Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012331.1 Corchorus olitorius cultivar O-4 contig12364, 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: 50377
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1496 original size:19 final size:19
Alignment explanation
Indices: 1456--1492 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1446 AATTTTTAAT
1456 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
1475 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
1493 ATAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:3907 original size:16 final size:16
Alignment explanation
Indices: 3866--3907 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3856 CCAAACCCAC
*
3866 CCGAACCCGAAATTAT
1 CCGAACCCGAAAATAT
* *
3882 CTGAATCCGAAAATAT
1 CCGAACCCGAAAATAT
3898 CCGAACCCGA
1 CCGAACCCGA
3908 TCCAAGACCG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.31, G:0.14, T:0.17
Consensus pattern (16 bp):
CCGAACCCGAAAATAT
Found at i:4113 original size:2 final size:2
Alignment explanation
Indices: 4106--4132 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4096 AAACTATTAA
4106 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4133 AAACTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4736 original size:29 final size:29
Alignment explanation
Indices: 4686--4742 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
4676 TCAATCTTTA
** *
4686 TATATATTGATAATAATGTTATATTATAT
1 TATATATTGATAATAAACTTATAATATAT
4715 TATATATT-ATCAATAAACTTATAATATA
1 TATATATTGAT-AATAAACTTATAATATA
4743 AAAGATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (29 bp):
TATATATTGATAATAAACTTATAATATAT
Found at i:4888 original size:16 final size:16
Alignment explanation
Indices: 4863--4952 Score: 76
Period size: 16 Copynumber: 5.7 Consensus size: 16
4853 CTACCCAAGA
*
4863 CCGAATCCGAAAATAC
1 CCGAACCCGAAAATAC
*
4879 CCGAACCCGAAAATAT
1 CCGAACCCGAAAATAC
**
4895 CCGAACCCG-ACTTAAC
1 CCGAACCCGAAAAT-AC
* *
4911 CTGAACCCAAAAATAC
1 CCGAACCCGAAAATAC
* * *
4927 CCAAACCTGAAAA-GC
1 CCGAACCCGAAAATAC
4942 CCGAACCCGAA
1 CCGAACCCGAA
4953 TCCGCCCGAA
Statistics
Matches: 56, Mismatches: 16, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
15 12 0.21
16 42 0.75
17 2 0.04
ACGTcount: A:0.42, C:0.36, G:0.12, T:0.10
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:10908 original size:34 final size:34
Alignment explanation
Indices: 10865--10933 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
10855 ACTCGCTATG
10865 CAATTTAGAATTAACATATATTGGTCTGGATAGC
1 CAATTTAGAATTAACATATATTGGTCTGGATAGC
*
10899 CAATTTAGAATTAACATATATTGGTGTGGATAGC
1 CAATTTAGAATTAACATATATTGGTCTGGATAGC
10933 C
1 C
10934 GAACTCCTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (34 bp):
CAATTTAGAATTAACATATATTGGTCTGGATAGC
Found at i:39493 original size:20 final size:21
Alignment explanation
Indices: 39456--39498 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
39446 ATCTCACACA
39456 AAGATTATCAAAAATCATAGG
1 AAGATTATCAAAAATCATAGG
*
39477 AAGATTA-CAAAATTCATAGG
1 AAGATTATCAAAAATCATAGG
39497 AA
1 AA
39499 AATTTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.23
Consensus pattern (21 bp):
AAGATTATCAAAAATCATAGG
Found at i:39572 original size:21 final size:21
Alignment explanation
Indices: 39546--39621 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
39536 CTTATGGAGT
* *
39546 TTATCACAATTTTATAGGTAA
1 TTATCAAAATTTAATAGGTAA
* **
39567 TTATCAAAATTTCATATGGTGG
1 TTATCAAAATTTAATA-GGTAA
39589 TTATCAAAATTTAATAGGTAA
1 TTATCAAAATTTAATAGGTAA
39610 TTATCAAAATTT
1 TTATCAAAATTT
39622 CATAAAAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 29 0.62
22 18 0.38
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (21 bp):
TTATCAAAATTTAATAGGTAA
Found at i:39585 original size:43 final size:43
Alignment explanation
Indices: 39502--39625 Score: 158
Period size: 43 Copynumber: 2.9 Consensus size: 43
39492 ATAGGAAAAT
* * * * * *
39502 TTATTAAAATTTTATAGTTAGGTTATCAAAGTTTCTTATGGAGT
1 TTATCAAAATTTTATAGGTA-ATTATCAAAATTTCATATGGAGG
* *
39546 TTATCACAATTTTATAGGTAATTATCAAAATTTCATATGGTGG
1 TTATCAAAATTTTATAGGTAATTATCAAAATTTCATATGGAGG
*
39589 TTATCAAAATTTAATAGGTAATTATCAAAATTTCATA
1 TTATCAAAATTTTATAGGTAATTATCAAAATTTCATA
39626 AAAATATTCA
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
43 53 0.76
44 17 0.24
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (43 bp):
TTATCAAAATTTTATAGGTAATTATCAAAATTTCATATGGAGG
Found at i:39593 original size:22 final size:21
Alignment explanation
Indices: 39458--39625 Score: 99
Period size: 22 Copynumber: 7.9 Consensus size: 21
39448 CTCACACAAA
* *
39458 GATTATCAAAA-ATCATAGGAA
1 GATTATCAAAATTTCATAGG-T
*
39479 GATTA-CAAAA-TTCATAGGAA
1 GATTATCAAAATTTCATAGG-T
* * * *
39499 AATTTATTAAAATTTTATAGTT
1 GA-TTATCAAAATTTCATAGGT
* * * *
39521 AGGTTATCAAAGTTTCTTATGGA
1 -GATTATCAAAATTTCATA-GGT
* * *
39544 GTTTATCACAATTTTATAGGT
1 GATTATCAAAATTTCATAGGT
*
39565 AATTATCAAAATTTCATATGGT
1 GATTATCAAAATTTCATA-GGT
* *
39587 GGTTATCAAAATTTAATAGGT
1 GATTATCAAAATTTCATAGGT
*
39608 AATTATCAAAATTTCATA
1 GATTATCAAAATTTCATA
39626 AAAATATTCA
Statistics
Matches: 111, Mismatches: 30, Indels: 12
0.73 0.20 0.08
Matches are distributed among these distances:
20 15 0.14
21 42 0.38
22 47 0.42
23 7 0.06
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (21 bp):
GATTATCAAAATTTCATAGGT
Found at i:41192 original size:5 final size:5
Alignment explanation
Indices: 41182--41206 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
41172 GTCTCGTTCT
41182 GTGTC GTGTC GTGTC GTGTC GTGTC
1 GTGTC GTGTC GTGTC GTGTC GTGTC
41207 AAGACCCGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.40, T:0.40
Consensus pattern (5 bp):
GTGTC
Found at i:45289 original size:31 final size:30
Alignment explanation
Indices: 45251--45329 Score: 99
Period size: 31 Copynumber: 2.7 Consensus size: 30
45241 GATCGTTTGA
*
45251 GAAGGGGCAAAGCGTCCAAAAATTGAGAGTT
1 GAAGGGGCAAAACGTCCAAAAATTGA-AGTT
*
45282 GAAGGGGCAAAATGTCC-AAAATTGAAGTT
1 GAAGGGGCAAAACGTCCAAAAATTGAAGTT
* *
45311 -CAGGGGTAAAACGTCCAAA
1 GAAGGGGCAAAACGTCCAAA
45330 CACTACAAGT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 13 0.31
29 6 0.14
30 8 0.19
31 15 0.36
ACGTcount: A:0.41, C:0.14, G:0.29, T:0.16
Consensus pattern (30 bp):
GAAGGGGCAAAACGTCCAAAAATTGAAGTT
Found at i:45326 original size:28 final size:30
Alignment explanation
Indices: 45251--45329 Score: 99
Period size: 28 Copynumber: 2.7 Consensus size: 30
45241 GATCGTTTGA
*
45251 GAAGGGGCAAAGCGTCCAAAAATTGAGAGTT
1 GAAGGGGCAAAACGTCC-AAAATTGAGAGTT
*
45282 GAAGGGGCAAAATGTCCAAAATTGA-AGTT
1 GAAGGGGCAAAACGTCCAAAATTGAGAGTT
* *
45311 -CAGGGGTAAAACGTCCAAA
1 GAAGGGGCAAAACGTCCAAA
45330 CACTACAAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 16 0.37
29 4 0.09
30 8 0.19
31 15 0.35
ACGTcount: A:0.41, C:0.14, G:0.29, T:0.16
Consensus pattern (30 bp):
GAAGGGGCAAAACGTCCAAAATTGAGAGTT
Found at i:49612 original size:17 final size:18
Alignment explanation
Indices: 49590--49624 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
49580 ACAAAAATTG
49590 AAATTGCTCAT-AAACAA
1 AAATTGCTCATGAAACAA
*
49607 AAATTGTTCATGAAACAA
1 AAATTGCTCATGAAACAA
49625 TATAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (18 bp):
AAATTGCTCATGAAACAA
Found at i:49768 original size:16 final size:16
Alignment explanation
Indices: 49747--49778 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
49737 ATTATTATTT
49747 TTATTAATAATATATA
1 TTATTAATAATATATA
*
49763 TTATTATTAATATATA
1 TTATTAATAATATATA
49779 AATAATTATA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTAATAATATATA
Found at i:49768 original size:25 final size:27
Alignment explanation
Indices: 49721--49770 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
49711 AATTTAAATA
49721 TATTAGATAATAGAATATTATTATTTT
1 TATTAGATAATAGAATATTATTATTTT
*
49748 TATTA-ATAATA-TATATTATTATT
1 TATTAGATAATAGAATATTATTATT
49771 AATATATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.50
26 6 0.27
27 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (27 bp):
TATTAGATAATAGAATATTATTATTTT
Found at i:49769 original size:19 final size:19
Alignment explanation
Indices: 49742--49794 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
49732 AGAATATTAT
*
49742 TATTTTTATTAATAATATA
1 TATTATTATTAATAATATA
49761 TATTATTATTAAT-ATATA
1 TATTATTATTAATAATATA
* *
49779 AATAATTATATAATAA
1 TATTATTAT-TAATAA
49795 ACGAACGTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 12 0.41
19 16 0.55
20 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTATTATTAATAATATA
Found at i:49866 original size:35 final size:35
Alignment explanation
Indices: 49820--49894 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
49810 TTATATAAAC
*
49820 GAACACTTAAATGAACAATAAACGAGTCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
49855 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
49890 GAACA
1 GAACA
49895 TAAACGAACT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (35 bp):
GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
Done.