Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014923.1 Corchorus olitorius cultivar O-4 contig14956, 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: 48820
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:688 original size:334 final size:332
Alignment explanation
Indices: 81--1807 Score: 2417
Period size: 334 Copynumber: 5.2 Consensus size: 332
71 CGGGGCCCAG
* * * *
81 GTACACGATTTCAGCCAAAATTTTGCAAAAACTGTCCTGAAAATTTTTTCCTCAATTTTTGGGCA
1 GTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCAATTTTTGGCCA
*
146 CAACACTCATAAAAAATATATAATTCAAGTCCAAATAGATTGAAGGGTTTTACACGCTTCAATTA
66 CAACACTCATAAAAAATATATAATTCAAGTCCAAATAGATTGAAGGGCTTTACACGCTTCAATTA
* * *
211 TCGTTTTTCCAATTTTTTCCGGATTAATTTCAAATTAAATCGAAACATTATTCAGATGCTCGAAT
131 TCGTTTTTCCTATTTTTTCCGGATTAATTTCTAATTAAATCGAAACATTATTCAGATGCTCGAAA
276 AAACAAATCCTTCAATCCAATGTATG-TGAGAATTGGTTAGATGAATATAGATATTTCAATGACA
196 AAACAAATCCTTCAATCCAATGTA-GCTGAGAATTGGTTAGATGAATATAGATATTTCAATGACA
* * *
340 CTAGGCGCCAAAAATCATGCAAAATTGTGTCGGGGCCCATGAACACGTTTTTAGCCAAAAACTGT
260 CTTGGCGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAGGAACACGTTTTTAGCCAAAAACTGT
405 GATGGTTA
325 GATGGTTA
413 GTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCAATTTTTGGCCA
1 GTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCAATTTTTGGCCA
*
478 CAACACTCATAAAAAAATATTTAATTCAAGTCCAAATAGATTGAAGGGCTTTACACGCTTCAATT
66 CAACACTCAT-AAAAAATATATAATTCAAGTCCAAATAGATTGAAGGGCTTTACACGCTTCAATT
* * *
543 ATTGTTTTTCCTATTTTTTTCCGGATTAATTTCTAATGAAATCGAAATATTATTCAGATGCTCGA
130 ATCGTTTTTCCTA-TTTTTTCCGGATTAATTTCTAATTAAATCGAAACATTATTCAGATGCTCGA
*
608 AAAAACAAATCCTTCAATCAAATGTAGCTGAGAATTGGTTAGATGAATATAGATATTTCAATGAC
194 AAAAACAAATCCTTCAATCCAATGTAGCTGAGAATTGGTTAGATGAATATAGATATTTCAATGAC
673 ACTTGGCGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAGGAACACGTTTTTAGCCAAAAACTG
259 ACTTGGCGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAGGAACACGTTTTTAGCCAAAAACTG
*
738 TGATGGATA
324 TGATGGTTA
* *
747 GTACACGATTTCGGCCAAAATTTTTCAAAAACTGTCCCGAAAAATTTTTCCTCAATTTTTGGACA
1 GTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCAATTTTTGGCCA
* * * * * * * * * * *
812 CAATACTCATAAAAGATATATAACTCAACG-CCAAAAAAATTTAACGGCTTTTCATG-TTTATAA
66 CAACACTCATAAAAAATATATAATTCAA-GTCCAAATAGATTGAAGGGCTTTACACGCTTCA-AT
* * * *
875 TATCGTTTTTCCTA--TTTTCTGAATTAATTTCTAATTAAATCGAAACATAATTCAGATGCTCGT
129 TATCGTTTTTCCTATTTTTTCCGGATTAATTTCTAATTAAATCGAAACATTATTCAGATGCTCGA
*** * * * * * * * *
938 AAAAACTTCTCCTTCAATCGATTGTAGCTAAGATTTGGTTAGATGAACATAGATATTTTAAGGAG
194 AAAAACAAATCCTTCAATCCAATGTAGCTGAGAATTGGTTAGATGAATATAGATATTTCAATGAC
* * * * * *
1003 TCTT-GCTGCAAAAAATCATCCAAAACTGTGTCGGGGCCTAGGAACTCGTTTTTAGCCAAAAATT
259 ACTTGGC-GCCAAAAATCATGCAAAACTGTGTCGGGGCCCAGGAACACGTTTTTAGCCAAAAACT
1067 GTGATGGTTA
323 GTGATGGTTA
* * * * *
1077 GTATACGATTTCGGCTAAAATTTTGCAAAAACTGTCCCGAAAATTTTTTCCTAAAGTTTTGGCCA
1 GTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCAATTTTTGGCCA
*
1142 CAACACTCATAAAAAATATATAATTCAAGTCCAAATAGAATGAAGGGCTTTACACGCTTCAATTA
66 CAACACTCATAAAAAATATATAATTCAAGTCCAAATAGATTGAAGGGCTTTACACGCTTCAATTA
* * * *
1207 TCGTTTTTCCTATTTTTTTTCGGGATTAATTTCTAATTAAATAGAAACATTATTTAGATGCT-TA
131 TCGTTTTTCCTA--TTTTTTCCGGATTAATTTCTAATTAAATCGAAACATTATTCAGATGCTCGA
* * *
1271 AAAAATAAATCCTTCAATCCATTGTAGCTAAGAATTGGTTAGATGAATATAGATATTTCAATGAC
194 AAAAACAAATCCTTCAATCCAATGTAGCTGAGAATTGGTTAGATGAATATAGATATTTCAATGAC
* * * *
1336 ACTTGGCGCCAAAAATCATGCAAAATTGTGTCGCGGCCCATGAACACGGTTTTAGCCAAAAACTG
259 ACTTGGCGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAGGAACACGTTTTTAGCCAAAAACTG
1401 TGATGGTTA
324 TGATGGTTA
* * *
1410 GTATAACTAACGTGCACGATTTCGGCCAAAATTTTACAAAAACTGTCTCGAAAAATGTTTCCTCA
1 G------T-A----CACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCA
* * *
1475 ATTTTTGGCCATAACACTCATAAAAAGTATATAATTCAAGTCCAAATAGATTGACGGGCTTTACA
55 ATTTTTGGCCACAACACTCATAAAAAATATATAATTCAAGTCCAAATAGATTGAAGGGCTTTACA
* * * *
1540 CGCTTCAATTATCGTTTTTCCTATTTGTTCGGGATTAATTTCTAATTAAATAGAAACATTATTTA
120 CGCTTCAATTATCGTTTTTCCTATTTTTTCCGGATTAATTTCTAATTAAATCGAAACATTATTCA
** * * * * *
1605 GATGCTTAAAAAAACAAATCCTTGAATTCAATTTAGATGAGAATTGGTTAGATGAATATACATAT
185 GATGCTCGAAAAAACAAATCCTTCAATCCAATGTAGCTGAGAATTGGTTAGATGAATATAGATAT
*
1670 TTCAATGACACTTGGCGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAGGAACACCTTTTTAGC
250 TTCAATGACACTTGGCGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAGGAACACGTTTTTAGC
1735 CAAAAACTGTGATGGTTA
315 CAAAAACTGTGATGGTTA
** *
1753 GTACACGATTTCGGAGAAAATTTTGCAAAAACTGTCCC-AAAATTTTTTTCCTCAA
1 GTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAA-ATTTTTCCTCAA
1808 CATCAAAAAA
Statistics
Matches: 1234, Mismatches: 135, Indels: 52
0.87 0.10 0.04
Matches are distributed among these distances:
329 3 0.00
330 278 0.23
331 7 0.01
332 115 0.09
333 230 0.19
334 295 0.24
336 1 0.00
337 1 0.00
339 1 0.00
340 1 0.00
342 47 0.04
343 128 0.10
344 127 0.10
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (332 bp):
GTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCAATTTTTGGCCA
CAACACTCATAAAAAATATATAATTCAAGTCCAAATAGATTGAAGGGCTTTACACGCTTCAATTA
TCGTTTTTCCTATTTTTTCCGGATTAATTTCTAATTAAATCGAAACATTATTCAGATGCTCGAAA
AAACAAATCCTTCAATCCAATGTAGCTGAGAATTGGTTAGATGAATATAGATATTTCAATGACAC
TTGGCGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAGGAACACGTTTTTAGCCAAAAACTGTG
ATGGTTA
Found at i:3096 original size:239 final size:241
Alignment explanation
Indices: 2653--3122 Score: 639
Period size: 239 Copynumber: 2.0 Consensus size: 241
2643 TTTCGGTCAA
* *
2653 AATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCAATTTTTGGGCATAACACTCATAAAAAATA
1 AATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCAATTTTTGGCCACAACACTCATAAAAAATA
* * * * * *
2718 TATATATCAAGTCCAAATAGATTGAAGGGCTTTACACGCTTCAATTATCGTCTTTCCTATTTTTT
66 TATATATCAAGTCCAAAAAAATTGAAGAGCTTTACACGCTTCAAATATAGTCTTTCCTATATTTT
* * * * *
2783 TCCGGATTAATTTTTAATTCAATCGAAATATCATTCAGATGCTCGAAAAAACAAATCCTTAAGTC
131 TCCGAATTAATTTTTAATTAAATCGAAACATAATTCAGATGCTCGAAAAAACAAATCCTTAAATC
*
2848 CAATGTGGCTTAAAATTGGTTAGATGAATATAGATATTTCAATTTC
196 CAATGTGGCTGAAAATTGGTTAGATGAATATAGATATTTCAATTTC
*
2894 AATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCAATTTTTGGCCACAATACTCATAAAAAATA
1 AATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCAATTTTTGGCCACAACACTCATAAAAAATA
* * *
2959 TATA-ACTCAACG-CCAAAAAAAATTTAAGAGCTTTTCATGCTT-ATAATATAGT-TTAT-C-AT
66 TATATA-TCAA-GTCC-AAAAAAATTGAAGAGCTTTACACGCTTCA-AATATAGTCTT-TCCTAT
* * *
3018 ATTTTT-CGAATTAATTTTTAATTAAATCGAAGCATAATTCAGATGCTTGTAAAAACAAATCCTT
126 ATTTTTCCGAATTAATTTTTAATTAAATCGAAACATAATTCAGATGCTCGAAAAAACAAATCCTT
* *
3082 AAATCCATTGTGGCTGAAATTTGGTTAGATGAATATAGATA
191 AAATCCAATGTGGCTGAAAATTGGTTAGATGAATATAGATA
3123 CTTTAAGGAG
Statistics
Matches: 201, Mismatches: 23, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
239 88 0.44
240 8 0.04
241 76 0.38
242 29 0.14
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (241 bp):
AATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCAATTTTTGGCCACAACACTCATAAAAAATA
TATATATCAAGTCCAAAAAAATTGAAGAGCTTTACACGCTTCAAATATAGTCTTTCCTATATTTT
TCCGAATTAATTTTTAATTAAATCGAAACATAATTCAGATGCTCGAAAAAACAAATCCTTAAATC
CAATGTGGCTGAAAATTGGTTAGATGAATATAGATATTTCAATTTC
Found at i:4160 original size:13 final size:13
Alignment explanation
Indices: 4142--4167 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4132 ACCTAAAACC
4142 GACTTCGTAATAT
1 GACTTCGTAATAT
4155 GACTTCGTAATAT
1 GACTTCGTAATAT
4168 TAGCAACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
GACTTCGTAATAT
Found at i:21523 original size:2 final size:2
Alignment explanation
Indices: 21516--21547 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21506 TAGGTTTATC
21516 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21548 GTCTTGATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28621 original size:21 final size:19
Alignment explanation
Indices: 28595--28652 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
28585 GCTGCTATAA
28595 TAATCTCATCTGTACAGTATC
1 TAATCTCATCTGTACA--ATC
* * *
28616 TAATCTAATATGTACAATG
1 TAATCTCATCTGTACAATC
*
28635 TAATTTCATCTGTACAAT
1 TAATCTCATCTGTACAAT
28653 TGCTAAACAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 17 0.55
21 14 0.45
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (19 bp):
TAATCTCATCTGTACAATC
Found at i:39255 original size:1 final size:1
Alignment explanation
Indices: 39218--39248 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
39208 TGTGGATCAG
39218 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
39249 AATTTTTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:39577 original size:2 final size:2
Alignment explanation
Indices: 39570--39598 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
39560 ATTAAGAGGG
39570 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
39599 TTTCTGTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:45779 original size:21 final size:21
Alignment explanation
Indices: 45753--45792 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
45743 TTGTTTGACA
* *
45753 ACTGTACAGATTAGATTATGT
1 ACTGTACAAATGAGATTATGT
45774 ACTGTACAAATGAGATTAT
1 ACTGTACAAATGAGATTAT
45793 TGAAACAGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (21 bp):
ACTGTACAAATGAGATTATGT
Found at i:46153 original size:4 final size:4
Alignment explanation
Indices: 46144--46170 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
46134 GTGGTAGGAG
46144 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
46171 ACGTAGTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Done.