Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014993.1 Corchorus capsularis cultivar CVL-1 contig15014, 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: 48691
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:967 original size:11 final size:11
Alignment explanation
Indices: 930--973 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
920 CCTATATATA
*
930 AAATAAATTAT
1 AAATTAATTAT
941 CAAA-TAATTAT
1 -AAATTAATTAT
952 AAATTAATTAT
1 AAATTAATTAT
*
963 AAATTTATTAT
1 AAATTAATTAT
974 GAATATACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 3 0.10
11 23 0.79
12 3 0.10
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:10165 original size:26 final size:26
Alignment explanation
Indices: 10148--10200 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
10138 TATTATCATT
10148 TTGAAAGTGGTACATATATATATATA
1 TTGAAAGTGGTACATATATATATATA
*
10174 TTGAAAGTGGTACATATATATACATA
1 TTGAAAGTGGTACATATATATATATA
10200 T
1 T
10201 ATATATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (26 bp):
TTGAAAGTGGTACATATATATATATA
Found at i:10192 original size:2 final size:2
Alignment explanation
Indices: 10187--10220 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
10177 AAAGTGGTAC
*
10187 AT AT AT AT AC 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
10221 GTGTTAGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16409 original size:2 final size:2
Alignment explanation
Indices: 16402--16426 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16392 AAATACATTG
16402 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 A
16427 ATTATGTTTG
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:37696 original size:30 final size:29
Alignment explanation
Indices: 37662--37725 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
37652 GAAGAGTGGA
*
37662 AAAAGCAGAACGAAGAGGATTTAGAGAGG
1 AAAAGAAGAACGAAGAGGATTTAGAGAGG
** * *
37691 CAAAAGAAGAGGGAAGAGTATTTGGAGAGG
1 -AAAAGAAGAACGAAGAGGATTTAGAGAGG
37721 AAAAG
1 AAAAG
37726 GAAAGAATGG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 5 0.17
30 24 0.83
ACGTcount: A:0.48, C:0.05, G:0.36, T:0.11
Consensus pattern (29 bp):
AAAAGAAGAACGAAGAGGATTTAGAGAGG
Found at i:43443 original size:38 final size:38
Alignment explanation
Indices: 43392--43464 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
43382 TAAGGTCCGC
*
43392 ATAATTGAGGTATTTTGCAAAATCGAACTTGAATTTTT
1 ATAATTGAGGTATTTTGCAAAATCAAACTTGAATTTTT
43430 ATAATTGAGGTATTTTGCAAAATCAAACTTGAATT
1 ATAATTGAGGTATTTTGCAAAATCAAACTTGAATT
43465 AAAAAAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (38 bp):
ATAATTGAGGTATTTTGCAAAATCAAACTTGAATTTTT
Found at i:43526 original size:96 final size:94
Alignment explanation
Indices: 43334--43522 Score: 299
Period size: 93 Copynumber: 2.0 Consensus size: 94
43324 ATAGGTCCGC
43334 ATAATTGAGGTATTTTACAAAATCAAACTTGAATTAAAAAAAAAAAATTAAGGTCCGCATAATTG
1 ATAATTGAGGTATTTTACAAAATCAAACTTGAATT--AAAAAAAAAATTAAGGTCCGCATAATTG
* * *
43399 AGGTATTTTGCAAAATCGAACTTGAATTTTT
64 AAGTATTTTGCAAAATCAAAATTGAATTTTT
* *
43430 ATAATTGAGGTATTTTGCAAAATCAAACTTGAATT-AAAAAAAAATTAAGGTCGGCATAATTGAA
1 ATAATTGAGGTATTTTACAAAATCAAACTTGAATTAAAAAAAAAATTAAGGTCCGCATAATTGAA
*
43494 GTATTTTGCAAAATCAAAATTGATTTTTT
66 GTATTTTGCAAAATCAAAATTGAATTTTT
43523 TTTAAAGTTT
Statistics
Matches: 87, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
93 53 0.61
96 34 0.39
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.34
Consensus pattern (94 bp):
ATAATTGAGGTATTTTACAAAATCAAACTTGAATTAAAAAAAAAATTAAGGTCCGCATAATTGAA
GTATTTTGCAAAATCAAAATTGAATTTTT
Found at i:48659 original size:2 final size:2
Alignment explanation
Indices: 48652--48691 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
48642 GTTATTATCT
48652 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.