Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012151.1 Corchorus olitorius cultivar O-4 contig12184, 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: 26817
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:7725 original size:100 final size:100
Alignment explanation
Indices: 7552--8151 Score: 897
Period size: 100 Copynumber: 6.0 Consensus size: 100
7542 ACTTTTATCT
7552 TTGACCTTAGAATTCGATCCGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAG
1 TTGACCTTAGAATTCGATCCGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAG
7617 CCCTGGACTCTTTGAGAGAACGACAACGTTCGTAA
66 CCCTGGACTCTTTGAGAGAACGACAACGTTCGTAA
*
7652 TTGACTTTAGAATTCGATCCGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAG
1 TTGACCTTAGAATTCGATCCGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAG
* *
7717 CCCTGGACTCTTTGAGAGAGCGACAATGTTCGTAA
66 CCCTGGACTCTTTGAGAGAACGACAACGTTCGTAA
* * *
7752 TTGAACTTAGAATTCGATCCGGACTCCCCGTGAGAACATCGAATCAAAGTTGGCCGAATGTAAAG
1 TTGACCTTAGAATTCGATCCGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAG
* * *
7817 CCCTAGACTCTTTGTGAGAACGGCAACGTTCGTAA
66 CCCTGGACTCTTTGAGAGAACGACAACGTTCGTAA
* * *
7852 TTGACCTTAGAATTCGATCCAGAGTCCCCGTGAGAACATCGATTCTAAGTTGGCCGAACGTAAAG
1 TTGACCTTAGAATTCGATCCGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAG
* *
7917 CCCTGGACTCTTTGTGAGAACGGCAACGTTCGTAA
66 CCCTGGACTCTTTGAGAGAACGACAACGTTCGTAA
** ** * *
7952 TTGACCTTAGACCTCGATTTGGACT--TCGATGAGAACATCGAATCTAAGTTAGCCGAACGTAAA
1 TTGACCTTAGAATTCGATCCGGACTCCCCG-TGAGAACATCGAATCTAAGTTGGCCGAACGTAAA
* *
8015 GCCCTGGACTCTTTGTGAGAACGGCAACGTTCGTAA
65 GCCCTGGACTCTTTGAGAGAACGACAACGTTCGTAA
* **
8051 TTGACCTTAG-ATCTTGATATGGACT--CCGATGAGAACATCGAATCTAAGTTGGCCGAACGTAA
1 TTGACCTTAGAAT-TCGATCCGGACTCCCCG-TGAGAACATCGAATCTAAGTTGGCCGAACGTAA
*
8113 AG-CCTGGACTCTTTGAGAGAACGACAATGTTCGTAA
64 AGCCCTGGACTCTTTGAGAGAACGACAACGTTCGTAA
8149 TTG
1 TTG
8152 TAACAAACAA
Statistics
Matches: 461, Mismatches: 37, Indels: 6
0.91 0.07 0.01
Matches are distributed among these distances:
98 36 0.08
99 125 0.27
100 300 0.65
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (100 bp):
TTGACCTTAGAATTCGATCCGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAG
CCCTGGACTCTTTGAGAGAACGACAACGTTCGTAA
Found at i:12098 original size:25 final size:25
Alignment explanation
Indices: 12064--12112 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
12054 TTCCAAGACA
*
12064 TTGCCGATCCTCCAATATCAATACC
1 TTGCCGATCCTCCAACATCAATACC
*
12089 TTGCCGATCCTCTAACATCAATAC
1 TTGCCGATCCTCCAACATCAATAC
12113 ATTGTCGAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.35, G:0.08, T:0.29
Consensus pattern (25 bp):
TTGCCGATCCTCCAACATCAATACC
Found at i:14701 original size:109 final size:109
Alignment explanation
Indices: 14505--14722 Score: 409
Period size: 109 Copynumber: 2.0 Consensus size: 109
14495 CTATTATATA
14505 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
1 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
14570 CAAAATGCAATGAACTACTGGATTTAAAGAAAAATACAAGCACC
66 CAAAATGCAATGAACTACTGGATTTAAAGAAAAATACAAGCACC
*
14614 TATTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
1 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
* *
14679 CAAAGTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
66 CAAAATGCAATGAACTACTGGATTTAAAGAAAAATACAAGCACC
14723 AAAATGACTA
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 106 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (109 bp):
TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
CAAAATGCAATGAACTACTGGATTTAAAGAAAAATACAAGCACC
Found at i:15376 original size:31 final size:31
Alignment explanation
Indices: 15305--15376 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
15295 GTCTATCAGC
*
15305 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
15336 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
15366 GTTTTAATTTG
1 -TTTTAATTTG
15377 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:15666 original size:13 final size:13
Alignment explanation
Indices: 15644--15678 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
15634 TATATTGATA
*
15644 ATAATGTTATATT
1 ATAATATTATATT
15657 ATAATATTATATT
1 ATAATATTATATT
15670 AT-ATATTAT
1 ATAATATTAT
15679 CAATAAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 7 0.33
13 14 0.67
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (13 bp):
ATAATATTATATT
Found at i:15870 original size:16 final size:16
Alignment explanation
Indices: 15851--15904 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
15841 CTGTCCGAGA
*
15851 CCGAACCC-AACATAAC
1 CCGAACCCGAAAAT-AC
*
15867 CCGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
15883 CCGAACCCGAAAA-AGC
1 CCGAACCCGAAAATA-C
15899 CCGAAC
1 CCGAAC
15905 TCGCCCAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 1 0.03
16 28 0.85
17 4 0.12
ACGTcount: A:0.41, C:0.41, G:0.15, T:0.04
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:17619 original size:32 final size:31
Alignment explanation
Indices: 17514--17702 Score: 132
Period size: 31 Copynumber: 6.1 Consensus size: 31
17504 GACACGTGGT
*
17514 ACGTGTC-CTTTTT-GTGCACGATG-CATGCC
1 ACGTGTCACTTTTTGGTACAC-ATGACATGCC
*** *
17543 ACGTGTCACTTTTTGGTACACATGGTGTGAC
1 ACGTGTCACTTTTTGGTACACATGACATGCC
* *
17574 ACGTGTCATTTTTTTGGTACATATGACATGCC
1 ACGTGTCA-CTTTTTGGTACACATGACATGCC
* * ** * *
17606 ACGCGTCACTTTTTGGTATATGTGACGTGTC
1 ACGTGTCACTTTTTGGTACACATGACATGCC
* * * * *
17637 ATGTGTCGCTTTTTGGTATACGTGACGTGCC
1 ACGTGTCACTTTTTGGTACACATGACATGCC
* * * * *
17668 ACATGTCGCTTCTTGGTACACGTGGCATGCC
1 ACGTGTCACTTTTTGGTACACATGACATGCC
17699 ACGT
1 ACGT
17703 CAGACATTGT
Statistics
Matches: 128, Mismatches: 28, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
29 7 0.05
30 9 0.07
31 88 0.69
32 24 0.19
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (31 bp):
ACGTGTCACTTTTTGGTACACATGACATGCC
Found at i:17650 original size:63 final size:62
Alignment explanation
Indices: 17537--17654 Score: 137
Period size: 63 Copynumber: 1.9 Consensus size: 62
17527 GTGCACGATG
* ** *
17537 CATGCCACGTGTCACTTTTTGGTACACATGGTGTGACACGTGTCATTTTTTTGGTACATATGA
1 CATGCCACGCGTCACTTTTTGGTACACATGACGTGACACGTGTCA-CTTTTTGGTACATATGA
* ** * * *
17600 CATGCCACGCGTCACTTTTTGGTATATGTGACGTGTCATGTGTCGCTTTTTGGTA
1 CATGCCACGCGTCACTTTTTGGTACACATGACGTGACACGTGTCACTTTTTGGTA
17655 TACGTGACGT
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
62 9 0.20
63 36 0.80
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39
Consensus pattern (62 bp):
CATGCCACGCGTCACTTTTTGGTACACATGACGTGACACGTGTCACTTTTTGGTACATATGA
Found at i:18106 original size:44 final size:44
Alignment explanation
Indices: 18056--18145 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
18046 TTTAAGCGGT
*
18056 AGTTCTCAAAAGATTTGTGAAAACCATTTTGAAGAGAATGAAAA
1 AGTTCTCAAAAGATTTGTGAAAACCATATTGAAGAGAATGAAAA
* *
18100 AGTTCTCAAAAGATTTGTGAAAGCCATATTGAAGAGAATGACAA
1 AGTTCTCAAAAGATTTGTGAAAACCATATTGAAGAGAATGAAAA
18144 AG
1 AG
18146 ATCAATTCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Consensus pattern (44 bp):
AGTTCTCAAAAGATTTGTGAAAACCATATTGAAGAGAATGAAAA
Found at i:18452 original size:37 final size:37
Alignment explanation
Indices: 18402--18472 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
18392 ATAGTGTAAA
* *
18402 TAGATCTTGATTACAGCGATTAGGGTTTGATTTTTAG
1 TAGATCTTAATTACAGCGATTAGGGTTGGATTTTTAG
*
18439 TAGATCTTAATTACAGTGATTAGGGTTGGATTTT
1 TAGATCTTAATTACAGCGATTAGGGTTGGATTTT
18473 ACAAACTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.44
Consensus pattern (37 bp):
TAGATCTTAATTACAGCGATTAGGGTTGGATTTTTAG
Found at i:21766 original size:6 final size:6
Alignment explanation
Indices: 21755--21836 Score: 141
Period size: 6 Copynumber: 13.8 Consensus size: 6
21745 ATCCAATGTA
21755 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
21803 TATATC TATATC TATATC --TATC TATATAC TATAT
1 TATATC TATATC TATATC TATATC TATAT-C TATAT
21837 AAGTCTAAAC
Statistics
Matches: 73, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.05
6 63 0.86
7 6 0.08
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATC
Found at i:22163 original size:25 final size:24
Alignment explanation
Indices: 22127--22173 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
22117 AATACTTACA
*
22127 TTAATTAAATTCTTAGGTATTTTC
1 TTAATTAAATTCTTACGTATTTTC
22151 TTAATTCAAATTCTTACGTATTT
1 TTAATT-AAATTCTTACGTATTT
22174 GTGCAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.30, C:0.11, G:0.06, T:0.53
Consensus pattern (24 bp):
TTAATTAAATTCTTACGTATTTTC
Found at i:22638 original size:204 final size:204
Alignment explanation
Indices: 22246--22658 Score: 681
Period size: 204 Copynumber: 2.0 Consensus size: 204
22236 TTCCTTAATA
*
22246 ATAAATAAATCGGATCTTTAATATCTTTTATAATTGTGAAATTTTTTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTGTGAAATTTTGTTTGACATTGATCTAATTT
* * *
22311 AATTTAATAAATCAACCACTAATGTTTAACTGATTGTTTTTGGTATAGTTCTATATATATAATAG
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTGTTTTTGGTATAGTTCTATATATATAATAA
*
22376 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTTAAAAATTAATAACAT
131 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
22441 TCACCATTG
196 TCACCATTG
* * *
22450 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGATATTTATCTAA-TT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTGTGAAATTTTGTTTGACATTGATCTAATTT
*
22514 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTT-T-TATATATAATAA
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTGTTTTTGGTATAGTTCTATATATATAATAA
22577 TAATGTGTTGTATCTTATT-ACTACAACTTTGTTAGTAATCTTAGACTTAAAAATTAAATTAATA
131 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTT--AAA--AAATTAATA
22641 ACATTCACCATTG
192 ACATTCACCATTG
22654 ATAAA
1 ATAAA
22659 GTTATTAAGC
Statistics
Matches: 196, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
200 29 0.15
201 30 0.15
202 3 0.02
203 49 0.25
204 85 0.43
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (204 bp):
ATAAATAAATCGGATCTTTAATATCTTTTATAATTGTGAAATTTTGTTTGACATTGATCTAATTT
AATTTAATAAATCAACCACTAATGTTCAACTAATTGTTTTTGGTATAGTTCTATATATATAATAA
TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
TCACCATTG
Found at i:23221 original size:36 final size:36
Alignment explanation
Indices: 23174--23243 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
23164 GAGATTTTGG
* *
23174 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAAGCAAAATCACAAAAAATGTAATA
*
23210 AGAAATATGATAAGCAAAATCACAAAAGATGTAA
1 AGAAATATGATAAGCAAAATCACAAAAAATGTAA
23244 GGTTATTGAA
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:0.60, C:0.07, G:0.11, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAAGCAAAATCACAAAAAATGTAATA
Found at i:24611 original size:58 final size:58
Alignment explanation
Indices: 24510--24622 Score: 174
Period size: 58 Copynumber: 1.9 Consensus size: 58
24500 AGCATCATGC
*
24510 CTCGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGT
1 CTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGT
* * *
24568 CTCGGTCCGAAAACGTCTTTTTTAATGCATCTAAT-AAAGAACATGTCACTTGATA
1 CTCGGTCCGAAAACGTCTTTTTT-AGGCATCTAATAAAAAAACATGTCACTCGATA
24623 TTTGATTAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
58 40 0.80
59 10 0.20
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (58 bp):
CTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGT
Done.