Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397269.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_12.1, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5666189
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 144833 characters in sequence are not A, C, G, or T
File 9 of 14
Found at i:3368188 original size:15 final size:15
Alignment explanation
Indices: 3368163--3368199 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3368153 ATAAGATTGA
3368163 AGAAA-GAGCAAGAAG
1 AGAAAGGAGCAA-AAG
3368178 A-AAAGGAGCAAAAG
1 AGAAAGGAGCAAAAG
3368192 AGAAAGGA
1 AGAAAGGA
3368200 AAAAGCAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.62, C:0.05, G:0.32, T:0.00
Consensus pattern (15 bp):
AGAAAGGAGCAAAAG
Found at i:3372126 original size:20 final size:20
Alignment explanation
Indices: 3372098--3372144 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
3372088 GAAAGAAATG
* **
3372098 TAAAAAAAAAAAAACTTGAT
1 TAAATAAAAAAAAACAAGAT
*
3372118 TAAATAAAAAGAAACAAGAT
1 TAAATAAAAAAAAACAAGAT
3372138 TAAATAA
1 TAAATAA
3372145 TAGATTTGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.70, C:0.04, G:0.06, T:0.19
Consensus pattern (20 bp):
TAAATAAAAAAAAACAAGAT
Found at i:3380301 original size:3 final size:3
Alignment explanation
Indices: 3380293--3380325 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
3380283 CTTGTGTAAT
*
3380293 ATC ATC ATC ATT ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
3380326 TGCTCAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:3383304 original size:34 final size:34
Alignment explanation
Indices: 3383250--3383333 Score: 114
Period size: 34 Copynumber: 2.5 Consensus size: 34
3383240 GATGGTACAC
* * * *
3383250 GCCAAAACTTTAGCAGCAGATGTTACATGCCAAG
1 GCCAAAGCTTCAGCATCAGATGTTACACGCCAAG
*
3383284 GTCAAAGCTTCAGCATCAGATGTTACACGCCAAG
1 GCCAAAGCTTCAGCATCAGATGTTACACGCCAAG
*
3383318 GCCAAGGCTTCAGCAT
1 GCCAAAGCTTCAGCAT
3383334 ATTACACACC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.20
Consensus pattern (34 bp):
GCCAAAGCTTCAGCATCAGATGTTACACGCCAAG
Found at i:3384694 original size:9 final size:11
Alignment explanation
Indices: 3384638--3384671 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
3384628 CGTAGTTTTT
3384638 TAAAATTAATA
1 TAAAATTAATA
3384649 TAAAATTAATA
1 TAAAATTAATA
3384660 -AAAATT-ATA
1 TAAAATTAATA
3384669 TAA
1 TAA
3384672 TAATAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 3 0.14
10 8 0.36
11 11 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAAATTAATA
Found at i:3392862 original size:21 final size:21
Alignment explanation
Indices: 3392837--3392876 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3392827 GTTTTGTTCC
*
3392837 TTAAATTTTAAAAATTTATAT
1 TTAAATATTAAAAATTTATAT
*
3392858 TTAAATATTCAAAATTTAT
1 TTAAATATTAAAAATTTAT
3392877 TTTCATTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAAATATTAAAAATTTATAT
Found at i:3395086 original size:55 final size:58
Alignment explanation
Indices: 3395027--3395133 Score: 157
Period size: 55 Copynumber: 1.9 Consensus size: 58
3395017 AATTAATCTA
*
3395027 TTAATAATTAATCTTTTAAATATTAATATTTTTAAT-A-TTAATATT-TTATTATAAT
1 TTAATAATTAATATTTTAAATATTAATATTTTTAATAATTTAATATTATTATTATAAT
* * *
3395082 TTAATCATTAATATTTTTAATATTAATATTTTTTATAATTTAATATTATTAT
1 TTAATAATTAATATTTTAAATATTAATATTTTTAATAATTTAATATTATTAT
3395134 GATTAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
55 32 0.71
56 1 0.02
57 8 0.18
58 4 0.09
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (58 bp):
TTAATAATTAATATTTTAAATATTAATATTTTTAATAATTTAATATTATTATTATAAT
Found at i:3395092 original size:40 final size:38
Alignment explanation
Indices: 3395045--3395129 Score: 152
Period size: 40 Copynumber: 2.2 Consensus size: 38
3395035 TAATCTTTTA
3395045 AATATTAATATTTTTAATATTAATATTTTATTATAATTT
1 AATATTAATATTTTTAATATTAATATTTT-TTATAATTT
3395084 AATCATTAATATTTTTAATATTAATATTTTTTATAATTT
1 AAT-ATTAATATTTTTAATATTAATATTTTTTATAATTT
3395123 AATATTA
1 AATATTA
3395130 TTATGATTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
38 4 0.09
39 15 0.33
40 26 0.58
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (38 bp):
AATATTAATATTTTTAATATTAATATTTTTTATAATTT
Found at i:3395110 original size:15 final size:15
Alignment explanation
Indices: 3394990--3395128 Score: 94
Period size: 15 Copynumber: 9.1 Consensus size: 15
3394980 TTTATTTTAT
3394990 TTTTTAAATATTAATAA
1 TTTTT-AATATTAAT-A
*
3395007 TTTATAAT-TTAATTAA
1 TTTTTAATATTAA-T-A
* *
3395023 TCTATTAATAATTAATC
1 T-TTTTAAT-ATTAATA
*
3395040 TTTTAAATATTAATA
1 TTTTTAATATTAATA
3395055 TTTTTAATATTAATA
1 TTTTTAATATTAATA
3395070 --TTT--TATT-ATA
1 TTTTTAATATTAATA
*
3395080 -ATTTAATCATTAATA
1 TTTTTAAT-ATTAATA
3395095 TTTTTAATATTAATA
1 TTTTTAATATTAATA
*
3395110 TTTTTTATAATTTAATA
1 TTTTTAAT-A-TTAATA
3395127 TT
1 TT
3395129 ATTATGATTA
Statistics
Matches: 100, Mismatches: 10, Indels: 24
0.75 0.07 0.18
Matches are distributed among these distances:
10 3 0.03
11 7 0.07
13 4 0.04
14 3 0.03
15 41 0.41
16 19 0.19
17 18 0.18
18 1 0.01
19 4 0.04
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTTTAATATTAATA
Found at i:3395144 original size:40 final size:40
Alignment explanation
Indices: 3395048--3395147 Score: 123
Period size: 40 Copynumber: 2.5 Consensus size: 40
3395038 TCTTTTAAAT
**
3395048 ATTAATATTTTTAATATTAATATTTTATTATAATTTAATC
1 ATTAATATTTAAAATATTAATATTTTATTATAATTTAATC
**
3395088 ATTAATATTTTTAATATTAATATTTT-TTATAATTTAAT-
1 ATTAATATTTAAAATATTAATATTTTATTATAATTTAATC
*
3395126 ATTATTATGATTAAAATATTAA
1 ATTAATAT--TTAAAATATTAA
3395148 AAATTTTAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
38 7 0.13
39 12 0.22
40 36 0.65
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (40 bp):
ATTAATATTTAAAATATTAATATTTTATTATAATTTAATC
Found at i:3395147 original size:55 final size:54
Alignment explanation
Indices: 3395033--3395157 Score: 137
Period size: 55 Copynumber: 2.3 Consensus size: 54
3395023 TCTATTAATA
* * *
3395033 ATTAATCTTTTAAATATTAATATTTTTAATATTAATATTTTATTATAATTTAATC
1 ATTAATATTTTTAATATTAATATTTTTAATATTAATA-TTTATTATAATTAAATC
* *
3395088 ATTAATATTTTTAATATTAATATTTTTTATAATTTAATA-TTATTATGATTAAAAT-
1 ATTAATATTTTTAATATTAATATTTTTAAT-A-TTAATATTTATTATAATT-AAATC
* *
3395143 ATTAAAAATTTTAAT
1 ATTAATATTTTTAAT
3395158 TAATTTCCAA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
55 50 0.83
56 4 0.07
57 6 0.10
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (54 bp):
ATTAATATTTTTAATATTAATATTTTTAATATTAATATTTATTATAATTAAATC
Found at i:3395438 original size:19 final size:20
Alignment explanation
Indices: 3395404--3395441 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3395394 TTAATTTTTC
*
3395404 TTTATTTTTATGTTTAATTT
1 TTTATTTTTATCTTTAATTT
3395424 TTTATTTTTA-CTTTAATT
1 TTTATTTTTATCTTTAATT
3395442 AAAATTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (20 bp):
TTTATTTTTATCTTTAATTT
Found at i:3395536 original size:8 final size:8
Alignment explanation
Indices: 3395507--3395559 Score: 63
Period size: 8 Copynumber: 6.5 Consensus size: 8
3395497 AATATTTTAT
3395507 TTAAAAT-
1 TTAAAATA
3395514 TTAAATATGA
1 TTAAA-AT-A
3395524 TTAAAATA
1 TTAAAATA
3395532 TTAAAATA
1 TTAAAATA
* *
3395540 TTAATATT
1 TTAAAATA
3395548 TTAAAATA
1 TTAAAATA
3395556 TTAA
1 TTAA
3395560 TTTTTTAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
7 5 0.13
8 27 0.69
9 2 0.05
10 5 0.13
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (8 bp):
TTAAAATA
Found at i:3395540 original size:19 final size:20
Alignment explanation
Indices: 3395486--3395540 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
3395476 ACATTAATTT
* * *
3395486 TTTAAAATATTAATATTTTA
1 TTTAAAATATTAAAATATGA
3395506 TTTAAAAT-TT-AAATATGA
1 TTTAAAATATTAAAATATGA
3395524 -TTAAAATATTAAAATAT
1 TTTAAAATATTAAAATAT
3395541 TAATATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 7 0.23
18 7 0.23
19 8 0.27
20 8 0.27
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
TTTAAAATATTAAAATATGA
Found at i:3395562 original size:14 final size:16
Alignment explanation
Indices: 3395478--3395566 Score: 80
Period size: 16 Copynumber: 5.8 Consensus size: 16
3395468 TAAGGTAAAC
*
3395478 ATTAATTTTTTAAAAT
1 ATTAATATTTTAAAAT
3395494 ATTAATATTTT---AT
1 ATTAATATTTTAAAAT
*
3395507 -TTAA-AATTTAAATAT
1 ATTAATATTTTAAA-AT
* *
3395522 GATTAAAATATTAAAAT
1 -ATTAATATTTTAAAAT
3395539 ATTAATATTTTAAAAT
1 ATTAATATTTTAAAAT
*
3395555 ATTAATTTTTTA
1 ATTAATATTTTA
3395567 GAATTTATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
11 4 0.07
12 4 0.07
13 2 0.03
15 2 0.03
16 35 0.59
17 6 0.10
18 6 0.10
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (16 bp):
ATTAATATTTTAAAAT
Found at i:3399852 original size:30 final size:30
Alignment explanation
Indices: 3399796--3399852 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
3399786 AAAATCTATA
**
3399796 AATTTTTAAAAAACATAAAAGTAATTTGTT
1 AATTTTTAAAAAACATAAAAAAAATTTGTT
*
3399826 AATTTTTAAAAATTC-TAAAAAAAATTT
1 AATTTTTAAAAA-ACATAAAAAAAATTT
3399853 TAAAACCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 22 0.96
31 1 0.04
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (30 bp):
AATTTTTAAAAAACATAAAAAAAATTTGTT
Found at i:3403706 original size:141 final size:147
Alignment explanation
Indices: 3403431--3403715 Score: 411
Period size: 141 Copynumber: 2.0 Consensus size: 147
3403421 TGTCATTGAC
3403431 CTTTTTATGGTTTTTTCCCTTAAATTTTGACTTAAATTTTAAATATATATATATATATATAAATC
1 CTTTTTATGGTTTTTTCCCTTAAATTTTGACTTAAATTTT-AATATATATATATATATATAAATC
* * * * *
3403496 TAAAAATTGAAGGTGACAAAGAGCAAATGGAATCCAAAAACCCGTTCCAAAAAATAAAAATTCAC
65 TAAAAATTGAAGGTGACAAAGAACAAACGGAATCCAAAAACCCATTCCAAAAAATAAAAATCCAA
*
3403561 ACTTGAATTGACAATGAA
130 ACTTGAATAGACAATGAA
* * *
3403579 CTTTTTATGGTTTTTT-CTTTGAATTTTTACTTAAATTTT-A-A-AT-T-TATATATATAAATCT
1 CTTTTTATGGTTTTTTCCCTTAAATTTTGACTTAAATTTTAATATATATATATATATATAAATCT
* * *
3403638 AAAAATTGAAGGTGACAAAGAATAAACGGAATCCAAAAACCCATTCCAAAAACTGAAAATCCAAA
66 AAAAATTGAAGGTGACAAAGAACAAACGGAATCCAAAAACCCATTCCAAAAAATAAAAATCCAAA
3403703 CTTGAATAGACAA
131 CTTGAATAGACAA
3403716 GAAATTAGAG
Statistics
Matches: 125, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
141 84 0.67
142 1 0.01
143 2 0.02
144 1 0.01
145 1 0.01
147 20 0.16
148 16 0.13
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (147 bp):
CTTTTTATGGTTTTTTCCCTTAAATTTTGACTTAAATTTTAATATATATATATATATATAAATCT
AAAAATTGAAGGTGACAAAGAACAAACGGAATCCAAAAACCCATTCCAAAAAATAAAAATCCAAA
CTTGAATAGACAATGAA
Found at i:3406616 original size:15 final size:17
Alignment explanation
Indices: 3406585--3406616 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
3406575 ATGCAACCGA
3406585 TTTATAGTTCAATGTTT
1 TTTATAGTTCAATGTTT
3406602 TTTAT-GTTC-ATGTTT
1 TTTATAGTTCAATGTTT
3406617 CTTTCTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (17 bp):
TTTATAGTTCAATGTTT
Found at i:3409386 original size:36 final size:36
Alignment explanation
Indices: 3409346--3409423 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 36
3409336 GTTTTTGGTT
* *
3409346 AAGGTTATGCCTAAT-TCTATGAAAAGGCATGCTGTG
1 AAGGTTATGCCTAATCT-TATGAAAAGGCATGCTATA
* * *
3409382 AAGGTTATGCTTAATCTTGTGAAAATGCATGCTATA
1 AAGGTTATGCCTAATCTTATGAAAAGGCATGCTATA
3409418 AAGGTT
1 AAGGTT
3409424 GCACCCAATC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
36 35 0.97
37 1 0.03
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (36 bp):
AAGGTTATGCCTAATCTTATGAAAAGGCATGCTATA
Found at i:3411456 original size:10 final size:10
Alignment explanation
Indices: 3411441--3411465 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3411431 GAATGTTCTT
3411441 TTTCATGAAA
1 TTTCATGAAA
3411451 TTTCATGAAA
1 TTTCATGAAA
3411461 TTTCA
1 TTTCA
3411466 CCCATTCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (10 bp):
TTTCATGAAA
Found at i:3422887 original size:22 final size:20
Alignment explanation
Indices: 3422861--3422907 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
3422851 TTGGAGCATC
*
3422861 AATAAATATTTTTTTTAAATAT
1 AATAAATA-ATTTTTTAAAT-T
3422883 AAT-AATAATTTTTTAAATT
1 AATAAATAATTTTTTAAATT
3422902 AATAAA
1 AATAAA
3422908 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 4 0.17
20 12 0.52
21 4 0.17
22 3 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATAAATAATTTTTTAAATT
Found at i:3432431 original size:88 final size:88
Alignment explanation
Indices: 3432280--3432453 Score: 285
Period size: 88 Copynumber: 2.0 Consensus size: 88
3432270 ACTTGGAGAG
* * * *
3432280 AGTACATGAGTGCTTGTTAAGAAACAAATTTACTGAACAAGACTCGCTATGAGAGTTCCATTTGG
1 AGTACATGAGCGCTTGTTAAGAAACAAATTCACTGAACAAGACCCGCTATGAAAGTTCCATTTGG
*
3432345 TATTTCATTCAAGTGTCTATGAA
66 TATTTCACTCAAGTGTCTATGAA
* *
3432368 AGTACATGGGCGCTTGTTAAGAAACAAATTCACTGAACAAGACCCGCTATGAAAGTTCTATTTGG
1 AGTACATGAGCGCTTGTTAAGAAACAAATTCACTGAACAAGACCCGCTATGAAAGTTCCATTTGG
3432433 TATTTCACTCAAGTGTCTATG
66 TATTTCACTCAAGTGTCTATG
3432454 GAAATACTCT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 79 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (88 bp):
AGTACATGAGCGCTTGTTAAGAAACAAATTCACTGAACAAGACCCGCTATGAAAGTTCCATTTGG
TATTTCACTCAAGTGTCTATGAA
Found at i:3443220 original size:35 final size:35
Alignment explanation
Indices: 3443190--3443273 Score: 132
Period size: 35 Copynumber: 2.4 Consensus size: 35
3443180 GAGGTTATGT
*
3443190 CTGATCTTGCAAAAGGCAAGTTGTAAAGGTTACAC
1 CTGATCCTGCAAAAGGCAAGTTGTAAAGGTTACAC
*
3443225 CTGATCCTGCAAAAGGCAAGTTGTGAAGGTTACAC
1 CTGATCCTGCAAAAGGCAAGTTGTAAAGGTTACAC
**
3443260 CCAATCCTGCAAAA
1 CTGATCCTGCAAAA
3443274 AGAATACTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (35 bp):
CTGATCCTGCAAAAGGCAAGTTGTAAAGGTTACAC
Found at i:3445026 original size:16 final size:17
Alignment explanation
Indices: 3444993--3445026 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3444983 CATAAATCTA
3444993 AAATTTAACTAATAAAC
1 AAATTTAACTAATAAAC
*
3445010 AAATTTAA-TAATTAAC
1 AAATTTAACTAATAAAC
3445026 A
1 A
3445027 CTTATTATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATTTAACTAATAAAC
Found at i:3447842 original size:27 final size:26
Alignment explanation
Indices: 3447791--3447844 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
3447781 ATTAAAATTT
*
3447791 AATAATATAAAAATATTTTACTTAAAA
1 AATAATATAAAAATAATTTA-TTAAAA
3447818 AATAATATATAATAATAATTT-TTAAAA
1 AATAATATA-AA-AATAATTTATTAAAA
3447845 TTATTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 15 0.62
28 2 0.08
29 7 0.29
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
AATAATATAAAAATAATTTATTAAAA
Found at i:3448919 original size:9 final size:9
Alignment explanation
Indices: 3448891--3448920 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3448881 AACATGATAG
3448891 ATACAATTA
1 ATACAATTA
*
3448900 ACACAATTA
1 ATACAATTA
3448909 ATACAATTA
1 ATACAATTA
3448918 ATA
1 ATA
3448921 TGCTTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (9 bp):
ATACAATTA
Found at i:3460295 original size:22 final size:22
Alignment explanation
Indices: 3460270--3460314 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3460260 GTGAGTACTT
* *
3460270 GTCGGATAGTTAGGAGAGTTAA
1 GTCGGATAGTTAGCAAAGTTAA
*
3460292 GTCGGATGGTTAGCAAAGTTAA
1 GTCGGATAGTTAGCAAAGTTAA
3460314 G
1 G
3460315 GAATTGGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.07, G:0.36, T:0.27
Consensus pattern (22 bp):
GTCGGATAGTTAGCAAAGTTAA
Found at i:3463014 original size:18 final size:18
Alignment explanation
Indices: 3462987--3463022 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3462977 TTTGATATTT
*
3462987 TTCAACCCAAAAATACCA
1 TTCAACCCAAAAACACCA
*
3463005 TTCAATCCAAAAACACCA
1 TTCAACCCAAAAACACCA
3463023 CATCTGATGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (18 bp):
TTCAACCCAAAAACACCA
Found at i:3464001 original size:15 final size:15
Alignment explanation
Indices: 3463981--3464012 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3463971 TAATGTTATA
3463981 ATTAAAATAAAATAT
1 ATTAAAATAAAATAT
3463996 ATTAAAATAAAATAT
1 ATTAAAATAAAATAT
3464011 AT
1 AT
3464013 ACTATAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATTAAAATAAAATAT
Found at i:3464418 original size:15 final size:15
Alignment explanation
Indices: 3464387--3464420 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3464377 ATTTTTCCTG
* *
3464387 CAATCACATTGCTTA
1 CAATCACATTACCTA
3464402 CAATCACATTACCTA
1 CAATCACATTACCTA
3464417 CAAT
1 CAAT
3464421 TAGATAGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.29, G:0.03, T:0.29
Consensus pattern (15 bp):
CAATCACATTACCTA
Found at i:3465270 original size:25 final size:25
Alignment explanation
Indices: 3465236--3465294 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
3465226 AATAAAATCT
3465236 CTATAATTATGATAA-TTCTCAATTC
1 CTATAATTATGATAATTTCT-AATTC
* *
3465261 CTATAATTATGGTGATTTCTAATTC
1 CTATAATTATGATAATTTCTAATTC
*
3465286 TTATAATTA
1 CTATAATTA
3465295 CGTGTATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 26 0.87
26 4 0.13
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (25 bp):
CTATAATTATGATAATTTCTAATTC
Found at i:3466722 original size:154 final size:157
Alignment explanation
Indices: 3466552--3466844 Score: 441
Period size: 157 Copynumber: 1.9 Consensus size: 157
3466542 TTTAAATTAT
* *
3466552 AAATAAAATATTAATATTTAAA-TGACCAATTATTAATATTTT-AAATCAATTATAAATTATTAA
1 AAATAAAAAATTAATATTTAAACT-ACCAATTATTAATATTTTAAAATAAATTATAAATTATTAA
* **
3466615 TATATATAA-TAAAATAAAAT-AAAAATAAATAATCATAATAACATTTAAATTATAAATTAAATA
65 TATATAAAAGTAAAATAAAATAAAAAATAAATAATCATAATAACATTTAAATTATAAAAAAAATA
*
3466678 TTATTATTTTTAATATTAATGATTAAAA
130 TTAATATTTTTAATATTAATGATTAAAA
* *
3466706 AAATAAAAAATTAATATTTAAACTACTAATTTTTAATATTTTAAAATAAATTATAAATTATTAAT
1 AAATAAAAAATTAATATTTAAACTACCAATTATTAATATTTTAAAATAAATTATAAATTATTAAT
* ** *
3466771 ATTTAAAAGTAAAATAACTTAAAAAATAAATAATCATAATAACATTTCAATTATAAAAAAAATAT
66 ATATAAAAGTAAAATAAAATAAAAAATAAATAATCATAATAACATTTAAATTATAAAAAAAATAT
3466836 TAATATTTT
131 TAATATTTT
3466845 ATAGTGTAAA
Statistics
Matches: 123, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
154 37 0.30
155 28 0.23
156 9 0.07
157 49 0.40
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.40
Consensus pattern (157 bp):
AAATAAAAAATTAATATTTAAACTACCAATTATTAATATTTTAAAATAAATTATAAATTATTAAT
ATATAAAAGTAAAATAAAATAAAAAATAAATAATCATAATAACATTTAAATTATAAAAAAAATAT
TAATATTTTTAATATTAATGATTAAAA
Found at i:3466869 original size:157 final size:154
Alignment explanation
Indices: 3466552--3466888 Score: 433
Period size: 157 Copynumber: 2.1 Consensus size: 154
3466542 TTTAAATTAT
* *
3466552 AAATAAAATATTAATATTTAAATGACCAATTATTAATATTTTAAATCAATTATAAATTATTAATA
1 AAATAAAAAATTAATATTTAAATGACCAATTATTAATATTTTAAATAAATTATAAATTATTAATA
* ** *
3466617 TATATAATAAAATAAAATAAAAATAAATAATCATAATAACATTTAAATTATAAATTAAATATTAT
66 TATAAAATAAAATAAAATAAAAATAAATAATCATAATAACATTTAAATTATAAAAAAAATATTAA
*
3466682 TATTTTTAATATTAATGATTAAAA
131 TATTTTTAATATAAATGATTAAAA
* *
3466706 AAATAAAAAATTAATATTTAAACT-ACTAATTTTTAATATTTTAAAATAAATTATAAATTATTAA
1 AAATAAAAAATTAATATTTAAA-TGACCAATTATTAATATTTT-AAATAAATTATAAATTATTAA
* ** *
3466770 TATTTAAAAGTAAAATAACTTAAAAAATAAATAATCATAATAACATTTCAATTATAAAAAAAATA
64 TATATAAAA-TAAAATAAAAT-AAAAATAAATAATCATAATAACATTTAAATTATAAAAAAAATA
* * * *
3466835 TTAATATTTTATAGTGTAAATGATTAGCTTAT
127 TTAATATTTT-TAATATAAATGATTA---AAA
*
3466867 AAATAAAATATTAATATTTAAA
1 AAATAAAAAATTAATATTTAAA
3466889 AAATAAAATA
Statistics
Matches: 157, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
154 37 0.24
155 28 0.18
156 9 0.06
157 49 0.31
158 12 0.08
161 22 0.14
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (154 bp):
AAATAAAAAATTAATATTTAAATGACCAATTATTAATATTTTAAATAAATTATAAATTATTAATA
TATAAAATAAAATAAAATAAAAATAAATAATCATAATAACATTTAAATTATAAAAAAAATATTAA
TATTTTTAATATAAATGATTAAAA
Found at i:3471436 original size:8 final size:8
Alignment explanation
Indices: 3471423--3471448 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3471413 TTTTATGGGA
3471423 TTTTCTTC
1 TTTTCTTC
3471431 TTTTCTTC
1 TTTTCTTC
3471439 TTTTCTTC
1 TTTTCTTC
3471447 TT
1 TT
3471449 CAGATTGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTCTTC
Found at i:3475897 original size:22 final size:22
Alignment explanation
Indices: 3475866--3475907 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3475856 ATTAAAATTT
*
3475866 TTATTTATAAATTA-AATAAATG
1 TTATTAAT-AATTATAATAAATG
3475888 TTATTAATAATTATAATAAA
1 TTATTAATAATTATAATAAA
3475908 AAAATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TTATTAATAATTATAATAAATG
Found at i:3479237 original size:2 final size:2
Alignment explanation
Indices: 3479230--3479258 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3479220 GAAAATGAAA
3479230 AT 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 AT A
3479259 AATGCTCTAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3480444 original size:494 final size:495
Alignment explanation
Indices: 3479581--3481246 Score: 1453
Period size: 494 Copynumber: 3.4 Consensus size: 495
3479571 TTACCTATTT
* * * * * ** * *
3479581 CATCTTTATAAGTTTTCACGTTAATTCTTACAGGTTTAAATTAAGGTTTTTCAACTACCT-ATTT
1 CATCTTAATAAGTTTTTACATTAATTC-AACAAGTTTATGTCAAGATTTTTCAACTA-CTAATTT
* * * * * * *
3479645 TCATTATAATAATTTTTATATTTACTATTATTCATTTATAAATTAAAATTTGTAAATCGTTATA-
64 TCACTATAATTATTTTTATAATTACTATTATTCATTTAAAAATTAAAATTTGTAAACCGTGAGAC
* * * * * *
3479709 A-TTTAAATTTAAGAATATAAATTTAAATATTTAATTTTTTAAAAAATTATATTTATTTGATTTA
129 ACTTTAAACTCAAGAATATAAATTTAAATATTTAA-TTTTTAAAAAAAT-TATGT-TTTAACTT-
* * * *** * * * * *
3479773 ATTAACTTATTACATTAAAT-TC-CATAGGTTTGCGTTAATGTTTTGATAGTGGTTATT-T-T-T
190 ATTAACGTGTTACATTAAATCTCACACA--TTTATATCAATATTTTGACATTGATTATTCTATAT
** * * * * * * *
3479833 TTATAAGTTTTTACGTTAATTTTTATAAGTTTAAATTAAAGTTTTTTAACTACTAATTTTTACTA
253 TTATAAAATTTTACATTAATTCTTACAA--AT-AGTGAAAGTTTTTTAAATACTAATTTTTACTA
* * *
3479898 TAATTATTTTTATCTTTAC-AGCTATTCATTTATAAGTTAAAGTTTGTAAACCGTTAAACACTTT
315 TAATTATTTTTATCTTTACTA-TTATTCATTTATAAATTAAAATTTGTAAACCGTTAAACACTTT
*
3479962 AAACTTGAAAATATAAATTTAAATATTTATTTTTTCTAAAAATAATATTTATTTGACTTAATTGA
379 AAACTTGAAAATATAAATTTAAATATTTA-TTTTTCTAAAAATTATATTTATTTGACTTAATTGA
* *
3480027 CTTGTTACATTAAATCTCATA-AGTTTACGTTAATATTTTGAC-GTTGCTTGTTC
443 CTTGTTACATTAAATCTCATATA-TTTACGTCAATATTTTAACAG-TGCTTGTTC
* * * * *
3480080 CCTCTTAATAAGTTTTTACATTAAATT-AATAAGTTTATGTTAAGATTTTTTAACTACTAGTTTT
1 CATCTTAATAAGTTTTTACATT-AATTCAACAAGTTTATGTCAAGATTTTTCAACTACTAATTTT
*** * * ** *
3480144 TGTTATAATTCTTTTTATATTTACTATTATTTGTTTAAAAATTAAAAATTTGT-AACCGTTAGAC
65 CACTATAATTATTTTTATAATTACTATTATTCATTTAAAAATT-AAAATTTGTAAACCGTGAGAC
* * **
3480208 ACTTTAAACTTAAGAATATAAATTTAAATGTTTAATTTCTT-AAAAGTTTATG-TTT-A-TT-TT
129 ACTTTAAACTCAAGAATATAAATTTAAATATTTAATTT-TTAAAAAAATTATGTTTTAACTTATT
* * *
3480268 -ACGTGTTACGTTAAGTCTCACA-AGTTTATATCAATATTTTGACATTGATTGTT-TCACT-TTT
193 AACGTGTTACATTAAATCTCACACA-TTTATATCAATATTTTGACATTGATTATTCT-A-TATTT
* * ** * * * * * *
3480329 ATAAAATTTTACGTTCATTCTTGTAAGT-TTGCATCCAGGTTTTTTAATTATTAATTTTTATTAT
255 ATAAAATTTTACATTAATTCTTACAAATAGTG-A---AAGTTTTTTAAATACTAATTTTTACTAT
* * *
3480393 AATTATCTTTATCTTTACTATTATTCATTTATAAATTAAAATTTATAAACCGTTAAATACTTTAA
316 AATTATTTTTATCTTTACTATTATTCATTTATAAATTAAAATTTGTAAACCGTTAAACACTTTAA
* * *
3480458 A-TTCTATAATATAAATTTAAATATTTAATTTTCTAAAAAATTATATTTATTTGACTTAATTGAC
381 ACTT-GAAAATATAAATTTAAATATTTATTTTTCT-AAAAATTATATTTATTTGACTTAATTGAC
** * * *
3480522 TTGTTAGGTTAAATCTCACATATTTATGTCAATATTTTAACAGTGTTTGTTC
444 TTGTTACATTAAATCTCATATATTTACGTCAATATTTTAACAGTGCTTGTTC
* * *
3480574 CATCTTTATAAGTTTTTACATTAATTCCTACAAGTTTATGTCAAGGTTTTTCAACTACTAATTTT
1 CATCTTAATAAGTTTTTACATTAATT-CAACAAGTTTATGTCAAGATTTTTCAACTACTAATTTT
* *
3480639 CACTATAATTATTTTTATAATTACTATTATTCATTTATAAATTAAAATTTGTAAACCGTGATACA
65 CACTATAATTATTTTTATAATTACTATTATTCATTTAAAAATTAAAATTTGTAAACCGTGAGACA
*
3480704 CTTTAAACTCGAGAATATAAATTTAAATATTTAATTTTTAAAAAAATTATGTTTATTTAACTTAA
130 CTTTAAACTCAAGAATATAAATTTAAATATTTAATTTTTAAAAAAATTATG--T-TTTAACTT-A
* * * * * *
3480769 TTAACTTGTTATATTAAATCTCACACATTTATGTCAATGTTTTGATATTGCTTATTCTATATTTA
191 TTAACGTGTTACATTAAATCTCACACATTTATATCAATATTTTGACATTGATTATTCTATATTTA
** *
3480834 TAAGTTTTTACATTAATTCTTACAAATAGTGAAAGTTTTTCAAATACTAATGTTTT-CTATAATT
256 TAAAATTTTACATTAATTCTTACAAATAGTGAAAGTTTTTTAAATACTAAT-TTTTACTATAATT
* * * **
3480898 ATTTTTATCCTTACTATCATT-AGTTTACAAATTAAAATTTGTAAATAGTTAAACACTTTAAACT
320 ATTTTTATCTTTACTATTATTCA-TTTATAAATTAAAATTTGTAAACCGTTAAACACTTTAAACT
* * * * * *
3480962 TGAGAATATAAATTTCAATGTTTAATTTCTCAAAAAATTATATTTATTTGA-TGAATTGACTTGT
384 TGAAAATATAAATTTAAATATTT-ATTTTTCTAAAAATTATATTTATTTGACTTAATTGACTTGT
* ** * * * * *
3481026 TATATTAAATCTCATGCATTTACGTCAATATCTAAACATTGCTTATTT
448 TACATTAAATCTCATATATTTACGTCAATATTTTAACAGTGCTTGTTC
* * ** * * * * *
3481074 CTTCTTTATAAG-TTTT---TTCGTT--AC---TTTATGTTAAAAATTTTCAATTACTAATTTCC
1 CATCTTAATAAGTTTTTACATTAATTCAACAAGTTTATGTCAAGATTTTTCAACTACTAATTTTC
** * * * * *
3481130 ACTATAATT-TTTTTATCCTTACTATTATTCATTTATAAATTAAAGTTTATAAACCGTTAAACAC
66 ACTATAATTATTTTTATAATTACTATTATTCATTTAAAAATTAAAATTTGTAAACCGTGAGACAC
* ** * * *
3481194 TTTAAACTCGAGTTTATAAAATTAAATATTTAATATTTCAAAAAATTATGTTT
131 TTTAAACTCAAGAATATAAATTTAAATATTTAATTTTTAAAAAAATTATGTTT
3481247 ATTTGACTTA
Statistics
Matches: 966, Mismatches: 160, Indels: 95
0.79 0.13 0.08
Matches are distributed among these distances:
486 2 0.00
487 1 0.00
489 94 0.10
490 36 0.04
491 35 0.04
492 6 0.01
493 16 0.02
494 230 0.24
495 123 0.13
496 7 0.01
497 2 0.00
498 73 0.08
499 44 0.05
500 98 0.10
501 113 0.12
502 11 0.01
503 3 0.00
504 68 0.07
505 4 0.00
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.48
Consensus pattern (495 bp):
CATCTTAATAAGTTTTTACATTAATTCAACAAGTTTATGTCAAGATTTTTCAACTACTAATTTTC
ACTATAATTATTTTTATAATTACTATTATTCATTTAAAAATTAAAATTTGTAAACCGTGAGACAC
TTTAAACTCAAGAATATAAATTTAAATATTTAATTTTTAAAAAAATTATGTTTTAACTTATTAAC
GTGTTACATTAAATCTCACACATTTATATCAATATTTTGACATTGATTATTCTATATTTATAAAA
TTTTACATTAATTCTTACAAATAGTGAAAGTTTTTTAAATACTAATTTTTACTATAATTATTTTT
ATCTTTACTATTATTCATTTATAAATTAAAATTTGTAAACCGTTAAACACTTTAAACTTGAAAAT
ATAAATTTAAATATTTATTTTTCTAAAAATTATATTTATTTGACTTAATTGACTTGTTACATTAA
ATCTCATATATTTACGTCAATATTTTAACAGTGCTTGTTC
Found at i:3480665 original size:21 final size:21
Alignment explanation
Indices: 3480640--3480682 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3480630 ACTAATTTTC
*
3480640 ACTATAATT-ATTTTTATAATT
1 ACTATAATTCATTTATA-AATT
*
3480661 ACTATTATTCATTTATAAATT
1 ACTATAATTCATTTATAAATT
3480682 A
1 A
3480683 AAATTTGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (21 bp):
ACTATAATTCATTTATAAATT
Found at i:3480665 original size:252 final size:251
Alignment explanation
Indices: 3479525--3481264 Score: 1524
Period size: 252 Copynumber: 7.0 Consensus size: 251
3479515 TTTATTATCA
* * * * * * * *
3479525 TAACTTGTTACGTTGAATCTCACAAGTTTACATCAATATTTTGATATTACCTATTTCATCTTTAT
1 TAACTTGTTACATTAAATCTCACAAGTTTACGTCAATATTTTGACAGTGCTTATTCCATCTTTAT
* * * ** *
3479590 AAGTTTTCACGTTAATTCTTACAGGTTTAAATTAAGGTTTTTCAACTACCT-ATTTTCATTATAA
66 AAGTTTTTACATTAATTCTTACAAGTTTATGTTAAGGTTTTTCAACTA-CTAATTTTCACTATAA
* * * *
3479654 TAATTTTTATATTTACTATTATTCATTTATAAATTAAAATTTGTAAATCGTTATA-A-TTTAAAT
130 TTATTTTTATCTTTACTATTATTCATTTATAAATTAAAATTTGTAAACCGTTAAACACTTTAAA-
* * *
3479717 TTAAGAATATAAATTTAAATATTTAATTTTTTAAAAAATTATATTTATTTGATTTAAT
194 TTGAGAATATAAATTTAAATATTTAATTTTCTAAAAAATTATATTTATTTGACTTAAT
* * * * * * *
3479775 TAACTTATTACATTAAAT-TC-CATAGGTTTGCGTTAATGTTTTGATAGTGGTTATT---TTTTT
1 TAACTTGTTACATTAAATCTCACA-A-GTTTACGTCAATATTTTGACAGTGCTTATTCCATCTTT
* * * ** * * *
3479835 ATAAGTTTTTACGTTAATTTTTATAAGTTTAAATTAAAGTTTTTTAACTACTAATTTTTACTATA
64 ATAAGTTTTTACATTAATTCTTACAAGTTTATGTTAAGGTTTTTCAACTACTAATTTTCACTATA
* * *
3479900 ATTATTTTTATCTTTAC-AGCTATTCATTTATAAGTTAAAGTTTGTAAACCGTTAAACACTTTAA
129 ATTATTTTTATCTTTACTA-TTATTCATTTATAAATTAAAATTTGTAAACCGTTAAACACTTTAA
* * *
3479964 ACTTGAAAATATAAATTTAAATATTTATTTTTTCT-AAAAATAATATTTATTTGACTTAAT
193 A-TTGAGAATATAAATTTAAATATTTA-ATTTTCTAAAAAATTATATTTATTTGACTTAAT
* * * * * *
3480024 TGACTTGTTACATTAAATCTCATAAGTTTACGTTAATATTTTGAC-GTTGCTTGTTCCCTCTTAA
1 TAACTTGTTACATTAAATCTCACAAGTTTACGTCAATATTTTGACAG-TGCTTATTCCATCTTTA
* * * * * * ***
3480088 TAAGTTTTTACATTAAAT-TAATAAGTTTATGTTAAGATTTTTTAACTACTAGTTTTTGTTATAA
65 TAAGTTTTTACATTAATTCTTACAAGTTTATGTTAAGGTTTTTCAACTACTAATTTTCACTATAA
* * ** * *
3480152 TTCTTTTTATATTTACTATTATTTGTTTAAAAATTAAAAATTTGT-AACCGTTAGACACTTTAAA
130 TTATTTTTATCTTTACTATTATTCATTTATAAATT-AAAATTTGTAAACCGTTAAACACTTTAAA
* * * * *
3480216 CTTAAGAATATAAATTTAAATGTTTAA-TTTCTTAAAAGTT-TA--TGTTT-A-TT--T
194 -TTGAGAATATAAATTTAAATATTTAATTTTCTAAAAAATTATATTTATTTGACTTAAT
* * * ** * * * *
3480267 T-ACGTGTTACGTTAAGTCTCACAAGTTTATATCAATATTTTGACATTGATTGTTTCA-CTTTTA
1 TAACTTGTTACATTAAATCTCACAAGTTTACGTCAATATTTTGACAGTGCTTATTCCATC-TTTA
** * * ** *** ** * * * * *
3480330 TAAAATTTTACGTTCATTCTTGTAAGTTTGCATCCAGGTTTTTTAATTATTAATTTTTATTATAA
65 TAAGTTTTTACATTAATTCTTACAAGTTTATGTTAAGGTTTTTCAACTACTAATTTTCACTATAA
* * *
3480395 TTATCTTTATCTTTACTATTATTCATTTATAAATTAAAATTTATAAACCGTTAAATACTTTAAAT
130 TTATTTTTATCTTTACTATTATTCATTTATAAATTAAAATTTGTAAACCGTTAAACACTTTAAAT
* *
3480460 TCTATAATATAAATTTAAATATTTAATTTTCTAAAAAATTATATTTATTTGACTTAAT
195 T-GAGAATATAAATTTAAATATTTAATTTTCTAAAAAATTATATTTATTTGACTTAAT
* ** * * * *
3480518 TGACTTGTTAGGTTAAATCTCACATA-TTTATGTCAATATTTTAACAGTGTTTGTTCCATCTTTA
1 TAACTTGTTACATTAAATCTCACA-AGTTTACGTCAATATTTTGACAGTGCTTATTCCATCTTTA
* *
3480582 TAAGTTTTTACATTAATTCCTACAAGTTTATGTCAAGGTTTTTCAACTACTAATTTTCACTATAA
65 TAAGTTTTTACATTAATTCTTACAAGTTTATGTTAAGGTTTTTCAACTACTAATTTTCACTATAA
** * *
3480647 TTATTTTTATAATTACTATTATTCATTTATAAATTAAAATTTGTAAACCGTGATACACTTTAAAC
130 TTATTTTTATCTTTACTATTATTCATTTATAAATTAAAATTTGTAAACCGTTAAACACTTTAAA-
* * *
3480712 TCGAGAATATAAATTTAAATATTTAATTTT-TAAAAAAATTATGTTTATTTAACTTAAT
194 TTGAGAATATAAATTTAAATATTTAATTTTCT-AAAAAATTATATTTATTTGACTTAAT
* * * * * * *
3480770 TAACTTGTTATATTAAATCTCACACA-TTTATGTCAATGTTTTGATATTGCTTATTCTATATTTA
1 TAACTTGTTACATTAAATCTCACA-AGTTTACGTCAATATTTTGACAGTGCTTATTCCATCTTTA
* * * * *
3480834 TAAGTTTTTACATTAATTCTTACAA--ATA-GTGAAAGTTTTTCAAATACTAATGTTT-TCTATA
65 TAAGTTTTTACATTAATTCTTACAAGTTTATGTTAAGGTTTTTCAACTACTAAT-TTTCACTATA
* * * **
3480895 ATTATTTTTATCCTTACTATCATT-AGTTTACAAATTAAAATTTGTAAATAGTTAAACACTTTAA
129 ATTATTTTTATCTTTACTATTATTCA-TTTATAAATTAAAATTTGTAAACCGTTAAACACTTTAA
* * *
3480959 ACTTGAGAATATAAATTTCAATGTTTAA-TTTCTCAAAAAATTATATTTATTTGA-TGAAT
193 A-TTGAGAATATAAATTTAAATATTTAATTTTCT-AAAAAATTATATTTATTTGACTTAAT
* * * ** * * *
3481018 TGACTTGTTATATTAAATCTCATGC-A-TTTACGTCAATATCTAAACATTGCTTATTTCTTCTTT
1 TAACTTGTTACATTAAATCTCA--CAAGTTTACGTCAATATTTTGACAGTGCTTATTCCATCTTT
*** * *
3481081 ATAAG---TT---TT--TTCGTTAC---TTTATGTTAAAAATTTTCAATTACTAATTTCCACTAT
64 ATAAGTTTTTACATTAATTC-TTACAAGTTTATGTTAAGGTTTTTCAACTACTAATTTTCACTAT
* * *
3481135 AATT-TTTTTATCCTTACTATTATTCATTTATAAATTAAAGTTTATAAACCGTTAAACACTTTAA
128 AATTATTTTTATCTTTACTATTATTCATTTATAAATTAAAATTTGTAAACCGTTAAACACTTTAA
* ** * *
3481199 ACTCGAGTTTATAAAATTAAATATTTAATATTTC-AAAAAATTATGTTTATTTGACTTAAT
193 A-TTGAGAATATAAATTTAAATATTTAAT-TTTCTAAAAAATTATATTTATTTGACTTAAT
3481259 TAACTT
1 TAACTT
3481265 CTTATGTTAA
Statistics
Matches: 1227, Mismatches: 216, Indels: 103
0.79 0.14 0.07
Matches are distributed among these distances:
240 100 0.08
241 42 0.03
242 76 0.06
243 103 0.08
244 11 0.01
245 6 0.00
246 4 0.00
247 113 0.09
248 67 0.05
249 226 0.18
250 56 0.05
251 109 0.09
252 311 0.25
253 3 0.00
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.48
Consensus pattern (251 bp):
TAACTTGTTACATTAAATCTCACAAGTTTACGTCAATATTTTGACAGTGCTTATTCCATCTTTAT
AAGTTTTTACATTAATTCTTACAAGTTTATGTTAAGGTTTTTCAACTACTAATTTTCACTATAAT
TATTTTTATCTTTACTATTATTCATTTATAAATTAAAATTTGTAAACCGTTAAACACTTTAAATT
GAGAATATAAATTTAAATATTTAATTTTCTAAAAAATTATATTTATTTGACTTAAT
Found at i:3480839 original size:746 final size:738
Alignment explanation
Indices: 3479641--3481010 Score: 1766
Period size: 746 Copynumber: 1.8 Consensus size: 738
3479631 TCAACTACCT
* * *
3479641 ATTTTCATTATAATAATTTTTATATTTACTATTATTCATTTATAAATTAAAATTTGTAAATCGTT
1 ATTTTCATTATAATAATCTTTATATTTACTATTATTCATTTATAAATTAAAATTTATAAACCGTT
* *
3479706 ATAATTTAAATTTAAGAATATAAATTTAAATATTTAATTTTTTAAAAAATTATATTTATTTGATT
66 ATAATTTAAATTTAAGAATATAAATTTAAATATTTAATTTTCTAAAAAATTATATTTATTTGACT
* * * * * *
3479771 TAATTAACTTATTACATTAAATTCCATAGGTTTGCGTTAATGTTTTGATAGTGGTTATTTTTTTA
131 TAATTAACTTATTACATTAAATTCCATA-GTTTACGTCAATATTTTAACAGTGGTTATTTCTTTA
* ** * * * *
3479836 TAAGTTTTTACGTTAATTTTTATAAGTTTAAATTAAAGTTTTTTAACTACTAATTTTTACTATAA
195 TAAGTTTTTACATTAATTCCTACAAGTTTAAATCAAAGTTTTTCAACTACTAATTTTCACTATAA
** * * *
3479901 TTATTTTTATCTTTACAGCTATTCATTTATAAGTTAAAGTTTGTAAACCGTTAAACACTTTAAAC
260 TTATTTTTATAATTACAGCTATTCATTTATAAATTAAAATTTGTAAACCGTGAAACACTTTAAAC
* * ** * *
3479966 TTGAAAATATAAATTTAAATATTTATTTTTTCTAAAAATAATATTTATTTGACTTAATTGACTTG
325 TCGAAAATATAAATTTAAATATTTAATTTTTAAAAAAATAATATTTATTTAACTTAATTAACTTG
* * * * * *
3480031 TTACATTAAATCTCATAAGTTTACGTTAATATTTTGACGTTGCTTGTTCCCTCTTAATAAGTTTT
390 TTACATTAAATCTCACAAGTTTACGTCAATATTTTGACATTGCTTATTCCATATTAATAAGTTTT
** * * * * * *
3480096 TACATTAAATTAATA-AGTTTA-TGTTAAGATTTTTTAACTACTAGT-TTTTGTTATAATTCTTT
455 TACATT-AATTAATACA-AATAGTG-AAAG-TTTTTCAAATACTAATGTTTT-CTATAATTATTT
* * * * *
3480158 TTATATTTACTATTATTTGTTTAAAAATTAAAAATTTGT-AACCGTTAGACACTTTAAACTTAAG
515 TTATACTTACTATCATTAGTTTAAAAATT-AAAATTTGTAAACAGTTAAACACTTTAAACTTAAG
* ** *
3480222 AATATAAATTTAAATGTTTAATTTCTTAAAAGTTTATGTTTATTTTACGTGTTACGTTAAGTCTC
579 AATATAAATTTAAATGTTTAATTTCTCAAAAAATTATATTTATTTTACGTGTTACGTTAAGTCTC
3480287 ACAAGTTTATATCAATATTTTGACATTGATTGTTTCACTTTTATAAAATTTTACGTTCATTCTTG
644 ACAAGTTTATATCAATATTTTGACATTGATTGTTTCACTTTTATAAAATTTTACGTTCATTCTTG
3480352 TAAGTTTGCATCCAGGTTTTTTAATTATTA
709 TAAGTTTGCATCCAGGTTTTTTAATTATTA
* * *
3480382 ATTTTTATTATAATTATCTTTATCTTTACTATTATTCATTTATAAATTAAAATTTATAAACCGTT
1 ATTTTCATTATAATAATCTTTATATTTACTATTATTCATTTATAAATTAAAATTTATAAACCGTT
* *
3480447 AAATACTTTAAATTCT-ATAATATAAATTTAAATATTTAATTTTCTAAAAAATTATATTTATTTG
66 --ATAATTTAAATT-TAAGAATATAAATTTAAATATTTAATTTTCTAAAAAATTATATTTATTTG
* * ** * * *
3480511 ACTTAATTGACTTGTTAGGTTAAATCTCACATA-TTTATGTCAATATTTTAACAGTGTTTGTTCC
128 ACTTAATTAACTTATTACATTAAAT-TC-CATAGTTTACGTCAATATTTTAACAGTGGTTATT--
** *
3480575 ATCTTTATAAGTTTTTACATTAATTCCTACAAGTTTATGTCAAGGTTTTTCAACTACTAATTTTC
189 -TCTTTATAAGTTTTTACATTAATTCCTACAAGTTTAAATCAAAGTTTTTCAACTACTAATTTTC
* *
3480640 ACTATAATTATTTTTATAATTACTA-TTATTCATTTATAAATTAAAATTTGTAAACCGTGATACA
253 ACTATAATTATTTTTATAATTAC-AGCTATTCATTTATAAATTAAAATTTGTAAACCGTGAAACA
* * *
3480704 CTTTAAACTCGAGAATATAAATTTAAATATTTAATTTTTAAAAAAATTATGTTTATTTAACTTAA
317 CTTTAAACTCGAAAATATAAATTTAAATATTTAATTTTTAAAAAAATAATATTTATTTAACTTAA
* * * * * *
3480769 TTAACTTGTTATATTAAATCTCACACA-TTTATGTCAATGTTTTGATATTGCTTATTCTATATTT
382 TTAACTTGTTACATTAAATCTCACA-AGTTTACGTCAATATTTTGACATTGCTTATTCCATATTA
**
3480833 ATAAGTTTTTACATTAATTCTTACAAATAGTGAAAGTTTTTCAAATACTAATGTTTTCTATAATT
446 ATAAGTTTTTACATTAATTAATACAAATAGTGAAAGTTTTTCAAATACTAATGTTTTCTATAATT
* * *
3480898 ATTTTTATCCTTACTATCATTAGTTTACAAATTAAAATTTGTAAATAGTTAAACACTTTAAACTT
511 ATTTTTATACTTACTATCATTAGTTTAAAAATTAAAATTTGTAAACAGTTAAACACTTTAAACTT
* *
3480963 GAGAATATAAATTTCAATGTTTAATTTCTCAAAAAATTATATTTATTT
576 AAGAATATAAATTTAAATGTTTAATTTCTCAAAAAATTATATTTATTT
3481011 GATGAATTGA
Statistics
Matches: 530, Mismatches: 85, Indels: 25
0.83 0.13 0.04
Matches are distributed among these distances:
741 59 0.11
743 107 0.20
744 111 0.21
745 19 0.04
746 232 0.44
747 2 0.00
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (738 bp):
ATTTTCATTATAATAATCTTTATATTTACTATTATTCATTTATAAATTAAAATTTATAAACCGTT
ATAATTTAAATTTAAGAATATAAATTTAAATATTTAATTTTCTAAAAAATTATATTTATTTGACT
TAATTAACTTATTACATTAAATTCCATAGTTTACGTCAATATTTTAACAGTGGTTATTTCTTTAT
AAGTTTTTACATTAATTCCTACAAGTTTAAATCAAAGTTTTTCAACTACTAATTTTCACTATAAT
TATTTTTATAATTACAGCTATTCATTTATAAATTAAAATTTGTAAACCGTGAAACACTTTAAACT
CGAAAATATAAATTTAAATATTTAATTTTTAAAAAAATAATATTTATTTAACTTAATTAACTTGT
TACATTAAATCTCACAAGTTTACGTCAATATTTTGACATTGCTTATTCCATATTAATAAGTTTTT
ACATTAATTAATACAAATAGTGAAAGTTTTTCAAATACTAATGTTTTCTATAATTATTTTTATAC
TTACTATCATTAGTTTAAAAATTAAAATTTGTAAACAGTTAAACACTTTAAACTTAAGAATATAA
ATTTAAATGTTTAATTTCTCAAAAAATTATATTTATTTTACGTGTTACGTTAAGTCTCACAAGTT
TATATCAATATTTTGACATTGATTGTTTCACTTTTATAAAATTTTACGTTCATTCTTGTAAGTTT
GCATCCAGGTTTTTTAATTATTA
Found at i:3482901 original size:32 final size:33
Alignment explanation
Indices: 3482865--3482937 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 33
3482855 TTGAAAATCT
3482865 AATATTTTCTATTATTTAGATAAAC-TATCAAA
1 AATATTTTCTATTATTTAGATAAACTTATCAAA
* * * * * *
3482897 AATATTTGCTATTGTTTGGATTATCTTATGAAA
1 AATATTTTCTATTATTTAGATAAACTTATCAAA
3482930 AATATTTT
1 AATATTTT
3482938 TCAGTATTCA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
32 20 0.61
33 13 0.39
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (33 bp):
AATATTTTCTATTATTTAGATAAACTTATCAAA
Found at i:3483889 original size:18 final size:18
Alignment explanation
Indices: 3483866--3483900 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3483856 TTTTGATAGA
3483866 AAAAAAAAAGAAAGAAAG
1 AAAAAAAAAGAAAGAAAG
*
3483884 AAAAAAAAAGGAAGAAA
1 AAAAAAAAAGAAAGAAA
3483901 AAGTTTTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAGAAAGAAAG
Found at i:3483893 original size:14 final size:15
Alignment explanation
Indices: 3483863--3483902 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
3483853 CAATTTTGAT
*
3483863 AGAAAAAAAAAAGAA
1 AGAAAGAAAAAAGAA
3483878 AGAAAGAAAAAA-AA
1 AGAAAGAAAAAAGAA
*
3483892 AGGAAGAAAAA
1 AGAAAGAAAAA
3483903 GTTTTGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AGAAAGAAAAAAGAA
Found at i:3494688 original size:19 final size:19
Alignment explanation
Indices: 3494664--3494708 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
3494654 TGACTACTTA
3494664 CTTGCCAAAGGATTTTATT
1 CTTGCCAAAGGATTTTATT
** *
3494683 CTTGCCACTGGATTTTGTT
1 CTTGCCAAAGGATTTTATT
3494702 CTTGCCA
1 CTTGCCA
3494709 CTCTTGTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (19 bp):
CTTGCCAAAGGATTTTATT
Found at i:3494709 original size:19 final size:19
Alignment explanation
Indices: 3494673--3494710 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3494663 ACTTGCCAAA
3494673 GGATTTTATTCTTGCCACT
1 GGATTTTATTCTTGCCACT
*
3494692 GGATTTTGTTCTTGCCACT
1 GGATTTTATTCTTGCCACT
3494711 CTTGTTTGTG
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:0.13, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
GGATTTTATTCTTGCCACT
Found at i:3495462 original size:3 final size:3
Alignment explanation
Indices: 3495454--3495490 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
3495444 AATTTTACCT
*
3495454 TTA TTA TTA TTA TTA TGA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3495491 CACGCACATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3508109 original size:12 final size:12
Alignment explanation
Indices: 3508094--3508159 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 12
3508084 TAACATGAGA
*
3508094 ATATACATATAC
1 ATATATATATAC
* *
3508106 ATATACATACAC
1 ATATATATATAC
* *
3508118 ATACATACATAC
1 ATATATATATAC
* *
3508130 ATACATACATAC
1 ATATATATATAC
*
3508142 ATATATATATAT
1 ATATATATATAC
3508154 ATATAT
1 ATATAT
3508160 GTACACTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (12 bp):
ATATATATATAC
Found at i:3508121 original size:16 final size:16
Alignment explanation
Indices: 3508096--3508146 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 16
3508086 ACATGAGAAT
*
3508096 ATACATATACATATAC
1 ATACACATACATATAC
3508112 ATACACATACATACATAC
1 ATACACATACAT--ATAC
3508130 ATACATACATACATATA
1 ATAC--ACATACATATA
3508147 TATATATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 11 0.37
18 11 0.37
20 8 0.27
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (16 bp):
ATACACATACATATAC
Found at i:3508123 original size:4 final size:4
Alignment explanation
Indices: 3508108--3508144 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
3508098 ACATATACAT
3508108 ATAC ATAC --AC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
3508145 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
4 29 0.94
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:3510641 original size:71 final size:71
Alignment explanation
Indices: 3510513--3510651 Score: 170
Period size: 71 Copynumber: 2.0 Consensus size: 71
3510503 ATTATATAAA
* * * * *
3510513 TGCTCAAATCAAATCAGTAGATTGTAAGAAAAGTTAAAGTAAAAAACCATACCCTTTAGACAGTT
1 TGCTCAAATCAAATCAATAGATTGTAAGAAAAATCAAAATAAAAAACCATACCCTTTAGACAATT
3510578 AAGAAG
66 AAGAAG
** *** * *
3510584 TGCTCAAATTGAATCAATAGATTGTAAGAAAAATCAAAATAAAAAGTTATACTCTTTAGGCAATT
1 TGCTCAAATCAAATCAATAGATTGTAAGAAAAATCAAAATAAAAAACCATACCCTTTAGACAATT
3510649 AAG
66 AAG
3510652 GTCATTAAGC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
71 56 1.00
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.27
Consensus pattern (71 bp):
TGCTCAAATCAAATCAATAGATTGTAAGAAAAATCAAAATAAAAAACCATACCCTTTAGACAATT
AAGAAG
Found at i:3511332 original size:33 final size:32
Alignment explanation
Indices: 3511290--3511353 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
3511280 AGTTGTTTTA
3511290 ATTTTATTTTAAT-TTTTGATTCTTATATTATAT
1 ATTTTATTTTAATATTTTGATT-TTA-ATTATAT
*
3511323 ATTTTATTTTAATATTTTTATTTTAATTATA
1 ATTTTATTTTAATATTTTGATTTTAATTATA
3511354 ACATTATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 6 0.21
33 16 0.55
34 7 0.24
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (32 bp):
ATTTTATTTTAATATTTTGATTTTAATTATAT
Found at i:3511341 original size:14 final size:15
Alignment explanation
Indices: 3511319--3511349 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
3511309 TTCTTATATT
3511319 ATATATTTTATTTTA
1 ATATATTTTATTTTA
3511334 ATAT-TTTTATTTTA
1 ATATATTTTATTTTA
3511348 AT
1 AT
3511350 TATAACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATATATTTTATTTTA
Found at i:3512844 original size:18 final size:18
Alignment explanation
Indices: 3512821--3512856 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3512811 TTTAAGAAGA
3512821 GTAAGCTTAACTATATGC
1 GTAAGCTTAACTATATGC
3512839 GTAAGCTTAACTATATGC
1 GTAAGCTTAACTATATGC
3512857 CTCTTTACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (18 bp):
GTAAGCTTAACTATATGC
Found at i:3525329 original size:21 final size:21
Alignment explanation
Indices: 3525305--3525348 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3525295 ATGATTATTT
3525305 ATTTAAAGTAAAAAT-ATAAAA
1 ATTT-AAGTAAAAATAATAAAA
* *
3525326 ATTTAATTAAATATAATAAAA
1 ATTTAAGTAAAAATAATAAAA
3525347 AT
1 AT
3525349 AAAATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
ATTTAAGTAAAAATAATAAAA
Found at i:3538522 original size:30 final size:31
Alignment explanation
Indices: 3538488--3538545 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
3538478 CTTCACTAAT
* *
3538488 AAATAAAGAT-AACAAATTTTAAGATTTCAA
1 AAATAAAGATAAAAAAAATTTAAGATTTCAA
*
3538518 AAATAAATATAAAAAAAATTTAAGATTT
1 AAATAAAGATAAAAAAAATTTAAGATTT
3538546 AATAGAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 9 0.38
31 15 0.62
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.31
Consensus pattern (31 bp):
AAATAAAGATAAAAAAAATTTAAGATTTCAA
Found at i:3546835 original size:2 final size:2
Alignment explanation
Indices: 3546828--3546869 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
3546818 ACATACACTC
* *
3546828 AT AT AT AT AT AT -T AT AT GT AT AT GT 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
3546869 A
1 A
3546870 CACACACATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3558619 original size:35 final size:34
Alignment explanation
Indices: 3558572--3558640 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 34
3558562 TAATAAATTT
* *
3558572 TAAATTTAAATAA-TCAAAAAAAAATTTCTCAAACA
1 TAAACTTAAATAACT-AAAAAAAAATATC-CAAACA
*
3558607 TAAACTTAAATAACTAAAAATAAATATCCAAACA
1 TAAACTTAAATAACTAAAAAAAAATATCCAAACA
3558641 ACAACATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
34 6 0.20
35 23 0.77
36 1 0.03
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (34 bp):
TAAACTTAAATAACTAAAAAAAAATATCCAAACA
Found at i:3558648 original size:40 final size:40
Alignment explanation
Indices: 3558603--3558691 Score: 142
Period size: 40 Copynumber: 2.2 Consensus size: 40
3558593 AAATTTCTCA
3558603 AACATAAACTTAAATAACTAAAAATAAATATCCAAACAAC
1 AACATAAACTTAAATAACTAAAAATAAATATCCAAACAAC
* *
3558643 AACATAAAATTAAATAATTAAAAATAAATATCCAAACAAC
1 AACATAAACTTAAATAACTAAAAATAAATATCCAAACAAC
* *
3558683 TACTTAAAC
1 AACATAAAC
3558692 AACATTACAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (40 bp):
AACATAAACTTAAATAACTAAAAATAAATATCCAAACAAC
Found at i:3559661 original size:22 final size:21
Alignment explanation
Indices: 3559613--3559661 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
3559603 ATGTAATTAA
* *
3559613 TAATATAATAATTTTTTAATT
1 TAATATAATAATTTATTAAAT
*
3559634 TAAATATATTAATGTTATTAAAT
1 T-AATATAATAAT-TTATTAAAT
3559657 TAATA
1 TAATA
3559662 ATTTGAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 14 0.61
23 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TAATATAATAATTTATTAAAT
Found at i:3563352 original size:2 final size:2
Alignment explanation
Indices: 3563345--3563427 Score: 69
Period size: 2 Copynumber: 41.0 Consensus size: 2
3563335 AAGAGTTTTC
* * * *
3563345 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA CA CA CA CTCA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -T-A TA TA
* * * *
3563389 TA TA AA T- TA TA TA TA TA TG TA TG TA TA TA TG 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
3563428 CATACACGCA
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
1 1 0.02
2 63 0.95
3 1 0.02
4 1 0.02
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (2 bp):
TA
Found at i:3569007 original size:23 final size:23
Alignment explanation
Indices: 3568966--3569030 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
3568956 AATTGAAAAT
** * *
3568966 AAAATTAAATTTAGGTTAATTAC
1 AAAATTAAATTTAATTTAACTAA
*
3568989 AAAATTAGATTTAATTTAACTAA
1 AAAATTAAATTTAATTTAACTAA
*
3569012 AAAATAAAATTTTAATTTA
1 AAAATTAAA-TTTAATTTA
3569031 CTTTTTAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 25 0.74
24 9 0.26
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (23 bp):
AAAATTAAATTTAATTTAACTAA
Found at i:3596965 original size:12 final size:12
Alignment explanation
Indices: 3596948--3596973 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3596938 TGATGAACAT
3596948 AAAAAAGAAAAA
1 AAAAAAGAAAAA
3596960 AAAAAAGAAAAA
1 AAAAAAGAAAAA
3596972 AA
1 AA
3596974 GCCAAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:3597176 original size:14 final size:15
Alignment explanation
Indices: 3597157--3597185 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3597147 TAAAGTACAC
3597157 AAAAAAAACA-AAAA
1 AAAAAAAACAGAAAA
3597171 AAAAAAAACAGAAAA
1 AAAAAAAACAGAAAA
3597186 CAAGAACTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.90, C:0.07, G:0.03, T:0.00
Consensus pattern (15 bp):
AAAAAAAACAGAAAA
Found at i:3605284 original size:33 final size:33
Alignment explanation
Indices: 3605247--3605309 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
3605237 TATGATTGTA
*
3605247 TTATTACAATATAAT-AATATGTTATGTCATCAT
1 TTATTACAATA-AATCAATATGTCATGTCATCAT
**
3605280 TTATTATGATAAATCAATATGTCATGTCAT
1 TTATTACAATAAATCAATATGTCATGTCAT
3605310 TATGAATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 3 0.12
33 23 0.88
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (33 bp):
TTATTACAATAAATCAATATGTCATGTCATCAT
Found at i:3606362 original size:27 final size:28
Alignment explanation
Indices: 3606336--3606387 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
3606326 TTTTATTTTA
*
3606336 TATAATTT-TTT-AAATATTAATAA-TT
1 TATAATTTATTTAAAAAATTAATAATTT
3606361 TATAATTTATTTAAAAAATTAATAATT
1 TATAATTTATTTAAAAAATTAATAATT
3606388 GATCATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.35
26 3 0.13
27 11 0.48
28 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
TATAATTTATTTAAAAAATTAATAATTT
Found at i:3606438 original size:16 final size:15
Alignment explanation
Indices: 3606393--3606440 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
3606383 TAATTGATCA
*
3606393 TTTAAATATTTATAT
1 TTTAAATATTAATAT
*
3606408 TTT-AATCAGTAATAT
1 TTTAAAT-ATTAATAT
3606423 TTTAAAATATTAATAT
1 TTT-AAATATTAATAT
3606439 TT
1 TT
3606441 AATTTATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 3 0.11
15 12 0.44
16 9 0.33
17 3 0.11
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (15 bp):
TTTAAATATTAATAT
Found at i:3606560 original size:19 final size:21
Alignment explanation
Indices: 3606517--3606563 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
3606507 TATATAATTA
3606517 ATTTAAAATATTAATAATTGGTC
1 ATTT-AAATATTAATAATT-GTC
3606540 ATTTAAATATTAAT-ATT-TC
1 ATTTAAATATTAATAATTGTC
3606559 ATTTA
1 ATTTA
3606564 TACTTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.29
21 3 0.12
22 10 0.42
23 4 0.17
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (21 bp):
ATTTAAATATTAATAATTGTC
Found at i:3606708 original size:41 final size:41
Alignment explanation
Indices: 3606663--3606795 Score: 133
Period size: 42 Copynumber: 3.2 Consensus size: 41
3606653 TAAAATTTTT
* * *
3606663 TATTTTATAATAATATTAATGATTGATAGTTTAA-ATATTAA
1 TATTTTATAATAAT-TTAATCATTAACAGTTTAATATATTAA
* *
3606704 TATTTTATTTATAATTTAATCATTAACATTTTAATATATTAA
1 TATTTTA-TAATAATTTAATCATTAACAGTTTAATATATTAA
* * * * * *
3606746 TATTTTATTTATACTTTACTAATTAACATTTTAAAATATTAA
1 TATTTTA-TAATAATTTAATCATTAACAGTTTAATATATTAA
3606788 TATTTTAT
1 TATTTTAT
3606796 TTATAATTGA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
41 23 0.28
42 58 0.72
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (41 bp):
TATTTTATAATAATTTAATCATTAACAGTTTAATATATTAA
Found at i:3606744 original size:42 final size:41
Alignment explanation
Indices: 3606692--3606803 Score: 179
Period size: 42 Copynumber: 2.7 Consensus size: 41
3606682 TGATTGATAG
*
3606692 TTTAAATATTAATATTTTATTTATAATTTAATCATTAACAT
1 TTTAAATATTAATATTTTATTTATAATTTAATAATTAACAT
* *
3606733 TTTAATATATTAATATTTTATTTATACTTTACTAATTAACAT
1 TTTAA-ATATTAATATTTTATTTATAATTTAATAATTAACAT
3606775 TTTAAAATATTAATATTTTATTTATAATT
1 TTT-AAATATTAATATTTTATTTATAATT
3606804 GAAATGTTAT
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
41 5 0.08
42 58 0.89
43 2 0.03
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (41 bp):
TTTAAATATTAATATTTTATTTATAATTTAATAATTAACAT
Found at i:3606750 original size:16 final size:16
Alignment explanation
Indices: 3606725--3606794 Score: 53
Period size: 16 Copynumber: 4.8 Consensus size: 16
3606715 TAATTTAATC
*
3606725 ATTAACATTTTAATAT
1 ATTAATATTTTAATAT
3606741 ATTAATA-TTT--TAT
1 ATTAATATTTTAATAT
* *
3606754 -TT-ATACTTTACTA-
1 ATTAATATTTTAATAT
* *
3606767 ATTAACATTTTAAAAT
1 ATTAATATTTTAATAT
3606783 ATTAATATTTTA
1 ATTAATATTTTA
3606795 TTTATAATTG
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
11 3 0.07
12 5 0.12
13 3 0.07
14 4 0.10
15 10 0.24
16 17 0.40
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTAATATTTTAATAT
Found at i:3612011 original size:18 final size:17
Alignment explanation
Indices: 3611990--3612026 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
3611980 GAATTATTTG
*
3611990 GACATTTTGGATTTTCTA
1 GACATTATGGATTTT-TA
3612008 GACATTATGGATTTTTA
1 GACATTATGGATTTTTA
3612025 GA
1 GA
3612027 ACCTCTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (17 bp):
GACATTATGGATTTTTA
Found at i:3613815 original size:33 final size:31
Alignment explanation
Indices: 3613778--3613894 Score: 117
Period size: 33 Copynumber: 3.9 Consensus size: 31
3613768 AATAAAAATT
3613778 ATTAAAATAAAATATATAATATAAGAATCAAAA
1 ATTAAAATAAAATATATAATATAAGAA--AAAA
3613811 ATTAAAATAAAATA-A-AATAT---AAAAAA
1 ATTAAAATAAAATATATAATATAAGAAAAAA
* *
3613837 ATTAAAAT---TTATATAATATAGGTAAAACAA
1 ATTAAAATAAAATATATAATATAAG-AAAA-AA
3613867 ATTAAAATAAAATATATAATATAA-AAAA
1 ATTAAAATAAAATATATAATATAAGAAAA
3613895 TCTATTAAAG
Statistics
Matches: 71, Mismatches: 3, Indels: 22
0.74 0.03 0.23
Matches are distributed among these distances:
23 2 0.03
24 1 0.01
25 5 0.07
26 12 0.17
28 2 0.03
29 4 0.06
30 10 0.14
31 9 0.13
32 1 0.01
33 25 0.35
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.28
Consensus pattern (31 bp):
ATTAAAATAAAATATATAATATAAGAAAAAA
Found at i:3613842 original size:16 final size:16
Alignment explanation
Indices: 3613762--3613845 Score: 59
Period size: 15 Copynumber: 5.2 Consensus size: 16
3613752 ATACTGTTAT
*
3613762 AATTAAAATAAAA-AT
1 AATTAAAATAAAATAA
*
3613777 TATTAAAATAAAAT-A
1 AATTAAAATAAAATAA
* *
3613792 TA-TAATATAAGAATCAAA
1 AATTAAAATAA-AAT--AA
3613810 AATTAAAATAAAATAA
1 AATTAAAATAAAATAA
*
3613826 AATATAAAA-AAATTAA
1 AAT-TAAAATAAAATAA
3613842 AATT
1 AATT
3613846 TATATAATAT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
14 7 0.12
15 18 0.32
16 14 0.25
17 5 0.09
18 5 0.09
19 7 0.12
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (16 bp):
AATTAAAATAAAATAA
Found at i:3613854 original size:25 final size:26
Alignment explanation
Indices: 3613825--3613894 Score: 59
Period size: 29 Copynumber: 2.5 Consensus size: 26
3613815 AAATAAAATA
* *
3613825 AAATATAAAAAAATTAAAATTTATATA
1 AAATATAAAAAAATTAAAA-TAAAATA
*
3613852 ATATAGGTAAAACAAATTAAAATAAAATA
1 AAATA--TAAAA-AAATTAAAATAAAATA
3613881 TATAATATAAAAAA
1 -A-AATATAAAAAA
3613895 TCTATTAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
27 4 0.12
28 2 0.06
29 15 0.44
30 10 0.29
31 3 0.09
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (26 bp):
AAATATAAAAAAATTAAAATAAAATA
Found at i:3613998 original size:60 final size:59
Alignment explanation
Indices: 3613924--3614123 Score: 189
Period size: 60 Copynumber: 3.4 Consensus size: 59
3613914 AATATAAGAT
* *
3613924 TATAATAATAAATAAAAATAAAATATGTGACATTAAAAATATATTTAAGAGATGATATTA
1 TATAAAAATAAATAAAAA-AAAATATATGACATTAAAAATATATTTAAGAGATGATATTA
* * * * * * *
3613984 TATAAAAATTAATAATAAAAAATATAAAT-ATATTAAAAATA-A---AATATATAAGA-T-
1 TATAAAAATAAATAA-AAAAAA-ATATATGACATTAAAAATATATTTAAGAGATGATATTA
* * *
3614038 TATAATAATAAATGAAAATAAAATATATGACATTAAAAATATATTTAAGAGATGGTATTA
1 TATAAAAATAAAT-AAAAAAAAATATATGACATTAAAAATATATTTAAGAGATGATATTA
* *
3614098 TATAAAAATTAATAATAAAAAATATA
1 TATAAAAATAAATAAAAAAAAATATA
3614124 AATATATTAA
Statistics
Matches: 107, Mismatches: 23, Indels: 21
0.71 0.15 0.14
Matches are distributed among these distances:
53 5 0.05
54 27 0.25
55 4 0.04
56 7 0.07
58 6 0.06
59 13 0.12
60 38 0.36
61 7 0.07
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (59 bp):
TATAAAAATAAATAAAAAAAAATATATGACATTAAAAATATATTTAAGAGATGATATTA
Found at i:3614009 original size:24 final size:24
Alignment explanation
Indices: 3613982--3614049 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
3613972 GAGATGATAT
3613982 TATATAAAAATTAATAATAAAAAA
1 TATATAAAAATTAATAATAAAAAA
* *
3614006 TATA-AATATATTAA-AA-ATAAAA
1 TATATAA-AAATTAATAATAAAAAA
* *
3614028 TATATAAGATTATAATAATAAA
1 TATATAAAAAT-TAATAATAAA
3614050 TGAAAATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
22 10 0.30
23 9 0.27
24 12 0.36
25 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (24 bp):
TATATAAAAATTAATAATAAAAAA
Found at i:3614021 original size:16 final size:16
Alignment explanation
Indices: 3614001--3614032 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
3613991 ATTAATAATA
3614001 AAAAATATAAATATATT
1 AAAAATA-AAATATATT
3614018 AAAAATAAAATATAT
1 AAAAATAAAATATAT
3614033 AAGATTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAAATAAAATATATT
Found at i:3614041 original size:114 final size:115
Alignment explanation
Indices: 3613905--3614134 Score: 417
Period size: 114 Copynumber: 2.0 Consensus size: 115
3613895 TCTATTAAAG
*
3613905 AAATAAAAAAATATAAGATTATAATAATAAATAAAAATAAAATATGTGACATTAAAAATATATTT
1 AAATAAAAAAATATAAGATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
3613970 AAGAGATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTAA
66 AAGAGATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTAA
* *
3614020 AAAT-AAAATATATAAGATTATAATAATAAATGAAAATAAAATATATGACATTAAAAATATATTT
1 AAATAAAAAAATATAAGATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
*
3614084 AAGAGATGGTATTATATAAAAATTAATAATAAAAAATATAAATATATTAA
66 AAGAGATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTAA
3614134 A
1 A
3614135 CTTGTATTTT
Statistics
Matches: 111, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
114 107 0.96
115 4 0.04
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.32
Consensus pattern (115 bp):
AAATAAAAAAATATAAGATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
AAGAGATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTAA
Found at i:3614334 original size:26 final size:26
Alignment explanation
Indices: 3614295--3614349 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
3614285 AGTACATTAC
3614295 TTGCAATCACCTAACATGTAATCACA
1 TTGCAATCACCTAACATGTAATCACA
* *
3614321 TTGCAATCATCTAATATGTAATCACA
1 TTGCAATCACCTAACATGTAATCACA
3614347 TTG
1 TTG
3614350 TATTGTAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (26 bp):
TTGCAATCACCTAACATGTAATCACA
Found at i:3623158 original size:24 final size:24
Alignment explanation
Indices: 3623131--3623202 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
3623121 TATCTATAAT
3623131 TAAAATTTTATAAATATTAATCAA
1 TAAAATTTTATAAATATTAATCAA
* *
3623155 TAAATGATTTTAT--ATA--CA-C-T
1 TAAA--ATTTTATAAATATTAATCAA
3623175 TAAAATTTTATAAATATTAATCAA
1 TAAAATTTTATAAATATTAATCAA
3623199 TAAA
1 TAAA
3623203 TGATTAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
18 7 0.19
20 7 0.19
21 1 0.03
22 2 0.06
23 1 0.03
24 11 0.31
26 7 0.19
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (24 bp):
TAAAATTTTATAAATATTAATCAA
Found at i:3626337 original size:25 final size:25
Alignment explanation
Indices: 3626308--3626368 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
3626298 ATACAAACGA
3626308 AATTAAAATTATATGAGAATTATTG
1 AATTAAAATTATATGAGAATTATTG
3626333 AATTAAAATTATATGAGAATTATTG
1 AATTAAAATTATATGAGAATTATTG
3626358 AATTAAAATTA
1 AATTAAAATTA
3626369 CCTGATTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (25 bp):
AATTAAAATTATATGAGAATTATTG
Found at i:3627195 original size:14 final size:16
Alignment explanation
Indices: 3627178--3627209 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3627168 TAATTAACAA
3627178 AATATTA-T-TATATT
1 AATATTAGTATATATT
3627192 AATATTAGTATATATT
1 AATATTAGTATATATT
3627208 AA
1 AA
3627210 GTTATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 1 0.06
16 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
AATATTAGTATATATT
Found at i:3637484 original size:21 final size:21
Alignment explanation
Indices: 3637458--3637510 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
3637448 AATATTATTT
3637458 TAAATATTTTAATACTAAATAA
1 TAAATATTTTAATA-TAAATAA
* *
3637480 -AAATA-TTTATTATTAATAA
1 TAAATATTTTAATATAAATAA
3637499 TAAATATTTTAA
1 TAAATATTTTAA
3637511 AAATATTTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 6 0.23
20 11 0.42
21 9 0.35
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAATATTTTAATATAAATAA
Found at i:3637711 original size:18 final size:18
Alignment explanation
Indices: 3637688--3637732 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
3637678 ATAGAAAAAA
3637688 TAGAAAATATCAACT-TTT
1 TAGAAAATATCAA-TATTT
*
3637706 TAGAAAAAATCAATATTT
1 TAGAAAATATCAATATTT
3637724 TCAGAAAAT
1 T-AGAAAAT
3637733 TATTTTTCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 16 0.70
19 6 0.26
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (18 bp):
TAGAAAATATCAATATTT
Found at i:3646997 original size:2 final size:2
Alignment explanation
Indices: 3646990--3647028 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
3646980 AAGAATATTC
* *
3646990 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AG AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3647029 AGAAATGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3656251 original size:18 final size:19
Alignment explanation
Indices: 3656228--3656265 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
3656218 ATTAAATCCT
3656228 ACTTTTCGAAAAAT-GCCA
1 ACTTTTCGAAAAATAGCCA
**
3656246 ACTTTTTTAAAAATAGCCA
1 ACTTTTCGAAAAATAGCCA
3656265 A
1 A
3656266 GTCCTTAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (19 bp):
ACTTTTCGAAAAATAGCCA
Found at i:3667002 original size:16 final size:16
Alignment explanation
Indices: 3666978--3667019 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3666968 GTGCATGCAG
*
3666978 AGATAGTGGTAAACAA
1 AGATTGTGGTAAACAA
**
3666994 AGATTGTGGTTTACAA
1 AGATTGTGGTAAACAA
3667010 AGATTGTGGT
1 AGATTGTGGT
3667020 TTAGTCCCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.05, G:0.29, T:0.31
Consensus pattern (16 bp):
AGATTGTGGTAAACAA
Found at i:3667020 original size:16 final size:16
Alignment explanation
Indices: 3666990--3667022 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3666980 ATAGTGGTAA
3666990 ACAAAGATTGTGGTTT
1 ACAAAGATTGTGGTTT
3667006 ACAAAGATTGTGGTTT
1 ACAAAGATTGTGGTTT
3667022 A
1 A
3667023 GTCCCACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (16 bp):
ACAAAGATTGTGGTTT
Found at i:3685730 original size:36 final size:36
Alignment explanation
Indices: 3685679--3685747 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
3685669 ATTGGCTATC
* *
3685679 ATATTAAAGCTTAATCAATATCTTTGGTTTCCTTTA
1 ATATTAAAGCCTAATCAATAGCTTTGGTTTCCTTTA
3685715 ATATTAAAGCCTAATCAATAGCTTTGGTTTCCT
1 ATATTAAAGCCTAATCAATAGCTTTGGTTTCCT
3685748 ATCTTTCACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.43
Consensus pattern (36 bp):
ATATTAAAGCCTAATCAATAGCTTTGGTTTCCTTTA
Found at i:3686014 original size:12 final size:12
Alignment explanation
Indices: 3685997--3686021 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3685987 GGTTTTCATC
3685997 TCTTCATTTTTT
1 TCTTCATTTTTT
3686009 TCTTCATTTTTT
1 TCTTCATTTTTT
3686021 T
1 T
3686022 TTCTTTCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCTTCATTTTTT
Found at i:3691324 original size:29 final size:30
Alignment explanation
Indices: 3691282--3691341 Score: 113
Period size: 29 Copynumber: 2.0 Consensus size: 30
3691272 GTATGTATAG
3691282 ATGCACAGGGTAATGACCTTGG-TTTTTTT
1 ATGCACAGGGTAATGACCTTGGCTTTTTTT
3691311 ATGCACAGGGTAATGACCTTGGCTTTTTTT
1 ATGCACAGGGTAATGACCTTGGCTTTTTTT
3691341 A
1 A
3691342 ATAATAGCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.40
Consensus pattern (30 bp):
ATGCACAGGGTAATGACCTTGGCTTTTTTT
Found at i:3704009 original size:50 final size:51
Alignment explanation
Indices: 3703952--3704058 Score: 164
Period size: 51 Copynumber: 2.1 Consensus size: 51
3703942 TTTACTTGAA
* **
3703952 TACATAAACCTT-AAACAATTGGGTCTTGCCCATCA-ACCATGTATAAACAT
1 TACATAAACCTTAAAACAATTGGGTCTTACCCATCACA-CATACATAAACAT
3704002 TACATAAACCTTAAAACAATTGGGTCTTACCCATCACACATACATAAACAT
1 TACATAAACCTTAAAACAATTGGGTCTTACCCATCACACATACATAAACAT
3704053 TACATA
1 TACATA
3704059 CATCATTTGC
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
50 12 0.23
51 39 0.75
52 1 0.02
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.27
Consensus pattern (51 bp):
TACATAAACCTTAAAACAATTGGGTCTTACCCATCACACATACATAAACAT
Found at i:3707458 original size:43 final size:42
Alignment explanation
Indices: 3707395--3707490 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 42
3707385 TTGAGAATTA
* * * *
3707395 ATTCTTTCTCTATGAGGTGTTGGTTCTTTTGGCTTAAGAATCG
1 ATTCTTTCTCCATAAAGTGTTGGTT-TTTTGACTTAAGAATCG
* *
3707438 ATTCTTTCTCCATAAAGTGTTGGTTTTTTTACTTAAGAATTG
1 ATTCTTTCTCCATAAAGTGTTGGTTTTTTGACTTAAGAATCG
3707480 ATTCTTTCTCC
1 ATTCTTTCTCC
3707491 CCATGGTCTT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 25 0.53
43 22 0.47
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.49
Consensus pattern (42 bp):
ATTCTTTCTCCATAAAGTGTTGGTTTTTTGACTTAAGAATCG
Found at i:3707486 original size:42 final size:43
Alignment explanation
Indices: 3707388--3707490 Score: 136
Period size: 43 Copynumber: 2.4 Consensus size: 43
3707378 CTTGCAATTG
* * * * *
3707388 AGAATTAATTCTTTCTCTATGAGGTGTTGGTTCTTTTGGCTTA
1 AGAATTGATTCTTTCTCCATAAAGTGTTGGTTCTTTTGACTTA
* *
3707431 AGAATCGATTCTTTCTCCATAAAGTGTTGGTT-TTTTTACTTA
1 AGAATTGATTCTTTCTCCATAAAGTGTTGGTTCTTTTGACTTA
3707473 AGAATTGATTCTTTCTCC
1 AGAATTGATTCTTTCTCC
3707491 CCATGGTCTT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 25 0.48
43 27 0.52
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.48
Consensus pattern (43 bp):
AGAATTGATTCTTTCTCCATAAAGTGTTGGTTCTTTTGACTTA
Found at i:3709234 original size:19 final size:19
Alignment explanation
Indices: 3709210--3709248 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3709200 ATCCAACAAG
3709210 AAAAATGA-AAATAAGTGAA
1 AAAAATGATAAA-AAGTGAA
*
3709229 AAAAATTATAAAAAGTGAA
1 AAAAATGATAAAAAGTGAA
3709248 A
1 A
3709249 GCAGCAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.18
Consensus pattern (19 bp):
AAAAATGATAAAAAGTGAA
Found at i:3718947 original size:15 final size:15
Alignment explanation
Indices: 3718927--3718956 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3718917 TCACATTATC
3718927 ATCTATTATTAACAT
1 ATCTATTATTAACAT
3718942 ATCTATTATTAACAT
1 ATCTATTATTAACAT
3718957 GTCAGTATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (15 bp):
ATCTATTATTAACAT
Found at i:3724603 original size:21 final size:22
Alignment explanation
Indices: 3724572--3724614 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
3724562 GGGGCACTTC
*
3724572 ACCTAAAATGTATCAATGCATT
1 ACCTAAAATGTATCAATACATT
*
3724594 ACCT-AAATGTATTAATACATT
1 ACCTAAAATGTATCAATACATT
3724615 TATTTGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.35
Consensus pattern (22 bp):
ACCTAAAATGTATCAATACATT
Found at i:3725328 original size:8 final size:8
Alignment explanation
Indices: 3725315--3725343 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
3725305 CTAGAGAATA
3725315 ATATATGT
1 ATATATGT
3725323 ATATATGT
1 ATATATGT
3725331 ATATATGT
1 ATATATGT
3725339 ATATA
1 ATATA
3725344 CGTGAATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (8 bp):
ATATATGT
Found at i:3726056 original size:2 final size:2
Alignment explanation
Indices: 3726051--3726100 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
3726041 AGAGGCTTTG
3726051 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
3726093 AT AT AT AT
1 AT AT AT AT
3726101 GATACAACTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3732223 original size:27 final size:27
Alignment explanation
Indices: 3732185--3732237 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
3732175 TCTATCAATA
3732185 CATTTGAGAATGTATCGATAGATTTGG
1 CATTTGAGAATGTATCGATAGATTTGG
3732212 CATTTGAGAATGTATCGATAGATTTG
1 CATTTGAGAATGTATCGATAGATTTG
3732238 CCCAAAGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.08, G:0.25, T:0.38
Consensus pattern (27 bp):
CATTTGAGAATGTATCGATAGATTTGG
Found at i:3739986 original size:31 final size:31
Alignment explanation
Indices: 3739942--3740005 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
3739932 AGAAACAGTC
*
3739942 TTGCACTGCTTTATCCACTATGGTAGCAGAA
1 TTGCACTGCTTTATCCACTATGATAGCAGAA
* *
3739973 TTGCAGTGGTTTATCCACTATGATAGCAGAA
1 TTGCACTGCTTTATCCACTATGATAGCAGAA
3740004 TT
1 TT
3740006 CATAACTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (31 bp):
TTGCACTGCTTTATCCACTATGATAGCAGAA
Found at i:3748276 original size:80 final size:80
Alignment explanation
Indices: 3748118--3748427 Score: 338
Period size: 80 Copynumber: 3.9 Consensus size: 80
3748108 CATGAGTTCC
* * * * * * *
3748118 ATTTATAAGATTAT-AATATGGATACCATGAAATGTATGTGTTAAGTATA-TCATGTACATTATG
1 ATTTATAAGGTTATGAA-ATGTATTCCATGAGATGTATATGTTAAG-ATAGTCATATACACTATG
* *
3748181 GGCTCAGTATGTAAGTG
64 GGCTAAGCATGTAAGTG
* *
3748198 ATTTATAAGGTTATGAAATGTATTCCACGAGATGTATATGTTGAGATAGTCATATACACTATGGG
1 ATTTATAAGGTTATGAAATGTATTCCATGAGATGTATATGTTAAGATAGTCATATACACTATGGG
*
3748263 CTAAGCATATAAGTG
66 CTAAGCATGTAAGTG
* * *
3748278 ATTTATGAGGTTATGAAATGTGTGT-CATGAGATGTATATGTTAAGATAGTCATATATACTATGG
1 ATTTATAAGGTTATGAAATGTAT-TCCATGAGATGTATATGTTAAGATAGTCATATACACTATGG
* *
3748342 GTTAATCATGTAAGTG
65 GCTAAGCATGTAAGTG
* * * * * * * * *
3748358 ATTTATGAGGTTATGAAATATATGCGATGATATGTATGTTTTGAGATAGTCATATACACTATGAG
1 ATTTATAAGGTTATGAAATGTATTCCATGAGATGTATATGTTAAGATAGTCATATACACTATGGG
3748423 CTAAG
66 CTAAG
3748428 TATGATTAAG
Statistics
Matches: 194, Mismatches: 32, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
79 3 0.02
80 188 0.97
81 3 0.02
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (80 bp):
ATTTATAAGGTTATGAAATGTATTCCATGAGATGTATATGTTAAGATAGTCATATACACTATGGG
CTAAGCATGTAAGTG
Found at i:3756352 original size:40 final size:40
Alignment explanation
Indices: 3756297--3756416 Score: 231
Period size: 40 Copynumber: 3.0 Consensus size: 40
3756287 ATTTGATGTT
3756297 CAAGTTTTGAACCTTGCTACTATTTAGGGCGAGCACTTTA
1 CAAGTTTTGAACCTTGCTACTATTTAGGGCGAGCACTTTA
*
3756337 CAAGTTTTGAACCTTGCTACTACTTAGGGCGAGCACTTTA
1 CAAGTTTTGAACCTTGCTACTATTTAGGGCGAGCACTTTA
3756377 CAAGTTTTGAACCTTGCTACTATTTAGGGCGAGCACTTTA
1 CAAGTTTTGAACCTTGCTACTATTTAGGGCGAGCACTTTA
3756417 TGAGAAATTT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (40 bp):
CAAGTTTTGAACCTTGCTACTATTTAGGGCGAGCACTTTA
Found at i:3757015 original size:15 final size:15
Alignment explanation
Indices: 3756995--3757031 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
3756985 TTTAGACAAA
3756995 GAAGAATCGATATCT
1 GAAGAATCGATATCT
*
3757010 GAAGAACCGATATCT
1 GAAGAATCGATATCT
3757025 GAAGAAT
1 GAAGAAT
3757032 GAAGAATTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.22
Consensus pattern (15 bp):
GAAGAATCGATATCT
Found at i:3759597 original size:33 final size:33
Alignment explanation
Indices: 3759553--3759651 Score: 126
Period size: 33 Copynumber: 3.0 Consensus size: 33
3759543 ACAACTTTTA
* *
3759553 CACTTGTTTTTTCAAGGATCAAGCAAAACCTAT
1 CACTTGCTTTTTCAAGGATCAAGCAGAACCTAT
* *
3759586 CACTTTCTTTTTCAAGGATCAAGTAGAACCTAT
1 CACTTGCTTTTTCAAGGATCAAGCAGAACCTAT
* * * *
3759619 TACTTGCTTTATCAAGGCTCAACCAGAACCTAT
1 CACTTGCTTTTTCAAGGATCAAGCAGAACCTAT
3759652 GCAACTACCT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.33
Consensus pattern (33 bp):
CACTTGCTTTTTCAAGGATCAAGCAGAACCTAT
Found at i:3759803 original size:30 final size:30
Alignment explanation
Indices: 3759764--3759824 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
3759754 GCTCAAGGCT
3759764 TGAAGAATGAGTACGAGTTTAGTTCAACAA
1 TGAAGAATGAGTACGAGTTTAGTTCAACAA
*
3759794 TGAATAATGAGTACGAGTTTAGTTCAACAA
1 TGAAGAATGAGTACGAGTTTAGTTCAACAA
3759824 T
1 T
3759825 TAACTAAGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (30 bp):
TGAAGAATGAGTACGAGTTTAGTTCAACAA
Found at i:3764803 original size:50 final size:49
Alignment explanation
Indices: 3764747--3764861 Score: 133
Period size: 50 Copynumber: 2.3 Consensus size: 49
3764737 TACTATCAAG
* *
3764747 GATTCTTACTTTTTAATGGGAAGCGATAA-CTCTCATATAATCCACAAAA
1 GATTCTTACTTTTTAATGGGAAGCGATAATCT-TCACACAATCCACAAAA
* * * * *
3764796 GAATTCTTGCTCTTTAATGGGAAGTGATAATCTTTACACAATCCACAACA
1 G-ATTCTTACTTTTTAATGGGAAGCGATAATCTTCACACAATCCACAAAA
*
3764846 GATTTTTACTTTTTAA
1 GATTCTTACTTTTTAA
3764862 CAGGATCAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
49 13 0.24
50 39 0.72
51 2 0.04
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (49 bp):
GATTCTTACTTTTTAATGGGAAGCGATAATCTTCACACAATCCACAAAA
Found at i:3764907 original size:35 final size:36
Alignment explanation
Indices: 3764853--3764920 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
3764843 ACAGATTTTT
* **
3764853 ACTTTTTAACAGGATCAAACGGTAACCCTTACAATG
1 ACTTTTTAACAAGATCAAACAATAACCCTTACAATG
3764889 ACTTTTT-ACAAGATCAAACAATAACCCTTACA
1 ACTTTTTAACAAGATCAAACAATAACCCTTACA
3764921 CAATCATCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 22 0.76
36 7 0.24
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.28
Consensus pattern (36 bp):
ACTTTTTAACAAGATCAAACAATAACCCTTACAATG
Found at i:3765450 original size:21 final size:20
Alignment explanation
Indices: 3765416--3765461 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
3765406 TTCAAATTTG
3765416 GCCT-TCTTTAGTCAACTAT
1 GCCTATCTTTAGTCAACTAT
3765435 GCCTATCTTATAGTCAACTAT
1 GCCTATCTT-TAGTCAACTAT
*
3765456 GACTAT
1 GCCTAT
3765462 TTAAAGTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 4 0.17
20 4 0.17
21 16 0.67
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (20 bp):
GCCTATCTTTAGTCAACTAT
Found at i:3766044 original size:28 final size:27
Alignment explanation
Indices: 3765987--3766236 Score: 168
Period size: 28 Copynumber: 9.3 Consensus size: 27
3765977 GAAAAAATTA
* *
3765987 TTACATGTCATGTTGAAAATGTAGTTG
1 TTACATGCCATGTTAAAAATGTAGTTG
*
3766014 TTACATACCATGTTAAAATATGTAGTTG
1 TTACATGCCATGTTAAAA-ATGTAGTTG
* * *
3766042 TTACATGTCATGTTAAAAAATGTAATTA
1 TTACATGCCATGTT-AAAAATGTAGTTG
* * * * *
3766070 TTACACGTCATGCTAAAAATTTAATTG
1 TTACATGCCATGTTAAAAATGTAGTTG
* * *
3766097 TTACA--CAAAGTTGAAAAATATAGTTG
1 TTACATGCCATGTT-AAAAATGTAGTTG
** * * * *
3766123 TTACAAACCGTGTTAAAGATTTAATTG
1 TTACATGCCATGTTAAAAATGTAGTTG
* * *
3766150 TTACACGTCATGTTAAAAAATGTA---A
1 TTACATGCCATGTT-AAAAATGTAGTTG
* * *
3766175 TTACATTCCATGTTGAAAATTTAGTTG
1 TTACATGCCATGTTAAAAATGTAGTTG
*
3766202 TTACATGCCATATTGAAAAATGTAGTTG
1 TTACATGCCATGTT-AAAAATGTAGTTG
*
3766230 TTGCATG
1 TTACATG
3766237 TTATAATGAA
Statistics
Matches: 172, Mismatches: 41, Indels: 19
0.74 0.18 0.08
Matches are distributed among these distances:
24 7 0.04
25 14 0.08
26 16 0.09
27 63 0.37
28 68 0.40
29 4 0.02
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (27 bp):
TTACATGCCATGTTAAAAATGTAGTTG
Found at i:3766115 original size:26 final size:28
Alignment explanation
Indices: 3766084--3766155 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 28
3766074 ACGTCATGCT
3766084 AAAAATTTAATTGTTACACAA-AGT-TG
1 AAAAATTTAATTGTTACACAACAGTGTG
* * * *
3766110 AAAAATATAGTTGTTACA-AACCGTGTT
1 AAAAATTTAATTGTTACACAACAGTGTG
*
3766137 AAAGATTTAATTGTTACAC
1 AAAAATTTAATTGTTACAC
3766156 GTCATGTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
25 2 0.06
26 18 0.50
27 16 0.44
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (28 bp):
AAAAATTTAATTGTTACACAACAGTGTG
Found at i:3766203 original size:52 final size:51
Alignment explanation
Indices: 3766014--3766225 Score: 158
Period size: 52 Copynumber: 4.0 Consensus size: 51
3766004 AATGTAGTTG
* *
3766014 TTACATACCATGTTAAAATATGTAGTTGTTACATGTCATGTTAAAAAATGTAA
1 TTACATACCATGTTAAAAT-T-TAATTGTTACACGTCATGTTAAAAAATGTAA
* * * * * **
3766067 TTATTACACGTCATGCTAAAAATTTAATTGTTACAC--AAAGTTGAAAAATATAGTTG
1 TTA-CATAC--CATG-TTAAAATTTAATTGTTACACGTCATGTT-AAAAA-AT-GTAA
* *
3766123 TTACAAACCGTGTTAAAGATTTAATTGTTACACGTCATGTTAAAAAATGTAA
1 TTACATACCATGTTAAA-ATTTAATTGTTACACGTCATGTTAAAAAATGTAA
* * * * * *
3766175 TTACATTCCATGTTGAAAATTTAGTTGTTACATGCCATATTGAAAAATGTA
1 TTACATACCATGTT-AAAATTTAATTGTTACACGTCATGTTAAAAAATGTA
3766226 GTTGTTGCAT
Statistics
Matches: 123, Mismatches: 25, Indels: 23
0.72 0.15 0.13
Matches are distributed among these distances:
52 45 0.37
53 30 0.24
54 13 0.11
55 19 0.15
56 10 0.08
57 6 0.05
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (51 bp):
TTACATACCATGTTAAAATTTAATTGTTACACGTCATGTTAAAAAATGTAA
Found at i:3766246 original size:28 final size:28
Alignment explanation
Indices: 3766190--3766249 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
3766180 TTCCATGTTG
* *
3766190 AAAATTTAGTTGTTACATGCCATATTGA
1 AAAATGTAGTTGTTACATGCCATAATGA
* **
3766218 AAAATGTAGTTGTTGCATGTTATAATGA
1 AAAATGTAGTTGTTACATGCCATAATGA
3766246 AAAA
1 AAAA
3766250 GTTGTTACAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.37
Consensus pattern (28 bp):
AAAATGTAGTTGTTACATGCCATAATGA
Found at i:3775666 original size:21 final size:21
Alignment explanation
Indices: 3775642--3775683 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3775632 GAAGGCTAAT
* *
3775642 AAATGTTCTCATTTCACTAGA
1 AAATATTCTAATTTCACTAGA
*
3775663 AAATATTCTAATTTCATTAGA
1 AAATATTCTAATTTCACTAGA
3775684 GTAATCCATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (21 bp):
AAATATTCTAATTTCACTAGA
Found at i:3795611 original size:34 final size:33
Alignment explanation
Indices: 3795538--3795636 Score: 90
Period size: 34 Copynumber: 2.9 Consensus size: 33
3795528 ATCAAGTATT
* *
3795538 AAACCCTCACAATGGCTTTTTACGGGAGCAACCA
1 AAACCCTTACAAT-GCTTTTTACGAGAGCAACCA
* * *
3795572 TAACCCTTACAATGCTTTTTCACGAGATCAAGCA
1 AAACCCTTACAATGCTTTTT-ACGAGAGCAACCA
* * * *
3795606 AAACCCATATAATGCCTTTTATCAAGAGCAA
1 AAACCCTTACAATGCTTTTTA-CGAGAGCAA
3795637 GCATAATCCA
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
33 8 0.15
34 44 0.85
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.25
Consensus pattern (33 bp):
AAACCCTTACAATGCTTTTTACGAGAGCAACCA
Found at i:3805440 original size:28 final size:28
Alignment explanation
Indices: 3805400--3805479 Score: 106
Period size: 28 Copynumber: 2.9 Consensus size: 28
3805390 GAGAAGTGGA
*
3805400 TAACCCATCAAAAGTGAATAAATACTTG
1 TAACCCATCAAAAGTGGATAAATACTTG
* * *
3805428 TAACCCATCAAAAATGGATGAATACTTT
1 TAACCCATCAAAAGTGGATAAATACTTG
* *
3805456 TAACCCACCAGAAGTGGATAAATA
1 TAACCCATCAAAAGTGGATAAATA
3805480 ATAAAAAAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (28 bp):
TAACCCATCAAAAGTGGATAAATACTTG
Found at i:3811106 original size:29 final size:30
Alignment explanation
Indices: 3811054--3811144 Score: 114
Period size: 30 Copynumber: 3.0 Consensus size: 30
3811044 AAAAAAAAAT
** *
3811054 TCAAATAGGTTTTTATATTTTTTATTTTG-C
1 TCAAATAAATTTTTATA-TTTTTATTTTGAA
3811084 TC-AATCAAATTTTTATATTTTTATTTTGAA
1 TCAAAT-AAATTTTTATATTTTTATTTTGAA
*
3811114 TCAAATAAGTTTTTATATTTTTATTTTGAA
1 TCAAATAAATTTTTATATTTTTATTTTGAA
3811144 T
1 T
3811145 AAACAAAAAC
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
29 14 0.26
30 37 0.69
31 3 0.06
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.58
Consensus pattern (30 bp):
TCAAATAAATTTTTATATTTTTATTTTGAA
Found at i:3821722 original size:20 final size:20
Alignment explanation
Indices: 3821697--3821749 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
3821687 GCTGCTATTT
* *
3821697 ATCTATCGATATATAGTATA
1 ATCTATCGATAGATAATATA
* *
3821717 ATCTATCGATAGATAATGTG
1 ATCTATCGATAGATAATATA
3821737 ATCTATCGATAGA
1 ATCTATCGATAGA
3821750 ATTTTCTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (20 bp):
ATCTATCGATAGATAATATA
Found at i:3821870 original size:25 final size:25
Alignment explanation
Indices: 3821824--3821871 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
3821814 AAGGTGAAAA
* *
3821824 TAAATATTTAGTAATTTTATATATT
1 TAAATATTTAATAATTTAATATATT
3821849 TAAATATTTAAATAA-TTAATATA
1 TAAATATTT-AATAATTTAATATA
3821872 AAAATATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TAAATATTTAATAATTTAATATATT
Found at i:3824519 original size:22 final size:21
Alignment explanation
Indices: 3824488--3824529 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
3824478 GTTGTTGTTG
3824488 TTTTTCTTCTTTTTCTCCCCTC
1 TTTTTCTTCTTTTTC-CCCCTC
*
3824510 TTTTTGTTCTTTTTCCCCCT
1 TTTTTCTTCTTTTTCCCCCT
3824530 TTAGATTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTTCTTCTTTTTCCCCCTC
Done.