Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 10 of 279
Found at i:3085370 original size:42 final size:42
Alignment explanation
Indices: 3085306--3085394 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
3085296 TCCTAATTGG
* *
3085306 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAATATAAAA
1 GAAAATAGTTCCCTTATCCTAATAAACTACTAAAAGATAAAA
* *
3085348 GAAAATAGTTCTCTTGTCCTAATAAACTACTAAAAGATAAAA
1 GAAAATAGTTCCCTTATCCTAATAAACTACTAAAAGATAAAA
*
3085390 TAAAA
1 GAAAA
3085395 ATATTCCTAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.51, C:0.13, G:0.07, T:0.29
Consensus pattern (42 bp):
GAAAATAGTTCCCTTATCCTAATAAACTACTAAAAGATAAAA
Found at i:3085441 original size:19 final size:18
Alignment explanation
Indices: 3085419--3085458 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
3085409 TGAATAAAAC
3085419 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAA-AT
3085438 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
3085456 TTA
1 TTA
3085459 AAATATATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:3091218 original size:14 final size:14
Alignment explanation
Indices: 3091187--3091217 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
3091177 TTCAATTGAA
3091187 TTTTATTTTTTTAT
1 TTTTATTTTTTTAT
3091201 TTTTA-TTTTTTAT
1 TTTTATTTTTTTAT
3091214 TTTT
1 TTTT
3091218 TGCAAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTATTTTTTTAT
Found at i:3093007 original size:2 final size:2
Alignment explanation
Indices: 3093000--3093026 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3092990 TTCATTTAAG
3093000 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
3093027 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3101701 original size:53 final size:54
Alignment explanation
Indices: 3101518--3101727 Score: 246
Period size: 55 Copynumber: 3.9 Consensus size: 54
3101508 ATTAGGGCTT
*
3101518 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGC-ATTGGTAA-GTTTCATAAGGA
* * * **
3101573 AAGGATATCATGTAAGACCACGTCAAGACATGGCATTCATAAGTTTCTATAAGGAA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTC-ATAAGG-A
* * * *
3101629 AAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTCAG-TTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTCATAAGGA
* * *
3101681 AAGGATACCATGTAAGACCATGTCGAGACATGGCAATGGTAAGTTTC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTC
3101728 CAAAGGATGC
Statistics
Matches: 129, Mismatches: 21, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
52 4 0.03
53 43 0.33
54 12 0.09
55 65 0.50
56 5 0.04
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTCATAAGGA
Found at i:3101724 original size:108 final size:110
Alignment explanation
Indices: 3101525--3101727 Score: 304
Period size: 108 Copynumber: 1.9 Consensus size: 110
3101515 CTTAAGGATA
*
3101525 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGAAAGGATATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGAAAGGATACCATGTAAGA
*
3101590 CCACGTCAAGACATGGCATTCATAAGTTTCTATAAGGAAAAGGTC
66 CCACGTCAAGACATGGCAATCATAAGTTTCTATAAGGAAAAGGTC
* *
3101635 CCATGTAAGACCATGCCAAGGCATGGC-ATTGGTCA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGAAAGGATACCATGTAAG
* * **
3101697 ACCATGTCGAGACATGGCAATGGTAAGTTTC
65 ACCACGTCAAGACATGGCAATCATAAGTTTC
3101728 CAAAGGATGC
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
107 3 0.04
108 47 0.56
109 7 0.08
110 27 0.32
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGAAAGGATACCATGTAAGA
CCACGTCAAGACATGGCAATCATAAGTTTCTATAAGGAAAAGGTC
Found at i:3101762 original size:49 final size:49
Alignment explanation
Indices: 3101681--3101774 Score: 134
Period size: 49 Copynumber: 1.9 Consensus size: 49
3101671 TTCATAAGGC
* * * *
3101681 AAGGATACCATGTAAGACCATGTCGAGACATGGCAATGGTAAGTTTCCA
1 AAGGATACCACGTAAGACCATGACAAGACATGGAAATGGTAAGTTTCCA
* *
3101730 AAGGATGCCACGTAAGACCATGACAAGTCATGGAAATGGTAAGTT
1 AAGGATACCACGTAAGACCATGACAAGACATGGAAATGGTAAGTT
3101775 ACCCGTGTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (49 bp):
AAGGATACCACGTAAGACCATGACAAGACATGGAAATGGTAAGTTTCCA
Found at i:3101986 original size:16 final size:16
Alignment explanation
Indices: 3101965--3101995 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3101955 ATAAATTTGA
3101965 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
3101981 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
3101996 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:3102595 original size:53 final size:54
Alignment explanation
Indices: 3102412--3102621 Score: 246
Period size: 55 Copynumber: 3.9 Consensus size: 54
3102402 ATTAGGGCTT
*
3102412 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGC-ATTGGTAA-GTTTCATAAGGA
* * * **
3102467 AAGGATATCATGTAAGACCACGTCAAGACATGGCATTCATAAGTTTCTATAAGGAA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTC-ATAAGG-A
* * * *
3102523 AAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTCAG-TTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTCATAAGGA
* * *
3102575 AAGGATACCATGTAAGACCATGTCGAGACATGGCAATGGTAAGTTTC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTC
3102622 CAAAGGATGC
Statistics
Matches: 129, Mismatches: 21, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
52 4 0.03
53 43 0.33
54 12 0.09
55 65 0.50
56 5 0.04
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTCATAAGGA
Found at i:3102618 original size:108 final size:110
Alignment explanation
Indices: 3102419--3102621 Score: 304
Period size: 108 Copynumber: 1.9 Consensus size: 110
3102409 CTTAAGGATA
*
3102419 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGAAAGGATATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGAAAGGATACCATGTAAGA
*
3102484 CCACGTCAAGACATGGCATTCATAAGTTTCTATAAGGAAAAGGTC
66 CCACGTCAAGACATGGCAATCATAAGTTTCTATAAGGAAAAGGTC
* *
3102529 CCATGTAAGACCATGCCAAGGCATGGC-ATTGGTCA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGAAAGGATACCATGTAAG
* * **
3102591 ACCATGTCGAGACATGGCAATGGTAAGTTTC
65 ACCACGTCAAGACATGGCAATCATAAGTTTC
3102622 CAAAGGATGC
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
107 3 0.04
108 47 0.56
109 7 0.08
110 27 0.32
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGAAAGGATACCATGTAAGA
CCACGTCAAGACATGGCAATCATAAGTTTCTATAAGGAAAAGGTC
Found at i:3102656 original size:49 final size:49
Alignment explanation
Indices: 3102575--3102668 Score: 134
Period size: 49 Copynumber: 1.9 Consensus size: 49
3102565 TTCATAAGGC
* * * *
3102575 AAGGATACCATGTAAGACCATGTCGAGACATGGCAATGGTAAGTTTCCA
1 AAGGATACCACGTAAGACCATGACAAGACATGGAAATGGTAAGTTTCCA
* *
3102624 AAGGATGCCACGTAAGACCATGACAAGTCATGGAAATGGTAAGTT
1 AAGGATACCACGTAAGACCATGACAAGACATGGAAATGGTAAGTT
3102669 ACCCGTGTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (49 bp):
AAGGATACCACGTAAGACCATGACAAGACATGGAAATGGTAAGTTTCCA
Found at i:3102880 original size:16 final size:16
Alignment explanation
Indices: 3102859--3102889 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3102849 ATAAATTTGA
3102859 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
3102875 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
3102890 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:3103177 original size:894 final size:894
Alignment explanation
Indices: 3101449--3103235 Score: 3565
Period size: 894 Copynumber: 2.0 Consensus size: 894
3101439 TTGACAGAGA
3101449 AGTAATTTTAAAAAGTTCTGGTTGAACCTTAGGAATGTGTAGGATACAAATGTCATGACATTAGG
1 AGTAATTTTAAAAAGTTCTGGTTGAACCTTAGGAATGTGTAGGATACAAATGTCATGACATTAGG
3101514 GCTTAAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGAAAGGAT
66 GCTTAAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGAAAGGAT
3101579 ATCATGTAAGACCACGTCAAGACATGGCATTCATAAGTTTCTATAAGGAAAAGGTCCCATGTAAG
131 ATCATGTAAGACCACGTCAAGACATGGCATTCATAAGTTTCTATAAGGAAAAGGTCCCATGTAAG
3101644 ACCATGCCAAGGCATGGCATTGGTCAGTTCATAAGGCAAGGATACCATGTAAGACCATGTCGAGA
196 ACCATGCCAAGGCATGGCATTGGTCAGTTCATAAGGCAAGGATACCATGTAAGACCATGTCGAGA
3101709 CATGGCAATGGTAAGTTTCCAAAGGATGCCACGTAAGACCATGACAAGTCATGGAAATGGTAAGT
261 CATGGCAATGGTAAGTTTCCAAAGGATGCCACGTAAGACCATGACAAGTCATGGAAATGGTAAGT
3101774 TACCCGTGTATCCTTAGTATTCCAAGTGGTTCGATGGGAAAATTAAGAGAGAATATCAAGGTAAG
326 TACCCGTGTATCCTTAGTATTCCAAGTGGTTCGATGGGAAAATTAAGAGAGAATATCAAGGTAAG
3101839 GTAAGGGAAGATGAGTTATACTAAAAATGGTAAGACAATTTCATGCTAGAAGCGCAAAGGTAAGT
391 GTAAGGGAAGATGAGTTATACTAAAAATGGTAAGACAATTTCATGCTAGAAGCGCAAAGGTAAGT
3101904 ATATAATGTTCATGTATGCTTGATAAAGAAAAAGGTAAGTAAAATGTATTAATAAATTTGATTAA
456 ATATAATGTTCATGTATGCTTGATAAAGAAAAAGGTAAGTAAAATGTATTAATAAATTTGATTAA
3101969 GTAAGTAAGTATTTAAGTAAGTGAGTAAGTGAAGAAGTTTAAAATATGTCAACGACAATTAATGA
521 GTAAGTAAGTATTTAAGTAAGTGAGTAAGTGAAGAAGTTTAAAATATGTCAACGACAATTAATGA
3102034 AGTTACATTAAGTAGTATCATGCCAAGTAGTAAGATGATTCTTATGAATGTTGTTATTTATTTGC
586 AGTTACATTAAGTAGTATCATGCCAAGTAGTAAGATGATTCTTATGAATGTTGTTATTTATTTGC
3102099 ATGCAAACTTACTAAGCTTAATGCTTACGCCTTTTATTTTCCTTCTTTTTATATTTTTGTCAAGC
651 ATGCAAACTTACTAAGCTTAATGCTTACGCCTTTTATTTTCCTTCTTTTTATATTTTTGTCAAGC
3102164 TAACTCGGGGATCGTAACGTATGTCGGAGGTCCAAGCACACTATCACAAGGATTACTTTGGTATA
716 TAACTCGGGGATCGTAACGTATGTCGGAGGTCCAAGCACACTATCACAAGGATTACTTTGGTATA
3102229 GCTAGACGTTTCATTTTGAGTATGGCATGTATAGCATCGTAGCCATTTTGTGTGTATGATCTTAT
781 GCTAGACGTTTCATTTTGAGTATGGCATGTATAGCATCGTAGCCATTTTGTGTGTATGATCTTAT
3102294 GATATGGCTAATGAATGGTATGTAAATGCTTGATAATGATTAGCTATTG
846 GATATGGCTAATGAATGGTATGTAAATGCTTGATAATGATTAGCTATTG
3102343 AGTAATTTTAAAAAGTTCTGGTTGAACCTTAGGAATGTGTAGGATACAAATGTCATGACATTAGG
1 AGTAATTTTAAAAAGTTCTGGTTGAACCTTAGGAATGTGTAGGATACAAATGTCATGACATTAGG
3102408 GCTTAAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGAAAGGAT
66 GCTTAAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGAAAGGAT
3102473 ATCATGTAAGACCACGTCAAGACATGGCATTCATAAGTTTCTATAAGGAAAAGGTCCCATGTAAG
131 ATCATGTAAGACCACGTCAAGACATGGCATTCATAAGTTTCTATAAGGAAAAGGTCCCATGTAAG
3102538 ACCATGCCAAGGCATGGCATTGGTCAGTTCATAAGGCAAGGATACCATGTAAGACCATGTCGAGA
196 ACCATGCCAAGGCATGGCATTGGTCAGTTCATAAGGCAAGGATACCATGTAAGACCATGTCGAGA
3102603 CATGGCAATGGTAAGTTTCCAAAGGATGCCACGTAAGACCATGACAAGTCATGGAAATGGTAAGT
261 CATGGCAATGGTAAGTTTCCAAAGGATGCCACGTAAGACCATGACAAGTCATGGAAATGGTAAGT
3102668 TACCCGTGTATCCTTAGTATTCCAAGTGGTTCGATGGGAAAATTAAGAGAGAATATCAAGGTAAG
326 TACCCGTGTATCCTTAGTATTCCAAGTGGTTCGATGGGAAAATTAAGAGAGAATATCAAGGTAAG
3102733 GTAAGGGAAGATGAGTTATACTAAAAATGGTAAGACAATTTCATGCTAGAAGCGCAAAGGTAAGT
391 GTAAGGGAAGATGAGTTATACTAAAAATGGTAAGACAATTTCATGCTAGAAGCGCAAAGGTAAGT
3102798 ATATAATGTTCATGTATGCTTGATAAAGAAAAAGGTAAGTAAAATGTATTAATAAATTTGATTAA
456 ATATAATGTTCATGTATGCTTGATAAAGAAAAAGGTAAGTAAAATGTATTAATAAATTTGATTAA
3102863 GTAAGTAAGTATTTAAGTAAGTGAGTAAGTGAAGAAGTTTAAAATATGTCAACGACAATTAATGA
521 GTAAGTAAGTATTTAAGTAAGTGAGTAAGTGAAGAAGTTTAAAATATGTCAACGACAATTAATGA
3102928 AGTTACATTAAGTAGTATCATGCCAAGTAGTAAGATGATTCTTATGAATGTTGTTATTTATTTGC
586 AGTTACATTAAGTAGTATCATGCCAAGTAGTAAGATGATTCTTATGAATGTTGTTATTTATTTGC
3102993 ATGCAAACTTACTAAGCTTAATGCTTACGCCTTTTATTTTCCTTCTTTTTATATTTTTGTCAAGC
651 ATGCAAACTTACTAAGCTTAATGCTTACGCCTTTTATTTTCCTTCTTTTTATATTTTTGTCAAGC
3103058 TAACTCGGGGATCGTAACGTATGTCGGAGGTCCAAGCACACTATCACAAGGATTACTTTGGTATA
716 TAACTCGGGGATCGTAACGTATGTCGGAGGTCCAAGCACACTATCACAAGGATTACTTTGGTATA
3103123 GCTAGACGTTTCATTTTGAGTATGGCATGTATAGCATCGTAGCCATTTTGTGTGTATGATCTTAT
781 GCTAGACGTTTCATTTTGAGTATGGCATGTATAGCATCGTAGCCATTTTGTGTGTATGATCTTAT
*
3103188 GATATGGCTAATGAATGGTATGTAAATTCTTGATAATGATTAGCTATT
846 GATATGGCTAATGAATGGTATGTAAATGCTTGATAATGATTAGCTATT
3103236 AGAATGGTTA
Statistics
Matches: 892, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
894 892 1.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (894 bp):
AGTAATTTTAAAAAGTTCTGGTTGAACCTTAGGAATGTGTAGGATACAAATGTCATGACATTAGG
GCTTAAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGAAAGGAT
ATCATGTAAGACCACGTCAAGACATGGCATTCATAAGTTTCTATAAGGAAAAGGTCCCATGTAAG
ACCATGCCAAGGCATGGCATTGGTCAGTTCATAAGGCAAGGATACCATGTAAGACCATGTCGAGA
CATGGCAATGGTAAGTTTCCAAAGGATGCCACGTAAGACCATGACAAGTCATGGAAATGGTAAGT
TACCCGTGTATCCTTAGTATTCCAAGTGGTTCGATGGGAAAATTAAGAGAGAATATCAAGGTAAG
GTAAGGGAAGATGAGTTATACTAAAAATGGTAAGACAATTTCATGCTAGAAGCGCAAAGGTAAGT
ATATAATGTTCATGTATGCTTGATAAAGAAAAAGGTAAGTAAAATGTATTAATAAATTTGATTAA
GTAAGTAAGTATTTAAGTAAGTGAGTAAGTGAAGAAGTTTAAAATATGTCAACGACAATTAATGA
AGTTACATTAAGTAGTATCATGCCAAGTAGTAAGATGATTCTTATGAATGTTGTTATTTATTTGC
ATGCAAACTTACTAAGCTTAATGCTTACGCCTTTTATTTTCCTTCTTTTTATATTTTTGTCAAGC
TAACTCGGGGATCGTAACGTATGTCGGAGGTCCAAGCACACTATCACAAGGATTACTTTGGTATA
GCTAGACGTTTCATTTTGAGTATGGCATGTATAGCATCGTAGCCATTTTGTGTGTATGATCTTAT
GATATGGCTAATGAATGGTATGTAAATGCTTGATAATGATTAGCTATTG
Found at i:3106155 original size:46 final size:46
Alignment explanation
Indices: 3106102--3106302 Score: 260
Period size: 46 Copynumber: 4.4 Consensus size: 46
3106092 GTTTGCCTCC
* * **
3106102 TGAAAGATACCTTGGCAACCTGATATGAAATGTGTAAGACCATGGT
1 TGAAAGATACCATGGCAACCTGACATGAAATGAATAAGACCATGGT
* *
3106148 TGAAAGATACCATGGCAACCTGATATAAAATGAATAAGACCATGGT
1 TGAAAGATACCATGGCAACCTGACATGAAATGAATAAGACCATGGT
* *
3106194 TGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGT
1 TGAAAGATACCATGGCAACCTGACATGAAATGAATAAGACCATGGT
* * *
3106240 TGAAAGATACCATGGCAACATGACA-GAAAATGAGTAAGACCATAGT
1 TGAAAGATACCATGGCAACCTGACATG-AAATGAATAAGACCATGGT
* * *
3106286 TTAAAGACACTATGGCA
1 TGAAAGATACCATGGCA
3106303 TCATGTCAAA
Statistics
Matches: 139, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 1 0.01
46 138 0.99
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (46 bp):
TGAAAGATACCATGGCAACCTGACATGAAATGAATAAGACCATGGT
Found at i:3110813 original size:93 final size:93
Alignment explanation
Indices: 3110701--3110872 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
3110691 GCCCATAAGT
* *
3110701 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
3110766 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* *
3110794 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
3110859 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
3110873 CAAACATCCT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:3110868 original size:46 final size:46
Alignment explanation
Indices: 3110693--3110868 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
3110683 TGTAACCCGC
* * *
3110693 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
* *
3110739 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-ATTTGCAT
* *
3110789 CTC-T---CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
*
3110832 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
3110869 TGCCCAAACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 1 0.01
43 8 0.07
44 1 0.01
46 65 0.59
47 28 0.25
49 1 0.01
50 6 0.05
51 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
Found at i:3113303 original size:30 final size:30
Alignment explanation
Indices: 3113259--3113347 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
3113249 CAAAGATAAC
*
3113259 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAACCCGGAATAAAGAAATCCAAGATA
*
3113288 GAGAAACCCGGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGGAATAAAGAAATCCAAG-ATA
* * *
3113318 AAGAGATCCAGG-ATAAAGAAACCCAAGATA
1 AAGA-AACCCGGAATAAAGAAATCCAAGATA
3113348 CGATACTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 9 0.18
30 34 0.68
31 7 0.14
ACGTcount: A:0.56, C:0.16, G:0.18, T:0.10
Consensus pattern (30 bp):
AAGAAACCCGGAATAAAGAAATCCAAGATA
Found at i:3113307 original size:15 final size:14
Alignment explanation
Indices: 3113259--3113341 Score: 58
Period size: 15 Copynumber: 5.6 Consensus size: 14
3113249 CAAAGATAAC
*
3113259 AAGAAAACCGAATA
1 AAGAAACCCGAATA
* *
3113273 AAGAAATCCAAGATA
1 AAGAAACCCGA-ATA
*
3113288 GAGAAACCCGGAATA
1 AAGAAACCC-GAATA
*
3113303 AAGAAATCCAGAATA
1 AAGAAA-CCCGAATA
* * *
3113318 AAGAGATCCAGGATA
1 AAGA-AACCCGAATA
3113333 AAGAAACCC
1 AAGAAACCC
3113342 AAGATACGAT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
14 12 0.22
15 38 0.70
16 4 0.07
ACGTcount: A:0.55, C:0.17, G:0.18, T:0.10
Consensus pattern (14 bp):
AAGAAACCCGAATA
Found at i:3113347 original size:15 final size:15
Alignment explanation
Indices: 3113270--3113347 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
3113260 AGAAAACCGA
3113270 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* **
3113285 ATAGAGAAA-CCCGG
1 ATAAAGAAATCCAAG
3113299 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
3113314 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
3113330 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
3113345 ATA
1 ATA
3113348 CGATACTATG
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
14 3 0.06
15 44 0.88
16 3 0.06
ACGTcount: A:0.55, C:0.15, G:0.18, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:3116385 original size:46 final size:48
Alignment explanation
Indices: 3116263--3116392 Score: 155
Period size: 46 Copynumber: 2.8 Consensus size: 48
3116253 TGTAACCCGC
*
3116263 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA--CCTAGTTACAT
* * *
3116313 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA-C-A-TTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTT-ACAT
3116356 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
3116393 TGCTCAACCA
Statistics
Matches: 70, Mismatches: 6, Indels: 12
0.80 0.07 0.14
Matches are distributed among these distances:
42 2 0.03
43 4 0.06
44 2 0.03
45 2 0.03
46 29 0.41
47 28 0.40
48 2 0.03
49 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (48 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTTACAT
Found at i:3116411 original size:46 final size:44
Alignment explanation
Indices: 3116268--3116411 Score: 132
Period size: 46 Copynumber: 3.1 Consensus size: 44
3116258 CCCGCCCATA
*
3116268 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT
* * * *
3116315 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCT
3116361 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CT
3116407 AGTGA
1 AGTGA
3116412 CATGTCACTT
Statistics
Matches: 79, Mismatches: 10, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
44 9 0.11
45 1 0.01
46 33 0.42
47 30 0.38
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCT
Found at i:3121414 original size:23 final size:23
Alignment explanation
Indices: 3121384--3121529 Score: 113
Period size: 22 Copynumber: 6.3 Consensus size: 23
3121374 GATGAACAAG
*
3121384 AAGCTCTAATGAGCTGAAACGGT
1 AAGCTCTAATGAGCTGAAACAGT
* *
3121407 AAGCTCT-ATCGAGTTG-AACAAT
1 AAGCTCTAAT-GAGCTGAAACAGT
* *
3121429 AAGCTCTATTGAGATG-AACAGT
1 AAGCTCTAATGAGCTGAAACAGT
3121451 AAGCTCATACA--AGCTGAAACAGT
1 AAGCTC-TA-ATGAGCTGAAACAGT
* *
3121474 AAGCTCCAATGAGCTGAAAATAGT
1 AAGCTCTAATGAGCTG-AAACAGT
* *
3121498 AAGCTCTTACGAGCTGATATATCAGT
1 AAGCTCTAATGAGCTGA-A-A-CAGT
3121524 AAGCTC
1 AAGCTC
3121530 ATACGATCTG
Statistics
Matches: 98, Mismatches: 14, Indels: 19
0.75 0.11 0.15
Matches are distributed among these distances:
21 1 0.01
22 34 0.35
23 33 0.34
24 20 0.20
25 1 0.01
26 9 0.09
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (23 bp):
AAGCTCTAATGAGCTGAAACAGT
Found at i:3121433 original size:45 final size:45
Alignment explanation
Indices: 3121376--3121514 Score: 138
Period size: 45 Copynumber: 3.1 Consensus size: 45
3121366 CCTAAGCTGA
* * * *
3121376 TGAACAAGAAGCTCTAATGAGCTGAAACGGTAAGCTC-TATCGAGT
1 TGAACAATAAGCTCTAATGAGCTGAAACAGTAAGCTCATA-CAAGC
* *
3121421 TGAACAATAAGCTCTATTGAGATG-AACAGTAAGCTCATACAAGC
1 TGAACAATAAGCTCTAATGAGCTGAAACAGTAAGCTCATACAAGC
* * * * *
3121465 TGAAACAGTAAGCTCCAATGAGCTGAAAATAGTAAGCTCTTACGAGC
1 TG-AACAATAAGCTCTAATGAGCTG-AAACAGTAAGCTCATACAAGC
3121512 TGA
1 TGA
3121515 TATATCAGTA
Statistics
Matches: 77, Mismatches: 13, Indels: 7
0.79 0.13 0.07
Matches are distributed among these distances:
44 16 0.21
45 41 0.53
46 1 0.01
47 19 0.25
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (45 bp):
TGAACAATAAGCTCTAATGAGCTGAAACAGTAAGCTCATACAAGC
Found at i:3121511 original size:24 final size:24
Alignment explanation
Indices: 3121448--3121535 Score: 90
Period size: 24 Copynumber: 3.6 Consensus size: 24
3121438 TGAGATGAAC
* *
3121448 AGTAAGCTCATACAAGCTG-AAAC
1 AGTAAGCTCATACGAGCTGAAAAT
*
3121471 AGTAAGCTCCA-ATGAGCTGAAAAT
1 AGTAAGCT-CATACGAGCTGAAAAT
* *
3121495 AGTAAGCTCTTACGAGCTGATATAT
1 AGTAAGCTCATACGAGCTGA-AAAT
3121520 CAGTAAGCTCATACGA
1 -AGTAAGCTCATACGA
3121536 TCTGTGGTGA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
23 15 0.28
24 21 0.40
25 3 0.06
26 14 0.26
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (24 bp):
AGTAAGCTCATACGAGCTGAAAAT
Found at i:3127530 original size:16 final size:17
Alignment explanation
Indices: 3127509--3127548 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3127499 TATGAACATT
*
3127509 AGACACAAACAAT-ATA
1 AGACACAAACAATAACA
*
3127525 AGACACAAGCAATAACA
1 AGACACAAACAATAACA
3127542 AGACACA
1 AGACACA
3127549 TAATGACGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.60, C:0.23, G:0.10, T:0.07
Consensus pattern (17 bp):
AGACACAAACAATAACA
Found at i:3132055 original size:32 final size:32
Alignment explanation
Indices: 3131998--3132058 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
3131988 TGGTAAGCCG
***
3131998 TGTGCGAGACACGAGCTCGGTAAATTGGGCCA
1 TGTGCGAGACACGAGCTCAAAAAATTGGGCCA
*
3132030 TGTGCGAGACACGGGCTCAAAAAATTGGG
1 TGTGCGAGACACGAGCTCAAAAAATTGGG
3132059 TCGTGTGGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.28, C:0.20, G:0.34, T:0.18
Consensus pattern (32 bp):
TGTGCGAGACACGAGCTCAAAAAATTGGGCCA
Found at i:3139877 original size:21 final size:21
Alignment explanation
Indices: 3139853--3139895 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3139843 TTTGTTTATG
3139853 TATCTCCTTACTTTGCTTCTT
1 TATCTCCTTACTTTGCTTCTT
3139874 TATCTCCTTACTTTGCTTCTT
1 TATCTCCTTACTTTGCTTCTT
3139895 T
1 T
3139896 CGTTGATGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.28, G:0.05, T:0.58
Consensus pattern (21 bp):
TATCTCCTTACTTTGCTTCTT
Found at i:3140777 original size:36 final size:36
Alignment explanation
Indices: 3140730--3140814 Score: 163
Period size: 36 Copynumber: 2.4 Consensus size: 36
3140720 TATTTAGCAT
3140730 ATAAAAATTATATACAATAGTTGATGTTTTTATAAA
1 ATAAAAATTATATACAATAGTTGATGTTTTTATAAA
3140766 ATAAAAATTATATACAATAGTTGATGTTTTTATAAA
1 ATAAAAATTATATACAATAGTTGATGTTTTTATAAA
3140802 AT-AAAATTATATA
1 ATAAAAATTATATA
3140815 TATATAGGGT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 11 0.22
36 38 0.78
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.41
Consensus pattern (36 bp):
ATAAAAATTATATACAATAGTTGATGTTTTTATAAA
Found at i:3145481 original size:23 final size:23
Alignment explanation
Indices: 3145437--3145481 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3145427 AGTATATAAT
* *
3145437 ATTATATATTTAAATTTTAAATG
1 ATTATATATTTAAATGTAAAATG
3145460 ATTATAT-TTTAATATGTAAAAT
1 ATTATATATTTAA-ATGTAAAAT
3145482 ATAGTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
ATTATATATTTAAATGTAAAATG
Found at i:3151157 original size:22 final size:22
Alignment explanation
Indices: 3151133--3151173 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3151123 ATAAAATTAA
3151133 AAAAG-AAAAAAGAATCAATCC
1 AAAAGTAAAAAAGAATCAATCC
*
3151154 AAAAGTAATAAAGAATCAAT
1 AAAAGTAAAAAAGAATCAAT
3151174 TCATTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.66, C:0.10, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAAGTAAAAAAGAATCAATCC
Found at i:3153515 original size:29 final size:28
Alignment explanation
Indices: 3153482--3153556 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 28
3153472 AATAAAAATA
3153482 AATAAAAGTTATAAAAAT-TATTAAATTTT
1 AATAAAA-TTATAAAAATAT-TTAAATTTT
* *
3153511 AATAAAAATATAAGAAATATTTAATTTTT
1 AATAAAATTATAA-AAATATTTAAATTTT
* *
3153540 ATTAAAAATTAGAAAAA
1 AAT-AAAATTATAAAAA
3153557 ATAATAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
28 5 0.13
29 24 0.63
30 9 0.24
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (28 bp):
AATAAAATTATAAAAATATTTAAATTTT
Found at i:3153531 original size:28 final size:29
Alignment explanation
Indices: 3153482--3153548 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
3153472 AATAAAAATA
*
3153482 AATAAAAGTTATAAAAATTA-TTAAATTTT
1 AATAAAA-ATATAAAAATTATTTAAATTTT
*
3153511 AATAAAAATATAAGAAA-TATTTAATTTTT
1 AATAAAAATATAA-AAATTATTTAAATTTT
*
3153540 ATTAAAAAT
1 AATAAAAAT
3153549 TAGAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 7 0.21
29 26 0.79
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (29 bp):
AATAAAAATATAAAAATTATTTAAATTTT
Found at i:3153916 original size:17 final size:18
Alignment explanation
Indices: 3153894--3153927 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3153884 TTTTATAAAA
3153894 TTTTACAAT-TTTATATT
1 TTTTACAATGTTTATATT
3153911 TTTTACAATGTTTATAT
1 TTTTACAATGTTTATAT
3153928 ATATTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTACAATGTTTATATT
Found at i:3153973 original size:20 final size:19
Alignment explanation
Indices: 3153902--3153977 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 19
3153892 AATTTTACAA
3153902 TTTTATATTTTTTACAATGTT
1 TTTTATATTTTTTA-AAT-TT
*
3153923 TATATATATTTTTCT-AATTT
1 T-TTTATATTTTT-TAAATTT
* *
3153943 TTAGTAAATTTTTTAAATATT
1 TT-TTATATTTTTTAAAT-TT
3153964 TTTTATATTTTTTA
1 TTTTATATTTTTTA
3153978 TTAAAGTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
19 2 0.04
20 24 0.53
21 8 0.18
22 10 0.22
23 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTTATATTTTTTAAATTT
Found at i:3153997 original size:10 final size:9
Alignment explanation
Indices: 3153870--3154031 Score: 96
Period size: 9 Copynumber: 17.0 Consensus size: 9
3153860 TATGCATTTA
3153870 ATAATTTTT
1 ATAATTTTT
*
3153879 ATGATTTTT
1 ATAATTTTT
*
3153888 ATAAAATTTT
1 AT-AATTTTT
*
3153898 ACAA-TTTT
1 ATAATTTTT
*
3153906 ATATTTTTT
1 ATAATTTTT
*
3153915 ACAATGTTTAT
1 ATAAT-TTT-T
3153926 ATATATTTTT
1 ATA-ATTTTT
*
3153936 CTAATTTTT
1 ATAATTTTT
3153945 AGTAAATTTTTT
1 A-T-AA-TTTTT
*
3153957 AAATATTTTTT
1 --ATAATTTTT
*
3153968 ATATTTTTT
1 ATAATTTTT
* *
3153977 ATTAAAGTTTA
1 A-T-AATTTTT
3153988 ATAATTTTT
1 ATAATTTTT
3153997 ATAATTTTT
1 ATAATTTTT
*
3154006 ATTGATTTTT
1 A-TAATTTTT
3154016 AT--TTTTT
1 ATAATTTTT
3154023 ATAATTTTT
1 ATAATTTTT
3154032 TTGCCACATG
Statistics
Matches: 120, Mismatches: 18, Indels: 30
0.71 0.11 0.18
Matches are distributed among these distances:
7 7 0.06
8 6 0.05
9 56 0.47
10 23 0.19
11 18 0.15
12 8 0.07
13 1 0.01
14 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (9 bp):
ATAATTTTT
Found at i:3154799 original size:14 final size:15
Alignment explanation
Indices: 3154780--3154808 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3154770 TTGTAGATAT
3154780 TATATATA-TAAAAA
1 TATATATACTAAAAA
3154794 TATATATACTAAAAA
1 TATATATACTAAAAA
3154809 CTTTTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
TATATATACTAAAAA
Found at i:3158780 original size:15 final size:16
Alignment explanation
Indices: 3158762--3158791 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3158752 AATATCTATT
3158762 TAATTA-CTAAAAATC
1 TAATTATCTAAAAATC
3158777 TAATTATCTAAAAAT
1 TAATTATCTAAAAAT
3158792 AAAAAAAGTT
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:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATTATCTAAAAATC
Found at i:3160183 original size:13 final size:13
Alignment explanation
Indices: 3160165--3160195 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3160155 CATGTAAATT
3160165 ATTTTTTATAATA
1 ATTTTTTATAATA
*
3160178 ATTTTTTATCATA
1 ATTTTTTATAATA
3160191 ATTTT
1 ATTTT
3160196 AGAAATTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTTTTTATAATA
Found at i:3161775 original size:20 final size:20
Alignment explanation
Indices: 3161729--3161780 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
3161719 GTGTGGTTAC
*
3161729 ACACGCCTGTGTGGCTTGGG
1 ACACGCTTGTGTGGCTTGGG
3161749 ACACGCTTGTGTGGCTTGGG
1 ACACGCTTGTGTGGCTTGGG
*
3161769 ACACGCTCGTGT
1 ACACGCTTGTGT
3161781 CCTCAGCCCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.25, G:0.37, T:0.27
Consensus pattern (20 bp):
ACACGCTTGTGTGGCTTGGG
Found at i:3163630 original size:49 final size:49
Alignment explanation
Indices: 3163558--3163795 Score: 388
Period size: 49 Copynumber: 4.9 Consensus size: 49
3163548 TCTATTGTGA
* * *
3163558 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGACTGTT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTT
3163607 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTT
3163656 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTT
*
3163705 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TAATT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACT-GTT
* * * *
3163754 GGTCGTATGTGTAGTACTATGTGCAGGCTACTATGCGTACCA
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCA
3163796 AATAGCTTTG
Statistics
Matches: 180, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
48 1 0.01
49 179 0.99
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (49 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTT
Found at i:3169586 original size:16 final size:16
Alignment explanation
Indices: 3169565--3169596 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3169555 GTTGTAATGC
3169565 CCCAAAAATCCCGAAA
1 CCCAAAAATCCCGAAA
*
3169581 CCCAAAAATCCTGAAA
1 CCCAAAAATCCCGAAA
3169597 TCTCGAACTT
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:0.34, G:0.06, T:0.09
Consensus pattern (16 bp):
CCCAAAAATCCCGAAA
Found at i:3170812 original size:419 final size:419
Alignment explanation
Indices: 3170034--3170872 Score: 1678
Period size: 419 Copynumber: 2.0 Consensus size: 419
3170024 GGGAGAAGTG
3170034 ATAGAGCCAAATGGAGAATTGGGCATGGGAAAATTCGGCTATAAGGCTTATAAATAGGTGCTGAA
1 ATAGAGCCAAATGGAGAATTGGGCATGGGAAAATTCGGCTATAAGGCTTATAAATAGGTGCTGAA
3170099 TGCTAGGGTATGAAGCTAATGACGAATTTCCTCCACTCTGTTACCAGAAACTCTTTTCTCTAAAA
66 TGCTAGGGTATGAAGCTAATGACGAATTTCCTCCACTCTGTTACCAGAAACTCTTTTCTCTAAAA
3170164 GCCGAAAACTCTCTGCCTTCTTTTCTTTTTCTTCTTCCTTGTGCCGAATTCTATTTTTCCTCTAC
131 GCCGAAAACTCTCTGCCTTCTTTTCTTTTTCTTCTTCCTTGTGCCGAATTCTATTTTTCCTCTAC
3170229 CTCATTGCTGACTTTTCTTTCTTTTTCCTTGGAGTCGAATAACCCTCTTTTGCAATACAAAATCG
196 CTCATTGCTGACTTTTCTTTCTTTTTCCTTGGAGTCGAATAACCCTCTTTTGCAATACAAAATCG
3170294 TAAAGGGCCGAACCTCTTTGGCCGAATACCCTTGGTGCAATCACTACTCCTACTTTGGTCAAATC
261 TAAAGGGCCGAACCTCTTTGGCCGAATACCCTTGGTGCAATCACTACTCCTACTTTGGTCAAATC
3170359 TAGTGGAATTAGTATTGGATCTTGGATCTTAGCTCATTGCCGAATTGCTCATTAGGTGTTGCGGT
326 TAGTGGAATTAGTATTGGATCTTGGATCTTAGCTCATTGCCGAATTGCTCATTAGGTGTTGCGGT
3170424 TTTGGTAAGTATTCCTCTTCCATTGGCTA
391 TTTGGTAAGTATTCCTCTTCCATTGGCTA
3170453 ATAGAGCCAAATGGAGAATTGGGCATGGGAAAATTCGGCTATAAGGCTTATAAATAGGTGCTGAA
1 ATAGAGCCAAATGGAGAATTGGGCATGGGAAAATTCGGCTATAAGGCTTATAAATAGGTGCTGAA
3170518 TGCTAGGGTATGAAGCTAATGACGAATTTCCTCCACTCTGTTACCAGAAACTCTTTTCTCTAAAA
66 TGCTAGGGTATGAAGCTAATGACGAATTTCCTCCACTCTGTTACCAGAAACTCTTTTCTCTAAAA
3170583 GCCGAAAACTCTCTGCCTTCTTTTCTTTTTCTTCTTCCTTGTGCCGAATTCTATTTTTCCTCTAC
131 GCCGAAAACTCTCTGCCTTCTTTTCTTTTTCTTCTTCCTTGTGCCGAATTCTATTTTTCCTCTAC
3170648 CTCATTGCTGACTTTTCTTTCTTTTTCCTTGGAGTCGAATAACCCTCTTTTGCAATACAAAATCG
196 CTCATTGCTGACTTTTCTTTCTTTTTCCTTGGAGTCGAATAACCCTCTTTTGCAATACAAAATCG
3170713 TAAAGGGCCGAACCTCTTTGGCCGAATACCCTTGGTGCAATCACTACTCCTACTTTGGTCAAATC
261 TAAAGGGCCGAACCTCTTTGGCCGAATACCCTTGGTGCAATCACTACTCCTACTTTGGTCAAATC
3170778 TAGTGGAATTAGTATTGGATCTTGGATCTTAGCTCATTGCCGAATTGCTCATTAGGTGTTGCGGT
326 TAGTGGAATTAGTATTGGATCTTGGATCTTAGCTCATTGCCGAATTGCTCATTAGGTGTTGCGGT
3170843 TTTGGTAAGTATTCCTCTTCCATTGGCTA
391 TTTGGTAAGTATTCCTCTTCCATTGGCTA
3170872 A
1 A
3170873 GGTTGGCCGA
Statistics
Matches: 420, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
419 420 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.36
Consensus pattern (419 bp):
ATAGAGCCAAATGGAGAATTGGGCATGGGAAAATTCGGCTATAAGGCTTATAAATAGGTGCTGAA
TGCTAGGGTATGAAGCTAATGACGAATTTCCTCCACTCTGTTACCAGAAACTCTTTTCTCTAAAA
GCCGAAAACTCTCTGCCTTCTTTTCTTTTTCTTCTTCCTTGTGCCGAATTCTATTTTTCCTCTAC
CTCATTGCTGACTTTTCTTTCTTTTTCCTTGGAGTCGAATAACCCTCTTTTGCAATACAAAATCG
TAAAGGGCCGAACCTCTTTGGCCGAATACCCTTGGTGCAATCACTACTCCTACTTTGGTCAAATC
TAGTGGAATTAGTATTGGATCTTGGATCTTAGCTCATTGCCGAATTGCTCATTAGGTGTTGCGGT
TTTGGTAAGTATTCCTCTTCCATTGGCTA
Found at i:3171510 original size:29 final size:29
Alignment explanation
Indices: 3171455--3171572 Score: 109
Period size: 29 Copynumber: 4.2 Consensus size: 29
3171445 GTGAGCATGA
* **
3171455 ATAT-AATATGATTTGGG-CTAACGGGCC
1 ATATGAATATGAATTGGGCCTAGTGGGCC
* *
3171482 ATATGAATGTGAATTGAGCCTAGTGGGCC
1 ATATGAATATGAATTGGGCCTAGTGGGCC
* *
3171511 ATAAGAATATGAACTGGGCC-AGATGGGCC
1 ATATGAATATGAATTGGGCCTAG-TGGGCC
* * *
3171540 ATTTGGATAAG-ATTGGGCCTAGTGGGCC
1 ATATGAATATGAATTGGGCCTAGTGGGCC
3171568 ATATG
1 ATATG
3171573 CATGTATGTA
Statistics
Matches: 72, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
27 4 0.06
28 29 0.40
29 39 0.54
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.26
Consensus pattern (29 bp):
ATATGAATATGAATTGGGCCTAGTGGGCC
Found at i:3174972 original size:22 final size:22
Alignment explanation
Indices: 3174945--3174995 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
3174935 AACCTTTTTA
*
3174945 CTTTCCCCCAATACTGTTACTT
1 CTTTCCCCCAAAACTGTTACTT
* *
3174967 CTTTCCCCTAAAACTTTTACTT
1 CTTTCCCCCAAAACTGTTACTT
3174989 CTTTCCC
1 CTTTCCC
3174996 ATCCCACCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.18, C:0.37, G:0.02, T:0.43
Consensus pattern (22 bp):
CTTTCCCCCAAAACTGTTACTT
Found at i:3177014 original size:24 final size:24
Alignment explanation
Indices: 3176984--3177064 Score: 162
Period size: 24 Copynumber: 3.4 Consensus size: 24
3176974 TTCTATTATT
3176984 TTATAAAATTAATTCTAATATATA
1 TTATAAAATTAATTCTAATATATA
3177008 TTATAAAATTAATTCTAATATATA
1 TTATAAAATTAATTCTAATATATA
3177032 TTATAAAATTAATTCTAATATATA
1 TTATAAAATTAATTCTAATATATA
3177056 TTATAAAAT
1 TTATAAAAT
3177065 ATCGAAAGTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (24 bp):
TTATAAAATTAATTCTAATATATA
Found at i:3189046 original size:14 final size:14
Alignment explanation
Indices: 3189027--3189100 Score: 52
Period size: 13 Copynumber: 5.6 Consensus size: 14
3189017 ATACAAAAGA
3189027 CATGAAACCATTAT
1 CATGAAACCATTAT
3189041 CATGAAA-CATT-T
1 CATGAAACCATTAT
* *
3189053 ACCT-AACCCATTAT
1 -CATGAAACCATTAT
3189067 CATGAAA-CATT-T
1 CATGAAACCATTAT
* *
3189079 ACCT-AACCCATTAT
1 -CATGAAACCATTAT
3189093 CATGAAAC
1 CATGAAAC
3189101 ATTTACCTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 16
0.65 0.12 0.24
Matches are distributed among these distances:
12 6 0.14
13 24 0.55
14 14 0.32
ACGTcount: A:0.41, C:0.26, G:0.05, T:0.28
Consensus pattern (14 bp):
CATGAAACCATTAT
Found at i:3189067 original size:26 final size:26
Alignment explanation
Indices: 3189034--3189172 Score: 242
Period size: 26 Copynumber: 5.3 Consensus size: 26
3189024 AGACATGAAA
3189034 CCATTATCATGAAACATTTACCTAAC
1 CCATTATCATGAAACATTTACCTAAC
3189060 CCATTATCATGAAACATTTACCTAAC
1 CCATTATCATGAAACATTTACCTAAC
3189086 CCATTATCATGAAACATTTACCTAAC
1 CCATTATCATGAAACATTTACCTAAC
*
3189112 CCATTATCATGGAACATTTACCTAAC
1 CCATTATCATGAAACATTTACCTAAC
* *
3189138 CTATTATCATGGAACATTTACCTAAC
1 CCATTATCATGAAACATTTACCTAAC
*
3189164 CTATTATCA
1 CCATTATCA
3189173 ATTTGTATCA
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 111 1.00
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (26 bp):
CCATTATCATGAAACATTTACCTAAC
Found at i:3193951 original size:9 final size:10
Alignment explanation
Indices: 3193918--3193953 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
3193908 GCCACAATCC
3193918 AATAACACTAA
1 AATAA-ACTAA
3193929 AATAAACTAA
1 AATAAACTAA
3193939 AATAAAC-AA
1 AATAAACTAA
3193948 AATAAA
1 AATAAA
3193954 AAATAACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 8 0.32
10 12 0.48
11 5 0.20
ACGTcount: A:0.72, C:0.11, G:0.00, T:0.17
Consensus pattern (10 bp):
AATAAACTAA
Found at i:3199704 original size:12 final size:13
Alignment explanation
Indices: 3199682--3199710 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3199672 TAAATAAATG
3199682 AATTAAAAAGCCA
1 AATTAAAAAGCCA
3199695 AATT-AAAAGCCA
1 AATTAAAAAGCCA
3199707 AATT
1 AATT
3199711 TTGTCCATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (13 bp):
AATTAAAAAGCCA
Found at i:3200583 original size:42 final size:42
Alignment explanation
Indices: 3200524--3200687 Score: 197
Period size: 42 Copynumber: 3.9 Consensus size: 42
3200514 TTAGGGTTAC
* *
3200524 TGAGATTACGTGTAAGACCATATCTGGGATATGGCATCTATA
1 TGAGATTACGTGTAAGACCATATCTAGGATATAGCATCTATA
* * * * *
3200566 TGAGATTTCGTGTAAGACCATATTTGGGATATGGCATCGATA
1 TGAGATTACGTGTAAGACCATATCTAGGATATAGCATCTATA
*
3200608 TGAGACTT-CGTGTAAGACCATATCTAGGCTATTAGCAT-TGATA
1 TGAGA-TTACGTGTAAGACCATATCTAGGATA-TAGCATCT-ATA
* *
3200651 CGAGATTACATGTAAGACCATATCTAGGATATAGCAT
1 TGAGATTACGTGTAAGACCATATCTAGGATATAGCAT
3200688 TGGTACGGTA
Statistics
Matches: 107, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
42 72 0.67
43 35 0.33
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.31
Consensus pattern (42 bp):
TGAGATTACGTGTAAGACCATATCTAGGATATAGCATCTATA
Found at i:3200681 original size:85 final size:84
Alignment explanation
Indices: 3200524--3200687 Score: 206
Period size: 85 Copynumber: 1.9 Consensus size: 84
3200514 TTAGGGTTAC
* * * * *
3200524 TGAGATTACGTGTAAGACCATATCTGGGATATGGCATCTATATGAGATTTCGTGTAAGACCATAT
1 TGAGATTACGTGTAAGACCATATCTAGGATATAGCATCTATACGAGATTACATGTAAGACCATAT
* * *
3200589 TTGGGATATGGCATCGATA
66 CTAGGATATAGCATCGATA
*
3200608 TGAGACTT-CGTGTAAGACCATATCTAGGCTATTAGCAT-TGATACGAGATTACATGTAAGACCA
1 TGAGA-TTACGTGTAAGACCATATCTAGGATA-TAGCATCT-ATACGAGATTACATGTAAGACCA
3200671 TATCTAGGATATAGCAT
63 TATCTAGGATATAGCAT
3200688 TGGTACGGTA
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
84 27 0.40
85 41 0.60
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.31
Consensus pattern (84 bp):
TGAGATTACGTGTAAGACCATATCTAGGATATAGCATCTATACGAGATTACATGTAAGACCATAT
CTAGGATATAGCATCGATA
Found at i:3204237 original size:40 final size:40
Alignment explanation
Indices: 3204183--3204298 Score: 121
Period size: 40 Copynumber: 3.0 Consensus size: 40
3204173 CGTTTGGATA
** *
3204183 AAAAACGCCACTAAAAATCAAGCATTAGTGGCGCTTTTAT-
1 AAAAACGCTGCTAAAAATCAAGCATTAGCGGCGCTTTT-TG
** * *
3204223 AAAAACGCTGCTAAAGGTCGAGCACTAGCGGCGCTTTTTG
1 AAAAACGCTGCTAAAAATCAAGCATTAGCGGCGCTTTTTG
* *
3204263 GAAAACGCTGCTAAAAAT-AAGCATTACCGGCG-TTTT
1 AAAAACGCTGCTAAAAATCAAGCATTAGCGGCGCTTTT
3204299 CCAAAAAGTG
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
38 4 0.06
39 12 0.19
40 46 0.74
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (40 bp):
AAAAACGCTGCTAAAAATCAAGCATTAGCGGCGCTTTTTG
Found at i:3204410 original size:41 final size:41
Alignment explanation
Indices: 3204353--3204596 Score: 407
Period size: 41 Copynumber: 6.0 Consensus size: 41
3204343 TGAGTTTTTG
*
3204353 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATTCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
*
3204394 GGGCCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
3204435 GGGCCTTTAGCGGCGTTTGTGAATAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
3204476 GGGCCTTTAGCGGCGTTTTTGAATAATCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
3204517 GGGCCTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTT
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
*
3204558 GGGCCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
3204597 CCGCTTTTGA
Statistics
Matches: 192, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 192 1.00
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.29
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
Found at i:3209251 original size:43 final size:43
Alignment explanation
Indices: 3209191--3209281 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
3209181 CTTTGAGTTC
* * * *
3209191 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
*
3209233 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATATTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
3209276 ATTACC
1 ATTACC
3209282 TTGCATATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
Found at i:3209545 original size:16 final size:16
Alignment explanation
Indices: 3209526--3209556 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3209516 TATTATTTGA
3209526 AAAAAATATATTTTTT
1 AAAAAATATATTTTTT
*
3209542 AAAAGATATATTTTT
1 AAAAAATATATTTTT
3209557 AGCGGCGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
AAAAAATATATTTTTT
Found at i:3209643 original size:43 final size:43
Alignment explanation
Indices: 3209554--3209758 Score: 260
Period size: 42 Copynumber: 4.8 Consensus size: 43
3209544 AAGATATATT
* *
3209554 TTTAGCGGCGTTTGTGGGAAAAAGCGCCGCTAAAGCTCAAT-ATC
1 TTTAGCGGCGTTTGTGGG-AAAAGCGCCGCTAAAGGTC-ATGGTC
* *
3209598 TTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
3209641 TTTAGCGACGTTTGTAGGG--AAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGT-GGGAAAAGCGCCGCTAAAGGTCATGGTC
*
3209683 TTTA-CTGGCATTTGTAGGG--AAGCGCCGCTAAAGGTCATGGTC
1 TTTAGC-GGCGTTTGT-GGGAAAAGCGCCGCTAAAGGTCATGGTC
3209725 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
3209759 TTAGCGACGC
Statistics
Matches: 145, Mismatches: 10, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
41 4 0.03
42 72 0.50
43 48 0.33
44 21 0.14
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:3211226 original size:13 final size:13
Alignment explanation
Indices: 3211208--3211232 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3211198 GTATTGATCA
3211208 TGTGTTCACACCT
1 TGTGTTCACACCT
3211221 TGTGTTCACACC
1 TGTGTTCACACC
3211233 ATGATGACCA
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:3212233 original size:99 final size:99
Alignment explanation
Indices: 3212026--3212225 Score: 391
Period size: 99 Copynumber: 2.0 Consensus size: 99
3212016 TCTTCATTGA
3212026 ACAAATATAACTCTTTGATTCAAGACGAACAAAACTTCATCGTTTGGACGATCGGGCAACGAAAA
1 ACAAATATAACTCTTTGATTCAAGACGAACAAAACTTCATCGTTTGGACGATCGGGCAACGAAAA
*
3212091 TGACTCGGATTCATCAACGAGGCCGGGGCGTATC
66 CGACTCGGATTCATCAACGAGGCCGGGGCGTATC
3212125 ACAAATATAACTCTTTGATTCAAGACGAACAAAACTTCATCGTTTGGACGATCGGGCAACGAAAA
1 ACAAATATAACTCTTTGATTCAAGACGAACAAAACTTCATCGTTTGGACGATCGGGCAACGAAAA
3212190 CGACTCGGATTCATCAACGAGGCCGGGGCGTATC
66 CGACTCGGATTCATCAACGAGGCCGGGGCGTATC
3212224 AC
1 AC
3212226 TACTATAATG
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.21
Consensus pattern (99 bp):
ACAAATATAACTCTTTGATTCAAGACGAACAAAACTTCATCGTTTGGACGATCGGGCAACGAAAA
CGACTCGGATTCATCAACGAGGCCGGGGCGTATC
Found at i:3226295 original size:25 final size:25
Alignment explanation
Indices: 3226267--3226324 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
3226257 TTTGAAACCA
* *
3226267 GTAAGCTCTAACGAGCTGCAAATCG
1 GTAAGCTCTAACGAGATACAAATCG
*
3226292 GTAAGGTCTAACGAGATACAAATCG
1 GTAAGCTCTAACGAGATACAAATCG
*
3226317 ATAAGCTC
1 GTAAGCTC
3226325 ATATGAGCTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (25 bp):
GTAAGCTCTAACGAGATACAAATCG
Found at i:3229372 original size:29 final size:29
Alignment explanation
Indices: 3229309--3229376 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
3229299 TAATCAACCA
3229309 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
3229338 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
3229367 CGCACACTTA
1 CGCACACTTA
3229377 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:3229507 original size:173 final size:173
Alignment explanation
Indices: 3229203--3229524 Score: 538
Period size: 173 Copynumber: 1.9 Consensus size: 173
3229193 CAAGGTACTC
* * *
3229203 ACCTTTTTCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATAGAAA
1 ACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATAGAAA
* *
3229268 ATATATACTGGGTTGCACACATAATGTTTAGTAATCAACCACGCACACTTAGTGCCATGCACTTT
66 ATATATACTGGGTTGCACACATAATGCTTAATAATCAACCACGCACACTTAGTGCCATGCACTTT
3229333 AAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCACACTT
131 AAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCACACTT
3229376 ACCTTTTCCGCT-TCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATAGAAA
1 ACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATAGAAA
* * * *
3229440 ATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGTACTT
66 ATATATACTGGGTT-GCACACATAATGCTTAATAATCAACCACGCACACTTAGTGCCATGCACTT
*
3229505 TAAACTCGCACACTTAGTGC
130 TAAACTCACACACTTAGTGC
3229525 TGTACAATTT
Statistics
Matches: 138, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
172 63 0.46
173 75 0.54
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (173 bp):
ACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATAGAAA
ATATATACTGGGTTGCACACATAATGCTTAATAATCAACCACGCACACTTAGTGCCATGCACTTT
AAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCACACTT
Found at i:3229516 original size:29 final size:30
Alignment explanation
Indices: 3229477--3229555 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
3229467 CTTAATAATC
3229477 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
3229507 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
3229536 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
3229556 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:3234432 original size:57 final size:57
Alignment explanation
Indices: 3234364--3234476 Score: 217
Period size: 57 Copynumber: 2.0 Consensus size: 57
3234354 AGGGTTTGAT
*
3234364 ACTCGAATTACGAGCTCAGTAGACTCAACAGGTAGAGTCTTACTGGATGCTAAGGTC
1 ACTCGAATTACGAACTCAGTAGACTCAACAGGTAGAGTCTTACTGGATGCTAAGGTC
3234421 ACTCGAATTACGAACTCAGTAGACTCAACAGGTAGAGTCTTACTGGATGCTAAGGT
1 ACTCGAATTACGAACTCAGTAGACTCAACAGGTAGAGTCTTACTGGATGCTAAGGT
3234477 TTCGCATACA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (57 bp):
ACTCGAATTACGAACTCAGTAGACTCAACAGGTAGAGTCTTACTGGATGCTAAGGTC
Found at i:3240450 original size:34 final size:34
Alignment explanation
Indices: 3240407--3240474 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
3240397 TTGGTTGCAT
3240407 TACTGATATTATAACTGTAATAGGCTAAGGCCCA
1 TACTGATATTATAACTGTAATAGGCTAAGGCCCA
* * * * *
3240441 TACTGATATTGTTATTGTATTGGGCTAAGGCCCA
1 TACTGATATTATAACTGTAATAGGCTAAGGCCCA
3240475 CATTAAAACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (34 bp):
TACTGATATTATAACTGTAATAGGCTAAGGCCCA
Found at i:3258094 original size:45 final size:45
Alignment explanation
Indices: 3258026--3258123 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
3258016 AAGAAGGGTG
* *
3258026 TAATCAACCTTCGTCAACGGTTTAAGCGGGCGAAACCACACTCTT
1 TAATCAACCTTCGTCAACAGTTTAAACGGGCGAAACCACACTCTT
* * * * *
3258071 TAATCGACCTTTGTCAACAGTTTAAACGGGCTAAGCCATACTCTT
1 TAATCAACCTTCGTCAACAGTTTAAACGGGCGAAACCACACTCTT
3258116 TCAATCAA
1 T-AATCAA
3258124 GGCAAGTATC
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
45 39 0.89
46 5 0.11
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.28
Consensus pattern (45 bp):
TAATCAACCTTCGTCAACAGTTTAAACGGGCGAAACCACACTCTT
Found at i:3260965 original size:43 final size:41
Alignment explanation
Indices: 3260910--3260996 Score: 104
Period size: 43 Copynumber: 2.1 Consensus size: 41
3260900 ATATCGTACA
** *
3260910 ATGCCAACGTCCCAAACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAAACAAGGTCTTACATG-AATCAAATA-CG
*
3260953 ATGCC-ACTGTCCCAGACAAGGTCTTACATGAATCAAATACG
1 ATGCCAAC-GTCCCAAACAAGGTCTTACATGAATCAAATACG
3260994 ATG
1 ATG
3260997 ACGCCAGACA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
41 5 0.13
42 10 0.26
43 24 0.62
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (41 bp):
ATGCCAACGTCCCAAACAAGGTCTTACATGAATCAAATACG
Found at i:3262025 original size:20 final size:20
Alignment explanation
Indices: 3262000--3262041 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3261990 ATAAGACAAG
3262000 TTCAATTAAGCACTTTCATA
1 TTCAATTAAGCACTTTCATA
3262020 TTCAATTAAGCACTTTCATA
1 TTCAATTAAGCACTTTCATA
3262040 TT
1 TT
3262042 TAACTATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (20 bp):
TTCAATTAAGCACTTTCATA
Found at i:3268425 original size:27 final size:27
Alignment explanation
Indices: 3268395--3268450 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
3268385 GAGCATAACC
* *
3268395 GTCATTCTACCATACAGGGGTATTACG
1 GTCATTCTACCATACAAGGGCATTACG
* * *
3268422 GTCATTTTGCCCTACAAGGGCATTACG
1 GTCATTCTACCATACAAGGGCATTACG
3268449 GT
1 GT
3268451 TATTTTCCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (27 bp):
GTCATTCTACCATACAAGGGCATTACG
Found at i:3269111 original size:49 final size:49
Alignment explanation
Indices: 3269016--3269127 Score: 129
Period size: 49 Copynumber: 2.3 Consensus size: 49
3269006 AAAGGGTGTG
* **
3269016 ATTACACTCC-TTTTACGGCTTTTCGATAGTAATGGTTTACGGTGTACA
1 ATTACACTCCTTTTTACGGCTTTTCGAAAGTAATGGTTTACAATGTACA
** *
3269064 ATTACACTCCTTTTTTTGGCGTTTT-GAAAGTAATGGTTTCCAATGTACA
1 ATTACACTCCTTTTTACGGC-TTTTCGAAAGTAATGGTTTACAATGTACA
* *
3269113 GTTACACACCTTTTT
1 ATTACACTCCTTTTT
3269128 CTGCAGAATC
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
48 10 0.19
49 40 0.74
50 4 0.07
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (49 bp):
ATTACACTCCTTTTTACGGCTTTTCGAAAGTAATGGTTTACAATGTACA
Found at i:3271858 original size:22 final size:22
Alignment explanation
Indices: 3271830--3271951 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
3271820 TTCCACATCC
3271830 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
3271852 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
3271876 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
3271899 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
3271923 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
3271946 ATCACA
1 ATCACA
3271952 CATACACATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:3271865 original size:47 final size:47
Alignment explanation
Indices: 3271802--3272100 Score: 406
Period size: 47 Copynumber: 6.3 Consensus size: 47
3271792 CCCTTCGGGA
* * *
3271802 CTTATCACATTTATACACT-TCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
3271849 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
* *
3271896 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
3271943 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
** * *
3271990 CTTATCACGCATACACATGTTCACATTCATCACATTGGTCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
3272037 CTTATCACGCATATATATACT-TTCACATTCATCACATTGGCCACTCGGC
1 CTTATCA--CATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
*
3272086 CCTATCACATATATA
1 CTTATCACATATATA
3272101 TACCTGTACA
Statistics
Matches: 230, Mismatches: 18, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
46 1 0.00
47 190 0.83
49 38 0.17
50 1 0.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
Found at i:3274230 original size:85 final size:85
Alignment explanation
Indices: 3274101--3274449 Score: 680
Period size: 85 Copynumber: 4.1 Consensus size: 85
3274091 TATTTTATTG
* *
3274101 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCGCTACCCCAACATGTTTATGACATGTTTT
3274166 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
3274186 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCGCTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCGCTACCCCAACATGTTTATGACATGTTTT
3274251 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
3274271 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCGCTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCGCTACCCCAACATGTTTATGACATGTTTT
3274336 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
3274356 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCGCTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCGCTACCCCAACATGTTTATGACATGTTTT
3274421 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
3274441 CCCATGCTC
1 CCCATGCTC
3274450 ATGGCCGGCC
Statistics
Matches: 262, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 262 1.00
ACGTcount: A:0.26, C:0.27, G:0.09, T:0.38
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCGCTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:3278430 original size:11 final size:14
Alignment explanation
Indices: 3278389--3278432 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
3278379 TATTTGTTTC
*
3278389 ATAAC-ATGCTATA
1 ATAACAATGTTATA
3278402 ATAACAATGTTATA
1 ATAACAATGTTATA
3278416 ATAACAATGTTATA
1 ATAACAATGTTATA
3278430 ATA
1 ATA
3278433 TATTAATCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 5 0.17
14 24 0.83
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (14 bp):
ATAACAATGTTATA
Found at i:3288171 original size:40 final size:40
Alignment explanation
Indices: 3288126--3288437 Score: 369
Period size: 40 Copynumber: 7.8 Consensus size: 40
3288116 ATAACCACAA
* * *
3288126 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* *
3288166 GCACAAATGCCTTCGGGTCATAGCCCGGATATACCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * * *
3288206 GCACAAAGGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* * *
3288246 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * *
3288286 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* * *
3288326 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * *
3288366 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* *
3288406 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
3288438 CATTCAAATG
Statistics
Matches: 229, Mismatches: 38, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
39 7 0.03
40 213 0.93
41 9 0.04
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:3288210 original size:80 final size:80
Alignment explanation
Indices: 3288126--3288437 Score: 455
Period size: 80 Copynumber: 3.9 Consensus size: 80
3288116 ATAACCACAA
* * * * * * * *
3288126 GCACAATTGCCTTCGGGTCTTAACCCGGGT-ATAGCAACTCGCACAAATGCCTTCGGGTCATAGC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAAC
*
3288190 CCGGATATACCAACTC
65 CCGGATATAGCAACTC
* *
3288206 GCACAAAGGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAACC
*
3288271 CGGGTATAGCAACTC
66 CGGATATAGCAACTC
*
3288286 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAACC
*
3288351 CGGGTATAGCAACTC
66 CGGATATAGCAACTC
* * *
3288366 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCATAAATGCCTTCGGGACTTAGCC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAACC
3288431 CGGATAT
66 CGGATAT
3288438 CATTCAAATG
Statistics
Matches: 213, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
80 210 0.99
81 3 0.01
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAACC
CGGATATAGCAACTC
Found at i:3288330 original size:120 final size:121
Alignment explanation
Indices: 3288106--3288436 Score: 418
Period size: 120 Copynumber: 2.8 Consensus size: 121
3288096 TCTTCGGAAT
* *
3288106 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATAAAACCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
* * *
3288170 AAATGCCTTCGGGTCATAGCCCGGAT-ATACCAACTCGCACAAAGGCCTTCGGGTC
66 AAATGCCTTCGGGTCTTAGCCCGGATAAAACCAACTAGCACAAAGGCCTTCGGGTC
*
3288225 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATAAAACCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
* **
3288290 AAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTAGCACAATTGCCTTCGGGTC
66 AAATGCCTTCGGGTCTTAGCCCGGATAAAACCAACTAGCACAAAGGCCTTCGGGTC
* * * * * * * * * * * *
3288345 TTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTAGCA
1 TTAGCCCGGATAAAACCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGT-ATAGCAACTCGCA
* *
3288409 TAAATGCCTTCGGGACTTAGCCCGGATA
65 CAAATGCCTTCGGGTCTTAGCCCGGATA
3288437 TCATTCAAAT
Statistics
Matches: 185, Mismatches: 24, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
119 4 0.02
120 175 0.95
121 6 0.03
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (121 bp):
TTAGCCCGGATAAAACCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
AAATGCCTTCGGGTCTTAGCCCGGATAAAACCAACTAGCACAAAGGCCTTCGGGTC
Found at i:3291499 original size:35 final size:35
Alignment explanation
Indices: 3291423--3291513 Score: 96
Period size: 35 Copynumber: 2.6 Consensus size: 35
3291413 CACAGGTAAG
* *
3291423 TACATGTAAGCTTATTTTGAACTTGTATATTCGGC
1 TACATGTAAGCTTATATTGAACTTGTATATTCGAC
* * * *
3291458 TGCATGTAAGGTTATATTGAA-TTTTAGTATTCGAT
1 TACATGTAAGCTTATATTGAACTTGTA-TATTCGAC
3291493 TACATGTGAA-CTTATATTGAA
1 TACATGT-AAGCTTATATTGAA
3291514 AATGTATACT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
34 4 0.09
35 40 0.87
36 2 0.04
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.43
Consensus pattern (35 bp):
TACATGTAAGCTTATATTGAACTTGTATATTCGAC
Found at i:3293601 original size:16 final size:15
Alignment explanation
Indices: 3293581--3293614 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3293571 CGTCACATCC
3293581 TAAAAATCGGGTTAG
1 TAAAAATCGGGTTAG
**
3293596 TAAAAATTTGGTTAG
1 TAAAAATCGGGTTAG
3293611 TAAA
1 TAAA
3293615 TTGAGAGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.32
Consensus pattern (15 bp):
TAAAAATCGGGTTAG
Found at i:3299717 original size:54 final size:54
Alignment explanation
Indices: 3299639--3299743 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
3299629 TAGCTTACCT
*
3299639 AGAGGTCCCATGTTCGAATATTCTATGTGTATAAAATGGAAATATTTTTATCCC
1 AGAGGTCCCATGTTCGAATATTCTATGTGTATAAAATGGAAACATTTTTATCCC
* * * *
3299693 AGAGGTCTCATTTTCGAATCTTCTATGTGTGTAAAATGGAAACATTTTTAT
1 AGAGGTCCCATGTTCGAATATTCTATGTGTATAAAATGGAAACATTTTTAT
3299744 TCCCTCTTAC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (54 bp):
AGAGGTCCCATGTTCGAATATTCTATGTGTATAAAATGGAAACATTTTTATCCC
Found at i:3301781 original size:21 final size:21
Alignment explanation
Indices: 3301732--3301798 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
3301722 CCTCTTTGAA
* * *
3301732 CCATAACCAATTCGTACCAAATA
1 CCAT-ACCATTTCATACC-AATT
*
3301755 CCATACTATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
3301776 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
3301797 CC
1 CC
3301799 CAAATACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 24 0.63
22 10 0.26
23 4 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:3302809 original size:47 final size:46
Alignment explanation
Indices: 3302756--3302857 Score: 132
Period size: 47 Copynumber: 2.2 Consensus size: 46
3302746 GTGGTTTAAC
*
3302756 CACATATCTGTCCTGGCAACTTGATTGCAATTATAGTGGCTCGACCA
1 CACATATCTGTCATGGCAACTTGATTGCAA-TATAGTGGCTCGACCA
* * * * *
3302803 CACATATCTTTTATGGCAGCTTGATTGTAATATAGTGGCTTGACCA
1 CACATATCTGTCATGGCAACTTGATTGCAATATAGTGGCTCGACCA
*
3302849 CATATATCT
1 CACATATCT
3302858 AATATGCCAG
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
46 23 0.48
47 25 0.52
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (46 bp):
CACATATCTGTCATGGCAACTTGATTGCAATATAGTGGCTCGACCA
Found at i:3302856 original size:46 final size:47
Alignment explanation
Indices: 3302769--3302857 Score: 135
Period size: 46 Copynumber: 1.9 Consensus size: 47
3302759 ATATCTGTCC
3302769 TGGCAACTTGATTGCAATTATAGTGGCTCGACCACACATATCTTTTA
1 TGGCAACTTGATTGCAATTATAGTGGCTCGACCACACATATCTTTTA
* * * *
3302816 TGGCAGCTTGATTGTAA-TATAGTGGCTTGACCACATATATCT
1 TGGCAACTTGATTGCAATTATAGTGGCTCGACCACACATATCT
3302858 AATATGCCAG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
46 23 0.61
47 15 0.39
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (47 bp):
TGGCAACTTGATTGCAATTATAGTGGCTCGACCACACATATCTTTTA
Found at i:3306027 original size:93 final size:93
Alignment explanation
Indices: 3305914--3306085 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
3305904 GCCCATAAGT
* *
3305914 GAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAATGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
3305979 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
3306007 GAACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAATGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
3306072 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
3306086 CAAATATCCT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAATGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:3306081 original size:46 final size:46
Alignment explanation
Indices: 3305906--3306081 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
3305896 TGTAACCCGC
* * *
3305906 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
3305952 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** * *
3305998 ACATCTCTCGAACTCGGACTCAACTCAATGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
3306045 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
3306082 TGCCCAAATA
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 68 0.63
47 31 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:3308497 original size:353 final size:353
Alignment explanation
Indices: 3307851--3308559 Score: 1089
Period size: 353 Copynumber: 2.0 Consensus size: 353
3307841 GCAAACCAAA
*
3307851 TATGAAAATATAATGAGACTAATTCTAAATTATCAATTAAACTACCTAAATTAAGATTTCTTCCT
1 TATGAAAATATAATGAGACTAATTCTAAATTATCAATTAAACTACCTAAACTAAGATTTCTTCCT
* * *
3307916 ATTGTATTCGACTATGCACATGATAAAAATGATGGTTGATTGATTAGTCAATTACTAATTAAGCC
66 ATTGTATTCGACTATGCAAATGATAAAAACGATGGTTGATTGATTAGTCAATTACTAACTAAGCC
* * ** **
3307981 AATAACCTATCTCGATTAGATTGCTTGCCACTCATCACTAGAATCTTGTCTTAGTCTCATCCTAA
131 AATAACCTATCCCAATTAGATCACTTGCCACTCATCACTAGAATCTCCTCTTAGTCTCATCCTAA
* * * *
3308046 TTCGGAATTGCCAACTAAGGTCTTCTCTTAGTCTCACTTAGACAAGTAGTTCTTCTCTCAATCTC
196 TTCGAAATTGACAACTAAGGTCTTCTCTCAATCTCACTTAGACAAGTAGTTCTTCTCTCAATCTC
* * *
3308111 ACTACCCAGTACAATTATATCGAACTGTTAAGGATAAACTCTCCTCTCTATCTTATTTATCTAGA
261 ACTACCCAGTACAATTATATCAAACTATTAAGGATAAACTCTCCTCTCTATCTTACTTATCTAGA
*
3308176 TTTTCCACTAGAAGCATCAATTTTAGCG
326 TTTTCCACTAGAAGCATCAATTCTAGCG
*
3308204 TATGAAAATATAATGAGACTAATTTTAAATTATCAATTAAACTACCTAAACTAAGATTTCTTCCT
1 TATGAAAATATAATGAGACTAATTCTAAATTATCAATTAAACTACCTAAACTAAGATTTCTTCCT
*
3308269 ATTGTATTCGACTATGCAAATGATAAAAACGATGGTTGATTGATTAGTCGATTACTAACTAAGCC
66 ATTGTATTCGACTATGCAAATGATAAAAACGATGGTTGATTGATTAGTCAATTACTAACTAAGCC
** *
3308334 AATAACCTATCCCAATTAGATCACTTGTGACTCCTCACTAGAATCTCCT-TTCAGTCTCATCCTA
131 AATAACCTATCCCAATTAGATCACTTGCCACTCATCACTAGAATCTCCTCTT-AGTCTCATCCTA
* * * * *
3308398 ATTTGAAATT-ACAACCTAAGTTTTTCTCTCAATCTCACTTTGACAAGTTGTTCTTCTCTCAATC
195 ATTCGAAATTGACAA-CTAAGGTCTTCTCTCAATCTCACTTAGACAAGTAGTTCTTCTCTCAATC
* * *
3308462 TCACTACTCGGTACAATTATATCAAACTATTAAGGATAAACTCTCCTCTCTATCTTGCTTATCTA
259 TCACTACCCAGTACAATTATATCAAACTATTAAGGATAAACTCTCCTCTCTATCTTACTTATCTA
* *
3308527 GATTTTCTACTAGAAGCATCAATTCTAGTG
324 GATTTTCCACTAGAAGCATCAATTCTAGCG
3308557 TAT
1 TAT
3308560 TAAGTAATTC
Statistics
Matches: 321, Mismatches: 33, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
352 5 0.02
353 316 0.98
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (353 bp):
TATGAAAATATAATGAGACTAATTCTAAATTATCAATTAAACTACCTAAACTAAGATTTCTTCCT
ATTGTATTCGACTATGCAAATGATAAAAACGATGGTTGATTGATTAGTCAATTACTAACTAAGCC
AATAACCTATCCCAATTAGATCACTTGCCACTCATCACTAGAATCTCCTCTTAGTCTCATCCTAA
TTCGAAATTGACAACTAAGGTCTTCTCTCAATCTCACTTAGACAAGTAGTTCTTCTCTCAATCTC
ACTACCCAGTACAATTATATCAAACTATTAAGGATAAACTCTCCTCTCTATCTTACTTATCTAGA
TTTTCCACTAGAAGCATCAATTCTAGCG
Found at i:3310128 original size:19 final size:19
Alignment explanation
Indices: 3310104--3310142 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3310094 TCAACCAAGA
* *
3310104 TTTTTACAATATTACATTT
1 TTTTTAAAATATTAAATTT
*
3310123 TTTTTAAAATTTTAAATTT
1 TTTTTAAAATATTAAATTT
3310142 T
1 T
3310143 ATGTTAGACC
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:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTAAAATATTAAATTT
Found at i:3322720 original size:18 final size:18
Alignment explanation
Indices: 3322699--3322756 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
3322689 TATATACTTA
3322699 CTTACTAAGCTATATAAG
1 CTTACTAAGCTATATAAG
* *
3322717 CTTACTTA--TATACTTA-
1 CTTACTAAGCTATA-TAAG
3322733 CTTACTAAGCTATATAAG
1 CTTACTAAGCTATATAAG
3322751 CTTACT
1 CTTACT
3322757 TTCTTTTCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 11 0.34
17 4 0.12
18 17 0.53
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (18 bp):
CTTACTAAGCTATATAAG
Found at i:3322731 original size:34 final size:34
Alignment explanation
Indices: 3322688--3322757 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
3322678 TTGTTATTAT
3322688 TTATATACTTACTTACTAAGCTATATAAGCTTAC
1 TTATATACTTACTTACTAAGCTATATAAGCTTAC
3322722 TTATATACTTACTTACTAAGCTATATAAGCTTAC
1 TTATATACTTACTTACTAAGCTATATAAGCTTAC
3322756 TT
1 TT
3322758 TCTTTTCTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (34 bp):
TTATATACTTACTTACTAAGCTATATAAGCTTAC
Found at i:3334063 original size:39 final size:40
Alignment explanation
Indices: 3334002--3334220 Score: 214
Period size: 40 Copynumber: 5.5 Consensus size: 40
3333992 AAGCCAAGTA
* * * *
3334002 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCTCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCACACAAATG
*
3334040 CCTTCGGGACATAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
* * * *
3334080 CCTTTGGGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
* * * *
3334120 CCTTCGGGACTTAGCCCGAAATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCG-GATATAGTAACTCACACAAATG
* * *
3334161 CCTTCGGGACTTAGCCCAGA-ACTAGTCACT-AGCGCAAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCA-CAC-AAATG
3334202 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
3334221 TTATCATCCA
Statistics
Matches: 154, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
38 12 0.08
39 16 0.10
40 65 0.42
41 61 0.40
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
Found at i:3334156 original size:41 final size:40
Alignment explanation
Indices: 3334036--3334219 Score: 228
Period size: 40 Copynumber: 4.5 Consensus size: 40
3334026 CTACTCTCTC
* * * * *
3334036 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCACACA
1 AATGCCTTCGGGACTTAGCCCGAATGTAATAACTCGCACA
* *
3334076 AATGCCTTTGGGACTTAGCCCGGATGTAATAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGAATGTAATAACTCGCACA
3334116 AATGCCTTCGGGACTTAGCCCGAAATGTAATAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCG-AATGTAATAACTCGCACA
* * *
3334157 AATGCCTTCGGGACTTAGCCCAGAA-CTAGTCACTAGCGCA-A
1 AATGCCTTCGGGACTTAGCCC-GAATGTAATAACT--CGCACA
3334198 AATGCCTTCGGGACTTAGCCCG
1 AATGCCTTCGGGACTTAGCCCG
3334220 GTTATCATCC
Statistics
Matches: 130, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
40 63 0.48
41 62 0.48
42 5 0.04
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGAATGTAATAACTCGCACA
Found at i:3334170 original size:81 final size:80
Alignment explanation
Indices: 3334036--3334219 Score: 235
Period size: 81 Copynumber: 2.3 Consensus size: 80
3334026 CTACTCTCTC
* * * * * *
3334036 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCACACAAATGCCTTTGGGACTTAGCCCGGAT
1 AATGCCTTCGGGACTTAGCCCGAATATAATAACTCACACAAATGCCTTCGGGACTTAGCCCAGAA
*
3334101 GTAATAACT-CGCACA
66 CTAATAACTACGCA-A
* *
3334116 AATGCCTTCGGGACTTAGCCCGAAATGTAATAACTCGCACAAATGCCTTCGGGACTTAGCCCAGA
1 AATGCCTTCGGGACTTAGCCCG-AATATAATAACTCACACAAATGCCTTCGGGACTTAGCCCAGA
* *
3334181 ACTAGTCACTAGCGCAA
65 ACTAATAACTA-CGCAA
3334198 AATGCCTTCGGGACTTAGCCCG
1 AATGCCTTCGGGACTTAGCCCG
3334220 GTTATCATCC
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
80 21 0.23
81 42 0.47
82 23 0.26
83 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGAATATAATAACTCACACAAATGCCTTCGGGACTTAGCCCAGAA
CTAATAACTACGCAA
Found at i:3341485 original size:52 final size:51
Alignment explanation
Indices: 3341423--3341522 Score: 132
Period size: 52 Copynumber: 1.9 Consensus size: 51
3341413 AATGGAAATC
3341423 GGCATTCCGTGCAATCTAACAAACAC-T-GAAATGTACAATTCAACTAATCTA
1 GGCATTCCGTGCAATCTAAC-AAC-CTTAGAAATGTACAATTCAACTAATCTA
* * *
3341474 NGGCATTCCGTGCAATCTCACAACCTTAGGAATGTACAATTCAGCTAAT
1 -GGCATTCCGTGCAATCTAACAACCTTAGAAATGTACAATTCAACTAAT
3341523 TATCAAGTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
50 1 0.02
51 4 0.09
52 38 0.88
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.26
Consensus pattern (51 bp):
GGCATTCCGTGCAATCTAACAACCTTAGAAATGTACAATTCAACTAATCTA
Found at i:3344583 original size:25 final size:28
Alignment explanation
Indices: 3344555--3344608 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
3344545 ATGTGAATGT
*
3344555 TGTG-ATGGTTTG-ATA-TCAATGGATG
1 TGTGAATGGTATGTATATTCAATGGATG
3344580 TGTGATATGGTATGTATATTCAATGGATG
1 TGTGA-ATGGTATGTATATTCAATGGATG
3344609 AACTTTGATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 4 0.17
27 7 0.29
28 3 0.12
29 10 0.42
ACGTcount: A:0.26, C:0.04, G:0.30, T:0.41
Consensus pattern (28 bp):
TGTGAATGGTATGTATATTCAATGGATG
Found at i:3354640 original size:40 final size:40
Alignment explanation
Indices: 3354561--3354737 Score: 207
Period size: 40 Copynumber: 4.5 Consensus size: 40
3354551 CGGATGATAA
* * * *
3354561 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * * * *
3354601 CTGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
* *
3354641 CCAGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
*
3354681 CCGGGCTAGGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
3354721 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
3354738 ATACTTGGGT
Statistics
Matches: 114, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
38 1 0.01
39 14 0.12
40 97 0.85
41 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:3354699 original size:80 final size:79
Alignment explanation
Indices: 3354561--3354737 Score: 241
Period size: 80 Copynumber: 2.2 Consensus size: 79
3354551 CGGATGATAA
* * * *
3354561 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATATCTGGGCTATGTCCCGAAGGCATTTA
1 CCGG-CTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAGGACCCGAAGGCATTTA
*
3354626 TGCTAG-TGATTATAT
65 TGCGAGTTG-TTATAT
* *
3354641 CCAGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAGGACCCGAAGGCATTTG
1 CC-GGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAGGACCCGAAGGCATTTA
3354706 TGCGAGTTGTTATAT
65 TGCGAGTTGTTATAT
3354721 CCGGCTAA-ATCCCGAAG
1 CCGGCTAAGA-CCCGAAG
3354738 ATACTTGGGT
Statistics
Matches: 87, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
78 1 0.01
79 13 0.15
80 69 0.79
81 4 0.05
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (79 bp):
CCGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAGGACCCGAAGGCATTTAT
GCGAGTTGTTATAT
Found at i:3355005 original size:22 final size:22
Alignment explanation
Indices: 3354965--3355006 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3354955 GAATGTGCAT
*
3354965 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
3354987 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
3355007 TCAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Found at i:3362773 original size:29 final size:27
Alignment explanation
Indices: 3362755--3362824 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
3362745 ATATTAAGTC
3362755 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
3362782 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
3362810 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
3362825 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:3362818 original size:28 final size:28
Alignment explanation
Indices: 3362755--3362852 Score: 126
Period size: 28 Copynumber: 3.5 Consensus size: 28
3362745 ATATTAAGTC
*
3362755 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
3362782 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * * *
3362810 CGCACACTTAGTGCTGTACAATTTAGACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
3362839 CGCACACTTAGTGC
1 CGCACACTTAGTGC
3362853 CAATCTCATG
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 22 0.35
28 23 0.37
29 18 0.29
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:3368745 original size:28 final size:27
Alignment explanation
Indices: 3368701--3368802 Score: 125
Period size: 28 Copynumber: 3.7 Consensus size: 27
3368691 GGCCCCTTTA
* *
3368701 GGCCTAATCTCATTCATATGGCCCATC
1 GGCCCAATCACATTCATATGGCCCATC
*
3368728 GGTCCCAATCACATTCATATGGCCCATTA
1 GG-CCCAATCACATTCATATGGCCCA-TC
*
3368757 GGCCCAATCAC-TTCCATATGGCCCGTC
1 GGCCCAATCACATT-CATATGGCCCATC
3368784 AGGCCCAATCACATTCATA
1 -GGCCCAATCACATTCATA
3368803 GTCATGCAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
27 5 0.08
28 55 0.85
29 5 0.08
ACGTcount: A:0.25, C:0.34, G:0.15, T:0.25
Consensus pattern (27 bp):
GGCCCAATCACATTCATATGGCCCATC
Found at i:3369029 original size:8 final size:8
Alignment explanation
Indices: 3369016--3369058 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
3369006 GTAGCCAAAC
*
3369016 TTTCGGCT
1 TTTCGGCA
3369024 TTTCGGCA
1 TTTCGGCA
*
3369032 TTTCGGCT
1 TTTCGGCA
*
3369040 TTTCAGCA
1 TTTCGGCA
*
3369048 TTTCGGGA
1 TTTCGGCA
3369056 TTT
1 TTT
3369059 ACCGATCTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (8 bp):
TTTCGGCA
Found at i:3369037 original size:16 final size:16
Alignment explanation
Indices: 3369016--3369053 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
3369006 GTAGCCAAAC
*
3369016 TTTCGGCTTTTCGGCA
1 TTTCGGCTTTTCAGCA
3369032 TTTCGGCTTTTCAGCA
1 TTTCGGCTTTTCAGCA
3369048 TTTCGG
1 TTTCGG
3369054 GATTTACCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.08, C:0.24, G:0.24, T:0.45
Consensus pattern (16 bp):
TTTCGGCTTTTCAGCA
Found at i:3373554 original size:71 final size:69
Alignment explanation
Indices: 3373405--3373584 Score: 209
Period size: 71 Copynumber: 2.6 Consensus size: 69
3373395 TTTTGGAAAG
* * *
3373405 CACATTAAGCATTTAAAATGGACTTAAATGAACACATTTTCAAGACAACAAATCAACCCTTTACA
1 CACATTAAGCATTTAAAATGAACGTAAATGAACACATTTTCAAGACAACAAATCAACACTTTACA
*
3373470 GCAG
66 GCAA
* * * * * * * *
3373474 CACATTAAGCATCTAAAATTAACGTGAGTGAACACATTTTTTTAAGATAACAAATTAGCACTTTA
1 CACATTAAGCATTTAAAATGAACGTAAATGAACACA--TTTTCAAGACAACAAATCAACACTTTA
3373539 CAGCAA
64 CAGCAA
*
3373545 CACATTAAGCATTT-AAATCGAACGTAAATGAAGACATTTT
1 CACATTAAGCATTTAAAAT-GAACGTAAATGAACACATTTT
3373585 TAATATAACA
Statistics
Matches: 91, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
69 34 0.37
70 4 0.04
71 53 0.58
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.28
Consensus pattern (69 bp):
CACATTAAGCATTTAAAATGAACGTAAATGAACACATTTTCAAGACAACAAATCAACACTTTACA
GCAA
Found at i:3381939 original size:28 final size:28
Alignment explanation
Indices: 3381874--3382024 Score: 214
Period size: 28 Copynumber: 5.4 Consensus size: 28
3381864 GAGATTGGCG
* * * *
3381874 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
3381903 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
3381931 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
3381959 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
3381987 CTAAGTGTGCAAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
3382014 CTGAGTGTGCG
1 CTAAGTGTGCG
3382025 GACTTAATAT
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 23 0.20
28 75 0.66
29 15 0.13
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:3387137 original size:26 final size:27
Alignment explanation
Indices: 3387108--3387161 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
3387098 TCACACAAGT
*
3387108 TAGTCATTT-ACGCACGAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
* *
3387134 TAGTCATTTAACACCCTAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
3387161 T
1 T
3387162 GGTAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (27 bp):
TAGTCATTTAACACACGAGGGGCAAAA
Found at i:3387239 original size:54 final size:54
Alignment explanation
Indices: 3387166--3387280 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
3387156 CAAAATGGTA
* *
3387166 ATTT-TACCCTACAATGGTATCTCGGTAATTCTATCCTACAGGGGTATTTCGGT
1 ATTTCTACCCTACAAGGGTATCTCGGTAATTCTATCCTACAGGGGTATTTCGAT
* * * *
3387219 ATTTCTACCCTACAAGGGTATTTTGGTAATTCTATTCTATAGGGGTATTTCGAT
1 ATTTCTACCCTACAAGGGTATCTCGGTAATTCTATCCTACAGGGGTATTTCGAT
*
3387273 AATTCTAC
1 ATTTCTAC
3387281 AACTTATCCA
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
53 4 0.07
54 50 0.93
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.40
Consensus pattern (54 bp):
ATTTCTACCCTACAAGGGTATCTCGGTAATTCTATCCTACAGGGGTATTTCGAT
Found at i:3387277 original size:27 final size:27
Alignment explanation
Indices: 3387162--3387279 Score: 128
Period size: 27 Copynumber: 4.4 Consensus size: 27
3387152 GGGGCAAAAT
* * ** *
3387162 GGTAATTTTACCCTACAATGGTATCTC
1 GGTAATTCTATCCTACAGGGGTATTTC
3387189 GGTAATTCTATCCTACAGGGGTATTTC
1 GGTAATTCTATCCTACAGGGGTATTTC
* * * *
3387216 GGTATTTCTACCCTACAAGGGTATTTT
1 GGTAATTCTATCCTACAGGGGTATTTC
* *
3387243 GGTAATTCTATTCTATAGGGGTATTTC
1 GGTAATTCTATCCTACAGGGGTATTTC
*
3387270 GATAATTCTA
1 GGTAATTCTA
3387280 CAACTTATCC
Statistics
Matches: 75, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 75 1.00
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.40
Consensus pattern (27 bp):
GGTAATTCTATCCTACAGGGGTATTTC
Found at i:3392692 original size:27 final size:26
Alignment explanation
Indices: 3392644--3392695 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
3392634 GCGAGGCTGC
*
3392644 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
3392670 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
3392696 TTGCAGCGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:3393709 original size:47 final size:47
Alignment explanation
Indices: 3393640--3393732 Score: 168
Period size: 47 Copynumber: 2.0 Consensus size: 47
3393630 GCCCTGTCCC
*
3393640 ACAAAAATCTGTTTATCTCTTAATATACTGCCCATATGATATTTTCA
1 ACAAAAATCTGTTTATCTCTTAATATACAGCCCATATGATATTTTCA
*
3393687 ACAAAAATCTGTTTATCTCTTAATATACAGCCCATATGATCTTTTC
1 ACAAAAATCTGTTTATCTCTTAATATACAGCCCATATGATATTTTC
3393733 GTTACTTCCT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.40
Consensus pattern (47 bp):
ACAAAAATCTGTTTATCTCTTAATATACAGCCCATATGATATTTTCA
Found at i:3394599 original size:27 final size:27
Alignment explanation
Indices: 3394569--3394746 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
3394559 ATATTGAGTC
* * * *
3394569 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
3394596 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
3394623 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
3394651 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
3394678 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
3394705 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
3394732 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
3394747 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:3394708 original size:82 final size:81
Alignment explanation
Indices: 3394590--3394745 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
3394580 TGCTATATAA
* *
3394590 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
3394655 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
3394672 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
3394736 CACTTAGTGC
65 CACTTAGTGC
3394746 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:3402077 original size:42 final size:43
Alignment explanation
Indices: 3402018--3402131 Score: 140
Period size: 42 Copynumber: 2.7 Consensus size: 43
3402008 AATTAAGAAG
* * * **
3402018 TCCGAACTCGTTGAGTGGTCCGGGTTCGTGATATATG-TGGCA
1 TCCGAACTCGTTGAGTGGTCCGAGTTCATGATAGATGCAAGCA
* *
3402060 TCCGAACTCGTTGAGTGGTCCGAGTTCATTATGGATGCAAGCA
1 TCCGAACTCGTTGAGTGGTCCGAGTTCATGATAGATGCAAGCA
* *
3402103 TCCGAGCTCGTTGAGTGGTCTGAGTTCAT
1 TCCGAACTCGTTGAGTGGTCCGAGTTCAT
3402132 AATGGATGTG
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
42 32 0.52
43 30 0.48
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.31
Consensus pattern (43 bp):
TCCGAACTCGTTGAGTGGTCCGAGTTCATGATAGATGCAAGCA
Found at i:3402118 original size:43 final size:43
Alignment explanation
Indices: 3402018--3402139 Score: 147
Period size: 43 Copynumber: 2.9 Consensus size: 43
3402008 AATTAAGAAG
* * * ** **
3402018 TCCGAACTCGTTGAGTGGTCCGGGTTCGTGATATATG-TGGCA
1 TCCGAACTCGTTGAGTGGTCCGAGTTCATAATGGATGCAAGCA
*
3402060 TCCGAACTCGTTGAGTGGTCCGAGTTCATTATGGATGCAAGCA
1 TCCGAACTCGTTGAGTGGTCCGAGTTCATAATGGATGCAAGCA
* *
3402103 TCCGAGCTCGTTGAGTGGTCTGAGTTCATAATGGATG
1 TCCGAACTCGTTGAGTGGTCCGAGTTCATAATGGATG
3402140 TGATACATGT
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
42 32 0.46
43 37 0.54
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.30
Consensus pattern (43 bp):
TCCGAACTCGTTGAGTGGTCCGAGTTCATAATGGATGCAAGCA
Found at i:3405620 original size:40 final size:40
Alignment explanation
Indices: 3405567--3406591 Score: 1987
Period size: 40 Copynumber: 25.6 Consensus size: 40
3405557 CATTGGATTA
* *
3405567 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATGATA
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
*
3405607 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATA
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
*
3405647 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATA
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
*
3405687 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATA
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
3405727 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
3405767 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
3405807 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
3405847 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
3405887 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
3405927 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
3405967 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
3406007 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
3406047 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
3406087 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
3406127 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
3406167 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
3406207 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
3406247 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
3406287 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
3406327 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
3406367 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
3406407 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
3406447 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
3406487 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
*
3406527 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATA
1 TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
*
3406567 TATCCGGGTTAAGACCCGAAGGCAA
1 TATCCGGGCTAAGACCCGAAGGCAA
3406592 ATGTGTTTGT
Statistics
Matches: 981, Mismatches: 4, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 981 1.00
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.22
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATG
Found at i:3408167 original size:13 final size:13
Alignment explanation
Indices: 3408149--3408173 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3408139 AATTGACCAC
3408149 ATGGCCATGTGAT
1 ATGGCCATGTGAT
3408162 ATGGCCATGTGA
1 ATGGCCATGTGA
3408174 CACTAAATTG
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:0.16, G:0.32, T:0.28
Consensus pattern (13 bp):
ATGGCCATGTGAT
Found at i:3419827 original size:34 final size:34
Alignment explanation
Indices: 3419781--3419862 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 34
3419771 GTAAACAGTT
* * *
3419781 TGGGCCTAAGCCC-TTATCAGTAGCAATATTAGTG
1 TGGGCCTTAGCCCATTA-CAGTAACAATAGTAGTG
*
3419815 TGGGCCTTAGCCCATTACAGTAACAGTAGTAGTG
1 TGGGCCTTAGCCCATTACAGTAACAATAGTAGTG
*
3419849 TAGGCCTTAGCCCA
1 TGGGCCTTAGCCCA
3419863 ATTCAATACA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
34 39 0.93
35 3 0.07
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (34 bp):
TGGGCCTTAGCCCATTACAGTAACAATAGTAGTG
Found at i:3428879 original size:22 final size:22
Alignment explanation
Indices: 3428851--3428897 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3428841 CCTTTTTGAA
3428851 CCCTTACCATTTCGTACCAAAT
1 CCCTTACCATTTCGTACCAAAT
*
3428873 CCCTTACCATTTCGTACCAATT
1 CCCTTACCATTTCGTACCAAAT
3428895 CCC
1 CCC
3428898 AAATACCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.40, G:0.04, T:0.32
Consensus pattern (22 bp):
CCCTTACCATTTCGTACCAAAT
Found at i:3429180 original size:41 final size:41
Alignment explanation
Indices: 3429135--3429255 Score: 123
Period size: 41 Copynumber: 3.1 Consensus size: 41
3429125 GTATCAAATT
3429135 TTTTCTTTATTTCTACTTGTGCTGAATCATTATCTAATCTA
1 TTTTCTTTATTTCTACTTGTGCTGAATCATTATCTAATCTA
* * ** * *
3429176 TTTTCTGT-TCT-TA-TTGTG-T-TTTCACTGTC-AAT-T-
1 TTTTCTTTATTTCTACTTGTGCTGAATCATTATCTAATCTA
*
3429209 CTTTCTTTATTTCTACTTGTGCTGAATCATTATCTAATCTA
1 TTTTCTTTATTTCTACTTGTGCTGAATCATTATCTAATCTA
3429250 TTTTCT
1 TTTTCT
3429256 GTTCTTATTG
Statistics
Matches: 58, Mismatches: 14, Indels: 16
0.66 0.16 0.18
Matches are distributed among these distances:
33 6 0.10
34 3 0.05
35 5 0.09
36 11 0.19
37 2 0.03
38 11 0.19
39 5 0.09
40 3 0.05
41 12 0.21
ACGTcount: A:0.18, C:0.17, G:0.08, T:0.56
Consensus pattern (41 bp):
TTTTCTTTATTTCTACTTGTGCTGAATCATTATCTAATCTA
Found at i:3429257 original size:74 final size:74
Alignment explanation
Indices: 3429131--3429273 Score: 277
Period size: 74 Copynumber: 1.9 Consensus size: 74
3429121 GGTCGTATCA
*
3429131 AATTTTTTCTTTATTTCTACTTGTGCTGAATCATTATCTAATCTATTTTCTGTTCTTATTGTGTT
1 AATTCTTTCTTTATTTCTACTTGTGCTGAATCATTATCTAATCTATTTTCTGTTCTTATTGTGTT
3429196 TTCACTGTC
66 TTCACTGTC
3429205 AATTCTTTCTTTATTTCTACTTGTGCTGAATCATTATCTAATCTATTTTCTGTTCTTATTGTGTT
1 AATTCTTTCTTTATTTCTACTTGTGCTGAATCATTATCTAATCTATTTTCTGTTCTTATTGTGTT
3429270 TTCA
66 TTCA
3429274 GCCTTTTTCT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.18, C:0.16, G:0.09, T:0.57
Consensus pattern (74 bp):
AATTCTTTCTTTATTTCTACTTGTGCTGAATCATTATCTAATCTATTTTCTGTTCTTATTGTGTT
TTCACTGTC
Found at i:3429267 original size:38 final size:38
Alignment explanation
Indices: 3429151--3429267 Score: 118
Period size: 38 Copynumber: 3.1 Consensus size: 38
3429141 TTATTTCTAC
3429151 TTGTGCTGAATCATTATCTAATCTATTTTCTGTTCTTA
1 TTGTGCTGAATCATTATCTAATCTATTTTCTGTTCTTA
** * * * *
3429189 TTGTG-T-TTTCACTGTC-AATTCTTTCTTTAT-TTC-TA
1 TTGTGCTGAATCATTATCTAA-TCTAT-TTTCTGTTCTTA
3429224 CTTGTGCTGAATCATTATCTAATCTATTTTCTGTTCTTA
1 -TTGTGCTGAATCATTATCTAATCTATTTTCTGTTCTTA
3429263 TTGTG
1 TTGTG
3429268 TTTTCAGCCT
Statistics
Matches: 59, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
35 4 0.07
36 18 0.31
37 10 0.17
38 23 0.39
39 4 0.07
ACGTcount: A:0.18, C:0.16, G:0.11, T:0.55
Consensus pattern (38 bp):
TTGTGCTGAATCATTATCTAATCTATTTTCTGTTCTTA
Found at i:3436556 original size:39 final size:39
Alignment explanation
Indices: 3436512--3437373 Score: 1661
Period size: 39 Copynumber: 22.1 Consensus size: 39
3436502 AATTATGTTA
*
3436512 CCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
* *
3436551 CCAGCACAAAGCCTGCGGGCCTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
3436590 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
3436629 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
3436668 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
3436707 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
3436746 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
3436785 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
3436824 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
3436863 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
3436902 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
3436941 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
3436980 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
3437019 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
3437058 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
3437097 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
3437136 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
3437175 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
3437214 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
*
3437253 CCAGCACGAAGCCTGCGGGACTTTAGCCCTGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
*
3437292 CCAGCACGAAGCCTGCGGGACTTTAGCCCTGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
* *
3437331 CCAGCACGAAGCCTGCAGGACTTTAGCCTGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
3437370 CCAG
1 CCAG
3437374 TGTCTTGCTT
Statistics
Matches: 816, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 816 1.00
ACGTcount: A:0.23, C:0.31, G:0.25, T:0.21
Consensus pattern (39 bp):
CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
Done.