Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013238.1 Corchorus olitorius cultivar O-4 contig13271, 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: 17813
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:3194 original size:17 final size:18
Alignment explanation
Indices: 3159--3194 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3149 CTCCTCTTGC
*
3159 ATGAAAACACTTGTTTTT
1 ATGAAAACAATTGTTTTT
3177 ATGAAAACAATT-TTTTT
1 ATGAAAACAATTGTTTTT
3194 A
1 A
3195 ACTACCCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (18 bp):
ATGAAAACAATTGTTTTT
Found at i:4428 original size:21 final size:21
Alignment explanation
Indices: 4404--4451 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
4394 GCAAGCTTGA
*
4404 CCGGGCAGGCGGCGCGGATGG
1 CCGGGCAGGCGACGCGGATGG
* * *
4425 CCGGGCATGTGACTCGGATGG
1 CCGGGCAGGCGACGCGGATGG
4446 CCGGGC
1 CCGGGC
4452 CATGGCCGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.10, C:0.29, G:0.50, T:0.10
Consensus pattern (21 bp):
CCGGGCAGGCGACGCGGATGG
Found at i:7386 original size:31 final size:32
Alignment explanation
Indices: 7349--7421 Score: 103
Period size: 31 Copynumber: 2.3 Consensus size: 32
7339 TCTATTCCTT
7349 ACTTCCCCGGAAAAAACCAGGAGAAAGTTTT-
1 ACTTCCCCGGAAAAAACCAGGAGAAAGTTTTA
* * * *
7380 CCTTCCCCAGCAATAACCAGGAGAAAGTTTTA
1 ACTTCCCCGGAAAAAACCAGGAGAAAGTTTTA
7412 ACTTCCCCGG
1 ACTTCCCCGG
7422 CAACAACGCC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
31 27 0.77
32 8 0.23
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.21
Consensus pattern (32 bp):
ACTTCCCCGGAAAAAACCAGGAGAAAGTTTTA
Found at i:9293 original size:19 final size:19
Alignment explanation
Indices: 9269--9307 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
9259 TCGCTCAATC
*
9269 AGAAGAATAGAGAATTAAG
1 AGAAGAAAAGAGAATTAAG
*
9288 AGAAGAAAAGTGAATTAAG
1 AGAAGAAAAGAGAATTAAG
9307 A
1 A
9308 TGTTCGAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (19 bp):
AGAAGAAAAGAGAATTAAG
Found at i:9704 original size:14 final size:13
Alignment explanation
Indices: 9679--9874 Score: 61
Period size: 14 Copynumber: 13.8 Consensus size: 13
9669 TAAATGTAAT
*
9679 GAAATTATATTTA
1 GAAATAATATTTA
*
9692 GAAGATAATATTTT
1 GAA-ATAATATTTA
* * *
9706 TAAATTATAGTTA
1 GAAATAATATTTA
9719 GAAAATAATATTT-
1 G-AAATAATATTTA
* *
9732 GCAAATTATAAATGTAA
1 G-AAA-TA-ATAT-TTA
* *
9749 TGAAATTACATTTA
1 -GAAATAATATTTA
*
9763 GAAAATAGTATTTA
1 G-AAATAATATTTA
*
9777 GAAATAATAAATGTAA
1 GAAATAAT--AT-TTA
* *
9793 TGAAATTACATTTA
1 -GAAATAATATTTA
* *
9807 GAAAATAGTATATA
1 G-AAATAATATTTA
*
9821 GAAATAATAAATGTAA
1 GAAATAAT--AT-TTA
*
9837 TGAAATTATATTTA
1 -GAAATAATATTTA
9851 GGAAATAATATTTA
1 -GAAATAATATTTA
*
9865 GAAATTATAT
1 GAAATAATAT
9875 ATAACGGTGT
Statistics
Matches: 131, Mismatches: 35, Indels: 34
0.65 0.17 0.17
Matches are distributed among these distances:
13 37 0.28
14 58 0.44
15 14 0.11
16 5 0.04
17 16 0.12
18 1 0.01
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.37
Consensus pattern (13 bp):
GAAATAATATTTA
Found at i:9719 original size:27 final size:27
Alignment explanation
Indices: 9680--9741 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
9670 AAATGTAATG
* * **
9680 AAATTATATTTAGAAGATAATATTTTT
1 AAATTATAGTTAGAAAATAATATTTGC
9707 AAATTATAGTTAGAAAATAATATTTGC
1 AAATTATAGTTAGAAAATAATATTTGC
9734 AAATTATA
1 AAATTATA
9742 AATGTAATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (27 bp):
AAATTATAGTTAGAAAATAATATTTGC
Found at i:9756 original size:44 final size:44
Alignment explanation
Indices: 9707--9869 Score: 238
Period size: 44 Copynumber: 3.7 Consensus size: 44
9697 TAATATTTTT
* * *
9707 AAATTATAGTTAGAAAATAATATTT-GCAAATTATAAATGTAATG
1 AAATTACATTTAGAAAATAATATTTAG-AAATAATAAATGTAATG
*
9751 AAATTACATTTAGAAAATAGTATTTAGAAATAATAAATGTAATG
1 AAATTACATTTAGAAAATAATATTTAGAAATAATAAATGTAATG
* *
9795 AAATTACATTTAGAAAATAGTATATAGAAATAATAAATGTAATG
1 AAATTACATTTAGAAAATAATATTTAGAAATAATAAATGTAATG
* *
9839 AAATTATATTTAGGAAATAATATTTAGAAAT
1 AAATTACATTTAGAAAATAATATTTAGAAAT
9870 TATATATAAC
Statistics
Matches: 109, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
44 108 0.99
45 1 0.01
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.35
Consensus pattern (44 bp):
AAATTACATTTAGAAAATAATATTTAGAAATAATAAATGTAATG
Found at i:9960 original size:32 final size:32
Alignment explanation
Indices: 9883--9960 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
9873 ATATAACGGT
* * * *
9883 GTTTTCTTTATTAAACGCCGCTAAATAGGGGC
1 GTTTTCTTCAATAGACGCCGCTAAATAAGGGC
9915 GTTTTCTTCAATAGACGCCGCTAAATAAGGGC
1 GTTTTCTTCAATAGACGCCGCTAAATAAGGGC
*
9947 GTTTTGTTCAATAG
1 GTTTTCTTCAATAG
9961 TGTCGAAACG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (32 bp):
GTTTTCTTCAATAGACGCCGCTAAATAAGGGC
Found at i:10638 original size:16 final size:16
Alignment explanation
Indices: 10617--10648 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10607 GAGAACATGA
*
10617 TTTGAGAAAGACCTTT
1 TTTGAGAAAAACCTTT
10633 TTTGAGAAAAACCTTT
1 TTTGAGAAAAACCTTT
10649 ATTACCTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (16 bp):
TTTGAGAAAAACCTTT
Found at i:14673 original size:26 final size:27
Alignment explanation
Indices: 14608--14679 Score: 92
Period size: 26 Copynumber: 2.7 Consensus size: 27
14598 CTAAAATGCC
* **
14608 AAATGACCAAAACGCCCCTGAGTATGC
1 AAATGACCAAAATGCCCCTGAGTATAA
*
14635 AAATGACCAAAATGCCCCT-AGTGTAA
1 AAATGACCAAAATGCCCCTGAGTATAA
*
14661 AAATGACCGAAATGCCCCT
1 AAATGACCAAAATGCCCCT
14680 TGGAGACCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 22 0.55
27 18 0.45
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.17
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAGTATAA
Done.