Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010261.1 Corchorus capsularis cultivar CVL-1 contig10282, 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: 28484
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2552 original size:16 final size:16
Alignment explanation
Indices: 2526--2578 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
2516 TGTCAACTTT
2526 TTTTATTAAAAAAATAA
1 TTTT-TTAAAAAAATAA
* *
2543 TTTTTTAAAAATAT-G
1 TTTTTTAAAAAAATAA
2558 TTTTTTGAAAAAAATATA
1 TTTTTT-AAAAAAATA-A
2576 TTT
1 TTT
2579 ATTGTTTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
15 6 0.21
16 16 0.55
17 4 0.14
18 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (16 bp):
TTTTTTAAAAAAATAA
Found at i:2883 original size:16 final size:17
Alignment explanation
Indices: 2839--2884 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
2829 TTTTTTTCAG
*
2839 TTTTTTAAAAAAAATTA
1 TTTTTTAATAAAAATTA
2856 TTTTTT--TGAAAAA-TA
1 TTTTTTAAT-AAAAATTA
2871 TTTTTTAATAAAAA
1 TTTTTTAATAAAAA
2885 AGTGACGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 8 0.32
16 10 0.40
17 7 0.28
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
TTTTTTAATAAAAATTA
Found at i:11733 original size:38 final size:38
Alignment explanation
Indices: 11682--11755 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
11672 AACCTCCAAT
11682 GTATCCAGTAATTACATTGGGCCTCCGATTATTCTGAA
1 GTATCCAGTAATTACATTGGGCCTCCGATTATTCTGAA
*
11720 GTATCCAGTAATTACATTGGGTCTCCGATTATTCTG
1 GTATCCAGTAATTACATTGGGCCTCCGATTATTCTG
11756 GAATCGAGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.36
Consensus pattern (38 bp):
GTATCCAGTAATTACATTGGGCCTCCGATTATTCTGAA
Found at i:12225 original size:201 final size:204
Alignment explanation
Indices: 11859--12225 Score: 519
Period size: 201 Copynumber: 1.8 Consensus size: 204
11849 CTTTAGAATT
*
11859 ATTATACAATACACTATCAATGGAGTTTAACATACTACACATGCTGAGGTTAACGGTTGACATGT
1 ATTATACAATACACTATCAATGGAGTTTAACAGACTACACATGCTGAGGTTAACGGTTGACATGT
* *
11924 GTCTTTTAGGAAATATAGTATTGAATTTTAAAAATAAAATTAATTCAGAAAATGGGTATGTGTCA
66 GTCTTTTAGGAAATATA-TATTGAATTCTAAAAACAAAATTAATTCAGAAAATGGGTATGTGTCA
* * *
11989 ATTCCTCACCCCGCTTGTGGAATCCAAATTTTACACTATCAATGTATCAAATAATTATCCTTTAC
130 ACTCCTCACCCCGCTTATGGAATCCAAAATTTACACTATCAATGTATCAAATAATTATCCTTTAC
12054 TTTATGGAAA
195 TTTATGGAAA
* * * * * *
12064 ATTATACAATACATTGTTAGTGGAGTTTAGCAGACTACACATGC-GAGGCTTAA-GGTTGATATG
1 ATTATACAATACACTATCAATGGAGTTTAACAGACTACACATGCTGAGG-TTAACGGTTGACATG
* *
12127 TGTCTTTTAGGGAATAT-T-TTTAATTCTAAAAACAAAATTAATTCAGAAAATGGGTATGTGTCA
65 TGTCTTTTAGGAAATATATATTGAATTCTAAAAACAAAATTAATTCAGAAAATGGGTATGTGTCA
* **
12190 ACTCCTCTCCTTGCTTAT-GAAGTCCAAAATTTACAC
130 ACTCCTCACCCCGCTTATGGAA-TCCAAAATTTACAC
12226 CGTCAATTCC
Statistics
Matches: 143, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
200 3 0.02
201 68 0.48
202 1 0.01
204 29 0.20
205 42 0.29
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (204 bp):
ATTATACAATACACTATCAATGGAGTTTAACAGACTACACATGCTGAGGTTAACGGTTGACATGT
GTCTTTTAGGAAATATATATTGAATTCTAAAAACAAAATTAATTCAGAAAATGGGTATGTGTCAA
CTCCTCACCCCGCTTATGGAATCCAAAATTTACACTATCAATGTATCAAATAATTATCCTTTACT
TTATGGAAA
Found at i:12780 original size:18 final size:17
Alignment explanation
Indices: 12753--12786 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
12743 TATATGCATG
12753 TATATTATATTTATATT
1 TATATTATATTTATATT
12770 TATATTTATATTTATAT
1 TATA-TTATATTTATAT
12787 AATCAATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATATTATATTTATATT
Found at i:17037 original size:23 final size:24
Alignment explanation
Indices: 17002--17052 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
16992 AAATTTTTTG
17002 TTTTCATTATTTA-AGAAAAAT-CT
1 TTTTCATTATTTAGA-AAAAATACT
* *
17025 TTTTTATTTTTTAGAAAAAATACT
1 TTTTCATTATTTAGAAAAAATACT
17049 TTTT
1 TTTT
17053 ATAAACTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (24 bp):
TTTTCATTATTTAGAAAAAATACT
Found at i:17184 original size:26 final size:26
Alignment explanation
Indices: 17148--17200 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
17138 TAAATCAACT
*
17148 ATGAGCAATATGAAAGTTGAAGAACA
1 ATGAACAATATGAAAGTTGAAGAACA
17174 ATGAACAATATGAAAGTTGAAGAACA
1 ATGAACAATATGAAAGTTGAAGAACA
17200 A
1 A
17201 ATACAATCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.53, C:0.08, G:0.21, T:0.19
Consensus pattern (26 bp):
ATGAACAATATGAAAGTTGAAGAACA
Found at i:27235 original size:11 final size:11
Alignment explanation
Indices: 27219--27251 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
27209 ATTAATATTT
27219 TAATTTTCTTA
1 TAATTTTCTTA
27230 TAATTTTCTTA
1 TAATTTTCTTA
27241 TAATTTTCTTA
1 TAATTTTCTTA
27252 ACACTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (11 bp):
TAATTTTCTTA
Done.