Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, 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: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 24 of 64
Found at i:3554203 original size:133 final size:133
Alignment explanation
Indices: 3553944--3554236 Score: 324
Period size: 133 Copynumber: 2.2 Consensus size: 133
3553934 TTATGAATCG
* * * *
3553944 AAAAT-ATGCTCGAAAGTCTTA-AAAATCATGTCCGAAGGTCTTACAGAATCGACTAGGATGACA
1 AAAATCATGCTCGGAGGTCTTACAAAATCATGTCCGAAGGTCTTACAGAATCGACGAGGATAACA
* * * * * * * * * *
3554007 TCGCAAGTCGAAAGATAAGGAATTGATCGGGACAACACCGCAAATCAAAATTATGTCCGGAGGTC
66 CCACAAGTCAAAAAATAAAGAATCGATCGAGACAACACCACAAATAAAAAATATGTCCGGAGGTC
3554072 TTA
131 TTA
*
3554075 AAAATCATGCTCGGAGGTCTTACAAAATCATGTCCAGAA-GTTTTACAGAATCGACGAGGATAAC
1 AAAATCATGCTCGGAGGTCTTACAAAATCATGTCC-GAAGGTCTTACAGAATCGACGAGGATAAC
* * *** *
3554139 ACCATAAGTCAAAAAATAAAGAATCGATCGAGATAACGTTACGAATAAAAAATATG-CCTGGAGG
65 ACCACAAGTCAAAAAATAAAGAATCGATCGAGACAACACCACAAATAAAAAATATGTCC-GGAGG
3554203 TCTTA
129 TCTTA
* * *
3554208 AAAATCATGTTCGGAGGTTTTACAGAATC
1 AAAATCATGCTCGGAGGTCTTACAAAATC
3554237 GACTGGTATA
Statistics
Matches: 134, Mismatches: 24, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
131 5 0.04
132 16 0.12
133 110 0.82
134 3 0.02
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (133 bp):
AAAATCATGCTCGGAGGTCTTACAAAATCATGTCCGAAGGTCTTACAGAATCGACGAGGATAACA
CCACAAGTCAAAAAATAAAGAATCGATCGAGACAACACCACAAATAAAAAATATGTCCGGAGGTC
TTA
Found at i:3554230 original size:110 final size:110
Alignment explanation
Indices: 3554074--3554399 Score: 352
Period size: 110 Copynumber: 2.9 Consensus size: 110
3554064 CGGAGGTCTT
* * *
3554074 AAAAATCATGCTCGGAGGTCTTACAAAATCATGTCCAGAAGTTTTACAGAATCGAC-GAGGATAA
1 AAAAAT-ATGCTCGGAGGTCTTA-AAAATCATGTTCGGAGGTTTTACAGAATCGACTG-GGATAA
** * *** *
3554138 CACCATAAGTCAAAAAATAAAGAATCGATCGAGATAACGTTACGAATA
63 CACCGCAAGTCAAAAAATAAAGAATCGATCGGGATAACACCACAAATA
* *
3554186 AAAAATATGC-CTGGAGGTCTTAAAAATCATGTTCGGAGGTTTTACAGAATCGACTGGTATAATA
1 AAAAATATGCTC-GGAGGTCTTAAAAATCATGTTCGGAGGTTTTACAGAATCGACTGGGATAACA
* * * * * *
3554250 TCGCAAGTCGAAAGATAAGGAATCGATCGGGATAACACCATAAATC
65 CCGCAAGTCAAAAAATAAAGAATCGATCGGGATAACACCACAAATA
* * * * * *
3554296 AAAATTATACTCGGAGGTCTTAGAAATCATGCTCGGAGCTCTTACAGAATCGACTGGGATAACAC
1 AAAAATATGCTCGGAGGTCTTAAAAATCATGTTCGGAGGTTTTACAGAATCGACTGGGATAACAC
* *
3554361 CGCAAGTTAAAAAAT-AAGAAATCGATCGGGATAGCACCA
66 CGCAAGTCAAAAAATAAAG-AATCGATCGGGATAACACCA
3554400 TGAATCAAAA
Statistics
Matches: 178, Mismatches: 32, Indels: 10
0.81 0.15 0.05
Matches are distributed among these distances:
109 2 0.01
110 154 0.87
111 16 0.09
112 6 0.03
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.22
Consensus pattern (110 bp):
AAAAATATGCTCGGAGGTCTTAAAAATCATGTTCGGAGGTTTTACAGAATCGACTGGGATAACAC
CGCAAGTCAAAAAATAAAGAATCGATCGGGATAACACCACAAATA
Found at i:3554443 original size:110 final size:110
Alignment explanation
Indices: 3554117--3554455 Score: 308
Period size: 110 Copynumber: 3.1 Consensus size: 110
3554107 TCCAGAAGTT
** * ***
3554117 TTACAGAATCGAC-GAGGATAACACCATAAGTCAAAAAATAA-AGAATCGATCGAGATAACGTTA
1 TTACAGAATCGACTG-GGATAACACCGCAAGTCAAAAAATAAGA-AATCGATCGGGATAACACCA
** * * * * * * *** * *
3554180 CGAATAAAAAATATGCCTGGAGGTCTTAAAAATCATGTTCGGAGGTT
64 TAAATCAAAATTATACCCGAAGGTCTTAGAAATCATACCCGGAGCTC
* * * * * *
3554227 TTACAGAATCGACTGGTATAATATCGCAAGTCGAAAGATAAGGAATCGATCGGGATAACACCATA
1 TTACAGAATCGACTGGGATAACACCGCAAGTCAAAAAATAAGAAATCGATCGGGATAACACCATA
* * * *
3554292 AATCAAAATTATACTCGGAGGTCTTAGAAATCATGCTCGGAGCTC
66 AATCAAAATTATACCCGAAGGTCTTAGAAATCATACCCGGAGCTC
* * *
3554337 TTACAGAATCGACTGGGATAACACCGCAAGTTAAAAAATAAGAAATCGATCGGGATAGCACCATG
1 TTACAGAATCGACTGGGATAACACCGCAAGTCAAAAAATAAGAAATCGATCGGGATAACACCATA
** *
3554402 AATCAAAATTATACCCGAAGGTCTT-GAAAGTTGTACCCGGAGGTC
66 AATCAAAATTATACCCGAAGGTCTTAGAAA-TCATACCCGGAGCTC
3554447 TTACA-AATC
1 TTACAGAATC
3554456 TTAAAATCTT
Statistics
Matches: 187, Mismatches: 39, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
109 8 0.04
110 178 0.95
111 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (110 bp):
TTACAGAATCGACTGGGATAACACCGCAAGTCAAAAAATAAGAAATCGATCGGGATAACACCATA
AATCAAAATTATACCCGAAGGTCTTAGAAATCATACCCGGAGCTC
Found at i:3554651 original size:41 final size:41
Alignment explanation
Indices: 3554572--3554687 Score: 137
Period size: 41 Copynumber: 2.8 Consensus size: 41
3554562 AGGTCTTTTC
* *
3554572 TGAGAAAGGTTCC-CTCTAAACGGAGGCTTTAAAATCTTGAT
1 TGAGAACGGTTCCTCT-TAAACAGAGGCTTTAAAATCTTGAT
* * * *
3554613 TGA-AATTGGTTTCTCTTAAATAGAGGCTTTGAAATCTTGAT
1 TGAGAA-CGGTTCCTCTTAAACAGAGGCTTTAAAATCTTGAT
*
3554654 TGAGAACGGTTCCTCTTAAACAGAGACTTTAAAA
1 TGAGAACGGTTCCTCTTAAACAGAGGCTTTAAAA
3554688 CTTTAAAAAC
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
40 2 0.03
41 56 0.90
42 4 0.06
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (41 bp):
TGAGAACGGTTCCTCTTAAACAGAGGCTTTAAAATCTTGAT
Found at i:3556407 original size:16 final size:16
Alignment explanation
Indices: 3556383--3556415 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3556373 AATTTGTCCC
3556383 TTTTGTTTGTTTTTTT
1 TTTTGTTTGTTTTTTT
*
3556399 TTTTTTTTGTTTTTTT
1 TTTTGTTTGTTTTTTT
3556415 T
1 T
3556416 ATGCCCTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (16 bp):
TTTTGTTTGTTTTTTT
Found at i:3564052 original size:13 final size:13
Alignment explanation
Indices: 3564036--3564070 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3564026 GTGTTTGTCA
3564036 CTTTTTTTTGTTT
1 CTTTTTTTTGTTT
*
3564049 CTTTTTTCTGTTT
1 CTTTTTTTTGTTT
*
3564062 GTTTTTTTT
1 CTTTTTTTT
3564071 TTTGTGGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.83
Consensus pattern (13 bp):
CTTTTTTTTGTTT
Found at i:3565631 original size:2 final size:2
Alignment explanation
Indices: 3565624--3565657 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3565614 TAGATTTCTA
3565624 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
3565658 TAAAGATCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3568565 original size:12 final size:12
Alignment explanation
Indices: 3568548--3568600 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 12
3568538 AATTTTAAAA
3568548 AATAAAATAATT
1 AATAAAATAATT
*
3568560 AATAAAACAATT
1 AATAAAATAATT
*
3568572 AATAAAAT-TTT
1 AATAAAATAATT
*
3568583 AAAAAAATAA--
1 AATAAAATAATT
3568593 AATAAAAT
1 AATAAAAT
3568601 GTGTGCATCA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 9 0.26
12 18 0.53
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (12 bp):
AATAAAATAATT
Found at i:3569028 original size:10 final size:10
Alignment explanation
Indices: 3569013--3569038 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3569003 AAAATTATCC
3569013 TTTTAATAAA
1 TTTTAATAAA
3569023 TTTTAATAAA
1 TTTTAATAAA
3569033 TTTTAA
1 TTTTAA
3569039 GATTTCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTTAATAAA
Found at i:3578412 original size:16 final size:18
Alignment explanation
Indices: 3578380--3578412 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3578370 TAAATTCAGA
3578380 TGCTGTAAAAAAGTATTT
1 TGCTGTAAAAAAGTATTT
3578398 TGCT-TAAAAAA-TATT
1 TGCTGTAAAAAAGTATT
3578413 AACTTATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (18 bp):
TGCTGTAAAAAAGTATTT
Found at i:3579324 original size:51 final size:50
Alignment explanation
Indices: 3579216--3579531 Score: 286
Period size: 51 Copynumber: 6.2 Consensus size: 50
3579206 AAACAGATGA
* * *
3579216 AATTTTAAAGTTGTTGAGCCT-TTCTTGAGAAGAGCTTTTTC-AG--A-AG
1 AATTTTAAAGTTGTTGAGCCTCTGC-TGAGAGGAGCTTTTCCAAGATAGAG
* * * *
3579262 AATTTTAAAGTTGTTGACCCTCTGCTAAAACGAGCTTTTCCAAGATAAGAG
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGAT-AGAG
* ** *
3579313 AATTTTAAAGTTGTTGAGCCTCTACTGAGATTAGCTTTTTCAAGAT-GAG
1 AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATAGAG
*
3579362 AATTTTAAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAATATGAGAG
1 AATTTT-AAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGAT-AGAG
* * * * *
3579414 ATTTTTTTTTAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAT-CAG
1 A---ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATAGAG
* *
3579466 ATTTTTAAAGTTTAAGTTGTTAAACCTCTGCTGAGAGGAGCTTTTCCAAGATGAGAG
1 AATTTTAAAG-TT--GTTG---AGCCTCTGCTGAGAGGAGCTTTTCCAAGAT-AGAG
3579523 AATTTTAAA
1 AATTTTAAA
3579532 CTACTGAGAG
Statistics
Matches: 220, Mismatches: 30, Indels: 29
0.79 0.11 0.10
Matches are distributed among these distances:
46 32 0.15
47 4 0.02
49 17 0.08
50 38 0.17
51 41 0.19
52 11 0.05
54 36 0.16
55 31 0.14
57 10 0.05
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (50 bp):
AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATAGAG
Found at i:3579472 original size:104 final size:102
Alignment explanation
Indices: 3579218--3579528 Score: 344
Period size: 104 Copynumber: 3.0 Consensus size: 102
3579208 ACAGATGAAA
* * *
3579218 TTTTAAAGTTGTTGAGCCTTTCTTGAGAAGAGCTTTTTC-AGA-AGAATTTT-AAAGTTGTTGAC
1 TTTTAAAGTTGTTGAGCCTCTATTGAGAAGAGCTTTTTCAAGATAGAATTTTAAAAGTTGTTGAA
* * * * *
3579280 CCTCTGCTAAAACGAGCTTTTCCAAGATAAGAGA--A
66 CCTCTGCTGAGAGGAGCTTTTCCAAGATGAGAGATTT
* **
3579315 TTTTAAAGTTGTTGAGCCTCTACTGAGATTAGCTTTTTCAAGATGAGAATTTTAAAAGTTGTTGA
1 TTTTAAAGTTGTTGAGCCTCTATTGAGAAGAGCTTTTTCAAGAT-AGAATTTTAAAAGTTGTTGA
* *
3579380 GCCTCTGCTGAGAGGAGCTTTTCCAATATGAGAGATTTT
65 ACCTCTGCTGAGAGGAGCTTTTCCAAGATGAGAGA-TTT
* * * *
3579419 TTTTTAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTTCAAGATCAGATTTTTAAAGTTTAAGTT
1 TTTTAAAGTTGTTGAGCCTCTATTGAGAAGAGCTTTTTCAAGAT-AGAATTTT-AA----AAGTT
* *
3579484 GTTAAACCTCTGCTGAGAGGAGCTTTTCCAAGATGAGAGAATT
60 GTTGAACCTCTGCTGAGAGGAGCTTTTCCAAGATGAGAGATTT
3579527 TT
1 TT
3579529 AAACTACTGA
Statistics
Matches: 179, Mismatches: 23, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
97 34 0.19
98 3 0.02
100 8 0.04
101 40 0.22
104 46 0.26
105 2 0.01
108 4 0.02
109 42 0.23
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.38
Consensus pattern (102 bp):
TTTTAAAGTTGTTGAGCCTCTATTGAGAAGAGCTTTTTCAAGATAGAATTTTAAAAGTTGTTGAA
CCTCTGCTGAGAGGAGCTTTTCCAAGATGAGAGATTT
Found at i:3579494 original size:55 final size:53
Alignment explanation
Indices: 3579269--3579517 Score: 213
Period size: 50 Copynumber: 4.7 Consensus size: 53
3579259 AAGAATTTTA
* * * * *** *
3579269 AAGTTGTTGACCCTCTGCTAAAACGAGCTTTTCCAAGATA-AGAGAATT-TTA
1 AAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATACAGATTTTTGTTT
* ** * * * **
3579320 AAGTTGTTGAGCCTCTACTGAGATTAGCTTTTTCAAGAT-GAGA-ATTT-TAA
1 AAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATACAGATTTTTGTTT
* * *
3579370 AAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAATATGAGAGATTTTTTTTT
1 AAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGAT-ACAGATTTTTGTTT
* *
3579424 AAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAT-CAGATTTTTAAAGTTT
1 AAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATACAGATTTTT---GTTT
* *
3579479 AAGTTGTTAAACCTCTGCTGAGAGGAGCTTTTCCAAGAT
1 AAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGAT
3579518 GAGAGAATTT
Statistics
Matches: 164, Mismatches: 26, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
50 39 0.24
51 35 0.21
52 12 0.07
53 3 0.02
54 37 0.23
55 38 0.23
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (53 bp):
AAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATACAGATTTTTGTTT
Found at i:3579799 original size:19 final size:19
Alignment explanation
Indices: 3579777--3579829 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
3579767 TTATTTATTA
3579777 TTTTTTT-TTTCTTTTTTCT
1 TTTTTTTCTTTCTTTTTT-T
*
3579796 TTTTTTTCCTTTCTTTCTTT
1 TTTTTTT-CTTTCTTTTTTT
3579816 TTTTTTTCTTTCTT
1 TTTTTTTCTTTCTT
3579830 ATCCGATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 14 0.45
20 8 0.26
21 9 0.29
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (19 bp):
TTTTTTTCTTTCTTTTTTT
Found at i:3579800 original size:15 final size:16
Alignment explanation
Indices: 3579780--3579829 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 16
3579770 TTTATTATTT
3579780 TTTTTTTCTTT-TTTC
1 TTTTTTTCTTTCTTTC
3579795 TTTTTTTTCCTTTCTTTC
1 -TTTTTTT-CTTTCTTTC
3579813 TTTTTTT-TTTCTTTC
1 TTTTTTTCTTTCTTTC
3579828 TT
1 TT
3579830 ATCCGATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.31
16 7 0.22
17 11 0.34
18 4 0.12
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTCTTTCTTTC
Found at i:3580815 original size:24 final size:24
Alignment explanation
Indices: 3580784--3580837 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
3580774 GGTAAAAAAA
*
3580784 ATTATTTTT-TTAATTTT-TTTATAT
1 ATTATTTTTGTT-ATTTTAATTAT-T
3580808 ATTATTTTTGTTATTTTAATTATT
1 ATTATTTTTGTTATTTTAATTATT
3580832 ATTATT
1 ATTATT
3580838 AATATTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 21 0.78
25 6 0.22
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (24 bp):
ATTATTTTTGTTATTTTAATTATT
Found at i:3580843 original size:21 final size:21
Alignment explanation
Indices: 3580783--3580844 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
3580773 AGGTAAAAAA
*
3580783 AATTATT-TTTTTAATTTTTT
1 AATTATTATTTTTAATATTTT
* **
3580803 TATATATTATTTTTGTTATTTT
1 AAT-TATTATTTTTAATATTTT
*
3580825 AATTATTATTATTAATATTT
1 AATTATTATTTTTAATATTT
3580845 ATACATGTAA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.06
21 18 0.56
22 12 0.38
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
AATTATTATTTTTAATATTTT
Found at i:3581319 original size:19 final size:20
Alignment explanation
Indices: 3581295--3581343 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
3581285 TTTCTTCAAA
3581295 ATTAAAAAAATAA-AAAATT
1 ATTAAAAAAATAATAAAATT
*
3581314 ATTAAAACAATTAATAAAATT
1 ATTAAAA-AAATAATAAAATT
3581335 A--AAAAAAAT
1 ATTAAAAAAAT
3581344 GTGTGCATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 3 0.12
19 11 0.42
20 5 0.19
21 7 0.27
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (20 bp):
ATTAAAAAAATAATAAAATT
Found at i:3581861 original size:11 final size:11
Alignment explanation
Indices: 3581845--3581871 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3581835 TTGATGACGA
3581845 TTTTATTTTAT
1 TTTTATTTTAT
3581856 TTTTATTTTAT
1 TTTTATTTTAT
3581867 TTTTA
1 TTTTA
3581872 AATTCATCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:3583635 original size:12 final size:13
Alignment explanation
Indices: 3583618--3583650 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
3583608 TTCAAACATC
3583618 TAAAAAATT-AAT
1 TAAAAAATTAAAT
3583630 TAAAAAATTAAAAT
1 TAAAAAATT-AAAT
3583644 TAAAAAA
1 TAAAAAA
3583651 ATGAAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
14 10 0.53
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
TAAAAAATTAAAT
Found at i:3583651 original size:15 final size:15
Alignment explanation
Indices: 3583619--3583673 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
3583609 TCAAACATCT
3583619 AAAAAATT--AATT-
1 AAAAAATTAAAATTA
3583631 AAAAAATTAAAATTA
1 AAAAAATTAAAATTA
*
3583646 AAAAAATGAAAATTCA
1 AAAAAATTAAAATT-A
3583662 ACAAAAA-TAAAA
1 A-AAAAATTAAAA
3583674 AGACTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
12 8 0.22
14 4 0.11
15 13 0.36
16 6 0.17
17 5 0.14
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.22
Consensus pattern (15 bp):
AAAAAATTAAAATTA
Found at i:3583764 original size:27 final size:28
Alignment explanation
Indices: 3583734--3583823 Score: 69
Period size: 28 Copynumber: 3.2 Consensus size: 28
3583724 TCTCTGAACC
*
3583734 TAAAATATC-TAAAAATTTTAAAAATTA
1 TAAAATATCTTAAAAATATTAAAAATTA
* * *
3583761 TAAAATTTTCTTTAAAAA-ACTGAAAATT-
1 TAAAA-TATC-TTAAAAATATTAAAAATTA
** *
3583789 TAAAATATCCAAAAAAATATGAAAAATTA
1 TAAAATAT-CTTAAAAATATTAAAAATTA
3583818 TAAAAT
1 TAAAAT
3583824 CTAAAAATTT
Statistics
Matches: 47, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
27 12 0.26
28 16 0.34
29 13 0.28
30 6 0.13
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (28 bp):
TAAAATATCTTAAAAATATTAAAAATTA
Found at i:3584406 original size:19 final size:19
Alignment explanation
Indices: 3584384--3584427 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
3584374 TTTTTCAACA
3584384 TTTTTAAAATTTTCAGAATT
1 TTTTTAAAATTTT-AGAATT
3584404 TTTTTAAAATTTTAG-ATT
1 TTTTTAAAATTTTAGAATT
3584422 TTTTTA
1 TTTTTA
3584428 TTTATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 9 0.38
19 2 0.08
20 13 0.54
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTTTAAAATTTTAGAATT
Found at i:3584463 original size:121 final size:118
Alignment explanation
Indices: 3584326--3584559 Score: 319
Period size: 121 Copynumber: 2.0 Consensus size: 118
3584316 TTGTTGGATT
** * * *
3584326 TTTAGGTAATTTTTAATTTTTTTAATTTTTATGATTTTTAAAAATTCTTTTTTCAACATTTTTAA
1 TTTAGGTAATTTTTAATTTTTGAAATTTTAAAGATTTTTAAAAATTCTTTTTTCAAAATTTTTAA
* *
3584391 AATTTTCA-GAATTTTTTTAAAATTTTAGATTTTTTTATT-TATTTTTTTTTTCGATG
66 AATTTTCAGGAA---TTTT-AAACTTTAGA-TTTTTTATTAAATTTTTTTTTTCGATG
* *
3584447 TTTAGGTAATTTTTAATTTTTGAAATTTTAAAGATTTTTTAAAATTCTTTTTTCAAAATTTTTTA
1 TTTAGGTAATTTTTAATTTTTGAAATTTTAAAGATTTTTAAAAATTCTTTTTTCAAAATTTTTAA
*
3584512 AATTTTTAGGAATTTTAAACTTTAGATTTTTTATTAAATTTTTTTTTT
66 AATTTTCAGGAATTTTAAACTTTAGATTTTTTATTAAATTTTTTTTTT
3584560 ATTTATTTGA
Statistics
Matches: 101, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
117 9 0.09
118 20 0.20
119 4 0.04
121 65 0.64
122 3 0.03
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (118 bp):
TTTAGGTAATTTTTAATTTTTGAAATTTTAAAGATTTTTAAAAATTCTTTTTTCAAAATTTTTAA
AATTTTCAGGAATTTTAAACTTTAGATTTTTTATTAAATTTTTTTTTTCGATG
Found at i:3597277 original size:14 final size:14
Alignment explanation
Indices: 3597253--3597290 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
3597243 ATCTTTTATT
3597253 TTTTTA-AAAATA-
1 TTTTTATAAAATAC
3597265 TATTTTATAAAATAC
1 T-TTTTATAAAATAC
3597280 TTTTTATAAAA
1 TTTTTATAAAA
3597291 GAAAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.04
13 5 0.22
14 16 0.70
15 1 0.04
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTTATAAAATAC
Found at i:3597451 original size:31 final size:31
Alignment explanation
Indices: 3597379--3597481 Score: 102
Period size: 31 Copynumber: 3.3 Consensus size: 31
3597369 TCTATTTTTG
* * *
3597379 AAAATGATTTGAAAATTTTTACATAATAT-TT
1 AAAATGATAT-AAAATTTTTACTTAATTTCTT
* * *
3597410 AACAA-GATATAGAGTTTTTATTTAATTTCTT
1 AA-AATGATATAAAATTTTTACTTAATTTCTT
* *
3597441 AAATTGATATAAAATTTTTACTTAATTTTTT
1 AAAATGATATAAAATTTTTACTTAATTTCTT
3597472 AAAATGATAT
1 AAAATGATAT
3597482 GTAATTTTAA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
30 14 0.25
31 41 0.72
32 2 0.04
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.48
Consensus pattern (31 bp):
AAAATGATATAAAATTTTTACTTAATTTCTT
Found at i:3597488 original size:31 final size:31
Alignment explanation
Indices: 3597372--3597489 Score: 98
Period size: 31 Copynumber: 3.8 Consensus size: 31
3597362 TAATAAATCT
* * *
3597372 ATTTTTGAAAATGATTTGAAAATTTTTACATA
1 ATTTTTTAAAATGATATG-AAATTTTTACTTA
* * *
3597404 A-TATTTAACAA-GATAT-AGAGTTTTTATTTA
1 ATTTTTTAA-AATGATATGA-AATTTTTACTTA
* * *
3597434 ATTTCTTAAATTGATATAAAATTTTTACTTA
1 ATTTTTTAAAATGATATGAAATTTTTACTTA
*
3597465 ATTTTTTAAAATGATATGTAATTTT
1 ATTTTTTAAAATGATATGAAATTTT
3597490 AACAAAATTG
Statistics
Matches: 66, Mismatches: 15, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
29 1 0.02
30 11 0.17
31 50 0.76
32 4 0.06
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (31 bp):
ATTTTTTAAAATGATATGAAATTTTTACTTA
Found at i:3597772 original size:22 final size:24
Alignment explanation
Indices: 3597747--3597797 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
3597737 AAAATATATA
3597747 TTTTATGGAT-AG-AAAATAACAT
1 TTTTATGGATAAGAAAAATAACAT
** *
3597769 TTTTATTTATAAGAAAAATAATAT
1 TTTTATGGATAAGAAAAATAACAT
3597793 TTTTA
1 TTTTA
3597798 ATATAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 8 0.33
23 2 0.08
24 14 0.58
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (24 bp):
TTTTATGGATAAGAAAAATAACAT
Found at i:3597795 original size:23 final size:21
Alignment explanation
Indices: 3597737--3597795 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 21
3597727 TTAATATTTT
3597737 AAAATATATATTTTATGGATAG
1 AAAATA-ATATTTTATGGATAG
* **
3597759 AAAATAACATTTTTATTTATAAG
1 AAAATAATA-TTTTATGGAT-AG
3597782 AAAAATAATATTTT
1 -AAAATAATATTTT
3597796 TAATATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
21 2 0.07
22 14 0.47
23 6 0.20
24 8 0.27
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (21 bp):
AAAATAATATTTTATGGATAG
Found at i:3597802 original size:23 final size:24
Alignment explanation
Indices: 3597759--3597803 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3597749 TTATGGATAG
*
3597759 AAAATAACATTTTTATTTATAAGA
1 AAAATAACATTTTTATATATAAGA
*
3597783 AAAATAATATTTTTA-ATATAA
1 AAAATAACATTTTTATATATAA
3597804 AATAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (24 bp):
AAAATAACATTTTTATATATAAGA
Found at i:3597849 original size:16 final size:17
Alignment explanation
Indices: 3597811--3597863 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
3597801 TAAAATAATT
* **
3597811 TTTTGATTTTAAAATGA
1 TTTTGAATTTAAAAAAA
*
3597828 TATTGAA-TTAAAAAAA
1 TTTTGAATTTAAAAAAA
3597844 TTTTGAATTTTAAAAAAA
1 TTTTGAA-TTTAAAAAAA
3597862 TT
1 TT
3597864 ATTTTCTGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 13 0.45
17 5 0.17
18 11 0.38
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (17 bp):
TTTTGAATTTAAAAAAA
Found at i:3601098 original size:202 final size:202
Alignment explanation
Indices: 3600752--3601118 Score: 471
Period size: 202 Copynumber: 1.8 Consensus size: 202
3600742 ATTATTTATC
* * *
3600752 TTGAAATTTTATTTAAATTCTTCCACCATTTAGAACAAATTTAAAGAAAATTTTCACTAAGAGAT
1 TTGAAACTTTATCTAAATTATTCCACCATTTAGAACAAATTTAAAGAAAATTTTCACTAAGAGAT
* * * *
3600817 TTCTTAGAAAATTTACCATTTGAAATTTCTAAGAATTTTATCATTGGATAATTATCATATATTTT
66 TTCTTAGAAAATTTACCATTTGAAATATCTAAGAATTTCATCATTGAATAATTATCATATATTCT
* *
3600882 CAACCAAAATTTTATTTTTTCCCTTTTTTATTTTTATTTTTTTGGATTGAAAATAAATATTGATT
131 CAACAAAAATTTTATTTTTTCCATTTTTTATTTTTATTTTTTTGGATTGAAAATAAATATTGATT
3600947 ATTGTTA
196 ATTGTTA
* * * *
3600954 TTGAAACTTTATCTAAATTATTTCACTATTTATG-ACAAATTTAGAGAAAATTTTTCACCTAGGA
1 TTGAAACTTTATCTAAATTATTCCACCATTTA-GAACAAATTTAAAGAAAA-TTTTCA-CTAAGA
3601018 -ATTT-TATAG-AAATTTACCATTTGAAATATCTATA-AATTTCATCATTGAATAATTA--ATAC
63 GATTTCT-TAGAAAATTTACCATTTGAAATATCTA-AGAATTTCATCATTGAATAATTATCATA-
**
3601077 TTATTCTCAA-AAAATATTTTATTTTTTTTATTTTTTATTTTT
125 -TATTCTCAACAAAA-ATTTTATTTTTTCCATTTTTTATTTTT
3601119 TTCTAATTTT
Statistics
Matches: 142, Mismatches: 15, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
200 3 0.02
201 3 0.02
202 116 0.82
203 15 0.11
204 5 0.04
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.48
Consensus pattern (202 bp):
TTGAAACTTTATCTAAATTATTCCACCATTTAGAACAAATTTAAAGAAAATTTTCACTAAGAGAT
TTCTTAGAAAATTTACCATTTGAAATATCTAAGAATTTCATCATTGAATAATTATCATATATTCT
CAACAAAAATTTTATTTTTTCCATTTTTTATTTTTATTTTTTTGGATTGAAAATAAATATTGATT
ATTGTTA
Found at i:3601128 original size:16 final size:16
Alignment explanation
Indices: 3601090--3601129 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
3601080 TTCTCAAAAA
3601090 ATATTTTATTTTTTTT
1 ATATTTTATTTTTTTT
*
3601106 ATTTTTTATTTTTTTCT
1 ATATTTTATTTTTTT-T
3601123 A-ATTTTA
1 ATATTTTA
3601130 ATTATGCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 19 0.90
17 2 0.10
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (16 bp):
ATATTTTATTTTTTTT
Found at i:3602072 original size:4 final size:4
Alignment explanation
Indices: 3602063--3602088 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3602053 AAGACCCAAA
3602063 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
3602089 CAATAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:3611324 original size:145 final size:145
Alignment explanation
Indices: 3611050--3611373 Score: 382
Period size: 145 Copynumber: 2.2 Consensus size: 145
3611040 ATTAAAAACT
* * * * **
3611050 ATGAAATATTATGAAATTAAGATTTAAAAAGTTTCATGAAAATCCGAGCTCAAAAAGGTTAAATT
1 ATGAAATATTATAAAATTAAAATCTAAAAAGTTTCATGAAAATCCAAGCTCAAAAAGGCCAAATT
* * * * * *
3611115 ACGAAAATACGCCTATAAATATATTTTGGTAATTTCACTCTTCTTGAGCTACTGTTATGATTTCA
66 ACAAAAATACGCCTATAAAGATATTTTGATAATTTCACACTTCTTAAGCTACTGATATGATTTCA
*
3611180 GATGCACCAAAAATC
131 AATGCACCAAAAATC
* ** * *
3611195 ATGAAATGTTATAAAATTAAAATCTGTAAAGTTTCATGAAATTCCAAGCTCAGAAAGGCCAAATT
1 ATGAAATATTATAAAATTAAAATCTAAAAAGTTTCATGAAAATCCAAGCTCAAAAAGGCCAAATT
* * * * *
3611260 ACAAAAATACTCCT-TAAAGGGTATTTTGATAATTTCACACTTCTTAAAG-TATTGATGTGGTTT
66 ACAAAAATACGCCTATAAA-GATATTTTGATAATTTCACACTTCTT-AAGCTACTGATATGATTT
3611323 CAAATGCACCAAAAATC
129 CAAATGCACCAAAAATC
* * *
3611340 ATAAAATATTATAAAAATAAAATATAAAAAGTTT
1 ATGAAATATTATAAAATTAAAATCTAAAAAGTTT
3611374 TACAAAAATT
Statistics
Matches: 148, Mismatches: 29, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
144 4 0.03
145 142 0.96
146 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (145 bp):
ATGAAATATTATAAAATTAAAATCTAAAAAGTTTCATGAAAATCCAAGCTCAAAAAGGCCAAATT
ACAAAAATACGCCTATAAAGATATTTTGATAATTTCACACTTCTTAAGCTACTGATATGATTTCA
AATGCACCAAAAATC
Found at i:3612384 original size:34 final size:34
Alignment explanation
Indices: 3612308--3612550 Score: 122
Period size: 34 Copynumber: 7.2 Consensus size: 34
3612298 AACGATTGAA
* * * *
3612308 ATTAAACCACGAATCAAAAAATAAAGAA-ACTAAA
1 ATTAAACCACGAGTCAGAAAATAAA-AAGACTGAG
* *
3612342 ATTGAACCACGAGTTAGAAAATAAAAAGACTGAG
1 ATTAAACCACGAGTCAGAAAATAAAAAGACTGAG
* * * *
3612376 ATTAAACCATGGGTCAAAAAATAACAAGA-TCGAG
1 ATTAAACCACGAGTCAGAAAATAAAAAGACT-GAG
* * * * *
3612410 GTTAAACTACGAATCAGAAAAT--AAAGACCGAT
1 ATTAAACCACGAGTCAGAAAATAAAAAGACTGAG
* * * *
3612442 ATTAATCCATGAGTTAGAAAATAAATAGACTGA-
1 ATTAAACCACGAGTCAGAAAATAAAAAGACTGAG
* * * *
3612475 AGTTGAATCACGAGTCA-AAAACTAAAGACA-ACAGGG
1 A-TTAAACCACGAGTCAGAAAA-TAAA-A-AGACTGAG
* * * * **
3612511 ATTGAACTACAAGTCAGAAAATAAAGAGACCAAG
1 ATTAAACCACGAGTCAGAAAATAAAAAGACTGAG
3612545 ATTAAA
1 ATTAAA
3612551 TTGCAAGTCA
Statistics
Matches: 152, Mismatches: 45, Indels: 24
0.69 0.20 0.11
Matches are distributed among these distances:
32 22 0.14
33 9 0.06
34 96 0.63
35 19 0.12
36 6 0.04
ACGTcount: A:0.52, C:0.14, G:0.16, T:0.18
Consensus pattern (34 bp):
ATTAAACCACGAGTCAGAAAATAAAAAGACTGAG
Found at i:3612850 original size:35 final size:35
Alignment explanation
Indices: 3612749--3612876 Score: 114
Period size: 35 Copynumber: 3.7 Consensus size: 35
3612739 AGACAACAGG
* * *
3612749 GATTGAATCACTAGTCAAAAAATGAAAATGATCGA
1 GATTGAACCACGAGTCAAAAAATGAAAATGACCGA
** * * * *
3612784 GATCAAACCACGAGTTAGAGAAT-AATGATGACCGA
1 GATTGAACCACGAGTCAAAAAATGAA-AATGACCGA
* * *
3612819 AATTGAACCACGAGTCAAAAAATGAAAATGACAGG
1 GATTGAACCACGAGTCAAAAAATGAAAATGACCGA
* *
3612854 GATTGAACCATGAGTCAATAAAT
1 GATTGAACCACGAGTCAAAAAAT
3612877 AATGATGACT
Statistics
Matches: 70, Mismatches: 21, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
34 2 0.03
35 66 0.94
36 2 0.03
ACGTcount: A:0.47, C:0.14, G:0.20, T:0.20
Consensus pattern (35 bp):
GATTGAACCACGAGTCAAAAAATGAAAATGACCGA
Found at i:3612863 original size:70 final size:70
Alignment explanation
Indices: 3612750--3612931 Score: 174
Period size: 70 Copynumber: 2.6 Consensus size: 70
3612740 GACAACAGGG
* * * ** * *
3612750 ATTGAATCACTAGTCAAAAAATGAAAATGATC-GAGATCAAACCACGAGTTAGA-GAATAATGAT
1 ATTGAACCACAAGTCAAAAAATGAAAATGA-CAGGGATTGAACCACGAGTCA-ATAAATAATGAT
3612813 GACCGA-A
64 GA-CGAGA
* *
3612820 ATTGAACCACGAGTCAAAAAATGAAAATGACAGGGATTGAACCATGAGTCAATAAATAATGATGA
1 ATTGAACCACAAGTCAAAAAATGAAAATGACAGGGATTGAACCACGAGTCAATAAATAATGATGA
*
3612885 CTAGA
66 CGAGA
* * * *
3612890 ATTGAACCACAAGCCAGAAACT-AAAGATAACAGGGATTGAAC
1 ATTGAACCACAAGTCAAAAAATGAAA-ATGACAGGGATTGAAC
3612932 TGTAAGTTAA
Statistics
Matches: 94, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
69 7 0.07
70 87 0.93
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (70 bp):
ATTGAACCACAAGTCAAAAAATGAAAATGACAGGGATTGAACCACGAGTCAATAAATAATGATGA
CGAGA
Found at i:3612885 original size:35 final size:35
Alignment explanation
Indices: 3612789--3612931 Score: 110
Period size: 35 Copynumber: 4.1 Consensus size: 35
3612779 ATCGAGATCA
* * * * *
3612789 AACCACGAGTTAGAGAATAATGATGACCGAAATTG
1 AACCACGAGTCAAAAAATAATGATGACAGGAATTG
* *
3612824 AACCACGAGTCAAAAAATGAA-AATGACAGGGATTG
1 AACCACGAGTCAAAAAAT-AATGATGACAGGAATTG
* *
3612859 AACCATGAGTCAATAAATAATGATGACTA-GAATTG
1 AACCACGAGTCAAAAAATAATGATGAC-AGGAATTG
* * * * * * *
3612894 AACCACAAGCCAGAAACTAAAGATAACAGGGATTG
1 AACCACGAGTCAAAAAATAATGATGACAGGAATTG
3612929 AAC
1 AAC
3612932 TGTAAGTTAA
Statistics
Matches: 84, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
34 3 0.04
35 78 0.93
36 3 0.04
ACGTcount: A:0.47, C:0.15, G:0.20, T:0.17
Consensus pattern (35 bp):
AACCACGAGTCAAAAAATAATGATGACAGGAATTG
Found at i:3613289 original size:105 final size:103
Alignment explanation
Indices: 3613167--3613512 Score: 315
Period size: 105 Copynumber: 3.3 Consensus size: 103
3613157 CAAGTTAGAG
* * *
3613167 ACTAAATACAATAGGGATTCAATCACGAGTCAAAAAATAAAAATGATCGAGATTAAACCATGTGT
1 ACTAAAGACAATAGGGATTAAATCACGAGTCAAAAAATAAAAA-GATCGAGATTAAACCAAGTGT
3613232 AAGAGAATAATGACAATCAAAATTGAACCGTGAGTCAAAA
65 -AGAGAATAATGACAATCAAAATTGAACCGTGAGTCAAAA
* * *
3613272 ACTAAAGACAATAGGGATTAAATTATGAGTCAAAAAATGAAAACGATC-AGAATTAAACCACAAG
1 ACTAAAGACAATAGGGATTAAATCACGAGTCAAAAAAT-AAAAAGATCGAG-ATTAAA-C-CAAG
* * * * * * *
3613336 T-CAGAGAATAATGACGATCGAAATTAAATCATGAGTCAGAA
62 TGTAGAGAATAATGACAATCAAAATTGAACCGTGAGTCAAAA
** * * * *
3613377 ACTAAAGATGATAGGGATTGAACCACGAGTCAAAAAATAAAAAGATTGCGATTAAACCGCAAGT-
1 ACTAAAGACAATAGGGATTAAATCACGAGTCAAAAAATAAAAAGATCGAGATTAAA-C-CAAGTG
* * **
3613441 TAGAGACTAAAGACAA-CAGGGATTGAACCGTGAGTCAAAA
64 TAGAGAATAATGACAATCA-AAATTGAACCGTGAGTCAAAA
* * * * *
3613481 AATGAAA-ACAATTGAGATTAAACCATGAGTCA
1 ACT-AAAGACAATAGGGATTAAATCACGAGTCA
3613513 GAGAATAATA
Statistics
Matches: 193, Mismatches: 41, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
103 1 0.01
104 70 0.36
105 113 0.59
106 5 0.03
107 4 0.02
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.20
Consensus pattern (103 bp):
ACTAAAGACAATAGGGATTAAATCACGAGTCAAAAAATAAAAAGATCGAGATTAAACCAAGTGTA
GAGAATAATGACAATCAAAATTGAACCGTGAGTCAAAA
Found at i:3613373 original size:35 final size:35
Alignment explanation
Indices: 3613193--3613377 Score: 97
Period size: 35 Copynumber: 5.3 Consensus size: 35
3613183 ATTCAATCAC
* ** * *
3613193 GAGTCAAAAAATAAAAATGATCGAGATTAAACCAT
1 GAGTCAGAAAATAATGACGATCGAAATTAAACCAT
* * * * * * *
3613228 GTGTAAGAGAATAATGACAATCAAAATTGAACCGT
1 GAGTCAGAAAATAATGACGATCGAAATTAAACCAT
* * * ** **
3613263 GAGTCA-AAAACTAAAGACAATAGGGATTAAATTAT
1 GAGTCAGAAAA-TAATGACGATCGAAATTAAACCAT
* * *
3613298 GAGTCAAAAAATGAA-AACGATC-AGAATTAAACCAC
1 GAGTCAGAAAAT-AATGACGATCGA-AATTAAACCAT
* * *
3613333 AAGTCAGAGAATAATGACGATCGAAATTAAATCAT
1 GAGTCAGAAAATAATGACGATCGAAATTAAACCAT
3613368 GAGTCAGAAA
1 GAGTCAGAAA
3613378 CTAAAGATGA
Statistics
Matches: 104, Mismatches: 40, Indels: 12
0.67 0.26 0.08
Matches are distributed among these distances:
34 5 0.05
35 92 0.88
36 7 0.07
ACGTcount: A:0.51, C:0.12, G:0.17, T:0.20
Consensus pattern (35 bp):
GAGTCAGAAAATAATGACGATCGAAATTAAACCAT
Found at i:3613527 original size:70 final size:69
Alignment explanation
Indices: 3613105--3613520 Score: 207
Period size: 70 Copynumber: 6.0 Consensus size: 69
3613095 AAAAATGAAA
* * * * * *
3613105 ACAACTGGGATTAAACCACGAGTCAAAAAATAAAAA-AGTTAAGATTAAACCGCAAGTTAGAGAC
1 ACAACAGGGATTGAACCACGAGTCAAAAAATAAAAAGA-TTGAGATTAAACCACAAGTCAGAGAA
*
3613169 TAAAT
65 TAAAG
* * * * *** *
3613174 ACAATAGGGATTCAATCACGAGTCAAAAAATAAAAATGATCGAGATTAAACCATGTGTAAGAGAA
1 ACAACAGGGATTGAACCACGAGTCAAAAAATAAAAA-GATTGAGATTAAACCACAAGTCAGAGAA
*
3613239 TAATG
65 TAAAG
** ** * * * ** ** * *
3613244 ACAATCA-AAATTGAACCGTGAGTCAAAAACTAAAGACA-ATAGGGATTAAATTATGAGTCAAAA
1 ACAA-CAGGGATTGAACCACGAGTCAAAAAATAAA-A-AGATTGAGATTAAACCACAAGTCAGAG
3613307 AATGAAA-
63 AAT-AAAG
* * * * * * * * * * * **
3613314 ACGATCA-GAATTAAACCACAAGTCAGAGAATAATGACGATCGAAATTAAATCATGAGTCAGA-A
1 AC-AACAGGGATTGAACCACGAGTCAAAAAATAA-AAAGATTGAGATTAAACCACAAGTCAGAGA
3613377 ACTAAAG
64 A-TAAAG
** * * * * *
3613384 ATGATAGGGATTGAACCACGAGTCAAAAAATAAAAAGATTGCGATTAAACCGCAAGTTAGAGACT
1 ACAACAGGGATTGAACCACGAGTCAAAAAATAAAAAGATTGAGATTAAACCACAAGTCAGAGAAT
3613449 AAAG
66 AAAG
** **
3613453 ACAACAGGGATTGAACCGTGAGTCAAAAAATGAAAACA-ATTGAGATTAAACCATGAGTCAGAGA
1 ACAACAGGGATTGAACCACGAGTCAAAAAAT-AAAA-AGATTGAGATTAAACCACAAGTCAGAGA
3613517 ATAA
64 ATAA
3613521 TAACAACTGA
Statistics
Matches: 254, Mismatches: 78, Indels: 29
0.70 0.22 0.08
Matches are distributed among these distances:
69 87 0.34
70 159 0.63
71 7 0.03
72 1 0.00
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.19
Consensus pattern (69 bp):
ACAACAGGGATTGAACCACGAGTCAAAAAATAAAAAGATTGAGATTAAACCACAAGTCAGAGAAT
AAAG
Found at i:3616424 original size:1 final size:1
Alignment explanation
Indices: 3616418--3616487 Score: 59
Period size: 1 Copynumber: 70.0 Consensus size: 1
3616408 CACCCATTCA
* ** * * * * **
3616418 TTTTTTTTTCTTTTTTCCTTTTATTTTTTTTTTCTTTTTCTTTTTTTTCTTTTTTTTCCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3616483 TTTTT
1 TTTTT
3616488 CACTGAGTGG
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.01, C:0.11, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:3616433 original size:9 final size:9
Alignment explanation
Indices: 3616419--3616484 Score: 71
Period size: 9 Copynumber: 6.9 Consensus size: 9
3616409 ACCCATTCAT
3616419 TTTTTTTTC
1 TTTTTTTTC
3616428 TTTTTTCCTT-
1 TTTTTT--TTC
*
3616438 TTATTTTTTT
1 TT-TTTTTTC
3616448 TTTCTTTTTC
1 TTT-TTTTTC
3616458 TTTTTTTTC
1 TTTTTTTTC
3616467 TTTTTTTTCC
1 TTTTTTTT-C
3616477 TTTTTTTT
1 TTTTTTTT
3616485 TTTCACTGAG
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
9 23 0.46
10 21 0.42
11 6 0.12
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:3616443 original size:23 final size:21
Alignment explanation
Indices: 3616418--3616487 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 21
3616408 CACCCATTCA
*
3616418 TTTTTTTTTCTTTTTTCCTTT
1 TTTTTTTTTTTTTTTTCCTTT
3616439 TATTTTTTTTTTCTTTTT-C--T
1 T-TTTTTTTTTT-TTTTTCCTTT
*
3616459 TTTTTTTCTTTTTTTTCCTTT
1 TTTTTTTTTTTTTTTTCCTTT
3616480 TTTTTTTT
1 TTTTTTTT
3616488 CACTGAGTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
18 5 0.12
19 10 0.24
20 2 0.05
21 9 0.22
22 10 0.24
23 5 0.12
ACGTcount: A:0.01, C:0.11, G:0.00, T:0.87
Consensus pattern (21 bp):
TTTTTTTTTTTTTTTTCCTTT
Found at i:3616445 original size:24 final size:24
Alignment explanation
Indices: 3616418--3616482 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 24
3616408 CACCCATTCA
3616418 TTTTTTTTTCTTTTTTCCTTTTAT
1 TTTTTTTTTCTTTTTTCCTTTTAT
* *
3616442 TTTTTTTTTC-TTTTTCTTTTTTT
1 TTTTTTTTTCTTTTTTCCTTTTAT
3616465 TCTTTTTTTTCCTTTTTT
1 T-TTTTTTTT-CTTTTTT
3616483 TTTTTCACTG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
23 12 0.33
24 18 0.50
25 1 0.03
26 5 0.14
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (24 bp):
TTTTTTTTTCTTTTTTCCTTTTAT
Found at i:3616668 original size:85 final size:86
Alignment explanation
Indices: 3616522--3616703 Score: 285
Period size: 85 Copynumber: 2.1 Consensus size: 86
3616512 ATACACTGTC
** *
3616522 ATATTGAGCCTTTACCACAACATACAGGATTCCATTTGGATATCTTCATCCTTAACCTTTAAATA
1 ATATTGAGGGTTTACCACAACATACAGGATTCCACTTGGATATCTTCATCCTTAACCTTTAAATA
*
3616587 TG-TTTTTTTTTTACTCTCTA
66 TGTTTTTTTTTTTACCCTCTA
* * *
3616607 ATATTGAGGGTTTGCCACAACATATAGGATTCCACTTGGATATCTTCATCCTTAACTTTTAAATA
1 ATATTGAGGGTTTACCACAACATACAGGATTCCACTTGGATATCTTCATCCTTAACCTTTAAATA
*
3616672 TGTTTTTTTTTTTGCCCTCTA
66 TGTTTTTTTTTTTACCCTCTA
3616693 ATATTGAGGGT
1 ATATTGAGGGT
3616704 GATCCTTAAT
Statistics
Matches: 88, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
85 61 0.69
86 27 0.31
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.43
Consensus pattern (86 bp):
ATATTGAGGGTTTACCACAACATACAGGATTCCACTTGGATATCTTCATCCTTAACCTTTAAATA
TGTTTTTTTTTTTACCCTCTA
Found at i:3620483 original size:29 final size:29
Alignment explanation
Indices: 3620449--3620510 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
3620439 GTTAAAAGTA
3620449 AAAAAAAATCAATAATGTTAATAAATTTAT
1 AAAAAAAA-CAATAATGTTAATAAATTTAT
*
3620479 AAAAAAAACAGTAATGTTAATAAATTTAT
1 AAAAAAAACAATAATGTTAATAAATTTAT
3620508 AAA
1 AAA
3620511 CAAACAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (29 bp):
AAAAAAAACAATAATGTTAATAAATTTAT
Found at i:3624625 original size:145 final size:145
Alignment explanation
Indices: 3624339--3624881 Score: 506
Period size: 145 Copynumber: 3.7 Consensus size: 145
3624329 TTAAAGTACT
* * *
3624339 AAAAATCATGAAATATTATGAAATTAAGATCTGAAAAAG-TTAATGAAAATCCAAGCTC-GGAAG
1 AAAAATCATGAAATATTATAAAATTAAGATCT-AAAAAGTTTTATGAAAATCCAAGCTCAGAAAG
* * * * * * * * *
3624402 GCTAAATTACGAAAATACTCATAGAAGGGTATTTTGGTAATTTCACAC-TTCTCAGGGTATTACT
65 ACCAAATTACGAAAATACCCCTACAAGGGTATTTTGGTAATTTCACACTTTTTGA-GGTACTATT
* *
3624466 ATGATTTCAGATGCATC
129 GTGATTTCAAATGCATC
* * **
3624483 AAAAATCATGAAATATTATAAAATTAAGATCTAAAAAGTTTTGTGAAATTATAAGCTCAGAAAGA
1 AAAAATCATGAAATATTATAAAATTAAGATCTAAAAAGTTTTATGAAAATCCAAGCTCAGAAAGA
* * * *
3624548 CCAAAGTACGAAAATACCCCTTA-AAAGGTATTTTCGTAATTTCACACTTTTTGAGGTACTGTTG
66 CCAAATTACGAAAATACCCC-TACAAGGGTATTTTGGTAATTTCACACTTTTTGAGGTACTATTG
* *
3624612 TGGTTTCAAATGCATA
130 TGATTTCAAATGCATC
* * * * * * *
3624628 AAAAATCATGAAATATTATAAAATTAAAATCTGAAAGGTTTCATGAAAATCCAAGCTAAAAAAAA
1 AAAAATCATGAAATATTATAAAATTAAGATCTAAAAAGTTTTATGAAAATCCAAGCTCAGAAAGA
* ** * * *
3624693 ACAAATTAAAAAAATACTCCTACAAGGGTATTTTGGTAATTTCACCCTTTTTTGGGGTACTATTG
66 CCAAATTACGAAAATACCCCTACAAGGGTATTTTGGTAATTTCACAC-TTTTTGAGGTACTATTG
* * *
3624758 TGATTT-TAAGGACACC
130 TGATTTCAAATG-CATC
* * ** * *
3624774 AAAAAT-ATTAAATATTATAAAATTAAGATCTAAAAAATTTTACAAAAATTCAAGCTCA-AAAAA
1 AAAAATCATGAAATATTATAAAATTAAGATCTAAAAAGTTTTATGAAAATCCAAGCTCAGAAAGA
** * * *
3624837 GTTAAATTATGAAAATGGCCCTTTACAAGGGTATTTTGGTAATTT
66 -CCAAATTACGAAAAT-ACCC-CTACAAGGGTATTTTGGTAATTT
3624882 TACCTTTCTC
Statistics
Matches: 323, Mismatches: 66, Indels: 17
0.80 0.16 0.04
Matches are distributed among these distances:
143 6 0.02
144 52 0.16
145 207 0.64
146 36 0.11
147 22 0.07
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (145 bp):
AAAAATCATGAAATATTATAAAATTAAGATCTAAAAAGTTTTATGAAAATCCAAGCTCAGAAAGA
CCAAATTACGAAAATACCCCTACAAGGGTATTTTGGTAATTTCACACTTTTTGAGGTACTATTGT
GATTTCAAATGCATC
Found at i:3637108 original size:13 final size:14
Alignment explanation
Indices: 3637083--3637111 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3637073 AAGTTAAAAA
3637083 AATTTTAAAAATAT
1 AATTTTAAAAATAT
3637097 AATTTT-AAAATAT
1 AATTTTAAAAATAT
3637110 AA
1 AA
3637112 AAAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTTTAAAAATAT
Found at i:3637130 original size:23 final size:25
Alignment explanation
Indices: 3637089--3637154 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 25
3637079 AAAAAATTTT
*
3637089 AAAAAT-ATAATTTTAAA--ATATAA
1 AAAAATAAAAATTTTAAATGATA-AA
*
3637112 AAAAATAAAAATTTTAAATGTTAAA
1 AAAAATAAAAATTTTAAATGATAAA
3637137 AAAAATAACATAATTTTA
1 AAAAATAA-A-AATTTTA
3637155 GGACATCCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
23 6 0.17
24 10 0.28
25 10 0.28
26 3 0.08
27 7 0.19
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (25 bp):
AAAAATAAAAATTTTAAATGATAAA
Found at i:3638757 original size:17 final size:17
Alignment explanation
Indices: 3638730--3638775 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
3638720 TTTTAATTTT
3638730 AAATTTATATTTAAAATA
1 AAATTT-TATTTAAAATA
*
3638748 AAATTTTATTTGAAATA
1 AAATTTTATTTAAAATA
3638765 AAATATTTATT
1 AAAT-TTTATT
3638776 ATATAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
AAATTTTATTTAAAATA
Found at i:3639346 original size:2 final size:2
Alignment explanation
Indices: 3639339--3639367 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3639329 ATTGACCATA
3639339 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3639368 TATTTATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3647138 original size:30 final size:31
Alignment explanation
Indices: 3647102--3647170 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
3647092 CAATCGAGAG
3647102 TTTAATTAAATAAAAA-TAAATGTTTAAAAA
1 TTTAATTAAATAAAAATTAAATGTTTAAAAA
** *
3647132 TTTAATTAGGTAAAAATTAAATTTTTAAAAA
1 TTTAATTAAATAAAAATTAAATGTTTAAAAA
*
3647163 TTCAATTA
1 TTTAATTA
3647171 TTCAAAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 14 0.41
31 20 0.59
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (31 bp):
TTTAATTAAATAAAAATTAAATGTTTAAAAA
Found at i:3647177 original size:15 final size:15
Alignment explanation
Indices: 3647112--3647178 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
3647102 TTTAATTAAA
3647112 TAAAAA-TAAATGT-T
1 TAAAAATTAAAT-TAT
* *
3647126 TAAAAATTTAATTAGG
1 TAAAAATTAAATTA-T
*
3647142 TAAAAATTAAATTTT
1 TAAAAATTAAATTAT
*
3647157 TAAAAATTCAATTAT
1 TAAAAATTAAATTAT
*
3647172 TCAAAAT
1 TAAAAAT
3647179 AAAAAATTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
14 7 0.17
15 23 0.55
16 12 0.29
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (15 bp):
TAAAAATTAAATTAT
Found at i:3648094 original size:14 final size:14
Alignment explanation
Indices: 3648075--3648102 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3648065 AGATAAACAC
3648075 CCCATAAGACTATT
1 CCCATAAGACTATT
3648089 CCCATAAGACTATT
1 CCCATAAGACTATT
3648103 AGAGATTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
CCCATAAGACTATT
Found at i:3650126 original size:28 final size:26
Alignment explanation
Indices: 3650065--3650126 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
3650055 ACCTTTGATT
*
3650065 ATATTCAAAAAATTCAATATTAACTA
1 ATATGCAAAAAATTCAATATTAACTA
*
3650091 ATATGCAAATAAATTCACTAATTAAACTA
1 ATATGCAAA-AAATTCAAT-ATT-AACTA
3650120 ATA-GCAA
1 ATATGCAA
3650127 CTAATTAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 8 0.26
27 8 0.26
28 7 0.23
29 8 0.26
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.31
Consensus pattern (26 bp):
ATATGCAAAAAATTCAATATTAACTA
Found at i:3650305 original size:16 final size:16
Alignment explanation
Indices: 3650281--3650313 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3650271 GTAAACAAGC
*
3650281 AATTGAAGATCCAATA
1 AATTAAAGATCCAATA
3650297 AATTAAAGATCCAATA
1 AATTAAAGATCCAATA
3650313 A
1 A
3650314 GTAAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.12, G:0.09, T:0.24
Consensus pattern (16 bp):
AATTAAAGATCCAATA
Found at i:3663397 original size:41 final size:42
Alignment explanation
Indices: 3663346--3663426 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 42
3663336 TAAAAGTAAT
* *
3663346 TTTAAATGAAGGTTAATAAAATC-TTCATTAAAAGTAAAAAC
1 TTTAAATGAAGATTAATAAAAGCTTTCATTAAAAGTAAAAAC
* *
3663387 TTTAAGTGAAGATTAATAAAAGCTTTCATTAAATGTAAAA
1 TTTAAATGAAGATTAATAAAAGCTTTCATTAAAAGTAAAA
3663427 TATATAGTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
41 20 0.57
42 15 0.43
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.33
Consensus pattern (42 bp):
TTTAAATGAAGATTAATAAAAGCTTTCATTAAAAGTAAAAAC
Found at i:3663658 original size:31 final size:31
Alignment explanation
Indices: 3663618--3663679 Score: 81
Period size: 33 Copynumber: 2.0 Consensus size: 31
3663608 GTTTGTAAAT
*
3663618 GACATTGA-CTTATTAAAAAAATGAGTGAGA
1 GACATTGACCTTATTAAAAAAATAAGTGAGA
*
3663648 GACATATGACTCTTGTTAAAAAAATAAGTGAG
1 GACAT-TGAC-CTTATTAAAAAAATAAGTGAG
3663680 GGTTATATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 5 0.19
31 3 0.11
33 19 0.70
ACGTcount: A:0.45, C:0.08, G:0.19, T:0.27
Consensus pattern (31 bp):
GACATTGACCTTATTAAAAAAATAAGTGAGA
Found at i:3664119 original size:21 final size:20
Alignment explanation
Indices: 3664095--3664145 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
3664085 TAATGGTGTG
* *
3664095 GTGAGATTAGTTATTATAATA
1 GTGAGATTA-ATATTATAAGA
3664116 GTGAGATTCAATATTATAAGA
1 GTGAGATT-AATATTATAAGA
*
3664137 GTAAGATTA
1 GTGAGATTA
3664146 CTATCAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (20 bp):
GTGAGATTAATATTATAAGA
Found at i:3664502 original size:24 final size:25
Alignment explanation
Indices: 3664453--3664504 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
3664443 ATAATTACTT
*
3664453 ATTTATTTAATAAATAATTGTATAA
1 ATTTATTTAATAAATAAATGTATAA
*
3664478 ATTTATTTTAT-AATAAATG-ACTAA
1 ATTTATTTAATAAATAAATGTA-TAA
3664502 ATT
1 ATT
3664505 AAAAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 1 0.04
24 13 0.54
25 10 0.42
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (25 bp):
ATTTATTTAATAAATAAATGTATAA
Found at i:3665009 original size:21 final size:24
Alignment explanation
Indices: 3664962--3665011 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 24
3664952 GTAACGATGG
* *
3664962 GATTAGATATTGTAGTGGTGATTA
1 GATTAGATATTGTAGTGGTAATAA
3664986 GATTAGATA-T-T-GTGGTAATAA
1 GATTAGATATTGTAGTGGTAATAA
3665007 GATTA
1 GATTA
3665012 AAATCAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 13 0.54
22 1 0.04
23 1 0.04
24 9 0.38
ACGTcount: A:0.34, C:0.00, G:0.26, T:0.40
Consensus pattern (24 bp):
GATTAGATATTGTAGTGGTAATAA
Found at i:3666175 original size:20 final size:20
Alignment explanation
Indices: 3666138--3666177 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3666128 CCAAGGTTAT
* * *
3666138 ATTTGGTCAAACTTGATCAA
1 ATTTAGTCAAAATCGATCAA
3666158 ATTTAGTCAAAATCGATCAA
1 ATTTAGTCAAAATCGATCAA
3666178 CAATGATCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (20 bp):
ATTTAGTCAAAATCGATCAA
Found at i:3667884 original size:22 final size:21
Alignment explanation
Indices: 3667858--3667902 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3667848 ATCGATCCTT
*
3667858 TCCCTTACCCAAAGGGATCGA
1 TCCCCTACCCAAAGGGATCGA
**
3667879 TCCCCTGGCCAAAGGGATCGA
1 TCCCCTACCCAAAGGGATCGA
3667900 TCC
1 TCC
3667903 ATTTTTCTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.36, G:0.22, T:0.18
Consensus pattern (21 bp):
TCCCCTACCCAAAGGGATCGA
Found at i:3674861 original size:24 final size:25
Alignment explanation
Indices: 3674813--3674882 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 25
3674803 TATCTAGAGT
*
3674813 GTAAATACAACCAATATCCAATACA
1 GTAAATACAACCAATATACAATACA
* *
3674838 GTAAATA-TACCAATATACATTACA
1 GTAAATACAACCAATATACAATACA
* * *
3674862 -CAAACAAAACCAATA-ACAATA
1 GTAAATACAACCAATATACAATA
3674883 TACATAATAC
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
23 9 0.24
24 21 0.57
25 7 0.19
ACGTcount: A:0.56, C:0.21, G:0.03, T:0.20
Consensus pattern (25 bp):
GTAAATACAACCAATATACAATACA
Found at i:3675643 original size:66 final size:66
Alignment explanation
Indices: 3675558--3675999 Score: 284
Period size: 66 Copynumber: 6.8 Consensus size: 66
3675548 CAAGAGCAAA
*
3675558 TAAGGCATTCAT-ATTAACAAACACCTTAATTGATCATATTTTATAAATTATAAAAAAAAAATTA
1 TAAGGCATTCATGA-TAACAAACACCTTAATTGATCATGTTTTATAAATTATAAAAAAAAAATTA
3675622 AT
65 AT
* * * *
3675624 TAAGGCGTTCATGATAACAAACACATTAATTGATCTTGTTTTATAAATTA-AAAAAAAAGATTAA
1 TAAGGCATTCATGATAACAAACACCTTAATTGATCATGTTTTATAAATTATAAAAAAAAAATTAA
3675688 T
66 T
* * * * * * * **** *
3675689 TAAGGCGTTCAT-ATTAACAAACGCTTTAATTGATGATGTTTCATAAA--AT-ATATACTTGTCA
1 TAAGGCATTCATGA-TAACAAACACCTTAATTGATCATGTTTTATAAATTATAAAAAAAAAATTA
3675750 AT
65 AT
* * * * *** * ****
3675752 TAAGGCGTTCTTGTTAACGAATGTCTTAATTGATCATGTTTTATAAATTATAAGAAATGTGTTAA
1 TAAGGCATTCATGATAACAAACACCTTAATTGATCATGTTTTATAAATTATAAAAAAAAAATTAA
3675817 T
66 T
* * *
3675818 TAAGGCATTCATGTTAACAAACACCTTAATTGATGA--ATTTA-AAA--A-AAAAAAAAAACTGT
1 TAAGGCATTCATGATAACAAACACCTTAATTGATCATGTTTTATAAATTATAAAAAAAAAA-T-T
3675877 CAAT
64 -AAT
* * * ** * * **** * *
3675881 TATGGCATTCCTGTTAACAAATGCCTTATTTGATGATGTTTTATAAATTAT--AAAACGTGTCAG
1 TAAGGCATTCATGATAACAAACACCTTAATTGATCATGTTTTATAAATTATAAAAAAAAAATTAA
3675944 T
66 T
* ** *
3675945 TAAGGCATTCAT-ATTAACCAATGCCTTAATTGATGATGTTTTATAAATTATAAAA
1 TAAGGCATTCATGA-TAACAAACACCTTAATTGATCATGTTTTATAAATTATAAAA
3676000 CTTGTCAATT
Statistics
Matches: 297, Mismatches: 60, Indels: 38
0.75 0.15 0.10
Matches are distributed among these distances:
60 5 0.02
61 2 0.01
62 1 0.00
63 83 0.28
64 52 0.18
65 60 0.20
66 88 0.30
67 5 0.02
68 1 0.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (66 bp):
TAAGGCATTCATGATAACAAACACCTTAATTGATCATGTTTTATAAATTATAAAAAAAAAATTAA
T
Found at i:3675718 original size:65 final size:65
Alignment explanation
Indices: 3675558--3675999 Score: 308
Period size: 63 Copynumber: 6.8 Consensus size: 65
3675548 CAAGAGCAAA
* * *
3675558 TAAGGCATTCATATTAACAAACACCTTAATTGATCATATTTTATAAATTATAAAAAAAAAATTAA
1 TAAGGCGTTCATATTAACAAACACCTTAATTGATCATGTTTTATAAATTA-AAAAAAAAGATTAA
3675623 T
65 T
* *
3675624 TAAGGCGTTCATGA-TAACAAACACATTAATTGATCTTGTTTTATAAATTAAAAAAAAAGATTAA
1 TAAGGCGTTCAT-ATTAACAAACACCTTAATTGATCATGTTTTATAAATTAAAAAAAAAGATTAA
3675688 T
65 T
* * * * * * * *** *
3675689 TAAGGCGTTCATATTAACAAACGCTTTAATTGATGATGTTTCATAAAAT-ATATACTTG-TCAAT
1 TAAGGCGTTCATATTAACAAACACCTTAATTGATCATGTTTTATAAATTAAAAAAAAAGATTAAT
* * * *** * * * *
3675752 TAAGGCGTTCTTGTTAACGAATGTCTTAATTGATCATGTTTTATAAATTATAAGAAATGTGTTAA
1 TAAGGCGTTCATATTAACAAACACCTTAATTGATCATGTTTTATAAATTAAAAAAAAAG-ATTAA
3675817 T
65 T
* * * * *
3675818 TAAGGCATTCATGTTAACAAACACCTTAATTGATGA--ATTTA-AAA--AAAAAAAAAAACTGTC
1 TAAGGCGTTCATATTAACAAACACCTTAATTGATCATGTTTTATAAATTAAAAAAAAAGA-T-T-
3675878 AAT
63 AAT
* * * * ** * * * *** * *
3675881 TATGGCATTCCTGTTAACAAATGCCTTATTTGATGATGTTTTATAAATTATAAAACGTG-TCAGT
1 TAAGGCGTTCATATTAACAAACACCTTAATTGATCATGTTTTATAAATTAAAAAAAAAGATTAAT
* * ** * *
3675945 TAAGGCATTCATATTAACCAATGCCTTAATTGATGATGTTTTATAAATTATAAAA
1 TAAGGCGTTCATATTAACAAACACCTTAATTGATCATGTTTTATAAATTAAAAAA
3676000 CTTGTCAATT
Statistics
Matches: 300, Mismatches: 63, Indels: 28
0.77 0.16 0.07
Matches are distributed among these distances:
61 7 0.02
62 1 0.00
63 81 0.27
64 65 0.22
65 59 0.20
66 81 0.27
67 1 0.00
68 5 0.02
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (65 bp):
TAAGGCGTTCATATTAACAAACACCTTAATTGATCATGTTTTATAAATTAAAAAAAAAGATTAAT
Found at i:3675781 original size:63 final size:64
Alignment explanation
Indices: 3675621--3676011 Score: 356
Period size: 63 Copynumber: 6.1 Consensus size: 64
3675611 AAAAAAAATT
* * ** * ** * *** *
3675621 AATTAAGGCGTTCATGATAACAAACACATTAATTGATCTTGTTTTATAAATTAAAAAAAAAGATT
1 AATTAAGGCATTCATGTTAACAAATGCCTTAATTGATGATGTTTTATAAATTATAAAACTTG-TC
* * * * * * *
3675686 AATTAAGGCGTTCATATTAACAAACGCTTTAATTGATGATGTTTCATAAAATAT-ATACTTGTC
1 AATTAAGGCATTCATGTTAACAAATGCCTTAATTGATGATGTTTTATAAATTATAAAACTTGTC
* * * * * *
3675749 AATTAAGGCGTTCTTGTTAACGAATGTCTTAATTGATCATGTTTTATAAATTATAAGAAATGTGT
1 AATTAAGGCATTCATGTTAACAAATGCCTTAATTGATGATGTTTTATAAATTATAA-AACT-TGT
*
3675814 T
64 C
** ** * ** *
3675815 AATTAAGGCATTCATGTTAACAAACACCTTAATTGATGAAT-TTAAAAAAAAAAAAAAAC-TGTC
1 AATTAAGGCATTCATGTTAACAAATGCCTTAATTGATG-ATGTTTTATAAATTATAAAACTTGTC
* * * *
3675878 AATTATGGCATTCCTGTTAACAAATGCCTTATTTGATGATGTTTTATAAATTATAAAACGTGTC
1 AATTAAGGCATTCATGTTAACAAATGCCTTAATTGATGATGTTTTATAAATTATAAAACTTGTC
* * *
3675942 AGTTAAGGCATTCATATTAACCAATGCCTTAATTGATGATGTTTTATAAATTATAAAACTTGTC
1 AATTAAGGCATTCATGTTAACAAATGCCTTAATTGATGATGTTTTATAAATTATAAAACTTGTC
3676006 AATTAA
1 AATTAA
3676012 AATATTTGTT
Statistics
Matches: 260, Mismatches: 60, Indels: 13
0.78 0.18 0.04
Matches are distributed among these distances:
62 2 0.01
63 94 0.36
64 70 0.27
65 49 0.19
66 43 0.17
67 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.37
Consensus pattern (64 bp):
AATTAAGGCATTCATGTTAACAAATGCCTTAATTGATGATGTTTTATAAATTATAAAACTTGTC
Found at i:3675878 original size:129 final size:127
Alignment explanation
Indices: 3675558--3675980 Score: 392
Period size: 129 Copynumber: 3.3 Consensus size: 127
3675548 CAAGAGCAAA
*
3675558 TAAGGCATTCATATTAACAAACACCTTAATTGATCATATTTTATAAATTATAAAAAAAAAA-T-T
1 TAAGGCATTCATATTAACAAACACCTTAATTGATGA-A-TTTA-AAA--A-AAAAAAAAAACTGT
* ** * * *
3675621 -AATTAAGGCGTTCATGATAACAAACACATTAATTGATCTTGTTTTATAAATTAAAAAAAAAG-A
60 CAATTAAGGCGTTCATGTTAACAATGAC-TTAATTGATCATGTTTTATAAATT-ATAAAAAAGTG
3675684 TTAAT
123 TTAAT
* * * ** * * * *
3675689 TAAGGCGTTCATATTAACAAACGCTTTAATTGATG-ATGTT-TCATAAAATATATACTTGTCAAT
1 TAAGGCATTCATATTAACAAACACCTTAATTGATGAAT-TTAAAAAAAAAAAAAAAC-TGTCAAT
* * *
3675752 TAAGGCGTTCTTGTTAACGAATGTCTTAATTGATCATGTTTTATAAATTATAAGAAATGTGTTAA
64 TAAGGCGTTCATGTTAAC-AATGACTTAATTGATCATGTTTTATAAATTATAA-AAAAGTGTTAA
3675817 T
127 T
*
3675818 TAAGGCATTCATGTTAACAAACACCTTAATTGATGAATTTAAAAAAAAAAAAAAACTGTCAATTA
1 TAAGGCATTCATATTAACAAACACCTTAATTGATGAATTTAAAAAAAAAAAAAAACTGTCAATTA
* * * * * * * * *
3675883 TGGCATTCCTGTTAACAAATGCCTTATTTGATGATGTTTTATAAATTAT-AAAACGTGTCAGT
66 AGGCGTTCATGTTAAC-AATGACTTAATTGATCATGTTTTATAAATTATAAAAAAGTGTTAAT
* **
3675945 TAAGGCATTCATATTAACCAATGCCTTAATTGATGA
1 TAAGGCATTCATATTAACAAACACCTTAATTGATGA
3675981 TGTTTTATAA
Statistics
Matches: 239, Mismatches: 43, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
124 7 0.03
126 1 0.00
127 46 0.19
128 48 0.20
129 95 0.40
130 11 0.05
131 31 0.13
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (127 bp):
TAAGGCATTCATATTAACAAACACCTTAATTGATGAATTTAAAAAAAAAAAAAAACTGTCAATTA
AGGCGTTCATGTTAACAATGACTTAATTGATCATGTTTTATAAATTATAAAAAAGTGTTAAT
Found at i:3676996 original size:14 final size:13
Alignment explanation
Indices: 3676972--3677021 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
3676962 CAAAAAGCAA
*
3676972 AGGAGAGAAAAGAG
1 AGGAGA-AAAAAAG
3676986 AGGAGAAAAAAA-
1 AGGAGAAAAAAAG
*
3676998 AAGAGAAAAAAAG
1 AGGAGAAAAAAAG
*
3677011 A-AAGAAAAAAA
1 AGGAGAAAAAAA
3677022 ATCTTGGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 20 0.62
13 6 0.19
14 6 0.19
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AGGAGAAAAAAAG
Found at i:3677003 original size:12 final size:12
Alignment explanation
Indices: 3676988--3677022 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
3676978 GAAAAGAGAG
3676988 GAGAAAAAAAAA
1 GAGAAAAAAAAA
3677000 GAGAAAAAAAGAA
1 GAGAAAAAAA-AA
3677013 -AGAAAAAAAA
1 GAGAAAAAAAA
3677023 TCTTGGTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 19 0.86
13 2 0.09
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
GAGAAAAAAAAA
Found at i:3678077 original size:30 final size:30
Alignment explanation
Indices: 3678038--3678096 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
3678028 CTAAACCCTA
*
3678038 AAACCTAAACCCTAA-TCAAACCCCAAACT
1 AAACCTAAACCCTAACTCAAACCCAAAACT
*
3678067 AAACCTTAAACCCTAACTTAAACCCAAAAC
1 AAACC-TAAACCCTAACTCAAACCCAAAAC
3678097 CTACCTAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 5 0.19
30 10 0.38
31 11 0.42
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.15
Consensus pattern (30 bp):
AAACCTAAACCCTAACTCAAACCCAAAACT
Found at i:3679286 original size:25 final size:25
Alignment explanation
Indices: 3679251--3679305 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
3679241 GTGAGTTTTA
3679251 CATTTCATGCATATTTTAACTATGT
1 CATTTCATGCATATTTTAACTATGT
* * *
3679276 TATTTCATGCATGTTTTAATTATGT
1 CATTTCATGCATATTTTAACTATGT
3679301 CATTT
1 CATTT
3679306 ATTATATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.13, G:0.09, T:0.53
Consensus pattern (25 bp):
CATTTCATGCATATTTTAACTATGT
Found at i:3680125 original size:11 final size:11
Alignment explanation
Indices: 3680092--3680127 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
3680082 TTATTCTAAG
3680092 CAAAAAAAAAA
1 CAAAAAAAAAA
*
3680103 AAAAAAAAAAA
1 CAAAAAAAAAA
*
3680114 CAAAACAAAAA
1 CAAAAAAAAAA
3680125 CAA
1 CAA
3680128 CAGAAATGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:3680374 original size:35 final size:37
Alignment explanation
Indices: 3680334--3680416 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 37
3680324 AGTAGGATAA
* *
3680334 TACATGCATTCCGTCTCAT-C-TATATCAATAAATAG
1 TACATGCATTCCATCTCATGCAAATATCAATAAATAG
* * * *
3680369 TACATGCATTCCATTTCATGCAAATGTTAATAAATGG
1 TACATGCATTCCATCTCATGCAAATATCAATAAATAG
3680406 TACATGCATTC
1 TACATGCATTC
3680417 ATCCTATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
35 17 0.43
36 1 0.03
37 22 0.55
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (37 bp):
TACATGCATTCCATCTCATGCAAATATCAATAAATAG
Found at i:3683258 original size:19 final size:19
Alignment explanation
Indices: 3683220--3683266 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
3683210 ATAAAGTGCC
*
3683220 ATGAAAAGAAAAATGAAAA
1 ATGAAAAGAAAAAAGAAAA
3683239 ATGAAAA-AAAAAAGAGAAA
1 ATGAAAAGAAAAAAGA-AAA
3683258 A--AAAAGAAA
1 ATGAAAAGAAA
3683267 GTTCACTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 4 0.16
18 10 0.40
19 11 0.44
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (19 bp):
ATGAAAAGAAAAAAGAAAA
Found at i:3686038 original size:70 final size:69
Alignment explanation
Indices: 3685923--3686064 Score: 168
Period size: 70 Copynumber: 2.0 Consensus size: 69
3685913 ATATCAAGGT
3685923 TTTTATTCAATTCTCTTAGTGATGATATTCGAGCTTTTTTATTTTAAATCTCTTAATGGTGACAT
1 TTTTATTCAATTCTCTTAGTGATGATATTCGAGCTTTTTTATTTTAAATCTC-TAATGGTGACA-
*
3685988 TTGAGC
64 GTGAGC
* *
3685994 TTTTATTCAA-TCTC-TAG-GATG-TGATATCTGAG-TTTTCTTTTTTTAAATCTCTCATGGTGA
1 TTTTATTCAATTCTCTTAGTGATGAT-AT-TC-GAGCTTTT-TTATTTTAAATCTCTAATGGTGA
3686054 CAGTGAGC
62 CAGTGAGC
3686062 TTT
1 TTT
3686065 CACAAAATCT
Statistics
Matches: 64, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
67 1 0.02
68 14 0.22
69 19 0.30
70 20 0.31
71 10 0.16
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.49
Consensus pattern (69 bp):
TTTTATTCAATTCTCTTAGTGATGATATTCGAGCTTTTTTATTTTAAATCTCTAATGGTGACAGT
GAGC
Found at i:3686119 original size:33 final size:33
Alignment explanation
Indices: 3685934--3686130 Score: 86
Period size: 33 Copynumber: 5.8 Consensus size: 33
3685924 TTTATTCAAT
*
3685934 TCTCTTAGTGATGATATTCGAGCTTTTTTATTTTAAA
1 TCTCTTAGTGGTGATATTCGAGCTTTTTTA----AAA
* * * *
3685971 TCTCTTAATGGTGACATTTGAGCTTTTATT-CAA
1 TCTCTTAGTGGTGATATTCGAGCTTTT-TTAAAA
*
3686004 TCTC-TAG-GATGTGATA-TCTGAGTTTTCTTTTTTTAAA
1 TCTCTTAGTG--GTGATATTC-GAG----CTTTTTTAAAA
* * * ***
3686041 TCTCTCA-TGGTGACAGT-GAGCTTTCACAAAA
1 TCTCTTAGTGGTGATATTCGAGCTTTTTTAAAA
* *
3686072 TCT-TTCGATAGTGATATTCGAGCTTTTTTAAAA
1 TCTCTTAG-TGGTGATATTCGAGCTTTTTTAAAA
*
3686105 TCTCTTAGTGGTGATATTTGAG-TTTT
1 TCTCTTAGTGGTGATATTCGAGCTTTT
3686131 CTTTGATGGT
Statistics
Matches: 118, Mismatches: 26, Indels: 37
0.65 0.14 0.20
Matches are distributed among these distances:
30 1 0.01
31 11 0.09
32 14 0.12
33 40 0.34
34 3 0.03
35 3 0.03
36 7 0.06
37 35 0.30
38 4 0.03
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (33 bp):
TCTCTTAGTGGTGATATTCGAGCTTTTTTAAAA
Found at i:3686240 original size:31 final size:32
Alignment explanation
Indices: 3686205--3686266 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
3686195 GGTGATATCC
3686205 AAAGT-TTGTGTTTT-ACTCAGTGGCGATATTT
1 AAAGTATT-TGTTTTCACTCAGTGGCGATATTT
*
3686236 AAAGTCATTTGTTTTCACTCAGTGGTGATAT
1 AAAGT-ATTTGTTTTCACTCAGTGGCGATAT
3686267 CCGAGTCCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 5 0.19
32 6 0.22
33 16 0.59
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.44
Consensus pattern (32 bp):
AAAGTATTTGTTTTCACTCAGTGGCGATATTT
Found at i:3690574 original size:7 final size:7
Alignment explanation
Indices: 3690564--3690631 Score: 54
Period size: 7 Copynumber: 10.1 Consensus size: 7
3690554 TCCCATGAAA
3690564 CCAAAAC
1 CCAAAAC
*
3690571 CCAAAAA
1 CCAAAAC
3690578 CCAAAA-
1 CCAAAAC
3690584 CCAAAAC
1 CCAAAAC
3690591 CCTAAAA-
1 CC-AAAAC
*
3690598 CCTAAAC
1 CCAAAAC
*
3690605 CCTAAA-
1 CCAAAAC
*
3690611 CCAAATC
1 CCAAAAC
*
3690618 CC-TAAC
1 CCAAAAC
3690624 CCAAAAC
1 CCAAAAC
3690631 C
1 C
3690632 AAATCCTAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
6 17 0.35
7 28 0.57
8 4 0.08
ACGTcount: A:0.53, C:0.40, G:0.00, T:0.07
Consensus pattern (7 bp):
CCAAAAC
Found at i:3690586 original size:20 final size:20
Alignment explanation
Indices: 3690561--3690605 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
3690551 AAATCCCATG
3690561 AAACCAAAACCCAAAAACCA
1 AAACCAAAACCCAAAAACCA
* *
3690581 AAACCAAAACCCTAAAACCT
1 AAACCAAAACCCAAAAACCA
3690601 AAACC
1 AAACC
3690606 CTAAACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.60, C:0.36, G:0.00, T:0.04
Consensus pattern (20 bp):
AAACCAAAACCCAAAAACCA
Found at i:3690620 original size:13 final size:12
Alignment explanation
Indices: 3690581--3690647 Score: 55
Period size: 13 Copynumber: 5.2 Consensus size: 12
3690571 CCAAAAACCA
3690581 AAACCAAAACCCT
1 AAACC-AAACCCT
3690594 AAAACCTAAACCCT
1 -AAACC-AAACCCT
3690608 AAACCAAATCCCT
1 AAACCAAA-CCCT
* *
3690621 AACCCAAAACC-
1 AAACCAAACCCT
3690632 AAATCCTAAACCCT
1 AAA-CC-AAACCCT
3690646 AA
1 AA
3690648 CCTAGACCCA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
11 2 0.05
12 7 0.16
13 21 0.48
14 14 0.32
ACGTcount: A:0.51, C:0.37, G:0.00, T:0.12
Consensus pattern (12 bp):
AAACCAAACCCT
Found at i:3690643 original size:19 final size:19
Alignment explanation
Indices: 3690584--3690644 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
3690574 AAAACCAAAA
*
3690584 CCAAAACCCTAAAACCTAAAC
1 CCAAAA-CC-AAATCCTAAAC
*
3690605 CCTAAACCAAATCCCT-AAC
1 CCAAAACCAAAT-CCTAAAC
3690624 CCAAAACCAAATCCTAAAC
1 CCAAAACCAAATCCTAAAC
3690643 CC
1 CC
3690645 TAACCTAGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
18 3 0.09
19 22 0.63
20 5 0.14
21 5 0.14
ACGTcount: A:0.48, C:0.41, G:0.00, T:0.11
Consensus pattern (19 bp):
CCAAAACCAAATCCTAAAC
Found at i:3690646 original size:7 final size:7
Alignment explanation
Indices: 3690587--3690663 Score: 53
Period size: 7 Copynumber: 12.0 Consensus size: 7
3690577 ACCAAAACCA
3690587 AAACCCT
1 AAACCCT
*
3690594 AAAACCT
1 AAACCCT
3690601 AAACCCT
1 AAACCCT
3690608 AAA-CC-
1 AAACCCT
3690613 AAATCCCT
1 AAA-CCCT
3690621 -AACCC-
1 AAACCCT
*
3690626 AAAACC-
1 AAACCCT
*
3690632 AAATCCT
1 AAACCCT
3690639 AAACCCT
1 AAACCCT
3690646 -AA-CCT
1 AAACCCT
*
3690651 AGACCC-
1 AAACCCT
3690657 AAACCCT
1 AAACCCT
3690664 CCCCAAACCC
Statistics
Matches: 55, Mismatches: 7, Indels: 16
0.71 0.09 0.21
Matches are distributed among these distances:
5 6 0.11
6 22 0.40
7 27 0.49
ACGTcount: A:0.45, C:0.40, G:0.01, T:0.13
Consensus pattern (7 bp):
AAACCCT
Found at i:3690758 original size:18 final size:19
Alignment explanation
Indices: 3690714--3690759 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
3690704 CATGCATTTG
* *
3690714 CATT-TCATTTTATTTTGT
1 CATTATCATGTTATTTTAT
3690732 CATTA-CATGTTATTTTAT
1 CATTATCATGTTATTTTAT
3690750 -ATTATCATGT
1 CATTATCATGT
3690760 GTTCTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.24, C:0.11, G:0.07, T:0.59
Consensus pattern (19 bp):
CATTATCATGTTATTTTAT
Found at i:3690811 original size:35 final size:34
Alignment explanation
Indices: 3690741--3690816 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 34
3690731 TCATTACATG
* ** * *
3690741 TTATTTTATATTATCATGTGTTCTTATTTTCTTA
1 TTATGTTATATTATCATGTAATCTCATATTCTTA
3690775 TTCATGTTATATTATCATGTAATCATCATATT-TTA
1 TT-ATGTTATATTATCATGTAATC-TCATATTCTTA
3690810 TTATGTT
1 TTATGTT
3690817 CATTCATCTC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
34 7 0.20
35 23 0.66
36 5 0.14
ACGTcount: A:0.25, C:0.09, G:0.07, T:0.59
Consensus pattern (34 bp):
TTATGTTATATTATCATGTAATCTCATATTCTTA
Found at i:3691897 original size:6 final size:6
Alignment explanation
Indices: 3691886--3691963 Score: 65
Period size: 6 Copynumber: 13.5 Consensus size: 6
3691876 AAATCTTATC
* *
3691886 TTAATT TTAATT TTGATT TTAA-T TTAA-T TTAAAT TTAA-T TTAATT
1 TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT
* * * *
3691931 ATTGATT TT-AGT TTGATT TTGATT TTAATT TTA
1 -TTAATT TTAATT TTAATT TTAATT TTAATT TTA
3691964 TTCTAGTTGT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
5 19 0.31
6 38 0.61
7 5 0.08
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (6 bp):
TTAATT
Found at i:3691920 original size:11 final size:11
Alignment explanation
Indices: 3691886--3691928 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
3691876 AAATCTTATC
*
3691886 TTAATTTTAATT
1 TTAA-TTTAAAT
* *
3691898 TTGATTTTAAT
1 TTAATTTAAAT
3691909 TTAATTTAAAT
1 TTAATTTAAAT
3691920 TTAATTTAA
1 TTAATTTAA
3691929 TTATTGATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 23 0.88
12 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (11 bp):
TTAATTTAAAT
Found at i:3692844 original size:17 final size:17
Alignment explanation
Indices: 3692796--3692854 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
3692786 TTCAAGAATG
3692796 ATGAATTTAGTTTTTCA-C
1 ATGAATTTA-TTTTT-AGC
*
3692814 ATGGCATTTA-TTTTAGC
1 AT-GAATTTATTTTTAGC
*
3692831 ATGAATTTATTTTTTGC
1 ATGAATTTATTTTTAGC
3692848 ATGAATT
1 ATGAATT
3692855 AATTATAGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
16 7 0.20
17 20 0.57
18 2 0.06
19 6 0.17
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.51
Consensus pattern (17 bp):
ATGAATTTATTTTTAGC
Found at i:3692927 original size:20 final size:20
Alignment explanation
Indices: 3692870--3693160 Score: 239
Period size: 20 Copynumber: 14.0 Consensus size: 20
3692860 TAGTATATTC
* *
3692870 CATGATTTTA-ATGTAATTG
1 CATGATTATATATTTAATTG
*
3692889 CATGTTTTATATATTTTTAATTG
1 CATG-ATTATATA--TTTAATTG
* *
3692912 CATGATTATATATTTATTTA
1 CATGATTATATATTTAATTG
* *
3692932 TAAGATTATATATGATTAATTG
1 CATGATTATATAT--TTAATTG
*
3692954 CATGATTATATATTGTTATTTG
1 CATGATTATATA-T-TTAATTG
* *
3692976 CATAATTATATATTTATTTG
1 CATGATTATATATTTAATTG
*
3692996 CAAGATTATATATTGTTAATTG
1 CATGATTATATA-T-TTAATTG
3693018 CATGATTATATATTTAATTG
1 CATGATTATATATTTAATTG
3693038 CATGATT-TATATTGTTAATTG
1 CATGATTATATA-T-TTAATTG
* *
3693059 CATGATTATGTATTTATTTG
1 CATGATTATATATTTAATTG
* *
3693079 CATGATT-TATATTGTTAGTTA
1 CATGATTATATA-T-TTAATTG
* *
3693100 CATGATTAGATATTTAATTA
1 CATGATTATATATTTAATTG
* *
3693120 CATG-TTTTACATTGTTAATTG
1 CATGATTATATA-T-TTAATTG
*
3693141 CATGATTCTATATTTAATTG
1 CATGATTATATATTTAATTG
3693161 TATGTCTATT
Statistics
Matches: 222, Mismatches: 32, Indels: 35
0.77 0.11 0.12
Matches are distributed among these distances:
19 15 0.07
20 85 0.38
21 43 0.19
22 67 0.30
23 12 0.05
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.52
Consensus pattern (20 bp):
CATGATTATATATTTAATTG
Found at i:3693061 original size:41 final size:41
Alignment explanation
Indices: 3692870--3693160 Score: 311
Period size: 41 Copynumber: 7.0 Consensus size: 41
3692860 TAGTATATTC
* *
3692870 CATGATTT-TAATG-TAATTGCATGTTTTATATATTTTTAATTG
1 CATGATTTATATTGTTAATTGCATG-ATTATATA--TTTAATTG
* ** *
3692912 CATGA-TTATATAT-TTATTTATAAGATTATATATGATTAATTG
1 CATGATTTATAT-TGTTAATTGCATGATTATATAT--TTAATTG
* * *
3692954 CATGATTATATATTGTTATTTGCATAATTATATATTTATTTG
1 CATGATT-TATATTGTTAATTGCATGATTATATATTTAATTG
*
3692996 CAAGATTATATATTGTTAATTGCATGATTATATATTTAATTG
1 CATGATT-TATATTGTTAATTGCATGATTATATATTTAATTG
* *
3693038 CATGATTTATATTGTTAATTGCATGATTATGTATTTATTTG
1 CATGATTTATATTGTTAATTGCATGATTATATATTTAATTG
* * * *
3693079 CATGATTTATATTGTTAGTTACATGATTAGATATTTAATTA
1 CATGATTTATATTGTTAATTGCATGATTATATATTTAATTG
* * *
3693120 CATGTTTTACATTGTTAATTGCATGATTCTATATTTAATTG
1 CATGATTTATATTGTTAATTGCATGATTATATATTTAATTG
3693161 TATGTCTATT
Statistics
Matches: 210, Mismatches: 31, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
40 1 0.00
41 103 0.49
42 76 0.36
43 9 0.04
44 21 0.10
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.52
Consensus pattern (41 bp):
CATGATTTATATTGTTAATTGCATGATTATATATTTAATTG
Found at i:3693227 original size:14 final size:14
Alignment explanation
Indices: 3693209--3693257 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
3693199 TGATTGTATA
3693209 ATTATTATTGCATG
1 ATTATTATTGCATG
* *
3693223 GTTATTTATT-CATT
1 ATTA-TTATTGCATG
3693237 ATTATTATTGCATG
1 ATTATTATTGCATG
3693251 ATT-TTAT
1 ATTATTAT
3693258 ATTTATTGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
13 9 0.31
14 15 0.52
15 5 0.17
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.57
Consensus pattern (14 bp):
ATTATTATTGCATG
Found at i:3693278 original size:19 final size:19
Alignment explanation
Indices: 3693241--3693284 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3693231 TTCATTATTA
* * *
3693241 TTATTGCATGATTTTATAT
1 TTATTGCATAATATGATAT
3693260 TTATTGCATAATATGATAT
1 TTATTGCATAATATGATAT
3693279 TATATT
1 T-TATT
3693285 AATTTTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.55
Consensus pattern (19 bp):
TTATTGCATAATATGATAT
Found at i:3693409 original size:20 final size:20
Alignment explanation
Indices: 3693386--3693435 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
3693376 GATTTCATGA
*
3693386 TTATATATTTGCATGGTATT
1 TTATATATTTGCATGGCATT
3693406 TTATAT-TGTTGCATGGCATT
1 TTATATAT-TTGCATGGCATT
3693426 TTATATATTT
1 TTATATATTT
3693436 ATAAAATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.24, C:0.06, G:0.14, T:0.56
Consensus pattern (20 bp):
TTATATATTTGCATGGCATT
Found at i:3693467 original size:8 final size:8
Alignment explanation
Indices: 3693456--3693497 Score: 66
Period size: 8 Copynumber: 5.1 Consensus size: 8
3693446 AAATATATAT
3693456 TTATATGA
1 TTATATGA
*
3693464 TTATTATTA
1 TTA-TATGA
3693473 TTATATGA
1 TTATATGA
3693481 TTATATGA
1 TTATATGA
3693489 TTATATGA
1 TTATATGA
3693497 T
1 T
3693498 ATAAATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
8 24 0.77
9 7 0.23
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.55
Consensus pattern (8 bp):
TTATATGA
Found at i:3693471 original size:3 final size:3
Alignment explanation
Indices: 3693463--3693566 Score: 110
Period size: 3 Copynumber: 35.7 Consensus size: 3
3693453 TATTTATATG
* * * * *
3693463 ATT ATT ATT ATT A-T ATG ATT A-T ATG ATT A-T ATG A-T ATA AAT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
3693508 ATT -TAT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3693553 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
3693567 GTATAATTGC
Statistics
Matches: 84, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
2 8 0.10
3 72 0.86
4 4 0.05
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:3693601 original size:26 final size:25
Alignment explanation
Indices: 3693572--3693634 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 25
3693562 ATTATGTATA
*
3693572 ATTGCATGA-ATGATTTTTATAATAT
1 ATTGCATGATAT-AATTTTATAATAT
*
3693597 GATTGCATGATATAATTTTATGATAT
1 -ATTGCATGATATAATTTTATAATAT
3693623 ATTTGCATGATA
1 A-TTGCATGATA
3693635 ATTTTAGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 1 0.03
26 30 0.91
27 2 0.06
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.46
Consensus pattern (25 bp):
ATTGCATGATATAATTTTATAATAT
Found at i:3696787 original size:12 final size:12
Alignment explanation
Indices: 3696770--3696796 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3696760 TAACACACTA
3696770 AAAAAAAATGGG
1 AAAAAAAATGGG
3696782 AAAAAAAATGGG
1 AAAAAAAATGGG
3696794 AAA
1 AAA
3696797 CCCACCAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.22, T:0.07
Consensus pattern (12 bp):
AAAAAAAATGGG
Found at i:3696871 original size:26 final size:26
Alignment explanation
Indices: 3696836--3696906 Score: 115
Period size: 26 Copynumber: 2.7 Consensus size: 26
3696826 ATACTCAAGA
* *
3696836 TCTTTGGTTGAAATTGGTGGCATAGC
1 TCTTTGGTTGGAATTGGTGGCAAAGC
*
3696862 TTTTTGGTTGGAATTGGTGGCAAAGC
1 TCTTTGGTTGGAATTGGTGGCAAAGC
3696888 TCTTTGGTTGGAATTGGTG
1 TCTTTGGTTGGAATTGGTG
3696907 ACTATCTGCC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.17, C:0.08, G:0.34, T:0.41
Consensus pattern (26 bp):
TCTTTGGTTGGAATTGGTGGCAAAGC
Found at i:3697393 original size:101 final size:101
Alignment explanation
Indices: 3697152--3697453 Score: 353
Period size: 101 Copynumber: 3.0 Consensus size: 101
3697142 TTGAAAAATT
* *
3697152 AATAATAAAATTTTTAATCCTATCAAACTATTAGAGGATTTAAATCTTGAATTAAGTTTTACCAA
1 AATAATAAAATTTTTAATCCTACCAAACTATTAGAGGATTTAAATCTTGAATTAAATTTTACCAA
* * * **
3697217 ACTATT-GAGGACTCAA-GAAATTTTTTTAAAATATT
66 ACTATTGGAAGACTTAATG-AATTTTTATAAAATAAA
* * * * *
3697252 AATAATAAAATTTTTAATCCGACCAAACTGTTGGAGGATTTAAATCTTGAATTAAATCTTATCAA
1 AATAATAAAATTTTTAATCCTACCAAACTATTAGAGGATTTAAATCTTGAATTAAATTTTACCAA
*
3697317 AATATTGGAAGACTTAATGAATTTTTCATAAAA-AAA
66 ACTATTGGAAGACTTAATGAATTTTT-ATAAAATAAA
* * * * * *
3697353 AATAATAAAATTTTCAATCTTACCAAACTATTTGATGATTTAAATATTGAATTAGATTTTACCAA
1 AATAATAAAATTTTTAATCCTACCAAACTATTAGAGGATTTAAATCTTGAATTAAATTTTACCAA
*
3697418 ACTATTGGAATG-TTTAATGAATTTTCT-TAAAATAAA
66 ACTATTGGAA-GACTTAATGAATTTT-TATAAAATAAA
3697454 TTTCATACAT
Statistics
Matches: 171, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
100 68 0.40
101 95 0.56
102 8 0.05
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (101 bp):
AATAATAAAATTTTTAATCCTACCAAACTATTAGAGGATTTAAATCTTGAATTAAATTTTACCAA
ACTATTGGAAGACTTAATGAATTTTTATAAAATAAA
Found at i:3699490 original size:24 final size:22
Alignment explanation
Indices: 3699463--3699508 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
3699453 AAATCAATTG
*
3699463 AAATAAATAAGATAGAAATAAAAT
1 AAATAAATAA-ATACAAA-AAAAT
3699487 AAATAAATAAATACAAAAAAAT
1 AAATAAATAAATACAAAAAAAT
3699509 TGGCTTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.24
23 6 0.29
24 10 0.48
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (22 bp):
AAATAAATAAATACAAAAAAAT
Found at i:3701100 original size:17 final size:18
Alignment explanation
Indices: 3701064--3701110 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
3701054 AGTTTTGCAA
* *
3701064 AAAATTCATAAAAATTTC
1 AAAATTCACAAAAATGTC
3701082 AAAATTCACAAAAA-GTC
1 AAAATTCACAAAAATGTC
* *
3701099 AAGATTCGCAAA
1 AAAATTCACAAA
3701111 GGTTTACAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.55, C:0.15, G:0.06, T:0.23
Consensus pattern (18 bp):
AAAATTCACAAAAATGTC
Found at i:3701247 original size:17 final size:16
Alignment explanation
Indices: 3701227--3701292 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 16
3701217 AAAATTCATA
3701227 AAAGATTCAAGTTTCGT
1 AAAGATTCAAGTTT-GT
3701244 AAAGATTCTAAAAGTTTGT
1 AAAGATTC---AAGTTTGT
*
3701263 AAATGATTCAAGATTGT
1 AAA-GATTCAAGTTTGT
3701280 CAAAGATTTCAAG
1 -AAAGA-TTCAAG
3701293 ATGCATAAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
17 17 0.40
18 9 0.21
19 5 0.12
20 11 0.26
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (16 bp):
AAAGATTCAAGTTTGT
Found at i:3701319 original size:18 final size:18
Alignment explanation
Indices: 3701258--3701319 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
3701248 ATTCTAAAAG
* *
3701258 TTTGTAAATGATTCAAGA
1 TTTGTAAAGGTTTCAAGA
*
3701276 -TTGTCAAAGATTTCAAGA
1 TTTGT-AAAGGTTTCAAGA
***
3701294 TGCATAAAGGTTTCAAGA
1 TTTGTAAAGGTTTCAAGA
3701312 TTTGTAAA
1 TTTGTAAA
3701320 TGTTCTATAT
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
17 4 0.12
18 27 0.84
19 1 0.03
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (18 bp):
TTTGTAAAGGTTTCAAGA
Found at i:3701437 original size:33 final size:34
Alignment explanation
Indices: 3701396--3701476 Score: 110
Period size: 33 Copynumber: 2.4 Consensus size: 34
3701386 CTTTTCAAAT
*
3701396 TCACAAGAATAGAAGATTCGCAA-GAATTTAGAA
1 TCACAAGAATAAAAGATTCGCAAGGAATTTAGAA
* ** *
3701429 TCACAAGAATAAAAGATTTGCAAGGTTTTTAGAT
1 TCACAAGAATAAAAGATTCGCAAGGAATTTAGAA
3701463 TCACAAGAATAAAA
1 TCACAAGAATAAAA
3701477 AATTTGTAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 21 0.50
34 21 0.50
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (34 bp):
TCACAAGAATAAAAGATTCGCAAGGAATTTAGAA
Found at i:3701467 original size:34 final size:34
Alignment explanation
Indices: 3701394--3701506 Score: 129
Period size: 34 Copynumber: 3.4 Consensus size: 34
3701384 CCCTTTTCAA
* * *
3701394 ATTCACAAGAATAGAAGATTCGCAA-GAATTTAG
1 ATTCACAAGAATAAAAGATTTGCAAGGTATTTAG
* *
3701427 AATCACAAGAATAAAAGATTTGCAAGGTTTTTAG
1 ATTCACAAGAATAAAAGATTTGCAAGGTATTTAG
* * * *
3701461 ATTCACAAGAATAAAAAATTTGTAAGGTCTTCAG
1 ATTCACAAGAATAAAAGATTTGCAAGGTATTTAG
*
3701495 ATTCGCAAGAAT
1 ATTCACAAGAAT
3701507 TCAAATTTGT
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
33 22 0.32
34 46 0.68
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (34 bp):
ATTCACAAGAATAAAAGATTTGCAAGGTATTTAG
Found at i:3701518 original size:33 final size:34
Alignment explanation
Indices: 3701429--3701519 Score: 112
Period size: 34 Copynumber: 2.7 Consensus size: 34
3701419 GAATTTAGAA
* * * *
3701429 TCACAAGAATAAAAGATTTGCAAGGTTTTTAGAT
1 TCACAAGAATAAAAAATTTGTAAGGTCTTCAGAT
3701463 TCACAAGAATAAAAAATTTGTAAGGTCTTCAGAT
1 TCACAAGAATAAAAAATTTGTAAGGTCTTCAGAT
* **
3701497 TCGCAAGAAT-TCAAATTTGTAAG
1 TCACAAGAATAAAAAATTTGTAAG
3701520 AAATTCATAT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 11 0.22
34 39 0.78
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (34 bp):
TCACAAGAATAAAAAATTTGTAAGGTCTTCAGAT
Found at i:3701526 original size:17 final size:17
Alignment explanation
Indices: 3701490--3701537 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
3701480 TTGTAAGGTC
* *
3701490 TTCAGATTCGCAAG-AA
1 TTCAAATTCGTAAGAAA
*
3701506 TTCAAATTTGTAAGAAA
1 TTCAAATTCGTAAGAAA
*
3701523 TTCATATTCGTAAGA
1 TTCAAATTCGTAAGA
3701538 TTAACAAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (17 bp):
TTCAAATTCGTAAGAAA
Found at i:3702769 original size:11 final size:10
Alignment explanation
Indices: 3702749--3702773 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3702739 TAAGTTATCC
3702749 TTTTTCTTTT
1 TTTTTCTTTT
3702759 TTTTTCTTTT
1 TTTTTCTTTT
3702769 TTTTT
1 TTTTT
3702774 ACACTTTTTT
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:3707871 original size:22 final size:21
Alignment explanation
Indices: 3707830--3707869 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3707820 GCTTTTGACC
3707830 TTTTTTTTTGTTTACTTTTGG
1 TTTTTTTTTGTTTACTTTTGG
*
3707851 TTTTTTTTTTTTTACTTTT
1 TTTTTTTTTGTTTACTTTT
3707870 TGAAAAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.05, G:0.07, T:0.82
Consensus pattern (21 bp):
TTTTTTTTTGTTTACTTTTGG
Found at i:3708948 original size:26 final size:25
Alignment explanation
Indices: 3708916--3708973 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
3708906 TTTTCCAATA
3708916 AAATTTTTGACAATTTTAATTAATT
1 AAATTTTTGACAATTTTAATTAATT
3708941 AAATTTTTGACAATTTTAATTAATT
1 AAATTTTTGACAATTTTAATTAATT
3708966 AAATTTTT
1 AAATTTTT
3708974 TGTTATCTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (25 bp):
AAATTTTTGACAATTTTAATTAATT
Found at i:3712052 original size:122 final size:120
Alignment explanation
Indices: 3711876--3712276 Score: 458
Period size: 122 Copynumber: 3.3 Consensus size: 120
3711866 TTTGTGCAGA
* * *
3711876 AAAAATTGATACTTTCAACTTTTCC-CCAAAATA-TTTTTTGGAAACTTTAATTTCGAGGAAAAT
1 AAAAATTGATACTTTCAACTTTTCCACAAAAATATTTTTTTAGAAACTTTAATTTCGAGAAAAAT
*** * **
3711939 TGATACTTTCAACTTTTCTTAAAAAAAAAACTTTTTTTTTGAAAA-TTTATTTTTAAG
66 TGATACTTTCAACTTTTCTT--CCCAAAAA-TTTTTTTTTGAAAACTTTAATTTCGAG
* * * *
3711996 GAAAATTGATACTTTCAATTTTTTTC-CAAAAATATTTTTTTAGAAACTTTAATTTCGAAAAAAA
1 AAAAATTGATACTTTCAA-CTTTTCCACAAAAATATTTTTTTAGAAACTTTAATTTCGAGAAAAA
*
3712060 TTGATACTTTCAACTTTTC--CCCAAAAAGGTTTTTTTTGAAAACTTTAATTTCGAG
65 TTGATACTTTCAACTTTTCTTCCCAAAAA-TTTTTTTTTGAAAACTTTAATTTCGAG
* * * * * **
3712115 AAAAATTGATACTTTCAACTTTTTCTCAAAAAAAAACTTTTTTTTGAAAATTTATTTTTAAGAAA
1 AAAAATTGATACTTTCAAC-TTTTC-CACAAAAATA-TTTTTTTAGAAACTTTAATTTCGAGAAA
* *
3712180 AATTGATACTTTTAAC-TTT-TTCCCAAAAATATTTTTTTGAAAACTTTAATTTCGAG
63 AATTGATACTTTCAACTTTTCTTCCCAAAAATTTTTTTTTGAAAACTTTAATTTCGAG
*
3712236 AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
1 AAAAATTGATACTTTCAACTTTTCCACAAAAATATTTTTTT
3712277 TTAATTTTAT
Statistics
Matches: 240, Mismatches: 32, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
118 25 0.10
119 37 0.15
120 23 0.10
121 65 0.27
122 90 0.38
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (120 bp):
AAAAATTGATACTTTCAACTTTTCCACAAAAATATTTTTTTAGAAACTTTAATTTCGAGAAAAAT
TGATACTTTCAACTTTTCTTCCCAAAAATTTTTTTTTGAAAACTTTAATTTCGAG
Found at i:3712217 original size:181 final size:180
Alignment explanation
Indices: 3711875--3712276 Score: 641
Period size: 181 Copynumber: 2.2 Consensus size: 180
3711865 TTTTGTGCAG
* * *
3711875 AAAAAATTGATACTTTCAACTTTTCCCC-AAAATATTTTTTGGAAACTTTAATTTCGAGGAAAAT
1 AAAAAATTGATACTTTCAACTTTTCCCCAAAAATTTTTTTTGAAAACTTTAATTTCGAGAAAAAT
*
3711939 TGATACTTTCAACTTTTCTTAAAAAAAAAACTTTTTTTTTGAAAATTTATTTTTAAGGAAAATTG
66 TGATACTTTCAACTTTTCTTAAAAAAAAAACTTTTTTTTTGAAAATTTATTTTTAAGAAAAATTG
* *
3712004 ATACTTTCAATTTTTTTCCAAAAATATTTTTTT-AGAAACTTTAATTTCGA
131 ATACTTTCAACTTTTTCCCAAAAATATTTTTTTGA-AAACTTTAATTTCGA
3712054 AAAAAATTGATACTTTCAACTTTTCCCCAAAAAGGTTTTTTTTGAAAACTTTAATTTCGAGAAAA
1 AAAAAATTGATACTTTCAACTTTTCCCCAAAAA--TTTTTTTTGAAAACTTTAATTTCGAGAAAA
*
3712119 ATTGATACTTTCAACTTTT-TCTCAAAAAAAAAC-TTTTTTTTGAAAATTTATTTTTAAGAAAAA
64 ATTGATACTTTCAACTTTTCT-TAAAAAAAAAACTTTTTTTTTGAAAATTTATTTTTAAGAAAAA
*
3712182 TTGATACTTTTAACTTTTTCCCAAAAATATTTTTTTGAAAACTTTAATTTCGA
128 TTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAAACTTTAATTTCGA
* *
3712235 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
1 AAAAAATTGATACTTTCAACTTTTCCCCAAAAAT-TTTTTTT
3712277 TTAATTTTAT
Statistics
Matches: 207, Mismatches: 10, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
179 29 0.14
180 11 0.05
181 109 0.53
182 58 0.28
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.44
Consensus pattern (180 bp):
AAAAAATTGATACTTTCAACTTTTCCCCAAAAATTTTTTTTGAAAACTTTAATTTCGAGAAAAAT
TGATACTTTCAACTTTTCTTAAAAAAAAAACTTTTTTTTTGAAAATTTATTTTTAAGAAAAATTG
ATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAAACTTTAATTTCGA
Found at i:3712318 original size:4 final size:4
Alignment explanation
Indices: 3712288--3712405 Score: 56
Period size: 4 Copynumber: 30.0 Consensus size: 4
3712278 TAATTTTATT
*
3712288 TAAA -AAA TAAA -AAA TAAA AAGAA TAAA TAAA TAAA -AGAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TA-AA TAAA TAAA TAAA TA-AA TAAA TAAA
* * * * *
3712335 TAAA -AATA GAAA GAAA -AAA AAAA CTAAA -CAA TCCTAA TATAA T-AA
1 TAAA TAA-A TAAA TAAA TAAA TAAA -TAAA TAAA T--AAA TA-AA TAAA
3712380 TAAA TAAA TAAA T-AA TAAA -AAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
3712406 AATAATAAAA
Statistics
Matches: 92, Mismatches: 6, Indels: 32
0.71 0.05 0.25
Matches are distributed among these distances:
3 23 0.25
4 54 0.59
5 12 0.13
6 3 0.03
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (4 bp):
TAAA
Found at i:3712408 original size:16 final size:16
Alignment explanation
Indices: 3712289--3712416 Score: 86
Period size: 16 Copynumber: 7.8 Consensus size: 16
3712279 AATTTTATTT
3712289 AAAA-AATAAAAAATA
1 AAAATAATAAAAAATA
*
3712304 AAAAGAATAAATAAAT-
1 AAAATAATAAA-AAATA
*
3712320 AAAAGAATAAATAAATA
1 AAAATAATAAA-AAATA
3712337 AAAATAGA-AAGAAAA-A
1 AAAATA-ATAA-AAAATA
* * *
3712353 AAAA-ACTAAACAATCCT
1 AAAATAATAAAAAAT--A
* *
3712370 AATATAATAATAAATAA
1 AAAATAATAAAAAAT-A
3712387 ATAAATAATAAAAAATA
1 A-AAATAATAAAAAATA
3712404 AAAATAATAAAAA
1 AAAATAATAAAAA
3712417 GAAACAAAAA
Statistics
Matches: 90, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
14 3 0.03
15 7 0.08
16 39 0.43
17 20 0.22
18 21 0.23
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAATAATAAAAAATA
Found at i:3712425 original size:19 final size:20
Alignment explanation
Indices: 3712385--3712426 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
3712375 AATAATAAAT
*
3712385 AAATAAATAATAAAAAATAA
1 AAATAAATAATAAAAAACAA
3712405 AAAT-AATAA-AAAGAAACAA
1 AAATAAATAATAAA-AAACAA
3712424 AAA
1 AAA
3712427 AAAAACCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 3 0.15
19 13 0.65
20 4 0.20
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (20 bp):
AAATAAATAATAAAAAACAA
Found at i:3712429 original size:23 final size:24
Alignment explanation
Indices: 3712381--3712430 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
3712371 ATATAATAAT
* *
3712381 AAATAAATAAATAATAAAAAATAA
1 AAATAAATAAATAAGAAAAAAAAA
3712405 AAAT-AATAAA-AAGAAACAAAAAA
1 AAATAAATAAATAAGAAA-AAAAAA
3712428 AAA
1 AAA
3712431 ACCTGGGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.22
23 14 0.61
24 4 0.17
ACGTcount: A:0.82, C:0.02, G:0.02, T:0.14
Consensus pattern (24 bp):
AAATAAATAAATAAGAAAAAAAAA
Found at i:3712719 original size:21 final size:22
Alignment explanation
Indices: 3712684--3712727 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
3712674 TTCAGCAGAA
*
3712684 CCCTTCTTCTCTTCTCTCTCTT
1 CCCTTCTTCTCTTCTCTCCCTT
3712706 CCCTTCTT-TCTTCTCTCCCTT
1 CCCTTCTTCTCTTCTCTCCCTT
3712727 C
1 C
3712728 TCTCTAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (22 bp):
CCCTTCTTCTCTTCTCTCCCTT
Found at i:3713299 original size:28 final size:28
Alignment explanation
Indices: 3713246--3713300 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
3713236 AAAAAGGAAA
*
3713246 AAAAAGAAAAAAATAGTAATAGATAATTT
1 AAAAAGAAAAAAATAG-AATAAATAATTT
*
3713275 AAAAAGAAAATAATTAG-ATAAATAAT
1 AAAAAGAAAA-AAATAGAATAAATAAT
3713301 AATATTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 8 0.35
29 10 0.43
30 5 0.22
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (28 bp):
AAAAAGAAAAAAATAGAATAAATAATTT
Done.