Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 120 of 345
Found at i:40215310 original size:24 final size:23
Alignment explanation
Indices: 40215273--40215340 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 23
40215263 GATATATCAT
*
40215273 CTCGTAAGATCTTACTGTTCCTAG
1 CTCGT-AGAGCTTACTGTTCCTAG
* *
40215297 CTCGTCAGAGCTTACTATTTCTAG
1 CTCGT-AGAGCTTACTGTTCCTAG
*
40215321 CTCAATAGAGCTTACTGTTC
1 CTC-GTAGAGCTTACTGTTC
40215341 ATCAGCTAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
24 35 0.97
25 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (23 bp):
CTCGTAGAGCTTACTGTTCCTAG
Found at i:40216320 original size:39 final size:39
Alignment explanation
Indices: 40216305--40216420 Score: 196
Period size: 39 Copynumber: 3.0 Consensus size: 39
40216295 CCGAACATAT
40216305 TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATATAA
1 TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATATAA
* *
40216344 TTCCAGCACATAGCCTACGGACCCTAAGTCCGGATATAA
1 TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATATAA
* *
40216383 TTCCAGCACATAGCCTGTGGACCCTAAGTCCGGATATA
1 TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATATA
40216421 CATCACTGAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 73 1.00
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (39 bp):
TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATATAA
Found at i:40221350 original size:67 final size:67
Alignment explanation
Indices: 40221268--40221400 Score: 212
Period size: 67 Copynumber: 2.0 Consensus size: 67
40221258 ATGGGTAGTG
* * * *
40221268 TTAGAAATGTTGGACCTAAATGTAAGCATTACAATGAGTGACATTATGGTGAATGTAGAATAATG
1 TTAGAAATGTTGGACCTAAATGCAAGCACTACAATAAGCGACATTATGGTGAATGTAGAATAATG
40221333 AC
66 AC
* *
40221335 TTAGAAATGTTGGACCTGAATGCAAGCACTACAATAAGCGATATTATGGTGAATGTAGAATAATG
1 TTAGAAATGTTGGACCTAAATGCAAGCACTACAATAAGCGACATTATGGTGAATGTAGAATAATG
40221400 A
66 A
40221401 GCGGAGCTTG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.29
Consensus pattern (67 bp):
TTAGAAATGTTGGACCTAAATGCAAGCACTACAATAAGCGACATTATGGTGAATGTAGAATAATG
AC
Found at i:40229617 original size:25 final size:26
Alignment explanation
Indices: 40229588--40229648 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 26
40229578 TTAATTAATA
40229588 TAAAATATTA-ATAATTCAAT-AAAT
1 TAAAATATTAGATAATTCAATAAAAT
*
40229612 TGAAAA-ATTAGATAATTGAATAAAAT
1 T-AAAATATTAGATAATTCAATAAAAT
40229638 TAAAAT-TTAGA
1 TAAAATATTAGA
40229649 AGAAAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
24 5 0.16
25 22 0.69
26 5 0.16
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (26 bp):
TAAAATATTAGATAATTCAATAAAAT
Found at i:40230356 original size:28 final size:28
Alignment explanation
Indices: 40230301--40230358 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
40230291 GCCTTTTGAA
* * *
40230301 AATATTTACAAAAAAGCATCTAATTTTT
1 AATATTTACAAAAAAGCAACCAAATTTT
* *
40230329 AATATTTACAAAAGAGTAACCAAATTTT
1 AATATTTACAAAAAAGCAACCAAATTTT
40230357 AA
1 AA
40230359 AAATAGTTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.34
Consensus pattern (28 bp):
AATATTTACAAAAAAGCAACCAAATTTT
Found at i:40230689 original size:26 final size:26
Alignment explanation
Indices: 40230660--40230711 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
40230650 ATAAAATGAA
40230660 TGAGATTTGATTCCGTTCAATTTTAT
1 TGAGATTTGATTCCGTTCAATTTTAT
*
40230686 TGAGATTTGATTTCGTTCAATTTTAT
1 TGAGATTTGATTCCGTTCAATTTTAT
40230712 CTCCCCAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.52
Consensus pattern (26 bp):
TGAGATTTGATTCCGTTCAATTTTAT
Found at i:40240672 original size:40 final size:40
Alignment explanation
Indices: 40240628--40240832 Score: 215
Period size: 40 Copynumber: 5.2 Consensus size: 40
40240618 GGGCTAAGTC
*
40240628 CCGAAGGCTTTTGTGCTAGTGACTATATCCGGACTAAGAT
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGACTAAGAT
* * *
40240668 CCGAAGGCACTTGTGCGAGTTG-CTATATCC-GAGCTAAGAC
1 CCGAAGGCATTTGTGCTAG-TGACTATATCCGGA-CTAAGAT
* *
40240708 CCGAAGGCATTTGTGCTAGCGACTATATCCGGGCTAAG-T
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGACTAAGAT
* * *
40240747 CCCGAAGGCATTTATGCTAGTGACTATATCCGGGCTAAGAC
1 -CCGAAGGCATTTGTGCTAGTGACTATATCCGGACTAAGAT
* * *
40240788 CCAAAGGCATTTGTGCGAGTTG-TTATATCCGG-CTAA-AT
1 CCGAAGGCATTTGTGCTAG-TGACTATATCCGGACTAAGAT
40240826 CCCGAAG
1 -CCGAAG
40240833 ATACTTGGGT
Statistics
Matches: 139, Mismatches: 18, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
38 1 0.01
39 12 0.09
40 121 0.87
41 5 0.04
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTGACTATATCCGGACTAAGAT
Found at i:40240815 original size:80 final size:80
Alignment explanation
Indices: 40240612--40240832 Score: 270
Period size: 80 Copynumber: 2.8 Consensus size: 80
40240602 TATTCGAATG
* * * *
40240612 ATATCTGGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAG-TCCCGAAGGC
*
40240676 ACTTGTGCGAGTTGCT
65 ACTTATGCGAGTTGCT
* *
40240692 ATATCCGAGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCA
* *
40240757 TTTATGCTAG-TGACT
66 CTTATGCGAGTTG-CT
* * * *
40240772 ATATCCGGGCTAAGACCCAAAGGCATTTGTGCGAGTTG-TTATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTCCCGAAG
40240833 ATACTTGGGT
Statistics
Matches: 123, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
79 17 0.14
80 105 0.85
81 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCA
CTTATGCGAGTTGCT
Found at i:40241100 original size:22 final size:22
Alignment explanation
Indices: 40241060--40241101 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
40241050 GAATGTGCAT
*
40241060 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
40241082 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
40241102 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:40242215 original size:24 final size:23
Alignment explanation
Indices: 40242188--40242280 Score: 80
Period size: 24 Copynumber: 3.8 Consensus size: 23
40242178 GTTACATATA
40242188 TCAGCTCATAAGAGCTTACTGTT
1 TCAGCTCATAAGAGCTTACTGTT
* *
40242211 CTCAGCTCGTTAGAGCTTACTGTT
1 -TCAGCTCATAAGAGCTTACTGTT
* *
40242235 TCCAGCTCGAT-AGTGCTTACTATT
1 T-CAGCTC-ATAAGAGCTTACTGTT
*
40242259 AATCAGCTCAGAAGGAGCTTAC
1 --TCAGCTCATAA-GAGCTTAC
40242281 CGATCATAGC
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
23 1 0.02
24 39 0.70
25 8 0.14
26 8 0.14
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (23 bp):
TCAGCTCATAAGAGCTTACTGTT
Found at i:40244006 original size:29 final size:29
Alignment explanation
Indices: 40243972--40244045 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
40243962 TAATCAACCG
*
40243972 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
40244001 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
40244030 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
40244046 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:40244868 original size:15 final size:15
Alignment explanation
Indices: 40244845--40244880 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
40244835 CTTAACATTT
* *
40244845 ACCACATATTGATTC
1 ACCAAATATCGATTC
40244860 ACCAAATATCGATTC
1 ACCAAATATCGATTC
40244875 ACCAAA
1 ACCAAA
40244881 CTCTTCATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.42, C:0.28, G:0.06, T:0.25
Consensus pattern (15 bp):
ACCAAATATCGATTC
Found at i:40248873 original size:18 final size:18
Alignment explanation
Indices: 40248852--40248888 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40248842 TCACAATCAA
40248852 TTTTCAATTCATACAATT
1 TTTTCAATTCATACAATT
* *
40248870 TTTTCAATTTATTCAATT
1 TTTTCAATTCATACAATT
40248888 T
1 T
40248889 AGTCCCTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.14, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTCAATTCATACAATT
Found at i:40262297 original size:27 final size:27
Alignment explanation
Indices: 40262255--40262614 Score: 439
Period size: 27 Copynumber: 13.6 Consensus size: 27
40262245 TACCGGAACT
* * *
40262255 CTTATGTGACAAAATGATGATTTTTCC
1 CTTATGTGATAAAATGACGATTTTGCC
* * *
40262282 CTCATATGATAAAATGATGATTTTGCC
1 CTTATGTGATAAAATGACGATTTTGCC
*
40262309 CTTATGTGATAAAATGATGATTTTGCC
1 CTTATGTGATAAAATGACGATTTTGCC
* *
40262336 CTTATGTAATAAAATGATGATTTTG-C
1 CTTATGTGATAAAATGACGATTTTGCC
* *
40262362 TTTATGTGATAAAATGACGAATTTGCC
1 CTTATGTGATAAAATGACGATTTTGCC
* *
40262389 TTTATATGATAAAATGACGAATTTT-CC
1 CTTATGTGATAAAATGACG-ATTTTGCC
* *
40262416 CTTATTTGATAAGATGACGATTTTGCC
1 CTTATGTGATAAAATGACGATTTTGCC
40262443 CTTATGTG-----ATGACGATTTTGCC
1 CTTATGTGATAAAATGACGATTTTGCC
* *
40262465 CTTATATAATAAAATGACGATTTTGCC
1 CTTATGTGATAAAATGACGATTTTGCC
40262492 CTTATGTGATAAAATGACGATTTTGCC
1 CTTATGTGATAAAATGACGATTTTGCC
*
40262519 CTTATGTGATAAAATGATGATTTTGCC
1 CTTATGTGATAAAATGACGATTTTGCC
* *
40262546 CATATGTGATAAAATGACAATTTT-CC
1 CTTATGTGATAAAATGACGATTTTGCC
* * * *
40262572 CATATGCGATAAAATGACAATTTTTCC
1 CTTATGTGATAAAATGACGATTTTGCC
40262599 CTTATGTGATAAAATG
1 CTTATGTGATAAAATG
40262615 CCCAAAATAC
Statistics
Matches: 296, Mismatches: 28, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
22 20 0.07
26 52 0.18
27 220 0.74
28 4 0.01
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (27 bp):
CTTATGTGATAAAATGACGATTTTGCC
Found at i:40262599 original size:183 final size:183
Alignment explanation
Indices: 40262268--40262610 Score: 519
Period size: 183 Copynumber: 1.9 Consensus size: 183
40262258 ATGTGACAAA
* * * * *
40262268 ATGATGATTTTTCCCTCATATGATAAAATGATGATTTTGCCCTTATGTGATAAAATGATGATTTT
1 ATGACGATTTTGCCCTCATATAATAAAATGACGATTTTGCCCTTATGTGATAAAATGACGATTTT
** ** *
40262333 GCCCTTATGTAATAAAATGATGATTTTGCTTTATGTGATAAAATGACGAATTTGCCTTTATATGA
66 GCCCTTATGTAATAAAATGATGATTTTGCCATATGTGATAAAATGACGAATTTGCCCATATACGA
*
40262398 TAAAATGACGAATTTTCCCTTATTTGATAAGATGACGATTTTGCCCTTATGTG
131 TAAAATGACGAATTTTCCCTTATGTGATAAGATGACGATTTTGCCCTTATGTG
*
40262451 ATGACGATTTTGCCCTTATATAATAAAATGACGATTTTGCCCTTATGTGATAAAATGACGATTTT
1 ATGACGATTTTGCCCTCATATAATAAAATGACGATTTTGCCCTTATGTGATAAAATGACGATTTT
* * *
40262516 GCCCTTATGTGATAAAATGATGATTTTGCCCATATGTGATAAAATGAC-AATTTTCCCATATGCG
66 GCCCTTATGTAATAAAATGATGATTTTG-CCATATGTGATAAAATGACGAATTTGCCCATATACG
40262580 ATAAAATGAC-AATTTTTCCCTTATGTGATAA
130 ATAAAATGACGAA-TTTTCCCTTATGTGATAA
40262611 AATGCCCAAA
Statistics
Matches: 143, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
182 2 0.01
183 124 0.87
184 17 0.12
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (183 bp):
ATGACGATTTTGCCCTCATATAATAAAATGACGATTTTGCCCTTATGTGATAAAATGACGATTTT
GCCCTTATGTAATAAAATGATGATTTTGCCATATGTGATAAAATGACGAATTTGCCCATATACGA
TAAAATGACGAATTTTCCCTTATGTGATAAGATGACGATTTTGCCCTTATGTG
Found at i:40262639 original size:80 final size:81
Alignment explanation
Indices: 40262473--40262643 Score: 186
Period size: 80 Copynumber: 2.1 Consensus size: 81
40262463 CCCTTATATA
* * * * **
40262473 ATAAAATGACGATTTTGCCCTTATGTGATAAAATGACGATTTTGCCCTTATGTGATAAAATGATG
1 ATAAAATGACAATTTTGCCCATATGCGATAAAATGACAATTTTGCCCTTATGTGATAAAATGACA
** ** *
40262538 ATTTTGCCCATATGTG
66 AAATACCCCATAAGTG
* *
40262554 ATAAAATGACAATTTT-CCCATATGCGATAAAATGACAATTTTTCCCTTATGTGATAAAATGCCC
1 ATAAAATGACAATTTTGCCCATATGCGATAAAATGACAATTTTGCCCTTATGTGATAAAATG-AC
40262618 AAAATACCCTCATAAG-G
65 AAAATACCC-CATAAGTG
40262635 -TAAAATGAC
1 ATAAAATGAC
40262644 TGCAATTCCC
Statistics
Matches: 75, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
80 50 0.67
81 20 0.27
82 5 0.07
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (81 bp):
ATAAAATGACAATTTTGCCCATATGCGATAAAATGACAATTTTGCCCTTATGTGATAAAATGACA
AAATACCCCATAAGTG
Found at i:40276784 original size:46 final size:48
Alignment explanation
Indices: 40276680--40276793 Score: 151
Period size: 48 Copynumber: 2.4 Consensus size: 48
40276670 TGTCTTCGAC
** * *
40276680 ATGGACTTACATGAATTATTCCTATCTCCAATGCCATATATATATAAT
1 ATGGACTTACATGGCTCATTCCTATCTCCAAAGCCATATATATATAAT
* * *
40276728 ATGGGCTTACATGGCTCATTCCTATCTCCAAAGCCATATA-A-CTGAT
1 ATGGACTTACATGGCTCATTCCTATCTCCAAAGCCATATATATATAAT
40276774 ATGGACTTACATGGCTCATT
1 ATGGACTTACATGGCTCATT
40276794 TCTGTCCTGT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 22 0.38
47 1 0.02
48 35 0.60
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (48 bp):
ATGGACTTACATGGCTCATTCCTATCTCCAAAGCCATATATATATAAT
Found at i:40276805 original size:5 final size:5
Alignment explanation
Indices: 40276795--40276819 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
40276785 TGGCTCATTT
40276795 CTGTC CTGTC CTGTC CTGTC CTGTC
1 CTGTC CTGTC CTGTC CTGTC CTGTC
40276820 AACCCCAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.20, T:0.40
Consensus pattern (5 bp):
CTGTC
Found at i:40281009 original size:40 final size:40
Alignment explanation
Indices: 40280947--40281164 Score: 298
Period size: 40 Copynumber: 5.5 Consensus size: 40
40280937 AAGCCAAGTA
* * * *
40280947 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
40280986 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
40281026 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
40281066 CCTTCGGGACTTAGCCCGGATATAGTAGCTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
40281106 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
40281146 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
40281165 TTATCATCCA
Statistics
Matches: 162, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
39 13 0.08
40 149 0.92
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:40282436 original size:10 final size:10
Alignment explanation
Indices: 40282421--40282450 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
40282411 CATGAGAGCT
40282421 TTTTTCTTTC
1 TTTTTCTTTC
40282431 TTTTTCTTTC
1 TTTTTCTTTC
40282441 TCTTTTCTTT
1 T-TTTTCTTT
40282451 TTTCATCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:40284357 original size:46 final size:48
Alignment explanation
Indices: 40284253--40284372 Score: 145
Period size: 48 Copynumber: 2.5 Consensus size: 48
40284243 TGTCTTCGAC
** * *
40284253 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATAAT
1 ATGGACTTACATGGCTAATTCCTGTCTCCAAAGCCATATATATATAAT
* * * *
40284301 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCCATATA-A-CTGAT
1 ATGGACTTACATGGCTAATTCCTGTCTCCAAAGCCATATATATATAAT
*
40284347 ATGGACTTACATGGCTAATTTCTGTC
1 ATGGACTTACATGGCTAATTCCTGTC
40284373 CTGTCCTGTC
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
46 26 0.42
47 1 0.02
48 35 0.56
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (48 bp):
ATGGACTTACATGGCTAATTCCTGTCTCCAAAGCCATATATATATAAT
Found at i:40284378 original size:5 final size:5
Alignment explanation
Indices: 40284368--40284392 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
40284358 TGGCTAATTT
40284368 CTGTC CTGTC CTGTC CTGTC CTGTC
1 CTGTC CTGTC CTGTC CTGTC CTGTC
40284393 AACCCCAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.20, T:0.40
Consensus pattern (5 bp):
CTGTC
Found at i:40288608 original size:48 final size:46
Alignment explanation
Indices: 40288535--40288654 Score: 123
Period size: 48 Copynumber: 2.6 Consensus size: 46
40288525 TGTCTTTGAC
** * * **
40288535 ATGGACTTACATGAATTATTTCTGTCTCCAATGCCATATATATATAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAACCATATA-A-ATAAT
* * * *
40288583 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAATCATATAACTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAACCATATAAATAAT
*
40288629 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
40288655 CTGTTCTGTC
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
46 27 0.45
47 1 0.02
48 32 0.53
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (46 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAACCATATAAATAAT
Found at i:40294965 original size:43 final size:43
Alignment explanation
Indices: 40294918--40295073 Score: 147
Period size: 43 Copynumber: 3.6 Consensus size: 43
40294908 TGCCATATCT
* * *
40294918 CAGATATGGTCTTACATGTTATCACATATCGATGCCATTGTCC
1 CAGACATGGTCTTACATGTAATCACATATCGATGCCAATGTCC
* * * * *
40294961 CAGATAGGGTCTTACAGGTAATTGA-TTAAT-GATGCCAATGTCC
1 CAGACATGGTCTTACATGTAA-TCACAT-ATCGATGCCAATGTCC
* * *
40295004 CAGACATGGTCTTACACGTAATCTCA-ATACAATGCCAATGTCC
1 CAGACATGGTCTTACATGTAATCACATAT-CGATGCCAATGTCC
* *
40295047 TAGACCTGGTCTTACATGTAATCACAT
1 CAGACATGGTCTTACATGTAATCACAT
40295074 TTCTGTAACC
Statistics
Matches: 90, Mismatches: 17, Indels: 11
0.76 0.14 0.09
Matches are distributed among these distances:
41 2 0.02
42 1 0.01
43 83 0.92
44 4 0.04
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (43 bp):
CAGACATGGTCTTACATGTAATCACATATCGATGCCAATGTCC
Found at i:40303207 original size:15 final size:17
Alignment explanation
Indices: 40303177--40303208 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
40303167 TTGACACTTG
40303177 TGAATGTGAGTTTGGTA
1 TGAATGTGAGTTTGGTA
40303194 TGAAT-TGA-TTTGGTA
1 TGAATGTGAGTTTGGTA
40303209 AAACATGCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (17 bp):
TGAATGTGAGTTTGGTA
Found at i:40304748 original size:11 final size:11
Alignment explanation
Indices: 40304733--40304777 Score: 56
Period size: 11 Copynumber: 3.9 Consensus size: 11
40304723 GCACAAAGCT
40304733 CATAAGAACATA
1 CATAA-AACATA
40304745 -ATAAAACCATA
1 CATAAAA-CATA
40304756 CTATAAAACATA
1 C-ATAAAACATA
40304768 CATAAAACAT
1 CATAAAACAT
40304778 TGGCTCGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 2 0.07
11 17 0.57
12 5 0.17
13 6 0.20
ACGTcount: A:0.60, C:0.18, G:0.02, T:0.20
Consensus pattern (11 bp):
CATAAAACATA
Found at i:40314667 original size:46 final size:47
Alignment explanation
Indices: 40314561--40314682 Score: 147
Period size: 46 Copynumber: 2.6 Consensus size: 47
40314551 TGTCTTCGAC
** * *
40314561 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC--A-ATATATCTAAT
* *
40314611 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATATCTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
*
40314657 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
40314683 CTGTCCTGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 34 0.53
50 30 0.47
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (47 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
Found at i:40317705 original size:12 final size:13
Alignment explanation
Indices: 40317687--40317718 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
40317677 TCGATATCTC
40317687 AATTTCAATTCAT
1 AATTTCAATTCAT
40317700 -ATTTCAATTCAT
1 AATTTCAATTCAT
40317712 AATTTCA
1 AATTTCA
40317719 CTTTCTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTTCAATTCAT
Found at i:40318124 original size:21 final size:21
Alignment explanation
Indices: 40318069--40318124 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
40318059 AGTAGTATAT
*
40318069 GACACATAAAGTGCCTGAAAC
1 GACACATATAGTGCCTGAAAC
** *
40318090 GACACACGTGGTGCCT-AATAC
1 GACACATATAGTGCCTGAA-AC
40318111 GACACATATAGTGC
1 GACACATATAGTGC
40318125 TTGATCGGAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (21 bp):
GACACATATAGTGCCTGAAAC
Found at i:40319389 original size:21 final size:20
Alignment explanation
Indices: 40319365--40319404 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
40319355 TCCTTTTCTT
40319365 TTTCTTT-TCTTCTTTGTTTTG
1 TTTCTTTCT-TTCTTT-TTTTG
40319386 TTTCTTTCTTTCTTTTTTT
1 TTTCTTTCTTTCTTTTTTT
40319405 ACTTTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 13 0.72
22 1 0.06
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (20 bp):
TTTCTTTCTTTCTTTTTTTG
Found at i:40319897 original size:11 final size:11
Alignment explanation
Indices: 40319876--40319905 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
40319866 TATTTCATAG
40319876 TATAA-TATAA
1 TATAATTATAA
40319886 TATAATTATAA
1 TATAATTATAA
40319897 TATAATTAT
1 TATAATTAT
40319906 TACAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TATAATTATAA
Found at i:40324298 original size:21 final size:21
Alignment explanation
Indices: 40324272--40324313 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
40324262 TAGATATCGT
* *
40324272 TAAATATGATATTAAAGAAAA
1 TAAATATGATATAAAAAAAAA
40324293 TAAATATGATATAAAAAAAAA
1 TAAATATGATATAAAAAAAAA
40324314 AAGAAGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (21 bp):
TAAATATGATATAAAAAAAAA
Found at i:40326217 original size:20 final size:21
Alignment explanation
Indices: 40326182--40326221 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
40326172 AAACACACAA
40326182 TTTAATCTATTTTTAAATAAC
1 TTTAATCTATTTTTAAATAAC
*
40326203 TTTAATTTA-TTTTAAATAA
1 TTTAATCTATTTTTAAATAA
40326222 ATAAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAATCTATTTTTAAATAAC
Found at i:40330672 original size:21 final size:21
Alignment explanation
Indices: 40330646--40330689 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
40330636 TTTTGAAGTC
40330646 TTTGAAGCACGATCTACCCAT
1 TTTGAAGCACGATCTACCCAT
*
40330667 TTTGAAGCATGATCTACCCAT
1 TTTGAAGCACGATCTACCCAT
40330688 TT
1 TT
40330690 CTAGCTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (21 bp):
TTTGAAGCACGATCTACCCAT
Found at i:40333289 original size:12 final size:12
Alignment explanation
Indices: 40333256--40333293 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
40333246 GCCATTCATT
*
40333256 ATTTTTATTTCA
1 ATTTTTATTTTA
*
40333268 ATTTAT-TTTTA
1 ATTTTTATTTTA
40333279 ATTTTTATTTTA
1 ATTTTTATTTTA
40333291 ATT
1 ATT
40333294 ACTAAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (12 bp):
ATTTTTATTTTA
Found at i:40341835 original size:62 final size:62
Alignment explanation
Indices: 40341737--40341855 Score: 211
Period size: 62 Copynumber: 1.9 Consensus size: 62
40341727 GTGGAATACG
* *
40341737 ATTGCTTGGTGAATGTATGAAGATGTATGGATTAAATACTAAGAGATAGTGAATGGTATTCC
1 ATTGCTTGGTGAATGTATGAAGATGTATGGAGTAAATACTAAGAGATAATGAATGGTATTCC
*
40341799 ATTGCTTGGTGAATGTATGAAGATGTATGGAGTAAATACTAGGAGATAATGAATGGT
1 ATTGCTTGGTGAATGTATGAAGATGTATGGAGTAAATACTAAGAGATAATGAATGGT
40341856 TTAATAACCT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (62 bp):
ATTGCTTGGTGAATGTATGAAGATGTATGGAGTAAATACTAAGAGATAATGAATGGTATTCC
Found at i:40343630 original size:50 final size:50
Alignment explanation
Indices: 40343518--40343648 Score: 169
Period size: 50 Copynumber: 2.6 Consensus size: 50
40343508 GTTATGATGC
* *
40343518 CGATGCCATGTCCCAGACATGGTCTTACACT-GACTATTGAAATCGAGGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGACTACTCAAATCGAGGT
* * * *
40343567 CGACGCCATGTCCCAAACATGGTCTTACACTAG-CT-CTCACATATCTATGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGACTACTCA-A-ATCGAGGT
40343617 CGATGCCATGTCCCAGACATGGTCTTACACTA
1 CGATGCCATGTCCCAGACATGGTCTTACACTA
40343649 ACACCTCTAT
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
48 2 0.03
49 32 0.45
50 37 0.52
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (50 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGACTACTCAAATCGAGGT
Found at i:40343685 original size:48 final size:50
Alignment explanation
Indices: 40343577--40343693 Score: 132
Period size: 48 Copynumber: 2.4 Consensus size: 50
40343567 CGACGCCATG
* * * **
40343577 TCCCAAACATGGTCTTACACTAGCTCTCACATATCTATGTCGATGCCATG
1 TCCCAAACATGGTCTTACACTAACCCTCACATATCTATGCCGATGCCACC
* * *
40343627 TCCCAGACATGGTCTTACACTAACACCTC-TATA-C-GTGCCGATGCCACC
1 TCCCAAACATGGTCTTACACTAAC-CCTCACATATCTATGCCGATGCCACC
40343675 TCCCAAACATGGTCTTACA
1 TCCCAAACATGGTCTTACA
40343694 TTGACACATC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
48 28 0.49
49 1 0.02
50 25 0.44
51 3 0.05
ACGTcount: A:0.26, C:0.33, G:0.14, T:0.26
Consensus pattern (50 bp):
TCCCAAACATGGTCTTACACTAACCCTCACATATCTATGCCGATGCCACC
Found at i:40348871 original size:40 final size:40
Alignment explanation
Indices: 40348827--40349008 Score: 249
Period size: 40 Copynumber: 4.6 Consensus size: 40
40348817 GCCACTAGCT
* * * *
40348827 CAAATGCCTTCGGGACTTTGCCCAGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCAGATATAATAACTCGCA
*
40348867 CAAATGCCTTCGGGACTTAGCCC-GGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCAGATATAATAACTCGCA
* * *
40348906 CAAATGCCTTCGGGACTTAGCCCGGACATAATAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCAGATATAATAACTCGCA
* * *
40348946 CAAACGCCTTCGGGACTTAGCCCAGATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCAGATATAATAACTCGCA
*
40348986 CGAATGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
40349009 GAAATTAGCC
Statistics
Matches: 128, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
39 36 0.28
40 92 0.72
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCAGATATAATAACTCGCA
Found at i:40348947 original size:79 final size:80
Alignment explanation
Indices: 40348827--40349009 Score: 251
Period size: 79 Copynumber: 2.3 Consensus size: 80
40348817 GCCACTAGCT
* * ** * * *
40348827 CAAATGCCTTCGGGACTTTGCCCAGTTATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCC-G
1 CAAATGCCTTCGGGACTTAGCCCGGACATAATAACTCGCACAAACGCCTTCGGGACTTAGCCCAG
*
40348891 GTATAATAACTCGCA
66 ATATAATAACTCGCA
*
40348906 CAAATGCCTTCGGGACTTAGCCCGGACATAATAGCTCGCACAAACGCCTTCGGGACTTAGCCCAG
1 CAAATGCCTTCGGGACTTAGCCCGGACATAATAACTCGCACAAACGCCTTCGGGACTTAGCCCAG
* *
40348971 ATATAGTAGCTCGCA
66 ATATAATAACTCGCA
*
40348986 CGAATGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
40349010 AAATTAGCCA
Statistics
Matches: 91, Mismatches: 12, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
79 55 0.60
80 36 0.40
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGACATAATAACTCGCACAAACGCCTTCGGGACTTAGCCCAG
ATATAATAACTCGCA
Found at i:40349032 original size:40 final size:39
Alignment explanation
Indices: 40348827--40349049 Score: 191
Period size: 40 Copynumber: 5.6 Consensus size: 39
40348817 GCCACTAGCT
* ** *
40348827 CAAATGCCTTCGGGACTTTGCCC-AGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGAAAT-TAG-AACTCGCA
** * *
40348867 CAAATGCCTTCGGGACTTAGCCCGGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGAAATTAGAACTCGCA
* * * *
40348906 CAAATGCCTTCGGGACTTAGCCCGGACATAATAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GAAATTAGAACTCGCA
* * *
40348946 CAAACGCCTTCGGGACTTAGCCC-AGATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGAAAT-TAG-AACTCGCA
* * * *
40348986 CGAATGCCTTCGGGACTTAGCCCGAAATTAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGAAATTAG-AACTCGCA
40349026 CAAATG-CTCTCGGGACTTAGCCCG
1 CAAATGCCT-TCGGGACTTAGCCCG
40349050 GTTATCATCC
Statistics
Matches: 154, Mismatches: 23, Indels: 12
0.81 0.12 0.06
Matches are distributed among these distances:
38 3 0.02
39 33 0.21
40 114 0.74
41 4 0.03
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGAAATTAGAACTCGCA
Found at i:40354722 original size:48 final size:47
Alignment explanation
Indices: 40354507--40354868 Score: 237
Period size: 48 Copynumber: 7.6 Consensus size: 47
40354497 TATGATGCTA
* * * *
40354507 ATGCCATGTCCCAGGCATGGTCTTACACTGGCTC-ATCCATCAAGT--CG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACACTAT--AT-ACGTGCCG
* * * * * *
40354554 ATGCCATGTCCCAAATATGGTCTTACATTGACTATCAAAATTGA-G-GCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTGAC-A-CTATA-T-ACGTGCCG
* * * * *
40354603 ATGCTATGTCCCAGACATGGTCTTACAC-CAGCTCTCACATATTCGTGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGA-CACT---ATATACGTGCCG
40354653 ATGCCATGTCCCAGACATGGTCTTACACTGACAGCTATATACGTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACA-CTATATACGTGCCG
* * * *
40354701 ATGCCATGTCCTAGACATGGTCTTACACTGAAACCTTTATACGTGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGACA-CTATATACGTGCCG
* * * *
40354749 ATGCCGTGTCCCAGACATGGTCTTACATTGACAC-GTCT-CGTAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACACTATATACGT-GCCG
* * *
40354795 ATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATA-ATGTGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACACT-ATATACGT-GCCG
* *
40354841 AT-ACATGTCCCAGACAT-ATCTTACACTG
1 ATGCCATGTCCCAGACATGGTCTTACACTG
40354869 GCATACATAT
Statistics
Matches: 250, Mismatches: 46, Indels: 39
0.75 0.14 0.12
Matches are distributed among these distances:
44 12 0.05
45 16 0.06
46 41 0.16
47 29 0.12
48 85 0.34
49 31 0.12
50 33 0.13
51 3 0.01
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (47 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGACACTATATACGTGCCG
Found at i:40356924 original size:30 final size:30
Alignment explanation
Indices: 40356842--40356929 Score: 131
Period size: 30 Copynumber: 2.9 Consensus size: 30
40356832 TATGGCCATG
* * *
40356842 ACACACGGGCGTGTGGCTTGCCCATGCGTC
1 ACACACGGGCGTGTGGCTTACCCGTGTGTC
*
40356872 ACACACGGGCGTGTGGCCTACCCGTGTGTC
1 ACACACGGGCGTGTGGCTTACCCGTGTGTC
*
40356902 ACACACGGGCGTGTGGTTTACCCGTGTG
1 ACACACGGGCGTGTGGCTTACCCGTGTG
40356930 AAAATACTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.14, C:0.31, G:0.34, T:0.22
Consensus pattern (30 bp):
ACACACGGGCGTGTGGCTTACCCGTGTGTC
Found at i:40358337 original size:52 final size:51
Alignment explanation
Indices: 40358208--40358339 Score: 185
Period size: 50 Copynumber: 2.6 Consensus size: 51
40358198 ATGTGTTCTG
* * * *
40358208 CATTTAATAAAGTCACGCATTATGTAACTCTCATGTTAGTTAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTTAAGTTTGCAT
* *
40358259 CA-TAAATTATGACATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTT-AAGTTTGCAT
*
40358310 CATTAAATTAAGTCATGCATTAAGTAACTC
1 CATTAAATTAAGTCATGCATTATGTAACTC
40358340 ATTTGTGCAT
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
50 32 0.46
51 14 0.20
52 24 0.34
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (51 bp):
CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTTAAGTTTGCAT
Found at i:40359923 original size:52 final size:52
Alignment explanation
Indices: 40359859--40359990 Score: 189
Period size: 50 Copynumber: 2.6 Consensus size: 52
40359849 ATCAAAAAAT
*
40359859 GAGTTACTTAATGCATGACTTAATTTAATGATGCAAACTTTAACTAACATG-G
1 GAGTTACATAATGCATGACTTAATTTAATGATGCAAAC-TTAACTAACATGAG
* *
40359911 GAGTTACATAATGCATGTCATAATTT-ATGATGCAAACTTAACTAACATGAG
1 GAGTTACATAATGCATGACTTAATTTAATGATGCAAACTTAACTAACATGAG
* *
40359962 G-GTTACATAATGCATGACTTTATTAAATG
1 GAGTTACATAATGCATGACTTAATTTAATG
40359991 CAGAACAAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
50 32 0.45
51 16 0.23
52 23 0.32
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (52 bp):
GAGTTACATAATGCATGACTTAATTTAATGATGCAAACTTAACTAACATGAG
Found at i:40364406 original size:20 final size:20
Alignment explanation
Indices: 40364383--40364433 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
40364373 AATTTGAAAA
40364383 AAAAAAGAAATTTGAAGTTG
1 AAAAAAGAAATTTGAAGTTG
*
40364403 AAAAAAGAATTTTGAAGTTG
1 AAAAAAGAAATTTGAAGTTG
40364423 AAAAAA-AAATT
1 AAAAAAGAAATT
40364434 GAAAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (20 bp):
AAAAAAGAAATTTGAAGTTG
Found at i:40365349 original size:13 final size:14
Alignment explanation
Indices: 40365313--40365358 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
40365303 TTGAGAGAAA
* *
40365313 AAGAAAAGAAATTG
1 AAGAAAAAAAAATG
*
40365327 AAGAAGAAAAAAT-
1 AAGAAAAAAAAATG
40365340 AAG-AAAAAAAATG
1 AAGAAAAAAAAATG
40365353 AAGAAA
1 AAGAAA
40365359 GAGAGAGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 8 0.31
13 6 0.23
14 12 0.46
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (14 bp):
AAGAAAAAAAAATG
Found at i:40367301 original size:50 final size:52
Alignment explanation
Indices: 40367245--40367363 Score: 172
Period size: 50 Copynumber: 2.3 Consensus size: 52
40367235 TTAATAAATT
* *
40367245 CATGCATTATGTAACTCTCATGTTAGTT-AAGTTTGCATCA-TAAATTATA-A
1 CATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGCACCATTAAATTA-AGA
*
40367295 CATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGCACCATTAAATTAAGT
1 CATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGCACCATTAAATTAAGA
*
40367347 CATGCATTAAGTAACTC
1 CATGCATTATGTAACTC
40367364 ATTTGTTCAT
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
50 27 0.44
51 12 0.19
52 23 0.37
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.37
Consensus pattern (52 bp):
CATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGCACCATTAAATTAAGA
Found at i:40387317 original size:16 final size:17
Alignment explanation
Indices: 40387296--40387363 Score: 68
Period size: 16 Copynumber: 4.0 Consensus size: 17
40387286 ACAATTAAAC
40387296 AACATT-TAACATACAT
1 AACATTCTAACATACAT
* * *
40387312 AACATTCTTACAATTAAAC
1 AACATTCTAAC-A-TACAT
40387331 AACATT-TAACATACAT
1 AACATTCTAACATACAT
*
40387347 AACATTCTTACATACAT
1 AACATTCTAACATACAT
40387364 TCATCATTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
16 15 0.37
17 13 0.32
18 4 0.10
19 9 0.22
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (17 bp):
AACATTCTAACATACAT
Found at i:40387332 original size:35 final size:35
Alignment explanation
Indices: 40387286--40387358 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
40387276 GACTTACAAA
40387286 ACAATTAAACAACATTTAACATACATAACATTCTT
1 ACAATTAAACAACATTTAACATACATAACATTCTT
40387321 ACAATTAAACAACATTTAACATACATAACATTCTT
1 ACAATTAAACAACATTTAACATACATAACATTCTT
40387356 ACA
1 ACA
40387359 TACATTCATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (35 bp):
ACAATTAAACAACATTTAACATACATAACATTCTT
Found at i:40387334 original size:19 final size:18
Alignment explanation
Indices: 40387285--40387341 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 18
40387275 GGACTTACAA
40387285 AACAATTAAACAACATTT
1 AACAATTAAACAACATTT
* *
40387303 AAC-A-TACATAACATTCT
1 AACAATTAAACAACATT-T
*
40387320 TACAATTAAACAACATTT
1 AACAATTAAACAACATTT
40387338 AACA
1 AACA
40387342 TACATAACAT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
16 9 0.30
17 4 0.13
18 8 0.27
19 9 0.30
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (18 bp):
AACAATTAAACAACATTT
Found at i:40387361 original size:17 final size:17
Alignment explanation
Indices: 40387304--40387363 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
40387294 ACAACATTTA
40387304 ACATACATAACATTCTT
1 ACATACATAACATTCTT
* * *
40387321 ACAATTAAACAACATT-TA
1 AC-A-TACATAACATTCTT
40387339 ACATACATAACATTCTT
1 ACATACATAACATTCTT
40387356 ACATACAT
1 ACATACAT
40387364 TCATCATTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 9 0.26
17 12 0.35
18 4 0.12
19 9 0.26
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.32
Consensus pattern (17 bp):
ACATACATAACATTCTT
Found at i:40388792 original size:41 final size:42
Alignment explanation
Indices: 40388718--40388796 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
40388708 AATACTCGAT
*
40388718 ATCTCGCACACTAACTGCCAATACATAGCCGAAGCTATTATA
1 ATCTCGCACACTAACTGCCAATACATAGACGAAGCTATTATA
* * *
40388760 ATCTTGCACACTAAGTGCC-TTACATAGACGAAGCTAT
1 ATCTCGCACACTAACTGCCAATACATAGACGAAGCTAT
40388797 CTCGGTCTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
41 16 0.48
42 17 0.52
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (42 bp):
ATCTCGCACACTAACTGCCAATACATAGACGAAGCTATTATA
Found at i:40388862 original size:40 final size:40
Alignment explanation
Indices: 40388721--40388906 Score: 187
Period size: 40 Copynumber: 4.6 Consensus size: 40
40388711 ACTCGATATC
* * **
40388721 TCGCACACTAACTGCCAATACATAGCCGAAGCTATT-ATAA
1 TCGCACACTAAGTGCC-ATATATAGCCGAAGCTATTCCGAA
* * * * **
40388761 TCTTGCACACTAAGTGCCTTACATAGACGAAGCTATCTCGGTC
1 TC--GCACACTAAGTGCCATATATAGCCGAAGCTAT-TCCGAA
* *
40388804 TCGCACACTAAGTACCATATATAGCCGAAGTTATTCCGAA
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATTCCGAA
* *
40388844 TCGCACACTAAATGCCATATATAGCCAAAGCTA-TCTCGAA
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATTC-CGAA
40388884 TCGCACACTAAGTGCCATATATA
1 TCGCACACTAAGTGCCATATATA
40388907 TATCCGAATC
Statistics
Matches: 121, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
39 2 0.02
40 60 0.50
41 43 0.36
42 14 0.12
43 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.25
Consensus pattern (40 bp):
TCGCACACTAAGTGCCATATATAGCCGAAGCTATTCCGAA
Found at i:40388875 original size:81 final size:80
Alignment explanation
Indices: 40388719--40388906 Score: 216
Period size: 81 Copynumber: 2.3 Consensus size: 80
40388709 ATACTCGATA
* * * * *
40388719 TCTCGCACACTAACTGCCAATACATAGCCGAAGCTATTATAATCTTGCACACTAAGTGCCTTACA
1 TCTCGCACACTAAGTGCC-ATATATAGCCGAAGCTATTAGAATC-TGCACACTAAATGCCATACA
*
40388784 TAGACGAAGCTATCTCGG
64 TAGACAAAGCTATCTC-G
* * * *
40388802 TCTCGCACACTAAGTACCATATATAGCCGAAGTTATTCCGAATC-GCACACTAAATGCCATATAT
1 TCTCGCACACTAAGTGCCATATATAGCCGAAGCTATT-AGAATCTGCACACTAAATGCCATACAT
*
40388866 AGCCAAAGCTATCTCG
65 AGACAAAGCTATCTCG
**
40388882 AATCGCACACTAAGTGCCATATATA
1 TCTCGCACACTAAGTGCCATATATA
40388907 TATCCGAATC
Statistics
Matches: 90, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
80 23 0.26
81 30 0.33
82 17 0.19
83 20 0.22
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (80 bp):
TCTCGCACACTAAGTGCCATATATAGCCGAAGCTATTAGAATCTGCACACTAAATGCCATACATA
GACAAAGCTATCTCG
Found at i:40389142 original size:29 final size:30
Alignment explanation
Indices: 40389100--40389157 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 30
40389090 TATCTTGATT
40389100 TAAATATAAT-AAAAAATAACTTATTTATC
1 TAAATATAATAAAAAAATAACTTATTTATC
40389129 TAAATATAATAAAAAAAATAACTTATTTA
1 TAAATATAAT-AAAAAAATAACTTATTTA
40389158 ATCATCTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 10 0.37
31 17 0.63
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (30 bp):
TAAATATAATAAAAAAATAACTTATTTATC
Found at i:40392724 original size:37 final size:37
Alignment explanation
Indices: 40392682--40392756 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
40392672 CAAATCTAAC
*
40392682 ACAACTAACTCAAAAGAACAAGTATACTGAGTAGTAG
1 ACAACTAACTCAAAAGAACAAGAATACTGAGTAGTAG
40392719 ACAACTAACTCAAAAGAACAAGAATACTGAGTAGTAG
1 ACAACTAACTCAAAAGAACAAGAATACTGAGTAGTAG
40392756 A
1 A
40392757 AGCAGGAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.17
Consensus pattern (37 bp):
ACAACTAACTCAAAAGAACAAGAATACTGAGTAGTAG
Found at i:40393893 original size:57 final size:57
Alignment explanation
Indices: 40393791--40393904 Score: 138
Period size: 57 Copynumber: 2.0 Consensus size: 57
40393781 TTTTTGTTTT
** * * * * *
40393791 TGCCAAAATCTGATGACGGCACTTGAGGTGCCAATTGCGGCTAGTAACCACCGCCAC
1 TGCCAAAATCTGATGACGGCACTTGAGGCACAAACTACGACTAGTAACCACCACCAC
* * *
40393848 TGCCAAAATTTGATGACGGCACTTGAGGCACAAACTATGATTAGTAACCACCACCAC
1 TGCCAAAATCTGATGACGGCACTTGAGGCACAAACTACGACTAGTAACCACCACCAC
40393905 GCACTACACC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (57 bp):
TGCCAAAATCTGATGACGGCACTTGAGGCACAAACTACGACTAGTAACCACCACCAC
Found at i:40401504 original size:21 final size:22
Alignment explanation
Indices: 40401458--40401505 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
40401448 TAAATACACT
**
40401458 TTTAATTTTTTTCAGAATTATT
1 TTTAATTTTTTTCAGAATTACA
*
40401480 TTTAATTTTTTT-ATAATTACA
1 TTTAATTTTTTTCAGAATTACA
40401501 TTTAA
1 TTTAA
40401506 AATTAATATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTAATTTTTTTCAGAATTACA
Found at i:40403691 original size:2 final size:2
Alignment explanation
Indices: 40403680--40403739 Score: 77
Period size: 2 Copynumber: 30.5 Consensus size: 2
40403670 TCATTTCATT
* * *
40403680 TA TA -A TA TA TA TA TA TA CA TA TA TA TA TG TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
40403721 TA TG TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
40403740 GTGCATTTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:40403705 original size:16 final size:16
Alignment explanation
Indices: 40403684--40403741 Score: 98
Period size: 16 Copynumber: 3.6 Consensus size: 16
40403674 TTCATTTATA
*
40403684 ATATATATATATACAT
1 ATATATATGTATACAT
40403700 ATATATATGTATACAT
1 ATATATATGTATACAT
*
40403716 ATATATATGTATATAT
1 ATATATATGTATACAT
40403732 ATATATATGT
1 ATATATATGT
40403742 GCATTTTAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (16 bp):
ATATATATGTATACAT
Found at i:40403894 original size:2 final size:2
Alignment explanation
Indices: 40403883--40403952 Score: 70
Period size: 2 Copynumber: 35.5 Consensus size: 2
40403873 TCATTTCATT
* * * * *
40403883 TA TA -A TA TA TA TA TA CA TA TA TA TA TA TG TG TA TA TT TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
40403924 TA TA TA TA CA TA TA TA TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40403953 GTGCAGCCTC
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (2 bp):
TA
Found at i:40403939 original size:203 final size:201
Alignment explanation
Indices: 40403543--40403940 Score: 661
Period size: 203 Copynumber: 2.0 Consensus size: 201
40403533 CTTGGGCAAA
* *
40403543 ATTTTAAGCCTTTTTTAGGCCCGGCCCGGCCCGAGCCCAATAAATGGGCCTAAATTTTTAGTTGA
1 ATTTTAAGCCTTTTTTAGGCCCGGCCCGGCCCGAGCCCAATAAATGAGCCTAAATTTTTAATTGA
*
40403608 GCTCGACCCGAACCCGGCCCGACCCGGCCTATGATCACCTCTATTAACAAGAAGATGTAAAATCA
66 GCTCGACCCGAACCCGGCCCGACCCGACCTATGATCACCTCTATTAACAAGAAGATGTAAAATCA
* * *
40403673 TTTCATTTATAATATATATATATACATATATATATGTATACATATATATATGTATATATATATAT
131 TTTCATTTATAATATATATATACACATATATATATGTATACATATATATATATATACATATATAT
40403738 ATGTGC
196 ATGTGC
*
40403744 ATTTTAAGCCTATTTTTTAGGCCCGGCCCGGCCCGAGCTCAATAAATGAGCCTAAATTTTTAATT
1 ATTTTAAGCC--TTTTTTAGGCCCGGCCCGGCCCGAGCCCAATAAATGAGCCTAAATTTTTAATT
*
40403809 GAGCTCGACCCGAACCCGGCCCGACCCGACTTATGATCACCTCTATTAACAAGAAGATGTAAAAT
64 GAGCTCGACCCGAACCCGGCCCGACCCGACCTATGATCACCTCTATTAACAAGAAGATGTAAAAT
* * * * *
40403874 CATTTCATTTATAATATATATATACATATATATATATGTGTATATTTATGTATATATACATATAT
129 CATTTCATTTATAATATATATATACACATATATATATGTATACATATATATATATATACATATAT
40403939 AT
194 AT
40403941 GTATATATAT
Statistics
Matches: 182, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
201 10 0.05
203 172 0.95
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.33
Consensus pattern (201 bp):
ATTTTAAGCCTTTTTTAGGCCCGGCCCGGCCCGAGCCCAATAAATGAGCCTAAATTTTTAATTGA
GCTCGACCCGAACCCGGCCCGACCCGACCTATGATCACCTCTATTAACAAGAAGATGTAAAATCA
TTTCATTTATAATATATATATACACATATATATATGTATACATATATATATATATACATATATAT
ATGTGC
Found at i:40405728 original size:52 final size:52
Alignment explanation
Indices: 40405663--40405769 Score: 214
Period size: 52 Copynumber: 2.1 Consensus size: 52
40405653 TGTGTCATTG
40405663 TATTTAATTACTCTTTAGAGTTATTCATCTTTTCCCATTAATATATAAAATA
1 TATTTAATTACTCTTTAGAGTTATTCATCTTTTCCCATTAATATATAAAATA
40405715 TATTTAATTACTCTTTAGAGTTATTCATCTTTTCCCATTAATATATAAAATA
1 TATTTAATTACTCTTTAGAGTTATTCATCTTTTCCCATTAATATATAAAATA
40405767 TAT
1 TAT
40405770 AATGAAAATG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.35, C:0.13, G:0.04, T:0.49
Consensus pattern (52 bp):
TATTTAATTACTCTTTAGAGTTATTCATCTTTTCCCATTAATATATAAAATA
Found at i:40420137 original size:13 final size:13
Alignment explanation
Indices: 40420119--40420144 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40420109 TTTGGAAGAA
40420119 ACTTCACAAAGCT
1 ACTTCACAAAGCT
40420132 ACTTCACAAAGCT
1 ACTTCACAAAGCT
40420145 CTGGGTTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (13 bp):
ACTTCACAAAGCT
Found at i:40433377 original size:597 final size:583
Alignment explanation
Indices: 40432237--40433422 Score: 1436
Period size: 597 Copynumber: 2.0 Consensus size: 583
40432227 CTGACCGCCT
* * * *
40432237 ATAAATGTGTTATCGTTTATAGTATAAGTAGCTCACCAAAAATATATAAAATTAAATCGACGGTT
1 ATAAATGTGTTATCGTTTATAGTATAAATAGCACACAAAAAATATATAAAATTAAATCGACGGTG
** **
40432302 TCCGCAAGCGTACAGGTCAAATTGTAATATAATATGTGTTACAACGGAACACCGGTAAGTATTCA
66 TCCGCAAGCGTACAGGAAAAATTGTAATATAATATGTGTTACAACGGAACACCAATAAGTATTCA
* *
40432367 GAGGATCGTACTCAAGAGAATGTAGATTAAAGAAATTAATGTTATATTAATTACAAACAATAATT
131 GAGGATCGTACTCAAGAGAATGTAGATTAAAGAAATTAATATTAAATTAATTACAAACAATAATT
*
40432432 AATATACTACTCGAGTCACAATTTAGTAGTGTGAATCCAAATTAATAATTTAATTAAACGAATTA
196 AATATACTACTCGAGTCACAAATTAGTAGTGTGAATCCAAATTAAT-ATTTAATTAAACGAATTA
* * * *
40432497 AATTAACTATCTTAAATTAATCTAATGGACTTTCCTATTTCTAGTGCTGACAACATGACTCTTTA
260 AATTAACTATCCTAAATTAACCTAATGGACTTTCCTATTCCTAGTGCTAACAACATGACTCTTTA
* *
40432562 ATTGATTAAATCCCTAATTATCTAATTAAATAATTAATTATCCTAAATTAAGTTCTTTATCACCC
325 ATCGATTAAATCCCTAATTATCTAATTAAATAATTAATTATCCTAAATTAAGTTATTTATCACCC
* * * * *
40432627 TTAGACTACCCTCCCGATTCATCTTTACTAAAGATTACCACCTAAGTCACCCTTCCGGTCTTTTC
390 TTAGACTACCCTCCCGATTCATCTTCACTAAAGATTACCACCAAAGGCACCCTTCCGATCTCTTC
* * *
40432692 CTAGGCATACGGATACCCTTCTGGTCTCACCACATGGCACAAGTTATACACCATAGGATACCTTT
455 CTAGGCATACGGATACCCTTCTGGTCTCACCACATAGCACAAGTTATACACCACAGGATACCCTT
* * * * * *
40432757 TCAGTCTCACTTGTCTTGATATTCTATCAGGGGCGTCACTATCTAATATACTAAGTACTCTTGA
520 CCAGTCTCACCTATCTCGATATTCTATCAGGGGCATCACTATCTAATATACTAAGTACTATTGA
* **
40432821 ATAAATGTGTTATCGTTTATAGTATAAATAGCACACAAAAAATATATAAAATTAAATTGGTGGTG
1 ATAAATGTGTTATCGTTTATAGTATAAATAGCACACAAAAAATATATAAAATTAAATCGACGGTG
* * * * *
40432886 TCTGCAAGCGTACAGGAAAAATTGTAATATAGTATTTTGTTACAATGGATA-ACTAATAAGTATT
66 TCCGCAAGCGTACAGGAAAAATTGTAATATAATA-TGTGTTACAACGGA-ACACCAATAAGTATT
* * * * *
40432950 CTGAGGATCGTA-TCCGAAGGGATTGCT-GATTAGAGAAATTAATATTAAATTAATTAGAGAA-A
129 CAGAGGATCGTACT-C-AAGAGAATG-TAGATTAAAGAAATTAATATTAAATTAATTACA-AACA
* * * *
40433012 ATAATTACTA-ATCTAGTTGAGTCACAAATTAGTGGTGTGAATCCAAATTAAT-TTTCAATTAAA
190 ATAATTAATATA-CTACTCGAGTCACAAATTAGTAGTGTGAATCCAAATTAATATTT-AATTAAA
* * **
40433075 CTAATTAGATTAACTATCCTAAATTAACCTAATGGACTTTCCTATTCCTAGTG-TCAACAATGTG
253 CGAATTAAATTAACTATCCTAAATTAACCTAATGGACTTTCCTATTCCTAGTGCT-AACAACATG
* * *
40433139 AGCCTCTAGCCTATGATCGATTGAATCCCTAATTATCTAATTAAATAATTAATTATCCTAAATTG
317 A--CTCT----T-TAATCGATTAAATCCCTAATTATCTAATTAAATAATTAATTATCCTAAATTA
* * *** * * *
40433204 AGTTATTTATCATCCTTAGTTAAGACTGCCCTTTTGGTTCATCTTCGCTAAGGATTACCACCAAA
375 AGTTATTTATCA-CC---CTT-AGACTACCCTCCCGATTCATCTTCACTAAAGATTACCACCAAA
** * ** *
40433269 GGCACCCTTTTGATCTCTTCCTAGGCATACGGATACCCTT-TCGGTCTCACTATTTAGCACATGT
435 GGCACCCTTCCGATCTCTTCCTAGGCATACGGATACCCTTCT-GGTCTCACCACATAGCACAAGT
** *
40433333 TATACATGACAGGATACCCTTCC-GATCTCACCTATCTCGATATTCTATTAGGGGCATCACTATC
499 TATACACCACAGGATACCCTTCCAG-TCTCACCTATCTCGATATTCTATCAGGGGCATCACTATC
*
40433397 TAATATACTAAGTATTATTGA
563 TAATATACTAAGTACTATTGA
40433418 ATAAA
1 ATAAA
40433423 CAACCAGTTT
Statistics
Matches: 506, Mismatches: 73, Indels: 33
0.83 0.12 0.05
Matches are distributed among these distances:
584 93 0.18
585 97 0.19
586 81 0.16
587 7 0.01
591 1 0.00
592 59 0.12
593 2 0.00
596 4 0.01
597 162 0.32
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (583 bp):
ATAAATGTGTTATCGTTTATAGTATAAATAGCACACAAAAAATATATAAAATTAAATCGACGGTG
TCCGCAAGCGTACAGGAAAAATTGTAATATAATATGTGTTACAACGGAACACCAATAAGTATTCA
GAGGATCGTACTCAAGAGAATGTAGATTAAAGAAATTAATATTAAATTAATTACAAACAATAATT
AATATACTACTCGAGTCACAAATTAGTAGTGTGAATCCAAATTAATATTTAATTAAACGAATTAA
ATTAACTATCCTAAATTAACCTAATGGACTTTCCTATTCCTAGTGCTAACAACATGACTCTTTAA
TCGATTAAATCCCTAATTATCTAATTAAATAATTAATTATCCTAAATTAAGTTATTTATCACCCT
TAGACTACCCTCCCGATTCATCTTCACTAAAGATTACCACCAAAGGCACCCTTCCGATCTCTTCC
TAGGCATACGGATACCCTTCTGGTCTCACCACATAGCACAAGTTATACACCACAGGATACCCTTC
CAGTCTCACCTATCTCGATATTCTATCAGGGGCATCACTATCTAATATACTAAGTACTATTGA
Found at i:40433742 original size:52 final size:52
Alignment explanation
Indices: 40433680--40433783 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
40433670 CATGAAAAGA
40433680 AAACTAAAAACTAAATAGTAAAACTATCTGTCTAGAATTGCTTATAATTTTG
1 AAACTAAAAACTAAATAGTAAAACTATCTGTCTAGAATTGCTTATAATTTTG
40433732 AAACTAAAAACTAAATAGTAAAACTATCTGTCTAGAATTGCTTATAATTTTG
1 AAACTAAAAACTAAATAGTAAAACTATCTGTCTAGAATTGCTTATAATTTTG
40433784 GTGACCTTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.35
Consensus pattern (52 bp):
AAACTAAAAACTAAATAGTAAAACTATCTGTCTAGAATTGCTTATAATTTTG
Found at i:40440737 original size:16 final size:16
Alignment explanation
Indices: 40440711--40440749 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
40440701 AACATTAATT
*
40440711 AATCTAATTAACCTAAA
1 AATC-AATTAAACTAAA
40440728 AATCAATTAAACTAAA
1 AATCAATTAAACTAAA
40440744 AATCAA
1 AATCAA
40440750 CCAATTAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (16 bp):
AATCAATTAAACTAAA
Found at i:40444122 original size:38 final size:38
Alignment explanation
Indices: 40444074--40444147 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
40444064 TGAGTTCGAA
**
40444074 TCCCTACGTTAGCAAGTGAATGTTATTTTTGGTTCGGT
1 TCCCTACGTTAGCAAAAGAATGTTATTTTTGGTTCGGT
*
40444112 TCCCTGCGTTAGCAAAAGAATGTTATTTTTGGTTCG
1 TCCCTACGTTAGCAAAAGAATGTTATTTTTGGTTCG
40444148 ATTATCAGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (38 bp):
TCCCTACGTTAGCAAAAGAATGTTATTTTTGGTTCGGT
Found at i:40444963 original size:13 final size:12
Alignment explanation
Indices: 40444946--40444983 Score: 58
Period size: 13 Copynumber: 3.0 Consensus size: 12
40444936 GGTGTGTCAG
40444946 CCCACACGGGCA
1 CCCACACGGGCA
40444958 CGCCACACGGGCAA
1 C-CCACACGGGC-A
40444972 CCCACACGGGCA
1 CCCACACGGGCA
40444984 TGTGGGCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.08
13 20 0.83
14 2 0.08
ACGTcount: A:0.26, C:0.47, G:0.26, T:0.00
Consensus pattern (12 bp):
CCCACACGGGCA
Found at i:40451956 original size:17 final size:17
Alignment explanation
Indices: 40451915--40451957 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
40451905 ACGAAGGCCA
*
40451915 GACCGTGCGCAAGACAC
1 GACCGTGTGCAAGACAC
40451932 GACCGTGTGCAAGACAC
1 GACCGTGTGCAAGACAC
40451949 GACCGTGTG
1 GACCGTGTG
40451958 AAAGCTAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.26, C:0.30, G:0.33, T:0.12
Consensus pattern (17 bp):
GACCGTGTGCAAGACAC
Found at i:40452597 original size:6 final size:6
Alignment explanation
Indices: 40452588--40452613 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
40452578 CTGATATGCA
40452588 TATCTG TATCTG TATCTG TATCTG TA
1 TATCTG TATCTG TATCTG TATCTG TA
40452614 ATGGTCTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.50
Consensus pattern (6 bp):
TATCTG
Found at i:40456887 original size:38 final size:38
Alignment explanation
Indices: 40456843--40456917 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
40456833 GAAATAGAAG
* *
40456843 TAAATAACATTAATATGAGTATTATGAAATACAGTATA
1 TAAATAAAATTAATATGAGTATTATCAAATACAGTATA
40456881 TAAATAAAATTAATATGAGTATTATCAAATACAGTAT
1 TAAATAAAATTAATATGAGTATTATCAAATACAGTAT
40456918 GTATGATCTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (38 bp):
TAAATAAAATTAATATGAGTATTATCAAATACAGTATA
Found at i:40457786 original size:29 final size:30
Alignment explanation
Indices: 40457744--40457804 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 30
40457734 ATACTAAGTA
40457744 AAAACGGTTACGATGATTTGCGAAT-AATG
1 AAAACGGTTACGATGATTTGCGAATAAATG
40457773 AAAACGGTTACGATGATTTGCGAATAAATG
1 AAAACGGTTACGATGATTTGCGAATAAATG
40457803 AA
1 AA
40457805 GAAGCTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (30 bp):
AAAACGGTTACGATGATTTGCGAATAAATG
Found at i:40458096 original size:47 final size:47
Alignment explanation
Indices: 40458027--40458120 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
40458017 ATGGAAAACC
*
40458027 AATATTACTAAGCAAAGAGCAAACTTTAAAAAAGCTCTTACTAAGCT
1 AATATTACTAAGCAAAGAGCAAACTTTAAAAAAGCTCATACTAAGCT
40458074 AATATTACTAAGCAAAGAGCAAACTTTAAAAAAGCTCATACTAAGCT
1 AATATTACTAAGCAAAGAGCAAACTTTAAAAAAGCTCATACTAAGCT
40458121 TTCACAATTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.24
Consensus pattern (47 bp):
AATATTACTAAGCAAAGAGCAAACTTTAAAAAAGCTCATACTAAGCT
Found at i:40459157 original size:43 final size:45
Alignment explanation
Indices: 40459072--40459159 Score: 126
Period size: 47 Copynumber: 2.0 Consensus size: 45
40459062 AAAAAACGCT
*
40459072 ACCAAGAAACAAAAAATAAAAGAGGAAGCAATGTGGAAGCAACCATA
1 ACCAAGAAACAAAAAATAAAAGAAGAAG--ATGTGGAAGCAACCATA
*
40459119 ACCAAGAAACAACAAA-AAAAGAAGAAG-TGTGGAAGCAACCA
1 ACCAAGAAACAAAAAATAAAAGAAGAAGATGTGGAAGCAACCA
40459160 CAACTGGACA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
43 14 0.36
46 10 0.26
47 15 0.38
ACGTcount: A:0.58, C:0.16, G:0.19, T:0.07
Consensus pattern (45 bp):
ACCAAGAAACAAAAAATAAAAGAAGAAGATGTGGAAGCAACCATA
Found at i:40460101 original size:26 final size:26
Alignment explanation
Indices: 40460068--40460120 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
40460058 AAGTTTACAT
40460068 AAAAAATATGTCTTTCAATCTTATAA
1 AAAAAATATGTCTTTCAATCTTATAA
40460094 AAAAAATATGTCTTTCAATCTTATAA
1 AAAAAATATGTCTTTCAATCTTATAA
40460120 A
1 A
40460121 TAACTTATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (26 bp):
AAAAAATATGTCTTTCAATCTTATAA
Found at i:40461555 original size:80 final size:78
Alignment explanation
Indices: 40461417--40461574 Score: 237
Period size: 80 Copynumber: 2.0 Consensus size: 78
40461407 TGGGCGAAAG
*
40461417 TAAAATGCTTGGCCCTTATAAAATAGAGTAATGACACTTTTAACCCTTCAATAATTAATAATTTA
1 TAAAATGCTTGCCCCTTATAAAATAGAGTAATGACACTTTTAACCCTTCAATAATTAATAATTTA
40461482 ATTTAATTTGCAAT
66 ATTTAATTT-CAAT
** *
40461496 TAAAAGTGCTTGCCCCTTATAAAATAGAGTAATGGTACTTTTAATCC-TCTAATAATTAATAATT
1 TAAAA-TGCTTGCCCCTTATAAAATAGAGTAATGACACTTTTAACCCTTC-AATAATTAATAATT
*
40461560 TAATTTGATTTCAAT
64 TAATTTAATTTCAAT
40461575 CTAACTCTTA
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
79 11 0.15
80 61 0.85
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.39
Consensus pattern (78 bp):
TAAAATGCTTGCCCCTTATAAAATAGAGTAATGACACTTTTAACCCTTCAATAATTAATAATTTA
ATTTAATTTCAAT
Found at i:40462315 original size:3 final size:3
Alignment explanation
Indices: 40462305--40462333 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
40462295 TTCACTTTTT
40462305 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40462334 ACTAAACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:40463913 original size:12 final size:12
Alignment explanation
Indices: 40463896--40463927 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
40463886 AAAGACTTCA
40463896 GAAGCCTTGGTT
1 GAAGCCTTGGTT
40463908 GAAGCCTTGGTT
1 GAAGCCTTGGTT
40463920 GAAGCCTT
1 GAAGCCTT
40463928 AAATTTGGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (12 bp):
GAAGCCTTGGTT
Found at i:40469623 original size:18 final size:18
Alignment explanation
Indices: 40469587--40469620 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40469577 TTTACACAAT
*
40469587 AAAAACAATTTCAAATTA
1 AAAAAAAATTTCAAATTA
40469605 AAAAAAAATTT-AAATT
1 AAAAAAAATTTCAAATT
40469621 TAACATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAAAAATTTCAAATTA
Found at i:40475078 original size:34 final size:34
Alignment explanation
Indices: 40475040--40475107 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
40475030 GAAGAAAATG
*
40475040 AAAGAAAAAAGGGTGTAATATATTAAAAGTTTAA
1 AAAGAAAAAAGGGTATAATATATTAAAAGTTTAA
*
40475074 AAAGAAAAAAGGGTATAATATCTTAAAAGTTTAA
1 AAAGAAAAAAGGGTATAATATATTAAAAGTTTAA
40475108 CACTTTGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.56, C:0.01, G:0.16, T:0.26
Consensus pattern (34 bp):
AAAGAAAAAAGGGTATAATATATTAAAAGTTTAA
Found at i:40482846 original size:28 final size:28
Alignment explanation
Indices: 40482806--40482861 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
40482796 CCACATTGGG
40482806 GTCACCGATATTTGCAAGCTAGGTTCCT
1 GTCACCGATATTTGCAAGCTAGGTTCCT
40482834 GTCACCGATATTTGCAAGCTAGGTTCCT
1 GTCACCGATATTTGCAAGCTAGGTTCCT
40482862 TCTTGGTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.32
Consensus pattern (28 bp):
GTCACCGATATTTGCAAGCTAGGTTCCT
Found at i:40484824 original size:22 final size:23
Alignment explanation
Indices: 40484790--40484834 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
40484780 ATCTTCCGCC
40484790 TATTAAAGAAAAAAAT-ACAAAA
1 TATTAAAGAAAAAAATAACAAAA
** *
40484812 TATTAAATTAAAATATAACAAAA
1 TATTAAAGAAAAAAATAACAAAA
40484835 AAAACTATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.24
Consensus pattern (23 bp):
TATTAAAGAAAAAAATAACAAAA
Found at i:40485794 original size:26 final size:26
Alignment explanation
Indices: 40485745--40485795 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
40485735 GGCGCAACTC
* *
40485745 TTTTTTATATTAAAATATATTTTTTG
1 TTTTTTATAATAAAATATAATTTTTG
40485771 TTTTTTA-AATAAAATATTAATTTTT
1 TTTTTTATAATAAAATA-TAATTTTT
40485796 TATATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTTTTATAATAAAATATAATTTTTG
Found at i:40486432 original size:21 final size:21
Alignment explanation
Indices: 40486395--40486434 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
40486385 TGACAAATGC
*
40486395 TTTTATTAAAATTATTTAAAA
1 TTTTATTAAAATAATTTAAAA
40486416 TTTTAATTAAAA-AATTTAA
1 TTTT-ATTAAAATAATTTAA
40486435 TACCCACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTATTAAAATAATTTAAAA
Found at i:40487012 original size:15 final size:15
Alignment explanation
Indices: 40486965--40487015 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
40486955 TTTGCTCTTA
40486965 TTATATTTTAATTAT
1 TTATATTTTAATTAT
*
40486980 TTAT-TTTTGAAATA-
1 TTATATTTT-AATTAT
40486994 TTATATTTTAATTAT
1 TTATATTTTAATTAT
40487009 TTATATT
1 TTATATT
40487016 ATTATTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 12 0.39
15 19 0.61
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
TTATATTTTAATTAT
Found at i:40487014 original size:20 final size:20
Alignment explanation
Indices: 40486991--40487028 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40486981 TATTTTTGAA
40486991 ATATTA-TATTTTAATTATTT
1 ATATTATTATTTT-ATTATTT
40487011 ATATTATTATTTTATTAT
1 ATATTATTATTTTATTAT
40487029 AAAATGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATATTATTATTTTATTATTT
Found at i:40487165 original size:34 final size:34
Alignment explanation
Indices: 40487127--40487196 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
40487117 ATGTGATGAG
40487127 AATAAATTTTTAATAAAATAAATTTAATTAATTA
1 AATAAATTTTTAATAAAATAAATTTAATTAATTA
* * *
40487161 AATAAATTTTTAGTGAAATAAGTTTAATTAATTA
1 AATAAATTTTTAATAAAATAAATTTAATTAATTA
40487195 AA
1 AA
40487197 AATTTTAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (34 bp):
AATAAATTTTTAATAAAATAAATTTAATTAATTA
Found at i:40487181 original size:16 final size:16
Alignment explanation
Indices: 40487127--40487172 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 16
40487117 ATGTGATGAG
40487127 AATAAATTTTTAATAA
1 AATAAATTTTTAATAA
*
40487143 AATAAATTTAATTAATTA
1 AATAAATTT--TTAATAA
40487161 AATAAATTTTTA
1 AATAAATTTTTA
40487173 GTGAAATAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 12 0.44
18 15 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AATAAATTTTTAATAA
Found at i:40490852 original size:58 final size:58
Alignment explanation
Indices: 40490779--40490898 Score: 188
Period size: 58 Copynumber: 2.1 Consensus size: 58
40490769 ATAATACGCA
40490779 GTAGGGCTAGCGTATATGCAGTACAGTGCAATG-TGGTAGTCCATTGTACAGATAAGTT
1 GTAGGGCTAGCGTATATGCAGTACAGTGCAATGCT-GTAGTCCATTGTACAGATAAGTT
* * **
40490837 GTAGGGCTAGTGTATATGTAGTACAGTGCAATGCTGTAGTCTGTTGTACAGATAAGTT
1 GTAGGGCTAGCGTATATGCAGTACAGTGCAATGCTGTAGTCCATTGTACAGATAAGTT
40490895 GTAG
1 GTAG
40490899 TTTAAACTAC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
58 56 0.98
59 1 0.02
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.32
Consensus pattern (58 bp):
GTAGGGCTAGCGTATATGCAGTACAGTGCAATGCTGTAGTCCATTGTACAGATAAGTT
Found at i:40496484 original size:22 final size:22
Alignment explanation
Indices: 40496459--40496500 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
40496449 CCATTTTTTA
40496459 AAAAGAAAAGAAAAAAGAAAGC
1 AAAAGAAAAGAAAAAAGAAAGC
**
40496481 AAAAGAAAAGCCAAAAGAAA
1 AAAAGAAAAGAAAAAAGAAA
40496501 AGGGAAGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAAGAAAAGAAAAAAGAAAGC
Found at i:40499303 original size:21 final size:21
Alignment explanation
Indices: 40499264--40499303 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
40499254 ACTCACACGT
** *
40499264 TCGTGTGTCCACCAGACACTA
1 TCGTGTGTCCAAAACACACTA
40499285 TCGTGTGTCCAAAACACAC
1 TCGTGTGTCCAAAACACAC
40499304 GCCCGTGAGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.23
Consensus pattern (21 bp):
TCGTGTGTCCAAAACACACTA
Found at i:40500825 original size:12 final size:12
Alignment explanation
Indices: 40500808--40500837 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
40500798 ATTTCAAACG
40500808 AAAATTTTAGCT
1 AAAATTTTAGCT
40500820 AAAATTTTAGCT
1 AAAATTTTAGCT
*
40500832 TAAATT
1 AAAATT
40500838 CTACAATCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (12 bp):
AAAATTTTAGCT
Found at i:40503696 original size:28 final size:28
Alignment explanation
Indices: 40503656--40503710 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
40503646 TAAACACATC
*
40503656 TGAAAAGGAATGCCTTTGTGGCAATATA
1 TGAAAAGAAATGCCTTTGTGGCAATATA
40503684 TGAAAAGAAATGCCTTTGTGGCAATAT
1 TGAAAAGAAATGCCTTTGTGGCAATAT
40503711 GTAGAAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (28 bp):
TGAAAAGAAATGCCTTTGTGGCAATATA
Found at i:40503718 original size:28 final size:27
Alignment explanation
Indices: 40503656--40503728 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 27
40503646 TAAACACATC
40503656 TGAAAAGGAATGCCTTTGTGGCAATATA
1 TGAAAA-GAATGCCTTTGTGGCAATATA
*
40503684 TGAAAAGAAATGCCTTTGTGGCAATATG
1 TGAAAAG-AATGCCTTTGTGGCAATATA
*
40503712 T-AGAAAGAATGACTTTG
1 TGA-AAAGAATGCCTTTG
40503729 CGGAAAACTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
27 11 0.27
28 30 0.73
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.29
Consensus pattern (27 bp):
TGAAAAGAATGCCTTTGTGGCAATATA
Found at i:40506560 original size:46 final size:46
Alignment explanation
Indices: 40506485--40506578 Score: 143
Period size: 46 Copynumber: 2.0 Consensus size: 46
40506475 CTTTTTCTTG
40506485 AAAGAATTTATATATAAATTCATAGGGTAAACTATTGCAAGGTATT
1 AAAGAATTTATATATAAATTCATAGGGTAAACTATTGCAAGGTATT
* * * * *
40506531 AAAGGATTTATATCTAAATTTATATGGTAAACTATTGTAAGGTATT
1 AAAGAATTTATATATAAATTCATAGGGTAAACTATTGCAAGGTATT
40506577 AA
1 AA
40506579 TCTTCATTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.43, C:0.05, G:0.15, T:0.37
Consensus pattern (46 bp):
AAAGAATTTATATATAAATTCATAGGGTAAACTATTGCAAGGTATT
Found at i:40507639 original size:35 final size:34
Alignment explanation
Indices: 40507593--40507661 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
40507583 GAGCTTAATT
40507593 ACAAATGTGTTAAAATCATTAATT-AAATATTTAAA
1 ACAAATGTGTTAAAATC--TAATTAAAATATTTAAA
*
40507628 ACAAATGTGTTAATATCTAATTACAAATATTTAA
1 ACAAATGTGTTAAAATCTAATTA-AAATATTTAA
40507662 TGGTTATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 5 0.16
35 26 0.84
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.38
Consensus pattern (34 bp):
ACAAATGTGTTAAAATCTAATTAAAATATTTAAA
Found at i:40508458 original size:34 final size:34
Alignment explanation
Indices: 40508411--40508479 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
40508401 AGTCGTTTCT
*
40508411 TGTCCTCAGGAAAGAGCAAAAGAAAAATGGAAAC
1 TGTCCTCAAGAAAGAGCAAAAGAAAAATGGAAAC
40508445 TGTCCTCAAGAAAGAGCAAAAGAAAAATGGAAAC
1 TGTCCTCAAGAAAGAGCAAAAGAAAAATGGAAAC
40508479 T
1 T
40508480 AAGAGAAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.51, C:0.14, G:0.22, T:0.13
Consensus pattern (34 bp):
TGTCCTCAAGAAAGAGCAAAAGAAAAATGGAAAC
Found at i:40512338 original size:23 final size:24
Alignment explanation
Indices: 40512301--40512390 Score: 121
Period size: 23 Copynumber: 3.8 Consensus size: 24
40512291 CGGCTTGTAA
40512301 GAGCTTACTGTTTTCAGCTCGTTG
1 GAGCTTACTGTTTTCAGCTCGTTG
40512325 GAGCTTA-TGTTTTCAGCTCGTTG
1 GAGCTTACTGTTTTCAGCTCGTTG
* * **
40512348 GAGCTTACTG-TTTCAACTCATAA
1 GAGCTTACTGTTTTCAGCTCGTTG
*
40512371 GAGCTTACTGTTTCCAGCTC
1 GAGCTTACTGTTTTCAGCTC
40512391 ATCAAAGCTT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
23 42 0.72
24 16 0.28
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.39
Consensus pattern (24 bp):
GAGCTTACTGTTTTCAGCTCGTTG
Found at i:40512383 original size:47 final size:47
Alignment explanation
Indices: 40512301--40512390 Score: 119
Period size: 47 Copynumber: 1.9 Consensus size: 47
40512291 CGGCTTGTAA
* * ** *
40512301 GAGCTTACTGTTTTCAGCTCGTTGGAGCTTATGTTTTCAGCTCGTTG
1 GAGCTTACTGTTTTCAACTCATAAGAGCTTATGTTTCCAGCTCGTTG
40512348 GAGCTTACTG-TTTCAACTCATAAGAGCTTACTGTTTCCAGCTC
1 GAGCTTACTGTTTTCAACTCATAAGAGCTTA-TGTTTCCAGCTC
40512391 ATCAAAGCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
46 16 0.43
47 21 0.57
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.39
Consensus pattern (47 bp):
GAGCTTACTGTTTTCAACTCATAAGAGCTTATGTTTCCAGCTCGTTG
Found at i:40512422 original size:23 final size:23
Alignment explanation
Indices: 40512298--40512426 Score: 111
Period size: 23 Copynumber: 5.5 Consensus size: 23
40512288 TATCGGCTTG
*
40512298 TAAGAGCTTACTGTTTTCAGCTCG
1 TAAGAGCTTACTG-TTTCAGCTCA
** *
40512322 TTGGAGCTTA-TGTTTTCAGCTCG
1 TAAGAGCTTACTG-TTTCAGCTCA
** *
40512345 TTGGAGCTTACTGTTTCAACTCA
1 TAAGAGCTTACTGTTTCAGCTCA
40512368 TAAGAGCTTACTGTTTCCAGCTCA
1 TAAGAGCTTACTGTTT-CAGCTCA
* *
40512392 TCAA-AGCTTACAGTTTTAGCTCA
1 T-AAGAGCTTACTGTTTCAGCTCA
40512415 -ATAGAGCTTACT
1 TA-AGAGCTTACT
40512427 ATCCATCAGC
Statistics
Matches: 90, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
21 1 0.01
22 1 0.01
23 58 0.64
24 28 0.31
25 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (23 bp):
TAAGAGCTTACTGTTTCAGCTCA
Found at i:40516802 original size:39 final size:40
Alignment explanation
Indices: 40516718--40516850 Score: 108
Period size: 40 Copynumber: 3.4 Consensus size: 40
40516708 ATCTCAGTCT
* ** * * * *
40516718 CGCACAATAAGTGCCATATATAGCCAAAACTAT-TCCAATT
1 CGCACACTAAGTGCTTTAGATAGCCAAAGCTATCT-CGATA
* *
40516758 CGCACACTAAGTGGTTT-GATAGCCAAAGCTATCTTGATA
1 CGCACACTAAGTGCTTTAGATAGCCAAAGCTATCTCGATA
* * * **
40516797 TGCACAATAAGTGCTTTATATAGGTAAAGCTATCTCGATA
1 CGCACACTAAGTGCTTTAGATAGCCAAAGCTATCTCGATA
*
40516837 CGCACACCAAGTGC
1 CGCACACTAAGTGC
40516851 CAAACATAAT
Statistics
Matches: 72, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
39 29 0.40
40 43 0.60
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.26
Consensus pattern (40 bp):
CGCACACTAAGTGCTTTAGATAGCCAAAGCTATCTCGATA
Found at i:40519519 original size:18 final size:18
Alignment explanation
Indices: 40519496--40519546 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
40519486 AGAAAATAAG
*
40519496 TAAAACTAAAACTCTTAA
1 TAAAACTAAAACTCTAAA
* *
40519514 TAAAACCTAATA-TAATAAA
1 TAAAA-CTAAAACT-CTAAA
40519533 TAAAACTAAAACTC
1 TAAAACTAAAACTC
40519547 CTATTGCAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 6
0.69 0.14 0.17
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.59, C:0.16, G:0.00, T:0.25
Consensus pattern (18 bp):
TAAAACTAAAACTCTAAA
Found at i:40524006 original size:22 final size:23
Alignment explanation
Indices: 40523965--40524028 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 23
40523955 ATGATTTAGG
* * *
40523965 GTTTAATGTTTAGGGGTTATTAT
1 GTTTAAGGTTTATGGATTATTAT
40523988 -TTTAAGGTTTATGGATTA-TAT
1 GTTTAAGGTTTATGGATTATTAT
* * *
40524009 GTTTAGGGATTATGGTTTAT
1 GTTTAAGGTTTATGGATTAT
40524029 GGTTTTAGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 3 0.09
22 30 0.91
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.52
Consensus pattern (23 bp):
GTTTAAGGTTTATGGATTATTAT
Found at i:40525808 original size:330 final size:333
Alignment explanation
Indices: 40525159--40525822 Score: 1136
Period size: 330 Copynumber: 2.0 Consensus size: 333
40525149 TATACCCAAG
* *
40525159 TACAAGATTTTGATTTTAAAAAAGCATCAGTCTTTGTTCTTTTGTGTATAAATCACGAGATTTGT
1 TACAAGATTTTGATTTTAAAAAAGCATCAGTCTTTGTTCTTTTATATATAAATCACGAGATTTGT
* *
40525224 TTGGTTTCTAAGAAAATATTTTATTCGTGTTTGGAAGATTTTCTTCGCCGTTTTAGAGGGTGTCT
66 TTGGTTTCTAAGAAAATATTTTATTCGTGTTTGGAAGATTTTCTTCACCATTTTAGAGGGTGTCT
* * * *
40525289 CTGTTTTTCTTTCTTTCGTTTTCTCTACAATCAAGTGGTTTTGATATTTTGATTTAAAGAGTTAC
131 CTATTTTTCTTTCTTTCATTTTATCT--AATCAAG-GGTTTTGAAATTTTGATTTAAAGAGTTAC
*
40525354 CCAATTGGATACGCAATTGTTGACGCTCTATAAAGTCTTAATCCCACCTCTTCATTTCATTTTCC
193 CCAATTGGATACGCAATCGTTGACGCTCTATAAAGTCTTAATCCCACCTCTTCATTTCATTTTCC
*
40525419 TGAGAAAATGTTGGACTTGACAGAAAATCCCAAGTTGGTAAGTATAATCTCTCTAGGTTTTCTTC
258 TGAGAAAATGTTGGACTTGACAGAAAATCCCAAGTTGGTAAGTATAATCTCTCTAGGTTTGCTTC
40525484 ATTTTTTCCCA
323 ATTTTTTCCCA
40525495 TACAAGATTTTGATTTTAAAAAAGCATCAGTCTTTGTTCTTTTATATATAAATCACGAGATTTGT
1 TACAAGATTTTGATTTTAAAAAAGCATCAGTCTTTGTTCTTTTATATATAAATCACGAGATTTGT
* *
40525560 TTGGTTTCTAATAAAATATTTTATTTGTGTTTGGAAGATTTTCTTCACCATTTTAGAGGGTGTCT
66 TTGGTTTCTAAGAAAATATTTTATTCGTGTTTGGAAGATTTTCTTCACCATTTTAGAGGGTGTCT
40525625 CTATTTTTCTTTCTTTCATTTTATCT-A-CAA-GGTTTTGAAATTTTGATTTAAAGAGTTACCCA
131 CTATTTTTCTTTCTTTCATTTTATCTAATCAAGGGTTTTGAAATTTTGATTTAAAGAGTTACCCA
* *
40525687 ATTGGATACGCAATCGTTGACGCTCTATAAAGTCTTAATTCCACCTCTTCATTTCATTTTCTTGA
196 ATTGGATACGCAATCGTTGACGCTCTATAAAGTCTTAATCCCACCTCTTCATTTCATTTTCCTGA
* *
40525752 GAAAATGTTGGACTTGACGGAAAATCCCAAGTTGGTAAGTATAATCTCTTTAGGTTTGCTTCATT
261 GAAAATGTTGGACTTGACAGAAAATCCCAAGTTGGTAAGTATAATCTCTCTAGGTTTGCTTCATT
40525817 TTTTCC
326 TTTTCC
40525823 GCCTTATTTA
Statistics
Matches: 312, Mismatches: 16, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
330 161 0.52
332 3 0.01
333 1 0.00
336 147 0.47
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.43
Consensus pattern (333 bp):
TACAAGATTTTGATTTTAAAAAAGCATCAGTCTTTGTTCTTTTATATATAAATCACGAGATTTGT
TTGGTTTCTAAGAAAATATTTTATTCGTGTTTGGAAGATTTTCTTCACCATTTTAGAGGGTGTCT
CTATTTTTCTTTCTTTCATTTTATCTAATCAAGGGTTTTGAAATTTTGATTTAAAGAGTTACCCA
ATTGGATACGCAATCGTTGACGCTCTATAAAGTCTTAATCCCACCTCTTCATTTCATTTTCCTGA
GAAAATGTTGGACTTGACAGAAAATCCCAAGTTGGTAAGTATAATCTCTCTAGGTTTGCTTCATT
TTTTCCCA
Found at i:40529564 original size:19 final size:19
Alignment explanation
Indices: 40529541--40529587 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
40529531 ATTTAATCTA
*
40529541 ATTTTTATTATTTATTTTT
1 ATTTTTATTATATATTTTT
* * *
40529560 GTTTTGATTCTATATTTTT
1 ATTTTTATTATATATTTTT
40529579 ATTTTTATT
1 ATTTTTATT
40529588 TTAATATTTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.19, C:0.02, G:0.04, T:0.74
Consensus pattern (19 bp):
ATTTTTATTATATATTTTT
Found at i:40529590 original size:5 final size:6
Alignment explanation
Indices: 40529513--40529589 Score: 55
Period size: 6 Copynumber: 12.5 Consensus size: 6
40529503 ACTTGATATA
* * * * * * *
40529513 TTTTAT TTATAT CTTTAT ATTTAA TCTAAT TTTTAT TATTTAT TTTTGT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T-TTTAT TTTTAT
* *
40529562 TTTGAT TCTATAT TTTTAT TTTTAT TTT
1 TTTTAT T-TTTAT TTTTAT TTTTAT TTT
40529590 AATATTTAAG
Statistics
Matches: 52, Mismatches: 17, Indels: 4
0.71 0.23 0.05
Matches are distributed among these distances:
6 42 0.81
7 10 0.19
ACGTcount: A:0.22, C:0.04, G:0.03, T:0.71
Consensus pattern (6 bp):
TTTTAT
Found at i:40529961 original size:43 final size:43
Alignment explanation
Indices: 40529848--40529961 Score: 140
Period size: 43 Copynumber: 2.7 Consensus size: 43
40529838 AATTTTTATA
* * **
40529848 AAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGTGCTGCT
1 AAAGGTCATGTTCTTTAGCGGCGTTTTTGGGAAAAGTGCCACT
* *
40529891 AAAGGTCATGTTTTTTAGTGGCGTTTTTAGGG-AAAGTGCCACT
1 AAAGGTCATGTTCTTTAGCGGCGTTTTT-GGGAAAAGTGCCACT
* *
40529934 AAAGATCATGTTCTTTAGCGGCATTTTT
1 AAAGGTCATGTTCTTTAGCGGCGTTTTT
40529962 TCACATAAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 57 0.95
44 3 0.05
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.36
Consensus pattern (43 bp):
AAAGGTCATGTTCTTTAGCGGCGTTTTTGGGAAAAGTGCCACT
Found at i:40533938 original size:21 final size:21
Alignment explanation
Indices: 40533912--40533958 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
40533902 GGGCATTACA
40533912 ATTTATAT-ATAGAAATATATT
1 ATTTATATAATA-AAATATATT
**
40533933 ATTTATATAATAATGTATATT
1 ATTTATATAATAAAATATATT
40533954 ATTTA
1 ATTTA
40533959 CAGGGGGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (21 bp):
ATTTATATAATAAAATATATT
Found at i:40538666 original size:46 final size:46
Alignment explanation
Indices: 40538613--40538881 Score: 299
Period size: 46 Copynumber: 5.8 Consensus size: 46
40538603 TATTTGGGCA
40538613 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
*** * * * *
40538659 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGA-GCG
* *
40538706 TCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
*** * * * *
40538752 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGA-GCG
* *
40538799 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * *
40538845 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40538882 GCGGGTTACA
Statistics
Matches: 181, Mismatches: 36, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
46 108 0.60
47 73 0.40
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:40538728 original size:47 final size:47
Alignment explanation
Indices: 40538609--40538827 Score: 239
Period size: 47 Copynumber: 4.7 Consensus size: 47
40538599 GGGATATTTG
*** * * *
40538609 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTA
*
40538656 -GCGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTA
* * *** * * *
40538702 GGCATCCGAGCTCATTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTA
*
40538749 -GCGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTA
*
40538795 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTC
40538828 ACTTATGGAT
Statistics
Matches: 140, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
46 69 0.49
47 71 0.51
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (47 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:40538768 original size:93 final size:93
Alignment explanation
Indices: 40538609--40538873 Score: 476
Period size: 93 Copynumber: 2.8 Consensus size: 93
40538599 GGGATATTTG
*
40538609 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
40538674 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
*
40538702 GGCATCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
40538767 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * *
40538795 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
*
40538860 TTGAGTCTGAGTTC
66 TTGAGTCCGAGTTC
40538874 ACTTATGGGC
Statistics
Matches: 165, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 165 1.00
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (93 bp):
GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:40541811 original size:15 final size:15
Alignment explanation
Indices: 40541791--40541859 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
40541781 GTATCTTGGG
40541791 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
40541806 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
40541821 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
40541836 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
40541851 TTTCTTTAT
1 TTTCTTTAT
40541860 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:40541860 original size:30 final size:30
Alignment explanation
Indices: 40541782--40541869 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
40541772 CATAGTATCG
* * * *
40541782 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
40541812 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
40541842 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
40541870 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:40544402 original size:46 final size:44
Alignment explanation
Indices: 40544244--40544416 Score: 204
Period size: 46 Copynumber: 3.8 Consensus size: 44
40544234 ATTTGGGCAT
*
40544244 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGC
*** * * *
40544288 CCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGA-GC
*
40544333 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-A-GC
*
40544381 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40544417 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
44 30 0.28
45 6 0.06
46 41 0.38
47 28 0.26
48 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (44 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGC
Found at i:40554624 original size:38 final size:38
Alignment explanation
Indices: 40554536--40554768 Score: 277
Period size: 38 Copynumber: 6.0 Consensus size: 38
40554526 AAACCCAAAC
* * *
40554536 ATAACACCAGCACAAAGCCTACGGGACTTTAAACTCAGAT
1 ATAATACCAGCACAAAGCCTACGGGA-TTT-AACCCGGAT
* * *
40554576 ATAATACCAGCACTAGGCCTACAGGATTTAACCCGGAT
1 ATAATACCAGCACAAAGCCTACGGGATTTAACCCGGAT
* *
40554614 ATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGAT
1 ATAATACCAGCACAAAGCCTACGGGATTTAACCCGGAT
* *
40554652 ATATTACCAGCACGAAGCCTACGGGATTTAACCCGGAT
1 ATAATACCAGCACAAAGCCTACGGGATTTAACCCGGAT
* *
40554690 ATATTACCAGCACAAAGCCTGCGGGATTTAACCCGGAT
1 ATAATACCAGCACAAAGCCTACGGGATTTAACCCGGAT
* * * * *
40554728 ATAATTCCAGCATATAGCCTGCGGGTCTTTAAGCCCGGAT
1 ATAATACCAGCACAAAGCCTACGGG-ATTTAA-CCCGGAT
40554768 A
1 A
40554769 CGATCTCAGC
Statistics
Matches: 172, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
38 134 0.78
39 8 0.05
40 30 0.17
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (38 bp):
ATAATACCAGCACAAAGCCTACGGGATTTAACCCGGAT
Found at i:40554729 original size:114 final size:118
Alignment explanation
Indices: 40554541--40554768 Score: 313
Period size: 114 Copynumber: 2.0 Consensus size: 118
40554531 CAAACATAAC
* * *
40554541 ACCAGCACAAAGCCTACGGGACTTTAAACTCAGATATAATACCAGCACTAGGCCTACAGGATTTA
1 ACCAGCACAAAGCCTACGGGACTTTAAACCCAGATATAATACCAGCACAAAGCCTACAGGATTTA
40554606 ACCCGGATATAATACCAGCACGA-AGCCTGCGGG-ATTTAA-CCCGGATATATT
66 ACCCGGATATAATACCAGCA-GATAGCCTGCGGGTATTTAAGCCCGGATATATT
* * * * *
40554657 ACCAGCACGAAGCCTACGGGA-TTT-AACCCGGATATATTACCAGCACAAAGCCTGCGGGATTTA
1 ACCAGCACAAAGCCTACGGGACTTTAAACCCAGATATAATACCAGCACAAAGCCTACAGGATTTA
* * *
40554720 ACCCGGATATAATTCCAGCATATAGCCTGCGGGTCTTTAAGCCCGGATA
66 ACCCGGATATAATACCAGCAGATAGCCTGCGGGTATTTAAGCCCGGATA
40554769 CGATCTCAGC
Statistics
Matches: 98, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
113 1 0.01
114 61 0.62
115 8 0.08
116 28 0.29
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (118 bp):
ACCAGCACAAAGCCTACGGGACTTTAAACCCAGATATAATACCAGCACAAAGCCTACAGGATTTA
ACCCGGATATAATACCAGCAGATAGCCTGCGGGTATTTAAGCCCGGATATATT
Found at i:40558701 original size:43 final size:43
Alignment explanation
Indices: 40558547--40558702 Score: 113
Period size: 43 Copynumber: 3.7 Consensus size: 43
40558537 TTTGTTCTCG
* * * *
40558547 TGTAAGA-CACGTCTAGGATGTTGGCATCGATATATGTGGTTACT
1 TGTAAGACCATGTCTAGGACGTTGGCATCG--ATATGTGATTACA
* * * * * *
40558591 TGTAAGACCATGTCTAGGACATCGGTATTG-TATTTGATT-CG
1 TGTAAGACCATGTCTAGGACGTTGGCATCGATATGTGATTACA
* * * *
40558632 TGTAAAACCCTGTCTGGGATAG-TGGCATCGATATGTGATTACA
1 TGTAAGACCATGTCTAGGA-CGTTGGCATCGATATGTGATTACA
* *
40558675 TGTAAGACCAGGTCTGGGACGTTGGCAT
1 TGTAAGACCATGTCTAGGACGTTGGCAT
40558703 TGTACGATAT
Statistics
Matches: 84, Mismatches: 23, Indels: 11
0.71 0.19 0.09
Matches are distributed among these distances:
41 22 0.26
42 16 0.19
43 23 0.27
44 7 0.08
45 16 0.19
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (43 bp):
TGTAAGACCATGTCTAGGACGTTGGCATCGATATGTGATTACA
Found at i:40560098 original size:50 final size:50
Alignment explanation
Indices: 40560023--40560127 Score: 210
Period size: 50 Copynumber: 2.1 Consensus size: 50
40560013 GAATATCAAT
40560023 GAATGAATAAAATTTTTAAAAAGTCATATTGAAGTTATTTTCTATTGACC
1 GAATGAATAAAATTTTTAAAAAGTCATATTGAAGTTATTTTCTATTGACC
40560073 GAATGAATAAAATTTTTAAAAAGTCATATTGAAGTTATTTTCTATTGACC
1 GAATGAATAAAATTTTTAAAAAGTCATATTGAAGTTATTTTCTATTGACC
40560123 GAATG
1 GAATG
40560128 TTGGCTAATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (50 bp):
GAATGAATAAAATTTTTAAAAAGTCATATTGAAGTTATTTTCTATTGACC
Done.