Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021864.1 Corchorus olitorius cultivar O-4 contig21897, 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: 11790
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:6421 original size:18 final size:18
Alignment explanation
Indices: 6384--6422 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6374 AAAGTTTTCA
* *
6384 AAATGGGATTTTCATTTG
1 AAATGGGATTTTAATGTG
*
6402 AAATTGGATTTTAATGTG
1 AAATGGGATTTTAATGTG
6420 AAA
1 AAA
6423 ACTTTGATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.41
Consensus pattern (18 bp):
AAATGGGATTTTAATGTG
Found at i:6839 original size:16 final size:15
Alignment explanation
Indices: 6820--6856 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
6810 AAATTCCCAT
*
6820 AAAAAATGATGAAATG
1 AAAAAATGA-AAAATG
6836 AAAAAATGAAAAATG
1 AAAAAATGAAAAATG
6851 AAAAAA
1 AAAAAA
6857 AATGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (15 bp):
AAAAAATGAAAAATG
Found at i:6842 original size:8 final size:8
Alignment explanation
Indices: 6820--6872 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
6810 AAATTCCCAT
6820 AAAAAATG
1 AAAAAATG
**
6828 ATGAAATG
1 AAAAAATG
6836 AAAAAATG
1 AAAAAATG
6844 -AAAAATG
1 AAAAAATG
6851 AAAAAAAATG
1 --AAAAAATG
*
6861 AAAAAATT
1 AAAAAATG
6869 AAAA
1 AAAA
6873 TAAAGGCACT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
7 7 0.19
8 23 0.62
10 7 0.19
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (8 bp):
AAAAAATG
Found at i:6857 original size:16 final size:16
Alignment explanation
Indices: 6820--6865 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
6810 AAATTCCCAT
*
6820 AAAAAATGATGAAATG-
1 AAAAAATGA-AAAATGA
6836 AAAAAATGAAAAATGAA
1 AAAAAATGAAAAATG-A
6853 AAAAAATGAAAAA
1 AAAAAATGAAAAA
6866 ATTAAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 5 0.19
16 9 0.33
17 13 0.48
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (16 bp):
AAAAAATGAAAAATGA
Found at i:9483 original size:163 final size:163
Alignment explanation
Indices: 9060--9485 Score: 582
Period size: 163 Copynumber: 2.6 Consensus size: 163
9050 TTCCATTTGA
* * * * * *
9060 TAAAACCTCCGGGTATCATTTCATTTTATCAAGTTTTTCACCAAAAATTCATGTTTAAGTTAAAA
1 TAAAACCTCCGGGTACCATTTGATTTCATCAAATTTTTCATCAAAAATTCAAGTTTAAG-----A
* * *
9125 TCCTTGGTCAAGGTCTCTATTCAGAGTTTGCGTTGGTAAGTCCTCCGGGCACAAATTCAGAAACC
61 TCCTTGTTTAAGGTCTCTATTCAGAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCAGAAACC
9190 TCCGAGTAGTAATTCTGATAAGTCCTCCGGGCAATCGG
126 TCCGAGTAGTAATTCTGATAAGTCCTCCGGGCAATCGG
* * * *
9228 TAAAACCTCCGGGTACCATTTGATTTCATCAAATTTTTCATCAAAAATTTAAGTATAAAATCCTG
1 TAAAACCTCCGGGTACCATTTGATTTCATCAAATTTTTCATCAAAAATTCAAGTTTAAGATCCTT
* * * *
9293 GTTTAAGGTCCCTATTCAGAGTTTGCATTGGTAAGTCTTCTGGGCACAAATTCAGAAACCTCCGG
66 GTTTAAGGTCTCTATTCAGAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCAGAAACCTCCGA
*
9358 GTAGTAATTCTGATAAGTCCTCTGGGCAATCGG
131 GTAGTAATTCTGATAAGTCCTCCGGGCAATCGG
* *
9391 TAAAACCTCCGGGTACCATTTGATTTCATCAAATTTTTCATCACAAATTCAGGTTTAAGATCCTT
1 TAAAACCTCCGGGTACCATTTGATTTCATCAAATTTTTCATCAAAAATTCAAGTTTAAGATCCTT
* * * * *
9456 GTTTAAAGTCTCAATTTAAAATTTGCATTG
66 GTTTAAGGTCTCTATTCAGAGTTTGCATTG
9486 ATAGGACCTC
Statistics
Matches: 228, Mismatches: 30, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
163 178 0.78
168 50 0.22
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (163 bp):
TAAAACCTCCGGGTACCATTTGATTTCATCAAATTTTTCATCAAAAATTCAAGTTTAAGATCCTT
GTTTAAGGTCTCTATTCAGAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCAGAAACCTCCGA
GTAGTAATTCTGATAAGTCCTCCGGGCAATCGG
Found at i:9650 original size:30 final size:30
Alignment explanation
Indices: 9616--10329 Score: 897
Period size: 30 Copynumber: 23.8 Consensus size: 30
9606 CTTTATCAGT
* *
9616 TTTATTTTAATCCTGATGGAGGAT-ATTTGC
1 TTTATTTTAATCCTGTTTGAGGATCA-TTGC
* *
9646 TTTATTTTAATCCTGGTTAAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
9676 TTTATTTTAATCCTGGTTGAGGATCGTTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
9706 TGTATGTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
9736 TTCATTTTAATCATGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
*
9766 TTTATTTTTTAA--CTGGTTGAGGAT-ATTTGC
1 TTTA--TTTTAATCCTGTTTGAGGATCA-TTGC
* * *
9796 TCTATGTTAAT-CTGGTTT-AGGATCATTAC
1 TTTATTTTAATCCT-GTTTGAGGATCATTGC
* * *
9825 TTCATTTTAATCCCGTTTGAGGATCATCGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
*
9855 TCTATTTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
9885 TTTATTTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
**
9915 TTTATTTTTGTCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
*
9945 TTTATTTTAATCCTGTTTGAGGATCATTTC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* **
9975 TTTATTTTAATCCTTTTTGAGGATCATTAA
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
10005 TTTTTTTTAGTCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
**
10035 TTTATTTTTGTCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
10065 TTTATTTTTATCCTGGTTGAGGAT-ATTTGC
1 TTTATTTTAATCCTGTTTGAGGATCA-TTGC
* * *
10095 TCTATGTTAATCCTGGTTT-AGGATCATTAC
1 TTTATTTTAATCCT-GTTTGAGGATCATTGC
* *
10125 TTCATTTTAATCCTGTTTGAGGATCATCGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
10155 TCTATTTTAATCCTGTTTG-GAAATCATTGC
1 TTTATTTTAATCCTGTTTGAG-GATCATTGC
*
10185 TTTATTTTAATCCTGTTTGAGGATCATTAC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
10215 TTTATTTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
*
10245 TTTATTTTAATCCTGTTTGAGGATCATTTC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* ** * *
10275 TTCATTTTAATTTTTTTTGAGGATCATTAC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
10305 TTTATTTTAATCCTGTTTGAGGATC
1 TTTATTTTAATCCTGTTTGAGGATC
10330 TGTAGACACT
Statistics
Matches: 593, Mismatches: 76, Indels: 30
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.01
29 29 0.05
30 547 0.92
31 6 0.01
32 6 0.01
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (30 bp):
TTTATTTTAATCCTGTTTGAGGATCATTGC
Found at i:10488 original size:27 final size:25
Alignment explanation
Indices: 10458--10507 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
10448 TTTTGTAGTA
10458 TTGAAATTTCGGTTTTGAAACCAAAGC
1 TTGAAATTTC--TTTTGAAACCAAAGC
* *
10485 TTGAATTTTCTTTTGAACCCAAA
1 TTGAAATTTCTTTTGAAACCAAA
10508 TTCTTGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.57
27 9 0.43
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (25 bp):
TTGAAATTTCTTTTGAAACCAAAGC
Found at i:10739 original size:9 final size:9
Alignment explanation
Indices: 10712--10745 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
10702 ACAAAACAAC
10712 AAAAAAAAT
1 AAAAAAAAT
10721 AATAAAAAAT
1 AA-AAAAAAT
*
10731 AAATAAAAT
1 AAAAAAAAT
10740 AAAAAA
1 AAAAAA
10746 GGAATGTCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAAAAAAT
Done.