Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020943.1 Corchorus olitorius cultivar O-4 contig20976, 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: 9763
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:3209 original size:12 final size:12
Alignment explanation
Indices: 3192--3227 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3182 TTGTTAACTA
3192 AATACTATTACT
1 AATACTATTACT
3204 AATACTATTACT
1 AATACTATTACT
3216 -AT--TATTACT
1 AATACTATTACT
3225 AAT
1 AAT
3228 TAAGGAACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 7 0.30
10 2 0.09
11 2 0.09
12 12 0.52
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (12 bp):
AATACTATTACT
Found at i:7069 original size:13 final size:13
Alignment explanation
Indices: 7038--7197 Score: 108
Period size: 13 Copynumber: 12.8 Consensus size: 13
7028 GTGAAACAAG
*
7038 TCTTCATCAAAAT
1 TCTTCATCAAAGT
*
7051 TATTCATCAAAGT
1 TCTTCATCAAAGT
*
7064 TCTTCAAC-AAG-
1 TCTTCATCAAAGT
*
7075 TCTCCA-CGAAAGT
1 TCTTCATC-AAAGT
*
7088 TATTCATCAAAGT
1 TCTTCATCAAAGT
*
7101 TCTTCAAC-AAG-
1 TCTTCATCAAAGT
* *
7112 TCTCCACCAAAGT
1 TCTTCATCAAAGT
*
7125 TATTCATCAAAGT
1 TCTTCATCAAAGT
*
7138 TCTTCAAC-AAG-
1 TCTTCATCAAAGT
7149 TCTTCATCAAATTGT
1 TCTTCATCAAA--GT
*
7164 TCTTCAAC-AAGT
1 TCTTCATCAAAGT
7176 T-TTCACTC--AGT
1 TCTTCA-TCAAAGT
7187 TCTTCATCAAA
1 TCTTCATCAAA
7198 TTTTCCACCA
Statistics
Matches: 114, Mismatches: 19, Indels: 28
0.71 0.12 0.17
Matches are distributed among these distances:
10 1 0.01
11 28 0.25
12 25 0.22
13 49 0.43
14 4 0.04
15 7 0.06
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.34
Consensus pattern (13 bp):
TCTTCATCAAAGT
Found at i:7073 original size:37 final size:37
Alignment explanation
Indices: 7032--7159 Score: 204
Period size: 37 Copynumber: 3.5 Consensus size: 37
7022 CCAAGAGTGA
* *
7032 AACAAGTCTTCATCAAAATTATTCATCAAAGTTCTTC
1 AACAAGTCTCCATCAAAGTTATTCATCAAAGTTCTTC
7069 AACAAGTCTCCA-CGAAAGTTATTCATCAAAGTTCTTC
1 AACAAGTCTCCATC-AAAGTTATTCATCAAAGTTCTTC
*
7106 AACAAGTCTCCACCAAAGTTATTCATCAAAGTTCTTC
1 AACAAGTCTCCATCAAAGTTATTCATCAAAGTTCTTC
*
7143 AACAAGTCTTCATCAAA
1 AACAAGTCTCCATCAAA
7160 TTGTTCTTCA
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
36 1 0.01
37 83 0.98
38 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.30
Consensus pattern (37 bp):
AACAAGTCTCCATCAAAGTTATTCATCAAAGTTCTTC
Found at i:7170 original size:26 final size:24
Alignment explanation
Indices: 7053--7192 Score: 101
Period size: 24 Copynumber: 5.7 Consensus size: 24
7043 ATCAAAATTA
7053 TTCATCAAAGTTCTTCAACAAGTC
1 TTCATCAAAGTTCTTCAACAAGTC
* * *
7077 TCCA-CGAAAGTTATTCATCAAAGTTC
1 TTCATC-AAAGTTCTTCAAC-AAG-TC
* * * *
7103 TTCAAC-AAG-TCTCCACCAAAGTTA
1 TTCATCAAAGTTCTTCAAC-AAG-TC
7127 TTCATCAAAGTTCTTCAACAAGTC
1 TTCATCAAAGTTCTTCAACAAGTC
*
7151 TTCATCAAATTGTTCTTCAACAAGTT
1 TTCATCAAA--GTTCTTCAACAAGTC
7177 TTCACTC--AGTTCTTCA
1 TTCA-TCAAAGTTCTTCA
7193 TCAAATTTTC
Statistics
Matches: 94, Mismatches: 13, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
23 9 0.10
24 40 0.43
25 13 0.14
26 29 0.31
27 3 0.03
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.34
Consensus pattern (24 bp):
TTCATCAAAGTTCTTCAACAAGTC
Done.