Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008788.1 Corchorus olitorius cultivar O-4 contig08815, 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, 732
Length: 1221
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:19 original size:12 final size:12
Alignment explanation
Indices: 3--27 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1 AA
3 ACATAATTTCAT
1 ACATAATTTCAT
15 ACATAATTTCAT
1 ACATAATTTCAT
27 A
1 A
28 AATTTTCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (12 bp):
ACATAATTTCAT
Found at i:84 original size:14 final size:14
Alignment explanation
Indices: 65--93 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
55 AGATAGAAAA
65 TCAAAAATATATTC
1 TCAAAAATATATTC
79 TCAAAAATATATTC
1 TCAAAAATATATTC
93 T
1 T
94 ATATATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (14 bp):
TCAAAAATATATTC
Found at i:125 original size:22 final size:22
Alignment explanation
Indices: 100--174 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
90 TTCTATATAT
*
100 AATAGAATAAATAGAATTATAG
1 AATAGAATAAATAGAATAATAG
*
122 AATA-AAGAATATAGAATAAATA-
1 AATAGAATAA-ATAGAAT-AATAG
144 AATAGAAT--ATAGAA-AATAG
1 AATAGAATAAATAGAATAATAG
*
163 AATAAAATAAAT
1 AATAGAATAAAT
175 TTCGAATTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 13
0.72 0.07 0.22
Matches are distributed among these distances:
18 4 0.09
19 7 0.16
20 6 0.14
21 6 0.14
22 15 0.35
23 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (22 bp):
AATAGAATAAATAGAATAATAG
Found at i:136 original size:14 final size:14
Alignment explanation
Indices: 101--168 Score: 75
Period size: 14 Copynumber: 4.7 Consensus size: 14
91 TCTATATATA
101 ATAGAATAAATAGAATT
1 ATAGAAT-AA-AGAA-T
118 ATAGAATAAAGAAT
1 ATAGAATAAAGAAT
*
132 ATAGAATAAATAA-
1 ATAGAATAAAGAAT
* *
145 ATAGAATATAGAAA
1 ATAGAATAAAGAAT
159 ATAGAATAAA
1 ATAGAATAAA
169 ATAAATTTCG
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
13 11 0.24
14 22 0.48
15 4 0.09
16 2 0.04
17 7 0.15
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (14 bp):
ATAGAATAAAGAAT
Found at i:148 original size:27 final size:28
Alignment explanation
Indices: 100--174 Score: 89
Period size: 27 Copynumber: 2.6 Consensus size: 28
90 TTCTATATAT
*
100 AATAGAATAAATAGAATTATAGAATAAAGAA
1 AATAGAATAAA-ATAA--ATAGAATAAAGAA
* *
131 TATAGAAT-AAATAAATAGAATATAGAA
1 AATAGAATAAAATAAATAGAATAAAGAA
158 AATAGAATAAAATAAAT
1 AATAGAATAAAATAAAT
175 TTCGAATTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
27 19 0.49
28 8 0.21
29 3 0.08
30 2 0.05
31 7 0.18
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (28 bp):
AATAGAATAAAATAAATAGAATAAAGAA
Found at i:174 original size:14 final size:13
Alignment explanation
Indices: 118--174 Score: 60
Period size: 14 Copynumber: 4.2 Consensus size: 13
108 AAATAGAATT
*
118 ATAGAATAAAGAAT
1 ATAGAATAAA-AAA
*
132 ATAGAATAAATAA
1 ATAGAATAAAAAA
*
145 ATAGAATATAGAAA
1 ATAGAATA-AAAAA
159 ATAGAATAAAATAA
1 ATAGAATAAAA-AA
173 AT
1 AT
175 TTCGAATTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 11 0.31
14 25 0.69
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.23
Consensus pattern (13 bp):
ATAGAATAAAAAA
Found at i:314 original size:15 final size:15
Alignment explanation
Indices: 294--322 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
284 GTTTTGCAGT
294 TATATAGTACTATAC
1 TATATAGTACTATAC
309 TATATAGTACTATA
1 TATATAGTACTATA
323 TCGAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (15 bp):
TATATAGTACTATAC
Done.