Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012331.1 Corchorus capsularis cultivar CVL-1 contig12352, 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: 17610
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.29
Found at i:689 original size:2 final size:2
Alignment explanation
Indices: 684--708 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
674 TACCAAAAAA
684 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
709 AATATTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5062 original size:2 final size:2
Alignment explanation
Indices: 5055--5080 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5045 CTCAGCACAT
5055 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5081 AGAGACTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5819 original size:5 final size:5
Alignment explanation
Indices: 5803--5852 Score: 59
Period size: 5 Copynumber: 10.2 Consensus size: 5
5793 AGTTCTTTTA
* *
5803 AAAAG -AAA- AAAAG AAAAA AAAAG AAGAAA AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG
5852 A
1 A
5853 GAGAACAAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
4 6 0.16
5 28 0.74
6 4 0.11
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:5825 original size:18 final size:19
Alignment explanation
Indices: 5802--5850 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
5792 GAGTTCTTTT
5802 AAAAAGAAAAAAAGAAAAAA
1 AAAAAGAAAAAAAG-AAAAA
5822 AAAGAAGAAAAAAAG-AAAA
1 AAA-AAGAAAAAAAGAAAAA
*
5841 GAAAAGAAAA
1 AAAAAGAAAA
5851 GAGAGAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 7 0.26
19 6 0.22
20 3 0.11
21 11 0.41
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAAAAGAAAAA
Found at i:5831 original size:21 final size:21
Alignment explanation
Indices: 5805--5848 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
5795 TTCTTTTAAA
5805 AAGAAAAAAAGAAAAAAAAAG
1 AAGAAAAAAAGAAAAAAAAAG
*
5826 AAGAAAAAAAGAAAAGAAAAG
1 AAGAAAAAAAGAAAAAAAAAG
5847 AA
1 AA
5849 AAGAGAGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (21 bp):
AAGAAAAAAAGAAAAAAAAAG
Found at i:5840 original size:26 final size:28
Alignment explanation
Indices: 5803--5857 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
5793 AGTTCTTTTA
5803 AAAAGAAAAAAAGAAAAAAAAAGA-AGA
1 AAAAGAAAAAAAGAAAAAAAAAGAGAGA
* *
5830 AAAA-AAGAAAAGAAAAGAAAAGAGAGA
1 AAAAGAAAAAAAGAAAAAAAAAGAGAGA
5857 A
1 A
5858 CAAGTAGTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (28 bp):
AAAAGAAAAAAAGAAAAAAAAAGAGAGA
Found at i:5852 original size:10 final size:10
Alignment explanation
Indices: 5808--5850 Score: 68
Period size: 10 Copynumber: 4.2 Consensus size: 10
5798 TTTTAAAAAG
5808 AAAAAAAGAA
1 AAAAAAAGAA
5818 AAAAAAAGAA
1 AAAAAAAGAA
5828 GAAAAAAAGAA
1 -AAAAAAAGAA
*
5839 AAGAAAAGAA
1 AAAAAAAGAA
5849 AA
1 AA
5851 GAGAGAACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 21 0.68
11 10 0.32
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:6255 original size:28 final size:28
Alignment explanation
Indices: 6184--6266 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 28
6174 TAGCCAAAGA
* * *
6184 TGCCGCAGCAACCCAAAAATTGC-AAAAT
1 TGCCGCAACTACCC-AAAATTACAAAAAT
* *
6212 TGCCGCGAGTACCCAAAATT-CAAAAATT
1 TGCCGCAACTACCCAAAATTACAAAAA-T
*
6240 TGCCGCAACTAGCCAAAATTACAAAAA
1 TGCCGCAACTACCCAAAATTACAAAAA
6267 CCCCGTAACT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.02
27 10 0.22
28 28 0.62
29 6 0.13
ACGTcount: A:0.43, C:0.27, G:0.13, T:0.17
Consensus pattern (28 bp):
TGCCGCAACTACCCAAAATTACAAAAAT
Found at i:6331 original size:46 final size:46
Alignment explanation
Indices: 6234--6324 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 46
6224 CCAAAATTCA
* *
6234 AAAATTTGCCGCAACTAGCCAAAATTACAAAAACCCCGTAACTAGCT
1 AAAA-TTGCCGCAACTAGCCAAAATTACAAAAACCCCGCAACAAGCT
* * * **
6281 AAAATTGTCGCAACTAGCCAAAATTGCAAGAATTCCGCAACAAG
1 AAAATTGCCGCAACTAGCCAAAATTACAAAAACCCCGCAACAAG
6325 ACAAAATCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
46 33 0.89
47 4 0.11
ACGTcount: A:0.43, C:0.25, G:0.13, T:0.19
Consensus pattern (46 bp):
AAAATTGCCGCAACTAGCCAAAATTACAAAAACCCCGCAACAAGCT
Found at i:13214 original size:3 final size:3
Alignment explanation
Indices: 13206--13241 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
13196 ATATATATAT
13206 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
13242 TCTTAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.