Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011192.1 Corchorus capsularis cultivar CVL-1 contig11213, 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: 34783
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2624 original size:58 final size:58
Alignment explanation
Indices: 2508--2626 Score: 143
Period size: 58 Copynumber: 2.1 Consensus size: 58
2498 AATTAACAAC
* * ** *
2508 TAAATAGCATTAATGTTAATTGATTGTAATTGATCAAAATTTTCATTTAACAATTAAT
1 TAAATAGCATTAATATTAATTAATTGTAATTGATCAAAATTTTCATAAAACAACTAAT
* *
2566 TAAATAGCATTATTATTAATTAATTTTAATTGATC-AAATTATTCA-AAAATCAACTAAT
1 TAAATAGCATTAATATTAATTAATTGTAATTGATCAAAATT-TTCATAAAA-CAACTAAT
2624 TAA
1 TAA
2627 TCAATCAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
57 7 0.13
58 45 0.87
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.42
Consensus pattern (58 bp):
TAAATAGCATTAATATTAATTAATTGTAATTGATCAAAATTTTCATAAAACAACTAAT
Found at i:2660 original size:30 final size:30
Alignment explanation
Indices: 2625--2683 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
2615 TCAACTAATT
*
2625 AATCAATCAAAAGTAATTAATATATTTCCC
1 AATCAACCAAAAGTAATTAATATATTTCCC
* *
2655 AATCAACCTAAAGTAATTAATTTATTTCC
1 AATCAACCAAAAGTAATTAATATATTTCC
2684 TTTTGTCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.36
Consensus pattern (30 bp):
AATCAACCAAAAGTAATTAATATATTTCCC
Found at i:2661 original size:192 final size:193
Alignment explanation
Indices: 2331--2681 Score: 632
Period size: 192 Copynumber: 1.8 Consensus size: 193
2321 AAACGGTTCC
* *
2331 TTAATTGATTGTAATTGATCAAAATTTTCATTTAACAATTGATTAAATAGAATTATTACTAATTG
1 TTAATTGATTGTAATTGATCAAAATTTTCATTTAACAATTAATTAAATAGAATTATTACTAATTA
2396 ATTTTAATTGATCAAATTATTCAAAAATCAACTAATTAATCAATCAAAAGAAATTAATATATTTC
66 ATTTTAATTGATCAAATTATTCAAAAATCAACTAATTAATCAATCAAAAGAAATTAATATATTTC
*
2461 CTAATCAACCTAAAGTAA-TAATTAATTTAATATTAGTAATTAACAACTAAATAGCATTAATG
131 CCAATCAACCTAAAGTAATTAATTAATTTAATATTAGTAATTAACAACTAAATAGCATTAATG
* *
2523 TTAATTGATTGTAATTGATCAAAATTTTCATTTAACAATTAATTAAATAGCATTATTATTAATTA
1 TTAATTGATTGTAATTGATCAAAATTTTCATTTAACAATTAATTAAATAGAATTATTACTAATTA
*
2588 ATTTTAATTGATCAAATTATTCAAAAATCAACTAATTAATCAATCAAAAGTAATTAATATATTTC
66 ATTTTAATTGATCAAATTATTCAAAAATCAACTAATTAATCAATCAAAAGAAATTAATATATTTC
*
2653 CCAATCAACCTAAAGTAATTAATTTATTT
131 CCAATCAACCTAAAGTAATTAATTAATTT
2682 CCTTTTGTCC
Statistics
Matches: 151, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
192 142 0.94
193 9 0.06
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (193 bp):
TTAATTGATTGTAATTGATCAAAATTTTCATTTAACAATTAATTAAATAGAATTATTACTAATTA
ATTTTAATTGATCAAATTATTCAAAAATCAACTAATTAATCAATCAAAAGAAATTAATATATTTC
CCAATCAACCTAAAGTAATTAATTAATTTAATATTAGTAATTAACAACTAAATAGCATTAATG
Found at i:7739 original size:31 final size:31
Alignment explanation
Indices: 7701--7763 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
7691 ACCGCATAAA
7701 AGTTAATTAATGATTGTTCCTAAATCCTAAT
1 AGTTAATTAATGATTGTTCCTAAATCCTAAT
7732 AGTTAATTAATGATTGTTCCTAAATCCTAAT
1 AGTTAATTAATGATTGTTCCTAAATCCTAAT
7763 A
1 A
7764 ATGTTAGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.41
Consensus pattern (31 bp):
AGTTAATTAATGATTGTTCCTAAATCCTAAT
Found at i:8387 original size:14 final size:15
Alignment explanation
Indices: 8348--8394 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
8338 ACAACGCAAC
8348 AAAAAC-AAAACGAAA
1 AAAAACAAAAACG-AA
8363 AGAAAACAAAAAC-AA
1 A-AAAACAAAAACGAA
*
8378 AAAAAGAAAAACGAA
1 AAAAACAAAAACGAA
8393 AA
1 AA
8395 CGATGTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.36
15 8 0.29
16 5 0.18
17 5 0.18
ACGTcount: A:0.81, C:0.11, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAACAAAAACGAA
Found at i:9345 original size:17 final size:17
Alignment explanation
Indices: 9307--9339 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
9297 CTCATGATAC
9307 CTAGGTAGTATGAGGTA
1 CTAGGTAGTATGAGGTA
9324 CTAGGTAGTATGAGGT
1 CTAGGTAGTATGAGGT
9340 GATAGGCTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.36, T:0.30
Consensus pattern (17 bp):
CTAGGTAGTATGAGGTA
Found at i:13897 original size:26 final size:26
Alignment explanation
Indices: 13862--13917 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
13852 ATGCGTGATT
13862 ATTTAATTTTTTACTATATTTTTTGG
1 ATTTAATTTTTTACTATATTTTTTGG
*
13888 ATTTAGTTTTTTACTATATTTTTTGG
1 ATTTAATTTTTTACTATATTTTTTGG
13914 ATTT
1 ATTT
13918 TTTCATAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.21, C:0.04, G:0.09, T:0.66
Consensus pattern (26 bp):
ATTTAATTTTTTACTATATTTTTTGG
Found at i:14628 original size:31 final size:31
Alignment explanation
Indices: 14559--14637 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
14549 ATTTTTACCC
* *
14559 ACCAATTTGAATCTAAACCTTTTAAAAGTTG
1 ACCAATTTGAACCTAAACCTTTTAAAAGGTG
*
14590 -CCTAATTTGAACCTAAACCTTTCT-AATGGTG
1 ACC-AATTTGAACCTAAACCTTT-TAAAAGGTG
*
14621 ACCAATTTGAGCCTAAA
1 ACCAATTTGAACCTAAA
14638 AACAAAAACG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 2 0.05
31 36 0.88
32 3 0.07
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.33
Consensus pattern (31 bp):
ACCAATTTGAACCTAAACCTTTTAAAAGGTG
Found at i:15563 original size:56 final size:56
Alignment explanation
Indices: 15477--15587 Score: 213
Period size: 56 Copynumber: 2.0 Consensus size: 56
15467 TCTACTCCTG
15477 AAAAAAAGGATTTAATATTAATATTAATTAAAAAAAATAGTAGGGAAAAATGCTTT
1 AAAAAAAGGATTTAATATTAATATTAATTAAAAAAAATAGTAGGGAAAAATGCTTT
*
15533 AAAAACAGGATTTAATATTAATATTAATTAAAAAAAATAGTAGGGAAAAATGCTT
1 AAAAAAAGGATTTAATATTAATATTAATTAAAAAAAATAGTAGGGAAAAATGCTT
15588 AAGGAAAATA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.30
Consensus pattern (56 bp):
AAAAAAAGGATTTAATATTAATATTAATTAAAAAAAATAGTAGGGAAAAATGCTTT
Found at i:16018 original size:15 final size:15
Alignment explanation
Indices: 15998--16028 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15988 TGACAAATGC
15998 CTAAAAAAAATAAGG
1 CTAAAAAAAATAAGG
*
16013 CTAAAAAAAATTAGG
1 CTAAAAAAAATAAGG
16028 C
1 C
16029 CCAAACTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.10, G:0.13, T:0.16
Consensus pattern (15 bp):
CTAAAAAAAATAAGG
Found at i:16513 original size:15 final size:15
Alignment explanation
Indices: 16480--16514 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
16470 AGATTTGTTC
* *
16480 GATTTCATGTTGTCT
1 GATTTCATGTTGACG
16495 GATTTCATGTTGACG
1 GATTTCATGTTGACG
16510 GATTT
1 GATTT
16515 GTCAGATTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.23, T:0.49
Consensus pattern (15 bp):
GATTTCATGTTGACG
Found at i:16778 original size:15 final size:15
Alignment explanation
Indices: 16758--16789 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
16748 TGACAAATGC
16758 CTAAAAAAAATAAGG
1 CTAAAAAAAATAAGG
*
16773 CTAAAAAAAATTAGG
1 CTAAAAAAAATAAGG
16788 CT
1 CT
16790 CAACCTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.19
Consensus pattern (15 bp):
CTAAAAAAAATAAGG
Found at i:16832 original size:33 final size:34
Alignment explanation
Indices: 16795--16858 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
16785 AGGCTCAACC
* *
16795 TATTTGCT-AGAAAAA-AAACACAAAGAAAAAGCA
1 TATTTG-TGAGAAAAAGAAAAACAAAAAAAAAGCA
16828 TATTTGTGAGAAAAAGAAAAACAAAAAAAAA
1 TATTTGTGAGAAAAAGAAAAACAAAAAAAAA
16859 AAAGAAAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 1 0.04
33 13 0.48
34 13 0.48
ACGTcount: A:0.64, C:0.08, G:0.12, T:0.16
Consensus pattern (34 bp):
TATTTGTGAGAAAAAGAAAAACAAAAAAAAAGCA
Found at i:17269 original size:24 final size:25
Alignment explanation
Indices: 17217--17274 Score: 84
Period size: 24 Copynumber: 2.4 Consensus size: 25
17207 TTCCTTTCTT
*
17217 GGATTTCATGTTGATGGATTTGTTC
1 GGATTTCATGTTGACGGATTTGTTC
17242 -GATTTCATGTTGACGGATTTG-TC
1 GGATTTCATGTTGACGGATTTGTTC
*
17265 GGATTGCATG
1 GGATTTCATG
17275 ATAGAGATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 2 0.07
24 28 0.93
ACGTcount: A:0.17, C:0.10, G:0.29, T:0.43
Consensus pattern (25 bp):
GGATTTCATGTTGACGGATTTGTTC
Found at i:18392 original size:12 final size:12
Alignment explanation
Indices: 18375--18417 Score: 61
Period size: 12 Copynumber: 3.5 Consensus size: 12
18365 GGGTTAGGTG
18375 TGGTGTTTGTGA
1 TGGTGTTTGTGA
18387 TGGTGTTTG-GA
1 TGGTGTTTGTGA
18398 TGTGGTGTTTGTGA
1 --TGGTGTTTGTGA
18412 TGGTGT
1 TGGTGT
18418 AAAGAGGAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 2 0.07
12 15 0.54
13 9 0.32
14 2 0.07
ACGTcount: A:0.07, C:0.00, G:0.44, T:0.49
Consensus pattern (12 bp):
TGGTGTTTGTGA
Found at i:18405 original size:13 final size:13
Alignment explanation
Indices: 18373--18413 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
18363 AGGGGTTAGG
18373 TGTGGTGTTT-G-
1 TGTGGTGTTTGGA
18384 TGATGGTGTTTGGA
1 TG-TGGTGTTTGGA
18398 TGTGGTGTTTGTGA
1 TGTGGTGTTTG-GA
18412 TG
1 TG
18414 GTGTAAAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.08
12 8 0.31
13 10 0.38
14 6 0.23
ACGTcount: A:0.07, C:0.00, G:0.44, T:0.49
Consensus pattern (13 bp):
TGTGGTGTTTGGA
Found at i:26082 original size:25 final size:25
Alignment explanation
Indices: 26050--26101 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
26040 AAAAAAACAT
* *
26050 AAAAATTATTTGAAAAACAAATTTA
1 AAAAATTATTTGAAAAAAAAATCTA
26075 AAAAATTATTTGAAAAAAAAATCTA
1 AAAAATTATTTGAAAAAAAAATCTA
26100 AA
1 AA
26102 CCCACCCGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (25 bp):
AAAAATTATTTGAAAAAAAAATCTA
Found at i:26085 original size:12 final size:13
Alignment explanation
Indices: 26050--26092 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
26040 AAAAAAACAT
26050 AAAAATTATTTGA
1 AAAAATTATTTGA
*
26063 AAAACA-AATTT-A
1 AAAA-ATTATTTGA
26075 AAAAATTATTTGA
1 AAAAATTATTTGA
26088 AAAAA
1 AAAAA
26093 AAATCTAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 1 0.04
12 9 0.36
13 14 0.56
14 1 0.04
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (13 bp):
AAAAATTATTTGA
Done.