Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012678.1 Corchorus olitorius cultivar O-4 contig12711, 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: 24210
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:12187 original size:2 final size:2
Alignment explanation
Indices: 12182--12207 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12172 ATACACACCC
12182 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
12208 TTCTCACAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12889 original size:29 final size:29
Alignment explanation
Indices: 12847--12936 Score: 171
Period size: 29 Copynumber: 3.1 Consensus size: 29
12837 GCAAAATCAG
12847 CATGTCTCTAGCCTCAAAATGTATGAATA
1 CATGTCTCTAGCCTCAAAATGTATGAATA
*
12876 CATGTCTCTAGCCTCAAAATATATGAATA
1 CATGTCTCTAGCCTCAAAATGTATGAATA
12905 CATGTCTCTAGCCTCAAAATGTATGAATA
1 CATGTCTCTAGCCTCAAAATGTATGAATA
12934 CAT
1 CAT
12937 TAATATATCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (29 bp):
CATGTCTCTAGCCTCAAAATGTATGAATA
Found at i:14820 original size:19 final size:18
Alignment explanation
Indices: 14782--14817 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
14772 TAAGCCCTTT
14782 TTTTATAGATTCATAAAA
1 TTTTATAGATTCATAAAA
14800 TTTTATAGATTCATAAAA
1 TTTTATAGATTCATAAAA
14818 ATTATATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (18 bp):
TTTTATAGATTCATAAAA
Found at i:14825 original size:19 final size:18
Alignment explanation
Indices: 14785--14825 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
14775 GCCCTTTTTT
*
14785 TATAGATTCATAAAATTT
1 TATAGATTCATAAAATTA
14803 TATAGATTCATAAAAATTA
1 TATAGATTCAT-AAAATTA
14822 TATA
1 TATA
14826 AAAAAATGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (18 bp):
TATAGATTCATAAAATTA
Found at i:14996 original size:22 final size:21
Alignment explanation
Indices: 14961--15012 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
14951 TCCGTTGACG
* *
14961 AAATAAT-TAAATAAAAGGAT
1 AAATAATAAAAATAAAACGAT
*
14981 AATTAAATAAAAATAAAACGAT
1 AAAT-AATAAAAATAAAACGAT
15003 AAATAATAAA
1 AAATAATAAA
15013 GATTCTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 3 0.12
21 9 0.35
22 14 0.54
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (21 bp):
AAATAATAAAAATAAAACGAT
Found at i:19498 original size:13 final size:13
Alignment explanation
Indices: 19480--19505 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19470 AAGGTAACAA
19480 CAAAAATCATCAC
1 CAAAAATCATCAC
19493 CAAAAATCATCAC
1 CAAAAATCATCAC
19506 TCATGCCAAG
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:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:23846 original size:11 final size:11
Alignment explanation
Indices: 23830--23855 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
23820 AGATAATTTC
23830 TTTTCTTCTAG
1 TTTTCTTCTAG
23841 TTTTCTTCTAG
1 TTTTCTTCTAG
23852 TTTT
1 TTTT
23856 ATAGGGCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Done.