Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019590.1 Corchorus olitorius cultivar O-4 contig19623, 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: 42765
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:5529 original size:16 final size:17
Alignment explanation
Indices: 5503--5534 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5493 AGTGCAAATT
5503 AAAATAGAAAAATAAAG
1 AAAATAGAAAAATAAAG
5520 AAAA-AGAAAAATAAA
1 AAAATAGAAAAATAAA
5535 ACGCAGTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAATAGAAAAATAAAG
Found at i:8813 original size:21 final size:21
Alignment explanation
Indices: 8788--8828 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
8778 CCTTGAGGAT
8788 GATGGAATCG-ATTCTCATAGG
1 GATGGAATCGAATTC-CATAGG
8809 GATGGAATCGAATTCCATAG
1 GATGGAATCGAATTCCATAG
8829 CCATTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.27
Consensus pattern (21 bp):
GATGGAATCGAATTCCATAGG
Found at i:11295 original size:12 final size:12
Alignment explanation
Indices: 11278--11320 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
11268 AAATCATACC
11278 AACAATTAAGAA
1 AACAATTAAGAA
*
11290 AACAATCAAG-A
1 AACAATTAAGAA
*
11301 AA-AATAAAGAA
1 AACAATTAAGAA
11312 AACAATTAA
1 AACAATTAA
11321 TTCGAAAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 6 0.23
11 6 0.23
12 14 0.54
ACGTcount: A:0.70, C:0.09, G:0.07, T:0.14
Consensus pattern (12 bp):
AACAATTAAGAA
Found at i:16223 original size:2 final size:2
Alignment explanation
Indices: 16211--16251 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
16201 AAACGTAATC
16211 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16252 AAAGTACGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16537 original size:60 final size:62
Alignment explanation
Indices: 16467--16584 Score: 195
Period size: 62 Copynumber: 1.9 Consensus size: 62
16457 ATTATATTTC
* * *
16467 TTAAGTGCCA-TTGTTTAAATTTTTA-CAGTTTTATTCTATTAAAAACTCTATTTTTACAGT
1 TTAAGTGCCATTTGTTTAAATTTTTACCAATTTTATTATACTAAAAACTCTATTTTTACAGT
16527 TTAAGTGCCATTTGTTTAAATTTTTACCAATTTTATTATACTAAAAACTCTATTTTTA
1 TTAAGTGCCATTTGTTTAAATTTTTACCAATTTTATTATACTAAAAACTCTATTTTTA
16585 TTTAATTAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
60 10 0.19
61 15 0.28
62 28 0.53
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (62 bp):
TTAAGTGCCATTTGTTTAAATTTTTACCAATTTTATTATACTAAAAACTCTATTTTTACAGT
Found at i:22624 original size:13 final size:12
Alignment explanation
Indices: 22599--22640 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
22589 ATTCTCATAA
22599 ATATTTTTATTT
1 ATATTTTTATTT
22611 ATATTTTATATTT
1 ATATTTT-TATTT
22624 AT-TTATTTATTT
1 ATATT-TTTATTT
22636 A-ATTT
1 ATATTT
22641 ACTCAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 1 0.04
12 17 0.63
13 9 0.33
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
ATATTTTTATTT
Found at i:23140 original size:19 final size:19
Alignment explanation
Indices: 23116--23153 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
23106 AAACCAACAT
23116 AGGAAAAAGTAAAA-AAAAA
1 AGGAAAAAG-AAAAGAAAAA
23135 AGGAAAAAGAAAAGAAAAA
1 AGGAAAAAGAAAAGAAAAA
23154 TTAGTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (19 bp):
AGGAAAAAGAAAAGAAAAA
Found at i:24685 original size:117 final size:117
Alignment explanation
Indices: 24479--24710 Score: 376
Period size: 117 Copynumber: 2.0 Consensus size: 117
24469 TGATCGACAA
* * *
24479 AGAACATGTTCTATAGGCTCTGGCCAGTGGTTTATAGTAACTGGAAAATGACCCTACTAACGAGT
1 AGAACATGTTCTATAGGCCCTGGCCAGTGGGTTATAGTAACTGGAAAACGACCCTACTAACGAGT
*
24544 TATAGTAGTTAGCTTAAGGCCCTGCTAACGGGTTATAGTAGTTAGCAATTTG
66 TATAGTAGTTAGCTTAAGGCCCTGCTAACGAGTTATAGTAGTTAGCAATTTG
* * * *
24596 AGAACATGTTCTATCGGCCCT-GCCAAGTGGGTTATAGTAACTGGAAAACGGCCCTGCTAACGGG
1 AGAACATGTTCTATAGGCCCTGGCC-AGTGGGTTATAGTAACTGGAAAACGACCCTACTAACGAG
24660 TTATAGTAGTTAGCTTAAGGCCCTGCTAACGAGTTATAGTAGTTAGCAATT
65 TTATAGTAGTTAGCTTAAGGCCCTGCTAACGAGTTATAGTAGTTAGCAATT
24711 GTCGATATCG
Statistics
Matches: 106, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
116 3 0.03
117 103 0.97
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (117 bp):
AGAACATGTTCTATAGGCCCTGGCCAGTGGGTTATAGTAACTGGAAAACGACCCTACTAACGAGT
TATAGTAGTTAGCTTAAGGCCCTGCTAACGAGTTATAGTAGTTAGCAATTTG
Found at i:29077 original size:7 final size:7
Alignment explanation
Indices: 29067--29107 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
29057 TATATTATAT
29067 AGTCTTG
1 AGTCTTG
29074 AGTCTTG
1 AGTCTTG
29081 AGTCTTG
1 AGTCTTG
*
29088 ACTCTTG
1 AGTCTTG
29095 AGTCTTG
1 AGTCTTG
*
29102 ACTCTT
1 AGTCTT
29108 TCTTTTACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.15, C:0.20, G:0.22, T:0.44
Consensus pattern (7 bp):
AGTCTTG
Found at i:29086 original size:14 final size:14
Alignment explanation
Indices: 29067--29107 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
29057 TATATTATAT
*
29067 AGTCTTGAGTCTTG
1 AGTCTTGACTCTTG
29081 AGTCTTGACTCTTG
1 AGTCTTGACTCTTG
29095 AGTCTTGACTCTT
1 AGTCTTGACTCTT
29108 TCTTTTACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.15, C:0.20, G:0.22, T:0.44
Consensus pattern (14 bp):
AGTCTTGACTCTTG
Found at i:29262 original size:51 final size:51
Alignment explanation
Indices: 29161--29332 Score: 299
Period size: 51 Copynumber: 3.3 Consensus size: 51
29151 GAATTATTGC
*
29161 GTTTGTGGTTGCTCATTAATTTCATATATTAATTTTTTTCTTTTTTTGGTTGT
1 GTTTGTCGTTGCTCATTAATTTC--ATATTAATTTTTTTCTTTTTTTGGTTGT
* *
29214 GTTTGTCGTTGCTCGTTAATTTCATATTAATTTTTTCCTTTTTTTGGTTGT
1 GTTTGTCGTTGCTCATTAATTTCATATTAATTTTTTTCTTTTTTTGGTTGT
29265 GTTTGTCGTTGCTCATTAATTTCATATTAATTTTTTTCTTTTTTTGGTTGT
1 GTTTGTCGTTGCTCATTAATTTCATATTAATTTTTTTCTTTTTTTGGTTGT
29316 GTTTGTCGTTGCTCATT
1 GTTTGTCGTTGCTCATT
29333 GACCGCAATT
Statistics
Matches: 114, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
51 93 0.82
53 21 0.18
ACGTcount: A:0.13, C:0.10, G:0.16, T:0.61
Consensus pattern (51 bp):
GTTTGTCGTTGCTCATTAATTTCATATTAATTTTTTTCTTTTTTTGGTTGT
Found at i:29717 original size:25 final size:25
Alignment explanation
Indices: 29683--29756 Score: 130
Period size: 25 Copynumber: 3.0 Consensus size: 25
29673 GATTAGTTTG
29683 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
29708 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
* *
29733 TAGAGACCGAGGGAGACTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
29757 GATTGTTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.35, C:0.20, G:0.32, T:0.12
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:32483 original size:49 final size:48
Alignment explanation
Indices: 32388--32518 Score: 167
Period size: 49 Copynumber: 2.7 Consensus size: 48
32378 GAGCGTGCCA
* * *
32388 ATCAATTTTGTCAAAAAAATTGATAAAAAGTGCAATGAAAATTAAAAG
1 ATCAATTTTGTCATAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
*
32436 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAG
1 ATCAATTTTGTCATAAAAATTGAGAAAAAG-TGCAATG-AAAAATAAAAG
* *
32485 TTCAATTTTAT-AGTAAAAATTGAGAAAAAGTGCA
1 ATCAATTTTGTCA-TAAAAATTGAGAAAAAGTGCA
32519 GGAAAAGTAA
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
48 32 0.44
49 41 0.56
ACGTcount: A:0.52, C:0.06, G:0.14, T:0.28
Consensus pattern (48 bp):
ATCAATTTTGTCATAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
Done.