Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013587.1 Corchorus olitorius cultivar O-4 contig13620, 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: 28088
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:64 original size:15 final size:15
Alignment explanation
Indices: 32--61 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
22 TAAATTTCAA
32 TAAAATAAAATATAT
1 TAAAATAAAATATAT
47 TAAAATAAAA-ATAT
1 TAAAATAAAATATAT
61 T
1 T
62 TAATTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAATAAAATATAT
Found at i:10781 original size:2 final size:2
Alignment explanation
Indices: 10770--10808 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
10760 TAATAGTAGG
10770 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10809 TACTAGTTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:11241 original size:110 final size:109
Alignment explanation
Indices: 11049--11265 Score: 371
Period size: 110 Copynumber: 2.0 Consensus size: 109
11039 GTCATTTTGA
* * *
11049 TGCTTGTATTTTTCTTTAAGTCCAATAGTTCATTGCACTTTGTATTGTTTGATATTTGTGCTTAT
1 TGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGATATGTATGCTTAT
11114 TTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATAGG
66 TTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATAGG
* *
11158 TGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCATTTTTGTATTGTTTGGTATGTATGCTTA
1 TGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCA-CTTTGTATTGTTTGATATGTATGCTTA
*
11223 TTTAATAGGTTCAATTGAATAAACCACACAATTAATAATAATA
65 TTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
11266 TATATAATAT
Statistics
Matches: 101, Mismatches: 6, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
109 36 0.36
110 65 0.64
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (109 bp):
TGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGATATGTATGCTTAT
TTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATAGG
Found at i:13593 original size:31 final size:31
Alignment explanation
Indices: 13525--13593 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
13515 TTTGCTGTGA
* *
13525 ATACCTATTTACTCATTATAATGAAGTAACAC
1 ATACATATTTACTCATTATAA-GAACTAACAC
*
13557 ATACATATTTACTCATTATCAA-AACTAAGAC
1 ATACATATTTACTCATTAT-AAGAACTAACAC
13588 ATACAT
1 ATACAT
13594 TTTGCTGAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 13 0.39
32 18 0.55
33 2 0.06
ACGTcount: A:0.43, C:0.19, G:0.04, T:0.33
Consensus pattern (31 bp):
ATACATATTTACTCATTATAAGAACTAACAC
Found at i:14514 original size:20 final size:20
Alignment explanation
Indices: 14491--14529 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
14481 CAGATTTGGA
14491 AGAGAATCAGTGGATTTTGT
1 AGAGAATCAGTGGATTTTGT
*
14511 AGAGAATCGGTGGATTTTG
1 AGAGAATCAGTGGATTTTG
14530 GAATGAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.05, G:0.33, T:0.33
Consensus pattern (20 bp):
AGAGAATCAGTGGATTTTGT
Found at i:16205 original size:16 final size:16
Alignment explanation
Indices: 16160--16207 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
16150 AAAAAATGGC
16160 TTTTTTTT-CATTTC-
1 TTTTTTTTCCATTTCT
* *
16174 TTTCTTTTCCTTTTCT
1 TTTTTTTTCCATTTCT
*
16190 TTTTTTTTCCACTTCT
1 TTTTTTTTCCATTTCT
16206 TT
1 TT
16208 CTTCTCCTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 7 0.26
15 5 0.19
16 15 0.56
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTTTCCATTTCT
Found at i:16218 original size:29 final size:29
Alignment explanation
Indices: 16160--16221 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
16150 AAAAAATGGC
* *
16160 TTTTTTTTCATTTCTTTCTTTTCCTTTTCT
1 TTTTTTTTCACTTCTTTCTTCTCC-TTTCT
16190 TTTTTTTTCCACTTCTTTCTTCTCC-TTCT
1 TTTTTTTT-CACTTCTTTCTTCTCCTTTCT
16219 TTT
1 TTT
16222 AGCCAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 7 0.24
30 8 0.28
31 14 0.48
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (29 bp):
TTTTTTTTCACTTCTTTCTTCTCCTTTCT
Done.