Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023926.1 Corchorus olitorius cultivar O-4 contig23959, 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: 49535
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:770 original size:17 final size:16
Alignment explanation
Indices: 750--785 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 16
740 CACAATATAT
750 ATATTATACTATAAAAA
1 ATATTAT-CTATAAAAA
767 ATA-TATCTATAAAAA
1 ATATTATCTATAAAAA
782 ATAT
1 ATAT
786 GGCTAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 12 0.67
16 3 0.17
17 3 0.17
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (16 bp):
ATATTATCTATAAAAA
Found at i:772 original size:2 final size:2
Alignment explanation
Indices: 707--762 Score: 62
Period size: 2 Copynumber: 27.5 Consensus size: 2
697 TGATTCTTTA
*
707 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT CAC A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT -AT AT AT AT AT
750 AT AT -T AT ACT AT A
1 AT AT AT AT A-T AT A
763 AAAAATATAT
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
1 2 0.04
2 41 0.84
3 6 0.12
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:785 original size:13 final size:15
Alignment explanation
Indices: 754--785 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
744 ATATATATAT
754 TATA-CTATAAAAAA
1 TATATCTATAAAAAA
768 TATATCTATAAAAAA
1 TATATCTATAAAAAA
783 TAT
1 TAT
786 GGCTAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.34
Consensus pattern (15 bp):
TATATCTATAAAAAA
Found at i:1672 original size:2 final size:2
Alignment explanation
Indices: 1665--1693 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1655 AATTACCTAC
1665 TA TA 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 TA TA T
1694 TAATTTGCAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6538 original size:21 final size:21
Alignment explanation
Indices: 6512--6559 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
6502 GGAATTACTG
6512 ATAAAAGTTGTATATATCTAT
1 ATAAAAGTTGTATATATCTAT
6533 ATAAAAGTTGTATATATCTAT
1 ATAAAAGTTGTATATATCTAT
6554 ATAAAA
1 ATAAAA
6560 AATTTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (21 bp):
ATAAAAGTTGTATATATCTAT
Found at i:6556 original size:23 final size:23
Alignment explanation
Indices: 6512--6578 Score: 79
Period size: 21 Copynumber: 3.1 Consensus size: 23
6502 GGAATTACTG
6512 ATAAAAGTTGTATATATC--TAT
1 ATAAAAGTTGTATATATCTATAT
6533 ATAAAAGTTGTATATATCTATAT
1 ATAAAAGTTGTATATATCTATAT
* * *
6556 A-AAAAATTTTA-AAATCTATAT
1 ATAAAAGTTGTATATATCTATAT
6577 AT
1 AT
6579 CTATAGATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
21 28 0.70
22 8 0.20
23 4 0.10
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (23 bp):
ATAAAAGTTGTATATATCTATAT
Found at i:6622 original size:19 final size:20
Alignment explanation
Indices: 6598--6644 Score: 87
Period size: 19 Copynumber: 2.4 Consensus size: 20
6588 ACTAATACTC
6598 TATATAAATTAATAATAA-T
1 TATATAAATTAATAATAATT
6617 TATATAAATTAATAATAATT
1 TATATAAATTAATAATAATT
6637 TATATAAA
1 TATATAAA
6645 AAATCAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TATATAAATTAATAATAATT
Found at i:10013 original size:25 final size:24
Alignment explanation
Indices: 9977--10023 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
9967 TCCTTCTATT
9977 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
10000 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
10024 AATTTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:16031 original size:76 final size:76
Alignment explanation
Indices: 15929--16231 Score: 534
Period size: 76 Copynumber: 4.0 Consensus size: 76
15919 ATTTCAAACA
* * * *
15929 AACGGTTGGGTGCCTAGACTGGCGCCCCCGTTCGTCTACCAGTGAGACAAAGCGTTCACGCAGAC
1 AACGGCTGAGTGCCTAGACTGGCGCCCCCGTTCGTCTACTAGTGAGACAAAGCGTCCACGCAGAC
15994 GCCGCTCACTC
66 GCCGCTCACTC
16005 AACGGCTGAGTGCCTAGACTGGCGCCCCCGTTCGTCTACTAGTGAGACAAAGCGTCCACGCAGAC
1 AACGGCTGAGTGCCTAGACTGGCGCCCCCGTTCGTCTACTAGTGAGACAAAGCGTCCACGCAGAC
16070 GCCGCTCACTC
66 GCCGCTCACTC
* * * *
16081 AACGGCTGAGTGCCTAGACTAGCGCCCTCATTCGTCTACTAGTGAGACAAAGCGTCCACGCAGAT
1 AACGGCTGAGTGCCTAGACTGGCGCCCCCGTTCGTCTACTAGTGAGACAAAGCGTCCACGCAGAC
16146 GCCGCTCACTC
66 GCCGCTCACTC
16157 AACGGCTGAGTGCCTAGACTGGCGCCCCCGTTCGTCTACTAGTGAGACAAAGCGTCCACGCAGAC
1 AACGGCTGAGTGCCTAGACTGGCGCCCCCGTTCGTCTACTAGTGAGACAAAGCGTCCACGCAGAC
16222 GCCGCTCACT
66 GCCGCTCACT
16232 AAACTATCAA
Statistics
Matches: 215, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 215 1.00
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.18
Consensus pattern (76 bp):
AACGGCTGAGTGCCTAGACTGGCGCCCCCGTTCGTCTACTAGTGAGACAAAGCGTCCACGCAGAC
GCCGCTCACTC
Found at i:19904 original size:23 final size:23
Alignment explanation
Indices: 19871--19914 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
19861 CCAACTTCCG
*
19871 AAATTCAAATTTTGAATTTTCAA
1 AAATTCAAATTTTGAAATTTCAA
*
19894 AAATTCGAATTTTGAAATTTC
1 AAATTCAAATTTTGAAATTTC
19915 GCGCCGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (23 bp):
AAATTCAAATTTTGAAATTTCAA
Found at i:30296 original size:26 final size:26
Alignment explanation
Indices: 30260--30311 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
30250 GGAAAAAAGT
30260 CTACCTGGTTAAGAAAAAGACATGAC
1 CTACCTGGTTAAGAAAAAGACATGAC
*
30286 CTACCTGGTTAAGAAAAATACATGAC
1 CTACCTGGTTAAGAAAAAGACATGAC
30312 AAAACTGTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.21
Consensus pattern (26 bp):
CTACCTGGTTAAGAAAAAGACATGAC
Found at i:34443 original size:31 final size:31
Alignment explanation
Indices: 34405--34463 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
34395 TTTGTAAAAC
*
34405 TTTTGAAATACCTATTATACCCTTATTTAAT
1 TTTTGAAACACCTATTATACCCTTATTTAAT
* *
34436 TTTTGAAACGCCTATTATATCCTTATTT
1 TTTTGAAACACCTATTATACCCTTATTT
34464 GTCTAACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (31 bp):
TTTTGAAACACCTATTATACCCTTATTTAAT
Found at i:40603 original size:80 final size:79
Alignment explanation
Indices: 40510--40665 Score: 249
Period size: 80 Copynumber: 2.0 Consensus size: 79
40500 TCGTTATGCA
40510 AACTCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAAGTCG
1 AACTCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAAGTCG
40575 TCTAAGATCCGTGC
66 TCTAAGATCCGTGC
* * * * **
40589 AACTCCCCCTCGTTTTTATTTCTCTTCCTAAAATAGGTTTTCCAGCCGACTTATCTTCAAAAGTC
1 AACT-CCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAAGTC
40654 GTCTAAGATCCG
65 GTCTAAGATCCG
40666 AAACCACTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
79 4 0.06
80 66 0.94
ACGTcount: A:0.24, C:0.31, G:0.12, T:0.33
Consensus pattern (79 bp):
AACTCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAAGTCG
TCTAAGATCCGTGC
Found at i:45489 original size:367 final size:367
Alignment explanation
Indices: 44809--45489 Score: 938
Period size: 367 Copynumber: 1.9 Consensus size: 367
44799 GCATAAAATA
* * * *
44809 TATAAAATAGAAAAGTATGAGAGTCATTTGATAACTAATTCAAATAAGAAATTATTTCTTAATGG
1 TATAAAATAGAAAAATATGAGAGTCATTTGATAAATAATCCAAATAAGAAAATATTTCTTAATGG
* * * *
44874 ATATCTTGAAATATAAAAATTCCCTTTTGAATCCTTTATGAAACTCGTAGCTCAAATTAACTTTC
66 AGATCTTGAAACATAAAAATTCCCTTTTGAAGCCTTTATGAAACTCGTAGATCAAATTAACTTTC
* * * * * *
44939 GGGTTCTTCATGAAAGTCGTAGATCATACAGTAACCTTTTAACCGACACTTGAATAACTTTAATC
131 GGGTCCTTCAAGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCAATC
* * ** ** * *
45004 GGACATGTGGATCGAAAATTATATGGTATTAAATAGACCAACAATGGAAACGACCAAATTTAGGA
196 GGACATGTGGATCAAAAATTATACGAAATTAAATAGACCAACAATCAAAACCACAAAATTTAGGA
* * *
45069 AGCATTTTTTTTGAATTAAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAAAAAAAATAATC
261 AGCATTTTTTTAGAATCAAAACATAAAAATTGGCTTTTGAGTCCTTCATGAAAAAAAAAATAATC
45134 TTAAACGTTAAATGAAGATAGAATTTGTAAAGAACTAAGTAG
326 TTAAACGTTAAATGAAGATAGAATTTGTAAAGAACTAAGTAG
* * * * *
45176 TATAAAGTAGAAAAATATGAGGGTTATTTGATAAATAATCCAAATAAGAAAATGTTTGTTAATGG
1 TATAAAATAGAAAAATATGAGAGTCATTTGATAAATAATCCAAATAAGAAAATATTTCTTAATGG
* *
45241 AGATCTTGAAGCAT-AAAATCTCCCTTTTG-AGCCTTTCATGAAACTCGTAGATCAAATTTAGCT
66 AGATCTTGAAACATAAAAAT-TCCCTTTTGAAGCCTTT-ATGAAACTCGTAGATCAAA-TTAACT
*
45304 TTCGGGTCCTTCAAGAAAGTCGTAAATCATGCAATAACCTTTTAACCGACACTTCAATAACTTCA
128 TTCGGGTCCTTCAAGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCA
* * **
45369 ATCGGATATGTGGA-CAAAAAATTATACGAAATTAAATTGACCGGCAATCAAAACCACAAAATTT
193 ATCGGACATGTGGATC-AAAAATTATACGAAATTAAATAGACCAACAATCAAAACCACAAAATTT
* * *
45433 CGGAAGCA-TTTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGTTCTTCATGAAAA
257 AGGAAGCATTTTTTTAGAATCAAAACATAAAAATTGGCTTTTGAGTCCTTCATGAAAA
45490 TTGTAGGTCA
Statistics
Matches: 270, Mismatches: 40, Indels: 8
0.85 0.13 0.03
Matches are distributed among these distances:
366 11 0.04
367 139 0.51
368 120 0.44
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.32
Consensus pattern (367 bp):
TATAAAATAGAAAAATATGAGAGTCATTTGATAAATAATCCAAATAAGAAAATATTTCTTAATGG
AGATCTTGAAACATAAAAATTCCCTTTTGAAGCCTTTATGAAACTCGTAGATCAAATTAACTTTC
GGGTCCTTCAAGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCAATC
GGACATGTGGATCAAAAATTATACGAAATTAAATAGACCAACAATCAAAACCACAAAATTTAGGA
AGCATTTTTTTAGAATCAAAACATAAAAATTGGCTTTTGAGTCCTTCATGAAAAAAAAAATAATC
TTAAACGTTAAATGAAGATAGAATTTGTAAAGAACTAAGTAG
Found at i:47657 original size:27 final size:29
Alignment explanation
Indices: 47601--47659 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 29
47591 GGAGATGGTT
*
47601 TTTGAGATGAGTGATATCTCTGGGAAATG
1 TTTGAGATGAGTGATATCTCTGAGAAATG
* *
47630 TTTGAGATG-TTGA-ATCTCTGAGAGATG
1 TTTGAGATGAGTGATATCTCTGAGAAATG
47657 TTT
1 TTT
47660 TTGTGAGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 15 0.56
28 3 0.11
29 9 0.33
ACGTcount: A:0.25, C:0.07, G:0.29, T:0.39
Consensus pattern (29 bp):
TTTGAGATGAGTGATATCTCTGAGAAATG
Found at i:47662 original size:29 final size:29
Alignment explanation
Indices: 47592--47677 Score: 77
Period size: 31 Copynumber: 2.9 Consensus size: 29
47582 ATAGATTCAG
* *
47592 GAGATGGTTTTTGAGATGAGTGATATCTCTGG
1 GAGAT-GTTTTTGAGATG-TTGA-ATCTCTGA
*
47624 GAAATG--TTTGAGATGTTGAATCTCTGA
1 GAGATGTTTTTGAGATGTTGAATCTCTGA
*
47651 GAGATGTTTTTGTGAGATGTAGAATCT
1 GAGATG-TTTT-TGAGATGTTGAATCT
47678 GCCTTGAAGC
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
27 12 0.27
28 3 0.07
29 9 0.20
30 2 0.04
31 15 0.33
32 4 0.09
ACGTcount: A:0.26, C:0.06, G:0.30, T:0.38
Consensus pattern (29 bp):
GAGATGTTTTTGAGATGTTGAATCTCTGA
Found at i:49506 original size:28 final size:30
Alignment explanation
Indices: 49443--49514 Score: 94
Period size: 28 Copynumber: 2.4 Consensus size: 30
49433 GCTTAAATAC
*
49443 CAAATAAATCCCTTATCTTTTTATTTTGGGA
1 CAAATAAATCCCTGATC-TTTTATTTTGGGA
* *
49474 CAAATAAATCTCTGATC-TTT-TTTTGGGT
1 CAAATAAATCCCTGATCTTTTATTTTGGGA
49502 CAAATAAATCCCT
1 CAAATAAATCCCT
49515 CAGCTTTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 19 0.51
29 3 0.08
31 15 0.41
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.42
Consensus pattern (30 bp):
CAAATAAATCCCTGATCTTTTATTTTGGGA
Done.