Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 14 of 117
Found at i:1439653 original size:5 final size:5
Alignment explanation
Indices: 1439630--1439669 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
1439620 GCTCGGATCG
*
1439630 CGGCT CGGCT TGG-T GCGGCT CGGCT CGGCT CGGCT CGGCT
1 CGGCT CGGCT CGGCT -CGGCT CGGCT CGGCT CGGCT CGGCT
1439670 TGGAGGGGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 1 0.03
5 29 0.94
6 1 0.03
ACGTcount: A:0.00, C:0.35, G:0.42, T:0.23
Consensus pattern (5 bp):
CGGCT
Found at i:1439679 original size:15 final size:15
Alignment explanation
Indices: 1439629--1439679 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
1439619 GGCTCGGATC
*
1439629 GCGGCTCGGCTTGGT
1 GCGGCTCGGCTTGGA
* *
1439644 GCGGCTCGGCTCGGC
1 GCGGCTCGGCTTGGA
*
1439659 TCGGCTCGGCTTGGA
1 GCGGCTCGGCTTGGA
*
1439674 GGGGCT
1 GCGGCT
1439680 GAGACGCGCG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.02, C:0.29, G:0.47, T:0.22
Consensus pattern (15 bp):
GCGGCTCGGCTTGGA
Found at i:1439909 original size:19 final size:19
Alignment explanation
Indices: 1439881--1439924 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1439871 AACGCCGGTA
*
1439881 CCGGATTCTGGAAATTTCG
1 CCGGAATCTGGAAATTTCG
*
1439900 CCGGAATCTGGGAATTTCG
1 CCGGAATCTGGAAATTTCG
*
1439919 TCGGAA
1 CCGGAA
1439925 ATTGGCCGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (19 bp):
CCGGAATCTGGAAATTTCG
Found at i:1439934 original size:11 final size:11
Alignment explanation
Indices: 1439920--1439945 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1439910 GGAATTTCGT
1439920 CGGAAATTGGC
1 CGGAAATTGGC
1439931 CGGAAATTGGC
1 CGGAAATTGGC
1439942 CGGA
1 CGGA
1439946 TGGTCGCCGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.19, G:0.38, T:0.15
Consensus pattern (11 bp):
CGGAAATTGGC
Found at i:1440024 original size:31 final size:31
Alignment explanation
Indices: 1439986--1440058 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
1439976 AAACTGGGTC
*
1439986 TGTCGCCGGAAACTTC-AAAGTTCGCCGAAAT
1 TGTCGCCGGAAAATTCAAAAG-TCGCCGAAAT
*
1440017 TGTCGCCGGAAAATTCAAAAGTCGCCGGAAT
1 TGTCGCCGGAAAATTCAAAAGTCGCCGAAAT
*
1440048 TTTCGCCGGAA
1 TGTCGCCGGAA
1440059 TCTGGAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 34 0.89
32 4 0.11
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (31 bp):
TGTCGCCGGAAAATTCAAAAGTCGCCGAAAT
Found at i:1440575 original size:40 final size:41
Alignment explanation
Indices: 1440474--1440575 Score: 113
Period size: 40 Copynumber: 2.5 Consensus size: 41
1440464 TAAAAAAAAA
* *
1440474 AATAATAATAATAATAAATATATAACTATATACATATAAATCT
1 AATAATAATAA-AATAAATAAATAAATATATACATATAAA-CT
*
1440517 AAT-CTAATAAAA-AAATAAATAAATATATACATA-ATAA-T
1 AATAATAATAAAATAAATAAATAAATATATACATATA-AACT
*
1440555 AATAATAATAAAATACATAAA
1 AATAATAATAAAATAAATAAA
1440576 ATACAAAAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
38 4 0.08
39 9 0.18
40 27 0.53
41 2 0.04
42 6 0.12
43 3 0.06
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (41 bp):
AATAATAATAAAATAAATAAATAAATATATACATATAAACT
Found at i:1440768 original size:1 final size:1
Alignment explanation
Indices: 1440758--1440871 Score: 93
Period size: 1 Copynumber: 114.0 Consensus size: 1
1440748 CAACTCAACA
* ** *** * * *
1440758 TTTTTATTTTTTGATTTTTTTTTTTTAAATTTTTGTTTTTTTGTTTTTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * *
1440823 TGTTTTTTTGTTTTTTTGTTTTTTATTTTTTATTTTTTATTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1440872 GCCGAAGCTC
Statistics
Matches: 88, Mismatches: 25, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 88 1.00
ACGTcount: A:0.07, C:0.00, G:0.06, T:0.87
Consensus pattern (1 bp):
T
Found at i:1440776 original size:14 final size:14
Alignment explanation
Indices: 1440757--1440867 Score: 106
Period size: 14 Copynumber: 7.9 Consensus size: 14
1440747 TCAACTCAAC
*
1440757 ATTTTTATTTTTTG
1 ATTTTTTTTTTTTG
*
1440771 ATTTTTTTTTTTTAA
1 ATTTTTTTTTTTT-G
1440786 ATTTTTGTTTTTTTG
1 ATTTTT-TTTTTTTG
*
1440801 TTTTTTTTTTTTTG
1 ATTTTTTTTTTTTG
1440815 -TTTTTTTTTGTTT-
1 ATTTTTTTTT-TTTG
*
1440828 -TTTTGTTTTTTTG
1 ATTTTTTTTTTTTG
1440841 -TTTTTTATTTTTT-
1 ATTTTTT-TTTTTTG
1440854 ATTTTTTATTTTTT
1 ATTTTTT-TTTTTT
1440868 TTTTGCCGAA
Statistics
Matches: 85, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
12 3 0.04
13 22 0.26
14 42 0.49
15 11 0.13
16 7 0.08
ACGTcount: A:0.08, C:0.00, G:0.06, T:0.86
Consensus pattern (14 bp):
ATTTTTTTTTTTTG
Found at i:1440819 original size:40 final size:40
Alignment explanation
Indices: 1440775--1440860 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
1440765 TTTTTGATTT
* *
1440775 TTTTTTTTTAAATTTTTGTTTTTTTGTTTTTTTTTTTTTG
1 TTTTTTTTTAAATTTTTGTTTTTTTGTTTTTTATTTTTTA
***
1440815 TTTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTATTTTTTA
1 TTTTTTTTTAAATTTTTGTTTTTTTGTTTTTTATTTTTTA
1440855 TTTTTT
1 TTTTTT
1440861 ATTTTTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.06, C:0.00, G:0.07, T:0.87
Consensus pattern (40 bp):
TTTTTTTTTAAATTTTTGTTTTTTTGTTTTTTATTTTTTA
Found at i:1440869 original size:40 final size:39
Alignment explanation
Indices: 1440787--1440872 Score: 136
Period size: 40 Copynumber: 2.2 Consensus size: 39
1440777 TTTTTTTAAA
* *
1440787 TTTTTGTTTTTTTGTTTTTTTTTTTTTGTTTTTTTTTGTT
1 TTTTTGTTTTTTTGTTTTTTATTTTTTATTTTTTTTT-TT
1440827 TTTTTGTTTTTTTGTTTTTTATTTTTTATTTTTTATTTTT
1 TTTTTGTTTTTTTGTTTTTTATTTTTTATTTTTT-TTTTT
1440867 TTTTTG
1 TTTTTG
1440873 CCGAAGCTCC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
40 40 0.93
41 3 0.07
ACGTcount: A:0.03, C:0.00, G:0.08, T:0.88
Consensus pattern (39 bp):
TTTTTGTTTTTTTGTTTTTTATTTTTTATTTTTTTTTTT
Found at i:1441046 original size:41 final size:41
Alignment explanation
Indices: 1440878--1441943 Score: 1494
Period size: 41 Copynumber: 26.0 Consensus size: 41
1440868 TTTTGCCGAA
* * *
1440878 GCTCCTCTAAACAGAGACTCAACGACTTTTG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
*
1440919 GCTCCTCTAAACAGAGGCA--ACGGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCAC-GACTTTGAAAAGTAAATT
*
1440959 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
*
1441001 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
1441042 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
1441084 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
1441125 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
1441167 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
*
1441209 GCTCCTCTAAACAGAGGCA--ACGGAACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCAC-G-ACTTTGAAAAGTAAATT
*
1441250 GCTCCTCTAAACAGAGGCA--ACGGAACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCAC-G-ACTTTGAAAAGTAAATT
** *
1441291 GCTCCTCTAAACAGAGATACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
1441332 GCTCCTCTAAACAGAGGCA--ACGGAACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCAC-G-ACTTTGAAAAGTAAATT
* *
1441373 GCTCCTCTCAACAGAGGTACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
*
1441415 GCTCCTCTAAACAGAGGCA--ACGGAACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCAC-G-ACTTTGAAAAGTAAATT
*
1441456 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1441497 GCTCCTCTAAACAGAGGCA--ACGAACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGAAAAGTAAATT
* *
1441537 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1441578 GCTCCTCTAAACAGAGGCA--ACGAACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGAAAAGTAAATT
*
1441618 GCTCCTCTAAACAGAGGTA--ACGAACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGAAAAGTAAATT
*
1441658 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1441699 GCTCCTCTAAACAGAGGCA--ACGAACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGAAAAGTAAATT
1441739 GCTCCTCTAAACAGAGGCA--ACGAACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGAAAAGTAAATT
* *
1441779 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATT
* *
1441821 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* * *
1441862 GCTCCTCTAAACAGAGGTACCACGACTTTAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1441903 GCTCCTCTAAACAGAGGCA--ACGGAACTTTGGAAAAGTAAAT
1 GCTCCTCTAAACAGAGGCACCAC-G-ACTTT-GAAAAGTAAAT
1441944 ACTCCTAGTC
Statistics
Matches: 952, Mismatches: 39, Indels: 67
0.90 0.04 0.06
Matches are distributed among these distances:
39 19 0.02
40 221 0.23
41 460 0.48
42 243 0.26
43 9 0.01
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:1441949 original size:82 final size:81
Alignment explanation
Indices: 1440878--1441943 Score: 1566
Period size: 83 Copynumber: 13.0 Consensus size: 81
1440868 TTTTGCCGAA
*
1440878 GCTCCTCTAAACAGA-G-ACTCAACGACTTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCAAC
1 GCTCCTCTAAACAGAGGTAC-C-ACGAC-TTTGAAAAATAAATTGCTCCTCTAAACAGAGGCAAC
* *
1440940 GGACTTTGGAAAGTAAATT
63 GAACTTTGAAAAGTAAATT
* * * *
1440959 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTCAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGTACCACGACTTT-GAAAAATAAATTGCTCCTCTAAACAGAGGCA--AC
1441024 G-ACTTTGAAAAGTAAATT
63 GAACTTTGAAAAGTAAATT
*
1441042 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGTACCACGACTTT-GAAAAATAAATTGCTCCTCTAAACAGAGGCA--AC
1441107 G-ACTTTGAAAAGTAAATT
63 GAACTTTGAAAAGTAAATT
*
1441125 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGTACCACGACTTT-GAAAAATAAATTGCTCCTCTAAACAGAGGCA--AC
1441190 G-ACTTTTGAAAAGTAAATT
63 GAAC-TTTGAAAAGTAAATT
*
1441209 GCTCCTCTAAACAGAGG--CAACGGAACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCAACG
1 GCTCCTCTAAACAGAGGTACCAC-G-ACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCAAC-
*
1441272 GAACTTTGAAAAATAAATT
63 GAACTTTGAAAAGTAAATT
*
1441291 GCTCCTCTAAACAGAGATACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGGA
1 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCAAC-GA
*
1441356 ACTTTGAAAAATAAATT
65 ACTTTGAAAAGTAAATT
* *
1441373 GCTCCTCTCAACAGAGGTACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGG
1 GCTCCTCTAAACAGAGGTACCACGACTTT-GAAAAATAAATTGCTCCTCTAAACAGAGGCAAC-G
*
1441438 AACTTTGAAAAATAAATT
64 AACTTTGAAAAGTAAATT
*
1441456 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAA
1 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGAA
1441521 CTTTGAAAAGTAAATT
66 CTTTGAAAAGTAAATT
1441537 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGAA
1 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGAA
1441602 CTTTGAAAAGTAAATT
66 CTTTGAAAAGTAAATT
* *
1441618 GCTCCTCTAAACAGAGGTA--ACGAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCAC
1 GCTCCTCTAAACAGAGGTACCACG-ACTTTGAAAAATAAATTGCTCCTCTAAACAGAGG--CAAC
1441681 G-ACTTTGAAAAGTAAATT
63 GAACTTTGAAAAGTAAATT
* *
1441699 GCTCCTCTAAACAGAGG--CAACGAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
1 GCTCCTCTAAACAGAGGTACCACG-ACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGA
1441762 ACTTTGAAAAGTAAATT
65 ACTTTGAAAAGTAAATT
*
1441779 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGTACCACGACTTTG-AAAAATAAATTGCTCCTCTAAACAGAGGCA--AC
*
1441844 G-ACTTTGAAAAATAAATT
63 GAACTTTGAAAAGTAAATT
*
1441862 GCTCCTCTAAACAGAGGTACCACGACTTTAAAAAATAAATTGCTCCTCTAAACAGAGGCAACGGA
1 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCAAC-GA
1441927 ACTTTGGAAAAGTAAAT
65 ACTTT-GAAAAGTAAAT
1441944 ACTCCTAGTC
Statistics
Matches: 931, Mismatches: 26, Indels: 54
0.92 0.03 0.05
Matches are distributed among these distances:
79 7 0.01
80 72 0.08
81 218 0.23
82 252 0.27
83 336 0.36
84 46 0.05
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (81 bp):
GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGAA
CTTTGAAAAGTAAATT
Found at i:1443145 original size:8 final size:8
Alignment explanation
Indices: 1443132--1443170 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
1443122 TTCGGATCTC
1443132 TTTTTTCA
1 TTTTTTCA
1443140 TTTTTTCA
1 TTTTTTCA
1443148 TTTTTTCA
1 TTTTTTCA
*
1443156 TTTTCTCA
1 TTTTTTCA
1443164 TTTTTTC
1 TTTTTTC
1443171 TTCTTTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTTCA
Found at i:1443187 original size:35 final size:35
Alignment explanation
Indices: 1443127--1443214 Score: 92
Period size: 35 Copynumber: 2.5 Consensus size: 35
1443117 TTCAATTCGG
*
1443127 ATCTCTTTT-TTCATTTTTTCATTTTTTCATTTTC-TC
1 ATCT-TTTTCTTCATTCTTTCATTTTTT--TTTTCATC
* *
1443163 AT-TTTTTCTTCTTTCTTTCTTTTTTTTTTTCATC
1 ATCTTTTTCTTCATTCTTTCATTTTTTTTTTCATC
*
1443197 ATCTTTTTTTTCATTCTT
1 ATCTTTTTCTTCATTCTT
1443215 CACCTATTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
33 5 0.11
34 8 0.18
35 29 0.66
36 2 0.05
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (35 bp):
ATCTTTTTCTTCATTCTTTCATTTTTTTTTTCATC
Found at i:1443602 original size:1 final size:1
Alignment explanation
Indices: 1443596--1443622 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1443586 CCTTTTGTGG
1443596 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1443623 CAAAAATTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1447113 original size:156 final size:156
Alignment explanation
Indices: 1446829--1447293 Score: 759
Period size: 156 Copynumber: 2.9 Consensus size: 156
1446819 TTAAAATTTT
* * * *
1446829 ACCAAGTAGTTAGTTGTTGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
1 ACCAAGTAATTAATTATCGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
*
1446894 AAATTCCCTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
66 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
*
1446959 GATTATTTAAAGAAAAATCAAGATCA
131 GATTATTTAAAGAAAAATCAAAATCA
*
1446985 ACCAATTAATTAATTATCGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
1 ACCAAGTAATTAATTATCGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
1447050 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
66 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
*
1447115 GATTAATTAAAGTAAAAAAAAATCAAAATCA
131 GATT-ATT----TAAAGAAAAATCAAAATCA
* *
1447146 GCCAAGTAATTAATTATCGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
1 ACCAAGTAATTAATTATCGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
* *
1447211 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTTTACTTGTAGAGGCTCCGTCGTC
66 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTG-TTTCACTTGCAGAGGCTCCGTCGTC
*
1447276 GGATTAATTAAAGAAAAA
130 GGATTATTTAAAGAAAAA
1447294 AGAAAAAAAA
Statistics
Matches: 288, Mismatches: 15, Indels: 11
0.92 0.05 0.04
Matches are distributed among these distances:
156 128 0.44
157 12 0.04
161 120 0.42
162 28 0.10
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (156 bp):
ACCAAGTAATTAATTATCGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
GATTATTTAAAGAAAAATCAAAATCA
Found at i:1447221 original size:161 final size:161
Alignment explanation
Indices: 1446829--1447307 Score: 774
Period size: 161 Copynumber: 3.0 Consensus size: 161
1446819 TTAAAATTTT
* * * *
1446829 ACCAAGTAGTTAGTTGTTGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
1 ACCAAGTAATTAATTATCGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
*
1446894 AAATTCCCTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
66 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
* *
1446959 GATT-ATT----TAAAGAAAAATCAAGATCA
131 GATTAATTAAAGTAAAAAAAAATCAAAATCA
*
1446985 ACCAATTAATTAATTATCGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
1 ACCAAGTAATTAATTATCGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
1447050 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
66 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
1447115 GATTAATTAAAGTAAAAAAAAATCAAAATCA
131 GATTAATTAAAGTAAAAAAAAATCAAAATCA
* *
1447146 GCCAAGTAATTAATTATCGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
1 ACCAAGTAATTAATTATCGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
* *
1447211 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTTTACTTGTAGAGGCTCCGTCGTC
66 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTG-TTTCACTTGCAGAGGCTCCGTCGTC
*
1447276 GGATTAATTAAAG-AAAAAAGAAA-AAAAATCA
130 GGATTAATTAAAGTAAAAAA-AAATCAAAATCA
1447307 A
1 A
1447308 GATCAAAATC
Statistics
Matches: 301, Mismatches: 15, Indels: 9
0.93 0.05 0.03
Matches are distributed among these distances:
156 128 0.43
157 3 0.01
161 131 0.44
162 39 0.13
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (161 bp):
ACCAAGTAATTAATTATCGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
GATTAATTAAAGTAAAAAAAAATCAAAATCA
Found at i:1447329 original size:14 final size:14
Alignment explanation
Indices: 1447322--1447361 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
1447312 AAAATCAAAG
1447322 TCAAAAAAAAAAAA
1 TCAAAAAAAAAAAA
1447336 TCAAAAAAAAAAAA
1 TCAAAAAAAAAAAA
1447350 --AAAAAAAAAAAA
1 TCAAAAAAAAAAAA
1447362 CCTGGAGCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 12 0.46
14 14 0.54
ACGTcount: A:0.90, C:0.05, G:0.00, T:0.05
Consensus pattern (14 bp):
TCAAAAAAAAAAAA
Found at i:1447330 original size:1 final size:1
Alignment explanation
Indices: 1447324--1447361 Score: 58
Period size: 1 Copynumber: 38.0 Consensus size: 1
1447314 AATCAAAGTC
**
1447324 AAAAAAAAAAAATCAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1447362 CCTGGAGCGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.95, C:0.03, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:1447400 original size:15 final size:16
Alignment explanation
Indices: 1447369--1447418 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
1447359 AAACCTGGAG
*
1447369 CGGCTCGGATCGCGGCT
1 CGGCTCGGCT-GCGGCT
*
1447386 CGGCTTGG-TGCGGCT
1 CGGCTCGGCTGCGGCT
1447401 CGGCTCGGCT-CGGCT
1 CGGCTCGGCTGCGGCT
1447416 CGG
1 CGG
1447419 AGGGGCTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 21 0.70
16 2 0.07
17 7 0.23
ACGTcount: A:0.02, C:0.34, G:0.44, T:0.20
Consensus pattern (16 bp):
CGGCTCGGCTGCGGCT
Found at i:1447404 original size:5 final size:5
Alignment explanation
Indices: 1447381--1447418 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
1447371 GCTCGGATCG
*
1447381 CGGCT CGGCT TGG-T GCGGCT CGGCT CGGCT CGGCT CGG
1 CGGCT CGGCT CGGCT -CGGCT CGGCT CGGCT CGGCT CGG
1447419 AGGGGCTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 1 0.03
5 27 0.93
6 1 0.03
ACGTcount: A:0.00, C:0.34, G:0.45, T:0.21
Consensus pattern (5 bp):
CGGCT
Found at i:1447662 original size:19 final size:19
Alignment explanation
Indices: 1447638--1447682 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1447628 GAACGCCGGT
*
1447638 ACCGGATTCTGGAAATTTC
1 ACCGGAATCTGGAAATTTC
*
1447657 ACCGGAATCTGGGAATTTC
1 ACCGGAATCTGGAAATTTC
*
1447676 GCCGGAA
1 ACCGGAA
1447683 ATTGGCCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (19 bp):
ACCGGAATCTGGAAATTTC
Found at i:1447771 original size:31 final size:31
Alignment explanation
Indices: 1447733--1447805 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
1447723 AAACTGGGTC
*
1447733 TGTCGCCGGAAACTTC-AAAGTTCGCCGAAAT
1 TGTCGCCGGAAAATTCAAAAG-TCGCCGAAAT
*
1447764 TGTCGCCGGAAAATTCAAAAGTCGCCGGAAT
1 TGTCGCCGGAAAATTCAAAAGTCGCCGAAAT
*
1447795 TTTCGCCGGAA
1 TGTCGCCGGAA
1447806 TCTGGAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 34 0.89
32 4 0.11
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (31 bp):
TGTCGCCGGAAAATTCAAAAGTCGCCGAAAT
Found at i:1448823 original size:26 final size:27
Alignment explanation
Indices: 1448794--1448852 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
1448784 TTAGTTAAAA
*
1448794 TAATAATATAAT-TTTTTATTTTTAGT
1 TAATAATATAATACTTTTATTTTTAGT
1448820 TAATAATATAATACTTTTATTTTTAGT
1 TAATAATATAATACTTTTATTTTTAGT
1448847 TAATAA
1 TAATAA
1448853 ATTTTTATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 12 0.39
27 19 0.61
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (27 bp):
TAATAATATAATACTTTTATTTTTAGT
Found at i:1448858 original size:21 final size:23
Alignment explanation
Indices: 1448796--1448860 Score: 62
Period size: 27 Copynumber: 2.7 Consensus size: 23
1448786 AGTTAAAATA
1448796 ATAATATAATTTTTTATTTTTAGTT
1 ATAATA-AA-TTTTTATTTTTAGTT
1448821 AATAATATAATACTTTTATTTTTAG-T
1 -ATAATA-AAT--TTTTATTTTTAGTT
1448847 -TAATAAATTTTTAT
1 ATAATAAATTTTTAT
1448861 ATAATAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
21 6 0.16
23 3 0.08
24 5 0.14
25 1 0.03
26 10 0.27
27 12 0.32
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (23 bp):
ATAATAAATTTTTATTTTTAGTT
Found at i:1448878 original size:15 final size:16
Alignment explanation
Indices: 1448860--1448895 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
1448850 TAAATTTTTA
1448860 TATAATAATAA-AATT
1 TATAATAATAATAATT
1448875 TATAA-AATAATAATT
1 TATAATAATAATAATT
1448890 TATAAT
1 TATAAT
1448896 TCAATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TATAATAATAATAATT
Found at i:1450619 original size:15 final size:16
Alignment explanation
Indices: 1450601--1450636 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
1450591 TTAATTTTTA
1450601 TATAATAATAA-AATT
1 TATAATAATAATAATT
1450616 TATAA-AATAATAATT
1 TATAATAATAATAATT
1450631 TATAAT
1 TATAAT
1450637 TCAATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TATAATAATAATAATT
Found at i:1454107 original size:13 final size:13
Alignment explanation
Indices: 1454074--1454112 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
1454064 AAAATAAAAT
1454074 ATTTTAATTTATTA
1 ATTTTAATTT-TTA
*
1454088 GTTTTAATTTTTA
1 ATTTTAATTTTTA
1454101 ATTTTAATTTTT
1 ATTTTAATTTTT
1454113 TAAAATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
ATTTTAATTTTTA
Found at i:1454112 original size:14 final size:14
Alignment explanation
Indices: 1454074--1454115 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
1454064 AAAATAAAAT
*
1454074 ATTTTAATTTATTA
1 ATTTTAATTTTTTA
*
1454088 GTTTTAA-TTTTTA
1 ATTTTAATTTTTTA
1454101 ATTTTAATTTTTTA
1 ATTTTAATTTTTTA
1454115 A
1 A
1454116 AATTATTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
ATTTTAATTTTTTA
Found at i:1455719 original size:13 final size:13
Alignment explanation
Indices: 1455701--1455730 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1455691 AGTTTATAAG
*
1455701 ATTATTACATATT
1 ATTATTACATATC
1455714 ATTATTACATATC
1 ATTATTACATATC
1455727 ATTA
1 ATTA
1455731 GGTCATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTATTACATATC
Found at i:1456997 original size:20 final size:21
Alignment explanation
Indices: 1456969--1457007 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1456959 GTAGACACAG
*
1456969 ATTTTTTTTGAAA-AAATTGA
1 ATTTATTTTGAAATAAATTGA
1456989 ATTTATTTTGAAATAAATT
1 ATTTATTTTGAAATAAATT
1457008 TGGAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (21 bp):
ATTTATTTTGAAATAAATTGA
Found at i:1458432 original size:11 final size:11
Alignment explanation
Indices: 1458416--1458449 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1458406 CAAATTAAAA
1458416 ATCAAATTTTT
1 ATCAAATTTTT
*
1458427 ATCAAATTTTG
1 ATCAAATTTTT
*
1458438 ATAAAATTTTT
1 ATCAAATTTTT
1458449 A
1 A
1458450 ATTTTTTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (11 bp):
ATCAAATTTTT
Found at i:1459599 original size:14 final size:14
Alignment explanation
Indices: 1459580--1459621 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1459570 ATTTTTCTTG
1459580 AATAAAAATGGAAC
1 AATAAAAATGGAAC
*
1459594 AATAAATATGGAAC
1 AATAAAAATGGAAC
1459608 -ATAGATAAATGGAA
1 AATA-A-AAATGGAA
1459622 AAACCAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 3 0.12
14 14 0.58
15 7 0.29
ACGTcount: A:0.60, C:0.05, G:0.17, T:0.19
Consensus pattern (14 bp):
AATAAAAATGGAAC
Found at i:1461525 original size:21 final size:21
Alignment explanation
Indices: 1461478--1461526 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1461468 AGTTGGCATG
*
1461478 AATTTATTTAATTTTAATAATT
1 AATTT-TTTAATTTTAATAAAT
*
1461500 AATTTTTTAA-TTTAGTAAAT
1 AATTTTTTAATTTTAATAAAT
1461520 ATATTTT
1 A-ATTTT
1461527 AATGGAATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 10 0.42
22 5 0.21
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
AATTTTTTAATTTTAATAAAT
Found at i:1465487 original size:22 final size:22
Alignment explanation
Indices: 1465459--1465503 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1465449 ATTAAAGAGA
1465459 AAAATTTGA-AAATTTTTTAAAT
1 AAAATTT-ATAAATTTTTTAAAT
*
1465481 AAAATTTATATATTTTTTAAAT
1 AAAATTTATAAATTTTTTAAAT
1465503 A
1 A
1465504 GGCATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
AAAATTTATAAATTTTTTAAAT
Found at i:1465958 original size:21 final size:21
Alignment explanation
Indices: 1465911--1465959 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1465901 GGTTGGCACG
*
1465911 AATTTATTTAATTTTAATAATT
1 AATTT-TTTAATTTTAATAAAT
*
1465933 AATTTTTTAA-TTTAGTAAAT
1 AATTTTTTAATTTTAATAAAT
1465953 ATATTTT
1 A-ATTTT
1465960 AATGGAATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 10 0.42
22 5 0.21
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
AATTTTTTAATTTTAATAAAT
Found at i:1467070 original size:34 final size:34
Alignment explanation
Indices: 1467021--1467106 Score: 127
Period size: 37 Copynumber: 2.4 Consensus size: 34
1467011 AAACTTTTAA
* *
1467021 TTATTTTTATTTGTTGAATACTAAAATATCTATT
1 TTATTTTAATATGTTGAATACTAAAATATCTATT
1467055 TTATTTTAATATGTTGTTGAATACTAAAATATCTATT
1 TTATTTTAATA---TGTTGAATACTAAAATATCTATT
1467092 TTATTTTAATATGTT
1 TTATTTTAATATGTT
1467107 AAACATGTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
34 13 0.28
37 34 0.72
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.56
Consensus pattern (34 bp):
TTATTTTAATATGTTGAATACTAAAATATCTATT
Found at i:1467079 original size:37 final size:37
Alignment explanation
Indices: 1467031--1467106 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
1467021 TTATTTTTAT
1467031 TTGTTGAATACTAAAATATCTATTTTATTTTAATATG
1 TTGTTGAATACTAAAATATCTATTTTATTTTAATATG
1467068 TTGTTGAATACTAAAATATCTATTTTATTTTAATATG
1 TTGTTGAATACTAAAATATCTATTTTATTTTAATATG
1467105 TT
1 TT
1467107 AAACATGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (37 bp):
TTGTTGAATACTAAAATATCTATTTTATTTTAATATG
Found at i:1467824 original size:17 final size:17
Alignment explanation
Indices: 1467802--1467834 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1467792 CCTTAAATCA
*
1467802 TTAAATCATTTTTTTCC
1 TTAAATAATTTTTTTCC
1467819 TTAAATAATTTTTTTC
1 TTAAATAATTTTTTTC
1467835 TTTTTTAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (17 bp):
TTAAATAATTTTTTTCC
Found at i:1469870 original size:20 final size:18
Alignment explanation
Indices: 1469846--1469893 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 18
1469836 TGTATATATT
1469846 TTTAAAATTTTTGTAATTA
1 TTTAAAATTTTT-TAATTA
**
1469865 TATTAAACAAATTTTAATTA
1 T-TTAAA-ATTTTTTAATTA
1469885 TTTAAAATT
1 TTTAAAATT
1469894 ATTATTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
18 1 0.04
19 6 0.26
20 12 0.52
21 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
TTTAAAATTTTTTAATTA
Found at i:1469910 original size:20 final size:20
Alignment explanation
Indices: 1469875--1469978 Score: 93
Period size: 23 Copynumber: 4.7 Consensus size: 20
1469865 TATTAAACAA
1469875 ATTTTAATTATTTAAAATTATT
1 ATTTT-ATT-TTTAAAATTATT
1469897 ATTTTATTTTTAAAATAATTATT
1 ATTTTATTTTT--AA-AATTATT
*
1469920 ATTTTATTTTTAAAATAATT
1 ATTTTATTTTTAAAATTATT
1469940 ATTTTTTATTATTTAATTAATT-TT
1 A--TTTTATT-TTTAA--AATTATT
1469964 ATTCTTATTTTTAAA
1 ATT-TTATTTTTAAA
1469979 TAATTTGATA
Statistics
Matches: 71, Mismatches: 2, Indels: 20
0.76 0.02 0.22
Matches are distributed among these distances:
20 11 0.15
21 5 0.07
22 21 0.30
23 28 0.39
24 3 0.04
25 3 0.04
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTATTTTTAAAATTATT
Found at i:1469948 original size:45 final size:45
Alignment explanation
Indices: 1469890--1469983 Score: 131
Period size: 45 Copynumber: 2.1 Consensus size: 45
1469880 AATTATTTAA
1469890 AATTATTATTTTATT-TTTAAAATAATTATTATT-TTATTTTTAAAAT
1 AATTATTATTTTATTATTT-AAATAATT-TTATTCTTATTTTT-AAAT
*
1469936 AATTATT-TTTTATTATTTAATTAATTTTATTCTTATTTTTAAAT
1 AATTATTATTTTATTATTTAAATAATTTTATTCTTATTTTTAAAT
1469980 AATT
1 AATT
1469984 TGATAAATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
44 13 0.29
45 22 0.49
46 10 0.22
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (45 bp):
AATTATTATTTTATTATTTAAATAATTTTATTCTTATTTTTAAAT
Found at i:1469984 original size:22 final size:23
Alignment explanation
Indices: 1469890--1469983 Score: 133
Period size: 23 Copynumber: 4.2 Consensus size: 23
1469880 AATTATTTAA
1469890 AATTATTATTTTATTTTTAAAAT
1 AATTATTATTTTATTTTTAAAAT
1469913 AATTATTATTTTATTTTTAAAAT
1 AATTATTATTTTATTTTTAAAAT
*
1469936 AATTATT-TTTTATTATTT-AATT
1 AATTATTATTTTATT-TTTAAAAT
1469958 AATT-TTATTCTTATTTTT-AAAT
1 AATTATTATT-TTATTTTTAAAAT
1469980 AATT
1 AATT
1469984 TGATAAATTT
Statistics
Matches: 66, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
21 2 0.03
22 26 0.39
23 38 0.58
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (23 bp):
AATTATTATTTTATTTTTAAAAT
Found at i:1470175 original size:40 final size:39
Alignment explanation
Indices: 1470079--1470175 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 39
1470069 TTTAGTATGG
* * *
1470079 AAAATATAGTTTA-ATATTAAGGAGATTACGATTTTCAAA
1 AAAATATAGTTTATATATAAAAGAGACTACGATTTT-AAA
* *
1470118 AAATTATAGTCTAATATATAAAAG-GACTACGATTTTTAAA
1 AAAATATAGT-TTATATATAAAAGAGACTACGA-TTTTAAA
1470158 AAAATCATAGTTTATATA
1 AAAAT-ATAGTTTATATA
1470176 GATAGAATTG
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
39 9 0.19
40 22 0.47
41 16 0.34
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.36
Consensus pattern (39 bp):
AAAATATAGTTTATATATAAAAGAGACTACGATTTTAAA
Found at i:1471503 original size:28 final size:25
Alignment explanation
Indices: 1471470--1471528 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 25
1471460 AAAAATTTAA
*
1471470 AATTCGACCCGAATCCAAATCTTTATTC
1 AATTCGAACCGAAT-CAAAT-TTTA-TC
* *
1471498 AATTCGAATCGAATCGAATTTTATC
1 AATTCGAACCGAATCAAATTTTATC
1471523 AATTCG
1 AATTCG
1471529 GTTTATCAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 8 0.29
26 4 0.14
27 4 0.14
28 12 0.43
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (25 bp):
AATTCGAACCGAATCAAATTTTATC
Found at i:1472414 original size:8 final size:8
Alignment explanation
Indices: 1472401--1472426 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1472391 TCAAACTAAA
1472401 ATTTTAAT
1 ATTTTAAT
1472409 ATTTTAAT
1 ATTTTAAT
1472417 ATTTTAAT
1 ATTTTAAT
1472425 AT
1 AT
1472427 AGTAGGTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATTTTAAT
Found at i:1476409 original size:34 final size:34
Alignment explanation
Indices: 1476355--1476513 Score: 192
Period size: 34 Copynumber: 4.7 Consensus size: 34
1476345 CAAAAAATAA
* *
1476355 TGGCATTTGTATCTAAAAAATGCCGCTATATTAG
1 TGGCATTTGAATCTAGAAAATGCCGCTATATTAG
* *
1476389 TGGCATTTAAACCTAGAAAATGCCGCTATATTAG
1 TGGCATTTGAATCTAGAAAATGCCGCTATATTAG
* * *
1476423 TGACATTTGAATCTAGAAAATGTCGCTATATTAA
1 TGGCATTTGAATCTAGAAAATGCCGCTATATTAG
* * * * **
1476457 AGGCATTTGTATCTAAAAAATACCATTATATTAG
1 TGGCATTTGAATCTAGAAAATGCCGCTATATTAG
*
1476491 TGGCATTTGTATCTAGAAAATGC
1 TGGCATTTGAATCTAGAAAATGC
1476514 TACTAGTTTA
Statistics
Matches: 104, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 104 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (34 bp):
TGGCATTTGAATCTAGAAAATGCCGCTATATTAG
Found at i:1476582 original size:34 final size:34
Alignment explanation
Indices: 1476458--1476627 Score: 110
Period size: 34 Copynumber: 5.0 Consensus size: 34
1476448 CTATATTAAA
* *
1476458 GGCATTTGTATCTAAAAAATACCATT-ATATTAGT
1 GGCATTTGTATCAAAAAAATGCCATTAAT-TTAGT
* * * * * *
1476492 GGCATTTGTATCTAGAAAATGCTACTAGTTTAGC
1 GGCATTTGTATCAAAAAAATGCCATTAATTTAGT
* *** *
1476526 AGCATTTGTAT-ATTTGAGATGCCATTAATTTAGT
1 GGCATTTGTATCA-AAAAAATGCCATTAATTTAGT
** * * *
1476560 GGTGTTTTTATCAAAAAAATGCCATTACTTTGGT
1 GGCATTTGTATCAAAAAAATGCCATTAATTTAGT
* * * *
1476594 GGCATTTGTATTAGAAAAATACCACTAATTTAGT
1 GGCATTTGTATCAAAAAAATGCCATTAATTTAGT
1476628 ACGTTTTCTA
Statistics
Matches: 98, Mismatches: 35, Indels: 6
0.71 0.25 0.04
Matches are distributed among these distances:
34 96 0.98
35 2 0.02
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (34 bp):
GGCATTTGTATCAAAAAAATGCCATTAATTTAGT
Found at i:1484845 original size:187 final size:187
Alignment explanation
Indices: 1484498--1484941 Score: 567
Period size: 187 Copynumber: 2.4 Consensus size: 187
1484488 TTATGAATGC
* * * * **
1484498 CTTCAATAATTTTCTTTTGAAAAA-TTTTGGAATTAGTAAAGGCATTTTTCAATGCAAAACGCAA
1 CTTCAATAATTTTCTTTT-AAAAATTTTTGGGATTATTAAAGGCATTTTTCAGTGAAAAACGCCT
* * * * *
1484562 TCAATATTTCACTATTCAAATTTTAAGATGATTAGTGAAGGCGTTTATTCTAGAAAATCACTTTC
65 TCAATATTCCACTACTCAAATTTTAAAATGATTAATGAAGGCGTTTATTCTAGAAAATCACCTTC
** *
1484627 ACTAATTCTTTTTAATTTACATACATAATTATTGAAT-GCATTTTTTTAGAAAAAACG-
130 ACTAATTCCATTTAATTTACATACATAATTATTG-ATGGCATTTTTTGAGAAAAAACGT
*
1484684 CTTTCAATAATTTTCTTTT-AAAATTTTTGGGATTATTAAAGGTATTTTTCAGTGAAAAACGCCT
1 C-TTCAATAATTTTCTTTTAAAAATTTTTGGGATTATTAAAGGCATTTTTCAGTGAAAAACGCCT
* * *
1484748 TCAATATTCCACTACTCAAATTTTAAAATGGTTAATGAATGTGTTTATTCTAGAAAAAAT-ACCT
65 TCAATATTCCACTACTCAAATTTTAAAATGATTAATGAAGGCGTTTATTCTAG--AAAATCACCT
* * *
1484812 TCACTAATTCCATTTAATTTACGTACATAATTATTGATGGCATTTTTTGAGAATAAATGT
128 TCACTAATTCCATTTAATTTACATACATAATTATTGATGGCATTTTTTGAGAAAAAACGT
* * * *
1484872 CTTCAATCATTTTCTTTTAAAAATTTTTGAGATTATTAAAGGCGTTTTTTAGT-ATAAAACGCCT
1 CTTCAATAATTTTCTTTTAAAAATTTTTGGGATTATTAAAGGCATTTTTCAGTGA-AAAACGCCT
1484936 TCAATA
65 TCAATA
1484942 ATGTTAAAGG
Statistics
Matches: 224, Mismatches: 26, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
185 4 0.02
186 82 0.37
187 87 0.39
188 51 0.23
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (187 bp):
CTTCAATAATTTTCTTTTAAAAATTTTTGGGATTATTAAAGGCATTTTTCAGTGAAAAACGCCTT
CAATATTCCACTACTCAAATTTTAAAATGATTAATGAAGGCGTTTATTCTAGAAAATCACCTTCA
CTAATTCCATTTAATTTACATACATAATTATTGATGGCATTTTTTGAGAAAAAACGT
Found at i:1485768 original size:13 final size:13
Alignment explanation
Indices: 1485730--1485770 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
1485720 TATATGATAT
1485730 TGGTATG-CTGAA
1 TGGTATGTCTGAA
*
1485742 TCGTATGT-TGAA
1 TGGTATGTCTGAA
*
1485754 TGGTATTTCTGAA
1 TGGTATGTCTGAA
1485767 TGGT
1 TGGT
1485771 TTGCTGAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.22, C:0.07, G:0.29, T:0.41
Consensus pattern (13 bp):
TGGTATGTCTGAA
Found at i:1487481 original size:21 final size:21
Alignment explanation
Indices: 1487437--1487481 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1487427 ATAAGTTTAA
* *
1487437 TATTAATTTGTTTATTATATT
1 TATTAATTTGTTTATAATACT
1487458 TATTAATTTGATTT-TAATACT
1 TATTAATTTG-TTTATAATACT
1487479 TAT
1 TAT
1487482 ATTTCATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (21 bp):
TATTAATTTGTTTATAATACT
Found at i:1488795 original size:28 final size:28
Alignment explanation
Indices: 1488764--1488856 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 28
1488754 TATTTCTAAG
1488764 AAAAATTGATACTTTCAACTTTTCCTC-
1 AAAAATTGATACTTTCAACTTTTCCTCA
* ** * *
1488791 AAAAATTTATTTTTTTGAAACTTTGAT-TTCCA
1 AAAAATTGA-TACTTT-CAACTTT--TCCT-CA
1488823 AGGAAAATTGATACTTTCAACTTTTCCTCA
1 A--AAAATTGATACTTTCAACTTTTCCTCA
1488853 AAAA
1 AAAA
1488857 TCCCTTTTTC
Statistics
Matches: 47, Mismatches: 10, Indels: 17
0.64 0.14 0.23
Matches are distributed among these distances:
27 8 0.17
28 7 0.15
29 6 0.13
30 5 0.11
31 3 0.06
32 7 0.15
33 4 0.09
34 7 0.15
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (28 bp):
AAAAATTGATACTTTCAACTTTTCCTCA
Found at i:1488835 original size:61 final size:57
Alignment explanation
Indices: 1488705--1489048 Score: 415
Period size: 61 Copynumber: 5.8 Consensus size: 57
1488695 TCTTGTGTAG
* *
1488705 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT-GAAATTTATTTTTAA
* **
1488763 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATTTATTTTTTTGAAACTTTGATTTCCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTTGAAA-TTT-ATTTTTAA
** *
1488824 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCCTTTTTCGAAAATTTATTTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAT-ATTTTTTTG-AAATTTA-TTTTTAA
* * * *
1488884 GAAAAATTAATATTTTCAACTTTTCCTCAAAAATATCTTTTTTGGAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATAT-TTTTTT-GAAA-TTT-ATTTTTAA
1488945 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCT-TTTTTTTGAAA-TTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA---TATTTTTTTGAAATTTATTTTTAA
1489003 GGAAAATTGATACTTTCAACTTTTCC-CTAAAAATATTTTTTTGAAA
1 GGAAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTTGAAA
1489049 ATTTTGATTT
Statistics
Matches: 250, Mismatches: 20, Indels: 34
0.82 0.07 0.11
Matches are distributed among these distances:
55 1 0.00
56 11 0.04
57 1 0.00
58 69 0.28
59 8 0.03
60 65 0.26
61 86 0.34
62 7 0.03
63 1 0.00
64 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (57 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAATTTATTTTTAA
Found at i:1488925 original size:119 final size:117
Alignment explanation
Indices: 1488705--1489058 Score: 491
Period size: 121 Copynumber: 3.0 Consensus size: 117
1488695 TCTTGTGTAG
* ** *
1488705 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAT-ATTTTTTTGGAAATTTATTTCTAAGAAAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCCTTTTTT-GAAATTTATTTTTAAGAAAAA
*
1488769 TTGATACTTTCAACTTTTCCTCAAAAATTTATTTTTTTGAAACTTTGATTTCCAA
65 TTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTTGAAATTTTGATTTCCAA
*
1488824 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCCTTTTTCGAAAATTTATTTTTTAAGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCCTTTTTTG-AAATTTA-TTTTTAAGAAAA
* * *
1488889 ATTAATATTTTCAACTTTTCCTCAAAAATATCTTTTTTGGAAATTTTGATTTTCAA
64 ATTGATACTTTCAACTTTTCCTCAAAAATAT-TTTTTT-GAAATTTTGATTTCCAA
*
1488945 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA-CCCTTTTTTTTGAAA-TTATTTTTAAGGAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCC--TTTTTTGAAATTTATTTTTAAGAAAA
1489008 ATTGATACTTTCAACTTTTCC-CTAAAAATATTTTTTTGAAAATTTTGATTT
64 ATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTTG-AAATTTTGATTT
1489059 TTATTTAAAG
Statistics
Matches: 213, Mismatches: 13, Indels: 19
0.87 0.05 0.08
Matches are distributed among these distances:
117 1 0.00
118 19 0.09
119 75 0.35
120 24 0.11
121 88 0.41
122 6 0.03
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (117 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCCTTTTTTGAAATTTATTTTTAAGAAAAAT
TGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAATTTTGATTTCCAA
Found at i:1489188 original size:17 final size:17
Alignment explanation
Indices: 1489064--1489198 Score: 73
Period size: 17 Copynumber: 7.6 Consensus size: 17
1489054 GATTTTTATT
*
1489064 TAAAGAAAATAGAAT-AA
1 TAAAAAAAATA-AATAAA
1489081 TAAAAAAAATAAATAAA
1 TAAAAAAAATAAATAAA
1489098 -AATAAAAAATAAAGTAAA
1 TAA-AAAAAATAAA-TAAA
1489116 -ACAAAAATAA-AAATAAGA
1 TA-AAAAA-AATAAATAA-A
*
1489134 TGAAGATAAAAA-ATATTAAA
1 T-AA-A-AAAAATA-AATAAA
*** *
1489154 TAAATCTAATCTAATAAA
1 TAAAAAAAAT-AAATAAA
*
1489172 TAAAACAAATAAATAAA
1 TAAAAAAAATAAATAAA
1489189 TAAAAAAAAT
1 TAAAAAAAAT
1489199 TCAAAAAAAA
Statistics
Matches: 94, Mismatches: 11, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
16 5 0.05
17 42 0.45
18 27 0.29
19 6 0.06
20 7 0.07
21 7 0.07
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.20
Consensus pattern (17 bp):
TAAAAAAAATAAATAAA
Found at i:1489450 original size:20 final size:19
Alignment explanation
Indices: 1489418--1489455 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
1489408 ACTCTTCCCC
1489418 TTTCTCTCTCTTCTTCTCTT
1 TTTCTCTCTCTTC-TCTCTT
1489438 TTTCTCTGC-CTTCTCTCT
1 TTTCTCT-CTCTTCTCTCT
1489456 AAAAGGCCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 11 0.65
21 1 0.06
ACGTcount: A:0.00, C:0.37, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTCTCTCTCTTCTCTCTT
Found at i:1489712 original size:26 final size:25
Alignment explanation
Indices: 1489672--1489727 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
1489662 GAATCTGGAA
*
1489672 ATTTCCCAGAAATTTCCAGAAAAATT
1 ATTTCCCAAAAATTTCCA-AAAAATT
*
1489698 -TTTCGCCAAAAATTTCTAAAAAATT
1 ATTTC-CCAAAAATTTCCAAAAAATT
1489723 ATTTC
1 ATTTC
1489728 TGATCCCTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (25 bp):
ATTTCCCAAAAATTTCCAAAAAATT
Found at i:1490045 original size:19 final size:17
Alignment explanation
Indices: 1490003--1490045 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
1489993 GCCATCCAAA
1490003 AAGAAAATAATAATAAT
1 AAGAAAATAATAATAAT
*
1490020 AAAAAAATACTATAATAAT
1 AAGAAAATA--ATAATAAT
*
1490039 TAGAAAA
1 AAGAAAA
1490046 GATAAATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 8 0.38
19 13 0.62
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (17 bp):
AAGAAAATAATAATAAT
Found at i:1490461 original size:1 final size:1
Alignment explanation
Indices: 1490455--1490588 Score: 88
Period size: 1 Copynumber: 134.0 Consensus size: 1
1490445 TCATTTTGTG
* * * * * * * * * **
1490455 TTTTTTTGTTTTTTTGTGTTTTTTTGTTTTTTTGTGTTTTTTTTGTGTTTTTTTGTTTTTTTTGG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * *
1490520 TTTTTTTTTGTTCTTTTTGTTTTTTTGTTCTTTTTGTTTTTTTTGTTTTTTTGTTTTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1490585 TTTT
1 TTTT
1490589 ACCAAAGCTC
Statistics
Matches: 95, Mismatches: 38, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 95 1.00
ACGTcount: A:0.01, C:0.01, G:0.13, T:0.85
Consensus pattern (1 bp):
T
Found at i:1490469 original size:18 final size:18
Alignment explanation
Indices: 1490448--1490588 Score: 182
Period size: 19 Copynumber: 7.8 Consensus size: 18
1490438 AACATTGTCA
1490448 TTTTGTGTTTTTTTGTTT
1 TTTTGTGTTTTTTTGTTT
1490466 TTTTGTGTTTTTTTGTTT
1 TTTTGTGTTTTTTTGTTT
1490484 TTTTGTGTTTTTTTTGTGTT
1 TTTTGTG-TTTTTTTGT-TT
1490504 TTTT-TGTTTTTTTTGGTTT
1 TTTTGTG-TTTTTTT-GTTT
*
1490523 TTTTTTGTTCTTTTTGTTT
1 TTTTGTGTT-TTTTTGTTT
*
1490542 TTTTGT-TCTTTTTGTTT
1 TTTTGTGTTTTTTTGTTT
1490559 TTTT-TGTTTTTTTGTTT
1 TTTTGTGTTTTTTTGTTT
*
1490576 TTTTAT-TTTTTTT
1 TTTTGTGTTTTTTT
1490589 ACCAAAGCTC
Statistics
Matches: 113, Mismatches: 3, Indels: 15
0.86 0.02 0.11
Matches are distributed among these distances:
16 1 0.01
17 34 0.30
18 27 0.24
19 36 0.32
20 15 0.13
ACGTcount: A:0.01, C:0.01, G:0.13, T:0.84
Consensus pattern (18 bp):
TTTTGTGTTTTTTTGTTT
Found at i:1490578 original size:8 final size:8
Alignment explanation
Indices: 1490448--1490587 Score: 142
Period size: 8 Copynumber: 16.8 Consensus size: 8
1490438 AACATTGTCA
*
1490448 TTTTGTGT
1 TTTTTTGT
1490456 TTTTTTGTT
1 TTTTTTG-T
1490465 TTTTTGTGT
1 TTTTT-TGT
1490474 TTTTTTGT
1 TTTTTTGT
1490482 TTTTTTG-
1 TTTTTTGT
*
1490489 -TGTTT-T
1 TTTTTTGT
*
1490495 TTTTGTGT
1 TTTTTTGT
1490503 TTTTTTGTT
1 TTTTTTG-T
1490512 TTTTTTGGTTT
1 TTTTTT-G--T
1490523 TTTTTTGT
1 TTTTTTGT
1490531 TCTTTTTGT
1 T-TTTTTGT
1490540 TTTTTTGT
1 TTTTTTGT
1490548 TCTTTTTGTT
1 T-TTTTTG-T
1490558 TTTTTTGT
1 TTTTTTGT
1490566 TTTTTTGT
1 TTTTTTGT
*
1490574 TTTTTTAT
1 TTTTTTGT
1490582 TTTTTT
1 TTTTTT
1490588 TACCAAAGCT
Statistics
Matches: 115, Mismatches: 6, Indels: 22
0.80 0.04 0.15
Matches are distributed among these distances:
6 4 0.03
7 3 0.03
8 55 0.48
9 39 0.34
10 6 0.05
11 8 0.07
ACGTcount: A:0.01, C:0.01, G:0.14, T:0.84
Consensus pattern (8 bp):
TTTTTTGT
Found at i:1490586 original size:10 final size:10
Alignment explanation
Indices: 1490448--1490588 Score: 133
Period size: 10 Copynumber: 15.2 Consensus size: 10
1490438 AACATTGTCA
*
1490448 TTTTGTGTTT
1 TTTTGTTTTT
1490458 TTTTG--TTT
1 TTTTGTTTTT
*
1490466 TTTTGTGTTT
1 TTTTGTTTTT
1490476 TTTTGTTTTT
1 TTTTGTTTTT
*
1490486 TTGTG-TTTT
1 TTTTGTTTTT
*
1490495 TTTTGTGTTT
1 TTTTGTTTTT
1490505 TTTTGTTTTT
1 TTTTGTTTTT
*
1490515 TTTGGTTTTT
1 TTTTGTTTTT
*
1490525 TTTTG-TTCT
1 TTTTGTTTTT
1490534 TTTTG--TTT
1 TTTTGTTTTT
*
1490542 TTTTG-TTCT
1 TTTTGTTTTT
1490551 TTTTG-TTTT
1 TTTTGTTTTT
1490560 TTTTG--TTT
1 TTTTGTTTTT
1490568 TTTTGTTTTT
1 TTTTGTTTTT
*
1490578 TTAT-TTTTT
1 TTTTGTTTTT
1490587 TT
1 TT
1490589 ACCAAAGCTC
Statistics
Matches: 113, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
8 23 0.20
9 38 0.34
10 52 0.46
ACGTcount: A:0.01, C:0.01, G:0.13, T:0.84
Consensus pattern (10 bp):
TTTTGTTTTT
Found at i:1490589 original size:9 final size:9
Alignment explanation
Indices: 1490448--1490588 Score: 173
Period size: 9 Copynumber: 15.3 Consensus size: 9
1490438 AACATTGTCA
1490448 TTTTGTGTTT
1 TTTTGT-TTT
1490458 TTTTG-TTT
1 TTTTGTTTT
1490466 TTTTGTGTTT
1 TTTTGT-TTT
1490476 TTTTGTTTT
1 TTTTGTTTT
1490485 TTTGTGTTTT
1 TTT-TGTTTT
1490495 TTTTGTGTTT
1 TTTTGT-TTT
1490505 TTTTGTTTT
1 TTTTGTTTT
1490514 TTTTGGTTTTT
1 TTTT-G-TTTT
*
1490525 TTTTGTTCT
1 TTTTGTTTT
1490534 TTTTG-TTT
1 TTTTGTTTT
*
1490542 TTTTGTTCT
1 TTTTGTTTT
1490551 TTTTGTTTT
1 TTTTGTTTT
1490560 TTTTG-TTT
1 TTTTGTTTT
1490568 TTTTGTTTT
1 TTTTGTTTT
1490577 TTTAT-TTTT
1 TTT-TGTTTT
1490586 TTT
1 TTT
1490589 ACCAAAGCTC
Statistics
Matches: 118, Mismatches: 4, Indels: 19
0.84 0.03 0.13
Matches are distributed among these distances:
8 23 0.19
9 52 0.44
10 35 0.30
11 8 0.07
ACGTcount: A:0.01, C:0.01, G:0.13, T:0.84
Consensus pattern (9 bp):
TTTTGTTTT
Found at i:1490680 original size:16 final size:16
Alignment explanation
Indices: 1490659--1490691 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1490649 CAGAGGCACC
1490659 ACGACTTTGGAAAGTA
1 ACGACTTTGGAAAGTA
1490675 ACGACTTTGGAAAGTA
1 ACGACTTTGGAAAGTA
1490691 A
1 A
1490692 ATTGCTCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24
Consensus pattern (16 bp):
ACGACTTTGGAAAGTA
Found at i:1490705 original size:57 final size:60
Alignment explanation
Indices: 1490615--1490733 Score: 199
Period size: 57 Copynumber: 2.0 Consensus size: 60
1490605 ACAGAGGCTC
1490615 AACGACTTTGAGAAACATAAATTGCTCCTCTAAACAGAGGCACCACGAC-TTTGGAAAGT
1 AACGACTTTGAGAAACATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGGAAAGT
* *
1490674 AACGACTTTG-GAAA-GTAAATTGCTCCTCTAAACAGAGGCACCATGACTTTTGGAAAGT
1 AACGACTTTGAGAAACATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGGAAAGT
1490732 AA
1 AA
1490734 ATTGCTCCTC
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
57 31 0.54
58 16 0.28
59 10 0.18
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (60 bp):
AACGACTTTGAGAAACATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGGAAAGT
Found at i:1490783 original size:41 final size:41
Alignment explanation
Indices: 1490677--1490775 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 41
1490667 GGAAAGTAAC
* *
1490677 GACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAT
1 GACTTTGGAAAGTAAATTGCTCCTCTAAACAGAAGCAACAT
1490718 GACTTTTGGAAAGTAAATTGCTCCTCTAAACAGAAGCAACA-
1 GAC-TTTGGAAAGTAAATTGCTCCTCTAAACAGAAGCAACAT
*
1490759 GAACTTTGGAAATTAAA
1 G-ACTTTGGAAAGTAAA
1490776 AGGCTCCTTG
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
41 16 0.30
42 37 0.70
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (41 bp):
GACTTTGGAAAGTAAATTGCTCCTCTAAACAGAAGCAACAT
Found at i:1492065 original size:8 final size:8
Alignment explanation
Indices: 1492024--1492083 Score: 50
Period size: 8 Copynumber: 7.2 Consensus size: 8
1492014 AATTTGAATA
1492024 TCTTTTTT
1 TCTTTTTT
* *
1492032 TCATTTTC
1 TCTTTTTT
1492040 TCATTTTTT
1 TC-TTTTTT
*
1492049 CCTTCTTTT
1 TCTT-TTTT
*
1492058 CTTTTTTTT
1 -TCTTTTTT
1492067 TCTTTTTT
1 TCTTTTTT
1492075 T-TTTTTT
1 TCTTTTTT
1492082 TC
1 TC
1492084 ATCTTCTTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
7 7 0.17
8 18 0.45
9 13 0.32
10 2 0.05
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (8 bp):
TCTTTTTT
Found at i:1492078 original size:15 final size:15
Alignment explanation
Indices: 1492026--1492100 Score: 78
Period size: 15 Copynumber: 4.6 Consensus size: 15
1492016 TTTGAATATC
1492026 TTTTTTTCATTTTCTCAT
1 TTTTTTTC-TTTTCT--T
1492044 TTTTTCCTTCTTTTCTT
1 TTTTT--TTCTTTTCTT
*
1492061 TTTTTTTCTTTTTTT
1 TTTTTTTCTTTTCTT
*
1492076 TTTTTTTCATCTTCTT
1 TTTTTTTC-TTTTCTT
1492092 TTTTTTTCT
1 TTTTTTTCT
1492101 CATTTTTCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
15 18 0.35
16 13 0.25
17 6 0.12
18 5 0.10
19 6 0.12
20 3 0.06
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTTCTTTTCTT
Found at i:1496131 original size:61 final size:59
Alignment explanation
Indices: 1496001--1496356 Score: 513
Period size: 61 Copynumber: 5.9 Consensus size: 59
1495991 TCTTGTGTAG
* *
1496001 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTT-ATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGGAAATTTGATTTCCAA
* *
1496059 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTTTTGAAACTTTGATTTCCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATAT-TTTTTTGGAAA-TTTGATTTCCAA
1496120 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATCTTTTTTGGAAATTTTGATATT-CAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATAT-TTTTTTGGAAA-TTTGAT-TTCCAA
*
1496181 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAATATATTTTTTTGAAACTTTGATTTCCAA
1 GGAAAATTGATACTTTCAACTTTTCCTC-AAAAATAT-TTTTTTGGAAA-TTTGATTTCCAA
* * **
1496243 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAATTT-ATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGGAAATTTGATTTCCAA
1496301 GGAAAATTGATACTTTCAACTTTTCC-CTAAAAATATTTTTTTGGAAATTTTGATTT
1 GGAAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTTGGAAA-TTTGATTT
1496357 TTATTTAAAG
Statistics
Matches: 273, Mismatches: 16, Indels: 16
0.90 0.05 0.05
Matches are distributed among these distances:
57 1 0.00
58 83 0.30
59 16 0.06
60 18 0.07
61 98 0.36
62 57 0.21
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.44
Consensus pattern (59 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGGAAATTTGATTTCCAA
Found at i:1496387 original size:17 final size:16
Alignment explanation
Indices: 1496362--1496516 Score: 71
Period size: 17 Copynumber: 8.8 Consensus size: 16
1496352 GATTTTTATT
*
1496362 TAAAGAAAATAGAATAA
1 TAAAAAAAATA-AATAA
1496379 TAAAAAAAATAAATAA
1 TAAAAAAAATAAATAA
*
1496395 AAATAAAAAATAAAGTAA
1 TAA-AAAAAATAAA-TAA
*
1496413 -AACAAAAATAAA-AA
1 TAAAAAAAATAAATAA
* *
1496427 TAAGATGAAGATAAAAAATAT
1 TAA-A--AA-A-AATAAATAA
*
1496448 TAAATAAATCTAATCTAATAAA
1 TAAA-AAA---AAT-AAAT-AA
*
1496470 TAAAACAAATAAATAAA
1 TAAAAAAAATAAAT-AA
* *
1496487 TAAATAAAACAAATAAA
1 TAAAAAAAATAAAT-AA
1496504 TAAAAAAAATAAA
1 TAAAAAAAATAAA
1496517 AAAAAAAGAC
Statistics
Matches: 108, Mismatches: 17, Indels: 26
0.72 0.11 0.17
Matches are distributed among these distances:
14 2 0.02
15 2 0.02
16 16 0.15
17 53 0.49
18 9 0.08
19 3 0.03
20 9 0.08
21 9 0.08
22 5 0.05
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.19
Consensus pattern (16 bp):
TAAAAAAAATAAATAA
Found at i:1496392 original size:4 final size:4
Alignment explanation
Indices: 1496385--1496507 Score: 57
Period size: 4 Copynumber: 30.8 Consensus size: 4
1496375 ATAATAAAAA
1496385 AAAT AAAT -AA- AAAT AAA- AAAT AAAGT AAA- ACAA- AAAT -AA- AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT A-AAT AAAT AAAT AAAT
* * * *
1496428 AAGAT GAAGAT AAA- AAAT -ATT AAAT AAAT CTAAT CTAAT AAAT AAAAC
1 AA-AT -AA-AT AAAT AAAT AAAT AAAT AAAT -AAAT -AAAT AAAT -AAAT
*
1496476 AAAT AAAT AAAT AAAT AAAAC AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAA
1496508 AAAAATAAAA
Statistics
Matches: 96, Mismatches: 8, Indels: 30
0.72 0.06 0.22
Matches are distributed among these distances:
3 19 0.20
4 50 0.52
5 22 0.23
6 5 0.05
ACGTcount: A:0.72, C:0.04, G:0.03, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:1496393 original size:13 final size:13
Alignment explanation
Indices: 1496377--1496523 Score: 93
Period size: 13 Copynumber: 10.8 Consensus size: 13
1496367 AAAATAGAAT
1496377 AATAAAAAAAATA
1 AATAAAAAAAATA
1496390 AATAAAAATAAA-A
1 AATAAAAA-AAATA
*
1496403 AATAAAGTAAAACAAA
1 AATAAA--AAAA-ATA
1496419 AATAAAAATAAGATGA
1 AATAAAAA-AA-AT-A
*
1496435 AGATAAAAAATATTA
1 A-ATAAAAAA-AATA
*** *
1496450 AATAAATCTAATCT
1 AATAAAAAAAAT-A
* *
1496464 AATAAATAAAACA
1 AATAAAAAAAATA
*
1496477 AAT-AAATAAATA
1 AATAAAAAAAATA
*
1496489 AATAAAACAAATA
1 AATAAAAAAAATA
1496502 AATAAAAAAAATA
1 AATAAAAAAAATA
1496515 AA-AAAAAAA
1 AATAAAAAAA
1496524 GACCTGGAGC
Statistics
Matches: 106, Mismatches: 17, Indels: 23
0.73 0.12 0.16
Matches are distributed among these distances:
12 16 0.15
13 42 0.40
14 21 0.20
15 8 0.08
16 11 0.10
17 8 0.08
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (13 bp):
AATAAAAAAAATA
Found at i:1496488 original size:21 final size:22
Alignment explanation
Indices: 1496464--1496517 Score: 92
Period size: 21 Copynumber: 2.5 Consensus size: 22
1496454 AATCTAATCT
1496464 AATAAATAAAACAAATAAAT-A
1 AATAAATAAAACAAATAAATAA
1496485 AATAAATAAAACAAATAAATAA
1 AATAAATAAAACAAATAAATAA
*
1496507 AAAAAATAAAA
1 AATAAATAAAA
1496518 AAAAAAGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.17
Consensus pattern (22 bp):
AATAAATAAAACAAATAAATAA
Found at i:1497407 original size:20 final size:20
Alignment explanation
Indices: 1497369--1497422 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 20
1497359 TAGCCATCCA
1497369 AAAAAGAAAATAATAATAAT
1 AAAAAGAAAATAATAATAAT
*
1497389 AAAAA-AAAATACTAGATAATT
1 AAAAAGAAAATAATA-ATAA-T
1497410 AGAAAAGATAAAT
1 A-AAAAGA-AAAT
1497423 CAAAAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 8 0.29
20 9 0.32
21 2 0.07
22 4 0.14
23 1 0.04
24 4 0.14
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.20
Consensus pattern (20 bp):
AAAAAGAAAATAATAATAAT
Found at i:1497462 original size:34 final size:35
Alignment explanation
Indices: 1497380--1497468 Score: 96
Period size: 34 Copynumber: 2.6 Consensus size: 35
1497370 AAAAGAAAAT
*
1497380 AATAATAATAAAAAAA-AATACTAGATAATTAGAA
1 AATAATAATAAAAAAATAATACTAGATAAATAGAA
* * *
1497414 AA-GATAAATCAAAAAATATTA-TAGGATAAATA-AA
1 AATAAT-AATAAAAAAATAATACTA-GATAAATAGAA
1497448 AATAATAATAAAAAAATAATA
1 AATAATAATAAAAAAATAATA
1497469 TCAGATATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
33 2 0.05
34 30 0.68
35 12 0.27
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.24
Consensus pattern (35 bp):
AATAATAATAAAAAAATAATACTAGATAAATAGAA
Found at i:1497523 original size:46 final size:45
Alignment explanation
Indices: 1497438--1497525 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 45
1497428 AATATTATAG
* *
1497438 GATAAATAAAAATAATAATAAAAAAATAATATCAGATATATAATTA
1 GATAAATAAAAATAAAAATAAAAAAATAATA-CAAATATATAATTA
1497484 GATAAATAAAAATACGAAAATAAATAAAATAA-A-AAATATATA
1 GATAAATAAAAATA--AAAATAAA-AAAATAATACAAATATATA
1497526 TATACATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
46 22 0.59
48 8 0.22
49 7 0.19
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (45 bp):
GATAAATAAAAATAAAAATAAAAAAATAATACAAATATATAATTA
Found at i:1498493 original size:35 final size:35
Alignment explanation
Indices: 1498454--1498522 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
1498444 TATATAAACA
*
1498454 AAATATTTTCTGGGCATAAA-TATACAACTGACTTC
1 AAATATTTTCTGAGCATAAACT-TACAACTGACTTC
* *
1498489 AAATATTTTTTGAGCATAAACTTACAATTGACTT
1 AAATATTTTCTGAGCATAAACTTACAACTGACTT
1498523 GACATATACA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 29 0.97
36 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (35 bp):
AAATATTTTCTGAGCATAAACTTACAACTGACTTC
Found at i:1501568 original size:37 final size:38
Alignment explanation
Indices: 1501490--1501568 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
1501480 AGATTCTCCA
*
1501490 TCAATTTAATAGAATTCTTAAAAAAATAGTTTTTTACC
1 TCAATTTAATAGAATTCTTAAAAAAATAGTTTTTCACC
** *
1501528 TCAATTTGGTAGAATTCTT-AAAAAATA-TTTCTTCATC
1 TCAATTTAATAGAATTCTTAAAAAAATAGTTT-TTCACC
1501565 TCAA
1 TCAA
1501569 GAGTATTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 3 0.08
37 16 0.44
38 17 0.47
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (38 bp):
TCAATTTAATAGAATTCTTAAAAAAATAGTTTTTCACC
Found at i:1508322 original size:13 final size:13
Alignment explanation
Indices: 1508284--1508323 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1508274 TTCACTGCTC
1508284 TTGAACATTTTCT
1 TTGAACATTTTCT
** *
1508297 TTGGTCATATTCT
1 TTGAACATTTTCT
1508310 TTGAACATTTTCT
1 TTGAACATTTTCT
1508323 T
1 T
1508324 CATGGCTTGT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.55
Consensus pattern (13 bp):
TTGAACATTTTCT
Found at i:1515218 original size:16 final size:16
Alignment explanation
Indices: 1515199--1515338 Score: 66
Period size: 16 Copynumber: 8.8 Consensus size: 16
1515189 TCTTTTGTAT
1515199 TTTATGTATT-TTATTA
1 TTTAT-TATTATTATTA
1515215 TTTATTATTATTATTA
1 TTTATTATTATTATTA
*
1515231 TATATTAATATATGTA-TA
1 TTTATT-AT-TAT-TATTA
*
1515249 TCT-TTATTTATTTATTTA
1 TTTATTA-TTA-TTA-TTA
* *
1515267 TTTATTTTCTATTAATA
1 TTTATTAT-TATTATTA
*
1515284 TTTA-TATGTATT-GTA
1 TTTATTAT-TATTATTA
1515299 TTTA-TA-TAGTTA-TA
1 TTTATTATTA-TTATTA
*
1515313 TATATTATTATT-TTA
1 TTTATTATTATTATTA
1515328 -TTATTATTATT
1 TTTATTATTATT
1515339 TTTTCTCTTT
Statistics
Matches: 99, Mismatches: 10, Indels: 32
0.70 0.07 0.23
Matches are distributed among these distances:
13 2 0.02
14 17 0.17
15 18 0.18
16 29 0.29
17 12 0.12
18 15 0.15
19 6 0.06
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (16 bp):
TTTATTATTATTATTA
Found at i:1515774 original size:25 final size:25
Alignment explanation
Indices: 1515740--1515793 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
1515730 CTGGGAGTAA
1515740 GAAAAATTTTT-TAAAAATTTTTGG
1 GAAAAATTTTTCTAAAAATTTTTGG
**
1515764 TGAAAAATTTTTCTGGAAATTTTTGG
1 -GAAAAATTTTTCTAAAAATTTTTGG
1515790 GAAA
1 GAAA
1515794 TTTCCAGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.39, C:0.02, G:0.17, T:0.43
Consensus pattern (25 bp):
GAAAAATTTTTCTAAAAATTTTTGG
Found at i:1516601 original size:62 final size:58
Alignment explanation
Indices: 1516446--1516669 Score: 319
Period size: 62 Copynumber: 3.8 Consensus size: 58
1516436 ATAAAAATCA
* *
1516446 AAATTTCCAAAAAAAATATTTTTGAGGAAAAATTGAAAGTATCAATTTTCCTTAAAAAT
1 AAATTT-CAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
* * *
1516505 AAATTTCCAAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGGAAAT
1 AAATTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
1516563 CAAAATTTCAAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
1 --AAATTTC--AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
* *
1516625 AAATTTC---CAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 AAATTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
1516670 TCCCACACAA
Statistics
Matches: 151, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
55 36 0.24
58 47 0.31
59 6 0.04
60 14 0.09
62 48 0.32
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.34
Consensus pattern (58 bp):
AAATTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
Found at i:1516602 original size:120 final size:116
Alignment explanation
Indices: 1516440--1516669 Score: 388
Period size: 120 Copynumber: 1.9 Consensus size: 116
1516430 CTTTAAATAA
*
1516440 AAATCAAAATTTCCAAAAAAAATATTTTTGAGGAAAAATTGAAAGTATCAATTTTCCTTAAAAAT
1 AAATCAAAATTTCAAAAAAAAATATTTTTGAGGAAAAATTGAAAGTATCAATTTTCCTTAAAAAT
1516505 AAATTTCCAAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGG
66 AAATTTCC--AAAA-TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGG
* *
1516559 AAATCAAAATTTCAAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAA
1 AAATCAAAATTTC-AAAAAAAAATATTTTTGAGGAAAAATTGAAAGTATCAATTTTCCTTAAAAA
*
1516624 TAAATTTCCAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
65 TAAATTTCCAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
1516670 TCCCACACAA
Statistics
Matches: 106, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
117 32 0.30
118 4 0.04
119 13 0.12
120 57 0.54
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (116 bp):
AAATCAAAATTTCAAAAAAAAATATTTTTGAGGAAAAATTGAAAGTATCAATTTTCCTTAAAAAT
AAATTTCCAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGG
Found at i:1520552 original size:20 final size:21
Alignment explanation
Indices: 1520527--1520574 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1520517 ATGATGAAAA
*
1520527 AAAAAAAAAAAAG-AAAAATG
1 AAAAAAAAGAAAGAAAAAATG
*
1520547 AGAAAAAAAGAAGGAAAAAATG
1 A-AAAAAAAGAAAGAAAAAATG
1520569 AAAAAA
1 AAAAAA
1520575 GGAGATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 15 0.62
22 8 0.33
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (21 bp):
AAAAAAAAGAAAGAAAAAATG
Found at i:1521870 original size:41 final size:40
Alignment explanation
Indices: 1521808--1522486 Score: 933
Period size: 41 Copynumber: 16.6 Consensus size: 40
1521798 TGATTGTCAG
*
1521808 GGAGTAATTTA-TTTTCCAAAGTTTCGTTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTT-CAAAG-TTCGTTGCCTCTGTTTAGA
1521849 GGAGCAATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAGA
* *
1521890 GGAGCAATTTATTTTTCCAAGTTCGTTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGA
*
1521930 GGAGCAATTTACTTTCCAAAG-TCGTGGTGCCTCTG-TTAGA
1 GGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAGA
1521970 GGAGCAATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAG-TTCGTTGCCTCTGTTTAGA
* *
1522011 GGAGCAATTTACTTTCCAATGTTCGGTTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAGTTC-GTTGCCTCTGTTTAGA
1522052 GGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGA
* * *
1522092 GGAGCAATTTATTTTTCCAAGTTCGTTGCCTTTGTTTAGA
1 GGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGA
* *
1522132 GGAGCAGCAATTTACTTTCCAAAG-TCATGGTGCCTCTGTTTAGA
1 -G-G-AGCAATTTACTTTTCAAAGTTC--GTTGCCTCTGTTTAGA
1522176 GGAGCAATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAG-TTCGTTGCCTCTGTTTAGA
1522217 GGAGCAATTTACTTTTCAAAGTTCAGTTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAGTTC-GTTGCCTCTGTTTAGA
*
1522258 GGAGCAATTTACTTTTCCAAAGTT-GTGGTACCTCTGTTTAGA
1 GGAGCAATTTACTTTT-CAAAGTTCGT--TGCCTCTGTTTAGA
*
1522300 GGAGCAATTTACTTTCCAAAGTTCGGTTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAGTTC-GTTGCCTCTGTTTAGA
*
1522341 GGAGCAATTTACTTTCCAAAG-TCGTGGTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAGA
1522382 GGAGCAATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAG-TTCGTTGCCTCTGTTTAGA
1522423 GGAGCAATTTACTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTT-CAAAGTTCGT--TGCCTCTGTTTAGA
* *
1522465 GGAACAATTTACTTTCCAAAGT
1 GGAGCAATTTACTTTTCAAAGT
1522487 CGTGGTGCCT
Statistics
Matches: 580, Mismatches: 27, Indels: 61
0.87 0.04 0.09
Matches are distributed among these distances:
39 10 0.02
40 132 0.23
41 315 0.54
42 84 0.14
43 25 0.04
44 14 0.02
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (40 bp):
GGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGA
Found at i:1522188 original size:124 final size:120
Alignment explanation
Indices: 1521808--1522486 Score: 933
Period size: 124 Copynumber: 5.5 Consensus size: 120
1521798 TGATTGTCAG
*
1521808 GGAGTAATTTA-TTTTCCAAAGTTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-T
1 GGAGCAATTTACTTTT-CAAAG-TTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTT
* *
1521871 CGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCC-AAGTTCGTTGCCTCTGTTTAGA
64 CGT--TGCCTCTGTTTAGAGGAGCAATTTA-CTTTCCAAAGTTCGGTGCCTCTGTTTAGA
*
1521930 GGAGCAATTTACTTTCCAAAG-TCGTGGTGCCTCTG-TTAGAGGAGCAATTTACTTTTCAAAGTT
1 GGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-T
*
1521993 TCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAATGTTCGGTTGCCTCTGTTTAGA
63 TCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTTCGG-TGCCTCTGTTTAGA
* *
1522052 GGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAGTTCG
1 GGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCG
*
1522117 TTGCCTTTGTTTAGAGGAGCAGCAATTTACTTTCCAAAG-TCATGGTGCCTCTGTTTAGA
66 TTGCCTCTGTTTAGA-G-G-AGCAATTTACTTTCCAAAGTTC--GGTGCCTCTGTTTAGA
1522176 GGAGCAATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTC
1 GGAGCAATTTACTTTTCAAAG-TTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTC
* *
1522241 AGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTTGTGGTACCTCTGTTTAGA
65 -GTTGCCTCTGTTTAGAGGAGCAATTTAC-TTTCCAAAGTT-CGGTGCCTCTGTTTAGA
* *
1522300 GGAGCAATTTACTTTCCAAAGTTCGGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAG-TC
1 GGAGCAATTTACTTTTCAAAGTTC-GTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTC
* *
1522364 GTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAGA
65 GT--TGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAG-TTCGGTGCCTCTGTTTAGA
* *
1522423 GGAGCAATTTACTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAACAATTTACTTTCCAAAGT
1 GGAGCAATTTACTTTT-CAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGT
1522487 CGTGGTGCCT
Statistics
Matches: 507, Mismatches: 23, Indels: 51
0.87 0.04 0.09
Matches are distributed among these distances:
120 9 0.02
121 83 0.16
122 86 0.17
123 68 0.13
124 201 0.40
125 45 0.09
126 15 0.03
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (120 bp):
GGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCG
TTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTTCGGTGCCTCTGTTTAGA
Found at i:1522224 original size:165 final size:162
Alignment explanation
Indices: 1521808--1522564 Score: 1008
Period size: 165 Copynumber: 4.5 Consensus size: 162
1521798 TGATTGTCAG
* * * *
1521808 GGAGTAATTTATTTTCCAAAGTTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCG
1 GGAGCAATTTACTTTCCAAAGTTTCGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCG
* *
1521873 TGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAGTTCGTTGCCTCTGTTTAGAGGAGCAAT
66 T-GTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAAT
1521938 TTAC-TTTCCAAAGTCGTGGTGCCTCTG-TTAGA
130 TTACTTTTCCAAAGTCGT-GTGCCTCTGTTTAGA
* * *
1521970 GGAGCAATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAATGTTC
1 GGAGCAATTTACTTTCCAAAGTTTCGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAG-TC
1522035 G-GTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAA
65 GTG-TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAA
* *
1522099 TTTATTTTTCC-AAGTTCGT-TGCCTTTGTTTAGA
129 TTTACTTTTCCAAAG-TCGTGTGCCTCTGTTTAGA
* *
1522132 GGAGCAGCAATTTACTTTCCAAAGTCAT-GGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAA
1 -G-G-AGCAATTTACTTTCCAAAGT-TTCGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAA
1522196 GTTTCGT-TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCAGTTGCCTCTGTTTAGAGG
62 G--TCGTGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTC-GTTGCCTCTGTTTAGAGG
* *
1522260 AGCAATTTACTTTTCCAAAGTTGTGGTACCTCTGTTTAGA
124 AGCAATTTACTTTTCCAAAGTCGT-GTGCCTCTGTTTAGA
1522300 GGAGCAATTTACTTTCCAAAG-TTCGGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTC
1 GGAGCAATTTACTTTCCAAAGTTTCGG-TGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTC
1522364 GTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAGAGGAGCA
65 GT-GTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-TTCGTTGCCTCTGTTTAGAGGAGCA
1522429 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGA
128 ATTTACTTTTCCAAAGTCGT-GTGCCTCTGTTTAGA
*
1522465 GGAACAATTTACTTTCCAAAGTCGTGGTGCCTCGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTA
1 GGAGCAATTTACTTTCCAAA------GT---T--TC--GGTGCCTCTGTTTAGAGGAGCAATTTA
* * *
1522530 TTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGC
53 CTTTCCAAAGTCG-TGTGCCTCTGTTTAGAGGAGC
1522565 TTTGGTCAAA
Statistics
Matches: 534, Mismatches: 26, Indels: 54
0.87 0.04 0.09
Matches are distributed among these distances:
161 8 0.01
162 128 0.24
163 18 0.03
164 3 0.01
165 254 0.48
166 45 0.08
167 4 0.01
168 12 0.02
171 1 0.00
175 1 0.00
177 2 0.00
178 55 0.10
179 3 0.01
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (162 bp):
GGAGCAATTTACTTTCCAAAGTTTCGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCG
TGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATT
TACTTTTCCAAAGTCGTGTGCCTCTGTTTAGA
Found at i:1522503 original size:13 final size:13
Alignment explanation
Indices: 1522485--1522510 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1522475 ACTTTCCAAA
1522485 GTCGTGGTGCCTC
1 GTCGTGGTGCCTC
1522498 GTCGTGGTGCCTC
1 GTCGTGGTGCCTC
1522511 TGTTTAGAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.31, G:0.38, T:0.31
Consensus pattern (13 bp):
GTCGTGGTGCCTC
Found at i:1522551 original size:54 final size:54
Alignment explanation
Indices: 1522444--1522551 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 54
1522434 CTTTTCCAAA
*
1522444 GTCGTGGTGCCTCTGTTTAGAGGAACAATTTACTTTCCAAAGTCGTGGTGCCTC
1 GTCGTGGTGCCTCTGTTTAGAGGAACAATTTACTTTCCAAAGTCGTGGAGCCTC
* * * *
1522498 GTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTTGAGCCTC
1 GTCGTGGTGCCTCTGTTTAGAGGAACAATTTACTTTCCAAAGTCGTGGAGCCTC
1522552 TGTTTAGAGG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (54 bp):
GTCGTGGTGCCTCTGTTTAGAGGAACAATTTACTTTCCAAAGTCGTGGAGCCTC
Found at i:1522810 original size:16 final size:16
Alignment explanation
Indices: 1522791--1522935 Score: 65
Period size: 16 Copynumber: 8.8 Consensus size: 16
1522781 TCTTTTGTAT
1522791 TTTATGTATT-TTATTA
1 TTTAT-TATTATTATTA
1522807 TTTATTATTATTATTA
1 TTTATTATTATTATTA
1522823 -TTATATATTAATATATGTA
1 TTTAT-TATT-AT-TAT-TA
1522842 TATCT-TTATTTATTTATTTA
1 T-T-TATTA-TTA-TTA-TTA
* *
1522862 TTTATTTTCTATTAATA
1 TTTATTAT-TATTATTA
*
1522879 TTTA-TATGTATT-GTA
1 TTTATTAT-TATTATTA
1522894 TTTA-TA-TAGTTATATA
1 TTTATTATTA-TTAT-TA
*
1522910 TATATTATTATT-TTA
1 TTTATTATTATTATTA
1522925 -TTATTATTATT
1 TTTATTATTATT
1522936 TTTTCTCTTT
Statistics
Matches: 103, Mismatches: 8, Indels: 38
0.69 0.05 0.26
Matches are distributed among these distances:
13 2 0.02
14 12 0.12
15 18 0.17
16 27 0.26
17 12 0.12
18 10 0.10
19 7 0.07
20 8 0.08
21 6 0.06
22 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64
Consensus pattern (16 bp):
TTTATTATTATTATTA
Found at i:1522819 original size:6 final size:6
Alignment explanation
Indices: 1522788--1522935 Score: 51
Period size: 6 Copynumber: 23.2 Consensus size: 6
1522778 TCTTCTTTTG
*
1522788 TATT-T TATGTAT T-TTAT TATTTAT TATTAT TATTAT TATATAT TAATA-
1 TATTAT TAT-TAT TATTAT TA-TTAT TATTAT TATTAT TAT-TAT TATTAT
* *
1522836 TATGTA- TATCT-T TATTTATT TATTTATT TATTTT CTATTAA TATT-T
1 TAT-TAT TAT-TAT TA-TTA-T TA-TTA-T TATTAT -TATTAT TATTAT
*
1522882 ATATGTAT T-GTATT TATATAGT TATATAT ATATTAT TATT-T TATTAT
1 -TAT-TAT TATTA-T TAT-TA-T TAT-TAT -TATTAT TATTAT TATTAT
1522929 TATTAT T
1 TATTAT T
1522936 TTTTCTCTTT
Statistics
Matches: 114, Mismatches: 10, Indels: 37
0.71 0.06 0.23
Matches are distributed among these distances:
5 16 0.14
6 48 0.42
7 26 0.23
8 24 0.21
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64
Consensus pattern (6 bp):
TATTAT
Found at i:1522838 original size:8 final size:7
Alignment explanation
Indices: 1522802--1522934 Score: 57
Period size: 6 Copynumber: 18.9 Consensus size: 7
1522792 TTATGTATTT
*
1522802 TATTATT
1 TATTATA
1522809 TATTAT-
1 TATTATA
1522815 TATTAT-
1 TATTATA
1522821 TATTATA
1 TATTATA
1522828 TATTAATA
1 TATT-ATA
1522836 TATGTATA
1 TAT-TATA
*
1522844 TCTT-TA
1 TATTATA
*
1522850 T-TTATT
1 TATTATA
*
1522856 TATTTATT
1 TA-TTATA
* *
1522864 TATTTTC
1 TATTATA
1522871 TATTA-A
1 TATTATA
1522877 TATT-TA
1 TATTATA
*
1522883 TATGTATTG
1 TAT-TA-TA
1522892 TATTTATA
1 TA-TTATA
1522900 TAGTTATA
1 TA-TTATA
1522908 TA-TATA
1 TATTATA
*
1522914 TTATTATTT
1 -TATTA-TA
1522923 TATTAT-
1 TATTATA
1522929 TATTAT
1 TATTAT
1522935 TTTTTCTCTT
Statistics
Matches: 102, Mismatches: 10, Indels: 29
0.72 0.07 0.21
Matches are distributed among these distances:
5 2 0.02
6 35 0.34
7 22 0.22
8 35 0.34
9 7 0.07
10 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (7 bp):
TATTATA
Found at i:1523072 original size:19 final size:20
Alignment explanation
Indices: 1523050--1523087 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1523040 TCTTTTCTAA
1523050 TTATCT-ATTATTATTTTTT
1 TTATCTGATTATTATTTTTT
* *
1523069 TTATTTGATTTTTATTTTT
1 TTATCTGATTATTATTTTT
1523088 CGAGGGCTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (20 bp):
TTATCTGATTATTATTTTTT
Found at i:1523394 original size:25 final size:25
Alignment explanation
Indices: 1523340--1523394 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1523330 TCTGGGAGTA
*
1523340 AGAAAAATTTTTTAGAAATTTTTGG
1 AGAAAAATTTTTTAGAAATTTCTGG
* *
1523365 TGAAAAATTTTTCTGGAAATTTCT-G
1 AGAAAAATTTTT-TAGAAATTTCTGG
1523390 AGAAA
1 AGAAA
1523395 TTTCCAGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (25 bp):
AGAAAAATTTTTTAGAAATTTCTGG
Found at i:1523924 original size:11 final size:11
Alignment explanation
Indices: 1523910--1524050 Score: 51
Period size: 11 Copynumber: 12.3 Consensus size: 11
1523900 TTTTTTTGGA
1523910 ATTTTTTATTT
1 ATTTTTTATTT
*
1523921 ATTTATTTGTTT
1 ATTT-TTTATTT
*
1523933 A-TTTGT-TTT
1 ATTTTTTATTT
1523942 ATTGTTTTA-TT
1 ATT-TTTTATTT
1523953 ATTTTTATTAGATTAT
1 A-TTTT-TT--ATT-T
*
1523969 ATTTATTTA-AT
1 ATTT-TTTATTT
1523980 ATTTTTTATCTTT
1 ATTTTTTA--TTT
*
1523993 ATCTTATT-TTT
1 AT-TTTTTATTT
**
1524004 ATTTTTTGCGTT
1 ATTTTTT-ATTT
* *
1524016 A-CTTTTCTTT
1 ATTTTTTATTT
*
1524026 GTTTTTTATTT
1 ATTTTTTATTT
1524037 ATTTTTTATTT
1 ATTTTTTATTT
1524048 ATT
1 ATT
1524051 ATTCTTTAAA
Statistics
Matches: 98, Mismatches: 14, Indels: 36
0.66 0.09 0.24
Matches are distributed among these distances:
9 4 0.04
10 14 0.14
11 48 0.49
12 14 0.14
13 4 0.04
14 5 0.05
15 6 0.06
16 3 0.03
ACGTcount: A:0.18, C:0.04, G:0.05, T:0.73
Consensus pattern (11 bp):
ATTTTTTATTT
Found at i:1523944 original size:17 final size:16
Alignment explanation
Indices: 1523910--1523961 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
1523900 TTTTTTTGGA
*
1523910 ATTT-TTTATTTATTT
1 ATTTGTTTATTTTTTT
1523925 ATTTGTTTATTTGTTTT
1 ATTTGTTTATTT-TTTT
1523942 A-TTGTTTTATTATTTTT
1 ATTTG-TTTATT-TTTTT
1523959 ATT
1 ATT
1523962 AGATTATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.13
16 10 0.32
17 15 0.48
18 2 0.06
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (16 bp):
ATTTGTTTATTTTTTT
Found at i:1524150 original size:58 final size:60
Alignment explanation
Indices: 1524061--1524178 Score: 177
Period size: 58 Copynumber: 2.0 Consensus size: 60
1524051 ATTCTTTAAA
1524061 TAAAAATCAAAATTTCCAAAAAAAATATTTTTGAGAAAAAATTGAAAGTATCAATTTTCCT
1 TAAAAAT-AAAATTTCCAAAAAAAATATTTTTGAGAAAAAATTGAAAGTATCAATTTTCCT
* * * *
1524122 TAAAAAT-AAATTTTC-AAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
1 TAAAAATAAAATTTCCAAAAAAAATATTTTTGAGAAAAAATTGAAAGTATCAATTTTCC
1524179 CCACACAAGA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 39 0.74
59 7 0.13
61 7 0.13
ACGTcount: A:0.48, C:0.08, G:0.09, T:0.34
Consensus pattern (60 bp):
TAAAAATAAAATTTCCAAAAAAAATATTTTTGAGAAAAAATTGAAAGTATCAATTTTCCT
Found at i:1526736 original size:144 final size:142
Alignment explanation
Indices: 1526473--1527218 Score: 1053
Period size: 144 Copynumber: 5.2 Consensus size: 142
1526463 TTCGACATGC
*
1526473 TTCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACCCAAAGTCAGTGAGAGAT
1 TTCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCAAAGTCAGTGAGAGAT
** *
1526538 TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATCGAGGTAAAGAGTGGA
66 TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGAT-GAGGTGGAGAATGGA
1526603 TAGACTGGTCAAGT
130 TA-ACTGGTCAAGT
*
1526617 TTCCTATGGAAGCAGGGATTGAACCAAAGAAATTATTTTGACTCAACTCAATA-TCAGTGAGAGA
1 TTCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCAA-AGTCAGTGAGAGA
* * * * **
1526681 TTTAAGCATGCCTATCTCTTGAGGTATCGATCCAGAAAACATATTTTGGTAGAGGTAGAGAAAAG
65 TTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGAT-GAGGTGGAGAATGG
*
1526746 ATAAGTTGGTCAAGT
129 ATAA-CTGGTCAAGT
*
1526761 TTCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGGCTCAACTCAAAGTCAGTGAGAGAT
1 TTCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCAAAGTCAGTGAGAGAT
* * * *
1526826 TTAAGCATCCTTATCTCTTGAGGTAACGACCCAGAAAACATATTATGATGAAGGTGGAGACTGGA
66 TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATG-AGGTGGAGAATGGA
1526891 TAAACTGGTCAAGT
130 T-AACTGGTCAAGT
* * * *
1526905 TTCTTATGGAAGCAGGGACTGAACCAGAGAAATTATTATGACTAAACTCAAAGTCAGTGAGAGAT
1 TTCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCAAAGTCAGTGAGAGAT
* * *
1526970 TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTATGGTGAAGGTGGAGAGTGGA
66 TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATG-AGGTGGAGAATGGA
1527035 TAAACTGGTCAAGT
130 T-AACTGGTCAAGT
* * * *
1527049 TTCTTATGGAAGCAGGAATTGAACCAGAGAAATTATTATGAATCAACTCAAAGTCAGTGAGAGAT
1 TTCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCAAAGTCAGTGAGAGAT
* * * * **
1527114 TTAAGCATCCCTATTTCTCGAGGTATCGATCCACAAAACATATTTTGATAGAGGTGGAGAACAGA
66 TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGAT-GAGGTGGAGAATGGA
*
1527179 TAAGTAGGTCAAGT
130 TAACT-GGTCAAGT
* *
1527193 TTCCTACGGAAGCAGGGATAGAACCA
1 TTCCTATGGAAGCAGGGATTGAACCA
1527219 CGTAGATAGT
Statistics
Matches: 544, Mismatches: 51, Indels: 14
0.89 0.08 0.02
Matches are distributed among these distances:
143 6 0.01
144 534 0.98
145 4 0.01
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (142 bp):
TTCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCAAAGTCAGTGAGAGAT
TTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATGAGGTGGAGAATGGAT
AACTGGTCAAGT
Found at i:1528141 original size:31 final size:31
Alignment explanation
Indices: 1528095--1528168 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 31
1528085 TAAATGAGTT
*
1528095 TAAAAGATTACTACAAACAATTAGATCATAAA
1 TAAAAAATTA-TACAAACAATTAGATCATAAA
1528127 TAAAAAATTATACAAACAATTAGATCATAAA
1 TAAAAAATTATACAAACAATTAGATCATAAA
1528158 TAAAAAATTAT
1 TAAAAAATTAT
1528169 GTAAAGAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 32 0.78
32 9 0.22
ACGTcount: A:0.59, C:0.09, G:0.04, T:0.27
Consensus pattern (31 bp):
TAAAAAATTATACAAACAATTAGATCATAAA
Found at i:1528861 original size:18 final size:18
Alignment explanation
Indices: 1528840--1528891 Score: 50
Period size: 23 Copynumber: 2.6 Consensus size: 18
1528830 ACATACTCTC
1528840 TGAACTAATCATATTCTT
1 TGAACTAATCATATTCTT
*
1528858 TGAACTTATGCTATCGTATTCTT
1 TGAAC-TA----ATCATATTCTT
1528881 TGAACTAATCA
1 TGAACTAATCA
1528892 AATATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
18 8 0.30
19 2 0.07
22 2 0.07
23 15 0.56
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (18 bp):
TGAACTAATCATATTCTT
Found at i:1530165 original size:18 final size:18
Alignment explanation
Indices: 1530131--1530165 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1530121 TATTTTATAA
* *
1530131 TAATATATTTATAAAAAT
1 TAATAAATTTAAAAAAAT
1530149 TAATAAATTTAAAAAAA
1 TAATAAATTTAAAAAAA
1530166 GAACTCTATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATAAATTTAAAAAAAT
Found at i:1530843 original size:19 final size:19
Alignment explanation
Indices: 1530821--1530857 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1530811 TAAAATTTGT
*
1530821 AAAATTAATAAATTATTTA
1 AAAATCAATAAATTATTTA
*
1530840 AAAATCCATAAATTATTT
1 AAAATCAATAAATTATTT
1530858 TTATGTCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATCAATAAATTATTTA
Found at i:1532831 original size:16 final size:17
Alignment explanation
Indices: 1532810--1532841 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1532800 TTTTTTTTAT
1532810 AAAAAATTG-CAATATA
1 AAAAAATTGTCAATATA
1532826 AAAAAATTGTCAATAT
1 AAAAAATTGTCAATAT
1532842 TGATATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.28
Consensus pattern (17 bp):
AAAAAATTGTCAATATA
Found at i:1533094 original size:75 final size:75
Alignment explanation
Indices: 1533015--1533165 Score: 275
Period size: 75 Copynumber: 2.0 Consensus size: 75
1533005 TATATGATAC
* *
1533015 ATCATTCAAAATTTTAAACTTGATAAATAGGTTTATAAGATTATTACATATCATTAGGTCATAAT
1 ATCATTCAAAATTTTAAACTCGATAAATAAGTTTATAAGATTATTACATATCATTAGGTCATAAT
*
1533080 TAAAATATTA
66 TAAAAAATTA
1533090 ATCATTCAAAATTTTAAACTCGATAAATAAGTTTATAAGATTATTACATATCATTAGGTCATAAT
1 ATCATTCAAAATTTTAAACTCGATAAATAAGTTTATAAGATTATTACATATCATTAGGTCATAAT
1533155 TAAAAAATTA
66 TAAAAAATTA
1533165 A
1 A
1533166 GTATATAGAC
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (75 bp):
ATCATTCAAAATTTTAAACTCGATAAATAAGTTTATAAGATTATTACATATCATTAGGTCATAAT
TAAAAAATTA
Found at i:1533284 original size:18 final size:18
Alignment explanation
Indices: 1533257--1533291 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1533247 TATTTTACAA
*
1533257 TAATATATTTATAAAAAT
1 TAATAAATTTATAAAAAT
*
1533275 TAATAAATTTTTAAAAA
1 TAATAAATTTATAAAAA
1533292 CTCTATCATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAAATTTATAAAAAT
Found at i:1534174 original size:17 final size:17
Alignment explanation
Indices: 1534132--1534174 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1534122 TTTAGTTAAT
*
1534132 TAATTTTTATATAATAA
1 TAATTTTTATAAAATAA
**
1534149 TAAAATTTATAAAATAA
1 TAATTTTTATAAAATAA
1534166 TAATTTTTA
1 TAATTTTTA
1534175 GTTCATAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATTTTTATAAAATAA
Found at i:1536426 original size:58 final size:59
Alignment explanation
Indices: 1536362--1536524 Score: 240
Period size: 61 Copynumber: 2.7 Consensus size: 59
1536352 GCTTTTGTAA
* *
1536362 AAGGAAAATTGATACTTTCAACTTTTTCTCGAAAATATTTTTTTG-AAAACTTATTTTC
1 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAAACTTATTTTC
* * *
1536420 AAGGAAAATTGATATTTTCAACTTTTCCTTAAAAATATTTTTTAGGAAAAAACTTATTTTC
1 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT-TG-AAAAACTTATTTTC
1536481 AA-GAAATATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
1 AAGGAAA-ATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
1536525 TGGAATTTTA
Statistics
Matches: 93, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
58 39 0.42
59 1 0.01
60 4 0.04
61 49 0.53
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (59 bp):
AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAAACTTATTTTC
Found at i:1537546 original size:14 final size:13
Alignment explanation
Indices: 1537503--1537669 Score: 68
Period size: 14 Copynumber: 11.6 Consensus size: 13
1537493 AAAAATAAAA
1537503 AATATATATATACAT
1 AATA-ATATATA-AT
* *
1537518 ATTAATAGATAAAT
1 AATAATATAT-AAT
1537532 AATAATATATGAAT
1 AATAATATAT-AAT
1537546 AGATAAATAATATATATT
1 A-AT-AAT-ATATA-A-T
*
1537564 AATAGATAAATAAT
1 AATA-ATATATAAT
* *
1537578 AATAAAAAATATAT
1 AATAATATATA-AT
* *
1537592 ATTAATAGATAAAT
1 AATAATATAT-AAT
*
1537606 AATAAAATATGAAT
1 AATAATATAT-AAT
1537620 AGATAA-ATAATAAT
1 A-ATAATAT-ATAAT
*
1537634 AAAAATATATATATT
1 AATAATATATA-A-T
*
1537649 AATAGATAAATAAT
1 AATA-ATATATAAT
1537663 AA-AATAT
1 AATAATAT
1537670 GTTAATAGAT
Statistics
Matches: 119, Mismatches: 18, Indels: 33
0.70 0.11 0.19
Matches are distributed among these distances:
12 3 0.03
13 13 0.11
14 58 0.49
15 19 0.16
16 15 0.13
17 9 0.08
18 2 0.02
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.34
Consensus pattern (13 bp):
AATAATATATAAT
Found at i:1537562 original size:21 final size:21
Alignment explanation
Indices: 1537516--1537708 Score: 126
Period size: 21 Copynumber: 9.0 Consensus size: 21
1537506 ATATATATAC
1537516 ATATTAATAGATAAATAATAAT
1 ATATTAATAGATAAATAAT-AT
*
1537538 ATATGAATAGATAAATAATAT
1 ATATTAATAGATAAATAATAT
1537559 ATATTAATAGATAAATAATA-
1 ATATTAATAGATAAATAATAT
** * *
1537579 ATAAAAAATATATATTAATAGATAA
1 AT-ATTAATAGATA--AATA-ATAT
* * * * *
1537604 ATAATAAAATATGAATAGATAA
1 ATATTAATAGATAAATA-ATAT
*
1537626 ATAATAATA-A-AAAT-ATAT
1 ATATTAATAGATAAATAATAT
1537644 ATATTAATAGATAAATAATAAAAT
1 ATATTAATAGATAAATAAT---AT
* *
1537668 ATGTTAATAGATAAATAATCT
1 ATATTAATAGATAAATAATAT
* *
1537689 TTATATATTA-ATAAATAATA
1 ATAT-TAATAGATAAATAATA
1537709 ATAGCAGTAA
Statistics
Matches: 141, Mismatches: 18, Indels: 25
0.77 0.10 0.14
Matches are distributed among these distances:
18 11 0.08
19 1 0.01
20 9 0.06
21 44 0.31
22 39 0.28
23 4 0.03
24 31 0.22
25 2 0.01
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.35
Consensus pattern (21 bp):
ATATTAATAGATAAATAATAT
Found at i:1537616 original size:74 final size:78
Alignment explanation
Indices: 1537516--1537686 Score: 235
Period size: 74 Copynumber: 2.2 Consensus size: 78
1537506 ATATATATAC
* **
1537516 ATATTAATAGATAAATAATAATATATGAATAGATAAATAATATATATTAATAGATA-AATAATA-
1 ATATTAATAGATAAATAATAAAATATGAATAGATAAATAATA-ATAAAAATAGATATAATAATAG
*
1537579 AT-AA-AA-AATAT
65 ATAAATAATAAAAT
* *
1537590 ATATTAATAGATAAATAATAAAATATGAATAGATAAATAATAATAAAAATATATATATTAATAGA
1 ATATTAATAGATAAATAATAAAATATGAATAGATAAATAATAATAAAAATAGATATAATAATAGA
1537655 TAAATAATAAAAT
66 TAAATAATAAAAT
*
1537668 ATGTTAATAGATAAATAAT
1 ATATTAATAGATAAATAAT
1537687 CTTTATATAT
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
73 10 0.12
74 47 0.55
75 2 0.02
76 2 0.02
77 2 0.02
78 22 0.26
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (78 bp):
ATATTAATAGATAAATAATAAAATATGAATAGATAAATAATAATAAAAATAGATATAATAATAGA
TAAATAATAAAAT
Found at i:1537734 original size:130 final size:127
Alignment explanation
Indices: 1537510--1537741 Score: 308
Period size: 130 Copynumber: 1.8 Consensus size: 127
1537500 AAAAATATAT
*
1537510 ATATACATATTAATAGATAAATAATAATATATGAATAGATAAATAATATATATTAATAGATAAAT
1 ATATACATATTAATAGATAAATAATAAAATATGAATAGATAAATAATATATATTAATAGATAAAT
* *
1537575 AATAATAAAAAATATATATTAATAGATAAATAATAAAATATGAATAGATAAATAATAATAAAA
66 AATAATAAAAAATATATATAAATAAATAAA-AATAAAATATGAATAGATAAATAATAATAAAA
* * * *
1537638 ATATATATATTAATAGATAAATAATAAAATATGTTAATAGATAAATAATCTTTATATATTA-ATA
1 ATATACATATTAATAGATAAATAATAAAATATG--AATAGATAAATAATATATAT-TAATAGATA
**
1537702 AATAATAATAGCAGTAATA-A-ATAAATAAATAAAAATAAAA
63 AATAATAATA--AAAAATATATATAAATAAATAAAAATAAAA
1537742 AATAAAAAAA
Statistics
Matches: 90, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
128 31 0.34
129 7 0.08
130 42 0.47
131 5 0.06
132 5 0.06
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (127 bp):
ATATACATATTAATAGATAAATAATAAAATATGAATAGATAAATAATATATATTAATAGATAAAT
AATAATAAAAAATATATATAAATAAATAAAAATAAAATATGAATAGATAAATAATAATAAAA
Found at i:1537750 original size:14 final size:14
Alignment explanation
Indices: 1537720--1537749 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1537710 TAGCAGTAAT
1537720 AAATAAATAAATAA
1 AAATAAATAAATAA
1537734 AAATAAA-AAATAA
1 AAATAAATAAATAA
1537747 AAA
1 AAA
1537750 AATGCAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAATAAATAAATAA
Found at i:1537920 original size:18 final size:18
Alignment explanation
Indices: 1537897--1537931 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1537887 CGCTCGACCT
1537897 TTTTTCTTTTTTTTTTGC
1 TTTTTCTTTTTTTTTTGC
1537915 TTTTTCTTTTTTTTTTG
1 TTTTTCTTTTTTTTTTG
1537932 TGTTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.86
Consensus pattern (18 bp):
TTTTTCTTTTTTTTTTGC
Found at i:1538054 original size:42 final size:41
Alignment explanation
Indices: 1537951--1538168 Score: 217
Period size: 42 Copynumber: 5.2 Consensus size: 41
1537941 TTTGATCAAA
* * **
1537951 GCTCCTCTAAGCA-AGGGCTCAACAACTTTGAGAAACATAAACAAA
1 GCTCCTCTAATCAGA-GGCTCAACGACTTTG-GAAA-AT-AA-ATT
* * *
1537996 GCTCCTATAATTAGAGGCTTAACGACTTTTGGAAAATAAATT
1 GCTCCTCTAATCAGAGGCTCAACGAC-TTTGGAAAATAAATT
* **
1538038 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAAAG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGGAAAATAAATT
* *
1538079 GCTCCTCTAATCAGAGGCTCAATGACTTTTGGAAAGTAAATT
1 GCTCCTCTAATCAGAGGCTCAACGAC-TTTGGAAAATAAATT
* *
1538121 GCTCCTCTAATCAGAGGCATC-ACAACTTT-GAAAGTAAATT
1 GCTCCTCTAATCAGAGGC-TCAACGACTTTGGAAAATAAATT
1538161 GCTCCTCT
1 GCTCCTCT
1538169 GAACAGATGC
Statistics
Matches: 149, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
40 19 0.13
41 40 0.27
42 56 0.38
43 4 0.03
44 2 0.01
45 23 0.15
46 5 0.03
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (41 bp):
GCTCCTCTAATCAGAGGCTCAACGACTTTGGAAAATAAATT
Found at i:1538113 original size:83 final size:83
Alignment explanation
Indices: 1537951--1538234 Score: 283
Period size: 83 Copynumber: 3.4 Consensus size: 83
1537941 TTTGATCAAA
* * *
1537951 GCTCCTCTAAGCA-AGGGCTCAACAACTTTGAGAAACATAAACAAAGCTCCTATAATTAGAGGCT
1 GCTCCTCTAATCAGA-GGCTCAACAACTTTGA-AAA-AT-AA-AAAGCTCCTCTAATCAGAGGCT
* * *
1538015 TAACGACTTTTGGAAAATAAATT
61 CAATGACTTTTGGAAAGTAAATT
* *
1538038 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAAAGGCTCCTCTAATCAGAGGCTCAATG
1 GCTCCTCTAATCAGAGGCTCAACAACTTTGAAAAATAAAAAGCTCCTCTAATCAGAGGCTCAATG
1538103 ACTTTTGGAAAGTAAATT
66 ACTTTTGGAAAGTAAATT
* ** * * *
1538121 GCTCCTCTAATCAGAGGCATC-ACAACTTTG-AAAGTAAATTGCTCCTCTGAA-CAGATGCACCA
1 GCTCCTCTAATCAGAGGC-TCAACAACTTTGAAAAATAAAAAGCTCCTCT-AATCAGAGGCTCAA
*
1538183 TAACTTTT-GAAAGTAAATT
64 TGACTTTTGGAAAGTAAATT
* * * *
1538202 TCTCCTCTAAACAAAGGTATC-ACAACTTTGAAA
1 GCTCCTCTAATCAGAGG-CTCAACAACTTTGAAA
1538235 GTAAATGCTC
Statistics
Matches: 172, Mismatches: 20, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
81 36 0.21
82 32 0.19
83 67 0.39
84 4 0.02
85 2 0.01
86 3 0.02
87 27 0.16
88 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (83 bp):
GCTCCTCTAATCAGAGGCTCAACAACTTTGAAAAATAAAAAGCTCCTCTAATCAGAGGCTCAATG
ACTTTTGGAAAGTAAATT
Found at i:1538165 original size:40 final size:40
Alignment explanation
Indices: 1538027--1538244 Score: 221
Period size: 41 Copynumber: 5.4 Consensus size: 40
1538017 ACGACTTTTG
* *
1538027 GAAAATAAATTGCTCCTCTAATCAGAGGC-TCAACGACTTT
1 GAAAGTAAATTGCTCCTCTAATCAGAGGCATC-ACAACTTT
* **
1538067 GAAAAATAAAAGGCTCCTCTAATCAGAGGC-TCA-ATGACTTTT
1 G-AAAGTAAATTGCTCCTCTAATCAGAGGCATCACA--AC-TTT
1538109 GGAAAGTAAATTGCTCCTCTAATCAGAGGCATCACAACTTT
1 -GAAAGTAAATTGCTCCTCTAATCAGAGGCATCACAACTTT
* * *
1538150 GAAAGTAAATTGCTCCTCTGAA-CAGATGCACCATAACTTTT
1 GAAAGTAAATTGCTCCTCT-AATCAGAGGCATCACAAC-TTT
* * * *
1538191 GAAAGTAAATTTCTCCTCTAAACAAAGGTATCACAACTTT
1 GAAAGTAAATTGCTCCTCTAATCAGAGGCATCACAACTTT
1538231 GAAAGTAAA-TGCTC
1 GAAAGTAAATTGCTC
1538245 ATTGATAATC
Statistics
Matches: 152, Mismatches: 16, Indels: 21
0.80 0.08 0.11
Matches are distributed among these distances:
39 4 0.03
40 47 0.31
41 66 0.43
42 30 0.20
43 4 0.03
44 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.28
Consensus pattern (40 bp):
GAAAGTAAATTGCTCCTCTAATCAGAGGCATCACAACTTT
Found at i:1544272 original size:20 final size:19
Alignment explanation
Indices: 1544247--1544292 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
1544237 TGGTATGTTT
1544247 GTGGGTAGGATGGCTATAGG
1 GTGGGTAGGATGGCTAT-GG
1544267 GTGGGTAGGATGGCTATGG
1 GTGGGTAGGATGGCTATGG
1544286 GATGGGT
1 G-TGGGT
1544293 TGGTATGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.17, C:0.04, G:0.52, T:0.26
Consensus pattern (19 bp):
GTGGGTAGGATGGCTATGG
Found at i:1545625 original size:15 final size:15
Alignment explanation
Indices: 1545601--1545631 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1545591 TGTTAAGTGT
*
1545601 AATGAGTGAAAATGC
1 AATGAATGAAAATGC
1545616 AATGAATGAAAATGC
1 AATGAATGAAAATGC
1545631 A
1 A
1545632 TGTATGCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.19
Consensus pattern (15 bp):
AATGAATGAAAATGC
Found at i:1548969 original size:58 final size:56
Alignment explanation
Indices: 1548836--1549053 Score: 249
Period size: 61 Copynumber: 3.7 Consensus size: 56
1548826 TTGTACAAGA
* *
1548836 AAAATTGATACTTTCAACTTTTCCCCCAAAAAACCCTTTTTTAGAAAA-TTACTTTTAAAG
1 AAAATTGATACTTTCAACTTTT-CCTCAAAATA---TTTTTTAGAAAACTTA-TTTTAAAG
*
1548896 AAAATTGATACTTTCAACTTTTCCTCGAAAATATTTTTTAGAAAACTTATTTTTAAG
1 AAAATTGATACTTTCAACTTTTCCTC-AAAATATTTTTTAGAAAACTTATTTTAAAG
** *
1548953 AAAATTTGATGTTTTCAACTTTTTCTCAGAAATATTTTTTAGGGAAAAACTTATTTTCAAAG
1 AAAA-TTGATACTTTCAACTTTTCCTCA-AAATATTTTTTA--G-AAAACTTATTTT-AAAG
*
1549015 AAAATTGATACTTTCAACTTTTCATCAAAAATATTTTTT
1 AAAATTGATACTTTCAACTTTTCCTC-AAAATATTTTTT
1549054 TTTGGAATTT
Statistics
Matches: 138, Mismatches: 11, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
57 24 0.17
58 34 0.25
59 3 0.02
60 28 0.20
61 41 0.30
62 8 0.06
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (56 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTAGAAAACTTATTTTAAAG
Found at i:1549096 original size:5 final size:5
Alignment explanation
Indices: 1549086--1549118 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
1549076 ATCATTTAAA
1549086 AAAAT AAAAT AAAAT AAAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AA
1549119 GGAATACTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Done.