Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021897.1 Corchorus olitorius cultivar O-4 contig21930, 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: 13636
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Found at i:1950 original size:21 final size:21
Alignment explanation
Indices: 1924--1978 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1914 CGGCCATTCA
**
1924 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCCAAGC
*
1945 CCGTGCCACCACCGGCCATGC
1 CCGTGCCACCACCGGCCAAGC
*
1966 CCGTGCCATCACC
1 CCGTGCCACCACC
1979 ATTCCAAGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.13
Consensus pattern (21 bp):
CCGTGCCACCACCGGCCAAGC
Found at i:3834 original size:11 final size:11
Alignment explanation
Indices: 3818--3865 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
3808 GAAGTTCGTG
3818 TTTGAAGACCA
1 TTTGAAGACCA
**
3829 TTTGAAGATAA
1 TTTGAAGACCA
3840 TTTGAAGA-C-
1 TTTGAAGACCA
3849 -TTGAAGACCA
1 TTTGAAGACCA
3859 -TTGAAGA
1 TTTGAAGA
3866 TTTATTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
8 7 0.22
9 1 0.03
10 7 0.22
11 17 0.53
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (11 bp):
TTTGAAGACCA
Found at i:5266 original size:15 final size:15
Alignment explanation
Indices: 5236--5277 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
5226 TTACTTTGCT
5236 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
5252 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
5267 TTGTTTTCTGT
1 TTGTTTTCTGT
5278 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:10071 original size:28 final size:27
Alignment explanation
Indices: 10033--10101 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
10023 ATCTAAGGGA
*
10033 ATTTTGGGTCATTTTCAAAATCCAGGGGC
1 ATTTT-GGTCATTTGC-AAATCCAGGGGC
**
10062 ATTTTGGTCATTTGCATGTCCAGGGGC
1 ATTTTGGTCATTTGCAAATCCAGGGGC
*
10089 ATTTTAGTCATTT
1 ATTTTGGTCATTT
10102 CAAGTACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
27 22 0.61
28 9 0.25
29 5 0.14
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (27 bp):
ATTTTGGTCATTTGCAAATCCAGGGGC
Found at i:11149 original size:23 final size:23
Alignment explanation
Indices: 11123--11169 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
11113 AGTTCAGGGC
11123 ACAAGATGGCTCACAAGCAGCAA
1 ACAAGATGGCTCACAAGCAGCAA
11146 ACAAGATGGCTCACAAGCAGCAA
1 ACAAGATGGCTCACAAGCAGCAA
11169 A
1 A
11170 TAGTTTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.26, G:0.21, T:0.09
Consensus pattern (23 bp):
ACAAGATGGCTCACAAGCAGCAA
Done.