Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 168 of 198
Found at i:52834509 original size:15 final size:15
Alignment explanation
Indices: 52834476--52834509 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
52834466 CAGAGATTTC
*
52834476 AACAGAACAAAGCAA
1 AACAGAACAAAACAA
*
52834491 AACAGAACAAAACAG
1 AACAGAACAAAACAA
52834506 AACA
1 AACA
52834510 ACGCAATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.21, G:0.12, T:0.00
Consensus pattern (15 bp):
AACAGAACAAAACAA
Found at i:52839229 original size:14 final size:15
Alignment explanation
Indices: 52839212--52839250 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
52839202 TTATTTATTA
52839212 AATTAATTTA-AATT
1 AATTAATTTACAATT
52839226 AATTAATTTACCAATT
1 AATTAATTTA-CAATT
*
52839242 AAATAATTT
1 AATTAATTT
52839251 TCTCAACCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.45
16 12 0.55
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTAATTTACAATT
Found at i:52846906 original size:12 final size:12
Alignment explanation
Indices: 52846889--52846942 Score: 65
Period size: 12 Copynumber: 4.5 Consensus size: 12
52846879 ACTTCACTTT
*
52846889 AAAAGAAACGAA
1 AAAAGAAAAGAA
52846901 AAAAGAAAAGAAA
1 AAAAGAAAAG-AA
52846914 AAAAGAAAAGAA
1 AAAAGAAAAGAA
* *
52846926 AAGA-AAAAGGA
1 AAAAGAAAAGAA
52846937 AAAAGA
1 AAAAGA
52846943 TAGGCCAAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
11 9 0.25
12 15 0.42
13 12 0.33
ACGTcount: A:0.80, C:0.02, G:0.19, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:52846909 original size:5 final size:5
Alignment explanation
Indices: 52846901--52846932 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
52846891 AAGAAACGAA
52846901 AAAAG AAAAG -AAA- AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
52846933 AGGAAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 6 0.24
5 19 0.76
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:52846917 original size:13 final size:13
Alignment explanation
Indices: 52846889--52846940 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
52846879 ACTTCACTTT
*
52846889 AAAAGAAACG-AA
1 AAAAGAAAAGAAA
52846901 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
52846914 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
* *
52846927 AGAA-AAAGGAAA
1 AAAAGAAAAGAAA
52846939 AA
1 AA
52846941 GATAGGCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
12 17 0.49
13 18 0.51
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAGAAA
Found at i:52846942 original size:18 final size:17
Alignment explanation
Indices: 52846889--52846933 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
52846879 ACTTCACTTT
**
52846889 AAAAGAAACGAAAAAAG
1 AAAAGAAAAAAAAAAAG
52846906 AAAAGAAAAAAAGAAAAG
1 AAAAGAAAAAAA-AAAAG
52846924 AAAAGAAAAA
1 AAAAGAAAAA
52846934 GGAAAAAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAAAAAAAG
Found at i:52850343 original size:46 final size:46
Alignment explanation
Indices: 52850240--52850492 Score: 451
Period size: 46 Copynumber: 5.6 Consensus size: 46
52850230 TACGTATGAT
* *
52850240 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
52850283 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
52850329 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
52850374 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
52850420 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
52850466 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
52850493 AGTACTCAAA
Statistics
Matches: 202, Mismatches: 4, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
43 10 0.05
44 5 0.02
45 64 0.32
46 123 0.61
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:52850359 original size:91 final size:91
Alignment explanation
Indices: 52850240--52850492 Score: 465
Period size: 91 Copynumber: 2.8 Consensus size: 91
52850230 TACGTATGAT
*
52850240 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
52850303 GATCAGATAAGTGTAGCTAAAGCTAC
66 GATCAGATAAGTGTAGCTAAAGCTAC
52850329 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
52850394 GATCAGATAAGTGTAGCTAAAGCTAC
66 GATCAGATAAGTGTAGCTAAAGCTAC
*
52850420 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTGTCACT
52850485 TGATCAGA
65 TGATCAGA
52850493 AGTACTCAAA
Statistics
Matches: 159, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
89 10 0.06
90 5 0.03
91 111 0.70
92 33 0.21
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (91 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
GATCAGATAAGTGTAGCTAAAGCTAC
Found at i:52855394 original size:37 final size:37
Alignment explanation
Indices: 52855352--52855537 Score: 300
Period size: 37 Copynumber: 5.0 Consensus size: 37
52855342 GGTAGTTTTA
*
52855352 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
52855389 GCTACACTTATTTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
52855426 GTTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
52855463 GTTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
52855500 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
52855537 G
1 G
52855538 TAGCTTCAGC
Statistics
Matches: 140, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 140 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:52855609 original size:45 final size:46
Alignment explanation
Indices: 52855500--52855623 Score: 191
Period size: 46 Copynumber: 2.8 Consensus size: 46
52855490 GTGATAAGTG
* *
52855500 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
52855546 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
52855591 GCTACGCTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
52855624 AGGTCATATG
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 20 0.27
46 41 0.56
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:52857225 original size:143 final size:143
Alignment explanation
Indices: 52856967--52857309 Score: 497
Period size: 143 Copynumber: 2.4 Consensus size: 143
52856957 GGGTGTTACA
* * * *
52856967 TTATCTCCCTGAAGTTACAGCGGAGCATACTGAAAATAGCGAATCTTATTTCCCTAGTGTTGTAG
1 TTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTAGTGTTGTAG
* * * * * * *
52857032 TGGAATAGATTAAAGTTACAAATTATGGCGAATTTTATCTTCTTAAAGTTGTAGTAGAGGAAATT
66 TGGAACAAATTAAAGCTACAAATTATGGCGAATCTTATCTTCCTAAAGTTGCAGTAGAGCAAATT
52857097 GAAGCCACCAACC
131 GAAGCCACCAACC
* * *
52857110 TTATCTCCCTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCTTGGTGTTGTAG
1 TTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTAGTGTTGTAG
* * * *
52857175 TGGAACAAATTATAGCTACAAATTATGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAGCAAATT
66 TGGAACAAATTAAAGCTACAAATTATGGCGAATCTTATCTTCCTAAAGTTGCAGTAGAGCAAATT
*
52857240 GACGCCACCAACC
131 GAAGCCACCAACC
* *
52857253 TTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACTGTGAATCTTATTTCCCTAG
1 TTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTAG
52857310 CACACTCTTA
Statistics
Matches: 176, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
143 176 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (143 bp):
TTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTAGTGTTGTAG
TGGAACAAATTAAAGCTACAAATTATGGCGAATCTTATCTTCCTAAAGTTGCAGTAGAGCAAATT
GAAGCCACCAACC
Found at i:52858437 original size:20 final size:22
Alignment explanation
Indices: 52858414--52858454 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
52858404 TTAAGTTAAT
52858414 ATTATTT-T-ATTTTTATATCC
1 ATTATTTATCATTTTTATATCC
*
52858434 ATTATTTATCTTTTTTATATC
1 ATTATTTATCATTTTTATATC
52858455 TAAATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 10 0.56
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTATTTATCATTTTTATATCC
Found at i:52858764 original size:22 final size:22
Alignment explanation
Indices: 52858694--52858771 Score: 70
Period size: 22 Copynumber: 3.4 Consensus size: 22
52858684 CTTTTAGTTC
*
52858694 TTATTTGTTTATTTAT-TTATT
1 TTATTTTTTTATTTATCTTATT
* *
52858715 ATT-TCTTTTTATTTAATTGGCTTGTT
1 -TTATTTTTTTATTT-A-T--CTTATT
52858741 TTATTTTTTTATTTATCTTATT
1 TTATTTTTTTATTTATCTTATT
52858763 TTATTTTTT
1 TTATTTTTT
52858772 CCCTTATTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
21 9 0.20
22 17 0.38
23 1 0.02
24 1 0.02
25 3 0.07
26 14 0.31
ACGTcount: A:0.17, C:0.04, G:0.05, T:0.74
Consensus pattern (22 bp):
TTATTTTTTTATTTATCTTATT
Found at i:52859866 original size:2 final size:2
Alignment explanation
Indices: 52859861--52859900 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
52859851 ATACTTACTC
52859861 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52859901 TAAAGGAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52873691 original size:17 final size:18
Alignment explanation
Indices: 52873667--52873713 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
52873657 GAATGTTTTT
52873667 GAAAGTGTCTCCGTGG-A
1 GAAAGTGTCTCCGTGGAA
* *
52873684 GGAAGTGTCTTCGTGGAA
1 GAAAGTGTCTCCGTGGAA
52873702 GAAAGT-TCTCCG
1 GAAAGTGTCTCCG
52873714 GTTTGGACGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (18 bp):
GAAAGTGTCTCCGTGGAA
Found at i:52882842 original size:24 final size:24
Alignment explanation
Indices: 52882792--52882843 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
52882782 AATCAAAGTC
* *
52882792 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
* *
52882816 AAATATATTATACTCATAAATATT
1 AAATATATTATACTAATAAATACT
52882840 AAAT
1 AAAT
52882844 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:52887302 original size:24 final size:24
Alignment explanation
Indices: 52887275--52887326 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
52887265 AATCAAAGTC
*
52887275 AAATATATTATGCTAATAAATACT
1 AAATATATTATACTAATAAATACT
* *
52887299 AAATATATTATACTCATAAGTACT
1 AAATATATTATACTAATAAATACT
52887323 AAAT
1 AAAT
52887327 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:52888142 original size:27 final size:27
Alignment explanation
Indices: 52888095--52888158 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
52888085 AAATATTCTC
52888095 TAAATTAAT-AAATATTAATTTATCAA
1 TAAATTAATAAAATATTAATTTATCAA
* *
52888121 TAAATTAATAAAATATTCATTTATCGA
1 TAAATTAATAAAATATTAATTTATCAA
*
52888148 TAAACTAATAA
1 TAAATTAATAA
52888159 CCTCGATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 9 0.26
27 25 0.74
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (27 bp):
TAAATTAATAAAATATTAATTTATCAA
Found at i:52896164 original size:12 final size:14
Alignment explanation
Indices: 52896134--52896165 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
52896124 AGAGTATTCT
52896134 ATGTTATAAATGAA
1 ATGTTATAAATGAA
52896148 ATGTT-TAAATG-A
1 ATGTTATAAATGAA
52896160 ATGTTA
1 ATGTTA
52896166 GATTTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.35
13 6 0.35
14 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.41
Consensus pattern (14 bp):
ATGTTATAAATGAA
Found at i:52896749 original size:29 final size:29
Alignment explanation
Indices: 52896704--52896763 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
52896694 CCACATGCCC
*
52896704 GTGTGCTAGGCCGTATGCAAGGTGTAGGG
1 GTGTGCTAGGCCATATGCAAGGTGTAGGG
52896733 GTGTGCTAGGCCATATGCAAGGTGTAGGG
1 GTGTGCTAGGCCATATGCAAGGTGTAGGG
52896762 GT
1 GT
52896764 CATACGGCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.18, C:0.13, G:0.43, T:0.25
Consensus pattern (29 bp):
GTGTGCTAGGCCATATGCAAGGTGTAGGG
Found at i:52897622 original size:42 final size:42
Alignment explanation
Indices: 52897576--52897706 Score: 106
Period size: 42 Copynumber: 3.1 Consensus size: 42
52897566 AGGCTGCACT
* *
52897576 GAAGCACATAAGTA-CTAAACGAAAACATGTAAGGGTTAAACA
1 GAAGCACAT-AGGAGCTAAACGAAAACATATAAGGGTTAAACA
* * * * *
52897618 GAAGCTCATAGGAGCTGAACGAAAACCTATAAGGGTTAATCT
1 GAAGCACATAGGAGCTAAACGAAAACATATAAGGGTTAAACA
* * * *
52897660 GAAGCTCAGAAGAGCTAAACTGAAACCCAT-T-AGGGTTAAACA
1 GAAGCACATAGGAGCTAAAC-GAAA-ACATATAAGGGTTAAACA
*
52897702 AAAGC
1 GAAGC
52897707 TCAAAAGAGT
Statistics
Matches: 71, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
41 3 0.04
42 61 0.86
43 5 0.07
44 2 0.03
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.18
Consensus pattern (42 bp):
GAAGCACATAGGAGCTAAACGAAAACATATAAGGGTTAAACA
Found at i:52897707 original size:42 final size:42
Alignment explanation
Indices: 52897605--52897732 Score: 141
Period size: 42 Copynumber: 3.0 Consensus size: 42
52897595 CGAAAACATG
* * *
52897605 TAAGGGTTAAACAGAAGCTCATAGGAGCTGAAC-GAAAACCTA
1 TAAGGGTTAAACAGAAGCTCAAAAGAGCTGAACTG-AAACCCA
* * * *
52897647 TAAGGGTTAATCTGAAGCTCAGAAGAGCTAAACTGAAACCCA
1 TAAGGGTTAAACAGAAGCTCAAAAGAGCTGAACTGAAACCCA
* * * *
52897689 TTAGGGTTAAACAAAAGCTCAAAAGAGTTGAACTGAAACTCA
1 TAAGGGTTAAACAGAAGCTCAAAAGAGCTGAACTGAAACCCA
52897731 TA
1 TA
52897733 TGAGTTAATT
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 69 0.99
43 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (42 bp):
TAAGGGTTAAACAGAAGCTCAAAAGAGCTGAACTGAAACCCA
Found at i:52897750 original size:20 final size:21
Alignment explanation
Indices: 52897658--52897756 Score: 56
Period size: 21 Copynumber: 4.8 Consensus size: 21
52897648 AAGGGTTAAT
* * *
52897658 CTGAAGCTCAGAAGAGCTAAA
1 CTGAAGCTCATAAGAGTTGAA
* * * * *
52897679 CTGAAACCCATTAGGGTTAAA
1 CTGAAGCTCATAAGAGTTGAA
** *
52897700 CAAAAGCTCAAAAGAGTTGAA
1 CTGAAGCTCATAAGAGTTGAA
* *
52897721 CTGAAACTCATATGAGTT-AA
1 CTGAAGCTCATAAGAGTTGAA
* *
52897741 TTGAAGCTCATGAGAG
1 CTGAAGCTCATAAGAG
52897757 CTACACGGAA
Statistics
Matches: 55, Mismatches: 23, Indels: 1
0.70 0.29 0.01
Matches are distributed among these distances:
20 14 0.25
21 41 0.75
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.21
Consensus pattern (21 bp):
CTGAAGCTCATAAGAGTTGAA
Found at i:52900679 original size:24 final size:24
Alignment explanation
Indices: 52900643--52900746 Score: 68
Period size: 24 Copynumber: 4.3 Consensus size: 24
52900633 TTCTTGATAT
* * *
52900643 ATGGCTATCCGGAGCTTCCCGTTA
1 ATGGCTCTTCGGAGCTTCCCATTA
*
52900667 ATGGCTCTTCGGAGCTACCCATTA
1 ATGGCTCTTCGGAGCTTCCCATTA
* * *
52900691 TTGGCTC-TCATGAGCTTCCTAATT-
1 ATGGCTCTTC-GGAGCTTCC-CATTA
* ** *
52900715 ATGGCACTTATGAGCTTCCCGTTA
1 ATGGCTCTTCGGAGCTTCCCATTA
52900739 CATGGCTC
1 -ATGGCTC
52900747 ACAGGAGCTT
Statistics
Matches: 61, Mismatches: 14, Indels: 9
0.73 0.17 0.11
Matches are distributed among these distances:
23 4 0.07
24 47 0.77
25 10 0.16
ACGTcount: A:0.18, C:0.28, G:0.21, T:0.33
Consensus pattern (24 bp):
ATGGCTCTTCGGAGCTTCCCATTA
Found at i:52901101 original size:13 final size:13
Alignment explanation
Indices: 52901083--52901107 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52901073 GTGTTTAGGA
52901083 AAATTTCCAAATC
1 AAATTTCCAAATC
52901096 AAATTTCCAAAT
1 AAATTTCCAAAT
52901108 TTTCTTTGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATTTCCAAATC
Found at i:52906847 original size:21 final size:21
Alignment explanation
Indices: 52906821--52906863 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
52906811 TTAATTTTCT
* *
52906821 ACTCCTATTAACAATCTAACA
1 ACTCCTACTAACAAGCTAACA
52906842 ACTCCTACTAACAAGCTAACA
1 ACTCCTACTAACAAGCTAACA
52906863 A
1 A
52906864 ATCTCCCTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.30, G:0.02, T:0.23
Consensus pattern (21 bp):
ACTCCTACTAACAAGCTAACA
Found at i:52906885 original size:21 final size:21
Alignment explanation
Indices: 52906861--52906903 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
52906851 AACAAGCTAA
*
52906861 CAAATCTCCCTAGGACTTAGT
1 CAAATCTCCCTAGGACTCAGT
*
52906882 CAAATCTCCTTAGGACTCAGT
1 CAAATCTCCCTAGGACTCAGT
52906903 C
1 C
52906904 TTATTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.28
Consensus pattern (21 bp):
CAAATCTCCCTAGGACTCAGT
Found at i:52915524 original size:10 final size:9
Alignment explanation
Indices: 52915485--52915604 Score: 77
Period size: 10 Copynumber: 13.1 Consensus size: 9
52915475 ACATGTAATA
*
52915485 AAAAATGAT
1 AAAAATTAT
52915494 AAAAA--AT
1 AAAAATTAT
*
52915501 AAAAATCAAT
1 AAAAAT-TAT
*
52915511 AAAAGTTAT
1 AAAAATTAT
52915520 AAAAATTATT
1 AAAAATTA-T
**
52915530 AAATTTTAAT
1 AAAAATT-AT
*
52915540 AAAAA-TAG
1 AAAAATTAT
*
52915548 AAAAA-TAG
1 AAAAATTAT
52915556 AAAAATTTAT
1 AAAAA-TTAT
52915566 AAAAATTTAT
1 AAAAA-TTAT
52915576 AAAAATTTAT
1 AAAAA-TTAT
*
52915586 AAAAATTGT
1 AAAAATTAT
*
52915595 AAAAAATAT
1 AAAAATTAT
52915604 A
1 A
52915605 TATATAAAAT
Statistics
Matches: 92, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
7 7 0.08
8 14 0.15
9 26 0.28
10 44 0.48
11 1 0.01
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:52915581 original size:20 final size:19
Alignment explanation
Indices: 52915511--52915703 Score: 92
Period size: 20 Copynumber: 9.9 Consensus size: 19
52915501 AAAAATCAAT
* *
52915511 AAAAGTTATAAAAATTATT
1 AAAATTTATAAAAATTATA
* *
52915530 AAATTTTAATAAAAA-TAGA
1 AAAATTT-ATAAAAATTATA
*
52915549 AAAA--TAGAAAAATTTATA
1 AAAATTTATAAAAA-TTATA
52915567 AAAATTTATAAAAATTTATA
1 AAAATTTATAAAAA-TTATA
*
52915587 AAAATTGTAAAAAATATATATA
1 AAAATT-TATAAAA-AT-TATA
* *
52915609 TAAAATATATAGAAA-TATA
1 -AAAATTTATAAAAATTATA
* * **
52915628 AAATTTTAT-AAAGTCGTA
1 AAAATTTATAAAAATTATA
* * *
52915646 AGAAAATTATAAAAAATGTA
1 A-AAATTTATAAAAATTATA
*
52915666 AAAATATAT-AAAATTCATAA
1 AAAATTTATAAAAATT-AT-A
* *
52915686 AAAAATTATAAAATTTAT
1 AAAATTTATAAAAATTAT
52915704 CGTACCAAAA
Statistics
Matches: 129, Mismatches: 30, Indels: 29
0.69 0.16 0.15
Matches are distributed among these distances:
16 6 0.05
17 3 0.02
18 22 0.17
19 27 0.21
20 43 0.33
21 13 0.10
22 10 0.08
23 5 0.04
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (19 bp):
AAAATTTATAAAAATTATA
Found at i:52915677 original size:10 final size:10
Alignment explanation
Indices: 52915556--52915698 Score: 66
Period size: 10 Copynumber: 14.4 Consensus size: 10
52915546 AGAAAAATAG
*
52915556 AAAAATTTAT
1 AAAAATATAT
*
52915566 AAAAATTTAT
1 AAAAATATAT
*
52915576 AAAAATTTAT
1 AAAAATATAT
* *
52915586 AAAAATTGTAA
1 AAAAA-TATAT
52915597 AAAATATATAT
1 AAAA-ATATAT
52915608 ATAAAATATAT
1 A-AAAATATAT
*
52915619 -AGAA-ATAT
1 AAAAATATAT
* *
52915627 AAAATTTTAT
1 AAAAATATAT
* *
52915637 -AAAGTCGTA-
1 AAAAAT-ATAT
52915646 AGAAAAT-TAT
1 A-AAAATATAT
*
52915656 AAAAA-ATGT
1 AAAAATATAT
52915665 AAAAATATAT
1 AAAAATATAT
* *
52915675 AAAATTCATAA
1 AAAAAT-ATAT
52915686 AAAAAT-TAT
1 AAAAATATAT
52915695 AAAA
1 AAAA
52915699 TTTATCGTAC
Statistics
Matches: 104, Mismatches: 17, Indels: 25
0.71 0.12 0.17
Matches are distributed among these distances:
8 4 0.04
9 28 0.27
10 39 0.38
11 29 0.28
12 4 0.04
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (10 bp):
AAAAATATAT
Found at i:52915920 original size:9 final size:9
Alignment explanation
Indices: 52915888--52916006 Score: 56
Period size: 8 Copynumber: 13.3 Consensus size: 9
52915878 TTTTTGATGC
52915888 ATTTTATATA
1 ATTTT-TATA
52915898 TATTTTT-T-
1 -ATTTTTATA
52915906 ATTTTTATA
1 ATTTTTATA
*
52915915 ATTTTTTTA
1 ATTTTTATA
* *
52915924 CTTTTTTCTA
1 -ATTTTTATA
*
52915934 ATTTATA-A
1 ATTTTTATA
*
52915942 TATATTTTAAA
1 -AT-TTTTATA
52915953 TATTTTTAT-
1 -ATTTTTATA
52915962 ATTTTTATTA
1 ATTTTTA-TA
* *
52915972 AATTTAAT-
1 ATTTTTATA
52915980 ATTTTTAT-
1 ATTTTTATA
52915988 A-TTTTAT-
1 ATTTTTATA
52915995 ATTTTTATA
1 ATTTTTATA
52916004 ATT
1 ATT
52916007 CTTTTACCAC
Statistics
Matches: 86, Mismatches: 12, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
7 13 0.15
8 22 0.26
9 20 0.23
10 22 0.26
11 9 0.10
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (9 bp):
ATTTTTATA
Found at i:52915965 original size:8 final size:8
Alignment explanation
Indices: 52915942--52916003 Score: 63
Period size: 8 Copynumber: 7.5 Consensus size: 8
52915932 TAATTTATAA
52915942 TATATTTT
1 TATATTTT
*
52915950 AAATATTTT
1 -TATATTTT
52915959 TATATTTT
1 TATATTTT
*
52915967 TATTAAATTT
1 TA-T-ATTTT
*
52915977 AATATTTT
1 TATATTTT
52915985 TATA-TTT
1 TATATTTT
52915992 TATATTTT
1 TATATTTT
52916000 TATA
1 TATA
52916004 ATTCTTTTAC
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
7 7 0.16
8 23 0.52
9 9 0.20
10 5 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TATATTTT
Found at i:52916005 original size:26 final size:26
Alignment explanation
Indices: 52915896--52916005 Score: 60
Period size: 26 Copynumber: 3.8 Consensus size: 26
52915886 GCATTTTATA
* *
52915896 TATATTTTTTATTTTTATAATTTTTT
1 TATATTTTATATTTTTATAATATTTT
* * *
52915922 TACTTTTTTCTA-ATTTATAATATATTT
1 TA-TATTTTATATTTTTATAATAT-TTT
52915949 TAAATATTTTTATATTTTTATTAAATTTAATATTTT
1 T--ATA-TTTTATA--TTT-TT--A--TAATATTTT
52915985 TATATTTTATATTTTTATAAT
1 TATATTTTATATTTTTATAAT
52916006 TCTTTTACCA
Statistics
Matches: 64, Mismatches: 7, Indels: 26
0.66 0.07 0.27
Matches are distributed among these distances:
26 15 0.23
27 11 0.17
28 2 0.03
29 7 0.11
30 2 0.03
31 3 0.05
32 1 0.02
33 9 0.14
34 3 0.05
35 1 0.02
36 4 0.06
37 6 0.09
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (26 bp):
TATATTTTATATTTTTATAATATTTT
Found at i:52917765 original size:31 final size:31
Alignment explanation
Indices: 52917707--52917765 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
52917697 GATGCAATTA
* * *
52917707 TATACCTAAAATTTTGATTATGGTTTAAATG
1 TATACATAAAATTTTAATTATGATTTAAATG
* *
52917738 TATACATAAAATTTTAATTTTTATTTAA
1 TATACATAAAATTTTAATTATGATTTAA
52917766 CCATACACAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (31 bp):
TATACATAAAATTTTAATTATGATTTAAATG
Found at i:52918136 original size:14 final size:14
Alignment explanation
Indices: 52918117--52918165 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
52918107 TAAATCGAAA
*
52918117 AAAATTTCATGTAT
1 AAAATTTCATGAAT
*
52918131 AAAATTGCATGAAAT
1 AAAATTTCATG-AAT
52918146 CAAAATTT-ATGAAT
1 -AAAATTTCATGAAT
52918160 AAAATT
1 AAAATT
52918166 ACATATTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 6 0.20
14 13 0.43
15 5 0.17
16 6 0.20
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (14 bp):
AAAATTTCATGAAT
Found at i:52928332 original size:20 final size:20
Alignment explanation
Indices: 52928286--52928338 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
52928276 AATTAAATCA
52928286 TAAGTATCGATACCCTACTC
1 TAAGTATCGATACCCTACTC
* * * *
52928306 GACGTATCAATACCTTACTC
1 TAAGTATCGATACCCTACTC
52928326 TAAGTATCGATAC
1 TAAGTATCGATAC
52928339 TATGCCCCTA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.30
Consensus pattern (20 bp):
TAAGTATCGATACCCTACTC
Found at i:52929876 original size:38 final size:38
Alignment explanation
Indices: 52929834--52929910 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
52929824 TGAATGCAAG
52929834 TTAACTTGGAATTTCAATCACACGATCACTTTTCTTAT
1 TTAACTTGGAATTTCAATCACACGATCACTTTTCTTAT
52929872 TTAACTTGGAATTTCAATCACACGATCACTTTTCTTAT
1 TTAACTTGGAATTTCAATCACACGATCACTTTTCTTAT
52929910 T
1 T
52929911 ATCACTATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.43
Consensus pattern (38 bp):
TTAACTTGGAATTTCAATCACACGATCACTTTTCTTAT
Found at i:52937532 original size:18 final size:18
Alignment explanation
Indices: 52937509--52937544 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
52937499 CAGGTAATTC
52937509 TTATTATTTTTTCTTTCT
1 TTATTATTTTTTCTTTCT
52937527 TTATTATTTTTTCTTTCT
1 TTATTATTTTTTCTTTCT
52937545 CGTGTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (18 bp):
TTATTATTTTTTCTTTCT
Found at i:52939693 original size:21 final size:21
Alignment explanation
Indices: 52939652--52939694 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
52939642 AATAAAGTAG
*
52939652 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
52939673 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
52939694 A
1 A
52939695 AATTCATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:52939994 original size:16 final size:16
Alignment explanation
Indices: 52939973--52940037 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
52939963 TTGATTTGCT
52939973 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
52939989 ATTACGTCTCTATTCC
1 ATTACGCCTCTATTCC
52940005 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
52940021 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
52940037 A
1 A
52940038 ATACAGCGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.20, C:0.35, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:52945805 original size:25 final size:26
Alignment explanation
Indices: 52945764--52945812 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
52945754 TGGACTATGT
52945764 TTTTGAATTTGGTTTT-GTTTTTGAG
1 TTTTGAATTTGGTTTTGGTTTTTGAG
*
52945789 TTTTGAA-TTGTTCTTTGGTTTTTG
1 TTTTGAATTTGGT-TTTGGTTTTTG
52945813 GAAGTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 10 0.48
26 7 0.33
ACGTcount: A:0.10, C:0.02, G:0.22, T:0.65
Consensus pattern (26 bp):
TTTTGAATTTGGTTTTGGTTTTTGAG
Found at i:52947933 original size:24 final size:24
Alignment explanation
Indices: 52947901--52947951 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
52947891 TACTTGGGTA
52947901 ATTTGTCGTCAATTCATCCTTTAC
1 ATTTGTCGTCAATTCATCCTTTAC
*
52947925 ATTTTTCGTCAATTCATCCTTTAC
1 ATTTGTCGTCAATTCATCCTTTAC
52947949 ATT
1 ATT
52947952 CGTAGTGCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.24, G:0.06, T:0.49
Consensus pattern (24 bp):
ATTTGTCGTCAATTCATCCTTTAC
Found at i:52948139 original size:68 final size:68
Alignment explanation
Indices: 52947990--52948141 Score: 232
Period size: 68 Copynumber: 2.2 Consensus size: 68
52947980 ATCATCAAAA
* * * * * **
52947990 TGCCATAGCCTAGCTATGGTCTTACATATAAGCACTGCCATGGTCCAACCATGGTCTTACGTTCA
1 TGCCATAACCCAGTTATGGTCTTACATATAAACACTACCATGGTCCAACCACAGTCTTACGTTCA
52948055 TAG
66 TAG
*
52948058 TGCCATAACCCAGTTATGGTCTTACATATAAACACTACCATGGTCCAACCACAGTCTTACGTTTA
1 TGCCATAACCCAGTTATGGTCTTACATATAAACACTACCATGGTCCAACCACAGTCTTACGTTCA
52948123 TAG
66 TAG
52948126 TGCCATAACCCAGTTA
1 TGCCATAACCCAGTTA
52948142 CGGTGTTATC
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 76 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (68 bp):
TGCCATAACCCAGTTATGGTCTTACATATAAACACTACCATGGTCCAACCACAGTCTTACGTTCA
TAG
Found at i:52949011 original size:12 final size:12
Alignment explanation
Indices: 52948996--52949022 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
52948986 TGCTTATATG
52948996 TAATATTATCTA
1 TAATATTATCTA
52949008 TAATATTATCTA
1 TAATATTATCTA
52949020 TAA
1 TAA
52949023 GTCTACTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (12 bp):
TAATATTATCTA
Found at i:52953783 original size:81 final size:81
Alignment explanation
Indices: 52953664--52953820 Score: 228
Period size: 81 Copynumber: 1.9 Consensus size: 81
52953654 AACCCGAAAA
* * *
52953664 GGTAAAATGACCAAAATACCCCCGAAGGGTATAATGACCAAAATACCTTCGA-AAGGTAAAATGA
1 GGTAAAATGACCAAAATACCCCCGAAAGGTATAATGACCAAAACACCCTC-ATAAGGTAAAATGA
52953728 CCAAAATACCCTCAAAG
65 CCAAAATACCCTCAAAG
*
52953745 GGTATAATGACCAAAATACCCCCGAAAGGTA-ATATGACCAAAACACCCTCATAAGGTAAAATGA
1 GGTAAAATGACCAAAATACCCCCGAAAGGTATA-ATGACCAAAACACCCTCATAAGGTAAAATGA
* *
52953809 CTAATATACCCT
65 CCAAAATACCCT
52953821 TAGAATTGGA
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
80 2 0.03
81 66 0.97
ACGTcount: A:0.45, C:0.23, G:0.15, T:0.18
Consensus pattern (81 bp):
GGTAAAATGACCAAAATACCCCCGAAAGGTATAATGACCAAAACACCCTCATAAGGTAAAATGAC
CAAAATACCCTCAAAG
Found at i:52953819 original size:27 final size:27
Alignment explanation
Indices: 52953648--52953820 Score: 199
Period size: 27 Copynumber: 6.4 Consensus size: 27
52953638 CGCAAATTAT
*
52953648 CAAAATAACC-CGAAAAGGTAAAATGAC
1 CAAAATACCCTCG-AAAGGTAAAATGAC
* * *
52953675 CAAAATACCCCCGAAGGGTATAATGAC
1 CAAAATACCCTCGAAAGGTAAAATGAC
*
52953702 CAAAATACCTTCGAAAGGTAAAATGAC
1 CAAAATACCCTCGAAAGGTAAAATGAC
*
52953729 CAAAATACCCTC-AAAGGGTATAATGAC
1 CAAAATACCCTCGAAA-GGTAAAATGAC
* *
52953756 CAAAATACCCCCGAAAGGTAATATGAC
1 CAAAATACCCTCGAAAGGTAAAATGAC
*
52953783 CAAAACACCCTC-ATAAGGTAAAATGAC
1 CAAAATACCCTCGA-AAGGTAAAATGAC
* *
52953810 TAATATACCCT
1 CAAAATACCCT
52953821 TAGAATTGGA
Statistics
Matches: 124, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
26 4 0.03
27 115 0.93
28 5 0.04
ACGTcount: A:0.46, C:0.23, G:0.14, T:0.17
Consensus pattern (27 bp):
CAAAATACCCTCGAAAGGTAAAATGAC
Found at i:52954218 original size:28 final size:28
Alignment explanation
Indices: 52954172--52954260 Score: 99
Period size: 28 Copynumber: 3.2 Consensus size: 28
52954162 ATTGTAATGT
* * * * * *
52954172 TTACTATATTAGGCAAAGGCCCATATTG
1 TTACTGTATTGGGCTAAGGCCCACACTA
52954200 TTACTGTATTGGGCTAAGGCCCACACTA
1 TTACTGTATTGGGCTAAGGCCCACACTA
* *
52954228 TTACTGTAATGGGCTAAGGCCCACATTA
1 TTACTGTATTGGGCTAAGGCCCACACTA
52954256 -TACTG
1 TTACTG
52954261 ATACTGTATA
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 5 0.09
28 48 0.91
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.30
Consensus pattern (28 bp):
TTACTGTATTGGGCTAAGGCCCACACTA
Found at i:52954521 original size:18 final size:18
Alignment explanation
Indices: 52954498--52954534 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
52954488 TAATAAGGCC
*
52954498 TTTAATTTGGTTTTAAAT
1 TTTAATTGGGTTTTAAAT
*
52954516 TTTAATTGGGTTTTCAAT
1 TTTAATTGGGTTTTAAAT
52954534 T
1 T
52954535 ACATATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.03, G:0.14, T:0.59
Consensus pattern (18 bp):
TTTAATTGGGTTTTAAAT
Found at i:52958723 original size:21 final size:21
Alignment explanation
Indices: 52958697--52958752 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
52958687 AACAGTGGTG
*
52958697 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
52958718 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
52958739 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
52958753 AACAGCGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:52962663 original size:13 final size:13
Alignment explanation
Indices: 52962609--52962665 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
52962599 TCTTCAATTA
* *
52962609 TTTTTCATCTAGT
1 TTTTTTATCAAGT
*
52962622 TCTTTTATCAAGT
1 TTTTTTATCAAGT
*
52962635 TTTTAATTACCAAGT
1 TTTT--TTATCAAGT
52962650 TTTTTTATCAAGT
1 TTTTTTATCAAGT
52962663 TTT
1 TTT
52962666 GCAGCAAGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
13 24 0.67
15 12 0.33
ACGTcount: A:0.23, C:0.12, G:0.07, T:0.58
Consensus pattern (13 bp):
TTTTTTATCAAGT
Found at i:52962673 original size:25 final size:24
Alignment explanation
Indices: 52962645--52962727 Score: 78
Period size: 25 Copynumber: 3.4 Consensus size: 24
52962635 TTTTAATTAC
* *
52962645 CAAGTTTTTTTATCAAGTTTTGCAG
1 CAAGTTTTTTTAT-AAGTTTTCCAT
*
52962670 CAAGTTCTTTTTA-AAGTTTTTCAT
1 CAAGTT-TTTTTATAAGTTTTCCAT
* * *
52962694 CAAGTCTTTTCATAAAATTTTCCAT
1 CAAGTTTTTTTAT-AAGTTTTCCAT
52962719 CAAGTTTTT
1 CAAGTTTTT
52962728 AATCATTTCG
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
23 5 0.10
24 14 0.29
25 23 0.48
26 6 0.12
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (24 bp):
CAAGTTTTTTTATAAGTTTTCCAT
Found at i:52962705 original size:13 final size:12
Alignment explanation
Indices: 52962609--52962732 Score: 70
Period size: 12 Copynumber: 9.8 Consensus size: 12
52962599 TCTTCAATTA
*
52962609 TTTTTCATCTAG
1 TTTTTCATCAAG
*
52962621 TTCTTTTATCAAG
1 TT-TTTCATCAAG
*
52962634 TTTTTAATTACCAAG
1 TTTTTCA-T--CAAG
*
52962649 TTTTTTTATCAAG
1 -TTTTTCATCAAG
* *
52962662 TTTTGCAGCAAG
1 TTTTTCATCAAG
* *
52962674 TTCTTT-TTAAAG
1 TT-TTTCATCAAG
52962686 TTTTTCATCAAG
1 TTTTTCATCAAG
* *
52962698 TCTTTTCATAAAA
1 T-TTTTCATCAAG
*
52962711 TTTTCCATCAAG
1 TTTTTCATCAAG
*
52962723 TTTTTAATCA
1 TTTTTCATCA
52962733 TTTCGTTTTT
Statistics
Matches: 84, Mismatches: 20, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
11 3 0.04
12 43 0.51
13 27 0.32
15 5 0.06
16 6 0.07
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.51
Consensus pattern (12 bp):
TTTTTCATCAAG
Found at i:52966519 original size:47 final size:47
Alignment explanation
Indices: 52966446--52966673 Score: 365
Period size: 47 Copynumber: 4.9 Consensus size: 47
52966436 ACAATACTAT
*
52966446 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTTCA-
1 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTTCAC
*
52966492 ACACTCAGTATGGTTTTCTTTATTGAAATACCATACTTACTTTTTCA-
1 A-ACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTTCAC
52966539 ACACTCAGTATGGTTTTCTTTATTGAAATACCATACCTAC-TTTTCAC
1 A-ACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTTCAC
* *
52966586 AACTCAGTATAGTTTTCTTTATTGAAATATCATACCTACTTTTT-AC
1 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTTCAC
*
52966632 AACTCAGTATGGTTTTCTTTATTGAAATACCATGCCTACTTT
1 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTT
52966674 ACACACTTTG
Statistics
Matches: 171, Mismatches: 8, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
46 84 0.49
47 87 0.51
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (47 bp):
AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTTCAC
Found at i:52966601 original size:46 final size:46
Alignment explanation
Indices: 52966446--52966678 Score: 353
Period size: 46 Copynumber: 5.0 Consensus size: 46
52966436 ACAATACTAT
*
52966446 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTTCA-
1 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTAC-TTTTCAC
*
52966492 ACACTCAGTATGGTTTTCTTTATTGAAATACCATACTTACTTTTTCA-
1 A-ACTCAGTATGGTTTTCTTTATTGAAATACCATACCTAC-TTTTCAC
52966539 ACACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTCAC
1 A-ACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTCAC
* * *
52966586 AACTCAGTATAGTTTTCTTTATTGAAATATCATACCTACTTTTTAC
1 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTCAC
* *
52966632 AACTCAGTATGGTTTTCTTTATTGAAATACCATGCCTACTTTACAC
1 AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTCAC
52966678 A
1 A
52966679 CTTTGCCATG
Statistics
Matches: 174, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
46 91 0.52
47 83 0.48
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.42
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTATTGAAATACCATACCTACTTTTCAC
Found at i:52968424 original size:23 final size:22
Alignment explanation
Indices: 52968398--52968442 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
52968388 ATCATCATAT
52968398 ACTTCCAACATGCATTCATAGAA
1 ACTTCCAAC-TGCATTCATAGAA
* * *
52968421 ACTTTCAACTTCTTTCATAGAA
1 ACTTCCAACTGCATTCATAGAA
52968443 TCAAAAACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (22 bp):
ACTTCCAACTGCATTCATAGAA
Found at i:52970177 original size:19 final size:19
Alignment explanation
Indices: 52970145--52970189 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
52970135 AATTTTCCTA
* *
52970145 TTATTATTATTATTATTA-T
1 TTATTTTTACTATT-TTATT
52970164 TTATTTTTACTATTTTATT
1 TTATTTTTACTATTTTATT
52970183 TTATTTT
1 TTATTTT
52970190 CATTTTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (19 bp):
TTATTTTTACTATTTTATT
Found at i:52971650 original size:12 final size:12
Alignment explanation
Indices: 52971607--52971706 Score: 58
Period size: 12 Copynumber: 8.0 Consensus size: 12
52971597 CTTTTCATCT
52971607 AGTTCTTTTATCA
1 AGTT-TTTTATCA
*
52971620 AGTTTTTAATTACCA
1 AG-TTTT--TTATCA
52971635 AGTTTTTTATCA
1 AGTTTTTTATCA
** *
52971647 AGTTTTGCAGCA
1 AGTTTTTTATCA
*
52971659 AGTTCTTTT-TAA
1 AGTT-TTTTATCA
* *
52971671 AGTTTTTCATAA
1 AGTTTTTTATCA
* *
52971683 AATTTTCTATCA
1 AGTTTTTTATCA
*
52971695 AGTTTTTAATCA
1 AGTTTTTTATCA
52971707 TTTCGTTTTT
Statistics
Matches: 65, Mismatches: 17, Indels: 11
0.70 0.18 0.12
Matches are distributed among these distances:
11 3 0.05
12 43 0.66
13 6 0.09
14 6 0.09
15 7 0.11
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (12 bp):
AGTTTTTTATCA
Found at i:52973798 original size:39 final size:39
Alignment explanation
Indices: 52973613--52973812 Score: 204
Period size: 39 Copynumber: 5.1 Consensus size: 39
52973603 ACTTCCAATA
* * ** *
52973613 CACCGGCACACAGCCTGCTAGGCACAAAGGCC-GAAAAAT
1 CACCGGCACAAAGCCTACTAGGCACTTA-GCCTGAATAAT
* *
52973652 CACAGGCACAAAGCCTACTAGGCACTTAGCCCGAATAAT
1 CACCGGCACAAAGCCTACTAGGCACTTAGCCTGAATAAT
* * * *
52973691 CACCGGCATAAAGCTTGCTAGGCATTTAGCCTGAATAAT
1 CACCGGCACAAAGCCTACTAGGCACTTAGCCTGAATAAT
* ** * *
52973730 CACCAGCACAAAATCTGCTAAGCACTTAGCCTGAATAAT
1 CACCGGCACAAAGCCTACTAGGCACTTAGCCTGAATAAT
* * * *
52973769 CACTGGCATAAAGCCTACTAGGCATTTAGCTTGAATAAT
1 CACCGGCACAAAGCCTACTAGGCACTTAGCCTGAATAAT
52973808 CACCG
1 CACCG
52973813 TATTTTTATT
Statistics
Matches: 131, Mismatches: 29, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
38 3 0.02
39 128 0.98
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.19
Consensus pattern (39 bp):
CACCGGCACAAAGCCTACTAGGCACTTAGCCTGAATAAT
Found at i:52979982 original size:24 final size:24
Alignment explanation
Indices: 52979948--52980033 Score: 75
Period size: 24 Copynumber: 3.6 Consensus size: 24
52979938 TCGAAAACCT
*
52979948 GGAGGCATGCCTGGTGGG-TTTCCA
1 GGAGGAATGCCTGG-GGGTTTTCCA
* *
52979972 GGTGGAATGCCTGGGGGTTTTCCC
1 GGAGGAATGCCTGGGGGTTTTCCA
* * * * *
52979996 GGAGGTATGCCTGGAGGTATGCCT
1 GGAGGAATGCCTGGGGGTTTTCCA
*
52980020 GGAGGTATGCCTGG
1 GGAGGAATGCCTGG
52980034 AGGCATGCCG
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 3 0.06
24 49 0.94
ACGTcount: A:0.13, C:0.19, G:0.43, T:0.26
Consensus pattern (24 bp):
GGAGGAATGCCTGGGGGTTTTCCA
Found at i:52980013 original size:12 final size:12
Alignment explanation
Indices: 52979996--52980058 Score: 90
Period size: 12 Copynumber: 5.2 Consensus size: 12
52979986 GGGTTTTCCC
52979996 GGAGGTATGCCT
1 GGAGGTATGCCT
52980008 GGAGGTATGCCT
1 GGAGGTATGCCT
52980020 GGAGGTATGCCT
1 GGAGGTATGCCT
* *
52980032 GGAGGCATGCCG
1 GGAGGTATGCCT
* *
52980044 GGTGGCATGCCT
1 GGAGGTATGCCT
52980056 GGA
1 GGA
52980059 AATGTTGATT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.16, C:0.19, G:0.44, T:0.21
Consensus pattern (12 bp):
GGAGGTATGCCT
Found at i:52980018 original size:36 final size:36
Alignment explanation
Indices: 52979978--52980058 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
52979968 TCCAGGTGGA
* * * * * *
52979978 ATGCCTGGGGGTTTTCCCGGAGGTATGCCTGGAGGT
1 ATGCCTGGAGGTATGCCCGGAGGCATGCCGGGAGGC
* *
52980014 ATGCCTGGAGGTATGCCTGGAGGCATGCCGGGTGGC
1 ATGCCTGGAGGTATGCCCGGAGGCATGCCGGGAGGC
52980050 ATGCCTGGA
1 ATGCCTGGA
52980059 AATGTTGATT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.14, C:0.21, G:0.42, T:0.23
Consensus pattern (36 bp):
ATGCCTGGAGGTATGCCCGGAGGCATGCCGGGAGGC
Found at i:52980034 original size:24 final size:24
Alignment explanation
Indices: 52979978--52980058 Score: 90
Period size: 24 Copynumber: 3.4 Consensus size: 24
52979968 TCCAGGTGGA
* * *
52979978 ATGCCTGGGGGTTTTCCCGGAGGT
1 ATGCCTGGAGGTATGCCCGGAGGT
*
52980002 ATGCCTGGAGGTATGCCTGGAGGT
1 ATGCCTGGAGGTATGCCCGGAGGT
* * * *
52980026 ATGCCTGGAGGCATGCCGGGTGGC
1 ATGCCTGGAGGTATGCCCGGAGGT
52980050 ATGCCTGGA
1 ATGCCTGGA
52980059 AATGTTGATT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.14, C:0.21, G:0.42, T:0.23
Consensus pattern (24 bp):
ATGCCTGGAGGTATGCCCGGAGGT
Found at i:52985525 original size:30 final size:30
Alignment explanation
Indices: 52985491--52985552 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
52985481 TCAAGTCCCA
* *
52985491 TAAAATTTATG-AAATTTTTATTAAATCTCT
1 TAAAATTTATGAAAATATTAATTAAAT-TCT
*
52985521 TAAAATTTTTGAAAATATTAATTAAATTCT
1 TAAAATTTATGAAAATATTAATTAAATTCT
52985551 TA
1 TA
52985553 TTTTTACTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (30 bp):
TAAAATTTATGAAAATATTAATTAAATTCT
Found at i:52988295 original size:3 final size:3
Alignment explanation
Indices: 52988287--52988331 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
52988277 GATCTGGAAT
52988287 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
52988332 GTGAAATCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:52988705 original size:13 final size:13
Alignment explanation
Indices: 52988653--52988705 Score: 79
Period size: 13 Copynumber: 4.1 Consensus size: 13
52988643 AGTTTGTCAA
*
52988653 TGCTTTTGAAATG
1 TGCTTTTGAAAAG
52988666 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
52988679 TGTTTTTGAGAAG
1 TGCTTTTGAAAAG
52988692 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
52988705 T
1 T
52988706 TTGGTTTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.43
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:53000288 original size:53 final size:53
Alignment explanation
Indices: 53000228--53000333 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
53000218 TCTCTTCCCA
*
53000228 AAAGTCTGACGTTAGTTTTCTTTTTTCTCTGCCATATTTTTTTCTCTTCTTTT
1 AAAGTCTGACGTTAGTTTTCTTTTTTCTCTGCCACATTTTTTTCTCTTCTTTT
53000281 AAAGTCTGACGTTAGTTTTCTTTTTTCTCTGCCACATTTTTTTCTCTTCTTTT
1 AAAGTCTGACGTTAGTTTTCTTTTTTCTCTGCCACATTTTTTTCTCTTCTTTT
53000334 TCCTGTAATT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.13, C:0.20, G:0.09, T:0.58
Consensus pattern (53 bp):
AAAGTCTGACGTTAGTTTTCTTTTTTCTCTGCCACATTTTTTTCTCTTCTTTT
Found at i:53001767 original size:22 final size:22
Alignment explanation
Indices: 53001726--53001767 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
53001716 CTCTCTGGGC
* *
53001726 TTTTTGGATTGTTTGGTTTAAA
1 TTTTTGGATTGGTTGCTTTAAA
*
53001748 TTTTTGGTTTGGTTGCTTTA
1 TTTTTGGATTGGTTGCTTTA
53001768 TGATTTCTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.12, C:0.02, G:0.24, T:0.62
Consensus pattern (22 bp):
TTTTTGGATTGGTTGCTTTAAA
Found at i:53011099 original size:51 final size:52
Alignment explanation
Indices: 53011035--53011372 Score: 340
Period size: 51 Copynumber: 6.7 Consensus size: 52
53011025 TATCGATGAA
* * * *
53011035 CACGTGTGTAGTACTGTGTAAAGGCTACTACGTGTATCGATAAATA-ATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTTGGT
* * *
53011086 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGT-TTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA-TATTTGGT
* **
53011137 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATGA--TGAA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATTTGGT
* * * * *
53011188 CAC--GTGTAGTACTAAGTGATGGCTACTATGTGTACC-AAAAAGATTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTTGGT
* * * *
53011237 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAATCG-TAAA-ATTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTTGGT
* * * * *
53011287 CACGTGTGTAGTACTATGTGACGGCTACTTCGTGAACCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTTGGT
* *
53011337 CACGTGTGTAGTACTATATGAAGGCTACTAAGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
53011373 TCGAATGATA
Statistics
Matches: 240, Mismatches: 37, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
47 1 0.00
48 4 0.02
49 34 0.14
50 85 0.35
51 113 0.47
52 3 0.01
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (52 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTTGGT
Found at i:53011236 original size:100 final size:99
Alignment explanation
Indices: 53011035--53011376 Score: 402
Period size: 100 Copynumber: 3.4 Consensus size: 99
53011025 TATCGATGAA
* * * *
53011035 CACGTGTGTAGTACTGTGTAAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAAT-AT-G-AACACGTGTAGTAC
*
53011100 TAAGTGAAGGCTACTATGTGTACCGAAAAGTTTTGGT
63 TAAGTGAAGGCTACTATGTGTACCGAAAAGATTTGGT
* *
53011137 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATGATGAACACGTGTAGTACTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAAT-ATGAACACGTGTAGTACTA
* *
53011202 AGTGATGGCTACTATGTGTACCAAAAAGATTTGGT
65 AGTGAAGGCTACTATGTGTACCGAAAAGATTTGGT
* * * *
53011237 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAATCG-TAAAATTTGATCACGTGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAT-AAATATGAACAC--GTGTAGTAC
* * * * * *
53011301 TATGTGACGGCTACT-TCGTGAACCGTAAA-ACTTGAT
63 TAAGTGAAGGCTACTAT-GTGTACCGAAAAGATTTGGT
* *
53011337 CACGTGTGTAGTACTATATGAAGGCTACTAAGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
53011377 ATGATAAAAG
Statistics
Matches: 211, Mismatches: 24, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
99 7 0.03
100 127 0.60
101 32 0.15
102 45 0.21
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (99 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATATGAACACGTGTAGTACTAA
GTGAAGGCTACTATGTGTACCGAAAAGATTTGGT
Found at i:53011409 original size:151 final size:152
Alignment explanation
Indices: 53011030--53011383 Score: 398
Period size: 151 Copynumber: 2.3 Consensus size: 152
53011020 TAAGGTATCG
* * * * *
53011030 ATGAACACGTGTGTAGTACTGTGTAAAGGCTACTACGTGTATCG-ATAAATAATGGTCACATGTG
1 ATGAACACGTGTGTAGTACTATATGAAGGCTACTAAGTGTATCGAAT-GATAATGGTCACATGTG
* * * *
53011094 TAGTACTAAGTGAAGGCTACTATGTGTACCGAAAAGTTTTGGTCACGTGTGTAGTACTGTGTGAA
65 TAGTACTATGTGAAGGCTACTATGTGAACCGAAAAG-TTTGATCACGTGTGTAGTACTATGTGAA
* **
53011159 GGCTACTACGTGTACCGATAAATG
129 GGCTACTACGTGAACCGATAAAAC
* * * * * * *
53011183 ATGAACAC--GTGTAGTACTA-AGTGATGGCTACTATGTGTACCAAAAAGAT-TTGGTCACGTGT
1 ATGAACACGTGTGTAGTACTATA-TGAAGGCTACTAAGTGTATC-GAATGATAATGGTCACATGT
*
53011244 GTAGTACTATGTGAAGGCTACTATGTGAATCGTAAAA-TTTGATCACGTGTGTAGTACTATGTGA
64 GTAGTACTATGTGAAGGCTACTATGTGAACCG-AAAAGTTTGATCACGTGTGTAGTACTATGTGA
* *
53011308 CGGCTACTTCGTGAACCG-TAAAAC
128 AGGCTACTACGTGAACCGATAAAAC
* *
53011332 TTGATCACGTGTGTAGTACTATATGAAGGCTACTAAGTGTATCGAATGATAA
1 ATGAACACGTGTGTAGTACTATATGAAGGCTACTAAGTGTATCGAATGATAA
53011384 AAGTAACATG
Statistics
Matches: 164, Mismatches: 29, Indels: 18
0.78 0.14 0.09
Matches are distributed among these distances:
149 10 0.06
150 45 0.27
151 93 0.57
152 7 0.04
153 9 0.05
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (152 bp):
ATGAACACGTGTGTAGTACTATATGAAGGCTACTAAGTGTATCGAATGATAATGGTCACATGTGT
AGTACTATGTGAAGGCTACTATGTGAACCGAAAAGTTTGATCACGTGTGTAGTACTATGTGAAGG
CTACTACGTGAACCGATAAAAC
Found at i:53013811 original size:25 final size:25
Alignment explanation
Indices: 53013733--53013862 Score: 84
Period size: 25 Copynumber: 5.2 Consensus size: 25
53013723 TTAGCTCTTT
* *
53013733 TGAGCATCCCGTTATATGGCTCTCA
1 TGAGCTTCCCGTTATATGGCTCGCA
* *** * *
53013758 CGAGCTTCCAAATAGT-TGGCTCTCT
1 TGAGCTTCCCGTTA-TATGGCTCGCA
*
53013783 TGAGCTTCCCGTTATATGGCTCACA
1 TGAGCTTCCCGTTATATGGCTCGCA
* * ** * *
53013808 TGAGCATCCTGTTCCATAGCTCGGA
1 TGAGCTTCCCGTTATATGGCTCGCA
*
53013833 AGAGCTTCCCGTTTATAT-GCTCGCA
1 TGAGCTTCCCG-TTATATGGCTCGCA
53013858 TGAGC
1 TGAGC
53013863 ATACCTGTAT
Statistics
Matches: 76, Mismatches: 26, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
24 1 0.01
25 70 0.92
26 5 0.07
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.31
Consensus pattern (25 bp):
TGAGCTTCCCGTTATATGGCTCGCA
Found at i:53015403 original size:40 final size:41
Alignment explanation
Indices: 53015359--53015559 Score: 162
Period size: 41 Copynumber: 4.9 Consensus size: 41
53015349 GAAATTCAAG
* * * *
53015359 ATAGCTTTGGTTATTAATGGCACTTAGTGTGTG-ATTTGGA
1 ATAGCTTTGGCTATTAATGGCACTTAGTGTGCGAAATTAGA
*
53015399 ATAGCTTTGGCTA-TATATGGCACTTAGTGTGCGAAATTATA
1 ATAGCTTTGGCTATTA-ATGGCACTTAGTGTGCGAAATTAGA
* * *
53015440 ATAGCTTCGGCTATGTAA-GGCACTTAGTGTAC-AGAATTATA
1 ATAGCTTTGGCTAT-TAATGGCACTTAGTGTGCGA-AATTAGA
* * *
53015481 ATAGCTTCGGCTAGGTAA-GGCACTTAGTGTGC-AGAATTATA
1 ATAGCTTTGGCTA-TTAATGGCACTTAGTGTGCGA-AATTAGA
* * * *
53015522 ATAGCTTTAGCTATATGATTGGCAATTAGTGTGTGAAA
1 ATAGCTTTGGCTAT-T-AATGGCACTTAGTGTGCGAAA
53015560 CATTGATTGT
Statistics
Matches: 136, Mismatches: 15, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
39 2 0.01
40 29 0.21
41 86 0.63
42 2 0.01
43 16 0.12
44 1 0.01
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.35
Consensus pattern (41 bp):
ATAGCTTTGGCTATTAATGGCACTTAGTGTGCGAAATTAGA
Found at i:53015462 original size:41 final size:41
Alignment explanation
Indices: 53015359--53015528 Score: 202
Period size: 41 Copynumber: 4.2 Consensus size: 41
53015349 GAAATTCAAG
* * * * **
53015359 ATAGCTTTGGTTAT-TAATGGCACTTAGTGTG-TGATTTGGA
1 ATAGCTTCGGCTATGTAA-GGCACTTAGTGTGCAGAATTATA
* * *
53015399 ATAGCTTTGGCTATATATGGCACTTAGTGTGC-GAAATTATA
1 ATAGCTTCGGCTATGTAAGGCACTTAGTGTGCAG-AATTATA
*
53015440 ATAGCTTCGGCTATGTAAGGCACTTAGTGTACAGAATTATA
1 ATAGCTTCGGCTATGTAAGGCACTTAGTGTGCAGAATTATA
*
53015481 ATAGCTTCGGCTAGGTAAGGCACTTAGTGTGCAGAATTATA
1 ATAGCTTCGGCTATGTAAGGCACTTAGTGTGCAGAATTATA
53015522 ATAGCTT
1 ATAGCTT
53015529 TAGCTATATG
Statistics
Matches: 115, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
40 27 0.23
41 87 0.76
42 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.35
Consensus pattern (41 bp):
ATAGCTTCGGCTATGTAAGGCACTTAGTGTGCAGAATTATA
Found at i:53023464 original size:25 final size:25
Alignment explanation
Indices: 53023386--53023477 Score: 105
Period size: 25 Copynumber: 3.7 Consensus size: 25
53023376 TTCTGTTGTA
*
53023386 TGGCTCTCACGAGCTTTCCGATAAT
1 TGGCTCTCACGAGCTTCCCGATAAT
*
53023411 TGGCTCTCACGAGCTTCCCAATAAT
1 TGGCTCTCACGAGCTTCCCGATAAT
** *
53023436 TGGCTCTCTTGAGCTTCCCG-TTAT
1 TGGCTCTCACGAGCTTCCCGATAAT
* *
53023460 ATGGCTCACATGAGCTTC
1 -TGGCTCTCACGAGCTTC
53023478 ATGTTCCATG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
24 3 0.05
25 55 0.95
ACGTcount: A:0.18, C:0.29, G:0.20, T:0.33
Consensus pattern (25 bp):
TGGCTCTCACGAGCTTCCCGATAAT
Found at i:53023705 original size:23 final size:23
Alignment explanation
Indices: 53023675--53023724 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
53023665 ATAATTGAAA
53023675 TACATGGATATGGTTGTACTTAT
1 TACATGGATATGGTTGTACTTAT
53023698 TACATGGATATGGTTGTACTTAT
1 TACATGGATATGGTTGTACTTAT
53023721 TACA
1 TACA
53023725 AGGACACATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (23 bp):
TACATGGATATGGTTGTACTTAT
Found at i:53026584 original size:2 final size:2
Alignment explanation
Indices: 53026577--53026623 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
53026567 TGTATGTATG
53026577 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
53026619 GA TA T
1 TA TA T
53026624 CACCAGCTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:53027106 original size:2 final size:2
Alignment explanation
Indices: 53027099--53027146 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
53027089 AGATTCCTGC
*
53027099 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53027141 AT AT AT
1 AT AT AT
53027147 TCATCTTATT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53034701 original size:95 final size:95
Alignment explanation
Indices: 53034587--53034766 Score: 315
Period size: 95 Copynumber: 1.9 Consensus size: 95
53034577 AAAAATATTT
* * *
53034587 ATATTATCAGCCGGCATCCCATGGGTAAAAGAAACTAGAATATTTTATTACAAGGTTGTTTAAAA
1 ATATGATCAGCCGACATCCCATGGGTAAAAGAAACTAGAATATTTTATTACAAGGCTGTTTAAAA
53034652 ATGAAAATAAAAAATCATGTGGCATTTCGC
66 ATGAAAATAAAAAATCATGTGGCATTTCGC
* *
53034682 ATATGATCAGCCGATATCCCATGGGTAAAATAAACTAGAATATTTTATTACAAGGCTGTTTAAAA
1 ATATGATCAGCCGACATCCCATGGGTAAAAGAAACTAGAATATTTTATTACAAGGCTGTTTAAAA
53034747 ATGAAAATAAAAAATCATGT
66 ATGAAAATAAAAAATCATGT
53034767 TCACACTCTA
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 80 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (95 bp):
ATATGATCAGCCGACATCCCATGGGTAAAAGAAACTAGAATATTTTATTACAAGGCTGTTTAAAA
ATGAAAATAAAAAATCATGTGGCATTTCGC
Found at i:53039462 original size:31 final size:31
Alignment explanation
Indices: 53039427--53039490 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
53039417 AATTAAGTCA
53039427 TTTTAATGATTGATATAAATTTGATAAATTT
1 TTTTAATGATTGATATAAATTTGATAAATTT
53039458 TTTTAATGATTGATATAAATTTGATAAATTT
1 TTTTAATGATTGATATAAATTTGATAAATTT
53039489 TT
1 TT
53039491 ACACGCATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (31 bp):
TTTTAATGATTGATATAAATTTGATAAATTT
Found at i:53049554 original size:12 final size:12
Alignment explanation
Indices: 53049537--53049571 Score: 63
Period size: 11 Copynumber: 3.0 Consensus size: 12
53049527 AAAAAACCAT
53049537 AAAATTATAAAA
1 AAAATTATAAAA
53049549 AAAATTAT-AAA
1 AAAATTATAAAA
53049560 AAAATTATAAAA
1 AAAATTATAAAA
53049572 TTTTTATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAATTATAAAA
Found at i:53049729 original size:21 final size:19
Alignment explanation
Indices: 53049704--53049764 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 19
53049694 AATTTTACAA
53049704 TTTTATAATTTTTCAAATTT
1 TTTTATAATTTTT-AAATTT
* *
53049724 TGTTTACAATTTTTATGATTT
1 T-TTTATAATTTTTA-AATTT
*
53049745 TTTAATAATTTTTAAATTT
1 TTTTATAATTTTTAAATTT
53049764 T
1 T
53049765 AAAAGGGCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
19 5 0.15
20 13 0.38
21 16 0.47
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTATAATTTTTAAATTT
Found at i:53064520 original size:41 final size:40
Alignment explanation
Indices: 53064464--53064608 Score: 129
Period size: 41 Copynumber: 3.6 Consensus size: 40
53064454 TGATTCGATA
53064464 CACCGGC-TTATAGCCTGCTAGACCTATAGTCCGAAATGTAT
1 CACCGGCATTA-AGCCTGCTAGACCTATAGTCCGAAAT-TAT
* * *
53064505 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTG-AATTAATT
1 CACCGGCATTAAGCCTGCTAGACCTATAGTCCGAAATT-A-T
* *
53064546 CACCGGCATTAAGCCTGCTAGGCAC-ATAG-CCTGAATTATAT
1 CACCGGCATTAAGCCTGCTAGAC-CTATAGTCC-GAAAT-TAT
**
53064587 CACC-GCATCCAGCCTGCTAGAC
1 CACCGGCATTAAGCCTGCTAGAC
53064609 AATAAGTCTG
Statistics
Matches: 86, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
39 1 0.01
40 20 0.23
41 58 0.67
42 6 0.07
43 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.24
Consensus pattern (40 bp):
CACCGGCATTAAGCCTGCTAGACCTATAGTCCGAAATTAT
Found at i:53065116 original size:2 final size:2
Alignment explanation
Indices: 53065109--53065138 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53065099 TCCAAGAGTT
53065109 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53065139 CTTTTATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53066968 original size:17 final size:18
Alignment explanation
Indices: 53066938--53066971 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
53066928 GTGATGTATC
53066938 TTATGAAATCAACTTATG
1 TTATGAAATCAACTTATG
*
53066956 TTAT-AAATGAACTTAT
1 TTATGAAATCAACTTAT
53066972 ACGAGATGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (18 bp):
TTATGAAATCAACTTATG
Found at i:53068593 original size:27 final size:26
Alignment explanation
Indices: 53068544--53068615 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
53068534 TTTGGGTTCA
*
53068544 AGTTTGGGTTCGAGGTTCGGGGTTTG
1 AGTTTGGGTTCGAGGTTCAGGGTTTG
*
53068570 AGTTTGGGATTCGAGG-TCTAGGGTTTA
1 AGTTTGGG-TTCGAGGTTC-AGGGTTTG
*
53068597 ATGTTTAGGGTTCAAGGTT
1 A-GTTT-GGGTTCGAGGTT
53068616 TGAGGTTTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
26 10 0.26
27 14 0.37
28 10 0.26
29 4 0.11
ACGTcount: A:0.15, C:0.07, G:0.39, T:0.39
Consensus pattern (26 bp):
AGTTTGGGTTCGAGGTTCAGGGTTTG
Found at i:53072000 original size:22 final size:22
Alignment explanation
Indices: 53071972--53072034 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
53071962 TTTATTGTTC
53071972 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
*
53071994 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTG
**
53072016 AGCCATGAGAGCTTAGTAC
1 AAACATGAGAGCTTAGTAC
53072035 TTGCATATGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:53077213 original size:19 final size:19
Alignment explanation
Indices: 53077189--53077227 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
53077179 AAATAATTTA
*
53077189 ATATAAATTA-TATATGTAT
1 ATATAAAATAGTATAT-TAT
53077208 ATATAAAATAGTATATTAT
1 ATATAAAATAGTATATTAT
53077227 A
1 A
53077228 AAACCATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (19 bp):
ATATAAAATAGTATATTAT
Found at i:53077342 original size:2 final size:2
Alignment explanation
Indices: 53077335--53077369 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
53077325 TTGGATTTAA
53077335 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53077370 AACTTAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53080689 original size:44 final size:44
Alignment explanation
Indices: 53080626--53080713 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
53080616 ACCAAAAACA
53080626 AATATAGGTGAAGTTGATTATACGCATGTCTTTTTAAATTTAAG
1 AATATAGGTGAAGTTGATTATACGCATGTCTTTTTAAATTTAAG
53080670 AATATAGGTGAAGTTGATTATACGCATGTCTTTTTAAATTTAAG
1 AATATAGGTGAAGTTGATTATACGCATGTCTTTTTAAATTTAAG
53080714 GCCAAAGATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (44 bp):
AATATAGGTGAAGTTGATTATACGCATGTCTTTTTAAATTTAAG
Found at i:53082428 original size:16 final size:16
Alignment explanation
Indices: 53082399--53082452 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
53082389 TTTGGTTCAC
* *
53082399 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
*
53082415 CGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
53082431 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
53082447 TGTAAT
1 TGTAAT
53082453 AAGAAATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.33, C:0.02, G:0.35, T:0.30
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:53082497 original size:45 final size:44
Alignment explanation
Indices: 53082431--53082521 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 44
53082421 GGAATAGAGG
**
53082431 TGTAATGGAATAGAGGTGTAATAAGAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGCCGTAAT-AGAAATCAACTGTTTGGTTGAA
* * ***
53082476 TGTAATGGAATTGAGCCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGCCGTAATAGAAATCAACTGTTTGGTTGAA
53082520 TG
1 TG
53082522 AAATAGAGGT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 20 0.51
45 19 0.49
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.35
Consensus pattern (44 bp):
TGTAATGGAATAGAGCCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:53082703 original size:16 final size:16
Alignment explanation
Indices: 53082666--53082707 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
53082656 TTAATCATAT
53082666 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATTA
53082682 TT-AAATATATTATTA
1 TTAAAATATATTATTA
53082697 TTAAAATATAT
1 TTAAAATATAT
53082708 AATTTAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.12
15 11 0.46
16 10 0.42
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAAATATATTATTA
Found at i:53082767 original size:61 final size:61
Alignment explanation
Indices: 53082699--53082999 Score: 257
Period size: 59 Copynumber: 5.0 Consensus size: 61
53082689 TATTATTATT
*
53082699 AAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCGAATC
1 AAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATC
* * * * * * * * * *
53082760 ATAATATATGATACT-ATAAAATT-TAAATTAA-C-ATAATTATTAT-TAAATATA-TTATTATT
1 AAAATATATAAT-TTAATAAAATTCTTAA-TAATCAAT-ATTCTTATATGAATTTACTCA-AATC
53082819 AAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATC
1 AAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATC
* * * * * * * * *
53082880 ATAATATATGATACT-ATAAAATT-TAAATTAA-C-ATAATTATTAT-TAAATATA-TTATAATT
1 AAAATATATAAT-TTAATAAAATTCTTAA-TAATCAAT-ATTCTTATATGAATTTACTCA-AATC
*
53082939 AAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
1 AAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATC
53083000 NNNNNNNNNN
Statistics
Matches: 180, Mismatches: 40, Indels: 40
0.69 0.15 0.15
Matches are distributed among these distances:
58 5 0.03
59 63 0.35
60 43 0.24
61 63 0.35
62 6 0.03
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (61 bp):
AAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATC
Found at i:53082813 original size:120 final size:120
Alignment explanation
Indices: 53082669--53082999 Score: 635
Period size: 120 Copynumber: 2.8 Consensus size: 120
53082659 ATCATATTTA
53082669 AACATAATTATTATTAAATATATTATTATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATTATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
53082734 TATTCTTATATGAATTTACTCGAATCATAATATATGATACTATAAAATTTAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATT
53082789 AACATAATTATTATTAAATATATTATTATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATTATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
53082854 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATT
* *
53082909 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATTATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
53082974 TATTCTTATATGAATTTACTCAAATC
66 TATTCTTATATGAATTTACTCAAATC
53083000 NNNNNNNNNN
Statistics
Matches: 208, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 208 1.00
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATTATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATT
Found at i:53082818 original size:18 final size:16
Alignment explanation
Indices: 53082786--53082827 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
53082776 TAAAATTTAA
*
53082786 ATTAACATA-ATTATT
1 ATTAAAATATATTATT
53082801 ATT-AAATATATTATT
1 ATTAAAATATATTATT
53082816 ATTAAAATATAT
1 ATTAAAATATAT
53082828 AATTTAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 12 0.50
16 8 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTAAAATATATTATT
Found at i:53082954 original size:14 final size:15
Alignment explanation
Indices: 53082905--53082956 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
53082895 ATAAAATTTA
53082905 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
53082920 TATTAAATATATTAT
1 AATTAAATATATTAT
53082935 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
53082948 AATTTAATA
1 AATTAAATA
53082957 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:53083192 original size:26 final size:25
Alignment explanation
Indices: 53083125--53083193 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 25
53083115 TAATTTTTCT
53083125 TATATGAATTTGTATAATTTAAAATAA
1 TATAT-AATTT-TATAATTTAAAATAA
* *
53083152 T-TATTATTACATATAATTTAATAATAA
1 TATATAATT--TTATAATTTAA-AATAA
53083179 TATATAATTTTATAA
1 TATATAATTTTATAA
53083194 AATTATTGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
25 3 0.09
26 18 0.53
27 7 0.21
28 6 0.18
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (25 bp):
TATATAATTTTATAATTTAAAATAA
Found at i:53083195 original size:47 final size:45
Alignment explanation
Indices: 53083144--53083287 Score: 109
Period size: 47 Copynumber: 3.1 Consensus size: 45
53083134 TTGTATAATT
53083144 TAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTTA
1 TAAAATAATTA-TATTA-ATATAATTTAATAATAATATATAATTTTA
* * ** * *
53083191 TAAAATTATTGATAATAAT-T--TTTCTTATATGAATTTATACA-ATT-
1 TAAAATAATT-ATATTAATATAATTTAATA-AT-AATATATA-ATTTTA
* *
53083235 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATAATT-ATATT-AATATAATTTAATAATAATATATAATTTTA
53083282 TAAAAT
1 TAAAAT
53083288 TCTTAATAAT
Statistics
Matches: 72, Mismatches: 15, Indels: 20
0.67 0.14 0.19
Matches are distributed among these distances:
43 5 0.07
44 15 0.21
45 14 0.19
46 11 0.15
47 21 0.29
48 6 0.08
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (45 bp):
TAAAATAATTATATTAATATAATTTAATAATAATATATAATTTTA
Found at i:53083200 original size:44 final size:44
Alignment explanation
Indices: 53083137--53083279 Score: 123
Period size: 45 Copynumber: 3.2 Consensus size: 44
53083127 TATGAATTTG
53083137 TATAA-TTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTTAAAATAATTATTATTA-ATATAATTTAATAATAATA
* * ** *
53083181 TATAATTTTATAA-AATTATTGA-TAATA-ATTTTTCTTATATGAATT
1 TATAATTTTAAAATAATTATT-ATTAATATA-ATTTAATA-AT-AATA
* * *
53083226 TATACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATA-ATTTTAAAATAATTATTATT-AATATAATTTAATAATAATA
53083272 TATAATTT
1 TATAATTT
53083280 CATAAAATTC
Statistics
Matches: 75, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
42 1 0.01
43 8 0.11
44 16 0.21
45 17 0.23
46 14 0.19
47 9 0.12
48 9 0.12
49 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (44 bp):
TATAATTTTAAAATAATTATTATTAATATAATTTAATAATAATA
Found at i:53083258 original size:91 final size:91
Alignment explanation
Indices: 53083103--53083319 Score: 319
Period size: 91 Copynumber: 2.4 Consensus size: 91
53083093 NNNNNNNAAT
* * * *
53083103 AATTA-TAACTAATAATTTTTCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATA
1 AATTATTAA-TAATAATTTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATA
*
53083167 ATTTAATAATAATATATAATTTTATAA
65 ATTTAATAATAATATATAATTTCATAA
*
53083194 AATTATTGATAATAATTTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
1 AATTATTAATAATAATTTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
*
53083259 TTTAATAATGATATATAATTTCATAA
66 TTTAATAATAATATATAATTTCATAA
* * *
53083285 AATTCTTAATAATAAAATGTTCTTATATGAATTTA
1 AATTATTAATAAT-AATTTTTCTTATATGAATTTA
53083320 CTAAAATCAA
Statistics
Matches: 113, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
91 92 0.81
92 21 0.19
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (91 bp):
AATTATTAATAATAATTTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
TTTAATAATAATATATAATTTCATAA
Found at i:53086422 original size:33 final size:33
Alignment explanation
Indices: 53086383--53086458 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
53086373 ATTATAAAGC
*
53086383 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
53086416 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
53086449 ATGTATAATT
1 ATGTATAATT
53086459 CAAGTTTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTAT
Found at i:53086556 original size:37 final size:37
Alignment explanation
Indices: 53086501--53086583 Score: 139
Period size: 37 Copynumber: 2.2 Consensus size: 37
53086491 GTATAAATAT
* *
53086501 ATTGATTAGTTCATTAAAGCATGTTCAAAGTTTTAAC
1 ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
*
53086538 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
1 ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
53086575 ATTGATTAG
1 ATTGATTAG
53086584 ATTATTTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (37 bp):
ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
Found at i:53087930 original size:69 final size:69
Alignment explanation
Indices: 53087820--53087948 Score: 195
Period size: 69 Copynumber: 1.9 Consensus size: 69
53087810 AATCAAGTTC
**
53087820 CAGTTTCATATTCTACTGGCTAACAAATCAAGAACAATTTCCAGCAGACAATCAAAACAACTGCC
1 CAGTTTCATATTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACAATCAAAACAACTGCC
53087885 GGAA
66 GGAA
* * * * *
53087889 CAGTTTCATCTTCTACTCACTAACAAATTAATAACATTTTCCAGCAGACTATCAAAACAA
1 CAGTTTCATATTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACAATCAAAACAA
53087949 TTTCCAGAAC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 53 1.00
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.26
Consensus pattern (69 bp):
CAGTTTCATATTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACAATCAAAACAACTGCC
GGAA
Found at i:53088807 original size:22 final size:23
Alignment explanation
Indices: 53088772--53088817 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
53088762 AAGCCTAACC
53088772 AACAACACAAAACA-CATCAACA
1 AACAACACAAAACAGCATCAACA
* * *
53088794 AACAACAGACAACAGTATCAACA
1 AACAACACAAAACAGCATCAACA
53088817 A
1 A
53088818 TATGCATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.61, C:0.28, G:0.04, T:0.07
Consensus pattern (23 bp):
AACAACACAAAACAGCATCAACA
Found at i:53089391 original size:36 final size:37
Alignment explanation
Indices: 53089307--53089414 Score: 137
Period size: 36 Copynumber: 2.9 Consensus size: 37
53089297 GGTAGAAACT
*
53089307 GAGCAAATCGGCCGAAAAAGAAAAGAAAAGAAACGGGGG
1 GAGCAAATCGGCAG-AAAAGAAAAGAAAAGAAAC-GGGG
* * * *
53089346 GAGCAAATCGGAAGAAAAGAAAATAAAATAAAC-TGG
1 GAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACGGGG
*
53089382 GAGCAAATCGGCAGAAAAGAAAAGCAAAGAAAC
1 GAGCAAATCGGCAGAAAAGAAAAGAAAAGAAAC
53089415 AAGGAAGCAG
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
36 31 0.52
38 17 0.28
39 12 0.20
ACGTcount: A:0.56, C:0.12, G:0.27, T:0.06
Consensus pattern (37 bp):
GAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACGGGG
Found at i:53096435 original size:79 final size:79
Alignment explanation
Indices: 53096337--53096495 Score: 207
Period size: 79 Copynumber: 2.0 Consensus size: 79
53096327 TTGTTAACAG
* ** *
53096337 AAATCGAATAAATTTTGTTGAACGA-CAAGAAT-AGAATTCTGAAACAGAATTGTTCAATTGATT
1 AAATCGAACAAATCCTGTTGAA-GAGCAAGAATAAG-ATCCTGAAACAGAATTGTTCAATTGATT
53096400 TCTGTTTGA-AAATAGA
64 TCTGTTT-ACAAATAGA
* * *
53096416 AAATCGAACAAATCCTGTTGAATAGTAGGAATAAGATCCTGAAACAGAATTGTTCAATTGATTTC
1 AAATCGAACAAATCCTGTTGAAGAGCAAGAATAAGATCCTGAAACAGAATTGTTCAATTGATTTC
53096481 TGTTTACAAATAGA
66 TGTTTACAAATAGA
53096495 A
1 A
53096496 TACAATTTCA
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
78 2 0.03
79 66 0.94
80 2 0.03
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (79 bp):
AAATCGAACAAATCCTGTTGAAGAGCAAGAATAAGATCCTGAAACAGAATTGTTCAATTGATTTC
TGTTTACAAATAGA
Found at i:53098465 original size:25 final size:25
Alignment explanation
Indices: 53098437--53098486 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
53098427 TATAATATAA
*
53098437 TAAA-AATAATAACATTAAAAAAAAT
1 TAAATAATAA-AACAGTAAAAAAAAT
*
53098462 TAAATAGTAAAACAGTAAAAAAAAT
1 TAAATAATAAAACAGTAAAAAAAAT
53098487 GGACTAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (25 bp):
TAAATAATAAAACAGTAAAAAAAAT
Found at i:53102186 original size:23 final size:23
Alignment explanation
Indices: 53102158--53102209 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
53102148 TAGATTTTTC
*
53102158 CTAAATATTGTCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
53102181 TTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
53102204 CTAAAT
1 CTAAAT
53102210 TTAAAATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.40
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:53103290 original size:31 final size:30
Alignment explanation
Indices: 53103255--53103355 Score: 123
Period size: 31 Copynumber: 3.3 Consensus size: 30
53103245 TTTAGGGGTT
*
53103255 AGGGTTAT-GTTTCAGGGGTTGGGGGGATTTA
1 AGGGTTATGGTTT-A-GGGTTAGGGGGATTTA
53103286 AGGGTTATGGGTTTAGGGTTAGGGGGATTTA
1 AGGGTTAT-GGTTTAGGGTTAGGGGGATTTA
* *
53103317 GGGGTTATGGGTTTAGGGTTAGAGGGATTTA
1 AGGGTTAT-GGTTTAGGGTTAGGGGGATTTA
*
53103348 TGGGTTAT
1 AGGGTTAT
53103356 TAAATTTTAT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
31 59 0.92
32 1 0.02
33 4 0.06
ACGTcount: A:0.18, C:0.01, G:0.45, T:0.37
Consensus pattern (30 bp):
AGGGTTATGGTTTAGGGTTAGGGGGATTTA
Found at i:53103305 original size:14 final size:14
Alignment explanation
Indices: 53103286--53103337 Score: 68
Period size: 14 Copynumber: 3.5 Consensus size: 14
53103276 GGGGGATTTA
53103286 AGGGTTATGGGTTT
1 AGGGTTATGGGTTT
*
53103300 AGGGTTAGGGGGATTT
1 AGGGTTA-TGGG-TTT
53103316 AGGGGTTATGGGTTT
1 A-GGGTTATGGGTTT
53103331 AGGGTTA
1 AGGGTTA
53103338 GAGGGATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 13 0.39
15 7 0.21
16 7 0.21
17 6 0.18
ACGTcount: A:0.17, C:0.00, G:0.46, T:0.37
Consensus pattern (14 bp):
AGGGTTATGGGTTT
Found at i:53103333 original size:15 final size:15
Alignment explanation
Indices: 53103282--53103334 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
53103272 GTTGGGGGGA
*
53103282 TTTAAGGGTTATGGG
1 TTTAGGGGTTATGGG
*
53103297 TTTA-GGGTTAGGGGG
1 TTTAGGGGTTA-TGGG
53103312 ATTTAGGGGTTATGGG
1 -TTTAGGGGTTATGGG
53103328 TTTAGGG
1 TTTAGGG
53103335 TTAGAGGGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 6 0.18
15 14 0.42
16 7 0.21
17 6 0.18
ACGTcount: A:0.17, C:0.00, G:0.45, T:0.38
Consensus pattern (15 bp):
TTTAGGGGTTATGGG
Found at i:53104174 original size:109 final size:109
Alignment explanation
Indices: 53103983--53104473 Score: 869
Period size: 109 Copynumber: 4.5 Consensus size: 109
53103973 NNNNNNNNNN
* *
53103983 AACCTTTATTTTATCTGCTAAAAATTATTAGTTTGCGGCCTTTTTCGTAAAAACGCCACAAAAAT
1 AACCTTTATTTTATCTGCTAAAAATTATTAGTTTGCGGCGTTTTTCGTAAAAACGCCACAAAAAA
53104048 TCATTTCATTTTGAACAAAACGACGTCGTTTTGTTATGCTAAAA
66 TCATTTCATTTTGAACAAAACGACGTCGTTTTGTTATGCTAAAA
* *
53104092 AACCTTTATTTTATCTGCTAAAAATTATTAGTTTGCGGCCTTTTTCGTAAAAACGCCACAAAAAT
1 AACCTTTATTTTATCTGCTAAAAATTATTAGTTTGCGGCGTTTTTCGTAAAAACGCCACAAAAAA
53104157 TCATTTCATTTTGAACAAAACGACGTCGTTTTGTTATGCTAAAA
66 TCATTTCATTTTGAACAAAACGACGTCGTTTTGTTATGCTAAAA
*
53104201 AGCCTTTATTTTATCTGCTAAAAATTATTAGTTTGCGGCGTTTTTCGTAAAAACGCCACAAAAAA
1 AACCTTTATTTTATCTGCTAAAAATTATTAGTTTGCGGCGTTTTTCGTAAAAACGCCACAAAAAA
53104266 TCATTTCATTTTGAACAAAACGACGTCGTTTTGTTATGCTAAAA
66 TCATTTCATTTTGAACAAAACGACGTCGTTTTGTTATGCTAAAA
* * * *
53104310 ATCATTTATTTTATATGCTAAAAATTATTAGTTTGCGGCGTTTTTCGTAAAAAAGCCACAAAAAA
1 AACCTTTATTTTATCTGCTAAAAATTATTAGTTTGCGGCGTTTTTCGTAAAAACGCCACAAAAAA
*
53104375 TCATTTCATTTTGAACAAAATGACGTCGTTTTGTTATGCTAAAA
66 TCATTTCATTTTGAACAAAACGACGTCGTTTTGTTATGCTAAAA
*
53104419 ATCCTTTATTTTATCTGCTAAAAATTATTAG-TTGCGGCGTTTTTCGT-AAAACGCC
1 AACCTTTATTTTATCTGCTAAAAATTATTAGTTTGCGGCGTTTTTCGTAAAAACGCC
53104474 GCTATTGCTT
Statistics
Matches: 371, Mismatches: 11, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
107 7 0.02
108 16 0.04
109 348 0.94
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (109 bp):
AACCTTTATTTTATCTGCTAAAAATTATTAGTTTGCGGCGTTTTTCGTAAAAACGCCACAAAAAA
TCATTTCATTTTGAACAAAACGACGTCGTTTTGTTATGCTAAAA
Found at i:53104683 original size:109 final size:109
Alignment explanation
Indices: 53104488--53104763 Score: 491
Period size: 109 Copynumber: 2.5 Consensus size: 109
53104478 TTGCTTATCT
*
53104488 TTTGCGGCGTTTTT-GATAAAAACGCCTCAAAAAATCATTTCATTTTGAACAAAACGACGTCGTT
1 TTTGCGGCGTTTTTCG-TAAAAACGCCACAAAAAATCATTTCATTTTGAACAAAACGACGTCGTT
* *
53104552 TTGTTATGCTAAAAATCTTTTATTTTATCTGCTAAAAATTATTAG
65 TTGTTATGCTAAAAAGCCTTTATTTTATCTGCTAAAAATTATTAG
* *
53104597 TTTGCGGCCTTTTTCGTAAAAACGCCACAAAAATTCATTTCATTTTGAACAAAACGACGTCGTTT
1 TTTGCGGCGTTTTTCGTAAAAACGCCACAAAAAATCATTTCATTTTGAACAAAACGACGTCGTTT
53104662 TGTTATGCTAAAAAGCCTTTATTTTATCTGCTAAAAATTATTAG
66 TGTTATGCTAAAAAGCCTTTATTTTATCTGCTAAAAATTATTAG
53104706 TTTGCGGCGTTTTTCGTAAAAACGCCACAAAAAATCATTTCATTTTGAACAAAACGAC
1 TTTGCGGCGTTTTTCGTAAAAACGCCACAAAAAATCATTTCATTTTGAACAAAACGAC
53104764 NNNNNNNNNN
Statistics
Matches: 159, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
109 158 0.99
110 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (109 bp):
TTTGCGGCGTTTTTCGTAAAAACGCCACAAAAAATCATTTCATTTTGAACAAAACGACGTCGTTT
TGTTATGCTAAAAAGCCTTTATTTTATCTGCTAAAAATTATTAG
Found at i:53104687 original size:256 final size:258
Alignment explanation
Indices: 53104232--53104731 Score: 898
Period size: 256 Copynumber: 1.9 Consensus size: 258
53104222 AAATTATTAG
53104232 TTTGCGGCGTTTTTCGTAAAAACGCCACAAAAAATCATTTCATTTTGAACAAAACGACGTCGTTT
1 TTTGCGGCGTTTTTCGTAAAAACGCCACAAAAAATCATTTCATTTTGAACAAAACGACGTCGTTT
*
53104297 TGTTATGCTAAAAATCATTTATTTTATATGCTAAAAATTATTAGTTTGCGGCGTTTTTCGTAAAA
66 TGTTATGCTAAAAATCATTTATTTTATATGCTAAAAATTATTAGTTTGCGGCCTTTTTCGTAAAA
* *
53104362 AAGCCACAAAAAATCATTTCATTTTGAACAAAATGACGTCGTTTTGTTATGCTAAAAATCCTTTA
131 AAGCCACAAAAAATCATTTCATTTTGAACAAAACGACGTCGTTTTGTTATGCTAAAAAGCCTTTA
53104427 TTTTATCTGCTAAAAATTATTAG-TTGCGGCGTTTTTCGT-AAAACGCCGCTATTGCTTATCT
196 TTTTATCTGCTAAAAATTATTAGTTTGCGGCGTTTTTCGTAAAAACGCCGCTATTGCTTATCT
*
53104488 TTTGCGGCGTTTTT-GATAAAAACGCCTCAAAAAATCATTTCATTTTGAACAAAACGACGTCGTT
1 TTTGCGGCGTTTTTCG-TAAAAACGCCACAAAAAATCATTTCATTTTGAACAAAACGACGTCGTT
* *
53104552 TTGTTATGCTAAAAATCTTTTATTTTATCTGCTAAAAATTATTAGTTTGCGGCCTTTTTCGTAAA
65 TTGTTATGCTAAAAATCATTTATTTTATATGCTAAAAATTATTAGTTTGCGGCCTTTTTCGTAAA
* *
53104617 AACGCCACAAAAATTCATTTCATTTTGAACAAAACGACGTCGTTTTGTTATGCTAAAAAGCCTTT
130 AAAGCCACAAAAAATCATTTCATTTTGAACAAAACGACGTCGTTTTGTTATGCTAAAAAGCCTTT
53104682 ATTTTATCTGCTAAAAATTATTAGTTTGCGGCGTTTTTCGTAAAAACGCC
195 ATTTTATCTGCTAAAAATTATTAGTTTGCGGCGTTTTTCGTAAAAACGCC
53104732 ACAAAAAATC
Statistics
Matches: 233, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
255 1 0.00
256 208 0.89
257 16 0.07
258 8 0.03
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.38
Consensus pattern (258 bp):
TTTGCGGCGTTTTTCGTAAAAACGCCACAAAAAATCATTTCATTTTGAACAAAACGACGTCGTTT
TGTTATGCTAAAAATCATTTATTTTATATGCTAAAAATTATTAGTTTGCGGCCTTTTTCGTAAAA
AAGCCACAAAAAATCATTTCATTTTGAACAAAACGACGTCGTTTTGTTATGCTAAAAAGCCTTTA
TTTTATCTGCTAAAAATTATTAGTTTGCGGCGTTTTTCGTAAAAACGCCGCTATTGCTTATCT
Found at i:53105279 original size:26 final size:27
Alignment explanation
Indices: 53105243--53105293 Score: 95
Period size: 26 Copynumber: 1.9 Consensus size: 27
53105233 CTTATATTTT
53105243 AGCTAGAAATCGACGATG-CCAGAAGA
1 AGCTAGAAATCGACGATGACCAGAAGA
53105269 AGCTAGAAATCGACGATGACCAGAA
1 AGCTAGAAATCGACGATGACCAGAA
53105294 ACTGTAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (27 bp):
AGCTAGAAATCGACGATGACCAGAAGA
Found at i:53107179 original size:2 final size:2
Alignment explanation
Indices: 53107172--53107250 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
53107162 NNNNNNNNTA
53107172 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
53107214 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
53107251 CCGATGCTAC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:53108000 original size:45 final size:42
Alignment explanation
Indices: 53107722--53108048 Score: 425
Period size: 42 Copynumber: 7.7 Consensus size: 42
53107712 ATTTACAAAC
*
53107722 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* *
53107764 AAAAAAGCCGCT--A-A--A-GTTCTTTAGCGGCGCTTTGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* * *
53107800 AAAAACGCCGTTAAAGAACATGTTCTTTAGCGGTGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* *
53107842 AAAAAGGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
*
53107884 AAAAACGCCGCTAAAGACAATGTTCTTTAGCGGCGCTTAGAAAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG--AA
*
53107928 AAAATGCCACGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAGGAAGA
1 AAAA----ACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTA-G-A-A
53107977 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG-A
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
*
53108018 AAAAACGCCGCTAAAGATCATGTTCTTTAGC
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGC
53108049 AGCGTTTATT
Statistics
Matches: 253, Mismatches: 18, Indels: 29
0.84 0.06 0.10
Matches are distributed among these distances:
36 30 0.12
37 1 0.00
38 1 0.00
39 2 0.01
40 1 0.00
41 32 0.13
42 104 0.41
44 7 0.03
45 34 0.13
48 35 0.14
49 6 0.02
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
Found at i:53108453 original size:21 final size:21
Alignment explanation
Indices: 53108426--53108475 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
53108416 TTTTGGCCTG
*
53108426 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
53108447 TTCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
53108468 CTCTGCTT
1 CTCTGCTT
53108476 TAAGTTGTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.02, C:0.44, G:0.18, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:53113973 original size:9 final size:9
Alignment explanation
Indices: 53113961--53114377 Score: 200
Period size: 9 Copynumber: 47.9 Consensus size: 9
53113951 ATTAAGTCAA
53113961 TTATGTAAG
1 TTATGTAAG
*
53113970 TTATGTACG
1 TTATGTAAG
53113979 TGTA--TAAG
1 T-TATGTAAG
53113987 TTATGTAAG
1 TTATGTAAG
53113996 TTATGT-A-
1 TTATGTAAG
*
53114003 TTAAGTAAG
1 TTATGTAAG
53114012 TTATGTAAG
1 TTATGTAAG
**
53114021 TTATCAAAG
1 TTATGTAAG
* *
53114030 TAATGTATG
1 TTATGTAAG
53114039 TTATGTAAG
1 TTATGTAAG
53114048 -T-TGTAAG
1 TTATGTAAG
*
53114055 TTAT-TATG
1 TTATGTAAG
53114063 TATTATGTAAG
1 --TTATGTAAG
53114074 -T-TGTAAG
1 TTATGTAAG
53114081 TTAAATGT-A-
1 TT--ATGTAAG
53114090 TTATGTAAG
1 TTATGTAAG
53114099 -T-TGTAAG
1 TTATGTAAG
*
53114106 TTAT-TATG
1 TTATGTAAG
53114114 TATTATGTAAG
1 --TTATGTAAG
53114125 -T-TGTAAG
1 TTATGTAAG
53114132 TTAAATGT-A-
1 TT--ATGTAAG
53114141 TTATGTAAG
1 TTATGTAAG
*
53114150 -T-TGTAGG
1 TTATGTAAG
*
53114157 TTAT-TATG
1 TTATGTAAG
53114165 TATTATGTAAG
1 --TTATGTAAG
*
53114176 TTATTTAAG
1 TTATGTAAG
**
53114185 TTACCTAAG
1 TTATGTAAG
53114194 TTAAATGT-A-
1 TT--ATGTAAG
53114203 TTATGTAAG
1 TTATGTAAG
53114212 -T-TGTAAG
1 TTATGTAAG
53114219 TTA--TAATG
1 TTATGTAA-G
53114227 TATTATGTAAG
1 --TTATGTAAG
53114238 -T-TGTAAG
1 TTATGTAAG
*
53114245 TTAT-TATG
1 TTATGTAAG
53114253 TATTATGTAAG
1 --TTATGTAAG
53114264 TTATGTAAG
1 TTATGTAAG
53114273 TTAAATGT-A-
1 TT--ATGTAAG
*
53114282 TTATGTAGG
1 TTATGTAAG
53114291 TTATGTAAG
1 TTATGTAAG
*
53114300 TTGTGTAAG
1 TTATGTAAG
** *
53114309 AGATTTAAG
1 TTATGTAAG
*
53114318 TTATGTGAG
1 TTATGTAAG
*
53114327 TTTTGT-A-
1 TTATGTAAG
53114334 TTATGTAAG
1 TTATGTAAG
53114343 TTATGTAAG
1 TTATGTAAG
* *
53114352 TTATTTAGG
1 TTATGTAAG
53114361 TTATGTAAG
1 TTATGTAAG
*
53114370 TTTTGTAA
1 TTATGTAA
53114378 TGTACAAGTG
Statistics
Matches: 310, Mismatches: 44, Indels: 108
0.67 0.10 0.23
Matches are distributed among these distances:
7 72 0.23
8 38 0.12
9 147 0.47
10 25 0.08
11 25 0.08
12 3 0.01
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:53114011 original size:42 final size:42
Alignment explanation
Indices: 53113960--53114045 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
53113950 TATTAAGTCA
* * *
53113960 ATTATGTAAGTTATGTACGTGTAT-AAGTTATGTAAGTTATGT
1 ATTAAGTAAGTTATGTAAGT-TATAAAGTAATGTAAGTTATGT
*
53114002 ATTAAGTAAGTTATGTAAGTTATCAAAGTAATGTATGTTATGT
1 ATTAAGTAAGTTATGTAAGTTAT-AAAGTAATGTAAGTTATGT
53114045 A
1 A
53114046 AGTTGTAAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 3 0.08
42 18 0.47
43 17 0.45
ACGTcount: A:0.35, C:0.02, G:0.20, T:0.43
Consensus pattern (42 bp):
ATTAAGTAAGTTATGTAAGTTATAAAGTAATGTAAGTTATGT
Done.