Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007415.1 Corchorus capsularis cultivar CVL-1 contig07436, 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: 7452
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Found at i:178 original size:37 final size:37
Alignment explanation
Indices: 123--215 Score: 125
Period size: 37 Copynumber: 2.5 Consensus size: 37
113 TTTTGCTTTC
123 TGTTTCCAACGTCCTATTTAATTTTGAC-TTTTACCTT
1 TGTTTCCAACGTCCTATTTAATTTTG-CTTTTTACCTT
** **
160 TGTTTCCAACGTTGTATTTAATTTTGCTTTTTGTCTT
1 TGTTTCCAACGTCCTATTTAATTTTGCTTTTTACCTT
*
197 TGTCTCCAACGTCCTATTT
1 TGTTTCCAACGTCCTATTT
216 GGGTTTAGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 1 0.02
37 47 0.98
ACGTcount: A:0.16, C:0.20, G:0.11, T:0.53
Consensus pattern (37 bp):
TGTTTCCAACGTCCTATTTAATTTTGCTTTTTACCTT
Found at i:863 original size:6 final size:6
Alignment explanation
Indices: 852--889 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
842 AAAAGTTTAA
*
852 ATCTAT ATCTAT ATCTAT ATTTATT ATCTAT A-CTAT AT
1 ATCTAT ATCTAT ATCTAT ATCTA-T ATCTAT ATCTAT AT
890 ATAAAAGTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 5 0.18
6 18 0.64
7 5 0.18
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.53
Consensus pattern (6 bp):
ATCTAT
Found at i:957 original size:30 final size:31
Alignment explanation
Indices: 916--985 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
906 GTGGAAACTT
* *
916 TATATTTTCCGATTGTA-CCCTTTTGTTTAAA
1 TATA-TTTCCGATTGTACCCCTTTTCTTAAAA
947 TATATTTCCGATTGTACCCCTTTTCTTAAAA
1 TATATTTCCGATTGTACCCCTTTTCTTAAAA
*
978 CATATTTC
1 TATATTTC
986 TAAATTGCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 12 0.34
31 23 0.66
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.49
Consensus pattern (31 bp):
TATATTTCCGATTGTACCCCTTTTCTTAAAA
Found at i:1162 original size:37 final size:37
Alignment explanation
Indices: 1107--1199 Score: 125
Period size: 37 Copynumber: 2.5 Consensus size: 37
1097 TTTTGCTTTC
1107 TGTTTCCAACGTCCTATTTAATTTTGAC-TTTTACCTT
1 TGTTTCCAACGTCCTATTTAATTTTG-CTTTTTACCTT
** **
1144 TGTTTCCAACGTTGTATTTAATTTTGCTTTTTGTCTT
1 TGTTTCCAACGTCCTATTTAATTTTGCTTTTTACCTT
*
1181 TGTCTCCAACGTCCTATTT
1 TGTTTCCAACGTCCTATTT
1200 GGGTTTAGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 1 0.02
37 47 0.98
ACGTcount: A:0.16, C:0.20, G:0.11, T:0.53
Consensus pattern (37 bp):
TGTTTCCAACGTCCTATTTAATTTTGCTTTTTACCTT
Found at i:3748 original size:33 final size:33
Alignment explanation
Indices: 3706--3855 Score: 230
Period size: 33 Copynumber: 4.5 Consensus size: 33
3696 TTTCAATGCC
3706 ATCAACCAAAACAGAATTATTTGCAATGTTATG
1 ATCAACCAAAACAGAATTATTTGCAATGTTATG
3739 ATCAACCAAAACATG-ATTATTTGCAATGTTATG
1 ATCAACCAAAACA-GAATTATTTGCAATGTTATG
*
3772 ATCAACCAAAACAGGATTATTTGCAATGTTATG
1 ATCAACCAAAACAGAATTATTTGCAATGTTATG
* ** *
3805 ATCAACCAAAACAAAATTATTTTTAATGCTATG
1 ATCAACCAAAACAGAATTATTTGCAATGTTATG
*
3838 TTCAACCAAAACAGAATT
1 ATCAACCAAAACAGAATT
3856 GTTTTCATCA
Statistics
Matches: 108, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
32 1 0.01
33 106 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.31
Consensus pattern (33 bp):
ATCAACCAAAACAGAATTATTTGCAATGTTATG
Found at i:5392 original size:10 final size:10
Alignment explanation
Indices: 5377--5412 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
5367 TTCAGGTCGA
5377 ATTTTTTTTT
1 ATTTTTTTTT
*
5387 ATTTTTTTTG
1 ATTTTTTTTT
*
5397 ATTTTTTTAT
1 ATTTTTTTTT
5407 ATTTTT
1 ATTTTT
5413 AGATATGACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:7396 original size:31 final size:31
Alignment explanation
Indices: 7337--7398 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
7327 AGTTTTGTAA
* * *
7337 AACTTTTTAAACGCCTATTGTACCTTTATTT
1 AACTTTTGAAACGCCTATTATACATTTATTT
*
7368 AACTTTTGAAACGCCTATTATATATTTATTT
1 AACTTTTGAAACGCCTATTATACATTTATTT
7399 GTCTAACATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.48
Consensus pattern (31 bp):
AACTTTTGAAACGCCTATTATACATTTATTT
Done.