Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019428.1 Corchorus olitorius cultivar O-4 contig19461, 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: 100849
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:11168 original size:14 final size:13
Alignment explanation
Indices: 11149--11187 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
11139 AAATTGTAAA
11149 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
11162 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
11176 ATTTAAAAAATT
1 ATTTAAAAAATT
11188 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:11386 original size:121 final size:126
Alignment explanation
Indices: 11173--11424 Score: 381
Period size: 121 Copynumber: 2.0 Consensus size: 126
11163 ATTTAAGAAA
11173 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAATAAAATAGTAAAATGGTAAAAATAAAAT
1 TATATTT-AAAAATTCTAATATATATAAGTTTTTAAATAAAATAGTAAAATGGT---AATAAAAT
* *
11238 AGATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAG
62 ACATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
*
11303 TATATTT-AAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGT-A-AAAAT-CA
1 TATATTTAAAAATTCTAATATATATAAG-TTTTTAAATAAAATAGTAAAATGGTAATAAAATACA
*
11364 TA-AA-GATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAAG
65 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
11424 T
1 T
11425 TTAAACAATG
Statistics
Matches: 117, Mismatches: 4, Indels: 11
0.89 0.03 0.08
Matches are distributed among these distances:
121 55 0.47
122 2 0.02
123 3 0.03
124 5 0.04
125 1 0.01
128 20 0.17
129 24 0.21
130 7 0.06
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (126 bp):
TATATTTAAAAATTCTAATATATATAAGTTTTTAAATAAAATAGTAAAATGGTAATAAAATACAT
ATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:15816 original size:1 final size:1
Alignment explanation
Indices: 15810--15845 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
15800 GGTTTTGGTG
15810 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
15846 CCGGCTGACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:22668 original size:15 final size:15
Alignment explanation
Indices: 22648--22677 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
22638 CAAATACTAC
22648 GATTGTGCAGAAGAA
1 GATTGTGCAGAAGAA
22663 GATTGTGCAGAAGAA
1 GATTGTGCAGAAGAA
22678 AAAAATTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (15 bp):
GATTGTGCAGAAGAA
Found at i:25652 original size:17 final size:17
Alignment explanation
Indices: 25630--25684 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
25620 GGATCACCCC
*
25630 AGATCACTAGTGATCTA
1 AGATCACCAGTGATCTA
*
25647 AGATCACCAGTGATGTA
1 AGATCACCAGTGATCTA
* * *
25664 AGATCATCGGTGATCAA
1 AGATCACCAGTGATCTA
25681 AGAT
1 AGAT
25685 TACATGGGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (17 bp):
AGATCACCAGTGATCTA
Found at i:31443 original size:21 final size:21
Alignment explanation
Indices: 31419--31481 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
31409 ATCATCCAAC
* *
31419 ACAGGTTCTGGCACTTCCACA
1 ACAGGTTCTAGCTCTTCCACA
* *
31440 ACAGCTTCTTGCTCTTCCACA
1 ACAGGTTCTAGCTCTTCCACA
*
31461 ATAGGTTCTAGCTCTTCCACA
1 ACAGGTTCTAGCTCTTCCACA
31482 GGCTTCTCCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.22, C:0.33, G:0.14, T:0.30
Consensus pattern (21 bp):
ACAGGTTCTAGCTCTTCCACA
Found at i:49562 original size:2 final size:2
Alignment explanation
Indices: 49557--49596 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
49547 TATGTCATAG
*
49557 AT AT AT AT AT AT AT AT AT AT AC 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 AT AT AT AT AT
49597 TCATCTCGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:54410 original size:15 final size:15
Alignment explanation
Indices: 54375--54416 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
54365 GGAGGAAAGG
*
54375 AAGGAAGG-GAAATG
1 AAGGAAGGAGAAATC
54389 AAGGGAAGGAGAAATC
1 AA-GGAAGGAGAAATC
*
54405 AAGGAAGAAGAA
1 AAGGAAGGAGAA
54417 GAGCAAGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 2 0.08
15 15 0.62
16 7 0.29
ACGTcount: A:0.55, C:0.02, G:0.38, T:0.05
Consensus pattern (15 bp):
AAGGAAGGAGAAATC
Found at i:57726 original size:48 final size:48
Alignment explanation
Indices: 57671--57805 Score: 143
Period size: 48 Copynumber: 2.8 Consensus size: 48
57661 TGCTCAAGAC
57671 TAACCATCACGA-TGGAAGGAT-ATCAAAATTGACCAAAAT-ATTAAAAAT
1 TAACCATCACGACT-GAAGG-TGATCAAAATTGACCAAAATGA-TAAAAAT
* * * *
57719 TAACCATCACGACTGAATGTGGTCTAAATTGACCAAAATGATAAAAGT
1 TAACCATCACGACTGAAGGTGATCAAAATTGACCAAAATGATAAAAAT
* * *
57767 TAACCATCACGAACCGAAGGTGA-AAAAATTAACCAAAAT
1 TAACCATCACG-ACTGAAGGTGATCAAAATTGACCAAAAT
57806 AGTAAAGGTT
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
47 1 0.01
48 62 0.85
49 10 0.14
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
TAACCATCACGACTGAAGGTGATCAAAATTGACCAAAATGATAAAAAT
Found at i:57817 original size:48 final size:49
Alignment explanation
Indices: 57695--57826 Score: 144
Period size: 48 Copynumber: 2.7 Consensus size: 49
57685 GAAGGATATC
* * * * **
57695 AAAATTGACCAAAATATTAAAAATTAACCATCACG-ACTGAATGTGGTC
1 AAAATTGACCAAAATAGTAAAAGTTAACCATCACGAACCGAAGGTGGAA
*
57743 TAAATTGACCAAAAT-GATAAAAGTTAACCATCACGAACCGAAGGT-GAA
1 AAAATTGACCAAAATAG-TAAAAGTTAACCATCACGAACCGAAGGTGGAA
* * *
57791 AAAATTAACCAAAATAGTAAAGGTTAATCATCACGA
1 AAAATTGACCAAAATAGTAAAAGTTAACCATCACGA
57827 TCCAAAGTGA
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
48 62 0.89
49 8 0.11
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (49 bp):
AAAATTGACCAAAATAGTAAAAGTTAACCATCACGAACCGAAGGTGGAA
Found at i:62860 original size:7 final size:7
Alignment explanation
Indices: 62821--62857 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
62811 TCGAGCAGAA
62821 CAGAAAC
1 CAGAAAC
62828 CAGAAAC
1 CAGAAAC
62835 CAGAAAC
1 CAGAAAC
62842 CAGAAAC
1 CAGAAAC
*
62849 CAAAAAC
1 CAGAAAC
62856 CA
1 CA
62858 AAATTGCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.59, C:0.30, G:0.11, T:0.00
Consensus pattern (7 bp):
CAGAAAC
Found at i:70226 original size:62 final size:63
Alignment explanation
Indices: 70152--70278 Score: 211
Period size: 62 Copynumber: 2.0 Consensus size: 63
70142 TCAGTCAGAG
* * *
70152 AGCACTACAGAACAATAGTTGAGACAAAAACAAAAAA-AATGAAAGAAATGTGCTCATTAATT
1 AGCACTAAAGAACAATAATTGAGACAAAAACAAAAAAGAATGAAAGAAATGTGCTAATTAATT
*
70214 AGCACTAAAGAACAATAATTGAGACAAAAACAAAAAAGAATGAAAGAAATGTGCTAATTGATT
1 AGCACTAAAGAACAATAATTGAGACAAAAACAAAAAAGAATGAAAGAAATGTGCTAATTAATT
70277 AG
1 AG
70279 TTGGTTTCTC
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
62 35 0.58
63 25 0.42
ACGTcount: A:0.54, C:0.11, G:0.16, T:0.19
Consensus pattern (63 bp):
AGCACTAAAGAACAATAATTGAGACAAAAACAAAAAAGAATGAAAGAAATGTGCTAATTAATT
Found at i:75481 original size:21 final size:21
Alignment explanation
Indices: 75436--75494 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
75426 CTGTTTGACA
* *
75436 ACTGTATAGATGAGATTA--C
1 ACTGTACAGATGAGATTATGT
*
75455 ACTGTACAGATTAGATTATGT
1 ACTGTACAGATGAGATTATGT
75476 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
75495 TAGAGCAGCG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.47
21 18 0.53
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (21 bp):
ACTGTACAGATGAGATTATGT
Found at i:80311 original size:30 final size:32
Alignment explanation
Indices: 80255--80318 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
80245 TAAATTAATC
80255 AACTAGGGATTTGGCTTTGACCAAAAA-AAAA
1 AACTAGGGATTTGGCTTTGACCAAAAAGAAAA
**
80286 AACTAGGGA-TTGGCTGTTG-GTAAAAAGAAAA
1 AACTAGGGATTTGGCT-TTGACCAAAAAGAAAA
80317 AA
1 AA
80319 AAATTGACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 11 0.38
31 18 0.62
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.22
Consensus pattern (32 bp):
AACTAGGGATTTGGCTTTGACCAAAAAGAAAA
Found at i:80633 original size:18 final size:18
Alignment explanation
Indices: 80590--80627 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
80580 CAAAATTAAA
80590 TATGAATTATGAAGAGTT
1 TATGAATTATGAAGAGTT
80608 TATGAATTATGAAGAGTT
1 TATGAATTATGAAGAGTT
80626 TA
1 TA
80628 GAAATTGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (18 bp):
TATGAATTATGAAGAGTT
Found at i:81612 original size:14 final size:14
Alignment explanation
Indices: 81593--81624 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
81583 GTTCGCTATA
81593 TGGATCCGAAATAT
1 TGGATCCGAAATAT
81607 TGGATCCGAAATAT
1 TGGATCCGAAATAT
81621 TGGA
1 TGGA
81625 CATCATGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.28
Consensus pattern (14 bp):
TGGATCCGAAATAT
Found at i:85633 original size:7 final size:7
Alignment explanation
Indices: 85621--85663 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
85611 ATCATTAAGA
85621 AAAAAAG
1 AAAAAAG
85628 AAAAAAG
1 AAAAAAG
*
85635 AAACAAG
1 AAAAAAG
*
85642 AAAAAAA
1 AAAAAAG
*
85649 AAAAAAA
1 AAAAAAG
85656 AAAAAAG
1 AAAAAAG
85663 A
1 A
85664 GAGAAAGAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.88, C:0.02, G:0.09, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:94854 original size:42 final size:42
Alignment explanation
Indices: 94795--94880 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
94785 GTACGTTAGC
94795 ATTTGCTGAGAACTCCTTTACTGTATGTTGCCTTGACAATTT
1 ATTTGCTGAGAACTCCTTTACTGTATGTTGCCTTGACAATTT
94837 ATTTGCTGAGAACTCCTTTACTGTATGTTGCCTTGACAATTT
1 ATTTGCTGAGAACTCCTTTACTGTATGTTGCCTTGACAATTT
94879 AT
1 AT
94881 GCTTCATAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (42 bp):
ATTTGCTGAGAACTCCTTTACTGTATGTTGCCTTGACAATTT
Done.