Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 10 of 284
Found at i:3211943 original size:9 final size:10
Alignment explanation
Indices: 3211918--3211950 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3211908 ATGTTGTTTA
*
3211918 ATTTGATATT
1 ATTTGTTATT
3211928 ATTTGTTATT
1 ATTTGTTATT
3211938 -TTTGTTATT
1 ATTTGTTATT
3211947 ATTT
1 ATTT
3211951 ATGTTATGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (10 bp):
ATTTGTTATT
Found at i:3214613 original size:26 final size:25
Alignment explanation
Indices: 3214569--3214622 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
3214559 TTTATGTGTT
*
3214569 TATTTTTTAAGTTTATTAAATAATA
1 TATTTTTTAAGTTTATTAAAAAATA
* *
3214594 TATTTTTATAATTTTTTTAAAAAATA
1 TATTTTT-TAAGTTTATTAAAAAATA
3214620 TAT
1 TAT
3214623 AGTTGCTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
TATTTTTTAAGTTTATTAAAAAATA
Found at i:3214931 original size:16 final size:16
Alignment explanation
Indices: 3214910--3214997 Score: 52
Period size: 16 Copynumber: 5.1 Consensus size: 16
3214900 TACAATTGTG
*
3214910 TAAATATTATTAAAAT
1 TAAATAATATTAAAAT
*
3214926 TAAATAATAATAAAACT
1 TAAATAATATTAAAA-T
* *
3214943 ATCAAAT-ATCAAATAATAT
1 -T-AAATAAT--ATTAAAAT
*
3214962 TAAAAGTACTATTAAAAT
1 T-AAA-TAATATTAAAAT
*
3214980 CAAATAATATTAAAAT
1 TAAATAATATTAAAAT
3214996 TA
1 TA
3214998 TCTAATATCA
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
16 25 0.45
17 4 0.07
18 13 0.24
19 6 0.11
20 7 0.13
ACGTcount: A:0.59, C:0.06, G:0.01, T:0.34
Consensus pattern (16 bp):
TAAATAATATTAAAAT
Found at i:3214973 original size:29 final size:28
Alignment explanation
Indices: 3214927--3215020 Score: 108
Period size: 26 Copynumber: 3.5 Consensus size: 28
3214917 TATTAAAATT
*
3214927 AAATAATAAT-AAA-ACTATCAAATATC
1 AAATAATATTAAAATACTATCAAATATC
*
3214953 AAATAATATTAAAAGTACTATTAAA-ATC
1 AAATAATATTAAAA-TACTATCAAATATC
*
3214981 AAATAATATTAAAAT--TATCTAATATC
1 AAATAATATTAAAATACTATCAAATATC
3215007 AAATAATAATTAAA
1 AAATAAT-ATTAAA
3215021 TATCTCAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
25 5 0.08
26 19 0.32
27 10 0.17
28 17 0.29
29 8 0.14
ACGTcount: A:0.60, C:0.07, G:0.01, T:0.32
Consensus pattern (28 bp):
AAATAATATTAAAATACTATCAAATATC
Found at i:3215005 original size:54 final size:55
Alignment explanation
Indices: 3214917--3215020 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 55
3214907 GTGTAAATAT
*
3214917 TATTAAAATTAAATAATAATAAAACTATCAAATATCAAATAAT-ATTAAAAGTAC
1 TATTAAAATCAAATAATAATAAAACTATCAAATATCAAATAATAATTAAAAGTAC
* * *
3214971 TATTAAAATCAAATAATATTAAAATTATCTAATATCAAATAATAATTAAA
1 TATTAAAATCAAATAATAATAAAACTATCAAATATCAAATAATAATTAAA
3215021 TATCTCAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
54 39 0.87
55 6 0.13
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.34
Consensus pattern (55 bp):
TATTAAAATCAAATAATAATAAAACTATCAAATATCAAATAATAATTAAAAGTAC
Found at i:3218828 original size:23 final size:23
Alignment explanation
Indices: 3218797--3218862 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 23
3218787 GTGAGGAACG
3218797 AACTAAAAACTAAACTAAAATTAC
1 AACTAAAAA-TAAACTAAAATTAC
*
3218821 AACTAAAAAGAAACCT-AAATTAC
1 AACTAAAAATAAA-CTAAAATTAC
*
3218844 AAATAAAAATAAAACTAAA
1 AACTAAAAAT-AAACTAAA
3218863 TAGGAGACGA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
23 20 0.56
24 16 0.44
ACGTcount: A:0.67, C:0.14, G:0.02, T:0.18
Consensus pattern (23 bp):
AACTAAAAATAAACTAAAATTAC
Found at i:3221121 original size:11 final size:11
Alignment explanation
Indices: 3221107--3221148 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
3221097 GCAAAAAAAA
3221107 AAAACTAAGAT
1 AAAACTAAGAT
*
3221118 AAAACTTAGA-
1 AAAACTAAGAT
*
3221128 GAAACTAAGACT
1 AAAACTAAGA-T
3221140 AAAACTAAG
1 AAAACTAAG
3221149 CTAATGTGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 8 0.32
11 9 0.36
12 8 0.32
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.17
Consensus pattern (11 bp):
AAAACTAAGAT
Found at i:3226039 original size:12 final size:12
Alignment explanation
Indices: 3226022--3226056 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
3226012 TTCTAATAAA
3226022 AATTATTATATT
1 AATTATTATATT
3226034 AATTA-TATTATT
1 AATTATTA-TATT
3226046 AATTATTATAT
1 AATTATTATAT
3226057 GTAGCTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
AATTATTATATT
Found at i:3226040 original size:9 final size:8
Alignment explanation
Indices: 3226023--3226056 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
3226013 TCTAATAAAA
3226023 ATTATTAT
1 ATTATTAT
3226031 ATTAATTAT
1 ATT-ATTAT
3226040 ATTATTA-
1 ATTATTAT
3226047 ATTATTAT
1 ATTATTAT
3226055 AT
1 AT
3226057 GTAGCTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.29
8 9 0.38
9 8 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
ATTATTAT
Found at i:3234457 original size:3 final size:3
Alignment explanation
Indices: 3234449--3234486 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3234439 TGTAAAATCA
3234449 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
3234487 TAGGGGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3234769 original size:6 final size:6
Alignment explanation
Indices: 3234746--3234778 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
3234736 CAAAGAATCT
*
3234746 AAAGG- AAAGGA AAGGGA AAAGGA AAAGGA AAAG
1 AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAG
3234779 TGGAGTTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:3238450 original size:94 final size:94
Alignment explanation
Indices: 3238280--3238499 Score: 422
Period size: 94 Copynumber: 2.3 Consensus size: 94
3238270 GGTGATTTGT
* *
3238280 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAGCCAGTATAAGACCATG
1 GTGCCAGTATAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAGCCAGTATAAGACCATG
3238345 TCTGGGACATGGCATCGGCGTAGAGGTGA
66 TCTGGGACATGGCATCGGCGTAGAGGTGA
3238374 GTGCCAGTATAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAGCCAGTATAAGACCATG
1 GTGCCAGTATAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAGCCAGTATAAGACCATG
3238439 TCTGGGACATGGCATCGGCGTAGAGGTGA
66 TCTGGGACATGGCATCGGCGTAGAGGTGA
3238468 GTGCCAGTATAAGACATGTCTGGGACATGCAT
1 GTGCCAGTATAAGACATGTCTGGGACATGCAT
3238500 TGGCTAAGAT
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 124 1.00
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (94 bp):
GTGCCAGTATAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAGCCAGTATAAGACCATG
TCTGGGACATGGCATCGGCGTAGAGGTGA
Found at i:3238588 original size:140 final size:140
Alignment explanation
Indices: 3238285--3238690 Score: 475
Period size: 140 Copynumber: 2.9 Consensus size: 140
3238275 TTTGTGTGCT
* * * ** *
3238285 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGC-CACATTATGAGAGCCAGTATAAGACCATGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAGA-GGTGAGTGCCAGTATAAGA-CATGTC
*
3238347 TGGGACATGGCATCGGCGTAGAGGTGAGTGCCAGTATAAGACATGTCTGGGACATGCATCAGCCA
64 TGGGACAT-GCATCGGCGTAGAGATGAGTGCCAGTATAAGACATGTCTGGGACATGCATCAGCCA
*
3238412 CATTATGAGAGCC
128 CATTACGAGAGCC
*
3238425 AGTATAAGACCATGTCTGGGACATGGCATCGGCGTAGAGGTGAGTGCCAGTATAAGACATGTCTG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAGAGGTGAGTGCCAGTATAAGACATGTCTG
* ** * *
3238490 GGACATGCATTGGC-TA-AGATTTGTGCTAGTGTAAGACATGTCTGGGACATGCATCAG-CATGT
66 GGACATGCATCGGCGTAGAGATGAGTGCCAGTATAAGACATGTCTGGGACATGCATCAGCCA---
3238552 CCA-TACGAGAGCC
128 -CATTACGAGAGCC
3238565 AGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAGAGGTGAGTGCCAGTATAAGACATGTCTG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAGAGGTGAGTGCCAGTATAAGACATGTCTG
* ** * * * *
3238630 GGACATGCATCAGCATGTCCATACGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC
66 GGACATGCATCGGC--GTAGAGATGAGTGCCAGTATAAGA-CATGTCTGGGACAT-GCATC
3238691 GACAACTTAT
Statistics
Matches: 229, Mismatches: 24, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
137 2 0.01
138 36 0.16
139 2 0.01
140 100 0.44
141 30 0.13
142 23 0.10
143 3 0.01
144 14 0.06
145 14 0.06
146 5 0.02
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (140 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAGAGGTGAGTGCCAGTATAAGACATGTCTG
GGACATGCATCGGCGTAGAGATGAGTGCCAGTATAAGACATGTCTGGGACATGCATCAGCCACAT
TACGAGAGCC
Found at i:3240110 original size:104 final size:104
Alignment explanation
Indices: 3239930--3240289 Score: 711
Period size: 104 Copynumber: 3.5 Consensus size: 104
3239920 GTTACAGTAC
3239930 ATATGCAAATAATATGCAATCTAAACAAGTATTTAACATATATTTAACATAATGAACGTAAATTT
1 ATATGCAAATAATATGCAATCTAAACAAGTATTTAACATATATTTAACATAATGAACGTAAATTT
3239995 GTATTTCATCAAATTACTTAAGCTTACTCATCACACATA
66 GTATTTCATCAAATTACTTAAGCTTACTCATCACACATA
3240034 ATATGCAAATAATATGCAATCTAAACAAGTATTTAACATATATTTAACATAATGAACGTAAATTT
1 ATATGCAAATAATATGCAATCTAAACAAGTATTTAACATATATTTAACATAATGAACGTAAATTT
3240099 GTATTTCATCAAATTACTTAAGCTTACTCATCACACATA
66 GTATTTCATCAAATTACTTAAGCTTACTCATCACACATA
3240138 ATATGCAAATAATATGCAATCTAAACAAGTATTTAACATATATTTAACATAATGAACGTAAATTT
1 ATATGCAAATAATATGCAATCTAAACAAGTATTTAACATATATTTAACATAATGAACGTAAATTT
3240203 GTATTTCATCAAATTACTTAAGCTTACTCATCACACATA
66 GTATTTCATCAAATTACTTAAGCTTACTCATCACACATA
*
3240242 ATATGCAAATAATATGCAATCTAAACAAGTATTTAACATACATTTAAC
1 ATATGCAAATAATATGCAATCTAAACAAGTATTTAACATATATTTAAC
3240290 TTATTTAATA
Statistics
Matches: 255, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 255 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (104 bp):
ATATGCAAATAATATGCAATCTAAACAAGTATTTAACATATATTTAACATAATGAACGTAAATTT
GTATTTCATCAAATTACTTAAGCTTACTCATCACACATA
Found at i:3241587 original size:19 final size:20
Alignment explanation
Indices: 3241553--3241590 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3241543 GGAAAATAAC
*
3241553 AAAAGAGAAGAGAAAACTTG
1 AAAAAAGAAGAGAAAACTTG
3241573 AAAAAAGAA-AGAAAACTT
1 AAAAAAGAAGAGAAAACTT
3241591 AAGAAGCTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.66, C:0.05, G:0.18, T:0.11
Consensus pattern (20 bp):
AAAAAAGAAGAGAAAACTTG
Found at i:3245834 original size:35 final size:35
Alignment explanation
Indices: 3245793--3245862 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
3245783 GGCTTGAGCA
3245793 ACACGAACCAAGTCGCAAAATGAAAATAATTTATT
1 ACACGAACCAAGTCGCAAAATGAAAATAATTTATT
*
3245828 ACACGAACCAAGTCGCAGAATGAAAATAATTTATT
1 ACACGAACCAAGTCGCAAAATGAAAATAATTTATT
3245863 TACTTTTGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (35 bp):
ACACGAACCAAGTCGCAAAATGAAAATAATTTATT
Found at i:3252723 original size:39 final size:40
Alignment explanation
Indices: 3252680--3252847 Score: 148
Period size: 40 Copynumber: 4.2 Consensus size: 40
3252670 CTCGTTCAAG
* * * *
3252680 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCATAC-AA
1 TGCCTTCGGGACTTAACCCGGATTATA-AAACTCACACGAA
* *
3252719 TGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
* * *
3252759 TGCCTTCGGGACTTAACCCGGAATTAGT--ATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTA-TAAAACTCACACGAA
* * * *
3252799 GGCCTTCGGGACTTAACCCGGAATTA-ATAACTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTATAAAACTCACACGAA
3252839 TGCCTTCGG
1 TGCCTTCGG
3252848 ATCTTAGTCC
Statistics
Matches: 111, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
39 26 0.23
40 81 0.73
41 3 0.03
42 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
Found at i:3252831 original size:80 final size:80
Alignment explanation
Indices: 3252715--3252900 Score: 229
Period size: 80 Copynumber: 2.3 Consensus size: 80
3252705 AGTAACTCAT
* * *
3252715 ACAATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTC-GGATCTTAACCCG
*
3252779 GA-ATTAGT-A-TCTCGC
65 GATA-TAGTCACT-TAGC
**
3252794 ACAAAGGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATGCCTTCGGATCTTAGTCC
1 ACAAA-GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATGCCTTCGGATCTTAACCC
3252858 GGATATAGTCACTTAGC
64 GGATATAGTCACTTAGC
*
3252875 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
3252901 CAGCATTCAA
Statistics
Matches: 94, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
79 11 0.12
80 72 0.77
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTCACTTAGC
Found at i:3252860 original size:40 final size:40
Alignment explanation
Indices: 3252717--3252900 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
3252707 TAACTCATAC
* *
3252717 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
3252757 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
3252797 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
3252837 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
3252878 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
3252901 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
39 8 0.06
40 105 0.85
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:3267230 original size:21 final size:22
Alignment explanation
Indices: 3267206--3267248 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3267196 CTGAGGATAC
*
3267206 GAGG-AATTGAACCACTGACCT
1 GAGGTAATTAAACCACTGACCT
*
3267227 GAGGTAATTAAACCACTTACCT
1 GAGGTAATTAAACCACTGACCT
3267249 ACAATAGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (22 bp):
GAGGTAATTAAACCACTGACCT
Found at i:3273101 original size:18 final size:18
Alignment explanation
Indices: 3273074--3273110 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3273064 TTCAAATTTT
3273074 ATAATCTCTATTAACCTA
1 ATAATCTCTATTAACCTA
*
3273092 ATAATTTCTATTAACCTA
1 ATAATCTCTATTAACCTA
3273110 A
1 A
3273111 CTCAGACTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAATCTCTATTAACCTA
Found at i:3274438 original size:24 final size:24
Alignment explanation
Indices: 3274391--3274460 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 24
3274381 AAAAGGGAGG
3274391 AAAAAGAAAAGAAAGAAATGATAAC
1 AAAAAGAAAAGAAAGAAA-GATAAC
* *
3274416 AAAAAGAAAAG-AAGGAAGAATAAG
1 AAAAAGAAAAGAAAGAAAG-ATAAC
* *
3274440 AAAAACAAAAAAAAAGAAAGA
1 AAAAA-GAAAAGAAAGAAAGA
3274461 AGAGGAAACG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
23 1 0.03
24 14 0.38
25 16 0.43
26 6 0.16
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.04
Consensus pattern (24 bp):
AAAAAGAAAAGAAAGAAAGATAAC
Found at i:3278301 original size:13 final size:13
Alignment explanation
Indices: 3278283--3278307 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3278273 TCTTTTCTTG
3278283 TTTTTATTTTTTA
1 TTTTTATTTTTTA
3278296 TTTTTATTTTTT
1 TTTTTATTTTTT
3278308 TTGTCTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:3279935 original size:5 final size:5
Alignment explanation
Indices: 3279925--3279952 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3279915 AGGAAAAAGA
3279925 AGATG AGATG AGATG AGATG AGATG AGA
1 AGATG AGATG AGATG AGATG AGATG AGA
3279953 ACAAGTGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.39, T:0.18
Consensus pattern (5 bp):
AGATG
Found at i:3283757 original size:24 final size:24
Alignment explanation
Indices: 3283721--3283784 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
3283711 GGATCAGTGA
* * *
3283721 CTGCATCTATATCTGAATCTGTGT
1 CTGCATTTGTATCTGAATCTGAGT
3283745 CTGCATTTGTATCTGAATCTGAGT
1 CTGCATTTGTATCTGAATCTGAGT
**
3283769 AAGCATTTGTATCTGA
1 CTGCATTTGTATCTGA
3283785 TTATGAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
CTGCATTTGTATCTGAATCTGAGT
Found at i:3286953 original size:5 final size:5
Alignment explanation
Indices: 3286945--3286982 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
3286935 ATTTAGATTA
3286945 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
3286983 TCATTATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:3286991 original size:3 final size:3
Alignment explanation
Indices: 3286941--3287035 Score: 71
Period size: 3 Copynumber: 33.3 Consensus size: 3
3286931 TTTTATTTAG
3286941 ATT ATAT ATT A-T ATT A-T ATT A-T ATT A-T ATT A-T ATT A-T ATT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
3286981 ATT CATT ATT ATA ATT ATT AATT TTT ATG GTT -TT A-T ATT ATT ATT
1 ATT -ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT
3287026 ATT ATT ATT A
1 ATT ATT ATT A
3287036 AATAAATTAA
Statistics
Matches: 74, Mismatches: 7, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
2 16 0.22
3 49 0.66
4 9 0.12
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:3287008 original size:16 final size:15
Alignment explanation
Indices: 3286957--3287032 Score: 57
Period size: 16 Copynumber: 4.9 Consensus size: 15
3286947 TATTATATTA
*
3286957 TATTATATTA-TATT
1 TATTATATTATTAAT
*
3286971 ATATTATATTATTCAT
1 -TATTATATTATTAAT
3286987 TATTATAATTATTAAT
1 TATTAT-ATTATTAAT
* *
3287003 TTTTATGGTT-TTATAT
1 TATTAT-ATTATTA-AT
3287019 TATTATTATTATTA
1 TATTA-TATTATTA
3287033 TTAAATAAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
15 19 0.40
16 25 0.52
17 4 0.08
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (15 bp):
TATTATATTATTAAT
Found at i:3287977 original size:45 final size:45
Alignment explanation
Indices: 3287926--3288032 Score: 162
Period size: 45 Copynumber: 2.4 Consensus size: 45
3287916 CGACTACTGT
*
3287926 TACTGTTACCGTTACTGTTATCGATTCGA-CACTTTGTGTGTCGAA
1 TACTGTTACCGTTACTGTTATAGATT-GAGCACTTTGTGTGTCGAA
* *
3287971 TACTGTTACCGTTACTGTTATAGATTTAGCACTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTATAGATTGAGCACTTTGTGTGTCGAA
*
3288016 TACTGTTACTGTTACTG
1 TACTGTTACCGTTACTG
3288033 CTACTGCTAC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
44 1 0.02
45 56 0.98
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.43
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTATAGATTGAGCACTTTGTGTGTCGAA
Found at i:3288026 original size:51 final size:50
Alignment explanation
Indices: 3287911--3288030 Score: 135
Period size: 45 Copynumber: 2.5 Consensus size: 50
3287901 CAGGCACTTA
* * *
3287911 TGTGCCGACTACTGTTACTGTTACCGTTACTGTTATCGATTCGACACTTTG
1 TGTGTCGA-TACTGTTACTGTTACCGTTACTGTTATAGATTAGACACTTTG
3287962 TGTGTCGA-A----TACTGTTACCGTTACTGTTATAGATTTAG-CACTTTG
1 TGTGTCGATACTGTTACTGTTACCGTTACTGTTATAGA-TTAGACACTTTG
*
3288007 TGTGTTGAATACTGTTACTGTTAC
1 TGTGTCG-ATACTGTTACTGTTAC
3288031 TGCTACTGCT
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
45 36 0.62
46 4 0.07
47 1 0.02
49 1 0.02
51 16 0.28
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (50 bp):
TGTGTCGATACTGTTACTGTTACCGTTACTGTTATAGATTAGACACTTTG
Found at i:3289680 original size:45 final size:44
Alignment explanation
Indices: 3289578--3289700 Score: 131
Period size: 45 Copynumber: 2.8 Consensus size: 44
3289568 CTGTAAATAG
* * * * *
3289578 GTTGTGCATCCATAGCCA-ATGGCAGATTTTATCTGCATTATTTT
1 GTTGTGTATCCACAGCCATA-GGCAGATTTCATCTACATGATTTT
* *
3289622 GTTGTGTACCCACAGCCATAGGCAGATTTCATCTACGATGCTTTT
1 GTTGTGTATCCACAGCCATAGGCAGATTTCATCTAC-ATGATTTT
* * *
3289667 GTTGTGTATCCACAACCATAGGTAGATTCCATCT
1 GTTGTGTATCCACAGCCATAGGCAGATTTCATCT
3289701 GTGGTGTTTT
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
44 29 0.44
45 37 0.56
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.36
Consensus pattern (44 bp):
GTTGTGTATCCACAGCCATAGGCAGATTTCATCTACATGATTTT
Found at i:3290190 original size:16 final size:17
Alignment explanation
Indices: 3290155--3290193 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3290145 TTAGGCTTAT
* *
3290155 TTTTATAATTCTTGTTA
1 TTTTATAATTCGTATTA
3290172 TTTTATAATT-GTATTA
1 TTTTATAATTCGTATTA
3290188 TTTTAT
1 TTTTAT
3290194 TTATATTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (17 bp):
TTTTATAATTCGTATTA
Found at i:3294403 original size:22 final size:22
Alignment explanation
Indices: 3294371--3294416 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
3294361 AGAAGAAAGC
*
3294371 TTATGAAGATCAGCACTAAATT
1 TTATGAAGATCAACACTAAATT
*
3294393 TTATGAGGATCAACACTAAATT
1 TTATGAAGATCAACACTAAATT
3294415 TT
1 TT
3294417 CTATTATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (22 bp):
TTATGAAGATCAACACTAAATT
Found at i:3296977 original size:262 final size:260
Alignment explanation
Indices: 3296508--3297028 Score: 880
Period size: 262 Copynumber: 2.0 Consensus size: 260
3296498 AATTTTTAAC
* *
3296508 GCAAAGACAATAACTGCCAATTCTAAGCATGTGTCGGATAATTTTTTTTGTACGGCTTCAATTGT
1 GCAAACACAATAACTGCCAATTCTAAGCATGTGTCGGATAATTTTTTTTGTACAGCTTCAATTGT
*
3296573 CGGTAAGCATATGCTATTACTTTGCCTTCCTGCATCAAAACACAGCCTAAACCATATAAAGAGCA
66 CGGTAAGCATATGCTATTACTTTGCCTTCCTGCATCAAAACACAACCTAAACCATATAAAGAGCA
* * *
3296638 TCACTGAAAATCACAAATTCTTTTCCCGATTCAGGCTGAACTAGAACGGGTGCTTCGGCCAACAG
131 TCACTAAAAATCACAAATTCTTTTCCCGATTCAAGCTAAACTAGAACGGGTGCTTCGGCCAACAG
* * *
3296703 TGTTTTCAACTGGTCAAAACTTTACTGACACTTGCCGGACCATTCTTATTTCACATCTTTCTATT
196 TGCTTTCAACTGGTCAAAACTTTACTGACACTTGCCAGACCATTCATATTTCACATCTTTCTATT
*
3296768 GCAAACACAATAACTGCCAATTCTAAGTCATGTGTTGGATAATTTTTTTTTGTACAGCTTCAATT
1 GCAAACACAATAACTGCCAATTCTAAG-CATGTGTCGGATAA-TTTTTTTTGTACAGCTTCAATT
* * *
3296833 GTCGGTAAGTATATGCTATTACTTTGCCTTCCTGTATCAAAACACAATCTAAACCATATAAAGAG
64 GTCGGTAAGCATATGCTATTACTTTGCCTTCCTGCATCAAAACACAACCTAAACCATATAAAGAG
* *
3296898 CATCACTAAAAATCACAAATTCTTTTCCCGATTCAAGCTAAACTATAACGGGTGCTTCGGTCAAC
129 CATCACTAAAAATCACAAATTCTTTTCCCGATTCAAGCTAAACTAGAACGGGTGCTTCGGCCAAC
*
3296963 AGTGCTTTCAACTGGTCGAAACTTTACTGACACTTGCCAGACCATTCATATTTCACATCTTTCTA
194 AGTGCTTTCAACTGGTCAAAACTTTACTGACACTTGCCAGACCATTCATATTTCACATCTTTCTA
3297028 T
259 T
3297029 AATAGTTGTG
Statistics
Matches: 243, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
260 26 0.11
261 13 0.05
262 204 0.84
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.32
Consensus pattern (260 bp):
GCAAACACAATAACTGCCAATTCTAAGCATGTGTCGGATAATTTTTTTTGTACAGCTTCAATTGT
CGGTAAGCATATGCTATTACTTTGCCTTCCTGCATCAAAACACAACCTAAACCATATAAAGAGCA
TCACTAAAAATCACAAATTCTTTTCCCGATTCAAGCTAAACTAGAACGGGTGCTTCGGCCAACAG
TGCTTTCAACTGGTCAAAACTTTACTGACACTTGCCAGACCATTCATATTTCACATCTTTCTATT
Found at i:3302014 original size:35 final size:35
Alignment explanation
Indices: 3301925--3302858 Score: 1685
Period size: 35 Copynumber: 26.7 Consensus size: 35
3301915 CCCGTGGCAA
* * * *
3301925 AGTTATGATACGTAGGTATGGCATTGTCCATACCG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
* * * ***
3301960 AGCT-TGATAA-GTAGTTATGGCATCGACCATACTG
1 AGTTATGA-AACGTAGGTATGGTATTTTCCATACTG
* * * **
3301994 AGCTATGATACGTAGGTATGGCATCGTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302029 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302064 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302099 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302134 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302169 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302204 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302239 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302274 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302309 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302344 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302379 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302414 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302449 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302484 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302519 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302554 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302589 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302624 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302659 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302694 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302729 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
3302764 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
*
3302799 AGTTATGAAACGTAGGTATGGTATTTTCCATACCG
1 AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
*
3302834 AG-TATGAAATGTAGGTATGGTATTT
1 AGTTATGAAACGTAGGTATGGTATTT
3302859 CAATGAGGAA
Statistics
Matches: 880, Mismatches: 16, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
34 50 0.06
35 830 0.94
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.36
Consensus pattern (35 bp):
AGTTATGAAACGTAGGTATGGTATTTTCCATACTG
Found at i:3305065 original size:38 final size:39
Alignment explanation
Indices: 3304986--3305079 Score: 127
Period size: 38 Copynumber: 2.4 Consensus size: 39
3304976 CACGGCATGA
* * * *
3304986 AAGTGCTATCAGGAGTACCGAAATACAATAGGGGCATGT
1 AAGTGCGATCAGGGGTACCGAAATACAACAGGGGCACGT
* *
3305025 AAGTGTGATCAGGGGTA-CGAAGTACAACAGGGGCACGT
1 AAGTGCGATCAGGGGTACCGAAATACAACAGGGGCACGT
3305063 AAGTGCGATCAGGGGTA
1 AAGTGCGATCAGGGGTA
3305080 TAATTATATA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
38 34 0.71
39 14 0.29
ACGTcount: A:0.33, C:0.15, G:0.34, T:0.18
Consensus pattern (39 bp):
AAGTGCGATCAGGGGTACCGAAATACAACAGGGGCACGT
Found at i:3305077 original size:20 final size:20
Alignment explanation
Indices: 3305015--3305077 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
3305005 GAAATACAAT
* *
3305015 AGGGGCATGTAAGTGTGATC
1 AGGGGCACGTAAGTGCGATC
* * *
3305035 AGGGGTACG-AAGTAC-AAC
1 AGGGGCACGTAAGTGCGATC
3305053 AGGGGCACGTAAGTGCGATC
1 AGGGGCACGTAAGTGCGATC
3305073 AGGGG
1 AGGGG
3305078 TATAATTATA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
18 10 0.30
19 9 0.27
20 14 0.42
ACGTcount: A:0.29, C:0.14, G:0.41, T:0.16
Consensus pattern (20 bp):
AGGGGCACGTAAGTGCGATC
Found at i:3306601 original size:25 final size:25
Alignment explanation
Indices: 3306567--3306617 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3306557 GATAGCATCC
*
3306567 GAACCATTAAAAAGTTTCTAGATGT
1 GAACCATTAAAAAGTTTCCAGATGT
* *
3306592 GAACCGTTAAAAGGTTTCCAGATGT
1 GAACCATTAAAAAGTTTCCAGATGT
3306617 G
1 G
3306618 TTGTCGAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (25 bp):
GAACCATTAAAAAGTTTCCAGATGT
Found at i:3311928 original size:17 final size:17
Alignment explanation
Indices: 3311908--3311940 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3311898 ATCATGAAGG
3311908 AAAGAATGAAATGAATA
1 AAAGAATGAAATGAATA
3311925 AAAGAATGAAATGAAT
1 AAAGAATGAAATGAAT
3311941 GCTAAGGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (17 bp):
AAAGAATGAAATGAATA
Found at i:3316886 original size:19 final size:20
Alignment explanation
Indices: 3316862--3316899 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3316852 CTTAATTTCG
3316862 ATGTTTGACCTC-AATCTCA
1 ATGTTTGACCTCGAATCTCA
*
3316881 ATGTTTGATCTCGAATCTC
1 ATGTTTGACCTCGAATCTC
3316900 TATAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTTTGACCTCGAATCTCA
Found at i:3317629 original size:34 final size:34
Alignment explanation
Indices: 3317549--3317636 Score: 97
Period size: 34 Copynumber: 2.6 Consensus size: 34
3317539 GCATAGTATT
* * *
3317549 TGCCACCGTATTGAAT-TGTTATAAGCATATTGAT
1 TGCCACCGTATTG-ATCTGTTAAAAGCATATTAAA
* * * *
3317583 TGCTATCATATTGTTCTGTTAAAAGCATATTAAA
1 TGCCACCGTATTGATCTGTTAAAAGCATATTAAA
3317617 TGCCACCGTATTGATCTGTT
1 TGCCACCGTATTGATCTGTT
3317637 TTGAAAATGC
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
33 1 0.02
34 41 0.98
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (34 bp):
TGCCACCGTATTGATCTGTTAAAAGCATATTAAA
Found at i:3319055 original size:79 final size:80
Alignment explanation
Indices: 3318935--3319131 Score: 285
Period size: 79 Copynumber: 2.5 Consensus size: 80
3318925 GATTTAGCCG
* * *
3318935 GATATAGCAACTCGCACAAATGCCTTCGGGTA-TTAGCCCGGATATTGTCACTAGCATAAATGCC
1 GATATAGCAACTAGCACAAATGCCTTCGGG-ACTTAGTCCGGATATAGTCACTAGCATAAATGCC
*
3318999 TTCGGGACTTAGCCCG
65 TTCGGGACTTAGCCCA
*
3319015 GATAT-GTC-GCTAGCACAAATGCCTTCGGGACTTAGTCCGGATATAGTCACTAGCATAAATGCC
1 GATATAG-CAACTAGCACAAATGCCTTCGGGACTTAGTCCGGATATAGTCACTAGCATAAATGCC
3319078 TTCGGGACTTAGCCCA
65 TTCGGGACTTAGCCCA
*
3319094 GATATAGCAACTCGCACAAATGCCTTC-GGATCTTAGTC
1 GATATAGCAACTAGCACAAATGCCTTCGGGA-CTTAGTC
3319132 TGGTTATCAT
Statistics
Matches: 105, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
78 1 0.01
79 74 0.70
80 30 0.29
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (80 bp):
GATATAGCAACTAGCACAAATGCCTTCGGGACTTAGTCCGGATATAGTCACTAGCATAAATGCCT
TCGGGACTTAGCCCA
Found at i:3319129 original size:40 final size:40
Alignment explanation
Indices: 3318919--3319122 Score: 256
Period size: 40 Copynumber: 5.2 Consensus size: 40
3318909 ACCCAAGTAT
* * *
3318919 CTTCGAGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* *
3318958 CTTCGGGTA-TTAGCCCGGATATTGTCACTAGCATAAATGC
1 CTTCGGG-ACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
3318998 CTTCGGGACTTAGCCCGGATAT-GTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
3319037 CTTCGGGACTTAGTCCGGATATAGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
3319077 CTTCGGGACTTAGCCCAGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
3319117 CTTCGG
1 CTTCGG
3319123 ATCTTAGTCT
Statistics
Matches: 146, Mismatches: 13, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
39 48 0.33
40 97 0.66
41 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:3329002 original size:21 final size:21
Alignment explanation
Indices: 3328978--3329017 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3328968 TTATCCCACA
3328978 TCAGAATTTTCATCATGAATT
1 TCAGAATTTTCATCATGAATT
* *
3328999 TCAGTATTTTCATCCTGAA
1 TCAGAATTTTCATCATGAA
3329018 AAAAGTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.42
Consensus pattern (21 bp):
TCAGAATTTTCATCATGAATT
Found at i:3333125 original size:62 final size:62
Alignment explanation
Indices: 3333025--3333187 Score: 206
Period size: 62 Copynumber: 2.6 Consensus size: 62
3333015 CACAAGCAAC
* * *
3333025 GGACACGGGCGTGTGTCTGGGCAGTGTAACTCACTGTTTGTGGCATAAAACCACACAGCT-AG
1 GGACACGGGCATGTGCCTAGGCAGTGTAACTCACTGTTTGTGGCATAAAACCACAC-GCTCAG
* * * *
3333087 GGGCACGGGCATGTGCCTAGGCCGTGTAACTCACTGTTTGTGGTATAAAACCACACGGTCAG
1 GGACACGGGCATGTGCCTAGGCAGTGTAACTCACTGTTTGTGGCATAAAACCACACGCTCAG
*
3333149 GGACACGGGCGTATGT-CC-AGGCTGTGTAACTCACTGTTT
1 GGACACGGGC--ATGTGCCTAGGCAGTGTAACTCACTGTTT
3333188 AATTTTTCGA
Statistics
Matches: 89, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
61 2 0.02
62 81 0.91
63 2 0.02
64 4 0.04
ACGTcount: A:0.22, C:0.23, G:0.31, T:0.24
Consensus pattern (62 bp):
GGACACGGGCATGTGCCTAGGCAGTGTAACTCACTGTTTGTGGCATAAAACCACACGCTCAG
Found at i:3351175 original size:51 final size:51
Alignment explanation
Indices: 3351099--3351199 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
3351089 CAGTGGAAGA
*
3351099 TATTAAACTTGAAATGTATAATGTAGTGTATTAATGAGTTAATTTTGTTGT
1 TATTAAACTTGAAATGTATAATGTAGTGTAGTAATGAGTTAATTTTGTTGT
3351150 TATTAAACTTGAAATGTATAATGTAGTGTAGTAATGAGTTAATTTTGTTG
1 TATTAAACTTGAAATGTATAATGTAGTGTAGTAATGAGTTAATTTTGTTG
3351200 CTATAGACCT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.46
Consensus pattern (51 bp):
TATTAAACTTGAAATGTATAATGTAGTGTAGTAATGAGTTAATTTTGTTGT
Found at i:3356088 original size:40 final size:40
Alignment explanation
Indices: 3356029--3356173 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
3356019 CATTTGAATG
* *
3356029 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGA-T
* *
3356069 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGAT
* *
3356109 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGAT
* * *
3356149 ATACCCGGGTTAAGACTCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
3356174 ATTGTGCTTG
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 92 0.97
41 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGAT
Found at i:3356192 original size:80 final size:80
Alignment explanation
Indices: 3356029--3356200 Score: 204
Period size: 80 Copynumber: 2.2 Consensus size: 80
3356019 CATTTGAATG
* * * * *
3356029 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCA
* *
3356094 TTTGTGCGAGTTGAT
66 ATTGTGCGAGTGGAT
* * *
3356109 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATACCCGGGTTAAGACTCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAG-TGACTATACCCGGGCTAAGACCCGAAGGC
** *
3356173 AATTGTGCTTGTGGTT
65 AATTGTGCGAGTGGAT
3356189 ATATCC-GGCTAA
1 ATATCCGGGCTAA
3356201 ATTCCGAAGA
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
79 6 0.08
80 70 0.90
81 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCA
ATTGTGCGAGTGGAT
Found at i:3358370 original size:43 final size:43
Alignment explanation
Indices: 3358305--3358453 Score: 235
Period size: 43 Copynumber: 3.5 Consensus size: 43
3358295 ATTTGAAAAA
* * *
3358305 AAACGCCGCTAAAGGTTATGGCCTTTAGCGACGCTTTTACCAC
1 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
* *
3358348 AAATGCCGCTAAAGCTCATGGCCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
*
3358391 ATACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
*
3358434 AAACGCCGCTAAAAGTCATG
1 AAACGCCGCTAAAGGTCATG
3358454 AAATTTAAAA
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 96 1.00
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
Found at i:3358637 original size:19 final size:19
Alignment explanation
Indices: 3358592--3358638 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
3358582 ATCAAATTAA
*
3358592 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
3358611 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
3358630 AATAAAAAT
1 AATAAAAAT
3358639 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:3360579 original size:46 final size:46
Alignment explanation
Indices: 3360526--3361050 Score: 535
Period size: 46 Copynumber: 11.3 Consensus size: 46
3360516 ATAATCCACA
3360526 ACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCACTTTAAC
* *
3360572 ACTTCAATTTACAGCAGTAAAACACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCACTTTAAC
* * ** * * *
3360618 ATTTCAATTAACAATATTTATAGCACTTCAATTTGCAACA-TTTAAGC
1 ACTTCAATTTACAGCATTCA-AACACTTCAATTTGCAGCACTTTAA-C
3360665 ACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCACTTTAAC
* * ** * * *
3360711 ATTTCAATTAACAATATTTATAGCACTTCAATTTGCAACA-TTTAAGC
1 ACTTCAATTTACAGCATTCA-AACACTTCAATTTGCAGCACTTTAA-C
3360758 ACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCACTTTAAC
* * ** * * *
3360804 ATTTCAATTAACAATATTTATAGCACTTCAATTTGCAACA-TTTAAGC
1 ACTTCAATTTACAGCATTCA-AACACTTCAATTTGCAGCACTTTAA-C
3360851 ACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCACTTTAAC
* * * * * *
3360897 ATTTCAATTAACAACATTTAAACA-TCTCAATTTCCAGCAAC-TAAAC
1 ACTTCAATTTACAGCATTCAAACACT-TCAATTTGCAGC-ACTTTAAC
* * * *
3360943 ACTTCAATTTGCAGTACTT-AAACACTCCAATTTACAGCACTTTAAC
1 ACTTCAATTTACAGCA-TTCAAACACTTCAATTTGCAGCACTTTAAC
* * * * *
3360989 ACTTCAATTTGCAGCACTT-TAACAGTTCAATTTACAACA-TTTAAAC
1 ACTTCAATTTACAGCA-TTCAAACACTTCAATTTGCAGCACTTT-AAC
* *
3361035 ACTTTAATTTGCAGCA
1 ACTTCAATTTACAGCA
3361051 CTTTAACATC
Statistics
Matches: 399, Mismatches: 65, Indels: 30
0.81 0.13 0.06
Matches are distributed among these distances:
45 6 0.02
46 274 0.69
47 119 0.30
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (46 bp):
ACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCACTTTAAC
Found at i:3360668 original size:93 final size:93
Alignment explanation
Indices: 3360548--3361050 Score: 712
Period size: 93 Copynumber: 5.4 Consensus size: 93
3360538 AGCATTCAAA
* * *
3360548 CACTTCAATTTGCAGCACTTTAA-CACTTCAATTTACAGCAGTAAAACACTTCAATTTGCAGCAC
1 CACTTCAATTTGCAACA-TTTAAGCACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCAC
3360612 TTTAACATTTCAATTAACAATATTTATAG
65 TTTAACATTTCAATTAACAATATTTATAG
3360641 CACTTCAATTTGCAACATTTAAGCACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCACT
1 CACTTCAATTTGCAACATTTAAGCACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCACT
3360706 TTAACATTTCAATTAACAATATTTATAG
66 TTAACATTTCAATTAACAATATTTATAG
3360734 CACTTCAATTTGCAACATTTAAGCACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCACT
1 CACTTCAATTTGCAACATTTAAGCACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCACT
3360799 TTAACATTTCAATTAACAATATTTATAG
66 TTAACATTTCAATTAACAATATTTATAG
3360827 CACTTCAATTTGCAACATTTAAGCACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCACT
1 CACTTCAATTTGCAACATTTAAGCACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCACT
* *
3360892 TTAACATTTCAATTAACAACATTTA-AA
66 TTAACATTTCAATTAACAATATTTATAG
* * ** * * * * *
3360919 CA-TCTCAATTTCCAGCAACTAAACACTTCAATTTGCAGTACTT-AAACACTCCAATTTACAGCA
1 CACT-TCAATTTGCAACATTTAAGCACTTCAATTTACAGCA-TTCAAACACTTCAATTTGCAGCA
* ** **
3360982 CTTTAACACTTCAATTTGCAGCACTTTA-A-
64 CTTTAACATTTCAATTAACAATA-TTTATAG
* * * * *
3361011 CAGTTCAATTTACAACATTTAAACACTTTAATTTGCAGCA
1 CACTTCAATTTGCAACATTTAAGCACTTCAATTTACAGCA
3361051 CTTTAACATC
Statistics
Matches: 381, Mismatches: 24, Indels: 11
0.92 0.06 0.03
Matches are distributed among these distances:
91 1 0.00
92 106 0.28
93 274 0.72
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.34
Consensus pattern (93 bp):
CACTTCAATTTGCAACATTTAAGCACTTCAATTTACAGCATTCAAACACTTCAATTTGCAGCACT
TTAACATTTCAATTAACAATATTTATAG
Found at i:3361058 original size:23 final size:22
Alignment explanation
Indices: 3360526--3361066 Score: 420
Period size: 23 Copynumber: 23.4 Consensus size: 22
3360516 ATAATCCACA
* *
3360526 ACTTCAATTTACAGCATTCAAAC
1 ACTTCAATTTGCAGCATT-TAAC
3360549 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTGCAGCA-TTTAAC
* **
3360572 ACTTCAATTTACAGCAGTAAAAC
1 ACTTCAATTTGCAGCA-TTTAAC
3360595 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTGCAGCA-TTTAAC
* ** **
3360618 ATTTCAATTAACAATATTTATAGC
1 ACTTCAATTTGCAGCATTTA-A-C
*
3360642 ACTTCAATTTGCAACATTTAAGC
1 ACTTCAATTTGCAGCATTTAA-C
* *
3360665 ACTTCAATTTACAGCATTCAAAC
1 ACTTCAATTTGCAGCATT-TAAC
3360688 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTGCAGCA-TTTAAC
* ** **
3360711 ATTTCAATTAACAATATTTATAGC
1 ACTTCAATTTGCAGCATTTA-A-C
*
3360735 ACTTCAATTTGCAACATTTAAGC
1 ACTTCAATTTGCAGCATTTAA-C
* *
3360758 ACTTCAATTTACAGCATTCAAAC
1 ACTTCAATTTGCAGCATT-TAAC
3360781 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTGCAGCA-TTTAAC
* ** **
3360804 ATTTCAATTAACAATATTTATAGC
1 ACTTCAATTTGCAGCATTTA-A-C
*
3360828 ACTTCAATTTGCAACATTTAAGC
1 ACTTCAATTTGCAGCATTTAA-C
* *
3360851 ACTTCAATTTACAGCATTCAAAC
1 ACTTCAATTTGCAGCATT-TAAC
3360874 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTGCAGCA-TTTAAC
* ** *
3360897 ATTTCAATTAACAACATTTAA-
1 ACTTCAATTTGCAGCATTTAAC
* * *
3360918 ACATCTCAATTTCCAGCAACTAAAC
1 AC-T-TCAATTTGCAGC-ATTTAAC
* *
3360943 ACTTCAATTTGCAGTACTTAAAC
1 ACTTCAATTTGCAGCA-TTTAAC
* *
3360966 ACTCCAATTTACAGCACTTTAAC
1 ACTTCAATTTGCAGCA-TTTAAC
3360989 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTGCAGCA-TTTAAC
* * *
3361012 AGTTCAATTTACAACATTTAAAC
1 ACTTCAATTTGCAGCATTT-AAC
*
3361035 ACTTTAATTTGCAGCACTTTAAC
1 ACTTCAATTTGCAGCA-TTTAAC
3361058 A-TCTCAATT
1 ACT-TCAATT
3361067 AACAACATTT
Statistics
Matches: 418, Mismatches: 79, Indels: 42
0.78 0.15 0.08
Matches are distributed among these distances:
21 1 0.00
22 23 0.06
23 319 0.76
24 73 0.17
25 2 0.00
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (22 bp):
ACTTCAATTTGCAGCATTTAAC
Found at i:3364019 original size:7 final size:7
Alignment explanation
Indices: 3364007--3364078 Score: 56
Period size: 7 Copynumber: 10.0 Consensus size: 7
3363997 ACTAATTAAT
3364007 CTAAACC
1 CTAAACC
3364014 CTAAACC
1 CTAAACC
*
3364021 TCTTAACC
1 -CTAAACC
*
3364029 C-ATATCC
1 CTA-AACC
*
3364036 CATAAACA
1 C-TAAACC
*
3364044 CTAAACT
1 CTAAACC
3364051 CTAAACC
1 CTAAACC
*
3364058 CTTAACC
1 CTAAACC
*
3364065 CTTAACC
1 CTAAACC
3364072 CTAAACC
1 CTAAACC
3364079 GTTACACCTT
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
7 42 0.81
8 9 0.17
9 1 0.02
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.22
Consensus pattern (7 bp):
CTAAACC
Found at i:3364077 original size:21 final size:21
Alignment explanation
Indices: 3364007--3364078 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
3363997 ACTAATTAAT
3364007 CTAAACCCTAAACCTCTTAACC
1 CTAAACCCTAAACC-CTTAACC
* * * *
3364029 C-ATATCCCATAAACACTAAACT
1 CTA-AACCC-TAAACCCTTAACC
*
3364051 CTAAACCCTTAACCCTTAACC
1 CTAAACCCTAAACCCTTAACC
3364072 CTAAACC
1 CTAAACC
3364079 GTTACACCTT
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
21 17 0.45
22 15 0.39
23 6 0.16
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.22
Consensus pattern (21 bp):
CTAAACCCTAAACCCTTAACC
Found at i:3364204 original size:14 final size:14
Alignment explanation
Indices: 3364187--3364255 Score: 57
Period size: 14 Copynumber: 4.6 Consensus size: 14
3364177 CCTTAAACCC
3364187 TAAACCATATATCT
1 TAAACCATATATCT
* *
3364201 TAAACTATAGTTAACTCA
1 TAAACCATA--T-A-TCT
* * *
3364219 TAAACCTTAAATCC
1 TAAACCATATATCT
3364233 TAAACCATATATCT
1 TAAACCATATATCT
3364247 TAAACCATA
1 TAAACCATA
3364256 AACCATAAAC
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
14 30 0.71
15 1 0.02
16 1 0.02
17 1 0.02
18 9 0.21
ACGTcount: A:0.45, C:0.22, G:0.01, T:0.32
Consensus pattern (14 bp):
TAAACCATATATCT
Found at i:3364204 original size:21 final size:21
Alignment explanation
Indices: 3364178--3364262 Score: 82
Period size: 21 Copynumber: 3.9 Consensus size: 21
3364168 ACTCCTAAAC
*
3364178 CTTAAACCCTAAACCATATAT
1 CTTAAACCATAAACCATATAT
* * *
3364199 CTTAAACTATAGTTAACTCATAAAC
1 CTTAAACCATA---AAC-CATATAT
3364224 CTTAAATCC-TAAACCATATAT
1 CTTAAA-CCATAAACCATATAT
3364245 CTTAAACCATAAACCATA
1 CTTAAACCATAAACCATA
3364263 AACTATAATG
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
20 2 0.04
21 29 0.57
22 3 0.06
24 3 0.06
25 13 0.25
26 1 0.02
ACGTcount: A:0.45, C:0.25, G:0.01, T:0.29
Consensus pattern (21 bp):
CTTAAACCATAAACCATATAT
Found at i:3364215 original size:46 final size:46
Alignment explanation
Indices: 3364162--3364251 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 46
3364152 CTTCAAATAC
*
3364162 TAGTTAACTCCTAAACCTTAAACCCTAAACCATATATCTTAAACTA
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACTA
*
3364208 TAGTTAACTCATAAACCTTAAATCCTAAACCATATATCTTAAAC
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAAC
3364252 CATAAACCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.42, C:0.24, G:0.02, T:0.31
Consensus pattern (46 bp):
TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACTA
Found at i:3364473 original size:41 final size:41
Alignment explanation
Indices: 3364427--3364684 Score: 281
Period size: 41 Copynumber: 6.4 Consensus size: 41
3364417 GTTATATGAC
* *
3364427 TTTTAGTGGCGTTTTACCAAAAGCGCCGCTAATGTTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
*
3364468 TTTTAGCGACGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* * * *
3364509 TTTTAGCAGCGTTTTTCCAAAAGTGCCGCTAATGCTCTAGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
** *
3364550 TTTTAGCGGCGTTTTTTCAAAAGCACCGCTAATG-TCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* * * * *
3364590 TTTTAACGGCGTTTTGCAAAAAGCACCGCT-ATGCTCT-AT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* ** * * *
3364629 TTTTTGCGGCGTTTTAGTAAAAAACGCCACTATTGCTCT-GT
1 TTTTAGCGGCGTTTTA-CCAAAAGCGCCGCTAATGCTCTGGT
*
3364670 TTTTAGTGGCGTTTT
1 TTTTAGCGGCGTTTT
3364685 TGATAAAACG
Statistics
Matches: 185, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
39 17 0.09
40 44 0.24
41 124 0.67
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
Found at i:3364693 original size:40 final size:41
Alignment explanation
Indices: 3364466--3364715 Score: 129
Period size: 41 Copynumber: 6.2 Consensus size: 41
3364456 TAATGTTCTG
* ** * * *
3364466 GTTTTTAGCGACGTTTTA-CCAAAAGCGCCGCTAATGCTCT
1 GTTTTTAGCGGCGTTTTAGTAAAAAACGCCACTATTGCTCT
* * ** * *
3364506 GGTTTTTAGCAGCGTTTT--TCCAAAAGTGCCGCTAATGCTCT
1 -GTTTTTAGCGGCGTTTTAGT-AAAAAACGCCACTATTGCTCT
* * * * * *
3364547 AGTTTTTAGCGGCGTTTT-TTCAAAAGCACCGCTAATG-TCT
1 -GTTTTTAGCGGCGTTTTAGTAAAAAACGCCACTATTGCTCT
* * * * *
3364587 GGTTTTTAACGGCGTTTT-GCAAAAAGCACCGCTA-TGCTCT
1 -GTTTTTAGCGGCGTTTTAGTAAAAAACGCCACTATTGCTCT
* *
3364627 ATTTTTTGCGGCGTTTTAGTAAAAAACGCCACTATTGCTCT
1 GTTTTTAGCGGCGTTTTAGTAAAAAACGCCACTATTGCTCT
* * * * *
3364668 GTTTTTAGTGGCGTTTTTG-ATAAAACGCCGCTATTGCTAT
1 GTTTTTAGCGGCGTTTTAGTAAAAAACGCCACTATTGCTCT
3364708 GTGTTTTA
1 GT-TTTTA
3364716 CAATTTTTGC
Statistics
Matches: 176, Mismatches: 27, Indels: 12
0.82 0.13 0.06
Matches are distributed among these distances:
39 16 0.09
40 67 0.38
41 92 0.52
42 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.38
Consensus pattern (41 bp):
GTTTTTAGCGGCGTTTTAGTAAAAAACGCCACTATTGCTCT
Found at i:3364991 original size:42 final size:42
Alignment explanation
Indices: 3364926--3365006 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 42
3364916 TCACAAAACT
* *
3364926 CACAAAGCAGTACATAGTAAGTCT-GTCGTTGAACACTTCAGA
1 CACAAAGCAATACATAGTAAGTCTCCT-GTTGAACACTTCAGA
3364968 CACAAAGCAATACATAG-AGAGTCTCCTGTTGAACACTTC
1 CACAAAGCAATACATAGTA-AGTCTCCTGTTGAACACTTC
3365007 GGATCAATCC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 1 0.03
42 33 0.94
43 1 0.03
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.23
Consensus pattern (42 bp):
CACAAAGCAATACATAGTAAGTCTCCTGTTGAACACTTCAGA
Found at i:3374057 original size:33 final size:32
Alignment explanation
Indices: 3373922--3374059 Score: 120
Period size: 33 Copynumber: 4.3 Consensus size: 32
3373912 GTGCATATTC
**
3373922 CCTTTTCAAGTG-ATACACATGAAGTGTACATAC
1 CCTTTTCAAGTGTATACACA--AAGTGTACATTT
* * **
3373955 CCTTTTCAATTTGTACACACAAAGTGTACATAA
1 CCTTTTCAA-GTGTATACACAAAGTGTACATTT
* *
3373988 CCTTTTCAAGTG--TACACATAGTGTACTTTT
1 CCTTTTCAAGTGTATACACAAAGTGTACATTT
* * *
3374018 CATTTTCAAGTGGTATACACAAAGTATACCTTT
1 CCTTTTCAAGT-GTATACACAAAGTGTACATTT
3374051 CCTTTTCAA
1 CCTTTTCAA
3374060 TACCACCCTT
Statistics
Matches: 86, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
30 23 0.27
31 1 0.01
32 2 0.02
33 52 0.60
34 2 0.02
35 6 0.07
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (32 bp):
CCTTTTCAAGTGTATACACAAAGTGTACATTT
Found at i:3374059 original size:63 final size:65
Alignment explanation
Indices: 3373922--3374046 Score: 155
Period size: 63 Copynumber: 1.9 Consensus size: 65
3373912 GTGCATATTC
* * * *
3373922 CCTTTTCAAGTGATACACATGAAGTGTACATACCCTTTTCAATTTGTACACACAAAGTGTACATA
1 CCTTTTCAAGTGATACACAT-AAGTGTACATACCATTTTCAAGTGGTACACACAAAGTATACATA
3373987 A
65 A
* ** *
3373988 CCTTTTCAAGTG-TACACAT-AGTGTACTTTTCATTTTCAAGTGGTATACACAAAGTATAC
1 CCTTTTCAAGTGATACACATAAGTGTACATACCATTTTCAAGTGGTACACACAAAGTATAC
3374047 CTTTCCTTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
63 32 0.63
65 7 0.14
66 12 0.24
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (65 bp):
CCTTTTCAAGTGATACACATAAGTGTACATACCATTTTCAAGTGGTACACACAAAGTATACATAA
Found at i:3375490 original size:62 final size:62
Alignment explanation
Indices: 3375366--3375518 Score: 166
Period size: 62 Copynumber: 2.5 Consensus size: 62
3375356 ACGGATACGA
* * * * *
3375366 GCGTGTGTCTAGGTCGTGTAACTCACTGTCTGTGGTATAAAACTACATAGCTAAGGATACGG
1 GCGTGTGCCTAGGCCGTGTAACTCACTGTCTGTGGTATAAAACCACAAAGCTAAGGACACGG
* *
3375428 GCGTGTGCCTAGGCCGTGTAACTCACTG-CTTGTGGTATAAAACCACACAATC-AATGACACGG
1 GCGTGTGCCTAGGCCGTGTAACTCACTGTC-TGTGGTATAAAACCACA-AAGCTAAGGACACGG
* * * * *
3375490 GCGTGTACCCAAGTCGCGTAACTCACTGT
1 GCGTGTGCCTAGGCCGTGTAACTCACTGT
3375519 TTAAGATTTT
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
61 1 0.01
62 73 0.96
63 2 0.03
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (62 bp):
GCGTGTGCCTAGGCCGTGTAACTCACTGTCTGTGGTATAAAACCACAAAGCTAAGGACACGG
Found at i:3381945 original size:12 final size:12
Alignment explanation
Indices: 3381930--3381956 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3381920 TCAATGTCAT
3381930 CTTCAACTTTAG
1 CTTCAACTTTAG
3381942 CTTCAACTTTAG
1 CTTCAACTTTAG
3381954 CTT
1 CTT
3381957 AGATTTCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.26, G:0.07, T:0.44
Consensus pattern (12 bp):
CTTCAACTTTAG
Found at i:3385730 original size:2 final size:2
Alignment explanation
Indices: 3385725--3385759 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3385715 GTAAAAAAAA
*
3385725 AT AT AT TT AT A- 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
3385760 CAAATTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3388972 original size:35 final size:35
Alignment explanation
Indices: 3388917--3388984 Score: 88
Period size: 34 Copynumber: 1.9 Consensus size: 35
3388907 TTTAGTAATT
3388917 TTTTATATTTTCTATAATTTT-ATGTAAATTTTTTAA
1 TTTTATATTTTCTATAATTTTGA--TAAATTTTTTAA
3388953 TTTTAT-TTTT-TAGTAATTTTGATAAATTTTTT
1 TTTTATATTTTCTA-TAATTTTGATAAATTTTTT
3388985 GTGATTTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
34 12 0.40
35 11 0.37
36 7 0.23
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.66
Consensus pattern (35 bp):
TTTTATATTTTCTATAATTTTGATAAATTTTTTAA
Found at i:3390415 original size:18 final size:18
Alignment explanation
Indices: 3390392--3390426 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3390382 ATCATCACAT
3390392 CATGAACATGATCATGAC
1 CATGAACATGATCATGAC
*
3390410 CATGAACTTGATCATGA
1 CATGAACATGATCATGA
3390427 TGGTGTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (18 bp):
CATGAACATGATCATGAC
Found at i:3393185 original size:12 final size:12
Alignment explanation
Indices: 3393170--3393194 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3393160 TTAATTTTTT
3393170 TAAAATTTTTAA
1 TAAAATTTTTAA
3393182 TAAAATTTTTAA
1 TAAAATTTTTAA
3393194 T
1 T
3393195 TAATAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAATTTTTAA
Found at i:3393405 original size:103 final size:106
Alignment explanation
Indices: 3393231--3393419 Score: 260
Period size: 103 Copynumber: 1.8 Consensus size: 106
3393221 TTTAATTCAT
* ** *
3393231 TTTTTCAATTAATAACTCTTTTATTTATATAAATAAAATAGTGTATGTGTAATTATATAATAAAA
1 TTTTTCAATTAATAACTCTTTTATTTATATAAATAAAATAATAAATATGTAATTATATAATAAAA
3393296 ATATAT-ATTTTTAT-TCTATGTGACATTATGTTTAAAATA
66 ATATATAATTTTTATATCTATGTGACATTATGTTTAAAATA
* * * *
3393335 TTTTT-AATTAATAATTTTTTTATTTATATAAATAAATTAATAAATATGTAATTATATAAT-GAA
1 TTTTTCAATTAATAACTCTTTTATTTATATAAATAAAATAATAAATATGTAATTATATAATAAAA
*
3393398 GTCATATAATTTTTATATCTAT
66 AT-ATATAATTTTTATATCTAT
3393420 CATTTTGTTA
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
102 3 0.04
103 52 0.71
104 13 0.18
105 5 0.07
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (106 bp):
TTTTTCAATTAATAACTCTTTTATTTATATAAATAAAATAATAAATATGTAATTATATAATAAAA
ATATATAATTTTTATATCTATGTGACATTATGTTTAAAATA
Found at i:3393484 original size:20 final size:20
Alignment explanation
Indices: 3393437--3393474 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3393427 TTAAATATAT
**
3393437 TTATATAAAAATTATTTTTA
1 TTATATAATTATTATTTTTA
3393457 TTATATAATTATTATTTT
1 TTATATAATTATTATTTT
3393475 ATTTGTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATATAATTATTATTTTTA
Found at i:3394294 original size:22 final size:24
Alignment explanation
Indices: 3394248--3394294 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
3394238 CACTGAAATT
*
3394248 AAATTATAATTTTTACTATAATAA
1 AAATTATAATTTTTACAATAATAA
*
3394272 AAATT-TAATTTTTA-AATATTAA
1 AAATTATAATTTTTACAATAATAA
3394294 A
1 A
3394295 TTAAAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 9 0.43
24 5 0.24
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
AAATTATAATTTTTACAATAATAA
Found at i:3396627 original size:20 final size:20
Alignment explanation
Indices: 3396577--3396630 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
3396567 GTACCAATCT
**
3396577 AGTATCGATACTTTTTGTCA
1 AGTATCGATAGATTTTGTCA
**
3396597 AGTATCGATAGATTTTGTTG
1 AGTATCGATAGATTTTGTCA
3396617 AGTATCGATAGATT
1 AGTATCGATAGATT
3396631 CAAAATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (20 bp):
AGTATCGATAGATTTTGTCA
Found at i:3399640 original size:3 final size:3
Alignment explanation
Indices: 3399632--3399666 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3399622 ATATTTTACC
3399632 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3399667 CATCATCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3414346 original size:28 final size:28
Alignment explanation
Indices: 3414314--3414372 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
3414304 ATTGCATGAC
* *
3414314 TATGAATATGATTGGGCCTGGTGGACCA
1 TATGAATATGATTAGGCCTGATGGACCA
3414342 TATGAATATGATTAGGCCTGATGGACCA
1 TATGAATATGATTAGGCCTGATGGACCA
3414370 TAT
1 TAT
3414373 AAATGTGGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.31
Consensus pattern (28 bp):
TATGAATATGATTAGGCCTGATGGACCA
Found at i:3417419 original size:19 final size:19
Alignment explanation
Indices: 3417395--3417444 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
3417385 ACTTCACTTA
* *
3417395 AAAAAAACAAGAGAAAAAG
1 AAAAAAACAAAAGAAAAAC
*
3417414 AAAAAAAGAAAAGAAAAAC
1 AAAAAAACAAAAGAAAAAC
*
3417433 AAAAAAAGAAAA
1 AAAAAAACAAAA
3417445 ACTGTAATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.84, C:0.04, G:0.12, T:0.00
Consensus pattern (19 bp):
AAAAAAACAAAAGAAAAAC
Found at i:3417423 original size:14 final size:15
Alignment explanation
Indices: 3417406--3417446 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
3417396 AAAAAACAAG
3417406 AGAAAAAGAAAAA-A
1 AGAAAAAGAAAAACA
3417420 AG-AAAAGAAAAACA
1 AGAAAAAGAAAAACA
3417434 A-AAAAAGAAAAAC
1 AGAAAAAGAAAAAC
3417447 TGTAATAGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (15 bp):
AGAAAAAGAAAAACA
Found at i:3418733 original size:43 final size:42
Alignment explanation
Indices: 3418686--3418857 Score: 184
Period size: 43 Copynumber: 4.0 Consensus size: 42
3418676 ACATAGGGTT
*
3418686 TCGATATGTGTTCTCATGTAAGACCATGTCTGGGACATTGGCA
1 TCGATATGTGAT-TCATGTAAGACCATGTCTGGGACATTGGCA
***
3418729 TCGATATGTGATTACATGTAAGACCATGTCTGGGACATCATCA
1 TCGATATGTGATT-CATGTAAGACCATGTCTGGGACATTGGCA
* * * * *
3418772 CCG-TATTTGATTCGTGTAAAGACCCTGTCTGGGACAGTGGCA
1 TCGATATGTGATTCATGT-AAGACCATGTCTGGGACATTGGCA
* * * *
3418814 TCGATATGAGATAGCATGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATGTGAT-TCATGTAAGACCATGTCTGGGACATTGGCA
3418857 T
1 T
3418858 TGTACGATAT
Statistics
Matches: 104, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
41 4 0.04
42 30 0.29
43 66 0.63
44 4 0.04
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (42 bp):
TCGATATGTGATTCATGTAAGACCATGTCTGGGACATTGGCA
Found at i:3424122 original size:5 final size:5
Alignment explanation
Indices: 3424114--3424155 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
3424104 ACAAAAACAA
* *
3424114 AAAAT AAAAG AAAAG AAAAG AAAA- AAGA- AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
3424156 AGAGGCCAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
4 6 0.18
5 27 0.82
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:3424138 original size:6 final size:6
Alignment explanation
Indices: 3424106--3424158 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
3424096 GGGGTGTTAC
*
3424106 AAAAAC AAAAA- ATAAAAG -AAAAG -AAAAG AAAAAAG AAAAAG -AAAAG
1 AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG -AAAAAG AAAAAG AAAAAG
3424152 AAAAAG A
1 AAAAAG A
3424159 GGCCAAGGCG
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
5 16 0.38
6 21 0.50
7 5 0.12
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:3424145 original size:18 final size:18
Alignment explanation
Indices: 3424106--3424156 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
3424096 GGGGTGTTAC
*
3424106 AAAAACAAAA-AATAAAAG
1 AAAAAGAAAAGAA-AAAAG
3424124 -AAAAGAAAAGAAAAAAG
1 AAAAAGAAAAGAAAAAAG
3424141 AAAAAGAAAAGAAAAA
1 AAAAAGAAAAGAAAAA
3424157 GAGGCCAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 13 0.43
18 17 0.57
ACGTcount: A:0.84, C:0.02, G:0.12, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAAG
Found at i:3425547 original size:143 final size:143
Alignment explanation
Indices: 3425283--3426089 Score: 1044
Period size: 143 Copynumber: 5.6 Consensus size: 143
3425273 TAGATCGAAG
* *
3425283 ATGGCAGATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCTCTCTG
1 ATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTG
* * * * * *
3425348 AAGTTGCAGGGGAGCAGATTGAAGACAACGAATCTTATTTCCCTGACATTGTAGTGGAACGGATT
66 AAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGACGTTGCAGTGGAACAGATT
3425413 AAAGCTACAAATT
131 AAAGCTACAAATT
* * * * * *
3425426 ATGGCAGATCTTATCTTCTTGAAGTTACAATAGAGCAGATTGAAGCCATCAGCCTTATCTCCCTA
1 ATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTG
* * * * **
3425491 AAGTTGCAGCGGAGTAGACTGAAGACAGTGAATCTTATTTCCCTGACATTACAGTGGAATGGATT
66 AAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGACGTTGCAGTGGAACAGATT
*
3425556 AAAGGTACAAATT
131 AAAGCTACAAATT
* * *
3425569 ACTGTG--GATCTTATCTTCTTGAAGTTGCAGTGGAGCAGATAGAAGCCACCAGCCTTATCTTCC
1 A-TG-GCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
* * *
3425632 TGAAGTTGCAGTGGAGCAGACTGAAGACAGTGAATCTTATTTCCTTGACGTTGCAGTGGAACAGA
64 TGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGACGTTGCAGTGGAACAGA
3425697 TTAAAGCTACAAATT
129 TTAAAGCTACAAATT
* * * * *
3425712 ATGGCGGATCTTATTTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAGCCTTATCTCTCTG
1 ATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTG
* * * * * *
3425777 AAGTTGCAGCGGAGCAGACTAAAGACAACAAATCTTATTTCCCCGATGTTGCAGTGGAATAGATT
66 AAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGACGTTGCAGTGGAACAGATT
* * *
3425842 GAAGCTACGAGTT
131 AAAGCTACAAATT
* * * * * *
3425855 ATGGCGGATCTCATCTTCCAGAAGTTACAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCTTA
1 ATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTG
* * *
3425920 AAGTTGAAGCGGAGCAGACTGAAGACAGCGAATTTTATTTCCCT-AGCGTTGCAGTGGAACATAT
66 AAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGA-CGTTGCAGTGGAACAGAT
* *
3425984 TAAAACTATAAATT
130 TAAAGCTACAAATT
* * * * *
3425998 ATGGCAAATCTTATCTTCCTAAAGTTGCAATGGAGTAGATTGAAGCCACCAGCCTTATCTCCTTG
1 ATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTG
*
3426063 AAGTTGCAGTGGAGCAGACTGAAGACA
66 AAGTTGCAGCGGAGCAGACTGAAGACA
3426090 ACAAATCCCA
Statistics
Matches: 578, Mismatches: 81, Indels: 10
0.86 0.12 0.01
Matches are distributed among these distances:
141 1 0.00
142 3 0.01
143 571 0.99
144 2 0.00
145 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (143 bp):
ATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTG
AAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGACGTTGCAGTGGAACAGATT
AAAGCTACAAATT
Found at i:3425676 original size:44 final size:44
Alignment explanation
Indices: 3425576--3425697 Score: 131
Period size: 44 Copynumber: 2.8 Consensus size: 44
3425566 ATTACTGTGG
* *
3425576 ATCTTATCTTCTTGAAGTTGCAGTGGAGCAGATAGAAGCCACCA
1 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATAGAAGACACCA
** **
3425620 GCCTTATCTTCCTGAAGTTGCAGTGGAGCAGACT-GAAGACAGTGA
1 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGA-TAGAAGACA-CCA
* *
3425665 ATCTTAT-TTCCTTGACGTTGCAGTGGAACAGAT
1 ATCTTATCTTCC-TGAAGTTGCAGTGGAGCAGAT
3425698 TAAAGCTACA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
44 40 0.62
45 25 0.38
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.29
Consensus pattern (44 bp):
ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATAGAAGACACCA
Found at i:3425808 original size:99 final size:99
Alignment explanation
Indices: 3425622--3425809 Score: 227
Period size: 99 Copynumber: 1.9 Consensus size: 99
3425612 AGCCACCAGC
* * * *
3425622 CTTATCTTCCTGAAGTTGCAGTGGAGCAGACTGAAGACAGTGAATCTTATTTCCTTGACGTTGCA
1 CTTATCTTCCTGAAGTTGCAGTGGAGCAGACTGAAGACACTGAACCTTATCTCCTTGAAGTTGCA
* * *
3425687 GTGGAACAGATTAAAGCTACAAATTATGGCGGAT
66 GCGGAACAGACTAAAGCAACAAATTATGGCGGAT
* * * * *
3425721 CTTATTTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCCACT-AGCCTTATCT-CTCTGAAGTTGC
1 CTTATCTTCCTGAAGTTGCAGTGGAGCAGACTGAAGACACTGAACCTTATCTCCT-TGAAGTTGC
*
3425784 AGCGGAGCAGACTAAAGACAACAAAT
65 AGCGGAACAGACTAAAG-CAACAAAT
3425810 CTTATTTCCC
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
97 2 0.03
98 29 0.39
99 43 0.58
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (99 bp):
CTTATCTTCCTGAAGTTGCAGTGGAGCAGACTGAAGACACTGAACCTTATCTCCTTGAAGTTGCA
GCGGAACAGACTAAAGCAACAAATTATGGCGGAT
Found at i:3426070 original size:44 final size:42
Alignment explanation
Indices: 3426007--3426149 Score: 111
Period size: 44 Copynumber: 3.5 Consensus size: 42
3425997 TATGGCAAAT
*
3426007 CTTATCTTCCTAAAGTTGCAATGGAGTAGATTGAAGCCACCAGC
1 CTTATC-TCCTTAAGTTGC-ATGGAGTAGATTGAAGCCACCAGC
* * *
3426051 CTTATCTCCTTGAAGTTGCAGTGGAGCAGACTGAAG--A-CA-A
1 CTTATCTCCTT-AAGTTGCA-TGGAGTAGATTGAAGCCACCAGC
** * *
3426091 CAAATC-CCATATGTTG--TGGAGTAGATTGAAGCCACCAGC
1 CTTATCTCCTTAAGTTGCATGGAGTAGATTGAAGCCACCAGC
*
3426130 CTTACCTCCTTAAAGTTGCA
1 CTTATCTCCTT-AAGTTGCA
3426150 GCAGAGCAGA
Statistics
Matches: 73, Mismatches: 16, Indels: 21
0.66 0.15 0.19
Matches are distributed among these distances:
35 13 0.18
37 1 0.01
38 7 0.10
39 6 0.08
40 7 0.10
41 7 0.10
42 1 0.01
43 5 0.07
44 26 0.36
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (42 bp):
CTTATCTCCTTAAGTTGCATGGAGTAGATTGAAGCCACCAGC
Found at i:3426088 original size:429 final size:429
Alignment explanation
Indices: 3425283--3426089 Score: 1154
Period size: 429 Copynumber: 1.9 Consensus size: 429
3425273 TAGATCGAAG
3425283 ATGGCAGATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCTCTCTG
1 ATGGCAGATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCTCTCTG
* * * * * * *
3425348 AAGTTGCAGGGGAGCAGATTGAAGACAACGAATCTTATTTCCCTGACATTGTAGTGGAACGGATT
66 AAGTTGCAGCGGAGCAGACTAAAGACAACAAATCTTATTTCCCCGACATTGCAGTGGAACAGATT
* ** *
3425413 AAAGCTACAAATTATGGCAGATCTTATCTTCTTGAAGTTACAATAGAGCAGATTGAAGCCATCAG
131 AAAGCTACAAATTATGGCAGATCTCATCTTCCAGAAGTTACAATAGAGCAGATTGAAGCCACCAG
* * *
3425478 CCTTATCTCCCTAAAGTTGCAGCGGAGTAGACTGAAGACAGTGAATCTTATTTCCCTGACATTAC
196 CCTTATCTCCCTAAAGTTGAAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGACATTAC
** ** * * * *
3425543 AGTGGAATGGATTAAAGGTACAAATTACTGTGGATCTTATCTTCTTGAAGTTGCAGTGGAGCAGA
261 AGTGGAACAGATTAAAACTACAAATTACTGTGAATCTTATCTTCCTAAAGTTGCAATGGAGCAGA
3425608 TAGAAGCCACCAGCCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTGAAGACAGTGAATCTTATT
326 TAGAAGCCACCAGCCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTGAAGACAGTGAATCTTATT
3425673 TCCTTGACGTTGCAGTGGAACAGATTAAAGCTACAAATT
391 TCCTTGACGTTGCAGTGGAACAGATTAAAGCTACAAATT
* * * * *
3425712 ATGGCGGATCTTATTTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAGCCTTATCTCTCTG
1 ATGGCAGATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCTCTCTG
** *
3425777 AAGTTGCAGCGGAGCAGACTAAAGACAACAAATCTTATTTCCCCGATGTTGCAGTGGAATAGATT
66 AAGTTGCAGCGGAGCAGACTAAAGACAACAAATCTTATTTCCCCGACATTGCAGTGGAACAGATT
* * * * * *
3425842 GAAGCTACGAGTTATGGCGGATCTCATCTTCCAGAAGTTACAGTGGAGCAGATTGAAGCCACCAG
131 AAAGCTACAAATTATGGCAGATCTCATCTTCCAGAAGTTACAATAGAGCAGATTGAAGCCACCAG
* * * *
3425907 CCTTATCTCCTTAAAGTTGAAGCGGAGCAGACTGAAGACAGCGAATTTTATTTCCCT-AGCGTTG
196 CCTTATCTCCCTAAAGTTGAAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGA-CATTA
* * *
3425971 CAGTGGAACATATTAAAACTATAAATTA-TG-GCAAATCTTATCTTCCTAAAGTTGCAATGGAGT
260 CAGTGGAACAGATTAAAACTACAAATTACTGTG--AATCTTATCTTCCTAAAGTTGCAATGGAGC
*
3426034 AGATTGAAGCCACCAGCCTTATC-TCCTTGAAGTTGCAGTGGAGCAGACTGAAGACA
323 AGATAGAAGCCACCAGCCTTATCTTCC-TGAAGTTGCAGTGGAGCAGACTGAAGACA
3426090 ACAAATCCCA
Statistics
Matches: 330, Mismatches: 44, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
427 1 0.00
428 6 0.02
429 323 0.98
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (429 bp):
ATGGCAGATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCTCTCTG
AAGTTGCAGCGGAGCAGACTAAAGACAACAAATCTTATTTCCCCGACATTGCAGTGGAACAGATT
AAAGCTACAAATTATGGCAGATCTCATCTTCCAGAAGTTACAATAGAGCAGATTGAAGCCACCAG
CCTTATCTCCCTAAAGTTGAAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGACATTAC
AGTGGAACAGATTAAAACTACAAATTACTGTGAATCTTATCTTCCTAAAGTTGCAATGGAGCAGA
TAGAAGCCACCAGCCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTGAAGACAGTGAATCTTATT
TCCTTGACGTTGCAGTGGAACAGATTAAAGCTACAAATT
Found at i:3426159 original size:79 final size:79
Alignment explanation
Indices: 3426028--3426280 Score: 346
Period size: 79 Copynumber: 3.2 Consensus size: 79
3426018 AAAGTTGCAA
* *
3426028 TGGAGTAGATTGAAGCCACCAGCCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTGAAGACAACA
1 TGGAGTAGATTGAAGCCACCAGCCTTATCTCCTTAAAGTTGCAGCGGAGCAGACTGAAGACAACA
* *
3426093 AATCCCATATGTTG
66 AATCCCATCTGTAG
* *
3426107 TGGAGTAGATTGAAGCCACCAGCCTTACCTCCTTAAAGTTGCAGCAGAGCAGACTGAAGACAACA
1 TGGAGTAGATTGAAGCCACCAGCCTTATCTCCTTAAAGTTGCAGCGGAGCAGACTGAAGACAACA
*
3426172 AATCCCATCTGCAG
66 AATCCCATCTGTAG
** * * * * **
3426186 TGGAACAGATTGAAGTCACCAGCCTTATCTCCCTAAAGCTGCAGCGGAGCAGACTGAAGATAGTA
1 TGGAGTAGATTGAAGCCACCAGCCTTATCTCCTTAAAGTTGCAGCGGAGCAGACTGAAGACAACA
*
3426251 AATCCCATCTCTAG
66 AATCCCATCTGTAG
3426265 TAGG-GTAGATTGAAGC
1 T-GGAGTAGATTGAAGC
3426281 TACTAATCCT
Statistics
Matches: 151, Mismatches: 22, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
79 149 0.99
80 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (79 bp):
TGGAGTAGATTGAAGCCACCAGCCTTATCTCCTTAAAGTTGCAGCGGAGCAGACTGAAGACAACA
AATCCCATCTGTAG
Found at i:3426899 original size:23 final size:23
Alignment explanation
Indices: 3426867--3426912 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3426857 AAGGTGGTTT
3426867 TCTTTCTG-TTTCTATTTTTTTCA
1 TCTTTCTGTTTTCT-TTTTTTTCA
*
3426890 TCTTTTTGTTTTCTTTTTTTTCA
1 TCTTTCTGTTTTCTTTTTTTTCA
3426913 AAGGAAGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.07, C:0.15, G:0.04, T:0.74
Consensus pattern (23 bp):
TCTTTCTGTTTTCTTTTTTTTCA
Found at i:3427553 original size:3 final size:3
Alignment explanation
Indices: 3427545--3427571 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3427535 TATATTTTAC
3427545 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
3427572 CATTTATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3427659 original size:71 final size:71
Alignment explanation
Indices: 3427575--3427717 Score: 277
Period size: 71 Copynumber: 2.0 Consensus size: 71
3427565 TTATTATCAT
3427575 TTATCAATATATTTGATTTCAAATTATATTCGTAATTTCATTTCTACTTTAACTTGTTTCTTTGT
1 TTATCAATATATTTGATTTCAAATTATATTCGTAATTTCATTTCTACTTTAACTTGTTTCTTTGT
3427640 TTTTGA
66 TTTTGA
*
3427646 TTATCTATATATTTGATTTCAAATTATATTCGTAATTTCATTTCTACTTTAACTTGTTTCTTTGT
1 TTATCAATATATTTGATTTCAAATTATATTCGTAATTTCATTTCTACTTTAACTTGTTTCTTTGT
3427711 TTTTGA
66 TTTTGA
3427717 T
1 T
3427718 CTTTTACAAA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.24, C:0.11, G:0.07, T:0.57
Consensus pattern (71 bp):
TTATCAATATATTTGATTTCAAATTATATTCGTAATTTCATTTCTACTTTAACTTGTTTCTTTGT
TTTTGA
Found at i:3431204 original size:42 final size:43
Alignment explanation
Indices: 3431103--3431344 Score: 332
Period size: 43 Copynumber: 5.7 Consensus size: 43
3431093 TGTGTTATCG
* * * * *
3431103 TGTAAGACCACGTATGGGATGTTGGCATCGACT-TATGATTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATC-AATATTTGA-TTACA
3431147 TGTAAGACCACGTCTGGGACGTTGGCATC-ATATTTGATTACA
1 TGTAAGACCACGTCTGGGACGTTGGCATCAATATTTGATTACA
**
3431189 TGTAAGACCTTGTCTGGGACAG-TGGCATCAATATTTGATTACA
1 TGTAAGACCACGTCTGGGAC-GTTGGCATCAATATTTGATTACA
3431232 TGTAAGACCACGTCTGGGACGTTGGCATC-ATATTTGATTACA
1 TGTAAGACCACGTCTGGGACGTTGGCATCAATATTTGATTACA
**
3431274 TGTAAGACCTTGTCTGGGACAG-TGGCATCAATATTTGATTACA
1 TGTAAGACCACGTCTGGGAC-GTTGGCATCAATATTTGATTACA
3431317 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
3431345 TGTACGAGCT
Statistics
Matches: 178, Mismatches: 13, Indels: 15
0.86 0.06 0.07
Matches are distributed among these distances:
42 70 0.39
43 81 0.46
44 27 0.15
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCAATATTTGATTACA
Found at i:3431257 original size:85 final size:85
Alignment explanation
Indices: 3431142--3431344 Score: 397
Period size: 85 Copynumber: 2.4 Consensus size: 85
3431132 GACTTATGAT
*
3431142 TTACGTGTAAGACCACGTCTGGGACGTTGGCATCATATTTGATTACATGTAAGACCTTGTCTGGG
1 TTACATGTAAGACCACGTCTGGGACGTTGGCATCATATTTGATTACATGTAAGACCTTGTCTGGG
3431207 ACAGTGGCATCAATATTTGA
66 ACAGTGGCATCAATATTTGA
3431227 TTACATGTAAGACCACGTCTGGGACGTTGGCATCATATTTGATTACATGTAAGACCTTGTCTGGG
1 TTACATGTAAGACCACGTCTGGGACGTTGGCATCATATTTGATTACATGTAAGACCTTGTCTGGG
3431292 ACAGTGGCATCAATATTTGA
66 ACAGTGGCATCAATATTTGA
3431312 TTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 TTACATGTAAGACCACGTCTGGGACGTTGGCAT
3431345 TGTACGAGCT
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 117 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (85 bp):
TTACATGTAAGACCACGTCTGGGACGTTGGCATCATATTTGATTACATGTAAGACCTTGTCTGGG
ACAGTGGCATCAATATTTGA
Found at i:3461900 original size:36 final size:36
Alignment explanation
Indices: 3461853--3461923 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
3461843 TCCTCTCCTC
3461853 AGTGAATCAGGTTAATGTACACACTTATTACACATA
1 AGTGAATCAGGTTAATGTACACACTTATTACACATA
3461889 AGTGAATCAGGTTAATGTACACACTTATTACACAT
1 AGTGAATCAGGTTAATGTACACACTTATTACACAT
3461924 TATTTTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (36 bp):
AGTGAATCAGGTTAATGTACACACTTATTACACATA
Found at i:3464789 original size:27 final size:27
Alignment explanation
Indices: 3464744--3464825 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
3464734 CTTAGTGTTC
*
3464744 CATCGGACTATC-CTATGTTTAATGTCT
1 CATCGGACTATCTC-GTGTTTAATGTCT
* *
3464771 CGTCAGG-CTATCTCGTGTTTAATGTCC
1 CATC-GGACTATCTCGTGTTTAATGTCT
*
3464798 CATCGGACTATCTTGTGTTTAATGTCT
1 CATCGGACTATCTCGTGTTTAATGTCT
3464825 C
1 C
3464826 TTTGAACTGT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
26 2 0.04
27 41 0.89
28 3 0.07
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.40
Consensus pattern (27 bp):
CATCGGACTATCTCGTGTTTAATGTCT
Found at i:3465031 original size:45 final size:44
Alignment explanation
Indices: 3464944--3465130 Score: 169
Period size: 45 Copynumber: 4.2 Consensus size: 44
3464934 TGGACTTAGT
* * * * **
3464944 CTTA-TTTACCATGATGCCATAACGTTTTTTAGCCATCATCTTA
1 CTTATTTTATCATGATGCCATAACATCTTTTAGCTATGGTCTTA
* * * *
3464987 CTTATTTATATCATGATGCGATAACATCCTTCAACTATGGTCTTA
1 CTTATTT-TATCATGATGCCATAACATCTTTTAGCTATGGTCTTA
* * * * *
3465032 CTTATCTTTACCATGGTGCCATAACATCTTTTAGTTATTGTCTAA
1 CTTAT-TTTATCATGATGCCATAACATCTTTTAGCTATGGTCTTA
* * * *
3465077 CATATTTTTATCATGAAGCTATAGCATCTTTTAGCTATGGTCTTA
1 CTTA-TTTTATCATGATGCCATAACATCTTTTAGCTATGGTCTTA
3465122 CTTATTTTA
1 CTTATTTTA
3465131 GGAATATAAC
Statistics
Matches: 111, Mismatches: 29, Indels: 7
0.76 0.20 0.05
Matches are distributed among these distances:
43 4 0.04
44 7 0.06
45 97 0.87
46 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.44
Consensus pattern (44 bp):
CTTATTTTATCATGATGCCATAACATCTTTTAGCTATGGTCTTA
Found at i:3465064 original size:90 final size:89
Alignment explanation
Indices: 3464944--3465130 Score: 214
Period size: 90 Copynumber: 2.1 Consensus size: 89
3464934 TGGACTTAGT
* * * * *
3464944 CTTA-TTTACCATGATGCCATAACGTTTTTTAGCCATCATCTTACTTATTTATATCATGATGCGA
1 CTTATTTTACCATGATGCCATAACATCTTTTAGCCATCATCTAACATATTTATATCATGAAGCGA
3465008 TAACATCCTTCAACTATGGTCTTA
66 TAACATCCTTCAACTATGGTCTTA
* ** ** * *
3465032 CTTATCTTTACCATGGTGCCATAACATCTTTTAGTTATTGTCTAACATATTTTTATCATGAAGCT
1 CTTAT-TTTACCATGATGCCATAACATCTTTTAGCCATCATCTAACATATTTATATCATGAAGCG
* * * *
3465097 ATAGCATCTTTTAGCTATGGTCTTA
65 ATAACATCCTTCAACTATGGTCTTA
3465122 CTTATTTTA
1 CTTATTTTA
3465131 GGAATATAAC
Statistics
Matches: 81, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
88 4 0.05
89 4 0.05
90 73 0.90
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.44
Consensus pattern (89 bp):
CTTATTTTACCATGATGCCATAACATCTTTTAGCCATCATCTAACATATTTATATCATGAAGCGA
TAACATCCTTCAACTATGGTCTTA
Found at i:3465731 original size:32 final size:32
Alignment explanation
Indices: 3465695--3465761 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
3465685 TTCATTCTCT
* * *
3465695 TTATCCCTACGCTTATAGAAGGATTAAGAACC
1 TTATCCCTACACTTATAGAAGGACTAAAAACC
* *
3465727 TTATCCTTACATTTATAGAAGGACTAAAAACC
1 TTATCCCTACACTTATAGAAGGACTAAAAACC
3465759 TTA
1 TTA
3465762 CTTGTTCACT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.31
Consensus pattern (32 bp):
TTATCCCTACACTTATAGAAGGACTAAAAACC
Found at i:3481551 original size:40 final size:40
Alignment explanation
Indices: 3481503--3481687 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
3481493 GCTACTCATT
*
3481503 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
3481543 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * *
3481583 CAAATGCCTTCGGG-CTTAGCCCAGAATTAGCATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
3481622 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
3481663 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
3481688 CATCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
38 2 0.02
39 31 0.26
40 75 0.62
41 13 0.11
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:3481620 original size:79 final size:80
Alignment explanation
Indices: 3481537--3481684 Score: 194
Period size: 79 Copynumber: 1.9 Consensus size: 80
3481527 GTTATAGTAA
* * *
3481537 CTCGCACAATTGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCACAAATGCCTTCGGG-CT
1 CTCGCACAAATGCCTTC-GGATCTTAACCCGGATATAGTAACTTAGCACAAA-GCCTTCGGGACT
3481599 TAGCCCAGAATTAGCAT
64 TAGCCCAGAATTAGCAT
** * *
3481616 CTCGCACAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTA
1 CTCGCACAAATGCCTTCGGATCTTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTA
3481681 GCCC
66 GCCC
3481685 GGACATCATT
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.05
79 40 0.68
80 16 0.27
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (80 bp):
CTCGCACAAATGCCTTCGGATCTTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTA
GCCCAGAATTAGCAT
Found at i:3489678 original size:39 final size:40
Alignment explanation
Indices: 3489561--3489745 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
3489551 GCTACTCGTT
*
3489561 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
3489601 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
3489641 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
3489680 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
*
3489721 CAAA-GCCTTCGGGACTTAGCTCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
3489746 CATCATTCAA
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 33 0.27
40 76 0.61
41 13 0.10
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:3489679 original size:79 final size:82
Alignment explanation
Indices: 3489561--3489745 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 82
3489551 GCTACTCGTT
* * *
3489561 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
3489624 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
3489641 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
3489704 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
*
3489721 CAAA-GCCTTCGGGACTTAGCTCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
3489746 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.60
80 33 0.37
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:3496547 original size:27 final size:27
Alignment explanation
Indices: 3496517--3496686 Score: 178
Period size: 27 Copynumber: 6.3 Consensus size: 27
3496507 GTAAAATGGC
* * * *
3496517 AATTTTACCCCACAAGGGTATCTCGGT
1 AATTCTACCCTACAGGGGTATTTCGGT
**
3496544 AATTCTACCCTACAGGGGTATTTCAAT
1 AATTCTACCCTACAGGGGTATTTCGGT
** * *
3496571 TTTTCCACCCTACAAGGGTATTTCGGT
1 AATTCTACCCTACAGGGGTATTTCGGT
* *
3496598 AATTCTATCCTACAGGGGTATTTCGCT
1 AATTCTACCCTACAGGGGTATTTCGGT
* **
3496625 AATTCTACCCTACAGGGGTAATTCAAT
1 AATTCTACCCTACAGGGGTATTTCGGT
* *
3496652 AATTCTACCCTACAGAGGTATTTTGGT
1 AATTCTACCCTACAGGGGTATTTCGGT
*
3496679 TATTCTAC
1 AATTCTAC
3496687 AACTTATCCA
Statistics
Matches: 115, Mismatches: 28, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 115 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (27 bp):
AATTCTACCCTACAGGGGTATTTCGGT
Found at i:3496629 original size:81 final size:81
Alignment explanation
Indices: 3496532--3496685 Score: 220
Period size: 81 Copynumber: 1.9 Consensus size: 81
3496522 TACCCCACAA
* * **
3496532 GGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCAATTTTTCCACCCTACA-AGGGTATTTCG
1 GGGTATCTCGCTAATTCTACCCTACAGGGGTAATTCAATAATTCCACCCTACAGA-GGTATTTCG
3496596 GTAATTCTATCCTACAG
65 GTAATTCTATCCTACAG
* * *
3496613 GGGTATTTCGCTAATTCTACCCTACAGGGGTAATTCAATAATTCTACCCTACAGAGGTATTTTGG
1 GGGTATCTCGCTAATTCTACCCTACAGGGGTAATTCAATAATTCCACCCTACAGAGGTATTTCGG
*
3496678 TTATTCTA
66 TAATTCTA
3496686 CAACTTATCC
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
81 63 0.98
82 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (81 bp):
GGGTATCTCGCTAATTCTACCCTACAGGGGTAATTCAATAATTCCACCCTACAGAGGTATTTCGG
TAATTCTATCCTACAG
Found at i:3500361 original size:44 final size:44
Alignment explanation
Indices: 3500292--3500378 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
3500282 ATGTATGAGT
*
3500292 CATCCGAGCTCGTTGAGTTGTTCCGAGTTCATTATGGATGCGAG
1 CATCCGAGCTCGTTGAGTTGGTCCGAGTTCATTATGGATGCGAG
*
3500336 CATCTGAGCTCGTTGAGTTGGTCCGAGTTCATTATGGATGCGA
1 CATCCGAGCTCGTTGAGTTGGTCCGAGTTCATTATGGATGCGA
3500379 TACATGTAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.18, C:0.20, G:0.30, T:0.32
Consensus pattern (44 bp):
CATCCGAGCTCGTTGAGTTGGTCCGAGTTCATTATGGATGCGAG
Found at i:3508661 original size:32 final size:32
Alignment explanation
Indices: 3508620--3508684 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
3508610 TGAGACTAAT
3508620 AGCAGGAATGAGGAATATAATCTCCTCAAACC
1 AGCAGGAATGAGGAATATAATCTCCTCAAACC
3508652 AGCAGGAATGAGGAATATAATCTCCTCAAACC
1 AGCAGGAATGAGGAATATAATCTCCTCAAACC
3508684 A
1 A
3508685 CCATGATCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (32 bp):
AGCAGGAATGAGGAATATAATCTCCTCAAACC
Found at i:3517242 original size:40 final size:40
Alignment explanation
Indices: 3517159--3517339 Score: 172
Period size: 40 Copynumber: 4.5 Consensus size: 40
3517149 AATCAAGCAT
** ** * *
3517159 CTTCGGGGTTTAG-CCGGATATAAACACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
3517197 CTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
3517237 CTTCGGGACTTAGCCCGGATATAGTCGA-TAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * * * *
3517277 CTTC-GAATCTTAGTCCGGATGTAGTCGCTTAGCACAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCAC-TAGCACAAATGC
3517318 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
3517340 CATTCGAGTA
Statistics
Matches: 115, Mismatches: 21, Indels: 11
0.78 0.14 0.07
Matches are distributed among these distances:
38 10 0.09
39 17 0.15
40 58 0.50
41 28 0.24
42 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:3518870 original size:25 final size:25
Alignment explanation
Indices: 3518842--3518892 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
3518832 AATTACATAT
3518842 ATTAGACAATAAATATCACATTCAA
1 ATTAGACAATAAATATCACATTCAA
3518867 ATTAGACAATAAATATCACATTCAA
1 ATTAGACAATAAATATCACATTCAA
3518892 A
1 A
3518893 CATTTCGGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.27
Consensus pattern (25 bp):
ATTAGACAATAAATATCACATTCAA
Found at i:3523404 original size:100 final size:100
Alignment explanation
Indices: 3523280--3523480 Score: 402
Period size: 100 Copynumber: 2.0 Consensus size: 100
3523270 GATAGTGTTG
3523280 TCCAACCAAAATTCAGCTTGCTTGGCATCATCGCTGTCTGTAGCTTTAAATTTAGTAGCCCCGTG
1 TCCAACCAAAATTCAGCTTGCTTGGCATCATCGCTGTCTGTAGCTTTAAATTTAGTAGCCCCGTG
3523345 TTTTCAGATTCTGTCAACTGGGGGCTTATTTGACC
66 TTTTCAGATTCTGTCAACTGGGGGCTTATTTGACC
3523380 TCCAACCAAAATTCAGCTTGCTTGGCATCATCGCTGTCTGTAGCTTTAAATTTAGTAGCCCCGTG
1 TCCAACCAAAATTCAGCTTGCTTGGCATCATCGCTGTCTGTAGCTTTAAATTTAGTAGCCCCGTG
3523445 TTTTCAGATTCTGTCAACTGGGGGCTTATTTGACC
66 TTTTCAGATTCTGTCAACTGGGGGCTTATTTGACC
3523480 T
1 T
3523481 TATTTGGTCA
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 101 1.00
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (100 bp):
TCCAACCAAAATTCAGCTTGCTTGGCATCATCGCTGTCTGTAGCTTTAAATTTAGTAGCCCCGTG
TTTTCAGATTCTGTCAACTGGGGGCTTATTTGACC
Found at i:3525289 original size:39 final size:40
Alignment explanation
Indices: 3525244--3525411 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
3525234 CGGGGTTTAG
* * *
3525244 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
3525283 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
3525323 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
3525363 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
3525404 CCGGATAT
1 CCGGATAT
3525412 CATTCGAGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.17
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:3525394 original size:41 final size:40
Alignment explanation
Indices: 3525267--3525411 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
3525257 CTCGCACAAG
* * * * *
3525267 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
3525307 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
3525347 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
3525388 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
3525412 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:3530415 original size:36 final size:36
Alignment explanation
Indices: 3530375--3530447 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
3530365 ATGCATGATG
3530375 TATGGCTAAATTAATAATTTAACTAGCAATGGTACA
1 TATGGCTAAATTAATAATTTAACTAGCAATGGTACA
* *
3530411 TATGGCTAAATTAATAATTTGACTAGTAATGGTACA
1 TATGGCTAAATTAATAATTTAACTAGCAATGGTACA
3530447 T
1 T
3530448 TTTCACTACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36
Consensus pattern (36 bp):
TATGGCTAAATTAATAATTTAACTAGCAATGGTACA
Found at i:3531320 original size:34 final size:34
Alignment explanation
Indices: 3531282--3531377 Score: 165
Period size: 34 Copynumber: 2.8 Consensus size: 34
3531272 CAGTAACAGT
3531282 AGCAGTCTGGGCCTTAGCCCATTTCAGTGATAAA
1 AGCAGTCTGGGCCTTAGCCCATTTCAGTGATAAA
*
3531316 AGCAGTCTGGGCCTTAGCCCTTTTCAGTGATAAA
1 AGCAGTCTGGGCCTTAGCCCATTTCAGTGATAAA
* *
3531350 ATCAGTCTGGGCCTTAGCCCATATCAGT
1 AGCAGTCTGGGCCTTAGCCCATTTCAGT
3531378 ACAGTATGCA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (34 bp):
AGCAGTCTGGGCCTTAGCCCATTTCAGTGATAAA
Found at i:3533095 original size:27 final size:27
Alignment explanation
Indices: 3533057--3533124 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
3533047 AGAGCATACG
* *
3533057 TGGGCCAAAGCCCATTACA-ATATCATT
1 TGGGCCAAAGCCCATAACAGA-ATCAAT
*
3533084 TGGGCCACAGCCCATAACAGAATCAAT
1 TGGGCCAAAGCCCATAACAGAATCAAT
*
3533111 TGGGCC-TAGCCCAT
1 TGGGCCAAAGCCCAT
3533125 CCTAGCCTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 7 0.19
27 28 0.78
28 1 0.03
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (27 bp):
TGGGCCAAAGCCCATAACAGAATCAAT
Found at i:3533572 original size:22 final size:22
Alignment explanation
Indices: 3533524--3533582 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
3533514 GTAAATACGT
*
3533524 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
3533546 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
3533568 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
3533583 GATCAGAATA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:3533773 original size:40 final size:41
Alignment explanation
Indices: 3533729--3533807 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
3533719 TAAAAGCCAC
3533729 CGGTGGATCCAC-ATCATCAAGCAACCATGCGATCCTCAAT
1 CGGTGGATCCACGATCATCAAGCAACCATGCGATCCTCAAT
* *
3533769 CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCA
1 CGGTGGATCCACGATCATCAAGCAACCATGCGATCCTCA
3533808 TATACTTCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 12 0.33
41 24 0.67
ACGTcount: A:0.27, C:0.33, G:0.22, T:0.19
Consensus pattern (41 bp):
CGGTGGATCCACGATCATCAAGCAACCATGCGATCCTCAAT
Found at i:3534073 original size:27 final size:27
Alignment explanation
Indices: 3534043--3534562 Score: 409
Period size: 27 Copynumber: 19.3 Consensus size: 27
3534033 AGACTACAAA
* *
3534043 GGTATTTCGATAATTCTACACAA-AAAG
1 GGTATTTCGATAATTTTACA-AATCAAG
* *
3534070 GGTATTTCGATAATTTTATAAATCGAG
1 GGTATTTCGATAATTTTACAAATCAAG
3534097 GGTATTTCGATAATTTTACAAATCAAG
1 GGTATTTCGATAATTTTACAAATCAAG
* * *
3534124 AGTATTTCGGTAATTTTACAAATCGAG
1 GGTATTTCGATAATTTTACAAATCAAG
* *
3534151 GGTATTTCGATAATTCTAC-ACTGCAAG
1 GGTATTTCGATAATTTTACAAAT-CAAG
*
3534178 GGTATTTCGATAATTTTACAAAT-TAG
1 GGTATTTCGATAATTTTACAAATCAAG
* * **
3534204 GGACATTTTGATAATTTTACAAAT-TGG
1 GG-TATTTCGATAATTTTACAAATCAAG
* *
3534231 AGGCATTTCGAAAATTTTACAAATCAAG
1 -GGTATTTCGATAATTTTACAAATCAAG
** * *
3534259 GGTATTTTAATAATTCTAC-ACTACAAG
1 GGTATTTCGATAATTTTACAAAT-CAAG
*
3534286 GGTATTTTGATAATTTTACAAATCGAA-
1 GGTATTTCGATAATTTTACAAATC-AAG
* *
3534313 GGTATTTCGGTAATTTTACAAATTGAA-
1 GGTATTTCGATAATTTTACAAA-TCAAG
* * *
3534340 GGTATTTCGATAATTCTAC-ACTACGAG
1 GGTATTTCGATAATTTTACAAAT-CAAG
* * * *
3534367 GGTGTTTCGGTTATTTTACAAATCAAA
1 GGTATTTCGATAATTTTACAAATCAAG
* *
3534394 GGTATCTCGTTAATTTTACAAATCGAA-
1 GGTATTTCGATAATTTTACAAATC-AAG
* * *
3534421 GGTATTTCGGTAATTCTAC-ACTACAAG
1 GGTATTTCGATAATTTTACAAAT-CAAG
* *
3534448 GGTATTTCAATAATTTTACAAATC-GG
1 GGTATTTCGATAATTTTACAAATCAAG
* *
3534474 GGTATTTC-AGTAATTTTCCAAA-CTAGG
1 GGTATTTCGA-TAATTTTACAAATC-AAG
* * *
3534501 GGTATTTTGGTAATTTTACTAATCAAG
1 GGTATTTCGATAATTTTACAAATCAAG
* * ** * *
3534528 GGTATTTTGGTAATTTTGTAAACCAAT
1 GGTATTTCGATAATTTTACAAATCAAG
3534555 GGTATTTC
1 GGTATTTC
3534563 AGTAATTCTA
Statistics
Matches: 398, Mismatches: 73, Indels: 44
0.77 0.14 0.09
Matches are distributed among these distances:
25 3 0.01
26 36 0.09
27 342 0.86
28 17 0.04
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (27 bp):
GGTATTTCGATAATTTTACAAATCAAG
Found at i:3539629 original size:43 final size:43
Alignment explanation
Indices: 3539571--3539655 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
3539561 AGGTCACATG
3539571 TGTGGTTCCAAGTGAAGGACACCATGCATACAAGAGAGCTACA
1 TGTGGTTCCAAGTGAAGGACACCATGCATACAAGAGAGCTACA
*
3539614 TGTGGTTCCAAGTGAAGGACACCATGTATACAAGAGAGCTAC
1 TGTGGTTCCAAGTGAAGGACACCATGCATACAAGAGAGCTAC
3539656 GAAATAAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (43 bp):
TGTGGTTCCAAGTGAAGGACACCATGCATACAAGAGAGCTACA
Found at i:3546333 original size:50 final size:50
Alignment explanation
Indices: 3546215--3546609 Score: 373
Period size: 50 Copynumber: 7.8 Consensus size: 50
3546205 GTTGTGAGAA
* * * *
3546215 CACATGTGTAGTACTATGTGCAAGCTACTATGTGTTTAAGACAG-TT-TTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTG--T-A-CCAGATTGTTAGGT
* *
3546267 CACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATTGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
** * * * * * *
3546317 TGCATGTGTAGTACTAAGTGCAGGCTACTATGAGTACCCGATAGCTTCGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTG-TTAGGT
* *
3546368 CACGTGTGTAGTACTAAGTACAGGCTACTACGTGTACCAGATTGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
* * * ** * * *
3546418 CGCATGTGCAGTACTAAGTGCAGGCTACTATGCATACTC-GATAGCTTTGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-CAGATTG-TTAGGT
* * * *
3546469 CACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTATCAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
* * * *
3546519 TACGTGTGTAGTACTAAGTGTAGGCTACTACATGTACCAGATTGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
* * * * *
3546569 CGCATGTGTAGAACTAAGTGTAGGCTACTATGCGTACCAGA
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA
3546610 GAGCTTCAGT
Statistics
Matches: 277, Mismatches: 60, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
48 3 0.01
49 3 0.01
50 164 0.59
51 78 0.28
52 29 0.10
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
Found at i:3546396 original size:101 final size:101
Alignment explanation
Indices: 3546266--3546548 Score: 442
Period size: 101 Copynumber: 2.8 Consensus size: 101
3546256 CAGTTTTAGG
*
3546266 TCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATTGTTAGGTTGCATGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGTTGCATGTGTAGTAC
3546331 TAAGTGCAGGCTACTATG-AGTACCCGATAGCTTCGA
66 TAAGTGCAGGCTACTATGCA-TACCCGATAGCTTCGA
* * *
3546367 TCACGTGTGTAGTACTAAGTACAGGCTACTACGTGTACCAGATTGTTAGGTCGCATGTGCAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGTTGCATGTGTAGTAC
* *
3546432 TAAGTGCAGGCTACTATGCATACTCGATAGCTTTGA
66 TAAGTGCAGGCTACTATGCATACCCGATAGCTTCGA
* * * * *
3546468 TCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTATCAGATGGTTAGGTTACGTGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGTTGCATGTGTAGTAC
*
3546533 TAAGTGTAGGCTACTA
66 TAAGTGCAGGCTACTA
3546549 CATGTACCAG
Statistics
Matches: 166, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
101 165 0.99
102 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (101 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGTTGCATGTGTAGTAC
TAAGTGCAGGCTACTATGCATACCCGATAGCTTCGA
Found at i:3546615 original size:151 final size:152
Alignment explanation
Indices: 3546261--3546615 Score: 437
Period size: 151 Copynumber: 2.3 Consensus size: 152
3546251 TAAGACAGTT
* * * * * * **
3546261 TTAGGTCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATTG-TTAGGTTGCATGTG
1 TTAGGTCGCATGTGTAGTACTAAGTGTAGGCTACTATGCGTACCAGATAGCTTAGATCACATGTG
* * * *
3546325 TAGTACTAAGTGCAGGCTACTATGAGTACCCGATAGCTTCGATCACGTGTGTAGTACTAAGTACA
66 TAGTACTAAGTGCAAGCTACTACGAGTACCAGATAGCTTAGATCACGTGTGTAGTACTAAGTACA
*
3546390 GGCTACTACGTGTACCAGATTG
131 GGCTACTACATGTACCAGATTG
* * * * *
3546412 TTAGGTCGCATGTGCAGTACTAAGTGCAGGCTACTATGCATACTC-GATAGCTTTGATCACGTGT
1 TTAGGTCGCATGTGTAGTACTAAGTGTAGGCTACTATGCGTAC-CAGATAGCTTAGATCACATGT
* * * * * **
3546476 GTAGTACTAAGTGCAAGCTACTACGTGTATCAGAT-GGTTAGGTTACGTGTGTAGTACTAAGTGT
65 GTAGTACTAAGTGCAAGCTACTACGAGTACCAGATAGCTTAGATCACGTGTGTAGTACTAAGTAC
3546540 AGGCTACTACATGTACCAGATTG
130 AGGCTACTACATGTACCAGATTG
* *
3546563 TTAGGTCGCATGTGTAGAACTAAGTGTAGGCTACTATGCGTACCAGAGAGCTT
1 TTAGGTCGCATGTGTAGTACTAAGTGTAGGCTACTATGCGTACCAGATAGCTT
3546616 CAGTTACAAG
Statistics
Matches: 171, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
150 1 0.01
151 131 0.77
152 39 0.23
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (152 bp):
TTAGGTCGCATGTGTAGTACTAAGTGTAGGCTACTATGCGTACCAGATAGCTTAGATCACATGTG
TAGTACTAAGTGCAAGCTACTACGAGTACCAGATAGCTTAGATCACGTGTGTAGTACTAAGTACA
GGCTACTACATGTACCAGATTG
Done.