Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004911.1 Corchorus capsularis cultivar CVL-1 contig04929, 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: 40627
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3776 original size:2 final size:2
Alignment explanation
Indices: 3769--3795 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3759 TAATTTGTAA
3769 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3796 AAGAAATACT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5410 original size:13 final size:13
Alignment explanation
Indices: 5394--5419 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5384 ACTAGCTAAA
5394 AACCCTCTTTAAG
1 AACCCTCTTTAAG
5407 AACCCTCTTTAAG
1 AACCCTCTTTAAG
5420 CTCTGACATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (13 bp):
AACCCTCTTTAAG
Found at i:8550 original size:19 final size:19
Alignment explanation
Indices: 8526--8562 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
8516 AAAAAGAATC
*
8526 TTTGTAATATATGTGTTTT
1 TTTGTAAGATATGTGTTTT
8545 TTTGTAAGATATGTGTTT
1 TTTGTAAGATATGTGTTT
8563 AGTGAACCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.59
Consensus pattern (19 bp):
TTTGTAAGATATGTGTTTT
Found at i:18138 original size:8 final size:8
Alignment explanation
Indices: 18125--18157 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
18115 TTTGAGTTGC
18125 AAAAAAAG
1 AAAAAAAG
18133 AAAAAAAG
1 AAAAAAAG
*
18141 -CAAAAAG
1 AAAAAAAG
18148 AAAAAAAG
1 AAAAAAAG
18156 AA
1 AA
18158 TAAACACTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:18147 original size:15 final size:15
Alignment explanation
Indices: 18127--18155 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
18117 TGAGTTGCAA
18127 AAAAAGAAAAAAAGC
1 AAAAAGAAAAAAAGC
18142 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
18156 AATAAACACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAGC
Found at i:25486 original size:31 final size:31
Alignment explanation
Indices: 25448--25510 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
25438 ACTCCGGAAA
25448 AATAGAAACCATGTTACTAAATTTTTTTATT
1 AATAGAAACCATGTTACTAAATTTTTTTATT
25479 AATAGAAACCATGTTACTAAATTTTTTTATT
1 AATAGAAACCATGTTACTAAATTTTTTTATT
25510 A
1 A
25511 TCTTATTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (31 bp):
AATAGAAACCATGTTACTAAATTTTTTTATT
Found at i:25937 original size:16 final size:16
Alignment explanation
Indices: 25916--25946 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25906 GGAGGTACGA
25916 ATAACATATAGATTTT
1 ATAACATATAGATTTT
*
25932 ATAACATATGGATTT
1 ATAACATATAGATTT
25947 ATTTTATATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (16 bp):
ATAACATATAGATTTT
Found at i:27893 original size:27 final size:28
Alignment explanation
Indices: 27863--27915 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
27853 GCGGTTTATT
27863 GCAATTTAAGCA-AGTC-TTAAGTTTCAA
1 GCAATTTAAGCATA-TCTTTAAGTTTCAA
27890 GCAATTTAAGCATATCTTTAAGTTTC
1 GCAATTTAAGCATATCTTTAAGTTTC
27916 GAGACCTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (28 bp):
GCAATTTAAGCATATCTTTAAGTTTCAA
Found at i:33389 original size:12 final size:12
Alignment explanation
Indices: 33368--33396 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
33358 AAGAAGTTTC
33368 TTTT-TCTTTAT
1 TTTTCTCTTTAT
33379 TTTTCTCTTTAT
1 TTTTCTCTTTAT
33391 TTTTCT
1 TTTTCT
33397 ATTGCTAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTCTCTTTAT
Found at i:40542 original size:30 final size:30
Alignment explanation
Indices: 40508--40568 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
40498 GAAGACCATG
* *
40508 AAGACGATGAACGTGAAAGAGAAGATGACA
1 AAGACAATGAACATGAAAGAGAAGATGACA
* *
40538 AAGACAATGAATATGAAGGAGAAGATGACA
1 AAGACAATGAACATGAAAGAGAAGATGACA
40568 A
1 A
40569 TGATAATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.52, C:0.08, G:0.28, T:0.11
Consensus pattern (30 bp):
AAGACAATGAACATGAAAGAGAAGATGACA
Done.