Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013687.1 Corchorus capsularis cultivar CVL-1 contig13708, 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: 17610
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Found at i:2588 original size:29 final size:29
Alignment explanation
Indices: 2546--2620 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
2536 ATCCTTCCTG
2546 AAATGTGGGAAAGGTGTGTTCCCAAAAAA
1 AAATGTGGGAAAGGTGTGTTCCCAAAAAA
*
2575 AAATGTGGGAAAGGTGTGTTGCCAAAAAA
1 AAATGTGGGAAAGGTGTGTTCCCAAAAAA
2604 AAATGTGGGAAAGGTGT
1 AAATGTGGGAAAGGTGT
2621 AAAATACAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.40, C:0.07, G:0.32, T:0.21
Consensus pattern (29 bp):
AAATGTGGGAAAGGTGTGTTCCCAAAAAA
Found at i:5144 original size:11 final size:11
Alignment explanation
Indices: 5108--5144 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
5098 CCATTATACT
5108 ATATCTAATTA
1 ATATCTAATTA
*
5119 ATAGCTAATTA
1 ATATCTAATTA
5130 ATATCTAATTA
1 ATATCTAATTA
5141 ATAT
1 ATAT
5145 AGTTAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (11 bp):
ATATCTAATTA
Found at i:8674 original size:2 final size:2
Alignment explanation
Indices: 8667--8698 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8657 CGGCTATCTT
8667 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
8699 ATGTTAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9685 original size:46 final size:46
Alignment explanation
Indices: 9618--9710 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
9608 AAATGGATTA
9618 CACAATAGGAGATAGTCCTCTCCTTTCCCATAATCCCACCCCGCCC
1 CACAATAGGAGATAGTCCTCTCCTTTCCCATAATCCCACCCCGCCC
* *
9664 CACAATAGGAGGTAGTCCTCTCCTTTCCCATAATCTCACCCCGCCC
1 CACAATAGGAGATAGTCCTCTCCTTTCCCATAATCCCACCCCGCCC
9710 C
1 C
9711 TTTCAGGATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.23, C:0.43, G:0.12, T:0.23
Consensus pattern (46 bp):
CACAATAGGAGATAGTCCTCTCCTTTCCCATAATCCCACCCCGCCC
Found at i:10459 original size:2 final size:2
Alignment explanation
Indices: 10437--10505 Score: 53
Period size: 2 Copynumber: 38.0 Consensus size: 2
10427 AAACCGTTTA
* *
10437 AT AT TT AT AT AT GT -T AT -T AT AT AT AT A- AT AT -T AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
10474 AT AT A- AA AT AT AT AT A- AA 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
10506 TAATTTCGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
1 7 0.13
2 48 0.87
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10472 original size:17 final size:18
Alignment explanation
Indices: 10451--10507 Score: 73
Period size: 17 Copynumber: 3.3 Consensus size: 18
10441 TTATATATGT
10451 TATTATATATATAATAT-
1 TATTATATATATAATATA
*
10468 TATTATATATAAAATATA
1 TATTATATATATAATATA
* *
10486 TATAAAATATAT-ATATA
1 TATTATATATATAATATA
10503 TATTA
1 TATTA
10508 ATTTCGAATC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
17 25 0.74
18 9 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTATATATATAATATA
Found at i:10485 original size:11 final size:11
Alignment explanation
Indices: 10471--10500 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
10461 ATAATATTAT
10471 TATATATAAAA
1 TATATATAAAA
10482 TATATATAAAA
1 TATATATAAAA
10493 TATATATA
1 TATATATA
10501 TATATTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TATATATAAAA
Found at i:17562 original size:2 final size:2
Alignment explanation
Indices: 17555--17586 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17545 AAAAAGAAAG
17555 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
17587 AAGCAAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.