Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015815.1 Corchorus olitorius cultivar O-4 contig15848, 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: 62189
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:18 original size:2 final size:2
Alignment explanation
Indices: 12--40 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2 ATACTATTAG
12 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41 TATTACTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6456 original size:19 final size:18
Alignment explanation
Indices: 6427--6468 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
6417 TGAGTAGTTT
* *
6427 TTAAGTAAAAATGTAATA
1 TTAAATAAAAATATAATA
6445 TATAAATAAAAATATAATA
1 T-TAAATAAAAATATAATA
6464 TTAAA
1 TTAAA
6469 ATAATTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
TTAAATAAAAATATAATA
Found at i:6472 original size:19 final size:19
Alignment explanation
Indices: 6432--6468 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
6422 AGTTTTTAAG
*
6432 TAAAAATGTAATATATAAA
1 TAAAAATATAATATATAAA
6451 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
6469 ATAATTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:48616 original size:20 final size:22
Alignment explanation
Indices: 48593--48632 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
48583 CGAGTTCGGC
48593 TCGAA-TTTTC-CGAGCCGAAT
1 TCGAATTTTTCTCGAGCCGAAT
48613 TCGAATTTTTCTCGAGCCGA
1 TCGAATTTTTCTCGAGCCGA
48633 GTCCGAGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.33
Consensus pattern (22 bp):
TCGAATTTTTCTCGAGCCGAAT
Found at i:52248 original size:26 final size:26
Alignment explanation
Indices: 52200--52251 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
52190 AAAATAGACA
*
52200 AATTAAACTAGAAAACAATAAAATAG
1 AATTAAACTAGAAAACAAGAAAATAG
* **
52226 AATTAAACTAGAGATTAAGAAAATAG
1 AATTAAACTAGAAAACAAGAAAATAG
52252 TTTGAGAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.21
Consensus pattern (26 bp):
AATTAAACTAGAAAACAAGAAAATAG
Found at i:58234 original size:12 final size:13
Alignment explanation
Indices: 58206--58235 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
58196 TGAAAAATGC
58206 AAAACAGAATTGA
1 AAAACAGAATTGA
58219 AAAACAGAATTGA
1 AAAACAGAATTGA
58232 AAAA
1 AAAA
58236 TGCAAAACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (13 bp):
AAAACAGAATTGA
Found at i:58244 original size:20 final size:20
Alignment explanation
Indices: 58173--58222 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
58163 TTCAAAAACT
58173 AATTGAAAAATGCAAAACAG
1 AATTGAAAAATGCAAAACAG
58193 AATTGAAAAATGCAAAACAG
1 AATTGAAAAATGCAAAACAG
58213 AATTGAAAAA
1 AATTGAAAAA
58223 CAGAATTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.62, C:0.08, G:0.14, T:0.16
Consensus pattern (20 bp):
AATTGAAAAATGCAAAACAG
Found at i:58273 original size:13 final size:13
Alignment explanation
Indices: 58257--58330 Score: 62
Period size: 14 Copynumber: 5.7 Consensus size: 13
58247 AAACAAAATT
58257 GAAATGCAAAACA
1 GAAATGCAAAACA
* *
58270 GAAACTTCAACACA
1 GAAA-TGCAAAACA
58284 GAAATGCAAAACA
1 GAAATGCAAAACA
*
58297 G-AA-GTAAAACA
1 GAAATGCAAAACA
* *
58308 GAAACTTCAACACA
1 GAAA-TGCAAAACA
*
58322 AAAATGCAA
1 GAAATGCAA
58331 TTGAAAAGTA
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
11 8 0.17
12 4 0.09
13 16 0.34
14 19 0.40
ACGTcount: A:0.58, C:0.19, G:0.12, T:0.11
Consensus pattern (13 bp):
GAAATGCAAAACA
Found at i:58286 original size:14 final size:13
Alignment explanation
Indices: 58257--58317 Score: 54
Period size: 13 Copynumber: 4.7 Consensus size: 13
58247 AAACAAAATT
*
58257 GAAATGCAAAACA
1 GAAATTCAAAACA
*
58270 GAAACTTCAACACA
1 GAAA-TTCAAAACA
*
58284 GAAATGCAAAACA
1 GAAATTCAAAACA
*
58297 G-AAGT-AAAACA
1 GAAATTCAAAACA
58308 GAAACTTCAA
1 GAAA-TTCAA
58318 CACAAAAATG
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
11 7 0.19
12 4 0.11
13 13 0.35
14 13 0.35
ACGTcount: A:0.57, C:0.18, G:0.13, T:0.11
Consensus pattern (13 bp):
GAAATTCAAAACA
Found at i:58306 original size:38 final size:38
Alignment explanation
Indices: 58264--58375 Score: 161
Period size: 38 Copynumber: 2.9 Consensus size: 38
58254 ATTGAAATGC
58264 AAAACAGAAACTTCAACACAGAAATGCAAAACAGAAGT
1 AAAACAGAAACTTCAACACAGAAATGCAAAACAGAAGT
* *** *
58302 AAAACAGAAACTTCAACACAAAAATGCAATTGAAAAGT
1 AAAACAGAAACTTCAACACAGAAATGCAAAACAGAAGT
* *
58340 AAAACAGAAACTTCAACACAGAATTGAAAAACAGAA
1 AAAACAGAAACTTCAACACAGAAATGCAAAACAGAA
58376 TTGTACCTGA
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 62 1.00
ACGTcount: A:0.59, C:0.17, G:0.12, T:0.12
Consensus pattern (38 bp):
AAAACAGAAACTTCAACACAGAAATGCAAAACAGAAGT
Done.