Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 370 of 378
Found at i:110622517 original size:33 final size:33
Alignment explanation
Indices: 110622470--110622535 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
110622460 ACCAATTTAA
110622470 AAAATAAAAAAATTTGACATTTTAATCCACCAT
1 AAAATAAAAAAATTTGACATTTTAATCCACCAT
* *
110622503 AAAATAGAAGAATTTGACATTTTAATCCACCAT
1 AAAATAAAAAAATTTGACATTTTAATCCACCAT
110622536 TCGTGTAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.30
Consensus pattern (33 bp):
AAAATAAAAAAATTTGACATTTTAATCCACCAT
Found at i:110627086 original size:21 final size:21
Alignment explanation
Indices: 110627060--110627102 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
110627050 CAGTAGGTTT
110627060 CATAAGGGTGGAGCTCCTTGG
1 CATAAGGGTGGAGCTCCTTGG
*
110627081 CATAAGGGTGGAGCTCTTTGG
1 CATAAGGGTGGAGCTCCTTGG
110627102 C
1 C
110627103 TTATCATCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.37, T:0.26
Consensus pattern (21 bp):
CATAAGGGTGGAGCTCCTTGG
Found at i:110629853 original size:33 final size:33
Alignment explanation
Indices: 110629785--110629881 Score: 85
Period size: 33 Copynumber: 2.9 Consensus size: 33
110629775 ATTTTTTTCA
* * *
110629785 TAAAAATAATTAAAAATGA-TATATATTA-AATTT
1 TAAAAAT-ATT-AAAATAACTATAAATTATAAATT
*
110629818 TAAAAATATTAAAATTACTATAAATTATAAATT
1 TAAAAATATTAAAATAACTATAAATTATAAATT
*
110629851 TAAAAA-A-TAAAAAAATCTAATAAATTATAAA
1 TAAAAATATTAAAATAA-CT-ATAAATTATAAA
110629882 AAATTGTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
31 12 0.22
32 14 0.25
33 29 0.53
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (33 bp):
TAAAAATATTAAAATAACTATAAATTATAAATT
Found at i:110629857 original size:34 final size:33
Alignment explanation
Indices: 110629811--110629881 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 33
110629801 TGATATATAT
* **
110629811 TAAATTTTAAAAATATTAAAAT-TACTATAAATTA
1 TAAATTTAAAAAATAAAAAAATCTA--ATAAATTA
110629845 TAAATTTAAAAAATAAAAAAATCTAATAAATTA
1 TAAATTTAAAAAATAAAAAAATCTAATAAATTA
110629878 TAAA
1 TAAA
110629882 AAATTGTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 12 0.36
34 19 0.58
35 2 0.06
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (33 bp):
TAAATTTAAAAAATAAAAAAATCTAATAAATTA
Found at i:110629891 original size:10 final size:10
Alignment explanation
Indices: 110629846--110629902 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
110629836 TATAAATTAT
110629846 AAATT-TAAA
1 AAATTATAAA
110629855 AAA-TA-AAA
1 AAATTATAAA
* *
110629863 AAA-TCTAAT
1 AAATTATAAA
110629872 AAATTATAAA
1 AAATTATAAA
*
110629882 AAATTGTAAA
1 AAATTATAAA
110629892 AAATTAATAAA
1 AAATT-ATAAA
110629903 GCTTATTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
8 8 0.21
9 8 0.21
10 18 0.47
11 4 0.11
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
AAATTATAAA
Found at i:110629895 original size:20 final size:19
Alignment explanation
Indices: 110629846--110629902 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 19
110629836 TATAAATTAT
110629846 AAATTTAAAAAA-TA-AAA
1 AAATTTAAAAAATTATAAA
* *
110629863 AAATCTAATAAATTATAAA
1 AAATTTAAAAAATTATAAA
110629882 AAATTGTAAAAAATTAATAAA
1 AAATT-TAAAAAATT-ATAAA
110629903 GCTTATTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 10 0.31
18 2 0.06
19 7 0.22
20 8 0.25
21 5 0.16
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (19 bp):
AAATTTAAAAAATTATAAA
Found at i:110629980 original size:20 final size:19
Alignment explanation
Indices: 110629956--110629998 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
110629946 TAAAAGATAA
*
110629956 TAAAAAAT-TGAAAAACAT
1 TAAAAAATATTAAAAACAT
*
110629974 ATAAAAAATATTTAAAACAT
1 -TAAAAAATATTAAAAACAT
110629994 TAAAA
1 TAAAA
110629999 TTGATATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (19 bp):
TAAAAAATATTAAAAACAT
Found at i:110630454 original size:9 final size:9
Alignment explanation
Indices: 110630442--110630611 Score: 58
Period size: 9 Copynumber: 17.8 Consensus size: 9
110630432 TTTATGATTT
110630442 TTTTTATAA
1 TTTTTATAA
*
110630451 TTTTTATTAG
1 TTTTTA-TAA
* *
110630461 TTTATATTGA
1 TTTTTA-TAA
* *
110630471 TTTTAATAC
1 TTTTTATAA
*
110630480 TTTTAAT-A
1 TTTTTATAA
* * *
110630488 GTTTTACAT
1 TTTTTATAA
*
110630497 TTTTTATGA
1 TTTTTATAA
110630506 TTTTTATAGAA
1 TTTTTAT--AA
* *
110630517 TTTTAATATG
1 TTTTTATA-A
110630527 TTTTTATAA
1 TTTTTATAA
110630536 TATTTTA-AA
1 T-TTTTATAA
*
110630545 TTTTTTAAATA
1 -TTTTTATA-A
110630556 TATTTTATTAA
1 T-TTTTA-TAA
110630567 -TTTTATAAA
1 TTTTTAT-AA
110630576 TTTTTATAA
1 TTTTTATAA
* *
110630585 TTTAGTAGAA
1 TTT-TTATAA
*
110630595 ATTTTATAA
1 TTTTTATAA
110630604 TATTTTAT
1 T-TTTTAT
110630612 TTTTAACAAT
Statistics
Matches: 117, Mismatches: 29, Indels: 29
0.67 0.17 0.17
Matches are distributed among these distances:
8 5 0.04
9 51 0.44
10 46 0.39
11 14 0.12
12 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:110630530 original size:21 final size:21
Alignment explanation
Indices: 110630501--110630562 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
110630491 TTACATTTTT
110630501 TATGATTTTTATAGA-ATTTTAA
1 TATG-TTTTTATA-ATATTTTAA
110630523 TATGTTTTTATAATATTTTAA
1 TATGTTTTTATAATATTTTAA
*
110630544 -AT-TTTTTAAATATATTTTA
1 TATGTTTTTATA-ATATTTTA
110630563 TTAATTTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 7 0.19
20 11 0.30
21 15 0.41
22 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (21 bp):
TATGTTTTTATAATATTTTAA
Found at i:110630555 original size:18 final size:19
Alignment explanation
Indices: 110630527--110630610 Score: 66
Period size: 19 Copynumber: 4.3 Consensus size: 19
110630517 TTTTAATATG
110630527 TTTTTATAATATTTTA-AAT
1 TTTTTA-AATATTTTATAAT
110630546 TTTTTAAATATATTTTATTAAT
1 TTTTT-AA-ATATTTTA-TAAT
*
110630568 TTTATAAAT-TTTTATAAT
1 TTTTTAAATATTTTATAAT
**
110630586 TTAGTAGAA-ATTTTATAAT
1 TTTTTA-AATATTTTATAAT
*
110630605 ATTTTA
1 TTTTTA
110630611 TTTTTAACAA
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
18 8 0.15
19 25 0.47
20 11 0.21
21 2 0.04
22 7 0.13
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTTAAATATTTTATAAT
Found at i:110630556 original size:31 final size:30
Alignment explanation
Indices: 110630517--110630585 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 30
110630507 TTTTATAGAA
*
110630517 TTTTAATATGTTTT-TATAATATTT-TAAATT
1 TTTTAATATATTTTAT-TAAT-TTTATAAATT
110630547 TTTTAAATATATTTTATTAATTTTATAAATT
1 TTTT-AATATATTTTATTAATTTTATAAATT
110630578 TTTATAAT
1 TTT-TAAT
110630586 TTAGTAGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
30 7 0.21
31 25 0.74
32 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (30 bp):
TTTTAATATATTTTATTAATTTTATAAATT
Found at i:110630558 original size:20 final size:20
Alignment explanation
Indices: 110630516--110630576 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 20
110630506 TTTTTATAGA
*
110630516 ATTTTAATATGTTTTTATA-AT
1 ATTTTAA-AT-TTTTTAAATAT
110630537 ATTTTAAATTTTTTAAATAT
1 ATTTTAAATTTTTTAAATAT
*
110630557 ATTTTATTAATTTTATAAAT
1 ATTTTA--AATTTTTTAAAT
110630577 TTTTATAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 7 0.20
20 10 0.29
21 7 0.20
22 11 0.31
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTTAAATTTTTTAAATAT
Found at i:110630610 original size:10 final size:10
Alignment explanation
Indices: 110630528--110630611 Score: 61
Period size: 9 Copynumber: 8.6 Consensus size: 10
110630518 TTTAATATGT
110630528 TTTTATAATA
1 TTTTATAATA
*
110630538 TTTTA-AATT
1 TTTTATAATA
*
110630547 TTTTAAATATA
1 TTTTATA-ATA
*
110630558 TTTTATTA-A
1 TTTTATAATA
110630567 TTTTATAA-A
1 TTTTATAATA
110630576 TTTT-T-ATA
1 TTTTATAATA
* *
110630584 ATTTAGTAGAAA
1 TTTTA-TA-ATA
110630596 TTTTATAATA
1 TTTTATAATA
110630606 TTTTAT
1 TTTTAT
110630612 TTTTAACAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
7 1 0.02
8 5 0.09
9 21 0.36
10 16 0.28
11 9 0.16
12 6 0.10
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (10 bp):
TTTTATAATA
Found at i:110633374 original size:12 final size:12
Alignment explanation
Indices: 110633341--110633374 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
110633331 CTTAATTCCA
*
110633341 TAACACACGACC
1 TAACACACGGCC
*
110633353 TAGCACACGGCC
1 TAACACACGGCC
110633365 TAACACACGG
1 TAACACACGG
110633375 GCGTGTGGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.38, G:0.18, T:0.09
Consensus pattern (12 bp):
TAACACACGGCC
Found at i:110645715 original size:80 final size:80
Alignment explanation
Indices: 110645609--110645761 Score: 297
Period size: 80 Copynumber: 1.9 Consensus size: 80
110645599 TTCTTATTGT
110645609 TTTTTTTATTTTGCTACTATTTTACTATTATGTTGCTACTTTGGGTTTTAACATTTTTATTCGGG
1 TTTTTTTATTTTGCTACTATTTTACTATTATGTTGCTACTTTGGGTTTTAACATTTTTATTCGGG
110645674 TCGGGCTTATTATTA
66 TCGGGCTTATTATTA
110645689 TTTTTTTATTTTGCTACTATTTTACTATTATGTTGCTACTTTGGGTTTTAACATTTTTATTCGGG
1 TTTTTTTATTTTGCTACTATTTTACTATTATGTTGCTACTTTGGGTTTTAACATTTTTATTCGGG
*
110645754 TTGGGCTT
66 TCGGGCTT
110645762 GGGTAAAATT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.57
Consensus pattern (80 bp):
TTTTTTTATTTTGCTACTATTTTACTATTATGTTGCTACTTTGGGTTTTAACATTTTTATTCGGG
TCGGGCTTATTATTA
Found at i:110648346 original size:13 final size:13
Alignment explanation
Indices: 110648328--110648372 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
110648318 TTTTAATTTC
*
110648328 AATTAAAATTATA
1 AATTAAAATAATA
110648341 AATTAAAATAATA
1 AATTAAAATAATA
* * *
110648354 ATTTAAAATGATC
1 AATTAAAATAATA
110648367 AATTAA
1 AATTAA
110648373 TTTATTATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (13 bp):
AATTAAAATAATA
Found at i:110649414 original size:19 final size:20
Alignment explanation
Indices: 110649367--110649416 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
110649357 TAACATGAAA
110649367 AAAATTATTAAAATATCATT
1 AAAATTATTAAAATATCATT
* * *
110649387 -CAATAATTAAAA-ATTATT
1 AAAATTATTAAAATATCATT
110649405 AAAATTATTAAA
1 AAAATTATTAAA
110649417 GACAAGTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATTATTAAAATATCATT
Found at i:110650670 original size:20 final size:20
Alignment explanation
Indices: 110650625--110650671 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
110650615 ATATTCAAAT
110650625 TAAATTTTTAAAAAATTATA
1 TAAATTTTTAAAAAATTATA
*
110650645 TTAATTATTTAAAAATATT-TA
1 TAAATT-TTTAAAAA-ATTATA
110650666 -AAATTT
1 TAAATTT
110650672 ATATTTCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 1 0.04
20 9 0.39
21 10 0.43
22 3 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAATTTTTAAAAAATTATA
Found at i:110653951 original size:23 final size:23
Alignment explanation
Indices: 110653907--110653951 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
110653897 GTGGTCCAAG
*
110653907 CTTATCTTTCCATATACTATAAT
1 CTTATCTTTCCATAAACTATAAT
110653930 CTTATCTTTCCATACAAC-ATAA
1 CTTATCTTTCCATA-AACTATAA
110653952 AAAATTCAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.42
Consensus pattern (23 bp):
CTTATCTTTCCATAAACTATAAT
Found at i:110655692 original size:24 final size:25
Alignment explanation
Indices: 110655660--110655724 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
110655650 GTGAATTTGG
* *
110655660 TTTTCATTTTTTTAATTTATT-AGT
1 TTTTAATTTTTTTAATTTATTGAAT
* *
110655684 TTTTAATTTGTTTAATTTTTTGAAT
1 TTTTAATTTTTTTAATTTATTGAAT
*
110655709 TTTAAATTTTTTTAAT
1 TTTTAATTTTTTTAAT
110655725 ATTACACTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 18 0.53
25 16 0.47
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.69
Consensus pattern (25 bp):
TTTTAATTTTTTTAATTTATTGAAT
Found at i:110658234 original size:23 final size:23
Alignment explanation
Indices: 110658190--110658265 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
110658180 TAAAAATAAT
110658190 AATAAAATAAAAGTT-T-TATTTTA
1 AATAAAATAAAA-TTATGT-TTTTA
110658213 AATAAAATAAAATTATGTTTTTAGAA
1 AATAAAATAAAATTATGTTTTT---A
*
110658239 AATAAAA-AAAATCA-G-TTTTA
1 AATAAAATAAAATTATGTTTTTA
110658259 AATAAAA
1 AATAAAA
110658266 AATCATGTCG
Statistics
Matches: 47, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
20 8 0.17
22 2 0.04
23 21 0.45
24 2 0.04
25 6 0.13
26 8 0.17
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.36
Consensus pattern (23 bp):
AATAAAATAAAATTATGTTTTTA
Found at i:110661237 original size:10 final size:11
Alignment explanation
Indices: 110661210--110661241 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
110661200 TCATAATATT
110661210 AATA-AATTTA
1 AATATAATTTA
110661220 AATATAATTTA
1 AATATAATTTA
110661231 AAT-TAATTTA
1 AATATAATTTA
110661241 A
1 A
110661242 TTTTTACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATATAATTTA
Found at i:110663908 original size:19 final size:19
Alignment explanation
Indices: 110663886--110663925 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
110663876 TTCTCTCTTC
* *
110663886 CTCTTATTCTTCAGTTTTT
1 CTCTCATTCTTCAATTTTT
110663905 CTCTCATTCTTCAATTTTT
1 CTCTCATTCTTCAATTTTT
110663924 CT
1 CT
110663926 TCTTTGTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.03, T:0.60
Consensus pattern (19 bp):
CTCTCATTCTTCAATTTTT
Found at i:110668892 original size:23 final size:23
Alignment explanation
Indices: 110668866--110668982 Score: 85
Period size: 23 Copynumber: 5.0 Consensus size: 23
110668856 TAAAGAACCA
110668866 TATCGGGAAGCTCACGAAGAGCC
1 TATCGGGAAGCTCACGAAGAGCC
* * * *
110668889 TATCGAGAAGCT-TCGGATAGCC
1 TATCGGGAAGCTCACGAAGAGCC
* * *
110668911 ATATATCGGGAAGTTCAAG-CGAGCAC
1 ---TATCGGGAAGCTCACGAAGAGC-C
**
110668937 TATCGGGAAGCTCATAAAGAGCC
1 TATCGGGAAGCTCACGAAGAGCC
**
110668960 TATTAGGAAGCTCACGAAGAGCC
1 TATCGGGAAGCTCACGAAGAGCC
110668983 ATATATCGGG
Statistics
Matches: 70, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
22 7 0.10
23 44 0.63
24 4 0.06
25 13 0.19
26 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.18
Consensus pattern (23 bp):
TATCGGGAAGCTCACGAAGAGCC
Found at i:110669070 original size:23 final size:22
Alignment explanation
Indices: 110669044--110669103 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 22
110669034 CACAATCTAT
*
110669044 CGGGACGCTCTGAAGAGCTATAA
1 CGGGAAGCTC-GAAGAGCTATAA
*
110669067 CGGGAAGCTCGCAAGAACCATATAA
1 CGGGAAGCTCG-AAG-AGC-TATAA
110669092 CGGGAAGCTCGA
1 CGGGAAGCTCGA
110669104 GAGGGCTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 1 0.03
23 12 0.38
24 3 0.09
25 16 0.50
ACGTcount: A:0.33, C:0.23, G:0.30, T:0.13
Consensus pattern (22 bp):
CGGGAAGCTCGAAGAGCTATAA
Found at i:110671170 original size:18 final size:18
Alignment explanation
Indices: 110671149--110671185 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
110671139 ATAATAAAAT
*
110671149 AATAAAATATCTCATTAA
1 AATAAAATATCTAATTAA
*
110671167 AATAATATATCTAATTAA
1 AATAAAATATCTAATTAA
110671185 A
1 A
110671186 TAATCATAAA
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:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (18 bp):
AATAAAATATCTAATTAA
Found at i:110676094 original size:5 final size:5
Alignment explanation
Indices: 110676060--110676093 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
110676050 TCAATTCATT
* *
110676060 TTTAA TTTAA TTTAA TTTAA TTTAT TTTAT TTTA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
110676094 TGCAAGAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (5 bp):
TTTAA
Found at i:110679849 original size:3 final size:3
Alignment explanation
Indices: 110679841--110679869 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
110679831 GTTGAAATTG
110679841 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
110679870 GCTATGGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:110680996 original size:3 final size:3
Alignment explanation
Indices: 110680988--110681047 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
110680978 ATATATGCAT
110680988 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
110681036 ATA ATA ATA ATA
1 ATA ATA ATA ATA
110681048 TCTACAATAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:110681433 original size:26 final size:27
Alignment explanation
Indices: 110681377--110681439 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
110681367 TAGCAATAAT
*
110681377 AATACTAATATAATAAATGTACTAGTG
1 AATAATAATATAATAAATGTACTAGTG
*
110681404 -ATAATAATATAAT-AATGGTAGTA-TG
1 AATAATAATATAATAAAT-GTACTAGTG
110681429 AATAAT-ATATA
1 AATAATAATATA
110681440 CAAAAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 10 0.31
26 22 0.69
ACGTcount: A:0.51, C:0.03, G:0.11, T:0.35
Consensus pattern (27 bp):
AATAATAATATAATAAATGTACTAGTG
Found at i:110681515 original size:22 final size:22
Alignment explanation
Indices: 110681471--110681521 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
110681461 ATGATATATG
**
110681471 AATATATACATATATGTATTAA
1 AATATATACATATATACATTAA
*
110681493 AATATATACATGATATACATAAA
1 AATATATACAT-ATATACATTAA
110681516 AATATA
1 AATATA
110681522 ATATTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (22 bp):
AATATATACATATATACATTAA
Found at i:110681769 original size:25 final size:25
Alignment explanation
Indices: 110681717--110681771 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
110681707 ATATATATAT
*
110681717 AATATAATTATTAAGAAAATACATAC
1 AATATAAGTATTAAGAAAATACA-AC
*
110681743 AATATATAGTATTAAGAATATAC-AC
1 AATATA-AGTATTAAGAAAATACAAC
110681768 AATA
1 AATA
110681772 CGTAGGGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 6 0.23
26 6 0.23
27 14 0.54
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.31
Consensus pattern (25 bp):
AATATAAGTATTAAGAAAATACAAC
Found at i:110682029 original size:16 final size:17
Alignment explanation
Indices: 110682003--110682045 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
110681993 ATGGGCATAA
110682003 TAAATATAATAATATATG
1 TAAA-ATAATAATATATG
*
110682021 -AAAATAATACTATATG
1 TAAAATAATAATATATG
110682037 TAAAA-AATA
1 TAAAATAATA
110682046 TGTATTGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (17 bp):
TAAAATAATAATATATG
Found at i:110682357 original size:15 final size:15
Alignment explanation
Indices: 110682334--110682369 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
110682324 AATACTAAAT
*
110682334 ATAAT-ATAATAGGA
1 ATAATAATAATAGCA
110682348 ATAATAATAATAGCA
1 ATAATAATAATAGCA
110682363 ATAATAA
1 ATAATAA
110682370 ATGTAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (15 bp):
ATAATAATAATAGCA
Found at i:110682394 original size:17 final size:18
Alignment explanation
Indices: 110682372--110682406 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
110682362 AATAATAAAT
110682372 GTAATA-ATATATAAAAG
1 GTAATACATATATAAAAG
110682389 GTAATACTATATATAAAA
1 GTAATAC-ATATATAAAA
110682407 AGTATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.31
Consensus pattern (18 bp):
GTAATACATATATAAAAG
Found at i:110683105 original size:17 final size:17
Alignment explanation
Indices: 110683079--110683119 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
110683069 TTTTATTGTA
110683079 TTATAT-TTTTAT-ATAT
1 TTATATGTTTT-TGATAT
110683095 TTATATGTTTTTGATAT
1 TTATATGTTTTTGATAT
*
110683112 ATATATGT
1 TTATATGT
110683120 GAAAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.63
Consensus pattern (17 bp):
TTATATGTTTTTGATAT
Found at i:110685060 original size:13 final size:13
Alignment explanation
Indices: 110685042--110685066 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
110685032 AACGATAAAG
110685042 TTAAAATGACATT
1 TTAAAATGACATT
110685055 TTAAAATGACAT
1 TTAAAATGACAT
110685067 CATTTCTAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (13 bp):
TTAAAATGACATT
Found at i:110687657 original size:91 final size:91
Alignment explanation
Indices: 110687498--110687679 Score: 319
Period size: 91 Copynumber: 2.0 Consensus size: 91
110687488 TTCAGTGTTG
*
110687498 AAATTAATTTTTTAGTCTGGTTGAATGCGTCTATTTCGATTCTTTATTCAACCAGTTTAAAGTAT
1 AAATTAATCTTTTAGTCTGGTTGAATGCGTCTATTTCGATTCTTTATTCAACCAGTTTAAAGTAT
110687563 TTCAAATCAGTACTCCAACCGACTCT
66 TTCAAATCAGTACTCCAACCGACTCT
* * * *
110687589 AAATTAATCTTTTAGTCTGGTTGAATGGGTTTGTTTCGATTCTTTATTCAACCAGTTTAAAGTCT
1 AAATTAATCTTTTAGTCTGGTTGAATGCGTCTATTTCGATTCTTTATTCAACCAGTTTAAAGTAT
110687654 TTCAAATCAGTACTCCAACCGACTCT
66 TTCAAATCAGTACTCCAACCGACTCT
110687680 TGATTTAATT
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 86 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (91 bp):
AAATTAATCTTTTAGTCTGGTTGAATGCGTCTATTTCGATTCTTTATTCAACCAGTTTAAAGTAT
TTCAAATCAGTACTCCAACCGACTCT
Found at i:110691910 original size:51 final size:52
Alignment explanation
Indices: 110691855--110691963 Score: 177
Period size: 51 Copynumber: 2.1 Consensus size: 52
110691845 TGATACAAAT
110691855 TGATAATAGGTTAGGTAAATG-TTCAATGATAAT-GGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTC-ATGATAATGGGTTAGGTAAATGTTCCA
* *
110691906 TGATAATGGGTTAGGTAAATGTTTCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCATGATAATGGGTTAGGTAAATGTTCCA
110691958 TGATAA
1 TGATAA
110691964 GAATTTCATG
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
51 28 0.52
52 26 0.48
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.37
Consensus pattern (52 bp):
TGATAATAGGTTAGGTAAATGTTTCATGATAATGGGTTAGGTAAATGTTCCA
Found at i:110691924 original size:26 final size:26
Alignment explanation
Indices: 110691855--110691963 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
110691845 TGATACAAAT
* *
110691855 TGATAATAGGTTAGGTAAATGTTCAA
1 TGATAATGGGTTAGGTAAATGTTCCA
110691881 TGATAAT-GGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
110691906 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
110691932 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
110691958 TGATAA
1 TGATAA
110691964 GAATTTCATG
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
25 24 0.30
26 56 0.70
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:110693440 original size:28 final size:25
Alignment explanation
Indices: 110693398--110693471 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 25
110693388 AAAAGTAGCT
* * *
110693398 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G--TGCA
110693426 AAATTACTGTTATACCCCTAGTGCA
1 AAATTACTGTTATACCCCTAGTGCA
* *
110693451 AAATTACCGTTATACCTCTAG
1 AAATTACTGTTATACCCCTAG
110693472 GGTTAATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
25 22 0.54
27 1 0.02
28 18 0.44
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (25 bp):
AAATTACTGTTATACCCCTAGTGCA
Found at i:110697690 original size:26 final size:26
Alignment explanation
Indices: 110697628--110697761 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
110697618 TGATACAAAT
*
110697628 TGATAATAGGTTAGGTAAATG-TTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
110697653 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
110697679 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
110697705 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
110697731 TGATAATGGGTTAGGTAAAT-TTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
110697756 TGATAA
1 TGATAA
110697762 GAATTTCATG
Statistics
Matches: 105, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
25 32 0.30
26 73 0.70
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:110699243 original size:28 final size:26
Alignment explanation
Indices: 110699201--110699271 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
110699191 AAAAGTAGCT
* * *
110699201 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-ATGCA
*
110699229 AAATTACTGTTATACCCCTAGGTGCA
1 AAATTACTGTTATACCCCTAGATGCA
*
110699255 AAATTACCGTTATACCC
1 AAATTACTGTTATACCC
110699272 TAGGGTTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
26 19 0.50
27 1 0.03
28 18 0.47
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGATGCA
Found at i:110699420 original size:27 final size:27
Alignment explanation
Indices: 110699379--110699490 Score: 109
Period size: 27 Copynumber: 4.1 Consensus size: 27
110699369 AGGAAGCGTC
*
110699379 CTGGTGGCTATGCCACAAATATCTGAT
1 CTGGTGGCTCTGCCACAAATATCTGAT
* * * *
110699406 CTAGTGGCTCTGCCACATATATTTGTT
1 CTGGTGGCTCTGCCACAAATATCTGAT
* *
110699433 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAAATATCTG-AT
* * * *
110699461 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAAATATCTGAT
110699487 CTGG
1 CTGG
110699491 CAGCCATGCT
Statistics
Matches: 70, Mismatches: 14, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
26 5 0.07
27 50 0.71
28 15 0.21
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAAATATCTGAT
Found at i:110699487 original size:54 final size:54
Alignment explanation
Indices: 110699379--110699490 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
110699369 AGGAAGCGTC
* *
110699379 CTGGTGGCTATGCCACAAATATCTGATCTAGTGGCTCTGCCACATATATTTGTT
1 CTGGTGGCTATGCCACAAATATCTGATCTAGTGACTCTGCCACATATATCTGTT
* * * * *
110699433 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAAATATCTG-ATCTAGTGACTCTGCCACATATATCTGTT
110699487 CTGG
1 CTGG
110699491 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 33 0.66
55 17 0.34
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAAATATCTGATCTAGTGACTCTGCCACATATATCTGTT
Found at i:110699576 original size:19 final size:22
Alignment explanation
Indices: 110699552--110699591 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
110699542 CTCCTCACAC
110699552 GGTGTA-A-GGTTGG-TATGGG
1 GGTGTATACGGTTGGATATGGG
110699571 GGTGTATACGGTTGGATATGG
1 GGTGTATACGGTTGGATATGG
110699592 TTGGGTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.17, C:0.03, G:0.47, T:0.33
Consensus pattern (22 bp):
GGTGTATACGGTTGGATATGGG
Found at i:110704312 original size:13 final size:13
Alignment explanation
Indices: 110704294--110704324 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
110704284 CAAATCGTTG
110704294 TAAATTTTTATTC
1 TAAATTTTTATTC
110704307 TAAATTTTTATTC
1 TAAATTTTTATTC
110704320 TAAAT
1 TAAAT
110704325 GGCTGACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (13 bp):
TAAATTTTTATTC
Found at i:110704837 original size:2 final size:2
Alignment explanation
Indices: 110704826--110704854 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
110704816 TCTTATAGTA
110704826 AT AT -T 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
110704855 GTTTCATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:110705374 original size:23 final size:23
Alignment explanation
Indices: 110705330--110705374 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
110705320 TTATATTAAA
**
110705330 ATTAAAAATAAAATGTAAATATG
1 ATTAAAAATAAAAAATAAATATG
*
110705353 ATTAAAAATAAAAAATATATAT
1 ATTAAAAATAAAAAATAAATAT
110705375 ATATTTAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (23 bp):
ATTAAAAATAAAAAATAAATATG
Found at i:110707933 original size:37 final size:37
Alignment explanation
Indices: 110707879--110707953 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
110707869 GCTTGAACTT
*
110707879 CATTATTTTAGAAAAGTAGACCATTGGCTCTGTACTA
1 CATTATTTTAGAAAAGTAGACCATCGGCTCTGTACTA
*
110707916 CATTATTTTAGATAAGTAGACCATCGGCTCTGTACTA
1 CATTATTTTAGAAAAGTAGACCATCGGCTCTGTACTA
110707953 C
1 C
110707954 GTACGTAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.35
Consensus pattern (37 bp):
CATTATTTTAGAAAAGTAGACCATCGGCTCTGTACTA
Found at i:110711731 original size:3 final size:3
Alignment explanation
Indices: 110711723--110711754 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
110711713 AATATGTAAA
110711723 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
110711755 ATAAATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:110711759 original size:4 final size:4
Alignment explanation
Indices: 110711750--110711785 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
110711740 TAATAATAAT
* *
110711750 AATA AATA AATA AATA AATA AATG AATA GATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA
110711786 GAAGGTCACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:110712013 original size:3 final size:3
Alignment explanation
Indices: 110711924--110711993 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
110711914 TATATGAATA
110711924 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
110711972 AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
110711994 GTTAAGTAGG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:110712071 original size:3 final size:3
Alignment explanation
Indices: 110712063--110712119 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
110712053 TATTAAAGAA
* * * **
110712063 AAT AAT AAT ACT AGT AAT AGT AAT AA- ATAT AAT GGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
110712108 AAT AAT AAT AAT
1 AAT AAT AAT AAT
110712120 CTAAACTTTG
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
2 1 0.02
3 41 0.95
4 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:110712421 original size:14 final size:14
Alignment explanation
Indices: 110712382--110712433 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
110712372 TAATGACAGC
110712382 AATAGTAATAATAAT
1 AATAGTAA-AATAAT
*
110712397 AAATAAT-AAATAAT
1 -AATAGTAAAATAAT
*
110712411 ACTAGTAAAATAAT
1 AATAGTAAAATAAT
110712425 AATAGTAAA
1 AATAGTAAA
110712434 TAAAATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 4 0.13
14 21 0.68
15 1 0.03
16 5 0.16
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (14 bp):
AATAGTAAAATAAT
Found at i:110714247 original size:5 final size:5
Alignment explanation
Indices: 110714237--110714290 Score: 60
Period size: 5 Copynumber: 11.0 Consensus size: 5
110714227 ATAGAAGATA
*
110714237 TTATT TTATT TTATT TTA-T TTAGT TT-TT TTATT TT-TAT TTATTT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTAT-T TTA-TT TTATT
110714286 TTATT
1 TTATT
110714291 AATTTAGGAT
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
4 8 0.19
5 30 0.70
6 4 0.09
7 1 0.02
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:110714252 original size:10 final size:10
Alignment explanation
Indices: 110714237--110714290 Score: 60
Period size: 9 Copynumber: 5.5 Consensus size: 10
110714227 ATAGAAGATA
110714237 TTATTTTATT
1 TTATTTTATT
110714247 TTATTTTA-T
1 TTATTTTATT
*
110714256 TTAGTTT-TT
1 TTATTTTATT
110714265 TTATTTT-TAT
1 TTATTTTAT-T
110714275 TTATTTTTATT
1 TTA-TTTTATT
110714286 TTATT
1 TTATT
110714291 AATTTAGGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 15 0.39
10 14 0.37
11 8 0.21
12 1 0.03
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.80
Consensus pattern (10 bp):
TTATTTTATT
Found at i:110714287 original size:23 final size:21
Alignment explanation
Indices: 110714235--110714290 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
110714225 AAATAGAAGA
110714235 TATTATTTTATTTTATTTTATT
1 TATT-TTTTATTTTATTTTATT
* *
110714257 TAGTTTTT-TTAT-TTTTATT
1 TATTTTTTATTTTATTTTATT
110714276 TA-TTTTTATTTTATT
1 TATTTTTTATTTTATT
110714291 AATTTAGGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 5 0.17
19 12 0.41
20 5 0.17
21 4 0.14
22 3 0.10
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.79
Consensus pattern (21 bp):
TATTTTTTATTTTATTTTATT
Found at i:110714295 original size:15 final size:16
Alignment explanation
Indices: 110714262--110714295 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
110714252 TTATTTAGTT
*
110714262 TTTTTATTTTTATTTA
1 TTTTTATTTTTATTAA
110714278 TTTTTA-TTTTATTAA
1 TTTTTATTTTTATTAA
110714293 TTT
1 TTT
110714296 AGGATTAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTATTTTTATTAA
Found at i:110722355 original size:96 final size:95
Alignment explanation
Indices: 110722169--110722360 Score: 278
Period size: 96 Copynumber: 2.0 Consensus size: 95
110722159 TGATTTATTT
*
110722169 TGAAGTTGGTACGATTATAGAGCTATAACGATACTAAAATAAAAATTTCACCTCTATTAAATTAA
1 TGAAGTTGATACGATTATAGAGCTATAACGATACTAAAATAAAAATTTCACCTCTATTAAATTAA
* *
110722234 ATAGGATTGTGCTAAATTCATATTATTCTTA
66 ATAGGATCGTGCTAAATTCAGATTATT-TTA
* * *
110722265 TGAAGTTGATATGATTATAGAGCTATAACGATATTAAAATAAAAATTTCACCTCTATTAGATTAA
1 TGAAGTTGATACGATTATAGAGCTATAACGATACTAAAATAAAAATTTCACCTCTATTAAATTAA
* * *
110722330 ATA-GACTCGTGTTAAGTTTAGATTATTTTA
66 ATAGGA-TCGTGCTAAATTCAGATTATTTTA
110722360 T
1 T
110722361 ATCTTAATTA
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
95 6 0.07
96 80 0.93
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (95 bp):
TGAAGTTGATACGATTATAGAGCTATAACGATACTAAAATAAAAATTTCACCTCTATTAAATTAA
ATAGGATCGTGCTAAATTCAGATTATTTTA
Found at i:110725626 original size:30 final size:30
Alignment explanation
Indices: 110725590--110725651 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
110725580 GAGCTAAGGG
110725590 TAAGAAGATCAATTGCCAGTTCATTAAATT
1 TAAGAAGATCAATTGCCAGTTCATTAAATT
110725620 TAAGAAGATCAATTGCCAGTTCATTAAATT
1 TAAGAAGATCAATTGCCAGTTCATTAAATT
110725650 TA
1 TA
110725652 CTATTTAGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (30 bp):
TAAGAAGATCAATTGCCAGTTCATTAAATT
Found at i:110726185 original size:41 final size:41
Alignment explanation
Indices: 110726140--110726224 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
110726130 TTTTGAAAGT
110726140 AAAGTGCGACATTATATTATAATGTCATTTTAAGTTATTTG
1 AAAGTGCGACATTATATTATAATGTCATTTTAAGTTATTTG
110726181 AAAGTGCGACATTATATTATAATGTCATTTTAAGTTATTTG
1 AAAGTGCGACATTATATTATAATGTCATTTTAAGTTATTTG
110726222 AAA
1 AAA
110726225 ATAAAGATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.42
Consensus pattern (41 bp):
AAAGTGCGACATTATATTATAATGTCATTTTAAGTTATTTG
Found at i:110726921 original size:47 final size:47
Alignment explanation
Indices: 110726809--110726921 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
110726799 TTCACAGTAA
* * *
110726809 TGCAGATAAACTGTCACTTAATAATATTGTGGATAAGCCACCACTTT
1 TGCAGATAAACTATCACTTAATAATATTATGGACAAGCCACCACTTT
* * * *
110726856 TGCAAATAAACCACCACTTTATAATATTATGGACAAGCCACCACTTT
1 TGCAGATAAACTATCACTTAATAATATTATGGACAAGCCACCACTTT
*
110726903 TGTAGATAAACTATCACTT
1 TGCAGATAAACTATCACTT
110726922 CTTCATTCTT
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 55 1.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (47 bp):
TGCAGATAAACTATCACTTAATAATATTATGGACAAGCCACCACTTT
Found at i:110749917 original size:17 final size:16
Alignment explanation
Indices: 110749897--110749944 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
110749887 TTAAATATTT
110749897 TATTATTATATTATTAC
1 TATT-TTATATTATTAC
* *
110749914 TATTTTGATATAATTAT
1 TATTTT-ATATTATTAC
110749931 TAATTTTATATTAT
1 T-ATTTTATATTAT
110749945 GTTTATAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 2 0.08
17 19 0.73
18 5 0.19
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (16 bp):
TATTTTATATTATTAC
Found at i:110754088 original size:24 final size:24
Alignment explanation
Indices: 110754061--110754109 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
110754051 TTTAGATGTT
110754061 GACATTGTTGAATATTTATTTTAA
1 GACATTGTTGAATATTTATTTTAA
110754085 GACATTGTTGAATATTTATTTTAA
1 GACATTGTTGAATATTTATTTTAA
110754109 G
1 G
110754110 TATTAAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (24 bp):
GACATTGTTGAATATTTATTTTAA
Found at i:110754665 original size:25 final size:25
Alignment explanation
Indices: 110754617--110754665 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
110754607 CATAATTGAA
* *
110754617 ATGAAATAGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
110754642 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
110754666 ATGTGTATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:110755109 original size:43 final size:43
Alignment explanation
Indices: 110755061--110755147 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
110755051 TTATGTGATT
* * *
110755061 AATATTGAAATGGGAAAGATGAGAAATGAATATGAGATGAGAA
1 AATATTGAAATGGAAAAGATGAAAAATGAATATGAAATGAGAA
* * *
110755104 AATATTGAAATGGAAAATATGAAAAATTATTATGAAATGAGAA
1 AATATTGAAATGGAAAAGATGAAAAATGAATATGAAATGAGAA
110755147 A
1 A
110755148 TGAAATATGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (43 bp):
AATATTGAAATGGAAAAGATGAAAAATGAATATGAAATGAGAA
Found at i:110756896 original size:17 final size:17
Alignment explanation
Indices: 110756846--110756896 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 17
110756836 TGGAAACATG
*
110756846 ATCTTCGAAGATATGCA
1 ATCTTAGAAGATATGCA
*
110756863 ATCTTAGATATGATATGTA
1 ATCTTAGA-A-GATATGCA
110756882 ATCTTAGAAGATATG
1 ATCTTAGAAGATATG
110756897 ATTTTGCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 13 0.43
18 2 0.07
19 15 0.50
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (17 bp):
ATCTTAGAAGATATGCA
Found at i:110756915 original size:22 final size:23
Alignment explanation
Indices: 110756868--110756922 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
110756858 ATGCAATCTT
* * *
110756868 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTTTGCAATCCTAGA
110756890 AGATATGATTTTGCAATCCTAG-
1 AGATATGATTTTGCAATCCTAGA
*
110756912 AGATTTGATTT
1 AGATATGATTT
110756923 GTAGATACCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (23 bp):
AGATATGATTTTGCAATCCTAGA
Found at i:110760298 original size:22 final size:22
Alignment explanation
Indices: 110760268--110760314 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
110760258 ATGGAATACA
110760268 AGCCCGGGAGTGCCAACATTGT
1 AGCCCGGGAGTGCCAACATTGT
*
110760290 AGCCGGGGAGTGCCAACATTGT
1 AGCCCGGGAGTGCCAACATTGT
110760312 AGC
1 AGC
110760315 TGACGCACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.26, G:0.34, T:0.17
Consensus pattern (22 bp):
AGCCCGGGAGTGCCAACATTGT
Found at i:110761297 original size:169 final size:169
Alignment explanation
Indices: 110761018--110761357 Score: 662
Period size: 169 Copynumber: 2.0 Consensus size: 169
110761008 CTTTTCCACT
*
110761018 AGCATGCATCCCCGAACCGATGGGCAAACCGAACAAGTGAATGCATTGTTGGATACGTATCTTCG
1 AGCATGCATCCCCAAACCGATGGGCAAACCGAACAAGTGAATGCATTGTTGGATACGTATCTTCG
110761083 GTACTATGTAAGTGCGACACAAAGGGATTGGCCGAAGTTGTTGGACGTGGCCCAATTTTCGTACA
66 GTACTATGTAAGTGCGACACAAAGGGATTGGCCGAAGTTGTTGGACGTGGCCCAATTTTCGTACA
110761148 ACTTACAATGAAGTGGGGCGACGAACCAGAGTCCGTTCG
131 ACTTACAATGAAGTGGGGCGACGAACCAGAGTCCGTTCG
*
110761187 AGCATGCATCCCCAAACCGATGGGCAAACCGAACAAGTGAATGCATTGTTGGATACGTATCTTTG
1 AGCATGCATCCCCAAACCGATGGGCAAACCGAACAAGTGAATGCATTGTTGGATACGTATCTTCG
110761252 GTACTATGTAAGTGCGACACAAAGGGATTGGCCGAAGTTGTTGGACGTGGCCCAATTTTCGTACA
66 GTACTATGTAAGTGCGACACAAAGGGATTGGCCGAAGTTGTTGGACGTGGCCCAATTTTCGTACA
110761317 ACTTACAATGAAGTGGGGCGACGAACCAGAGTCCGTTCG
131 ACTTACAATGAAGTGGGGCGACGAACCAGAGTCCGTTCG
110761356 AG
1 AG
110761358 ATAGTGACGG
Statistics
Matches: 169, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
169 169 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (169 bp):
AGCATGCATCCCCAAACCGATGGGCAAACCGAACAAGTGAATGCATTGTTGGATACGTATCTTCG
GTACTATGTAAGTGCGACACAAAGGGATTGGCCGAAGTTGTTGGACGTGGCCCAATTTTCGTACA
ACTTACAATGAAGTGGGGCGACGAACCAGAGTCCGTTCG
Found at i:110763460 original size:15 final size:15
Alignment explanation
Indices: 110763440--110763470 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
110763430 AACCTATAGG
110763440 ATATACAATAACTTA
1 ATATACAATAACTTA
110763455 ATATACAATAACTTA
1 ATATACAATAACTTA
110763470 A
1 A
110763471 GTTAGCAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (15 bp):
ATATACAATAACTTA
Found at i:110769722 original size:31 final size:31
Alignment explanation
Indices: 110769684--110769744 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
110769674 AAATTACATA
110769684 AAAAAAATTCATTTAAGTTACTAAACTATTC
1 AAAAAAATTCATTTAAGTTACTAAACTATTC
* * *
110769715 AAAAAAATTTATTTAAGTTATTAGACTATT
1 AAAAAAATTCATTTAAGTTACTAAACTATT
110769745 AAGCCTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (31 bp):
AAAAAAATTCATTTAAGTTACTAAACTATTC
Found at i:110771523 original size:2 final size:2
Alignment explanation
Indices: 110771516--110771541 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
110771506 CATAATTTTC
110771516 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
110771542 GAAATCTCTA
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):
TA
Found at i:110773330 original size:22 final size:22
Alignment explanation
Indices: 110773305--110773348 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
110773295 TAGTCATATA
110773305 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
110773327 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
110773349 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:110773443 original size:15 final size:15
Alignment explanation
Indices: 110773423--110773479 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
110773413 ATTCAATATT
110773423 AATATTTTAATAATA
1 AATATTTTAATAATA
*
110773438 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
110773457 AATATATTAATAATA
1 AATATTTTAATAATA
*
110773472 AATGTTTT
1 AATATTTT
110773480 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:110775482 original size:24 final size:24
Alignment explanation
Indices: 110775438--110775483 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
110775428 AACATTATAT
* *
110775438 AAAAAGTTAAAATAGATAATAACA
1 AAAAAGTAAAAATAGAAAATAACA
110775462 AAAAACGTAAAAATA-AAAATAA
1 AAAAA-GTAAAAATAGAAAATAA
110775484 AAATAAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.17
Consensus pattern (24 bp):
AAAAAGTAAAAATAGAAAATAACA
Found at i:110775599 original size:29 final size:28
Alignment explanation
Indices: 110775567--110775686 Score: 68
Period size: 29 Copynumber: 4.1 Consensus size: 28
110775557 TATTAATATA
110775567 AATAGAAATATAATAAATAGAAATATAAT
1 AATAGAAA-ATAATAAATAGAAATATAAT
* *
110775596 AATAGTTGAAAT-ATAAATAGATAA-ATAAA
1 AATAG--AAAATAATAAATAGA-AATATAAT
* * *
110775625 AATTAGATAAATAAT-AATAGTATTAGAAT
1 AA-TAGA-AAATAATAAATAGAAATATAAT
* * *
110775654 AACA-AAATAAATATAAATAGAAACATAAT
1 AATAGAAA-ATA-ATAAATAGAAATATAAT
110775683 AATA
1 AATA
110775687 ATAGCAATAA
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
26 2 0.03
27 3 0.04
28 4 0.06
29 47 0.70
30 9 0.13
31 2 0.03
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (28 bp):
AATAGAAAATAATAAATAGAAATATAAT
Found at i:110775608 original size:17 final size:15
Alignment explanation
Indices: 110775564--110775611 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
110775554 GTATATTAAT
110775564 ATAAATAGAAATATA
1 ATAAATAGAAATATA
110775579 ATAAATAGAAATATA
1 ATAAATAGAAATATA
*
110775594 ATAATAGTTGAAATATA
1 ATAA-A-TAGAAATATA
110775611 A
1 A
110775612 ATAGATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 19 0.63
16 1 0.03
17 10 0.33
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.29
Consensus pattern (15 bp):
ATAAATAGAAATATA
Found at i:110775611 original size:44 final size:44
Alignment explanation
Indices: 110775561--110775645 Score: 122
Period size: 44 Copynumber: 1.9 Consensus size: 44
110775551 TTAGTATATT
110775561 AATATAAATAGA-AATATAATAAA-TAGA-AATATAATAATAGTTGA
1 AATATAAATAGATAA-ATAA-AAATTAGATAA-ATAATAATAGTTGA
110775605 AATATAAATAGATAAATAAAAATTAGATAAATAATAATAGT
1 AATATAAATAGATAAATAAAAATTAGATAAATAATAATAGT
110775646 ATTAGAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
43 3 0.08
44 31 0.82
45 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.29
Consensus pattern (44 bp):
AATATAAATAGATAAATAAAAATTAGATAAATAATAATAGTTGA
Found at i:110775631 original size:15 final size:14
Alignment explanation
Indices: 110775561--110775674 Score: 65
Period size: 15 Copynumber: 7.9 Consensus size: 14
110775551 TTAGTATATT
*
110775561 AATATAAATAGA-A
1 AATAAAAATAGATA
110775574 ATATAATAAATAGA-A
1 A-ATAA-AAATAGATA
* *
110775589 ATATAATAATAGTTGA
1 A-ATAAAAATAGAT-A
*
110775605 AATATAAATAGATA
1 AATAAAAATAGATA
110775619 AATAAAAATTAGATA
1 AATAAAAA-TAGATA
*
110775634 AATAATAATAGTATTA
1 AATAAAAATAG-A-TA
*
110775650 GAATAACAA-A-ATA
1 -AATAAAAATAGATA
*
110775663 AATATAAATAGA
1 AATAAAAATAGA
110775675 AACATAATAA
Statistics
Matches: 80, Mismatches: 11, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
12 6 0.08
13 4 0.05
14 21 0.26
15 37 0.46
16 5 0.06
17 7 0.09
ACGTcount: A:0.63, C:0.01, G:0.08, T:0.28
Consensus pattern (14 bp):
AATAAAAATAGATA
Found at i:110781156 original size:9 final size:9
Alignment explanation
Indices: 110781142--110781170 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
110781132 ATGTGGACAT
110781142 GATTATGTG
1 GATTATGTG
110781151 GATTATGTG
1 GATTATGTG
110781160 GATTATGTG
1 GATTATGTG
110781169 GA
1 GA
110781171 AACTATTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.34, T:0.41
Consensus pattern (9 bp):
GATTATGTG
Found at i:110782308 original size:5 final size:5
Alignment explanation
Indices: 110782293--110782322 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
110782283 CTAAATTCCT
110782293 TAAAA TAAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA T-AAAA TAAAA TAAAA TAAAA TAAA
110782323 TTCTAAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:110786937 original size:5 final size:5
Alignment explanation
Indices: 110786927--110786960 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
110786917 AATCATTATA
110786927 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
110786961 TAACCAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:110798707 original size:107 final size:107
Alignment explanation
Indices: 110798515--110798735 Score: 293
Period size: 107 Copynumber: 2.1 Consensus size: 107
110798505 TTGCTATCTT
* * * *
110798515 ATTTTG-AAAATGTCAAAACTTTCCTCGCCAAATGCTTTTAAATGTGTTTTAGTGTAAAATAGCA
1 ATTTTGCAAAATGTCAAAACTTTCCTCACCAAATGCTTTCAAATGGGTTTTAGTATAAAATAGCA
**
110798579 AAATTCAAATAAGTCCAAAGTTTTATGTTTTTCCCCCTCCAA
66 AAATTCAAATAAGTCCAAAGTTTTATGTTTCACCCCCTCCAA
* * * ** *
110798621 ATTTTGCAAAATGTCAAAGCTTTCCTCATCAATTGCTTTCAAATGGGTTTTAGTATAATTTGGTC
1 ATTTTGCAAAATGTCAAAACTTTCCTCACCAAATGCTTTCAAATGGGTTTTAGTATAAAATAG-C
**
110798686 -GGATTCAAATAAGTCCAAAGTTTTATGTTTCACCCCCTCCAA
65 AAAATTCAAATAAGTCCAAAGTTTTATGTTTCACCCCCTCCAA
110798728 ATTTTGCA
1 ATTTTGCA
110798736 TTGTAGGGAT
Statistics
Matches: 99, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
106 6 0.06
107 92 0.93
108 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.38
Consensus pattern (107 bp):
ATTTTGCAAAATGTCAAAACTTTCCTCACCAAATGCTTTCAAATGGGTTTTAGTATAAAATAGCA
AAATTCAAATAAGTCCAAAGTTTTATGTTTCACCCCCTCCAA
Found at i:110799428 original size:29 final size:29
Alignment explanation
Indices: 110799361--110799428 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
110799351 ATTAGATATA
*
110799361 AATTAAAAAAAAATCAATTAAGCTCTTTT
1 AATTAAAAAAAAATCAATTAAACTCTTTT
* * *
110799390 AA-AAATAAAAAAAT-AATTATAATTTTTTT
1 AATTAA-AAAAAAATCAATTA-AACTCTTTT
110799419 AATTAAAAAA
1 AATTAAAAAA
110799429 TAACAATACC
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
28 7 0.23
29 22 0.71
30 2 0.06
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (29 bp):
AATTAAAAAAAAATCAATTAAACTCTTTT
Found at i:110799549 original size:17 final size:18
Alignment explanation
Indices: 110799527--110799562 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
110799517 TATTTTTTAA
110799527 TAAAATATTTATAA-TTT
1 TAAAATATTTATAACTTT
*
110799544 TAAAATGTTTATAACTTT
1 TAAAATATTTATAACTTT
110799562 T
1 T
110799563 TTTAATAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
TAAAATATTTATAACTTT
Found at i:110799572 original size:13 final size:14
Alignment explanation
Indices: 110799549--110799580 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
110799539 AATTTTAAAA
110799549 TGTTT-ATAACTTT
1 TGTTTAATAACTTT
110799562 T-TTTAATAACTTT
1 TGTTTAATAACTTT
110799575 TGTTTA
1 TGTTTA
110799581 TAGTTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 10 0.59
14 4 0.24
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (14 bp):
TGTTTAATAACTTT
Found at i:110802261 original size:3 final size:3
Alignment explanation
Indices: 110802253--110802285 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
110802243 GATTATATGC
110802253 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
110802286 TTAATATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:110803113 original size:131 final size:133
Alignment explanation
Indices: 110802930--110803181 Score: 305
Period size: 131 Copynumber: 1.9 Consensus size: 133
110802920 AGATTCGATA
* * * *
110802930 TTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTTGCGTTTGCTCAAAATAAT
1 TTTGACAATTCGCGGAATCATGCCCTAACGTGTTGGGTTGCAATTCTGCGTTTGCTCAAAACAAT
* *
110802995 CGAATATCCCTTCAAAATTTCACTCGTGTCTTCTAA-AAATC-CTTTAAAACGAAGGCAATACTT
66 CGAATATCCCTTCAAAATTTCACTCATGT-TTCTAAGAAAACACTTTAAAACGAAGGCAATACTT
110803058 TGTG
130 TGTG
* * * * *
110803062 TTTGACAATTCG-GGAATCATGCCCTATCGTGTTGGGTTGTGACTTCT-CGTTTGGTCAAAACAT
1 TTTGACAATTCGCGGAATCATGCCCTAACGTGTTGGGTTG-CAATTCTGCGTTTGCTCAAAACAA
* * *** *
110803125 TCGAATATTCCTTTAGGTTTTCACTCATGTTTTTAAGAAAACACTTTAAAACGAAGG
65 TCGAATATCCCTTCAAAATTTCACTCATGTTTCTAAGAAAACACTTTAAAACGAAGG
110803182 TGATGTTCAA
Statistics
Matches: 100, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
130 5 0.05
131 66 0.66
132 29 0.29
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (133 bp):
TTTGACAATTCGCGGAATCATGCCCTAACGTGTTGGGTTGCAATTCTGCGTTTGCTCAAAACAAT
CGAATATCCCTTCAAAATTTCACTCATGTTTCTAAGAAAACACTTTAAAACGAAGGCAATACTTT
GTG
Found at i:110803409 original size:132 final size:133
Alignment explanation
Indices: 110802898--110803426 Score: 416
Period size: 132 Copynumber: 4.0 Consensus size: 133
110802888 ACAATTTTTT
* * * * * *
110802898 AAAATTCTTTAAAACGAA-GACGA-GATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
1 AAAACTCTTTAAAACGAAGGA-AATG-TTCGATGTTTGGCAATTCGGGGAATAGTGCCCTATCGT
* * * * * *
110802961 GTTGGGTTGCAAT-TT-TGCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCACTCGTGT
64 GCTGGGTTGCAATCTTCT-CGTTTGTTCAAAACAATCGAATATCCCTTCAGAATTTCACTCATAT
*
110803024 CTTCTA
128 TTTCTA
* * * *
110803030 AAAA-TCCTTTAAAACGAAGGCAATACTTTG-TGTTTGACAATTC-GGGAATCA-TGCCCTATCG
1 AAAACT-CTTTAAAACGAAGGAAAT-GTTCGATGTTTGGCAATTCGGGGAAT-AGTGCCCTATCG
* ** * * * * ** *
110803091 TGTTGGGTTGTGA-CTTCTCGTTTGGTCAAAACATTCGAATATTCCTTTAGGTTTTCACTCATGT
63 TGCTGGGTTGCAATCTTCTCGTTTGTTCAAAACAATCGAATATCCCTTCAGAATTTCACTCATAT
110803155 TTT-TAA
128 TTTCT-A
* ** * * * * *
110803161 GAAAACACTTTAAAACGAAGGTGATGTTCAATGTTTGGCGATT-TGAGAATCGTGCCCTATCGTG
1 -AAAACTCTTTAAAACGAAGGAAATGTTCGATGTTTGGCAATTCGGGGAATAGTGCCCTATCGTG
* ** * * * * * * * *
110803225 CTGGGTCGCGCTTTTTTCATTGGTTCAAAACAATTGAAGATCCCTTTAGAATTTCACTCACATTT
65 CTGGGTTGCAATCTTCTCGTTTGTTCAAAACAATCGAATATCCCTTCAGAATTTCACTCATATTT
110803290 TCTA
130 TCTA
* * *
110803294 AAAACTCTTAAAAACGAAAGAAATGTTCGATGTTTGGCAATTCGGGGAATAGTGCCTTATCGTGC
1 AAAACTCTTTAAAACGAAGGAAATGTTCGATGTTTGGCAATTCGGGGAATAGTGCCCTATCGTGC
* * * * *
110803359 TGGGTTGCAATCTCCT-GTTTGTTCAAAATAATCGAATATCTCTTCGGAATTTCACTCGTATTTT
66 TGGGTTGCAATCTTCTCGTTTGTTCAAAACAATCGAATATCCCTTCAGAATTTCACTCATATTTT
110803423 CTA
131 CTA
110803426 A
1 A
110803427 GGTGAGGCAA
Statistics
Matches: 306, Mismatches: 75, Indels: 32
0.74 0.18 0.08
Matches are distributed among these distances:
130 1 0.00
131 70 0.23
132 160 0.52
133 74 0.24
134 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (133 bp):
AAAACTCTTTAAAACGAAGGAAATGTTCGATGTTTGGCAATTCGGGGAATAGTGCCCTATCGTGC
TGGGTTGCAATCTTCTCGTTTGTTCAAAACAATCGAATATCCCTTCAGAATTTCACTCATATTTT
CTA
Found at i:110805368 original size:11 final size:11
Alignment explanation
Indices: 110805352--110805381 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
110805342 TAACATTAAG
110805352 AATATATATAT
1 AATATATATAT
*
110805363 AATATAAATAT
1 AATATATATAT
110805374 AATATATA
1 AATATATA
110805382 CAATATACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATATATAT
Found at i:110806117 original size:12 final size:12
Alignment explanation
Indices: 110806100--110806129 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
110806090 GGTGGTAGAC
110806100 AATGGGAGGAAA
1 AATGGGAGGAAA
110806112 AATGGGAGGAAA
1 AATGGGAGGAAA
110806124 AATGGG
1 AATGGG
110806130 GCAAGTGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.43, T:0.10
Consensus pattern (12 bp):
AATGGGAGGAAA
Found at i:110806260 original size:37 final size:35
Alignment explanation
Indices: 110806168--110806259 Score: 143
Period size: 36 Copynumber: 2.6 Consensus size: 35
110806158 GTTTTTTTAG
110806168 TTTTTTTTT--GTTAGGTTTTTCTTTTTTCTTCTT
1 TTTTTTTTTGGGTTAGGTTTTTCTTTTTTCTTCTT
*
110806201 TTTTTTTTGGGGGTTAGGTTTTTCTTTTTTTCTTCTT
1 TTTTTTTT-TGGGTTAGGTTTTTC-TTTTTTCTTCTT
110806238 TTTTTTTTTGGGTTAGGTTTTT
1 TTTTTTTTTGGGTTAGGTTTTT
110806260 TGGGGGCTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
33 8 0.15
36 25 0.47
37 20 0.38
ACGTcount: A:0.03, C:0.07, G:0.16, T:0.74
Consensus pattern (35 bp):
TTTTTTTTTGGGTTAGGTTTTTCTTTTTTCTTCTT
Found at i:110818541 original size:12 final size:12
Alignment explanation
Indices: 110818524--110818558 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
110818514 AAATATACAT
110818524 GAATTGTCACGC
1 GAATTGTCACGC
110818536 GAATTGTCACGC
1 GAATTGTCACGC
110818548 GAATTGTCACG
1 GAATTGTCACG
110818559 TCAATATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (12 bp):
GAATTGTCACGC
Found at i:110820958 original size:15 final size:15
Alignment explanation
Indices: 110820938--110820971 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
110820928 TCTACCCGTG
**
110820938 ATTTTTCCTGATAAA
1 ATTTTTCCACATAAA
110820953 ATTTTTCCACATAAA
1 ATTTTTCCACATAAA
110820968 ATTT
1 ATTT
110820972 ATGTATTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.47
Consensus pattern (15 bp):
ATTTTTCCACATAAA
Found at i:110821373 original size:50 final size:50
Alignment explanation
Indices: 110821298--110821397 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
110821288 GTATGAATGT
*
110821298 AAGACAAATATCGTTAATTTTAAACAAAAGTGATTAATCTATCAATGGTG
1 AAGACAAATATCGTTAATTTTAAACAAAAGTAATTAATCTATCAATGGTG
*
110821348 AAGACAAATATCGTTAATTTTAAACAAAAGTAATTTATCTATCAATGGTG
1 AAGACAAATATCGTTAATTTTAAACAAAAGTAATTAATCTATCAATGGTG
110821398 TTGCAAGCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (50 bp):
AAGACAAATATCGTTAATTTTAAACAAAAGTAATTAATCTATCAATGGTG
Found at i:110834861 original size:16 final size:16
Alignment explanation
Indices: 110834840--110834870 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
110834830 TGAATTTTTT
110834840 TTAATTTTTAAAAATC
1 TTAATTTTTAAAAATC
110834856 TTAATTTTTAAAAAT
1 TTAATTTTTAAAAAT
110834871 AAATTAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAATTTTTAAAAATC
Found at i:110836084 original size:23 final size:24
Alignment explanation
Indices: 110836034--110836084 Score: 79
Period size: 22 Copynumber: 2.2 Consensus size: 24
110836024 TTTTCTTTAA
*
110836034 AATTATTGATTGAAATAAAATTAT
1 AATTTTTGATTGAAATAAAATTAT
110836058 -ATTTTTGA-TGAAATAAAATTAT
1 AATTTTTGATTGAAATAAAATTAT
110836080 AATTT
1 AATTT
110836085 CCTAAATCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (24 bp):
AATTTTTGATTGAAATAAAATTAT
Found at i:110837202 original size:12 final size:12
Alignment explanation
Indices: 110837185--110837209 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
110837175 GAGAGAAGCT
110837185 TTAATTAAATGA
1 TTAATTAAATGA
110837197 TTAATTAAATGA
1 TTAATTAAATGA
110837209 T
1 T
110837210 GGGTGATTTC
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (12 bp):
TTAATTAAATGA
Found at i:110839273 original size:16 final size:17
Alignment explanation
Indices: 110839252--110839286 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
110839242 TAATATTTAG
110839252 GAAAATTA-TTAATTGA
1 GAAAATTACTTAATTGA
110839268 GAAAATTATCTTAATTGA
1 GAAAATTA-CTTAATTGA
110839286 G
1 G
110839287 GGGTTAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.37
Consensus pattern (17 bp):
GAAAATTACTTAATTGA
Found at i:110844248 original size:10 final size:10
Alignment explanation
Indices: 110844233--110844265 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
110844223 TATCAAGAAC
110844233 TTAATTCAAA
1 TTAATTCAAA
*
110844243 TTAATTCGAA
1 TTAATTCAAA
110844253 TTAA-TCAAA
1 TTAATTCAAA
110844262 TTAA
1 TTAA
110844266 AATCACATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.39
Consensus pattern (10 bp):
TTAATTCAAA
Found at i:110860205 original size:12 final size:12
Alignment explanation
Indices: 110860188--110860219 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
110860178 ATAGTAGGTA
110860188 GTATTTGGTGAT
1 GTATTTGGTGAT
110860200 GTATTTGGTGAT
1 GTATTTGGTGAT
110860212 GTATTTGG
1 GTATTTGG
110860220 CTATAAATGT
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:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (12 bp):
GTATTTGGTGAT
Found at i:110865574 original size:28 final size:29
Alignment explanation
Indices: 110865543--110865607 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
110865533 TTTTTAAAAA
110865543 ATATTTTTTAAT-TCT-TTTATTTTTCTTT
1 ATATTTTTT-ATCTCTCTTTATTTTTCTTT
* * *
110865571 ATATTATTTCTCTCTCTTTATTTTTTTTT
1 ATATTTTTTATCTCTCTTTATTTTTCTTT
*
110865600 CTATTTTT
1 ATATTTTT
110865608 CTTCATTACT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 1 0.03
28 11 0.37
29 18 0.60
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (29 bp):
ATATTTTTTATCTCTCTTTATTTTTCTTT
Found at i:110866860 original size:192 final size:191
Alignment explanation
Indices: 110866529--110867036 Score: 845
Period size: 192 Copynumber: 2.6 Consensus size: 191
110866519 GATTAATGTG
* *
110866529 AAATGCACTAGTGGCCCCAAATTGAGTAGACTTTATAGTCTTTGGCACTAACTTCCTCATCTATA
1 AAATGCACTAGTGGCCCCAAATTGAGTGGACTTTATAGTCTTTGGCACTAACTTCCTCATCTGTA
* *
110866594 TCTTGCTCAAAAACCGTAAGTCCATGACCATCACCTACAAATGAAAGTGTGATAAAAGGAATCTT
66 TCTTGCTCAAAAACCATAAGTCCATCACCATCACCTACAAATGAAAGTGTGATAAAAGGAATCTT
* *
110866659 TTGGGATTAATGTGAAATCAATGAAGCTTGAAACCCACCATTGTTGACCATTCTTTATTTA
131 TTGGGATTAATGTGAAATCAATGAAGCGTAAAACCCACCATTGTTGACCATTCTTTATTTA
* *
110866720 AAATAGCACTAGTTGCCCCAAATTGAGTGGACTTTGTAGTCTTTGGCACTAACTTCCTCATCTGT
1 AAAT-GCACTAGTGGCCCCAAATTGAGTGGACTTTATAGTCTTTGGCACTAACTTCCTCATCTGT
* * *
110866785 ATTTTGCTCAAAAACCATAAGTCCATCACCGTAACCTACAAATGAAAGTGTGATAAAAGGAATCT
65 ATCTTGCTCAAAAACCATAAGTCCATCACCATCACCTACAAATGAAAGTGTGATAAAAGGAATCT
*
110866850 TTTGGGATTAATGTGAAATCAATGAAGCGTAAAACCCGCCATTGTTGACCATTCTTTATTTA
130 TTTGGGATTAATGTGAAATCAATGAAGCGTAAAACCCACCATTGTTGACCATTCTTTATTTA
* * *
110866912 AGATGGTACTAGTGGCCCTAAATTGAGTGGACTTTATAGTCTTTGGCACTAACTTCCTCATCTGT
1 AAAT-GCACTAGTGGCCCCAAATTGAGTGGACTTTATAGTCTTTGGCACTAACTTCCTCATCTGT
* *
110866977 ATCTTGCTCAAAAACCATGAGTCCATCACCATCACCTACAATTGAAAGTGTGATAAAAGG
65 ATCTTGCTCAAAAACCATAAGTCCATCACCATCACCTACAAATGAAAGTGTGATAAAAGG
110867037 TTTTGTAGTA
Statistics
Matches: 293, Mismatches: 23, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
191 4 0.01
192 289 0.99
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (191 bp):
AAATGCACTAGTGGCCCCAAATTGAGTGGACTTTATAGTCTTTGGCACTAACTTCCTCATCTGTA
TCTTGCTCAAAAACCATAAGTCCATCACCATCACCTACAAATGAAAGTGTGATAAAAGGAATCTT
TTGGGATTAATGTGAAATCAATGAAGCGTAAAACCCACCATTGTTGACCATTCTTTATTTA
Found at i:110873094 original size:19 final size:18
Alignment explanation
Indices: 110873070--110873117 Score: 78
Period size: 19 Copynumber: 2.6 Consensus size: 18
110873060 ACGTAAAAAG
110873070 TAAAAAGTAAAAGATGAAA
1 TAAAAA-TAAAAGATGAAA
110873089 TAAAAATAAAAAGATGAAA
1 TAAAAAT-AAAAGATGAAA
110873108 TAAAAATAAA
1 TAAAAATAAA
110873118 TAACAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (18 bp):
TAAAAATAAAAGATGAAA
Found at i:110874035 original size:16 final size:16
Alignment explanation
Indices: 110874005--110874052 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
110873995 GAAAATTAAT
110874005 ATAAAATCT-AAAAT-A
1 ATAAAAT-TAAAAATAA
110874020 ATAATAATTAAAAATAA
1 ATAA-AATTAAAAATAA
110874037 ATAAAATT-AAAATAA
1 ATAAAATTAAAAATAA
110874052 A
1 A
110874053 CTTAAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.43
16 12 0.40
17 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAAATAA
Found at i:110874051 original size:11 final size:11
Alignment explanation
Indices: 110873996--110874066 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
110873986 ATAGCTTAAG
*
110873996 AAAATTAATAT
1 AAAATTAAAAT
110874007 AAAATCTAAAAT
1 AAAAT-TAAAAT
*
110874019 AATAA-T-AATT
1 AA-AATTAAAAT
*
110874029 AAAAAT-AAAT
1 AAAATTAAAAT
110874039 AAAATTAAAAT
1 AAAATTAAAAT
*
110874050 AAACTTAAAAT
1 AAAATTAAAAT
*
110874061 AGAATT
1 AAAATT
110874067 TCCTATTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 2 0.04
10 14 0.29
11 24 0.49
12 7 0.14
13 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:110878298 original size:19 final size:18
Alignment explanation
Indices: 110878274--110878321 Score: 78
Period size: 19 Copynumber: 2.6 Consensus size: 18
110878264 ACGTAAAAAG
110878274 TAAAAAGTAAAAGATGAAA
1 TAAAAA-TAAAAGATGAAA
110878293 TAAAAATAAAAAGATGAAA
1 TAAAAAT-AAAAGATGAAA
110878312 TAAAAATAAA
1 TAAAAATAAA
110878322 TAACAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (18 bp):
TAAAAATAAAAGATGAAA
Found at i:110879238 original size:16 final size:16
Alignment explanation
Indices: 110879208--110879255 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
110879198 GAAAATTAAT
110879208 ATAAAATCT-AAAAT-A
1 ATAAAAT-TAAAAATAA
110879223 ATAATAATTAAAAATAA
1 ATAA-AATTAAAAATAA
110879240 ATAAAATT-AAAATAA
1 ATAAAATTAAAAATAA
110879255 A
1 A
110879256 CTTAAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.43
16 12 0.40
17 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAAATAA
Found at i:110879254 original size:11 final size:11
Alignment explanation
Indices: 110879199--110879269 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
110879189 ATAGCTTAAG
*
110879199 AAAATTAATAT
1 AAAATTAAAAT
110879210 AAAATCTAAAAT
1 AAAAT-TAAAAT
*
110879222 AATAA-T-AATT
1 AA-AATTAAAAT
*
110879232 AAAAAT-AAAT
1 AAAATTAAAAT
110879242 AAAATTAAAAT
1 AAAATTAAAAT
*
110879253 AAACTTAAAAT
1 AAAATTAAAAT
*
110879264 AGAATT
1 AAAATT
110879270 TCCTATTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 2 0.04
10 14 0.29
11 24 0.49
12 7 0.14
13 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:110881027 original size:49 final size:49
Alignment explanation
Indices: 110880955--110881048 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 49
110880945 TCTAGAAGGG
* * * *
110880955 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGCAATGT
1 ATAAACAGCGATAAGAGTGTAGACAATGAAAGACCAAGTTTAGCAATGT
110881004 ATAAACAGCGATAAGAGTGTAGACAATGAAAGACCAAGTTTAGCA
1 ATAAACAGCGATAAGAGTGTAGACAATGAAAGACCAAGTTTAGCA
110881049 TTGCATAGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.21
Consensus pattern (49 bp):
ATAAACAGCGATAAGAGTGTAGACAATGAAAGACCAAGTTTAGCAATGT
Found at i:110886246 original size:20 final size:20
Alignment explanation
Indices: 110886203--110886246 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
110886193 TTATTTACAT
110886203 AGAATAAATTTTATTTTTGG
1 AGAATAAATTTTATTTTTGG
*
110886223 -GAATAAGTTTTATTTTTGG
1 AGAATAAATTTTATTTTTGG
110886242 AGAAT
1 AGAAT
110886247 TTCAATCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (20 bp):
AGAATAAATTTTATTTTTGG
Found at i:110889638 original size:30 final size:30
Alignment explanation
Indices: 110889604--110889694 Score: 80
Period size: 30 Copynumber: 3.0 Consensus size: 30
110889594 AGTGGGAGTA
110889604 GTGGTTATAACAGTGAAGAAGTGATGGAAG
1 GTGGTTATAACAGTGAAGAAGTGATGGAAG
* * * * *
110889634 GTGGTTTTGA-AGGGAGTGATAGTG--GGAGTG
1 GTGGTTATAACAGTGA-AGA-AGTGATGGA-AG
*
110889664 GTGGTTATAACAGTGAGGAAGTGATGGAAG
1 GTGGTTATAACAGTGAAGAAGTGATGGAAG
110889694 G
1 G
110889695 CCTCCAACCA
Statistics
Matches: 45, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
29 11 0.24
30 23 0.51
31 11 0.24
ACGTcount: A:0.30, C:0.02, G:0.43, T:0.25
Consensus pattern (30 bp):
GTGGTTATAACAGTGAAGAAGTGATGGAAG
Found at i:110889671 original size:60 final size:60
Alignment explanation
Indices: 110889578--110889694 Score: 189
Period size: 60 Copynumber: 1.9 Consensus size: 60
110889568 TTATATTTGC
*
110889578 TTTTGAAAGGTGTGACAGTGGGAGTAGTGGTTATAACAGTGAAGAAGTGATGGAAGGTGG
1 TTTTGAAAGGAGTGACAGTGGGAGTAGTGGTTATAACAGTGAAGAAGTGATGGAAGGTGG
* * * *
110889638 TTTTGAAGGGAGTGATAGTGGGAGTGGTGGTTATAACAGTGAGGAAGTGATGGAAGG
1 TTTTGAAAGGAGTGACAGTGGGAGTAGTGGTTATAACAGTGAAGAAGTGATGGAAGG
110889695 CCTCCAACCA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.29, C:0.03, G:0.42, T:0.26
Consensus pattern (60 bp):
TTTTGAAAGGAGTGACAGTGGGAGTAGTGGTTATAACAGTGAAGAAGTGATGGAAGGTGG
Found at i:110892117 original size:28 final size:28
Alignment explanation
Indices: 110892086--110892143 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
110892076 ATTCATTTAG
110892086 TTTGGAACTACAAGTCTCTTATATTTCT
1 TTTGGAACTACAAGTCTCTTATATTTCT
110892114 TTTGGAACTACAAGTCTCTTATATTTCT
1 TTTGGAACTACAAGTCTCTTATATTTCT
110892142 TT
1 TT
110892144 CTTTATTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.48
Consensus pattern (28 bp):
TTTGGAACTACAAGTCTCTTATATTTCT
Found at i:110893795 original size:19 final size:20
Alignment explanation
Indices: 110893766--110893831 Score: 75
Period size: 19 Copynumber: 3.3 Consensus size: 20
110893756 TATTTTTATA
110893766 TTTT-ATATTTTTTGTAAAT
1 TTTTAATATTTTTTGTAAAT
110893785 TTTTAAT-TTTTTTGT-AAT
1 TTTTAATATTTTTTGTAAAT
*
110893803 TTTTAAATATTCTTTTTTACAAT
1 TTTT-AATATT-TTTTGTA-AAT
110893826 TTTTAA
1 TTTTAA
110893832 GGTTTTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
18 7 0.17
19 15 0.38
20 4 0.10
21 5 0.12
22 2 0.05
23 7 0.17
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTTAATATTTTTTGTAAAT
Found at i:110897108 original size:17 final size:17
Alignment explanation
Indices: 110897086--110897126 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
110897076 ATAGATTGAG
*
110897086 TTAATTAGAAAGAAGTT
1 TTAATTAGAAAGAAATT
110897103 TTAATTAGAAAGAAATT
1 TTAATTAGAAAGAAATT
*
110897120 TCAATTA
1 TTAATTA
110897127 ATCAACCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (17 bp):
TTAATTAGAAAGAAATT
Found at i:110903342 original size:15 final size:14
Alignment explanation
Indices: 110903310--110903347 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
110903300 TATTCATTAA
110903310 AATATTATA-AAAT
1 AATATTATATAAAT
*
110903323 AATATTATATATAT
1 AATATTATATAAAT
110903337 ATATATTATAT
1 A-ATATTATAT
110903348 GTTTGAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.41
14 4 0.18
15 9 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATATTATATAAAT
Found at i:110903618 original size:18 final size:19
Alignment explanation
Indices: 110903538--110903618 Score: 53
Period size: 18 Copynumber: 4.4 Consensus size: 19
110903528 CTTATAAAAA
110903538 TATTTAATAAATTATATTG
1 TATTTAATAAATTATATTG
* * * *
110903557 -AATAAATTAAA-AATATTT
1 TATTTAA-TAAATTATATTG
* * *
110903575 TATCATAATAAATTTTATTT
1 TAT-TTAATAAATTATATTG
110903595 TA-TTAATAAA-TATATTG
1 TATTTAATAAATTATATTG
110903612 TATTTAA
1 TATTTAA
110903619 AAGTTTATTC
Statistics
Matches: 45, Mismatches: 12, Indels: 11
0.66 0.18 0.16
Matches are distributed among these distances:
17 7 0.16
18 20 0.44
19 9 0.20
20 9 0.20
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (19 bp):
TATTTAATAAATTATATTG
Done.