Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008345.1 Corchorus capsularis cultivar CVL-1 contig08366, 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: 24312
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:3974 original size:17 final size:16
Alignment explanation
Indices: 3941--3978 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
3931 AAGTCAACGT
3941 CCCGAACCCGCCCGAA
1 CCCGAACCCGCCCGAA
*
3957 CCCGAACCCGATCCGAA
1 CCCGAACCCG-CCCGAA
3974 CCCGA
1 CCCGA
3979 GATCAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.26, C:0.53, G:0.18, T:0.03
Consensus pattern (16 bp):
CCCGAACCCGCCCGAA
Found at i:4748 original size:17 final size:18
Alignment explanation
Indices: 4726--4776 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 18
4716 TCGAAAGTGA
4726 ACCCGAACCCG-ACCCGG
1 ACCCGAACCCGAACCCGG
4743 ACCCGAACCCGAACCC-G
1 ACCCGAACCCGAACCCGG
* *
4760 ATCCGAGCCCGAACCCG
1 ACCCGAACCCGAACCCG
4777 AAAATACCCG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 26 0.87
18 4 0.13
ACGTcount: A:0.25, C:0.51, G:0.22, T:0.02
Consensus pattern (18 bp):
ACCCGAACCCGAACCCGG
Found at i:4754 original size:23 final size:23
Alignment explanation
Indices: 4724--4778 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
4714 TATCGAAAGT
4724 GAACCCGAACCCGACCCG-GACCC
1 GAACCCGAACCCGACCCGAG-CCC
*
4747 GAACCCGAACCCGATCCGAGCCC
1 GAACCCGAACCCGACCCGAGCCC
4770 GAACCCGAA
1 GAACCCGAA
4779 AATACCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 29 0.97
24 1 0.03
ACGTcount: A:0.29, C:0.47, G:0.22, T:0.02
Consensus pattern (23 bp):
GAACCCGAACCCGACCCGAGCCC
Found at i:4765 original size:11 final size:11
Alignment explanation
Indices: 4726--4778 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
4716 TCGAAAGTGA
4726 ACCCGAACCCG
1 ACCCGAACCCG
*
4737 ACCCGGACCCG
1 ACCCGAACCCG
4748 AACCCGAACCCG
1 -ACCCGAACCCG
* *
4760 ATCCGAGCCCG
1 ACCCGAACCCG
4771 AACCCGAA
1 -ACCCGAA
4779 AATACCCGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
11 19 0.56
12 15 0.44
ACGTcount: A:0.28, C:0.49, G:0.21, T:0.02
Consensus pattern (11 bp):
ACCCGAACCCG
Found at i:4788 original size:16 final size:16
Alignment explanation
Indices: 4767--4837 Score: 108
Period size: 16 Copynumber: 4.5 Consensus size: 16
4757 CCGATCCGAG
4767 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
4783 CCCGAACCCGAAAAAA
1 CCCGAACCCGAAAATA
*
4799 CCTGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
4815 CCCGAACCCG-AAGTA
1 CCCGAACCCGAAAATA
4830 CCCGAACC
1 CCCGAACC
4838 AGCCCAATTG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
15 12 0.24
16 38 0.76
ACGTcount: A:0.41, C:0.39, G:0.14, T:0.06
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:4794 original size:6 final size:6
Alignment explanation
Indices: 4724--4778 Score: 69
Period size: 6 Copynumber: 9.5 Consensus size: 6
4714 TATCGAAAGT
* * *
4724 GAACCC GAACCC G-ACCC GGACCC GAACCC GAACCC G-ATCC GAGCCC
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC
4770 GAACCC GAA
1 GAACCC GAA
4779 AATACCCGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
5 9 0.21
6 33 0.79
ACGTcount: A:0.29, C:0.47, G:0.22, T:0.02
Consensus pattern (6 bp):
GAACCC
Found at i:5277 original size:15 final size:15
Alignment explanation
Indices: 5257--5286 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5247 TTGGAGTTGT
*
5257 TTTTTTTTTTTTTGA
1 TTTTTTTTCTTTTGA
5272 TTTTTTTTCTTTTGA
1 TTTTTTTTCTTTTGA
5287 GAGATAATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (15 bp):
TTTTTTTTCTTTTGA
Found at i:12891 original size:19 final size:21
Alignment explanation
Indices: 12866--12924 Score: 77
Period size: 19 Copynumber: 2.9 Consensus size: 21
12856 ACAATTTATG
*
12866 TACTGTACAGATGAAATTA-C
1 TACTGTACAGATCAAATTAGC
12886 -ACTGTACAGATCAAATTAGC
1 TACTGTACAGATCAAATTAGC
* *
12906 TATTGTACAGATCATATTA
1 TACTGTACAGATCAAATTA
12925 TTAGAGCAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.50
20 1 0.03
21 16 0.47
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (21 bp):
TACTGTACAGATCAAATTAGC
Found at i:22184 original size:25 final size:25
Alignment explanation
Indices: 22156--22218 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
22146 AACCCAATTT
22156 TCAACCATTGTTAACCATTGTAAAA
1 TCAACCATTGTTAACCATTGTAAAA
* * *
22181 TCAACCTTTGTCAACCATTTTAAAA
1 TCAACCATTGTTAACCATTGTAAAA
*
22206 CCAACCATT-TTAA
1 TCAACCATTGTTAA
22219 AACTCTGGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 3 0.09
25 29 0.91
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (25 bp):
TCAACCATTGTTAACCATTGTAAAA
Found at i:22210 original size:15 final size:15
Alignment explanation
Indices: 22192--22221 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
22182 CAACCTTTGT
22192 CAACCATTTTAAAAC
1 CAACCATTTTAAAAC
22207 CAACCATTTTAAAAC
1 CAACCATTTTAAAAC
22222 TCTGGTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (15 bp):
CAACCATTTTAAAAC
Found at i:24257 original size:2 final size:2
Alignment explanation
Indices: 24250--24290 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
24240 TTAAATAATA
* *
24250 AT AT AT AT AT TT A- AT AT AA 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
24291 TAAGTCAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24269 original size:25 final size:27
Alignment explanation
Indices: 24235--24286 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 27
24225 AGACCCATTC
*
24235 TTAATTTAAATA-ATA-ATATATATAT
1 TTAATATAAATATATATATATATATAT
24260 TTAATATAAATATATATATATATATAT
1 TTAATATAAATATATATATATATATAT
24287 ATATTAAGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 11 0.46
26 3 0.12
27 10 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
TTAATATAAATATATATATATATATAT
Done.