Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012092.1 Corchorus olitorius cultivar O-4 contig12125, 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: 22573
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2004 original size:2 final size:2
Alignment explanation
Indices: 1997--2021 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1987 TTAACAAAAG
1997 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2022 TTGAAAACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2051 original size:119 final size:118
Alignment explanation
Indices: 1885--2118 Score: 450
Period size: 119 Copynumber: 2.0 Consensus size: 118
1875 CTTAAACTAA
*
1885 ATATATATATATATATATTTGAAAACCATGTGATTCTTTTTTTTTTTTTGAAAAAATAATTAAGA
1 ATATATATATATATATATTTGAAAACCATGTGATTCGTTTTTTTTTTTTGAAAAAATAATTAAGA
1950 AAAGACAAACATTAGGTACAACATAATTGAGCAAAATTTAACAAAAGTATATAT
66 AAAGACAAACATTAGGTACAACATAATTGAGC-AAATTTAACAAAAGTATATAT
2004 ATATATATATATATATATTTGAAAACCATGTGATTCGTTTTTTTTTTTTGAAAAAATAATTAAGA
1 ATATATATATATATATATTTGAAAACCATGTGATTCGTTTTTTTTTTTTGAAAAAATAATTAAGA
2069 AAAGACAAACATTAGGTACAACATAATTGAGCAAATTTAACAAAAGTATA
66 AAAGACAAACATTAGGTACAACATAATTGAGCAAATTTAACAAAAGTATA
2119 CTGTAATGAA
Statistics
Matches: 114, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
118 18 0.16
119 96 0.84
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (118 bp):
ATATATATATATATATATTTGAAAACCATGTGATTCGTTTTTTTTTTTTGAAAAAATAATTAAGA
AAAGACAAACATTAGGTACAACATAATTGAGCAAATTTAACAAAAGTATATAT
Found at i:5149 original size:439 final size:439
Alignment explanation
Indices: 4174--5214 Score: 1349
Period size: 439 Copynumber: 2.4 Consensus size: 439
4164 GTTCTTCATG
* * * * *
4174 TAGACACTTGAATCACCTTAATGGGACAAATAGAAA-ACAAAA-ACAAAAGTCAAAG-CG-----
1 TAGACACTTGAATCACCTTGATCGGACAAATA-AAACAAAAAATACAAAAATAAAAGCCGAAACA
* *
4231 TTAAATCGTCCAACCTATAATTGTAAAGGATTCAATAGCATGAAA-CATAAAAGTATGAGGGTCA
65 TTAAATCGTCCAACCTATAATTGTAAAGGATTAAATAGCAT-AAAGCATAAAAGTAT-AGGATCA
* * * * *
4295 TTAGATAAATAATCCAGCAAAAAAAATATTAGTTTATGAAGACAAAACATAAAAATTCCCTCTTG
128 TTTGATAAATAATCCAGCAAAAAATATATTTGTTTATGGAGACAAAACATAAAAATTCCCTCTCG
* * *
4360 AATCCTCCACGAAACTCATTAATCAAATTCAACTTTCATGCCCTTAATGAAAGTCACAGATCACA
193 AACCCTCCACGAAACTCATTAATCAAATTCAACTTTCAGGCCCTTAACGAAAGTCACAGATCACA
* * *
4425 CCAATAACCTTTTAAACGACACTTGAACAACTTCAACCGGACAAGTGGACCAAAAATTATGCGAT
258 CCAATAACCTTTTAAACGACACTTGAACAACCTCAACCGGACAAGTGGACCAAAAATTATACAAT
* * * *
4490 ATTAAATATATCAGCAATCGAAACAACAAAATTTAAGAAACATTTTTTAGAATCAAAACATTAAA
323 ATTAAACAGACCAGCAATCGAAACAACAAAATTTAAGAAACATTTTTTAGAATCAAAACATGAAA
** * *
4555 ATTGGCTTCTGAGTTTTTTATGAAAGTTGTAGATCATGAGATTACCTTTTAA
388 ATTGGCTTCTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAA
* * ** *
4607 TAGACACTTGAATCACCTTGATCGGACAAATAGAACAGAAAATACAAAAATAAAAGCCGACGCGT
1 TAGACACTTGAATCACCTTGATCGGACAAATAAAACAAAAAATACAAAAATAAAAGCCGAAACAT
* *
4672 TAAATCGTTCAACCCATAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATAAGGATCATT
66 TAAATCGTCCAACCTATAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTAT-AGGATCATT
* * *
4737 TGATAAATAATCCAGCAAAAAATATATTTGTTTATGGAGACCAAACATAAAAATTTCTTCTCGAA
130 TGATAAATAATCCAGCAAAAAATATATTTGTTTATGGAGACAAAACATAAAAATTCCCTCTCGAA
* * * * *
4802 CCCTCCACGAAACTCATTAATCAAATTCAGCTTTCAGGTCCTTGACGAAAGTCATAGATCACA-T
195 CCCTCCACGAAACTCATTAATCAAATTCAACTTTCAGGCCCTTAACGAAAGTCACAGATCACACC
* * * *
4866 AATAACCTTTTAACCGACACTTGAACAACCTCAATCGGACAAGTGGATCGAAAATTATACAATAT
260 AATAACCTTTTAAACGACACTTGAACAACCTCAACCGGACAAGTGGACCAAAAATTATACAATAT
* * *
4931 TAGACAGACC-GACAATC-AAGACCACAAAATTTAAGAAGCATTTTTTAGAATCAAAACATGAAA
325 TAAACAGACCAG-CAATCGAA-ACAACAAAATTTAAGAAACATTTTTTAGAATCAAAACATGAAA
4994 ATTGG-TT-TGCAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAA
388 ATTGGCTTCTG-AGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAA
* * * *
5045 TAGACACTTGAATCACCTTGATCGGACAAGTAAAATAAAAAATA-AAAGAATTAAAGTCGAAACA
1 TAGACACTTGAATCACCTTGATCGGACAAATAAAACAAAAAATACAAA-AATAAAAGCCGAAACA
* * * *
5109 TTCAATCGTCCAACCTAGAATTTGTGAGGGATTAAATAGCATAAAGCATAAAAGTATAGTGATCA
65 TTAAATCGTCCAACCTATAA-TTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATAG-GATCA
* * *
5174 TTTGATAAATAGTCCAGTAAAAAAT-TATTTGTTTATTGAGA
128 TTTGATAAATAATCCAGCAAAAAATATATTTGTTTATGGAGA
5215 GCGGGGCCCA
Statistics
Matches: 530, Mismatches: 63, Indels: 25
0.86 0.10 0.04
Matches are distributed among these distances:
432 2 0.00
433 35 0.07
434 11 0.02
435 2 0.00
437 5 0.01
438 126 0.24
439 179 0.34
440 170 0.32
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.27
Consensus pattern (439 bp):
TAGACACTTGAATCACCTTGATCGGACAAATAAAACAAAAAATACAAAAATAAAAGCCGAAACAT
TAAATCGTCCAACCTATAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATAGGATCATTT
GATAAATAATCCAGCAAAAAATATATTTGTTTATGGAGACAAAACATAAAAATTCCCTCTCGAAC
CCTCCACGAAACTCATTAATCAAATTCAACTTTCAGGCCCTTAACGAAAGTCACAGATCACACCA
ATAACCTTTTAAACGACACTTGAACAACCTCAACCGGACAAGTGGACCAAAAATTATACAATATT
AAACAGACCAGCAATCGAAACAACAAAATTTAAGAAACATTTTTTAGAATCAAAACATGAAAATT
GGCTTCTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAA
Found at i:6541 original size:22 final size:22
Alignment explanation
Indices: 6515--7115 Score: 269
Period size: 22 Copynumber: 26.7 Consensus size: 22
6505 TTACATTGGA
6515 AGGTTATCAAAATTTCATAGTG
1 AGGTTATCAAAATTTCATAGTG
* * *
6537 TGGTTACCAAAATTTCA-AATGG
1 AGGTTATCAAAATTTCATAGT-G
* *
6559 AGATTATC-AAACTTCATAGTG
1 AGGTTATCAAAATTTCATAGTG
**
6580 TA-GTTATCAAAATTTCATACAG
1 -AGGTTATCAAAATTTCATAGTG
* * *
6602 AGGTTA-CTAATATTTCATAAAATTAA
1 AGGTTATC-AAAATTTCAT---AGT-G
* *
6628 AGGTTATCAAAATTTCTTAGGG
1 AGGTTATCAAAATTTCATAGTG
* *
6650 AGGTTAACAAAATTTCATACG-A
1 AGGTTATCAAAATTTCATA-GTG
** *
6672 AGGTTATTGAAATTTTATAGTG
1 AGGTTATCAAAATTTCATAGTG
* *
6694 TGGTTATCAAAATTTCATAAG-A
1 AGGTTATCAAAATTTCAT-AGTG
*
6716 AGGTTA-CAAAAATTTCATAGGAAGG
1 AGGTTATC-AAAATTTCATA-G--TG
* *
6741 AGGTCATCAAAATTTTC-TAGAG
1 AGGTTATCAAAA-TTTCATAGTG
* * *
6763 TGGTTAAT-AAAATTCCATAGGG
1 AGGTT-ATCAAAATTTCATAGTG
* * * *
6785 AGGTTATGAAAATTTTATGGAG
1 AGGTTATCAAAATTTCATAGTG
*
6807 AGGTTATCAAAATTAT-ATAGAGAG
1 AGGTTATCAAAATT-TCAT--AGTG
* * * *
6831 AGGATATCACAGTTTCATTCTTATAGGG
1 AGGTTATCA-A----AATT-TCATAGTG
** **
6859 AGGTTATTGAAATTTCAGGGT-
1 AGGTTATCAAAATTTCATAGTG
*
6880 ATGGTTATCAAAATTTTATGAG-G
1 A-GGTTATCAAAATTTCAT-AGTG
*
6903 ATGTTATCAAAATTTCCATAGTG
1 AGGTTATCAAAATTT-CATAGTG
* *
6926 CGGTTA-CCAAATTT-ATAGTG
1 AGGTTATCAAAATTTCATAGTG
* * *
6946 TGATTATCAAAATTTCATAGGG
1 AGGTTATCAAAATTTCATAGTG
* *** *
6968 AGATTATCAAAATTTCACCTTA
1 AGGTTATCAAAATTTCATAGTG
* *
6990 AGGTTATAAAAATTTAATAGTG
1 AGGTTATCAAAATTTCATAGTG
* * * * *
7012 TGTTTATCAAAATTTTACAATG
1 AGGTTATCAAAATTTCATAGTG
* * *
7034 TGGTTATCAAATTTTCATAGGG
1 AGGTTATCAAAATTTCATAGTG
*
7056 AGGTTATCAAAATTTCATAATG
1 AGGTTATCAAAATTTCATAGTG
**
7078 AGGTTATCAATTTTTCATAGTG
1 AGGTTATCAAAATTTCATAGTG
*
7100 TGGTTAT-AAATATTTC
1 AGGTTATCAAA-ATTTC
7116 TACGTTAGAG
Statistics
Matches: 428, Mismatches: 110, Indels: 82
0.69 0.18 0.13
Matches are distributed among these distances:
20 10 0.02
21 35 0.08
22 303 0.71
23 19 0.04
24 12 0.03
25 13 0.03
26 19 0.04
27 2 0.00
28 9 0.02
29 4 0.01
30 2 0.00
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGTG
Found at i:6548 original size:44 final size:43
Alignment explanation
Indices: 6498--6593 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 43
6488 TGATAATCAA
* * * *
6498 ACCAAAATTAC-ATTGGAAGGTTATCAAAATTTCATAGTGTGGTT
1 ACCAAAATTACAAATGG-AGATTATC-AAACTTCATAGTGTAGTT
*
6542 ACCAAAATTTCAAATGGAGATTATCAAACTTCATAGTGTAGTT
1 ACCAAAATTACAAATGGAGATTATCAAACTTCATAGTGTAGTT
*
6585 ATCAAAATT
1 ACCAAAATT
6594 TCATACAGAG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
43 24 0.53
44 17 0.38
45 4 0.09
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (43 bp):
ACCAAAATTACAAATGGAGATTATCAAACTTCATAGTGTAGTT
Found at i:6752 original size:113 final size:112
Alignment explanation
Indices: 6514--6820 Score: 314
Period size: 113 Copynumber: 2.7 Consensus size: 112
6504 ATTACATTGG
* * * * * * * * *
6514 AAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCAAATGGAGATTATCAAACTTCATAGT
1 AAGGTTATCAAAATTTCTTAGAGTGGTTAACAAAATTTCATACGGAGGTTATGAAATTTTATAGT
* * *
6579 GTAGTTATCAAAATTTCATACAGAGGTTACTAATATTTCATAAAATTA
66 GTGGTTATCAAAATTTCATACAGAGGTTACAAAAATTTCATAAAA-TA
* * *
6627 AAGGTTATCAAAATTTCTTAGGGAGGTTAACAAAATTTCATACGAAGGTTATTGAAATTTTATAG
1 AAGGTTATCAAAATTTCTTAGAGTGGTTAACAAAATTTCATACGGAGGTTA-TGAAATTTTATAG
* *
6692 TGTGGTTATCAAAATTTCATA-AGAAGGTTACAAAAATTTCATAGGAA-G
65 TGTGGTTATCAAAATTTCATACAG-AGGTTACAAAAATTTCATA-AAATA
* * * * * *
6740 GAGGTCATCAAAATTT-TCTAGAGTGGTTAATAAAATTCCATAGGGAGGTTATGAAAATTTTATG
1 AAGGTTATCAAAATTTCT-TAGAGTGGTTAACAAAATTTCATACGGAGGTTATG-AAATTTTATA
* *
6804 GAGAGGTTATCAAAATT
64 GTGTGGTTATCAAAATT
6821 ATATAGAGAG
Statistics
Matches: 162, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
112 3 0.02
113 110 0.68
114 47 0.29
115 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (112 bp):
AAGGTTATCAAAATTTCTTAGAGTGGTTAACAAAATTTCATACGGAGGTTATGAAATTTTATAGT
GTGGTTATCAAAATTTCATACAGAGGTTACAAAAATTTCATAAAATA
Found at i:21473 original size:15 final size:16
Alignment explanation
Indices: 21442--21481 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
21432 TTACTCTGCT
21442 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
21458 TTGTTTTCTA-TTTAA
1 TTGTTTTCTAGTTTAA
*
21473 TTGCTTTCT
1 TTGTTTTCT
21482 GTCAATCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:21861 original size:24 final size:22
Alignment explanation
Indices: 21834--21882 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
21824 TTGTTTTGTG
21834 TTTTGCGTAAAAAAAAGAAATAGT
1 TTTTGCGTAAAAAAAA-AAATA-T
* *
21858 TTTTGCGTTATAAAAAAAATAT
1 TTTTGCGTAAAAAAAAAAATAT
21880 TTT
1 TTT
21883 CTTTATTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 5 0.22
24 14 0.61
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.39
Consensus pattern (22 bp):
TTTTGCGTAAAAAAAAAAATAT
Done.