Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 171 of 349
Found at i:55327844 original size:21 final size:21
Alignment explanation
Indices: 55327818--55327857 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55327808 CACTTGACAT
*
55327818 AGGGGCACATGCCCATGTGAA
1 AGGGGCACACGCCCATGTGAA
*
55327839 AGGGGCACACGCCCTTGTG
1 AGGGGCACACGCCCATGTG
55327858 GCCAATTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.28, G:0.35, T:0.15
Consensus pattern (21 bp):
AGGGGCACACGCCCATGTGAA
Found at i:55329074 original size:47 final size:48
Alignment explanation
Indices: 55329005--55329268 Score: 161
Period size: 47 Copynumber: 5.6 Consensus size: 48
55328995 GTACCAATGG
* * * *
55329005 CATGTCCTAGACACAGTCTTATACTGGCTCAT-ATCCCAA-GTCGATGC
1 CATGTCCCAGACA-TGTCTTACACTGGCTCATCATCCCAAGGCCGATGC
* * ** *
55329052 CATGTCCCAGACATGGTCTTATACTGACT-ATCATCTCGTA-GCCGAT-A
1 CATGTCCCAGACAT-GTCTTACACTGGCTCATCATC-CCAAGGCCGATGC
* * ** * * *
55329099 CATGTCCCAGACATGTCTTACACTGGCTTAT-GTTTCAAGGTCGTTGG
1 CATGTCCCAGACATGTCTTACACTGGCTCATCATCCCAAGGCCGATGC
* * * * * *
55329146 C-TGTCCTAGACATGTCTTACACTAGC-CCTCGTCTCAATGCCGATGC
1 CATGTCCCAGACATGTCTTACACTGGCTCATCATCCCAAGGCCGATGC
***** *
55329192 CATGTCCCAGACATGATCTTACACTGGCTC-TCATAATGTGGCTGATG-
1 CATGTCCCAGACATG-TCTTACACTGGCTCATCATCCCAAGGCCGATGC
55329239 CATGTCCCAGACATGATCTTACACTGGCTC
1 CATGTCCCAGACATG-TCTTACACTGGCTC
55329269 TCAAAATGTG
Statistics
Matches: 171, Mismatches: 36, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
45 2 0.01
46 54 0.32
47 87 0.51
48 27 0.16
49 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.30
Consensus pattern (48 bp):
CATGTCCCAGACATGTCTTACACTGGCTCATCATCCCAAGGCCGATGC
Found at i:55329269 original size:47 final size:47
Alignment explanation
Indices: 55329187--55329314 Score: 213
Period size: 47 Copynumber: 2.7 Consensus size: 47
55329177 TCTCAATGCC
*
55329187 GATGCCATGTCCCAGACATGATCTTACACTGGCTCTCATAATGTGGCT
1 GATG-CATGTCCCAGACATGATCTTACACTGGCTCTCAAAATGTGGCT
55329235 GATGCATGTCCCAGACATGATCTTACACTGGCTCTCAAAATGTGGCT
1 GATGCATGTCCCAGACATGATCTTACACTGGCTCTCAAAATGTGGCT
* *
55329282 GATGCATGTCCCATACATG-TCTTACACTAGCTC
1 GATGCATGTCCCAGACATGATCTTACACTGGCTC
55329315 ACACACGAAT
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
46 13 0.17
47 60 0.78
48 4 0.05
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (47 bp):
GATGCATGTCCCAGACATGATCTTACACTGGCTCTCAAAATGTGGCT
Found at i:55332947 original size:40 final size:40
Alignment explanation
Indices: 55332715--55332940 Score: 298
Period size: 40 Copynumber: 5.7 Consensus size: 40
55332705 TTGAATGATG
* * * *
55332715 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA-GTTACTAAA
* *
55332755 TCCGGACTAAGAT-CCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
55332795 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
55332835 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
55332875 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
55332916 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
55332941 AACGAGTAGA
Statistics
Matches: 171, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
39 1 0.01
40 160 0.94
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:55332958 original size:120 final size:120
Alignment explanation
Indices: 55332715--55332973 Score: 287
Period size: 120 Copynumber: 2.2 Consensus size: 120
55332705 TTGAATGATG
* * *
55332715 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAGGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
** *
55332780 GTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
66 GTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTTAATAAA
* * **
55332835 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-GTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCGAGGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
55332898 TTGTGCGAGTTACTATAA-CCGGGCTATG-TCCCGAAGGCATTTGAACGAG-TAGATATA
64 TTGTACGAGTTACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGTTA-ATAAA
* *
55332955 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
55332974 TATGTGATTT
Statistics
Matches: 118, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
119 18 0.15
120 90 0.76
121 10 0.08
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTTAATAAA
Found at i:55339973 original size:47 final size:48
Alignment explanation
Indices: 55339904--55340025 Score: 153
Period size: 47 Copynumber: 2.6 Consensus size: 48
55339894 GCTGGTGCCG
* * * * *
55339904 ATGCCATGTCCTAGACACGGTCTTATACTGGCTCAT-ATCTC-AAGTCA
1 ATGCCATGTCCCAAACATGGTCTTACACTGACT-ATCATCTCGAAGTCA
*
55339951 ATGCCATGTCCCAAACATGGTCTTACACTGACTATCATCTCGTAGTCA
1 ATGCCATGTCCCAAACATGGTCTTACACTGACTATCATCTCGAAGTCA
55339999 ATG-CATGTCCCAAACAT-GTCTTACACT
1 ATGCCATGTCCCAAACATGGTCTTACACT
55340026 TGCTTACGTC
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
46 12 0.18
47 47 0.70
48 8 0.12
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.30
Consensus pattern (48 bp):
ATGCCATGTCCCAAACATGGTCTTACACTGACTATCATCTCGAAGTCA
Found at i:55344758 original size:46 final size:46
Alignment explanation
Indices: 55344708--55344880 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
55344698 TGGTTGAGCA
* *
55344708 TCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
55344754 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* * * *
55344801 TCCGAACTCATTGAATTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
55344847 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
55344881 GGGGCGGGTT
Statistics
Matches: 102, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 58 0.57
47 27 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:55344864 original size:93 final size:93
Alignment explanation
Indices: 55344705--55344875 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
55344695 GGATGGTTGA
* * * * *
55344705 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAATTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
55344770 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
55344798 GCATCCGAACTCATTGAATTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCATTGAATTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
55344863 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
55344876 ACTTAGGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCATTGAATTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:55346675 original size:17 final size:18
Alignment explanation
Indices: 55346645--55346679 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
55346635 TTTACTTAAA
*
55346645 TTTTTTTCTAAATTGGCC
1 TTTTTATCTAAATTGGCC
55346663 TTTTTATCT-AATTGGCC
1 TTTTTATCTAAATTGGCC
55346680 CATTACTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (18 bp):
TTTTTATCTAAATTGGCC
Found at i:55350954 original size:13 final size:13
Alignment explanation
Indices: 55350936--55350962 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55350926 TTCAATGCCA
55350936 GCACTGAAAATAC
1 GCACTGAAAATAC
55350949 GCACTGAAAATAC
1 GCACTGAAAATAC
55350962 G
1 G
55350963 ATTACTAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (13 bp):
GCACTGAAAATAC
Found at i:55351798 original size:19 final size:19
Alignment explanation
Indices: 55351774--55351815 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
55351764 TAAAAGCAAC
55351774 ACAACATCAACCCAAATAA
1 ACAACATCAACCCAAATAA
* **
55351793 ACAACATGATTCCAAATAA
1 ACAACATCAACCCAAATAA
55351812 ACAA
1 ACAA
55351816 AAAAAACAAT
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:0.57, C:0.26, G:0.02, T:0.14
Consensus pattern (19 bp):
ACAACATCAACCCAAATAA
Found at i:55354461 original size:24 final size:25
Alignment explanation
Indices: 55354416--55354462 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
55354406 ATGACCAAAA
* *
55354416 ATTGATTTAAAATCAAACTTAATAG
1 ATTGATTTAAAATAAAAATTAATAG
*
55354441 ATTGA-TTAAATTAAAAATTAAT
1 ATTGATTTAAAATAAAAATTAAT
55354463 TAATATAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.38
Consensus pattern (25 bp):
ATTGATTTAAAATAAAAATTAATAG
Found at i:55354566 original size:90 final size:90
Alignment explanation
Indices: 55354460--55354858 Score: 618
Period size: 90 Copynumber: 4.4 Consensus size: 90
55354450 ATTAAAAATT
* *
55354460 AATTAATATAATAGTACAGTAGCATAAATTAAACAAAAAAAAGTATGTTAAACTACATTTTAAAC
1 AATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAGTATGTTAAACTACAGTTTAAAC
55354525 TTTAAAGTTAGTTAATTGAAGCCTA
66 TTTAAAGTTAGTTAATTGAAGCCTA
* * * *
55354550 AATTAATATAAGAGTACAATAGCATAAATTAAACAAAAAAAAAGTTTGTTAAGCTACTGTTTAAA
1 AATTAATATAATAGTACAATAGCATAAATTAAAC-AAAAAAAAGTATGTTAAACTACAGTTTAAA
* *
55354615 CTTTAAAATTAGTTAATTGAAGCCCA
65 CTTTAAAGTTAGTTAATTGAAGCCTA
*
55354641 AATTAATATAATAGTACAAGTACTACAGCATAAATTAAACAAAAAAAAGTATGTTAGACTACAGT
1 AATTAATATAATAGTAC-A--A-T--AGCATAAATTAAACAAAAAAAAGTATGTTAAACTACAGT
55354706 TTAAACTTTAAAGTTAGTTAATTGAAGCCTA
60 TTAAACTTTAAAGTTAGTTAATTGAAGCCTA
* *
55354737 AATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAGTCTGTTAAACCACAGTTTAAAC
1 AATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAGTATGTTAAACTACAGTTTAAAC
55354802 TTTAAAGTTAGTTAATTGAAGCCTA
66 TTTAAAGTTAGTTAATTGAAGCCTA
* *
55354827 AATTAATATAATAGTACAACAACATAAATTAA
1 AATTAATATAATAGTACAATAGCATAAATTAA
55354859 TTAATTGAAG
Statistics
Matches: 282, Mismatches: 20, Indels: 14
0.89 0.06 0.04
Matches are distributed among these distances:
90 129 0.46
91 66 0.23
92 2 0.01
93 1 0.00
94 1 0.00
95 2 0.01
96 67 0.24
97 14 0.05
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (90 bp):
AATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAGTATGTTAAACTACAGTTTAAAC
TTTAAAGTTAGTTAATTGAAGCCTA
Found at i:55354769 original size:187 final size:186
Alignment explanation
Indices: 55354480--55354845 Score: 642
Period size: 187 Copynumber: 2.0 Consensus size: 186
55354470 ATAGTACAGT
*
55354480 AGCATAAATTAAACAAAAAAAAGTATGTTAAACTACATTTTAAACTTTAAAGTTAGTTAATTGAA
1 AGCATAAATTAAACAAAAAAAAGTATGTTAAACTACAGTTTAAACTTTAAAGTTAGTTAATTGAA
* * * *
55354545 GCCTAAATTAATATAAGAGTACAATAGCATAAATTAAACAAAAAAAAAGTTTGTTAAGCTACTGT
66 GCCTAAATTAATATAAGAGTACAATAGCATAAATTAAAC-AAAAAAAAGTCTGTTAAACCACAGT
55354610 TTAAACTTTAAAATTAGTTAATTGAAGCCCAAATTAATATAATAGTACAAGTACTAC
130 TTAAACTTTAAAATTAGTTAATTGAAGCCCAAATTAATATAATAGTACAAGTACTAC
*
55354667 AGCATAAATTAAACAAAAAAAAGTATGTTAGACTACAGTTTAAACTTTAAAGTTAGTTAATTGAA
1 AGCATAAATTAAACAAAAAAAAGTATGTTAAACTACAGTTTAAACTTTAAAGTTAGTTAATTGAA
*
55354732 GCCTAAATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAGTCTGTTAAACCACAGTT
66 GCCTAAATTAATATAAGAGTACAATAGCATAAATTAAACAAAAAAAAGTCTGTTAAACCACAGTT
* *
55354797 TAAACTTTAAAGTTAGTTAATTGAAGCCTAAATTAATATAATAGTACAA
131 TAAACTTTAAAATTAGTTAATTGAAGCCCAAATTAATATAATAGTACAA
55354846 CAACATAAAT
Statistics
Matches: 170, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
186 69 0.41
187 101 0.59
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (186 bp):
AGCATAAATTAAACAAAAAAAAGTATGTTAAACTACAGTTTAAACTTTAAAGTTAGTTAATTGAA
GCCTAAATTAATATAAGAGTACAATAGCATAAATTAAACAAAAAAAAGTCTGTTAAACCACAGTT
TAAACTTTAAAATTAGTTAATTGAAGCCCAAATTAATATAATAGTACAAGTACTAC
Found at i:55360014 original size:18 final size:18
Alignment explanation
Indices: 55359984--55360029 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
55359974 GAGTGTGGTT
55359984 GTGTGGG-CCACACGAGC
1 GTGTGGGCCCACACGAGC
*
55360001 GTGTGGGCCCACACGGGC
1 GTGTGGGCCCACACGAGC
* *
55360019 ATGTTGGCCCA
1 GTGTGGGCCCA
55360030 TAACTCTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.15, C:0.30, G:0.39, T:0.15
Consensus pattern (18 bp):
GTGTGGGCCCACACGAGC
Found at i:55367115 original size:18 final size:18
Alignment explanation
Indices: 55367082--55367128 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
55367072 CGAATCTGGT
*
55367082 CGTGTGGG-CAACACGGG
1 CGTGTGGGCCCACACGGG
55367099 CGTGTGGGCCCACACGGG
1 CGTGTGGGCCCACACGGG
*
55367117 CATGTGGGCCCA
1 CGTGTGGGCCCA
55367129 TTACTCTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 8 0.30
18 19 0.70
ACGTcount: A:0.15, C:0.30, G:0.43, T:0.13
Consensus pattern (18 bp):
CGTGTGGGCCCACACGGG
Found at i:55368237 original size:20 final size:20
Alignment explanation
Indices: 55368212--55368256 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
55368202 ATGGGCTAAA
* *
55368212 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
55368232 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
55368252 ATGAA
1 ATGAA
55368257 TACATGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:55369302 original size:42 final size:42
Alignment explanation
Indices: 55369236--55369354 Score: 141
Period size: 43 Copynumber: 2.8 Consensus size: 42
55369226 GGATTATTGG
* *
55369236 GATTACGTGTAAGACCATATCTGGGATATGGCATCGATAGGA
1 GATTACGTGTAAGACCATATCTGGGATATGGCATCAATACGA
* * * *
55369278 GACTT-TGTGTAAGACCATAGCTGGGCTATTAGCATCAATACGA
1 GA-TTACGTGTAAGACCATATCTGGGATA-TGGCATCAATACGA
* *
55369321 GATTACATATAAGACCATATCTGGGATATGGCAT
1 GATTACGTGTAAGACCATATCTGGGATATGGCAT
55369355 TGGTACAGTA
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
42 29 0.47
43 33 0.53
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (42 bp):
GATTACGTGTAAGACCATATCTGGGATATGGCATCAATACGA
Found at i:55384646 original size:24 final size:24
Alignment explanation
Indices: 55384618--55384678 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
55384608 AACCGTATTT
* * *
55384618 GCACACATAGTGCTA-ATTACACTC
1 GCACACATAGTGCCATAGTAAAC-C
55384642 GCACACATAGTGCCATAGTAAACC
1 GCACACATAGTGCCATAGTAAACC
55384666 GCACACATAGTGC
1 GCACACATAGTGC
55384679 ATTGGATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 28 0.85
25 5 0.15
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (24 bp):
GCACACATAGTGCCATAGTAAACC
Found at i:55393675 original size:39 final size:34
Alignment explanation
Indices: 55393595--55393694 Score: 110
Period size: 34 Copynumber: 2.8 Consensus size: 34
55393585 TCTGTCCTAT
*
55393595 TACTGTTACTGAAATGGGCTAAGGCCCGCACTTA
1 TACTGTTACTGAAATGGGCTAAGGCCCGAACTTA
* *
55393629 TACTGTTACTGTAATGGGCTAAGGCCCTAACTGATA
1 TACTGTTACTGAAATGGGCTAAGGCCCGAACT--TA
* *
55393665 CTGGACTGTTACTGAAACGGGCTTAGGCCC
1 -T--ACTGTTACTGAAATGGGCTAAGGCCC
55393695 AGACTGTATT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
34 29 0.53
36 2 0.04
37 1 0.02
39 23 0.42
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (34 bp):
TACTGTTACTGAAATGGGCTAAGGCCCGAACTTA
Found at i:55394322 original size:19 final size:21
Alignment explanation
Indices: 55394294--55394334 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
55394284 GGGGAGAAAG
55394294 TTGGGAGGAA-GT-AAAAGTT
1 TTGGGAGGAATGTAAAAAGTT
*
55394313 TTGGGGGGAATGTAAAAAGTT
1 TTGGGAGGAATGTAAAAAGTT
55394334 T
1 T
55394335 CAGAGGTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 2 0.11
21 8 0.42
ACGTcount: A:0.34, C:0.00, G:0.37, T:0.29
Consensus pattern (21 bp):
TTGGGAGGAATGTAAAAAGTT
Found at i:55395650 original size:16 final size:16
Alignment explanation
Indices: 55395624--55395656 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
55395614 GGAAGGACCT
55395624 AAAAAAGAAAGATAAAC
1 AAAAAAGAAAGA-AAAC
55395641 AAAAAA-AAAGAAAAC
1 AAAAAAGAAAGAAAAC
55395656 A
1 A
55395657 TAATATGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 5 0.31
17 6 0.38
ACGTcount: A:0.82, C:0.06, G:0.09, T:0.03
Consensus pattern (16 bp):
AAAAAAGAAAGAAAAC
Found at i:55397458 original size:46 final size:45
Alignment explanation
Indices: 55397400--55397571 Score: 166
Period size: 46 Copynumber: 3.7 Consensus size: 45
55397390 CTCGTAGCTA
* * *
55397400 ATGCATGTCCCAGACATGTCTTATACTGGCTTACGTCCCGAGGCTG
1 ATGCATGTCCCAGACATGTCTTACACTAGCTT-CGTCCCGAGGCCG
* * *
55397446 ATGCATGTCCCAGACATGTCCTACACTAGCACTCGTCCC-ACTGCCG
1 ATGCATGTCCCAGACATGTCTTACACTAGC-TTCGTCCCGA-GGCCG
* * *** *
55397492 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCG
1 ATG-CATGTCCCAGACAT-GTCTTACACTAGCT-TCGTCCCGAGGCCG
*
55397540 ATGCATGTCCGAGACATGTCTTACACTAGCTT
1 ATGCATGTCCCAGACATGTCTTACACTAGCTT
55397572 ACACAAATGA
Statistics
Matches: 103, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
45 2 0.02
46 52 0.50
47 28 0.27
48 21 0.20
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.27
Consensus pattern (45 bp):
ATGCATGTCCCAGACATGTCTTACACTAGCTTCGTCCCGAGGCCG
Found at i:55405031 original size:49 final size:47
Alignment explanation
Indices: 55404971--55405150 Score: 153
Period size: 49 Copynumber: 3.8 Consensus size: 47
55404961 TGGGTAAAGT
55404971 GCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTATCATCTTTGA
1 GCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTA-CATCTTTGA
* *
55405019 GGCCGATGCCATGTCCCAG-CAATGGTCTTACACTAGCTCCCACATAACTTTGTA
1 -GCCGATGCCATGTCCTAGAC-ATGGTCTTACACTGGCT---ACAT--CTTTG-A
* *
55405073 ---GATGCCATGTCCTAGACATGGTCTTACACTGAC-ACATCTCAT-A
1 GCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTACATCT-TTGA
*
55405116 GCCGATG-CATGTACC-AGACAT-GTCTTATACTGGCT
1 GCCGATGCCATGT-CCTAGACATGGTCTTACACTGGCT
55405151 TACGTCCCGG
Statistics
Matches: 109, Mismatches: 8, Indels: 32
0.73 0.05 0.21
Matches are distributed among these distances:
43 1 0.01
44 13 0.12
45 12 0.11
46 10 0.09
48 1 0.01
49 33 0.30
50 28 0.26
51 4 0.04
52 1 0.01
53 5 0.05
54 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (47 bp):
GCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTACATCTTTGA
Found at i:55417868 original size:25 final size:25
Alignment explanation
Indices: 55417840--55417918 Score: 78
Period size: 25 Copynumber: 3.3 Consensus size: 25
55417830 CGAATGGCCA
55417840 ATGTGATGAATGTGAACATGCATAT
1 ATGTGATGAATGTGAACATGCATAT
* * *
55417865 ATGTGAT-AAGGCCG-A-ATGGC-CA-
1 ATGTGATGAATG-TGAACAT-GCATAT
55417887 ATGTGATGAATGTGAACATGCATAT
1 ATGTGATGAATGTGAACATGCATAT
55417912 ATGTGAT
1 ATGTGAT
55417919 AAGGCCGAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 8 0.20
23 9 0.22
24 9 0.22
25 15 0.37
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (25 bp):
ATGTGATGAATGTGAACATGCATAT
Found at i:55418033 original size:47 final size:47
Alignment explanation
Indices: 55417793--55418025 Score: 385
Period size: 47 Copynumber: 5.0 Consensus size: 47
55417783 TTAGGATTTT
** * *
55417793 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
55417840 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
55417887 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
55417934 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
55417981 ATGTGATGAATATGAACATGCATATATGTGGTAAAGCCGAATGGC
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGC
55418026 TAGTGTGAAA
Statistics
Matches: 175, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 175 1.00
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:55418078 original size:94 final size:92
Alignment explanation
Indices: 55417793--55418080 Score: 260
Period size: 94 Copynumber: 3.1 Consensus size: 92
55417783 TTAGGATTTT
* ** * * * * *
55417793 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATATGAACATGCATATATGTGATAAAGCCGAATGGCCAATGTGATAAATGTG-AGA
* * * *
55417858 TGCATATATGTGATAAGGCCGAATGGCCA
65 -GCATATGTGCGATAAGGCCGAACGACCA
* * *
55417887 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
1 ATGTGATGAATATGAACATGCATATATGTGATAAAGCCGAATGGCCAATGTGATAAATGTGAG-A
* * *
55417952 TGCATATGTGTGATAAGGCCGAATGGCCA
65 -GCATATGTGCGATAAGGCCGAACGACCA
* * *
55417981 ATGTGATGAATATGAACATGCATATATGTGGTAAAGCCGAATGGCTAGTGTGA-AATATGT-AG-
1 ATGTGATGAATATGAACATGCATATATGTGATAAAGCCGAATGGCCAATGTGATAA-ATGTGAGA
*
55418043 GCA-ATGTGCGTATATTGTGGCCGAACGACCAA
65 GCATATGTGCG-ATA---AGGCCGAACGACC-A
55418075 ATGTGA
1 ATGTGA
55418081 AAGGTGTGTA
Statistics
Matches: 171, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
89 6 0.04
90 6 0.04
93 14 0.08
94 145 0.85
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (92 bp):
ATGTGATGAATATGAACATGCATATATGTGATAAAGCCGAATGGCCAATGTGATAAATGTGAGAG
CATATGTGCGATAAGGCCGAACGACCA
Found at i:55418333 original size:37 final size:37
Alignment explanation
Indices: 55418188--55418332 Score: 245
Period size: 37 Copynumber: 3.9 Consensus size: 37
55418178 GGAAATATAT
55418188 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
55418225 TCCGGGTAAGACCCGATGACTACATGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
55418262 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* * *
55418299 TCCAGGTAAGACCCGATAACTTCGTGTGGAGATT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT
55418333 TCGTCTGAGC
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 102 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:55421697 original size:43 final size:43
Alignment explanation
Indices: 55421602--55421709 Score: 146
Period size: 43 Copynumber: 2.5 Consensus size: 43
55421592 ATCGAGATGT
* *
55421602 GATTACATGTAAGACCATGTCTGGGACATTGACATCGTATTGA
1 GATTACGTGTAAGACCATGTCTGGGACATTGACATCGTAATGA
* *
55421645 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTTAAT-C
1 GATTACGTGTAAGACCATGTCTGGGACATTGACATCG-TAATGA
* *
55421688 GATTTCGTGTAAGACCTTGTCT
1 GATTACGTGTAAGACCATGTCT
55421710 ACGATAGTGG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 55 0.95
44 3 0.05
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (43 bp):
GATTACGTGTAAGACCATGTCTGGGACATTGACATCGTAATGA
Found at i:55423244 original size:6 final size:6
Alignment explanation
Indices: 55423233--55423277 Score: 56
Period size: 6 Copynumber: 7.2 Consensus size: 6
55423223 GAAGTCTAAG
55423233 AAATAA AAAT-A AAATAACCA AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAAT-A--A AAATAA AAATAA AAATAA AAATAA A
55423278 CATGAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
5 5 0.14
6 24 0.69
8 1 0.03
9 5 0.14
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:55423285 original size:18 final size:16
Alignment explanation
Indices: 55423233--55423293 Score: 50
Period size: 20 Copynumber: 3.4 Consensus size: 16
55423223 GAAGTCTAAG
55423233 AAATAAAAATAAAATAACCA
1 AAATAAAAAT-AAA-AA--A
55423253 AAATAAAAATAAAAATAA
1 AAATAAAAAT-AAAA-AA
* *
55423271 AAATAAACATGAAAAA
1 AAATAAAAATAAAAAA
55423287 AAATAAA
1 AAATAAA
55423294 GAAAATAGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
16 9 0.24
17 3 0.08
18 10 0.26
19 1 0.03
20 15 0.39
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.15
Consensus pattern (16 bp):
AAATAAAAATAAAAAA
Found at i:55423286 original size:26 final size:26
Alignment explanation
Indices: 55423233--55423293 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
55423223 GAAGTCTAAG
*
55423233 AAATAAAAATAAAATAACCAAAATAA
1 AAATAAAAATAAAATAAACAAAATAA
55423259 AAATAAAAATAAAAATAAACATGAAA-AA
1 AAATAAAAAT-AAAATAAACA--AAATAA
55423287 AAATAAA
1 AAATAAA
55423294 GAAAATAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 10 0.32
27 9 0.29
28 9 0.29
29 3 0.10
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.15
Consensus pattern (26 bp):
AAATAAAAATAAAATAAACAAAATAA
Found at i:55424953 original size:22 final size:22
Alignment explanation
Indices: 55424928--55424976 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
55424918 TAACAATTAT
*
55424928 AATAA-AATTAATAAGAATAAAA
1 AATAAGAATAAATAA-AATAAAA
*
55424950 AATAAGAATAAATAAAGTAAAA
1 AATAAGAATAAATAAAATAAAA
55424972 AATAA
1 AATAA
55424977 TAAAGACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.20
Consensus pattern (22 bp):
AATAAGAATAAATAAAATAAAA
Found at i:55424955 original size:13 final size:13
Alignment explanation
Indices: 55424937--55424961 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55424927 TAATAAAATT
55424937 AATAAGAATAAAA
1 AATAAGAATAAAA
55424950 AATAAGAATAAA
1 AATAAGAATAAA
55424962 TAAAGTAAAA
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:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (13 bp):
AATAAGAATAAAA
Found at i:55426302 original size:15 final size:17
Alignment explanation
Indices: 55426284--55426315 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
55426274 TAGCATAATT
55426284 TACCAAA-TCA-ATTCA
1 TACCAAACTCACATTCA
55426299 TACCAAACTCACATTCA
1 TACCAAACTCACATTCA
55426316 CAAGTATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (17 bp):
TACCAAACTCACATTCA
Found at i:55427392 original size:24 final size:27
Alignment explanation
Indices: 55427360--55427411 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 27
55427350 AGTTCATGAA
55427360 ATATTAAAG-TATTTAA-ATAC-AACT
1 ATATTAAAGCTATTTAACATACGAACT
55427384 ATATTAAAGCTTATTTAACATACGAACT
1 ATATTAAAGC-TATTTAACATACGAACT
55427412 TACCTCGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 9 0.38
26 7 0.29
27 4 0.17
28 4 0.17
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.37
Consensus pattern (27 bp):
ATATTAAAGCTATTTAACATACGAACT
Found at i:55433337 original size:385 final size:385
Alignment explanation
Indices: 55432605--55433366 Score: 1073
Period size: 385 Copynumber: 2.0 Consensus size: 385
55432595 TAGCTAATGC
* * *
55432605 TTGGTAGTTTATTTTGGAGAATGGCTAAACACTCCTCGTTGAGCTCCACAGTTGATAGCTCTTCA
1 TTGGTAATTTAATTTGGAGAATGGCTAAACACTCCTCGTTGAGCTCCACAGTGGATAGCTCTTCA
* *
55432670 AACTCCCTTTTATTTGTTAATAACTCATTTAAAAATTTTGCATATGCTGGCATCTACGAAATAGC
66 AAATCCCTTTTATTTGTTAATAACTCATTTAAAAATTTTGCATATGCTAGCATCTACGAAATAGC
* * * *
55432735 TTCAACGAAAGGTAAGTTAATATGTATTTTTTAAAACGTTTAAGAAATTTGCCAAATTGTTCATC
131 TTCAACAAAAGGCAAGTTAATATGTATTGTTTAAAACGTTTAAGAAATTTACCAAATTGTTCATC
*
55432800 CATGCGGTCTTTCTTCAAATTTGCTTGGTATGGCATCGGTGGTTTGTATTCTTTAAGCACCGATG
196 CATGCGGTCTTTCTTCAAATTTGCTAGGTATGGCATCGGTGGTTTGTATTCTTTAAGCACCGATG
* * * *
55432865 TTTGATTTTTTTGGTTTCTAGCACCCCATCATCTTTCTTATTAGTTTCTGGTTTCAGCTTCTTTT
261 TTTGATTTTTTTGGTTTCTACCACCCCATCATCTTTCCTATCAGTTTCTGGCTTCAGCTTCTTTT
* *
55432930 CAGGTTCACACAACTTCTTCCCATTCCTCAATGTAATTGCCTTAACA-GCTAATGCTTAG
326 CAGGTTCACACAACTCCTTCCCATTCCTCAATGTAAATGCCTTAACATGCTAATGCTTAG
* * * * *
55432989 TTGGTAATTTAATTTGGAGAATTGTTGAACACTCCTCGTTGAGTTCTACAGTGGATAGCTCTTCA
1 TTGGTAATTTAATTTGGAGAATGGCTAAACACTCCTCGTTGAGCTCCACAGTGGATAGCTCTTCA
* ** * * *
55433054 AAAT-TCTTTATATTTGTTAATAGTTCCTTTAAAAATTTTGCATATGTTAGCATCTATGAAATAG
66 AAATCCCTTT-TATTTGTTAATAACTCATTTAAAAATTTTGCATATGCTAGCATCTACGAAATAG
* * * *
55433118 GTTCAACAAAAGGCAGGTTAATATGTAATTGTTTGAAACGTTTAAGACATTTACCAAATTGTTCA
130 CTTCAACAAAAGGCAAGTTAATATGT-ATTGTTTAAAACGTTTAAGAAATTTACCAAATTGTTCA
* * * *
55433183 TCCATGCGGTCTTTCTTCAACTTTGCTAGGTATGGTATCGGTGTTTTGTATTCTTTAAGTACC-A
194 TCCATGCGGTCTTTCTTCAAATTTGCTAGGTATGGCATCGGTGGTTTGTATTCTTTAAGCACCGA
** * *
55433247 GTGTTTGAATTTTTTTGGTTTCTACCA-CCTGTTATCTTTCCTATCGGTTTCTGGCTTCAGCTTC
259 -TGTTTG-ATTTTTTTGGTTTCTACCACCCCATCATCTTTCCTATCAGTTTCTGGCTTCAGCTTC
** * *
55433311 TTTTTGGGTTCAGATAACTCCTTCCCATTCCTCAATGTAAATGCCTTAACATGCTA
322 TTTTCAGGTTCACACAACTCCTTCCCATTCCTCAATGTAAATGCCTTAACATGCTA
55433367 TTATGGGTTG
Statistics
Matches: 330, Mismatches: 43, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
383 4 0.01
384 131 0.40
385 173 0.52
386 22 0.07
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (385 bp):
TTGGTAATTTAATTTGGAGAATGGCTAAACACTCCTCGTTGAGCTCCACAGTGGATAGCTCTTCA
AAATCCCTTTTATTTGTTAATAACTCATTTAAAAATTTTGCATATGCTAGCATCTACGAAATAGC
TTCAACAAAAGGCAAGTTAATATGTATTGTTTAAAACGTTTAAGAAATTTACCAAATTGTTCATC
CATGCGGTCTTTCTTCAAATTTGCTAGGTATGGCATCGGTGGTTTGTATTCTTTAAGCACCGATG
TTTGATTTTTTTGGTTTCTACCACCCCATCATCTTTCCTATCAGTTTCTGGCTTCAGCTTCTTTT
CAGGTTCACACAACTCCTTCCCATTCCTCAATGTAAATGCCTTAACATGCTAATGCTTAG
Found at i:55439856 original size:28 final size:28
Alignment explanation
Indices: 55439824--55439954 Score: 151
Period size: 29 Copynumber: 4.6 Consensus size: 28
55439814 TACCTGTATT
* *
55439824 TGGCCCATTAAGCCC-AGTCATATTCATA
1 TGGCCCATTAGGCCCAAATCATATT-ATA
55439852 TGGCCCATTAGGCCCAAATCACT-TGTATA
1 TGGCCCATTAGGCCCAAATCA-TAT-TATA
55439881 TGGCCCATTAGGCCCAAATCACT-TGTATA
1 TGGCCCATTAGGCCCAAATCA-TAT-TATA
*
55439910 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCATA-TTATA
*
55439939 TGGCCCGTTAGGCCCA
1 TGGCCCATTAGGCCCA
55439955 GCCACATTCA
Statistics
Matches: 94, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
28 14 0.15
29 77 0.82
30 3 0.03
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.27
Consensus pattern (28 bp):
TGGCCCATTAGGCCCAAATCATATTATA
Found at i:55439889 original size:29 final size:29
Alignment explanation
Indices: 55439849--55439954 Score: 187
Period size: 29 Copynumber: 3.7 Consensus size: 29
55439839 AGTCATATTC
55439849 ATATGGCCCATTAGGCCCAAATCACTTGT
1 ATATGGCCCATTAGGCCCAAATCACTTGT
55439878 ATATGGCCCATTAGGCCCAAATCACTTGT
1 ATATGGCCCATTAGGCCCAAATCACTTGT
55439907 ATATGGCCCATTAGGCCCAAATCACATT-T
1 ATATGGCCCATTAGGCCCAAATCAC-TTGT
*
55439936 ATATGGCCCGTTAGGCCCA
1 ATATGGCCCATTAGGCCCA
55439955 GCCACATTCA
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
29 73 0.97
30 2 0.03
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.26
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCCAAATCACTTGT
Found at i:55440197 original size:8 final size:8
Alignment explanation
Indices: 55440186--55440240 Score: 65
Period size: 8 Copynumber: 6.9 Consensus size: 8
55440176 ACTTTCAGCT
55440186 TTTCGGCA
1 TTTCGGCA
* *
55440194 TTTCAGCT
1 TTTCGGCA
* *
55440202 TTTAGACA
1 TTTCGGCA
*
55440210 TTTCGGCT
1 TTTCGGCA
55440218 TTTCGGCA
1 TTTCGGCA
55440226 TTTCGGCA
1 TTTCGGCA
55440234 TTTCGGC
1 TTTCGGC
55440241 TTTTGCCAAT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.42
Consensus pattern (8 bp):
TTTCGGCA
Found at i:55440199 original size:16 final size:16
Alignment explanation
Indices: 55440178--55440240 Score: 81
Period size: 16 Copynumber: 3.9 Consensus size: 16
55440168 GTAGCCAAAC
55440178 TTTCAGCTTTTCGGCA
1 TTTCAGCTTTTCGGCA
* *
55440194 TTTCAGCTTTTAGACA
1 TTTCAGCTTTTCGGCA
*
55440210 TTTCGGCTTTTCGGCA
1 TTTCAGCTTTTCGGCA
* *
55440226 TTTCGGCATTTCGGC
1 TTTCAGCTTTTCGGC
55440241 TTTTGCCAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.43
Consensus pattern (16 bp):
TTTCAGCTTTTCGGCA
Found at i:55444618 original size:73 final size:67
Alignment explanation
Indices: 55444475--55444618 Score: 162
Period size: 73 Copynumber: 2.1 Consensus size: 67
55444465 GAGGAAGCGT
* * * * *
55444475 TCTGGTAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACTTCGTCATAA
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACCTAGCCACAA
55444540 TA
66 TA
* * *
55444542 TCTGGCAGCCTCGCTGCAATCTGTTGGCTTCGCCACACATATATATATCTGTTCTGGTGGCCTAG
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCG-C-CAC----ATATATCTGTTCTGGTGACCTAG
55444607 CCACAATA
60 CCACAATA
55444615 TCTG
1 TCTG
55444619 TATCTGCTGA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
67 29 0.46
68 1 0.02
69 3 0.05
73 30 0.48
ACGTcount: A:0.19, C:0.28, G:0.22, T:0.32
Consensus pattern (67 bp):
TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACCTAGCCACAA
TA
Found at i:55452827 original size:39 final size:39
Alignment explanation
Indices: 55452661--55452921 Score: 320
Period size: 39 Copynumber: 6.6 Consensus size: 39
55452651 GCTCCTCGTT
* *
55452661 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
55452701 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
55452741 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTA-CTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
55452779 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
55452818 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
* * *
55452857 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT-ATC-TCGCA
55452898 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
55452922 CATCATTCAA
Statistics
Matches: 203, Mismatches: 10, Indels: 17
0.88 0.04 0.07
Matches are distributed among these distances:
38 38 0.19
39 93 0.46
40 61 0.30
41 11 0.05
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:55460709 original size:39 final size:39
Alignment explanation
Indices: 55460666--55460874 Score: 323
Period size: 39 Copynumber: 5.3 Consensus size: 39
55460656 GCTCCTCGTT
* * *
55460666 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTA-ATCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCA
* * *
55460705 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
55460745 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
55460784 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
55460823 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
55460862 CAAATGCCTTCGG
1 CAAATGCCTTCGG
55460875 ATCTTAGTCC
Statistics
Matches: 162, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
39 141 0.87
40 21 0.13
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:55460767 original size:78 final size:80
Alignment explanation
Indices: 55460666--55460925 Score: 340
Period size: 78 Copynumber: 3.3 Consensus size: 80
55460656 GCTCCTCGTT
* * * *
55460666 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTA-ATCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGGACTTAGCCCG
55460729 GATTTAGTAACTCGCA
65 GATTTAGTAACTCGCA
55460745 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGACTTAGCCCGG
* *
55460808 AATTAGTATCTCGCA
66 ATTTAGTAACTCGCA
*
55460823 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGA-CTTAGCCCG
* * *
55460886 GATAT-GTCACTTAGCA
65 GATTTAGTAAC-TCGCA
55460902 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
55460926 CATCATTCAA
Statistics
Matches: 163, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
77 11 0.07
78 102 0.63
79 50 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGACTTAGCCCGG
ATTTAGTAACTCGCA
Found at i:55460919 original size:117 final size:119
Alignment explanation
Indices: 55460666--55460925 Score: 331
Period size: 117 Copynumber: 2.2 Consensus size: 119
55460656 GCTCCTCGTT
* *
55460666 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAATCGCACAAATGCCTTCGGGACTTAACCCGG
* *
55460730 ATTTAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
66 AATTAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTAGCA
* *
55460784 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTA-ATCGCACAAATGCCTTCGGGACTTAACCCG
* * *
55460846 GAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG-A-TATGTCA-CTTAGCA
65 GAATTAGTAACTCGCACAAATGCCTTCGG-GCTTAGCCCGGAATTA-GT-ATC-TAGCA
55460902 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
55460926 CATCATTCAA
Statistics
Matches: 126, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
116 11 0.09
117 66 0.52
118 49 0.39
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (119 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAATCGCACAAATGCCTTCGGGACTTAACCCGG
AATTAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTAGCA
Found at i:55462018 original size:13 final size:13
Alignment explanation
Indices: 55462000--55462024 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55461990 AGGATGAGCA
55462000 TTTTTTTTCTTTG
1 TTTTTTTTCTTTG
55462013 TTTTTTTTCTTT
1 TTTTTTTTCTTT
55462025 CTAGTTTCGG
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:0.00, C:0.08, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTTTTCTTTG
Found at i:55470208 original size:21 final size:20
Alignment explanation
Indices: 55470180--55470219 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
55470170 TAGTAGATGG
55470180 CCTAACCACACGGGCGTGTC
1 CCTAACCACACGGGCGTGTC
*
55470200 CCTAGACCACACGGGTGTGT
1 CCTA-ACCACACGGGCGTGT
55470220 GAGCCCTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.17
Consensus pattern (20 bp):
CCTAACCACACGGGCGTGTC
Found at i:55481718 original size:50 final size:50
Alignment explanation
Indices: 55481604--55481929 Score: 314
Period size: 50 Copynumber: 6.7 Consensus size: 50
55481594 TGACATGTGT
* * * *
55481604 GCTAGTGTAAGA-CATGTTTGGGACATGGCATCGGCATTGAG--ACGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATATGAGA
*
55481651 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATATGAAA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATATGAGA
* * * * *
55481701 GCTAGTGTAAGATCATGTCTAGGACATGGCATCAG-CTTG-G-TATGTG-
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATATGAGA
* * * * *
55481747 TC-AATGTAAGACCATGTCTGGGACATGGCATCGGCATCGACAAATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATATGAGA
* *
55481796 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATATATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATATGAGA
* * * ** * *
55481846 G-TCAGTGTAAGATCATGTCTGGGATATGGCATC-GACT-TTGATGTGTGA
1 GCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATATGAGA
* * **
55481894 GCAAGTGTAAAACCATGTCCAGGACATGGCATCGGC
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
55481930 ATCTTAGCCT
Statistics
Matches: 226, Mismatches: 42, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
45 28 0.12
46 3 0.01
47 16 0.07
48 63 0.28
49 8 0.04
50 108 0.48
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (50 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATATGAGA
Found at i:55481769 original size:95 final size:95
Alignment explanation
Indices: 55481656--55481828 Score: 283
Period size: 95 Copynumber: 1.8 Consensus size: 95
55481646 CGAGAGCTAG
* * * * *
55481656 TGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATATGAAAGCTAGTGTAAGATCATGTCT
1 TGTAAGACCATGTCTGGGACATGGCATCGGCATCGACAAATGAAAGCCAGTGTAAGACCATGTCT
55481721 AGGACATGGCATCAGCTTGGTATGTGTCAA
66 AGGACATGGCATCAGCTTGGTATGTGTCAA
*
55481751 TGTAAGACCATGTCTGGGACATGGCATCGGCATCGACAAATGAGAGCCAGTGTAAGACCATGTCT
1 TGTAAGACCATGTCTGGGACATGGCATCGGCATCGACAAATGAAAGCCAGTGTAAGACCATGTCT
*
55481816 GGGACATGGCATC
66 AGGACATGGCATC
55481829 GGCCTCGATA
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
95 71 1.00
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.24
Consensus pattern (95 bp):
TGTAAGACCATGTCTGGGACATGGCATCGGCATCGACAAATGAAAGCCAGTGTAAGACCATGTCT
AGGACATGGCATCAGCTTGGTATGTGTCAA
Found at i:55481877 original size:145 final size:144
Alignment explanation
Indices: 55481598--55481932 Score: 446
Period size: 145 Copynumber: 2.3 Consensus size: 144
55481588 TTTAGGTGAC
* * * * *
55481598 ATGTGTGCTAGTGTAAGA-CATGTTTGGGACATGGCATCGGCATTGAGACGAGAGCTAGTGTAAG
1 ATGTGTGCAAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAAACGAGAGCCAGTGTAAG
55481662 ACCATGTCTGGGACATGGCATCGGCCTCGAGATATGAAAGCTAGTGTAAGATCATGTCTAGGACA
66 ACCATGTCTGGGACATGGCATCGGCCTCGAGATATGAAAGCTAGTGTAAGATCATGTCTAGGACA
55481727 TGGCATC-AGCTTGG
131 TGGCATCGA-CTTGG
*
55481741 TATGTGT-CAA-TGTAAGACCATGTCTGGGACATGGCATCGGCATCGACAAATGAGAGCCAGTGT
1 -ATGTGTGCAAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCG--AAACGAGAGCCAGTGT
* * *
55481804 AAGACCATGTCTGGGACATGGCATCGGCCTCGATATATGAGAG-TCAGTGTAAGATCATGTCTGG
63 AAGACCATGTCTGGGACATGGCATCGGCCTCGAGATATGAAAGCT-AGTGTAAGATCATGTCTAG
* *
55481868 GATATGGCATCGACTTTG
127 GACATGGCATCGACTTGG
* **
55481886 ATGTGTGAGCAAGTGTAAAACCATGTCCAGGACATGGCATCGGCATC
1 ATGTGT--GCAAGTGTAAGACCATGTCTGGGACATGGCATCGGCATC
55481933 TTAGCCTATG
Statistics
Matches: 168, Mismatches: 14, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
142 7 0.04
143 27 0.16
144 13 0.08
145 86 0.51
146 1 0.01
147 3 0.02
148 31 0.18
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (144 bp):
ATGTGTGCAAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAAACGAGAGCCAGTGTAAG
ACCATGTCTGGGACATGGCATCGGCCTCGAGATATGAAAGCTAGTGTAAGATCATGTCTAGGACA
TGGCATCGACTTGG
Found at i:55505792 original size:26 final size:26
Alignment explanation
Indices: 55505733--55505843 Score: 132
Period size: 27 Copynumber: 4.2 Consensus size: 26
55505723 AGGAAGCGTC
* * *
55505733 CTGGTGGCTATGCCATAATTATCTGAT
1 CTGGTGGCTCTGCCA-CATTATCTGTT
*
55505760 CTAGTGGCTCTGCCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGTT
*
55505786 CTGGTGGCTCTGCCACGATTATCTGTAC
1 CTGGTGGCTCTGCCAC-ATTATCTGT-T
* *
55505814 CTGGTGACTCTGCCACATTATCTATT
1 CTGGTGGCTCTGCCACATTATCTGTT
55505840 CTGG
1 CTGG
55505844 CAGCTATGCT
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
26 28 0.38
27 30 0.41
28 15 0.21
ACGTcount: A:0.17, C:0.25, G:0.22, T:0.36
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:55505843 original size:54 final size:53
Alignment explanation
Indices: 55505733--55505852 Score: 150
Period size: 54 Copynumber: 2.2 Consensus size: 53
55505723 AGGAAGCGTC
* * * *
55505733 CTGGTGGCTATGCCATAATTATCTGATCTAGTGGCTCTGCCACATTATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGACCTAGTGACTCTGCCACATTATCTATT
* * *
55505786 CTGGTGGCTCTGCCACGATTATCTGTACCTGGTGACTCTGCCACATTATCTATT
1 CTGGTGGCTATGCCACAATTATCTG-ACCTAGTGACTCTGCCACATTATCTATT
**
55505840 CTGGCAGCTATGC
1 CTGGTGGCTATGC
55505853 TGCATATTTC
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
53 22 0.39
54 34 0.61
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (53 bp):
CTGGTGGCTATGCCACAATTATCTGACCTAGTGACTCTGCCACATTATCTATT
Found at i:55512164 original size:25 final size:25
Alignment explanation
Indices: 55512122--55512178 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
55512112 GTAAGGAGGG
55512122 GATAA-GGGAGAAGATTTAGGAGCT
1 GATAAGGGGAGAAGATTTAGGAGCT
*
55512146 GATAAGGGGAGAAGTTTTAGGAGCT
1 GATAAGGGGAGAAGATTTAGGAGCT
*
55512171 GATTAGGG
1 GATAAGGG
55512179 AAGGCAGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 5 0.17
25 25 0.83
ACGTcount: A:0.33, C:0.04, G:0.40, T:0.23
Consensus pattern (25 bp):
GATAAGGGGAGAAGATTTAGGAGCT
Found at i:55513626 original size:27 final size:26
Alignment explanation
Indices: 55513594--55513688 Score: 109
Period size: 27 Copynumber: 3.5 Consensus size: 26
55513584 CTATGCCATG
55513594 ATTATCTGATCTGGTGGCTCTGACAC
1 ATTATCTGATCTGGTGGCTCTGACAC
* *
55513620 ATATATCTGTTCTGGTGGCTCTGCCAC
1 AT-TATCTGATCTGGTGGCTCTGACAC
* * *
55513647 GATTATCTGTATCTAGTGACTCTGTCAC
1 -ATTATCTG-ATCTGGTGGCTCTGACAC
*
55513675 ATTATCTGTTCTGG
1 ATTATCTGATCTGG
55513689 CAGCTATGCT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
26 6 0.10
27 36 0.62
28 16 0.28
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.39
Consensus pattern (26 bp):
ATTATCTGATCTGGTGGCTCTGACAC
Found at i:55513681 original size:54 final size:54
Alignment explanation
Indices: 55513577--55513697 Score: 163
Period size: 54 Copynumber: 2.2 Consensus size: 54
55513567 AGGAAGCGTC
* * *
55513577 CTGGTGGCTATGCCATGATTATCTGATCTGGTGGCTCTGACACATATATCTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTAGTGACTCTGACACATATATCTGTT
* *
55513631 CTGGTGGCTCTGCCACGATTATCTGTATCTAGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACGATTATCTG-ATCTAGTGACTCTGACACATATATCTGTT
**
55513685 CTGGCAGCTATGC
1 CTGGTGGCTATGC
55513698 TGCATATTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 41 0.71
55 17 0.29
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.36
Consensus pattern (54 bp):
CTGGTGGCTATGCCACGATTATCTGATCTAGTGACTCTGACACATATATCTGTT
Found at i:55529336 original size:43 final size:43
Alignment explanation
Indices: 55529276--55529361 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
55529266 GAGATATGTG
* ** * *
55529276 GCATCCGAGCTCATTGAGTGGTTTGATTTCATTATGGATGCGA
1 GCATCCAAGCTCATTGAGTGGTCCGAGTTCATAATGGATGCGA
*
55529319 GCATCCAAGCTCGTTGAGTGGTCCGAGTTCATAATGGATGCGA
1 GCATCCAAGCTCATTGAGTGGTCCGAGTTCATAATGGATGCGA
55529362 TACATGTAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (43 bp):
GCATCCAAGCTCATTGAGTGGTCCGAGTTCATAATGGATGCGA
Found at i:55529399 original size:51 final size:51
Alignment explanation
Indices: 55529320--55529419 Score: 137
Period size: 51 Copynumber: 2.0 Consensus size: 51
55529310 TGGATGCGAG
* *
55529320 CATCCAAGCTCGTTGAGTGGTCCGAGTTCATAATGGATGCGATACATGTAA
1 CATCCAAGCTCGTTGAGAGGTCCAAGTTCATAATGGATGCGATACATGTAA
* * * * *
55529371 CATCCGAGCTCGTTTAGAGGTCCAAGTTCATTATGGATGTGTTACATGT
1 CATCCAAGCTCGTTGAGAGGTCCAAGTTCATAATGGATGCGATACATGT
55529420 TATAAGGTAG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (51 bp):
CATCCAAGCTCGTTGAGAGGTCCAAGTTCATAATGGATGCGATACATGTAA
Found at i:55542465 original size:15 final size:16
Alignment explanation
Indices: 55542441--55542482 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
55542431 CACAACTAAT
*
55542441 CGAAAAAGAAG-AAAA
1 CGAAGAAGAAGAAAAA
*
55542456 CGAAGGAGAAGAAAAA
1 CGAAGAAGAAGAAAAA
55542472 CGAAGAAGAAG
1 CGAAGAAGAAG
55542483 GGAAAAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.64, C:0.07, G:0.29, T:0.00
Consensus pattern (16 bp):
CGAAGAAGAAGAAAAA
Found at i:55548685 original size:28 final size:30
Alignment explanation
Indices: 55548622--55548685 Score: 78
Period size: 33 Copynumber: 2.1 Consensus size: 30
55548612 ACACCTGTGT
*
55548622 GCCTTGCCCATGTGGGTCACACGATCCAAATTG
1 GCCTTGCCCATGTGGATCACACGATCC--A-TG
55548655 GCCTTGCCCATGTGGATCACACGA-CC-TG
1 GCCTTGCCCATGTGGATCACACGATCCATG
55548683 GCC
1 GCC
55548686 CAGGTTTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 5 0.17
32 2 0.07
33 23 0.77
ACGTcount: A:0.19, C:0.34, G:0.25, T:0.22
Consensus pattern (30 bp):
GCCTTGCCCATGTGGATCACACGATCCATG
Found at i:55549165 original size:19 final size:19
Alignment explanation
Indices: 55549107--55549167 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 19
55549097 CACAACTAAT
55549107 AGAAAAAGAAGAAAATGAATG
1 AGAAAAAGAAGAAAA-GAA-G
* *
55549128 AGAAGAAAAACAGAGAAGAAG
1 AGAA-AAAGA-AGAAAAGAAG
*
55549149 GGAAAAAGAAGAAAAGAAG
1 AGAAAAAGAAGAAAAGAAG
55549168 TTCGACAGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
19 9 0.27
20 4 0.12
21 8 0.24
22 7 0.21
23 5 0.15
ACGTcount: A:0.67, C:0.02, G:0.28, T:0.03
Consensus pattern (19 bp):
AGAAAAAGAAGAAAAGAAG
Found at i:55558079 original size:51 final size:48
Alignment explanation
Indices: 55558016--55558145 Score: 145
Period size: 49 Copynumber: 2.6 Consensus size: 48
55558006 AAGTCGCATG
* *
55558016 TGTAGTACTAAGTGCGGGCTACTATGCGTACTC-AATGACTTCGATCACGTA
1 TGTAGTACTAAGTGCAGGCTACTATGCGTAC-CGAATG--TT-GATCACATA
* * * * *
55558067 TGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATTGTTGATCGCATG
1 TGTAGTACTAAGTGCAGGCTACTATGCGTACC-GAATGTTGATCACATA
55558116 TGTAGTACTAAGTGCAGGCTACTATGCGTA
1 TGTAGTACTAAGTGCAGGCTACTATGCGTA
55558146 TCAGATAGCT
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
49 34 0.50
50 3 0.04
51 28 0.41
52 3 0.04
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (48 bp):
TGTAGTACTAAGTGCAGGCTACTATGCGTACCGAATGTTGATCACATA
Found at i:55558132 original size:49 final size:47
Alignment explanation
Indices: 55557968--55558139 Score: 173
Period size: 51 Copynumber: 3.5 Consensus size: 47
55557958 TACACGTGTA
* * *
55557968 TAGTACTAAGTGTAGGCTACTACGTGTATCATACTGTTAAGTCGCATGTG
1 TAGTACTAAGTGCAGGCTACTACGTGTACCA-A-TGTTGA-TCGCATGTG
* * * * * *
55558018 TAGTACTAAGTGCGGGCTACTATGCGTACTCAATGACTTCGATCACGTATG
1 TAGTACTAAGTGCAGGCTACTACGTGTAC-CAATG--TT-GATCGCATGTG
*
55558069 TAGTACTAAGTGCAGGCTACTACGTGTACCGGATTGTTGATCGCATGTG
1 TAGTACTAAGTGCAGGCTACTACGTGTACC--AATGTTGATCGCATGTG
55558118 TAGTACTAAGTGCAGGCTACTA
1 TAGTACTAAGTGCAGGCTACTA
55558140 TGCGTATCAG
Statistics
Matches: 100, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
49 32 0.32
50 28 0.28
51 36 0.36
52 4 0.04
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (47 bp):
TAGTACTAAGTGCAGGCTACTACGTGTACCAATGTTGATCGCATGTG
Found at i:55558268 original size:27 final size:26
Alignment explanation
Indices: 55558238--55558289 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
55558228 GGGAAAATCG
55558238 ATAAAGTGGTAATATGTG-AAAGTTATT
1 ATAAAGT-G-AATATGTGCAAAGTTATT
* *
55558265 ATAAGGTGAATATGTGCAAATTTAT
1 ATAAAGTGAATATGTGCAAAGTTAT
55558290 GTTTATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 8 0.36
26 8 0.36
27 6 0.27
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.37
Consensus pattern (26 bp):
ATAAAGTGAATATGTGCAAAGTTATT
Found at i:55562296 original size:24 final size:24
Alignment explanation
Indices: 55562264--55562311 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
55562254 GCTTAGGGTT
* *
55562264 AGTTGACGTCCATTGGCCTAATTC
1 AGTTGACGTCCACTAGCCTAATTC
55562288 AGTTGACGTCCACTAGCCTAATTC
1 AGTTGACGTCCACTAGCCTAATTC
55562312 CCTCATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (24 bp):
AGTTGACGTCCACTAGCCTAATTC
Found at i:55562420 original size:21 final size:21
Alignment explanation
Indices: 55562396--55562442 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
55562386 TCTACTCACT
55562396 ATGTTGAAACATCGGCA-TTTC
1 ATGTTGAAACAT-GGCAGTTTC
*
55562417 ATGTTGCAACATGGCAGTTTC
1 ATGTTGAAACATGGCAGTTTC
55562438 ATGTT
1 ATGTT
55562443 CTTATGCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (21 bp):
ATGTTGAAACATGGCAGTTTC
Found at i:55569771 original size:20 final size:20
Alignment explanation
Indices: 55569728--55569769 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
55569718 TAAAGAAAGT
**
55569728 AAATGCAATGGAAAATAATG
1 AAATGCAAAAGAAAATAATG
55569748 AAATGCAAAAGAAAATAA-G
1 AAATGCAAAAGAAAATAATG
55569767 AAA
1 AAA
55569770 ATTTGAAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.64, C:0.05, G:0.17, T:0.14
Consensus pattern (20 bp):
AAATGCAAAAGAAAATAATG
Found at i:55572489 original size:30 final size:30
Alignment explanation
Indices: 55572455--55572516 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
55572445 TAATTTGGGA
*
55572455 AGGGTTATAATTGAGCCTTGTAAAAACTAG
1 AGGGTTATAATTAAGCCTTGTAAAAACTAG
*
55572485 AGGGTTATAGTTAAGCCTTGTAAAAACTAG
1 AGGGTTATAATTAAGCCTTGTAAAAACTAG
55572515 AG
1 AG
55572517 TTCTAGTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (30 bp):
AGGGTTATAATTAAGCCTTGTAAAAACTAG
Found at i:55575040 original size:19 final size:21
Alignment explanation
Indices: 55574997--55575041 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
55574987 TTGGAATTGG
55574997 ATTTTTCTGCTTTATTTATTA
1 ATTTTTCTGCTTTATTTATTA
* *
55575018 ATTTTT-TG-TTTATTTGTTT
1 ATTTTTCTGCTTTATTTATTA
55575037 ATTTT
1 ATTTT
55575042 ACAGATTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 14 0.64
20 2 0.09
21 6 0.27
ACGTcount: A:0.16, C:0.04, G:0.07, T:0.73
Consensus pattern (21 bp):
ATTTTTCTGCTTTATTTATTA
Found at i:55577263 original size:30 final size:30
Alignment explanation
Indices: 55577224--55577281 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
55577214 AACATTCCCC
*
55577224 CTAGTTTTTCAAGGCTAAATTAGAATCTCT
1 CTAGCTTTTCAAGGCTAAATTAGAATCTCT
*
55577254 CTAGCTTTTCAAGGCTTAATTAGAATCT
1 CTAGCTTTTCAAGGCTAAATTAGAATCT
55577282 TCCCTAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (30 bp):
CTAGCTTTTCAAGGCTAAATTAGAATCTCT
Found at i:55578550 original size:18 final size:18
Alignment explanation
Indices: 55578502--55578552 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
55578492 TGTAAATGGA
**
55578502 TCATTTTCATTTTTATTT
1 TCATTTTCATTTCCATTT
* * *
55578520 TCGTTTCCGTTTCCATTT
1 TCATTTTCATTTCCATTT
55578538 TCATTTTCATTTCCA
1 TCATTTTCATTTCCA
55578553 AATAATTTCA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.14, C:0.22, G:0.04, T:0.61
Consensus pattern (18 bp):
TCATTTTCATTTCCATTT
Found at i:55578566 original size:5 final size:6
Alignment explanation
Indices: 55578502--55578549 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
55578492 TGTAAATGGA
* * * * *
55578502 TCATTT TCATTT TTATTT TCGTTT CCGTTT CCATTT TCATTT TCATTT
1 TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT
55578550 CCAAATAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.12, C:0.19, G:0.04, T:0.65
Consensus pattern (6 bp):
TCATTT
Found at i:55584128 original size:22 final size:20
Alignment explanation
Indices: 55584103--55584157 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 20
55584093 AGTAGTGAAT
55584103 ATAATTATATTATTTGGTAAAA
1 ATAATTATATTATTT--TAAAA
55584125 ATAA--ATATTAATTTTAAAA
1 ATAATTATATT-ATTTTAAAA
55584144 AT-ATTAT-TTATTTT
1 ATAATTATATTATTTT
55584158 TAATTTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
18 6 0.20
19 9 0.30
20 7 0.23
21 4 0.13
22 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
ATAATTATATTATTTTAAAA
Found at i:55584156 original size:18 final size:19
Alignment explanation
Indices: 55584103--55584157 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
55584093 AGTAGTGAAT
55584103 ATAATTATATTATTTGGTAAAA
1 ATAATTAT-TTATTT--TAAAA
* *
55584125 ATAAATATTAATTTTAAAA
1 ATAATTATTTATTTTAAAA
55584144 AT-ATTATTTATTTT
1 ATAATTATTTATTTT
55584158 TAATTTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 10 0.34
19 7 0.24
21 5 0.17
22 7 0.24
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (19 bp):
ATAATTATTTATTTTAAAA
Found at i:55584488 original size:2 final size:2
Alignment explanation
Indices: 55584481--55584534 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
55584471 ATATGGAAAA
55584481 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
55584523 AG AG AG AG AG AG
1 AG AG AG AG AG AG
55584535 GGGGGAGAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:55588592 original size:27 final size:27
Alignment explanation
Indices: 55588511--55588606 Score: 74
Period size: 26 Copynumber: 3.6 Consensus size: 27
55588501 TGTGAAAAAG
* * *
55588511 ATTTAACATAAATAAAATAT-AATC-A
1 ATTTAAAATAAATAATATATAAAGCAA
*
55588536 ATTTGAAATAAAATAATATATAAAGCAA
1 ATTTAAAAT-AAATAATATATAAAGCAA
* * *
55588564 ATTTCAAATAAATAATATGTTAAA-TAA
1 ATTTAAAATAAATAATAT-ATAAAGCAA
*
55588591 A-TTAAAATGAATAATA
1 ATTTAAAATAAATAATA
55588607 CACAAAGTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
25 7 0.12
26 23 0.40
27 15 0.26
28 13 0.22
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.32
Consensus pattern (27 bp):
ATTTAAAATAAATAATATATAAAGCAA
Found at i:55588718 original size:27 final size:28
Alignment explanation
Indices: 55588680--55588736 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 28
55588670 GTAAATGAGA
55588680 AATTTAAAATAAAT-TATATACAAAAAT
1 AATTTAAAATAAATATATATACAAAAAT
* *
55588707 AATTTAAAATAAATATATATATAAATAT
1 AATTTAAAATAAATATATATACAAAAAT
55588735 AA
1 AA
55588737 CCCAAAGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (28 bp):
AATTTAAAATAAATATATATACAAAAAT
Found at i:55588736 original size:28 final size:28
Alignment explanation
Indices: 55588654--55588736 Score: 98
Period size: 29 Copynumber: 3.0 Consensus size: 28
55588644 ATAAAAGAGC
* *
55588654 TTAAAATAAATA-ATATGTAAATGAGAAAT
1 TTAAAATAAATATATATATAAAT-A-TAAT
* *
55588683 TTAAAATAAAT-TATATACAAAAATAAT
1 TTAAAATAAATATATATATAAATATAAT
55588710 TTAAAATAAATATATATATAAATATAA
1 TTAAAATAAATATATATATAAATATAA
55588737 CCCAAAGTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
27 14 0.30
28 14 0.30
29 18 0.39
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (28 bp):
TTAAAATAAATATATATATAAATATAAT
Found at i:55588795 original size:27 final size:25
Alignment explanation
Indices: 55588754--55588819 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 25
55588744 TAACATATAC
55588754 ATATATAAAAG-TTTTAAGATAAGGA
1 ATATATAAAAGTTTTTAA-ATAAGGA
* *
55588779 GTATATAAAAGAATTTTTAAATAAGTA
1 ATATATAAAAG--TTTTTAAATAAGGA
55588806 ATATATAGAAAGTT
1 ATATATA-AAAGTT
55588820 CAAAATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 10 0.29
26 2 0.06
27 12 0.35
28 10 0.29
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.35
Consensus pattern (25 bp):
ATATATAAAAGTTTTTAAATAAGGA
Found at i:55590054 original size:25 final size:25
Alignment explanation
Indices: 55590000--55590061 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
55589990 TATTTTAAAC
*
55590000 TATTATTTATTTTAATTTTCATATA
1 TATTATTTATTTTAATTTTCATACA
* * *
55590025 CATTATTTGTTTTAATTATT-ATGCA
1 TATTATTTATTTTAATT-TTCATACA
55590050 TATTA-TTATTTT
1 TATTATTTATTTT
55590062 TTTAGATGCC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 6 0.20
25 22 0.73
26 2 0.07
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (25 bp):
TATTATTTATTTTAATTTTCATACA
Found at i:55590249 original size:27 final size:27
Alignment explanation
Indices: 55590192--55590250 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
55590182 TTGAACTTTC
* *
55590192 TATATATTACTTATTTAAAAATTCTTT
1 TATATACTACTTATTTAAAAATTCTTA
* *
55590219 TATATACTCCTTATCTTAAAACTT-TTA
1 TATATACTACTTAT-TTAAAAATTCTTA
55590246 TATAT
1 TATAT
55590251 GTATATGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.53
Consensus pattern (27 bp):
TATATACTACTTATTTAAAAATTCTTA
Found at i:55590321 original size:27 final size:28
Alignment explanation
Indices: 55590267--55590350 Score: 100
Period size: 29 Copynumber: 3.0 Consensus size: 28
55590257 GTTACTTTGG
55590267 ATTATATTTATATATATATTTATTTTAA
1 ATTATATTTATATATATATTTATTTTAA
* *
55590295 ATTATTTTTGTATATA-ATTTATTTTAA
1 ATTATATTTATATATATATTTATTTTAA
* *
55590322 ATTTCTCATTTACATAT-TATTTATTTTAA
1 A-TTAT-ATTTATATATATATTTATTTTAA
55590351 GCTCTTTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
27 12 0.26
28 17 0.36
29 18 0.38
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.61
Consensus pattern (28 bp):
ATTATATTTATATATATATTTATTTTAA
Found at i:55590453 original size:27 final size:25
Alignment explanation
Indices: 55590423--55590486 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 25
55590413 TTTATCTAAC
* *
55590423 ATATTATTTATTTGAAATTTGCTTTAT
1 ATATTATTTATTTCAAA-TTG-ATTAT
55590450 ATATTATTTTATTTCAAATTGATTAT
1 ATATTA-TTTATTTCAAATTGATTAT
*
55590476 ATTTTATTTAT
1 ATATTATTTAT
55590487 GTTAAATCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 5 0.15
26 9 0.27
27 9 0.27
28 10 0.30
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (25 bp):
ATATTATTTATTTCAAATTGATTAT
Found at i:55592342 original size:11 final size:11
Alignment explanation
Indices: 55592326--55592350 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55592316 CGTGGAGATA
55592326 AGTGAGCAACG
1 AGTGAGCAACG
55592337 AGTGAGCAACG
1 AGTGAGCAACG
55592348 AGT
1 AGT
55592351 CGCAGCCTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.16, G:0.36, T:0.12
Consensus pattern (11 bp):
AGTGAGCAACG
Found at i:55592586 original size:19 final size:18
Alignment explanation
Indices: 55592564--55592611 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
55592554 CTTCCTTTCT
55592564 TTTGCATTCATTCCATACA
1 TTTGCATTCATTCCAT-CA
*
55592583 TTTGCATTGCATTGCATCA
1 TTTGCATT-CATTCCATCA
55592602 TTTGCATTCA
1 TTTGCATTCA
55592612 ACTTTCACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 2 0.07
19 18 0.67
20 7 0.26
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (18 bp):
TTTGCATTCATTCCATCA
Found at i:55596479 original size:64 final size:64
Alignment explanation
Indices: 55596406--55596533 Score: 195
Period size: 64 Copynumber: 2.0 Consensus size: 64
55596396 TCATTCATAA
55596406 CACATCTAGTTAGGAGCAT-TTGATTCATTTCAATCATAACATCCTAATTAATTGACATAAGCAT
1 CACATCTAGTTAGGAGCATCTT-ATTCATTTCAATCATAACATCCTAATTAATTGACATAAGCAT
** * * *
55596470 CACATCTAGTTAGGAGCATCTTATTCATTTCGGTCATAGCATCCTAATTATTTGGCATAAGCAT
1 CACATCTAGTTAGGAGCATCTTATTCATTTCAATCATAACATCCTAATTAATTGACATAAGCAT
55596534 AGATACATGA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
64 56 0.97
65 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (64 bp):
CACATCTAGTTAGGAGCATCTTATTCATTTCAATCATAACATCCTAATTAATTGACATAAGCAT
Found at i:55596844 original size:132 final size:132
Alignment explanation
Indices: 55596601--55597651 Score: 1534
Period size: 132 Copynumber: 8.0 Consensus size: 132
55596591 GTGAATTTGT
* * *
55596601 AGATCTTATCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGGTC-AATCTTATCTCTCTGAAG
1 AGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAGACGG-CGAATCTTGTCTCTCTGAAG
* *
55596665 TTGCAATGGAGCAAATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGAT
65 TTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGAT
55596730 TGC
130 TGC
* * * * *
55596733 AAATCTTGTCTCCTTGAAGTTGCAGTGGAACAGATTGAAGACGGTGAATCTTGTCTCTCTGAAGT
1 AGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGAAGT
* * * * *
55596798 TGCAATGGAGCAAATTTAAGCCACAATCCTATCTCCCTACGTAGTAGTGGAGTAGGCTGAAGATT
66 TGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATT
55596863 GC
131 GC
* ** *
55596865 AGATCTTGTCTCCCTGAAGTTACAGTGGAATAGATTAAAGAAGGCGAATCTTGTCTCTCTGAAGT
1 AGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGAAGT
* * *
55596930 TGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAACAGTAATGGAGTAGGCTAAAGATT
66 TGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATT
55596995 GC
131 GC
* * * **
55596997 AGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAGATGACGAATCTTGTCTCCCT-AACC
1 AGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGAAGT
* * * *
55597061 AGTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTAGAGTAGGTTGAAGATT
66 TGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATT
55597126 GC
131 GC
* * *
55597128 AGATCTTGTCTCCCTGAAATT-CTAGTGGAACAGATCGAAGATGGTGAATCTTGTCTCTCTGAAG
1 AGATCTTGTCTCCCTGAAGTTAC-AGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGAAG
* *
55597192 TTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGGAGTAGTGGAGTAGGTTGAAGAT
65 TTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGAT
*
55597257 TAC
130 TGC
* * * * *
55597260 AGATTTTGTCTCCCTGAAGTTACAATGGAACAGATTGAAGAAGGCGAATCTTGTTTCTCTGAAGT
1 AGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGAAGT
* *
55597325 TGCAGTGGAGTAGATTTAAGCCACTATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATT
66 TGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATT
55597390 GC
131 GC
* * **
55597392 AGATCTTGTCTCCCTAAAGTTACAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCCCT-AACC
1 AGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGAAGT
*** * *
55597456 AATAGTGAAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTAAAGATT
66 TGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATT
55597521 GC
131 GC
*
55597523 AGATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGAAGT
1 AGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGAAGT
* * * *
55597588 TGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTGAGCAGCAGTGGAGCAGACTGAAGAT
66 TGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGAT
55597652 AGTGAATCTC
Statistics
Matches: 822, Mismatches: 92, Indels: 10
0.89 0.10 0.01
Matches are distributed among these distances:
130 1 0.00
131 235 0.29
132 585 0.71
133 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.27
Consensus pattern (132 bp):
AGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGAAGT
TGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATT
GC
Found at i:55596945 original size:45 final size:44
Alignment explanation
Indices: 55596603--55597603 Score: 268
Period size: 45 Copynumber: 22.8 Consensus size: 44
55596593 GAATTTGTAG
* * * *
55596603 ATCTTATCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGGTCA
1 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAGG-CA
* * * * * * *
55596648 ATCTTATCTCTCTGAAGTTGCAATGGAGCAAATTTAAGCCA--CC
1 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-AAGGCA
* * ** * * ** **
55596691 ATCCTATCTCCCT-AAGCAGTAGTGGAGTAGGCTGAAGATTGCAA
1 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAGGC-A
* * * *
55596735 ATCTTGTCTCCTTGAAGTTGCAGTGGAACAGATTGAAGACGGTGA
1 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAGG-CA
* * * * *
55596780 ATCTTGTCTCTCTGAAGTTGCAATGGAGCAAATTTAAGCCA--CA
1 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-AAGGCA
* * * * * * ** **
55596823 ATCCTATCTCCCT-ACGTAGTAGTGGAGTAGGCTGAAGATTGCA
1 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAGGCA
* ** *
55596866 GATCTTGTCTCCCTGAAGTTACAGTGGAATAGATTAAAGAAGGCGA
1 -ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAGGC-A
* * * *
55596912 ATCTTGTCTCTCTGAAGTTGCAGTGGAGCAGATTTAAGCCA--CC
1 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-AAGGCA
* * *** * * * ** * **
55596955 ATCCTATCTCCCT-AAACAGTAATGGAGTAGGCTAAAGATTGCA
1 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAGGCA
* * * * *
55596998 GATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAGATGACGA
1 -ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAGGC-A
*** * * * *
55597044 ATCTTGTCTCCCT-AACCAGTAGTGGAGCAGATTTAAGCCA--CC
1 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-AAGGCA
* * ** * * * * **
55597086 ATCCTATCTCCCT-AAGCAGTAGTAGAGTAGGTTGAAGATTGCA
1 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAGGCA
* * * * *
55597129 GATCTTGTCTCCCTGAAATT-CTAGTGGAACAGATCGAAGATGGTGA
1 -ATCTTGTCTCCCTGAAGTTGC-AGTGGAGCAGATTGAAGAAGG-CA
* * * *
55597175 ATCTTGTCTCTCTGAAGTTGCAGTGGAGCAGATTTAAGCCA--CC
1 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-AAGGCA
* * ** * * * ***
55597218 ATCCTATCTCCCT-AAGGAGTAGTGGAGTAGGTTGAAGATTACA
1 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAGGCA
* * * *
55597261 GATTTTGTCTCCCTGAAGTTACAATGGAACAGATTGAAGAAGGCGA
1 -ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAGGC-A
* * * * * *
55597307 ATCTTGTTTCTCTGAAGTTGCAGTGGAGTAGATTTAAGCCA--CT
1 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-AAGGCA
* * ** * * ** **
55597350 ATCCTATCTCCCT-AAGCAGTAGTGGAGTAGGCTGAAGATTGCA
1 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAGGCA
* * * * *
55597393 GATCTTGTCTCCCTAAAGTTACAGTGGAACAGATCGAAGACGGCGA
1 -ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAGGC-A
***** * * * *
55597439 ATCTTGTCTCCCT-AACCAATAGTGAAGCAGATTTAAGCCA--CC
1 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-AAGGCA
* * ** * * ** * **
55597481 ATCCTATCTCCCT-AAGCAGTAGTGGAGTAGGCTAAAGATTGCA
1 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAGGCA
* * *
55597524 GATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGGCGA
1 -ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAGGC-A
*
55597570 ATCTTGTCTCTCTGAAGTTGCAGTGGAGCAGATT
1 ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATT
55597604 TAAGCCACCA
Statistics
Matches: 659, Mismatches: 253, Indels: 88
0.66 0.25 0.09
Matches are distributed among these distances:
42 139 0.21
43 62 0.09
44 109 0.17
45 340 0.52
46 9 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
ATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAGGCA
Found at i:55597197 original size:263 final size:264
Alignment explanation
Indices: 55596601--55597651 Score: 1518
Period size: 263 Copynumber: 4.0 Consensus size: 264
55596591 GTGAATTTGT
* * * *
55596601 AGATCTTATCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGGTC-AATCTTATCTCTCTGAAG
1 AGATCTTGTCTCCCTGAAATTACAGTGGAACAGATCGAAGACGG-CGAATCTTGTCTCTCTGAAG
* * *
55596665 TTGCAATGGAGCAAATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGAT
65 TTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTAAAGAT
* * * * *
55596730 TGCAAATCTTGTCTCCTTGAAGTTGCAGTGGAACAGATTGAAGACGGTGAATCTTGTCTCTCTGA
130 TGCAGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGA
* * * * *
55596795 AGTTGCAATGGAGCAAATTTAAGCCACAATCCTATCTCCCTACGTAGTAGTGGAGTAGGCTGAAG
195 AGTTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAG
55596860 ATTGC
260 ATTGC
* * ** *
55596865 AGATCTTGTCTCCCTGAAGTTACAGTGGAATAGATTAAAGAAGGCGAATCTTGTCTCTCTGAAGT
1 AGATCTTGTCTCCCTGAAATTACAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGAAGT
* *
55596930 TGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAACAGTAATGGAGTAGGCTAAAGATT
66 TGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTAAAGATT
* * *
55596995 GCAGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAGATGACGAATCTTGTCTCCCT-AA
131 GCAGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGAA
*** * * *
55597059 CCAGTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTAGAGTAGGTTGAAGA
196 GTTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGA
55597124 TTGC
261 TTGC
* *
55597128 AGATCTTGTCTCCCTGAAATT-CTAGTGGAACAGATCGAAGATGGTGAATCTTGTCTCTCTGAAG
1 AGATCTTGTCTCCCTGAAATTAC-AGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGAAG
* * *
55597192 TTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGGAGTAGTGGAGTAGGTTGAAGAT
65 TTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTAAAGAT
* * * * * *
55597257 TACAGATTTTGTCTCCCTGAAGTTACAATGGAACAGATTGAAGAAGGCGAATCTTGTTTCTCTGA
130 TGCAGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGA
* *
55597322 AGTTGCAGTGGAGTAGATTTAAGCCACTATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAG
195 AGTTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAG
55597387 ATTGC
260 ATTGC
* *
55597392 AGATCTTGTCTCCCT-AAAGTTACAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCCCT-AAC
1 AGATCTTGTCTCCCTGAAA-TTACAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGAAG
**** *
55597455 CAATAGTGAAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTAAAGAT
65 TTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTAAAGAT
*
55597520 TGCAGATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGA
130 TGCAGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGA
* * * *
55597585 AGTTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTGAGCAGCAGTGGAGCAGACTGAAG
195 AGTTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAG
55597650 AT
260 AT
55597652 AGTGAATCTC
Statistics
Matches: 699, Mismatches: 83, Indels: 11
0.88 0.10 0.01
Matches are distributed among these distances:
262 1 0.00
263 413 0.59
264 284 0.41
265 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.27
Consensus pattern (264 bp):
AGATCTTGTCTCCCTGAAATTACAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGAAGT
TGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTAAAGATT
GCAGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGAA
GTTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGA
TTGC
Found at i:55597401 original size:395 final size:395
Alignment explanation
Indices: 55596601--55597651 Score: 1638
Period size: 395 Copynumber: 2.7 Consensus size: 395
55596591 GTGAATTTGT
* * * * * *
55596601 AGATCTTATCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGGTC-AATCTTATCTCTCTGAAG
1 AGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAGAC-GACGAATCTTGTCTCCCT-AAC
** * * *
55596665 TTGCAATGGAGCAAATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGAT
64 CAGTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGAT
* * *
55596730 TGCAAATCTTGTCTCCTTGAAGTTGCAGTGGAACAGATTGAAGACGGTGAATCTTGTCTCTCTGA
129 TGCAGATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGGTGAATCTTGTCTCTCTGA
* * * * *
55596795 AGTTGCAATGGAGCAAATTTAAGCCACAATCCTATCTCCCTACGTAGTAGTGGAGTAGGCTGAAG
194 AGTTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAG
* * *
55596860 ATTGCAGATCTTGTCTCCCTGAAGTTACAGTGGAATAGATTAAAGAAGGCGAATCTTGTCTCTCT
259 ATTACAGATCTTGTCTCCCTGAAGTTACAATGGAACAGATTAAAGAAGGCGAATCTTGTCTCTCT
55596925 GAAGTTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAACAGTAATGGAGTAGGCTAA
324 GAAGTTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAACAGTAATGGAGTAGGCTAA
55596990 AGATTGC
389 AGATTGC
*
55596997 AGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAGATGACGAATCTTGTCTCCCTAACCA
1 AGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAGACGACGAATCTTGTCTCCCTAACCA
* *
55597062 GTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTAGAGTAGGTTGAAGATTG
66 GTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTG
* *
55597127 CAGATCTTGTCTCCCTGAAATT-CTAGTGGAACAGATCGAAGATGGTGAATCTTGTCTCTCTGAA
131 CAGATCTTGTCTCCCTGAAGTTGC-AGTGGAACAGATCGAAGACGGTGAATCTTGTCTCTCTGAA
* *
55597191 GTTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGGAGTAGTGGAGTAGGTTGAAGA
195 GTTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGA
* * *
55597256 TTACAGATTTTGTCTCCCTGAAGTTACAATGGAACAGATTGAAGAAGGCGAATCTTGTTTCTCTG
260 TTACAGATCTTGTCTCCCTGAAGTTACAATGGAACAGATTAAAGAAGGCGAATCTTGTCTCTCTG
* * * * *
55597321 AAGTTGCAGTGGAGTAGATTTAAGCCACTATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAA
325 AAGTTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAACAGTAATGGAGTAGGCTAAA
55597386 GATTGC
390 GATTGC
* *
55597392 AGATCTTGTCTCCCTAAAGTTACAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCCCTAACCA
1 AGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAGACGACGAATCTTGTCTCCCTAACCA
* * *
55597457 ATAGTGAAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTAAAGATTG
66 GTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTG
*
55597522 CAGATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGGCGAATCTTGTCTCTCTGAAG
131 CAGATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGGTGAATCTTGTCTCTCTGAAG
* * * *
55597587 TTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTGAGCAGCAGTGGAGCAGACTGAAGAT
196 TTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGAT
55597652 AGTGAATCTC
Statistics
Matches: 599, Mismatches: 53, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
394 1 0.00
395 546 0.91
396 52 0.09
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.27
Consensus pattern (395 bp):
AGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAGACGACGAATCTTGTCTCCCTAACCA
GTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTG
CAGATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGGTGAATCTTGTCTCTCTGAAG
TTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGAT
TACAGATCTTGTCTCCCTGAAGTTACAATGGAACAGATTAAAGAAGGCGAATCTTGTCTCTCTGA
AGTTGCAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAACAGTAATGGAGTAGGCTAAAG
ATTGC
Found at i:55600788 original size:23 final size:20
Alignment explanation
Indices: 55600739--55600776 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
55600729 AATATCTTAT
55600739 TAAAATAT-TAATTAAATAA
1 TAAAATATCTAATTAAATAA
*
55600758 T-AATTATCTAATTAAATAA
1 TAAAATATCTAATTAAATAA
55600777 CTATAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAAATATCTAATTAAATAA
Found at i:55601480 original size:37 final size:37
Alignment explanation
Indices: 55601410--55601483 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
55601400 TTTTAATAAC
* * **
55601410 ATTATTAAATATAATTTAATCATATTTTAATATAATT
1 ATTATTAAATACAATTTAATAATATAATAATATAATT
55601447 ATTATTAAATACAATTTAATAATAATAAT-ATATAATT
1 ATTATTAAATACAATTTAATAAT-ATAATAATATAATT
55601484 TAATAACATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 29 0.91
38 3 0.09
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTATTAAATACAATTTAATAATATAATAATATAATT
Found at i:55602505 original size:17 final size:17
Alignment explanation
Indices: 55602483--55602517 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
55602473 AATAATATAA
55602483 TAAGCACAATTGAATAT
1 TAAGCACAATTGAATAT
55602500 TAAGCACAATTGAATAT
1 TAAGCACAATTGAATAT
55602517 T
1 T
55602518 TAAAATTCAC
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:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (17 bp):
TAAGCACAATTGAATAT
Found at i:55602924 original size:40 final size:40
Alignment explanation
Indices: 55602847--55602925 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
55602837 AAAACACACC
** *
55602847 AATTTGGCACCTAGTGCCTCATTGGATAATTCGAAGTAAT
1 AATTTGGCACCTAGTGCCTCATTGGATAAACCAAAGTAAT
* *
55602887 AATTTGGCATCC-AGTGTCTCATTGGCTAAACCAAAGTAA
1 AATTTGGCA-CCTAGTGCCTCATTGGATAAACCAAAGTAA
55602926 ATTGACACCC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 31 0.94
41 2 0.06
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (40 bp):
AATTTGGCACCTAGTGCCTCATTGGATAAACCAAAGTAAT
Found at i:55603966 original size:21 final size:21
Alignment explanation
Indices: 55603940--55604008 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 21
55603930 GTTTCATTAT
55603940 TATATAATATAATATATAATA
1 TATATAATATAATATATAATA
*
55603961 TATATACT-TAA-ATATTAAGGTA
1 TATATAATATAATATA-TAA--TA
*
55603983 TA-ATATTATAATATTATAATA
1 TATATAATATAATA-TATAATA
55604004 TATAT
1 TATAT
55604009 TTTAACTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
19 3 0.08
20 6 0.15
21 15 0.38
22 9 0.23
23 4 0.10
24 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (21 bp):
TATATAATATAATATATAATA
Found at i:55607049 original size:35 final size:35
Alignment explanation
Indices: 55607009--55607079 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
55606999 TAAGGAGTCC
55607009 ATTTTATTTGTAGCGTCTATATCCATTTTTAATGA
1 ATTTTATTTGTAGCGTCTATATCCATTTTTAATGA
55607044 ATTTTATTTGTAGCGTCTATATCCATTTTTAATGA
1 ATTTTATTTGTAGCGTCTATATCCATTTTTAATGA
55607079 A
1 A
55607080 CTATCAAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (35 bp):
ATTTTATTTGTAGCGTCTATATCCATTTTTAATGA
Found at i:55616881 original size:17 final size:17
Alignment explanation
Indices: 55616849--55616883 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
55616839 TTTTTTTATT
55616849 ATAACAATAAAAGTAAA
1 ATAACAATAAAAGTAAA
55616866 ATAA-AATAAAATGTAAA
1 ATAACAATAAAA-GTAAA
55616883 A
1 A
55616884 GGCAAAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.20
Consensus pattern (17 bp):
ATAACAATAAAAGTAAA
Found at i:55619840 original size:20 final size:20
Alignment explanation
Indices: 55619807--55619844 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
55619797 ACTAATTGTG
*
55619807 CATGTTATGCTTAAATGTTT
1 CATGTGATGCTTAAATGTTT
*
55619827 CATGTGATGGTTAAATGT
1 CATGTGATGCTTAAATGT
55619845 GGTATATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.45
Consensus pattern (20 bp):
CATGTGATGCTTAAATGTTT
Found at i:55621600 original size:52 final size:54
Alignment explanation
Indices: 55621467--55621602 Score: 143
Period size: 52 Copynumber: 2.5 Consensus size: 54
55621457 TTATGAACCC
* **
55621467 ACCATTGCCATGCCTTGGCATGGTCTTACATGGGATATTTGCCTTATCGTAGTTT
1 ACCAATGCCATGCCTTGGCATGGTCTTACAT-GGATATTTGCCTTATCGTAAATT
* * * * * *
55621522 ATCAATGCCATGTCTTGACATGGTCTTACAT-GAT-TTT-CTTTCCTTGTAAATT
1 ACCAATGCCATGCCTTGGCATGGTCTTACATGGATATTTGCCTT-ATCGTAAATT
*
55621574 ACCAATTCCATGCCTTGGCATGGTCTTAC
1 ACCAATGCCATGCCTTGGCATGGTCTTAC
55621603 TTGGTATCGT
Statistics
Matches: 67, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
51 3 0.04
52 34 0.51
53 3 0.04
55 27 0.40
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.39
Consensus pattern (54 bp):
ACCAATGCCATGCCTTGGCATGGTCTTACATGGATATTTGCCTTATCGTAAATT
Found at i:55631001 original size:23 final size:23
Alignment explanation
Indices: 55630966--55631025 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
55630956 TGTCCCAATG
55630966 CACACGGGCGTGTGCATTGCCTC
1 CACACGGGCGTGTGCATTGCCTC
* *
55630989 TACACGGGTGTGTGCATTGCCTC
1 CACACGGGCGTGTGCATTGCCTC
*
55631012 CACACGGGCATGTG
1 CACACGGGCGTGTG
55631026 AGGTTTAAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.15, C:0.30, G:0.32, T:0.23
Consensus pattern (23 bp):
CACACGGGCGTGTGCATTGCCTC
Found at i:55634000 original size:30 final size:30
Alignment explanation
Indices: 55633942--55634000 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
55633932 GATTTTGAGC
* **
55633942 CTAGAGGCAAAATGGTTATTTTGTCAAAGT
1 CTAGAGGCAAAATGGTCATTTTACCAAAGT
* *
55633972 CTAGGGGCAAAATGGTCGTTTTACCAAAG
1 CTAGAGGCAAAATGGTCATTTTACCAAAG
55634001 ATATGAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (30 bp):
CTAGAGGCAAAATGGTCATTTTACCAAAGT
Found at i:55634395 original size:46 final size:44
Alignment explanation
Indices: 55634338--55634513 Score: 162
Period size: 46 Copynumber: 3.8 Consensus size: 44
55634328 CCACTTGTGT
*
55634338 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCC-CATTA-GA
*
55634384 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATTGG--CATTGAGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCCATT-AGA
* * * *
55634429 CGAGTGCTAGTGTAAGACATTTCTAGGACATGCATCGGCCTCGA-CACGTA
1 -GA--GCCAGTGTAAGACATGTCTGGGACATGCATCGGCC-C-ATTA-G-A
55634479 -AGCCAGTGTAAGACATGTCTGGGACATGCATCGGC
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGC
55634514 TACGAGATGT
Statistics
Matches: 108, Mismatches: 10, Indels: 24
0.76 0.07 0.17
Matches are distributed among these distances:
45 6 0.06
46 53 0.49
47 26 0.24
48 19 0.18
49 2 0.02
50 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.23
Consensus pattern (44 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCCATTAGA
Found at i:55641251 original size:40 final size:40
Alignment explanation
Indices: 55641146--55641322 Score: 236
Period size: 40 Copynumber: 4.5 Consensus size: 40
55641136 CGGATGATAA
* *
55641146 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
55641186 TCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
55641225 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
55641265 CCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
55641305 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
55641323 TACTTGGTTT
Statistics
Matches: 124, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
39 50 0.40
40 74 0.60
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:55641311 original size:79 final size:79
Alignment explanation
Indices: 55641146--55641322 Score: 234
Period size: 79 Copynumber: 2.2 Consensus size: 79
55641136 CGGATGATAA
* ** *
55641146 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTTCGGGCTAAGCCCGAAGGCATTTGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCATTTGA
*
55641211 GCGAGTTACTATAT
66 GCAAGTTACTATAT
*
55641225 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAG-CCCGAAGGCATTT
55641289 GAGCAAG-TAGCTATAT
64 GAGCAAGTTA-CTATAT
* *
55641305 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
55641323 TACTTGGTTT
Statistics
Matches: 87, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
78 2 0.02
79 59 0.68
80 26 0.30
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCATTTGA
GCAAGTTACTATAT
Found at i:55647498 original size:40 final size:40
Alignment explanation
Indices: 55647404--55647548 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
55647394 TACTCGAATG
*
55647404 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
55647445 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
55647485 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
55647525 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
55647549 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:55649995 original size:28 final size:28
Alignment explanation
Indices: 55649957--55650109 Score: 238
Period size: 28 Copynumber: 5.5 Consensus size: 28
55649947 TAAATTGTAC
*
55649957 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
55649985 AGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
55650013 AGCACT-AGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
55650040 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
55650068 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
* *
55650095 AGCACTGAGTATGCG
1 AGCACTAAGTGTGCG
55650110 GACTTAATAT
Statistics
Matches: 118, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
27 49 0.42
28 69 0.58
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:55650034 original size:55 final size:55
Alignment explanation
Indices: 55649957--55650109 Score: 236
Period size: 55 Copynumber: 2.8 Consensus size: 55
55649947 TAAATTGTAC
*
55649957 AGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGATTATGTAGCACTAAGTGTGCGAATTTGATTATAT
*
55650013 AGCACT-AGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAG-TTGATTATGTAGCACTAAGTGTGCGAATTTGATTATAT
* * *
55650068 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTATGCG
1 AGCACTAAGTGTGCGAGTTGATTATGTAGCACTAAGTGTGCG
55650110 GACTTAATAT
Statistics
Matches: 90, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
55 74 0.82
56 16 0.18
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.33
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATAT
Found at i:55658939 original size:40 final size:40
Alignment explanation
Indices: 55658845--55658989 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
55658835 TACTCGAATG
*
55658845 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
55658886 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
55658926 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
55658966 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
55658990 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:55663664 original size:39 final size:40
Alignment explanation
Indices: 55663610--55663852 Score: 320
Period size: 40 Copynumber: 6.2 Consensus size: 40
55663600 GATGATAACT
* *
55663610 GGGCTAAG-CCCGAAGGCATTTGTGCTAGTGACTA-ATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCC
* * **
55663649 GGGCTAAG-CCCGAAGGCATTTGTGCTAGTGACTA-ATTTT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCC
55663688 GGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
*
55663727 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
*
55663767 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
* *
55663807 GGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCC
55663847 -GGCTAA
1 GGGCTAA
55663853 ATTCTGAAGG
Statistics
Matches: 191, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
39 86 0.45
40 105 0.55
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
Found at i:55666448 original size:26 final size:24
Alignment explanation
Indices: 55666418--55666467 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
55666408 AAATAAAAAA
*
55666418 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
55666444 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
55666468 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:55666487 original size:21 final size:21
Alignment explanation
Indices: 55666438--55666496 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
55666428 ATAATAAATC
*
55666438 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
55666458 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
55666480 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
55666497 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:55669036 original size:43 final size:42
Alignment explanation
Indices: 55668985--55669083 Score: 128
Period size: 43 Copynumber: 2.3 Consensus size: 42
55668975 GAAATCTGAG
* *
55668985 CTCGTTGAGTGGTCCTAG-TTCGTGATATATGTAAGAATCCTAA
1 CTCGTTGAGTGGTCCAAGATT-GTGATATATGT-AGAATCCGAA
* * *
55669028 CTTGTTGAGTGGTCCAAGATTGTGATATATGTAGCATCCGAG
1 CTCGTTGAGTGGTCCAAGATTGTGATATATGTAGAATCCGAA
55669070 CTCGTTGAGTGGTC
1 CTCGTTGAGTGGTC
55669084 TGATTTCATT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
42 20 0.41
43 27 0.55
44 2 0.04
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.34
Consensus pattern (42 bp):
CTCGTTGAGTGGTCCAAGATTGTGATATATGTAGAATCCGAA
Found at i:55669135 original size:43 final size:42
Alignment explanation
Indices: 55669056--55669143 Score: 113
Period size: 43 Copynumber: 2.1 Consensus size: 42
55669046 ATTGTGATAT
* ** * *
55669056 ATGTAGCATCCGAGCTCGTTGAGTGGTCTGATTTCATTATGG
1 ATGTAGCATCCGAGCTCGTTAAGTGGTCCAAGTTCATAATGG
*
55669098 ATGTGAGCATCTGAGCTCGTTAAGTGGTCCAAGTTCATAATGG
1 ATGT-AGCATCCGAGCTCGTTAAGTGGTCCAAGTTCATAATGG
55669141 ATG
1 ATG
55669144 CGATACATGT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 4 0.10
43 35 0.90
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (42 bp):
ATGTAGCATCCGAGCTCGTTAAGTGGTCCAAGTTCATAATGG
Found at i:55672591 original size:70 final size:70
Alignment explanation
Indices: 55672429--55672591 Score: 218
Period size: 70 Copynumber: 2.3 Consensus size: 70
55672419 CATGCCAAAA
* * ** * **
55672429 TTGTGAAACGTAGGTATGGTATCATCCATACTGATTTGTGAAACGTAGGTATGGTATTAACCATA
1 TTGTGAAACGTAGGTATGGTATTATCCATACTGAGTTAAGAAACATAGGTATGACATTAACCATA
*
55672494 CTGAG
66 CCGAG
**
55672499 TTGTGAAACGTAGGTATGGTATTATCCATACTGAGTTAAGAAACATAGGTATGACATTTCCCATA
1 TTGTGAAACGTAGGTATGGTATTATCCATACTGAGTTAAGAAACATAGGTATGACATTAACCATA
55672564 CCGAG
66 CCGAG
* *
55672569 TTGTAAAATGTAGGTATGGTATT
1 TTGTGAAACGTAGGTATGGTATT
55672592 TCAATGAGGA
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
70 81 1.00
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.33
Consensus pattern (70 bp):
TTGTGAAACGTAGGTATGGTATTATCCATACTGAGTTAAGAAACATAGGTATGACATTAACCATA
CCGAG
Found at i:55672593 original size:35 final size:34
Alignment explanation
Indices: 55672429--55672593 Score: 195
Period size: 35 Copynumber: 4.7 Consensus size: 34
55672419 CATGCCAAAA
* *
55672429 TTGTGAAACGTAGGTATGGTATCATCCATACTGAT
1 TTGTGAAACGTAGGTATGGTAT-TTCCATACTGAG
*
55672464 TTGTGAAACGTAGGTATGGTATTAACCATACTGAG
1 TTGTGAAACGTAGGTATGGTATT-TCCATACTGAG
55672499 TTGTGAAACGTAGGTATGGTATTATCCATACTGAG
1 TTGTGAAACGTAGGTATGGTATT-TCCATACTGAG
** * ** *
55672534 TTAAGAAACATAGGTATGACATTTCCCATACCGAG
1 TTGTGAAACGTAGGTATGGTATTT-CCATACTGAG
* *
55672569 TTGTAAAATGTAGGTATGGTATTTC
1 TTGTGAAACGTAGGTATGGTATTTC
55672594 AATGAGGAAA
Statistics
Matches: 111, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
34 2 0.02
35 109 0.98
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (34 bp):
TTGTGAAACGTAGGTATGGTATTTCCATACTGAG
Found at i:55674482 original size:22 final size:22
Alignment explanation
Indices: 55674457--55674498 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
55674447 CATAAAATAA
55674457 AAAAAGAA-AAATGAATCAATCC
1 AAAAAGAATAAA-GAATCAATCC
*
55674479 AAAAATAATAAAGAATCAAT
1 AAAAAGAATAAAGAATCAAT
55674499 TCATTCCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.67, C:0.10, G:0.07, T:0.17
Consensus pattern (22 bp):
AAAAAGAATAAAGAATCAATCC
Found at i:55674857 original size:11 final size:11
Alignment explanation
Indices: 55674843--55674872 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
55674833 TTAGCCCATC
55674843 ATTAATTAGAA
1 ATTAATTAGAA
55674854 ATTAATTAGAA
1 ATTAATTAGAA
*
55674865 CTTAATTA
1 ATTAATTA
55674873 CTAGAGTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (11 bp):
ATTAATTAGAA
Found at i:55680513 original size:16 final size:15
Alignment explanation
Indices: 55680481--55680526 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
55680471 AATTTAATTT
*
55680481 TTTTA-TTTT-TTTA
1 TTTTATTTTTCTTTC
*
55680494 TTTTCTTTTTCTTCTC
1 TTTTATTTTTCTT-TC
55680510 TTTTATTTTTCTTTC
1 TTTTATTTTTCTTTC
55680525 TT
1 TT
55680527 CTCACATTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 4 0.15
14 4 0.15
15 6 0.22
16 13 0.48
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTATTTTTCTTTC
Found at i:55680526 original size:20 final size:21
Alignment explanation
Indices: 55680489--55680529 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
55680479 TTTTTTATTT
*
55680489 TTTTATTTTCTTTTTCTTCTC
1 TTTTATTTTCTCTTTCTTCTC
55680510 TTTTATTTT-TCTTTCTTCTC
1 TTTTATTTTCTCTTTCTTCTC
55680530 ACATTCTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTATTTTCTCTTTCTTCTC
Found at i:55683357 original size:27 final size:27
Alignment explanation
Indices: 55683315--55683395 Score: 144
Period size: 27 Copynumber: 3.0 Consensus size: 27
55683305 TTGTTGGTCA
*
55683315 AGAGTAGTTTTTTATTGGTTCGGGTTT
1 AGAGTAGTTTTCTATTGGTTCGGGTTT
*
55683342 AGAGTAGGTTTCTATTGGTTCGGGTTT
1 AGAGTAGTTTTCTATTGGTTCGGGTTT
55683369 AGAGTAGTTTTCTATTGGTTCGGGTTT
1 AGAGTAGTTTTCTATTGGTTCGGGTTT
55683396 CGAACAATCT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.15, C:0.06, G:0.31, T:0.48
Consensus pattern (27 bp):
AGAGTAGTTTTCTATTGGTTCGGGTTT
Done.