Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008612.1 Corchorus capsularis cultivar CVL-1 contig08633, 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: 58879
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:8211 original size:6 final size:6
Alignment explanation
Indices: 8202--8234 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
8192 AAAGAGCGAA
*
8202 AAAATG AAAATG AAAGTG AAAATG AAAATG AAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAA
8235 GAAAGTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:9686 original size:35 final size:33
Alignment explanation
Indices: 9640--9756 Score: 101
Period size: 35 Copynumber: 3.4 Consensus size: 33
9630 GTTCAAAGGT
*
9640 ATTGACCCAGGGCAGTCTC-CATTCAGTAAATTTCA
1 ATTGACCCAGGGC-GTCTCTC-TTCAAT-AATTTCA
* *
9675 ATTGATCCAGGGCGATCTCTCTTCAATACTTTCA
1 ATTGACCCAGGGCG-TCTCTCTTCAATAATTTCA
* **
9709 ATTGACCCAGGGCGGTCTTTCTTCAGATGCTTTCA
1 ATTGACCCAGGGC-GTCTCTCTTCA-ATAATTTCA
*
9744 AGTTGATCCAGGG
1 A-TTGACCCAGGG
9757 AGATTATTCT
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
34 28 0.40
35 31 0.44
36 11 0.16
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (33 bp):
ATTGACCCAGGGCGTCTCTCTTCAATAATTTCA
Found at i:9713 original size:34 final size:35
Alignment explanation
Indices: 9670--9756 Score: 122
Period size: 34 Copynumber: 2.5 Consensus size: 35
9660 ATTCAGTAAA
9670 TTTCAATTGATCCAGGGCGATCTCTCTTCA-ATAC
1 TTTCAATTGATCCAGGGCGATCTCTCTTCAGATAC
* * * *
9704 TTTCAATTGACCCAGGGCGGTCTTTCTTCAGATGC
1 TTTCAATTGATCCAGGGCGATCTCTCTTCAGATAC
9739 TTTCAAGTTGATCCAGGG
1 TTTCAA-TTGATCCAGGG
9757 AGATTATTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 27 0.59
35 9 0.20
36 10 0.22
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (35 bp):
TTTCAATTGATCCAGGGCGATCTCTCTTCAGATAC
Found at i:9911 original size:8 final size:8
Alignment explanation
Indices: 9898--9947 Score: 57
Period size: 8 Copynumber: 6.2 Consensus size: 8
9888 AAGGTGGTCT
9898 TTCTTCAA
1 TTCTTCAA
9906 TTCTTCAA
1 TTCTTCAA
*
9914 TTAC-ACAA
1 TT-CTTCAA
*
9922 TGCTTCAA
1 TTCTTCAA
9930 TTCTTCAA
1 TTCTTCAA
*
9938 TGCTTCAA
1 TTCTTCAA
9946 TT
1 TT
9948 TACTTCAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
7 1 0.03
8 32 0.94
9 1 0.03
ACGTcount: A:0.28, C:0.24, G:0.04, T:0.44
Consensus pattern (8 bp):
TTCTTCAA
Found at i:9994 original size:36 final size:35
Alignment explanation
Indices: 9954--10157 Score: 153
Period size: 36 Copynumber: 5.7 Consensus size: 35
9944 AATTTACTTC
*
9954 AATGACCCAGGGTGGTTTTTCTTCAGTTTGAGTCGG
1 AATGATCCAGGGTGGTTTTTCTTCAGTTT-AGTCGG
* * *
9990 AATGATCGAGGGTGGTTGTTCTTCAGTTTATTCCGG
1 AATGATCCAGGGTGGTTTTTCTTCAGTTTAGT-CGG
** ** * * * *
10026 AATGATTGAGGGTGGTCGTTCTCCAATTTATTTCAG
1 AATGATCCAGGGTGGTTTTTCTTCAGTTTA-GTCGG
* * * *
10062 -TTGACCCAAGGTGGTCTTTCTTCAGTTTACGTCGG
1 AATGATCCAGGGTGGTTTTTCTTCAGTTTA-GTCGG
* * *
10097 AATGATCGAGGGTGGTCGTTT-TTCA-TTTCAGTTTGG
1 AATGATCCAGGGTGGT-TTTTCTTCAGTTT-AG-TCGG
10133 AATGATCCAGGGTGGTTTTTCTTCA
1 AATGATCCAGGGTGGTTTTTCTTCA
10158 CTTACTTATT
Statistics
Matches: 133, Mismatches: 28, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
35 33 0.25
36 95 0.71
37 5 0.04
ACGTcount: A:0.18, C:0.16, G:0.28, T:0.39
Consensus pattern (35 bp):
AATGATCCAGGGTGGTTTTTCTTCAGTTTAGTCGG
Found at i:10145 original size:107 final size:106
Alignment explanation
Indices: 9943--10148 Score: 274
Period size: 107 Copynumber: 1.9 Consensus size: 106
9933 TTCAATGCTT
* * *
9943 CAATTTACTTCAATGACCCAGGGTGGTTTTTCTTCAGTTTGAGTCGGAATGATCGAGGGTGGTTG
1 CAATTTACTTCAATGACCCAAGGTGGTCTTTCTTCAGTTTGAGTCGGAATGATCGAGGGTGGTCG
**
10008 TTCTTCAGTTTATTCCGGAATGATTGAGGGTGGTCGTTCTC
66 TTCTTCAGTTTATTCCGGAATGATCCAGGGTGGTCGTTCTC
* *
10049 CAATTTATTTCAGTTGACCCAAGGTGGTCTTTCTTCAGTTT-ACGTCGGAATGATCGAGGGTGGT
1 CAATTTACTTCA-ATGACCCAAGGTGGTCTTTCTTCAGTTTGA-GTCGGAATGATCGAGGGTGGT
* *
10113 CGTTTTTCA-TTTCAGTT-TGGAATGATCCAGGGTGGT
64 CGTTCTTCAGTTT-A-TTCCGGAATGATCCAGGGTGGT
10149 TTTTCTTCAC
Statistics
Matches: 87, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
106 15 0.17
107 70 0.80
108 2 0.02
ACGTcount: A:0.18, C:0.16, G:0.28, T:0.38
Consensus pattern (106 bp):
CAATTTACTTCAATGACCCAAGGTGGTCTTTCTTCAGTTTGAGTCGGAATGATCGAGGGTGGTCG
TTCTTCAGTTTATTCCGGAATGATCCAGGGTGGTCGTTCTC
Found at i:18120 original size:9 final size:9
Alignment explanation
Indices: 18106--18137 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
18096 TACTGATTTT
18106 GGCCCAGTA
1 GGCCCAGTA
18115 GGCCCAGTA
1 GGCCCAGTA
*
18124 GGCCCATTA
1 GGCCCAGTA
18133 GGCCC
1 GGCCC
18138 GGTTGAGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.19, C:0.38, G:0.31, T:0.12
Consensus pattern (9 bp):
GGCCCAGTA
Found at i:41340 original size:11 final size:10
Alignment explanation
Indices: 41322--41355 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
41312 GAAGTTCTTG
41322 TTTTGAAGAT
1 TTTTGAAGAT
41332 TTCTTGAAGAT
1 TT-TTGAAGAT
41343 ATTTTGAAGAT
1 -TTTTGAAGAT
41354 TT
1 TT
41356 GAAGACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:42898 original size:29 final size:29
Alignment explanation
Indices: 42856--42913 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
42846 TCACAATTGC
42856 CCTACTTGCCCTAGCTAGTTTAGTTAGTT
1 CCTACTTGCCCTAGCTAGTTTAGTTAGTT
42885 CCTACTTGCCCTAGCTAGTTTAGTTAGTT
1 CCTACTTGCCCTAGCTAGTTTAGTTAGTT
42914 TTTGTGGGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.41
Consensus pattern (29 bp):
CCTACTTGCCCTAGCTAGTTTAGTTAGTT
Found at i:46356 original size:21 final size:22
Alignment explanation
Indices: 46332--46373 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
46322 ACGAGCCATA
*
46332 TCCGCG-CTATGCCCGGCCTTG
1 TCCGCGACCATGCCCGGCCTTG
46353 TCCGCGCACCATGCCCGGCCT
1 TCCGCG-ACCATGCCCGGCCT
46374 ATGCCACTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
23 12 0.67
ACGTcount: A:0.07, C:0.48, G:0.26, T:0.19
Consensus pattern (22 bp):
TCCGCGACCATGCCCGGCCTTG
Found at i:49651 original size:33 final size:33
Alignment explanation
Indices: 49604--49669 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
49594 GCCGCGGAAC
*
49604 ACCGGCCACATGACTCGGCCATGCCCGGCCACA
1 ACCGGCCACATGACTCGACCATGCCCGGCCACA
* *
49637 ACCGTCCACATGACTCGATCATGCCCGGCCACA
1 ACCGGCCACATGACTCGACCATGCCCGGCCACA
49670 TGATTTGACC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.44, G:0.21, T:0.12
Consensus pattern (33 bp):
ACCGGCCACATGACTCGACCATGCCCGGCCACA
Found at i:49668 original size:23 final size:23
Alignment explanation
Indices: 49642--49692 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
49632 CCACAACCGT
*
49642 CCACATGACTCGATCATGCCCGG
1 CCACATGACTCGACCATGCCCGG
* *
49665 CCACATGATTTGACCATGCCCGG
1 CCACATGACTCGACCATGCCCGG
49688 CCACA
1 CCACA
49693 ACCGGCCACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.24, C:0.39, G:0.20, T:0.18
Consensus pattern (23 bp):
CCACATGACTCGACCATGCCCGG
Found at i:53142 original size:13 final size:13
Alignment explanation
Indices: 53124--53153 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
53114 TATTGTTTGT
53124 TTTATTAAATTGC
1 TTTATTAAATTGC
*
53137 TTTATTAATTTGC
1 TTTATTAAATTGC
53150 TTTA
1 TTTA
53154 GATTTAGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.60
Consensus pattern (13 bp):
TTTATTAAATTGC
Found at i:54460 original size:13 final size:14
Alignment explanation
Indices: 54436--54467 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
54426 GAATTAAAAT
54436 TAAATCTAACTAAG
1 TAAATCTAACTAAG
54450 TAAAT-TAACTAAG
1 TAAATCTAACTAAG
54463 -AAATC
1 TAAATC
54468 AATCAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.24
13 8 0.47
14 5 0.29
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.28
Consensus pattern (14 bp):
TAAATCTAACTAAG
Found at i:57302 original size:13 final size:12
Alignment explanation
Indices: 57284--57326 Score: 54
Period size: 10 Copynumber: 3.7 Consensus size: 12
57274 TGAAACTTGA
57284 AAAATAAAGACAT
1 AAAATAAAG-CAT
57297 AAAATAAAG-A-
1 AAAATAAAGCAT
57307 AAAATAAAGCAT
1 AAAATAAAGCAT
*
57319 AAACTAAA
1 AAAATAAA
57327 TAACTAAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 9 0.33
11 2 0.07
12 7 0.26
13 9 0.33
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAATAAAGCAT
Found at i:57309 original size:22 final size:22
Alignment explanation
Indices: 57282--57326 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
57272 AATGAAACTT
57282 GAAAAATAAAGACATAAAATAAA
1 GAAAAATAAAG-CATAAAATAAA
*
57305 GAAAAATAAAGCATAAACTAAA
1 GAAAAATAAAGCATAAAATAAA
57327 TAACTAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.71, C:0.07, G:0.09, T:0.13
Consensus pattern (22 bp):
GAAAAATAAAGCATAAAATAAA
Done.