JAL-724 JAL-715 refactor and create new test for RSBS framework and Multi-harmony...

[jalview.git] / examples / testdata / smad.fa

diff --git a/examples/testdata/smad.fa b/examples/testdata/smad.fa
new file mode 100644 (file)
index 0000000..6a3b27b
--- /dev/null
+++ b/examples/testdata/smad.fa
@@ -0,0 +1,132 @@
+>gi|7160686|emb|CAB76819.1|/1-465
+DVQAVAYEEPKHWCSIVYYELNNRVGEAFHASSTSILVDGFTDPSNNKNRFCLGLLSNVNRNSTIENTRRHI
+GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPTTVCKIPSGCSLKIFNNQEF----AQLLAQSVNH
+GFETVYELTKMCTLRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS
+>gi|61967924|gb|AAX56944.1|/1-465
+DVQAVAYEEPKHWCSIVYYELNNRVGEAFHASSTSILVDGFTDPSNNKNRFCLGLLSNVNRNSTIENTRRHI
+GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPTTVCKIPSGCSLKIFNNQEF----AQLLAQSVNH
+GFETVYELTKMCTLRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS
+>gi|11464653|gb|AAG35265.1|/1-455
+TMHPVNYQEPKYWCSIVYYELNNRVGEAFNASQLSIIIDGFTDPSNNSDRFCLGLLSNVNRNSTIENTRRHI
+GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHNFHPTTVCKIPPGCSLKIFSNQEF----AHLLSRTVHH
+GFEAVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWVEIHLNGPLQWLDRVLTQMGTPRNPISSVS
+>gi|6273783|gb|AAF06361.1|/1-472
+DVHPVAYQEPKHWCSIVYYELNNRVGEAFLASSTSVLVDGFTDPSNNRNRFCLGLLSNVNRNSTIENTRRHI
+GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPTTVCKIPSRCSLKIFNNQEF----AELLAQSVNH
+GFEAVYELTKMCTIRMSFVKGWGAKYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS
+>gi|11907945|gb|AAG41407.1|/1-465
+DVQAVAYEEPKHWCSIVYYELNNRVGEAFHASSTSVLVDGFTDPSNNKNRFCLGLLSNVNRNSTIENTRRHI
+GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPTTVCKIPSGCSLKIFNNQEF----AQLLAQSVNH
+GFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS
+>gi|29725652|gb|AAO88909.1|/1-465
+DVQAVAYEEPKHWCSIVYYELNNRVGEAFHASSTSVLVDGFTDPSNNKNRFCLGLLSNVNRNSTIENTRRHI
+GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPTTVCKIPSGCSLKIFNNQEF----AQLLAQSVNH
+GFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS
+>gi|1654323|gb|AAC50790.1|/1-465
+DVQAVAYEEPKHWCSIVYYELNNRVGEAFHASSTSVLVDGFTDPSNNKNRFCLGLLSNVNRNSTIENTRRHI
+GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPTTVCKIPSGCSLKIFNNQEF----AQLLAQSVNH
+GFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS
+>gi|3192871|gb|AAC19116.1|/1-468
+DVQAVAYEEPKHWCSIVYYELNNRVGEAFHASSTSVLVDGFTDPSNNKNRFCLGLLSNVNRNSTIENTRRHI
+GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPTTVCKIPSGCSLKIFNNQEF----AQLLAQSVNH
+GFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS
+>gi|55926152|ref|NP_001007481.1|/1-464
+DVQAVAYEEPKHWCSIVYYELNNRVGEAFHASSTSVLVDGFTDPSNNRNRFCLGLLSNVNRNSTIENTRRHI
+GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNFHHGFHPTTVCKIPSGCSLKIFNNQEF----AQLLAQSVNH
+GFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS
+>gi|61967926|gb|AAX56945.1|/1-465
+DVQPVAYEEPKHWCSIVYYELNNRVGEAFHASSTSVLVDGFTDPSNNKNRFCLGLLSNVNRNSTIENTRRHI
+GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPTTVCKIPSGCSLKIFNNQEF----AQLLAQSVNH
+GFEAVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPLNPISSVS
+>gi|2360958|gb|AAB92396.1|/1-465
+DVQPVAYEEPKHWCSIVYYELNNRVGEAFHASSTSVLVDGFTDPSNNKSRFCLGLLSNVNRNSTIENTRRHI
+GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNFHHGFHPTTVCKIPSSCSLKIFNNQEF----AQLLAQSVNH
+GFEAVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPLNPISSVS
+>gi|5706366|dbj|BAA83093.1|/1-465
+DVQPVAYEEPKHWCSIVYYELNNRVGEAFHASSTSVLVDGFTDPANNKSRFCLGLLSNVNRNSTIENTRRHI
+GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNFHHGFHPTTVCKIPSSCSLKIFNNQEF----AQLLAQSVNH
+GFEAVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPLNPISSVS
+>gi|3982649|gb|AAC83580.1|/1-465
+DVQPVAYEEPKHWCSIVYYELNNRVGEAFHASSTSVLVDGFTDPSNNKSRFCLGLLSNVNRNSTIENTRRHI
+GKGVHLYYVGGEVYAECLSDSSIFVQSRNCNFHHGFHPTTVCKIPSSCSLKIFNNQEF----AQLLAQSVNH
+GFEAVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPLNPISSVS
+>gi|6288777|gb|AAF06738.1|/1-464
+DVQPVEYQEPSHWCSIVYYELNNRVGEAYHASSTSVLVDGFTDPSNNKNRFCLGLLSNVNRNSTIENTRRHI
+GKGVHLYYVGGEVYAECLSDTSIFVQSRNCNYHHGFHPTTVCKIPSGCSLKIFNNQEF----AQLLAQSVNH
+GFEAVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEVHLHGPLQWLDKVLTQMGSPLNPISSVS
+>gi|61967928|gb|AAX56946.1|/1-476
+NFRPVCYEEPQHWCSVAYYELNNRVGETFQASSRSILIDGFTDPSNNKNRFCLGLLSNVNRNSTIENTRRHI
+GKGVHLYYVGGEVYAECVSDSSIFVQSRNCNYQHGFHPATVCKIPSGCSLKIFNNQLF----AQPLAQSVNH
+GFEVVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS
+>gi|2689629|gb|AAC53515.1|/1-434
+DFRPVCYEEPLHWCSVAYYELNNRVGETFQASSRSVLIDGFTDPSNNRNRFCLGLLSNVNRNSTIENTRRHI
+GKGVHLYYVGGEVYAECVSDSSIFVQSRNCNYQHGFHPATVCKIPSGCSLKVFNNQLFAQLLAQLLAQSVHH
+GFEVVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS
+>gi|22532988|gb|AAF77079.2|/1-428
+DFRPVCYEEPQHWCSVAYYELNNRVGETFQASSRSVLIDGFTDPSNNRNRFCLGLLSNVNRNSTIENTRRHI
+GKGVHLYYVGGEVYAECVSDSSIFVQSRNCNYQHGFHPATVCKIPSGCSLKVFNNQLF----AQLLAQSVHH
+GFEVVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS
+>gi|2967646|gb|AAC39657.1|/1-467
+DLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNS-ERFCLGLLSNVNRNATVEMTRRHI
+GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ
+GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSVRCSSMS
+>gi|45331050|gb|AAS57861.1|/1-468
+DLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNS-ERFCLGLLSNVNRNATVEMTRRHI
+GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYDWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ
+GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSVRCSSMS
+>gi|5360217|dbj|BAA81909.1|/1-467
+DLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNS-ERFCLGLLSNVNRNATVEMTRRHI
+GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ
+GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSVRCSSMS
+>gi|6288775|gb|AAF06737.1|/1-468
+DLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNS-ERFCLCLLSNVNRNATVEMTRRHI
+GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ
+GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSVRCSSMS
+>gi|58047721|gb|AAH89184.1|/1-467
+DLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNS-ERFCLGLLSNVNRNATVEMTRRHI
+GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ
+GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSVRCSSMS
+>gi|4009524|gb|AAD11458.1|/1-486
+DAAPVMYHEPAFWCSISYYELNTRVGETFHASQPSITVDGFTDPSNS-ERFCLGLLSNVNRNEVVEQTRRHI
+GKGVRLYYIGGEVFAECLSDSSIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLSQSVSQ
+GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDRVLTQMGSPRLPCSSMS
+>gi|40254710|ref|NP_571441.2|/1-468
+DLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNS-ERFCLGLLSNVNRNATVEMTRRHI
+GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ
+GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSVRCSSMS
+>gi|18655485|pdb|1KHX|A|/22-227
+DLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNS-ERFCLGLLSNVNRNATVEMTRRHI
+GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ
+GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSVRCSSMS
+>gi|13992583|emb|CAC38118.1|/1-425
+DLQPVTYCEPAFWCSISYYELNQRVGETFHASQPSMTVDGFTDPSNS-ERFCLGLLSNVNRNAAVELTRRHI
+GRGVRLYYIGGEVFAECLSDNAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ
+GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSIRCSSVS
+>gi|11875329|dbj|BAB19634.1|/1-425
+DLQPVTYCEPAFWCSISYYELNQRVGETFHASQPSMTVDGFTDPSNS-ERFCLGLLSNVNRNAAVELTRRHI
+GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ
+GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSIRCSSVS
+>gi|45331052|gb|AAS57862.1|/1-422
+DLQPVTYCESAFWCSISYYELNQRVGETFHASQPSLTVDGFTDPSNA-ERFCLGLLSNVNRNAAVELTRRHI
+GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ
+GFEAVYRLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPNLRCSSVS
+>gi|18418623|gb|AAL68976.1|/1-425
+DLQPVTYCEPAFWCSISYYELNQRVGETFHASQPSMTVDGFTDPSNS-ERFCLGLLSNVNRNAAVELTRRHI
+GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ
+GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSIRCSSVS
+>gi|2564493|gb|AAB81755.1|/1-425
+DLQPVTYCEPAFWCSISYYELNQRVGETFHASQPSMTVDGFTDPSNS-ERLCLGLLSNVNRNAAVELTRRHI
+GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ
+GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSIRCSSVS
+>gi|6981174|ref|NP_037227.1|/1-425
+DLQPVTYCEPAFWCSISYYELNQRVGETFHASQPSMTVDGFTDPSNS-ERFCLGLLSNVNRNAAVELTRRHI
+GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ
+GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSIRCSSVS
+>gi|45383213|ref|NP_989806.1|/1-426
+DLQPVTYCEPAFWCSISYYELNQRVGETFHASQPSMTVDGFTDPSNS-ERFCLGLLSNVNRNAAVELTRRHI
+GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ
+GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSIRCSSVS
+>gi|47523074|ref|NP_999302.1|/1-425
+DLQPVTYCEPAFWCSISYYELNQRVGETFHASQPSMTVDGFTDPSNS-ERFCLGLLSNVNRNAAVELTRRHI
+GRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEF----AALLAQSVNQ
+GFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSIRCSSVS