Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021684.1 Corchorus olitorius cultivar O-4 contig21717, 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: 13116
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:3280 original size:22 final size:21
Alignment explanation
Indices: 3214--3663 Score: 196
Period size: 22 Copynumber: 20.5 Consensus size: 21
3204 TTATCAAATT
* * *
3214 AAATTTCATTGGGGGTTATAA
1 AAATTTCATAGGAGGTTATCA
* ***
3235 AAATTTAATAGCGTTCTTAT-A
1 AAATTTCATAG-GAGGTTATCA
*
3256 AAATTTTCATAGGAGGTTAACA
1 AAA-TTTCATAGGAGGTTATCA
* *
3278 AAATTTTATAAGGAGGTTATAA
1 AAATTTCAT-AGGAGGTTATCA
* *
3300 AACATTT-ATAGAGATGCTATCA
1 AA-ATTTCATAG-GAGGTTATCA
*
3322 AAATTTCATAAGATGGTTATCA
1 AAATTTCATAGGA-GGTTATCA
* *
3344 AAATTTCATGAGGTGGTTTTCA
1 AAATTTCAT-AGGAGGTTATCA
3366 AAATTTCAT--GAGGTTATCA
1 AAATTTCATAGGAGGTTATCA
*
3385 AAATTTTATAGGGAGGTTTAT-A
1 AAATTTCATA-GGAGG-TTATCA
3407 AATATTTCATAGTGAGG-TATCA
1 AA-ATTTCATAG-GAGGTTATCA
*
3429 CAATTTCAT-GGTATGGTTATCA
1 AAATTTCATAGG-A-GGTTATCA
* * * * *
3451 AAATTTTCATAATGTGATTACCG
1 AAA-TTTCAT-AGGAGGTTATCA
* * *
3474 ATATTTTATATGAAGGTTATCA
1 AAATTTCATA-GGAGGTTATCA
* * *
3496 AAATTTCATAATGTGCGCTTACCA
1 AAATTTCAT-A-G-GAGGTTATCA
* * *
3520 ACATTTCATTGGGAGGTTATGA
1 AAATTTCA-TAGGAGGTTATCA
* *
3542 AAATTTCATAAGGTGATTATCA
1 AAATTTCAT-AGGAGGTTATCA
* * *
3564 AAATTTCATTATGTGGTTATTA
1 AAATTTCA-TAGGAGGTTATCA
* *
3586 AAATTTTTATAGG-GAGTGTAACA
1 AAA-TTTCATAGGAG-GT-TATCA
* * *
3609 AAATTTTATAGGAAAGTTAACA
1 AAATTTCATAGG-AGGTTATCA
* * *
3631 AAATTCCATATGGTGGTTCTCA
1 AAATTTCATA-GGAGGTTATCA
*
3653 AAATTTTATAG
1 AAATTTCATAG
3664 TATCATCATA
Statistics
Matches: 321, Mismatches: 74, Indels: 68
0.69 0.16 0.15
Matches are distributed among these distances:
19 17 0.05
20 2 0.01
21 46 0.14
22 188 0.59
23 53 0.17
24 13 0.04
25 2 0.01
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (21 bp):
AAATTTCATAGGAGGTTATCA
Found at i:3740 original size:19 final size:20
Alignment explanation
Indices: 3690--3741 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
3680 TTATATTGTA
3690 ATTATCAAAATTTTATATGG
1 ATTATCAAAATTTTATATGG
*
3710 GTTATCAAAATTTTATA-GTG
1 ATTATCAAAATTTTATATG-G
3730 ATTAT-AAAATTT
1 ATTATCAAAATTT
3742 CATAAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (20 bp):
ATTATCAAAATTTTATATGG
Found at i:3806 original size:2 final size:2
Alignment explanation
Indices: 3799--3838 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3789 TAAAACTAAG
3799 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3839 ACATAAATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4853 original size:35 final size:35
Alignment explanation
Indices: 4807--4874 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
4797 AATGTTTAAG
* * *
4807 ATGTCTAAGGCTGTAAGGTGAGTTTTTATGTGAAT
1 ATGTCTAAGGCTGTAACGTAAATTTTTATGTGAAT
4842 ATGTCTAAGGCTGTAACGTAAATTTTTATGTGA
1 ATGTCTAAGGCTGTAACGTAAATTTTTATGTGA
4875 TAACTAAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.28, C:0.07, G:0.25, T:0.40
Consensus pattern (35 bp):
ATGTCTAAGGCTGTAACGTAAATTTTTATGTGAAT
Found at i:11718 original size:21 final size:21
Alignment explanation
Indices: 11692--11825 Score: 198
Period size: 21 Copynumber: 6.4 Consensus size: 21
11682 TGCTAGAAGT
11692 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
11713 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
11734 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
11755 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
* *
11776 TCATTGGCGAAGGTTCCAAGA
1 TCATTGGAGAAGGTTCCAAGC
*
11797 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
11818 ACATTGGA
1 TCATTGGA
11826 ATTGTCTAAG
Statistics
Matches: 105, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
20 2 0.02
21 103 0.98
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:12720 original size:21 final size:21
Alignment explanation
Indices: 12696--12812 Score: 157
Period size: 21 Copynumber: 5.6 Consensus size: 21
12686 CTTAGGCATT
*
12696 TCCAATGAACTTGAAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
12717 TCCAATGATCTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
12738 TCCAATGAACTTGGAACCTGC
1 TCCAATGAACTTGGAACCTTC
*
12759 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAACTTGGAACCTT-C
*
12780 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAACTTGGAACCTT-C
12801 TCCAATGAACTT
1 TCCAATGAACTT
12813 CTAGCATCTT
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
20 2 0.02
21 86 0.98
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.29
Consensus pattern (21 bp):
TCCAATGAACTTGGAACCTTC
Done.