Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009476.1 Kokia drynarioides strain JFW-HI SEQ_124184, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3190
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Found at i:1494 original size:217 final size:215
Alignment explanation
Indices: 1--3183 Score: 3000
Period size: 216 Copynumber: 14.7 Consensus size: 215
* * * * * * * * *
1 TAAAAGCTTGACAAGTTTAGAAGTTTGTCTAAGAATCAAGAGAGAAATAATCTCACATAAATATG
1 TAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTTCACGTAAATAAG
* * * ** *
66 ATTTTAATTCAAAGACCAATAGTTGTTGACAAAATGACAAACTATTTAGATAAAATGATGCAATT
66 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATT
* * * * * *
131 TTTCGAACATGCAATGTTCTAAAAAAATCT-CTAGAAGGAATGGATCA-CATAGAATACTTTAAG
131 TCTCGAGCATGGAATGTTC--GAAAAAT-TGCTTGAAGGAATGGATCATC-TTGAATACTTTAAG
*
194 GAACCTAAGTTATAAAAGAACTCA-
192 GAACCGAAGTTATAAAAGAACT-AG
* * * * * * * * * *
218 TAAAAGTTAGACTAGTTC-GAAAGTTCATCCAATAACTAAGGGAGAGACAATTCCCACGTCATTA
1 TAAAAGTTTGACAAGTTCAG-AAGTTCGTCCAAGAACCAAGAGAGAAACAATT-TCACGTAAATA
* * * *
282 AGTTTTTAATTTAAAGACCAAAAGTTGTTTACAAAATGACAAAATATTTAGGCCGAATGATGCGA
64 AGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA
* * * * ** *
347 TTTCCCGA-CATGGAATGTTTGGAATAA-TGCTCGAAAAAATGGATCGTCTTGAATACTTTAAGG
129 TTTCTCGAGCATGGAATG-TTCGAAAAATTGCTTGAAGGAATGGATCATCTTGAATACTTTAAGG
410 AA-CGAAAGTTATAAAAGAACTCA-
193 AACCG-AAGTTATAAAAGAACT-AG
* * * * *
433 TAAAAGCTTGAAAAGTTCAGAAGTTCGTCTAAGAACTAAGAGAAAAACAATTCTCACGTAAATAA
1 TAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATT-TCACGTAAATAA
* * * * * * *
498 GTTTTTAATTCAAAGAGCAAAAGTTGTTTACAGAACGTCAAACTATTTAAACCAAAAGATTCGAT
65 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* * * * *
563 TT-TCGGAGAATGGAATGTTC-AAAAATTGC-TCAATGAAGTGGATCAT-TTATAATACTTCAAG
130 TTCTC-GAGCATGGAATGTTCGAAAAATTGCTTGAAGGAA-TGGATCATCTT-GAATACTTTAAG
* * * *
624 GAACAGAAGTTTTAAATTGAACTTG
192 GAACCGAAGTTATAAA-AGAACTAG
* * ** *
649 TAAAAGTTTGACAAGTTCGGAGGTTCGTCCAAGAACCAAGAGAGAAACAAATCCCACGTCAATAA
1 TAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAAC-AATTTCACGTAAATAA
* * * *
714 GTTTTTTATTCAAAGACCGAAAGTTGTTTACAAAATGACAAAGTATTTAGATCAAATGATGCGAT
65 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* * * * * * *
779 TTTTTGAACATTGAATGTTCGAAAAATTTG-TAGAAGGAATGGATCGCA-C-AGAATGCTTTAAG
130 TTCTCGAGCATGGAATGTTCGAAAAA-TTGCTTGAAGGAATGGAT--CATCTTGAATACTTTAAG
*
841 GAACCTAAGTTATAAAAGAACTAG
192 GAACCGAAGTTATAAAAGAACTAG
** * * * * *
865 TAAAAGTTTGACAAGTTCCTAAGTTCATCCAAGAACTAGGAGAGAAACAATTCTCTCGTAAATAG
1 TAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATT-TCACGTAAATAA
* * *
930 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAATATTTAGACCAAATGATACAAT
65 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* * * ** *
995 TTCTCGAGCATGGAATGTTTGGAATATTGCTTGAAATAATCGATCATCTTGAATACTTTAAGGAA
130 TTCTCGAGCATGGAATGTTCGAAAAATTGCTTGAAGGAATGGATCATCTTGAATACTTTAAGGAA
* * * **
1060 CCAAAGTTAAAAAAGAATTCT
195 CCGAAGTTATAAAAGAACTAG
* * * * * *
1081 TGAAAGCTTGAAAAGTTCAGAAGTTCGTCTAAGAACCAAGAGAGAAACGATTCTCACATAAATAA
1 TAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATT-TCACGTAAATAA
* * * * *
1146 GTTTTTAATTTAAAGACAAAAAGTTGTTTACAAAATGACAAACTATTTAAACCAAGTGATGCAAT
65 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* * * *
1211 TTCTCGAGCATGGAATGTTCGCAAAATTGC-TCAGAGAAATGGATCATCTTGAATACTTTGAGGA
130 TTCTCGAGCATGGAATGTTCGAAAAATTGCTTGA-AGGAATGGATCATCTTGAATACTTTAAGGA
*
1275 ACCGAAGTTACT-ACAGTAA-TAG
194 ACCGAAGTTA-TAAAAG-AACTAG
** * *
1297 TAAAAGTTTTCCTAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTTACACATAAATAA
1 TAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTT-CACGTAAATAA
* * ** * * *
1362 GTATTTAATTCAATGACCGAAATTTTGTCTACAAAATGACAAACTATTTTGACCGAATGATGCG-
65 GTTTTTAATTCAAAGACC-AAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA
* * * * * *
1426 TAGTCCCGAGCATGGGATGTTCGGAATATTGCTTGAAGGAATGGATCACCTTGAATACTTTAAGG
129 T-TTCTCGAGCATGGAATGTTCGAAAAATTGCTTGAAGGAATGGATCATCTTGAATACTTTAAGG
* *
1491 AACCAAAGTTATTATAAAAGAAATAG
193 AACCGAAG---TTATAAAAGAACTAG
* * * * * * * * * *
1517 TAAAAGCTGGACAAG-TCAGAAGTTTGTCTAAGAATCAAAAGTGAAATAAATCTC-C-CAAATAT
1 TAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAA-CAATTTCACGTAAATA-
* * *
1579 A-TTTTTAATTCAAAGACCAAAAAGTTGTTTGCAAAATGACAAACTATTTAGACCGAATGATGCT
64 AGTTTTTAATTCAAAGACC-AAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCG
* * * * * *
1643 ATTTCTCGAGCATGGAATGTTTGAAATATTGATCGAAGGAATGTATCGTCTTGAATACTTTAAGG
128 ATTTCTCGAGCATGGAATGTTCGAAAAATTGCTTGAAGGAATGGATCATCTTGAATACTTTAAGG
* *
1708 AACCAAAGTTATAAAAGAACTCG
193 AACCGAAGTTATAAAAGAACTAG
* * * * * *
1731 TAAAAGCTTGACTAGTTCAGAAGTTCATCTAAGAACCAA-AGGAGAAATAATTCTCACGTAAACA
1 TAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGA-GAGAAACAATT-TCACGTAAATA
* *** * * * * *
1795 TGTTTTTAATTTGCAGACCAAAACTTGGTTTTCAAAATGAAAAACTATTTAGACCAAAAGATGCA
64 AGTTTTTAATTCAAAGACCAAAAGTT-GTTTACAAAATGACAAACTATTTAGACCAAATGATGCG
* * * * * * *
1860 ATTTCTCGAGCATGAAATGTTTGGAAAATTGC-TCATAGAAATGGATGATCTTGAATACTTTATG
128 ATTTCTCGAGCATGGAATGTTCGAAAAATTGCTTGA-AGGAATGGATCATCTTGAATACTTTAAG
* * *
1924 GAACCGAAGTTGTAAAATAACTCG
192 GAACCGAAGTTATAAAAGAACTAG
* * * * * *
1948 TAAAAGTTTTACAAGTCCGGTAGTTCGACCAAGAACCAAGAGAGAAACAATTTTCACATAAATAA
1 TAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAA-TTTCACGTAAATAA
* *
2013 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAAACCAAAAT-ATTCGA
65 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACC-AAATGATGCGA
** * * * * * *
2077 TTTC-CGGAAAATGGATTGTTC-AAAAATTGCTCG-ATGAAGTGGATCATTTATAGAACACTTCA
129 TTTCTC-GAGCATGGAATGTTCGAAAAATTGCTTGAAGGAA-TGGATCATCT-T-GAATACTTTA
* *
2139 AGGAACCGAAGTTTTAAAAGAACTTG
190 AGGAACCGAAGTTATAAAAGAACTAG
* * ** *
2165 TAAAAGTTTGACAAGTTCGGAGGTTCGTCCAAGAACCAAGAGAGAAACAAATCCCACGTCAATAA
1 TAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAAC-AATTTCACGTAAATAA
* * * * * * **
2230 GTTTTTAATTCAATGACCAAAACTTGTTTACAAAATGACAATCTATTTAGATCACATAATAAGAT
65 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* * * * * ** *
2295 TT-TCCAAACATTGAATGTTCGAAAAATTTG-TAGAAGGAATGGATC-GCAAAGAATGCTTTAAG
130 TTCT-CGAGCATGGAATGTTCGAAAAA-TTGCTTGAAGGAATGGATCATC-TTGAATACTTTAAG
** *
2357 GAACATAAGTTATAAAAGAACTCG
192 GAACCGAAGTTATAAAAGAACTAG
* * * * ** *
2381 TAAATGTTTGACAAGTTCGGGAGTTCATCCAAGAAATAAGAGAGAAACAATTCTCACGAAAATAA
1 TAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATT-TCACGTAAATAA
* * *
2446 GTTTTTAATTCAAAGACCAAAATTTGTTTACAAAATGACAAAATATTTAGACCGAATGATGCGAT
65 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* * * * * * *
2511 TTCTCGAGCATGGAATGTTTGGAATATTGCTTGAAAGAATGAATCGTCTTGAATACTTTGAGGAA
130 TTCTCGAGCATGGAATGTTCGAAAAATTGCTTGAAGGAATGGATCATCTTGAATACTTTAAGGAA
* * *
2576 TC-AATGTTATAAAAGAAGTCG
195 CCGAA-GTTATAAAAGAACTAG
* * * * *
2597 TAAAAGCTTGAAAAGTTCAGAAGTACATCTAAGAACCAAGAGAGAAACAATTCTCACGTAAATAA
1 TAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATT-TCACGTAAATAA
* * * *
2662 GTTTTCAATTCAAAGGCCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAGTGATGCAAT
65 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* * * *
2727 TTC-CGGAGCATGGAATGTTCGCAAAATTGCTCGAAGAAACGGATCATCTTGAATACTTTAAGGA
130 TTCTC-GAGCATGGAATGTTCGAAAAATTGCTTGAAGGAATGGATCATCTTGAATACTTTAAGGA
* *
2791 ACCGAAGTTATAACAGAAATAG
194 ACCGAAGTTATAAAAGAACTAG
** * *
2813 TAAAAGTTTTCCTAGTTC-GAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTTACACATAAATA
1 TAAAAGTTTGACAAGTTCAG-AAGTTCGTCCAAGAACCAAGAGAGAAACAATTT-CACGTAAATA
* * * * *
2877 AGTATTTAATTCAATGACCAAAAGTTGTTTACAAAATGACAAGCTATTTTGACCGAATGATGCGA
64 AGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA
* *
2942 TTTCTCGAGCATGGAATGTTCGAAATATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGA
129 TTTCTCGAGCATGGAATGTTCGAAAAATTGCTTGAAGGAATGGATCATCTTGAATACTTTAAGGA
* * *
3007 ACTGAAGTTATAAAAGAAATTG
194 ACCGAAGTTATAAAAGAACTAG
* * * * * * *
3029 TAAAAGCTTGACAAGTTCTGAAGCTT-GTCTAAGAATCAAGAGAGAAATAATTTCACATAAATAT
1 TAAAAGTTTGACAAGTTCAGAAG-TTCGTCCAAGAACCAAGAGAGAAACAATTTCACGTAAATAA
* * * * **
3093 GATCTAAATTCAAAAACCAAAAGTTGTTTACAAAATGACAAACTATTTAGATAAAATGATGCGAT
65 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* * * * *
3158 TTTTCGAACTTGCAATGTTCAAAAAA
130 TTCTCGAGCATGGAATGTTCGAAAAA
3184 ATTTCTA
Statistics
Matches: 2412, Mismatches: 476, Indels: 158
0.79 0.16 0.05
Matches are distributed among these distances:
214 48 0.02
215 338 0.14
216 1215 0.50
217 648 0.27
218 101 0.04
219 39 0.02
220 23 0.01
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (215 bp):
TAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTTCACGTAAATAAG
TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATT
TCTCGAGCATGGAATGTTCGAAAAATTGCTTGAAGGAATGGATCATCTTGAATACTTTAAGGAAC
CGAAGTTATAAAAGAACTAG
Done.