Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022405.1 Corchorus olitorius cultivar O-4 contig22438, 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: 18266
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4072 original size:7 final size:7
Alignment explanation
Indices: 4038--4090 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
4028 TCTCTTGCAG
4038 ATAATAT
1 ATAATAT
4045 ATATATAT
1 ATA-ATAT
4053 ATATATAT
1 ATA-ATAT
4061 ATAATAT
1 ATAATAT
* *
4068 TTAATAA
1 ATAATAT
4075 ATAATA-
1 ATAATAT
4081 ATAATA-
1 ATAATAT
4087 ATAA
1 ATAA
4091 GAAAGGAGAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
6 10 0.24
7 17 0.40
8 15 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATAATAT
Found at i:4074 original size:10 final size:11
Alignment explanation
Indices: 4038--4067 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
4028 TCTCTTGCAG
4038 ATAATATATAT
1 ATAATATATAT
4049 ATATATATATAT
1 ATA-ATATATAT
4061 ATAATAT
1 ATAATAT
4068 TTAATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATAATATATAT
Found at i:4114 original size:7 final size:7
Alignment explanation
Indices: 4095--4123 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
4085 TAATAAGAAA
4095 GGAGATT
1 GGAGATT
4102 -GAGATT
1 GGAGATT
4108 GGAGATT
1 GGAGATT
4115 GGAGATT
1 GGAGATT
4122 GG
1 GG
4124 GGGAGGAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.28, C:0.00, G:0.45, T:0.28
Consensus pattern (7 bp):
GGAGATT
Found at i:4920 original size:31 final size:32
Alignment explanation
Indices: 4875--4942 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
4865 CGGACTGACC
* *
4875 TGACCTTAGACCCAGCA-GACTCGAGACCCGAA
1 TGACCTGAGACCCAG-ATGACTCGAAACCCGAA
*
4907 TGACCTGA-ACCCAGATGAGTCGAAACCCGAA
1 TGACCTGAGACCCAGATGACTCGAAACCCGAA
4938 TGACC
1 TGACC
4943 CAAGAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 1 0.03
31 24 0.75
32 7 0.22
ACGTcount: A:0.32, C:0.32, G:0.22, T:0.13
Consensus pattern (32 bp):
TGACCTGAGACCCAGATGACTCGAAACCCGAA
Found at i:5546 original size:105 final size:102
Alignment explanation
Indices: 5371--5579 Score: 296
Period size: 105 Copynumber: 2.0 Consensus size: 102
5361 TAATATATCT
* *
5371 AAGTTTTTTAATAAAATTAGTAAAATGATAAAAAAATAATAGGTATAAGGATATTAGATTTAATT
1 AAGTATTTTAATAAAATTAGTAAAATGATAAAAAAATAATAGGTATAAGGATATTAGATTTAATC
**
5436 AAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAA
66 AAATAAAAATAGAGTTTTTAGTTGAACAAAACTATAA
* *
5473 AAGTATTTTAATTAAAA-TAGTAAAATGGTAAAAATAA-AATAGTACTTATAAGGATATTAGATT
1 AAGTATTTTAA-TAAAATTAGTAAAATGATAAAAA-AATAATAG---GTATAAGGATATTAGATT
*
5536 TAATCAAATAAAAATAGAGTTTTTAGTTGAACAAAATTATAA
61 TAATCAAATAAAAATAGAGTTTTTAGTTGAACAAAACTATAA
5578 AA
1 AA
5580 ATTTAAGCAA
Statistics
Matches: 95, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
102 31 0.33
103 7 0.07
105 57 0.60
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.34
Consensus pattern (102 bp):
AAGTATTTTAATAAAATTAGTAAAATGATAAAAAAATAATAGGTATAAGGATATTAGATTTAATC
AAATAAAAATAGAGTTTTTAGTTGAACAAAACTATAA
Found at i:9370 original size:17 final size:17
Alignment explanation
Indices: 9329--9370 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
9319 GATTAAATTG
*
9329 ATTTTTGCTTGCATGTT
1 ATTTTTGCTTGAATGTT
*
9346 ATTATTGCTTGAAT-TT
1 ATTTTTGCTTGAATGTT
9362 AGTTTTTGC
1 A-TTTTTGC
9371 ATTTATATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.17, C:0.10, G:0.17, T:0.57
Consensus pattern (17 bp):
ATTTTTGCTTGAATGTT
Found at i:11542 original size:30 final size:29
Alignment explanation
Indices: 11469--11546 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
11459 TTGCTTATTC
* * *
11469 TATCTTTCAATTG-TTGATTTGAATTGCCA
1 TATCTTGCTATTGATTGA-TTGAATTGCAA
11498 TATCTTGCTATTGATTGATTGAATTGCAA
1 TATCTTGCTATTGATTGATTGAATTGCAA
*
11527 TTAT-TTGTTAGTTGATTGAT
1 -TATCTTGCTA-TTGATTGAT
11547 AGATTGTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 26 0.62
30 16 0.38
ACGTcount: A:0.24, C:0.09, G:0.17, T:0.50
Consensus pattern (29 bp):
TATCTTGCTATTGATTGATTGAATTGCAA
Found at i:13283 original size:45 final size:42
Alignment explanation
Indices: 13219--13312 Score: 145
Period size: 45 Copynumber: 2.2 Consensus size: 42
13209 AGCAACAATT
*
13219 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGAAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGAT--A-GAGTAG
13264 AATATTAGCTTTATTTTGATGAATTACCTAGAGATAGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATAGAGTAG
13306 AAT-TTAG
1 AATATTAG
13313 ATAATGCACT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 9 0.19
43 1 0.02
45 34 0.71
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.38
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATAGAGTAG
Found at i:14056 original size:3 final size:3
Alignment explanation
Indices: 14048--14110 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
14038 GTTCGATTTC
14048 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
14096 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
14111 ATATATATAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Done.