Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022261.1 Corchorus olitorius cultivar O-4 contig22294, 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: 11349
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Found at i:1391 original size:13 final size:13
Alignment explanation
Indices: 1373--1397 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1363 TTGAAATTCC
1373 AAATAATATTTAT
1 AAATAATATTTAT
1386 AAATAATATTTA
1 AAATAATATTTA
1398 AAACATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:1911 original size:190 final size:190
Alignment explanation
Indices: 1582--1929 Score: 615
Period size: 190 Copynumber: 1.8 Consensus size: 190
1572 TTACAAGTTA
* *
1582 CCCCATACTGTTGTATGCTCAGTATTTGGCATTTCTAATGCTGACATTTATCCAAAGTTAATTGG
1 CCCCAAACTGTTGTATGCTCAATATTTGGCATTTCTAATGCTGACATTTATCCAAAGTTAATTGG
*
1647 TTGGGAGAAAACCAATATATATTATTATACATTTACAATTCCAAATAATATTTAGACCATTGAAT
66 TTGGGAGAAAACCAATATATATTATTATACATTTACAATTCCAAATAATATTTAGAACATTGAAT
*
1712 TAAAATTCTTTTTCTAACAATATTACATCTATACCTTTTATTTATTACTATTAAAATTAT
131 TAAAATTCTTTTTCTAAAAATATTACATCTATACCTTTTATTTATTACTATTAAAATTAT
* * *
1772 CCCCAAACTGTTGTATGCTCAATATTTGGCTTTTTTAATGCTGGCATTTATCCAAAGTTAATTGG
1 CCCCAAACTGTTGTATGCTCAATATTTGGCATTTCTAATGCTGACATTTATCCAAAGTTAATTGG
1837 TTGGGAGAAAACCAATATATATTATTATACATTTACAATTCCAAATAATATTTAGAACATTGAAT
66 TTGGGAGAAAACCAATATATATTATTATACATTTACAATTCCAAATAATATTTAGAACATTGAAT
* *
1902 TATAATTCTTTTTTTAAAAATATTACAT
131 TAAAATTCTTTTTCTAAAAATATTACAT
1930 AAAATAAAAT
Statistics
Matches: 149, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
190 149 1.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (190 bp):
CCCCAAACTGTTGTATGCTCAATATTTGGCATTTCTAATGCTGACATTTATCCAAAGTTAATTGG
TTGGGAGAAAACCAATATATATTATTATACATTTACAATTCCAAATAATATTTAGAACATTGAAT
TAAAATTCTTTTTCTAAAAATATTACATCTATACCTTTTATTTATTACTATTAAAATTAT
Found at i:3651 original size:27 final size:27
Alignment explanation
Indices: 3621--3702 Score: 155
Period size: 27 Copynumber: 3.0 Consensus size: 27
3611 TTAATCTATG
*
3621 AGCCAACAAACTCCTTCCCCAACAAAC
1 AGCCAACAAACCCCTTCCCCAACAAAC
3648 AGCCAACAAACCCCTTCCCCAACAAAC
1 AGCCAACAAACCCCTTCCCCAACAAAC
3675 AGCCAACAAACCCCTTCCCCAACAAAC
1 AGCCAACAAACCCCTTCCCCAACAAAC
3702 A
1 A
3703 AACCCAGTGA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.41, C:0.46, G:0.04, T:0.09
Consensus pattern (27 bp):
AGCCAACAAACCCCTTCCCCAACAAAC
Found at i:3671 original size:16 final size:16
Alignment explanation
Indices: 3650--3701 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
3640 CAACAAACAG
3650 CCAACAAACCCCTTCC
1 CCAACAAACCCCTTCC
**
3666 CCAACAAA---C--AG
1 CCAACAAACCCCTTCC
3677 CCAACAAACCCCTTCC
1 CCAACAAACCCCTTCC
3693 CCAACAAAC
1 CCAACAAAC
3702 AAACCCAGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 10
0.66 0.10 0.24
Matches are distributed among these distances:
11 8 0.30
13 1 0.04
14 1 0.04
16 17 0.63
ACGTcount: A:0.40, C:0.50, G:0.02, T:0.08
Consensus pattern (16 bp):
CCAACAAACCCCTTCC
Found at i:4156 original size:19 final size:19
Alignment explanation
Indices: 4128--4176 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
4118 TTTATAGAAT
4128 TATATATATAACTTATA-A
1 TATATATATAACTTATATA
4146 TATAGTATATAACTTATATA
1 TATA-TATATAACTTATATA
*
4166 TATATTTATAA
1 TATATATATAA
4177 GTCGATTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 4 0.14
19 19 0.68
20 5 0.18
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (19 bp):
TATATATATAACTTATATA
Found at i:4508 original size:14 final size:14
Alignment explanation
Indices: 4491--4539 Score: 84
Period size: 14 Copynumber: 3.6 Consensus size: 14
4481 GATAGAAATG
4491 TTTTCTTTTTTCGT
1 TTTTCTTTTTTCGT
4505 TTTTCTTTTTTCGT
1 TTTTCTTTTTTCGT
4519 TTTTCTTTTTTC-T
1 TTTTCTTTTTTCGT
4532 TTTT-TTTT
1 TTTTCTTTT
4540 CTTTTTTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.11
13 5 0.14
14 26 0.74
ACGTcount: A:0.00, C:0.12, G:0.04, T:0.84
Consensus pattern (14 bp):
TTTTCTTTTTTCGT
Found at i:4546 original size:7 final size:7
Alignment explanation
Indices: 4491--4536 Score: 74
Period size: 7 Copynumber: 6.6 Consensus size: 7
4481 GATAGAAATG
4491 TTTTCTT
1 TTTTCTT
*
4498 TTTTCGT
1 TTTTCTT
4505 TTTTCTT
1 TTTTCTT
*
4512 TTTTCGT
1 TTTTCTT
4519 TTTTCTT
1 TTTTCTT
4526 TTTTCTT
1 TTTTCTT
4533 TTTT
1 TTTT
4537 TTTCTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (7 bp):
TTTTCTT
Found at i:4685 original size:27 final size:29
Alignment explanation
Indices: 4602--4680 Score: 149
Period size: 29 Copynumber: 2.7 Consensus size: 29
4592 CAAATAATAA
4602 ATAAAAACTAAGAAATATGTAGTAGTAAT
1 ATAAAAACTAAGAAATATGTAGTAGTAAT
4631 ATAAAAACTAAGAAATATGTAGTAGTAAT
1 ATAAAAACTAAGAAATATGTAGTAGTAAT
*
4660 ATAAAAACTAAGAAATGTGTA
1 ATAAAAACTAAGAAATATGTA
4681 TGTAAAAAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.56, C:0.04, G:0.14, T:0.27
Consensus pattern (29 bp):
ATAAAAACTAAGAAATATGTAGTAGTAAT
Found at i:5260 original size:14 final size:15
Alignment explanation
Indices: 5236--5266 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
5226 TGTGTTTTAA
5236 TTACATATTTTATAT
1 TTACATATTTTATAT
5251 TTAC-TATTTTATAT
1 TTACATATTTTATAT
5265 TT
1 TT
5267 TTTTGTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (15 bp):
TTACATATTTTATAT
Found at i:5819 original size:41 final size:41
Alignment explanation
Indices: 5757--5839 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
5747 AACTAATGAC
* *
5757 TTTCTTTTCTTAACTAAATTTTCTTAAAA-ACACTTATAAAA
1 TTTCATTTCTTAACTAAATTTTCTTAAAAGA-ACTCATAAAA
*
5798 TTTCATTTCTTAACTGAATTTTCTTAAAAGAACTCATAAAA
1 TTTCATTTCTTAACTAAATTTTCTTAAAAGAACTCATAAAA
5839 T
1 T
5840 AAAACAGCCG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 37 0.97
42 1 0.03
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (41 bp):
TTTCATTTCTTAACTAAATTTTCTTAAAAGAACTCATAAAA
Found at i:7360 original size:201 final size:200
Alignment explanation
Indices: 7008--7570 Score: 849
Period size: 201 Copynumber: 2.8 Consensus size: 200
6998 AATATTATTA
7008 GGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATATTTAATATTAATACATAT
1 GGGTTAAGAAGTTGACACATACCCCATTTCATAATTAA-TAAATATATTTAATATTAATACATAT
* * *
7073 TCCCCTAGGGGACACATGTCGACCCTTAAACCCCGCACATGCAGTCTGCTAAACTCCAGTGACGG
65 TCCCCTAGGGGACACATGTCGACCCTTAAACCCCGCACGTGCAATCTGCTAAACTCCACTGACGG
* * * * *
7138 TTTATTGTATAATTCTTCTTATCGGATTATTATACAATACACTATCAGTGTAAATTTTGGACTCC
130 TGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTATCAGTGTAAAATTTAGACTCC
7203 ATAAGC
195 ATAAGC
* *
7209 GGGTTAAGAAGTTGACACATACCCCATTTCATACTTAAGAAAATATATTTAATATTAATACATAT
1 GGGTTAAGAAGTTGACACATACCCCATTTCATAATTAA-TAAATATATTTAATATTAATACATAT
** *
7274 T-CCCTAAGGGGACACATGTTAACCCTTAAACCCCGCACGTGCAATCTGCTAAACTCCACTAACG
65 TCCCCT-AGGGGACACATGTCGACCCTTAAACCCCGCACGTGCAATCTGCTAAACTCCACTGACG
* * *
7338 GTGTATTGTATACTTTTTCTTATAGGATTATTATACAATTCACTATTAGTGTAAAATTTAGACTC
129 GTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTATCAGTGTAAAATTTAGACTC
*
7403 CATAAGT
194 CATAAGC
* *
7410 GGGTTAAGAGGTTGACACATACCCCATTTCATAATTAATTAATATATTTAATATTAATACATATT
1 GGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATAAATATATTTAATATTAATACATATT
* * * * * **
7475 CCCCTAGGGGACACATGTCGACCCTTAAACCCCGCACGTACAATATACTAAACTCTATTGACATT
66 CCCCTAGGGGACACATGTCGACCCTTAAACCCCGCACGTGCAATCTGCTAAACTCCACTGACGGT
*
7540 GTATTGTATAATTTTTCTTGTAGGATTATTA
131 GTATTGTATAATTTTTCTTATAGGATTATTA
7571 ATTTATTGAG
Statistics
Matches: 326, Mismatches: 34, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
200 108 0.33
201 218 0.67
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (200 bp):
GGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATAAATATATTTAATATTAATACATATT
CCCCTAGGGGACACATGTCGACCCTTAAACCCCGCACGTGCAATCTGCTAAACTCCACTGACGGT
GTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTATCAGTGTAAAATTTAGACTCCA
TAAGC
Found at i:7672 original size:21 final size:21
Alignment explanation
Indices: 7643--7690 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
7633 TTGATATATG
*
7643 CTTTATAGT-AGCATTATTAAA
1 CTTTTTAGTAAGC-TTATTAAA
7664 CTTTTTAGTAAGCTTATTAAA
1 CTTTTTAGTAAGCTTATTAAA
*
7685 GTTTTT
1 CTTTTT
7691 TATGATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.50
Consensus pattern (21 bp):
CTTTTTAGTAAGCTTATTAAA
Done.