Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011392.1 Corchorus capsularis cultivar CVL-1 contig11413, 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: 9557
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Found at i:749 original size:38 final size:38
Alignment explanation
Indices: 717--941 Score: 264
Period size: 38 Copynumber: 6.0 Consensus size: 38
707 AATTAAGGAC
* *
717 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGC
1 CAAAGTAAGAGTAATCAGTAAAATTGATAATTAAGAGT
755 CAAAGTAAGAGTAATCAGTAAAATTGATAATTAAGAGT
1 CAAAGTAAGAGTAATCAGTAAAATTGATAATTAAGAGT
*
793 CAAAGTAAGAGTAATCAGTAAAGTTGATAATTAAGAGT
1 CAAAGTAAGAGTAATCAGTAAAATTGATAATTAAGAGT
* * *
831 CAAAGTAAGAATAATCAGTAAAATTGATAATCAAGGGT
1 CAAAGTAAGAGTAATCAGTAAAATTGATAATTAAGAGT
* * *
869 CAAGGTAAAAATAGTAATCAGT-AAA-TCAGTAATTAAGAGT
1 CAAAGT---AAGAGTAATCAGTAAAATTGA-TAATTAAGAGT
* * *
909 C-AAG--GGATTAATCAGT-AAATTGATACTTAAGAG
1 CAAAGTAAGAGTAATCAGTAAAATTGATAATTAAGAG
942 AGAGAGTAAA
Statistics
Matches: 163, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
34 21 0.13
35 2 0.01
38 112 0.69
39 4 0.02
40 13 0.08
41 11 0.07
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.26
Consensus pattern (38 bp):
CAAAGTAAGAGTAATCAGTAAAATTGATAATTAAGAGT
Found at i:960 original size:114 final size:113
Alignment explanation
Indices: 707--965 Score: 269
Period size: 114 Copynumber: 2.3 Consensus size: 113
697 ACCTTAATAA
* *
707 AATTAAG-GACCAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGCCAAAGTAAGAGTAATC
1 AATTAAGAGA-CAAAGTAAGAGTAATCAGTAAAATTGATAATCAAGAGCCAAAGTAAGAGTAATC
*
771 AGTAAAATTGATAATTAAGAGTCAAAGTAAGAGTAATCAGTAAAGTTGAT
65 AGTAAAATAGATAATTAAGAGTCAAAG-AAGAGTAATCAGTAAAGTTGAT
* * * * * *
821 AATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATCAAGGGTCAAGGTAAAAATAGTAA
1 AATTAAGAGACAAAGTAAGAGTAATCAGTAAAATTGATAATCAAGAGCCAAAGT---AAGAGTAA
* *
886 TCAGT-AAATCAG-TAATTAAGAGTC-AAG-GGATTAATCAGTAAA-TTGAT
63 TCAGTAAAAT-AGATAATTAAGAGTCAAAGAAGAGTAATCAGTAAAGTTGAT
* * * *
933 ACTTAAGAGAGAGAGTAAAAGAGTAATCGGTAA
1 AATTAAGAGACAAAGT--AAGAGTAATCAGTAA
966 TTAAGAAAGG
Statistics
Matches: 121, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
112 17 0.14
113 13 0.11
114 58 0.48
115 4 0.03
116 16 0.13
117 13 0.11
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.25
Consensus pattern (113 bp):
AATTAAGAGACAAAGTAAGAGTAATCAGTAAAATTGATAATCAAGAGCCAAAGTAAGAGTAATCA
GTAAAATAGATAATTAAGAGTCAAAGAAGAGTAATCAGTAAAGTTGAT
Found at i:1030 original size:33 final size:32
Alignment explanation
Indices: 949--1035 Score: 129
Period size: 32 Copynumber: 2.7 Consensus size: 32
939 GAGAGAGAGT
* *
949 AAAAGAGTAATCGGTAATTAAGAAAGGAAGTA
1 AAAAGACTAATCAGTAATTAAGAAAGGAAGTA
*
981 AAAAGATTAATCAGTAATTAAGAAAGGAAGTA
1 AAAAGACTAATCAGTAATTAAGAAAGGAAGTA
1013 AAAAGGACTAATCAGTAAATTAA
1 AAAA-GACTAATCAGT-AATTAA
1036 TAATTAAGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 34 0.68
33 10 0.20
34 6 0.12
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.21
Consensus pattern (32 bp):
AAAAGACTAATCAGTAATTAAGAAAGGAAGTA
Found at i:1274 original size:14 final size:14
Alignment explanation
Indices: 1257--1292 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1247 GTAAAAAGCT
1257 AAGAGTAATCAGTA
1 AAGAGTAATCAGTA
1271 AAGAGTAATCAGTA
1 AAGAGTAATCAGTA
*
1285 AAAAGTAA
1 AAGAGTAA
1293 AAAATGGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.19
Consensus pattern (14 bp):
AAGAGTAATCAGTA
Found at i:1421 original size:26 final size:25
Alignment explanation
Indices: 1383--1440 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
1373 CAAGTGAAAT
* *
1383 ATGGTATTGAGTACGAA-GGTCAAAAA
1 ATGGTATTAAGTA-AAAGGGTC-AAAA
*
1409 ATGGTGTTAAGTAAAAGGGTCAAAA
1 ATGGTATTAAGTAAAAGGGTCAAAA
1434 ATGGTAT
1 ATGGTAT
1441 CCATAAGAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 12 0.44
26 15 0.56
ACGTcount: A:0.41, C:0.05, G:0.28, T:0.26
Consensus pattern (25 bp):
ATGGTATTAAGTAAAAGGGTCAAAA
Found at i:1509 original size:15 final size:15
Alignment explanation
Indices: 1489--1518 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1479 AAAGAGTAAG
*
1489 AAAAATGGTAAAAGT
1 AAAAATGATAAAAGT
1504 AAAAATGATAAAAGT
1 AAAAATGATAAAAGT
1519 GGCAAAAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (15 bp):
AAAAATGATAAAAGT
Found at i:1525 original size:24 final size:24
Alignment explanation
Indices: 1489--1534 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1479 AAAGAGTAAG
*
1489 AAAAATGGTAAAAGTAAAAATGAT
1 AAAAATGGCAAAAGTAAAAATGAT
*
1513 AAAAGTGGCAAAAGTAAAAATG
1 AAAAATGGCAAAAGTAAAAATG
1535 GTAATCAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.61, C:0.02, G:0.20, T:0.17
Consensus pattern (24 bp):
AAAAATGGCAAAAGTAAAAATGAT
Done.