Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007738.1 Hibiscus syriacus cultivar Beakdansim tig00109997_pilon, 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: 150216
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:4596 original size:22 final size:21
Alignment explanation
Indices: 4564--4607 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
4554 GACTTATGAG
4564 AAAAAATATAAA-TATAAATAT
1 AAAAAATATAAAGTA-AAATAT
4585 AAAAAATCATAAAGTAAAATAT
1 AAAAAAT-ATAAAGTAAAATAT
4607 A
1 A
4608 GATATAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.33
22 12 0.57
23 2 0.10
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (21 bp):
AAAAAATATAAAGTAAAATAT
Found at i:5138 original size:15 final size:15
Alignment explanation
Indices: 5118--5184 Score: 100
Period size: 15 Copynumber: 4.5 Consensus size: 15
5108 TTTCGGAAAA
*
5118 TGAATTACTGAAATT
1 TGAATTACTGGAATT
5133 TGAATTACTGGAATT
1 TGAATTACTGGAATT
5148 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
5163 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
5177 TGAATTAC
1 TGAATTAC
5185 ATTTTTTGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
14 12 0.25
15 36 0.75
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.37
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:5564 original size:26 final size:26
Alignment explanation
Indices: 5529--5612 Score: 86
Period size: 24 Copynumber: 3.3 Consensus size: 26
5519 CTTTATTAAA
5529 TATTATTTAAATATATAAATATATTAT
1 TATTA-TTAAATATATAAATATATTAT
*
5556 TATTATTAAATA-A-AAAAATATTAT
1 TATTATTAAATATATAAATATATTAT
* * *
5580 ATATTATAAAAAATAT-AATATCTTA-
1 -TATTATTAAATATATAAATATATTAT
5605 TATTATTA
1 TATTATTA
5613 TAATTGATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
24 17 0.35
25 11 0.23
26 15 0.31
27 5 0.10
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (26 bp):
TATTATTAAATATATAAATATATTAT
Found at i:5565 original size:18 final size:18
Alignment explanation
Indices: 5521--5567 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
5511 TTAAATATCT
5521 TTATTAAATATTATTTAA
1 TTATTAAATATTATTTAA
* *
5539 ATATATAAATA-TATTATTA
1 TTAT-TAAATATTATT-TAA
5558 TTATTAAATA
1 TTATTAAATA
5568 AAAAAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATTAAATATTATTTAA
Found at i:5592 original size:19 final size:19
Alignment explanation
Indices: 5568--5606 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5558 TTATTAAATA
*
5568 AAAAAATATTATATATTAT
1 AAAAAATATAATATATTAT
*
5587 AAAAAATATAATATCTTAT
1 AAAAAATATAATATATTAT
5606 A
1 A
5607 TTATTATAAT
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:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAAATATAATATATTAT
Found at i:5697 original size:21 final size:21
Alignment explanation
Indices: 5639--5707 Score: 95
Period size: 21 Copynumber: 3.2 Consensus size: 21
5629 ATACTAAAAA
* *
5639 TATT-AAAATATATCTTATAT
1 TATTAAAAACATATATTATAT
5659 TATTATAAAACATAATATTATAT
1 TATTA-AAAACAT-ATATTATAT
5682 TATTAAAAACATATATTATAT
1 TATTAAAAACATATATTATAT
5703 TATTA
1 TATTA
5708 TATTTAATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
20 4 0.09
21 14 0.32
22 13 0.30
23 13 0.30
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (21 bp):
TATTAAAAACATATATTATAT
Found at i:10134 original size:2 final size:2
Alignment explanation
Indices: 10129--10170 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
10119 ACACACACAC
10129 AT AT AT AT AT AT AT 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 AT AT AT AT
10171 TCTCAGCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11476 original size:14 final size:14
Alignment explanation
Indices: 11457--11483 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11447 CGACCGCGTA
11457 GGGCCCCAAAAAAT
1 GGGCCCCAAAAAAT
11471 GGGCCCCAAAAAA
1 GGGCCCCAAAAAA
11484 GAATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.30, G:0.22, T:0.04
Consensus pattern (14 bp):
GGGCCCCAAAAAAT
Found at i:12776 original size:111 final size:109
Alignment explanation
Indices: 12577--12812 Score: 332
Period size: 111 Copynumber: 2.1 Consensus size: 109
12567 GCCTATTTTC
* *
12577 TAGATATACTCGATTTCGGGCCCCCTATTTTTATGTTTTTAATGGCAACAACTGATATATACTCG
1 TAGATATACTCGATTTCGGGCCCCCTATTTTTATGTTCTTAATGACAACAACTGATATATACTCG
*
12642 ATTTCGGGGCCCCTATTTTTATGCTTCTTAATGACAACAACTGA
66 ATTTCGGGGCCCCTATTTTTATGCTTCTTAATGACAACAACGGA
* * * * *
12686 TAGATATATTTGATTTCGGG-TCCCTATTTTTATGCTTCTTAATGACAATAATTGATAGATATAC
1 TAGATATACTCGATTTCGGGCCCCCTATTTTTATG-TTCTTAATGACAACAACTGAT--ATATAC
* *
12750 TCGATATTC-GGGCCCTTATTTTTATGCTTCTTAATGGCAACAACGGA
63 TCGAT-TTCGGGGCCCCTATTTTTATGCTTCTTAATGACAACAACGGA
12797 TAGATATACTCGATTT
1 TAGATATACTCGATTT
12813 TGAGGCCCAT
Statistics
Matches: 111, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
108 13 0.12
109 35 0.32
111 60 0.54
112 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (109 bp):
TAGATATACTCGATTTCGGGCCCCCTATTTTTATGTTCTTAATGACAACAACTGATATATACTCG
ATTTCGGGGCCCCTATTTTTATGCTTCTTAATGACAACAACGGA
Found at i:12799 original size:56 final size:55
Alignment explanation
Indices: 12577--12828 Score: 339
Period size: 56 Copynumber: 4.6 Consensus size: 55
12567 GCCTATTTTC
* *
12577 TAGATATACTCGATTTCGGGCCCCCTATTTTTATG-TTTTTAATGGCAACAACTGA
1 TAGATATACTCGATTTCGGG-CCCCTATTTTTATGCTTCTTAATGACAACAACTGA
12632 T--ATATACTCGATTTCGGGGCCCCTATTTTTATGCTTCTTAATGACAACAACTGA
1 TAGATATACTCGATTTC-GGGCCCCTATTTTTATGCTTCTTAATGACAACAACTGA
* * * * *
12686 TAGATATATTTGATTTCGGGTCCCTATTTTTATGCTTCTTAATGACAATAATTGA
1 TAGATATACTCGATTTCGGGCCCCTATTTTTATGCTTCTTAATGACAACAACTGA
* * *
12741 TAGATATACTCGATATTCGGGCCCTTATTTTTATGCTTCTTAATGGCAACAACGGA
1 TAGATATACTCGAT-TTCGGGCCCCTATTTTTATGCTTCTTAATGACAACAACTGA
* *
12797 TAGATATACTCGATTTTGAGGCCCATATTTTT
1 TAGATATACTCGATTTCG-GGCCCCTATTTTT
12829 TGGGGGCCTG
Statistics
Matches: 174, Mismatches: 17, Indels: 11
0.86 0.08 0.05
Matches are distributed among these distances:
53 28 0.16
54 22 0.13
55 51 0.29
56 73 0.42
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (55 bp):
TAGATATACTCGATTTCGGGCCCCTATTTTTATGCTTCTTAATGACAACAACTGA
Found at i:14173 original size:2 final size:2
Alignment explanation
Indices: 14166--14203 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
14156 ACCAAACACA
14166 AT AT AT AT AT 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 AT AT
14204 TTGAATCTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14980 original size:16 final size:16
Alignment explanation
Indices: 14961--15005 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
14951 GTTTATGTAA
14961 AAAAATATTTAAATTT
1 AAAAATATTTAAATTT
**
14977 AAAAATATAAAAATTT
1 AAAAATATTTAAATTT
*
14993 ATTAAATATTTAA
1 A-AAAATATTTAA
15006 TCAAGTAGGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAAATATTTAAATTT
Found at i:19830 original size:23 final size:23
Alignment explanation
Indices: 19775--19836 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
19765 GGATGTAATC
*
19775 GAACATAAGCGAACAAAAAAAAAT
1 GAACATAAACGAAC-AAAAAAAAT
* * * *
19799 GAACGTAAACGAACACAATAAGT
1 GAACATAAACGAACAAAAAAAAT
19822 GAACATAAACGAACA
1 GAACATAAACGAACA
19837 TAAATGAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 20 0.62
24 12 0.38
ACGTcount: A:0.60, C:0.16, G:0.15, T:0.10
Consensus pattern (23 bp):
GAACATAAACGAACAAAAAAAAT
Found at i:20009 original size:34 final size:34
Alignment explanation
Indices: 19969--20045 Score: 127
Period size: 34 Copynumber: 2.3 Consensus size: 34
19959 TATTAAAATT
19969 TATTGGGCTTCAATATTTTAAATGGGTCTATAGA
1 TATTGGGCTTCAATATTTTAAATGGGTCTATAGA
*
20003 TATTGGGCTTTAATATTTTAAATGGGTCTATAGA
1 TATTGGGCTTCAATATTTTAAATGGGTCTATAGA
* *
20037 GATTAGGCT
1 TATTGGGCT
20046 AAACATAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.42
Consensus pattern (34 bp):
TATTGGGCTTCAATATTTTAAATGGGTCTATAGA
Found at i:20098 original size:14 final size:14
Alignment explanation
Indices: 20046--20098 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
20036 AGATTAGGCT
20046 AAACATAAATGAAC
1 AAACATAAATGAAC
* *
20060 ACACATAAACGAAC
1 AAACATAAATGAAC
*
20074 GAACAT--A--AAC
1 AAACATAAATGAAC
20084 AAACATAAATGAAC
1 AAACATAAATGAAC
20098 A
1 A
20099 TATTATCGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
10 8 0.27
12 2 0.07
14 20 0.67
ACGTcount: A:0.62, C:0.19, G:0.08, T:0.11
Consensus pattern (14 bp):
AAACATAAATGAAC
Found at i:24163 original size:2 final size:2
Alignment explanation
Indices: 24156--24181 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24146 ACAAGATAGA
24156 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
24182 TTTAACACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26654 original size:14 final size:14
Alignment explanation
Indices: 26613--26655 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
26603 TATGAAGAAC
26613 ATGAACGAACATAA
1 ATGAACGAACATAA
* * *
26627 ATAAATGAATATAA
1 ATGAACGAACATAA
*
26641 ATGAACAAACATAA
1 ATGAACGAACATAA
26655 A
1 A
26656 CAAATGGGTT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.63, C:0.09, G:0.09, T:0.19
Consensus pattern (14 bp):
ATGAACGAACATAA
Found at i:26794 original size:2 final size:2
Alignment explanation
Indices: 26787--26813 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
26777 TATTTTCAAG
26787 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
26814 GTTGGGTTGC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26928 original size:47 final size:47
Alignment explanation
Indices: 26859--26951 Score: 168
Period size: 47 Copynumber: 2.0 Consensus size: 47
26849 GATTTTAAAA
*
26859 AATAACATAATACGAAATGAATTAGGACTAAGTAATGAAATCGAGAC
1 AATAACATAATACGAAATGAATTAGGACTAAATAATGAAATCGAGAC
*
26906 AATAACATAATACGAAATGAATTAGGACTAAATAATGAAATTGAGA
1 AATAACATAATACGAAATGAATTAGGACTAAATAATGAAATCGAGA
26952 AAATCAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.53, C:0.09, G:0.16, T:0.23
Consensus pattern (47 bp):
AATAACATAATACGAAATGAATTAGGACTAAATAATGAAATCGAGAC
Found at i:27744 original size:10 final size:11
Alignment explanation
Indices: 27713--27744 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
27703 CATACTTAAA
*
27713 GTTTAGTTTTT
1 GTTTCGTTTTT
27724 GTTTCGTTTTT
1 GTTTCGTTTTT
27735 GTTTCGTTTT
1 GTTTCGTTTT
27745 AGTACCTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.03, C:0.06, G:0.19, T:0.72
Consensus pattern (11 bp):
GTTTCGTTTTT
Found at i:30964 original size:13 final size:13
Alignment explanation
Indices: 30946--30972 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30936 CTCTTCACAA
30946 ACTGATCTGAAAT
1 ACTGATCTGAAAT
30959 ACTGATCTGAAAT
1 ACTGATCTGAAAT
30972 A
1 A
30973 TTGAAAATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ACTGATCTGAAAT
Found at i:33890 original size:3 final size:3
Alignment explanation
Indices: 33882--33991 Score: 211
Period size: 3 Copynumber: 36.7 Consensus size: 3
33872 TTTTTACCCA
33882 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
33930 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
33978 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
33992 AATATATATT
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 105 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:36001 original size:6 final size:7
Alignment explanation
Indices: 35980--36004 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
35970 TGTCTCCATT
35980 AATTAAA
1 AATTAAA
35987 AATTAAA
1 AATTAAA
35994 AATTAAA
1 AATTAAA
36001 AATT
1 AATT
36005 TATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATTAAA
Found at i:46736 original size:10 final size:10
Alignment explanation
Indices: 46718--46765 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
46708 GCTTGAAGAG
*
46718 AAAAGAGAAA
1 AAAAAAGAAA
46728 AAAAAAG-AA
1 AAAAAAGAAA
46737 AAAAAAGAAA
1 AAAAAAGAAA
*
46747 AAGAAAAAAAA
1 AA-AAAAGAAA
46758 AGAAAAAG
1 A-AAAAAG
46766 GGGGGTCAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 9 0.28
10 10 0.31
11 12 0.38
12 1 0.03
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:46738 original size:9 final size:9
Alignment explanation
Indices: 46726--46764 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
46716 AGAAAAGAGA
46726 AAAAAAAAG
1 AAAAAAAAG
46735 AAAAAAAAG
1 AAAAAAAAG
*
46744 -AAAAAGA-
1 AAAAAAAAG
46751 AAAAAAAAG
1 AAAAAAAAG
46760 AAAAA
1 AAAAA
46765 GGGGGGTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
8 12 0.46
9 14 0.54
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:46753 original size:25 final size:26
Alignment explanation
Indices: 46716--46764 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
46706 ATGCTTGAAG
46716 AGAAAAGAGAAAAAAAAAGAAAAAAA
1 AGAAAAGAGAAAAAAAAAGAAAAAAA
46742 AGAAAA-AGAAAAAAAAAGAAAAA
1 AGAAAAGAGAAAAAAAAAGAAAAA
46765 GGGGGGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (26 bp):
AGAAAAGAGAAAAAAAAAGAAAAAAA
Found at i:46754 original size:16 final size:15
Alignment explanation
Indices: 46725--46765 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
46715 GAGAAAAGAG
46725 AAAA-AAAAAGAAAA
1 AAAAGAAAAAGAAAA
46739 AAAAGAAAAAGAAAAA
1 AAAAGAAAAAG-AAAA
46755 AAAAGAAAAAG
1 AAAAGAAAAAG
46766 GGGGGTCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.16
15 6 0.24
16 15 0.60
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAGAAAA
Found at i:47103 original size:16 final size:16
Alignment explanation
Indices: 47077--47121 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
47067 TTTGAATACA
*
47077 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
47094 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
47109 ATTCAATTTATTT
1 ATTCAATTTATTT
47122 TTGAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:48060 original size:83 final size:83
Alignment explanation
Indices: 47921--48461 Score: 956
Period size: 83 Copynumber: 6.5 Consensus size: 83
47911 CAATATACTC
*
47921 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTGGACAGAATCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
**
47986 TAGAAGATGAATTTGTTA
66 TAGAAGATGAATTTGCCA
48004 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
**
48069 TAGAAGATGAATTTGTTA
66 TAGAAGATGAATTTGCCA
48087 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
*
48152 TGGAAGATGAATTTGCCA
66 TAGAAGATGAATTTGCCA
*
48170 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCACTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
**
48235 TAGAAGATGAATTTGTTA
66 TAGAAGATGAATTTGCCA
48253 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
* *
48318 TGGAATATGAATTTGCCA
66 TAGAAGATGAATTTGCCA
*
48336 ATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
*
48401 TGGAAGATGAATTTGCCA
66 TAGAAGATGAATTTGCCA
*
48419 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
48462 TGGTAGGAAC
Statistics
Matches: 441, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 441 1.00
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAATCATTGAATT
TAGAAGATGAATTTGCCA
Found at i:49384 original size:113 final size:113
Alignment explanation
Indices: 49186--49743 Score: 817
Period size: 113 Copynumber: 5.0 Consensus size: 113
49176 CAAAGATTCC
49186 AATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
49251 AGGAAGAAGAAATTCACAATGAGAAGAATTTGTTCAACCTTTTGCTCA
66 AGGAAGAAGAAATTCACAATGAGAAGAATTTGTTCAACCTTTTGCTCA
*
49299 AATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAAAGAGAAGAACTCATCTGAAGA
1 AATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
49364 AGGAAGAAGAAATTCACAATGAGAAGAATTTGTTCAACCTTTTGCTCA
66 AGGAAGAAGAAATTCACAATGAGAAGAATTTGTTCAACCTTTTGCTCA
49412 AATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
49477 AGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTT--T--
66 AGGAAGAAGAAATTCACAATGAGAAGAATTTGTTCAACCTTTTGCTCA
* * * * * * * * * *
49520 -TTTCATCATTTAATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTAA
1 AATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAA--C-TCATCTGA
49584 AGAAGGAAGAAGAAATTCACAATGAGAAGAATTTGTTCAACCTTTTGCTCA
63 AGAAGGAAGAAGAAATTCACAATGAGAAGAATTTGTTCAACCTTTTGCTCA
* * * *
49635 AATCCATCACTTGATGGAGCAGCTTTTCCAGAT-AAGTTCATAATGAGAAGAACTCATCTAAAGA
1 AATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
49699 AGGAAGAA-AAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGC
66 AGGAAGAAGAAA-TTCACAATGAGAAGAATTTGTTCAACCTTTTGC
49744 ATAATTCTAT
Statistics
Matches: 401, Mismatches: 34, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
107 43 0.11
109 1 0.00
110 44 0.11
111 8 0.02
112 53 0.13
113 211 0.53
115 18 0.04
116 23 0.06
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.28
Consensus pattern (113 bp):
AATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAATTCACAATGAGAAGAATTTGTTCAACCTTTTGCTCA
Found at i:50069 original size:3 final size:3
Alignment explanation
Indices: 50061--50116 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
50051 TTTTTACCCA
*
50061 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
50109 TAT TAT TA
1 TAT TAT TA
50117 AATATATATT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:74418 original size:124 final size:124
Alignment explanation
Indices: 74198--74450 Score: 506
Period size: 124 Copynumber: 2.0 Consensus size: 124
74188 CTCGGTGTGC
74198 TTATGTAGGGTAACTATAGTTGAAATAATTGCTGGATTTGGAAAGGATCGAATAGCGATTGTAAA
1 TTATGTAGGGTAACTATAGTTGAAATAATTGCTGGATTTGGAAAGGATCGAATAGCGATTGTAAA
74263 CATATTAAGTAATCGTTTTATGTTGAGAAGGAACTTTATAAATCCATAGAAAATAAGAT
66 CATATTAAGTAATCGTTTTATGTTGAGAAGGAACTTTATAAATCCATAGAAAATAAGAT
74322 TTATGTAGGGTAACTATAGTTGAAATAATTGCTGGATTTGGAAAGGATCGAATAGCGATTGTAAA
1 TTATGTAGGGTAACTATAGTTGAAATAATTGCTGGATTTGGAAAGGATCGAATAGCGATTGTAAA
74387 CATATTAAGTAATCGTTTTATGTTGAGAAGGAACTTTATAAATCCATAGAAAATAAGAT
66 CATATTAAGTAATCGTTTTATGTTGAGAAGGAACTTTATAAATCCATAGAAAATAAGAT
74446 TTATG
1 TTATG
74451 AAGGAGGGAG
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 129 1.00
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (124 bp):
TTATGTAGGGTAACTATAGTTGAAATAATTGCTGGATTTGGAAAGGATCGAATAGCGATTGTAAA
CATATTAAGTAATCGTTTTATGTTGAGAAGGAACTTTATAAATCCATAGAAAATAAGAT
Found at i:75272 original size:54 final size:54
Alignment explanation
Indices: 75208--75424 Score: 247
Period size: 54 Copynumber: 4.0 Consensus size: 54
75198 AGAAGCTCTT
* *
75208 AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTACATTTGTTCCTTCTTCAAAG
1 AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTCCACTTGTTCCTTCTTCAAAG
* * * *
75262 AGAGCTGAAACAATGGCTGCTGCCAGTGCTATTCCGCTTGTTCCTTCTTCAAAG
1 AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTCCACTTGTTCCTTCTTCAAAG
** * * * * *
75316 AGAGCCGAAACAATGGTTGTTTCCAGTGTTATTCC-GTTAGTTCCTACTTCGAAG
1 AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTCCACTT-GTTCCTTCTTCAAAG
* * * * **
75370 CGAGCTGAAAAAATGGTCGCACCCAGTGTTATTCCACTTGTTCCTTCTTCAAAG
1 AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTCCACTTGTTCCTTCTTCAAAG
75424 A
1 A
75425 ACAAATTACA
Statistics
Matches: 136, Mismatches: 25, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
53 2 0.01
54 132 0.97
55 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (54 bp):
AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTCCACTTGTTCCTTCTTCAAAG
Found at i:75343 original size:108 final size:108
Alignment explanation
Indices: 75208--75424 Score: 283
Period size: 108 Copynumber: 2.0 Consensus size: 108
75198 AGAAGCTCTT
* * *
75208 AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTACATTTGTTCCTTCTTCAAAGAGAGCTGAAAC
1 AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTACATTAGTTCCTACTTCAAAGAGAGCTGAAAA
** *
75273 AATGG-CTGCTGCCAGTGCTATTCCGCTTGTTCCTTCTTCAAAG
66 AATGGTC-GCACCCAGTGCTATTCCACTTGTTCCTTCTTCAAAG
** * * * * * *
75316 AGAGCCGAAACAATGGTTGTTTCCAGTGTTATTCCGTTAGTTCCTACTTCGAAGCGAGCTGAAAA
1 AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTACATTAGTTCCTACTTCAAAGAGAGCTGAAAA
*
75381 AATGGTCGCACCCAGTGTTATTCCACTTGTTCCTTCTTCAAAG
66 AATGGTCGCACCCAGTGCTATTCCACTTGTTCCTTCTTCAAAG
75424 A
1 A
75425 ACAAATTACA
Statistics
Matches: 93, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
108 92 0.99
109 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (108 bp):
AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTACATTAGTTCCTACTTCAAAGAGAGCTGAAAA
AATGGTCGCACCCAGTGCTATTCCACTTGTTCCTTCTTCAAAG
Found at i:91847 original size:20 final size:20
Alignment explanation
Indices: 91796--91847 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
91786 CCACTCTGCA
*
91796 GTATCGATACCATATCTAAG
1 GTATCGATACCCTATCTAAG
91816 GTATCGATACCCTATCTAAG
1 GTATCGATACCCTATCTAAG
91836 GTATCGATACCC
1 GTATCGATACCC
91848 CTATAGCTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (20 bp):
GTATCGATACCCTATCTAAG
Found at i:92699 original size:3 final size:3
Alignment explanation
Indices: 92691--92737 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
92681 AAAATATCAT
*
92691 TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
92738 TGTGTTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:101045 original size:18 final size:18
Alignment explanation
Indices: 101022--101067 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
101012 CGTATTTCAA
*
101022 CACATATCCGATCATCGG
1 CACATACCCGATCATCGG
101040 CACATACCCGATCATCGG
1 CACATACCCGATCATCGG
101058 CACATACCCG
1 CACATACCCG
101068 GACTGCCGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.28, C:0.39, G:0.15, T:0.17
Consensus pattern (18 bp):
CACATACCCGATCATCGG
Found at i:111197 original size:28 final size:28
Alignment explanation
Indices: 111153--111209 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
111143 CTCTCCGTTC
*
111153 ATATTAGGTCGTTGAGCCAATGCTTGAA
1 ATATTAGGTCGTCGAGCCAATGCTTGAA
* *
111181 ATATTATGTCGTCGAGCTAATGCTTGAA
1 ATATTAGGTCGTCGAGCCAATGCTTGAA
111209 A
1 A
111210 GCAACGACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (28 bp):
ATATTAGGTCGTCGAGCCAATGCTTGAA
Found at i:122237 original size:21 final size:21
Alignment explanation
Indices: 122211--122253 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
122201 ATTTAACGTG
122211 TTATTTGTTTTATAATTACAA
1 TTATTTGTTTTATAATTACAA
122232 TTATTTGTTTTATAATTACAA
1 TTATTTGTTTTATAATTACAA
122253 T
1 T
122254 ATTGAGCAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (21 bp):
TTATTTGTTTTATAATTACAA
Found at i:122658 original size:36 final size:36
Alignment explanation
Indices: 122609--122705 Score: 176
Period size: 36 Copynumber: 2.7 Consensus size: 36
122599 TTTTAGCCGC
122609 GATAAATGTAATTAAACGATTTTGATATAACAAAGG
1 GATAAATGTAATTAAACGATTTTGATATAACAAAGG
* *
122645 GCTAAATGTAATTAAACGATTTTGATATAATAAAGG
1 GATAAATGTAATTAAACGATTTTGATATAACAAAGG
122681 GATAAATGTAATTAAACGATTTTGA
1 GATAAATGTAATTAAACGATTTTGA
122706 AATTTGTAAC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.33
Consensus pattern (36 bp):
GATAAATGTAATTAAACGATTTTGATATAACAAAGG
Found at i:128349 original size:21 final size:21
Alignment explanation
Indices: 128325--128385 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
128315 GGCAACCAAC
128325 TTTGAAAAATGTTTTTCAAAG
1 TTTGAAAAATGTTTTTCAAAG
**
128346 TTTGGTAAATG--TTTC----
1 TTTGAAAAATGTTTTTCAAAG
128361 TTTGAAAAATGTTTTTCAAAG
1 TTTGAAAAATGTTTTTCAAAG
128382 TTTG
1 TTTG
128386 GTAAAGTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 9 0.30
17 4 0.13
19 4 0.13
21 13 0.43
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.48
Consensus pattern (21 bp):
TTTGAAAAATGTTTTTCAAAG
Found at i:128371 original size:36 final size:35
Alignment explanation
Indices: 128324--128394 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 35
128314 TGGCAACCAA
128324 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAA-GTTT
128360 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
128395 GATAGATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 4 0.11
36 31 0.89
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (35 bp):
CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
Found at i:129414 original size:21 final size:21
Alignment explanation
Indices: 129388--129430 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
129378 ATTTAACGTG
129388 TTATTTGTTTTATAATTACAA
1 TTATTTGTTTTATAATTACAA
129409 TTATTTGTTTTATAATTACAA
1 TTATTTGTTTTATAATTACAA
129430 T
1 T
129431 ATTGAGCAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (21 bp):
TTATTTGTTTTATAATTACAA
Found at i:135506 original size:24 final size:26
Alignment explanation
Indices: 135452--135503 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
135442 ATAACCACAC
*
135452 CAATATATAAGTTCAAACATCCATAATA
1 CAATAAATAAGTTCAAACATCC--AATA
*
135480 CAATAAATAAGTTCAAATATCCAA
1 CAATAAATAAGTTCAAACATCCAA
135504 CAACAAAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
28 20 0.91
ACGTcount: A:0.52, C:0.17, G:0.04, T:0.27
Consensus pattern (26 bp):
CAATAAATAAGTTCAAACATCCAATA
Found at i:137507 original size:20 final size:20
Alignment explanation
Indices: 137460--137515 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
137450 AAAACCAGTA
* *
137460 CCCCAGTGGGGTATCGATTT
1 CCCCAGGGGGGTATCGAATT
137480 CCCCAGGGGGGTATC-AATT
1 CCCCAGGGGGGTATCGAATT
*
137499 CCCCTAGGGGGGAATCG
1 CCCC-AGGGGGGTATCG
137516 GTTCCCCTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.23
20 24 0.77
ACGTcount: A:0.18, C:0.27, G:0.34, T:0.21
Consensus pattern (20 bp):
CCCCAGGGGGGTATCGAATT
Found at i:137520 original size:20 final size:20
Alignment explanation
Indices: 137478--137544 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 20
137468 GGGTATCGAT
* **
137478 TTCCCC-AGGGGGGTATCAA
1 TTCCCCTAGGGGGGAATCGG
137497 TTCCCCTAGGGGGGAATCGG
1 TTCCCCTAGGGGGGAATCGG
*
137517 TTCCCCTTCAAAGGGGGAATCGG
1 TTCCCC-T--AGGGGGGAATCGG
137540 TTCCC
1 TTCCC
137545 TCATGAGAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.15
20 16 0.40
21 1 0.03
23 17 0.43
ACGTcount: A:0.18, C:0.28, G:0.31, T:0.22
Consensus pattern (20 bp):
TTCCCCTAGGGGGGAATCGG
Found at i:141572 original size:15 final size:15
Alignment explanation
Indices: 141552--141590 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
141542 TTCTTGTTCC
141552 TCTTCATCGAAACCT
1 TCTTCATCGAAACCT
*
141567 TCTTCATCGGAACCT
1 TCTTCATCGAAACCT
141582 TCTTCATCG
1 TCTTCATCG
141591 CTCCATGTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.21, C:0.33, G:0.10, T:0.36
Consensus pattern (15 bp):
TCTTCATCGAAACCT
Found at i:144078 original size:20 final size:21
Alignment explanation
Indices: 144043--144090 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
144033 GTAGTGGGTT
144043 AAACCTACCATAAGGGG-TTCG
1 AAACC-ACCATAAGGGGTTTCG
*
144064 AAACCACCTTAAGGGGTTTCG
1 AAACCACCATAAGGGGTTTCG
144085 AAACCA
1 AAACCA
144091 AGCTCAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (21 bp):
AAACCACCATAAGGGGTTTCG
Found at i:145428 original size:23 final size:23
Alignment explanation
Indices: 145384--145428 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
145374 CATTCAATAG
*
145384 CTTCTAGAAGACCCAGTCAGCAA
1 CTTCTAGAAGACCCAATCAGCAA
* *
145407 CTTCTAGAAGATCCAATTAGCA
1 CTTCTAGAAGACCCAATCAGCA
145429 GTGGCGTGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.22
Consensus pattern (23 bp):
CTTCTAGAAGACCCAATCAGCAA
Found at i:148266 original size:2 final size:2
Alignment explanation
Indices: 148259--148307 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
148249 TAATTTGTGC
*
148259 AT AT AT AT AT AT AT -T AT AT -T AT TT 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 AT AT AT AT
148299 AT AT AT AT A
1 AT AT AT AT A
148308 CTACTTTCTC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:149857 original size:20 final size:21
Alignment explanation
Indices: 149832--149873 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
149822 ATTTAACGTG
149832 TTATTTG-TTTATAATTACAA
1 TTATTTGTTTTATAATTACAA
149852 TTATTTGTTTTATAATTACAA
1 TTATTTGTTTTATAATTACAA
149873 T
1 T
149874 ATTGAGCAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (21 bp):
TTATTTGTTTTATAATTACAA
Done.