Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008929.1 Corchorus capsularis cultivar CVL-1 contig08950, 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: 26353
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Found at i:805 original size:16 final size:14
Alignment explanation
Indices: 780--831 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 14
770 ACCCAAAATT
*
780 AAAAACAAAAAAGA
1 AAAAAAAAAAAAGA
*
794 AAAAAAGAAAAACGA
1 AAAAAA-AAAAAAGA
809 AAAAAAAGAAAAAGA
1 AAAAAAA-AAAAAGA
824 AAATAAAA
1 AAA-AAAA
832 GGAGATCCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 6 0.19
15 22 0.69
16 4 0.12
ACGTcount: A:0.85, C:0.04, G:0.10, T:0.02
Consensus pattern (14 bp):
AAAAAAAAAAAAGA
Found at i:832 original size:16 final size:15
Alignment explanation
Indices: 787--832 Score: 67
Period size: 16 Copynumber: 3.0 Consensus size: 15
777 ATTAAAAACA
787 AAAAAG-AAAAAAAG
1 AAAAAGAAAAAAAAG
801 AAAAACGAAAAAAAAG
1 AAAAA-GAAAAAAAAG
817 AAAAAGAAAATAAAAG
1 AAAAAGAAAA-AAAAG
833 GAGATCCGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.17
15 6 0.21
16 18 0.62
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:3067 original size:16 final size:16
Alignment explanation
Indices: 3048--3101 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
3038 TATTCAAGTT
3048 TCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTC
3064 TCGGGTCATAT-GGGT-
1 TCGGGTCAT-TCGGGTC
*
3079 TCCAGGTCATTCGGGTC
1 T-CGGGTCATTCGGGTC
3096 TCGGGT
1 TCGGGT
3102 TGGGCGGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 2 0.06
16 28 0.88
17 2 0.06
ACGTcount: A:0.09, C:0.22, G:0.37, T:0.31
Consensus pattern (16 bp):
TCGGGTCATTCGGGTC
Found at i:4973 original size:104 final size:103
Alignment explanation
Indices: 4794--5055 Score: 348
Period size: 104 Copynumber: 2.5 Consensus size: 103
4784 TTGGCATGGT
* * *
4794 GGACAAAAATTGTTCTTTACAATTTTTTAGTTTGTTTGAACCTTGTCTAGGAGTTTCACATGGTG
1 GGACAATAATTGTGCTTTACAATTTTTTAGTTTGTTTGAAGCTTGTCTAGGAGTTTCACATGGTG
*
4859 GAGAGAGTGGATTGAATAAAGGTTTGTCAACC-TGCTA
66 GAGAGAGTGGATTGAATAAAGGTTTGTCAACCTTACTA
* * ** *
4896 GGGACAATAATTGTGCTTTCCAATTTTTTAGATTTGTTTGAAGCTTGTCTAGTAGTTTGGCTTGG
1 -GGACAATAATTGTGCTTTACAATTTTTTAG-TTTGTTTGAAGCTTGTCTAGGAGTTTCACATGG
* * *
4961 TGGAGAGAGTGGATTGAATAAGGGTTTGTCTACCTTATTA
64 TGGAGAGAGTGGATTGAATAAAGGTTTGTCAACCTTACTA
* *
5001 GGACAATAATTGTGCTTTATC-ATTTTTCAGTTTTATTTGAAGCTTGTCTAGGAGT
1 GGACAATAATTGTGCTTTA-CAATTTTTTAG-TTTGTTTGAAGCTTGTCTAGGAGT
5056 GGTTGGAAAA
Statistics
Matches: 139, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
103 27 0.19
104 108 0.78
105 4 0.03
ACGTcount: A:0.25, C:0.11, G:0.24, T:0.40
Consensus pattern (103 bp):
GGACAATAATTGTGCTTTACAATTTTTTAGTTTGTTTGAAGCTTGTCTAGGAGTTTCACATGGTG
GAGAGAGTGGATTGAATAAAGGTTTGTCAACCTTACTA
Found at i:11358 original size:31 final size:31
Alignment explanation
Indices: 11284--11422 Score: 110
Period size: 31 Copynumber: 4.5 Consensus size: 31
11274 ATTGGTTAAT
* *
11284 TGCTCAAATAAGAGCCTAATGTCTGTCAAAA
1 TGCTCAAATAAGGGCCTAACGTCTGTCAAAA
* *
11315 TACTCAAATAAGGGCTTAACGT-TGTCGAAAA
1 TGCTCAAATAAGGGCCTAACGTCTGTC-AAAA
* * **
11346 TGCTCAAATAAGGG-C--ACGATCTTTTAATT
1 TGCTCAAATAAGGGCCTAACG-TCTGTCAAAA
*
11375 TGGC-CAAATAAGGGCCTAACGT-TATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTCTGTC-AAAA
*
11406 TGCTCAAATAAGAGCCT
1 TGCTCAAATAAGGGCCT
11423 GGTGTCGAAA
Statistics
Matches: 84, Mismatches: 15, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
28 3 0.04
29 14 0.17
30 13 0.15
31 51 0.61
32 3 0.04
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTCTGTCAAAA
Found at i:11562 original size:60 final size:60
Alignment explanation
Indices: 11462--11580 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 60
11452 AGTGACGCCA
* * *
11462 GGCCCTTATTTGAGCATTATCGATAACGTTAGGCCATTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTATCAATAACATTAGGCCATTATTTGACCAAATTAAAAGATCG
* *
11522 GGCCCTTATTTGAGCATTTTCAATAACATTAGGTCC-TTATTTGATCAAATTAAAAGATC
1 GGCCCTTATTTGAGCATTATCAATAACATTAGG-CCATTATTTGACCAAATTAAAAGATC
11581 AGATCCTTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
60 51 0.96
61 2 0.04
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTATCAATAACATTAGGCCATTATTTGACCAAATTAAAAGATCG
Found at i:14177 original size:15 final size:15
Alignment explanation
Indices: 14157--14187 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
14147 ACTAATTAAG
14157 AAAAGATATCACAAT
1 AAAAGATATCACAAT
14172 AAAAGATATCACAAT
1 AAAAGATATCACAAT
14187 A
1 A
14188 GAGTCTATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (15 bp):
AAAAGATATCACAAT
Found at i:20125 original size:16 final size:15
Alignment explanation
Indices: 20106--20166 Score: 59
Period size: 16 Copynumber: 3.9 Consensus size: 15
20096 ATCGGGTTTG
*
20106 GGTTGAATTTGAGTCA
1 GGTT-AATTTGGGTCA
* *
20122 GGTTAATTCGGGTTCG
1 GGTTAATTTGGG-TCA
20138 GGTTGAATTTGGGTCA
1 GGTT-AATTTGGGTCA
*
20154 GGTTAATTCGGGT
1 GGTTAATTTGGGT
20167 TCGGGTTCAG
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
15 14 0.38
16 16 0.43
17 7 0.19
ACGTcount: A:0.18, C:0.08, G:0.36, T:0.38
Consensus pattern (15 bp):
GGTTAATTTGGGTCA
Found at i:20173 original size:16 final size:16
Alignment explanation
Indices: 20122--20173 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
20112 ATTTGAGTCA
20122 GGTTAATTCGGGTTCG
1 GGTTAATTCGGGTTCG
* *
20138 GGTTGAATTTGGG-TCA
1 GGTT-AATTCGGGTTCG
20154 GGTTAATTCGGGTTCG
1 GGTTAATTCGGGTTCG
20170 GGTT
1 GGTT
20174 CAGTTTGGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 7 0.23
16 16 0.53
17 7 0.23
ACGTcount: A:0.13, C:0.10, G:0.38, T:0.38
Consensus pattern (16 bp):
GGTTAATTCGGGTTCG
Found at i:20181 original size:32 final size:32
Alignment explanation
Indices: 20097--20183 Score: 138
Period size: 32 Copynumber: 2.7 Consensus size: 32
20087 CAGGCTTGAA
* *
20097 TCGGGTTTGGGTTGAATTTGAGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
20129 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
* *
20161 TCGGGTTCGGGTTCAGTTTGGGT
1 TCGGGTTCGGGTTGAATTTGGGT
20184 TTTGGCCAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.14, C:0.09, G:0.38, T:0.39
Consensus pattern (32 bp):
TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
Found at i:20355 original size:16 final size:16
Alignment explanation
Indices: 20336--20411 Score: 89
Period size: 16 Copynumber: 4.8 Consensus size: 16
20326 GGATTCGGGT
*
20336 TTTTTCGGGTTTGAGC
1 TTTTTCGGGTTCGAGC
*
20352 TTTTTCGGGTTCGAGT
1 TTTTTCGGGTTCGAGC
** *
20368 TTTTTCGGGTTTAAAC
1 TTTTTCGGGTTCGAGC
* *
20384 TTTTTCGGGTTCGGGT
1 TTTTTCGGGTTCGAGC
20400 TTTTTCGGGTTC
1 TTTTTCGGGTTC
20412 AGGTTCAGGT
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.07, C:0.13, G:0.29, T:0.51
Consensus pattern (16 bp):
TTTTTCGGGTTCGAGC
Found at i:20375 original size:32 final size:32
Alignment explanation
Indices: 20329--20410 Score: 137
Period size: 32 Copynumber: 2.6 Consensus size: 32
20319 AATTTTAGGA
* *
20329 TTCGGGTTTTTTCGGGTTTGAGCTTTTTCGGG
1 TTCGGGTTTTTTCGGGTTTAAACTTTTTCGGG
*
20361 TTCGAGTTTTTTCGGGTTTAAACTTTTTCGGG
1 TTCGGGTTTTTTCGGGTTTAAACTTTTTCGGG
20393 TTCGGGTTTTTTCGGGTT
1 TTCGGGTTTTTTCGGGTT
20411 CAGGTTCAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.06, C:0.12, G:0.30, T:0.51
Consensus pattern (32 bp):
TTCGGGTTTTTTCGGGTTTAAACTTTTTCGGG
Found at i:22840 original size:41 final size:41
Alignment explanation
Indices: 22795--22880 Score: 163
Period size: 41 Copynumber: 2.1 Consensus size: 41
22785 TGTTTTAACA
22795 ATTTTTTCTTTTTTGGTTTTTAAAGAAGCAAAGCAAAGTTC
1 ATTTTTTCTTTTTTGGTTTTTAAAGAAGCAAAGCAAAGTTC
*
22836 ATTTTTTCTTTTTTGTTTTTTAAAGAAGCAAAGCAAAGTTC
1 ATTTTTTCTTTTTTGGTTTTTAAAGAAGCAAAGCAAAGTTC
22877 ATTT
1 ATTT
22881 GAACCTGATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (41 bp):
ATTTTTTCTTTTTTGGTTTTTAAAGAAGCAAAGCAAAGTTC
Found at i:24003 original size:16 final size:16
Alignment explanation
Indices: 23962--24006 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
23952 TCGGATTTTG
**
23962 TCGGTTTCGGGTTATC
1 TCGGTTTCGGGTTAAA
*
23978 TC-GATTCGGGTTAAA
1 TCGGTTTCGGGTTAAA
23993 TCGGTTTCGGGTTA
1 TCGGTTTCGGGTTA
24007 TAGTACTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.13, C:0.16, G:0.31, T:0.40
Consensus pattern (16 bp):
TCGGTTTCGGGTTAAA
Found at i:26177 original size:2 final size:2
Alignment explanation
Indices: 26170--26225 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
26160 GATATCTAGC
26170 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
* *
26212 CT TT AT AT -T AT AT A
1 AT AT AT AT AT AT AT A
26226 AGTCTAAACT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Done.