Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021398.1 Corchorus olitorius cultivar O-4 contig21431, 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: 83859
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:13863 original size:16 final size:16
Alignment explanation
Indices: 13842--13873 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
13832 TATCCTTAAG
13842 TTAGAGATCAAAAACA
1 TTAGAGATCAAAAACA
*
13858 TTAGAGATCTAAAACA
1 TTAGAGATCAAAAACA
13874 AAGAAGCACA
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:0.53, C:0.12, G:0.12, T:0.22
Consensus pattern (16 bp):
TTAGAGATCAAAAACA
Found at i:14801 original size:16 final size:16
Alignment explanation
Indices: 14780--14811 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
14770 AACAAAATAC
*
14780 TACTTCATTTACAGAT
1 TACTTCATATACAGAT
14796 TACTTCATATACAGAT
1 TACTTCATATACAGAT
14812 AACTGTAAGG
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:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (16 bp):
TACTTCATATACAGAT
Found at i:21820 original size:13 final size:13
Alignment explanation
Indices: 21802--21828 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21792 TTTTATTATC
21802 TATCTATACTATA
1 TATCTATACTATA
21815 TATCTATACTATA
1 TATCTATACTATA
21828 T
1 T
21829 TAAAAAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (13 bp):
TATCTATACTATA
Found at i:22051 original size:130 final size:131
Alignment explanation
Indices: 21912--22174 Score: 411
Period size: 130 Copynumber: 2.0 Consensus size: 131
21902 GCCATTAGAC
21912 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
* * * * *
21977 TTTAATTTTTACCATTTTACTATTTTAATT-AAAAACTTATATATATTAGAATTTTTTAAATATA
66 TTTAATTTTTACCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAAATTTTAAAATATA
22041 T
131 T
* * * * *
22042 TTTTATAGTTTTACTCAACTAAAAACTCTTTTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
* *
22107 TTTTATTTTTATCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAAATTTTAAAATATA
66 TTTAATTTTTACCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAAATTTTAAAATATA
22172 T
131 T
22173 TT
1 TT
22175 CTTAAATGAC
Statistics
Matches: 120, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
130 86 0.72
131 34 0.28
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.49
Consensus pattern (131 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
TTTAATTTTTACCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAAATTTTAAAATATA
T
Found at i:24362 original size:25 final size:24
Alignment explanation
Indices: 24311--24367 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
24301 GTCAGTCTTG
*
24311 AATTT-TTTAATGTTTAATTCTTA
1 AATTTATTTAATGTTTAATTATTA
*
24334 AATTTATTTAATGTCTTAATTATTC
1 AATTTATTTAATGT-TTAATTATTA
24359 AATTTATTT
1 AATTTATTT
24368 TACAATCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (24 bp):
AATTTATTTAATGTTTAATTATTA
Found at i:26811 original size:30 final size:30
Alignment explanation
Indices: 26775--26834 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
26765 TATACATTTA
* *
26775 AGTATGAGCCCGTTCGTATGTGGGAAATGG
1 AGTATGAGCCCGTTCATATGTGAGAAATGG
*
26805 AGTATGAGCCCGTTTATATGTGAGAAATGG
1 AGTATGAGCCCGTTCATATGTGAGAAATGG
26835 TGTACCGCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.28
Consensus pattern (30 bp):
AGTATGAGCCCGTTCATATGTGAGAAATGG
Found at i:28979 original size:32 final size:32
Alignment explanation
Indices: 28943--29003 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
28933 AAATATGTTT
*
28943 GAAAAATAAGGGTATAATGGTCGATTCAATTA
1 GAAAAATAAGGGTATAATAGTCGATTCAATTA
28975 GAAAAATAAGGGTATAATAGTCGATTCAA
1 GAAAAATAAGGGTATAATAGTCGATTCAA
29004 AAGTTTTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.46, C:0.07, G:0.21, T:0.26
Consensus pattern (32 bp):
GAAAAATAAGGGTATAATAGTCGATTCAATTA
Found at i:29635 original size:25 final size:24
Alignment explanation
Indices: 29607--29658 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
29597 GTGGATTGTA
*
29607 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
29632 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
29656 AAA
1 AAA
29659 AATTCAAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.31
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:29667 original size:22 final size:25
Alignment explanation
Indices: 29607--29667 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 25
29597 GTGGATTGTA
* *
29607 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTCAAGAATTAAGACATT
*
29632 AAATAAATTTAAGAATTAA-ACATT
1 AAATAAATTCAAGAATTAAGACATT
29656 -AA-AAATTCAAGA
1 AAATAAATTCAAGA
29668 CTGACCCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 9 0.27
23 2 0.06
24 5 0.15
25 17 0.52
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.30
Consensus pattern (25 bp):
AAATAAATTCAAGAATTAAGACATT
Found at i:29788 original size:16 final size:17
Alignment explanation
Indices: 29754--29830 Score: 56
Period size: 16 Copynumber: 4.8 Consensus size: 17
29744 AAAACCCGAA
*
29754 CCAGCATGACCCTAAAC
1 CCAGCATGACCCGAAAC
*
29771 CCAGCA-GACCCGAGAC
1 CCAGCATGACCCGAAAC
* *
29787 CC-GAATGACCTG-AAC
1 CCAGCATGACCCGAAAC
* *
29802 CAAG-ATGAGCCGAAAC
1 CCAGCATGACCCGAAAC
*
29818 CC-GAATGACCCGA
1 CCAGCATGACCCGA
29831 GAAAATTACC
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
15 12 0.26
16 28 0.61
17 6 0.13
ACGTcount: A:0.35, C:0.36, G:0.21, T:0.08
Consensus pattern (17 bp):
CCAGCATGACCCGAAAC
Found at i:30693 original size:166 final size:166
Alignment explanation
Indices: 30511--30843 Score: 648
Period size: 166 Copynumber: 2.0 Consensus size: 166
30501 AATTCTAATA
30511 TATAAAAGTAAAAATTAAATAGTTATAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTAT
1 TATAAAAGTAAAAATTAAATAGTTATAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTAT
*
30576 AAAAGTTTAAATAATGGCATTTAAGAAATATATTCGAAAAATAAGGGTATAATGGACAGATATAT
66 AAAAGTTTAAATAATGACATTTAAGAAATATATTCGAAAAATAAGGGTATAATGGACAGATATAT
*
30641 ACGAAAAATAAGGATATAATAGGTGATTCAAAAGTT
131 ACGAAAAATAAGGATATAATAAGTGATTCAAAAGTT
30677 TATAAAAGTAAAAATTAAATAGTTATAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTAT
1 TATAAAAGTAAAAATTAAATAGTTATAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTAT
30742 AAAAGTTTAAATAATGACATTTAAGAAATATATTCGAAAAATAAGGGTATAATGGACAGATATAT
66 AAAAGTTTAAATAATGACATTTAAGAAATATATTCGAAAAATAAGGGTATAATGGACAGATATAT
30807 ACGAAAAATAAGGATATAATAAGTGATTCAAAAGTT
131 ACGAAAAATAAGGATATAATAAGTGATTCAAAAGTT
30843 T
1 T
30844 TACAAAACTC
Statistics
Matches: 165, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
166 165 1.00
ACGTcount: A:0.51, C:0.04, G:0.14, T:0.31
Consensus pattern (166 bp):
TATAAAAGTAAAAATTAAATAGTTATAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTAT
AAAAGTTTAAATAATGACATTTAAGAAATATATTCGAAAAATAAGGGTATAATGGACAGATATAT
ACGAAAAATAAGGATATAATAAGTGATTCAAAAGTT
Found at i:58332 original size:101 final size:102
Alignment explanation
Indices: 58157--58361 Score: 342
Period size: 101 Copynumber: 2.0 Consensus size: 102
58147 ATTTTGATAC
* * * *
58157 AGTGATTAATGCATATGTTGTTTTCCCTAAGTTTTAATATATGATTTGATTTTGTCCTTAATTCT
1 AGTGATTAATGCATATATTGTTTTCCCTAAGTTTTAATATATGATTTGATTCTATCCTTAATCCT
58222 ATCATAAAAAGGAAAAATAACAC-ATATATGTTAATG
66 ATCATAAAAAGGAAAAATAACACAATATATGTTAATG
58258 AGTGATTAATGCATATATTGTTTTCCCTAAGTTTTAATAT-TGGATTTGATTCTATCCTTAATCC
1 AGTGATTAATGCATATATTGTTTTCCCTAAGTTTTAATATAT-GATTTGATTCTATCCTTAATCC
58322 TATCATAAAAAGGAAAAATAACACATATATATGTTAATG
65 TATCATAAAAAGGAAAAATAACACA-ATATATGTTAATG
58361 A
1 A
58362 AAAATTACCT
Statistics
Matches: 97, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
100 1 0.01
101 82 0.85
103 14 0.14
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (102 bp):
AGTGATTAATGCATATATTGTTTTCCCTAAGTTTTAATATATGATTTGATTCTATCCTTAATCCT
ATCATAAAAAGGAAAAATAACACAATATATGTTAATG
Found at i:58859 original size:16 final size:16
Alignment explanation
Indices: 58838--58868 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58828 ATAATTATTA
58838 ATATATTAATAATAAT
1 ATATATTAATAATAAT
*
58854 ATATATTATTAATAA
1 ATATATTAATAATAA
58869 AAATTATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATATTAATAATAAT
Found at i:59022 original size:18 final size:18
Alignment explanation
Indices: 58995--59029 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
58985 AATTATTACA
58995 TTGTTCATGAACAATTTT
1 TTGTTCATGAACAATTTT
*
59013 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
59030 CAGTTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:62444 original size:29 final size:29
Alignment explanation
Indices: 62402--62462 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
62392 TACAATTCAA
62402 AACAATACTCCTAAATCTAATGTGTATTT
1 AACAATACTCCTAAATCTAATGTGTATTT
62431 AACAATACTCCTAAATCTAATGTGTATTT
1 AACAATACTCCTAAATCTAATGTGTATTT
62460 AAC
1 AAC
62463 GGTGAAGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (29 bp):
AACAATACTCCTAAATCTAATGTGTATTT
Found at i:65704 original size:31 final size:31
Alignment explanation
Indices: 65668--65744 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 31
65658 ATGGAGCTTT
**
65668 AAGAAGGCAGTTATAAATTTTGAAAAAAAAGAAG
1 AAGAAGGCAGTTATAAA--TTGCCAAAAAA-AAG
*
65702 AAGAATGCAG-T-T-AATTGCCAAAAAAAAG
1 AAGAAGGCAGTTATAAATTGCCAAAAAAAAG
65730 AAGAAGGCAGTTATA
1 AAGAAGGCAGTTATA
65745 GATTATGATG
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
28 12 0.33
29 10 0.28
30 1 0.03
31 2 0.06
32 1 0.03
33 1 0.03
34 9 0.25
ACGTcount: A:0.53, C:0.06, G:0.21, T:0.19
Consensus pattern (31 bp):
AAGAAGGCAGTTATAAATTGCCAAAAAAAAG
Found at i:81452 original size:49 final size:47
Alignment explanation
Indices: 81351--81492 Score: 160
Period size: 49 Copynumber: 3.0 Consensus size: 47
81341 GAGCGTGCCA
* * * * *
81351 ATCAATTTTGTCAAAAAATTGATAAAAAGTACGATGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
81398 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAATG-AAAAATAAAAG
* * * *
81447 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAGTGAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAATGAAAAATAAA
81493 GGATTGCTTG
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
47 12 0.15
48 28 0.35
49 41 0.51
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.27
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
Found at i:83397 original size:30 final size:30
Alignment explanation
Indices: 83361--83553 Score: 180
Period size: 30 Copynumber: 6.4 Consensus size: 30
83351 ACCACTTTCA
*
83361 GTGCCATCATCTTCGGTGCCATC-AGTTTTG
1 GTGCCATCATCTTCGGTGCCATCGA-TGTTG
* *
83391 GTGCCATCATTTTCGGTGCCGTCGATGTTG
1 GTGCCATCATCTTCGGTGCCATCGATGTTG
* * *
83421 GTGTCATCAGT-TTTGGTGCCATC-ATCTTCG
1 GTGCCATCA-TCTTCGGTGCCATCGATGTT-G
* * * * *
83451 GTGTCGTCGATGTT-GGTGTCATC-AGTTTTG
1 GTGCCATC-ATCTTCGGTGCCATCGA-TGTTG
* *
83481 GTGCCATCATCTTCGGTGTCGTCGATGTTG
1 GTGCCATCATCTTCGGTGCCATCGATGTTG
*
83511 GTGCCATCATCTTCGGTGCCGTCGATGTTG
1 GTGCCATCATCTTCGGTGCCATCGATGTTG
83541 GTGCCATCATCTT
1 GTGCCATCATCTT
83554 TTTCCATGAC
Statistics
Matches: 139, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
29 8 0.06
30 122 0.88
31 9 0.06
ACGTcount: A:0.11, C:0.23, G:0.27, T:0.38
Consensus pattern (30 bp):
GTGCCATCATCTTCGGTGCCATCGATGTTG
Found at i:83450 original size:75 final size:74
Alignment explanation
Indices: 83361--83550 Score: 242
Period size: 75 Copynumber: 2.5 Consensus size: 74
83351 ACCACTTTCA
* * * *
83361 GTGCCATCATCTTCGGTGCCATC-AGTTTTGGTGCCATCATTTTCGGTGCCGTCGATGTT-GGTG
1 GTGCCATCATCTTCGGTGCCGTCGA-TGTTGGTGCCATCATTTT-GGTGCCATC-ATCTTCGGTG
*
83424 TCATC-AGTTTTG
63 TCATCGA-TGTTG
* *
83436 GTGCCATCATCTTCGGTGTCGTCGATGTTGGTGTCATCAGTTTTGGTGCCATCATCTTCGGTGTC
1 GTGCCATCATCTTCGGTGCCGTCGATGTTGGTGCCATCA-TTTTGGTGCCATCATCTTCGGTGTC
*
83501 GTCGATGTTG
65 ATCGATGTTG
83511 GTGCCATCATCTTCGGTGCCGTCGATGTTGGTGCCATCAT
1 GTGCCATCATCTTCGGTGCCGTCGATGTTGGTGCCATCAT
83551 CTTTTTCCAT
Statistics
Matches: 101, Mismatches: 10, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
74 5 0.05
75 90 0.89
76 6 0.06
ACGTcount: A:0.12, C:0.23, G:0.28, T:0.37
Consensus pattern (74 bp):
GTGCCATCATCTTCGGTGCCGTCGATGTTGGTGCCATCATTTTGGTGCCATCATCTTCGGTGTCA
TCGATGTTG
Found at i:83530 original size:45 final size:45
Alignment explanation
Indices: 83375--83519 Score: 254
Period size: 45 Copynumber: 3.2 Consensus size: 45
83365 CATCATCTTC
* *
83375 GGTGCCATCAGTTTTGGTGCCATCATTTTCGGTGCCGTCGATGTT
1 GGTGCCATCAGTTTTGGTGCCATCATCTTCGGTGTCGTCGATGTT
*
83420 GGTGTCATCAGTTTTGGTGCCATCATCTTCGGTGTCGTCGATGTT
1 GGTGCCATCAGTTTTGGTGCCATCATCTTCGGTGTCGTCGATGTT
*
83465 GGTGTCATCAGTTTTGGTGCCATCATCTTCGGTGTCGTCGATGTT
1 GGTGCCATCAGTTTTGGTGCCATCATCTTCGGTGTCGTCGATGTT
83510 GGTGCCATCA
1 GGTGCCATCA
83520 TCTTCGGTGC
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 96 1.00
ACGTcount: A:0.12, C:0.21, G:0.29, T:0.38
Consensus pattern (45 bp):
GGTGCCATCAGTTTTGGTGCCATCATCTTCGGTGTCGTCGATGTT
Done.