Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006197.1 Corchorus capsularis cultivar CVL-1 contig06215, 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: 18861
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:1009 original size:41 final size:40
Alignment explanation
Indices: 859--1010 Score: 157
Period size: 41 Copynumber: 3.7 Consensus size: 40
849 GTAATTCAAG
* * *
859 GTGACAA-TCTCTGGTGTCAATAGTAATTATAATTTACTAGA
1 GTGACAACT-TCTGGTGTCAA-AGTAATTTTAATTTACCAAA
* *
900 GTAAC-ACTTCTTGTGTCAAAGGTAATTTTAATTTACCAAA
1 GTGACAACTTCTGGTGTCAAA-GTAATTTTAATTTACCAAA
* * *
940 ATGACAACTTCTAGTGTCAGCAA-AAATTTTAATTTACCAAA
1 GTGACAACTTCTGGTGTCA--AAGTAATTTTAATTTACCAAA
981 GTGACAACTTCTGGTGTCAAAGGTAATTTT
1 GTGACAACTTCTGGTGTCAAA-GTAATTTT
1011 CAATATTATT
Statistics
Matches: 92, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
39 3 0.03
40 30 0.33
41 57 0.62
43 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (40 bp):
GTGACAACTTCTGGTGTCAAAGTAATTTTAATTTACCAAA
Found at i:3219 original size:12 final size:12
Alignment explanation
Indices: 3202--3247 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
3192 TGCCGGCGAT
3202 GCAGGCTGGCCA
1 GCAGGCTGGCCA
*
3214 GCAGGCTTGGGCCT
1 GCAGGC-T-GGCCA
3228 GCTAGGCTGGCCA
1 GC-AGGCTGGCCA
3241 GCAGGCT
1 GCAGGCT
3248 TGGGCCTGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 11 0.38
13 7 0.24
14 7 0.24
15 4 0.14
ACGTcount: A:0.13, C:0.30, G:0.41, T:0.15
Consensus pattern (12 bp):
GCAGGCTGGCCA
Found at i:3235 original size:27 final size:27
Alignment explanation
Indices: 3203--3261 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
3193 GCCGGCGATG
3203 CAGGCTGGCCAGCAGGCTTGGGCCTGC
1 CAGGCTGGCCAGCAGGCTTGGGCCTGC
*
3230 TAGGCTGGCCAGCAGGCTTGGGCCTGC
1 CAGGCTGGCCAGCAGGCTTGGGCCTGC
3257 CAGGC
1 CAGGC
3262 CTGCTGCGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.12, C:0.32, G:0.41, T:0.15
Consensus pattern (27 bp):
CAGGCTGGCCAGCAGGCTTGGGCCTGC
Found at i:3870 original size:162 final size:162
Alignment explanation
Indices: 3603--3925 Score: 646
Period size: 162 Copynumber: 2.0 Consensus size: 162
3593 GTATTGGTTA
3603 TTGTGAATGGTTATAATTATGATTTTACCCATAAGTTTTAGAAAATGCCAATTTAGCCACGGAAA
1 TTGTGAATGGTTATAATTATGATTTTACCCATAAGTTTTAGAAAATGCCAATTTAGCCACGGAAA
3668 GAGGCTTTAAACTCCTAGAACCATTCTGAAAGTAAATAAAGCCTTAGTTGGGCACGTGTATGAGT
66 GAGGCTTTAAACTCCTAGAACCATTCTGAAAGTAAATAAAGCCTTAGTTGGGCACGTGTATGAGT
3733 CTTTATTAGTATTAAATAAAGTAATATCTTAG
131 CTTTATTAGTATTAAATAAAGTAATATCTTAG
3765 TTGTGAATGGTTATAATTATGATTTTACCCATAAGTTTTAGAAAATGCCAATTTAGCCACGGAAA
1 TTGTGAATGGTTATAATTATGATTTTACCCATAAGTTTTAGAAAATGCCAATTTAGCCACGGAAA
3830 GAGGCTTTAAACTCCTAGAACCATTCTGAAAGTAAATAAAGCCTTAGTTGGGCACGTGTATGAGT
66 GAGGCTTTAAACTCCTAGAACCATTCTGAAAGTAAATAAAGCCTTAGTTGGGCACGTGTATGAGT
3895 CTTTATTAGTATTAAATAAAGTAATATCTTA
131 CTTTATTAGTATTAAATAAAGTAATATCTTA
3926 TGCTACTAAT
Statistics
Matches: 161, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
162 161 1.00
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (162 bp):
TTGTGAATGGTTATAATTATGATTTTACCCATAAGTTTTAGAAAATGCCAATTTAGCCACGGAAA
GAGGCTTTAAACTCCTAGAACCATTCTGAAAGTAAATAAAGCCTTAGTTGGGCACGTGTATGAGT
CTTTATTAGTATTAAATAAAGTAATATCTTAG
Found at i:4269 original size:31 final size:32
Alignment explanation
Indices: 4234--4294 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
4224 AACTTGCCTC
4234 ATGAATGTTC-AAATTT-AGAACAATTTGCCCT
1 ATGAATGTTCTAAATTTAAG-ACAATTTGCCCT
*
4265 ATGAATTTTCTAAATTTAAGACAATTTGCC
1 ATGAATGTTCTAAATTTAAGACAATTTGCC
4295 ATGATATAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 9 0.33
32 16 0.59
33 2 0.07
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (32 bp):
ATGAATGTTCTAAATTTAAGACAATTTGCCCT
Found at i:8062 original size:16 final size:16
Alignment explanation
Indices: 8041--8129 Score: 108
Period size: 16 Copynumber: 5.6 Consensus size: 16
8031 GAACTCGCCC
8041 GACCCGAGACCCGAAT
1 GACCCGAGACCCGAAT
* *
8057 GACCCGAAATCCGAAT
1 GACCCGAGACCCGAAT
8073 GACCCGTA-ACCCGAAT
1 GACCCG-AGACCCGAAT
* *
8089 GATCCGAGACCCGTAT
1 GACCCGAGACCCGAAT
*
8105 GACCCGAAACCCGAAT
1 GACCCGAGACCCGAAT
*
8121 AACCCGAGA
1 GACCCGAGA
8130 AGTTAACCCG
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
15 1 0.02
16 59 0.97
17 1 0.02
ACGTcount: A:0.34, C:0.35, G:0.21, T:0.10
Consensus pattern (16 bp):
GACCCGAGACCCGAAT
Found at i:9022 original size:9 final size:9
Alignment explanation
Indices: 8996--9072 Score: 64
Period size: 9 Copynumber: 9.6 Consensus size: 9
8986 GATCCGAAAT
8996 CCGAATGAC
1 CCGAATGAC
9005 CCG---GAC
1 CCGAATGAC
9011 CCGAATGAC
1 CCGAATGAC
9020 CCG-A-GAC
1 CCGAATGAC
*
9027 CCGTATGAC
1 CCGAATGAC
9036 CCGAA--AC
1 CCGAATGAC
*
9043 CCGTATGAC
1 CCGAATGAC
9052 CCG-A-GAC
1 CCGAATGAC
*
9059 TCGAATGAC
1 CCGAATGAC
9068 CCGAA
1 CCGAA
9073 ACCTGAATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 18
0.71 0.05 0.23
Matches are distributed among these distances:
6 6 0.11
7 17 0.31
8 4 0.07
9 28 0.51
ACGTcount: A:0.30, C:0.36, G:0.23, T:0.10
Consensus pattern (9 bp):
CCGAATGAC
Found at i:9022 original size:47 final size:48
Alignment explanation
Indices: 8971--9071 Score: 143
Period size: 47 Copynumber: 2.1 Consensus size: 48
8961 AACCCGCCCA
* *
8971 ACCCGAGACCCGGTA-GATCCGAAATCCGAATGACCCG-GACCCGAATG
1 ACCCGAGACCC-GTATGACCCGAAACCCGAATGACCCGAGACCCGAATG
* *
9018 ACCCGAGACCCGTATGACCCGAAACCCGTATGACCCGAGACTCGAATG
1 ACCCGAGACCCGTATGACCCGAAACCCGAATGACCCGAGACCCGAATG
9066 ACCCGA
1 ACCCGA
9072 AACCTGAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
46 3 0.06
47 30 0.62
48 15 0.31
ACGTcount: A:0.30, C:0.36, G:0.24, T:0.11
Consensus pattern (48 bp):
ACCCGAGACCCGTATGACCCGAAACCCGAATGACCCGAGACCCGAATG
Found at i:9029 original size:16 final size:16
Alignment explanation
Indices: 8996--9087 Score: 114
Period size: 16 Copynumber: 5.8 Consensus size: 16
8986 GATCCGAAAT
8996 CCGAATGACCCG-GAC
1 CCGAATGACCCGAGAC
9011 CCGAATGACCCGAGAC
1 CCGAATGACCCGAGAC
* *
9027 CCGTATGACCCGAAAC
1 CCGAATGACCCGAGAC
*
9043 CCGTATGACCCGAGAC
1 CCGAATGACCCGAGAC
* *
9059 TCGAATGACCCGAAAC
1 CCGAATGACCCGAGAC
* *
9075 CTGAATAACCCGA
1 CCGAATGACCCGA
9088 ACCGAAAAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
15 12 0.18
16 55 0.82
ACGTcount: A:0.32, C:0.36, G:0.22, T:0.11
Consensus pattern (16 bp):
CCGAATGACCCGAGAC
Found at i:9086 original size:48 final size:47
Alignment explanation
Indices: 8989--9088 Score: 128
Period size: 48 Copynumber: 2.1 Consensus size: 47
8979 CCCGGTAGAT
* * * *
8989 CCGAAATCCGAATGACCCGGACCCGAATGACCCGAGACCCGTATGAC
1 CCGAAACCCGAATGACCCGGACCCGAATGACCCGAAACCCGAATAAC
* * *
9036 CCGAAACCCGTATGACCCGAGACTCGAATGACCCGAAACCTGAATAAC
1 CCGAAACCCGAATGACCCG-GACCCGAATGACCCGAAACCCGAATAAC
9084 CCGAA
1 CCGAA
9089 CCGAAAAAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
47 17 0.38
48 28 0.62
ACGTcount: A:0.33, C:0.35, G:0.21, T:0.11
Consensus pattern (47 bp):
CCGAAACCCGAATGACCCGGACCCGAATGACCCGAAACCCGAATAAC
Found at i:10226 original size:10 final size:11
Alignment explanation
Indices: 10201--10240 Score: 57
Period size: 10 Copynumber: 3.7 Consensus size: 11
10191 ATTATGCATG
10201 TTTTTATAGCTA
1 TTTTTATA-CTA
10213 TTTTTATA-TA
1 TTTTTATACTA
10223 TTTTT-TACTA
1 TTTTTATACTA
10233 TTTTTATA
1 TTTTTATA
10241 TGTGTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 2 0.08
10 14 0.54
11 2 0.08
12 8 0.31
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (11 bp):
TTTTTATACTA
Found at i:10235 original size:20 final size:21
Alignment explanation
Indices: 10210--10251 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
10200 GTTTTTATAG
10210 CTATTTTTATATAT-TTTTTA
1 CTATTTTTATATATGTTTTTA
*
10230 CTATTTTTATATGTGTTTTTA
1 CTATTTTTATATATGTTTTTA
10251 C
1 C
10252 CCTATTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (21 bp):
CTATTTTTATATATGTTTTTA
Found at i:17337 original size:87 final size:87
Alignment explanation
Indices: 17239--17501 Score: 508
Period size: 87 Copynumber: 3.0 Consensus size: 87
17229 TATATTTAAT
17239 ATTTTAATTCTTTTAATATGTTATATAATCTTTTTATTTTAGACAAACTCTTAACCATTTTTAAT
1 ATTTTAATTCTTTTAATATGTTATATAATCTTTTTATTTTAGACAAACTCTTAACCATTTTTAAT
17304 CTCAACCAAACTCCAAATTTTA
66 CTCAACCAAACTCCAAATTTTA
17326 ATTTTAATTCTTTTAATATGTTATATAATCTTTTTATTTTAGACAAACTCTTAACCATTTTTAAT
1 ATTTTAATTCTTTTAATATGTTATATAATCTTTTTATTTTAGACAAACTCTTAACCATTTTTAAT
17391 CTCAACCAAACTCCAAATTTTA
66 CTCAACCAAACTCCAAATTTTA
*
17413 ATTTTAATTCTTTTATTATGTTATATAATCTTTTTATTTTAGACAAACTCTTAACCATTTTTAAT
1 ATTTTAATTCTTTTAATATGTTATATAATCTTTTTATTTTAGACAAACTCTTAACCATTTTTAAT
*
17478 CTCAACCAAACTCCCAATTTTA
66 CTCAACCAAACTCCAAATTTTA
17500 AT
1 AT
17502 CTCAATTAAT
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 174 1.00
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.48
Consensus pattern (87 bp):
ATTTTAATTCTTTTAATATGTTATATAATCTTTTTATTTTAGACAAACTCTTAACCATTTTTAAT
CTCAACCAAACTCCAAATTTTA
Done.