Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014799.1 Corchorus olitorius cultivar O-4 contig14832, 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: 34878
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:259 original size:21 final size:22
Alignment explanation
Indices: 220--260 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
210 TTAATTTACA
*
220 TGTAAATTCGTTTTATTACAGT
1 TGTAAATTCGTCTTATTACAGT
*
242 TGTAATTTCGTCTT-TTACA
1 TGTAAATTCGTCTTATTACA
261 ATTAATTACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.51
Consensus pattern (22 bp):
TGTAAATTCGTCTTATTACAGT
Found at i:413 original size:31 final size:32
Alignment explanation
Indices: 363--451 Score: 128
Period size: 31 Copynumber: 2.8 Consensus size: 32
353 TTTGTCTTGT
* *
363 TTTGCATTTAATGCATTGCAGTTTTGGCTTTA
1 TTTGCATTTAATGCATTGCAATTTTGGCTTCA
395 TTTGCATTTAA-GCATTGCAATTTTGGCTTCA
1 TTTGCATTTAATGCATTGCAATTTTGGCTTCA
*
426 TTTGCATTTAATG-ACTTGAAATTTTG
1 TTTGCATTTAATGCA-TTGCAATTTTG
452 TCCTCTATCT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
31 30 0.58
32 22 0.42
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.48
Consensus pattern (32 bp):
TTTGCATTTAATGCATTGCAATTTTGGCTTCA
Found at i:451 original size:63 final size:63
Alignment explanation
Indices: 322--451 Score: 145
Period size: 63 Copynumber: 2.1 Consensus size: 63
312 CCGTTGCAAA
* * ** * * ** * *
322 TTTGGCTTTTTTTGCAATTATGGGTTGTAATTTTGTCTTGTTTTGCATTTAATGCATTGCAGT
1 TTTGGCTTTATTTGCAATTAAGCATTGCAATTTTGGCTTCATTTGCATTTAATGCATTGAAAT
*
385 TTTGGCTTTATTTGCATTTAAGCATTGCAATTTTGGCTTCATTTGCATTTAATG-ACTTGAAAT
1 TTTGGCTTTATTTGCAATTAAGCATTGCAATTTTGGCTTCATTTGCATTTAATGCA-TTGAAAT
448 TTTG
1 TTTG
452 TCCTCTATCT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
62 1 0.02
63 54 0.98
ACGTcount: A:0.19, C:0.11, G:0.18, T:0.52
Consensus pattern (63 bp):
TTTGGCTTTATTTGCAATTAAGCATTGCAATTTTGGCTTCATTTGCATTTAATGCATTGAAAT
Found at i:1209 original size:32 final size:31
Alignment explanation
Indices: 1172--1260 Score: 97
Period size: 32 Copynumber: 2.8 Consensus size: 31
1162 ATTTCAACTG
1172 ATTAAATGCAAATAAGGCCAAATTTACAAGCC
1 ATTAAATGCAAATAA-GCCAAATTTACAAGCC
* * * *
1204 ATTAAATGCGAATTAAGACAAAATAACAAGCC
1 ATTAAATGC-AAATAAGCCAAATTTACAAGCC
* *
1236 ATTAATTGCAAAAAATGCCAAATTT
1 ATTAAATGCAAATAA-GCCAAATTT
1261 GCAACCGAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
31 4 0.09
32 36 0.80
33 5 0.11
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (31 bp):
ATTAAATGCAAATAAGCCAAATTTACAAGCC
Found at i:4401 original size:2 final size:2
Alignment explanation
Indices: 4394--4430 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4384 CACGGCTTAA
4394 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4431 ATAAGTAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4671 original size:5 final size:5
Alignment explanation
Indices: 4661--4690 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
4651 CTTGGTGAGT
4661 TTTTC TTTTC TTTTC TTTTC TTTT- TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T
4691 CCTTCGCCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:5229 original size:49 final size:49
Alignment explanation
Indices: 5119--5220 Score: 151
Period size: 49 Copynumber: 2.2 Consensus size: 49
5109 TTTATCTGGC
5119 ATATTTTCTTTGTCATTACTAATATAATAATAATTACTTATTGTTAATT
1 ATATTTTCTTTGTCATTACTAATATAATAATAATTACTTATTGTTAATT
* *
5168 ATATTTTCTTTGTGATTACT-A-AT-ATAATAATTAC-TATTGTTGATT
1 ATATTTTCTTTGTCATTACTAATATAATAATAATTACTTATTGTTAATT
5213 AT-TTTTCT
1 ATATTTTCT
5221 AATCTTTGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
44 6 0.12
45 12 0.24
46 11 0.22
47 2 0.04
48 1 0.02
49 19 0.37
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.55
Consensus pattern (49 bp):
ATATTTTCTTTGTCATTACTAATATAATAATAATTACTTATTGTTAATT
Found at i:20725 original size:38 final size:39
Alignment explanation
Indices: 20683--20760 Score: 131
Period size: 38 Copynumber: 2.0 Consensus size: 39
20673 GGAATTGCAA
*
20683 TGAGATTTCACTGGGTTTGTTTGTTGGGAAAGG-GTTTG
1 TGAGATTTCACTCGGTTTGTTTGTTGGGAAAGGAGTTTG
*
20721 TGAGATTTCACTCGGTTTGTTTGTTGGGGAAGGAGTTTG
1 TGAGATTTCACTCGGTTTGTTTGTTGGGAAAGGAGTTTG
20760 T
1 T
20761 TGGCTCATAG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
38 31 0.84
39 6 0.16
ACGTcount: A:0.15, C:0.06, G:0.36, T:0.42
Consensus pattern (39 bp):
TGAGATTTCACTCGGTTTGTTTGTTGGGAAAGGAGTTTG
Found at i:24512 original size:24 final size:24
Alignment explanation
Indices: 24485--24535 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
24475 ATCGCAAGTC
24485 AAATGAATACAATCAAAATTTAAG
1 AAATGAATACAATCAAAATTTAAG
24509 AAATGAATACAATCAAAATTTAAG
1 AAATGAATACAATCAAAATTTAAG
24533 AAA
1 AAA
24536 ATCAAAGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.61, C:0.08, G:0.08, T:0.24
Consensus pattern (24 bp):
AAATGAATACAATCAAAATTTAAG
Done.