Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024559.1 Corchorus olitorius cultivar O-4 contig24592, 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: 13676
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Found at i:332 original size:4 final size:4
Alignment explanation
Indices: 323--567 Score: 90
Period size: 4 Copynumber: 61.0 Consensus size: 4
313 AAAAGTATAG
*
323 ATAA ATAA ATAA ATAA ATAA ATAA ATAA GAAAA ATAA AGTAA GA-ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA -ATAA ATAA A-TAA -ATA-A
* * * * * * * *
370 ATAG ATAA ATAA A-AA GATAA ATAG GTAT ATAG ATAA TTAG ATAA ATAG
1 ATAA ATAA ATAA ATAA -ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* * * * * * ** * *
418 GTAG GTAA AAAA AGTAG ATAA TAGTAA ATAA ATAG AT-A ATGG CTAA ATTA
1 ATAA ATAA ATAA A-TAA ATAA -A-TAA ATAA ATAA ATAA ATAA ATAA ATAA
* * * * * *
468 ATAA ATAA ATAG ATAA AT-A GTAA ATAA ATAG AT-A ATAG TTAA ATTA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* * * * * *
514 ATAA ATAA ATAG ATAA AT-A GTAA ATAA ATAG AT-A ATAG TTAA ATTA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
560 ATAA ATAA
1 ATAA ATAA
568 TAATTTAAAA
Statistics
Matches: 171, Mismatches: 55, Indels: 30
0.67 0.21 0.12
Matches are distributed among these distances:
3 12 0.07
4 141 0.82
5 14 0.08
6 4 0.02
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:464 original size:19 final size:18
Alignment explanation
Indices: 422--569 Score: 99
Period size: 19 Copynumber: 8.0 Consensus size: 18
412 AAATAGGTAG
*
422 GTAAAAAAAGTAGATAATA
1 GTAAATAAA-TAGATAATA
*
441 GTAAATAAATAGATAATG
1 GTAAATAAATAGATAATA
* *
459 GCTAAATTAATAAATAA-A
1 G-TAAATAAATAGATAATA
*
477 -TAGATAAATAG-TAA-A
1 GTAAATAAATAGATAATA
*
492 -TAAATAGATAATAGTTAAATTA
1 GTAAAT--A-AATAGAT-AA-TA
*
514 ATAAATAAATAGATAAATA
1 GTAAATAAATAGAT-AATA
533 GTAAATAAATAGATAATA
1 GTAAATAAATAGATAATA
* *
551 GTTAAATTAATAAATAATA
1 G-TAAATAAATAGATAATA
570 ATTTAAAAAA
Statistics
Matches: 106, Mismatches: 13, Indels: 20
0.76 0.09 0.14
Matches are distributed among these distances:
15 8 0.08
16 8 0.08
17 1 0.01
18 19 0.18
19 52 0.49
20 11 0.10
21 1 0.01
22 1 0.01
23 5 0.05
ACGTcount: A:0.60, C:0.01, G:0.10, T:0.29
Consensus pattern (18 bp):
GTAAATAAATAGATAATA
Found at i:477 original size:27 final size:25
Alignment explanation
Indices: 442--567 Score: 96
Period size: 27 Copynumber: 5.3 Consensus size: 25
432 TAGATAATAG
442 TAAATAAATAGATAATGGCTAAATTAA
1 TAAATAAATAGATAAT-G-TAAATTAA
*
469 TAAATAAATAG---A--TAAA-TAG
1 TAAATAAATAGATAATGTAAATTAA
488 TAAATAAATAGATAATAGTTAAATTAA
1 TAAATAAATAGATAAT-G-TAAATTAA
*
515 TAAATAAATAG---A--TAAA-TAG
1 TAAATAAATAGATAATGTAAATTAA
534 TAAATAAATAGATAATAGTTAAATTAA
1 TAAATAAATAGATAAT-G-TAAATTAA
561 TAAATAA
1 TAAATAA
568 TAATTTAAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 32
0.69 0.03 0.28
Matches are distributed among these distances:
19 26 0.33
20 8 0.10
22 2 0.03
24 2 0.03
26 8 0.10
27 33 0.42
ACGTcount: A:0.60, C:0.01, G:0.09, T:0.30
Consensus pattern (25 bp):
TAAATAAATAGATAATGTAAATTAA
Found at i:489 original size:46 final size:46
Alignment explanation
Indices: 423--567 Score: 247
Period size: 46 Copynumber: 3.2 Consensus size: 46
413 AATAGGTAGG
* * *
423 TAAAAAAAGTAGAT-AATAGTAAATAAATAGATAATGGCTAAATTAA
1 TAAATAAA-TAGATAAATAGTAAATAAATAGATAATAGTTAAATTAA
469 TAAATAAATAGATAAATAGTAAATAAATAGATAATAGTTAAATTAA
1 TAAATAAATAGATAAATAGTAAATAAATAGATAATAGTTAAATTAA
515 TAAATAAATAGATAAATAGTAAATAAATAGATAATAGTTAAATTAA
1 TAAATAAATAGATAAATAGTAAATAAATAGATAATAGTTAAATTAA
561 TAAATAA
1 TAAATAA
568 TAATTTAAAA
Statistics
Matches: 95, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
45 5 0.05
46 90 0.95
ACGTcount: A:0.61, C:0.01, G:0.10, T:0.29
Consensus pattern (46 bp):
TAAATAAATAGATAAATAGTAAATAAATAGATAATAGTTAAATTAA
Found at i:1007 original size:26 final size:26
Alignment explanation
Indices: 975--1026 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
965 TGAAATTAAA
975 AACCTAAATTAATTAAACCATAACCC
1 AACCTAAATTAATTAAACCATAACCC
1001 AACCTAAATTAATTAAACCATAACCC
1 AACCTAAATTAATTAAACCATAACCC
1027 CAAGGTCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (26 bp):
AACCTAAATTAATTAAACCATAACCC
Found at i:6053 original size:27 final size:27
Alignment explanation
Indices: 5992--6086 Score: 118
Period size: 27 Copynumber: 3.4 Consensus size: 27
5982 GGTAGGGGAC
* **
5992 CAAATGACCAAAATGCCCCTCTAAATGCA
1 CAAATGACCAAAATGCCCC-C-GAATGTG
6021 CAAATGACCAAAATGCCCCCGAATGTG
1 CAAATGACCAAAATGCCCCCGAATGTG
* *
6048 CAAATGACTAAAATGCCCCCGAATATG
1 CAAATGACCAAAATGCCCCCGAATGTG
*
6075 CCAATGACCAAA
1 CAAATGACCAAA
6087 TGACCCCTAG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 39 0.66
28 1 0.02
29 19 0.32
ACGTcount: A:0.41, C:0.29, G:0.14, T:0.16
Consensus pattern (27 bp):
CAAATGACCAAAATGCCCCCGAATGTG
Found at i:11936 original size:29 final size:30
Alignment explanation
Indices: 11889--11948 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
11879 AAAGTTCATG
* *
11889 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGAC-CATTGAAGAATTATTTCAAGA
11920 TTTGAAGA-CATTGAAGAATTATTTCAAGA
1 TTTGAAGACCATTGAAGAATTATTTCAAGA
11949 GGAAAGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 19 0.70
31 8 0.30
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.35
Consensus pattern (30 bp):
TTTGAAGACCATTGAAGAATTATTTCAAGA
Found at i:13663 original size:39 final size:38
Alignment explanation
Indices: 13603--13676 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 38
13593 TCTCTTGGTG
* *
13603 TCTGCGTTTTTTATCTTAAAAAAAAATTAGTTTTTCTTT
1 TCTGCGTTTTTTATCTAAAAAAAAAAAT-GTTTTTCTTT
13642 TCTGCGTTTTTTA-CTAAAAAAAAAAAATGTTTTTC
1 TCTGCGTTTTTTATCT-AAAAAAAAAAATGTTTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
38 9 0.28
39 23 0.72
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (38 bp):
TCTGCGTTTTTTATCTAAAAAAAAAAATGTTTTTCTTT
Done.