Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017086.1 Corchorus olitorius cultivar O-4 contig17119, 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: 27730
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:8568 original size:32 final size:33
Alignment explanation
Indices: 8489--8568 Score: 130
Period size: 31 Copynumber: 2.5 Consensus size: 33
8479 GTTTTTCTAT
8489 TTTAAGGCTCAAATTG-GTCAACTTTTGAAAGG
1 TTTAAGGCTCAAATTGAGTCAACTTTTGAAAGG
*
8521 TTT-AGACTCAAATTGAGT-AACTTTTGAAAGG
1 TTTAAGGCTCAAATTGAGTCAACTTTTGAAAGG
8552 TTTAAGGCTCAAATTGA
1 TTTAAGGCTCAAATTGA
8569 TGGCTAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
31 27 0.61
32 17 0.39
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (33 bp):
TTTAAGGCTCAAATTGAGTCAACTTTTGAAAGG
Found at i:16450 original size:21 final size:21
Alignment explanation
Indices: 16424--16463 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
16414 ATTGGATATA
16424 TGAAACCCCAAGGTTTCAATT
1 TGAAACCCCAAGGTTTCAATT
16445 TGAAACCCCAAGGTTTCAA
1 TGAAACCCCAAGGTTTCAA
16464 GCTTTTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (21 bp):
TGAAACCCCAAGGTTTCAATT
Found at i:16806 original size:20 final size:21
Alignment explanation
Indices: 16767--16808 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
16757 CCTCTCATGG
**
16767 AGCTTGGGATTTTCTTCATCA
1 AGCTTGGGATTTTCACCATCA
16788 AGCTT-GGATTTTCACCATCA
1 AGCTTGGGATTTTCACCATCA
16808 A
1 A
16809 ATATCTCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (21 bp):
AGCTTGGGATTTTCACCATCA
Found at i:19615 original size:108 final size:108
Alignment explanation
Indices: 19422--19642 Score: 388
Period size: 108 Copynumber: 2.0 Consensus size: 108
19412 AAAGAGGGAA
* *
19422 CTTAATAAACTACTCCTTTGTTTTTGGAAGTGGAGTACACGGGGTTCGGTATCACAAATATCAAC
1 CTTAATAAACTACTCCTCTGTTTTTGGAAGTGGAGCACACGGGGTTCGGTATCACAAATATCAAC
* * *
19487 CTTCGCGTCAGTCACGACCCAAAATTATGAGTATGCAAAGCAC
66 CTTCGCGTCAGTCACAACCCAAAATCACGAGTATGCAAAGCAC
19530 CTTAATAAACTACTCCTCTGTTTTTGGAAGTGGAGCACACGGGGTTCGGTATCACAAATATCAAC
1 CTTAATAAACTACTCCTCTGTTTTTGGAAGTGGAGCACACGGGGTTCGGTATCACAAATATCAAC
*
19595 CTTCGCGTCAGTCACAACCCAAAATCACGAGTATGCAAGGCAC
66 CTTCGCGTCAGTCACAACCCAAAATCACGAGTATGCAAAGCAC
19638 CTTAA
1 CTTAA
19643 ATGCGTAAGT
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 107 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (108 bp):
CTTAATAAACTACTCCTCTGTTTTTGGAAGTGGAGCACACGGGGTTCGGTATCACAAATATCAAC
CTTCGCGTCAGTCACAACCCAAAATCACGAGTATGCAAAGCAC
Found at i:20787 original size:20 final size:21
Alignment explanation
Indices: 20748--20789 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
20738 CCTCTCACGG
**
20748 AGCTTGGGATTTTCTTCATCA
1 AGCTTGGGATTTTCACCATCA
20769 AGCTT-GGATTTTCACCATCA
1 AGCTTGGGATTTTCACCATCA
20789 A
1 A
20790 ATATATCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (21 bp):
AGCTTGGGATTTTCACCATCA
Found at i:24222 original size:86 final size:86
Alignment explanation
Indices: 24076--24249 Score: 303
Period size: 86 Copynumber: 2.0 Consensus size: 86
24066 ATTTCAGCTT
*
24076 AAAATTCGTTCTATAACTACCCCAAAAGGCTTGTCGAAATTCTGACCAGAAACATATATTAGTGT
1 AAAATTCGTTCTATAACTACCCCAAAAGGCTTGTCAAAATTCTGACCAGAAACATATATTAGTGT
* *
24141 TTTTCAGAACTGTTGACACTC
66 TTTTCAGAACTCTGGACACTC
* *
24162 AAAATTCGTTCTATAACTACCCCAAAAGGCTTGTCAAAATTCTGACCAGAAATATCTATTAGTGT
1 AAAATTCGTTCTATAACTACCCCAAAAGGCTTGTCAAAATTCTGACCAGAAACATATATTAGTGT
24227 TTTTCAGAACTCTGGACACTC
66 TTTTCAGAACTCTGGACACTC
24248 AA
1 AA
24250 CGAAAAAATT
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 83 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.31
Consensus pattern (86 bp):
AAAATTCGTTCTATAACTACCCCAAAAGGCTTGTCAAAATTCTGACCAGAAACATATATTAGTGT
TTTTCAGAACTCTGGACACTC
Found at i:26788 original size:17 final size:17
Alignment explanation
Indices: 26766--26799 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
26756 TTGGATTGAT
26766 ACAATCATATAATGGAG
1 ACAATCATATAATGGAG
26783 ACAATCATATAATGGAG
1 ACAATCATATAATGGAG
26800 GACTACTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.24
Consensus pattern (17 bp):
ACAATCATATAATGGAG
Done.