Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021011.1 Corchorus olitorius cultivar O-4 contig21044, 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: 26101
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Found at i:2458 original size:18 final size:19
Alignment explanation
Indices: 2425--2460 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2415 TGAAGATTTA
2425 TTGAAGATAAATTGAAGAC
1 TTGAAGATAAATTGAAGAC
*
2444 TTGAAGAT-CATTGAAGA
1 TTGAAGATAAATTGAAGA
2461 ATTATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (19 bp):
TTGAAGATAAATTGAAGAC
Found at i:16326 original size:16 final size:15
Alignment explanation
Indices: 16288--16329 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
16278 ACAGAGATTG
*
16288 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
16303 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
16318 ACTAGAAAACAA
1 AC-AGAAAACAA
16330 AGCAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:19306 original size:22 final size:22
Alignment explanation
Indices: 19280--19327 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
19270 CAAAATAAGT
19280 AATAAAATTCAAAGGTAGATTC
1 AATAAAATTCAAAGGTAGATTC
19302 AATAAAATTCAAAGGTAGATTC
1 AATAAAATTCAAAGGTAGATTC
19324 AATA
1 AATA
19328 CCTTGTCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.27
Consensus pattern (22 bp):
AATAAAATTCAAAGGTAGATTC
Found at i:20476 original size:86 final size:84
Alignment explanation
Indices: 20316--20476 Score: 241
Period size: 86 Copynumber: 1.9 Consensus size: 84
20306 ATTAACACTC
* *
20316 AAATAATAATAAAGTTGAATAATAATGAGAATATTCTCTAAATCTTGCCAAATTGTGGAAGGTTT
1 AAATAATAATAAAGTTGAAGAATAATGAGAATATTCTCTAAATCTTGCCAAATTGTGGAAGATTT
*
20381 AGAAGATATTTTAAGAAAT
66 AGAAAATATTTTAAGAAAT
* * *
20400 AAATAAATTATAAAGATTGAAGAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGAT
1 AAAT-AATAATAAAG-TTGAAGAATAATGAGAATATTCTCTAAATCTTGCCAAATTGTGGAAGAT
*
20465 TTGGAAAATATT
64 TTAGAAAATATT
20477 AAATAAAATA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
84 4 0.06
85 9 0.13
86 55 0.81
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.34
Consensus pattern (84 bp):
AAATAATAATAAAGTTGAAGAATAATGAGAATATTCTCTAAATCTTGCCAAATTGTGGAAGATTT
AGAAAATATTTTAAGAAAT
Found at i:20486 original size:86 final size:84
Alignment explanation
Indices: 20316--20497 Score: 235
Period size: 86 Copynumber: 2.2 Consensus size: 84
20306 ATTAACACTC
* *
20316 AAATAATAATAAAGTTGAATAATAATGAGAATATTCTCTAAATCTTGCCAAATTGTGGAAGGTTT
1 AAATAATAATAAAGTTGAAGAATAATGAGAATATTCTCTAAATCTTGCCAAATTGTGGAAGATTT
* * *
20381 AGAAGATATTTTAAGAAAT
66 AGAAAATATTTAAAAAAAT
* * *
20400 AAATAAATTATAAAGATTGAAGAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGAT
1 AAAT-AATAATAAAG-TTGAAGAATAATGAGAATATTCTCTAAATCTTGCCAAATTGTGGAAGAT
*
20465 TTGGAAAATA-TTAAATAAAAT
64 TTAGAAAATATTTAAA-AAAAT
20486 -AATAATAA-AAAG
1 AAATAATAATAAAG
20498 AAGTTCAGAT
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
83 4 0.05
84 8 0.09
85 16 0.19
86 57 0.67
ACGTcount: A:0.48, C:0.05, G:0.15, T:0.32
Consensus pattern (84 bp):
AAATAATAATAAAGTTGAAGAATAATGAGAATATTCTCTAAATCTTGCCAAATTGTGGAAGATTT
AGAAAATATTTAAAAAAAT
Done.