Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020559.1 Corchorus olitorius cultivar O-4 contig20592, 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: 16408
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:6424 original size:15 final size:16
Alignment explanation
Indices: 6391--6430 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
6381 TTACTTTGCT
6391 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
6407 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
6422 TTGCTTTCT
1 TTGTTTTCT
6431 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:8581 original size:13 final size:13
Alignment explanation
Indices: 8563--8588 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8553 CTTGGCATGA
8563 GTGATGATTTTTG
1 GTGATGATTTTTG
8576 GTGATGATTTTTG
1 GTGATGATTTTTG
8589 TTGTTATCTT
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:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:11468 original size:39 final size:40
Alignment explanation
Indices: 11412--11492 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
11402 TTTAATTCCT
11412 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
11452 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
11491 AT
1 AT
11493 TTTTAGGTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:11856 original size:206 final size:201
Alignment explanation
Indices: 11607--12019 Score: 661
Period size: 206 Copynumber: 2.0 Consensus size: 201
11597 TTCCTTAATA
* * *
11607 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTGA-T-T
1 ATAAATAAATCAGATCTTAATATCTTTTATAATTTTAAAATTTTGTTTGACATTGATCTAATTAT
*
11670 TAATTTAATAAATCAACCACTAATGTTCAACTTAAATTTTTTTTGGTATAGTTCTATATATATAA
66 TAATTTAATAAATCAACCACTAATGTTCAAC-T--ACTTTTTTTGGTATAGTT-T-TATATATAA
*
11735 TAGTAATGTCTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTT-AAAAAATTAATA
126 TAATAATG--TTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAAATTAATA
11799 ACATTCACCATTG
189 ACATTCACCATTG
11812 ATAAATAAATCAGATCTTTAATATCTTTTATAATTTTAAAATTTTGTTTGACATTGATCTAATTA
1 ATAAATAAATCAGATC-TTAATATCTTTTATAATTTTAAAATTTTGTTTGACATTGATCTAATT-
*
11877 ATTAATTTAATAAATCAACCCCTAATGTTCAACTACTTTTTTTGGTATAGTTTTATATATAATAA
64 ATTAATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTGGTATAGTTTTATATATAATAA
*
11942 TGATGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAAATTAATAACATT
129 TAATGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAAATTAATAACATT
12007 CACCATTG
194 CACCATTG
12015 ATAAA
1 ATAAA
12020 GTTATTAAGC
Statistics
Matches: 196, Mismatches: 7, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
202 42 0.21
203 30 0.15
204 15 0.08
205 16 0.08
206 60 0.31
207 1 0.01
208 1 0.01
209 31 0.16
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.44
Consensus pattern (201 bp):
ATAAATAAATCAGATCTTAATATCTTTTATAATTTTAAAATTTTGTTTGACATTGATCTAATTAT
TAATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTGGTATAGTTTTATATATAATAATA
ATGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAAATTAATAACATTCA
CCATTG
Found at i:12582 original size:36 final size:36
Alignment explanation
Indices: 12535--12604 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
12525 GAGATTTTGG
* *
12535 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
12571 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
12605 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:15535 original size:31 final size:31
Alignment explanation
Indices: 15497--15558 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
15487 GAGTTTTGTA
* * *
15497 AAACTTTTGAATCACCTATTATACCCTTATT
1 AAACTTTTAAATCACCTATCACACCCTTATT
**
15528 AAACTTTTAAATTGCCTATCACACCCTTATT
1 AAACTTTTAAATCACCTATCACACCCTTATT
15559 TTTCGAATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.40
Consensus pattern (31 bp):
AAACTTTTAAATCACCTATCACACCCTTATT
Found at i:15709 original size:93 final size:93
Alignment explanation
Indices: 15597--15778 Score: 292
Period size: 93 Copynumber: 2.0 Consensus size: 93
15587 TTTAAATTTG
*
15597 TATAATTTTAGTCAACTAAAAACTCTATTTTTACTTAATTAAATCTAATATCCTTATAACTATTT
1 TATAATTTTACTCAACTAAAAACTCTATTTTTACTTAATTAAATCTAATATCCTTATAACTATTT
* * *
15662 TATTTTTACCATTTTACTATTTTACTTT
66 TATTTGTACCATATTACTAATTTACTTT
* * *
15690 TATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTATTT
1 TATAATTTTACTCAACTAAAAACTCTATTTTTACTTAATTAAATCTAATATCCTTATAACTATTT
*
15755 TATTTGTACGATATTACTAATTTA
66 TATTTGTACCATATTACTAATTTA
15779 ATTAAAAAGT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 81 1.00
ACGTcount: A:0.34, C:0.14, G:0.02, T:0.50
Consensus pattern (93 bp):
TATAATTTTACTCAACTAAAAACTCTATTTTTACTTAATTAAATCTAATATCCTTATAACTATTT
TATTTGTACCATATTACTAATTTACTTT
Done.