Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 165 of 259
Found at i:53606528 original size:4 final size:4
Alignment explanation
Indices: 53606519--53606553 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
53606509 ATGTACACCA
53606519 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
53606554 ACTCATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:53609694 original size:21 final size:21
Alignment explanation
Indices: 53609665--53609704 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53609655 TGACTACAAA
*
53609665 TCAGATTTTTGCTCCTGATTT
1 TCAGATTTTTCCTCCTGATTT
*
53609686 TCAGTTTTTTCCTCCTGAT
1 TCAGATTTTTCCTCCTGAT
53609705 AAAATTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.23, G:0.12, T:0.53
Consensus pattern (21 bp):
TCAGATTTTTCCTCCTGATTT
Found at i:53613829 original size:39 final size:39
Alignment explanation
Indices: 53613786--53613865 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
53613776 TGTAATTGTA
53613786 AATCAACCAGCTATTTGGAGTTGCGATTGTAAATCAACT
1 AATCAACCAGCTATTTGGAGTTGCGATTGTAAATCAACT
** *
53613825 AATCAATGAGCTGTTTGGAGTTGCGATTGTAAATCAACT
1 AATCAACCAGCTATTTGGAGTTGCGATTGTAAATCAACT
53613864 AA
1 AA
53613866 CTTAGAAGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (39 bp):
AATCAACCAGCTATTTGGAGTTGCGATTGTAAATCAACT
Found at i:53613941 original size:94 final size:94
Alignment explanation
Indices: 53613832--53614017 Score: 282
Period size: 94 Copynumber: 2.0 Consensus size: 94
53613822 ACTAATCAAT
* * * * *
53613832 GAGCTGTTTGGAGTTGCGATTGTAAATCAACTAACTTAGAAGAAATTGTTCATGATCGTAAATCA
1 GAGCTATTTGGAGTTGAGATCGTAAATCAACTAACTCAGAAGAAATTGTTCATGATCATAAATCA
*
53613897 ATGAACTTAGGTTATGATCGTAAATCAGC
66 ATGAACTCAGGTTATGATCGTAAATCAGC
* * *
53613926 GAGCTATTTGGAGTTGAGATCGTAAATCAGCTAACTCAGAATAAATTGTTCATGATTATAAATCA
1 GAGCTATTTGGAGTTGAGATCGTAAATCAACTAACTCAGAAGAAATTGTTCATGATCATAAATCA
*
53613991 ATGAACTCAGGTTGTGATCGTAAATCA
66 ATGAACTCAGGTTATGATCGTAAATCA
53614018 ATGAGCCTTA
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
94 82 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (94 bp):
GAGCTATTTGGAGTTGAGATCGTAAATCAACTAACTCAGAAGAAATTGTTCATGATCATAAATCA
ATGAACTCAGGTTATGATCGTAAATCAGC
Found at i:53614111 original size:130 final size:130
Alignment explanation
Indices: 53613911--53614248 Score: 435
Period size: 130 Copynumber: 2.6 Consensus size: 130
53613901 ACTTAGGTTA
* * * * * *
53613911 TGATCGTAAATCAGCGAGCTATTTGGAGTTGA-GATCGTAAATCAGCTAACTCAGAATAAATTGT
1 TGATCATAAATCAACGAGTTGTTTGGAGTT-ACAATCGTAAATCAGCTAACTCAGAAGAAATTGT
* * *
53613975 TCATGATTATAAATCAATGAACTCAGGTTGTGATCGTAAATCAATGAGCCTTAATAATATCAACC
65 TCATGATTATAAATCAATGAACTCAGGTGGTGATCGTAAATCAATAAGCCTTAAAAATATCAACC
53614040 G
130 G
** * * * *
53614041 TGATTGTAAATCAATGAGTTGTTTGGAGTTACAATTGTAAATCAGCTAACTAAAAAGAAATTGTT
1 TGATCATAAATCAACGAGTTGTTTGGAGTTACAATCGTAAATCAGCTAACTCAGAAGAAATTGTT
* * * *
53614106 CATGATTGTAAATCAATGAACTTAGGTGGTGATCGTAAATCAATAAGCCTTAAAAATATCAGCTG
66 CATGATTATAAATCAATGAACTCAGGTGGTGATCGTAAATCAATAAGCCTTAAAAATATCAACCG
* * * *
53614171 TGATCATAAATCAGCGAGTTGTTTGGAGTTGCGATCGTAAATCAACTAACTCAGAAGAAATTGTT
1 TGATCATAAATCAACGAGTTGTTTGGAGTTACAATCGTAAATCAGCTAACTCAGAAGAAATTGTT
* *
53614236 TATGATCATAAAT
66 CATGATTATAAAT
53614249 TAGTGAGCCT
Statistics
Matches: 177, Mismatches: 30, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
129 1 0.01
130 176 0.99
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (130 bp):
TGATCATAAATCAACGAGTTGTTTGGAGTTACAATCGTAAATCAGCTAACTCAGAAGAAATTGTT
CATGATTATAAATCAATGAACTCAGGTGGTGATCGTAAATCAATAAGCCTTAAAAATATCAACCG
Found at i:53614724 original size:63 final size:63
Alignment explanation
Indices: 53614625--53614751 Score: 236
Period size: 63 Copynumber: 2.0 Consensus size: 63
53614615 TCTTGTAGGG
* *
53614625 CCCTTCCTAATTGGGATCCATCTTTCCTTGCTGCGATGTTGGTAAATTGGCTTTAATATTCCT
1 CCCTTCCCAATTGGGATCCATCTTTCCTTGCTGCGATGTTGGTAAATTGGCTTCAATATTCCT
53614688 CCCTTCCCAATTGGGATCCATCTTTCCTTGCTGCGATGTTGGTAAATTGGCTTCAATATTCCT
1 CCCTTCCCAATTGGGATCCATCTTTCCTTGCTGCGATGTTGGTAAATTGGCTTCAATATTCCT
53614751 C
1 C
53614752 AAGACTAGAC
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.39
Consensus pattern (63 bp):
CCCTTCCCAATTGGGATCCATCTTTCCTTGCTGCGATGTTGGTAAATTGGCTTCAATATTCCT
Found at i:53639758 original size:15 final size:17
Alignment explanation
Indices: 53639737--53639777 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
53639727 TAATTTTTTA
53639737 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
53639753 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
53639769 AAAATTATA
1 AAAATTATA
53639778 TTTTTACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:53639806 original size:23 final size:22
Alignment explanation
Indices: 53639767--53639811 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
53639757 TATTAAAATA
* * *
53639767 ATAAAATTATATTTTTACTTTC
1 ATAAAAATATATATTTAATTTC
53639789 ATAAAAATATATAATTTAATTTC
1 ATAAAAATATAT-ATTTAATTTC
53639812 GACCTTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAAAAATATATATTTAATTTC
Found at i:53640443 original size:13 final size:13
Alignment explanation
Indices: 53640425--53640450 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53640415 AATTAATGTT
53640425 TTGATAGGGATAA
1 TTGATAGGGATAA
53640438 TTGATAGGGATAA
1 TTGATAGGGATAA
53640451 GTTTTCAGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
TTGATAGGGATAA
Found at i:53643093 original size:48 final size:49
Alignment explanation
Indices: 53643041--53643133 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
53643031 TTGTTTGAAC
*
53643041 ATTTGTGTTTGATATGCAAA-AAATGGAGAAAGTTAAATTTATATAAAA
1 ATTTGTGTTTAATATGCAAATAAATGGAGAAAGTTAAATTTATATAAAA
53643089 ATTTGTGTTTAATATGCAAATAAATGGAGAAAGTTAAATTTATAT
1 ATTTGTGTTTAATATGCAAATAAATGGAGAAAGTTAAATTTATAT
53643134 CTACTTCCAT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 19 0.44
49 24 0.56
ACGTcount: A:0.44, C:0.02, G:0.16, T:0.38
Consensus pattern (49 bp):
ATTTGTGTTTAATATGCAAATAAATGGAGAAAGTTAAATTTATATAAAA
Found at i:53652669 original size:5 final size:5
Alignment explanation
Indices: 53652659--53652688 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
53652649 CTATTGTGAA
*
53652659 TTGTG TTGTG TTGTG TTGTG TTATG TTGTG
1 TTGTG TTGTG TTGTG TTGTG TTGTG TTGTG
53652689 GGAATGATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.03, C:0.00, G:0.37, T:0.60
Consensus pattern (5 bp):
TTGTG
Found at i:53655353 original size:27 final size:27
Alignment explanation
Indices: 53655311--53655442 Score: 173
Period size: 27 Copynumber: 4.9 Consensus size: 27
53655301 GTCACTAGAC
53655311 ACAGATAT-TGTGGCAGAGCCACCAGA
1 ACAGATATATGTGGCAGAGCCACCAGA
53655337 ACAGATATATGTGGCAGAGCCACCAGA
1 ACAGATATATGTGGCAGAGCCACCAGA
* * *
53655364 TCAGATA-ATTGTGGCATAGCCACCAGG
1 ACAGATATA-TGTGGCAGAGCCACCAGA
53655391 ACAGATATATGTGGCAGAGCCACCA-A
1 ACAGATATATGTGGCAGAGCCACCAGA
*
53655417 ATCAGATA-ATTGTGGCATAGCCACCA
1 A-CAGATATA-TGTGGCAGAGCCACCA
53655443 AGACGCTTCC
Statistics
Matches: 94, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
26 11 0.12
27 82 0.87
28 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (27 bp):
ACAGATATATGTGGCAGAGCCACCAGA
Found at i:53655385 original size:54 final size:54
Alignment explanation
Indices: 53655312--53655442 Score: 228
Period size: 54 Copynumber: 2.4 Consensus size: 54
53655302 TCACTAGACA
* *
53655312 CAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGCCACCAGAT
1 CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGCCACCAAAT
*
53655365 CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGCCACCAAAT
1 CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGCCACCAAAT
53655419 CAGATAATTGTGGCATAGCCACCA
1 CAGATAATTGTGGCATAGCCACCA
53655443 AGACGCTTCC
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 5 0.07
54 69 0.93
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.18
Consensus pattern (54 bp):
CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGCCACCAAAT
Found at i:53655849 original size:8 final size:8
Alignment explanation
Indices: 53655833--53655862 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
53655823 CTCAAAATAC
53655833 CGGCTTTT
1 CGGCTTTT
*
53655841 CGGCATTT
1 CGGCTTTT
53655849 CGGCTTTT
1 CGGCTTTT
53655857 CGGCTT
1 CGGCTT
53655863 GTGCCGATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.03, C:0.27, G:0.27, T:0.43
Consensus pattern (8 bp):
CGGCTTTT
Found at i:53657076 original size:26 final size:26
Alignment explanation
Indices: 53657046--53657120 Score: 141
Period size: 26 Copynumber: 2.9 Consensus size: 26
53657036 CCCATGATGG
53657046 AACATTTACCTAACCCATTATCATGA
1 AACATTTACCTAACCCATTATCATGA
*
53657072 AACATTTACCTAACCCATTATCATGG
1 AACATTTACCTAACCCATTATCATGA
53657098 AACATTTACCTAACCCATTATCA
1 AACATTTACCTAACCCATTATCA
53657121 ATTTGTACCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.31
Consensus pattern (26 bp):
AACATTTACCTAACCCATTATCATGA
Found at i:53670543 original size:17 final size:17
Alignment explanation
Indices: 53670523--53670569 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
53670513 TTTTACCCAT
*
53670523 TAAATTCTTTTAATTCA
1 TAAATTCTTCTAATTCA
*
53670540 TAAAATTC-ACTAATTCA
1 T-AAATTCTTCTAATTCA
53670557 -AAATTCTTCTAAT
1 TAAATTCTTCTAAT
53670570 GTCTTAGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 6 0.24
16 5 0.20
17 8 0.32
18 6 0.24
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATTCTTCTAATTCA
Found at i:53671067 original size:32 final size:32
Alignment explanation
Indices: 53671026--53671089 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
53671016 AAGCTTTAGG
53671026 GCCATTTATAACCTTGGAAACAAGAAATTGAC
1 GCCATTTATAACCTTGGAAACAAGAAATTGAC
*
53671058 GCCATTTATAACGTTGGAAACAAGAAATTGAC
1 GCCATTTATAACCTTGGAAACAAGAAATTGAC
53671090 TCTTACACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (32 bp):
GCCATTTATAACCTTGGAAACAAGAAATTGAC
Found at i:53673830 original size:80 final size:79
Alignment explanation
Indices: 53673697--53673903 Score: 335
Period size: 80 Copynumber: 2.6 Consensus size: 79
53673687 TGAATGATAT
*
53673697 CCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
*
53673762 TGCGAGTTGCTATAC
66 TGCGAG-TGATATAC
*
53673777 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
*
53673842 TGCGAGTGATATAT
66 TGCGAGTGATATAC
* * *
53673856 CCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGATTATATCC-GGCTAA
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAA
53673904 ATTCCGAAGA
Statistics
Matches: 119, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
78 6 0.05
79 44 0.37
80 69 0.58
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (79 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
TGCGAGTGATATAC
Found at i:53673912 original size:39 final size:40
Alignment explanation
Indices: 53673693--53673903 Score: 293
Period size: 40 Copynumber: 5.3 Consensus size: 40
53673683 CATTTGAATG
* *
53673693 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
53673733 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
53673773 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
53673813 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
*
53673852 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
53673892 ATATCC-GGCTAA
1 ATATCCGGGCTAA
53673904 ATTCCGAAGA
Statistics
Matches: 149, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
39 44 0.30
40 103 0.69
41 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:53681798 original size:40 final size:40
Alignment explanation
Indices: 53681740--53681950 Score: 273
Period size: 40 Copynumber: 5.3 Consensus size: 40
53681730 ATTTGAATGA
*
53681740 TATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTT
* * * * *
53681780 TATCCGGGCTAAGACCCGAAGGCATTTGTACGAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TGATTT
* * *
53681820 TACCCGGGTTAAGACCCGAAGGCAGTTGTGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTT
*
53681860 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTT
* * * *
53681900 TATACGGGCTAAGACCCGAAGGCATTTGTGCTTGTGATTA
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTT
53681940 TATCC-GGCTAA
1 TATCCGGGCTAA
53681951 ATTCCGAAGA
Statistics
Matches: 148, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
39 8 0.05
40 138 0.93
41 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.28
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTT
Found at i:53696813 original size:14 final size:14
Alignment explanation
Indices: 53696794--53696823 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53696784 TATTTTCAAG
53696794 ATAGATTAACGCAT
1 ATAGATTAACGCAT
*
53696808 ATAGATTCACGCAT
1 ATAGATTAACGCAT
53696822 AT
1 AT
53696824 TTATAAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (14 bp):
ATAGATTAACGCAT
Found at i:53705225 original size:21 final size:20
Alignment explanation
Indices: 53705196--53705250 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
53705186 AAAAACACTT
53705196 TAAC-TGATTGAAGAAAAGTC
1 TAACTTGATTGAA-AAAAGTC
** *
53705216 TAACTTGATTGAAACCATTC
1 TAACTTGATTGAAAAAAGTC
*
53705236 TAACTTGATTTAAAA
1 TAACTTGATTGAAAA
53705251 GTTGACTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 21 0.72
21 8 0.28
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
TAACTTGATTGAAAAAAGTC
Found at i:53708218 original size:10 final size:10
Alignment explanation
Indices: 53708203--53708233 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
53708193 TAAATAAAAC
53708203 ATAACATAAA
1 ATAACATAAA
53708213 ATAACATAAA
1 ATAACATAAA
*
53708223 ATAAAATAAA
1 ATAACATAAA
53708233 A
1 A
53708234 CAAAGTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (10 bp):
ATAACATAAA
Found at i:53708220 original size:15 final size:15
Alignment explanation
Indices: 53708200--53708231 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
53708190 AATTAAATAA
*
53708200 AACATAACATAAAAT
1 AACATAAAATAAAAT
53708215 AACATAAAATAAAAT
1 AACATAAAATAAAAT
53708230 AA
1 AA
53708232 AACAAAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (15 bp):
AACATAAAATAAAAT
Found at i:53709078 original size:12 final size:14
Alignment explanation
Indices: 53709061--53709093 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
53709051 TAAAGAAATA
53709061 ATAAATTG-AT-TG
1 ATAAATTGAATATG
53709073 ATAAATTGAATATG
1 ATAAATTGAATATG
53709087 ATAAATT
1 ATAAATT
53709094 ACAATTTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 2 0.11
14 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (14 bp):
ATAAATTGAATATG
Found at i:53709759 original size:34 final size:34
Alignment explanation
Indices: 53709679--53709759 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
53709669 TTATAGTTTT
* * *
53709679 AATATTGGTGTGAAAGTCAATGATATATTTTAAG
1 AATATTGGTATGGAACTCAATGATATATTTTAAG
* * * *
53709713 CATATTGTTATGGAACTCAATGGTATGTTTTAAG
1 AATATTGGTATGGAACTCAATGATATATTTTAAG
53709747 AATATTGGTATGG
1 AATATTGGTATGG
53709760 TGATAGAAAG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.33, C:0.05, G:0.22, T:0.40
Consensus pattern (34 bp):
AATATTGGTATGGAACTCAATGATATATTTTAAG
Found at i:53718117 original size:26 final size:26
Alignment explanation
Indices: 53718081--53718191 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
53718071 AGCCTGGCTG
* * *
53718081 CCAGAATAGATAATGTGACAAAGTCA
1 CCAGAATAGATAATGTGGCAGAGCCA
53718107 CCAGAATAGATAATCGTGGCAGAGCCA
1 CCAGAATAGATAAT-GTGGCAGAGCCA
*
53718134 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAATAGATA-ATGTGGCAGAGCCA
*
53718161 CCAG-ATCAGATAATTGTGGCATAGCCA
1 CCAGAAT-AGATAA-TGTGGCAGAGCCA
53718188 CCAG
1 CCAG
53718192 GACGCTTCCT
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 16 0.21
27 57 0.76
28 2 0.03
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAATAGATAATGTGGCAGAGCCA
Found at i:53719635 original size:24 final size:24
Alignment explanation
Indices: 53719608--53719678 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
53719598 CTAGATTTTC
**
53719608 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
53719632 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
53719656 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
53719679 CTCCTGACAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.25, C:0.38, G:0.01, T:0.35
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:53721775 original size:19 final size:18
Alignment explanation
Indices: 53721751--53721786 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
53721741 TGATATATTT
53721751 TATTAATAAATAAAGTAAA
1 TATTAATAAAT-AAGTAAA
*
53721770 TATTAATTAATAAGTAA
1 TATTAATAAATAAGTAA
53721787 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (18 bp):
TATTAATAAATAAGTAAA
Found at i:53722706 original size:38 final size:38
Alignment explanation
Indices: 53722654--53722733 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
53722644 TTTAATAAGT
* ** *
53722654 ATATGGATACATGAAATGGACCATGATTTGGATTAATG
1 ATATAGATACATGAAATAAACCATGATTTAGATTAATG
*
53722692 ATATAGATATATGAAATAAACCATGATTTAGATTAATG
1 ATATAGATACATGAAATAAACCATGATTTAGATTAATG
53722730 ATAT
1 ATAT
53722734 GGATTATAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.34
Consensus pattern (38 bp):
ATATAGATACATGAAATAAACCATGATTTAGATTAATG
Found at i:53726056 original size:20 final size:21
Alignment explanation
Indices: 53726018--53726056 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53726008 TTATTTTATG
53726018 TTTTAACCTTTATTATAACTA
1 TTTTAACCTTTATTATAACTA
*
53726039 TTTTAACTTTTATT-TAAC
1 TTTTAACCTTTATTATAAC
53726057 ACATAAACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTAACCTTTATTATAACTA
Found at i:53735745 original size:42 final size:42
Alignment explanation
Indices: 53735685--53735796 Score: 170
Period size: 42 Copynumber: 2.7 Consensus size: 42
53735675 AATGCAGGGG
* ** *
53735685 ACACACGGCCAATCCACATGCCCATGTGCTAGGCCGTGTGTC
1 ACACACGGTCAAGACACATGCCCGTGTGCTAGGCCGTGTGTC
* *
53735727 ACACACGGTCAAGACACATGCCTGTGTGCTAGGTCGTGTGTC
1 ACACACGGTCAAGACACATGCCCGTGTGCTAGGCCGTGTGTC
53735769 ACACACGGTCAAGACACATGCCCGTGTG
1 ACACACGGTCAAGACACATGCCCGTGTG
53735797 TCTACCCATG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.20
Consensus pattern (42 bp):
ACACACGGTCAAGACACATGCCCGTGTGCTAGGCCGTGTGTC
Found at i:53741940 original size:31 final size:31
Alignment explanation
Indices: 53741897--53741958 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
53741887 GCTCGATCAC
53741897 TCAAAGAATACCCGTCCGGGCTAGATCCTTT
1 TCAAAGAATACCCGTCCGGGCTAGATCCTTT
*
53741928 TCAAGGAATACCCGTCCGGGCTAGATCCTTT
1 TCAAAGAATACCCGTCCGGGCTAGATCCTTT
53741959 CTATATTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (31 bp):
TCAAAGAATACCCGTCCGGGCTAGATCCTTT
Found at i:53744775 original size:35 final size:35
Alignment explanation
Indices: 53744729--53744837 Score: 200
Period size: 35 Copynumber: 3.1 Consensus size: 35
53744719 GCTCAGGGCT
*
53744729 TTAACATAATAAAATTTTTATTTTAATATAAAAGG
1 TTAACATAATAAAATTTTTATTTTAATACAAAAGG
53744764 TTAACATAATAAAATTTTTATTTTAATACAAAAGG
1 TTAACATAATAAAATTTTTATTTTAATACAAAAGG
*
53744799 TTAACATAATAAAATTTTTATTTTAATACAAGAGG
1 TTAACATAATAAAATTTTTATTTTAATACAAAAGG
53744834 TTAA
1 TTAA
53744838 TGTTTATTTT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 72 1.00
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (35 bp):
TTAACATAATAAAATTTTTATTTTAATACAAAAGG
Found at i:53748121 original size:13 final size:13
Alignment explanation
Indices: 53748103--53748127 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53748093 GCCAACCATT
53748103 TATAGATTTTTTC
1 TATAGATTTTTTC
53748116 TATAGATTTTTT
1 TATAGATTTTTT
53748128 TGTTTTAAAT
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:0.24, C:0.04, G:0.08, T:0.64
Consensus pattern (13 bp):
TATAGATTTTTTC
Found at i:53758864 original size:31 final size:31
Alignment explanation
Indices: 53758826--53758907 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 31
53758816 ATGGGGGTAG
* * ** *
53758826 GACACTGTATCTATTCTTATCTGTTTTGCAT
1 GACACTGTATTTATTCTGATCTACTCTGCAT
*
53758857 GACACTGTATTTGTTCTGATCTACTCTGCAT
1 GACACTGTATTTATTCTGATCTACTCTGCAT
53758888 GACACTGTATTTATTCTGAT
1 GACACTGTATTTATTCTGAT
53758908 ATGTTATGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.21, C:0.20, G:0.15, T:0.45
Consensus pattern (31 bp):
GACACTGTATTTATTCTGATCTACTCTGCAT
Found at i:53771866 original size:20 final size:20
Alignment explanation
Indices: 53771841--53771887 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
53771831 CTTCCAGACA
53771841 ACGTCGTGACATGATTTTTC
1 ACGTCGTGACATGATTTTTC
*
53771861 ACGTCGTGACGTGATTTTTC
1 ACGTCGTGACATGATTTTTC
53771881 ACGTCGT
1 ACGTCGT
53771888 CTCGGCATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
ACGTCGTGACATGATTTTTC
Found at i:53780020 original size:27 final size:26
Alignment explanation
Indices: 53779990--53780069 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 26
53779980 GCACATAATT
53779990 AGGAAGCACTC-TCTCGAGCCATATAAC
1 AGGAAGC-CTCATCT-GAGCCATATAAC
* *
53780017 AGGAAG-CTCATGTGAGCCATATAAT
1 AGGAAGCCTCATCTGAGCCATATAAC
* *
53780042 AGGAAG-CTTATCCGAG-C-TATAAC
1 AGGAAGCCTCATCTGAGCCATATAAC
53780065 AGGAA
1 AGGAA
53780070 ACTTATAAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
23 10 0.22
24 1 0.02
25 27 0.59
26 2 0.04
27 6 0.13
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (26 bp):
AGGAAGCCTCATCTGAGCCATATAAC
Found at i:53780068 original size:23 final size:25
Alignment explanation
Indices: 53780004--53780075 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 25
53779994 AGCACTCTCT
* *
53780004 CGAGCCATATAACAGGAAGCTCATG
1 CGAGCCATATAACAGGAAGCTTATC
* *
53780029 TGAGCCATATAATAGGAAGCTTATC
1 CGAGCCATATAACAGGAAGCTTATC
*
53780054 CGAG-C-TATAACAGGAAACTTAT
1 CGAGCCATATAACAGGAAGCTTAT
53780076 AAGAGTTTAG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
23 15 0.38
24 1 0.03
25 24 0.60
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (25 bp):
CGAGCCATATAACAGGAAGCTTATC
Found at i:53783464 original size:56 final size:56
Alignment explanation
Indices: 53783397--53783509 Score: 190
Period size: 56 Copynumber: 2.0 Consensus size: 56
53783387 TTATTTACTC
* *
53783397 TAACTTCCAGAAGAATGATGACATAAACATTTATCAAATCTCTGCAAGTGATCATT
1 TAACTTCCAGAAGAATAATGACATAAACATTTACCAAATCTCTGCAAGTGATCATT
* *
53783453 TAACTTCCAGAAGAATAATGATATAAACATTTACCAAATCTCTTCAAGTGATCATT
1 TAACTTCCAGAAGAATAATGACATAAACATTTACCAAATCTCTGCAAGTGATCATT
53783509 T
1 T
53783510 GAAAAACTAG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.32
Consensus pattern (56 bp):
TAACTTCCAGAAGAATAATGACATAAACATTTACCAAATCTCTGCAAGTGATCATT
Found at i:53788504 original size:60 final size:54
Alignment explanation
Indices: 53788386--53788493 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
53788376 AAATTAACCA
* *
53788386 TGATAATGTATGATTATCATGATTTTGATTATTACATTATCTTTAAATAAAATT
1 TGATAATGTATGATTATCATGATTTTGATTATTAAATTATCTTTAAAGAAAATT
*
53788440 TGATAATGTATGGTTATCATGATTTTGATTATTAAATTATCTTTAAAGAAAATT
1 TGATAATGTATGATTATCATGATTTTGATTATTAAATTATCTTTAAAGAAAATT
53788494 GAACTGTGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (54 bp):
TGATAATGTATGATTATCATGATTTTGATTATTAAATTATCTTTAAAGAAAATT
Found at i:53790455 original size:27 final size:27
Alignment explanation
Indices: 53790422--53790477 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
53790412 CTTTGGAAAA
53790422 ATTACAATTTTTCCCCTAAACTTTTGC
1 ATTACAATTTTTCCCCTAAACTTTTGC
53790449 ATTACAATTTTTCCCCTAAACTTTTGC
1 ATTACAATTTTTCCCCTAAACTTTTGC
53790476 AT
1 AT
53790478 ATTTACACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.27, C:0.25, G:0.04, T:0.45
Consensus pattern (27 bp):
ATTACAATTTTTCCCCTAAACTTTTGC
Found at i:53794015 original size:22 final size:22
Alignment explanation
Indices: 53793958--53794005 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
53793948 TCACTTGCCG
53793958 AGAAACACCTTCATATTGTAAT
1 AGAAACACCTTCATATTGTAAT
53793980 AGAAACACCTTCATATTGTAAT
1 AGAAACACCTTCATATTGTAAT
53794002 AGAA
1 AGAA
53794006 TTTCTTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (22 bp):
AGAAACACCTTCATATTGTAAT
Found at i:53797520 original size:15 final size:15
Alignment explanation
Indices: 53797500--53797529 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
53797490 TAAAGCCTCC
53797500 TTTTAAACAATCATT
1 TTTTAAACAATCATT
53797515 TTTTAAACAATCATT
1 TTTTAAACAATCATT
53797530 GTTTCTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTTAAACAATCATT
Found at i:53820016 original size:19 final size:19
Alignment explanation
Indices: 53819994--53820032 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
53819984 ATTTTGCTAA
*
53819994 TTTTAGATTTTTATATATT
1 TTTTAGAATTTTATATATT
* *
53820013 TTTTTGAATTTTCTATATT
1 TTTTAGAATTTTATATATT
53820032 T
1 T
53820033 ATAAATTGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTTAGAATTTTATATATT
Found at i:53820022 original size:27 final size:28
Alignment explanation
Indices: 53819992--53820065 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 28
53819982 TAATTTTGCT
53819992 AATTTTAGATTTTTATATATT-TTTTTG
1 AATTTTAGATTTTTATATATTGTTTTTG
** * * *
53820019 AATTTTCTATATTTATAAATTGTTTTTT
1 AATTTTAGATTTTTATATATTGTTTTTG
*
53820047 ATTTTTATGATTTTTATAT
1 AATTTTA-GATTTTTATAT
53820066 TTATAAAAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
27 17 0.49
28 10 0.29
29 8 0.23
ACGTcount: A:0.27, C:0.01, G:0.05, T:0.66
Consensus pattern (28 bp):
AATTTTAGATTTTTATATATTGTTTTTG
Found at i:53820050 original size:37 final size:37
Alignment explanation
Indices: 53819975--53820072 Score: 107
Period size: 36 Copynumber: 2.7 Consensus size: 37
53819965 ACATCATAAT
* *
53819975 TTTTTTTTAATTTTGCTA-ATTT-TAGATTTTTATATA
1 TTTTTTTGAATTTT-CTATATTTATAAATTTTTATATA
*
53820011 TTTTTTTGAATTTTCTATATTTATAAATTGTTT-TTTA
1 TTTTTTTGAATTTTCTATATTTATAAATT-TTTATATA
*
53820048 TTTTTATG-ATTTT-TATATTTATAAA
1 TTTTTTTGAATTTTCTATATTTATAAA
53820073 AAAATTAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
35 15 0.27
36 22 0.40
37 15 0.27
38 3 0.05
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (37 bp):
TTTTTTTGAATTTTCTATATTTATAAATTTTTATATA
Found at i:53821118 original size:11 final size:11
Alignment explanation
Indices: 53821102--53821127 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
53821092 TTAAAATATG
53821102 ATAAACAAATA
1 ATAAACAAATA
53821113 ATAAACAAATA
1 ATAAACAAATA
53821124 ATAA
1 ATAA
53821128 TAAAAACAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (11 bp):
ATAAACAAATA
Found at i:53828106 original size:3 final size:3
Alignment explanation
Indices: 53828098--53828136 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
53828088 TCCTGTTACC
53828098 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
53828137 TCCAATTTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:53838911 original size:20 final size:19
Alignment explanation
Indices: 53838888--53838929 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
53838878 AATAAATTTT
*
53838888 AAATTATTTTAAATATAATA
1 AAATAATTTT-AATATAATA
*
53838908 AAATAATTTTTATATAATA
1 AAATAATTTTAATATAATA
53838927 AAA
1 AAA
53838930 AATAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATAATTTTAATATAATA
Found at i:53838933 original size:26 final size:27
Alignment explanation
Indices: 53838898--53838973 Score: 95
Period size: 26 Copynumber: 2.9 Consensus size: 27
53838888 AAATTATTTT
*
53838898 AAATATAATAAAA-TAATTTTTATATA
1 AAATAAAATAAAATTAATTTTTATATA
*
53838924 ATAA-AAAATAAAATTAA-TTATATATA
1 A-AATAAAATAAAATTAATTTTTATATA
53838950 AAATAAAATAAAAATTAATTTTTA
1 AAATAAAAT-AAAATTAATTTTTA
53838974 AACATTCATT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
25 2 0.05
26 23 0.55
27 13 0.31
28 4 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
AAATAAAATAAAATTAATTTTTATATA
Found at i:53838957 original size:27 final size:26
Alignment explanation
Indices: 53838904--53838970 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
53838894 TTTTAAATAT
* *
53838904 AATAAAA-TAATTTTTATATAATAAAA
1 AATAAAATTAATTTATATAAAAT-AAA
53838930 AATAAAATTAATTATATATAAAAT-AA
1 AATAAAATTAATT-TATATAAAATAAA
53838956 AATAAAAATTAATTT
1 AAT-AAAATTAATTT
53838971 TTAAACATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
26 13 0.36
27 15 0.42
28 8 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
AATAAAATTAATTTATATAAAATAAA
Found at i:53839266 original size:13 final size:14
Alignment explanation
Indices: 53839250--53839278 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
53839240 ATTTTAGTCA
53839250 TTAATTTA-ATTTT
1 TTAATTTATATTTT
53839263 TTAATTTATATTTT
1 TTAATTTATATTTT
53839277 TT
1 TT
53839279 GTCAAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTAATTTATATTTT
Found at i:53839925 original size:35 final size:35
Alignment explanation
Indices: 53839868--53839935 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
53839858 AAAGCCTACT
* * *
53839868 GAATCTTAATTTGATTAATATTAGTATAATTGTCA
1 GAATCTTAACTTAATTAATATTAGCATAATTGTCA
**
53839903 GAATCTTAACTTAATTTGTATTAGCATAATTGT
1 GAATCTTAACTTAATTAATATTAGCATAATTGT
53839936 TAATATAAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (35 bp):
GAATCTTAACTTAATTAATATTAGCATAATTGTCA
Found at i:53840871 original size:15 final size:16
Alignment explanation
Indices: 53840851--53840880 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
53840841 TGATTTTTCT
53840851 AAAAAAGAAA-TAAAA
1 AAAAAAGAAACTAAAA
53840866 AAAAAAGAAACTAAA
1 AAAAAAGAAACTAAA
53840881 CAATTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.83, C:0.03, G:0.07, T:0.07
Consensus pattern (16 bp):
AAAAAAGAAACTAAAA
Found at i:53846079 original size:30 final size:30
Alignment explanation
Indices: 53846043--53846102 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
53846033 AATAATCTTC
53846043 TAATTAAACTCTGTTTATTTGTTTCAATCA
1 TAATTAAACTCTGTTTATTTGTTTCAATCA
53846073 TAATTAAACTCTGTTTATTTGTTTCAATCA
1 TAATTAAACTCTGTTTATTTGTTTCAATCA
53846103 AACTCTGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (30 bp):
TAATTAAACTCTGTTTATTTGTTTCAATCA
Found at i:53853892 original size:14 final size:15
Alignment explanation
Indices: 53853875--53853908 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
53853865 TTAAATGCTG
53853875 AAAAAA-TAAATATT
1 AAAAAAGTAAATATT
*
53853889 AAAAAAGTAAGTATT
1 AAAAAAGTAAATATT
53853904 AAAAA
1 AAAAA
53853909 TTTAAAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (15 bp):
AAAAAAGTAAATATT
Found at i:53856579 original size:37 final size:37
Alignment explanation
Indices: 53856526--53856612 Score: 147
Period size: 37 Copynumber: 2.4 Consensus size: 37
53856516 GTTTATTTCC
*
53856526 TAAAATAAAATCTTTAAAAGATAATATAATATTAAAA
1 TAAAATAAAATTTTTAAAAGATAATATAATATTAAAA
* *
53856563 TAAAATAAAATTTTTAAAAGATAATATTATTTTAAAA
1 TAAAATAAAATTTTTAAAAGATAATATAATATTAAAA
53856600 TAAAATAAAATTT
1 TAAAATAAAATTT
53856613 GAAAAAAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (37 bp):
TAAAATAAAATTTTTAAAAGATAATATAATATTAAAA
Found at i:53856586 original size:16 final size:16
Alignment explanation
Indices: 53856564--53856605 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
53856554 ATATTAAAAT
53856564 AAAATAAAATT-TTTA
1 AAAATAAAATTATTTA
* *
53856579 AAAGATAATATTATTTT
1 AAA-ATAAAATTATTTA
53856596 AAAATAAAAT
1 AAAATAAAAT
53856606 AAAATTTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 3 0.14
16 13 0.59
17 6 0.27
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
AAAATAAAATTATTTA
Found at i:53856606 original size:18 final size:18
Alignment explanation
Indices: 53856527--53856622 Score: 77
Period size: 18 Copynumber: 5.3 Consensus size: 18
53856517 TTTATTTCCT
*
53856527 AAAATAAAATCTTTAAAAG
1 AAAATATAAT-TTTAAAAG
* * *
53856546 ATAATATAATATTAAAAT
1 AAAATATAATTTTAAAAG
*
53856564 AAAATAAAATTTTTAAAAG
1 AAAATATAA-TTTTAAAAG
* * *
53856583 ATAATATTATTTTAAAAT
1 AAAATATAATTTTAAAAG
* *
53856601 AAAATAAAATTTGAAAA-
1 AAAATATAATTTTAAAAG
53856618 AAAAT
1 AAAAT
53856623 CTGCATGTAA
Statistics
Matches: 60, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
17 5 0.08
18 34 0.57
19 21 0.35
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (18 bp):
AAAATATAATTTTAAAAG
Found at i:53860812 original size:5 final size:5
Alignment explanation
Indices: 53860801--53860862 Score: 74
Period size: 5 Copynumber: 12.6 Consensus size: 5
53860791 AAATAGAAAG
* * *
53860801 ATTTT GTTTT GTTTT ATTTT ATTTT ATTTT -TATT A-TTT ATATTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT-TTT ATTTT
53860850 ATTTT ATTTT ATT
1 ATTTT ATTTT ATT
53860863 AATTTAGGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
4 6 0.12
5 39 0.78
6 5 0.10
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:53860846 original size:29 final size:29
Alignment explanation
Indices: 53860813--53860868 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
53860803 TTTGTTTTGT
53860813 TTTATTTTATTTTATTTTTATT-ATTTATA
1 TTTATTTTATTTTA-TTTTATTAATTTATA
53860842 TTTATTTTATTTTATTTTATTAATTTA
1 TTTATTTTATTTTATTTTATTAATTTA
53860869 GGTTAGGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (29 bp):
TTTATTTTATTTTATTTTATTAATTTATA
Found at i:53861721 original size:16 final size:16
Alignment explanation
Indices: 53861700--53861751 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
53861690 AAATCCCAAT
53861700 TTAATTTTTTATTTAG
1 TTAATTTTTTATTTAG
*
53861716 TTAATTATTTATCTTAG
1 TTAATTTTTTAT-TTAG
*
53861733 -CAATTTTAATTATTTAG
1 TTAATTTT--TTATTTAG
53861750 TT
1 TT
53861752 TCTACTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
16 16 0.57
17 8 0.29
18 4 0.14
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.62
Consensus pattern (16 bp):
TTAATTTTTTATTTAG
Found at i:53864424 original size:16 final size:14
Alignment explanation
Indices: 53864397--53864430 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
53864387 TTAGTACTTA
53864397 TTTTTTTCTTCTTT
1 TTTTTTTCTTCTTT
53864411 TTTTTTTCTT-TTCT
1 TTTTTTTCTTCTT-T
53864425 TTTTTT
1 TTTTTT
53864431 AAATTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 17 0.89
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTCTTCTTT
Found at i:53864718 original size:118 final size:118
Alignment explanation
Indices: 53864556--53864789 Score: 380
Period size: 118 Copynumber: 2.0 Consensus size: 118
53864546 TATTTCCGGT
* *
53864556 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
1 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTAACACGAAGTAGAATGACAACCCAAGCAC
*
53864621 CCTACCCC-AGTTACTCAGTCAGTCACGATTTGAGCCATACTCATAACCTCGGC
66 CCTACCCCGA-TTACTCAGTCAGTCACAATTTGAGCCATACTCATAACCTCGGC
**** *
53864674 TAGCGGAGTTTTACTTGTCACGTTACACAACCTTTTAACACGAAGTAGAATGACAACCCAAGCAC
1 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTAACACGAAGTAGAATGACAACCCAAGCAC
53864739 CCTACCCCGATTACTCAGTCAGTCACAATTTGAGCCATACTCATAACCTCG
66 CCTACCCCGATTACTCAGTCAGTCACAATTTGAGCCATACTCATAACCTCG
53864790 AAAAACATTT
Statistics
Matches: 107, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
118 106 0.99
119 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (118 bp):
TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTAACACGAAGTAGAATGACAACCCAAGCAC
CCTACCCCGATTACTCAGTCAGTCACAATTTGAGCCATACTCATAACCTCGGC
Found at i:53865633 original size:42 final size:42
Alignment explanation
Indices: 53865568--53865690 Score: 140
Period size: 42 Copynumber: 2.9 Consensus size: 42
53865558 GGTTTTGGGG
* * *
53865568 ATTCTAAGGCTGAAATAGGACTGTTTGGCTGCA-GAGATATAGC
1 ATTCT-AGGCTGGAATAGAACTGTTTGGCAGCATG-GATATAGC
* *
53865611 ATTCTGGGCTGGAATAGAACTGTTTGGCAGCATGGATATGGC
1 ATTCTAGGCTGGAATAGAACTGTTTGGCAGCATGGATATAGC
* * * *
53865653 ATTTTAGGTTGGAATAGAACTGTTTGGTACCATGGATA
1 ATTCTAGGCTGGAATAGAACTGTTTGGCAGCATGGATA
53865691 GGGTTGTTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 63 0.91
43 6 0.09
ACGTcount: A:0.28, C:0.12, G:0.29, T:0.31
Consensus pattern (42 bp):
ATTCTAGGCTGGAATAGAACTGTTTGGCAGCATGGATATAGC
Found at i:53865801 original size:8 final size:8
Alignment explanation
Indices: 53865790--53865844 Score: 94
Period size: 8 Copynumber: 6.9 Consensus size: 8
53865780 ATTTAAATAA
53865790 AATAAAAT
1 AATAAAAT
53865798 AATAAAAT
1 AATAAAAT
53865806 AATAAAAT
1 AATAAAAT
53865814 AATAAAAT
1 AATAAAAT
53865822 AATAAAAT
1 AATAAAAT
53865830 AAT-AAAT
1 AATAAAAT
53865837 AAATAAAA
1 -AATAAAA
53865845 ATAAAAATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
7 4 0.09
8 38 0.84
9 3 0.07
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:53865822 original size:24 final size:24
Alignment explanation
Indices: 53865783--53865844 Score: 99
Period size: 24 Copynumber: 2.5 Consensus size: 24
53865773 TATTAATATT
53865783 TAAATAAAATAAAATAATAAAATAA
1 TAAAT-AAATAAAATAATAAAATAA
53865808 TAAA-ATAATAAAATAATAAAATAA
1 TAAATA-AATAAAATAATAAAATAA
53865832 TAAATAAATAAAA
1 TAAATAAATAAAA
53865845 ATAAAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
23 1 0.03
24 29 0.83
25 5 0.14
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (24 bp):
TAAATAAATAAAATAATAAAATAA
Found at i:53865852 original size:16 final size:16
Alignment explanation
Indices: 53865783--53865855 Score: 89
Period size: 16 Copynumber: 4.5 Consensus size: 16
53865773 TATTAATATT
53865783 TAAATAAAATAAAATAA
1 TAAAT-AAATAAAATAA
53865800 TAAA-ATAATAAAATAA
1 TAAATA-AATAAAATAA
53865816 TAAA-ATAATAAAATAA
1 TAAATA-AATAAAATAA
53865832 TAAATAAATAAAAATAA
1 TAAATAAAT-AAAATAA
53865849 -AAATAAA
1 TAAATAAA
53865856 GATTAGGTTG
Statistics
Matches: 53, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.02
16 40 0.75
17 12 0.23
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
TAAATAAATAAAATAA
Found at i:53873096 original size:6 final size:6
Alignment explanation
Indices: 53873080--53873114 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
53873070 TTTGTTTTGT
53873080 TTTATTA TTTATA TTTATA TTTATA TTTAT- TTTAT
1 TTTA-TA TTTATA TTTATA TTTATA TTTATA TTTAT
53873115 TAATTTAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.18
6 19 0.68
7 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTATA
Found at i:53877850 original size:169 final size:169
Alignment explanation
Indices: 53877557--53877894 Score: 473
Period size: 169 Copynumber: 2.0 Consensus size: 169
53877547 CCTTCAATAG
* * * * *
53877557 TAACCCACAAGACCCAAAAAACTACGGATCTTAAAAATGTTCCTAGGTTGTTTCTAATCAAGTAC
1 TAACCCACAAGACCCAAAAAAATACAGATCTTAAAAAGGTTCCTAGGCTGTTTCTAATCAAGCAC
* * *
53877622 AGCCTCAATCTTTCTAGGATCAACTCAGATCTATTCAGCAAAAACTAAGTACCCTAGAAATGTTA
66 AGCCTCAACCTTTCTAGGATCAACTCAGATCCATTCAGCAAAAACTAAGTACACTAGAAATGTTA
* * * *
53877687 TTTCCTGTAATCATAATTCACATTTGCTCAACTTAGCGT
131 TTTCCCGTAACCAGAATTCACATTTACTCAACTTAGCGT
* * *
53877726 TAACCCGCAAGACCCAAAAAAATGCAGAT-TTCAAAAAGGTTCCTAGGCTGTTTCCT-ATCACGC
1 TAACCCACAAGACCCAAAAAAATACAGATCTT-AAAAAGGTTCCTAGGCTGTTT-CTAATCAAGC
* * * *
53877789 ACGGCCTCAACCTTTCTAGGATCAACTCAGATCCATTCAGTAGAAACTACGTACACTAGAAATGT
64 ACAGCCTCAACCTTTCTAGGATCAACTCAGATCCATTCAGCAAAAACTAAGTACACTAGAAATGT
53877854 TATTTCCCGTAACCAGAATTCACATTTACTCAACTTAGCGT
129 TATTTCCCGTAACCAGAATTCACATTTACTCAACTTAGCGT
53877895 AAAGCTACTT
Statistics
Matches: 148, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
168 2 0.01
169 144 0.97
170 2 0.01
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (169 bp):
TAACCCACAAGACCCAAAAAAATACAGATCTTAAAAAGGTTCCTAGGCTGTTTCTAATCAAGCAC
AGCCTCAACCTTTCTAGGATCAACTCAGATCCATTCAGCAAAAACTAAGTACACTAGAAATGTTA
TTTCCCGTAACCAGAATTCACATTTACTCAACTTAGCGT
Found at i:53878923 original size:27 final size:27
Alignment explanation
Indices: 53878893--53878955 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
53878883 ACGGATTAGT
*
53878893 ACAATAATCTCATCAGAAGTACACTCA
1 ACAATAATCTCACCAGAAGTACACTCA
* *
53878920 ACAATAATCTGACCGGAAGTACACTCA
1 ACAATAATCTCACCAGAAGTACACTCA
53878947 ACAATAATC
1 ACAATAATC
53878956 CCCAAGTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.44, C:0.25, G:0.10, T:0.21
Consensus pattern (27 bp):
ACAATAATCTCACCAGAAGTACACTCA
Found at i:53885457 original size:31 final size:31
Alignment explanation
Indices: 53885419--53885478 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
53885409 TTAAGTGTAA
** *
53885419 AATCAAATAATTACGGTACAAATATATTAAG
1 AATCAAATAATTACAATACAAATAAATTAAG
*
53885450 AATCAAATTATTACAATACAAATAAATTA
1 AATCAAATAATTACAATACAAATAAATTA
53885479 TAAAGTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.30
Consensus pattern (31 bp):
AATCAAATAATTACAATACAAATAAATTAAG
Found at i:53895504 original size:39 final size:39
Alignment explanation
Indices: 53895450--53895561 Score: 161
Period size: 39 Copynumber: 2.8 Consensus size: 39
53895440 ACATGATACT
*
53895450 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTAC
*
53895489 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTATGTAC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTAC
* * * *
53895528 TGGAAATATATCCGGGCTTAAAGTCCCGCAGGCT
1 TGGAAACATATCCGGACTTGAGGT-CCGCAGGCT
53895562 TTTTGCTAGA
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
39 57 0.86
40 9 0.14
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (39 bp):
TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTAC
Found at i:53897062 original size:19 final size:19
Alignment explanation
Indices: 53897038--53897075 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
53897028 TCTTTTGTAT
53897038 ATGATAATACTCTTTAACC
1 ATGATAATACTCTTTAACC
53897057 ATGATAATACTCTTTAACC
1 ATGATAATACTCTTTAACC
53897076 CTCCGGCGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (19 bp):
ATGATAATACTCTTTAACC
Found at i:53898154 original size:117 final size:119
Alignment explanation
Indices: 53897889--53898162 Score: 392
Period size: 121 Copynumber: 2.3 Consensus size: 119
53897879 TAGAAAGGGA
* *
53897889 AAGTATCCAAAGTCCTAACAAAACATAATTATACAATTACAAGTCATGCACATCATCTAATATAG
1 AAGTATCCAAAGTCCTAACAAAACCTAATTATACAATTACAAGTCATGCACATCATCTAAGATAG
* * *
53897954 GTAATGTATCCAAGAAAGGTTCAAAATATAATATTATCAAAGAAAGTTCAAAGAGG
66 GTAATGTA--CAAGAAAAGTTCAAAATATAATACTACCAAAGAAAGTTCAAAGAGG
* * *
53898010 AAGTATCCAAAGTCCTAACAAAACCTAATTATACAATTACAAGTCATGCATATCATCTCAGATTG
1 AAGTATCCAAAGTCCTAACAAAACCTAATTATACAATTACAAGTCATGCACATCATCTAAGATAG
* *
53898075 GTAATGTA-AAGAAAAGTTC-AAATATAATACTACC-ATGAAAAGTTCAAAGATG
66 GTAATGTACAAGAAAAGTTCAAAATATAATACTACCAAAG-AAAGTTCAAAGAGG
* *
53898127 AAGTATTCAAAGTTCTAACAAAACCTAATTATACAA
1 AAGTATCCAAAGTCCTAACAAAACCTAATTATACAA
53898163 AGCCCAAAAA
Statistics
Matches: 140, Mismatches: 12, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
116 2 0.01
117 60 0.43
118 10 0.07
121 68 0.49
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (119 bp):
AAGTATCCAAAGTCCTAACAAAACCTAATTATACAATTACAAGTCATGCACATCATCTAAGATAG
GTAATGTACAAGAAAAGTTCAAAATATAATACTACCAAAGAAAGTTCAAAGAGG
Found at i:53903867 original size:3 final size:3
Alignment explanation
Indices: 53903859--53903901 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
53903849 ACAAATTAAA
* *
53903859 AAT AAT AAT ATT AAT AAT AAT ATT AAT AAT AAT -AT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
53903902 AAAATTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:53903876 original size:12 final size:12
Alignment explanation
Indices: 53903859--53903901 Score: 79
Period size: 12 Copynumber: 3.7 Consensus size: 12
53903849 ACAAATTAAA
53903859 AATAATAATATT
1 AATAATAATATT
53903871 AATAATAATATT
1 AATAATAATATT
53903883 AATAATAATA-T
1 AATAATAATATT
53903894 AATAATAA
1 AATAATAA
53903902 AAAATTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 9 0.29
12 22 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AATAATAATATT
Found at i:53903877 original size:15 final size:15
Alignment explanation
Indices: 53903853--53903897 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
53903843 TGTAAAACAA
*
53903853 ATTAAAAATAATAAT
1 ATTAATAATAATAAT
*
53903868 ATTAATAATAATATT
1 ATTAATAATAATAAT
*
53903883 AATAATAAT-ATAAT
1 ATTAATAATAATAAT
53903897 A
1 A
53903898 ATAAAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTAATAATAATAAT
Found at i:53903961 original size:17 final size:17
Alignment explanation
Indices: 53903932--53903973 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
53903922 TATATAAAAG
53903932 GATATAAATAAATAAAT
1 GATATAAATAAATAAAT
53903949 GATA-AAATAAAATAAAT
1 GATATAAAT-AAATAAAT
53903966 GTATATAA
1 G-ATATAA
53903974 GAAAAAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.18
17 13 0.59
18 3 0.14
19 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (17 bp):
GATATAAATAAATAAAT
Found at i:53904399 original size:13 final size:13
Alignment explanation
Indices: 53904381--53904407 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53904371 TTAAAAGAAG
53904381 ATAAATAAAATAA
1 ATAAATAAAATAA
53904394 ATAAATAAAATAA
1 ATAAATAAAATAA
53904407 A
1 A
53904408 ACAGAACAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
ATAAATAAAATAA
Found at i:53907000 original size:20 final size:21
Alignment explanation
Indices: 53906977--53907015 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
53906967 TGAGATTAAT
*
53906977 GAGGATT-TTTAAAATTTTGA
1 GAGGATTAATTAAAATTTTGA
*
53906997 GAGGCTTAATTAAAATTTT
1 GAGGATTAATTAAAATTTT
53907016 TTAAAATTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.44
Consensus pattern (21 bp):
GAGGATTAATTAAAATTTTGA
Found at i:53907338 original size:21 final size:21
Alignment explanation
Indices: 53907312--53907354 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
53907302 TTTCCAAGTA
53907312 TATTTA-CGGAAATGGACCGAT
1 TATTTACCGGAAA-GGACCGAT
*
53907333 TATTTACCGGAAAGGGCCGAT
1 TATTTACCGGAAAGGACCGAT
53907354 T
1 T
53907355 TTGGCAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (21 bp):
TATTTACCGGAAAGGACCGAT
Found at i:53907632 original size:21 final size:22
Alignment explanation
Indices: 53907608--53907650 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
53907598 GTTTTACTAA
53907608 AATAATCTA-GGTTTAGAGTTT
1 AATAATCTAGGGTTTAGAGTTT
* *
53907629 AATAATTTAGGGTTTAGGGTTT
1 AATAATCTAGGGTTTAGAGTTT
53907651 TCTACAGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.30, C:0.02, G:0.23, T:0.44
Consensus pattern (22 bp):
AATAATCTAGGGTTTAGAGTTT
Found at i:53907873 original size:122 final size:124
Alignment explanation
Indices: 53907648--53907910 Score: 381
Period size: 122 Copynumber: 2.1 Consensus size: 124
53907638 GGGTTTAGGG
*
53907648 TTTTCTACAGTAGTTCCTAAAAAATAATTTTGAGAAGACGTTTTTGAACAAAGAGTGTAAAAAAC
1 TTTTCTACAGTAGTTCCTAAAAAATAA-TTTGAGAAGACGTTTCTGAACAAAGAGTGTAAAAAAC
* * * *
53907713 GCTTTAAGCAGGATGCACTGTCAGCAAAAGTACTGAAAAATA-CTCCCACGTGGACACTAT
65 GCTTAAAGCAGAATCCACTGTCAGCAAAAGTACAGAAAAA-AGCTCCCACGTGGACACTAT
*
53907773 TTTTCTACAGTAGTTCCTAAAAAA-AA-TTGAGAAGACGTTTCTGAACAAATAGTGTAAAAAACG
1 TTTTCTACAGTAGTTCCTAAAAAATAATTTGAGAAGACGTTTCTGAACAAAGAGTGTAAAAAACG
* * * *
53907836 CTTCAAAG-AGAATCCACTGTCAGTAAAATTACAGAAAAAAGCTCCCACGTGGACGCTCT
66 CTT-AAAGCAGAATCCACTGTCAGCAAAAGTACAGAAAAAAGCTCCCACGTGGACACTAT
53907895 TTTTCTACAGTAGTTC
1 TTTTCTACAGTAGTTC
53907911 ATGTTTGGCC
Statistics
Matches: 126, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
121 1 0.01
122 96 0.76
123 3 0.02
124 2 0.02
125 24 0.19
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (124 bp):
TTTTCTACAGTAGTTCCTAAAAAATAATTTGAGAAGACGTTTCTGAACAAAGAGTGTAAAAAACG
CTTAAAGCAGAATCCACTGTCAGCAAAAGTACAGAAAAAAGCTCCCACGTGGACACTAT
Found at i:53911311 original size:27 final size:27
Alignment explanation
Indices: 53911271--53911359 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 27
53911261 CCATCAACGA
*
53911271 TGGT-AATATAATCGGCACACAG-CAC
1 TGGTAAATATGATCGGCACACAGCCAC
* * *
53911296 TGGGTAAATATGATCGACACAGAGTCA-
1 T-GGTAAATATGATCGGCACACAGCCAC
* * *
53911323 TCGATAAATATGATAGGCACATAGCCAC
1 T-GGTAAATATGATCGGCACACAGCCAC
53911351 TGGTAAATA
1 TGGTAAATA
53911360 CGATTTGCAC
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
25 1 0.02
26 3 0.06
27 43 0.86
28 3 0.06
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.22
Consensus pattern (27 bp):
TGGTAAATATGATCGGCACACAGCCAC
Found at i:53911821 original size:27 final size:26
Alignment explanation
Indices: 53911802--53911886 Score: 107
Period size: 27 Copynumber: 3.2 Consensus size: 26
53911792 GGTATTTTAG
*
53911802 TAATTTTACAAATTGAGGGTATTTCGA
1 TAATTTTACAAATCG-GGGTATTTCGA
*
53911829 TAATTTCACAAATCGGAGGTATTTCGA
1 TAATTTTACAAATCGG-GGTATTTCGA
* *
53911856 TAATTTTACAAACCGGGGGTATTTCAA
1 TAATTTTACAAATC-GGGGTATTTCGA
53911883 TAAT
1 TAAT
53911887 CTAAACAGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
26 1 0.02
27 48 0.94
28 2 0.04
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (26 bp):
TAATTTTACAAATCGGGGTATTTCGA
Found at i:53912113 original size:18 final size:18
Alignment explanation
Indices: 53912092--53912127 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
53912082 AAAGTTTGTC
53912092 ACTAATCGAGGATTTTAT
1 ACTAATCGAGGATTTTAT
53912110 ACTAATCGAGGATTTTAT
1 ACTAATCGAGGATTTTAT
53912128 CCGTGCGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (18 bp):
ACTAATCGAGGATTTTAT
Found at i:53913254 original size:24 final size:24
Alignment explanation
Indices: 53913226--53913289 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 24
53913216 CTCATTAAAT
*
53913226 CTCTCCATAAATCACTC-ATTGATT
1 CTCTCCATAAATCACTCTA-TGATA
* *
53913250 TTCTCC-TAATATCTCTCTATGATA
1 CTCTCCATAA-ATCACTCTATGATA
*
53913274 CACTCCATAAATCACT
1 CTCTCCATAAATCACT
53913290 TCAACCTCTC
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
23 3 0.10
24 24 0.77
25 4 0.13
ACGTcount: A:0.30, C:0.30, G:0.03, T:0.38
Consensus pattern (24 bp):
CTCTCCATAAATCACTCTATGATA
Found at i:53914401 original size:14 final size:14
Alignment explanation
Indices: 53914365--53914395 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
53914355 TATTAGTTAT
*
53914365 ATACATAATACTAA
1 ATACAAAATACTAA
53914379 ATACAAAATACTAA
1 ATACAAAATACTAA
53914393 ATA
1 ATA
53914396 TGAAATGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (14 bp):
ATACAAAATACTAA
Found at i:53915356 original size:18 final size:19
Alignment explanation
Indices: 53915312--53915357 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
53915302 ACAGACTGTT
*
53915312 ATAAAAAATTATAAAATAC
1 ATAAATAATTATAAAATAC
* *
53915331 A-AATTAATTA-AAATTAC
1 ATAAATAATTATAAAATAC
53915348 ATAAATAATT
1 ATAAATAATT
53915358 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 7 0.32
18 14 0.64
19 1 0.05
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAATAATTATAAAATAC
Found at i:53915577 original size:21 final size:21
Alignment explanation
Indices: 53915544--53915597 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
53915534 TAAAGAGAGT
** *
53915544 TTTGAGAAATTTAATAAGAAA
1 TTTGAGAGCTTTAAGAAGAAA
* *
53915565 TTTGAGAGCTTTAGGGAGAAA
1 TTTGAGAGCTTTAAGAAGAAA
53915586 TTTGAGAGCTTT
1 TTTGAGAGCTTT
53915598 TTTGTTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (21 bp):
TTTGAGAGCTTTAAGAAGAAA
Found at i:53915925 original size:29 final size:30
Alignment explanation
Indices: 53915868--53915930 Score: 69
Period size: 29 Copynumber: 2.1 Consensus size: 30
53915858 CGTTTTGCCA
* *
53915868 AAATCGGCCCTTTCTGGTAAATAATGTT-G
1 AAATCAGCCCTTTCTGATAAATAATGTTGG
53915897 AAATCAGCCCATTTCT-ATAAAT-ATAGTTGG
1 AAATCAGCCC-TTTCTGATAAATAAT-GTTGG
53915927 AAAT
1 AAAT
53915931 GGACCTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
28 2 0.07
29 17 0.59
30 10 0.34
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (30 bp):
AAATCAGCCCTTTCTGATAAATAATGTTGG
Found at i:53929644 original size:15 final size:15
Alignment explanation
Indices: 53929624--53929653 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
53929614 TGTTAAAAAA
53929624 TGGATAATTTTGTTG
1 TGGATAATTTTGTTG
53929639 TGGATAATTTTGTTG
1 TGGATAATTTTGTTG
53929654 GTTCATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (15 bp):
TGGATAATTTTGTTG
Found at i:53929799 original size:17 final size:17
Alignment explanation
Indices: 53929756--53929798 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
53929746 TATTTAATCT
* *
53929756 AATTCATTTGATATATTC
1 AATT-ATTTTATATATTA
53929774 AATTATTTTATATATTA
1 AATTATTTTATATATTA
53929791 AA-TATTTT
1 AATTATTTT
53929799 TTAAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 6 0.26
17 13 0.57
18 4 0.17
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (17 bp):
AATTATTTTATATATTA
Found at i:53936828 original size:17 final size:18
Alignment explanation
Indices: 53936801--53936846 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
53936791 GTAGTAATTT
53936801 TATAT-TATTATAAT-TG
1 TATATATATTATAATGTG
* *
53936817 TGTATATATTAT-GTGTG
1 TATATATATTATAATGTG
53936834 TATATATATTATA
1 TATATATATTATA
53936847 TGCATATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (18 bp):
TATATATATTATAATGTG
Found at i:53937880 original size:13 final size:13
Alignment explanation
Indices: 53937864--53937888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53937854 TTTAAACCAA
53937864 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
53937877 ACTTTTCAAAAG
1 ACTTTTCAAAAG
53937889 TATTACCAAA
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:0.20, G:0.08, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:53938619 original size:15 final size:17
Alignment explanation
Indices: 53938594--53938631 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
53938584 TCAATTACTT
*
53938594 CATACATATATTT-TTA
1 CATAAATATATTTATTA
53938610 -ATAAATATATTTATTA
1 CATAAATATATTTATTA
53938626 CATAAA
1 CATAAA
53938632 AAAAATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 11 0.58
16 3 0.16
17 5 0.26
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (17 bp):
CATAAATATATTTATTA
Found at i:53943800 original size:33 final size:33
Alignment explanation
Indices: 53943745--53943854 Score: 80
Period size: 33 Copynumber: 3.3 Consensus size: 33
53943735 TAGTCCAACT
** * * *
53943745 ATGGTCTTACACATATATTGCCATGACCCTGCC
1 ATGGTCTTACATTTATAGTGCCATAACCCAGCC
* **
53943778 ATGGTCTTACATTTGTAGTGCCATAACCCAGTT
1 ATGGTCTTACATTTATAGTGCCATAACCCAGCC
* * * *
53943811 ATGGTCTTATCA-TTA-GGATGTCATAGCCCAGCT
1 ATGGTCTTA-CATTTATAG-TGCCATAACCCAGCC
53943844 ATGGTCTTACA
1 ATGGTCTTACA
53943855 CATATATTTA
Statistics
Matches: 62, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
32 3 0.05
33 57 0.92
34 2 0.03
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.34
Consensus pattern (33 bp):
ATGGTCTTACATTTATAGTGCCATAACCCAGCC
Found at i:53946962 original size:47 final size:49
Alignment explanation
Indices: 53946844--53947023 Score: 191
Period size: 46 Copynumber: 3.8 Consensus size: 49
53946834 TGTAACCCGC
* * * *
53946844 CCATAAGCGAAATCGGACTCAACTCAATGAGCTCGG--G-C-GTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCAGTT-ACAT
53946890 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCC-AGTTACAT
* * *
53946940 -C-TTA-TGAACTCGGACTCAACTCAACGAGCTCGGA---CATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCAGTTACAT
* *
53946983 CCATAAGTGAACTCGGACTTAACTCAACGAGCTCAGATGCC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCC
53947024 CAAATATCCT
Statistics
Matches: 113, Mismatches: 10, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
43 6 0.05
44 2 0.02
45 2 0.02
46 61 0.54
47 30 0.27
48 3 0.03
49 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (49 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCAGTTACAT
Found at i:53951828 original size:22 final size:23
Alignment explanation
Indices: 53951803--53951867 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 23
53951793 TATTGAAAAT
*
53951803 ACATGTTCATAATATATA-TAAA
1 ACATATTCATAATATATATTAAA
53951825 ACATATAT-ATAATATAATATTAAA
1 ACATAT-TCATAATAT-ATATTAAA
* *
53951849 ACGTTTTACATAATATATA
1 ACATATT-CATAATATATA
53951868 CACATATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
22 12 0.34
23 5 0.14
24 11 0.31
25 7 0.20
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (23 bp):
ACATATTCATAATATATATTAAA
Found at i:53951943 original size:21 final size:21
Alignment explanation
Indices: 53951913--53951956 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
53951903 ATTAATAATA
53951913 ATACTAATAT-TACATAAAGAT
1 ATACTAATATATA-ATAAAGAT
* *
53951934 ATACTTATATATATTAAAGAT
1 ATACTAATATATAATAAAGAT
53951955 AT
1 AT
53951957 GTGCATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.39
Consensus pattern (21 bp):
ATACTAATATATAATAAAGAT
Found at i:53954065 original size:73 final size:74
Alignment explanation
Indices: 53953977--53954563 Score: 707
Period size: 78 Copynumber: 7.7 Consensus size: 74
53953967 GCGTGAGCTA
*
53953977 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAG
53954041 CGTGTCCTG
66 CGTGTCCTG
**
53954050 AGGCTCAACTCACCTCTCGCAACGTGAGTTGATCTTTTTGAAAAAACAGAAATTGAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTTTG-AAAAACAGAAATTGAAAATACCTC
* *
53954115 GGCGTGTGACCCG
64 AGCGTGT--CCTG
* **
53954128 AGGCTTAACTCACCTCTCGCAACGTGAGTTGATCTTTTTGAAAAAACAGAAATTGAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTTTG-AAAAACAGAAATTGAAAATACCTC
* **
53954193 GGCGTGTGACCCA
64 AGCGTGT--CCTG
** *
53954206 AGGCTCAACTCACCTCTCGCAACGTGAGTTGATCTTTTTGAAAAAACAGAAATTGAAAATACCCC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTTTG-AAAAACAGAAATTGAAAATACCTC
* *
53954271 GGCGTGTCTTG
64 AGCGTGTCCTG
*
53954282 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAG
53954346 CGTGTCCTG
66 CGTGTCCTG
53954355 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACATAAATTGAACAGGAATTGA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAC----A--G---A--AATTGA
* *
53954419 AAATACCTCAACGTGTCTTG
55 AAATACCTCAGCGTGTCCTG
*
53954439 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAATTGAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-TTGAAAAACAGAAATTGAAAATACCTCA
** *
53954504 ATGTGTCTTG
65 GCGTGTCCTG
* *
53954514 AGGCTCAACTCACCTATCGTAATATGAGTTGATTTTTTCG--AAACAGAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT-GAAAAACAGAAAT
53954564 AAAAACATCA
Statistics
Matches: 469, Mismatches: 26, Indels: 38
0.88 0.05 0.07
Matches are distributed among these distances:
73 114 0.24
74 8 0.02
75 66 0.14
76 60 0.13
77 2 0.00
78 149 0.32
79 1 0.00
80 1 0.00
82 2 0.00
84 55 0.12
85 3 0.01
86 8 0.02
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (74 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAG
CGTGTCCTG
Found at i:53954464 original size:84 final size:75
Alignment explanation
Indices: 53954406--53954550 Score: 222
Period size: 75 Copynumber: 1.9 Consensus size: 75
53954396 AACATAAATT
*
53954406 GAACAGGAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 GAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
53954471 TTTTCTTGAAAA
66 -TTT-TTGAAAA
* * *
53954483 G--CAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCACCTATCGTAATATGAGTTGA
1 GAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
53954546 TTTTT
66 TTTTT
53954551 TCGAAACAGA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
73 2 0.03
74 3 0.05
75 58 0.91
77 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (75 bp):
GAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
TTTTTGAAAA
Found at i:53954490 original size:232 final size:225
Alignment explanation
Indices: 53953976--53954550 Score: 728
Period size: 232 Copynumber: 2.5 Consensus size: 225
53953966 CGCGTGAGCT
*
53953976 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAAATTACCTCA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCA
* **
53954040 GCGTGTCCTGAGGCTCAACTCACCTCTCGCAACGTGAGTTGATCTTTTTGAAAAAACAGAAATTG
66 GCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAAACAGAAATTG
* * *
53954105 AAAATACCTCGGCGTGTGACCCGAGGCTTAACTCACCTCTCGCAACGTGAGTTGATCTTTTTGAA
129 AAAATACCTCAGCGTGT-ACCCGAGGCTCAACTCACCTCTCGCAACATGAGTTGA-CTTTTTGAA
**
53954170 AAAACAGAAATTGAAAATACCTCGGCGTGTGACCC
192 AAAACAGAAATTGAAAATACCTCAACGTGT-ACCC
** *
53954205 AAGGCTCAACTCACCTCTCGCAACGTGAGTTGATCTTTTTGAAAAAACAGAAATTGAAAATACCC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTTTG-AAAAACAGAAATTGAAAATACCT
*
53954270 CGGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAACAGAAATTG
64 CAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTG
* * *
53954334 AAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAA
129 AAAATACCTCAGCGTGTACCCGAGGCTCAACTCACCTCTCGCAACATGAGTTGACTTTTTG----
* **
53954397 ACATAAATTGAACAGGAATTGAAAATACCTCAACGTGT-CTT
190 --A-AAA---AACAGAAATTGAAAATACCTCAACGTGTACCC
* *
53954438 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAATTGAAAATACCTC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-TTGAAAAACAGAAATTGAAAATACCTC
** * *
53954503 AATGTGTCTTGAGGCTCAACTCACCTATCGTAATATGAGTTGATTTTT
65 AGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
53954551 TCGAAACAGA
Statistics
Matches: 303, Mismatches: 29, Indels: 25
0.85 0.08 0.07
Matches are distributed among these distances:
225 6 0.02
227 32 0.11
229 60 0.20
230 6 0.02
231 7 0.02
232 132 0.44
233 35 0.12
235 25 0.08
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (225 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCA
GCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTGAA
AATACCTCAGCGTGTACCCGAGGCTCAACTCACCTCTCGCAACATGAGTTGACTTTTTGAAAAAA
CAGAAATTGAAAATACCTCAACGTGTACCC
Found at i:53966634 original size:15 final size:14
Alignment explanation
Indices: 53966614--53966644 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
53966604 TAATTAAGAG
53966614 TATATATGTCATATA
1 TATATATGT-ATATA
53966629 TATATATGTATATA
1 TATATATGTATATA
53966643 TA
1 TA
53966645 AATAGTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (14 bp):
TATATATGTATATA
Found at i:53966929 original size:21 final size:23
Alignment explanation
Indices: 53966899--53966944 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
53966889 ATTAATAATA
53966899 ATACTAATAT-TACA-TAAAGAT
1 ATACTAATATATACATTAAAGAT
* *
53966920 ATACTTATATATATATTAAAGAT
1 ATACTAATATATACATTAAAGAT
53966943 AT
1 AT
53966945 GTGCATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 3 0.14
23 9 0.43
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (23 bp):
ATACTAATATATACATTAAAGAT
Found at i:53968522 original size:9 final size:9
Alignment explanation
Indices: 53968508--53968532 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
53968498 TTGGACTTTA
53968508 TTTATTTGG
1 TTTATTTGG
53968517 TTTATTTGG
1 TTTATTTGG
53968526 TTTATTT
1 TTTATTT
53968533 ATTTTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.16, T:0.72
Consensus pattern (9 bp):
TTTATTTGG
Found at i:53969125 original size:73 final size:73
Alignment explanation
Indices: 53968966--53969538 Score: 680
Period size: 73 Copynumber: 7.5 Consensus size: 73
53968956 ACGTGAGCTA
** * *
53968966 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAACATTAATTAAAAATACCTTA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG--AAAAACAGAAATTGAAAATACCTCA
* *
53969031 GCGTGCCCCG
64 GCGTGTCCTG
* * * *
53969041 AAGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTGAAATTACCTCAGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGC
53969106 GTGTCCTG
66 GTGTCCTG
*
53969114 AGGCTCAACTCACCTCTCGCAACATGAGTTGATCTTTTTGAAAAAAACAGAAATTGAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTG--AAAAACAGAAATTGAAAATACCT
* *
53969179 CGGCGTGTGACCCG
62 CAGCGTGT--CCTG
*
53969193 AGGCTCAACTCACCTCTCGCAACATGAGTTGATCTTTTTGAAAAAAACAGAAATTGAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTG--AAAAACAGAAATTGAAAATACCT
53969258 C-GACGTGTCCTG
62 CAG-CGTGTCCTG
*
53969270 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTCAGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGC
53969335 GTGTCCTG
66 GTGTCCTG
53969343 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAACAGGAATTGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC----A--G---A--AATTGAA
* *
53969408 AATACCTCAACGTGTCTTG
55 AATACCTCAGCGTGTCCTG
* * *
53969427 AGGCTCAATTCACCTCTCGCAATATGAGTTGATTTTCTTGAAGAGCAGAAATTGAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT-TTGAAAAACAGAAATTGAAAATACCTCA
** *
53969492 ATGTGTCTTG
64 GCGTGTCCTG
* *
53969502 AGGCTCAACTCACCTATCGTAATATGAGTTGATTTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
53969539 TCGAAACAGA
Statistics
Matches: 447, Mismatches: 30, Indels: 44
0.86 0.06 0.08
Matches are distributed among these distances:
73 134 0.30
74 4 0.01
75 102 0.23
77 64 0.14
78 1 0.00
79 75 0.17
80 1 0.00
82 2 0.00
84 54 0.12
85 3 0.01
86 7 0.02
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (73 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAGC
GTGTCCTG
Found at i:53969372 original size:229 final size:228
Alignment explanation
Indices: 53968966--53969538 Score: 773
Period size: 229 Copynumber: 2.5 Consensus size: 228
53968956 ACGTGAGCTA
** * *
53968966 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAAAACATTAATTAAAAATACCTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAAACAGAAATTGAAAATACCTC
* * * * * *
53969030 AGCGTGCCCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTGAA
66 AACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
53969095 ATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAACATGAGTTGATCTTTTTG-A-A-A
131 ATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAACATGAGTTGA--TTTTTGAACATA
**
53969157 AA-AACAGAAATTGAAAATACCTCGGCGTGTGACCCG
194 AATAACAGAAATTGAAAATACCTCAACGTGT--CCCG
*
53969193 AGGCTCAACTCACCTCTCGCAACATGAGTTGATCTTTTTGAAAAAAACAGAAATTGAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTTTGAAAAAAACAGAAATTGAAAATACCT
*
53969258 CGACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGA
65 CAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGA
*
53969323 AATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
130 AATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAACATGAGTTGATTTTTG---AACA
* **
53969388 TAAATTGAACAGGAATTGAAAATACCTCAACGTGTCTTG
192 TAAA-T-AACAGAAATTGAAAATACCTCAACGTGTCCCG
* * *
53969427 AGGCTCAATTCACCTCTCGCAATATGAGTTGATTTTCTTG--AAGAGCAGAAATTGAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-TTGAAAAAAACAGAAATTGAAAATACCT
* * * *
53969490 CAATGTGTCTTGAGGCTCAACTCACCTATCGTAATATGAGTTGATTTTT
65 CAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
53969539 TCGAAACAGA
Statistics
Matches: 307, Mismatches: 27, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
227 37 0.12
229 136 0.44
231 1 0.00
232 66 0.21
233 6 0.02
234 36 0.12
236 25 0.08
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (228 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAAACAGAAATTGAAAATACCTC
AACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
ATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAACATGAGTTGATTTTTGAACATAAA
TAACAGAAATTGAAAATACCTCAACGTGTCCCG
Found at i:53969440 original size:157 final size:149
Alignment explanation
Indices: 53968966--53969538 Score: 704
Period size: 150 Copynumber: 3.7 Consensus size: 149
53968956 ACGTGAGCTA
** * *
53968966 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAAAACATTAATTAAAAATACCTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG--AAAAACAGAAATTGAAAATACCTC
* * * * *
53969030 AGCGTGCCCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTG--AAAAATAGAAATTG
64 AGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAACAGAAATTG
* *
53969093 AAATTACCTCAGCGTGTCCTG
129 AAAATACCTCAACGTGTCCTG
*
53969114 AGGCTCAACTCACCTCTCGCAACATGAGTTGATCTTTTTGAAAAAAACAGAAATTGAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTTTG--AAAAACAGAAATTGAAAATACCT
* * *
53969179 CGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAACATGAGTTGATCTTTTTGAAAAAAACAGA
63 CAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAAAACAGA
*
53969244 AATTGAAAATACCTCGACGTGTCCTG
124 AATTGAAAATACCTCAACGTGTCCTG
*
53969270 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAG
53969334 CGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAACA
66 CGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG----A-A-AAA---AACA
* *
53969399 GGAATTGAAAATACCTCAACGTGTCTTG
122 GAAATTGAAAATACCTCAACGTGTCCTG
* * *
53969427 AGGCTCAATTCACCTCTCGCAATATGAGTTGATTTTCTTGAAGAGCAGAAATTGAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-TTGAAAAACAGAAATTGAAAATACCTCA
** * * *
53969492 ATGTGTCTTGAGGCTCAACTCACCTATCGTAATATGAGTTGATTTTT
65 GCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
53969539 TCGAAACAGA
Statistics
Matches: 375, Mismatches: 31, Indels: 27
0.87 0.07 0.06
Matches are distributed among these distances:
148 37 0.10
150 67 0.18
152 63 0.17
153 1 0.00
154 15 0.04
156 62 0.17
157 60 0.16
158 3 0.01
159 67 0.18
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (149 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAG
CGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAACAGAAATTGAA
AATACCTCAACGTGTCCTG
Found at i:53969452 original size:84 final size:76
Alignment explanation
Indices: 53969394--53969538 Score: 211
Period size: 75 Copynumber: 1.9 Consensus size: 76
53969384 AACATAAATT
* *
53969394 GAACAGGAATTGAAAATACCTCAACGTGTCTTGAGGCTCAATTCACCTCTCGCAATATGAGTTGA
1 GAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* *
53969459 -TTTTCTTGAA
66 TTTTTCATAAA
* * * *
53969469 GAGCAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCACCTATCGTAATATGAGTTGA
1 GAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
53969534 TTTTT
66 TTTTT
53969539 TCGAAACAGA
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
75 59 0.94
76 4 0.06
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (76 bp):
GAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
TTTTTCATAAA
Found at i:53973346 original size:11 final size:11
Alignment explanation
Indices: 53973330--53973370 Score: 82
Period size: 11 Copynumber: 3.7 Consensus size: 11
53973320 GTTTGGAAAT
53973330 GATTCGACGAA
1 GATTCGACGAA
53973341 GATTCGACGAA
1 GATTCGACGAA
53973352 GATTCGACGAA
1 GATTCGACGAA
53973363 GATTCGAC
1 GATTCGAC
53973371 AGTTGGAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.20
Consensus pattern (11 bp):
GATTCGACGAA
Found at i:53977409 original size:39 final size:36
Alignment explanation
Indices: 53977366--53977447 Score: 83
Period size: 39 Copynumber: 2.2 Consensus size: 36
53977356 GATGACTATA
*
53977366 TAAAAACTTTCAATAAAAAAATATAATTTTATTAAATAT
1 TAAAAACTAT-AATAAAAAAATAT-ATTTT-TTAAATAT
* * * *
53977405 TAAAATAGTATAATATAAATATATATTTTTTAAATTT
1 TAAAA-ACTATAATAAAAAAATATATTTTTTAAATAT
53977442 TAAAAA
1 TAAAAA
53977448 TAATATAGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
36 1 0.03
37 12 0.32
38 5 0.14
39 16 0.43
40 3 0.08
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (36 bp):
TAAAAACTATAATAAAAAAATATATTTTTTAAATAT
Found at i:53977985 original size:33 final size:34
Alignment explanation
Indices: 53977905--53977991 Score: 92
Period size: 33 Copynumber: 2.6 Consensus size: 34
53977895 TGACTATATA
* *
53977905 AAATTTACAATAAATAAAAAAATATAAAATTTTATT
1 AAATTTA-AA-AAATAATATAATATAAAATTTTATT
53977941 AAATATT--AAAATAATATAATAT-AAATATTT-TT
1 AAAT-TTAAAAAATAATATAATATAAAAT-TTTATT
53977973 AAATTTAAAAAATAATATA
1 AAATTTAAAAAATAATATA
53977992 TACGAGTCTA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
31 2 0.04
32 10 0.22
33 26 0.58
34 1 0.02
36 4 0.09
37 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (34 bp):
AAATTTAAAAAATAATATAATATAAAATTTTATT
Found at i:53980663 original size:30 final size:31
Alignment explanation
Indices: 53980579--53980683 Score: 88
Period size: 30 Copynumber: 3.5 Consensus size: 31
53980569 ATATATTTTT
* * * *
53980579 AATTTTTTAAA-TTTTAATTAGATTTTTCAA
1 AATTTTTGAAAGTTTTAATTAAATCTATCAA
* ** * * *
53980609 AATTTTTTAATTTTTTTATAAAATCTCT-AA
1 AATTTTTGAAAGTTTTAATTAAATCTATCAA
53980639 AATTTTTGAAAGTTTTAATTAAATCTATCAA
1 AATTTTTGAAAGTTTTAATTAAATCTATCAA
**
53980670 AATTCGTGAAAGTT
1 AATTTTTGAAAGTT
53980684 CTCACTAAGA
Statistics
Matches: 59, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
30 34 0.58
31 25 0.42
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (31 bp):
AATTTTTGAAAGTTTTAATTAAATCTATCAA
Found at i:53981121 original size:9 final size:9
Alignment explanation
Indices: 53981109--53981151 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
53981099 AAATAATGCA
53981109 GTTAATTCG
1 GTTAATTCG
*
53981118 GTTAATTTG
1 GTTAATTCG
* *
53981127 GGTAATTCA
1 GTTAATTCG
53981136 GTTAATTCG
1 GTTAATTCG
53981145 GTTAATT
1 GTTAATT
53981152 TTATACTTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.47
Consensus pattern (9 bp):
GTTAATTCG
Found at i:53981299 original size:20 final size:20
Alignment explanation
Indices: 53981274--53981321 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
53981264 GTCGGTTAAT
53981274 TCGGTTAATGTTATTTCGGA
1 TCGGTTAATGTTATTTCGGA
53981294 TCGGTTAATGTTATTTCGGA
1 TCGGTTAATGTTATTTCGGA
53981314 TCGGTTAA
1 TCGGTTAA
53981322 CCGATTGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.21, C:0.10, G:0.25, T:0.44
Consensus pattern (20 bp):
TCGGTTAATGTTATTTCGGA
Found at i:53982553 original size:8 final size:8
Alignment explanation
Indices: 53982535--53982568 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
53982525 TTTGTTTTCT
53982535 TTATATATA
1 TTAT-TATA
53982544 TTATTATA
1 TTATTATA
53982552 TTATTATA
1 TTATTATA
53982560 TTACTTATA
1 TTA-TTATA
53982569 AAATATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.62
9 9 0.38
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (8 bp):
TTATTATA
Found at i:53984448 original size:20 final size:21
Alignment explanation
Indices: 53984409--53984448 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53984399 TAATTAGATA
*
53984409 AATTGTTAAAAAATTGAAATG
1 AATTGTTAAAAAAATGAAATG
53984430 AATTGTTAAAAAAAT-AAAT
1 AATTGTTAAAAAAATGAAAT
53984449 TAGAAAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (21 bp):
AATTGTTAAAAAAATGAAATG
Done.