Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013455.1 Kokia drynarioides strain JFW-HI SEQ_128481, 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: 55814
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 88 characters in sequence are not A, C, G, or T
Found at i:630 original size:23 final size:24
Alignment explanation
Indices: 604--665 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 24
594 ACGCTAGCGT
604 GCTTACTGTTTCGCACTTCGTG-A
1 GCTTACTGTTTCGCACTTCGTGTA
* *
627 GCTTACTGTTTCGCATTTTGTGTA
1 GCTTACTGTTTCGCACTTCGTGTA
*
651 -CTTACTATTTCGCAC
1 GCTTACTGTTTCGCAC
666 ATTGTGTGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 33 0.97
24 1 0.03
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (24 bp):
GCTTACTGTTTCGCACTTCGTGTA
Found at i:670 original size:23 final size:23
Alignment explanation
Indices: 604--672 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
594 ACGCTAGCGT
604 GCTTACTGTTTCGCACTTCGTG-A
1 GCTTACTGTTTCGCACTT-GTGTA
*
627 GCTTACTGTTTCGCATTTTGTGTA
1 GCTTACTGTTTCGCA-CTTGTGTA
*
651 -CTTACTATTTCGCACATTGTGT
1 GCTTACTGTTTCGCAC-TTGTGT
673 GTCTACTGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 37 0.93
24 3 0.08
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTGTGTA
Found at i:732 original size:23 final size:23
Alignment explanation
Indices: 703--748 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
693 TGCGCCTATT
703 GATTGCACTGTATGTGCCTACTG
1 GATTGCACTGTATGTGCCTACTG
* *
726 GATTGCACTGTGTGTGCTTACTG
1 GATTGCACTGTATGTGCCTACTG
749 TTTCCCCAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.15, C:0.20, G:0.28, T:0.37
Consensus pattern (23 bp):
GATTGCACTGTATGTGCCTACTG
Found at i:7405 original size:5 final size:5
Alignment explanation
Indices: 7395--7421 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
7385 CATGACAACT
7395 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
7422 ATTTAAGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:9206 original size:2 final size:2
Alignment explanation
Indices: 9194--9227 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
9184 ATTGTAGCAA
*
9194 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9228 TTGCATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15159 original size:6 final size:6
Alignment explanation
Indices: 15148--15188 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
15138 AATAAAATTA
15148 GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTT
1 GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTT
15189 GTAGAATACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (6 bp):
GGGTTT
Found at i:19922 original size:15 final size:15
Alignment explanation
Indices: 19904--19937 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
19894 TTTCTCCTAA
19904 CTTTCTTTTTTTTT-T
1 CTTT-TTTTTTTTTCT
19919 CTTTTTTTTTTTTCT
1 CTTTTTTTTTTTTCT
19934 CTTT
1 CTTT
19938 GAAACACTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
CTTTTTTTTTTTTCT
Found at i:19925 original size:10 final size:11
Alignment explanation
Indices: 19905--19929 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19895 TTCTCCTAAC
19905 TTTCTTTTTTT
1 TTTCTTTTTTT
19916 TTTCTTTTTTT
1 TTTCTTTTTTT
19927 TTT
1 TTT
19930 TTCTCTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:19927 original size:13 final size:13
Alignment explanation
Indices: 19909--19933 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19899 CCTAACTTTC
19909 TTTTTTTTTTCTT
1 TTTTTTTTTTCTT
19922 TTTTTTTTTTCT
1 TTTTTTTTTTCT
19934 CTTTGAAACA
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTTTTTTTCTT
Found at i:22787 original size:6 final size:6
Alignment explanation
Indices: 22776--22810 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
22766 CACCCACTCT
22776 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTC
22811 ACGTGTTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CTCTCC
Found at i:24510 original size:3 final size:3
Alignment explanation
Indices: 24502--24557 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
24492 TCACCTCCAT
24502 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
24550 TTC TTC TT
1 TTC TTC TT
24558 GCATTTTATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:32588 original size:40 final size:40
Alignment explanation
Indices: 32541--32620 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
32531 GTAATATACA
*
32541 ATACCACTATAATGTAAAACTTTAAAATTTTAAAATGACT
1 ATACCACTATAATGTAAAACTTTAAAAATTTAAAATGACT
32581 ATACCACTATAATGTAAAACTTTAAAAATTTAAAATGACT
1 ATACCACTATAATGTAAAACTTTAAAAATTTAAAATGACT
32621 TTATATAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (40 bp):
ATACCACTATAATGTAAAACTTTAAAAATTTAAAATGACT
Found at i:35198 original size:2 final size:2
Alignment explanation
Indices: 35191--35217 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35181 CCTTTCTGCA
35191 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
35218 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:38834 original size:17 final size:17
Alignment explanation
Indices: 38794--38835 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
38784 GAAAATTACT
38794 AAAATTATTAAAAATAAG
1 AAAATT-TTAAAAATAAG
*
38812 AAAATTTTATAACATAA-
1 AAAATTTTA-AAAATAAG
38829 AAAATTT
1 AAAATTT
38836 CTTTAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAATTTTAAAAATAAG
Found at i:38845 original size:11 final size:11
Alignment explanation
Indices: 38829--38855 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
38819 TATAACATAA
38829 AAAATTTCTTT
1 AAAATTTCTTT
38840 AAAATTTCTTT
1 AAAATTTCTTT
38851 AAAAT
1 AAAAT
38856 ATTAAAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (11 bp):
AAAATTTCTTT
Found at i:39390 original size:20 final size:20
Alignment explanation
Indices: 39346--39383 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39336 GTAGCAATTT
*
39346 TTAATTTTTATAATATTTTA
1 TTAAATTTTATAATATTTTA
39366 TTAAATTTTAT-ATATTTT
1 TTAAATTTTATAATATTTT
39384 TCTTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTAAATTTTATAATATTTTA
Found at i:39730 original size:29 final size:25
Alignment explanation
Indices: 39684--39751 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 25
39674 GATGTAGCAA
*
39684 TTTTTA-ATTTTTATATTTATTCATTAG
1 TTTTTATAATTTTATATTT-TT-A-TAG
39711 TTTTTATAATTTTATCATTTTTATAG
1 TTTTTATAATTTTAT-ATTTTTATAG
39737 TATTTTATATATTTT
1 T-TTTTATA-ATTTT
39752 TCTAAAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
26 4 0.11
27 14 0.39
28 14 0.39
29 4 0.11
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (25 bp):
TTTTTATAATTTTATATTTTTATAG
Found at i:39732 original size:9 final size:8
Alignment explanation
Indices: 39683--39751 Score: 50
Period size: 9 Copynumber: 7.8 Consensus size: 8
39673 AGATGTAGCA
39683 ATTTTTA-
1 ATTTTTAT
39690 ATTTTTAT
1 ATTTTTAT
39698 ATTTATTCATT
1 ATTT-TT-A-T
39709 AGTTTTTAT
1 A-TTTTTAT
*
39718 AATTTTAT
1 ATTTTTAT
39726 CATTTTTAT
1 -ATTTTTAT
39735 AGTATTTTAT
1 A-T-TTTTAT
39745 ATATTTT
1 AT-TTTT
39752 TCTAAAAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
7 7 0.13
8 11 0.21
9 18 0.35
10 9 0.17
11 4 0.08
12 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (8 bp):
ATTTTTAT
Found at i:39752 original size:29 final size:30
Alignment explanation
Indices: 39683--39752 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 30
39673 AGATGTAGCA
39683 ATTTT-TAATTTTTATATTTATTCATTAGT
1 ATTTTATAATTTTTATATTTATTCATTAGT
39712 -TTTTATAA-TTTTATCATTT-TT-A-TAGT
1 ATTTTATAATTTTTAT-ATTTATTCATTAGT
39738 ATTTTATATATTTTT
1 ATTTTATA-ATTTTT
39753 CTAAAAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
26 4 0.11
27 8 0.22
28 13 0.36
29 11 0.31
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (30 bp):
ATTTTATAATTTTTATATTTATTCATTAGT
Found at i:39937 original size:30 final size:29
Alignment explanation
Indices: 39882--39961 Score: 101
Period size: 30 Copynumber: 2.8 Consensus size: 29
39872 CTTTTACTTA
*
39882 AAAAATTAATTAAGTCC-TCTAAAATAAT
1 AAAAATAAATTAAGTCCTTCTAAAATAAT
*
39910 AAAAAGTAAATTAAGTCCTTGTAAAATAAT
1 AAAAA-TAAATTAAGTCCTTCTAAAATAAT
*
39940 AGAAAATCAATTAAG-CCTTCTA
1 A-AAAATAAATTAAGTCCTTCTA
39962 TGTCATCATT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
28 5 0.11
29 17 0.38
30 19 0.42
31 4 0.09
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.30
Consensus pattern (29 bp):
AAAAATAAATTAAGTCCTTCTAAAATAAT
Found at i:48286 original size:25 final size:25
Alignment explanation
Indices: 48242--48298 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
48232 TAATTTAGTT
*
48242 TACTATTTTTTAATATTTATAAGTAA
1 TACTATTTTTAAATATTTATAA-TAA
48268 TACTATTTTTAAATA-TTATAATAA
1 TACTATTTTTAAATATTTATAATAA
48292 TA-TATTT
1 TACTATTT
48299 GATAGATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 5 0.17
24 5 0.17
25 6 0.20
26 14 0.47
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (25 bp):
TACTATTTTTAAATATTTATAATAA
Found at i:52366 original size:29 final size:28
Alignment explanation
Indices: 52322--52719 Score: 311
Period size: 28 Copynumber: 13.8 Consensus size: 28
52312 AAGACTTCCG
* * * *
52322 AACTCTCCAACAATTAGATTTTGATCCCA
1 AACT-TCCAAAAATTACATTTTTACCCCA
* *
52351 AACTTTCTAAAAATTATATTTTTAACCCTCGA
1 AAC-TTCCAAAAATTACATTTTT-ACCC-C-A
*
52383 ACCTTCCAAAAATTACATTTTTACTCCCA
1 AACTTCCAAAAATTACATTTTTAC-CCCA
*
52412 AACTTCTCAAAAATTACATTTTCACCCTCA
1 AACTTC-CAAAAATTACATTTTTACCC-CA
* *
52442 AACTTCCAAAAATCACA-TTTCACCCTCA
1 AACTTCCAAAAATTACATTTTTACCC-CA
52470 AACTTCCAAAAATTACATTTTT-CCCCTA
1 AACTTCCAAAAATTACATTTTTACCCC-A
* *
52498 AACTTCCAAAAATTATATTTTTGCCCCA
1 AACTTCCAAAAATTACATTTTTACCCCA
* * *
52526 AACTTCCAAAAATTTCATTTTTACCTCG
1 AACTTCCAAAAATTACATTTTTACCCCA
* * * *
52554 AACTTTCAAAAATTATATTTTTAACCTCG
1 AACTTCCAAAAATTACATTTTT-ACCCCA
* *
52583 AACTTCCAAAAAATATATTTTTACCCCCA
1 AACTTCCAAAAATTACATTTTTA-CCCCA
* * * *
52612 AACATT-CAAAAATGACATTTTGATCCCG
1 AAC-TTCCAAAAATTACATTTTTACCCCA
* * *
52640 AACTTTCCAAAAAATACCA-TTTTGCCCACT
1 AAC-TTCCAAAAATTA-CATTTTTACCC-CA
* *
52670 AACATCC-AAAATTACATTTTTACCCTCG
1 AACTTCCAAAAATTACATTTTTACCC-CA
* *
52698 AACATCCAAAAATCACCATTTT
1 AACTTCCAAAAATTA-CATTTT
52720 GCCCTCGAAT
Statistics
Matches: 305, Mismatches: 45, Indels: 37
0.79 0.12 0.10
Matches are distributed among these distances:
27 3 0.01
28 125 0.41
29 108 0.35
30 46 0.15
31 20 0.07
32 3 0.01
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (28 bp):
AACTTCCAAAAATTACATTTTTACCCCA
Found at i:52607 original size:57 final size:58
Alignment explanation
Indices: 52322--52709 Score: 283
Period size: 57 Copynumber: 6.7 Consensus size: 58
52312 AAGACTTCCG
* * * * * * *
52322 AACTCTCCAACAATTAGATTTTGATCC-CAAACTTTCTAAAAATTATATTTTTAACCCTCGA
1 AACT-TCCAAAAATTACATTTTTAACCTCAAAC-TTCCAAAAAATACATTTTT-ACCCTC-A
* * * *
52383 ACCTTCCAAAAATTACATTTTT-ACTCCCAAACTTCTCAAAAATTACATTTTCACCCTCA
1 AACTTCCAAAAATTACATTTTTAAC-CTCAAACTTC-CAAAAAATACATTTTTACCCTCA
* * * * *
52442 AACTTCCAAAAATCACA-TTTCACCCTCAAACTTCCAAAAATTACATTTTTCCCCT-A
1 AACTTCCAAAAATTACATTTTTAACCTCAAACTTCCAAAAAATACATTTTTACCCTCA
* * * * * *
52498 AACTTCCAAAAATTATATTTTT-GCCCCAAACTTCCAAAAATTTCATTTTTA-CCTCG
1 AACTTCCAAAAATTACATTTTTAACCTCAAACTTCCAAAAAATACATTTTTACCCTCA
* * * * *
52554 AACTTTCAAAAATTATATTTTTAACCTCGAACTTCCAAAAAATATATTTTTACCCCCA
1 AACTTCCAAAAATTACATTTTTAACCTCAAACTTCCAAAAAATACATTTTTACCCTCA
* * * * * * *
52612 AACATT-CAAAAATGACATTTTGATCC-CGAACTTTCCAAAAAATACCA-TTTTGCCCACT
1 AAC-TTCCAAAAATTACATTTTTAACCTCAAAC-TTCCAAAAAATA-CATTTTTACCCTCA
* * * *
52670 AACATCC-AAAATTACATTTTTACCCTCGAACATCCAAAAA
1 AACTTCCAAAAATTACATTTTTAACCTCAAACTTCCAAAAA
52710 TCACCATTTT
Statistics
Matches: 269, Mismatches: 45, Indels: 30
0.78 0.13 0.09
Matches are distributed among these distances:
55 3 0.01
56 62 0.23
57 74 0.28
58 63 0.23
59 21 0.08
60 25 0.09
61 21 0.08
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.33
Consensus pattern (58 bp):
AACTTCCAAAAATTACATTTTTAACCTCAAACTTCCAAAAAATACATTTTTACCCTCA
Found at i:52716 original size:57 final size:58
Alignment explanation
Indices: 52389--52723 Score: 201
Period size: 58 Copynumber: 5.8 Consensus size: 58
52379 TCGAACCTTC
* * * * *
52389 CAAAAATTACATTTTT-ACTCCCAAACTTCTCAAAAATTA-CATTTTCACCCTCAAAC-TT
1 CAAAAATTACATTTTTAAC-CTCGAACTTC-CAAAAAATACCATTTT-GCCCACAAACATT
* * * * * *
52447 CCAAAAATCACA-TTTCACCCTCAAACTTCCAAAAATTA-CATTTTTCCC-CTAAAC-TT
1 -CAAAAATTACATTTTTAACCTCGAACTTCCAAAAAATACCATTTTGCCCAC-AAACATT
* * * * ** ** * * *
52503 CCAAAAATTATATTTTT-GCCCCAAACTTCC-AAAAATTTCATTTTTACCTCGAACTTT
1 -CAAAAATTACATTTTTAACCTCGAACTTCCAAAAAATACCATTTTGCCCACAAACATT
* * * *
52560 CAAAAATTATATTTTTAACCTCGAACTTCCAAAAAATA-TATTTTTACCCCCAAACATT
1 CAAAAATTACATTTTTAACCTCGAACTTCCAAAAAATACCA-TTTTGCCCACAAACATT
* * * *
52618 CAAAAATGACATTTTGATCC-CGAACTTTCCAAAAAATACCATTTTGCCCACTAACA-T
1 CAAAAATTACATTTTTAACCTCGAAC-TTCCAAAAAATACCATTTTGCCCACAAACATT
* * *
52675 CCAAAATTACATTTTTACCCTCGAACATCC-AAAAATCACCATTTTGCCC
1 CAAAAATTACATTTTTAACCTCGAACTTCCAAAAAAT-ACCATTTTGCCC
52724 TCGAATTTTC
Statistics
Matches: 226, Mismatches: 37, Indels: 28
0.78 0.13 0.10
Matches are distributed among these distances:
55 6 0.03
56 64 0.28
57 69 0.31
58 75 0.33
59 12 0.05
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (58 bp):
CAAAAATTACATTTTTAACCTCGAACTTCCAAAAAATACCATTTTGCCCACAAACATT
Found at i:52724 original size:29 final size:28
Alignment explanation
Indices: 52649--52728 Score: 99
Period size: 28 Copynumber: 2.8 Consensus size: 28
52639 GAACTTTCCA
* *
52649 AAAAATACCATTTTGCCCACTAACATCC
1 AAAAATACCATTTTGCCCTCGAACATCC
* *
52677 AAAATTA-CATTTTTACCCTCGAACATCC
1 AAAAATACCA-TTTTGCCCTCGAACATCC
52705 AAAAATCACCATTTTGCCCTCGAA
1 AAAAAT-ACCATTTTGCCCTCGAA
52729 TTTTCCAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
27 2 0.05
28 26 0.60
29 13 0.30
30 2 0.05
ACGTcount: A:0.38, C:0.30, G:0.05, T:0.28
Consensus pattern (28 bp):
AAAAATACCATTTTGCCCTCGAACATCC
Found at i:54694 original size:23 final size:22
Alignment explanation
Indices: 54664--54737 Score: 103
Period size: 23 Copynumber: 3.3 Consensus size: 22
54654 GAAACAATAA
54664 GCACACACAGTGCAATCTAGTAG
1 GCACACACAGTGCAATC-AGTAG
54687 GCACACACAGTGCAATCAGTAG
1 GCACACACAGTGCAATCAGTAG
* * *
54709 GCGCACATAGCGCAAATCAGTAG
1 GCACACACAGTGC-AATCAGTAG
54732 GCACAC
1 GCACAC
54738 GAGGTGCGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.33
23 31 0.67
ACGTcount: A:0.35, C:0.28, G:0.23, T:0.14
Consensus pattern (22 bp):
GCACACACAGTGCAATCAGTAG
Found at i:54753 original size:23 final size:23
Alignment explanation
Indices: 54726--54801 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
54716 TAGCGCAAAT
* *
54726 CAGTAGGCACACGAGGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
* *
54749 TAGTAAGCACACAAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
54772 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
54795 CAGTAAG
1 CAGTAAG
54802 GGTGCTAGCG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.42, C:0.20, G:0.28, T:0.11
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGCGAAA
Done.