Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021888.1 Corchorus olitorius cultivar O-4 contig21921, 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: 22183
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:14 original size:2 final size:2
Alignment explanation
Indices: 8--41 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1 CATGTAA
8 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42 TCTAATGACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13448 original size:18 final size:18
Alignment explanation
Indices: 13427--13488 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
13417 TTGTAGATTT
13427 CTTATGACATTAATCATG
1 CTTATGACATTAATCATG
* *
13445 CTTATG-CAATAGAT--TT
1 CTTATGACATTA-ATCATG
13461 CTTATGACATTTAATCATG
1 CTTATGACA-TTAATCATG
13480 CTTAT-ACAT
1 CTTATGACAT
13489 GGCAGCTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
16 7 0.20
17 9 0.26
18 13 0.37
19 6 0.17
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (18 bp):
CTTATGACATTAATCATG
Found at i:13871 original size:20 final size:17
Alignment explanation
Indices: 13827--13881 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 17
13817 GCCATGTCAT
13827 TTTTTTTATTAAAAAATTA
1 TTTTTTTA--AAAAAATTA
13846 TTTTTTTAAAAAAATATA
1 TTTTTTTAAAAAAAT-TA
13864 TATATTTTTAAAAAAATT
1 T-T-TTTTTAAAAAAATT
13882 GGGTGAGGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.21
18 3 0.09
19 10 0.30
20 13 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTTTTAAAAAAATTA
Found at i:14810 original size:30 final size:31
Alignment explanation
Indices: 14774--14842 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
14764 GTTCAAATGG
14774 GTCCCTGAAGT-AAACTT-AGTGAGCAATTGA
1 GTCCCTGAAGTGAAA-TTAAGTGAGCAATTGA
* *
14804 GTCCCTGAAGTGAAATTAATTGAGCAATTGG
1 GTCCCTGAAGTGAAATTAAGTGAGCAATTGA
14835 GTCCCTGA
1 GTCCCTGA
14843 CTATTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
30 13 0.37
31 22 0.63
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (31 bp):
GTCCCTGAAGTGAAATTAAGTGAGCAATTGA
Found at i:14874 original size:12 final size:12
Alignment explanation
Indices: 14857--14882 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
14847 TTTTTTTAAA
14857 AAAATATTTTTT
1 AAAATATTTTTT
14869 AAAATATTTTTT
1 AAAATATTTTTT
14881 AA
1 AA
14883 TCAAAAAATA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
AAAATATTTTTT
Found at i:17316 original size:29 final size:30
Alignment explanation
Indices: 17255--17334 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
17245 GCTAAATATC
* **
17255 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT-CTTTCCGGA
17286 CAAAATAATCCCTTATGTTTT-TTTCCGGA
1 CAAAATAATCCCTTATGTTTTCTTTCCGGA
* *
17315 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
17335 CAAAAATGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 24 0.55
31 20 0.45
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTCCGGA
Found at i:17493 original size:31 final size:31
Alignment explanation
Indices: 17458--17552 Score: 149
Period size: 29 Copynumber: 3.1 Consensus size: 31
17448 AAGGGACTGA
17458 TTTGTCCCAAAAGAAAAACATAAGAGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGAGATTTT
*
17489 TTTGTCCCAAAAGAAAAACATAAGGGA--TT
1 TTTGTCCCAAAAGAAAAACATAAGAGATTTT
*
17518 TTTGTCCCAAAAGAAAAATATAAGAGAATTTT
1 TTTGTCCCAAAAGAAAAACATAAGAG-ATTTT
17550 TTT
1 TTT
17553 AGTATTTAGT
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
29 26 0.45
30 1 0.02
31 26 0.45
32 5 0.09
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAGAGATTTT
Found at i:17529 original size:29 final size:29
Alignment explanation
Indices: 17458--17550 Score: 132
Period size: 31 Copynumber: 3.1 Consensus size: 29
17448 AAGGGACTGA
*
17458 TTTGTCCCAAAAGAAAAACATAAGAGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGA--TT
17489 TTTGTCCCAAAAGAAAAACATAAGGGATT
1 TTTGTCCCAAAAGAAAAACATAAGGGATT
* *
17518 TTTGTCCCAAAAGAAAAATATAAGAGAATT
1 TTTGTCCCAAAAGAAAAACATAAG-GGATT
17548 TTT
1 TTT
17551 TTAGTATTTA
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
29 25 0.43
30 7 0.12
31 26 0.45
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (29 bp):
TTTGTCCCAAAAGAAAAACATAAGGGATT
Found at i:18290 original size:126 final size:126
Alignment explanation
Indices: 18157--18396 Score: 315
Period size: 127 Copynumber: 1.9 Consensus size: 126
18147 CTTATTTTTC
* ** * *
18157 AAATATATTTTTTAAAT-ACCATT-TTTAAACTTTTACAATTTTACTCAATTAGAAATTCTATTT
1 AAATATATTTCTTAAATGA-CATTATTTAAACTTTTACAATTTTACTCAACCAAAAAATCTATTT
* *
18220 TTATTTAATCAAA-TCTAATATATTTTATAACTATTTTATTTTTACCATTTTACTATTTTAATT
65 TTATTTAATCAAATTC-AATAT-TTTTATAACAATTTTATCTTTACCATTTTACTATTTTAATT
* * **
18283 AAATATATTTCTTAAATGACATTATTTAAACTTTTACAGTTTTATTTTACCAAAAAATCTATTTT
1 AAATATATTTCTTAAATGACATTATTTAAACTTTTACAATTTTACTCAACCAAAAAATCTATTTT
* *
18348 TATTTAATTAAATTCAATATTTTTATAACAATTTTATCTTTGCCATTTT
66 TATTTAATCAAATTCAATATTTTTATAACAATTTTATCTTTACCATTTT
18397 TTTTAGGGAA
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
126 46 0.47
127 50 0.51
128 2 0.02
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.52
Consensus pattern (126 bp):
AAATATATTTCTTAAATGACATTATTTAAACTTTTACAATTTTACTCAACCAAAAAATCTATTTT
TATTTAATCAAATTCAATATTTTTATAACAATTTTATCTTTACCATTTTACTATTTTAATT
Found at i:18503 original size:14 final size:15
Alignment explanation
Indices: 18486--18514 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
18476 GGAGGAGAAG
18486 GAAAAAA-GAAAAAA
1 GAAAAAAGGAAAAAA
18500 GAAAAAAGGAAAAAA
1 GAAAAAAGGAAAAAA
18515 ATCAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
GAAAAAAGGAAAAAA
Found at i:18804 original size:29 final size:30
Alignment explanation
Indices: 18762--18835 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 30
18752 CTAATTTTGG
* *
18762 AAACGTAAGGGATTAATTTGTCCCGAAA-A
1 AAACATAAGGGATTAATTTGTCCCAAAACA
*
18791 AAACATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTAATTTGTCCCAAAA-CA
18822 AAACATAAGGGATT
1 AAACATAAGGGATT
18836 TTTCTGGGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 25 0.62
31 15 0.38
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (30 bp):
AAACATAAGGGATTAATTTGTCCCAAAACA
Done.