Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 215 of 313
Found at i:66134324 original size:16 final size:15
Alignment explanation
Indices: 66134300--66134344 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
66134290 ATGAAGAGTA
66134300 ATCAAAATAAAAATG
1 ATCAAAATAAAAATG
* *
66134315 ATCTAAAATATAAGTG
1 ATC-AAAATAAAAATG
*
66134331 TTCAAAATAAAAAT
1 ATCAAAATAAAAAT
66134345 AATTTAAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27
Consensus pattern (15 bp):
ATCAAAATAAAAATG
Found at i:66135712 original size:16 final size:15
Alignment explanation
Indices: 66135691--66135745 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
66135681 TCTAGGTATG
66135691 TGAAGAGACTTGAAGA
1 TGAAGAGACTTGAA-A
66135707 TGAAGAG--TTAGAAA
1 TGAAGAGACTT-GAAA
66135721 TGTGAAGAGACTTGAATA
1 --TGAAGAGACTTGAA-A
66135739 TGAAGAG
1 TGAAGAG
66135746 TTACACACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
14 3 0.09
15 3 0.09
16 21 0.64
17 3 0.09
18 3 0.09
ACGTcount: A:0.44, C:0.04, G:0.31, T:0.22
Consensus pattern (15 bp):
TGAAGAGACTTGAAA
Found at i:66135729 original size:32 final size:32
Alignment explanation
Indices: 66135688--66135748 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
66135678 GTTTCTAGGT
66135688 ATGTGAAGAGACTTGAAGATGAAGAGTTAGAA
1 ATGTGAAGAGACTTGAAGATGAAGAGTTAGAA
*
66135720 ATGTGAAGAGACTTGAATATGAAGAGTTA
1 ATGTGAAGAGACTTGAAGATGAAGAGTTA
66135749 CACACATGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.43, C:0.03, G:0.30, T:0.25
Consensus pattern (32 bp):
ATGTGAAGAGACTTGAAGATGAAGAGTTAGAA
Found at i:66135818 original size:39 final size:39
Alignment explanation
Indices: 66135764--66135853 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 39
66135754 ATGCATGTAG
*
66135764 ATGAATAGTCACAACTCCTATAGCATTTAAGTGATGAAA
1 ATGAATAGTCACAACTCCTATAGCACTTAAGTGATGAAA
* *
66135803 ATGAATAGTCACAACTCCTATAGCACTTAAGTGATGTAG
1 ATGAATAGTCACAACTCCTATAGCACTTAAGTGATGAAA
66135842 ATGAATAGTCAC
1 ATGAATAGTCAC
66135854 TTACAACTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (39 bp):
ATGAATAGTCACAACTCCTATAGCACTTAAGTGATGAAA
Found at i:66141131 original size:16 final size:16
Alignment explanation
Indices: 66141110--66141141 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
66141100 TATCCTCAAC
66141110 CAACAATTATTCTAAA
1 CAACAATTATTCTAAA
*
66141126 CAACAATTATTTTAAA
1 CAACAATTATTCTAAA
66141142 TAATAGGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (16 bp):
CAACAATTATTCTAAA
Found at i:66141539 original size:26 final size:26
Alignment explanation
Indices: 66141501--66141550 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
66141491 GTTATTAAAT
* **
66141501 TTTAATAAGATTATTATTAAATATAA
1 TTTAATAAAATTAAAATTAAATATAA
66141527 TTTAATAAAATTAAAATTAAATAT
1 TTTAATAAAATTAAAATTAAATAT
66141551 TTTAGTCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
TTTAATAAAATTAAAATTAAATATAA
Found at i:66141581 original size:10 final size:10
Alignment explanation
Indices: 66141568--66141593 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
66141558 ATTTTTTAAC
66141568 ATAATATTTA
1 ATAATATTTA
66141578 ATAATATTTA
1 ATAATATTTA
66141588 ATAATA
1 ATAATA
66141594 AATTTAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
ATAATATTTA
Found at i:66141987 original size:26 final size:27
Alignment explanation
Indices: 66141952--66142026 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 27
66141942 ATAAAAAATC
66141952 AAAACTCATAGTTCTTTATGTTATTCA
1 AAAACTCATAGTTCTTTATGTTATTCA
*
66141979 AAAAC-CATAGTCCTTGATTTTATGTTATTCA
1 AAAACTCATAG---TT--CTTTATGTTATTCA
66142010 AAAACTCATAGTTCTTT
1 AAAACTCATAGTTCTTT
66142027 GTATTATTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
26 5 0.12
27 8 0.20
29 4 0.10
31 18 0.45
32 5 0.12
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (27 bp):
AAAACTCATAGTTCTTTATGTTATTCA
Found at i:66145715 original size:30 final size:29
Alignment explanation
Indices: 66145679--66145735 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
66145669 TCCGAGCTTT
66145679 GGGGCAAAAGTGTAATTATGTAAAAGTTTA
1 GGGGCAAAAGTGTAATT-TGTAAAAGTTTA
* *
66145709 GGGGCAAAATTGTAATTTTTAAAAGTT
1 GGGGCAAAAGTGTAATTTGTAAAAGTT
66145736 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.33
Consensus pattern (29 bp):
GGGGCAAAAGTGTAATTTGTAAAAGTTTA
Found at i:66148636 original size:17 final size:17
Alignment explanation
Indices: 66148603--66148640 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
66148593 AGGTATTACA
*
66148603 TTATGATTCTGTTATTT
1 TTATGATTCTATTATTT
66148620 TTATG-TTCTATTCATTT
1 TTATGATTCTATT-ATTT
66148637 TTAT
1 TTAT
66148641 TTTTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.18, C:0.08, G:0.08, T:0.66
Consensus pattern (17 bp):
TTATGATTCTATTATTT
Found at i:66153700 original size:37 final size:37
Alignment explanation
Indices: 66153643--66153768 Score: 157
Period size: 37 Copynumber: 3.4 Consensus size: 37
66153633 GTCCAACTGA
* *
66153643 AACATGCCAAATG-TTCATAAGATCTAATCCACCTAAT
1 AACAAGCCAAATGCTT-ATAAGAGCTAATCCACCTAAT
*
66153680 AACACA-CCAAATGCTTATAAGAGCTAATCCACCTGAT
1 AACA-AGCCAAATGCTTATAAGAGCTAATCCACCTAAT
**
66153717 AACAAGCCAGGTGCTTATAAGAGCTAATCCACCTAAT
1 AACAAGCCAAATGCTTATAAGAGCTAATCCACCTAAT
* *
66153754 AACATGCCAGATGCT
1 AACAAGCCAAATGCT
66153769 CCGAAAAGCT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
36 1 0.01
37 75 0.96
38 2 0.03
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.23
Consensus pattern (37 bp):
AACAAGCCAAATGCTTATAAGAGCTAATCCACCTAAT
Found at i:66153779 original size:37 final size:37
Alignment explanation
Indices: 66153659--66153768 Score: 159
Period size: 37 Copynumber: 3.0 Consensus size: 37
66153649 CCAAATGTTC
* *
66153659 ATAAGATCTAATCCACCTAATAACACA-CCAAATGCTT
1 ATAAGAGCTAATCCACCTAATAACA-AGCCAGATGCTT
* *
66153696 ATAAGAGCTAATCCACCTGATAACAAGCCAGGTGCTT
1 ATAAGAGCTAATCCACCTAATAACAAGCCAGATGCTT
*
66153733 ATAAGAGCTAATCCACCTAATAACATGCCAGATGCT
1 ATAAGAGCTAATCCACCTAATAACAAGCCAGATGCT
66153769 CCGAAAAGCT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
36 1 0.02
37 64 0.98
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.23
Consensus pattern (37 bp):
ATAAGAGCTAATCCACCTAATAACAAGCCAGATGCTT
Found at i:66157596 original size:13 final size:13
Alignment explanation
Indices: 66157580--66157604 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66157570 TATAAAGCCG
66157580 TAAATATTTTTAT
1 TAAATATTTTTAT
66157593 TAAATATTTTTA
1 TAAATATTTTTA
66157605 GAGTCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTTTAT
Found at i:66159025 original size:53 final size:53
Alignment explanation
Indices: 66158945--66159050 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
66158935 TAGATCAGGA
*
66158945 ACAAGTGGAAAACCGAGGGAAAGAGAAAGTATCGAATAGTCTTTGTACCTTTG
1 ACAAGTGGAAAACCGAAGGAAAGAGAAAGTATCGAATAGTCTTTGTACCTTTG
66158998 ACAAGTGGAAAACCGAAGGAAAGAGAAAGTATCGAATAGTCTTTGTACCTTTG
1 ACAAGTGGAAAACCGAAGGAAAGAGAAAGTATCGAATAGTCTTTGTACCTTTG
66159051 TCATTGCTAC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (53 bp):
ACAAGTGGAAAACCGAAGGAAAGAGAAAGTATCGAATAGTCTTTGTACCTTTG
Found at i:66171964 original size:35 final size:35
Alignment explanation
Indices: 66171925--66171995 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
66171915 TTGATTCAAA
*
66171925 TTTCCAAGGTCCATCTCGATTTGTCTTTGAGTTGT
1 TTTCCAAGGTCCATCTCGACTTGTCTTTGAGTTGT
66171960 TTTCCAAGGTCCATCTCGACTTGTCTTTGAGTTGT
1 TTTCCAAGGTCCATCTCGACTTGTCTTTGAGTTGT
66171995 T
1 T
66171996 CATTCATGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (35 bp):
TTTCCAAGGTCCATCTCGACTTGTCTTTGAGTTGT
Found at i:66176216 original size:25 final size:25
Alignment explanation
Indices: 66176186--66176236 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
66176176 TGTAGCTACG
66176186 TTCTGACCCACAGCTCGTGTGAGCA
1 TTCTGACCCACAGCTCGTGTGAGCA
** *
66176211 TTCTGATTCATAGCTCGTGTGAGCA
1 TTCTGACCCACAGCTCGTGTGAGCA
66176236 T
1 T
66176237 ACATGTATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.31
Consensus pattern (25 bp):
TTCTGACCCACAGCTCGTGTGAGCA
Found at i:66184227 original size:17 final size:17
Alignment explanation
Indices: 66184205--66184269 Score: 69
Period size: 17 Copynumber: 3.7 Consensus size: 17
66184195 TAATCTTAGA
66184205 GTTCTAATTGTATACAG
1 GTTCTAATTGTATACAG
*
66184222 GTTCTAATTGTGT-CTTAG
1 GTTCTAATTGTATAC--AG
66184240 AGTTCTAATTGTATACAG
1 -GTTCTAATTGTATACAG
* *
66184258 CTTTTAATTGTA
1 GTTCTAATTGTA
66184270 GCCTTTGATG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
16 1 0.03
17 22 0.55
18 4 0.10
19 12 0.30
20 1 0.03
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (17 bp):
GTTCTAATTGTATACAG
Found at i:66184245 original size:36 final size:36
Alignment explanation
Indices: 66184198--66184268 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
66184188 GATTATGTAA
*
66184198 TCTTAGAGTTCTAATTGTATACAGGTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
*
66184234 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGT
66184269 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:0.25, C:0.11, G:0.17, T:0.46
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
Found at i:66184246 original size:19 final size:19
Alignment explanation
Indices: 66184197--66184253 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
66184187 TGATTATGTA
66184197 ATCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
66184216 ATAC--AG-GTTCTAATTGT
1 AT-CTTAGAGTTCTAATTGT
*
66184233 GTCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
66184252 AT
1 AT
66184254 ACAGCTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
16 1 0.03
17 12 0.38
18 4 0.12
19 14 0.44
20 1 0.03
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.46
Consensus pattern (19 bp):
ATCTTAGAGTTCTAATTGT
Found at i:66188577 original size:17 final size:17
Alignment explanation
Indices: 66188555--66188618 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
66188545 AATCTTAGAG
66188555 TTCTAATTGTATACAAC
1 TTCTAATTGTATACAAC
* *
66188572 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--A-AC
*
66188591 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAAC
*
66188608 TTTTAATTGTA
1 TTCTAATTGTA
66188619 GCATTTGATG
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.57
18 2 0.05
19 12 0.32
20 1 0.03
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (17 bp):
TTCTAATTGTATACAAC
Found at i:66188594 original size:36 final size:36
Alignment explanation
Indices: 66188547--66188617 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
66188537 GATTATGTAA
66188547 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
* *
66188583 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGT
66188618 AGCATTTGAT
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:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
Found at i:66188596 original size:19 final size:19
Alignment explanation
Indices: 66188546--66188602 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
66188536 TGATTATGTA
66188546 ATCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
*
66188565 ATAC--A-ACTTCTAATTGT
1 AT-CTTAGAGTTCTAATTGT
*
66188582 GTCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
66188601 AT
1 AT
66188603 ACAGCTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 1 0.03
17 12 0.40
18 2 0.07
19 14 0.47
20 1 0.03
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (19 bp):
ATCTTAGAGTTCTAATTGT
Found at i:66188916 original size:48 final size:48
Alignment explanation
Indices: 66188825--66188917 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
66188815 GGGAATTTTG
**
66188825 TTGAATCCTTTATCATTACAAGTTAGGCCGACTTAGGTGTTTTTACGT
1 TTGAATCCTTTATCATTACAAGTTAGGCCGACTTAGGCATTTTTACGT
* *
66188873 TTGAATCCTTTATCATTGCAAGTTAGGCTGACTTAGGCATTTTTA
1 TTGAATCCTTTATCATTACAAGTTAGGCCGACTTAGGCATTTTTA
66188918 AGCAAAGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (48 bp):
TTGAATCCTTTATCATTACAAGTTAGGCCGACTTAGGCATTTTTACGT
Found at i:66197136 original size:104 final size:104
Alignment explanation
Indices: 66196950--66197140 Score: 229
Period size: 104 Copynumber: 1.8 Consensus size: 104
66196940 CACAGCCTGG
* * * * * * *
66196950 CACATGCTTGTGTCCTTGCCCCTGTGGCTCCCACGGCATGACACACATACGTGTTATCTGGCTGT
1 CACATGCTCGTGCCCTTGCCCCTGTGGCTCACACAGCATGACACACATACGTGTCATCTGCCCGT
*
66197015 GTGGTTATAAACCGTAAACAGTGAGTCACATGGCTTGGA
66 GTGCTTATAAACCGTAAACAGTGAGTCACATGGCTTGGA
* * * * * *
66197054 CACATGCTCGTGCCCTTGCTCTTGTGTCTCACACAGCCTGACACTCATCCGTGTCATCTGCCCGT
1 CACATGCTCGTGCCCTTGCCCCTGTGGCTCACACAGCATGACACACATACGTGTCATCTGCCCGT
* **
66197119 GTGCTTCTAAATTGTAAACAGT
66 GTGCTTATAAACCGTAAACAGT
66197141 AAGTTACACG
Statistics
Matches: 70, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
104 70 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (104 bp):
CACATGCTCGTGCCCTTGCCCCTGTGGCTCACACAGCATGACACACATACGTGTCATCTGCCCGT
GTGCTTATAAACCGTAAACAGTGAGTCACATGGCTTGGA
Found at i:66197778 original size:20 final size:20
Alignment explanation
Indices: 66197753--66197795 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
66197743 AACTCAATTG
66197753 AAAGAGGAAATAGAAA-AAGA
1 AAAGAGGAAA-AGAAAGAAGA
66197773 AAAGAGGAAAAGAAAGAAGA
1 AAAGAGGAAAAGAAAGAAGA
66197793 AAA
1 AAA
66197796 TAATGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (20 bp):
AAAGAGGAAAAGAAAGAAGA
Found at i:66201163 original size:23 final size:22
Alignment explanation
Indices: 66201111--66201163 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
66201101 TCCACGTCTT
*
66201111 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
66201133 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
66201156 TTTCTTTT
1 TTTCTTTT
66201164 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:66205819 original size:119 final size:120
Alignment explanation
Indices: 66205637--66205859 Score: 292
Period size: 119 Copynumber: 1.9 Consensus size: 120
66205627 TACTCGTTCA
* *
66205637 AATGCCTTTGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
66205702 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
66205757 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
66205819 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
66205860 CATCATTCGA
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
118 4 0.04
119 66 0.74
120 19 0.21
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:66205859 original size:40 final size:40
Alignment explanation
Indices: 66205616--66205859 Score: 282
Period size: 40 Copynumber: 6.1 Consensus size: 40
66205606 CGGAATTTAA
** * *
66205616 CCGGATATAGCT-ACTCGTTCAAATGCCTTTGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
66205656 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
66205696 CCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
66205736 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
66205775 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
66205815 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
66205855 CCGGA
1 CCGGA
66205860 CATCATTCGA
Statistics
Matches: 178, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
38 2 0.01
39 32 0.18
40 132 0.74
41 12 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:66212257 original size:49 final size:49
Alignment explanation
Indices: 66212143--66212592 Score: 750
Period size: 49 Copynumber: 9.3 Consensus size: 49
66212133 TTATTACATT
* * * * * * *
66212143 TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
66212190 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
** *
66212239 TATACACTTTCACATTCATCACATTAGCCATTCGGCCTTATCAC--ATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
*
66212286 TATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
66212335 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
66212384 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
66212433 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
66212482 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
*
66212531 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAAATATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
66212580 TATACA--TTCACAT
1 TATACACTTTCACAT
66212593 CACAATTATC
Statistics
Matches: 383, Mismatches: 16, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
47 87 0.23
49 296 0.77
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (49 bp):
TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
Found at i:66218253 original size:40 final size:40
Alignment explanation
Indices: 66218209--66218428 Score: 190
Period size: 40 Copynumber: 5.7 Consensus size: 40
66218199 GCTACTCGTT
* *
66218209 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTC-CAA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGC-A
66218249 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
66218289 CAAATGCCTTTGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * * *
66218329 CCAA-----TCGGG-CTTAGCCCGGAATAAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * * *
66218363 CAAATGCCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
66218404 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
66218429 CATCATTCGA
Statistics
Matches: 148, Mismatches: 21, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
34 24 0.16
35 4 0.03
38 2 0.01
39 2 0.01
40 102 0.69
41 14 0.09
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:66219621 original size:55 final size:56
Alignment explanation
Indices: 66219555--66219673 Score: 222
Period size: 55 Copynumber: 2.1 Consensus size: 56
66219545 TATTAGTTTA
66219555 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACAT-TT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
66219610 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
66219666 TTGCCCAT
1 TTGCCCAT
66219674 CATCCCTTGT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
55 52 0.84
56 10 0.16
ACGTcount: A:0.23, C:0.24, G:0.08, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:66221973 original size:23 final size:23
Alignment explanation
Indices: 66221947--66222012 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
66221937 TTGAACCATA
**
66221947 ACCATTTCATACCAAATCGTATT
1 ACCATTTCATACCAAATCACATT
66221970 ACCATTTCGA-ACCAAATCACATT
1 ACCATTTC-ATACCAAATCACATT
*
66221993 ACCATTTCATAACAAA-CACA
1 ACCATTTCATACCAAATCACA
66222013 AAACCAAACT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
22 5 0.13
23 32 0.84
24 1 0.03
ACGTcount: A:0.41, C:0.29, G:0.03, T:0.27
Consensus pattern (23 bp):
ACCATTTCATACCAAATCACATT
Found at i:66225050 original size:22 final size:23
Alignment explanation
Indices: 66225013--66225080 Score: 79
Period size: 22 Copynumber: 3.0 Consensus size: 23
66225003 TTATGGTTAC
66225013 TTAAGTGTTCTAAATAGATTTAA
1 TTAAGTGTTCTAAATAGATTTAA
* *
66225036 TTCA-TGTT-TATAATATGA-TTAC
1 TTAAGTGTTCTA-AATA-GATTTAA
66225058 TTAAGTGTTCTAAATAGATTTAA
1 TTAAGTGTTCTAAATAGATTTAA
66225081 GTCAAATTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
21 2 0.06
22 16 0.44
23 16 0.44
24 2 0.06
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.46
Consensus pattern (23 bp):
TTAAGTGTTCTAAATAGATTTAA
Found at i:66225066 original size:23 final size:23
Alignment explanation
Indices: 66224999--66225077 Score: 76
Period size: 22 Copynumber: 3.5 Consensus size: 23
66224989 AAGTTGACAA
*
66224999 TAAATTATGGTTACTTAAGTGTTC
1 TAAA-TATGATTACTTAAGTGTTC
* *
66225023 TAAATA-GATTTAATTCA-TGTT-
1 TAAATATGA-TTACTTAAGTGTTC
66225044 TATAATATGATTACTTAAGTGTTC
1 TA-AATATGATTACTTAAGTGTTC
66225068 TAAATA-GATT
1 TAAATATGATT
66225078 TAAGTCAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
21 2 0.04
22 19 0.42
23 18 0.40
24 6 0.13
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (23 bp):
TAAATATGATTACTTAAGTGTTC
Found at i:66228678 original size:41 final size:40
Alignment explanation
Indices: 66228585--66228685 Score: 148
Period size: 40 Copynumber: 2.5 Consensus size: 40
66228575 GAAAAATGGT
* *
66228585 GCTATTGCTTTACCATTAGCGGCGTTTATGAAAAAACACA
1 GCTATTGCTTTACCTTTTGCGGCGTTTATGAAAAAACACA
* *
66228625 GCTATTGTTTTACCTTTTGCGGCGTTTATGAGAAAAACACC
1 GCTATTGCTTTACCTTTTGCGGCGTTTATGA-AAAAACACA
*
66228666 GCTACTGCTTTACCTTTTGC
1 GCTATTGCTTTACCTTTTGC
66228686 AGCTTTTTTC
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
40 28 0.52
41 26 0.48
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.36
Consensus pattern (40 bp):
GCTATTGCTTTACCTTTTGCGGCGTTTATGAAAAAACACA
Found at i:66230251 original size:19 final size:19
Alignment explanation
Indices: 66230224--66230261 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
66230214 TAAAATCAAT
66230224 TTTTCTAAAAATATT-TTTA
1 TTTTCT-AAAATATTATTTA
*
66230243 TTTTGTAAAATATTATTTA
1 TTTTCTAAAATATTATTTA
66230262 CCAATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (19 bp):
TTTTCTAAAATATTATTTA
Found at i:66234766 original size:16 final size:15
Alignment explanation
Indices: 66234745--66234788 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
66234735 TTTTAAAGGT
*
66234745 TAATTAAGTAATTTGA
1 TAATTAAGTAA-ATGA
*
66234761 TAATTAAGTTAAATGT
1 TAATTAAG-TAAATGA
66234777 TAATTAAGTAAA
1 TAATTAAGTAAA
66234789 AGACGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.16
16 18 0.72
17 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (15 bp):
TAATTAAGTAAATGA
Found at i:66234779 original size:32 final size:31
Alignment explanation
Indices: 66234716--66234787 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
66234706 TGGATAGGTT
*
66234716 TTAATGTAATTATGATAATTTTTAAAGGTTAA
1 TTAA-GTAATTATGATAATTGTTAAAGGTTAA
*
66234748 TTAAGTAATT-TGATAATTAAGTTAAATGTTAA
1 TTAAGTAATTATGATAATT--GTTAAAGGTTAA
66234780 TTAAGTAA
1 TTAAGTAA
66234788 AAGACGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
30 8 0.22
31 6 0.17
32 22 0.61
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.44
Consensus pattern (31 bp):
TTAAGTAATTATGATAATTGTTAAAGGTTAA
Found at i:66235588 original size:40 final size:39
Alignment explanation
Indices: 66235531--66235673 Score: 155
Period size: 40 Copynumber: 3.6 Consensus size: 39
66235521 ATACACTTAT
66235531 GTGCCCCTGTGTGTACTTCGGTACCCCTAATTTCACATAC
1 GTGCCCCTGT-TGTACTTCGGTACCCCTAATTTCACATAC
* * *
66235571 GTGCCCCTAGTTTTACTTCAGTACCCCTGAA-TGCACATAC
1 GTGCCCCT-GTTGTACTTCGGTACCCCT-AATTTCACATAC
* * *
66235611 GTGCCCATGTTTGTACTTTGGTACCCCTAATTGT-AGATAC
1 GTGCCCCTG-TTGTACTTCGGTACCCCTAATT-TCACATAC
*
66235651 GTGCCCCTGGTTGTACTTTGGTA
1 GTGCCCCT-GTTGTACTTCGGTA
66235674 ATCCTGAATT
Statistics
Matches: 87, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
39 3 0.03
40 79 0.91
41 5 0.06
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.34
Consensus pattern (39 bp):
GTGCCCCTGTTGTACTTCGGTACCCCTAATTTCACATAC
Found at i:66235680 original size:80 final size:80
Alignment explanation
Indices: 66235531--66235682 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
66235521 ATACACTTAT
* * *
66235531 GTGCCCCTGTGTGTACTTCGGTACCCCTAATTTCACATACGTGCCCCTAGTTTTACTTCAGTACC
1 GTGCCCATGTGTGTACTTCGGTACCCCTAATTTCACATACGTGCCCCTAGTTGTACTTCAGTAAC
66235596 CCTGAATGCACATAC
66 CCTGAATGCACATAC
* * * * **
66235611 GTGCCCATGTTTGTACTTTGGTACCCCTAATTGT-AGATACGTGCCCCTGGTTGTACTTTGGTAA
1 GTGCCCATGTGTGTACTTCGGTACCCCTAATT-TCACATACGTGCCCCTAGTTGTACTTCAGTAA
*
66235675 TCCTGAAT
65 CCCTGAAT
66235683 TAAATAATAT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
80 60 0.98
81 1 0.02
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.34
Consensus pattern (80 bp):
GTGCCCATGTGTGTACTTCGGTACCCCTAATTTCACATACGTGCCCCTAGTTGTACTTCAGTAAC
CCTGAATGCACATAC
Found at i:66237833 original size:50 final size:50
Alignment explanation
Indices: 66237730--66238019 Score: 312
Period size: 50 Copynumber: 5.7 Consensus size: 50
66237720 TAAAGAGATT
* *
66237730 CCATGTAAGACCATGTCTGGGACATGACATTAGCATCCTTGAGATCATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA--C-TGAG---ATGAGAGGTC
* *
66237786 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGACGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTC
* *
66237836 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATGGGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTC
** * * * * **
66237886 CCCCGTAAGACCATGTCTGTGACATGGCATGGGCACCGATATGAGAACTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTC
* * * * * **
66237936 CCATGTAAGACCATATCTGGGATATGGCATTGGCAGT-ACATGAAACATC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTC
* *
66237985 CCATGTAATACCATGTCTGGGACATGGCTTTGGCA
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA
66238020 TGTTATTATC
Statistics
Matches: 202, Mismatches: 32, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
49 39 0.19
50 126 0.62
53 4 0.02
54 1 0.00
56 32 0.16
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.23
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTC
Found at i:66243469 original size:24 final size:24
Alignment explanation
Indices: 66243435--66243524 Score: 92
Period size: 24 Copynumber: 3.8 Consensus size: 24
66243425 TATCTATGAC
* *
66243435 GCCTTTTTGGTGTATTCTATTAAT
1 GCCTTTATGGTGTATTCTATAAAT
66243459 GCCTTTATGGTGTATTCTATAAAT
1 GCCTTTATGGTGTATTCTATAAAT
* * * *
66243483 ACC-CTATTGGCGTTTTCTATAAAT
1 GCCTTTA-TGGTGTATTCTATAAAT
* *
66243507 TCCTTTGTGGTGTATTCT
1 GCCTTTATGGTGTATTCT
66243525 GTGTTGCCTT
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
23 2 0.04
24 50 0.94
25 1 0.02
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.49
Consensus pattern (24 bp):
GCCTTTATGGTGTATTCTATAAAT
Found at i:66245724 original size:19 final size:20
Alignment explanation
Indices: 66245700--66245742 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
66245690 GCATTAGAAC
66245700 TTTTATTTT-TATTTACTTA-
1 TTTTATTTTAT-TTTACTTAG
66245719 TTTTATTTTATTTTACTTAG
1 TTTTATTTTATTTTACTTAG
66245739 TTTT
1 TTTT
66245743 TTAATCACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTATTTTATTTTACTTAG
Found at i:66250776 original size:14 final size:13
Alignment explanation
Indices: 66250757--66250790 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
66250747 GTAGTTTCAA
66250757 AAAAAAAGAATTCG
1 AAAAAAA-AATTCG
66250771 -AAAAAAAATTCG
1 AAAAAAAAATTCG
66250783 AAAAAAAA
1 AAAAAAAA
66250791 TTGTATACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.74, C:0.06, G:0.09, T:0.12
Consensus pattern (13 bp):
AAAAAAAAATTCG
Found at i:66250786 original size:11 final size:12
Alignment explanation
Indices: 66250758--66250792 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
66250748 TAGTTTCAAA
66250758 AAAAAAGAATTCG
1 AAAAAA-AATTCG
66250771 AAAAAAAATTCG
1 AAAAAAAATTCG
66250783 AAAAAAAATT
1 AAAAAAAATT
66250793 GTATACGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 16 0.73
13 6 0.27
ACGTcount: A:0.69, C:0.06, G:0.09, T:0.17
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:66252279 original size:96 final size:96
Alignment explanation
Indices: 66252167--66252359 Score: 377
Period size: 96 Copynumber: 2.0 Consensus size: 96
66252157 TCCGTTCTTT
66252167 CCCTAATACTTCTTCTACGACTAGGTGGGAGCAAGGGTCCAACAAACGAGACTTGCCGAGTCGAA
1 CCCTAATACTTCTTCTACGACTAGGTGGGAGCAAGGGTCCAACAAACGAGACTTGCCGAGTCGAA
*
66252232 ATAAAGAAGTAAGTGGAGCTACCAAATTCAA
66 ATAAAGAAGTAAGCGGAGCTACCAAATTCAA
66252263 CCCTAATACTTCTTCTACGACTAGGTGGGAGCAAGGGTCCAACAAACGAGACTTGCCGAGTCGAA
1 CCCTAATACTTCTTCTACGACTAGGTGGGAGCAAGGGTCCAACAAACGAGACTTGCCGAGTCGAA
66252328 ATAAAGAAGTAAGCGGAGCTACCAAATTCAA
66 ATAAAGAAGTAAGCGGAGCTACCAAATTCAA
66252359 C
1 C
66252360 AAACCAATGG
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (96 bp):
CCCTAATACTTCTTCTACGACTAGGTGGGAGCAAGGGTCCAACAAACGAGACTTGCCGAGTCGAA
ATAAAGAAGTAAGCGGAGCTACCAAATTCAA
Found at i:66257540 original size:19 final size:19
Alignment explanation
Indices: 66257518--66257556 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
66257508 AAATAATTCG
*
66257518 AAAAAAAATTTGAAAAAAA
1 AAAAAAAATTCGAAAAAAA
*
66257537 AAAAAGAATTCGAAAAAAA
1 AAAAAAAATTCGAAAAAAA
66257556 A
1 A
66257557 TTCGAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.13
Consensus pattern (19 bp):
AAAAAAAATTCGAAAAAAA
Found at i:66257541 original size:31 final size:31
Alignment explanation
Indices: 66257503--66257568 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
66257493 TTGTAGTTTC
* *
66257503 AAAAAAAATAATTCGAAAAAAAATTTGAAAA
1 AAAAAAAAGAATTCGAAAAAAAATTCGAAAA
66257534 AAAAAAAAGAATTCGAAAAAAAATTCGAAAA
1 AAAAAAAAGAATTCGAAAAAAAATTCGAAAA
66257565 AAAA
1 AAAA
66257569 TTGTATACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.73, C:0.05, G:0.08, T:0.15
Consensus pattern (31 bp):
AAAAAAAAGAATTCGAAAAAAAATTCGAAAA
Found at i:66257552 original size:11 final size:12
Alignment explanation
Indices: 66257505--66257570 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
66257495 GTAGTTTCAA
66257505 AAAAAATAATTCG
1 AAAAAA-AATTCG
*
66257518 AAAAAAAATTTG
1 AAAAAAAATTCG
66257530 -AAAAAAA----
1 AAAAAAAATTCG
*
66257537 AAAAAGAATTCG
1 AAAAAAAATTCG
66257549 AAAAAAAATTCG
1 AAAAAAAATTCG
66257561 AAAAAAAATT
1 AAAAAAAATT
66257571 GTATACGGTC
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
8 6 0.13
11 7 0.16
12 26 0.58
13 6 0.13
ACGTcount: A:0.70, C:0.05, G:0.08, T:0.18
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:66257552 original size:14 final size:13
Alignment explanation
Indices: 66257535--66257568 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
66257525 ATTTGAAAAA
66257535 AAAAAAAGAATTCG
1 AAAAAAA-AATTCG
66257549 -AAAAAAAATTCG
1 AAAAAAAAATTCG
66257561 AAAAAAAA
1 AAAAAAAA
66257569 TTGTATACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.74, C:0.06, G:0.09, T:0.12
Consensus pattern (13 bp):
AAAAAAAAATTCG
Found at i:66257568 original size:16 final size:18
Alignment explanation
Indices: 66257518--66257556 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
66257508 AAATAATTCG
*
66257518 AAAAAA-AATTTGAAAAAA
1 AAAAAAGAATTCG-AAAAA
66257536 AAAAAAGAATTCGAAAAA
1 AAAAAAGAATTCGAAAAA
66257554 AAA
1 AAA
66257557 TTCGAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.13
Consensus pattern (18 bp):
AAAAAAGAATTCGAAAAA
Found at i:66258677 original size:30 final size:31
Alignment explanation
Indices: 66258641--66258703 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 31
66258631 TGGGCAGAAA
66258641 TGAAAGCCATAATGAGAAAGCG-TTCATTCC
1 TGAAAGCCATAATGAGAAAGCGATTCATTCC
66258671 TGAAAGCCATAATGAGAAAGCGATTCATTCC
1 TGAAAGCCATAATGAGAAAGCGATTCATTCC
66258702 TG
1 TG
66258704 CTTACTATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.24
Consensus pattern (31 bp):
TGAAAGCCATAATGAGAAAGCGATTCATTCC
Found at i:66270202 original size:31 final size:29
Alignment explanation
Indices: 66270144--66270202 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
66270134 ATTTATCTAA
*
66270144 AAGATAAACATTAAATTTAATTTAATAAT
1 AAGATAAACATTAAATTTAAATTAATAAT
* *
66270173 AAGATAATCACTTTAATATTAAATTAATAA
1 AAGATAAACA-TTAAAT-TTAAATTAATAA
66270203 AATACCATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.36
30 5 0.20
31 11 0.44
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.37
Consensus pattern (29 bp):
AAGATAAACATTAAATTTAAATTAATAAT
Found at i:66273880 original size:21 final size:22
Alignment explanation
Indices: 66273850--66273892 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
66273840 TCTTGTTCAA
66273850 TCTCAATCTCGTTT-TTCTTTT
1 TCTCAATCTCGTTTATTCTTTT
* *
66273871 TCTCACTCTCTTTTATTCTTTT
1 TCTCAATCTCGTTTATTCTTTT
66273893 CTTGAGTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.09, C:0.26, G:0.02, T:0.63
Consensus pattern (22 bp):
TCTCAATCTCGTTTATTCTTTT
Found at i:66282177 original size:17 final size:17
Alignment explanation
Indices: 66282155--66282197 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
66282145 AGATCTCCGA
66282155 CGAGCTTCCAAATCGAT
1 CGAGCTTCCAAATCGAT
*
66282172 CGAGCTTCCAAATCGGT
1 CGAGCTTCCAAATCGAT
66282189 CGAGCTTCC
1 CGAGCTTCC
66282198 GATAATCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.23
Consensus pattern (17 bp):
CGAGCTTCCAAATCGAT
Found at i:66290779 original size:94 final size:94
Alignment explanation
Indices: 66290520--66290772 Score: 497
Period size: 94 Copynumber: 2.7 Consensus size: 94
66290510 TAAAAAGGGG
66290520 ATTTGATATATTCCTTATCAGATAAGGAAATAGAATTTAATTATTATTTAAAAGAGTTTTAGATA
1 ATTTGATATATTCCTTATCAGATAAGGAAATAGAATTTAATTATTATTTAAAAGAGTTTTAGATA
66290585 GATAATAATTAAAAATCAAAATCAAAAGA
66 GATAATAATTAAAAATCAAAATCAAAAGA
66290614 ATTTGATATATTCCTTATCAGATAAGGAAATAGAATTTAATTATTATTTAAAAGAGTTTTAGATA
1 ATTTGATATATTCCTTATCAGATAAGGAAATAGAATTTAATTATTATTTAAAAGAGTTTTAGATA
66290679 GATAATAATTAAAAATCAAAATCAAAAGA
66 GATAATAATTAAAAATCAAAATCAAAAGA
*
66290708 ATTTGATATATTCCTTATCAGATAAGGAAATAGAATTTAGTTATTATTTAAAAGAGTTTTAGATA
1 ATTTGATATATTCCTTATCAGATAAGGAAATAGAATTTAATTATTATTTAAAAGAGTTTTAGATA
66290773 ATTAATACTT
Statistics
Matches: 158, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 158 1.00
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (94 bp):
ATTTGATATATTCCTTATCAGATAAGGAAATAGAATTTAATTATTATTTAAAAGAGTTTTAGATA
GATAATAATTAAAAATCAAAATCAAAAGA
Found at i:66290835 original size:46 final size:48
Alignment explanation
Indices: 66290785--66290899 Score: 171
Period size: 48 Copynumber: 2.4 Consensus size: 48
66290775 TAATACTTAT
* *
66290785 ATTATTATTTAAAAGAGTTTTAGAT-AAATAATA-AAAATAGAATTTA
1 ATTATTATTTAAAAGAGTTTTAAATAAAATAATATAAAATAGAATTAA
* *
66290831 ATTATTATTTAAAAGAGTTTTAAATAAAATATTATTAAATAGAATTAA
1 ATTATTATTTAAAAGAGTTTTAAATAAAATAATATAAAATAGAATTAA
*
66290879 AATATTATTTAAAAGAGTTTT
1 ATTATTATTTAAAAGAGTTTT
66290900 TAAAATTCAA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
46 24 0.39
47 7 0.11
48 31 0.50
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (48 bp):
ATTATTATTTAAAAGAGTTTTAAATAAAATAATATAAAATAGAATTAA
Found at i:66302540 original size:50 final size:50
Alignment explanation
Indices: 66302465--66302564 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
66302455 GAACTGGAGT
66302465 TACAGAGGATGAGTGATCTTCAACAGGTTTGGTGGCTTTCTTCACTGATC
1 TACAGAGGATGAGTGATCTTCAACAGGTTTGGTGGCTTTCTTCACTGATC
*
66302515 TACAGAGGATGAGTGATCTTCAACAGGTTTGGTGGCTTTCTTCATTGATC
1 TACAGAGGATGAGTGATCTTCAACAGGTTTGGTGGCTTTCTTCACTGATC
66302565 CTCTCATTCT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (50 bp):
TACAGAGGATGAGTGATCTTCAACAGGTTTGGTGGCTTTCTTCACTGATC
Found at i:66311608 original size:27 final size:27
Alignment explanation
Indices: 66311578--66311755 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
66311568 ATATTGAGCC
* *
66311578 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
66311605 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
66311632 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
66311660 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
66311687 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
66311714 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
66311741 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
66311756 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:66311690 original size:55 final size:54
Alignment explanation
Indices: 66311578--66311755 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
66311568 ATATTGAGCC
* * * * *
66311578 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
66311632 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
66311687 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
66311741 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
66311756 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:66312949 original size:1 final size:1
Alignment explanation
Indices: 66312943--66312998 Score: 94
Period size: 1 Copynumber: 56.0 Consensus size: 1
66312933 GAATGAACTC
* *
66312943 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
66312999 CTTTCTTCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.02, C:0.00, G:0.02, T:0.96
Consensus pattern (1 bp):
T
Found at i:66319633 original size:27 final size:27
Alignment explanation
Indices: 66319603--66319780 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
66319593 ATATTGAGCC
* *
66319603 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
66319630 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
66319657 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
66319685 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
66319712 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
66319739 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
66319766 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
66319781 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:66319715 original size:55 final size:54
Alignment explanation
Indices: 66319603--66319780 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
66319593 ATATTGAGCC
* * * * *
66319603 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
66319657 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
66319712 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
66319766 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
66319781 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:66327780 original size:27 final size:27
Alignment explanation
Indices: 66327750--66327927 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
66327740 ATATTGAGCC
* *
66327750 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
66327777 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
66327804 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
66327832 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
66327859 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
66327886 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
66327913 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
66327928 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:66327862 original size:55 final size:54
Alignment explanation
Indices: 66327750--66327927 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
66327740 ATATTGAGCC
* * * * *
66327750 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
66327804 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
66327859 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
66327913 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
66327928 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:66337411 original size:27 final size:27
Alignment explanation
Indices: 66337381--66337558 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
66337371 ATATTGAGCC
* *
66337381 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
66337408 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
66337435 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
66337463 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
66337490 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
66337517 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
66337544 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
66337559 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:66337493 original size:55 final size:54
Alignment explanation
Indices: 66337381--66337558 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
66337371 ATATTGAGCC
* * * * *
66337381 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
66337435 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
66337490 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
66337544 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
66337559 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:66340470 original size:42 final size:43
Alignment explanation
Indices: 66340370--66340483 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 43
66340360 AACTCGTACA
* ***
66340370 ATGCCAACGTCCCAGACGCAGTCTTACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACGCGGTCTTACACAAAATCAAATATCG
66340413 ATGCC-ACTGTCCCAGACAG-GGTCTTACACAAAATCAAATA-CG
1 ATGCCAAC-GTCCCAGAC-GCGGTCTTACACAAAATCAAATATCG
*
66340455 ATGCCAACGTCCCAGACGTGGTCTTACAC
1 ATGCCAACGTCCCAGACGCGGTCTTACAC
66340484 GAAACCACAT
Statistics
Matches: 63, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
41 1 0.02
42 28 0.44
43 33 0.52
44 1 0.02
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.21
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGCGGTCTTACACAAAATCAAATATCG
Found at i:66348484 original size:20 final size:20
Alignment explanation
Indices: 66348411--66348485 Score: 60
Period size: 20 Copynumber: 3.8 Consensus size: 20
66348401 TGCAAAACAA
* *
66348411 GGGCACCAAAGTGTAATCAG
1 GGGCACCAGAGTGCAATCAG
* * * *
66348431 GGGCATCGGAGTGCAGTCAA
1 GGGCACCAGAGTGCAATCAG
* * *
66348451 GAGCACGAGTGTGCAATCAG
1 GGGCACCAGAGTGCAATCAG
*
66348471 GGGCACCCGAGTGCA
1 GGGCACCAGAGTGCA
66348486 GTCAAGGGAA
Statistics
Matches: 38, Mismatches: 17, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.28, C:0.23, G:0.36, T:0.13
Consensus pattern (20 bp):
GGGCACCAGAGTGCAATCAG
Found at i:66348543 original size:18 final size:21
Alignment explanation
Indices: 66348496--66348547 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
66348486 GTCAAGGGAA
66348496 CAAATGCACTATCGGGGGCAC
1 CAAATGCACTATCGGGGGCAC
*
66348517 CAGAATGCA-T-TCGGGGGC-T
1 CA-AATGCACTATCGGGGGCAC
66348536 CAAATGCACTAT
1 CAAATGCACTAT
66348548 TAGGGACCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 6 0.22
19 3 0.11
20 9 0.33
21 3 0.11
22 6 0.22
ACGTcount: A:0.29, C:0.25, G:0.27, T:0.19
Consensus pattern (21 bp):
CAAATGCACTATCGGGGGCAC
Found at i:66351228 original size:28 final size:28
Alignment explanation
Indices: 66351121--66351233 Score: 108
Period size: 28 Copynumber: 4.1 Consensus size: 28
66351111 AGCATGGCCG
* * *
66351121 CCAGAACAGATAA-TT-TGACAGAGTCA
1 CCAGATCAGATAATTTGTGGCAGAGCCA
* **
66351147 CCAGATACAGATAA-TCGTGGCAGAATCA
1 CCAGAT-CAGATAATTTGTGGCAGAGCCA
* *
66351175 CCAGAACAGA-AATATGTGGCAGAGCCA
1 CCAGATCAGATAATTTGTGGCAGAGCCA
*
66351202 CCAGATCAGATAATTTGTGGCATAGCCA
1 CCAGATCAGATAATTTGTGGCAGAGCCA
66351230 CCAG
1 CCAG
66351234 GACGCTACCT
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
26 7 0.10
27 31 0.44
28 33 0.46
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (28 bp):
CCAGATCAGATAATTTGTGGCAGAGCCA
Found at i:66351232 original size:55 final size:54
Alignment explanation
Indices: 66351112--66351233 Score: 131
Period size: 55 Copynumber: 2.2 Consensus size: 54
66351102 GAATTATGCA
* * *
66351112 GCATGGCCGCCAGAACAGATAATTTGACAGAGTCACCAGATACAGATAATCGTG
1 GCATAGCCACCAGAACAGATAATTTGACAGAGCCACCAGATACAGATAATCGTG
* ** * *
66351166 GCAGAATCACCAGAACAGA-AATATGTGGCAGAGCCACCAGAT-CAGATAATTTGTG
1 GCATAGCCACCAGAACAGATAAT-T-TGACAGAGCCACCAGATACAGATAA-TCGTG
66351221 GCATAGCCACCAG
1 GCATAGCCACCAG
66351234 GACGCTACCT
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
53 3 0.06
54 22 0.41
55 29 0.54
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (54 bp):
GCATAGCCACCAGAACAGATAATTTGACAGAGCCACCAGATACAGATAATCGTG
Found at i:66351386 original size:28 final size:28
Alignment explanation
Indices: 66351339--66351431 Score: 159
Period size: 28 Copynumber: 3.3 Consensus size: 28
66351329 AAATTAACCC
* *
66351339 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
66351367 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
*
66351395 TAGGGGTATAATGGTAATATTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
66351423 TAGGGGTAT
1 TAGGGGTAT
66351432 TCTAGTAAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 62 1.00
ACGTcount: A:0.32, C:0.08, G:0.27, T:0.33
Consensus pattern (28 bp):
TAGGGGTATAATGGTAATTTTGCATACA
Found at i:66358325 original size:13 final size:13
Alignment explanation
Indices: 66358309--66358354 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
66358299 TTCTTTCATC
66358309 ATAATAAAATAAA
1 ATAATAAAATAAA
66358322 ATAATAAAAGTAAA
1 ATAATAAAA-TAAA
* *
66358336 ACAAAAAAATAAAA
1 ATAATAAAAT-AAA
66358350 ATAAT
1 ATAAT
66358355 TAAGCGGCCT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (13 bp):
ATAATAAAATAAA
Found at i:66358341 original size:19 final size:19
Alignment explanation
Indices: 66358313--66358349 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
66358303 TTCATCATAA
* *
66358313 TAAAATAAAATAATAAAAG
1 TAAAACAAAAAAATAAAAG
66358332 TAAAACAAAAAAATAAAA
1 TAAAACAAAAAAATAAAA
66358350 ATAATTAAGC
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:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (19 bp):
TAAAACAAAAAAATAAAAG
Found at i:66358824 original size:27 final size:27
Alignment explanation
Indices: 66358788--66358899 Score: 104
Period size: 27 Copynumber: 4.1 Consensus size: 27
66358778 AGCATGGCTG
*
66358788 CCAGAACAGATAAT-TTGACAGAGTCA
1 CCAGAACAGATAATATTGGCAGAGTCA
** *
66358814 CCAGATACAGATAATCGTGGCAGAATCA
1 CCAGA-ACAGATAATATTGGCAGAGTCA
*
66358842 CCAGAACAGA-AATATGTGGCAGAGCCA
1 CCAGAACAGATAATAT-TGGCAGAGTCA
* * *
66358869 CCAGATCAGATAAT-TGTGGCATAGCCA
1 CCAGAACAGATAATAT-TGGCAGAGTCA
66358896 CCAG
1 CCAG
66358900 GACGCTTCCT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 8 0.11
27 48 0.66
28 17 0.23
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (27 bp):
CCAGAACAGATAATATTGGCAGAGTCA
Found at i:66358898 original size:54 final size:54
Alignment explanation
Indices: 66358788--66358899 Score: 138
Period size: 54 Copynumber: 2.1 Consensus size: 54
66358778 AGCATGGCTG
* *
66358788 CCAGAACAGATAATTTGACAGAGTCACCAGATACAGATAATCGTGGCAGAATCA
1 CCAGAACAGATAATTTGACAGAGCCACCAGATACAGATAATCGTGGCAGAACCA
* * * *
66358842 CCAGAACAGA-AATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAAT-T-TGACAGAGCCACCAGATACAGATAATCGTGGCAGAACCA
66358896 CCAG
1 CCAG
66358900 GACGCTTCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
53 3 0.06
54 32 0.64
55 15 0.30
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATAATTTGACAGAGCCACCAGATACAGATAATCGTGGCAGAACCA
Found at i:66359052 original size:28 final size:28
Alignment explanation
Indices: 66359005--66359097 Score: 159
Period size: 28 Copynumber: 3.3 Consensus size: 28
66358995 AAATTAACCC
* *
66359005 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
66359033 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
*
66359061 TAGGGGTATAATGGTAATTTTGTATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
66359089 TAGGGGTAT
1 TAGGGGTAT
66359098 TCTAGTACAT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 62 1.00
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.35
Consensus pattern (28 bp):
TAGGGGTATAATGGTAATTTTGCATACA
Found at i:66366788 original size:42 final size:42
Alignment explanation
Indices: 66366742--66366829 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
66366732 CAATATGTAC
*
66366742 GAAGGGGTTACATTCAAATACTATAGTTTCAGATTGCATATT
1 GAAGGGGTTACATTCAAATACCATAGTTTCAGATTGCATATT
66366784 GAAGGGGTTACATTCAAATACCATAGTTTCAGATTGCATATT
1 GAAGGGGTTACATTCAAATACCATAGTTTCAGATTGCATATT
66366826 GAAG
1 GAAG
66366830 TGTGTTTGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.33
Consensus pattern (42 bp):
GAAGGGGTTACATTCAAATACCATAGTTTCAGATTGCATATT
Found at i:66373978 original size:116 final size:116
Alignment explanation
Indices: 66373774--66374156 Score: 694
Period size: 116 Copynumber: 3.3 Consensus size: 116
66373764 NNNNNNNNNN
66373774 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
66373839 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
66 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
66373890 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
66373955 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
66 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
* * * *
66374006 AACATTTTGAATATTTTTATATTATTTCATGTGATAATATAAAATGTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
* * *
66374071 TATAATTTACTTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAGC
66 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
*
66374122 AATATTTTGAATATTTTTATATTATTTCATGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAAT
66374157 AAAATATAAA
Statistics
Matches: 258, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 258 1.00
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.48
Consensus pattern (116 bp):
AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC
Found at i:66377408 original size:126 final size:125
Alignment explanation
Indices: 66377178--66377715 Score: 826
Period size: 126 Copynumber: 4.3 Consensus size: 125
66377168 GCCCAAGTTA
* *
66377178 TTTCAGAAACCACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
**
66377243 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTATGCAGACACGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTT-ACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
* * * *
66377304 TTTCAGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
*
66377369 TGCATCCTGCTTGAAGCGTTTTTACCACTATTTGCGCAGACACGTTTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTTA-CACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
* * * * * **
66377430 TTTCAGAGACTATTATAGCAAAATAGCATCCACGTGGAAGCTTCTTTCAGTACTTTTGCTGGCAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
* *
66377495 TGCATCCTGCTTGAAGCGTTTTTTACACTATTTGCACAGACACGTCTTCTAAAAATTA-TT
66 TGCATCCTGCTTGAAGCG-TTTTTACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
* * *
66377555 TTTCAGATACTATTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
* *
66377620 TGCATCCTGCTTGAAGCGTTTTTGGCACTATTTGCGCAGACACGTCTTCTCAAATTTATTT
66 TGCATCCTGCTTGAAGCGTTTTT-ACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
66377681 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGT
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGT
66377716 AGAAGCTTTT
Statistics
Matches: 377, Mismatches: 31, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
124 5 0.01
125 110 0.29
126 256 0.68
127 6 0.02
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (125 bp):
TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
TGCATCCTGCTTGAAGCGTTTTTACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
Found at i:66377681 original size:251 final size:252
Alignment explanation
Indices: 66377178--66377723 Score: 842
Period size: 251 Copynumber: 2.2 Consensus size: 252
66377168 GCCCAAGTTA
* * * *
66377178 TTTCAGAAACCACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
1 TTTCAGAGACTACTATAGCAAAAGAGCGTCCACGTGGAAGCTTCTTTCAGTACTTTTGCTGAAAA
** *
66377243 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTATGCAGACACGTCTTCTCAAAATTATTTTTTC
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTACACAGACACGTCTTCTAAAAATTATTTTTTC
66377308 AGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAATGCA
131 AGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAATGCA
*
66377373 TCCTGCTTGAAGCGTTTTTACCACTATTTGCGCAGACACGTTTTCTCAAAATTATTT
196 TCCTGCTTGAAGCGTTTTTACCACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
* * * **
66377430 TTTCAGAGACTATTATAGCAAAATAGCATCCACGTGGAAGCTTCTTTCAGTACTTTTGCTGGCAA
1 TTTCAGAGACTACTATAGCAAAAGAGCGTCCACGTGGAAGCTTCTTTCAGTACTTTTGCTGAAAA
* *
66377495 TGCATCCTGCTTGAAGCGTTTTTTACACTATTTGCACAGACACGTCTTCTAAAAATTA-TTTTTC
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTACACAGACACGTCTTCTAAAAATTATTTTTTC
* * * * * * *
66377559 AGATACTATTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCA
131 AGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAATGCA
** *
66377624 TCCTGCTTGAAGCGTTTTTGGCACTATTTGCGCAGACACGTCTTCTCAAATTTATTT
196 TCCTGCTTGAAGCGTTTTTACCACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
* *
66377681 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTAGAAGCTT
1 TTTCAGAGACTACTATAGCAAAAGAGCGTCCACGTGGAAGCTT
66377724 TTTTAGATTA
Statistics
Matches: 264, Mismatches: 30, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
251 155 0.59
252 109 0.41
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33
Consensus pattern (252 bp):
TTTCAGAGACTACTATAGCAAAAGAGCGTCCACGTGGAAGCTTCTTTCAGTACTTTTGCTGAAAA
TGCATCCTGCTTGAAGCGTTTTTGACACTATTTACACAGACACGTCTTCTAAAAATTATTTTTTC
AGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAATGCA
TCCTGCTTGAAGCGTTTTTACCACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
Found at i:66377977 original size:95 final size:98
Alignment explanation
Indices: 66377832--66378006 Score: 250
Period size: 95 Copynumber: 1.8 Consensus size: 98
66377822 CCTAAAATCC
* * ** * *
66377832 TAATCTATTTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTTATTTGA
1 TAATCTATATTTTTTAAAATTTATAATTAATTTAATCAACAAACACTAAACCCTAATTTATTTAA
66377897 -TTTTTTCCTTAAAAACCATAAACACTAAACCA
66 TTTTTTTCCTTAAAAACCATAAACACTAAACCA
*
66377929 TAATCTA-ATTTTTT-AAA-TTAGTAATTAATTTAATTAACAAACACTAAACCCTAATTTATTTA
1 TAATCTATATTTTTTAAAATTTA-TAATTAATTTAATCAACAAACACTAAACCCTAATTTATTTA
66377991 ATTTTTTTCCTTAAAA
65 ATTTTTTTCCTTAAAA
66378007 CCCTAAAATT
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
94 3 0.04
95 39 0.57
96 20 0.29
97 7 0.10
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.43
Consensus pattern (98 bp):
TAATCTATATTTTTTAAAATTTATAATTAATTTAATCAACAAACACTAAACCCTAATTTATTTAA
TTTTTTTCCTTAAAAACCATAAACACTAAACCA
Found at i:66386347 original size:48 final size:48
Alignment explanation
Indices: 66386228--66386396 Score: 146
Period size: 48 Copynumber: 3.6 Consensus size: 48
66386218 TGATATGTGT
* * ** *
66386228 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-A-TTACGA-GA
1 GCTAGTGTAACACATGTCTGGGACATGCATCGGCCTCGAGAGAC-ACAA
* * * ** * * *
66386274 GCCAATGTAAAACATGTCTCAGACATGTATCGGCTTTGAGAGACACAA
1 GCTAGTGTAACACATGTCTGGGACATGCATCGGCCTCGAGAGACACAA
** * *
66386322 GCTAGTGTAGGACATGTCTGGGACATGCATCGGCCTCGAGATATACAA
1 GCTAGTGTAACACATGTCTGGGACATGCATCGGCCTCGAGAGACACAA
*
66386370 GCTAGTGTAACACCTGTCTGGGACATG
1 GCTAGTGTAACACATGTCTGGGACATG
66386397 GAATCGACAC
Statistics
Matches: 94, Mismatches: 26, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
46 28 0.30
47 2 0.02
48 64 0.68
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (48 bp):
GCTAGTGTAACACATGTCTGGGACATGCATCGGCCTCGAGAGACACAA
Found at i:66386477 original size:49 final size:48
Alignment explanation
Indices: 66386320--66386492 Score: 138
Period size: 49 Copynumber: 3.5 Consensus size: 48
66386310 TGAGAGACAC
* * *
66386320 AAGCTAGTGTAGGACATGTCTGGGACATG-CATCGGCCTCGAGATAT-A
1 AAGC-AGTGTAAGACATGTCTGGGACACGACATCGGCCTCGATATATGA
* * * * *
66386367 CAAGCTAGTGTAACACCTGTCTGGGACATGGA-ATCGACAC-CGATAGATGA
1 -AAGC-AGTGTAAGACATGTCTGGGACA-CGACATCGGC-CTCGATATATGA
* * * *
66386417 GAGCCAATGTAAGACCTGTCTGGGACACGACATCGGCCTCAATATATGA
1 AAG-CAGTGTAAGACATGTCTGGGACACGACATCGGCCTCGATATATGA
*
66386466 AAGTCAGTGTAAGACATGTCTAGGACA
1 AAG-CAGTGTAAGACATGTCTGGGACA
66386493 TGGCATCAAC
Statistics
Matches: 99, Mismatches: 19, Indels: 13
0.76 0.15 0.10
Matches are distributed among these distances:
48 27 0.27
49 69 0.70
50 3 0.03
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (48 bp):
AAGCAGTGTAAGACATGTCTGGGACACGACATCGGCCTCGATATATGA
Found at i:66394154 original size:94 final size:94
Alignment explanation
Indices: 66394034--66394206 Score: 276
Period size: 94 Copynumber: 1.8 Consensus size: 94
66394024 ACCACATTAT
66394034 GAGAGCCAGTGTAAGACATGTCTGGGACAGGCA-TAGGCCTCGAGAGACACAAGCTAGTGTAAGA
1 GAGAGCCAGTGTAAGACATGTCTGGGACAGGCATTA-GCCTCGAGAGACACAAGCTAGTGTAAGA
66394098 CATGTTTGGGACATGTATCAGTATTGAAAC
65 CATGTTTGGGACATGTATCAGTATTGAAAC
* * * * *
66394128 GAGAGCTAGTGTAAGACATGTGTGGGACATGCATTAGCCTCGAGATATACAAGCTAGTGTAAGAC
1 GAGAGCCAGTGTAAGACATGTCTGGGACAGGCATTAGCCTCGAGAGACACAAGCTAGTGTAAGAC
*
66394193 CTGTTTGGGACATG
66 ATGTTTGGGACATG
66394207 CGTCTGTAAC
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
94 70 0.97
95 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (94 bp):
GAGAGCCAGTGTAAGACATGTCTGGGACAGGCATTAGCCTCGAGAGACACAAGCTAGTGTAAGAC
ATGTTTGGGACATGTATCAGTATTGAAAC
Found at i:66394202 original size:48 final size:46
Alignment explanation
Indices: 66394041--66394207 Score: 169
Period size: 48 Copynumber: 3.5 Consensus size: 46
66394031 TATGAGAGCC
* *
66394041 AGTGTAAGACATGTCTGGGACAGGCA-TAGGCCTCGAGAGACACAAGCT
1 AGTGTAAGACATGTTTGGGACATGCATTA-GCCTCGAGA-A-ACAAGCT
* * ***
66394089 AGTGTAAGACATGTTTGGGACATGTATCAG--TATTGAAACGAGAGCT
1 AGTGTAAGACATGTTTGGGACATGCATTAGCCTCGAGAAAC-A-AGCT
*
66394135 AGTGTAAGACATGTGTGGGACATGCATTAGCCTCGAGATATACAAGCT
1 AGTGTAAGACATGTTTGGGACATGCATTAGCCTCGAGA-A-ACAAGCT
*
66394183 AGTGTAAGACCTGTTTGGGACATGC
1 AGTGTAAGACATGTTTGGGACATGC
66394208 GTCTGTAACA
Statistics
Matches: 97, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
44 2 0.02
45 2 0.02
46 34 0.35
48 54 0.56
49 3 0.03
50 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTTTGGGACATGCATTAGCCTCGAGAAACAAGCT
Found at i:66395378 original size:23 final size:21
Alignment explanation
Indices: 66395306--66395380 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
66395296 CCTGATCAGT
** *
66395306 ATACGACACATAAAGTGCCTA
1 ATACGACACACGAGGTGCCTA
* * *
66395327 AAACTACGCACGAGGTGCCTA
1 ATACGACACACGAGGTGCCTA
*
66395348 ATATGACACACGAGGTGCCTGAA
1 ATACGACACACGAGGTGCCT--A
66395371 ATACGACACA
1 ATACGACACA
66395381 TAAAGTGCCT
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
21 31 0.76
23 10 0.24
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (21 bp):
ATACGACACACGAGGTGCCTA
Found at i:66395388 original size:23 final size:23
Alignment explanation
Indices: 66395306--66395392 Score: 67
Period size: 23 Copynumber: 4.0 Consensus size: 23
66395296 CCTGATCAGT
*
66395306 ATACGACACATAAAGTGCCTAAA
1 ATACGACACATAAAGTGCCTGAA
* *
66395329 ACTACG-CAC--GAGGTGCCT--A
1 A-TACGACACATAAAGTGCCTGAA
* ** *
66395348 ATATGACACACGAGGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
66395371 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
66395393 TCAGTAAAGC
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
18 3 0.06
19 5 0.10
21 16 0.31
23 23 0.45
24 4 0.08
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAA
Found at i:66397375 original size:49 final size:49
Alignment explanation
Indices: 66397321--66397497 Score: 157
Period size: 49 Copynumber: 3.6 Consensus size: 49
66397311 TGTTGTGTGT
*
66397321 CAGTGTAAGACTTGTTTGGGACATGGCATCGACAC-CGATAGAT-GAGAGC
1 CAGTGTAAGACTTGTCTGGGACATGGCATCGAC-CTCGATAGATGGA-AGC
* * * *
66397370 CAGTGTAAGACCTATCTGGGACATGGCATC-AGCCTCGATATATGGAAGT
1 CAGTGTAAGACTTGTCTGGGACATGGCATCGA-CCTCGATAGATGGAAGC
* * * * **
66397419 TAGTGTAAGACTTGTCTAGGACATGGCATCGACTTTGAT-G-TGCTAGC
1 CAGTGTAAGACTTGTCTGGGACATGGCATCGACCTCGATAGATGGAAGC
* * *
66397466 TAGTGTAAGACCATGTCTAGGACATGGCATCG
1 CAGTGTAAGA-CTTGTCTGGGACATGGCATCG
66397498 GCATCTTATT
Statistics
Matches: 107, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
47 14 0.13
48 22 0.21
49 68 0.64
50 3 0.03
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (49 bp):
CAGTGTAAGACTTGTCTGGGACATGGCATCGACCTCGATAGATGGAAGC
Found at i:66399010 original size:169 final size:169
Alignment explanation
Indices: 66398731--66399235 Score: 992
Period size: 169 Copynumber: 3.0 Consensus size: 169
66398721 TCCACATGGG
*
66398731 CGTATGCCCCTATCTCGAGTTACATTTTTTTAAAGTCTTTAAAGATGTTAAGTTTAATCCCGGAT
1 CGTATGCCCCTATCTCGAGTTACATTTTTTTAAAGTCTTTAAAGATGTTCAGTTTAATCCCGGAT
66398796 AGTTTCCCAAGGATGATTTGGGCCTTGTAGGCTCGTATTGAGAATTTTTAGATTAAGAGCGAAAA
66 AGTTTCCCAAGGATGATTTGGGCCTTGTAGGCTCGTATTGAGAATTTTTAGATTAAGAGCGAAAA
66398861 GTTTTAAATTTGATCTAGTTTTTATAACTCAGAAATGTT
131 GTTTTAAATTTGATCTAGTTTTTATAACTCAGAAATGTT
66398900 CGTATGCCCCTATCTCGAGTTACATTTTTTTAAAGTCTTTAAAGATGTTCAGTTTAATCCCGGAT
1 CGTATGCCCCTATCTCGAGTTACATTTTTTTAAAGTCTTTAAAGATGTTCAGTTTAATCCCGGAT
66398965 AGTTTCCCAAGGATGATTTGGGCCTTGTAGGCTCGTATTGAGAATTTTTAGATTAAGAGCGAAAA
66 AGTTTCCCAAGGATGATTTGGGCCTTGTAGGCTCGTATTGAGAATTTTTAGATTAAGAGCGAAAA
66399030 GTTTTAAATTTGATCTAGTTTTTATAACTCAGAAATGTT
131 GTTTTAAATTTGATCTAGTTTTTATAACTCAGAAATGTT
66399069 CGTATGCCCCTATCTCGAGTTACATTTTTTTAAAGTCTTTAAAGATGTTCAGTTTAATCCCGGAT
1 CGTATGCCCCTATCTCGAGTTACATTTTTTTAAAGTCTTTAAAGATGTTCAGTTTAATCCCGGAT
66399134 AGTTTCCCAAGGATGATTTGGGCCTTGTAGGCTCGTATTGAGAATTTTTAGATTAAGAGCGAAAA
66 AGTTTCCCAAGGATGATTTGGGCCTTGTAGGCTCGTATTGAGAATTTTTAGATTAAGAGCGAAAA
*
66399199 GTTTTAAATTTGATCTAGTTTTTATAACTCACAAATG
131 GTTTTAAATTTGATCTAGTTTTTATAACTCAGAAATG
66399236 ATCGAATACA
Statistics
Matches: 334, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
169 334 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (169 bp):
CGTATGCCCCTATCTCGAGTTACATTTTTTTAAAGTCTTTAAAGATGTTCAGTTTAATCCCGGAT
AGTTTCCCAAGGATGATTTGGGCCTTGTAGGCTCGTATTGAGAATTTTTAGATTAAGAGCGAAAA
GTTTTAAATTTGATCTAGTTTTTATAACTCAGAAATGTT
Found at i:66403514 original size:44 final size:43
Alignment explanation
Indices: 66403451--66403537 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 43
66403441 AATTTAAAGC
*
66403451 TCCATAAATCTTGTGAGGAAGTTAAGAACCAATCTTCCCTACA
1 TCCATAAATCTTGTGAGGAAGTTAAGAACAAATCTTCCCTACA
66403494 NTCCATAAAT-TCTGTGAGGAAGTTAAGAACAAATCTTCCCTACA
1 -TCCATAAATCT-TGTGAGGAAGTTAAGAACAAATCTTCCCTACA
66403538 CCCCAAGTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
43 1 0.02
44 40 0.98
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (43 bp):
TCCATAAATCTTGTGAGGAAGTTAAGAACAAATCTTCCCTACA
Found at i:66404987 original size:26 final size:26
Alignment explanation
Indices: 66404948--66405031 Score: 75
Period size: 26 Copynumber: 3.3 Consensus size: 26
66404938 AGTAGTTCCA
**
66404948 AGTGAAACAAGGTGTATAGAAGCTTT
1 AGTGAAACGGGGTGTATAGAAGCTTT
* * *
66404974 AGTGAAACGGGGTGTTTTG-A-TTTT
1 AGTGAAACGGGGTGTATAGAAGCTTT
* **
66404998 AGTGAAA-TGGGCATATAGAAGCTTT
1 AGTGAAACGGGGTGTATAGAAGCTTT
66405023 AGTGAAACG
1 AGTGAAACG
66405032 AAGCATTTTG
Statistics
Matches: 43, Mismatches: 12, Indels: 6
0.70 0.20 0.10
Matches are distributed among these distances:
23 6 0.14
24 11 0.26
25 11 0.26
26 15 0.35
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (26 bp):
AGTGAAACGGGGTGTATAGAAGCTTT
Found at i:66406455 original size:15 final size:16
Alignment explanation
Indices: 66406426--66406455 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
66406416 TTGAAAAAGT
66406426 TTTCAAATATATTTGG
1 TTTCAAATATATTTGG
66406442 TTTCAAAT-TATTTG
1 TTTCAAATATATTTG
66406456 CTCTATCACG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (16 bp):
TTTCAAATATATTTGG
Found at i:66406738 original size:13 final size:13
Alignment explanation
Indices: 66406722--66406746 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66406712 TTTTTTTTTT
66406722 TAAATTAAATTTC
1 TAAATTAAATTTC
66406735 TAAATTAAATTT
1 TAAATTAAATTT
66406747 AATTTCAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAATTAAATTTC
Found at i:66407500 original size:3 final size:3
Alignment explanation
Indices: 66407492--66407519 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
66407482 GGTGGAAATG
66407492 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
66407520 TGCATTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:66410862 original size:23 final size:23
Alignment explanation
Indices: 66410834--66410881 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
66410824 TTAACAAGTA
66410834 AAAACTCATTCTAACAAAACATC
1 AAAACTCATTCTAACAAAACATC
66410857 AAAACTCATTCTAACAAAACATC
1 AAAACTCATTCTAACAAAACATC
66410880 AA
1 AA
66410882 TCAATTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.54, C:0.25, G:0.00, T:0.21
Consensus pattern (23 bp):
AAAACTCATTCTAACAAAACATC
Found at i:66412415 original size:24 final size:24
Alignment explanation
Indices: 66412385--66412475 Score: 128
Period size: 24 Copynumber: 3.8 Consensus size: 24
66412375 ATTGACATTT
66412385 AAATCCGCACACATAGTGCTATAC
1 AAATCCGCACACATAGTGCTATAC
* *
66412409 AAGTCCGCACACATAGTGCCATAC
1 AAATCCGCACACATAGTGCTATAC
* * *
66412433 AATTTCGCACACATAGTGCTATTC
1 AAATCCGCACACATAGTGCTATAC
*
66412457 AAATTCGCACACATAGTGC
1 AAATCCGCACACATAGTGC
66412476 CGAAGTCAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (24 bp):
AAATCCGCACACATAGTGCTATAC
Found at i:66412842 original size:11 final size:10
Alignment explanation
Indices: 66412821--66412846 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
66412811 TAAAACTTGA
66412821 TTTTTTATTT
1 TTTTTTATTT
66412831 TTTTTTATTT
1 TTTTTTATTT
66412841 TTTTTT
1 TTTTTT
66412847 CACCTTAGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:66412950 original size:10 final size:10
Alignment explanation
Indices: 66412935--66412961 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
66412925 AAAACACCTA
66412935 TATATATATG
1 TATATATATG
66412945 TATATATATG
1 TATATATATG
66412955 TATATAT
1 TATATAT
66412962 GGTAACCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (10 bp):
TATATATATG
Found at i:66414070 original size:30 final size:30
Alignment explanation
Indices: 66414034--66414093 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
66414024 TTTGAACCGA
*
66414034 ATCATACAACATCTTAGTGTCCCTATTATG
1 ATCATACAACATCATAGTGTCCCTATTATG
66414064 ATCATACAACATCATAGTGTCCCTATTATG
1 ATCATACAACATCATAGTGTCCCTATTATG
66414094 GGCCTACGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (30 bp):
ATCATACAACATCATAGTGTCCCTATTATG
Found at i:66428330 original size:27 final size:28
Alignment explanation
Indices: 66428273--66428342 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
66428263 NNNNNNNNNN
* *
66428273 AGCACTAAGTGTGCGAGTTTGATTGTGT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
66428301 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
*
66428328 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
66428343 GACTTAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.24, C:0.13, G:0.31, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:66428353 original size:27 final size:27
Alignment explanation
Indices: 66428273--66428355 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
66428263 NNNNNNNNNN
* * * *
66428273 AGCACTAAGTGTGCGAGTTTGATTGTGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
66428301 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
66428328 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
66428355 A
1 A
66428356 TTTTTGAATC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
27 28 0.58
28 20 0.42
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:66433021 original size:39 final size:40
Alignment explanation
Indices: 66432817--66433039 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
66432807 TTGAATGCTG
* * * * * *
66432817 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
66432857 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
66432897 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
66432937 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
66432977 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
66433016 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
66433040 TGAACGAGGA
Statistics
Matches: 161, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 35 0.22
40 118 0.73
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:66433059 original size:79 final size:80
Alignment explanation
Indices: 66432892--66433074 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
66432882 GTGCGAGATA
* * *
66432892 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
66432957 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
66432972 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
66433036 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
66433051 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
66433075 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:66439411 original size:28 final size:28
Alignment explanation
Indices: 66439346--66439467 Score: 165
Period size: 28 Copynumber: 4.4 Consensus size: 28
66439336 GAGATTGGTG
* * * *
66439346 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
66439375 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
66439403 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
66439431 CTAAGTGTGCAAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
66439458 CTGAGTGTGC
1 CTAAGTGTGC
66439468 AGACTTAATA
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
27 23 0.27
28 47 0.55
29 15 0.18
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:66439458 original size:55 final size:57
Alignment explanation
Indices: 66439346--66439467 Score: 167
Period size: 55 Copynumber: 2.2 Consensus size: 57
66439336 GAGATTGGTG
* * * *
66439346 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCAAGTTTGATTATATAGCA
* *
66439403 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCAAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCAAGTTTGATTATATAGCA
*
66439458 CTGAGTGTGC
1 CTAAGTGTGC
66439468 AGACTTAATA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
55 22 0.38
56 21 0.36
57 15 0.26
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (57 bp):
CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCAAGTTTGATTATATAGCA
Found at i:66439479 original size:27 final size:27
Alignment explanation
Indices: 66439371--66439481 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
66439361 TAAATTGTAC
** * *
66439371 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGC-AACTTGAATATAT
** *
66439399 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGC-AACTTGAATATAT
* *
66439427 AGCACTAAGTGTGCAAGTTGATTATAT
1 AGCACTAAGTGTGCAACTTGAATATAT
*
66439454 AGCACTGAGTGTGCAGACTT-AATATAT
1 AGCACTAAGTGTGCA-ACTTGAATATAT
66439481 A
1 A
66439482 CTTTTGAATC
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
27 32 0.42
28 44 0.58
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCAACTTGAATATAT
Found at i:66440795 original size:38 final size:38
Alignment explanation
Indices: 66440744--66440820 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
66440734 AGTGTAGTCG
*
66440744 CACCCTGTAATAGGGGATAATTTAACTAATAAACTGTA
1 CACCCTGTAATAGGGGATAACTTAACTAATAAACTGTA
66440782 CACCCTGTAATAGGGGATAACTTAACTAATAAACTGTA
1 CACCCTGTAATAGGGGATAACTTAACTAATAAACTGTA
66440820 C
1 C
66440821 TAATTGGCCC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (38 bp):
CACCCTGTAATAGGGGATAACTTAACTAATAAACTGTA
Found at i:66442628 original size:26 final size:26
Alignment explanation
Indices: 66442598--66442678 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
66442588 CAATAGTCTG
*
66442598 TACACGTAGTAGCTTGCACTTAGTAC
1 TACACGTAGTAGCCTGCACTTAGTAC
* * * *
66442624 TACACAT-GT-GACCT-CAC-CATCTAA
1 TACACGTAGTAG-CCTGCACTTA-GTAC
66442648 TACACGTAGTAGCCTGCACTTAGTAC
1 TACACGTAGTAGCCTGCACTTAGTAC
66442674 TACAC
1 TACAC
66442679 ACGTGATCAC
Statistics
Matches: 40, Mismatches: 9, Indels: 12
0.66 0.15 0.20
Matches are distributed among these distances:
23 1 0.03
24 12 0.30
25 9 0.22
26 17 0.43
27 1 0.03
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (26 bp):
TACACGTAGTAGCCTGCACTTAGTAC
Found at i:66442668 original size:50 final size:48
Alignment explanation
Indices: 66442557--66442742 Score: 182
Period size: 50 Copynumber: 3.8 Consensus size: 48
66442547 CTGGTACGCA
* *
66442557 TAGTAGCCTGCACTTAGTACTACACATGCGACAAT-A-GTCTGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGAC-CTCACATCTGTACACG
* * *
66442604 TAGTAGCTTGCACTTAGTACTACACATGTGACCTCACCATCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTCA-CATCT-GTACACG
* * * * *
66442654 TAGTAGCCTGCACTTAGTACTACACACGTGA--TCACAGTTTTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTCACA----TC-TGTACACG
66442705 TAGTAGCCTGCACTTAGTACTACACATGCGACCTCACA
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTCACA
66442743 ATAGATCATT
Statistics
Matches: 115, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
46 1 0.01
47 33 0.29
48 3 0.03
49 3 0.03
50 35 0.30
51 35 0.30
53 5 0.04
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.26
Consensus pattern (48 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCTCACATCTGTACACG
Found at i:66442731 original size:101 final size:97
Alignment explanation
Indices: 66442557--66442741 Score: 253
Period size: 101 Copynumber: 1.9 Consensus size: 97
66442547 CTGGTACGCA
* * * *
66442557 TAGTAGCCTGCACTTAGTACTACACATGCGACAATAGTCTGTACACGTAGTAGCTTGCACTTAGT
1 TAGTAGCCTGCACTTAGTACTACACACGCGACAATAGTCGGTACACATAGTAGCCTGCACTTAGT
*
66442622 ACTACACATGTGACCTCACCATCTAATACACG
66 ACTACACATGCGACCTCACCATCTAATACACG
* ** *
66442654 TAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-CA-A-TAGTC-GGTACACATAGTAGCCTGCACT
66442719 TAGTACTACACATGCGACCTCAC
62 TAGTACTACACATGCGACCTCAC
66442742 AATAGATCAT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
97 29 0.39
98 2 0.03
99 1 0.01
100 3 0.04
101 40 0.53
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (97 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACAATAGTCGGTACACATAGTAGCCTGCACTTAGT
ACTACACATGCGACCTCACCATCTAATACACG
Found at i:66447368 original size:29 final size:28
Alignment explanation
Indices: 66447332--66447409 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
66447322 TCATGAGATT
66447332 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
66447362 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
66447389 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
66447410 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:66447628 original size:175 final size:174
Alignment explanation
Indices: 66447362--66447690 Score: 595
Period size: 175 Copynumber: 1.9 Consensus size: 174
66447352 AAATTGTACA
66447362 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
* * *
66447427 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTACGACCTTACCGAGTCAA
66447492 TTTTGGACAGCGGAAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGG-AAAAGGTAAGTGTGCGAACTTGAAATGCATG
* *
66447537 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
*
66447602 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTACGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTACGACCTTACCGAGTCAA
66447667 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
66447691 ACCTTGAGTA
Statistics
Matches: 148, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
174 11 0.07
175 137 0.93
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTACGACCTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:66452786 original size:50 final size:51
Alignment explanation
Indices: 66452674--66452920 Score: 241
Period size: 50 Copynumber: 4.8 Consensus size: 51
66452664 CATTTGGGTA
* * * *
66452674 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGTATTGACATCCTTGAGATC
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--AAGATC
*
66452728 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGA-C
1 A--AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATC
* *
66452780 AAGAGGTCCCATGTAAGACCATATCTGGGACATGG-AGTTGGCACCAAGATG
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCA-TTGGCACCAAGATC
** * * *
66452831 AA-AGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATAT-
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATC
* ** * ** *
66452880 GAGAACTCCCATGTAAGACCATATCTTTGATATGGCATTGG
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
66452921 AAGTACACGA
Statistics
Matches: 163, Mismatches: 24, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
49 1 0.01
50 113 0.69
51 3 0.02
52 2 0.01
53 3 0.02
54 1 0.01
55 2 0.01
56 38 0.23
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (51 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATC
Found at i:66452873 original size:100 final size:104
Alignment explanation
Indices: 66452674--66452905 Score: 271
Period size: 100 Copynumber: 2.2 Consensus size: 104
66452664 CATTTGGGTA
* *
66452674 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGTATTGACATCCTTGAGATCATGAGAGGTCC
1 AAGAGATCCCATGTAAGACCATATCTGGGACATGGTATTGACATCC-T-AGATCATGAAAGGTCC
* * *
66452739 CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGAC
64 CACGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGAC
* * *
66452780 AAGAGGTCCCATGTAAGACCATATCTGGGACATGG-AGTTGGCA-CC-A-A-GATGAAAGGTCCC
1 AAGAGATCCCATGTAAGACCATATCTGGGACATGGTA-TTGACATCCTAGATCATGAAAGGTCCC
* *
66452840 CCGTAAGACCATGTCTGGGACATGGCATGGGCACC--GAT
65 ACGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGAC
*
66452878 ATGAGAACTCCCATGTAAGACCATATCT
1 AAGAG-A-TCCCATGTAAGACCATATCT
66452906 TTGATATGGC
Statistics
Matches: 111, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
98 6 0.05
100 62 0.56
101 1 0.01
102 1 0.01
105 3 0.03
106 38 0.34
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (104 bp):
AAGAGATCCCATGTAAGACCATATCTGGGACATGGTATTGACATCCTAGATCATGAAAGGTCCCA
CGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGAC
Found at i:66456621 original size:17 final size:17
Alignment explanation
Indices: 66456599--66456631 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
66456589 TCTCCAATCG
66456599 GGTTATTACCAGTTACA
1 GGTTATTACCAGTTACA
*
66456616 GGTTATTACTAGTTAC
1 GGTTATTACCAGTTAC
66456632 TGGTAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.39
Consensus pattern (17 bp):
GGTTATTACCAGTTACA
Found at i:66460444 original size:53 final size:50
Alignment explanation
Indices: 66460310--66460501 Score: 204
Period size: 53 Copynumber: 3.7 Consensus size: 50
66460300 ATTTTGGTAA
* * * *
66460310 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATATAAGACCATGTTTGGGACATGGCGTTGGCA-CC--GAGA-C--G
*
66460366 AGAGGTCCCATATAAGACCATGTTTGAGACATGGCGTTGGCACCGAGACG
1 AGAGGTCCCATATAAGACCATGTTTGGGACATGGCGTTGGCACCGAGACG
* *
66460416 AGAGGTCCCATGTCATAAGACCATGTTTGGGACATTGCGTTGGCACCGAGATG
1 AGAGGTCCCA--T-ATAAGACCATGTTTGGGACATGGCGTTGGCACCGAGACG
*** *
66460469 AGAGGTCCCCCGTAAGACCATGTCTGGGACATG
1 AGAGGTCCCATATAAGACCATGTTTGGGACATG
66460502 ACTTTGGCTT
Statistics
Matches: 120, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
50 30 0.25
52 2 0.02
53 49 0.41
55 2 0.02
56 37 0.31
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATATAAGACCATGTTTGGGACATGGCGTTGGCACCGAGACG
Found at i:66461073 original size:26 final size:25
Alignment explanation
Indices: 66461018--66461066 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
66461008 GATTTTGCTA
*
66461018 ATGAATGATGTTTAAATATCTAATG
1 ATGAATGATGTTAAAATATCTAATG
* *
66461043 ATGAATGGTTGTTAAAATGTCTAA
1 ATGAAT-GATGTTAAAATATCTAA
66461067 GTATGAAGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 6 0.30
26 14 0.70
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39
Consensus pattern (25 bp):
ATGAATGATGTTAAAATATCTAATG
Found at i:66463156 original size:18 final size:18
Alignment explanation
Indices: 66463120--66463157 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
66463110 TCGAATTTCG
*
66463120 AATTCGAATAACTCAAAT
1 AATTCGAATAAATCAAAT
*
66463138 AATTCGAATAAATCGAAT
1 AATTCGAATAAATCAAAT
66463156 AA
1 AA
66463158 CAAACTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.13, G:0.08, T:0.26
Consensus pattern (18 bp):
AATTCGAATAAATCAAAT
Done.