Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008900.1 Corchorus capsularis cultivar CVL-1 contig08921, 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: 28337
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:2987 original size:32 final size:32
Alignment explanation
Indices: 2951--3057 Score: 105
Period size: 32 Copynumber: 3.3 Consensus size: 32
2941 AGATTATATA
*
2951 TAGCGGCGTTTTG-GATCAGAGACGCCACCATT
1 TAGCGGCGTTTTGAGATCAG-GACGCCACTATT
* *
2983 TAGCGGCGTCTGTGACATTC--GACGCCACTATT
1 TAGCGGCGT-TTTGAGA-TCAGGACGCCACTATT
* *
3015 TAGCGGCGTCTGTGACATC-GGACGCCACTATT
1 TAGCGGCGT-TTTGAGATCAGGACGCCACTATT
3047 TAGCGGCGTTT
1 TAGCGGCGTTT
3058 AGGGCCTAGA
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
31 3 0.04
32 58 0.87
33 3 0.04
34 1 0.01
35 2 0.03
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.27
Consensus pattern (32 bp):
TAGCGGCGTTTTGAGATCAGGACGCCACTATT
Found at i:3219 original size:113 final size:114
Alignment explanation
Indices: 3017--3303 Score: 470
Period size: 113 Copynumber: 2.5 Consensus size: 114
3007 CCACTATTTA
* * *
3017 GCGGCGTCTGTGACATCGGACGCCACTATTTAGCGGCGTTTAGGGCCTAGACGCCGCTATTTGTT
1 GCGGCGTCCGGGACATCAGACGCCACTATTTAGCGGCGTTTAGGGCCTAGACGCCGCTATTTGTT
* * *
3082 AGGCTTCATTTTTACTCAATTTGCATTTCTCCG-AAAAAATTAATTATG
66 AGACTTCATTTTTACTCAAATTGCATTTCTCCGAAAAAAATTAATTATC
*
3130 GCGGCGTCCGGGACATAAGACGCCACTATTTAGCGGCGTTTAGGGCCTAGACGCCGCTATTTGTT
1 GCGGCGTCCGGGACATCAGACGCCACTATTTAGCGGCGTTTAGGGCCTAGACGCCGCTATTTGTT
3195 AGACTTCATTTTTACTCAAATTGCATTTCTCCGAAAAAAATTAATTATC
66 AGACTTCATTTTTACTCAAATTGCATTTCTCCGAAAAAAATTAATTATC
* *
3244 GCGGCGTCCGGGATC-CCAGACGCCACTATTTAGCGGCGTTTAGTGCCTAGACGCCGCTAT
1 GCGGCGTCCGGGA-CATCAGACGCCACTATTTAGCGGCGTTTAGGGCCTAGACGCCGCTAT
3304 ATTCAATTTT
Statistics
Matches: 162, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
113 92 0.57
114 69 0.43
115 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (114 bp):
GCGGCGTCCGGGACATCAGACGCCACTATTTAGCGGCGTTTAGGGCCTAGACGCCGCTATTTGTT
AGACTTCATTTTTACTCAAATTGCATTTCTCCGAAAAAAATTAATTATC
Found at i:5292 original size:30 final size:31
Alignment explanation
Indices: 5232--5297 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
5222 AAGGGTCCTT
5232 TGGCCGGTTGTGCGCGGATGCCCACATGCGA
1 TGGCCGGTTGTGCGCGGATGCCCACATGCGA
* *
5263 TGGCCGGTTGTG-GCCGGTTGCTC-CATGCGA
1 TGGCCGGTTGTGCG-CGGATGCCCACATGCGA
5293 TGGCC
1 TGGCC
5298 CATGCGATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 13 0.41
31 19 0.59
ACGTcount: A:0.09, C:0.29, G:0.39, T:0.23
Consensus pattern (31 bp):
TGGCCGGTTGTGCGCGGATGCCCACATGCGA
Found at i:7381 original size:13 final size:13
Alignment explanation
Indices: 7363--7388 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7353 ATTATCATTC
7363 AAAGCTTCTTTAA
1 AAAGCTTCTTTAA
7376 AAAGCTTCTTTAA
1 AAAGCTTCTTTAA
7389 TCTCACTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
AAAGCTTCTTTAA
Found at i:13712 original size:33 final size:33
Alignment explanation
Indices: 13675--13749 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
13665 GAAAACAAAC
* *
13675 CTGTTTTGGTTGATCATAGTATT-ACAAATAATT
1 CTGTTTTGGATGATCATAGCATTGA-AAATAATT
13708 CTGTTTTGGATGATCATAGCATTGAAAATAATT
1 CTGTTTTGGATGATCATAGCATTGAAAATAATT
*
13741 TTGTTTTGG
1 CTGTTTTGG
13750 GTGAAGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 37 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.08, G:0.19, T:0.45
Consensus pattern (33 bp):
CTGTTTTGGATGATCATAGCATTGAAAATAATT
Found at i:14828 original size:33 final size:33
Alignment explanation
Indices: 14786--14992 Score: 263
Period size: 33 Copynumber: 6.3 Consensus size: 33
14776 TTGGAGAACT
* *
14786 TTATTTTCAATATTATGTTCAACCAAAACAGAA
1 TTATTTTCAATACTATGATCAACCAAAACAGAA
* * *
14819 TTATTTTCAATATTATGTTCACCCAAAACAGAA
1 TTATTTTCAATACTATGATCAACCAAAACAGAA
* *
14852 TTATTTTCAATATTATGTTCAACCAAAACAGAA
1 TTATTTTCAATACTATGATCAACCAAAACAGAA
* *
14885 TTATTTGCAATGCTATGATCAACCAAAACAGAA
1 TTATTTTCAATACTATGATCAACCAAAACAGAA
* * *
14918 TTATTTGCAATACTATGATCAACTAAAA-ATAAA
1 TTATTTTCAATACTATGATCAACCAAAACA-GAA
* *
14951 TTATTTGCAATACTATGATCAACCAAAACAGAT
1 TTATTTTCAATACTATGATCAACCAAAACAGAA
*
14984 TTGTTTTCA
1 TTATTTTCA
14993 TCATAATTAG
Statistics
Matches: 158, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
32 1 0.01
33 156 0.99
34 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.35
Consensus pattern (33 bp):
TTATTTTCAATACTATGATCAACCAAAACAGAA
Found at i:14911 original size:66 final size:66
Alignment explanation
Indices: 14786--14992 Score: 290
Period size: 66 Copynumber: 3.1 Consensus size: 66
14776 TTGGAGAACT
* * * *
14786 TTATTTTCAATATTATGTTCAACCAAAACAGAATTATTTTCAATATTATGTTCACCCAAAACAGA
1 TTATTTTCAATATTATGTTCAACCAAAACAGAATTATTTGCAATACTATGATCAACCAAAACAGA
14851 A
66 A
*
14852 TTATTTTCAATATTATGTTCAACCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGA
1 TTATTTTCAATATTATGTTCAACCAAAACAGAATTATTTGCAATACTATGATCAACCAAAACAGA
14917 A
66 A
* * * * *
14918 TTATTTGCAATACTATGATCAACTAAAA-ATAAATTATTTGCAATACTATGATCAACCAAAACAG
1 TTATTTTCAATATTATGTTCAACCAAAACA-GAATTATTTGCAATACTATGATCAACCAAAACAG
*
14982 AT
65 AA
*
14984 TTGTTTTCA
1 TTATTTTCA
14993 TCATAATTAG
Statistics
Matches: 126, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
65 1 0.01
66 125 0.99
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.35
Consensus pattern (66 bp):
TTATTTTCAATATTATGTTCAACCAAAACAGAATTATTTGCAATACTATGATCAACCAAAACAGA
A
Done.