Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016983.1 Corchorus olitorius cultivar O-4 contig17016, 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: 11582
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:3468 original size:23 final size:21
Alignment explanation
Indices: 3437--3484 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
3427 AAAAAACCAA
*
3437 GCTCCGTGCTTATTTTCTCTTTG
1 GCTCCGTGC-CATTTTC-CTTTG
* *
3460 GCTCTGTGCCATTTTCCTTTT
1 GCTCCGTGCCATTTTCCTTTG
3481 GCTC
1 GCTC
3485 ATCACGAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 8 0.36
22 6 0.27
23 8 0.36
ACGTcount: A:0.04, C:0.29, G:0.17, T:0.50
Consensus pattern (21 bp):
GCTCCGTGCCATTTTCCTTTG
Found at i:4891 original size:11 final size:10
Alignment explanation
Indices: 4875--4926 Score: 54
Period size: 11 Copynumber: 5.1 Consensus size: 10
4865 AAATTCGTGT
4875 TTGAAGACTTA
1 TTGAAGA-TTA
*
4886 TTGAAGATAA
1 TTGAAGATTA
4896 TTTGAAGA-T-
1 -TTGAAGATTA
4905 TTGAAGATTA
1 TTGAAGATTA
4915 TTGAAGAATTA
1 TTGAAG-ATTA
4926 T
1 T
4927 CTCAAGAGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
8 7 0.20
9 1 0.03
10 8 0.23
11 19 0.54
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.38
Consensus pattern (10 bp):
TTGAAGATTA
Found at i:4910 original size:19 final size:18
Alignment explanation
Indices: 4886--4921 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4876 TGAAGACTTA
4886 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
4905 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
4922 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:6126 original size:47 final size:47
Alignment explanation
Indices: 6057--6169 Score: 208
Period size: 47 Copynumber: 2.4 Consensus size: 47
6047 TAGCAAATCG
6057 TTAAGCCTTGACGGGTAATTGATTAGCTAGGAAGTAAAAGGGGTAAT
1 TTAAGCCTTGACGGGTAATTGATTAGCTAGGAAGTAAAAGGGGTAAT
*
6104 TTAAGCCTTGACAGGTAATTGATTAGCTAGGAAGTAAAAGGGGTAAT
1 TTAAGCCTTGACGGGTAATTGATTAGCTAGGAAGTAAAAGGGGTAAT
*
6151 TTAAGTCTTGACGGGTAAT
1 TTAAGCCTTGACGGGTAAT
6170 CTTATCTAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 63 1.00
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.29
Consensus pattern (47 bp):
TTAAGCCTTGACGGGTAATTGATTAGCTAGGAAGTAAAAGGGGTAAT
Found at i:6787 original size:31 final size:31
Alignment explanation
Indices: 6747--6818 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
6737 TGCATTTTTG
*
6747 AAAAAAAAAACGAGTTTTTGCGTTTTC-TAA
1 AAAAAAAAAACGAGTTTCTGCGTTTTCATAA
***
6777 AATAAAAAAAATTTGTTTCTGCGTTTTCATAA
1 AA-AAAAAAAACGAGTTTCTGCGTTTTCATAA
*
6809 GAAAAAAAAA
1 AAAAAAAAAA
6819 TATTTTCTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 2 0.06
31 29 0.83
32 4 0.11
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (31 bp):
AAAAAAAAAACGAGTTTCTGCGTTTTCATAA
Found at i:6819 original size:31 final size:31
Alignment explanation
Indices: 6760--6819 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
6750 AAAAAAACGA
*
6760 GTTTTTGCGTTTTCTAAAATAAAAAAAATTT
1 GTTTCTGCGTTTTCTAAAATAAAAAAAATTT
*
6791 GTTTCTGCGTTTTCATAAGA-AAAAAAAAT
1 GTTTCTGCGTTTTC-TAAAATAAAAAAAAT
6820 ATTTTCTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (31 bp):
GTTTCTGCGTTTTCTAAAATAAAAAAAATTT
Found at i:6826 original size:30 final size:30
Alignment explanation
Indices: 6761--6826 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
6751 AAAAAACGAG
*
6761 TTTT-TGCGTTTTCTAAAATAAAAAAAATT
1 TTTTCTGCGTTTTCTAAAATAAAAAAAATA
*
6790 TGTTTCTGCGTTTTCATAAGA-AAAAAAAATA
1 T-TTTCTGCGTTTTC-TAAAATAAAAAAAATA
6821 TTTTCT
1 TTTTCT
6827 TTATTTTCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 1 0.03
30 8 0.25
31 19 0.59
32 4 0.12
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (30 bp):
TTTTCTGCGTTTTCTAAAATAAAAAAAATA
Found at i:10152 original size:11 final size:10
Alignment explanation
Indices: 10136--10187 Score: 54
Period size: 11 Copynumber: 5.1 Consensus size: 10
10126 AAGTTCGTGT
10136 TTGAAGACTTA
1 TTGAAGA-TTA
*
10147 TTGAAGATAA
1 TTGAAGATTA
10157 TTTGAAGA-T-
1 -TTGAAGATTA
10166 TTGAAGATTA
1 TTGAAGATTA
10176 TTGAAGAATTA
1 TTGAAG-ATTA
10187 T
1 T
10188 CTCAAGAGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
8 7 0.20
9 1 0.03
10 8 0.23
11 19 0.54
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.38
Consensus pattern (10 bp):
TTGAAGATTA
Found at i:10171 original size:19 final size:18
Alignment explanation
Indices: 10147--10182 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10137 TGAAGACTTA
10147 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
10166 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
10183 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.