Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019829.1 Corchorus olitorius cultivar O-4 contig19862, 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: 26299
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:566 original size:16 final size:16
Alignment explanation
Indices: 547--577 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
537 ATATTCTAAG
547 AATACATTTTTCTACT
1 AATACATTTTTCTACT
563 AATACATTTTTCTAC
1 AATACATTTTTCTAC
578 CAAGCAATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.48
Consensus pattern (16 bp):
AATACATTTTTCTACT
Found at i:671 original size:15 final size:17
Alignment explanation
Indices: 646--678 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
636 TAAAAAGTTA
646 TTTAAATAAAA-TATTT
1 TTTAAATAAAATTATTT
662 TTTAAA-AAAATTATTT
1 TTTAAATAAAATTATTT
678 T
1 T
679 CTTCTGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAAATAAAATTATTT
Found at i:783 original size:60 final size:60
Alignment explanation
Indices: 706--822 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
696 TATAGATAAT
* * *
706 AAACAAGCAATTTAGGATATAACGTTTTCTGCCGCAAGCAATTAAGGATATAACGTTACA
1 AAACAAACAATTAAGGATATAACGTTTTCTACCGCAAGCAATTAAGGATATAACGTTACA
* *** *
766 AAACAAACAATTAAGGATATAACGTTTTTTATTTCAAGCAATTAAGGATATGACGTT
1 AAACAAACAATTAAGGATATAACGTTTTCTACCGCAAGCAATTAAGGATATAACGTT
823 TTCGATTTCA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (60 bp):
AAACAAACAATTAAGGATATAACGTTTTCTACCGCAAGCAATTAAGGATATAACGTTACA
Found at i:811 original size:31 final size:31
Alignment explanation
Indices: 709--849 Score: 151
Period size: 31 Copynumber: 4.6 Consensus size: 31
699 AGATAATAAA
* ****
709 CAAGCAATTTAGGATATAACGTTTTCTGCCG
1 CAAGCAATTAAGGATATAACGTTTTCTATTT
* ***
740 CAAGCAATTAAGGATATAACG-TTAC-AAAA
1 CAAGCAATTAAGGATATAACGTTTTCTATTT
* *
769 CAAACAATTAAGGATATAACGTTTTTTATTT
1 CAAGCAATTAAGGATATAACGTTTTCTATTT
* *
800 CAAGCAATTAAGGATATGACGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTTCTATTT
831 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
850 TCAGTTAGGG
Statistics
Matches: 91, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
29 20 0.22
30 5 0.05
31 66 0.73
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTCTATTT
Found at i:1042 original size:29 final size:31
Alignment explanation
Indices: 968--1034 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
958 CCTAACGGAC
968 TATATCCTTAATTGCTCGTTTTTCGTAACGT
1 TATATCCTTAATTGCTCGTTTTTCGTAACGT
*
999 TATATCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCTTAATTGCTCGTTTTTCGTAACGT
1028 TATATCC
1 TATATCC
1035 CAAATTGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.49
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGTTTTTCGTAACGT
Found at i:18534 original size:22 final size:22
Alignment explanation
Indices: 18506--18573 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 22
18496 ATATATACTA
18506 TTAAATAAATAATAAATATATT
1 TTAAATAAATAATAAATATATT
18528 TTAAAT-AATAA-ATAATGA-ATT
1 TTAAATAAATAATA-AAT-ATATT
**
18549 CAAAATAAATAAATAATATATATT
1 TTAAATAAAT-AATAA-ATATATT
18573 T
1 T
18574 AATTACTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
20 1 0.03
21 15 0.42
22 10 0.28
23 4 0.11
24 6 0.17
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (22 bp):
TTAAATAAATAATAAATATATT
Found at i:21491 original size:1 final size:1
Alignment explanation
Indices: 21485--21514 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
21475 CTATGGGCTG
21485 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
21515 AATTGTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.