Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009696.1 Corchorus olitorius cultivar O-4 contig09728, 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: 14956
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Found at i:1177 original size:9 final size:9
Alignment explanation
Indices: 1157--1212 Score: 87
Period size: 9 Copynumber: 6.3 Consensus size: 9
1147 TTAAATAATT
1157 TAATTTCC-
1 TAATTTCCA
1165 TAATTTCCA
1 TAATTTCCA
*
1174 TAATTTCCC
1 TAATTTCCA
1183 TAATTTCCA
1 TAATTTCCA
*
1192 TAATTTCCC
1 TAATTTCCA
1201 TAATTTCCA
1 TAATTTCCA
1210 TAA
1 TAA
1213 GTAATTTGGG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
8 8 0.19
9 35 0.81
ACGTcount: A:0.30, C:0.25, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATTTCCA
Found at i:1186 original size:18 final size:18
Alignment explanation
Indices: 1157--1212 Score: 105
Period size: 18 Copynumber: 3.2 Consensus size: 18
1147 TTAAATAATT
1157 TAATTT-CCTAATTTCCA
1 TAATTTCCCTAATTTCCA
1174 TAATTTCCCTAATTTCCA
1 TAATTTCCCTAATTTCCA
1192 TAATTTCCCTAATTTCCA
1 TAATTTCCCTAATTTCCA
1210 TAA
1 TAA
1213 GTAATTTGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 6 0.16
18 32 0.84
ACGTcount: A:0.30, C:0.25, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATTTCCCTAATTTCCA
Found at i:3551 original size:35 final size:35
Alignment explanation
Indices: 3512--3583 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
3502 CAAGTATTCG
3512 AATCCGAGACCTCCAACAAGAAGTCCCAAGCTCAT
1 AATCCGAGACCTCCAACAAGAAGTCCCAAGCTCAT
3547 AATCCGAGACCTCCAACAAGAAGTCCCAAGCTCAT
1 AATCCGAGACCTCCAACAAGAAGTCCCAAGCTCAT
3582 AA
1 AA
3584 CCACTGGGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.39, C:0.33, G:0.14, T:0.14
Consensus pattern (35 bp):
AATCCGAGACCTCCAACAAGAAGTCCCAAGCTCAT
Found at i:12219 original size:103 final size:102
Alignment explanation
Indices: 12012--12218 Score: 344
Period size: 103 Copynumber: 2.0 Consensus size: 102
12002 GAATAAATTC
*
12012 AAATCTTATTACACCTGTTTTAAATAAAGCAGTACTGCATGATTTGAAAATATGCTCTCCAATAA
1 AAATCTTATTACACCTGTTTTAAATAAAGCAATACTGCATGATTTGAAAATATGCTCTCCAATAA
* * *
12077 CATGTTTATCTCCAATTTACTAAAATTACCAGGCAAAA
66 CATGTTTATCTCCAATCTACT-AAATAACCAGGAAAAA
*
12115 AAATCTTATTACACCTTTTTTAAATAAAGCAATACTGCATGATTTGAAAATATGCTCTCCAATAA
1 AAATCTTATTACACCTGTTTTAAATAAAGCAATACTGCATGATTTGAAAATATGCTCTCCAATAA
*
12180 CATGTTTATCTCCAATCTAGT-AATAACCAGGAAAAA
66 CATGTTTATCTCCAATCTACTAAATAACCAGGAAAAA
12216 AAA
1 AAA
12219 AGCTATAGAG
Statistics
Matches: 98, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
101 16 0.16
103 82 0.84
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (102 bp):
AAATCTTATTACACCTGTTTTAAATAAAGCAATACTGCATGATTTGAAAATATGCTCTCCAATAA
CATGTTTATCTCCAATCTACTAAATAACCAGGAAAAA
Done.