Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018546.1 Corchorus olitorius cultivar O-4 contig18579, 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: 25061
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Found at i:2498 original size:13 final size:13
Alignment explanation
Indices: 2480--2504 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2470 ATTCTTAATT
2480 TTATTTATTATTA
1 TTATTTATTATTA
2493 TTATTTATTATT
1 TTATTTATTATT
2505 CCTACTATAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:3462 original size:51 final size:51
Alignment explanation
Indices: 3386--3495 Score: 129
Period size: 51 Copynumber: 2.2 Consensus size: 51
3376 TGTTATTTCT
* *
3386 AAGAGAAAAACACGTGTACAGTGTTTG-TATGTCCGGAGACAAGAT-TGAAAC
1 AAGAGAAAAACACGTGAACAGTGTTTGAT-TATCCGGAGACAAGATCT-AAAC
* *
3437 AAGAGAAAAACAC-TGAAAGAGTGTTTGATTATCCTGAGACAAGATCTAAAC
1 AAGAGAAAAACACGTG-AACAGTGTTTGATTATCCGGAGACAAGATCTAAAC
3488 AAG-GAAAA
1 AAGAGAAAA
3496 GTTGATGAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
50 7 0.13
51 43 0.83
52 2 0.04
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.20
Consensus pattern (51 bp):
AAGAGAAAAACACGTGAACAGTGTTTGATTATCCGGAGACAAGATCTAAAC
Found at i:15510 original size:15 final size:15
Alignment explanation
Indices: 15490--15519 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
15480 AATATAAGTT
15490 GTCCTGATGGTGTGC
1 GTCCTGATGGTGTGC
15505 GTCCTGATGGTGTGC
1 GTCCTGATGGTGTGC
15520 TATTTCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.20, G:0.40, T:0.33
Consensus pattern (15 bp):
GTCCTGATGGTGTGC
Found at i:15755 original size:27 final size:27
Alignment explanation
Indices: 15748--15828 Score: 144
Period size: 27 Copynumber: 3.0 Consensus size: 27
15738 CCGAAAATCA
*
15748 TCTCATGACCATCAGGATCCAATTTTG
1 TCTCATGACCATCGGGATCCAATTTTG
15775 TCTCATGACCATCGGGATCCAATTTTG
1 TCTCATGACCATCGGGATCCAATTTTG
*
15802 TCTCATGACCATCGGGATACAATTTTG
1 TCTCATGACCATCGGGATCCAATTTTG
15829 GAAACCAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (27 bp):
TCTCATGACCATCGGGATCCAATTTTG
Found at i:15788 original size:54 final size:54
Alignment explanation
Indices: 15724--15828 Score: 140
Period size: 54 Copynumber: 1.9 Consensus size: 54
15714 CCAAATTGCA
*
15724 CATGACCATCGGGA-CCGAAAATCATCTCATGACCATCAGGATCCAATTTTGTCT
1 CATGACCATCGGGATCC-AAAATCATCTCATGACCATCAGGATACAATTTTGTCT
** ** *
15778 CATGACCATCGGGATCCAATTTTGTCTCATGACCATCGGGATACAATTTTG
1 CATGACCATCGGGATCCAAAATCATCTCATGACCATCAGGATACAATTTTG
15829 GAAACCAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
54 42 0.95
55 2 0.05
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29
Consensus pattern (54 bp):
CATGACCATCGGGATCCAAAATCATCTCATGACCATCAGGATACAATTTTGTCT
Found at i:16482 original size:46 final size:46
Alignment explanation
Indices: 16389--17030 Score: 1044
Period size: 46 Copynumber: 14.1 Consensus size: 46
16379 TCATCAAATC
* *
16389 CTCCATCCTGATGGCATAAATTT-TTTACACCATCAGAACCAATTT
1 CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGAACCAATTT
16434 CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGAACCAATTT
1 CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGAACCAATTT
* *
16480 CTCCATCCTGATGGTATAAGTTTCTTCACACCATCAGAACCAAATT
1 CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGAACCAATTT
* * *
16526 CTCCATCCTGATGGTATAAGTTTCTTGACACCATCAGAACCAAATT
1 CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGAACCAATTT
*
16572 CTCCATCCTGATGGCATAAATTTC-TCACACCATCAGAACCAATTT
1 CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGAACCAATTT
*
16617 CTCCATCCTGATGGCATAAATTTC-TCACACCATCAGAACCAATTT
1 CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGAACCAATTT
*
16662 CTCCATCCTGATGGCATAAATTTC-TCACACCATCAGAACCAATTT
1 CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGAACCAATTT
* *
16707 CTCCATCCTGATGGCATAAATTTC-TCACACCATCAGAAACAATTT
1 CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGAACCAATTT
* * *
16752 CTCCATCCTGATGGCATAAATTTTTTCACACCATCAGAACTAATTT
1 CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGAACCAATTT
*
16798 CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGAACTAATTT
1 CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGAACCAATTT
*
16844 CTCCATCTTGATGGTATAAATTTCTTCACACCATCA-AGACCAATTT
1 CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGA-ACCAATTT
* *
16890 CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGGACTAATTT
1 CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGAACCAATTT
*
16936 CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGGACCAATTT
1 CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGAACCAATTT
*
16982 CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGAACTAATTT
1 CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGAACCAATTT
17028 CTC
1 CTC
17031 TGTGCCGAAT
Statistics
Matches: 570, Mismatches: 23, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
45 199 0.35
46 371 0.65
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.32
Consensus pattern (46 bp):
CTCCATCCTGATGGTATAAATTTCTTCACACCATCAGAACCAATTT
Found at i:16616 original size:22 final size:22
Alignment explanation
Indices: 16590--16754 Score: 90
Period size: 22 Copynumber: 7.4 Consensus size: 22
16580 TGATGGCATA
16590 AATTTCTCACACCATCAGAACC
1 AATTTCTCACACCATCAGAACC
* * **
16612 AATTTCTC-CATCCTGAT-GGCATA
1 AATTTCTCACA-CC--ATCAGAACC
16635 AATTTCTCACACCATCAGAACC
1 AATTTCTCACACCATCAGAACC
* * **
16657 AATTTCTC-CATCCTGAT-GGCATA
1 AATTTCTCACA-CC--ATCAGAACC
16680 AATTTCTCACACCATCAGAACC
1 AATTTCTCACACCATCAGAACC
* * **
16702 AATTTCTC-CATCCTGAT-GGCATA
1 AATTTCTCACA-CC--ATCAGAACC
*
16725 AATTTCTCACACCATCAGAAAC
1 AATTTCTCACACCATCAGAACC
16747 AATTTCTC
1 AATTTCTC
16755 CATCCTGATG
Statistics
Matches: 104, Mismatches: 24, Indels: 30
0.66 0.15 0.19
Matches are distributed among these distances:
21 12 0.12
22 44 0.42
23 36 0.35
24 12 0.12
ACGTcount: A:0.32, C:0.31, G:0.08, T:0.29
Consensus pattern (22 bp):
AATTTCTCACACCATCAGAACC
Found at i:21635 original size:22 final size:19
Alignment explanation
Indices: 21598--21657 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
21588 TAGTAAATAG
* *
21598 AATCCTAAATTAGGGACTA
1 AATCTTAAATCAGGGACTA
* *
21617 AATTGCATTTAATCAGGGAATA
1 AA-T-C-TTAAATCAGGGACTA
21639 AATCTTAAATCAGGGACTA
1 AATCTTAAATCAGGGACTA
21658 GGCCGCATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
19 15 0.47
20 2 0.06
21 2 0.06
22 13 0.41
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (19 bp):
AATCTTAAATCAGGGACTA
Done.