Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 1 of 206
Found at i:3148 original size:2 final size:2
Alignment explanation
Indices: 3136--3167 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3126 CAGGGAGACC
*
3136 GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3168 TGGCTAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:9206 original size:36 final size:36
Alignment explanation
Indices: 9159--9230 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
9149 TGCGACCAGA
9159 ACCTATTCACTTAAAAGATTACAACTCAATTTCCCT
1 ACCTATTCACTTAAAAGATTACAACTCAATTTCCCT
9195 ACCTATTCACTTAAAAGATTACAACTCAATTTCCCT
1 ACCTATTCACTTAAAAGATTACAACTCAATTTCCCT
9231 TCATGTAAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (36 bp):
ACCTATTCACTTAAAAGATTACAACTCAATTTCCCT
Found at i:13792 original size:23 final size:23
Alignment explanation
Indices: 13760--13912 Score: 141
Period size: 23 Copynumber: 6.7 Consensus size: 23
13750 ACTCGTTTGT
* * *
13760 ACACCACAATTTGCAGCACTTAA
1 ACACCTCAATTTACAGCATTTAA
* * *
13783 ACACTTCAATTTACATCATTTGA
1 ACACCTCAATTTACAGCATTTAA
* *
13806 GCACCTCAATTTACAGCAATTAA
1 ACACCTCAATTTACAGCATTTAA
*
13829 ACACTTCAATTTACAGCATTTAA
1 ACACCTCAATTTACAGCATTTAA
* *
13852 ACACCTCAACTTACAACACTTT-A
1 ACACCTCAATTTACAGCA-TTTAA
* * *
13875 ACATCC-CAATTAACAACATTTAT
1 ACA-CCTCAATTTACAGCATTTAA
13898 ACACCTCAA-TTACAG
1 ACACCTCAATTTACAG
13913 NNNNNNNNNN
Statistics
Matches: 104, Mismatches: 22, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
22 9 0.09
23 90 0.87
24 5 0.05
ACGTcount: A:0.39, C:0.27, G:0.05, T:0.29
Consensus pattern (23 bp):
ACACCTCAATTTACAGCATTTAA
Found at i:13823 original size:46 final size:46
Alignment explanation
Indices: 13760--13912 Score: 166
Period size: 46 Copynumber: 3.3 Consensus size: 46
13750 ACTCGTTTGT
* * * *
13760 ACACCACAATTTGCAGCACTTAAACACTTCAATTTACATCATTTGA
1 ACACCTCAATTTACAGCACTTAAACACTTCAATTTACAGCATTTAA
* *
13806 GCACCTCAATTTACAGCAATTAAACACTTCAATTTACAGCATTTAA
1 ACACCTCAATTTACAGCACTTAAACACTTCAATTTACAGCATTTAA
* * * * * * *
13852 ACACCTCAACTTACAACACTTTAACA-TCCCAATTAACAACATTTAT
1 ACACCTCAATTTACAGCACTTAAACACT-TCAATTTACAGCATTTAA
13898 ACACCTCAA-TTACAG
1 ACACCTCAATTTACAG
13913 NNNNNNNNNN
Statistics
Matches: 90, Mismatches: 16, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
45 6 0.07
46 84 0.93
ACGTcount: A:0.39, C:0.27, G:0.05, T:0.29
Consensus pattern (46 bp):
ACACCTCAATTTACAGCACTTAAACACTTCAATTTACAGCATTTAA
Found at i:13885 original size:69 final size:69
Alignment explanation
Indices: 13760--13912 Score: 159
Period size: 69 Copynumber: 2.2 Consensus size: 69
13750 ACTCGTTTGT
* * * * * * * *
13760 ACACCACAATTTGCAGCACTTAAACACTTCAATTTACATCATTTGAGCACCTCAATTTACAGCAA
1 ACACCTCAATTTACAGCACTTAAACACCTCAACTTACAACATTTGAACACCTCAATTAACAACAA
13825 TTAA
66 TTAA
* *
13829 ACACTTCAATTTACAGCATTTAAACACCTCAACTTACAACACTTT-AACATCC-CAATTAACAAC
1 ACACCTCAATTTACAGCACTTAAACACCTCAACTTACAACA-TTTGAACA-CCTCAATTAACAAC
* *
13892 ATTTAT
64 AATTAA
13898 ACACCTCAA-TTACAG
1 ACACCTCAATTTACAG
13913 NNNNNNNNNN
Statistics
Matches: 69, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
68 6 0.09
69 58 0.84
70 5 0.07
ACGTcount: A:0.39, C:0.27, G:0.05, T:0.29
Consensus pattern (69 bp):
ACACCTCAATTTACAGCACTTAAACACCTCAACTTACAACATTTGAACACCTCAATTAACAACAA
TTAA
Found at i:14091 original size:46 final size:45
Alignment explanation
Indices: 14016--14127 Score: 143
Period size: 46 Copynumber: 2.4 Consensus size: 45
14006 NNNNNNNCAA
* *
14016 TTCAATTTGCAATACTTAAAACACTTCAATTTACAACATTTAAACAC
1 TTCAATTTGCAACACTT--AACACTTCAATTCACAACATTTAAACAC
* * **
14063 TTCAATTTGCAGCACGTTAACACTTCAATTCACAGCATTTAAATTC
1 TTCAATTTGCAACAC-TTAACACTTCAATTCACAACATTTAAACAC
14109 TTCAATTTGCAACACTTAA
1 TTCAATTTGCAACACTTAA
14128 ATAGGGCTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
45 4 0.07
46 38 0.67
47 13 0.23
48 2 0.04
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (45 bp):
TTCAATTTGCAACACTTAACACTTCAATTCACAACATTTAAACAC
Found at i:14129 original size:23 final size:23
Alignment explanation
Indices: 14016--14128 Score: 111
Period size: 23 Copynumber: 4.9 Consensus size: 23
14006 NNNNNNNCAA
*
14016 TTCAATTTGCAATACTTAAAACAC
1 TTCAATTTGCAACACTT-AAACAC
* *
14040 TTCAATTTACAACATTTAAACAC
1 TTCAATTTGCAACACTTAAACAC
*
14063 TTCAATTTGCAGCACGTT-AACAC
1 TTCAATTTGCAACAC-TTAAACAC
** * * **
14086 TTCAATTCACAGCATTTAAATTC
1 TTCAATTTGCAACACTTAAACAC
14109 TTCAATTTGCAACACTTAAA
1 TTCAATTTGCAACACTTAAA
14129 TAGGGCTTTA
Statistics
Matches: 72, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
22 2 0.03
23 54 0.75
24 16 0.22
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (23 bp):
TTCAATTTGCAACACTTAAACAC
Found at i:14638 original size:15 final size:15
Alignment explanation
Indices: 14618--14646 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
14608 TTTAAGACAA
14618 CATGAATACTTACAG
1 CATGAATACTTACAG
14633 CATGAATACTTACA
1 CATGAATACTTACA
14647 TTTTAATCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (15 bp):
CATGAATACTTACAG
Found at i:22355 original size:31 final size:30
Alignment explanation
Indices: 22290--22386 Score: 115
Period size: 31 Copynumber: 3.2 Consensus size: 30
22280 AAACCCCTAG
*
22290 ATCCCAAGCCGGGATATCCT-AGAATAAGAT
1 ATCCCAAGCCGGGATATCCTGA-AATAGGAT
* *
22320 ATCCCAAACCGGGATGTCCCTGAAATAGGAT
1 ATCCCAAGCCGGGATAT-CCTGAAATAGGAT
* *
22351 ATCCCAAGCCGGGATATACCTGGAATGGGAT
1 ATCCCAAGCCGGGATAT-CCTGAAATAGGAT
22382 ATCCC
1 ATCCC
22387 TGGCTGGAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
30 15 0.26
31 41 0.72
32 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.20
Consensus pattern (30 bp):
ATCCCAAGCCGGGATATCCTGAAATAGGAT
Found at i:22628 original size:31 final size:29
Alignment explanation
Indices: 22573--22649 Score: 109
Period size: 31 Copynumber: 2.6 Consensus size: 29
22563 AAGAATGAAT
*
22573 TAAATTCAGTGCTTACTAACGTTGTAAAA
1 TAAATTCAGTGCTTATTAACGTTGTAAAA
* *
22602 TAAATTTAGTGCTTATTAAAACGTTGTGAAA
1 TAAATTCAGTGCTTATT--AACGTTGTAAAA
22633 TAAATTCAGTGCTTATT
1 TAAATTCAGTGCTTATT
22650 TACAAGGACT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 15 0.36
31 27 0.64
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.39
Consensus pattern (29 bp):
TAAATTCAGTGCTTATTAACGTTGTAAAA
Found at i:31187 original size:21 final size:21
Alignment explanation
Indices: 31155--31196 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
31145 TCCTGCAGCA
31155 TAAAAAATCTGAACCGGACAC
1 TAAAAAATCTGAACCGGACAC
31176 TAAAAGAA-CTGAACCGGACAC
1 TAAAA-AATCTGAACCGGACAC
31197 GTGAAATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.12
Consensus pattern (21 bp):
TAAAAAATCTGAACCGGACAC
Found at i:32134 original size:40 final size:40
Alignment explanation
Indices: 32079--32162 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
32069 CTACGTGCGT
32079 CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
1 CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
32119 CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
1 CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
32159 CACA
1 CACA
32163 GATGCAGTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.38, C:0.38, G:0.12, T:0.12
Consensus pattern (40 bp):
CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
Found at i:36600 original size:22 final size:23
Alignment explanation
Indices: 36574--36616 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
36564 ATTTAGAATT
*
36574 TAAAC-TAAAATGATAAATTTTG
1 TAAACATAAAAGGATAAATTTTG
*
36596 TAAACATTAAAGGATAAATTT
1 TAAACATAAAAGGATAAATTT
36617 GTTGAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (23 bp):
TAAACATAAAAGGATAAATTTTG
Found at i:37106 original size:35 final size:35
Alignment explanation
Indices: 37067--37206 Score: 199
Period size: 35 Copynumber: 4.0 Consensus size: 35
37057 ACTCAACCTT
** *
37067 TGCAATCGACAGTCAGTCGCATGGCTCGCAAGCAG
1 TGCAATCGGTAGTCAGTCGCACGGCTCGCAAGCAG
*
37102 TGCAATCGGTAGTCAGTCGCGCGGCTCGCAAGCAG
1 TGCAATCGGTAGTCAGTCGCACGGCTCGCAAGCAG
* *
37137 TGCAATCGGTAGTCAGTCGCGCGGATCGCAAGCAG
1 TGCAATCGGTAGTCAGTCGCACGGCTCGCAAGCAG
* * *
37172 TGCAATCGGTAGTCAGTTGCGCAGCTCGCAAGCAG
1 TGCAATCGGTAGTCAGTCGCACGGCTCGCAAGCAG
37207 CAAGTTCGTC
Statistics
Matches: 97, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 97 1.00
ACGTcount: A:0.23, C:0.27, G:0.32, T:0.18
Consensus pattern (35 bp):
TGCAATCGGTAGTCAGTCGCACGGCTCGCAAGCAG
Found at i:43805 original size:4 final size:4
Alignment explanation
Indices: 43796--43853 Score: 116
Period size: 4 Copynumber: 14.5 Consensus size: 4
43786 CTCCCTCAGA
43796 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
43844 ATGT ATGT AT
1 ATGT ATGT AT
43854 AACTGGATTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:46806 original size:35 final size:35
Alignment explanation
Indices: 46753--46853 Score: 166
Period size: 35 Copynumber: 2.9 Consensus size: 35
46743 AGCTTGCTGA
*
46753 TTGCGAGCTGCGCAACTGACTACCGATTGCACTGC
1 TTGCGAGCTGCGCGACTGACTACCGATTGCACTGC
*
46788 TTGCGAGCCGCGCGACTGACTACCGATTGCACTGC
1 TTGCGAGCTGCGCGACTGACTACCGATTGCACTGC
* *
46823 TTGCGAGTTGCGCGACTGACTGCCGATTGCA
1 TTGCGAGCTGCGCGACTGACTACCGATTGCA
46854 AGGGTTGAGT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 61 1.00
ACGTcount: A:0.18, C:0.31, G:0.29, T:0.23
Consensus pattern (35 bp):
TTGCGAGCTGCGCGACTGACTACCGATTGCACTGC
Found at i:46852 original size:19 final size:19
Alignment explanation
Indices: 46797--46852 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
46787 CTTGCGAGCC
*
46797 GCGCGACTGACTACCGATT
1 GCGCGACTGACTGCCGATT
46816 --GC-ACTG-CTTG-CGAGTT
1 GCGCGACTGAC-TGCCGA-TT
46832 GCGCGACTGACTGCCGATT
1 GCGCGACTGACTGCCGATT
46851 GC
1 GC
46853 AAGGGTTGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
15 4 0.14
16 7 0.24
17 2 0.07
18 2 0.07
19 10 0.34
20 4 0.14
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.23
Consensus pattern (19 bp):
GCGCGACTGACTGCCGATT
Found at i:46871 original size:33 final size:34
Alignment explanation
Indices: 46767--46871 Score: 95
Period size: 35 Copynumber: 3.1 Consensus size: 34
46757 GAGCTGCGCA
** ** *
46767 ACTGACTACCGATTGCACTGCTTGCGAGCCGCGCG
1 ACTGACTACCGATTGCAAGGCTT-CGAGTTGAGCG
** *
46802 ACTGACTACCGATTGCACTGCTTGCGAGTTGCGCG
1 ACTGACTACCGATTGCAAGGCTT-CGAGTTGAGCG
* *
46837 ACTGACTGCCGATTGCAAGGGTT-GAGTTGAGCG
1 ACTGACTACCGATTGCAAGGCTTCGAGTTGAGCG
46870 AC
1 AC
46872 GGAAAGAGGC
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
33 11 0.17
35 52 0.83
ACGTcount: A:0.19, C:0.28, G:0.30, T:0.23
Consensus pattern (34 bp):
ACTGACTACCGATTGCAAGGCTTCGAGTTGAGCG
Found at i:47216 original size:36 final size:36
Alignment explanation
Indices: 47175--47245 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
47165 GATTATTTAA
*
47175 TCTTAGAGTTTTAATTGTATACAACTTCTAATTATG
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTATG
* * *
47211 TCTTAGAGTTCTGATTGTATACAGCTTTTAATTAT
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTAT
47246 AGCCTTTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAACTTCTAATTATG
Found at i:52316 original size:36 final size:36
Alignment explanation
Indices: 52275--52345 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
52265 GATTATTTAA
*
52275 TCTTAGAGTTTTAATTGTATACAGCTTCTAATTATG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
*
52311 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTAT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTAT
52346 AGCCTTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
Found at i:62834 original size:54 final size:54
Alignment explanation
Indices: 62714--62835 Score: 181
Period size: 54 Copynumber: 2.3 Consensus size: 54
62704 TAATAATAAT
* * * * *
62714 TTTAACCGTTAACATTTATAAATTATGTCAATTTATTCTTGGTTCTGAAACGAA
1 TTTAACCATCAACATTTATAAATTATGTCAATTTAATCTTGATTCTAAAACGAA
*
62768 TTTAACTATCAACATTTATAAATTATGTCAATTTAATCTTGATTCTAAAACGAA
1 TTTAACCATCAACATTTATAAATTATGTCAATTTAATCTTGATTCTAAAACGAA
*
62822 TTTAACCCTCAACA
1 TTTAACCATCAACA
62836 AATTCACATT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 60 1.00
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (54 bp):
TTTAACCATCAACATTTATAAATTATGTCAATTTAATCTTGATTCTAAAACGAA
Found at i:63224 original size:18 final size:18
Alignment explanation
Indices: 63201--63241 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
63191 ATATTAATTT
63201 TATAACTTTTCATACTTA
1 TATAACTTTTCATACTTA
63219 TATAACTTTTCATACTTA
1 TATAACTTTTCATACTTA
*
63237 GATAA
1 TATAA
63242 ATAAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.37, C:0.15, G:0.02, T:0.46
Consensus pattern (18 bp):
TATAACTTTTCATACTTA
Found at i:65616 original size:7 final size:7
Alignment explanation
Indices: 65606--65639 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
65596 TATAATGATA
65606 ATTATTT
1 ATTATTT
65613 ATTATTT
1 ATTATTT
65620 ATTATTT
1 ATTATTT
65627 ATTA-TT
1 ATTATTT
65633 ATTATTT
1 ATTATTT
65640 TAAAATTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
ATTATTT
Found at i:67333 original size:6 final size:6
Alignment explanation
Indices: 67324--67353 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
67314 TATATGTAAT
67324 AGTATC AGTATC AGTATC AGTATC AGTATC
1 AGTATC AGTATC AGTATC AGTATC AGTATC
67354 TATATGTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (6 bp):
AGTATC
Found at i:71381 original size:22 final size:22
Alignment explanation
Indices: 71353--71402 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
71343 CTTCTTTACA
*
71353 TGTTTTATTATTGTTATATCAT
1 TGTTTTACTATTGTTATATCAT
*
71375 TGTTTTACTATTGTTATATTAT
1 TGTTTTACTATTGTTATATCAT
*
71397 TATTTT
1 TGTTTT
71403 GCCATCATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.04, G:0.08, T:0.66
Consensus pattern (22 bp):
TGTTTTACTATTGTTATATCAT
Found at i:78573 original size:17 final size:17
Alignment explanation
Indices: 78551--78585 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
78541 CTTTGGGCTG
* *
78551 TGATTTGAATGGGGTTT
1 TGATTTCAATGGGCTTT
78568 TGATTTCAATGGGCTTT
1 TGATTTCAATGGGCTTT
78585 T
1 T
78586 TGGAACAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.29, T:0.49
Consensus pattern (17 bp):
TGATTTCAATGGGCTTT
Found at i:88403 original size:18 final size:18
Alignment explanation
Indices: 88355--88405 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
88345 TTATGCAACG
*
88355 TGTTATTTTTTAAATAAT
1 TGTTATTTTTTAAAAAAT
* *
88373 T-TAATTGTATTAAAAAAT
1 TGTTATT-TTTTAAAAAAT
88391 TGTTATTTTTTAAAA
1 TGTTATTTTTTAAAA
88406 GAAAATATGC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 4 0.15
18 18 0.69
19 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (18 bp):
TGTTATTTTTTAAAAAAT
Found at i:100312 original size:21 final size:21
Alignment explanation
Indices: 100283--100332 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
100273 AGAATAGATT
* *
100283 TAATATTTATTGTTTAAACAA
1 TAATATTTATTGTGTAAAAAA
*
100304 TATTATTTATTGTGTAAAAAA
1 TAATATTTATTGTGTAAAAAA
100325 TAATATTT
1 TAATATTT
100333 TTAAAGTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (21 bp):
TAATATTTATTGTGTAAAAAA
Found at i:108326 original size:19 final size:19
Alignment explanation
Indices: 108304--108350 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
108294 AATTTAGAAT
108304 TAATAATATATATTAAAT-A
1 TAATAATATA-ATTAAATAA
*
108323 TAATAATATAATTTAATAA
1 TAATAATATAATTAAATAA
*
108342 TAAAAATAT
1 TAATAATAT
108351 CAAAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAATAATATAATTAAATAA
Found at i:108414 original size:25 final size:25
Alignment explanation
Indices: 108385--108432 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
108375 TTATAGATTG
*
108385 TTCAAATCAATTATTACCCAATTCA
1 TTCAAATCAATTATTACCAAATTCA
108410 TTCAAATCAATTATTACCAAATT
1 TTCAAATCAATTATTACCAAATT
108433 TGAATTTGGA
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:0.42, C:0.21, G:0.00, T:0.38
Consensus pattern (25 bp):
TTCAAATCAATTATTACCAAATTCA
Found at i:109257 original size:6 final size:6
Alignment explanation
Indices: 109243--109284 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
109233 ACTCAACGTA
* *
109243 AATCGC AATCAC AATCAC AATCAC AATCAC AATCAC ATTCAC
1 AATCAC AATCAC AATCAC AATCAC AATCAC AATCAC AATCAC
109285 GCTTTTCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.45, C:0.33, G:0.02, T:0.19
Consensus pattern (6 bp):
AATCAC
Found at i:115409 original size:19 final size:19
Alignment explanation
Indices: 115385--115421 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
115375 AAACACCTAA
115385 TATTTATTTATTAAGTATT
1 TATTTATTTATTAAGTATT
115404 TATTTATTTATTAAGTAT
1 TATTTATTTATTAAGTAT
115422 GCAAAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
TATTTATTTATTAAGTATT
Found at i:149883 original size:28 final size:28
Alignment explanation
Indices: 149851--149906 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
149841 CATCATTTTA
*
149851 TGTGTATAATCACACTAAATCAAAATTT
1 TGTGTATAATCACAATAAATCAAAATTT
* *
149879 TGTGTATAATTACAATAAATTAAAATTT
1 TGTGTATAATCACAATAAATCAAAATTT
149907 CATATATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (28 bp):
TGTGTATAATCACAATAAATCAAAATTT
Found at i:149914 original size:28 final size:28
Alignment explanation
Indices: 149855--149915 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
149845 ATTTTATGTG
* ** *
149855 TATAATCACACTAAATCAAAATTTTGTG
1 TATAATCACAATAAATCAAAATTTCATA
* *
149883 TATAATTACAATAAATTAAAATTTCATA
1 TATAATCACAATAAATCAAAATTTCATA
149911 TATAA
1 TATAA
149916 AATTGTATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (28 bp):
TATAATCACAATAAATCAAAATTTCATA
Found at i:154395 original size:6 final size:6
Alignment explanation
Indices: 154380--154423 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
154370 ATGTTACTCG
*
154380 GAGT-T GAGTGT GAGTGT GGGTGT GAGTGT GAGTGT GAGTGT GAG
1 GAGTGT GAGTGT GAGTGT GAGTGT GAGTGT GAGTGT GAGTGT GAG
154424 ATACAGAGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 4 0.11
6 32 0.89
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (6 bp):
GAGTGT
Found at i:159319 original size:18 final size:19
Alignment explanation
Indices: 159287--159325 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
159277 AGTTCTTTTT
159287 TTTTCCTATTATATTAGTA
1 TTTTCCTATTATATTAGTA
*
159306 TTTT-CTATTCTATTAGTA
1 TTTTCCTATTATATTAGTA
159324 TT
1 TT
159326 AGATTAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.23, C:0.10, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTTCCTATTATATTAGTA
Found at i:160466 original size:29 final size:29
Alignment explanation
Indices: 160418--160475 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
160408 AAATGAAAAT
*
160418 TTTTAAATTTTTAAATAATTTAATAATTA
1 TTTTAAATTTTTAAATAATTGAATAATTA
160447 TTTTATAATTTTGT-AA-AATTGAATAATTA
1 TTTTA-AATTTT-TAAATAATTGAATAATTA
160476 ATAAAGAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 17 0.65
30 8 0.31
31 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (29 bp):
TTTTAAATTTTTAAATAATTGAATAATTA
Found at i:162089 original size:63 final size:62
Alignment explanation
Indices: 161972--162101 Score: 156
Period size: 63 Copynumber: 2.1 Consensus size: 62
161962 ATGCACTTAA
* * *
161972 AAAATTGGCATGAATAAATCAATATGTAAATCCCACTTCGACCTGACTTCCAAAAATTATCTT
1 AAAATCGGCATGAAGAAATCAATATGTAAATCCCACTTCGACCTAACTTCC-AAAATTATCTT
* * * *
162035 AAAATCGGCATGAAGAAATCAGTACT-TAAATCCGACTTTGACAC-AACTTTCAAAATTATCTT
1 AAAATCGGCATGAAGAAATCAATA-TGTAAATCCCACTTCGAC-CTAACTTCCAAAATTATCTT
162097 AAAAT
1 AAAAT
162102 TTGTAGACCG
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
62 16 0.28
63 40 0.69
64 2 0.03
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (62 bp):
AAAATCGGCATGAAGAAATCAATATGTAAATCCCACTTCGACCTAACTTCCAAAATTATCTT
Found at i:170431 original size:20 final size:21
Alignment explanation
Indices: 170402--170442 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
170392 AAATGTAATT
*
170402 ATTATTTTAT-TTTATTTAAA
1 ATTATATTATGTTTATTTAAA
*
170422 ATTATATTATGTTTTTTTAAA
1 ATTATATTATGTTTATTTAAA
170443 CAATTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
ATTATATTATGTTTATTTAAA
Found at i:171667 original size:19 final size:20
Alignment explanation
Indices: 171645--171683 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
171635 AAAGTTTTCT
*
171645 AAAATTTTAAATAT-ATTAA
1 AAAATGTTAAATATAATTAA
*
171664 AAAATGTTAAGTATAATTAA
1 AAAATGTTAAATATAATTAA
171684 TTTTAAAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAATGTTAAATATAATTAA
Found at i:171707 original size:17 final size:17
Alignment explanation
Indices: 171685--171723 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
171675 TATAATTAAT
171685 TTTAAAAGTTTAATATA
1 TTTAAAAGTTTAATATA
*
171702 TTTAAAATTTTAATATA
1 TTTAAAAGTTTAATATA
*
171719 CTTAA
1 TTTAA
171724 TACATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (17 bp):
TTTAAAAGTTTAATATA
Found at i:171796 original size:26 final size:26
Alignment explanation
Indices: 171763--171867 Score: 84
Period size: 25 Copynumber: 4.3 Consensus size: 26
171753 AGATTTTCTT
171763 AATATATTTAAAATTTTAAAAAATTA
1 AATATATTTAAAATTTTAAAAAATTA
*
171789 AATATA-TTAAAATTTTAAATATATTA
1 AATATATTTAAAATTTTAAA-AAATTA
* *
171815 AA-A-ATAT-ATATTTT-AAAAA-T-
1 AATATATTTAAAATTTTAAAAAATTA
* * *
171835 -ATATA-TTAAAATTTTAATATATTT
1 AATATATTTAAAATTTTAAAAAATTA
171859 AATATATTT
1 AATATATTT
171868 TTAATAGATA
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
19 1 0.02
20 2 0.03
21 8 0.13
22 5 0.08
23 3 0.05
24 7 0.11
25 20 0.33
26 15 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
AATATATTTAAAATTTTAAAAAATTA
Found at i:171798 original size:17 final size:17
Alignment explanation
Indices: 171778--171818 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
171768 ATTTAAAATT
171778 TTAAAAAATTAAATATA
1 TTAAAAAATTAAATATA
**
171795 TTAAAATTTTAAATATA
1 TTAAAAAATTAAATATA
171812 TTAAAAA
1 TTAAAAA
171819 TATATATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAAATTAAATATA
Found at i:171800 original size:15 final size:15
Alignment explanation
Indices: 171782--171857 Score: 66
Period size: 15 Copynumber: 5.0 Consensus size: 15
171772 AAAATTTTAA
171782 AAAATTAAATATATT
1 AAAATTAAATATATT
171797 AAAATTTTAAATATATT
1 AAAA--TTAAATATATT
* * *
171814 AAAAATATATATTTT
1 AAAATTAAATATATT
*
171829 AAAA--ATATATATT
1 AAAATTAAATATATT
*
171842 AAAATTTTAATATATT
1 AAAA-TTAAATATATT
171858 TAATATATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
13 12 0.24
15 16 0.32
16 7 0.14
17 15 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATTAAATATATT
Found at i:171840 original size:17 final size:16
Alignment explanation
Indices: 171778--171845 Score: 54
Period size: 17 Copynumber: 4.4 Consensus size: 16
171768 ATTTAAAATT
171778 TTAAAAAATTAAATATA
1 TTAAAAAA-TAAATATA
**
171795 TTAAAATTTTAAATATA
1 TTAAAA-AATAAATATA
*
171812 TT-AAAAATATATAT-
1 TTAAAAAATAAATATA
*
171826 TTTAAAAAT--ATATA
1 TTAAAAAATAAATATA
171840 TTAAAA
1 TTAAAA
171846 TTTTAATATA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
13 4 0.10
14 7 0.17
15 12 0.29
16 3 0.07
17 16 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAAAAATAAATATA
Found at i:171913 original size:17 final size:17
Alignment explanation
Indices: 171890--171958 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
171880 GAGAGAAGAT
*
171890 TTTTTAATATATTTAAAA
1 TTTTAAATATA-TTAAAA
*
171908 TTTTAAA-AAACTTAAAAA
1 TTTTAAATATA-TT-AAAA
**
171926 AATTAAATATATTAAAA
1 TTTTAAATATATTAAAA
*
171943 TTTTAAATATGTTAAA
1 TTTTAAATATATTAAA
171959 GAAAATGTTG
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
17 21 0.52
18 17 0.43
19 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (17 bp):
TTTTAAATATATTAAAA
Found at i:171958 original size:35 final size:37
Alignment explanation
Indices: 171895--171964 Score: 99
Period size: 35 Copynumber: 1.9 Consensus size: 37
171885 AAGATTTTTT
171895 AATATATTTAAAATTTTAAAAAACTTAAA-AAAATTA
1 AATATATTTAAAATTTTAAAAAACTTAAAGAAAATTA
* **
171931 AATATA-TTAAAATTTTAAATATGTTAAAGAAAAT
1 AATATATTTAAAATTTTAAAAAACTTAAAGAAAAT
171965 GTTGAGTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (37 bp):
AATATATTTAAAATTTTAAAAAACTTAAAGAAAATTA
Found at i:172002 original size:18 final size:17
Alignment explanation
Indices: 171981--172044 Score: 74
Period size: 17 Copynumber: 3.6 Consensus size: 17
171971 TATAATCGAT
171981 TTAAAATTTTTAATATA
1 TTAAAATTTTTAATATA
* *
171998 CTTAATATATTTAAATATA
1 -TTAAAAT-TTTTAATATA
* *
172017 TTAAAATTTTGAACATA
1 TTAAAATTTTTAATATA
172034 TTAAAATTTTT
1 TTAAAATTTTT
172045 TTAAGTATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
17 18 0.46
18 12 0.31
19 9 0.23
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (17 bp):
TTAAAATTTTTAATATA
Found at i:172064 original size:80 final size:80
Alignment explanation
Indices: 171900--172070 Score: 184
Period size: 80 Copynumber: 2.1 Consensus size: 80
171890 TTTTTAATAT
* *
171900 ATTTAAAA-TTTTAAAAAACTTAAAAAAATTAAATATATTAAAATTTTAAATATGTTAAAGAAAA
1 ATTTAAAATTTTTAAAAAACTTAAAAAAATTAAATATATTAAAATTTTAAACATATTAAAGAAAA
* * *
171964 TGTTGAGTATAATCG
66 TGTTAAGTATAACCA
* * * * * * ***
171979 ATTTAAAATTTTTAATATACTTAATATATTTAAATATATTAAAATTTTGAACATATTAAA-ATTT
1 ATTTAAAATTTTTAAAAAACTTAAAAAAATTAAATATATTAAAATTTTAAACATATTAAAGAAAA
*
172043 TTTTAAGTATAACCA
66 TGTTAAGTATAACCA
172058 ATTTTAAAATTTT
1 A-TTTAAAATTTT
172071 AATTTATTTT
Statistics
Matches: 75, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
79 21 0.28
80 54 0.72
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.43
Consensus pattern (80 bp):
ATTTAAAATTTTTAAAAAACTTAAAAAAATTAAATATATTAAAATTTTAAACATATTAAAGAAAA
TGTTAAGTATAACCA
Found at i:173727 original size:32 final size:32
Alignment explanation
Indices: 173678--173740 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
173668 GGCATAAATG
*
173678 TATATATATTATAAATATTTAAAGTTAAAAGA
1 TATATATATTATAAATATTAAAAGTTAAAAGA
173710 TATATAATATTAT-AATATTAAAAGTTAAAAG
1 TATAT-ATATTATAAATATTAAAAGTTAAAAG
173741 TTAAGTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 22 0.76
33 7 0.24
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (32 bp):
TATATATATTATAAATATTAAAAGTTAAAAGA
Found at i:174569 original size:24 final size:23
Alignment explanation
Indices: 174542--174588 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
174532 ATTGAAATAG
174542 ATTGATTTAGTATGTGA-TGAATTT
1 ATTGATTTA-TAT-TGATTGAATTT
174566 ATTGATTTATATTGATTGAATTT
1 ATTGATTTATATTGATTGAATTT
174589 GTATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 3 0.14
23 10 0.45
24 9 0.41
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (23 bp):
ATTGATTTATATTGATTGAATTT
Found at i:174845 original size:37 final size:38
Alignment explanation
Indices: 174746--174846 Score: 98
Period size: 37 Copynumber: 2.6 Consensus size: 38
174736 CTTCGAGTCA
*
174746 ATGAGACACTGGGTGTCAATTTATTACTCCGGATTAATTCG
1 ATGAGACACTGGGTGTCAA--T-TTACTCCGGATTAATCCG
* * * *
174787 ATGAGGCACTGGGCG-CTAATTTACTTCGGTTTAA-CCG
1 ATGAGACACTGGGTGTC-AATTTACTCCGGATTAATCCG
*
174824 ATGAGACACTAGGTGTCAATTTA
1 ATGAGACACTGGGTGTCAATTTA
174847 TTACTTTGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
37 20 0.40
38 13 0.26
39 1 0.02
40 1 0.02
41 15 0.30
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (38 bp):
ATGAGACACTGGGTGTCAATTTACTCCGGATTAATCCG
Found at i:175718 original size:31 final size:31
Alignment explanation
Indices: 175665--175735 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
175655 TTTTGTGTTG
*
175665 CTTATTGTTCAAGATTGTAGGGAATGGTAAA
1 CTTATTGTTCAAGATTGCAGGGAATGGTAAA
*
175696 CTTATT-TTCCAAGCTTGCAGGGAATGGTAAA
1 CTTATTGTT-CAAGATTGCAGGGAATGGTAAA
*
175727 CTTCTTGTT
1 CTTATTGTT
175736 AAAGTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 2 0.06
31 31 0.89
32 2 0.06
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.38
Consensus pattern (31 bp):
CTTATTGTTCAAGATTGCAGGGAATGGTAAA
Found at i:182850 original size:2 final size:2
Alignment explanation
Indices: 182843--182889 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
182833 TTTTACAGCC
182843 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
182885 AT AT A
1 AT AT A
182890 AAGTGACTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:194207 original size:31 final size:31
Alignment explanation
Indices: 194171--194239 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
194161 GTTACAAAAT
194171 GTTATTGAACTATTCAAAAAATTTTATTTAA
1 GTTATTGAACTATTCAAAAAATTTTATTTAA
* *
194202 GTTATTGAACTATTCGAAAATTTTTATTTAA
1 GTTATTGAACTATTCAAAAAATTTTATTTAA
194233 GTTATTG
1 GTTATTG
194240 GGTTGTTAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.48
Consensus pattern (31 bp):
GTTATTGAACTATTCAAAAAATTTTATTTAA
Found at i:207484 original size:6 final size:6
Alignment explanation
Indices: 207475--207505 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
207465 AATAACATTG
207475 AATTTA AATTTA AATTTA AATTTA AATTTA A
1 AATTTA AATTTA AATTTA AATTTA AATTTA A
207506 TTTTGTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:213630 original size:172 final size:171
Alignment explanation
Indices: 213328--213636 Score: 469
Period size: 172 Copynumber: 1.8 Consensus size: 171
213318 AATGTCATTG
* * *
213328 ACAATACATGACATAAAATCAAATAATTCTTGTACTGAAATAAATACTAAATCTTAAAACATCCA
1 ACAATACATGACATAAAATCAAAGAATTCTTGTACTGAAATAAAGACTAAATCTTAAAACAACCA
*
213393 ACCATCTTTCGATTTCCCAATCTGTGAAACTAAAGAACTATGGAACTCAAACCCAAGATAACTGC
66 ACCATCTTTCGATTTCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAAGATAACTGC
213458 AGACATGGAGGAGAAACATGAACACAACATGTATGCCACTA
131 AGACATGGAGGAGAAACATGAACACAACATGTATGCCACTA
* * * *
213499 ACAATACATGACAATACAATCAAAGAATGTC-TGTACTGAAATAAAGACTAAATCTTCAGATAAC
1 ACAATACATGAC-ATAAAATCAAAGAAT-TCTTGTACTGAAATAAAGACTAAATCTTAAAACAAC
** * *
213563 CAACTGTCTTTCGATTATCCCAATTTGTGAAACTAAAGAAATATGGAACTCAAACCC-AGTTAAC
64 CAACCATCTTTCGATT-TCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAAGATAAC
213627 TGCAGACATG
128 TGCAGACATG
213637 TCATAGAAAC
Statistics
Matches: 123, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
171 12 0.10
172 71 0.58
173 40 0.33
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.24
Consensus pattern (171 bp):
ACAATACATGACATAAAATCAAAGAATTCTTGTACTGAAATAAAGACTAAATCTTAAAACAACCA
ACCATCTTTCGATTTCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAAGATAACTGC
AGACATGGAGGAGAAACATGAACACAACATGTATGCCACTA
Found at i:213856 original size:148 final size:147
Alignment explanation
Indices: 213509--213925 Score: 511
Period size: 148 Copynumber: 2.8 Consensus size: 147
213499 ACAATACATG
* * **
213509 ACAATACAATCAAAGAATGTCTGTACTGAAATAAAGACTAAATCTTCAGATAACCAACTGTCTTT
1 ACAATACAATCAAAGAATGTCTGTACTGAAATAAAGACTGAATCTTCACATAACCAACCATCTTT
* * *
213574 CGATTATCCCAATTTGTGAAACTAAAGAAATATGGAACTCAAACCCAGTTAACTGCAGACATGTC
66 CGATTATCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAGTTAACTGCAAACACGTC
*
213639 ATAGAAACACGCCACCA
131 ATACAAACACGCCACCA
* *
213656 ACAACACAATCAAAGAATGTCTGTACTGAAATAAAGACTGTATCTTCACATAACCAACCATCTTT
1 ACAATACAATCAAAGAATGTCTGTACTGAAATAAAGACTGAATCTTCACATAACCAACCATCTTT
* * * *
213721 CGGTTATCTCAATCTGTGAAACAAAAGAAATATGGAACTCAAACCCA--TATCATAG-AAACACG
66 CGATTATCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAGTTAAC-T-GCAAACACG
* * * *
213783 AATACA-ACATATATGCCACTA
129 --T-CATACAAACACGCCACCA
* * * * *
213804 ACAATACAATCAAAGAATGTCCGTACTGAATTGAAGACTGCATCTTCACATAACCACCCAT-TTC
1 ACAATACAATCAAAGAATGTCTGTACTGAAATAAAGACTGAATCTTCACATAACCAACCATCTT-
* * *
213868 TCGATTATCCCAATCAGTGAAACTAAAGAAATATGGAACTCTAACCCAGATAACTGCA
65 TCGATTATCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAGTTAACTGCA
213926 GACAACTGAG
Statistics
Matches: 231, Mismatches: 30, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
145 3 0.01
146 6 0.03
147 105 0.45
148 110 0.48
149 4 0.02
150 3 0.01
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.24
Consensus pattern (147 bp):
ACAATACAATCAAAGAATGTCTGTACTGAAATAAAGACTGAATCTTCACATAACCAACCATCTTT
CGATTATCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAGTTAACTGCAAACACGTC
ATACAAACACGCCACCA
Found at i:214194 original size:164 final size:163
Alignment explanation
Indices: 213968--214388 Score: 553
Period size: 164 Copynumber: 2.6 Consensus size: 163
213958 CACATGAATA
* * * *
213968 ATGCCACAAACAATACATGACAATAAAATCAAAGAATGCCCATACTGCAATAAAGACTAAATCTT
1 ATGCCACCAACAATACACGACAATAAAATCAAAGAATGCCTATACTACAATAAAGACTAAATCTT
* ** * *
214033 CACACATCCATCTGACTTTCAATCAGTCAAACTAAAATACTACAGAACACAAACCTGAGACA-AA
66 CACACATCCAACCAACTTTCAATCAGTCAAACTAAAATACTACAGAACAAAAACCCGAGACACAA
* **
214097 CAG-CGACTTGTCGGAG-GAACATGAACACAACATAT
131 CAGAC-ACAT-T-GGAGAG-ACACCAACACAACATAT
* *
214132 ATGCCACCAACAATACACAACAATAAAATCAAGGAATGCCTATACTACAATAAAGACTAAATCTT
1 ATGCCACCAACAATACACGACAATAAAATCAAAGAATGCCTATACTACAATAAAGACTAAATCTT
* *
214197 CACACATCCAACCAACTTTCAATCAGTCAAACTAAAGTACTACAGAACAAAAACCCGAGACAGCC
66 CACACATCCAACCAACTTTCAATCAGTCAAACTAAAATACTACAGAACAAAAACCCGAGACA-CA
**
214262 ACAGACACATTGGAGAGACACCAACATGACATAT
130 ACAGACACATTGGAGAGACACCAACACAACATAT
* *
214296 ATGTCACCAACAATACACGACAATAAAATCAAAGAAAGCCTATACTACAATAAAGACTAAAT-TT
1 ATGCCACCAACAATACACGACAATAAAATCAAAGAATGCCTATACTACAATAAAGACTAAATCTT
* * *
214360 CCATATATACAACCAACTTTCAATCAGTC
66 -CACACATCCAACCAACTTTCAATCAGTC
214389 GGAGGAACAT
Statistics
Matches: 227, Mismatches: 25, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
163 2 0.01
164 215 0.95
165 2 0.01
166 7 0.03
167 1 0.00
ACGTcount: A:0.46, C:0.25, G:0.10, T:0.19
Consensus pattern (163 bp):
ATGCCACCAACAATACACGACAATAAAATCAAAGAATGCCTATACTACAATAAAGACTAAATCTT
CACACATCCAACCAACTTTCAATCAGTCAAACTAAAATACTACAGAACAAAAACCCGAGACACAA
CAGACACATTGGAGAGACACCAACACAACATAT
Found at i:214490 original size:116 final size:116
Alignment explanation
Indices: 214285--214504 Score: 309
Period size: 116 Copynumber: 1.9 Consensus size: 116
214275 AGAGACACCA
* * *
214285 ACATGACATATATGTCACCAACAATACACGACAATAAAATCAAAGAAAGCCTATACTACAATAAA
1 ACATGACATATATGCCACCAACAATACACAACAACAAAATCAAAGAAAGCCTATACTACAATAAA
* *
214350 GACTAAATTTCCATATATACAACCAACTTTCAATCAGTCGGAGGAACATAG
66 GACTAAATCTCCACATATACAACCAACTTTCAATCAGTCGGAGGAACATAG
* * * * * *
214401 ACATGACATATATGCCACTAACAATACATAACAACACAATCAAAGAATGCCTGT-GTAACAATAA
1 ACATGACATATATGCCACCAACAATACACAACAACAAAATCAAAGAAAGCCTATACT-ACAATAA
214465 AGACTAAATCTCCACATAT-CTAACCAACTTTCAATCAGTC
65 AGACTAAATCTCCACATATAC-AACCAACTTTCAATCAGTC
214505 AAACTAAAGT
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
115 2 0.02
116 89 0.98
ACGTcount: A:0.45, C:0.23, G:0.09, T:0.22
Consensus pattern (116 bp):
ACATGACATATATGCCACCAACAATACACAACAACAAAATCAAAGAAAGCCTATACTACAATAAA
GACTAAATCTCCACATATACAACCAACTTTCAATCAGTCGGAGGAACATAG
Found at i:217498 original size:48 final size:48
Alignment explanation
Indices: 217426--217521 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
217416 TTTCTTTGCT
* *
217426 TAAAAACGCCTAAGTCAGCCTAACTTGCAGCGATAAAGGATTCAACAG
1 TAAAAACGCCTAAGTCAGCCTAACTCGCAACGATAAAGGATTCAACAG
*
217474 TAAAAACGCCTAAGTCAGCTTAACTCGCAACGATAAAGGATTCAACAG
1 TAAAAACGCCTAAGTCAGCCTAACTCGCAACGATAAAGGATTCAACAG
217522 AATTCACTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.19
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTCGCAACGATAAAGGATTCAACAG
Found at i:217816 original size:36 final size:36
Alignment explanation
Indices: 217746--217816 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
217736 TACAATTAAA
* * * *
217746 AGCTGTATACAATTAGAACTCTAAGCTTAGATAATC
1 AGCTATATACAATTAAAACTCTAAGATTACATAATC
*
217782 AGCTATATACAATTAAAACTCTAAGATTCCATAAT
1 AGCTATATACAATTAAAACTCTAAGATTACATAAT
217817 TATATCTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (36 bp):
AGCTATATACAATTAAAACTCTAAGATTACATAATC
Found at i:218269 original size:15 final size:15
Alignment explanation
Indices: 218249--218282 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
218239 GAAATTAAGG
218249 TTTTTAAAAAATTCA
1 TTTTTAAAAAATTCA
* *
218264 TTTTTACAATATTCA
1 TTTTTAAAAAATTCA
218279 TTTT
1 TTTT
218283 AATTAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTTTAAAAAATTCA
Found at i:221742 original size:16 final size:16
Alignment explanation
Indices: 221718--221761 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
221708 CACTATTTTT
221718 TTTTCAAAAATGTA-TA
1 TTTTCAAAAAT-TATTA
*
221734 TTTTGAAAAAATTATTA
1 TTTT-CAAAAATTATTA
221751 TTTTCAAAAAT
1 TTTTCAAAAAT
221762 ACTATTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (16 bp):
TTTTCAAAAATTATTA
Found at i:221743 original size:17 final size:17
Alignment explanation
Indices: 221718--221760 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
221708 CACTATTTTT
221718 TTTTC-AAAAATGTA-TA
1 TTTTCAAAAAAT-TATTA
*
221734 TTTTGAAAAAATTATTA
1 TTTTCAAAAAATTATTA
221751 TTTTCAAAAA
1 TTTTCAAAAA
221761 TACTATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (17 bp):
TTTTCAAAAAATTATTA
Found at i:222833 original size:20 final size:20
Alignment explanation
Indices: 222808--222847 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
222798 CGTAAAATGA
*
222808 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
222828 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
222848 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:222837 original size:34 final size:35
Alignment explanation
Indices: 222793--222859 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
222783 CAGTAAAATA
*
222793 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
222827 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
222860 CTGGGTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:222863 original size:14 final size:15
Alignment explanation
Indices: 222787--222863 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
222777 GATTGCCAGT
* *
222787 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
222801 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
222815 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
222835 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
222850 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
222864 GTTTGATTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:225977 original size:16 final size:14
Alignment explanation
Indices: 225956--225989 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
225946 AATTGGGCTG
225956 GAAAAATACGAAACAA
1 GAAAAATA-GAAA-AA
225972 GAAAAATAGAAAAA
1 GAAAAATAGAAAAA
225986 GAAA
1 GAAA
225990 TTTTTAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 4 0.22
16 8 0.44
ACGTcount: A:0.74, C:0.06, G:0.15, T:0.06
Consensus pattern (14 bp):
GAAAAATAGAAAAA
Found at i:230725 original size:4 final size:4
Alignment explanation
Indices: 230716--230755 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
230706 AATGCACCTG
*
230716 GTAT GTAT GTAT GTAT GTAT GTAT GCAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
230756 CAAGGCGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (4 bp):
GTAT
Found at i:232043 original size:268 final size:268
Alignment explanation
Indices: 231282--232076 Score: 1263
Period size: 259 Copynumber: 3.0 Consensus size: 268
231272 TGGTTGTCAT
* * *
231282 CCCACTTCGGTAAAATCTGGGATTGCGTATGCTCTTTACATTCAAGTCAGCTTTAAGTTGGATTC
1 CCCACATCGGTTAAATCTGGGATTGCGTATGCTCTTTACATTCGAGTCAGCTTTAAGTTGGATTC
*
231347 CGTTATATTGTTGTTGTTGTTATTGCATGTTCGAGTTTATCACA-TGATAGGCTATTATATTATC
66 CGTTATATTGTTATTGTTGTTATTGCATGTTCGAGTTTATCACACT-ATAGGCTATTATATTATC
*
231411 TGCATATGGAGGTTTTTACTGCAGCCAATTGGTTTTAGCCTGCCAAAGTTCTTCCCCTTTGTTGT
130 TGCCTATGGAGGTTTTTACTGCAGCCAATTGGTTTTAGCCTGCCAAAGTTCTTCCCCTTTGTTGT
* *
231476 AGTTTTCAGGGGATAAGCCTGCTCATTTGGAGGAACTCAGGTTGCAACCGGTTGATCCAAATGAT
195 AGTTTCCAGGGGATAAGCCTGCTCATTTGGAGGAACTCGGGTTGCAACCGGTTGATCCAAATGAT
231541 GTAAGGAAG
260 GTAAGGAAG
* * * *
231550 CCTACATCGGTTAAATCCGGGATTGCGTATGCTCTTTACGTTCGAGTCAGCATTAAGTTGGATTC
1 CCCACATCGGTTAAATCTGGGATTGCGTATGCTCTTTACATTCGAGTCAGCTTTAAGTTGGATTC
*
231615 CG-TA-A----TA---TTGTTATTGCATGTTCGAGTTTATCACACGATAGGCTATTATATTATCT
66 CGTTATATTGTTATTGTTGTTATTGCATGTTCGAGTTTATCACACTATAGGCTATTATATTATCT
* *
231671 GCCTATGGAGGTTTTTACTGCAGCCAATTGGTTTTAGCCTGCCGAAGTTCTCCCCCTTTGTTGTA
131 GCCTATGGAGGTTTTTACTGCAGCCAATTGGTTTTAGCCTGCCAAAGTTCTTCCCCTTTGTTGTA
231736 GTTTCCAGGGGATAAGCCTGCTCATTTGGAGGAACTCGGGTTGCAACCGGTTGATCCAAATGATG
196 GTTTCCAGGGGATAAGCCTGCTCATTTGGAGGAACTCGGGTTGCAACCGGTTGATCCAAATGATG
231801 TAAGGAAG
261 TAAGGAAG
* * * *
231809 CCCACATTGGTTAAATTTGGGATTGCGTATGCTCTTTACATTTGAGTCAGTTTTAAGTTGGA-TC
1 CCCACATCGGTTAAATCTGGGATTGCGTATGCTCTTTACATTCGAGTCAGCTTTAAGTTGGATTC
* *
231873 CTGTTATATTGTTATTGTTGTTATTGCATGTTTGAGTTTATCACACTATAGGCGATTATATTATC
66 C-GTTATATTGTTATTGTTGTTATTGCATGTTCGAGTTTATCACACTATAGGCTATTATATTATC
* *
231938 TACCTATGGAGGTCTTTTACTGCAGCCAATTGGTTTTAGCCTGCCAAAGTTCTTCCCC-TTATTG
130 TGCCTATGGAGGT-TTTTACTGCAGCCAATTGGTTTTAGCCTGCCAAAGTTCTTCCCCTTTGTTG
**
232002 TAGTTTCCAGGGGATAAGCCTGCTCATTTGGAGGAACTCGGGTTGCAACCGGTTGATCTGAATGA
194 TAGTTTCCAGGGGATAAGCCTGCTCATTTGGAGGAACTCGGGTTGCAACCGGTTGATCCAAATGA
232067 TGTAAGGAAG
259 TGTAAGGAAG
232077 GACCAAAAAT
Statistics
Matches: 484, Mismatches: 31, Indels: 24
0.90 0.06 0.04
Matches are distributed among these distances:
258 3 0.01
259 235 0.49
260 2 0.00
261 1 0.00
262 1 0.00
265 2 0.00
266 1 0.00
267 2 0.00
268 195 0.40
269 42 0.09
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (268 bp):
CCCACATCGGTTAAATCTGGGATTGCGTATGCTCTTTACATTCGAGTCAGCTTTAAGTTGGATTC
CGTTATATTGTTATTGTTGTTATTGCATGTTCGAGTTTATCACACTATAGGCTATTATATTATCT
GCCTATGGAGGTTTTTACTGCAGCCAATTGGTTTTAGCCTGCCAAAGTTCTTCCCCTTTGTTGTA
GTTTCCAGGGGATAAGCCTGCTCATTTGGAGGAACTCGGGTTGCAACCGGTTGATCCAAATGATG
TAAGGAAG
Found at i:237923 original size:39 final size:39
Alignment explanation
Indices: 237879--237963 Score: 163
Period size: 39 Copynumber: 2.2 Consensus size: 39
237869 ATGTTAAAAT
237879 TTTATAATGTGTTTTCTTAGGGAAATTTTTTTACCTTAA
1 TTTATAATGTGTTTTCTTAGGGAAATTTTTTTACCTTAA
237918 TTTATAATGTGTTTTCTTAGGGAAATTTTTTTACCTTAA
1 TTTATAATGTGTTTTCTTAGGGAAATTTTTTTACCTTAA
237957 TTT-TAAT
1 TTTATAAT
237964 TTTAAATTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 4 0.09
39 42 0.91
ACGTcount: A:0.26, C:0.07, G:0.12, T:0.55
Consensus pattern (39 bp):
TTTATAATGTGTTTTCTTAGGGAAATTTTTTTACCTTAA
Found at i:246281 original size:67 final size:67
Alignment explanation
Indices: 246173--246302 Score: 260
Period size: 67 Copynumber: 1.9 Consensus size: 67
246163 CATTCACAGC
246173 CGTGAATATATTGATAAACAGTTCATAAATCATTCTGGTCCTGTTCGTTTATCAACTAAATAATA
1 CGTGAATATATTGATAAACAGTTCATAAATCATTCTGGTCCTGTTCGTTTATCAACTAAATAATA
246238 TT
66 TT
246240 CGTGAATATATTGATAAACAGTTCATAAATCATTCTGGTCCTGTTCGTTTATCAACTAAATAA
1 CGTGAATATATTGATAAACAGTTCATAAATCATTCTGGTCCTGTTCGTTTATCAACTAAATAA
246303 ATGAATATGA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (67 bp):
CGTGAATATATTGATAAACAGTTCATAAATCATTCTGGTCCTGTTCGTTTATCAACTAAATAATA
TT
Found at i:249018 original size:21 final size:21
Alignment explanation
Indices: 248977--249026 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
248967 ATATTTTTTA
*
248977 TAAAAA-TTAAAATAATCATTT
1 TAAAAATTTAAAATAAT-AATT
248998 TAAAAATTTAAAAT-ATAATT
1 TAAAAATTTAAAATAATAATT
*
249018 TAATAATTT
1 TAAAAATTT
249027 TGAAAAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 11 0.42
21 8 0.31
22 7 0.27
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAAAATTTAAAATAATAATT
Found at i:250731 original size:7 final size:7
Alignment explanation
Indices: 250719--250749 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
250709 AGGTCAAGCC
250719 CCTACCT
1 CCTACCT
250726 CCTACCT
1 CCTACCT
250733 CCTACCT
1 CCTACCT
250740 CCTACCT
1 CCTACCT
250747 CCT
1 CCT
250750 CCCTTCGCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.58, G:0.00, T:0.29
Consensus pattern (7 bp):
CCTACCT
Found at i:252253 original size:104 final size:104
Alignment explanation
Indices: 252073--252280 Score: 416
Period size: 104 Copynumber: 2.0 Consensus size: 104
252063 TTATAAAAAG
252073 ATAGTTTCATTTCATTAGGCTTTTTCATGGGCACGGTGAAACAACCAGTGGTTTAAAGCAAAAAA
1 ATAGTTTCATTTCATTAGGCTTTTTCATGGGCACGGTGAAACAACCAGTGGTTTAAAGCAAAAAA
252138 GAAAATCCAAAAATGGGACAAACAAGTGAAACTCAGAGT
66 GAAAATCCAAAAATGGGACAAACAAGTGAAACTCAGAGT
252177 ATAGTTTCATTTCATTAGGCTTTTTCATGGGCACGGTGAAACAACCAGTGGTTTAAAGCAAAAAA
1 ATAGTTTCATTTCATTAGGCTTTTTCATGGGCACGGTGAAACAACCAGTGGTTTAAAGCAAAAAA
252242 GAAAATCCAAAAATGGGACAAACAAGTGAAACTCAGAGT
66 GAAAATCCAAAAATGGGACAAACAAGTGAAACTCAGAGT
252281 TTAAACAATC
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.24
Consensus pattern (104 bp):
ATAGTTTCATTTCATTAGGCTTTTTCATGGGCACGGTGAAACAACCAGTGGTTTAAAGCAAAAAA
GAAAATCCAAAAATGGGACAAACAAGTGAAACTCAGAGT
Found at i:253174 original size:67 final size:67
Alignment explanation
Indices: 252984--253175 Score: 233
Period size: 67 Copynumber: 2.8 Consensus size: 67
252974 GTTTACAAAA
** * *
252984 GCATAGCCTTTGTTTGACCTGGTGCTGCAACAATGGTGAACTAAAGTAAAGGGAAGAAATTGCAA
1 GCATAGCCTTTGTTTGATTTAGTGCTGCAACAATGGTGAACT----CAAA-GG--GAAATTGCAA
253049 GTAATGTAT
59 GTAATGTAT
* * **
253058 GTATAGCCTTTTTTTGATTTAGTGCTGCAACAATGGTGAACTCTTAGGGAAATTGC-AGATAATG
1 GCATAGCCTTTGTTTGATTTAGTGCTGCAACAATGGTGAACTCAAAGGGAAATTGCAAG-TAATG
253122 TAT
65 TAT
253125 GCATAGCCTTTGTTTGATTTAGTGCTGCAACAATGGTGAACTCAAAGGGAA
1 GCATAGCCTTTGTTTGATTTAGTGCTGCAACAATGGTGAACTCAAAGGGAA
253176 GTGATAAAAT
Statistics
Matches: 105, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
66 2 0.02
67 63 0.60
69 2 0.02
70 1 0.01
74 37 0.35
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (67 bp):
GCATAGCCTTTGTTTGATTTAGTGCTGCAACAATGGTGAACTCAAAGGGAAATTGCAAGTAATGT
AT
Found at i:253862 original size:196 final size:194
Alignment explanation
Indices: 253436--253921 Score: 601
Period size: 194 Copynumber: 2.5 Consensus size: 194
253426 AATTATAATT
* * *
253436 CCCAAAGATGAAAAAAAAATCAGTTTAATCCTTTTAAAATTCTAAAAT-A-AA-TATATAAAA-A
1 CCCAAAGAT--AAAAAAATTCAGTTTAATCCCTTTAAAATTCTAAAATAACAAGCATATAAAAGA
*
253497 TAAAATTGTACTTTTGACCCCTTAAAATTTTCATAATATACTTTTGGGCCCTCAAAAGGCAAATT
64 TAAAATTGTACTTTTGACCCCTT-AAATTTT-ATAATATACTTTTGAGCCCTCAAAAGGCAAATT
* **
253562 ATCAATTTAGTCCCTTGAAGTTTTTAATATTACATTTTAATTTAATAGTAAAAATACACTTTGAC
127 ATCAATTTAGTCCCTTGAAGTTTTTAAAATTACAAGTTAATTTAATAGTAAAAATACACTTTGAC
*
253627 CTC
192 ATC
** * * * * *
253630 CATAGAGAT-GAAAATTTCAGTTTAATCCCCTTAAAATTCGAAAATAACAAGCATATACAAAGAT
1 CCCAAAGATAAAAAAATTCAGTTTAATCCCTTTAAAATTCTAAAATAACAAGCATATA-AAAGAT
** * * * *
253694 AAAATTACACTTTTGACCCATTAAAGTTTTATAATTTA-TTTTTAGCCC-CAAAAGGGGAAATTA
65 AAAATTGTACTTTTGACCCCTTAAA-TTTTATAATATACTTTTGAGCCCTCAAAA-GGCAAATTA
* * * * *
253757 TCATTTTAGTCCCTTTAAGTTTTTAAAATTATAAGTTAATTTAAATGGTAAAAATACACTTTGGC
128 TCAATTTAGTCCCTTGAAGTTTTTAAAATTACAAGTTAATTT-AATAGTAAAAATACACTTTGAC
253822 ATC
192 ATC
253825 CCCAAAGATAAAAAAATTCAGTTTAATCCCTTTAAAATTCTAAAATAACAAGCATATAAAAGATA
1 CCCAAAGATAAAAAAATTCAGTTTAATCCCTTTAAAATTCTAAAATAACAAGCATATAAAAGATA
253890 AAATTGTAC-TTTGACCCCTATAAATTTTATAA
66 AAATTGTACTTTTGACCCCT-TAAATTTTATAA
253922 GCTTACGGTT
Statistics
Matches: 246, Mismatches: 36, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
191 30 0.12
192 1 0.00
193 7 0.03
194 80 0.33
195 59 0.24
196 69 0.28
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.35
Consensus pattern (194 bp):
CCCAAAGATAAAAAAATTCAGTTTAATCCCTTTAAAATTCTAAAATAACAAGCATATAAAAGATA
AAATTGTACTTTTGACCCCTTAAATTTTATAATATACTTTTGAGCCCTCAAAAGGCAAATTATCA
ATTTAGTCCCTTGAAGTTTTTAAAATTACAAGTTAATTTAATAGTAAAAATACACTTTGACATC
Found at i:255080 original size:23 final size:23
Alignment explanation
Indices: 255054--255099 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
255044 GCCTATGGTG
255054 ATAGATCACTTAACCTCTTATGT
1 ATAGATCACTTAACCTCTTATGT
255077 ATAGATCACTTAACCTCTTATGT
1 ATAGATCACTTAACCTCTTATGT
255100 CTAGTCCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (23 bp):
ATAGATCACTTAACCTCTTATGT
Found at i:256941 original size:31 final size:31
Alignment explanation
Indices: 256904--256979 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
256894 TAAGTGTACG
* *
256904 TTTAATTTAAGTTACTAAATTATTCGAAAGT
1 TTTAATTTAAGTCACTAAATTATTCGAAAAT
*
256935 TTTAATTGAAGTCACTAAATTATTCGAAAAT
1 TTTAATTTAAGTCACTAAATTATTCGAAAAT
*
256966 TTTTATTTAAGTCA
1 TTTAATTTAAGTCA
256980 TTAGGCTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (31 bp):
TTTAATTTAAGTCACTAAATTATTCGAAAAT
Found at i:258888 original size:26 final size:26
Alignment explanation
Indices: 258859--258922 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
258849 TAAACCAAAT
*
258859 TTTTTAAAAGTACTTCTGAAAAATAC
1 TTTTTAAAAGTACTTCTCAAAAATAC
* * *
258885 TTTTCTACAA-CACTTTTCAAAAATAC
1 TTTT-TAAAAGTACTTCTCAAAAATAC
258911 TTTTTAAAAGTA
1 TTTTTAAAAGTA
258923 ATGAAAAACT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
25 4 0.13
26 22 0.73
27 4 0.13
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (26 bp):
TTTTTAAAAGTACTTCTCAAAAATAC
Found at i:258912 original size:13 final size:13
Alignment explanation
Indices: 258877--258919 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
258867 AGTACTTCTG
258877 AAAAATACTTTTC
1 AAAAATACTTTTC
* * *
258890 TACAACACTTTTC
1 AAAAATACTTTTC
*
258903 AAAAATACTTTTT
1 AAAAATACTTTTC
258916 AAAA
1 AAAA
258920 GTAATGAAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAAATACTTTTC
Found at i:277718 original size:3 final size:3
Alignment explanation
Indices: 277710--277740 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
277700 GGAAACCAGT
277710 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
277741 AGCTTAACGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:289877 original size:315 final size:315
Alignment explanation
Indices: 289213--290166 Score: 1569
Period size: 315 Copynumber: 3.0 Consensus size: 315
289203 TCAATATAAA
* * *
289213 TTTTTAAA--AATTTAGTGTAAAAAAACCCTTATTCCTGTCCTTTGCTCGTATAATTTTCTCGAA
1 TTTTTAAATTAATTTAGTGTAAAAAAA-TCTTATTCCTGCCCTTTGCTCGTATTATTTTCTCGAA
*
289276 TTTTATTACTTTCAATAAAAATATATTATTTTTGTATTTTATTATTTTATATTATTTCAGTACAT
65 TTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACAT
* *
289341 TTTTTTTGAAATATTTGTATTCATTATTTCTGAATTTTTAAAAAATTTAGTAAAAGACTCTTACT
130 TTTGTTTGAAATATTTGTATTCATTATTTCTGAATTTTTAAAAAATTTAGTAAAACACTCTTACT
289406 TCGGCCCTTTGTTCGTATTTTTGTCTCCGCATTTTATTACTTTAAAAAA-ATCATAATTTCTAAT
195 TCGGCCCTTTGTTCGTATTTTT-TCTCCGCATTTTATTACTTTAAAAAATATCATAATTTCTAAT
*
289470 TTTATAATTTTGCATTATTTCAGTGCATTATGTTTGAAATTTATTAATTTAGTGTGT
259 TTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAATTTATTAATTTAGTGTGT
* *
289527 TTTTTAAATTAATTTAGTGTAAAAAACTCTTATTCCTGCCCTTTGCTCGTATTATTTTCTCAAAT
1 TTTTTAAATTAATTTAGTGTAAAAAAATCTTATTCCTGCCCTTTGCTCGTATTATTTTCTCGAAT
*
289592 TTTATTACTTTCAATAAAAATATATTATTTTCGTATATTATTATTTTATATTATTTCAGTACATT
66 TTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATT
* *
289657 TTGTTTGAAATATTTGTATTCATTATTTCTGAATTTTTAAAAAATTTAGTACAATACTCTTACTT
131 TTGTTTGAAATATTTGTATTCATTATTTCTGAATTTTTAAAAAATTTAGTAAAACACTCTTACTT
289722 CGGCCCTTTGTTCGTATTTTTTCTCCGCA-TTTATTACTTTAAAAAATATCATAATTTCTAATTT
196 CGGCCCTTTGTTCGTATTTTTTCTCCGCATTTTATTACTTTAAAAAATATCATAATTTCTAATTT
* *
289786 TATAATTTTACATTACTTCAGTGCATTATGTTTGAAATTTATTAATTTAGTGTAT
261 TATAATTTTACATTATTTCAGTGCATTATGTTTGAAATTTATTAATTTAGTGTGT
* *
289841 TTTTTAAATTAATTTAGTGTAAAAAAATCTTTATTCCTGCCATTTACTCGTATTATTTTC-CTGA
1 TTTTTAAATTAATTTAGTGTAAAAAAATC-TTATTCCTGCCCTTTGCTCGTATTATTTTCTC-GA
*
289905 ATTTTATTACTTACAATAAAAATATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACA
64 ATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACA
* * * *
289970 TTTTGTTTGAAATATTTGTATTAATTATTTCTAAATTTTAAAAAAAAATTAGTAAAACACTCTTA
129 TTTTGTTTGAAATATTTGTATTCATTATTTCTGAATTTT-TAAAAAATTTAGTAAAACACTCTTA
* * *
290035 CTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTACTTT-AAAAATACCATAATTTTTA
193 CTTCGGCCCTTTGTTCGTA-TTTTTTCTCCGCATTTTATTACTTTAAAAAATATCATAATTTCTA
* * *
290099 ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGT
257 ATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAATTTATTAATTTAGTGTGT
290158 TTTTTAAAT
1 TTTTTAAAT
290167 ATATCATTTT
Statistics
Matches: 599, Mismatches: 33, Indels: 13
0.93 0.05 0.02
Matches are distributed among these distances:
313 17 0.03
314 114 0.19
315 309 0.52
316 55 0.09
317 93 0.16
318 11 0.02
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.51
Consensus pattern (315 bp):
TTTTTAAATTAATTTAGTGTAAAAAAATCTTATTCCTGCCCTTTGCTCGTATTATTTTCTCGAAT
TTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATT
TTGTTTGAAATATTTGTATTCATTATTTCTGAATTTTTAAAAAATTTAGTAAAACACTCTTACTT
CGGCCCTTTGTTCGTATTTTTTCTCCGCATTTTATTACTTTAAAAAATATCATAATTTCTAATTT
TATAATTTTACATTATTTCAGTGCATTATGTTTGAAATTTATTAATTTAGTGTGT
Found at i:290550 original size:23 final size:23
Alignment explanation
Indices: 290524--290592 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
290514 TTCCCTCTTC
290524 TTCTTCTCCTTCCTTTTCTTTCA
1 TTCTTCTCCTTCCTTTTCTTTCA
*
290547 TTCTT-T--TT-C-TTTCTTT-T
1 TTCTTCTCCTTCCTTTTCTTTCA
* *
290564 TTCTTCTCCTTTCATTTTCTTTCC
1 TTCTTCTCC-TTCCTTTTCTTTCA
290588 TTCTT
1 TTCTT
290593 TTTCTTTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 13
0.69 0.06 0.25
Matches are distributed among these distances:
17 5 0.14
18 8 0.22
19 1 0.03
20 2 0.06
21 2 0.06
22 1 0.03
23 12 0.33
24 5 0.14
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (23 bp):
TTCTTCTCCTTCCTTTTCTTTCA
Found at i:290556 original size:14 final size:13
Alignment explanation
Indices: 290496--290603 Score: 69
Period size: 14 Copynumber: 7.9 Consensus size: 13
290486 AAAAATTACC
290496 TTTT-TTTCTTTCT
1 TTTTCTTTC-TTCT
* * *
290509 TTTCCTTCCCTCT
1 TTTTCTTTCTTCT
* *
290522 TCTTCTTCTCCTTCC
1 TTTTCTT-T-CTTCT
290537 TTTTCTTTCATTCT
1 TTTTCTTTC-TTCT
290551 TTTTCTTTC-T-T
1 TTTTCTTTCTTCT
*
290562 TTTTCTTCTCCTTTCA
1 TTTTCTT-T-C-TTCT
290578 TTTTCTTTCCTTCT
1 TTTTCTTT-CTTCT
290592 TTTTCTTTCTTC
1 TTTTCTTTCTTC
290604 CCTCTCCTTT
Statistics
Matches: 74, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
11 8 0.11
12 2 0.03
13 17 0.23
14 27 0.36
15 13 0.18
16 7 0.09
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTCTTTCTTCT
Found at i:290560 original size:10 final size:10
Alignment explanation
Indices: 290542--290637 Score: 61
Period size: 10 Copynumber: 9.1 Consensus size: 10
290532 CTTCCTTTTC
*
290542 TTTCATTCTT
1 TTTCTTTCTT
290552 TTTCTTTCTT
1 TTTCTTTCTT
*
290562 TTT-TCTTCTCC
1 TTTCT-TTCT-T
*
290573 TTTCATTT-TC
1 TTTC-TTTCTT
*
290583 TTTCCTTCTT
1 TTTCTTTCTT
290593 TTTCTTTCTT
1 TTTCTTTCTT
* *
290603 CCCTCTCCTTTCCT
1 ---T-TTCTTTCTT
290617 TTTCTTTCTT
1 TTTCTTTCTT
290627 TTTCTTTCTT
1 TTTCTTTCTT
290637 T
1 T
290638 ATTTCTTCTC
Statistics
Matches: 68, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
9 3 0.04
10 49 0.72
11 5 0.07
12 2 0.03
13 2 0.03
14 7 0.10
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:290620 original size:38 final size:38
Alignment explanation
Indices: 290524--290653 Score: 156
Period size: 38 Copynumber: 3.4 Consensus size: 38
290514 TTCCCTCTTC
*
290524 TTCTTCTCC-TTCCTTTTCTTTCATTCTTTTTCTTTCTTTT
1 TTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTC---T
*
290564 TTCTTCTCCTTTCATTTTCTTTCCTTCTTTTTCTTTCT
1 TTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCT
* * * *
290602 TCCCTCTCCTTTCCTTTTCTTT-CTTTTTCTTTCTTTAT
1 TTCTTCTCCTTTCCTTTTCTTTCCTTCTT-TTTCTTTCT
290640 TTCTTCTCCTTTCC
1 TTCTTCTCCTTTCC
290654 CTCTCCTTCT
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
37 5 0.06
38 40 0.51
40 9 0.11
41 25 0.32
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (38 bp):
TTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCT
Found at i:290626 original size:34 final size:34
Alignment explanation
Indices: 290552--290636 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
290542 TTTCATTCTT
* * *
290552 TTTCTTTCTTTTTTCTTCTCCTTTCATTTTCTTTC
1 TTTCTTT-TTCTTTCTTCTCCTCTCATTTCCTTTC
* *
290587 CTTCTTTTTCTTTCTTC-CCTCTCCTTTCCTTTTC
1 TTTCTTTTTCTTTCTTCTCCTCTCATTTCC-TTTC
290621 TTTCTTTTTCTTTCTT
1 TTTCTTTTTCTTTCTT
290637 TATTTCTTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
33 9 0.21
34 28 0.65
35 6 0.14
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.69
Consensus pattern (34 bp):
TTTCTTTTTCTTTCTTCTCCTCTCATTTCCTTTC
Found at i:291059 original size:18 final size:19
Alignment explanation
Indices: 291032--291067 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
291022 CTCTATTTTT
291032 ATTATATTTATCA-ATTTA
1 ATTATATTTATCATATTTA
*
291050 ATTATTTTTATCATATTT
1 ATTATATTTATCATATTT
291068 TATGACAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTATATTTATCATATTTA
Found at i:295167 original size:3 final size:3
Alignment explanation
Indices: 295159--295192 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
295149 TGTTTGTACA
*
295159 TCT TCT TCT TCT TCT TCT TCT TTT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
295193 TTTAAATTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:295193 original size:12 final size:12
Alignment explanation
Indices: 295159--295195 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
295149 TGTTTGTACA
*
295159 TCTTCTTCTTCT
1 TCTTCTTCTTTT
295171 TCTTCTTCTTTT
1 TCTTCTTCTTTT
295183 TCTTCTTCTTTT
1 TCTTCTTCTTTT
295195 T
1 T
295196 AAATTCTGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TCTTCTTCTTTT
Found at i:302385 original size:77 final size:77
Alignment explanation
Indices: 302258--302411 Score: 281
Period size: 77 Copynumber: 2.0 Consensus size: 77
302248 ATTTATCGGA
* *
302258 ATGGTCCTTTTCCGCGAAATCACGTCCACGTTAGCGCGATGTCAAGGTACGCGCCAGGAGATCGC
1 ATGGTCCTTTTCCGCGAAATCACGTCAACGTCAGCGCGATGTCAAGGTACGCGCCAGGAGATCGC
302323 GTCCACGTCAGC
66 GTCCACGTCAGC
*
302335 ATGGTCCTTTTCCGCGAAATCACGTCAACGTCAGCGCGATGTCAGGGTACGCGCCAGGAGATCGC
1 ATGGTCCTTTTCCGCGAAATCACGTCAACGTCAGCGCGATGTCAAGGTACGCGCCAGGAGATCGC
302400 GTCCACGTCAGC
66 GTCCACGTCAGC
302412 GCGAGTTACT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 74 1.00
ACGTcount: A:0.21, C:0.31, G:0.28, T:0.20
Consensus pattern (77 bp):
ATGGTCCTTTTCCGCGAAATCACGTCAACGTCAGCGCGATGTCAAGGTACGCGCCAGGAGATCGC
GTCCACGTCAGC
Found at i:309768 original size:15 final size:17
Alignment explanation
Indices: 309730--309763 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
309720 TTTATTAACA
309730 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
309747 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
309764 TTTATAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:309777 original size:16 final size:15
Alignment explanation
Indices: 309730--309777 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
309720 TTTATTAACA
*
309730 ATTTTATTAAATTATAT
1 ATTTTA-TAAAAT-TAT
*
309747 ATTTTATTAAATTAT
1 ATTTTATAAAATTAT
309762 ATTTTATAACAATTAT
1 ATTTTATAA-AATTAT
309778 GTTAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.41
16 10 0.37
17 6 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTATAAAATTAT
Found at i:309955 original size:39 final size:41
Alignment explanation
Indices: 309910--310015 Score: 135
Period size: 44 Copynumber: 2.5 Consensus size: 41
309900 TTTCCTTATG
* *
309910 CTATTACACCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
309950 C-ATTACGCCTCTATTCCATTACATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTCTATT-C----CATTCAACCAAACAAAAGAATTAC
309995 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
310016 ACGCCTCTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
39 13 0.23
40 2 0.04
41 4 0.07
44 19 0.33
45 5 0.09
46 14 0.25
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:309990 original size:44 final size:46
Alignment explanation
Indices: 309927--310017 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
309917 ACCTCTATTC
*
309927 CATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
309971 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
310017 C
1 C
310018 GCCTCTATTC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 19 0.43
45 4 0.09
46 21 0.48
ACGTcount: A:0.38, C:0.31, G:0.04, T:0.26
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
Found at i:310018 original size:16 final size:16
Alignment explanation
Indices: 309997--310033 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
309987 AGAATTACCT
309997 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
310013 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
310029 ATTAC
1 ATTAC
310034 AGCGAACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.22, C:0.35, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:310197 original size:22 final size:21
Alignment explanation
Indices: 310172--310222 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 21
310162 TACTTTGATC
*
310172 AATTTTAATTTTTGTATTTATT
1 AATTTTAATTTTTATATTT-TT
310194 AATTTTAATTTTTATATTTTT
1 AATTTTAATTTTTATATTTTT
*
310215 AATATTAA
1 AATTTTAA
310223 AACTTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
AATTTTAATTTTTATATTTTT
Found at i:310351 original size:15 final size:15
Alignment explanation
Indices: 310325--310366 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
310315 TTATTTACTG
310325 AATAAAATTTTAAAAT
1 AATAAAA-TTTAAAAT
**
310341 AATAAAATTTAATTT
1 AATAAAATTTAAAAT
310356 AAT-AAATTTAA
1 AATAAAATTTAA
310367 TATTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 8 0.33
15 9 0.38
16 7 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATAAAATTTAAAAT
Found at i:310364 original size:14 final size:15
Alignment explanation
Indices: 310325--310367 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
310315 TTATTTACTG
**
310325 AATAAAATTTTAAAAT
1 AATAAAA-TTTAATTT
310341 AATAAAATTTAATTT
1 AATAAAATTTAATTT
310356 AAT-AAATTTAAT
1 AATAAAATTTAAT
310368 ATTTTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 9 0.36
15 9 0.36
16 7 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATAAAATTTAATTT
Found at i:324888 original size:31 final size:29
Alignment explanation
Indices: 324853--324926 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 29
324843 TTAACGGCTC
324853 AGTGACTAAAATGTTACAACACGTT-AACATA
1 AGTGACTAAAATGTT--AACA-GTTAAACATA
* * *
324884 AGTGATTAAAACG-TAACATTTCAAACATA
1 AGTGACTAAAATGTTAACAGTT-AAACATA
324913 AGTGACTAAAATGT
1 AGTGACTAAAATGT
324927 AACCTAAGGG
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
27 2 0.06
28 4 0.11
29 17 0.49
30 1 0.03
31 11 0.31
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.27
Consensus pattern (29 bp):
AGTGACTAAAATGTTAACAGTTAAACATA
Found at i:327398 original size:14 final size:15
Alignment explanation
Indices: 327373--327401 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
327363 ATATGATTTG
327373 ATAAAAATAATTAAA
1 ATAAAAATAATTAAA
327388 ATAAAAA-AATTAAA
1 ATAAAAATAATTAAA
327402 CTTATCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
ATAAAAATAATTAAA
Found at i:328846 original size:16 final size:16
Alignment explanation
Indices: 328820--328868 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
328810 AATAATATTT
328820 AAAAATATAATTAATGA
1 AAAAAT-TAATTAATGA
328837 AAAAATTAATTCAA-GA
1 AAAAATTAATT-AATGA
328853 AAAATATTACATTAAT
1 AAAA-ATTA-ATTAAT
328869 TAAGTTAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
16 11 0.39
17 14 0.50
18 3 0.11
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (16 bp):
AAAAATTAATTAATGA
Found at i:329014 original size:27 final size:27
Alignment explanation
Indices: 328981--329033 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
328971 AAACGATTAT
328981 TAAACTATTCA-AAAGTTTTCATTTAAG
1 TAAACTATTCAGAAA-TTTTCATTTAAG
*
329008 TAAACTATTTAGAAATTTTCATTTAA
1 TAAACTATTCAGAAATTTTCATTTAA
329034 TTCATTAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (27 bp):
TAAACTATTCAGAAATTTTCATTTAAG
Found at i:332464 original size:11 final size:11
Alignment explanation
Indices: 332448--332481 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
332438 CTTTATGTTC
332448 AAAAAAAA-AA
1 AAAAAAAAGAA
332458 AAAAAAAAGAA
1 AAAAAAAAGAA
*
332469 AAGAAAAAGAA
1 AAAAAAAAGAA
332480 AA
1 AA
332482 CTTACATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:336423 original size:25 final size:25
Alignment explanation
Indices: 336378--336425 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
336368 TATTAAGTAG
336378 TTTTAAATCATATATTATGTTATAC
1 TTTTAAATCATATATTATGTTATAC
336403 TTTTAAATCATATATTATGTTAT
1 TTTTAAATCATATATTATGTTAT
336426 TTTGAAGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.54
Consensus pattern (25 bp):
TTTTAAATCATATATTATGTTATAC
Found at i:336630 original size:22 final size:23
Alignment explanation
Indices: 336582--336630 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
336572 TAACATGTGA
* **
336582 TTTTTTTAAAATATTTTATTATG
1 TTTTTATAAAATATTTTATTAAC
*
336605 TTTTTATAAAATA-TTTGTTAAC
1 TTTTTATAAAATATTTTATTAAC
336627 TTTT
1 TTTT
336631 AATTTTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (23 bp):
TTTTTATAAAATATTTTATTAAC
Found at i:336782 original size:17 final size:16
Alignment explanation
Indices: 336753--336787 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
336743 AGTAAAAAAT
336753 AAAAATATAAAATTAA
1 AAAAATATAAAATTAA
*
336769 AAAAATTATGAAATTAA
1 AAAAA-TATAAAATTAA
336786 AA
1 AA
336788 CATTTCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAAATATAAAATTAA
Found at i:336979 original size:14 final size:14
Alignment explanation
Indices: 336960--336990 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
336950 CGGTTGAGTA
336960 AATAAAATTTTTAT
1 AATAAAATTTTTAT
336974 AAT-AAATTTTTAT
1 AATAAAATTTTTAT
336987 AATA
1 AATA
336991 TAATCTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.81
14 3 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATAAAATTTTTAT
Found at i:336992 original size:18 final size:19
Alignment explanation
Indices: 336971--337010 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
336961 ATAAAATTTT
336971 TATAA-TAAATTTTTATAA
1 TATAACTAAATTTTTATAA
*
336989 TATAATCTGAATTTTTATAA
1 TATAA-CTAAATTTTTATAA
337009 TA
1 TA
337011 AATTTTGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
20 14 0.74
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (19 bp):
TATAACTAAATTTTTATAA
Found at i:337033 original size:21 final size:19
Alignment explanation
Indices: 337008--337062 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
336998 AATTTTTATA
*
337008 ATAAATTTTGAATATTATTTG
1 ATAAATTTT-AAAATT-TTTG
*
337029 ATAAAATTTTAAAATTTTTT
1 AT-AAATTTTAAAATTTTTG
337049 ATAAATATTTAAAA
1 ATAAAT-TTTAAAA
337063 AAATTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 4 0.13
20 12 0.40
21 7 0.23
22 7 0.23
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (19 bp):
ATAAATTTTAAAATTTTTG
Found at i:337063 original size:21 final size:21
Alignment explanation
Indices: 336998--337063 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
336988 ATATAATCTG
*
336998 AATTTTTATAATAAAT-TTTGAA
1 AATTTTT-T-ATAAATATTTAAA
* * *
337020 TATTATTTGATAAA-ATTTTAA
1 AATT-TTTTATAAATATTTAAA
337041 AATTTTTTATAAATATTTAAA
1 AATTTTTTATAAATATTTAAA
337062 AA
1 AA
337064 AATTAAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
20 8 0.23
21 21 0.60
22 3 0.09
23 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (21 bp):
AATTTTTTATAAATATTTAAA
Found at i:337135 original size:18 final size:18
Alignment explanation
Indices: 337084--337135 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 18
337074 TAAGTAAATA
337084 AAAAAT-TATAA-ATCTT
1 AAAAATATATAATATCTT
337100 ATAAAATATAT-AT-T-TT
1 A-AAAATATATAATATCTT
337116 AAAAATATATAATATCTT
1 AAAAATATATAATATCTT
337134 AA
1 AA
337136 TGTTATTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
15 9 0.30
16 6 0.20
17 8 0.27
18 7 0.23
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAAATATATAATATCTT
Found at i:338700 original size:138 final size:137
Alignment explanation
Indices: 338468--338734 Score: 327
Period size: 138 Copynumber: 1.9 Consensus size: 137
338458 ATAATGAGAT
338468 TTTTCAGGAATTTTCCAGGTTCTTGATTATAACTTGAAATGTAGCCTACAAAAGTTGAAAGGCAT
1 TTTTCAGGAATTTTCCAGGTTCTTGATTATAACTTGAAATGTAGCCTACAAAAGTTGAAAGGCAT
* ** ** *
338533 TGTAAGGGCTAGGGTGTTTTAGTGTTGAATCCGGGCTATTTGGACTTTAATTATTGATGCTAGAA
66 CGTAAGGGCTAGGGTGTGGTAGTACTGAATCCGGGCTATTTAGACTTTAATTATTGATGCTAGAA
338598 ATGGGAA
131 ATGGGAA
* * * * * * * * *
338605 TTTTCAGGGATTTATCCGGGTTCTTGATTATAGCTTGTAATGTGGCTTACTAAAGTTGAATGGTA
1 TTTTCAGGAATTT-TCCAGGTTCTTGATTATAACTTGAAATGTAGCCTACAAAAGTTGAAAGGCA
* * * * * * *
338670 TCGTGATGGTTTGGGTGTGGTAGTACTGAATCCGGGCTATTTAGATTTTAGTTATTGGTGCTAGA
65 TCGTAAGGGCTAGGGTGTGGTAGTACTGAATCCGGGCTATTTAGACTTTAATTATTGATGCTAGA
338735 TGGGTATAGA
Statistics
Matches: 107, Mismatches: 22, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
137 12 0.11
138 95 0.89
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.38
Consensus pattern (137 bp):
TTTTCAGGAATTTTCCAGGTTCTTGATTATAACTTGAAATGTAGCCTACAAAAGTTGAAAGGCAT
CGTAAGGGCTAGGGTGTGGTAGTACTGAATCCGGGCTATTTAGACTTTAATTATTGATGCTAGAA
ATGGGAA
Found at i:340516 original size:14 final size:12
Alignment explanation
Indices: 340481--340511 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
340471 ACTTAAATGA
340481 AATTTTTTAAAT
1 AATTTTTTAAAT
340493 AA-TTTTTAAAT
1 AATTTTTTAAAT
340504 AATTTTTT
1 AATTTTTT
340512 TTAAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
AATTTTTTAAAT
Found at i:343034 original size:140 final size:140
Alignment explanation
Indices: 342822--343086 Score: 385
Period size: 140 Copynumber: 1.9 Consensus size: 140
342812 TTCTATCATG
* * *
342822 TTAATTTAAAATATTGTTTATATCATTATATTTTTAATGGTTGAACTTTTACATAAATAAATAAT
1 TTAATTTAAAATACTGTTTATATCATTATATTTTTAATGGTTCAACTTTTACATAAATAAACAAT
* *
342887 TAAAAAAATAATTT-A-TTATTTCAAAC-TTGACATACATTATTTAATTTACGTCAATAAAACAA
66 T-AAAAAAT--TTTAATTTATTTCAAACTTTAACATACATTATTTAATTTACGTAAATAAAACAA
342949 ATAAAATTTTATA
128 ATAAAATTTTATA
*
342962 TTAATTTAAAATACTGTTTATATCATTATATTTTTAATGGTTACAATTTTTACATAAAATAAACA
1 TTAATTTAAAATACTGTTTATATCATTATATTTTTAATGGTT-CAACTTTTACAT-AAATAAACA
* *
343027 ATT-AAAAATTTTAATTTATTTCAAACTTTAACATACGTTATTTTATTTACGTAAATAAAA
64 ATTAAAAAATTTTAATTTATTTCAAACTTTAACATACATTATTTAATTTACGTAAATAAAA
343087 TGAGAATAGT
Statistics
Matches: 112, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
138 3 0.03
139 1 0.01
140 58 0.52
141 39 0.35
142 11 0.10
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.45
Consensus pattern (140 bp):
TTAATTTAAAATACTGTTTATATCATTATATTTTTAATGGTTCAACTTTTACATAAATAAACAAT
TAAAAAATTTTAATTTATTTCAAACTTTAACATACATTATTTAATTTACGTAAATAAAACAAATA
AAATTTTATA
Found at i:346848 original size:23 final size:23
Alignment explanation
Indices: 346759--346848 Score: 89
Period size: 23 Copynumber: 4.0 Consensus size: 23
346749 ATCTGATCAG
346759 TATACGACACAT-AAGTGCCTGGA
1 TATACGACACATAAAGTGCCT-GA
** *
346782 -AT--GACACACGAGGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
* * *
346802 AATACGACAAATAAAGTGCTTGA
1 TATACGACACATAAAGTGCCTGA
346825 TATACGACACATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
346848 T
1 T
346849 CGGCAAAGCC
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
20 8 0.15
21 9 0.17
22 2 0.04
23 34 0.64
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (23 bp):
TATACGACACATAAAGTGCCTGA
Found at i:348534 original size:26 final size:26
Alignment explanation
Indices: 348505--348579 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 26
348495 AAAATATAAT
*
348505 AATATAATATAATTAATATAATTTAC
1 AATATAATATAAATAATATAATTTAC
*
348531 AATATAATA-AAATAATAATAATATAC
1 AATATAATATAAATAAT-ATAATTTAC
* *
348557 ATTATCAT-TAAATAATAT-ATTTA
1 AATATAATATAAATAATATAATTTA
348580 TATATTTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
24 4 0.10
25 8 0.19
26 30 0.71
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (26 bp):
AATATAATATAAATAATATAATTTAC
Found at i:348829 original size:14 final size:14
Alignment explanation
Indices: 348795--348832 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
348785 ACTAGCTTCG
348795 TAAATATTTA-TAA
1 TAAATATTTACTAA
*
348808 TAAATATTTACTTA
1 TAAATATTTACTAA
*
348822 TTAATATTTAC
1 TAAATATTTAC
348833 GAGTCTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (14 bp):
TAAATATTTACTAA
Done.