Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009963.1 Corchorus capsularis cultivar CVL-1 contig09984, 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: 31332
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:1029 original size:32 final size:34
Alignment explanation
Indices: 982--1069 Score: 135
Period size: 34 Copynumber: 2.6 Consensus size: 34
972 GATGACCCGT
**
982 GCCGCCCCAAGAGGGCGGCTT-ACCA-TGGGCAG
1 GCCGCCCCACTAGGGCGGCTTCACCATTGGGCAG
1014 GCCGCCCCACTAGGGCGGCTTCACCATTGGGCAG
1 GCCGCCCCACTAGGGCGGCTTCACCATTGGGCAG
*
1048 GCCGCCCCACTGGGGCGGCTTC
1 GCCGCCCCACTAGGGCGGCTTC
1070 GCCACGACAG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 19 0.37
33 4 0.08
34 28 0.55
ACGTcount: A:0.14, C:0.39, G:0.35, T:0.12
Consensus pattern (34 bp):
GCCGCCCCACTAGGGCGGCTTCACCATTGGGCAG
Found at i:1341 original size:14 final size:15
Alignment explanation
Indices: 1312--1353 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
1302 GGCTCAGTGT
*
1312 AAAAGTGTAAAAAGGGT
1 AAAAGTGT--AAAGGGC
1329 AAAAGT-TAAAGGGC
1 AAAAGTGTAAAGGGC
1343 AAAAGTGTAAA
1 AAAAGTGTAAA
1354 AAGTGGGGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 12 0.52
15 4 0.17
16 1 0.04
17 6 0.26
ACGTcount: A:0.55, C:0.02, G:0.26, T:0.17
Consensus pattern (15 bp):
AAAAGTGTAAAGGGC
Found at i:1519 original size:18 final size:18
Alignment explanation
Indices: 1471--1523 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
1461 TATAAAGTAA
1471 AATTATAAATCAGAAAATAT
1 AATTATAAAT-A-AAAATAT
* *
1491 ATATAAT-AATAATAATAT
1 A-ATTATAAATAAAAATAT
1509 AATTATAAATAAAAA
1 AATTATAAATAAAAA
1524 AAAATCACCA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
17 4 0.15
18 14 0.52
19 1 0.04
20 4 0.15
21 4 0.15
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
AATTATAAATAAAAATAT
Found at i:4075 original size:15 final size:16
Alignment explanation
Indices: 4049--4078 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4039 TCTGTAACAG
4049 TAAAAGAAAAAAAATT
1 TAAAAGAAAAAAAATT
4065 TAAAA-AAAAAAAAT
1 TAAAAGAAAAAAAAT
4079 ACTATAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAAAAAATT
Found at i:4970 original size:3 final size:3
Alignment explanation
Indices: 4962--4990 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4952 TTCTGAGTTT
4962 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
4991 TTATTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:21004 original size:18 final size:18
Alignment explanation
Indices: 20964--21006 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
20954 TCCTATTGCT
20964 GTTTT-TTTTCAGATCCA
1 GTTTTGTTTTCAGATCCA
*
20981 GGTTTGTTTTCAGATCCA
1 GTTTTGTTTTCAGATCCA
*
20999 TTTTTGTT
1 GTTTTGTT
21007 CTCTCAGCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.14, C:0.14, G:0.16, T:0.56
Consensus pattern (18 bp):
GTTTTGTTTTCAGATCCA
Found at i:21180 original size:14 final size:14
Alignment explanation
Indices: 21161--21197 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
21151 AAAAGGTCAC
21161 TTTCTTTTCTTTTT
1 TTTCTTTTCTTTTT
*
21175 TTTCTTTTTTTTTT
1 TTTCTTTTCTTTTT
21189 TTTCCTTTT
1 TTT-CTTTT
21198 GTTCCCTCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTCTTTTCTTTTT
Found at i:27315 original size:26 final size:26
Alignment explanation
Indices: 27253--27317 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 26
27243 TCTGTCAACC
*
27253 AAAAAAAA-AATCTAAAACAAAAAAG
1 AAAAAAAACAAACTAAAACAAAAAAG
*
27278 TAAAAACTAACAAACTAAAACAAAAGAA-
1 -AAAAA-AAACAAACTAAAACAAAA-AAG
27306 AAAAAAAACAAA
1 AAAAAAAACAAA
27318 AAATAACAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 11 0.33
27 7 0.21
28 13 0.39
29 2 0.06
ACGTcount: A:0.78, C:0.11, G:0.03, T:0.08
Consensus pattern (26 bp):
AAAAAAAACAAACTAAAACAAAAAAG
Found at i:28714 original size:2 final size:2
Alignment explanation
Indices: 28707--28733 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28697 CCTCTACTCC
28707 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
28734 CCTATTGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.