Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023916.1 Corchorus olitorius cultivar O-4 contig23949, 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: 18438
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:7815 original size:26 final size:27
Alignment explanation
Indices: 7781--7841 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
7771 CGGGCTTTAA
* *
7781 ATTT-TTTTTTTACCCATTTGGGCTTC
1 ATTTATTTTCTTACCCATTTGGACTTC
**
7807 ATTTATTTTCTTATGCATTTGGACTTC
1 ATTTATTTTCTTACCCATTTGGACTTC
7834 -TTTCATTT
1 ATTT-ATTT
7842 ACATGCATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.15, C:0.16, G:0.10, T:0.59
Consensus pattern (27 bp):
ATTTATTTTCTTACCCATTTGGACTTC
Found at i:9346 original size:14 final size:14
Alignment explanation
Indices: 9327--9355 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
9317 AGATAGAAAA
9327 TCAAAAATATATTC
1 TCAAAAATATATTC
9341 TCAAAAATATATTC
1 TCAAAAATATATTC
9355 T
1 T
9356 ATATATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (14 bp):
TCAAAAATATATTC
Found at i:9530 original size:19 final size:19
Alignment explanation
Indices: 9502--9541 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
9492 ATAATCCAGA
* *
9502 AATTATAAATTTCTAAAAT
1 AATTAGAAATTTATAAAAT
9521 AATTAGAAATTTATAAAAT
1 AATTAGAAATTTATAAAAT
9540 AA
1 AA
9542 AGTAAAAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
AATTAGAAATTTATAAAAT
Found at i:10201 original size:18 final size:20
Alignment explanation
Indices: 10178--10230 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
10168 AATATACTTA
10178 CTAATA-TA-CTTATTCGAT
1 CTAATAGTATCTTATTCGAT
*
10196 CTAATAAGTATCTTGTTCGAT
1 CTAAT-AGTATCTTATTCGAT
10217 CTAATAAGTATCTT
1 CTAAT-AGTATCTT
10231 GGGTATTGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 5 0.16
19 1 0.03
20 2 0.06
21 23 0.74
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.43
Consensus pattern (20 bp):
CTAATAGTATCTTATTCGAT
Found at i:10216 original size:21 final size:21
Alignment explanation
Indices: 10190--10231 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
10180 AATATACTTA
10190 TTCGATCTAATAAGTATCTTG
1 TTCGATCTAATAAGTATCTTG
10211 TTCGATCTAATAAGTATCTTG
1 TTCGATCTAATAAGTATCTTG
10232 GGTATTGAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (21 bp):
TTCGATCTAATAAGTATCTTG
Found at i:10560 original size:27 final size:27
Alignment explanation
Indices: 10524--10669 Score: 220
Period size: 27 Copynumber: 5.2 Consensus size: 27
10514 AGAACTCCGA
10524 ATCATTCTCTTGAAGCTCATCCTTTTC
1 ATCATTCTCTTGAAGCTCATCCTTTTC
10551 ATCATTCTCTTGAAGCTCATCCTTTTC
1 ATCATTCTCTTGAAGCTCATCCTTTTC
10578 ATCATTCTCTTGAAGCTCATCCTTTTC
1 ATCATTCTCTTGAAGCTCATCCTTTTC
* *
10605 ATCATAAATGATCCGCTGAAGCTCATCCTTTTC
1 ATCAT---T-CT-C-TTGAAGCTCATCCTTTTC
10638 ATCATTCTCTTGAAGCTCATCCTTTTC
1 ATCATTCTCTTGAAGCTCATCCTTTTC
10665 ATCAT
1 ATCAT
10670 AAATGATCTG
Statistics
Matches: 109, Mismatches: 4, Indels: 12
0.87 0.03 0.10
Matches are distributed among these distances:
27 81 0.74
28 1 0.01
29 1 0.01
30 2 0.02
31 1 0.01
32 1 0.01
33 22 0.20
ACGTcount: A:0.21, C:0.29, G:0.08, T:0.42
Consensus pattern (27 bp):
ATCATTCTCTTGAAGCTCATCCTTTTC
Found at i:10636 original size:60 final size:59
Alignment explanation
Indices: 10524--10677 Score: 246
Period size: 60 Copynumber: 2.7 Consensus size: 59
10514 AGAACTCCGA
* *
10524 ATCATTCTCTTGAAGCTCATCCTTTTCATCAT---T-CT-CTTGAAGCTCATCCTTTTC
1 ATCATTCTCTTGAAGCTCATCCTTTTCATCATAAATGATCCCTGAAGCTCATCCTTTTC
10578 ATCATTCTCTTGAAGCTCATCCTTTTCATCATAAATGATCCGCTGAAGCTCATCCTTTTC
1 ATCATTCTCTTGAAGCTCATCCTTTTCATCATAAATGATCC-CTGAAGCTCATCCTTTTC
10638 ATCATTCTCTTGAAGCTCATCCTTTTCATCATAAATGATC
1 ATCATTCTCTTGAAGCTCATCCTTTTCATCATAAATGATC
10678 TGCTTGCCCC
Statistics
Matches: 92, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
54 32 0.35
57 1 0.01
58 1 0.01
59 1 0.01
60 57 0.62
ACGTcount: A:0.23, C:0.28, G:0.08, T:0.41
Consensus pattern (59 bp):
ATCATTCTCTTGAAGCTCATCCTTTTCATCATAAATGATCCCTGAAGCTCATCCTTTTC
Done.