Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018041.1 Corchorus olitorius cultivar O-4 contig18074, 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: 32034
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:7505 original size:3 final size:3
Alignment explanation
Indices: 7492--7521 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
7482 TGAAAAATGC
7492 AAT AAT AAAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AA
7522 AAGAACATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:11087 original size:22 final size:22
Alignment explanation
Indices: 11059--11113 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
11049 GTTCATGGGC
*
11059 CGGGCCGGGTCGGATTCGGGTT
1 CGGGCCGGGCCGGATTCGGGTT
11081 CGGGCCGGGCCGGATTCGGGTT
1 CGGGCCGGGCCGGATTCGGGTT
*
11103 TGGGCCGGGCC
1 CGGGCCGGGCC
11114 CAAGCTTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.04, C:0.27, G:0.51, T:0.18
Consensus pattern (22 bp):
CGGGCCGGGCCGGATTCGGGTT
Found at i:16266 original size:27 final size:27
Alignment explanation
Indices: 16233--16306 Score: 139
Period size: 27 Copynumber: 2.7 Consensus size: 27
16223 ATCTAATCTT
16233 AAAATGACCAAAATGCCCCTGAACTTA
1 AAAATGACCAAAATGCCCCTGAACTTA
*
16260 AAAATGACCAAAATGTCCCTGAACTTA
1 AAAATGACCAAAATGCCCCTGAACTTA
16287 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
16307 AAATGATCCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.45, C:0.26, G:0.11, T:0.19
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAACTTA
Found at i:20217 original size:19 final size:19
Alignment explanation
Indices: 20195--20242 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
20185 TTAAATTTTC
20195 TATTTTAAAATTTAA-ACTT
1 TATTTTAAAA-TTAATACTT
*
20214 TATTTTAAAATTAATATTT
1 TATTTTAAAATTAATACTT
20233 TATTTTAAAA
1 TATTTTAAAA
20243 ATAAAATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTTAAAATTAATACTT
Found at i:21128 original size:6 final size:6
Alignment explanation
Indices: 21117--21181 Score: 71
Period size: 6 Copynumber: 11.0 Consensus size: 6
21107 GTTCTTTTTA
* * *
21117 TTCTTT TTCTTT TTC-TC TTCTTC TTCTTC TTCTTCT TTCTTT TTCTTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTT-T TTCTTT TTCTTT
*
21165 TTCTTT TT-TCT TTCTTT
1 TTCTTT TTCTTT TTCTTT
21182 CTTTCTTCCT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
5 8 0.15
6 39 0.75
7 5 0.10
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (6 bp):
TTCTTT
Found at i:21140 original size:3 final size:3
Alignment explanation
Indices: 21117--21169 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
21107 GTTCTTTTTA
* * *
21117 TTC TTT TTC TTT TTC -TC TTC TTC TTC TTC TTC TTC TTTC TTT TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC
*
21162 TTT TTC TT
1 TTC TTC TT
21170 TTTTCTTTCT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (3 bp):
TTC
Found at i:21188 original size:19 final size:19
Alignment explanation
Indices: 21117--21181 Score: 70
Period size: 17 Copynumber: 3.7 Consensus size: 19
21107 GTTCTTTTTA
21117 TTCTT-TTTCTTTTTCTC-
1 TTCTTCTTTCTTTTTCTCT
*
21134 TTCTTC-TTCTTCTTCTTCT
1 TTCTTCTTTCTTTTTC-TCT
21153 TTCTT-TTTCTTTTTCT-T
1 TTCTTCTTTCTTTTTCTCT
21170 TT-TTCTTTCTTT
1 TTCTTCTTTCTTT
21182 CTTTCTTCCT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
16 2 0.05
17 23 0.56
18 3 0.07
19 13 0.32
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (19 bp):
TTCTTCTTTCTTTTTCTCT
Found at i:25003 original size:42 final size:44
Alignment explanation
Indices: 24952--25045 Score: 122
Period size: 45 Copynumber: 2.2 Consensus size: 44
24942 CGTCCATTAC
* *
24952 CTAA-ATTCTA-C-TCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTTCCATCTCTAGATAATTCATCAAAATAAAA
* *
24993 CTAATATTCTACTCTTCCATCTTTAGATAATTTATCAAAATAAAA
1 CTAATATTCTAC-CTTCCATCTCTAGATAATTCATCAAAATAAAA
25038 CTAATATT
1 CTAATATT
25046 AATTGTTGCT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
44 1 0.02
45 34 0.76
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.37
Consensus pattern (44 bp):
CTAATATTCTACCTTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:27341 original size:11 final size:11
Alignment explanation
Indices: 27325--27351 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
27315 CAAGGGTAAG
27325 CTTTTCTTTTT
1 CTTTTCTTTTT
27336 CTTTTCTTTTT
1 CTTTTCTTTTT
27347 CTTTT
1 CTTTT
27352 TAATTTAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
CTTTTCTTTTT
Done.