Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022824.1 Corchorus olitorius cultivar O-4 contig22857, 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: 14094
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:3739 original size:26 final size:26
Alignment explanation
Indices: 3710--3784 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
3700 AAATAAAAGG
3710 AAGAT-GGAT-TAATCAATATGCAATGC
1 AAGATAGGATATAAT-AA-ATGCAATGC
* *
3736 AAGATATGATATACTAAATGCAATGC
1 AAGATAGGATATAATAAATGCAATGC
* **
3762 AAGATATGATATGCTAAATGCAA
1 AAGATAGGATATAATAAATGCAA
3785 CACTAAAGGT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 36 0.82
27 5 0.11
28 3 0.07
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.27
Consensus pattern (26 bp):
AAGATAGGATATAATAAATGCAATGC
Found at i:4924 original size:8 final size:10
Alignment explanation
Indices: 4889--4934 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
4879 AGCTCGTGAC
4889 TGAAGACTTAT
1 TGAAGAC-TAT
*
4900 TGAAGACAATT
1 TGAAGACTA-T
4911 TGAAGA-TA-
1 TGAAGACTAT
4919 TGAAGACTAT
1 TGAAGACTAT
4929 TGAAGA
1 TGAAGA
4935 ATTATTTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
8 6 0.20
9 2 0.07
10 8 0.27
11 14 0.47
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.28
Consensus pattern (10 bp):
TGAAGACTAT
Found at i:5991 original size:18 final size:18
Alignment explanation
Indices: 5956--5991 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5946 ATTGGCATAC
*
5956 ATTAATTTAATCAGAGTA
1 ATTAATTTAATCAAAGTA
*
5974 ATTAATTTAATTAAAGTA
1 ATTAATTTAATCAAAGTA
5992 CTTTCATAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (18 bp):
ATTAATTTAATCAAAGTA
Found at i:6924 original size:23 final size:24
Alignment explanation
Indices: 6880--6924 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
6870 TCATGCATCC
* *
6880 TCATGTCAACATTGCATTTTTAAG
1 TCATGGCAACATTACATTTTTAAG
6904 TCATGGCAACA-TACATTTTTA
1 TCATGGCAACATTACATTTTTA
6925 GCATTGCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (24 bp):
TCATGGCAACATTACATTTTTAAG
Found at i:9277 original size:16 final size:17
Alignment explanation
Indices: 9248--9288 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
9238 CAAAAAGGTT
9248 TTCAAAAATCCAAAAAA
1 TTCAAAAATCCAAAAAA
*
9265 TTCAAAACT-CAAAAAA
1 TTCAAAAATCCAAAAAA
*
9281 ATCAAAAA
1 TTCAAAAA
9289 GAATTTCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (17 bp):
TTCAAAAATCCAAAAAA
Found at i:9342 original size:34 final size:34
Alignment explanation
Indices: 9304--9576 Score: 271
Period size: 34 Copynumber: 7.7 Consensus size: 34
9294 TCATTCAAGT
* * *
9304 TTTTCAAATTGGGAAACTTCCAACCAGGTTTAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAGGTTTAAG
*
9338 TTTTCAAATTGGAAAAGTTCCCATCAGGTTTAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAGGTTTAAG
* * *
9372 TTTCCAGACTGGGAAAGTTCCCATCAGGTTTAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAGGTTTAAG
* *
9406 TTTTCAAATTGGGAAAGTTCCCACCAGTTTTTAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAG-GTTTAAG
*
9441 TTTTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAG
1 TTTTCAAATTGGGAAAGTTCCCA-TCAGGTTT--AAG
* * * *
9478 TTTTTAAATTGGGATAA-TTTCCATCATGTTTTAG
1 TTTTCAAATTGGGA-AAGTTCCCATCAGGTTTAAG
* *
9512 TTTTCAATTTAGGGAAAGTTCCCGTCATTTTCA-GTTTTAG
1 TTTTCAAATT-GGGAAAGTT-CC--CA---TCAGGTTTAAG
*
9552 TTTTCAAAGTGGGAAAGTTCCCATC
1 TTTTCAAATTGGGAAAGTTCCCATC
9577 CAAAGCACTT
Statistics
Matches: 202, Mismatches: 24, Indels: 27
0.80 0.09 0.11
Matches are distributed among these distances:
33 2 0.01
34 95 0.47
35 39 0.19
36 12 0.06
37 21 0.10
38 6 0.03
39 9 0.04
40 15 0.07
41 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (34 bp):
TTTTCAAATTGGGAAAGTTCCCATCAGGTTTAAG
Found at i:9372 original size:17 final size:17
Alignment explanation
Indices: 9352--9407 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
9342 CAAATTGGAA
9352 AAGTTCCCATCAGGTTT
1 AAGTTCCCATCAGGTTT
* * * **
9369 AAGTTTCCAGACTGG-GA
1 AAGTTCCCA-TCAGGTTT
9386 AAGTTCCCATCAGGTTT
1 AAGTTCCCATCAGGTTT
9403 AAGTT
1 AAGTT
9408 TTCAAATTGG
Statistics
Matches: 27, Mismatches: 10, Indels: 4
0.66 0.24 0.10
Matches are distributed among these distances:
16 3 0.11
17 21 0.78
18 3 0.11
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (17 bp):
AAGTTCCCATCAGGTTT
Found at i:10668 original size:25 final size:26
Alignment explanation
Indices: 10620--10680 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 26
10610 ATTGCCATAG
*
10620 TTTAGATTTAATTTACTTTACTTTATT
1 TTTAG-TTTAATTTACTTTACTTTATA
*
10647 TTTAGTTTAATTT-CTTTTCTTTATA
1 TTTAGTTTAATTTACTTTACTTTATA
*
10672 TTTATTTTA
1 TTTAGTTTA
10681 TTCAATCCCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 18 0.58
26 8 0.26
27 5 0.16
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.67
Consensus pattern (26 bp):
TTTAGTTTAATTTACTTTACTTTATA
Done.