Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 12 of 208
Found at i:3653459 original size:18 final size:18
Alignment explanation
Indices: 3653415--3653561 Score: 81
Period size: 17 Copynumber: 8.3 Consensus size: 18
3653405 ACGAAAGCAT
*
3653415 GAAAA-TTTTGAAAACAC
1 GAAAATTTTTTAAAACAC
* *
3653432 GGGAATTTTTTTAAAACAC
1 -GAAAATTTTTTAAAACAC
* *
3653451 GAAAA-TTTTTGAAACAT
1 GAAAATTTTTTAAAACAC
* *
3653468 GAGAATTTTTT--GACAC
1 GAAAATTTTTTAAAACAC
** *
3653484 GAAAA-TTTCGAAAACAT
1 GAAAATTTTTTAAAACAC
** *
3653501 GAATTTTTTTTAAAATAC
1 GAAAATTTTTTAAAACAC
*
3653519 G-AATTTTTTTAAAAACAC
1 GAAAATTTTTT-AAAACAC
*
3653537 GAGAATTTTTTTGAAAACAC
1 GA-AAATTTTTT-AAAACAC
3653557 GAAAA
1 GAAAA
3653562 CATGAAAATT
Statistics
Matches: 96, Mismatches: 25, Indels: 15
0.71 0.18 0.11
Matches are distributed among these distances:
15 3 0.03
16 7 0.07
17 28 0.29
18 27 0.28
19 13 0.14
20 18 0.19
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (18 bp):
GAAAATTTTTTAAAACAC
Found at i:3653499 original size:33 final size:34
Alignment explanation
Indices: 3653415--3653622 Score: 103
Period size: 36 Copynumber: 6.1 Consensus size: 34
3653405 ACGAAAGCAT
* *
3653415 GAAAATTTTGAAAACACGGGAATTTTTTTAAAACAC
1 GAAAATTTTGAAAACATGAGAA-TTTTTT-AAACAC
*
3653451 GAAAATTTTTG-AAACATGAGAATTTTTT-GACAC
1 GAAAA-TTTTGAAAACATGAGAATTTTTTAAACAC
* * *
3653484 GAAAATTTCGAAAACATGA-ATTTTTTTTAAAATAC
1 GAAAATTTTGAAAACATGAGA-ATTTTTT-AAACAC
** * * *
3653519 GAATTTTTTTAAAAACACGAGAATTTTTT-----T
1 GAA-AATTTTGAAAACATGAGAATTTTTTAAACAC
*** * **
3653549 GAAAA-CACGAAAACATGAAAATTTTGAAAACAC
1 GAAAATTTTGAAAACATGAGAATTTTTTAAACAC
*
3653582 AAAAATTTTTG-AAACATGAGAATTTTTTGAAAACAC
1 GAAAA-TTTTGAAAACATGAGAATTTTTT--AAACAC
3653618 GAAAA
1 GAAAA
3653623 CACGAAAAAA
Statistics
Matches: 123, Mismatches: 33, Indels: 32
0.65 0.18 0.17
Matches are distributed among these distances:
28 14 0.11
30 3 0.02
32 5 0.04
33 27 0.22
34 14 0.11
35 13 0.11
36 41 0.33
37 6 0.05
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (34 bp):
GAAAATTTTGAAAACATGAGAATTTTTTAAACAC
Found at i:3653542 original size:20 final size:20
Alignment explanation
Indices: 3653501--3653558 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
3653491 TCGAAAACAT
* *
3653501 GAATTTTTTTTAAAATAC--
1 GAATTTTTTTAAAAACACGA
3653519 GAATTTTTTTAAAAACACGA
1 GAATTTTTTTAAAAACACGA
*
3653539 GAATTTTTTTGAAAACACGA
1 GAATTTTTTTAAAAACACGA
3653559 AAACATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
18 16 0.46
20 19 0.54
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (20 bp):
GAATTTTTTTAAAAACACGA
Found at i:3653579 original size:17 final size:17
Alignment explanation
Indices: 3653557--3653622 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
3653547 TTGAAAACAC
*
3653557 GAAAACATGAAAATTTT
1 GAAAACACGAAAATTTT
*
3653574 GAAAACACAAAAATTTTT
1 GAAAACACGAAAA-TTTT
* *
3653592 G-AAACATGAGAATTTTTT
1 GAAAACACGA-AA-ATTTT
3653610 GAAAACACGAAAA
1 GAAAACACGAAAA
3653623 CACGAAAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
17 17 0.45
18 14 0.37
19 7 0.18
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (17 bp):
GAAAACACGAAAATTTT
Found at i:3653593 original size:18 final size:18
Alignment explanation
Indices: 3653566--3653622 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
3653556 CGAAAACATG
3653566 AAAA-TTTTGAAAACACA
1 AAAATTTTTGAAAACACA
*
3653583 AAAATTTTTG-AAACATGA
1 AAAATTTTTGAAAACA-CA
* *
3653601 GAATTTTTTGAAAACACGA
1 AAAATTTTTGAAAACAC-A
3653620 AAA
1 AAA
3653623 CACGAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
17 9 0.29
18 14 0.45
19 8 0.26
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.28
Consensus pattern (18 bp):
AAAATTTTTGAAAACACA
Found at i:3653624 original size:44 final size:43
Alignment explanation
Indices: 3653574--3653665 Score: 105
Period size: 44 Copynumber: 2.1 Consensus size: 43
3653564 TGAAAATTTT
** * *
3653574 GAAAACAC-AAAAATTTTTGAAACATGAGAATTTTTTGAAAACAC
1 GAAAACACAAAAAAAATTT-AAACACGAGAA-TTTTTGAAAACAA
*
3653618 GAAAACACGAAAAAAAATTTAAACACGGGAATTTTTGAAAACAA
1 GAAAACAC-AAAAAAAATTTAAACACGAGAATTTTTGAAAACAA
3653662 GAAA
1 GAAA
3653666 TTTTTTTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
44 24 0.59
45 9 0.22
46 8 0.20
ACGTcount: A:0.54, C:0.11, G:0.13, T:0.22
Consensus pattern (43 bp):
GAAAACACAAAAAAAATTTAAACACGAGAATTTTTGAAAACAA
Found at i:3653642 original size:62 final size:61
Alignment explanation
Indices: 3653524--3653671 Score: 158
Period size: 62 Copynumber: 2.4 Consensus size: 61
3653514 AATACGAATT
* * * *
3653524 TTTTTAAAAACACGAGAATTTTTTTGAAAACACGAAAACATGAAAATTTTGAAAACACAAAAA
1 TTTTTGAAAACAAGAGAA-TTTTTTGAAAACACGAAAACACGAAAAATTT-AAAACACAAAAA
* ***
3653587 TTTTTG-AAACATGAGAATTTTTTGAAAACACGAAAACACGAAAAAAAATTT-AAACACGGGAA
1 TTTTTGAAAACAAGAGAATTTTTTGAAAACACGAAAACACG---AAAAATTTAAAACACAAAAA
3653649 TTTTTGAAAACAAGA-AATTTTTT
1 TTTTTGAAAACAAGAGAATTTTTT
3653672 TTTAAAAACA
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
61 22 0.30
62 32 0.44
63 12 0.16
64 7 0.10
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.29
Consensus pattern (61 bp):
TTTTTGAAAACAAGAGAATTTTTTGAAAACACGAAAACACGAAAAATTTAAAACACAAAAA
Found at i:3653679 original size:21 final size:22
Alignment explanation
Indices: 3653649--3653691 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
3653639 AACACGGGAA
*
3653649 TTTTTGAAAACA-AGAAATTTT
1 TTTTTAAAAACACAGAAATTTT
*
3653670 TTTTTAAAAACACGGAAATTTT
1 TTTTTAAAAACACAGAAATTTT
3653692 AAAACATGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (22 bp):
TTTTTAAAAACACAGAAATTTT
Found at i:3653693 original size:17 final size:17
Alignment explanation
Indices: 3653671--3653723 Score: 74
Period size: 16 Copynumber: 3.2 Consensus size: 17
3653661 AGAAATTTTT
3653671 TTTTAAAAACACGGAAA
1 TTTTAAAAACACGGAAA
*
3653688 TTTT-AAAACATGGAAA
1 TTTTAAAAACACGGAAA
*
3653704 CTTTAAAAACAC-GAAA
1 TTTTAAAAACACGGAAA
3653720 TTTT
1 TTTT
3653724 TTTTTAAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 21 0.68
17 10 0.32
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.30
Consensus pattern (17 bp):
TTTTAAAAACACGGAAA
Found at i:3653734 original size:20 final size:21
Alignment explanation
Indices: 3653709--3653749 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3653699 GGAAACTTTA
3653709 AAAACACGAA-ATTTTT-TTTT
1 AAAACAC-AAGATTTTTATTTT
3653729 AAAACACAAGATTTTTATTTT
1 AAAACACAAGATTTTTATTTT
3653750 TTTTATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 13 0.68
21 4 0.21
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (21 bp):
AAAACACAAGATTTTTATTTT
Found at i:3653896 original size:20 final size:20
Alignment explanation
Indices: 3653867--3653904 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3653857 GGGATTCTAA
3653867 TAAAACACGAGAATTTTTAT
1 TAAAACACGAGAATTTTTAT
* *
3653887 TAAAATACGAGGATTTTT
1 TAAAACACGAGAATTTTT
3653905 GAATATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (20 bp):
TAAAACACGAGAATTTTTAT
Found at i:3654166 original size:19 final size:19
Alignment explanation
Indices: 3654126--3654168 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
3654116 AACACCATTT
*
3654126 AAATACATTAAATAAAATA
1 AAATACATTAAATAAAAAA
* *
3654145 AAATAGATTAAAAAGAAAAA
1 AAATACATTAAATA-AAAAA
3654165 AAAT
1 AAAT
3654169 TACCCAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (19 bp):
AAATACATTAAATAAAAAA
Found at i:3654367 original size:14 final size:14
Alignment explanation
Indices: 3654350--3654390 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3654340 TTACTTTTTT
3654350 CTCTCTTTTTCTTC
1 CTCTCTTTTTCTTC
*
3654364 CTCTTTTTTTCTTC
1 CTCTCTTTTTCTTC
* *
3654378 TTCTCTTCTTCTT
1 CTCTCTTTTTCTT
3654391 GTCTCAAAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (14 bp):
CTCTCTTTTTCTTC
Found at i:3655018 original size:30 final size:29
Alignment explanation
Indices: 3654981--3655106 Score: 107
Period size: 30 Copynumber: 4.2 Consensus size: 29
3654971 ATTGAGAGTT
3654981 TAGGGGTCAAA-GTGAAATTTTGAGAAAGTA
1 TAGGGGTCAAATGT-AAATTTT-AGAAAGTA
* * *
3655011 TAAGGGTCGAAATGT-AATTTTATAAAGTT
1 TAGGGGTC-AAATGTAAATTTTAGAAAGTA
* *
3655040 TTGGGGTTAAAATGTAAATTTTAGAAAAGT-
1 TAGGGG-TCAAATGTAAATTTTAG-AAAGTA
*
3655070 TTGGGGTCAAATTGTAAATTTT-GAGAAGTA
1 TAGGGGTCAAA-TGTAAATTTTAGA-AAGTA
3655100 TAGGGGT
1 TAGGGGT
3655107 TAAAATGCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
28 1 0.01
29 25 0.32
30 43 0.54
31 8 0.10
32 2 0.03
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (29 bp):
TAGGGGTCAAATGTAAATTTTAGAAAGTA
Found at i:3655509 original size:57 final size:56
Alignment explanation
Indices: 3655448--3655638 Score: 165
Period size: 57 Copynumber: 3.6 Consensus size: 56
3655438 ATATATTTTA
* *
3655448 TCTGACATGTGAAGAAATGATTGTCTAAAATGGCTGCTGTTTCCAGAACTTATCATG
1 TCTGACAT-TGAAGAAATGGTTGTCTAAAATGGCTGCTGTTTCCAGAACTTATTATG
* * * * *
3655505 TCTGACATTTAAGAAATGGTTGTCCAAAATGAACT--TGTTTTCATAACTTATTATG
1 TCTGACATTGAAGAAATGGTTGTCTAAAATG-GCTGCTGTTTCCAGAACTTATTATG
* *
3655560 TCTG--A-T------AT--TTGTCTAAAATGGCTGCTCTTTCCTGAACTTATTATG
1 TCTGACATTGAAGAAATGGTTGTCTAAAATGGCTGCTGTTTCCAGAACTTATTATG
* *
3655605 TCTGATATATGAAGAAACGGTTGTCTAAAATGGC
1 TCTGACAT-TGAAGAAATGGTTGTCTAAAATGGC
3655639 GTTGCTTGGT
Statistics
Matches: 105, Mismatches: 14, Indels: 30
0.70 0.09 0.20
Matches are distributed among these distances:
43 2 0.02
44 11 0.10
45 20 0.19
46 2 0.02
47 1 0.01
49 1 0.01
52 1 0.01
53 1 0.01
55 22 0.21
56 20 0.19
57 24 0.23
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (56 bp):
TCTGACATTGAAGAAATGGTTGTCTAAAATGGCTGCTGTTTCCAGAACTTATTATG
Found at i:3655535 original size:56 final size:55
Alignment explanation
Indices: 3655448--3655569 Score: 138
Period size: 55 Copynumber: 2.2 Consensus size: 55
3655438 ATATATTTTA
* * *
3655448 TCTGACATGTGAAGAAATGATTGTCTAAAATG-GCTGCTGTTTCCAGAACTTATCATG
1 TCTGACAT-TTAAGAAATGATTGTCCAAAATGAACT--TGTTTCCAGAACTTATCATG
* * * *
3655505 TCTGACATTTAAGAAATGGTTGTCCAAAATGAACTTGTTTTCATAACTTATTATG
1 TCTGACATTTAAGAAATGATTGTCCAAAATGAACTTGTTTCCAGAACTTATCATG
*
3655560 TCTGATATTT
1 TCTGACATTT
3655570 GTCTAAAATG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
55 26 0.46
56 20 0.36
57 10 0.18
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (55 bp):
TCTGACATTTAAGAAATGATTGTCCAAAATGAACTTGTTTCCAGAACTTATCATG
Found at i:3655563 original size:55 final size:54
Alignment explanation
Indices: 3655417--3655569 Score: 146
Period size: 57 Copynumber: 2.7 Consensus size: 54
3655407 TTTCTAGCAG
* * * *
3655417 AAAATGACTGTTGTTTTCATAA-TATATTTTATCTGACATGTGAAGAAATGATTGTCT
1 AAAATGAC--TTGTTTTCATAACT-TATTATGTCTGACAT-TTAAGAAATGATTGTCC
* * * * *
3655474 AAAATGGCTGCTGTTTCCAGAACTTATCATGTCTGACATTTAAGAAATGGTTGTCC
1 AAAATGACT--TGTTTTCATAACTTATTATGTCTGACATTTAAGAAATGATTGTCC
*
3655530 AAAATGAACTTGTTTTCATAACTTATTATGTCTGATATTT
1 AAAATG-ACTTGTTTTCATAACTTATTATGTCTGACATTT
3655570 GTCTAAAATG
Statistics
Matches: 78, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
55 27 0.35
56 20 0.26
57 30 0.38
58 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (54 bp):
AAAATGACTTGTTTTCATAACTTATTATGTCTGACATTTAAGAAATGATTGTCC
Found at i:3655578 original size:44 final size:45
Alignment explanation
Indices: 3655524--3655612 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 45
3655514 TAAGAAATGG
3655524 TTGTCCAAAATGAACTTG-T-TTTCAT-AACTTATTATGTCTGATAT
1 TTGTCCAAAATG-AC-TGCTCTTTCATGAACTTATTATGTCTGATAT
* * *
3655568 TTGTCTAAAATGGCTGCTCTTTCCTGAACTTATTATGTCTGATAT
1 TTGTCCAAAATGACTGCTCTTTCATGAACTTATTATGTCTGATAT
3655613 ATGAAGAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
42 2 0.05
43 2 0.05
44 16 0.41
45 19 0.49
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (45 bp):
TTGTCCAAAATGACTGCTCTTTCATGAACTTATTATGTCTGATAT
Found at i:3655940 original size:50 final size:49
Alignment explanation
Indices: 3655885--3655979 Score: 136
Period size: 49 Copynumber: 1.9 Consensus size: 49
3655875 TATCTAAAAA
*
3655885 TCTAAATAAAAAAATATAAAATTACGTCGTTTTGATAAATATTTACTTCC
1 TCTAAA-AAAAAAAGATAAAATTACGTCGTTTTGATAAATATTTACTTCC
** * *
3655935 TCTAAAATTAAAAGGTAAAATTACGTTGTTTTGATAAATATTTAC
1 TCTAAAAAAAAAAGATAAAATTACGTCGTTTTGATAAATATTTAC
3655980 CCATCAACCT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
49 34 0.85
50 6 0.15
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.39
Consensus pattern (49 bp):
TCTAAAAAAAAAAGATAAAATTACGTCGTTTTGATAAATATTTACTTCC
Found at i:3662335 original size:66 final size:66
Alignment explanation
Indices: 3662259--3662388 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 66
3662249 AACTCTTGAG
*
3662259 TCGTCCCCCCACTCTCTTGTAGGGCTTTGACCAAC-TCCGGATTATCAATTTGAACTATTCTTTA
1 TCGTCCCCCCACTCTCTTGTAGGGCTTTGACC-ACTTCCGGATTATCAATTTGAACTACTCTTTA
3662323 CT
65 CT
*
3662325 TCGTCCCCCCACTCTTTTGTAGGGCTTTGACCACTTCCGGATTATCAATTTGAACTACTCTTTA
1 TCGTCCCCCCACTCTCTTGTAGGGCTTTGACCACTTCCGGATTATCAATTTGAACTACTCTTTA
3662389 TTTTATGTCT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
65 2 0.03
66 59 0.97
ACGTcount: A:0.19, C:0.30, G:0.14, T:0.37
Consensus pattern (66 bp):
TCGTCCCCCCACTCTCTTGTAGGGCTTTGACCACTTCCGGATTATCAATTTGAACTACTCTTTAC
T
Found at i:3666854 original size:19 final size:19
Alignment explanation
Indices: 3666822--3666869 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
3666812 AAACTTTTTC
3666822 TTGTTGTT-TTTCACTATT
1 TTGTTGTTATTTCACTATT
3666840 TTGTTGTTATTTCACTATT
1 TTGTTGTTATTTCACTATT
*
3666859 ATGTTGTTATT
1 TTGTTGTTATT
3666870 GTTTGGATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.15, C:0.08, G:0.12, T:0.65
Consensus pattern (19 bp):
TTGTTGTTATTTCACTATT
Found at i:3673507 original size:91 final size:91
Alignment explanation
Indices: 3673342--3673522 Score: 258
Period size: 91 Copynumber: 2.0 Consensus size: 91
3673332 CTCTTACGTG
3673342 GGAACAATTACCTAGTTCAAGCACTAACATGAGAACAATTACCAAGTTTAAGGATTAACTTGAAC
1 GGAACAATTACCTAGTTCAAGCACTAACATGAGAACAATTACCAAGTTTAAGGATTAACTTGAAC
*
3673407 AAAAAAAAAGTCCATACCCCAATGTA
66 AAAAAAAAAGTCCAAACCCCAATGTA
* * * * *
3673433 GGAACAATTACCTAGTTCAAGC-CTTAACATGTGAACAATTCCCAAGTTTATGGATTAAATTTGG
1 GGAACAATTACCTAGTTCAAGCAC-TAACATGAGAACAATTACCAAGTTTAAGGATT-AACTTGA
**
3673497 AC-AAAAAAAAGTTTAAACCCCAATGT
64 ACAAAAAAAAAGTCCAAACCCCAATGT
3673523 GAGAATTTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
90 1 0.01
91 72 0.90
92 7 0.09
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.25
Consensus pattern (91 bp):
GGAACAATTACCTAGTTCAAGCACTAACATGAGAACAATTACCAAGTTTAAGGATTAACTTGAAC
AAAAAAAAAGTCCAAACCCCAATGTA
Found at i:3676081 original size:2 final size:2
Alignment explanation
Indices: 3676074--3676100 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3676064 TCAAATAGAA
3676074 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3676101 AATGAATTAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3678555 original size:2 final size:2
Alignment explanation
Indices: 3678548--3678589 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3678538 TCTCAATCCA
3678548 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
3678590 TTCAATACCA
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:3678756 original size:2 final size:2
Alignment explanation
Indices: 3678751--3678776 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3678741 TTATTATCAC
3678751 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
3678777 GTCATGACTA
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:3679674 original size:38 final size:37
Alignment explanation
Indices: 3679605--3679677 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
3679595 TTTTCATAAT
* *
3679605 TTCACTTTTTCACTTTTAATCACTATTCAATTCAAAA
1 TTCACTTTTCCACTTTTAATCAATATTCAATTCAAAA
3679642 TTCACTTTTCCA-TTTTCAAGTCAATATTCAATTCAA
1 TTCACTTTTCCACTTTT-AA-TCAATATTCAATTCAA
3679678 TTCCACACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.32, C:0.22, G:0.01, T:0.45
Consensus pattern (37 bp):
TTCACTTTTCCACTTTTAATCAATATTCAATTCAAAA
Found at i:3679708 original size:23 final size:22
Alignment explanation
Indices: 3679665--3679708 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
3679655 TTTCAAGTCA
3679665 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
3679688 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
3679709 TTAATCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:3679822 original size:23 final size:23
Alignment explanation
Indices: 3679796--3679917 Score: 208
Period size: 23 Copynumber: 5.3 Consensus size: 23
3679786 ATAAGTGCCA
3679796 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
3679819 CACTGAAATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
3679842 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
3679865 CACTGATATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
3679888 CGCTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
3679911 CACTGAT
1 CACTGAT
3679918 CAATAACACT
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 91 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:3695543 original size:20 final size:20
Alignment explanation
Indices: 3695515--3695552 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3695505 ATAATTTTGT
3695515 AAACCCAAAACTTAAACCAC
1 AAACCCAAAACTTAAACCAC
*
3695535 AAACTCAAAACTTAAACC
1 AAACCCAAAACTTAAACC
3695553 CGAACATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.32, G:0.00, T:0.13
Consensus pattern (20 bp):
AAACCCAAAACTTAAACCAC
Found at i:3708777 original size:31 final size:31
Alignment explanation
Indices: 3708742--3708810 Score: 113
Period size: 31 Copynumber: 2.2 Consensus size: 31
3708732 TGTCCCAGAA
3708742 GGTCACTTTAAAATAGCGTTA-TTTTAATTTT
1 GGTCACTTTAAAATAGCGTTATTTTTAA-TTT
*
3708773 GGTCAATTTAAAATAGCGTTATTTTTAATTT
1 GGTCACTTTAAAATAGCGTTATTTTTAATTT
3708804 GGTCACT
1 GGTCACT
3708811 CTAATTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 29 0.83
32 6 0.17
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.46
Consensus pattern (31 bp):
GGTCACTTTAAAATAGCGTTATTTTTAATTT
Found at i:3714776 original size:19 final size:19
Alignment explanation
Indices: 3714731--3714790 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
3714721 GTTTCTCTCA
*
3714731 ATAAAAGTTACAAAATAATTT
1 ATAAAAATT-CAAAAT-ATTT
*
3714752 -TTAAAATTCAAAATATTT
1 ATAAAAATTCAAAATATTT
*
3714770 ATAAAAATTCCAAAT-TTT
1 ATAAAAATTCAAAATATTT
3714788 ATA
1 ATA
3714791 TGTTTTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.29
19 18 0.53
20 6 0.18
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (19 bp):
ATAAAAATTCAAAATATTT
Found at i:3718632 original size:22 final size:23
Alignment explanation
Indices: 3718588--3718632 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
3718578 TTAATTTAAT
*
3718588 TTTTATTTTTTCATTTTTTATGA
1 TTTTATTTTTTCATTTTTCATGA
3718611 TTTTA-TTTTT-ATTTGTTCATGA
1 TTTTATTTTTTCATTT-TTCATGA
3718633 CTCAGTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 11 0.55
23 5 0.25
ACGTcount: A:0.18, C:0.04, G:0.07, T:0.71
Consensus pattern (23 bp):
TTTTATTTTTTCATTTTTCATGA
Found at i:3725057 original size:131 final size:128
Alignment explanation
Indices: 3724651--3725125 Score: 400
Period size: 131 Copynumber: 3.7 Consensus size: 128
3724641 AAAATTGTTT
* * * * *
3724651 TGTTGTAATTAGTAATAAGAAAATTAAATTATGTAACGATATTTTAAGGTTATTGCTAATATTTT
1 TGTTGTAATTAGTAAGAAGAAAATTAAATTACGTAACGACATTTTAAGATTGTTGCTAATATTTT
* * *
3724716 AATGTTTAACAACAATTTATTTTGTCCGTGTA-AATTTTATTAAGAATATGCACCA-ACAAA--A
66 AACGTTTAACAACAATTTATTTTAT-CGT-TACAATTTTATTAAGAAT-T-CACAAGACAAATCA
3724777 GA
127 GA
* * *
3724779 TGTTGTGATTCGTAA-ATAGAAAATCAAATTACGTAACGACATTTTAAAGA-TGTTGCTAATATT
1 TGTTGTAATTAGTAAGA-AGAAAATTAAATTACGTAACGACATTTT-AAGATTGTTGCTAATATT
* * * * * *
3724842 TTCACATTT---AAC--TTTTTTTTTTCGTTACAAATTTTATTAGGAATTCACAACGACAAGTCG
64 TTAACGTTTAACAACAATTTATTTTATCGTTAC-AATTTTATTAAGAATTCACAA-GACAAATC-
* *
3724902 CGT
126 AGA
* * * * *
3724905 TGTTGTGAA-TACTAAGCAGAAAGTTAAATTACGTAAAGACAATTTAAGATTGTTGCTAATATTT
1 TGTTGT-AATTAGTAAGAAGAAAATTAAATTACGTAACGACATTTTAAGATTGTTGCTAATATTT
*
3724969 TAACGTTTAACAACAACTTATTTTATCGTTACACATTTTATTAAGAATTCACAATGACAAATCAT
65 TAACGTTTAACAACAATTTATTTTATCGTTACA-ATTTTATTAAGAATTCACAA-GACAAATCA-
*
3725034 GC
127 GA
* * * * ** * *
3725036 TGCTGTAATTAATAAGAAGAAAATTAAATGACATAACGACATTTTAA-AGTCATTGCTAACATTA
1 TGTTGTAATTAGTAAGAAGAAAATTAAATTACGTAACGACATTTTAAGA-TTGTTGCTAATATTT
** *
3725100 TAATATTTAACGACAATTTATTTTAT
65 TAACGTTTAACAACAATTTATTTTAT
3725126 TGTTGCATAT
Statistics
Matches: 275, Mismatches: 51, Indels: 39
0.75 0.14 0.11
Matches are distributed among these distances:
121 6 0.02
122 4 0.01
123 26 0.09
125 7 0.03
126 55 0.20
127 2 0.01
128 56 0.20
129 6 0.02
130 4 0.01
131 109 0.40
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (128 bp):
TGTTGTAATTAGTAAGAAGAAAATTAAATTACGTAACGACATTTTAAGATTGTTGCTAATATTTT
AACGTTTAACAACAATTTATTTTATCGTTACAATTTTATTAAGAATTCACAAGACAAATCAGA
Found at i:3730786 original size:30 final size:30
Alignment explanation
Indices: 3730734--3730794 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
3730724 TTACAAAGGC
* *
3730734 ATTGGTGGTGTAGGGGGTTTAGGCGGTGGA
1 ATTGGAGGTCTAGGGGGTTTAGGCGGTGGA
*
3730764 ATTGGAGGTCTAGGTGGG-TTAGGGGGTGGA
1 ATTGGAGGTCTAGG-GGGTTTAGGCGGTGGA
3730794 A
1 A
3730795 CTGGTGGCGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.16, C:0.03, G:0.52, T:0.28
Consensus pattern (30 bp):
ATTGGAGGTCTAGGGGGTTTAGGCGGTGGA
Found at i:3730820 original size:42 final size:42
Alignment explanation
Indices: 3730766--3730861 Score: 165
Period size: 42 Copynumber: 2.3 Consensus size: 42
3730756 GCGGTGGAAT
*
3730766 TGGAGGTCTAGGTGGGTTAGGGGGTGGAACTGGTGGCGGAGG
1 TGGAGGTCTAGGTGGGTTAGGGGGTGGAACCGGTGGCGGAGG
* *
3730808 TGGAGGTCTAGGTGGTTTAGGGGGTGGAACCGGTGGCGGAGT
1 TGGAGGTCTAGGTGGGTTAGGGGGTGGAACCGGTGGCGGAGG
3730850 TGGAGGTCTAGG
1 TGGAGGTCTAGG
3730862 CGGTGGGACC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.15, C:0.08, G:0.54, T:0.23
Consensus pattern (42 bp):
TGGAGGTCTAGGTGGGTTAGGGGGTGGAACCGGTGGCGGAGG
Found at i:3730867 original size:33 final size:33
Alignment explanation
Indices: 3730825--3730900 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
3730815 CTAGGTGGTT
* *
3730825 TAGGGGGTGGAACCGGTGGCGGAGTTGGAGGTC
1 TAGGCGGTGGAACCGGGGGCGGAGTTGGAGGTC
* *
3730858 TAGGCGGTGGGACCGGGGGTGGAGTTGGAGGTC
1 TAGGCGGTGGAACCGGGGGCGGAGTTGGAGGTC
*
3730891 TAGGTGGTGG
1 TAGGCGGTGG
3730901 TGGTTGTCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.13, C:0.11, G:0.57, T:0.20
Consensus pattern (33 bp):
TAGGCGGTGGAACCGGGGGCGGAGTTGGAGGTC
Found at i:3730928 original size:66 final size:67
Alignment explanation
Indices: 3730858--3731022 Score: 176
Period size: 66 Copynumber: 2.5 Consensus size: 67
3730848 GTTGGAGGTC
* * * *
3730858 TAGGCGGTGGGA-CCGGGGGTGGAGTTGGAGGT-CTAGGTGGTGGTGGTTGTCCAGGTACAGGTG
1 TAGGCGGTGGGAGCCGGAGGTCGAGGTGGAGGTGCT-GGTGGTGGTGGTTGTCCAGATACAGGTG
3730921 GTG
65 GTG
* * * * * *
3730924 TAGGCAG-CGGAGCTGGAGGTCTAGGTGGTGGTGGTGGTGGTGGTGGTTGTCCAGATACAGGTGG
1 TAGGCGGTGGGAGCCGGAGGTCGAGGTGGAGGTGCTGGTGGTGGTGGTTGTCCAGATACAGGTGG
3730988 TG
66 TG
* * *
3730990 TAGGCGGT-GGAGCTGGAGGTCTAGGTGGTGGTG
1 TAGGCGGTGGGAGCCGGAGGTCGAGGTGGAGGTG
3731023 GCAGCGGAAT
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
65 3 0.04
66 81 0.95
67 1 0.01
ACGTcount: A:0.13, C:0.10, G:0.52, T:0.25
Consensus pattern (67 bp):
TAGGCGGTGGGAGCCGGAGGTCGAGGTGGAGGTGCTGGTGGTGGTGGTTGTCCAGATACAGGTGG
TG
Found at i:3731023 original size:66 final size:66
Alignment explanation
Indices: 3730893--3731023 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 66
3730883 TGGAGGTCTA
*
3730893 GGTGGTGGTGGTTGTCCAGGTACAGGTGGTGTAGGCAGCGGAGCTGGAGGTCTAGGTGGTGGTGG
1 GGTGGTGGTGGTTGTCCAGATACAGGTGGTGTAGGCAGCGGAGCTGGAGGTCTAGGTGGTGGTGG
3730958 T
66 T
* *
3730959 GGTGGTGGTGGTTGTCCAGATACAGGTGGTGTAGGCGGTGGAGCTGGAGGTCTAGGTGGTGGTGG
1 GGTGGTGGTGGTTGTCCAGATACAGGTGGTGTAGGCAGCGGAGCTGGAGGTCTAGGTGGTGGTGG
3731024 CAGCGGAATA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.12, C:0.10, G:0.52, T:0.26
Consensus pattern (66 bp):
GGTGGTGGTGGTTGTCCAGATACAGGTGGTGTAGGCAGCGGAGCTGGAGGTCTAGGTGGTGGTGG
T
Found at i:3735163 original size:50 final size:50
Alignment explanation
Indices: 3735041--3735333 Score: 487
Period size: 50 Copynumber: 5.8 Consensus size: 50
3735031 GATAATAACA
* ** *
3735041 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* ** *
3735092 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCACATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
3735142 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
3735192 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACATCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
3735242 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
3735292 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
3735334 TTACCCAAAT
Statistics
Matches: 226, Mismatches: 16, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
50 193 0.85
51 33 0.15
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:3750161 original size:6 final size:7
Alignment explanation
Indices: 3750136--3750160 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3750126 ATTCAACAAA
3750136 AAAAATT
1 AAAAATT
3750143 AAAAATT
1 AAAAATT
3750150 AAAAATT
1 AAAAATT
3750157 AAAA
1 AAAA
3750161 TACTTTAATG
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAAATT
Found at i:3755104 original size:4 final size:4
Alignment explanation
Indices: 3755095--3755142 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
3755085 ATCTTAATCC
* * * * *
3755095 TTTA TTTA TTCA TTTA TTTA TTTG TTTG TTTA TTTA TATC TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
3755143 AAACTTTCTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:3755401 original size:26 final size:26
Alignment explanation
Indices: 3755372--3755441 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 26
3755362 AAATATACGT
*
3755372 ATACTTATATATATATATATCTTATA
1 ATACTTATATATACATATATCTTATA
* * *
3755398 ATACATATATGTACATATATTTTATA
1 ATACTTATATATACATATATCTTATA
3755424 AT--TTATATATACATATAT
1 ATACTTATATATACATATAT
3755442 ATATTTGTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 14 0.37
26 24 0.63
ACGTcount: A:0.43, C:0.07, G:0.01, T:0.49
Consensus pattern (26 bp):
ATACTTATATATACATATATCTTATA
Found at i:3756946 original size:10 final size:11
Alignment explanation
Indices: 3756919--3756945 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3756909 ATAATAAAAA
3756919 TAAAAATATTT
1 TAAAAATATTT
3756930 TAAAAATATTT
1 TAAAAATATTT
3756941 TAAAA
1 TAAAA
3756946 TTAAAAAATA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TAAAAATATTT
Found at i:3760359 original size:3 final size:3
Alignment explanation
Indices: 3760351--3760432 Score: 164
Period size: 3 Copynumber: 27.3 Consensus size: 3
3760341 CTCAACTGCA
3760351 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3760399 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3760433 GAGAAGAAAA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3761643 original size:51 final size:51
Alignment explanation
Indices: 3761553--3761649 Score: 131
Period size: 51 Copynumber: 1.9 Consensus size: 51
3761543 ATATTTTTTT
* * * *
3761553 ATTTTTTAGAATTAGGACCAAATTGAGAATATTTGTAAATTTTGAGGGTTA
1 ATTTTTTAAAATTAGGACCAAATTGAGAATATATATAAATGTTGAGGGTTA
* * *
3761604 ATTTTTTAAAATTAGGACTAAATTGATATTATATATAAATGTTGAG
1 ATTTTTTAAAATTAGGACCAAATTGAGAATATATATAAATGTTGAG
3761650 AGCTAAATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 39 1.00
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.42
Consensus pattern (51 bp):
ATTTTTTAAAATTAGGACCAAATTGAGAATATATATAAATGTTGAGGGTTA
Found at i:3767115 original size:3 final size:3
Alignment explanation
Indices: 3767107--3767144 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3767097 ATAGTCCTTG
3767107 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3767145 GTTAATGTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3772808 original size:20 final size:20
Alignment explanation
Indices: 3772783--3772822 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3772773 CGTAAAATGA
*
3772783 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
3772803 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
3772823 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:3772812 original size:34 final size:35
Alignment explanation
Indices: 3772768--3772834 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3772758 CAGTAAAATA
*
3772768 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
3772802 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
3772835 CCGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:3784312 original size:18 final size:19
Alignment explanation
Indices: 3784279--3784316 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3784269 AGACTCTAGG
*
3784279 TCTGATTCTTTTCAATCAT
1 TCTGATTCTCTTCAATCAT
3784298 TCTGATT-TCTTCAATCAT
1 TCTGATTCTCTTCAATCAT
3784316 T
1 T
3784317 GCCTGCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (19 bp):
TCTGATTCTCTTCAATCAT
Found at i:3788900 original size:18 final size:19
Alignment explanation
Indices: 3788873--3788912 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
3788863 AGCAATTATT
3788873 TTTTTAATATTTAAAAATA
1 TTTTTAATATTTAAAAATA
* *
3788892 TTTTT-ATATTTTATAATA
1 TTTTTAATATTTAAAAATA
3788910 TTT
1 TTT
3788913 CAATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTAATATTTAAAAATA
Found at i:3789841 original size:21 final size:21
Alignment explanation
Indices: 3789796--3789843 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3789786 TGAAATTTAT
* *
3789796 TTTTTATTTTTATTTTACAAT
1 TTTTAATTTTTATTTTACAAA
3789817 TTTTAATTTTTATATTT-CAAA
1 TTTTAATTTTTAT-TTTACAAA
3789838 TTTTAA
1 TTTTAA
3789844 AATTTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTAATTTTTATTTTACAAA
Found at i:3792352 original size:51 final size:51
Alignment explanation
Indices: 3792289--3792390 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 51
3792279 TTTTTTTTAT
* * * *
3792289 TTTTTTAGAATTAGGATCAAATTAAGAATATTTGTAAATTTTGAGGGTTAA
1 TTTTTTAAAATTAGGATCAAATTAAGAATATATATAAATGTTGAGGGTTAA
* * * *
3792340 TTTTTTAAAATTAGGATTAAATTGATATTATATATAAATGTTGAGGGTTAA
1 TTTTTTAAAATTAGGATCAAATTAAGAATATATATAAATGTTGAGGGTTAA
3792391 ATTTGTTATT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.38, C:0.01, G:0.17, T:0.44
Consensus pattern (51 bp):
TTTTTTAAAATTAGGATCAAATTAAGAATATATATAAATGTTGAGGGTTAA
Found at i:3798752 original size:18 final size:19
Alignment explanation
Indices: 3798725--3798769 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
3798715 AGCAATTATT
3798725 TTTTTAATATTTAAAAATA
1 TTTTTAATATTTAAAAATA
* *
3798744 TTTTT-ATATTTTATAATA
1 TTTTTAATATTTAAAAATA
3798762 -TTTTAATA
1 TTTTTAATA
3798770 ATTTTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 4 0.17
18 14 0.61
19 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTTAATATTTAAAAATA
Found at i:3798754 original size:29 final size:28
Alignment explanation
Indices: 3798721--3798812 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 28
3798711 CGTTAGCAAT
3798721 TATTTTTTTAATATTTAAAAATATTTTTA
1 TATTTTTTTAATATTTAAAAAT-TTTTTA
* *
3798750 TA-TTTTATAATATTTTAATAATTTTTATA
1 TATTTTTTTAATA-TTTAAAAATTTTT-TA
* * * *
3798779 TAGTTTTTGAATTTTTAAAAATTTATT-
1 TATTTTTTTAATATTTAAAAATTTTTTA
3798806 TATTTTT
1 TATTTTT
3798813 GACATGGCAA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
27 6 0.12
28 14 0.27
29 25 0.48
30 7 0.13
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (28 bp):
TATTTTTTTAATATTTAAAAATTTTTTA
Found at i:3798762 original size:10 final size:10
Alignment explanation
Indices: 3798724--3798778 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
3798714 TAGCAATTAT
*
3798724 TTTTTTAATA
1 TTTTATAATA
* *
3798734 TTTAAAAATA
1 TTTTATAATA
3798744 TTTT-T-ATA
1 TTTTATAATA
3798752 TTTTATAATA
1 TTTTATAATA
3798762 TTTTAATAAT-
1 TTTT-ATAATA
3798772 TTTTATA
1 TTTTATA
3798779 TAGTTTTTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
8 7 0.19
9 4 0.11
10 21 0.57
11 5 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTTATAATA
Found at i:3799319 original size:16 final size:15
Alignment explanation
Indices: 3799291--3799320 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
3799281 TATGAACTAA
3799291 TTTCTTTTATATATT
1 TTTCTTTTATATATT
3799306 TTTCTTTATATATAT
1 TTTCTTT-TATATAT
3799321 ATTTACAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTCTTTTATATATT
Found at i:3800960 original size:560 final size:560
Alignment explanation
Indices: 3799901--3801022 Score: 2235
Period size: 560 Copynumber: 2.0 Consensus size: 560
3799891 TTTAGGGGAG
3799901 TTCTATTCACGCAATCAAGGATTGCCCACACCCATACACGTGTGGAAAAACTTGGTGACAACTTA
1 TTCTATTCACGCAATCAAGGATTGCCCACACCCATACACGTGTGGAAAAACTTGGTGACAACTTA
3799966 TATTCAGGTCAATTTCTTTGCCTCGAATTTGGTGGGTTAGGTGATGGCTAATTTGAATATGTCCA
66 TATTCAGGTCAATTTCTTTGCCTCGAATTTGGTGGGTTAGGTGATGGCTAATTTGAATATGTCCA
3800031 CTATCCATGTTTGTTGTAATGCCCCTTGGGACACTCTATTTGGAATTGAATGTTGGAAGCCTTGG
131 CTATCCATGTTTGTTGTAATGCCCCTTGGGACACTCTATTTGGAATTGAATGTTGGAAGCCTTGG
*
3800096 AAGTAGCGTAATTCTCTAGTGTCATTTGTATTTTAAGAATTTTTAAGGTTCAGACGGAATACTTT
196 AAGTAGCGTAATTCTCTAGTGTCATTTGTATTTTAAGAATTCTTAAGGTTCAGACGGAATACTTT
3800161 CACATATAAGTTATTGATTCATTCCATTGCATCGTTTTATAACTATAATTTCGTAAAGTTCCCAT
261 CACATATAAGTTATTGATTCATTCCATTGCATCGTTTTATAACTATAATTTCGTAAAGTTCCCAT
3800226 CTTTCACACATTTCTATCAACTATTTCAATTTTGCAATTCAATCCAAATGCTAGTTAACATTTTA
326 CTTTCACACATTTCTATCAACTATTTCAATTTTGCAATTCAATCCAAATGCTAGTTAACATTTTA
3800291 TGACCATTTATAATTATAAAAAAACTTACAATTATTCACTAAAAAGGAAATTTAACAAAATAACC
391 TGACCATTTATAATTATAAAAAAACTTACAATTATTCACTAAAAAGGAAATTTAACAAAATAACC
3800356 CCTATACGAACTTACCTCAATAAAATGATTTGAGTTAAATGGTTTGAGTTATTCGAGTTATTCAG
456 CCTATACGAACTTACCTCAATAAAATGATTTGAGTTAAATGGTTTGAGTTATTCGAGTTATTCAG
3800421 ATAAACTCAAATAAAAAAATTAATTTTTTTGGATAAATGT
521 ATAAACTCAAATAAAAAAATTAATTTTTTTGGATAAATGT
3800461 TTCTATTCACGCAATCAAGGATTGCCCACACCCATACACGTGTGGAAAAACTTGGTGACAACTTA
1 TTCTATTCACGCAATCAAGGATTGCCCACACCCATACACGTGTGGAAAAACTTGGTGACAACTTA
3800526 TATTCAGGTCAATTTCTTTGCCTCGAATTTGGTGGGTTAGGTGATGGCTAATTTGAATATGTCCA
66 TATTCAGGTCAATTTCTTTGCCTCGAATTTGGTGGGTTAGGTGATGGCTAATTTGAATATGTCCA
3800591 CTATCCATGTTTGTTGTAATGCCCCTTGGGACACTCTATTTGGAATTGAATGTTGGAAGCCTTGG
131 CTATCCATGTTTGTTGTAATGCCCCTTGGGACACTCTATTTGGAATTGAATGTTGGAAGCCTTGG
3800656 AAGTAGCGTAATTCTCTAGTGTCATTTGTATTTTAAGAATTCTTAAGGTTCAGACGGAATACTTT
196 AAGTAGCGTAATTCTCTAGTGTCATTTGTATTTTAAGAATTCTTAAGGTTCAGACGGAATACTTT
3800721 CACATATAAGTTATTGATTCATTCCATTGCATCGTTTTATAACTATAATTTCGTAAAGTTCCCAT
261 CACATATAAGTTATTGATTCATTCCATTGCATCGTTTTATAACTATAATTTCGTAAAGTTCCCAT
3800786 CTTTCACACATTTCTATCAACTATTTCAATTTTGCAATTCAATCCAAATGCTAGTTAACATTTTA
326 CTTTCACACATTTCTATCAACTATTTCAATTTTGCAATTCAATCCAAATGCTAGTTAACATTTTA
3800851 TGACCATTTATAATTATAAAAAAACTTACAATTATTCACTAAAAAGGAAATTTAACAAAATAACC
391 TGACCATTTATAATTATAAAAAAACTTACAATTATTCACTAAAAAGGAAATTTAACAAAATAACC
3800916 CCTATACGAACTTACCTCAATAAAATGATTTGAGTTAAATGGTTTGAGTTATTCGAGTTATTCAG
456 CCTATACGAACTTACCTCAATAAAATGATTTGAGTTAAATGGTTTGAGTTATTCGAGTTATTCAG
3800981 ATAAACTCAAATAAAAAAATTAATTTTTTTGGATAAATGT
521 ATAAACTCAAATAAAAAAATTAATTTTTTTGGATAAATGT
3801021 TT
1 TT
3801023 ACCTTTTCTA
Statistics
Matches: 561, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
560 561 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (560 bp):
TTCTATTCACGCAATCAAGGATTGCCCACACCCATACACGTGTGGAAAAACTTGGTGACAACTTA
TATTCAGGTCAATTTCTTTGCCTCGAATTTGGTGGGTTAGGTGATGGCTAATTTGAATATGTCCA
CTATCCATGTTTGTTGTAATGCCCCTTGGGACACTCTATTTGGAATTGAATGTTGGAAGCCTTGG
AAGTAGCGTAATTCTCTAGTGTCATTTGTATTTTAAGAATTCTTAAGGTTCAGACGGAATACTTT
CACATATAAGTTATTGATTCATTCCATTGCATCGTTTTATAACTATAATTTCGTAAAGTTCCCAT
CTTTCACACATTTCTATCAACTATTTCAATTTTGCAATTCAATCCAAATGCTAGTTAACATTTTA
TGACCATTTATAATTATAAAAAAACTTACAATTATTCACTAAAAAGGAAATTTAACAAAATAACC
CCTATACGAACTTACCTCAATAAAATGATTTGAGTTAAATGGTTTGAGTTATTCGAGTTATTCAG
ATAAACTCAAATAAAAAAATTAATTTTTTTGGATAAATGT
Found at i:3801752 original size:21 final size:21
Alignment explanation
Indices: 3801726--3801788 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
3801716 TTTGAAATTT
*
3801726 ATTTTTTATTTTTATTTTAAA
1 ATTTTTAATTTTTATTTTAAA
*
3801747 ATTTTTAATTTTTATATTTCAA
1 ATTTTTAATTTTTAT-TTTAAA
* *
3801769 ATTTTAAATTTTAATTTTAA
1 ATTTTTAATTTTTATTTTAA
3801789 TTATTAGTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
21 18 0.50
22 18 0.50
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTTTAATTTTTATTTTAAA
Found at i:3805994 original size:10 final size:10
Alignment explanation
Indices: 3805970--3806032 Score: 60
Period size: 10 Copynumber: 6.6 Consensus size: 10
3805960 ACCAGAAAAG
3805970 TATAAA-AAT
1 TATAAATAAT
*
3805979 TGTAAATAAT
1 TATAAATAAT
* *
3805989 TATAAAGAAA
1 TATAAATAAT
3805999 T-TAAA-AAT
1 TATAAATAAT
*
3806007 GATAAATAAT
1 TATAAATAAT
*
3806017 TGTAAATAAT
1 TATAAATAAT
3806027 TATAAA
1 TATAAA
3806033 AAAGATAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
8 2 0.05
9 13 0.31
10 27 0.64
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.33
Consensus pattern (10 bp):
TATAAATAAT
Found at i:3806042 original size:38 final size:37
Alignment explanation
Indices: 3805971--3806044 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 37
3805961 CCAGAAAAGT
*
3805971 ATAAAAATTGTAAATAATTATAAAGAAATTAAAAATG
1 ATAAAAATTGTAAATAATTATAAAGAAAATAAAAATG
3806008 ATAAATAATTGTAAATAATTATAAA-AAAGATAAAAAT
1 ATAAA-AATTGTAAATAATTATAAAGAAA-ATAAAAAT
3806045 TACAAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
37 8 0.24
38 26 0.76
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (37 bp):
ATAAAAATTGTAAATAATTATAAAGAAAATAAAAATG
Found at i:3813296 original size:179 final size:179
Alignment explanation
Indices: 3812985--3813341 Score: 624
Period size: 179 Copynumber: 2.0 Consensus size: 179
3812975 AAGCATCAAT
*
3812985 CATTAGCTTTGCATCTTCAAAACCTTTTACCTAAAGGAAGATTTAAATGCACAAGGACATAAACT
1 CATTAGCTTTGCATCTTCAAAACCTTTTACCTAAAGGAAGAATTAAATGCACAAGGACATAAACT
3813050 TCAAAAGAGATTCATCATTAAACATTAAATGCTTCCCTAGATAATGGTGTAGAAATACAGAATGA
66 TCAAAAGAGATTCATCATTAAACATTAAATGCTTCCCTAGATAATGGTGTAGAAATACAGAATGA
*
3813115 ACGGAACAAATTCAAAATCAAACCTATATCTATTATGAAGAGACTAAAA
131 ACGGAACAAATTCAAAATCAAACCTATACCTATTATGAAGAGACTAAAA
*
3813164 CATTAGCTTTGCATCTTCAAAACCTTTTTCCTAAAGGAAGAATTAAATGCACAAGGACATAAACT
1 CATTAGCTTTGCATCTTCAAAACCTTTTACCTAAAGGAAGAATTAAATGCACAAGGACATAAACT
* * * * * *
3813229 TCAAAAGAGGTTCATCATTAAACATTAGATTCTTCCCTAGGTAATGGTGTAGAAATGCAGGATGA
66 TCAAAAGAGATTCATCATTAAACATTAAATGCTTCCCTAGATAATGGTGTAGAAATACAGAATGA
*
3813294 ACGGCACAAATTCAAAATCAAACCTATACCTATTATGAAGAGACTAAA
131 ACGGAACAAATTCAAAATCAAACCTATACCTATTATGAAGAGACTAAA
3813342 GCCAGTGTAG
Statistics
Matches: 168, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
179 168 1.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (179 bp):
CATTAGCTTTGCATCTTCAAAACCTTTTACCTAAAGGAAGAATTAAATGCACAAGGACATAAACT
TCAAAAGAGATTCATCATTAAACATTAAATGCTTCCCTAGATAATGGTGTAGAAATACAGAATGA
ACGGAACAAATTCAAAATCAAACCTATACCTATTATGAAGAGACTAAAA
Found at i:3814430 original size:18 final size:18
Alignment explanation
Indices: 3814407--3814451 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
3814397 GAAATTAGCA
3814407 GATGATCA-AAACAATGGT
1 GATGATCATAAAC-ATGGT
* *
3814425 GATGATCATCATCATGGT
1 GATGATCATAAACATGGT
3814443 GATGATCAT
1 GATGATCAT
3814452 CATGGAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (18 bp):
GATGATCATAAACATGGT
Found at i:3814445 original size:15 final size:15
Alignment explanation
Indices: 3814427--3814456 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3814417 ACAATGGTGA
3814427 TGATCATCATCATGG
1 TGATCATCATCATGG
*
3814442 TGATGATCATCATGG
1 TGATCATCATCATGG
3814457 AACAGAGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (15 bp):
TGATCATCATCATGG
Found at i:3814452 original size:18 final size:18
Alignment explanation
Indices: 3814420--3814454 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3814410 GATCAAAACA
3814420 ATGGTGATGATCATCATC
1 ATGGTGATGATCATCATC
3814438 ATGGTGATGATCATCAT
1 ATGGTGATGATCATCAT
3814455 GGAACAGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (18 bp):
ATGGTGATGATCATCATC
Found at i:3818422 original size:32 final size:32
Alignment explanation
Indices: 3818382--3818452 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
3818372 AATTTTAACC
*
3818382 CAATAACTTTAAACAAAAAATTTCAAACAGTT
1 CAATAACTTTAAACAAAAAATTTCAAACAATT
* * * *
3818414 CAATAAC-TTGAAGAAAAATTTTCAAATAATT
1 CAATAACTTTAAACAAAAAATTTCAAACAATT
3818445 CAATAACT
1 CAATAACT
3818453 ATTTTGTATC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 26 0.79
32 7 0.21
ACGTcount: A:0.52, C:0.14, G:0.04, T:0.30
Consensus pattern (32 bp):
CAATAACTTTAAACAAAAAATTTCAAACAATT
Found at i:3825111 original size:21 final size:22
Alignment explanation
Indices: 3825085--3825127 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3825075 TAAAAAAACT
**
3825085 TTATATAT-TTTATTTTTTAAA
1 TTATATATATTTAAATTTTAAA
3825106 TTATATATATTTAAATTTTAAA
1 TTATATATATTTAAATTTTAAA
3825128 CAATGGTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATATATATTTAAATTTTAAA
Found at i:3826582 original size:9 final size:9
Alignment explanation
Indices: 3826570--3826600 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3826560 ACTTTTAAAC
*
3826570 ATTTTTAAT
1 ATTTTTATT
3826579 ATTTTTATT
1 ATTTTTATT
3826588 ATTTTTATT
1 ATTTTTATT
3826597 ATTT
1 ATTT
3826601 GTAAGAGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
ATTTTTATT
Found at i:3834425 original size:2 final size:2
Alignment explanation
Indices: 3834418--3834453 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3834408 ATCCGATTCA
3834418 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
3834454 TGGCCCTACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3837984 original size:38 final size:38
Alignment explanation
Indices: 3837932--3838014 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 38
3837922 ATTTGCCGGC
*
3837932 TTACTGATTAGGCACTTATG-TGCCGACTACTGTTACTG
1 TTACTGATTAGGCACTT-TGATGCCGAATACTGTTACTG
* *
3837970 TTACTGATTCGGCACTTTGTATGTCGAATACTGTTACTG
1 TTACTGATTAGGCACTTTG-ATGCCGAATACTGTTACTG
3838009 TTACTG
1 TTACTG
3838015 TTACCGACTC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
37 2 0.05
38 16 0.40
39 22 0.55
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (38 bp):
TTACTGATTAGGCACTTTGATGCCGAATACTGTTACTG
Found at i:3838010 original size:45 final size:45
Alignment explanation
Indices: 3837959--3838156 Score: 290
Period size: 45 Copynumber: 4.4 Consensus size: 45
3837949 ATGTGCCGAC
*
3837959 TACTGTTACTGTTACTGATTCGGCACTTTGTATGTCGAATACTGT
1 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
* *
3838004 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
*
3838049 TACTGTTACTGTTA-TCGATTCGGCACTCTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACT-GATTCGGCACTTTGTGTGTCGAATACTGT
* * * * *
3838094 TACAGTTACTGTTACAGGTTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
3838139 TACTGTTACTGATTACTG
1 TACTGTTACTG-TTACTG
3838157 TATACTGGTG
Statistics
Matches: 136, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
45 131 0.96
46 5 0.04
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (45 bp):
TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
Found at i:3838013 original size:39 final size:39
Alignment explanation
Indices: 3837932--3838152 Score: 183
Period size: 45 Copynumber: 5.2 Consensus size: 39
3837922 ATTTGCCGGC
* * * *
3837932 TTACTGATTAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
*
3837970 TTACTGATTCGGCACTTTGTATGTCGAATACTGTTACTG
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
*
3838009 TTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTAC---T---GATTCGGCACTTTGTGTGTCGAATACTGTTACTG
* *
3838054 TTACTGTTATCGATTCGGCACTCTGTGTGTCGAATACTGTTACAG
1 TTAC-----T-GATTCGGCACTTTGTGTGTCGAATACTGTTACTG
* *
3838099 TTACTGTTACAGGTTCAGCACTTTGTGTGTTGAATACTGTTACTG
1 TTACTG----A--TTCGGCACTTTGTGTGTCGAATACTGTTACTG
3838144 TTACTGATT
1 TTACTGATT
3838153 ACTGTATACT
Statistics
Matches: 152, Mismatches: 16, Indels: 29
0.77 0.08 0.15
Matches are distributed among these distances:
38 14 0.09
39 26 0.17
40 1 0.01
41 1 0.01
42 1 0.01
43 1 0.01
45 106 0.70
47 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (39 bp):
TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
Found at i:3839666 original size:22 final size:23
Alignment explanation
Indices: 3839618--3839665 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
3839608 CCCGTTTTCT
*
3839618 AAACGGGCTTCATTTTTTTTGCA
1 AAACGGGCTTCATTTTTTTTCCA
*
3839641 AAACGGGCTTCATTTTTTTCCCA
1 AAACGGGCTTCATTTTTTTTCCA
3839664 AA
1 AA
3839666 CTCATATTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.40
Consensus pattern (23 bp):
AAACGGGCTTCATTTTTTTTCCA
Found at i:3840738 original size:33 final size:33
Alignment explanation
Indices: 3840696--3840766 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3840686 GTGGCATAAG
*
3840696 GCCCACCTTACCATGAAAACCCCAACATCATGC
1 GCCCACCTTACCATGAAAAACCCAACATCATGC
*
3840729 GCCCACCTTACCATGAAAAACCCAATATCATGC
1 GCCCACCTTACCATGAAAAACCCAACATCATGC
*
3840762 ACCCA
1 GCCCA
3840767 ACACCACAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.35, C:0.41, G:0.08, T:0.15
Consensus pattern (33 bp):
GCCCACCTTACCATGAAAAACCCAACATCATGC
Found at i:3841117 original size:15 final size:15
Alignment explanation
Indices: 3841076--3841117 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3841066 GAGAGTAATG
3841076 GGAA-AAGAAGA-AGA
1 GGAAGAAGAAGAGA-A
3841090 GGAAGAAGAAGAGAA
1 GGAAGAAGAAGAGAA
*
3841105 GGAAGAGGAAGAG
1 GGAAGAAGAAGAG
3841118 CCTATACTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 4 0.16
15 20 0.80
16 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (15 bp):
GGAAGAAGAAGAGAA
Found at i:3846141 original size:17 final size:17
Alignment explanation
Indices: 3846119--3846152 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3846109 ATTGTTGTCC
3846119 CTTATCGAATTTTTTAA
1 CTTATCGAATTTTTTAA
3846136 CTTATCGAATTTTTTAA
1 CTTATCGAATTTTTTAA
3846153 GTGCCTGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (17 bp):
CTTATCGAATTTTTTAA
Found at i:3847936 original size:14 final size:15
Alignment explanation
Indices: 3847919--3847951 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3847909 GTTGAAATAA
3847919 ATTTTTT-TAAATTT
1 ATTTTTTATAAATTT
*
3847933 ATTTTTTATGAATTT
1 ATTTTTTATAAATTT
3847948 ATTT
1 ATTT
3847952 AATTGAACCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
ATTTTTTATAAATTT
Found at i:3850770 original size:3 final size:3
Alignment explanation
Indices: 3850762--3850812 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
3850752 ATTTGACCTA
3850762 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3850810 ATT
1 ATT
3850813 TGATATTAAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3850871 original size:2 final size:2
Alignment explanation
Indices: 3850864--3850896 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3850854 ATTGCTAATT
*
3850864 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3850897 CTTGACATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3863469 original size:63 final size:67
Alignment explanation
Indices: 3863331--3863471 Score: 150
Period size: 69 Copynumber: 2.1 Consensus size: 67
3863321 GAAATATCAA
* * * *
3863331 AATT-TTTGTATTTAAGATTTCTGTTTCGAGTTCGATTTTTAAATAAATTTTTATTTGTTACCCG
1 AATTATTTATATTTAAGATTTCTGTCTCGAGTTCAATTTTTAAATAAATTTTTA-TTGTT--CCA
*
3863395 TTATC
63 TAATC
*
3863400 AA-TATTTATATTTAAGATTTCTGTCTCGAGTTTAATTTTTAAAT-AATTTTTA-T-TT-CATAA
1 AATTATTTATATTTAAGATTTCTGTCTCGAGTTCAATTTTTAAATAAATTTTTATTGTTCCATAA
*
3863460 TG
66 TC
3863462 AATTATTTAT
1 AATTATTTAT
3863472 TGTTATATTA
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
62 6 0.10
63 7 0.11
65 2 0.03
66 1 0.02
68 9 0.14
69 38 0.60
ACGTcount: A:0.29, C:0.08, G:0.09, T:0.54
Consensus pattern (67 bp):
AATTATTTATATTTAAGATTTCTGTCTCGAGTTCAATTTTTAAATAAATTTTTATTGTTCCATAA
TC
Found at i:3863988 original size:31 final size:31
Alignment explanation
Indices: 3863930--3863994 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
3863920 ATAAAAATTC
** *
3863930 AATGACTTAAATAAAAACTTTTGAATAGTTT
1 AATGACTTAAATAAAAACTTTCAAATAGCTT
*
3863961 AATGACTTAAATGAAAACTTTCAAATAGCTT
1 AATGACTTAAATAAAAACTTTCAAATAGCTT
3863992 AAT
1 AAT
3863995 AACCATTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.35
Consensus pattern (31 bp):
AATGACTTAAATAAAAACTTTCAAATAGCTT
Found at i:3864274 original size:20 final size:19
Alignment explanation
Indices: 3864252--3864323 Score: 94
Period size: 19 Copynumber: 3.7 Consensus size: 19
3864242 AAAATTTCAA
3864252 AAAAAATTCAAAATAATTT
1 AAAAAATTCAAAATAATTT
3864271 AAAAAATTCAAAATAAATTT
1 AAAAAATTCAAAAT-AATTT
*
3864291 -TAAAATTCAAAAT-ATTT
1 AAAAAATTCAAAATAATTT
3864308 ATAAAAATTTCAAAAT
1 A-AAAAA-TTCAAAAT
3864324 TTATATATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.09
19 30 0.64
20 13 0.28
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAAATTCAAAATAATTT
Found at i:3864284 original size:38 final size:39
Alignment explanation
Indices: 3864242--3864326 Score: 90
Period size: 38 Copynumber: 2.2 Consensus size: 39
3864232 ACTCTTAACA
3864242 AAAATTTCAAA-AAAAATTCAAAATAATTTA-AAAAA-TTC
1 AAAATTT-AAATAAAAATTCAAAAT-ATTTATAAAAATTTC
*
3864280 AAAA--TAAATTTTAAAATTCAAAATATTTATAAAAATTTC
1 AAAATTTAAA--TAAAAATTCAAAATATTTATAAAAATTTC
3864319 AAAATTTA
1 AAAATTTA
3864327 TATATATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
35 3 0.08
36 1 0.03
37 5 0.13
38 21 0.54
39 7 0.18
41 2 0.05
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (39 bp):
AAAATTTAAATAAAAATTCAAAATATTTATAAAAATTTC
Found at i:3874852 original size:26 final size:28
Alignment explanation
Indices: 3874818--3874876 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 28
3874808 GGCCCAACCC
* *
3874818 ATATTAAATATATATAT-ATTTAATAT-
1 ATATAAAATATATATATGATTTAAAATA
*
3874844 ATATAAAATATATATTTGATTTAAAATA
1 ATATAAAATATATATATGATTTAAAATA
3874872 ATATA
1 ATATA
3874877 TATTTGATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 15 0.54
27 8 0.29
28 5 0.18
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
ATATAAAATATATATATGATTTAAAATA
Found at i:3874868 original size:18 final size:18
Alignment explanation
Indices: 3874847--3874897 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 18
3874837 TTAATATATA
3874847 TAAAATATATATTTGATT
1 TAAAATATATATTTGATT
3874865 TAAAATAATATATATTTGATT
1 T--AA-AATATATATTTGATT
* *
3874886 AAAAATAAATAT
1 TAAAATATATAT
3874898 ATATATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 9 0.32
19 2 0.07
20 2 0.07
21 15 0.54
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (18 bp):
TAAAATATATATTTGATT
Found at i:3877451 original size:2 final size:2
Alignment explanation
Indices: 3877444--3877487 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3877434 ACATGCCATT
3877444 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3877486 TC
1 TC
3877488 ACACACACTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3877492 original size:2 final size:2
Alignment explanation
Indices: 3877487--3877538 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
3877477 CTCTCTCTCT
* * *
3877487 CA CA CA CA CT CT CT CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3877529 CA CA CA CA CA
1 CA CA CA CA CA
3877539 TCCCCTTCCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (2 bp):
CA
Found at i:3877498 original size:16 final size:16
Alignment explanation
Indices: 3877479--3877527 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
3877469 CTCTCTCTCT
*
3877479 CTCTCTCTCACACACA
1 CTCTCTCACACACACA
3877495 CTCTCTCACACACACA
1 CTCTCTCACACACACA
* * *
3877511 CACACACACACACACA
1 CTCTCTCACACACACA
3877527 C
1 C
3877528 ACACACACAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.35, C:0.51, G:0.00, T:0.14
Consensus pattern (16 bp):
CTCTCTCACACACACA
Found at i:3877498 original size:18 final size:18
Alignment explanation
Indices: 3877477--3877531 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
3877467 CTCTCTCTCT
* *
3877477 CTCTCTCTCTCACACACA
1 CTCTCTCACACACACACA
3877495 CTCTCTCACACACACACA
1 CTCTCTCACACACACACA
* * *
3877513 CACACACACACACACACA
1 CTCTCTCACACACACACA
3877531 C
1 C
3877532 ACACACATCC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.35, C:0.51, G:0.00, T:0.15
Consensus pattern (18 bp):
CTCTCTCACACACACACA
Found at i:3884643 original size:31 final size:31
Alignment explanation
Indices: 3884602--3884662 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
3884592 GAAATGATTA
* *
3884602 CTAAATTATTCACAAGTTTTCATTTAAGTCG
1 CTAAACTATTCAAAAGTTTTCATTTAAGTCG
*
3884633 CTAAACTATTCAAAAGTTTTTATTTAAGTC
1 CTAAACTATTCAAAAGTTTTCATTTAAGTC
3884663 ATTGAGCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (31 bp):
CTAAACTATTCAAAAGTTTTCATTTAAGTCG
Found at i:3889972 original size:9 final size:9
Alignment explanation
Indices: 3889952--3890000 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
3889942 TGTATGATTC
*
3889952 AATTAGGTT
1 AATTCGGTT
*
3889961 AATTCGGGT
1 AATTCGGTT
3889970 AATTCGGTT
1 AATTCGGTT
*
3889979 AATTTGGTT
1 AATTCGGTT
*
3889988 AATTCGGCT
1 AATTCGGTT
3889997 AATT
1 AATT
3890001 TTTAACCAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:3891986 original size:25 final size:26
Alignment explanation
Indices: 3891939--3891988 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
3891929 AACCCGGCCC
* * *
3891939 ATTTTTAAAATAAACATTAAAAAAGT
1 ATTTTAAAAATAAAAAATAAAAAAGT
3891965 ATTTTAAAAATAAAAAATAAAAAA
1 ATTTTAAAAATAAAAAATAAAAAA
3891989 ATTTATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (26 bp):
ATTTTAAAAATAAAAAATAAAAAAGT
Found at i:3891997 original size:28 final size:26
Alignment explanation
Indices: 3891939--3892001 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
3891929 AACCCGGCCC
* * *
3891939 ATTTTTAAAATAAACATTAAAAAAGT
1 ATTTTAAAAATAAAAATAAAAAAAGT
*
3891965 ATTTTAAAAATAAAAAATAAAAAAATTT
1 ATTTTAAAAAT-AAAAATAAAAAAA-GT
3891993 ATTTTAAAA
1 ATTTTAAAA
3892002 GTATTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 10 0.32
27 11 0.35
28 10 0.32
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (26 bp):
ATTTTAAAAATAAAAATAAAAAAAGT
Found at i:3900661 original size:15 final size:15
Alignment explanation
Indices: 3900641--3900671 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3900631 ATTTAGAATC
3900641 TAAGCCCACGTATAG
1 TAAGCCCACGTATAG
3900656 TAAGCCCACGTATAG
1 TAAGCCCACGTATAG
3900671 T
1 T
3900672 TTGGAACTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (15 bp):
TAAGCCCACGTATAG
Found at i:3907243 original size:24 final size:24
Alignment explanation
Indices: 3907193--3907244 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
3907183 AATTAAAGTC
* **
3907193 AAATATATTATGCCAATAAATGTT
1 AAATATATTATACCAATAAATACT
3907217 AAATATATTATACTC-ATAAATACT
1 AAATATATTATAC-CAATAAATACT
3907241 AAAT
1 AAAT
3907245 CTTCTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACCAATAAATACT
Found at i:3909053 original size:14 final size:14
Alignment explanation
Indices: 3909030--3909063 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
3909020 TGGTATGAGT
3909030 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
3909043 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
3909057 TTATAGG
1 TTATAGG
3909064 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:3921054 original size:2 final size:2
Alignment explanation
Indices: 3921047--3921093 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
3921037 GGAAGGGATT
3921047 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3921089 TA TA T
1 TA TA T
3921094 NNNNNNNNNN
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3921787 original size:13 final size:13
Alignment explanation
Indices: 3921769--3921794 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3921759 AAGAGTACAA
3921769 AATTAAATTAAAT
1 AATTAAATTAAAT
3921782 AATTAAATTAAAT
1 AATTAAATTAAAT
3921795 TATGTTAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATTAAATTAAAT
Found at i:3923975 original size:19 final size:18
Alignment explanation
Indices: 3923944--3923988 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
3923934 TTATTTTGGT
3923944 GATT-TTTTTTAAACATA
1 GATTATTTTTTAAACATA
*
3923961 GATTATTTTTATAAATATA
1 GATTATTTTT-TAAACATA
3923980 -A-TATTTTTT
1 GATTATTTTTT
3923989 TAGACTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.04
17 11 0.44
18 6 0.24
19 7 0.28
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (18 bp):
GATTATTTTTTAAACATA
Found at i:3923989 original size:19 final size:20
Alignment explanation
Indices: 3923945--3923990 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
3923935 TATTTTGGTG
3923945 ATTTTTTT-TAAACATAGAT
1 ATTTTTTTATAAACATAGAT
* *
3923964 -TATTTTTATAAATATA-AT
1 ATTTTTTTATAAACATAGAT
3923982 ATTTTTTTA
1 ATTTTTTTA
3923991 GACTATTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
ATTTTTTTATAAACATAGAT
Found at i:3925109 original size:17 final size:17
Alignment explanation
Indices: 3925087--3925120 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3925077 ACTTGGATTA
3925087 AATTGATTTAATTAAAT
1 AATTGATTTAATTAAAT
*
3925104 AATTGATTTTATTAAAT
1 AATTGATTTAATTAAAT
3925121 CTGTTGGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
AATTGATTTAATTAAAT
Found at i:3926040 original size:21 final size:21
Alignment explanation
Indices: 3926014--3926055 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3926004 TTAGAAACTC
3926014 GATTAAGCATGACGTTGACTT
1 GATTAAGCATGACGTTGACTT
*
3926035 GATTAAGCATGAGGTTGACTT
1 GATTAAGCATGACGTTGACTT
3926056 ACTAATGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (21 bp):
GATTAAGCATGACGTTGACTT
Found at i:3926823 original size:21 final size:20
Alignment explanation
Indices: 3926776--3926823 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
3926766 GCCCAGCTTG
*
3926776 GATACC-TTAACAAAATATT
1 GATACCTTTAACAAAATATC
* *
3926795 GGTACCTTTCACAAAAGTATC
1 GATACCTTTAACAAAA-TATC
3926816 GATACCTT
1 GATACCTT
3926824 GCCTAGTAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 5 0.22
20 8 0.35
21 10 0.43
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (20 bp):
GATACCTTTAACAAAATATC
Found at i:3929240 original size:2 final size:2
Alignment explanation
Indices: 3929233--3929276 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3929223 AAACCAACAA
3929233 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3929275 TC
1 TC
3929277 CCATTATTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3929984 original size:3 final size:3
Alignment explanation
Indices: 3929976--3930004 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3929966 ACTAGATGGG
3929976 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
3930005 AAGTGAGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:3933078 original size:15 final size:16
Alignment explanation
Indices: 3933058--3933089 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3933048 TGTAATTATA
3933058 TTTTTCTT-TTAATTT
1 TTTTTCTTATTAATTT
3933073 TTTTTCTTATTAATTT
1 TTTTTCTTATTAATTT
3933089 T
1 T
3933090 GTATAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTCTTATTAATTT
Found at i:3934177 original size:5 final size:5
Alignment explanation
Indices: 3934167--3934196 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
3934157 ATTTCTAGTT
3934167 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
3934197 TAATTTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:3935814 original size:83 final size:83
Alignment explanation
Indices: 3935675--3935838 Score: 267
Period size: 83 Copynumber: 2.0 Consensus size: 83
3935665 GCTTCGCTCT
*
3935675 TGTGTATGCTATGTTTTATCATGAATTTTGACATTCCATTGGAAATGATTATGTGAACACTT-TG
1 TGTGTATGCTATGTTTTATCATGAATTTTGAAATTCCATTGGAAATGATTATGTGAACA-TTCTG
*
3935739 GGGATTTAAATAGATCCCC
65 CGGATTTAAATAGATCCCC
* *
3935758 TGTGTATGTTATGTTTTATCATGAATTTTGAAATTTCATTGGAAATGATTATGTGAACATTCTGC
1 TGTGTATGCTATGTTTTATCATGAATTTTGAAATTCCATTGGAAATGATTATGTGAACATTCTGC
*
3935823 GGCTTTAAATAGATCC
66 GGATTTAAATAGATCC
3935839 ATTAATTTGT
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
82 2 0.03
83 73 0.97
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (83 bp):
TGTGTATGCTATGTTTTATCATGAATTTTGAAATTCCATTGGAAATGATTATGTGAACATTCTGC
GGATTTAAATAGATCCCC
Found at i:3941439 original size:89 final size:89
Alignment explanation
Indices: 3941259--3941427 Score: 275
Period size: 89 Copynumber: 1.9 Consensus size: 89
3941249 AGCACCGAAC
* * *
3941259 TGAATAAGTAATTCGTAAAACTAACTCGACTCACTATTAAACATGGTTTGCATAGATGGTACTCG
1 TGAATAAGTAATTCGTAAAACTAACTCAACTCACGATTAAACATGGTTTACATAGATGGTACTCG
3941324 AACATAGGTATATAAGCTCTGAAT
66 AACATAGGTATATAAGCTCTGAAT
* * *
3941348 TGAATAATTAATTCGTAAAACTAATTCAACTCACGATTAATCATGGTTTACATAGATGGTACTCG
1 TGAATAAGTAATTCGTAAAACTAACTCAACTCACGATTAAACATGGTTTACATAGATGGTACTCG
*
3941413 AACGTAGGTATATAA
66 AACATAGGTATATAA
3941428 CTTGATAATT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
89 73 1.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (89 bp):
TGAATAAGTAATTCGTAAAACTAACTCAACTCACGATTAAACATGGTTTACATAGATGGTACTCG
AACATAGGTATATAAGCTCTGAAT
Found at i:3943691 original size:147 final size:147
Alignment explanation
Indices: 3943406--3943694 Score: 551
Period size: 148 Copynumber: 2.0 Consensus size: 147
3943396 AAAGCAGCTC
3943406 TTTAATTCTAGAACTGCAACAAATTATGATTAAATTACTGAAAACAAGGCAAACCCAAATAAAAA
1 TTTAATTCTAGAACTGCAACAAATTATGATTAAATTACTGAAAACAAGGCAAACCCAAATAAAAA
*
3943471 ATTCTCAAAAAATTAAACTTCCCCATTCTAAATCATTTAGTCTTCCAATAAAATCCCAAACAATC
66 ATTCTCAAAAAATTAAACTTCCCAATTCTAAATCATTTAGTCTTCCAATAAAATCCCAAACAATC
3943536 ATTAAAAAAAAGGGTAG
131 ATTAAAAAAAAGGGTAG
*
3943553 TTTAATTCTAGAACTGCAACAAATTATGATTAAATTACTGAAAACAAGTCAAACCCAAATAAAAA
1 TTTAATTCTAGAACTGCAACAAATTATGATTAAATTACTGAAAACAAGGCAAACCCAAAT-AAAA
3943618 AATTCTCAAAAAATTAAACTTCCCAATTCTAAATCATTTAGTCTTCCAATAAAATCCCAAACAAT
65 AATTCTCAAAAAATTAAACTTCCCAATTCTAAATCATTTAGTCTTCCAATAAAATCCCAAACAAT
3943683 CATTAAAAAAAA
130 CATTAAAAAAAA
3943695 AAAAGGTAGT
Statistics
Matches: 139, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
147 59 0.42
148 80 0.58
ACGTcount: A:0.49, C:0.18, G:0.06, T:0.27
Consensus pattern (147 bp):
TTTAATTCTAGAACTGCAACAAATTATGATTAAATTACTGAAAACAAGGCAAACCCAAATAAAAA
ATTCTCAAAAAATTAAACTTCCCAATTCTAAATCATTTAGTCTTCCAATAAAATCCCAAACAATC
ATTAAAAAAAAGGGTAG
Found at i:3943725 original size:148 final size:146
Alignment explanation
Indices: 3943422--3943725 Score: 461
Period size: 148 Copynumber: 2.1 Consensus size: 146
3943412 TCTAGAACTG
3943422 CAACAAATTATGATTAAATTACTGAAAACAAGGCAAACCCAAATAAAAAATTCTCAAAAAATTAA
1 CAACAAATTATGATTAAATTACTGAAAACAAGGCAAACCCAAATAAAAAATTCTCAAAAAATTAA
* *
3943487 ACTTCCCCATTCTAAATCATTTAGTCTTCCAATAAAATCCCAAACAATCATTAAAAAAAAGGGTA
66 ACTTCCCAATTCTAAATCATTTAGTCTTCCAATAAAATCCCAAACAATCATTAAAAAAAAAGGTA
* * * * *
3943552 GTTTAATTCTAGAACTG
131 G-TTAAATCAAAAAATC
*
3943569 CAACAAATTATGATTAAATTACTGAAAACAAGTCAAACCCAAATAAAAAAATTCTCAAAAAATTA
1 CAACAAATTATGATTAAATTACTGAAAACAAGGCAAACCCAAAT-AAAAAATTCTCAAAAAATTA
3943634 AACTTCCCAATTCTAAATCATTTAGTCTTCCAATAAAATCCCAAACAATCATTAAAAAAAAAAAA
65 AACTTCCCAATTCTAAATCATTTAGTCTTCCAATAAAATCCCAAACAATCATT---AAAAAAAAA
3943699 GGTAG-TAAAT-AAAAATATC
127 GGTAGTTAAATCAAAAA-ATC
3943718 CAA-AAATT
1 CAACAAATT
3943726 TTCAGGTGGG
Statistics
Matches: 144, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
147 43 0.30
148 80 0.56
149 8 0.06
151 13 0.09
ACGTcount: A:0.51, C:0.17, G:0.06, T:0.26
Consensus pattern (146 bp):
CAACAAATTATGATTAAATTACTGAAAACAAGGCAAACCCAAATAAAAAATTCTCAAAAAATTAA
ACTTCCCAATTCTAAATCATTTAGTCTTCCAATAAAATCCCAAACAATCATTAAAAAAAAAGGTA
GTTAAATCAAAAAATC
Found at i:3943764 original size:148 final size:145
Alignment explanation
Indices: 3943462--3943758 Score: 311
Period size: 148 Copynumber: 2.0 Consensus size: 145
3943452 AGGCAAACCC
*
3943462 AAAT-AAAAAATTCTCAAAAAATTAAACTTCCCCATTCTAAATCATTTAGTCTTCCAATAAAATC
1 AAATAAAAAAATTCTCAAAAAATTAAACTTCCCAATTCTAAATCATTTAGTCTTCCAATAAAATC
* * * * * * * *
3943526 CCAAACAATCATTAAAAAAAAGGGTAGTTTAATTCTAGAACTGCAACAAATTATGATTAAATTAC
66 CCAAACAATCATTAAAAAAAAAGGTAG-TTAAATCAAAAAATCCAACAAATTAT-ATCAAATGAC
* * ***
3943591 TGAAAACAAGTCAAACCC
129 CGAAAACAAG-AAAAAAA
3943609 AAATAAAAAAATTCTCAAAAAATTAAACTTCCCAATTCTAAATCATTTAGTCTTCCAATAAAATC
1 AAATAAAAAAATTCTCAAAAAATTAAACTTCCCAATTCTAAATCATTTAGTCTTCCAATAAAATC
**
3943674 CCAAACAATCATTAAAAAAAAAAAAGGTAG-TAAAT-AAAAATATCCAA-AAATT-T-TCAGGTG
66 CCAAACAATCATT---AAAAAAAAAGGTAGTTAAATCAAAAA-ATCCAACAAATTATATCAAAT-
3943734 GGACCCGAAAACAA-AAAAAAA
126 -GA-CCGAAAACAAGAAAAAAA
3943755 AAAT
1 AAAT
3943759 CTAAAACAAT
Statistics
Matches: 126, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
145 3 0.02
146 7 0.06
147 6 0.05
148 89 0.71
149 8 0.06
151 13 0.10
ACGTcount: A:0.52, C:0.17, G:0.07, T:0.25
Consensus pattern (145 bp):
AAATAAAAAAATTCTCAAAAAATTAAACTTCCCAATTCTAAATCATTTAGTCTTCCAATAAAATC
CCAAACAATCATTAAAAAAAAAGGTAGTTAAATCAAAAAATCCAACAAATTATATCAAATGACCG
AAAACAAGAAAAAAA
Found at i:3945872 original size:3 final size:3
Alignment explanation
Indices: 3945864--3945890 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3945854 GTTGATCCTT
3945864 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
3945891 GTCTTCGCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:3955223 original size:20 final size:20
Alignment explanation
Indices: 3955198--3955237 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3955188 TTAAAAACCA
3955198 GCCTTCTACAGCCACTGGTT
1 GCCTTCTACAGCCACTGGTT
* *
3955218 GCCTTCTACGGCCGCTGGTT
1 GCCTTCTACAGCCACTGGTT
3955238 ATGTGGGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.10, C:0.35, G:0.25, T:0.30
Consensus pattern (20 bp):
GCCTTCTACAGCCACTGGTT
Found at i:3961926 original size:16 final size:16
Alignment explanation
Indices: 3961887--3961928 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
3961877 TGATTGTACT
3961887 ATATTTTTCTATTTCTA
1 ATATTTTT-TATTTCTA
3961904 ATA-TTTTTATTT-TA
1 ATATTTTTTATTTCTA
3961918 ATAATTTTTTA
1 AT-ATTTTTTA
3961929 ATAATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 4 0.17
15 6 0.26
16 10 0.43
17 3 0.13
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (16 bp):
ATATTTTTTATTTCTA
Found at i:3961942 original size:12 final size:12
Alignment explanation
Indices: 3961909--3961942 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
3961899 TTCTAATATT
3961909 TTTATTTTAATAA
1 TTTA-TTTAATAA
3961922 TTT-TTTAATAA
1 TTTATTTAATAA
3961933 TTTATTTAAT
1 TTTATTTAAT
3961943 CAAACTGGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.55
12 6 0.30
13 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTATTTAATAA
Found at i:3961986 original size:17 final size:18
Alignment explanation
Indices: 3961953--3961987 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3961943 CAAACTGGAC
3961953 CAACTACTCGAACCAATT
1 CAACTACTCGAACCAATT
*
3961971 CAACTACT-GGACCAATT
1 CAACTACTCGAACCAATT
3961988 ATAAAAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.37, C:0.31, G:0.09, T:0.23
Consensus pattern (18 bp):
CAACTACTCGAACCAATT
Found at i:3966327 original size:14 final size:11
Alignment explanation
Indices: 3966297--3966326 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3966287 ATATACAAAC
3966297 AATAATAACAA
1 AATAATAACAA
3966308 AATAATAACAA
1 AATAATAACAA
*
3966319 TATAATAA
1 AATAATAA
3966327 TGAAATTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (11 bp):
AATAATAACAA
Found at i:3968583 original size:3 final size:3
Alignment explanation
Indices: 3968575--3968602 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3968565 ACAGCCACAC
3968575 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3968603 TTCTCTCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3972442 original size:31 final size:31
Alignment explanation
Indices: 3972383--3972452 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
3972373 GAAACCTTTA
* * * * *
3972383 AAGTTTAGGCTTCAATGTGAGAATAATTGTT
1 AAGTTTAGGCTCCAATATAAGAACAATTGTC
*
3972414 AAGTTTATGCTCCAATATAAGAACAATTGTC
1 AAGTTTAGGCTCCAATATAAGAACAATTGTC
3972445 AAGTTTAG
1 AAGTTTAG
3972453 AGATAAAGTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.36
Consensus pattern (31 bp):
AAGTTTAGGCTCCAATATAAGAACAATTGTC
Found at i:3975249 original size:30 final size:31
Alignment explanation
Indices: 3975191--3975260 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
3975181 AACAATTAAA
* * *
3975191 AAAAATTTTGGATAGTTGATTGACTTAAATG
1 AAAATTTTTGAATAGTTGAATGACTTAAATG
* *
3975222 AAAATTTTTGAATAGTTTAATGA-TTAAATT
1 AAAATTTTTGAATAGTTGAATGACTTAAATG
*
3975252 ATAATTTTT
1 AAAATTTTT
3975261 TTTAGTTAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 14 0.42
31 19 0.58
ACGTcount: A:0.40, C:0.01, G:0.13, T:0.46
Consensus pattern (31 bp):
AAAATTTTTGAATAGTTGAATGACTTAAATG
Done.