Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015994.1 Corchorus capsularis cultivar CVL-1 contig16015, 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: 20225
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:2659 original size:19 final size:18
Alignment explanation
Indices: 2635--2670 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2625 TGAAGATTTC
2635 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
2654 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
2671 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:6923 original size:33 final size:32
Alignment explanation
Indices: 6875--6984 Score: 98
Period size: 33 Copynumber: 3.3 Consensus size: 32
6865 AAGCCGTGCA
* *
6875 ACACCGGCCACGCGACTTGGA-GATGCCCGGCC
1 ACACCGGCCACGCGACAT-GACCATGCCCGGCC
*
6907 ATCACCGGCCATGCGACATGACCATGCCCGGCC
1 A-CACCGGCCACGCGACATGACCATGCCCGGCC
** * *
6940 ACAACCGGCCACATGAC-TCGGCCATGCCCTGCC
1 AC-ACCGGCCACGCGACAT-GACCATGCCCGGCC
6973 ACAACCGGCCAC
1 AC-ACCGGCCAC
6985 ATGATCCTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
32 5 0.08
33 61 0.92
ACGTcount: A:0.22, C:0.44, G:0.25, T:0.10
Consensus pattern (32 bp):
ACACCGGCCACGCGACATGACCATGCCCGGCC
Found at i:8068 original size:33 final size:33
Alignment explanation
Indices: 7999--8071 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
7989 ATGACCCATC
* * *
7999 CCGCCCCAGGAGGGCGGCTTACCATGGCTCAAG
1 CCGCCCCACGAGGGCAGCTTACCATGGCGCAAG
* *
8032 CCGCCCCACTAGGGCAGCTTCACCATGG-GCAGG
1 CCGCCCCACGAGGGCAGCTT-ACCATGGCGCAAG
8065 CCGCCCC
1 CCGCCCC
8072 GGGGGGCGTC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 27 0.79
34 7 0.21
ACGTcount: A:0.16, C:0.42, G:0.30, T:0.11
Consensus pattern (33 bp):
CCGCCCCACGAGGGCAGCTTACCATGGCGCAAG
Found at i:8182 original size:17 final size:16
Alignment explanation
Indices: 8135--8186 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
8125 CTCCATGGCT
8135 GAGCCGTCCTAGTGGG
1 GAGCCGTCCTAGTGGG
* **
8151 GAGGC-TCCGCCGTGGCG
1 GAGCCGTCC-TAGTGG-G
8168 GAGCCGTCCTAGTGGG
1 GAGCCGTCCTAGTGGG
8184 GAG
1 GAG
8187 GCTCAGTGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
15 3 0.11
16 12 0.44
17 9 0.33
18 3 0.11
ACGTcount: A:0.12, C:0.27, G:0.46, T:0.15
Consensus pattern (16 bp):
GAGCCGTCCTAGTGGG
Found at i:9073 original size:28 final size:28
Alignment explanation
Indices: 9041--9099 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
9031 AAAAGACAAA
* *
9041 TGAGACGCCTGAAACGATGGAAGAGACT
1 TGAGACACCTGAAACGAAGGAAGAGACT
9069 TGAGACACCTGAAACGAAGGAAGAGACT
1 TGAGACACCTGAAACGAAGGAAGAGACT
9097 TGA
1 TGA
9100 TTGGTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.17, G:0.31, T:0.14
Consensus pattern (28 bp):
TGAGACACCTGAAACGAAGGAAGAGACT
Found at i:11898 original size:28 final size:28
Alignment explanation
Indices: 11823--11916 Score: 91
Period size: 28 Copynumber: 3.2 Consensus size: 28
11813 TATCAAAATA
* * *
11823 AAAATAAAAATCATTTTCTTCTTTAAAAAAG
1 AAAA-AAAAATTATTTT-TT-TTAAAAAAAC
*
11854 AAAAAAAAATGGT-TTTTTTTTGAAAAAAC
1 AAAAAAAAAT--TATTTTTTTTAAAAAAAC
*
11883 AAAAAAAAATTATTTTTATTAAAAAAAC
1 AAAAAAAAATTATTTTTTTTAAAAAAAC
11911 AAAAAA
1 AAAAAA
11917 TTAGGGGCAA
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
27 1 0.02
28 20 0.36
29 18 0.33
30 8 0.15
31 8 0.15
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.32
Consensus pattern (28 bp):
AAAAAAAAATTATTTTTTTTAAAAAAAC
Found at i:11898 original size:29 final size:28
Alignment explanation
Indices: 11823--11916 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 28
11813 TATCAAAATA
*
11823 AAAATAAAAATCATTTTCTTCTTTAAAAAAG
1 AAAA-AAAAATCATTTT-TT-TTTAAAAAAC
**
11854 AAAAAAAAATGGTTTTTTTTTGAAAAAAC
1 AAAAAAAAATCATTTTTTTTT-AAAAAAC
* * *
11883 AAAAAAAAATTATTTTTATTAAAAAAAC
1 AAAAAAAAATCATTTTTTTTTAAAAAAC
11911 AAAAAA
1 AAAAAA
11917 TTAGGGGCAA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
28 16 0.29
29 25 0.45
30 10 0.18
31 4 0.07
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.32
Consensus pattern (28 bp):
AAAAAAAAATCATTTTTTTTTAAAAAAC
Found at i:12004 original size:31 final size:29
Alignment explanation
Indices: 11934--12005 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 29
11924 CAAATGTGCA
11934 AATTGGTCCCTGAAGTGAACTTAGTGAGC
1 AATTGGTCCCTGAAGTGAACTTAGTGAGC
* *
11963 AATTGAGTCCCTGAAGTTG-AGTTAATTGAGC
1 AATTG-GTCCCTGAAG-TGAACTT-AGTGAGC
11994 AATTAGGTCCCT
1 AATT-GGTCCCT
12006 CACCCAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
29 5 0.14
30 13 0.35
31 18 0.49
32 1 0.03
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (29 bp):
AATTGGTCCCTGAAGTGAACTTAGTGAGC
Found at i:12318 original size:2 final size:2
Alignment explanation
Indices: 12313--12337 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12303 CATATATATA
12313 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
12338 AAAATGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:13022 original size:178 final size:178
Alignment explanation
Indices: 12698--13035 Score: 443
Period size: 178 Copynumber: 1.9 Consensus size: 178
12688 CAGATTAAGG
* * *
12698 TGATTTAAGTGTCTATTAAAATATTGTTCTATGATCTACAACTTTCATGAAGGACTCGGAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGGAAACTA
* * * *
12763 AATTTAATATTTCAAGTATTAAAAATGCTTCCGAAAAATTTGTTGTTTCGGTTAACAGGAATAGA
66 AATTCAATAGTTCAAGTATAAAAAATGCTTCCGAAAAATTAGTTGTTTCGGTTAACAGGAATAGA
* * * *
12828 TGGTCCACTTAATATTATATAACTTT-TGCTCCAGATGTCTGATTGAGA
131 CGGACCACTAAATATTACATAA-TTTGTGCTCCAGATGTCTGATTGAGA
* * * * *
12876 TGATTCAAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGACT-TGAGAATT
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGGA-AACT
12940 AAATTCAAT-GTTCAAGGTATAAAAAATGCTTCC-AAAGAATTAGTTGTTTCGGTTAAC-GGAAA
65 AAATTCAATAGTTCAA-GTATAAAAAATGCTTCCGAAA-AATTAGTTGTTTCGGTTAACAGG-AA
*
13002 TAGACGGACTACTAAATATTACATAATTTGTGCT
127 TAGACGGACCACTAAATATTACATAATTTGTGCT
13036 TATGGTGGAA
Statistics
Matches: 138, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
177 15 0.11
178 123 0.89
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (178 bp):
TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGGAAACTA
AATTCAATAGTTCAAGTATAAAAAATGCTTCCGAAAAATTAGTTGTTTCGGTTAACAGGAATAGA
CGGACCACTAAATATTACATAATTTGTGCTCCAGATGTCTGATTGAGA
Found at i:14772 original size:2 final size:2
Alignment explanation
Indices: 14765--14792 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
14755 GAAGATGTGA
14765 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14793 TAAGAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18513 original size:28 final size:28
Alignment explanation
Indices: 18482--18539 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
18472 AAAGAGAAAG
* * *
18482 GAGACGCCTGAAACGATGGAAGAGACTT
1 GAGACACCTGAAACAAAGGAAGAGACTT
*
18510 GAGACACCTGAAACAAAGGATGAGACTT
1 GAGACACCTGAAACAAAGGAAGAGACTT
18538 GA
1 GA
18540 TTGGTTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.40, C:0.17, G:0.29, T:0.14
Consensus pattern (28 bp):
GAGACACCTGAAACAAAGGAAGAGACTT
Done.