Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024720.1 Corchorus olitorius cultivar O-4 contig24753, 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: 14851
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:656 original size:17 final size:18
Alignment explanation
Indices: 636--681 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
626 TATCTACTTA
*
636 TGTATTCTAA-CTGATCT
1 TGTACTCTAATCTGATCT
653 TGTACTCTAAATCTGATCT
1 TGTACTCT-AATCTGATCT
672 TGTACTCTAA
1 TGTACTCTAA
682 ATCTCAGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 7 0.27
18 4 0.15
19 15 0.58
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (18 bp):
TGTACTCTAATCTGATCT
Found at i:670 original size:19 final size:19
Alignment explanation
Indices: 646--685 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
636 TGTATTCTAA
646 CTGATCTTGTACTCTAAAT
1 CTGATCTTGTACTCTAAAT
665 CTGATCTTGTACTCTAAAT
1 CTGATCTTGTACTCTAAAT
684 CT
1 CT
686 CAGCTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (19 bp):
CTGATCTTGTACTCTAAAT
Found at i:9313 original size:26 final size:26
Alignment explanation
Indices: 9252--9301 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
9242 CTCTACACAG
9252 AATCATTCTCTCCACTCTCACTCTGC
1 AATCATTCTCTCCACTCTCACTCTGC
9278 AATCATTCTCTCCACTCTCACTCT
1 AATCATTCTCTCCACTCTCACTCT
9302 TCGATCACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.20, C:0.42, G:0.02, T:0.36
Consensus pattern (26 bp):
AATCATTCTCTCCACTCTCACTCTGC
Found at i:11177 original size:20 final size:20
Alignment explanation
Indices: 11152--11214 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
11142 CATGCATATC
11152 ATATTTACTTGTCATAAACT
1 ATATTTACTTGTCATAAACT
** *
11172 ATATTTGTTTG-CAT-ATC-
1 ATATTTACTTGTCATAAACT
11189 ATATTTACTTGTCATAAACT
1 ATATTTACTTGTCATAAACT
11209 ATATTT
1 ATATTT
11215 GTTTGCATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 9 0.26
18 5 0.15
19 5 0.15
20 15 0.44
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.49
Consensus pattern (20 bp):
ATATTTACTTGTCATAAACT
Found at i:11185 original size:37 final size:37
Alignment explanation
Indices: 11144--11228 Score: 170
Period size: 37 Copynumber: 2.3 Consensus size: 37
11134 CCTAATTGCA
11144 TGCATATCATATTTACTTGTCATAAACTATATTTGTT
1 TGCATATCATATTTACTTGTCATAAACTATATTTGTT
11181 TGCATATCATATTTACTTGTCATAAACTATATTTGTT
1 TGCATATCATATTTACTTGTCATAAACTATATTTGTT
11218 TGCATATCATA
1 TGCATATCATA
11229 CCACCTTAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (37 bp):
TGCATATCATATTTACTTGTCATAAACTATATTTGTT
Found at i:13296 original size:30 final size:31
Alignment explanation
Indices: 13233--13297 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
13223 GAAAGCGATT
* *
13233 AATTTAGTCCATGTACTCACAAGATTTGGTC
1 AATTTAATCCATGTACTCACAAGATTGGGTC
*
13264 AATTTAATCCTTGTACTCACAAG-TTGGGTC
1 AATTTAATCCATGTACTCACAAGATTGGGTC
13294 AATT
1 AATT
13298 AAGTCTAGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 10 0.32
31 21 0.68
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (31 bp):
AATTTAATCCATGTACTCACAAGATTGGGTC
Done.