Refine dataset 130217001630855CAIFx7efltEgYJVBUdSRb

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History

Step 1: 1000 unaligned sequences → New tree, 23:28:56
Step 2: 334 unaligned sequences → New tree, 23:59:41
Step 3: 285 unaligned sequences → Aligned, 00:05:17
Step 4: 58 sequences × 0 gap-free sites → Clipped, 00:10:01
Step 5: 51 sequences × 17 gap-free sites → Clipped, 00:17:04
Step 6: 49 sequences × 89 gap-free sites →
Refine dataset

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Realign the selected sequences (alignment→reset; numbering→reset)
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Clip the selected sequences (alignment→kept; numbering→kept)
  
 removes redundant sequences. help
 increases the number of gap-free sites. help
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Select / Unselect representative organisms:
 HOMSA XENTR ORYLA

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   1 HOMSA|gi|5729790|ref|NP_006556.1| transcriptional repressor CTCF isoform 1 [Homo sapiens]
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   2 PELSI|ENSPSIP00000003796 pep:novel scaffold:PelSin_1.0:JH205822.1:16124:37080:-1 gene:ENSPSIG00000003593 transcript:ENSPSIT00000003816 gene_biotype:protein_coding transcript_biotype:protein_coding
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   3 gi|171474905|gb|ACB47393.1| CCCTC-binding factor [Pogona vitticeps]
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   7 gi|327281289|ref|XP_003225381.1| PREDICTED: transcriptional repressor CTCF-like [Anolis carolinensis]
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   8 MONDO|ENSMODP00000007129 pep:novel chromosome:BROADO5:1:685282646:685300408:1 gene:ENSMODG00000005757 transcript:ENSMODT00000007273 gene_biotype:protein_coding transcript_biotype:protein_coding
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   9 SARHA|ENSSHAP00000004296 pep:novel scaffold:DEVIL7.0:GL834762.1:75014:90492:1 gene:ENSSHAG00000003783 transcript:ENSSHAT00000004340 gene_biotype:protein_coding transcript_biotype:protein_coding
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   10 MACEU|ENSMEUP00000005228 pep:novel genescaffold:Meug_1.0:GeneScaffold_6565:184:14145:1 gene:ENSMEUG00000005728 transcript:ENSMEUT00000005742 gene_biotype:protein_coding transcript_biotype:protein_coding
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   4 gi|396094|emb|CAA80319.1| CTCF protein [Gallus gallus]
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   5 gi|326927215|ref|XP_003209788.1| PREDICTED: transcriptional repressor CTCF-like [Meleagris gallopavo]
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   6 MELGA|ENSMGAP00000001773 pep:novel chromosome:UMD2:13:1721989:1735383:-1 gene:ENSMGAG00000002200 transcript:ENSMGAT00000002439 gene_biotype:protein_coding transcript_biotype:protein_coding
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   11 SARHA|ENSSHAP00000004295 pep:novel scaffold:DEVIL7.0:GL834762.1:75014:90492:1 gene:ENSSHAG00000003783 transcript:ENSSHAT00000004339 gene_biotype:protein_coding transcript_biotype:protein_coding
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   12 gi|224063911|ref|XP_002196108.1| PREDICTED: CCCTC-binding factor (zinc finger protein) [Taeniopygia guttata]
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   14 gi|34785484|gb|AAH57697.1| Ctcf protein [Xenopus laevis]
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   15 gi|11878220|gb|AAG40852.1|AF305695_1 transcriptional repressor [Xenopus laevis]
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   16 XENTR|ENSXETP00000062683 pep:known scaffold:JGI_4.2:GL172782.1:1468935:1488905:1 gene:ENSXETG00000015615 transcript:ENSXETT00000060905 gene_biotype:protein_coding transcript_biotype:protein_coding
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   17 gi|170284950|gb|AAI61099.1| ctcf protein [Xenopus (Silurana) tropicalis]
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   18 LATCH|ENSLACP00000011174 pep:novel scaffold:LatCha1:JH126699.1:452823:489575:1 gene:ENSLACG00000009833 transcript:ENSLACT00000011258 gene_biotype:protein_coding transcript_biotype:protein_coding
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   25 ORENI|ENSONIP00000007230 pep:novel scaffold:Orenil1.0:GL831150.1:2536970:2540553:1 gene:ENSONIG00000005736 transcript:ENSONIT00000007235 gene_biotype:protein_coding transcript_biotype:protein_coding
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   26 gi|348509710|ref|XP_003442390.1| PREDICTED: transcriptional repressor CTCF-like [Oreochromis niloticus]
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   27 ORENI|ENSONIP00000007229 pep:novel scaffold:Orenil1.0:GL831150.1:2536889:2541050:1 gene:ENSONIG00000005736 transcript:ENSONIT00000007234 gene_biotype:protein_coding transcript_biotype:protein_coding
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   28 TAKRU|ENSTRUP00000045998 pep:novel scaffold:FUGU4:scaffold_14:1533474:1536803:-1 gene:ENSTRUG00000017943 transcript:ENSTRUT00000046152 gene_biotype:protein_coding transcript_biotype:protein_coding
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   29 TAKRU|ENSTRUP00000045999 pep:novel scaffold:FUGU4:scaffold_14:1533474:1536800:-1 gene:ENSTRUG00000017943 transcript:ENSTRUT00000046153 gene_biotype:protein_coding transcript_biotype:protein_coding
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   30 TETNI|ENSTNIP00000012180 pep:novel chromosome:TETRAODON8:5:5277710:5281213:1 gene:ENSTNIG00000009314 transcript:ENSTNIT00000012371 gene_biotype:protein_coding transcript_biotype:protein_coding
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   31 gi|47230373|emb|CAF99566.1| unnamed protein product [Tetraodon nigroviridis]
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   32 GASAC|ENSGACP00000020939 pep:novel group:BROADS1:groupII:11613372:11616719:-1 gene:ENSGACG00000015865 transcript:ENSGACT00000020979 gene_biotype:protein_coding transcript_biotype:protein_coding
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   33 GASAC|ENSGACP00000020941 pep:novel group:BROADS1:groupII:11613372:11616695:-1 gene:ENSGACG00000015865 transcript:ENSGACT00000020981 gene_biotype:protein_coding transcript_biotype:protein_coding
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   34 ORYLA|ENSORLP00000011017 pep:known chromosome:MEDAKA1:3:20410268:20415910:-1 gene:ENSORLG00000008771 transcript:ENSORLT00000011018 gene_biotype:protein_coding transcript_biotype:protein_coding
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   35 ORENI|ENSONIP00000005164 pep:novel scaffold:Orenil1.0:GL831206.1:2751803:2762795:1 gene:ENSONIG00000004097 transcript:ENSONIT00000005168 gene_biotype:protein_coding transcript_biotype:protein_coding
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   36 gi|348523553|ref|XP_003449288.1| PREDICTED: transcriptional repressor CTCF-like [Oreochromis niloticus]
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   37 ORYLA|ENSORLP00000022986 pep:novel ultracontig:MEDAKA1:ultracontig72:341588:352749:1 gene:ENSORLG00000018357 transcript:ENSORLT00000022987 gene_biotype:protein_coding transcript_biotype:protein_coding
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   38 GADMO|ENSGMOP00000006796 pep:novel genescaffold:gadMor1:GeneScaffold_4125:40745:45236:1 gene:ENSGMOG00000006386 transcript:ENSGMOT00000006994 gene_biotype:protein_coding transcript_biotype:protein_coding
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   39 GASAC|ENSGACP00000003270 pep:novel group:BROADS1:groupXIX:1433175:1439803:1 gene:ENSGACG00000002504 transcript:ENSGACT00000003281 gene_biotype:protein_coding transcript_biotype:protein_coding
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   19 gi|126632718|emb|CAM56716.1| CCCTC-binding factor (zinc finger protein) [Danio rerio]
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   41 SARHA|ENSSHAP00000015681 pep:novel scaffold:DEVIL7.0:GL834666.1:1222728:1242523:1 gene:ENSSHAG00000013360 transcript:ENSSHAT00000015809 gene_biotype:protein_coding transcript_biotype:protein_coding
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   42 SARHA|ENSSHAP00000015680 pep:novel scaffold:DEVIL7.0:GL834666.1:1220619:1244690:1 gene:ENSSHAG00000013360 transcript:ENSSHAT00000015808 gene_biotype:protein_coding transcript_biotype:protein_coding
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   43 MONDO|ENSMODP00000020611 pep:novel chromosome:BROADO5:1:486248077:486266900:1 gene:ENSMODG00000016490 transcript:ENSMODT00000020976 gene_biotype:protein_coding transcript_biotype:protein_coding
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   44 ORNAN|ENSOANP00000025255 pep:known ultracontig:OANA5:Ultra516:6791142:6804936:-1 gene:ENSOANG00000009260 transcript:ENSOANT00000029059 gene_biotype:protein_coding transcript_biotype:protein_coding
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   46 HOMSA|gi|29570785|ref|NP_542185.2| transcriptional repressor CTCFL [Homo sapiens]
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   47 PELSI|ENSPSIP00000012493 pep:novel scaffold:PelSin_1.0:JH209331.1:1517019:1535688:1 gene:ENSPSIG00000011195 transcript:ENSPSIT00000012554 gene_biotype:protein_coding transcript_biotype:protein_coding
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   48 gi|171474913|gb|ACB47397.1| brother of regulator of imprinted sites [Pogona vitticeps]
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   49 ANOCA|ENSACAP00000016003 pep:novel scaffold:AnoCar2.0:GL343217.1:1034665:1047855:1 gene:ENSACAG00000016243 transcript:ENSACAT00000016323 gene_biotype:protein_coding transcript_biotype:protein_coding
 +reg Begin: End:
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   50 SARHA|ENSSHAP00000001830 pep:novel scaffold:DEVIL7.0:GL867782.1:14413:31463:1 gene:ENSSHAG00000001630 transcript:ENSSHAT00000001851 gene_biotype:protein_coding transcript_biotype:protein_coding
 +reg Begin: End:
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   40 PETMA|ENSPMAP00000004689 pep:putative scaffold:Pmarinus_7.0:GL483954:4616:13063:1 gene:ENSPMAG00000004257 transcript:ENSPMAT00000004708 gene_biotype:protein_coding transcript_biotype:protein_coding
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   54 BRAFL|gi|260819198|ref|XP_002604924.1| hypothetical protein BRAFLDRAFT_217118 [Branchiostoma floridae]
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   53 MACEU|ENSMEUP00000007622 pep:novel genescaffold:Meug_1.0:GeneScaffold_3588:549:7519:-1 gene:ENSMEUG00000008337 transcript:ENSMEUT00000008359 gene_biotype:protein_coding transcript_biotype:protein_coding
 +reg Begin: End:
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   55 OIKDI|GSOIDT00001753001
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   56 CIOIN|ENSCINP00000013892 pep:known scaffold:KH:HT000097.1:44901:51453:1 gene:ENSCING00000006765 transcript:ENSCINT00000013892 gene_biotype:protein_coding transcript_biotype:protein_coding
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   57 CIOIN|ENSCINP00000031196 pep:known scaffold:KH:HT000097.1:44901:51453:1 gene:ENSCING00000006765 transcript:ENSCINT00000036493 gene_biotype:protein_coding transcript_biotype:protein_coding
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   58 STRPU|gi|72028083|ref|XP_797592.1| PREDICTED: uncharacterized protein LOC593001 [Strongylocentrotus purpuratus]
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MAYSCRIPT
Archaeopteryx home:
https://sites.google.com/site/cmzmasek/home/software/archaeopteryx
Archaeopteryx references:
Zmasek and Eddy (2001)
Han and Zmasek (2009)
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