Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022244.1 Corchorus olitorius cultivar O-4 contig22277, 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: 13846
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5761 original size:51 final size:51
Alignment explanation
Indices: 5702--5822 Score: 190
Period size: 51 Copynumber: 2.4 Consensus size: 51
5692 AAAAAATTGT
* *
5702 GTGC-TGTTTCATTCAAACTTTTTCTTTTCCATTTAATGACCGTAGCTTAC
1 GTGCTTGTTTCATTCAAACTTTTTCTTTTCCATTTAATGACCGTAACGTAC
**
5752 GTGCTTGTTTCATTCAAACTTTTTCTTTTCCATTTAATGGTCGTAACGTAC
1 GTGCTTGTTTCATTCAAACTTTTTCTTTTCCATTTAATGACCGTAACGTAC
*
5803 ATGCTTGTTTCATTCAAACT
1 GTGCTTGTTTCATTCAAACT
5823 CAGAATATTG
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 4 0.06
51 61 0.94
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (51 bp):
GTGCTTGTTTCATTCAAACTTTTTCTTTTCCATTTAATGACCGTAACGTAC
Found at i:5934 original size:16 final size:16
Alignment explanation
Indices: 5913--5950 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
5903 GACAACTTTG
5913 AAAATATAATGTGCAA
1 AAAATATAATGTGCAA
5929 AAAATATAATGTGCAA
1 AAAATATAATGTGCAA
5945 AAAATA
1 AAAATA
5951 CTGTTGATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.61, C:0.05, G:0.11, T:0.24
Consensus pattern (16 bp):
AAAATATAATGTGCAA
Found at i:12809 original size:39 final size:40
Alignment explanation
Indices: 12753--12833 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
12743 TTTAATTCCT
12753 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
12793 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
12832 AT
1 AT
12834 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:13195 original size:204 final size:201
Alignment explanation
Indices: 12944--13350 Score: 717
Period size: 204 Copynumber: 2.0 Consensus size: 201
12934 CCTTAATAAT
12944 AATAAATCAGATCTTAATATCTTTTATAAATTTTGAAATTTTGTTTGACATTGATCTAATTTAAT
1 AATAAATCAGATCTTAATATCTTTTATAAATTTTGAAATTTTGTTTGACATTGATCTAATTTAAT
* * *
13009 TTAATTAATCTACCACTAATGTTCAACTAATTTTTTTGGTATAGTTATATATATATAATAGTAAT
66 TTAATAAATCAACCACTAATGTTCAACTAATTTTTTTGGTATAGTT-T-TATATATAATAATAAT
13074 GTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTTAAAAAATTAATAACATTCA
129 GTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGAC-TTAAAAAATTAATAACATTCA
13139 CCATTGATA
193 CCATTGATA
*
13148 AATAAATCGGATCTTTAATATCTTTTAT-AATTTTGAAATTTTGTTTGACATTGATCTAATTTAA
1 AATAAATCAGATC-TTAATATCTTTTATAAATTTTGAAATTTTGTTTGACATTGATCTAATTTAA
* *
13212 TTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGTATAGTTTTATATATAATAATAATG
65 TTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTGGTATAGTTTTATATATAATAATAATG
13277 TGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCACC
130 TGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCACC
13342 ATTGATA
195 ATTGATA
13349 AA
1 AA
13351 GTTATTAAGC
Statistics
Matches: 196, Mismatches: 6, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
201 32 0.16
202 58 0.30
203 1 0.01
204 91 0.46
205 14 0.07
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.44
Consensus pattern (201 bp):
AATAAATCAGATCTTAATATCTTTTATAAATTTTGAAATTTTGTTTGACATTGATCTAATTTAAT
TTAATAAATCAACCACTAATGTTCAACTAATTTTTTTGGTATAGTTTTATATATAATAATAATGT
GTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCACCA
TTGATA
Done.