Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021898.1 Corchorus olitorius cultivar O-4 contig21931, 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: 17044
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:1148 original size:76 final size:76
Alignment explanation
Indices: 1011--1161 Score: 173
Period size: 76 Copynumber: 2.0 Consensus size: 76
1001 ACAAGGACCC
* * *
1011 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCATTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
1076 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * **
1087 CGACTCCAGCTGGGTGCCCACATGGTT-TATGTGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGGTTGCAT-TG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
1149 GATGGGCTGTGTC
63 GATGGGCAGTGTC
1162 TTAGCTCATC
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
75 5 0.08
76 56 0.89
77 2 0.03
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCATTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:8135 original size:19 final size:19
Alignment explanation
Indices: 8088--8136 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
8078 TTTAATGTGG
8088 GTATACTTG-TTTGTACAT
1 GTATACTTGTTTTGTACAT
*
8106 GT-TATTTGTTTTGTA-AGT
1 GTATACTTGTTTTGTACA-T
8124 GTATACTTGTTTT
1 GTATACTTGTTTT
8137 CACACATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 6 0.23
18 11 0.42
19 9 0.35
ACGTcount: A:0.18, C:0.06, G:0.18, T:0.57
Consensus pattern (19 bp):
GTATACTTGTTTTGTACAT
Found at i:8197 original size:16 final size:15
Alignment explanation
Indices: 8167--8211 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
8157 ATATCATCAT
*
8167 AATATATCCTTAAAA
1 AATAAATCCTTAAAA
8182 AATAAATCCTTTAAAA
1 AATAAATCC-TTAAAA
* *
8198 AATACATTCTTAAA
1 AATAAATCCTTAAA
8212 TATCCTAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (15 bp):
AATAAATCCTTAAAA
Found at i:8851 original size:2 final size:2
Alignment explanation
Indices: 8844--8881 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
8834 AATGGGTAGG
8844 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8882 TGGTTTTCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9008 original size:3 final size:3
Alignment explanation
Indices: 9002--9030 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
8992 AATACTAATA
9002 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
9031 AACAAGCAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:10074 original size:2 final size:2
Alignment explanation
Indices: 10069--10097 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10059 AATGTGTGTG
10069 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10098 TAGATTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12269 original size:19 final size:19
Alignment explanation
Indices: 12247--12283 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
12237 CAAAAGCATT
12247 AGTTCATGTAAAAAGAATC
1 AGTTCATGTAAAAAGAATC
12266 AGTTCATGTAAAAAGAAT
1 AGTTCATGTAAAAAGAAT
12284 TGATATAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.27
Consensus pattern (19 bp):
AGTTCATGTAAAAAGAATC
Found at i:13344 original size:13 final size:13
Alignment explanation
Indices: 13302--13346 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
13292 TCATGCACCC
*
13302 AAAACAATTTATTT
1 AAAACAATTTA-AT
*
13316 AAAACCATTT-AT
1 AAAACAATTTAAT
13328 AAAACAATTTAAT
1 AAAACAATTTAAT
13341 AAAACA
1 AAAACA
13347 GTAATGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 10 0.37
13 8 0.30
14 9 0.33
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAACAATTTAAT
Done.