Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009008.1 Corchorus capsularis cultivar CVL-1 contig09029, 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: 29587
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:8570 original size:2 final size:2
Alignment explanation
Indices: 8563--8601 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
8553 ACCCCTTACA
* *
8563 AT AT AT AT AT AT AT AC AT AT AC AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8602 CTAATTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:9794 original size:31 final size:29
Alignment explanation
Indices: 9759--9829 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
9749 TTGGACGGCT
* *
9759 TGCCCCTAATTGACGCCAAATTGAAATGTTG
1 TGCCCCAAATTGA--CCAAATTGAAACGTTG
*
9790 TGCCCCAAATAGACCAAATTGAAACGTTG
1 TGCCCCAAATTGACCAAATTGAAACGTTG
9819 TGCCCCAAATT
1 TGCCCCAAATT
9830 AGGCCGAGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 25 0.69
31 11 0.31
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (29 bp):
TGCCCCAAATTGACCAAATTGAAACGTTG
Found at i:12096 original size:3 final size:3
Alignment explanation
Indices: 12088--12117 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
12078 TAACCACAAC
12088 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12118 TTGCTATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:12312 original size:22 final size:22
Alignment explanation
Indices: 12274--12355 Score: 85
Period size: 22 Copynumber: 3.7 Consensus size: 22
12264 ATTATTACAC
*
12274 TATGAAATCAATGATAATCTCCA
1 TATGAAAT-TATGATAATCTCCA
*
12297 TATGAAATTATGATAATC-ACA
1 TATGAAATTATGATAATCTCCA
* * *
12318 CTATGAAATTTTGATAACCTCCT
1 -TATGAAATTATGATAATCTCCA
*
12341 TATGAAATTTTGATA
1 TATGAAATTATGATA
12356 GCATTCGTGG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
21 2 0.04
22 40 0.78
23 9 0.18
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (22 bp):
TATGAAATTATGATAATCTCCA
Found at i:12346 original size:44 final size:45
Alignment explanation
Indices: 12270--12355 Score: 120
Period size: 44 Copynumber: 1.9 Consensus size: 45
12260 AGCTATTATT
*
12270 ACACTATGAAATCAATGATAATCTCCATATGAAATTATGATAATC
1 ACACTATGAAATCAATGATAACCTCCATATGAAATTATGATAATC
** * *
12315 ACACTATGAAAT-TTTGATAACCTCCTTATGAAATTTTGATA
1 ACACTATGAAATCAATGATAACCTCCATATGAAATTATGATA
12356 GCATTCGTGG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 24 0.67
45 12 0.33
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (45 bp):
ACACTATGAAATCAATGATAACCTCCATATGAAATTATGATAATC
Found at i:16306 original size:22 final size:21
Alignment explanation
Indices: 16276--16316 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
16266 AATTCTTGCT
*
16276 TCTTGAAATAATTCTTCAATGA
1 TCTTCAAATAA-TCTTCAATGA
*
16298 TCTTCAAATTATCTTCAAT
1 TCTTCAAATAATCTTCAAT
16317 AAAGACCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.34, C:0.17, G:0.05, T:0.44
Consensus pattern (21 bp):
TCTTCAAATAATCTTCAATGA
Found at i:22908 original size:19 final size:19
Alignment explanation
Indices: 22884--22923 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
22874 GCCAACGCAC
* *
22884 GTCGGTTGCATCGGTTCCG
1 GTCGGTAGCATCGGTTACG
*
22903 GTCGGTAGCTTCGGTTACG
1 GTCGGTAGCATCGGTTACG
22922 GT
1 GT
22924 TTTTTTTCCC
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:0.07, C:0.23, G:0.38, T:0.33
Consensus pattern (19 bp):
GTCGGTAGCATCGGTTACG
Found at i:23148 original size:30 final size:31
Alignment explanation
Indices: 23110--23178 Score: 108
Period size: 30 Copynumber: 2.3 Consensus size: 31
23100 ATCATGAGGT
23110 AATC-CTAAC-TTAGCAAAATCGGTTC-AATC
1 AATCTCTAACGTT-GCAAAATCGGTTCAAATC
23139 AATCTCTAACGTTGCAAAATCGGTTCAAATC
1 AATCTCTAACGTTGCAAAATCGGTTCAAATC
23170 AATCTCTAA
1 AATCTCTAA
23179 TGTCAATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
29 4 0.11
30 18 0.49
31 15 0.41
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (31 bp):
AATCTCTAACGTTGCAAAATCGGTTCAAATC
Found at i:27346 original size:30 final size:31
Alignment explanation
Indices: 27312--27377 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 31
27302 ATGAGGTAAT
* *
27312 TCTAACTTTGCAAAATCGGCTC-AATTAGTC
1 TCTAACGTTGCAAAATCGGCTCAAATCAGTC
*
27342 TCTAACGTTGCAAAATCGGTTCAAATCAGTC
1 TCTAACGTTGCAAAATCGGCTCAAATCAGTC
27373 TCTAA
1 TCTAA
27378 TGTCAATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 20 0.62
31 12 0.38
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (31 bp):
TCTAACGTTGCAAAATCGGCTCAAATCAGTC
Found at i:27721 original size:5 final size:5
Alignment explanation
Indices: 27711--27744 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
27701 CCATAAAATT
27711 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
27745 ACTATCCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Done.