Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003970.1 Corchorus capsularis cultivar CVL-1 contig03978, 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: 10525
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Found at i:752 original size:16 final size:16
Alignment explanation
Indices: 731--765 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
721 TCTGAATCTA
* *
731 GTTTATTTGTTTGTTT
1 GTTTATTTGATAGTTT
747 GTTTATTTGATAGTTT
1 GTTTATTTGATAGTTT
763 GTT
1 GTT
766 AAGTAGGGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.20, T:0.69
Consensus pattern (16 bp):
GTTTATTTGATAGTTT
Found at i:2959 original size:6 final size:6
Alignment explanation
Indices: 2939--2978 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
2929 CACTATCGAC
2939 TTCTTT CTT-TTT TTCTTT TTCTTT TTC-TT TT-TTT TTCTTT
1 TTCTTT -TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
2979 CTTTTCGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
5 10 0.33
6 18 0.60
7 2 0.07
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTCTTT
Found at i:2961 original size:14 final size:14
Alignment explanation
Indices: 2942--2983 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2932 TATCGACTTC
2942 TTTCTTTTTTTCTT
1 TTTCTTTTTTTCTT
2956 TTTC--TTTTTCTT
1 TTTCTTTTTTTCTT
2968 TTT-TTTTCTTTCTT
1 TTTCTTTT-TTTCTT
2982 TT
1 TT
2984 CGATTTTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 11 0.44
13 2 0.08
14 12 0.48
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTCTTTTTTTCTT
Found at i:2965 original size:20 final size:20
Alignment explanation
Indices: 2942--2983 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2932 TATCGACTTC
2942 TTTCTTTTTTTCTT-TTTCTT
1 TTTCTTTTTTT-TTCTTTCTT
2962 TTTCTTTTTTTTTCTTTCTT
1 TTTCTTTTTTTTTCTTTCTT
2982 TT
1 TT
2984 CGATTTTCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (20 bp):
TTTCTTTTTTTTTCTTTCTT
Found at i:3743 original size:22 final size:23
Alignment explanation
Indices: 3707--3750 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
3697 AGATAGTTGG
*
3707 GTAAAAATAATGAAAATTATAGC
1 GTAAAAATAAAGAAAATTATAGC
3730 GTAAAAA-AAAGAAAATTATAG
1 GTAAAAATAAAGAAAATTATAG
3751 ATATCATTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.61, C:0.02, G:0.14, T:0.23
Consensus pattern (23 bp):
GTAAAAATAAAGAAAATTATAGC
Found at i:3851 original size:30 final size:30
Alignment explanation
Indices: 3817--3875 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
3807 ATGAAAGATA
*
3817 AATTATTTTAAGAAGTTAAAAAGAAAAAAG
1 AATTATTTTAAGAAGTCAAAAAGAAAAAAG
*
3847 AATTATTTTAAGGAGTCAAAAAGAAAAAA
1 AATTATTTTAAGAAGTCAAAAAGAAAAAA
3876 TTCAACGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.59, C:0.02, G:0.14, T:0.25
Consensus pattern (30 bp):
AATTATTTTAAGAAGTCAAAAAGAAAAAAG
Found at i:4136 original size:73 final size:74
Alignment explanation
Indices: 4047--4196 Score: 198
Period size: 74 Copynumber: 2.0 Consensus size: 74
4037 TAAATCTTTA
* * *
4047 GGGGACCAAATTATAAACTTTT-C-ATTTTTTTCAATTGAAATGTATATATCTTAAAGAATTCTT
1 GGGGACCAAATTATAAA-TTTTCCGATTTTTTTCAATTGAAATGCATATATATGAAAGAATTCTT
4110 GGCAA-TTTGG
65 GG-AAGTTTGG
* * * *
4120 GGGGGCCAAATTATAAATTTTCCGATTTTTTTCATTTGAAGTGCATATATATGAAAGATTTCTTG
1 GGGGACCAAATTATAAATTTTCCGATTTTTTTCAATTGAAATGCATATATATGAAAGAATTCTTG
4185 GAAGTTTGG
66 GAAGTTTGG
4194 GGG
1 GGG
4197 AGGGGGGGCA
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
72 4 0.06
73 19 0.28
74 44 0.66
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (74 bp):
GGGGACCAAATTATAAATTTTCCGATTTTTTTCAATTGAAATGCATATATATGAAAGAATTCTTG
GAAGTTTGG
Found at i:4331 original size:19 final size:19
Alignment explanation
Indices: 4304--4343 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4294 GGAATAAAAA
* *
4304 ACCGTAACCGAAGCTACCG
1 ACCGGAACCGAAGCAACCG
*
4323 ACCGGAACCGACGCAACCG
1 ACCGGAACCGAAGCAACCG
4342 AC
1 AC
4344 GTGCGTAGAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.40, G:0.23, T:0.05
Consensus pattern (19 bp):
ACCGGAACCGAAGCAACCG
Found at i:7950 original size:13 final size:13
Alignment explanation
Indices: 7932--7962 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
7922 CAATTAGAAC
*
7932 AATAAAATCATAA
1 AATAAAATCAAAA
7945 AATAAAATCAAAA
1 AATAAAATCAAAA
7958 AATAA
1 AATAA
7963 CATATGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (13 bp):
AATAAAATCAAAA
Done.