Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 307 of 444
Found at i:88457085 original size:15 final size:15
Alignment explanation
Indices: 88457065--88457121 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
88457055 ATTCAATATT
88457065 AATATTTTAATAATA
1 AATATTTTAATAATA
*
88457080 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
88457099 AATATATTAATAATA
1 AATATTTTAATAATA
88457114 AATATTTT
1 AATATTTT
88457122 GTAGTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 17 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:88461937 original size:31 final size:31
Alignment explanation
Indices: 88461860--88461942 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 31
88461850 CAAGAATTGA
* *
88461860 ATTAAATCAAAATTTCATGTATACAGTTGCAC
1 ATTAAATC-AAAGTTCATGTATACAATTGCAC
* *
88461892 A--AAATCAAAGTTCATGTATACAATTGTAT
1 ATTAAATCAAAGTTCATGTATACAATTGCAC
88461921 ATTAAATCATAA-TTCATGTATA
1 ATTAAATCA-AAGTTCATGTATA
88461943 ATTTTAAGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
29 20 0.45
30 5 0.11
31 16 0.36
32 3 0.07
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.36
Consensus pattern (31 bp):
ATTAAATCAAAGTTCATGTATACAATTGCAC
Found at i:88465007 original size:209 final size:209
Alignment explanation
Indices: 88464647--88465276 Score: 1251
Period size: 209 Copynumber: 3.0 Consensus size: 209
88464637 ATAACATGAT
*
88464647 TAAGATCTCTGGATACATGTCTAATGTACCACTACCTTTCAGTTCTCAAAATTCTTCGGATCCTC
1 TAAGATCTCTAGATACATGTCTAATGTACCACTACCTTTCAGTTCTCAAAATTCTTCGGATCCTC
88464712 CTAAGCACTGTAATACTAGAATTTGTCAACCAACTTTCTTGTAATGCTCAAACCACCTCCAAATT
66 CTAAGCACTGTAATACTAGAATTTGTCAACCAACTTTCTTGTAATGCTCAAACCACCTCCAAATT
88464777 ATTAGATTGGATCATGACCCTTCTGAATCTTTTACTGAGCACCACTAAAAGACCATTTAAAATTC
131 ATTAGATTGGATCATGACCCTTCTGAATCTTTTACTGAGCACCACTAAAAGACCATTTAAAATTC
88464842 CCCATAACTCAGCC
196 CCCATAACTCAGCC
88464856 TAAGATCTCTAGATACATGTCTAATGTACCACTACCTTTCAGTTCTCAAAATTCTTCGGATCCTC
1 TAAGATCTCTAGATACATGTCTAATGTACCACTACCTTTCAGTTCTCAAAATTCTTCGGATCCTC
88464921 CTAAGCACTGTAATACTAGAATTTGTCAACCAACTTTCTTGTAATGCTCAAACCACCTCCAAATT
66 CTAAGCACTGTAATACTAGAATTTGTCAACCAACTTTCTTGTAATGCTCAAACCACCTCCAAATT
88464986 ATTAGATTGGATCATGACCCTTCTGAATCTTTTACTGAGCACCACTAAAAGACCATTTAAAATTC
131 ATTAGATTGGATCATGACCCTTCTGAATCTTTTACTGAGCACCACTAAAAGACCATTTAAAATTC
88465051 CCCATAACTCAGCC
196 CCCATAACTCAGCC
88465065 TAAGATCTCTAGATACATGTCTAATGTACCACTACCTTTCAGTTCTCAAAATTCTTCGGATCCTC
1 TAAGATCTCTAGATACATGTCTAATGTACCACTACCTTTCAGTTCTCAAAATTCTTCGGATCCTC
88465130 CTAAGCACTGTAATACTAGAATTTGTCAACCAACTTTCTTGTAATGCTCAAACCACCTCCAAATT
66 CTAAGCACTGTAATACTAGAATTTGTCAACCAACTTTCTTGTAATGCTCAAACCACCTCCAAATT
88465195 ATTAGATTGGATCATGACCCTTCTGAATCTTTTACTGAGCACCACTAAAAGACCATTTAAAATTC
131 ATTAGATTGGATCATGACCCTTCTGAATCTTTTACTGAGCACCACTAAAAGACCATTTAAAATTC
88465260 CCCATAACTCAGCC
196 CCCATAACTCAGCC
88465274 TAA
1 TAA
88465277 AAAATCGTGC
Statistics
Matches: 420, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
209 420 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (209 bp):
TAAGATCTCTAGATACATGTCTAATGTACCACTACCTTTCAGTTCTCAAAATTCTTCGGATCCTC
CTAAGCACTGTAATACTAGAATTTGTCAACCAACTTTCTTGTAATGCTCAAACCACCTCCAAATT
ATTAGATTGGATCATGACCCTTCTGAATCTTTTACTGAGCACCACTAAAAGACCATTTAAAATTC
CCCATAACTCAGCC
Found at i:88466139 original size:25 final size:26
Alignment explanation
Indices: 88466102--88466155 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
88466092 ATACCCCTTT
88466102 TCACCTATTCATTCAACACAACTCTC
1 TCACCTATTCATTCAACACAACTCTC
* **
88466128 TCACCT-TTCATTCCACACTTCTCTC
1 TCACCTATTCATTCAACACAACTCTC
88466153 TCA
1 TCA
88466156 TTTTCTATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.24, C:0.41, G:0.00, T:0.35
Consensus pattern (26 bp):
TCACCTATTCATTCAACACAACTCTC
Found at i:88470653 original size:24 final size:23
Alignment explanation
Indices: 88470624--88470765 Score: 90
Period size: 24 Copynumber: 5.9 Consensus size: 23
88470614 AGCCTTATAA
*
88470624 CGGGAAGCTCACACAGAGCCATGT
1 CGGGAAGCTCACA-AGAGCCATAT
* * * *
88470648 CGGGAAGCTTATC-CGTGCAATAT
1 CGGGAAGCTCA-CAAGAGCCATAT
* *
88470671 AATGGGAAGCTCATAAGAGCCATAAT
1 --CGGGAAGCTCACAAGAGCCAT-AT
* * *
88470697 CAGGAAGTTCACATAGAACCATAT
1 CGGGAAGCTCACA-AGAGCCATAT
*
88470721 CAGGAAGCTCACGAAGAGCC-TAT
1 CGGGAAGCTCAC-AAGAGCCATAT
*
88470744 CGAGAAGCTCACAAAGAGCCAT
1 CGGGAAGCTCAC-AAGAGCCAT
88470766 GTAACGGGAA
Statistics
Matches: 89, Mismatches: 21, Indels: 16
0.71 0.17 0.13
Matches are distributed among these distances:
23 26 0.29
24 38 0.43
25 23 0.26
26 2 0.02
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (23 bp):
CGGGAAGCTCACAAGAGCCATAT
Found at i:88473540 original size:24 final size:24
Alignment explanation
Indices: 88473513--88473563 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 24
88473503 TTTACGACAT
88473513 AGACAACTTCAAAGCT-TTCCAAAG
1 AGACAACTTCAAAG-TGTTCCAAAG
88473537 AGACAACTTCAAAGTGTTCCAAAG
1 AGACAACTTCAAAGTGTTCCAAAG
88473561 AGA
1 AGA
88473564 TCTTCACTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.20
Consensus pattern (24 bp):
AGACAACTTCAAAGTGTTCCAAAG
Found at i:88476087 original size:21 final size:22
Alignment explanation
Indices: 88476034--88476087 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
88476024 GGGGGTCCAA
* *
88476034 ACGCCCGTGTGAAAGGTAGCAC
1 ACGCCCGTGTGAAAGGAAGAAC
* * *
88476056 ACGACCATGTGACA-GAAGAAC
1 ACGCCCGTGTGAAAGGAAGAAC
88476077 ACGCCCGTGTG
1 ACGCCCGTGTG
88476088 GTGCAGGTAC
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.30, C:0.28, G:0.30, T:0.13
Consensus pattern (22 bp):
ACGCCCGTGTGAAAGGAAGAAC
Found at i:88487940 original size:39 final size:39
Alignment explanation
Indices: 88487886--88488117 Score: 371
Period size: 39 Copynumber: 6.0 Consensus size: 39
88487876 AATTATATTA
* **
88487886 CCAGCACAAAGCCTGCAGGACTTTAGCTTGGATACATTT
1 CCAGCACGAAGCCTGCAGGACTTTAGCCCGGATACATTT
*
88487925 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCAGGACTTTAGCCCGGATACATTT
* *
88487964 CCAGCACGAAGCCTGCGGGACTTTAGCCCGAATACATTT
1 CCAGCACGAAGCCTGCAGGACTTTAGCCCGGATACATTT
88488003 CCAGCACGAAG-C--CAGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCAGGACTTTAGCCCGGATACATTT
88488039 CCAGCACGAAGCCTGCAGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCAGGACTTTAGCCCGGATACATTT
* *
88488078 CCAGCACGAAGCCTGCGGGACTTTAGCCCAGATACATTT
1 CCAGCACGAAGCCTGCAGGACTTTAGCCCGGATACATTT
88488117 C
1 C
88488118 TAATGTCTTG
Statistics
Matches: 181, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
36 33 0.18
37 1 0.01
38 1 0.01
39 146 0.81
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (39 bp):
CCAGCACGAAGCCTGCAGGACTTTAGCCCGGATACATTT
Found at i:88488101 original size:114 final size:114
Alignment explanation
Indices: 88487901--88488117 Score: 391
Period size: 114 Copynumber: 1.9 Consensus size: 114
88487891 ACAAAGCCTG
** *
88487901 CAGGACTTTAGCTTGGATACATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCC
1 CAGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCAGGACTTTAGCCCGGATACATTTCC
88487966 AGCACGAAGCCTGCGGGACTTTAGCCC-GAATACATTTCCAGCACGAAGC
66 AGCACGAAGCCTGCGGGACTTTAGCCCAG-ATACATTTCCAGCACGAAGC
88488015 CAGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCAGGACTTTAGCCCGGATACATTTCC
1 CAGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCAGGACTTTAGCCCGGATACATTTCC
88488080 AGCACGAAGCCTGCGGGACTTTAGCCCAGATACATTTC
66 AGCACGAAGCCTGCGGGACTTTAGCCCAGATACATTTC
88488118 TAATGTCTTG
Statistics
Matches: 99, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
114 98 0.99
115 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.22
Consensus pattern (114 bp):
CAGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCAGGACTTTAGCCCGGATACATTTCC
AGCACGAAGCCTGCGGGACTTTAGCCCAGATACATTTCCAGCACGAAGC
Found at i:88497425 original size:16 final size:16
Alignment explanation
Indices: 88497404--88497437 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
88497394 TGAGAAAGGA
88497404 AGTTCAACTAGTAATG
1 AGTTCAACTAGTAATG
88497420 AGTTCAACTAGTAATG
1 AGTTCAACTAGTAATG
88497436 AG
1 AG
88497438 GAAACCAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (16 bp):
AGTTCAACTAGTAATG
Found at i:88498156 original size:27 final size:26
Alignment explanation
Indices: 88498126--88498178 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 26
88498116 GAAAAAAGTC
88498126 TTTCTTAAAGAACCTCTTAAGCATTTT
1 TTTCTTAAAGAACCTCTTAAGC-TTTT
88498153 TTTCTTAAAGAACCTCTTAAGCTTTT
1 TTTCTTAAAGAACCTCTTAAGCTTTT
88498179 CTTCAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.45
Consensus pattern (26 bp):
TTTCTTAAAGAACCTCTTAAGCTTTT
Found at i:88498188 original size:27 final size:27
Alignment explanation
Indices: 88498131--88498188 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
88498121 AAGTCTTTCT
* *
88498131 TAAAGAACCTCTTAAGCATTTTTTTCT
1 TAAAGAACCTCTTAAGCATTTTCTTCA
88498158 TAAAGAACCTCTTAAGC-TTTTCTTCAA
1 TAAAGAACCTCTTAAGCATTTTCTTC-A
88498185 TAAA
1 TAAA
88498189 ACTCTCATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (27 bp):
TAAAGAACCTCTTAAGCATTTTCTTCA
Found at i:88500510 original size:19 final size:19
Alignment explanation
Indices: 88500483--88500520 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
88500473 ACTAATCTCG
*
88500483 ATACGTATTTCTATACTCA
1 ATACATATTTCTATACTCA
88500502 ATACATATTTCTATACTCA
1 ATACATATTTCTATACTCA
88500521 GTAGTGCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.42
Consensus pattern (19 bp):
ATACATATTTCTATACTCA
Found at i:88507678 original size:16 final size:15
Alignment explanation
Indices: 88507654--88507683 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
88507644 AACTATTTTA
88507654 TTACAAATTTCACTC
1 TTACAAATTTCACTC
88507669 TTACATAATTTCACT
1 TTACA-AATTTCACT
88507684 TACTCCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.43
Consensus pattern (15 bp):
TTACAAATTTCACTC
Found at i:88508014 original size:50 final size:50
Alignment explanation
Indices: 88507893--88508170 Score: 285
Period size: 50 Copynumber: 5.6 Consensus size: 50
88507883 ATCTAGTACG
* * * * *
88507893 CATAGTAGCTTGCACTTAGTACTACACATGCGACC-AACAATCCGATACA
1 CATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACA
88507942 C--AGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACA
1 CATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACA
* * * ** * * * *
88507990 CGTAGTAGCCTACACTTAGCACTACACACGTGATCGAAACTATCGGGTACG
1 CATAGTAGCCTGCACTTAGTACTACACACGTGA-CCTAACCATCTGATACA
* * * * *
88508041 CATAATAGCCTGCACTTAGTACTACACATGCT-ACCTAATCATCTGGTATA
1 CATAGTAGCCTGCACTTAGTACTACACACG-TGACCTAACCATCTGATACA
* * *
88508091 CATAGTAGCCTGCACTTAGTACTACACACGTGACCTAAAACCATTTTAAACA
1 CATAGTAGCCTGCACTTAGTACTACACACGTGACCT--AACCATCTGATACA
*
88508143 CATAGTAGCCTGCACATAGTACTACACA
1 CATAGTAGCCTGCACTTAGTACTACACA
88508171 TGTGTTCTCA
Statistics
Matches: 187, Mismatches: 34, Indels: 13
0.80 0.15 0.06
Matches are distributed among these distances:
47 29 0.16
48 13 0.07
49 2 0.01
50 70 0.37
51 37 0.20
52 36 0.19
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (50 bp):
CATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACA
Found at i:88517108 original size:29 final size:29
Alignment explanation
Indices: 88517076--88517144 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
88517066 TCTTTTCTCT
88517076 CACTTTTCTACTCCCTCTTCTCATCCCTC
1 CACTTTTCTACTCCCTCTTCTCATCCCTC
88517105 CACTTTTCTACTCCCTCTTCTCATCCCTC
1 CACTTTTCTACTCCCTCTTCTCATCCCTC
88517134 CACTTTTCTAC
1 CACTTTTCTAC
88517145 CCAACTAAGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.12, C:0.46, G:0.00, T:0.42
Consensus pattern (29 bp):
CACTTTTCTACTCCCTCTTCTCATCCCTC
Found at i:88517119 original size:17 final size:16
Alignment explanation
Indices: 88517074--88517121 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 16
88517064 TTTCTTTTCT
88517074 CTCACTTTTCTACTCC
1 CTCACTTTTCTACTCC
*
88517090 CT--CTTCTC-A-TCC
1 CTCACTTTTCTACTCC
88517102 CTCCACTTTTCTACTCC
1 CT-CACTTTTCTACTCC
88517119 CTC
1 CTC
88517122 TTCTCATCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
12 5 0.20
13 1 0.04
14 5 0.20
15 5 0.20
16 4 0.16
17 5 0.20
ACGTcount: A:0.10, C:0.48, G:0.00, T:0.42
Consensus pattern (16 bp):
CTCACTTTTCTACTCC
Found at i:88519464 original size:80 final size:80
Alignment explanation
Indices: 88519374--88519535 Score: 306
Period size: 80 Copynumber: 2.0 Consensus size: 80
88519364 CTAATACATT
*
88519374 CACTTACCCCAAGTCCTCACTCACAAATCACAATAACTCTCCAATAAAGTGCCTAAAATAAAAGT
1 CACTTACCCCAAATCCTCACTCACAAATCACAATAACTCTCCAATAAAGTGCCTAAAATAAAAGT
88519439 GCAAAAATATTCACA
66 GCAAAAATATTCACA
*
88519454 CACTTACCCCAAATCCTCACTCACAAATCACAATAACTCTCCAATAAAGTGCCTAATATAAAAGT
1 CACTTACCCCAAATCCTCACTCACAAATCACAATAACTCTCCAATAAAGTGCCTAAAATAAAAGT
88519519 GCAAAAATATTCACA
66 GCAAAAATATTCACA
88519534 CA
1 CA
88519536 TTTAAGCGTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.44, C:0.29, G:0.06, T:0.22
Consensus pattern (80 bp):
CACTTACCCCAAATCCTCACTCACAAATCACAATAACTCTCCAATAAAGTGCCTAAAATAAAAGT
GCAAAAATATTCACA
Found at i:88520548 original size:109 final size:109
Alignment explanation
Indices: 88520349--88520565 Score: 364
Period size: 108 Copynumber: 2.0 Consensus size: 109
88520339 AACTCATGCA
* *
88520349 TTGAAATTTTAAAAGGTTATTCGGTTATTTGGGTCAAACGAAACAAATCGAAACCCAGCACGTAG
1 TTGAAATTTTAAAAGGTTATTCGGTTATTTGGGTCAAACGAAACAAATCGAAACCCAACACGTAA
* * *
88520414 GGCACAATCTTTTGAATCTCCAAAAAAGGAAATATTGCCTTTAT
66 GGCACAATCTTTCGAATCCCCAAAAAACGAAATATTGCCTTTAT
*
88520458 TTGAAATTTTAAAAGGTTGTTCGGTTATTTGGGTCAAACGAAA-AAATCGAAACCCAACACGTAA
1 TTGAAATTTTAAAAGGTTATTCGGTTATTTGGGTCAAACGAAACAAATCGAAACCCAACACGTAA
*
88520522 GGCACGATCTTTCGAATCCCCAAAAAACGAAATATTGCCTTTAT
66 GGCACAATCTTTCGAATCCCCAAAAAACGAAATATTGCCTTTAT
88520566 GTTTAAAAAT
Statistics
Matches: 101, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
108 59 0.58
109 42 0.42
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.29
Consensus pattern (109 bp):
TTGAAATTTTAAAAGGTTATTCGGTTATTTGGGTCAAACGAAACAAATCGAAACCCAACACGTAA
GGCACAATCTTTCGAATCCCCAAAAAACGAAATATTGCCTTTAT
Found at i:88521342 original size:3 final size:3
Alignment explanation
Indices: 88521328--88521388 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
88521318 GTTTAATGGT
* *
88521328 ATA ATC ATA ATA ATA ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
88521376 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
88521389 ATGATCCAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:88521413 original size:7 final size:7
Alignment explanation
Indices: 88521336--88521413 Score: 53
Period size: 6 Copynumber: 11.7 Consensus size: 7
88521326 GTATAATCAT
88521336 AATAAT-
1 AATAATA
88521342 AATAAT-
1 AATAATA
88521348 AATAATGA
1 AATAAT-A
88521356 TAATAAT-
1 -AATAATA
88521363 AATAAT-
1 AATAATA
88521369 AATAAT-
1 AATAATA
88521375 AATAAT-
1 AATAATA
88521381 AATAATA
1 AATAATA
* *
88521388 AATGATCC
1 AATAAT-A
88521396 AA-AATA
1 AATAATA
88521402 AATAATA
1 AATAATA
*
88521409 TATAA
1 AATAA
88521414 AAGTTTAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
6 38 0.62
7 15 0.25
8 2 0.03
9 6 0.10
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (7 bp):
AATAATA
Found at i:88521630 original size:26 final size:27
Alignment explanation
Indices: 88521599--88521658 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
88521589 GAAAAGAGCC
* *
88521599 AAAATATATGA-TATACAAAATAATTT
1 AAAATACATGAGTATAAAAAATAATTT
*
88521625 AGAATACATGATGTATAAAAAATAATTT
1 AAAATACATGA-GTATAAAAAATAATTT
88521653 AAAATA
1 AAAATA
88521659 AATAATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 9 0.32
28 19 0.68
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.32
Consensus pattern (27 bp):
AAAATACATGAGTATAAAAAATAATTT
Found at i:88522774 original size:22 final size:21
Alignment explanation
Indices: 88522749--88522796 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
88522739 TGTTCAATCA
88522749 CTGTTCTATATTGTTTCTGCCT
1 CTGTTCTATATTGTTT-TGCCT
* *
88522771 CTGTTCTGTATTGTTTTGCTT
1 CTGTTCTATATTGTTTTGCCT
88522792 CTGTT
1 CTGTT
88522797 TCGCCTCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.06, C:0.19, G:0.17, T:0.58
Consensus pattern (21 bp):
CTGTTCTATATTGTTTTGCCT
Found at i:88528836 original size:5 final size:5
Alignment explanation
Indices: 88528826--88528878 Score: 106
Period size: 5 Copynumber: 10.6 Consensus size: 5
88528816 CTGTGTGTTC
88528826 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
88528876 TTT
1 TTT
88528879 TTTACAAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:88529703 original size:20 final size:20
Alignment explanation
Indices: 88529656--88529704 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
88529646 AGAACTAAAC
*
88529656 AGAACA-AACAAAGCAGAGT
1 AGAACAGAACAAAGCAGACT
*
88529675 AGAATAGAACAAAGCAGAACT
1 AGAACAGAACAAAGCAG-ACT
88529696 -GAACAGAAC
1 AGAACAGAAC
88529705 TACACAAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 5 0.20
20 18 0.72
21 2 0.08
ACGTcount: A:0.57, C:0.16, G:0.20, T:0.06
Consensus pattern (20 bp):
AGAACAGAACAAAGCAGACT
Found at i:88550028 original size:25 final size:24
Alignment explanation
Indices: 88549968--88550028 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
88549958 AATTTTATCA
*
88549968 AAAATATTT-TTTATTATATAATT
1 AAAATATTTATTTATTATATAAAT
* * *
88549991 ATCAATAATTATTTGATTTTATAAAT
1 A-AAATATTTATTT-ATTATATAAAT
88550017 AAAATATTTATT
1 AAAATATTTATT
88550029 AAATAAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
23 1 0.03
24 6 0.21
25 12 0.41
26 10 0.34
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
AAAATATTTATTTATTATATAAAT
Found at i:88550049 original size:29 final size:29
Alignment explanation
Indices: 88550013--88550092 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 29
88550003 TTGATTTTAT
88550013 AAATAAAATATTTATTAAATAAAAATATG-
1 AAATAAAATATTTATTAAATAAAAAT-TGA
* * *
88550042 AAGTAAAAAATTTA--AAA-AAAACTTGA
1 AAATAAAATATTTATTAAATAAAAATTGA
* *
88550068 AAATAATATATTTATTAATTAAAAA
1 AAATAAAATATTTATTAAATAAAAA
88550093 AAATTTGAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
25 2 0.05
26 16 0.41
27 3 0.08
28 2 0.05
29 16 0.41
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (29 bp):
AAATAAAATATTTATTAAATAAAAATTGA
Found at i:88551369 original size:64 final size:64
Alignment explanation
Indices: 88551291--88551417 Score: 182
Period size: 64 Copynumber: 2.0 Consensus size: 64
88551281 TGTTTAGTCT
* *
88551291 GGTTCATCTGATGACAAAGATTTGTATATTTCTATAGATGAAACCAAGTTTTGTTTGAATGTCC
1 GGTTCATCTAATGACAAAGATTTGTATATTTCAATAGATGAAACCAAGTTTTGTTTGAATGTCC
* * * * * *
88551355 GGTTCATCTAATGACAAAGATTTTTATGTTTCAATTGATTAAACTAAGTTTTGTTTGATTGTC
1 GGTTCATCTAATGACAAAGATTTGTATATTTCAATAGATGAAACCAAGTTTTGTTTGAATGTC
88551418 TGGATTGTAG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (64 bp):
GGTTCATCTAATGACAAAGATTTGTATATTTCAATAGATGAAACCAAGTTTTGTTTGAATGTCC
Found at i:88552488 original size:153 final size:150
Alignment explanation
Indices: 88552208--88552489 Score: 381
Period size: 153 Copynumber: 1.9 Consensus size: 150
88552198 TCTGAGTAAA
*
88552208 ATAGCTTGTGTGTGCTTGCAGCTGCTAGCTTTCAGTTGACTGGATAGGCAATTCTAATCCTGTAA
1 ATAGCTTGTGTGTGCATGCAGCTGCTAGCTTTCAGTTGACTGGATAGGCAATTCTAATCCTGTAA
*
88552273 AAAAAGAGCCAAATCTTGTGTTTGCAAAAGGTGCACAAGGGGAGCAATTAGGGGATTGGGAGGGG
66 AAAAAGAGCAAAATCTTGTGTTTGCAAAAGGTGCACAAGGGGAGCAATTAGGGGATTGGGAGGGG
88552338 CCCCATGTCCCCTAAACATG
131 CCCCATGTCCCCTAAACATG
* * * * ** *
88552358 ATAGCTTGTGTGTGCATGCAGTTGCTAGGTTTTAGTTGATTGGGATAGGCGGTTCTAATCCCTCT
1 ATAGCTTGTGTGTGCATGCAGCTGCTAGCTTTCAGTTGACT-GGATAGGCAATTCTAAT-CCT-G
* * *
88552423 TAAAAGAAA-AGGAAAAT-TTGGTGTTTGCAAAAGGTGCAGAAGGGGAGCAATT-GGGTGATTTG
63 TAAAA-AAAGAGCAAAATCTT-GTGTTTGCAAAAGGTGCACAAGGGGAGCAATTAGGG-GATTGG
88552485 GAGGG
125 GAGGG
88552490 CTTATATTTC
Statistics
Matches: 114, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
150 36 0.32
151 15 0.13
152 8 0.07
153 52 0.46
154 3 0.03
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.28
Consensus pattern (150 bp):
ATAGCTTGTGTGTGCATGCAGCTGCTAGCTTTCAGTTGACTGGATAGGCAATTCTAATCCTGTAA
AAAAAGAGCAAAATCTTGTGTTTGCAAAAGGTGCACAAGGGGAGCAATTAGGGGATTGGGAGGGG
CCCCATGTCCCCTAAACATG
Found at i:88556334 original size:2 final size:2
Alignment explanation
Indices: 88556327--88556357 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
88556317 ATTCCTAAAT
88556327 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 T
88556358 TTCACTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:88563364 original size:16 final size:19
Alignment explanation
Indices: 88563345--88563383 Score: 57
Period size: 16 Copynumber: 2.2 Consensus size: 19
88563335 TTACGAAGAT
88563345 AAAAAATC-T-GTG-AGGA
1 AAAAAATCTTAGTGAAGGA
88563361 AAAAAATCTTAGTGAAGGA
1 AAAAAATCTTAGTGAAGGA
88563380 AAAA
1 AAAA
88563384 GAATACACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.40
17 1 0.05
18 3 0.15
19 8 0.40
ACGTcount: A:0.56, C:0.05, G:0.21, T:0.18
Consensus pattern (19 bp):
AAAAAATCTTAGTGAAGGA
Found at i:88578837 original size:2 final size:2
Alignment explanation
Indices: 88578830--88578859 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
88578820 AATAAATAAT
88578830 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
88578860 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:88578864 original size:2 final size:2
Alignment explanation
Indices: 88578859--88578883 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
88578849 ATATATATAT
88578859 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
88578884 TTTGTTAATG
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:88579889 original size:15 final size:15
Alignment explanation
Indices: 88579852--88579890 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
88579842 AAATATTATA
88579852 AAAGAG-GAAAAAAT
1 AAAGAGAGAAAAAAT
*
88579866 AAA-ATAGAAAAAAT
1 AAAGAGAGAAAAAAT
88579880 AAAGAGAGAAA
1 AAAGAGAGAAA
88579891 TAATGTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 1 0.05
14 14 0.67
15 6 0.29
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (15 bp):
AAAGAGAGAAAAAAT
Found at i:88581875 original size:17 final size:16
Alignment explanation
Indices: 88581853--88581885 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
88581843 TAAAAAGGAA
88581853 AAAAATAATATTTTTAT
1 AAAAATAAT-TTTTTAT
88581870 AAAAATAATTTTTTAT
1 AAAAATAATTTTTTAT
88581886 TTTTTTGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAAAATAATTTTTTAT
Found at i:88582035 original size:64 final size:64
Alignment explanation
Indices: 88581865--88582040 Score: 183
Period size: 66 Copynumber: 2.7 Consensus size: 64
88581855 AAATAATATT
* * * * * * * **
88581865 TTTATAAAAATAATTTTTTATTTTTTTGGTGCCAGTGTTGAAGTGACCGATACCACTTCAAAGT
1 TTTAAAAAAATGATTTTTTGTTTTTTTGGTGTCGGTGTTGAAGTGGCCGACACCACTTCAAAAC
* * * *
88581929 TTTAAAAAAAATGATTTTTTGCGTTTTTGGGTGTCGATGTTGAAGTGGCC-AGCACCAGTTCAAA
1 TTT-AAAAAAATGATTTTTTG-TTTTTTTGGTGTCGGTGTTGAAGTGGCCGA-CACCACTTCAAA
88581993 AC
63 AC
* *
88581995 TTTAAAAAAATGATCTTTTGTTTTTTTGGTGTTGGTGTTGAAGTGG
1 TTTAAAAAAATGATTTTTTGTTTTTTTGGTGTCGGTGTTGAAGTGG
88582041 GCGGTATCTG
Statistics
Matches: 91, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
64 25 0.27
65 31 0.34
66 35 0.38
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.41
Consensus pattern (64 bp):
TTTAAAAAAATGATTTTTTGTTTTTTTGGTGTCGGTGTTGAAGTGGCCGACACCACTTCAAAAC
Found at i:88582054 original size:64 final size:62
Alignment explanation
Indices: 88581933--88582068 Score: 148
Period size: 64 Copynumber: 2.2 Consensus size: 62
88581923 CAAAGTTTTA
*
88581933 AAAAAAATGATTTTTTGCGTTTTTGGGTGTCGATGTTGAAGTGGCCAGCACCAGTTCAAAACTTT
1 AAAAAAATGATCTTTTGCGTTTTTGGGTGTCGATGTTGAAGTGGCCAGCACCAGTTCAAAA---T
* * * * * * * * *
88581998 AAAAAAATGATCTTTTG-TTTTTTTGGTGTTGGTGTTGAAGTGGGCGGTATCTGTTCAAAAT
1 AAAAAAATGATCTTTTGCGTTTTTGGGTGTCGATGTTGAAGTGGCCAGCACCAGTTCAAAAT
88582059 AAAAAAATGA
1 AAAAAAATGA
88582069 ATTGAGGAGG
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
61 11 0.18
64 34 0.56
65 16 0.26
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.37
Consensus pattern (62 bp):
AAAAAAATGATCTTTTGCGTTTTTGGGTGTCGATGTTGAAGTGGCCAGCACCAGTTCAAAAT
Found at i:88582607 original size:6 final size:6
Alignment explanation
Indices: 88582596--88582637 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
88582586 AATTAATTAT
* *
88582596 ATTAAA ATTAAA ATTAAA ATTAAA A-TATA ATTAAA AATAAA A
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA A
88582638 ATATATATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
ATTAAA
Found at i:88582638 original size:18 final size:17
Alignment explanation
Indices: 88582580--88582642 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 17
88582570 TGAAAAATAT
*
88582580 AATAAAAAT-TAATTAT
1 AATAAAAATATAATTAA
* * *
88582596 ATTAAAATTAAAATTAA
1 AATAAAAATATAATTAA
*
88582613 AATTAAAATATAATTAAA
1 AATAAAAATATAATT-AA
88582631 AATAAAAATATA
1 AATAAAAATATA
88582643 TATTTATTAT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
16 7 0.19
17 16 0.44
18 13 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAAAAATATAATTAA
Found at i:88583372 original size:23 final size:23
Alignment explanation
Indices: 88583311--88583375 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
88583301 ACTTTTTAAC
88583311 TTTTA-ATTTTTTTACTAATAATAT
1 TTTTATATTTTTTT--TAATAATAT
* *
88583335 TTTTAT-TTGTGTTTTAGTAATAT
1 TTTTATATT-TTTTTTAATAATAT
88583358 TTTTATATTTTTTTTAAT
1 TTTTATATTTTTTTTAAT
88583376 CTCAAAGGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
23 21 0.62
24 9 0.26
25 4 0.12
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.68
Consensus pattern (23 bp):
TTTTATATTTTTTTTAATAATAT
Found at i:88583980 original size:2 final size:2
Alignment explanation
Indices: 88583969--88584008 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
88583959 AAATCATTTT
88583969 TA TA -A 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 TA TA T
88584009 TAGGTTAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:88584254 original size:17 final size:16
Alignment explanation
Indices: 88584216--88584257 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
88584206 ATTATCACTT
* *
88584216 TAAAATTAAAAAAATT
1 TAAAATTTAAAAAATA
88584232 TAAAATTTAAAAAATA
1 TAAAATTTAAAAAATA
88584248 TATAAATTTA
1 TA-AAATTTA
88584258 TTAAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAAATTTAAAAAATA
Found at i:88585268 original size:16 final size:16
Alignment explanation
Indices: 88585231--88585270 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
88585221 CAATGATGAA
88585231 AGAAAATTGAAGGAAT
1 AGAAAATTGAAGGAAT
*
88585247 -GAAAAATTGAAGGGAT
1 AG-AAAATTGAAGGAAT
88585263 AGAAAATT
1 AGAAAATT
88585271 AAAAAGATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 1 0.05
16 19 0.90
17 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.25, T:0.20
Consensus pattern (16 bp):
AGAAAATTGAAGGAAT
Found at i:88585504 original size:27 final size:27
Alignment explanation
Indices: 88585466--88585519 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
88585456 ACACACTCAA
*
88585466 AATTTATTTTATTTTCATTTTTTCTTT
1 AATTTATTTTATTTCCATTTTTTCTTT
88585493 AATTTATTTTATTTCCATTTTTTCTTT
1 AATTTATTTTATTTCCATTTTTTCTTT
88585520 CTTTCCCCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (27 bp):
AATTTATTTTATTTCCATTTTTTCTTT
Found at i:88586819 original size:17 final size:18
Alignment explanation
Indices: 88586783--88586820 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
88586773 ATATTAATTT
*
88586783 ATTATTTGAGTAATTAAA
1 ATTATTTAAGTAATTAAA
*
88586801 ATTATTTAAGTTA-TAAA
1 ATTATTTAAGTAATTAAA
88586818 ATT
1 ATT
88586821 TAACTGGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (18 bp):
ATTATTTAAGTAATTAAA
Found at i:88587020 original size:18 final size:18
Alignment explanation
Indices: 88586997--88587032 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
88586987 CGCCACTTGG
88586997 CTAGTTCAACCAATTCAA
1 CTAGTTCAACCAATTCAA
*
88587015 CTAGTTCAATCAATTCAA
1 CTAGTTCAACCAATTCAA
88587033 TAAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.25, G:0.06, T:0.31
Consensus pattern (18 bp):
CTAGTTCAACCAATTCAA
Found at i:88591414 original size:22 final size:23
Alignment explanation
Indices: 88591372--88591414 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
88591362 GGAAGATACC
88591372 AACAACATGAATGTCATAAATAT
1 AACAACATGAATGTCATAAATAT
88591395 AACAACA-GAACTG-CATAAAT
1 AACAACATGAA-TGTCATAAAT
88591415 TAAAGTAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.53, C:0.16, G:0.09, T:0.21
Consensus pattern (23 bp):
AACAACATGAATGTCATAAATAT
Found at i:88597235 original size:91 final size:91
Alignment explanation
Indices: 88597110--88597292 Score: 217
Period size: 91 Copynumber: 2.0 Consensus size: 91
88597100 ATTTTTGTAC
* * * *
88597110 AAAAACAATTAAGCCCCTCCTTTTTTTTGTACTCAATT-GAGCACTTAAACTTTCAAAATGTATT
1 AAAAACAATTAAGCCCATCCTTTTTTTTGTACTCAATTGGA-CAATTAAACTTTCAAAATGCATC
* *
88597174 AAAAAGACTCTCAAACTTCTTCAAAAA
65 AAAAAGACCCTCAAAATTCTTCAAAAA
* * * *
88597201 AAAAAGCAATTAAGCTCATGCTTTTTTTT-TACTCAATTGGATAATTGAACTTTCAAAATGCATC
1 AAAAA-CAATTAAGCCCATCCTTTTTTTTGTACTCAATTGGACAATTAAACTTTCAAAATGCATC
* * *
88597265 AAAAATACCCTTAAAATTTTTCAAAAA
65 AAAAAGACCCTCAAAATTCTTCAAAAA
88597292 A
1 A
88597293 TAATTAAGCC
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
91 55 0.71
92 22 0.29
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (91 bp):
AAAAACAATTAAGCCCATCCTTTTTTTTGTACTCAATTGGACAATTAAACTTTCAAAATGCATCA
AAAAGACCCTCAAAATTCTTCAAAAA
Found at i:88597392 original size:10 final size:10
Alignment explanation
Indices: 88597352--88597398 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
88597342 TAAATTTTAG
88597352 AAAAATTATT
1 AAAAATTATT
** *
88597362 AAATTTTAAT
1 AAAAATTATT
88597372 AAAAATT-TT
1 AAAAATTATT
*
88597381 AAAATTTATT
1 AAAAATTATT
88597391 AAAAATTA
1 AAAAATTA
88597399 GATTTTTTTA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
9 7 0.25
10 21 0.75
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
AAAAATTATT
Found at i:88597457 original size:19 final size:19
Alignment explanation
Indices: 88597343--88597458 Score: 85
Period size: 19 Copynumber: 6.2 Consensus size: 19
88597333 AACAAATAAT
* *
88597343 AAATTTTAGAAAAATTATT
1 AAATTTTATAAAAATTATA
*
88597362 AAATTTTAATAAAAATTTTA
1 AAATTTT-ATAAAAATTATA
*
88597382 AAA-TTTATTAAAAATTAGA
1 AAATTTTA-TAAAAATTATA
*** *
88597401 TTTTTTTATAAAAATTGTA
1 AAATTTTATAAAAATTATA
** *
88597420 AAA-AATA-AAAAATTGTA
1 AAATTTTATAAAAATTATA
*
88597437 AAATTTTATAAAAATCATA
1 AAATTTTATAAAAATTATA
88597456 AAA
1 AAA
88597459 AAATAAACGA
Statistics
Matches: 73, Mismatches: 19, Indels: 10
0.72 0.19 0.10
Matches are distributed among these distances:
17 13 0.18
18 5 0.07
19 39 0.53
20 16 0.22
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (19 bp):
AAATTTTATAAAAATTATA
Found at i:88600848 original size:132 final size:131
Alignment explanation
Indices: 88600602--88600972 Score: 449
Period size: 132 Copynumber: 2.8 Consensus size: 131
88600592 CAAGTATTCT
* * * *
88600602 TTTAAAAATTCTTTACAACGAAGACGAGATTCAATATTTGGCAATTCACGGAATAGTGCCCTAAC
1 TTTAAAAATTCTTTAAAACGAAGACGAGATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAAC
* *
88600667 GTATTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCACTCACGC
66 GTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTCACTCACGC
88600732 C
131 C
* * * * *
88600733 TTTCAAAAATTCTTTAAAACGAAGACGAGGTTTGATGTTTGGCAATTCGCGGAAGCGTACCCTAA
1 TTT-AAAAATTCTTTAAAACGAAGACGAGATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAA
* * *
88600798 CGTGTTGGGTTGCAATTTCGCGTTTGCTCGAAATAATCGAATGTCACTTCAAAATTTCATTCACG
65 CGTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTCACTCACG
*
88600863 TC
130 CC
** * * * *
88600865 TATT-AAAA-TCCCTAAAACGAAGGCGATATGCGATATTTGGCAATTCGTGGAATCGTGCCCTAA
1 T-TTAAAAATTCTTTAAAACGAAGACGAGATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAA
* ** * * * * *
88600928 CATGTTGGGTCACAATTTCCCATTTGTTTAAAATAATCAAATATC
65 CGTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATATC
88600973 CCTCAGGTCT
Statistics
Matches: 202, Mismatches: 36, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
130 79 0.39
131 7 0.03
132 114 0.56
133 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (131 bp):
TTTAAAAATTCTTTAAAACGAAGACGAGATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAAC
GTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTCACTCACGC
C
Found at i:88601786 original size:10 final size:10
Alignment explanation
Indices: 88601755--88601800 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
88601745 ACACTATATA
88601755 TTTTATAATT
1 TTTTATAATT
*
88601765 TTTTACAATT
1 TTTTATAATT
88601775 TTTTAT-A-T
1 TTTTATAATT
*
88601783 TTTTCTAATT
1 TTTTATAATT
*
88601793 TTTAATAA
1 TTTTATAA
88601801 ATTTAATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
8 6 0.21
9 2 0.07
10 21 0.72
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTATAATT
Found at i:88602084 original size:89 final size:89
Alignment explanation
Indices: 88601914--88602086 Score: 224
Period size: 89 Copynumber: 1.9 Consensus size: 89
88601904 TTGAAAAAAA
* * *
88601914 TTTGAGAGTTTTTTTAATGCATTTTGAAAGTTCAAGCACCCAATTAAGTGCAAAAAAAAAAGTAC
1 TTTGAGAGTTTTTTTAATGCATTTTAAAAGTTCAAGCACCCAAATAAGTGCAAAAAAAAAAGTAA
* **
88601979 GAGCTTAATTGTTTTTTTTAAAGG
66 GAGCTTAAATACTTTTTTTAAAGG
* * * *
88602003 TTTGAGGGCTTTTTTT-ATGCATTTTAAAAGTTTAAGTACCCAAATGAGTGCAAAAAAAAAAAG-
1 TTTGAGAG-TTTTTTTAATGCATTTTAAAAGTTCAAGCACCCAAATAAGTGC-AAAAAAAAAAGT
88602066 AAGAGCTTAAATACTTTTTTT
64 AAGAGCTTAAATACTTTTTTT
88602087 GAAAAAATTT
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
89 54 0.75
90 18 0.25
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (89 bp):
TTTGAGAGTTTTTTTAATGCATTTTAAAAGTTCAAGCACCCAAATAAGTGCAAAAAAAAAAGTAA
GAGCTTAAATACTTTTTTTAAAGG
Found at i:88602727 original size:15 final size:15
Alignment explanation
Indices: 88602709--88602738 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
88602699 AACAATAACA
88602709 TTTTCGAGATTTTAT
1 TTTTCGAGATTTTAT
*
88602724 TTTTCTAGATTTTAT
1 TTTTCGAGATTTTAT
88602739 ATAAGATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (15 bp):
TTTTCGAGATTTTAT
Found at i:88606241 original size:64 final size:64
Alignment explanation
Indices: 88606092--88606400 Score: 404
Period size: 64 Copynumber: 4.8 Consensus size: 64
88606082 CAAGTTCATC
* * * *
88606092 TAAATAATTGAAGTTGATATAAGAATGAAAATTCAATAAAAAAATATATACATAATGCAAATATA
1 TAAATAATTGAAGTTGATACAAGAATGAAAATTCAAT-ACATAAT-T-TACATAAAGCAAATATA
88606157 TG
63 TG
* * * * * *
88606159 TAAATAATTGAAGTTGATACTATAATGAAAATTCAATACATAACTTACATAAAGTAAATAAACG
1 TAAATAATTGAAGTTGATACAAGAATGAAAATTCAATACATAATTTACATAAAGCAAATATATG
*
88606223 TAAATAATTGAAGTTGATACAAGAATGAAAATTCAATACATAATTTACATAAAACAAATATATG
1 TAAATAATTGAAGTTGATACAAGAATGAAAATTCAATACATAATTTACATAAAGCAAATATATG
* * ** * *
88606287 TAAATAATTGAAATTGATACAAGAATGAGAATTTTATATATAATTTACATAATGCAAATATATG
1 TAAATAATTGAAGTTGATACAAGAATGAAAATTCAATACATAATTTACATAAAGCAAATATATG
* *
88606351 TAAATAATTGAAGTTGATAC-AGTAATGAAAATTGAATATATAATTTACAT
1 TAAATAATTGAAGTTGATACAAG-AATGAAAATTCAATACATAATTTACAT
88606401 TCTATTTGGC
Statistics
Matches: 213, Mismatches: 28, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
63 2 0.01
64 172 0.81
65 1 0.00
66 4 0.02
67 34 0.16
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.32
Consensus pattern (64 bp):
TAAATAATTGAAGTTGATACAAGAATGAAAATTCAATACATAATTTACATAAAGCAAATATATG
Found at i:88607542 original size:27 final size:27
Alignment explanation
Indices: 88607510--88607918 Score: 371
Period size: 27 Copynumber: 15.3 Consensus size: 27
88607500 GTAGGGCAAA
* * *
88607510 TCAGTCATTTTACCTTACAGGGATATT
1 TCAGTCATTTTACCGTATAGGGGTATT
*
88607537 ACAGTCATTTTACCGTATAGGGGTATT
1 TCAGTCATTTTACCGTATAGGGGTATT
*
88607564 ACAGTCATTTTACCGTATAGGGGTATT
1 TCAGTCATTTTACCGTATAGGGGTATT
*
88607591 TCAGTCATTTTACCGTATAGGGGTATC
1 TCAGTCATTTTACCGTATAGGGGTATT
*
88607618 TC-GATCATTTTACCCTAT-GAGGGTATT
1 TCAG-TCATTTTACCGTATAG-GGGTATT
* *
88607645 TCGGTCATTTTACCTTATA-GGGTATT
1 TCAGTCATTTTACCGTATAGGGGTATT
* *
88607671 TC-GATCATTTTACCCTATAGCGGTATT
1 TCAG-TCATTTTACCGTATAGGGGTATT
*
88607698 TCGGTCATTTTATCC-TAT-GGGGTATT
1 TCAGTCATTTTA-CCGTATAGGGGTATT
* * ** *
88607724 TCGGTTATTTTACTTTATGGGGGTATT
1 TCAGTCATTTTACCGTATAGGGGTATT
*
88607751 TC-GATCATTTTACCCTAT-GAGGGTATT
1 TCAG-TCATTTTACCGTATAG-GGGTATT
* * *
88607778 TCGGTCATTTTACCTTATAGAGGTATT
1 TCAGTCATTTTACCGTATAGGGGTATT
* *
88607805 TCGGTCA-TTTACCCTAT-GGAGGTATT
1 TCAGTCATTTTACCGTATAGG-GGTATT
* *
88607831 TCATTCA-TTTACCCTAT-GGAGGTATT
1 TCAGTCATTTTACCGTATAGG-GGTATT
*
88607857 TCATTCATTTTATCC-TATAGGGGTATT
1 TCAGTCATTTTA-CCGTATAGGGGTATT
88607884 TCAGTCATTTTATCC-TAT-GAGGGTATT
1 TCAGTCATTTTA-CCGTATAG-GGGTATT
*
88607911 TCGGTCAT
1 TCAGTCAT
88607919 ACATGGCCCA
Statistics
Matches: 338, Mismatches: 25, Indels: 38
0.84 0.06 0.09
Matches are distributed among these distances:
25 3 0.01
26 95 0.28
27 230 0.68
28 10 0.03
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.42
Consensus pattern (27 bp):
TCAGTCATTTTACCGTATAGGGGTATT
Found at i:88607756 original size:133 final size:131
Alignment explanation
Indices: 88607513--88607918 Score: 500
Period size: 133 Copynumber: 3.0 Consensus size: 131
88607503 GGGCAAATCA
* * * * *
88607513 GTCATTTTACCTTACAGGGATATTAC-AGTCATTTTACCGTATAGGGGTATTACAGTCATTTTAC
1 GTCATTTTACCTTATAGGG-TATTTCGA-TCATTTTACCCTATAGAGGTATTTCAGTCATTTTAC
* *
88607577 CGTATAGGGGTATTTCAGTCATTTTAC-CGTATAGGGGTATCTCGATCATTTTACCCTATGAGGG
64 C-TAT-GGGGTATTTC-GTTATTTTACTC-TATAGGGGTATTTCGATCATTTTACCCTATGAGGG
88607641 TATTTCG
125 TATTTCG
* *
88607648 GTCATTTTACCTTATAGGGTATTTCGATCATTTTACCCTATAGCGGTATTTCGGTCATTTTATCC
1 GTCATTTTACCTTATAGGGTATTTCGATCATTTTACCCTATAGAGGTATTTCAGTCATTTTA-CC
* *
88607713 TATGGGGTATTTCGGTTATTTTACTTTATGGGGGTATTTCGATCATTTTACCCTATGAGGGTATT
65 TATGGGGTATTTC-GTTATTTTACTCTATAGGGGTATTTCGATCATTTTACCCTATGAGGGTATT
88607778 TCG
129 TCG
* * *
88607781 GTCATTTTACCTTATAGAGGTATTTCGGTCA-TTTACCCTATGGAGGTATTTCATTCA-TTTACC
1 GTCATTTTACCTTATAG-GGTATTTCGATCATTTTACCCTATAGAGGTATTTCAGTCATTTTA-C
* *
88607844 CTATGGAGGTATTTCATTCATTTTA-TCCTATAGGGGTATTTC-AGTCATTTTATCCTATGAGGG
64 CTATGG-GGTATTTCGTT-ATTTTACT-CTATAGGGGTATTTCGA-TCATTTTACCCTATGAGGG
88607907 TATTTCG
125 TATTTCG
88607914 GTCAT
1 GTCAT
88607919 ACATGGCCCA
Statistics
Matches: 242, Mismatches: 21, Indels: 18
0.86 0.07 0.06
Matches are distributed among these distances:
132 15 0.06
133 155 0.64
134 51 0.21
135 21 0.09
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.42
Consensus pattern (131 bp):
GTCATTTTACCTTATAGGGTATTTCGATCATTTTACCCTATAGAGGTATTTCAGTCATTTTACCT
ATGGGGTATTTCGTTATTTTACTCTATAGGGGTATTTCGATCATTTTACCCTATGAGGGTATTTC
G
Found at i:88613074 original size:21 final size:21
Alignment explanation
Indices: 88613048--88613130 Score: 114
Period size: 21 Copynumber: 4.0 Consensus size: 21
88613038 CAGATACGAC
88613048 AACAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
*
88613069 AACAGAAGCTCAAAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
* *
88613090 AACAGAAGCTCGTAAGAGTTG
1 AACAGAAGCTCATAAGAGCTG
*
88613111 AACAGAAACTCGA-AAGAGCT
1 AACAGAAGCTC-ATAAGAGCT
88613131 AAATAGAAAG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:88613107 original size:42 final size:42
Alignment explanation
Indices: 88613048--88613130 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
88613038 CAGATACGAC
*
88613048 AACAGAAGCTCATAAGAGCTGAACAGAAGCTCAAAAGAGCTG
1 AACAGAAGCTCATAAGAGCTGAACAGAAACTCAAAAGAGCTG
* * *
88613090 AACAGAAGCTCGTAAGAGTTGAACAGAAACTCGAAAGAGCT
1 AACAGAAGCTCATAAGAGCTGAACAGAAACTCAAAAGAGCT
88613131 AAATAGAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTGAACAGAAACTCAAAAGAGCTG
Found at i:88617295 original size:23 final size:23
Alignment explanation
Indices: 88617253--88617310 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
88617243 ATCAAAAGAA
*
88617253 AGATCCAAAA-G-AAAAAAAATG
1 AGATCCAAAAGGTTAAAAAAATG
88617274 AGATCCAAAAGGTTAAAAAAATG
1 AGATCCAAAAGGTTAAAAAAATG
88617297 AGATCCAAAAGGTT
1 AGATCCAAAAGGTT
88617311 CACCTGGATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 10 0.29
22 1 0.03
23 23 0.68
ACGTcount: A:0.57, C:0.10, G:0.17, T:0.16
Consensus pattern (23 bp):
AGATCCAAAAGGTTAAAAAAATG
Found at i:88619821 original size:46 final size:44
Alignment explanation
Indices: 88619756--88619876 Score: 145
Period size: 46 Copynumber: 2.7 Consensus size: 44
88619746 GACGAGAGCT
* *
88619756 AGTGTAAGACTTGTCTGGGACATGCATCAGCCT-CGAGATGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-GCCTACAAG-T-TAAGCC
* * *
88619802 AGTGTAAGACATGTTTGGGACATGCATCGGCTACAAGTTAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGCCTACAAGTTAAGCC
88619846 AGTGTAAGACCATGTCTGGGACATGGCATCG
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCG
88619877 ATATCCTATC
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
44 14 0.21
45 17 0.26
46 35 0.53
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGCCTACAAGTTAAGCC
Found at i:88620868 original size:28 final size:28
Alignment explanation
Indices: 88620828--88620894 Score: 134
Period size: 28 Copynumber: 2.4 Consensus size: 28
88620818 CACACTGGCT
88620828 AGGACACGGGCGTGTCATGGCCATGTGA
1 AGGACACGGGCGTGTCATGGCCATGTGA
88620856 AGGACACGGGCGTGTCATGGCCATGTGA
1 AGGACACGGGCGTGTCATGGCCATGTGA
88620884 AGGACACGGGC
1 AGGACACGGGC
88620895 CAGAGACACG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.22, C:0.22, G:0.40, T:0.15
Consensus pattern (28 bp):
AGGACACGGGCGTGTCATGGCCATGTGA
Found at i:88623375 original size:49 final size:49
Alignment explanation
Indices: 88623311--88623829 Score: 903
Period size: 49 Copynumber: 10.5 Consensus size: 49
88623301 TACATATATG
*
88623311 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATA
* *
88623360 TGTGATAAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATA
* * *
88623409 TGTGATCAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTA--TGTATA
* *
88623460 TGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATA
88623509 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATA
88623558 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTA--TGTATA
*
88623609 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGCATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATA
88623658 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATA
*
88623707 TGTGATGAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATA
88623756 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATA
*
88623805 TGTGATGAGGCCTAATGGCCAATGT
1 TGTGATGAGGCCTAATGGCCGATGT
88623830 AAAATATATG
Statistics
Matches: 453, Mismatches: 13, Indels: 8
0.96 0.03 0.02
Matches are distributed among these distances:
49 356 0.79
51 97 0.21
ACGTcount: A:0.27, C:0.10, G:0.34, T:0.29
Consensus pattern (49 bp):
TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATA
Found at i:88623571 original size:149 final size:149
Alignment explanation
Indices: 88623311--88623829 Score: 934
Period size: 149 Copynumber: 3.5 Consensus size: 149
88623301 TACATATATG
* *
88623311 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATATGTGATAAGGCCTAAT
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAAT
* * *
88623376 GGCCGATGTGATGAACGTGAAAGTGTATGTATATGTGATCAGGCCTAATGGCCGATGTGATGAAT
66 GGCCGATGTGGTGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAATGGCCGATGTGATGAAC
88623441 GTGAAAGTGTATGTGTATA
131 GTGAAAGTGTATGTGTATA
* *
88623460 TGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATATGTGATGAGGCCTAAT
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAAT
*
88623525 GGCCGATGTGGTGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAATGGCCGATGTGGTGAAC
66 GGCCGATGTGGTGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAATGGCCGATGTGATGAAC
88623590 GTGAAAGTGTATGTGTATA
131 GTGAAAGTGTATGTGTATA
*
88623609 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGCATATGTGATGAGGCCTAAT
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAAT
88623674 GGCCGATGTGGTGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAATGGCCGATGTGATGAAC
66 GGCCGATGTGGTGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAATGGCCGATGTGATGAAC
88623739 GTGAAAGTGTA--TGTATA
131 GTGAAAGTGTATGTGTATA
88623756 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAAT
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAAT
*
88623821 GGCCAATGT
66 GGCCGATGT
88623830 AAAATATATG
Statistics
Matches: 358, Mismatches: 12, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
147 78 0.22
149 280 0.78
ACGTcount: A:0.27, C:0.10, G:0.34, T:0.29
Consensus pattern (149 bp):
TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAAT
GGCCGATGTGGTGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAATGGCCGATGTGATGAAC
GTGAAAGTGTATGTGTATA
Found at i:88623661 original size:198 final size:197
Alignment explanation
Indices: 88623311--88623829 Score: 905
Period size: 198 Copynumber: 2.6 Consensus size: 197
88623301 TACATATATG
* *
88623311 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATATGTGATAAGGCCTAAT
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAAT
* * *
88623376 GGCCGATGTGATGAACGTGAAAGTGTATGTATATGTGATCAGGCCTAATGGCCGATGTGATGAAT
66 GGCCGATGTGGTGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAATGGCCGATGTGATGAAC
* *
88623441 GTGAAAGTGTATGTGTATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGT
131 GTGAAAGTGTA-GTGCATATGTGATGAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATGT
88623506 ATA
195 ATA
88623509 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAAT
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAAT
*
88623574 GGCCGATGTGGTGAACGTGAAAGTGTATGTGTATATGTGATGAGGCCTAATGGCCGATGTGGTGA
66 GGCCGATGTGGTGAACGTGAAAGTGTA--TGTATATGTGATGAGGCCTAATGGCCGATGTGATGA
*
88623639 ACGTGAAAGTGTA-TGCATATGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATG
129 ACGTGAAAGTGTAGTGCATATGTGATGAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATG
88623703 TATA
194 TATA
*
88623707 TGTGATGAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAAT
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAAT
*
88623772 GGCCGATGTGGTGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAATGGCCAATGT
66 GGCCGATGTGGTGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAATGGCCGATGT
88623830 AAAATATATG
Statistics
Matches: 308, Mismatches: 11, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
196 30 0.10
198 232 0.75
200 46 0.15
ACGTcount: A:0.27, C:0.10, G:0.34, T:0.29
Consensus pattern (197 bp):
TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAAT
GGCCGATGTGGTGAACGTGAAAGTGTATGTATATGTGATGAGGCCTAATGGCCGATGTGATGAAC
GTGAAAGTGTAGTGCATATGTGATGAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATGTA
TA
Found at i:88623987 original size:37 final size:37
Alignment explanation
Indices: 88623932--88624046 Score: 212
Period size: 37 Copynumber: 3.1 Consensus size: 37
88623922 GTTCCGGGCG
* *
88623932 AGACTCGATGACTACGTGTGGAGATTATGACTGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGACCGGGTA
88623969 AGACCCGATGACTACGTGTGGAGATTATGACCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGACCGGGTA
88624006 AGACCCGATGACTACGTGTGGAGATTATGACCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGACCGGGTA
88624043 AGAC
1 AGAC
88624047 TTCTTTTATA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 76 1.00
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (37 bp):
AGACCCGATGACTACGTGTGGAGATTATGACCGGGTA
Found at i:88625998 original size:27 final size:27
Alignment explanation
Indices: 88625960--88626013 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
88625950 TGATCCAATT
88625960 GTGTATATATATATAAGTAAAAAATAA
1 GTGTATATATATATAAGTAAAAAATAA
88625987 GTGTATATATATATAAGTAAAAAATAA
1 GTGTATATATATATAAGTAAAAAATAA
88626014 CCATTATTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (27 bp):
GTGTATATATATATAAGTAAAAAATAA
Found at i:88627671 original size:13 final size:14
Alignment explanation
Indices: 88627632--88627663 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
88627622 CCTTAAACCT
*
88627632 TAAATCATAAAACA
1 TAAAACATAAAACA
88627646 TAAAACATAAAACA
1 TAAAACATAAAACA
88627660 TAAA
1 TAAA
88627664 CCTTAAACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAAACATAAAACA
Found at i:88627686 original size:14 final size:16
Alignment explanation
Indices: 88627664--88627696 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
88627654 AAAACATAAA
88627664 CCTTAAACCCCT-ACC
1 CCTTAAACCCCTAACC
88627679 CCTT-AACCCCTAACC
1 CCTTAAACCCCTAACC
88627694 CCT
1 CCT
88627697 AACACTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.24, C:0.55, G:0.00, T:0.21
Consensus pattern (16 bp):
CCTTAAACCCCTAACC
Found at i:88627686 original size:21 final size:22
Alignment explanation
Indices: 88627661--88627734 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 22
88627651 CATAAAACAT
* *
88627661 AAACCTTAAACCCCTACCCCTT
1 AAACCTTAAACCCCTAACACTT
* *
88627683 AACCCCT-AACCCCTAACACTT
1 AAACCTTAAACCCCTAACACTT
88627704 AAACCTTAAACCCC-AATC-CTT
1 AAACCTTAAACCCCTAA-CACTT
*
88627725 AAACCATAAA
1 AAACCTTAAA
88627735 TCATAAACCA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
21 31 0.72
22 12 0.28
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (22 bp):
AAACCTTAAACCCCTAACACTT
Found at i:88627734 original size:7 final size:7
Alignment explanation
Indices: 88627724--88627777 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
88627714 CCCCAATCCT
88627724 TAAACCA
1 TAAACCA
*
88627731 TAAATCA
1 TAAACCA
88627738 TAAACCA
1 TAAACCA
* *
88627745 TAATCCC
1 TAAACCA
88627752 TAAACCCA
1 TAAA-CCA
*
88627760 TAATCCA
1 TAAACCA
*
88627767 TAAACCT
1 TAAACCA
88627774 TAAA
1 TAAA
88627778 ATAGTAATAT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
7 32 0.86
8 5 0.14
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCA
Found at i:88627734 original size:28 final size:29
Alignment explanation
Indices: 88627703--88627772 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
88627693 CCCTAACACT
* * *
88627703 TAAACCTTAAACCCCAATCCTTAAA-CCA
1 TAAACCATAAACCACAATCCCTAAACCCA
* *
88627731 TAAATCATAAACCATAATCCCTAAACCCA
1 TAAACCATAAACCACAATCCCTAAACCCA
*
88627760 TAATCCATAAACC
1 TAAACCATAAACC
88627773 TTAAAATAGT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
28 20 0.59
29 14 0.41
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (29 bp):
TAAACCATAAACCACAATCCCTAAACCCA
Found at i:88627741 original size:14 final size:14
Alignment explanation
Indices: 88627718--88627772 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
88627708 CTTAAACCCC
*
88627718 AATCCTTAAACCAT
1 AATCCATAAACCAT
88627732 AAAT-CATAAACCAT
1 -AATCCATAAACCAT
*
88627746 AATCCCTAAACCCAT
1 AATCCATAAA-CCAT
88627761 AATCCATAAACC
1 AATCCATAAACC
88627773 TTAAAATAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 3 0.09
14 16 0.46
15 16 0.46
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (14 bp):
AATCCATAAACCAT
Found at i:88627762 original size:15 final size:15
Alignment explanation
Indices: 88627718--88627772 Score: 62
Period size: 15 Copynumber: 3.8 Consensus size: 15
88627708 CTTAAACCCC
*
88627718 AATCCTTAAA-CCAT
1 AATCCATAAACCCAT
88627732 AAAT-CATAAA-CCAT
1 -AATCCATAAACCCAT
*
88627746 AATCCCTAAACCCAT
1 AATCCATAAACCCAT
88627761 AATCCATAAACC
1 AATCCATAAACC
88627773 TTAAAATAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
13 3 0.09
14 14 0.40
15 18 0.51
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (15 bp):
AATCCATAAACCCAT
Found at i:88627834 original size:14 final size:14
Alignment explanation
Indices: 88627660--88627835 Score: 52
Period size: 14 Copynumber: 12.4 Consensus size: 14
88627650 ACATAAAACA
88627660 TAAACCTTAAACCCC
1 TAAACCTTAAA-CCC
** *
88627675 TACCCCTTAACCCC
1 TAAACCTTAAACCC
* * *
88627689 TAACCCCT-AACACT
1 TAAACCTTAAAC-CC
88627703 TAAACCTTAAACCC
1 TAAACCTTAAACCC
* * *
88627717 CAATCCTTAAACCA
1 TAAACCTTAAACCC
* * *
88627731 TAAATCATAAACCA
1 TAAACCTTAAACCC
* *
88627745 TAATCCCTAAACCC
1 TAAACCTTAAACCC
* * *
88627759 ATAATCCATAAACCT
1 -TAAACCTTAAACCC
* *
88627774 TAAA-ATAGTAATA-TC
1 TAAACCT--TAA-ACCC
*
88627789 TAAACATTAAACCC
1 TAAACCTTAAACCC
* * *
88627803 TTAACCATATACCC
1 TAAACCTTAAACCC
* *
88627817 TAAACCCTAAACCT
1 TAAACCTTAAACCC
88627831 TAAAC
1 TAAAC
88627836 TATAATGATA
Statistics
Matches: 116, Mismatches: 37, Indels: 17
0.68 0.22 0.10
Matches are distributed among these distances:
13 3 0.03
14 80 0.69
15 30 0.26
16 3 0.03
ACGTcount: A:0.43, C:0.34, G:0.01, T:0.23
Consensus pattern (14 bp):
TAAACCTTAAACCC
Found at i:88628275 original size:40 final size:40
Alignment explanation
Indices: 88628224--88628386 Score: 220
Period size: 40 Copynumber: 4.1 Consensus size: 40
88628214 TTTTTGTAGT
* * *
88628224 GTTTTCCAAAAAGCGCCGCTAATGGTCGACCTATAGCGGC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
* *
88628264 GTTTTTCAAAAAGCACCGCTAATGCTTGATCTATAGCGGC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
* * * *
88628304 ATTTTTCAAAAAGCGCCGCTAATTCTCAATCTATAGTGGC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
**
88628344 -TTTTTTTAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
88628383 GTTT
1 GTTT
88628387 CTTTATCCAA
Statistics
Matches: 106, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 34 0.32
40 72 0.68
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (40 bp):
GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
Found at i:88628375 original size:79 final size:80
Alignment explanation
Indices: 88628225--88628382 Score: 219
Period size: 79 Copynumber: 2.0 Consensus size: 80
88628215 TTTTGTAGTG
* *
88628225 TTTTCCAAAAAGCGCCGCTAATGGTCGACCTATAGCGGCGTTTTTCAAAAAGCACCGCTAATGCT
1 TTTTCCAAAAAGCGCCGCTAATGCTCAACCTATAGCGGCGTTTTTCAAAAAGCACCGCTAATGCT
*
88628290 TGATCTATAGCGGCA
66 CGATCTATAGCGGCA
* * * * ** *
88628305 TTTTTCAAAAAGCGCCGCTAATTCTCAATCTATAGTGGC-TTTTTTTAAAAGCGCCGCTAATGCT
1 TTTTCCAAAAAGCGCCGCTAATGCTCAACCTATAGCGGCGTTTTTCAAAAAGCACCGCTAATGCT
88628369 CGATCTATAGCGGC
66 CGATCTATAGCGGC
88628383 GTTTCTTTAT
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
79 35 0.51
80 33 0.49
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (80 bp):
TTTTCCAAAAAGCGCCGCTAATGCTCAACCTATAGCGGCGTTTTTCAAAAAGCACCGCTAATGCT
CGATCTATAGCGGCA
Found at i:88630382 original size:2 final size:2
Alignment explanation
Indices: 88630377--88630403 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
88630367 ATAAAATAAT
88630377 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 T
88630404 TTTGCATTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:88630880 original size:20 final size:20
Alignment explanation
Indices: 88630855--88630893 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
88630845 TGTTTTTATA
88630855 AAAATATAC-AAGAAAACTTC
1 AAAATA-ACTAAGAAAACTTC
*
88630875 AAAATACCTAAGAAAACTT
1 AAAATAACTAAGAAAACTT
88630894 TAAATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.59, C:0.15, G:0.05, T:0.21
Consensus pattern (20 bp):
AAAATAACTAAGAAAACTTC
Found at i:88631480 original size:2 final size:2
Alignment explanation
Indices: 88631473--88631499 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
88631463 CCATTAAAGT
88631473 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 T
88631500 TTTTAATTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:88632706 original size:2 final size:2
Alignment explanation
Indices: 88632699--88632723 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
88632689 TTCCTATCAC
88632699 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 A
88632724 CACGTATAGC
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:88633140 original size:24 final size:23
Alignment explanation
Indices: 88633096--88633140 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
88633086 TAAACATAAA
* **
88633096 AAAATGTTAAAATAATTATATAT
1 AAAATGTAAAAATAAAAATATAT
88633119 AAAATGTAATAAATAAAAATAT
1 AAAATGTAA-AAATAAAAATAT
88633141 GTATAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (23 bp):
AAAATGTAAAAATAAAAATATAT
Found at i:88639989 original size:85 final size:85
Alignment explanation
Indices: 88639824--88639995 Score: 213
Period size: 85 Copynumber: 2.0 Consensus size: 85
88639814 ATGTATTAAT
* * * * *
88639824 AGGAAACGCTAATGGAAAGGTGCAGTGATACAAAGTCTCAAAAGATGGAGGAATCATAGGATAAT
1 AGGAAACGCTAATGCAAAGGTGAAGTGACACAAAGTCTCAAAAGATGGAGAAATCAAAGGATAAT
* *
88639889 ACAAAGAGTACTGAGTGAGG
66 ACAAAAACTACTGAGTGAGG
* *
88639909 AGGAAATGCTAATGCAAAGGTGAAGTGACGCAACA-TCTCAAAAGATGGAGAAATCAAAGGATAA
1 AGGAAACGCTAATGCAAAGGTGAAGTGACACAA-AGTCTCAAAAGATGGAGAAATCAAAGGATAA
* *
88639973 TA-AAGAAACTATTGAGTTAGG
65 TACAA-AAACTACTGAGTGAGG
88639994 AG
1 AG
88639996 AGACAGTTTG
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
84 2 0.03
85 71 0.96
86 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.27, T:0.18
Consensus pattern (85 bp):
AGGAAACGCTAATGCAAAGGTGAAGTGACACAAAGTCTCAAAAGATGGAGAAATCAAAGGATAAT
ACAAAAACTACTGAGTGAGG
Found at i:88647374 original size:6 final size:6
Alignment explanation
Indices: 88647363--88647402 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
88647353 CCAATTGACA
* *
88647363 TAGGAT TAGGAT TAGGAT TAGGAT TAGGAC TAGGAG TAGG
1 TAGGAT TAGGAT TAGGAT TAGGAT TAGGAT TAGGAT TAGG
88647403 TATAGAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.33, C:0.03, G:0.38, T:0.28
Consensus pattern (6 bp):
TAGGAT
Found at i:88647887 original size:17 final size:18
Alignment explanation
Indices: 88647855--88647888 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
88647845 TTATTGCACA
*
88647855 TTTTGTTTTTGGTATGTT
1 TTTTGTTTTTGCTATGTT
88647873 TTTTGTTTTT-CTATGT
1 TTTTGTTTTTGCTATGT
88647889 AGGCCACTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.06, C:0.03, G:0.18, T:0.74
Consensus pattern (18 bp):
TTTTGTTTTTGCTATGTT
Found at i:88649187 original size:21 final size:22
Alignment explanation
Indices: 88649143--88649193 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
88649133 ATTGAATAAA
**
88649143 ATTATAATAAGATGTTATTTGT
1 ATTATAATAAGATGTTATAAGT
*
88649165 ATTA-AATAAGCTGTTATAAGT
1 ATTATAATAAGATGTTATAAGT
88649186 ATGTATAA
1 AT-TATAA
88649194 CTGATAATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 16 0.67
22 6 0.25
23 2 0.08
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.43
Consensus pattern (22 bp):
ATTATAATAAGATGTTATAAGT
Found at i:88649595 original size:42 final size:43
Alignment explanation
Indices: 88649527--88649607 Score: 114
Period size: 42 Copynumber: 1.9 Consensus size: 43
88649517 CTCTCTGTTG
88649527 TGTAGGTTAACTCGGACAAGTAACCAGACACTA-TATGTCTCA
1 TGTAGGTTAACTCGGACAAGTAACCAGACACTATTATGTCTCA
*
88649569 TGTAGGTTAACTC-GA-AAGGGTGACCAGACACTATTATGT
1 TGTAGGTTAACTCGGACAA--GTAACCAGACACTATTATGT
88649608 GATTCACGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
40 2 0.06
41 2 0.06
42 26 0.74
43 5 0.14
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (43 bp):
TGTAGGTTAACTCGGACAAGTAACCAGACACTATTATGTCTCA
Found at i:88649649 original size:46 final size:46
Alignment explanation
Indices: 88649586--88650018 Score: 418
Period size: 46 Copynumber: 9.4 Consensus size: 46
88649576 TAACTCGAAA
* * *
88649586 GGGTGACCAGACACTATTATGTGATTCACGTAGGTTCAACCCTAAC
1 GGGTGACCAGGCACTATTATCTGATTCGCGTAGGTTCAACCCTAAC
* * * * *
88649632 GAGTGACCAGGCGCTATTATCTGATTCCCTTAGGTTAAACCCTAAC
1 GGGTGACCAGGCACTATTATCTGATTCGCGTAGGTTCAACCCTAAC
** ** * *
88649678 GAATGACCAGGCGTTATTATCTGATTTGCGTAGATTCAACCCTAAC
1 GGGTGACCAGGCACTATTATCTGATTCGCGTAGGTTCAACCCTAAC
* * * * * * *
88649724 GGGTGACTATGCATTATTATTTGATTCACGTAGGTTAAACCCTAAA
1 GGGTGACCAGGCACTATTATCTGATTCGCGTAGGTTCAACCCTAAC
* * * * * * *
88649770 GGATGACTAGACACTATTATCTGATTCACATAGGCTCAACCCTAAT
1 GGGTGACCAGGCACTATTATCTGATTCGCGTAGGTTCAACCCTAAC
* * *
88649816 GGGTGA-CTGGACGCTATTATCTGATTCGCGTAGGTTCAACCCTAAT
1 GGGTGACCAGG-CACTATTATCTGATTCGCGTAGGTTCAACCCTAAC
* * * * * *
88649862 GGGTGACCAAGCACTATTATTTGATTTGCATAGGTTTAACCTTAAC
1 GGGTGACCAGGCACTATTATCTGATTCGCGTAGGTTCAACCCTAAC
* * * * *
88649908 GGTTGACCAGACACTATTATCTGATTTGCATAGGTTCAACCCTAAT
1 GGGTGACCAGGCACTATTATCTGATTCGCGTAGGTTCAACCCTAAC
* * * * *
88649954 GGGTGACCAGGCGCTATTATCTAATTCGTGTAGGTTTAACCCTAAT
1 GGGTGACCAGGCACTATTATCTGATTCGCGTAGGTTCAACCCTAAC
*
88650000 GGGTGACCAGACACTATTA
1 GGGTGACCAGGCACTATTA
88650019 CTTTCACCTG
Statistics
Matches: 317, Mismatches: 68, Indels: 4
0.81 0.17 0.01
Matches are distributed among these distances:
45 1 0.00
46 314 0.99
47 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (46 bp):
GGGTGACCAGGCACTATTATCTGATTCGCGTAGGTTCAACCCTAAC
Found at i:88649834 original size:138 final size:138
Alignment explanation
Indices: 88649586--88650018 Score: 505
Period size: 138 Copynumber: 3.1 Consensus size: 138
88649576 TAACTCGAAA
* * * * *
88649586 GGGTGACC-AGACACTATTATGTGATTCACGTAGGTTCAACCCT-AACGAGTGACCAGGCGCTAT
1 GGGTGACCAAG-CACTATTATTTGATTCACGTAGGTTAAACCCTAAAGGA-TGACCAGACACTAT
* * * * ** * * *
88649649 TATCTGATTCCCTTAGGTTAAACCCTAACGAATGACCAGGCGTTATTATCTGATTTGCGTAGATT
64 TATCTGATTCACATAGGTTCAACCCTAATGGGTGACCAGGCGCTATTATCTGATTCGCGTAGGTT
*
88649714 CAACCCTAAC
129 CAACCCTAAT
* * * *
88649724 GGGTGACTATGCATTATTATTTGATTCACGTAGGTTAAACCCTAAAGGATGACTAGACACTATTA
1 GGGTGACCAAGCACTATTATTTGATTCACGTAGGTTAAACCCTAAAGGATGACCAGACACTATTA
* *
88649789 TCTGATTCACATAGGCTCAACCCTAATGGGTGA-CTGGACGCTATTATCTGATTCGCGTAGGTTC
66 TCTGATTCACATAGGTTCAACCCTAATGGGTGACCAGG-CGCTATTATCTGATTCGCGTAGGTTC
88649853 AACCCTAAT
130 AACCCTAAT
** * * * * *
88649862 GGGTGACCAAGCACTATTATTTGATTTGCATAGGTTTAACCTTAACGGTTGACCAGACACTATTA
1 GGGTGACCAAGCACTATTATTTGATTCACGTAGGTTAAACCCTAAAGGATGACCAGACACTATTA
** * * *
88649927 TCTGATTTGCATAGGTTCAACCCTAATGGGTGACCAGGCGCTATTATCTAATTCGTGTAGGTTTA
66 TCTGATTCACATAGGTTCAACCCTAATGGGTGACCAGGCGCTATTATCTGATTCGCGTAGGTTCA
88649992 ACCCTAAT
131 ACCCTAAT
88650000 GGGTGACC-AGACACTATTA
1 GGGTGACCAAG-CACTATTA
88650019 CTTTCACCTG
Statistics
Matches: 251, Mismatches: 39, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
137 5 0.02
138 238 0.95
139 8 0.03
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (138 bp):
GGGTGACCAAGCACTATTATTTGATTCACGTAGGTTAAACCCTAAAGGATGACCAGACACTATTA
TCTGATTCACATAGGTTCAACCCTAATGGGTGACCAGGCGCTATTATCTGATTCGCGTAGGTTCA
ACCCTAAT
Found at i:88653044 original size:19 final size:20
Alignment explanation
Indices: 88653020--88653059 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
88653010 CACTCCCTGC
88653020 TGTGTTGCGAA-ATA-CCCCT
1 TGTGTTGC-AACATAGCCCCT
88653039 TGTGTTGCAACATAGCCCCT
1 TGTGTTGCAACATAGCCCCT
88653059 T
1 T
88653060 TGTAGCCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 11 0.58
20 6 0.32
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (20 bp):
TGTGTTGCAACATAGCCCCT
Found at i:88657679 original size:26 final size:25
Alignment explanation
Indices: 88657625--88657680 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
88657615 TTTGCCCGGG
* *
88657625 TTTAAACCCAAACCCATTTACCCCT
1 TTTAAACCCAAACCCATTGACCCCA
*
88657650 TTTACAACCCAAACCCGGTTGA-CCCA
1 TTTA-AACCCAAACCC-ATTGACCCCA
88657676 TTTAA
1 TTTAA
88657681 TAACCCCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 5 0.19
26 18 0.69
27 3 0.12
ACGTcount: A:0.32, C:0.36, G:0.05, T:0.27
Consensus pattern (25 bp):
TTTAAACCCAAACCCATTGACCCCA
Found at i:88657685 original size:27 final size:26
Alignment explanation
Indices: 88657629--88657695 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 26
88657619 CCCGGGTTTA
* * *
88657629 AACCCAAACCCATTTACCCCTTTTAC
1 AACCCAAACCCATTGACCCATTTAAC
* *
88657655 AACCCAAACCCGGTTGACCCATTTAAT
1 AACCCAAACCC-ATTGACCCATTTAAC
88657682 AACCCCTAAACCCA
1 AA-CCC-AAACCCA
88657696 AACTAAACCT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
26 11 0.34
27 12 0.38
28 3 0.09
29 6 0.19
ACGTcount: A:0.34, C:0.40, G:0.04, T:0.21
Consensus pattern (26 bp):
AACCCAAACCCATTGACCCATTTAAC
Found at i:88659590 original size:3 final size:3
Alignment explanation
Indices: 88659582--88659636 Score: 85
Period size: 3 Copynumber: 18.3 Consensus size: 3
88659572 ATCACTTTGC
*
88659582 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
88659627 TTA TTA TTA T
1 TTA TTA TTA T
88659637 CAGTATCATT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.92
4 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:88663364 original size:22 final size:23
Alignment explanation
Indices: 88663339--88663384 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
88663329 CAACCAAACC
88663339 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
88663361 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
88663384 A
1 A
88663385 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:88663390 original size:23 final size:23
Alignment explanation
Indices: 88663346--88663390 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
88663336 ACCAATTCAA
*
88663346 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
88663369 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
88663391 CACATACGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:88685652 original size:17 final size:19
Alignment explanation
Indices: 88685621--88685660 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
88685611 AATAAAAATA
*
88685621 ATAAAAATATTAATTTA-G
1 ATAAAAATATGAATTTATG
88685639 ATAAAAATA-GAATTTATG
1 ATAAAAATATGAATTTATG
88685657 ATAA
1 ATAA
88685661 TAATTTGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (19 bp):
ATAAAAATATGAATTTATG
Found at i:88687072 original size:13 final size:13
Alignment explanation
Indices: 88687054--88687088 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
88687044 AATCGTACAT
88687054 GGGCGTGTCACAC
1 GGGCGTGTCACAC
88687067 GGGCGTGTCACAC
1 GGGCGTGTCACAC
*
88687080 GGACGTGTC
1 GGGCGTGTC
88687089 CCTGCCGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.14, C:0.29, G:0.40, T:0.17
Consensus pattern (13 bp):
GGGCGTGTCACAC
Found at i:88697654 original size:90 final size:92
Alignment explanation
Indices: 88697496--88697681 Score: 286
Period size: 90 Copynumber: 2.0 Consensus size: 92
88697486 TAAATGCAGT
* * * * *
88697496 AATTCGCGGAGTGGGGGTATCCTATAGTTATAGTAGATTAATACACAATCTGTACAAGACATAGT
1 AATTCGCAGAGTGAGGGTATCCTATAGTTATAGTAGATTAATACACAATCTGTACAAGAAAAAAT
88697561 TGCTTCTGAATCAC-AA-ACTTGCACA
66 TGCTTCTGAATCACAAATACTTGCACA
* *
88697586 AATTCGCAGAGTGATGGTATCTTATAGTTATAGTAGATTAATACACAATCTGTACAAGAAAAAAT
1 AATTCGCAGAGTGAGGGTATCCTATAGTTATAGTAGATTAATACACAATCTGTACAAGAAAAAAT
88697651 TGCTTCTGAATCACAAAATACTTGCACA
66 TGCTTCTGAATCAC-AAATACTTGCACA
88697679 AAT
1 AAT
88697682 AGCTATCTCA
Statistics
Matches: 86, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
90 72 0.84
92 2 0.02
93 12 0.14
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (92 bp):
AATTCGCAGAGTGAGGGTATCCTATAGTTATAGTAGATTAATACACAATCTGTACAAGAAAAAAT
TGCTTCTGAATCACAAATACTTGCACA
Found at i:88698316 original size:21 final size:20
Alignment explanation
Indices: 88698287--88698325 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
88698277 ACGCCCACGA
88698287 AAAGATCGCTTGGATTTAAG
1 AAAGATCGCTTGGATTTAAG
88698307 AAAGAGTCGCTTGGATTTA
1 AAAGA-TCGCTTGGATTTA
88698326 TCCATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (20 bp):
AAAGATCGCTTGGATTTAAG
Found at i:88698490 original size:15 final size:14
Alignment explanation
Indices: 88698468--88698504 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
88698458 TTTATCATAT
*
88698468 AAATATATAATTTA
1 AAATATATAAATTA
88698482 AATATATATAAATTA
1 AA-ATATATAAATTA
88698497 AAATATAT
1 AAATATAT
88698505 TAATAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATATATAAATTA
Found at i:88698500 original size:16 final size:16
Alignment explanation
Indices: 88698470--88698536 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 16
88698460 TATCATATAA
*
88698470 ATATAT-AATTTAAAT
1 ATATATAAATTAAAAT
88698485 ATATATAAATTAAAAT
1 ATATATAAATTAAAAT
*
88698501 ATAT-TAATAATATAGAAT
1 ATATAT-A-AAT-TAAAAT
88698519 AATATATAAA-TAAAAT
1 -ATATATAAATTAAAAT
88698535 AT
1 AT
88698537 GCGTTATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
15 9 0.21
16 18 0.42
17 3 0.07
18 7 0.16
19 5 0.12
20 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (16 bp):
ATATATAAATTAAAAT
Found at i:88698559 original size:14 final size:16
Alignment explanation
Indices: 88698540--88698576 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
88698530 AAAATATGCG
88698540 TTATATA-TAAAT-AA
1 TTATATATTAAATAAA
*
88698554 TTATATATTTAATAAA
1 TTATATATTAAATAAA
88698570 TTATATA
1 TTATATA
88698577 CCTAATGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 4 0.20
16 9 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTATATATTAAATAAA
Found at i:88702274 original size:30 final size:29
Alignment explanation
Indices: 88702215--88702275 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
88702205 AAGTACGATG
* *
88702215 TTATACATGAATTTTAATTTTATGTAATT
1 TTATACATGAATATTAATTTAATGTAATT
88702244 TTATACATGAAATATTAATTTAAT-TCAATT
1 TTATACATG-AATATTAATTTAATGT-AATT
88702274 TT
1 TT
88702276 TGCAAATCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 10 0.36
30 18 0.64
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (29 bp):
TTATACATGAATATTAATTTAATGTAATT
Found at i:88705135 original size:90 final size:89
Alignment explanation
Indices: 88705007--88705176 Score: 243
Period size: 90 Copynumber: 1.9 Consensus size: 89
88704997 TGCCAACACT
* * *
88705007 ATATCCCAGATATGGTCTTACATGGGATCACCACTCGATGCCAATGCCATGTCCCAGACATGGTC
1 ATATCCCAGATATGGTCTTACAT-GGATAACCAATCGATGCCAATGCCATATCCCAGACATGGTC
88705072 TTACATGGGATCTCAAATTAACGCC
65 TTACATGGGATCTCAAATTAACGCC
* * *
88705097 ATATCCCAGATATGGTCTTACAT-GATAACACATATCGATGCCGATGCCATATTCCAGATATGGT
1 ATATCCCAGATATGGTCTTACATGGATAAC-CA-ATCGATGCCAATGCCATATCCCAGACATGGT
*
88705161 CTTATATGGGATCTCA
64 CTTACATGGGATCTCA
88705177 TTAACCTGAA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
88 5 0.07
89 2 0.03
90 64 0.90
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (89 bp):
ATATCCCAGATATGGTCTTACATGGATAACCAATCGATGCCAATGCCATATCCCAGACATGGTCT
TACATGGGATCTCAAATTAACGCC
Found at i:88707397 original size:66 final size:66
Alignment explanation
Indices: 88707291--88707423 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
88707281 TCATCGATCA
88707291 CAATCATTTGTGCTAATCCTTTCCTACATACTTCTTGATCAAATCTCCAAGTTGAAAGATGCCTT
1 CAATCATTTGTGCTAATCCTTTCCTACATACTTCTTGATCAAATCTCCAAGTTGAAAGATGCCTT
88707356 C
66 C
* *
88707357 CAATCATTTGTGCTAATCCTTTTCTACATGCTTCTTGATCAAATCTCCAAGTTGAAAGATGCCTT
1 CAATCATTTGTGCTAATCCTTTCCTACATACTTCTTGATCAAATCTCCAAGTTGAAAGATGCCTT
88707422 C
66 C
88707423 C
1 C
88707424 CCCTTTCAAC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (66 bp):
CAATCATTTGTGCTAATCCTTTCCTACATACTTCTTGATCAAATCTCCAAGTTGAAAGATGCCTT
C
Found at i:88709648 original size:5 final size:5
Alignment explanation
Indices: 88709638--88709673 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
88709628 ATTTTTATGA
*
88709638 TTGGG TTGGG TTGGG TTGGG TTGGG TTGGT TTGGG T
1 TTGGG TTGGG TTGGG TTGGG TTGGG TTGGG TTGGG T
88709674 ACTTAGGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.56, T:0.44
Consensus pattern (5 bp):
TTGGG
Found at i:88712435 original size:16 final size:16
Alignment explanation
Indices: 88712414--88712447 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
88712404 ATTGCTATGT
88712414 TCTTTTTAATTTAGAA
1 TCTTTTTAATTTAGAA
88712430 TCTTTTTAATTTAGAA
1 TCTTTTTAATTTAGAA
88712446 TC
1 TC
88712448 CTTAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.56
Consensus pattern (16 bp):
TCTTTTTAATTTAGAA
Found at i:88713579 original size:43 final size:43
Alignment explanation
Indices: 88713442--88713613 Score: 186
Period size: 43 Copynumber: 4.0 Consensus size: 43
88713432 CATAGGATTC
* * * * *
88713442 CGATATGTGATTTCGTGAAAGACCACGTCTGAGACGTTGGCAT
1 CGATATATGATTTCGTGTAAGACCATGTCTGGGACATTGGCAT
* *
88713485 CGATTTAAGATTTACGTGTAAGACCATGTCTGGGACATTGGCAT
1 CGATATATGATTT-CGTGTAAGACCATGTCTGGGACATTGGCAT
* * *
88713529 C-TTATATGATTTCGTGTAAGACCGTGTCTGGGACAATGGCAT
1 CGATATATGATTTCGTGTAAGACCATGTCTGGGACATTGGCAT
* * * *
88713571 CGATATATGATTACATGTAAAACC-TCGTCTAGGACATTGGCAT
1 CGATATATGATTTCGTGTAAGACCAT-GTCTGGGACATTGGCAT
88713614 TGTACAAACT
Statistics
Matches: 108, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
42 30 0.28
43 51 0.47
44 27 0.25
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.31
Consensus pattern (43 bp):
CGATATATGATTTCGTGTAAGACCATGTCTGGGACATTGGCAT
Found at i:88721629 original size:20 final size:19
Alignment explanation
Indices: 88721600--88721637 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
88721590 TTGTTCAGTG
88721600 TTGAAATTTTTGGAGGGAA
1 TTGAAATTTTTGGAGGGAA
88721619 TTGAAATTTTTGGAGGGAA
1 TTGAAATTTTTGGAGGGAA
88721638 AGATTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.37
Consensus pattern (19 bp):
TTGAAATTTTTGGAGGGAA
Found at i:88721865 original size:49 final size:49
Alignment explanation
Indices: 88721803--88721944 Score: 149
Period size: 49 Copynumber: 2.9 Consensus size: 49
88721793 GTCGTATTGC
* *
88721803 AACTCGGGCTCCCAGTTTACGGTGGTTATACAATCATGGGTTCAAGTAT
1 AACTCGGGCTCCCAGTTGACGGTGGTTATACAATCACGGGTTCAAGTAT
* * ** * * *
88721852 AACTAGGGCTCCCAGCTGACGGCAGTTATGCAGTCACGGGTTGAAGTAT
1 AACTCGGGCTCCCAGTTGACGGTGGTTATACAATCACGGGTTCAAGTAT
* * * ** *
88721901 AACTCGAGCCCCCAGTTGATGGTGGTTATGTAGTCACGGGTTCA
1 AACTCGGGCTCCCAGTTGACGGTGGTTATACAATCACGGGTTCA
88721945 TATTACATGC
Statistics
Matches: 75, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
49 75 1.00
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (49 bp):
AACTCGGGCTCCCAGTTGACGGTGGTTATACAATCACGGGTTCAAGTAT
Found at i:88724801 original size:40 final size:40
Alignment explanation
Indices: 88724746--88724930 Score: 273
Period size: 40 Copynumber: 4.6 Consensus size: 40
88724736 CGGATGATAA
* * *
88724746 CCGGGCTAAGTCCCGAAGGAATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
88724786 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
88724826 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
88724866 CCAGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
**
88724906 ATGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
88724931 AGCTAGTAGC
Statistics
Matches: 133, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 132 0.99
41 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:88724971 original size:80 final size:79
Alignment explanation
Indices: 88724742--88724963 Score: 254
Period size: 80 Copynumber: 2.8 Consensus size: 79
88724732 TATTCGGATG
* * * *
88724742 ATAACCGGGCTAAGTCCCGAAGGAATTTGTGCTAGT-GACTAATTCCGGGCTAAGTCCCGAAGGC
1 ATAAACGGGCTAAGTCCCGAAGGCATTTGAGCTAGTAG-CT-ATTCCAGGCTAAGTCCCGAAGGC
88724806 ATTTGTGCAAGTTACT
64 ATTTGTGCAAGTTACT
** *
88724822 ATATCCGGGCTAAGTCCCGAAGGCATTTGTA-CGAGTTA-CTATATCCAGGCTAAGTCCCGAAGG
1 ATAAACGGGCTAAGTCCCGAAGGCATTTG-AGCTAG-TAGCTAT-TCCAGGCTAAGTCCCGAAGG
*
88724885 CATTTGTGCGAGTTACT
63 CATTTGTGCAAGTTACT
* * * *
88724902 ATAAATGGGCTAAGTCCCGAAGGCATTTGAGCTAGTAGCTGTGTCC-GGCTAAATCTCGAAGG
1 ATAAACGGGCTAAGTCCCGAAGGCATTTGAGCTAGTAGCTAT-TCCAGGCTAAGTCCCGAAGG
88724964 TACTTTGTTG
Statistics
Matches: 122, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
79 19 0.16
80 102 0.84
81 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
ATAAACGGGCTAAGTCCCGAAGGCATTTGAGCTAGTAGCTATTCCAGGCTAAGTCCCGAAGGCAT
TTGTGCAAGTTACT
Found at i:88734720 original size:1 final size:1
Alignment explanation
Indices: 88734714--88734740 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
88734704 CTTAAATCTG
88734714 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
88734741 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:88743838 original size:36 final size:37
Alignment explanation
Indices: 88743771--88743842 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
88743761 TAATTAAACT
88743771 TAATCACTTTAATATCAAATTTAATCTAATATTAAAA
1 TAATCACTTTAATATCAAATTTAATCTAATATTAAAA
* * * *
88743808 TAATCACTTTATTATTATA-TTAATTTAATATTAAA
1 TAATCACTTTAATATCAAATTTAATCTAATATTAAA
88743843 TCTTATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 15 0.48
37 16 0.52
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (37 bp):
TAATCACTTTAATATCAAATTTAATCTAATATTAAAA
Found at i:88743929 original size:20 final size:18
Alignment explanation
Indices: 88743882--88743988 Score: 69
Period size: 20 Copynumber: 5.8 Consensus size: 18
88743872 CAAGATAAAC
88743882 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
88743899 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
* *
88743919 ATTAAATTAATATAATAGT
1 ATTAAATTAATAT-TTAAT
* *
88743938 ATGAACATAAATA-TTAA-
1 ATTAA-ATTAATATTTAAT
*
88743955 ATTAAATTTAATATTAAACT
1 ATTAAA-TTAATATTTAA-T
*
88743975 ATTAAAATAATATT
1 ATTAAATTAATATT
88743989 ATTTTTGGAA
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
16 1 0.01
17 17 0.25
18 7 0.10
19 17 0.25
20 27 0.39
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:88746272 original size:40 final size:42
Alignment explanation
Indices: 88746186--88746272 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
88746176 ACACGCCCAT
* *
88746186 GTGTGAACCCGTGTGACACACACGACCAATAGACATGCTCGT
1 GTGTGAACCCGTGTGACACACACGACCAATAGACACGCTCGC
*
88746228 GTGTGAACCCGTGTGACACACACGGCCAATAGACACG-TC-C
1 GTGTGAACCCGTGTGACACACACGACCAATAGACACGCTCGC
88746268 GTGTG
1 GTGTG
88746273 TCTAAGCCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
40 5 0.12
41 2 0.05
42 35 0.83
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (42 bp):
GTGTGAACCCGTGTGACACACACGACCAATAGACACGCTCGC
Found at i:88747277 original size:22 final size:23
Alignment explanation
Indices: 88747200--88747305 Score: 90
Period size: 24 Copynumber: 4.5 Consensus size: 23
88747190 GAATCATGGT
**
88747200 CAGTAAGCTCCTCCTGAGCTAATAAA
1 CAGTAAGCT-CTATTGAGCT-A-AAA
* *
88747226 TAGTAAGCTCTATTAAGCTAAAAA
1 CAGTAAGCTCTATTGAGCT-AAAA
*
88747250 CGGTAAGCTCTATTGAGCT-AAA
1 CAGTAAGCTCTATTGAGCTAAAA
* *
88747272 CAGTAAGCTCT-TTCGAGCTGAAT
1 CAGTAAGCTCTATT-GAGCTAAAA
88747295 CAGTAAGCTCT
1 CAGTAAGCTCT
88747306 TACGAGCTGT
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
21 2 0.03
22 18 0.26
23 13 0.19
24 19 0.28
25 9 0.13
26 8 0.12
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (23 bp):
CAGTAAGCTCTATTGAGCTAAAA
Found at i:88747302 original size:23 final size:23
Alignment explanation
Indices: 88747247--88747314 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
88747237 ATTAAGCTAA
*
88747247 AAACGGTAAGCTCTATT-GAGCT-
1 AAACAGTAAGCTCT-TTCGAGCTG
88747269 AAACAGTAAGCTCTTTCGAGCTG
1 AAACAGTAAGCTCTTTCGAGCTG
* *
88747292 AATCAGTAAGCTCTTACGAGCTG
1 AAACAGTAAGCTCTTTCGAGCTG
88747315 TGGTGAGTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
21 2 0.05
22 18 0.44
23 21 0.51
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (23 bp):
AAACAGTAAGCTCTTTCGAGCTG
Found at i:88752420 original size:105 final size:105
Alignment explanation
Indices: 88752230--88752549 Score: 379
Period size: 105 Copynumber: 3.0 Consensus size: 105
88752220 ATCAATGCAT
* * * * *
88752230 TATAGGTAACAACATCAGGCTCAATGCCTTGATTGCTCATTTTGTCAACAATATCTTCAGCTTCA
1 TATACGTAACAACATTAGGCTCAATGCCTTGCTTTCTCATTGTGTCAACAATATCTTCAGCTTCA
*
88752295 AAAACCATCCCCTCCTTACAAAGTGCATCGACCAATATAC
66 AAAACCATCCCCTCCTTACAAAGTGCATCAACCAATATAC
* * * *
88752335 TATACGTGACAACATTAGGCTCAATGCCTTGCTTTATCATTGTCTCAACAATATCTTTAGCTTCA
1 TATACGTAACAACATTAGGCTCAATGCCTTGCTTTCTCATTGTGTCAACAATATCTTCAGCTTCA
** * * *
88752400 GGAATCATCCCTTCCTTACAATGTGCATCAACCAATATAC
66 AAAACCATCCCCTCCTTACAAAGTGCATCAACCAATATAC
* *** *
88752440 TATATGTAACAACATTAGGCTCAATGCCTTGCTTTCTCATTGTGTCAATGGTATCTACAGCTTCA
1 TATACGTAACAACATTAGGCTCAATGCCTTGCTTTCTCATTGTGTCAACAATATCTTCAGCTTCA
* *** * * * * *
88752505 GAAATTGTCCCCTCCTTGCAATGTGCATCAATCAACATAT
66 AAAACCATCCCCTCCTTACAAAGTGCATCAACCAATATAC
88752545 TATAC
1 TATAC
88752550 ATGAAAATAT
Statistics
Matches: 182, Mismatches: 33, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
105 182 1.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (105 bp):
TATACGTAACAACATTAGGCTCAATGCCTTGCTTTCTCATTGTGTCAACAATATCTTCAGCTTCA
AAAACCATCCCCTCCTTACAAAGTGCATCAACCAATATAC
Found at i:88754845 original size:10 final size:10
Alignment explanation
Indices: 88754830--88754859 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
88754820 TATGAAAATG
88754830 CAAATATAGA
1 CAAATATAGA
88754840 CAAATATAGA
1 CAAATATAGA
*
88754850 CAAATTTAGA
1 CAAATATAGA
88754860 GTTTATAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.23
Consensus pattern (10 bp):
CAAATATAGA
Done.