Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008267.1 Corchorus capsularis cultivar CVL-1 contig08288, 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: 24383
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:2028 original size:10 final size:10
Alignment explanation
Indices: 2013--2064 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
2003 TAAAGGATCA
2013 TGTGGCCGGT
1 TGTGGCCGGT
*
2023 TGTGGCCGGG
1 TGTGGCCGGT
**
2033 CATGGCCGAGT
1 TGTGGCCG-GT
2044 CATGTGGCCGGT
1 --TGTGGCCGGT
2056 TGTGGCCGG
1 TGTGGCCGG
2065 GCATGGCCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
10 24 0.73
11 1 0.03
12 2 0.06
13 6 0.18
ACGTcount: A:0.06, C:0.23, G:0.48, T:0.23
Consensus pattern (10 bp):
TGTGGCCGGT
Found at i:2118 original size:33 final size:32
Alignment explanation
Indices: 2014--2154 Score: 147
Period size: 33 Copynumber: 4.3 Consensus size: 32
2004 AAAGGATCAT
** * **
2014 GTGGCCGGTTGTGGCCGGGCATGGCCGAGTCAT
1 GTGGCCGG-TGTGGCCGGGCATCTCCAAGTCGC
** * *
2047 GTGGCCGGTTGTGGCCGGGCATGGCCATGTCAC
1 GTGGCCGG-TGTGGCCGGGCATCTCCAAGTCGC
2080 GTGGCCGGTGATGGCCGGGCATCTCCAAGTCGC
1 GTGGCCGGTG-TGGCCGGGCATCTCCAAGTCGC
* *
2113 ATGGCCGGTGTTGCGCGGGCATCTCCAAGTCGC
1 GTGGCCGGTGTGGC-CGGGCATCTCCAAGTCGC
2146 GTGGCCGGT
1 GTGGCCGGT
2155 CACAAGTGCT
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
32 5 0.05
33 91 0.95
ACGTcount: A:0.10, C:0.28, G:0.42, T:0.21
Consensus pattern (32 bp):
GTGGCCGGTGTGGCCGGGCATCTCCAAGTCGC
Found at i:4755 original size:20 final size:21
Alignment explanation
Indices: 4716--4755 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4706 CAAATGCTCA
*
4716 ACTTAAGGAGTCAAACGACTT
1 ACTTAAAGAGTCAAACGACTT
*
4737 ACTTAAAGAG-CAAATGACT
1 ACTTAAAGAGTCAAACGACT
4756 CAAGATCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23
Consensus pattern (21 bp):
ACTTAAAGAGTCAAACGACTT
Found at i:8517 original size:156 final size:154
Alignment explanation
Indices: 8044--8551 Score: 500
Period size: 156 Copynumber: 3.3 Consensus size: 154
8034 CAAACTTAAG
**
8044 ATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAGTTTGGGGTGAGAAACC-ACTTCACTAAGA
1 ATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAGTTTGGGGTGAGAAACCAACTTCACTATCA
* * * *
8108 TAGAGAGTTCAGTTTTACTTAGAATTTTTTCCATAGTCTTATGGAGATAGTCTAAGT-CTTGTGG
66 -AGAGAGTTCGGTTTTACTT-GAATTTTTTCCATAGTCTTATGGAGATAATCTAAATCCCTGTGG
* * ** *
8172 CTAAGTTTCATCTCAATTGGACTTAGT
129 CAAAGTTTCAGCT-TTTTGGACTTAGA
* ** ** *
8199 ATGAAAAACTTAT-TTAAGTTTTTCAGTTAAGGATGGTTTGGGGTGTCAAACCAACTTCTCTATG
1 ATGAAAAACTTATGCT-AGTTTTTCAGTTAAGGACAGTTTGGGGTGAGAAACCAACTTCACTAT-
* * * *
8263 CTAGGGAGTTTGGTTTTAC-T---TTTTTTCCATTAGTCTTATGGAGATAATCT-AAGCCTACTG
64 CAAGAGAGTTCGGTTTTACTTGAATTTTTTCCA-TAGTCTTATGGAGATAATCTAAATCC--CT-
* *
8323 GTGG-AAA--ATCAGATTTATTGGACTTAGA
125 GTGGCAAAGTTTCAGCTTT-TTGGACTTAGA
* * * * * *
8351 ATGAAGAACTTATGCTAGTTTTTCATTTAAGGACAATTTGGGGAGAGAAACCAAGTTCACCATCA
1 ATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAGTTTGGGGTGAGAAACCAACTTCACTATCA
* * *
8416 AGAAGAGCTCGGTTTTACTTGGAATTTTTTCCATAGTCTTGTGGAGAGAATCTAAATCCCT-TGG
66 AG-AGAGTTCGGTTTTACTT-GAATTTTTTCCATAGTCTTATGGAGATAATCTAAATCCCTGTGG
*
8480 CAAAGTTTCAGCTTTTTCAGACTTAGA
129 CAAAGTTTCAGCTTTTT-GGACTTAGA
* *
8507 ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTG
1 ATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAGTTTGGGGTG
8552 TGAAGTCTAG
Statistics
Matches: 283, Mismatches: 49, Indels: 41
0.76 0.13 0.11
Matches are distributed among these distances:
151 13 0.05
152 95 0.34
153 5 0.02
154 7 0.02
155 54 0.19
156 96 0.34
157 13 0.05
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (154 bp):
ATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAGTTTGGGGTGAGAAACCAACTTCACTATCA
AGAGAGTTCGGTTTTACTTGAATTTTTTCCATAGTCTTATGGAGATAATCTAAATCCCTGTGGCA
AAGTTTCAGCTTTTTGGACTTAGA
Found at i:8922 original size:17 final size:17
Alignment explanation
Indices: 8900--8936 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
8890 ATTATCCAGC
8900 ACCTCATGCTACCTAGT
1 ACCTCATGCTACCTAGT
8917 ACCTCATGCTACCTAGT
1 ACCTCATGCTACCTAGT
8934 ACC
1 ACC
8937 ATGAGGGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.38, G:0.11, T:0.27
Consensus pattern (17 bp):
ACCTCATGCTACCTAGT
Found at i:9471 original size:17 final size:17
Alignment explanation
Indices: 9445--9481 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
9435 TCCCCCTCAT
9445 GGTACCAGGTAGCATGA
1 GGTACCAGGTAGCATGA
*
9462 GGTACTAGGTAGCATGA
1 GGTACCAGGTAGCATGA
9479 GGT
1 GGT
9482 GCTGGATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.27, C:0.14, G:0.38, T:0.22
Consensus pattern (17 bp):
GGTACCAGGTAGCATGA
Found at i:10353 original size:155 final size:156
Alignment explanation
Indices: 9821--10367 Score: 570
Period size: 156 Copynumber: 3.5 Consensus size: 156
9811 GCAAACTAGA
* * *
9821 TTTCACACCTCAAACTGTCCCTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGA
1 TTTCTCACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGA
* * * * * * *
9886 GCTGAAACTTTGCCAAGGGA-CTGAGATTCTCTCCACAAGACTATGGAAAAAATTCCAAGTCAAA
66 GATGAAACTTTGCCACGAGACCT-AGATTATCTCCATAAGACTATGGAAAAAATTCTAAGTAAAA
* * * * *
9950 CCGAGCTCTCCT-TGATGGTGAACTTGG
130 TCGAACTC-CCTATCATAGTGAAGTTGG
* * *
9977 TTTCTCCCCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAATAA
1 TTTCTCACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGA
* * * * *
10041 GTCTG--A-TTTTCCACCAGTAGGCTTAGATTATCTCCTTAAGACTATGGAAAAAATTCTAAGTA
66 G-ATGAAACTTTGCCA-C-G-AGACCTAGATTATCTCCATAAGACTATGGAAAAAATTCTAAGTA
* * *
10103 AAATCAAACTCCCTAGCATAGAGAAGTTGG
127 AAATCGAACTCCCTATCATAGTGAAGTTGG
** * * ** *
10133 TTTGACACCCCAAACTGTCCTTAACTGAAAAACTTGCATAAGTTTTTCAAACTAAGTC-CAATTG
1 TTTCTCACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAA-TG
* * * *
10197 AGATGAAACTTAGCCACGAGACCTAGACTATCTCCATAAGACTATGGAAAAAATTATAATTAAAA
65 AGATGAAACTTTGCCACGAGACCTAGATTATCTCCATAAGACTATGGAAAAAATTCTAAGTAAAA
10262 TCGAACTCCCTATCATAGTGAAGTT-G
130 TCGAACTCCCTATCATAGTGAAGTTGG
* * * * **
10288 TTTCTCACCCTAAACTGTCCTTAACTGAAAAACTAGCATAAGTTTTTGATTTTAAGTCTGTTTGA
1 TTTCTCACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGA
* *
10353 GATAAAACTTGGCCA
66 GATGAAACTTTGCCA
10368 AGGTAACCTA
Statistics
Matches: 323, Mismatches: 57, Indels: 23
0.80 0.14 0.06
Matches are distributed among these distances:
153 6 0.02
154 1 0.00
155 76 0.24
156 228 0.71
157 5 0.02
158 2 0.01
159 5 0.02
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.30
Consensus pattern (156 bp):
TTTCTCACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGA
GATGAAACTTTGCCACGAGACCTAGATTATCTCCATAAGACTATGGAAAAAATTCTAAGTAAAAT
CGAACTCCCTATCATAGTGAAGTTGG
Found at i:14815 original size:16 final size:16
Alignment explanation
Indices: 14794--14851 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
14784 GTCGAGACTC
14794 GAATGACCCGTAACTCA
1 GAATGACCCGTAAC-CA
* * *
14811 G-ATGATCCGAAACCC
1 GAATGACCCGTAACCA
*
14826 GAATGACCCGTAACCC
1 GAATGACCCGTAACCA
*
14842 GAGTGACCCG
1 GAATGACCCG
14852 AGACCTGTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
15 2 0.06
16 31 0.91
17 1 0.03
ACGTcount: A:0.31, C:0.33, G:0.22, T:0.14
Consensus pattern (16 bp):
GAATGACCCGTAACCA
Found at i:14864 original size:32 final size:32
Alignment explanation
Indices: 14793--14867 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
14783 AGTCGAGACT
* *
14793 CGAATGACCCGTAACTCAGATGATCCGAAACC
1 CGAATGACCCGTAACCCAGATGACCCGAAACC
*
14825 CGAATGACCCGTAACCC-GAGTGACCCGAGACC
1 CGAATGACCCGTAACCCAGA-TGACCCGAAACC
* *
14857 TGTATGACCCG
1 CGAATGACCCG
14868 AGAAGTTAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 2 0.05
32 35 0.95
ACGTcount: A:0.29, C:0.33, G:0.23, T:0.15
Consensus pattern (32 bp):
CGAATGACCCGTAACCCAGATGACCCGAAACC
Found at i:15565 original size:14 final size:16
Alignment explanation
Indices: 15542--15575 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
15532 GCTTTCTGTA
15542 TTTTATTTGCT-TCCT
1 TTTTATTTGCTCTCCT
15557 TTTTA-TTGCTCTCCT
1 TTTTATTTGCTCTCCT
15572 TTTT
1 TTTT
15576 TTTTTTACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.06, C:0.21, G:0.06, T:0.68
Consensus pattern (16 bp):
TTTTATTTGCTCTCCT
Found at i:15931 original size:2 final size:2
Alignment explanation
Indices: 15924--15954 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15914 AAATTAAAAC
15924 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15955 GTGGCATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24157 original size:141 final size:141
Alignment explanation
Indices: 23972--24259 Score: 567
Period size: 141 Copynumber: 2.0 Consensus size: 141
23962 GAAGGCCAGA
23972 TCTTTGTTTAACAATGGATAATGAGTTTAGTAAATTAAAATGCAGTAGTTTATGAAAAGTATAGA
1 TCTTTGTTTAACAATGGATAATGAGTTTAGTAAATTAAAATGCAGTAGTTTATGAAAAGTATAGA
24037 TATTGTACTACGTCTATTATTATTTTGAAGCATCAGATGCTTTTCACCTTATTTAATAAAAATTT
66 TATTGTACTACGTCTATTATTATTTTGAAGCATCAGATGCTTTTCACCTTATTTAATAAAAATTT
24102 AATTCTTTTTT
131 AATTCTTTTTT
*
24113 TCTTTGTTTAACAATGGCTAATGAGTTTAGTAAATTAAAATGCAGTAGTTTATGAAAAGTATAGA
1 TCTTTGTTTAACAATGGATAATGAGTTTAGTAAATTAAAATGCAGTAGTTTATGAAAAGTATAGA
24178 TATTGTACTACGTCTATTATTATTTTGAAGCATCAGATGCTTTTCACCTTATTTAATAAAAATTT
66 TATTGTACTACGTCTATTATTATTTTGAAGCATCAGATGCTTTTCACCTTATTTAATAAAAATTT
24243 AATTCTTTTTT
131 AATTCTTTTTT
24254 TCTTTG
1 TCTTTG
24260 GTTTTAACTT
Statistics
Matches: 146, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 146 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (141 bp):
TCTTTGTTTAACAATGGATAATGAGTTTAGTAAATTAAAATGCAGTAGTTTATGAAAAGTATAGA
TATTGTACTACGTCTATTATTATTTTGAAGCATCAGATGCTTTTCACCTTATTTAATAAAAATTT
AATTCTTTTTT
Found at i:24353 original size:2 final size:2
Alignment explanation
Indices: 24346--24383 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
24336 AAGCTTAAAC
24346 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Done.