Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 140 of 410
Found at i:42425608 original size:40 final size:40
Alignment explanation
Indices: 42425553--42425633 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
42425543 TTTTTATGCT
42425553 TAGTAAGTCTCAAGGAATAAAATCAGCTTTAATTAAAGCA
1 TAGTAAGTCTCAAGGAATAAAATCAGCTTTAATTAAAGCA
42425593 TAGTAAGTCTCAAGGAATAAAATCAGCTTTAATTAAAGCA
1 TAGTAAGTCTCAAGGAATAAAATCAGCTTTAATTAAAGCA
42425633 T
1 T
42425634 TACATTCACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.28
Consensus pattern (40 bp):
TAGTAAGTCTCAAGGAATAAAATCAGCTTTAATTAAAGCA
Found at i:42426051 original size:40 final size:40
Alignment explanation
Indices: 42426001--42426107 Score: 133
Period size: 40 Copynumber: 2.7 Consensus size: 40
42425991 TATCACGATT
** *
42426001 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
* * *
42426041 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAGCCACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
* * *
42426081 GCACCATTGCCTTCGGGTCTTAACCCG
1 GCACAAATGCCTTCGGGTCTTAGCCCG
42426108 ATTATAATTT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
Found at i:42433979 original size:50 final size:48
Alignment explanation
Indices: 42433861--42433987 Score: 139
Period size: 50 Copynumber: 2.6 Consensus size: 48
42433851 TATAATGCTG
* *
42433861 ATGCCATGTCCCAAACATGGTCTTACACT-GGCTTATACGTCAAGTCG
1 ATGCCATGTCCCAAACATGGTCTTACACTAGGCTTATACATCAAGTCA
* * * * **
42433908 ACGCCATGTCCCAGACATGGTCTTACACTAGCTCTTATATATCCGTGTCA
1 ATGCCATGTCCCAAACATGGTCTTACACTAG-GCTTATACAT-CAAGTCA
* *
42433958 ATGCCATGTTCCAAACATGGTCTTCCACTA
1 ATGCCATGTCCCAAACATGGTCTTACACTA
42433988 ACACCTCTAT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
47 27 0.42
48 1 0.02
49 7 0.11
50 30 0.46
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (48 bp):
ATGCCATGTCCCAAACATGGTCTTACACTAGGCTTATACATCAAGTCA
Found at i:42434027 original size:48 final size:47
Alignment explanation
Indices: 42433860--42434077 Score: 173
Period size: 48 Copynumber: 4.6 Consensus size: 47
42433850 GTATAATGCT
* **
42433860 GATGCCATGTCCCAAACATGGTCTTACACT--GGC-TTATACGTCAAGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAACACATTATACGT---GTC
* * * *
42433907 GACGCCATGTCCCAGACATGGTCTTACACTAGCTCTTATATATCCGTGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAACAC--AT-TATACGTGTC
* * * * *
42433957 AATGCCATGTTCCAAACATGGTCTTCCACTAACACCTCTATACGTGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAACACAT-TATACGTGTC
* * *
42434005 GATGCAATGTCCCAGACATGGTCTTTCACTGACACATT-T-CGTAGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAACACATTATACGT-GTC
42434051 GAT--CATGTCCCAGACAT-GTCTTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
42434078 GGCTTACATC
Statistics
Matches: 140, Mismatches: 24, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
43 9 0.06
44 13 0.09
45 3 0.02
46 7 0.05
47 29 0.21
48 40 0.29
49 1 0.01
50 31 0.22
52 1 0.01
53 6 0.04
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (47 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAACACATTATACGTGTC
Found at i:42434112 original size:46 final size:45
Alignment explanation
Indices: 42434055--42434220 Score: 151
Period size: 46 Copynumber: 3.6 Consensus size: 45
42434045 GTAGTCGATC
*
42434055 ATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCTGATGT
1 ATGTCCCAGACATGTCTTACACTGGCTTACATCTC-AGGCCGATGT
* * *
42434101 ATGTCCCAGACATGTCTTACACTAGC-TATCGA-CTCAATGCCAAT-T
1 ATGTCCCAGACATGTCTTACACTGGCTTA-C-ATCTC-AGGCCGATGT
** * *
42434146 CCATGTCCCAGACATGGTCTTACACTGGCTCCCATAAT-ATGGCCGATGC
1 --ATGTCCCAGACAT-GTCTTACACTGGCTTACAT-CTCA-GGCCGATGT
42434195 ATGTCCCAGACATGTCTTACACTGGC
1 ATGTCCCAGACATGTCTTACACTGGC
42434221 ACACAAATAA
Statistics
Matches: 98, Mismatches: 12, Indels: 20
0.75 0.09 0.15
Matches are distributed among these distances:
45 3 0.03
46 47 0.48
47 29 0.30
48 18 0.18
49 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.28
Consensus pattern (45 bp):
ATGTCCCAGACATGTCTTACACTGGCTTACATCTCAGGCCGATGT
Found at i:42438668 original size:40 final size:40
Alignment explanation
Indices: 42438608--42438828 Score: 247
Period size: 40 Copynumber: 5.5 Consensus size: 40
42438598 TATTCGAATG
*
42438608 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
* * *
42438648 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-TT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-TGACT
* *
42438688 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
*
42438728 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
* * * * *
42438768 ATATTCAGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-TGACT
42438808 ATATCC-GGCTAA-ATCCTGAAG
1 ATATCCGGGCTAAGATCC-GAAG
42438829 ATACTTGGGT
Statistics
Matches: 154, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
38 3 0.02
39 11 0.07
40 135 0.88
41 5 0.03
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
Found at i:42439096 original size:22 final size:22
Alignment explanation
Indices: 42439056--42439097 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
42439046 GAATGTGCAT
*
42439056 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
42439078 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
42439098 TCGAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Found at i:42446824 original size:40 final size:41
Alignment explanation
Indices: 42446764--42446984 Score: 282
Period size: 40 Copynumber: 5.6 Consensus size: 41
42446754 TATTCGAATG
42446764 ATATCCGGGCTAAG-TCCCGAAGGC-TATTGTGCTAGTGACT
1 ATATCCGGGCTAAGATCCCGAAGGCAT-TTGTGCTAGTGACT
* *
42446804 ATATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCCGAAGGCATTTGTGCTAG-TGACT
* *
42446844 ATATCCGGGCTAAGA-CCCGAAGGTATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCCGAAGGCATTTGTGCTAGTGACT
*
42446884 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGATCCCGAAGGCATTTGTGCTAGTGACT
* *
42446924 ATATCCGGGCTAAGA-CCCGAAGGCATTTGTGCGAGTTG-TT
1 ATATCCGGGCTAAGATCCCGAAGGCATTTGTGCTAG-TGACT
42446964 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGATCCCGAAG
42446985 ATACTTGGGT
Statistics
Matches: 160, Mismatches: 12, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
38 1 0.01
39 14 0.09
40 139 0.87
41 6 0.04
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (41 bp):
ATATCCGGGCTAAGATCCCGAAGGCATTTGTGCTAGTGACT
Found at i:42447252 original size:22 final size:22
Alignment explanation
Indices: 42447212--42447253 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
42447202 GAATGTGCAT
*
42447212 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
42447234 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
42447254 TCGAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Found at i:42451663 original size:16 final size:16
Alignment explanation
Indices: 42451622--42451664 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
42451612 GTAGCCAAAC
*
42451622 TTTCGGCTTTTTGGCA
1 TTTCGGCTTTTCGGCA
***
42451638 TTTTAACTTTTCGGCA
1 TTTCGGCTTTTCGGCA
42451654 TTTCGGCTTTT
1 TTTCGGCTTTT
42451665 GCCGATCTAC
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (16 bp):
TTTCGGCTTTTCGGCA
Found at i:42470955 original size:40 final size:40
Alignment explanation
Indices: 42470842--42470941 Score: 123
Period size: 40 Copynumber: 2.5 Consensus size: 40
42470832 GGATATAACG
* * * *
42470842 ACTCGCTCAAATGCCTTCGGGAC-AAAGCCCGG-TTATAGTA
1 ACTCGCACGAATGCCTTCGGGACTTAA-CCCGGATT-TATTA
42470882 ACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTATTA
1 ACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTATTA
*
42470922 ACTCGCACGAATGGCTTCGG
1 ACTCGCACGAATGCCTTCGG
42470942 ATCTTAGTCC
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
40 49 0.92
41 4 0.08
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
ACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTATTA
Found at i:42471689 original size:2 final size:2
Alignment explanation
Indices: 42471682--42471707 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42471672 ATGTGCAAAC
42471682 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
42471708 GCTAGAGCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42479804 original size:40 final size:40
Alignment explanation
Indices: 42479751--42479850 Score: 114
Period size: 40 Copynumber: 2.5 Consensus size: 40
42479741 GGATATAACG
* *
42479751 ACTCGCTCAAATGCCTTCGGGAC-AAAGCCCGG-TTATAGTA
1 ACTCGCACGAATGCCTTCGGGACTAAA-CCCGGATT-TAGTA
* * *
42479791 ACTCGCACGAATGCCTTCGTGACTTAACCCGGATTTATTA
1 ACTCGCACGAATGCCTTCGGGACTAAACCCGGATTTAGTA
*
42479831 ACTCGCACGAATGGCTTCGG
1 ACTCGCACGAATGCCTTCGG
42479851 ATCTTAGTCC
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
40 47 0.92
41 4 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
ACTCGCACGAATGCCTTCGGGACTAAACCCGGATTTAGTA
Found at i:42482066 original size:40 final size:39
Alignment explanation
Indices: 42481898--42482068 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
42481888 AGAAATTGAA
* *
42481898 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
42481938 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
42481978 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
42482018 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
42482058 TGATATCCGGG
1 TGATATCCGGG
42482069 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:42489979 original size:40 final size:39
Alignment explanation
Indices: 42489810--42489991 Score: 161
Period size: 40 Copynumber: 4.5 Consensus size: 39
42489800 AGAAATTGAA
* * *
42489810 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
42489851 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
* *
42489890 -GCTATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 TG--ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
42489931 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
42489971 TGATATCCGGGTTAAGTCCCG
1 TGATATCCGGGCTAAGACCCG
42489992 TTAGGCCTTG
Statistics
Matches: 113, Mismatches: 22, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
38 4 0.04
39 3 0.03
40 82 0.73
41 24 0.21
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:42496908 original size:40 final size:40
Alignment explanation
Indices: 42496821--42496970 Score: 123
Period size: 40 Copynumber: 3.8 Consensus size: 40
42496811 AATTGAATGA
* * * **
42496821 TATCCGGGCTAAGCCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC-GAGTCA-TAC
* * *
42496861 TAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGT--CATAC
*
42496902 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTCATAC
*
42496941 TATCCGGGCTAAGA-CCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
42496971 AAATCGTGAT
Statistics
Matches: 89, Mismatches: 13, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
38 1 0.01
39 17 0.19
40 71 0.80
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTCATAC
Found at i:42496984 original size:39 final size:40
Alignment explanation
Indices: 42496902--42497002 Score: 114
Period size: 39 Copynumber: 2.5 Consensus size: 40
42496892 TAGTGGCTAC
* * **
42496902 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTCT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAATCATGAT
* *
42496942 ATCCGGGCTAAGA-CCGAAGGCATTTGTGCAAATCGTGAT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAATCATGAT
* * *
42496981 ATCCGGGTTAAGTCCCGTAGGC
1 ATCCGGGCTAAGACCCGAAGGC
42497003 CTTGGTGCGG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
39 31 0.61
40 20 0.39
ACGTcount: A:0.24, C:0.25, G:0.29, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAATCATGAT
Found at i:42510020 original size:40 final size:39
Alignment explanation
Indices: 42509855--42510038 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
42509845 AAATTGAATG
* * *
42509855 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
42509895 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
42509935 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
42509975 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
42510014 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
42510039 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:42510063 original size:80 final size:81
Alignment explanation
Indices: 42509895--42510083 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
42509885 GCTGGAAATT
* * * *
42509895 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
42509960 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
42509976 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
42510039 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
42510055 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
42510084 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:42517839 original size:40 final size:39
Alignment explanation
Indices: 42517751--42517934 Score: 140
Period size: 40 Copynumber: 4.6 Consensus size: 39
42517741 AAATTGAATG
* * * *
42517751 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGCAA-T-TG-TGCAAGTCGT
* * * *
42517791 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTCG-T
* *
42517831 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTC-GT
* * *
42517871 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTCGT
* * *
42517910 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
42517935 CTTGGTGCGG
Statistics
Matches: 116, Mismatches: 21, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
37 4 0.03
38 2 0.02
39 5 0.04
40 103 0.89
41 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTCGT
Found at i:42517959 original size:80 final size:81
Alignment explanation
Indices: 42517791--42517979 Score: 195
Period size: 80 Copynumber: 2.4 Consensus size: 81
42517781 GCTGGAAATT
* * * *
42517791 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTATATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTATATCCGGGCTAAGACCCGAAGGCA
*
42517856 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * *
42517872 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ATATCCGGGCTAAGACCCGAAGGC
* * * *
42517935 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
42517951 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
42517980 ATCGAGTAGC
Statistics
Matches: 87, Mismatches: 19, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
79 2 0.02
80 85 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTATATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:42524289 original size:20 final size:20
Alignment explanation
Indices: 42524229--42524289 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
42524219 ATAAATATGG
*
42524229 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
42524249 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
42524269 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
42524289 T
1 T
42524290 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:42524366 original size:24 final size:24
Alignment explanation
Indices: 42524339--42524481 Score: 200
Period size: 24 Copynumber: 6.0 Consensus size: 24
42524329 GAGGAAGTGA
42524339 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
42524363 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
42524387 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
42524410 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * * *
42524434 GAAAGGGCTTTTGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
42524458 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
42524482 ATGATAAAGC
Statistics
Matches: 109, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
23 23 0.21
24 76 0.70
25 10 0.09
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:42524432 original size:47 final size:47
Alignment explanation
Indices: 42524339--42524481 Score: 198
Period size: 47 Copynumber: 3.0 Consensus size: 47
42524329 GAGGAAGTGA
42524339 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
42524387 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * * *
42524434 GAAAGGGCTTTTGCCCTAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
42524482 ATGATAAAGC
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
47 42 0.48
48 34 0.39
49 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:42524455 original size:71 final size:72
Alignment explanation
Indices: 42524339--42524482 Score: 211
Period size: 71 Copynumber: 2.0 Consensus size: 72
42524329 GAGGAAGTGA
*
42524339 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
42524402 CCAGTTAT
65 CCAGTTAT
** * * *
42524410 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCTAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
42524475 CAGTTAT
66 CAGTTAT
42524482 A
1 A
42524483 TGATAAAGCA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
71 53 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:42524708 original size:31 final size:31
Alignment explanation
Indices: 42524673--42524736 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
42524663 CGTTTACAGT
42524673 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
42524704 AAAGGCTTCGGCCCAGTGTTATGGAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
42524735 AA
1 AA
42524737 CATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:42526173 original size:56 final size:56
Alignment explanation
Indices: 42526101--42526211 Score: 147
Period size: 56 Copynumber: 2.0 Consensus size: 56
42526091 TCTTACATGT
*
42526101 AATCACATATCAATGCC-ACTGTCCTAGACA-G-GGTCTTACTCGTACACATATATCGG
1 AATCACATATCAATGCCAAC-GT-ATAGA-ATGTGGTCTTACTCGTACACATATATCGG
* *
42526157 AATCACATATCGATGCCAACGTATATAATGTGGTCTTACTCGTACACATATATCG
1 AATCACATATCAATGCCAACGTATAGAATGTGGTCTTACTCGTACACATATATCG
42526212 ATGCCATGGC
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
54 1 0.02
55 4 0.08
56 42 0.86
57 2 0.04
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (56 bp):
AATCACATATCAATGCCAACGTATAGAATGTGGTCTTACTCGTACACATATATCGG
Found at i:42529698 original size:36 final size:36
Alignment explanation
Indices: 42529651--42529723 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
42529641 TAAGTGTCCG
42529651 ATATCGAGATAGCTTTGGTTTATTAAAATGGCACTA
1 ATATCGAGATAGCTTTGGTTTATTAAAATGGCACTA
42529687 ATATCGAGATAGCTTTGGTTTATTAAAATGGCACTA
1 ATATCGAGATAGCTTTGGTTTATTAAAATGGCACTA
42529723 A
1 A
42529724 GTGTGCGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (36 bp):
ATATCGAGATAGCTTTGGTTTATTAAAATGGCACTA
Found at i:42534325 original size:20 final size:19
Alignment explanation
Indices: 42534306--42534356 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
42534296 TAAGAAGCAC
42534306 CAAATTGCAAACAAGGGCA
1 CAAATTGCAAACAAGGGCA
* *
42534325 CAAATGTGCGAACAGGGGCA
1 CAAAT-TGCAAACAAGGGCA
*
42534345 TCAAAATGCAAA
1 -CAAATTGCAAA
42534357 TAGGGACACC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 5 0.19
20 17 0.65
21 4 0.15
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.12
Consensus pattern (19 bp):
CAAATTGCAAACAAGGGCA
Found at i:42541484 original size:40 final size:40
Alignment explanation
Indices: 42541417--42541584 Score: 151
Period size: 40 Copynumber: 4.2 Consensus size: 40
42541407 AAATTGAATG
* * * * *
42541417 ATATCCGGGCTAAGCCCCAAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
42541457 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
42541497 ATATTCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
42541537 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
42541577 ATATCCGG
1 ATATCCGG
42541585 TTATATTCCG
Statistics
Matches: 102, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
39 3 0.03
40 97 0.95
41 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:42549103 original size:40 final size:39
Alignment explanation
Indices: 42549046--42549230 Score: 180
Period size: 40 Copynumber: 4.7 Consensus size: 39
42549036 TCGAATGATG
* *
42549046 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGACTAAGTCCCGAAGGCATTTGTGC-AAGT-ACTAAA
*
42549086 TCCGGACTAAGAT-CCGAAGGCATTTGTCCAAGTTACTAAA
1 TCCGGACTAAG-TCCCGAAGGCATTTGTGCAAG-TACTAAA
*
42549126 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTACTAAA
1 TCCGGACTAAG-TCCCGAAGGCATTTGTGCAAGTACTAAA
** **
42549165 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGCTACTATAA
1 TCCGGACTAAGTCCCGAAGGCATTTGTGCAAG-TACTA-AA
* * *
42549206 -CCGGGCTATGTCCCGAAGGTATTTG
1 TCCGGACTAAGTCCCGAAGGCATTTG
42549231 AACGAGTAGC
Statistics
Matches: 128, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
38 1 0.01
39 34 0.27
40 83 0.65
41 10 0.08
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (39 bp):
TCCGGACTAAGTCCCGAAGGCATTTGTGCAAGTACTAAA
Found at i:42549202 original size:79 final size:80
Alignment explanation
Indices: 42549046--42549263 Score: 216
Period size: 79 Copynumber: 2.7 Consensus size: 80
42549036 TCGAATGATG
* **
42549046 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGT-ACTATATCCGGGTTAAGATCCGAAGGCATT
*
42549110 TGTCCAAGTTACTA-AA
64 TGTCCAAGCTACTATAA
* *
42549126 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTACTATATCCGGGTTAAGAT-CCGAAGGCATT
***
42549189 TGTGTGAGCTACTATAA
64 TGTCCAAGCTACTATAA
* * **
42549206 -CCGGGCTATGTCCCGAAGGTATTTGAACGAGTAGCTATATCC-GGTTAA-ACTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTA-CTATATCCGGGTTAAGA-TCCGAAGG
42549264 TACGTGATTC
Statistics
Matches: 115, Mismatches: 15, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
78 2 0.02
79 74 0.64
80 31 0.27
81 8 0.07
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATATCCGGGTTAAGATCCGAAGGCATTTG
TCCAAGCTACTATAA
Found at i:42558613 original size:34 final size:33
Alignment explanation
Indices: 42558555--42558648 Score: 89
Period size: 34 Copynumber: 2.8 Consensus size: 33
42558545 ATGCATTTTG
*
42558555 GATACTGTACTGAAATGGGCTAAGGCACACATT
1 GATACTGTACTGAAATGGGCTAAGGCACACACT
* * * *
42558588 GATACTGTTACTGTATTGGGTTAAGGCCCACACT
1 GATACTG-TACTGAAATGGGCTAAGGCACACACT
* * * *
42558622 GATATTGCGACTGATATGGGCTTAGGC
1 GATACTG-TACTGAAATGGGCTAAGGC
42558649 CCAGACTGTT
Statistics
Matches: 47, Mismatches: 13, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
33 7 0.15
34 40 0.85
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (33 bp):
GATACTGTACTGAAATGGGCTAAGGCACACACT
Found at i:42559638 original size:55 final size:55
Alignment explanation
Indices: 42559577--42559707 Score: 172
Period size: 55 Copynumber: 2.4 Consensus size: 55
42559567 TCCATGCCTT
* *
42559577 TGCCCGTGTGCAACATTGACTTCAACACACAGCCATGGCACACGCCCGTGTGACC
1 TGCCCGTGTACAACACTGACTTCAACACACAGCCATGGCACACGCCCGTGTGACC
* * * * *
42559632 TGCCCGTGTACGATACTGACTTTAAGACACAGCCATGGCACACGCCCGTGTGGCC
1 TGCCCGTGTACAACACTGACTTCAACACACAGCCATGGCACACGCCCGTGTGACC
* * *
42559687 TACCCATGTTCAACACTGACT
1 TGCCCGTGTACAACACTGACT
42559708 AAAAAGTTTA
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 64 1.00
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (55 bp):
TGCCCGTGTACAACACTGACTTCAACACACAGCCATGGCACACGCCCGTGTGACC
Found at i:42560627 original size:44 final size:46
Alignment explanation
Indices: 42560573--42560737 Score: 176
Period size: 46 Copynumber: 3.6 Consensus size: 46
42560563 TACATGTGCT
* *
42560573 GATGCATGTCCCAAACATGTCTTACACTAGCACAAC-TCTTA-GCT
1 GATGCATGTCCCAAACATGTCTTACACTAGCACATCATCTTACGCC
* * * * *
42560617 GATGCGTGTCCCAGACACGTCTTACACTAGCTATCATCATC-GAGGCC
1 GATGCATGTCCCAAACATGTCTTACACTAGC-A-CATCATCTTACGCC
* * *
42560664 GATGCATGTCCCAAACATGTCTTATACTGGAAC-TCATCTCTACGCC
1 GATGCATGTCCCAAACATGTCTTACACTAGCACATCATCT-TACGCC
*
42560710 GATGCCTGTCCCAAACATGTCTTACACT
1 GATGCATGTCCCAAACATGTCTTACACT
42560738 GGCGCACAAG
Statistics
Matches: 99, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
44 33 0.33
45 2 0.02
46 35 0.35
47 29 0.29
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (46 bp):
GATGCATGTCCCAAACATGTCTTACACTAGCACATCATCTTACGCC
Found at i:42566144 original size:39 final size:39
Alignment explanation
Indices: 42566097--42566279 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
42566087 AATGTTCGAG
42566097 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
42566136 TGATATCCGGGCTAAGCCCGAAGGCAATTGGGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
42566175 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* ** *
42566214 TGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
42566254 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
42566280 GTTTGAACGA
Statistics
Matches: 126, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 88 0.70
40 38 0.30
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:42573575 original size:39 final size:39
Alignment explanation
Indices: 42573528--42573710 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
42573518 AATGTTCGAG
42573528 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
42573567 TGATATCCGGGCTAAGCCCGAAGGCAATTGGGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
42573606 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* ** *
42573645 TGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
42573685 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
42573711 GTTTGAACGA
Statistics
Matches: 126, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 88 0.70
40 38 0.30
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:42575904 original size:49 final size:49
Alignment explanation
Indices: 42575665--42575909 Score: 224
Period size: 49 Copynumber: 4.9 Consensus size: 49
42575655 TCTATTGTGA
* * * * *
42575665 GGTCGCATGTGTAGTACTAAGTGTAGGCTACTATGCGTACCCA-AAAACTGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCAGATAA-T-T
* * * ** ** *
42575716 GATCACGTGTGTAGGACTAAGTGCAGGCTACTACGTGTATTAGATGGTGA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAAT-T
* * *
42575766 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGACT-GTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TAATT
** *
42575815 GGTTGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * *
42575864 GGTCACATGTGTAGTACTATGTGCAGGCTATTATGCGTACCAGATA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
42575910 GCTTTGGCTA
Statistics
Matches: 161, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
48 1 0.01
49 80 0.50
50 46 0.29
51 34 0.21
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.29
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:42580804 original size:49 final size:50
Alignment explanation
Indices: 42580749--42580994 Score: 300
Period size: 49 Copynumber: 4.9 Consensus size: 50
42580739 ATCTATTGTG
* * *
42580749 AGGTCACATGCGTAGTACTAAGTGCAGGCTACTATGTGTACTAGATTATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
* *
42580799 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAA-TT
* * * * * **
42580849 CA-ATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGCATCAGATGGTT
1 -AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
** *
42580899 AGGTCATGTGTGTAGTACTAAGTGCAGGCTACTATGTATACCAGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
* *
42580949 A-GTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATA
42580995 GCTTTGGCTA
Statistics
Matches: 165, Mismatches: 27, Indels: 9
0.82 0.13 0.04
Matches are distributed among these distances:
49 83 0.50
50 45 0.27
51 37 0.22
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
Found at i:42580934 original size:101 final size:98
Alignment explanation
Indices: 42580752--42580981 Score: 300
Period size: 101 Copynumber: 2.3 Consensus size: 98
42580742 TATTGTGAGG
* * * *
42580752 TCACATGCGTAGTACTAAGTGCAGGCTACTATGTGTACTAGATTATTGGTCACATGTGTAGTACT
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGCACTAGATGATTGGTCACATGTGTAGTACT
* *
42580817 AAGTGCAGGCTACTATGCGTACCCGATAACTTCAA
66 AAGTGCAGGCTACTATGCATACCAGATAA-TT-AA
* * **
42580852 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGCA-TCAGATGGTTAGGTCATGTGTGTAGTA
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGCACT-AGATGATT-GGTCACATGTGTAGTA
* *
42580916 CTAAGTGCAGGCTACTATGTATACCAGATAATTAG
64 CTAAGTGCAGGCTACTATGCATACCAGATAATTAA
*
42580951 TCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 TCACATGTGTAGTACTAAGTGCAGGCTACTA
42580982 TGCGTACCAG
Statistics
Matches: 114, Mismatches: 14, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
99 31 0.27
100 41 0.36
101 42 0.37
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (98 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGCACTAGATGATTGGTCACATGTGTAGTACT
AAGTGCAGGCTACTATGCATACCAGATAATTAA
Found at i:42589867 original size:27 final size:27
Alignment explanation
Indices: 42589837--42589899 Score: 90
Period size: 28 Copynumber: 2.3 Consensus size: 27
42589827 TTTAAAACTC
*
42589837 TAGGGGTATATCGGTAATTTTGCTCTT
1 TAGGGGTATATCAGTAATTTTGCTCTT
* *
42589864 TAGGGGTAATTTTAGTAATTTTGCTCTT
1 TAGGGGT-ATATCAGTAATTTTGCTCTT
42589892 TAGGGGTA
1 TAGGGGTA
42589900 ATTTCGTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 8 0.25
28 24 0.75
ACGTcount: A:0.21, C:0.08, G:0.27, T:0.44
Consensus pattern (27 bp):
TAGGGGTATATCAGTAATTTTGCTCTT
Found at i:42589885 original size:28 final size:28
Alignment explanation
Indices: 42589850--42589903 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
42589840 GGGTATATCG
42589850 GTAATTTTGCTCTTTAGGGGTAATTTTA
1 GTAATTTTGCTCTTTAGGGGTAATTTTA
42589878 GTAATTTTGCTCTTTAGGGGTAATTT
1 GTAATTTTGCTCTTTAGGGGTAATTT
42589904 CGTGATCTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.20, C:0.07, G:0.22, T:0.50
Consensus pattern (28 bp):
GTAATTTTGCTCTTTAGGGGTAATTTTA
Found at i:42592277 original size:86 final size:86
Alignment explanation
Indices: 42592132--42592307 Score: 343
Period size: 86 Copynumber: 2.0 Consensus size: 86
42592122 GTAATTATTT
*
42592132 CAAACAAGTTGGTTAATAATAAAAAATTCATGAATTTCATTAATATACTTTGTATAATTTTCCTC
1 CAAACAAGTTGGTTAATAAAAAAAAATTCATGAATTTCATTAATATACTTTGTATAATTTTCCTC
42592197 ATATGGTTCTTTCACACAAAG
66 ATATGGTTCTTTCACACAAAG
42592218 CAAACAAGTTGGTTAATAAAAAAAAATTCATGAATTTCATTAATATACTTTGTATAATTTTCCTC
1 CAAACAAGTTGGTTAATAAAAAAAAATTCATGAATTTCATTAATATACTTTGTATAATTTTCCTC
42592283 ATATGGTTCTTTCACACAAAG
66 ATATGGTTCTTTCACACAAAG
42592304 CAAA
1 CAAA
42592308 ATAAAAGAAA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 89 1.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (86 bp):
CAAACAAGTTGGTTAATAAAAAAAAATTCATGAATTTCATTAATATACTTTGTATAATTTTCCTC
ATATGGTTCTTTCACACAAAG
Found at i:42593407 original size:58 final size:58
Alignment explanation
Indices: 42593288--42593404 Score: 141
Period size: 57 Copynumber: 2.0 Consensus size: 58
42593278 AAATGGTAAG
* * * * * *
42593288 AATGGAGAAATGGGTAATATTTGGAAATGATTAGGGTTTTCTTCAAAATGAAAATGAA
1 AATGGAGAAATGGGTAATATTTGAAAATGAATAGGGTTTTATCCAAAATAAAAATAAA
42593346 AATGGAGAAAT-GG-AATCATTTGAAAATGAAT-GTGGTTTTATCCAAAATAAAAATAAA
1 AATGGAGAAATGGGTAAT-ATTTGAAAATGAATAG-GGTTTTATCCAAAATAAAAATAAA
42593403 AA
1 AA
42593405 ATGAAAATGA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
56 4 0.08
57 36 0.71
58 11 0.22
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.29
Consensus pattern (58 bp):
AATGGAGAAATGGGTAATATTTGAAAATGAATAGGGTTTTATCCAAAATAAAAATAAA
Found at i:42596817 original size:48 final size:48
Alignment explanation
Indices: 42596692--42597062 Score: 189
Period size: 48 Copynumber: 7.7 Consensus size: 48
42596682 TGATATGTGC
*
42596692 GCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCACAATA-TG-A-GA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-G--ACAATATTGTAGGA
* * *
42596740 GCCAGTTTGTAAGACCATGTTTGGAACATGGCATCGACAATATTGTAGGA
1 GCTAG--TGTAAGACCATGTCTGGGACATGGCATCGACAATATTGTAGGA
* * ** * * *
42596790 GCTAGTGTAAGACCATGCCTGGGACATGGCATCGGCGTTGTTAT-GTGT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGACAATATTGTAG-GA
* * * * *
42596838 GCTAGTGTAAGACCATGTCTGGGATATGGCGTCG---GTGTCGTCATGTGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGACAATATTGT-A-G-GA
* * * *
42596886 GCCAATGTAAGACCATGTCTGGGACATGGCATCGGC---ATTGAGACGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGACAATATTG-TA-G-GA
* * * * *
42596934 GCTAGTTTAAGACAATGTCTGGGACATGGCATCAGCCTCGACA-TGT--GA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-G--ACAATATTGTAGGA
* * * * * *
42596982 GCTAGTGTAAAACCATGTCTGGGACATGGCATTGGC-CTCGACATGT--TA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGACAAT--A-TTGTAGGA
42597030 GCTAGTGTAAGACCATGTCTGGGACATGGCATC
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC
42597063 AGCAATTCAC
Statistics
Matches: 255, Mismatches: 46, Indels: 44
0.74 0.13 0.13
Matches are distributed among these distances:
45 5 0.02
46 1 0.00
47 8 0.03
48 203 0.80
49 3 0.01
50 31 0.12
51 1 0.00
53 2 0.01
54 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (48 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGACAATATTGTAGGA
Found at i:42596908 original size:96 final size:96
Alignment explanation
Indices: 42596795--42597065 Score: 328
Period size: 96 Copynumber: 2.8 Consensus size: 96
42596785 TAGGAGCTAG
* * **
42596795 TGTAAGACCATGCCTGGGACATGGCATCGGCGTTGTTATGTGTGCTAGTGTAAGACCATGTCTGG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCATTGACATGTGTGCTAGTGTAAGACCATGTCTGG
* * * ** *
42596860 GATATGGCGTCGGTGTCGTCATGTGAGCCAA
66 GACATGGCATCAGCCTCGACATGTGAGCCAA
* * * * * *
42596891 TGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGAGCTAGTTTAAGACAATGTCTGG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCATTGACATGTGTGCTAGTGTAAGACCATGTCTGG
* *
42596956 GACATGGCATCAGCCTCGACATGTGAGCTAG
66 GACATGGCATCAGCCTCGACATGTGAGCCAA
* * * *
42596987 TGTAAAACCATGTCTGGGACATGGCATTGGCCTCGACATGT-TAGCTAGTGTAAGACCATGTCTG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCATTGACATGTGT-GCTAGTGTAAGACCATGTCTG
42597051 GGACATGGCATCAGC
65 GGACATGGCATCAGC
42597066 AATTCACCCT
Statistics
Matches: 147, Mismatches: 27, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
96 147 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (96 bp):
TGTAAGACCATGTCTGGGACATGGCATCGGCATTGACATGTGTGCTAGTGTAAGACCATGTCTGG
GACATGGCATCAGCCTCGACATGTGAGCCAA
Found at i:42596959 original size:144 final size:142
Alignment explanation
Indices: 42596683--42597062 Score: 422
Period size: 144 Copynumber: 2.6 Consensus size: 142
42596673 ACATTTTGGT
* * * * *
42596683 GATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCACAAT-ATGAGAGCCAGTT
1 GATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTC-GTCATGTGAGCCA--A
* * * *
42596747 TGTAAGACCATGTTTGGAACATGGCATCGACAATATTGTAGGAGCTAGTGTAAGACCATGCCTGG
63 TGTAAGACCATGTCTGGGACATGGCATCGAC-A-ATTGGAGGAGCTAGTGTAAGACAATGCCTGG
* * *
42596812 GACATGGCATCGGCGTT
126 GACATGGCATCAGCCTC
* * * **
42596829 GTTATGTGTGCTAGTGTAAGACCATGTCTGGGATATGGCGTCGGTGTCGTCATGTGAGCCAATGT
1 GATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGTCATGTGAGCCAATGT
* * *
42596894 AAGACCATGTCTGGGACATGGCATCGGC-ATTGAGACGAGAGCTAGTTTAAGACAATGTCTGGGA
66 AAGACCATGTCTGGGACATGGCATCGACAATTG-GA-G-GAGCTAGTGTAAGACAATGCCTGGGA
42596958 CATGGCATCAGCCTC
128 CATGGCATCAGCCTC
* * * * * * * *
42596973 GACATGTGAGCTAGTGTAAAACCATGTCTGGGACATGGCATTGGCCTCGACATGTTAGCTAGTGT
1 GATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGTCATGTGAGCCAATGT
42597038 AAGACCATGTCTGGGACATGGCATC
66 AAGACCATGTCTGGGACATGGCATC
42597063 AGCAATTCAC
Statistics
Matches: 198, Mismatches: 32, Indels: 10
0.82 0.13 0.04
Matches are distributed among these distances:
141 4 0.02
142 1 0.01
143 1 0.01
144 140 0.71
145 1 0.01
146 51 0.26
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (142 bp):
GATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGTCATGTGAGCCAATGT
AAGACCATGTCTGGGACATGGCATCGACAATTGGAGGAGCTAGTGTAAGACAATGCCTGGGACAT
GGCATCAGCCTC
Found at i:42616769 original size:25 final size:24
Alignment explanation
Indices: 42616740--42616828 Score: 63
Period size: 25 Copynumber: 3.6 Consensus size: 24
42616730 CATTTAACAA
42616740 GAAGCTCATGTGAGCCATGTAATGG
1 GAAGCTCATGTGAGCCAT-TAATGG
* ** * * *
42616765 GAAGCTTATCCGGGCTATATAACGG
1 GAAGCTCATGTGAGCCAT-TAATGG
** *
42616790 GAAGCTCATAAGAGCCA-TAATCAG
1 GAAGCTCATGTGAGCCATTAAT-GG
42616814 GAAGCTCATGTGAGC
1 GAAGCTCATGTGAGC
42616829 AAATAACAGG
Statistics
Matches: 47, Mismatches: 16, Indels: 3
0.71 0.24 0.05
Matches are distributed among these distances:
23 3 0.06
24 14 0.30
25 30 0.64
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.21
Consensus pattern (24 bp):
GAAGCTCATGTGAGCCATTAATGG
Found at i:42616820 original size:24 final size:24
Alignment explanation
Indices: 42616789--42616869 Score: 76
Period size: 24 Copynumber: 3.3 Consensus size: 24
42616779 CTATATAACG
42616789 GGAAGCTCATAAGAGCCATAATCA
1 GGAAGCTCATAAGAGCCATAATCA
** *
42616813 GGAAGCTCATGTGAGCAAATAA-CA
1 GGAAGCTCATAAGAGC-CATAATCA
* *
42616837 GGTAGCTC-TGAAGAGCCATTAATTA
1 GGAAGCTCAT-AAGAGCCA-TAATCA
42616862 GGAAGCTC
1 GGAAGCTC
42616870 CAGATAGCCA
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
23 2 0.05
24 30 0.68
25 12 0.27
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.20
Consensus pattern (24 bp):
GGAAGCTCATAAGAGCCATAATCA
Found at i:42648050 original size:13 final size:13
Alignment explanation
Indices: 42648032--42648057 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42648022 GAAAAGAGAA
42648032 ATTCCCCCAAAGT
1 ATTCCCCCAAAGT
42648045 ATTCCCCCAAAGT
1 ATTCCCCCAAAGT
42648058 GCCGAATACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.38, G:0.08, T:0.23
Consensus pattern (13 bp):
ATTCCCCCAAAGT
Found at i:42655751 original size:22 final size:21
Alignment explanation
Indices: 42655720--42655776 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
42655710 TTTATTACAC
* *
42655720 CGACAATAAGCTTGAATAACA
1 CGACACTAAGCTTAAATAACA
*
42655741 TCGACACTAAGCCTAAATAACA
1 -CGACACTAAGCTTAAATAACA
*
42655763 CCAGCACTAAGCTT
1 CGA-CACTAAGCTT
42655777 TCTAGGCACT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 2 0.07
22 27 0.93
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.19
Consensus pattern (21 bp):
CGACACTAAGCTTAAATAACA
Found at i:42655798 original size:38 final size:38
Alignment explanation
Indices: 42655745--42655838 Score: 145
Period size: 38 Copynumber: 2.5 Consensus size: 38
42655735 ATAACATCGA
* *
42655745 CACTAAGCCTAAATAACACCAGCACTAAGCTTTCTAGG
1 CACTAAGCCTAAATAACACCAGCACTAAGCCTGCTAGG
42655783 CACTAAGGCCT-AATAACACCAGCACTAAGCCTGCTAGG
1 CACTAA-GCCTAAATAACACCAGCACTAAGCCTGCTAGG
*
42655821 CACTAAGCCTGAATAACA
1 CACTAAGCCTAAATAACA
42655839 ACTACACTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
37 4 0.08
38 44 0.85
39 4 0.08
ACGTcount: A:0.37, C:0.30, G:0.15, T:0.18
Consensus pattern (38 bp):
CACTAAGCCTAAATAACACCAGCACTAAGCCTGCTAGG
Found at i:42658436 original size:16 final size:16
Alignment explanation
Indices: 42658417--42658448 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42658407 AATTGTTTTA
42658417 TTACAAAATTTCACTT
1 TTACAAAATTTCACTT
*
42658433 TTACATAATTTCACTT
1 TTACAAAATTTCACTT
42658449 ACTCCATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
TTACAAAATTTCACTT
Found at i:42658706 original size:78 final size:78
Alignment explanation
Indices: 42658577--42658733 Score: 296
Period size: 78 Copynumber: 2.0 Consensus size: 78
42658567 AGTAAATTTC
42658577 CCGTTGAACTCATCGGAATAATAACATATACCCGGTGGCTTGTGCATATACCACCCTTGTAATCG
1 CCGTTGAACTCATCGGAATAATAACATATACCCGGTGGCTTGTGCATATACCACCCTTGTAATCG
42658642 AAGCTCTCTAGTA
66 AAGCTCTCTAGTA
* *
42658655 CCGTTGAACTCATCGGAATAATAATATATATCCGGTGGCTTGTGCATATACCACCCTTGTAATCG
1 CCGTTGAACTCATCGGAATAATAACATATACCCGGTGGCTTGTGCATATACCACCCTTGTAATCG
42658720 AAGCTCTCTAGTA
66 AAGCTCTCTAGTA
42658733 C
1 C
42658734 ACATAGTAGC
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (78 bp):
CCGTTGAACTCATCGGAATAATAACATATACCCGGTGGCTTGTGCATATACCACCCTTGTAATCG
AAGCTCTCTAGTA
Found at i:42658762 original size:26 final size:26
Alignment explanation
Indices: 42658731--42658812 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
42658721 AGCTCTCTAG
42658731 TACACATAGTAGCCTGCACTTAGTAC
1 TACACATAGTAGCCTGCACTTAGTAC
* * *
42658757 TACACAT-G-AGACCTATCAATCT-G--G
1 TACACATAGTAG-CCT-GCACT-TAGTAC
*
42658781 TACACGTAGTAGCCTGCACTTAGTAC
1 TACACATAGTAGCCTGCACTTAGTAC
42658807 TACACA
1 TACACA
42658813 CGTGACTTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 16
0.62 0.12 0.25
Matches are distributed among these distances:
23 1 0.03
24 12 0.30
25 8 0.20
26 18 0.45
27 1 0.03
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.26
Consensus pattern (26 bp):
TACACATAGTAGCCTGCACTTAGTAC
Found at i:42658936 original size:101 final size:100
Alignment explanation
Indices: 42658730--42659123 Score: 393
Period size: 101 Copynumber: 3.9 Consensus size: 100
42658720 AAGCTCTCTA
* * * *
42658730 GTACACATAGTAGCCTGCACTTAGTACTACACATGAGACCTATCAATCTGGTACACGTAGTAGCC
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAATCAATCGGGTACACATAGTAGCC
* * * * *
42658795 TGCACTTAGTACTACACACGTGACTTATCCATCTG
66 TACACTTAGTACTACACACGAGACCTATCAATCCG
* * * * *
42658830 ATACACGTAGTAGCCTGCACTTAGTACTACACATGTGATCGAAGTTAA-CGGGTACGCATAGTAG
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-TCAATCGGGTACACATAGTAG
*
42658894 CCTACACTTAGTACTACACATGAGACCTATCAATCCG
64 CCTACACTTAGTACTACACACGAGACCTATCAATCCG
* * * *
42658931 GTACACATAGTAGCCTGCACTTAGTACTACAAATGTGACCTAA-CCATCTGATACACATAGTAGC
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACC-AATCAATCGGGTACACATAGTAGC
* * * * * * *
42658995 TTGCACTTAGTACAACACAC-ATGA-TTGAAACTATCGG
65 CTACACTTAGTACTACACACGA-GACCT--ATCAATCCG
* * * * *
42659032 GTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCTAA-CAATCTGGTACACGTAGTAGC
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACC-AATCAATCGGGTACACATAGTAGC
* *
42659096 CTGCACTTAGTACTACACACGTGACCTA
65 CTACACTTAGTACTACACACGAGACCTA
42659124 AAACTGTTTT
Statistics
Matches: 242, Mismatches: 43, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
99 3 0.01
100 69 0.29
101 166 0.69
102 4 0.02
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.25
Consensus pattern (100 bp):
GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAATCAATCGGGTACACATAGTAGCC
TACACTTAGTACTACACACGAGACCTATCAATCCG
Found at i:42658942 original size:151 final size:151
Alignment explanation
Indices: 42658730--42659124 Score: 619
Period size: 151 Copynumber: 2.6 Consensus size: 151
42658720 AAGCTCTCTA
* *
42658730 GTACACATAGTAGCCTGCACTTAGTACTACACATGAGACCTATCAATCTGGTACACGTAGTAGCC
1 GTACGCATAGTAGCCTACACTTAGTACTACACATGAGACCTATCAATCTGGTACACGTAGTAGCC
* * * *
42658795 TGCACTTAGTACTACACACGTGACTTATCCATCTGATACACGTAGTAGCCTGCACTTAGTACTAC
66 TGCACTTAGTACTACACACGTGACCTAACCATCTGATACACATAGTAGCCTGCACTTAGTACAAC
** **
42658860 ACATGTGATCGAAGTTAACGG
131 ACACATGATCGAAACTAACGG
* *
42658881 GTACGCATAGTAGCCTACACTTAGTACTACACATGAGACCTATCAATCCGGTACACATAGTAGCC
1 GTACGCATAGTAGCCTACACTTAGTACTACACATGAGACCTATCAATCTGGTACACGTAGTAGCC
* * *
42658946 TGCACTTAGTACTACAAATGTGACCTAACCATCTGATACACATAGTAGCTTGCACTTAGTACAAC
66 TGCACTTAGTACTACACACGTGACCTAACCATCTGATACACATAGTAGCCTGCACTTAGTACAAC
* *
42659011 ACACATGATTGAAACTATCGG
131 ACACATGATCGAAACTAACGG
* *
42659032 GTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTAGTAGCC
1 GTACGCATAGTAGCCTACACTTAGTACTACACATGAGACCTATCAATCTGGTACACGTAGTAGCC
42659097 TGCACTTAGTACTACACACGTGACCTAA
66 TGCACTTAGTACTACACACGTGACCTAA
42659125 AACTGTTTTA
Statistics
Matches: 221, Mismatches: 23, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
151 221 1.00
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (151 bp):
GTACGCATAGTAGCCTACACTTAGTACTACACATGAGACCTATCAATCTGGTACACGTAGTAGCC
TGCACTTAGTACTACACACGTGACCTAACCATCTGATACACATAGTAGCCTGCACTTAGTACAAC
ACACATGATCGAAACTAACGG
Found at i:42659124 original size:50 final size:50
Alignment explanation
Indices: 42658730--42659124 Score: 443
Period size: 50 Copynumber: 7.9 Consensus size: 50
42658720 AAGCTCTCTA
* *
42658730 GTACACATAGTAGCCTGCACTTAGTACTACACATGAGACCTATCAATCTG
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTG
* * * * *
42658780 GTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACTTATCCATCTG
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTG
* * * * * *
42658830 ATACACGTAGTAGCCTGCACTTAGTACTACACATGTGATCGAAGTTAA-CGG
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAA--CAATCTG
* * * * *
42658881 GTACGCATAGTAGCCTACACTTAGTACTACACATGAGACCTATCAATCCG
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTG
* *
42658931 GTACACATAGTAGCCTGCACTTAGTACTACAAATGTGACCTAACCATCTG
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTG
* * * ** * * *
42658981 ATACACATAGTAGCTTGCACTTAGTACAACACACATGA-TTGAAACTATCGG
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCT--AACAATCTG
* * *
42659032 GTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCTAACAATCTG
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTG
* *
42659082 GTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
1 GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAA
42659125 AACTGTTTTA
Statistics
Matches: 283, Mismatches: 56, Indels: 12
0.81 0.16 0.03
Matches are distributed among these distances:
49 3 0.01
50 204 0.72
51 74 0.26
52 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (50 bp):
GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAATCTG
Found at i:42666406 original size:48 final size:47
Alignment explanation
Indices: 42666335--42666456 Score: 156
Period size: 48 Copynumber: 2.6 Consensus size: 47
42666325 TGACATTGGG
42666335 TGATATGTGTGCCAGTGTAAGACCATGTCCAGGACATGGCATCAGAGT
1 TGATA-GTGTGCCAGTGTAAGACCATGTCCAGGACATGGCATCAGAGT
* ** * *
42666383 TGATAGGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCGT
1 TGATA-GTGTGCCAGTGTAAGACCATGTCCAGGACATGGCATCAGAGT
* *
42666431 TGACA-TGAGCCAGTGTAAGACCATGT
1 TGATAGTGTGCCAGTGTAAGACCATGT
42666457 TTGGGGCACG
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
46 19 0.29
48 46 0.71
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.25
Consensus pattern (47 bp):
TGATAGTGTGCCAGTGTAAGACCATGTCCAGGACATGGCATCAGAGT
Found at i:42673249 original size:23 final size:23
Alignment explanation
Indices: 42673197--42673310 Score: 63
Period size: 23 Copynumber: 4.8 Consensus size: 23
42673187 GAGCTAATAT
*
42673197 GGTAAGCTC-TATCGAGCAG-AAC
1 GGTAAGCTCATA-CGAGCTGAAAC
* *
42673219 AGCAAGCTCATACGAGCTGAAAC
1 GGTAAGCTCATACGAGCTGAAAC
* * *
42673242 GGTAAGCTCCA-ATGAGTTGAAAAT
1 GGTAAGCT-CATACGAGCTG-AAAC
** *
42673266 AATAAGCTCTTACGAGCTGATATATC
1 GGTAAGCTCATACGAGCTGA-A-A-C
*
42673292 GGCAAGCTCATACGAGCTG
1 GGTAAGCTCATACGAGCTG
42673311 TGGTGAGTCT
Statistics
Matches: 66, Mismatches: 18, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
22 13 0.20
23 19 0.29
24 18 0.27
25 1 0.02
26 15 0.23
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (23 bp):
GGTAAGCTCATACGAGCTGAAAC
Found at i:42674908 original size:13 final size:13
Alignment explanation
Indices: 42674890--42674926 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
42674880 AGTAATCAAA
*
42674890 CACGGGCGTGTGC
1 CACGGGCGTGTAC
42674903 CACGGGCGTGTAC
1 CACGGGCGTGTAC
42674916 CACGGGCGTGT
1 CACGGGCGTGT
42674927 CCCTGCCTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.11, C:0.30, G:0.43, T:0.16
Consensus pattern (13 bp):
CACGGGCGTGTAC
Found at i:42678147 original size:80 final size:80
Alignment explanation
Indices: 42678063--42678211 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
42678053 TATGGTAACC
* * * *
42678063 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
42678127 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
42678143 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
42678208 CCGG
66 CCGG
42678212 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:42678153 original size:40 final size:38
Alignment explanation
Indices: 42678104--42678211 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
42678094 ATCACGATTT
*
42678104 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
42678144 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
42678184 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
42678212 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:42689053 original size:40 final size:39
Alignment explanation
Indices: 42689001--42689107 Score: 137
Period size: 40 Copynumber: 2.7 Consensus size: 39
42688991 GGAAATTATA
* *
42689001 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC-AT
1 CCGGGCTAAGACCCGAAGGC-ATTGTGCGAGT--CATACTAT
*
42689041 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTCTAT
1 CCGGGCTAAGACCCGAAGGCATT-GTGCGAGTCATACTAT
42689081 CCGGGCTAAGACCCGAAGGCATTGTGC
1 CCGGGCTAAGACCCGAAGGCATTGTGC
42689108 ACGTGGTTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
38 1 0.02
39 9 0.15
40 51 0.84
ACGTcount: A:0.23, C:0.26, G:0.30, T:0.21
Consensus pattern (39 bp):
CCGGGCTAAGACCCGAAGGCATTGTGCGAGTCATACTAT
Found at i:42691780 original size:26 final size:27
Alignment explanation
Indices: 42691721--42691786 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 27
42691711 AATTGTACAG
* ***
42691721 CACTAAGTGTGCGAGTTTGATTCTATA
1 CACTAAGTGTGCGAGTCTGAAAATATA
42691748 CACTAAGTGTGCGAG-CTGAAAATATA
1 CACTAAGTGTGCGAGTCTGAAAATATA
42691774 CACTAAGTGTGCG
1 CACTAAGTGTGCG
42691787 GATTCACTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
26 20 0.57
27 15 0.43
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (27 bp):
CACTAAGTGTGCGAGTCTGAAAATATA
Found at i:42694596 original size:40 final size:40
Alignment explanation
Indices: 42694551--42694680 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
42694541 CGGAATACAA
42694551 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* ** *
42694591 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
42694631 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
42694671 CCGGATATAA
1 CCGGATATAA
42694681 TTTCCAGCAT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 3 0.04
40 73 0.96
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:42694695 original size:40 final size:40
Alignment explanation
Indices: 42694551--42694718 Score: 153
Period size: 40 Copynumber: 4.2 Consensus size: 40
42694541 CGGAATACAA
* **
42694551 CCGGATATAACCACGTGCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAATCACCAGCAC-AATTGCCTTCGGGTCTTAGC
* *
42694591 CCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-CAGCAC-AATTGCCTTCGGGTCTTAGC
* ** * *
42694631 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC
** * * *
42694671 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC
42694711 CCGGATAT
1 CCGGATAT
42694719 CATTCAATTT
Statistics
Matches: 104, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 2 0.02
40 102 0.98
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC
Found at i:42702628 original size:39 final size:39
Alignment explanation
Indices: 42702585--42702713 Score: 145
Period size: 39 Copynumber: 3.3 Consensus size: 39
42702575 CGGAATACAA
42702585 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAG
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAG
* ** *
42702624 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAG
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAG
* * *
42702663 CCCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 -CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTT-AG
42702704 CCGGATATAA
1 CCGGATATAA
42702714 TTTCCAGCAT
Statistics
Matches: 74, Mismatches: 12, Indels: 7
0.80 0.13 0.08
Matches are distributed among these distances:
38 1 0.01
39 36 0.49
40 36 0.49
41 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (39 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAG
Found at i:42702691 original size:40 final size:40
Alignment explanation
Indices: 42702601--42702710 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 40
42702591 ATAACCACGT
*
42702601 GCACGAATGCCTTCGGGTCTTAG-CCGGATAGAATGACTC
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
*
42702640 GCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTA-GCCACTA
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATG--ACTA
*
42702680 GCAC-AATTGCCTTCGGGTCTTAACCCGGATA
1 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATA
42702711 TAATTTCCAG
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
38 1 0.02
39 27 0.43
40 35 0.56
ACGTcount: A:0.22, C:0.28, G:0.26, T:0.24
Consensus pattern (40 bp):
GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
Found at i:42702728 original size:40 final size:40
Alignment explanation
Indices: 42702585--42702747 Score: 136
Period size: 40 Copynumber: 4.1 Consensus size: 40
42702575 CGGAATACAA
**
42702585 CCGGATATAACCACGTGCACGAA-TGCCTTCGGGTCTTAG-
1 CCGGATATAACCACCAGCAC-AATTGCCTTCGGGTCTTAGC
* **
42702624 CCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-CAGCAC-AATTGCCTTCGGGTCTTAGC
* * * *
42702664 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAGC
*** * * *
42702704 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAGC
42702744 CCGG
1 CCGG
42702748 GTATCATTCA
Statistics
Matches: 99, Mismatches: 21, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
39 36 0.36
40 63 0.64
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (40 bp):
CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAGC
Found at i:42704955 original size:37 final size:37
Alignment explanation
Indices: 42704896--42705004 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
42704886 AGCTCAGACG
* *
42704896 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
42704933 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
42704970 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
42705005 ATATATTTCC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:42705263 original size:47 final size:47
Alignment explanation
Indices: 42705210--42705403 Score: 289
Period size: 47 Copynumber: 4.1 Consensus size: 47
42705200 TATATATATT
* * * * *
42705210 TCACATTGACCATTCAGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * *
42705257 CCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
42705304 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* **
42705351 TCACATTGGCCATTCGGCCTTATCTCATATATGCACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
42705398 TCACAT
1 TCACAT
42705404 AAAATCCTAA
Statistics
Matches: 133, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 133 1.00
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:42705330 original size:22 final size:22
Alignment explanation
Indices: 42705303--42705374 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
42705293 GCTCACATTC
42705303 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
42705325 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
42705349 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
42705372 ATC
1 ATC
42705375 TCATATATGC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 13 0.35
23 7 0.19
24 7 0.19
25 10 0.27
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:42705404 original size:25 final size:25
Alignment explanation
Indices: 42705325--42705404 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 25
42705315 ATTCGGCCTT
**
42705325 ATCACATATATGCATGTTCACATTC
1 ATCACATATATGCACATTCACATTC
* * *
42705350 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATGCACATTC-ACATTC
*
42705372 ATCTCATATATGCACATTCACATTC
1 ATCACATATATGCACATTCACATTC
42705397 ATCACATA
1 ATCACATA
42705405 AAATCCTAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 10
0.67 0.17 0.17
Matches are distributed among these distances:
22 9 0.22
23 6 0.15
24 6 0.15
25 19 0.47
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.34
Consensus pattern (25 bp):
ATCACATATATGCACATTCACATTC
Found at i:42710158 original size:24 final size:24
Alignment explanation
Indices: 42710129--42710176 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
42710119 AACCTATGAG
*
42710129 TATTTGCACAATTTCAGTCCATAT
1 TATTTGCACAATTTCAATCCATAT
42710153 TATTTGCACAATTTCAATCCATAT
1 TATTTGCACAATTTCAATCCATAT
42710177 AACTATATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (24 bp):
TATTTGCACAATTTCAATCCATAT
Found at i:42718606 original size:22 final size:22
Alignment explanation
Indices: 42718581--42718635 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
42718571 TGCTGCAACT
42718581 GTGGAGTGTAGGGCTGGTACAG
1 GTGGAGTGTAGGGCTGGTACAG
42718603 GTGGAGTGTAGGGCTGGTACAG
1 GTGGAGTGTAGGGCTGGTACAG
42718625 GTGGAGTGTAG
1 GTGGAGTGTAG
42718636 CGGATGGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.18, C:0.07, G:0.51, T:0.24
Consensus pattern (22 bp):
GTGGAGTGTAGGGCTGGTACAG
Found at i:42719305 original size:44 final size:44
Alignment explanation
Indices: 42719249--42719334 Score: 172
Period size: 44 Copynumber: 2.0 Consensus size: 44
42719239 TTAAATAGAA
42719249 TAAAACTTAATTTGTTGTTCGTGGACAAGTAATAAGCTTAAAAC
1 TAAAACTTAATTTGTTGTTCGTGGACAAGTAATAAGCTTAAAAC
42719293 TAAAACTTAATTTGTTGTTCGTGGACAAGTAATAAGCTTAAA
1 TAAAACTTAATTTGTTGTTCGTGGACAAGTAATAAGCTTAAA
42719335 GTGTGGCAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (44 bp):
TAAAACTTAATTTGTTGTTCGTGGACAAGTAATAAGCTTAAAAC
Found at i:42730799 original size:16 final size:17
Alignment explanation
Indices: 42730778--42730811 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42730768 TGTAACGCCT
42730778 CAAAAAT-CTCAAATCC
1 CAAAAATCCTCAAATCC
*
42730794 CAAAAATCCTGAAATCC
1 CAAAAATCCTCAAATCC
42730811 C
1 C
42730812 GAACTTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.47, C:0.32, G:0.03, T:0.18
Consensus pattern (17 bp):
CAAAAATCCTCAAATCC
Found at i:42732283 original size:29 final size:29
Alignment explanation
Indices: 42732241--42732361 Score: 129
Period size: 29 Copynumber: 4.2 Consensus size: 29
42732231 GTGAGCATGA
* **
42732241 ATATG-AGGTGATTTGGGCCTAACGGGCC
1 ATATGAAGGTGAATTGGGCCTAATAGGCC
* *
42732269 ATATAAAGGTGATTTGGGCCTAATAGGCC
1 ATATGAAGGTGAATTGGGCCTAATAGGCC
** *
42732298 ATATGAATATGAATTGGGCCTAATACGCC
1 ATATGAAGGTGAATTGGGCCTAATAGGCC
* *
42732327 ATATGAATGTGAATTGGGCCTGAT-GGCCC
1 ATATGAAGGTGAATTGGGCCTAATAGG-CC
42732356 ATATGA
1 ATATGA
42732362 GTAAGATGGG
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
28 5 0.06
29 75 0.94
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (29 bp):
ATATGAAGGTGAATTGGGCCTAATAGGCC
Found at i:42733459 original size:17 final size:18
Alignment explanation
Indices: 42733426--42733460 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42733416 CTTTAAGAAG
42733426 GGTTTTCAATGAAAACAC
1 GGTTTTCAATGAAAACAC
*
42733444 GGTTTTCACT-AAAACAC
1 GGTTTTCAATGAAAACAC
42733461 TTCAATGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAC
Found at i:42745572 original size:12 final size:12
Alignment explanation
Indices: 42745555--42745579 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42745545 CATTACTAGT
42745555 ACCGATTTCTTC
1 ACCGATTTCTTC
42745567 ACCGATTTCTTC
1 ACCGATTTCTTC
42745579 A
1 A
42745580 AAGCCAAACC
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:0.20, C:0.32, G:0.08, T:0.40
Consensus pattern (12 bp):
ACCGATTTCTTC
Found at i:42748269 original size:40 final size:39
Alignment explanation
Indices: 42748104--42748287 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
42748094 AAATTGAATG
* * *
42748104 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
42748144 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
42748184 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
42748224 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
42748263 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
42748288 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:42748312 original size:80 final size:81
Alignment explanation
Indices: 42748144--42748332 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
42748134 GCTGGAAATT
* * * *
42748144 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
42748209 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
42748225 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
42748288 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
42748304 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
42748333 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:42751350 original size:40 final size:40
Alignment explanation
Indices: 42751223--42751352 Score: 145
Period size: 40 Copynumber: 3.2 Consensus size: 40
42751213 ATGCTGGAAA
* * * *
42751223 TTATATCCGGGTTAAGACCCGAAGGCAATTGCGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * ***
42751263 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGACA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
*
42751303 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
42751343 TTATATCCGG
1 TTATATCCGG
42751353 TTATATTCCG
Statistics
Matches: 71, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
39 1 0.01
40 70 0.99
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:42751351 original size:80 final size:80
Alignment explanation
Indices: 42751185--42751352 Score: 198
Period size: 80 Copynumber: 2.1 Consensus size: 80
42751175 AAATTGAATG
* *
42751185 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCA
42751250 ATTGCGCTAGTGGCT
66 ATTGCGCTAGTGGCT
* * * * *
42751265 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATTCTATCCGGGCTAAGACCCGAAGG
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTG-GAAATTATATCCGGGCTAAGACCCGAAGG
* * *
42751328 CATTTGTGC-ACGTGGTT
64 CAATTGCGCTA-GTGGCT
42751345 ATATCCGG
1 ATATCCGG
42751353 TTATATTCCG
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
79 5 0.07
80 69 0.93
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.22
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCA
ATTGCGCTAGTGGCT
Found at i:42761972 original size:46 final size:46
Alignment explanation
Indices: 42761919--42762094 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
42761909 TATTTGGGCA
42761919 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
42761965 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
42762012 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
42762058 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42762095 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:42762074 original size:93 final size:93
Alignment explanation
Indices: 42761915--42762086 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
42761905 AGGATATTTG
* *
42761915 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
42761980 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
42762008 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
42762073 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
42762087 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:42765059 original size:15 final size:15
Alignment explanation
Indices: 42765039--42765107 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
42765029 GTATCTTGGG
42765039 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
42765054 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
42765069 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
42765084 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
42765099 TTTCTTTAT
1 TTTCTTTAT
42765108 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:42765108 original size:30 final size:30
Alignment explanation
Indices: 42765030--42765117 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
42765020 CATAGTATCG
* * * *
42765030 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
42765060 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
42765090 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
42765118 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:42767532 original size:46 final size:46
Alignment explanation
Indices: 42767482--42767657 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
42767472 TATTTGGGCA
42767482 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
42767528 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
42767575 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
42767621 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42767658 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:42767637 original size:93 final size:93
Alignment explanation
Indices: 42767478--42767649 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
42767468 TGGATATTTG
* *
42767478 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
42767543 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
42767571 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
42767636 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
42767650 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:42769031 original size:24 final size:24
Alignment explanation
Indices: 42769004--42769049 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
42768994 GTGATCAGTC
**
42769004 AAGCAACTGAAATGTACCTAAATT
1 AAGCAACCAAAATGTACCTAAATT
**
42769028 AAGCCTCCAAAATGTACCTAAA
1 AAGCAACCAAAATGTACCTAAA
42769050 ATGTACATAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.46, C:0.22, G:0.11, T:0.22
Consensus pattern (24 bp):
AAGCAACCAAAATGTACCTAAATT
Found at i:42771120 original size:24 final size:23
Alignment explanation
Indices: 42771087--42771188 Score: 102
Period size: 24 Copynumber: 4.4 Consensus size: 23
42771077 GATGATAAAC
42771087 AGTAAGCTCTATTGAGCTGAAAAT
1 AGTAAGCTCTATTGAGCTG-AAAT
* *
42771111 GGTAAGCTCTATTGAGCT-TAAT
1 AGTAAGCTCTATTGAGCTGAAAT
42771133 AGTAAGCTCT-TTGGAGCTG-AAT
1 AGTAAGCTCTATT-GAGCTGAAAT
* * * *
42771155 CGGTAGGCTCCAGTGAGCTGAAAT
1 -AGTAAGCTCTATTGAGCTGAAAT
42771179 AGTAAGCTCT
1 AGTAAGCTCT
42771189 TAGGAGCTAT
Statistics
Matches: 63, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
21 2 0.03
22 20 0.32
23 20 0.32
24 21 0.33
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (23 bp):
AGTAAGCTCTATTGAGCTGAAAT
Found at i:42771142 original size:46 final size:46
Alignment explanation
Indices: 42771087--42771196 Score: 127
Period size: 46 Copynumber: 2.4 Consensus size: 46
42771077 GATGATAAAC
* * *
42771087 AGTAAGCTCTATT-GAGCTGAAAAT-GGTAAGCTCTATTGAGCT-TAAT
1 AGTAAGCTCT-TTGGAGCTG--AATCGGTAAGCTCCAGTGAGCTGAAAT
*
42771133 AGTAAGCTCTTTGGAGCTGAATCGGTAGGCTCCAGTGAGCTGAAAT
1 AGTAAGCTCTTTGGAGCTGAATCGGTAAGCTCCAGTGAGCTGAAAT
*
42771179 AGTAAGCTCTTAGGAGCT
1 AGTAAGCTCTTTGGAGCT
42771197 ATGGTGAGTC
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
44 3 0.05
45 17 0.30
46 36 0.64
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (46 bp):
AGTAAGCTCTTTGGAGCTGAATCGGTAAGCTCCAGTGAGCTGAAAT
Found at i:42771195 original size:23 final size:22
Alignment explanation
Indices: 42771087--42771196 Score: 71
Period size: 23 Copynumber: 4.8 Consensus size: 22
42771077 GATGATAAAC
*
42771087 AGTAAGCTCTATTGAGCTGAAAAT
1 AGTAAGCTCTA-GGAGCTG-AAAT
* * *
42771111 GGTAAGCTCTATTGAGCT-TAAT
1 AGTAAGCTCTA-GGAGCTGAAAT
*
42771133 AGTAAGCTCTTTGGAGCTG-AAT
1 AGTAAGCTC-TAGGAGCTGAAAT
* * *
42771155 CGGTAGGCTCCAGTGAGCTGAAAT
1 -AGTAAGCTCTAG-GAGCTGAAAT
42771179 AGTAAGCTCTTAGGAGCT
1 AGTAAGCTC-TAGGAGCT
42771197 ATGGTGAGTC
Statistics
Matches: 68, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
22 20 0.29
23 26 0.38
24 22 0.32
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (22 bp):
AGTAAGCTCTAGGAGCTGAAAT
Found at i:42775416 original size:29 final size:29
Alignment explanation
Indices: 42775383--42775565 Score: 226
Period size: 29 Copynumber: 6.3 Consensus size: 29
42775373 AAAAGCATGA
*
42775383 ATATGAATGTGATTTGGGCCTAATGGGGC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
42775412 ATATGAATGTGATTTGTGCCTAATGGGCA
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
42775441 ATATGAATGTGATTTTGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
42775470 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* * * *
42775499 TTACGATTATGATTTAGGG-CTAATGGGCC
1 ATATGAATGTGATTT-GGGCCTAATGGGCC
*** *
42775528 ATATGAACAAGATTT-GGCCTAGTGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
42775556 ATATGCATGT
1 ATATGAATGT
42775566 ATGTAGACTT
Statistics
Matches: 131, Mismatches: 21, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
27 2 0.02
28 15 0.11
29 111 0.85
30 3 0.02
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:42779831 original size:28 final size:29
Alignment explanation
Indices: 42779748--42779843 Score: 158
Period size: 29 Copynumber: 3.3 Consensus size: 29
42779738 GAAAGCATGA
42779748 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
42779777 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
42779806 ATATGAATGAGA-TTGGGCCTAGTGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
42779834 ATATGCATGT
1 ATATGAATGT
42779844 ATGTAGACTT
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
28 23 0.37
29 40 0.63
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.30
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:42783748 original size:29 final size:29
Alignment explanation
Indices: 42783715--42783815 Score: 184
Period size: 29 Copynumber: 3.5 Consensus size: 29
42783705 GTGACGAGAT
*
42783715 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
42783744 TGGCACTGAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
42783773 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
42783802 TGGCACTAAGTGTG
1 TGGCACTAAGTGTG
42783816 TGAGCTCGAA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 69 1.00
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:42783845 original size:58 final size:58
Alignment explanation
Indices: 42783711--42783837 Score: 168
Period size: 58 Copynumber: 2.2 Consensus size: 58
42783701 TACGGTGACG
* *
42783711 AGAT-TGGCACTAAGTGTGCATGCTGGAAAAATATGGCACTGAGTGTGCATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAAAATATGGCACTAAGTGTGCATGCTCGAA
* * *
42783768 ATATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGTGA-GCTCGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAAAATATGGCACTAAGTGTG-CATGCTCGAA
* *
42783826 GGGTATGGCACT
1 AGATATGGCACT
42783838 GTGTGTGCGG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 3 0.05
58 56 0.93
59 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.26
Consensus pattern (58 bp):
AGATATGGCACTAAGTGTGCATGCTGGAAAAATATGGCACTAAGTGTGCATGCTCGAA
Found at i:42791756 original size:29 final size:29
Alignment explanation
Indices: 42791717--42791791 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
42791707 GGTTGAGAGA
* *
42791717 ATGGCACTAAGTGTGCGGGCTTGAAA-TGC
1 ATGGCACTAAGTGTGCGAG-TTGAAAGTAC
*
42791746 ATGGCACTAAGTGTGCGAGTTTAAAGTAC
1 ATGGCACTAAGTGTGCGAGTTGAAAGTAC
42791775 ATGGCACTAAGTGTGCG
1 ATGGCACTAAGTGTGCG
42791792 TGGTTGATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
28 5 0.12
29 37 0.88
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (29 bp):
ATGGCACTAAGTGTGCGAGTTGAAAGTAC
Found at i:42794918 original size:46 final size:43
Alignment explanation
Indices: 42794775--42794910 Score: 123
Period size: 47 Copynumber: 3.0 Consensus size: 43
42794765 CCTGCCCCTA
42794775 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATTT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCA-TT
* * * * *
42794822 CA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATA
1 -AGTGAACTCGGACTCAACTCAACGAGTTC-G-GATGC-CAACCATT
42794868 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT
42794911 CCTAGTGACA
Statistics
Matches: 73, Mismatches: 10, Indels: 14
0.75 0.10 0.14
Matches are distributed among these distances:
44 9 0.12
45 2 0.03
46 27 0.37
47 28 0.38
48 2 0.03
49 4 0.05
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (43 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATT
Found at i:42799672 original size:30 final size:30
Alignment explanation
Indices: 42799637--42799736 Score: 123
Period size: 29 Copynumber: 3.4 Consensus size: 30
42799627 AGCTATCCCC
42799637 TTCATATTTTGATGGTCGTCACCATCCCTT
1 TTCATATTTTGATGGTCGTCACCATCCCTT
* * *
42799667 GTCATA-GTTGATGGTCGTCACCATTCCTT
1 TTCATATTTTGATGGTCGTCACCATCCCTT
* * *
42799696 TTCAT-TATTGATGGTTGTCACTATCCCTT
1 TTCATATTTTGATGGTCGTCACCATCCCTT
*
42799725 TTCATAATTTGA
1 TTCATATTTTGA
42799737 CAGGCGAAGC
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
29 49 0.84
30 9 0.16
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.44
Consensus pattern (30 bp):
TTCATATTTTGATGGTCGTCACCATCCCTT
Found at i:42799776 original size:30 final size:30
Alignment explanation
Indices: 42799742--42799856 Score: 131
Period size: 30 Copynumber: 3.8 Consensus size: 30
42799732 TTTGACAGGC
* * * * *
42799742 GAAGCTATCCCTTTCCGTAGTTCGATAGTT
1 GAAGCTATCCCTTTTCATTGATCGATAGTA
* * *
42799772 GAAGCTATCTCTTTTCATTGGTCGATACTA
1 GAAGCTATCCCTTTTCATTGATCGATAGTA
*
42799802 GAAGCTATCCCTTTTCATTGATCGATAGTC
1 GAAGCTATCCCTTTTCATTGATCGATAGTA
* *
42799832 GAAGCTATCCCTTTTTATTGGTCGA
1 GAAGCTATCCCTTTTCATTGATCGA
42799857 CGATCATCAA
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (30 bp):
GAAGCTATCCCTTTTCATTGATCGATAGTA
Found at i:42799809 original size:60 final size:60
Alignment explanation
Indices: 42799742--42799856 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
42799732 TTTGACAGGC
* * * *
42799742 GAAGCTATCCCTTTCCGTAGTTCGATAGTTGAAGCTATCTCTTTTCATTGGTCGATACTA
1 GAAGCTATCCCTTTCCATAGATCGATAGTCGAAGCTATCCCTTTTCATTGGTCGATACTA
* * *
42799802 GAAGCTATCCCTTTTCATTGATCGATAGTCGAAGCTATCCCTTTTTATTGGTCGA
1 GAAGCTATCCCTTTCCATAGATCGATAGTCGAAGCTATCCCTTTTCATTGGTCGA
42799857 CGATCATCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (60 bp):
GAAGCTATCCCTTTCCATAGATCGATAGTCGAAGCTATCCCTTTTCATTGGTCGATACTA
Found at i:42806147 original size:16 final size:17
Alignment explanation
Indices: 42806126--42806158 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
42806116 TAGATAGCCG
*
42806126 AATACATGT-ATTTATA
1 AATACATATAATTTATA
42806142 AATACATATAATTTATA
1 AATACATATAATTTATA
42806159 CTCATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (17 bp):
AATACATATAATTTATA
Found at i:42811376 original size:57 final size:57
Alignment explanation
Indices: 42811310--42811425 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 57
42811300 AAATTTGAGT
42811310 AAAACTTGGTAACCCAATTTGGTACGTTTCAAAATGAAAAGTCCTGGTAATACCTCG
1 AAAACTTGGTAACCCAATTTGGTACGTTTCAAAATGAAAAGTCCTGGTAATACCTCG
*
42811367 AAAACTTGGTGACCCAATTTGGTACGTTTCAAAATGAAAAGTCCTGGTAATACCTCG
1 AAAACTTGGTAACCCAATTTGGTACGTTTCAAAATGAAAAGTCCTGGTAATACCTCG
42811424 AA
1 AA
42811426 CCCTATCCCG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (57 bp):
AAAACTTGGTAACCCAATTTGGTACGTTTCAAAATGAAAAGTCCTGGTAATACCTCG
Found at i:42815329 original size:62 final size:64
Alignment explanation
Indices: 42815156--42815332 Score: 152
Period size: 66 Copynumber: 2.8 Consensus size: 64
42815146 ATGGAGCGTA
** * * * *
42815156 GCTAGGTCACATGTATGGTGCTGAGTG-CACATCATGTGTACTAGAGAGCTACAGACATTATGAT
1 GCTAGGTCACATGGGTGGTACTAAGTGTCAC--CATGTGTACAAGAGAGCTACAGACATAAT-AT
42815220 GT
63 GT
* * *
42815222 GCTAGGTTC-CATGGGTGATA-TATGTTGTACACCATGTAG-ACAAGAGAGCTAC-GAGATAA-A
1 GCTAGG-TCACATGGGTGGTACTAAG-TGT-CACCATGT-GTACAAGAGAGCTACAGACATAATA
42815282 T-T
62 TGT
42815284 GGCTAGGTCACATGGGTGGTACTAAGTGTCACCATGTGTACAAGAGAGC
1 -GCTAGGTCACATGGGTGGTACTAAGTGTCACCATGTGTACAAGAGAGC
42815333 CGAATTATAT
Statistics
Matches: 91, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
61 1 0.01
62 21 0.23
63 21 0.23
64 3 0.03
65 7 0.08
66 32 0.35
67 3 0.03
68 3 0.03
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (64 bp):
GCTAGGTCACATGGGTGGTACTAAGTGTCACCATGTGTACAAGAGAGCTACAGACATAATATGT
Found at i:42828516 original size:38 final size:38
Alignment explanation
Indices: 42828465--42828619 Score: 249
Period size: 38 Copynumber: 4.0 Consensus size: 38
42828455 GATGTGTATG
42828465 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGC
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGC
42828503 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGC
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGC
*
42828541 AATGTGCGAGA-TATGATATCCGGGCTAAGCCCGAAGGC
1 AATGTGCGA-ATTGTGATATCCGGGCTAAGCCCGAAGGC
* *
42828579 AATTGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGC
1 AA-TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGC
42828619 A
1 A
42828620 TTTGTGCGGG
Statistics
Matches: 109, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
38 75 0.69
39 24 0.22
40 10 0.09
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (38 bp):
AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGC
Found at i:42828643 original size:40 final size:40
Alignment explanation
Indices: 42828484--42828663 Score: 145
Period size: 38 Copynumber: 4.6 Consensus size: 40
42828474 ATTGTGATAT
* * *** *
42828484 CCGGGCTAAG-CCCGAAGGCA-ATGTGCGAATTGTGATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA
* * ** *
42828522 CCGGGCTAAG-CCCGAAGGCA-ATGTGCGAGATATGATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA
* *** *
42828560 CCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTGTGATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA
* *
42828599 CCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTACCATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA
* *
42828639 CCGGGCTATGTCCCGAAGGCGTTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
42828664 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
38 55 0.44
39 24 0.19
40 45 0.36
ACGTcount: A:0.23, C:0.22, G:0.32, T:0.22
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA
Found at i:42836843 original size:40 final size:40
Alignment explanation
Indices: 42836799--42837011 Score: 218
Period size: 40 Copynumber: 5.3 Consensus size: 40
42836789 GCTACTCGTT
* * * * *
42836799 CAAATACCTTTGGGACATAGCCTGG-TTATAGTAGCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TAGTAACTCGCA
*
42836839 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* **
42836879 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAGTAACTCGCA
* **
42836919 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAGTAACTCGCA
* * **
42836959 CAAATGCCTT-TGGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAGTAACTCGCA
42836999 CAAATGCCTTCGG
1 CAAATGCCTTCGG
42837012 ATCTTAGTCT
Statistics
Matches: 160, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
39 3 0.02
40 154 0.96
41 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.29
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:42837014 original size:40 final size:40
Alignment explanation
Indices: 42836827--42837064 Score: 347
Period size: 40 Copynumber: 6.0 Consensus size: 40
42836817 AGCCTGGTTA
* **
42836827 TAGTAGCTCGCACAAATGCCTTCGGGA-CTTAACCCGGATT
1 TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATT
42836867 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATT
1 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATT
42836907 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATT
1 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATT
*
42836947 TAGTAACTCGCACAAATGCCTTTGGATCTTAGTCCGGATT
1 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATT
* *
42836987 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCTGGATA
1 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATT
* * *
42837027 TAGTCACTTAGCACAAA-GCCTTCGGGA-CTTAGCCCGGA
1 TAGTAAC-TCGCACAAATGCCTTC-GGATCTTAGTCCGGA
42837065 CATCATTTGA
Statistics
Matches: 184, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
39 3 0.02
40 170 0.92
41 11 0.06
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (40 bp):
TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATT
Found at i:42837661 original size:22 final size:21
Alignment explanation
Indices: 42837636--42837678 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
42837626 ACCACACACA
* *
42837636 AATGGAATACATTTTACTAACT
1 AATGCAATACATATTA-TAACT
*
42837658 AATGCATTACATATTATAACT
1 AATGCAATACATATTATAACT
42837679 CAATACGCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (21 bp):
AATGCAATACATATTATAACT
Found at i:42837786 original size:2 final size:2
Alignment explanation
Indices: 42837779--42837808 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42837769 ATGTGCAAAC
42837779 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42837809 TGTGACAGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42839584 original size:40 final size:40
Alignment explanation
Indices: 42839499--42839649 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
42839489 AATTGAATGA
* * *
42839499 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
42839539 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
42839580 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
42839619 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
42839650 ACATGGTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:42839663 original size:40 final size:40
Alignment explanation
Indices: 42839536--42839665 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
42839526 ATGCTGGAAA
* * * *
42839536 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
42839576 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
*
42839616 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
42839656 TTATATCCGG
1 TTATATCCGG
42839666 TTATGTTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:42842950 original size:30 final size:30
Alignment explanation
Indices: 42842914--42843044 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
42842904 GACAAGATTG
* * * * *
42842914 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
42842944 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
42842972 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
42843002 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
42843031 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
42843045 GATTCACTAT
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 20 0.22
30 46 0.50
31 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:42843005 original size:58 final size:58
Alignment explanation
Indices: 42842914--42843044 Score: 174
Period size: 58 Copynumber: 2.2 Consensus size: 58
42842904 GACAAGATTG
* * * * * *
42842914 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAG-CTGAAATATATA
*
42842972 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTG-AAATATATA
42843031 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
42843045 GATTCACTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
57 2 0.03
58 41 0.64
59 21 0.33
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTGAAATATATA
Found at i:42850688 original size:40 final size:40
Alignment explanation
Indices: 42850603--42850753 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
42850593 AATTGAATGA
* * *
42850603 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
42850643 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
42850684 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
42850723 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
42850754 ACATGGTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:42850767 original size:40 final size:40
Alignment explanation
Indices: 42850640--42850769 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
42850630 ATGCTGGAAA
* * * *
42850640 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
42850680 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
*
42850720 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
42850760 TTATATCCGG
1 TTATATCCGG
42850770 TTATATTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:42854100 original size:30 final size:29
Alignment explanation
Indices: 42854015--42854142 Score: 149
Period size: 30 Copynumber: 4.5 Consensus size: 29
42854005 GACAAGATTG
* * * *
42854015 GCACTAAGTGTGCG-GTTTAAAATTGTACA
1 GCACTAAGTGTGCGAG-CTGAAATTATATA
*
42854044 GCACTAAGTGTGCGAGTTTG--ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAATTATATA
42854072 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTG-AAATTATATA
42854102 GCACTAAGTGTGCGAGCTGAAA--ATATA
1 GCACTAAGTGTGCGAGCTGAAATTATATA
42854129 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
42854143 GATTCACTAT
Statistics
Matches: 91, Mismatches: 4, Indels: 10
0.87 0.04 0.10
Matches are distributed among these distances:
27 21 0.23
28 22 0.24
29 17 0.19
30 31 0.34
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGCTGAAATTATATA
Done.