Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017012.1 Corchorus olitorius cultivar O-4 contig17045, 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: 37564
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:2082 original size:30 final size:30
Alignment explanation
Indices: 2048--2105 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
2038 ACTGTCATAC
2048 TCATCTCCTCCTTCACATTCATTGTCTTTG
1 TCATCTCCTCCTTCACATTCATTGTCTTTG
*
2078 TCATCTTCTCCTTCACATTCATTGTCTT
1 TCATCTCCTCCTTCACATTCATTGTCTT
2106 CATGGTCTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.14, C:0.33, G:0.05, T:0.48
Consensus pattern (30 bp):
TCATCTCCTCCTTCACATTCATTGTCTTTG
Found at i:2848 original size:39 final size:33
Alignment explanation
Indices: 2790--2864 Score: 78
Period size: 36 Copynumber: 2.1 Consensus size: 33
2780 CAGATACAGT
*
2790 TGAATGATGAAATTGAGATTGAGAGAGAGCTTTGTC
1 TGAATAATGAAATTGAGATT-AG-G-GAGCTTTGTC
*
2826 TGAATAATGAAGATTGGTAGATTTGGGAGCTTTGTC
1 TGAATAATGAA-ATT-G-AGATTAGGGAGCTTTGTC
2862 TGA
1 TGA
2865 TTTTCACCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
36 23 0.68
37 4 0.12
38 2 0.06
39 5 0.15
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (33 bp):
TGAATAATGAAATTGAGATTAGGGAGCTTTGTC
Found at i:3012 original size:14 final size:14
Alignment explanation
Indices: 2993--3020 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2983 AACAATGTCT
2993 GAATTATCCTTATG
1 GAATTATCCTTATG
3007 GAATTATCCTTATG
1 GAATTATCCTTATG
3021 TAATATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (14 bp):
GAATTATCCTTATG
Found at i:4725 original size:12 final size:13
Alignment explanation
Indices: 4702--4737 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
4692 GAGTGAGGTG
*
4702 TTTTCCTTTTTTC
1 TTTTTCTTTTTTC
4715 TTTTT-TTTTTTC
1 TTTTTCTTTTTTC
4727 TTTTTCTTTTT
1 TTTTTCTTTTT
4738 GGAAGTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:5070 original size:29 final size:31
Alignment explanation
Indices: 5038--5102 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
5028 TATGGGATTT
5038 ATTTGTCCCAAA-AAAA-AGTAAAGGGGCTA
1 ATTTGTCCCAAATAAAATAGTAAAGGGGCTA
* *
5067 ATTTGTCCCAAATAAAATAGTTAAGGGGCTG
1 ATTTGTCCCAAATAAAATAGTAAAGGGGCTA
5098 ATTTG
1 ATTTG
5103 GGTATTAAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 12 0.38
30 4 0.12
31 16 0.50
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (31 bp):
ATTTGTCCCAAATAAAATAGTAAAGGGGCTA
Found at i:12366 original size:6 final size:6
Alignment explanation
Indices: 12357--12406 Score: 61
Period size: 6 Copynumber: 8.7 Consensus size: 6
12347 CGTTTCCGTT
*
12357 TTTTTG TTTTTTG TTTTTG -TTTTG TTTTTG -TTTCG TTTTTG -TTTTG
1 TTTTTG -TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
12403 TTTT
1 TTTT
12407 CAAAATTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 14 0.37
6 18 0.47
7 6 0.16
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.82
Consensus pattern (6 bp):
TTTTTG
Found at i:12381 original size:11 final size:11
Alignment explanation
Indices: 12365--12406 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
12355 TTTTTTTGTT
12365 TTTTGTTTTTG
1 TTTTGTTTTTG
12376 TTTTGTTTTTG
1 TTTTGTTTTTG
*
12387 TTTCGTTTTTG
1 TTTTGTTTTTG
12398 TTTTGTTTT
1 TTTTGTTTT
12407 CAAAATTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.00, C:0.02, G:0.17, T:0.81
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:14717 original size:30 final size:30
Alignment explanation
Indices: 14683--14755 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
14673 CCAATAATGC
*
14683 CATCTTCATCACTTAATGGTTGATCCCTCG
1 CATCTTCATCACTTAATGGTTGATCCCTCA
* * *
14713 CATCTTCCTCCCTTATTGGTTGATCCCTCA
1 CATCTTCATCACTTAATGGTTGATCCCTCA
14743 CATCTTCATCACT
1 CATCTTCATCACT
14756 ATCAGAGGGG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.18, C:0.34, G:0.10, T:0.38
Consensus pattern (30 bp):
CATCTTCATCACTTAATGGTTGATCCCTCA
Found at i:17022 original size:20 final size:20
Alignment explanation
Indices: 16997--17037 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
16987 TTTTGTTTCC
16997 AAAAAACGAAAA-TGGCAACA
1 AAAAAAC-AAAATTGGCAACA
17017 AAAAAACAAAATTGGCAACA
1 AAAAAACAAAATTGGCAACA
17037 A
1 A
17038 TGCCAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.66, C:0.15, G:0.12, T:0.07
Consensus pattern (20 bp):
AAAAAACAAAATTGGCAACA
Found at i:17661 original size:15 final size:15
Alignment explanation
Indices: 17642--17684 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
17632 ACATCTTAAT
*
17642 ATTATAATTATTA-A
1 ATTATTATTATTATA
17656 ACTTATTATTATTATA
1 A-TTATTATTATTATA
17672 ATTATTATTATTA
1 ATTATTATTATTA
17685 GTGGTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 1 0.04
15 23 0.88
16 2 0.08
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTATTATTATTATA
Found at i:17664 original size:109 final size:106
Alignment explanation
Indices: 17475--17671 Score: 297
Period size: 109 Copynumber: 1.8 Consensus size: 106
17465 CCGGATTTTA
* *
17475 TTTCCATATTAAAAAAGTCTAAAATAATAACAATTATTTTTACGTTAAACAACTTATTATTATAA
1 TTTCCATATTAAAAAAGTCTAAAATAATAACAAATATTTTTACGTTAAACAACTTAATATTATAA
17540 TTATTAAAATTATTATTAGTTATATATATAATTACGTTTTCC
66 TTATTAAAATTATTATTA-TTATATATATAATTACGTTTTCC
* * *
17582 TTTCCATATTACAAAAGTCTAATATAATACTAACAAAT-TTTTTACGTTAAACATCTTAATATTA
1 TTTCCATATTAAAAAAGTCT-A-A-AATAATAACAAATATTTTTACGTTAAACAACTTAATATTA
*
17646 TAATTATTAAACTTATTATTATTATA
63 TAATTATTAAAATTATTATTATTATA
17672 ATTATTATTA
Statistics
Matches: 81, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
107 19 0.23
108 6 0.07
109 45 0.56
110 11 0.14
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (106 bp):
TTTCCATATTAAAAAAGTCTAAAATAATAACAAATATTTTTACGTTAAACAACTTAATATTATAA
TTATTAAAATTATTATTATTATATATATAATTACGTTTTCC
Found at i:17679 original size:18 final size:19
Alignment explanation
Indices: 17658--17707 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
17648 ATTATTAAAC
*
17658 TTATTATTAT-TATAATTA
1 TTATTATTATGTAAAATTA
17676 TTATTATTAGTGGTAAAATTA
1 TTATTATTA-T-GTAAAATTA
17697 TTATTAGTTAT
1 TTATTA-TTAT
17708 ATGATCATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 9 0.33
19 1 0.04
21 14 0.52
22 3 0.11
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (19 bp):
TTATTATTATGTAAAATTA
Found at i:19012 original size:22 final size:22
Alignment explanation
Indices: 18982--19023 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
18972 AAGATAATAA
* *
18982 TATAGTTTTTAGAATAATCACT
1 TATACTTTTTAGAACAATCACT
19004 TATACTTTTTAGAACAATCA
1 TATACTTTTTAGAACAATCA
19024 TTGAAGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (22 bp):
TATACTTTTTAGAACAATCACT
Found at i:20453 original size:29 final size:29
Alignment explanation
Indices: 20420--20478 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
20410 CAAACTAAAT
*
20420 AATTATGTAGCACGTTTATTGG-TAGATGG
1 AATTATGTAGCACGTATA-TGGATAGATGG
20449 AATTATGTAGCACGTATATGGATAGATGG
1 AATTATGTAGCACGTATATGGATAGATGG
20478 A
1 A
20479 TAGATGGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 3 0.11
29 25 0.89
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (29 bp):
AATTATGTAGCACGTATATGGATAGATGG
Found at i:20535 original size:2 final size:2
Alignment explanation
Indices: 20528--20557 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20518 TTCTACCATC
20528 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20558 GAGATCATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28499 original size:34 final size:34
Alignment explanation
Indices: 28434--28529 Score: 147
Period size: 34 Copynumber: 2.8 Consensus size: 34
28424 CTTGGGCCGC
* * * *
28434 GCGCCTGGCCTAGGCGCTGGGGCCGCACTGGCCTG
1 GCGCCTAGCCTA-GCGTTTGGGCCGCGCTGGCCTG
28469 GCGCCTAGCCTAGCGTTTGGGCCGCGCTGGCCTG
1 GCGCCTAGCCTAGCGTTTGGGCCGCGCTGGCCTG
28503 GCGCCTAGCCTAGCGTTTGGGCCGCGC
1 GCGCCTAGCCTAGCGTTTGGGCCGCGC
28530 CAGGCAGGCC
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 46 0.81
35 11 0.19
ACGTcount: A:0.06, C:0.36, G:0.40, T:0.18
Consensus pattern (34 bp):
GCGCCTAGCCTAGCGTTTGGGCCGCGCTGGCCTG
Found at i:33938 original size:19 final size:18
Alignment explanation
Indices: 33905--33940 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
33895 TGAAAATAAT
33905 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
33923 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
33941 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Done.