Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 253 of 259
Found at i:79388520 original size:34 final size:33
Alignment explanation
Indices: 79388449--79388520 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 33
79388439 CTTGATTTGG
**
79388449 TTTTTAATATTATTTTACTCAAAATCAGTCTAT
1 TTTTTAATATTATTTTACTCAAAATCAAACTAT
*
79388482 TTTTTAA-ATTTATATTTACTCAAAATTAAACTCAT
1 TTTTTAATA-TTAT-TTTACTCAAAATCAAACT-AT
79388517 TTTT
1 TTTT
79388521 CAAAACTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 1 0.03
33 11 0.33
34 15 0.45
35 6 0.18
ACGTcount: A:0.35, C:0.11, G:0.01, T:0.53
Consensus pattern (33 bp):
TTTTTAATATTATTTTACTCAAAATCAAACTAT
Found at i:79388774 original size:53 final size:49
Alignment explanation
Indices: 79388674--79388782 Score: 137
Period size: 53 Copynumber: 2.1 Consensus size: 49
79388664 TTTTCTTATA
* * *
79388674 AATTTTTAATAGTTTCTATATTTTTTATATCTTTATAATAAATTTTAAT
1 AATTTTTAAAAGTTTCTATATTTTTTATATCTTTATAATAAACTTTAAC
* *
79388723 AATTTTCTAAAAGTTTTCTATATTTTTTTTTATCTTTTATAATGAACTTTAAC
1 AATTTT-TAAAAG-TTTCTATA-TTTTTTATATC-TTTATAATAAACTTTAAC
79388776 AATTTTT
1 AATTTTT
79388783 TATATTTTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
49 6 0.12
50 5 0.10
51 8 0.16
52 11 0.22
53 21 0.41
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (49 bp):
AATTTTTAAAAGTTTCTATATTTTTTATATCTTTATAATAAACTTTAAC
Found at i:79388782 original size:83 final size:84
Alignment explanation
Indices: 79388693--79388895 Score: 222
Period size: 83 Copynumber: 2.4 Consensus size: 84
79388683 TAGTTTCTAT
* * *
79388693 ATTTTTTATATCTTTATAATAAATTTTAATAATTTTCTA-AAAGTTTTCTATATTTT-TTTTTAT
1 ATTTTTTATATCTTTATAATAAATTTTAATAATTTTCTATAAA-TTTT-AAAATTTTATTTGTAT
*
79388756 CTTTTATAATGAACTTTAACA
64 CTTTTATAATAAACTTTAACA
** *
79388777 ATTTTTTATAT-TTT-T-A-AAATGTTTTCTATATTGTTTTATAAATTTTAAAATTTTATTTGTA
1 ATTTTTTATATCTTTATAATAAAT-TTTAATA-ATT-TTCTATAAATTTTAAAATTTTATTTGTA
*
79388838 TCTTTTATAATAAACTTTAA-T
63 TCTTTTATAATAAACTTTAACA
*
79388859 ATTTTTTATATCTTTTATAATAAAATTTAATAATTTT
1 ATTTTTTATATC-TTTATAATAAATTTTAATAATTTT
79388896 ATTTTTTTTA
Statistics
Matches: 98, Mismatches: 11, Indels: 20
0.76 0.09 0.16
Matches are distributed among these distances:
80 4 0.04
81 6 0.06
82 21 0.21
83 35 0.36
84 19 0.19
85 4 0.04
86 6 0.06
87 3 0.03
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (84 bp):
ATTTTTTATATCTTTATAATAAATTTTAATAATTTTCTATAAATTTTAAAATTTTATTTGTATCT
TTTATAATAAACTTTAACA
Found at i:79388806 original size:20 final size:19
Alignment explanation
Indices: 79388770--79388808 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
79388760 TATAATGAAC
79388770 TTTAACAATTTTTTATATT
1 TTTAACAATTTTTTATATT
79388789 TTTAA-AATGTTTTCTATATT
1 TTTAACAAT-TTTT-TATATT
79388809 GTTTTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 9 0.50
20 6 0.33
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTAACAATTTTTTATATT
Found at i:79388874 original size:31 final size:31
Alignment explanation
Indices: 79388836--79388895 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
79388826 ATTTTATTTG
* *
79388836 TATCTTTTATAATAAACTTTAATATTTTTTA
1 TATCTTTTATAATAAAATTTAATAATTTTTA
79388867 TATCTTTTATAATAAAATTTAATAATTTT
1 TATCTTTTATAATAAAATTTAATAATTTT
79388896 ATTTTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (31 bp):
TATCTTTTATAATAAAATTTAATAATTTTTA
Found at i:79389187 original size:21 final size:23
Alignment explanation
Indices: 79389145--79389192 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 23
79389135 TATTTTATAA
**
79389145 TAAAATTTATTTTTCTATATTTC
1 TAAAATTTATTTTAATATATTTC
*
79389168 TAAAATTT-TTTTAATA-ATTTT
1 TAAAATTTATTTTAATATATTTC
79389189 TAAA
1 TAAA
79389193 TGTTCTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 8 0.36
22 6 0.27
23 8 0.36
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
TAAAATTTATTTTAATATATTTC
Found at i:79389625 original size:19 final size:18
Alignment explanation
Indices: 79389601--79389650 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
79389591 AAATGTTTTC
79389601 TATATTGTTTTATAAATTT
1 TATATT-TTTTATAAATTT
*
79389620 TATATTTTATAATAAATTT
1 TATATTTT-TTATAAATTT
79389639 TAT-TTTTTTATA
1 TATATTTTTTATA
79389651 TTTCGAACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 18 0.64
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TATATTTTTTATAAATTT
Found at i:79389685 original size:19 final size:18
Alignment explanation
Indices: 79389659--79389698 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
79389649 TATTTCGAAC
*
79389659 AAATTTTTAATAATTTTT
1 AAATTTTTAATAAATTTT
*
79389677 AAATGTTTTTATAAATTTT
1 AAAT-TTTTAATAAATTTT
79389696 AAA
1 AAA
79389699 AAAATTACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
AAATTTTTAATAAATTTT
Found at i:79390039 original size:12 final size:12
Alignment explanation
Indices: 79390019--79390059 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
79390009 CTCTGTTTCA
*
79390019 TTGTCTACCATC
1 TTGTTTACCATC
79390031 TTGTTTACCATC
1 TTGTTTACCATC
79390043 TTGTTTACCATC
1 TTGTTTACCATC
79390055 TTGTT
1 TTGTT
79390060 CTTGCTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.15, C:0.24, G:0.10, T:0.51
Consensus pattern (12 bp):
TTGTTTACCATC
Found at i:79401616 original size:5 final size:5
Alignment explanation
Indices: 79401595--79401633 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
79401585 ATATATTTCA
* *
79401595 AAAAT AAAAA ACAAAT ATAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAA
79401634 TTGAAGTGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:79407268 original size:16 final size:16
Alignment explanation
Indices: 79407247--79407280 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
79407237 CCCCAAGACT
*
79407247 TTTTTATTATTATTAA
1 TTTTTATTATTATAAA
*
79407263 TTTTTATTTTTATAAA
1 TTTTTATTATTATAAA
79407279 TT
1 TT
79407281 GGACCACCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTATTATTATAAA
Found at i:79407546 original size:17 final size:17
Alignment explanation
Indices: 79407524--79407557 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
79407514 TTGATTAACA
*
79407524 ATTATTTTTTAATTTTT
1 ATTATTTTTCAATTTTT
79407541 ATTATTTTTCAATTTTT
1 ATTATTTTTCAATTTTT
79407558 CTTACCAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
ATTATTTTTCAATTTTT
Found at i:79421993 original size:32 final size:32
Alignment explanation
Indices: 79421957--79422033 Score: 91
Period size: 33 Copynumber: 2.4 Consensus size: 32
79421947 AACTTTTCCG
* ** *
79421957 GAAAATATTTTCAGAAAATCTGTCAAACAGCA
1 GAAAATATTTTCACAAAATCAATCAAACACCA
* *
79421989 GAAAATATTTTACACAGATTCAATCAAACACCA
1 GAAAATATTTT-CACAAAATCAATCAAACACCA
79422022 GAAAATATTTTC
1 GAAAATATTTTC
79422034 CTGTAAGTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 12 0.32
33 26 0.68
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.27
Consensus pattern (32 bp):
GAAAATATTTTCACAAAATCAATCAAACACCA
Found at i:79422280 original size:26 final size:26
Alignment explanation
Indices: 79422251--79422303 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
79422241 ATGTAATTGA
79422251 ATATAAGTA-TATTTATTTAAATTTTT
1 ATATAAGTACTA-TTATTTAAATTTTT
**
79422277 ATATCCGTACTATTATTTAAATTTTT
1 ATATAAGTACTATTATTTAAATTTTT
79422303 A
1 A
79422304 ATTGAGTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.55
Consensus pattern (26 bp):
ATATAAGTACTATTATTTAAATTTTT
Found at i:79422793 original size:24 final size:23
Alignment explanation
Indices: 79422748--79422793 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
79422738 CTCAACTAAA
* *
79422748 ATTTTATTTTAATATTTTTATAC
1 ATTTTATTTTAATACTTCTATAC
*
79422771 ATTTTAATTTTATTACTTCTATA
1 ATTTT-ATTTTAATACTTCTATA
79422794 AGTTGTACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (23 bp):
ATTTTATTTTAATACTTCTATAC
Found at i:79427127 original size:30 final size:30
Alignment explanation
Indices: 79427091--79427148 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
79427081 AGCTAGATTG
79427091 TAAATTGGTAACCAAACTCCAAAATATTTA
1 TAAATTGGTAACCAAACTCCAAAATATTTA
*
79427121 TAAATTGGTAACCGAACTCCAAAATATT
1 TAAATTGGTAACCAAACTCCAAAATATT
79427149 GTAGTTGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.29
Consensus pattern (30 bp):
TAAATTGGTAACCAAACTCCAAAATATTTA
Found at i:79435326 original size:21 final size:21
Alignment explanation
Indices: 79435284--79435322 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
79435274 TAAAATTTAA
*
79435284 AATTTTAATATGGATAAAATT
1 AATTTTAATAAGGATAAAATT
79435305 AATTTTAA-AAGGATAAAA
1 AATTTTAATAAGGATAAAA
79435323 ATTATAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (21 bp):
AATTTTAATAAGGATAAAATT
Found at i:79441123 original size:20 final size:20
Alignment explanation
Indices: 79441086--79441123 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
79441076 AATTTAATAC
*
79441086 ACTAAAATTTTATCATTTCA
1 ACTAAAATTTAATCATTTCA
79441106 ACTAAAACTTTAAT-ATTT
1 ACTAAAA-TTTAATCATTT
79441124 TTAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (20 bp):
ACTAAAATTTAATCATTTCA
Found at i:79441720 original size:31 final size:30
Alignment explanation
Indices: 79441682--79441745 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
79441672 CTTAACTATT
* *
79441682 TTTAATTATATTTA-AAAATATAATATAATCA
1 TTTAATTA-AGTTATAAAATATAAT-TAATAA
*
79441713 TTTAATTAAGTTATTAAATATAATTAATAA
1 TTTAATTAAGTTATAAAATATAATTAATAA
79441743 TTT
1 TTT
79441746 TATATAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 12 0.41
31 17 0.59
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (30 bp):
TTTAATTAAGTTATAAAATATAATTAATAA
Found at i:79441739 original size:22 final size:23
Alignment explanation
Indices: 79441714--79441757 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
79441704 ATATAATCAT
79441714 TTAATTAA-GTTAT-TAAATATAA
1 TTAA-TAATGTTATATAAATATAA
*
79441736 TTAATAATTTTATATAAATATA
1 TTAATAATGTTATATAAATATA
79441758 TATTTACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 3 0.16
22 8 0.42
23 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATAATGTTATATAAATATAA
Found at i:79448394 original size:6 final size:6
Alignment explanation
Indices: 79448383--79448408 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
79448373 CTTTTGTTGT
79448383 TAAATA TAAATA TAAATA TAAATA TA
1 TAAATA TAAATA TAAATA TAAATA TA
79448409 TGTATATCTC
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATA
Found at i:79449434 original size:29 final size:29
Alignment explanation
Indices: 79449379--79449434 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
79449369 ATTAATAAAA
* *
79449379 ATAAAATTATACTTTAATCTCTCAAAATG
1 ATAAAATTATAATTTAATCCCTCAAAATG
* *
79449408 ATAAAATTTTAATTTAATCCCTTAAAA
1 ATAAAATTATAATTTAATCCCTCAAAA
79449435 AATATATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.39
Consensus pattern (29 bp):
ATAAAATTATAATTTAATCCCTCAAAATG
Found at i:79453119 original size:21 final size:21
Alignment explanation
Indices: 79453093--79453133 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
79453083 ATCTGCTCAA
* *
79453093 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
79453114 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
79453134 TCGCTTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:79467669 original size:15 final size:16
Alignment explanation
Indices: 79467636--79467671 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
79467626 CTTAATCCTA
79467636 TTTTTGATAAATTATT
1 TTTTTGATAAATTATT
79467652 TTTTTGATAAATTATT
1 TTTTTGATAAATTATT
79467668 TTTT
1 TTTT
79467672 AATTTAACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (16 bp):
TTTTTGATAAATTATT
Found at i:79467757 original size:34 final size:35
Alignment explanation
Indices: 79467709--79467779 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 35
79467699 TGGCAGGTGC
79467709 CTTAAGGGGGTGAGTCAAGGTGAATACTGATGCAG
1 CTTAAGGGGGTGAGTCAAGGTGAATACTGATGCAG
79467744 CTTAA-GGGGTGAGTCAAGGTGAATACTGATGCAG
1 CTTAAGGGGGTGAGTCAAGGTGAATACTGATGCAG
79467778 CT
1 CT
79467780 GTGTATGATG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 31 0.86
35 5 0.14
ACGTcount: A:0.28, C:0.13, G:0.35, T:0.24
Consensus pattern (35 bp):
CTTAAGGGGGTGAGTCAAGGTGAATACTGATGCAG
Found at i:79471837 original size:6 final size:6
Alignment explanation
Indices: 79471826--79471854 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
79471816 AAATATCGTA
79471826 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
79471855 TATATACTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:79479134 original size:22 final size:24
Alignment explanation
Indices: 79479093--79479148 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
79479083 ACTTCAATTT
79479093 TTTATATTTTTTATACATTTA-AAA
1 TTTA-ATTTTTTATACATTTAGAAA
*
79479117 TTTAATTTTTT-TATATTTAGAAA
1 TTTAATTTTTTATACATTTAGAAA
79479140 TTTAATTTT
1 TTTAATTTT
79479149 AAAATTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 7 0.23
23 19 0.63
24 4 0.13
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTAATTTTTTATACATTTAGAAA
Found at i:79499045 original size:10 final size:10
Alignment explanation
Indices: 79499030--79499058 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
79499020 TTTCTATTTA
79499030 GTTGGTTGGG
1 GTTGGTTGGG
79499040 GTTGGTTGGG
1 GTTGGTTGGG
79499050 GTTGGTTGG
1 GTTGGTTGG
79499059 TTGGTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.59, T:0.41
Consensus pattern (10 bp):
GTTGGTTGGG
Found at i:79510690 original size:29 final size:31
Alignment explanation
Indices: 79510657--79510725 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 31
79510647 TAAAAATATT
* *
79510657 AATTTAACTCTTTTGAAAAT-TAAT-AGTCA
1 AATTTAACTCTTTTGAAAATATAATGAATAA
* *
79510686 AATTTGACTCTTTTTAAAATATAATGAATAA
1 AATTTAACTCTTTTGAAAATATAATGAATAA
79510717 AATTTAACT
1 AATTTAACT
79510726 GAAAAATAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 18 0.55
30 4 0.12
31 11 0.33
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (31 bp):
AATTTAACTCTTTTGAAAATATAATGAATAA
Found at i:79515252 original size:3 final size:3
Alignment explanation
Indices: 79515244--79515293 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
79515234 ATTAATTTGA
79515244 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
79515292 AT
1 AT
79515294 GGTTAGAAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:79519461 original size:19 final size:21
Alignment explanation
Indices: 79519425--79519467 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
79519415 TAATACTTTC
79519425 AAAATAATATTTATTTTTTTAT
1 AAAATAATA-TTATTTTTTTAT
79519447 AAAATAATA-TA-TTTTTTAT
1 AAAATAATATTATTTTTTTAT
79519466 AA
1 AA
79519468 TTTCACAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.48
20 2 0.10
22 9 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAAATAATATTATTTTTTTAT
Found at i:79536028 original size:18 final size:18
Alignment explanation
Indices: 79536000--79536042 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
79535990 CTATATAATT
*
79536000 ATTACTAATACATAATATA
1 ATTATTAATACAT-ATATA
79536019 A-TATTAATACATATATA
1 ATTATTAATACATATATA
79536036 ATTATTA
1 ATTATTA
79536043 TTGTAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 6 0.27
18 15 0.68
19 1 0.05
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTATTAATACATATATA
Found at i:79537432 original size:16 final size:16
Alignment explanation
Indices: 79537410--79537478 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
79537400 TTTGGTTCGC
79537410 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
79537426 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
79537442 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
79537459 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
79537475 TGTA
1 TGTA
79537479 ATAGCTAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:79537456 original size:33 final size:32
Alignment explanation
Indices: 79537410--79537478 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
79537400 TTTGGTTCGC
79537410 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
*
79537442 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGCGTATTGGATTAGAGG
79537475 TGTA
1 TGTA
79537479 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAGAGGCGTATTGGATTAGAGG
Found at i:79537543 original size:44 final size:45
Alignment explanation
Indices: 79537459--79537549 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
79537449 GGATTAGAGG
* * *
79537459 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
79537504 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
79537548 TG
1 TG
79537550 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:79537736 original size:18 final size:17
Alignment explanation
Indices: 79537715--79537749 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
79537705 TTATTATTAA
*
79537715 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
79537733 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
79537750 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:79537911 original size:120 final size:120
Alignment explanation
Indices: 79537698--79537960 Score: 508
Period size: 120 Copynumber: 2.2 Consensus size: 120
79537688 ATCATATTTA
79537698 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
79537763 TATTCTTATGTTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
79537818 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
79537883 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
79537938 AACATAATTATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
79537961 AACTTGAAAT
Statistics
Matches: 141, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 141 1.00
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:79542562 original size:32 final size:30
Alignment explanation
Indices: 79542526--79542596 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
79542516 TAAATCCCTT
*
79542526 TTTATAGATAATATAACATTTATAAATATGAA
1 TTTATAGA-AATATAACATTTATAAAAAT-AA
* *
79542558 TTTATA-ACATATAATATTTATAAAAATAA
1 TTTATAGAAATATAACATTTATAAAAATAA
79542587 TTT-TAGAAAT
1 TTTATAGAAAT
79542597 TGTCGAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
28 2 0.06
29 8 0.24
30 17 0.50
31 1 0.03
32 6 0.18
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (30 bp):
TTTATAGAAATATAACATTTATAAAAATAA
Found at i:79542586 original size:15 final size:15
Alignment explanation
Indices: 79542535--79542596 Score: 65
Period size: 15 Copynumber: 4.2 Consensus size: 15
79542525 TTTTATAGAT
*
79542535 AATATAACATTTATA
1 AATATAATATTTATA
*
79542550 AATATGA-ATTTATA
1 AATATAATATTTATA
79542564 ACATATAATATTTATA
1 A-ATATAATATTTATA
* *
79542580 AAAATAAT-TTTAGA
1 AATATAATATTTATA
79542594 AAT
1 AAT
79542597 TGTCGAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
14 15 0.38
15 17 0.43
16 8 0.20
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (15 bp):
AATATAATATTTATA
Found at i:79543525 original size:19 final size:21
Alignment explanation
Indices: 79543491--79543537 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
79543481 TGTATACTTA
79543491 TATTTATATGATCATATCATC
1 TATTTATATGATCATATCATC
79543512 TATTT-TAT-ATCATATCA--
1 TATTTATATGATCATATCATC
79543529 TATTTATAT
1 TATTTATAT
79543538 AATAATCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.20
18 3 0.12
19 9 0.36
20 3 0.12
21 5 0.20
ACGTcount: A:0.34, C:0.11, G:0.02, T:0.53
Consensus pattern (21 bp):
TATTTATATGATCATATCATC
Found at i:79553127 original size:17 final size:18
Alignment explanation
Indices: 79553086--79553128 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
79553076 TTGTAAGATA
79553086 ATATAATTATATTAACTT
1 ATATAATTATATTAACTT
**
79553104 ATA-AATTATA-TATTTT
1 ATATAATTATATTAACTT
79553120 ATATAATTA
1 ATATAATTA
79553129 ATAAAATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 12 0.55
18 3 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATAATTATATTAACTT
Found at i:79553706 original size:20 final size:20
Alignment explanation
Indices: 79553681--79553730 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
79553671 TGGCTTAAAA
79553681 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
79553701 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
79553718 GTGGTAGTGGATT
1 TTGGTAGTGGATT
79553731 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:79558345 original size:20 final size:20
Alignment explanation
Indices: 79558320--79558369 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
79558310 TGGCTTAAAA
79558320 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
79558340 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
79558357 GTGGTAGTGGATT
1 TTGGTAGTGGATT
79558370 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:79561480 original size:20 final size:20
Alignment explanation
Indices: 79561442--79561481 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
79561432 TTGAGTTTGG
**
79561442 AATTTGGGGTTCATTATTCA
1 AATTTGGGGTTCAGGATTCA
*
79561462 AATTTGGGGTTTAGGATTCA
1 AATTTGGGGTTCAGGATTCA
79561482 TGATTCAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.42
Consensus pattern (20 bp):
AATTTGGGGTTCAGGATTCA
Found at i:79562391 original size:18 final size:18
Alignment explanation
Indices: 79562368--79562404 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
79562358 CAATCAATAC
79562368 AGTTGCTCCCAAAAAGTA
1 AGTTGCTCCCAAAAAGTA
79562386 AGTTGCTCCCAAAAAGTA
1 AGTTGCTCCCAAAAAGTA
79562404 A
1 A
79562405 AGATACTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.22
Consensus pattern (18 bp):
AGTTGCTCCCAAAAAGTA
Found at i:79564133 original size:17 final size:18
Alignment explanation
Indices: 79564108--79564146 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
79564098 TTAGCATTTG
*
79564108 TTGTGAACTTGTTTAAC-
1 TTGTCAACTTGTTTAACA
79564125 TTGTCAACTTGTTTAACA
1 TTGTCAACTTGTTTAACA
79564143 TTGT
1 TTGT
79564147 ATTTAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.49
Consensus pattern (18 bp):
TTGTCAACTTGTTTAACA
Found at i:79575273 original size:28 final size:28
Alignment explanation
Indices: 79575215--79575269 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
79575205 ATAATTTAGA
*
79575215 TAATGTTATTTAACATTATAACATTCTC
1 TAATGTTATTTAACATAATAACATTCTC
*
79575243 TAATTTTATTTATA-ATAATAAC-TTCTC
1 TAATGTTATTTA-ACATAATAACATTCTC
79575270 CTAACTCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 18 0.75
29 1 0.04
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (28 bp):
TAATGTTATTTAACATAATAACATTCTC
Found at i:79579366 original size:15 final size:14
Alignment explanation
Indices: 79579346--79579384 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
79579336 AAATTAAATT
79579346 ATTAAACGTGTCAAA
1 ATTAAA-GTGTCAAA
* *
79579361 ATTAAAATATCAAA
1 ATTAAAGTGTCAAA
79579375 ATTAAAGTGT
1 ATTAAAGTGT
79579385 ATTTTAAGCA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (14 bp):
ATTAAAGTGTCAAA
Found at i:79597688 original size:69 final size:70
Alignment explanation
Indices: 79597576--79597749 Score: 262
Period size: 69 Copynumber: 2.5 Consensus size: 70
79597566 CCAACAATAC
* *
79597576 TAACTACGATTATAAGTAATTTCTAGACACCAGA-AACCACTCAGTCGCATTCCAAAATGCAGTC
1 TAACTACGATTATAAGTAATTTCTAGACATCAGAGAACCACTCAGTCGCATTCCAAAATGCAATC
79597640 AATTA
66 AATTA
* * *
79597645 TAACTATGATTATAAGTAATTTCTAGACATCAGAGATCC-CTCAGTTGCATTCCAAAATGCAATC
1 TAACTACGATTATAAGTAATTTCTAGACATCAGAGAACCACTCAGTCGCATTCCAAAATGCAATC
*
79597709 AGTTA
66 AATTA
* *
79597714 TAACTACGATTTTAAGTAATTTCTACACATCAGAGA
1 TAACTACGATTATAAGTAATTTCTAGACATCAGAGA
79597750 CCATCATTCA
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
69 92 0.97
70 3 0.03
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (70 bp):
TAACTACGATTATAAGTAATTTCTAGACATCAGAGAACCACTCAGTCGCATTCCAAAATGCAATC
AATTA
Found at i:79600266 original size:81 final size:82
Alignment explanation
Indices: 79600126--79600326 Score: 307
Period size: 81 Copynumber: 2.4 Consensus size: 82
79600116 AAATAAAAGA
* * **
79600126 AAAGCTTTGATTTAATGATCGTCTAAACTTGATCTTAAATAAATGTGGGTTGATTGGATAAATCA
1 AAAGCTTTGATCTAATGATCGTCTAAACTTAATCTTAAATAAATGTGGGCCGATTGGATAAATCA
79600191 TATTT-TTTT-CCTTGAT
66 T-TTTATTTTCCCTTGAT
*
79600207 AAAGTTTTGATCTAATGATCGTCTAAACTTAATCTTAAATAAATGTGGGCCGATTGGATAAATCA
1 AAAGCTTTGATCTAATGATCGTCTAAACTTAATCTTAAATAAATGTGGGCCGATTGGATAAATCA
79600272 TTTTATTTTGCCCCTTGAT
66 TTTTATTTT--CCCTTGAT
*
79600291 AAAGCTTTGATCTAATGATCGTATAAACTTAATCTT
1 AAAGCTTTGATCTAATGATCGTCTAAACTTAATCTT
79600327 TGATAGACTT
Statistics
Matches: 109, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
80 3 0.03
81 65 0.60
84 41 0.38
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (82 bp):
AAAGCTTTGATCTAATGATCGTCTAAACTTAATCTTAAATAAATGTGGGCCGATTGGATAAATCA
TTTTATTTTCCCTTGAT
Found at i:79605116 original size:19 final size:21
Alignment explanation
Indices: 79605088--79605144 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
79605078 ATATTAATTA
79605088 AAATTTTAAAAATATAA-AAT
1 AAATTTTAAAAATATAATAAT
** *
79605108 TTA-TTT-AAATTATAATAAT
1 AAATTTTAAAAATATAATAAT
79605127 AAATTTTAAAAATATAAT
1 AAATTTTAAAAATATAAT
79605145 TACTAAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
18 8 0.29
19 7 0.25
20 4 0.14
21 9 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATTTTAAAAATATAATAAT
Found at i:79613157 original size:9 final size:10
Alignment explanation
Indices: 79613143--79613192 Score: 50
Period size: 9 Copynumber: 4.9 Consensus size: 10
79613133 GTTATATACG
79613143 TATATATT-T
1 TATATATTAT
79613152 TATATATTAT
1 TATATATTAT
*
79613162 TAT-TTTTAT
1 TATATATTAT
79613171 TATACATATTAT
1 TAT--ATATTAT
79613183 GTATATATTA
1 -TATATATTA
79613193 AATATCGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
9 16 0.47
10 4 0.12
11 6 0.18
12 5 0.15
13 3 0.09
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (10 bp):
TATATATTAT
Found at i:79614806 original size:22 final size:25
Alignment explanation
Indices: 79614781--79614826 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
79614771 AAAGAGCACA
79614781 AATGTGCT-A-AAT-GGAGAGCATT
1 AATGTGCTAATAATCGGAGAGCATT
*
79614803 AATGTGTTAATAATCGGAGAGCAT
1 AATGTGCTAATAATCGGAGAGCAT
79614827 GCTAAGGTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 1 0.05
24 3 0.15
25 9 0.45
ACGTcount: A:0.37, C:0.09, G:0.26, T:0.28
Consensus pattern (25 bp):
AATGTGCTAATAATCGGAGAGCATT
Found at i:79616392 original size:42 final size:38
Alignment explanation
Indices: 79616316--79616393 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 38
79616306 AATTTAATGG
* *
79616316 GATGTTTAAAACAAATAATAATGGAAAAATTATATTGA
1 GATGTTTAAAACAAATAATAATAGAAAAAATATATTGA
*
79616354 GATGTTTAAAAATAAATAATAATATAGATAAAAATATATT
1 GATGTTT-AAAACAAATAAT-A-ATAGA-AAAAATATATT
79616394 ATACGAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 7 0.21
39 11 0.33
40 1 0.03
41 4 0.12
42 10 0.30
ACGTcount: A:0.55, C:0.01, G:0.10, T:0.33
Consensus pattern (38 bp):
GATGTTTAAAACAAATAATAATAGAAAAAATATATTGA
Found at i:79621541 original size:26 final size:26
Alignment explanation
Indices: 79621500--79621549 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
79621490 TAATAACGGA
*
79621500 TTGCTCTATTCGTATTATTTTGTTAC
1 TTGCTCTATTCGTATTATTATGTTAC
**
79621526 TTGCTCTATTTTTATTATTATGTT
1 TTGCTCTATTCGTATTATTATGTT
79621550 TTTATAGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.16, C:0.12, G:0.10, T:0.62
Consensus pattern (26 bp):
TTGCTCTATTCGTATTATTATGTTAC
Found at i:79623301 original size:16 final size:16
Alignment explanation
Indices: 79623277--79623317 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
79623267 AATTTTGTAT
*
79623277 CGACACAACTC-AAGCC
1 CGACCCAACTCGAA-CC
79623293 CGACCCAACTCGAACC
1 CGACCCAACTCGAACC
79623309 CGACCCAAC
1 CGACCCAAC
79623318 CCATTATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.34, C:0.49, G:0.12, T:0.05
Consensus pattern (16 bp):
CGACCCAACTCGAACC
Found at i:79623523 original size:22 final size:23
Alignment explanation
Indices: 79623498--79623540 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
79623488 TTGAGATGTT
79623498 TAAAAATAAATAATA-ATATAGA
1 TAAAAATAAATAATATATATAGA
*
79623520 TAAAAATATATAATATATATA
1 TAAAAATAAATAATATATATA
79623541 CAAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
TAAAAATAAATAATATATATAGA
Found at i:79623534 original size:19 final size:18
Alignment explanation
Indices: 79623505--79623547 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
79623495 GTTTAAAAAT
79623505 AAATAATAATATAGATAA
1 AAATAATAATATAGATAA
* *
79623523 AAATATATAATATATATAC
1 AAATA-ATAATATAGATAA
79623542 AAATAA
1 AAATAA
79623548 AAAGATATCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (18 bp):
AAATAATAATATAGATAA
Found at i:79623547 original size:25 final size:22
Alignment explanation
Indices: 79623498--79623555 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
79623488 TTGAGATGTT
* *
79623498 TAAAAATAAATAATAATATAGA
1 TAAAAATATATAATAATATAAA
79623520 TAAAAATATATAATATATATACAAA
1 TAAAAATATATAATA-ATAT--AAA
*
79623545 TAAAAAGATAT
1 TAAAAATATAT
79623556 CCATCGACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 14 0.47
23 4 0.13
25 12 0.40
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (22 bp):
TAAAAATATATAATAATATAAA
Found at i:79624428 original size:15 final size:16
Alignment explanation
Indices: 79624398--79624436 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
79624388 TAATAAAAAT
79624398 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
79624415 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
79624430 ATAATTT
1 ATAATTT
79624437 TTAAAAGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:79624888 original size:22 final size:22
Alignment explanation
Indices: 79624849--79624907 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
79624839 GTTTTAAGAA
*
79624849 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
79624870 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
79624892 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
79624908 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:79624924 original size:26 final size:24
Alignment explanation
Indices: 79624878--79624937 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
79624868 ATTTGTTTTA
*
79624878 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
79624902 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
* *
79624928 TTTTTTATTT
1 ATATTTATTT
79624938 AATGAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:79626287 original size:59 final size:59
Alignment explanation
Indices: 79626217--79626336 Score: 231
Period size: 59 Copynumber: 2.0 Consensus size: 59
79626207 CAGTTGGTTA
*
79626217 TTTCGATTAATCAACTTTTTTTTTACTATAGTTTCTTTTTTTAAAAAAGTTGAGTTTGG
1 TTTCGATTAATCAACTTTTTTTTTACTATAGTTTCTTTTTTAAAAAAAGTTGAGTTTGG
79626276 TTTCGATTAATCAACTTTTTTTTTACTATAGTTTCTTTTTTAAAAAAAGTTGAGTTTGG
1 TTTCGATTAATCAACTTTTTTTTTACTATAGTTTCTTTTTTAAAAAAAGTTGAGTTTGG
79626335 TT
1 TT
79626337 GGAAGATTGA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.26, C:0.08, G:0.12, T:0.54
Consensus pattern (59 bp):
TTTCGATTAATCAACTTTTTTTTTACTATAGTTTCTTTTTTAAAAAAAGTTGAGTTTGG
Found at i:79633384 original size:16 final size:17
Alignment explanation
Indices: 79633348--79633388 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
79633338 AAATTTAAAG
* *
79633348 TTTTAGTATTTATTTTA
1 TTTTAATATTTATTATA
79633365 TTTTAATATTTA-TATA
1 TTTTAATATTTATTATA
79633381 TTTTAATA
1 TTTTAATA
79633389 AAAGATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (17 bp):
TTTTAATATTTATTATA
Found at i:79635048 original size:14 final size:14
Alignment explanation
Indices: 79635029--79635072 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
79635019 AATTTTAAGT
79635029 AAATAATAATTTAA
1 AAATAATAATTTAA
*
79635043 AAATAATTAATATAA
1 AAATAA-TAATTTAA
*
79635058 AAA-AACAATTTAA
1 AAATAATAATTTAA
79635071 AA
1 AA
79635073 TAAAATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 8 0.31
14 8 0.31
15 10 0.38
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATAATAATTTAA
Found at i:79635058 original size:15 final size:14
Alignment explanation
Indices: 79635029--79635088 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 14
79635019 AATTTTAAGT
*
79635029 AAATAATAATTTAA
1 AAATAATAATATAA
79635043 AAATAATTAATATAA
1 AAATAA-TAATATAA
* *
79635058 AAA-AACAATTTAA
1 AAATAATAATATAA
*
79635071 AATAAAATATATATAA
1 AA-ATAATA-ATATAA
79635087 AA
1 AA
79635089 CAATCTAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
13 8 0.22
14 9 0.24
15 13 0.35
16 7 0.19
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATAATAATATAA
Found at i:79635067 original size:28 final size:27
Alignment explanation
Indices: 79635036--79635098 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 27
79635026 AGTAAATAAT
79635036 AATTTAAAAATAATTAATATA-AAAAAAC
1 AATTTAAAAATAA--AATATATAAAAAAC
*
79635064 AATTT-AAAATAAAATATATATAAAAC
1 AATTTAAAAATAAAATATATAAAAAAC
*
79635090 AATCTAAAA
1 AATTTAAAA
79635099 TGACTAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 6 0.19
26 10 0.32
27 10 0.32
28 5 0.16
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (27 bp):
AATTTAAAAATAAAATATATAAAAAAC
Found at i:79635224 original size:26 final size:25
Alignment explanation
Indices: 79635195--79635252 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 25
79635185 ATAAAACAGT
*
79635195 TTTAAA-AAATAATACTGTAAAAGAAA
1 TTTAAAGAAATAACA-TGTAAAA-AAA
*
79635221 TTTAAAGTAAATAACATGTAAAATAA
1 TTTAAAG-AAATAACATGTAAAAAAA
79635247 TTTAAA
1 TTTAAA
79635253 CCAAGTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 14 0.50
27 7 0.25
28 7 0.25
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (25 bp):
TTTAAAGAAATAACATGTAAAAAAA
Found at i:79635242 original size:27 final size:27
Alignment explanation
Indices: 79635201--79635252 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
79635191 CAGTTTTAAA
*
79635201 AAATAATACTGTAAAAGAAATTTAAAGT
1 AAATAACACTGTAAAA-AAATTTAAAGT
*
79635229 AAATAACA-TGTAAAATAATTTAAA
1 AAATAACACTGTAAAAAAATTTAAA
79635253 CCAAGTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
27 7 0.32
28 7 0.32
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.29
Consensus pattern (27 bp):
AAATAACACTGTAAAAAAATTTAAAGT
Found at i:79636016 original size:18 final size:17
Alignment explanation
Indices: 79635967--79636024 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
79635957 ATAATGAAAG
*
79635967 ATAATGATAAAATAATA
1 ATAATGCTAAAATAATA
*
79635984 ATAA-ACTAAGGAATAATA
1 ATAATGCTAA--AATAATA
79636002 ATAATGCTAACAATAAT-
1 ATAATGCTAA-AATAATA
79636019 ATAATG
1 ATAATG
79636025 TAAGTAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 3 0.09
17 10 0.29
18 17 0.50
19 4 0.12
ACGTcount: A:0.59, C:0.05, G:0.09, T:0.28
Consensus pattern (17 bp):
ATAATGCTAAAATAATA
Found at i:79639869 original size:17 final size:18
Alignment explanation
Indices: 79639847--79639880 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
79639837 TACTTTTAAT
79639847 AATTT-AAAATTTAAAAA
1 AATTTAAAAATTTAAAAA
79639864 AATTTAAAAATTTAAAA
1 AATTTAAAAATTTAAAA
79639881 TAAAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AATTTAAAAATTTAAAAA
Found at i:79647382 original size:20 final size:20
Alignment explanation
Indices: 79647357--79647394 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
79647347 GCTTTTATCT
79647357 AATATATTGTTT-AAATTTGA
1 AATATA-TGTTTGAAATTTGA
79647377 AATATATGTTTGAAATTT
1 AATATATGTTTGAAATTT
79647395 TATCTAGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (20 bp):
AATATATGTTTGAAATTTGA
Found at i:79648144 original size:6 final size:6
Alignment explanation
Indices: 79648133--79648163 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
79648123 GATCAGTTGA
79648133 AGGTGC AGGTGC AGGTGC AGGTGC AGGTGC A
1 AGGTGC AGGTGC AGGTGC AGGTGC AGGTGC A
79648164 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.16, G:0.48, T:0.16
Consensus pattern (6 bp):
AGGTGC
Found at i:79650951 original size:26 final size:27
Alignment explanation
Indices: 79650922--79650978 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
79650912 AAAGTAAACA
* *
79650922 ATAAAACA-GTTTAAAATGAATAATAC
1 ATAAAACATATTTAAAATAAATAATAC
79650948 ATAAAACATATTTAAAATAAATAATAC
1 ATAAAACATATTTAAAATAAATAATAC
79650975 -TAAA
1 ATAAA
79650979 GAAGCCTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 12 0.43
27 16 0.57
ACGTcount: A:0.61, C:0.07, G:0.04, T:0.28
Consensus pattern (27 bp):
ATAAAACATATTTAAAATAAATAATAC
Found at i:79651014 original size:26 final size:25
Alignment explanation
Indices: 79650931--79651014 Score: 80
Period size: 26 Copynumber: 3.2 Consensus size: 25
79650921 AATAAAACAG
*
79650931 TTTAAAATGAATAATACATAAA-ACATA
1 TTTAAAATAAATAATACA-AAAGA-A-A
* *
79650958 TTTAAAATAAATAATACTAAAGAAG
1 TTTAAAATAAATAATACAAAAGAAA
**
79650983 CCTAAAATAAATAAATACAAAAGAAA
1 TTTAAAATAAAT-AATACAAAAGAAA
79651009 TTTAAA
1 TTTAAA
79651015 GCTGAATAAC
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
25 10 0.22
26 19 0.41
27 17 0.37
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.26
Consensus pattern (25 bp):
TTTAAAATAAATAATACAAAAGAAA
Found at i:79651271 original size:19 final size:17
Alignment explanation
Indices: 79651247--79651282 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
79651237 AATAAAAAGG
79651247 TATTTAATAGTTTTCAAAA
1 TATTTAATA-TTTT-AAAA
79651266 TATTTAATATTTTAAAA
1 TATTTAATATTTTAAAA
79651283 CAAATAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 4 0.24
19 9 0.53
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
TATTTAATATTTTAAAA
Found at i:79651380 original size:25 final size:26
Alignment explanation
Indices: 79651330--79651386 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
79651320 CCAGAATATG
* *
79651330 TAAAAATTTAGAATACATGATGATAA
1 TAAAAATTTAAAATACATAATGATAA
79651356 TAAAAATTTAAAATACATAAT-ATAA
1 TAAAAATTTAAAATACATAATGATAA
*
79651381 GAAAAA
1 TAAAAA
79651387 ACAAGCTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 9 0.32
26 19 0.68
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (26 bp):
TAAAAATTTAAAATACATAATGATAA
Found at i:79653971 original size:30 final size:31
Alignment explanation
Indices: 79653935--79654027 Score: 88
Period size: 30 Copynumber: 3.1 Consensus size: 31
79653925 TAAATAAATC
79653935 ATATCATTTATGCTAAATTTATCATTGAGAT
1 ATATCATTTATGCTAAATTTATCATTGAGAT
* * * *
79653966 A-ATCATTT-T--TAATTATTATTAAAT-AAAT
1 ATATCATTTATGCTAAAT-TTA-TCATTGAGAT
79653994 CATATCATTTATGCTAAATTTATCATTGAGAT
1 -ATATCATTTATGCTAAATTTATCATTGAGAT
79654026 AT
1 AT
79654028 TATCTAGTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
27 4 0.09
28 6 0.13
29 5 0.11
30 14 0.30
31 7 0.15
32 6 0.13
33 4 0.09
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (31 bp):
ATATCATTTATGCTAAATTTATCATTGAGAT
Found at i:79653980 original size:60 final size:60
Alignment explanation
Indices: 79653910--79654026 Score: 234
Period size: 60 Copynumber: 1.9 Consensus size: 60
79653900 AGATTTCTGA
79653910 ATTTTTAATTATTATTAAATAAATCATATCATTTATGCTAAATTTATCATTGAGATAATC
1 ATTTTTAATTATTATTAAATAAATCATATCATTTATGCTAAATTTATCATTGAGATAATC
79653970 ATTTTTAATTATTATTAAATAAATCATATCATTTATGCTAAATTTATCATTGAGATA
1 ATTTTTAATTATTATTAAATAAATCATATCATTTATGCTAAATTTATCATTGAGATA
79654027 TTATCTAGTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (60 bp):
ATTTTTAATTATTATTAAATAAATCATATCATTTATGCTAAATTTATCATTGAGATAATC
Found at i:79654572 original size:17 final size:16
Alignment explanation
Indices: 79654546--79654586 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
79654536 ATATCGTACA
*
79654546 TATTTTTATTACATTT
1 TATTTTTATTACATGT
*
79654562 TATTATTTATTATATGT
1 TATT-TTTATTACATGT
79654579 TATTTTTA
1 TATTTTTA
79654587 AATATGAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (16 bp):
TATTTTTATTACATGT
Found at i:79655465 original size:12 final size:11
Alignment explanation
Indices: 79655437--79655467 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
79655427 ATAATAAATC
79655437 AAAAATATTAA
1 AAAAATATTAA
79655448 AAAAATATTAA
1 AAAAATATTAA
79655459 AATAAATAT
1 AA-AAATAT
79655468 CTTTCAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAAATATTAA
Found at i:79658711 original size:20 final size:20
Alignment explanation
Indices: 79658688--79658737 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
79658678 AAATCTAAAT
79658688 TAAAATACTAAAAGTCAGGA
1 TAAAATACTAAAAGTCAGGA
* * *
79658708 TAAAATACTGAAATTTAGGA
1 TAAAATACTAAAAGTCAGGA
79658728 TAAGAATACT
1 TAA-AATACT
79658738 GATGTGGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.26
Consensus pattern (20 bp):
TAAAATACTAAAAGTCAGGA
Found at i:79660355 original size:17 final size:19
Alignment explanation
Indices: 79660321--79660357 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
79660311 CTATATTATG
*
79660321 TTTTAAATATATATTATTT
1 TTTTAAATATATAATATTT
79660340 TTTTAAA-AT-TAATATTT
1 TTTTAAATATATAATATTT
79660357 T
1 T
79660358 AGATGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 2 0.12
19 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTAAATATATAATATTT
Found at i:79671722 original size:22 final size:22
Alignment explanation
Indices: 79671671--79671731 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
79671661 ATAAGTAAAT
* *
79671671 ACAAAAATAA-AGGAAAATATA
1 ACAAAAATAATAGAAAAATACA
* *
79671692 ATAACAATAATAGAAAAATACA
1 ACAAAAATAATAGAAAAATACA
* *
79671714 ACAATAATAATAGTAAAA
1 ACAAAAATAATAGAAAAA
79671732 GATATAATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 8 0.25
22 24 0.75
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.18
Consensus pattern (22 bp):
ACAAAAATAATAGAAAAATACA
Found at i:79671831 original size:3 final size:3
Alignment explanation
Indices: 79671823--79672021 Score: 84
Period size: 3 Copynumber: 65.7 Consensus size: 3
79671813 AAAGTAGTGC
* *
79671823 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-C TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * *
79671870 GTTA TAA TGAA -AG TAA TGA TAA TGA TGA T-A TAT TAGA TAA TAA TAG
1 -TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
* * * * * * *
79671916 TAA -AA TAA TAA GTAA CAA TGA TAAA TTA TAA TAA TAG TGA TGA GAA
1 TAA TAA TAA TAA -TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
* * * * * * *
79671962 TAA TAA GTGA TGA TAA TAA CAA TAA CAA TAG TAG TAA TAA T-A TAT
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
79672007 TAG TAA TACA TAA TA
1 TAA TAA TA-A TAA TA
79672022 GAGTAGTAAA
Statistics
Matches: 147, Mismatches: 37, Indels: 24
0.71 0.18 0.12
Matches are distributed among these distances:
2 8 0.05
3 123 0.84
4 16 0.11
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:79671972 original size:16 final size:15
Alignment explanation
Indices: 79671945--79671980 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
79671935 GATAAATTAT
79671945 AATAATAGTGATGAG
1 AATAATAGTGATGAG
*
79671960 AATAATAAGTGATGAT
1 AATAAT-AGTGATGAG
79671976 AATAA
1 AATAA
79671981 CAATAACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (15 bp):
AATAATAGTGATGAG
Found at i:79672115 original size:16 final size:15
Alignment explanation
Indices: 79672086--79672128 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
79672076 TATACGTATG
*
79672086 AAAAATAATGATAGT
1 AAAAATAATAATAGT
79672101 AAAATATAATAATAGT
1 AAAA-ATAATAATAGT
*
79672117 AATAATAATAAT
1 AAAAATAATAAT
79672129 GGAATGAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (15 bp):
AAAAATAATAATAGT
Found at i:79672353 original size:3 final size:3
Alignment explanation
Indices: 79672339--79672374 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
79672329 AAATATACAC
79672339 TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
79672375 TTAAAATGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:79672916 original size:25 final size:27
Alignment explanation
Indices: 79672862--79672916 Score: 78
Period size: 25 Copynumber: 2.1 Consensus size: 27
79672852 AAAAATCCCC
* *
79672862 TCTTGAATCTCCAAAAAAAAAATTTCT
1 TCTTGAATCTCCAAAAAAAAAATCTAT
79672889 TCTTGAATCT-C-AAAAAAAAATCTAT
1 TCTTGAATCTCCAAAAAAAAAATCTAT
79672914 TCT
1 TCT
79672917 GTCCAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 15 0.58
26 1 0.04
27 10 0.38
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.35
Consensus pattern (27 bp):
TCTTGAATCTCCAAAAAAAAAATCTAT
Found at i:79673402 original size:16 final size:17
Alignment explanation
Indices: 79673365--79673402 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
79673355 TGACTTGAAT
79673365 TAAA-CCCAAATAACCC
1 TAAACCCCAAATAACCC
*
79673381 TGAACCCCAAATAACCC
1 TAAACCCCAAATAACCC
79673398 -AAACC
1 TAAACC
79673403 GAAAATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.47, C:0.39, G:0.03, T:0.11
Consensus pattern (17 bp):
TAAACCCCAAATAACCC
Found at i:79682471 original size:48 final size:48
Alignment explanation
Indices: 79682367--79682646 Score: 271
Period size: 48 Copynumber: 5.8 Consensus size: 48
79682357 TGAGATTCAA
* * * *
79682367 TGTAAGTCCATGTCTGGGGCATGGCATCGGC-ATCCGAGA-AGTGTGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCAGCGAT--GATATA-TGTGCCAG
* * * * * *
79682416 TGAAAGACCATGTCTAGGATATAGTATCAGCGATGATATATGTGCCTG
1 TGTAAGACCATGTCTGGGACATGGCATCAGCGATGATATATGTGCCAG
* * *
79682464 TGTAAGACTATGTCTGGGACATGGCATC-GATGATGATATATGTGCCTG
1 TGTAAGACCATGTCTGGGACATGGCATCAG-CGATGATATATGTGCCAG
* * *
79682512 TGTAAGACCATGTCTGGGACATGGCATCAACAATAATATATGTGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCAGCGATGATATATGTGCCAG
* * * *
79682560 TGTAAGACCATGTCTGGGACATGGAATCGGTGATTATATATGTGCC-G
1 TGTAAGACCATGTCTGGGACATGGCATCAGCGATGATATATGTGCCAG
* * **
79682607 TTATAAGACCATGTTTGGGACATGGCATTGGCGATGATAT
1 -TGTAAGACCATGTCTGGGACATGGCATCAGCGATGATAT
79682647 TTGGATTCAT
Statistics
Matches: 191, Mismatches: 35, Indels: 11
0.81 0.15 0.05
Matches are distributed among these distances:
47 2 0.01
48 163 0.85
49 24 0.13
50 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.28
Consensus pattern (48 bp):
TGTAAGACCATGTCTGGGACATGGCATCAGCGATGATATATGTGCCAG
Found at i:79682660 original size:144 final size:144
Alignment explanation
Indices: 79682408--79682682 Score: 329
Period size: 144 Copynumber: 1.9 Consensus size: 144
79682398 ATCCGAGAAG
* * * *
79682408 TGTGCCAGTGAAAGACCATGTCTAGGATATAGTATCAGCGATGATATATGTGCCTGTGTAAGACT
1 TGTGCCAGTGAAAGACCATGTCTAGGACATAGAATCAGCGATGATATATGTGCCTGTATAAGACC
* * * * **
79682473 ATGTCTGGGACATGGCATCGATGATGATATATGTGCCTGTGTAAGACCATGTCTGGGACATGGCA
66 ATGTCTGGGACATGGCATCGACGATGATATATGTGACTATGTAAAACCATGTCTAAGACATGGCA
79682538 TCAACAATAATATA
131 TCAACAATAATATA
* * * * * *
79682552 TGTGCCAGTGTAAGACCATGTCTGGGACATGGAATCGGTGATTATATATGTGCC-GTTATAAGAC
1 TGTGCCAGTGAAAGACCATGTCTAGGACATAGAATCAGCGATGATATATGTGCCTG-TATAAGAC
* * * * *
79682616 CATGTTTGGGACATGGCATTGGCGATGATATTTG-GATTCATGTAAAACCATGTCTAAGACATGG
65 CATGTCTGGGACATGGCATCGACGATGATATATGTGACT-ATGTAAAACCATGTCTAAGACATGG
79682680 CAT
129 CAT
79682683 TGATACTTTG
Statistics
Matches: 108, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
143 3 0.03
144 105 0.97
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (144 bp):
TGTGCCAGTGAAAGACCATGTCTAGGACATAGAATCAGCGATGATATATGTGCCTGTATAAGACC
ATGTCTGGGACATGGCATCGACGATGATATATGTGACTATGTAAAACCATGTCTAAGACATGGCA
TCAACAATAATATA
Found at i:79691415 original size:45 final size:41
Alignment explanation
Indices: 79691356--79691465 Score: 107
Period size: 45 Copynumber: 2.6 Consensus size: 41
79691346 TTTGGTTCGC
* *
79691356 TGTATTGGATTAGAGGTGTAATAGCAAATCAACTGTTTGGTT
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGG-T
* * ***
79691398 GAATGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGT
1 ---TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGT
79691441 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
79691466 TAATGGAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
39 20 0.36
40 2 0.04
43 1 0.02
44 11 0.20
45 21 0.38
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (41 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGT
Found at i:79691692 original size:61 final size:61
Alignment explanation
Indices: 79691627--79691814 Score: 199
Period size: 61 Copynumber: 3.1 Consensus size: 61
79691617 TTATAATTAA
*
79691627 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTATTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * *
79691688 AATATATGATACT-ATAAAA-TATAAATTAA-C-ATAATTATTAT-TAAATATA-TTATAATTAA
1 AATATATAAT-TTAATAAAATTATTAA-TAATCAAT-ATTCTTATATGAATTTACTCA-AATCAT
*
79691747 AATATATAATTTAATAATATTATTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTATTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
79691808 AATATAT
1 AATATAT
79691815 GATACTATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 20
0.71 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 29 0.30
60 25 0.26
61 37 0.38
62 3 0.03
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTATTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
Found at i:79691739 original size:15 final size:15
Alignment explanation
Indices: 79691711--79691769 Score: 61
Period size: 15 Copynumber: 4.0 Consensus size: 15
79691701 ATAAAATATA
79691711 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
79691726 TATTAAATATATTAT
1 AATTAAATATATTAT
79691741 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
79691754 AATTTAATAATATTAT
1 AATTAAAT-ATATTAT
79691770 TAATAATCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 9 0.24
14 6 0.16
15 19 0.51
16 3 0.08
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:79691741 original size:120 final size:120
Alignment explanation
Indices: 79691595--79691844 Score: 464
Period size: 120 Copynumber: 2.1 Consensus size: 120
79691585 ATCATATTTA
* *
79691595 AACATAATTATTATTAAGTATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAATCAA
79691660 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
*
79691715 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAATATTATTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAATCAA
*
79691780 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
79691835 AACATAATTA
1 AACATAATTA
79691845 ATAAAAATAT
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 126 1.00
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:79691770 original size:44 final size:43
Alignment explanation
Indices: 79691688--79691772 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
79691678 CTCAAATCAT
* *
79691688 AATATATGATACTATAAAATATAAATTAACATAATTATTATTA
1 AATATATGATAATATAAAATATAAATTAAAATAATTATTATTA
* *
79691731 AATATATTATAAT-TAAAATATATAATT-TAATAA-TATTATTA
1 AATATATGATAATATAAAATATA-AATTAAAATAATTATTATTA
79691772 A
1 A
79691773 TAATCAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
41 9 0.24
42 13 0.35
43 15 0.41
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (43 bp):
AATATATGATAATATAAAATATAAATTAAAATAATTATTATTA
Found at i:79691857 original size:103 final size:103
Alignment explanation
Indices: 79691740--79691979 Score: 338
Period size: 103 Copynumber: 2.3 Consensus size: 103
79691730 AAATATATTA
* * * * * *
79691740 TAATTAAAATATATAATTTAATAATATTATTAATAATCAATATTCTTATATGAATTTACTCAAAT
1 TAATAAAAATATATAATTTAATAAAAATATTAATAATAAATATTCTTATATGAATTTAATAAAAT
* *
79691805 CATAATATATGATACTATAAAATATAATTTAACATAAT
66 CATAATATATAATACTATAAAATATAATTTAAAATAAT
* *
79691843 TAATAAAAATATATAATTTAATAAAAATCTTAATATTAAATATTCTTATATGAATTTAATAAAAT
1 TAATAAAAATATATAATTTAATAAAAATATTAATAATAAATATTCTTATATGAATTTAATAAAAT
*
79691908 CATAATATATAATACTATATAATATAATTTAAAATAAT
66 CATAATATATAATACTATAAAATATAATTTAAAATAAT
* **
79691946 TATTATTAA-ATATAATTTAATAAAAATATATAAT
1 TAATAAAAATATATAATTTAATAAAAATAT-TAAT
79691980 TTAACATAAT
Statistics
Matches: 121, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
102 19 0.16
103 102 0.84
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.42
Consensus pattern (103 bp):
TAATAAAAATATATAATTTAATAAAAATATTAATAATAAATATTCTTATATGAATTTAATAAAAT
CATAATATATAATACTATAAAATATAATTTAAAATAAT
Found at i:79691884 original size:19 final size:18
Alignment explanation
Indices: 79691838--79691983 Score: 62
Period size: 18 Copynumber: 8.5 Consensus size: 18
79691828 ATAATTTAAC
79691838 ATAA-TTAATAAAAATAT
1 ATAATTTAATAAAAATAT
*
79691855 ATAATTTAATAAAAATCT
1 ATAATTTAATAAAAATAT
****
79691873 -TAATATTAAATATTCTTAT
1 ATAAT-TT-AATAAAAATAT
*
79691892 ATGAATTTAAT-AAAAT-C
1 AT-AATTTAATAAAAATAT
* * *
79691909 ATAATAT-ATAATACTAT
1 ATAATTTAATAAAAATAT
* *
79691926 ATAATATAATTTAAAATA-
1 ATAATTTAA-TAAAAATAT
* *
79691944 ATTA-TT-AT--TAA-AT
1 ATAATTTAATAAAAATAT
79691957 ATAATTTAATAAAAATAT
1 ATAATTTAATAAAAATAT
79691975 ATAATTTAA
1 ATAATTTAA
79691984 CATAATTATT
Statistics
Matches: 91, Mismatches: 23, Indels: 29
0.64 0.16 0.20
Matches are distributed among these distances:
12 1 0.01
13 5 0.05
14 2 0.02
15 5 0.05
16 8 0.09
17 20 0.22
18 30 0.33
19 14 0.15
20 3 0.03
21 3 0.03
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (18 bp):
ATAATTTAATAAAAATAT
Found at i:79691937 original size:38 final size:37
Alignment explanation
Indices: 79691853--79691939 Score: 97
Period size: 37 Copynumber: 2.3 Consensus size: 37
79691843 TAATAAAAAT
* * *
79691853 ATATAATTTAATAAAAATCTTAATATTAAATATTCTT
1 ATATAATTTAATAAAAATCATAATATTAAATATTATA
79691890 ATATGAATTTAAT-AAAATCATAATA-TATAATACTATATA
1 ATAT-AATTTAATAAAAATCATAATATTA-AATA-T-TATA
79691929 ATATAATTTAA
1 ATATAATTTAA
79691940 AATAATTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
36 2 0.05
37 19 0.44
38 16 0.37
39 6 0.14
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.43
Consensus pattern (37 bp):
ATATAATTTAATAAAAATCATAATATTAAATATTATA
Found at i:79692924 original size:21 final size:22
Alignment explanation
Indices: 79692891--79692946 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
79692881 AAAATATTAA
* *
79692891 ATTATATAAATTTTATATTTA-T
1 ATTA-ATATATTTTATAATTAGT
79692913 ATTAATATATTTTTATAATTAGT
1 ATTAATATA-TTTTATAATTAGT
79692936 -TTAA-ATATTTT
1 ATTAATATATTTT
79692947 TTAAACATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 4 0.13
21 7 0.23
22 18 0.60
23 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
ATTAATATATTTTATAATTAGT
Found at i:79692947 original size:21 final size:22
Alignment explanation
Indices: 79692901--79692947 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
79692891 ATTATATAAA
*
79692901 TTTTATATTTATATTAATATAT
1 TTTTATAATTATATTAATATAT
79692923 TTTTATAATTAGT-TTAA-ATAT
1 TTTTATAATTA-TATTAATATAT
79692944 TTTT
1 TTTT
79692948 TAAACATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 8 0.35
22 14 0.61
23 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTTATAATTATATTAATATAT
Found at i:79693387 original size:28 final size:30
Alignment explanation
Indices: 79693343--79693403 Score: 92
Period size: 28 Copynumber: 2.1 Consensus size: 30
79693333 TTTTCGTTAA
79693343 TTTAAAATTTAATCTCTTT-A-TTTTTATT
1 TTTAAAATTTAATCTCTTTCATTTTTTATT
79693371 TTTAAGAATTTAA-CTCTTTCATTTTTTATT
1 TTTAA-AATTTAATCTCTTTCATTTTTTATT
79693401 TTT
1 TTT
79693404 TAACTTCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 11 0.37
29 8 0.27
30 11 0.37
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.64
Consensus pattern (30 bp):
TTTAAAATTTAATCTCTTTCATTTTTTATT
Found at i:79697623 original size:26 final size:27
Alignment explanation
Indices: 79697565--79697635 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 27
79697555 TGTCGTTTAC
** *
79697565 ATAATTAAAATAT-AAAATAGTATATT
1 ATAATTAAAATATAAAAATAAAACATT
*
79697591 ATGATTAAAATATAAAAATAAAACATT
1 ATAATTAAAATATAAAAATAAAACATT
79697618 A-AATTAAAAT-TGAAAAAT
1 ATAATTAAAATAT-AAAAAT
79697636 CATATTGATA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
25 1 0.03
26 26 0.68
27 11 0.29
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (27 bp):
ATAATTAAAATATAAAAATAAAACATT
Found at i:79697796 original size:17 final size:18
Alignment explanation
Indices: 79697761--79697799 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
79697751 AAAATCCAAC
79697761 TAAATAAAAAAATGAAATT
1 TAAATAAAAAAAT-AAATT
* *
79697780 TAAATAAAAAGATAATTT
1 TAAATAAAAAAATAAATT
79697798 TA
1 TA
79697800 TTTTTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (18 bp):
TAAATAAAAAAATAAATT
Found at i:79703916 original size:6 final size:6
Alignment explanation
Indices: 79703905--79703944 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
79703895 GGCCTAATAT
79703905 TGCCTA TGCCTA TGCCTA TGCCTA TGCCTA TGCCTA TGCC
1 TGCCTA TGCCTA TGCCTA TGCCTA TGCCTA TGCCTA TGCC
79703945 ATCTATCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.15, C:0.35, G:0.17, T:0.33
Consensus pattern (6 bp):
TGCCTA
Found at i:79706170 original size:26 final size:28
Alignment explanation
Indices: 79706129--79706195 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 28
79706119 TCTAAGATAA
* * *
79706129 AAATTAATCCCGATGCTCAAT-C-CAAC
1 AAATTAAACCCAATGCCCAATACACAAC
*
79706155 AAATTAAACCCAATGCCCAATACACAAT
1 AAATTAAACCCAATGCCCAATACACAAC
*
79706183 AAACTAAACCCAA
1 AAATTAAACCCAA
79706196 ACCCGATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 18 0.53
27 1 0.03
28 15 0.44
ACGTcount: A:0.48, C:0.30, G:0.04, T:0.18
Consensus pattern (28 bp):
AAATTAAACCCAATGCCCAATACACAAC
Found at i:79706242 original size:22 final size:23
Alignment explanation
Indices: 79706216--79706258 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
79706206 AAAAAATAAT
* *
79706216 AATTT-AAGAATTAAATTTAAAG
1 AATTTAAAGAATAAAACTTAAAG
79706238 AATTTAAAGAATAAAACTTAA
1 AATTTAAAGAATAAAACTTAA
79706259 TTCAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (23 bp):
AATTTAAAGAATAAAACTTAAAG
Found at i:79714745 original size:6 final size:6
Alignment explanation
Indices: 79714730--79714761 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
79714720 GGAATACACC
*
79714730 GTAACG GTAACA GTAACA GTAACA GTAACA GT
1 GTAACA GTAACA GTAACA GTAACA GTAACA GT
79714762 CAGGTACAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.19
Consensus pattern (6 bp):
GTAACA
Found at i:79716867 original size:109 final size:109
Alignment explanation
Indices: 79716673--79716978 Score: 429
Period size: 109 Copynumber: 2.8 Consensus size: 109
79716663 TAAATTCAAT
* * * * * * * *
79716673 AGGATATTTGGCAATTCGGTTAAACGAG--AAATCGAAACCCAGTATCTTAGGGCACG-TTCCTT
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGTACCTTAGGGCACGTTTTCTC
* *
79716735 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGAA
66 GAATTTCCAAACGCAAAATATTGCCTTATTTTGAAATTTTTAAA
* * * * *
79716779 AGGATATTTAGCTATTTGGTTGAATGAGAAAAATCTATACCCAGTACCTTAGGGCATGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGTACCTTAGGGCACGTTTTCTC
*
79716844 GAATTTCCAAACACAAAATATTGCCTTATTTTGAAATTTTTAAA
66 GAATTTCCAAACGCAAAATATTGCCTTATTTTGAAATTTTTAAA
*
79716888 ATGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGTACCTTAGGGCACGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGTACCTTAGGGCACGTTTTCTC
*
79716953 GAATTTCCAAACGCTAAATATTGCCT
66 GAATTTCCAAACGCAAAATATTGCCT
79716979 CAATCGAAAA
Statistics
Matches: 175, Mismatches: 22, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
106 23 0.13
108 24 0.14
109 128 0.73
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Consensus pattern (109 bp):
AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGTACCTTAGGGCACGTTTTCTC
GAATTTCCAAACGCAAAATATTGCCTTATTTTGAAATTTTTAAA
Found at i:79717850 original size:20 final size:20
Alignment explanation
Indices: 79717814--79717853 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
79717804 TCCTATTGTT
79717814 GTTTTGTTACTGTTTGCTGC
1 GTTTTGTTACTGTTTGCTGC
*
79717834 GTTTCTGTTTCTG-TTGCTGC
1 GTTT-TGTTACTGTTTGCTGC
79717854 TTCCGTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.03, C:0.17, G:0.25, T:0.55
Consensus pattern (20 bp):
GTTTTGTTACTGTTTGCTGC
Found at i:79718755 original size:20 final size:20
Alignment explanation
Indices: 79718719--79718758 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
79718709 TCCTATTGTT
79718719 GTTTTGTTACTGTTTGCTGC
1 GTTTTGTTACTGTTTGCTGC
*
79718739 GTTTCTGTTTCTG-TTGCTGC
1 GTTT-TGTTACTGTTTGCTGC
79718759 TTCCGTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.03, C:0.17, G:0.25, T:0.55
Consensus pattern (20 bp):
GTTTTGTTACTGTTTGCTGC
Found at i:79723322 original size:26 final size:26
Alignment explanation
Indices: 79723292--79723399 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
79723282 TGAAATGCCC
*
79723292 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
79723318 ATCATGGAACATTTACATAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
79723344 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
79723370 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
79723396 ATCA
1 ATCA
79723400 ATTTGTATCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:79724844 original size:3 final size:3
Alignment explanation
Indices: 79724832--79724868 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
79724822 ATATAAAACC
*
79724832 ATA ATAA ATA ATA ATA ATA ATA AGA ATA ATA ATA ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
79724869 TACATATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:79732248 original size:19 final size:19
Alignment explanation
Indices: 79732206--79732248 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
79732196 TTTTAATGTA
79732206 TATTTTTAAAATTTTAAAT
1 TATTTTTAAAATTTTAAAT
* ** *
79732225 AATTTTTATTATTTTTAAT
1 TATTTTTAAAATTTTAAAT
79732244 TATTT
1 TATTT
79732249 ATTTAATTAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTTTAAAATTTTAAAT
Found at i:79751176 original size:18 final size:18
Alignment explanation
Indices: 79751149--79751191 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
79751139 ATTTTCAGAT
79751149 ATTTA-AAAAATTTTAAAA
1 ATTTATAAAAA-TTTAAAA
*
79751167 ATTTATAAAAATTTCAAA
1 ATTTATAAAAATTTAAAA
79751185 ATTTATA
1 ATTTATA
79751192 TTTTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTATAAAAATTTAAAA
Found at i:79754289 original size:5 final size:5
Alignment explanation
Indices: 79754279--79754333 Score: 110
Period size: 5 Copynumber: 11.0 Consensus size: 5
79754269 TTACTGCAAC
79754279 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
79754329 ATTTT
1 ATTTT
79754334 TGAACCAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 50 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:79759564 original size:13 final size:13
Alignment explanation
Indices: 79759526--79759565 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
79759516 ACATAAGATC
79759526 AATTACTTGATTA
1 AATTACTTGATTA
* *
79759539 AATTATTTTATTA
1 AATTACTTGATTA
*
79759552 AATTACCTGATTA
1 AATTACTTGATTA
79759565 A
1 A
79759566 TTTAACTATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.47
Consensus pattern (13 bp):
AATTACTTGATTA
Found at i:79769940 original size:27 final size:27
Alignment explanation
Indices: 79769902--79769957 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
79769892 CTAGTTTGCG
79769902 TTGCCTTTAATATTTTTTTATAAACTA
1 TTGCCTTTAATATTTTTTTATAAACTA
79769929 TTGCCTTTAATATTTTTTTATAAACTA
1 TTGCCTTTAATATTTTTTTATAAACTA
79769956 TT
1 TT
79769958 TTAATATTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.11, G:0.04, T:0.57
Consensus pattern (27 bp):
TTGCCTTTAATATTTTTTTATAAACTA
Found at i:79776347 original size:15 final size:15
Alignment explanation
Indices: 79776326--79776367 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
79776316 AAAAAGTAAA
*
79776326 AAAAATTAAATTTGC
1 AAAAATTAAATTTAC
*
79776341 TAAAATTAAATTTAC
1 AAAAATTAAATTTAC
*
79776356 AAAAACTAAATT
1 AAAAATTAAATT
79776368 GAAATTTGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (15 bp):
AAAAATTAAATTTAC
Done.