Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 143 of 161
Found at i:44582903 original size:73 final size:73
Alignment explanation
Indices: 44582728--44583005 Score: 301
Period size: 73 Copynumber: 3.8 Consensus size: 73
44582718 GCTGAATTGG
* * * *
44582728 TTGACTTGATTGTATCCCTTAAGGGATTTAGCTCTA-TCGATTAAGTGAGAGCAAGTTTGTGAAA
1 TTGACTTGATTGCATCCCTTAAGGGATTTGGCTCTACT-AATTAAGTGAGAGCAAATTTGTGAAA
*
44582792 GTCAAAGTGT
65 -TCAAAATGT
* * * * *
44582802 TTAATTTGATTACATCCTTTAAGGGATTTGGCTCTACTAATTAAGTGGGAG-AAATTATGTGAAA
1 TTGACTTGATTGCATCCCTTAAGGGATTTGGCTCTACTAATTAAGTGAGAGCAAATT-TGTGAAA
44582866 TCAAAATGT
65 TCAAAATGT
* * * * * * *
44582875 TTGACTTGATTGCATCCTTTAAGAGATTTGGCTCTACCAATTGAGTGAGAACAAGTCTGTGGAAA
1 TTGACTTGATTGCATCCCTTAAGGGATTTGGCTCTACTAATTAAGTGAGAGCAAATTTGT-GAAA
*
44582940 TCAAATTG-
65 TCAAAATGT
* * * *
44582948 TTGACTTGATTGCATCCCCTGAGGGATTTGGCTTTATTAATTAAGTGAGAGCAAATTT
1 TTGACTTGATTGCATCCCTTAAGGGATTTGGCTCTACTAATTAAGTGAGAGCAAATTT
44583006 TTGGAACATA
Statistics
Matches: 168, Mismatches: 32, Indels: 9
0.80 0.15 0.04
Matches are distributed among these distances:
73 105 0.62
74 62 0.37
75 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.36
Consensus pattern (73 bp):
TTGACTTGATTGCATCCCTTAAGGGATTTGGCTCTACTAATTAAGTGAGAGCAAATTTGTGAAAT
CAAAATGT
Found at i:44583020 original size:147 final size:147
Alignment explanation
Indices: 44582728--44583004 Score: 351
Period size: 147 Copynumber: 1.9 Consensus size: 147
44582718 GCTGAATTGG
* * * * * *
44582728 TTGACTTGATTGTATCCCTTAAGGGATTTAGCTCTATCGATTAAGTGAGAGCAAGTTTGTGAAAG
1 TTGACTTGATTGCATCCCTTAAGAGATTTAGCTCTACCAATTAAGTGAGAACAAGTCTGTGAAAG
* ** *
44582793 TCAAAGTGTTTAATTTGATTACATCCTTTAAGGGATTTGGCTCTACTAATTAAGTGGGAGAAATT
66 TCAAAGTGTTTAACTTGATTACATCCCCTAAGGGATTTGGCTCTACTAATTAAGTGAGAGAAATT
44582858 ATGTGAAATCAAAATGT
131 ATGTGAAATCAAAATGT
* * *
44582875 TTGACTTGATTGCATCCTTTAAGAGATTTGGCTCTACCAATTGAGTGAGAACAAGTCTGTGGAAA
1 TTGACTTGATTGCATCCCTTAAGAGATTTAGCTCTACCAATTAAGTGAGAACAAGTCTGT-GAAA
* * * * * *
44582940 -TCAAATTG-TTGACTTGATTGCATCCCCTGAGGGATTTGGCTTTATTAATTAAGTGAGAGCAAA
65 GTCAAAGTGTTTAACTTGATTACATCCCCTAAGGGATTTGGCTCTACTAATTAAGTGAGAG-AAA
44583003 TT
129 TT
44583005 TTTGGAACAT
Statistics
Matches: 109, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
146 42 0.39
147 63 0.58
148 4 0.04
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (147 bp):
TTGACTTGATTGCATCCCTTAAGAGATTTAGCTCTACCAATTAAGTGAGAACAAGTCTGTGAAAG
TCAAAGTGTTTAACTTGATTACATCCCCTAAGGGATTTGGCTCTACTAATTAAGTGAGAGAAATT
ATGTGAAATCAAAATGT
Found at i:44583050 original size:147 final size:147
Alignment explanation
Indices: 44582728--44583053 Score: 338
Period size: 147 Copynumber: 2.2 Consensus size: 147
44582718 GCTGAATTGG
* * * * * * *
44582728 TTGACTTGATTGTATCCCTTAAGGGATTTAGCTCTATCGATTAAGTGAGAGCAAGTTTGTGAAAG
1 TTGACTTGATTGAATCCTTTAAGGGATTTGGCTCTACCAATTAAGTGAGAACAAGTCTGTGAAAG
* ** *
44582793 TCAAAGTGTTTAATTTGATTACATCCTTTAAGGGATTTGGCTCTACTAATTAAGTGGGAGAAATT
66 TCAAAGTGTTTAACTTGATTACATCCCCTAAGGGATTTGGCTCTACTAATTAAGTGAGAGAAATT
*
44582858 ATGTGAAATCAAAATGT
131 ATGTGAAATCAAAATGC
* * *
44582875 TTGACTTGATTGCATCCTTTAAGAGATTTGGCTCTACCAATTGAGTGAGAACAAGTCTGTGGAAA
1 TTGACTTGATTGAATCCTTTAAGGGATTTGGCTCTACCAATTAAGTGAGAACAAGTCTGT-GAAA
* * * * * *
44582940 -TCAAATTG-TTGACTTGATTGCATCCCCTGAGGGATTTGGCTTTATTAATTAAGTGAGAGCAAA
65 GTCAAAGTGTTTAACTTGATTACATCCCCTAAGGGATTTGGCTCTACTAATTAAGTGAGAG-AAA
*
44583003 TT-TTTGGAACAT-AAAATGC
129 TTATGT-GAA-ATCAAAATGC
** * *
44583022 TTGTTTTGATTTAAT-CTCTTGAGGGATTTGGC
1 TTGACTTGATTGAATCCT-TTAAGGGATTTGGC
44583054 CTTACTCATA
Statistics
Matches: 147, Mismatches: 27, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
146 46 0.31
147 95 0.65
148 6 0.04
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (147 bp):
TTGACTTGATTGAATCCTTTAAGGGATTTGGCTCTACCAATTAAGTGAGAACAAGTCTGTGAAAG
TCAAAGTGTTTAACTTGATTACATCCCCTAAGGGATTTGGCTCTACTAATTAAGTGAGAGAAATT
ATGTGAAATCAAAATGC
Found at i:44584978 original size:4 final size:4
Alignment explanation
Indices: 44584969--44584993 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
44584959 TTTGCAAATT
44584969 TTAG TTAG TTAG TTAG TTAG TTAG T
1 TTAG TTAG TTAG TTAG TTAG TTAG T
44584994 ATAATCAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TTAG
Found at i:44605168 original size:5 final size:5
Alignment explanation
Indices: 44605158--44605189 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
44605148 TATCACTACT
44605158 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA
44605190 TAGTGTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:44609931 original size:14 final size:14
Alignment explanation
Indices: 44609912--44609940 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
44609902 CTGTGCTACT
44609912 TCCAGGAGAAAGTA
1 TCCAGGAGAAAGTA
44609926 TCCAGGAGAAAGTA
1 TCCAGGAGAAAGTA
44609940 T
1 T
44609941 GGAGAGACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.14, G:0.28, T:0.17
Consensus pattern (14 bp):
TCCAGGAGAAAGTA
Found at i:44613814 original size:76 final size:75
Alignment explanation
Indices: 44613688--44613861 Score: 240
Period size: 76 Copynumber: 2.3 Consensus size: 75
44613678 TGTCCGTTAT
* * * * * * * *
44613688 CGGTGGATTCAGAACTTAGTAACCACCAGTGATTTGGGGAATCAGGACTTATCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAGTGAATCGAGGAATCAGCACTTAGCAACCCCTTTCAC
44613753 ATTCAAAAATA
66 ATT-AAAAATA
*
44613764 CGGTGGAATCAGCACTTAGCAACCACCAGTGAATCGAGGAATTAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAGTGAATCGAGGAATCAGCACTTAGCAACCCCTTTCAC
*
44613829 ATTTAAAATA
66 ATTAAAAATA
*
44613839 CGGTGGGATCAGCACTTAGCAAC
1 CGGTGGAATCAGCACTTAGCAAC
44613862 AACCCTTTCA
Statistics
Matches: 87, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
75 28 0.32
76 59 0.68
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (75 bp):
CGGTGGAATCAGCACTTAGCAACCACCAGTGAATCGAGGAATCAGCACTTAGCAACCCCTTTCAC
ATTAAAAATA
Found at i:44613883 original size:45 final size:42
Alignment explanation
Indices: 44613801--44613981 Score: 182
Period size: 42 Copynumber: 4.5 Consensus size: 42
44613791 AGTGAATCGA
* *
44613801 GGAATTAGCACTTAGCAACCCCTTTCACATTTAAAATACGGT
1 GGAATCAGCACTTAGCAACCCCTTTCACATTAAAAATACGGT
*
44613843 GGGATCAGCACTTAGCAACAACCCTTTCACATTCAAAAATACGGT
1 GGAATCAGCACTTAGCAAC--CCCTTTCACATT-AAAAATACGGT
* * * *
44613888 GGAATCAGCACTTAGCAA--CC--AC-CAGT--GAAT-C-GA
1 GGAATCAGCACTTAGCAACCCCTTTCACATTAAAAATACGGT
* *
44613921 GGAATTAGCACTTAGCAACCCCTTTCACATTTAAAATACGGT
1 GGAATCAGCACTTAGCAACCCCTTTCACATTAAAAATACGGT
*
44613963 GGGATCAGCACTTAGCAAC
1 GGAATCAGCACTTAGCAAC
44613982 AACCAATGAT
Statistics
Matches: 112, Mismatches: 15, Indels: 24
0.74 0.10 0.16
Matches are distributed among these distances:
33 18 0.16
34 1 0.01
35 5 0.04
37 1 0.01
38 6 0.05
39 1 0.01
40 3 0.03
41 3 0.03
42 35 0.31
44 12 0.11
45 27 0.24
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCCCTTTCACATTAAAAATACGGT
Found at i:44613886 original size:120 final size:120
Alignment explanation
Indices: 44613728--44614083 Score: 491
Period size: 120 Copynumber: 3.1 Consensus size: 120
44613718 GATTTGGGGA
* *
44613728 ATCAGGACTTATCAAC--CCCTTTCACATTCAAAAATACGGTGGAATCAGCACTTAGCAACCACC
1 ATCAGCACTTAGCAACAACCCTTTCACATTCAAAAATACGGTGGAATCAGCACTTAGCAACCACC
44613791 AGTGAATCGAGGAATTAGCACTTAGCAACCCCTTTCACATTTAAAATACGGTGGG
66 AGTGAATCGAGGAATTAGCACTTAGCAACCCCTTTCACATTTAAAATACGGTGGG
44613846 ATCAGCACTTAGCAACAACCCTTTCACATTCAAAAATACGGTGGAATCAGCACTTAGCAACCACC
1 ATCAGCACTTAGCAACAACCCTTTCACATTCAAAAATACGGTGGAATCAGCACTTAGCAACCACC
44613911 AGTGAATCGAGGAATTAGCACTTAGCAACCCCTTTCACATTTAAAATACGGTGGG
66 AGTGAATCGAGGAATTAGCACTTAGCAACCCCTTTCACATTTAAAATACGGTGGG
* *
44613966 ATCAGCACTTAGCAACAA--C---CA-A-T----GATTCGG-GGAATCAGCACTTAGCAACC-CC
1 ATCAGCACTTAGCAACAACCCTTTCACATTCAAAAATACGGTGGAATCAGCACTTAGCAACCACC
* * * *
44614018 --T---TCGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGA
66 AGTGAATCGAGGAATTAGCACTTAGCAACCCCTTTCACATTTAAAATACGGTGGG
*
44614068 ATCAGCACTTATCAAC
1 ATCAGCACTTAGCAAC
44614084 CACCAATGAT
Statistics
Matches: 227, Mismatches: 9, Indels: 20
0.89 0.04 0.08
Matches are distributed among these distances:
102 60 0.26
105 1 0.00
107 2 0.01
108 20 0.09
109 5 0.02
113 1 0.00
114 1 0.00
115 2 0.01
118 15 0.07
120 120 0.53
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (120 bp):
ATCAGCACTTAGCAACAACCCTTTCACATTCAAAAATACGGTGGAATCAGCACTTAGCAACCACC
AGTGAATCGAGGAATTAGCACTTAGCAACCCCTTTCACATTTAAAATACGGTGGG
Found at i:44613975 original size:75 final size:76
Alignment explanation
Indices: 44613846--44614019 Score: 260
Period size: 75 Copynumber: 2.3 Consensus size: 76
44613836 ATACGGTGGG
*
44613846 ATCAGCACTTAGCAACAACCCTTTCACATTCAAAAATACGGTGGAATCAGCACTTAGCAACCACC
1 ATCAGCACTTAGCAAC--CCCTTTCACATTCAAAAATACGGTGGAATCAGCACTTAGCAACAACC
*
44613911 AGTGAATCGAGGA
64 AATGAATCGAGGA
* * *
44613924 ATTAGCACTTAGCAACCCCTTTCACATT-TAAAATACGGTGGGATCAGCACTTAGCAACAACCAA
1 ATCAGCACTTAGCAACCCCTTTCACATTCAAAAATACGGTGGAATCAGCACTTAGCAACAACCAA
* *
44613988 TGATTCGGGGA
66 TGAATCGAGGA
44613999 ATCAGCACTTAGCAACCCCTT
1 ATCAGCACTTAGCAACCCCTT
44614020 CGGGGAATCA
Statistics
Matches: 88, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
75 61 0.69
76 12 0.14
78 15 0.17
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (76 bp):
ATCAGCACTTAGCAACCCCTTTCACATTCAAAAATACGGTGGAATCAGCACTTAGCAACAACCAA
TGAATCGAGGA
Found at i:44614008 original size:33 final size:33
Alignment explanation
Indices: 44613966--44614144 Score: 139
Period size: 27 Copynumber: 5.5 Consensus size: 33
44613956 ATACGGTGGG
*
44613966 ATCAGCACTTAGCAACAACCAATGATTCGGGGA
1 ATCAGCACTTAGCAACCACCAATGATTCGGGGA
44613999 ATCAGCACTTAGCAACC-CC-----TTCGGGGA
1 ATCAGCACTTAGCAACCACCAATGATTCGGGGA
* * *
44614026 ATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGA
1 ATCAGCACTTAGCAA-CCAC--CA-A--T--GATTCGG-GGA
*
44614068 ATCAGCACTTATCAACCACCAATGATTCGGGGA
1 ATCAGCACTTAGCAACCACCAATGATTCGGGGA
*
44614101 ATCAGCACTTAGCAACC-CC-----TTGGGGGA
1 ATCAGCACTTAGCAACCACCAATGATTCGGGGA
44614128 ATCAGCACTTAGCAACC
1 ATCAGCACTTAGCAACC
44614145 CCCTTTATAT
Statistics
Matches: 123, Mismatches: 8, Indels: 36
0.74 0.05 0.22
Matches are distributed among these distances:
27 47 0.38
28 2 0.02
29 1 0.01
31 1 0.01
32 4 0.03
33 35 0.28
34 5 0.04
36 1 0.01
38 1 0.01
39 2 0.02
41 7 0.06
42 17 0.14
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.20
Consensus pattern (33 bp):
ATCAGCACTTAGCAACCACCAATGATTCGGGGA
Found at i:44614072 original size:102 final size:102
Alignment explanation
Indices: 44613888--44614149 Score: 407
Period size: 102 Copynumber: 2.5 Consensus size: 102
44613878 AAAATACGGT
* * *
44613888 GGAATCAGCACTTAGCAACCACCAGTGAATCGAGGAATTAGCACTTAGCAACCCCTTTCACATTT
1 GGAATCAGCACTTAGCAACC-CC--T---TCGGGGAATCAGCACTTAGCAACCCCCTTCACATTT
*
44613953 AAAATACGGTGGGATCAGCACTTAGCAACAACCAATGATTCGG
60 AAAATACGGTGGAATCAGCACTTAGCAACAACCAATGATTCGG
44613996 GGAATCAGCACTTAGCAACCCCTTCGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATA
1 GGAATCAGCACTTAGCAACCCCTTCGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATA
* *
44614061 CGGTGGAATCAGCACTTATCAACCACCAATGATTCGG
66 CGGTGGAATCAGCACTTAGCAACAACCAATGATTCGG
*
44614098 GGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTT
1 GGAATCAGCACTTAGCAACCCCTTCGGGGAATCAGCACTTAGCAACCCCCTT
44614150 TATATTCAAT
Statistics
Matches: 147, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
102 124 0.84
105 1 0.01
107 2 0.01
108 20 0.14
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (102 bp):
GGAATCAGCACTTAGCAACCCCTTCGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATA
CGGTGGAATCAGCACTTAGCAACAACCAATGATTCGG
Found at i:44618273 original size:37 final size:36
Alignment explanation
Indices: 44618230--44618307 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 36
44618220 GTTTTAAGTG
*
44618230 ATTTGTTCCTATGTAACTTTGTCTAGTTGTTTTGTA
1 ATTTGTTCCTATGTAACTTTGTCTAGTTCTTTTGTA
44618266 TATTTGTTCCTATGTAACTTTGTCTAGTTCTTTTGTA
1 -ATTTGTTCCTATGTAACTTTGTCTAGTTCTTTTGTA
44618303 ATTTG
1 ATTTG
44618308 ATAGCAAAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
36 5 0.12
37 35 0.88
ACGTcount: A:0.17, C:0.12, G:0.15, T:0.56
Consensus pattern (36 bp):
ATTTGTTCCTATGTAACTTTGTCTAGTTCTTTTGTA
Found at i:44630819 original size:18 final size:20
Alignment explanation
Indices: 44630782--44630821 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
44630772 ACCTAACACG
*
44630782 AATTAAAATTAGACCATATT
1 AATTAAAATTAGAACATATT
44630802 AATT-AAATTA-AACATATT
1 AATTAAAATTAGAACATATT
44630820 AA
1 AA
44630822 CATCACAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 6 0.32
20 4 0.21
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (20 bp):
AATTAAAATTAGAACATATT
Found at i:44636627 original size:40 final size:41
Alignment explanation
Indices: 44636520--44636663 Score: 220
Period size: 41 Copynumber: 3.5 Consensus size: 41
44636510 TTTAACATAT
*
44636520 TCACCGGCACTTAGCCTACTAGGCTTATAGA-CTGATTCAGA
1 TCACCGGCACTTAGCCTACTAGGTTTATA-ACCTGATTCAGA
*
44636561 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTACTAGGTTTATAACCTGATTCAGA
*
44636602 TCACCGGCAC-TAGCCTACTAGGTTTATAACCTAATTCAGA
1 TCACCGGCACTTAGCCTACTAGGTTTATAACCTGATTCAGA
* *
44636642 TCACCGGCACTGAGCCTGCTAG
1 TCACCGGCACTTAGCCTACTAG
44636664 ACATAAAGTC
Statistics
Matches: 95, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
40 39 0.41
41 56 0.59
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTACTAGGTTTATAACCTGATTCAGA
Found at i:44644607 original size:40 final size:41
Alignment explanation
Indices: 44644510--44644716 Score: 337
Period size: 41 Copynumber: 5.1 Consensus size: 41
44644500 TCTGATAGGC
*
44644510 CTAGGTTTATAACCTAATTCAGATCACCGGCACTTAGCCTG
1 CTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCCTG
* *
44644551 CTAGGTTTATAACCTGATTCAGATCACCGACAC-TAGCTTG
1 CTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCCTG
* * *
44644591 CTAGGTTGATAGCCTGATTCAGATCACCGACAC-TAGCCTG
1 CTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCCTG
*
44644631 CTAGGTTTATAACCTAATTCAGATCACCGGCACTTAGCCTG
1 CTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCCTG
44644672 CTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCCTG
1 CTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCCTG
44644713 CTAG
1 CTAG
44644717 ACATAAAGTC
Statistics
Matches: 154, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 72 0.47
41 82 0.53
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (41 bp):
CTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCCTG
Found at i:44644932 original size:78 final size:78
Alignment explanation
Indices: 44644819--44644974 Score: 294
Period size: 78 Copynumber: 2.0 Consensus size: 78
44644809 TATAAGAAAA
44644819 TCTAGATATTCTTTATATCACACATAAATCTTTTCAATAATCGTATCTCAGCAAGAATTGAATTA
1 TCTAGATATTCTTTATATCACACATAAATCTTTTCAATAATCGTATCTCAGCAAGAATTGAATTA
*
44644884 TATTCCAATCTTC
66 TATTCAAATCTTC
*
44644897 TCTAGATATTCTTTATATCATACATAAATCTTTTCAATAATCGTATCTCAGCAAGAATTGAATTA
1 TCTAGATATTCTTTATATCACACATAAATCTTTTCAATAATCGTATCTCAGCAAGAATTGAATTA
44644962 TATTCAAATCTTC
66 TATTCAAATCTTC
44644975 GTAGCAAACA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.40
Consensus pattern (78 bp):
TCTAGATATTCTTTATATCACACATAAATCTTTTCAATAATCGTATCTCAGCAAGAATTGAATTA
TATTCAAATCTTC
Found at i:44647764 original size:18 final size:18
Alignment explanation
Indices: 44647719--44647764 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
44647709 AAGCTTCCGC
44647719 AATAAGTAACGTTTTGAA
1 AATAAGTAACGTTTTGAA
44647737 AATTAA-TAACGTTTTG-A
1 AA-TAAGTAACGTTTTGAA
44647754 AATAGAGTAAC
1 AATA-AGTAAC
44647765 TTTATGACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.08
17 4 0.16
18 16 0.64
19 3 0.12
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.33
Consensus pattern (18 bp):
AATAAGTAACGTTTTGAA
Found at i:44674969 original size:44 final size:41
Alignment explanation
Indices: 44674872--44675203 Score: 195
Period size: 44 Copynumber: 7.6 Consensus size: 41
44674862 GAAGATGGCA
* * * * *
44674872 AGTCTTATCTCCCTGAAATAGCAATGGAGCAGATTAAAGTCGAT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAAA-AC-CT
*
44674916 AGT-TCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCT
1 AGTCT-TATCTCCCTGAAGTTGCAGTGGAGCAGA-TAAAACCT
* * *** *
44674958 CAGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCGCATCT
1 -AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAAACCT
* *
44675000 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAA--AACCT
* * * ** *
44675044 AGTCTTATC-CTCCTGAAGTTACAGTGGGGCAAACTGAAATTGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGA-T-AAA--ACCT
* * * *
44675089 AGTCTTATCTTCCTGAAGTTGCAGTGGAGAAGACTAAAATTGGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAAAA---CCT
* *
44675134 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T-AA-AACCT
44675178 AGTCTTATC-CTCCTGAAGTTGCAGTG
1 AGTCTTATCTC-CCTGAAGTTGCAGTG
44675204 AGGCAGACTG
Statistics
Matches: 237, Mismatches: 32, Indels: 38
0.77 0.10 0.12
Matches are distributed among these distances:
40 21 0.09
41 9 0.04
42 6 0.03
43 13 0.05
44 113 0.48
45 71 0.30
46 2 0.01
47 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (41 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAAACCT
Found at i:44675050 original size:84 final size:88
Alignment explanation
Indices: 44674921--44675212 Score: 268
Period size: 89 Copynumber: 3.3 Consensus size: 88
44674911 TCGATAGTTC
* * * *
44674921 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAA-AACCTCAGATCTTATCTCTCTGAAGTTGCAG-
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAATAAGC-AAG-TCTTATCTCTCTGAAGTTGCAGT
* * * *
44674984 AGAGCAGATC-G-CA-T-CTAGTCT
64 GGAGCAGAACTGAAATTGCAAGTCT
*
44675005 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATC-CTCCTGAAGTTACAGT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAA-TAAGCAAGTCTTATCTCT-CTGAAGTTGCAGT
*
44675069 GGGGCA-AACTGAAATTGGCAAGTCT
64 GGAGCAGAACTGAAATT-GCAAGTCT
* * *
44675094 TATCTTCCTGAAGTTGCAGTGGAGAAGACTAA-AATTGGCAAGTCTTATCTCCCTGAAGTTGCAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAATAA---GCAAGTCTTATCTCTCTGAAGTTGCAG
*
44675158 TGGAGCAG-ACT-AAATAAGCAAGTCT
63 TGGAGCAGAACTGAAAT-TGCAAGTCT
44675183 TATC-CTCCTGAAGTTGCAGT-GAGGCAGACT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGACT
44675213 GAAGATGGCA
Statistics
Matches: 173, Mismatches: 18, Indels: 29
0.79 0.08 0.13
Matches are distributed among these distances:
83 2 0.01
84 50 0.29
85 7 0.04
86 4 0.02
87 3 0.02
88 2 0.01
89 72 0.42
90 32 0.18
91 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (88 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACTAATAAGCAAGTCTTATCTCTCTGAAGTTGCAGTGG
AGCAGAACTGAAATTGCAAGTCT
Found at i:44675105 original size:45 final size:44
Alignment explanation
Indices: 44675000--44675212 Score: 275
Period size: 45 Copynumber: 4.8 Consensus size: 44
44674990 GATCGCATCT
* *
44675000 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTAAATAAGCA
* * * * **
44675044 AGTCTTATCCTCCTGAAGTTACAGTGGGGCAAACTGAAATTGGCA
1 AGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACT-AAATAAGCA
* **
44675089 AGTCTTATCTTCCTGAAGTTGCAGTGGAGAAGACTAAAATTGGCA
1 AGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACT-AAATAAGCA
*
44675134 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAGCA
1 AGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTAAATAAGCA
*
44675178 AGTCTTATCCTCCTGAAGTTGCAGT-GAGGCAGACT
1 AGTCTTATCTTCCTGAAGTTGCAGTGGA-GCAGACT
44675213 GAAGATGGCA
Statistics
Matches: 147, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
43 2 0.01
44 67 0.46
45 78 0.53
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
AGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTAAATAAGCA
Found at i:44675113 original size:89 final size:89
Alignment explanation
Indices: 44675000--44675212 Score: 279
Period size: 89 Copynumber: 2.4 Consensus size: 89
44674990 GATCGCATCT
* *
44675000 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGCAAGTCTTATC-CTCCTGAAGT
1 AGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTAAAATAAGCAAGTCTTATCTC-CCTGAAGT
* **
44675063 TACAGTGGGGCAAACTGAAATTGGCA
65 TACAGTGGAGCAAACT-AAATAAGCA
* **
44675089 AGTCTTATCTTCCTGAAGTTGCAGTGGAGAAGACTAAAATTGGCAAGTCTTATCTCCCTGAAGTT
1 AGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTAAAATAAGCAAGTCTTATCTCCCTGAAGTT
* *
44675154 GCAGTGGAGCAGACTAAATAAGCA
66 ACAGTGGAGCAAACTAAATAAGCA
*
44675178 AGTCTTATCCTCCTGAAGTTGCAGT-GAGGCAGACT
1 AGTCTTATCTTCCTGAAGTTGCAGTGGA-GCAGACT
44675213 GAAGATGGCA
Statistics
Matches: 109, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
88 2 0.02
89 70 0.64
90 36 0.33
91 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (89 bp):
AGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTAAAATAAGCAAGTCTTATCTCCCTGAAGTT
ACAGTGGAGCAAACTAAATAAGCA
Found at i:44675412 original size:19 final size:19
Alignment explanation
Indices: 44675388--44675466 Score: 79
Period size: 19 Copynumber: 4.0 Consensus size: 19
44675378 AATTTTTAAG
44675388 GATATGCAATCTTAAATAT
1 GATATGCAATCTTAAATAT
*
44675407 GATATGCAATC-CAAGATAT
1 GATATGCAATCTTAA-ATAT
** *
44675426 GATATATATAATCTTAGATAT
1 G--ATATGCAATCTTAAATAT
44675447 GATATGCAATCTTAGAATAT
1 GATATGCAATCTTA-AATAT
44675467 ATGATTTTGT
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
18 2 0.04
19 27 0.57
20 4 0.09
21 13 0.28
22 1 0.02
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAAATAT
Found at i:44676915 original size:98 final size:98
Alignment explanation
Indices: 44676795--44676991 Score: 367
Period size: 98 Copynumber: 2.0 Consensus size: 98
44676785 TTAAAAATAA
* *
44676795 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTA
1 TAAAGGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTA
44676860 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
44676893 TAAAGGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTA
44676958 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
44676991 T
1 T
44676992 TTTATTGTAC
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTA
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:44681937 original size:18 final size:17
Alignment explanation
Indices: 44681895--44681938 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
44681885 TGTCGTTCGT
44681895 TTTCAAAACATTATTCA
1 TTTCAAAACATTATTCA
* *
44681912 TTTACAAATCGTTATTCAA
1 TTT-CAAAACATTATTC-A
44681931 TTTCAAAA
1 TTTCAAAA
44681939 TGTTATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.14
18 15 0.68
19 4 0.18
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.41
Consensus pattern (17 bp):
TTTCAAAACATTATTCA
Found at i:44681943 original size:18 final size:17
Alignment explanation
Indices: 44681895--44681945 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
44681885 TGTCGTTCGT
**
44681895 TTTCAAAACATTATTCA
1 TTTCAAAATGTTATTCA
44681912 TTT-ACAAATCGTTATTCAA
1 TTTCA-AAAT-GTTATTC-A
44681931 TTTCAAAATGTTATT
1 TTTCAAAATGTTATT
44681946 TTTTTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
16 1 0.04
17 6 0.21
18 12 0.43
19 8 0.29
20 1 0.04
ACGTcount: A:0.37, C:0.14, G:0.04, T:0.45
Consensus pattern (17 bp):
TTTCAAAATGTTATTCA
Found at i:44684949 original size:24 final size:24
Alignment explanation
Indices: 44684922--44684970 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
44684912 CAAAGTCAAC
* *
44684922 TATATTATGCTAATAAATGCTAAA
1 TATATTATACTAATAAATACTAAA
*
44684946 TATATTATACTCATAAATACTAAA
1 TATATTATACTAATAAATACTAAA
44684970 T
1 T
44684971 CTTCTAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (24 bp):
TATATTATACTAATAAATACTAAA
Found at i:44692008 original size:497 final size:497
Alignment explanation
Indices: 44691074--44692029 Score: 1822
Period size: 497 Copynumber: 1.9 Consensus size: 497
44691064 ATAGTATATG
44691074 TATTATGATATGATGTATATTAATTGGGTCGAATAGGTGATTAAGTAAATAATATTGATATGTTT
1 TATTATGATATGATGTATATTAATTGGGTCGAATAGGTGATTAAGTAAATAATATTGATATGTTT
44691139 AAATTTTAAAGAATAAATTGCTTATGTATTAAAAGTAGTAAAGCAAGACTGGTTTTTAGTTGGTT
66 AAATTTTAAAGAATAAATTGCTTATGTATTAAAAGTAGTAAAGCAAGACTGGTTTTTAGTTGGTT
*
44691204 AAGTAATCTATATGTGCAAATGTGATTTATATGATTTAACTGCTAGTTACTATTTGAGTTTAAAA
131 AAGTAATCTATATATGCAAATGTGATTTATATGATTTAACTGCTAGTTACTATTTGAGTTTAAAA
44691269 TTTTCGTGATTGAATTAATATAATTTGTGCATAATTTAAAATGAAAGACTGTTCTGAGTTGTGTT
196 TTTTCGTGATTGAATTAATATAATTTGTGCATAATTTAAAATGAAAGACTGTTCTGAGTTGTGTT
*
44691334 TTGGTCGGTAATGCCTCGTGACCCTAATCCGGCGACGGATATGGGCTAGGGGTGTTACATTTGAT
261 TTGGTCGGTAATGCCTCGTGACCCTAATCCGGCGACGGATACGGGCTAGGGGTGTTACATTTGAT
*
44691399 TGGTACCAGAGCTATGGTTTAGTCGATTCTAGGACTAGCGTAGTGCGTGTGAGTCTAGCTATACA
326 TGGTACCAGAGCTATGGTTTAGTCGATTCTAGGACTAACGTAGTGCGTGTGAGTCTAGCTATACA
*
44691464 TGCCATATTCTTATATTGCGATAGTGTGATGATTCCAAACATTTGAAAATGTGTTTTCATATAGT
391 TGCCATATTCTTATATTGCGATAGTATGATGATTCCAAACATTTGAAAATGTGTTTTCATATAGT
44691529 AAATATTAATTAGGTCGAATAGGTGATTAAGTAGATAGTAAA
456 AAATATTAATTAGGTCGAATAGGTGATTAAGTAGATAGTAAA
44691571 TATTATGATATGATGTATATTAATTGGGTCGAATAGGTGATTAAGTAAATAATATTGATATGTTT
1 TATTATGATATGATGTATATTAATTGGGTCGAATAGGTGATTAAGTAAATAATATTGATATGTTT
* * *
44691636 AAATTTTAAAGCATAAATTGCTTATGTATTAAAAGTAGTAAAGCATGATTGGTTTTTAGTTGGTT
66 AAATTTTAAAGAATAAATTGCTTATGTATTAAAAGTAGTAAAGCAAGACTGGTTTTTAGTTGGTT
*
44691701 AAGTAATCTATATATGCGAATGTGATTTATATGATTTAACTGCTAGTTACTATTTGAGTTTAAAA
131 AAGTAATCTATATATGCAAATGTGATTTATATGATTTAACTGCTAGTTACTATTTGAGTTTAAAA
*
44691766 TTTTCGTGATTGAATTAATATAATTTGTGCATAATTTAAAATGAAAGATTGTTCTGAGTTGTGTT
196 TTTTCGTGATTGAATTAATATAATTTGTGCATAATTTAAAATGAAAGACTGTTCTGAGTTGTGTT
44691831 TTGGTCGGTAATGCCTCGTGACCCTAATCCGGCGACGGATACGGGCTAGGGGTGTTACATTTGAT
261 TTGGTCGGTAATGCCTCGTGACCCTAATCCGGCGACGGATACGGGCTAGGGGTGTTACATTTGAT
44691896 TGGTACCAGAGCTATGGTTTAGTCGATTCTAGGACTAACGTAGTGCGTGTGAGTCTAGCTATACA
326 TGGTACCAGAGCTATGGTTTAGTCGATTCTAGGACTAACGTAGTGCGTGTGAGTCTAGCTATACA
*
44691961 TGCCATATTCTTATATTGCGATAGTATGATGATTCCAAACATTTGAAAATGTGTTTTCATATTGT
391 TGCCATATTCTTATATTGCGATAGTATGATGATTCCAAACATTTGAAAATGTGTTTTCATATAGT
44692026 AAAT
456 AAAT
44692030 GGATCCTGAT
Statistics
Matches: 449, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
497 449 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (497 bp):
TATTATGATATGATGTATATTAATTGGGTCGAATAGGTGATTAAGTAAATAATATTGATATGTTT
AAATTTTAAAGAATAAATTGCTTATGTATTAAAAGTAGTAAAGCAAGACTGGTTTTTAGTTGGTT
AAGTAATCTATATATGCAAATGTGATTTATATGATTTAACTGCTAGTTACTATTTGAGTTTAAAA
TTTTCGTGATTGAATTAATATAATTTGTGCATAATTTAAAATGAAAGACTGTTCTGAGTTGTGTT
TTGGTCGGTAATGCCTCGTGACCCTAATCCGGCGACGGATACGGGCTAGGGGTGTTACATTTGAT
TGGTACCAGAGCTATGGTTTAGTCGATTCTAGGACTAACGTAGTGCGTGTGAGTCTAGCTATACA
TGCCATATTCTTATATTGCGATAGTATGATGATTCCAAACATTTGAAAATGTGTTTTCATATAGT
AAATATTAATTAGGTCGAATAGGTGATTAAGTAGATAGTAAA
Found at i:44696524 original size:24 final size:24
Alignment explanation
Indices: 44696509--44696560 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
44696499 AATCAAAGTC
44696509 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
44696533 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
44696557 AAAT
1 AAAT
44696561 CTTCTATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:44707207 original size:15 final size:14
Alignment explanation
Indices: 44707185--44707219 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
44707175 CCCCAACCCT
*
44707185 TAAACCATAATCCC
1 TAAACCATAATCCA
44707199 TAAATCCATAATCCA
1 TAAA-CCATAATCCA
44707214 TAAACC
1 TAAACC
44707220 TTAAAATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCATAATCCA
Found at i:44707248 original size:7 final size:7
Alignment explanation
Indices: 44707234--44707282 Score: 53
Period size: 7 Copynumber: 7.0 Consensus size: 7
44707224 AATAGTAACT
44707234 CCTAAAC
1 CCTAAAC
*
44707241 CTTAAAC
1 CCTAAAC
44707248 CCTAAAC
1 CCTAAAC
** *
44707255 TATATAC
1 CCTAAAC
44707262 CCTAAAC
1 CCTAAAC
*
44707269 CATAAAC
1 CCTAAAC
44707276 CCTAAAC
1 CCTAAAC
44707283 TATAATGATA
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.20
Consensus pattern (7 bp):
CCTAAAC
Found at i:44707253 original size:14 final size:14
Alignment explanation
Indices: 44707143--44707282 Score: 70
Period size: 14 Copynumber: 9.8 Consensus size: 14
44707133 CTTTCTTGAC
*
44707143 AAACCTTAAACCCTT
1 AAACCCTAAA-CCTT
* *
44707158 AACCCCTAAACATT
1 AAACCCTAAACCTT
* *
44707172 AAACCCCAACCCTT
1 AAACCCTAAACCTT
* * *
44707186 AAACCATAATCCCT
1 AAACCCTAAACCTT
* * *
44707200 AAATCCATAATCCAT
1 AAA-CCCTAAACCTT
* *
44707215 AAACCTTAAA--AT
1 AAACCCTAAACCTT
44707227 AGTAACTCCTAAACCTT
1 A--AAC-CCTAAACCTT
44707244 AAACCCTAAA-CTAT
1 AAACCCTAAACCT-T
* *
44707258 ATACCCTAAACCAT
1 AAACCCTAAACCTT
44707272 AAACCCTAAAC
1 AAACCCTAAAC
44707283 TATAATGATA
Statistics
Matches: 98, Mismatches: 19, Indels: 17
0.73 0.14 0.13
Matches are distributed among these distances:
12 3 0.03
13 2 0.02
14 61 0.62
15 30 0.31
17 2 0.02
ACGTcount: A:0.44, C:0.33, G:0.01, T:0.22
Consensus pattern (14 bp):
AAACCCTAAACCTT
Found at i:44707274 original size:28 final size:28
Alignment explanation
Indices: 44707211--44707287 Score: 102
Period size: 28 Copynumber: 2.7 Consensus size: 28
44707201 AATCCATAAT
* *
44707211 CCATAAACCTTAAAATAGTAACTCCTAAA
1 CCATAAACCCTAAACTA-TAACTCCTAAA
*
44707240 CCTTAAACCCTAAACTATATAC-CCTAAA
1 CCATAAACCCTAAACTATA-ACTCCTAAA
44707268 CCATAAACCCTAAACTATAA
1 CCATAAACCCTAAACTATAA
44707288 TGATAATTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 1 0.02
28 26 0.60
29 16 0.37
ACGTcount: A:0.47, C:0.29, G:0.01, T:0.23
Consensus pattern (28 bp):
CCATAAACCCTAAACTATAACTCCTAAA
Found at i:44707287 original size:14 final size:14
Alignment explanation
Indices: 44707234--44707287 Score: 74
Period size: 14 Copynumber: 3.9 Consensus size: 14
44707224 AATAGTAACT
44707234 CCTAAACCT-TAAAC
1 CCTAAA-CTATAAAC
*
44707248 CCTAAACTATATAC
1 CCTAAACTATAAAC
*
44707262 CCTAAACCATAAAC
1 CCTAAACTATAAAC
44707276 CCTAAACTATAA
1 CCTAAACTATAA
44707288 TGATAATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 2 0.06
14 33 0.94
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.22
Consensus pattern (14 bp):
CCTAAACTATAAAC
Found at i:44710890 original size:77 final size:76
Alignment explanation
Indices: 44710570--44710902 Score: 309
Period size: 77 Copynumber: 4.3 Consensus size: 76
44710560 AGAAATTACT
* ** * * * *
44710570 TAAATCAAGG-AATAATTACTTAATACATGAAATGTTGGTGAAAACATGAAAAGATTTTTAAAAA
1 TAAATC-AGGAAAGAATTACTTAATACATGAAATGTTACTTAAAACATGAAAAGGTTTCTAAGAA
*
44710634 ATTAAGCAATTC
65 ATTAAGTAATTC
* * *
44710646 GTAAATCA-TAAACGAATCACTTAATACATGAAATGTTACTTAAAACGTGAAAAAGGTTTCTAAG
1 -TAAATCAGGAAA-GAATTACTTAATACATGAAATGTTACTTAAAACATG-AAAAGGTTTCTAAG
*
44710710 AAATTAAATAATTC
63 AAATTAAGTAATTC
* * * * **
44710724 TTAAATCAGGTAA-AATTACTTAAAACAT-AAACGATTA-TGTATAACATGAAGTGGTTTCTAAG
1 -TAAATCAGGAAAGAATTACTTAATACATGAAATG-TTACT-TAAAACATGAAAAGGTTTCTAAG
*
44710786 AAATTAAGTTATTCC
63 AAATTAAGTAATT-C
* * * *
44710801 TAAATCATGAAAGAATTACTTAATCCATTAAATGTTACTTAAAACATGAAAAGGTTTCCAAGAAA
1 TAAATCAGGAAAGAATTACTTAATACATGAAATGTTACTTAAAACATGAAAAGGTTTCTAAGAAA
44710866 TTAAGTAATTC
66 TTAAGTAATTC
* *
44710877 ATAAAATTA-GAAAGTATTACTTAATA
1 -T-AAATCAGGAAAGAATTACTTAATA
44710903 TTAAACCTGT
Statistics
Matches: 207, Mismatches: 37, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
76 42 0.20
77 123 0.59
78 40 0.19
79 2 0.01
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.32
Consensus pattern (76 bp):
TAAATCAGGAAAGAATTACTTAATACATGAAATGTTACTTAAAACATGAAAAGGTTTCTAAGAAA
TTAAGTAATTC
Found at i:44711041 original size:16 final size:16
Alignment explanation
Indices: 44711006--44711045 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
44710996 TTGATAAAAT
* * *
44711006 TAAAACTAATTGTTAT
1 TAAAATTAATTGTCAG
44711022 TAAAATTAATTGTCAG
1 TAAAATTAATTGTCAG
44711038 TAAAATTA
1 TAAAATTA
44711046 TCAAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (16 bp):
TAAAATTAATTGTCAG
Found at i:44711106 original size:66 final size:68
Alignment explanation
Indices: 44711036--44711179 Score: 193
Period size: 75 Copynumber: 2.0 Consensus size: 68
44711026 ATTAATTGTC
* *
44711036 AGTAAAATTATCAAATTATTAATTG-TTAATTG-TATTAATTGTTGTAATAAAATCTAACATTTG
1 AGTAAAATTATCAAATTATTAATTGATTAATTGTTATTAATTGTTGTAACAAAATCTAAAATTTG
44711099 ATT
66 ATT
44711102 AGTAAAATTATCAAATTATTAATTGTATTAATTGTTAATTATATTAATTGTTGTAACAAAATCTA
1 AGTAAAATTATCAAATTATTAATTG-ATTAATTG-----T-TATTAATTGTTGTAACAAAATCTA
44711167 AAATTTGATT
59 AAATTTGATT
44711177 AGT
1 AGT
44711180 TTACATTTTT
Statistics
Matches: 67, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
66 25 0.37
68 7 0.10
75 35 0.52
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (68 bp):
AGTAAAATTATCAAATTATTAATTGATTAATTGTTATTAATTGTTGTAACAAAATCTAAAATTTG
ATT
Found at i:44711139 original size:16 final size:16
Alignment explanation
Indices: 44711115--44711153 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
44711105 AAAATTATCA
* *
44711115 AATTATTAATTGTATT
1 AATTGTTAATTATATT
44711131 AATTGTTAATTATATT
1 AATTGTTAATTATATT
44711147 AATTGTT
1 AATTGTT
44711154 GTAACAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (16 bp):
AATTGTTAATTATATT
Found at i:44711405 original size:20 final size:20
Alignment explanation
Indices: 44711380--44711436 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
44711370 CTTTCTACAG
44711380 TGAAAACATAAAAATAAAAT
1 TGAAAACATAAAAATAAAAT
* *
44711400 TGAAAACTTAAACTAA-AAACT
1 TGAAAACATAAA--AATAAAAT
44711421 T--AAACATAAAAATAAA
1 TGAAAACATAAAAATAAA
44711437 TATATATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
17 2 0.06
18 3 0.10
19 8 0.26
20 11 0.35
21 5 0.16
22 2 0.06
ACGTcount: A:0.67, C:0.09, G:0.04, T:0.21
Consensus pattern (20 bp):
TGAAAACATAAAAATAAAAT
Found at i:44711418 original size:13 final size:14
Alignment explanation
Indices: 44711402--44711432 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
44711392 AATAAAATTG
44711402 AAAACTTAAAC-TA
1 AAAACTTAAACATA
44711415 AAAACTTAAACATA
1 AAAACTTAAACATA
44711429 AAAA
1 AAAA
44711433 TAAATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAACTTAAACATA
Found at i:44711469 original size:16 final size:16
Alignment explanation
Indices: 44711450--44711482 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
44711440 ATATTTTTTT
44711450 AAACATAAAAAACTTA
1 AAACATAAAAAACTTA
44711466 AAACATAAAAAACTTA
1 AAACATAAAAAACTTA
44711482 A
1 A
44711483 TATATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (16 bp):
AAACATAAAAAACTTA
Found at i:44711495 original size:44 final size:40
Alignment explanation
Indices: 44711407--44711495 Score: 99
Period size: 44 Copynumber: 2.1 Consensus size: 40
44711397 AATTGAAAAC
*
44711407 TTAAACTAAAAACTTAAACATAAAAATAAATATATATTTTT
1 TTAAACTAAAAACTTAAACATAAAAATAAATATATA-TTAT
*
44711448 TTAAACATAAAAAACTTAAAACATAAAAAACTTAATATATA-TAT
1 TTAAAC-T-AAAAACTT-AAACAT-AAAAA-TAAATATATATTAT
44711492 TTAA
1 TTAA
44711496 TATATTTTCG
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
41 6 0.15
42 1 0.02
43 8 0.20
44 12 0.29
45 5 0.12
46 9 0.22
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (40 bp):
TTAAACTAAAAACTTAAACATAAAAATAAATATATATTAT
Found at i:44711748 original size:19 final size:19
Alignment explanation
Indices: 44711724--44711760 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
44711714 TCATGGAAGA
44711724 ATTACTT-AATACATGAAAC
1 ATTACTTGAAT-CATGAAAC
44711743 ATTACTTGAATCATGAAA
1 ATTACTTGAATCATGAAA
44711761 TGGTGTCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (19 bp):
ATTACTTGAATCATGAAAC
Found at i:44711866 original size:75 final size:76
Alignment explanation
Indices: 44711687--44711891 Score: 245
Period size: 75 Copynumber: 2.7 Consensus size: 76
44711677 TAATTTGTAT
* * *
44711687 TTTCTATGAAATTAAGTAATTCCAAAATCATGGAAGAATTACTTAATACATGAAACATTACTTGA
1 TTTCTAAGAAATTAAGTAATTTCTAAATCATGGAAGAATTACTTAATACATGAAACA-TACTTGA
44711752 ATCATGAAATGG
65 ATCATGAAATGG
* * *
44711764 TGTCTAA-AGAATTAAGTAA-TTCATAAATCATGGAAGAATTATTTAATATATGAAACA-ACTTG
1 TTTCTAAGA-AATTAAGTAATTTC-TAAATCATGGAAGAATTACTTAATACATGAAACATACTTG
*
44711826 CATCATGAAATGG
64 AATCATGAAATGG
* * ** **
44711839 TTTCTAAGAAATTAAATAATTTCTAAATTACAGAAGAAAAACTTAATACATGA
1 TTTCTAAGAAATTAAGTAATTTCTAAATCATGGAAGAATTACTTAATACATGA
44711892 TATATTACTG
Statistics
Matches: 108, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
75 55 0.51
76 7 0.06
77 46 0.43
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.32
Consensus pattern (76 bp):
TTTCTAAGAAATTAAGTAATTTCTAAATCATGGAAGAATTACTTAATACATGAAACATACTTGAA
TCATGAAATGG
Found at i:44712284 original size:41 final size:41
Alignment explanation
Indices: 44712222--44712332 Score: 170
Period size: 41 Copynumber: 2.7 Consensus size: 41
44712212 GAAAATATAT
44712222 ACCTA-TAGGCTCAAGGCCTAATATGATACACCGGCACGAA
1 ACCTACTAGGCTCAAGGCCTAATATGATACACCGGCACGAA
* *
44712262 ACCTGCTAGGCGCAAGGCCTAATATGATACACCGGCACGAA
1 ACCTACTAGGCTCAAGGCCTAATATGATACACCGGCACGAA
* * *
44712303 GCCTACTAGACTCAAGGCCTGATATGATAC
1 ACCTACTAGGCTCAAGGCCTAATATGATAC
44712333 TGAAAGTAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 4 0.06
41 59 0.94
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.18
Consensus pattern (41 bp):
ACCTACTAGGCTCAAGGCCTAATATGATACACCGGCACGAA
Found at i:44713614 original size:25 final size:26
Alignment explanation
Indices: 44713572--44713627 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 26
44713562 TTTTCTCAAA
* *
44713572 ATTTTACCCGGGGTAAAATTGTCATG
1 ATTTTACCCAGGGTAAAATTGACATG
44713598 ATTTTA-CCAGGGTAAAATTGACATG
1 ATTTTACCCAGGGTAAAATTGACATG
44713623 ATTTT
1 ATTTT
44713628 GGGATGATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 22 0.79
26 6 0.21
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (26 bp):
ATTTTACCCAGGGTAAAATTGACATG
Found at i:44716884 original size:16 final size:16
Alignment explanation
Indices: 44716863--44716893 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
44716853 TTTATAATTG
44716863 TGTTGGTGGCCCTATA
1 TGTTGGTGGCCCTATA
44716879 TGTTGGTGGCCCTAT
1 TGTTGGTGGCCCTAT
44716894 TAAGAGTGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.10, C:0.19, G:0.32, T:0.39
Consensus pattern (16 bp):
TGTTGGTGGCCCTATA
Found at i:44719347 original size:9 final size:9
Alignment explanation
Indices: 44719327--44719393 Score: 82
Period size: 9 Copynumber: 7.4 Consensus size: 9
44719317 TTTGGTTAAA
44719327 AATTAACCG
1 AATTAACCG
44719336 AATT-ACCGG
1 AATTAACC-G
44719345 AATTAACCG
1 AATTAACCG
44719354 AATTAACCG
1 AATTAACCG
*
44719363 AATTAACTG
1 AATTAACCG
** *
44719372 AATTATTCA
1 AATTAACCG
44719381 AATTAACCG
1 AATTAACCG
44719390 AATT
1 AATT
44719394 GAATCACTAC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
8 3 0.06
9 42 0.88
10 3 0.06
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:44719360 original size:27 final size:27
Alignment explanation
Indices: 44719326--44719393 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
44719316 TTTTGGTTAA
*
44719326 AAATTAACCGAATTACCGGAATTAACC
1 AAATTAACCGAATTAACGGAATTAACC
* * **
44719353 GAATTAACCGAATTAACTGAATTATTC
1 AAATTAACCGAATTAACGGAATTAACC
44719380 AAATTAACCGAATT
1 AAATTAACCGAATT
44719394 GAATCACTAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (27 bp):
AAATTAACCGAATTAACGGAATTAACC
Found at i:44724680 original size:5 final size:5
Alignment explanation
Indices: 44724670--44724696 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
44724660 TGAGCATTCG
44724670 ATCGA ATCGA ATCGA ATCGA ATCGA AT
1 ATCGA ATCGA ATCGA ATCGA ATCGA AT
44724697 AAAAAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (5 bp):
ATCGA
Found at i:44725313 original size:20 final size:20
Alignment explanation
Indices: 44725288--44725327 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
44725278 CGTAAAATGA
*
44725288 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
44725308 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
44725328 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:44725317 original size:34 final size:35
Alignment explanation
Indices: 44725273--44725339 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
44725263 CAGTAAAATA
*
44725273 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
44725307 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
44725340 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:44725343 original size:14 final size:15
Alignment explanation
Indices: 44725267--44725343 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
44725257 GATTGCCAGT
* *
44725267 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
44725281 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
44725295 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
44725315 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
44725330 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
44725344 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:44725625 original size:25 final size:23
Alignment explanation
Indices: 44725580--44725626 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
44725570 GTAATTTGTG
*
44725580 TTAAAAAAACAAGTATTGAATAA
1 TTAAAAAAACAAGTATGGAATAA
*
44725603 TTAAAAAAATAAGTTACTGGAATA
1 TTAAAAAAACAAG-TA-TGGAATA
44725627 TCGATAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 2 0.10
25 6 0.30
ACGTcount: A:0.57, C:0.04, G:0.11, T:0.28
Consensus pattern (23 bp):
TTAAAAAAACAAGTATGGAATAA
Found at i:44726257 original size:9 final size:9
Alignment explanation
Indices: 44726243--44726279 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
44726233 TATAGTTTAA
44726243 TATTCGAAT
1 TATTCGAAT
44726252 TATTCGAAT
1 TATTCGAAT
* *
44726261 TATTTGAGT
1 TATTCGAAT
44726270 TATTCGAAT
1 TATTCGAAT
44726279 T
1 T
44726280 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:44729673 original size:23 final size:19
Alignment explanation
Indices: 44729650--44729687 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
44729640 CCACTGTCAC
44729650 CCACCGTAATCAAATTTGT
1 CCACCGTAATCAAATTTGT
44729669 CCACCGTAATCAAATTTGT
1 CCACCGTAATCAAATTTGT
44729688 TATTAACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (19 bp):
CCACCGTAATCAAATTTGT
Found at i:44731634 original size:21 final size:21
Alignment explanation
Indices: 44731605--44731647 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
44731595 CAAAAGTTAT
*
44731605 TTCAATTT-ATTTAATTTTGAA
1 TTCAATTTAATTT-ATGTTGAA
*
44731626 TTCAGTTTAATTTATGTTGAA
1 TTCAATTTAATTTATGTTGAA
44731647 T
1 T
44731648 ATAAAAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.56
Consensus pattern (21 bp):
TTCAATTTAATTTATGTTGAA
Found at i:44733158 original size:14 final size:14
Alignment explanation
Indices: 44733139--44733165 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44733129 TGATCTTTAG
44733139 TTTAAATTTTGATT
1 TTTAAATTTTGATT
44733153 TTTAAATTTTGAT
1 TTTAAATTTTGAT
44733166 ATATCTAGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTAAATTTTGATT
Found at i:44735775 original size:36 final size:35
Alignment explanation
Indices: 44735676--44735795 Score: 136
Period size: 36 Copynumber: 3.3 Consensus size: 35
44735666 CTCTATGTTT
44735676 TGGTGTGTTTCGGTTGGACTAGCTCTT-TGGAGCCAT-
1 TGGTGTGTTTCGG-TGGACTAGCTCTTAT-GAG-CATC
* *
44735712 TGGTATGTTATCAGGTGGACTGGCTCTTATGAGCATC
1 TGGTGTGTT-TC-GGTGGACTAGCTCTTATGAGCATC
* *
44735749 TGGTGTGTTTCGGATGGATTAGCTCTTATGATCATC
1 TGGTGTGTTTCGG-TGGACTAGCTCTTATGAGCATC
44735785 TGGTGTGTTTC
1 TGGTGTGTTTC
44735796 AGTTGGAATA
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
35 2 0.03
36 43 0.59
37 25 0.34
38 3 0.04
ACGTcount: A:0.14, C:0.15, G:0.31, T:0.40
Consensus pattern (35 bp):
TGGTGTGTTTCGGTGGACTAGCTCTTATGAGCATC
Found at i:44739116 original size:146 final size:147
Alignment explanation
Indices: 44738848--44739144 Score: 533
Period size: 146 Copynumber: 2.0 Consensus size: 147
44738838 CTATTGATCT
*
44738848 TGGTTTTTTGCTTGCTTCTTCTTGACCCAACTAAAATTGTCAGTATGTCCAGACTTTTGGCAAAA
1 TGGTTTTTTGCTTGCTTCTTCTTGACCCAACAAAAATTGTCAGTATGTCCAGACTTTTGGCAAAA
*
44738913 AAATACACTGAAATTTGGACTTGTCTTTTTCCTTGAATCGACAATCCTTTTCAGCATGATTTGTC
66 AAATACACAGAAATTTGGACTTGTCTTTTTCCTTGAATCGACAATCCTTTTCAGCATGATTTGTC
44738978 CTCTTACAAATAGGACA
131 CTCTTACAAATAGGACA
* *
44738995 TGGTTTTTTGCTTGCTTCTTCTTGACCCAACAAAAATTTTTAGTATGTCCAGACTTTTGGC-AAA
1 TGGTTTTTTGCTTGCTTCTTCTTGACCCAACAAAAATTGTCAGTATGTCCAGACTTTTGGCAAAA
* *
44739059 AAATACACAGAAATTTGGACTTGTCTTTTTCCTTGAATCGTCAATCCTTTTTAGCATGATTTGTC
66 AAATACACAGAAATTTGGACTTGTCTTTTTCCTTGAATCGACAATCCTTTTCAGCATGATTTGTC
44739124 CTCTTACAAATAGGACA
131 CTCTTACAAATAGGACA
44739141 TGGT
1 TGGT
44739145 GGAAATTTTC
Statistics
Matches: 144, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
146 86 0.60
147 58 0.40
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (147 bp):
TGGTTTTTTGCTTGCTTCTTCTTGACCCAACAAAAATTGTCAGTATGTCCAGACTTTTGGCAAAA
AAATACACAGAAATTTGGACTTGTCTTTTTCCTTGAATCGACAATCCTTTTCAGCATGATTTGTC
CTCTTACAAATAGGACA
Found at i:44744553 original size:14 final size:14
Alignment explanation
Indices: 44744534--44744565 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
44744524 TCCAATCACC
44744534 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
44744548 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
44744562 GGGC
1 GGGC
44744566 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:44747179 original size:42 final size:41
Alignment explanation
Indices: 44747120--44747273 Score: 157
Period size: 42 Copynumber: 3.7 Consensus size: 41
44747110 NNNNNNNNNN
*
44747120 TGCCGATGGTGCCCGAGGCTCCCGCACATCGAAGCACCGAGG
1 TGCCGATGGTGCCCGAGGCTCCCGCACATCCAAGCACC-AGG
* * ** * *
44747162 TGCCGATGGCGCCCGAGGCTCCTGCA-ATACCAAGGGCTTAGTT
1 TGCCGATGGTGCCCGAGGCTCCCGCACAT-CCAAGCAC-CAG-G
* * * *
44747205 TGCCGATGGTGTCCGGGGCTCCTGCACATCCTAGCACCAGGG
1 TGCCGATGGTGCCCGAGGCTCCCGCACATCCAAGCACCA-GG
44747247 TGCCGATGGTGCCCGAGGCTCCCGCAC
1 TGCCGATGGTGCCCGAGGCTCCCGCAC
44747274 GACCAAGGGC
Statistics
Matches: 89, Mismatches: 18, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
41 2 0.02
42 56 0.63
43 29 0.33
44 2 0.02
ACGTcount: A:0.16, C:0.34, G:0.32, T:0.17
Consensus pattern (41 bp):
TGCCGATGGTGCCCGAGGCTCCCGCACATCCAAGCACCAGG
Found at i:44747263 original size:85 final size:85
Alignment explanation
Indices: 44747120--44747283 Score: 231
Period size: 85 Copynumber: 1.9 Consensus size: 85
44747110 NNNNNNNNNN
* *
44747120 TGCCGATGGTGCCCGAGGCTCCCGCACATCGAAGCACCGAGGTGCCGATGGCGCCCGAGGCTCCT
1 TGCCGATGGTGCCCGAGGCTCCCGCACATCCAAGCACCGAGGTGCCGATGGCGCCCGAGGCTCCC
*
44747185 GCAATACCAAGGGCTTAGTT
66 GCAAGACCAAGGGCTTAGTT
* * * * *
44747205 TGCCGATGGTGTCCGGGGCTCCTGCACATCCTAGCACC-AGGGTGCCGATGGTGCCCGAGGCTCC
1 TGCCGATGGTGCCCGAGGCTCCCGCACATCCAAGCACCGA-GGTGCCGATGGCGCCCGAGGCTCC
*
44747269 CGCACGACCAAGGGC
65 CGCAAGACCAAGGGC
44747284 CTATGCTACC
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
84 1 0.01
85 68 0.99
ACGTcount: A:0.17, C:0.34, G:0.33, T:0.16
Consensus pattern (85 bp):
TGCCGATGGTGCCCGAGGCTCCCGCACATCCAAGCACCGAGGTGCCGATGGCGCCCGAGGCTCCC
GCAAGACCAAGGGCTTAGTT
Found at i:44747367 original size:24 final size:24
Alignment explanation
Indices: 44747291--44747369 Score: 106
Period size: 24 Copynumber: 3.3 Consensus size: 24
44747281 GGCCTATGCT
* *
44747291 ACCGGAACGGTTCACCGGAGCACC
1 ACCGGGACGGTTCGCCGGAGCACC
44747315 GA-CGGGACGGTTCGCCGGAGCACC
1 -ACCGGGACGGTTCGCCGGAGCACC
* *
44747339 GCCGGGACGGATCGCCGGAGCACC
1 ACCGGGACGGTTCGCCGGAGCACC
44747363 ACCGGGA
1 ACCGGGA
44747370 ACCTAACCGG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
24 47 0.98
25 1 0.02
ACGTcount: A:0.20, C:0.35, G:0.38, T:0.06
Consensus pattern (24 bp):
ACCGGGACGGTTCGCCGGAGCACC
Found at i:44747703 original size:42 final size:41
Alignment explanation
Indices: 44747588--44747786 Score: 168
Period size: 42 Copynumber: 4.7 Consensus size: 41
44747578 TTGGTGCTGA
* * *
44747588 AGGCTCCCGCACATCATAGCACCGAGGTGCCGATGGTCTCCG
1 AGGCTCCCGCACATC-CAGCACCAAGGTGCCGATGGTGTCCG
* ** * * *
44747630 AGGCTCCC-CACAACCAAGGGCCTAGTTTGCCGGTGGTGTCCG
1 AGGCTCCCGCACATCC-AGCACCAAG-GTGCCGATGGTGTCCG
*
44747672 ATGCTCCCGCACATCCATGCACCAAGGTGCCGATGGTG-CTCG
1 AGGCTCCCGCACATCCA-GCACCAAGGTGCCGATGGTGTC-CG
* * * *
44747714 AGGCTCCCGCACATCCCAGCATCAAGGTTACCGATGGTGGCTG
1 AGGCTCCCGCACAT-CCAGCACCAAGG-TGCCGATGGTGTCCG
*
44747757 AGGCTCCCACACATCCGAGCCACCAAGGTG
1 AGGCTCCCGCACATCC-AG-CACCAAGGTG
44747787 ATGGAGGCTC
Statistics
Matches: 125, Mismatches: 22, Indels: 19
0.75 0.13 0.11
Matches are distributed among these distances:
41 12 0.10
42 64 0.51
43 41 0.33
44 8 0.06
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.17
Consensus pattern (41 bp):
AGGCTCCCGCACATCCAGCACCAAGGTGCCGATGGTGTCCG
Found at i:44747762 original size:43 final size:43
Alignment explanation
Indices: 44747674--44747785 Score: 133
Period size: 43 Copynumber: 2.6 Consensus size: 43
44747664 GGTGTCCGAT
*
44747674 GCTCCCGCACAT-CCATGCACCAAGGTGCCGATGGTGCTCGAG
1 GCTCCCGCACATCCCATGCACCAAGGTACCGATGGTGCTCGAG
*
44747716 GCTCCCGCACATCCCA-GCATCAAGGTTACCGATGGTGGCT-GAG
1 GCTCCCGCACATCCCATGCACCAAGG-TACCGATGGT-GCTCGAG
* *
44747759 GCTCCCACACATCCGA-GCCACCAAGGT
1 GCTCCCGCACATCCCATG-CACCAAGGT
44747786 GATGGAGGCT
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
42 20 0.33
43 31 0.51
44 10 0.16
ACGTcount: A:0.21, C:0.37, G:0.26, T:0.16
Consensus pattern (43 bp):
GCTCCCGCACATCCCATGCACCAAGGTACCGATGGTGCTCGAG
Found at i:44749112 original size:14 final size:14
Alignment explanation
Indices: 44749093--44749124 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
44749083 TCCAATCACC
44749093 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
44749107 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
44749121 GGGC
1 GGGC
44749125 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:44749362 original size:30 final size:29
Alignment explanation
Indices: 44749297--44749364 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
44749287 GAAAGTTATG
* *
44749297 AATTTAATTTTTATACTTTTATTTGATTA
1 AATTTAGTTTTTATACTTTTATTTGAGTA
* *
44749326 ATTTTAGTTTTTATATTTTTTATATT-AGTA
1 AATTTAGTTTTTATA-CTTTTAT-TTGAGTA
44749356 AATTTAGTT
1 AATTTAGTT
44749365 CTTACATTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 13 0.41
30 17 0.53
31 2 0.06
ACGTcount: A:0.29, C:0.01, G:0.06, T:0.63
Consensus pattern (29 bp):
AATTTAGTTTTTATACTTTTATTTGAGTA
Found at i:44761807 original size:46 final size:44
Alignment explanation
Indices: 44761755--44761863 Score: 134
Period size: 46 Copynumber: 2.4 Consensus size: 44
44761745 TTTTTAAATC
*
44761755 TAGTATTATTTAATATTTAAGCT-TAAC-ATTGTTTTAAATTTATCAT
1 TAGTATTATTTAATATTTAA--TAT-ACTATTATTTTAAA-TTATCAT
44761801 TAGTATTATTTTAATATTTAATATACTATTATTTTAAATTATCAT
1 TAGTATTA-TTTAATATTTAATATACTATTATTTTAAATTATCAT
*
44761846 TAATATTATTTAA-ATTTA
1 TAGTATTATTTAATATTTA
44761864 TCATACATGA
Statistics
Matches: 58, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
43 5 0.09
44 5 0.09
45 17 0.29
46 19 0.33
47 12 0.21
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.54
Consensus pattern (44 bp):
TAGTATTATTTAATATTTAATATACTATTATTTTAAATTATCAT
Found at i:44761885 original size:45 final size:45
Alignment explanation
Indices: 44761790--44761916 Score: 134
Period size: 45 Copynumber: 2.8 Consensus size: 45
44761780 ACATTGTTTT
* * *
44761790 AAATTTATCATTAGTATTATTTTAATATTTAAT-ATACTATTATTTT
1 AAATTTATCATTAATATTATTTTAA-ATTT-ATCATACTATAATTTG
44761836 AAA-TTATCATTAATATTA-TTTAAATTTATCATACATGATAATTTG
1 AAATTTATCATTAATATTATTTTAAATTTATCATAC-T-ATAATTTG
* * *
44761881 AAATTTATCATGTACTATAATTTTAAACTTATCATA
1 AAATTTATCAT-TAATATTATTTTAAATTTATCATA
44761917 TCATTATTTA
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
42 2 0.03
43 8 0.12
44 6 0.09
45 23 0.33
46 10 0.14
47 6 0.09
48 14 0.20
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (45 bp):
AAATTTATCATTAATATTATTTTAAATTTATCATACTATAATTTG
Found at i:44761887 original size:24 final size:21
Alignment explanation
Indices: 44761787--44761916 Score: 84
Period size: 24 Copynumber: 5.7 Consensus size: 21
44761777 TTAACATTGT
* *
44761787 TTTAAATTTATCATTAGTATTAT
1 TTTAAATTTATCA-TACTA-TAA
*
44761810 TTTAATATTTAAT-ATACTATTAT
1 TTTAA-ATTT-ATCATACTA-TAA
* *
44761833 TTTAAA-TTATCATTAATATTA
1 TTTAAATTTATCA-TACTATAA
44761854 TTTAAATTTATCATACATGATAA
1 TTTAAATTTATCATAC-T-ATAA
44761877 TTTGAAATTTATCATGTACTATAA
1 TTT-AAATTTATCA--TACTATAA
*
44761901 TTTTAAACTTATCATA
1 -TTTAAATTTATCATA
44761917 TCATTATTTA
Statistics
Matches: 89, Mismatches: 7, Indels: 23
0.75 0.06 0.19
Matches are distributed among these distances:
20 2 0.02
21 12 0.13
22 14 0.16
23 24 0.27
24 28 0.31
25 6 0.07
26 3 0.03
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (21 bp):
TTTAAATTTATCATACTATAA
Found at i:44765918 original size:41 final size:40
Alignment explanation
Indices: 44765853--44765998 Score: 125
Period size: 41 Copynumber: 3.6 Consensus size: 40
44765843 GTATCATATC
* *
44765853 AGGCCTTGAGCCTAGC-AGATTTCGTGCCGGTGTATTGTATT
1 AGGCCTTGAGCCTATCAAG-CTTCGTGCCGGTGTATT-TATT
* * *
44765894 AGGCTTTGAGCCTATCAAGCTTCGTGCCGGTATATATTTTT
1 AGGCCTTGAGCCTATCAAGCTTCGTGCCGGTGTAT-TTATT
* * * * * * *
44765935 GGGCCTTGAGCTTAGT-AGGCTTTGTGCCGATGTATCATATC
1 AGGCCTTGAGCCTA-TCAAGCTTCGTGCCGGTGTAT-TTATT
44765976 AGGCCTTGAGCCTATCAAGCTTC
1 AGGCCTTGAGCCTATCAAGCTTC
44765999 TTCGAAGTCT
Statistics
Matches: 81, Mismatches: 20, Indels: 8
0.74 0.18 0.07
Matches are distributed among these distances:
40 1 0.01
41 76 0.94
42 4 0.05
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.34
Consensus pattern (40 bp):
AGGCCTTGAGCCTATCAAGCTTCGTGCCGGTGTATTTATT
Found at i:44766436 original size:77 final size:77
Alignment explanation
Indices: 44766265--44766669 Score: 274
Period size: 77 Copynumber: 5.3 Consensus size: 77
44766255 TTTTCTTTTG
* * * ** ** * *
44766265 TAATTTAGAAATTATTTAATTTCTTAGAAACCATTTCATGATGCAAGT--TGTTTCATATATTAA
1 TAATTTAGGAATTAATTAATTTCTTAGAAACCATTTCATGTTTTAAGTAAAATTTAATAGATTAA
*
44766328 GTAATTCTTCCA
66 GTAATTCTTTCA
* * * * * * *
44766340 TGATTTCGGAATTACTTAATTTCTTAAAAATCATTTCATGTTTTAAGTAAAATTTTATATATTAA
1 TAATTTAGGAATTAATTAATTTCTTAGAAACCATTTCATGTTTTAAGTAAAATTTAATAGATTAA
44766405 GTAATAT-TTTC-
66 GTAAT-TCTTTCA
* * * * * *
44766416 TAATTTTATGAATTAATTAATTTCTTGGAAGCCTTTTCATGTTTTAAGTAACATTTAATGGATTA
1 TAA-TTTAGGAATTAATTAATTTCTTAGAAACCATTTCATGTTTTAAGTAAAATTTAATAGATTA
44766481 AGTAATTCTTTCA
65 AGTAATTCTTTCA
* * ** *
44766494 TGATTTAGGAA-TAACTTAATTTCTTAGAAACCACTTCATGTTTTACA-TAATCGTTT-AT-GTT
1 TAATTTAGGAATTAA-TTAATTTCTTAGAAACCATTTCATGTTTTA-AGTAA-AATTTAATAG-A
*
44766555 TTAAGTAATT-TTACA
62 TTAAGTAATTCTTTCA
* * * ** ** * *
44766570 TGATTTAAGAATTATTTAATTTCTTAGAAACTTTTTTCACATTTTAAGTAACATTTCAT-GTATT
1 TAATTTAGGAATTAATTAATTTCTTAGAAAC-CATTTCATGTTTTAAGTAAAATTTAATAG-ATT
*
44766634 AAGTGATTCGTTT-A
64 AAGTAATTC-TTTCA
* * *
44766648 TGATTTACGAATTACTTAATTT
1 TAATTTAGGAATTAATTAATTT
44766670 TTTTTAAAAT
Statistics
Matches: 266, Mismatches: 48, Indels: 29
0.78 0.14 0.08
Matches are distributed among these distances:
75 39 0.15
76 42 0.16
77 154 0.58
78 29 0.11
79 2 0.01
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (77 bp):
TAATTTAGGAATTAATTAATTTCTTAGAAACCATTTCATGTTTTAAGTAAAATTTAATAGATTAA
GTAATTCTTTCA
Found at i:44766532 original size:154 final size:154
Alignment explanation
Indices: 44766323--44766669 Score: 414
Period size: 154 Copynumber: 2.3 Consensus size: 154
44766313 TGTTTCATAT
* * * *
44766323 ATTAAGTAATTCTTCCATGATTTCGGAATTACTTAATTTCTTAAAAATCATTTCATGTTTTA-AG
1 ATTAAGTAATTCTTTCATGATTTAGGAATTACTTAATTTCTTAAAAACCACTTCATGTTTTACA-
* * * * *
44766387 TAAAATTTTATATATTAAGTAATATTTTC-TAATTTTATGAATTAATTAATTTCTTGGAAGC-CT
65 TAAAAGTTTATATATTAAGTAAT-TTTACATAA-TTTAAGAATTAATTAATTTCTTAGAAACTCT
**
44766450 TTTCATGTTTTAAGTAACATTTAATGG
128 TTTCACATTTTAAGTAACATTTAATGG
* *
44766477 ATTAAGTAATTCTTTCATGATTTAGGAATAACTTAATTTCTTAGAAACCACTTCATGTTTTACAT
1 ATTAAGTAATTCTTTCATGATTTAGGAATTACTTAATTTCTTAAAAACCACTTCATGTTTTACAT
** * * * * *
44766542 AATCGTTTATGTTTTAAGTAATTTTACATGATTTAAGAATTATTTAATTTCTTAGAAACTTTTTT
66 AAAAGTTTATATATTAAGTAATTTTACATAATTTAAGAATTAATTAATTTCTTAGAAACTCTTTT
* *
44766607 CACATTTTAAGTAACATTTCATGT
131 CACATTTTAAGTAACATTTAATGG
* *
44766631 ATTAAGTGATTCGTTT-ATGATTTACGAATTACTTAATTT
1 ATTAAGTAATTC-TTTCATGATTTAGGAATTACTTAATTT
44766670 TTTTTAAAAT
Statistics
Matches: 164, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
153 28 0.17
154 132 0.80
155 4 0.02
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (154 bp):
ATTAAGTAATTCTTTCATGATTTAGGAATTACTTAATTTCTTAAAAACCACTTCATGTTTTACAT
AAAAGTTTATATATTAAGTAATTTTACATAATTTAAGAATTAATTAATTTCTTAGAAACTCTTTT
CACATTTTAAGTAACATTTAATGG
Found at i:44768314 original size:76 final size:78
Alignment explanation
Indices: 44768173--44768332 Score: 202
Period size: 76 Copynumber: 2.1 Consensus size: 78
44768163 AGGTATGAGG
* * *
44768173 TTCGAACATAAATATGTATGCATATAATCAAGTTATTGAGTTGGGAATTAATGTATGAATTTTAT
1 TTCGAACATAAATATGTATGCATATAATCAAGTAATTGAGTTGGAAATTAAAGTATGAATTTTAT
*
44768238 AATT-ATAGGGAGA
66 -ATTCATAGAGAGA
* * *
44768251 TTCGAACAT-AA-ATGTATGCCTTTAATCAAGTAATTGAGTTGGAAATTAAAGTATG-TTTCTTA
1 TTCGAACATAAATATGTATGCATATAATCAAGTAATTGAGTTGGAAATTAAAGTATGAATT-TTA
*
44768313 TATTCATAGAGAGG
65 TATTCATAGAGAGA
44768327 TTCGAA
1 TTCGAA
44768333 TATAGAGATT
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
75 5 0.07
76 56 0.78
77 2 0.03
78 9 0.12
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (78 bp):
TTCGAACATAAATATGTATGCATATAATCAAGTAATTGAGTTGGAAATTAAAGTATGAATTTTAT
ATTCATAGAGAGA
Found at i:44771544 original size:109 final size:109
Alignment explanation
Indices: 44771355--44772232 Score: 1472
Period size: 109 Copynumber: 8.1 Consensus size: 109
44771345 AAAATTTAGG
* * *
44771355 AGGATATTTGGCTATTTGGTCGAACGAG--AAACCAAAACCCAGCACATTAGGGCACGTTTTCTT
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
*
44771418 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGAA
* * *
44771462 AGGATATTTGGCTATTTGGTTGAATGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTT
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
*
44771527 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGAA
* * * *
44771571 AGGATATTTGGCTATTTGGTTGAATGAGAAAAATCGAAACCCAGCACATTAGGGCACATTTTCTT
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
*
44771636 GAATTTCCAAATGCAAAACATTGCCTTATTTTGAAATTTTTGAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGAA
* *
44771680 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACATTTTCTT
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
*
44771745 GAATTTCCAAATGCAAAACATTGCCTTATTTTGAAATTTTTGAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGAA
* *
44771789 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATTGAAACCTAGCACATTAGGGCACGTTTTCTC
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
*
44771854 GAATTTCCAAACGCAAAACATTGCCTTATTTTGGAATTTTTGAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGAA
* * *
44771898 AGGATATTTGGCTATTTGGTCGAACGATAAAAATGGAAACCCAGCACATTTGGGCACGTTTTCTC
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
*
44771963 GAATTTCCAAACGCAAAACATTGCCTTATTTTGGAATTTTTGAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGAA
* *
44772007 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATTGAAACCCAGCACATTAGGGCACATTTTCTC
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* *
44772072 GAATTTCCAAACGCAAAACAATGCCTTATTTTGAAATTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGAA
*
44772116 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTTGGGCACGTTTTCTC
1 AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* *
44772181 GAATTTCCAAAAGCAAAACATTGCCTTATTTTGAAATTTTTTAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGAA
44772225 AGGATATT
1 AGGATATT
44772233 AGTACGCGTA
Statistics
Matches: 737, Mismatches: 32, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
107 26 0.04
109 711 0.96
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (109 bp):
AGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGAA
Found at i:44772538 original size:14 final size:15
Alignment explanation
Indices: 44772505--44772540 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
44772495 TATATATTTC
44772505 AAAAT-TAT-TATAT
1 AAAATATATGTATAT
44772518 AAAATATATGTATAT
1 AAAATATATGTATAT
44772533 -AAATATAT
1 AAAATATAT
44772541 AAGTAAGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.24
14 11 0.52
15 5 0.24
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
AAAATATATGTATAT
Found at i:44783286 original size:24 final size:23
Alignment explanation
Indices: 44783253--44783317 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 23
44783243 AAACTATGTC
44783253 AAATTTAAATAATAATACATAGT-
1 AAATTTAAATAATAATACATA-TA
44783276 AAATTTCAAATAATAATACATATA
1 AAATTT-AAATAATAATACATATA
*
44783300 AAACTTAAAATAATAATA
1 AAA-TTTAAATAATAATA
44783318 AAAGAAACTC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
23 7 0.18
24 29 0.76
25 2 0.05
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (23 bp):
AAATTTAAATAATAATACATATA
Found at i:44783853 original size:17 final size:17
Alignment explanation
Indices: 44783827--44783860 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
44783817 AAAAACTATT
*
44783827 ACCTATACTAAAACAAA
1 ACCTAAACTAAAACAAA
*
44783844 ACCTAAACTAAAGCAAA
1 ACCTAAACTAAAACAAA
44783861 GCCCTGCGCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.24, G:0.03, T:0.15
Consensus pattern (17 bp):
ACCTAAACTAAAACAAA
Found at i:44787127 original size:82 final size:82
Alignment explanation
Indices: 44787006--44787465 Score: 662
Period size: 82 Copynumber: 5.6 Consensus size: 82
44786996 TGGATTAGTG
* * * * **
44787006 TCGCTAATGATCAGAGTTTTAGCGGTGTTTTTGAT-AAAGCGCCGCTAATGCTCTGGGTTTTAA-
1 TCGCTAATGCTCTGGGTTTTAGCGGCGTTTTTG-TGAAAGCGCCGCTAATGCTCAAGG-TTTAAG
44787069 CGGCGTTTTTGTGGAAGCA
64 CGGCGTTTTTGTGGAAGCA
44787088 -CAGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATGCTCAAGGTTTAAGC
1 TC-GCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATGCTCAAGGTTTAAGC
44787152 GGCGTTTTTGTGGAAGCA
65 GGCGTTTTTGTGGAAGCA
44787170 TCGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATGCTCAAGGTTTAAGCG
1 TCGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATGCTCAAGGTTTAAGCG
44787235 GCGTTTTTGTGGAAGCA
66 GCGTTTTTGTGGAAGCA
44787252 TCGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATGCTCAAGGTTTAAGCG
1 TCGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATGCTCAAGGTTTAAGCG
44787317 GCGTTTTTGTGGAAGCA
66 GCGTTTTTGTGGAAGCA
* * * * *
44787334 TCGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTTAAAGCGCTGCTAATGCTCTAGGTTTTAGCA
1 TCGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATGCTCAAGGTTTAAGCG
* * *
44787399 GCATTTTT-TAAGAAGCG
66 GCGTTTTTGT-GGAAGCA
* * **
44787416 CCACTAATGCTC-GAGGTTTTAGCGGCGTTTTCT-AAAAAGCGCCGCTAATG
1 TCGCTAATGCTCTG-GGTTTTAGCGGCGTTTT-TGTGAAAGCGCCGCTAATG
44787466 GTCGGGGTTT
Statistics
Matches: 352, Mismatches: 19, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
81 9 0.03
82 341 0.97
83 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.33
Consensus pattern (82 bp):
TCGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATGCTCAAGGTTTAAGCG
GCGTTTTTGTGGAAGCA
Found at i:44787475 original size:41 final size:41
Alignment explanation
Indices: 44787007--44787541 Score: 553
Period size: 41 Copynumber: 13.1 Consensus size: 41
44786997 GGATTAGTGT
* * * *
44787007 CGCTAATGATCAGAGTTTTAGCGGTGTTTTTGAT-AAAGCGC
1 CGCTAATGCTCTGGGTTTTAGCGGCGTTTTTG-TGAAAGCGC
* * *
44787048 CGCTAATGCTCTGGGTTTTAACGGCGTTTTTGTGGAAGCAC
1 CGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGAAAGCGC
*
44787089 AGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGAAAGCGC
1 CGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGAAAGCGC
** * * **
44787130 CGCTAATGCTCAAGGTTTAAGCGGCGTTTTTGTGGAAGCAT
1 CGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGAAAGCGC
44787171 CGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGAAAGCGC
1 CGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGAAAGCGC
** * * **
44787212 CGCTAATGCTCAAGGTTTAAGCGGCGTTTTTGTGGAAGCAT
1 CGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGAAAGCGC
44787253 CGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGAAAGCGC
1 CGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGAAAGCGC
** * * **
44787294 CGCTAATGCTCAAGGTTTAAGCGGCGTTTTTGTGGAAGCAT
1 CGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGAAAGCGC
*
44787335 CGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTTAAAGCGC
1 CGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGAAAGCGC
* * * * *
44787376 TGCTAATGCTCTAGGTTTTAGCAGCATTTTT-TAAGAAGCGC
1 CGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGA-AAGCGC
* **
44787417 CACTAATGCTC-GAGGTTTTAGCGGCGTTTTCT-AAAAAGCGC
1 CGCTAATGCTCTG-GGTTTTAGCGGCGTTTT-TGTGAAAGCGC
* * *** * *
44787458 CGCTAATGGTCGGGGTTTTAATAGCATTTTTGAGAAAGCGC
1 CGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGAAAGCGC
* * * *
44787499 CACT-ATGCTC-GGGTTTTTAGAGTCGTTCTTT-TTAAAGCGC
1 CGCTAATGCTCTGGG-TTTTAGCGGCGTT-TTTGTGAAAGCGC
44787539 CGC
1 CGC
44787542 AAAAAATATT
Statistics
Matches: 409, Mismatches: 77, Indels: 17
0.81 0.15 0.03
Matches are distributed among these distances:
39 3 0.01
40 26 0.06
41 376 0.92
42 4 0.01
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (41 bp):
CGCTAATGCTCTGGGTTTTAGCGGCGTTTTTGTGAAAGCGC
Found at i:44787601 original size:16 final size:15
Alignment explanation
Indices: 44787568--44787622 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 15
44787558 TAATTGGTTT
*
44787568 ATTATTT-ATATT-A
1 ATTATTTAAAATTGA
44787581 ATTATTTAAAATTGA
1 ATTATTTAAAATTGA
**
44787596 ACTTATTTCTAATTGA
1 A-TTATTTAAAATTGA
44787612 A-TATTTAAAAT
1 ATTATTTAAAAT
44787623 CTTCAGAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
13 7 0.21
14 12 0.35
15 2 0.06
16 13 0.38
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (15 bp):
ATTATTTAAAATTGA
Found at i:44787945 original size:14 final size:15
Alignment explanation
Indices: 44787915--44787953 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
44787905 AGGGAGTATA
*
44787915 TATGGATTTAGGGAT
1 TATGGATTTAAGGAT
44787930 TATGGA-TTAAGGAT
1 TATGGATTTAAGGAT
44787944 TAT-GATTTAA
1 TATGGATTTAA
44787954 TTAAGGGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 2 0.09
14 14 0.64
15 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.41
Consensus pattern (15 bp):
TATGGATTTAAGGAT
Found at i:44787993 original size:22 final size:22
Alignment explanation
Indices: 44787958--44788048 Score: 62
Period size: 22 Copynumber: 4.2 Consensus size: 22
44787948 ATTTAATTAA
*
44787958 GGGTT-GGGATTTAAGGTTTAG
1 GGGTTAGGGGTTTAAGGTTTAG
* *
44787979 GGGTTAGGGGTTTAAGGGTTAT
1 GGGTTAGGGGTTTAAGGTTTAG
*** *
44788001 ACATTAGGGG-TTAAGAGTTAAG
1 GGGTTAGGGGTTTAAG-GTTTAG
**
44788023 GATTTA-GGGTTTAAGGTTTCAG
1 GGGTTAGGGGTTTAAGGTTT-AG
44788045 GGGT
1 GGGT
44788049 CGAGTTAGGG
Statistics
Matches: 51, Mismatches: 15, Indels: 7
0.70 0.21 0.10
Matches are distributed among these distances:
21 16 0.31
22 35 0.69
ACGTcount: A:0.23, C:0.02, G:0.40, T:0.35
Consensus pattern (22 bp):
GGGTTAGGGGTTTAAGGTTTAG
Found at i:44788258 original size:14 final size:15
Alignment explanation
Indices: 44788232--44788269 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
44788222 TATATATATA
44788232 TATGGATTTAGGGAT
1 TATGGATTTAGGGAT
44788247 TATGGA-TTAGGGAT
1 TATGGATTTAGGGAT
44788261 TATGG-TTTA
1 TATGGATTTA
44788270 ATTAAGGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (15 bp):
TATGGATTTAGGGAT
Found at i:44789285 original size:43 final size:43
Alignment explanation
Indices: 44789226--44789452 Score: 294
Period size: 43 Copynumber: 5.3 Consensus size: 43
44789216 TTTTAGAAAT
**
44789226 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
*
44789269 AAACGCCGCAAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
*
44789312 AAACGCCGCTAAAGACCATGTCCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * * **
44789355 AAACGCTGCTATAGACCATGATCTTTAGCGGCGCTTTTTTCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * * * * * * *
44789398 AGACGCCGCTAAAGAACA-AACCTTTTGTGGCGCTTCTCGCAA
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
44789440 AAACGCCGCTAAA
1 AAACGCCGCTAAA
44789453 AACATAATCT
Statistics
Matches: 160, Mismatches: 24, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 28 0.17
43 132 0.82
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:44789907 original size:23 final size:23
Alignment explanation
Indices: 44789857--44789908 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
44789847 GTTAGGTGTC
* *
44789857 AGTATAAAGACATGTCAGATATG
1 AGTATGAAGACATGTCAGAGATG
* * *
44789880 GGTATGAAGGCATGTCTGAGATG
1 AGTATGAAGACATGTCAGAGATG
44789903 AGTATG
1 AGTATG
44789909 TTCAATTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.27
Consensus pattern (23 bp):
AGTATGAAGACATGTCAGAGATG
Found at i:44792111 original size:8 final size:8
Alignment explanation
Indices: 44792098--44792122 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
44792088 AGGGAAAAAA
44792098 ATTTAACC
1 ATTTAACC
44792106 ATTTAACC
1 ATTTAACC
44792114 ATTTAACC
1 ATTTAACC
44792122 A
1 A
44792123 AGGGGATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (8 bp):
ATTTAACC
Found at i:44792566 original size:19 final size:19
Alignment explanation
Indices: 44792540--44792586 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
44792530 CTGAAACCAA
44792540 AATTTATAATAGGCATTCT
1 AATTTATAATAGGCATTCT
*
44792559 AGTTTATAATAGGCATTCT
1 AATTTATAATAGGCATTCT
44792578 AATTTATAA
1 AATTTATAA
44792587 CAGATTCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.43
Consensus pattern (19 bp):
AATTTATAATAGGCATTCT
Found at i:44794379 original size:26 final size:26
Alignment explanation
Indices: 44794349--44794401 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
44794339 AATAAATTAA
44794349 ATTCTTGTATATTGCATATCAATTTT
1 ATTCTTGTATATTGCATATCAATTTT
*
44794375 ATTCTTGTATATTGCATATTAATTTT
1 ATTCTTGTATATTGCATATCAATTTT
44794401 A
1 A
44794402 AATTAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.09, G:0.08, T:0.55
Consensus pattern (26 bp):
ATTCTTGTATATTGCATATCAATTTT
Found at i:44794671 original size:87 final size:90
Alignment explanation
Indices: 44794570--44794753 Score: 266
Period size: 87 Copynumber: 2.1 Consensus size: 90
44794560 AGCAACTTAT
* * *
44794570 CCCTAAACCTTATTTAATATATAAATTAAAA-ACACTAATTAATCTAAATCCTAAACCCTAAC-C
1 CCCTAAACATTATTTAATATATAAATTAAAACAAACTAATTAATCTAAACCCTAAACCCTAACTC
*
44794633 CTAACTC-GACCCCAAATCCCTAAC
66 CTAACTCTGACCCCAAACCCCTAAC
*
44794657 CCCTAAACATTATTTAATATATAAATTAAAACAAACTAATTAATTTAAACCCTAAACCCTAACTC
1 CCCTAAACATTATTTAATATATAAATTAAAACAAACTAATTAATCTAAACCCTAAACCCTAACTC
* * *
44794722 TTAACTCTTGACCTCTAACCCCTAAC
66 CTAACTC-TGACCCCAAACCCCTAAC
44794748 CCCTAA
1 CCCTAA
44794754 CTCGACACCA
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
87 30 0.35
88 28 0.33
89 7 0.08
91 20 0.24
ACGTcount: A:0.42, C:0.29, G:0.01, T:0.28
Consensus pattern (90 bp):
CCCTAAACATTATTTAATATATAAATTAAAACAAACTAATTAATCTAAACCCTAAACCCTAACTC
CTAACTCTGACCCCAAACCCCTAAC
Found at i:44794816 original size:21 final size:22
Alignment explanation
Indices: 44794774--44794816 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
44794764 AATCAATAAA
* * *
44794774 CCCTGAATTCCTAACTCTTAAC
1 CCCTGAATCCCTAACCCCTAAC
44794796 CCCT-AATCCCTAACCCCTAAC
1 CCCTGAATCCCTAACCCCTAAC
44794817 TCATAAACCT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.28, C:0.44, G:0.02, T:0.26
Consensus pattern (22 bp):
CCCTGAATCCCTAACCCCTAAC
Found at i:44794866 original size:14 final size:15
Alignment explanation
Indices: 44794849--44794881 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
44794839 CTTAAATCAG
44794849 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
44794863 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
44794878 AATC
1 AATC
44794882 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:44795350 original size:41 final size:41
Alignment explanation
Indices: 44795295--44795439 Score: 184
Period size: 41 Copynumber: 3.5 Consensus size: 41
44795285 TTGCGGCACT
* * *
44795295 TTTTTCAAAAACGCCGCTAAAGATCTAATCATTAGCGGCGC
1 TTTTCCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGC
* *
44795336 TTTTCCAAAAACGCCGCTAAAGATATGGGCATTAGCGGCGC
1 TTTTCCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGC
* * *
44795377 TTTTCCAAAAATGCCGCTAAAGATCTGAGCATTGGCAGCGC
1 TTTTCCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGC
*
44795418 -TTTCCTTAAAAATGCCGCTAAA
1 TTTTCC--AAAAACGCCGCTAAA
44795440 TCCCCGAAAG
Statistics
Matches: 92, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
40 5 0.05
41 72 0.78
42 15 0.16
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (41 bp):
TTTTCCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGC
Found at i:44795946 original size:16 final size:16
Alignment explanation
Indices: 44795898--44795948 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
44795888 TCGTTGCTCA
* *
44795898 TCTACCGTCACACTCG
1 TCTACCGTCGCACTCC
* **
44795914 TCAACCGTCGCTGTCC
1 TCTACCGTCGCACTCC
44795930 TCTACCGTCGCACTCC
1 TCTACCGTCGCACTCC
44795946 TCT
1 TCT
44795949 GTCGTCGGAG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.14, C:0.45, G:0.14, T:0.27
Consensus pattern (16 bp):
TCTACCGTCGCACTCC
Found at i:44797468 original size:19 final size:19
Alignment explanation
Indices: 44797431--44797483 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 19
44797421 ACATTACTTA
* **
44797431 TTAATATTTATATACATTT
1 TTAATATATATATTTATTT
44797450 TTAATATATATATTTATTT
1 TTAATATATATATTTATTT
** *
44797469 AAAATTTATATATTT
1 TTAATATATATATTT
44797484 TTTCAAAACT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTAATATATATATTTATTT
Found at i:44797491 original size:19 final size:19
Alignment explanation
Indices: 44797456--44797496 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
44797446 ATTTTTAATA
*
44797456 TATATATTTATTTAAAATT
1 TATATATTTATTTAAAACT
44797475 TATATATTT-TTTCAAAACT
1 TATATATTTATTT-AAAACT
44797494 TAT
1 TAT
44797497 CAATCATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATATTTATTTAAAACT
Found at i:44797625 original size:12 final size:12
Alignment explanation
Indices: 44797608--44797632 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44797598 TACATAATAC
44797608 ATAACTTACATA
1 ATAACTTACATA
44797620 ATAACTTACATA
1 ATAACTTACATA
44797632 A
1 A
44797633 CTTATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:44797646 original size:12 final size:12
Alignment explanation
Indices: 44797631--44797659 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
44797621 TAACTTACAT
44797631 AACTTATATATA
1 AACTTATATATA
44797643 AACTTATATATA
1 AACTTATATATA
44797655 AACTT
1 AACTT
44797660 GCATAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (12 bp):
AACTTATATATA
Found at i:44798368 original size:43 final size:43
Alignment explanation
Indices: 44798193--44798352 Score: 196
Period size: 43 Copynumber: 3.7 Consensus size: 43
44798183 TCACCAAACA
* * * *
44798193 ATAGCAGCGTTTGTGGG-AAAGCACCGTTAAAAGTCATGATCT
1 ATAGCAGCATTTGTGGGAAAAGCGCCGCTAAAAGTCATGACCT
* * *
44798235 ATAGCGGCATTTGTGGGAAAAGCGTCGCTAAAGGTCATGACCT
1 ATAGCAGCATTTGTGGGAAAAGCGCCGCTAAAAGTCATGACCT
* * *
44798278 ATAGCGGCATTTGCGGGAAAAGAGCCGCTAAAAGTCATGACCT
1 ATAGCAGCATTTGTGGGAAAAGCGCCGCTAAAAGTCATGACCT
* * *
44798321 TTAGCAGCGTTTGTGGGGAAAGCGCCGCTAAA
1 ATAGCAGCATTTGTGGGAAAAGCGCCGCTAAA
44798353 GAACAAGACC
Statistics
Matches: 100, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 15 0.15
43 85 0.85
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (43 bp):
ATAGCAGCATTTGTGGGAAAAGCGCCGCTAAAAGTCATGACCT
Found at i:44798839 original size:17 final size:19
Alignment explanation
Indices: 44798801--44798839 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
44798791 GCATTCTTGA
44798801 ATATGAATTGACAGATATT
1 ATATGAATTGACAGATATT
*
44798820 ATATGATTTGAC-GA-ATT
1 ATATGAATTGACAGATATT
44798837 ATA
1 ATA
44798840 GTTTTGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 2 0.11
19 11 0.58
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.38
Consensus pattern (19 bp):
ATATGAATTGACAGATATT
Found at i:44801133 original size:36 final size:35
Alignment explanation
Indices: 44801077--44801164 Score: 113
Period size: 36 Copynumber: 2.5 Consensus size: 35
44801067 ACATCGATAT
*
44801077 TCCAACTGGAACACACCAGATGATCATAAGAGCTAA
1 TCCAACTGAAACACACCAGATGATCATAAGAGC-AA
* *
44801113 TCCATCTGAAACACACCAGATGCTCATAAGAGCAA
1 TCCAACTGAAACACACCAGATGATCATAAGAGCAA
* *
44801148 TCTACCTGATAACACAC
1 TCCAACTGA-AACACAC
44801165 TAATGGCTCG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 9 0.20
36 37 0.80
ACGTcount: A:0.40, C:0.28, G:0.14, T:0.18
Consensus pattern (35 bp):
TCCAACTGAAACACACCAGATGATCATAAGAGCAA
Found at i:44803501 original size:17 final size:18
Alignment explanation
Indices: 44803470--44803503 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44803460 GTAATTAAAA
44803470 TAAAAAAAATGTTGAAAG
1 TAAAAAAAATGTTGAAAG
*
44803488 TAAAAGAAAT-TTGAAA
1 TAAAAAAAATGTTGAAA
44803504 TAGCAGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.24
Consensus pattern (18 bp):
TAAAAAAAATGTTGAAAG
Found at i:44803724 original size:19 final size:18
Alignment explanation
Indices: 44803683--44803725 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
44803673 ACTAAAGATC
*
44803683 AAATTTAAAATAATTAAA
1 AAATTTAAAATAATCAAA
44803701 AAATTTAACAAT-ATCAAA
1 AAATTTAA-AATAATCAAA
44803719 ATAATTT
1 A-AATTT
44803726 GATCTTTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATTTAAAATAATCAAA
Found at i:44814545 original size:62 final size:62
Alignment explanation
Indices: 44814448--44814573 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
44814438 TTTTTGTTCT
44814448 AATTTAGCCCTATTTTTATAAGAATTTGAATTTAACATACCAACTTCATTCCTGATAAGAAA
1 AATTTAGCCCTATTTTTATAAGAATTTGAATTTAACATACCAACTTCATTCCTGATAAGAAA
*
44814510 AATTTAGCCCTATTTTTATAAGAATTTGAATTTAACATACCAATTTCATTCCTGATAAGAAA
1 AATTTAGCCCTATTTTTATAAGAATTTGAATTTAACATACCAACTTCATTCCTGATAAGAAA
44814572 AA
1 AA
44814574 CTCAAATTTA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (62 bp):
AATTTAGCCCTATTTTTATAAGAATTTGAATTTAACATACCAACTTCATTCCTGATAAGAAA
Found at i:44816342 original size:41 final size:41
Alignment explanation
Indices: 44816285--44816362 Score: 156
Period size: 41 Copynumber: 1.9 Consensus size: 41
44816275 AAAGGTTTAA
44816285 GACTTCAAAAGCAAGAAGGACATTATCAATTATCATAGTGT
1 GACTTCAAAAGCAAGAAGGACATTATCAATTATCATAGTGT
44816326 GACTTCAAAAGCAAGAAGGACATTATCAATTATCATA
1 GACTTCAAAAGCAAGAAGGACATTATCAATTATCATA
44816363 TGCCCTTGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (41 bp):
GACTTCAAAAGCAAGAAGGACATTATCAATTATCATAGTGT
Found at i:44816984 original size:12 final size:12
Alignment explanation
Indices: 44816951--44816984 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
44816941 GTTTTATATC
44816951 GAAATTGTGAAA
1 GAAATTGTGAAA
*
44816963 G-AATTATGAAA
1 GAAATTGTGAAA
44816974 GAAATTGTGAA
1 GAAATTGTGAA
44816985 TATCTTCCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (12 bp):
GAAATTGTGAAA
Found at i:44819509 original size:23 final size:21
Alignment explanation
Indices: 44819462--44819513 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
44819452 CCTAACTTTG
**
44819462 TAAAAATTCTTAAAAAAATTG
1 TAAAAATTCTTAAAAAAATCA
*
44819483 TAAAAATTCTTAATTATAAATCA
1 TAAAAATTCTTAA--AAAAATCA
44819506 TAAAAATT
1 TAAAAATT
44819514 GTAAAATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 13 0.50
23 13 0.50
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (21 bp):
TAAAAATTCTTAAAAAAATCA
Found at i:44821654 original size:25 final size:25
Alignment explanation
Indices: 44821624--44821705 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
44821614 GGACACACCG
44821624 TAGCTCTTATGAG-TGTCCTGTTAAT
1 TAGCTCTTATGAGCT-TCCTGTTAAT
* ** * *
44821649 TGGCTCTTCGGAGCTTCCCGATAAT
1 TAGCTCTTATGAGCTTCCTGTTAAT
44821674 TAGCTCTTATGAGCTTCCTGATTAA-
1 TAGCTCTTATGAGCTTCCTG-TTAAT
44821699 TAGCTCT
1 TAGCTCT
44821706 CCGGAGCTTC
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
25 41 0.91
26 4 0.09
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.39
Consensus pattern (25 bp):
TAGCTCTTATGAGCTTCCTGTTAAT
Found at i:44821705 original size:50 final size:50
Alignment explanation
Indices: 44821624--44821720 Score: 144
Period size: 50 Copynumber: 1.9 Consensus size: 50
44821614 GGACACACCG
* *
44821624 TAGCTCTTATGAGTGTCCTGTTAATTGGCTCTTCGGAGCTTCCCGATAAT
1 TAGCTCTTATGAGTGTCCTGTTAATTAGCTCTCCGGAGCTTCCCGATAAT
44821674 TAGCTCTTATGAGCT-TCCTGATTAA-TAGCTCTCCGGAGCTTCCCGAT
1 TAGCTCTTATGAG-TGTCCTG-TTAATTAGCTCTCCGGAGCTTCCCGAT
44821721 TAAAGGCTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
50 38 0.88
51 5 0.12
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.36
Consensus pattern (50 bp):
TAGCTCTTATGAGTGTCCTGTTAATTAGCTCTCCGGAGCTTCCCGATAAT
Found at i:44821712 original size:25 final size:26
Alignment explanation
Indices: 44821644--44821723 Score: 101
Period size: 25 Copynumber: 3.2 Consensus size: 26
44821634 GAGTGTCCTG
*
44821644 TTAATTGGCTCTTCGGAGCTTCCCGA
1 TTAATTAGCTCTTCGGAGCTTCCCGA
** *
44821670 -TAATTAGCTCTTATGAGCTTCCTGA
1 TTAATTAGCTCTTCGGAGCTTCCCGA
*
44821695 TTAA-TAGCTCTCCGGAGCTTCCCGA
1 TTAATTAGCTCTTCGGAGCTTCCCGA
44821720 TTAA
1 TTAA
44821724 AGGCTCTTTC
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
25 42 0.93
26 3 0.07
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (26 bp):
TTAATTAGCTCTTCGGAGCTTCCCGA
Found at i:44821869 original size:25 final size:25
Alignment explanation
Indices: 44821814--44821874 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
44821804 ATTGGCTCAC
44821814 ATGAGCTTCCCGTTATATGGCTCTG
1 ATGAGCTTCCCGTTATATGGCTCTG
* * *
44821839 AAGAGCTTCTCGTTTATAT-GCTCTT
1 ATGAGCTTCCCG-TTATATGGCTCTG
44821864 ATGAGCATTCC
1 ATGAGC-TTCC
44821875 TGAATATGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 20 0.69
26 9 0.31
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.38
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATATGGCTCTG
Found at i:44823912 original size:26 final size:26
Alignment explanation
Indices: 44823584--44823911 Score: 428
Period size: 26 Copynumber: 12.7 Consensus size: 26
44823574 ACACGAATAA
44823584 AAATTACCAAAATACCCTCGATGGGT
1 AAATTACCAAAATACCCTCGATGGGT
*
44823610 AAATTACCAAAATACCCTCGATGTGT
1 AAATTACCAAAATACCCTCGATGGGT
*
44823636 AAATTACCAAAATACCCTCAATGGGT
1 AAATTACCAAAATACCCTCGATGGGT
* *
44823662 AAATTA-CAGAAATACCCTCAATAGGT
1 AAATTACCA-AAATACCCTCGATGGGT
** *
44823688 AAATTACTGAAATACCATCGATGGGT
1 AAATTACCAAAATACCCTCGATGGGT
* *
44823714 AAATTATCGAAATACCCTCGATGGGT
1 AAATTACCAAAATACCCTCGATGGGT
* *
44823740 AAATCA-CAGAAATACCCTCAATGGGT
1 AAATTACCA-AAATACCCTCGATGGGT
* *
44823766 AAATTATCGAAA-ACCCTCGATGGGT
1 AAATTACCAAAATACCCTCGATGGGT
*
44823791 AAATTGCCAAAATACCCTCGATGGGT
1 AAATTACCAAAATACCCTCGATGGGT
44823817 AAATTACCAAAATACCCTCGATGGGT
1 AAATTACCAAAATACCCTCGATGGGT
* * *
44823843 AAATTACCAAAATACTCTCAATAGGT
1 AAATTACCAAAATACCCTCGATGGGT
* *
44823869 AAATTACTAAAATACCCCCGATGGGT
1 AAATTACCAAAATACCCTCGATGGGT
* *
44823895 AAATTATCGAAATACCC
1 AAATTACCAAAATACCC
44823912 CTGTAGGGTA
Statistics
Matches: 264, Mismatches: 33, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
25 24 0.09
26 239 0.91
27 1 0.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (26 bp):
AAATTACCAAAATACCCTCGATGGGT
Found at i:44824147 original size:27 final size:27
Alignment explanation
Indices: 44824106--44824170 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
44824096 ATGGAGGAAG
* * *
44824106 TACTGTTTCTTGTGGCTCTGCCACA-A
1 TACTGTTACTGGTGGCTATGCCACATA
44824132 TCACTGTTACTGGTGGCTATGCCACATA
1 T-ACTGTTACTGGTGGCTATGCCACATA
44824160 TACTG-TACTGG
1 TACTGTTACTGG
44824171 CAGCTCGGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.21
27 25 0.74
28 2 0.06
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTATGCCACATA
Found at i:44828001 original size:18 final size:17
Alignment explanation
Indices: 44827974--44828032 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
44827964 ACGGAAAAAC
*
44827974 AAGATGAAGATGAAGATG
1 AAGATAAAGAT-AAGATG
*
44827992 AAGATAAAGATAACATTG
1 AAGATAAAGATAAGA-TG
* *
44828010 GAGATAGAGATAGAGATG
1 AAGATAAAGATA-AGATG
44828028 AAGAT
1 AAGAT
44828033 GATGATAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 3 0.09
18 28 0.85
19 2 0.06
ACGTcount: A:0.51, C:0.02, G:0.29, T:0.19
Consensus pattern (17 bp):
AAGATAAAGATAAGATG
Found at i:44837043 original size:26 final size:27
Alignment explanation
Indices: 44836992--44837045 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
44836982 TATACAATAT
* *
44836992 TTAATTTTATATAATAAAAATTAAAAA
1 TTAATTATATATAATAAAAATAAAAAA
44837019 TTAATTATATA-AATAAAAATAAAAAA
1 TTAATTATATATAATAAAAATAAAAAA
44837045 T
1 T
44837046 AAAAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
TTAATTATATATAATAAAAATAAAAAA
Found at i:44837994 original size:17 final size:19
Alignment explanation
Indices: 44837967--44838004 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
44837957 AATACAAATT
44837967 AACCCTCAGCCC-AAACTA
1 AACCCTCAGCCCAAAACTA
44837985 AACCCT-AGCCCAAAACTA
1 AACCCTCAGCCCAAAACTA
44838003 AA
1 AA
44838005 AAAAATTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.45, C:0.39, G:0.05, T:0.11
Consensus pattern (19 bp):
AACCCTCAGCCCAAAACTA
Found at i:44838220 original size:20 final size:21
Alignment explanation
Indices: 44838183--44838230 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
44838173 TGGTAGAGAA
44838183 AAAAATAAACAAAC-AAAAG-C
1 AAAAA-AAACAAACAAAAAGAC
*
44838203 AAAAAAAACAAATGAAAAAGAC
1 AAAAAAAACAAA-CAAAAAGAC
44838225 AAAAAA
1 AAAAAA
44838231 GAATAACGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.29
20 5 0.21
21 5 0.21
22 7 0.29
ACGTcount: A:0.79, C:0.10, G:0.06, T:0.04
Consensus pattern (21 bp):
AAAAAAAACAAACAAAAAGAC
Found at i:44839155 original size:56 final size:55
Alignment explanation
Indices: 44839062--44839170 Score: 164
Period size: 56 Copynumber: 2.0 Consensus size: 55
44839052 CCTTAATGAC
* * * *
44839062 TCTTATTTATTTATAGTTTCAGCCCCTAAATTTTGGTTCGATTCCGGTATCATCAT
1 TCTTATTTATTTACAGTTTCAGCCCCCAAATTCTGGTTCGA-TCCAGTATCATCAT
*
44839118 TCTTATTTATTTACAGTTTCAGCCCCCAGATTCTGGTTCGATCCAGTATCATC
1 TCTTATTTATTTACAGTTTCAGCCCCCAAATTCTGGTTCGATCCAGTATCATC
44839171 CTTAGTTCTT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
55 11 0.23
56 37 0.77
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.43
Consensus pattern (55 bp):
TCTTATTTATTTACAGTTTCAGCCCCCAAATTCTGGTTCGATCCAGTATCATCAT
Found at i:44841427 original size:13 final size:13
Alignment explanation
Indices: 44841409--44841433 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44841399 TAAGTTATAT
44841409 GTGTGAAAATTTC
1 GTGTGAAAATTTC
44841422 GTGTGAAAATTT
1 GTGTGAAAATTT
44841434 GATAGTTTGA
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Done.