Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015762.1 Corchorus olitorius cultivar O-4 contig15795, 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: 40766
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1043 original size:2 final size:2
Alignment explanation
Indices: 1036--1074 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1026 TTGCGCGTTC
1036 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1075 AACTAGTGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8709 original size:40 final size:39
Alignment explanation
Indices: 8655--9050 Score: 309
Period size: 39 Copynumber: 10.1 Consensus size: 39
8645 ACAAAAACAA
* *
8655 GATTTTGAAATTAACTGATAAAACAATAATCCTAAATAG
1 GATTTTGAAATTAACTGATAAAACAATGATCCTGAATAG
* * *
8694 GATTTTTGAAATTAACTGGTAAAGCAACGATCCTGAATAG
1 GA-TTTTGAAATTAACTGATAAAACAATGATCCTGAATAG
* * * *
8734 GATTTCGAAATAAACTGATCAAGA-AATGATCCTGAATGG
1 GATTTTGAAATTAACTGAT-AAAACAATGATCCTGAATAG
** * * * * * *
8773 GATCCTAAAATTGACTGGTAAATCAATGATCTTGTATAG
1 GATTTTGAAATTAACTGATAAAACAATGATCCTGAATAG
* ** *
8812 GATTTCGAAATTAA-TAGATAAGGCAATGATCCTGGATAG
1 GATTTTGAAATTAACT-GATAAAACAATGATCCTGAATAG
* * *
8851 GATTTCGAAATTAACTGATAAGACAATGATCCTGAGTAG
1 GATTTTGAAATTAACTGATAAAACAATGATCCTGAATAG
* * *
8890 GATTCTGAAATTAATTTGATAAAGCAATGATCCAT-AATAG
1 GATTTTGAAATTAA-CTGATAAAACAATGATCC-TGAATAG
* * * *
8930 GATTGTGAAATTAACTTGATAAAACAATGATCTTGAGTAA
1 GATTTTGAAATTAAC-TGATAAAACAATGATCCTGAATAG
* * * **
8970 GATTGTG--ATTCACTGGTAAAGA-AATGATCCTGAGCAG
1 GATTTTGAAATTAACTGATAAA-ACAATGATCCTGAATAG
* * * * *
9007 GATTCTGAAATTAATTTGACAAAGCAATGATCCTGAGTAG
1 GATTTTGAAATTAA-CTGATAAAACAATGATCCTGAATAG
9047 GATT
1 GATT
9051 AACATTAACT
Statistics
Matches: 282, Mismatches: 61, Indels: 27
0.76 0.16 0.07
Matches are distributed among these distances:
37 24 0.09
38 9 0.03
39 131 0.46
40 117 0.41
41 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.30
Consensus pattern (39 bp):
GATTTTGAAATTAACTGATAAAACAATGATCCTGAATAG
Found at i:9016 original size:77 final size:76
Alignment explanation
Indices: 8836--9088 Score: 233
Period size: 77 Copynumber: 3.2 Consensus size: 76
8826 TAGATAAGGC
* * *
8836 AATGATCCTG-GATAGGATTTCGAAATTAAC-TGATAAGACAATGATCCTGAGTAGGATTCTGAA
1 AATGATCCTGAG-CAGGATTT-GAAATTAACTTGATAAAACAATGATCCTGAGTAGGATTATG--
* * *
8899 ATTAATTTGATAAAGC
62 ATTAA-CTGGTAAAGA
** * * *
8915 AATGATCCAT-AATAGGATTGTGAAATTAACTTGATAAAACAATGATCTTGAGTAAGATTGTGAT
1 AATGATCC-TGAGCAGGATT-TGAAATTAACTTGATAAAACAATGATCCTGAGTAGGATTATGAT
*
8979 TCACTGGTAAAGA
64 TAACTGGTAAAGA
* * * **
8992 AATGATCCTGAGCAGGATTCTGAAATTAATTTGACAAAGCAATGATCCTGAGTAGGATTAACATT
1 AATGATCCTGAGCAGGATT-TGAAATTAACTTGATAAAACAATGATCCTGAGTAGGATTATGATT
*
9057 AACTGGTAAAAAA
65 AACTGGT-AAAGA
*
9070 AATGATCATGAGCAGGATT
1 AATGATCCTGAGCAGGATT
9089 AAAACACATA
Statistics
Matches: 145, Mismatches: 23, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
76 1 0.01
77 65 0.45
78 26 0.18
79 24 0.17
80 29 0.20
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (76 bp):
AATGATCCTGAGCAGGATTTGAAATTAACTTGATAAAACAATGATCCTGAGTAGGATTATGATTA
ACTGGTAAAGA
Found at i:9107 original size:117 final size:118
Alignment explanation
Indices: 8864--9107 Score: 268
Period size: 117 Copynumber: 2.1 Consensus size: 118
8854 TTCGAAATTA
* *
8864 ACTGAT-AAGACAATGATCCTGAGTAGGATTCTGAAATTAATTTGATAAAGCAATGATCCATAAT
1 ACTGATAAAGACAATGATCCTGAGCAGGATTCTGAAATTAATTTGACAAAGCAATGATCCATAAT
* * * * *** **
8928 AGGATTGTGAAATTAACTTGATAAAACAATGATCTTGAGTAAGATTGTGATTC
66 AGGATTGTGAAATTAACTGGATAAAAAAATGATCATGAGCAAGATTAAAACAC
* *
8981 ACTGGTAAAGA-AATGATCCTGAGCAGGATTCTGAAATTAATTTGACAAAGCAATGATCC-TGAG
1 ACTGATAAAGACAATGATCCTGAGCAGGATTCTGAAATTAATTTGACAAAGCAATGATCCAT-AA
*
9044 TAGGA-T-T-AACATTAACTGG-TAAAAAAAATGATCATGAGCAGGATTAAAACAC
65 TAGGATTGTGAA-ATTAACTGGAT-AAAAAAATGATCATGAGCAAGATTAAAACAC
9096 ATACTGATAAAG
1 --ACTGATAAAG
9108 CAAAATAGTC
Statistics
Matches: 106, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
114 3 0.03
115 31 0.29
116 2 0.02
117 66 0.62
118 4 0.04
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.28
Consensus pattern (118 bp):
ACTGATAAAGACAATGATCCTGAGCAGGATTCTGAAATTAATTTGACAAAGCAATGATCCATAAT
AGGATTGTGAAATTAACTGGATAAAAAAATGATCATGAGCAAGATTAAAACAC
Found at i:9461 original size:145 final size:141
Alignment explanation
Indices: 9138--9521 Score: 520
Period size: 145 Copynumber: 2.6 Consensus size: 141
9128 ATATGGAATG
* * * *
9138 CCCGGAGGACTTGTTAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCC-AGAGGTCTGACAAA
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGA-AGGTCTTACAAA
* *
9202 TGTAAACTCTGAGTAAAGACCTTGAGCAAGG-TTTATTGAAATTTAAAGCAAATTTAATTAAAAA
65 TGCAAACTC-------A-ACCTTGAGCAAGGTTTTATTGAAACTTAAAGCAAATTTAATTAAAAA
9266 CTTGATGAAATGAGATGATA
122 CTTGATGAAATGAGATGATA
* *
9286 CCCGGAGGATTTATCAGAATTAATAGCCGGAGGTTTCTGAAATTATGCCCGAAGGTCTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGAAGGTCTTACAAAT
* * *
9351 GCAAACTCAACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACGCAACTTTGATTAAGAACTTGA
66 GCAAACTCAACCTTGAGCAAGGTTTT-A--TTGAAACTTAAA-GCAAATTTAATTAAAAACTTGA
*
9416 TGATATGAGATGATA
127 TGAAATGAGATGATA
*
9431 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCTCGAAGGTCTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGAAGGTCTTACAAAT
9496 GCAAACTCAACCTTGAGCAAGGTTTT
66 GCAAACTCAACCTTGAGCAAGGTTTT
9522 TAAAACTTAA
Statistics
Matches: 215, Mismatches: 15, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
140 13 0.06
141 4 0.02
142 1 0.00
144 11 0.05
145 121 0.56
148 64 0.30
149 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (141 bp):
CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGAAGGTCTTACAAAT
GCAAACTCAACCTTGAGCAAGGTTTTATTGAAACTTAAAGCAAATTTAATTAAAAACTTGATGAA
ATGAGATGATA
Found at i:18216 original size:2 final size:2
Alignment explanation
Indices: 18209--18246 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
18199 ACTCGTTTCT
18209 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
18247 ACTAACCGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:20600 original size:138 final size:137
Alignment explanation
Indices: 20339--20616 Score: 531
Period size: 138 Copynumber: 2.0 Consensus size: 137
20329 AACAAGGTAA
20339 CTAACAATGTAAAGGGGTCAATTGGGTCCAATTGAAGCAAAATTGGCCCAAGAAGCAAGGCCCGA
1 CTAACAATGTAAAGGGGTCAATTGGGTCCAATTGAAGCAAAATTGGCCCAAGAAGCAAGGCCCGA
20404 AAGGAAAATAATCAAAACAACCTAAAGAAAAGATTGGCCCATTTGCTCCAAAAGAAATTTGGAAA
66 AAGGAAAATAATCAAAACAACCTAAAGAAAAGATTGGCCCATTTGCTCCAAAAGAAA-TTGGAAA
20469 AGTGTATC
130 AGTGTATC
20477 CTAACAATGTAAAGGGGTCAATTGGGTCCAATTGAAGCAAAATTGGCCCAAGAAGCAAGGCCCGA
1 CTAACAATGTAAAGGGGTCAATTGGGTCCAATTGAAGCAAAATTGGCCCAAGAAGCAAGGCCCGA
20542 AAGGAAAATAATCAAAACAACCT-AAGAAAAGATTGGCCCATTTGCTCCAAAAGAAAATTGGAAA
66 AAGGAAAATAATCAAAACAACCTAAAGAAAAGATTGGCCCATTTGCTCCAAAAG-AAATTGGAAA
20606 AGTGTATC
130 AGTGTATC
20614 CTA
1 CTA
20617 CATAAATATA
Statistics
Matches: 139, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
137 48 0.35
138 91 0.65
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.19
Consensus pattern (137 bp):
CTAACAATGTAAAGGGGTCAATTGGGTCCAATTGAAGCAAAATTGGCCCAAGAAGCAAGGCCCGA
AAGGAAAATAATCAAAACAACCTAAAGAAAAGATTGGCCCATTTGCTCCAAAAGAAATTGGAAAA
GTGTATC
Found at i:36575 original size:1 final size:1
Alignment explanation
Indices: 36571--36624 Score: 63
Period size: 1 Copynumber: 54.0 Consensus size: 1
36561 TAAGGTTTTT
* * * * *
36571 AAAAAAAAAACAAAAAAAACAAAAAAAAACAAAAAACAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
36625 CACCGAACCA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:36587 original size:8 final size:8
Alignment explanation
Indices: 36574--36622 Score: 71
Period size: 8 Copynumber: 5.9 Consensus size: 8
36564 GGTTTTTAAA
36574 AAAAAAAC
1 AAAAAAAC
36582 AAAAAAAAC
1 -AAAAAAAC
*
36591 AAAAAAAA
1 AAAAAAAC
36599 ACAAAAAAC
1 A-AAAAAAC
36608 AAAAAAAC
1 AAAAAAAC
36616 AAAAAAA
1 AAAAAAA
36623 AACACCGAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
8 22 0.59
9 15 0.41
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:36587 original size:9 final size:9
Alignment explanation
Indices: 36573--36623 Score: 79
Period size: 9 Copynumber: 5.9 Consensus size: 9
36563 AGGTTTTTAA
36573 AAAAAAAAC
1 AAAAAAAAC
36582 AAAAAAAAC
1 AAAAAAAAC
36591 AAAAAAAA-
1 AAAAAAAAC
*
36599 ACAAAAAAC
1 AAAAAAAAC
36608 -AAAAAAAC
1 AAAAAAAAC
36616 AAAAAAAA
1 AAAAAAAA
36624 ACACCGAACC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
8 14 0.37
9 24 0.63
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:36609 original size:26 final size:25
Alignment explanation
Indices: 36571--36626 Score: 96
Period size: 25 Copynumber: 2.2 Consensus size: 25
36561 TAAGGTTTTT
36571 AAAA-AAAAAACAAAAAAAACAAAAA
1 AAAACAAAAAAC-AAAAAAACAAAAA
36596 AAAACAAAAAACAAAAAAACAAAAA
1 AAAACAAAAAACAAAAAAACAAAAA
36621 AAAACA
1 AAAACA
36627 CCGAACCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 23 0.77
26 7 0.23
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (25 bp):
AAAACAAAAAACAAAAAAACAAAAA
Found at i:37216 original size:29 final size:30
Alignment explanation
Indices: 37155--37229 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
37145 GCTAAATACC
* * *
37155 CAAAAAAATCCCTTATGTTTTGCTTTTAGGA
1 CAAAATAATCCCTTATATTTT-CTTTCAGGA
*
37186 CAAAATAATCCCTTATATTTT-TTTCGGGA
1 CAAAATAATCCCTTATATTTTCTTTCAGGA
*
37215 CAAATTAATCCCTTA
1 CAAAATAATCCCTTA
37230 CGTTTCAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 20 0.51
31 19 0.49
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (30 bp):
CAAAATAATCCCTTATATTTTCTTTCAGGA
Found at i:37391 original size:31 final size:32
Alignment explanation
Indices: 37356--37421 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 32
37346 AAGGGACTGA
*
37356 TTTGTCCCAAAAGAAAAACATAAG-GGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGAGAATTTT
*
37387 TTTGTCCCAAAAGAAAAATATAAGAGAATTTT
1 TTTGTCCCAAAAGAAAAACATAAGAGAATTTT
37419 TTT
1 TTT
37422 AGTATTTAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 23 0.72
32 9 0.28
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (32 bp):
TTTGTCCCAAAAGAAAAACATAAGAGAATTTT
Found at i:38532 original size:29 final size:31
Alignment explanation
Indices: 38429--38522 Score: 149
Period size: 31 Copynumber: 3.1 Consensus size: 31
38419 ACTAAATACT
*
38429 AAAAAAAT-CCTTAATGTTTTTCTTTTGGAAC
1 AAAAAAATCCCTT-ATGTTTTTCTTTTGGGAC
38460 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
38491 AAAAAAATCCCTTATG-TTTT-TTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
38520 AAA
1 AAA
38523 TTAGTCCCTT
Statistics
Matches: 61, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
29 12 0.20
30 4 0.07
31 41 0.67
32 4 0.07
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (31 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
Found at i:38733 original size:31 final size:30
Alignment explanation
Indices: 38666--38740 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
38656 CTCATTTTTG
*
38666 AAACGTAAGGGATTAATTTGTCCCGAAAAA
1 AAACATAAGGGATTAATTTGTCCCGAAAAA
*
38696 AAACATAAGGGATTATTTTGTCCC-AAAAGCA
1 AAACATAAGGGATTAATTTGTCCCGAAAA--A
38727 AAACATAAGGGATT
1 AAACATAAGGGATT
38741 TTTCTGGGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
29 4 0.10
30 22 0.54
31 15 0.37
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (30 bp):
AAACATAAGGGATTAATTTGTCCCGAAAAA
Found at i:39453 original size:16 final size:16
Alignment explanation
Indices: 39432--39463 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39422 GGGTAATTAA
*
39432 AAAAAATTGTTTTCAT
1 AAAAAAGTGTTTTCAT
39448 AAAAAAGTGTTTTCAT
1 AAAAAAGTGTTTTCAT
39464 GATAGAGGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (16 bp):
AAAAAAGTGTTTTCAT
Found at i:40344 original size:19 final size:18
Alignment explanation
Indices: 40320--40355 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
40310 TGAAGATTTA
40320 TTGAAGATAATTTGAAGAC
1 TTGAAGATAA-TTGAAGAC
*
40339 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
40356 ATTATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAC
Done.