Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010875.1 Corchorus capsularis cultivar CVL-1 contig10896, 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: 18651
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2179 original size:2 final size:2
Alignment explanation
Indices: 2167--2208 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2157 TTGTTTACTC
*
2167 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2209 TCTAATTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:5719 original size:15 final size:16
Alignment explanation
Indices: 5699--5729 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5689 TTTAGGTTGC
5699 GGTTTA-AAAAAGTTT
1 GGTTTAGAAAAAGTTT
5714 GGTTTAGAAAAAGTTT
1 GGTTTAGAAAAAGTTT
5730 TTTCGAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.39
Consensus pattern (16 bp):
GGTTTAGAAAAAGTTT
Found at i:8105 original size:56 final size:55
Alignment explanation
Indices: 7950--8113 Score: 173
Period size: 56 Copynumber: 3.0 Consensus size: 55
7940 ACCTAATACT
*
7950 ATTTATAACATTACTTATAAAGGGTAGTACTTGGTACCAAAACTATTTAATTAATC
1 ATTTATAACATTACTTATAAAGGGTAGTACTTGGTA-CAAAACTATTTAATTAACC
* *
8006 AGTTATAATAACATTAC-T-T--A---TA-TACTTGGTACGAAAACCATTTAATTTACC
1 A-TT-T-ATAACATTACTTATAAAGGGTAGTACTTGGTAC-AAAACTATTTAATTAACC
* *
8057 ATTTATTACATTACTTATAAAGGGTAGTACTTGGTATCAGAACTATTTAATTAACC
1 ATTTATAACATTACTTATAAAGGGTAGTACTTGGTA-CAAAACTATTTAATTAACC
8113 A
1 A
8114 CAGATATACT
Statistics
Matches: 88, Mismatches: 7, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
48 9 0.10
49 2 0.02
50 4 0.05
51 25 0.28
52 3 0.03
55 3 0.03
56 26 0.30
57 4 0.05
58 2 0.02
59 10 0.11
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (55 bp):
ATTTATAACATTACTTATAAAGGGTAGTACTTGGTACAAAACTATTTAATTAACC
Found at i:9408 original size:2 final size:2
Alignment explanation
Indices: 9396--9429 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
9386 TTATTAAAAC
*
9396 TA TA GTA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9430 CAAGTGTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:11206 original size:2 final size:2
Alignment explanation
Indices: 11199--11226 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11189 CAATAACTCG
11199 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11227 TTTGCCCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14816 original size:2 final size:2
Alignment explanation
Indices: 14809--14834 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14799 CAAAAGTAGC
14809 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
14835 TTACCAACAA
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):
AT
Found at i:15571 original size:13 final size:13
Alignment explanation
Indices: 15555--15588 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
15545 GAAAAATGAT
15555 AAAAAAAAAAGGA
1 AAAAAAAAAAGGA
*
15568 AAAAAGAAAAGGA
1 AAAAAAAAAAGGA
15581 AACAAAAA
1 AA-AAAAA
15589 GATTATATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGGA
Done.