Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011388.1 Corchorus capsularis cultivar CVL-1 contig11409, 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: 3358
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.28
Found at i:550 original size:38 final size:38
Alignment explanation
Indices: 518--715 Score: 324
Period size: 38 Copynumber: 5.2 Consensus size: 38
508 AATTAAGGAC
* *
518 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGC
1 CAAAGTAAGAGTAATCAGTAAAATTGATAATTAAGAGT
*
556 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
1 CAAAGTAAGAGTAATCAGTAAAATTGATAATTAAGAGT
594 CAAAGTAAGAGTAATCAGTAAAATTGATAATTAAGAGT
1 CAAAGTAAGAGTAATCAGTAAAATTGATAATTAAGAGT
*
632 CAAAGTAAGAGTAATCAGTAAAGTTGATAATTAAGAGT
1 CAAAGTAAGAGTAATCAGTAAAATTGATAATTAAGAGT
* * *
670 CAAAGTAAGAATAATCAGTAAAATTGATAATCAAGGGT
1 CAAAGTAAGAGTAATCAGTAAAATTGATAATTAAGAGT
*
708 CAAGGTAA
1 CAAAGTAA
716 AAATAGTAAT
Statistics
Matches: 152, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 152 1.00
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (38 bp):
CAAAGTAAGAGTAATCAGTAAAATTGATAATTAAGAGT
Found at i:636 original size:76 final size:76
Alignment explanation
Indices: 518--780 Score: 331
Period size: 76 Copynumber: 3.5 Consensus size: 76
508 AATTAAGGAC
* *
518 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGA
1 CAAAGTAAGAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGA
583 TAATTAAGAGT
66 TAATTAAGAGT
* *
594 CAAAGTAAGAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAGTAATCAGTAAAGTTGA
1 CAAAGTAAGAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGA
659 TAATTAAGAGT
66 TAATTAAGAGT
* * * * *
670 CAAAGTAAGAATAATCAGTAAAATTGATAATCAAGGGTCAAGGTAAAAATAGTAATAAGT-AAA-
1 CAAAGTAAGAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGT---AATAGTAATCAGTAAAAT
*
733 TCAGTAATTAAGAGT
63 TGA-TAATTAAGAGT
* * *
748 C-AAG--GGATTAATCAGT-AAATTGATACTTAAGAG
1 CAAAGTAAGAGTAATCAGTAAAATTGATAATTAAGAG
781 AGAGAGTAAA
Statistics
Matches: 166, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
74 14 0.08
75 10 0.06
76 112 0.67
77 5 0.03
78 14 0.08
79 11 0.07
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.26
Consensus pattern (76 bp):
CAAAGTAAGAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGA
TAATTAAGAGT
Found at i:799 original size:114 final size:112
Alignment explanation
Indices: 518--799 Score: 302
Period size: 114 Copynumber: 2.5 Consensus size: 112
508 AATTAAGGAC
* * *
518 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGA
1 CAAAG-AAGAGTAATCAGT-AAATTGATAATTAAGAGACAAAGTAAGAGTAATCAGTAAAATTGA
* * *
583 TAATTAAGAGTCAAAGTAAGAGTAATCAGTAAAATTGATAATTAAGAGT
64 TAATCAAGAGTCAAAGTAAGAGTAATAAGTAAAATAGATAATTAAGAGT
* *
632 CAAAGTAAGAGTAATCAGTAAAGTTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGA
1 CAAAG-AAGAGTAATCAGTAAA-TTGATAATTAAGAGACAAAGTAAGAGTAATCAGTAAAATTGA
* * *
697 TAATCAAGGGTCAAGGTAAAAATAGTAATAAGT-AAATCAG-TAATTAAGAGT
64 TAATCAAGAGTCAAAGT---AAGAGTAATAAGTAAAAT-AGATAATTAAGAGT
* * * * *
748 C-AAG-GGATTAATCAGTAAATTGATACTTAAGAGAGAGAGTAAAAGAGTAATC
1 CAAAGAAGAGTAATCAGTAAATTGATAATTAAGAGACAAAGT--AAGAGTAATC
800 GATAATTAAG
Statistics
Matches: 144, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
112 17 0.12
113 16 0.11
114 80 0.56
115 3 0.02
116 16 0.11
117 12 0.08
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (112 bp):
CAAAGAAGAGTAATCAGTAAATTGATAATTAAGAGACAAAGTAAGAGTAATCAGTAAAATTGATA
ATCAAGAGTCAAAGTAAGAGTAATAAGTAAAATAGATAATTAAGAGT
Found at i:869 original size:33 final size:32
Alignment explanation
Indices: 788--874 Score: 122
Period size: 32 Copynumber: 2.7 Consensus size: 32
778 GAGAGAGAGT
*
788 AAAAGAGTAATC-GATAATTAAGAAAGGAAGTA
1 AAAAGACTAATCAG-TAATTAAGAAAGGAAGTA
*
820 AAAAGATTAATCAGTAATTAAGAAAGGAAGTA
1 AAAAGACTAATCAGTAATTAAGAAAGGAAGTA
852 AAAAGGACTAATCAGTAAATTAA
1 AAAA-GACTAATCAGT-AATTAA
875 TAATTAAGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
32 33 0.66
33 11 0.22
34 6 0.12
ACGTcount: A:0.56, C:0.05, G:0.18, T:0.21
Consensus pattern (32 bp):
AAAAGACTAATCAGTAATTAAGAAAGGAAGTA
Found at i:1142 original size:14 final size:14
Alignment explanation
Indices: 1121--1155 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1111 GTAAAAAGGT
1121 AAAGTAATCAGTAA
1 AAAGTAATCAGTAA
*
1135 AGAGTAATCAGTAA
1 AAAGTAATCAGTAA
1149 AAAGTAA
1 AAAGTAA
1156 AAATGGCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.57, C:0.06, G:0.17, T:0.20
Consensus pattern (14 bp):
AAAGTAATCAGTAA
Found at i:1295 original size:25 final size:26
Alignment explanation
Indices: 1245--1302 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
1235 CAAGTGAAAT
*
1245 ATGGTATTGAGTAAGAAGGTCAAAAA
1 ATGGTATTAAGTAAGAAGGTCAAAAA
*
1271 ATGGTGTTAAGTAA-AAGGGTC-AAAA
1 ATGGTATTAAGTAAGAA-GGTCAAAAA
1296 ATGGTAT
1 ATGGTAT
1303 CCATAAGAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 12 0.43
26 16 0.57
ACGTcount: A:0.43, C:0.03, G:0.28, T:0.26
Consensus pattern (26 bp):
ATGGTATTAAGTAAGAAGGTCAAAAA
Found at i:1371 original size:15 final size:15
Alignment explanation
Indices: 1351--1380 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1341 AAAGAGTAAG
*
1351 AAAAATGGTAAAAGT
1 AAAAATGATAAAAGT
1366 AAAAATGATAAAAGT
1 AAAAATGATAAAAGT
1381 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:1387 original size:24 final size:24
Alignment explanation
Indices: 1351--1396 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1341 AAAGAGTAAG
*
1351 AAAAATGGTAAAAGTAAAAATGAT
1 AAAAATGGCAAAAGTAAAAATGAT
*
1375 AAAAGTGGCAAAAGTAAAAATG
1 AAAAATGGCAAAAGTAAAAATG
1397 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.