Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020059.1 Corchorus olitorius cultivar O-4 contig20092, 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: 36999
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:2840 original size:18 final size:18
Alignment explanation
Indices: 2813--2852 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
2803 CAACGAACTC
*
2813 CTCTGGCAACTCAATGTT
1 CTCTGCCAACTCAATGTT
2831 CTCTGCCAACTCAATGTT
1 CTCTGCCAACTCAATGTT
2849 CTCT
1 CTCT
2853 ACCTTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (18 bp):
CTCTGCCAACTCAATGTT
Found at i:4698 original size:23 final size:23
Alignment explanation
Indices: 4672--4715 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
4662 TATGGTAACT
4672 GGATTCAAAAATCATATTGATCC
1 GGATTCAAAAATCATATTGATCC
*
4695 GGATTCAAAAATCTTATTGAT
1 GGATTCAAAAATCATATTGAT
4716 TAGCTATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (23 bp):
GGATTCAAAAATCATATTGATCC
Found at i:5955 original size:29 final size:28
Alignment explanation
Indices: 5880--5963 Score: 82
Period size: 27 Copynumber: 3.0 Consensus size: 28
5870 GTGGGCTGAA
* *
5880 ATCT-TAATTTGGTATCAAACCTTTTAA
1 ATCTCTAATTTAGTATCAAACCTTTTAT
* *
5907 ATCTC-AACTTAGTATGAAACCTTTTAT
1 ATCTCTAATTTAGTATCAAACCTTTTAT
* * *
5934 TTCTACTAATTTAGTACCAAACGTTTTAT
1 ATCT-CTAATTTAGTATCAAACCTTTTAT
5963 A
1 A
5964 AATAAACCAA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
27 25 0.57
28 1 0.02
29 18 0.41
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (28 bp):
ATCTCTAATTTAGTATCAAACCTTTTAT
Found at i:23095 original size:13 final size:13
Alignment explanation
Indices: 23077--23102 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23067 AAACCCTTGG
23077 GGATGAAACATCT
1 GGATGAAACATCT
23090 GGATGAAACATCT
1 GGATGAAACATCT
23103 CATGATGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
GGATGAAACATCT
Found at i:30535 original size:21 final size:20
Alignment explanation
Indices: 30511--30554 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
30501 AGCACAATTA
30511 AAATCG-AAATTGAAAGTAAAG
1 AAATCGAAAATT-AAAG-AAAG
30532 AAATCGAAAATTAAAGAAAG
1 AAATCGAAAATTAAAGAAAG
30552 AAA
1 AAA
30555 AGGAAAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 10 0.45
22 5 0.23
ACGTcount: A:0.64, C:0.05, G:0.16, T:0.16
Consensus pattern (20 bp):
AAATCGAAAATTAAAGAAAG
Found at i:30560 original size:20 final size:22
Alignment explanation
Indices: 30517--30564 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
30507 ATTAAAATCG
*
30517 AAATTGAAAGTAAAGAAATCGA
1 AAATTGAAAGTAAAGAAAACGA
*
30539 AAATT-AAAG-AAAGAAAAGGA
1 AAATTGAAAGTAAAGAAAACGA
30559 AAATTG
1 AAATTG
30565 CGATTAGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 14 0.61
21 4 0.17
22 5 0.22
ACGTcount: A:0.62, C:0.02, G:0.19, T:0.17
Consensus pattern (22 bp):
AAATTGAAAGTAAAGAAAACGA
Found at i:33780 original size:2 final size:2
Alignment explanation
Indices: 33773--33805 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
33763 AGAAAATCCT
33773 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
33806 TTGTTTACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Done.