Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013751.1 Corchorus olitorius cultivar O-4 contig13784, 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: 65630
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1961 original size:128 final size:128
Alignment explanation
Indices: 1772--2030 Score: 407
Period size: 128 Copynumber: 2.0 Consensus size: 128
1762 GTCATTTAAG
* *
1772 AAATATATTTTAAAAATTCTAATATATCTAAGTTTTTTAATTAAATTAGTAAAATGGTAAAAATA
1 AAATATATTTAAAAAATTCTAATATA-CTAAGTTTTTTAATCAAATTAGTAAAATGGTAAAAATA
* * *
1837 AAATAGGTATAAAGATATTAGATTTTATTAAATAGAAATAGAGTTTTTAGTTGAGTAAAATTATA
65 AAATAGGTATAAAGATATTAGATTTAATTAAATA-AAA-AAAGTTTTTAGTTGAGTAAAACTATA
1902 A
128 A
1903 AAATATA-TTAAAAAATTCTAATATA-TAAGATTTTTTAATCAAA-TAGTAAAATGGTAAAAATA
1 AAATATATTTAAAAAATTCTAATATACTAAG-TTTTTTAATCAAATTAGTAAAATGGTAAAAATA
*
1965 AAATAGTTATAAAGATATTAGATTTAATTAAATAAAAAAAGTTTTTAGTTGAGTAAAACTATAA
65 AAATAGGTATAAAGATATTAGATTTAATTAAATAAAAAAAGTTTTTAGTTGAGTAAAACTATAA
2029 AA
1 AA
2031 GTTTAAACAA
Statistics
Matches: 121, Mismatches: 6, Indels: 7
0.90 0.04 0.05
Matches are distributed among these distances:
126 27 0.22
127 3 0.02
128 55 0.45
129 12 0.10
130 17 0.14
131 7 0.06
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (128 bp):
AAATATATTTAAAAAATTCTAATATACTAAGTTTTTTAATCAAATTAGTAAAATGGTAAAAATAA
AATAGGTATAAAGATATTAGATTTAATTAAATAAAAAAAGTTTTTAGTTGAGTAAAACTATAA
Found at i:5198 original size:24 final size:24
Alignment explanation
Indices: 5171--5218 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5161 AAAGTTATCC
5171 CCAAACTGCTATATGCTCAGTATT
1 CCAAACTGCTATATGCTCAGTATT
* * *
5195 CCAAACTGCTGTCTGCTTAGTATT
1 CCAAACTGCTATATGCTCAGTATT
5219 TCGCTCTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (24 bp):
CCAAACTGCTATATGCTCAGTATT
Found at i:5318 original size:13 final size:13
Alignment explanation
Indices: 5300--5324 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5290 TTGGAATTCC
5300 AAATAATATTTAT
1 AAATAATATTTAT
5313 AAATAATATTTA
1 AAATAATATTTA
5325 GAACATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:5639 original size:66 final size:66
Alignment explanation
Indices: 5533--5664 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
5523 ATCTAGTAAT
5533 CGATTAAAGATATCTAATCGGCTTGAATTTTATGTGCACGACTAGAGTATTAAATTCAATGCTTT
1 CGATTAAAGATATCTAATCGGCTTGAATTTTATGTGCACGACTAGAGTATTAAATTCAATGCTTT
5598 A
66 A
5599 CGATTAAAGATATCTAATCGGCTTGAATTTTATGTGCACGACTAGAGTATTAAATTCAATGCTTT
1 CGATTAAAGATATCTAATCGGCTTGAATTTTATGTGCACGACTAGAGTATTAAATTCAATGCTTT
5664 A
66 A
5665 TCATATTTTC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (66 bp):
CGATTAAAGATATCTAATCGGCTTGAATTTTATGTGCACGACTAGAGTATTAAATTCAATGCTTT
A
Found at i:6070 original size:21 final size:20
Alignment explanation
Indices: 6040--6078 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
6030 GAAATTAATA
6040 AGAAAATAATAATTATTTTC
1 AGAAAATAATAATTATTTTC
6060 AGAATAATAATAATTATTT
1 AGAA-AATAATAATTATTT
6079 CATATGTGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
AGAAAATAATAATTATTTTC
Found at i:10364 original size:44 final size:44
Alignment explanation
Indices: 10314--10403 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
10304 TCCTCCTTGG
*
10314 ATCTTCTTTGATAATAATCCTCCACATGCATGGATCTTCTTTCA
1 ATCTTCTTTGATAATAATCCTCCACATACATGGATCTTCTTTCA
*
10358 ATCTTCTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCA
1 ATCTTCTTTGATAATAATCCTCCACATACATGGATCTTCTTTCA
10402 AT
1 AT
10404 AATCCTCTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (44 bp):
ATCTTCTTTGATAATAATCCTCCACATACATGGATCTTCTTTCA
Found at i:19787 original size:20 final size:21
Alignment explanation
Indices: 19742--19799 Score: 91
Period size: 20 Copynumber: 2.8 Consensus size: 21
19732 CATCGAATTC
19742 AAAATTAGGGTTCTTGAGTTT
1 AAAATTAGGGTTCTTGAGTTT
* *
19763 CAAATTAGGTTTCTTGAG-TT
1 AAAATTAGGGTTCTTGAGTTT
19783 AAAATTAGGGTTCTTGA
1 AAAATTAGGGTTCTTGA
19800 ATTATTGAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.41
Consensus pattern (21 bp):
AAAATTAGGGTTCTTGAGTTT
Found at i:29611 original size:91 final size:91
Alignment explanation
Indices: 29394--29655 Score: 386
Period size: 91 Copynumber: 2.9 Consensus size: 91
29384 CGTATATGCG
29394 TAAATTGAGCTATTATGATCATGCAAAAGCATCGTTTAAGCATGATAACATGTTTTATCA-TTTT
1 TAAATTGAGCTATTATGATCATGCAAAAGCATCGTTTAAGCATGATAACATGTTTTATCATTTTT
* * **
29458 TCGATGGAAGTTTACGCCTATATGTA
66 TCGATGGAAGTATATGCCTATATACA
29484 TAAATTGAGCTATTATGATCATGCAAAAGCATCGTTTAAGCATGATAACATGTTTTATCATTTTT
1 TAAATTGAGCTATTATGATCATGCAAAAGCATCGTTTAAGCATGATAACATGTTTTATCATTTTT
29549 TCGATGGAAGTATATGCCTATATACA
66 TCGATGGAAGTATATGCCTATATACA
* * * * * * * *
29575 TAAATTGAGCTAATATGATCATCCAAGAGCAACGTTTAAACATGCTTACATGTTTTATCATATTT
1 TAAATTGAGCTATTATGATCATGCAAAAGCATCGTTTAAGCATGATAACATGTTTTATCATTTTT
29640 T-GAT-GATAGTATATGC
66 TCGATGGA-AGTATATGC
29656 TTAGTATGAT
Statistics
Matches: 158, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
89 2 0.01
90 72 0.46
91 84 0.53
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (91 bp):
TAAATTGAGCTATTATGATCATGCAAAAGCATCGTTTAAGCATGATAACATGTTTTATCATTTTT
TCGATGGAAGTATATGCCTATATACA
Found at i:30041 original size:44 final size:44
Alignment explanation
Indices: 29992--30077 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
29982 ATCCAAGATA
*
29992 CCGGCTGGCAAGCGGTGGAGAGCCGACCTCGACCAAGCACGGTC
1 CCGGCTGGCAAGCAGTGGAGAGCCGACCTCGACCAAGCACGGTC
* * *
30036 CCGGCTGGCAGGCAGTGGAGAGCTGACCTTGACCAAGCACGG
1 CCGGCTGGCAAGCAGTGGAGAGCCGACCTCGACCAAGCACGG
30078 ATGAAGAGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.21, C:0.31, G:0.37, T:0.10
Consensus pattern (44 bp):
CCGGCTGGCAAGCAGTGGAGAGCCGACCTCGACCAAGCACGGTC
Found at i:30077 original size:115 final size:116
Alignment explanation
Indices: 29925--30149 Score: 398
Period size: 115 Copynumber: 1.9 Consensus size: 116
29915 GTGATACTGA
*
29925 CTGGCAGGCGGTGGAGAGCCGACCTTGACCAAGCACGGATGAAGAGCCCTCTTAAGGATCCA-AG
1 CTGGCAGGCAGTGGAGAGCCGACCTTGACCAAGCACGGATGAAGAGCCCTCTTAAGGATCCAGAG
29989 ATACCGGCTGGCAAGCGGTGGAGAGCCGACCTCGACCAAGCACGGTCCCGG
66 ATACCGGCTGGCAAGCGGTGGAGAGCCGACCTCGACCAAGCACGGTCCCGG
* *
30040 CTGGCAGGCAGTGGAGAGCTGACCTTGACCAAGCACGGATGAAGAGCCCTCTTAAGGGTCCAGAG
1 CTGGCAGGCAGTGGAGAGCCGACCTTGACCAAGCACGGATGAAGAGCCCTCTTAAGGATCCAGAG
* *
30105 ATACCGGCTGGCAGGCGGTGGAGAGCCGACCTTGACCAAGCACGG
66 ATACCGGCTGGCAAGCGGTGGAGAGCCGACCTCGACCAAGCACGG
30150 ATGAAGAACC
Statistics
Matches: 104, Mismatches: 5, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
115 59 0.57
116 45 0.43
ACGTcount: A:0.24, C:0.28, G:0.35, T:0.13
Consensus pattern (116 bp):
CTGGCAGGCAGTGGAGAGCCGACCTTGACCAAGCACGGATGAAGAGCCCTCTTAAGGATCCAGAG
ATACCGGCTGGCAAGCGGTGGAGAGCCGACCTCGACCAAGCACGGTCCCGG
Found at i:30118 original size:72 final size:72
Alignment explanation
Indices: 30036--30220 Score: 271
Period size: 72 Copynumber: 2.6 Consensus size: 72
30026 AAGCACGGTC
* * *
30036 CCGGCTGGCAGGCAGTGGAGAGCTGACCTTGACCAAGCACGGATGAAGAGCCCTCTTAAGGGTCC
1 CCGGCTGGCAGGCGGTGGAGAGCCGACCTTGACCAAGCACGGATGAAGAACCCTCTTAAGGGTCC
*
30101 AGAGATA
66 AGAGAGA
*
30108 CCGGCTGGCAGGCGGTGGAGAGCCGACCTTGACCAAGCACGGATGAAGAACCTTCTTAAGGGTCC
1 CCGGCTGGCAGGCGGTGGAGAGCCGACCTTGACCAAGCACGGATGAAGAACCCTCTTAAGGGTCC
*
30173 AGTGAGA
66 AGAGAGA
* * * * *
30180 CCGGCTGACAAGTGGTGAAGAGCCGACCTCGACCAAGCACG
1 CCGGCTGGCAGGCGGTGGAGAGCCGACCTTGACCAAGCACG
30221 ACATCGGCTA
Statistics
Matches: 102, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 102 1.00
ACGTcount: A:0.26, C:0.26, G:0.34, T:0.14
Consensus pattern (72 bp):
CCGGCTGGCAGGCGGTGGAGAGCCGACCTTGACCAAGCACGGATGAAGAACCCTCTTAAGGGTCC
AGAGAGA
Found at i:31155 original size:5 final size:5
Alignment explanation
Indices: 31145--31208 Score: 119
Period size: 5 Copynumber: 12.8 Consensus size: 5
31135 CTAACCCTAA
*
31145 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATAGT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
31195 ATATT ATATT ATAT
1 ATATT ATATT ATAT
31209 ATTATCTTAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 57 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:32371 original size:74 final size:75
Alignment explanation
Indices: 32249--32389 Score: 214
Period size: 74 Copynumber: 1.9 Consensus size: 75
32239 TATGAACTAC
* * *
32249 TCGGTGGACCTTGAATCAAGACTGGACCCGGGTTCCTCTCCCAACATATATGGTGAATTCC-AGC
1 TCGGTGGACCTTGAACCAAGACAGGACCCGGATTCCTCTCCCAACATATATGGTGAATTCCTAGC
32313 TATGGGCTAT
66 TATGGGCTAT
* *
32323 TCGGTGGACCTTGAACCAAGACAAGG-CCTGGATTCCTCTCCCAGCATATATGGTGAATTCCTAG
1 TCGGTGGACCTTGAACCAAGAC-AGGACCCGGATTCCTCTCCCAACATATATGGTGAATTCCTAG
32387 CTA
65 CTA
32390 GCTAACACTC
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
74 53 0.88
75 7 0.12
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.26
Consensus pattern (75 bp):
TCGGTGGACCTTGAACCAAGACAGGACCCGGATTCCTCTCCCAACATATATGGTGAATTCCTAGC
TATGGGCTAT
Found at i:34640 original size:4 final size:4
Alignment explanation
Indices: 34633--34671 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
34623 GCAATATATA
34633 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
34672 ACTATATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:35813 original size:2 final size:2
Alignment explanation
Indices: 35806--35845 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
35796 AAGGGTAAAC
* *
35806 TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35846 ATGCCAAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:37389 original size:12 final size:12
Alignment explanation
Indices: 37364--37401 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
37354 CTTTGTTTCA
37364 TATATATATATAT
1 TATATAT-TATAT
37377 TATATATTATAT
1 TATATATTATAT
*
37389 TATATATCATAT
1 TATATATTATAT
37401 T
1 T
37402 TTGTTCTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 17 0.71
13 7 0.29
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:38117 original size:20 final size:20
Alignment explanation
Indices: 38092--38130 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38082 TCTGCTTCTT
*
38092 TTGTTTGCTTTGATTTTGTC
1 TTGTTTGCTTTGATATTGTC
*
38112 TTGTTTTCTTTGATATTGT
1 TTGTTTGCTTTGATATTGT
38131 TCTCTGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.08, G:0.18, T:0.67
Consensus pattern (20 bp):
TTGTTTGCTTTGATATTGTC
Found at i:40581 original size:29 final size:29
Alignment explanation
Indices: 40548--40604 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
40538 ATAAGTGTGG
*
40548 TATGGAAGGTGTAGAGTCAGATTAATAAC
1 TATGGAAGGTGTAGAGCCAGATTAATAAC
40577 TATGGAAGGTGTAGAGCCAGATTAATAA
1 TATGGAAGGTGTAGAGCCAGATTAATAA
40605 ATGTATGTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.39, C:0.07, G:0.28, T:0.26
Consensus pattern (29 bp):
TATGGAAGGTGTAGAGCCAGATTAATAAC
Found at i:41478 original size:20 final size:20
Alignment explanation
Indices: 41453--41499 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
41443 TCAATATAAG
*
41453 AAAAAACCATCATTTACGAA
1 AAAAAAACATCATTTACGAA
*
41473 AAAAAAACATCATTTACTAA
1 AAAAAAACATCATTTACGAA
41493 AAAAAAA
1 AAAAAAA
41500 GAATGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.64, C:0.15, G:0.02, T:0.19
Consensus pattern (20 bp):
AAAAAAACATCATTTACGAA
Found at i:46084 original size:16 final size:18
Alignment explanation
Indices: 46057--46093 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
46047 ATATTTATCC
46057 TTTAATGGGTAG-TTTTA
1 TTTAATGGGTAGTTTTTA
46074 TTTAA-GGGTAGTTTTTA
1 TTTAATGGGTAGTTTTTA
46091 TTT
1 TTT
46094 TGTTTTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.57
Consensus pattern (18 bp):
TTTAATGGGTAGTTTTTA
Found at i:64980 original size:2 final size:2
Alignment explanation
Indices: 64973--65022 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
64963 GGCGCAACAA
64973 AT AT AT AT AT AT AT A- AT AT A- AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65012 AT AT AT AT AT A
1 AT AT AT AT AT A
65023 CCCATAAATC
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 42 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.