Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015503.1 Corchorus capsularis cultivar CVL-1 contig15524, 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: 8466
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32
Found at i:1283 original size:2 final size:2
Alignment explanation
Indices: 1270--1309 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
1260 ATTTATAAAC
*
1270 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1310 TCATATAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3187 original size:19 final size:19
Alignment explanation
Indices: 3160--3204 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
3150 CGCGACCCGC
3160 TGTTCTTCTTCTTTTTTTT
1 TGTTCTTCTTCTTTTTTTT
*
3179 TGTTTTTCTTCTTTTTTTT
1 TGTTCTTCTTCTTTTTTTT
*
3198 TCTTCTT
1 TGTTCTT
3205 TATAGGCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (19 bp):
TGTTCTTCTTCTTTTTTTT
Found at i:3193 original size:16 final size:16
Alignment explanation
Indices: 3165--3204 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
3155 CCCGCTGTTC
3165 TTCTTCTT-TTTTTTT
1 TTCTTCTTCTTTTTTT
*
3180 GTTTTTCTTCTTTTTTT
1 -TTCTTCTTCTTTTTTT
3197 TTCTTCTT
1 TTCTTCTT
3205 TATAGGCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (16 bp):
TTCTTCTTCTTTTTTT
Found at i:3199 original size:13 final size:14
Alignment explanation
Indices: 3176--3205 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3166 TCTTCTTTTT
3176 TTTTGTTTTTCTTC
1 TTTTGTTTTTCTTC
3190 TTTT-TTTTTCTTC
1 TTTTGTTTTTCTTC
3203 TTT
1 TTT
3206 ATAGGCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.83
Consensus pattern (14 bp):
TTTTGTTTTTCTTC
Found at i:4817 original size:21 final size:21
Alignment explanation
Indices: 4791--4835 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
4781 CGCATCGCCA
4791 TTCGTCAGGTGTTTTTTATAT
1 TTCGTCAGGTGTTTTTTATAT
4812 TTCGTCAGGTGTTTTTTATAT
1 TTCGTCAGGTGTTTTTTATAT
4833 TTC
1 TTC
4836 AATAGTCGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.11, G:0.18, T:0.58
Consensus pattern (21 bp):
TTCGTCAGGTGTTTTTTATAT
Found at i:8428 original size:13 final size:13
Alignment explanation
Indices: 8410--8444 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
8400 AAAAGCCTTT
8410 AAAGAAGAAAAAA
1 AAAGAAGAAAAAA
8423 AAAGAAGAAAAAA
1 AAAGAAGAAAAAA
8436 AAAGAAGAA
1 AAAGAAGAA
8445 CAGCGGGTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAGAAGAAAAAA
Found at i:8430 original size:16 final size:16
Alignment explanation
Indices: 8411--8444 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
8401 AAAGCCTTTA
8411 AAGAAGAAAAAAAAAG
1 AAGAAGAAAAAAAAAG
8427 AAGAA-AAAAAAAGAAG
1 AAGAAGAAAAAAA-AAG
8443 AA
1 AA
8445 CAGCGGGTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAGAAGAAAAAAAAAG
Done.