Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016144.1 Corchorus capsularis cultivar CVL-1 contig16165, 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: 48115
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:288 original size:40 final size:40
Alignment explanation
Indices: 233--317 Score: 161
Period size: 40 Copynumber: 2.1 Consensus size: 40
223 GTTACACTAC
233 GAACATGTGTGTAATGCAAAATTAACCCATTAAAATGCTT
1 GAACATGTGTGTAATGCAAAATTAACCCATTAAAATGCTT
273 GAACATGTGTGTAATGCAAAATTAACCCATTAAAATGCTT
1 GAACATGTGTGTAATGCAAAATTAACCCATTAAAATGCTT
*
313 AAACA
1 GAACA
318 AATTAAAACG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.28
Consensus pattern (40 bp):
GAACATGTGTGTAATGCAAAATTAACCCATTAAAATGCTT
Found at i:1602 original size:13 final size:13
Alignment explanation
Indices: 1584--1609 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1574 AAGATATGGA
1584 TAGATAACAAAGG
1 TAGATAACAAAGG
1597 TAGATAACAAAGG
1 TAGATAACAAAGG
1610 AACATCTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.23, T:0.15
Consensus pattern (13 bp):
TAGATAACAAAGG
Found at i:9288 original size:19 final size:18
Alignment explanation
Indices: 9264--9302 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
9254 TAAAGAATTC
*
9264 TTGAAGATAATTTGAAGAA
1 TTGAAGACAA-TTGAAGAA
*
9283 TTGAAGACCATTGAAGAA
1 TTGAAGACAATTGAAGAA
9301 TT
1 TT
9303 ATTTCAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAA
Found at i:10610 original size:20 final size:21
Alignment explanation
Indices: 10574--10621 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
10564 TAGATTTAGA
* *
10574 TTTAATTTACTTTGCTTTGTT
1 TTTAATTTACATTGCTTTCTT
10595 TTTAATTTA-ATTGCTTTCTT
1 TTTAATTTACATTGCTTTCTT
10615 TTTAATT
1 TTTAATT
10622 GATAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.67
Consensus pattern (21 bp):
TTTAATTTACATTGCTTTCTT
Found at i:14540 original size:21 final size:21
Alignment explanation
Indices: 14503--14544 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
14493 CATGTCTCGA
14503 CTAGCGCTGGGCGCCCATGTG
1 CTAGCGCTGGGCGCCCATGTG
*
14524 CTAG-GCTTGGCGCCCCATGTG
1 CTAGCGCTGGGCG-CCCATGTG
14545 GTTTGCCTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.10, C:0.33, G:0.36, T:0.21
Consensus pattern (21 bp):
CTAGCGCTGGGCGCCCATGTG
Found at i:21610 original size:17 final size:17
Alignment explanation
Indices: 21588--21623 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
21578 GGCATACAAC
21588 ACCTAGAAAGAACTAAA
1 ACCTAGAAAGAACTAAA
*
21605 ACCTAGAAAGAACTTAA
1 ACCTAGAAAGAACTAAA
21622 AC
1 AC
21624 AAAAATCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.19, G:0.11, T:0.14
Consensus pattern (17 bp):
ACCTAGAAAGAACTAAA
Found at i:26115 original size:30 final size:30
Alignment explanation
Indices: 26081--26141 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
26071 AAGACATCAA
*
26081 TGGATGGAGGAGTCGCAACAAAGATGCCAT
1 TGGATGGAGGAATCGCAACAAAGATGCCAT
*
26111 TGGATGGAGGAATCGCACCAAAGATGCCAT
1 TGGATGGAGGAATCGCAACAAAGATGCCAT
26141 T
1 T
26142 TGATCCTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.18, G:0.31, T:0.18
Consensus pattern (30 bp):
TGGATGGAGGAATCGCAACAAAGATGCCAT
Found at i:32324 original size:3 final size:3
Alignment explanation
Indices: 32311--32361 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
32301 ATTTTGGTTA
*
32311 AAG ACG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
32359 AAG
1 AAG
32362 CTCGACCTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:33300 original size:29 final size:29
Alignment explanation
Indices: 33268--33324 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
33258 TTTTGTTCAT
33268 ATCAAAAACACAAAACAATTAATTAACAC
1 ATCAAAAACACAAAACAATTAATTAACAC
* * *
33297 ATCAAAAACGCATAAGAATTAATTAACA
1 ATCAAAAACACAAAACAATTAATTAACA
33325 TATATATGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.60, C:0.18, G:0.04, T:0.19
Consensus pattern (29 bp):
ATCAAAAACACAAAACAATTAATTAACAC
Found at i:42249 original size:28 final size:28
Alignment explanation
Indices: 42209--42291 Score: 121
Period size: 28 Copynumber: 3.0 Consensus size: 28
42199 GATGCCACAA
42209 ATGAACTCCGCGATTGAGTATAAACTAC
1 ATGAACTCCGCGATTGAGTATAAACTAC
*
42237 ATGAACTCCGCGATTGAGTATACACTAC
1 ATGAACTCCGCGATTGAGTATAAACTAC
* * * *
42265 ATGAACTCTGTGATTGAGAATGAACTA
1 ATGAACTCCGCGATTGAGTATAAACTA
42292 ATATGACGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (28 bp):
ATGAACTCCGCGATTGAGTATAAACTAC
Found at i:42909 original size:26 final size:26
Alignment explanation
Indices: 42877--42927 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
42867 TTTCAAATGT
*
42877 TAAGACATTATGAAAAAGCCACGTTA
1 TAAGACATCATGAAAAAGCCACGTTA
*
42903 TAAGACATCATGAAGAAGCCACGTT
1 TAAGACATCATGAAAAAGCCACGTT
42928 TGCAAACTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.22
Consensus pattern (26 bp):
TAAGACATCATGAAAAAGCCACGTTA
Found at i:43182 original size:16 final size:17
Alignment explanation
Indices: 43137--43174 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
43127 ATTTAAAGGG
43137 TAAAAATAAGTT--AAAA
1 TAAAAATAA-TTGAAAAA
43153 TAAAAATAATTGAAAAA
1 TAAAAATAATTGAAAAA
43170 TAAAA
1 TAAAA
43175 GAAATGAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 2 0.10
16 9 0.45
17 9 0.45
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (17 bp):
TAAAAATAATTGAAAAA
Found at i:45486 original size:12 final size:11
Alignment explanation
Indices: 45469--45509 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
45459 TTCATTAACT
45469 ATAAATAATAA
1 ATAAATAATAA
45480 GATAAATAA-AA
1 -ATAAATAATAA
45491 AT-AATAATAA
1 ATAAATAATAA
45501 ATTAAATAA
1 A-TAAATAA
45510 ATTAAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 5 0.19
10 5 0.19
11 3 0.12
12 13 0.50
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (11 bp):
ATAAATAATAA
Done.