Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr10
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: 21822658
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 1067834 characters in sequence are not A, C, G, or T
File 9 of 59
Found at i:3312149 original size:28 final size:29
Alignment explanation
Indices: 3312111--3312165 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
3312101 ATTTAAAAAA
*
3312111 ATTTAAGTAAATTTTTAT-TATTTATTAC
1 ATTTAAGTAAATTTGTATATATTTATTAC
*
3312139 ATTTAATTAAATTTGTATATATTTATT
1 ATTTAAGTAAATTTGTATATATTTATT
3312166 TTGATTCGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (29 bp):
ATTTAAGTAAATTTGTATATATTTATTAC
Found at i:3312226 original size:22 final size:22
Alignment explanation
Indices: 3312157--3312229 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 22
3312147 AAATTTGTAT
* **
3312157 ATATTTATT-TTGATTCGAATA
1 ATATTTATTATTAATTAAAATA
* *
3312178 A-ATTT-TTA-TAATTAAATTG
1 ATATTTATTATTAATTAAAATA
*
3312197 ATAATTATTATTAATTAAAATA
1 ATATTTATTATTAATTAAAATA
3312219 ATATTTATTAT
1 ATATTTATTAT
3312230 GTTATGTTGA
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
19 9 0.23
20 7 0.18
21 4 0.10
22 19 0.49
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (22 bp):
ATATTTATTATTAATTAAAATA
Found at i:3320557 original size:19 final size:20
Alignment explanation
Indices: 3320535--3320576 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
3320525 TATAAAAAAA
3320535 TTAAAAAAATTAAAATTT-T
1 TTAAAAAAATTAAAATTTGT
* *
3320554 TTAAATAATTTAAAATTTGT
1 TTAAAAAAATTAAAATTTGT
3320574 TTA
1 TTA
3320577 GATATTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAAAAAAATTAAAATTTGT
Found at i:3326115 original size:29 final size:29
Alignment explanation
Indices: 3326060--3326115 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
3326050 AAAATTGATG
* * * **
3326060 AAATTAAAATATAATGATAAATTTTAATA
1 AAATTAAAATACAATAAGAAAACTTAATA
3326089 AAATTAAAATACAATAAGAAAACTTAA
1 AAATTAAAATACAATAAGAAAACTTAA
3326116 CAACGAGCCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (29 bp):
AAATTAAAATACAATAAGAAAACTTAATA
Found at i:3341355 original size:19 final size:21
Alignment explanation
Indices: 3341317--3341356 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
3341307 CCACTCATGC
*
3341317 CACATTGTACATTAAATCAAG
1 CACATTGTACAATAAATCAAG
3341338 CACATTG-ACAAT-AATCAAG
1 CACATTGTACAATAAATCAAG
3341357 TTTTCTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.25
Consensus pattern (21 bp):
CACATTGTACAATAAATCAAG
Found at i:3341476 original size:2 final size:2
Alignment explanation
Indices: 3341469--3341495 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3341459 AATATTATGC
3341469 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
3341496 CAAGCATGTA
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:3341479 original size:37 final size:39
Alignment explanation
Indices: 3341404--3341483 Score: 121
Period size: 37 Copynumber: 2.1 Consensus size: 39
3341394 TAACCTTTTC
3341404 TATAACATATAAAAAACATATTTATGGCATATATATATA
1 TATAACATATAAAAAACATATTTATGGCATATATATATA
*
3341443 TNATAACATATAAAACA-ATA-TTAT-GCATATATATATA
1 T-ATAACATATAAAAAACATATTTATGGCATATATATATA
3341480 TATA
1 TATA
3341484 TATATATATA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
36 3 0.08
37 14 0.36
38 4 0.10
39 4 0.10
40 14 0.36
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.36
Consensus pattern (39 bp):
TATAACATATAAAAAACATATTTATGGCATATATATATA
Found at i:3341493 original size:39 final size:38
Alignment explanation
Indices: 3341410--3341493 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 38
3341400 TTTCTATAAC
* *
3341410 ATATAAAAAACATATTTATGGCATATATATATATNATA
1 ATATATAAAACATATTTATGGCATATATATATATTATA
*
3341448 ACATATAAAACA-ATATTAT-GCATATATATATATATATA
1 ATATATAAAACATAT-TTATGGCATATATATATAT-TATA
3341486 TATATATA
1 -ATATATA
3341494 TACAAGCATG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
37 16 0.41
38 17 0.44
39 6 0.15
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.38
Consensus pattern (38 bp):
ATATATAAAACATATTTATGGCATATATATATATTATA
Found at i:3341603 original size:37 final size:37
Alignment explanation
Indices: 3341561--3341694 Score: 110
Period size: 37 Copynumber: 3.4 Consensus size: 37
3341551 TCGTGTGCAC
*
3341561 CCCCACATCGCGCACAACTAATGCCATCATGTGCTCT
1 CCCCACATCACGCACAACTAATGCCATCATGTGCTCT
* *
3341598 CCCCACATCACGCACACGGCATATAT-CATCATCATCTTGTGCAC-
1 CCCCACATCACGCACA--AC-TA-ATGC--CATCA---TGTGCTCT
* * *
3341642 CCCTACATCACGCACAACTAATGTCATAATGTGCTCT
1 CCCCACATCACGCACAACTAATGCCATCATGTGCTCT
*
3341679 CCCCACATCGCGCACA
1 CCCCACATCACGCACA
3341695 TGGCGTATAT
Statistics
Matches: 76, Mismatches: 10, Indels: 22
0.70 0.09 0.20
Matches are distributed among these distances:
36 6 0.08
37 29 0.38
39 5 0.07
40 5 0.07
41 4 0.05
42 6 0.08
44 15 0.20
45 6 0.08
ACGTcount: A:0.27, C:0.40, G:0.12, T:0.22
Consensus pattern (37 bp):
CCCCACATCACGCACAACTAATGCCATCATGTGCTCT
Found at i:3341662 original size:81 final size:82
Alignment explanation
Indices: 3341546--3341769 Score: 319
Period size: 81 Copynumber: 2.7 Consensus size: 82
3341536 ACATAGCCGG
*
3341546 AGTCATCGTGTGCACCCCCACATCGCGCACAACTAATGCCATCATGTGCTCTCCCCACATCACGC
1 AGTCATCTTGTGCACCCCCACATCGCGCACAACTAATGCCATCATGTGCTCTCCCCACATCACGC
3341611 ACACGGCATATATCATC
66 ACACGGCATATATCATC
* * * * *
3341628 A-TCATCTTGTGCACCCCTACATCACGCACAACTAATGTCATAATGTGCTCTCCCCACATCGCGC
1 AGTCATCTTGTGCACCCCCACATCGCGCACAACTAATGCCATCATGTGCTCTCCCCACATCACGC
* *
3341692 ACATGGCGTATATCATC
66 ACACGGCATATATCATC
* *
3341709 AGT-AT-TGTGTGCACCCCCATATCGCGCACAACTAATGCCATCATGTGCTCCCCCCCACATC
1 AGTCATCT-TGTGCACCCCCACATCGCGCACAACTAATGCCATCATGTGCT-CTCCCCACATC
3341770 GCACACATAG
Statistics
Matches: 125, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
80 1 0.01
81 112 0.90
82 12 0.10
ACGTcount: A:0.25, C:0.38, G:0.14, T:0.23
Consensus pattern (82 bp):
AGTCATCTTGTGCACCCCCACATCGCGCACAACTAATGCCATCATGTGCTCTCCCCACATCACGC
ACACGGCATATATCATC
Found at i:3346712 original size:29 final size:29
Alignment explanation
Indices: 3346679--3346734 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
3346669 ATTTAAAAAC
3346679 ATTCAAATAAGTCCTTAT-TGTTTTATTAT
1 ATTCAAATAAGTCCTTATAT-TTTTATTAT
* *
3346708 ATTCAATTAAGTTCTTATATTTTTATT
1 ATTCAAATAAGTCCTTATATTTTTATT
3346735 TTTGACAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.55
Consensus pattern (29 bp):
ATTCAAATAAGTCCTTATATTTTTATTAT
Found at i:3349387 original size:2 final size:2
Alignment explanation
Indices: 3349380--3349407 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3349370 AAACCCCAAA
3349380 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3349408 TGTATCTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3357360 original size:15 final size:15
Alignment explanation
Indices: 3357342--3357394 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
3357332 CACAAATGCT
*
3357342 AAGGAAACGAATGGC
1 AAGGAAACGAATGAC
*
3357357 AAGGACACGAATGAC
1 AAGGAAACGAATGAC
*
3357372 AAGGACACGAATGAC
1 AAGGAAACGAATGAC
3357387 AAGGAAAC
1 AAGGAAAC
3357395 AAACAGCATC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.49, C:0.17, G:0.28, T:0.06
Consensus pattern (15 bp):
AAGGAAACGAATGAC
Found at i:3359343 original size:19 final size:20
Alignment explanation
Indices: 3359299--3359338 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3359289 TATTATTATG
* *
3359299 AAAATATTTATTTTTAAAAT
1 AAAATATGTATTTTAAAAAT
3359319 AAAATATGTATTTTAAAAAT
1 AAAATATGTATTTTAAAAAT
3359339 TAATAAAATA
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:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
AAAATATGTATTTTAAAAAT
Found at i:3374164 original size:29 final size:27
Alignment explanation
Indices: 3374130--3374200 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 27
3374120 CATTCAACGT
* *
3374130 AATAAAAGAATAAGCACTTGATTGAGGGT
1 AATAAAAGAATAAG--CTTGATTGAGAGA
* *
3374159 ATTAAAGGAATATAGCTTGATTGAGAGA
1 AATAAAAGAATA-AGCTTGATTGAGAGA
3374187 AATAAAAGAATAAG
1 AATAAAAGAATAAG
3374201 AAATTATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
27 2 0.06
28 21 0.60
29 10 0.29
30 2 0.06
ACGTcount: A:0.49, C:0.04, G:0.23, T:0.24
Consensus pattern (27 bp):
AATAAAAGAATAAGCTTGATTGAGAGA
Found at i:3377730 original size:53 final size:52
Alignment explanation
Indices: 3377654--3377761 Score: 146
Period size: 53 Copynumber: 2.1 Consensus size: 52
3377644 AATTTTGATA
* *
3377654 TTTTATGAAATATTTTAACGGTTAAAATTTGAGATTTTATTT-AAGTTTGACAT
1 TTTTATGAAATATTGTAACGGTTAAAATTTGAAATTTTATTTCAA-TTTGA-AT
* * *
3377707 TTTTATGTAATATTGTCATGGTTAAAATTTGAAATTTTATTTCAATTTGAAT
1 TTTTATGAAATATTGTAACGGTTAAAATTTGAAATTTTATTTCAATTTGAAT
3377759 TTT
1 TTT
3377762 AAGAGTCCTA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
52 5 0.10
53 42 0.86
54 2 0.04
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.52
Consensus pattern (52 bp):
TTTTATGAAATATTGTAACGGTTAAAATTTGAAATTTTATTTCAATTTGAAT
Found at i:3389952 original size:38 final size:36
Alignment explanation
Indices: 3389902--3389981 Score: 117
Period size: 38 Copynumber: 2.2 Consensus size: 36
3389892 TACTGAGAGG
3389902 ATAAAAAAAATCACAAGCTATGAGATGATAAT-GAGA
1 ATAAAAAAAATCACAAGCTATGAGATGATAATAG-GA
*
3389938 ATAAAAAGATAATCACAAGCTGTGAGATGATAATAGGA
1 ATAAAAA-A-AATCACAAGCTATGAGATGATAATAGGA
3389976 ATAAAA
1 ATAAAA
3389982 TGACAACCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
36 7 0.17
37 1 0.03
38 31 0.77
39 1 0.03
ACGTcount: A:0.55, C:0.07, G:0.17, T:0.20
Consensus pattern (36 bp):
ATAAAAAAAATCACAAGCTATGAGATGATAATAGGA
Found at i:3395707 original size:12 final size:11
Alignment explanation
Indices: 3395673--3395706 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3395663 TTTTCTTAAG
3395673 TTATATAAAAA
1 TTATATAAAAA
*
3395684 TTATACTCAAAA
1 TTATA-TAAAAA
3395696 TTATATAAAAA
1 TTATATAAAAA
3395707 AATCCTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (11 bp):
TTATATAAAAA
Found at i:3398306 original size:2 final size:2
Alignment explanation
Indices: 3398301--3398337 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
3398291 CAAGTACACA
3398301 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3398338 ATTTTAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3405797 original size:29 final size:29
Alignment explanation
Indices: 3405755--3405812 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
3405745 TATTATAGGT
*
3405755 TATTCAATTATTGGAATTAATAATATTTG
1 TATTCAATTATTGGAATCAATAATATTTG
*
3405784 TATTCAATTATTGGAATCAATAATGTTTG
1 TATTCAATTATTGGAATCAATAATATTTG
3405813 AACCACTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (29 bp):
TATTCAATTATTGGAATCAATAATATTTG
Found at i:3411708 original size:18 final size:18
Alignment explanation
Indices: 3411687--3411721 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3411677 TTATTTTTAA
3411687 TTATAT-TTTTTCAAATTT
1 TTATATATTTTT-AAATTT
3411705 TTATATATTTTTAAATT
1 TTATATATTTTTAAATT
3411722 AAATACTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATATATTTTTAAATTT
Found at i:3411885 original size:2 final size:2
Alignment explanation
Indices: 3411878--3411929 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
3411868 TGTTTTCACA
3411878 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
3411920 AT AT AT AT AT
1 AT AT AT AT AT
3411930 CAAGTAGATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3420621 original size:21 final size:21
Alignment explanation
Indices: 3420597--3420636 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3420587 TATAAATTAC
*
3420597 AATTAACTCTCGATTACGATG
1 AATTAACTCTCAATTACGATG
* *
3420618 AATTTATTCTCAATTACGA
1 AATTAACTCTCAATTACGA
3420637 AAGAAAATCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (21 bp):
AATTAACTCTCAATTACGATG
Found at i:3425409 original size:16 final size:16
Alignment explanation
Indices: 3425389--3425426 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3425379 GTTAATTTTT
3425389 TTTAAAA-AAAATTGA
1 TTTAAAATAAAATTGA
*
3425404 TATTAAAATAAATTTGA
1 T-TTAAAATAAAATTGA
3425421 TTTAAA
1 TTTAAA
3425427 CTCGATTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 11 0.55
17 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (16 bp):
TTTAAAATAAAATTGA
Found at i:3432089 original size:21 final size:21
Alignment explanation
Indices: 3432063--3432107 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
3432053 TGGACCAATT
3432063 ATTC-AAAAGAGAAAAAGAGGG
1 ATTCAAAAAGAG-AAAAGAGGG
*
3432084 ATTCAAAAAGAGAAAAGTGGG
1 ATTCAAAAAGAGAAAAGAGGG
3432105 ATT
1 ATT
3432108 TAAATTATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.53, C:0.04, G:0.27, T:0.16
Consensus pattern (21 bp):
ATTCAAAAAGAGAAAAGAGGG
Found at i:3442096 original size:20 final size:20
Alignment explanation
Indices: 3442069--3442113 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
3442059 AATAATGATT
3442069 TTTA-ATATTAAATT-TTTA
1 TTTATATATTAAATTATTTA
*
3442087 TTATATATATTATATTATTTA
1 TT-TATATATTAAATTATTTA
3442108 TTTATA
1 TTTATA
3442114 AATTTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 2 0.09
19 2 0.09
20 13 0.57
21 6 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATATATTAAATTATTTA
Found at i:3445140 original size:84 final size:84
Alignment explanation
Indices: 3444982--3445140 Score: 189
Period size: 84 Copynumber: 1.9 Consensus size: 84
3444972 GCTCCAATTC
* * * *
3444982 TTCATTTTTTTAATGGTAATTTCTTGGTAATTGATCTGTTAGTTATAGTTATATAGGGATTATTG
1 TTCATTTTTTTAATGCTAATCTCTTGATAATTGATCTGTTAGTTATAGTTATATAGGGATAATTG
* **
3445047 TGGTGAAATATAATAATGA
66 TCGACAAATATAATAATGA
* *
3445066 TTCATTTTTTTACTGCTAATCTCTTGATGATTGAT-TCGTTAGTTATAGTTA-ATA-GGATAATT
1 TTCATTTTTTTAATGCTAATCTCTTGATAATTGATCT-GTTAGTTATAGTTATATAGGGATAATT
3445128 GTTACGACAAATA
65 G-T-CGACAAATA
3445141 GATGAGATGG
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
82 8 0.13
83 5 0.08
84 50 0.79
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.47
Consensus pattern (84 bp):
TTCATTTTTTTAATGCTAATCTCTTGATAATTGATCTGTTAGTTATAGTTATATAGGGATAATTG
TCGACAAATATAATAATGA
Found at i:3464136 original size:20 final size:21
Alignment explanation
Indices: 3464091--3464137 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
3464081 GGGCTCGGTT
3464091 ATATTTTATTAATTAAAATTA
1 ATATTTTATTAATTAAAATTA
* *
3464112 A-ATTTTATTTATTTAAA-TA
1 ATATTTTATTAATTAAAATTA
3464131 ATATTTT
1 ATATTTT
3464138 TTAGATATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 3 0.13
20 19 0.83
21 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTTTATTAATTAAAATTA
Found at i:3469430 original size:14 final size:14
Alignment explanation
Indices: 3469411--3469459 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 14
3469401 TTTGAGAGTA
3469411 AAAATAATATTTAT
1 AAAATAATATTTAT
3469425 AAAATAATCATATTA-
1 AAAATAAT-AT-TTAT
3469440 AAAATTTAATATTTAT
1 AAAA--TAATATTTAT
3469456 AAAA
1 AAAA
3469460 ATAAAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
14 8 0.27
15 9 0.30
16 9 0.30
17 4 0.13
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
AAAATAATATTTAT
Found at i:3472946 original size:7 final size:7
Alignment explanation
Indices: 3472936--3472986 Score: 66
Period size: 7 Copynumber: 7.1 Consensus size: 7
3472926 TATCAGAGGT
3472936 AAAAATA
1 AAAAATA
3472943 AAAAATA
1 AAAAATA
3472950 AAAAATA
1 AAAAATA
*
3472957 AAAAAGA
1 AAAAATA
*
3472964 AAAAAGA
1 AAAAATA
*
3472971 AAAAAGA
1 AAAAATA
3472978 AAAATATA
1 AAAA-ATA
3472986 A
1 A
3472987 TTAAAAGACA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
7 38 0.93
8 3 0.07
ACGTcount: A:0.84, C:0.00, G:0.06, T:0.10
Consensus pattern (7 bp):
AAAAATA
Found at i:3472955 original size:14 final size:14
Alignment explanation
Indices: 3472936--3472986 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
3472926 TATCAGAGGT
*
3472936 AAAAATAAAAAATA
1 AAAAATAAAAAAGA
3472950 AAAAATAAAAAAGA
1 AAAAATAAAAAAGA
*
3472964 AAAAAGAAAAAAGA
1 AAAAATAAAAAAGA
3472978 AAAATATAA
1 AAAA-ATAA
3472987 TTAAAAGACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
14 30 0.91
15 3 0.09
ACGTcount: A:0.84, C:0.00, G:0.06, T:0.10
Consensus pattern (14 bp):
AAAAATAAAAAAGA
Found at i:3487950 original size:14 final size:14
Alignment explanation
Indices: 3487931--3487957 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3487921 CTTTTTCATC
3487931 ATATATATATACAT
1 ATATATATATACAT
3487945 ATATATATATACA
1 ATATATATATACA
3487958 CATCAAGCAT
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:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATATATACAT
Found at i:3489529 original size:25 final size:25
Alignment explanation
Indices: 3489482--3489531 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3489472 AAAGAAATAA
* **
3489482 AAACTTTTTATTTCTATACATAAAT
1 AAACTTTCTATTTAAATACATAAAT
*
3489507 AAACTTTCTATTTAAATATATAAAT
1 AAACTTTCTATTTAAATACATAAAT
3489532 GATAAAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (25 bp):
AAACTTTCTATTTAAATACATAAAT
Found at i:3492733 original size:21 final size:25
Alignment explanation
Indices: 3492686--3492735 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3492676 AAAGAAATAA
3492686 AAACTTTTTATTTCTATACATAAAT
1 AAACTTTTTATTTCTATACATAAAT
*
3492711 AAACTTTTTA-TTCAAATACATAAAT
1 AAACTTTTTATTTC-TATACATAAAT
3492736 GATAAAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (25 bp):
AAACTTTTTATTTCTATACATAAAT
Found at i:3502362 original size:87 final size:86
Alignment explanation
Indices: 3502261--3502428 Score: 246
Period size: 87 Copynumber: 1.9 Consensus size: 86
3502251 ATTTCTCTTA
* *
3502261 TTTGGGATAATTGTGCTTGTTTGGATTTTGTAAAATAAATTTTCATGTTTGTTGTCAATTTGGAT
1 TTTGGGATAATTGTGCTTGTTTGGAATTTGTAAAATAAATTTCCATGTTTGTTGTCAATTTGGAT
* * *
3502326 GTATTTTCCAATTTTTTCTAC
66 ATAATTTCCAAGTTTTTCTAC
* * * *
3502347 TTTGGGATAATTTGTGCTTGTTTGGAATTTGTATAATAAGTTTCCATGTTTGTTGTGAATTTGGC
1 TTTGGGATAA-TTGTGCTTGTTTGGAATTTGTAAAATAAATTTCCATGTTTGTTGTCAATTTGGA
3502412 TATAATTTCCAAGTTTT
65 TATAATTTCCAAGTTTT
3502429 ATGAATTGGA
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
86 10 0.14
87 62 0.86
ACGTcount: A:0.22, C:0.08, G:0.19, T:0.51
Consensus pattern (86 bp):
TTTGGGATAATTGTGCTTGTTTGGAATTTGTAAAATAAATTTCCATGTTTGTTGTCAATTTGGAT
ATAATTTCCAAGTTTTTCTAC
Found at i:3505991 original size:32 final size:32
Alignment explanation
Indices: 3505955--3506015 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
3505945 TTGTTTGGAT
3505955 TTTGTATAATAAATTTCCATA-TTTGTTGCCAA
1 TTTGTATAATAAATTTCCA-ACTTTGTTGCCAA
3505987 TTTGTATAATAAATTTCCAACTTTGTTGC
1 TTTGTATAATAAATTTCCAACTTTGTTGC
3506016 AAACTTAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.48
Consensus pattern (32 bp):
TTTGTATAATAAATTTCCAACTTTGTTGCCAA
Found at i:3506784 original size:21 final size:21
Alignment explanation
Indices: 3506732--3506961 Score: 120
Period size: 21 Copynumber: 10.1 Consensus size: 21
3506722 GCGACTAGTG
* *
3506732 TTTAGGCATTGCGTGACTGAC
1 TTTAGGCATTGCGTGACTAAT
*
3506753 TTT-GGATATTGCGTGACTAAT
1 TTTAGG-CATTGCGTGACTAAT
3506774 TTTAGGCATTGCGTGACTAATTT
1 TTTAGGCATTGCGTGACTAA--T
* *
3506797 TTGATAAAGCATTGCGTGACTAGTT
1 TT--T-AGGCATTGCGTGACTA-AT
*
3506822 TCTAGTAAGGCATTGCGTGACTAGT
1 T-T--T-AGGCATTGCGTGACTAAT
* ** * *
3506847 TGATAGGCATTGTATGACTGAC
1 T-TTAGGCATTGCGTGACTAAT
* *
3506869 TTTGGGCATTGCGTGACTAGTTT
1 TTTAGGCATTGCGTGACTA--AT
*
3506892 TTGATATGGCATTGCGTGACTAGCT
1 TT--TA-GGCATTGCGTGACTA-AT
** *
3506917 GATAGGCATTGCGTGACTAAC
1 TTTAGGCATTGCGTGACTAAT
* *
3506938 TTTGGGCATTGCGTGACTAGT
1 TTTAGGCATTGCGTGACTAAT
3506959 TTT
1 TTT
3506962 TGATAAGGTA
Statistics
Matches: 159, Mismatches: 36, Indels: 28
0.71 0.16 0.13
Matches are distributed among these distances:
20 2 0.01
21 63 0.40
22 31 0.19
23 8 0.05
25 7 0.04
26 48 0.30
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (21 bp):
TTTAGGCATTGCGTGACTAAT
Found at i:3506815 original size:26 final size:26
Alignment explanation
Indices: 3506777--3507154 Score: 308
Period size: 26 Copynumber: 15.6 Consensus size: 26
3506767 GACTAATTTT
*
3506777 AGGCATTGCGTGACTAATTTTTGATA
1 AGGCATTGCGTGACTAGTTTTTGATA
* *
3506803 AAGCATTGCGTGACTAGTTTCT-AGTA
1 AGGCATTGCGTGACTAGTTTTTGA-TA
3506829 AGGCATTGCGTGACTAG---TTGAT-
1 AGGCATTGCGTGACTAGTTTTTGATA
** **
3506851 AGGCATTGTATGACT-GACTTTG---
1 AGGCATTGCGTGACTAGTTTTTGATA
3506873 -GGCATTGCGTGACTAGTTTTTGATA
1 AGGCATTGCGTGACTAGTTTTTGATA
* *
3506898 TGGCATTGCGTGACTAG---CTGAT-
1 AGGCATTGCGTGACTAGTTTTTGATA
**
3506920 AGGCATTGCGTGACTA-ACTTTG---
1 AGGCATTGCGTGACTAGTTTTTGATA
3506942 -GGCATTGCGTGACTAGTTTTTGATA
1 AGGCATTGCGTGACTAGTTTTTGATA
* *
3506967 AGGTATTACGTGACTAGTTTTTGATA
1 AGGCATTGCGTGACTAGTTTTTGATA
* * * *
3506993 AGGTATTACGTGACTAGTTTCTAATA
1 AGGCATTGCGTGACTAGTTTTTGATA
**
3507019 AGGCATTGCGTGACTA-ACTTTG---
1 AGGCATTGCGTGACTAGTTTTTGATA
* *
3507041 -GGCATTACGTGATTAGTTTTTGATA
1 AGGCATTGCGTGACTAGTTTTTGATA
* *
3507066 AGGCATTGCGTGATTAGTTTCTGATA
1 AGGCATTGCGTGACTAGTTTTTGATA
* * *
3507092 AGGTATTGCGTGATTAGTTTCTGATA
1 AGGCATTGCGTGACTAGTTTTTGATA
*
3507118 AGGCATTACGTGACTAG---TTGAT-
1 AGGCATTGCGTGACTAGTTTTTGATA
3507140 AGGCATTGCGTGACT
1 AGGCATTGCGTGACT
3507155 TGTTAGTAAG
Statistics
Matches: 291, Mismatches: 38, Indels: 50
0.77 0.10 0.13
Matches are distributed among these distances:
21 41 0.14
22 55 0.19
23 10 0.03
24 6 0.02
25 3 0.01
26 176 0.60
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (26 bp):
AGGCATTGCGTGACTAGTTTTTGATA
Found at i:3506887 original size:69 final size:69
Alignment explanation
Indices: 3506805--3506985 Score: 274
Period size: 69 Copynumber: 2.6 Consensus size: 69
3506795 TTTTGATAAA
* * *
3506805 GCATTGCGTGACTAGTTTCT-AGTAAGGCATTGCGTGACTAGTTGATAGGCATTGTATGACTGAC
1 GCATTGCGTGACTAGTTTTTGA-TAAGGCATTGCGTGACTAGTTGATAGGCATTGCATGACTAAC
3506869 TTTGG
65 TTTGG
* * *
3506874 GCATTGCGTGACTAGTTTTTGATATGGCATTGCGTGACTAGCTGATAGGCATTGCGTGACTAACT
1 GCATTGCGTGACTAGTTTTTGATAAGGCATTGCGTGACTAGTTGATAGGCATTGCATGACTAACT
3506939 TTGG
66 TTGG
* *
3506943 GCATTGCGTGACTAGTTTTTGATAAGGTATTACGTGACTAGTT
1 GCATTGCGTGACTAGTTTTTGATAAGGCATTGCGTGACTAGTT
3506986 TTTGATAAGG
Statistics
Matches: 101, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
69 100 0.99
70 1 0.01
ACGTcount: A:0.22, C:0.14, G:0.28, T:0.36
Consensus pattern (69 bp):
GCATTGCGTGACTAGTTTTTGATAAGGCATTGCGTGACTAGTTGATAGGCATTGCATGACTAACT
TTGG
Found at i:3507052 original size:99 final size:97
Alignment explanation
Indices: 3506735--3507133 Score: 424
Period size: 99 Copynumber: 4.2 Consensus size: 97
3506725 ACTAGTGTTT
* ** * *
3506735 AGGCATTGCGTGACTGACTTTGGATATTGCGTGACTA--ATTT-TAGGCATTGCGTGACTAATTT
1 AGGCATTGCGTGACTAACTTTGGGCATTGCGTGACTAGTTTTTGTAGGCATTGCGTGACTAGTTT
* *
3506797 TTGATAAAGCATTGCGTGACTAGTTTCTAGTA
66 TTGATAAGGCATTGCGTGACTAGTTTCTAATA
* * ** **
3506829 AGGCATTGCGTGACT-AGTTGATAGGCATTGTATGACT-GACTTTG--GGCATTGCGTGACTAGT
1 AGGCATTGCGTGACTAACTT--TGGGCATTGCGTGACTAGTTTTTGTAGGCATTGCGTGACTAGT
* *
3506890 TTTTGATATGGCATTGCGTGACTAG---CTGAT-
64 TTTTGATAAGGCATTGCGTGACTAGTTTCTAATA
* *
3506920 AGGCATTGCGTGACTAACTTTGGGCATTGCGTGACTAGTTTTTGATAAGGTATTACGTGACTAGT
1 AGGCATTGCGTGACTAACTTTGGGCATTGCGTGACTAGTTTTTG-T-AGGCATTGCGTGACTAGT
* *
3506985 TTTTGATAAGGTATTACGTGACTAGTTTCTAATA
64 TTTTGATAAGGCATTGCGTGACTAGTTTCTAATA
* * *
3507019 AGGCATTGCGTGACTAACTTTGGGCATTACGTGATTAGTTTTTGATAAGGCATTGCGTGATTAGT
1 AGGCATTGCGTGACTAACTTTGGGCATTGCGTGACTAGTTTTTG-T-AGGCATTGCGTGACTAGT
* * * *
3507084 TTCTGATAAGGTATTGCGTGATTAGTTTCTGATA
64 TTTTGATAAGGCATTGCGTGACTAGTTTCTAATA
*
3507118 AGGCATTACGTGACTA
1 AGGCATTGCGTGACTA
3507134 GTTGATAGGC
Statistics
Matches: 256, Mismatches: 34, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
90 13 0.05
91 20 0.08
92 6 0.02
93 3 0.01
94 15 0.06
95 87 0.34
96 3 0.01
98 4 0.02
99 105 0.41
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (97 bp):
AGGCATTGCGTGACTAACTTTGGGCATTGCGTGACTAGTTTTTGTAGGCATTGCGTGACTAGTTT
TTGATAAGGCATTGCGTGACTAGTTTCTAATA
Found at i:3507169 original size:23 final size:23
Alignment explanation
Indices: 3507116--3507224 Score: 114
Period size: 23 Copynumber: 4.8 Consensus size: 23
3507106 TAGTTTCTGA
* *
3507116 TAAGGCATTACGTGACTAGTT-G
1 TAAGGCATTGCGTGACTTGTTAG
3507138 -ATAGGCATTGCGTGACTTGTTAG
1 TA-AGGCATTGCGTGACTTGTTAG
* * *
3507161 TAAGACATTGCGTGATTTGTTAA
1 TAAGGCATTGCGTGACTTGTTAG
** *
3507184 TAAGGCATTGTATGACTAGTTAG
1 TAAGGCATTGCGTGACTTGTTAG
*
3507207 TAAGGCATTGTGTGACTT
1 TAAGGCATTGCGTGACTT
3507225 AGGCATTGCT
Statistics
Matches: 71, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
21 1 0.01
22 17 0.24
23 52 0.73
24 1 0.01
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.36
Consensus pattern (23 bp):
TAAGGCATTGCGTGACTTGTTAG
Found at i:3507270 original size:22 final size:21
Alignment explanation
Indices: 3507245--3507313 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 21
3507235 TAAAAATCAG
3507245 TCACGTAATGTCTAAAAACTAA
1 TCACGTAATG-CTAAAAACTAA
*
3507267 TCACGTAATGCCT-AAAACCAA
1 TCACGTAATG-CTAAAAACTAA
* *
3507288 TCACGTAACGCTTAAAAACTAG
1 TCACGTAATGC-TAAAAACTAA
3507310 TCAC
1 TCAC
3507314 ACAGTGATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 1 0.03
21 17 0.43
22 22 0.55
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.23
Consensus pattern (21 bp):
TCACGTAATGCTAAAAACTAA
Found at i:3507289 original size:21 final size:21
Alignment explanation
Indices: 3507245--3507304 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
3507235 TAAAAATCAG
* *
3507245 TCACGTAATGTCTAAAAACTAA
1 TCACGTAATGCCT-AAAACCAA
3507267 TCACGTAATGCCTAAAACCAA
1 TCACGTAATGCCTAAAACCAA
* *
3507288 TCACGTAACGCTTAAAA
1 TCACGTAATGCCTAAAA
3507305 ACTAGTCACA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 22 0.65
22 12 0.35
ACGTcount: A:0.43, C:0.23, G:0.10, T:0.23
Consensus pattern (21 bp):
TCACGTAATGCCTAAAACCAA
Found at i:3508060 original size:2 final size:2
Alignment explanation
Indices: 3508053--3508096 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3508043 CAATTTTCTC
3508053 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
3508095 AT
1 AT
3508097 GTTTCCACTC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3513100 original size:22 final size:21
Alignment explanation
Indices: 3513051--3513100 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 21
3513041 TTTTACTTAC
3513051 TTAT-TATATATATTTTTATA
1 TTATATATATATATTTTTATA
3513071 TTGCATATATATA-ACTTTTT-TA
1 TT--ATATATATATA-TTTTTATA
3513093 TTATATAT
1 TTATATAT
3513101 TATTAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
20 8 0.31
22 7 0.27
23 11 0.42
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (21 bp):
TTATATATATATATTTTTATA
Found at i:3515164 original size:16 final size:16
Alignment explanation
Indices: 3515140--3515198 Score: 68
Period size: 16 Copynumber: 3.6 Consensus size: 16
3515130 TAAGTTCATC
3515140 TTTTT-TTTCTATATT
1 TTTTTATTTCTATATT
3515155 TTTTTATTTCCTCAT-TT
1 TTTTTATTT-CT-ATATT
*
3515172 TATTTTTTTTCTATATT
1 T-TTTTATTTCTATATT
3515189 TTTTTATTTC
1 TTTTTATTTC
3515199 CTCATTTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
15 5 0.14
16 13 0.35
17 10 0.27
18 9 0.24
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTATTTCTATATT
Found at i:3515183 original size:34 final size:34
Alignment explanation
Indices: 3515140--3515228 Score: 137
Period size: 34 Copynumber: 2.6 Consensus size: 34
3515130 TAAGTTCATC
3515140 TTTTTTTTCTATATTTTTTTATTTCCTCATTTTA
1 TTTTTTTTCTATATTTTTTTATTTCCTCATTTTA
*
3515174 TTTTTTTTCTATATTTTTTTATTTCCTCATTTTG
1 TTTTTTTTCTATATTTTTTTATTTCCTCATTTTA
3515208 TTTGTTTGTT-TAT-TTTTTTTA
1 TTT-TTT-TTCTATATTTTTTTA
3515229 GGGAGAATCA
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
34 44 0.85
35 6 0.12
36 2 0.04
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.75
Consensus pattern (34 bp):
TTTTTTTTCTATATTTTTTTATTTCCTCATTTTA
Found at i:3515205 original size:16 final size:16
Alignment explanation
Indices: 3515152--3515206 Score: 65
Period size: 17 Copynumber: 3.3 Consensus size: 16
3515142 TTTTTTCTAT
3515152 ATTTTTTTATTTCCTC
1 ATTTTTTTATTTCCTC
* * *
3515168 ATTTTATTTTTTTTCTAT
1 ATTTT-TTTATTTCCT-C
3515186 ATTTTTTTATTTCCTC
1 ATTTTTTTATTTCCTC
3515202 ATTTT
1 ATTTT
3515207 GTTTGTTTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
16 10 0.32
17 16 0.52
18 5 0.16
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.73
Consensus pattern (16 bp):
ATTTTTTTATTTCCTC
Found at i:3523043 original size:19 final size:19
Alignment explanation
Indices: 3523019--3523056 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3523009 TCATTTAACT
*
3523019 TATTGGAGTATGATTTGAG
1 TATTGGAATATGATTTGAG
3523038 TATTGGAATATGATTTGAG
1 TATTGGAATATGATTTGAG
3523057 GTTTAGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAATATGATTTGAG
Found at i:3526420 original size:18 final size:18
Alignment explanation
Indices: 3526397--3526435 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3526387 TTCACTATCA
*
3526397 TCTGTGTGAAATTGTTAT
1 TCTGTGTGAAATAGTTAT
*
3526415 TCTGTGTGAAGTAGTTAT
1 TCTGTGTGAAATAGTTAT
3526433 TCT
1 TCT
3526436 ACTTGTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.08, G:0.23, T:0.49
Consensus pattern (18 bp):
TCTGTGTGAAATAGTTAT
Found at i:3529625 original size:18 final size:16
Alignment explanation
Indices: 3529595--3529629 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
3529585 TTCTTATTTT
3529595 TATATACACAATATAA
1 TATATACACAATATAA
3529611 TATATATCACAAATATAA
1 TATATA-CAC-AATATAA
3529629 T
1 T
3529630 TTTGATTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 3 0.18
18 8 0.47
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.34
Consensus pattern (16 bp):
TATATACACAATATAA
Found at i:3530683 original size:30 final size:30
Alignment explanation
Indices: 3530647--3530712 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
3530637 TAGGGTACCC
3530647 TATAAACAATGGTGTTTGGATTCGAACTCG
1 TATAAACAATGGTGTTTGGATTCGAACTCG
3530677 TATAAACAATGGTGTTTGGATTCGAACTCG
1 TATAAACAATGGTGTTTGGATTCGAACTCG
3530707 TATAAA
1 TATAAA
3530713 GAGGGAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (30 bp):
TATAAACAATGGTGTTTGGATTCGAACTCG
Found at i:3533416 original size:19 final size:19
Alignment explanation
Indices: 3533394--3533442 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
3533384 TATAAACATT
3533394 ATATATTATACATTATAT-A
1 ATATATTATA-ATTATATAA
*
3533413 ATATATATATAATTGTATAA
1 ATATAT-TATAATTATATAA
*
3533433 ACATATTATA
1 ATATATTATA
3533443 TATACATGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (19 bp):
ATATATTATAATTATATAA
Found at i:3533416 original size:44 final size:44
Alignment explanation
Indices: 3533368--3533468 Score: 143
Period size: 44 Copynumber: 2.3 Consensus size: 44
3533358 AAATATTATG
3533368 AATATATATATAATTGTATAAACAT-TATATATTATACAT-TATAT
1 AATATATATATAATTGTATAAACATAT-TATA-TATACATGTATAT
*
3533412 AATATATATATAATTGTATAAACATATTATATATACATGTATTT
1 AATATATATATAATTGTATAAACATATTATATATACATGTATAT
* *
3533456 AATTTATACATAA
1 AATATATATATAA
3533469 ACATTATTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
43 7 0.13
44 44 0.85
45 1 0.02
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.45
Consensus pattern (44 bp):
AATATATATATAATTGTATAAACATATTATATATACATGTATAT
Found at i:3533421 original size:25 final size:22
Alignment explanation
Indices: 3533369--3533446 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 22
3533359 AATATTATGA
*
3533369 ATATATATATAATTGTATAAAC
1 ATATATATATAATTATATAAAC
3533391 ATTATATATTATACATTATAT--A-
1 A-TATATA-TATA-ATTATATAAAC
*
3533413 ATATATATATAATTGTATAAAC
1 ATATATATATAATTATATAAAC
3533435 ATATTATATATA
1 ATA-TATATATA
3533447 CATGTATTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
19 6 0.13
20 4 0.09
21 7 0.15
22 5 0.11
23 15 0.32
24 4 0.09
25 6 0.13
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.45
Consensus pattern (22 bp):
ATATATATATAATTATATAAAC
Found at i:3533490 original size:22 final size:21
Alignment explanation
Indices: 3533438--3533500 Score: 74
Period size: 23 Copynumber: 2.9 Consensus size: 21
3533428 TATAAACATA
*
3533438 TTAT-ATATACATGTATTTAAT
1 TTATAATAAACAT-TATTTAAT
3533459 TTATACATAAACATTATTATAAT
1 TTATA-ATAAACATTATT-TAAT
*
3533482 TTATAATAAACTTTATTTA
1 TTATAATAAACATTATTTA
3533501 TATGATTGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
21 6 0.16
22 15 0.41
23 16 0.43
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (21 bp):
TTATAATAAACATTATTTAAT
Found at i:3533502 original size:23 final size:23
Alignment explanation
Indices: 3533446--3533498 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
3533436 TATTATATAT
3533446 ACATGTATT-TAATTTATACATAA
1 ACAT-TATTATAATTTATACATAA
3533469 ACATTATTATAATTTATA-ATAA
1 ACATTATTATAATTTATACATAA
*
3533491 ACTTTATT
1 ACATTATT
3533499 TATATGATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 15 0.54
23 13 0.46
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (23 bp):
ACATTATTATAATTTATACATAA
Found at i:3533658 original size:2 final size:2
Alignment explanation
Indices: 3533651--3533684 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3533641 AGCAAGATTT
3533651 TA TA TA TA TA T- 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 TA TA TA TA T
3533685 TTAATTTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3533681 original size:23 final size:22
Alignment explanation
Indices: 3533651--3533711 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
3533641 AGCAAGATTT
3533651 TATATATATATTATATATATATA
1 TATATATATATTATA-ATATATA
*
3533674 TATATATATATT-TAATTTATA
1 TATATATATATTATAATATATA
* *
3533695 CATAAATATTATTATAA
1 TATATATA-TATTATAA
3533712 CTTTTAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 12 0.36
22 6 0.18
23 15 0.45
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TATATATATATTATAATATATA
Found at i:3533926 original size:15 final size:15
Alignment explanation
Indices: 3533888--3533928 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 15
3533878 TTTTATATAC
3533888 ATATATT-TAATT-T
1 ATATATTATAATTGT
3533901 ATA-ATTA-AATTGT
1 ATATATTATAATTGT
3533914 ATATATTATAATTGT
1 ATATATTATAATTGT
3533929 GGATGAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 7 0.29
13 7 0.29
14 4 0.17
15 6 0.25
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (15 bp):
ATATATTATAATTGT
Found at i:3534221 original size:1 final size:1
Alignment explanation
Indices: 3534215--3534244 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
3534205 AGTTAATGTG
3534215 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3534245 CATGTTCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3541109 original size:4 final size:4
Alignment explanation
Indices: 3541102--3541148 Score: 87
Period size: 4 Copynumber: 12.0 Consensus size: 4
3541092 CCTTTCTTTT
3541102 TGTA TGTA TGTA TGTA T-TA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
3541149 AGCATCTGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.07
4 39 0.93
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:3541290 original size:126 final size:126
Alignment explanation
Indices: 3541129--3541356 Score: 341
Period size: 126 Copynumber: 1.8 Consensus size: 126
3541119 TATGTATGTA
* * * * *
3541129 TGTATGTATGTATGTATGTAAGCATCTGAGTATGTTAATTTTTGCATATATGCATCTGGGTATCT
1 TGTATGTATGGATGGATGTAAGCATCTGAGTATGTTAATTTATGCAAATATGCATCTGGGTATCA
3541194 CTTTGTTTGTTAAAAT-TCTGATAAATGATTAATGGGTTTTTTTTCCCGATTTTGAGGTTTG
66 CTTTGTTTGTTAAAATAT-TGATAAATGATTAATGGGTTTTTTTTCCCGATTTTGAGGTTTG
** * * * *
3541255 TGTATGTATGGATGGATGTGTGCATTTGGGTATGTTTATTTATGCAAATATGCATCTGGGTTTCA
1 TGTATGTATGGATGGATGTAAGCATCTGAGTATGTTAATTTATGCAAATATGCATCTGGGTATCA
3541320 CTTTGTTTGTTAAAATATTGATAAATGATTAATGGGT
66 CTTTGTTTGTTAAAATATTGATAAATGATTAATGGGT
3541357 ACCGATGGGT
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
126 89 0.99
127 1 0.01
ACGTcount: A:0.24, C:0.07, G:0.22, T:0.46
Consensus pattern (126 bp):
TGTATGTATGGATGGATGTAAGCATCTGAGTATGTTAATTTATGCAAATATGCATCTGGGTATCA
CTTTGTTTGTTAAAATATTGATAAATGATTAATGGGTTTTTTTTCCCGATTTTGAGGTTTG
Found at i:3543775 original size:2 final size:2
Alignment explanation
Indices: 3543768--3543794 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3543758 CCCAAGTAAT
3543768 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
3543795 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3543799 original size:2 final size:2
Alignment explanation
Indices: 3543794--3543818 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3543784 TCTCTCTCTC
3543794 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 T
3543819 CCCCCTCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3547693 original size:2 final size:2
Alignment explanation
Indices: 3547686--3547726 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3547676 GAAAAGGTTG
3547686 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3547727 TCATCCTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3548978 original size:12 final size:13
Alignment explanation
Indices: 3548955--3548987 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3548945 TAACACTTTT
3548955 TTATTCTTTTCTC
1 TTATTCTTTTCTC
3548968 TTATT-TTTTCTC
1 TTATTCTTTTCTC
*
3548980 TTGTTCTT
1 TTATTCTT
3548988 GATGGAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.06, C:0.18, G:0.03, T:0.73
Consensus pattern (13 bp):
TTATTCTTTTCTC
Found at i:3553143 original size:2 final size:2
Alignment explanation
Indices: 3553136--3553184 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
3553126 NNNNNNNNNN
*
3553136 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3553178 TA TA TA T
1 TA TA TA T
3553185 TTCAAATTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3557554 original size:19 final size:19
Alignment explanation
Indices: 3557530--3557567 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3557520 AAAAAAAAGG
3557530 GTCTTAGATTGTAATTCAT
1 GTCTTAGATTGTAATTCAT
3557549 GTCTTAGATTGTAATTCAT
1 GTCTTAGATTGTAATTCAT
3557568 TCTCTTCGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (19 bp):
GTCTTAGATTGTAATTCAT
Found at i:3558536 original size:3 final size:3
Alignment explanation
Indices: 3558528--3558564 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3558518 TGTATTTGCT
3558528 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3558565 GATTTTTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3558909 original size:12 final size:12
Alignment explanation
Indices: 3558872--3558912 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
3558862 ATTCTCTTTA
3558872 TCTCTCCCTCTC
1 TCTCTCCCTCTC
*
3558884 CCTCTCCCTCTC
1 TCTCTCCCTCTC
* *
3558896 TCTCTCTCTTTC
1 TCTCTCCCTCTC
3558908 TCTCT
1 TCTCT
3558913 AACGTCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (12 bp):
TCTCTCCCTCTC
Found at i:3560645 original size:32 final size:33
Alignment explanation
Indices: 3560601--3560665 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
3560591 CCCTCCAAAG
3560601 TTTTAAAAATTTATAAATTT-TTTAAAATTTTA
1 TTTTAAAAATTTATAAATTTATTTAAAATTTTA
* * *
3560633 TTTTAAATATTTATAATTTTATTTATAATTTTA
1 TTTTAAAAATTTATAAATTTATTTAAAATTTTA
3560666 GTATCTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (33 bp):
TTTTAAAAATTTATAAATTTATTTAAAATTTTA
Found at i:3560655 original size:12 final size:12
Alignment explanation
Indices: 3560609--3560665 Score: 59
Period size: 12 Copynumber: 5.1 Consensus size: 12
3560599 AGTTTTAAAA
*
3560609 ATTTATAAATTT
1 ATTTATAATTTT
*
3560621 -TTTAAAATTTT
1 ATTTATAATTTT
*
3560632 ATTT-TAA--AT
1 ATTTATAATTTT
3560641 ATTTATAATTTT
1 ATTTATAATTTT
3560653 ATTTATAATTTT
1 ATTTATAATTTT
3560665 A
1 A
3560666 GTATCTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
9 5 0.14
10 3 0.08
11 11 0.31
12 17 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTTATAATTTT
Found at i:3560975 original size:29 final size:28
Alignment explanation
Indices: 3560943--3561012 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 28
3560933 ACCTATAGTT
*
3560943 AATTAATTAAATTAAAATTAAAATATAAA
1 AATTAATTAAATTAAAATAAAAATAT-AA
*
3560972 AATTTAATTAAA-TATAATAAAAATATAA
1 AA-TTAATTAAATTAAAATAAAAATATAA
*
3561000 AATTATTTAAATT
1 AATTAATTAAATT
3561013 TTTTTGAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 8 0.22
28 5 0.14
29 14 0.39
30 9 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
AATTAATTAAATTAAAATAAAAATATAA
Found at i:3566702 original size:33 final size:33
Alignment explanation
Indices: 3566655--3567455 Score: 309
Period size: 33 Copynumber: 24.3 Consensus size: 33
3566645 AAGCATGGCT
* * *
3566655 ACCTTAGGTGAAGAAACTCTTAGCATTCCCGCA
1 ACCTTGGGTGAAGAAACTCCTAGCATTCCCACA
*
3566688 AGCTTGGGTGAAGAAACTCCTAGCATTCCCACA
1 ACCTTGGGTGAAGAAACTCCTAGCATTCCCACA
* * * *
3566721 AGCTTGGATGAAGAAACGCCTAGCGTTCCCACA
1 ACCTTGGGTGAAGAAACTCCTAGCATTCCCACA
3566754 ACCTTGGGTGAAGAAACTCCTAGCATTCCCACA
1 ACCTTGGGTGAAGAAACTCCTAGCATTCCCACA
* * * *
3566787 ACCTTGGGTGAAGAAATTCTTACCATTCCCTCA
1 ACCTTGGGTGAAGAAACTCCTAGCATTCCCACA
* * ****
3566820 ACCTTGGGCGAAGAAACTCCTATC-TATCCTGTG
1 ACCTTGGGTGAAGAAACTCCTAGCAT-TCCCACA
** * * * *
3566853 ACCTTGGCAGAAGAAACCCCTACCATTACCATA
1 ACCTTGGGTGAAGAAACTCCTAGCATTCCCACA
** *
3566886 ACCTTGGGCCAAGAAACTCCT-G-ACTTACACACA
1 ACCTTGGGTGAAGAAACTCCTAGCA-TT-CCCACA
* * **
3566919 ACATTGGGTGCAGAAACTCC-AGTCATTCCTTCA
1 ACCTTGGGTGAAGAAACTCCTAG-CATTCCCACA
***
3566952 ACCTTGGACAAAGAAACTCCT-GTCATTCCTC-CA
1 ACCTTGGGTGAAGAAACTCCTAG-CATTCC-CACA
3566985 ACCTTGGGTGAAGAAACTCCT-GCCATTCCTC-CA
1 ACCTTGGGTGAAGAAACTCCTAG-CATTCC-CACA
* * * * * * * ***
3567018 ACCTTGAGCGATGAAATTTCGACCA-TCACTGTA
1 ACCTTGGGTGAAGAAACTCCTAGCATTC-CCACA
* * * ** * *
3567051 ACCCTGGGTCAGGAAACTCAGACCATTCCTACA
1 ACCTTGGGTGAAGAAACTCCTAGCATTCCCACA
* * * * * * ***
3567084 A--TTGTCGCTGAGGAAACTACAACCGTTCTTGCA
1 ACCTTG--GGTGAAGAAACTCCTAGCATTCCCACA
* * * * *
3567117 ACCTTGGTTGAGGAAACTAC-AACTATTCCTACA
1 ACCTTGGGTGAAGAAACTCCTAGC-ATTCCCACA
** *
3567150 ACCTTGCATGAAGAAACT-CTAGCTGTTCCCACA
1 ACCTTGGGTGAAGAAACTCCTAGC-ATTCCCACA
* *
3567183 ACCTTGGCTG-AGAGAACTCC-AACTATTCCCACA
1 ACCTTGGGTGAAGA-AACTCCTAGC-ATTCCCACA
* * * *
3567216 ACCTTGGGTGAGGAAACTGCGA-CTATTCCCACC
1 ACCTTGGGTGAAGAAACTCCTAGC-ATTCCCACA
* *** * *
3567249 ACCTTGGG-CAAGGAAACTGAAAGTATTCCCAAA
1 ACCTTGGGTGAA-GAAACTCCTAGCATTCCCACA
*
3567282 ACCTTGGGTGAGGAAACTTCAACTA--ATT-CCACA
1 ACCTTGGGTGAAGAAAC-TC--CTAGCATTCCCACA
* * *
3567315 ACCTTGGGTGAGGAAACTTCTA-CTATTCCAACA
1 ACCTTGGGTGAAGAAACTCCTAGC-ATTCCCACA
* * * * * *
3567348 ACCTTGGCTGAGGAAATTCC-AACTAATCCGACA
1 ACCTTGGGTGAAGAAACTCCTAGC-ATTCCCACA
* ** * * *
3567381 ACCGTGACTGAGGAAACTTCGA-CTATTCCCACA
1 ACCTTGGGTGAAGAAACTCCTAGC-ATTCCCACA
* * * *
3567414 ACCTTGGGCGAGGAAACT-GTGGCTATTCCCACA
1 ACCTTGGGTGAAGAAACTCCTAGC-ATTCCCACA
*
3567447 ACGTTGGGT
1 ACCTTGGGT
3567456 TTGGAAGCTT
Statistics
Matches: 595, Mismatches: 138, Indels: 70
0.74 0.17 0.09
Matches are distributed among these distances:
30 3 0.01
31 3 0.01
32 17 0.03
33 552 0.93
34 15 0.03
35 4 0.01
36 1 0.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (33 bp):
ACCTTGGGTGAAGAAACTCCTAGCATTCCCACA
Found at i:3569905 original size:20 final size:21
Alignment explanation
Indices: 3569870--3569908 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3569860 CCTTACAAAA
*
3569870 GATAATATTAAAAAATAAACT
1 GATAAAATTAAAAAATAAACT
3569891 GATAAAATT-AAAAATAAA
1 GATAAAATTAAAAAATAAA
3569909 TAAATAGCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (21 bp):
GATAAAATTAAAAAATAAACT
Found at i:3570024 original size:25 final size:25
Alignment explanation
Indices: 3569996--3570048 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
3569986 GGCTAATATG
*
3569996 AGAAACCAAATAACCACCAAA-TAAA
1 AGAAAACAAATAACCA-CAAAGTAAA
*
3570021 AGAAAATAAATAACCACAAAGTAAA
1 AGAAAACAAATAACCACAAAGTAAA
3570046 AGA
1 AGA
3570049 CATGTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.66, C:0.17, G:0.08, T:0.09
Consensus pattern (25 bp):
AGAAAACAAATAACCACAAAGTAAA
Found at i:3572971 original size:2 final size:2
Alignment explanation
Indices: 3572959--3572997 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
3572949 TCACTTTTCC
*
3572959 CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3572998 GTTTCTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
CT
Found at i:3588526 original size:2 final size:2
Alignment explanation
Indices: 3588519--3588551 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3588509 CTGGTTTCTT
3588519 TA TA TA 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 TA TA TA T
3588552 TTGTTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3605657 original size:5 final size:5
Alignment explanation
Indices: 3605651--3605680 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3605641 CCCCCCCCAA
*
3605651 AAAAA AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
3605681 CAGGTTCCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:3605837 original size:3 final size:3
Alignment explanation
Indices: 3605829--3605870 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
3605819 CATATGGATG
3605829 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3605871 ATGTTGAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:3608115 original size:2 final size:2
Alignment explanation
Indices: 3608108--3608173 Score: 69
Period size: 2 Copynumber: 32.5 Consensus size: 2
3608098 ACCTTATTAT
* * ** **
3608108 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TNN NN NN TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
3608151 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
3608174 CTTGATTGAC
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3608775 original size:22 final size:23
Alignment explanation
Indices: 3608737--3608781 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
3608727 TAGATATTGA
*
3608737 TAAAATATATAAAAATTATTTTT
1 TAAAATATATAAAAATTAATTTT
3608760 TAAAATA-A-AAATAATTAATTTT
1 TAAAATATATAAA-AATTAATTTT
3608782 AACAAGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 3 0.15
22 10 0.50
23 7 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAAATATATAAAAATTAATTTT
Found at i:3611922 original size:2 final size:2
Alignment explanation
Indices: 3611915--3611970 Score: 71
Period size: 2 Copynumber: 28.5 Consensus size: 2
3611905 TTTCAAAAGG
*
3611915 AT AT AT AT AT AT AT AT -T TT AT AT AT AT AT AT AT AT CAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
*
3611957 AT AT GT A- AT AT AT A
1 AT AT AT AT AT AT AT A
3611971 AGAATACAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.04
2 44 0.92
3 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3611938 original size:15 final size:15
Alignment explanation
Indices: 3611918--3611970 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
3611908 CAAAAGGATA
3611918 TATATATATATATTT
1 TATATATATATATTT
*
3611933 TATATATATATA-TA
1 TATATATATATATTT
*
3611947 TATCATATATATATGT
1 TAT-ATATATATATTT
*
3611963 AATATATA
1 TATATATA
3611971 AGAATACAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 4 0.12
15 26 0.81
16 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
TATATATATATATTT
Found at i:3611938 original size:17 final size:17
Alignment explanation
Indices: 3611916--3611960 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
3611906 TTCAAAAGGA
*
3611916 TATATATATATATATTT
1 TATATATATATATATAT
3611933 TATATATATATATATAT
1 TATATATATATATATAT
*
3611950 CATATATATAT
1 TATATATATAT
3611961 GTAATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:3611939 original size:19 final size:19
Alignment explanation
Indices: 3611915--3611960 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
3611905 TTTCAAAAGG
**
3611915 ATATATATATATATATTTT
1 ATATATATATATATATCAT
3611934 ATATATATATATATATCAT
1 ATATATATATATATATCAT
3611953 ATATATAT
1 ATATATAT
3611961 GTAATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
ATATATATATATATATCAT
Found at i:3613937 original size:2 final size:2
Alignment explanation
Indices: 3613930--3613955 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3613920 NTAAGTAAGA
3613930 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
3613956 GTGATGGAAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3619749 original size:2 final size:2
Alignment explanation
Indices: 3619742--3619786 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
3619732 TTACATAATC
*
3619742 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3619784 AT A
1 AT A
3619787 AAATAAACAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3623011 original size:15 final size:15
Alignment explanation
Indices: 3622991--3623032 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
3622981 TAGAATTGAT
*
3622991 CATGACATTCATGTG
1 CATGACATTCATGGG
3623006 CATGACATTCATGGG
1 CATGACATTCATGGG
3623021 CATGACATTCAT
1 CATGACATTCAT
3623033 CATTTATGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (15 bp):
CATGACATTCATGGG
Found at i:3627206 original size:2 final size:2
Alignment explanation
Indices: 3627199--3627226 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3627189 TGAAATTCAG
3627199 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
3627227 GTAGGGNAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3627260 original size:2 final size:2
Alignment explanation
Indices: 3627253--3627281 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3627243 TGAAATTCAG
3627253 TA 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 TA T
3627282 GGGGAAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3631786 original size:53 final size:53
Alignment explanation
Indices: 3631706--3631813 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
3631696 TATAAACAGA
3631706 CAATTTAATTAGAATCATTCCTTTCAAGTTAAGAGCAAGACTGGTTCTTTCTG
1 CAATTTAATTAGAATCATTCCTTTCAAGTTAAGAGCAAGACTGGTTCTTTCTG
3631759 CAATTTAATTAGAATCATTCCTTTCAAGTTAAGAGCAAGACTGGTTCTTTCTG
1 CAATTTAATTAGAATCATTCCTTTCAAGTTAAGAGCAAGACTGGTTCTTTCTG
3631812 CA
1 CA
3631814 TGCACACAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.37
Consensus pattern (53 bp):
CAATTTAATTAGAATCATTCCTTTCAAGTTAAGAGCAAGACTGGTTCTTTCTG
Found at i:3642231 original size:15 final size:14
Alignment explanation
Indices: 3642199--3642233 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3642189 AGTAAAAATT
*
3642199 TTTTTATTTTAAGC
1 TTTTTATTTTAAAC
3642213 TTTTTATTTTAAAC
1 TTTTTATTTTAAAC
*
3642227 ATTTTAT
1 TTTTTAT
3642234 CAAAGAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.66
Consensus pattern (14 bp):
TTTTTATTTTAAAC
Found at i:3649063 original size:6 final size:6
Alignment explanation
Indices: 3649049--3649106 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
3649039 CGGGCCTTTG
* * * * * * *
3649049 CCCTCT CCCTAT CCCTTT CTCTGT CCCTCT CCCTTT CCCTTT CCCTGT
1 CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT
3649097 CCCTCT CCCT
1 CCCTCT CCCT
3649107 GCTCTTTTCC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.02, C:0.55, G:0.03, T:0.40
Consensus pattern (6 bp):
CCCTCT
Found at i:3649075 original size:12 final size:12
Alignment explanation
Indices: 3649049--3649107 Score: 64
Period size: 12 Copynumber: 4.9 Consensus size: 12
3649039 CGGGCCTTTG
* *
3649049 CCCTCTCCCTAT
1 CCCTTTCCCTGT
*
3649061 CCCTTTCTCTGT
1 CCCTTTCCCTGT
* *
3649073 CCCTCTCCCTTT
1 CCCTTTCCCTGT
3649085 CCCTTTCCCTGT
1 CCCTTTCCCTGT
*
3649097 CCCTCTCCCTG
1 CCCTTTCCCTG
3649108 CTCTTTTCCC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.02, C:0.54, G:0.05, T:0.39
Consensus pattern (12 bp):
CCCTTTCCCTGT
Found at i:3649075 original size:18 final size:18
Alignment explanation
Indices: 3649043--3649107 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
3649033 CGATCCCGGG
*
3649043 CCTTTGCCCTCTCCCTATC
1 CCTTT-CCCTGTCCCTATC
* *
3649062 CCTTTCTCTGTCCCTCTC
1 CCTTTCCCTGTCCCTATC
* *
3649080 CCTTTCCCTTTCCCTGTC
1 CCTTTCCCTGTCCCTATC
*
3649098 CCTCTCCCTG
1 CCTTTCCCTG
3649108 CTCTTTTCCC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
18 33 0.87
19 5 0.13
ACGTcount: A:0.02, C:0.52, G:0.06, T:0.40
Consensus pattern (18 bp):
CCTTTCCCTGTCCCTATC
Found at i:3649076 original size:24 final size:24
Alignment explanation
Indices: 3649049--3649106 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
3649039 CGGGCCTTTG
*
3649049 CCCTCTCCCTATCCCTTTCTCTGT
1 CCCTCTCCCTATCCCTTTCCCTGT
*
3649073 CCCTCTCCCTTTCCCTTTCCCTGT
1 CCCTCTCCCTATCCCTTTCCCTGT
3649097 CCCTCTCCCT
1 CCCTCTCCCT
3649107 GCTCTTTTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.02, C:0.55, G:0.03, T:0.40
Consensus pattern (24 bp):
CCCTCTCCCTATCCCTTTCCCTGT
Found at i:3654177 original size:26 final size:25
Alignment explanation
Indices: 3654149--3654196 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
3654139 GTTTTATTTA
3654149 AAAAAATAA-AAAATATAATAATTCT
1 AAAAAATAATAAAATATAA-AATTCT
*
3654174 AAAAATTAATAAAATATAAAATT
1 AAAAAATAATAAAATATAAAATT
3654197 ATATTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (25 bp):
AAAAAATAATAAAATATAAAATTCT
Found at i:3658255 original size:6 final size:7
Alignment explanation
Indices: 3658227--3658257 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
3658217 AACAACAGAA
3658227 TAATTATT
1 TAATT-TT
3658235 TAATTTT
1 TAATTTT
3658242 TAATTTT
1 TAATTTT
3658249 TAATTTT
1 TAATTTT
3658256 TA
1 TA
3658258 TATAGAACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.78
8 5 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TAATTTT
Found at i:3663126 original size:1 final size:1
Alignment explanation
Indices: 3663117--3663156 Score: 62
Period size: 1 Copynumber: 40.0 Consensus size: 1
3663107 CCCCTCTCCA
* *
3663117 CCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCNCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
3663157 AAAAAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.03, C:0.95, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:3667833 original size:28 final size:29
Alignment explanation
Indices: 3667759--3667835 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
3667749 CAATCTTAAT
3667759 TATAAAGACTTATTTGAATCGAAATAAAAA
1 TATAAA-ACTTATTTGAATCGAAATAAAAA
* * * *
3667789 TATAAGAGTTTTGTTGAAT-GTAATAAAAA
1 TATAAAACTTAT-TTGAATCGAAATAAAAA
3667818 -ATAATAACTTATTTGAAT
1 TATAA-AACTTATTTGAAT
3667836 TTTTTTCGAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
28 10 0.26
29 17 0.45
30 11 0.29
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.36
Consensus pattern (29 bp):
TATAAAACTTATTTGAATCGAAATAAAAA
Found at i:3667919 original size:21 final size:20
Alignment explanation
Indices: 3667872--3667921 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
3667862 AACTATACAT
**
3667872 AATATTTAAAAAATTTCTTA
1 AATATTTAAAAAATTTAATA
*
3667892 AATTATTTAAAAATTTTAAATA
1 AA-TATTTAAAAAATTT-AATA
3667914 AATATTTA
1 AATATTTA
3667922 TATTTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 19 0.76
22 4 0.16
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATTTAAAAAATTTAATA
Found at i:3668013 original size:31 final size:30
Alignment explanation
Indices: 3667948--3668006 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
3667938 AATCAAGTTC
*
3667948 TTATACTTTTATTTTGAATCAAACAAGTCA
1 TTATACTTTTATTTTGAATCAAACAAATCA
* *
3667978 TTATACTTTTTATTTTGACTCAAATAAAT
1 TTATAC-TTTTATTTTGAATCAAACAAAT
3668007 TTTTATAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (30 bp):
TTATACTTTTATTTTGAATCAAACAAATCA
Found at i:3671503 original size:21 final size:22
Alignment explanation
Indices: 3671475--3671528 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 22
3671465 AAATACAGAG
* *
3671475 AATAAATAAATAAAATTATTTA
1 AATAAATAAATAAAAATAATTA
*
3671497 AA-AAAT-ATTAAAAATAATTA
1 AATAAATAAATAAAAATAATTA
3671517 AATAAA-AAATAA
1 AATAAATAAATAA
3671529 TTCACTAGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
20 13 0.50
21 11 0.42
22 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
AATAAATAAATAAAAATAATTA
Found at i:3671777 original size:28 final size:28
Alignment explanation
Indices: 3671723--3671791 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
3671713 TCCAATCGAG
* *
3671723 TTTAAATTTTGTAATATTTAAGTATTTTA
1 TTTAAATTTT-AAATATTTAAGTATTTAA
**
3671752 -TTAAATTTTAAATATTTACTTAATTTAA
1 TTTAAATTTTAAATATTTAAGT-ATTTAA
*
3671780 TTTAAATATTAA
1 TTTAAATTTTAA
3671792 TTGAGTTCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
27 9 0.27
28 14 0.42
29 10 0.30
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (28 bp):
TTTAAATTTTAAATATTTAAGTATTTAA
Found at i:3671778 original size:27 final size:28
Alignment explanation
Indices: 3671724--3671778 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
3671714 CCAATCGAGT
* *
3671724 TTAAATTTTGTAATATTTAAGTATTTTA
1 TTAAATTTTGAAATATTTAAGTAATTTA
**
3671752 TTAAATTTT-AAATATTTACTTAATTTA
1 TTAAATTTTGAAATATTTAAGTAATTTA
3671779 ATTTAAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (28 bp):
TTAAATTTTGAAATATTTAAGTAATTTA
Found at i:3675538 original size:39 final size:39
Alignment explanation
Indices: 3675476--3675555 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
3675466 GTTTAGTGAA
*
3675476 GGCCATTAGATATGCATTAATACCACTTCGTAGCTATGT
1 GGCCATTAGATATCCATTAATACCACTTCGTAGCTATGT
*
3675515 GGCCATTAGATATCCATTGATACCACTTCGTAGCTATGT
1 GGCCATTAGATATCCATTAATACCACTTCGTAGCTATGT
3675554 GG
1 GG
3675556 TATCATTTGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (39 bp):
GGCCATTAGATATCCATTAATACCACTTCGTAGCTATGT
Found at i:3678563 original size:33 final size:33
Alignment explanation
Indices: 3678506--3678571 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3678496 AGAAGCCCTC
3678506 CTTTCAAAGCAACCATCCCCTAATATTTTTATT
1 CTTTCAAAGCAACCATCCCCTAATATTTTTATT
* *
3678539 CTTTGAAAGCAACTA-CCCCATAATATTTTTATT
1 CTTTCAAAGCAACCATCCCC-TAATATTTTTATT
3678572 ATTATTCTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 4 0.13
33 26 0.87
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (33 bp):
CTTTCAAAGCAACCATCCCCTAATATTTTTATT
Found at i:3680912 original size:2 final size:2
Alignment explanation
Indices: 3680905--3680931 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3680895 TCGTCACTGG
3680905 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
3680932 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3680936 original size:2 final size:2
Alignment explanation
Indices: 3680931--3680969 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3680921 TCTCTCTCTC
*
3680931 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3680970 GCGTATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3692616 original size:40 final size:40
Alignment explanation
Indices: 3692568--3692646 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
3692558 TTGGTTATTT
*
3692568 TTCACCTTAGTGGGG-TTCTGAACCTTGCCAAGATTGGTGA
1 TTCACCTTAGTGGGGTTTCT-AACCTCGCCAAGATTGGTGA
*
3692608 TTCACCTTAGTGGGGTTTCTAACCTCGCCACGATTGGTG
1 TTCACCTTAGTGGGGTTTCTAACCTCGCCAAGATTGGTG
3692647 TCTTTCACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 32 0.89
41 4 0.11
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.33
Consensus pattern (40 bp):
TTCACCTTAGTGGGGTTTCTAACCTCGCCAAGATTGGTGA
Found at i:3717369 original size:26 final size:28
Alignment explanation
Indices: 3717339--3717402 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 28
3717329 ATAAAATTTT
* *
3717339 ATTTAATTTAAGAT-A-AAAATATAAGA
1 ATTTAATTTAAGATAACAAAAAATAAAA
*
3717365 ATTTAATTTAATATAACAAAAAATAAAA
1 ATTTAATTTAAGATAACAAAAAATAAAA
3717393 ATTT-ATTTAA
1 ATTTAATTTAA
3717403 TTTTTTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 13 0.39
27 7 0.21
28 13 0.39
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (28 bp):
ATTTAATTTAAGATAACAAAAAATAAAA
Found at i:3724581 original size:1 final size:1
Alignment explanation
Indices: 3724570--3724600 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
3724560 TGTCTCTTTC
*
3724570 TTTTGTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3724601 GGGGGGGGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:3736299 original size:3 final size:3
Alignment explanation
Indices: 3736291--3736336 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3736281 TATAGCAATT
3736291 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3736337 GTTCAATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3737994 original size:23 final size:23
Alignment explanation
Indices: 3737968--3738011 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3737958 TAATATTAAT
3737968 TTAATTAA-ATAAAAAATAAAAAA
1 TTAATTAACAT-AAAAATAAAAAA
*
3737991 TTAATTAACATAATAATAAAA
1 TTAATTAACATAAAAATAAAA
3738012 TAAAATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
TTAATTAACATAAAAATAAAAAA
Found at i:3738221 original size:142 final size:142
Alignment explanation
Indices: 3738035--3738319 Score: 428
Period size: 142 Copynumber: 2.0 Consensus size: 142
3738025 TTTTTAAAAG
* * **
3738035 TAATTTTAAAATATTAAACCTATTTCTTTATTTGTGTTTCTTTTTTCTTTTTTAGCTCATCTACC
1 TAATTTAAAAATATTAAACCTAGTTCTTTATTTGAATTTCTTTTTTCTTTTTTAGCTCATCTACC
* * * * *
3738100 AATGATAATTTTTCTACGTTGCATATCTACACGTACAGCTAATCTAATGCCTATATATTGAATTC
66 AATGACAAATTCTCTACGTCGCATATCTACACGTACAGCTAATCTAATACCTATATATTGAATTC
3738165 TTAAACTTGATT
131 TTAAACTTGATT
* *
3738177 TAATTTAAAAATATTAAATCTAGTTCTTTATTTGCAATTT-TTTTTTCTTTTTTAGTTCATCTAC
1 TAATTTAAAAATATTAAACCTAGTTCTTTATTTG-AATTTCTTTTTTCTTTTTTAGCTCATCTAC
* *
3738241 CAATGACAAATTCTCTACGTCGCATATCTACCCGTACAGCTAATCTAATACCTATTTATTGAATT
65 CAATGACAAATTCTCTACGTCGCATATCTACACGTACAGCTAATCTAATACCTATATATTGAATT
*
3738306 CTTAAATTTGATT
130 CTTAAACTTGATT
3738319 T
1 T
3738320 TCTAAATTTC
Statistics
Matches: 128, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
142 125 0.98
143 3 0.02
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.47
Consensus pattern (142 bp):
TAATTTAAAAATATTAAACCTAGTTCTTTATTTGAATTTCTTTTTTCTTTTTTAGCTCATCTACC
AATGACAAATTCTCTACGTCGCATATCTACACGTACAGCTAATCTAATACCTATATATTGAATTC
TTAAACTTGATT
Found at i:3738441 original size:8 final size:8
Alignment explanation
Indices: 3738428--3738455 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
3738418 GCGAGCTAAA
3738428 TGCTTGAG
1 TGCTTGAG
3738436 TGCTTGAG
1 TGCTTGAG
3738444 TGCTTGAG
1 TGCTTGAG
3738452 TGCT
1 TGCT
3738456 GCTTATCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.14, G:0.36, T:0.39
Consensus pattern (8 bp):
TGCTTGAG
Found at i:3738473 original size:3 final size:3
Alignment explanation
Indices: 3738467--3738492 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3738457 CTTATCTATC
3738467 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
3738493 AATTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3753933 original size:103 final size:103
Alignment explanation
Indices: 3753754--3753961 Score: 416
Period size: 103 Copynumber: 2.0 Consensus size: 103
3753744 ATTTGTATGA
3753754 ATTCTATTCTTTATAGGACTTAAAATAATGAAACCGAAAATGTTGATCAAAGCCAGTTGTGATTA
1 ATTCTATTCTTTATAGGACTTAAAATAATGAAACCGAAAATGTTGATCAAAGCCAGTTGTGATTA
3753819 CCCTGTATGGTAGAACTGTAATTATTTTGGAATGAGAT
66 CCCTGTATGGTAGAACTGTAATTATTTTGGAATGAGAT
3753857 ATTCTATTCTTTATAGGACTTAAAATAATGAAACCGAAAATGTTGATCAAAGCCAGTTGTGATTA
1 ATTCTATTCTTTATAGGACTTAAAATAATGAAACCGAAAATGTTGATCAAAGCCAGTTGTGATTA
3753922 CCCTGTATGGTAGAACTGTAATTATTTTGGAATGAGAT
66 CCCTGTATGGTAGAACTGTAATTATTTTGGAATGAGAT
3753960 AT
1 AT
3753962 ATTCTTCCTA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (103 bp):
ATTCTATTCTTTATAGGACTTAAAATAATGAAACCGAAAATGTTGATCAAAGCCAGTTGTGATTA
CCCTGTATGGTAGAACTGTAATTATTTTGGAATGAGAT
Done.