Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016067.1 Corchorus olitorius cultivar O-4 contig16100, 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: 8639
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Found at i:949 original size:26 final size:27
Alignment explanation
Indices: 919--977 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
909 CATTTTTTTC
919 AAATATATTTCTAAATT-GT-CATTATT-
1 AAATATATTT-T-AATTAGTCCATTATTG
945 AAATAATATTTTAATTAGTCCATTATTG
1 AAAT-ATATTTTAATTAGTCCATTATTG
973 AAATA
1 AAATA
978 ATTGAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
25 4 0.14
26 7 0.24
27 14 0.48
28 4 0.14
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (27 bp):
AAATATATTTTAATTAGTCCATTATTG
Found at i:2735 original size:35 final size:35
Alignment explanation
Indices: 2688--2759 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
2678 GATCCTTTTT
* *
2688 GATATTGGAGTTAGTA-AGATATTAAGGTGTTTGGA
1 GATATTGAAGTTAGTAGA-ATATTAAGGTGTTTAGA
* *
2723 GATATTGAAGTTAGTGGAATCTTAAGGTGTTTAGA
1 GATATTGAAGTTAGTAGAATATTAAGGTGTTTAGA
2758 GA
1 GA
2760 GCTTAAGATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 31 0.97
36 1 0.03
ACGTcount: A:0.32, C:0.01, G:0.31, T:0.36
Consensus pattern (35 bp):
GATATTGAAGTTAGTAGAATATTAAGGTGTTTAGA
Found at i:3518 original size:22 final size:21
Alignment explanation
Indices: 3461--3617 Score: 124
Period size: 22 Copynumber: 7.2 Consensus size: 21
3451 CTATAAAAAA
*
3461 TCATAGGAAGGTTA-CAAAA-T
1 TCATAGGTA-GTTATCAAAATT
* *
3481 TCATAGGAAAGTTTATTAAAATT
1 TCATAGG-TAG-TTATCAAAATT
* *
3504 TCATAGTTAGGTTATCAAAGTT
1 TCATAGGTA-GTTATCAAAATT
*
3526 TCTTATA-G-AGTTTATCACAATT
1 TC--ATAGGTAG-TTATCAAAATT
* *
3548 TTATAGGTAATTATCAAAATT
1 TCATAGGTAGTTATCAAAATT
3569 TCATATGGTAGTTATCAAAATT
1 TCATA-GGTAGTTATCAAAATT
*
3591 TAATAGGGTAGTTATCAAAATT
1 TCATA-GGTAGTTATCAAAATT
3613 TCATA
1 TCATA
3618 AAAATATTCA
Statistics
Matches: 110, Mismatches: 16, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
20 11 0.10
21 21 0.19
22 67 0.61
23 8 0.07
24 3 0.03
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (21 bp):
TCATAGGTAGTTATCAAAATT
Found at i:3548 original size:44 final size:44
Alignment explanation
Indices: 3490--3617 Score: 143
Period size: 44 Copynumber: 2.9 Consensus size: 44
3480 TTCATAGGAA
* * * * *
3490 AGTTTATTAAAATTTCATAGTTAGGTTATCAAAGTTTCTTATAG-
1 AGTTTATCAAAATTTAATAGGTA-GTTATCAAAATTTCATATAGT
* * * *
3534 AGTTTATCACAATTTTATAGGTAATTATCAAAATTTCATATGGT
1 AGTTTATCAAAATTTAATAGGTAGTTATCAAAATTTCATATAGT
3578 AG-TTATCAAAATTTAATAGGGTAGTTATCAAAATTTCATA
1 AGTTTATCAAAATTTAATA-GGTAGTTATCAAAATTTCATA
3618 AAAATATTCA
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
43 30 0.42
44 41 0.58
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (44 bp):
AGTTTATCAAAATTTAATAGGTAGTTATCAAAATTTCATATAGT
Found at i:3584 original size:43 final size:44
Alignment explanation
Indices: 3515--3617 Score: 129
Period size: 43 Copynumber: 2.4 Consensus size: 44
3505 CATAGTTAGG
* * * *
3515 TTATCAAAGTTTCTTATAGAGTTTATCACAATTTTATA-GGTAA
1 TTATCAAAATTTCATATAGAGTTTATCAAAATTTAATAGGGTAA
* *
3558 TTATCAAAATTTCATATGGTAG-TTATCAAAATTTAATAGGGTAG
1 TTATCAAAATTTCATATAG-AGTTTATCAAAATTTAATAGGGTAA
3602 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
3618 AAAATATTCA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
43 30 0.58
44 22 0.42
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.42
Consensus pattern (44 bp):
TTATCAAAATTTCATATAGAGTTTATCAAAATTTAATAGGGTAA
Found at i:3831 original size:48 final size:47
Alignment explanation
Indices: 3774--3867 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 47
3764 ATTTTAATTT
* *
3774 TTATAATATTTATTAATCAATATATTAATTATACAACTAATAATTTTC
1 TTATAATATTCATTAATCAACATATTAATTATACAACTAAT-ATTTTC
*
3822 TTATAATATTCATTAATCAACATATTAATTATACAATTAATATTTT
1 TTATAATATTCATTAATCAACATATTAATTATACAACTAATATTTT
3868 AATTTTCTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
47 5 0.12
48 38 0.88
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.48
Consensus pattern (47 bp):
TTATAATATTCATTAATCAACATATTAATTATACAACTAATATTTTC
Found at i:4026 original size:88 final size:89
Alignment explanation
Indices: 3863--4038 Score: 291
Period size: 88 Copynumber: 2.0 Consensus size: 89
3853 TACAATTAAT
* * *
3863 ATTTTAATTTTCTTAACATACCTTAGCAATGTATGGTATAAATATTTCAATTTTCTTAATTTGGA
1 ATTTTAATTTTCTTAACACACCTTAGCAATGTATGGTATAAATATTTCAATTTTCATAATTTAGA
3928 TTTGATTAAATTTACGCCAAACTG
66 TTTGATTAAATTTACGCCAAACTG
* *
3952 ATTTTCATTTTCTTAACACACCTTAGCAATGTATGGT-TAAATATTTTAATTTTCATAATTTAGA
1 ATTTTAATTTTCTTAACACACCTTAGCAATGTATGGTATAAATATTTCAATTTTCATAATTTAGA
*
4016 TTTGATTAAATTTACTCCAAACT
66 TTTGATTAAATTTACGCCAAACT
4039 CTCGGTTTGG
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
88 46 0.57
89 35 0.43
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (89 bp):
ATTTTAATTTTCTTAACACACCTTAGCAATGTATGGTATAAATATTTCAATTTTCATAATTTAGA
TTTGATTAAATTTACGCCAAACTG
Found at i:6370 original size:2 final size:2
Alignment explanation
Indices: 6363--6417 Score: 74
Period size: 2 Copynumber: 27.5 Consensus size: 2
6353 CAGGCAAAAC
* * * *
6363 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT GT AT GT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6405 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
6418 GTGCAATACT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Done.