Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 16 of 93
Found at i:7376465 original size:28 final size:28
Alignment explanation
Indices: 7376434--7376591 Score: 122
Period size: 28 Copynumber: 5.7 Consensus size: 28
7376424 AGCGTGCAAT
* *
7376434 AATTAAATTTTTTAATATAATGTGTAAC
1 AATTAAATTTTTTAATATGATATGTAAC
* * **
7376462 AATTAAA-TCTTCAGCATGATATGTAAC
1 AATTAAATTTTTTAATATGATATGTAAC
* * *
7376489 AATTACATTTTTTAACATAATATGTAAC
1 AATTAAATTTTTTAATATGATATGTAAC
* *
7376517 AATTAAA-TTTTTAATCTGACATGTAAC
1 AATTAAATTTTTTAATATGATATGTAAC
* * * ** *
7376544 AGTTACATTTTTCAATATGACGTGTAAT
1 AATTAAATTTTTTAATATGATATGTAAC
* **
7376572 AGTTAAATTTTAAAATATGA
1 AATTAAATTTTTTAATATGA
7376592 CGTATAATAC
Statistics
Matches: 103, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
27 41 0.40
28 62 0.60
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (28 bp):
AATTAAATTTTTTAATATGATATGTAAC
Found at i:7376500 original size:55 final size:54
Alignment explanation
Indices: 7376434--7376584 Score: 158
Period size: 55 Copynumber: 2.8 Consensus size: 54
7376424 AGCGTGCAAT
* * *
7376434 AATTAAATTTTTTAATATAATGTGTAACAATTAAATCTTCAGCATGATATGTAAC
1 AATTACATTTTTTAATATAATGTGTAACAATTAAATCTTAAGC-TGACATGTAAC
* * * *
7376489 AATTACATTTTTTAACATAATATGTAACAATTAAATTTTTAATCTGACATGTAAC
1 AATTACATTTTTTAATATAATGTGTAACAATTAAA-TCTTAAGCTGACATGTAAC
* * * * * * *
7376544 AGTTACATTTTTCAATATGACGTGTAATAGTTAAATTTTAA
1 AATTACATTTTTTAATATAATGTGTAACAATTAAATCTTAA
7376585 AATATGACGT
Statistics
Matches: 80, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
54 6 0.08
55 69 0.86
56 5 0.06
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (54 bp):
AATTACATTTTTTAATATAATGTGTAACAATTAAATCTTAAGCTGACATGTAAC
Found at i:7376592 original size:28 final size:27
Alignment explanation
Indices: 7376519--7376600 Score: 83
Period size: 28 Copynumber: 3.0 Consensus size: 27
7376509 TATGTAACAA
* * * *
7376519 TTAAATTTTTAATCTGACATGTAACAG
1 TTAAATTTTAAATATGACGTGTAATAG
* *
7376546 TTACATTTTTCAATATGACGTGTAATAG
1 TTA-AATTTTAAATATGACGTGTAATAG
*
7376574 TTAAATTTTAAAATATGACGTATAATA
1 TTAAATTTT-AAATATGACGTGTAATA
7376601 CAACATTTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
27 8 0.18
28 37 0.82
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (27 bp):
TTAAATTTTAAATATGACGTGTAATAG
Found at i:7383173 original size:32 final size:31
Alignment explanation
Indices: 7383137--7383202 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 31
7383127 CTTAATTTGA
*
7383137 TTTTTTTTAATTTAAAAATTATTGTGAAGTNG
1 TTTTTTTTAATTTAAAAATTATTATGAAGT-G
*
7383169 TTTTTTTTAATTTAAAAGTTATTATGAAGT-
1 TTTTTTTTAATTTAAAAATTATTATGAAGTG
7383199 TTTT
1 TTTT
7383203 ATAAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 4 0.12
32 28 0.88
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.58
Consensus pattern (31 bp):
TTTTTTTTAATTTAAAAATTATTATGAAGTG
Found at i:7389710 original size:2 final size:2
Alignment explanation
Indices: 7389703--7389773 Score: 85
Period size: 2 Copynumber: 37.0 Consensus size: 2
7389693 CAACTTACTA
7389703 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
7389744 AT -T GT AT AA AT AT AT -T CT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7389774 TTAATTTATA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
1 3 0.05
2 57 0.95
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7391114 original size:6 final size:6
Alignment explanation
Indices: 7391105--7391153 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
7391095 AAAAATAATG
* * *
7391105 AAAAAC AAAAAC AATAAC -AAAA- AATAA- AAAAAC AAGAAC AAAAAC
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
7391150 AAAA
1 AAAA
7391154 GCTGGTTATC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
5 10 0.29
6 25 0.71
ACGTcount: A:0.82, C:0.12, G:0.02, T:0.04
Consensus pattern (6 bp):
AAAAAC
Found at i:7391126 original size:27 final size:27
Alignment explanation
Indices: 7391095--7391153 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
7391085 GTTAAAAAGT
*
7391095 AAAAATAATGAAAAACAAAAACAATAACA
1 AAAAATAA--AAAAACAAAAACAAAAACA
*
7391124 AAAAATAAAAAAACAAGAACAAAAACA
1 AAAAATAAAAAAACAAAAACAAAAACA
7391151 AAA
1 AAA
7391154 GCTGGTTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 20 0.71
29 8 0.29
ACGTcount: A:0.80, C:0.10, G:0.03, T:0.07
Consensus pattern (27 bp):
AAAAATAAAAAAACAAAAACAAAAACA
Found at i:7395338 original size:23 final size:24
Alignment explanation
Indices: 7395308--7395359 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
7395298 ATTTTCGGTT
*
7395308 AAAAAATAA-AAATAA-TGAAAAAC
1 AAAAAATAACAAA-AAGTAAAAAAC
7395331 AAAAAATAACAAAAAGTAAAAAAC
1 AAAAAATAACAAAAAGTAAAAAAC
7395355 AAAAA
1 AAAAA
7395360 CCAAAGCAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.81, C:0.06, G:0.04, T:0.10
Consensus pattern (24 bp):
AAAAAATAACAAAAAGTAAAAAAC
Found at i:7397952 original size:22 final size:22
Alignment explanation
Indices: 7397927--7397985 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
7397917 ATATTACTGA
** *
7397927 TTTTTAGGTATTGTGTCACTAG
1 TTTTTAGGTATTACGACACTAG
* *
7397949 TTTTTAAGTATTACGAGACTAG
1 TTTTTAGGTATTACGACACTAG
*
7397971 TTTTTAGGCATTACG
1 TTTTTAGGTATTACG
7397986 TGACTTAATC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.46
Consensus pattern (22 bp):
TTTTTAGGTATTACGACACTAG
Found at i:7397990 original size:22 final size:22
Alignment explanation
Indices: 7397944--7397990 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
7397934 GTATTGTGTC
*
7397944 ACTAGTTTTTAAGTATTACGAG
1 ACTAGTTTTTAAGCATTACGAG
* *
7397966 ACTAGTTTTTAGGCATTACGTG
1 ACTAGTTTTTAAGCATTACGAG
7397988 ACT
1 ACT
7397991 TAATCATTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (22 bp):
ACTAGTTTTTAAGCATTACGAG
Found at i:7398039 original size:22 final size:22
Alignment explanation
Indices: 7397990--7398040 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
7397980 ATTACGTGAC
* *
7397990 TTAATCATTGCGTGACTGAGTT
1 TTAAGCATTGCATGACTGAGTT
* * *
7398012 TCAAGCATTGCATGACTTATTT
1 TTAAGCATTGCATGACTGAGTT
7398034 TTAAGCA
1 TTAAGCA
7398041 ATGTCTAAGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (22 bp):
TTAAGCATTGCATGACTGAGTT
Found at i:7398076 original size:23 final size:23
Alignment explanation
Indices: 7398045--7398130 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
7398035 TAAGCAATGT
* *
7398045 CTAAGTCACATAATGTCTTACTAA
1 CTAA-TCACGTAATGCCTTACTAA
*
7398069 CTAATCACGCAATGCCTTACTAA
1 CTAATCACGTAATGCCTTACTAA
*
7398092 CTAGTCACGTAATGCCTTACTAA
1 CTAATCACGTAATGCCTTACTAA
* *
7398115 CAAATCACGCAATGCC
1 CTAATCACGTAATGCC
7398131 ATATCAGTCA
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
23 50 0.93
24 4 0.07
ACGTcount: A:0.35, C:0.28, G:0.10, T:0.27
Consensus pattern (23 bp):
CTAATCACGTAATGCCTTACTAA
Found at i:7398172 original size:22 final size:22
Alignment explanation
Indices: 7398142--7398229 Score: 54
Period size: 22 Copynumber: 4.0 Consensus size: 22
7398132 TATCAGTCAA
*
7398142 TCACACAATACCTAAAAATTAG
1 TCACGCAATACCTAAAAATTAG
* * * *
7398164 TCACGCAATGCTTTAAAACTAG
1 TCACGCAATACCTAAAAATTAG
** *
7398186 TCACGTTATATCC--AAAATCAG
1 TCACGCAATA-CCTAAAAATTAG
* **
7398207 TCATGCAATGTCTAAAAATTAG
1 TCACGCAATACCTAAAAATTAG
7398229 T
1 T
7398230 AACATAATGC
Statistics
Matches: 46, Mismatches: 17, Indels: 6
0.67 0.25 0.09
Matches are distributed among these distances:
20 1 0.02
21 12 0.26
22 32 0.70
23 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.28
Consensus pattern (22 bp):
TCACGCAATACCTAAAAATTAG
Found at i:7398238 original size:22 final size:22
Alignment explanation
Indices: 7398219--7398261 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
7398209 ATGCAATGTC
* *
7398219 TAAAAATTAGTAACATAATGCT
1 TAAAAACTAATAACATAATGCT
*
7398241 TAAAAACTAATCACATAATGC
1 TAAAAACTAATAACATAATGC
7398262 CCCAAAATCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.28
Consensus pattern (22 bp):
TAAAAACTAATAACATAATGCT
Found at i:7398520 original size:51 final size:51
Alignment explanation
Indices: 7398397--7398525 Score: 159
Period size: 52 Copynumber: 2.5 Consensus size: 51
7398387 ACAAAGAATA
* * * *
7398397 CTCAAAATGCTCAAAGGTTTTTTTTCATATATCAAAAATTATTTCAAAATG
1 CTCAAAATGCTCAAAAGTTTTTCTTCATATATCAAAAACTATTTCAAAAAG
* * * *
7398448 CTTAAAAATGCTCAAAAGTTTTTCTTCATGTATTAAAAACTATTTTAAAAAG
1 C-TCAAAATGCTCAAAAGTTTTTCTTCATATATCAAAAACTATTTCAAAAAG
* *
7398500 CTCAAAATGCTTAAACGTTTTTCTTC
1 CTCAAAATGCTCAAAAGTTTTTCTTC
7398526 TAGTAAAGAA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
51 23 0.35
52 43 0.65
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.40
Consensus pattern (51 bp):
CTCAAAATGCTCAAAAGTTTTTCTTCATATATCAAAAACTATTTCAAAAAG
Found at i:7404512 original size:16 final size:15
Alignment explanation
Indices: 7404493--7404522 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
7404483 TTTTAAATTT
7404493 TTAAAAATTAAAATCA
1 TTAAAAA-TAAAATCA
7404509 TTAAAAATAAAATC
1 TTAAAAATAAAATC
7404523 CACATAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (15 bp):
TTAAAAATAAAATCA
Found at i:7404709 original size:14 final size:14
Alignment explanation
Indices: 7404668--7404713 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
7404658 AATAGAATTG
7404668 AAAAAA-ATAAATA
1 AAAAAATATAAATA
*
7404681 ATAATAATATAAATA
1 A-AAAAATATAAATA
*
7404696 AAAAAATTTAAATA
1 AAAAAATATAAATA
7404710 AAAA
1 AAAA
7404714 CTTTACTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 1 0.04
14 19 0.68
15 8 0.29
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAAAATATAAATA
Found at i:7414259 original size:2 final size:2
Alignment explanation
Indices: 7414252--7414375 Score: 104
Period size: 2 Copynumber: 64.5 Consensus size: 2
7414242 NNNNNNNNNN
*
7414252 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
7414293 CT GAT A- AA AT TT CAT CCT -T AT AT -T A- AT -T AT -T AT -T CAT
1 AT -AT AT AT AT AT -AT -AT AT AT AT AT AT AT AT AT AT AT AT -AT
7414330 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7414371 AT AT A
1 AT AT A
7414376 AAGAGTAAAT
Statistics
Matches: 103, Mismatches: 7, Indels: 24
0.77 0.05 0.18
Matches are distributed among these distances:
1 9 0.09
2 89 0.86
3 5 0.05
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7415994 original size:26 final size:26
Alignment explanation
Indices: 7415961--7416033 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
7415951 TTTGTAAATT
*
7415961 TTAAAATATTAATATTA-TATATATAA
1 TTAAAATATTAATAATATTA-ATATAA
* * *
7415987 TTGAAATATTATTAATATTAATATGA
1 TTAAAATATTAATAATATTAATATAA
7416013 TTAAAATATTAA-AATATTAAT
1 TTAAAATATTAATAATATTAAT
7416034 TTTTTAAACT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
25 9 0.22
26 29 0.73
27 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (26 bp):
TTAAAATATTAATAATATTAATATAA
Found at i:7416009 original size:15 final size:15
Alignment explanation
Indices: 7415965--7416016 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 15
7415955 TAAATTTTAA
7415965 AATATTAATATTATAT
1 AATATTAATATTAT-T
7415981 ATATAATTGAAATATTATT
1 A-AT-ATT--AATATTATT
*
7416000 AATATTAATATGATT
1 AATATTAATATTATT
7416015 AA
1 AA
7416017 AATATTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
15 10 0.32
16 1 0.03
17 5 0.16
18 5 0.16
19 2 0.06
20 8 0.26
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (15 bp):
AATATTAATATTATT
Found at i:7416025 original size:8 final size:8
Alignment explanation
Indices: 7415990--7416032 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
7415980 TATATAATTG
7415990 AAATATTA
1 AAATATTA
*
7415998 TTAATATTA
1 -AAATATTA
*
7416007 ATATGATTA
1 AAAT-ATTA
7416016 AAATATTA
1 AAATATTA
7416024 AAATATTA
1 AAATATTA
7416032 A
1 A
7416033 TTTTTTAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 15 0.52
9 14 0.48
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (8 bp):
AAATATTA
Found at i:7416082 original size:16 final size:16
Alignment explanation
Indices: 7416002--7416088 Score: 54
Period size: 16 Copynumber: 5.4 Consensus size: 16
7415992 ATATTATTAA
*
7416002 TATTAATATGATTAAAA
1 TATTAATAT-ATTAAAT
* *
7416019 TATTAAAATATTAATT
1 TATTAATATATTAAAT
*
7416035 TTTTAA-ACTATT-AAT
1 TATTAATA-TATTAAAT
* *
7416050 GT-TTTATTTATTAAAT
1 -TATTAATATATTAAAT
*
7416066 TATTAATATATTTAAT
1 TATTAATATATTAAAT
*
7416082 TTTTAAT
1 TATTAAT
7416089 GAGTATAAAT
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
15 11 0.20
16 35 0.65
17 8 0.15
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (16 bp):
TATTAATATATTAAAT
Found at i:7416130 original size:22 final size:23
Alignment explanation
Indices: 7416103--7416162 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
7416093 ATAAATAAAA
*
7416103 ATAAAA-ATTATTAATATTTTA-
1 ATAAAATATTATTAATATTATAC
*
7416124 ATCAAAATAATATTAA-ATTATAC
1 AT-AAAATATTATTAATATTATAC
7416147 ATAAAATATTATTAAT
1 ATAAAATATTATTAAT
7416163 TAAANNNNNN
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 2 0.06
22 21 0.66
23 9 0.28
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (23 bp):
ATAAAATATTATTAATATTATAC
Found at i:7416899 original size:2 final size:2
Alignment explanation
Indices: 7416892--7416925 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
7416882 NNNNNNNNNN
7416892 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7416926 GTTGCTTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7419416 original size:2 final size:2
Alignment explanation
Indices: 7419409--7419438 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7419399 GGACATACAT
7419409 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
7419439 AAGAATGGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:7419529 original size:2 final size:2
Alignment explanation
Indices: 7419522--7419553 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
7419512 ATCAGTTGTN
7419522 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
7419554 GAAAAATGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7419610 original size:116 final size:115
Alignment explanation
Indices: 7419409--7419636 Score: 431
Period size: 116 Copynumber: 2.0 Consensus size: 115
7419399 GGACATACAT
7419409 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAATGGGGAGGATGGAAGAATATTAATTGAAAA
1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAATGGGGAGGATGGAAGAATATTAATTGAAAA
7419474 ATTAATAGGCAATGAGTCAATGGCCTCGACTCAGAGTCATCAGTTGTNAGA
66 ATTAATAGGCAATGAGTCAATGGCCTCGACTCAGAGTCATCAGTTGT-AGA
7419525 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGGAAA-AATGGGGAGGATGGAAGAATATTAATTGAAA
1 GAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAAAGAATGGGGAGGATGGAAGAATATTAATTGAAA
7419589 AATTAATAGGCAATGAGTCAATGGCCTCGACTCAGAGTCATCAGTTGT
65 AATTAATAGGCAATGAGTCAATGGCCTCGACTCAGAGTCATCAGTTGT
7419637 TGTTTATGTA
Statistics
Matches: 111, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
116 107 0.96
117 4 0.04
ACGTcount: A:0.41, C:0.08, G:0.33, T:0.18
Consensus pattern (115 bp):
GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAATGGGGAGGATGGAAGAATATTAATTGAAAA
ATTAATAGGCAATGAGTCAATGGCCTCGACTCAGAGTCATCAGTTGTAGA
Found at i:7427846 original size:30 final size:29
Alignment explanation
Indices: 7427801--7427866 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
7427791 CAATCAAGTT
* *
7427801 TATTTATTTTTTATTTTAAATTAAATAAA
1 TATTTATTTTCTATTTTAAATCAAATAAA
* *
7427830 TTTTTATATTTCTATTTTGAATCAAATAAA
1 TATTTAT-TTTCTATTTTAAATCAAATAAA
7427860 TATTTAT
1 TATTTAT
7427867 GATTAATGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 6 0.19
30 25 0.81
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (29 bp):
TATTTATTTTCTATTTTAAATCAAATAAA
Found at i:7438377 original size:2 final size:2
Alignment explanation
Indices: 7438370--7438405 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
7438360 NNNNNNNNNN
7438370 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7438406 TCTTACTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7439023 original size:8 final size:8
Alignment explanation
Indices: 7439010--7439036 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
7439000 ACAAAATAAA
7439010 AAATAATT
1 AAATAATT
7439018 AAATAATT
1 AAATAATT
7439026 AAATAATT
1 AAATAATT
7439034 AAA
1 AAA
7439037 AAGGTGGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAATAATT
Found at i:7439661 original size:16 final size:16
Alignment explanation
Indices: 7439640--7439671 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
7439630 GACGTGGTAC
*
7439640 AAAATTTTTTTTTTTG
1 AAAATTTTTTTATTTG
7439656 AAAATTTTTTTATTTG
1 AAAATTTTTTTATTTG
7439672 CCATGTGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (16 bp):
AAAATTTTTTTATTTG
Found at i:7440392 original size:22 final size:23
Alignment explanation
Indices: 7440367--7440415 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
7440357 TTAAAATTTC
* *
7440367 AAAATTTAATAA-TATATTTTTG
1 AAAATTTAAAAATTATATTTTTA
*
7440389 AAAATTTAAAAATTTTATTTTTA
1 AAAATTTAAAAATTATATTTTTA
7440412 AAAA
1 AAAA
7440416 AATTTATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AAAATTTAAAAATTATATTTTTA
Found at i:7440435 original size:24 final size:25
Alignment explanation
Indices: 7440389--7440435 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
7440379 TATATTTTTG
* *
7440389 AAAATTTAAAAATTTTATTTTTAAA
1 AAAATTTAAAAATTTCATCTTTAAA
*
7440414 AAAATTT-ATAATTTCATCTTTA
1 AAAATTTAAAAATTTCATCTTTA
7440436 TAAATATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (25 bp):
AAAATTTAAAAATTTCATCTTTAAA
Found at i:7445741 original size:5 final size:5
Alignment explanation
Indices: 7445701--7445751 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
7445691 ACATATAAGT
* *
7445701 AAATA GAATA TAAATA ATAATA ATAATA ATAT- AAATA AAATA AAATA
1 AAATA AAATA -AAATA A-AATA A-AATA AAATA AAATA AAATA AAATA
7445748 AAAT
1 AAAT
7445752 TGAGTCAGCT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 3 0.08
5 21 0.54
6 15 0.38
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (5 bp):
AAATA
Found at i:7460189 original size:28 final size:29
Alignment explanation
Indices: 7460144--7460205 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
7460134 ATTAAGTGAC
* *
7460144 ATTTTAATTAATAAAAAT-TAATTATAAA
1 ATTTTAATTAATAAAAATAAAAATATAAA
* **
7460172 ATTTTATTTAATTTAAATAAAAATATAAA
1 ATTTTAATTAATAAAAATAAAAATATAAA
7460201 ATTTT
1 ATTTT
7460206 GATGATATAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
ATTTTAATTAATAAAAATAAAAATATAAA
Found at i:7469605 original size:37 final size:35
Alignment explanation
Indices: 7469564--7469633 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 35
7469554 ATTGCGCTAG
7469564 GGTAAAAAATTAGACTTTCTAGGAGATCAATTGTTAA
1 GGTAAAAAATT-GACTTT-TAGGAGATCAATTGTTAA
* *
7469601 GGTAAAATATTGCCTTTTAGGAGATCAATTGTT
1 GGTAAAAAATTGACTTTTAGGAGATCAATTGTT
7469634 GTATTGATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 16 0.52
36 5 0.16
37 10 0.32
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.36
Consensus pattern (35 bp):
GGTAAAAAATTGACTTTTAGGAGATCAATTGTTAA
Found at i:7475731 original size:30 final size:29
Alignment explanation
Indices: 7475695--7475771 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 29
7475685 AATTGTTAAT
**
7475695 TATAAAAATTTATTTAATTTAAAATA-AAAA
1 TATAAAAATTTATTTAAAGT--AATAGAAAA
*
7475725 TATAAAAATTTAATTGAAAGTAATAGAAAA
1 TATAAAAATTT-ATTTAAAGTAATAGAAAA
7475755 -ATAAAAATTTATTTAAA
1 TATAAAAATTTATTTAAA
7475772 TATTTTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 6 0.15
29 14 0.34
30 15 0.37
31 6 0.15
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (29 bp):
TATAAAAATTTATTTAAAGTAATAGAAAA
Found at i:7479166 original size:30 final size:30
Alignment explanation
Indices: 7479132--7479212 Score: 105
Period size: 29 Copynumber: 2.7 Consensus size: 30
7479122 ATTTGTAGAG
7479132 ATAAAATTATAAAATTTTTAAAAA-ATAAAA
1 ATAAAATTATAAAA-TTTTAAAAAGATAAAA
*
7479162 ATAAAAATT-TAAAATTTAAAAAAGATAAAA
1 AT-AAAATTATAAAATTTTAAAAAGATAAAA
*
7479192 AT-AAATTATAAAAATTTAAAA
1 ATAAAATTATAAAATTTTAAAA
7479213 TTTTTGGAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
28 5 0.11
29 19 0.42
30 15 0.33
31 6 0.13
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (30 bp):
ATAAAATTATAAAATTTTAAAAAGATAAAA
Found at i:7479196 original size:22 final size:23
Alignment explanation
Indices: 7479158--7479205 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 23
7479148 TTTAAAAAAT
7479158 AAAAATAAAAATTTAAAATT-TAA
1 AAAAATAAAAA-TTAAAATTATAA
7479181 AAAAGATAAAAA-T-AAATTATAA
1 AAAA-ATAAAAATTAAAATTATAA
7479203 AAA
1 AAA
7479206 TTTAAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 5 0.22
22 7 0.30
23 4 0.17
24 7 0.30
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (23 bp):
AAAAATAAAAATTAAAATTATAA
Found at i:7480602 original size:47 final size:48
Alignment explanation
Indices: 7480474--7480605 Score: 137
Period size: 50 Copynumber: 2.7 Consensus size: 48
7480464 AGAAATATTA
*
7480474 AAAATATATAGT-AAATAAATAATTCCTT-AAATTTTGAAAGGAACTCTT
1 AAAATATATA-TAAAATAAAAAATT-CTTAAAATTTTGAAAGGAACTCTT
* **
7480522 AAAAAATATATAATAAATAAAAAATTCCAAAAATTTTGAAAGG-A-TCATT
1 AAAATATATAT-A-AAATAAAAAATTCTTAAAATTTTGAAAGGAACTC-TT
* *
7480571 AATATATATATAAAATAAAAAATTTTTAAAATTTT
1 AAAATATATATAAAATAAAAAATTCTTAAAATTTT
7480606 TCAACCCCCC
Statistics
Matches: 70, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
47 21 0.30
48 12 0.17
49 13 0.19
50 24 0.34
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (48 bp):
AAAATATATATAAAATAAAAAATTCTTAAAATTTTGAAAGGAACTCTT
Found at i:7480716 original size:3 final size:3
Alignment explanation
Indices: 7480710--7480744 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
7480700 GTCCCATGAC
7480710 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
7480745 TATTATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:7480749 original size:3 final size:3
Alignment explanation
Indices: 7480743--7480768 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
7480733 AATAATAATA
7480743 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
7480769 CTAAATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:7482380 original size:6 final size:6
Alignment explanation
Indices: 7482369--7482395 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
7482359 GAGAGAATGC
7482369 ATGTGG ATGTGG ATGTGG ATGTGG ATG
1 ATGTGG ATGTGG ATGTGG ATGTGG ATG
7482396 GCTACTGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.48, T:0.33
Consensus pattern (6 bp):
ATGTGG
Found at i:7482992 original size:2 final size:2
Alignment explanation
Indices: 7482985--7483019 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
7482975 GTTAAAGGCA
7482985 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7483020 GAACATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7483925 original size:11 final size:11
Alignment explanation
Indices: 7483909--7483942 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
7483899 GATTTTTATA
*
7483909 TAAAAAGTAAT
1 TAAAAAATAAT
7483920 TAAAAAATAAT
1 TAAAAAATAAT
7483931 TATAAAAATAAT
1 TA-AAAAATAAT
7483943 CATAATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (11 bp):
TAAAAAATAAT
Found at i:7483937 original size:12 final size:12
Alignment explanation
Indices: 7483907--7483947 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
7483897 TAGATTTTTA
7483907 TATAAAAAGTAAT
1 TATAAAAA-TAAT
7483920 TA-AAAAATAAT
1 TATAAAAATAAT
7483931 TATAAAAATAAT
1 TATAAAAATAAT
*
7483943 CATAA
1 TATAA
7483948 TATATATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 6 0.23
12 18 0.69
13 2 0.08
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (12 bp):
TATAAAAATAAT
Found at i:7485384 original size:3 final size:3
Alignment explanation
Indices: 7485376--7485422 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
7485366 AAATACATAT
* *
7485376 ATA ATA ATA ATA ATTA ATA ATA ATA ATA GTA ACA ATA ATA AT- ATA
1 ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
7485421 AT
1 AT
7485423 GCTACTGTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:7500678 original size:3 final size:3
Alignment explanation
Indices: 7500670--7500694 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
7500660 AAAGGGCATT
7500670 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
7500695 ACTGATGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:7504348 original size:2 final size:2
Alignment explanation
Indices: 7504341--7504378 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
7504331 TTACTAATAC
7504341 TA TA TA TA TA TA 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 TA TA TA TA TA TA
7504379 AAGAAAAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7508798 original size:33 final size:33
Alignment explanation
Indices: 7508760--7508827 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
7508750 CTCAACTGCT
*
7508760 TTCCAGTTAGTAAAATGATATTTTATTGTAATG
1 TTCCAGTTAGTAAAATGATATTTTATTCTAATG
7508793 TTCCAGTTAGTAAAATGATATTTTATTCTAATG
1 TTCCAGTTAGTAAAATGATATTTTATTCTAATG
7508826 TT
1 TT
7508828 ATGTGCTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.32, C:0.07, G:0.13, T:0.47
Consensus pattern (33 bp):
TTCCAGTTAGTAAAATGATATTTTATTCTAATG
Found at i:7509281 original size:2 final size:2
Alignment explanation
Indices: 7509274--7509310 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
7509264 CCCAAGTACT
7509274 TC TC TC TC TC TC TC TC TC -C T- TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
7509311 ATATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:7509368 original size:2 final size:2
Alignment explanation
Indices: 7509361--7509397 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
7509351 CNAATTACTT
7509361 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
7509398 ATATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:7509402 original size:2 final size:2
Alignment explanation
Indices: 7509397--7509433 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
7509387 TCTCTCTCTC
7509397 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7509434 GTATGTATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7516322 original size:45 final size:45
Alignment explanation
Indices: 7516258--7516488 Score: 219
Period size: 45 Copynumber: 5.1 Consensus size: 45
7516248 TTTAATGAAA
* * *
7516258 TTACACGTTATGTAAAAAAACATGTGACAAGCCATGGTTAGGTTG
1 TTACACGTCATGTACAAAAACATGTAACAAGCCATGGTTAGGTTG
* * *
7516303 TTACACGTCATATACAAAAACATGTAACAAGCCATGATTAGATTG
1 TTACACGTCATGTACAAAAACATGTAACAAGCCATGGTTAGGTTG
** * * *
7516348 TTACACCCCATATACAAAAACATGTTACATGCCATGGTTAGGTTG
1 TTACACGTCATGTACAAAAACATGTAACAAGCCATGGTTAGGTTG
* *** * * ** *
7516393 CTACATACCATGTACACAAATATGTAACAAGTTATAGTTAGGTTG
1 TTACACGTCATGTACAAAAACATGTAACAAGCCATGGTTAGGTTG
* * * * * **
7516438 TTACATGTCATGTACAAAAATATGTGACAAGTCATGGATAATTTG
1 TTACACGTCATGTACAAAAACATGTAACAAGCCATGGTTAGGTTG
7516483 TTACAC
1 TTACAC
7516489 ACCATAGTTA
Statistics
Matches: 152, Mismatches: 34, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 152 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (45 bp):
TTACACGTCATGTACAAAAACATGTAACAAGCCATGGTTAGGTTG
Found at i:7516505 original size:66 final size:66
Alignment explanation
Indices: 7516426--7516554 Score: 168
Period size: 66 Copynumber: 2.0 Consensus size: 66
7516416 GTAACAAGTT
* * * ** *
7516426 ATAGTTAGGTTGTTACATGTCATGTACAAAAATATGTGACAAGTCATGGATAATTTGTTACACAC
1 ATAGTTAGATTGTTACACGCCATGTACAAAAATATGTGACAAACCATGGATAAGTTGTTACACAC
7516491 C
66 C
** * *
7516492 ATAGTTAGATTGTTGTACGCCATGTATAAAAATATGTGACAAACCATGGTTAAGTTGTTACAC
1 ATAGTTAGATTGTTACACGCCATGTACAAAAATATGTGACAAACCATGGATAAGTTGTTACAC
7516555 GTCATGTTGA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (66 bp):
ATAGTTAGATTGTTACACGCCATGTACAAAAATATGTGACAAACCATGGATAAGTTGTTACACAC
C
Found at i:7516679 original size:45 final size:45
Alignment explanation
Indices: 7516628--7516734 Score: 169
Period size: 45 Copynumber: 2.4 Consensus size: 45
7516618 AAAAAATAAC
* * * *
7516628 GTTGTTATACGTCATGTACAAAAACATGTGACAAGTTATGGTTAG
1 GTTGTTACACATCATGTACAAAAACATGTGACAAGTAATAGTTAG
7516673 GTTGTTACACATCATGTACAAAAACATGTGACAAGTAATAGTTAG
1 GTTGTTACACATCATGTACAAAAACATGTGACAAGTAATAGTTAG
*
7516718 GTTGTTACACACCATGT
1 GTTGTTACACATCATGT
7516735 TGAAAAAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.32
Consensus pattern (45 bp):
GTTGTTACACATCATGTACAAAAACATGTGACAAGTAATAGTTAG
Found at i:7516872 original size:26 final size:26
Alignment explanation
Indices: 7516826--7516883 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
7516816 TATAAAAACA
* *
7516826 TATTACACGTCATGGTTAAAAAA-ATT
1 TATTATACGTCATGATTAAAAAATA-T
7516852 TATTATACGTCAT-ATTGAAAAAATAT
1 TATTATACGTCATGATT-AAAAAATAT
7516878 TATTAT
1 TATTAT
7516884 TACACGATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 2 0.07
26 25 0.89
27 1 0.04
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (26 bp):
TATTATACGTCATGATTAAAAAATAT
Found at i:7516878 original size:23 final size:24
Alignment explanation
Indices: 7516818--7516880 Score: 65
Period size: 26 Copynumber: 2.6 Consensus size: 24
7516808 ACGTTATATA
* * *
7516818 TAAAAACATATTACACGTCATGGT
1 TAAAAAAATATTATACGTCATGAT
7516842 TAAAAAAATTTATTATACGTCAT-AT
1 TAAAAAAA--TATTATACGTCATGAT
*
7516867 TGAAAAAATATTAT
1 TAAAAAAATATTAT
7516881 TATTACACGA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
23 6 0.18
24 7 0.21
25 8 0.24
26 12 0.36
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.35
Consensus pattern (24 bp):
TAAAAAAATATTATACGTCATGAT
Found at i:7522079 original size:2 final size:2
Alignment explanation
Indices: 7522072--7522118 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
7522062 TGTACTGTTG
*
7522072 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
7522114 GA GA G
1 GA GA G
7522119 GATAGACAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:7536484 original size:21 final size:21
Alignment explanation
Indices: 7536423--7536493 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 21
7536413 TTAAAAAATA
7536423 TTTTTTAAAA-AAATT-TAAT
1 TTTTTTAAAATAAATTATAAT
* *
7536442 TTTTTTCAAAT-ATTATATTAAT
1 TTTTTTAAAATAAAT-TA-TAAT
7536464 TTTTTTAAAATAAATTATAAT
1 TTTTTTAAAATAAATTATAAT
*
7536485 TTCTTTAAA
1 TTTTTTAAA
7536494 TGTTAGACAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 11 0.26
20 1 0.02
21 12 0.29
22 16 0.38
23 2 0.05
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTTTAAAATAAATTATAAT
Found at i:7536779 original size:23 final size:23
Alignment explanation
Indices: 7536748--7536793 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
7536738 TAGAATAATA
* *
7536748 ATTCTTAATTCTATTAGGATAAG
1 ATTCATAATTATATTAGGATAAG
7536771 ATTCATAATTATATTAGGATAAG
1 ATTCATAATTATATTAGGATAAG
7536794 GTTATTGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (23 bp):
ATTCATAATTATATTAGGATAAG
Found at i:7537311 original size:2 final size:2
Alignment explanation
Indices: 7537304--7537411 Score: 127
Period size: 2 Copynumber: 55.5 Consensus size: 2
7537294 GCCTTTGACG
7537304 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
7537346 AT AN CT TT GACG AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT -A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7537389 A- AT AT A- AT AT A- AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
7537412 GCTAAGCAAA
Statistics
Matches: 92, Mismatches: 7, Indels: 14
0.81 0.06 0.12
Matches are distributed among these distances:
1 5 0.05
2 86 0.93
3 1 0.01
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:7537973 original size:2 final size:2
Alignment explanation
Indices: 7537968--7537993 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7537958 GTGTGTGTGT
7537968 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
7537994 ATGGGACTTG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:7538086 original size:12 final size:12
Alignment explanation
Indices: 7538069--7538095 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
7538059 ACAACTCAGT
7538069 GAAGACAGCAAA
1 GAAGACAGCAAA
7538081 GAAGACAGCAAA
1 GAAGACAGCAAA
7538093 GAA
1 GAA
7538096 TGAATCCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.15, G:0.26, T:0.00
Consensus pattern (12 bp):
GAAGACAGCAAA
Found at i:7544308 original size:40 final size:40
Alignment explanation
Indices: 7544264--7544343 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
7544254 AAGGTTATCC
7544264 CACACAAGAGGTGGAGAACCTTGGAACAAATATTTATTCT
1 CACACAAGAGGTGGAGAACCTTGGAACAAATATTTATTCT
7544304 CACACAAGAGGTGGAGAACCTTGGAACAAATATTTATTCT
1 CACACAAGAGGTGGAGAACCTTGGAACAAATATTTATTCT
7544344 TTCTGTTTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (40 bp):
CACACAAGAGGTGGAGAACCTTGGAACAAATATTTATTCT
Found at i:7546769 original size:23 final size:23
Alignment explanation
Indices: 7546742--7546785 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
7546732 GTGAGAAGAG
* *
7546742 AAGGAGAAAACAAGAAAAAAAAA
1 AAGGAAAAAAAAAGAAAAAAAAA
7546765 AAGGAAAAAAAAAGAAAAAAA
1 AAGGAAAAAAAAAGAAAAAAA
7546786 GAAACAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (23 bp):
AAGGAAAAAAAAAGAAAAAAAAA
Found at i:7546782 original size:18 final size:18
Alignment explanation
Indices: 7546749--7546795 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 18
7546739 GAGAAGGAGA
7546749 AAACAAGAAAAAAAAAAAGG
1 AAACAA-AAAAAAAAAAA-G
7546769 AAA-AAAAAAGAAAAAAAG
1 AAACAAAAAA-AAAAAAAG
7546787 AAACAAAAA
1 AAACAAAAA
7546796 CAATATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 8 0.32
19 14 0.56
20 3 0.12
ACGTcount: A:0.85, C:0.04, G:0.11, T:0.00
Consensus pattern (18 bp):
AAACAAAAAAAAAAAAAG
Found at i:7546795 original size:23 final size:23
Alignment explanation
Indices: 7546748--7546795 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
7546738 AGAGAAGGAG
* **
7546748 AAAACAAGAAAAAAAAAAAGGAA
1 AAAAAAAGAAAAAAAAAAACAAA
*
7546771 AAAAAAAGAAAAAAAGAAACAAA
1 AAAAAAAGAAAAAAAAAAACAAA
7546794 AA
1 AA
7546796 CAATATATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.85, C:0.04, G:0.10, T:0.00
Consensus pattern (23 bp):
AAAAAAAGAAAAAAAAAAACAAA
Found at i:7547038 original size:150 final size:150
Alignment explanation
Indices: 7546883--7547164 Score: 456
Period size: 150 Copynumber: 1.9 Consensus size: 150
7546873 GTATAAGTAC
** ** * ** *
7546883 AAGAATTTTTGAAGTATTTTGACCAAAATGTAAAAATCAATAAGATTTTCAATTAGTATATTAAT
1 AAGAATTACTGAAGTATTTTGACCAAAATAAAAAAATCAATAAAATTTTCAATTAAAATATTAAC
*
7546948 AACATTAATATAAAACTTAACTAAAAGGTAATATTTATAAACAAAATTGAGCCAATAATTTCTAA
66 AACATTAATATAAAACTTAACTAAAAGGTAATATCTATAAACAAAATTGAGCCAATAATTTCTAA
7547013 ACTTTTTAATACCACTTCGT
131 ACTTTTTAATACCACTTCGT
7547033 AAGAATTACTGAAGTATTTTGACCAAAATAAAAAAATCAATAAAATTTTCAATTAAAATATTAAC
1 AAGAATTACTGAAGTATTTTGACCAAAATAAAAAAATCAATAAAATTTTCAATTAAAATATTAAC
* * *
7547098 AACATTAATATAAAATTTAACTAAAAGGTAATATCTATAAACAAAATTTAGCCAATAATTTTTAA
66 AACATTAATATAAAACTTAACTAAAAGGTAATATCTATAAACAAAATTGAGCCAATAATTTCTAA
7547163 AC
131 AC
7547165 CCTTAAATAC
Statistics
Matches: 120, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
150 120 1.00
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (150 bp):
AAGAATTACTGAAGTATTTTGACCAAAATAAAAAAATCAATAAAATTTTCAATTAAAATATTAAC
AACATTAATATAAAACTTAACTAAAAGGTAATATCTATAAACAAAATTGAGCCAATAATTTCTAA
ACTTTTTAATACCACTTCGT
Found at i:7547416 original size:45 final size:46
Alignment explanation
Indices: 7547352--7547445 Score: 172
Period size: 45 Copynumber: 2.0 Consensus size: 46
7547342 GTTTATTGCG
7547352 TAGTTCCAAGATGAGGCTATCGTTTCATGGATATA-AATGAATCTA
1 TAGTTCCAAGATGAGGCTATCGTTTCATGGATATACAATGAATCTA
7547397 TAGTTCCAAGATGAGGCTATCGTTTCATGGATATACCAATGAATCTA
1 TAGTTCCAAGATGAGGCTATCGTTTCATGGATATA-CAATGAATCTA
7547444 TA
1 TA
7547446 AAGGAGATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
45 35 0.74
47 12 0.26
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (46 bp):
TAGTTCCAAGATGAGGCTATCGTTTCATGGATATACAATGAATCTA
Found at i:7561021 original size:32 final size:34
Alignment explanation
Indices: 7560983--7561048 Score: 100
Period size: 32 Copynumber: 2.0 Consensus size: 34
7560973 CAACATTCCA
7560983 CAACCACACCCCACTTTCACTGG-CA-CCAAAAG
1 CAACCACACCCCACTTTCACTGGCCACCCAAAAG
* *
7561015 CAACCACACCCCTCTTTCATTGGCCACCCAAAAG
1 CAACCACACCCCACTTTCACTGGCCACCCAAAAG
7561049 GTATGCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 21 0.70
33 2 0.07
34 7 0.23
ACGTcount: A:0.32, C:0.44, G:0.09, T:0.15
Consensus pattern (34 bp):
CAACCACACCCCACTTTCACTGGCCACCCAAAAG
Found at i:7567376 original size:73 final size:73
Alignment explanation
Indices: 7567254--7567393 Score: 190
Period size: 73 Copynumber: 1.9 Consensus size: 73
7567244 CGTCCACAAA
* *
7567254 AATTATAATTTAAGTCTTCAAATTAATATCTTAATTATCAAAATCTGAAATTTTGCATTCAAATC
1 AATTATAATTTAAATCTTCAAATTAATATCTTAATTATCAAAATCTGAAATTTTACATTCAAATC
7567319 TTGAGACC
66 TTGAGACC
* * * *** * *
7567327 AATTATATTTTAAATTTTCAAATTAATATCTTAATTGTTGGAATTTGAAATTTTACATTCGAATC
1 AATTATAATTTAAATCTTCAAATTAATATCTTAATTATCAAAATCTGAAATTTTACATTCAAATC
7567392 TT
66 TT
7567394 AAAAGTAGGG
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
73 57 1.00
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (73 bp):
AATTATAATTTAAATCTTCAAATTAATATCTTAATTATCAAAATCTGAAATTTTACATTCAAATC
TTGAGACC
Found at i:7573498 original size:34 final size:37
Alignment explanation
Indices: 7573450--7573584 Score: 127
Period size: 34 Copynumber: 3.6 Consensus size: 37
7573440 AATAAATAAT
* * *
7573450 TAAACACCATATAATTTATTTTTT-A-GTAAAAA-AG
1 TAAACACTATATAATTTATTTTTTAAGGAAAAAACAA
*
7573484 TAAACACTAGATAATTTATTTTTTAATGGAAAAAACAA
1 TAAACACTATATAATTTATTTTTTAA-GGAAAAAACAA
7573522 TAAACACTATATAATTTA-TTTTTAA-GAATGTAAAACCAA
1 TAAACACTATATAATTTATTTTTTAAGGAA---AAAA-CAA
* * *
7573561 TTAACACAATATATTTTATTTTTT
1 TAAACACTATATAATTTATTTTTT
7573585 CTTAAAGAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
34 22 0.26
35 4 0.05
37 13 0.15
38 22 0.26
39 18 0.21
40 5 0.06
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (37 bp):
TAAACACTATATAATTTATTTTTTAAGGAAAAAACAA
Found at i:7573536 original size:38 final size:37
Alignment explanation
Indices: 7573450--7573584 Score: 141
Period size: 39 Copynumber: 3.6 Consensus size: 37
7573440 AATAAATAAT
* *
7573450 TAAACACCATATAATTTATTTTTT-A-GTAAAAA-AG
1 TAAACACTATATAATTTATTTTTTAATGTAAAAACAA
* *
7573484 TAAACACTAGATAATTTATTTTTTAATGGAAAAAACAA
1 TAAACACTATATAATTTATTTTTTAAT-GTAAAAACAA
* *
7573522 TAAACACTATATAATTTATTTTTAAGAATGTAAAACCAA
1 TAAACACTATATAATTTATTTTT--TAATGTAAAAACAA
* * *
7573561 TTAACACAATATATTTTATTTTTT
1 TAAACACTATATAATTTATTTTTT
7573585 CTTAAAGAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
34 22 0.27
35 1 0.01
37 6 0.07
38 23 0.28
39 28 0.34
40 3 0.04
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (37 bp):
TAAACACTATATAATTTATTTTTTAATGTAAAAACAA
Found at i:7575881 original size:20 final size:21
Alignment explanation
Indices: 7575838--7575889 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
7575828 GTTTTTACGT
* *
7575838 ATTGCGTAACTGATTTTGGAC
1 ATTGCGTGACTGATCTTGGAC
*
7575859 ATTGCGTGACTGA-CTTGGGC
1 ATTGCGTGACTGATCTTGGAC
7575879 ATTGCGTGACT
1 ATTGCGTGACT
7575890 AGTTTTTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.19, C:0.17, G:0.29, T:0.35
Consensus pattern (21 bp):
ATTGCGTGACTGATCTTGGAC
Found at i:7575915 original size:26 final size:26
Alignment explanation
Indices: 7575876--7576132 Score: 178
Period size: 26 Copynumber: 10.7 Consensus size: 26
7575866 GACTGACTTG
7575876 GGCATTGCGTGACTAGTTTTTGATAA
1 GGCATTGCGTGACTAGTTTTTGATAA
* * *
7575902 GGCATTGCGCGACTAGTTTCTAATAA
1 GGCATTGCGTGACTAGTTTTTGATAA
*
7575928 GACATTGCGTGACTAG---TTGAT-A
1 GGCATTGCGTGACTAGTTTTTGATAA
* **
7575950 GGCATTGCATGACT-GACTTTG-T--
1 GGCATTGCGTGACTAGTTTTTGATAA
* *
7575972 -GTATTACGTGACTAGTTTTTGATAA
1 GGCATTGCGTGACTAGTTTTTGATAA
* *
7575997 GACATTGCGTGACTA---ATTGAT-A
1 GGCATTGCGTGACTAGTTTTTGATAA
*
7576019 GGCATTGCGTGACTAGTTTTTAATAA
1 GGCATTGCGTGACTAGTTTTTGATAA
** * * *
7576045 AACATTGCGTGACTAATTTCTAATAA
1 GGCATTGCGTGACTAGTTTTTGATAA
*
7576071 GGTATTGCGTGACTAG---TTGAT-A
1 GGCATTGCGTGACTAGTTTTTGATAA
* * *
7576093 GGTATTGCGTGAC---TTGTAG-TAA
1 GGCATTGCGTGACTAGTTTTTGATAA
7576115 GGCATTGCGTGACTAGTT
1 GGCATTGCGTGACTAGTT
7576133 AGTAAAGCAT
Statistics
Matches: 179, Mismatches: 33, Indels: 39
0.71 0.13 0.16
Matches are distributed among these distances:
21 12 0.07
22 62 0.35
23 13 0.07
24 3 0.02
25 6 0.03
26 83 0.46
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (26 bp):
GGCATTGCGTGACTAGTTTTTGATAA
Found at i:7576051 original size:95 final size:93
Alignment explanation
Indices: 7575857--7576058 Score: 221
Period size: 95 Copynumber: 2.1 Consensus size: 93
7575847 CTGATTTTGG
* * *
7575857 ACATTGCGTGACTGACTTGGGCATTGCGTGACTAGTTTTTGATAAGGCATTGCGCGACTAGTTTC
1 ACATTGCGTGACTGACTTGGGCATTACGTGACTAGTTTTTGATAAGACATTGCGCGACTAG-ATC
* *
7575922 TAATAAGACATTGCGTGACTAGTTGATAG
65 TAATAAGACATTGCGTGACTAGTTAATAA
* * * * *
7575951 GCATTGCATGACTGACTTTGTGTATTACGTGACTAGTTTTTGATAAGACATTGCGTGACTA-AT-
1 ACATTGCGTGACTGAC-TTGGGCATTACGTGACTAGTTTTTGATAAGACATTGCGCGACTAGATC
* *
7576014 TGAT-AGGCATTGCGTGACTAGTTTTTAATAAA
65 TAATAAGACATTGCGTGACTAG---TTAAT-AA
7576046 ACATTGCGTGACT
1 ACATTGCGTGACT
7576059 AATTTCTAAT
Statistics
Matches: 89, Mismatches: 14, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
91 16 0.18
92 3 0.03
93 1 0.01
94 18 0.20
95 51 0.57
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (93 bp):
ACATTGCGTGACTGACTTGGGCATTACGTGACTAGTTTTTGATAAGACATTGCGCGACTAGATCT
AATAAGACATTGCGTGACTAGTTAATAA
Found at i:7576202 original size:22 final size:22
Alignment explanation
Indices: 7576171--7576309 Score: 169
Period size: 22 Copynumber: 6.4 Consensus size: 22
7576161 CTTAAAAATC
*
7576171 AGTCATGCAATGCCTAGAAACT
1 AGTCACGCAATGCCTAGAAACT
7576193 AGTCACGCAATGCCTA-AAA-T
1 AGTCACGCAATGCCTAGAAACT
* *
7576213 CAATCACGTAATGCCTAGAAACT
1 -AGTCACGCAATGCCTAGAAACT
7576236 AGTCACGCAATGCCTAGAAACT
1 AGTCACGCAATGCCTAGAAACT
7576258 AGTCACGCAATGCCTA-AAA-T
1 AGTCACGCAATGCCTAGAAACT
* * * *
7576278 CAATCACGTAATGCCTAAAAACC
1 -AGTCACGCAATGCCTAGAAACT
7576301 AGTCACGCA
1 AGTCACGCA
7576310 GTGATTAAGT
Statistics
Matches: 101, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
20 2 0.02
21 34 0.34
22 64 0.63
23 1 0.01
ACGTcount: A:0.39, C:0.27, G:0.15, T:0.19
Consensus pattern (22 bp):
AGTCACGCAATGCCTAGAAACT
Found at i:7576226 original size:43 final size:43
Alignment explanation
Indices: 7576165--7576309 Score: 179
Period size: 43 Copynumber: 3.3 Consensus size: 43
7576155 GCATTACTTA
*
7576165 AAAATCAGTCATGCAATGCCTAGAAACTAGTCACGCAATGCCT
1 AAAATCAGTCACGCAATGCCTAGAAACTAGTCACGCAATGCCT
* *
7576208 AAAATCAATCACGTAATGCCTAGAAACTAGTCACGCAATGCCT
1 AAAATCAGTCACGCAATGCCTAGAAACTAGTCACGCAATGCCT
* *
7576251 AGAAA-CTAGTCACGCAATGCCTA-AAA-TCAATCACGTAATGCCT
1 A-AAATC-AGTCACGCAATGCCTAGAAACT-AGTCACGCAATGCCT
*
7576294 AAAAACCAGTCACGCA
1 -AAAATCAGTCACGCA
7576310 GTGATTAAGT
Statistics
Matches: 90, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
42 1 0.01
43 70 0.78
44 19 0.21
ACGTcount: A:0.40, C:0.26, G:0.14, T:0.19
Consensus pattern (43 bp):
AAAATCAGTCACGCAATGCCTAGAAACTAGTCACGCAATGCCT
Found at i:7576252 original size:65 final size:65
Alignment explanation
Indices: 7576163--7576309 Score: 258
Period size: 65 Copynumber: 2.3 Consensus size: 65
7576153 AGGCATTACT
* *
7576163 TAAAAATCAGTCATGCAATGCCTAGAAACTAGTCACGCAATGCCTAAAATCAATCACGTAATGCC
1 TAAAAACCAGTCACGCAATGCCTAGAAACTAGTCACGCAATGCCTAAAATCAATCACGTAATGCC
* *
7576228 TAGAAACTAGTCACGCAATGCCTAGAAACTAGTCACGCAATGCCTAAAATCAATCACGTAATGCC
1 TAAAAACCAGTCACGCAATGCCTAGAAACTAGTCACGCAATGCCTAAAATCAATCACGTAATGCC
7576293 TAAAAACCAGTCACGCA
1 TAAAAACCAGTCACGCA
7576310 GTGATTAAGT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 76 1.00
ACGTcount: A:0.40, C:0.26, G:0.14, T:0.20
Consensus pattern (65 bp):
TAAAAACCAGTCACGCAATGCCTAGAAACTAGTCACGCAATGCCTAAAATCAATCACGTAATGCC
Found at i:7577216 original size:20 final size:20
Alignment explanation
Indices: 7577182--7577231 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
7577172 ATTTCTCACA
*
7577182 ATTTTTTCTTGCTTTTTCTTC
1 ATTTTTT-TTACTTTTTCTTC
*
7577203 ATTTTTTTTACTTTTTTTTC
1 ATTTTTTTTACTTTTTCTTC
*
7577223 -TTTGTTTTA
1 ATTTTTTTTA
7577232 AGAAATGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 8 0.31
20 11 0.42
21 7 0.27
ACGTcount: A:0.08, C:0.12, G:0.04, T:0.76
Consensus pattern (20 bp):
ATTTTTTTTACTTTTTCTTC
Found at i:7585708 original size:2 final size:2
Alignment explanation
Indices: 7585701--7585727 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7585691 CTTCAAATAA
7585701 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
7585728 ATCAATTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7585844 original size:18 final size:18
Alignment explanation
Indices: 7585821--7585857 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
7585811 AAAAAAAAGA
*
7585821 AAAAGCTTGTTAGTCTAG
1 AAAAGCTTGCTAGTCTAG
*
7585839 AAAAGCTTGCTAGTTTAG
1 AAAAGCTTGCTAGTCTAG
7585857 A
1 A
7585858 TTTTAATAAT
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:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (18 bp):
AAAAGCTTGCTAGTCTAG
Found at i:7587564 original size:16 final size:16
Alignment explanation
Indices: 7587543--7587580 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
7587533 GCCAAAATAA
7587543 TTTATTTTTTGAATTT
1 TTTATTTTTTGAATTT
**
7587559 TTTATTTTTTTTATTT
1 TTTATTTTTTGAATTT
7587575 TTTATT
1 TTTATT
7587581 AATAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTATTTTTTGAATTT
Found at i:7587805 original size:16 final size:15
Alignment explanation
Indices: 7587769--7587802 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
7587759 AATTAATTTT
*
7587769 AAAATTTTTTTAATA
1 AAAATATTTTTAATA
*
7587784 TAAATATTTTTAATA
1 AAAATATTTTTAATA
7587799 AAAA
1 AAAA
7587803 ATACGATACG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAATATTTTTAATA
Found at i:7588397 original size:428 final size:419
Alignment explanation
Indices: 7587608--7588438 Score: 1563
Period size: 428 Copynumber: 2.0 Consensus size: 419
7587598 AATATATATC
7587608 TTATTTAAAAATATATATTATAAAGGAATAAATTGAGAGTTTAAATTAAAAAAATAATAATCTTT
1 TTATTTAAAAATATATATTATAAAGGAATAAATTGAGAGTTTAAATTAAAAAAATAATAATCTTT
7587673 TCGATTTATGTCATATAATCTTTAATTTTATTAATAAATATATTTTTTAACTCTTTTTTTATTTT
66 TCGATTTATGTCATATAATCTTTAATTTTATTAATAAATATATTTTTTAACTCTTTTTTTATTTT
*
7587738 ACATGTGTACATGTTGTTTATAATTAATTTTAAAATTTTTTTAATATAAATATTTTTAATAAAAA
131 ACATGTGTACATGTTGTTTATAATTAATTTTAAAATTTTTTTAATATAAATATTTATAATAAAAA
7587803 ATACGATACGTATCTTAATTTAAGAATGATGCTTGATACAATAATCAATAATCAATATAACATTA
196 ATACGATACGTATCTTAATTTAAGAATGATGCTTGATACAATAATCAATAATCAATATAACATTA
7587868 ATATATTTATTTGATTAATTGAAAATATATTAACGAGTTCGAGGGGTTAAATGCAACAAATTCTT
261 ATATATTTATTTGATTAATTGAAAATATATTAACGAGTTCGAGGGGTTAAATGCAACAAATTCTT
7587933 TCTTGATGGCAAGAATTCAAGAAATACAAAACATTAATGGTACTCTATAAAACAAACAACAAAGG
326 TCTTGATGGCAAGAATTCAAGAAATACAAAACATTAATGGTACTCTATAAAACAAACAACAAAGG
7587998 CAAGGGCAAACCANATGAGAAATGTATGTT
391 CAAGGGCAAACCA-ATGAGAAATGTATGTT
7588028 TTATTTAAAAATATATATTATAAAGGAATAAATTGAGAGTTTAAATTAAAAAAATAATAATCTTT
1 TTATTTAAAAATATATATTATAAAGGAATAAATTGAGAGTTTAAATTAAAAAAATAATAATCTTT
7588093 TCGATTTATGTCATATAATCTTTAATTTTATTAATAAATATATTTTTTAACTCTTTTTTTATTTT
66 TCGATTTATGTCATATAATCTTTAATTTTATTAATAAATATATTTTTTAACTCTTTTTTTATTTT
*
7588158 ACATGTGTACATGTTGTTTATAATTAATTTTAAAATTTTTTATTATATACAATATAATACTCGAT
131 ACATGTGTACATGTTGTTTATAATTAATTTTAAAATTTTTT-TAATATA-AATAT--T--T--AT
7588223 AATAAAAAATACGATACGTATCTTAATTTAAGAATGATGCTTGATACAATAATCAATAATCAATA
188 AATAAAAAATACGATACGTATCTTAATTTAAGAATGATGCTTGATACAATAATCAATAATCAATA
7588288 TAACATTAATATATTTATTTGATTAATTGAAAATATATTAACGAGTTCGAGGGGTTAAATGCAAC
253 TAACATTAATATATTTATTTGATTAATTGAAAATATATTAACGAGTTCGAGGGGTTAAATGCAAC
7588353 AAATTCTTTCTTGATGGCAAGAATTCAAGAAATACAAAACATTAATGGTACTCTATAAAACAAAC
318 AAATTCTTTCTTGATGGCAAGAATTCAAGAAATACAAAACATTAATGGTACTCTATAAAACAAAC
7588418 AACAAAGGCAAGGGCAAACCA
383 AACAAAGGCAAGGGCAAACCA
7588439 TACAGGGCTA
Statistics
Matches: 401, Mismatches: 2, Indels: 8
0.98 0.00 0.02
Matches are distributed among these distances:
420 171 0.43
421 6 0.01
422 5 0.01
424 1 0.00
426 1 0.00
428 217 0.54
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.39
Consensus pattern (419 bp):
TTATTTAAAAATATATATTATAAAGGAATAAATTGAGAGTTTAAATTAAAAAAATAATAATCTTT
TCGATTTATGTCATATAATCTTTAATTTTATTAATAAATATATTTTTTAACTCTTTTTTTATTTT
ACATGTGTACATGTTGTTTATAATTAATTTTAAAATTTTTTTAATATAAATATTTATAATAAAAA
ATACGATACGTATCTTAATTTAAGAATGATGCTTGATACAATAATCAATAATCAATATAACATTA
ATATATTTATTTGATTAATTGAAAATATATTAACGAGTTCGAGGGGTTAAATGCAACAAATTCTT
TCTTGATGGCAAGAATTCAAGAAATACAAAACATTAATGGTACTCTATAAAACAAACAACAAAGG
CAAGGGCAAACCAATGAGAAATGTATGTT
Found at i:7588510 original size:40 final size:40
Alignment explanation
Indices: 7588466--7588542 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
7588456 ACTGCAACTT
* *
7588466 AATGGAGACCGCTATGGAAGGTTATAAGGGACAATATAAA
1 AATGGAGACCGCCATAGAAGGTTATAAGGGACAATATAAA
7588506 AATGGAGACCGCCATAGAAGGTTATAAGGGACAATAT
1 AATGGAGACCGCCATAGAAGGTTATAAGGGACAATAT
7588543 GAAGCTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.42, C:0.12, G:0.27, T:0.19
Consensus pattern (40 bp):
AATGGAGACCGCCATAGAAGGTTATAAGGGACAATATAAA
Found at i:7592463 original size:17 final size:17
Alignment explanation
Indices: 7592410--7592464 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
7592400 TTATATTATA
7592410 CTAAAATTGAGAAAAAC
1 CTAAAATTGAGAAAAAC
** *
7592427 CTAATTTTCA-AAAAA-
1 CTAAAATTGAGAAAAAC
*
7592442 -AAAAATTGAGAAAAAC
1 CTAAAATTGAGAAAAAC
7592458 CTAAAAT
1 CTAAAAT
7592465 GAAAATAGTG
Statistics
Matches: 27, Mismatches: 8, Indels: 6
0.66 0.20 0.15
Matches are distributed among these distances:
14 5 0.19
15 5 0.19
16 5 0.19
17 12 0.44
ACGTcount: A:0.60, C:0.11, G:0.07, T:0.22
Consensus pattern (17 bp):
CTAAAATTGAGAAAAAC
Found at i:7595079 original size:20 final size:20
Alignment explanation
Indices: 7595054--7595108 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
7595044 AAGCTCTACA
7595054 TCCTTTCAGACTTCTGAAAG
1 TCCTTTCAGACTTCTGAAAG
7595074 TCCTTTCAGACTTCTGAAAG
1 TCCTTTCAGACTTCTGAAAG
7595094 TCCTTTCAGACTTCT
1 TCCTTTCAGACTTCT
7595109 TGTATGCAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.22, C:0.27, G:0.13, T:0.38
Consensus pattern (20 bp):
TCCTTTCAGACTTCTGAAAG
Found at i:7595552 original size:33 final size:33
Alignment explanation
Indices: 7595515--7595584 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
7595505 TGATTTTCAG
7595515 CTGATGAAGAAGACTCAGTGAA-CTGATCTGCAC
1 CTGATGAAGAAGACTCAG-GAAGCTGATCTGCAC
* * *
7595548 CTGATGGAGAAGATTCTGGAAGCTGATCTGCAC
1 CTGATGAAGAAGACTCAGGAAGCTGATCTGCAC
7595581 CTGA
1 CTGA
7595585 CAGAGAAGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 3 0.09
33 30 0.91
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (33 bp):
CTGATGAAGAAGACTCAGGAAGCTGATCTGCAC
Found at i:7605447 original size:2 final size:2
Alignment explanation
Indices: 7605440--7605482 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
7605430 TGTCTTTAAC
7605440 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7605482 A
1 A
7605483 CACCTCAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7618107 original size:67 final size:66
Alignment explanation
Indices: 7618017--7618154 Score: 240
Period size: 67 Copynumber: 2.1 Consensus size: 66
7618007 CTTTTCTTTT
* * *
7618017 GCTTTTGCAATTTGTGGGTTTTAAAGTTTACTTAAGCTCTATTTTTAGAGTTTAAGGCCGCATGA
1 GCTTTTGCAATTTGTGGATTTTAAAGTTTACTTAAACTCTATTTTTAAAGTTTAAGGCCGCATGA
7618082 G
66 G
7618083 GCTTTTGCAATTTTGTGGATTTTAAAGTTTACTTAAACTCTATTTTTAAAGTTTAAGGCCGCATG
1 GCTTTTGCAA-TTTGTGGATTTTAAAGTTTACTTAAACTCTATTTTTAAAGTTTAAGGCCGCATG
7618148 AG
65 AG
7618150 GCTTT
1 GCTTT
7618155 ACTGATATAG
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
66 10 0.15
67 58 0.85
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.43
Consensus pattern (66 bp):
GCTTTTGCAATTTGTGGATTTTAAAGTTTACTTAAACTCTATTTTTAAAGTTTAAGGCCGCATGA
G
Found at i:7618251 original size:76 final size:75
Alignment explanation
Indices: 7618120--7618270 Score: 225
Period size: 76 Copynumber: 2.0 Consensus size: 75
7618110 TTTACTTAAA
*
7618120 CTCTATTTTTAAAGTTTAAGGCCGCATGAGGCTTTACTGATATAGGACCCTCATGAGAGATA-AA
1 CTCTATTTTTAAAGTTTAAGGCCGCACGAGGCTTTACTGATATAGGACCCTCATGAGAGATACAA
7618184 AGAGTCGAGGT
66 AG-GTCGAGGT
* * *
7618195 CTCTATTTTTAGAGTTTTAGGGCCGCACGAGGCTTTACTGATATGGGATCCC-CATGAGAGATAC
1 CTCTATTTTTAAAG-TTTAAGGCCGCACGAGGCTTTACTGATATAGGA-CCCTCATGAGAGATAC
7618259 AAAGGTCGAGGT
64 AAAGGTCGAGGT
7618271 AGATCTGAAC
Statistics
Matches: 69, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
75 13 0.19
76 49 0.71
77 7 0.10
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (75 bp):
CTCTATTTTTAAAGTTTAAGGCCGCACGAGGCTTTACTGATATAGGACCCTCATGAGAGATACAA
AGGTCGAGGT
Found at i:7618698 original size:21 final size:21
Alignment explanation
Indices: 7618672--7618715 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
7618662 AACCAGGAAT
7618672 GAATAGCACTTTATTTGATAA
1 GAATAGCACTTTATTTGATAA
7618693 GAATAGCACTTTATTTGATAA
1 GAATAGCACTTTATTTGATAA
7618714 GA
1 GA
7618716 TTTAATACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (21 bp):
GAATAGCACTTTATTTGATAA
Found at i:7627114 original size:2 final size:2
Alignment explanation
Indices: 7627109--7627159 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
7627099 AGAGAGAGAG
*
7627109 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
7627150 AA AT AT AT AT
1 AT AT AT AT AT
7627160 NNNNNNNNNN
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:7627184 original size:2 final size:2
Alignment explanation
Indices: 7627177--7627201 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7627167 NNNNNNATAT
7627177 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
7627202 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7627206 original size:2 final size:2
Alignment explanation
Indices: 7627201--7627240 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
7627191 AGAGAGAGAG
7627201 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7627241 GATGAAGATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7628004 original size:6 final size:6
Alignment explanation
Indices: 7627993--7628020 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
7627983 TAACTTCCCC
7627993 TTTGAT TTTGAT TTTGAT TTTGAT TTTG
1 TTTGAT TTTGAT TTTGAT TTTGAT TTTG
7628021 TGTATGCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.18, T:0.68
Consensus pattern (6 bp):
TTTGAT
Found at i:7634167 original size:21 final size:20
Alignment explanation
Indices: 7634129--7634170 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
7634119 CTTTTCATTG
7634129 TTGCTTTTGCTACTTGCTTT
1 TTGCTTTTGCTACTTGCTTT
* *
7634149 TTGCTATTTTCTATTTGCTTT
1 TTGCT-TTTGCTACTTGCTTT
7634170 T
1 T
7634171 GAAAAGTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.07, C:0.17, G:0.12, T:0.64
Consensus pattern (20 bp):
TTGCTTTTGCTACTTGCTTT
Found at i:7636302 original size:33 final size:34
Alignment explanation
Indices: 7636265--7636336 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 34
7636255 TCTTCTTTCA
** *
7636265 TTAATTACTCAAA-TTCGCTTTTGTAT-AATTTTT
1 TTAATTACT-AAATTTAACTTTTGCATAAATTTTT
7636298 TTAATTACTAAATTTAACTTTTGCATAAATTTTT
1 TTAATTACTAAATTTAACTTTTGCATAAATTTTT
7636332 TTAAT
1 TTAAT
7636337 ACATATGAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 3 0.09
33 19 0.56
34 12 0.35
ACGTcount: A:0.32, C:0.10, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAATTACTAAATTTAACTTTTGCATAAATTTTT
Found at i:7637150 original size:16 final size:16
Alignment explanation
Indices: 7637129--7637169 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
7637119 TTGTTTTATC
7637129 GCCTTTAACATATCAT
1 GCCTTTAACATATCAT
7637145 GCCTTTAACATATCAT
1 GCCTTTAACATATCAT
*
7637161 TCCTTTAAC
1 GCCTTTAAC
7637170 TATGTTATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.29, C:0.27, G:0.05, T:0.39
Consensus pattern (16 bp):
GCCTTTAACATATCAT
Found at i:7639882 original size:14 final size:13
Alignment explanation
Indices: 7639841--7639896 Score: 62
Period size: 13 Copynumber: 4.3 Consensus size: 13
7639831 ATTTGAATTA
7639841 TTAT-TATTATTT
1 TTATCTATTATTT
*
7639853 TTATC-ATCATTTT
1 TTATCTATTA-TTT
7639866 TTATCTATTATTAT
1 TTATCTATTATT-T
*
7639880 TTATTTATTATTT
1 TTATCTATTATTT
7639893 TTAT
1 TTAT
7639897 TGAGTAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 7 0.19
13 15 0.41
14 15 0.41
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATCTATTATTT
Found at i:7640909 original size:12 final size:12
Alignment explanation
Indices: 7640892--7640939 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
7640882 TCTCTTCTAT
*
7640892 TTTTTTATTTCA
1 TTTTTCATTTCA
7640904 TTTTTTTCATTTTCA
1 --TTTTTCA-TTTCA
7640919 -TTTTCATTTCA
1 TTTTTCATTTCA
7640930 TTTTTCATTT
1 TTTTTCATTT
7640940 TTTTATTTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
11 5 0.16
12 15 0.48
14 6 0.19
15 5 0.16
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTCATTTCA
Found at i:7640910 original size:14 final size:15
Alignment explanation
Indices: 7640890--7640947 Score: 68
Period size: 15 Copynumber: 3.9 Consensus size: 15
7640880 TCTCTCTTCT
7640890 ATTTTTTT-A-TTTC
1 ATTTTTTTCATTTTC
7640903 ATTTTTTTCATTTTC
1 ATTTTTTTCATTTTC
7640918 ATTTTCATTTCATTTTTC
1 ATTTT--TTTCA-TTTTC
7640936 ATTTTTTT-ATTT
1 ATTTTTTTCATTT
7640948 GTTGTTTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
13 8 0.20
14 4 0.10
15 10 0.25
16 3 0.08
17 5 0.12
18 10 0.25
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTTTTTCATTTTC
Found at i:7640941 original size:7 final size:6
Alignment explanation
Indices: 7640907--7640940 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
7640897 TATTTCATTT
7640907 TTTTCA TTTTCA TTTTCA -TTTCA TTTTTCA TTTT
1 TTTTCA TTTTCA TTTTCA TTTTCA -TTTTCA TTTT
7640941 TTTATTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 16 0.62
7 5 0.19
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTCA
Found at i:7643209 original size:26 final size:26
Alignment explanation
Indices: 7643179--7643271 Score: 91
Period size: 26 Copynumber: 3.6 Consensus size: 26
7643169 TGGGTTAAAG
7643179 TATCCATTCACTTCTGATGGTAAAAT
1 TATCCATTCACTTCTGATGGTAAAAT
* *
7643205 TATCCA-TCTATTTCT-AGTCGTAAAAT
1 TATCCATTC-ACTTCTGA-TGGTAAAAT
* * * * *
7643231 TATCAATGCATTTCTGGTGGCAAAAT
1 TATCCATTCACTTCTGATGGTAAAAT
7643257 TATCCATTCACTTCT
1 TATCCATTCACTTCT
7643272 TGTAGAATTA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
25 3 0.06
26 49 0.92
27 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (26 bp):
TATCCATTCACTTCTGATGGTAAAAT
Found at i:7644778 original size:13 final size:12
Alignment explanation
Indices: 7644749--7644802 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
7644739 TTATCCCCAA
*
7644749 CTTCTTCTATTTC
1 CTTCTTCT-TTTT
7644762 CTTCTTCTTCTTT
1 CTTCTTCTT-TTT
7644775 CTTCCTTCTTTTT
1 CTT-CTTCTTTTT
* *
7644788 TTTCTTCTTCTT
1 CTTCTTCTTTTT
7644800 CTT
1 CTT
7644803 TTACCTTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
12 11 0.31
13 18 0.51
14 6 0.17
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.69
Consensus pattern (12 bp):
CTTCTTCTTTTT
Found at i:7646548 original size:19 final size:18
Alignment explanation
Indices: 7646512--7646561 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
7646502 ATTTTAATTA
7646512 TTATTAA-ATAATA-AAT
1 TTATTAATATAATATAAT
7646528 TTATTAATATAATATATAT
1 TTATTAATATAATATA-AT
*
7646547 TTATGAATATAATAT
1 TTATTAATATAATAT
7646562 TAAATAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 7 0.23
17 6 0.20
18 1 0.03
19 16 0.53
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TTATTAATATAATATAAT
Found at i:7675979 original size:8 final size:8
Alignment explanation
Indices: 7675971--7676031 Score: 59
Period size: 8 Copynumber: 7.6 Consensus size: 8
7675961 TATGTTAATA
*
7675971 TATATATA
1 TATATATG
7675979 TATATATG
1 TATATATG
*
7675987 TATGTATG
1 TATATATG
*
7675995 TATGTATG
1 TATATATG
*
7676003 TATGTATG
1 TATATATG
* *
7676011 TATGTATA
1 TATATATG
*
7676019 TGTATATG
1 TATATATG
7676027 TATAT
1 TATAT
7676032 GCAGTTTCTT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (8 bp):
TATATATG
Found at i:7675982 original size:4 final size:4
Alignment explanation
Indices: 7675983--7676017 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
7675973 TATATATATA
7675983 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
7676018 ATGTATATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:7675985 original size:12 final size:12
Alignment explanation
Indices: 7675968--7676031 Score: 74
Period size: 12 Copynumber: 5.3 Consensus size: 12
7675958 TTTTATGTTA
* *
7675968 ATATATATATAT
1 ATATATGTATGT
7675980 ATATATGTATGT
1 ATATATGTATGT
*
7675992 ATGTATGTATGT
1 ATATATGTATGT
*
7676004 ATGTATGTATGT
1 ATATATGTATGT
* *
7676016 ATATGTATATGT
1 ATATATGTATGT
7676028 ATAT
1 ATAT
7676032 GCAGTTTCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (12 bp):
ATATATGTATGT
Found at i:7679542 original size:2 final size:2
Alignment explanation
Indices: 7679537--7679579 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
7679527 TTTTAATTAA
*
7679537 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7679579 A
1 A
7679580 CAAGAGAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7682890 original size:2 final size:2
Alignment explanation
Indices: 7682883--7682908 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7682873 TGCAAAAATG
7682883 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
7682909 AATGTAAAGA
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:7704400 original size:20 final size:20
Alignment explanation
Indices: 7704375--7704419 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
7704365 TTTCTTTTTT
* *
7704375 TATTTTGATATG-TGATTCAA
1 TATTTTG-TATGATAATTAAA
7704395 TATTTTGTATGATAATTAAA
1 TATTTTGTATGATAATTAAA
7704415 TATTT
1 TATTT
7704420 GTTTAAGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.53
Consensus pattern (20 bp):
TATTTTGTATGATAATTAAA
Found at i:7705669 original size:21 final size:21
Alignment explanation
Indices: 7705645--7705699 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 21
7705635 AAATTATGGG
7705645 GAATCGACCTAAGTTATTGGA
1 GAATCGACCTAAGTTATTGGA
*
7705666 GAATCAACCGATCTAAGTTATTGGA
1 GAAT----CGACCTAAGTTATTGGA
7705691 GAATCGACC
1 GAATCGACC
7705700 AAATTGTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
21 8 0.29
25 20 0.71
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (21 bp):
GAATCGACCTAAGTTATTGGA
Found at i:7713911 original size:20 final size:20
Alignment explanation
Indices: 7713886--7713927 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
7713876 TAAAGAGGCT
7713886 TAAGGTGTTCAAGAACTGTC
1 TAAGGTGTTCAAGAACTGTC
7713906 TAAGGTGTTCAAGAACTGTC
1 TAAGGTGTTCAAGAACTGTC
7713926 TA
1 TA
7713928 CCTCCTGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (20 bp):
TAAGGTGTTCAAGAACTGTC
Found at i:7723818 original size:25 final size:25
Alignment explanation
Indices: 7723758--7723821 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
7723748 TTAATAAACG
* * *
7723758 TAATTATAGGAATTAGAAATCATCA
1 TAATTATAGGGATTAGAAACCACCA
* *
7723783 TAATTATAGGGATTGGGAACCACCA
1 TAATTATAGGGATTAGAAACCACCA
7723808 TAATTATAGGGATT
1 TAATTATAGGGATT
7723822 TTATTTTCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (25 bp):
TAATTATAGGGATTAGAAACCACCA
Found at i:7728502 original size:33 final size:33
Alignment explanation
Indices: 7728460--7728522 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
7728450 ATTTATTCTC
7728460 ATCATACTGTTATACTGGTTAGTTTGTTATGTT
1 ATCATACTGTTATACTGGTTAGTTTGTTATGTT
7728493 ATCATACTGTTATACTGGTTAGTTTGTTAT
1 ATCATACTGTTATACTGGTTAGTTTGTTAT
7728523 ATTTATTCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.22, C:0.10, G:0.17, T:0.51
Consensus pattern (33 bp):
ATCATACTGTTATACTGGTTAGTTTGTTATGTT
Found at i:7740954 original size:18 final size:18
Alignment explanation
Indices: 7740910--7740954 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
7740900 GATTTTACCT
7740910 TTTAATTTT-TTTATGAA
1 TTTAATTTTATTTATGAA
*
7740927 -TTAACTTTTATTTATTAA
1 TTTAA-TTTTATTTATGAA
7740945 TTTAATTTTA
1 TTTAATTTTA
7740955 ATTAATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 4 0.17
17 4 0.17
18 12 0.50
19 4 0.17
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTAATTTTATTTATGAA
Found at i:7743584 original size:90 final size:90
Alignment explanation
Indices: 7743486--7743655 Score: 295
Period size: 90 Copynumber: 1.9 Consensus size: 90
7743476 GTAATTATTT
** *
7743486 TGTTTTTTTTTCTAATTTATTTATTTGGTACTCTCTCAATTATTGTTTATTCGATTATTTGTTGC
1 TGTTTTTTTCCCTAATTTATTTATTTGGTACTCTCTCAATTATTGTTTATTCAATTATTTGTTGC
7743551 ATAAAAATTAATGAATATGAATAGC
66 ATAAAAATTAATGAATATGAATAGC
*
7743576 TGTTTTTTTCCCTAATTTATTTATTTTGTACTCTCTCAATTATTGTTTATTCAATTATTTGTTGC
1 TGTTTTTTTCCCTAATTTATTTATTTGGTACTCTCTCAATTATTGTTTATTCAATTATTTGTTGC
*
7743641 ATAAAAATTGATGAA
66 ATAAAAATTAATGAA
7743656 AAATTTGTTA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 75 1.00
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.53
Consensus pattern (90 bp):
TGTTTTTTTCCCTAATTTATTTATTTGGTACTCTCTCAATTATTGTTTATTCAATTATTTGTTGC
ATAAAAATTAATGAATATGAATAGC
Done.