Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold47
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: 2157611
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 149227 characters in sequence are not A, C, G, or T
File 14 of 15
Found at i:1864680 original size:14 final size:15
Alignment explanation
Indices: 1864661--1864689 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1864651 AATTAAAAAA
1864661 TCAAAAACTT-GAAC
1 TCAAAAACTTCGAAC
1864675 TCAAAAACTTCGAAC
1 TCAAAAACTTCGAAC
1864690 CTAAAATCAC
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:0.48, C:0.24, G:0.07, T:0.21
Consensus pattern (15 bp):
TCAAAAACTTCGAAC
Found at i:1865880 original size:18 final size:17
Alignment explanation
Indices: 1865859--1865950 Score: 63
Period size: 18 Copynumber: 5.5 Consensus size: 17
1865849 TGATTAATTT
1865859 ATAATATATAATATTAAA
1 ATAATATAT-ATATTAAA
*
1865877 ATAATAAATAT-TTAAAA
1 ATAATATATATATT-AAA
1865894 ATTAAT-TATATA-TATAA
1 A-TAATATATATATTA-AA
* *
1865911 AT-ATA-A-ATTTTAAT
1 ATAATATATATATTAAA
1865925 A-AATATATATATTAAA
1 ATAATATATATATTAAA
1865941 ATTAATATAT
1 A-TAATATAT
1865951 TATAACAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 22
0.67 0.07 0.26
Matches are distributed among these distances:
14 7 0.12
15 6 0.11
16 11 0.19
17 14 0.25
18 19 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAATATATATATTAAA
Found at i:1865939 original size:16 final size:15
Alignment explanation
Indices: 1865861--1865952 Score: 55
Period size: 16 Copynumber: 5.9 Consensus size: 15
1865851 ATTAATTTAT
1865861 AATATATAATATT-AA
1 AATATAT-ATATTAAA
*
1865876 AATAATAAATATTTAAA
1 AAT-ATATATA-TTAAA
*
1865893 AAT-TAATTATATATATA
1 AATAT-A-TATAT-TAAA
* *
1865910 AATATAAATTTTAATA
1 AATATATATATTAA-A
1865926 AATATATATATTAAA
1 AATATATATATTAAA
*
1865941 ATTA-ATATATTA
1 AATATATATATTA
1865953 TAACAAAATT
Statistics
Matches: 60, Mismatches: 9, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
14 8 0.13
15 13 0.22
16 23 0.38
17 15 0.25
18 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATATATATTAAA
Found at i:1865999 original size:62 final size:63
Alignment explanation
Indices: 1865853--1866002 Score: 154
Period size: 64 Copynumber: 2.4 Consensus size: 63
1865843 TTAATATGAT
*
1865853 TAATTT-ATAATATATAATATTAAAATAATAAATATTTAAAAATTAATTATATATATAAATATAA
1 TAATTTAATAATATATAATATTAAAATAAT-AATATTTAAAAA-TAATTATATATATAAAAATAA
* *
1865917 -ATTTTAATAA-ATATATATATTAAAATTAAT-ATATTATAACAA-AATT-T-TACT-TAAAAAT
1 TAATTTAATAATATATA-ATATTAAAA-TAATAATATT-TAAAAATAATTATATA-TATAAAAAT
1865975 AA
62 AA
1865977 TAATTTAATAATATATTAATATTAAA
1 TAATTTAATAATATA-TAATATTAAA
1866003 TTACTTTAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
60 10 0.14
61 11 0.15
62 15 0.20
63 16 0.22
64 18 0.24
65 4 0.05
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (63 bp):
TAATTTAATAATATATAATATTAAAATAATAATATTTAAAAATAATTATATATATAAAAATAA
Found at i:1866138 original size:16 final size:16
Alignment explanation
Indices: 1866083--1866139 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
1866073 TAAACTCGAC
1866083 ACTTAAA-AAAGTTCAA
1 ACTTAAATAAA-TTCAA
*
1866099 A-TTCAAATAAATT-TA
1 ACTT-AAATAAATTCAA
*
1866114 ACCTAAATAAATTCAA
1 ACTTAAATAAATTCAA
1866130 ACTTAAATAA
1 ACTTAAATAA
1866140 TAAAAACCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 13 0.39
16 17 0.52
17 3 0.09
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.30
Consensus pattern (16 bp):
ACTTAAATAAATTCAA
Found at i:1878154 original size:2 final size:2
Alignment explanation
Indices: 1878109--1878135 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1878099 CCTTTGGATC
1878109 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1878136 CACACACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1880825 original size:86 final size:88
Alignment explanation
Indices: 1880704--1880877 Score: 289
Period size: 86 Copynumber: 2.0 Consensus size: 88
1880694 CAGTAAAACA
*
1880704 AACTTCAAACAGGAAAATTTTCTAAACATCAGAAAACATGGTCTTTCGAAACAAGGAATTAAGTT
1 AACTTCAAACAGGAAAATTTTCTAAACATCAGAAAACATGGTCTTTCGAAACAAGGAATGAAGTT
*
1880769 CCTATATTGTCAAGAAGCATGAT
66 CCTATATTCTCAAGAAGCATGAT
* * *
1880792 AACTTCAAACA-GAAAA-TTTCTAAACATTAGAAAACCTGGTCTTTCGAAACAAGGACTGAAGTT
1 AACTTCAAACAGGAAAATTTTCTAAACATCAGAAAACATGGTCTTTCGAAACAAGGAATGAAGTT
1880855 CCTATATTCTCAAGAAGCATGAT
66 CCTATATTCTCAAGAAGCATGAT
1880878 TTGCTCAGTC
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
86 65 0.80
87 5 0.06
88 11 0.14
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.27
Consensus pattern (88 bp):
AACTTCAAACAGGAAAATTTTCTAAACATCAGAAAACATGGTCTTTCGAAACAAGGAATGAAGTT
CCTATATTCTCAAGAAGCATGAT
Found at i:1886850 original size:14 final size:14
Alignment explanation
Indices: 1886827--1886863 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1886817 AATCAAATCA
1886827 TATTAAATTATATT
1 TATTAAATTATATT
* *
1886841 TATTATATTATTTT
1 TATTAAATTATATT
1886855 TATTAAATT
1 TATTAAATT
1886864 TAAAAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTAAATTATATT
Found at i:1886936 original size:26 final size:26
Alignment explanation
Indices: 1886907--1886968 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
1886897 AATAATTCAC
1886907 TAATTTATGAAGTTAATA-TTTTA-TTT
1 TAATTTAT-AA-TTAATATTTTTATTTT
*
1886933 TAATTTATTATTAATATTTTTATTTT
1 TAATTTATAATTAATATTTTTATTTT
1886959 TAATTT-TAAT
1 TAATTTATAAT
1886969 AATTTATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 6 0.19
25 9 0.28
26 17 0.53
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (26 bp):
TAATTTATAATTAATATTTTTATTTT
Found at i:1886971 original size:24 final size:24
Alignment explanation
Indices: 1886920--1886971 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1886910 TTTATGAAGT
*
1886920 TAATATTTTATTTTAATTTATTAT
1 TAATATTTTATTTTAATTTATTAA
1886944 TAATATTTTTATTTTTAA-TT-TTAA
1 TAATA-TTTTA-TTTTAATTTATTAA
1886968 TAAT
1 TAAT
1886972 TTATTTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 12 0.48
25 7 0.28
26 6 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TAATATTTTATTTTAATTTATTAA
Found at i:1887105 original size:19 final size:19
Alignment explanation
Indices: 1887028--1887107 Score: 58
Period size: 19 Copynumber: 4.2 Consensus size: 19
1887018 TAAAAAATTT
*
1887028 TAAATTATTATA-TTAA-A
1 TAAATTATTTTATTTAATA
* *
1887045 TAAATTATGTTTAATGTATTA
1 TAAATTAT-TTT-ATTTAATA
* * *
1887066 AAAATTA-TTAAATTAATTA
1 TAAATTATTTTATTTAA-TA
1887085 TAAATTATTTTATTTAATA
1 TAAATTATTTTATTTAATA
1887104 TAAA
1 TAAA
1887108 AAATTATCTT
Statistics
Matches: 46, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
17 8 0.17
18 5 0.11
19 17 0.37
20 9 0.20
21 7 0.15
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
TAAATTATTTTATTTAATA
Found at i:1887342 original size:10 final size:10
Alignment explanation
Indices: 1887327--1887396 Score: 54
Period size: 10 Copynumber: 6.9 Consensus size: 10
1887317 TTGAATCAAG
1887327 TTAAATTAAT
1 TTAAATTAAT
1887337 TTAAATT-AT
1 TTAAATTAAT
*
1887346 TATAAATTTAT
1 T-TAAATTAAT
1887357 CTTAAATGTAAT
1 -TTAAAT-TAAT
* * *
1887369 ATAATTTAAA
1 TTAAATTAAT
*
1887379 TTAAATTTA-
1 TTAAATTAAT
1887388 TTAAATTAA
1 TTAAATTAA
1887397 ATGCATAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
9 11 0.23
10 22 0.46
11 11 0.23
12 4 0.08
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (10 bp):
TTAAATTAAT
Found at i:1887363 original size:21 final size:20
Alignment explanation
Indices: 1887328--1887390 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
1887318 TGAATCAAGT
*
1887328 TAAATTAATTTAAATTATTA
1 TAAATTTATTTAAATTATTA
*
1887348 TAAATTTATCTTAAATGTAATA
1 TAAATTTAT-TTAAAT-TATTA
*
1887370 T-AATTTAAATTAAATTTATTA
1 TAAATTT-ATTTAAA-TTATTA
1887391 AATTAAATGC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
20 8 0.23
21 20 0.57
22 7 0.20
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
TAAATTTATTTAAATTATTA
Found at i:1887591 original size:3 final size:3
Alignment explanation
Indices: 1887585--1887612 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1887575 TTTTATTTGG
1887585 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1887613 AATTTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1888244 original size:14 final size:15
Alignment explanation
Indices: 1888213--1888258 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
1888203 TTTAAAAAAA
*
1888213 TAATATCTTATAAATT
1 TAATAT-TTATAATTT
1888229 TAATATTTA-AATTT
1 TAATATTTATAATTT
*
1888243 TAACATTTATAATTT
1 TAATATTTATAATTT
1888258 T
1 T
1888259 TTTTTTTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 12 0.44
15 9 0.33
16 6 0.22
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATATTTATAATTT
Found at i:1888531 original size:2 final size:2
Alignment explanation
Indices: 1888524--1888563 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1888514 TGTTCTGCTG
*
1888524 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1888564 CTATGCAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1900591 original size:240 final size:239
Alignment explanation
Indices: 1900169--1900647 Score: 940
Period size: 240 Copynumber: 2.0 Consensus size: 239
1900159 TAAAGGACAG
1900169 TTATAATTGTTTTTATTATTATTTTTTTTTCATTTGATCGTTCATTATATCATAAAAGTGATGAG
1 TTATAATTGTTTTTATTATTATTTTTTTTTCATTTGATCGTTCATTATATCATAAAAGTGATGAG
*
1900234 AAATCTTGTTGTAAACCAATATTTGTTAATAGCAAAGTGTTTTGTGTGATTTATACATTATAATG
66 AAATCTTGTTGTAAACCAATATTTGTTAATAGCAAAGTGTTTTGTGTGATTTATACATTATAATA
1900299 CTACTAATAATAACCATGAAATCTTATATGATTAACTTTAGCGGCTAAAAGCAGCCCTTGAAGGT
131 CTACTAATAATAACCATGAAATCTTATATGATTAACTTTAGCGGCTAAAAGCAGCCCTTGAAGGT
1900364 GCTTTGACACTATGATTTTGATTCATCCTTGTTATTATGTACTA
196 GCTTTGACACTATGATTTTGATTCATCCTTGTTATTATGTACTA
1900408 TTATAATTGTTTTTATTATTATTTTTTTTTTCATTTGATCGTTCATTATATCATAAAAGTGATGA
1 TTATAATTGTTTTTATTATTA-TTTTTTTTTCATTTGATCGTTCATTATATCATAAAAGTGATGA
1900473 GAAATCTTGTTGTAAACCAATATTTGTTAATAGCAAAGTGTTTTGTGTGATTTATACATTATAAT
65 GAAATCTTGTTGTAAACCAATATTTGTTAATAGCAAAGTGTTTTGTGTGATTTATACATTATAAT
1900538 ACTACTAATAATAACCATGAAATCTTATATGATTAACTTTAGCGGCTAAAAGCAGCCCTTGAAGG
130 ACTACTAATAATAACCATGAAATCTTATATGATTAACTTTAGCGGCTAAAAGCAGCCCTTGAAGG
1900603 TGCTTTGACACTATGATTTTGATTCATCCTTGTTATTATGTACTA
195 TGCTTTGACACTATGATTTTGATTCATCCTTGTTATTATGTACTA
1900648 CTGACTACGC
Statistics
Matches: 238, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
239 21 0.09
240 217 0.91
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.44
Consensus pattern (239 bp):
TTATAATTGTTTTTATTATTATTTTTTTTTCATTTGATCGTTCATTATATCATAAAAGTGATGAG
AAATCTTGTTGTAAACCAATATTTGTTAATAGCAAAGTGTTTTGTGTGATTTATACATTATAATA
CTACTAATAATAACCATGAAATCTTATATGATTAACTTTAGCGGCTAAAAGCAGCCCTTGAAGGT
GCTTTGACACTATGATTTTGATTCATCCTTGTTATTATGTACTA
Found at i:1904844 original size:3 final size:3
Alignment explanation
Indices: 1904836--1904891 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
1904826 ATGTATCTGT
1904836 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1904884 AT- ATA ATA
1 ATA ATA ATA
1904892 GGAATGGTGG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1905302 original size:16 final size:16
Alignment explanation
Indices: 1905237--1905336 Score: 62
Period size: 16 Copynumber: 6.2 Consensus size: 16
1905227 CAAAATCGAC
*
1905237 TGATTCGAAATTCGAAA
1 TGATTCG-AACTCGAAA
*
1905254 TAATTC-ATACTCGAAA
1 TGATTCGA-ACTCGAAA
*
1905270 TGATTCGAA-TCCAAAA
1 TGATTCGAACT-CGAAA
*
1905286 TGATTTGAACTCGAAA
1 TGATTCGAACTCGAAA
**
1905302 TGACCCGAA-TCCGAAA
1 TGATTCGAACT-CGAAA
* * *
1905318 TAATTCAAACTTGAAA
1 TGATTCGAACTCGAAA
1905334 TGA
1 TGA
1905337 CACGGACAAT
Statistics
Matches: 62, Mismatches: 15, Indels: 13
0.69 0.17 0.14
Matches are distributed among these distances:
15 3 0.05
16 51 0.82
17 8 0.13
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (16 bp):
TGATTCGAACTCGAAA
Found at i:1905302 original size:32 final size:32
Alignment explanation
Indices: 1905251--1905337 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 32
1905241 TCGAAATTCG
* **
1905251 AAATAATTCATACTCGAAATGATTCGAATCCA
1 AAATAATTCAAACTCGAAATGACCCGAATCCA
* ** *
1905283 AAATGATTTGAACTCGAAATGACCCGAATCCG
1 AAATAATTCAAACTCGAAATGACCCGAATCCA
*
1905315 AAATAATTCAAACTTGAAATGAC
1 AAATAATTCAAACTCGAAATGAC
1905338 ACGGACAATT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (32 bp):
AAATAATTCAAACTCGAAATGACCCGAATCCA
Found at i:1906201 original size:16 final size:16
Alignment explanation
Indices: 1906156--1906235 Score: 70
Period size: 16 Copynumber: 5.0 Consensus size: 16
1906146 CAAATTCGAT
*
1906156 TGACCCGAATTCGAAA
1 TGACTCGAATTCGAAA
* ** *
1906172 TAACTTAAACTCGAAA
1 TGACTCGAATTCGAAA
*
1906188 TGGCTCGAATTCGAAA
1 TGACTCGAATTCGAAA
* *
1906204 TAACTCGAATTTGAAA
1 TGACTCGAATTCGAAA
* *
1906220 TGACCCGAACTCGAAA
1 TGACTCGAATTCGAAA
1906236 ATAAATCAAA
Statistics
Matches: 47, Mismatches: 17, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (16 bp):
TGACTCGAATTCGAAA
Found at i:1906220 original size:32 final size:32
Alignment explanation
Indices: 1906156--1906245 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
1906146 CAAATTCGAT
*
1906156 TGACCCGAATTCGAAATAACTTAAACTCGAAA
1 TGACCCGAATTCGAAATAACTCAAACTCGAAA
* * * * *
1906188 TGGCTCGAATTCGAAATAACTCGAATTTGAAA
1 TGACCCGAATTCGAAATAACTCAAACTCGAAA
* *
1906220 TGACCCGAACTCGAAAATAAATCAAA
1 TGACCCGAATTCG-AAATAACTCAAA
1906246 ATTTTTAAAA
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
32 36 0.78
33 10 0.22
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.22
Consensus pattern (32 bp):
TGACCCGAATTCGAAATAACTCAAACTCGAAA
Found at i:1907599 original size:3 final size:3
Alignment explanation
Indices: 1907591--1907621 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1907581 AATCCTCATC
1907591 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1907622 GTTAAAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1919909 original size:21 final size:23
Alignment explanation
Indices: 1919869--1919911 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
1919859 AATGCAGACA
*
1919869 AAAAACACCTTTATAATTGAAAC
1 AAAAACACATTTATAATTGAAAC
1919892 AAAAACA-ATTTA-AATTGAAA
1 AAAAACACATTTATAATTGAAA
1919912 TAATTAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 4 0.21
23 7 0.37
ACGTcount: A:0.58, C:0.12, G:0.05, T:0.26
Consensus pattern (23 bp):
AAAAACACATTTATAATTGAAAC
Found at i:1920764 original size:6 final size:6
Alignment explanation
Indices: 1920729--1920763 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1920719 TAAAAAAATA
*
1920729 AATTTT AATTTT AATTTT AATTTT AATTTC AATTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTT
1920764 CGGATGATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (6 bp):
AATTTT
Found at i:1922071 original size:3 final size:3
Alignment explanation
Indices: 1922051--1922086 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
1922041 CATCCAAATT
* *
1922051 CAG CAA CAG CAA CAG CAG CAG CAG CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
1922087 AAACAGCAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.39, C:0.33, G:0.28, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:1925939 original size:21 final size:21
Alignment explanation
Indices: 1925913--1925964 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
1925903 AATGGTTACA
*
1925913 ATTTATATATTTTTTTATTAT
1 ATTTATATAATTTTTTATTAT
1925934 ATTTATATAATTTTTTATTAT
1 ATTTATATAATTTTTTATTAT
*
1925955 AATTATATAA
1 ATTTATATAA
1925965 AAATTATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTATATAATTTTTTATTAT
Found at i:1926019 original size:15 final size:16
Alignment explanation
Indices: 1925975--1926029 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
1925965 AAATTATTAT
1925975 ATATTAAAAATTTTTAAA
1 ATATTAAAAA--TTTAAA
*
1925993 ATATTAATAATTTAAA
1 ATATTAAAAATTTAAA
*
1926009 TTA-TAAAAATTTAAAA
1 ATATTAAAAATTT-AAA
1926025 ATATT
1 ATATT
1926030 TTTATATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
15 8 0.26
16 13 0.42
17 1 0.03
18 9 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATTAAAAATTTAAA
Found at i:1926044 original size:32 final size:33
Alignment explanation
Indices: 1925969--1926044 Score: 77
Period size: 32 Copynumber: 2.3 Consensus size: 33
1925959 ATATAAAAAT
*
1925969 TATTATA-TATTAAAAATTTTTAAAATATTAATA
1 TATTATATTA-TAAAAATTTTAAAAATATTAATA
* **
1926002 -ATTTAAATTATAAAAA-TTTAAAAATATTTTTA
1 TA-TTATATTATAAAAATTTTAAAAATATTAATA
1926034 TATTATATTAT
1 TATTATATTAT
1926045 TTATATATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
32 22 0.63
33 11 0.31
34 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (33 bp):
TATTATATTATAAAAATTTTAAAAATATTAATA
Found at i:1926051 original size:16 final size:16
Alignment explanation
Indices: 1926026--1926071 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
1926016 AATTTAAAAA
*
1926026 TATTTTTATATTATAT
1 TATTTATATATTATAT
1926042 TATTTATATATTATAT
1 TATTTATATATTATAT
*
1926058 TATATATTATATTA
1 TATTTA-TATATTA
1926072 CGTAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 20 0.74
17 7 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTATATATTATAT
Found at i:1926062 original size:12 final size:12
Alignment explanation
Indices: 1926037--1926071 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1926027 ATTTTTATAT
1926037 TATATTAT-TTA
1 TATATTATATTA
1926048 TATATTATATTA
1 TATATTATATTA
1926060 TATATTATATTA
1 TATATTATATTA
1926072 CGTAATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATTATATTA
Found at i:1926395 original size:6 final size:6
Alignment explanation
Indices: 1926384--1926436 Score: 52
Period size: 6 Copynumber: 8.2 Consensus size: 6
1926374 TATAAGCATA
* *
1926384 TTAATT TTAATT TTAATT TAAAAAAT TTAATT AATTAATT TTAATT TTAATT
1 TTAATT TTAATT TTAATT T--TAATT TTAATT --TTAATT TTAATT TTAATT
1926436 T
1 T
1926437 AATCTAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
6 29 0.74
8 10 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
TTAATT
Found at i:1926533 original size:16 final size:16
Alignment explanation
Indices: 1926500--1926590 Score: 85
Period size: 16 Copynumber: 5.7 Consensus size: 16
1926490 AAAATGACAC
*
1926500 AAATTTAGAAT-ATCTT
1 AAATTTAAAATAAT-TT
**
1926516 AAATTTAAAATTGTTT
1 AAATTTAAAATAATTT
1926532 AAATTTAAAATAATTT
1 AAATTTAAAATAATTT
* *
1926548 AAACTTAAAATGATTT
1 AAATTTAAAATAATTT
* * *
1926564 GATTTTAAAATAACTT
1 AAATTTAAAATAATTT
*
1926580 GAATTTAAAAT
1 AAATTTAAAAT
1926591 GACTCAAACT
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
16 61 0.98
17 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (16 bp):
AAATTTAAAATAATTT
Found at i:1926591 original size:32 final size:32
Alignment explanation
Indices: 1926500--1926592 Score: 107
Period size: 32 Copynumber: 2.9 Consensus size: 32
1926490 AAAATGACAC
* *
1926500 AAATTTAGAATATCTTAAATTTAAAATTG-TTT
1 AAATTTAAAATAACTTAAATTTAAAA-TGATTT
* *
1926532 AAATTTAAAATAATTTAAACTTAAAATGATTT
1 AAATTTAAAATAACTTAAATTTAAAATGATTT
* * *
1926564 GATTTTAAAATAACTTGAATTTAAAATGA
1 AAATTTAAAATAACTTAAATTTAAAATGA
1926593 CTCAAACTTG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 2 0.04
32 49 0.96
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (32 bp):
AAATTTAAAATAACTTAAATTTAAAATGATTT
Found at i:1928775 original size:51 final size:51
Alignment explanation
Indices: 1928715--1928813 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
1928705 AAGAAAAAAA
* *
1928715 TTCTGATATTATCCGGCAACTTGTCAACATAATTATTGAGAATGATCAACT
1 TTCTGATATTATCCAGCAACCTGTCAACATAATTATTGAGAATGATCAACT
** *
1928766 TTCTGATATTATTTAGCAACCTGTCAACATAATTGTTGAGAATGATCA
1 TTCTGATATTATCCAGCAACCTGTCAACATAATTATTGAGAATGATCA
1928814 GCAGTTATCA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (51 bp):
TTCTGATATTATCCAGCAACCTGTCAACATAATTATTGAGAATGATCAACT
Found at i:1935798 original size:77 final size:78
Alignment explanation
Indices: 1935676--1935836 Score: 288
Period size: 77 Copynumber: 2.1 Consensus size: 78
1935666 CAACAAATAG
1935676 GAAACAAAAACAAAACCAAGAAAAAAAAAAAGTATAAAACAAGGAGATTTTATTTCTAATAAAAA
1 GAAACAAAAACAAAACC-A-AAAAAAAAAAAGTATAAAACAAGGAGATTTTATTTCTAATAAAAA
1935741 GCTGAAATTACTGAA
64 GCTGAAATTACTGAA
*
1935756 GAAACAAAAACAAAACC-AAAAAAAAAGAGTATAAAACAAGGAGATTTTATTTCTAATAAAAAGC
1 GAAACAAAAACAAAACCAAAAAAAAAAAAGTATAAAACAAGGAGATTTTATTTCTAATAAAAAGC
1935820 TGAAATTACTGAA
66 TGAAATTACTGAA
1935833 GAAA
1 GAAA
1935837 AACTCCATCA
Statistics
Matches: 80, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
77 63 0.79
80 17 0.21
ACGTcount: A:0.60, C:0.10, G:0.12, T:0.19
Consensus pattern (78 bp):
GAAACAAAAACAAAACCAAAAAAAAAAAAGTATAAAACAAGGAGATTTTATTTCTAATAAAAAGC
TGAAATTACTGAA
Found at i:1937765 original size:2 final size:2
Alignment explanation
Indices: 1937758--1937795 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1937748 CTATATCTAG
1937758 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
1937796 CACTTCATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1940675 original size:19 final size:19
Alignment explanation
Indices: 1940648--1940687 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1940638 ATTTAATCTG
*
1940648 ATTATTTTAATAATTTTTT
1 ATTAATTTAATAATTTTTT
*
1940667 ATTAATTTAATTATTTTTT
1 ATTAATTTAATAATTTTTT
1940686 AT
1 AT
1940688 CGATTTATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTAATTTAATAATTTTTT
Found at i:1940693 original size:19 final size:19
Alignment explanation
Indices: 1940653--1940694 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1940643 ATCTGATTAT
*
1940653 TTTAATAATTTTTTATTAA
1 TTTAATAATTTTTTATCAA
* *
1940672 TTTAATTATTTTTTATCGA
1 TTTAATAATTTTTTATCAA
1940691 TTTA
1 TTTA
1940695 TCATATTCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTAATAATTTTTTATCAA
Found at i:1942101 original size:16 final size:14
Alignment explanation
Indices: 1942079--1942116 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 14
1942069 AAAACTTATT
1942079 AAATTATATGATAAA
1 AAATTATAT-ATAAA
1942094 ATAATTATA-ATAAA
1 A-AATTATATATAAA
1942108 AAATTATAT
1 AAATTATAT
1942117 TTATATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 7 0.33
14 6 0.29
15 1 0.05
16 7 0.33
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (14 bp):
AAATTATATATAAA
Found at i:1942544 original size:6 final size:6
Alignment explanation
Indices: 1942492--1942531 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
1942482 TTTCCTTACC
*
1942492 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTCT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
1942532 CTCTCTCTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
CTTTTT
Found at i:1943046 original size:8 final size:8
Alignment explanation
Indices: 1943006--1943045 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1942996 GCTATAAATG
1943006 CATATATA
1 CATATATA
*
1943014 CATACATA
1 CATATATA
*
1943022 CATACATA
1 CATATATA
1943030 CATATATA
1 CATATATA
*
1943038 TATATATA
1 CATATATA
1943046 TCTTTATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (8 bp):
CATATATA
Found at i:1943046 original size:12 final size:12
Alignment explanation
Indices: 1943006--1943037 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1942996 GCTATAAATG
1943006 CATATATACATA
1 CATATATACATA
*
1943018 CATACATACATA
1 CATATATACATA
1943030 CATATATA
1 CATATATA
1943038 TATATATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (12 bp):
CATATATACATA
Found at i:1945170 original size:2 final size:2
Alignment explanation
Indices: 1945163--1945195 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1945153 CTAGAGGAGG
1945163 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1945196 CTTATGCTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1945579 original size:2 final size:2
Alignment explanation
Indices: 1945572--1945599 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1945562 CCAACTCTAT
1945572 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1945600 CTTCAGACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1947550 original size:70 final size:70
Alignment explanation
Indices: 1947437--1947567 Score: 235
Period size: 70 Copynumber: 1.9 Consensus size: 70
1947427 ATATTCAGAG
1947437 AAACAAGAAGGAAGATGCATTCATCGTAATATTATGACATCATTTTGTATATATATATATATATA
1 AAACAAGAAGGAAGATGCATTCATCGTAATATTATGACATCATTTTGTATATATATATATATATA
1947502 TATAT
66 TATAT
* * *
1947507 AAACAATAAGGAAGATGCATTCATCGTAATATTATGACATCATTTTGTGTGTATATATATA
1 AAACAAGAAGGAAGATGCATTCATCGTAATATTATGACATCATTTTGTATATATATATATA
1947568 AAGTGATCAC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 58 1.00
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (70 bp):
AAACAAGAAGGAAGATGCATTCATCGTAATATTATGACATCATTTTGTATATATATATATATATA
TATAT
Found at i:1951773 original size:2 final size:2
Alignment explanation
Indices: 1951766--1951802 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1951756 AAGTGAGACA
1951766 AT AT AT AT 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 AT AT AT AT A
1951803 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1951807 original size:2 final size:2
Alignment explanation
Indices: 1951802--1951838 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1951792 ATATATATAT
1951802 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1951839 TTGAAATTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1954049 original size:19 final size:20
Alignment explanation
Indices: 1954025--1954072 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1954015 ACAATTCATG
1954025 ATGTATCGATA-TAATG-AAC
1 ATGTATCGATACTAA-GCAAC
* *
1954044 ATGTATCAATACTAAGCAAT
1 ATGTATCGATACTAAGCAAC
1954064 ATGTATCGA
1 ATGTATCGA
1954073 CACATCTGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACTAAGCAAC
Found at i:1961085 original size:16 final size:16
Alignment explanation
Indices: 1961064--1961127 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 16
1961054 TTCTATTTAT
1961064 TTTTAAAATATTAATA
1 TTTTAAAATATTAATA
1961080 TTTT-AAATAGTT-ATA
1 TTTTAAAATA-TTAATA
1961095 TTTTAATCATAATATTAA-A
1 TTTT-A--A-AATATTAATA
1961114 TTATTAAAATATTA
1 TT-TTAAAATATTA
1961128 TAGTAATATT
Statistics
Matches: 40, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
15 12 0.30
16 13 0.32
17 1 0.03
19 7 0.17
20 7 0.17
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (16 bp):
TTTTAAAATATTAATA
Found at i:1961087 original size:15 final size:15
Alignment explanation
Indices: 1961060--1961100 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
1961050 TAAATTCTAT
1961060 TTAT-TTTTAAAATA-
1 TTATATTTT-AAATAG
1961074 TTAATATTTTAAATAG
1 TT-ATATTTTAAATAG
1961090 TTATATTTTAA
1 TTATATTTTAA
1961101 TCATAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.08
15 16 0.67
16 6 0.25
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
TTATATTTTAAATAG
Found at i:1961197 original size:21 final size:20
Alignment explanation
Indices: 1961172--1961217 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
1961162 TAGAACATTA
1961172 ATTAT-ACAAATATTTAAAAAT
1 ATTATAACAAATA-TT-AAAAT
*
1961193 ATTATAATAAATATTAAAAT
1 ATTATAACAAATATTAAAAT
1961213 ATTAT
1 ATTAT
1961218 TTTACAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 10 0.43
21 7 0.30
22 6 0.26
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTATAACAAATATTAAAAT
Found at i:1961646 original size:16 final size:16
Alignment explanation
Indices: 1961625--1961670 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 16
1961615 ATAAAATTGT
1961625 TTTATTAAATAATAAA
1 TTTATTAAATAATAAA
1961641 TTTATTAAAATAATAAA
1 TTTATT-AAATAATAAA
1961658 TTATATT-AATAAT
1 TT-TATTAAATAAT
1961671 TTATTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 12 0.43
17 12 0.43
18 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTTATTAAATAATAAA
Found at i:1961653 original size:17 final size:17
Alignment explanation
Indices: 1961625--1961709 Score: 72
Period size: 17 Copynumber: 5.1 Consensus size: 17
1961615 ATAAAATTGT
1961625 TTTATT-AAATAATAAA
1 TTTATTAAAATAATAAA
1961641 TTTATTAAAATAATAAA
1 TTTATTAAAATAATAAA
**
1961658 TTATATT--AATAATTTA
1 TT-TATTAAAATAATAAA
1961674 -TTATTAAAAATAATATAA
1 TTTATT-AAAATAATA-AA
*
1961692 TATTTTTAAAAT-ATAAA
1 T-TTATTAAAATAATAAA
1961709 T
1 T
1961710 ATATATGTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 15
0.74 0.07 0.20
Matches are distributed among these distances:
14 4 0.07
15 1 0.02
16 13 0.23
17 21 0.38
18 8 0.14
19 5 0.09
20 4 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTATTAAAATAATAAA
Found at i:1961695 original size:20 final size:22
Alignment explanation
Indices: 1961672--1961712 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
1961662 ATTAATAATT
1961672 TATTATTAAAA-AT-AATATAA
1 TATTATTAAAATATAAATATAA
*
1961692 TATTTTTAAAATATAAATATA
1 TATTATTAAAATATAAATATA
1961713 TATGTTTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TATTATTAAAATATAAATATAA
Found at i:1961720 original size:21 final size:20
Alignment explanation
Indices: 1961677--1961720 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
1961667 TAATTTATTA
*
1961677 TTAAAAATAATATAATATTT
1 TTAAAAATAATATAATATGT
1961697 TTAAAATATAA-ATATATATGT
1 TTAAAA-ATAATATA-ATATGT
1961718 TTA
1 TTA
1961721 GTAATATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
TTAAAAATAATATAATATGT
Found at i:1962358 original size:16 final size:16
Alignment explanation
Indices: 1962331--1962372 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1962321 ACTGTACTAA
*
1962331 TTTTTTTGTTTACTTT
1 TTTTTTTGTTTAATTT
1962347 TTTATTTT-TTTAATTT
1 TTT-TTTTGTTTAATTT
1962363 TTTTTTTGTT
1 TTTTTTTGTT
1962373 ATTGATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 4 0.17
16 15 0.65
17 4 0.17
ACGTcount: A:0.10, C:0.02, G:0.05, T:0.83
Consensus pattern (16 bp):
TTTTTTTGTTTAATTT
Found at i:1969081 original size:7 final size:7
Alignment explanation
Indices: 1969069--1969097 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1969059 ATACCTCAAA
1969069 TAAATAT
1 TAAATAT
1969076 TAAATAT
1 TAAATAT
1969083 TAAATA-
1 TAAATAT
1969089 TAAATAT
1 TAAATAT
1969096 TA
1 TA
1969098 GTAAATTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TAAATAT
Found at i:1969094 original size:13 final size:14
Alignment explanation
Indices: 1969069--1969097 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1969059 ATACCTCAAA
1969069 TAAATATTAAATAT
1 TAAATATTAAATAT
1969083 TAAATA-TAAATAT
1 TAAATATTAAATAT
1969096 TA
1 TA
1969098 GTAAATTCTA
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):
TAAATATTAAATAT
Found at i:1969172 original size:12 final size:11
Alignment explanation
Indices: 1969151--1969205 Score: 53
Period size: 12 Copynumber: 5.1 Consensus size: 11
1969141 AATTATTAAA
1969151 AATATAAAAAT
1 AATATAAAAAT
1969162 AATAGTAAAAA-
1 AATA-TAAAAAT
* *
1969173 AATTTAAAATT
1 AATATAAAAAT
1969184 AAT-T-AAAAT
1 AATATAAAAAT
1969193 AATCATAAAAAT
1 AAT-ATAAAAAT
1969205 A
1 A
1969206 TTTTTTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
9 7 0.19
10 6 0.17
11 11 0.31
12 12 0.33
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:1969175 original size:22 final size:20
Alignment explanation
Indices: 1969148--1969205 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
1969138 TGAAATTATT
1969148 AAAAATATAAAAATAATAGTAA
1 AAAAATATAAAAATAAT--TAA
* *
1969170 AAAAATTTAAAATTAATTAA
1 AAAAATATAAAAATAATTAA
*
1969190 AATAATCATAAAAATA
1 AAAAAT-ATAAAAATA
1969206 TTTTTTTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 8 0.27
21 7 0.23
22 15 0.50
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (20 bp):
AAAAATATAAAAATAATTAA
Found at i:1969525 original size:4 final size:4
Alignment explanation
Indices: 1969516--1969546 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1969506 TTTTAACATC
1969516 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
1969547 TGTGTTAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:1970461 original size:2 final size:2
Alignment explanation
Indices: 1970454--1970481 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1970444 ACTTATTGTT
1970454 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1970482 AATATCAGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1970942 original size:11 final size:12
Alignment explanation
Indices: 1970921--1970945 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1970911 TCGATCTTTC
1970921 TTTCTTTTTTTT
1 TTTCTTTTTTTT
1970933 TTTCTTTTTTTT
1 TTTCTTTTTTTT
1970945 T
1 T
1970946 CTTATTTCCT
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:1973991 original size:7 final size:7
Alignment explanation
Indices: 1973981--1974014 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
1973971 AGATGATAAA
1973981 AATATAT
1 AATATAT
1973988 AATATAT
1 AATATAT
1973995 AATATAT
1 AATATAT
1974002 AATATAT
1 AATATAT
1974009 AATATA
1 AATATA
1974015 ATGTGGTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AATATAT
Found at i:1974196 original size:2 final size:2
Alignment explanation
Indices: 1974189--1974214 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1974179 AGATCTATGC
1974189 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
1974215 TTGCATTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1976504 original size:3 final size:3
Alignment explanation
Indices: 1976496--1976527 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1976486 CCTTTTTCTT
1976496 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1976528 TCTGTGAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1981815 original size:2 final size:2
Alignment explanation
Indices: 1981808--1981842 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1981798 AATCTTATTG
1981808 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1981843 TCATGTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1985698 original size:72 final size:72
Alignment explanation
Indices: 1985618--1985774 Score: 305
Period size: 72 Copynumber: 2.2 Consensus size: 72
1985608 GGAATCATTT
1985618 GTAGGAAAAGAAAATGAAAGAGTTTTCTGAAAAGATGCAGAAACATACAGTCAGAAAACTAGGAC
1 GTAGGAAAAGAAAATGAAAGAGTTTTCTGAAAAGATGCAGAAACATACAGTCAGAAAACTAGGAC
1985683 TGGAGTA
66 TGGAGTA
*
1985690 GTAGGAAAAGAAAATGAAAGAGTTTTCTGAAAAGATGGAGAAACATACAGTCAGAAAACTAGGAC
1 GTAGGAAAAGAAAATGAAAGAGTTTTCTGAAAAGATGCAGAAACATACAGTCAGAAAACTAGGAC
1985755 TGGAGTA
66 TGGAGTA
1985762 GTAGGAAAAGAAA
1 GTAGGAAAAGAAA
1985775 CTAAGAGCAA
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 84 1.00
ACGTcount: A:0.48, C:0.08, G:0.26, T:0.17
Consensus pattern (72 bp):
GTAGGAAAAGAAAATGAAAGAGTTTTCTGAAAAGATGCAGAAACATACAGTCAGAAAACTAGGAC
TGGAGTA
Found at i:1988396 original size:12 final size:12
Alignment explanation
Indices: 1988379--1988404 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1988369 ATATCTTCTC
1988379 TTTTTATTATTA
1 TTTTTATTATTA
1988391 TTTTTATTATTA
1 TTTTTATTATTA
1988403 TT
1 TT
1988405 AGTATTATAT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTATTATTA
Found at i:1996778 original size:28 final size:26
Alignment explanation
Indices: 1996724--1996789 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 26
1996714 AATTACGGTA
* *
1996724 TAAAAAAAAATTTTGGTAATTCGTTT
1 TAAAAAAAAATTTTGATAATTCATTT
*
1996750 TAAAAGAATAAATTTTGATAATTTATTT
1 TAAAA-AA-AAATTTTGATAATTCATTT
1996778 TAAGAAACAAAA
1 TAA-AAA-AAAA
1996790 GTAGTTTTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 5 0.15
27 2 0.06
28 23 0.70
29 3 0.09
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (26 bp):
TAAAAAAAAATTTTGATAATTCATTT
Found at i:1997081 original size:21 final size:19
Alignment explanation
Indices: 1997055--1997101 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 19
1997045 CTATTTTTTC
1997055 ATTATATAAAATATAATATAT
1 ATTATATAAAA-ATAA-ATAT
1997076 ATTATATAAAAATAAATAT
1 ATTATATAAAAATAAATAT
1997095 ATCTATA
1 AT-TATA
1997102 ATATTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.24
20 8 0.32
21 11 0.44
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTATATAAAAATAAATAT
Found at i:1997096 original size:23 final size:22
Alignment explanation
Indices: 1997055--1997117 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
1997045 CTATTTTTTC
*
1997055 ATTATATAAAATATA-ATATAT
1 ATTATATAAAATAAATATATAT
*
1997076 ATTATATAAAAATAAATATATCT
1 ATTATAT-AAAATAAATATATAT
* *
1997099 ATAATATTAATATAAATAT
1 ATTATA-TAAAATAAATAT
1997118 TAAAAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 7 0.20
22 7 0.20
23 20 0.57
24 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTATATAAAATAAATATATAT
Found at i:1997417 original size:21 final size:20
Alignment explanation
Indices: 1997375--1997423 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1997365 TTTTTTAATA
*
1997375 AAAAGTATTTTTATTTAATTT
1 AAAA-TATTTTTATTAAATTT
*
1997396 ATAATATTTTTATTAAATTTT
1 AAAATATTTTTATTAAA-TTT
1997417 AAAATAT
1 AAAATAT
1997424 AAATAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
AAAATATTTTTATTAAATTT
Found at i:2002713 original size:25 final size:26
Alignment explanation
Indices: 2002685--2002794 Score: 66
Period size: 25 Copynumber: 4.2 Consensus size: 26
2002675 ATAAATTATG
2002685 AATTACA-TATTATAAATAAATAAAA
1 AATTACATTATTATAAATAAATAAAA
* *
2002710 AATTA-ATTTTTATAGATAAATATAAA
1 AATTACATTATTATAAATAAATA-AAA
* * * * * *
2002736 TTATAAGATCTATCTGTATTATAAACT-ATA
1 -AATTACAT-TAT-TATA-AATAAA-TAAAA
2002766 AATTACA-TATTATAAATAAATAAAA
1 AATTACATTATTATAAATAAATAAAA
2002791 AATT
1 AATT
2002795 GAATCGTGCA
Statistics
Matches: 62, Mismatches: 14, Indels: 18
0.66 0.15 0.19
Matches are distributed among these distances:
24 2 0.03
25 29 0.47
26 6 0.10
27 6 0.10
28 2 0.03
29 6 0.10
30 5 0.08
31 5 0.08
32 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (26 bp):
AATTACATTATTATAAATAAATAAAA
Found at i:2002923 original size:3 final size:3
Alignment explanation
Indices: 2002915--2002949 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
2002905 TATCTGTAAA
*
2002915 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2002950 AAAAAATCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:2003081 original size:17 final size:17
Alignment explanation
Indices: 2003039--2003085 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
2003029 CTCTCTCTCT
*
2003039 CTCTCTCTCTCTGCAAA
1 CTCTCTCTCTCTTCAAA
*
2003056 ATCAT-TCTCTCTTCAAA
1 CTC-TCTCTCTCTTCAAA
2003073 CTCTCTCTCTCTT
1 CTCTCTCTCTCTT
2003086 TCTATCGAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 1 0.04
17 23 0.92
18 1 0.04
ACGTcount: A:0.17, C:0.38, G:0.02, T:0.43
Consensus pattern (17 bp):
CTCTCTCTCTCTTCAAA
Found at i:2007464 original size:27 final size:27
Alignment explanation
Indices: 2007411--2007547 Score: 175
Period size: 27 Copynumber: 4.9 Consensus size: 27
2007401 GGAACATCTT
2007411 TTGGAACTTCAGTTTCAACAGCAGCGGCAG
1 TTGGAACTTCAG---CAACAGCAGCGGCAG
2007441 TTGGAACTTCAGCAACAGCAGCGGCAG
1 TTGGAACTTCAGCAACAGCAGCGGCAG
2007468 TTGGAACTTCAGCAACAGCAGCGGCAG
1 TTGGAACTTCAGCAACAGCAGCGGCAG
** * * *
2007495 TTGGAACTTCAGCGGCAGAAACAGCAG
1 TTGGAACTTCAGCAACAGCAGCGGCAG
2007522 TTGGAACTTCAGTGGCAACAGCAGCG
1 TTGGAACTTCA---GCAACAGCAGCG
2007548 CCGTCACCAC
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
27 75 0.80
30 19 0.20
ACGTcount: A:0.29, C:0.24, G:0.29, T:0.18
Consensus pattern (27 bp):
TTGGAACTTCAGCAACAGCAGCGGCAG
Found at i:2011127 original size:42 final size:42
Alignment explanation
Indices: 2011068--2011158 Score: 155
Period size: 42 Copynumber: 2.2 Consensus size: 42
2011058 CTATTACGTG
* * *
2011068 ATAATTATTAATTAATAATTAAATGATATATATAAATGTAAA
1 ATAATTATTAATAAATAATTAAATGATACATAAAAATGTAAA
2011110 ATAATTATTAATAAATAATTAAATGATACATAAAAATGTAAA
1 ATAATTATTAATAAATAATTAAATGATACATAAAAATGTAAA
2011152 ATAATTA
1 ATAATTA
2011159 GAAGAGACAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.37
Consensus pattern (42 bp):
ATAATTATTAATAAATAATTAAATGATACATAAAAATGTAAA
Found at i:2015221 original size:78 final size:78
Alignment explanation
Indices: 2015076--2015254 Score: 216
Period size: 78 Copynumber: 2.3 Consensus size: 78
2015066 TTTTGGAGAT
* ** * * *
2015076 AATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGATTAGAAAAAAAATCGGGATTAGA
1 AATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGATTAGAAAAAAAAGCGGGATTAGA
2015141 GTATCCCCTCGAA
66 GTATCCCCTCGAA
* ** * * *
2015154 AATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-ATTTTGGGAATAAAGCGGGGTTGG
1 AATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGA-TTAGAAAAAAAAGCGGGATTAG
*
2015218 AGTATCCCCTCGGA
65 AGTATCCCCTCGAA
*
2015232 AGTAACGGGGTTGGAGTATCCCC
1 AATAACGGGGTTGGAGTATCCCC
2015255 GATGAAATAA
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
77 1 0.01
78 85 0.99
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.23
Consensus pattern (78 bp):
AATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGATTAGAAAAAAAAGCGGGATTAGA
GTATCCCCTCGAA
Found at i:2015265 original size:28 final size:28
Alignment explanation
Indices: 2015209--2015280 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
2015199 GGGAATAAAG
** *
2015209 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
2015237 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
**
2015265 CAAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
2015281 TCGACTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:2015400 original size:52 final size:51
Alignment explanation
Indices: 2015268--2015447 Score: 175
Period size: 52 Copynumber: 3.5 Consensus size: 51
2015258 GAAATAACAA
* * * * *
2015268 GGTTGGAGTATCCTCGACTGT-GAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTGG--TGTTTGAAAATAAAACCGG
* **
2015320 AGTTGGAGTATCCCCGATTAAAGG-AAAATTGGTGTTTCGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-GTGGAAAAATTGGTGTTT-GAAAATAAAACCGG
* * * *
2015372 GGTTAGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTGA-AAATAAAACCGG
* *
2015424 GGTTGGAATATCCCCGATGGTGGA
1 GGTTGGAGTATCCCCGATTGTGGA
2015448 GAATTGATAA
Statistics
Matches: 105, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
51 7 0.07
52 89 0.85
53 8 0.08
54 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTGAAAATAAAACCGG
Found at i:2017823 original size:13 final size:13
Alignment explanation
Indices: 2017805--2017830 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2017795 ACAAAGATCC
2017805 ATGTATCGATACA
1 ATGTATCGATACA
2017818 ATGTATCGATACA
1 ATGTATCGATACA
2017831 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2017826 original size:33 final size:33
Alignment explanation
Indices: 2017784--2017850 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2017774 AAAATTTCCA
***
2017784 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2017817 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2017850 A
1 A
2017851 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2017894 original size:19 final size:18
Alignment explanation
Indices: 2017870--2017937 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
2017860 CAGTAGCTAA
2017870 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2017889 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2017904 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2017921 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2017938 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2017910 original size:13 final size:13
Alignment explanation
Indices: 2017892--2017916 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2017882 ACAATACTTA
2017892 TGTATCGATACAT
1 TGTATCGATACAT
2017905 TGTATCGATACA
1 TGTATCGATACA
2017917 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2017914 original size:32 final size:32
Alignment explanation
Indices: 2017873--2017935 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2017863 TAGCTAATTA
*
2017873 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2017905 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2017936 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2018626 original size:46 final size:48
Alignment explanation
Indices: 2018573--2018710 Score: 136
Period size: 50 Copynumber: 2.8 Consensus size: 48
2018563 GCTTAGAGCC
* * * *
2018573 AACAATTACG-ATCT-TTTCTATTTTCAAAGGGTGGTGAAGAATAGTA
1 AACAATTACGCACCTCTTTCGATTGTCAAAGGGTGGTGAAAAATAGTA
* *
2018619 AACAATTACGGTCACCTCTTTCGATTGTCAAAGGTTGGTGAAAAATAGTC
1 AACAATTAC-G-CACCTCTTTCGATTGTCAAAGGGTGGTGAAAAATAGTA
* * * *
2018669 AACAATTACGGTCACCTCTCTCGATTGTTAAACGTTGGTGAA
1 AACAATTAC-G-CACCTCTTTCGATTGTCAAAGGGTGGTGAA
2018711 TAGTCAAATC
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
46 9 0.11
47 1 0.01
49 3 0.04
50 66 0.84
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (48 bp):
AACAATTACGCACCTCTTTCGATTGTCAAAGGGTGGTGAAAAATAGTA
Found at i:2018658 original size:50 final size:50
Alignment explanation
Indices: 2018587--2018710 Score: 176
Period size: 50 Copynumber: 2.5 Consensus size: 50
2018577 ATTACGATCT
* * * *
2018587 TTTCTATTTTCAAAGGGTGGTGAAGAATAGTAAACAATTACGGTCACCTC
1 TTTCGATTGTCAAAGGTTGGTGAAAAATAGTAAACAATTACGGTCACCTC
*
2018637 TTTCGATTGTCAAAGGTTGGTGAAAAATAGTCAACAATTACGGTCACCTC
1 TTTCGATTGTCAAAGGTTGGTGAAAAATAGTAAACAATTACGGTCACCTC
* * *
2018687 TCTCGATTGTTAAACGTTGGTGAA
1 TTTCGATTGTCAAAGGTTGGTGAA
2018711 TAGTCAAATC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (50 bp):
TTTCGATTGTCAAAGGTTGGTGAAAAATAGTAAACAATTACGGTCACCTC
Found at i:2023128 original size:50 final size:50
Alignment explanation
Indices: 2023069--2023224 Score: 199
Period size: 50 Copynumber: 3.1 Consensus size: 50
2023059 AGATGCTTCG
* *
2023069 AGTCAACAATTATGGTCACCTTTCTCTATTATCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGTCACCTTTCTCTATTGTCAAAGGTTGGTGAAGAAT
* *
2023119 AGTCAACAATTACGGTCACCTCTCT-TGATTGTCAAAGGTGGGTGAAGAAT
1 AGTCAACAATTACGGTCACCTTTCTCT-ATTGTCAAAGGTTGGTGAAGAAT
* * * * *
2023169 AGTCAACAATTGCAGCCACCTCTT-TCGATTGTCAAAGGTTTGTGAAGAAT
1 AGTCAACAATTACGGTCACCT-TTCTCTATTGTCAAAGGTTGGTGAAGAAT
2023219 AGTCAA
1 AGTCAA
2023225 ATCACTTTGC
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
49 1 0.01
50 90 0.98
51 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (50 bp):
AGTCAACAATTACGGTCACCTTTCTCTATTGTCAAAGGTTGGTGAAGAAT
Found at i:2028072 original size:8 final size:8
Alignment explanation
Indices: 2028059--2028117 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 8
2028049 TGTATAAAAT
2028059 TTAATATA
1 TTAATATA
2028067 TTAATA-A
1 TTAATATA
*
2028074 TTTATATTA
1 TTAATA-TA
*
2028083 TATAAAAT-
1 T-TAATATA
2028091 TTAATATA
1 TTAATATA
*
2028099 TTTATATA
1 TTAATATA
*
2028107 TTTATATA
1 TTAATATA
2028115 TTA
1 TTA
2028118 TATTTTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
7 11 0.27
8 24 0.59
9 3 0.07
10 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
TTAATATA
Found at i:2028077 original size:16 final size:15
Alignment explanation
Indices: 2027980--2028117 Score: 67
Period size: 16 Copynumber: 9.0 Consensus size: 15
2027970 AGTGGATGCG
2027980 ATAATTTATATATTA
1 ATAATTTATATATTA
2027995 AT-ATTT-TAT-TTA
1 ATAATTTATATATTA
* * *
2028007 TGTTATTTTTATATT-
1 -ATAATTTATATATTA
2028022 ATAATTT-TATA-TA
1 ATAATTTATATATTA
*
2028035 A-AATTTTATGTATTTGTA
1 ATAA-TTTA--TATAT-TA
*
2028053 TAAAATTTAATATATTA
1 -ATAATTT-ATATATTA
2028070 ATAATTTATATTATATA
1 ATAATTTATA-TAT-TA
*
2028087 A-AATTTAATATATTT
1 ATAATTT-ATATATTA
2028102 ATATATTTATATATTA
1 ATA-ATTTATATATTA
2028118 TATTTTATTT
Statistics
Matches: 96, Mismatches: 8, Indels: 37
0.68 0.06 0.26
Matches are distributed among these distances:
12 6 0.06
13 12 0.12
14 13 0.14
15 10 0.10
16 30 0.31
17 12 0.12
18 6 0.06
19 4 0.04
20 3 0.03
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
ATAATTTATATATTA
Found at i:2028087 original size:32 final size:33
Alignment explanation
Indices: 2028051--2028113 Score: 110
Period size: 32 Copynumber: 1.9 Consensus size: 33
2028041 TATGTATTTG
2028051 TATAAAATTTAATATATTAATA-ATTTATATTA
1 TATAAAATTTAATATATTAATATATTTATATTA
*
2028083 TATAAAATTTAATATATTTATATATTTATAT
1 TATAAAATTTAATATATTAATATATTTATAT
2028114 ATTATATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 21 0.72
33 8 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
TATAAAATTTAATATATTAATATATTTATATTA
Found at i:2028103 original size:20 final size:20
Alignment explanation
Indices: 2028027--2028106 Score: 77
Period size: 20 Copynumber: 4.4 Consensus size: 20
2028017 ATATTATAAT
* *
2028027 TTTATATAAAATTTTATGTA
1 TTTATATAAAATTTAATATA
*
2028047 TTTGTATAAAATTTAATATA
1 TTTATATAAAATTTAATATA
2028067 -TTA-AT--AA-TT--TATA
1 TTTATATAAAATTTAATATA
2028080 -TTATATAAAATTTAATATA
1 TTTATATAAAATTTAATATA
2028099 TTTATATA
1 TTTATATA
2028107 TTTATATATT
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
13 7 0.14
14 2 0.04
15 2 0.04
16 4 0.08
17 2 0.04
18 2 0.04
19 6 0.12
20 24 0.49
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTATATAAAATTTAATATA
Found at i:2028182 original size:17 final size:17
Alignment explanation
Indices: 2028152--2028192 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
2028142 ATATCAAATA
2028152 TAAAATTAATTTTTATT
1 TAAAATTAATTTTTATT
2028169 TAAATATTAATTTTT-TT
1 TAAA-ATTAATTTTTATT
2028186 TATAAAT
1 TA-AAAT
2028193 GATACAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TAAAATTAATTTTTATT
Found at i:2028331 original size:2 final size:2
Alignment explanation
Indices: 2028324--2028361 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2028314 CTTCCTTCCA
2028324 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2028362 AAATTAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2028911 original size:20 final size:19
Alignment explanation
Indices: 2028863--2028913 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
2028853 CGTATATAAT
2028863 AAATATAATT-ATTTATTA
1 AAATATAATTAATTTATTA
*
2028881 AATTTAATAATTAATTTATTA
1 AA-AT-ATAATTAATTTATTA
2028902 AAATATTAATTA
1 AAATA-TAATTA
2028914 TATAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 2 0.07
19 2 0.07
20 13 0.48
21 10 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATATAATTAATTTATTA
Found at i:2030112 original size:107 final size:106
Alignment explanation
Indices: 2029882--2030112 Score: 225
Period size: 107 Copynumber: 2.2 Consensus size: 106
2029872 CCTGCCATGA
* * * ** * *
2029882 ATTATTATTATTATTATGCAAAGTGGGTAAGGTCAGGTAAGGTCCAGCCTAGGAAAATTAAGAAA
1 ATTATTATTATTTTTTTACAAAGAAGGTAAAGTCAGGTAAGGTCCAGCCAAGGAAAATTAAGAAA
*
2029947 GTAAAATTTGCTAGCCTCGACTCTCCTTGAATTATTTGAGT
66 GTAAAATTTGCTAGCCTCGACTCGCCTTGAATTATTTGAGT
* * * *
2029988 ATCATTTATTGTCTTTTTACAAAGAAGGTAAAGTCAGGTCAA-GTCCAGCCAATGAAAATTAAGA
1 ATTA-TTATTATTTTTTTACAAAGAAGGTAAAGTCAGGT-AAGGTCCAGCCAAGGAAAATTAAGA
** * * * *
2030052 GGGTGAAATTTGCT-GCTTGCAAGCCTCGCCTTGAATTATTT-ATT
64 AAGTAAAATTTGCTAGCCT-C--GACTCGCCTTGAATTATTTGAGT
*
2030096 TTTATTATTATTTTTTT
1 ATTATTATTATTTTTTT
2030113 TTAAAAAAAA
Statistics
Matches: 98, Mismatches: 22, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
106 6 0.06
107 69 0.70
108 6 0.06
109 17 0.17
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (106 bp):
ATTATTATTATTTTTTTACAAAGAAGGTAAAGTCAGGTAAGGTCCAGCCAAGGAAAATTAAGAAA
GTAAAATTTGCTAGCCTCGACTCGCCTTGAATTATTTGAGT
Found at i:2030584 original size:13 final size:13
Alignment explanation
Indices: 2030566--2030591 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2030556 TTAACTATCT
2030566 ATAATTCTCAACC
1 ATAATTCTCAACC
2030579 ATAATTCTCAACC
1 ATAATTCTCAACC
2030592 CCACCTCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAATTCTCAACC
Found at i:2036339 original size:3 final size:3
Alignment explanation
Indices: 2036331--2036359 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2036321 TCCGGCACAA
2036331 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2036360 AAATCTTACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2037161 original size:31 final size:31
Alignment explanation
Indices: 2037126--2037188 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
2037116 ATTTATCCTA
2037126 TACCTATTCTTTTTCTTCATCAATGGCCTTC
1 TACCTATTCTTTTTCTTCATCAATGGCCTTC
2037157 TACCTATTCTTTTTCTTCATCAATGGCCTTC
1 TACCTATTCTTTTTCTTCATCAATGGCCTTC
2037188 T
1 T
2037189 CCCTTTTGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.16, C:0.29, G:0.06, T:0.49
Consensus pattern (31 bp):
TACCTATTCTTTTTCTTCATCAATGGCCTTC
Found at i:2037195 original size:25 final size:28
Alignment explanation
Indices: 2037133--2037195 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 28
2037123 CTATACCTAT
2037133 TCTTTTTCTTCATCAATGGCCTTCTACC
1 TCTTTTTCTTCATCAATGGCCTTCTACC
2037161 TATTCTTTTTCTTCATCAATGGCCTTCT-CC
1 ---TCTTTTTCTTCATCAATGGCCTTCTACC
2037191 -CTTTT
1 TCTTTT
2037196 GGTTCCACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 5 0.16
30 2 0.06
31 25 0.78
ACGTcount: A:0.13, C:0.30, G:0.06, T:0.51
Consensus pattern (28 bp):
TCTTTTTCTTCATCAATGGCCTTCTACC
Found at i:2037569 original size:22 final size:21
Alignment explanation
Indices: 2037544--2037587 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
2037534 TGCATCTCTC
*
2037544 TTCTTTTCTACTCTCTATTATT
1 TTCTTCTCTACTCTCTA-TATT
*
2037566 TTCTTCTCTATTCTCTATATT
1 TTCTTCTCTACTCTCTATATT
2037587 T
1 T
2037588 GCTTGCATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.14, C:0.23, G:0.00, T:0.64
Consensus pattern (21 bp):
TTCTTCTCTACTCTCTATATT
Found at i:2039458 original size:13 final size:13
Alignment explanation
Indices: 2039440--2039464 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2039430 TATAAAGTGT
2039440 TGTATCGATACAA
1 TGTATCGATACAA
2039453 TGTATCGATACA
1 TGTATCGATACA
2039465 TATTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2039546 original size:13 final size:13
Alignment explanation
Indices: 2039528--2039552 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2039518 ATTACTCAAA
2039528 TGTATCGATACAT
1 TGTATCGATACAT
2039541 TGTATCGATACA
1 TGTATCGATACA
2039553 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2039603 original size:52 final size:50
Alignment explanation
Indices: 2039541--2039689 Score: 181
Period size: 52 Copynumber: 2.9 Consensus size: 50
2039531 ATCGATACAT
* *
2039541 TGTATCGATACACTGATCTTTGTATCGATACATGAAGGCAAATTTGCCCAAA
1 TGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAAA
* * * *
2039593 TGTATCGATACATTATAAAATGTATCGATACATGCATGCAAATTTGCCCAGA
1 TGTATCGATACACTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAAA
*
2039645 TGTATCGATACACTATTAAATGTATCGATACATGCAGGTAAATTT
1 TGTATCGATACACTATT--ATGTATCGATACATGCAGGCAAATTT
2039690 TCATATTTCG
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
51 2 0.02
52 81 0.98
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (50 bp):
TGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAAA
Found at i:2041312 original size:13 final size:13
Alignment explanation
Indices: 2041294--2041318 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2041284 TATAAAGTGT
2041294 TGTATCGATACAA
1 TGTATCGATACAA
2041307 TGTATCGATACA
1 TGTATCGATACA
2041319 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2041399 original size:13 final size:13
Alignment explanation
Indices: 2041381--2041405 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2041371 ATTACTCAAA
2041381 TGTATCGATACAT
1 TGTATCGATACAT
2041394 TGTATCGATACA
1 TGTATCGATACA
2041406 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2041456 original size:52 final size:50
Alignment explanation
Indices: 2041394--2041542 Score: 181
Period size: 52 Copynumber: 2.9 Consensus size: 50
2041384 ATCGATACAT
* *
2041394 TGTATCGATACACTGATCTTTGTATCGATACATGAAGGCAAATTTGCCCAAA
1 TGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAAA
* * * *
2041446 TGTATCGATACATTATAAAATGTATCGATACATGCATGCAAATTTGCCCAGA
1 TGTATCGATACACTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAAA
*
2041498 TGTATCGATACACTATTAAATGTATCGATACATGCAGGTAAATTT
1 TGTATCGATACACTATT--ATGTATCGATACATGCAGGCAAATTT
2041543 TCATATTTCG
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
51 2 0.02
52 81 0.98
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (50 bp):
TGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAAA
Found at i:2048372 original size:11 final size:11
Alignment explanation
Indices: 2048358--2048431 Score: 73
Period size: 11 Copynumber: 6.6 Consensus size: 11
2048348 AAGTGATGAA
2048358 AAAAAAACAAC
1 AAAAAAACAAC
2048369 -AAAAAA-AAC
1 AAAAAAACAAC
*
2048378 AAAAAAACAAAA
1 AAAAAAAC-AAC
2048390 AACAAAAACAA-
1 AA-AAAAACAAC
*
2048401 AACAAAAACAAA
1 AA-AAAAACAAC
2048413 AAAAAAACACAC
1 AAAAAAACA-AC
2048425 AAAAAAA
1 AAAAAAA
2048432 AGTTGCAAAG
Statistics
Matches: 55, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
9 3 0.05
10 12 0.22
11 18 0.33
12 16 0.29
13 6 0.11
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAC
Found at i:2048376 original size:17 final size:16
Alignment explanation
Indices: 2048356--2048432 Score: 91
Period size: 18 Copynumber: 4.4 Consensus size: 16
2048346 AAAAGTGATG
*
2048356 AAAAAAAAACAACAAA
1 AAAAAAAAAAAACAAA
2048372 AAAAACAAAAAAACAAA
1 AAAAA-AAAAAAACAAA
2048389 AAACAAAAACAAAACAAA
1 AAA-AAAAA-AAAACAAA
2048407 AACAAAAAAAAAACACACA
1 AA-AAAAAAAAAACA-A-A
2048426 AAAAAAA
1 AAAAAAA
2048433 GTTGCAAAGG
Statistics
Matches: 54, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
16 5 0.09
17 22 0.41
18 23 0.43
19 4 0.07
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAACAAA
Found at i:2048383 original size:24 final size:25
Alignment explanation
Indices: 2048356--2048417 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 25
2048346 AAAAGTGATG
*
2048356 AAAAAAAAACAACAAAAAAAACAAAA
1 AAAAAAAAACAA-AAACAAAACAAAA
2048382 AAACAAAAAACAAAAACAAAACAAAA
1 AAA-AAAAAACAAAAACAAAACAAAA
2048408 ACAAAAAAAA
1 A-AAAAAAAA
2048418 AACACACAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
26 22 0.67
27 11 0.33
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (25 bp):
AAAAAAAAACAAAAACAAAACAAAA
Found at i:2048431 original size:24 final size:23
Alignment explanation
Indices: 2048357--2048432 Score: 88
Period size: 24 Copynumber: 3.3 Consensus size: 23
2048347 AAAGTGATGA
*
2048357 AAAAAAAAC-AACAAAAAAA-AC
1 AAAAAAAACAAAAAAAAAAACAC
2048378 -AAAAAAACAAAAAACAAAAACA-
1 AAAAAAAACAAAAAA-AAAAACAC
2048400 AAACAAAAACAAAAAAAAAACACAC
1 AAA-AAAAACAAAAAAAAAA-ACAC
2048425 AAAAAAAA
1 AAAAAAAA
2048433 GTTGCAAAGG
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
20 8 0.17
21 4 0.09
22 5 0.11
23 7 0.15
24 20 0.43
25 3 0.06
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (23 bp):
AAAAAAAACAAAAAAAAAAACAC
Found at i:2048432 original size:1 final size:1
Alignment explanation
Indices: 2048356--2048419 Score: 56
Period size: 1 Copynumber: 64.0 Consensus size: 1
2048346 AAAAGTGATG
* * * * * * * *
2048356 AAAAAAAAACAACAAAAAAAACAAAAAAACAAAAAACAAAAACAAAACAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2048420 CACACAAAAA
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2048692 original size:16 final size:16
Alignment explanation
Indices: 2048671--2048724 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
2048661 TGTTCTTTTC
2048671 CAAAAAAGAAACAAAA
1 CAAAAAAGAAACAAAA
2048687 CAAAAAAGAAA-AAAA
1 CAAAAAAGAAACAAAA
*
2048702 CAAACAAACAAAC-AAA
1 CAAA-AAAGAAACAAAA
2048718 CAAAAAA
1 CAAAAAA
2048725 AAAGAAGGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
15 11 0.31
16 24 0.69
ACGTcount: A:0.81, C:0.15, G:0.04, T:0.00
Consensus pattern (16 bp):
CAAAAAAGAAACAAAA
Found at i:2048708 original size:4 final size:4
Alignment explanation
Indices: 2048679--2048721 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
2048669 TCCAAAAAAG
* *
2048679 AAAC AAAAC AAA- AAAG AAAA AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC -AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
2048722 AAAAAAGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
3 3 0.09
4 28 0.80
5 4 0.11
ACGTcount: A:0.81, C:0.16, G:0.02, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:2049740 original size:34 final size:34
Alignment explanation
Indices: 2049685--2049886 Score: 259
Period size: 34 Copynumber: 6.0 Consensus size: 34
2049675 AAGTCCACGT
2049685 CTCCGTGGCACC---TTCTTTTCAAAGCCCACAA
1 CTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAA
* *
2049716 CTCCGTGACACCTTTTTCTTTTCAAGGCCCACAA
1 CTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAA
* ** *
2049750 CTCCGTGACACCTTTTTCTTTTTTAAGTCCACAA
1 CTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAA
* *
2049784 CTCTGTGGCACCTTTTTCTTTTTAAAGCCCACAA
1 CTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAA
* *
2049818 CTTCGTGGCACCTTTTTCTTTTCAAAGCCTACAA
1 CTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAA
2049852 CTCCGTGGCACTCTTTTTCCCTTTT-AAAGCCCACA
1 CTCCGTGGCAC-CTTTTT--CTTTTCAAAGCCCACA
2049887 CAAGTCGGTG
Statistics
Matches: 149, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
31 11 0.07
34 118 0.79
35 6 0.04
36 9 0.06
37 5 0.03
ACGTcount: A:0.20, C:0.33, G:0.11, T:0.35
Consensus pattern (34 bp):
CTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAA
Found at i:2049952 original size:32 final size:32
Alignment explanation
Indices: 2049877--2050224 Score: 526
Period size: 32 Copynumber: 10.8 Consensus size: 32
2049867 TTTCCCTTTT
2049877 AAAGCCCACACAAGTCGGTGGCAACCCTTCT-
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTC
* *
2049908 AAAGCCCGCACAAGTCGGGGGCAACCCTTCTC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTC
*
2049940 AGAGCCCACACAAGTCGGTGGCAAACCCTTCTC
1 AAAGCCCACACAAGTCGGTGGC-AACCCTTCTC
2049973 TAAAGCCCACACAAGTCGGTGGCAACCCTTCT-
1 -AAAGCCCACACAAGTCGGTGGCAACCCTTCTC
*
2050005 AAAGCCAACACAAGTCGGTGGCAACCCTTCTC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTC
* * *
2050037 AGAGCCCACACAAGTCGATGGCAAAACCTTCTC
1 AAAGCCCACACAAGTCGGTGGC-AACCCTTCTC
2050070 TAAAGCCCACACAAGTCGGTGGCAACCCTTCTC
1 -AAAGCCCACACAAGTCGGTGGCAACCCTTCTC
*
2050103 AAAGCCCACACAAGTCGGTGGCAA-CCTTTTC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTC
2050134 TAAAGCCCACACAAGTCGGTGGCAACCCTTCTC
1 -AAAGCCCACACAAGTCGGTGGCAACCCTTCTC
2050167 AAAGCCCACACAAGTCGGTGGC-ACCCTT-TC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTC
*
2050197 TAAAGCCCACACAAGTCAGTGGCAACCC
1 -AAAGCCCACACAAGTCGGTGGCAACCC
2050225 CTCTAAGCCC
Statistics
Matches: 290, Mismatches: 17, Indels: 19
0.89 0.05 0.06
Matches are distributed among these distances:
30 2 0.01
31 92 0.32
32 112 0.39
33 43 0.15
34 41 0.14
ACGTcount: A:0.29, C:0.35, G:0.20, T:0.16
Consensus pattern (32 bp):
AAAGCCCACACAAGTCGGTGGCAACCCTTCTC
Found at i:2049986 original size:97 final size:97
Alignment explanation
Indices: 2049876--2050224 Score: 571
Period size: 97 Copynumber: 3.6 Consensus size: 97
2049866 TTTTCCCTTT
* *
2049876 TAAAGCCCACACAAGTCGGTGGCAACCCTTCTAAAGCCCGCACAAGTCGGGGGCAACCCTTCTCA
1 TAAAGCCCACACAAGTCGGTGGCAACCCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCA
2049941 GAGCCCACACAAGTCGGTGGCAAACCCTTCTC
66 GAGCCCACACAAGTCGGTGGCAAACCCTTCTC
*
2049973 TAAAGCCCACACAAGTCGGTGGCAACCCTTCTAAAGCCAACACAAGTCGGTGGCAACCCTTCTCA
1 TAAAGCCCACACAAGTCGGTGGCAACCCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCA
* *
2050038 GAGCCCACACAAGTCGATGGCAAAACCTTCTC
66 GAGCCCACACAAGTCGGTGGCAAACCCTTCTC
*
2050070 TAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCGGTGGCAA-CCTTTTC
1 TAAAGCCCACACAAGTCGGTGGCAACCCTTCT-AAAGCCCACACAAGTCGGTGGCAACCCTTCTC
*
2050134 TAAAGCCCACACAAGTCGGTGGC-AACCCTTCTC
65 -AGAGCCCACACAAGTCGGTGGCAAACCCTTCTC
*
2050167 -AAAGCCCACACAAGTCGGTGGC-ACCCTTTCTAAAGCCCACACAAGTCAGTGGCAACCC
1 TAAAGCCCACACAAGTCGGTGGCAACCC-TTCTAAAGCCCACACAAGTCGGTGGCAACCC
2050225 CTCTAAGCCC
Statistics
Matches: 237, Mismatches: 11, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
95 27 0.11
96 28 0.12
97 139 0.59
98 43 0.18
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.16
Consensus pattern (97 bp):
TAAAGCCCACACAAGTCGGTGGCAACCCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCA
GAGCCCACACAAGTCGGTGGCAAACCCTTCTC
Found at i:2050381 original size:92 final size:92
Alignment explanation
Indices: 2050224--2050591 Score: 619
Period size: 92 Copynumber: 4.0 Consensus size: 92
2050214 AGTGGCAACC
2050224 CCTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
1 CCTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
2050289 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
2050316 CCTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
1 CCTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
*
2050381 AGCTGGCCTTCAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * *
2050408 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
1 CCTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
* *
2050473 AGCTAGCCTTGAATCAGTACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * * *
2050500 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAA
1 CCTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CTTCTTTAAGTCCAA
2050565 TGTAGCTGGCCTTGAATCAGCACATTG
63 TGTAGCTGGCCTTGAATCAGCACATTG
2050592 ACATCCTTTT
Statistics
Matches: 261, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
92 221 0.85
94 2 0.01
95 38 0.15
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (92 bp):
CCTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCA
Done.