Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 182 of 208
Found at i:55673579 original size:22 final size:22
Alignment explanation
Indices: 55673551--55673593 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
55673541 ATAAGCTCCT
*
55673551 TTACATTCAATTAATAAATGTA
1 TTACATTCAATCAATAAATGTA
55673573 TTACATTCAATCAATAAATGT
1 TTACATTCAATCAATAAATGT
55673594 GAATTAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.40
Consensus pattern (22 bp):
TTACATTCAATCAATAAATGTA
Found at i:55676754 original size:3 final size:3
Alignment explanation
Indices: 55676746--55676798 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
55676736 CATTTAACTG
55676746 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
55676794 TAT TA
1 TAT TA
55676799 ACTAGATGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:55679787 original size:101 final size:102
Alignment explanation
Indices: 55679665--55679849 Score: 302
Period size: 101 Copynumber: 1.8 Consensus size: 102
55679655 AAAGTGATAG
* * *
55679665 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACATGTGTAGTACTATGTGCAGGCCACTACGTGTATCAGATAGTGAT-GGTCACATGTGTAGT
55679728 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
*
55679766 TCACATGTGTAGTACTATGTGCAGGCCACTACGTGTATCGGATAGTGATGGTCACATGTGTAGTA
1 TCACATGTGTAGTACTATGTGCAGGCCACTACGTGTATCAGATAGTGATGGTCACATGTGTAGTA
*
55679831 CTATGTGCATGCTACTATG
66 CTATGTGCAGGCTACTATG
55679850 TGAACCGGTA
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
101 39 0.51
102 34 0.44
103 4 0.05
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (102 bp):
TCACATGTGTAGTACTATGTGCAGGCCACTACGTGTATCAGATAGTGATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:55679808 original size:51 final size:49
Alignment explanation
Indices: 55679664--55679847 Score: 217
Period size: 51 Copynumber: 3.7 Consensus size: 49
55679654 GAAAGTGATA
* * *
55679664 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGA-ATGATAG
1 GTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATA-G-TTG
* * * *
55679714 GTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCG
1 GTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAG-TT-G
* *
55679765 ATCACATGTGTAGTACTATGTGCAGGCCACTACGTGTATCGGATAGTGATG
1 GTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGT--TG
*
55679816 GTCACATGTGTAGTACTATGTGCATGCTACTA
1 GTCACATGTGTAGTACTATGTGCAGGCTACTA
55679848 TGTGAACCGG
Statistics
Matches: 113, Mismatches: 17, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
50 40 0.35
51 72 0.64
52 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (49 bp):
GTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTTG
Found at i:55679851 original size:26 final size:26
Alignment explanation
Indices: 55679770--55679851 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
55679760 CTTCGATCAC
* *
55679770 ATGTGTAGTACTATGTGCAGGCCACT
1 ATGTGTAGTACTATGTGCATGCTACT
* * *
55679796 ACGTGTA-T-CGGATAGTG-ATGGTCAC-
1 ATGTGTAGTAC-TAT-GTGCATGCT-ACT
55679821 ATGTGTAGTACTATGTGCATGCTACT
1 ATGTGTAGTACTATGTGCATGCTACT
55679847 ATGTG
1 ATGTG
55679852 AACCGGTATC
Statistics
Matches: 41, Mismatches: 8, Indels: 14
0.65 0.13 0.22
Matches are distributed among these distances:
24 1 0.02
25 16 0.39
26 23 0.56
27 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (26 bp):
ATGTGTAGTACTATGTGCATGCTACT
Found at i:55679857 original size:102 final size:101
Alignment explanation
Indices: 55679665--55679857 Score: 298
Period size: 102 Copynumber: 1.9 Consensus size: 101
55679655 AAAGTGATAG
* * *
55679665 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGAATGATAGGTCGCATGTGTAGTAC
1 TCACATGTGTAGTACTATGTGCAGGCCACTACGTGTATCAGAATGATAGGTCACATGTGTAGTAC
*
55679730 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
66 TATGTGCAGGCTACTATGCGAACCGGATAGCTTCGA
*
55679766 TCACATGTGTAGTACTATGTGCAGGCCACTACGTGTATCGGATAGTGAT-GGTCACATGTGTAGT
1 TCACATGTGTAGTACTATGTGCAGGCCACTACGTGTATCAGA-A-TGATAGGTCACATGTGTAGT
* *
55679830 ACTATGTGCATGCTACTATGTGAACCGG
64 ACTATGTGCAGGCTACTATGCGAACCGG
55679858 TATCATTAAT
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
101 39 0.47
102 40 0.48
103 4 0.05
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (101 bp):
TCACATGTGTAGTACTATGTGCAGGCCACTACGTGTATCAGAATGATAGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGAACCGGATAGCTTCGA
Found at i:55679944 original size:46 final size:43
Alignment explanation
Indices: 55679853--55679937 Score: 116
Period size: 46 Copynumber: 1.9 Consensus size: 43
55679843 TACTATGTGA
*
55679853 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTGATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGATCCC
* *
55679896 ACCGGATATCATTGATTACAAAGGGTGGTTGCTGTGTGCTGA
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGA
55679938 ATCCACCATG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 5 0.14
44 11 0.31
45 2 0.06
46 18 0.50
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGATCCC
Found at i:55680096 original size:16 final size:16
Alignment explanation
Indices: 55680075--55680106 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
55680065 TGATTGAAAG
*
55680075 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
55680091 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
55680107 CCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:55685652 original size:91 final size:91
Alignment explanation
Indices: 55685497--55685846 Score: 655
Period size: 91 Copynumber: 3.8 Consensus size: 91
55685487 TTAAATGTAT
*
55685497 AAATTATATATCATTATTAAATTATATTTAATACTAATTATTTTAAATTATATAAATTCATATAA
1 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
55685562 GAAAATTTATTATCAAGAATTTTATG
66 GAAAATTTATTATCAAGAATTTTATG
55685588 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
1 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
55685653 GAAAATTTATTATCAAGAATTTTATG
66 GAAAATTTATTATCAAGAATTTTATG
*
55685679 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATAAAA
1 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
55685744 GAAAATTTATTATCAAGAATTTTATG
66 GAAAATTTATTATCAAGAATTTTATG
* * *
55685770 AAATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAAATTATACAAATTCATATAA
1 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
55685835 GAAAATTTATTA
66 GAAAATTTATTA
55685847 GTTATAATTA
Statistics
Matches: 253, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 253 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (91 bp):
AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
GAAAATTTATTATCAAGAATTTTATG
Found at i:55685865 original size:91 final size:91
Alignment explanation
Indices: 55685497--55686001 Score: 650
Period size: 91 Copynumber: 5.5 Consensus size: 91
55685487 TTAAATGTAT
*
55685497 AAATTATATATCATTATTAAATTATATTTAATACTAATTATTTTAAATTATATAAATTCATATAA
1 AAATTATATATCATTATTAAATTATATTTAATAATAATTATTTTAAATTATATAAATTCATATAA
55685562 GAAAATTTATTATCAAGAATTTTATG
66 GAAAATTTATTATCAAGAATTTTATG
*
55685588 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
1 AAATTATATATCATTATTAAATTATATTTAATAATAATTATTTTAAATTATATAAATTCATATAA
55685653 GAAAATTTATTATCAAGAATTTTATG
66 GAAAATTTATTATCAAGAATTTTATG
* *
55685679 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATAAAA
1 AAATTATATATCATTATTAAATTATATTTAATAATAATTATTTTAAATTATATAAATTCATATAA
55685744 GAAAATTTATTATCAAGAATTTTATG
66 GAAAATTTATTATCAAGAATTTTATG
* *
55685770 AAATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAAATTATACAAATTCATATAA
1 AAATTATATATCATTATTAAATTATATTTAATAATAATTATTTTAAATTATATAAATTCATATAA
* * *
55685835 GAAAATTTATTAGT-TATAATTATT-TT
66 GAAAATTTATTA-TCAAGAATT-TTATG
* * * * * * *
55685861 AAATTTTAT-TAAATCA-TATATTTTA-TTAAGAAT-ATTGATTATTAAGAATTTTATTAAATT-
1 AAATTATATAT-CATTATTAAATTATATTTAATAATAATT-ATT-TT-A-AATTATA-TAAATTC
* * * * *
55685921 ATATAAGAATATTGATTATTAAAAATTTTATT
60 ATATAAGAAAATTTATTATCAAGAATTTTATG
*
55685953 AAATTATATAT-TTTAATTATAA-TATATTTAATAATAATTATGTTTAAAT
1 AAATTATATATCATT-ATTA-AATTATATTTAATAATAATTAT-TTTAAAT
55686002 ATGCTTAAAT
Statistics
Matches: 370, Mismatches: 27, Indels: 33
0.86 0.06 0.08
Matches are distributed among these distances:
88 3 0.01
89 10 0.03
90 10 0.03
91 275 0.74
92 44 0.12
93 12 0.03
94 12 0.03
95 4 0.01
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (91 bp):
AAATTATATATCATTATTAAATTATATTTAATAATAATTATTTTAAATTATATAAATTCATATAA
GAAAATTTATTATCAAGAATTTTATG
Found at i:55685902 original size:16 final size:16
Alignment explanation
Indices: 55685883--55685942 Score: 66
Period size: 16 Copynumber: 3.4 Consensus size: 16
55685873 ATCATATATT
55685883 TTATTAAGAATATTGA
1 TTATTAAGAATATTGA
*
55685899 TTATTAAGAATTTTATTAAA
1 TTATTAAGAA---TATT-GA
55685919 TTATATAAGAATATTGA
1 TTAT-TAAGAATATTGA
55685936 TTATTAA
1 TTATTAA
55685943 AAATTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
16 13 0.35
17 5 0.14
18 4 0.11
19 4 0.11
20 5 0.14
21 6 0.16
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (16 bp):
TTATTAAGAATATTGA
Found at i:55685930 original size:37 final size:37
Alignment explanation
Indices: 55685883--55685962 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 37
55685873 ATCATATATT
*
55685883 TTAT-TAAGAATATTGATTATTAAGAATTTTATTAAA
1 TTATATAAGAATATTGATTATTAAAAATTTTATTAAA
55685919 TTATATAAGAATATTGATTATTAAAAATTTTATTAAA
1 TTATATAAGAATATTGATTATTAAAAATTTTATTAAA
55685956 TTATATA
1 TTATATA
55685963 TTTTAATTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
36 4 0.10
37 38 0.90
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.47
Consensus pattern (37 bp):
TTATATAAGAATATTGATTATTAAAAATTTTATTAAA
Found at i:55685979 original size:16 final size:16
Alignment explanation
Indices: 55685958--55685999 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
55685948 TTATTAAATT
*
55685958 ATATATTTTAATTATA
1 ATATATTTTAATAATA
55685974 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
55685989 AT-TATGTTTAA
1 ATATAT-TTTAA
55686000 ATATGCTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:55685984 original size:15 final size:15
Alignment explanation
Indices: 55685949--55685990 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
55685939 TTAAAAATTT
*
55685949 TATTAAATTAT-ATA
1 TATTTAATTATAATA
55685963 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
55685977 TATTTAATAATAAT
1 TATTTAATTATAAT
55685991 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:55686234 original size:16 final size:16
Alignment explanation
Indices: 55686213--55686277 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
55686203 TTGATTTGCT
55686213 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
55686229 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
55686245 ATTACGTCTCTATTCC
1 ATTACGCCTCTATTCC
55686261 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
55686277 A
1 A
55686278 ATACAGCGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.20, C:0.35, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:55697445 original size:27 final size:28
Alignment explanation
Indices: 55697417--55697470 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
55697407 AAATAGGATA
*
55697417 AAAT-AAATAATAA-GTTAATAATAATT
1 AAATAAAATAATAATGGTAATAATAATT
*
55697443 AAATAAAATAATAATGGTATTAATAATT
1 AAATAAAATAATAATGGTAATAATAATT
55697471 GGGGAAATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 9 0.38
28 11 0.46
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (28 bp):
AAATAAAATAATAATGGTAATAATAATT
Found at i:55698758 original size:28 final size:27
Alignment explanation
Indices: 55698690--55698758 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
55698680 TATATATATA
* * *
55698690 ATATATACGTATAGGGGTTTTGTTATTT
1 ATATATA-ATATATGGGTTTTGGTATTT
*
55698718 ATATATAATATATGGGTTTTGGTGTTAT
1 ATATATAATATATGGGTTTTGGTATT-T
*
55698746 ATGTATAATATAT
1 ATATATAATATAT
55698759 TTACGTGGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 15 0.43
28 20 0.57
ACGTcount: A:0.30, C:0.01, G:0.19, T:0.49
Consensus pattern (27 bp):
ATATATAATATATGGGTTTTGGTATTT
Found at i:55698844 original size:29 final size:28
Alignment explanation
Indices: 55698787--55698854 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
55698777 CACATAGTAC
*
55698787 ATATATATGCGTGGTTTTGCTATACATA
1 ATATATATGCGTGGTTTTACTATACATA
* * *
55698815 ATATATATGTGTGGGTTTTATTATATATA
1 ATATATATGCGT-GGTTTTACTATACATA
*
55698844 ATAAATATGCG
1 ATATATATGCG
55698855 GTTATAGATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 11 0.33
29 22 0.67
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (28 bp):
ATATATATGCGTGGTTTTACTATACATA
Found at i:55702502 original size:22 final size:22
Alignment explanation
Indices: 55702457--55702503 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
55702447 TTTTTGTAAA
*
55702457 AAGGATAAAGTGTTTAAAATGTT
1 AAGGATAAAGTG-TTAAAACGTT
55702480 AAGGACTAAAGTG-TAAAACGTT
1 AAGGA-TAAAGTGTTAAAACGTT
55702502 AA
1 AA
55702504 AATATTTGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
23 5 0.23
24 7 0.32
ACGTcount: A:0.47, C:0.04, G:0.21, T:0.28
Consensus pattern (22 bp):
AAGGATAAAGTGTTAAAACGTT
Found at i:55708385 original size:40 final size:40
Alignment explanation
Indices: 55708327--55708467 Score: 203
Period size: 40 Copynumber: 3.5 Consensus size: 40
55708317 ATCGTCAGAT
*
55708327 CAATCG-AACACACCAGACAGAAGCTCATAAGAGGTAATC
1 CAATCGAAACACACCAGACAGAAGCTCATAAAAGGTAATC
* *
55708366 CAATCGAAACACACTAGACAGAAGCTCATAACAGGTAATC
1 CAATCGAAACACACCAGACAGAAGCTCATAAAAGGTAATC
* * * * *
55708406 CAACCGAAACACGCCAGATAAAAGCTCATAAAAGCTAATC
1 CAATCGAAACACACCAGACAGAAGCTCATAAAAGGTAATC
55708446 CAATCGAAACACACCAGACAGA
1 CAATCGAAACACACCAGACAGA
55708468 GAGTATAACA
Statistics
Matches: 88, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
39 6 0.07
40 82 0.93
ACGTcount: A:0.46, C:0.27, G:0.15, T:0.12
Consensus pattern (40 bp):
CAATCGAAACACACCAGACAGAAGCTCATAAAAGGTAATC
Found at i:55713217 original size:56 final size:56
Alignment explanation
Indices: 55713151--55713262 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
55713141 TATAACAAGT
*
55713151 ATGAGAATTGGGATATTTGTGAAACAAATGAAATATGATAGCATATGTAAGTTGAA
1 ATGAGAATTGGGATATTTGTGAAACAAATGAAATATAATAGCATATGTAAGTTGAA
*
55713207 ATGAGAATTGGGATATTTGTGAAACAAATGAAATATAATAGCATGTGTAAGTTGAA
1 ATGAGAATTGGGATATTTGTGAAACAAATGAAATATAATAGCATATGTAAGTTGAA
55713263 TATAGTATGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.43, C:0.04, G:0.23, T:0.30
Consensus pattern (56 bp):
ATGAGAATTGGGATATTTGTGAAACAAATGAAATATAATAGCATATGTAAGTTGAA
Found at i:55714679 original size:27 final size:27
Alignment explanation
Indices: 55714649--55714708 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
55714639 TTTCATCTCT
55714649 TAGGGGTATAACAATCATTTTACCTTA
1 TAGGGGTATAACAATCATTTTACCTTA
** *
55714676 TAGGGGTATTTCGATCATTTTACCTTA
1 TAGGGGTATAACAATCATTTTACCTTA
55714703 TGAGGG
1 T-AGGG
55714709 TATTTTGGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (27 bp):
TAGGGGTATAACAATCATTTTACCTTA
Found at i:55714709 original size:27 final size:27
Alignment explanation
Indices: 55714663--55714927 Score: 322
Period size: 27 Copynumber: 9.9 Consensus size: 27
55714653 GGTATAACAA
* *
55714663 TCATTTTACCTTAT-AGGGGTATTTCGA
1 TCATTTTACCCTATGA-GGGTATTTCGG
* *
55714690 TCATTTTACCTTATGAGGGTATTTTGG
1 TCATTTTACCCTATGAGGGTATTTCGG
* *
55714717 TCA-TTTACCCTATGGGGGTATTTCAG
1 TCATTTTACCCTATGAGGGTATTTCGG
* * * *
55714743 TCATTCTACCTTATGGGGGTATTTGGG
1 TCATTTTACCCTATGAGGGTATTTCGG
55714770 TCATTTTACCCTATGAGGGTATTTCGG
1 TCATTTTACCCTATGAGGGTATTTCGG
* *
55714797 TTATTCTACCCTATGAGGGTATTTCGG
1 TCATTTTACCCTATGAGGGTATTTCGG
* * *
55714824 CCATTTTACCCTATGGGGGTATTTTGG
1 TCATTTTACCCTATGAGGGTATTTCGG
*
55714851 TCATTCTACCCTATG-GGGATATTTCGG
1 TCATTTTACCCTATGAGGG-TATTTCGG
* *
55714878 TCATTCTACCCTATGAGGGTATTTCAG
1 TCATTTTACCCTATGAGGGTATTTCGG
55714905 TCATTTTACCCTATG-GGGTATTT
1 TCATTTTACCCTATGAGGGTATTT
55714928 TACTGCAGGT
Statistics
Matches: 208, Mismatches: 26, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
26 33 0.16
27 171 0.82
28 4 0.02
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTATGAGGGTATTTCGG
Found at i:55714846 original size:81 final size:81
Alignment explanation
Indices: 55714663--55714927 Score: 374
Period size: 81 Copynumber: 3.3 Consensus size: 81
55714653 GGTATAACAA
* * * * *
55714663 TCATTTTACCTTATAGGGGTATTTCGATCATTTTACCTTATGAGGGTATTTTGGTCATT-TACCC
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCGGTCATTCTACCC
*
55714727 TATGGGGGTATTTCAG
66 TATGAGGGTATTTCAG
* * * *
55714743 TCATTCTACCTTATGGGGGTATTTGGGTCATTTTACCCTATGAGGGTATTTCGGTTATTCTACCC
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCGGTCATTCTACCC
*
55714808 TATGAGGGTATTTCGG
66 TATGAGGGTATTTCAG
* * *
55714824 CCATTTTACCCTATGGGGGTATTTTGGTCATTCTACCCTATG-GGGATATTTCGGTCATTCTACC
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGG-TATTTCGGTCATTCTACC
55714888 CTATGAGGGTATTTCAG
65 CTATGAGGGTATTTCAG
55714905 TCATTTTACCCTAT-GGGGTATTT
1 TCATTTTACCCTATGGGGGTATTT
55714928 TACTGCAGGT
Statistics
Matches: 166, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
80 64 0.39
81 102 0.61
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (81 bp):
TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCGGTCATTCTACCC
TATGAGGGTATTTCAG
Found at i:55717876 original size:27 final size:27
Alignment explanation
Indices: 55717859--55718286 Score: 465
Period size: 27 Copynumber: 15.9 Consensus size: 27
55717849 GGGTATAACA
*
55717859 GTCATTTTACCCTATAGGGGTATTTCG
1 GTCATTCTACCCTATAGGGGTATTTCG
* * * *
55717886 ATCATTTTACCCTATGGGGGTATTTTG
1 GTCATTCTACCCTATAGGGGTATTTCG
* **
55717913 GTCATTCTACCCTATAAGGGTATTTTA
1 GTCATTCTACCCTATAGGGGTATTTCG
55717940 GTCATTCTACCCTATA-GGGTATTTCG
1 GTCATTCTACCCTATAGGGGTATTTCG
* * *
55717966 ATCATTCTA-CCTTTTGAGGGTATTTCG
1 GTCATTCTACCCTATAG-GGGTATTTCG
* * *
55717993 GTCATTTTACCCTATGGGGGTATTTTG
1 GTCATTCTACCCTATAGGGGTATTTCG
* **
55718020 GTCATTCTACCCTATAAGGGTATTTTA
1 GTCATTCTACCCTATAGGGGTATTTCG
55718047 GTCATTCTACCCTATA-GGGTATTTCG
1 GTCATTCTACCCTATAGGGGTATTTCG
* * *
55718073 ATCATTCTA-CCTTTTGAGGGTATTTCG
1 GTCATTCTACCCTATAG-GGGTATTTCG
* *
55718100 ATCATTTTACCCTATAGGGGTATTTCG
1 GTCATTCTACCCTATAGGGGTATTTCG
*
55718127 GTCATTCTACCATAT-GGAGGTATTTCG
1 GTCATTCTACCCTATAGG-GGTATTTCG
* * *
55718154 GTCATTTTATCCTATGGGGGTATTTCG
1 GTCATTCTACCCTATAGGGGTATTTCG
*
55718181 GTTACTT-TACCCTATAGGGGTATTTCG
1 GTCA-TTCTACCCTATAGGGGTATTTCG
* *
55718208 GTCATTCTACCCTAT-GAGAGTATTTCA
1 GTCATTCTACCCTATAG-GGGTATTTCG
* *
55718235 GTTATTTTACCCTATAGGGGTATTTCG
1 GTCATTCTACCCTATAGGGGTATTTCG
* *
55718262 GTCATTTTACCTTATAGGGGTATTT
1 GTCATTCTACCCTATAGGGGTATTT
55718287 TGGTGCAGCT
Statistics
Matches: 341, Mismatches: 48, Indels: 24
0.83 0.12 0.06
Matches are distributed among these distances:
25 8 0.02
26 37 0.11
27 281 0.82
28 15 0.04
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (27 bp):
GTCATTCTACCCTATAGGGGTATTTCG
Found at i:55717998 original size:107 final size:107
Alignment explanation
Indices: 55717876--55718286 Score: 513
Period size: 107 Copynumber: 3.8 Consensus size: 107
55717866 TACCCTATAG
* *
55717876 GGGTATTTCGATCATTTTACCCTATGGGGGTATTTTGGTCATTCTACCCTATAAGGGTATTTTAG
1 GGGTATTTCGATCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCCTATAAGGGTATTTCAG
55717941 TCATTCTACCCTATAGGGTATTTCGATCATTCTACCTTTTGA
66 TCATTCTACCCTATAGGGTATTTCGATCATTCTACCTTTTGA
* * *
55717983 GGGTATTTCGGTCATTTTACCCTATGGGGGTATTTTGGTCATTCTACCCTATAAGGGTATTTTAG
1 GGGTATTTCGATCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCCTATAAGGGTATTTCAG
55718048 TCATTCTACCCTATAGGGTATTTCGATCATTCTACCTTTTGA
66 TCATTCTACCCTATAGGGTATTTCGATCATTCTACCTTTTGA
* * * *
55718090 GGGTATTTCGATCATTTTACCCTATAGGGGTATTTCGGTCATTCTACCATAT-GGAGGTATTTCG
1 GGGTATTTCGATCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCCTATAAG-GGTATTTCA
* * * * * * *
55718154 GTCATTTTATCCTATGGGGGTATTTCGGTTACTT-TACCCTAT-A
65 GTCATTCTACCCTAT-AGGGTATTTCGATCA-TTCTACCTTTTGA
* * * * * * * * *
55718197 GGGGTATTTCGGTCATTCTACCCTATGAGAGTATTTCAGTTATTTTACCCTATAGGGGTATTTCG
1 -GGGTATTTCGATCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCCTATAAGGGTATTTCA
* *
55718262 GTCATTTTACCTTATAGGGGTATTT
65 GTCATTCTACCCTATA-GGGTATTT
55718287 TGGTGCAGCT
Statistics
Matches: 271, Mismatches: 27, Indels: 11
0.88 0.09 0.04
Matches are distributed among these distances:
106 1 0.00
107 175 0.65
108 91 0.34
109 4 0.01
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (107 bp):
GGGTATTTCGATCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCCTATAAGGGTATTTCAG
TCATTCTACCCTATAGGGTATTTCGATCATTCTACCTTTTGA
Found at i:55719004 original size:24 final size:25
Alignment explanation
Indices: 55718972--55719018 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
55718962 CCCAAATCCT
*
55718972 AATATTCTCTCCTCAAATCTCTCCA
1 AATATTCTCCCCTCAAATCTCTCCA
*
55718997 AATA-TCTCCCCTCAATTCTCTC
1 AATATTCTCCCCTCAAATCTCTC
55719019 TATGACCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.26, C:0.38, G:0.00, T:0.36
Consensus pattern (25 bp):
AATATTCTCCCCTCAAATCTCTCCA
Found at i:55723774 original size:31 final size:31
Alignment explanation
Indices: 55723736--55723812 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
55723726 CGTCACAGGC
* *
55723736 CGTGTGGGCCACACT-GGCTAGGCTAGTTAGG
1 CGTGTGGGCCACA-TGGGCTAGGCCAATTAGG
* *
55723767 CGTGTGGGCCACATGGGTTGGGCCAATTAGG
1 CGTGTGGGCCACATGGGCTAGGCCAATTAGG
55723798 CTGTGTGGGCCACAT
1 C-GTGTGGGCCACAT
55723813 AGGAGTATGG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
30 1 0.03
31 26 0.65
32 13 0.32
ACGTcount: A:0.16, C:0.22, G:0.39, T:0.23
Consensus pattern (31 bp):
CGTGTGGGCCACATGGGCTAGGCCAATTAGG
Found at i:55723815 original size:18 final size:17
Alignment explanation
Indices: 55723763--55723825 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
55723753 CTAGGCTAGT
55723763 TAGGCGTGTGGGCCACA
1 TAGGCGTGTGGGCCACA
55723780 T-GG-GT-TGGGCCA-A
1 TAGGCGTGTGGGCCACA
55723793 TTAGGCTGTGTGGGCCACA
1 -TAGGC-GTGTGGGCCACA
* *
55723812 TAGGAGTATGGGCC
1 TAGGCGTGTGGGCC
55723826 TATTTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 1 0.03
14 8 0.21
15 4 0.11
16 2 0.05
17 11 0.29
18 11 0.29
19 1 0.03
ACGTcount: A:0.17, C:0.19, G:0.41, T:0.22
Consensus pattern (17 bp):
TAGGCGTGTGGGCCACA
Found at i:55725925 original size:39 final size:40
Alignment explanation
Indices: 55725816--55725925 Score: 125
Period size: 40 Copynumber: 2.8 Consensus size: 40
55725806 GTTTGGATAA
* * *
55725816 AAAACGCCGCTGAAAATCGAGAATTAGAGGCGCTTTATGG
1 AAAACGCCGCTGAAAATCGAGCATTAGCGGCACTTTATGG
* * *
55725856 AAAACGCCGCT-AAAGATCAAGCATTTGCGGCACTTTTTGG
1 AAAACGCCGCTGAAA-ATCGAGCATTAGCGGCACTTTATGG
* *
55725896 AACACGCCGTTGAAAAT-GAGCATTAGCGGC
1 AAAACGCCGCTGAAAATCGAGCATTAGCGGC
55725926 GTTTTTCCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
39 14 0.24
40 41 0.71
41 3 0.05
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (40 bp):
AAAACGCCGCTGAAAATCGAGCATTAGCGGCACTTTATGG
Found at i:55726056 original size:41 final size:41
Alignment explanation
Indices: 55725983--55726204 Score: 311
Period size: 41 Copynumber: 5.4 Consensus size: 41
55725973 TTTTGACCTT
*
55725983 TCGGGGCTTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGC
1 TCGGGGCTTTAGCGGCGTTTCTGAAAAAGCACCGCTAATGC
* *
55726024 TCGAGGCTTTAGCGACGTTTCT-AAAAAGGCACCGCTAATGC
1 TCGGGGCTTTAGCGGCGTTTCTGAAAAA-GCACCGCTAATGC
** *
55726065 TCGGGGCTTTAGCGGCGTTTCTGAAAAAGTGCCGCTAATAC
1 TCGGGGCTTTAGCGGCGTTTCTGAAAAAGCACCGCTAATGC
*
55726106 TCGGGGCTTTAGCGGCGTTTCTGAAAAAGCGCCGCTAATGC
1 TCGGGGCTTTAGCGGCGTTTCTGAAAAAGCACCGCTAATGC
* * * * * *
55726147 TCAGGGCTTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATTC
1 TCGGGGCTTTAGCGGCGTTTCTGAAAAAGCACCGCTAATGC
55726188 TCGGGGCTTTAGCGGCG
1 TCGGGGCTTTAGCGGCG
55726205 CTTTTTAAAA
Statistics
Matches: 162, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
40 5 0.03
41 152 0.94
42 5 0.03
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.27
Consensus pattern (41 bp):
TCGGGGCTTTAGCGGCGTTTCTGAAAAAGCACCGCTAATGC
Found at i:55726591 original size:15 final size:15
Alignment explanation
Indices: 55726571--55726600 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55726561 ACTATCTTAA
*
55726571 GGTTTATGGATTATG
1 GGTTTAGGGATTATG
55726586 GGTTTAGGGATTATG
1 GGTTTAGGGATTATG
55726601 ATATATGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (15 bp):
GGTTTAGGGATTATG
Found at i:55726659 original size:21 final size:20
Alignment explanation
Indices: 55726604--55726659 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 20
55726594 GATTATGATA
55726604 TATGATTTAAGGGTTAGGGTT
1 TATGATTT-AGGGTTAGGGTT
* *
55726625 TAAGGTTTAGGGGTTAGGGGTT
1 TATGATTTA-GGGTTA-GGGTT
55726647 TATGATTTAGGGT
1 TATGATTTAGGGT
55726660 GTAAGGGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.03
21 16 0.55
22 12 0.41
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (20 bp):
TATGATTTAGGGTTAGGGTT
Found at i:55726887 original size:22 final size:22
Alignment explanation
Indices: 55726860--55726918 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
55726850 TTAAGAGTTG
55726860 GGGTTTAAGGTTTAGGGGTTAA
1 GGGTTTAAGGTTTAGGGGTTAA
*
55726882 GGGTTTAGAGG-ATAGGGGTTAA
1 GGGTTTA-AGGTTTAGGGGTTAA
*
55726904 GGGTTTAGGGTTTAG
1 GGGTTTAAGGTTTAG
55726919 ATTTATTAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.84
23 3 0.09
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.34
Consensus pattern (22 bp):
GGGTTTAAGGTTTAGGGGTTAA
Found at i:55734019 original size:15 final size:15
Alignment explanation
Indices: 55733999--55734029 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
55733989 CCAACCTTCA
55733999 AATTTTACCTCAATT
1 AATTTTACCTCAATT
55734014 AATTTTACCTCAATT
1 AATTTTACCTCAATT
55734029 A
1 A
55734030 TACATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTTACCTCAATT
Found at i:55737601 original size:16 final size:16
Alignment explanation
Indices: 55737580--55737618 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
55737570 TTGATTTGCT
*
55737580 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
**
55737596 ATTACACCTCTATTCC
1 ATTACACAGCTATTCC
55737612 ATTACAC
1 ATTACAC
55737619 CTCTAATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:55737619 original size:16 final size:16
Alignment explanation
Indices: 55737592--55737633 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
55737582 TACACAGCTT
55737592 TTCCATTACACCTCTA
1 TTCCATTACACCTCTA
55737608 TTCCATTACACCTCTA
1 TTCCATTACACCTCTA
* *
55737624 ATCCAATACA
1 TTCCATTACA
55737634 GCGAACCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
TTCCATTACACCTCTA
Found at i:55739292 original size:13 final size:13
Alignment explanation
Indices: 55739270--55739303 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
55739260 ATTGCTCATT
*
55739270 TATTTAAACATAA
1 TATTTTAACATAA
55739283 TATTTTAACATAA
1 TATTTTAACATAA
55739296 TATTTTAA
1 TATTTTAA
55739304 TTCTAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (13 bp):
TATTTTAACATAA
Found at i:55739640 original size:36 final size:36
Alignment explanation
Indices: 55739574--55739646 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
55739564 TCATGATCTT
* * * *
55739574 TAGCGGCGTTTGTGGTAGAAGCGTTGCTAAAGGTCA
1 TAGCGGCGTTTGTGGGAAAAGCGCTACTAAAGGTCA
* *
55739610 TAGCGGCGTTTGTGGGAAAAGTGCTACTAAATGTCA
1 TAGCGGCGTTTGTGGGAAAAGCGCTACTAAAGGTCA
55739646 T
1 T
55739647 GATCTTTAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.25, C:0.14, G:0.33, T:0.29
Consensus pattern (36 bp):
TAGCGGCGTTTGTGGGAAAAGCGCTACTAAAGGTCA
Found at i:55743055 original size:43 final size:43
Alignment explanation
Indices: 55742992--55743079 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
55742982 TTTTGGGATG
*
55742992 TTAGCACACTGATGGTCGGCACCCCTTTACCAGATAAATCTTT
1 TTAGCACACTGATGGCCGGCACCCCTTTACCAGATAAATCTTT
*
55743035 TTAGCACACTGATGGCCGGCACCCCTTTACCAGATAAATTTTT
1 TTAGCACACTGATGGCCGGCACCCCTTTACCAGATAAATCTTT
55743078 TT
1 TT
55743080 TGGGTGCTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (43 bp):
TTAGCACACTGATGGCCGGCACCCCTTTACCAGATAAATCTTT
Found at i:55743263 original size:54 final size:52
Alignment explanation
Indices: 55743119--55743321 Score: 165
Period size: 54 Copynumber: 3.8 Consensus size: 52
55743109 CATTTTAAAA
* * * *
55743119 TTAAAAAA-ATTGGGTGCTAAGACACTGATGGCCGGCACCCCAGTATCAAATT
1 TTAAAAAATTTTGGGTGCT-GGACACTGATGGCCGGCACCTCAGTACCAAATT
* * * * *** **
55743171 TTAAAAAAATTGGGGTACTGGAACATTGATGATAGGCACCTTTGTACCAAAATT
1 TTAAAAAATTTTGGGTGCTGG-ACACTGATGGCCGGCACCTCAGTACC-AAATT
* * *
55743225 TTAAAAAATTTTGGGTGCTAGGACAATGATGGCCGGCACATCAGTACCATATT
1 TTAAAAAATTTTGGGTGCT-GGACACTGATGGCCGGCACCTCAGTACCAAATT
*
55743278 TAAAAAATATATTTTGAGGTGCTGAGACACTGATGGCCGGCACC
1 T-TAAAA-A-ATTTTG-GGTGCTG-GACACTGATGGCCGGCACC
55743322 CCAATACTAG
Statistics
Matches: 116, Mismatches: 26, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
52 9 0.08
53 30 0.26
54 44 0.38
55 3 0.03
56 7 0.06
57 23 0.20
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (52 bp):
TTAAAAAATTTTGGGTGCTGGACACTGATGGCCGGCACCTCAGTACCAAATT
Found at i:55743340 original size:57 final size:56
Alignment explanation
Indices: 55743232--55743341 Score: 132
Period size: 57 Copynumber: 1.9 Consensus size: 56
55743222 ATTTTAAAAA
* * * *
55743232 ATTTTGGGTGCTAGGACAATGATGGCCGGCACATCAGTACCATATTTAAAAAATAT
1 ATTTTGGGTGCTAGGACAATGATGGCCGGCACACCAATACCAGATTAAAAAAATAT
* * *
55743288 ATTTTGAGGTGCT-GAGACACTGATGGCCGGCACCCCAATACTAGATTAAAAAAA
1 ATTTTG-GGTGCTAG-GACAATGATGGCCGGCACACCAATACCAGATTAAAAAAA
55743342 AAAAGGATGT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
56 7 0.16
57 38 0.84
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (56 bp):
ATTTTGGGTGCTAGGACAATGATGGCCGGCACACCAATACCAGATTAAAAAAATAT
Found at i:55743947 original size:90 final size:90
Alignment explanation
Indices: 55743792--55743997 Score: 270
Period size: 90 Copynumber: 2.3 Consensus size: 90
55743782 ACTACTATTC
* * * * * *
55743792 AAAATGGTTGTATTATTTTTGTATATGTAAATCAATTTTAGTCCGTATTATTTGTTGGTCGAATT
1 AAAATGTTTGTATTATTTTTGGATCTGTAAATAAATTTTAGTCCGTATTATTTATTGGTCAAATT
* * *
55743857 TTATATTTTCGTATATCAGTTTTGT
66 TTATATTTTCATATATCAATTTTCT
*
55743882 AAAATGTTTGTATTATTTTTGGATCTGTAAA-AATATTTTAGTCCGTATTTTTTATTGGTCAAAT
1 AAAATGTTTGTATTATTTTTGGATCTGTAAATAA-ATTTTAGTCCGTATTATTTATTGGTCAAAT
55743946 TTTATATTTTCATATATCAATTTTCT
65 TTTATATTTTCATATATCAATTTTCT
* * * *
55743972 AGAATGTTCGTAATAATTTTGGATCT
1 AAAATGTTTGTATTATTTTTGGATCT
55743998 ATGCAAAAAA
Statistics
Matches: 101, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
89 1 0.01
90 100 0.99
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.51
Consensus pattern (90 bp):
AAAATGTTTGTATTATTTTTGGATCTGTAAATAAATTTTAGTCCGTATTATTTATTGGTCAAATT
TTATATTTTCATATATCAATTTTCT
Found at i:55751551 original size:46 final size:45
Alignment explanation
Indices: 55751480--55751618 Score: 197
Period size: 46 Copynumber: 3.0 Consensus size: 45
55751470 ACAATGCTAT
*
55751480 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTT-ACTGAAATACCATACCTACGTTTCAC
* *
55751526 AACTCAATATGGTTTTCGTTGCTGAAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTC-TTACTGAAATACCATACCTACGTTTCAC
* * *
55751572 AACTCAGTATGGTTTTCTTTACTGAATTACCATACCTATGTTCCAC
1 AACTCAGTATGGTTTTC-TTACTGAAATACCATACCTACGTTTCAC
55751618 A
1 A
55751619 CTTTGCCATG
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
46 81 0.98
47 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (45 bp):
AACTCAGTATGGTTTTCTTACTGAAATACCATACCTACGTTTCAC
Found at i:55756535 original size:13 final size:13
Alignment explanation
Indices: 55756517--55756544 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
55756507 TCTAATTAGG
55756517 GTCACACGCCCGT
1 GTCACACGCCCGT
55756530 GTCACACGCCCGT
1 GTCACACGCCCGT
55756543 GT
1 GT
55756545 ACCGGGTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.43, G:0.25, T:0.18
Consensus pattern (13 bp):
GTCACACGCCCGT
Found at i:55756581 original size:25 final size:25
Alignment explanation
Indices: 55756526--55756581 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
55756516 GGTCACACGC
*
55756526 CCGTGTCACACGCCCGTGTACCGGG
1 CCGTGTCACACGCCCGTGTACCAGG
** *
55756551 TTGTGTCACACGCCCGTGTGCCAGG
1 CCGTGTCACACGCCCGTGTACCAGG
55756576 CCGTGT
1 CCGTGT
55756582 AACTTTCTGA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.11, C:0.36, G:0.32, T:0.21
Consensus pattern (25 bp):
CCGTGTCACACGCCCGTGTACCAGG
Found at i:55758292 original size:102 final size:102
Alignment explanation
Indices: 55758160--55758511 Score: 668
Period size: 102 Copynumber: 3.5 Consensus size: 102
55758150 TCGGAATAGG
*
55758160 CCACCGTATTTTAAATTTTAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTT
1 CCACCGTATTTTAAATTTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTT
55758225 GATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATT
66 GATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATT
* *
55758262 CCACCGTATTTTAAATATGAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCT
1 CCACCGTATTTTAAATTTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTT
55758327 GATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATT
66 GATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATT
*
55758364 CCACCGTATTTTAAATTTTAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTT
1 CCACCGTATTTTAAATTTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTT
55758429 GATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATT
66 GATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATT
55758466 CCACCGTATTTTAAATTTGAAGGGGGTTGCTAAGTGCTGATTCCCC
1 CCACCGTATTTTAAATTTGAAGGGGGTTGCTAAGTGCTGATTCCCC
55758512 GACTCATTGG
Statistics
Matches: 243, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 243 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.33
Consensus pattern (102 bp):
CCACCGTATTTTAAATTTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTT
GATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATT
Found at i:55758500 original size:75 final size:75
Alignment explanation
Indices: 55758413--55758696 Score: 478
Period size: 75 Copynumber: 3.8 Consensus size: 75
55758403 ATTCCCCCAA
* * *
55758413 GGGGTTGCTAAGTGTTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTT
1 GGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGAATCCACCGTATCTT
*
55758478 AAATTTGAAG
66 AAATGTGAAG
* *
55758488 GGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGTTGATTCCACCGTATCTT
1 GGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGAATCCACCGTATCTT
55758553 AAATGTGAAG
66 AAATGTGAAG
* *
55758563 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGAACCCACCGTATCTT
1 GGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGAATCCACCGTATCTT
*
55758628 AAATGTGAAA
66 AAATGTGAAG
*
55758638 GGGGTTGCTAAGTGCTGATTCCCCCACTCATTGGTGGTTGCTAAGTGCTGAATCCACCG
1 GGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGAATCCACCG
55758697 ATAACGGTTA
Statistics
Matches: 197, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 197 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.32
Consensus pattern (75 bp):
GGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGAATCCACCGTATCTT
AAATGTGAAG
Found at i:55758507 original size:42 final size:41
Alignment explanation
Indices: 55758448--55758659 Score: 177
Period size: 42 Copynumber: 5.5 Consensus size: 41
55758438 ACTCATTGGT
55758448 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATTTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTA-TTTAAATTTGAAGGG
* * *
55758490 GGTTGCTAAGTGCTGATTCC-CCG-A-CT-CA-TT---GGT
1 GGTTGCTAAGTGCTGATTCCACCGTATTTAAATTTGAAGGG
* *
55758523 GGTTGCTAAGTGTTGATTCCACCGTATCTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTAT-TTAAATTTGAAGGG
* * *
55758565 GGTTGCTAAGTGCTGATTCC-CCG-A-AT-CA-TT---GGT
1 GGTTGCTAAGTGCTGATTCCACCGTATTTAAATTTGAAGGG
** * *
55758598 GGTTGCTAAGTGCTGAACCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTAT-TTAAATTTGAAGGG
55758640 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
55758660 CCCACTCATT
Statistics
Matches: 130, Mismatches: 22, Indels: 36
0.69 0.12 0.19
Matches are distributed among these distances:
33 41 0.32
34 6 0.05
35 2 0.02
36 3 0.02
37 4 0.03
38 4 0.03
39 2 0.02
40 2 0.02
41 6 0.05
42 60 0.46
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACCGTATTTAAATTTGAAGGG
Found at i:55765991 original size:33 final size:33
Alignment explanation
Indices: 55765919--55766477 Score: 235
Period size: 33 Copynumber: 16.5 Consensus size: 33
55765909 ATAAAAAGGG
*
55765919 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
55765946 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
* * * *
55765979 GGATGCTAAGTGCTGATTCGACCGTATTTTAAATATGAAGGG
1 GGTTGCTAAGTGCTGATTC--CCCTA--TT-CAT-T---GGT
*
55766021 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
* *
55766048 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
* *
55766081 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATTAAAAGGG
1 GGTTGCTAAGTGCTGATTCC-CC-TA--TT-CATT----GGT
*
55766123 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
55766150 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
* *
55766183 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATTTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CC-TA--TT-CA-TT---GGT
*
55766225 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
* *
55766252 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
* * *
55766285 GGTTGCTAAGTGTTGATTCCACCGTATCTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CC-TA--TT-CAT-T---GGT
*
55766327 GGTTGCTTAGTGCTGATTCCCC----CGA--GG-
1 GGTTGCTAAGTGCTGATTCCCCTATTC-ATTGGT
*
55766354 GGTTGCTAAGTGCTGATTCCCCTAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
* ** * *
55766387 GGTTGCTAAGTGATGAACCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CC-TA--TT-CAT-TG---GT
* *
55766429 GGTTGCTAAGTGCTGATTCCCCCACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
55766462 GGTTGCTAAGTGCTGA
1 GGTTGCTAAGTGCTGA
55766478 ATCCACCGAT
Statistics
Matches: 411, Mismatches: 44, Indels: 148
0.68 0.07 0.25
Matches are distributed among these distances:
27 109 0.27
28 8 0.02
30 1 0.00
31 9 0.02
32 10 0.02
33 114 0.28
34 9 0.02
35 10 0.02
36 2 0.00
37 9 0.02
38 11 0.03
39 6 0.01
40 3 0.01
41 8 0.02
42 102 0.25
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
Found at i:55766090 original size:102 final size:102
Alignment explanation
Indices: 55765914--55766452 Score: 891
Period size: 102 Copynumber: 5.3 Consensus size: 102
55765904 ATTGAATAAA
*
55765914 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCTACTCATTGGT
* * *
55765979 GGATGCTAAGTGCTGATTCGACCGTATTTTAAATATG
66 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTG
*
55766016 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCTACTCATTGGT
*
55766081 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAAT-TAA
66 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGT-G
*
55766118 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCTACTCATTGGT
*
55766183 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATTTG
66 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTG
*
55766220 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCTACTCATTGGT
* *
55766285 GGTTGCTAAGTGTTGATTCCACCGTATCTTAAATGTG
66 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTG
* * *
55766322 AAGGGGGTTGCTTAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCTAATCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCTACTCATTGGT
* ** *
55766387 GGTTGCTAAGTGATGAACCCACCGTATCTTAAATGTG
66 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTG
*
55766424 AAAGGGGTTGCTAAGTGCTGATTCCCCCA
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCA
55766453 CTCATTGGTG
Statistics
Matches: 412, Mismatches: 23, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
101 1 0.00
102 410 1.00
103 1 0.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (102 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCTACTCATTGGT
GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTG
Found at i:55776979 original size:37 final size:38
Alignment explanation
Indices: 55776898--55776981 Score: 102
Period size: 38 Copynumber: 2.3 Consensus size: 38
55776888 ACAAAAAATG
* * *
55776898 ATAAAAAA-ATAAAATTCAATAAAATTTATTAAATTTT
1 ATAAAAAATATAAAAATCAATAAAATTGATAAAATTTT
*
55776935 AATAAAAATTATAAAAATCAA-AAAATTGA-AAAATTTT
1 -ATAAAAAATATAAAAATCAATAAAATTGATAAAATTTT
55776972 ATAAAAAATA
1 ATAAAAAATA
55776982 AAATATATAG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
36 9 0.22
37 7 0.17
38 14 0.35
39 10 0.25
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.32
Consensus pattern (38 bp):
ATAAAAAATATAAAAATCAATAAAATTGATAAAATTTT
Found at i:55777324 original size:20 final size:20
Alignment explanation
Indices: 55777299--55777347 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
55777289 GCTGACAAAA
55777299 CAGTCACTCTGATTTCAATT
1 CAGTCACTCTGATTTCAATT
*
55777319 CAGTCACTCTGATTTGAATT
1 CAGTCACTCTGATTTCAATT
55777339 CAGTCACTC
1 CAGTCACTC
55777348 AACTTTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (20 bp):
CAGTCACTCTGATTTCAATT
Found at i:55777376 original size:30 final size:32
Alignment explanation
Indices: 55777335--55777408 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 32
55777325 CTCTGATTTG
55777335 AATTCAGTCACTCAAC-TT-TCAAAAAATAACA
1 AATT-AGTCACTCAACGTTATCAAAAAATAACA
* *
55777366 AATTAGTCACT-AACGTTATCAAAAAGTGACA
1 AATTAGTCACTCAACGTTATCAAAAAATAACA
*
55777397 AATCAGTCACTC
1 AATTAGTCACTC
55777409 GTTAACATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 3 0.08
30 9 0.24
31 25 0.68
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.26
Consensus pattern (32 bp):
AATTAGTCACTCAACGTTATCAAAAAATAACA
Found at i:55777783 original size:28 final size:29
Alignment explanation
Indices: 55777752--55777807 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
55777742 ATTTTTCGTC
*
55777752 TTTTTA-ATAAAT-GACCAATATTTTTAT
1 TTTTTACATAAATGGACCAATATGTTTAT
*
55777779 TTTTTACATAAATGGCCCAATATGTTTAT
1 TTTTTACATAAATGGACCAATATGTTTAT
55777808 ATTTCTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.24
28 6 0.24
29 13 0.52
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (29 bp):
TTTTTACATAAATGGACCAATATGTTTAT
Found at i:55779568 original size:13 final size:13
Alignment explanation
Indices: 55779550--55779574 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55779540 TATTTTATTT
55779550 TATAAAATATATA
1 TATAAAATATATA
55779563 TATAAAATATAT
1 TATAAAATATAT
55779575 TTGCAAATGC
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TATAAAATATATA
Found at i:55779576 original size:27 final size:26
Alignment explanation
Indices: 55779553--55779601 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
55779543 TTTATTTTAT
*
55779553 AAAATATATATATAAAATATA-TTTG
1 AAAATACATATATAAAATATATTTTG
* *
55779578 CAAATGCATATATAAAATATATTT
1 AAAATACATATATAAAATATATTT
55779602 GCAAACTTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (26 bp):
AAAATACATATATAAAATATATTTTG
Found at i:55783116 original size:18 final size:19
Alignment explanation
Indices: 55783075--55783121 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
55783065 AAAAAAAAAC
*
55783075 ATTTTAAAATTGAATAACG
1 ATTTGAAAATTGAATAACG
* *
55783094 ATTTGTAAATT-AATAATG
1 ATTTGAAAATTGAATAACG
*
55783112 TTTTGAAAAT
1 ATTTGAAAAT
55783122 GAACGACACG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.43
Consensus pattern (19 bp):
ATTTGAAAATTGAATAACG
Found at i:55783798 original size:30 final size:30
Alignment explanation
Indices: 55783764--55783821 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
55783754 TTTTATTTTA
* *
55783764 AATTTTATTATTATTTTAAAGGCATTTGTT
1 AATTTTAGTATTACTTTAAAGGCATTTGTT
* *
55783794 AATTTTGGTATTACTTTAGAGGCATTTG
1 AATTTTAGTATTACTTTAAAGGCATTTG
55783822 CTTGTTAAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.28, C:0.05, G:0.16, T:0.52
Consensus pattern (30 bp):
AATTTTAGTATTACTTTAAAGGCATTTGTT
Found at i:55785396 original size:31 final size:31
Alignment explanation
Indices: 55785330--55785406 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 31
55785320 ATACATAAAC
* * * *
55785330 TTCAATTACACACCTGAAACTTGAATTGTGG
1 TTCAAATATACACATGAAACTTGAATTGTGA
* *
55785361 TTCAAATATATACATGAAACGTTG-ATTTTGA
1 TTCAAATATACACATGAAAC-TTGAATTGTGA
*
55785392 TTCAATTATACACAT
1 TTCAAATATACACAT
55785407 TTAAAAAATG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
31 34 0.92
32 3 0.08
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (31 bp):
TTCAAATATACACATGAAACTTGAATTGTGA
Found at i:55794358 original size:138 final size:138
Alignment explanation
Indices: 55794107--55794382 Score: 525
Period size: 138 Copynumber: 2.0 Consensus size: 138
55794097 AACATTACAG
*
55794107 TTGGCTGAAAGATCTTCAGTACATCTGAAAGGAGTATTGGAACATGCGTTGGTTAAAGTGTGCAG
1 TTGGCTGAAAGATCTTCAGTACATCTGAAAGGAGTATTGGAACATGCGTTGGTTAAAGTGTACAG
55794172 TTTCATTATTCCAACAGATTTTGTGGTTTTAGACTTTGAAGAAGATTGTAAGATACCAATCTTAT
66 TTTCATTATTCCAACAGATTTTGTGGTTTTAGACTTTGAAGAAGATTGTAAGATACCAATCTTAT
55794237 TAGGAAGA
131 TAGGAAGA
*
55794245 TTGGCTGAAAGATCTTCAGTACATCTGAAAGGAGTATTGGAACATGTGTTGGTTAAAGTGTACAG
1 TTGGCTGAAAGATCTTCAGTACATCTGAAAGGAGTATTGGAACATGCGTTGGTTAAAGTGTACAG
*
55794310 TTTCATTATTCCAACAGATTTTGTGGTTTTAGACTTTGAAGAATATTGTAAGATACCAATCTTAT
66 TTTCATTATTCCAACAGATTTTGTGGTTTTAGACTTTGAAGAAGATTGTAAGATACCAATCTTAT
55794375 TAGGAAGA
131 TAGGAAGA
55794383 CCTTTTCTAG
Statistics
Matches: 135, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
138 135 1.00
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.35
Consensus pattern (138 bp):
TTGGCTGAAAGATCTTCAGTACATCTGAAAGGAGTATTGGAACATGCGTTGGTTAAAGTGTACAG
TTTCATTATTCCAACAGATTTTGTGGTTTTAGACTTTGAAGAAGATTGTAAGATACCAATCTTAT
TAGGAAGA
Found at i:55805663 original size:20 final size:20
Alignment explanation
Indices: 55805625--55805662 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55805615 TCGTTCCAAG
*
55805625 TTTTTTACGCTCTTCTTTTA
1 TTTTTCACGCTCTTCTTTTA
*
55805645 TTTTTCACGTTCTT-TTTT
1 TTTTTCACGCTCTTCTTTT
55805663 TTGCAGTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.08, C:0.18, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTTCACGCTCTTCTTTTA
Found at i:55807609 original size:30 final size:30
Alignment explanation
Indices: 55807573--55807635 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
55807563 CCAAAGTGAT
*
55807573 AACTAAATTATACTTTGTCTTTATTACCAA
1 AACTAAATTATACTTCGTCTTTATTACCAA
*
55807603 AACTAAATTATACTTCGTCTTTATTGCCAA
1 AACTAAATTATACTTCGTCTTTATTACCAA
55807633 AAC
1 AAC
55807636 CACCCTAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.40
Consensus pattern (30 bp):
AACTAAATTATACTTCGTCTTTATTACCAA
Found at i:55815024 original size:16 final size:16
Alignment explanation
Indices: 55815002--55815048 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
55814992 TTATTTTGAA
55815002 ATTAAAAGTATAAAATT
1 ATTAAAA-TATAAAATT
55815019 -TTAAAATATATAAATT
1 ATTAAAATATA-AAATT
*
55815035 AATAAAAATATAAA
1 -ATTAAAATATAAA
55815049 TCTTTATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.15
16 11 0.42
17 2 0.08
18 9 0.35
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
ATTAAAATATAAAATT
Found at i:55815107 original size:17 final size:17
Alignment explanation
Indices: 55815093--55815146 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
55815083 GTTATTTTCC
*
55815093 TTTTTATATATTTTTAA
1 TTTTTATAAATTTTTAA
*
55815110 TTTTTATAAATTTATAAA
1 TTTTTATAAATTT-TTAA
*
55815128 TTGTATTATAAAATTTTAA
1 TT-T-TTATAAATTTTTAA
55815147 AAATATTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 12 0.40
18 5 0.17
19 4 0.13
20 9 0.30
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTTTATAAATTTTTAA
Found at i:55815774 original size:45 final size:45
Alignment explanation
Indices: 55815721--55816501 Score: 1030
Period size: 45 Copynumber: 17.4 Consensus size: 45
55815711 TCCTATACTA
* * *
55815721 GCAGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCCTATATTG
1 GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTG
* * * *
55815766 GTAGCGAAGTAGATCAAAGATAGCAGATCTTATCTTCCTATATTG
1 GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTG
* * * * *
55815811 GTAACGAAGTAGATCGAAGAAAACAGATCTTGTCTTCTTGTATTG
1 GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTG
* *
55815856 GCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTG
1 GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTG
* * *
55815901 GTAGCGAAGTAGATCGAATATAGCAGATCTTGTCTTCCTGTACTG
1 GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTG
* * * * *
55815946 GCACCGAAGTAGATTGAAGATAACAGAACTTGTCTTCCTGTACTG
1 GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTG
* * *
55815991 GCAGCGAAGTAGATCAAAGATAACAGATCTTATCTTCCTGTATTG
1 GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTG
*
55816036 GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTACTG
1 GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTG
* * *
55816081 GCAGTGAAGTAGATTGAAGATAACAGA----GTCTTCCTGTATTG
1 GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTG
* * *
55816122 GCAGCGAAGTAGATCGAAGATAGCAGATTTTGTCTTCCTGTACTA
1 GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTG
*
55816167 GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCGTATTG
1 GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTG
* * *
55816212 GCAGCGAAGTAGATCGAAGGTAGTAGATCTTGTCTTCTTGTATTG
1 GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTG
* * *
55816257 GCAGCAAAGTAGATCGAAGATAGCAGATTTTGTCTTCCTGTACTG
1 GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTG
*
55816302 GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTG
1 GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTG
* *
55816347 GTAGCGAAGTAGATCGAAGATAACAGATCTTGTCTTCCTGTATTG
1 GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTG
* * * * *
55816392 GCAGCAAAGTAGATCAAAGATAACGGATCTCGTCTTCCTGTATTG
1 GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTG
** * * * * *
55816437 ATAGCGAAGTAGATCGAAAACAACAGATCTTATTTTCCTGTATTG
1 GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTG
* *
55816482 ACAGCAAAGTAGATCGAAGA
1 GCAGCGAAGTAGATCGAAGA
55816502 CAGAAGTAAC
Statistics
Matches: 644, Mismatches: 88, Indels: 8
0.87 0.12 0.01
Matches are distributed among these distances:
41 37 0.06
45 607 0.94
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.29
Consensus pattern (45 bp):
GCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTG
Found at i:55816699 original size:44 final size:44
Alignment explanation
Indices: 55816596--55816713 Score: 139
Period size: 44 Copynumber: 2.7 Consensus size: 44
55816586 CAGATCGCAT
* * * ** * *
55816596 CCAAT-CTCATCTCCCCGAGGTTACAGTAGAGTAGATTGAATAAG
1 CCAATCCT-ATCTCCCTGAGGTTGCAGTGGAACAGATTGAAGAAA
*
55816640 CCAATCTTATCTCCCTGAGGTTGCAGTGGAACAGATTGAAGAAA
1 CCAATCCTATCTCCCTGAGGTTGCAGTGGAACAGATTGAAGAAA
*
55816684 CCAATCCTATCTCCCTGAAGTTGCAGTGGA
1 CCAATCCTATCTCCCTGAGGTTGCAGTGGA
55816714 GTGGATCAGA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 62 0.98
45 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (44 bp):
CCAATCCTATCTCCCTGAGGTTGCAGTGGAACAGATTGAAGAAA
Found at i:55831697 original size:15 final size:17
Alignment explanation
Indices: 55831677--55831716 Score: 66
Period size: 15 Copynumber: 2.5 Consensus size: 17
55831667 GTCTTGATTC
55831677 TTAAAATTTTAAA-AA-
1 TTAAAATTTTAAACAAT
55831692 TTAAAATTTTAAACAAT
1 TTAAAATTTTAAACAAT
55831709 TTAAAATT
1 TTAAAATT
55831717 AAAAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 13 0.57
16 2 0.09
17 8 0.35
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAAATTTTAAACAAT
Found at i:55834220 original size:29 final size:29
Alignment explanation
Indices: 55834186--55834272 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
55834176 ATTTTATAGT
*
55834186 GCCACATGGCCGTGTGGTAGACTATGTGC
1 GCCACACGGCCGTGTGGTAGACTATGTGC
* * *
55834215 GCCACACGGCTGTGTGTTAAGCCT-TGTGC
1 GCCACACGGCCGTGTGGT-AGACTATGTGC
* * *
55834244 GCCACACAGCCGTGTGGTAGGCCATGTGC
1 GCCACACGGCCGTGTGGTAGACTATGTGC
55834273 CAGTCCATGT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
28 3 0.06
29 40 0.85
30 4 0.09
ACGTcount: A:0.16, C:0.28, G:0.33, T:0.23
Consensus pattern (29 bp):
GCCACACGGCCGTGTGGTAGACTATGTGC
Found at i:55835379 original size:6 final size:6
Alignment explanation
Indices: 55835362--55835408 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
55835352 TTTGGACTAA
** *
55835362 GTTTTCG GTTTTG GTTTT- GTTTTG GGCTTG ATTTTG GTTTTG GTTTT
1 GTTTT-G GTTTTG GTTTTG GTTTTG GTTTTG GTTTTG GTTTTG GTTTT
55835409 TTATCTATCG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
5 5 0.15
6 23 0.70
7 5 0.15
ACGTcount: A:0.02, C:0.04, G:0.30, T:0.64
Consensus pattern (6 bp):
GTTTTG
Found at i:55837198 original size:16 final size:16
Alignment explanation
Indices: 55837173--55837206 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55837163 TGACTATATA
*
55837173 TAAAATTTTAATAAAT
1 TAAAAATTTAATAAAT
*
55837189 TAAAAATTTATTAAAT
1 TAAAAATTTAATAAAT
55837205 TA
1 TA
55837207 TTAAATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAAATTTAATAAAT
Found at i:55837227 original size:24 final size:25
Alignment explanation
Indices: 55837184--55837233 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
55837174 AAAATTTTAA
*
55837184 TAAATTAAAAATTTATTAAAT-TAT
1 TAAATTAAAAATATATTAAATATAT
55837208 TAAATTAAAAATA-ATATAAATATAT
1 TAAATTAAAAATATAT-TAAATATAT
55837233 T
1 T
55837234 TTTCAGAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 2 0.09
24 17 0.74
25 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
TAAATTAAAAATATATTAAATATAT
Found at i:55843588 original size:38 final size:38
Alignment explanation
Indices: 55843457--55843597 Score: 140
Period size: 38 Copynumber: 3.7 Consensus size: 38
55843447 CCACTGTATT
* *
55843457 ACTGAAAACATGTTAAACATG-CTTACTGCTACTGTTGA
1 ACTGAAAACATGTTAAGCATGTC-TACTGTTACTGTTGA
* * ** * * *
55843495 ACCGAATACATGTTAAGCATCCCTACTATTATTGTTAA
1 ACTGAAAACATGTTAAGCATGTCTACTGTTACTGTTGA
** * *
55843533 ACTGAATGCATGATAAGCATGTCTAATGTTACTGTTGA
1 ACTGAAAACATGTTAAGCATGTCTACTGTTACTGTTGA
*
55843571 ACTAAAAACATGTTAAGCATGTCTACT
1 ACTGAAAACATGTTAAGCATGTCTACT
55843598 ATTTTTACAA
Statistics
Matches: 80, Mismatches: 22, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
38 79 0.99
39 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (38 bp):
ACTGAAAACATGTTAAGCATGTCTACTGTTACTGTTGA
Found at i:55843881 original size:20 final size:21
Alignment explanation
Indices: 55843856--55843896 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
55843846 CAATTTGTAC
*
55843856 TACTGGTAGTT-ATCTACAAA
1 TACTGGTAGTTCATCCACAAA
*
55843876 TACTGGTGGTTCATCCACAAA
1 TACTGGTAGTTCATCCACAAA
55843897 CTGGAGTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Consensus pattern (21 bp):
TACTGGTAGTTCATCCACAAA
Found at i:55847677 original size:22 final size:21
Alignment explanation
Indices: 55847650--55847712 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
55847640 TTGGACCGGC
* *
55847650 TAATAACATTAAAAAATTATAA
1 TAATAAAATT-AAAAATTAAAA
55847672 TAATAAAATTAAAAATTAAAA
1 TAATAAAATTAAAAATTAAAA
* *
55847693 T-ATAGAAATTTAAATTTAAA
1 TAATA-AAATTAAAAATTAAA
55847713 TTTAGGCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 3 0.08
21 24 0.67
22 9 0.25
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
TAATAAAATTAAAAATTAAAA
Found at i:55853275 original size:30 final size:27
Alignment explanation
Indices: 55853210--55853285 Score: 102
Period size: 25 Copynumber: 2.8 Consensus size: 27
55853200 ATCCATATTT
*
55853210 ATGGAAAGTCAAAGATAAGGGTATCAA
1 ATGGAAAGTCAAAGATATGGGTATCAA
55853237 AT--AAAGTCAAAGATATGGGTATCAAA
1 ATGGAAAGTCAAAGATATGGGTATC-AA
55853263 TATTGGAAAGTCAAAGATATGGG
1 -A-TGGAAAGTCAAAGATATGGG
55853286 AATTGGGATA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
25 20 0.47
26 2 0.05
27 3 0.07
28 1 0.02
30 17 0.40
ACGTcount: A:0.46, C:0.07, G:0.25, T:0.22
Consensus pattern (27 bp):
ATGGAAAGTCAAAGATATGGGTATCAA
Found at i:55860225 original size:33 final size:32
Alignment explanation
Indices: 55860126--55860236 Score: 125
Period size: 32 Copynumber: 3.4 Consensus size: 32
55860116 TAGAGGAATA
* *** *
55860126 TTGTTATCATTTAACAAAATGCTAGTTGATGT
1 TTGTTATCATTTCACAAAATAAAAGTTGATAT
* *
55860158 TTGTTATCATTTTACAAAATTAAAGTTG-TAAT
1 TTGTTATCATTTCACAAAATAAAAGTTGAT-AT
*
55860190 TTGTTATAATTTCACAAAATAAAAAGTTGATAT
1 TTGTTATCATTTCACAAAAT-AAAAGTTGATAT
55860223 TTGTTATCATTTCA
1 TTGTTATCATTTCA
55860237 TATAACATTC
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
31 1 0.01
32 43 0.64
33 22 0.33
34 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (32 bp):
TTGTTATCATTTCACAAAATAAAAGTTGATAT
Found at i:55861186 original size:18 final size:17
Alignment explanation
Indices: 55861161--55861204 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
55861151 ATTACATACC
55861161 AAAGAATATAAAAAACA
1 AAAGAATATAAAAAACA
* *
55861178 AATAGAATATTACAAACA
1 AA-AGAATATAAAAAACA
55861196 AAAGAATAT
1 AAAGAATAT
55861205 TGGTGGCGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.68, C:0.07, G:0.07, T:0.18
Consensus pattern (17 bp):
AAAGAATATAAAAAACA
Found at i:55861203 original size:17 final size:17
Alignment explanation
Indices: 55861151--55861205 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
55861141 GATAGTGACG
* *
55861151 ATTACATACCAAAGAAT
1 ATTACAAACAAAAGAAT
* *
55861168 ATAAAAAACAAATAGAAT
1 ATTACAAACAAA-AGAAT
55861186 ATTACAAACAAAAGAAT
1 ATTACAAACAAAAGAAT
55861203 ATT
1 ATT
55861206 GGTGGCGATT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.62, C:0.11, G:0.05, T:0.22
Consensus pattern (17 bp):
ATTACAAACAAAAGAAT
Found at i:55863619 original size:13 final size:13
Alignment explanation
Indices: 55863601--55863628 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
55863591 AAAGGGCGCC
55863601 TTTCAGAAACGTT
1 TTTCAGAAACGTT
55863614 TTTCAGAAACGTT
1 TTTCAGAAACGTT
55863627 TT
1 TT
55863629 AGATATCCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTTCAGAAACGTT
Found at i:55864305 original size:11 final size:11
Alignment explanation
Indices: 55864289--55864318 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
55864279 TTTAAAAAAA
55864289 TTAAAATATTT
1 TTAAAATATTT
55864300 TTAAAATA-TT
1 TTAAAATATTT
55864310 TTAAAATAT
1 TTAAAATAT
55864319 AAAAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TTAAAATATTT
Found at i:55867140 original size:14 final size:14
Alignment explanation
Indices: 55867121--55867150 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55867111 TGATTGTTTT
*
55867121 TAATCTAAATTTAC
1 TAATCTAAATTAAC
55867135 TAATCTAAATTAAC
1 TAATCTAAATTAAC
55867149 TA
1 TA
55867151 CGAACGCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:55870375 original size:27 final size:27
Alignment explanation
Indices: 55870337--55870677 Score: 412
Period size: 27 Copynumber: 12.6 Consensus size: 27
55870327 TGCTTGGGAA
55870337 CCATAGGGTAAAATGACCGAAATACCC
1 CCATAGGGTAAAATGACCGAAATACCC
55870364 CCATAGGGTAAAATGACCGAAATACCC
1 CCATAGGGTAAAATGACCGAAATACCC
* * * *
55870391 CCGTAGGGTAGAATAACCGAAATACCT
1 CCATAGGGTAAAATGACCGAAATACCC
* * * *
55870418 TCATAGGATAAAATGATCGAAGTACCC
1 CCATAGGGTAAAATGACCGAAATACCC
* * *
55870445 CCATAAGATAAAATGACTGAAATACCC
1 CCATAGGGTAAAATGACCGAAATACCC
* *
55870472 CCATAGGATAAAATGACCGAATTACCC
1 CCATAGGGTAAAATGACCGAAATACCC
* * * *
55870499 TCATAAGGTAGAATGACCGAATTACCC
1 CCATAGGGTAAAATGACCGAAATACCC
* * *
55870526 TCATAAGGTAAAATGACTGAAATACCC
1 CCATAGGGTAAAATGACCGAAATACCC
* *
55870553 CCATAAGGTAAAATGACAGAAATACCC
1 CCATAGGGTAAAATGACCGAAATACCC
* *
55870580 CAATAGGGTAAAATGATCGAAATACCC
1 CCATAGGGTAAAATGACCGAAATACCC
* * * *
55870607 CTATAAGGTAGAATGAACGAAATACCC
1 CCATAGGGTAAAATGACCGAAATACCC
*
55870634 TCATAGGGTAAAATGACCGAAATACCC
1 CCATAGGGTAAAATGACCGAAATACCC
*
55870661 CCATAGGATAAAATGAC
1 CCATAGGGTAAAATGAC
55870678 TATTATACCC
Statistics
Matches: 270, Mismatches: 44, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 270 1.00
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.18
Consensus pattern (27 bp):
CCATAGGGTAAAATGACCGAAATACCC
Found at i:55872460 original size:40 final size:40
Alignment explanation
Indices: 55872407--55872634 Score: 321
Period size: 40 Copynumber: 5.7 Consensus size: 40
55872397 TAGAGCATTC
* * *
55872407 TTTCAATAGATTCAGTAGGTATAGCTTGAAAGCGCATACG
1 TTTCAATAGATTCACTAGGTATGGCTCGAAAGCGCATACG
* * * * *
55872447 TTTTAGTATATTCACTAGGTATGGCTCGAAAGCACATACA
1 TTTCAATAGATTCACTAGGTATGGCTCGAAAGCGCATACG
*
55872487 TTTCAATAGATTCACTAGGTATGGCTCGAAAGTGCATACG
1 TTTCAATAGATTCACTAGGTATGGCTCGAAAGCGCATACG
* * * **
55872527 TTTTAGTAGATTCACTAGGTATGGCTCGAAAGCACATTTG
1 TTTCAATAGATTCACTAGGTATGGCTCGAAAGCGCATACG
*
55872567 TTTAAATAGATTCACTAGGTATGGCTCGAAAGCGCATACG
1 TTTCAATAGATTCACTAGGTATGGCTCGAAAGCGCATACG
55872607 TTTCAATAGATTCACTAGGTATGGCTCG
1 TTTCAATAGATTCACTAGGTATGGCTCG
55872635 TCTGAGCACC
Statistics
Matches: 162, Mismatches: 26, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 162 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (40 bp):
TTTCAATAGATTCACTAGGTATGGCTCGAAAGCGCATACG
Found at i:55872540 original size:80 final size:80
Alignment explanation
Indices: 55872407--55872634 Score: 357
Period size: 80 Copynumber: 2.9 Consensus size: 80
55872397 TAGAGCATTC
* * * *
55872407 TTTCAATAGATTCAGTAGGTATAGCTTGAAAGCGCATACGTTTTAGTATATTCACTAGGTATGGC
1 TTTCAATAGATTCACTAGGTATGGCTCGAAAGCGCATACGTTTTAGTAGATTCACTAGGTATGGC
55872472 TCGAAAGCACATACA
66 TCGAAAGCACATACA
*
55872487 TTTCAATAGATTCACTAGGTATGGCTCGAAAGTGCATACGTTTTAGTAGATTCACTAGGTATGGC
1 TTTCAATAGATTCACTAGGTATGGCTCGAAAGCGCATACGTTTTAGTAGATTCACTAGGTATGGC
***
55872552 TCGAAAGCACATTTG
66 TCGAAAGCACATACA
* * *
55872567 TTTAAATAGATTCACTAGGTATGGCTCGAAAGCGCATACGTTTCAATAGATTCACTAGGTATGGC
1 TTTCAATAGATTCACTAGGTATGGCTCGAAAGCGCATACGTTTTAGTAGATTCACTAGGTATGGC
55872632 TCG
66 TCG
55872635 TCTGAGCACC
Statistics
Matches: 136, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 136 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (80 bp):
TTTCAATAGATTCACTAGGTATGGCTCGAAAGCGCATACGTTTTAGTAGATTCACTAGGTATGGC
TCGAAAGCACATACA
Found at i:55875367 original size:28 final size:28
Alignment explanation
Indices: 55875327--55875382 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
55875317 CAAATAACAA
55875327 GTTTATTTCCATCACTTTCCATCACATT
1 GTTTATTTCCATCACTTTCCATCACATT
55875355 GTTTATTTCCATCACTTTCCATCACATT
1 GTTTATTTCCATCACTTTCCATCACATT
55875383 AACCGTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.29, G:0.04, T:0.46
Consensus pattern (28 bp):
GTTTATTTCCATCACTTTCCATCACATT
Found at i:55875648 original size:14 final size:14
Alignment explanation
Indices: 55875629--55875660 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
55875619 ATCAAAACAC
55875629 ATAAATATAATACA
1 ATAAATATAATACA
*
55875643 ATAAATATAGTACA
1 ATAAATATAATACA
55875657 ATAA
1 ATAA
55875661 TATCATTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.28
Consensus pattern (14 bp):
ATAAATATAATACA
Found at i:55876589 original size:29 final size:29
Alignment explanation
Indices: 55876540--55876623 Score: 125
Period size: 29 Copynumber: 2.9 Consensus size: 29
55876530 GGCTGACATC
* *
55876540 GGTGCCGCCTGTCAGGAAGGCTTCACTAGT
1 GGTGCTGCCT-TCAGGCAGGCTTCACTAGT
55876570 GGTGCTGCCTTCAGGCAGGCTTCACTAGT
1 GGTGCTGCCTTCAGGCAGGCTTCACTAGT
55876599 GGTG-TCGCCTTCAGGCAGGCTTCAC
1 GGTGCT-GCCTTCAGGCAGGCTTCAC
55876624 CATTAAATGT
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
28 1 0.02
29 41 0.80
30 9 0.18
ACGTcount: A:0.14, C:0.29, G:0.32, T:0.25
Consensus pattern (29 bp):
GGTGCTGCCTTCAGGCAGGCTTCACTAGT
Found at i:55876938 original size:27 final size:28
Alignment explanation
Indices: 55876888--55876956 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
55876878 AAATAAAAAA
*
55876888 TTACCAAAATGT-TATAACTTTTTTTTAT
1 TTACCAAAATATATATAAC-TTTTTTTAT
55876916 TTACCAAAATATATATAA-TTTTTTTAT
1 TTACCAAAATATATATAACTTTTTTTAT
*
55876943 TCACCAAAATATAT
1 TTACCAAAATATAT
55876957 CAAAAAAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 22 0.58
28 11 0.29
29 5 0.13
ACGTcount: A:0.39, C:0.12, G:0.01, T:0.48
Consensus pattern (28 bp):
TTACCAAAATATATATAACTTTTTTTAT
Found at i:55876973 original size:9 final size:9
Alignment explanation
Indices: 55876957--55877001 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
55876947 CAAAATATAT
55876957 CAAAAAAAA
1 CAAAAAAAA
*
55876966 C-TAAAAAA
1 CAAAAAAAA
55876974 CAAAAAAAA
1 CAAAAAAAA
*
55876983 GAAAAAAAA
1 CAAAAAAAA
*
55876992 GAAAAAAAA
1 CAAAAAAAA
55877001 C
1 C
55877002 CTGAACTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
8 7 0.23
9 24 0.77
ACGTcount: A:0.84, C:0.09, G:0.04, T:0.02
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:55877177 original size:18 final size:17
Alignment explanation
Indices: 55877154--55877332 Score: 81
Period size: 18 Copynumber: 10.5 Consensus size: 17
55877144 GAAGGAGAGG
55877154 GGAAG-AAGAAGAAAGAAA
1 GGAAGAAAGAA-AAAG-AA
55877172 GGAAGAAAGAAAAAGAA
1 GGAAGAAAGAAAAAGAA
* *
55877189 GG-A-AAAGGAAAGGAGA
1 GGAAGAAAGAAAAAGA-A
55877205 GGAAAGAAAGAAAAAGAA
1 GG-AAGAAAGAAAAAGAA
** *
55877223 GGAAAGAAAAGGAAATGGGA
1 GG-AAG-AAA-GAAAAAGAA
*
55877243 GGAAAGAAAGAAAAATAA
1 GG-AAGAAAGAAAAAGAA
* *
55877261 GGAAAGAAA-AGGAAAGGA
1 GG-AAGAAAGA-AAAAGAA
55877279 GG-AGAAA-AAAAA-AA
1 GGAAGAAAGAAAAAGAA
* * *
55877293 GAAAG-AAGAAGAAGAG
1 GGAAGAAAGAAAAAGAA
*
55877309 GGAAGGAAGGAAAAA-AA
1 GGAA-GAAAGAAAAAGAA
55877326 -GAAGAAA
1 GGAAGAAA
55877333 ATAAGGTAAT
Statistics
Matches: 124, Mismatches: 24, Indels: 29
0.70 0.14 0.16
Matches are distributed among these distances:
14 4 0.03
15 21 0.17
16 17 0.14
17 7 0.06
18 43 0.35
19 20 0.16
20 12 0.10
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (17 bp):
GGAAGAAAGAAAAAGAA
Found at i:55877187 original size:10 final size:10
Alignment explanation
Indices: 55877156--55877227 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 10
55877146 AGGAGAGGGG
*
55877156 AAGAAGAAGA
1 AAGAAAAAGA
55877166 AAGAAAGGAAGA
1 AAGAAA--AAGA
55877178 AAGAAAAAGA
1 AAGAAAAAGA
* *
55877188 AGGAAAAGGA
1 AAGAAAAAGA
55877198 AAGGAGAGGAAAGA
1 AA-GA-A--AAAGA
55877212 AAGAAAAAGA
1 AAGAAAAAGA
*
55877222 AGGAAA
1 AAGAAA
55877228 GAAAAGGAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 28 0.56
11 2 0.04
12 12 0.24
13 2 0.04
14 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:55877187 original size:22 final size:23
Alignment explanation
Indices: 55877156--55877237 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 23
55877146 AGGAGAGGGG
*
55877156 AAGAAGAAGAAAG-AAAGGAAGA
1 AAGAAAAAGAAAGAAAAGGAAGA
*
55877178 AAGAAAAAGAAGGAAAAGGAA-A
1 AAGAAAAAGAAAGAAAAGGAAGA
* * *
55877200 GGAGAGGAAAGAAAGAAAAAGAAGGA
1 -AAGA-AAAAGAAAGAAAAGGAA-GA
*
55877226 AAGAAAAGGAAA
1 AAGAAAAAGAAA
55877238 TGGGAGGAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
22 12 0.26
23 10 0.22
24 20 0.43
25 3 0.07
26 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAAAGGAAGA
Found at i:55877193 original size:14 final size:13
Alignment explanation
Indices: 55877159--55877232 Score: 51
Period size: 14 Copynumber: 5.1 Consensus size: 13
55877149 AGAGGGGAAG
55877159 AAGAAGAAAG-AA
1 AAGAAGAAAGAAA
*
55877171 AGGAAGAAAGAAA
1 AAGAAGAAAGAAA
55877184 AAGAAGGAAAAGGAAA
1 AAGAA-G-AAA-GAAA
55877200 GGAGAGGAAAGAAAGAAA
1 --A-A-G-AAGAAAGAAA
55877218 AAGAAGGAAAGAAA
1 AAGAA-GAAAGAAA
55877232 A
1 A
55877233 GGAAATGGGA
Statistics
Matches: 50, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
12 9 0.18
13 8 0.16
14 11 0.22
15 4 0.08
16 5 0.10
18 5 0.10
19 4 0.08
20 2 0.04
21 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAGAAA
Found at i:55877232 original size:38 final size:36
Alignment explanation
Indices: 55877174--55877328 Score: 158
Period size: 38 Copynumber: 4.2 Consensus size: 36
55877164 GAAAGAAAGG
55877174 AAGAAAGAAAAAGAAG--GAAAAGGAAAGGAGAGGA
1 AAGAAAGAAAAAGAAGAAGAAAAGGAAAGGAGAGGA
55877208 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAATGG-GAGGA
1 AAGAAAGAAAAAGAA-G-AAGAAAAGGAAA-GGAGAGGA
*
55877246 AAGAAAGAAAAATAAGGAAAGAAAAGGAAAGGAG-GAGA
1 AAGAAAGAAAAAGAA-G-AAGAAAAGGAAAGGAGAG-GA
* * * *
55877284 AAAAAAAAAGAAAGAAGAAGAAGAGGGAAGGA-AGGA
1 AAGAAAGAA-AAAGAAGAAGAAAAGGAAAGGAGAGGA
*
55877320 AAAAAAGAA
1 AAGAAAGAA
55877329 GAAAATAAGG
Statistics
Matches: 105, Mismatches: 7, Indels: 16
0.82 0.05 0.12
Matches are distributed among these distances:
34 15 0.14
35 1 0.01
36 10 0.10
37 17 0.16
38 55 0.52
39 7 0.07
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.01
Consensus pattern (36 bp):
AAGAAAGAAAAAGAAGAAGAAAAGGAAAGGAGAGGA
Found at i:55877234 original size:10 final size:10
Alignment explanation
Indices: 55877176--55877276 Score: 72
Period size: 10 Copynumber: 10.5 Consensus size: 10
55877166 AAGAAAGGAA
*
55877176 GAAAGAAAAA
1 GAAAGAAAAG
*
55877186 GAAGGAAAAG
1 GAAAGAAAAG
* *
55877196 GAAAGGAGAG
1 GAAAGAAAAG
55877206 GAAAG-AAA-
1 GAAAGAAAAG
55877214 GAAA-AAGAAG
1 GAAAGAA-AAG
55877224 GAAAGAAAAG
1 GAAAGAAAAG
**
55877234 GAAATG-GGAG
1 GAAA-GAAAAG
55877244 GAAAG-AAA-
1 GAAAGAAAAG
55877252 GAAA-AATAAG
1 GAAAGAA-AAG
55877262 GAAAGAAAAG
1 GAAAGAAAAG
55877272 GAAAG
1 GAAAG
55877277 GAGGAGAAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
8 10 0.14
9 8 0.11
10 49 0.68
11 5 0.07
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:55877270 original size:76 final size:74
Alignment explanation
Indices: 55877155--55877338 Score: 182
Period size: 71 Copynumber: 2.5 Consensus size: 74
55877145 AAGGAGAGGG
* * * * * *
55877155 GAAGAAGAA-GAAAGAAAGG-AAGAAAGAAAAAGAAGGAAAAGGAAAGGAGAGGA-AAG-AAAGA
1 GAAGAA-AAGGAAAGGAAGGAAAGAAAGAAAAATAAGG-AAAGAAAAGGAAAGGAGGAGAAAAAA
*
55877216 AAAAG-AAGGA
64 AAAAGAAAGAA
*
55877226 -AAGAAAAGGAAATGGGAGGAAAGAAAGAAAAATAAGGAAAGAAAAGGAAAGGAGGAGAAAAAAA
1 GAAGAAAAGGAAA-GGAAGGAAAGAAAGAAAAATAAGGAAAGAAAAGGAAAGGAGGAGAAAAAAA
55877290 AAAGAAAGAA
65 AAAGAAAGAA
* * *
55877300 GAAGAAGAGGGAAGGAAGGAAAAAAAGAAGAAAATAAGG
1 GAAGAAAAGGAAAGGAAGGAAAGAAAG-A-AAAATAAGG
55877339 TAATTATTNN
Statistics
Matches: 92, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
69 2 0.02
70 9 0.10
71 18 0.20
72 18 0.20
73 9 0.10
74 16 0.17
75 11 0.12
76 9 0.10
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.02
Consensus pattern (74 bp):
GAAGAAAAGGAAAGGAAGGAAAGAAAGAAAAATAAGGAAAGAAAAGGAAAGGAGGAGAAAAAAAA
AAGAAAGAA
Found at i:55880719 original size:26 final size:27
Alignment explanation
Indices: 55880671--55880737 Score: 102
Period size: 26 Copynumber: 2.5 Consensus size: 27
55880661 AAATAAAAAA
*
55880671 TTACCAAATTAT-TATAACTTTTTTTAT
1 TTACCAAAATATATATAAC-TTTTTTAT
55880698 TTACCAAAATATATATAA-TTTTTTAT
1 TTACCAAAATATATATAACTTTTTTAT
55880724 TTACCAAAATATAT
1 TTACCAAAATATAT
55880738 CAAAAAAAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
26 22 0.58
27 11 0.29
28 5 0.13
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.49
Consensus pattern (27 bp):
TTACCAAAATATATATAACTTTTTTAT
Found at i:55880913 original size:18 final size:18
Alignment explanation
Indices: 55880886--55880920 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
55880876 AACACACTAA
55880886 ATTAATAAATT-TAAAAC
1 ATTAATAAATTATAAAAC
55880903 ATTATATAAATTATAAAA
1 ATTA-ATAAATTATAAAA
55880921 TTAGAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 7 0.44
19 5 0.31
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
ATTAATAAATTATAAAAC
Found at i:55882810 original size:18 final size:18
Alignment explanation
Indices: 55882784--55882820 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
55882774 ATCCCAATGA
* *
55882784 TCGCCACCACCTTCTTCT
1 TCGCAACCACATTCTTCT
55882802 TCGCAACCACATTCTTCT
1 TCGCAACCACATTCTTCT
55882820 T
1 T
55882821 TACCACCAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.16, C:0.43, G:0.05, T:0.35
Consensus pattern (18 bp):
TCGCAACCACATTCTTCT
Found at i:55883666 original size:3 final size:3
Alignment explanation
Indices: 55883658--55883728 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
55883648 AGTAACATCT
55883658 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55883706 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
55883729 TAAAATTTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:55884115 original size:27 final size:27
Alignment explanation
Indices: 55884036--55884116 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 27
55884026 TGGTTGGCAG
* *
55884036 GACTGGTGCCGCCAATCTGCTTCCCTC
1 GACTGATGCCGCCAACCTGCTTCCCTC
* *
55884063 GACTGGTGCCGCCAACCTGCTTCCCTT
1 GACTGATGCCGCCAACCTGCTTCCCTC
**
55884090 GTTTGATGCCGCCAACCTGCTTCCCTC
1 GACTGATGCCGCCAACCTGCTTCCCTC
55884117 CACCCAAGGA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.11, C:0.41, G:0.21, T:0.27
Consensus pattern (27 bp):
GACTGATGCCGCCAACCTGCTTCCCTC
Found at i:55884211 original size:27 final size:28
Alignment explanation
Indices: 55884175--55884230 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 28
55884165 AGTTTTTTTG
55884175 ATATATTTTGGTAAAT-AAAAAAATTAT
1 ATATATTTTGGTAAATAAAAAAAATTAT
*
55884202 ATATTTTTTGGTAAATAAAAAAAATTAT
1 ATATATTTTGGTAAATAAAAAAAATTAT
55884230 A
1 A
55884231 ACATTTTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 15 0.56
28 12 0.44
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (28 bp):
ATATATTTTGGTAAATAAAAAAAATTAT
Found at i:55884237 original size:27 final size:27
Alignment explanation
Indices: 55884179--55884242 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
55884169 TTTTTGATAT
*
55884179 ATTTTGGTAAATAAAAAAATTATATAT
1 ATTTTGGTAAATAAAAAAATTATATAC
*
55884206 TTTTTGGTAAATAAAAAAAATTATA-AC
1 ATTTTGGTAAAT-AAAAAAATTATATAC
*
55884233 ATTTTAGTAA
1 ATTTTGGTAA
55884243 TTTTTTATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 20 0.62
28 12 0.38
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.41
Consensus pattern (27 bp):
ATTTTGGTAAATAAAAAAATTATATAC
Found at i:55885735 original size:44 final size:44
Alignment explanation
Indices: 55885669--55885756 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
55885659 AATGACATTC
* *
55885669 TCTTTCTCTCCTTAACCTAACTTAATATGTGTAATTTATGTGTG
1 TCTTTCTCTCCTTAACCTAACTTAAAATGTGCAATTTATGTGTG
* *
55885713 TCTTTCTCTCTTTAATCC-AACTTAAAATGTGCCATTTATGTGTG
1 TCTTTCTCTCCTTAA-CCTAACTTAAAATGTGCAATTTATGTGTG
55885757 CTTACATGGC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 37 0.95
45 2 0.05
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.47
Consensus pattern (44 bp):
TCTTTCTCTCCTTAACCTAACTTAAAATGTGCAATTTATGTGTG
Found at i:55887489 original size:24 final size:25
Alignment explanation
Indices: 55887462--55887514 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
55887452 ATATGGAAAG
*
55887462 AAATAATTAAGAT-T-TTATGCTAAT
1 AAATAATTAA-ATATATTATACTAAT
*
55887486 AAAT-GTTAAATATATTATACTAAT
1 AAATAATTAAATATATTATACTAAT
55887510 AAATA
1 AAATA
55887515 CTAAATCTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
22 2 0.08
23 5 0.21
24 17 0.71
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.40
Consensus pattern (25 bp):
AAATAATTAAATATATTATACTAAT
Found at i:55888623 original size:21 final size:21
Alignment explanation
Indices: 55888597--55888661 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
55888587 ATGAACGATG
*
55888597 AATGATTACATAATT-ATTTGT
1 AATGATTGCAT-ATTGATTTGT
55888618 AATGATTGCATATTGATTTGT
1 AATGATTGCATATTGATTTGT
55888639 AATGATTGCATATTGATTTGT
1 AATGATTGCATATTGATTTGT
55888660 AA
1 AA
55888662 ATCCTATGGC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
20 3 0.07
21 39 0.93
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (21 bp):
AATGATTGCATATTGATTTGT
Found at i:55890131 original size:32 final size:32
Alignment explanation
Indices: 55890095--55890157 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
55890085 GGTTTTAAAA
55890095 TTATTATGTTTTAAAG-TTGTTAGATATTGAAT
1 TTATTATGTTTT-AAGCTTGTTAGATATTGAAT
*
55890127 TTATTATGTTTTAAGCTTGTTGGATATTGAA
1 TTATTATGTTTTAAGCTTGTTAGATATTGAA
55890158 ATGATTGACA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 3 0.10
32 26 0.90
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (32 bp):
TTATTATGTTTTAAGCTTGTTAGATATTGAAT
Found at i:55891136 original size:21 final size:20
Alignment explanation
Indices: 55891112--55891187 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 20
55891102 TCATCAAGGA
*
55891112 TATGTAATCTTAGATATGAT
1 TATGCAATCTTAGATATGAT
55891132 ATATGCAATCTTAGATATG--
1 -TATGCAATCTTAGATATGAT
55891151 TATGCAATCTTAGAAGATATGAT
1 TATGCAATCTT---AGATATGAT
* *
55891174 TTTGTAATCTTAGA
1 TATGCAATCTTAGA
55891188 GATTTAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
18 11 0.23
20 3 0.06
21 24 0.51
23 9 0.19
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.41
Consensus pattern (20 bp):
TATGCAATCTTAGATATGAT
Found at i:55891156 original size:18 final size:19
Alignment explanation
Indices: 55891110--55891164 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 19
55891100 AATCATCAAG
*
55891110 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
55891129 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
55891150 G-TATGCAATCTTAGA
1 GATATGCAATCTTAGA
55891165 AGATATGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 14 0.42
19 1 0.03
21 18 0.55
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:55893383 original size:2 final size:2
Alignment explanation
Indices: 55893376--55893406 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
55893366 AAAGCACAAC
55893376 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 A
55893407 CGTGTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55900788 original size:7 final size:7
Alignment explanation
Indices: 55900778--55900802 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
55900768 TGATGATTGA
55900778 TTTTTAT
1 TTTTTAT
55900785 TTTTTAT
1 TTTTTAT
55900792 TTTTTAT
1 TTTTTAT
55900799 TTTT
1 TTTT
55900803 GTTTATATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:55905269 original size:13 final size:13
Alignment explanation
Indices: 55905223--55905271 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
55905213 TTTCTCATTT
*
55905223 CTTTTGAAAAGTG
1 CTTTTGAAAAATG
* **
55905236 CTGTAAAAAAATG
1 CTTTTGAAAAATG
*
55905249 CTTATGAAAAATG
1 CTTTTGAAAAATG
55905262 CTTTTGAAAA
1 CTTTTGAAAA
55905272 GCTTGGTCTA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (13 bp):
CTTTTGAAAAATG
Found at i:55906807 original size:18 final size:19
Alignment explanation
Indices: 55906767--55906810 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
55906757 GTTTGATGGA
*
55906767 GTTT-ATTTTTTAATTCTT
1 GTTTAATTTTTTAATTCAT
*
55906785 TTTTAATTTTTTAATT-AT
1 GTTTAATTTTTTAATTCAT
55906803 GTTTAATT
1 GTTTAATT
55906811 ATAATTAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (19 bp):
GTTTAATTTTTTAATTCAT
Found at i:55907104 original size:16 final size:18
Alignment explanation
Indices: 55907067--55907101 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
55907057 AATATTAAGA
55907067 ATTT-TATTAAATTATAT
1 ATTTATATTAAATTATAT
55907084 ATTTATATTAAATTATAT
1 ATTTATATTAAATTATAT
55907102 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTATATTAAATTATAT
Found at i:55907113 original size:16 final size:17
Alignment explanation
Indices: 55907074--55907119 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
55907064 AGAATTTTAT
* *
55907074 TAAATTATATATTTATAT
1 TAAATTATAT-TTAATAA
55907092 TAAATTATATTTAATAA
1 TAAATTATATTTAATAA
55907109 T-AATTAT-TTTA
1 TAAATTATATTTA
55907120 GATTATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 4 0.15
16 6 0.23
17 6 0.23
18 10 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAAATTATATTTAATAA
Found at i:55907115 original size:26 final size:25
Alignment explanation
Indices: 55907086--55907142 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
55907076 AATTATATAT
55907086 TTATATTAAATTATATTTAATAATAA
1 TTATATTAAATTATATTTAATAAT-A
* * * *
55907112 TTATTTTAGATTATATTTTATAGTA
1 TTATATTAAATTATATTTAATAATA
55907137 TTATAT
1 TTATAT
55907143 ATTATGATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (25 bp):
TTATATTAAATTATATTTAATAATA
Found at i:55907147 original size:120 final size:120
Alignment explanation
Indices: 55906990--55907593 Score: 940
Period size: 120 Copynumber: 5.1 Consensus size: 120
55906980 CCACAAAATC
*
55906990 AATTATTTTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAT
1 AATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAT
*
55907055 TTAATATTAAGAATTTTATTAAATTATATA-TTTATATTAAATTATATTTAATAAT
66 TTAATATTAAGAATTTTATTAAATTATATATTTTA-ATTAAAATATATTTAATAAT
*
55907110 AATTATTTTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAT
1 AATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATA-
* *
55907175 TTTAATATTAAGAATTTTATTAAATTATAT-TTTTTATTAAATTATATTTAATAAT
65 TTTAATATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAT
* * *
55907230 TATTATTTTAAATTATATTTTATACTATTATATATTATAATTTTAGTAAATTCATATAAGAATAT
1 AATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAT
*
55907295 TTAATATTAAGAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAAT
66 TTAATATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAT
*
55907350 AATTATTTCAAATTATA-TTT-TA-TA-TAT-TA-TA--ATTTTAGTAAATTCATATAAGAATAT
1 AATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAT
* * * *
55907407 TGATTATTAAGAATTTTATTAAATCATATATTTTAATTAAAATGTATTTAATAAT
66 TTAATATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAT
* * *
55907462 AATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATAT
1 AATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAT
* *
55907527 TGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAT
66 TTAATATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAT
*
55907582 AATTATGTTAAA
1 AATTATTTTAAA
55907594 ATATGATTAA
Statistics
Matches: 454, Mismatches: 19, Indels: 22
0.92 0.04 0.04
Matches are distributed among these distances:
112 93 0.20
113 3 0.01
114 4 0.01
115 4 0.01
116 5 0.01
117 4 0.01
118 4 0.01
119 32 0.07
120 272 0.60
121 33 0.07
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAT
TTAATATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAT
Found at i:55907209 original size:17 final size:17
Alignment explanation
Indices: 55907189--55907223 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
55907179 ATATTAAGAA
55907189 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
55907206 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
55907223 T
1 T
55907224 AATAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATTAAATTATATT
Found at i:55907232 original size:13 final size:13
Alignment explanation
Indices: 55907214--55907271 Score: 64
Period size: 13 Copynumber: 4.3 Consensus size: 13
55907204 TTTTTTATTA
*
55907214 AATTATATTTAAT
1 AATTATATTTTAT
55907227 AATTATTATTTTA-
1 AATTA-TATTTTAT
55907240 AATTATATTTTAT
1 AATTATATTTTAT
*
55907253 ACTATTATATATTAT
1 A--ATTATATTTTAT
55907268 AATT
1 AATT
55907272 TTAGTAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
12 7 0.18
13 14 0.36
14 6 0.15
15 12 0.31
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (13 bp):
AATTATATTTTAT
Done.