Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000163.1 Corchorus capsularis cultivar CVL-1 contig00163, 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: 1840
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Found at i:446 original size:15 final size:14
Alignment explanation
Indices: 426--459 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
416 TGAGTATTTG
426 AATTTTTAATGTTTT
1 AATTTTTAAT-TTTT
441 AATTTTTAATTTTT
1 AATTTTTAATTTTT
455 AATTT
1 AATTT
460 ATACTAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (14 bp):
AATTTTTAATTTTT
Found at i:449 original size:7 final size:7
Alignment explanation
Indices: 426--459 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
416 TGAGTATTTG
426 AATTTTT
1 AATTTTT
433 AATGTTTT
1 AAT-TTTT
441 AATTTTT
1 AATTTTT
448 AATTTTT
1 AATTTTT
455 AATTT
1 AATTT
460 ATACTAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (7 bp):
AATTTTT
Found at i:1331 original size:17 final size:17
Alignment explanation
Indices: 1309--1352 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1299 GTTTCGATGG
1309 CAAATTAA-TATGTCAAA
1 CAAATTAATTA-GTCAAA
1326 CAAATTAATTAGTCAAA
1 CAAATTAATTAGTCAAA
*
1343 CAAATAAATT
1 CAAATTAATT
1353 GATAGTCTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 23 0.92
18 2 0.08
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.30
Consensus pattern (17 bp):
CAAATTAATTAGTCAAA
Found at i:1522 original size:58 final size:59
Alignment explanation
Indices: 1432--1550 Score: 204
Period size: 58 Copynumber: 2.0 Consensus size: 59
1422 TTAGAGGAGC
*
1432 TGATCTTAGTAACTCGAAATTTCAACAATAATCTCCACC-AAAAAAATCTCTACAATAA
1 TGATCTTAGTAACTCAAAATTTCAACAATAATCTCCACCAAAAAAAATCTCTACAATAA
* *
1490 TGATCTTAGTAACTCAAAATTTCTACAATAATCTTCACCAAAAAAAATCTCTACAATAA
1 TGATCTTAGTAACTCAAAATTTCAACAATAATCTCCACCAAAAAAAATCTCTACAATAA
1549 TG
1 TG
1551 GTGTATCAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
58 36 0.63
59 21 0.37
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (59 bp):
TGATCTTAGTAACTCAAAATTTCAACAATAATCTCCACCAAAAAAAATCTCTACAATAA
Found at i:1536 original size:28 final size:28
Alignment explanation
Indices: 1456--1549 Score: 84
Period size: 28 Copynumber: 3.3 Consensus size: 28
1446 CGAAATTTCA
*
1456 ACAATAATCTCCACC-AAAAAAATCTCT
1 ACAATAATCTTCACCAAAAAAAATCTCT
** ** *
1483 ACAATAATGATCTT-AGTAACTCAAAATTTCT
1 ACAAT-A--ATCTTCACCAA-AAAAAATCTCT
1514 ACAATAATCTTCACCAAAAAAAATCTCT
1 ACAATAATCTTCACCAAAAAAAATCTCT
1542 ACAATAAT
1 ACAATAAT
1550 GGTGTATCAA
Statistics
Matches: 50, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
27 5 0.10
28 22 0.44
29 4 0.08
30 6 0.12
31 13 0.26
ACGTcount: A:0.48, C:0.22, G:0.02, T:0.28
Consensus pattern (28 bp):
ACAATAATCTTCACCAAAAAAAATCTCT
Done.