Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397271.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_89.0, whole genome shotgun sequence
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: 4184555
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 83639 characters in sequence are not A, C, G, or T
File 9 of 11
Found at i:3165613 original size:167 final size:167
Alignment explanation
Indices: 3165315--3165889 Score: 792
Period size: 167 Copynumber: 3.4 Consensus size: 167
3165305 TTATATTACT
* *
3165315 TATAAAATTTTTCATAATAGTTGAA-TTCGTAAACTAACAATTGTAAAATTAATTTATATTACTT
1 TATAAAATTTTT-ATATTAGTTGAACTT-GTAAACTAACAAATGTAAAATTAATTTATATTACTT
* * * * *
3165379 ATGATGCAAACTTGAATATATAAACTTTTTATATTACTTAAACTTGTAAACTAACAAATGTAAAA
64 ATGATGCAAACTTAAATATATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGCAAAA
3165444 TTAATTTATATTACTTGAACTATAATGCAAACTTAAATA
129 TTAATTTATATTACTTGAACTATAATGCAAACTTAAATA
* *
3165483 TGTAAAATTTTTATATTAGTTGAATTTGTAAACTAACAAATGTAAAATTAATTTATATTACTTAT
1 TATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTAATTTATATTACTTAT
*
3165548 GATACAAACTTAAATATATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGCAAAATT
66 GATGCAAACTTAAATATATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGCAAAATT
* * * *
3165613 AATTTATATTACTTGAATTATGATACAAATTTAAATA
131 AATTTATATTACTTGAACTATAATGCAAACTTAAATA
* *
3165650 TATAAACTTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTATTTTATATTACTTGA
1 TATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTAATTTATATTAC-T--
* * *
3165715 ACTATGATGTAAACTTAAATATATAAAATTTTTATATTAGTTGAACTTGTAAACTAATAAATACA
63 --TATGATGCAAACTTAAATATATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGCA
* *
3165780 AATTTAATTTATATTACTTGAACTGTATATGATGTAAACTTAAATA
126 AAATTAATTTATATTACTTGAAC--TATA--ATGCAAACTTAAATA
* * *
3165826 TATAAATTAAAGTTTTATATTAGTTGAACTTGTAAATTAACAAATGTAAAATTAATATATATTA
1 TAT--A--AAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTAATTTATATTA
3165890 ATTGAACTAT
Statistics
Matches: 361, Mismatches: 32, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
167 197 0.55
168 14 0.04
172 80 0.22
174 3 0.01
176 15 0.04
178 1 0.00
180 51 0.14
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (167 bp):
TATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTAATTTATATTACTTAT
GATGCAAACTTAAATATATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGCAAAATT
AATTTATATTACTTGAACTATAATGCAAACTTAAATA
Found at i:3165789 original size:253 final size:258
Alignment explanation
Indices: 3165315--3165912 Score: 822
Period size: 253 Copynumber: 2.3 Consensus size: 258
3165305 TTATATTACT
* *
3165315 TATAAAATTTTTCATAATAGTTGAA-TTCGTAAACTAACAATTGTAAAATTAATTTATATTAC--
1 TATAAAATTTTT-ATATTAGTTGAACTT-GTAAACTAACAAATGTAAAATTAATTTATATTACTT
*
3165377 ---TTATGATGCAAACTTGAATATATAAACTTTTTATATTACTTAAACTTGTAAACTAACAAATG
64 GAATTATGATGCAAACTTAAATATATAAACTTTTTATATTACTTAAACTTGTAAACTAACAAATG
*
3165439 TAAAATTAATTTATATTACTTGAACTATAATGCAAACTTAAATATGTAAAATTTTTATATTAGTT
129 TAAAATTAATTTATATTACTTGAACTATAATGCAAACTTAAATATATAAAATTTTTATATTAGTT
* **
3165504 GAATTTGTAAACTAACAAATGTAAAATTAATTTATATTACTT-A-TG-AT-A-CAAACTTAAATA
194 GAACTTGTAAACTAACAAATACAAAATTAATTTATATTACTTAACTGTATGAGCAAACTTAAATA
*
3165564 TATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGCAAAATTAATTTATATTACTTGA
1 TATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTAATTTATATTACTTGA
* * * *
3165629 ATTATGATACAAATTTAAATATATAAACTTTTTATATTAGTTGAACTTGTAAACTAACAAATGTA
66 ATTATGATGCAAACTTAAATATATAAACTTTTTATATTACTTAAACTTGTAAACTAACAAATGTA
* * *
3165694 AAATTATTTTATATTACTTGAACTATGATGTAAACTTAAATATATAAAATTTTTATATTAGTTGA
131 AAATTAATTTATATTACTTGAACTATAATGCAAACTTAAATATATAAAATTTTTATATTAGTTGA
* * *
3165759 ACTTGTAAACTAATAAATACAAATTTAATTTATATTACTTGAACTGTATATGATGTAAACTTAAA
196 ACTTGTAAACTAACAAATACAAAATTAATTTATATTACTT-AACTG--TATGA-GCAAACTTAAA
3165824 TA
257 TA
* * * *
3165826 TATAAATTAAAGTTTTATATTAGTTGAACTTGTAAATTAACAAATGTAAAATTAATATATATTAA
1 TAT--A--AAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTAATTTATATTAC
*
3165891 TTGAACTATGATGCAAACTTAA
62 TTGAATTATGATGCAAACTTAA
3165913 TAACATATCA
Statistics
Matches: 304, Mismatches: 26, Indels: 21
0.87 0.07 0.06
Matches are distributed among these distances:
248 43 0.14
249 14 0.05
253 155 0.51
255 1 0.00
256 2 0.01
259 2 0.01
260 1 0.00
262 14 0.05
264 1 0.00
266 71 0.23
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (258 bp):
TATAAAATTTTTATATTAGTTGAACTTGTAAACTAACAAATGTAAAATTAATTTATATTACTTGA
ATTATGATGCAAACTTAAATATATAAACTTTTTATATTACTTAAACTTGTAAACTAACAAATGTA
AAATTAATTTATATTACTTGAACTATAATGCAAACTTAAATATATAAAATTTTTATATTAGTTGA
ACTTGTAAACTAACAAATACAAAATTAATTTATATTACTTAACTGTATGAGCAAACTTAAATA
Found at i:3170862 original size:121 final size:120
Alignment explanation
Indices: 3170649--3170889 Score: 430
Period size: 121 Copynumber: 2.0 Consensus size: 120
3170639 TGTAAATGTC
3170649 AAAAAGTTATCTCTAATTCATCTTGGTTTCTTGGACTAAACACTAATCTTTTAATGTGAAAATTT
1 AAAAAGTTATCTCTAATTCATCTTGGTTTCTTGGACTAAACACTAATCTTTTAATGTGAAAATTT
3170714 TTATGATGTAAAAGATGTATTCAAATTAGTTAGTTATCAAGTTGAACATTAGTAA
66 TTATGATGTAAAAGATGTATTCAAATTAGTTAGTTATCAAGTTGAACATTAGTAA
3170769 AAAAAGTTATCTCTAATTCATCTTGGTTTCTTTGTG-CTAAACACTAATCTTTTAATGTGAAAAT
1 AAAAAGTTATCTCTAATTCATCTTGGTTTC-TTG-GACTAAACACTAATCTTTTAATGTGAAAAT
* * *
3170833 TTTTGTGATGTAAAAGATGTATTCAAATTAGTTGGTTATCAATTTGAACATTAGTAA
64 TTTTATGATGTAAAAGATGTATTCAAATTAGTTAGTTATCAAGTTGAACATTAGTAA
3170890 GGTTGTAGGC
Statistics
Matches: 116, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
120 30 0.26
121 85 0.73
122 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (120 bp):
AAAAAGTTATCTCTAATTCATCTTGGTTTCTTGGACTAAACACTAATCTTTTAATGTGAAAATTT
TTATGATGTAAAAGATGTATTCAAATTAGTTAGTTATCAAGTTGAACATTAGTAA
Found at i:3179257 original size:25 final size:25
Alignment explanation
Indices: 3179223--3179297 Score: 123
Period size: 25 Copynumber: 3.0 Consensus size: 25
3179213 TAAAAAATAA
3179223 TTTTATTTATATTTAATTAAATTTT
1 TTTTATTTATATTTAATTAAATTTT
3179248 TTTTATTTATATTTAATTAAATTTT
1 TTTTATTTATATTTAATTAAATTTT
* **
3179273 TTTTATTTAAATTTAAAAAAATTTT
1 TTTTATTTATATTTAATTAAATTTT
3179298 ATAATTAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (25 bp):
TTTTATTTATATTTAATTAAATTTT
Found at i:3181063 original size:47 final size:47
Alignment explanation
Indices: 3181010--3181197 Score: 189
Period size: 48 Copynumber: 3.9 Consensus size: 47
3181000 CAAGCTCTGG
* *
3181010 CCTAGACTAATAGCATAAAAAACTAAGCCTAATATTGTTTATTTTGA
1 CCTAGACTAATAGCATAAAAAACTAAGCCCAATATTGTTTATTATGA
* *
3181057 CCTAGACTATAATAGCATAAATAACCTAA-CTCCAATATTGTTTATTCTGA
1 CCTAGAC--TAATAGCATAAA-AAACTAAGC-CCAATATTGTTTATTATGA
* * * * * *
3181107 TCTAAATTAATAGTATAAAAAGACTAATCCCAATATTGTTTATTATGG
1 CCTAGACTAATAGCATAAAAA-ACTAAGCCCAATATTGTTTATTATGA
* * * **
3181155 CCTAGACAAATAACATAAAAGACTAAGCTTAATATTGTTTATT
1 CCTAGACTAATAGCATAAAAAACTAAGCCCAATATTGTTTATT
3181198 CTAACCCTAA
Statistics
Matches: 115, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
47 28 0.24
48 46 0.40
49 14 0.12
50 27 0.23
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.35
Consensus pattern (47 bp):
CCTAGACTAATAGCATAAAAAACTAAGCCCAATATTGTTTATTATGA
Found at i:3181145 original size:98 final size:94
Alignment explanation
Indices: 3181017--3181199 Score: 235
Period size: 98 Copynumber: 1.9 Consensus size: 94
3181007 TGGCCTAGAC
* * *
3181017 TAATAGCATAAAAAACTAAGCCTAATATTGTTTATTTTGACCTAGACTATAATAGCATAAATA-A
1 TAATAGCATAAAAAACTAAGCCCAATATTGTTTATTATGACCTAGAC-A-AATAACATAAA-AGA
3181081 CCTAA-CTCCAATATTGTTTATTCTGATCTAAAT
63 -CTAAGCT-CAATATTGTTTATTCTGATCTAAAT
* * *
3181114 TAATAGTATAAAAAGACTAATCCCAATATTGTTTATTATGGCCTAGACAAATAACATAAAAGACT
1 TAATAGCATAAAAA-ACTAAGCCCAATATTGTTTATTATGACCTAGACAAATAACATAAAAGACT
*
3181179 AAGCTTAATATTGTTTATTCT
65 AAGCTCAATATTGTTTATTCT
3181200 AACCCTAACT
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
95 20 0.26
96 13 0.17
97 14 0.18
98 29 0.38
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (94 bp):
TAATAGCATAAAAAACTAAGCCCAATATTGTTTATTATGACCTAGACAAATAACATAAAAGACTA
AGCTCAATATTGTTTATTCTGATCTAAAT
Found at i:3186511 original size:48 final size:48
Alignment explanation
Indices: 3186426--3186714 Score: 129
Period size: 48 Copynumber: 6.0 Consensus size: 48
3186416 CAGTCAACAA
* * ** *
3186426 GCCTAGATAAATAACATAAATAAACTATGCCCAATATTGTTTATTCTG
1 GCCTAGACAAATAACATAAATAAACTAAGAACAATATTGCTTATTCTG
* * * * *
3186474 GCCTAGACAAATAACATAAATATATTAAGAACTATATTGCTTGTTTTG
1 GCCTAGACAAATAACATAAATAAACTAAGAACAATATTGCTTATTCTG
* ** ** *
3186522 GCCTAGACTAATAGTATAAA-AAACCTAAGCTCAATATTG-TTCATTTTG
1 GCCTAGACAAATAACATAAATAAA-CTAAGAACAATATTGCTT-ATTCTG
* * * *** * **
3186570 ACCCAAACTATAATAACATAAATAAACTAACTCCAACATTATTTATTCTG
1 GCCTAGAC-A-AATAACATAAATAAACTAAGAACAATATTGCTTATTCTG
** * *** * * *
3186620 GCCTAGA-ATAATAGTATGAAA-AGACTAATCCCAGTATTGTTTATTTTG
1 GCCTAGACA-AATAACAT-AAATAAACTAAGAACAATATTGCTTATTCTG
* ** ** *
3186668 GCCTAGACAAGTAACATAAA-AGGCTAAGCTCAATATTGTTTATTCTG
1 GCCTAGACAAATAACATAAATAAACTAAGAACAATATTGCTTATTCTG
3186715 ACACAAACTC
Statistics
Matches: 182, Mismatches: 51, Indels: 17
0.73 0.20 0.07
Matches are distributed among these distances:
47 29 0.16
48 116 0.64
49 4 0.02
50 28 0.15
51 5 0.03
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (48 bp):
GCCTAGACAAATAACATAAATAAACTAAGAACAATATTGCTTATTCTG
Found at i:3200012 original size:55 final size:57
Alignment explanation
Indices: 3199951--3200057 Score: 150
Period size: 55 Copynumber: 1.9 Consensus size: 57
3199941 TAAAATAAAA
* *
3199951 TATATAATATAAG-AATCAA-AAATTAAACTAAAATA-A-AATATAAGAAATTAAAGTT
1 TATATAATATAAGTAA--AAGAAATTAAAATAAAATATATAATATAAAAAATTAAAGTT
3200006 TATATAATATAAGTAAAAGAAATTAAAATAAAATATATAATATAAAAAATTA
1 TATATAATATAAGTAAAAGAAATTAAAATAAAATATATAATATAAAAAATTA
3200058 TATAAAAGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
54 2 0.04
55 28 0.61
56 3 0.07
57 13 0.28
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (57 bp):
TATATAATATAAGTAAAAGAAATTAAAATAAAATATATAATATAAAAAATTAAAGTT
Found at i:3200083 original size:34 final size:33
Alignment explanation
Indices: 3200031--3200116 Score: 102
Period size: 33 Copynumber: 2.5 Consensus size: 33
3200021 AAAGAAATTA
3200031 AAAT-AAAATATATAATATAAAAAATTATATAAAAG
1 AAATGAAAATA-A-AATATAAAAAATTATA-AAAAG
* * *
3200066 AAATGAAAATAAAATATATAAGATTATAATAAG
1 AAATGAAAATAAAATATAAAAAATTATAAAAAG
*
3200099 AAATGTAAATAAAATATA
1 AAATGAAAATAAAATATA
3200117 TTTAAGAGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
33 21 0.46
34 14 0.30
35 5 0.11
36 6 0.13
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (33 bp):
AAATGAAAATAAAATATAAAAAATTATAAAAAG
Found at i:3200923 original size:23 final size:22
Alignment explanation
Indices: 3200897--3200939 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
3200887 TTTTGTTTTA
*
3200897 ATTTCTTCTTTTTTTATATTTGC
1 ATTTCTTATTTTTTTA-ATTTGC
*
3200920 ATTTTTTATTTTTTTAATTT
1 ATTTCTTATTTTTTTAATTT
3200940 CTGTTTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.74
Consensus pattern (22 bp):
ATTTCTTATTTTTTTAATTTGC
Found at i:3213073 original size:44 final size:44
Alignment explanation
Indices: 3213010--3213266 Score: 211
Period size: 44 Copynumber: 5.7 Consensus size: 44
3213000 TATTTTTCTA
* *
3213010 TATATTTTTTGTTATCTAGTTGAACTAAACTAGACTAATTTAGT
1 TATATTTTTTGTTATCTAGTTGAACTCAACTAGACTCATTTAGT
* * * * *
3213054 TATATTTTTTTTTATCTAGTTGAACTCAATTGGACTTATTTAGG
1 TATATTTTTTGTTATCTAGTTGAACTCAACTAGACTCATTTAGT
* * * *
3213098 TATATATTTTGTTATCTAGTTGATCTCAACTGGGCTCATTTAGT
1 TATATTTTTTGTTATCTAGTTGAACTCAACTAGACTCATTTAGT
* * *
3213142 TACATATTTTGTTATTTATAGTT-AATCTCAACTAGACTCATTTA-T
1 TATATTTTTTGTTA--TCTAGTTGAA-CTCAACTAGACTCATTTAGT
* * * *
3213187 GTATATATTTTGTTATCTA--T-AATTGATCTTA-ACTCATTTAGGTT
1 -TATATTTTTTGTTATCTAGTTGAACTCAAC-TAGACTCATTTA-G-T
3213231 CTACATATTTTTTGTTCATCTAGTTGAACTCAACTA
1 -T--ATATTTTTTGTT-ATCTAGTTGAACTCAACTA
3213267 CACTTATGGT
Statistics
Matches: 171, Mismatches: 28, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
41 12 0.07
42 5 0.03
44 93 0.54
45 2 0.01
46 46 0.27
47 5 0.03
49 3 0.02
50 5 0.03
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49
Consensus pattern (44 bp):
TATATTTTTTGTTATCTAGTTGAACTCAACTAGACTCATTTAGT
Found at i:3213172 original size:90 final size:87
Alignment explanation
Indices: 3213010--3213205 Score: 234
Period size: 90 Copynumber: 2.2 Consensus size: 87
3213000 TATTTTTCTA
*
3213010 TATATTTTTTGTTATCTAGTTGAACTAAACTAGACTAATTTAGTTATATTTTTTTTTATCTAGTT
1 TATATATTTTGTTATCTAGTTGAACTAAACTAGACTAATTTAGTTATATTTTTTTTTA-CTAGTT
* * *
3213075 GAACTCAATTGGACTTATTTAGG
65 GAACTCAACTAGACTCATTTAGG
* * * * *
3213098 TATATATTTTGTTATCTAGTTGATCTCAACTGGGCTCATTTAGTTACATATTTTGTTATTTA-TA
1 TATATATTTTGTTATCTAGTTGAACTAAACTAGACTAATTTAGTT--ATATTTT-TT-TTTACTA
*
3213162 GTT-AATCTCAACTAGACTCATTTATG
62 GTTGAA-CTCAACTAGACTCATTTAGG
3213188 TATATATTTTGTTATCTA
1 TATATATTTTGTTATCTA
3213206 TAATTGATCT
Statistics
Matches: 93, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
88 39 0.42
89 2 0.02
90 46 0.49
91 2 0.02
92 4 0.04
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.50
Consensus pattern (87 bp):
TATATATTTTGTTATCTAGTTGAACTAAACTAGACTAATTTAGTTATATTTTTTTTTACTAGTTG
AACTCAACTAGACTCATTTAGG
Found at i:3213537 original size:16 final size:16
Alignment explanation
Indices: 3213503--3213537 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3213493 ATATATTAAA
* *
3213503 TTAGTGATAGAATTTT
1 TTAGTGATAGAAATCT
3213519 TTAGTGATAGAAATCT
1 TTAGTGATAGAAATCT
3213535 TTA
1 TTA
3213538 AAAATGAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (16 bp):
TTAGTGATAGAAATCT
Found at i:3216414 original size:2 final size:2
Alignment explanation
Indices: 3216402--3216441 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3216392 TAATGCAACA
*
3216402 AT AT GT 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 AT
3216442 GTATTGCCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3226056 original size:28 final size:29
Alignment explanation
Indices: 3226001--3226056 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
3225991 CGAGCAAATA
**
3226001 AAAGAAGAGAAAAGAAATTGAAGGAAAAG
1 AAAGAAGAGAAAAGAAATTGAACCAAAAG
* *
3226030 AAAGAA-AGAATAGAACTTGAACCAAAA
1 AAAGAAGAGAAAAGAAATTGAACCAAAA
3226057 ATGTTATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.64, C:0.05, G:0.21, T:0.09
Consensus pattern (29 bp):
AAAGAAGAGAAAAGAAATTGAACCAAAAG
Found at i:3235307 original size:61 final size:61
Alignment explanation
Indices: 3235233--3235356 Score: 239
Period size: 61 Copynumber: 2.0 Consensus size: 61
3235223 ACAGTTTATC
*
3235233 ACCATCAAGGACCTTATTTCATAAAAAGCTAAGTCCAATGCCATCTTAATTGCTAGCTTGT
1 ACCATCAAAGACCTTATTTCATAAAAAGCTAAGTCCAATGCCATCTTAATTGCTAGCTTGT
3235294 ACCATCAAAGACCTTATTTCATAAAAAGCTAAGTCCAATGCCATCTTAATTGCTAGCTTGT
1 ACCATCAAAGACCTTATTTCATAAAAAGCTAAGTCCAATGCCATCTTAATTGCTAGCTTGT
3235355 AC
1 AC
3235357 ACATTTGGCC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.31
Consensus pattern (61 bp):
ACCATCAAAGACCTTATTTCATAAAAAGCTAAGTCCAATGCCATCTTAATTGCTAGCTTGT
Found at i:3235845 original size:31 final size:31
Alignment explanation
Indices: 3235810--3235881 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
3235800 AGCTTTATTT
**
3235810 AATTTAGATCTTGTATTATAGAATTTTGTTC
1 AATTTAGATCTTACATTATAGAATTTTGTTC
*
3235841 AATTTAG-TCCTTACATTATAGAGTTTTGTTC
1 AATTTAGAT-CTTACATTATAGAATTTTGTTC
3235872 AATTTA-ATCT
1 AATTTAGATCT
3235882 CGGTACTCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 3 0.08
31 33 0.92
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.50
Consensus pattern (31 bp):
AATTTAGATCTTACATTATAGAATTTTGTTC
Found at i:3235899 original size:31 final size:29
Alignment explanation
Indices: 3235831--3235912 Score: 76
Period size: 31 Copynumber: 2.7 Consensus size: 29
3235821 TGTATTATAG
* *
3235831 AATTTTGTTCAATTTAGTCCTTACATTAT
1 AATTTTGTTCAATTTAATCCGTACATTAT
3235860 AGAGTTTTGTTCAATTTAATCTCGGTAC-TCTAT
1 A-A-TTTTGTTCAATTTAATC-C-GTACAT-TAT
* *
3235893 AATTTTGTTTAATTTTATCC
1 AATTTTGTTCAATTTAATCC
3235913 TTATGACATG
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
29 1 0.02
30 2 0.05
31 31 0.70
32 3 0.07
33 7 0.16
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.51
Consensus pattern (29 bp):
AATTTTGTTCAATTTAATCCGTACATTAT
Found at i:3240153 original size:49 final size:49
Alignment explanation
Indices: 3240014--3240442 Score: 143
Period size: 48 Copynumber: 8.5 Consensus size: 49
3240004 TATAGATGGG
** * *
3240014 GAGCTTTTCTAATCATTTTAAAGTGGTAGTAGTCACTTTTA-AAAATGAT
1 GAGCTTTTCTAATCATTTTAAAGTTATAGTAG-CCCTTTTAGAAAATGAA
* * * *
3240063 GAGCTTTTTTCAATCATTTTAAAGCTACA-TAGCCCGGTTTAGAAAA-GAA
1 GAGCTTTTCT-AATCATTTTAAAGTTATAGTAGCCC-TTTTAGAAAATGAA
* *
3240112 GAGCTTTTCTAATTATTTTAAAGTTATAGTAACCTCTTTTAGAAATGAGGTGGAAAAAGA
1 GAGCTTTTCTAATCATTTTAAAGTTATAGTAGCC-CTTTTAGAAA--A--T-G----A-A
* * * * *
3240172 GAAGAGTTTTTTTTAATCATTTTAAAGTTGT-GTAGCCTCGTTTT--AAGATAAA
1 G-AG-CTTTT--CTAATCATTTTAAAGTTATAGTAGCC-C-TTTTAGAAAATGAA
* * * * *
3240224 GAG-TTTTATCAATCATTTTAAAGTTGTA-TAGCCTTATTTAG-AGATGGA
1 GAGCTTTTCT-AATCATTTTAAAGTTATAGTAGCCCT-TTTAGAAAATGAA
* * * *
3240272 GAGCTTTTCTAATTATTTTAAAGTTGTAGTAGCATCTTTTAG-AGATG-A
1 GAGCTTTTCTAATCATTTTAAAGTTATAGTAGC-CCTTTTAGAAAATGAA
* * * * * * * *
3240320 GAAGAATTTTTTAATTATTTCAAAGTTGTA-TAGCCTTGTTTA-AAGATAAA
1 G-AG-CTTTTCTAATCATTTTAAAGTTATAGTAGCCCT-TTTAGAAAATGAA
* * * * *
3240370 GAGCTTTT-TCAATCATTTTAAAGTT-TTGTAGCCTTGTTTA-TAGATAAA
1 GAGCTTTTCT-AATCATTTTAAAGTTATAGTAGCCCT-TTTAGAAAATGAA
* *
3240418 GAACTTTTTTAATCATTTTAAAGTT
1 GAGCTTTTCTAATCATTTTAAAGTT
3240443 GCATAATCTC
Statistics
Matches: 302, Mismatches: 41, Indels: 75
0.72 0.10 0.18
Matches are distributed among these distances:
46 1 0.00
47 6 0.02
48 125 0.41
49 79 0.26
50 44 0.15
51 3 0.01
52 2 0.01
53 1 0.00
55 1 0.00
58 1 0.00
59 1 0.00
60 3 0.01
61 2 0.01
62 6 0.02
63 7 0.02
64 20 0.07
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.41
Consensus pattern (49 bp):
GAGCTTTTCTAATCATTTTAAAGTTATAGTAGCCCTTTTAGAAAATGAA
Found at i:3240355 original size:146 final size:146
Alignment explanation
Indices: 3240180--3240443 Score: 386
Period size: 146 Copynumber: 1.8 Consensus size: 146
3240170 GAGAAGAGTT
* * *
3240180 TTTTTTAATCATTTTAAAGTTGTGTAGCCTCGTTTTAAGATAAAGAG-TTTTATCAATCATTTTA
1 TTTTTTAATCATTTCAAAGTTGTATAGCCTCGTTTAAAGATAAAGAGCTTTT-TCAATCATTTTA
** * *
3240244 AAGTTGTATAGCCTTATTTAGAGATGGAGAGCTTTTCTAATTATTTTAAAGTTGTAGTAGCATCT
65 AAGTTGTATAGCCTTATTTAGAGATAAAGAACTTTTCTAATCATTTTAAAGTTGTAGTAGCATCT
3240309 TTTAGAGATGAGAAGAA
130 TTTAGAGATGAGAAGAA
* *
3240326 TTTTTTAATTATTTCAAAGTTGTATAGCCTTGTTTAAAGATAAAGAGCTTTTTCAATCATTTTAA
1 TTTTTTAATCATTTCAAAGTTGTATAGCCTCGTTTAAAGATAAAGAGCTTTTTCAATCATTTTAA
* * * * *
3240391 AGTTTTGTAGCCTTGTTTATAGATAAAGAACTTTTTTAATCATTTTAAAGTTG
66 AGTTGTATAGCCTTATTTAGAGATAAAGAACTTTTCTAATCATTTTAAAGTTG
3240444 CATAATCTCG
Statistics
Matches: 103, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
146 99 0.96
147 4 0.04
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (146 bp):
TTTTTTAATCATTTCAAAGTTGTATAGCCTCGTTTAAAGATAAAGAGCTTTTTCAATCATTTTAA
AGTTGTATAGCCTTATTTAGAGATAAAGAACTTTTCTAATCATTTTAAAGTTGTAGTAGCATCTT
TTAGAGATGAGAAGAA
Found at i:3240457 original size:48 final size:48
Alignment explanation
Indices: 3240180--3240571 Score: 322
Period size: 48 Copynumber: 8.1 Consensus size: 48
3240170 GAGAAGAGTT
*
3240180 TTTTTTAATCATTTTAAAGTTGTGTAGCCTCGTTTTA-AGATAAAGAG-
1 TTTTTTAATCATTTTAAAGTTGTATAGCCTCG-TTTAGAGATAAAGAGC
* ** **
3240227 TTTTATCAATCATTTTAAAGTTGTATAGCCTTATTTAGAGATGGAGAGC
1 TTTT-TTAATCATTTTAAAGTTGTATAGCCTCGTTTAGAGATAAAGAGC
* * * * *
3240276 TTTTCTAATTATTTTAAAGTTGTAGTAGCATCTTTTAGAGATGAGAAGA-A
1 TTTTTTAATCATTTTAAAGTTGTA-TAGCCTCGTTTAGAGAT-A-AAGAGC
* * * *
3240326 TTTTTTAATTATTTCAAAGTTGTATAGCCTTGTTTAAAGATAAAGAGC
1 TTTTTTAATCATTTTAAAGTTGTATAGCCTCGTTTAGAGATAAAGAGC
* * * * * *
3240374 TTTTTCAATCATTTTAAAGTTTTGTAGCCTTGTTTATAGATAAAGAAC
1 TTTTTTAATCATTTTAAAGTTGTATAGCCTCGTTTAGAGATAAAGAGC
* ** * * *
3240422 TTTTTTAATCATTTTAAAGTTGCATAATCTCGTTTAGAAATAAGGAGT
1 TTTTTTAATCATTTTAAAGTTGTATAGCCTCGTTTAGAGATAAAGAGC
* * ** ** * *
3240470 TTTTTTAACTTATTTTAAAGCTACATAGTGTCATTTAGAGATGAAGAGC
1 TTTTTTAA-TCATTTTAAAGTTGTATAGCCTCGTTTAGAGATAAAGAGC
* * ** * * *
3240519 TTTTTTCTATCATTTAAAAGTTACATAACCTCATTTCGAGATAAAGAGC
1 TTTTTT-AATCATTTTAAAGTTGTATAGCCTCGTTTAGAGATAAAGAGC
3240568 TTTT
1 TTTT
3240572 CAATTCTTTA
Statistics
Matches: 276, Mismatches: 60, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
47 12 0.04
48 135 0.49
49 103 0.37
50 23 0.08
51 3 0.01
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (48 bp):
TTTTTTAATCATTTTAAAGTTGTATAGCCTCGTTTAGAGATAAAGAGC
Found at i:3240523 original size:49 final size:47
Alignment explanation
Indices: 3240406--3240571 Score: 143
Period size: 49 Copynumber: 3.4 Consensus size: 47
3240396 TGTAGCCTTG
* * * * *
3240406 TTTATAGATAAAGAACTTTTTTAATCATTTTAAAGTTGCATAATCTCG
1 TTTAGAGAT-AAGAGCTTTTTTAATCATTTTAAAGCTACATAATCTCA
* * * * *
3240454 TTTAGAAATAAGGAGTTTTTTTAACTTATTTTAAAGCTACATAGTGTCA
1 TTTAGAGATAA-GAGCTTTTTTAA-TCATTTTAAAGCTACATAATCTCA
* * * *
3240503 TTTAGAGATGAAGAGCTTTTTTCTATCATTTAAAAGTTACATAACCTCA
1 TTTAGAGAT-AAGAGCTTTTTT-AATCATTTTAAAGCTACATAATCTCA
*
3240552 TTTCGAGATAAAGAGCTTTT
1 TTTAGAGAT-AAGAGCTTTT
3240572 CAATTCTTTA
Statistics
Matches: 93, Mismatches: 21, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
47 2 0.02
48 17 0.18
49 71 0.76
50 3 0.03
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (47 bp):
TTTAGAGATAAGAGCTTTTTTAATCATTTTAAAGCTACATAATCTCA
Found at i:3240524 original size:146 final size:145
Alignment explanation
Indices: 3240204--3240572 Score: 343
Period size: 146 Copynumber: 2.5 Consensus size: 145
3240194 TAAAGTTGTG
* *
3240204 TAGCCTCGTTTTAAGATAAAGAG-TTTTATCAATCATTTTAAAGTTGTATAGCCTTATTTAGAGA
1 TAGCCTC-ATTTAAGATAAAGAGCTTTTTTCAATCATTTTAAAGTTGTATAGCCTTATTTAGAGA
** * * * * *
3240268 TGGAGAGCTTTTCTAATTATTTTAAAGTTGTAGTAGCATCTTTTAGAGATGAGAAGAATTTTTTA
65 TAAAGAACTTTTCTAATCATTTTAAAGTTGCAGTA-CATCTTTTAGAAATAAGAAGAATTTTTTA
* **
3240333 ATTATTTCAAAGTTGTA
129 ATTATTTCAAAGCTACA
** * * * *
3240350 TAGCCTTGTTTAAAGATAAAGAGC-TTTTTCAATCATTTTAAAGTTTTGTAGCCTTGTTTATAGA
1 TAGCCTCATTT-AAGATAAAGAGCTTTTTTCAATCATTTTAAAGTTGTATAGCCTTATTTAGAGA
* * *
3240414 TAAAGAACTTTTTTAATCATTTTAAAGTTGCA-TA-ATCTCGTTTAGAAATAAGGAG-TTTTTTT
65 TAAAGAACTTTTCTAATCATTTTAAAGTTGCAGTACATCT--TTTAGAAATAAGAAGAATTTTTT
*
3240476 AACTTATTTTAAAGCTACA
128 AA-TTATTTCAAAGCTACA
** * * * ** * * *
3240495 TAGTGTCATTTAGAGATGAAGAGCTTTTTTCTATCATTTAAAAGTTACATAACCTCATTTCGAGA
1 TAGCCTCATTTA-AGATAAAGAGCTTTTTTCAATCATTTTAAAGTTGTATAGCCTTATTTAGAGA
*
3240560 TAAAGAGCTTTTC
65 TAAAGAACTTTTC
3240573 AATTCTTTAA
Statistics
Matches: 178, Mismatches: 38, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
143 4 0.02
144 9 0.05
145 46 0.26
146 119 0.67
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (145 bp):
TAGCCTCATTTAAGATAAAGAGCTTTTTTCAATCATTTTAAAGTTGTATAGCCTTATTTAGAGAT
AAAGAACTTTTCTAATCATTTTAAAGTTGCAGTACATCTTTTAGAAATAAGAAGAATTTTTTAAT
TATTTCAAAGCTACA
Found at i:3241794 original size:15 final size:16
Alignment explanation
Indices: 3241759--3241796 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3241749 TAATAAAAGT
* *
3241759 TAAATAAAAGAATTTA
1 TAAATAAAAGAAATCA
3241775 TAAATAAAA-AAATCA
1 TAAATAAAAGAAATCA
3241790 TAAATAA
1 TAAATAA
3241797 GTAAAAGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (16 bp):
TAAATAAAAGAAATCA
Found at i:3245649 original size:16 final size:16
Alignment explanation
Indices: 3245628--3245673 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
3245618 AAATTTTAAA
3245628 AAACTTTTTAAAAAAT
1 AAACTTTTTAAAAAAT
*
3245644 AAACTTTTTTAAAAAT
1 AAACTTTTTAAAAAAT
*
3245660 AAA-ATTTTAAAAAA
1 AAACTTTTTAAAAAA
3245674 AATTCTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (16 bp):
AAACTTTTTAAAAAAT
Found at i:3245669 original size:14 final size:13
Alignment explanation
Indices: 3245618--3245686 Score: 52
Period size: 13 Copynumber: 5.1 Consensus size: 13
3245608 TAAATTAAAT
3245618 AAATTTT-AAAAA
1 AAATTTTAAAAAA
**
3245630 ACTTTTTAAAAAA
1 AAATTTTAAAAAA
3245643 TAAACTTTTTTAAAAATA
1 -AAA---TTTTAAAAA-A
3245661 AAATTTT-AAAAA
1 AAATTTTAAAAAA
*
3245673 AAATTCTAAAAAA
1 AAATTTTAAAAAA
3245686 A
1 A
3245687 GTTTTCGAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
12 12 0.27
13 15 0.33
14 5 0.11
17 12 0.27
18 1 0.02
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (13 bp):
AAATTTTAAAAAA
Found at i:3247012 original size:42 final size:42
Alignment explanation
Indices: 3246965--3247049 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 42
3246955 ATGAGGTACA
* * * * *
3246965 ACCTCGTCTATGGACGAAAGGGCCGTGTGTGAGGGCA-GAGAG
1 ACCTCGCCCATGGACGAAAAGGACGTGGGTGAGGG-AGGAGAG
3247007 ACCTCGCCCATGGACGAAAAGGACGTGGGTGAGGGAGGAGAG
1 ACCTCGCCCATGGACGAAAAGGACGTGGGTGAGGGAGGAGAG
3247049 A
1 A
3247050 GAGCATACCA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.03
42 36 0.97
ACGTcount: A:0.27, C:0.19, G:0.41, T:0.13
Consensus pattern (42 bp):
ACCTCGCCCATGGACGAAAAGGACGTGGGTGAGGGAGGAGAG
Found at i:3247928 original size:7 final size:7
Alignment explanation
Indices: 3247916--3247945 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3247906 TCACCCCTTT
3247916 TTACCCA
1 TTACCCA
3247923 TTACCCA
1 TTACCCA
3247930 TTACCCA
1 TTACCCA
*
3247937 TTGCCCA
1 TTACCCA
3247944 TT
1 TT
3247946 TGTAGGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.23, C:0.40, G:0.03, T:0.33
Consensus pattern (7 bp):
TTACCCA
Found at i:3258822 original size:29 final size:29
Alignment explanation
Indices: 3258782--3258838 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
3258772 GTCCTCGTAC
3258782 AATAATTTGTAAAAATTGAGCCCCTGTAT
1 AATAATTTGTAAAAATTGAGCCCCTGTAT
*
3258811 AATAATTTGTAAAAATTGAGTCCCTGTA
1 AATAATTTGTAAAAATTGAGCCCCTGTA
3258839 CTTTCCAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (29 bp):
AATAATTTGTAAAAATTGAGCCCCTGTAT
Found at i:3263483 original size:26 final size:25
Alignment explanation
Indices: 3263393--3263482 Score: 69
Period size: 25 Copynumber: 3.6 Consensus size: 25
3263383 TTTAATTATT
*
3263393 ATTTTATCATCAAAAGTGGATGGAT-
1 ATTTTATCAT-AAAAGTGGATAGATA
* * **
3263418 ATTTTATTATTTAAA-TTTA-AGAATA
1 ATTTTATCA-TAAAAGTGGATAG-ATA
*
3263443 ATTTTACCACTAAAAGTGGATAGATA
1 ATTTTATCA-TAAAAGTGGATAGATA
3263469 ATTTTATCATAAAA
1 ATTTTATCATAAAA
3263483 AATGGATGGA
Statistics
Matches: 48, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
23 1 0.02
24 4 0.08
25 27 0.56
26 14 0.29
27 2 0.04
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (25 bp):
ATTTTATCATAAAAGTGGATAGATA
Found at i:3263488 original size:26 final size:26
Alignment explanation
Indices: 3263440--3263489 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3263430 AAATTTAAGA
*
3263440 ATAATTTTACCACTAAAAGTGGATAG
1 ATAATTTTACCACTAAAAATGGATAG
*
3263466 ATAATTTTATCA-TAAAAAATGGAT
1 ATAATTTTACCACT-AAAAATGGAT
3263490 GGATGCTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 20 0.95
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (26 bp):
ATAATTTTACCACTAAAAATGGATAG
Found at i:3263609 original size:28 final size:28
Alignment explanation
Indices: 3263543--3263615 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
3263533 AATCACCCAC
* *
3263543 CAAAAGTAGATGTATACTTGTAACTTAA
1 CAAAAGTAGATGAATACTTGTAACGTAA
* *
3263571 CATAAA-CAGATGAATACTT-TCAACGTAT
1 CA-AAAGTAGATGAATACTTGT-AACGTAA
3263599 CAAAAGTAGATGAATAC
1 CAAAAGTAGATGAATAC
3263616 CTTAATCCAC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
27 4 0.11
28 30 0.81
29 3 0.08
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (28 bp):
CAAAAGTAGATGAATACTTGTAACGTAA
Found at i:3279750 original size:27 final size:28
Alignment explanation
Indices: 3279697--3279751 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
3279687 TATATGATTA
*
3279697 TATATTTAATTTACAAAATATTTATAATC
1 TATATTTAATTTA-AAAATATTAATAATC
* *
3279726 TATATTTCATTT-AAAATGTTAATAAT
1 TATATTTAATTTAAAAATATTAATAAT
3279752 TTACAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 12 0.52
29 11 0.48
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (28 bp):
TATATTTAATTTAAAAATATTAATAATC
Found at i:3279864 original size:42 final size:43
Alignment explanation
Indices: 3279770--3279870 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
3279760 AAAACATTAA
* * ** **
3279770 TTTTATTATTTT-ATTTTATTCTTTATTTTTAAAATATTTTAT
1 TTTTATAATTTTAATTTAATTCTTTAAGTTTAAAATATTAAAT
* *
3279812 TATTAAAATTTTAATTTAATT-TTTAAGTTTAAAATATTAAAT
1 TTTTATAATTTTAATTTAATTCTTTAAGTTTAAAATATTAAAT
3279854 TTTTATAATTTATAATT
1 TTTTATAATTT-TAATT
3279871 AAAACTTAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
42 35 0.74
43 12 0.26
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (43 bp):
TTTTATAATTTTAATTTAATTCTTTAAGTTTAAAATATTAAAT
Found at i:3285601 original size:15 final size:17
Alignment explanation
Indices: 3285575--3285607 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3285565 AGAGAGAGAG
3285575 AGAGGTA-TTTTTTGAA
1 AGAGGTATTTTTTTGAA
3285591 AGAGG-ATTTTTTTGAA
1 AGAGGTATTTTTTTGAA
3285607 A
1 A
3285608 AAAATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 15 0.94
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.42
Consensus pattern (17 bp):
AGAGGTATTTTTTTGAA
Found at i:3288676 original size:19 final size:20
Alignment explanation
Indices: 3288631--3288683 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 20
3288621 ATTTACTATT
* *
3288631 TAATTTTAGTTTTAGTTTAT
1 TAATTTTAATTTTAGTTTAA
* *
3288651 TAGTTTTAATTTT-TTTTAA
1 TAATTTTAATTTTAGTTTAA
*
3288670 TAATTTTAAATTTA
1 TAATTTTAATTTTA
3288684 ATTGTTTGGA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (20 bp):
TAATTTTAATTTTAGTTTAA
Found at i:3298316 original size:25 final size:25
Alignment explanation
Indices: 3298282--3298359 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
3298272 TTAAAAGAAT
*
3298282 TTAAATAAATTATTATTTTTTATAA
1 TTAATTAAATTATTATTTTTTATAA
* *
3298307 TTAATTAAATTTTTATATTTTTAT-T
1 TTAATTAAATTATTAT-TTTTTATAA
*
3298332 TTAAATTAAA-TA--AATTTTTATAA
1 TT-AATTAAATTATTATTTTTTATAA
3298355 TTAAT
1 TTAAT
3298360 AACTAATTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
22 10 0.23
23 3 0.07
25 17 0.39
26 14 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TTAATTAAATTATTATTTTTTATAA
Found at i:3298321 original size:18 final size:18
Alignment explanation
Indices: 3298298--3298359 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 18
3298288 AAATTATTAT
3298298 TTTTTATAATTAATTAAA
1 TTTTTATAATTAATTAAA
*
3298316 TTTTTAT-ATT--TT-TA
1 TTTTTATAATTAATTAAA
*
3298330 -TTTTA-AATTAAATAAA
1 TTTTTATAATTAATTAAA
3298346 TTTTTATAATTAAT
1 TTTTTATAATTAAT
3298360 AACTAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
13 8 0.24
14 1 0.03
15 3 0.09
16 1 0.03
17 8 0.24
18 13 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTTATAATTAATTAAA
Found at i:3298395 original size:22 final size:23
Alignment explanation
Indices: 3298365--3298418 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
3298355 TTAATAACTA
* *
3298365 ATTAATTATTAT-TAATCAAAAT
1 ATTATTTATTATATAATAAAAAT
3298387 ATTATTTATTATATAATAAAAAT
1 ATTATTTATTATATAATAAAAAT
3298410 A-TATTTATT
1 ATTATTTATT
3298419 TATTTTATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 19 0.66
23 10 0.34
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTATTTATTATATAATAAAAAT
Found at i:3298421 original size:23 final size:22
Alignment explanation
Indices: 3298348--3298418 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
3298338 TAAATAAATT
* **
3298348 TTTATAATTAATAACTA-ATTA
1 TTTATTATTAATAAAAATATTA
* *
3298369 ATTATTATTAATCAAAATATTA
1 TTTATTATTAATAAAAATATTA
3298391 TTTATTATATAATAAAAATA-TA
1 TTTATTAT-TAATAAAAATATTA
3298413 TTTATT
1 TTTATT
3298419 TATTTTATCT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
21 12 0.29
22 19 0.46
23 10 0.24
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTATTATTAATAAAAATATTA
Found at i:3304065 original size:12 final size:12
Alignment explanation
Indices: 3304044--3304075 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3304034 ATAACGTAAC
3304044 TATCACATAAAT
1 TATCACATAAAT
*
3304056 TATCATATAAAT
1 TATCACATAAAT
3304068 TATCACAT
1 TATCACAT
3304076 CAATCAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.38
Consensus pattern (12 bp):
TATCACATAAAT
Found at i:3314980 original size:15 final size:15
Alignment explanation
Indices: 3314936--3314987 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
3314926 TAAGTTTGAT
3314936 AAATATTAATATTTA
1 AAATATTAATATTTA
** *
3314951 ATTTA-AAATAGTTTA
1 AAATATTAATA-TTTA
3314966 AAATATTAATATTTA
1 AAATATTAATATTTA
*
3314981 AATTATT
1 AAATATT
3314988 CAACATTATT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
14 4 0.14
15 20 0.71
16 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
AAATATTAATATTTA
Found at i:3315433 original size:33 final size:33
Alignment explanation
Indices: 3315391--3315464 Score: 98
Period size: 32 Copynumber: 2.3 Consensus size: 33
3315381 CATGATGGTG
*
3315391 GAAAATATTTTTC-ATAGAATGATCCAAACAACA
1 GAAAATATTTTTCAACAG-ATGATCCAAACAACA
* *
3315424 GAAAATA-TTTTCAACAGTTTATCCAAACAACA
1 GAAAATATTTTTCAACAGATGATCCAAACAACA
3315456 GAAAATATT
1 GAAAATATT
3315465 AAATTTTCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 25 0.69
33 11 0.31
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.28
Consensus pattern (33 bp):
GAAAATATTTTTCAACAGATGATCCAAACAACA
Found at i:3316843 original size:19 final size:19
Alignment explanation
Indices: 3316819--3316864 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
3316809 GAAGCTTTCA
3316819 CTCTTGGTTAGGAATTCTT
1 CTCTTGGTTAGGAATTCTT
3316838 CTCTTGGTTAGGAATTCTT
1 CTCTTGGTTAGGAATTCTT
3316857 CTCTTGGT
1 CTCTTGGT
3316865 GTTCTCTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.13, C:0.17, G:0.22, T:0.48
Consensus pattern (19 bp):
CTCTTGGTTAGGAATTCTT
Found at i:3320015 original size:15 final size:15
Alignment explanation
Indices: 3319975--3320018 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
3319965 GAATGAATTA
*
3319975 CATTGAAAGGCTGAT
1 CATTGAAAGGTTGAT
3319990 CATTGAAAGGTTGAT
1 CATTGAAAGGTTGAT
3320005 CATTGAAAGGTTGA
1 CATTGAAAGGTTGA
3320019 GTCAAACCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (15 bp):
CATTGAAAGGTTGAT
Found at i:3320408 original size:35 final size:35
Alignment explanation
Indices: 3320332--3320555 Score: 150
Period size: 35 Copynumber: 6.3 Consensus size: 35
3320322 GTTGTACCTT
* * *
3320332 ATTAATTAAATAT-TTTAATTAAATCATTGGGCCTA
1 ATTAATTAAAT-TGTTTAATTAAGTCATTGAGCTTA
**
3320367 GCTAATTAAATTGTTTAATTAAGTCATTGAGCTTA
1 ATTAATTAAATTGTTTAATTAAGTCATTGAGCTTA
* **** * *
3320402 ATTAATTAAGTTAAACAATTAATTTATT-AGACTTA
1 ATTAATTAAATTGTTTAATTAAGTCATTGAG-CTTA
* * * *
3320437 ATTGATTAAATTTATTTAATTAAGTCATTGGGCATA
1 ATTAATTAAA-TTGTTTAATTAAGTCATTGAGCTTA
* * ** *
3320473 ATTGATTAAAATTGTTTAATTAAATTGTTTG-GTTTA
1 ATTAATT-AAATTGTTTAATT-AAGTCATTGAGCTTA
* *
3320509 ATTAATTAAATTGTTTAATTAAGTTATTTGA-CCTA
1 ATTAATTAAATTGTTTAATTAAGTCA-TTGAGCTTA
*
3320544 ATTGATTAAATT
1 ATTAATTAAATT
3320556 AAACAATTAA
Statistics
Matches: 145, Mismatches: 36, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
34 6 0.04
35 88 0.61
36 41 0.28
37 10 0.07
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (35 bp):
ATTAATTAAATTGTTTAATTAAGTCATTGAGCTTA
Found at i:3320515 original size:107 final size:105
Alignment explanation
Indices: 3320327--3320555 Score: 244
Period size: 107 Copynumber: 2.2 Consensus size: 105
3320317 ATTAAGTTGT
* * * * *
3320327 ACCTTATTAATTAAATATTTTAATTAAATCATTGGGCCTAGCTAATTAAATTGTTTAATTAAGTC
1 ACCTAATTGATTAAATTTTTTAATTAAATCATTGGGCATAACTAATTAAATTGTTTAATTAAGTC
* *
3320392 ATTGAGCTTAATTAATTAAGTTAAACAATTAATTTATTAG
66 ATTGAGCTTAATTAATTAAATTAAACAATTAAGTTATTAG
* * * *
3320432 ACTTAATTGATTAAATTTATTTAATTAAGTCATTGGGCATAATTGATTAAAATTGTTTAATTAAA
1 ACCTAATTGATTAAATTT-TTTAATTAAATCATTGGGCATAACTAATT-AAATTGTTTAATT-AA
* ** * **** *
3320497 TTGTTTG-GTTTAATTAATTAAATTGTTTAATTAAGTTATTTG
63 GTCATTGAGCTTAATTAATTAAATTAAACAATTAAGTTATTAG
3320539 ACCTAATTGATTAAATT
1 ACCTAATTGATTAAATT
3320556 AAACAATTAA
Statistics
Matches: 100, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
105 14 0.14
106 24 0.24
107 56 0.56
108 6 0.06
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (105 bp):
ACCTAATTGATTAAATTTTTTAATTAAATCATTGGGCATAACTAATTAAATTGTTTAATTAAGTC
ATTGAGCTTAATTAATTAAATTAAACAATTAAGTTATTAG
Found at i:3320526 original size:71 final size:71
Alignment explanation
Indices: 3320369--3320565 Score: 200
Period size: 71 Copynumber: 2.8 Consensus size: 71
3320359 TGGGCCTAGC
* * * * *
3320369 TAATTAAATTGTTTAATTAAGTCATTGAGCTTAATTAATT-AAGTTAAACAATTAATTTATTAGA
1 TAATTAAATTGTTTAATTAAGTCATTGGGCATAATTGATTAAAATTAAACAATTAAATTATTAGA
3320433 CTTAAT
66 CTTAAT
* * **** * *
3320439 TGATTAAATTTATTTAATTAAGTCATTGGGCATAATTGATTAAAATTGTTTAATTAAATTGTTTG
1 TAATTAAA-TTGTTTAATTAAGTCATTGGGCATAATTGATTAAAATTAAACAATTAAATTATTAG
**
3320504 GTTTAAT
65 ACTTAAT
* * * *
3320511 TAATTAAATTGTTTAATTAAGTTATTTGACCTAATTGATT-AAATTAAACAATTAA
1 TAATTAAATTGTTTAATTAAGTCATTGGGCATAATTGATTAAAATTAAACAATTAA
3320566 GTTGATTGAG
Statistics
Matches: 100, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
70 18 0.18
71 55 0.55
72 27 0.27
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.46
Consensus pattern (71 bp):
TAATTAAATTGTTTAATTAAGTCATTGGGCATAATTGATTAAAATTAAACAATTAAATTATTAGA
CTTAAT
Found at i:3330188 original size:36 final size:36
Alignment explanation
Indices: 3330148--3330239 Score: 130
Period size: 36 Copynumber: 2.6 Consensus size: 36
3330138 ATGTACTGCT
* *
3330148 TTTTATGGGTCAAGTACAACCTTTCAATACAATGCC
1 TTTTATGGATCAAGCACAACCTTTCAATACAATGCC
* ** *
3330184 TTTTATAGATCAAGCACAATTTTTCAATACATTGCC
1 TTTTATGGATCAAGCACAACCTTTCAATACAATGCC
3330220 TTTTATGGATCAAGCACAAC
1 TTTTATGGATCAAGCACAAC
3330240 ATATCTACCT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.35
Consensus pattern (36 bp):
TTTTATGGATCAAGCACAACCTTTCAATACAATGCC
Found at i:3335677 original size:21 final size:21
Alignment explanation
Indices: 3335653--3335698 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
3335643 CATCAGTACC
*
3335653 TAAAGAAAATATTCAAACATG
1 TAAAGAAAATATACAAACATG
*
3335674 TAAAGAAAATATACAAATATG
1 TAAAGAAAATATACAAACATG
3335695 TAAA
1 TAAA
3335699 TCACACAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.24
Consensus pattern (21 bp):
TAAAGAAAATATACAAACATG
Found at i:3337569 original size:121 final size:122
Alignment explanation
Indices: 3337430--3337662 Score: 362
Period size: 121 Copynumber: 1.9 Consensus size: 122
3337420 AAATACCCTA
* *
3337430 ATTTAAAAGGTATTTTTGTTGAAACTTTAGGGTATTTTTGT-TATTTTGTTGCCTGACATTAATT
1 ATTTAAAAGGTATATTTGTTGAAACTTAAGGGTATTTTTGTAT-TTTTGTTGCCTGACATTAATT
* * * *
3337494 TCATAACACCCTA-ATGAGAGAATGAAGCCTCAAGGTGCAAAAAAAAGTAACCCTCAT
65 TCATAACACCCTAGATGACAAAAGGAAACCTCAAGGTGCAAAAAAAAGTAACCCTCAT
*
3337551 ATTTAAAAGGTATATTTGTTGAAACTTAAGGGTATTTTTGTATTTTTGTTGTCTGACATTAATTT
1 ATTTAAAAGGTATATTTGTTGAAACTTAAGGGTATTTTTGTATTTTTGTTGCCTGACATTAATTT
*
3337616 CATAACACCCTATGATGACAAAAGGAAACTTCAAGGTGCAAAAAAAA
66 CATAACACCCTA-GATGACAAAAGGAAACCTCAAGGTGCAAAAAAAA
3337663 ATCACAGGGT
Statistics
Matches: 101, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
121 72 0.71
122 1 0.01
123 28 0.28
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (122 bp):
ATTTAAAAGGTATATTTGTTGAAACTTAAGGGTATTTTTGTATTTTTGTTGCCTGACATTAATTT
CATAACACCCTAGATGACAAAAGGAAACCTCAAGGTGCAAAAAAAAGTAACCCTCAT
Found at i:3338894 original size:2 final size:2
Alignment explanation
Indices: 3338887--3338920 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3338877 CTTTTCTACT
3338887 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3338921 AGGAAAATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3344567 original size:2 final size:2
Alignment explanation
Indices: 3344560--3344602 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3344550 CTTAGAGAAT
*
3344560 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC GC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3344602 T
1 T
3344603 TTCGTTTCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.02, T:0.49
Consensus pattern (2 bp):
TC
Found at i:3357969 original size:9 final size:10
Alignment explanation
Indices: 3357956--3357988 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3357946 CAAGTAAGCT
3357956 TCATTCATT-
1 TCATTCATTA
3357965 TCATTCATTA
1 TCATTCATTA
*
3357975 ACATTCATTA
1 TCATTCATTA
3357985 TCAT
1 TCAT
3357989 GTGCTGAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.48
Consensus pattern (10 bp):
TCATTCATTA
Found at i:3359347 original size:20 final size:21
Alignment explanation
Indices: 3359321--3359368 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
3359311 AGATGAGAGT
3359321 CATCTATCA-ATAAATCTGGC
1 CATCTATCAGATAAATCTGGC
* *
3359341 TATCTAT-AGATAAATTTGGC
1 CATCTATCAGATAAATCTGGC
3359361 CATCTATC
1 CATCTATC
3359369 CATAGATGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.35
Consensus pattern (21 bp):
CATCTATCAGATAAATCTGGC
Found at i:3361080 original size:31 final size:32
Alignment explanation
Indices: 3361045--3361143 Score: 107
Period size: 31 Copynumber: 3.2 Consensus size: 32
3361035 AAGAAAAAGA
3361045 GAAAAATGTTGAGAGACTAAATTACAAATA-T
1 GAAAAATGTTGAGAGACTAAATTACAAATATT
* * *
3361076 G-AAAAGGTTTAGAGGACCAAATTACAAATATT
1 GAAAAATGTTGAGA-GACTAAATTACAAATATT
* *
3361108 AAAAAAT-TTGAAAGA-TGAAATTACAAATATT
1 GAAAAATGTTGAGAGACT-AAATTACAAATATT
3361139 GAAAA
1 GAAAA
3361144 GTTTGGAGAA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
30 10 0.18
31 36 0.65
32 5 0.09
33 4 0.07
ACGTcount: A:0.54, C:0.06, G:0.15, T:0.25
Consensus pattern (32 bp):
GAAAAATGTTGAGAGACTAAATTACAAATATT
Found at i:3361345 original size:25 final size:25
Alignment explanation
Indices: 3361308--3361398 Score: 146
Period size: 25 Copynumber: 3.6 Consensus size: 25
3361298 AAGAAAATAA
* *
3361308 AATCCCTACAATTATGATGATTCCC
1 AATCCCTATAATTATGGTGATTCCC
*
3361333 AATCCCTATAATTATGGTGAATCCC
1 AATCCCTATAATTATGGTGATTCCC
*
3361358 AATCCCTATAATTATGGTAATTCCC
1 AATCCCTATAATTATGGTGATTCCC
3361383 AATCCCTATAATTATG
1 AATCCCTATAATTATG
3361399 TTTATTAATA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 61 1.00
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.34
Consensus pattern (25 bp):
AATCCCTATAATTATGGTGATTCCC
Found at i:3366007 original size:25 final size:25
Alignment explanation
Indices: 3365970--3366059 Score: 110
Period size: 25 Copynumber: 3.6 Consensus size: 25
3365960 AAGAAAATAA
* *
3365970 AATCCCTACAATTATGATGATTCCT
1 AATCCCTATAATTATGGTGATTCCT
*
3365995 AATCCCTATAATTATGGTGAAT-CT
1 AATCCCTATAATTATGGTGATTCCT
* * *
3366019 CAATCTCTATAATTATGGTAATTCCC
1 -AATCCCTATAATTATGGTGATTCCT
3366045 AATCCCTATAATTAT
1 AATCCCTATAATTAT
3366060 ATTTATTAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
24 2 0.04
25 52 0.95
26 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (25 bp):
AATCCCTATAATTATGGTGATTCCT
Found at i:3369928 original size:10 final size:10
Alignment explanation
Indices: 3369913--3369943 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3369903 TTAAGTGAGT
3369913 TGACTTGGGC
1 TGACTTGGGC
3369923 TGACTTGGGC
1 TGACTTGGGC
*
3369933 TGACTTAGGC
1 TGACTTGGGC
3369943 T
1 T
3369944 TTTTTTGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.13, C:0.19, G:0.35, T:0.32
Consensus pattern (10 bp):
TGACTTGGGC
Found at i:3370115 original size:25 final size:24
Alignment explanation
Indices: 3370081--3370140 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
3370071 TTAAATAGTT
**
3370081 AATAAAATTAATCTTCATGTAATA
1 AATAAAATTAATCTTCACATAATA
*
3370105 AATAAATATTAATCTTTACATAATA
1 AATAAA-ATTAATCTTCACATAATA
3370130 AATAAACATTA
1 AATAAA-ATTA
3370141 GTTTCAAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 6 0.19
25 25 0.81
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (24 bp):
AATAAAATTAATCTTCACATAATA
Found at i:3372961 original size:85 final size:86
Alignment explanation
Indices: 3372818--3373051 Score: 339
Period size: 85 Copynumber: 2.7 Consensus size: 86
3372808 TACTCAAACA
* * * * *
3372818 TTAATTCTAGCATATTGCCAATCATTTTAATTGA-AAATCTAAAAAATAATTTTAAACATTAATT
1 TTAATTCTAGCATATTGCAAATCATTTTAATTGATATATCCAAAATATAATTCTAAACATTAATT
*
3372882 CTCAAACATAATTCTTAATGT
66 CCCAAACATAATTCTTAATGT
* * *
3372903 TTAATTCTATCATATTGCTAATCATTTTAATT-ATATATCCAAATTATAATTCTAAACATTAATT
1 TTAATTCTAGCATATTGCAAATCATTTTAATTGATATATCCAAAATATAATTCTAAACATTAATT
3372967 CCCAAACATAATTCTTAATGT
66 CCCAAACATAATTCTTAATGT
*
3372988 TTAATTCTAGCATATTGCACAAATCATTTTAATTGAT-TATCCAAACTATAATTCTAAACATTAA
1 TTAATTCTAGCATATTG--CAAATCATTTTAATTGATATATCCAAAATATAATTCTAAACATTAA
3373052 CCTCTTTGAA
Statistics
Matches: 134, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
84 1 0.01
85 91 0.68
87 40 0.30
88 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.04, T:0.41
Consensus pattern (86 bp):
TTAATTCTAGCATATTGCAAATCATTTTAATTGATATATCCAAAATATAATTCTAAACATTAATT
CCCAAACATAATTCTTAATGT
Found at i:3375315 original size:18 final size:18
Alignment explanation
Indices: 3375235--3375315 Score: 76
Period size: 18 Copynumber: 4.5 Consensus size: 18
3375225 TGTGATGCTA
3375235 TTGTAAATGTTGATGATG
1 TTGTAAATGTTGATGATG
* * *
3375253 ATGTAAATATTGATGTTG
1 TTGTAAATGTTGATGATG
*
3375271 TTAG-AAAT-TGTGATGTTG
1 TT-GTAAATGT-TGATGATG
* *
3375289 ATGTAAATGTTTATGATG
1 TTGTAAATGTTGATGATG
3375307 TTGTAAATG
1 TTGTAAATG
3375316 ATACTGGTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
17 2 0.04
18 47 0.92
19 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (18 bp):
TTGTAAATGTTGATGATG
Found at i:3376630 original size:13 final size:13
Alignment explanation
Indices: 3376612--3376699 Score: 56
Period size: 13 Copynumber: 6.7 Consensus size: 13
3376602 CCCAAAGGCC
3376612 AAGAAGGAAGAAA
1 AAGAAGGAAGAAA
* *
3376625 AAGAAGAAAGGAA
1 AAGAAGGAAGAAA
3376638 AAG-A-GAGAGCAAA
1 AAGAAGGA-AG-AAA
* *
3376651 AAGAAGTAGGAAA
1 AAGAAGGAAGAAA
*
3376664 AA-AAAGAAGGAAA
1 AAGAAGGAA-GAAA
* *
3376677 AAGAAAGAAAAAA
1 AAGAAGGAAGAAA
3376690 AGAGAAGGAA
1 A-AGAAGGAA
3376700 TAGGGGCCAC
Statistics
Matches: 57, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
11 1 0.02
12 6 0.11
13 34 0.60
14 15 0.26
15 1 0.02
ACGTcount: A:0.69, C:0.01, G:0.28, T:0.01
Consensus pattern (13 bp):
AAGAAGGAAGAAA
Found at i:3376641 original size:26 final size:26
Alignment explanation
Indices: 3376612--3376699 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
3376602 CCCAAAGGCC
3376612 AAGAAGGAAGAAAAAGAAGAAAGGAA
1 AAGAAGGAAGAAAAAGAAGAAAGGAA
*
3376638 AAG-A-GAGAGCAAAAAGAAG-TAGGAA
1 AAGAAGGA-AG-AAAAAGAAGAAAGGAA
* * *
3376663 AAAAAAGAAGGAAAAAGAAAGAAA-AAA
1 AAGAAGGAA-GAAAAAG-AAGAAAGGAA
3376690 AGAGAAGGAA
1 A-AGAAGGAA
3376700 TAGGGGCCAC
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
24 2 0.04
25 10 0.21
26 20 0.42
27 9 0.19
28 7 0.15
ACGTcount: A:0.69, C:0.01, G:0.28, T:0.01
Consensus pattern (26 bp):
AAGAAGGAAGAAAAAGAAGAAAGGAA
Found at i:3378787 original size:59 final size:59
Alignment explanation
Indices: 3378719--3378830 Score: 188
Period size: 59 Copynumber: 1.9 Consensus size: 59
3378709 TTAGGTTAGT
* *
3378719 TTTTATTTGGAATCTAAGAATTTTTTACGCTCCTACTTCTACTTAAAATATTGGAAAGC
1 TTTTATTTGGAATCTAAGAATTTTTCAAGCTCCTACTTCTACTTAAAATATTGGAAAGC
* *
3378778 TTTTATTTGGAGTCTAAGAATTTTTCAAGCTCCTACTTCTACTTAATATATTG
1 TTTTATTTGGAATCTAAGAATTTTTCAAGCTCCTACTTCTACTTAAAATATTG
3378831 CAATAAGAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.45
Consensus pattern (59 bp):
TTTTATTTGGAATCTAAGAATTTTTCAAGCTCCTACTTCTACTTAAAATATTGGAAAGC
Found at i:3397560 original size:23 final size:23
Alignment explanation
Indices: 3397530--3397574 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
3397520 TGATAGTATG
*
3397530 ATCATATTGACATAACATTGACT
1 ATCATATTGACATAACACTGACT
3397553 ATCATATTGACATAACACTGAC
1 ATCATATTGACATAACACTGAC
3397575 ATGTGGACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (23 bp):
ATCATATTGACATAACACTGACT
Found at i:3409834 original size:28 final size:28
Alignment explanation
Indices: 3409785--3409846 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
3409775 TTATAATGGG
* *
3409785 TTACATGTCCCTAAGATGTTTTGATAGA
1 TTACATGTCCCTAACATATTTTGATAGA
* *
3409813 TTACATGTCCTTAACATATTTTGATAGG
1 TTACATGTCCCTAACATATTTTGATAGA
3409841 TTACAT
1 TTACAT
3409847 ATCTTTACCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (28 bp):
TTACATGTCCCTAACATATTTTGATAGA
Found at i:3409929 original size:35 final size:35
Alignment explanation
Indices: 3409889--3409993 Score: 201
Period size: 35 Copynumber: 3.0 Consensus size: 35
3409879 TGTTATGTAC
3409889 ATGCCTTCACATGTTTCAACATGTTTTGAAAACAT
1 ATGCCTTCACATGTTTCAACATGTTTTGAAAACAT
*
3409924 ATGCCTTCACATGTTTCAACATGTTTTGAAAACAC
1 ATGCCTTCACATGTTTCAACATGTTTTGAAAACAT
3409959 ATGCCTTCACATGTTTCAACATGTTTTGAAAACAT
1 ATGCCTTCACATGTTTCAACATGTTTTGAAAACAT
3409994 TCTCAAATTT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.36
Consensus pattern (35 bp):
ATGCCTTCACATGTTTCAACATGTTTTGAAAACAT
Found at i:3420174 original size:12 final size:12
Alignment explanation
Indices: 3420157--3420186 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3420147 ATATGTATAC
3420157 TATATATGTGCA
1 TATATATGTGCA
*
3420169 TATATATGTGTA
1 TATATATGTGCA
3420181 TATATA
1 TATATA
3420187 CATATGTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (12 bp):
TATATATGTGCA
Found at i:3420185 original size:14 final size:14
Alignment explanation
Indices: 3420150--3420226 Score: 54
Period size: 14 Copynumber: 5.7 Consensus size: 14
3420140 TACACACATA
3420150 TGTATACTATATATG
1 TGTATA-TATATATG
*
3420165 TG--CATATATATG
1 TGTATATATATATG
* *
3420177 TGTATATATACATA
1 TGTATATATATATG
* *
3420191 TG--TACACATATG
1 TGTATATATATATG
*
3420203 TGTATATATACATG
1 TGTATATATATATG
*
3420217 TGTACATATA
1 TGTATATATA
3420227 CACACATGTG
Statistics
Matches: 46, Mismatches: 12, Indels: 9
0.69 0.18 0.13
Matches are distributed among these distances:
12 18 0.39
13 1 0.02
14 25 0.54
15 2 0.04
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (14 bp):
TGTATATATATATG
Found at i:3420201 original size:26 final size:26
Alignment explanation
Indices: 3420172--3420222 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
3420162 ATGTGCATAT
3420172 ATATGTGTATATATACATATGTACAC
1 ATATGTGTATATATACATATGTACAC
*
3420198 ATATGTGTATATATACATGTGTACA
1 ATATGTGTATATATACATATGTACA
3420223 TATACACACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (26 bp):
ATATGTGTATATATACATATGTACAC
Found at i:3420215 original size:16 final size:16
Alignment explanation
Indices: 3420193--3420271 Score: 67
Period size: 16 Copynumber: 5.1 Consensus size: 16
3420183 TATACATATG
*
3420193 TACACATATGTGTATA
1 TACACACATGTGTATA
*
3420209 T--ATACATGTGTACATA
1 TACACACATGTGT--ATA
3420225 TACACACATGTG--TA
1 TACACACATGTGTATA
* *
3420239 TACACATATGTATATA
1 TACACACATGTGTATA
*
3420255 TACACACATGTATATA
1 TACACACATGTGTATA
3420271 T
1 T
3420272 GCTTTCGCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
14 20 0.39
16 23 0.45
18 8 0.16
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.35
Consensus pattern (16 bp):
TACACACATGTGTATA
Found at i:3420227 original size:14 final size:14
Alignment explanation
Indices: 3420167--3420228 Score: 65
Period size: 14 Copynumber: 4.6 Consensus size: 14
3420157 TATATATGTG
*
3420167 CATATATATGTGTA
1 CATATACATGTGTA
* *
3420181 TATATACATATGTA
1 CATATACATGTGTA
*
3420195 CACAT--ATGTGTA
1 CATATACATGTGTA
*
3420207 TATATACATGTGTA
1 CATATACATGTGTA
3420221 CATATACA
1 CATATACA
3420229 CACATGTGTA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
12 9 0.24
14 28 0.76
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (14 bp):
CATATACATGTGTA
Found at i:3420240 original size:14 final size:14
Alignment explanation
Indices: 3420222--3420270 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
3420212 ACATGTGTAC
3420222 ATATACACACATGT
1 ATATACACACATGT
* *
3420236 GTATACACATATGTAT
1 ATATACACACATG--T
3420252 ATATACACACATGT
1 ATATACACACATGT
3420266 ATATA
1 ATATA
3420271 TGCTTTCGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 17 0.59
16 12 0.41
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (14 bp):
ATATACACACATGT
Found at i:3420258 original size:30 final size:30
Alignment explanation
Indices: 3420188--3420270 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 30
3420178 GTATATATAC
* * * *
3420188 ATATGTACACATATGTGTATATATACATGTGT
1 ATATATACACACATGTG--TATACACATATGT
*
3420220 ACATATACACACATGTGTATACACATATGT
1 ATATATACACACATGTGTATACACATATGT
*
3420250 ATATATACACACATGTATATA
1 ATATATACACACATGTGTATA
3420271 TGCTTTCGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 30 0.68
32 14 0.32
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (30 bp):
ATATATACACACATGTGTATACACATATGT
Found at i:3424205 original size:27 final size:28
Alignment explanation
Indices: 3424175--3424228 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
3424165 TGTATGAATA
* *
3424175 TAAAAATAAACA-ATGATTTTTATAAAT
1 TAAAAATAAAAATATAATTTTTATAAAT
*
3424202 TAAAATTAAAAATATAATTTTTATAAA
1 TAAAAATAAAAATATAATTTTTATAAA
3424229 AAACAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (28 bp):
TAAAAATAAAAATATAATTTTTATAAAT
Found at i:3425890 original size:112 final size:112
Alignment explanation
Indices: 3425761--3425983 Score: 387
Period size: 114 Copynumber: 2.0 Consensus size: 112
3425751 CTTTTTCGTC
*
3425761 AAAAAAAAATCCATGCTTTTATATATATCTATAATATATAGATAAAAATT-AAAAAAA-ATATTT
1 AAAAAAAAATCCATGCTTTTACATATATCTATAATATATAGATAAAAATTAAAAAAAATATATTT
3425824 TTATACATACCATAGGCCAAGGAAATTTAAACTCGCCCCTGAGGCCA
66 TTATACATACCATAGGCCAAGGAAATTTAAACTCGCCCCTGAGGCCA
3425871 AAAAAAGAATATCCATGCTTTTACATATATCTATAATATATAGATAAAAATTAAAAAAAATATAT
1 AAAAAA-AA-ATCCATGCTTTTACATATATCTATAATATATAGATAAAAATTAAAAAAAATATAT
* *
3425936 TTTTATACATACCATAGGCCAGGGAAATTTAAACTCTCCCCTGAGGCC
64 TTTTATACATACCATAGGCCAAGGAAATTTAAACTCGCCCCTGAGGCC
3425984 CCAACAACCC
Statistics
Matches: 106, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
110 6 0.06
111 2 0.02
112 41 0.39
113 7 0.07
114 50 0.47
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (112 bp):
AAAAAAAAATCCATGCTTTTACATATATCTATAATATATAGATAAAAATTAAAAAAAATATATTT
TTATACATACCATAGGCCAAGGAAATTTAAACTCGCCCCTGAGGCCA
Found at i:3429576 original size:17 final size:16
Alignment explanation
Indices: 3429516--3429576 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
3429506 GTCTTTTTTT
*
3429516 ATTTATTTTTTTCTGG
1 ATTTTTTTTTTTCTGG
* * *
3429532 ATTTTTTTTTTCCAGA
1 ATTTTTTTTTTTCTGG
**
3429548 ATTTTGCTTTTTCTGG
1 ATTTTTTTTTTTCTGG
3429564 ATTTTTTTGTTTT
1 ATTTTTTT-TTTT
3429577 TATTTTTAAT
Statistics
Matches: 33, Mismatches: 11, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
16 29 0.88
17 4 0.12
ACGTcount: A:0.11, C:0.08, G:0.11, T:0.69
Consensus pattern (16 bp):
ATTTTTTTTTTTCTGG
Found at i:3430078 original size:34 final size:34
Alignment explanation
Indices: 3430030--3430102 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
3430020 CAATAATTGG
3430030 TACATTGGACGAAACTCTAGTGCAACAAATCTGA
1 TACATTGGACGAAACTCTAGTGCAACAAATCTGA
* *
3430064 TACATTGGATGAAACTCTAGTGCAACAATTCTGA
1 TACATTGGACGAAACTCTAGTGCAACAAATCTGA
3430098 TACAT
1 TACAT
3430103 CCTTGTATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (34 bp):
TACATTGGACGAAACTCTAGTGCAACAAATCTGA
Found at i:3434994 original size:31 final size:31
Alignment explanation
Indices: 3434944--3435016 Score: 110
Period size: 31 Copynumber: 2.3 Consensus size: 31
3434934 TTTAAAACTC
*
3434944 ATAAAGAAACTGGTTAACAAATTCAACCGGTAA
1 ATAAA-AAA-TGGTAAACAAATTCAACCGGTAA
3434977 ATAAAAAATGGTAAACAAATTCAACCGGTAA
1 ATAAAAAATGGTAAACAAATTCAACCGGTAA
*
3435008 ACAAAAAAT
1 ATAAAAAAT
3435017 CCTCCCTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 30 0.79
32 3 0.08
33 5 0.13
ACGTcount: A:0.55, C:0.14, G:0.12, T:0.19
Consensus pattern (31 bp):
ATAAAAAATGGTAAACAAATTCAACCGGTAA
Found at i:3435008 original size:17 final size:17
Alignment explanation
Indices: 3434959--3435012 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
3434949 GAAACTGGTT
3434959 AACAAATTCAACCGGTA
1 AACAAATTCAACCGGTA
* **
3434976 AATAAA---AAATGGTA
1 AACAAATTCAACCGGTA
3434990 AACAAATTCAACCGGTA
1 AACAAATTCAACCGGTA
3435007 AACAAA
1 AACAAA
3435013 AAATCCTCCC
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
14 11 0.39
17 17 0.61
ACGTcount: A:0.56, C:0.17, G:0.11, T:0.17
Consensus pattern (17 bp):
AACAAATTCAACCGGTA
Found at i:3435652 original size:226 final size:227
Alignment explanation
Indices: 3435277--3435695 Score: 599
Period size: 226 Copynumber: 1.8 Consensus size: 227
3435267 ATACAAGGTA
* * * *
3435277 AAATAATTAAATTTAAAATTTTAACTTAAATGTGTAAGAGTTAACGTAACAAGTCAAATAGGAAA
1 AAATAATTAAATTTAAAATCTTAACATAAATGTATAAGAATTAACGTAACAAGTCAAATAGGAAA
* * * * * **
3435342 AAATTTAATTTTAATGAAAAATAAATATTTAAATTTATATTTTCAAATTAAAAGTGTTTAATGAT
66 AAATTTAATTGTAATGAAAAACAAACATTTAAATTTACATTCTCAAATTAAAAGTGTTTAACAAT
* *
3435407 ATATAAATTTAAATTTTTAAATAAATAATAAT-A-ATAAAAATAATTATAGTTCAAAATTGATAT
131 ATACAAATTTAAATTTTTAAATAAAAAATAATAAGATAAAAATAATTATAGTTCAAAATTGATAT
3435470 AGATAACCTTGACGTAAAAACTTAGAAAAGTG
196 AGATAACCTTGACGTAAAAACTTAGAAAAGTG
* * * *
3435502 AAATAATTAAATTTTAAATCTTAACATAAATGTATGAGAATTAACGTAACAAGTCAATTAAGTAA
1 AAATAATTAAATTTAAAATCTTAACATAAATGTATAAGAATTAACGTAACAAGTCAAAT-AGGAA
* * * * *
3435567 AAATTTTAATTGTAGTGAAAAACAAACATTTAAATTTACATTCTCAGATTTAAAGTGTTTTACAA
65 AAAATTTAATTGTAATGAAAAACAAACATTTAAATTTACATTCTCAAATTAAAAGTGTTTAACAA
*
3435632 TATACAAATTTTAATTTTTAAATAAAAAATAATAAAGATAAAAATAATTATAGTTCAAAATTGA
130 TATACAAATTTAAATTTTTAAATAAAAAATAAT-AAGATAAAAATAATTATAGTTCAAAATTGA
3435696 CATAAAAAAG
Statistics
Matches: 167, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
225 52 0.31
226 87 0.52
228 1 0.01
229 27 0.16
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.36
Consensus pattern (227 bp):
AAATAATTAAATTTAAAATCTTAACATAAATGTATAAGAATTAACGTAACAAGTCAAATAGGAAA
AAATTTAATTGTAATGAAAAACAAACATTTAAATTTACATTCTCAAATTAAAAGTGTTTAACAAT
ATACAAATTTAAATTTTTAAATAAAAAATAATAAGATAAAAATAATTATAGTTCAAAATTGATAT
AGATAACCTTGACGTAAAAACTTAGAAAAGTG
Found at i:3436097 original size:198 final size:200
Alignment explanation
Indices: 3435716--3436103 Score: 543
Period size: 198 Copynumber: 1.9 Consensus size: 200
3435706 CTTTGATGTT
* * * * *
3435716 AAACTGTAAGAATTGATGAAAAACTTATAAAGGTAGAATAATTAAATTTTAAATCTTAACATAAA
1 AAACTGTAACAATTGACGAAAAACTTATAAAGATAAAATAACTAAATTTTAAATCTTAACATAAA
* *
3435781 CGTGTGAAAGTTAATGTAACAAGTCAATTAAGTAAAAAAAAAATCTAATTTTAGTGAAAAATAAA
66 CATGTGAAAGTTAATGTAACAAGTCAATTAAGT-AAAAAAAAATCTAATTTTAATGAAAAATAAA
* **
3435846 TATTTAAATTTATATTCTTTGACTAAAAATGTTTGACGATATACAAATTTTAATTTTTAAGTTTT
130 TATTTAAAATTATATTCTTTGACTAAAAATAATTGACGATATACAAATTTTAATTTTTAAGTTTT
3435911 AACATA
195 AACATA
* * * *
3435917 AAACTGTAACAATTGACGTTAAAACTTTTAAAGATAAAATAACTAAATTTT-GATCTTAACGTAA
1 AAACTGTAACAATTGACG-AAAAACTTATAAAGATAAAATAACTAAATTTTAAATCTTAACATAA
3435981 ACATGTGAAAGTTAATAG-AACAAGTCAATTAAGT-AAAAAAAAT-TAATTTTAATGAAAAATAA
65 ACATGTGAAAGTTAAT-GTAACAAGTCAATTAAGTAAAAAAAAATCTAATTTTAATGAAAAATAA
* * * *
3436043 ATATTTAAAATTATATT-TTTAGGCTAAAAGTAATTGACGATATATAATTTTTAATTTTTAA
129 ATATTTAAAATTATATTCTTT-GACTAAAAATAATTGACGATATACAAATTTTAATTTTTAA
3436104 ATAATAATAA
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
197 3 0.02
198 68 0.41
199 9 0.05
201 58 0.35
202 28 0.17
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.36
Consensus pattern (200 bp):
AAACTGTAACAATTGACGAAAAACTTATAAAGATAAAATAACTAAATTTTAAATCTTAACATAAA
CATGTGAAAGTTAATGTAACAAGTCAATTAAGTAAAAAAAAATCTAATTTTAATGAAAAATAAAT
ATTTAAAATTATATTCTTTGACTAAAAATAATTGACGATATACAAATTTTAATTTTTAAGTTTTA
ACATA
Found at i:3436467 original size:250 final size:250
Alignment explanation
Indices: 3435904--3437728 Score: 1369
Period size: 251 Copynumber: 7.4 Consensus size: 250
3435894 TTTAATTTTT
* * * * * * * * **
3435904 AAGTTTTAACATAAAACTGTAACAATTGACGTTAAAACTTTTAAAGATAAAATAACTAAATTTT-
1 AAGTCTTAACGTAAAATTATAAGAATTGACGTAAAAACTTATAAAGGTGGAATAACTAAATTTTA
* * * * * * *
3435968 GATCTTAACGTAAACATGTGAAAGTTAATAG-AACAAGTCAATTAAGTAAAAAAAATTAATTTTA
66 AATCTTAACGTAAATATATGAGAGTTAA-CGTAATAAGTCAATTAAGTAAAAAAATTTAATTTTA
* * * * * *
3436032 ATGAAAAATAAATATTTAAAATTATATTTTTAGGCTAAAAGTAATTGACGATATAT-AATTTTTA
130 ATGAAAAATAAATATTTAAATTTATATTCTCAGGCTAAAAGTATTTAACGATAT-TCAAATTTTA
* * * * * *
3436096 ATTTTTAAAT-AATAATAAT-A-ATAATAA-AATTATAGTTCAAAATTGATATAGAC
194 ATTTTTTAATAAAGAATAATAAGATAAAAATAATTATAGTTCAAAATTGACATAAAA
* * * *
3436149 AA-TCCTTGACGTAAAATTACAAGAATTGACATAAAAACTTATAAAGGTGGAATAGCTAAATTTT
1 AAGT-CTTAACGTAAAATTATAAGAATTGACGTAAAAACTTATAAAGGTGGAATAACTAAATTTT
* * * *
3436213 AAATCTTAATGTAAATAT-TGAAAGTTAACGTAATGAGTTAATTAAGTAAAAAAATTTAATTTTA
65 AAATCTTAACGTAAATATATGAGAGTTAACGTAATAAGTCAATTAAGTAAAAAAATTTAATTTTA
* * * * ** ** * *
3436277 ATGAAAAACAAACATTTATATTTATATTATTGGGCTAAAAACATTTAATGATATTCAAATTTTTA
130 ATGAAAAATAAATATTTAAATTTATATTCTCAGGCTAAAAGTATTTAACGATATTCAAATTTTAA
*
3436342 TTTTTTAATAAATAATAATACAGATAAAAATAATTATAGTTCAAAATTGACATAAAA
195 TTTTTTAATAAAGAATAATA-AGATAAAAATAATTATAGTTCAAAATTGACATAAAA
* * * * *
3436399 AAGTCTTGACGTTAAATTGTAAGAATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATGTTA
1 AAGTCTTAACGTAAAATTATAAGAATTGACGTAAAAACTTATAAAGGTGGAATAACTAAATTTTA
* * * * * *
3436464 AATCTTAACGTAAATGTATGAGAATTAACGTAATAAGTCAATGAAGTAAAAATATCTAATTTTAG
66 AATCTTAACGTAAATATATGAGAGTTAACGTAATAAGTCAATTAAGTAAAAAAATTTAATTTTAA
* *** *
3436529 TGAAAAATAAATATGTAAATTTATATTCTCAAATTAAAAGTATTTAACGATATACAAATTTTAAT
131 TGAAAAATAAATATTTAAATTTATATTCTCAGGCTAAAAGTATTTAACGATATTCAAATTTTAAT
* * * *
3436594 TTTTAAATAAAGAATAATAAGGATAAACATAATTATAGTTCAAAATGGATATAGAAA
196 TTTTTAATAAAGAATAATAA-GATAAAAATAATTATAGTTCAAAATTGACATA-AAA
* * * * *
3436651 AACT-TTAACGTAAAA-CAGTAAGAATTGACGT-AAAATTTATAAAAGTGGAATAATTAAATTTT
1 AAGTCTTAACGTAAAATTA-TAAGAATTGACGTAAAAACTTATAAAGGTGGAATAACTAAATTTT
* * ** * * * **
3436713 AAATCTTAACATAAATGA-GTGAGAGTTAATATAAGAAGTTAATTGAG-AAAAAAAAATAATTTT
65 AAATCTTAACGTAAAT-ATATGAGAGTTAACGTAATAAGTCAATTAAGTAAAAAAATTTAATTTT
* * *** * *
3436776 ATTAAAAAATAAATATTTAAATTTATATTCTCAAAATAAAAGTATTTAACAATATACAAATTTTA
129 AATGAAAAATAAATATTTAAATTTATATTCTCAGGCTAAAAGTATTTAACGATATTCAAATTTTA
********** * *
3436841 A-----T-AT------T--TAA-ATAAANNNNNNNNNNGCTT-AAAATTGACATATAT
194 ATTTTTTAATAAAGAATAATAAGATAAAAATAATTATAG-TTCAAAATTGACATAAAA
* * ********** *
3436883 AAGCCTTAACGTAAAACTATAAGAATTNNNNNNNNNNCTTATAAAGGTGGAATAATTAAA-TTTA
1 AAGTCTTAACGTAAAATTATAAGAATTGACGTAAAAACTTATAAAGGTGGAATAACTAAATTTTA
* ** * ** * *
3436947 AAT-TTAACCTAAACGTGTGAGAGTTAAAATAACAAGTCAATTAAGT-AAAAAGTTTAAATTTTA
66 AATCTTAACGTAAATATATGAGAGTTAACGTAATAAGTCAATTAAGTAAAAAAATTT-AATTTTA
* * * * * * * *
3437010 GTGAAAAATAAATATTAAAATATATATTCTTAGACTAAATA-TGTTTAACAATATACAAATTTTA
130 ATGAAAAATAAATATTTAAATTTATATTCTCAGGCTAAA-AGTATTTAACGATATTCAAATTTTA
* * *
3437074 ATTTTTAAATAAAGAATAATGAGGATAAAAAT-ATTATAGTTTAAAATTGACA-AAAA
194 ATTTTTTAATAAAGAATAAT-AAGATAAAAATAATTATAGTTCAAAATTGACATAAAA
** * * * * * * *
3437130 TAAG-CTTTAATATAAAACTGTAATAATTAACGTAAATACTTATAAAGGTGAAATAATTAAATTT
1 -AAGTC-TTAACGTAAAATTATAAGAATTGACGTAAAAACTTATAAAGGTGGAATAACTAAATTT
* ** * * * * * *
3437194 TAAATCTCAATATAAATGTGTGACAGCTAACCT-ACAAGTCAATTAAGTAAAAAAAATTTAAGTT
64 TAAATCTTAACGTAAATATATGAGAGTTAACGTAATAAGTCAATTAAGT-AAAAAAATTTAA-TT
* * *
3437258 TTAGTGAAAAATAAATATTTAAATTTATATTCT-AGTGTTAAAAGCATTTAACGATATAT-AAAT
127 TTAATGAAAAATAAATATTTAAATTTATATTCTCAG-GCTAAAAGTATTTAACGATAT-TCAAAT
*
3437321 TTTAATTTTTAAAT-AA-AA-AAT-A-ATAAAAATAATTATAGTTCAAAATTGACATAAATA
190 TTTAATTTTTTAATAAAGAATAATAAGATAAAAATAATTATAGTTCAAAATTGACATAAA-A
* * * *
3437378 AA-TCTTGACGAAAAATTATAACAATTGACGTAAAAACGTATAAAGGTGGAATAACTAAATTTTA
1 AAGTCTTAACGTAAAATTATAAGAATTGACGTAAAAACTTATAAAGGTGGAATAACTAAATTTTA
* * * * * * *
3437442 AATCTTAATGTAAATATATTAGATTTAACATAATAAGTTAATTAAGT-AAAAAATCTAATTTCAA
66 AATCTTAACGTAAATATATGAGAGTTAACGTAATAAGTCAATTAAGTAAAAAAATTTAATTTTAA
* * * * * *
3437506 TGAAAAATAAACATTTATATTTATATTATCGGGCTAAAAGTATGTAGCGATATTCAAATTTT--T
131 TGAAAAATAAATATTTAAATTTATATTCTCAGGCTAAAAGTATTTAACGATATTCAAATTTTAAT
* * * * **
3437569 ATTTTAAGTAAAGAATAATAAAGATAACAATAATTATAATT-AAAAGTT-ATTATTGAA
196 TTTTTAA-TAAAGAATAAT-AAGATAAAAATAATTATAGTTCAAAA-TTGA-CATAAAA
* * * * * * * *
3437626 AAGACTTAACGTAAAGTTATAAGAATTAAAGTAAAATCTTATAAACGTGAAATAAGC-AAATTTA
1 AAGTCTTAACGTAAAATTATAAGAATTGACGTAAAAACTTATAAAGGTGGAATAA-CTAAATTTT
* * *
3437690 AAATCTTAATGTAAATGTATGAGAGTTAACGTAACAAGT
65 AAATCTTAACGTAAATATATGAGAGTTAACGTAATAAGT
3437729 GGTAATAATA
Statistics
Matches: 1257, Mismatches: 255, Indels: 132
0.76 0.16 0.08
Matches are distributed among these distances:
232 43 0.03
233 104 0.08
234 25 0.02
235 3 0.00
237 1 0.00
239 2 0.00
242 6 0.00
243 4 0.00
244 59 0.05
245 167 0.13
246 115 0.09
247 25 0.02
248 69 0.05
249 211 0.17
250 186 0.15
251 231 0.18
252 6 0.00
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.34
Consensus pattern (250 bp):
AAGTCTTAACGTAAAATTATAAGAATTGACGTAAAAACTTATAAAGGTGGAATAACTAAATTTTA
AATCTTAACGTAAATATATGAGAGTTAACGTAATAAGTCAATTAAGTAAAAAAATTTAATTTTAA
TGAAAAATAAATATTTAAATTTATATTCTCAGGCTAAAAGTATTTAACGATATTCAAATTTTAAT
TTTTTAATAAAGAATAATAAGATAAAAATAATTATAGTTCAAAATTGACATAAAA
Found at i:3436674 original size:251 final size:248
Alignment explanation
Indices: 3435908--3436853 Score: 948
Period size: 250 Copynumber: 3.8 Consensus size: 248
3435898 ATTTTTAAGT
* * * * * ** *
3435908 TTTAACATAAAACTGTAACAATTGACGTTAAAACTT-TTAAAGATAAAATAACTAAATTTT-GAT
1 TTTAACGTAAAACAGTAAGAATTGACGTAAAAACTTATAAAAG-TGGAATAACTAAATTTTAAAT
* * * * *
3435971 CTTAACGTAAACATGTGAAAGTTAATAG-AACAAGTCAATTAAGTAAAAAAAATTAATTTTAATG
65 CTTAACGTAAATATATGAAAGTTAA-CGTAATAAGTCAATGAAGT-AAAAAAATTAATTTTAATG
* * * ** * * * *
3436035 AAAAATAAATATTTAAAATTATATTTTTAGGCTAAAAGTAATTGACGATATATAATTTTTAATTT
128 AAAAATAAATATTTAAATTTATATTCTCAAACTAAAAGTATTTAACGATATACAAATTTTAATTT
* *
3436100 TTAAAT-AATAATAAT-A-ATAATAA-AATTATAGTTCAAAATTGATATAGACAATC
193 TTAAATAAATAATAATAAGATAA-AATAATTATAGTTCAAAATTGATATAGAAAAAC
* * * * * * *
3436153 CTTGACGTAAAATTA-CAAGAATTGACATAAAAACTTATAAAGGTGGAATAGCTAAATTTTAAAT
1 TTTAACGTAAAA-CAGTAAGAATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAAAT
* * * *
3436217 CTTAATGTAAATAT-TGAAAGTTAACGTAATGAGTTAATTAAGTAAAAAAATTTAATTTTAATGA
65 CTTAACGTAAATATATGAAAGTTAACGTAATAAGTCAATGAAGTAAAAAAA-TTAATTTTAATGA
* * * * **** ** * * *
3436281 AAAACAAACATTTATATTTATATTATTGGGCTAAAAACATTTAATGATATTCAAATTTTTATTTT
129 AAAATAAATATTTAAATTTATATTCTCAAACTAAAAGTATTTAACGATATACAAATTTTAATTTT
* * *
3436346 TTAATAAATAATAATACAGATAAAAATAATTATAGTTCAAAATTGACATA-AAAAAG
194 TAAATAAATAATAATA-AGAT-AAAATAATTATAGTTCAAAATTGATATAGAAAAAC
* * ** *
3436402 TCTTGACGTTAAATTGTAAGAATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATGTTAAAT
1 T-TTAACGTAAAACAGTAAGAATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAAAT
* * *
3436467 CTTAACGTAAATGTATGAGAA-TTAACGTAATAAGTCAATGAAGTAAAAATATCTAATTTTAGTG
65 CTTAACGTAAATATATGA-AAGTTAACGTAATAAGTCAATGAAGTAAAAAAAT-TAATTTTAATG
* *
3436531 AAAAATAAATATGTAAATTTATATTCTCAAATTAAAAGTATTTAACGATATACAAATTTTAATTT
128 AAAAATAAATATTTAAATTTATATTCTCAAACTAAAAGTATTTAACGATATACAAATTTTAATTT
* *
3436596 TTAAATAAAGAATAATAAGGATAAACATAATTATAGTTCAAAATGGATATAGAAAAAC
193 TTAAATAAATAATAATAA-GATAAA-ATAATTATAGTTCAAAATTGATATAGAAAAAC
* *
3436654 TTTAACGTAAAACAGTAAGAATTGACGT-AAAATTTATAAAAGTGGAATAATTAAATTTTAAATC
1 TTTAACGTAAAACAGTAAGAATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAAATC
* * * ** * * * * * *
3436718 TTAACATAAATGA-GTGAGAGTTAATATAAGAAGTTAATTG-AGAAAAAAAAATAATTTTATTAA
66 TTAACGTAAAT-ATATGAAAGTTAACGTAATAAGTCAA-TGAAGTAAAAAAATTAATTTTAATGA
* * *
3436781 AAAATAAATATTTAAATTTATATTCTCAAAATAAAAGTATTTAACAATATACAAATTTTAATATT
129 AAAATAAATATTTAAATTTATATTCTCAAACTAAAAGTATTTAACGATATACAAATTTTAATTTT
3436846 TAAATAAA
194 TAAATAAA
3436854 NNNNNNNNNN
Statistics
Matches: 579, Mismatches: 100, Indels: 40
0.81 0.14 0.06
Matches are distributed among these distances:
244 8 0.01
245 130 0.22
246 27 0.05
248 1 0.00
249 88 0.15
250 162 0.28
251 155 0.27
252 8 0.01
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.35
Consensus pattern (248 bp):
TTTAACGTAAAACAGTAAGAATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAAATC
TTAACGTAAATATATGAAAGTTAACGTAATAAGTCAATGAAGTAAAAAAATTAATTTTAATGAAA
AATAAATATTTAAATTTATATTCTCAAACTAAAAGTATTTAACGATATACAAATTTTAATTTTTA
AATAAATAATAATAAGATAAAATAATTATAGTTCAAAATTGATATAGAAAAAC
Found at i:3437038 original size:482 final size:466
Alignment explanation
Indices: 3436436--3437337 Score: 1011
Period size: 482 Copynumber: 1.9 Consensus size: 466
3436426 GACGTAAAAA
* * ** *
3436436 CTTATAAAAGTGGAATAACTAAATGTTAAATCTTAACGTAAATGTATGAGAATTAACGTAATAAG
1 CTTATAAAAGTGGAATAACTAAATGTTAAATCTTAACCTAAACGTATGAGAATTAAAATAACAAG
* *
3436501 TCAATGAAGTAAAAATATCTAATTTTAGTGAAAAATAAATATGTAAATTTATATTCTCAAATTAA
66 TCAATGAAGTAAAAATATCTAATTTTAGTGAAAAATAAATATGTAAATATATATTCTCAAACTAA
* *
3436566 A-AGTATTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAACATAATTAT
131 ATA-TATTTAACAATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAAT-ATTAT
* * * *
3436630 AGTTCAAAATGGATATAGAAA-AA-CTTTAACGTAAAACAGTAAGAATTGACGTAAA-ATTTATA
194 AGTTCAAAATGGACA-A-AAATAAGCTTTAACATAAAACAGTAAGAATTAACGTAAATACTTATA
* * * * * * *
3436692 AAAGTGGAATAATTAAATTTTAAATCTTAACATAAATGAGTGAGAGTTAATATAAGAAGTTAATT
257 AAAGTGAAATAATTAAATTTTAAATCTCAACATAAATGAGTGACAGCTAACAT-ACAAGTCAATT
* *
3436757 GAG-AAAAAAAA-ATAA-TTTTATTAAAAAATAAATATTTAAATTTATATTCTCA-AAATAAAAG
321 AAGTAAAAAAAATATAAGTTTTAGTAAAAAATAAATATTTAAATTTATATTCT-AGAAATAAAAG
*
3436818 TATTTAACAATATACAAATTTTAATATTTAAATAAANNNNNNNNNNGCTTAAAATTGACATATAT
385 CATTTAACAATATACAAATTTTAATATTTAAATAAA----------GCTTAAAATTGACATATAT
3436883 AAGCCTTAACGTAAAACTATAAGAATT
440 AAGCCTTAACGTAAAACTATAAGAATT
* * * *
3436910 NNNNNNNNNNCTTATAAAGGTGGAATAATTAAAT-TTAAAT-TTAACCTAAACGTGTGAGAGTTA
1 ----------CTTATAAAAGTGGAATAACTAAATGTTAAATCTTAACCTAAACGTATGAGAATTA
*
3436973 AAATAACAAGTCAATTAAGTAAAAAGT-T-TAAATTTTAGTGAAAAATAAATAT-TAAAATATAT
56 AAATAACAAGTCAATGAAGTAAAAA-TATCT-AATTTTAGTGAAAAATAAATATGT-AAATATAT
* * * *
3437035 ATTCTTAGACTAAATATGTTTAACAATATACAAATTTTAATTTTTAAATAAAGAATAATGAGGAT
118 ATTCTCAAACTAAATATATTTAACAATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGAT
* * * * *
3437100 AAAAATATTATAGTTTAAAATTGACAAAAATAAGCTTTAATATAAAACTGTAATAATTAACGTAA
183 AAAAATATTATAGTTCAAAATGGACAAAAATAAGCTTTAACATAAAACAGTAAGAATTAACGTAA
* * * *
3437165 ATACTTATAAAGGTGAAATAATTAAATTTTAAATCTCAATATAAATGTGTGACAGCTAACCTACA
248 ATACTTATAAAAGTGAAATAATTAAATTTTAAATCTCAACATAAATGAGTGACAGCTAACATACA
* * **
3437230 AGTCAATTAAGTAAAAAAAATTTAAGTTTTAGTGAAAAATAAATATTTAAATTTATATTCTAGTG
313 AGTCAATTAAGTAAAAAAAATATAAGTTTTAGTAAAAAATAAATATTTAAATTTATATTCTAGAA
* * * *
3437295 TTAAAAGCATTTAACGATATATAAATTTTAATTTTTAAATAAA
378 ATAAAAGCATTTAACAATATACAAATTTTAATATTTAAATAAA
3437338 AAATAATAAA
Statistics
Matches: 358, Mismatches: 49, Indels: 22
0.83 0.11 0.05
Matches are distributed among these distances:
479 3 0.01
480 3 0.01
481 57 0.16
482 190 0.53
483 12 0.03
484 93 0.26
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.34
Consensus pattern (466 bp):
CTTATAAAAGTGGAATAACTAAATGTTAAATCTTAACCTAAACGTATGAGAATTAAAATAACAAG
TCAATGAAGTAAAAATATCTAATTTTAGTGAAAAATAAATATGTAAATATATATTCTCAAACTAA
ATATATTTAACAATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATATTATAG
TTCAAAATGGACAAAAATAAGCTTTAACATAAAACAGTAAGAATTAACGTAAATACTTATAAAAG
TGAAATAATTAAATTTTAAATCTCAACATAAATGAGTGACAGCTAACATACAAGTCAATTAAGTA
AAAAAAATATAAGTTTTAGTAAAAAATAAATATTTAAATTTATATTCTAGAAATAAAAGCATTTA
ACAATATACAAATTTTAATATTTAAATAAAGCTTAAAATTGACATATATAAGCCTTAACGTAAAA
CTATAAGAATT
Found at i:3437331 original size:251 final size:246
Alignment explanation
Indices: 3436920--3437728 Score: 714
Period size: 249 Copynumber: 3.3 Consensus size: 246
3436910 NNNNNNNNNN
** * *
3436920 CTTATAAAGGTGGAATAATTAAA-TTTAAAT-TTAACCTAAACGTGTGAGAGTTAAAATAACAAG
1 CTTATAAAGGTGGAATAATTAAATTTTAAATCTTAATATAAATGTGTGAGAGTTAACATAACAAG
* * * *
3436983 TCAATTAAGTAAAAAGTTTAAATTTTAGTGAAAAATAAATATTAAAATATATATTCTTAGACTAA
66 TCAATTAAGTAAAAAATTT-AATTTTAGTGAAAAATAAATATTTAAATTTATATTC-TAGGCTAA
* *
3437048 ATATG-TTTAACAATATACAAATTTTAATTTTTAAATAAAGAATAATGAGGATAAAAAT-ATTAT
129 A-A-GATTTAACGATATATAAATTTTAATTTTTAAATAAAGAATAAT-A-GATAAAAATAATTAT
* * * * * *
3437111 AGTTTAAAATTGACAAAAAT-AAGCTTTAATATAAAACTGTAATAATTAACGTAAATA
190 AGTTCAAAATTGACAAAAATAAAGCTTGAAGA-AAAACTATAACAATTAACGTAAAAA
* * * * *
3437168 CTTATAAAGGTGAAATAATTAAATTTTAAATCTCAATATAAATGTGTGACAGCTAACCT-ACAAG
1 CTTATAAAGGTGGAATAATTAAATTTTAAATCTTAATATAAATGTGTGAGAGTTAACATAACAAG
*
3437232 TCAATTAAGTAAAAAAAATTTAAGTTTTAGTGAAAAATAAATATTTAAATTTATATTCTAGTGTT
66 TCAATTAAGT--AAAAAATTTAA-TTTTAGTGAAAAATAAATATTTAAATTTATATTCTAG-GCT
3437297 AAAAGCATTTAACGATATATAAATTTTAATTTTTAAAT-AA-AA-AATA-ATAAAAATAATTATA
127 AAAAG-ATTTAACGATATATAAATTTTAATTTTTAAATAAAGAATAATAGATAAAAATAATTATA
* * * * *
3437358 GTTCAAAATTGACATAAATAAATCTTGACGAAAAATTATAACAATTGACGTAAAAA
191 GTTCAAAATTGACAAAAATAAAGCTTGAAGAAAAACTATAACAATTAACGTAAAAA
* * * * * * * *
3437414 CGTATAAAGGTGGAATAACTAAATTTTAAATCTTAATGTAAATATATTAGATTTAACATAATAAG
1 CTTATAAAGGTGGAATAATTAAATTTTAAATCTTAATATAAATGTGTGAGAGTTAACATAACAAG
* * * * * * * *
3437479 TTAATTAAGTAAAAAATCTAATTTCAATGAAAAATAAACATTTATATTTATATTATCGGGCTAAA
66 TCAATTAAGTAAAAAATTTAATTTTAGTGAAAAATAAATATTTAAATTTATATTCT-AGGCTAAA
* * * * *
3437544 AGTATGTAGCGATAT-TCAAATTTTTA-TTTTAAGTAAAGAATAATAAAGATAACAATAATTATA
130 AG-ATTTAACGATATAT-AAATTTTAATTTTTAAATAAAGAATAAT--AGATAAAAATAATTATA
* * *** * ** * * *
3437607 ATT-AAAAGTT-ATTATTGA-AAAGACTT-AACGTAAAGTTATAAGAATTAAAGTAAAAT
191 GTTCAAAA-TTGA-CAAAAATAAAG-CTTGAA-GAAAAACTATAACAATTAACGTAAAAA
* * ** * * * *
3437663 CTTATAAACGTGAAATAAGCAAATTTAAAATCTTAATGTAAATGTATGAGAGTTAACGTAACAAG
1 CTTATAAAGGTGGAATAATTAAATTTTAAATCTTAATATAAATGTGTGAGAGTTAACATAACAAG
3437728 T
66 T
3437729 GGTAATAATA
Statistics
Matches: 460, Mismatches: 78, Indels: 45
0.79 0.13 0.08
Matches are distributed among these distances:
243 8 0.02
244 57 0.12
245 21 0.05
246 93 0.20
247 21 0.05
248 35 0.08
249 125 0.27
250 27 0.06
251 73 0.16
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.34
Consensus pattern (246 bp):
CTTATAAAGGTGGAATAATTAAATTTTAAATCTTAATATAAATGTGTGAGAGTTAACATAACAAG
TCAATTAAGTAAAAAATTTAATTTTAGTGAAAAATAAATATTTAAATTTATATTCTAGGCTAAAA
GATTTAACGATATATAAATTTTAATTTTTAAATAAAGAATAATAGATAAAAATAATTATAGTTCA
AAATTGACAAAAATAAAGCTTGAAGAAAAACTATAACAATTAACGTAAAAA
Found at i:3441608 original size:171 final size:170
Alignment explanation
Indices: 3441286--3443357 Score: 1834
Period size: 171 Copynumber: 12.1 Consensus size: 170
3441276 TAGGTAATGA
* * ** * * *
3441286 TCAATGGATGGCTTTCGCTTTACGTTTCTCAAGATAAACCTCCAATTATGATTTGTTTGAATC-A
1 TCAATGGATGGCTTTCGCTTCATGTTTCTCAAGGCAAACATCCAATTATGATCTGTTTTAA-CAA
* * * * *
3441350 AAAATGAAAAAAATTTAACTTAAAATCATTTATAAGATTATAAAACCATTT-AACGCGAATAATT
65 AAAATGAAAAAAATTCAACTTAAAATCATTTATAAGATTATAAAATC-TTTGAAAGCGAGTAACT
* * *
3441414 AGGCTTTCGAAGGCATGAGTGACTATAAATGGACTTATCTTG
129 AGTCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTG
* * * *
3441456 TCAATGCATGGCTTTGGCTTCAAGTTT-TCCAAGGCTAACATCCAATTATGATCTGTTTTAACAA
1 TCAATGGATGGCTTTCGCTTCATGTTTCT-CAAGGCAAACATCCAATTATGATCTGTTTTAACAA
* * *
3441520 AAAATGAAACAAAATTTAACTTAAAATCATTTATAAGATTATAAAATCTTTGAAAGCTAGTAATT
65 AAAATGAAA-AAAATTCAACTTAAAATCATTTATAAGATTATAAAATCTTTGAAAGCGAGTAACT
* * * * *
3441585 AATCTTTCAAAGGTATAAGTGACTATATATGGACTTTTCTTA
129 AGTCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTG
* * * * * ** * * ** ***
3441627 TCAATAGATGGTTTTCACTTTACGTTT-TTGAGGTAAACATCCAATTATGATCTATTGCAAGTGA
1 TCAATGGATGGCTTTCGCTTCATGTTTCTCAAGGCAAACATCCAATTATGATCTGTTTTAACAAA
* * *
3441691 AAATAAAAAAAATT-AACTTAAAATCATTTATAAGATTATAAAA-CTATGTAAAACGAGTAACTA
66 AAATGAAAAAAATTCAACTTAAAATCATTTATAAGATTATAAAATCTTTG-AAAGCGAGTAACTA
* * * *
3441754 GTCTTTCAAAAGTATGAGTGACTATAAATAGACTTTTCTTA
130 GTCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTG
* * * ** ** * * * *
3441795 TCGATGGATAGCTTTCACTTCACATTTCTCAAGATAAATATCCAATTAT-ACTATGTTTTACCCA
1 TCAATGGATGGCTTTCGCTTCATGTTTCTCAAGGCAAACATCCAATTATGA-TCTGTTTTAACAA
* * * * *
3441859 GAAATAAAAAAACAAGTTTAACTTAAAATCATTTATAAGATTATAAAACCATTT-AAAGTGAGTA
65 AAAAT-GAAAAA-AA-TTCAACTTAAAATCATTTATAAGATTATAAAATC-TTTGAAAGCGAGTA
* * * *
3441923 AATAATCTTTCAAAGGCATGAATGACTATAAATGAACTTTTCTTG
126 ACTAGTCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTG
* * * * * * *
3441968 TCACTGAATGACTTT-GCTTCATGGTTCTCTAGGCAAACATCCAGTTATGATCTGCTTTAACAAA
1 TCAATGGATGGCTTTCGCTTCATGTTTCTCAAGGCAAACATCCAATTATGATCTGTTTTAACAAA
* * * * * *
3442032 CAATGAAAAACAATTCAACATAAAATGATGTATAAGATTAT-AAATCCATTT-AAAGCAAGTAAT
66 AAATGAAAAA-AATTCAACTTAAAATCATTTATAAGATTATAAAAT-C-TTTGAAAGCGAGTAAC
* * *** *
3442095 TAGTTTTTCGAATATATGAGTGACTATAAATGGACTTTTCTTA
128 TAGTCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTG
* * * * * * * ** *
3442138 TTAATGGATAGCTTTTGCTTCACGTTTTTCAAGACGAACATTTAATTATGATCTGTTTTAACCAA
1 TCAATGGATGGCTTTCGCTTCATGTTTCTCAAGGCAAACATCCAATTATGATCTGTTTTAACAAA
* *
3442203 AAATGAAAAAAAAATT-AACTTAAAATCATTTATAAGATTATAAAATCATTGAAAGCAAGTAACT
66 AAATG--AAAAAAATTCAACTTAAAATCATTTATAAGATTATAAAATCTTTGAAAGCGAGTAACT
* * *
3442267 AGTCTTTTAAAGGCATGAGTGACTATAAATGGACTATTCTTA
129 AGTCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTG
* ** *
3442309 TCAATGGATGGCTTTCGCTTTATGTTTCTCAAGAAAAACATCCAATTATGATCTGTTTGAATC-A
1 TCAATGGATGGCTTTCGCTTCATGTTTCTCAAGGCAAACATCCAATTATGATCTGTTTTAA-CAA
* * * *
3442373 AAAATGAAAAAAAATTCAACTTAAAATCATTTAGAATATTAT-AAATCTATTTAAAGC-ATGTAG
65 AAAATG-AAAAAAATTCAACTTAAAATCATTTATAAGATTATAAAATCT-TTGAAAGCGA-GTAA
* * * * *
3442436 TTAGTTTTTCGAAGGTATGAGTGACTATAAATAGACTTTTCTTG
127 CTAGTCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTG
* * ** ** *
3442480 TCAATGGATGGTTTTTG-TTTTTGTTTTACGTTTCTTAAGATAAACATCCAATTATGATATGTTT
1 TCAATGGATGGCTTTCGCTTCATG-TTT-C---TC--AAGGCAAACATCCAATTATGATCTGTTT
*** * * * *
3442544 TAATTGAAAATGAAAAAAACTTCAACTTAAAATGATTTATAAGATTACAAAA-CTATTTAAAGCA
59 TAACAAAAAATGAAAAAAA-TTCAACTTAAAATCATTTATAAGATTATAAAATCT-TTGAAAGCG
* * * **
3442608 AGTAAGTAGTCTTTCGAAGGCATGAGTGATTATAAATAAACTTTGT-TTG
122 AGTAACTAGTCTTTCAAAGGCATGAGTGACTATAAATGGACTTT-TCTTG
* ** ** * * * *
3442657 TCGATGGATGGCTTTTACTTCATGTTTCTTGAGGCAAACATCTAAATATGATCTATTTTAGCCAA
1 TCAATGGATGGCTTTCGCTTCATGTTTCTCAAGGCAAACATCCAATTATGATCTGTTTTA-ACAA
* * * * *
3442722 AAAA-GAAAAAAAGTTTAACTTAAAATCATTTATAAGATTATAAAACCATTCAACA-CGAGTAAT
65 AAAATGAAAAAAA-TTCAACTTAAAATCATTTATAAGATTATAAAATCTTTGAA-AGCGAGTAAC
* * * *
3442785 TAGGCTTTCGAAA-GTATGAGTGACTATAAATAGATTTTTCTTG
128 TAGTCTTTC-AAAGGCATGAGTGACTATAAATGGACTTTTCTTG
* * * * * *
3442828 TCAATAGATAGCTTTTGCTTCATGTTTCTCAAGGCTAACATCTAATTATGATCTGTTTTAATAAA
1 TCAATGGATGGCTTTCGCTTCATGTTTCTCAAGGCAAACATCCAATTATGATCTGTTTTAACAAA
* * * *
3442893 AAATGAAAACAAATTCAACTTAAAATCATTTAAAAGAGTATAAAACCATTGAAAGCGAGTAACTA
66 AAATGAAAA-AAATTCAACTTAAAATCATTTATAAGATTATAAAATCTTTGAAAGCGAGTAACTA
* *
3442958 GTCTTTCAAAGGCATGAGTGACTGTAAATGGACTTTTCTTA
130 GTCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTG
* ** ** * * *
3442999 TCAATGGATGGCTTTCGTTTCACATTTCTTGAGACAAACATCCAATTATGATTTGTTTTAACTAA
1 TCAATGGATGGCTTTCGCTTCATGTTTCTCAAGGCAAACATCCAATTATGATCTGTTTTAACAAA
* * * *
3443064 AATTGAAAAAGAATTCAACATAAAATGATTTATAAGATTAT-AAATCCATTT-AAAGTGAGTAAC
66 AAATGAAAAA-AATTCAACTTAAAATCATTTATAAGATTATAAAAT-C-TTTGAAAGCGAGTAAC
* * ** * * * *
3443127 TAATTTTTTGAAGGAATGAATAACTATAAATTGACTTTTCTTG
128 TAGTCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTG
* * * * * *
3443170 TCATTGGATGGCTTTCGCTTTATGTTTTTCAAGGCAAACATCCAATTATGATATGTTTTAGCCAA
1 TCAATGGATGGCTTTCGCTTCATGTTTCTCAAGGCAAACATCCAATTATGATCTGTTTTAACAAA
*
3443235 AAATGAAAAAAAAATTCAACTTAGAATCATTTATAAGATTATAAAA-CTATTGAAAGCGAGTAAC
66 AAATG--AAAAAAATTCAACTTAAAATCATTTATAAGATTATAAAATCT-TTGAAAGCGAGTAAC
* * * *
3443299 TAGTCTTTCGAAGACATAAATGACTATAAATGGACTTTTCTTG
128 TAGTCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTG
* **
3443342 TTAAAAGATGGCTTTC
1 TCAATGGATGGCTTTC
3443358 ATATCCAAAA
Statistics
Matches: 1546, Mismatches: 302, Indels: 106
0.79 0.15 0.05
Matches are distributed among these distances:
167 4 0.00
168 98 0.06
169 37 0.02
170 222 0.14
171 792 0.51
172 146 0.09
173 99 0.06
174 1 0.00
175 4 0.00
176 8 0.01
177 126 0.08
178 9 0.01
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (170 bp):
TCAATGGATGGCTTTCGCTTCATGTTTCTCAAGGCAAACATCCAATTATGATCTGTTTTAACAAA
AAATGAAAAAAATTCAACTTAAAATCATTTATAAGATTATAAAATCTTTGAAAGCGAGTAACTAG
TCTTTCAAAGGCATGAGTGACTATAAATGGACTTTTCTTG
Found at i:3442427 original size:342 final size:342
Alignment explanation
Indices: 3441285--3443340 Score: 2072
Period size: 342 Copynumber: 6.0 Consensus size: 342
3441275 TTAGGTAATG
* * * *
3441285 ATCAATGGATGGCTTTCGCTTTACGTTTCTCAAGATAAACCTCCAATTATGATTTGTTTGAATCA
1 ATCAATGGATGGCTTTCGCTTTACGTTTCTCGAGACAAACATCCAATTATGATCTGTTTGAATCA
* *
3441350 AAAATG-AAAAAAATTTAACTTAAAATCATTTATAAGATTATAAAACCATTTAACGCGAA-TAAT
66 AAAATGAAAAAAAATTCAACTTAAAATCATTTATAAGATTATAAAACCATTTAAAGC-AAGTAAT
* ** * * * * *
3441413 TAGGCTTTCGAAGGCATGAGTGACTATAAATGGACTTATCTTGTCAATGCATGGCTTTGGCTTCA
130 TAGTCTTTCGAAGATATGAGTGACTATAAATAGACTTTTCTTGTCAATGGATAGCTTTTGCTTCA
* * * * * * * *
3441478 AGTTTTCCAAGGCTAACATCCAATTATGATCTGTTTTAACAAAAAATG-AAACAAAATTTAACTT
195 CGTTTTTCAAGACAAACATCCAATTATGATATGTTTTAACCAAAAATGAAAAAAAAATTCAACTT
* * * * * *
3441542 AAAATCATTTATAAGATTATAAAATCTTTGAAAGCTAGTAATTAATCTTTCAAAGGTATAAGTGA
260 AAAATCATTTATAAGATTATAAAA-CATTGAAAGCGAGTAACTAGTCTTTCAAAGGCATGAGTGA
*
3441607 CTATATATGGACTTTTCTT
324 CTATAAATGGACTTTTCTT
* * * * ** *
3441626 ATCAATAGATGGTTTTCACTTTACGTTT-TTGAGGTAAACATCCAATTATGATCT-ATTGCAAGT
1 ATCAATGGATGGCTTTCGCTTTACGTTTCTCGAGACAAACATCCAATTATGATCTGTTTG-AA-T
* * * * *
3441689 -GAAAAT-AAAAAAAATT-AACTTAAAATCATTTATAAGATTATAAAACTATGTAAAACGAGTAA
64 CAAAAATGAAAAAAAATTCAACTTAAAATCATTTATAAGATTATAAAACCATTTAAAGCAAGTAA
* * * * **
3441751 CTAGTCTTTC-AAAAGTATGAGTGACTATAAATAGACTTTTCTTATCGATGGATAGCTTTCACTT
129 TTAGTCTTTCGAAGA-TATGAGTGACTATAAATAGACTTTTCTTGTCAATGGATAGCTTTTGCTT
* * * * * * *
3441815 CACATTTCTCAAGATAAATATCCAATTAT-ACTATGTTTTACCCAGAAAT-AAAAAAACAAGTTT
193 CACGTTTTTCAAGACAAACATCCAATTATGA-TATGTTTTAACCAAAAATGAAAAAAA-AA-TTC
* * * *
3441878 AACTTAAAATCATTTATAAGATTATAAAACCATTTAAAGTGAGTAAATAATCTTTCAAAGGCATG
255 AACTTAAAATCATTTATAAGATTATAAAA-CATTGAAAGCGAGTAACTAGTCTTTCAAAGGCATG
* *
3441943 AATGACTATAAATGAACTTTTCTT
319 AGTGACTATAAATGGACTTTTCTT
* * * * * * * * * *
3441967 GTCACTGAATGACTTT-GCTTCATGGTTCTCTAGGCAAACATCCAGTTATGATCTGCTTT-AA-C
1 ATCAATGGATGGCTTTCGCTTTACGTTTCTCGAGACAAACATCCAATTATGATCTG-TTTGAATC
* * * * *
3442029 AAACAATGAAAAACAATTCAACATAAAATGATGTATAAGATTATAAATCCATTTAAAGCAAGTAA
65 AAA-AATGAAAAAAAATTCAACTTAAAATCATTTATAAGATTATAAAACCATTTAAAGCAAGTAA
* * * * *
3442094 TTAGTTTTTCGAATATATGAGTGACTATAAATGGACTTTTCTTATTAATGGATAGCTTTTGCTTC
129 TTAGTCTTTCGAAGATATGAGTGACTATAAATAGACTTTTCTTGTCAATGGATAGCTTTTGCTTC
* ** *
3442159 ACGTTTTTCAAGACGAACATTTAATTATGATCTGTTTTAACCAAAAATGAAAAAAAAATT-AACT
194 ACGTTTTTCAAGACAAACATCCAATTATGATATGTTTTAACCAAAAATGAAAAAAAAATTCAACT
* *
3442223 TAAAATCATTTATAAGATTATAAAATCATTGAAAGCAAGTAACTAGTCTTTTAAAGGCATGAGTG
259 TAAAATCATTTATAAGATTATAAAA-CATTGAAAGCGAGTAACTAGTCTTTCAAAGGCATGAGTG
*
3442288 ACTATAAATGGACTATTCTT
323 ACTATAAATGGACTTTTCTT
* * *
3442308 ATCAATGGATGGCTTTCGCTTTATGTTTCTCAAGAAAAACATCCAATTATGATCTGTTTGAATCA
1 ATCAATGGATGGCTTTCGCTTTACGTTTCTCGAGACAAACATCCAATTATGATCTGTTTGAATCA
* * * * * *
3442373 AAAATGAAAAAAAATTCAACTTAAAATCATTTAGAATATTATAAATCTATTTAAAGCATGTAGTT
66 AAAATGAAAAAAAATTCAACTTAAAATCATTTATAAGATTATAAAACCATTTAAAGCAAGTAATT
* * * *
3442438 AGTTTTTCGAAGGTATGAGTGACTATAAATAGACTTTTCTTGTCAATGGATGGTTTTTGTTTTTG
131 AGTCTTTCGAAGATATGAGTGACTATAAATAGACTTTTCTTGTCAATGGA------TAGCTTTTG
* * * *** *
3442503 TTTTACGTTTCTT-AAGATAAACATCCAATTATGATATGTTTTAATTGAAAATG-AAAAAAACTT
190 CTTCACGTTT-TTCAAGACAAACATCCAATTATGATATGTTTTAACCAAAAATGAAAAAAAAATT
* * * * * *
3442566 CAACTTAAAATGATTTATAAGATTACAAAACTATTTAAAGCAAGTAAGTAGTCTTTCGAAGGCAT
254 CAACTTAAAATCATTTATAAGATTATAAAAC-ATTGAAAGCGAGTAACTAGTCTTTCAAAGGCAT
* **
3442631 GAGTGATTATAAATAAACTTTGT-TT
318 GAGTGACTATAAATGGACTTT-TCTT
* * ** * * * * * * * * **
3442656 GTCGATGGATGGCTTTTACTTCATGTTTCTTGAGGCAAACATCTAAATATGATCTATTTTAGCCA
1 ATCAATGGATGGCTTTCGCTTTACGTTTCTCGAGACAAACATCCAATTATGATCTGTTTGAATCA
* * * * *
3442721 AAAAAGAAAAAAAGTTTAACTTAAAATCATTTATAAGATTATAAAACCATTCAACA-CGAGTAAT
66 AAAATGAAAAAAAATTCAACTTAAAATCATTTATAAGATTATAAAACCATTTAA-AGCAAGTAAT
* * *
3442785 TAGGCTTTCGAA-AGTATGAGTGACTATAAATAGATTTTTCTTGTCAATAGATAGCTTTTGCTTC
130 TAGTCTTTCGAAGA-TATGAGTGACTATAAATAGACTTTTCTTGTCAATGGATAGCTTTTGCTTC
* * * * * * ** *
3442849 ATGTTTCTCAAGGCTAACATCTAATTATGATCTGTTTTAATAAAAAATG-AAAACAAATTCAACT
194 ACGTTTTTCAAGACAAACATCCAATTATGATATGTTTTAACCAAAAATGAAAAAAAAATTCAACT
* *
3442913 TAAAATCATTTAAAAGAGTATAAAACCATTGAAAGCGAGTAACTAGTCTTTCAAAGGCATGAGTG
259 TAAAATCATTTATAAGATTATAAAA-CATTGAAAGCGAGTAACTAGTCTTTCAAAGGCATGAGTG
*
3442978 ACTGTAAATGGACTTTTCTT
323 ACTATAAATGGACTTTTCTT
* * * *
3442998 ATCAATGGATGGCTTTCG-TTTCACATTTCTTGAGACAAACATCCAATTATGATTTGTTTTAA-C
1 ATCAATGGATGGCTTTCGCTTT-ACGTTTCTCGAGACAAACATCCAATTATGATCTGTTTGAATC
* * * * * **
3443061 TAAAATTGAAAAAGAATTCAACATAAAATGATTTATAAGATTATAAATCCATTTAAAGTGAGTAA
65 -AAAAATGAAAAAAAATTCAACTTAAAATCATTTATAAGATTATAAAACCATTTAAAGCAAGTAA
* * * * * * * * * *
3443126 CTAATTTTTTGAAGGA-ATGAATAACTATAAATTGACTTTTCTTGTCATTGGATGGCTTTCGCTT
129 TTAGTCTTTCGAA-GATATGAGTGACTATAAATAGACTTTTCTTGTCAATGGATAGCTTTTGCTT
* * * *
3443190 TATGTTTTTCAAGGCAAACATCCAATTATGATATGTTTTAGCCAAAAATGAAAAAAAAATTCAAC
193 CACGTTTTTCAAGACAAACATCCAATTATGATATGTTTTAACCAAAAATGAAAAAAAAATTCAAC
* * * * *
3443255 TTAGAATCATTTATAAGATTATAAAACTATTGAAAGCGAGTAACTAGTCTTTCGAAGACATAAAT
258 TTAAAATCATTTATAAGATTATAAAAC-ATTGAAAGCGAGTAACTAGTCTTTCAAAGGCATGAGT
3443320 GACTATAAATGGACTTTTCTT
322 GACTATAAATGGACTTTTCTT
3443341 GTTAAAAGAT
Statistics
Matches: 1408, Mismatches: 263, Indels: 86
0.80 0.15 0.05
Matches are distributed among these distances:
338 4 0.00
339 130 0.09
340 48 0.03
341 244 0.17
342 463 0.33
343 225 0.16
344 12 0.01
347 10 0.01
348 268 0.19
349 4 0.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (342 bp):
ATCAATGGATGGCTTTCGCTTTACGTTTCTCGAGACAAACATCCAATTATGATCTGTTTGAATCA
AAAATGAAAAAAAATTCAACTTAAAATCATTTATAAGATTATAAAACCATTTAAAGCAAGTAATT
AGTCTTTCGAAGATATGAGTGACTATAAATAGACTTTTCTTGTCAATGGATAGCTTTTGCTTCAC
GTTTTTCAAGACAAACATCCAATTATGATATGTTTTAACCAAAAATGAAAAAAAAATTCAACTTA
AAATCATTTATAAGATTATAAAACATTGAAAGCGAGTAACTAGTCTTTCAAAGGCATGAGTGACT
ATAAATGGACTTTTCTT
Found at i:3442876 original size:690 final size:680
Alignment explanation
Indices: 3441348--3443342 Score: 2301
Period size: 690 Copynumber: 2.9 Consensus size: 680
3441338 TTGTTTGAAT
* *
3441348 CAAAAATGAAAAAAATTTAACTTAAAATCATTTATAAGATTATAAAACCATTTAACGCGAATAAT
1 CAAAAATGAAAAAAATTTAACTTAAAATCATTTATAAGATTATAAAACCATTTAACACGAGTAAT
* * * * *
3441413 TAGGCTTTCGAAGGCATGAGTGACTATAAATGGACTTATCTTGTCAATGCATGGCTTTGGCTTCA
66 TAGGCTTTCGAAAGTATGAGTGACTATAAATGGACTTTTCTTGTCAATG-ATAGCTTTTGCTTCA
* * *
3441478 AGTTTTCCAAGGCTAACATCCAATTATGATCTGTTTTAACAAAAAATGAAACAAAATTTAACTTA
130 AGTTTT-CAAGGCTAACATCTAATTATGATCTGTTTTAACAAAAAATGAAAAAAAAATTAACTTA
* * * * * *
3441543 AAATCATTTATAAGATTATAAAATCTTTGAAAGCTAGTAATTAATCTTTCAAAGGTATAAGTGAC
194 AAATCATTTATAAGATTATAAAATCATTGAAAGCAAGTAACTAGTCTTTCAAAGGCATGAGTGAC
* * * * **
3441608 TATATATGGACTTTTCTTATCAATAGATGGTTTTCACTTTACGTTT-TTGAGGTAAACATCCAAT
259 TATAAATGGACTTTTCTTATCAATGGATGGCTTTCGCTTTACGTTTCTTGAGAAAAACATCCAAT
* *
3441672 TATGATCT-ATTGCAAGT-GAAAAT-AAAAAAAATT-AACTTAAAATCATTTATAAGATTATAAA
324 TATGATCTGTTTG-AA-TCAAAAATGAAAAAAAATTCAACTTAAAATCATTTATAAGATTATAAA
* * * * * *
3441733 ACTATGTAAAACGAGTAACTAGTCTTTCAAAAGTATGAGTGACTATAAATAGACTTTTC-T-T--
387 TCTATTTAAAGC-AGTAACTAGTTTTTCGAAGGTATGAGTGACTATAAATAGACTTTTCTTGTCA
* * *** * * *
3441794 ATCGATGG-ATAGCTTTCACTTCACATTTCTCAAGATAAATATCCAATTAT-ACTATGTTTTACC
451 ATGGATGGTTTAG-TTTTTGTTTAC-TTTCT-AAGATAAACATCCAATTATGA-TATGTTTTAAC
* * * *
3441857 CAGAAAT-AAAAAAACAAGTTTAACTTAAAATCATTTATAAGATTATAAAACCATTTAAAGTGAG
512 CAAAAATGAAAAAAAC---TTCAACTTAAAATCATTTATAAGATTATAAAACTATTTAAAGCGAG
* * * *
3441921 TAAATAATCTTTCAAAGGCATGAATGACTATAAATGAACTTTTCTTGTCACTGAATGACTTTGCT
574 TAAATAGTCTTTCGAAGGCATGAATGACTATAAATAAACTTTTCTTGTCACTGAATGACTTTACT
** *
3441986 TCATGGTTCTCTAGGCAAACATCCAGTTATGATCTGCTTTAA
639 TCATGGTTCTCTAGGCAAACATCCAAATATGATCTACTTTAA
* * * * * *
3442028 CAAACAATGAAAAACAATTCAACATAAAATGATGTATAAGATTATAAATCCATTTAA-AGCAAGT
1 CAAA-AATGAAAAA-AATTTAACTTAAAATCATTTATAAGATTATAAAACCATTTAACA-CGAGT
** * *
3442092 AATTAGTTTTTCGAATA-TATGAGTGACTATAAATGGACTTTTCTTATTAATGGATAGCTTTTGC
63 AATTAGGCTTTCGAA-AGTATGAGTGACTATAAATGGACTTTTCTTGTCAAT-GATAGCTTTTGC
* * * * *
3442156 TTCACGTTTTTCAAGACGAACATTTAATTATGATCTGTTTTAACCAAAAATGAAAAAAAAATTAA
126 TTCAAG-TTTTCAAGGCTAACATCTAATTATGATCTGTTTTAACAAAAAATGAAAAAAAAATTAA
*
3442221 CTTAAAATCATTTATAAGATTATAAAATCATTGAAAGCAAGTAACTAGTCTTTTAAAGGCATGAG
190 CTTAAAATCATTTATAAGATTATAAAATCATTGAAAGCAAGTAACTAGTCTTTCAAAGGCATGAG
* * **
3442286 TGACTATAAATGGACTATTCTTATCAATGGATGGCTTTCGCTTTATGTTTCTCAAGAAAAACATC
255 TGACTATAAATGGACTTTTCTTATCAATGGATGGCTTTCGCTTTACGTTTCTTGAGAAAAACATC
* *
3442351 CAATTATGATCTGTTTGAATCAAAAATGAAAAAAAATTCAACTTAAAATCATTTAGAATATTATA
320 CAATTATGATCTGTTTGAATCAAAAATGAAAAAAAATTCAACTTAAAATCATTTATAAGATTATA
**
3442416 AATCTATTTAAAGCATGTAGTTAGTTTTTCGAAGGTATGAGTGACTATAAATAGACTTTTCTTGT
385 AATCTATTTAAAGCA-GTAACTAGTTTTTCGAAGGTATGAGTGACTATAAATAGACTTTTCTTGT
*
3442481 CAATGGATGGTTTTTGTTTTTGTTTTACGTTTCTTAAGATAAACATCCAATTATGATATGTTTTA
449 CAATGGATGG-TTTAGTTTTTG-TTTAC-TTTC-TAAGATAAACATCCAATTATGATATGTTTTA
*** * * *
3442546 ATTGAAAATGAAAAAAACTTCAACTTAAAATGATTTATAAGATTACAAAACTATTTAAAGCAAGT
510 ACCAAAAATGAAAAAAACTTCAACTTAAAATCATTTATAAGATTATAAAACTATTTAAAGCGAGT
* * * * *
3442611 AAGTAGTCTTTCGAAGGCATGAGTGATTATAAATAAACTTTGT-TTGTCGA-TGGATGGCTTTTA
575 AAATAGTCTTTCGAAGGCATGAATGACTATAAATAAACTTT-TCTTGTC-ACTGAATGAC-TTTA
* * * *
3442674 CTTCATGTTTCT-TGAGGCAAACATCTAAATATGATCTATTTTAGC
637 CTTCATGGTTCTCT-AGGCAAACATCCAAATATGATCTACTTTA-A
* *
3442719 CAAAAAAGAAAAAAAGTTTAACTTAAAATCATTTATAAGATTATAAAACCATTCAACACGAGTAA
1 CAAAAATGAAAAAAA-TTTAACTTAAAATCATTTATAAGATTATAAAACCATTTAACACGAGTAA
* *
3442784 TTAGGCTTTCGAAAGTATGAGTGACTATAAATAGATTTTTCTTGTCAATAGATAGCTTTTGCTTC
65 TTAGGCTTTCGAAAGTATGAGTGACTATAAATGGACTTTTCTTGTCAAT-GATAGCTTTTGCTTC
* * *
3442849 ATGTTTCTCAAGGCTAACATCTAATTATGATCTGTTTTAATAAAAAATG-AAAACAAATTCAACT
129 AAGTTT-TCAAGGCTAACATCTAATTATGATCTGTTTTAACAAAAAATGAAAAAAAAATT-AACT
* * * *
3442913 TAAAATCATTTAAAAGAGTATAAAACCATTGAAAGCGAGTAACTAGTCTTTCAAAGGCATGAGTG
192 TAAAATCATTTATAAGATTATAAAATCATTGAAAGCAAGTAACTAGTCTTTCAAAGGCATGAGTG
* * *
3442978 ACTGTAAATGGACTTTTCTTATCAATGGATGGCTTTCG-TTTCACATTTCTTGAGACAAACATCC
257 ACTATAAATGGACTTTTCTTATCAATGGATGGCTTTCGCTTT-ACGTTTCTTGAGAAAAACATCC
* * * * * *
3443042 AATTATGATTTGTTTTAA-CTAAAATTGAAAAAGAATTCAACATAAAATGATTTATAAGATTATA
321 AATTATGATCTGTTTGAATC-AAAAATGAAAAAAAATTCAACTTAAAATCATTTATAAGATTATA
* * * * * * * *
3443106 AATCCATTTAAAGTGAGTAACTAATTTTTTGAAGGAATGAATAACTATAAATTGACTTTTCTTGT
385 AATCTATTTAAAG-CAGTAACTAGTTTTTCGAAGGTATGAGTGACTATAAATAGACTTTTCTTGT
* * * ** *
3443171 CATTGGATGGCTTTCGCTTTATG-TT--TTTC-AAGGCAAACATCCAATTATGATATGTTTTAGC
449 CAATGGATGG-TTTAG-TTTTTGTTTACTTTCTAAGATAAACATCCAATTATGATATGTTTTAAC
* * *
3443232 CAAAAATGAAAAAAAAATTCAACTTAGAATCATTTATAAGATTATAAAACTATTGAAAGCGAGTA
512 CAAAAATG-AAAAAAACTTCAACTTAAAATCATTTATAAGATTATAAAACTATTTAAAGCGAGTA
* * * **
3443297 ACTAGTCTTTCGAAGACATAAATGACTATAAATGGACTTTTCTTGT
576 AATAGTCTTTCGAAGGCATGAATGACTATAAATAAACTTTTCTTGT
3443343 TAAAAGATGG
Statistics
Matches: 1112, Mismatches: 165, Indels: 71
0.82 0.12 0.05
Matches are distributed among these distances:
680 4 0.00
681 9 0.01
682 247 0.22
683 34 0.03
684 49 0.04
685 162 0.15
686 5 0.00
687 1 0.00
689 116 0.10
690 423 0.38
691 52 0.05
692 10 0.01
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.35
Consensus pattern (680 bp):
CAAAAATGAAAAAAATTTAACTTAAAATCATTTATAAGATTATAAAACCATTTAACACGAGTAAT
TAGGCTTTCGAAAGTATGAGTGACTATAAATGGACTTTTCTTGTCAATGATAGCTTTTGCTTCAA
GTTTTCAAGGCTAACATCTAATTATGATCTGTTTTAACAAAAAATGAAAAAAAAATTAACTTAAA
ATCATTTATAAGATTATAAAATCATTGAAAGCAAGTAACTAGTCTTTCAAAGGCATGAGTGACTA
TAAATGGACTTTTCTTATCAATGGATGGCTTTCGCTTTACGTTTCTTGAGAAAAACATCCAATTA
TGATCTGTTTGAATCAAAAATGAAAAAAAATTCAACTTAAAATCATTTATAAGATTATAAATCTA
TTTAAAGCAGTAACTAGTTTTTCGAAGGTATGAGTGACTATAAATAGACTTTTCTTGTCAATGGA
TGGTTTAGTTTTTGTTTACTTTCTAAGATAAACATCCAATTATGATATGTTTTAACCAAAAATGA
AAAAAACTTCAACTTAAAATCATTTATAAGATTATAAAACTATTTAAAGCGAGTAAATAGTCTTT
CGAAGGCATGAATGACTATAAATAAACTTTTCTTGTCACTGAATGACTTTACTTCATGGTTCTCT
AGGCAAACATCCAAATATGATCTACTTTAA
Found at i:3445480 original size:19 final size:20
Alignment explanation
Indices: 3445458--3445495 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
3445448 AGCACGAAGA
*
3445458 ATCAAGCAA-AGAAAGCAAT
1 ATCAAACAACAGAAAGCAAT
*
3445477 ATCAAACAACGGAAAGCAA
1 ATCAAACAACAGAAAGCAA
3445496 AATATGATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.58, C:0.18, G:0.16, T:0.08
Consensus pattern (20 bp):
ATCAAACAACAGAAAGCAAT
Found at i:3462876 original size:49 final size:50
Alignment explanation
Indices: 3462816--3462914 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 50
3462806 ATACATCATA
* * * * * *
3462816 AAAAACATATTCATTTCAGCTTAATTTAAGCTCATGCATATCAAGCATTC
1 AAAAACATATTCAATTAAGCTCAATTCAAACTCATGCACATCAAGCATTC
3462866 AAAAA-ATATTCAATTAAGCTCAATTCAAACTCATGCACATCAAGCATTC
1 AAAAACATATTCAATTAAGCTCAATTCAAACTCATGCACATCAAGCATTC
3462915 CTAGTTCTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
49 38 0.88
50 5 0.12
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.30
Consensus pattern (50 bp):
AAAAACATATTCAATTAAGCTCAATTCAAACTCATGCACATCAAGCATTC
Found at i:3472300 original size:250 final size:249
Alignment explanation
Indices: 3471847--3473696 Score: 2094
Period size: 250 Copynumber: 7.4 Consensus size: 249
3471837 ATTTTTTACT
* * * * * * * ***
3471847 TTTATAATTTTTTAAGTCAACTGTTACAGTTTTACGTCAAGATTTATCTATGTTAATTTTGTTCT
1 TTTATAAGTTTTTACGTCAATTCTTACAATTTTACGTCAAGACTTATCTATGTCAATTTTAAACT
* * * * *
3471912 ATAATTATTTTTATTATTTTTATTTTTATTTTAAAATTAAAATTTATATATCGTTAAACACTTTT
66 ATAATTATTTTTATTCTTATTATTTTTATTTAAAAATTAAAATTTGTATATCGTTAAATACTTTT
* * * *
3471977 AGTCTGAGAATATATATTTAAATATTTATTTTTTATTAAAATTAAATTTTTTTATTTAATTGAA-
131 AGTC-GAGAATATAAATTTAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATT-AAC
* * * * * * *
3472041 TTGTTACGTTAACACTCAAACGTTTACGTTAAGATTTAAAATTTAATTATTCCATA
194 TTATTACGTTAACTCTCACACATTTATGTTAAGATTTAAAATTTAGTTATTCCATC
* * * *
3472097 TTTATAAATTTTTACGTCAATTCTTACAGTTTTACGTTAAGACTTATCTATGTCAATTTTAAATT
1 TTTATAAGTTTTTACGTCAATTCTTACAATTTTACGTCAAGACTTATCTATGTCAATTTTAAACT
* * * *
3472162 ATAATTATTTTTATTCTTATTATTTTTGTTTAAAAATTAAAATGTGTATATTGTTACATACTTTT
66 ATAATTATTTTTATTCTTATTATTTTTATTTAAAAATTAAAATTTGTATATCGTTAAATACTTTT
* * * * * *
3472227 AGCTCGATAATATAAATATAAATACTTATTTTTCATTAAAATGAGATTTGTTTACTCAATTAACT
131 AG-TCGAGAATATAAATTTAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTAACT
* * * *
3472292 TATTACGTTAAATCTTACACATTTATGTTAAGATTTAAAATTTAGTTATTCTACC
195 TATTACGTTAACTCTCACACATTTATGTTAAGATTTAAAATTTAGTTATTCCATC
* * * * * *
3472347 TTTGTAAGTTTTAACGTTAATTTTTACAATTTTACATCAAGACTTATATATGTCAATTTTAAACT
1 TTTATAAGTTTTTACGTCAATTCTTACAATTTTACGTCAAGACTTATCTATGTCAATTTTAAACT
* * *
3472412 ATAACTATTTTTA-TCTTTATTATTTTTATTTAAAAAGTAAAATTTATATATCGTTAAATACTTT
66 ATAATTATTTTTATTC-TTATTATTTTTATTTAAAAATTAAAATTTGTATATCGTTAAATACTTT
* * * *
3472476 TATTCCAAGAATATAAATTTAAATA-TT-TTTTTCAATAAAATTAGATTTTTTTACTTAATTGAC
130 TAGT-CGAGAATATAAATTTAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTAAC
* * * *
3472539 TTGTTATGTTAACTCTCACACATTTATGTT-AGATTTAAAATTTAATTATTTCATC
194 TTATTACGTTAACTCTCACACATTTATGTTAAGATTTAAAATTTAGTTATTCCATC
* ** * * * * *
3472594 TTTATAAATTTTTACGTTTATTCTTACAATTTTACGTCAAGATTTTTTTGTGTCTATTTTAAACT
1 TTTATAAGTTTTTACGTCAATTCTTACAATTTTACGTCAAGACTTATCTATGTCAATTTTAAACT
* * *
3472659 ATAATTATTTTTATCCTTATTATTCTTTATTCAAAAATTAAAATTTGTATATCG--AAACACTTT
66 ATAATTATTTTTATTCTTATTATT-TTTATTTAAAAATTAAAATTTGTATATCGTTAAATACTTT
* * * * *
3472722 TAGTCCAAAAATATAAATTT-AA-ATTT-TTTTTCACTAAAATTAGATTTTTTTACTTAATTGAT
130 TAGT-CGAGAATATAAATTTAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTAAC
* * * * * *
3472784 TTGTTATGTTAACTCTCACACTTTTACGTTAAAATTTAAAATTTAGTTATTCTA-C
194 TTATTACGTTAACTCTCACACATTTATGTTAAGATTTAAAATTTAGTTATTCCATC
* * * * * *
3472839 TTTTATAAGTTTTTATGTCGATTCTTACAGTTTTATGTTAAGACTTATCTATGTCAATTTTAAAT
1 -TTTATAAGTTTTTACGTCAATTCTTACAATTTTACGTCAAGACTTATCTATGTCAATTTTAAAC
* * **
3472904 TATAATTATTTTTATTCTTATT-TTTTTATTTAAAAATTAAAATTTGAATATTGTTACGTACTTT
65 TATAATTATTTTTATTCTTATTATTTTTATTTAAAAATTAAAATTTGTATATCGTTAAATACTTT
** * * ** * *
3472968 TAACCCGATAATATAAATATAAATGCTTATTTTTCATTAAAATTAGACTTTTTAACTTAATTAAC
130 T-AGTCGAGAATATAAATTTAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTAAC
* ** * *
3473033 TTATTACGTTAACTCTTACACATTTACATTAAGATTTAAAATTTAGTTATTTCACC
194 TTATTACGTTAACTCTCACACATTTATGTTAAGATTTAAAATTTAGTTATTCCATC
* * *
3473089 TTTATAGGTTTTTACGTTAATTCTTACAATTTTACGTCAAGGCTTATCTATGTCAATTTTAAACT
1 TTTATAAGTTTTTACGTCAATTCTTACAATTTTACGTCAAGACTTATCTATGTCAATTTTAAACT
* *
3473154 ATAATTATTTTTA-TCTTTATTATTTTTATTTAAAAATTAAAATTTATATA-CGTTAAATAATTT
66 ATAATTATTTTTATTC-TTATTATTTTTATTTAAAAATTAAAATTTGTATATCGTTAAATACTTT
* * * * *
3473217 TATTCTAAGAATATAAATTTAAATATTTGTTTTTCAATAAAATTAAATTTTTTTACTTAATTAAC
130 TAGTC-GAGAATATAAATTTAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTAAC
* * * *
3473282 TTATT-CTATTAACTCTTACACATTTATGTTAAGATTTAAAATTTAATTATTTCATC
194 TTATTAC-GTTAACTCTCACACATTTATGTTAAGATTTAAAATTTAGTTATTCCATC
* * * * * * * * *
3473338 TTCATAAGTTTTTA-GATCAATTCTTATAACTTTACGTTAAGATTTTTCTATATCCATCTTAAAC
1 TTTATAAGTTTTTACG-TCAATTCTTACAATTTTACGTCAAGACTTATCTATGTCAATTTTAAAC
* * * *
3473402 TATAACTATTTTAATCCTTATTATTCTTTATTTAAAAATTAAAATTTGTATATCGTTAAACACTT
65 TATAATTATTTTTATTCTTATTATT-TTTATTTAAAAATTAAAATTTGTATATCGTTAAATACTT
* * * *
3473467 TTAGTCTGAAAATATAAATTTAAATATTTATTTTTTACTAAAATTAGATTTTTTTACTTAATTGA
129 TTAGTC-GAGAATATAAATTTAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTAA
* * * * ** * *
3473532 TTTATTACGTTAACTATGATATGTTTATGTTAAAATTTAAAATTTAGTTATTCCAAC
193 CTTATTACGTTAACTCTCACACATTTATGTTAAGATTTAAAATTTAGTTATTCCATC
* * * * *
3473589 TTTAAAAGTTTTTATGTTAATTCTTACAATTTTACGTCAAGACTTATCTATATCAATTTTAAACC
1 TTTATAAGTTTTTACGTCAATTCTTACAATTTTACGTCAAGACTTATCTATGTCAATTTTAAACT
*
3473654 ATAATTATTTTTATCCTTATTATTTTTATTTAAAAATTAAAAT
66 ATAATTATTTTTATTCTTATTATTTTTATTTAAAAATTAAAAT
3473697 NNNNNNNNNN
Statistics
Matches: 1350, Mismatches: 224, Indels: 52
0.83 0.14 0.03
Matches are distributed among these distances:
244 27 0.02
245 69 0.05
246 136 0.10
247 98 0.07
248 92 0.07
249 336 0.25
250 403 0.30
251 187 0.14
252 2 0.00
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.50
Consensus pattern (249 bp):
TTTATAAGTTTTTACGTCAATTCTTACAATTTTACGTCAAGACTTATCTATGTCAATTTTAAACT
ATAATTATTTTTATTCTTATTATTTTTATTTAAAAATTAAAATTTGTATATCGTTAAATACTTTT
AGTCGAGAATATAAATTTAAATATTTATTTTTCATTAAAATTAGATTTTTTTACTTAATTAACTT
ATTACGTTAACTCTCACACATTTATGTTAAGATTTAAAATTTAGTTATTCCATC
Found at i:3473529 original size:18 final size:18
Alignment explanation
Indices: 3473497--3473534 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
3473487 TAAATATTTA
3473497 TTTTTTACTAAAATTAGAT
1 TTTTTTACTAAAATT-GAT
*
3473516 TTTTTTACT-TAATTGAT
1 TTTTTTACTAAAATTGAT
3473533 TT
1 TT
3473535 ATTACGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 4 0.22
19 9 0.50
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (18 bp):
TTTTTTACTAAAATTGAT
Found at i:3475910 original size:20 final size:20
Alignment explanation
Indices: 3475885--3475923 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
3475875 TTAGTCTATG
3475885 GAATTAAATTAGTTAATTTC
1 GAATTAAATTAGTTAATTTC
3475905 GAATTAAATTAGTTAATTT
1 GAATTAAATTAGTTAATTT
3475924 AACGATTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (20 bp):
GAATTAAATTAGTTAATTTC
Found at i:3481071 original size:17 final size:17
Alignment explanation
Indices: 3481042--3481074 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3481032 TTCTTCATAA
3481042 AATAAAACTTCTTATTG
1 AATAAAACTTCTTATTG
3481059 AATAATAAC-TCTTATT
1 AATAA-AACTTCTTATT
3481075 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (17 bp):
AATAAAACTTCTTATTG
Found at i:3481252 original size:31 final size:31
Alignment explanation
Indices: 3481217--3481351 Score: 142
Period size: 31 Copynumber: 4.5 Consensus size: 31
3481207 TAAGACAATG
**
3481217 CTTGTCTTTGATTAAGAC-AAAAATATTTTAT
1 CTTGTCTTAAATTAAGACAAAAAATATTTT-T
*
3481248 CTTGTC-TAAATTGAGAC---AAATATGTTTT
1 CTTGTCTTAAATTAAGACAAAAAATAT-TTTT
*
3481276 CTTGTC-TAGATTAAGACAAAAAATATTTTT
1 CTTGTCTTAAATTAAGACAAAAAATATTTTT
* *
3481306 CTTATCTTAAATTAAGACTAAAAATA-TTTT
1 CTTGTCTTAAATTAAGACAAAAAATATTTTT
3481336 CTTGTC-TAAATTAAGA
1 CTTGTCTTAAATTAAGA
3481352 TAAACATGTT
Statistics
Matches: 90, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
28 22 0.24
29 13 0.14
30 26 0.29
31 29 0.32
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (31 bp):
CTTGTCTTAAATTAAGACAAAAAATATTTTT
Found at i:3481267 original size:30 final size:30
Alignment explanation
Indices: 3481227--3481351 Score: 152
Period size: 30 Copynumber: 4.2 Consensus size: 30
3481217 CTTGTCTTTG
3481227 ATTAAGAC-AAAAATATTTTATCTTGTCTAA
1 ATTAAGACAAAAAATATTTT-TCTTGTCTAA
* *
3481257 ATTGAGAC---AAATATGTTTTCTTGTCTAG
1 ATTAAGACAAAAAATAT-TTTTCTTGTCTAA
*
3481285 ATTAAGACAAAAAATATTTTTCTTATCTTAA
1 ATTAAGACAAAAAATATTTTTCTTGTC-TAA
*
3481316 ATTAAGACTAAAAATA-TTTTCTTGTCTAA
1 ATTAAGACAAAAAATATTTTTCTTGTCTAA
3481345 ATTAAGA
1 ATTAAGA
3481352 TAAACATGTT
Statistics
Matches: 83, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
28 22 0.27
29 13 0.16
30 25 0.30
31 23 0.28
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.41
Consensus pattern (30 bp):
ATTAAGACAAAAAATATTTTTCTTGTCTAA
Found at i:3481349 original size:60 final size:58
Alignment explanation
Indices: 3481227--3481351 Score: 171
Period size: 60 Copynumber: 2.1 Consensus size: 58
3481217 CTTGTCTTTG
* * * * *
3481227 ATTAAGACAAAAATATTTTATCTTGTCTAAATTGAGACAAATATGTTTTCTTGTCTAG
1 ATTAAGACAAAAATATTTTATCTTATCTAAATTAAGACAAAAATATTTTCTTGTCTAA
3481285 ATTAAGACAAAAAATATTTT-TCTTATCTTAAATTAAGACTAAAAATATTTTCTTGTCTAA
1 ATTAAGAC-AAAAATATTTTATCTTATC-TAAATTAAGAC-AAAAATATTTTCTTGTCTAA
3481345 ATTAAGA
1 ATTAAGA
3481352 TAAACATGTT
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
58 14 0.24
59 21 0.36
60 24 0.41
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.41
Consensus pattern (58 bp):
ATTAAGACAAAAATATTTTATCTTATCTAAATTAAGACAAAAATATTTTCTTGTCTAA
Found at i:3483464 original size:16 final size:17
Alignment explanation
Indices: 3483443--3483474 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3483433 TTTTATTATT
3483443 TTTAG-TTATTTTTCTA
1 TTTAGTTTATTTTTCTA
3483459 TTTAGTTTATTTTTCT
1 TTTAGTTTATTTTTCT
3483475 TAAGTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.72
Consensus pattern (17 bp):
TTTAGTTTATTTTTCTA
Found at i:3500891 original size:74 final size:73
Alignment explanation
Indices: 3500737--3500883 Score: 199
Period size: 74 Copynumber: 2.0 Consensus size: 73
3500727 TTTTTGTCAT
*
3500737 AAATTTTAGATGGTAAAATAGACTTGAAATGGAGTATTCTAGTAATGTCAAATTTTATGCATGTT
1 AAATTTTAGATGATAAAATAGACTTGAAATGGAGTATTCTAGTAATGTCAAATTTTATG-ATGTT
*
3500802 TAAGAGGAA
65 TAAGAGAAA
* * * * *
3500811 AAATTTTAGATGATAAGATATATTTGAAAT-GAGATATTTTAGTAATGTCAAATTTTGTG-TGTT
1 AAATTTTAGATGATAAAATAGACTTGAAATGGAG-TATTCTAGTAATGTCAAATTTTATGATGTT
3500874 TAAGAGAAA
65 TAAGAGAAA
3500883 A
1 A
3500884 CATATTTTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
72 13 0.20
73 3 0.05
74 49 0.75
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.37
Consensus pattern (73 bp):
AAATTTTAGATGATAAAATAGACTTGAAATGGAGTATTCTAGTAATGTCAAATTTTATGATGTTT
AAGAGAAA
Found at i:3508354 original size:28 final size:28
Alignment explanation
Indices: 3508323--3508377 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
3508313 AGGTTCAAAC
3508323 ATAACCATTGCTTTTTCAAGAATCAAGT
1 ATAACCATTGCTTTTTCAAGAATCAAGT
3508351 ATAACCATTGCTTTTTCAAGAATCAAG
1 ATAACCATTGCTTTTTCAAGAATCAAG
3508378 CACAACCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (28 bp):
ATAACCATTGCTTTTTCAAGAATCAAGT
Found at i:3508384 original size:28 final size:28
Alignment explanation
Indices: 3508325--3508384 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
3508315 GTTCAAACAT
* *
3508325 AACCATTGCTTTTTCAAGAATCAAGTAT
1 AACCATTGCTTTTTCAAGAATCAAGCAC
3508353 AACCATTGCTTTTTCAAGAATCAAGCAC
1 AACCATTGCTTTTTCAAGAATCAAGCAC
3508381 AACC
1 AACC
3508385 TTTAAACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (28 bp):
AACCATTGCTTTTTCAAGAATCAAGCAC
Found at i:3508483 original size:64 final size:64
Alignment explanation
Indices: 3508364--3508484 Score: 161
Period size: 64 Copynumber: 1.9 Consensus size: 64
3508354 ACCATTGCTT
* **
3508364 TTTCAAGAATCAAGCACAACCTTTAAACATTACCTTTTAAAGGCTAAGGTGTAACCTCTATGCC
1 TTTCAAGAATCAAGCACAACCTTTAAACACTACCTTTTAAAGGCTAAGGAATAACCTCTATGCC
* * * * **
3508428 TTTCAAGGATCAAGTACAACCTTTAAATACTATCTTTTGTAGGCTAAGGAATAACCT
1 TTTCAAGAATCAAGCACAACCTTTAAACACTACCTTTTAAAGGCTAAGGAATAACCT
3508485 TTCTCTTTTA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 48 1.00
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (64 bp):
TTTCAAGAATCAAGCACAACCTTTAAACACTACCTTTTAAAGGCTAAGGAATAACCTCTATGCC
Found at i:3509126 original size:20 final size:20
Alignment explanation
Indices: 3509087--3509150 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
3509077 AAACTAATTT
* *
3509087 AAACAAGTTTAAAAACCATTC
1 AAACAAG-TTCAAAATCATTC
3509108 AAACAAGTTCAAAATCATTC
1 AAACAAGTTCAAAATCATTC
* * *
3509128 AAGCAATTTCAAGACTCATTC
1 AAACAAGTTCAA-AATCATTC
3509149 AA
1 AA
3509151 GTAATTTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 21 0.57
21 16 0.43
ACGTcount: A:0.48, C:0.20, G:0.06, T:0.25
Consensus pattern (20 bp):
AAACAAGTTCAAAATCATTC
Found at i:3509148 original size:21 final size:20
Alignment explanation
Indices: 3509098--3509157 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
3509088 AACAAGTTTA
* * *
3509098 AAAACCATTCAAACAAGTTC
1 AAAATCATTCAAGCAATTTC
3509118 AAAATCATTCAAGCAATTTC
1 AAAATCATTCAAGCAATTTC
* *
3509138 AAGACTCATTCAAGTAATTT
1 AA-AATCATTCAAGCAATTT
3509158 TAAACCTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 19 0.56
21 15 0.44
ACGTcount: A:0.45, C:0.20, G:0.07, T:0.28
Consensus pattern (20 bp):
AAAATCATTCAAGCAATTTC
Found at i:3509248 original size:22 final size:22
Alignment explanation
Indices: 3509189--3509290 Score: 106
Period size: 21 Copynumber: 4.8 Consensus size: 22
3509179 ACTTAGGATC
3509189 TTTAAAACTCAATT-AAACAAG
1 TTTAAAACTCAATTCAAACAAG
*
3509210 TTTAAAA-TCTATTCAAACAAG
1 TTTAAAACTCAATTCAAACAAG
* *
3509231 GTTAAACACTC-ATTCAAACAAC
1 TTTAAA-ACTCAATTCAAACAAG
*
3509253 TTTAAAAATC-ATTCAAACAAG
1 TTTAAAACTCAATTCAAACAAG
*
3509274 TTCAAAGA-TCAATTCAA
1 TTTAAA-ACTCAATTCAA
3509291 GTAATTTTAA
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
20 5 0.07
21 39 0.57
22 23 0.33
23 2 0.03
ACGTcount: A:0.49, C:0.18, G:0.05, T:0.28
Consensus pattern (22 bp):
TTTAAAACTCAATTCAAACAAG
Found at i:3509289 original size:43 final size:44
Alignment explanation
Indices: 3509190--3509290 Score: 124
Period size: 43 Copynumber: 2.4 Consensus size: 44
3509180 CTTAGGATCT
*
3509190 TTAAA-ACTCAATT-AAACAAGTTTAAAATCTATTCAAACAAGG
1 TTAAACACTCAATTCAAACAACTTTAAAATCTATTCAAACAAGG
3509232 TTAAACACTC-ATTCAAACAACTTTAAAAATC-ATTCAAACAA-G
1 TTAAACACTCAATTCAAACAACTTT-AAAATCTATTCAAACAAGG
*
3509274 TTCAAAGA-TCAATTCAA
1 TT-AAACACTCAATTCAA
3509291 GTAATTTTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
42 13 0.25
43 33 0.63
44 6 0.12
ACGTcount: A:0.50, C:0.18, G:0.05, T:0.28
Consensus pattern (44 bp):
TTAAACACTCAATTCAAACAACTTTAAAATCTATTCAAACAAGG
Found at i:3510088 original size:22 final size:22
Alignment explanation
Indices: 3510040--3510091 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
3510030 TTGCACTACA
**
3510040 GGTTTTTAGACATTGTGTTATT
1 GGTTTTTAGACATTGTGAAATT
* **
3510062 AGTTTTTAGGTATTGTGAAATT
1 GGTTTTTAGACATTGTGAAATT
3510084 GGTTTTTA
1 GGTTTTTA
3510092 AGCATTGCGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.02, G:0.23, T:0.54
Consensus pattern (22 bp):
GGTTTTTAGACATTGTGAAATT
Found at i:3510098 original size:22 final size:22
Alignment explanation
Indices: 3510040--3510098 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
3510030 TTGCACTACA
**
3510040 GGTTTTT-AGACATTGTGTTATT
1 GGTTTTTAAG-CATTGTGAAATT
* * *
3510062 AGTTTTTAGGTATTGTGAAATT
1 GGTTTTTAAGCATTGTGAAATT
3510084 GGTTTTTAAGCATTG
1 GGTTTTTAAGCATTG
3510099 CGTGACTTAA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.22, C:0.03, G:0.24, T:0.51
Consensus pattern (22 bp):
GGTTTTTAAGCATTGTGAAATT
Found at i:3510216 original size:22 final size:22
Alignment explanation
Indices: 3510191--3510239 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3510181 CATATCAACC
*
3510191 AGTCACATAATACATAAAAATT
1 AGTCACATAATACATAAAAACT
** *
3510213 AGTCATGTAATACTTAAAAACT
1 AGTCACATAATACATAAAAACT
3510235 AGTCA
1 AGTCA
3510240 AAAAATGCCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.29
Consensus pattern (22 bp):
AGTCACATAATACATAAAAACT
Found at i:3510275 original size:22 final size:22
Alignment explanation
Indices: 3510198--3510277 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 22
3510188 ACCAGTCACA
* *
3510198 TAATACATAAAAATTAGTCATG
1 TAATACTTAAAAACTAGTCATG
**
3510220 TAATACTTAAAAACTAGTCAAA
1 TAATACTTAAAAACTAGTCATG
* * ** *
3510242 AAATGCCGAAAAACTAGTTATG
1 TAATACTTAAAAACTAGTCATG
3510264 TAATACTTAAAAAC
1 TAATACTTAAAAAC
3510278 CACCAAAACT
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.28
Consensus pattern (22 bp):
TAATACTTAAAAACTAGTCATG
Found at i:3510476 original size:50 final size:50
Alignment explanation
Indices: 3510379--3510504 Score: 180
Period size: 50 Copynumber: 2.5 Consensus size: 50
3510369 CTTGGCGAAG
*
3510379 AATGCTCAAAATGTTCAAAGGTTTATCTTCATGTATCAAAAACCACTCAAA
1 AATGCTCAAAATGCTCAAAGGTTT-TCTTCATGTATCAAAAACCACTCAAA
* * * * *
3510430 AATGCTTAAAATACTCAAAGGTTTTCTTCGTGTATTAAAAACCACTCCAA
1 AATGCTCAAAATGCTCAAAGGTTTTCTTCATGTATCAAAAACCACTCAAA
*
3510480 AATGCTCAAAATGCTTAAAGGTTTT
1 AATGCTCAAAATGCTCAAAGGTTTT
3510505 TCTTTTAGGC
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 45 0.68
51 21 0.32
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (50 bp):
AATGCTCAAAATGCTCAAAGGTTTTCTTCATGTATCAAAAACCACTCAAA
Found at i:3510826 original size:29 final size:28
Alignment explanation
Indices: 3510771--3510826 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
3510761 TTTATGATTT
* *
3510771 TGAACTTTAGATCAAACTAAATGTTTTG
1 TGAACTTTAAATCAAACTAAACGTTTTG
* *
3510799 TGAACTTTAAATCCAAATTCAACGTTTT
1 TGAACTTTAAAT-CAAACTAAACGTTTT
3510827 CAGAATGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (28 bp):
TGAACTTTAAATCAAACTAAACGTTTTG
Found at i:3517641 original size:2 final size:2
Alignment explanation
Indices: 3517634--3517665 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3517624 ACAAAGAAAT
*
3517634 AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3517666 GNNNNNNNNN
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3517875 original size:61 final size:61
Alignment explanation
Indices: 3517800--3517915 Score: 214
Period size: 61 Copynumber: 1.9 Consensus size: 61
3517790 ATCCATTAGT
3517800 TATTCCGATGATTCTTTGACTAGCTTTCCATTCTTTCAACATCCCTCCATGGATTTATGGG
1 TATTCCGATGATTCTTTGACTAGCTTTCCATTCTTTCAACATCCCTCCATGGATTTATGGG
* *
3517861 TATTCCGATGATTCTTTGACTAGCTTTCCATTCTTTTAGCATCCCTCCATGGATT
1 TATTCCGATGATTCTTTGACTAGCTTTCCATTCTTTCAACATCCCTCCATGGATT
3517916 CAGTAGTTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.42
Consensus pattern (61 bp):
TATTCCGATGATTCTTTGACTAGCTTTCCATTCTTTCAACATCCCTCCATGGATTTATGGG
Found at i:3519267 original size:2 final size:2
Alignment explanation
Indices: 3519260--3519300 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3519250 CATGTCTGTG
*
3519260 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3519301 GCTACACATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3535710 original size:18 final size:18
Alignment explanation
Indices: 3535684--3535775 Score: 60
Period size: 19 Copynumber: 4.9 Consensus size: 18
3535674 TTTCAAATAA
* *
3535684 AAATGAATGTGTATAATC
1 AAATCAATGTTTATAATC
*
3535702 AAATCAATGTTTCA-AATAA
1 AAATCAATGTTT-ATAAT-C
*
3535721 AAATGAATGTTTATAATC
1 AAATCAATGTTTATAATC
* * *
3535739 AAATCTAAGTATTTCTAATG
1 AAATC-AA-TGTTTATAATC
*
3535759 AAAACGAATGTTTATAA
1 AAATC-AATGTTTATAA
3535776 AGCTCAGTAG
Statistics
Matches: 56, Mismatches: 13, Indels: 9
0.72 0.17 0.12
Matches are distributed among these distances:
18 18 0.32
19 24 0.43
20 14 0.25
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.35
Consensus pattern (18 bp):
AAATCAATGTTTATAATC
Found at i:3535724 original size:37 final size:39
Alignment explanation
Indices: 3535673--3535775 Score: 147
Period size: 37 Copynumber: 2.7 Consensus size: 39
3535663 ATATCTGTGC
*
3535673 ATTTCAAATAAAAATGAATGTGTATAATCAAATC-AA-T
1 ATTTCAAATAAAAATGAATGTTTATAATCAAATCTAAGT
*
3535710 GTTTCAAATAAAAATGAATGTTTATAATCAAATCTAAGT
1 ATTTCAAATAAAAATGAATGTTTATAATCAAATCTAAGT
* * *
3535749 ATTTCTAATGAAAACGAATGTTTATAA
1 ATTTCAAATAAAAATGAATGTTTATAA
3535776 AGCTCAGTAG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
37 32 0.55
38 2 0.03
39 24 0.41
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.35
Consensus pattern (39 bp):
ATTTCAAATAAAAATGAATGTTTATAATCAAATCTAAGT
Found at i:3535729 original size:19 final size:19
Alignment explanation
Indices: 3535674--3535732 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
3535664 TATCTGTGCA
3535674 TTTCAAATAAAAATGAATG
1 TTTCAAATAAAAATGAATG
* * *
3535693 TGT-ATAAT-CAAATCAATG
1 TTTCA-AATAAAAATGAATG
3535711 TTTCAAATAAAAATGAATG
1 TTTCAAATAAAAATGAATG
3535730 TTT
1 TTT
3535733 ATAATCAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.36
Consensus pattern (19 bp):
TTTCAAATAAAAATGAATG
Done.