Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012858.1 Corchorus olitorius cultivar O-4 contig12891, 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: 8196
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Found at i:2577 original size:23 final size:23
Alignment explanation
Indices: 2540--2587 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
2530 TACATTACCG
*
2540 AAACGCAAATTTATGAGCCAACA
1 AAACGCAAATCTATGAGCCAACA
*
2563 AAACGCTAATCTATGAGCCAACA
1 AAACGCAAATCTATGAGCCAACA
2586 AA
1 AA
2588 CCCCTTCCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.23, G:0.12, T:0.17
Consensus pattern (23 bp):
AAACGCAAATCTATGAGCCAACA
Found at i:3462 original size:16 final size:15
Alignment explanation
Indices: 3441--3488 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
3431 AATTTTCTCG
3441 GGTCATTCGGGTTTC
1 GGTCATTCGGGTTTC
*
3456 GGCTCATTTGGG-TTC
1 GG-TCATTCGGGTTTC
*
3471 AGGTCATTCGGGTCTC
1 -GGTCATTCGGGTTTC
3487 GG
1 GG
3489 GTCTGCTGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.08, C:0.21, G:0.35, T:0.35
Consensus pattern (15 bp):
GGTCATTCGGGTTTC
Found at i:5289 original size:12 final size:12
Alignment explanation
Indices: 5272--5301 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
5262 TACTATCTAC
5272 CAAACAAATAAA
1 CAAACAAATAAA
5284 CAAACAAATAAA
1 CAAACAAATAAA
5296 CTAAAC
1 C-AAAC
5302 TCACATTCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.70, C:0.20, G:0.00, T:0.10
Consensus pattern (12 bp):
CAAACAAATAAA
Found at i:5462 original size:30 final size:30
Alignment explanation
Indices: 5422--5499 Score: 147
Period size: 30 Copynumber: 2.6 Consensus size: 30
5412 TACGTATTAA
*
5422 ATATACACATTGTTAATTTCTTTTGGCAGC
1 ATATATACATTGTTAATTTCTTTTGGCAGC
5452 ATATATACATTGTTAATTTCTTTTGGCAGC
1 ATATATACATTGTTAATTTCTTTTGGCAGC
5482 ATATATACATTGTTAATT
1 ATATATACATTGTTAATT
5500 AATAAATAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (30 bp):
ATATATACATTGTTAATTTCTTTTGGCAGC
Found at i:5537 original size:28 final size:28
Alignment explanation
Indices: 5497--5553 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
5487 TACATTGTTA
*
5497 ATTAATAAATAAAGTCATTCTAATATAT
1 ATTAATAAATAAAGTAATTCTAATATAT
* * *
5525 ATTAATATATAAAGTAATTTTAATGTAT
1 ATTAATAAATAAAGTAATTCTAATATAT
5553 A
1 A
5554 GCTATAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (28 bp):
ATTAATAAATAAAGTAATTCTAATATAT
Found at i:7325 original size:27 final size:27
Alignment explanation
Indices: 7283--7343 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
7273 TCCTCATTTT
* *
7283 AGGGGTAAAATTGTAATTTTATCAATC
1 AGGGGTAAAATAGTAAATTTATCAATC
* * *
7310 AGGGGTAATATAGTAAATTTGTCCATC
1 AGGGGTAAAATAGTAAATTTATCAATC
*
7337 ACGGGTA
1 AGGGGTA
7344 TTTTGGTAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (27 bp):
AGGGGTAAAATAGTAAATTTATCAATC
Done.