Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017874.1 Corchorus olitorius cultivar O-4 contig17907, 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: 2767
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:448 original size:22 final size:22
Alignment explanation
Indices: 423--464 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
413 TTTTTGGACA
*
423 CAATTTTCCCTATTTTTTTCCT
1 CAATTTTCCCTATTTATTTCCT
*
445 CAATTTTCCGTATTTATTTC
1 CAATTTTCCCTATTTATTTC
465 TGATAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.17, C:0.24, G:0.02, T:0.57
Consensus pattern (22 bp):
CAATTTTCCCTATTTATTTCCT
Found at i:1232 original size:327 final size:331
Alignment explanation
Indices: 631--1245 Score: 707
Period size: 327 Copynumber: 1.9 Consensus size: 331
621 AAACCCTAAC
** * *
631 GTACACGATTTCGGCTAAAATTTTATAAAAACTGACCCGAAAGATTTTGCCTCAATTTTTAGCCA
1 GTACACGATTTCGGCTAAAATTTTATAAAAACTGACCAAAAAAATTTTGCCTCAATTTTTAGACA
* * * * * *
696 TAATATTCGAGAAAAATATACGACTCAAGCCAACAATATTGAAGGGATTTTCATGCTTCTAATAT
66 GAATACTCGAGAAAAATATACAACTCAAGCCAAAAAGATTGAAGGGATTTTCAAGCTTCTAATAT
* * **
761 AGTTTTTCATATTTGCTTCCCAATTAATTTCTAAGAAAATCAAAACAAGATTCTGATCCTCGTAA
131 AGTTTTT-ATATTTGCTT-CCAATTAATTTCTAAGAAAAGCAAAACAAGATCCAAATCCTCGTAA
* * * *
826 AAACAAATCCTCAAATCTATTGTGGCTAAGATTTCGTTAGATAAATATAGATATGTCAAGGAGTC
194 AAACAAATCATCAAATCCAATGTGACTAAGATTTCGTTAGATAAATATAGATATGTCAAGGAGTC
* *
891 TGCGCGCCAAAAATCATGCAAAACTGAGGCGGGGCCCGAAACACGTTTTTAGCAAAAAAAAACTG
259 TGCGCGCAAAAAATCAAGCAAAACTGAGGCGGGGCCCGAAACACGTTTTTAGCAAAAAAAAACTG
956 TGACGGTA
324 TGACGGTA
* * *
964 GTACACGATTTCGGCTAAAATTTTAT-AAAAGTGGATTCAAAAAAATTTT-CCTCAATTTTTGGA
1 GTACACGATTTCGGCTAAAATTTTATAAAAACT-GA-CCAAAAAAATTTTGCCTCAATTTTTAGA
* *
1027 CAGAATACTCGTA-AAATATATATAACTCAACGCCAAAAAGATTGAA-GGACTTTTCAAGCTTCT
64 CAGAATACTCG-AGAAAAATATACAACTCAA-GCCAAAAAGATTGAAGGGA-TTTTCAAGCTTCT
* ** * *
1090 AATATCA-TTTTT-T-TTT-C-T-GAATTAATTTCTAATTAAAGCGAAACAAGATCCAAATGCTC
126 AATAT-AGTTTTTATATTTGCTTCCAATTAATTTCTAAGAAAAGCAAAACAAGATCCAAATCCTC
* ** * * *
1149 GTAAAAACAATTCATTTAATCCAATGTGACTGAGATTTTGTTAGACT-AATATAGATATTTCAAG
190 GTAAAAACAAATCATCAAATCCAATGTGACTAAGATTTCGTTAGA-TAAATATAGATATGTCAAG
*
1213 GAGTCTG-GACAG-AAAAAATCAAGGAAAACTGAG
254 GAGTCTGCG-C-GCAAAAAATCAAGCAAAACTGAG
1246 CTGGGGCACT
Statistics
Matches: 236, Mismatches: 37, Indels: 24
0.79 0.12 0.08
Matches are distributed among these distances:
326 1 0.00
327 110 0.47
328 2 0.01
329 1 0.00
330 1 0.00
331 3 0.01
332 6 0.03
333 66 0.28
334 45 0.19
335 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.30
Consensus pattern (331 bp):
GTACACGATTTCGGCTAAAATTTTATAAAAACTGACCAAAAAAATTTTGCCTCAATTTTTAGACA
GAATACTCGAGAAAAATATACAACTCAAGCCAAAAAGATTGAAGGGATTTTCAAGCTTCTAATAT
AGTTTTTATATTTGCTTCCAATTAATTTCTAAGAAAAGCAAAACAAGATCCAAATCCTCGTAAAA
ACAAATCATCAAATCCAATGTGACTAAGATTTCGTTAGATAAATATAGATATGTCAAGGAGTCTG
CGCGCAAAAAATCAAGCAAAACTGAGGCGGGGCCCGAAACACGTTTTTAGCAAAAAAAAACTGTG
ACGGTA
Found at i:1565 original size:333 final size:322
Alignment explanation
Indices: 448--1645 Score: 999
Period size: 326 Copynumber: 3.6 Consensus size: 322
438 TTTTCCTCAA
* * * * *
448 TTTTCCGTATTTATTTCTGATAAAAATGAAAC-CGATTTTCTGATGCTCGTAAAAATAAATCCTT
1 TTTTCCGAATTAATTTCTAATAAAAATGAAACAAGA--TTCTGATGCTCGTAAAAACAAATCCTT
* * *
512 AAATCCAAAGTGGTTGAGATTTCGTTAGATAAATATAGATATTTCAAGGAGTTTGGGTGACAAAA
64 AAATCCAATGTGGCTGAGATTTCGTTAGATAAATATAGATATTTCAAGGAGTCTGGGTGACAAAA
* * * ** *
577 ATCAAGAAAAAATGTGCCGGGGCTGCGTAATGCGTTTTTAGCAAAAACCCTAA--CGTACACGAT
129 ATCAAGAAAAACTGAGCCGGGGC-CCGTAATGCGTTTTTAGCAAAAACTGTAAGTAGTACACGAT
* * * * * * *
640 TTCGGCTAAAATTTTATAAAAACTGACCCG-AAAGATTTTGCCTCAATTTTTAGCCATAATATTC
193 TTCGGCTAAAATTTTAT-AAAATTGTCCCGAAAAG-TTTTTCCTCAATTTTTGGACACAATACTC
* * * * * * *
704 GAGAAAAATATACGACTCA-AGCCAACAATATTGAAGGGATTTTCATGCTTCTAATATAGTTTTT
256 -ATAAAAATATACAACTCACA-CCAA-AAGATTGAAGGGCTTTTCAAGCTTCTAATATCG-ATTT
768 CATATT
317 CATATT
* * * * * *
774 TGCTTCCCAATTAATTTCTAA-GAAAATCAAAACAAGATTCTGATCCTCGTAAAAACAAATCCTC
1 T-TTTCCGAATTAATTTCTAATAAAAAT-GAAACAAGATTCTGATGCTCGTAAAAACAAATCCTT
* * * * * * *
838 AAATCTATTGTGGCTAAGATTTCGTTAGATAAATATAGATATGTCAAGGAGTCTGCGCGCCAAAA
64 AAATCCAATGTGGCTGAGATTTCGTTAGATAAATATAGATATTTCAAGGAGTCTGGGTGACAAAA
* * * * ** *
903 ATCATGCAAAACTGAGGCGGGGCCCGAAACACGTTTTTAGCAAAAAAAAACTGTGACGGTAGTAC
129 ATCAAGAAAAACTGAGCCGGGGCCCGTAATGCGTTTTTAGC----AAAAACTGT-A-AGTAGTAC
* * * ** *
968 ACGATTTCGGCTAAAATTTTATAAAAGTGGAT-TCAAAAAAATTTTCCTCAATTTTTGGACAGAA
188 ACGATTTCGGCTAAAATTTTATAAAA-TTG-TCCCGAAAAGTTTTTCCTCAATTTTTGGACACAA
* * * *
1032 TACTCGTAAAATATATATAACTCAACGCCAAAAAGATTGAAGGACTTTTCAAGCTTCTAATATC-
251 TACTCATAAAA-ATATACAACTC-ACACC-AAAAGATTGAAGGGCTTTTCAAGCTTCTAATATCG
1096 A-TT--T-TT
313 ATTTCATATT
* * ** * ** * * *
1102 TTTTCTGAATTAATTTCTAATTAAAGCGAAACAAGATCCAAATGCTCGTAAAAACAATTCATTTA
1 TTTTCCGAATTAATTTCTAATAAAAATGAAACAAGATTCTGATGCTCGTAAAAACAAATCCTTAA
* * **
1167 ATCCAATGTGACTGAGATTTTGTTAGACT-AATATAGATATTTCAAGGAGTCTGGACAGA-AAAA
66 ATCCAATGTGGCTGAGATTTCGTTAGA-TAAATATAGATATTTCAAGGAGTCTGG-GTGACAAAA
* * * *
1230 ATCAAGGAAAACTGAGCTGGGGCACTGTAATGCGTTTTTAGTAAAAACTGTAATGTTTTAGTACA
129 ATCAAGAAAAACTGAGCCGGGGC-CCGTAATGCGTTTTTAGCAAAAACTGTAA-G---TAGTACA
* * * ** *
1295 CGTTTTCAGCGAAAATTTTGCAAAGATTGTCCCGAAAAGTTTTTCCTCAAATTTTGGACACAATA
189 CGATTTCGGCTAAAATTTTATAAA-ATTGTCCCGAAAAGTTTTTCCTCAATTTTTGGACACAATA
* * *
1360 CTCATAAAAGGTATACAATTCGACACCGAAAAGATTGAAGGGCTTTTCAAGCTTCTAATTTCGAT
253 CTCATAAAA-ATATACAACTC-ACACC-AAAAGATTGAAGGGCTTTTCAAGCTTCTAATATCGAT
1425 TTCACTAATT
315 TTCA-T-ATT
* * * *
1435 TTTTCCGTATTTATTTCTAATAAAAATGAAAC-CGATTTCTTATGCTCGT-AAAACGAAATCCTT
1 TTTTCCGAATTAATTTCTAATAAAAATGAAACAAGA-TTCTGATGCTCGTAAAAAC-AAATCCTT
* * * *
1498 AAATCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTTGGGTGACAAAA
64 AAATCCAATGTGGCTGAGATTTCGTTAGATAAATATAGATATTTCAAGGAGTCTGGGTGACAAAA
* * * * * * *
1563 ATCAAGAAAAATTGTGCCAGGGCCCCGGAATGCGTTTTTAGCAAAAACCCTG-ATGGTTAATACC
129 ATCAAGAAAAACTGAGCC-GGGGCCCGTAATGCGTTTTTAGCAAAAA--CTGTA-AG-TAGTACA
1627 CGATTTCGGCTAAAATTTT
189 CGATTTCGGCTAAAATTTT
1646 GCAAAAATTG
Statistics
Matches: 682, Mismatches: 147, Indels: 80
0.75 0.16 0.09
Matches are distributed among these distances:
323 2 0.00
324 9 0.01
325 15 0.02
326 211 0.31
327 133 0.20
328 25 0.04
329 8 0.01
330 1 0.00
331 3 0.00
332 40 0.06
333 191 0.28
334 39 0.06
335 5 0.01
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (322 bp):
TTTTCCGAATTAATTTCTAATAAAAATGAAACAAGATTCTGATGCTCGTAAAAACAAATCCTTAA
ATCCAATGTGGCTGAGATTTCGTTAGATAAATATAGATATTTCAAGGAGTCTGGGTGACAAAAAT
CAAGAAAAACTGAGCCGGGGCCCGTAATGCGTTTTTAGCAAAAACTGTAAGTAGTACACGATTTC
GGCTAAAATTTTATAAAATTGTCCCGAAAAGTTTTTCCTCAATTTTTGGACACAATACTCATAAA
AATATACAACTCACACCAAAAGATTGAAGGGCTTTTCAAGCTTCTAATATCGATTTCATATT
Found at i:1784 original size:146 final size:146
Alignment explanation
Indices: 1512--1801 Score: 393
Period size: 146 Copynumber: 2.0 Consensus size: 146
1502 CCAATGTGGT
* * *
1512 TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTTGGGTGACAAAAATCAAGAAAAATTG
1 TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGGGACAAAAATCAAGAAAAACTG
* * * *
1577 TGCCAGGGCCCCGGAATGCGTTTTTAGCAAAAACCCTGATGGTTAATACCCGATTTCGGCTAAAA
66 AGCCAGGGCACCGGAACGCGTTTTTAGCAAAAACCCTGATGGTTAATACACGATTTCGGCTAAAA
1642 TTTTGCAAAAATTGGC
131 TTTTGCAAAAATTGGC
* * *
1658 TGAGATTTTGTTAGATTAATATAGATATTTCAAGGAGTCTGGGCGGA-AAAAATCAAGCAAAACT
1 TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGG-GGACAAAAATCAAGAAAAACT
*** * * * * *
1722 GAGTTGGGGCACTGGAACGCGTTTTTAGCAAAAACCCTGATGGTTAGTACACGTTTTTGGCTAAT
65 GAGCCAGGGCACCGGAACGCGTTTTTAGCAAAAACCCTGATGGTTAATACACGATTTCGGCTAAA
*
1787 CTTTTGCAAAAATTG
130 ATTTTGCAAAAATTG
1802 TCTCGAAAAT
Statistics
Matches: 124, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
146 122 0.98
147 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (146 bp):
TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGGGACAAAAATCAAGAAAAACTG
AGCCAGGGCACCGGAACGCGTTTTTAGCAAAAACCCTGATGGTTAATACACGATTTCGGCTAAAA
TTTTGCAAAAATTGGC
Found at i:2082 original size:479 final size:479
Alignment explanation
Indices: 1178--2134 Score: 1540
Period size: 479 Copynumber: 2.0 Consensus size: 479
1168 TCCAATGTGA
*
1178 CTGAGATTTTGTTAGACTAATATAGATATTTCAAGGAGTCTGGACAGAAAAAATCAAGGAAAACT
1 CTGAGATTTTGTTAGACTAATATAGATATTTCAAGGAGTCTGGACAGAAAAAATCAAGCAAAACT
* * * ** *
1243 GAGCTGGGGCACTGTAATGCGTTTTTAGTAAAAACTGTAATGTTTTAGTACACGTTTTCAGCGAA
66 GAGCTGGGGCACTGGAACGCGTTTTTAGCAAAAACCCTAATGTGTTAGTACACGTTTTCAGCGAA
*
1308 AATTTTGCAAAGATTGTCCCGAAAAGTTTTTCCTCAAATTTTGGACACAATACTCATAAAAGGTA
131 AATTTTGCAAAAATTGTCCCGAAAAGTTTTTCCTCAAATTTTGGACACAATACTCATAAAAGGTA
*
1373 TACAATTCGACACCGAAAAGATTGAAGGGCTTTTCAAGCTTCTAATTTCGATTTCACTAATTTTT
196 TACAATTCGACACCGAAAAGATTGAAGGGCTTTTCAAGCTTCTAAATTCGATTTCACTAATTTTT
* *
1438 TCCGTATTTATTTCTAATAAAAATGAAACCGATTTCTTATGCTCGTAAAACGAAATCCTTAAATC
261 TCCGTATTTATTTCTAATAAAAATGAAACCGATTTCTGATGCTCGTAAAAAGAAATCCTTAAATC
1503 CAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTTGGGTGACAAAAATCAA
326 CAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTTGGGTGACAAAAATCAA
* * * * *
1568 GAAAAATTGTGCCAGGGCCCCGGAATGCGTTTTTAGCAAAAACCCTGATGGTTAATACCCGATTT
391 GAAAAACTGGGCCAGGGCCCCGAAATGCATTTTTAGCAAAAACCCTGATGGTTAATACACGATTT
1633 CGGCTAAAATTTTGCAAAAATTGG
456 CGGCTAAAATTTTGCAAAAATTGG
* * *
1657 CTGAGATTTTGTTAGATTAATATAGATATTTCAAGGAGTCTGGGCGGAAAAAATCAAGCAAAACT
1 CTGAGATTTTGTTAGACTAATATAGATATTTCAAGGAGTCTGGACAGAAAAAATCAAGCAAAACT
* * ** *
1722 GAGTTGGGGCACTGGAACGCGTTTTTAGCAAAAACCCTGATG-GTTAGTACACGTTTTTGGCTAA
66 GAGCTGGGGCACTGGAACGCGTTTTTAGCAAAAACCCTAATGTGTTAGTACACGTTTTCAGCGAA
** * **
1786 TCTTTTGCAAAAATTGTCTCGAAAA-TCTTTTCCTCAGTTTTTGGACACAATACTCATAAAAGGT
131 AATTTTGCAAAAATTGTCCCGAAAAGT-TTTTCCTCAAATTTTGGACACAATACTCATAAAAGGT
* * * **
1850 ATACAATTCGACACTGAAAATATTGAAGGGTTTTTCATTCTTCTAAATTCGATTTCACTAATTTT
195 ATACAATTCGACACCGAAAAGATTGAAGGGCTTTTCAAGCTTCTAAATTCGATTTCACTAA-TTT
* *
1915 TTTCCGTATTTATTTCTAATAAAAATGAAACCGATTTCTGATGCTCGTAAAAATAAATCCTTTAA
259 TTTCCGTATTTATTTCTAATAAAAATGAAACCGATTTCTGATGCTCGTAAAAAGAAATCCTTAAA
1980 TCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTTGGGTGACAAAAATC
324 TCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTTGGGTGACAAAAATC
* *
2045 AAGAAAAACTGGGCCGGGGCCCCGAAATGCATTTTTAGCAAAAACCCTGATGGTTAGTACACGAT
389 AAGAAAAACTGGGCCAGGGCCCCGAAATGCATTTTTAGCAAAAACCCTGATGGTTAATACACGAT
2110 TTCGGCTAAAATTTTGCAAAAATTG
454 TTCGGCTAAAATTTTGCAAAAATTG
2135 ACCCAAAAGA
Statistics
Matches: 438, Mismatches: 38, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
477 1 0.00
478 129 0.29
479 308 0.70
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (479 bp):
CTGAGATTTTGTTAGACTAATATAGATATTTCAAGGAGTCTGGACAGAAAAAATCAAGCAAAACT
GAGCTGGGGCACTGGAACGCGTTTTTAGCAAAAACCCTAATGTGTTAGTACACGTTTTCAGCGAA
AATTTTGCAAAAATTGTCCCGAAAAGTTTTTCCTCAAATTTTGGACACAATACTCATAAAAGGTA
TACAATTCGACACCGAAAAGATTGAAGGGCTTTTCAAGCTTCTAAATTCGATTTCACTAATTTTT
TCCGTATTTATTTCTAATAAAAATGAAACCGATTTCTGATGCTCGTAAAAAGAAATCCTTAAATC
CAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTTGGGTGACAAAAATCAA
GAAAAACTGGGCCAGGGCCCCGAAATGCATTTTTAGCAAAAACCCTGATGGTTAATACACGATTT
CGGCTAAAATTTTGCAAAAATTGG
Done.