Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021262.1 Corchorus olitorius cultivar O-4 contig21295, 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: 37290
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:1839 original size:58 final size:58
Alignment explanation
Indices: 1728--1840 Score: 147
Period size: 58 Copynumber: 1.9 Consensus size: 58
1718 ATTAATCAAA
* * *
1728 TATCAAGTGGCATGTTCTTTATTAGATGCATAAAAAAAGACATTTTCGGACCGAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACATTTTAGAACCGAGACT
* * * *
1786 TATCGAGTGACATGTTTTTTTATTAGATGC-TTAAAAAAGACGTTTTAGAACCGAG
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAAGACATTTTAGAACCGAG
1841 GCATGATGCT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
58 33 0.70
59 14 0.30
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACATTTTAGAACCGAGACT
Found at i:3156 original size:36 final size:36
Alignment explanation
Indices: 3109--3178 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
3099 TTCAATAACC
* *
3109 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
3145 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
3179 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:4052 original size:203 final size:201
Alignment explanation
Indices: 3691--4099 Score: 739
Period size: 203 Copynumber: 2.0 Consensus size: 201
3681 GCTTAATAAC
*
3691 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTAATAAG
1 TTTATCAATGGTGAATGTTATTAATGTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTAATAAG
* * *
3756 ATACAACACATTATTATTATATATATAACTATACCAAAAAAAATTAGTTGAATATTAGTGGTTGA
66 ATACAACACATTACTATTATATATATAACTATACCAAAAAAAATCAGTTGAACATTAGTGGTTGA
3821 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
131 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
3886 GATTTA
196 GATTTA
3892 TTTATCAATGGTGAATGTTATTAATGTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATGTTTTAAGTCTAAGATTACTAACAAAGTTGTAGT-AATAA
3957 GATACAACACATTACTATTATATATATAGAACTATA-CAAAAAAAATCAGTTGAACATTAGTGGT
65 GATACAACACATTACTATTATATATAT--AACTATACCAAAAAAAATCAGTTGAACATTAGTGGT
*
4021 TGATTTATTAAATTAAATTAGATCAATGTCAAACGAAATTTCAAAATTATAAAAGATATTAAAGA
128 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
4086 TCCGATTTA
193 TCCGATTTA
4095 TTTAT
1 TTTAT
4100 TATTAAGGAA
Statistics
Matches: 200, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
201 58 0.29
202 31 0.16
203 104 0.52
204 7 0.04
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (201 bp):
TTTATCAATGGTGAATGTTATTAATGTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTAATAAG
ATACAACACATTACTATTATATATATAACTATACCAAAAAAAATCAGTTGAACATTAGTGGTTGA
TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
GATTTA
Found at i:4263 original size:39 final size:40
Alignment explanation
Indices: 4209--4289 Score: 155
Period size: 39 Copynumber: 2.0 Consensus size: 40
4199 ATACCTAAGA
4209 ATTTAATTAATGTAAGTATTTTAGTTATTATAT-TATTAC
1 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
4248 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
4288 AT
1 AT
4290 AGGAATTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 33 0.80
40 8 0.20
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.53
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
Found at i:4524 original size:6 final size:6
Alignment explanation
Indices: 4506--4541 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
4496 ATTTAGACTT
4506 ATATAG TATATAG ATATAG AATATAG ATATAG ATAT
1 ATATAG -ATATAG ATATAG -ATATAG ATATAG ATAT
4542 TTGGAAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 16 0.57
7 12 0.43
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (6 bp):
ATATAG
Found at i:4524 original size:13 final size:12
Alignment explanation
Indices: 4506--4541 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
4496 ATTTAGACTT
4506 ATATAGTATATAG
1 ATATAG-ATATAG
4519 ATATAGAATATAG
1 ATATAG-ATATAG
4532 ATATAGATAT
1 ATATAGATAT
4542 TTGGAAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (12 bp):
ATATAGATATAG
Found at i:12708 original size:58 final size:58
Alignment explanation
Indices: 12618--12735 Score: 218
Period size: 58 Copynumber: 2.0 Consensus size: 58
12608 AAATGACCAA
*
12618 GATGAAAGTATCAAATGAAATGTATTTCTAATCAATTCCAACTTCAATGAAACCAAAT
1 GATGAAAGTATCAAATGAAATGCATTTCTAATCAATTCCAACTTCAATGAAACCAAAT
*
12676 GATGAAAGTATCAAATGAAATGCATTTCTAATCAATTCCAACTTCAATGCAACCAAAT
1 GATGAAAGTATCAAATGAAATGCATTTCTAATCAATTCCAACTTCAATGAAACCAAAT
12734 GA
1 GA
12736 CTAGGCATGA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (58 bp):
GATGAAAGTATCAAATGAAATGCATTTCTAATCAATTCCAACTTCAATGAAACCAAAT
Found at i:12923 original size:31 final size:31
Alignment explanation
Indices: 12885--13087 Score: 226
Period size: 31 Copynumber: 6.5 Consensus size: 31
12875 ACGGTGTCCG
* * *
12885 ATGTGGCATGGCACGTGTACCAAAAAGCGAC
1 ATGTGGCACGCCACGTGTACCAAAAAGTGAC
*
12916 ATGTGGCACGCCACGTGTACCAAAAAGCGAC
1 ATGTGGCACGCCACGTGTACCAAAAAGTGAC
*
12947 ATGTGGCACGCCACGTGTATCAAAAAGTGAC
1 ATGTGGCACGCCACGTGTACCAAAAAGTGAC
** * *
12978 ATGTATCACGCCATGTGTATCAAAAAGTGAC
1 ATGTGGCACGCCACGTGTACCAAAAAGTGAC
** * *
13009 ATGTATCACGCCATGTGTACCCAAAAGTGAC
1 ATGTGGCACGCCACGTGTACCAAAAAGTGAC
* * **
13040 ATGTGGCATGCCATGTGTTTCAAAAAGTGAC
1 ATGTGGCACGCCACGTGTACCAAAAAGTGAC
* * *
13071 ACGTGACATGCCACGTG
1 ATGTGGCACGCCACGTG
13088 CGCAAAAGGA
Statistics
Matches: 154, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 154 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.21
Consensus pattern (31 bp):
ATGTGGCACGCCACGTGTACCAAAAAGTGAC
Found at i:13035 original size:93 final size:93
Alignment explanation
Indices: 12899--13071 Score: 256
Period size: 93 Copynumber: 1.9 Consensus size: 93
12889 GGCATGGCAC
*
12899 GTGTACCAAAAAGCGACATGTGGCACGCCACGTGTACCAAAAAGCGACATGTGGCACGCCACGTG
1 GTGTACCAAAAAGCGACATGTAGCACGCCACGTGTACCAAAAAGCGACATGTGGCACGCCACGTG
12964 TATCAAAAAGTGACATGTATCACGCCAT
66 TATCAAAAAGTGACATGTATCACGCCAT
* * * * * * * *
12992 GTGTATCAAAAAGTGACATGTATCACGCCATGTGTACCCAAAAGTGACATGTGGCATGCCATGTG
1 GTGTACCAAAAAGCGACATGTAGCACGCCACGTGTACCAAAAAGCGACATGTGGCACGCCACGTG
*
13057 TTTCAAAAAGTGACA
66 TATCAAAAAGTGACA
13072 CGTGACATGC
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.21
Consensus pattern (93 bp):
GTGTACCAAAAAGCGACATGTAGCACGCCACGTGTACCAAAAAGCGACATGTGGCACGCCACGTG
TATCAAAAAGTGACATGTATCACGCCAT
Found at i:32415 original size:20 final size:20
Alignment explanation
Indices: 32390--32429 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
32380 AAAAACACTT
32390 TGTTTCGATTCGTATTCCAA
1 TGTTTCGATTCGTATTCCAA
*
32410 TGTTTCGGTTCGTATTCCAA
1 TGTTTCGATTCGTATTCCAA
32430 AAGCGGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.45
Consensus pattern (20 bp):
TGTTTCGATTCGTATTCCAA
Found at i:34090 original size:24 final size:24
Alignment explanation
Indices: 34063--34110 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
34053 TGAAAAACTT
**
34063 TTTTAATGGTAGAAGAAATAAGAA
1 TTTTAATAATAGAAGAAATAAGAA
34087 TTTTAATAATAGAAGAAATAAGAA
1 TTTTAATAATAGAAGAAATAAGAA
34111 ATAGGGAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (24 bp):
TTTTAATAATAGAAGAAATAAGAA
Found at i:34646 original size:18 final size:19
Alignment explanation
Indices: 34608--34650 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
34598 ACTGAGACTC
*
34608 AAACT-AACTGACTCAACA
1 AAACTGAACTGACTCAAAA
34626 AAACTGAACTGACT-AAAA
1 AAACTGAACTGACTCAAAA
34644 AAACTGA
1 AAACTGA
34651 CTAAACCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.53, C:0.21, G:0.09, T:0.16
Consensus pattern (19 bp):
AAACTGAACTGACTCAAAA
Done.