Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011534.1 Corchorus capsularis cultivar CVL-1 contig11555, 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: 7334
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:1766 original size:6 final size:7
Alignment explanation
Indices: 1750--1775 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1740 ACGGAGCTAA
1750 GGGGGCG
1 GGGGGCG
1757 GGGGGCG
1 GGGGGCG
1764 GGGGGCG
1 GGGGGCG
1771 GGGGG
1 GGGGG
1776 AGGTGACTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.88, T:0.00
Consensus pattern (7 bp):
GGGGGCG
Found at i:2736 original size:14 final size:15
Alignment explanation
Indices: 2710--2738 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2700 TGGCAAAGTG
2710 AATCCGATCCGAAAA
1 AATCCGATCCGAAAA
2725 AATCCG-TCCGAAAA
1 AATCCGATCCGAAAA
2739 CCTAATTCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.28, G:0.14, T:0.14
Consensus pattern (15 bp):
AATCCGATCCGAAAA
Found at i:2853 original size:32 final size:32
Alignment explanation
Indices: 2817--2930 Score: 165
Period size: 32 Copynumber: 3.6 Consensus size: 32
2807 TGAACTCGAC
*
2817 AAAACCCGAACTCGAAAAAGCTCAAACCCGAA
1 AAAACCCGAACCCGAAAAAGCTCAAACCCGAA
* *
2849 AAAACACGAACCCGAAAAAGCTCAACCCCGAA
1 AAAACCCGAACCCGAAAAAGCTCAAACCCGAA
** *
2881 AAAATTCGAACCCGAAAAAACTCAAACCCGAA
1 AAAACCCGAACCCGAAAAAGCTCAAACCCGAA
*
2913 AAAACCCGAATCCGAAAA
1 AAAACCCGAACCCGAAAA
2931 TTTATGAAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 72 1.00
ACGTcount: A:0.52, C:0.31, G:0.11, T:0.06
Consensus pattern (32 bp):
AAAACCCGAACCCGAAAAAGCTCAAACCCGAA
Found at i:2927 original size:16 final size:16
Alignment explanation
Indices: 2817--2930 Score: 122
Period size: 16 Copynumber: 7.1 Consensus size: 16
2807 TGAACTCGAC
* *
2817 AAAACCCGAACTCGAA
1 AAAACTCGAACCCGAA
* *
2833 AAAGCTCAAACCCGAA
1 AAAACTCGAACCCGAA
*
2849 AAAACACGAACCCGAA
1 AAAACTCGAACCCGAA
*
2865 AAAGCTC-AACCCCGAA
1 AAAACTCGAA-CCCGAA
*
2881 AAAATTCGAACCCGAA
1 AAAACTCGAACCCGAA
*
2897 AAAACTCAAACCCGAA
1 AAAACTCGAACCCGAA
* *
2913 AAAACCCGAATCCGAA
1 AAAACTCGAACCCGAA
2929 AA
1 AA
2931 TTTATGAAAA
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
15 2 0.03
16 76 0.95
17 2 0.03
ACGTcount: A:0.52, C:0.31, G:0.11, T:0.06
Consensus pattern (16 bp):
AAAACTCGAACCCGAA
Found at i:3148 original size:31 final size:31
Alignment explanation
Indices: 3078--3216 Score: 197
Period size: 31 Copynumber: 4.4 Consensus size: 31
3068 ACCCAAACAG
*
3078 AACCCTAACCCGAATTAACCTGACCCAAATT
1 AACCCGAACCCGAATTAACCTGACCCAAATT
3109 CAACCCGAACCCGAATTAACCTGACCCAAATT
1 -AACCCGAACCCGAATTAACCTGACCCAAATT
* *
3141 AACCCGAACCTGAATTAACCTGACCCGAATT
1 AACCCGAACCCGAATTAACCTGACCCAAATT
* * * *
3172 AACTCGAACCCGAATTAACCTGATCAAAATCC
1 AACCCGAACCCGAATTAACCTGACCCAAAT-T
3204 AACCCGAACCCGA
1 AACCCGAACCCGA
3217 CTCAAACCCG
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
31 54 0.56
32 42 0.44
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (31 bp):
AACCCGAACCCGAATTAACCTGACCCAAATT
Found at i:3184 original size:16 final size:16
Alignment explanation
Indices: 3084--3194 Score: 131
Period size: 16 Copynumber: 7.1 Consensus size: 16
3074 ACAGAACCCT
3084 AACCCGAATTAACCTG
1 AACCCGAATTAACCTG
* *
3100 -ACCCAAATTCAACCCG
1 AACCCGAATT-AACCTG
3116 AACCCGAATTAACCTG
1 AACCCGAATTAACCTG
* *
3132 -ACCCAAATTAACCCG
1 AACCCGAATTAACCTG
*
3147 AACCTGAATTAACCTG
1 AACCCGAATTAACCTG
3163 -ACCCGAATTAA-CTCG
1 AACCCGAATTAACCT-G
3178 AACCCGAATTAACCTG
1 AACCCGAATTAACCTG
3194 A
1 A
3195 TCAAAATCCA
Statistics
Matches: 79, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
14 2 0.03
15 32 0.41
16 35 0.44
17 10 0.13
ACGTcount: A:0.38, C:0.33, G:0.11, T:0.18
Consensus pattern (16 bp):
AACCCGAATTAACCTG
Found at i:3777 original size:15 final size:15
Alignment explanation
Indices: 3757--3790 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
3747 TTTATAACCC
*
3757 AAAAAAAAAGAAGAG
1 AAAAAAAAAGAAAAG
3772 AAAAAAAAAGAAAAG
1 AAAAAAAAAGAAAAG
3787 AAAA
1 AAAA
3791 GAAACCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAGAAAAG
Found at i:3785 original size:20 final size:19
Alignment explanation
Indices: 3757--3794 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3747 TTTATAACCC
*
3757 AAAAAAAAAGAAGAGAAAA
1 AAAAAAAAAGAAAAGAAAA
3776 AAAAAGAAAAGAAAAGAAA
1 AAAAA-AAAAGAAAAGAAA
3795 CCACATCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAGAAAAGAAAA
Found at i:4123 original size:16 final size:16
Alignment explanation
Indices: 4115--4206 Score: 105
Period size: 16 Copynumber: 5.8 Consensus size: 16
4105 TCGGATTCGG
4115 GTTTTTTCGGGTTTGA
1 GTTTTTTCGGGTTTGA
* * * *
4131 GCTTTTCCGGATTCG-
1 GTTTTTTCGGGTTTGA
* *
4146 GATTTTTCAGGTTTGA
1 GTTTTTTCGGGTTTGA
* *
4162 GCTTTTTCGGGTTTGT
1 GTTTTTTCGGGTTTGA
4178 GTTTTTTCGGGTTTGA
1 GTTTTTTCGGGTTTGA
4194 GTTTTTTCGGGTT
1 GTTTTTTCGGGTT
4207 CAGGTTTTGT
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
15 10 0.16
16 51 0.84
ACGTcount: A:0.07, C:0.11, G:0.29, T:0.53
Consensus pattern (16 bp):
GTTTTTTCGGGTTTGA
Found at i:4142 original size:32 final size:32
Alignment explanation
Indices: 4102--4222 Score: 138
Period size: 32 Copynumber: 3.8 Consensus size: 32
4092 TTTTCATAAA
4102 TTTTCGGATTCGGGTTTTTTCGGGTTTGAGCT
1 TTTTCGGATTCGGGTTTTTTCGGGTTTGAGCT
* * *
4134 TTTCCGGATTC-GGATTTTTCAGGTTTGAGCT
1 TTTTCGGATTCGGGTTTTTTCGGGTTTGAGCT
* * * *
4165 TTTTCGGGTTTGTGTTTTTTCGGGTTTGAGTT
1 TTTTCGGATTCGGGTTTTTTCGGGTTTGAGCT
* *
4197 TTTTCGGGTTCAGGTTTTGTT-GGGTT
1 TTTTCGGATTCGGGTTTT-TTCGGGTT
4223 CAGATTCAGG
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
31 26 0.35
32 46 0.62
33 2 0.03
ACGTcount: A:0.07, C:0.11, G:0.31, T:0.52
Consensus pattern (32 bp):
TTTTCGGATTCGGGTTTTTTCGGGTTTGAGCT
Found at i:5340 original size:3 final size:3
Alignment explanation
Indices: 5332--5369 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5322 TACAATACAC
5332 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5370 ATTTTGGGCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Done.