Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021326.1 Corchorus olitorius cultivar O-4 contig21359, 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: 17146
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2628 original size:16 final size:16
Alignment explanation
Indices: 2607--2639 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2597 AATTAATCTA
2607 AAATTAAAGCTAAACT
1 AAATTAAAGCTAAACT
*
2623 AAATTAAATCTAAACT
1 AAATTAAAGCTAAACT
2639 A
1 A
2640 TGTCAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.12, G:0.03, T:0.27
Consensus pattern (16 bp):
AAATTAAAGCTAAACT
Found at i:3828 original size:18 final size:18
Alignment explanation
Indices: 3796--3834 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
3786 ACCCTCTTCT
3796 AAAACTAGAAAGAAAACTA
1 AAAACTAGAAAGAAAA-TA
*
3815 AAAACTAG-ACGAAAATA
1 AAAACTAGAAAGAAAATA
3832 AAA
1 AAA
3835 TTACAGATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 6 0.32
19 8 0.42
ACGTcount: A:0.69, C:0.10, G:0.10, T:0.10
Consensus pattern (18 bp):
AAAACTAGAAAGAAAATA
Found at i:4592 original size:17 final size:16
Alignment explanation
Indices: 4570--4603 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4560 ATTTTGTTCT
*
4570 TATTCTTTTTATGCTCA
1 TATTCTTCTTAT-CTCA
4587 TATTCTTCTTATCTCA
1 TATTCTTCTTATCTCA
4603 T
1 T
4604 CATATCTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.18, C:0.21, G:0.03, T:0.59
Consensus pattern (16 bp):
TATTCTTCTTATCTCA
Found at i:14624 original size:39 final size:40
Alignment explanation
Indices: 14568--14648 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
14558 TTTAATTCCT
14568 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
14608 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
14647 AT
1 AT
14649 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:15116 original size:202 final size:202
Alignment explanation
Indices: 14759--15167 Score: 734
Period size: 202 Copynumber: 2.0 Consensus size: 202
14749 TTCCTTAATA
*
14759 ATAAATAAATCGGATCTTTAATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAA
1 ATAAATAAATCGAATCTTTAATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAA
*
14824 TTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAGTA
66 TTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAATA
*
14889 ATGTGTTTAATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
131 ATGTGTTTAATCTTATTCACTACAACTTTGTCAGTAATCTTAGACTTAAAAAATTAATAACATTC
14954 ACCATTG
196 ACCATTG
14961 ATAAATAAATCGAATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGAATCTTT-A-ATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
*
15026 AATTTAATAATTCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTT-T-TATATATAATAA
64 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAA
15089 TAATGTGTTGT-ATCTTATTCACTACAACTTTGTCAGTAATCTTAGACTTAAAAAATTAATAACA
129 TAATGTGTT-TAATCTTATTCACTACAACTTTGTCAGTAATCTTAGACTTAAAAAATTAATAACA
15153 TTCACCATTG
193 TTCACCATTG
15163 ATAAA
1 ATAAA
15168 GTTATTAAGC
Statistics
Matches: 200, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
202 105 0.52
203 3 0.01
204 92 0.46
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (202 bp):
ATAAATAAATCGAATCTTTAATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAA
TTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAATA
ATGTGTTTAATCTTATTCACTACAACTTTGTCAGTAATCTTAGACTTAAAAAATTAATAACATTC
ACCATTG
Found at i:15735 original size:36 final size:36
Alignment explanation
Indices: 15688--15757 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
15678 GAGATTTTGG
* *
15688 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
15724 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
15758 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Done.