Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015142.1 Corchorus olitorius cultivar O-4 contig15175, 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: 36808
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:255 original size:48 final size:47
Alignment explanation
Indices: 180--314 Score: 157
Period size: 49 Copynumber: 2.8 Consensus size: 47
170 GAGCGTGCCA
* * * *
180 ATCAATTTTATCAAAAAATTGATAAAAAGTGCAGTGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAGTGAAAAATAAAAG
227 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGT-AAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGC-AGTGAAAAATAAAAG
* * *
276 TTCAATTTTGTAGTAAAAATTGAGAAAAAATGCAG-GAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAGTGAAA
315 TGTAAAGGAT
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
47 16 0.21
48 18 0.24
49 39 0.51
50 3 0.04
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAGTGAAAAATAAAAG
Found at i:281 original size:49 final size:50
Alignment explanation
Indices: 193--309 Score: 161
Period size: 49 Copynumber: 2.4 Consensus size: 50
183 AATTTTATCA
* * **
193 AAAAATTGATAAAAAG-TGC-AGTGAAAATTAAAAGATCAATTTTGTCTT
1 AAAAATTGAGAAAAAGATGCAAGTGAAAAATAAAAGATCAATTTTGTAGT
*
241 AAAAATTGAGAAAAAGATGCAAGT-AAAAATAAAAGTTCAATTTTGTAGT
1 AAAAATTGAGAAAAAGATGCAAGTGAAAAATAAAAGATCAATTTTGTAGT
290 AAAAATTGAGAAAAA-ATGCA
1 AAAAATTGAGAAAAAGATGCA
310 GGAAATGTAA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
48 20 0.32
49 39 0.63
50 3 0.05
ACGTcount: A:0.53, C:0.05, G:0.15, T:0.26
Consensus pattern (50 bp):
AAAAATTGAGAAAAAGATGCAAGTGAAAAATAAAAGATCAATTTTGTAGT
Found at i:1605 original size:9 final size:9
Alignment explanation
Indices: 1591--1620 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1581 TGAAATCATT
1591 TAATTTCCA
1 TAATTTCCA
*
1600 TAATTTCCC
1 TAATTTCCA
1609 TAATTTCCA
1 TAATTTCCA
1618 TAA
1 TAA
1621 GTAATTTGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.43
Consensus pattern (9 bp):
TAATTTCCA
Found at i:3511 original size:23 final size:20
Alignment explanation
Indices: 3481--3540 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 20
3471 AACTTAACAT
3481 ATAT-ATATTATGTTTATTA
1 ATATGATATTATGTTTATTA
3500 ATAATGTGATATT-TGTATTATTA
1 AT-A--TGATATTATGT-TTATTA
3523 ATATG-TATTATGTTTATT
1 ATATGATATTATGTTTATT
3541 TAACAGTGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
19 11 0.31
20 6 0.17
22 5 0.14
23 13 0.37
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (20 bp):
ATATGATATTATGTTTATTA
Found at i:3543 original size:20 final size:19
Alignment explanation
Indices: 3481--3540 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 19
3471 AACTTAACAT
*
3481 ATATATATTATGTTTATTA
1 ATATGTATTATGTTTATTA
*
3500 ATAATGTGATATTTGTATTATTA
1 AT-ATGT-AT-TATGT-TTATTA
3523 ATATGTATTATGTTTATT
1 ATATGTATTATGTTTATT
3541 TAACAGTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
19 7 0.21
20 7 0.21
21 4 0.12
22 8 0.24
23 8 0.24
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (19 bp):
ATATGTATTATGTTTATTA
Found at i:4876 original size:18 final size:18
Alignment explanation
Indices: 4853--4887 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4843 ACAAAAATTG
4853 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
4871 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
4888 TGCAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:4945 original size:2 final size:2
Alignment explanation
Indices: 4938--4966 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4928 ATTATACAAT
4938 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4967 ATAATTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5283 original size:16 final size:16
Alignment explanation
Indices: 5262--5293 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5252 ATTATAATTT
5262 TTATTAATAATATATA
1 TTATTAATAATATATA
*
5278 TTATTATTAATATATA
1 TTATTAATAATATATA
5294 AATAATAATT
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:5304 original size:18 final size:18
Alignment explanation
Indices: 5264--5314 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
5254 TATAATTTTT
* * *
5264 ATTAATAATATATATTATT
1 ATTAAT-ATATAAATAATA
5283 ATTAATATATAAATAATA
1 ATTAATATATAAATAATA
5301 ATT-ATATAATAAAT
1 ATTAATAT-ATAAAT
5315 GAACGTTCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 4 0.14
18 18 0.64
19 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTAATATATAAATAATA
Found at i:5378 original size:35 final size:35
Alignment explanation
Indices: 5339--5412 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 35
5329 TATATAAACG
5339 AACACTTAAATGAACAATAAACGAACATGTTCGTA
1 AACACTTAAATGAACAATAAACGAACATGTTCGTA
* *
5374 AACACTTAAATGAACAATAAACGAGCATGTTCGTG
1 AACACTTAAATGAACAATAAACGAACATGTTCGTA
5409 AACA
1 AACA
5413 TAAACGAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.22
Consensus pattern (35 bp):
AACACTTAAATGAACAATAAACGAACATGTTCGTA
Found at i:5557 original size:24 final size:23
Alignment explanation
Indices: 5512--5557 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
5502 ACGAACATAA
*
5512 ACGAGCTTTAATCGAGCCCGTTC
1 ACGAGCTTTAATCGAACCCGTTC
* *
5535 ACGAGCTGTTCATCGAACTCGTT
1 ACGAGCT-TTAATCGAACCCGTT
5558 GTTCATTTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (23 bp):
ACGAGCTTTAATCGAACCCGTTC
Found at i:10765 original size:14 final size:13
Alignment explanation
Indices: 10746--10784 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
10736 AAATTGTAAA
10746 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
10759 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
10773 ATTTAAAAAATT
1 ATTTAAAAAATT
10785 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:11005 original size:123 final size:128
Alignment explanation
Indices: 10770--11025 Score: 387
Period size: 123 Copynumber: 2.0 Consensus size: 128
10760 ATTTAAGAAA
10770 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---
* * *
10835 ATAGGTATAAGGATATTGGAATTAAATAAATAGAAATAGAGTTTTTAGTTGAGTAAAAATGTAAA
63 ATA-GTATAAGGATATTAGAATTAAATAAATAAAAATAGAGTTTTTAGTTGAGTAAAAATATAAA
10900 AG
127 AG
10902 TATATTTAAAAAATTCTAATATATATAAG-TTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATATA
* * *
10965 -TA-AA-GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
66 GTATAAGGATATTAGAATTAAATAAATAAAAATAGAGTTTTTAGTTGAGTAAAAATATAAAAG
11025 T
1 T
11026 TTAAACAATG
Statistics
Matches: 118, Mismatches: 6, Indels: 9
0.89 0.05 0.07
Matches are distributed among these distances:
123 51 0.43
124 2 0.02
125 2 0.02
127 2 0.02
131 32 0.27
132 29 0.25
ACGTcount: A:0.50, C:0.01, G:0.12, T:0.37
Consensus pattern (128 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATATA
GTATAAGGATATTAGAATTAAATAAATAAAAATAGAGTTTTTAGTTGAGTAAAAATATAAAAG
Found at i:23355 original size:17 final size:17
Alignment explanation
Indices: 23335--23376 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
23325 TTTGATAACC
23335 GGTGATCTT-GCATCACT
1 GGTGATCTTAG-ATCACT
23352 GGTGATCTTAGATCACT
1 GGTGATCTTAGATCACT
*
23369 AGTGATCT
1 GGTGATCT
23377 GGGGGGTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 22 0.96
18 1 0.04
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (17 bp):
GGTGATCTTAGATCACT
Found at i:25709 original size:25 final size:25
Alignment explanation
Indices: 25675--25748 Score: 148
Period size: 25 Copynumber: 3.0 Consensus size: 25
25665 CCAAACAATC
25675 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
25700 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
25725 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
25749 CAAACTAACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.12, C:0.32, G:0.20, T:0.35
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:30393 original size:527 final size:526
Alignment explanation
Indices: 29400--30452 Score: 1865
Period size: 527 Copynumber: 2.0 Consensus size: 526
29390 GCCGCCTGAT
29400 TGTTGACTCCATGTGTTTTTGATGATAACAAAACATTCTATTTAGTGTGACTAATCAAGCTATCT
1 TGTTGACTCCATGTGTTTTTGATGATAACAAAACATTCTATTTAGTGTGACTAATCAAGCTATCT
29465 AGTGTGCAGTGTTTAACTGAGCAGTTTACTTAACGAATCGTTATGGCCAAACCAATCCACACAAA
66 AGTGTGCAGTGTTTAACTGAGCAGTTTACTTAACGAATCGTTATGGCCAAACCAATCCACACAAA
29530 GCTCATTAGCACAGAGGAAGCATACTATGATTAAAGCCCTCATGAAAGGCACAAGTCAAGAAGGA
131 GCTCATTAGCACAGAGGAAGCATACTATGATTAAAGCCCTCATGAAAGGCACAAGTCAAGAAGGA
* * *
29595 TTGAGGAAGGCTTAGCTCAACACATCAAGATATAAGTATATCATCAATGGAACTAACGCCAAGAA
196 TTGAGGAAGGCTTAGCTCAACACATCAAGATAGAAGTACATCATCAAAGGAACTAACGCCAAGAA
* *
29660 GCAGGAGCTACAAGTTATTGAAGATAAGGTATTCAGTTGAAGCAAGTATTACTGCTAACAATGTG
261 GCAGAAGCTACAAGTTATTGAAGATAAGGTATTCAGTTGAAGCAAGTATTACTGCCAACAATGTG
29725 GAACATGACTTTAGTGGGATTAACGCCAGAAGCAGAAGACACAAGAAACAAGTCATTGTAGATAA
326 GAACATGACTTTAGTGGGATTAACGCCAGAAGCAGAAGACACAAGAAACAAGTCATTGTAGATAA
* ** *
29790 GGTATTCGGTTGAAGTAAGGATTAGTGTTAACAATGAGGAGCATCACTTTAGTGGGCTACCAGAA
391 GGTATTCGGTTGAAGCAAGGATTAGTGCCAACAATGAGGAGCATCACTTTAATGGGCTACCAGAA
**
29855 ATCGTCAGCCAGTCAGATTTTGCCAACGTCAGAAAAAGTCAAGACAATGGCTATAATTCAAATGG
456 ATCGTCAGCCAGTCAGATTTTGCCAACGTCAG-AAAAGTCAAGACAATAACTATAATTCAAATGG
29920 TTCTTTC
520 TTCTTTC
* *
29927 TGTTGACTCCATGTGTTTTTGATGATAACAAAACATTCTATTTAGTGTGACTAATTAAGTTATCT
1 TGTTGACTCCATGTGTTTTTGATGATAACAAAACATTCTATTTAGTGTGACTAATCAAGCTATCT
* * * *
29992 AGTGTGCAGTGTTTAATTGAGCAGTTTCCTTAACGAATGGTTATGGCCAAACCAATCTACACAAA
66 AGTGTGCAGTGTTTAACTGAGCAGTTTACTTAACGAATCGTTATGGCCAAACCAATCCACACAAA
*
30057 GCTCATTAGCTCAGAGGAAGCATACTATGATTAAAGCCCTCATGAAAGGCACAAGTCAAGAAGGA
131 GCTCATTAGCACAGAGGAAGCATACTATGATTAAAGCCCTCATGAAAGGCACAAGTCAAGAAGGA
*
30122 TTGAGGAAGGCTTAGCTCAACACATCAAGATAGAAGTACATCATCAAAGGGACTAACGCC-AGAA
196 TTGAGGAAGGCTTAGCTCAACACATCAAGATAGAAGTACATCATCAAAGGAACTAACGCCAAGAA
* *
30186 GCAGAAGCTACAAGTTATTGTAGATAAGGTATTCAGTTGAAGCAAGTATTAGTGCCAACAATGTG
261 GCAGAAGCTACAAGTTATTGAAGATAAGGTATTCAGTTGAAGCAAGTATTACTGCCAACAATGTG
* * *
30251 GAACATGACTTTAGTGGGATTAACGCCAGAAGTAGAAGACACAAGACACAAGTCATTTTAGATAA
326 GAACATGACTTTAGTGGGATTAACGCCAGAAGCAGAAGACACAAGAAACAAGTCATTGTAGATAA
30316 GGTATTCGGTTGAAGCAAGGATTAGTGCCAACAATGAGGAGCATCACTTTAATGGGACTACCAGA
391 GGTATTCGGTTGAAGCAAGGATTAGTGCCAACAATGAGGAGCATCACTTTAATGGG-CTACCAGA
30381 AATCGTCAGCCAGTCAGATTTTGCCAACGTCAGAAAAGTCAAGACAATAACTATAATTCAAATGG
455 AATCGTCAGCCAGTCAGATTTTGCCAACGTCAGAAAAGTCAAGACAATAACTATAATTCAAATGG
30446 TTCTTTC
520 TTCTTTC
30453 AACGCCATAA
Statistics
Matches: 501, Mismatches: 24, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
526 216 0.43
527 285 0.57
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (526 bp):
TGTTGACTCCATGTGTTTTTGATGATAACAAAACATTCTATTTAGTGTGACTAATCAAGCTATCT
AGTGTGCAGTGTTTAACTGAGCAGTTTACTTAACGAATCGTTATGGCCAAACCAATCCACACAAA
GCTCATTAGCACAGAGGAAGCATACTATGATTAAAGCCCTCATGAAAGGCACAAGTCAAGAAGGA
TTGAGGAAGGCTTAGCTCAACACATCAAGATAGAAGTACATCATCAAAGGAACTAACGCCAAGAA
GCAGAAGCTACAAGTTATTGAAGATAAGGTATTCAGTTGAAGCAAGTATTACTGCCAACAATGTG
GAACATGACTTTAGTGGGATTAACGCCAGAAGCAGAAGACACAAGAAACAAGTCATTGTAGATAA
GGTATTCGGTTGAAGCAAGGATTAGTGCCAACAATGAGGAGCATCACTTTAATGGGCTACCAGAA
ATCGTCAGCCAGTCAGATTTTGCCAACGTCAGAAAAGTCAAGACAATAACTATAATTCAAATGGT
TCTTTC
Found at i:32693 original size:29 final size:30
Alignment explanation
Indices: 32624--32696 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 30
32614 CAAAGCTTTG
*
32624 ACACGAGTGCA-AACCCACACTCAAAACAA
1 ACACAAGTGCACAACCCACACTCAAAACAA
* * * **
32653 TCCCAAGCGCACAACCCACACT-TGAACAA
1 ACACAAGTGCACAACCCACACTCAAAACAA
32682 ACACAAGTGCACAAC
1 ACACAAGTGCACAAC
32697 ACGAACTTAA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
29 24 0.71
30 10 0.29
ACGTcount: A:0.44, C:0.37, G:0.11, T:0.08
Consensus pattern (30 bp):
ACACAAGTGCACAACCCACACTCAAAACAA
Done.