Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 173 of 318
Found at i:53836128 original size:24 final size:24
Alignment explanation
Indices: 53836045--53836128 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 24
53836035 GGAGGAAGTG
* *
53836045 TAAAAGGGCTATGCCCCAGTTTACC
1 TAAAAGGGCTTTGCCCCAGTTTA-T
*
53836070 GAAAAGGGCTTTGCCCCAGTTTAT
1 TAAAAGGGCTTTGCCCCAGTTTAT
*
53836094 CAAAAAGGGCTTTGCCCCAG-TTAT
1 -TAAAAGGGCTTTGCCCCAGTTTAT
53836118 TAAAAGAGGCT
1 TAAAAG-GGCT
53836129 AGGCCTCTAG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.10
24 8 0.15
25 39 0.75
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (24 bp):
TAAAAGGGCTTTGCCCCAGTTTAT
Found at i:53836372 original size:31 final size:31
Alignment explanation
Indices: 53836334--53836411 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
53836324 TTGTTACCGT
53836334 AAAGGCTTTGGCCCAGTGATATGAATAATGA
1 AAAGGCTTTGGCCCAGTGATATGAATAATGA
*
53836365 AAAGGCTTTGGCCCAGTGATATGAATAATGT
1 AAAGGCTTTGGCCCAGTGATATGAATAATGA
53836396 AAAGG-TTTCGGCCCAG
1 AAAGGCTTT-GGCCCAG
53836412 ATATGCTGAG
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 3 0.07
31 42 0.93
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (31 bp):
AAAGGCTTTGGCCCAGTGATATGAATAATGA
Found at i:53838077 original size:24 final size:24
Alignment explanation
Indices: 53838025--53838078 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
53838015 GATTAGGTGG
53838025 TGTGTGACAGCCAATGTACACGGC
1 TGTGTGACAGCCAATGTACACGGC
* * *
53838049 CGTGTGACAGCCCATGT-CTCAGGC
1 TGTGTGACAGCCAATGTACAC-GGC
53838073 TGTGTG
1 TGTGTG
53838079 TACCAAAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.19, C:0.26, G:0.31, T:0.24
Consensus pattern (24 bp):
TGTGTGACAGCCAATGTACACGGC
Found at i:53839382 original size:32 final size:32
Alignment explanation
Indices: 53839346--53839410 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
53839336 AAATATGCTA
53839346 AGTGATTTTTTCTCATACCTATATCAACTAAC
1 AGTGATTTTTTCTCATACCTATATCAACTAAC
*
53839378 AGTGATTTTTTCTCTTACCTATATCAACTAAC
1 AGTGATTTTTTCTCATACCTATATCAACTAAC
53839410 A
1 A
53839411 TTTTTCCTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.42
Consensus pattern (32 bp):
AGTGATTTTTTCTCATACCTATATCAACTAAC
Found at i:53839414 original size:28 final size:29
Alignment explanation
Indices: 53839349--53839421 Score: 94
Period size: 32 Copynumber: 2.4 Consensus size: 29
53839339 TATGCTAAGT
53839349 GATTTTTTCTCATACCTATATCAACTAAC
1 GATTTTTTCTCATACCTATATCAACTAAC
*
53839378 AGTGATTTTTTCTCTTACCTATATCAACTAAC
1 ---GATTTTTTCTCATACCTATATCAACTAAC
*
53839410 -ATTTTTCCTCAT
1 GATTTTTTCTCAT
53839422 TTCACAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 10 0.26
32 28 0.74
ACGTcount: A:0.27, C:0.23, G:0.04, T:0.45
Consensus pattern (29 bp):
GATTTTTTCTCATACCTATATCAACTAAC
Found at i:53845128 original size:27 final size:27
Alignment explanation
Indices: 53845074--53845153 Score: 99
Period size: 27 Copynumber: 2.9 Consensus size: 27
53845064 TTAGAATACT
* *
53845074 TTAGTTTACTAAAATTACCGAAATACCC
1 TTAGTTT-GTAAAATTACTGAAATACCC
*
53845102 TTAGTTTGTAAAAATACTGAAATACCC
1 TTAGTTTGTAAAATTACTGAAATACCC
*
53845129 -TCGATTTGTAAAATTACTGAAATAC
1 TTAG-TTTGTAAAATTACTGAAATAC
53845154 TTTCGACTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
26 2 0.04
27 37 0.80
28 7 0.15
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (27 bp):
TTAGTTTGTAAAATTACTGAAATACCC
Found at i:53845159 original size:27 final size:27
Alignment explanation
Indices: 53845083--53845172 Score: 110
Period size: 27 Copynumber: 3.3 Consensus size: 27
53845073 TTTAGTTTAC
* *
53845083 TAAAATTACCGAAATACCCTTAG-TTTG
1 TAAAATTACTGAAATA-CCTTCGATTTG
* *
53845110 TAAAAATACTGAAATACCCTCGATTTG
1 TAAAATTACTGAAATACCTTCGATTTG
* *
53845137 TAAAATTACTGAAATACTTTCGACTTG
1 TAAAATTACTGAAATACCTTCGATTTG
53845164 TAAAATTAC
1 TAAAATTAC
53845173 CAAAGTACCC
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
26 4 0.07
27 50 0.93
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (27 bp):
TAAAATTACTGAAATACCTTCGATTTG
Found at i:53845388 original size:27 final size:27
Alignment explanation
Indices: 53845178--53845387 Score: 271
Period size: 27 Copynumber: 7.8 Consensus size: 27
53845168 ATTACCAAAG
53845178 TACCC-CGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
53845204 TACCCTCGATTTATATAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
53845231 TACCC-CTGATTTACATAATTATCGTTT
1 TACCCTC-GATTTACAGAATTACCGTTT
* *
53845258 TACCCTCGACTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
53845285 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * * **
53845312 TACCCACGATTAATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
53845339 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
53845366 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
53845388 TAAAATACCC
Statistics
Matches: 159, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
26 6 0.04
27 152 0.96
28 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:53845396 original size:27 final size:27
Alignment explanation
Indices: 53845339--53845589 Score: 136
Period size: 27 Copynumber: 9.3 Consensus size: 27
53845329 ATTACTATTT
* *****
53845339 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTTGATTTACAAAATTACCAAAA
* *
53845366 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTTGATTTACAAAATTACCAAAA
** *
53845393 TACCCTT-AGTTTGTAAAAGTACCAAAA
1 TACCCTTGA-TTTACAAAATTACCAAAA
* **
53845420 TACCCCT-AGTTTTTAAAATTACCAAAA
1 TACCCTTGA-TTTACAAAATTACCAAAA
* *** *
53845447 TACCCTTGGTTTGTGAAATTACCGAAA
1 TACCCTTGATTTACAAAATTACCAAAA
* **
53845474 TACCC-TAATTTGTAAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACCAAAA
* *
53845500 TACCCCTGATTTACAAAGTTA-CAGAAA
1 TACCCTTGATTTACAAAATTACCA-AAA
*
53845527 TACCCTTGACTTT-CTAAAAATTA-TAGAAA
1 TACCCTTGA-TTTAC--AAAATTACCA-AAA
* * **
53845556 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGATTTACAAAATTACCAAAA
53845583 TACCCTT
1 TACCCTT
53845590 AGTTTGTAGA
Statistics
Matches: 181, Mismatches: 34, Indels: 18
0.78 0.15 0.08
Matches are distributed among these distances:
26 25 0.14
27 130 0.72
28 7 0.04
29 19 0.10
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (27 bp):
TACCCTTGATTTACAAAATTACCAAAA
Found at i:53845424 original size:54 final size:54
Alignment explanation
Indices: 53845366--53845504 Score: 165
Period size: 54 Copynumber: 2.6 Consensus size: 54
53845356 ATTACTGTTT
* * *
53845366 TACCCTCGATTTACAAAATTACTAAAATACCCTTAGTTTGTAAAAGTACCAAAA
1 TACCCTCAATTTATAAAATTACCAAAATACCCTTAGTTTGTAAAAGTACCAAAA
* * * * * *
53845420 TACCC-CTAGTTTTTAAAATTACCAAAATACCCTTGGTTTGTGAAATTACCGAAA
1 TACCCTC-AATTTATAAAATTACCAAAATACCCTTAGTTTGTAAAAGTACCAAAA
*
53845474 TACCCT-AATTTGTAAAATTACCAAAATACCC
1 TACCCTCAATTTATAAAATTACCAAAATACCC
53845505 CTGATTTACA
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
53 24 0.33
54 48 0.67
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.31
Consensus pattern (54 bp):
TACCCTCAATTTATAAAATTACCAAAATACCCTTAGTTTGTAAAAGTACCAAAA
Found at i:53845528 original size:80 final size:81
Alignment explanation
Indices: 53845381--53845534 Score: 208
Period size: 80 Copynumber: 1.9 Consensus size: 81
53845371 TCGATTTACA
* * *
53845381 AAATTACTAAAATACCCTTAGTTTGTAAAAGTACCAAAATACCCCTAGTTTTTAAAATTACCAAA
1 AAATTACCAAAATACCCTTAATTTGTAAAAGTACCAAAATACCCCTAGTATTTAAAATTACCAAA
53845446 ATACCCTTGGTTTGTG
66 ATACCCTTGGTTTGTG
* *
53845462 AAATTACCGAAATACCC-TAATTTGTAAAATTACCAAAATACCCCT-G-ATTTACAAAGTTA-CA
1 AAATTACCAAAATACCCTTAATTTGTAAAAGTACCAAAATACCCCTAGTATTTA-AAA-TTACCA
53845523 GAAATACCCTTG
64 -AAATACCCTTG
53845535 ACTTTCTAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
78 4 0.06
79 6 0.09
80 40 0.62
81 15 0.23
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (81 bp):
AAATTACCAAAATACCCTTAATTTGTAAAAGTACCAAAATACCCCTAGTATTTAAAATTACCAAA
ATACCCTTGGTTTGTG
Found at i:53845594 original size:27 final size:27
Alignment explanation
Indices: 53845375--53845594 Score: 144
Period size: 27 Copynumber: 8.1 Consensus size: 27
53845365 TTACCCTCGA
*
53845375 TTTACAAAATTACTAAAATACCCTTAG
1 TTTACAAAATTACCAAAATACCCTTAG
** * *
53845402 TTTGTAAAAGTACCAAAATACCCCTAG
1 TTTACAAAATTACCAAAATACCCTTAG
** *
53845429 TTTTTAAAATTACCAAAATACCCTTGG
1 TTTACAAAATTACCAAAATACCCTTAG
*** * *
53845456 TTTGTGAAATTACCGAAATACCC-TAA
1 TTTACAAAATTACCAAAATACCCTTAG
** *
53845482 TTTGTAAAATTACCAAAATACCCCT-G
1 TTTACAAAATTACCAAAATACCCTTAG
* *
53845508 ATTTACAAAGTTA-CAGAAATACCCTTGAC
1 -TTTACAAAATTACCA-AAATACCCTT-AG
* * *
53845537 TTT-CTAAAAATTA-TAGAAATACCATTGG
1 TTTAC--AAAATTACCA-AAATACCCTTAG
**
53845565 TTTACAAAATTACTGAAATACCCTTAG
1 TTTACAAAATTACCAAAATACCCTTAG
53845592 TTT
1 TTT
53845595 GTAGATTTAC
Statistics
Matches: 154, Mismatches: 30, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
26 24 0.16
27 105 0.68
28 7 0.05
29 18 0.12
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.33
Consensus pattern (27 bp):
TTTACAAAATTACCAAAATACCCTTAG
Found at i:53845712 original size:27 final size:27
Alignment explanation
Indices: 53845635--53845712 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
53845625 AAATGACTAA
* *
53845635 AATACCCCTAT-TAGGTAAAAAGACCGT
1 AATACCCCTGTAT-GGTAAAATGACCGT
* *
53845662 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTATGGTAAAATGACCGT
53845689 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCTGTATGGTAAAATGAC
53845713 GAATATGCCC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 1 0.02
27 40 0.95
28 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTATGGTAAAATGACCGT
Found at i:53846889 original size:25 final size:25
Alignment explanation
Indices: 53846860--53846907 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
53846850 TTATAACATG
* * *
53846860 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
53846885 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
53846908 GTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:53846958 original size:9 final size:9
Alignment explanation
Indices: 53846946--53847002 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
53846936 TTTGATAAAC
53846946 ATGATATGT
1 ATGATATGT
*
53846955 ATGATATGCAC
1 ATGATATG--T
*
53846966 ATGACATGT
1 ATGATATGT
*
53846975 ATGATATGCAC
1 ATGATATG--T
53846986 ATGATATGT
1 ATGATATGT
53846995 ATGATATG
1 ATGATATG
53847003 CACACGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:53846969 original size:20 final size:20
Alignment explanation
Indices: 53846944--53847006 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
53846934 ATTTTGATAA
53846944 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
53846964 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
53846984 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
53847004 ACA
1 ACA
53847007 CGAGATGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:53847116 original size:24 final size:23
Alignment explanation
Indices: 53847060--53847226 Score: 228
Period size: 24 Copynumber: 7.0 Consensus size: 23
53847050 GAGGAAGTGA
53847060 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
53847083 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
53847106 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
53847130 CAAAAGGGCTTACGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
53847154 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
53847177 AAAAAGGGCTTTTGCCCCAGTTATT
1 -AAAAGGGCTTATGCCCCAGTTA-T
*
53847202 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
53847226 A
1 A
53847227 TGATAAAGCA
Statistics
Matches: 130, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
23 43 0.33
24 76 0.58
25 11 0.08
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:53847129 original size:47 final size:47
Alignment explanation
Indices: 53847060--53847226 Score: 230
Period size: 47 Copynumber: 3.5 Consensus size: 47
53847050 GAGGAAGTGA
*
53847060 AAAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTAT
* *
53847106 CAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTACGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTAT
* *
53847154 TAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTA-T
*
53847202 AAAAGAGGC-TAGGCCTCCAGTTATA
1 AAAAG-GGCTTATGCC-CCAGTTATA
53847227 TGATAAAGCA
Statistics
Matches: 108, Mismatches: 8, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
47 65 0.60
48 31 0.29
49 12 0.11
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTAT
Found at i:53847176 original size:71 final size:71
Alignment explanation
Indices: 53847060--53847225 Score: 262
Period size: 71 Copynumber: 2.3 Consensus size: 71
53847050 GAGGAAGTGA
* *
53847060 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
1 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCA
53847125 GTTATC
66 GTTATC
*
53847131 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTTTGCCCCA
1 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCA
*
53847196 GTTATT
66 GTTATC
*
53847202 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTACGCC-CCAGTTAT
53847226 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
71 77 0.88
72 11 0.12
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.27
Consensus pattern (71 bp):
AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCA
GTTATC
Found at i:53847454 original size:31 final size:31
Alignment explanation
Indices: 53847419--53847482 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
53847409 CGTTTACCGT
*
53847419 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
53847450 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
53847481 AA
1 AA
53847483 TATGAAAGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:53857512 original size:46 final size:46
Alignment explanation
Indices: 53857445--53857573 Score: 231
Period size: 46 Copynumber: 2.8 Consensus size: 46
53857435 TGTAACCCGC
* * *
53857445 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
53857491 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
53857537 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
53857574 TGCCCAAATA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 80 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:53863359 original size:12 final size:13
Alignment explanation
Indices: 53863344--53863492 Score: 121
Period size: 12 Copynumber: 12.4 Consensus size: 13
53863334 AATCTGAATA
53863344 AGAATCAGTAA-C
1 AGAATCAGTAATC
53863356 AGAATCAG-AATC
1 AGAATCAGTAATC
*
53863368 AGAATCAGT-ATT
1 AGAATCAGTAATC
53863380 AGTAA-CAG--ATC
1 AG-AATCAGTAATC
53863391 AGAATCAG-AATC
1 AGAATCAGTAATC
53863403 AGAATCAGTAA-C
1 AGAATCAGTAATC
*
53863415 AGAATCA-AAATC
1 AGAATCAGTAATC
*
53863427 AGAATCAGT-ATT
1 AGAATCAGTAATC
53863439 AGTAA-CAG-AATC
1 AG-AATCAGTAATC
53863451 AGAATCAG-AATC
1 AGAATCAGTAATC
* *
53863463 AGAATTAGGTGA-C
1 AGAATCA-GTAATC
53863476 AGAATCA-TAATC
1 AGAATCAGTAATC
53863488 AGAAT
1 AGAAT
53863493 GTGAATACAA
Statistics
Matches: 113, Mismatches: 10, Indels: 28
0.75 0.07 0.19
Matches are distributed among these distances:
10 2 0.02
11 15 0.13
12 81 0.72
13 14 0.12
14 1 0.01
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (13 bp):
AGAATCAGTAATC
Found at i:53863364 original size:6 final size:6
Alignment explanation
Indices: 53863332--53863467 Score: 138
Period size: 6 Copynumber: 22.8 Consensus size: 6
53863322 AACCAAAATG
* * * *
53863332 AGAATC TGAATA AGAATC AGTAA-C AGAATC AGAATC AGAATC AGTATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC
*
53863380 AGTAA-C AG-ATC AGAATC AGAATC AGAATC AGTAA-C AGAATC AAAATC
1 AG-AATC AGAATC AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC
* *
53863427 AGAATC AGTATT AGTAA-C AGAATC AGAATC AGAATC AGAAT
1 AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGAAT
53863468 TAGGTGACAG
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
4 1 0.01
5 9 0.08
6 91 0.85
7 6 0.06
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.21
Consensus pattern (6 bp):
AGAATC
Found at i:53863366 original size:30 final size:30
Alignment explanation
Indices: 53863332--53863492 Score: 225
Period size: 30 Copynumber: 5.4 Consensus size: 30
53863322 AACCAAAATG
* * *
53863332 AGAATCTGAATAAGAATCAGTAACAGAATC
1 AGAATCAGAATCAGAATTAGTAACAGAATC
*
53863362 AGAATCAGAATCAGTATTAGTAACAG-ATC
1 AGAATCAGAATCAGAATTAGTAACAGAATC
*
53863391 AGAATCAGAATCAGAATCAGTAACAGAATC
1 AGAATCAGAATCAGAATTAGTAACAGAATC
* *
53863421 AAAATCAGAATCAGTATTAGTAACAGAATC
1 AGAATCAGAATCAGAATTAGTAACAGAATC
*
53863451 AGAATCAGAATCAGAATTAGGTGACAGAATC
1 AGAATCAGAATCAGAATTA-GTAACAGAATC
*
53863482 ATAATCAGAAT
1 AGAATCAGAAT
53863493 GTGAATACAA
Statistics
Matches: 116, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
29 27 0.23
30 69 0.59
31 20 0.17
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (30 bp):
AGAATCAGAATCAGAATTAGTAACAGAATC
Found at i:53863659 original size:27 final size:26
Alignment explanation
Indices: 53863610--53863691 Score: 83
Period size: 27 Copynumber: 3.1 Consensus size: 26
53863600 AGCATGGCTG
* ** *
53863610 CCAGAACAGATATCGTGATAGAGTCA
1 CCAGAACAGATATTGTGGCAGAGCCA
*
53863636 CTAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATTGTGGCAGAGCCA
* *
53863663 CCAGAATCAGATAATGTGGCAAAGCCA
1 CCAGAA-CAGATATTGTGGCAGAGCCA
53863690 CC
1 CC
53863692 TAACAGAATA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
26 5 0.11
27 41 0.89
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATATTGTGGCAGAGCCA
Found at i:53863896 original size:22 final size:22
Alignment explanation
Indices: 53863848--53863906 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
53863838 GTAAATACGT
*
53863848 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
53863870 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
53863892 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
53863907 TAATAACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:53864033 original size:27 final size:26
Alignment explanation
Indices: 53863994--53864076 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
53863984 TCGATCGGTC
*
53863994 AACAGATATTGTGACAGAGTCACCAG
1 AACAGATATTGTGACAGAGCCACCAG
53864020 ATACAGATATTGTGACAGAGCCACCAG
1 A-ACAGATATTGTGACAGAGCCACCAG
* * *
53864047 AACAGATATTTATGGCATAGCCACCAG
1 AACAGATA-TTGTGACAGAGCCACCAG
53864074 AAC
1 AAC
53864077 GCTTCCTCCG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 8 0.16
27 43 0.84
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (26 bp):
AACAGATATTGTGACAGAGCCACCAG
Found at i:53864305 original size:27 final size:27
Alignment explanation
Indices: 53864275--53864415 Score: 169
Period size: 27 Copynumber: 5.3 Consensus size: 27
53864265 GGGGAAAAAT
* * * *
53864275 GGTAATTTTACCCCACAAAGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
53864302 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
53864329 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
53864356 GAT-ATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
53864382 GGTAATTCTACCCTAC-AGGAGTATTCC
1 GGTAATTCTACCCTACAAGG-GTATTTC
*
53864409 AGTAATT
1 GGTAATT
53864416 TCACAATTGA
Statistics
Matches: 98, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
26 25 0.26
27 73 0.74
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:53864322 original size:54 final size:53
Alignment explanation
Indices: 53864264--53864394 Score: 122
Period size: 53 Copynumber: 2.5 Consensus size: 53
53864254 TTAACACCCT
*
53864264 AGGGGAAAAAT-GGTAATTT-TACCCCACAAAGGTATCTCGGTAATTCTACCCTAC
1 AGGGG-AAAATCGGT-ATTTCTACCCCACAAAGGTATCTCGAT-ATTCTACCCTAC
* ** * * *
53864318 AGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTCGATATTCTACCCTAC
1 AGGGGAAAATCGGTATTTCTACCCCACAAAGGTATCTCGATATTCTACCCTAC
* ** *
53864371 AGGGGTATTTCGGTAATTCTACCC
1 AGGGGAAAATCGGTATTTCTACCC
53864395 TACAGGAGTA
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
53 41 0.61
54 26 0.39
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (53 bp):
AGGGGAAAATCGGTATTTCTACCCCACAAAGGTATCTCGATATTCTACCCTAC
Found at i:53864373 original size:53 final size:54
Alignment explanation
Indices: 53864279--53864406 Score: 181
Period size: 53 Copynumber: 2.4 Consensus size: 54
53864269 AAAAATGGTA
* * * *
53864279 ATTT-TACCCCACAAAGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGGT
1 ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTCGGT
53864332 ATTTCTACCCTACAAGGGTATTTCGAT-ATTCTACCCTACAGGGGTATTTCGGT
1 ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTCGGT
*
53864385 AATTCTACCCTAC-AGGAGTATT
1 ATTTCTACCCTACAAGG-GTATT
53864407 CCAGTAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
52 3 0.04
53 47 0.69
54 18 0.26
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (54 bp):
ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTCGGT
Found at i:53864459 original size:27 final size:27
Alignment explanation
Indices: 53864424--53865007 Score: 615
Period size: 27 Copynumber: 21.3 Consensus size: 27
53864414 TTTCACAATT
** *
53864424 GAGGGTAAAACAGTAATTTTGTAAATC
1 GAGGGTAAAATGGTAATTCTGTAAATC
* * * ** *
53864451 GAGGGTAAAACGATAATTTTACAAATT
1 GAGGGTAAAATGGTAATTCTGTAAATC
* *
53864478 GAGGGTAAAACGGTAATTCTATAAATC
1 GAGGGTAAAATGGTAATTCTGTAAATC
* *
53864505 GAGGGCAAAATAGTAATTCTGTAAA-C
1 GAGGGTAAAATGGTAATTCTGTAAATC
*
53864531 TGAGGGTAAAATGGTAATGCTGTAAATC
1 -GAGGGTAAAATGGTAATTCTGTAAATC
53864559 GAGGGTAAAATGGTAATTCTGTAAA-C
1 GAGGGTAAAATGGTAATTCTGTAAATC
*
53864585 TGAGGGTAAAACGGTAATTCTGTAAATC
1 -GAGGGTAAAATGGTAATTCTGTAAATC
*** * ** *
53864613 GAGGGTAAAACAATAATTTTACAAATT
1 GAGGGTAAAATGGTAATTCTGTAAATC
*
53864640 GAGGGTAAAACGGTAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTCTGTAAATC
53864667 GAGGGTAAAATGGTAATTCTGTAAA-C
1 GAGGGTAAAATGGTAATTCTGTAAATC
*
53864693 TGAGGGTAAAACGGTAATTCTGTAAATC
1 -GAGGGTAAAATGGTAATTCTGTAAATC
53864721 GAGGGTAAAATAGGGTAAAATGGTAATACTGTAAATC
1 GAGGGTAAAAT--GGT--AA---T--T-CTGTAAATC
53864758 GAGGGTAAAATGGTAATTCTGTAAA-C
1 GAGGGTAAAATGGTAATTCTGTAAATC
* *
53864784 TGAGGGTAAAACT-GTAATTCTATAAATT
1 -GAGGGTAAAA-TGGTAATTCTGTAAATC
* * ** *
53864812 GAGGGTAAAACGGTAATTTTACAAATT
1 GAGGGTAAAATGGTAATTCTGTAAATC
53864839 GAGGGTAAAATGGTAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTCTGTAAATC
53864866 GAGGGTAAAATGGTAATTCTGTAAA-C
1 GAGGGTAAAATGGTAATTCTGTAAATC
* *
53864892 TGAGGGTAAAACGGTAATTCTATAAATC
1 -GAGGGTAAAATGGTAATTCTGTAAATC
* *
53864920 GAGGGTAAAATAGTAATTCTATAAA-C
1 GAGGGTAAAATGGTAATTCTGTAAATC
*
53864946 TGAGGGTAAAATGGTAATGCTGTAAATC
1 -GAGGGTAAAATGGTAATTCTGTAAATC
* *
53864974 AAGGGTAAAATGGTAATTCTATAAATC
1 GAGGGTAAAATGGTAATTCTGTAAATC
*
53865001 GGGGGTA
1 GAGGGTA
53865008 CTTTGGTAAT
Statistics
Matches: 478, Mismatches: 55, Indels: 48
0.82 0.09 0.08
Matches are distributed among these distances:
26 6 0.01
27 432 0.90
28 7 0.01
29 3 0.01
30 1 0.00
31 2 0.00
33 2 0.00
34 1 0.00
35 3 0.01
36 1 0.00
37 20 0.04
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (27 bp):
GAGGGTAAAATGGTAATTCTGTAAATC
Found at i:53864740 original size:37 final size:37
Alignment explanation
Indices: 53864695--53864768 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
53864685 CTGTAAACTG
*
53864695 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAT
1 AGGGTAAAACGGTAATACTGTAAATCGAGGGTAAAAT
*
53864732 AGGGTAAAATGGTAATACTGTAAATCGAGGGTAAAAT
1 AGGGTAAAACGGTAATACTGTAAATCGAGGGTAAAAT
53864769 GGTAATTCTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.42, C:0.07, G:0.27, T:0.24
Consensus pattern (37 bp):
AGGGTAAAACGGTAATACTGTAAATCGAGGGTAAAAT
Found at i:53864741 original size:64 final size:64
Alignment explanation
Indices: 53864668--53864794 Score: 204
Period size: 64 Copynumber: 2.0 Consensus size: 64
53864658 CTGTAAATCG
*
53864668 AGGGTAAAATGGTAATTCTGTAAA-CTGAGGGTAAAACGGTAATTCTGTAAA-TCGAGGGTAAAA
1 AGGGTAAAATGGTAATACTGTAAATC-GAGGGTAAAACGGTAATTCTGTAAACT-GAGGGTAAAA
53864731 T
64 T
*
53864732 AGGGTAAAATGGTAATACTGTAAATCGAGGGTAAAATGGTAATTCTGTAAACTGAGGGTAAAA
1 AGGGTAAAATGGTAATACTGTAAATCGAGGGTAAAACGGTAATTCTGTAAACTGAGGGTAAAA
53864795 CTGTAATTCT
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
64 57 0.97
65 2 0.03
ACGTcount: A:0.40, C:0.07, G:0.27, T:0.26
Consensus pattern (64 bp):
AGGGTAAAATGGTAATACTGTAAATCGAGGGTAAAACGGTAATTCTGTAAACTGAGGGTAAAAT
Found at i:53865196 original size:107 final size:108
Alignment explanation
Indices: 53865066--53865261 Score: 270
Period size: 107 Copynumber: 1.8 Consensus size: 108
53865056 AGGATATTTC
* * *
53865066 AGTAATTTTGCAAACTGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTTAGTAATTTTAC
1 AGTAATTTTACAAACTGAGGGTATTTCGATAATTTTACAAACCAAGGGTATTTTAGTAATTTTAC
**
53865131 AAA-TTGGGGTATTTTGGTGATTTAATAAACCAAGGGTATTCT
66 AAACCAGGGGTATTTTGGTGATTTAATAAACCAAGGGTATTCT
* * ** * *
53865173 AGTAATTTTACAAACT-AGAGGTATTTTGGTAATTTTGTAAACCAATGGTATTTTGGTAATTTTA
1 AGTAATTTTACAAACTGAG-GGTATTTCGATAATTTTACAAACCAAGGGTATTTTAGTAATTTTA
53865237 CAAACCAGGGGTATTTTGGTGATTT
65 CAAACCAGGGGTATTTTGGTGATTT
53865262 GGTAAACTAA
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
106 2 0.03
107 56 0.74
108 18 0.24
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.40
Consensus pattern (108 bp):
AGTAATTTTACAAACTGAGGGTATTTCGATAATTTTACAAACCAAGGGTATTTTAGTAATTTTAC
AAACCAGGGGTATTTTGGTGATTTAATAAACCAAGGGTATTCT
Found at i:53865241 original size:27 final size:27
Alignment explanation
Indices: 53865003--53865261 Score: 198
Period size: 27 Copynumber: 9.6 Consensus size: 27
53864993 TATAAATCGG
* ** *
53865003 GGGTACTTTGGTAATTTTACAAGTCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
** * *
53865030 GGGTATTTCAGTAATTTTACAAATCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
* ** * **
53865057 GGATATTTCAGTAATTTTGCAAACTGA
1 GGGTATTTTGGTAATTTTACAAACCAA
* * * *
53865084 GGGTATTTCGATAATTTTACAAATCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
* ***
53865111 GGGTATTTTAGTAATTTTACAAA-TTG
1 GGGTATTTTGGTAATTTTACAAACCAA
* * *
53865137 GGGTATTTTGGTGATTTAATAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
* * *
53865164 GGGTATTCTAGTAATTTTACAAA-CTA
1 GGGTATTTTGGTAATTTTACAAACCAA
**
53865190 GAGGTATTTTGGTAATTTTGTAAACCAA
1 G-GGTATTTTGGTAATTTTACAAACCAA
* *
53865218 TGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
*
53865245 GGGTATTTTGGTGATTT
1 GGGTATTTTGGTAATTT
53865262 GGTAAACTAA
Statistics
Matches: 185, Mismatches: 44, Indels: 6
0.79 0.19 0.03
Matches are distributed among these distances:
26 22 0.12
27 161 0.87
28 2 0.01
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAA
Found at i:53865250 original size:54 final size:54
Alignment explanation
Indices: 53865110--53865268 Score: 221
Period size: 54 Copynumber: 3.0 Consensus size: 54
53865100 TTACAAATCG
* *
53865110 AGGGTATTTTAGTAATTTTACAAA-TTGGGGTATTTTGGTGATTTAATAAACCA
1 AGGGTATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTGATTTAGTAAACCA
* * * *
53865163 AGGGTATTCTAGTAATTTTACAAACTAGAGGTATTTTGGTAATTTTGTAAACCA
1 AGGGTATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTGATTTAGTAAACCA
* * * *
53865217 ATGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTGATTTGGTAAAC
1 AGGGTATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTGATTTAGTAAAC
53865269 TAAAGTATTC
Statistics
Matches: 92, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
53 23 0.25
54 69 0.75
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (54 bp):
AGGGTATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTGATTTAGTAAACCA
Found at i:53867245 original size:15 final size:15
Alignment explanation
Indices: 53867225--53867254 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53867215 ACATGGTATC
53867225 CTATCTCGGATTTCT
1 CTATCTCGGATTTCT
*
53867240 CTATCTTGGATTTCT
1 CTATCTCGGATTTCT
53867255 TTACATGCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.13, T:0.50
Consensus pattern (15 bp):
CTATCTCGGATTTCT
Found at i:53874472 original size:120 final size:120
Alignment explanation
Indices: 53874263--53874488 Score: 266
Period size: 120 Copynumber: 1.9 Consensus size: 120
53874253 ACTACTCGTT
53874263 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAGATGCCTTCGGGACTTAACCCGA
1 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAGATGCCTTCGGGACTTAACCCGA
* * *
53874328 ATTTAGTAACTCATACAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCACA
66 ATATAGTAACTCACACAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCACA
* * **
53874383 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAGTAACTCGCAC-GAATGCCTTC-GGATCTTAGT
1 CAAATGCCTTCGGGA-CATAGCCCGG-TTATAGTAACTCGCACAG-ATGCCTTCGGGA-CTTAAC
* * *
53874444 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
62 CCGAATATAGTAACTCA-CACAAATGCCTTCGGGACTTAGCCCGGA
53874489 CATCATTCGA
Statistics
Matches: 90, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
119 7 0.08
120 73 0.81
121 10 0.11
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAGATGCCTTCGGGACTTAACCCGA
ATATAGTAACTCACACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACA
Found at i:53874488 original size:40 final size:41
Alignment explanation
Indices: 53874263--53874488 Score: 218
Period size: 40 Copynumber: 5.6 Consensus size: 41
53874253 ACTACTCGTT
* *
53874263 CAAATGCCTTCGGGA-CATAGCCCGG-TTATAGTAAC-TCGCA
1 CAAATGCCTTC-GGATCTTAGCCCGGATT-TAGTAACTTAGCA
* * * * *
53874303 CAGATGCCTTCGGGA-CTTAACCCGAATTTAGTAACTCA-TA
1 CAAATGCCTTC-GGATCTTAGCCCGGATTTAGTAACTTAGCA
* *
53874343 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCA-CA
1 CAAATGCCTTCGGATCTTAGCCCGGATTTAGTAACTTAGCA
* *
53874383 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAAC-TCGCA
1 CAAATGCCTTCGGATCTTAGCCCGGATTTAGTAACTTAGCA
* * * *
53874423 CGAATGCCTTCGGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGATCTTAGCCCGGATTTAGTAACTTAGCA
53874464 CAAA-GCCTTCGGGA-CTTAGCCCGGA
1 CAAATGCCTTC-GGATCTTAGCCCGGA
53874489 CATCATTCGA
Statistics
Matches: 160, Mismatches: 20, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
39 3 0.02
40 145 0.91
41 12 0.08
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (41 bp):
CAAATGCCTTCGGATCTTAGCCCGGATTTAGTAACTTAGCA
Found at i:53874488 original size:80 final size:80
Alignment explanation
Indices: 53874263--53874488 Score: 262
Period size: 80 Copynumber: 2.8 Consensus size: 80
53874253 ACTACTCGTT
* * * * * *
53874263 CAAATGCCTTCGGGA-CATAGCCCGGTTATAGTAAC-TCGCACAGATGCCTTCGGGACTTAACCC
1 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTAACTTAGCACA-AAGCCTTCGGGACTTAGCCC
* *
53874326 GAATTTAGTAACTCATA
64 GGATTTAGTAACTCACA
* * *
53874343 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCA-CACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGATCTTAGTCCGGATATAGTAACTTAGCACAAA-GCCTTCGGGA-CTTAGCCC
*
53874406 GGATTTAGTAACTCGCA
64 GGATTTAGTAACTCACA
* *
53874423 CGAATGCCTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGATCTTAGTCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGG
53874488 A
66 A
53874489 CATCATTCGA
Statistics
Matches: 123, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
79 7 0.06
80 107 0.87
81 9 0.07
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (80 bp):
CAAATGCCTTCGGATCTTAGTCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGG
ATTTAGTAACTCACA
Found at i:53877364 original size:22 final size:22
Alignment explanation
Indices: 53877331--53877384 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
53877321 TTTATGGCCT
53877331 TTAA-CCGTCCTGTCTACGGAG
1 TTAAGCCGTCCTGTCTACGGAG
* *
53877352 TTGAGTCGTCCTGTCTACGGAG
1 TTAAGCCGTCCTGTCTACGGAG
53877374 TTAAGCCGTCC
1 TTAAGCCGTCC
53877385 CGTTGACTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.30
Consensus pattern (22 bp):
TTAAGCCGTCCTGTCTACGGAG
Found at i:53880699 original size:30 final size:30
Alignment explanation
Indices: 53880658--53880721 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
53880648 AATCAGAAGT
*
53880658 TTTGGCACTAAGTGGGCGATTTAAACTAGC
1 TTTGCCACTAAGTGGGCGATTTAAACTAGC
* *
53880688 TTTGCCACTAAGTGTGCGATTTACACTAGC
1 TTTGCCACTAAGTGGGCGATTTAAACTAGC
53880718 TTTG
1 TTTG
53880722 GCTACTTGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.34
Consensus pattern (30 bp):
TTTGCCACTAAGTGGGCGATTTAAACTAGC
Found at i:53888653 original size:52 final size:52
Alignment explanation
Indices: 53888575--53888680 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 52
53888565 AAGGAGAAGG
53888575 TAAGTTTGGTGAGTTCATGATTTGAGAATGAATGACGTTTTTAATATAATCT
1 TAAGTTTGGTGAGTTCATGATTTGAGAATGAATGACGTTTTTAATATAATCT
* *
53888627 TAAGTTTGGTGAGTTCATGATTTGAGAATGAATGATGTTTTTGATATAATCT
1 TAAGTTTGGTGAGTTCATGATTTGAGAATGAATGACGTTTTTAATATAATCT
53888679 TA
1 TA
53888681 CATTATGTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.30, C:0.05, G:0.22, T:0.43
Consensus pattern (52 bp):
TAAGTTTGGTGAGTTCATGATTTGAGAATGAATGACGTTTTTAATATAATCT
Found at i:53894336 original size:30 final size:28
Alignment explanation
Indices: 53894296--53894396 Score: 103
Period size: 28 Copynumber: 3.5 Consensus size: 28
53894286 GACAAGATTG
* * *
53894296 GCACTGAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--AATTATACA
* *
53894326 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAATTATACA
* * *
53894354 GCACTAAGTGTGCGAGCTGAATATATATA
1 GCACTAAGTGTGCGAGTTTAAT-TATACA
53894383 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
53894397 GATTCACTAT
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
28 25 0.40
29 20 0.32
30 17 0.27
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATACA
Found at i:53894360 original size:28 final size:29
Alignment explanation
Indices: 53894325--53894396 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 29
53894315 AAAATTGTAC
*
53894325 AGCACTAAGTGTGCGAGTTTG-AT-TATAT
1 AGCACTAAGTGTGCGAG-CTGAATATATAT
53894353 AGCACTAAGTGTGCGAGCTGAATATATAT
1 AGCACTAAGTGTGCGAGCTGAATATATAT
53894382 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
53894397 GATTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 2 0.05
28 19 0.46
29 20 0.49
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (29 bp):
AGCACTAAGTGTGCGAGCTGAATATATAT
Found at i:53899792 original size:47 final size:46
Alignment explanation
Indices: 53899724--53899940 Score: 165
Period size: 46 Copynumber: 4.6 Consensus size: 46
53899714 ATTGAGGGCT
*
53899724 AGTGTAAGACATGTCTGGGACATGCATCAGCCA-TATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCATTA-GATGAGAGCC
* * * * *
53899770 AGTGTAAGACCATGTCTAGGACACGGCATC-GGCATTGAGATGAGTGCT
1 AGTGTAAGA-CATGTCTGGGACA-TGCATCAGCCATT-AGATGAGAGCC
* * *
53899818 AGTGTAAGACATGTCCGGGACATGCATCAGCC-TCGAGACAT-A-AGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAT-TAG--ATGAGAGCC
* ** * ** * *
53899864 AGTGTAAGACATGTTTGGGACATGCATTGGCTACGAGATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCATTAGATGAGAGCC
53899910 AGTGTAAGACCATGTCTGGGACATGGCATCA
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCA
53899941 ACACAAGACA
Statistics
Matches: 135, Mismatches: 23, Indels: 24
0.74 0.13 0.13
Matches are distributed among these distances:
44 2 0.01
45 1 0.01
46 61 0.45
47 42 0.31
48 28 0.21
49 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCATTAGATGAGAGCC
Found at i:53899979 original size:140 final size:140
Alignment explanation
Indices: 53899721--53899981 Score: 319
Period size: 140 Copynumber: 1.9 Consensus size: 140
53899711 GTTATTGAGG
* *
53899721 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCATATTATGAGAGCCAGTGTAAGACCATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCAGATGATGAGAGCCAGTGTAAGACCATGTC
** ** ** *
53899786 TAGGACACGGCATCGGCATTGAGATGAGTGCTAGTGTAAGACATGTCCGGGACATGCATCAGCCT
66 TAGGACACGGCATCAACATCAAGACAAGTGCTAGTGTAAGACATGTCCAGGACATGCATCAGCCT
53899851 CGAGACATAA
131 CGAGACATAA
* ** * * *
53899861 GCTAGTGTAAGACATGTTTGGGACATGCATTGGCTACGA-GATGATAGTCAGTGTAAGACCATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCA-GATGATGAGAGCCAGTGTAAGACCATGT
* * * *
53899925 CTGGGACATGGCATCAACA-CAAGACAAGTGCTAGTGTAAGACCGTGTCTAGGACATG
65 CTAGGACACGGCATCAACATCAAGACAAGTGCTAGTGTAAGA-CATGTCCAGGACATG
53899982 GCAGCGGCAC
Statistics
Matches: 100, Mismatches: 19, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
139 18 0.18
140 81 0.81
141 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (140 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCAGATGATGAGAGCCAGTGTAAGACCATGTC
TAGGACACGGCATCAACATCAAGACAAGTGCTAGTGTAAGACATGTCCAGGACATGCATCAGCCT
CGAGACATAA
Found at i:53902551 original size:24 final size:24
Alignment explanation
Indices: 53902486--53902552 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
53902476 GGAAGCTCAT
* *
53902486 AAGAGCTATAATTGGGAAGTTGACA
1 AAGAACTAT-ATTGGGAAGTTCACA
*
53902511 AAGAACTATATCGGGAAGTTCACA
1 AAGAACTATATTGGGAAGTTCACA
*
53902535 AAGAACTATATTAGGAAG
1 AAGAACTATATTGGGAAG
53902553 CTCTGGATAG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
24 29 0.78
25 8 0.22
ACGTcount: A:0.43, C:0.10, G:0.24, T:0.22
Consensus pattern (24 bp):
AAGAACTATATTGGGAAGTTCACA
Found at i:53904780 original size:50 final size:50
Alignment explanation
Indices: 53904390--53904783 Score: 400
Period size: 50 Copynumber: 7.8 Consensus size: 50
53904380 ATTGTGAGAA
* *
53904390 CACATGTGTAGTACTATGTGCAGGCTACTATGTGT-CTA-ATACGGTTTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATA--G--TTAGGT
* * * *
53904442 CA-AGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTATATTGTTAGGT
1 CACA-TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGT
* * * * * *
53904492 CGCATGTGTAGTACTAAGTACAGGCTATTATGCGTACCAGATAGCTTCGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAG-TTAGGT
** * * *
53904543 CACATGTGTAGTACTAAGTGCAGGCTACTACATATATCAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGT
* * * * * *
53904593 CACGTGTGTAGTACCAAGTGCAGGCTATTATGT-TACCCGATAGCTTCGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAG-TTAGGT
* * * *
53904643 CACGTGTGTAGTACTAAGTGCAGGCTACTGTGTGTATCAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGT
* * *
53904693 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGT
* * *
53904743 CACATATGTAGTACTAAGTGCTGGCTACTATGCGTACCAGA
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGA
53904784 GAGCTTCGGT
Statistics
Matches: 284, Mismatches: 51, Indels: 16
0.81 0.15 0.05
Matches are distributed among these distances:
49 7 0.02
50 192 0.68
51 48 0.17
52 32 0.11
53 3 0.01
54 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGT
Found at i:53909609 original size:190 final size:190
Alignment explanation
Indices: 53909286--53909663 Score: 747
Period size: 190 Copynumber: 2.0 Consensus size: 190
53909276 AGGTAATGTT
*
53909286 GCCAAATTTTCAATGCAAACACAATGGTTGCTAATTTAAGATCATGTATTGGGTAATTCTTCTCA
1 GCCAAATTTTCAATGCAAACACAATAGTTGCTAATTTAAGATCATGTATTGGGTAATTCTTCTCA
53909351 TGTGGTTTTAAGCATAGGCTATTACTTTACCTTCTTGCATCAATACACAACCTAAACCATTTAAT
66 TGTGGTTTTAAGCATAGGCTATTACTTTACCTTCTTGCATCAATACACAACCTAAACCATTTAAT
53909416 GATGCATCACTATAAATTATAAATTCCTTACTCGATTCAGGCTGAACTAACATGGGTGTC
131 GATGCATCACTATAAATTATAAATTCCTTACTCGATTCAGGCTGAACTAACATGGGTGTC
53909476 GCCAAATTTTCAATGCAAACACAATAGTTGCTAATTTAAGATCATGTATTGGGTAATTCTTCTCA
1 GCCAAATTTTCAATGCAAACACAATAGTTGCTAATTTAAGATCATGTATTGGGTAATTCTTCTCA
53909541 TGTGGTTTTAAGCATAGGCTATTACTTTACCTTCTTGCATCAATACACAACCTAAACCATTTAAT
66 TGTGGTTTTAAGCATAGGCTATTACTTTACCTTCTTGCATCAATACACAACCTAAACCATTTAAT
53909606 GATGCATCACTATAAATTATAAATTCCTTACTCGATTCAGGCTGAACTAACATGGGTG
131 GATGCATCACTATAAATTATAAATTCCTTACTCGATTCAGGCTGAACTAACATGGGTG
53909664 CTTCAATCAA
Statistics
Matches: 187, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
190 187 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (190 bp):
GCCAAATTTTCAATGCAAACACAATAGTTGCTAATTTAAGATCATGTATTGGGTAATTCTTCTCA
TGTGGTTTTAAGCATAGGCTATTACTTTACCTTCTTGCATCAATACACAACCTAAACCATTTAAT
GATGCATCACTATAAATTATAAATTCCTTACTCGATTCAGGCTGAACTAACATGGGTGTC
Found at i:53916562 original size:13 final size:13
Alignment explanation
Indices: 53916526--53916563 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
53916516 GTAAAAAAGG
*
53916526 ATATTTGAAACGA
1 ATATTTGAAATGA
53916539 ATATTTGAAATGA
1 ATATTTGAAATGA
*
53916552 ATATGTGAAATG
1 ATATTTGAAATG
53916564 TTAAATGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.34
Consensus pattern (13 bp):
ATATTTGAAATGA
Found at i:53918425 original size:2 final size:2
Alignment explanation
Indices: 53918418--53918455 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
53918408 TGCAATCGCC
53918418 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53918456 CTGTTCTGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53928828 original size:27 final size:27
Alignment explanation
Indices: 53928798--53928850 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
53928788 AGAAAATAAT
*
53928798 CGTAATGCCCCTATAGGGAAAAATGAC
1 CGTAATACCCCTATAGGGAAAAATGAC
* *
53928825 CGTAATACCCCTATATGGTAAAATGA
1 CGTAATACCCCTATAGGGAAAAATGA
53928851 TGATTATGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.23
Consensus pattern (27 bp):
CGTAATACCCCTATAGGGAAAAATGAC
Found at i:53938699 original size:46 final size:44
Alignment explanation
Indices: 53938596--53938707 Score: 154
Period size: 46 Copynumber: 2.5 Consensus size: 44
53938586 TGCCGATGCC
*
53938596 ATGTCCCAGACATGGTCTTACACTGGCACATTTCATGGTAGATGC
1 ATGTCCCAGACAT-GTCTTACACTGGCACATTTCATGGTAGATGA
* *
53938641 ATGTCCCAGACATGTCTTACACTGGCTTACATCTTGA-GGTCGATGA
1 ATGTCCCAGACATGTCTTACACTGGC--ACAT-TTCATGGTAGATGA
53938687 ATGTCCCAGACATGTCTTACA
1 ATGTCCCAGACATGTCTTACA
53938708 TTAGCACTCG
Statistics
Matches: 61, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
44 13 0.21
45 13 0.21
46 32 0.52
47 3 0.05
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (44 bp):
ATGTCCCAGACATGTCTTACACTGGCACATTTCATGGTAGATGA
Found at i:53939188 original size:30 final size:30
Alignment explanation
Indices: 53939152--53939227 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
53939142 TCATAGTTGG
*
53939152 GCAAAATGACCAATTTTCCCCTGGACTTTT
1 GCAAAATGACCAATTTTCCCCTAGACTTTT
* ***
53939182 GCAAAATAACCAATACGCCCCTAGACTTTT
1 GCAAAATGACCAATTTTCCCCTAGACTTTT
*
53939212 ACAAAATGACC-ATTTT
1 GCAAAATGACCAATTTT
53939228 ACACCTAAGC
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
29 2 0.06
30 34 0.94
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (30 bp):
GCAAAATGACCAATTTTCCCCTAGACTTTT
Found at i:53939873 original size:20 final size:20
Alignment explanation
Indices: 53939848--53939892 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
53939838 AAACTTGACA
53939848 ACTTTAGCTATCAAATTAGG
1 ACTTTAGCTATCAAATTAGG
53939868 ACTTTAGCTATCAAATTAGG
1 ACTTTAGCTATCAAATTAGG
53939888 ACTTT
1 ACTTT
53939893 TGCACTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (20 bp):
ACTTTAGCTATCAAATTAGG
Found at i:53946244 original size:40 final size:40
Alignment explanation
Indices: 53946200--53946387 Score: 270
Period size: 40 Copynumber: 4.7 Consensus size: 40
53946190 ATAACCACAA
* *
53946200 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* *
53946240 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
53946280 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* * *
53946320 GCACAAATGCCTTTGGGTCTTAACCCGGATATAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAT-AGCAACTC
* * *
53946360 GCATAAATGCCTTCGGGACTTAGCCCGG
1 GCACAAATGCCTTCGGGTCTTAACCCGG
53946388 GTATCATTCA
Statistics
Matches: 134, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 132 0.99
41 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
Found at i:53946303 original size:80 final size:79
Alignment explanation
Indices: 53946180--53946391 Score: 309
Period size: 80 Copynumber: 2.7 Consensus size: 79
53946170 TCTTCGAAAT
* *
53946180 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
53946244 AAATGCCTTCGGGTC
65 AAATGCCTTCGGGTC
* *
53946259 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCAC
1 TTAGCCCGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
*
53946324 AAATGCCTTTGGGTC
65 AAATGCCTTCGGGTC
* * * *
53946339 TTAACCCGGATATAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGGGTAT
1 TTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTAT
53946392 CATTCAATTG
Statistics
Matches: 119, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
79 5 0.04
80 113 0.95
81 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (79 bp):
TTAGCCCGGATATAACACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACA
AATGCCTTCGGGTC
Found at i:53949721 original size:46 final size:45
Alignment explanation
Indices: 53949666--53949833 Score: 174
Period size: 46 Copynumber: 3.6 Consensus size: 45
53949656 TTTCATGGTT
*
53949666 GATGCATGTCCCAGACATGCCTTACACTGGCTTACATCTTGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTT-CATCTTGAGGCC
* * * * * * *
53949712 GATGCATGTCCCAAACATTTCTTACACTAGCACTCGTCTTAATGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGC-TTCATCTTGAGGCC
* ** *
53949758 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TCATCTTGAGGCC
*
53949806 GATGCATGTCCCAGATATGTCTTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
53949834 AGCTCACACA
Statistics
Matches: 97, Mismatches: 21, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
46 50 0.52
47 25 0.26
48 22 0.23
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTTCATCTTGAGGCC
Found at i:53949806 original size:94 final size:92
Alignment explanation
Indices: 53949666--53949836 Score: 236
Period size: 94 Copynumber: 1.8 Consensus size: 92
53949656 TTTCATGGTT
** *
53949666 GATGCATGTCCCAGACATGCCTTACACTGGCTTACATCTTGAGGCCGATGCATGTCCCAAACATT
1 GATGCATGTCCCAGACATGCCTTACACTGGCTTACATAATGAGGCCGATGCATGTCCCAAACATG
53949731 TCTTACACTAGCACTCGTCTTAATGCC
66 TCTTACACTAGCACTCGTCTTAATGCC
* * * * *
53949758 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCT-CATAATGTGGCCGATGCATGTCCCAGAT
1 GATG-CATGTCCCAGACAT-GCCTTACACTGGCT-TACATAATGAGGCCGATGCATGTCCCAAAC
53949822 ATGTCTTACACTAGC
63 ATGTCTTACACTAGC
53949837 TCACACAAGT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
92 4 0.06
93 13 0.19
94 50 0.74
95 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (92 bp):
GATGCATGTCCCAGACATGCCTTACACTGGCTTACATAATGAGGCCGATGCATGTCCCAAACATG
TCTTACACTAGCACTCGTCTTAATGCC
Found at i:53951620 original size:46 final size:46
Alignment explanation
Indices: 53951570--53951742 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
53951560 TGGTTAAGCA
*
53951570 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * *
53951616 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG
* *
53951661 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCAATTATGGATGCAAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * *
53951709 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
53951743 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 5 0.05
45 4 0.04
46 59 0.55
47 29 0.27
48 4 0.04
50 6 0.06
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:53951726 original size:93 final size:93
Alignment explanation
Indices: 53951567--53951737 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
53951557 GGATGGTTAA
* * * *
53951567 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAATTATGGATGCAAACGCCCGAACTCGTTGAGT
53951632 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
53951660 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAATTATGGATGCAAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAATTATGGATGCAAACGCCCGAACTCGTTGAGT
*
53951725 TGAGTCTGAGTTC
66 TGAGTCCGAGTTC
53951738 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAATTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:53954037 original size:28 final size:27
Alignment explanation
Indices: 53954004--53954059 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
53953994 TTAGAATACT
*
53954004 TTAGTTTACTAAAATTACCGAAATACCC
1 TTAGTTT-CTAAAAATACCGAAATACCC
* *
53954032 TTAGTTTGTAAAAATACTGAAATACCC
1 TTAGTTTCTAAAAATACCGAAATACCC
53954059 T
1 T
53954060 CGATTTGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (27 bp):
TTAGTTTCTAAAAATACCGAAATACCC
Found at i:53954043 original size:27 final size:28
Alignment explanation
Indices: 53954013--53954112 Score: 100
Period size: 27 Copynumber: 3.7 Consensus size: 28
53954003 TTTAGTTTAC
53954013 TAAAATTACCGAAATACCCTTAG-TTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
* * *
53954040 TAAAAATACTGAAATACCC-TCGATTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
** * *
53954067 TAAAATTATTGAAATA-CCTTCGACTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
53954094 TAAAATTACC-AAAGTACCC
1 TAAAATTACCGAAA-TACCC
53954113 CCGATTTACA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
26 7 0.11
27 52 0.85
28 2 0.03
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (28 bp):
TAAAATTACCGAAATACCCTTAGATTTG
Found at i:53954125 original size:27 final size:27
Alignment explanation
Indices: 53954095--53954156 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
53954085 TTCGACTTGT
53954095 AAAATTACCAAAGTACCCCCGATTTAC
1 AAAATTACCAAAGTACCCCCGATTTAC
****
53954122 AAAATTACCGTTTTACCCCCGATTTAC
1 AAAATTACCAAAGTACCCCCGATTTAC
*
53954149 ATAATTAC
1 AAAATTAC
53954157 TTTTTACCCC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.29
Consensus pattern (27 bp):
AAAATTACCAAAGTACCCCCGATTTAC
Found at i:53954155 original size:81 final size:81
Alignment explanation
Indices: 53954054--53954355 Score: 246
Period size: 81 Copynumber: 3.7 Consensus size: 81
53954044 AATACTGAAA
** * * * *
53954054 TACCCTCGATTTGTAAAATTATTGAAATACCTTCGACTTGTAAAATTACCAAAGTACCCCCGATT
1 TACCCTCGATTTACAAAATTACTGAAATACCTTCGATTTGTAAAATTACCAAATTACCCTCGATT
53954119 TACAAAATTACCGTTT
66 TACAAAATTACCGTTT
* * *** ** ** * * *** *
53954135 TACCCCCGATTTACATAATTACT-TTTTACCCCCGATTTACATAATTATCGTTTTACCCTCGACT
1 TACCCTCGATTTACAAAATTACTGAAATACCTTCGATTTGTAAAATTACCAAATTACCCTCGATT
* *
53954199 TATAGAATTACCGTTT
66 TACAAAATTACCGTTT
* *** * * **** *
53954215 TACCCTCGATTTACAGAATTACTGTTTTACCTTCGATTTATATAATTACTGTTTTACCCTTGATT
1 TACCCTCGATTTACAAAATTACTGAAATACCTTCGATTTGTAAAATTACCAAATTACCCTCGATT
*
53954280 TACAAAATTACTGTTT
66 TACAAAATTACCGTTT
* * * *
53954296 TACCCTCGATTTACAAAATTACTAAAATACCTTTGGTTTGTAAAATTACCAAAATACCCT
1 TACCCTCGATTTACAAAATTACTGAAATACCTTCGATTTGTAAAATTACCAAATTACCCT
53954356 TGGTTTGTGA
Statistics
Matches: 171, Mismatches: 49, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
80 60 0.35
81 111 0.65
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.38
Consensus pattern (81 bp):
TACCCTCGATTTACAAAATTACTGAAATACCTTCGATTTGTAAAATTACCAAATTACCCTCGATT
TACAAAATTACCGTTT
Found at i:53954167 original size:27 final size:26
Alignment explanation
Indices: 53954108--53954318 Score: 224
Period size: 27 Copynumber: 7.9 Consensus size: 26
53954098 ATTACCAAAG
* *
53954108 TACCCCCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAAAATTA-CTTTT
* *
53954135 TACCCCCGATTTACATAATTACTTTT
1 TACCCTCGATTTACAAAATTACTTTT
* * *
53954161 TACCCCCGATTTACATAATTATCGTTT
1 TACCCTCGATTTACAAAATTA-CTTTT
* * * *
53954188 TACCCTCGACTTATAGAATTACCGTTT
1 TACCCTCGATTTACAAAATTA-CTTTT
*
53954215 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACT-TTT
* * *
53954242 TACCTTCGATTTATATAATTACTGTTT
1 TACCCTCGATTTACAAAATTACT-TTT
*
53954269 TACCCTTGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACT-TTT
53954296 TACCCTCGATTTACAAAATTACT
1 TACCCTCGATTTACAAAATTACT
53954319 AAAATACCTT
Statistics
Matches: 163, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 26 0.16
27 137 0.84
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.41
Consensus pattern (26 bp):
TACCCTCGATTTACAAAATTACTTTT
Found at i:53954208 original size:107 final size:108
Alignment explanation
Indices: 53954081--53954326 Score: 289
Period size: 107 Copynumber: 2.3 Consensus size: 108
53954071 ATTATTGAAA
* *
53954081 TACCTTCGACTTGTAAAATTACCAAAGTACCCCCGATTTACAAAATTACCGTTTTACCCCCGATT
1 TACCCTCGACTTATAAAATTACCAAAGTACCCCCGATTTACAAAATTACCGTTTTACCCCCGATT
*
53954146 TACATAATTACT-TTTTACCCCCGATTTACATAATTA-TCGTTT
66 TACATAATTACTGTTTTACCCCCGATTTACAAAATTACT-GTTT
* **** * * * **
53954188 TACCCTCGACTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTACTGTTTTACCTTCGATT
1 TACCCTCGACTTATAAAATTACCAAAGTACCCCCGATTTACAAAATTACCGTTTTACCCCCGATT
* **
53954253 TATATAATTACTGTTTTACCCTTGATTTACAAAATTACTGTTT
66 TACATAATTACTGTTTTACCCCCGATTTACAAAATTACTGTTT
* * * *
53954296 TACCCTCGATTTACAAAATTACTAAAATACC
1 TACCCTCGACTTATAAAATTACCAAAGTACC
53954327 TTTGGTTTGT
Statistics
Matches: 113, Mismatches: 24, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
107 64 0.57
108 48 0.42
109 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.39
Consensus pattern (108 bp):
TACCCTCGACTTATAAAATTACCAAAGTACCCCCGATTTACAAAATTACCGTTTTACCCCCGATT
TACATAATTACTGTTTTACCCCCGATTTACAAAATTACTGTTT
Found at i:53954318 original size:54 final size:54
Alignment explanation
Indices: 53954108--53954318 Score: 273
Period size: 54 Copynumber: 3.9 Consensus size: 54
53954098 ATTACCAAAG
* * *
53954108 TACCCCCGATTTACAAAATTACCGTTTTACCCCCGATTTACATAATTACT-TTT
1 TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTACATAATTACTGTTT
* * * * * *
53954161 TACCCCCGATTTACATAATTA-TCGTTTTACCCTCGACTTATAGAATTACCGTTT
1 TACCCTCGATTTACAAAATTACT-GTTTTACCCTCGATTTACATAATTACTGTTT
* * *
53954215 TACCCTCGATTTACAGAATTACTGTTTTACCTTCGATTTATATAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTACATAATTACTGTTT
* *
53954269 TACCCTTGATTTACAAAATTACTGTTTTACCCTCGATTTACAAAATTACT
1 TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTACATAATTACT
53954319 AAAATACCTT
Statistics
Matches: 137, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
53 42 0.31
54 94 0.69
55 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.41
Consensus pattern (54 bp):
TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTACATAATTACTGTTT
Found at i:53954326 original size:27 final size:27
Alignment explanation
Indices: 53954215--53954490 Score: 117
Period size: 27 Copynumber: 10.1 Consensus size: 27
53954205 ATTACCGTTT
* ****
53954215 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTAAAA
* * * ****
53954242 TACCTTCGATTTATATAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTAAAA
* ****
53954269 TACCCTTGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTAAAA
53954296 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* * * ** *
53954323 TACCTTTGGTTTGTAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* * *** *
53954350 TACCCTTGGTTTGTGAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* ** *
53954377 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
*
53954404 TACCC-CTGATTTACAAAGTTAC-AGAAA
1 TACCCTC-GATTTACAAAATTACTA-AAA
* * *
53954431 CACCCTTGACTTTATAAAAATTA-TAGAAA
1 TACCCTCGA-TTTA-CAAAATTACTA-AAA
* * * *
53954460 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTCGATTTACAAAATTACTAAAA
53954487 TACC
1 TACC
53954491 TTTGGTTTGT
Statistics
Matches: 205, Mismatches: 37, Indels: 14
0.80 0.14 0.05
Matches are distributed among these distances:
26 2 0.01
27 177 0.86
28 9 0.04
29 17 0.08
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.36
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTAAAA
Found at i:53954341 original size:54 final size:54
Alignment explanation
Indices: 53954095--53954344 Score: 171
Period size: 54 Copynumber: 4.6 Consensus size: 54
53954085 TTCGACTTGT
* * ** * *
53954095 AAAATTACCAAAGTACCCCCGATTTACAAAATTACCGTTTTACCCCCGATTTAC
1 AAAATTACTAAAATACCCTTGATTTACAAAATTACTGTTTTACCCTCGATTTAC
* *** ** * * *
53954149 ATAATTACT-TTTTACCCCCGATTTACATAATTA-TCGTTTTACCCTCGACTTAT
1 AAAATTACTAAAATACCCTTGATTTACAAAATTACT-GTTTTACCCTCGATTTAC
* ***** * * * *
53954202 AGAATTACCGTTTTACCCTCGATTTACAGAATTACTGTTTTACCTTCGATTTAT
1 AAAATTACTAAAATACCCTTGATTTACAAAATTACTGTTTTACCCTCGATTTAC
* ****
53954256 ATAATTACTGTTTTACCCTTGATTTACAAAATTACTGTTTTACCCTCGATTTAC
1 AAAATTACTAAAATACCCTTGATTTACAAAATTACTGTTTTACCCTCGATTTAC
* * **
53954310 AAAATTACTAAAATACCTTTGGTTTGTAAAATTAC
1 AAAATTACTAAAATACCCTTGATTTACAAAATTAC
53954345 CAAAATACCC
Statistics
Matches: 162, Mismatches: 31, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
53 42 0.26
54 119 0.73
55 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (54 bp):
AAAATTACTAAAATACCCTTGATTTACAAAATTACTGTTTTACCCTCGATTTAC
Found at i:53954356 original size:81 final size:81
Alignment explanation
Indices: 53954008--53954357 Score: 240
Period size: 81 Copynumber: 4.3 Consensus size: 81
53953998 AATACTTTAG
* * *** **
53954008 TTTACTAAAATTACCGAAATACCCTTAGTTTGTA-AAAA-TACTGAAATACCCTCGATTTGTAAA
1 TTTA-TAAAATTACCGAAATACCCTT-GATT-TACAAAATTACCGTTTTACCCTCGATTTACAAA
*
53954071 ATTATTGAAATACCTTCGA
63 ATTACTGAAATACCTTCGA
* * ** * *
53954090 CTTGTAAAATTACC-AAAGTACCCCCGATTTACAAAATTACCGTTTTACCCCCGATTTACATAAT
1 TTTATAAAATTACCGAAA-TACCCTTGATTTACAAAATTACCGTTTTACCCTCGATTTACAAAAT
*** **
53954154 TACT-TTTTACCCCCGA
65 TACTGAAATACCTTCGA
* * * *** * * * * *
53954170 TTTACATAATTATCGTTTTACCCTCGACTTATAGAATTACCGTTTTACCCTCGATTTACAGAATT
1 TTTATAAAATTACCGAAATACCCTTGATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATT
***
53954235 ACTGTTTTACCTTCGA
66 ACTGAAATACCTTCGA
* * *** *
53954251 TTTATATAATTACTGTTTTACCCTTGATTTACAAAATTACTGTTTTACCCTCGATTTACAAAATT
1 TTTATAAAATTACCGAAATACCCTTGATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATT
* * *
53954316 ACTAAAATACCTTTGG
66 ACTGAAATACCTTCGA
* *
53954332 TTTGTAAAATTACCAAAATACCCTTG
1 TTTATAAAATTACCGAAATACCCTTG
53954358 GTTTGTGAAA
Statistics
Matches: 206, Mismatches: 57, Indels: 11
0.75 0.21 0.04
Matches are distributed among these distances:
79 2 0.01
80 70 0.34
81 132 0.64
82 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.38
Consensus pattern (81 bp):
TTTATAAAATTACCGAAATACCCTTGATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATT
ACTGAAATACCTTCGA
Found at i:53954381 original size:81 final size:83
Alignment explanation
Indices: 53954296--53954501 Score: 195
Period size: 81 Copynumber: 2.5 Consensus size: 83
53954286 ATTACTGTTT
* *
53954296 TACCCTCGATTTACAAAATTACTAAAATACCTTTGGTTTGTAAAATTACCA-AAATACCCTTG-G
1 TACCCTCGATTTACAAAATTACTAAAATACCTTTGGTTTGTAAAATTA-CAGAAACACCCTTGAC
* *
53954359 TTTGT-GAAATTACCA-AAA
65 TTTATAAAAATTA-CAGAAA
* ** * ** * ** *
53954377 TACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAGTTACAGAAACACCCTTGACT
1 TACCCTCGATTTACAAAATTACTAAAATACCTTTGGTTTGTAAAATTACAGAAACACCCTTGACT
*
53954442 TTATAAAAATTATAGAAA
66 TTATAAAAATTACAGAAA
* * * *
53954460 TACCATTGGTTTACAAAATTACTGAAATACCTTTGGTTTGTA
1 TACCCTCGATTTACAAAATTACTAAAATACCTTTGGTTTGTA
53954502 GATGTACCAA
Statistics
Matches: 93, Mismatches: 28, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
80 2 0.02
81 48 0.52
82 5 0.05
83 38 0.41
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (83 bp):
TACCCTCGATTTACAAAATTACTAAAATACCTTTGGTTTGTAAAATTACAGAAACACCCTTGACT
TTATAAAAATTACAGAAA
Found at i:53954498 original size:27 final size:27
Alignment explanation
Indices: 53954269--53954490 Score: 151
Period size: 27 Copynumber: 8.1 Consensus size: 27
53954259 ATTACTGTTT
****
53954269 TACCCTTGATTTACAAAATTACTGTTT
1 TACCCTTGATTTACAAAATTACTAAAA
*
53954296 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTTGATTTACAAAATTACTAAAA
* * ** *
53954323 TACCTTTGGTTTGTAAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACTAAAA
* *** *
53954350 TACCCTTGGTTTGTGAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACTAAAA
** ** *
53954377 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACTAAAA
* *
53954404 TACCCCTGATTTACAAAGTTAC-AGAAA
1 TACCCTTGATTTACAAAATTACTA-AAA
* *
53954431 CACCCTTGACTTTATAAAAATTA-TAGAAA
1 TACCCTTGA-TTTA-CAAAATTACTA-AAA
* * *
53954460 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGATTTACAAAATTACTAAAA
53954487 TACC
1 TACC
53954491 TTTGGTTTGT
Statistics
Matches: 158, Mismatches: 32, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
26 1 0.01
27 131 0.83
28 9 0.06
29 17 0.11
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (27 bp):
TACCCTTGATTTACAAAATTACTAAAA
Found at i:53954573 original size:27 final size:27
Alignment explanation
Indices: 53954552--53954639 Score: 97
Period size: 27 Copynumber: 3.3 Consensus size: 27
53954542 ACCCCTATTA
53954552 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAAAGACCGTAAAGCCCCTGTAG
**
53954579 GGTAAAGTGACCGTAAAGCCCCTGTAG
1 GGTAAAAAGACCGTAAAGCCCCTGTAG
* ** **
53954606 AGTAAAGTGACCGTAATA-CCCCTGTCT
1 GGTAAAAAGACCGTAA-AGCCCCTGTAG
53954633 GGTAAAA
1 GGTAAAA
53954640 TGACGAATAT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
27 52 0.98
28 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (27 bp):
GGTAAAAAGACCGTAAAGCCCCTGTAG
Found at i:53954643 original size:27 final size:26
Alignment explanation
Indices: 53954543--53954643 Score: 96
Period size: 27 Copynumber: 3.7 Consensus size: 26
53954533 GACTAAAATA
* *
53954543 CCCCTATTAGGTAAAAAGACCGTAAAG
1 CCCCTGTT-GGTAAAATGACCGTAAAG
* *
53954570 CCCCTGTAGGGTAAAGTGACCGTAAAG
1 CCCCTGT-TGGTAAAATGACCGTAAAG
* *
53954597 CCCCTGTAGAGTAAAGTGACCGTAATA-
1 CCCCTGTTG-GTAAAATGACCGTAA-AG
53954624 CCCCTGTCTGGTAAAATGAC
1 CCCCTGT-TGGTAAAATGAC
53954644 GAATATGCCC
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
26 1 0.02
27 60 0.95
28 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.21
Consensus pattern (26 bp):
CCCCTGTTGGTAAAATGACCGTAAAG
Found at i:53955474 original size:26 final size:26
Alignment explanation
Indices: 53955445--53955568 Score: 214
Period size: 26 Copynumber: 4.8 Consensus size: 26
53955435 GAGGAAGTGC
53955445 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
53955471 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
53955497 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
53955523 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
53955549 AAAAGGGCTT-TGCCCTAGTT
1 AAAAGGGCTTATGCCCCAGTT
53955569 ATTAAAGAGG
Statistics
Matches: 93, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
25 9 0.10
26 84 0.90
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:53955772 original size:42 final size:42
Alignment explanation
Indices: 53955713--53955804 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
53955703 TAGTCTCCCC
* ** *
53955713 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
53955755 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
53955797 AAATGGGC
1 AAATGGGC
53955805 CTATAGGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:53957637 original size:22 final size:22
Alignment explanation
Indices: 53957604--53957667 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
53957594 AACAGTGGAG
* *
53957604 CACCATAA-TGCTATTCAGACAA
1 CACCA-AAGTGCTAGTCAGAAAA
* *
53957626 CACCGAAGTGCTAGTCAAAAAA
1 CACCAAAGTGCTAGTCAGAAAA
53957648 CACCAAAGTGCTAGTCAGAA
1 CACCAAAGTGCTAGTCAGAA
53957668 CGGAAAGCAC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 2 0.06
22 33 0.94
ACGTcount: A:0.42, C:0.25, G:0.16, T:0.17
Consensus pattern (22 bp):
CACCAAAGTGCTAGTCAGAAAA
Found at i:53957713 original size:27 final size:27
Alignment explanation
Indices: 53957626--53957743 Score: 86
Period size: 27 Copynumber: 4.6 Consensus size: 27
53957616 ATTCAGACAA
*
53957626 CACCGAAGTGCTAGTC--AAAA-A-A-
1 CACCGAAGTGCTAATCAGAAAAGAGAG
* * ** *
53957648 CACCAAAGTGCTAGTCAGAACGGAAAG
1 CACCGAAGTGCTAATCAGAAAAGAGAG
* * *
53957675 CACCAAAATGCTAATCA-AAACAGTGAG
1 CACCGAAGTGCTAATCAGAAA-AGAGAG
* *
53957702 CACTGAAGTGCTAATTAGAAAAGAGAG
1 CACCGAAGTGCTAATCAGAAAAGAGAG
53957729 CACCGAAGTGCTAAT
1 CACCGAAGTGCTAAT
53957744 TTCCATTCAT
Statistics
Matches: 74, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
22 15 0.20
24 2 0.03
25 1 0.01
26 3 0.04
27 50 0.68
28 3 0.04
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.15
Consensus pattern (27 bp):
CACCGAAGTGCTAATCAGAAAAGAGAG
Found at i:53963084 original size:301 final size:301
Alignment explanation
Indices: 53962542--53963144 Score: 1206
Period size: 301 Copynumber: 2.0 Consensus size: 301
53962532 GGTGAACTAG
53962542 TACGGGTGCTTCAGTCAACAAAGCTTTCAATCTATCAAAACTCTACTCGCATATATCAGACCACT
1 TACGGGTGCTTCAGTCAACAAAGCTTTCAATCTATCAAAACTCTACTCGCATATATCAGACCACT
53962607 CAAATTTTACATCTTTTTGCAACAGACGAGTCTTTGCAGCAACTATCATCGAGAATCCTTTTACA
66 CAAATTTTACATCTTTTTGCAACAGACGAGTCTTTGCAGCAACTATCATCGAGAATCCTTTTACA
53962672 AACATCCGATAATATCCAGGTAGTCCTAGAAAACTTCTAACTTCACACATTTTTCAGTGGTTTCC
131 AACATCCGATAATATCCAGGTAGTCCTAGAAAACTTCTAACTTCACACATTTTTCAGTGGTTTCC
53962737 AGTTAACAATAGCTAAAATTTTATCCGGGTCCACTCTGATGCCTTTATCAGATACTATATGTCCA
196 AGTTAACAATAGCTAAAATTTTATCCGGGTCCACTCTGATGCCTTTATCAGATACTATATGTCCA
53962802 AGGAAACCAACTTTTCAAAGCCAAAATTCACATTTACTGAA
261 AGGAAACCAACTTTTCAAAGCCAAAATTCACATTTACTGAA
53962843 TACGGGTGCTTCAGTCAACAAAGCTTTCAATCTATCAAAACTCTACTCGCATATATCAGACCACT
1 TACGGGTGCTTCAGTCAACAAAGCTTTCAATCTATCAAAACTCTACTCGCATATATCAGACCACT
53962908 CAAATTTTACATCTTTTTGCAACAGACGAGTCTTTGCAGCAACTATCATCGAGAATCCTTTTACA
66 CAAATTTTACATCTTTTTGCAACAGACGAGTCTTTGCAGCAACTATCATCGAGAATCCTTTTACA
53962973 AACATCCGATAATATCCAGGTAGTCCTAGAAAACTTCTAACTTCACACATTTTTCAGTGGTTTCC
131 AACATCCGATAATATCCAGGTAGTCCTAGAAAACTTCTAACTTCACACATTTTTCAGTGGTTTCC
53963038 AGTTAACAATAGCTAAAATTTTATCCGGGTCCACTCTGATGCCTTTATCAGATACTATATGTCCA
196 AGTTAACAATAGCTAAAATTTTATCCGGGTCCACTCTGATGCCTTTATCAGATACTATATGTCCA
53963103 AGGAAACCAACTTTTCAAAGCCAAAATTCACATTTACTGAA
261 AGGAAACCAACTTTTCAAAGCCAAAATTCACATTTACTGAA
53963144 T
1 T
53963145 TTGGCATATA
Statistics
Matches: 302, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
301 302 1.00
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (301 bp):
TACGGGTGCTTCAGTCAACAAAGCTTTCAATCTATCAAAACTCTACTCGCATATATCAGACCACT
CAAATTTTACATCTTTTTGCAACAGACGAGTCTTTGCAGCAACTATCATCGAGAATCCTTTTACA
AACATCCGATAATATCCAGGTAGTCCTAGAAAACTTCTAACTTCACACATTTTTCAGTGGTTTCC
AGTTAACAATAGCTAAAATTTTATCCGGGTCCACTCTGATGCCTTTATCAGATACTATATGTCCA
AGGAAACCAACTTTTCAAAGCCAAAATTCACATTTACTGAA
Found at i:53966292 original size:16 final size:15
Alignment explanation
Indices: 53966271--53966308 Score: 67
Period size: 16 Copynumber: 2.5 Consensus size: 15
53966261 CATAAATGTA
53966271 TTTTTTTCACTTCTTT
1 TTTTTTTCACTT-TTT
53966287 TTTTTTTCACTTTTT
1 TTTTTTTCACTTTTT
53966302 TTTTTTT
1 TTTTTTT
53966309 GAGAATAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTTCACTTTTT
Found at i:53966390 original size:29 final size:29
Alignment explanation
Indices: 53966355--53966412 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
53966345 TAACAAAAAA
53966355 ACATAGTTAAGCAACTAACCAAATCAAGT
1 ACATAGTTAAGCAACTAACCAAATCAAGT
53966384 ACATAGTTAAGCAACTAACCAAATCAAGT
1 ACATAGTTAAGCAACTAACCAAATCAAGT
53966413 CTCGACAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (29 bp):
ACATAGTTAAGCAACTAACCAAATCAAGT
Found at i:53967455 original size:14 final size:14
Alignment explanation
Indices: 53967429--53967497 Score: 59
Period size: 14 Copynumber: 4.6 Consensus size: 14
53967419 ATGATAATAG
53967429 TAAAAAAAT-GAAA
1 TAAAAAAATAGAAA
*
53967442 GAAAAAAATAGAAA
1 TAAAAAAATAGAAA
*
53967456 AAAATAGAAATAGTAAAA
1 TAAA-A-AAATAG--AAA
*
53967474 TAAAAATAATAAAAA
1 TAAAAA-AATAGAAA
53967489 TAAAAAAAT
1 TAAAAAAAT
53967498 TTTAAAAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
13 8 0.17
14 10 0.22
15 10 0.22
16 7 0.15
17 5 0.11
18 6 0.13
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (14 bp):
TAAAAAAATAGAAA
Found at i:53967458 original size:9 final size:10
Alignment explanation
Indices: 53967441--53967465 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
53967431 AAAAAATGAA
53967441 AGAAAAAAAT
1 AGAAAAAAAT
53967451 AGAAAAAAAT
1 AGAAAAAAAT
53967461 AGAAA
1 AGAAA
53967466 TAGTAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (10 bp):
AGAAAAAAAT
Found at i:53967473 original size:24 final size:24
Alignment explanation
Indices: 53967424--53967497 Score: 80
Period size: 23 Copynumber: 3.1 Consensus size: 24
53967414 TTGTAATGAT
*
53967424 AATAGTAAAAAAAT-GAAAGAAAAA
1 AATAG-AAAAAAATAGAAATAAAAA
**
53967448 AATAGAAAAAAATAGAAATAGTAA
1 AATAGAAAAAAATAGAAATAAAAA
* *
53967472 AATA-AAAATAATAAAAATAAAAA
1 AATAGAAAAAAATAGAAATAAAAA
53967495 AAT
1 AAT
53967498 TTTAAAAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
23 26 0.62
24 16 0.38
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (24 bp):
AATAGAAAAAAATAGAAATAAAAA
Found at i:53967495 original size:17 final size:18
Alignment explanation
Indices: 53967475--53967517 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
53967465 ATAGTAAAAT
53967475 AAAAATAATAAAAA-TAA
1 AAAAATAATAAAAATTAA
**
53967492 AAAAATTTTAAAAATTAA
1 AAAAATAATAAAAATTAA
*
53967510 AAATATAA
1 AAAAATAA
53967518 GTATAAGAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAATAATAAAAATTAA
Found at i:53967584 original size:22 final size:20
Alignment explanation
Indices: 53967550--53967601 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
53967540 AATTAATTAG
* *
53967550 TAAAATAAGAATAAATAATA
1 TAAAATAAAAATAAATAAAA
53967570 TAACAATTAAAAATAAATAAAA
1 TAA-AA-TAAAAATAAATAAAA
53967592 TAAAATAAAA
1 TAAAATAAAA
53967602 TTGGGGTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 8 0.29
21 4 0.14
22 16 0.57
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (20 bp):
TAAAATAAAAATAAATAAAA
Found at i:53970390 original size:84 final size:84
Alignment explanation
Indices: 53970249--53970418 Score: 322
Period size: 84 Copynumber: 2.0 Consensus size: 84
53970239 AACCTCGTGG
*
53970249 TAGGGAGTTCAACCACTGCTTAGCCTTATTTCTCAATGAGAAGAGGAATAACCGTAGGTGAATGG
1 TAGGGAGTTCAACCACTGCTTAACCTTATTTCTCAATGAGAAGAGGAATAACCGTAGGTGAATGG
53970314 CATCATCAGAAACATCATT
66 CATCATCAGAAACATCATT
*
53970333 TAGGGAGTTCAACCACTGCTTAACCTTATTTCTTAATGAGAAGAGGAATAACCGTAGGTGAATGG
1 TAGGGAGTTCAACCACTGCTTAACCTTATTTCTCAATGAGAAGAGGAATAACCGTAGGTGAATGG
53970398 CATCATCAGAAACATCATT
66 CATCATCAGAAACATCATT
53970417 TA
1 TA
53970419 TCTTGAAAGT
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (84 bp):
TAGGGAGTTCAACCACTGCTTAACCTTATTTCTCAATGAGAAGAGGAATAACCGTAGGTGAATGG
CATCATCAGAAACATCATT
Found at i:53974866 original size:41 final size:41
Alignment explanation
Indices: 53974821--53974989 Score: 139
Period size: 41 Copynumber: 4.1 Consensus size: 41
53974811 GCACAAACAT
* *
53974821 CCTTCGGAA-TCAAGCCCGATTCTTAGCACTGGCTCAAAAGC
1 CCTTCGGAACT-AAGCCCGATTATGAGCACTGGCTCAAAAGC
* * * * *
53974862 CCTTC-GAGACCAAGCTCGGATTA-GACCACTGGCTCGAAGGC
1 CCTTCGGA-ACTAAGC-CCGATTATGAGCACTGGCTCAAAAGC
* * * *
53974903 CCTTTGGAACTAAGTCCGGTTATGA-CACTGGCTCTAAAGC
1 CCTTCGGAACTAAGCCCGATTATGAGCACTGGCTCAAAAGC
* ** * *
53974943 CCTTCGAAACTAAGTTCGGTTATTAGCACTGGCTCAAAAGC
1 CCTTCGGAACTAAGCCCGATTATGAGCACTGGCTCAAAAGC
53974984 CCTTCG
1 CCTTCG
53974990 AGACCAAGCT
Statistics
Matches: 103, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
40 41 0.40
41 55 0.53
42 7 0.07
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (41 bp):
CCTTCGGAACTAAGCCCGATTATGAGCACTGGCTCAAAAGC
Found at i:53974990 original size:41 final size:41
Alignment explanation
Indices: 53974843--53974990 Score: 167
Period size: 41 Copynumber: 3.6 Consensus size: 41
53974833 AGCCCGATTC
* * *
53974843 TTAGCACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGG--A
1 TTAGCACTGGCTCAAAAGCCCTTCGAAACTAAGTTCGGTTA
* * * * *
53974882 TTAGACCACTGGCTCGAAGGCCCTTTGGAACTAAGTCCGGTTA
1 TTAG--CACTGGCTCAAAAGCCCTTCGAAACTAAGTTCGGTTA
* *
53974925 TGA-CACTGGCTCTAAAGCCCTTCGAAACTAAGTTCGGTTA
1 TTAGCACTGGCTCAAAAGCCCTTCGAAACTAAGTTCGGTTA
53974965 TTAGCACTGGCTCAAAAGCCCTTCGA
1 TTAGCACTGGCTCAAAAGCCCTTCGA
53974991 GACCAAGCTC
Statistics
Matches: 88, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
39 4 0.05
40 34 0.39
41 47 0.53
43 3 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (41 bp):
TTAGCACTGGCTCAAAAGCCCTTCGAAACTAAGTTCGGTTA
Found at i:53984159 original size:152 final size:152
Alignment explanation
Indices: 53983893--53984322 Score: 618
Period size: 152 Copynumber: 2.8 Consensus size: 152
53983883 AAAGATAGAG
* * *
53983893 CATTAGCGGCGTTTTTGAGAAAGCGCCGC-ATAGATCAA-CTTATAGCGGCGCATTTTTAAAAAC
1 CATTAGCGGCGTTTTTAAGAAAGCGCCGCTATAGGTCAATC-TATAGCGGCGCTTTTTTAAAAAC
* * * *
53983956 GCCACTAAAAGATTAAAGAGAACGGTGACGTTTTTTTAGCTTCAGTGGCATTAGCGGCGCTTTCC
65 GCCGCTAAAAGATTAAAAAGAACGATGTCGTTTTTTTAGCTTCAGTGGCATTAGCGGCGCTTTCC
53984021 AAAAAACGCCGCAATAGATCCAA
130 AAAAAACGCCGCAATAGATCCAA
* *
53984044 CATTAGCGGCGTTTTTAAGAAAGCGCCGCTATAGGTCAATCTATAACGGCACTTTTTTAAAAACG
1 CATTAGCGGCGTTTTTAAGAAAGCGCCGCTATAGGTCAATCTATAGCGGCGCTTTTTTAAAAACG
* * * *
53984109 ACGCTAAAAGATTAAAAAGAACGACGTTGTTTTTTTAGCTTCAGTGGCATTAGCGGCGC-TTCCC
66 CCGCTAAAAGATTAAAAAGAACGATGTCGTTTTTTTAGCTTCAGTGGCATTAGCGGCGCTTTCCA
*
53984173 AAAAATGCCGCAATAGATCCAA
131 AAAAACGCCGCAATAGATCCAA
** * *
53984195 CATTAGCGGCGTTTTTAAGAAAGCGCCGCTATA-GTTGATCTATAGCGGCGCTTTTTAAAAAAAG
1 CATTAGCGGCGTTTTTAAGAAAGCGCCGCTATAGGTCAATCTATAGCGGCGCTTTTTTAAAAACG
*
53984259 CCGCTAAAAGATTAAACA-AACGATGTCGTTTTTCTTTGAGCTTCAGTGGCATTAGCGGCGCTTT
66 CCGCTAAAAGATTAAAAAGAACGATGTCG-TTTT-TTT-AGCTTCAGTGGCATTAGCGGCGCTTT
53984323 ATGGAAAACG
Statistics
Matches: 249, Mismatches: 24, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
149 8 0.03
150 45 0.18
151 89 0.36
152 104 0.42
153 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (152 bp):
CATTAGCGGCGTTTTTAAGAAAGCGCCGCTATAGGTCAATCTATAGCGGCGCTTTTTTAAAAACG
CCGCTAAAAGATTAAAAAGAACGATGTCGTTTTTTTAGCTTCAGTGGCATTAGCGGCGCTTTCCA
AAAAACGCCGCAATAGATCCAA
Found at i:53984633 original size:10 final size:10
Alignment explanation
Indices: 53984618--53984644 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
53984608 TGGATAGGAC
53984618 CAAATTATAA
1 CAAATTATAA
53984628 CAAATTATAA
1 CAAATTATAA
53984638 CAAATTA
1 CAAATTA
53984645 AATAAGGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (10 bp):
CAAATTATAA
Found at i:53984946 original size:21 final size:21
Alignment explanation
Indices: 53984920--53984972 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
53984910 AAATCTCTAG
53984920 TTAAACCCTAAACTA-TAAACC
1 TTAAACCCTAAA-TATTAAACC
53984941 TTAAACCCTAAATATTAAACC
1 TTAAACCCTAAATATTAAACC
* *
53984962 TTGAATCCTAA
1 TTAAACCCTAA
53984973 GCCATAAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.45, C:0.25, G:0.02, T:0.28
Consensus pattern (21 bp):
TTAAACCCTAAATATTAAACC
Found at i:53985001 original size:29 final size:29
Alignment explanation
Indices: 53984969--53985041 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 29
53984959 ACCTTGAATC
*
53984969 CTAAGCCATAAAACCC-TAAACTATAGACA
1 CTAAACCATAAAACCCTTAAA-TATAGACA
* *
53984998 CTAAACCCTTAAACCCTTAAATATAGATTC-
1 CTAAACCATAAAACCCTTAAATATAGA--CA
*
53985028 CTAAATCATAAAAC
1 CTAAACCATAAAAC
53985042 TGTTAACCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
29 19 0.54
30 15 0.43
31 1 0.03
ACGTcount: A:0.47, C:0.26, G:0.04, T:0.23
Consensus pattern (29 bp):
CTAAACCATAAAACCCTTAAATATAGACA
Found at i:53985098 original size:21 final size:21
Alignment explanation
Indices: 53985074--53985129 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
53985064 GGCCTAAATT
**
53985074 ATAAACCCTAAATCTTAAACC
1 ATAAACCCTAAATCCAAAACC
53985095 ATAAACCCTAAATCCAAAACC
1 ATAAACCCTAAATCCAAAACC
*
53985116 ATAAAACCTTAAAT
1 AT-AAACCCTAAAT
53985130 TATAGATAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 21 0.68
22 10 0.32
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (21 bp):
ATAAACCCTAAATCCAAAACC
Found at i:53985478 original size:3 final size:3
Alignment explanation
Indices: 53985470--53985505 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
53985460 AACCATGTAT
53985470 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
53985506 AAGAGAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:53987176 original size:39 final size:38
Alignment explanation
Indices: 53987125--53987202 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 38
53987115 AATAACTTAA
* * *
53987125 ATGTTATAATACATGATTTATCTCAATTACATTCATAT
1 ATGTTATAATACATAATATATCTCAATTACATCCATAT
53987163 ATGTTATATATACATAATATATCTCAATTACATCCATAT
1 ATGTTATA-ATACATAATATATCTCAATTACATCCATAT
53987202 A
1 A
53987203 AATATATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 8 0.22
39 28 0.78
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.42
Consensus pattern (38 bp):
ATGTTATAATACATAATATATCTCAATTACATCCATAT
Found at i:53989491 original size:24 final size:24
Alignment explanation
Indices: 53989464--53989510 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
53989454 ATTATTATTG
*
53989464 AAATATTCTCGTCCGTTTTATCAC
1 AAATATTATCGTCCGTTTTATCAC
53989488 AAATATTATCGTCCGTTTTATCA
1 AAATATTATCGTCCGTTTTATCA
53989511 TTTAAGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.43
Consensus pattern (24 bp):
AAATATTATCGTCCGTTTTATCAC
Found at i:53989769 original size:39 final size:40
Alignment explanation
Indices: 53989721--53989827 Score: 135
Period size: 47 Copynumber: 2.5 Consensus size: 40
53989711 AGGTTCAATC
53989721 TTATTTTAATTAATATAATTTGGATTAATTTATTTAAATA
1 TTATTTTAATTAATATAATTTGGATTAATTTATTTAAATA
53989761 TTATTTAATTAATATAATAATATAATTTGGATTAATTTATTTAAATA
1 TTA-TT--TT-A-AT--TAATATAATTTGGATTAATTTATTTAAATA
*
53989808 TTA-TTAAATTAATATAATTT
1 TTATTTTAATTAATATAATTT
53989828 TTATAAATAT
Statistics
Matches: 59, Mismatches: 1, Indels: 15
0.79 0.01 0.20
Matches are distributed among these distances:
39 11 0.19
40 3 0.05
41 4 0.07
42 1 0.02
43 3 0.05
44 1 0.02
45 3 0.05
47 33 0.56
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (40 bp):
TTATTTTAATTAATATAATTTGGATTAATTTATTTAAATA
Found at i:53989785 original size:47 final size:47
Alignment explanation
Indices: 53989731--53989825 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
53989721 TTATTTTAAT
*
53989731 TAATATAATTTGGATTAATTTATTTAAATATTATTTAATTAATATAA
1 TAATATAATTTGGATTAATTTATTTAAATATTATTAAATTAATATAA
53989778 TAATATAATTTGGATTAATTTATTTAAATATTATTAAATTAATATAA
1 TAATATAATTTGGATTAATTTATTTAAATATTATTAAATTAATATAA
53989825 T
1 T
53989826 TTTTATAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (47 bp):
TAATATAATTTGGATTAATTTATTTAAATATTATTAAATTAATATAA
Found at i:53989826 original size:29 final size:29
Alignment explanation
Indices: 53989793--53989859 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
53989783 TAATTTGGAT
*
53989793 TAATTTATT-TAAATATTATTAAATTAATA
1 TAATTT-TTATAAATATTATTAAATTAAAA
*
53989822 TAATTTTTATAAATATTATTTAATTAAAA
1 TAATTTTTATAAATATTATTAAATTAAAA
53989851 TAAATTTTT
1 T-AATTTTT
53989860 TTCCATGTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 2 0.06
29 25 0.74
30 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TAATTTTTATAAATATTATTAAATTAAAA
Found at i:53989855 original size:39 final size:39
Alignment explanation
Indices: 53989746--53989856 Score: 113
Period size: 39 Copynumber: 2.9 Consensus size: 39
53989736 TAATTTGGAT
*
53989746 TAATTTATT-TAAATATTATTTAATTAATAT-AA-TAATA
1 TAATTT-TTATAAATATTATTTAATTAAAATAAATTAATA
** * * * *
53989783 TAATTTGGATTAAT-TTATTTAAATATTATTAAATTAATA
1 TAATTTTTATAAATATTATTTAATTA-AAATAAATTAATA
53989822 TAATTTTTATAAATATTATTTAATTAAAATAAATT
1 TAATTTTTATAAATATTATTTAATTAAAATAAATT
53989857 TTTTTCCATG
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
36 10 0.18
37 11 0.20
38 2 0.04
39 23 0.41
40 10 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (39 bp):
TAATTTTTATAAATATTATTTAATTAAAATAAATTAATA
Found at i:53990148 original size:9 final size:9
Alignment explanation
Indices: 53990129--53990283 Score: 204
Period size: 9 Copynumber: 17.2 Consensus size: 9
53990119 TATATACTTG
53990129 AACTTACAT
1 AACTTACAT
* *
53990138 AACTCATAT
1 AACTTACAT
53990147 AACTTACAT
1 AACTTACAT
*
53990156 AACTTATAT
1 AACTTACAT
53990165 AACTTACAT
1 AACTTACAT
53990174 AACTTACAT
1 AACTTACAT
*
53990183 AACTCACAT
1 AACTTACAT
53990192 AA-TTCACAT
1 AACTT-ACAT
*
53990201 AACTTATAT
1 AACTTACAT
53990210 AACTTACAT
1 AACTTACAT
53990219 AACTTACAT
1 AACTTACAT
*
53990228 AACTCACAT
1 AACTTACAT
*
53990237 AACTTACAA
1 AACTTACAT
*
53990246 AACTTACAG
1 AACTTACAT
53990255 AACTTACAT
1 AACTTACAT
*
53990264 AACTGACAT
1 AACTTACAT
*
53990273 AACTTATAT
1 AACTTACAT
53990282 AA
1 AA
53990284 TACATAAATA
Statistics
Matches: 126, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
8 1 0.01
9 123 0.98
10 2 0.02
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:53992072 original size:12 final size:12
Alignment explanation
Indices: 53992039--53992073 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
53992029 AAGATCGAGG
*
53992039 GATGAATCTAAT
1 GATGAATCTGAT
53992051 GATGAATCTGAT
1 GATGAATCTGAT
53992063 GATGAATCTGA
1 GATGAATCTGA
53992074 CGAAGAGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.31
Consensus pattern (12 bp):
GATGAATCTGAT
Found at i:53995850 original size:21 final size:21
Alignment explanation
Indices: 53995824--53995885 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
53995814 AACTTAGAGC
*
53995824 GGAGGCAGCGGCAACAGCGAG
1 GGAGGCAGCGGCAGCAGCGAG
*
53995845 GGAGGCAGCGGCAGCAGCGTG
1 GGAGGCAGCGGCAGCAGCGAG
* *
53995866 GGAGGAAGAGGCAGCAGCGA
1 GGAGGCAGCGGCAGCAGCGA
53995886 TGGCAGCAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.27, C:0.21, G:0.50, T:0.02
Consensus pattern (21 bp):
GGAGGCAGCGGCAGCAGCGAG
Found at i:53995896 original size:21 final size:21
Alignment explanation
Indices: 53995826--53995896 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
53995816 CTTAGAGCGG
* * * *
53995826 AGGCAGCGGCAACAGCGAGGG
1 AGGCAGAGGCAGCAGCGTGGC
* *
53995847 AGGCAGCGGCAGCAGCGTGGG
1 AGGCAGAGGCAGCAGCGTGGC
*
53995868 AGGAAGAGGCAGCAGCGATGGC
1 AGGCAGAGGCAGCAGCG-TGGC
53995890 A-GCAGAG
1 AGGCAGAG
53995897 TAGAGCAGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 39 0.91
22 4 0.09
ACGTcount: A:0.28, C:0.21, G:0.48, T:0.03
Consensus pattern (21 bp):
AGGCAGAGGCAGCAGCGTGGC
Found at i:54002768 original size:17 final size:18
Alignment explanation
Indices: 54002741--54002797 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
54002731 CCAGTCTTTC
*
54002741 TTTTTATTTTTATTTATT
1 TTTTTCTTTTTATTTATT
54002759 TTTTTCTTTTATTATTTA-T
1 TTTTTC-TTT-TTATTTATT
*
54002778 TTTTTCTTTTTTTTTATT
1 TTTTTCTTTTTATTTATT
54002796 TT
1 TT
54002798 ATTTTAGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 6 0.18
18 11 0.32
19 10 0.29
20 7 0.21
ACGTcount: A:0.12, C:0.04, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTCTTTTTATTTATT
Found at i:54002775 original size:20 final size:19
Alignment explanation
Indices: 54002747--54002797 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
54002737 TTTCTTTTTA
54002747 TTTTTATTTATTTTTTTCT
1 TTTTTATTTATTTTTTTCT
54002766 TTTATTATTTA-TTTTTTCT
1 TTT-TTATTTATTTTTTTCT
54002785 TTTTT-TTTATTTT
1 TTTTTATTTATTTT
54002798 ATTTTAGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.13
18 5 0.17
19 14 0.47
20 7 0.23
ACGTcount: A:0.12, C:0.04, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTATTTATTTTTTTCT
Found at i:54002776 original size:24 final size:23
Alignment explanation
Indices: 54002737--54002802 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 23
54002727 CAACCCAGTC
54002737 TTTCTTTTTATTTTTATTTATTT-T
1 TTTC-TTTTATTTTTATTT-TTTCT
54002761 TTTCTTTTATTATTTATTTTTTCT
1 TTTCTTTTATT-TTTATTTTTTCT
*
54002785 TTTTTTTTA-TTTTATTTT
1 TTTCTTTTATTTTTATTTT
54002803 AGTTAAATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
22 8 0.21
23 11 0.28
24 20 0.51
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.83
Consensus pattern (23 bp):
TTTCTTTTATTTTTATTTTTTCT
Found at i:54002802 original size:20 final size:20
Alignment explanation
Indices: 54002737--54002802 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 20
54002727 CAACCCAGTC
54002737 TTTCTTTTTATTTT-TATTTAT
1 TTTCTTTTT-TTTTAT-TTTAT
*
54002758 TTT-TTTCTTTTATTATTTATTT
1 TTTCTTT-TTTT-TTATTT-TAT
54002780 TTTCTTTTTTTTTATTTTAT
1 TTTCTTTTTTTTTATTTTAT
54002800 TTT
1 TTT
54002803 AGTTAAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
20 10 0.26
21 15 0.39
22 10 0.26
23 3 0.08
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTCTTTTTTTTTATTTTAT
Found at i:54003906 original size:118 final size:115
Alignment explanation
Indices: 54003683--54003892 Score: 384
Period size: 118 Copynumber: 1.8 Consensus size: 115
54003673 TGTTTTCCAT
*
54003683 GGTTATGAGTAGCTTAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTCTA
1 GGTTATGAGTAGCTAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTCTA
54003748 CTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCACTAGCCGA
66 CTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCACTAGCCGA
54003798 GGTTATGAGTATGGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTA--GCT-AAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
54003863 CTACTTCGCGTCAAAAGGTTGTGTGACGTG
63 CTACTTCGCGTCAAAAGGTTGTGTGACGTG
54003893 TTGGGTAAAA
Statistics
Matches: 91, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
115 11 0.12
117 3 0.03
118 77 0.85
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.29
Consensus pattern (115 bp):
GGTTATGAGTAGCTAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTCTA
CTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCACTAGCCGA
Found at i:54008370 original size:21 final size:21
Alignment explanation
Indices: 54008336--54008376 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
54008326 ATTTTTTTTG
*
54008336 AAAAAAAATTAAAAAAATAGC
1 AAAAAAAATCAAAAAAATAGC
* *
54008357 AAAAAAAGTCAAAACAATAG
1 AAAAAAAATCAAAAAAATAG
54008377 TTTATGGTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.12
Consensus pattern (21 bp):
AAAAAAAATCAAAAAAATAGC
Found at i:54017339 original size:10 final size:9
Alignment explanation
Indices: 54017314--54017338 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
54017304 AAAGTAAGAC
54017314 AAAAAAATA
1 AAAAAAATA
54017323 AAAAAAATA
1 AAAAAAATA
54017332 AAAAAAA
1 AAAAAAA
54017339 ACCCAATAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAATA
Found at i:54023289 original size:6 final size:6
Alignment explanation
Indices: 54023271--54023358 Score: 65
Period size: 6 Copynumber: 14.3 Consensus size: 6
54023261 AAGAAACATT
*
54023271 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATCAG- GTGACAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
** * *
54023320 ATCAGA ATTGGT ATCAGGTA A-CAGA ATCAAA ATCAGA AT
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
54023359 GTGAATGCAA
Statistics
Matches: 64, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
5 4 0.06
6 51 0.80
7 7 0.11
8 2 0.03
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:54023292 original size:18 final size:18
Alignment explanation
Indices: 54023271--54023358 Score: 65
Period size: 19 Copynumber: 4.8 Consensus size: 18
54023261 AAGAAACATT
54023271 ATCAGAA-CTAGAATCAGA
1 ATCAGAATC-AGAATCAGA
54023289 ATCAGAATCAGAATCAG-
1 ATCAGAATCAGAATCAGA
*
54023306 GTGACAGAATCAGAATCAGA
1 AT--CAGAATCAGAATCAGA
** *
54023326 ATTGGTATCAGGTAA-CAGA
1 ATCAGAATCA-G-AATCAGA
*
54023345 ATCAAAATCAGAAT
1 ATCAGAATCAGAAT
54023359 GTGAATGCAA
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
17 3 0.06
18 21 0.39
19 27 0.50
20 3 0.06
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (18 bp):
ATCAGAATCAGAATCAGA
Found at i:54023315 original size:31 final size:31
Alignment explanation
Indices: 54023280--54023358 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
54023270 TATCAGAACT
*
54023280 AGAATCAGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAGAATCAGAATCAGAATCAGGTAAC
** *
54023311 AGAATCAGAATCAGAATTGGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGAATCAGGTAAC
*
54023342 AGAATCAAAATCAGAAT
1 AGAATCAGAATCAGAAT
54023359 GTGAATGCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.47, C:0.14, G:0.20, T:0.19
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGAATCAGGTAAC
Found at i:54023531 original size:27 final size:27
Alignment explanation
Indices: 54023501--54023562 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
54023491 AGTAAGTTGA
*
54023501 GGCAAAGCC-TCCAGAA-CAGATATTTGT
1 GGCAAAGCCAT-CAGAATCAGATA-ATGT
*
54023528 GGCATAGCCATCAGAATCAGATAATGT
1 GGCAAAGCCATCAGAATCAGATAATGT
54023555 GGCAAAGC
1 GGCAAAGC
54023563 TACTTAACAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 23 0.77
28 7 0.23
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.19
Consensus pattern (27 bp):
GGCAAAGCCATCAGAATCAGATAATGT
Found at i:54025524 original size:29 final size:29
Alignment explanation
Indices: 54025491--54025564 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
54025481 CCTTCGAGCT
54025491 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
54025520 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
54025549 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
54025565 ATCTCGTCAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:54025525 original size:58 final size:58
Alignment explanation
Indices: 54025432--54025564 Score: 133
Period size: 58 Copynumber: 2.3 Consensus size: 58
54025422 ATACTCGATT
* * * * *
54025432 TCGCACACTTAGTGCCATGCGATTTAAGCCCGCACACACAGTGCCATGCCCTTCGAGC
1 TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC
* * * ** * *
54025490 TCGCACACTTAGTGCCAT-ATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGC
1 TCGCACACTTAGTGCCATGAGATTT-AAGCACGCACACACAGTGCCATACACTTCCAGC
*
54025548 ACGCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
54025565 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
57 4 0.07
58 57 0.93
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (58 bp):
TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC
Done.