JAL-1684 updated fragment alignment for example and added aligned protein and cDNA

diff --git a/examples/estrogenReceptorCdna_aln.fa b/examples/estrogenReceptorCdna_aln.fa
new file mode 100644 (file)
index 0000000..2f121db
--- /dev/null
+++ b/examples/estrogenReceptorCdna_aln.fa
@@ -0,0 +1,320 @@
+>EMBLCDS|ADZ17331/1-1593 Homo sapiens (human) estrogen nuclear receptor beta variant a
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------atggatataaaaaactcaccatctagccttaattctccttcctcctacaactgcagtcaatccatc
+------------------ttacccctggagcacggctccatatacataccttcctcctatgtagacagccac
+catgaatatccagccatgacattctatagccctgctgtgatgaattacagcattcccagcaatgtcactaac
+ttggaaggtgggcctggtcggcagacc---------------------acaagccca---------------
+---------------aatgtgttgtggccaacacctgggcacctttctcctttagtggtccatcgccagtta
+tcacatctgtat------------------------------------------------------------
+------------------------------------------------------------------------
+gcggaacctcaaaagagtccctggtgtgaagcaagatcgctagaacacaccttacctgtaaacagagagaca
+ctgaaa------------------------------aggaaggttagtgggaac------------------
+---------------------------cgttgcgccagccctgttactggtcca------------------
+------------------------------------------------------------------------
+---------------------------------------------------------ggttcaaagagggat
+gctcacttc---------------------------------------------------------------
+------------------------------------tgcgctgtctgcagcgattacgcatcgggatatcac
+tatggagtctggtcgtgtgaaggatgtaaggccttttttaaaagaagcattcaaggacataatgattatatt
+tgtccagctacaaatcagtgtacaatcgataaaaaccggcgcaagagctgccaggcctgccgacttcggaag
+tgttacgaagtgggaatggtgaagtgtggctcccggagagagagatgt---gggtaccgccttgtgcggaga
+cagagaagtgccgacgagcagctgcactgtgccggcaaggccaagagaagtggcggccac------------
+---------------------------gcgccccgagtgcgggagctgctgctggacgccctgagccccgag
+cagctagtgctcaccctcctggaggct---gagccgccccatgtgctgatcagc------------------
+------------------------------------------------------------------cgc---
+cccagtgcgcccttcaccgaggcctccatgatgatgtccctgaccaagttggccgacaaggagttggtacac
+atgatcagctgggccaagaagattcccggctttgtggagctcagcctgttcgaccaagtgcggctcttggag
+agctgttggatggaggtgttaatgatggggctgatgtggcgctcaattgac------caccccggcaagctc
+atctttgctccagatcttgttctggacagggatgaggggaaatgcgtagaaggaattctggaaatctttgac
+atgctcctggcaact---------acttcaaggtttcgagagttaaaactccaacacaaagaatatctctgt
+gtcaaggccatgatcctgctcaattccagtatgtaccctctggtcacagcgacc---caggatgctgacagc
+agccggaagctggctcacttgctgaacgccgtgaccgatgctttggtttgggtgattgccaagagcggcatc
+tcctcccagcagcaatccatgcgcctggctaacctcctgatgctcctgtcccacgtcaggcatgcgagtaac
+aagggcatggaacatctgctcaac------atgaagtgcaaaaatgtg---------gtcccagtgtatgac
+ctgctgctggagatgctgaatgcccacgtgcttcgcgggtgcaagtcctccatcacggggtccgagtgcagc
+ccggcagaggacagtaaaagcaaagagggctcccagaacccacagtctcagtga
+>EMBLCDS|AAK93056/1-1455 Drosophila melanogaster (fruit fly) GH28308p
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+---------------------------------atgtccgacggcgtcagcatcttgcacatcaaacaggag
+gtggacactccatcggcgtcctgctttagtcccagctccaagtcaacggccacgcagagtggcacaaacggc
+ctgaaa------------------------------------------tcctcgccc---------------
+---------------tcggtttcgccggaaaggcagctctgcagctcgacgacctctctatcctgcgatttg
+cacaatgtatcc------------------------------------------------------------
+---------------------------------------------------------ttaagcaatgatggc
+gatagtctgaaaggaagtggtacaagtggcggcaatggcggaggaggaggtggtggtacgagtggtggaaat
+gcgacc------------------------------------------------------------------
+------------------------------aatgcgagtgccggagctggatcg------------------
+------------------------------------------------------------------------
+---------------------------------------------------------ggatccgtcagggac
+gagctccgccgattg---------------------------------------------------------
+------------------------------------tgtttggtttgtggcgatgtggccagtggattccac
+tatggtgtggcgagttgtgaggcttgcaaagcgttctttaaacgcaccatccaaggcaacatcgagtacacg
+tgtccggcgaacaacgagtgtgagattaacaagcggagacgcaaggcctgccaagcgtgtcgcttccagaaa
+tgtctactaatgggcatgctcaaggagggtgtgcgcttggatcgagttcgtggaggacggcagaagtaccga
+aggaatcctgtatcaaactcttaccagactatgcagctgctataccaatccaacaccacctcgctg------
+---------------------------tgcgatgtcaagatactggaggtgctcaattcatatgagccggat
+gccttgagcgtccaaacg------------ccgccgccgcaagtccacacgactagcataactaatgatgag
+gcctcatcctcctcgggcagcataaaactggagtccagcgttgttacgcccaatgggacttgcattttccaa
+aacaacaacaacaatgatcccaatgagatactaagcgtccttagtgatatttacgacaaggaattggtcagc
+gtcattggctgggccaagcagatacctggctttatagatctgccacttaacgaccagatgaagcttctccag
+gtgtcgtgggcagagatcctgacgctccagctgaccttccggtccctaccg------ttcaatggcaagtta
+tgcttcgccacggatgtctggatggatgaacatttggccaaggagtgc---ggttacacggagttctactac
+cactgcgtccagatc---------gcacagcgcatggaaagaatatcgccacgaagggaggagtactacttg
+ctaaaggcgctcctgctggccaactgcgacattctgctg------------------gatgatcagagttcc
+ctgcgcgcatttcgtgatacgattcttaattctctaaacgatgtggtctacttgctgcgtcattcgtcggcc
+gtgtcgcatcagcaa---------------caattgctgcttttgctgccttcgctgcggcaggcggatgat
+atcctgcgaagattttggcgtgga------attgcacgcgatgaagtc---------attaccatgaagaaa
+ctgttcctcgagatgctcgag---------------------------------------------------
+---------------------------------------ccgctggccaggtga
+>EMBLCDS|BAA89539/1-2133 Anguilla japonica (Japanese eel) progesterone receptor
+------------------------------------------------------------------------
+------------------------------------------------------------atggacaacaat
+caccaagacaagatggaaagtctatacacgccagccagagcatcaccaactcctgatgcagaatcgattaaa
+agagccaggaatttgattaaaacatactcggagtcttttgggagttatgtggaggagatagttcgagacgac
+tcgaataacatacaatctttgagcagcgtccctctcttgatgcgtaattttggaaacatggacaccctaacc
+tgcgcacctggctcgggtagtgacagtgagatttggaaagactttgttgttcccgggaactctgtggtaagc
+aaagacacctgtggtcatgttgaaatatccactaaagccgaaaatttgtcttgggctgccgcgcccttaagt
+agagaagaaaccctcgcgaaaggaactgttacggtcccagcgactgtgcctaaagaaagttttaccgcaaca
+---------------tcaaacacttcttcagccagtggaatctctattaaagatgaacaacaatctttgctc
+aaaatggaaccacagtcttctgacttttgtccttatacagcaaatataccgaaattgaatccatcttatctg
+accaatactgcgagtacgaaacaacttggatatggc------------gaacagccg---------------
+---------------gacacttcagcgcactcctctccacctgctcagaagattgttttagatactgctcga
+tactcggccgat------------------------------------------------------------
+------------------------------------------ttatgttcggataaccctttaccgcaagcg
+acaaatatcaaaacagatccttgtagtagtttctcttctttcgttggagaagggatccttactagggcatct
+atgggctactcacagcaagcgattcagacattgccggtgcacaagagtgaaccg------------------
+---------------------------ttcaggttgtctgcttcgagcgcgcccgcggattctccgttttgg
+tgccaatcc---------------------------------------------------------------
+------------------------------------------------------acgggtccttctgaggat
+catcatctgcagattgactatctatctcccgctggactccacagcacatgcaaatacagttccacgaacgcg
+tacagctcctatttaggtgtgctgccccagagggtgtgcgtcatctgtggggatgaagcatcaggctgtcac
+tatggtgtcctcacctgtggcagctgtaaggtgttctttaagagggcagtggaaggccatcataactacttg
+tgtgctggacggaatgactgcatcgtggacaagatccgtaggaaaaactgtcctgcttgtcgcctcagaaag
+tgctaccaggcgggaatgatactgggaggtcggaagctgaagaagttg---ggggctctgaaggcagcaggg
+ctgacccaggccctggtggcccactcactgactcctcggaggctctctggtgacagccaggccctg------
+---------------------------atgcccctgggctgccttccaggggtccgggagctgcacctttcc
+ccacagatcatcagcgtgctggagagcattgagcctgaggtggtgtactctggt------------------
+------------------------------------------------------------------tatgac
+aactcccagcctgacatgcccaatatgctgctcaacagcctcaaccgcttatgtgagaggcagctgctgagg
+attgtcaagtggtccaagtctttaccaggttttcgcagtttacacatcaatgaccaaatggctctgatccag
+tactcctggatgagcttaatggtattttctttgggttggcggtctttccaaaatgtcaccagtgattacctg
+tactttgcacctgacctcattctcaacgaagagtatatgaggaggtct------------ccaatatttgac
+ctgtgcatggccatgcagttcatccctcaagagtttgccaatctccaggtgaccaaggaggagtttctgtgc
+atgaaggtcttgctgttgctcaac------acagtgcctctg---------------gaggggttgaagagc
+cagccacagtttgatgagatgaggcagaattacatccatgaactcaccaaggccattcacctgcgagagaat
+ggtgtggtcgcctgctcccagcgtttctaccacctgaccaagctgatggaccacatgcatgacattgtgaag
+aagctccacctgtactgcctgagcactttcattcaggcagatgccatgcgg------gtagagttccccgag
+atgatgtcagaagtcatcgcctcccagctg------------------------------------------
+------------cctcgggtgctcgctggaatggtgaaaccccttctttttcacaccaaatga
+>EMBLCDS|AHW56473/1-1590 Homo sapiens (human) partial estrogen receptor 2 isoform A
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------atggatataaaaaactcaccatctagccttaattctccttcctcctacaactgcagtcaatccatc
+------------------ttacccctggagcacggctccatatacataccttcctcctatgtagacagccac
+catgaatatccagccatgacattctatagccctgctgtgatgaattacagcattcccagcaatgtcactaac
+ttggaaggtgggcctggtcggcagacc---------------------acaagccca---------------
+---------------aatgtgttgtggccaacacctgggcacctttctcctttagtggtccatcgccagtta
+tcacatctgtat------------------------------------------------------------
+------------------------------------------------------------------------
+gcggaacctcaaaagagtccctggtgtgaagcaagatcgctagaacacaccttacctgtaaacagagagaca
+ctgaaa------------------------------aggaaggttagtgggaac------------------
+---------------------------cgttgcgccagccctgttactggtcca------------------
+------------------------------------------------------------------------
+---------------------------------------------------------ggttcaaagagggat
+gctcacttc---------------------------------------------------------------
+------------------------------------tgcgctgtctgcagcgattacgcatcgggatatcac
+tatggagtctggtcgtgtgaaggatgtaaggccttttttaaaagaagcattcaaggacataatgattatatt
+tgtccagctacaaatcagtgtacaatcgataaaaaccggcgcaagagctgccaggcctgccgacttcggaag
+tgttacgaagtgggaatggtgaagtgtggctcccggagagagagatgt---gggtaccgccttgtgcggaga
+cagagaagtgccgacgagcagctgcactgtgccggcaaggccaagagaagtggcggccac------------
+---------------------------gcgccccgagtgcgggagctgctgctggacgccctgagccccgag
+cagctagtgctcaccctcctggaggct---gagccgccccatgtgctgatcagc------------------
+------------------------------------------------------------------cgc---
+cccagtgcgcccttcaccgaggcctccatgatgatgtccctgaccaagttggccgacaaggagttggtacac
+atgatcagctgggccaagaagattcccggctttgtggagctcagcctgttcgaccaagtgcggctcttggag
+agctgttggatggaggtgttaatgatggggctgatgtggcgctcaattgac------caccccggcaagctc
+atctttgctccagatcttgttctggacagggatgaggggaaatgcgtagaaggaattctggaaatctttgac
+atgctcctggcaact---------acttcaaggtttcgagagttaaaactccaacacaaagaatatctctgt
+gtcaaggccatgatcctgctcaattccagtatgtaccctctggtcacagcgacc---caggatgctgacagc
+agccggaagctggctcacttgctgaacgccgtgaccgatgctttggtttgggtgattgccaagagcggcatc
+tcctcccagcagcaatccatgcgcctggctaacctcctgatgctcctgtcccacgtcaggcatgcgagtaac
+aagggcatggaacatctgctcaac------atgaagtgcaaaaatgtg---------gtcccagtgtatgac
+ctgctgctggagatgctgaatgcccacgtgcttcgcgggtgcaagtcctccatcacggggtccgagtgcagc
+ccggcagaggacagtaaaagcaaagagggctcccagaacccacagtctcag
+>EMBLCDS|BAA75464/1-2547 Anguilla japonica (Japanese eel) androgen receptor alpha
+atggagattccagttgggttaggaggagtttcagatgccacaaacgccgtttttcgcggaccttaccaaaac
+gttttccacagccttcaagtggcatttcagagtcacggtgccgtctccaggagcttagattttccaaataca
+aagtacggttttttacaaaacagacatttctgtgaaatgcgtcaggagaacaagcagccgccatgcaaagga
+ctcggcctattttacgggaaccatcgtaattcggacactgggacaaacgaagacgacatcgcttgtttttcc
+agacagtccgacgctgaagccagacctggtattttttctgaaagctcattggatactggagacgagattact
+tgcaaactccagtcagacaaccaaggggtaagagcgagcggtcctctcctaccgggctctagcggctgcaat
+tcgggacaaaagtcctcccttgcttgtacgtcccaacaaagggagacaacatctcaaagtgacacctgcgca
+ggagagagctgctcggaacatcaagcaactaccatttcggaaactgcgcgcgaattgtgcaacgccgtttcc
+gtgtcgctgggcttgaatttagatcttaatgatatgaatgacctaagttcaaaccaaatatcgtctaccgaa
+agtgacacaagtcaagccatctacttatttgaatcttcacctgggtatactggggtcggactgaacgccttg
+gtaagagactgtaaatgtcagagtgcacgcgaagggacatcgacacaacagtacgaccgcggggcaatgttt
+aagataaaccgtgtaaatgacttgccgcttcagccagcacccccgcgacacaccagcattagcgatgctaaa
+tgggacatggaagcaggtttgtgtgcgcagatggagcacaaagactctgaaaagtgcgcgaatatggatggt
+gcacactccacttctgtcttctcccagttcgaccaactgttgccagtaaacgcgtcgcactacagtcagaac
+gtttcggtcagagtggaaccacaaagtgatttctctccgattttgtacaaatcacctggtattcagaaaaat
+gccgaaaagtacaatgtccaatatgatgccacaattaaatcagaagatgggaaaacgacatctgaacgggaa
+tggggttttcagtacaggtacaatgaaagctgcagcacaccgtcagcacctcctagacattgtgcacatcag
+aacagggccggaccgtacaaccagttcttttttaatccatttgaatatgcgaaaagaggtgttgtctcaagg
+gaaggatattctctcgaacatgggttcccaaacaatctcgctcggacaccctactctggttccttgaaaaac
+gaactaggagatcgtctgagtgggccataccctgacgtcagttacaggtacgagggcgagcgggagaacgtg
+ttccccgtggagttcttctttccgccgcagaggacctgcctgatctgcggggacgaggcctcgggctgtcac
+tatggagccctcacctgcggcagctgcaaggtgttcttcaagagggccgcggaagggaaacagaagtacctg
+tgcgccagcatcaatgattgcaccattgataaacttcgaaggaagaactgcccctcttgccgtctcaaaagg
+tgctttgctgccggaatgaccctt---------------------------ggagcgcggaagctgaagaag
+atcgggcaaatgagggcccccgaggatggccaggggcagggcccggcggaagcggagctgagcgtc------
+---------------------------tcccccaagtacgacctg------------ggcttccacacccag
+tccatgttcctcaacatcctggaggccatcgagccggaggtggtgaacgccggg------------------
+------------------------------------------------------------------cacgac
+tatggccagccggactctgcggccagcctgctgaccagcctcaacgagctcggagaacggcaactcgtcaag
+gtcgtcaagtgggccaagggcatgccaggttttcggagtctgtacgtggatgaccagatgacagtcatccag
+cactcctggatggcagtgatggtgttcgctctgggctggaggtcatttaagaatgtgaagtccaggatgctt
+tactttgctcctgaccttgttttcaacgagcaccgaatgcaggtgtcc------------accatgtatgaa
+cactgcatccggatgaagaacttctcccaggagtttgctatgctgcaggtctcccaggaagagttcctgtgc
+atgaaagctctgcttctcttcagc------accatccccgtt---------------gaagggctgaagggg
+cagaatttctttgacgagctgcggaggagctacattaacgagctggaccggctggttagcttcaggagcaag
+tccagc------tgttccgagaggttccagcagctcacccgcctcctggactccctccaacctgttctgaag
+aagctccaccagtttacgttcgaccttttcgtccagtcccagaacctctccaaccaagtttgctttcccgag
+atgatctcagagatcatatccgtgcacgtg------------------------------------------
+------------ccaaagattctcgctggcacggtgaagccaatcctcttccacaagtag
+>EMBLCDS|AAA17402/1-1032 Serinus canaria (common canary) partial androgen receptor
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------gaagcctccgggtgccac
+tacggagccctgacgtgtgggagctgcaaagtgttcttcaaacgggcagctgaaggtaaacagaagtacctc
+tgtgccagccgcaacgactgcaccatcgacaagttccggcggaaaaactgcccctcctgccgcctgcgcaag
+tgctacgaggccgggatgacgctt---------------------------ggagcccgcaagctgaagaaa
+ctgggtaacctgaaggcacaggacgacatagagggagccagctcgtccagcccaacggaggagcaa------
+---------------------------gctcccaagctggtgatgacacgcattgatggctacgagtgccag
+cccatcttcctcaacgtcctggaggccatcgagcctggggtggtgtgtgctggc------------------
+------------------------------------------------------------------catgac
+aacagccagcctgactccttctccaacctgctgaccagcctgaatgagcttggggagaggcagctggtctac
+gtggtcaaatgggcaaaggctctgccaggatttcgcaacctgcatgtggatgaccagatgtcaataatccag
+tactcttggatgggcctgatggtgtttgctatggggtggagatccttcaccaacgtcaattccaggatgctt
+tactttgctccagacctggtcttcaatgagtaccgcatgcacaaatcc------------aggatgtacagc
+cagtgcatcaggatgcggcacctctcccaggaattcgggtggcttcagatcacaccccaggggttcctctgt
+atgaaggctctcctcttcttcagt------attattccagtg---------------gatggcctgaagaac
+cagaagctcttcgatgagctccgcatgaattacatcaaggaacttgaccgtatcattgcctgcaagaggaag
+aaccccacctcatgctcccggaggttttaccagctcaccaaggtcctggactccgtgactccgattgccaag
+gacctgcatcagtttacatttgatctcctaatcaaggcacacatggtgagc------gtggactacccagaa
+atgatggctgagatcatctctgtgcaggtt------------------------------------------
+------------cccaagatcctgtct
+>EMBLCDS|AAL37553/1-1455 Drosophila melanogaster (fruit fly) estrogen-related receptor
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+---------------------------------atgtccgacggcgtcagcatcttgcacatcaaacaggag
+gtggacactccatcggcgtcctgctttagtcccagctccaagtcaacggccacgcagagtggcacaaacggc
+ctgaaa------------------------------------------tcctcgccc---------------
+---------------tcggtttcgccggaaaggcagctctgcagctcgacgacctctctatcctgcgatttg
+cacaatgtatcc------------------------------------------------------------
+---------------------------------------------------------ttaagcaatgatggc
+gatagtctgaaaggaagtggtacaagtggcggcaatggcggaggaggaggtggtggtacgagtggtggaaat
+gcgacc------------------------------------------------------------------
+------------------------------aatgcgagtgccggagctggatcg------------------
+------------------------------------------------------------------------
+---------------------------------------------------------ggatccgtcagggac
+gagctccgccgattg---------------------------------------------------------
+------------------------------------tgtttggtttgtggcgatgtggccagtggattccac
+tatggtgtggcgagttgtgaggcttgcaaagcgttctttaaacgcaccatccaaggcaacatcgagtacacg
+tgtccggcgaacaacgagtgtgagattaacaagcggagacgcaaggcctgccaagcgtgtcgcttccagaaa
+tgtctactaatgggcatgctcaaggagggtgtgcgcttggatcgagttcgtggaggacggcagaagtaccga
+aggaatcctgtatcaaactcttaccagactatgcagctgctataccaatccaacaccacctcgctg------
+---------------------------tgcgatgtcaagatactggaggtgctcaattcatatgagccggat
+gccttgagcgtccaaacg------------ccgccgccgcaagtccacacgactagcataactaatgatgag
+gcctcatcctcctcgggcagcataaaactggagtccagcgttgttacgcccaatgggacttgcattttccaa
+aacaacaacaacaatgatcccaatgagatactaagcgtccttagtgatatttacgacaaggaattggtcagc
+gtcattggctgggccaagcagatacctggctttatagatctgccacttaacgaccagatgaagcttctccag
+gtgtcgtgggcagagatcctgacgctccagctgaccttccggtccctaccg------ttcaatggcaagtta
+tgcttcgccacggatgtctggatggatgaacatttggccaaggagtgc---ggttacacggagttctactac
+cactgcgtccagatc---------gcacagcgcatggaaagaatatcgccacgaagggaggagtactacttg
+ctaaaggcgctcctgctggccaactgcgacattctgctg------------------gatgatcagagttcc
+ctgcgcgcatttcgtgatacgattcttaattctctaaacgatgtggtctacttgctgcgtcattcgtcggcc
+gtgtcgcatcagcaa---------------caattgctgcttttgctgccttcgctgcggcaggcggatgat
+atcctgcgaagattttggcgtgga------attgcacgcgatgaagtc---------attaccatgaagaaa
+ctgttcctcgagatgctcgag---------------------------------------------------
+---------------------------------------ccgctggccaggtga
+>EMBLCDS|AAK20929/1-1662 Petromyzon marinus (sea lamprey) partial estrogen receptor
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+---------------------------------------------------------gcacgaggcttcagc
+gaggcacatggctacgagtactccggggcctcgctctaccagccactgcctccctcgtgcacagagttctca
+---------------------------------attggagctcatcaacaacaacaacatcagcaccagcat
+caccagcaccagcatcagcagcaccaccaccagcagcagcagcagcagccacagccgcagcagaatggagtt
+ttgggcgaggggcagagttcccatctctcttatcttccgccctcgaccgagctgccc---------------
+---------------cagtacgtgccctccagccccagcgcgccctacagcatggagctcggggcagggcgt
+cctcacggctacgac---------------------------------------------------------
+------------------------------------------ccagggccacagagcctctacaggggcggt
+gtggagagcagcgcccccccgtacagcgagcagcagcaggtggtgggcggcggcggagccatgtcggccatg
+ggcttg---------------------------------------acagagcca------------------
+---------------------------cgccacgtcagctccggatcgctaccc------------------
+------------------------------------------------------------------------
+---------------------------------------------------------agcagcacgaggccc
+gagcgcagcacccagttc------------------------------------------------------
+------------------------------------tgtgccgtgtgcagcgactatgcctcggggtaccac
+tacggcgtgtggtcctgcgagggctgcaaagccttcttcaagcgcagcacgcaaggccacaatgactacatg
+tgcccggccaccaaccagtgcaccatcgacaggaaccgtcgcaagagctgtcaggcttgccgcctgcgtaag
+tgctacgaagtgggcatggtcaaa---ggcgttcgcaaggaccgcaaa---ggctttcgaggggtcaagcac
+aaacgtaagcgccccatcccccaaaagaatgggggagaaggaggtgccggcggcggccaagacgtgagcgag
+acgaggcctcagggtgagaggccctccgggccgagggaccgggagagcgccgtcagctcactcgaggctgac
+caggtgatctcggctcttctggaggct---gagccacccaccgtactgtcctcg------------------
+------------------------------------------------------------------tatgac
+cccgacaagcctgtgacggaggcctcgctcatggctgctctcaccagcctggctgaccgagagctcgtgcac
+atgatcacctgggctaagaagattccaggattcacggccatcgggctgagtgaccaggtgcagctgctggag
+tgctgctggctggagatcctaatcgtggggctcatctggaggtctatcgat------cgccctggtcagctc
+cactttgctccaaacctcatcctaggaagggaggacgcgcgcaatgtggagggcatgctggacatgttcgac
+atgctgctcgtcacc---------gtgagtcgcttccgtgagctgcatctccgccgggaggaatacgtctgc
+ctcaaggccatgatcctcctcaactcgggggtgtttttctgcctctccaattccgccggggagcagacgaat
+gtgcagctcatccagcagatcctcgagaaggtgatggacgccctgggcagcaccatcggccacattgaggcg
+tccccgccgcaacactcgcgtcgcctctcccagctgctcctgctgctttcacagatccggcacattagcaac
+aagggcatcgagcatctcaacagc------atgaagcgtaagaatgtg---------atcccgctatacgac
+ctgctccttgagctgctggacgctcacagcctgcag---------------------aatactggcttacgg
+acgtcgcccccaccgcaggatttcagggcaaccctcgtgccg

diff --git a/examples/estrogenReceptorCdna_frag.fa b/examples/estrogenReceptorCdna_frag.fa
index da5f5c8..c44766d 100644 (file)
--- a/examples/estrogenReceptorCdna_frag.fa
+++ b/examples/estrogenReceptorCdna_frag.fa
@@ -1,12 +1,32 @@
->EMBLCDS|BAA89539/1111-1224 Anguilla japonica (Japanese eel) progesterone receptor
+>EMBLCDS|ADZ17331/532-675 Homo sapiens (human) estrogen nuclear receptor beta variant a
+caaggacataatgattatatttgtccagctacaaatcagtgtacaatcgataaaaaccggcgcaagagctgc
+caggcctgccgacttcggaagtgttacgaagtgggaatggtgaagtgtggctcccggagagagagatgt---
+ggg
+>EMBLCDS|AAK93056/430-576 Drosophila melanogaster (fruit fly) GH28308p
+caaggcaacatcgagtacacgtgtccggcgaacaacgagtgtgagattaacaagcggagacgcaaggcctgc
+caagcgtgtcgcttccagaaatgtctactaatgggcatgctcaaggagggtgtgcgcttggatcgagttcgt
+gga
+>EMBLCDS|BAA89539/1111-1254 Anguilla japonica (Japanese eel) progesterone receptor
 gaaggccatcataactacttgtgtgctggacggaatgactgcatcgtggacaagatccgtaggaaaaactgt
-cctgcttgtcgcctcagaaagtgctaccaggcgggaatgata---
->EMBLCDS|BAA75464/1564-1677 Anguilla japonica (Japanese eel) androgen receptor alpha
+cctgcttgtcgcctcagaaagtgctaccaggcgggaatgatactgggaggtcggaagctgaagaagttg---
+ggg
+>EMBLCDS|AHW56473/532-675 Homo sapiens (human) partial estrogen receptor 2 isoform A
+caaggacataatgattatatttgtccagctacaaatcagtgtacaatcgataaaaaccggcgcaagagctgc
+caggcctgccgacttcggaagtgttacgaagtgggaatggtgaagtgtggctcccggagagagagatgt---
+ggg
+>EMBLCDS|BAA75464/1564-1683 Anguilla japonica (Japanese eel) androgen receptor alpha
 gaagggaaacagaagtacctgtgcgccagcatcaatgattgcaccattgataaacttcgaaggaagaactgc
-ccctcttgccgtctcaaaaggtgctttgctgccggaatgacc---
->EMBLCDS|AAA17402/70-183 Serinus canaria (common canary) partial androgen receptor
+ccctcttgccgtctcaaaaggtgctttgctgccggaatgaccctt---------------------------
+gga
+>EMBLCDS|AAA17402/70-189 Serinus canaria (common canary) partial androgen receptor
 gaaggtaaacagaagtacctctgtgccagccgcaacgactgcaccatcgacaagttccggcggaaaaactgc
-ccctcctgccgcctgcgcaagtgctacgaggccgggatgacg---
->EMBLCDS|AAK20929/592-708 Petromyzon marinus (sea lamprey) partial estrogen receptor
+ccctcctgccgcctgcgcaagtgctacgaggccgggatgacgctt---------------------------
+gga
+>EMBLCDS|AAL37553/430-576 Drosophila melanogaster (fruit fly) estrogen-related receptor
+caaggcaacatcgagtacacgtgtccggcgaacaacgagtgtgagattaacaagcggagacgcaaggcctgc
+caagcgtgtcgcttccagaaatgtctactaatgggcatgctcaaggagggtgtgcgcttggatcgagttcgt
+gga
+>EMBLCDS|AAK20929/592-732 Petromyzon marinus (sea lamprey) partial estrogen receptor
 caaggccacaatgactacatgtgcccggccaccaaccagtgcaccatcgacaggaaccgtcgcaagagctgt
-caggcttgccgcctgcgtaagtgctacgaagtgggcatggtcaaa
+caggcttgccgcctgcgtaagtgctacgaagtgggcatggtcaaa---ggcgttcgcaaggaccgcaaa---
+ggc

diff --git a/examples/estrogenReceptorProtein_aln.fa b/examples/estrogenReceptorProtein_aln.fa
new file mode 100644 (file)
index 0000000..353c68c
--- /dev/null
+++ b/examples/estrogenReceptorProtein_aln.fa
@@ -0,0 +1,112 @@
+>UNIPROT|Q7LCB3/1-530 estrogen nuclear receptor beta variant a
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+--------------------------MDIKNSPSSLNSPSSYNCSQSI------LPLEHGSIYIPSSYVDSH
+HEYPAMTFYSPAVMNYSIPSNVTNLEGGPGRQT-------TSP----------NVLWPTPGHLSPLVVHRQL
+SHLY--------------------------------------------AEPQKSPWCEARSLEHTLPVNRET
+LK----------RKVSGN---------------RCASPVTGP------------------------------
+-------------------GSKRDAHF---------------------------------CAVCSDYASGYH
+YGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMVKCGSRRERC-GYRLVRR
+QRSADEQLHCAGKAKRSGGH-------------APRVRELLLDALSPEQLVLTLLEA-EPPHVLIS------
+----------------------R-PSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLE
+SCWMEVLMMGLMWRSID--HPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLAT---TSRFRELKLQHKEYLC
+VKAMILLNSSMYPLVTAT-QDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASN
+KGMEHLLN--MKCKNV---VPVYDLLLEMLNAHVLRGCKSSITGSECSPAEDSKSKEGSQNPQSQ---
+>UNIPROT|Q9VSE9/1-484 GH28308p
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+-----------------------------------------------------------MSDGVSILHIKQE
+VDTPSASCFSPSSKSTATQSGTNGLK--------------SSP----------SVSPERQLCSSTTSLSCDL
+HNVS---------------------------------------LSNDGDSLKGSGTSGGNGGGGGGGTSGGN
+AT--------------------------------NASAGAGS------------------------------
+-------------------GSVRDELRRL-------------------------------CLVCGDVASGFH
+YGVASCEACKAFFKRTIQGNIEYTCPANNECEINKRRRKACQACRFQKCLLMGMLKEGVRLDRVRGGRQKYR
+RNPVSNSYQTMQLLYQSNTTSL-----------CDVKILEVLNSYEPDALSVQT----PPPQVHTTSITNDE
+ASSSSGSIKLESSVVTPNGTCIFQNNNNNDPNEILSVLSDIYDKELVSVIGWAKQIPGFIDLPLNDQMKLLQ
+VSWAEILTLQLTFRSLP--FNGKLCFATDVWMDEHLAKEC-GYTEFYYHCVQI---AQRMERISPRREEYYL
+LKALLLANCDILL------DDQSSLRAFRDTILNSLNDVVYLLRHSSAVSHQQ-----QLLLLLPSLRQADD
+ILRRFWRG--IARDEV---ITMKKLFLEMLE------------------------------PLAR---
+>UNIPROT|Q9IBD5/1-710 progesterone receptor
+--------------------------------------------MDNNHQDKMESLYTPARASPTPDAESIK
+RARNLIKTYSESFGSYVEEIVRDDSNNIQSLSSVPLLMRNFGNMDTLTCAPGSGSDSEIWKDFVVPGNSVVS
+KDTCGHVEISTKAENLSWAAAPLSREETLAKGTVTVPATVPKESFTAT-----SNTSSASGISIKDEQQSLL
+KMEPQSSDFCPYTANIPKLNPSYLTNTASTKQLGYG----EQP----------DTSAHSSPPAQKIVLDTAR
+YSAD----------------------------------LCSDNPLPQATNIKTDPCSSFSSFVGEGILTRAS
+MGYSQQAIQTLPVHKSEP---------------FRLSASSAPADSPFWCQS---------------------
+------------------TGPSEDHHLQIDYLSPAGLHSTCKYSSTNAYSSYLGVLPQRVCVICGDEASGCH
+YGVLTCGSCKVFFKRAVEGHHNYLCAGRNDCIVDKIRRKNCPACRLRKCYQAGMILGGRKLKKL-GALKAAG
+LTQALVAHSLTPRRLSGDSQAL-----------MPLGCLPGVRELHLSPQIISVLESIEPEVVYSG------
+----------------------YDNSQPDMPNMLLNSLNRLCERQLLRIVKWSKSLPGFRSLHINDQMALIQ
+YSWMSLMVFSLGWRSFQNVTSDYLYFAPDLILNEEYMRRS----PIFDLCMAMQFIPQEFANLQVTKEEFLC
+MKVLLLLN--TVPL-----EGLKSQPQFDEMRQNYIHELTKAIHLRENGVVACSQRFYHLTKLMDHMHDIVK
+KLHLYCLSTFIQADAMR--VEFPEMMSEVIASQL------------------PRVLAGMVKPLLFHTK
+>UNIPROT|Q7LCB3/1-530 estrogen receptor 2 isoform A
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+--------------------------MDIKNSPSSLNSPSSYNCSQSI------LPLEHGSIYIPSSYVDSH
+HEYPAMTFYSPAVMNYSIPSNVTNLEGGPGRQT-------TSP----------NVLWPTPGHLSPLVVHRQL
+SHLY--------------------------------------------AEPQKSPWCEARSLEHTLPVNRET
+LK----------RKVSGN---------------RCASPVTGP------------------------------
+-------------------GSKRDAHF---------------------------------CAVCSDYASGYH
+YGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMVKCGSRRERC-GYRLVRR
+QRSADEQLHCAGKAKRSGGH-------------APRVRELLLDALSPEQLVLTLLEA-EPPHVLIS------
+----------------------R-PSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLE
+SCWMEVLMMGLMWRSID--HPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLAT---TSRFRELKLQHKEYLC
+VKAMILLNSSMYPLVTAT-QDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASN
+KGMEHLLN--MKCKNV---VPVYDLLLEMLNAHVLRGCKSSITGSECSPAEDSKSKEGSQNPQSQ---
+>UNIPROT|Q9YGV9/1-848 androgen receptor alpha
+MEIPVGLGGVSDATNAVFRGPYQNVFHSLQVAFQSHGAVSRSLDFPNTKYGFLQNRHFCEMRQENKQPPCKG
+LGLFYGNHRNSDTGTNEDDIACFSRQSDAEARPGIFSESSLDTGDEITCKLQSDNQGVRASGPLLPGSSGCN
+SGQKSSLACTSQQRETTSQSDTCAGESCSEHQATTISETARELCNAVSVSLGLNLDLNDMNDLSSNQISSTE
+SDTSQAIYLFESSPGYTGVGLNALVRDCKCQSAREGTSTQQYDRGAMFKINRVNDLPLQPAPPRHTSISDAK
+WDMEAGLCAQMEHKDSEKCANMDGAHSTSVFSQFDQLLPVNASHYSQNVSVRVEPQSDFSPILYKSPGIQKN
+AEKYNVQYDATIKSEDGKTTSEREWGFQYRYNESCSTPSAPPRHCAHQNRAGPYNQFFFNPFEYAKRGVVSR
+EGYSLEHGFPNNLARTPYSGSLKNELGDRLSGPYPDVSYRYEGERENVFPVEFFFPPQRTCLICGDEASGCH
+YGALTCGSCKVFFKRAAEGKQKYLCASINDCTIDKLRRKNCPSCRLKRCFAAGMTL---------GARKLKK
+IGQMRAPEDGQGQGPAEAELSV-----------SPKYDL----GFHTQSMFLNILEAIEPEVVNAG------
+----------------------HDYGQPDSAASLLTSLNELGERQLVKVVKWAKGMPGFRSLYVDDQMTVIQ
+HSWMAVMVFALGWRSFKNVKSRMLYFAPDLVFNEHRMQVS----TMYEHCIRMKNFSQEFAMLQVSQEEFLC
+MKALLLFS--TIPV-----EGLKGQNFFDELRRSYINELDRLVSFRSKSS--CSERFQQLTRLLDSLQPVLK
+KLHQFTFDLFVQSQNLSNQVCFPEMISEIISVHV------------------PKILAGTVKPILFHK-
+>UNIPROT|Q91445/1-344 androgen receptor
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+------------------------------------------------------------------EASGCH
+YGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTL---------GARKLKK
+LGNLKAQDDIEGASSSSPTEEQ-----------APKLVMTRIDGYECQPIFLNVLEAIEPGVVCAG------
+----------------------HDNSQPDSFSNLLTSLNELGERQLVYVVKWAKALPGFRNLHVDDQMSIIQ
+YSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHKS----RMYSQCIRMRHLSQEFGWLQITPQGFLC
+MKALLFFS--IIPV-----DGLKNQKLFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKVLDSVTPIAK
+DLHQFTFDLLIKAHMVS--VDYPEMMAEIISVQV------------------PKILS-----------
+>UNIPROT|Q9VSE9/1-484 estrogen-related receptor
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+-----------------------------------------------------------MSDGVSILHIKQE
+VDTPSASCFSPSSKSTATQSGTNGLK--------------SSP----------SVSPERQLCSSTTSLSCDL
+HNVS---------------------------------------LSNDGDSLKGSGTSGGNGGGGGGGTSGGN
+AT--------------------------------NASAGAGS------------------------------
+-------------------GSVRDELRRL-------------------------------CLVCGDVASGFH
+YGVASCEACKAFFKRTIQGNIEYTCPANNECEINKRRRKACQACRFQKCLLMGMLKEGVRLDRVRGGRQKYR
+RNPVSNSYQTMQLLYQSNTTSL-----------CDVKILEVLNSYEPDALSVQT----PPPQVHTTSITNDE
+ASSSSGSIKLESSVVTPNGTCIFQNNNNNDPNEILSVLSDIYDKELVSVIGWAKQIPGFIDLPLNDQMKLLQ
+VSWAEILTLQLTFRSLP--FNGKLCFATDVWMDEHLAKEC-GYTEFYYHCVQI---AQRMERISPRREEYYL
+LKALLLANCDILL------DDQSSLRAFRDTILNSLNDVVYLLRHSSAVSHQQ-----QLLLLLPSLRQADD
+ILRRFWRG--IARDEV---ITMKKLFLEMLE------------------------------PLAR---
+>UNIPROT|Q90ZM8/1-554 estrogen receptor
+------------------------------------------------------------------------
+------------------------------------------------------------------------
+-------------------ARGFSEAHGYEYSGASLYQPLPPSCTEFS-----------IGAHQQQQHQHQH
+HQHQHQQHHHQQQQQQPQPQQNGVLGEGQSSHLSYLPPSTELP----------QYVPSSPSAPYSMELGAGR
+PHGYD---------------------------------PGPQSLYRGGVESSAPPYSEQQQVVGGGGAMSAM
+GL-------------TEP---------------RHVSSGSLP------------------------------
+-------------------SSTRPERSTQF------------------------------CAVCSDYASGYH
+YGVWSCEGCKAFFKRSTQGHNDYMCPATNQCTIDRNRRKSCQACRLRKCYEVGMVK-GVRKDRK-GFRGVKH
+KRKRPIPQKNGGEGGAGGGQDVSETRPQGERPSGPRDRESAVSSLEADQVISALLEA-EPPTVLSS------
+----------------------YDPDKPVTEASLMAALTSLADRELVHMITWAKKIPGFTAIGLSDQVQLLE
+CCWLEILIVGLIWRSID--RPGQLHFAPNLILGREDARNVEGMLDMFDMLLVT---VSRFRELHLRREEYVC
+LKAMILLNSGVFFCLSNSAGEQTNVQLIQQILEKVMDALGSTIGHIEASPPQHSRRLSQLLLLLSQIRHISN
+KGIEHLNS--MKRKNV---IPLYDLLLELLDAHSLQ-------NTGLRTSPPPQDFRATLVP------

diff --git a/examples/estrogenReceptorProtein_frag.fa b/examples/estrogenReceptorProtein_frag.fa
index c9e31aa..efd89bf 100644 (file)
--- a/examples/estrogenReceptorProtein_frag.fa
+++ b/examples/estrogenReceptorProtein_frag.fa
@@ -1,8 +1,16 @@
->UNIPROT|Q9IBD5/371-408
-EGHHNYLCAGRNDCIVDKIRRKNCPACRLRKCYQAGMI-
->UNIPROT|Q9YGV9/522-559
-EGKQKYLCASINDCTIDKLRRKNCPSCRLKRCFAAGMT-
->UNIPROT|Q90ZM7/97-134
-EGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCIQAGMT-
->UNIPROT|Q90ZM8/198-236
-QGHNDYMCPATNQCTIDRNRRKSCQACRLRKCYEVGMVK
+>UNIPROT|Q7LCB3/178-225 estrogen nuclear receptor beta variant a
+QGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMVKCGSRRERC-G
+>UNIPROT|Q9VSE9/144-192 GH28308p
+QGNIEYTCPANNECEINKRRRKACQACRFQKCLLMGMLKEGVRLDRVRG
+>UNIPROT|Q9IBD5/371-418 progesterone receptor
+EGHHNYLCAGRNDCIVDKIRRKNCPACRLRKCYQAGMILGGRKLKKL-G
+>UNIPROT|Q7LCB3/178-225 estrogen receptor 2 isoform A
+QGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMVKCGSRRERC-G
+>UNIPROT|Q9YGV9/522-561 androgen receptor alpha
+EGKQKYLCASINDCTIDKLRRKNCPSCRLKRCFAAGMTL---------G
+>UNIPROT|Q91445/24-63 androgen receptor
+EGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTL---------G
+>UNIPROT|Q9VSE9/144-192 estrogen-related receptor
+QGNIEYTCPANNECEINKRRRKACQACRFQKCLLMGMLKEGVRLDRVRG
+>UNIPROT|Q90ZM8/198-244 estrogen receptor
+QGHNDYMCPATNQCTIDRNRRKSCQACRLRKCYEVGMVK-GVRKDRK-G