Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020429.1 Corchorus olitorius cultivar O-4 contig20462, 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: 6775
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Found at i:594 original size:14 final size:14
Alignment explanation
Indices: 577--614 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
567 TGAGTTTGCA
577 ATTTTATTTTATTT
1 ATTTTATTTTATTT
591 A-TTTATTATTATTT
1 ATTTTATT-TTATTT
*
605 ATTATATTTT
1 ATTTTATTTT
615 TTTTGAGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 6 0.29
14 10 0.48
15 5 0.24
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
ATTTTATTTTATTT
Found at i:667 original size:5 final size:5
Alignment explanation
Indices: 649--697 Score: 52
Period size: 5 Copynumber: 10.6 Consensus size: 5
639 TATATAGTAG
* *
649 TAAGA T-AG- TAAGA TAAGA TAAAA T-A-T TAAGA TAAGA TAAGA TAAGA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA
695 TAA
1 TAA
698 AATGGGATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
3 2 0.05
4 6 0.16
5 29 0.78
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.24
Consensus pattern (5 bp):
TAAGA
Found at i:691 original size:28 final size:26
Alignment explanation
Indices: 649--700 Score: 86
Period size: 28 Copynumber: 1.9 Consensus size: 26
639 TATATAGTAG
649 TAAGATAGTAAGATAAGATAAAATAT
1 TAAGATAGTAAGATAAGATAAAATAT
675 TAAGATAAGATAAGATAAGATAAAAT
1 TAAGAT-AG-TAAGATAAGATAAAAT
701 GGGATGAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 6 0.25
27 2 0.08
28 16 0.67
ACGTcount: A:0.60, C:0.00, G:0.15, T:0.25
Consensus pattern (26 bp):
TAAGATAGTAAGATAAGATAAAATAT
Found at i:3242 original size:2 final size:2
Alignment explanation
Indices: 3235--3273 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3225 ATGGATATCT
3235 TA TA TA TA TA 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 TA TA TA TA TA T
3274 TCTTTTTGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4417 original size:31 final size:31
Alignment explanation
Indices: 4382--4443 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
4372 ACCATGATAT
4382 AACCTTTATTAACTCGCTTTCCATTTTTCTC
1 AACCTTTATTAACTCGCTTTCCATTTTTCTC
*
4413 AACCTTTATTAACTCGTTTTCCATTTTTCTC
1 AACCTTTATTAACTCGCTTTCCATTTTTCTC
4444 GACTAATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.19, C:0.27, G:0.03, T:0.50
Consensus pattern (31 bp):
AACCTTTATTAACTCGCTTTCCATTTTTCTC
Found at i:6679 original size:13 final size:13
Alignment explanation
Indices: 6661--6702 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
6651 ATTAAAAGAT
6661 AAAAGAAAATCTA
1 AAAAGAAAATCTA
6674 AAAAG-AAAT-T-
1 AAAAGAAAATCTA
6684 AAAAGAAAATCTA
1 AAAAGAAAATCTA
6697 AAAAGA
1 AAAAGA
6703 TAAAAAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 5 0.19
11 5 0.19
12 5 0.19
13 11 0.42
ACGTcount: A:0.71, C:0.05, G:0.10, T:0.14
Consensus pattern (13 bp):
AAAAGAAAATCTA
Found at i:6693 original size:11 final size:12
Alignment explanation
Indices: 6660--6699 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
6650 TATTAAAAGA
6660 TAAAAGAAAATC
1 TAAAAGAAAATC
6672 TAAAA-AGAAAT-
1 TAAAAGA-AAATC
6683 TAAAAGAAAATC
1 TAAAAGAAAATC
6695 TAAAA
1 TAAAA
6700 AGATAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.17
Consensus pattern (12 bp):
TAAAAGAAAATC
Found at i:6710 original size:23 final size:23
Alignment explanation
Indices: 6661--6713 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
6651 ATTAAAAGAT
*
6661 AAAAGAAAATCTAAAAAGAAATT
1 AAAAGAAAATCTAAAAAGAAATA
6684 AAAAGAAAATCTAAAAAGATAA-A
1 AAAAGAAAATCTAAAAAGA-AATA
6707 AAAAGAA
1 AAAAGAA
6714 CGCAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 26 0.93
24 2 0.07
ACGTcount: A:0.74, C:0.04, G:0.09, T:0.13
Consensus pattern (23 bp):
AAAAGAAAATCTAAAAAGAAATA
Done.