Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021760.1 Corchorus olitorius cultivar O-4 contig21793, 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: 15789
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:3111 original size:22 final size:23
Alignment explanation
Indices: 3072--3114 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
3062 AATCCTAATC
3072 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
3095 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
3115 ACTCCTTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Found at i:4222 original size:26 final size:26
Alignment explanation
Indices: 4183--4237 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
4173 GTTAATGGCA
4183 AATGCAAGTCGAGATTGGAAATTATG
1 AATGCAAGTCGAGATTGGAAATTATG
* * *
4209 AATGCAGGTGGAGATTTGAAATTATG
1 AATGCAAGTCGAGATTGGAAATTATG
4235 AAT
1 AAT
4238 ATCTTTATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.05, G:0.27, T:0.29
Consensus pattern (26 bp):
AATGCAAGTCGAGATTGGAAATTATG
Found at i:4846 original size:50 final size:52
Alignment explanation
Indices: 4775--4887 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
4765 AAAATGATGC
* * *
4775 TATTAA-ATTCCTATCTATATTTGC-T-CATACTTTCTATTACATGTTTTCT
1 TATTAAGAGTCCTACCTATATTTGCTTACATACTTTCTATTACATCTTTTCT
*
4824 TATTAAGAGTCCTACCTGTATTTGCTTTACATACTTTCTATTACATCTTTTCT
1 TATTAAGAGTCCTACCTATATTTGC-TTACATACTTTCTATTACATCTTTTCT
4877 TATTAAGAGTC
1 TATTAAGAGTC
4888 TTCATATAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
49 6 0.11
50 15 0.27
52 1 0.02
53 34 0.61
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.50
Consensus pattern (52 bp):
TATTAAGAGTCCTACCTATATTTGCTTACATACTTTCTATTACATCTTTTCT
Found at i:6678 original size:18 final size:18
Alignment explanation
Indices: 6663--6697 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
6653 TCAATAATAG
6663 TTCTTGGCAAAATAATGA
1 TTCTTGGCAAAATAATGA
6681 TTCTTGGCAAAATAATG
1 TTCTTGGCAAAATAATG
6698 GTTGTAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.34
Consensus pattern (18 bp):
TTCTTGGCAAAATAATGA
Found at i:6731 original size:10 final size:10
Alignment explanation
Indices: 6702--6732 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
6692 ATAATGGTTG
*
6702 TAAAAGCCTG
1 TAAAAGCCTT
6712 TAAAAGCCTT
1 TAAAAGCCTT
6722 TAAAAGCCTT
1 TAAAAGCCTT
6732 T
1 T
6733 GAATTGGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (10 bp):
TAAAAGCCTT
Found at i:7165 original size:10 final size:10
Alignment explanation
Indices: 7150--7186 Score: 74
Period size: 10 Copynumber: 3.7 Consensus size: 10
7140 AGAGTAGCAA
7150 GCTTTTAAAG
1 GCTTTTAAAG
7160 GCTTTTAAAG
1 GCTTTTAAAG
7170 GCTTTTAAAG
1 GCTTTTAAAG
7180 GCTTTTA
1 GCTTTTA
7187 CAACCATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.43
Consensus pattern (10 bp):
GCTTTTAAAG
Found at i:11890 original size:6 final size:6
Alignment explanation
Indices: 11879--11925 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
11869 ATTTCTTATT
* *
11879 GGACTC GGACTC GGACCC GGACTC GGACTC GGACTC GGACTC AGACT
1 GGACTC GGACTC GGACTC GGACTC GGACTC GGACTC GGACTC GGACT
11926 TGAGAGTAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.19, C:0.34, G:0.32, T:0.15
Consensus pattern (6 bp):
GGACTC
Found at i:12607 original size:36 final size:36
Alignment explanation
Indices: 12567--12637 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
12557 TAAATCCCTC
* *
12567 CTCTTCATGGAATGCATATTGGTATATTCATTGATT
1 CTCTTCATGAAATGCATATTGGTATATACATTGATT
12603 CTCTTCATGAAATGCATATTGGTATATACATTGAT
1 CTCTTCATGAAATGCATATTGGTATATACATTGAT
12638 GAGTGAGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.42
Consensus pattern (36 bp):
CTCTTCATGAAATGCATATTGGTATATACATTGATT
Found at i:12858 original size:3 final size:3
Alignment explanation
Indices: 12850--12888 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
12840 ATAAATATAA
12850 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
12889 AATAATAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:12907 original size:4 final size:4
Alignment explanation
Indices: 12898--12927 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
12888 TAATAATAAT
12898 AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
12928 CTCATTCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Done.