Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017526.1 Corchorus olitorius cultivar O-4 contig17559, 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: 13497
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:1233 original size:29 final size:28
Alignment explanation
Indices: 1201--1299 Score: 90
Period size: 29 Copynumber: 3.4 Consensus size: 28
1191 TGCACAAACA
* * *
1201 ACCAAAATGTCCCAGGATTTGCGGAAATG
1 ACCAAAATG-CCCTGGATTTGAGAAAATG
* * * *
1230 ACCATAATGCCACTGAATGTGAAAAAATG
1 ACCAAAATGCC-CTGGATTTGAGAAAATG
**
1259 ACCAAAATGCCCCTGGATTTTTGAAAATG
1 ACCAAAATG-CCCTGGATTTGAGAAAATG
1288 ACCAAAATGCCC
1 ACCAAAATGCCC
1300 CTAGATGATC
Statistics
Matches: 55, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
28 5 0.09
29 48 0.87
30 2 0.04
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (28 bp):
ACCAAAATGCCCTGGATTTGAGAAAATG
Found at i:5260 original size:15 final size:15
Alignment explanation
Indices: 5240--5270 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5230 CTTGTTTTCT
5240 TTTCAAATAAGTCCC
1 TTTCAAATAAGTCCC
*
5255 TTTCAATTAAGTCCC
1 TTTCAAATAAGTCCC
5270 T
1 T
5271 GAAACTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.39
Consensus pattern (15 bp):
TTTCAAATAAGTCCC
Found at i:6618 original size:87 final size:87
Alignment explanation
Indices: 6468--6726 Score: 484
Period size: 87 Copynumber: 3.0 Consensus size: 87
6458 TCGGCCCTTC
*
6468 ACTCTTCTTTGTCCCTTCTCACAAGAATGA-TCATTTCAAATCAATACAAAGAGTATTTCAATTT
1 ACTCCTCTTTGTCCCTTCTCACAAGAATGAGTCATTTCAAATCAATACAAAGAGTATTTCAATTT
*
6532 AATGCAACTTTAATCCGCATAT
66 AATGCAACTCTAATCCGCATAT
*
6554 ACTCCTCTTTGTCCCTTCTCACAAGAATGAGTCATTTCAAATCAATATAAAGAGTATTTCAATTT
1 ACTCCTCTTTGTCCCTTCTCACAAGAATGAGTCATTTCAAATCAATACAAAGAGTATTTCAATTT
6619 AATGCAACTCTAATCCGCATAT
66 AATGCAACTCTAATCCGCATAT
6641 ACTCCTCTTTGTCCCTTCTCACAAGAATGAGTCATTTCAAATCAATACAAAGAGTATTTCAATTT
1 ACTCCTCTTTGTCCCTTCTCACAAGAATGAGTCATTTCAAATCAATACAAAGAGTATTTCAATTT
6706 AATGCAACTCTAATCCGCATA
66 AATGCAACTCTAATCCGCATA
6727 GAATATACGT
Statistics
Matches: 168, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
86 29 0.17
87 139 0.83
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (87 bp):
ACTCCTCTTTGTCCCTTCTCACAAGAATGAGTCATTTCAAATCAATACAAAGAGTATTTCAATTT
AATGCAACTCTAATCCGCATAT
Found at i:8304 original size:2 final size:2
Alignment explanation
Indices: 8297--8322 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8287 ATAATATAGC
8297 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
8323 TTGACAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11157 original size:33 final size:33
Alignment explanation
Indices: 11115--11188 Score: 148
Period size: 33 Copynumber: 2.2 Consensus size: 33
11105 AGGAAAGCCT
11115 GGTCGCGACCTATGCGCGACTGGGCCATGGCCA
1 GGTCGCGACCTATGCGCGACTGGGCCATGGCCA
11148 GGTCGCGACCTATGCGCGACTGGGCCATGGCCA
1 GGTCGCGACCTATGCGCGACTGGGCCATGGCCA
11181 GGTCGCGA
1 GGTCGCGA
11189 TCCGCGCGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.15, C:0.32, G:0.38, T:0.15
Consensus pattern (33 bp):
GGTCGCGACCTATGCGCGACTGGGCCATGGCCA
Found at i:13246 original size:160 final size:160
Alignment explanation
Indices: 13026--13350 Score: 641
Period size: 160 Copynumber: 2.0 Consensus size: 160
13016 ATTGAAAATT
13026 TTGCACTGTTTGACTGTTTCCCTTTTATTATTGGTGGACTTCCAAGAAAATGATATATATTGACT
1 TTGCACTGTTTGACTGTTTCCCTTTTATTATTGGTGGACTTCCAAGAAAATGATATATATTGACT
13091 GAATTTGGTATGCAGATAAATCTAGGCTATATATATGGTCATTGAAAACTATATGAAAGCCATGT
66 GAATTTGGTATGCAGATAAATCTAGGCTATATATATGGTCATTGAAAACTATATGAAAGCCATGT
*
13156 AGGAGAATCGAAATAGTAAAACTAGTTTGA
131 AGGAGAATCGAAATAGTAAAACTAATTTGA
13186 TTGCACTGTTTGACTGTTTCCCTTTTATTATTGGTGGACTTCCAAGAAAATGATATATATTGACT
1 TTGCACTGTTTGACTGTTTCCCTTTTATTATTGGTGGACTTCCAAGAAAATGATATATATTGACT
13251 GAATTTGGTATGCAGATAAATCTAGGCTATATATATGGTCATTGAAAACTATATGAAAGCCATGT
66 GAATTTGGTATGCAGATAAATCTAGGCTATATATATGGTCATTGAAAACTATATGAAAGCCATGT
13316 AGGAGAATCGAAATAGTAAAACTAATTTGA
131 AGGAGAATCGAAATAGTAAAACTAATTTGA
13346 TTGCA
1 TTGCA
13351 ATTTGCATGA
Statistics
Matches: 164, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 164 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (160 bp):
TTGCACTGTTTGACTGTTTCCCTTTTATTATTGGTGGACTTCCAAGAAAATGATATATATTGACT
GAATTTGGTATGCAGATAAATCTAGGCTATATATATGGTCATTGAAAACTATATGAAAGCCATGT
AGGAGAATCGAAATAGTAAAACTAATTTGA
Done.