Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007324.1 Corchorus capsularis cultivar CVL-1 contig07345, 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: 25997
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:1395 original size:70 final size:67
Alignment explanation
Indices: 1282--1417 Score: 202
Period size: 70 Copynumber: 2.0 Consensus size: 67
1272 AACAACTAAG
* * *
1282 GAAAAAAATGGTGGAAGCATCATTAATTACATCTCAATGCTAAAATTAGCACATATAAAGACAAT
1 GAAAAAAATGGTAGAAACACCATTAATTACATCTCAATGCTAAAATT---ACATATAAAGACAAT
1347 GCATA
63 GCATA
1352 GAAAAAAATGGTAGAAACACCATTAATTACATC-CAAATGCTAAAATTACATATAAAGACAATGC
1 GAAAAAAATGGTAGAAACACCATTAATTACATCTC-AATGCTAAAATTACATATAAAGACAATGC
1416 AT
65 AT
1418 TTCAAGTAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
67 19 0.31
69 1 0.02
70 42 0.68
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.24
Consensus pattern (67 bp):
GAAAAAAATGGTAGAAACACCATTAATTACATCTCAATGCTAAAATTACATATAAAGACAATGCA
TA
Found at i:1543 original size:17 final size:17
Alignment explanation
Indices: 1485--1543 Score: 84
Period size: 17 Copynumber: 3.5 Consensus size: 17
1475 ATCACCCCTC
*
1485 AGATTACTAGTGAT-CTA
1 AGATCACTAGTGATGC-A
*
1502 AGATCACCAGTGATGCA
1 AGATCACTAGTGATGCA
1519 AGATCACTAGTGATGCA
1 AGATCACTAGTGATGCA
1536 AGATCACT
1 AGATCACT
1544 GATAATCTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
17 37 0.97
18 1 0.03
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (17 bp):
AGATCACTAGTGATGCA
Found at i:4431 original size:18 final size:18
Alignment explanation
Indices: 4408--4442 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4398 AAAATAAGTA
*
4408 TTTGGTTGCATATATCTT
1 TTTGGTTACATATATCTT
*
4426 TTTGGTTACATGTATCT
1 TTTGGTTACATATATCT
4443 GGTCCAATAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.54
Consensus pattern (18 bp):
TTTGGTTACATATATCTT
Found at i:7229 original size:20 final size:20
Alignment explanation
Indices: 7204--7243 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
7194 GAGTTTTTTT
* *
7204 TTTTTTTGCTTGTTTGTTTG
1 TTTTTTAGCTTGTTAGTTTG
*
7224 TTTTTTAGTTTGTTAGTTTG
1 TTTTTTAGCTTGTTAGTTTG
7244 CTTGCTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.03, G:0.20, T:0.72
Consensus pattern (20 bp):
TTTTTTAGCTTGTTAGTTTG
Found at i:19920 original size:30 final size:30
Alignment explanation
Indices: 19882--19945 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
19872 ACTTTATGTT
* *
19882 TTTCGATTGTA-CTTTTTTTTTAAAACATA
1 TTTCGATTGTACCCTTTTTTATAAAACATA
*
19911 TTTCAGATTGTACCCTTTTTTATAAAATATA
1 TTTC-GATTGTACCCTTTTTTATAAAACATA
19942 TTTC
1 TTTC
19946 TAAATTGTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 4 0.13
30 7 0.23
31 19 0.63
ACGTcount: A:0.28, C:0.12, G:0.06, T:0.53
Consensus pattern (30 bp):
TTTCGATTGTACCCTTTTTTATAAAACATA
Found at i:20112 original size:37 final size:37
Alignment explanation
Indices: 20070--20160 Score: 119
Period size: 37 Copynumber: 2.5 Consensus size: 37
20060 TTGTTTTTTG
*
20070 TTTCCAACGTGCTATTTAATTTTGGCTTTTGTCTTTA
1 TTTCCAACGTCCTATTTAATTTTGGCTTTTGTCTTTA
** ** *
20107 TTTCCAACGTTTTATTTAATTTTGTTTTTTGTCTTTG
1 TTTCCAACGTCCTATTTAATTTTGGCTTTTGTCTTTA
*
20144 TCTCCAACGTCCTATTT
1 TTTCCAACGTCCTATTT
20161 GGGCTTAGAT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.15, C:0.18, G:0.11, T:0.56
Consensus pattern (37 bp):
TTTCCAACGTCCTATTTAATTTTGGCTTTTGTCTTTA
Found at i:21387 original size:7 final size:7
Alignment explanation
Indices: 21356--21385 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
21346 AAGAAAGAAA
21356 TTTGTTT
1 TTTGTTT
21363 TTTGTTT
1 TTTGTTT
21370 TTTGTTT
1 TTTGTTT
21377 TTT-TTT
1 TTTGTTT
21383 TTT
1 TTT
21386 TTGGACGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (7 bp):
TTTGTTT
Found at i:22971 original size:20 final size:21
Alignment explanation
Indices: 22938--22981 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
22928 TTTGCCATCA
22938 TTTTGGGCTTTAAACTTGGGC
1 TTTTGGGCTTTAAACTTGGGC
22959 TTTTGGG-TTTAAACTTGGGC
1 TTTTGGGCTTTAAACTTGGGC
22979 TTT
1 TTT
22982 GCGTAGTAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.14, C:0.11, G:0.27, T:0.48
Consensus pattern (21 bp):
TTTTGGGCTTTAAACTTGGGC
Found at i:23172 original size:12 final size:12
Alignment explanation
Indices: 23155--23180 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
23145 GAATGTCATC
23155 TTCATTTATCCA
1 TTCATTTATCCA
23167 TTCATTTATCCA
1 TTCATTTATCCA
23179 TT
1 TT
23181 TACATCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (12 bp):
TTCATTTATCCA
Found at i:25965 original size:48 final size:48
Alignment explanation
Indices: 25884--25997 Score: 142
Period size: 48 Copynumber: 2.4 Consensus size: 48
25874 TTTCACTTGC
25884 TTTTTCCTAAAACGCCCTTCCCGGATGGAAGGCACTAATCTCTACCTG
1 TTTTTCCTAAAACGCCCTTCCCGGATGGAAGGCACTAATCTCTACCTG
* * * * * *
25932 TTTTT-CTCAAAATGCCCTTCCCGGACT-GCAGGCATTTATTTTTACCTG
1 TTTTTCCT-AAAACGCCCTTCCCGGA-TGGAAGGCACTAATCTCTACCTG
25980 TTTTTCCTAAAACGCCCT
1 TTTTTCCTAAAACGCCCT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
47 2 0.04
48 51 0.91
49 3 0.05
ACGTcount: A:0.21, C:0.30, G:0.14, T:0.35
Consensus pattern (48 bp):
TTTTTCCTAAAACGCCCTTCCCGGATGGAAGGCACTAATCTCTACCTG
Done.