Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 152 of 198
Found at i:48123137 original size:12 final size:12
Alignment explanation
Indices: 48123120--48123154 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
48123110 ATTAATATAT
48123120 ATACATATCATG
1 ATACATATCATG
48123132 ATACATATCATG
1 ATACATATCATG
48123144 ATACATATCAT
1 ATACATATCAT
48123155 TCTCTTACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (12 bp):
ATACATATCATG
Found at i:48123299 original size:21 final size:21
Alignment explanation
Indices: 48123275--48123333 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
48123265 CAAAAACTTG
*
48123275 TAAGAGCTGAACAGAAACTCA
1 TAAGAGCTAAACAGAAACTCA
* *
48123296 TAAGAGTTAAACAGAAGCTCGA
1 TAAGAGCTAAACAGAAACTC-A
*
48123318 -AAGAACTAAACAGAAA
1 TAAGAGCTAAACAGAAA
48123334 GTAAAACATG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.53, C:0.15, G:0.19, T:0.14
Consensus pattern (21 bp):
TAAGAGCTAAACAGAAACTCA
Found at i:48128340 original size:127 final size:126
Alignment explanation
Indices: 48128111--48128631 Score: 619
Period size: 127 Copynumber: 4.2 Consensus size: 126
48128101 TAAGGCCAAG
* * * *
48128111 CAGAAACTATTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTCTGTAATTTTGCTGACAGTGC
1 CAGAAACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* * * *
48128176 ATCTTGCTTAAAGCGTTTTTGGCACTATTTTTTCAGAATAGCCTTCTCAAAATTATTTTTT
66 ATCTTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAATCGTCTTCTCAAAATTATTTTTT
* * *
48128237 CA-AGAACTACTGTATAAAAAGAGCGTCTACATGGGAGCTTTTTTCAGTAATTTTTGTTGACAGT
1 CAGA-AACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGTAA-TTTTGCTGACAGT
* * *
48128301 GCAT-TCTGCTTGAAGCGTTTTTAACACTATTTTTTCAGAACCGTCTTTTCAAAATTATTTTTT
64 GCATCT-TGCTTGAAGCGTTTTTGACACTATTTTTTCAGAATCGTCTTCTCAAAATTATTTTTT
* * * * *
48128364 CGGAAACTATTGTAAAAAAAGAGCGTCCACGTGGGAGGTTTTTT-AGTAATTTTGCTGACAGTGC
1 CAGAAACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* * * * *
48128428 ATCATGTTTGAAGCGTTTTTGACA-TAATTTTTTTTAGAAT-TTCTTCT--TAATTATTTTTT
66 ATCTTGCTTGAAGCGTTTTTGACACT-A-TTTTTTCAGAATCGTCTTCTCAAAATTATTTTTT
* * * * *
48128487 CAGAAACTACTATAGAAAAATAACGTCCA-AGTGGGAG-TTTTTTCAGTACTTTTGCTAACAGTG
1 CAGAAACTACTGTAGAAAAAGAGCGTCCACA-TGGGAGCTTTTTTCAGTAATTTTGCTGACAGTG
* * * *
48128550 CATCTTGCTTGAAGCGTTTTTGTCACTATTTTTTCATAATCGTTTTCTCAAAATTAATTTTT
65 CATCTTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAATCGTCTTCTCAAAATTATTTTTT
*
48128612 CAGAAACTACTATAGAAAAA
1 CAGAAACTACTGTAGAAAAA
48128632 AAAAAATACA
Statistics
Matches: 335, Mismatches: 47, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
122 16 0.05
123 85 0.25
124 2 0.01
125 71 0.21
126 58 0.17
127 102 0.30
128 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (126 bp):
CAGAAACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
ATCTTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAATCGTCTTCTCAAAATTATTTTTT
Found at i:48128828 original size:27 final size:28
Alignment explanation
Indices: 48128791--48128868 Score: 115
Period size: 28 Copynumber: 2.9 Consensus size: 28
48128781 TTAATTAATG
* *
48128791 TTTTTT-AAAT-CTTAAACCCTGATTTA
1 TTTTTTAAAATCCCTAAACCCTAATTTA
*
48128817 TTTTTTAAAATCCCCAAACCCTAATTTA
1 TTTTTTAAAATCCCTAAACCCTAATTTA
48128845 TTTTTTAAAATCCCTAAACCCTAA
1 TTTTTTAAAATCCCTAAACCCTAA
48128869 ATAAATAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.13
27 4 0.09
28 36 0.78
ACGTcount: A:0.35, C:0.22, G:0.01, T:0.42
Consensus pattern (28 bp):
TTTTTTAAAATCCCTAAACCCTAATTTA
Found at i:48134660 original size:10 final size:11
Alignment explanation
Indices: 48134605--48134691 Score: 79
Period size: 11 Copynumber: 7.9 Consensus size: 11
48134595 TTTTGTAGGT
48134605 TTTTGGTGCTG
1 TTTTGGTGCTG
* *
48134616 TTTTGTTGTTG
1 TTTTGGTGCTG
* *
48134627 TTGGTGATGCTG
1 TT-TTGGTGCTG
*
48134639 TTTTTTGTGCTG
1 -TTTTGGTGCTG
48134651 -TTTGGTGCTG
1 TTTTGGTGCTG
*
48134661 TTTTGATGCTG
1 TTTTGGTGCTG
*
48134672 TTTTGGTGTTG
1 TTTTGGTGCTG
48134683 TTTT-GTGCT
1 TTTTGGTGCT
48134692 ACTTTTTGTG
Statistics
Matches: 60, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
10 13 0.22
11 33 0.55
12 12 0.20
13 2 0.03
ACGTcount: A:0.02, C:0.07, G:0.32, T:0.59
Consensus pattern (11 bp):
TTTTGGTGCTG
Found at i:48134697 original size:22 final size:22
Alignment explanation
Indices: 48134651--48134708 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
48134641 TTTTGTGCTG
*
48134651 TTTGGTGCTGTTTTGATGCTGT
1 TTTGGTGCTGTTTTGATGCTCT
*
48134673 TTTGGTGTTGTTTTG-TGCTACT
1 TTTGGTGCTGTTTTGATGCT-CT
* *
48134695 TTTTGTGGTGTTTT
1 TTTGGTGCTGTTTT
48134709 ATTGTTCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 4 0.13
22 27 0.87
ACGTcount: A:0.03, C:0.07, G:0.29, T:0.60
Consensus pattern (22 bp):
TTTGGTGCTGTTTTGATGCTCT
Found at i:48135236 original size:3 final size:3
Alignment explanation
Indices: 48135222--48135252 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
48135212 CCAATAAATA
*
48135222 ATG ATG ACG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
48135253 AAACAAAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.03, G:0.32, T:0.29
Consensus pattern (3 bp):
ATG
Found at i:48136858 original size:8 final size:8
Alignment explanation
Indices: 48136801--48136866 Score: 53
Period size: 8 Copynumber: 8.0 Consensus size: 8
48136791 TTTTAGCAAT
*
48136801 TTTATCTA
1 TTTATATA
48136809 TTTATATA
1 TTTATATA
48136817 TATATATATA
1 T-T-TATATA
*
48136827 TATTATAAA
1 T-TTATATA
*
48136836 TTTCTA-A
1 TTTATATA
*
48136843 TTTTTATA
1 TTTATATA
48136851 TTTATATA
1 TTTATATA
*
48136859 TTTTTATA
1 TTTATATA
48136867 AATTTATAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
7 6 0.12
8 27 0.55
9 7 0.14
10 9 0.18
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (8 bp):
TTTATATA
Found at i:48136884 original size:36 final size:33
Alignment explanation
Indices: 48136808--48136899 Score: 103
Period size: 36 Copynumber: 2.7 Consensus size: 33
48136798 AATTTTATCT
* * *
48136808 ATTTATATATATATATATATATTATAAATTTCTA
1 ATTTTTATATTTATATAT-TATTATAAATTTATA
*
48136842 ATTTTTATATTTATATATTTTTATAAATTTATA
1 ATTTTTATATTTATATATTATTATAAATTTATA
*
48136875 ATTTGTTTTAGATTTATATATTATT
1 A--T-TTTTATATTTATATATTATT
48136900 TTTTGAATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
33 14 0.29
34 16 0.33
35 1 0.02
36 18 0.37
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (33 bp):
ATTTTTATATTTATATATTATTATAAATTTATA
Found at i:48136901 original size:18 final size:17
Alignment explanation
Indices: 48136821--48136901 Score: 60
Period size: 18 Copynumber: 4.7 Consensus size: 17
48136811 TATATATATA
* *
48136821 TATATATATTATAAATT
1 TATATATTTTTTAAATT
* *
48136838 TCTA-A-TTTTTATATT
1 TATATATTTTTTAAATT
48136853 TATATATTTTTATAAATT
1 TATATATTTTT-TAAATT
*
48136871 TATA-ATTTGTTTTAGATT
1 TATATA-TT-TTTTAAATT
48136889 TATATATTATTTT
1 TATATATT-TTTT
48136902 TTGAATAAAG
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
15 10 0.20
16 2 0.04
17 8 0.16
18 26 0.52
19 4 0.08
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (17 bp):
TATATATTTTTTAAATT
Found at i:48137121 original size:28 final size:28
Alignment explanation
Indices: 48137090--48137145 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
48137080 TATCGTTATC
48137090 TTTTAATAAAATTTATATAATTTTTAAT
1 TTTTAATAAAATTTATATAATTTTTAAT
* * * *
48137118 TTTTTATAAATTTTTTATGATTTTTAAT
1 TTTTAATAAAATTTATATAATTTTTAAT
48137146 AATTTTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTTAATAAAATTTATATAATTTTTAAT
Found at i:48137141 original size:9 final size:9
Alignment explanation
Indices: 48137099--48137159 Score: 54
Period size: 8 Copynumber: 6.7 Consensus size: 9
48137089 CTTTTAATAA
*
48137099 AATTTATAT
1 AATTTTTAT
48137108 AATTTTTA-
1 AATTTTTAT
*
48137116 ATTTTTTAT
1 AATTTTTAT
48137125 AAATTTTTTAT
1 -AA-TTTTTAT
*
48137136 GATTTTTAAT
1 AATTTTT-AT
48137146 AATTTTTA-
1 AATTTTTAT
48137154 AATTTT
1 AATTTT
48137160 AAAAAGACTT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
8 13 0.30
9 13 0.30
10 10 0.23
11 7 0.16
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (9 bp):
AATTTTTAT
Found at i:48137153 original size:10 final size:10
Alignment explanation
Indices: 48137090--48137154 Score: 55
Period size: 10 Copynumber: 6.6 Consensus size: 10
48137080 TATCGTTATC
*
48137090 TTTTAATAAA
1 TTTTAATAAT
*
48137100 ATTTATATAAT
1 TTTTA-ATAAT
48137111 TTTTAAT--T
1 TTTTAATAAT
48137119 TTTT-ATAAAT
1 TTTTAAT-AAT
* *
48137129 TTTTTATGAT
1 TTTTAATAAT
48137139 TTTTAATAAT
1 TTTTAATAAT
48137149 TTTTAA
1 TTTTAA
48137155 ATTTTAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
7 2 0.05
8 5 0.11
10 27 0.61
11 10 0.23
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:48137189 original size:7 final size:7
Alignment explanation
Indices: 48137177--48137202 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
48137167 CTTAATTGAT
48137177 TTTTAAA
1 TTTTAAA
48137184 TTTTAAA
1 TTTTAAA
48137191 TTTTAAA
1 TTTTAAA
48137198 TTTTA
1 TTTTA
48137203 GTCTTATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTTAAA
Found at i:48138804 original size:2 final size:2
Alignment explanation
Indices: 48138797--48138835 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
48138787 CCAATACATC
48138797 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
48138836 ACATTTTCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48145524 original size:2 final size:2
Alignment explanation
Indices: 48145517--48145549 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
48145507 CACTTTTAAT
48145517 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48145550 TTACATAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48146134 original size:15 final size:15
Alignment explanation
Indices: 48146114--48146166 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
48146104 TTAGCTAAAT
48146114 TTAAAATTATAAAAA
1 TTAAAATTATAAAAA
*
48146129 TTAAAAATTTTAAAAA
1 TT-AAAATTATAAAAA
*
48146145 ATAAAATTATAAAAA
1 TTAAAATTATAAAAA
48146160 -TAAAATT
1 TTAAAATT
48146167 TAACATAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
14 7 0.21
15 14 0.41
16 13 0.38
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAAAATTATAAAAA
Found at i:48146135 original size:16 final size:16
Alignment explanation
Indices: 48146110--48146164 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 16
48146100 TATTTTAGCT
*
48146110 AAATTTAAAATTATAA
1 AAATTAAAAATTATAA
*
48146126 AAATTAAAAATTTTAA
1 AAATTAAAAATTATAA
*
48146142 AAAAT-AAAATTATAA
1 AAATTAAAAATTATAA
48146157 AAA-TAAAA
1 AAATTAAAA
48146165 TTTAACATAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
14 1 0.03
15 15 0.44
16 18 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATTAAAAATTATAA
Found at i:48146279 original size:16 final size:16
Alignment explanation
Indices: 48146258--48146288 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
48146248 AATTAAAATG
48146258 CATTCATATCACCAAC
1 CATTCATATCACCAAC
48146274 CATTCATATCACCAA
1 CATTCATATCACCAA
48146289 TATTAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.35, G:0.00, T:0.26
Consensus pattern (16 bp):
CATTCATATCACCAAC
Found at i:48149076 original size:14 final size:15
Alignment explanation
Indices: 48149054--48149130 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
48149044 CATCCAAACG
48149054 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
48149068 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
48149083 ACAGAAAAATAAAACATTTT
1 CCAG-AAAAT----CATTTT
48149103 CCA-AAAATCATTTT
1 CCAGAAAATCATTTT
* *
48149117 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
48149131 ACTGGCAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 12 0.24
16 4 0.08
18 5 0.10
20 8 0.16
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:48149114 original size:34 final size:35
Alignment explanation
Indices: 48149058--48149124 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
48149048 CAAACGCCAG
* *
48149058 AAAATATTTTCCAGTAAATCATTTTACAGAAAAAT
1 AAAACATTTTCCAGAAAATCATTTTACAGAAAAAT
*
48149093 AAAACATTTTCCA-AAAATCATTTTACGGAAAA
1 AAAACATTTTCCAGAAAATCATTTTACAGAAAA
48149125 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGAAAATCATTTTACAGAAAAAT
Found at i:48150752 original size:14 final size:14
Alignment explanation
Indices: 48150733--48150759 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
48150723 CAGAAGTTGG
48150733 GAAATTGGGGAAAA
1 GAAATTGGGGAAAA
48150747 GAAATTGGGGAAA
1 GAAATTGGGGAAA
48150760 TCTAATTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.37, T:0.15
Consensus pattern (14 bp):
GAAATTGGGGAAAA
Found at i:48151077 original size:10 final size:11
Alignment explanation
Indices: 48151055--48151079 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
48151045 GTTGCTAAGC
48151055 TTTAAATTTTT
1 TTTAAATTTTT
48151066 TTTAAATTTTT
1 TTTAAATTTTT
48151077 TTT
1 TTT
48151080 CTCTGATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTAAATTTTT
Found at i:48151544 original size:41 final size:42
Alignment explanation
Indices: 48151477--48151575 Score: 121
Period size: 41 Copynumber: 2.4 Consensus size: 42
48151467 TAAAATAATT
** *
48151477 TTTTGCGGCGTTTTTCTCATGTACGCCGCTACT-GCT-TAACC
1 TTTTGCGGCGTTTTTCTCATAAACGCCACTA-TAGCTCTAACC
* * *
48151518 TTTTGCGGCATTTTTCTCATAAACGCCATTATAGCTCTAATC
1 TTTTGCGGCGTTTTTCTCATAAACGCCACTATAGCTCTAACC
48151560 TTTTGCGGCGTTTTTC
1 TTTTGCGGCGTTTTTC
48151576 GATTAGCGCC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
40 1 0.02
41 29 0.59
42 19 0.39
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.42
Consensus pattern (42 bp):
TTTTGCGGCGTTTTTCTCATAAACGCCACTATAGCTCTAACC
Found at i:48151982 original size:34 final size:37
Alignment explanation
Indices: 48151939--48152006 Score: 97
Period size: 35 Copynumber: 1.9 Consensus size: 37
48151929 GATGTTGTTT
*
48151939 TTAATAA-TTTTAATTTATTAT-TAT-TTTATAATTC
1 TTAATAATTTTTAATTAATTATCTATGTTTATAATTC
*
48151973 TTAATAATTTTTAATTAATTCTCTATGTTTATAA
1 TTAATAATTTTTAATTAATTATCTATGTTTATAA
48152007 ATATTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 7 0.24
35 12 0.41
36 3 0.10
37 7 0.24
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (37 bp):
TTAATAATTTTTAATTAATTATCTATGTTTATAATTC
Found at i:48168586 original size:17 final size:17
Alignment explanation
Indices: 48168550--48168597 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
48168540 CATTGTCCCC
* *
48168550 AATGTACTGAC-ATTAA
1 AATGTAATGACAATAAA
48168566 AATGTAATGACAATAAA
1 AATGTAATGACAATAAA
* *
48168583 AATGAAATTACAATA
1 AATGTAATGACAATA
48168598 TATACTTATC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 10 0.37
17 17 0.63
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.27
Consensus pattern (17 bp):
AATGTAATGACAATAAA
Found at i:48179193 original size:45 final size:45
Alignment explanation
Indices: 48179142--48179231 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
48179132 TTGCTTGCAA
*
48179142 ACATCACAAATCTCTCAAGGTTAGTAATTTCACATATACGAAAAC
1 ACATCACAAATCTCACAAGGTTAGTAATTTCACATATACGAAAAC
48179187 ACATCACAAATCTCACAAGGTTAGTAATTTCACATATACGAAAAC
1 ACATCACAAATCTCACAAGGTTAGTAATTTCACATATACGAAAAC
48179232 GTGTAACTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (45 bp):
ACATCACAAATCTCACAAGGTTAGTAATTTCACATATACGAAAAC
Found at i:48179530 original size:25 final size:25
Alignment explanation
Indices: 48179498--48179565 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
48179488 ACATAAGAAT
* *
48179498 AATGCTCACACAAGCTGTAATTGTA
1 AATGCTCACACAAGCTGTAACTATA
* ** *
48179523 ATTGCTCACATGAGTTGTAACTATA
1 AATGCTCACACAAGCTGTAACTATA
48179548 AATGCTCACACAAGCTGT
1 AATGCTCACACAAGCTGT
48179566 GAAATGGGAC
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (25 bp):
AATGCTCACACAAGCTGTAACTATA
Found at i:48190243 original size:4 final size:4
Alignment explanation
Indices: 48190234--48190319 Score: 99
Period size: 4 Copynumber: 21.5 Consensus size: 4
48190224 TAAATTAAGA
48190234 AATT AATT AATT AA-- AATT AATT AATT AAATT AATT AA-- AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT -AATT AATT AATT AATT AATT
*
48190279 AATT AAATT AATT AAATT AATT AATT AAATT AATT GATT AA
1 AATT -AATT AATT -AATT AATT AATT -AATT AATT AATT AA
48190320 AAATATTTAT
Statistics
Matches: 72, Mismatches: 2, Indels: 16
0.80 0.02 0.18
Matches are distributed among these distances:
2 4 0.06
4 52 0.72
5 16 0.22
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (4 bp):
AATT
Found at i:48190265 original size:13 final size:13
Alignment explanation
Indices: 48190233--48190320 Score: 109
Period size: 13 Copynumber: 7.2 Consensus size: 13
48190223 TTAAATTAAG
48190233 AAATTAATTAATT
1 AAATTAATTAATT
48190246 AAAATTAATTAATT
1 -AAATTAATTAATT
48190260 AAATTAATT-A--
1 AAATTAATTAATT
48190270 AAATTAATTAATT
1 AAATTAATTAATT
48190283 --A--AATTAATT
1 AAATTAATTAATT
48190292 AAATTAATTAATT
1 AAATTAATTAATT
*
48190305 AAATTAATTGATT
1 AAATTAATTAATT
48190318 AAA
1 AAA
48190321 AATATTTATT
Statistics
Matches: 66, Mismatches: 1, Indels: 15
0.80 0.01 0.18
Matches are distributed among these distances:
9 8 0.12
10 9 0.14
11 3 0.05
12 1 0.02
13 32 0.48
14 13 0.20
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (13 bp):
AAATTAATTAATT
Found at i:48190266 original size:9 final size:9
Alignment explanation
Indices: 48190217--48190320 Score: 93
Period size: 9 Copynumber: 12.3 Consensus size: 9
48190207 CGAATTGAGA
48190217 AAATT-ATT
1 AAATTAATT
*
48190225 AAATTAA-G
1 AAATTAATT
48190233 AAATTAATT
1 AAATTAATT
48190242 -AATTAAAATT
1 AAATT--AATT
48190252 -AATTAATT
1 AAATTAATT
48190260 AAATTAATT
1 AAATTAATT
48190269 -AA--AATT
1 AAATTAATT
48190275 -AATTAATT
1 AAATTAATT
48190283 AAATTAATT
1 AAATTAATT
48190292 AAATTAATT
1 AAATTAATT
48190301 -AATTAAATT
1 AAATT-AATT
*
48190310 -AATTGATT
1 AAATTAATT
48190318 AAA
1 AAA
48190321 AATATTTATT
Statistics
Matches: 83, Mismatches: 3, Indels: 19
0.79 0.03 0.18
Matches are distributed among these distances:
6 6 0.07
8 33 0.40
9 36 0.43
10 8 0.10
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (9 bp):
AAATTAATT
Found at i:48192197 original size:13 final size:13
Alignment explanation
Indices: 48192175--48192204 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
48192165 GTTAAGAAAA
*
48192175 TAATTGAATTAAT
1 TAATTAAATTAAT
48192188 TAATTAAATTAAT
1 TAATTAAATTAAT
48192201 TAAT
1 TAAT
48192205 ATTATGGGAA
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:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
TAATTAAATTAAT
Found at i:48197996 original size:19 final size:18
Alignment explanation
Indices: 48197961--48197996 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
48197951 TTGCTATGTT
*
48197961 ATTTTATATTATGTTTAA
1 ATTTTATATTATATTTAA
48197979 ATTTTATGATTATATTTA
1 ATTTTAT-ATTATATTTA
48197997 TTAATTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (18 bp):
ATTTTATATTATATTTAA
Found at i:48201478 original size:33 final size:33
Alignment explanation
Indices: 48201436--48201512 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
48201426 TGACATTCAC
**
48201436 AGAGTAAGTCTATTAGGATAATAAACACAGCAT
1 AGAGTAAGTCTATTAGGATAATAAACACAAAAT
* * *
48201469 AGAGTAAGTCGATTCGGATAGTAAACACAAAAT
1 AGAGTAAGTCTATTAGGATAATAAACACAAAAT
*
48201502 AGATTAAGTCT
1 AGAGTAAGTCT
48201513 GACAGGACAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (33 bp):
AGAGTAAGTCTATTAGGATAATAAACACAAAAT
Found at i:48203698 original size:21 final size:21
Alignment explanation
Indices: 48203672--48203718 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
48203662 TCAAAGCAGT
* *
48203672 GGTATCGCGAGATCCCCTTAG
1 GGTATCACGAGATCCCCCTAG
*
48203693 GGTATCACTAGATCCCCCTAG
1 GGTATCACGAGATCCCCCTAG
48203714 GGTAT
1 GGTAT
48203719 TGCAATATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.26
Consensus pattern (21 bp):
GGTATCACGAGATCCCCCTAG
Found at i:48207281 original size:21 final size:21
Alignment explanation
Indices: 48207257--48207297 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
48207247 ATTTTAGGAA
48207257 AATTATTTAATATGAAAAATT
1 AATTATTTAATATGAAAAATT
* * *
48207278 AATTGTTTAATTTGGAAAAT
1 AATTATTTAATATGAAAAAT
48207298 AGAGAAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (21 bp):
AATTATTTAATATGAAAAATT
Found at i:48211350 original size:22 final size:23
Alignment explanation
Indices: 48211311--48211353 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
48211301 ATAGAACAAG
48211311 TGAAAAAATCATTAAATTTTCTA
1 TGAAAAAATCATTAAATTTTCTA
*
48211334 TGAAAAACTCATT-AATTTTC
1 TGAAAAAATCATTAAATTTTC
48211354 AGAACAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.40
Consensus pattern (23 bp):
TGAAAAAATCATTAAATTTTCTA
Found at i:48227096 original size:26 final size:26
Alignment explanation
Indices: 48227061--48227135 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 26
48227051 ACATATATTG
48227061 TTACTGGCAGCTTTGCTGCGATACTGA
1 TTACTGGCAGCTTTGCTGCGATACT-A
* **
48227088 -TACTAGCAGCTTCACTGCGATACTA
1 TTACTGGCAGCTTTGCTGCGATACTA
*
48227113 TTACTGGCAACTTTGCTGCGATA
1 TTACTGGCAGCTTTGCTGCGATA
48227136 TTGGTGTGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
25 1 0.03
26 39 0.98
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCTGCGATACTA
Found at i:48232367 original size:15 final size:15
Alignment explanation
Indices: 48232347--48232376 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
48232337 TTTCCCATTG
48232347 TTATTTTTATTTTTA
1 TTATTTTTATTTTTA
48232362 TTATTTTTATTTTTA
1 TTATTTTTATTTTTA
48232377 ATACAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TTATTTTTATTTTTA
Found at i:48244785 original size:61 final size:62
Alignment explanation
Indices: 48244663--48244785 Score: 158
Period size: 61 Copynumber: 2.0 Consensus size: 62
48244653 AGCACACTGC
48244663 AACTGGAAAGGCTATACAAAATACTATTGCAAAAAAAATCAGATCAATTTGCTAATAGAAAT
1 AACTGGAAAGGCTATACAAAATACTATTGCAAAAAAAATCAGATCAATTTGCTAATAGAAAT
* * * * ** * * *
48244725 AACTGGAAAGGCTATATAGAATATTGTTGC-AGTAGAATCAGATCATTTTGCTAATGGAAAT
1 AACTGGAAAGGCTATACAAAATACTATTGCAAAAAAAATCAGATCAATTTGCTAATAGAAAT
48244786 GCTATAGCAA
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
61 26 0.50
62 26 0.50
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (62 bp):
AACTGGAAAGGCTATACAAAATACTATTGCAAAAAAAATCAGATCAATTTGCTAATAGAAAT
Found at i:48260463 original size:27 final size:27
Alignment explanation
Indices: 48260425--48260478 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
48260415 AAGTGAAGGC
48260425 CATAATTTGAATATGTCTTCTGCAATT
1 CATAATTTGAATATGTCTTCTGCAATT
48260452 CATAATTTGAATATGTCTTCTGCAATT
1 CATAATTTGAATATGTCTTCTGCAATT
48260479 AACTCATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (27 bp):
CATAATTTGAATATGTCTTCTGCAATT
Found at i:48260671 original size:44 final size:44
Alignment explanation
Indices: 48260563--48260652 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
48260553 TAATTGTAAT
* * * * *
48260563 TTAAATTCTAATTATTTTTAAATGTGTATTTATCACAACTTCTA
1 TTAAATTATAACTATTTTTAAATATATAATTATCACAACTTCTA
*
48260607 TTAAATTATAACTATTTTTAAATATATAATTATCACAACTTTTA
1 TTAAATTATAACTATTTTTAAATATATAATTATCACAACTTCTA
48260651 TT
1 TT
48260653 TTATTTAAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (44 bp):
TTAAATTATAACTATTTTTAAATATATAATTATCACAACTTCTA
Found at i:48264719 original size:2 final size:2
Alignment explanation
Indices: 48264712--48264739 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
48264702 GCATCCATAA
48264712 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48264740 CAACCACCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48264970 original size:41 final size:41
Alignment explanation
Indices: 48264868--48264973 Score: 167
Period size: 41 Copynumber: 2.6 Consensus size: 41
48264858 ACTAGCAATT
* * * *
48264868 AGCCTGCTGGACGTAAAGTCCGAAATATTTCACCGGCGTCA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
*
48264909 AGCCTGCTAGACGTATAGTCTGAAACATTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
48264950 AGCCTGCTAGACGTAAAGTCTGAA
1 AGCCTGCTAGACGTAAAGTCTGAA
48264974 TTATCTCATT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
Found at i:48272839 original size:41 final size:41
Alignment explanation
Indices: 48272737--48272842 Score: 176
Period size: 41 Copynumber: 2.6 Consensus size: 41
48272727 ACTGGCAATT
* * *
48272737 AGCCTGCTAGACGTAAAGTCCGAAATATTTCACCGGCGTCA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
*
48272778 AGCCTGCTAGACGTATAGTCTGAAACATTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
48272819 AGCCTGCTAGACGTAAAGTCTGAA
1 AGCCTGCTAGACGTAAAGTCTGAA
48272843 TTATCTCATT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
Found at i:48279503 original size:23 final size:23
Alignment explanation
Indices: 48279477--48279528 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
48279467 TTGACTATTT
*
48279477 CTGTAATATCCCGAAAATTACTA
1 CTGTAATACCCCGAAAATTACTA
48279500 CTGTAATACCCCGAAAATTACTA
1 CTGTAATACCCCGAAAATTACTA
*
48279523 CAGTAA
1 CTGTAA
48279529 GAAAGTAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (23 bp):
CTGTAATACCCCGAAAATTACTA
Found at i:48282707 original size:24 final size:25
Alignment explanation
Indices: 48282675--48282721 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
48282665 GTGTATATGC
48282675 ATGTCATAAAATTTATGA-TATAAGT
1 ATGTCATAAAA-TTATGATTATAAGT
*
48282700 ATGT-ATAATATTATGATTATAA
1 ATGTCATAAAATTATGATTATAA
48282722 TTATACTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 10 0.50
25 4 0.20
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.43
Consensus pattern (25 bp):
ATGTCATAAAATTATGATTATAAGT
Found at i:48283883 original size:30 final size:30
Alignment explanation
Indices: 48283845--48283927 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 30
48283835 GAGAATATAA
* * * *
48283845 TGCTCACACAAGCTGATAGTATATCAGGGT
1 TGCTCACACAAGCTAACAGTATAACAGAGT
* * *
48283875 TTCTCACACAGGCTAACATTATAACAGAGT
1 TGCTCACACAAGCTAACAGTATAACAGAGT
*
48283905 TGCTCACACAAGCTAACATTATA
1 TGCTCACACAAGCTAACAGTATA
48283928 TTGAGACTAC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.27
Consensus pattern (30 bp):
TGCTCACACAAGCTAACAGTATAACAGAGT
Found at i:48292715 original size:25 final size:25
Alignment explanation
Indices: 48292687--48292738 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
48292677 CACTAATAGT
48292687 GTGGAAAGAGTTGGGTGGTGGTTAG
1 GTGGAAAGAGTTGGGTGGTGGTTAG
48292712 GTGGAAAGAGTTGGGTGGTGGTTAG
1 GTGGAAAGAGTTGGGTGGTGGTTAG
48292737 GT
1 GT
48292739 CAGATAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.52, T:0.29
Consensus pattern (25 bp):
GTGGAAAGAGTTGGGTGGTGGTTAG
Found at i:48301764 original size:18 final size:18
Alignment explanation
Indices: 48301741--48301783 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
48301731 TGCCAGATGC
* *
48301741 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
48301759 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
48301777 GTTTCCT
1 GTATCCT
48301784 TTTTCTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:48302049 original size:21 final size:21
Alignment explanation
Indices: 48302024--48302071 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
48302014 CCAACACCGA
48302024 CAACCAG-ATCCCCTACCGGAG
1 CAACCAGAATCCCC-ACCGGAG
* *
48302045 GAACCAGAATCCCCGCCGGAG
1 CAACCAGAATCCCCACCGGAG
48302066 CAACCA
1 CAACCA
48302072 CAACCCTCGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.31, C:0.42, G:0.21, T:0.06
Consensus pattern (21 bp):
CAACCAGAATCCCCACCGGAG
Found at i:48302082 original size:21 final size:21
Alignment explanation
Indices: 48302039--48302085 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
48302029 AGATCCCCTA
* *
48302039 CCGGAGGAACCAGAATCCCCG
1 CCGGAGCAACCACAATCCCCG
48302060 CCGGAGCAACCACAA-CCCTCG
1 CCGGAGCAACCACAATCCC-CG
48302081 CCGGA
1 CCGGA
48302086 AGCTGGACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.28, C:0.43, G:0.26, T:0.04
Consensus pattern (21 bp):
CCGGAGCAACCACAATCCCCG
Found at i:48302857 original size:96 final size:94
Alignment explanation
Indices: 48302716--48302987 Score: 341
Period size: 96 Copynumber: 2.8 Consensus size: 94
48302706 AACCTCAAAT
*
48302716 CCTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACTTAACCCTAATCTAATTTTTTAAAAA
1 CCTAATTTATTTGA-TTTTTACTTAAAAACCCTAAACACTAAACCCTAATCTAA-TTTTTAAAAA
48302781 TCTATAATTAATTTAATCAAGTAACCCTAAAC
64 T-TATAATTAATTTAATCAAGTAACCCTAAAC
* * * *
48302813 CCTAATTTATTTGATTTTTCCTTAAAAACCCTTAACTCTAAACCCTAATCTAACTTTTTAAAAAA
1 CCTAATTTATTTGATTTTTACTTAAAAACCCTAAACACTAAACCCTAATCTAA-TTTTTAAAAAT
* * *
48302878 AATTAATTAAATTACTCAAGTAACCCTAAAC
65 TA-TAATTAATTTAATCAAGTAACCCTAAAC
* ** * * *
48302909 CCTAATTTAATTT-ATTTTTTCTTAAAAAACAATAAACACGAAA-CCTAATCCAATTTTGAAAAA
1 CCTAATTT-ATTTGATTTTTACTT-AAAAACCCTAAACACTAAACCCTAATCTAATTTTTAAAAA
48302972 TTATAATTAATTTAAT
64 TTATAATTAATTTAAT
48302988 TGACAAACCC
Statistics
Matches: 151, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
94 11 0.07
95 11 0.07
96 97 0.64
97 32 0.21
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.38
Consensus pattern (94 bp):
CCTAATTTATTTGATTTTTACTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTAAAAATT
ATAATTAATTTAATCAAGTAACCCTAAAC
Found at i:48304477 original size:22 final size:21
Alignment explanation
Indices: 48304447--48304487 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
48304437 GATGATTTAT
48304447 AAATATCAAAAATTTAAATAG
1 AAATATCAAAAATTTAAATAG
**
48304468 AAATAATCAATTATTTAAAT
1 AAAT-ATCAAAAATTTAAAT
48304488 TAGTCTAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (21 bp):
AAATATCAAAAATTTAAATAG
Found at i:48316175 original size:57 final size:54
Alignment explanation
Indices: 48316064--48316171 Score: 141
Period size: 57 Copynumber: 2.0 Consensus size: 54
48316054 CCCCCTTACA
48316064 TCCCTCTCTCTCTTCCCCACCATCCCTCCCCTTACTCTGATTCTCTCTCCCTCCC
1 TCCCTCTCTCTCTTCCCCACCATCCCT-CCCTTACTCTGATTCTCTCTCCCTCCC
*
48316119 TCCCTCTCCCTCTCTTCCCCACCATCCCT-TCTTGCACTCTGATTCT-T-TCCCTC
1 TCCCTCT--CTCTCTTCCCCACCATCCCTCCCTT--ACTCTGATTCTCTCTCCCTC
48316172 TCCCCCATCG
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
55 16 0.33
56 1 0.02
57 31 0.65
ACGTcount: A:0.07, C:0.54, G:0.03, T:0.36
Consensus pattern (54 bp):
TCCCTCTCTCTCTTCCCCACCATCCCTCCCTTACTCTGATTCTCTCTCCCTCCC
Found at i:48319265 original size:27 final size:27
Alignment explanation
Indices: 48319227--48319281 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
48319217 GTTCAACGGG
48319227 TATGAAAAGGGAAGCAACGGTAAGTGT
1 TATGAAAAGGGAAGCAACGGTAAGTGT
*
48319254 TATGAAAAGGGAAGGAACGGTAAGTGT
1 TATGAAAAGGGAAGCAACGGTAAGTGT
48319281 T
1 T
48319282 CCAATGGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.35, T:0.20
Consensus pattern (27 bp):
TATGAAAAGGGAAGCAACGGTAAGTGT
Found at i:48320036 original size:13 final size:13
Alignment explanation
Indices: 48320018--48320045 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
48320008 CATATTAGTC
48320018 GTATAGATATTTG
1 GTATAGATATTTG
48320031 GTATAGATATTTG
1 GTATAGATATTTG
48320044 GT
1 GT
48320046 CATTTTATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (13 bp):
GTATAGATATTTG
Found at i:48321488 original size:13 final size:13
Alignment explanation
Indices: 48321470--48321496 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
48321460 GATCATTGAT
48321470 CTGCAACAACTCG
1 CTGCAACAACTCG
48321483 CTGCAACAACTCG
1 CTGCAACAACTCG
48321496 C
1 C
48321497 ATCAGCTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.41, G:0.15, T:0.15
Consensus pattern (13 bp):
CTGCAACAACTCG
Found at i:48321771 original size:27 final size:27
Alignment explanation
Indices: 48321740--48321901 Score: 150
Period size: 27 Copynumber: 6.0 Consensus size: 27
48321730 TACCGAAATA
*
48321740 CCCCTATAGGATAAAATGA-CAGTAATG
1 CCCCTATAGGGTAAAATGATCA-TAATG
* * *
48321767 CCCCTATAAGGTAAAACGA-CTATAATAC
1 CCCCTATAGGGTAAAATGATC-ATAAT-G
* *
48321795 CCCCGA-AGGGTAAAATGACCATAATG
1 CCCCTATAGGGTAAAATGATCATAATG
* * * *
48321821 CCCTTGTAGAGTAAAACGATCATAATG
1 CCCCTATAGGGTAAAATGATCATAATG
* * *
48321848 CCCCTGTAGGGTAAAATTATCGTAATG
1 CCCCTATAGGGTAAAATGATCATAATG
*
48321875 CCCCTGTAGGGTAAAATGATCATAATG
1 CCCCTATAGGGTAAAATGATCATAATG
48321902 TCATGGTGGG
Statistics
Matches: 110, Mismatches: 21, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
26 3 0.03
27 100 0.91
28 7 0.06
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.23
Consensus pattern (27 bp):
CCCCTATAGGGTAAAATGATCATAATG
Found at i:48321901 original size:54 final size:54
Alignment explanation
Indices: 48321751--48321901 Score: 178
Period size: 54 Copynumber: 2.8 Consensus size: 54
48321741 CCCTATAGGA
* * * *
48321751 TAAAATGACAGTAATGCCCCTATAAGGTAAAACGA-CTATAATACCCCCGAAGGG
1 TAAAATGACCGTAATGCCCCTGTAGGGTAAAACGATC-ATAATGCCCCCGAAGGG
* * * * *
48321805 TAAAATGACCATAATGCCCTTGTAGAGTAAAACGATCATAATGCCCCTGTAGGG
1 TAAAATGACCGTAATGCCCCTGTAGGGTAAAACGATCATAATGCCCCCGAAGGG
* * *
48321859 TAAAATTATCGTAATGCCCCTGTAGGGTAAAATGATCATAATG
1 TAAAATGACCGTAATGCCCCTGTAGGGTAAAACGATCATAATG
48321902 TCATGGTGGG
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
54 80 0.99
55 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (54 bp):
TAAAATGACCGTAATGCCCCTGTAGGGTAAAACGATCATAATGCCCCCGAAGGG
Found at i:48322101 original size:27 final size:27
Alignment explanation
Indices: 48322063--48322127 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
48322053 ATGGAGGAAG
48322063 TACTG-TACTGGTGGCTCT-GCCACA-A
1 TACTGTTACTGGTGGCT-TGGCCACATA
48322088 TCACTGTTACTGGTGGCTTGGCCACATA
1 T-ACTGTTACTGGTGGCTTGGCCACATA
*
48322116 TACTATTACTGG
1 TACTGTTACTGG
48322128 CAATGTTGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 1 0.03
26 5 0.14
27 27 0.77
28 2 0.06
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTTGGCCACATA
Found at i:48322212 original size:32 final size:32
Alignment explanation
Indices: 48322171--48322405 Score: 178
Period size: 32 Copynumber: 7.4 Consensus size: 32
48322161 GCTGCGATAC
*
48322171 TACTGATGGCTTTGTGCCGGTCATAGTA-TCGT
1 TACTGATGGCTTTGTGCCGATCATAGTACT-GT
* *
48322203 TACTGATGGCTTTGTGTCGATCATATTACTGT
1 TACTGATGGCTTTGTGCCGATCATAGTACTGT
* * * *
48322235 TACCGATGGCTGTGTGCTGATCAT-TTCACTGT
1 TACTGATGGCTTTGTGCCGATCATAGT-ACTGT
* * ** *
48322267 TACAGATGGCTGTGTGCCGATCATAACACTGC
1 TACTGATGGCTTTGTGCCGATCATAGTACTGT
* *
48322299 TACTGATGGCTTTGTGTCGATCAT-GTTACCGT
1 TACTGATGGCTTTGTGCCGATCATAG-TACTGT
*
48322331 TACTGATGG-TTGTGTGTCGATCATA-TCACTGCT
1 TACTGATGGCTT-TGTGCCGATCATAGT-ACTG-T
* * * * *
48322364 T-TTGATGGCTTTATGCCAATCACATTACTG-
1 TACTGATGGCTTTGTGCCGATCATAGTACTGT
*
48322394 TACTTATGGCTT
1 TACTGATGGCTT
48322406 GTAGCCATTC
Statistics
Matches: 165, Mismatches: 27, Indels: 23
0.77 0.13 0.11
Matches are distributed among these distances:
30 1 0.01
31 13 0.08
32 145 0.88
33 6 0.04
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATAGTACTGT
Found at i:48322370 original size:64 final size:63
Alignment explanation
Indices: 48322173--48322375 Score: 207
Period size: 64 Copynumber: 3.2 Consensus size: 63
48322163 TGCGATACTA
* * *
48322173 CTGATGGCTTTGTGCCGGTCATAG-TATCGTTACTGATGGCTT-TGTGTCGATCATATTACTG-T
1 CTGATGGCTTTGTG-CGATCAT-GTTACCGTTACTGATGG-TTGTGTGTCGATCATATCACTGCT
48322235 T
63 T
* * * * * * *
48322236 ACCGATGGCTGTGTGCTGATCAT-TTCACTGTTACAGATGGCTGTGTGCCGATCATAACACTGCT
1 -CTGATGGCTTTGTGC-GATCATGTT-ACCGTTACTGATGGTTGTGTGTCGATCATATCACTGCT
*
48322300 A
63 T
48322301 CTGATGGCTTTGTGTCGATCATGTTACCGTTACTGATGGTTGTGTGTCGATCATATCACTGCTT
1 CTGATGGCTTTGTG-CGATCATGTTACCGTTACTGATGGTTGTGTGTCGATCATATCACTGCTT
*
48322365 TTGATGGCTTT
1 CTGATGGCTTT
48322376 ATGCCAATCA
Statistics
Matches: 112, Mismatches: 20, Indels: 14
0.77 0.14 0.10
Matches are distributed among these distances:
63 3 0.03
64 105 0.94
65 4 0.04
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.38
Consensus pattern (63 bp):
CTGATGGCTTTGTGCGATCATGTTACCGTTACTGATGGTTGTGTGTCGATCATATCACTGCTT
Found at i:48324362 original size:2 final size:2
Alignment explanation
Indices: 48324355--48324396 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
48324345 ATAATGAAAG
*
48324355 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48324397 TCGGTTGTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:48335174 original size:22 final size:21
Alignment explanation
Indices: 48335125--48335201 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 21
48335115 CCCCATATTT
** *
48335125 TTAGGGTTTTAATT-ATTTAA
1 TTAGGGTTTTGGTTAATTAAA
*
48335145 TTATGGTTTGTGGTTAATTAAA
1 TTAGGGTTT-TGGTTAATTAAA
*
48335167 TTAGGGTTTAAT-GTTTATTAAA
1 TTAGGGTTT--TGGTTAATTAAA
48335189 TTAGGGTTTTGGT
1 TTAGGGTTTTGGT
48335202 GGTTTTTTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
20 9 0.20
21 5 0.11
22 31 0.67
23 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (21 bp):
TTAGGGTTTTGGTTAATTAAA
Found at i:48341692 original size:139 final size:139
Alignment explanation
Indices: 48341442--48341715 Score: 467
Period size: 139 Copynumber: 2.0 Consensus size: 139
48341432 TGTTGATGCG
* * *
48341442 TTTTAATTTTAATCAGCGTACAGCCATGTCTATGAGTATTTACCCATGGGAAATGGGGAAAGCAT
1 TTTTAATTTTAACCAGCGTACAACCATGTCTATGAGTATTTACCCATGGGAAATCGGGAAAGCAT
48341507 CTTGTTTCTGTGCATGCATGTTAGCGATGTGCTAAATGAATGCTACAATTTTCCAAAGTTGCGCC
66 CTTGTTTCTGTGCATGCATGTTAGCGATGTGCTAAATGAATGCTACAATTTTCCAAAGTTGCGCC
48341572 TTTTCGTCA
131 TTTTCGTCA
* * *
48341581 TTTTATTTTTAACCAGTGTACAACCATGTCTATGTGTATTTACCCATGGGAAATCGGGAAAGCAT
1 TTTTAATTTTAACCAGCGTACAACCATGTCTATGAGTATTTACCCATGGGAAATCGGGAAAGCAT
* * *
48341646 CTTGTTTCTGTGCATGCATGTTAGTGATGTGTTGAATGAATGCTACAATTTTCCAAAGTTGCGCC
66 CTTGTTTCTGTGCATGCATGTTAGCGATGTGCTAAATGAATGCTACAATTTTCCAAAGTTGCGCC
48341711 TTTTC
131 TTTTC
48341716 TTCTTCATTT
Statistics
Matches: 126, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
139 126 1.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (139 bp):
TTTTAATTTTAACCAGCGTACAACCATGTCTATGAGTATTTACCCATGGGAAATCGGGAAAGCAT
CTTGTTTCTGTGCATGCATGTTAGCGATGTGCTAAATGAATGCTACAATTTTCCAAAGTTGCGCC
TTTTCGTCA
Found at i:48343286 original size:16 final size:16
Alignment explanation
Indices: 48343265--48343295 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48343255 TTGAAAGAGT
48343265 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
48343281 TTTCAAATTTATATG
1 TTTCAAATATATATG
48343296 CTTTGACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:48346365 original size:14 final size:14
Alignment explanation
Indices: 48346343--48346372 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
48346333 AACATAATAG
48346343 ATTAATAAATATTT
1 ATTAATAAATATTT
*
48346357 ATTATTAAATATTT
1 ATTAATAAATATTT
48346371 AT
1 AT
48346373 AAATTGCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTAATAAATATTT
Found at i:48366974 original size:15 final size:16
Alignment explanation
Indices: 48366956--48366990 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
48366946 ATAAAAACAA
48366956 TTATATATTATTT-AT
1 TTATATATTATTTAAT
*
48366971 TTATTTATTATTTAAT
1 TTATATATTATTTAAT
48366987 TTAT
1 TTAT
48366991 TCATTTCTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATATATTATTTAAT
Found at i:48367102 original size:22 final size:21
Alignment explanation
Indices: 48367047--48367102 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 21
48367037 GAAATATTAC
48367047 AAAATTAAATATACTTTTCATA
1 AAAATTAAATATAC-TTTCATA
* * *
48367069 AAAAATATATATGA-TTTCAGTT
1 AAAATTAAATAT-ACTTTCA-TA
48367091 AAAATTAAATAT
1 AAAATTAAATAT
48367103 TTAAATTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
21 5 0.19
22 21 0.78
23 1 0.04
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (21 bp):
AAAATTAAATATACTTTCATA
Found at i:48369149 original size:23 final size:23
Alignment explanation
Indices: 48369119--48369172 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
48369109 ATTTTTTGGG
* *
48369119 TTTTTTGTTTAATTTCTTTGAAT
1 TTTTTTGTTAAATTTCTTTAAAT
48369142 TTTTTTGTTAAATTTCTTTAAAT
1 TTTTTTGTTAAATTTCTTTAAAT
48369165 TCTTTTTG
1 T-TTTTTG
48369173 ATTTTTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.19, C:0.06, G:0.07, T:0.69
Consensus pattern (23 bp):
TTTTTTGTTAAATTTCTTTAAAT
Found at i:48382262 original size:42 final size:42
Alignment explanation
Indices: 48382203--48382286 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
48382193 ATGTTTCAAG
48382203 AAGAATTGTTGTGTTGGAAGTTTATTTGTTGTTGTTCAGGCT
1 AAGAATTGTTGTGTTGGAAGTTTATTTGTTGTTGTTCAGGCT
48382245 AAGAATTGTTGTGTTGGAAGTTTATTTGTTGTTGTTCAGGCT
1 AAGAATTGTTGTGTTGGAAGTTTATTTGTTGTTGTTCAGGCT
48382287 TCCGTCTGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.19, C:0.05, G:0.29, T:0.48
Consensus pattern (42 bp):
AAGAATTGTTGTGTTGGAAGTTTATTTGTTGTTGTTCAGGCT
Found at i:48390273 original size:32 final size:33
Alignment explanation
Indices: 48390202--48390275 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 33
48390192 AGACTAACCC
48390202 GAAAATA-AAGCAAATAAAGAAGAGATTGCAAA
1 GAAAATAGAAGCAAATAAAGAAGAGATTGCAAA
*
48390234 GAGAAATAGAAG-AAATTAAA-AGAGAGATTG-AGA
1 GA-AAATAGAAGCAAA-TAAAGA-AGAGATTGCAAA
48390267 GAAAATAGA
1 GAAAATAGA
48390276 GAGAGGGAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
32 9 0.24
33 13 0.35
34 15 0.41
ACGTcount: A:0.61, C:0.03, G:0.23, T:0.14
Consensus pattern (33 bp):
GAAAATAGAAGCAAATAAAGAAGAGATTGCAAA
Found at i:48400649 original size:21 final size:22
Alignment explanation
Indices: 48400609--48400663 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
48400599 TTTCCCCCCA
*
48400609 TTGCATGTGGCTATACAA-TTGT
1 TTGCA-GTGGCTATACAATTTAT
**
48400631 TTGCAGTGGCTATGTAATTTAT
1 TTGCAGTGGCTATACAATTTAT
*
48400653 TTACAGTGGCT
1 TTGCAGTGGCT
48400664 CCATCTACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.22, C:0.13, G:0.24, T:0.42
Consensus pattern (22 bp):
TTGCAGTGGCTATACAATTTAT
Found at i:48400968 original size:70 final size:70
Alignment explanation
Indices: 48400874--48401004 Score: 235
Period size: 70 Copynumber: 1.9 Consensus size: 70
48400864 GAATGCTTTG
* * *
48400874 AAATGTTTGAAATTGTGTTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGCTCA
1 AAATGTTTGAAATGGTGCTATTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGCTCA
48400939 CTGAT
66 CTGAT
48400944 AAATGTTTGAAATGGTGCTATTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTG
1 AAATGTTTGAAATGGTGCTATTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTG
48401005 AAATGAGTTA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 58 1.00
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.45
Consensus pattern (70 bp):
AAATGTTTGAAATGGTGCTATTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGCTCA
CTGAT
Found at i:48405860 original size:92 final size:91
Alignment explanation
Indices: 48405703--48405911 Score: 242
Period size: 92 Copynumber: 2.3 Consensus size: 91
48405693 TTGATTTTAG
* ** *
48405703 TAAATTCATATAAAGACAATTTATTATTGAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATAT-AAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
48405768 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
* *
48405795 TAAATTCATATAAGAAAATTTATTATCAAGCATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
*
48405859 TATGTAATAATTATTATTTTAGATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * * *
48405887 CAATTTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
48405912 GTTATAATTA
Statistics
Matches: 100, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
90 1 0.01
91 32 0.32
92 64 0.64
93 3 0.03
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:48406017 original size:16 final size:16
Alignment explanation
Indices: 48405996--48406037 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
48405986 TTATTAAATT
*
48405996 ATATATTTTAATTATA
1 ATATATTTTAATAATA
48406012 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
48406027 AT-TATGTTTAA
1 ATATAT-TTTAA
48406038 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:48406022 original size:15 final size:15
Alignment explanation
Indices: 48405941--48406028 Score: 55
Period size: 15 Copynumber: 6.1 Consensus size: 15
48405931 ATTTTAAATC
*
48405941 ATATATTATAATTAAA
1 ATATATT-TAATTATA
48405957 ATATATTTAA-TAT-
1 ATATATTTAATTATA
*
48405970 -TA-ATTT-ATTAAGA
1 ATATATTTAATT-ATA
* *
48405983 ATTTTATTAAATTAT-
1 A-TATATTTAATTATA
48405998 ATAT-TTTAATTATA
1 ATATATTTAATTATA
*
48406012 ATATATTTAATAATA
1 ATATATTTAATTATA
48406027 AT
1 AT
48406029 TATGTTTAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 19
0.67 0.10 0.23
Matches are distributed among these distances:
10 1 0.02
11 5 0.09
12 3 0.05
13 8 0.15
14 8 0.15
15 16 0.29
16 11 0.20
17 3 0.05
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
ATATATTTAATTATA
Found at i:48406047 original size:55 final size:53
Alignment explanation
Indices: 48405915--48406059 Score: 157
Period size: 55 Copynumber: 2.6 Consensus size: 53
48405905 TTTATTAGTT
* *
48405915 ATAATTATTTTAAATTATTTTAAATCATATATTATAATTAAAATATATTTAATA
1 ATAATTATTTTAAA-TATATTAAATTATATATTATAATTAAAATATATTTAATA
* * * * *
48405969 TTAATT-TATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATA
1 ATAATTAT-TTTA-AA-TATATTAAATTATATATTATAATTAAAATATATTTAATA
*
48406024 ATAATTATGTTTAAATATGATTAAATTATTTATTAT
1 ATAATTAT-TTTAAATAT-ATTAAATTATATATTAT
48406060 TGATATTAAT
Statistics
Matches: 74, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
53 1 0.01
54 10 0.14
55 59 0.80
56 4 0.05
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (53 bp):
ATAATTATTTTAAATATATTAAATTATATATTATAATTAAAATATATTTAATA
Found at i:48406184 original size:30 final size:27
Alignment explanation
Indices: 48406133--48406189 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 27
48406123 ATAACAATAC
*
48406133 TTATATATTAATTATTAACAATATTTA
1 TTATATATTAATTAATAACAATATTTA
48406160 TTATATATTAAATAATAATAACAATATTTA
1 TTATATATT-AAT--TAATAACAATATTTA
48406190 ACAATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 9 0.35
28 3 0.12
30 14 0.54
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (27 bp):
TTATATATTAATTAATAACAATATTTA
Found at i:48406201 original size:16 final size:16
Alignment explanation
Indices: 48406176--48406206 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48406166 ATTAAATAAT
48406176 AATAACAATATTTAAC
1 AATAACAATATTTAAC
*
48406192 AATAATAATATTTAA
1 AATAACAATATTTAA
48406207 TAATTTACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAACAATATTTAAC
Found at i:48406271 original size:18 final size:17
Alignment explanation
Indices: 48406243--48406277 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
48406233 ATTATTAAGA
*
48406243 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
48406260 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
48406278 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:48408366 original size:109 final size:109
Alignment explanation
Indices: 48408221--48408433 Score: 390
Period size: 109 Copynumber: 2.0 Consensus size: 109
48408211 GAGAAAGGTG
* *
48408221 TTTTGTCCCAAAAGTATTCGGCCATAGATTTTAAGATAATTTCAAGTCTTTTTCTTGTAATTTTT
1 TTTTGTCCCAAAAGCATTCGACCATAGATTTTAAGATAATTTCAAGTCTTTTTCTTGTAATTTTT
48408286 ATAGATTTAAGGTAATGGGAGCTTGATTTAACTAACCAATGTAA
66 ATAGATTTAAGGTAATGGGAGCTTGATTTAACTAACCAATGTAA
*
48408330 TTTTTTCCCAAAAGCATTCGACCATAGATTTTAAGATAATTTCAAGTCTTTTTCTTGTAATTTTT
1 TTTTGTCCCAAAAGCATTCGACCATAGATTTTAAGATAATTTCAAGTCTTTTTCTTGTAATTTTT
*
48408395 ATAGATTTAAGGTAATGGGAGCTTGATTTAAGTAACCAA
66 ATAGATTTAAGGTAATGGGAGCTTGATTTAACTAACCAA
48408434 AATACCAATT
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 100 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.41
Consensus pattern (109 bp):
TTTTGTCCCAAAAGCATTCGACCATAGATTTTAAGATAATTTCAAGTCTTTTTCTTGTAATTTTT
ATAGATTTAAGGTAATGGGAGCTTGATTTAACTAACCAATGTAA
Found at i:48414004 original size:68 final size:68
Alignment explanation
Indices: 48413908--48414111 Score: 196
Period size: 68 Copynumber: 3.0 Consensus size: 68
48413898 ACTTCTAGCG
* * * *
48413908 AACTCTATTGG-TTGCCTTAGCCAAGCTATGATTTTACACCTTGTAACCCCATGTTTAATGTCTT
1 AACTCAATTGGATT-CCATAGCCAAGCTATGGTCTTACACCTTGTAACCCCATGTTTAATGTCTT
* *
48413972 GGCG
65 GACA
* * ** ** ** * * *
48413976 GACTCTATT-TTTTGTTATAGCCAAGCTATGGTCTTACATTTTGTAACCTCATATTTAATGTCCT
1 AACTCAATTGGATT-CCATAGCCAAGCTATGGTCTTACACCTTGTAACCCCATGTTTAATGTCTT
*
48414040 GATA
65 GACA
* *
48414044 AACTCAATTGGATTCCATAGCCGAGCTATGGTCTTACACCTTGTAACCCCATGATTAATGTCTTG
1 AACTCAATTGGATTCCATAGCCAAGCTATGGTCTTACACCTTGTAACCCCATGTTTAATGTCTTG
48414109 ACA
66 ACA
48414112 GACTTTATAT
Statistics
Matches: 105, Mismatches: 29, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
68 103 0.98
69 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (68 bp):
AACTCAATTGGATTCCATAGCCAAGCTATGGTCTTACACCTTGTAACCCCATGTTTAATGTCTTG
ACA
Found at i:48416787 original size:2 final size:2
Alignment explanation
Indices: 48416780--48416806 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
48416770 AATCAACTTT
48416780 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
48416807 ATTAGTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:48418918 original size:21 final size:21
Alignment explanation
Indices: 48418892--48418942 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
48418882 AAGGCTCCTG
48418892 ATGTGATTGCTAGTACATTCT
1 ATGTGATTGCTAGTACATTCT
48418913 ATGTGATTGCTAGTACATTCT
1 ATGTGATTGCTAGTACATTCT
48418934 ATGTGATTG
1 ATGTGATTG
48418943 ATGTTACTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.43
Consensus pattern (21 bp):
ATGTGATTGCTAGTACATTCT
Found at i:48423585 original size:2 final size:2
Alignment explanation
Indices: 48423578--48423606 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
48423568 AAACGTGGTT
48423578 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
48423607 AAAGCAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:48427367 original size:21 final size:20
Alignment explanation
Indices: 48427322--48427395 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 20
48427312 TTAATTTATT
48427322 AAATT-TTAATTTTTATAAC
1 AAATTATTAATTTTTATAAC
*
48427341 -ATTTATTAATTTTTATATAC
1 AAATTATTAATTTTTATA-AC
* * *
48427361 AAATTATTGATTTTTTTAAT
1 AAATTATTAATTTTTATAAC
48427381 AATATTACTTAATTT
1 AA-ATTA-TTAATTT
48427396 AATTAGAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
18 3 0.07
19 12 0.27
20 5 0.11
21 18 0.41
22 6 0.14
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (20 bp):
AAATTATTAATTTTTATAAC
Found at i:48432992 original size:14 final size:13
Alignment explanation
Indices: 48432966--48433015 Score: 59
Period size: 12 Copynumber: 3.9 Consensus size: 13
48432956 ATTTATTTGA
48432966 AATATAATAATAT
1 AATATAATAATAT
48432979 AATATAATTAATAT
1 AATATAA-TAATAT
* *
48432993 AAT-TTACAATAT
1 AATATAATAATAT
48433005 AATA-AATAATA
1 AATATAATAATA
48433016 ATATACTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
12 13 0.42
13 9 0.29
14 9 0.29
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATAATAATAT
Found at i:48435526 original size:54 final size:54
Alignment explanation
Indices: 48435463--48435695 Score: 227
Period size: 54 Copynumber: 4.1 Consensus size: 54
48435453 AGTATCATAT
*
48435463 ATTATGATTTGAGTAAATTCATATAAAAATATTAATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
*
48435517 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
* * * * * * * *
48435571 ATTATATATTTTAATTATAATAT-ATTTAATAATAATTATGTTAAATT-ATATTTTATAGTATCA
1 ATTAT-GA-TTTGAGTA-AAT-TCATATAAGAAT-ATTA-ATT--ATTAAGAATTT-TA-T-T-A
48435634 TA
54 -A
*
48435636 TATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
1 -ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
48435691 ATTAT
1 ATTAT
48435696 ATATTTTAAT
Statistics
Matches: 143, Mismatches: 20, Indels: 32
0.73 0.10 0.16
Matches are distributed among these distances:
54 62 0.43
55 2 0.01
56 7 0.05
57 12 0.08
58 5 0.03
59 7 0.05
60 10 0.07
61 7 0.05
62 5 0.03
63 12 0.08
64 7 0.05
65 2 0.01
66 5 0.03
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (54 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
Found at i:48435563 original size:28 final size:27
Alignment explanation
Indices: 48435478--48435563 Score: 63
Period size: 28 Copynumber: 3.1 Consensus size: 27
48435468 GATTTGAGTA
*
48435478 AATTCATATAAAAATATTAATTATTAAG
1 AATTCATAT-AAAATATTGATTATTAAG
* * *
48435506 AATT-TTATTAAAT-TATGA-T-TTGAG
1 AATTCATATAAAATAT-TGATTATTAAG
48435530 TAAATTCATATAAGAATATTGATTATTAAG
1 --AATTCATATAA-AATATTGATTATTAAG
48435560 AATT
1 AATT
48435564 TTATTAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 16
0.65 0.11 0.24
Matches are distributed among these distances:
24 4 0.09
25 2 0.05
26 10 0.23
27 7 0.16
28 14 0.33
29 2 0.05
30 4 0.09
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (27 bp):
AATTCATATAAAATATTGATTATTAAG
Found at i:48435595 original size:16 final size:16
Alignment explanation
Indices: 48435574--48435620 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
48435564 TTATTAAATT
48435574 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
48435590 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
48435605 AT-TATGTTAAATTATA
1 ATATAT-TTTAATTATA
48435621 TTTTATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:48435642 original size:120 final size:121
Alignment explanation
Indices: 48435517--48435737 Score: 435
Period size: 120 Copynumber: 1.8 Consensus size: 121
48435507 ATTTTATTAA
48435517 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
1 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
48435582 TAATTATAATATATTTAATAATAATTATG-TTAAATTATATTTTATAGTATCATAT
66 TAATTATAATATATTTAATAATAATTATGTTTAAATTATATTTTATAGTATCATAT
48435637 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
1 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
48435702 TAATTATAATATATTTAATAATAATTATGTTTAAAT
66 TAATTATAATATATTTAATAATAATTATGTTTAAAT
48435738 ATGATTAAAT
Statistics
Matches: 100, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
120 94 0.94
121 6 0.06
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (121 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
TAATTATAATATATTTAATAATAATTATGTTTAAATTATATTTTATAGTATCATAT
Found at i:48435715 original size:16 final size:16
Alignment explanation
Indices: 48435694--48435735 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
48435684 TTATTAAATT
*
48435694 ATATATTTTAATTATA
1 ATATATTTTAATAATA
48435710 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
48435725 AT-TATGTTTAA
1 ATATAT-TTTAA
48435736 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:48435720 original size:15 final size:15
Alignment explanation
Indices: 48435685--48435726 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
48435675 TTAAGAATTT
*
48435685 TATTAAATTAT-ATA
1 TATTTAATTATAATA
48435699 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
48435713 TATTTAATAATAAT
1 TATTTAATTATAAT
48435727 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:48435865 original size:18 final size:17
Alignment explanation
Indices: 48435837--48435871 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
48435827 AATTATAAGA
*
48435837 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
48435854 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
48435872 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:48435871 original size:16 final size:16
Alignment explanation
Indices: 48435837--48435894 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
48435827 AATTATAAGA
48435837 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
48435854 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
48435870 A-TTTAA-TAATAAT-T
1 ATTTTAATTAA-AATAT
48435884 ATGTTTAATTA
1 AT-TTTAATTA
48435895 TGATTAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 5 0.14
15 8 0.22
16 10 0.28
17 7 0.19
18 6 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:48437491 original size:84 final size:84
Alignment explanation
Indices: 48437397--48437564 Score: 309
Period size: 84 Copynumber: 2.0 Consensus size: 84
48437387 TATGGATTAA
* *
48437397 ATTGAATACTAGAAGTACTTAATTGATTGAAATTATCTATTTAGATCAAGATAAATCACATTCGG
1 ATTGAATACTAGAAGTACTTAATTGATTGAAATTATCTATTTAGATCAAGATAAACCACATTCAG
48437462 ACTTAAATCGAGGAAAAGC
66 ACTTAAATCGAGGAAAAGC
*
48437481 ATTGAATACTAGAAGTACTTAATTGCTTGAAATTATCTATTTAGATCAAGATAAACCACATTCAG
1 ATTGAATACTAGAAGTACTTAATTGATTGAAATTATCTATTTAGATCAAGATAAACCACATTCAG
48437546 ACTTAAATCGAGGAAAAGC
66 ACTTAAATCGAGGAAAAGC
48437565 TAAATCTTCA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (84 bp):
ATTGAATACTAGAAGTACTTAATTGATTGAAATTATCTATTTAGATCAAGATAAACCACATTCAG
ACTTAAATCGAGGAAAAGC
Found at i:48439595 original size:16 final size:16
Alignment explanation
Indices: 48439574--48439623 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 16
48439564 ATATTTAACT
48439574 ATATAATAAATTATTA
1 ATATAATAAATTATTA
48439590 ATATAAT---TTATTA
1 ATATAATAAATTATTA
* *
48439603 TTTTAATAAATTATTTA
1 ATATAATAAATTA-TTA
48439620 ATAT
1 ATAT
48439624 TTTTATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 11 0.42
16 10 0.38
17 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:48439599 original size:29 final size:30
Alignment explanation
Indices: 48439566--48439623 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
48439556 AATTACTTAT
48439566 ATTTAACTA-TATAATAAATTA-TTAATATA
1 ATTT-ACTATTATAATAAATTATTTAATATA
* *
48439595 ATTTATTATTTTAATAAATTATTTAATAT
1 ATTTACTATTATAATAAATTATTTAATAT
48439624 TTTTATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 15 0.60
30 7 0.28
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
ATTTACTATTATAATAAATTATTTAATATA
Found at i:48439628 original size:29 final size:30
Alignment explanation
Indices: 48439577--48439642 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 30
48439567 TTTAACTATA
48439577 TAATAAATTATTAATATAATTTA-TTATTT
1 TAATAAATTATTAATATAATTTATTTATTT
*
48439606 TAATAAATTATTTAATAT-TTTTATTTTATTT
1 TAATAAATTA-TTAATATAATTTA-TTTATTT
48439637 TAATAA
1 TAATAA
48439643 TAAATATCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 14 0.42
30 7 0.21
31 12 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
TAATAAATTATTAATATAATTTATTTATTT
Found at i:48439654 original size:19 final size:19
Alignment explanation
Indices: 48439632--48439668 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
48439622 ATTTTTATTT
*
48439632 TATTTTAATAATAAATATC
1 TATTATAATAATAAATATC
*
48439651 TATTATAATTATAAATAT
1 TATTATAATAATAAATAT
48439669 ATTAACAATA
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:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTATAATAATAAATATC
Found at i:48442402 original size:21 final size:22
Alignment explanation
Indices: 48442377--48442421 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
48442367 TTAAAAAAAT
48442377 AAAATCAAT-AAAAT-TATTTTA
1 AAAAT-AATAAAAATATATTTTA
*
48442398 AAAATTATAAAAATATATTTTA
1 AAAATAATAAAAATATATTTTA
48442420 AA
1 AA
48442422 TATTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 10 0.48
22 9 0.43
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAATAATAAAAATATATTTTA
Found at i:48443428 original size:42 final size:42
Alignment explanation
Indices: 48443362--48443441 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
48443352 ATGGTGATGC
* * *
48443362 GAACCCACCATGTGTGAGCTCATGTAAAGATGCAAACTCAGT
1 GAACCCACCACGTGCGAGCCCATGTAAAGATGCAAACTCAGT
* *
48443404 GAACCCATCACGTGCGAGCCCATGTAAGGATGCAAACT
1 GAACCCACCACGTGCGAGCCCATGTAAAGATGCAAACT
48443442 ATACAAGCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.19
Consensus pattern (42 bp):
GAACCCACCACGTGCGAGCCCATGTAAAGATGCAAACTCAGT
Found at i:48444904 original size:31 final size:31
Alignment explanation
Indices: 48444866--48444927 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
48444856 ACAGATAGAC
48444866 TTAGACCAATTGATACTTATCTCATTCATAT
1 TTAGACCAATTGATACTTATCTCATTCATAT
48444897 TTAGACCAATTGATACTTATCTCATTCATAT
1 TTAGACCAATTGATACTTATCTCATTCATAT
48444928 CTACGAATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (31 bp):
TTAGACCAATTGATACTTATCTCATTCATAT
Found at i:48452424 original size:11 final size:11
Alignment explanation
Indices: 48452410--48452443 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
48452400 ATATTTAATT
*
48452410 TCAATTTTCTC
1 TCAAGTTTCTC
48452421 TCAAGTTTCTC
1 TCAAGTTTCTC
*
48452432 TTAAGTTTCTC
1 TCAAGTTTCTC
48452443 T
1 T
48452444 TAACTCCCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.18, C:0.24, G:0.06, T:0.53
Consensus pattern (11 bp):
TCAAGTTTCTC
Found at i:48452444 original size:11 final size:11
Alignment explanation
Indices: 48452415--48452446 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
48452405 TAATTTCAAT
*
48452415 TTTCTCTCAAG
1 TTTCTCTTAAG
48452426 TTTCTCTTAAG
1 TTTCTCTTAAG
48452437 TTTCTCTTAA
1 TTTCTCTTAA
48452447 CTCCCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.22, G:0.06, T:0.53
Consensus pattern (11 bp):
TTTCTCTTAAG
Found at i:48452491 original size:12 final size:12
Alignment explanation
Indices: 48452452--48452495 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
48452442 CTTAACTCCC
*
48452452 TTTTTTTAAATA
1 TTTTTTAAAATA
* *
48452464 ATTTTAAAAATA
1 TTTTTTAAAATA
48452476 TTTTTTAAAAT-
1 TTTTTTAAAATA
48452487 TTTTTTAAA
1 TTTTTTAAA
48452496 CCATAAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTTTTAAAATA
Found at i:48454298 original size:18 final size:18
Alignment explanation
Indices: 48454271--48454309 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
48454261 CAGGTGCGTT
*
48454271 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
48454289 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
48454307 TCC
1 TCC
48454310 CTTTCCCAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:48454732 original size:9 final size:9
Alignment explanation
Indices: 48454718--48454749 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
48454708 TATTTGTACA
48454718 AATATTTTG
1 AATATTTTG
48454727 AATATTTTG
1 AATATTTTG
48454736 AATATTTTG
1 AATATTTTG
48454745 -ATATT
1 AATATT
48454750 ATTTGATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.22
9 18 0.78
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (9 bp):
AATATTTTG
Found at i:48454784 original size:25 final size:25
Alignment explanation
Indices: 48454748--48454795 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
48454738 TATTTTGATA
48454748 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
48454773 TTATTTGGTGTAATAAAATAGAA
1 TTATTTGATGTAATAAAATAGAA
48454796 ATTTTTGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.40
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:48454812 original size:9 final size:9
Alignment explanation
Indices: 48454798--48454834 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
48454788 AAATAGAAAT
48454798 TTTTGAATA
1 TTTTGAATA
48454807 TTTTGAATA
1 TTTTGAATA
48454816 TTTTGAATA
1 TTTTGAATA
48454825 TTTTG-ATA
1 TTTTGAATA
48454833 TT
1 TT
48454835 ATTTGAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 5 0.18
9 23 0.82
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (9 bp):
TTTTGAATA
Found at i:48454952 original size:44 final size:45
Alignment explanation
Indices: 48454865--48455633 Score: 875
Period size: 44 Copynumber: 17.4 Consensus size: 45
48454855 ATTAATACCT
*
48454865 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCT-ATTAAATTAAAAACCCTAACCTAA
* * *
48454911 TTAAATTAAAAACCCTAACC-CTTAACTTAAAAACTCTAACCTAA
1 TTAAATTAAAAACCCTAACCTATTAAATTAAAAACCCTAACCTAA
* *
48454955 TTAAATTAAAAACCCTAACC-CTTAAATTAAAAAGCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTATTAAATTAAAAACCCTAACCTAA
* * *
48454999 TTAACTTAAAAACCCTAACC-CTTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTATTAAATTAAAAACCCTAACCTAA
* *
48455043 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAATCCTAACC--C
1 TTAAATTAAAAACCCTAACCT-ATTAAATTAAAAACCCTAACCTAA
* * *
48455087 TTAACTTAAAAACCTTAACCTAATTAAATT-AAAACCCTAACC--C
1 TTAAATTAAAAACCCTAACCT-ATTAAATTAAAAACCCTAACCTAA
* * *
48455130 TTAACTTAAAAACCCTAACCTGATTAACTTAAAAACCCTAACC--C
1 TTAAATTAAAAACCCTAACCT-ATTAAATTAAAAACCCTAACCTAA
* *
48455174 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACC--C
1 TTAAATTAAAAACCCTAACCT-ATTAAATTAAAAACCCTAACCTAA
* *
48455218 TTAACTTAAAAACACTAACCTAATTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCT-ATTAAATTAAAAACCCTAACCTAA
* * *
48455264 TTAAATTAAAAACCCTAACC-CTTAACTTAAAAATCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTATTAAATTAAAAACCCTAACCTAA
* *
48455308 TTAAATT---AACTCTAACCTAATTAAATTAAAAACCCTAACC--C
1 TTAAATTAAAAACCCTAACCT-ATTAAATTAAAAACCCTAACCTAA
*
48455349 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCT-ATTAAATTAAAAACCCTAACCTAA
* *
48455395 TTAAATTAAAAACCCTAACC-CTTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTATTAAATTAAAAACCCTAACCTAA
*
48455439 TTAAATTAAAAACCCTAACC-CTTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTATTAAATTAAAAACCCTAACCTAA
* * **
48455483 TTAAATTAAAAAACCTAACCTAATTAACTTAAAAACCCTAACCTCG
1 TTAAATTAAAAACCCTAACCT-ATTAAATTAAAAACCCTAACCTAA
* * * * *
48455529 TTAACTTAAAAACCCTAACC-CTTAACTTAAAAACACTAAACC--C
1 TTAAATTAAAAACCCTAACCTATTAAATTAAAAACCCT-AACCTAA
* ** * *
48455572 TTAACTTAAAAATTCTAACC-CTTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTATTAAATTAAAAACCCTAACCTAA
*
48455616 TTAAATTTAAAACCCTAA
1 TTAAATTAAAAACCCTAA
48455634 ACGAAATTAA
Statistics
Matches: 646, Mismatches: 60, Indels: 36
0.87 0.08 0.05
Matches are distributed among these distances:
41 15 0.02
42 4 0.01
43 91 0.14
44 420 0.65
45 4 0.01
46 112 0.17
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.26
Consensus pattern (45 bp):
TTAAATTAAAAACCCTAACCTATTAAATTAAAAACCCTAACCTAA
Found at i:48454972 original size:67 final size:66
Alignment explanation
Indices: 48454861--48455612 Score: 940
Period size: 67 Copynumber: 11.4 Consensus size: 66
48454851 AACAATTAAT
* * *
48454861 ACCT-TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACC
1 ACCTATTAAATTAAAAACCCTAACC--CTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACC
48454925 CTA
64 CTA
* * * * * * *
48454928 ACC-CTTAACTTAAAAACTCTAACCTAATTAAATTAAAAACCCTAACC--CTTAAATTAAAAAGC
1 ACCTATTAAATTAAAAACCCTAACC--CTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACC
48454990 CTA
64 CTA
*
48454993 ACCTAATTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCC
1 ACCT-ATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCC
48455058 TA
65 TA
* *
48455060 ACCTAATTAAATTAAAAATCCTAACCCTTAACTTAAAAACCTTAACCTAATTAAATT-AAAACCC
1 ACCT-ATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCC
48455124 TA
65 TA
* * * * *
48455126 ACC-CTTAACTTAAAAACCCTAACCTGATTAACTTAAAAACCCTAACC--CTTAACTTAAAAACC
1 ACCTATTAAATTAAAAACCCTAACC--CTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACC
48455188 CTA
64 CTA
*
48455191 ACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACACTAACCTAATTAAATTAAAAACCC
1 ACCT-ATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCC
48455256 TA
65 TA
* *
48455258 ACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAATCCTAACCTAATTAAATT---AACTC
1 ACCT-ATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCC
48455320 TA
65 TA
48455322 ACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCC
1 ACCT-ATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCC
48455387 TA
65 TA
48455389 ACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCC
1 ACCT-ATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCC
48455454 TA
65 TA
* * * * *
48455456 ACC-CTTAAATTAAAAACCCTAACCTAATTAAATTAAAAAACCTAACCTAATTAACTTAAAAACC
1 ACCTATTAAATTAAAAACCCTAACC--CTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACC
48455520 CTA
64 CTA
* * * * * **
48455523 ACCTCGTTAACTTAAAAACCCTAACCCTTAACTTAAAAACACTAAACC--CTTAACTTAAAAATT
1 ACCT-ATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCT-AACCTAATTAAATTAAAAACC
48455586 CTA
64 CTA
* *
48455589 ACC-CTTAACTTAAAAACCCTAACC
1 ACCTATTAAATTAAAAACCCTAACC
48455613 TAATTAAATT
Statistics
Matches: 620, Mismatches: 45, Indels: 43
0.88 0.06 0.06
Matches are distributed among these distances:
64 106 0.17
65 89 0.14
66 49 0.08
67 353 0.57
68 4 0.01
69 19 0.03
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (66 bp):
ACCTATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCT
A
Found at i:48455238 original size:198 final size:198
Alignment explanation
Indices: 48454865--48455612 Score: 1043
Period size: 198 Copynumber: 3.8 Consensus size: 198
48454855 ATTAATACCT
*
48454865 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
1 TTAAATTAAAAACCCTAACC-AATTAAATTAAAAA-CCTAACCTAATTAAATTAAAAACCCTAAC
* * *
48454930 C-CTTAACTTAAAAACTCTAACCTAATTAAATTAAAAACCCTAACCCTTAAATTAAAAAGCCTAA
64 CTCTTAACTTAAAAACCCTAACC--ATTAACTTAAAAACCCTAACCCTTAAATTAAAAACCCTAA
*
48454994 CCTAATTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCT
127 CCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCT
48455059 AACCTAA
192 AACCTAA
* * *
48455066 TTAAATTAAAAATCCTAACC-CTTAACTTAAAAACCTTAACCTAATTAAATT-AAAACCCTAACC
1 TTAAATTAAAAACCCTAACCAATTAAATTAAAAACC-TAACCTAATTAAATTAAAAACCCTAACC
*
48455129 -CTTAACTTAAAAACCCTAACCTGATTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAC
65 TCTTAACTTAAAAACCCTAACC--ATTAACTTAAAAACCCTAACCCTTAAATTAAAAACCCTAAC
*
48455193 CTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACACTAACCTAATTAAATTAAAAACCCTA
128 CTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
48455258 ACCTAA
193 ACCTAA
* * *
48455264 TTAAATTAAAAACCCTAACC-CTTAACTTAAAAATCCTAACCTAATTAAATT---AACTCTAACC
1 TTAAATTAAAAACCCTAACCAATTAAATTAAAAA-CCTAACCTAATTAAATTAAAAACCCTAACC
* * * *
48455325 TAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAA
65 T-CTTAACTTAAAAACCCTAACCATTAACTTAAAAACCCTAACC--CTTAAATTAAAAACCCTAA
48455390 CCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCT
127 CCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCT
*
48455455 AACC--C
192 AACCTAA
*
48455460 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAAACCTAACCTAATTAACTTAAAAACCCTAAC
1 TTAAATTAAAAACCCTAACC-AATTAAATT-AAAAACCTAACCTAATTAAATTAAAAACCCTAAC
* * * **
48455525 CTCGTTAACTTAAAAACCCTAACCCTTAACTTAAAAACACTAAACCCTTAACTTAAAAATTCTAA
64 CTC-TTAACTTAAAAACCCTAACCATTAACTTAAAAACCCT-AACCCTTAAATTAAAAACCCTAA
* *
48455590 CC--CTTAACTTAAAAACCCTAACC
127 CCTAATTAAATTAAAAACCCTAACC
48455613 TAATTAAATT
Statistics
Matches: 500, Mismatches: 33, Indels: 31
0.89 0.06 0.05
Matches are distributed among these distances:
196 49 0.10
198 334 0.67
199 33 0.07
200 17 0.03
201 63 0.13
202 4 0.01
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (198 bp):
TTAAATTAAAAACCCTAACCAATTAAATTAAAAACCTAACCTAATTAAATTAAAAACCCTAACCT
CTTAACTTAAAAACCCTAACCATTAACTTAAAAACCCTAACCCTTAAATTAAAAACCCTAACCTA
ATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACC
TAA
Found at i:48459200 original size:123 final size:123
Alignment explanation
Indices: 48458891--48459240 Score: 513
Period size: 123 Copynumber: 2.8 Consensus size: 123
48458881 CCCAAACATG
*
48458891 CTACTGTAGCAAAAGCGCGTCCACGAGGGCACGATTTTCACAAATTCTTCTCAAATAGCATCCTC
1 CTACTGTAGCAAAAGCGCGTCCACTAGGGCACGA-TTTCACAAATTCTTCTCAAATAGCATCCT-
* * * **** *
48458956 CTAGAAGTGATTTTATACTATTTGCTCAGAAACATCAAAAAAAGTTTTTTTTTCCATGAC
64 ATAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAGAAAATTCTTCCATGAC
* *
48459016 TTACTGTAGCAAAAGCGTGTCCACTAGGGCACGATTTCACAAATTCTTCTCAAATAGCATCCTGA
1 CTACTGTAGCAAAAGCGCGTCCACTAGGGCACGATTTCACAAATTCTTCTCAAATAGCATCCT-A
*
48459081 TAGAAGCGATTTTATACTATTTTCTCAGAAACGTCAAAAAAA-AAAATTCTTCCATGAC
65 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAGAAAATTCTTCCATGAC
* * *
48459139 CTACTGTGGCAAAAGCGCGTCCACTAGGGCACGATTTCACAAATTCTTCTTAAATAACATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACTAGGGCACGATTTCACAAATTCTTCTCAAATAGCATCCTA-
*
48459204 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAA
65 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
48459241 CTCGAAATTA
Statistics
Matches: 204, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
122 1 0.00
123 104 0.51
124 68 0.33
125 31 0.15
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.30
Consensus pattern (123 bp):
CTACTGTAGCAAAAGCGCGTCCACTAGGGCACGATTTCACAAATTCTTCTCAAATAGCATCCTAT
AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAGAAAATTCTTCCATGAC
Found at i:48462057 original size:38 final size:38
Alignment explanation
Indices: 48461985--48462058 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
48461975 TCGTTTTAGT
48461985 GAAATTATATTTGCCCATGGTTTTTTATCCTCTTCGAA
1 GAAATTATATTTGCCCATGGTTTTTTATCCTCTTCGAA
*
48462023 GAAATTATATTTGTCCATGGTTTTTTATCCTCTTCG
1 GAAATTATATTTGCCCATGGTTTTTTATCCTCTTCG
48462059 GGATTTAGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.47
Consensus pattern (38 bp):
GAAATTATATTTGCCCATGGTTTTTTATCCTCTTCGAA
Found at i:48467035 original size:12 final size:12
Alignment explanation
Indices: 48467018--48467062 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
48467008 TTTATCTTGA
48467018 TAAATATAATAT
1 TAAATATAATAT
48467030 TAAATATAATAT
1 TAAATATAATAT
*
48467042 TAAATCT--TAT
1 TAAATATAATAT
48467052 TAAA-ATAATAT
1 TAAATATAATAT
48467063 AATGTTTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 1 0.03
10 7 0.24
11 3 0.10
12 18 0.62
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (12 bp):
TAAATATAATAT
Found at i:48471980 original size:27 final size:27
Alignment explanation
Indices: 48471950--48472006 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
48471940 GCCTCTAGCA
* * *
48471950 ATCCATGCTTCGCCAAGCCCATTGGTG
1 ATCCATACTTCGCCAAGCCCACTAGTG
* *
48471977 ATCCTTACTTTGCCAAGCCCACTAGTG
1 ATCCATACTTCGCCAAGCCCACTAGTG
48472004 ATC
1 ATC
48472007 ATAGTTCTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.21, C:0.33, G:0.18, T:0.28
Consensus pattern (27 bp):
ATCCATACTTCGCCAAGCCCACTAGTG
Found at i:48472425 original size:24 final size:24
Alignment explanation
Indices: 48472398--48472450 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
48472388 TTTTTAGAAG
* *
48472398 ATTTAGTATTTATGAGTATAACAT
1 ATTTAGCATTTATGAGCATAACAT
* *
48472422 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAACAT
48472446 ATTTA
1 ATTTA
48472451 ACTTTGATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAACAT
Done.