Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 180 of 235
Found at i:61157531 original size:18 final size:18
Alignment explanation
Indices: 61157508--61157542 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
61157498 TTTATAATAC
*
61157508 TATATATTATGTTATTTT
1 TATATATTATGTAATTTT
61157526 TATATATTATGTAATTT
1 TATATATTATGTAATTT
61157543 AGTACACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
TATATATTATGTAATTTT
Found at i:61163958 original size:18 final size:18
Alignment explanation
Indices: 61163916--61163958 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
61163906 ATAATTTAAA
* *
61163916 ATATAATTTTATTAATTT
1 ATATAAATTTATTAATAT
61163934 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
*
61163952 ATGTAAA
1 ATATAAA
61163959 AATAACTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
ATATAAATTTATTAATAT
Found at i:61167941 original size:48 final size:48
Alignment explanation
Indices: 61167889--61167983 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
61167879 TTAACCTAAG
61167889 CCCATTTTAGGTCCACCCATATTATTTTTTATTTTAAAATATTTATTA
1 CCCATTTTAGGTCCACCCATATTATTTTTTATTTTAAAATATTTATTA
**
61167937 CCCATTTTAGGTCTGCCCATATTATTTTTTATTTTAAAATATTTATT
1 CCCATTTTAGGTCCACCCATATTATTTTTTATTTTAAAATATTTATT
61167984 TTATTTTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.27, C:0.16, G:0.05, T:0.52
Consensus pattern (48 bp):
CCCATTTTAGGTCCACCCATATTATTTTTTATTTTAAAATATTTATTA
Found at i:61187601 original size:43 final size:43
Alignment explanation
Indices: 61187446--61187602 Score: 162
Period size: 43 Copynumber: 3.7 Consensus size: 43
61187436 TGTGTTATCG
* *
61187446 TGTAAGACCACGTCTGGGACGTTGGCATCGACT-TATGATTTACA
1 TGTAAGACCACGTCTGGGACGTTGGCATC-AATATTTGA-TTACA
** * *
61187490 TGTAAGACCACGTCTCGGG-CGTTGGCAT-TGTATTTGATTTCG
1 TGTAAGACCACGTCT-GGGACGTTGGCATCAATATTTGATTACA
61187532 TGTAAGACC-CTGTCTGGGACAG-TGGCATCAATATTTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCAATATTTGATTACA
* *
61187575 TGTAAGACCACATCTAGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
61187603 TGTACGAGCT
Statistics
Matches: 94, Mismatches: 11, Indels: 17
0.77 0.09 0.14
Matches are distributed among these distances:
41 4 0.04
42 25 0.27
43 37 0.39
44 25 0.27
45 3 0.03
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCAATATTTGATTACA
Found at i:61189423 original size:40 final size:40
Alignment explanation
Indices: 61189356--61189532 Score: 234
Period size: 40 Copynumber: 4.5 Consensus size: 40
61189346 ACCCAAGTAT
*
61189356 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
61189395 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
61189435 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * *
61189475 CTTCGGGACATAGCCCGGATATAGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
61189515 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
61189533 TTATCATCCG
Statistics
Matches: 120, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.01
39 13 0.11
40 104 0.87
41 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:61202681 original size:8 final size:9
Alignment explanation
Indices: 61202659--61202683 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
61202649 TTTGAGCTCG
61202659 GTTTTTGAT
1 GTTTTTGAT
61202668 GTTTTTGAT
1 GTTTTTGAT
61202677 GTTTTTG
1 GTTTTTG
61202684 TGATCGTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (9 bp):
GTTTTTGAT
Found at i:61213330 original size:6 final size:6
Alignment explanation
Indices: 61213319--61213350 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
61213309 TCACCCCTAA
61213319 AACCCT AACCCT AACCCT AACCCT AACCCT AA
1 AACCCT AACCCT AACCCT AACCCT AACCCT AA
61213351 AAAAATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.38, C:0.47, G:0.00, T:0.16
Consensus pattern (6 bp):
AACCCT
Found at i:61214917 original size:66 final size:67
Alignment explanation
Indices: 61214783--61214920 Score: 215
Period size: 66 Copynumber: 2.1 Consensus size: 67
61214773 GATGGTAATG
* * ** *
61214783 TTGTTTCTTGAAGGTTGTAACTTGCTAGGTTTTGTTTTAGGTGCTATTAGTGTTCTGTCATAGTT
1 TTGTTTCTTGAAGGCTGTAACTTGCTAGGTTTTGTTTTAGGCGCTATTAGTGTTCCATCACAGTT
61214848 TC
66 TC
*
61214850 TTGTTTCTTGAAGGCTGTAACTTGCTAGG-TTTGTTTTAGGCGCTATTCGTGTTCCATCACAGTT
1 TTGTTTCTTGAAGGCTGTAACTTGCTAGGTTTTGTTTTAGGCGCTATTAGTGTTCCATCACAGTT
61214914 TC
66 TC
61214916 TTGTT
1 TTGTT
61214921 GATAGCAATG
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
66 37 0.57
67 28 0.43
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.49
Consensus pattern (67 bp):
TTGTTTCTTGAAGGCTGTAACTTGCTAGGTTTTGTTTTAGGCGCTATTAGTGTTCCATCACAGTT
TC
Found at i:61219531 original size:16 final size:17
Alignment explanation
Indices: 61219507--61219543 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
61219497 CCACAGAATT
*
61219507 TTTTTTTTTTTTTGTA-
1 TTTTATTTTTTTTGTAC
61219523 TTTTATTTTTTTTGTAC
1 TTTTATTTTTTTTGTAC
61219540 TTTT
1 TTTT
61219544 TTAATCACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.08, C:0.03, G:0.05, T:0.84
Consensus pattern (17 bp):
TTTTATTTTTTTTGTAC
Found at i:61227043 original size:77 final size:77
Alignment explanation
Indices: 61226916--61227072 Score: 314
Period size: 77 Copynumber: 2.0 Consensus size: 77
61226906 CGTAATGTCG
61226916 ATTTCAATGTACATAATACCAATCACTTACTCATGGAGCAATCAAAGCATAACTCATAATAGCAT
1 ATTTCAATGTACATAATACCAATCACTTACTCATGGAGCAATCAAAGCATAACTCATAATAGCAT
61226981 TAAATAATTTGA
66 TAAATAATTTGA
61226993 ATTTCAATGTACATAATACCAATCACTTACTCATGGAGCAATCAAAGCATAACTCATAATAGCAT
1 ATTTCAATGTACATAATACCAATCACTTACTCATGGAGCAATCAAAGCATAACTCATAATAGCAT
61227058 TAAATAATTTGA
66 TAAATAATTTGA
61227070 ATT
1 ATT
61227073 CACATAATAC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 80 1.00
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.31
Consensus pattern (77 bp):
ATTTCAATGTACATAATACCAATCACTTACTCATGGAGCAATCAAAGCATAACTCATAATAGCAT
TAAATAATTTGA
Found at i:61228874 original size:27 final size:27
Alignment explanation
Indices: 61228844--61229021 Score: 189
Period size: 27 Copynumber: 6.6 Consensus size: 27
61228834 ATATTGAGCC
* *
61228844 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
61228871 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
61228898 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** * *
61228926 CGCACACTTAGTGCCGCATGATCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
61228953 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
61228980 CGCACACTTAGTGCAACATAGTCAAAC-
1 CGCACACTTAGTGCTACATAATC-AACT
61229007 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
61229022 GTACAATTTA
Statistics
Matches: 127, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:61228983 original size:82 final size:81
Alignment explanation
Indices: 61228864--61229020 Score: 235
Period size: 82 Copynumber: 1.9 Consensus size: 81
61228854 GTGCTATATA
* *
61228864 ATCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGC
1 ATCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAAC-CGC
61228929 ACACTTAGTGCCGCATG
65 ACACTTAGTGCCGCATG
* * **
61228946 ATCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAACCGC
1 ATCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAACCGC
61229010 ACACTTAGTGC
65 ACACTTAGTGC
61229021 TGTACAATTT
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 53 0.78
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.26
Consensus pattern (81 bp):
ATCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAACCGCA
CACTTAGTGCCGCATG
Found at i:61233560 original size:35 final size:35
Alignment explanation
Indices: 61233521--61233590 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
61233511 GCACTCAGGT
*
61233521 TTAACAAATCTCGAGTTCCTTACACTGGCTACCGA
1 TTAACAAATCTCGAGTTCCCTACACTGGCTACCGA
*
61233556 TTAACAAATCTCGAGTTCCCTACACTGGCTGCCGA
1 TTAACAAATCTCGAGTTCCCTACACTGGCTACCGA
61233591 AGTAGTCTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (35 bp):
TTAACAAATCTCGAGTTCCCTACACTGGCTACCGA
Found at i:61236064 original size:46 final size:46
Alignment explanation
Indices: 61235973--61236100 Score: 206
Period size: 46 Copynumber: 2.8 Consensus size: 46
61235963 TGTAACCCGC
* * *
61235973 CCATAAGAGAACTCGGACTCAACT-AACGAGCTCAGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
61236018 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
61236064 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
61236101 TGCTCAACCA
Statistics
Matches: 78, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
45 25 0.32
46 53 0.68
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:61237899 original size:14 final size:15
Alignment explanation
Indices: 61237860--61237901 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
61237850 NNNNNNNATA
*
61237860 ATTATTATTAAATAT
1 ATTATAATTAAATAT
61237875 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
61237889 A-TATAATTTAATA
1 ATTATAATTAAATA
61237902 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:61238039 original size:28 final size:27
Alignment explanation
Indices: 61237975--61238052 Score: 67
Period size: 28 Copynumber: 3.0 Consensus size: 27
61237965 AGATAATTTG
*
61237975 AAATAATTA-ATATTAAATATATTTTA
1 AAATAATTATATATTAAATAAATTTTA
*
61238001 ATTAA-AA-TATATGATTTAATAAATTTTA
1 A--AATAATTATAT-ATTAAATAAATTTTA
*
61238029 AAATAATTATA-ACT-AATAAATTTT
1 AAATAATTATATATTAAATAAATTTT
61238053 CTTATATGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
25 10 0.23
26 7 0.16
27 6 0.14
28 20 0.47
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (27 bp):
AAATAATTATATATTAAATAAATTTTA
Found at i:61238073 original size:101 final size:98
Alignment explanation
Indices: 61237967--61238249 Score: 281
Period size: 91 Copynumber: 3.0 Consensus size: 98
61237957 ACTATAAAAG
* *
61237967 ATAATTTGAAATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAATTTTAAAA
1 ATAATTTAAAATAATTAATATTAAATATAATTTAA-TAAAATATAT-ATTT-ATAAATTTTAAAA
*
61238032 TAATT-ATAACTAATAAATTTTCTTATATGAATTTGT
63 TAATTCATAA-TAATAAATTTTCTTATATGAATTTAT
* * * *
61238068 ATAATTTAAAATAATTATTATTACATATAATTTAAT--AATA-ATA--TAT-AATTTCATAA-AA
1 ATAATTTAAAATAATTAATATTAAATATAATTTAATAAAATATATATTTATAAATTTTAAAATAA
* *
61238126 TTCTTGATAATAAATTTTCTTATATGAATTTAT
66 TTCATAATAATAAATTTTCTTATATGAATTTAT
* * * *
61238159 ACAATTTAAAATAATTAATATTAAATATAATTTAAT--AAT-GATA--TAT-AATTTCATAA-AA
1 ATAATTTAAAATAATTAATATTAAATATAATTTAATAAAATATATATTTATAAATTTTAAAATAA
* *
61238217 TTCTTAATAATAAAATGTTCTTATATGAATTTA
66 TTCATAATAAT-AAATTTTCTTATATGAATTTA
61238250 CTAAAATCAA
Statistics
Matches: 165, Mismatches: 14, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
91 93 0.56
92 30 0.18
93 2 0.01
94 1 0.01
96 1 0.01
97 2 0.01
98 4 0.02
100 1 0.01
101 31 0.19
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.46
Consensus pattern (98 bp):
ATAATTTAAAATAATTAATATTAAATATAATTTAATAAAATATATATTTATAAATTTTAAAATAA
TTCATAATAATAAATTTTCTTATATGAATTTAT
Found at i:61238077 original size:47 final size:46
Alignment explanation
Indices: 61238008--61238175 Score: 136
Period size: 47 Copynumber: 3.7 Consensus size: 46
61237998 TTAATTAAAA
61238008 TATATG-ATTTA-ATAAATTTTAAAATAATTATAACTAATAAATTTTCT
1 TATATGAATTTATAT-AA-TTTAAAATAATTATAA-TAATAAATTTTCT
* * **
61238055 TATATGAATTTGTATAATTTAAAATAATTATTATTACATATAA-TTTAA
1 TATATGAATTTATATAATTTAAAATAATTA-TAATA-ATA-AATTTTCT
* * *
61238103 TA-AT-AA--TATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAATTTATATAATTT-AAAATAATT-ATAATAATAAATTTTCT
*
61238146 TATATGAATTTATACAATTTAAAATAATTA
1 TATATGAATTTATATAATTTAAAATAATTA
61238176 ATATTAAATA
Statistics
Matches: 94, Mismatches: 14, Indels: 27
0.70 0.10 0.20
Matches are distributed among these distances:
42 2 0.02
43 8 0.09
44 18 0.19
45 5 0.05
46 5 0.05
47 36 0.38
48 16 0.17
49 4 0.04
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTTTCT
Found at i:61238097 original size:26 final size:28
Alignment explanation
Indices: 61238067--61238127 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
61238057 TATGAATTTG
*
61238067 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
61238093 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
61238121 TAAAATT
1 TATAATT
61238128 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:61238137 original size:91 final size:91
Alignment explanation
Indices: 61238042--61238249 Score: 344
Period size: 91 Copynumber: 2.3 Consensus size: 91
61238032 TAATTATAAC
* * * *
61238042 TAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
61238107 AATATATAATTTCATAAAATTCTTGA
66 AATATATAATTTCATAAAATTCTTAA
61238133 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
61238198 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
61238224 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
61238250 CTAAAATCAA
Statistics
Matches: 109, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
91 89 0.82
92 20 0.18
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTAA
Found at i:61238209 original size:44 final size:43
Alignment explanation
Indices: 61238067--61238209 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 43
61238057 TATGAATTTG
* *
61238067 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
** * * * *
61238111 TATAATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATTTA
1 TATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
*
61238158 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
61238202 TATAATTT
1 TATAATTT
61238210 CATAAAATTC
Statistics
Matches: 74, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
43 3 0.04
44 32 0.43
45 7 0.09
46 7 0.09
47 22 0.30
48 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:61238224 original size:47 final size:47
Alignment explanation
Indices: 61238092--61238230 Score: 137
Period size: 47 Copynumber: 3.0 Consensus size: 47
61238082 TTATTATTAC
* *
61238092 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
* * * ** *
61238139 AT-T--TTCTTAT-ATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAATT-TAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
61238183 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
61238230 A
1 A
61238231 ATGTTCTTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
44 20 0.29
45 13 0.19
46 13 0.19
47 23 0.33
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:61244529 original size:26 final size:26
Alignment explanation
Indices: 61244500--61244607 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
61244490 TGGTACAAAT
61244500 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
61244526 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
61244552 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
61244578 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
61244604 TGAT
1 TGAT
61244608 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:61246228 original size:27 final size:27
Alignment explanation
Indices: 61246188--61246299 Score: 120
Period size: 27 Copynumber: 4.1 Consensus size: 27
61246178 AGGAAGCGTC
*
61246188 CTGGTGGCTATGCCACAAATATCTGAT
1 CTGGTGGCTCTGCCACAAATATCTGAT
*
61246215 CTGGTGGCTCTGCCACATATATCT-ATT
1 CTGGTGGCTCTGCCACAAATATCTGA-T
* *
61246242 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAAATATCTG-AT
* * * *
61246270 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAAATATCTGAT
61246296 CTGG
1 CTGG
61246300 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 6 0.08
27 52 0.70
28 15 0.20
29 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAAATATCTGAT
Found at i:61246292 original size:54 final size:54
Alignment explanation
Indices: 61246188--61246299 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
61246178 AGGAAGCGTC
*
61246188 CTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCTATT
1 CTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCTATT
* * * * *
61246242 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCTATT
61246296 CTGG
1 CTGG
61246300 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 33 0.65
55 18 0.35
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCTATT
Found at i:61247832 original size:21 final size:19
Alignment explanation
Indices: 61247808--61247846 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
61247798 GTTTCTCATG
61247808 GCCTCCTCAGGCTCCCATGTA
1 GCCTCCTCA-GC-CCCATGTA
*
61247829 GCCTCTTCAGCCCCATGT
1 GCCTCCTCAGCCCCATGT
61247847 CTTTGCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 2 0.12
21 8 0.47
ACGTcount: A:0.13, C:0.44, G:0.18, T:0.26
Consensus pattern (19 bp):
GCCTCCTCAGCCCCATGTA
Found at i:61253798 original size:43 final size:42
Alignment explanation
Indices: 61253751--61253924 Score: 188
Period size: 43 Copynumber: 4.1 Consensus size: 42
61253741 ATATGGTCTT
* * ** *
61253751 TAGCGGCGTTTTTGGGAAAAATGCTGCTAAAGGTCATGTTATA
1 TAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCATGTT-TA
*
61253794 TAGCGGCGTTTGTAGGAAAAGCGCCACTAAAGGTCATGTTTA
1 TAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCATGTTTA
* * **
61253836 TAGCGGTGTTTGTAAGAAAAGCGCCGCTAAAGGTCACATTCTA
1 TAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCATGTT-TA
* * *
61253879 TAGCGGCGTTTATTA-GAAAAGCACCGTTAAAGGTCATGTTTTA
1 TAGCGGCGTTT-GTAGGAAAAGCGCCGCTAAAGGTCATG-TTTA
61253922 TAG
1 TAG
61253925 TGACTTTTGT
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
42 37 0.33
43 70 0.63
44 4 0.04
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (42 bp):
TAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCATGTTTA
Found at i:61253855 original size:42 final size:43
Alignment explanation
Indices: 61253776--61253924 Score: 192
Period size: 43 Copynumber: 3.5 Consensus size: 43
61253766 GAAAAATGCT
*
61253776 GCTAAAGGTCATGTTATATAGCGGCGTTTGTAGGAAAAGCGCC
1 GCTAAAGGTCATGTTATATAGCGGCGTTTGTAAGAAAAGCGCC
* *
61253819 ACTAAAGGTCATGTT-TATAGCGGTGTTTGTAAGAAAAGCGCC
1 GCTAAAGGTCATGTTATATAGCGGCGTTTGTAAGAAAAGCGCC
** * * * *
61253861 GCTAAAGGTCACATTCTATAGCGGCGTTTATTAGAAAAGCACC
1 GCTAAAGGTCATGTTATATAGCGGCGTTTGTAAGAAAAGCGCC
* *
61253904 GTTAAAGGTCATGTTTTATAG
1 GCTAAAGGTCATGTTATATAG
61253925 TGACTTTTGT
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 37 0.41
43 54 0.59
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (43 bp):
GCTAAAGGTCATGTTATATAGCGGCGTTTGTAAGAAAAGCGCC
Found at i:61253966 original size:85 final size:85
Alignment explanation
Indices: 61253777--61253966 Score: 199
Period size: 85 Copynumber: 2.2 Consensus size: 85
61253767 AAAAATGCTG
* *
61253777 CTAAAGGTCATGTTATATAGCGGCGTTTGTAGGAAAAGCGCCACTAAAGGTCATGTTTATAGCGG
1 CTAAAGGTCATGTTATATAGCGGCGTTTGTAGGAAAAGCACCACTAAAGGTCATGTTTATAGCGC
* *
61253842 TGTTTGTAAGAAAAGCGCCG
66 TGTTTGTAAGAAAAGCACCA
** * * ** *
61253862 CTAAAGGTCACATTCTATAGCGGCGTTTATTA-GAAAAGCACCGTTAAAGGTCATGTTTTATAGT
1 CTAAAGGTCATGTTATATAGCGGCGTTT-GTAGGAAAAGCACCACTAAAGGTCATG-TTTATAGC
* *
61253926 GACT-TTTGT-TGTAAAAG-ATCA
64 G-CTGTTTGTAAG-AAAAGCACCA
61253947 CTAAAGGTCATGTTATATAG
1 CTAAAGGTCATGTTATATAG
61253967 GGACATTTTT
Statistics
Matches: 85, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
85 64 0.75
86 20 0.24
87 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (85 bp):
CTAAAGGTCATGTTATATAGCGGCGTTTGTAGGAAAAGCACCACTAAAGGTCATGTTTATAGCGC
TGTTTGTAAGAAAAGCACCA
Found at i:61276236 original size:72 final size:72
Alignment explanation
Indices: 61276160--61276303 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
61276150 AAATCTCCAC
61276160 AACTATAAAATGATATGTTACACAAATCAAAAGGTCATTAAAGGGTTGTAATGGGGCTTGGGTTA
1 AACTATAAAATGATATGTTACACAAATCAAAAGGTCATTAAAGGGTTGTAATGGGGCTTGGGTTA
61276225 AAGGTGT
66 AAGGTGT
61276232 AACTATAAAATGATATGTTACACAAATCAAAAGGTCATTAAAGGGTTGTAATGGGGCTTGGGTTA
1 AACTATAAAATGATATGTTACACAAATCAAAAGGTCATTAAAGGGTTGTAATGGGGCTTGGGTTA
61276297 AAGGTGT
66 AAGGTGT
61276304 GGATAAAGGC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (72 bp):
AACTATAAAATGATATGTTACACAAATCAAAAGGTCATTAAAGGGTTGTAATGGGGCTTGGGTTA
AAGGTGT
Found at i:61279313 original size:93 final size:93
Alignment explanation
Indices: 61279138--61279865 Score: 1413
Period size: 93 Copynumber: 7.8 Consensus size: 93
61279128 ATCCATAAGT
* * * *
61279138 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTG-ACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAAGGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
61279202 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
61279230 GAACTCGGACTCAACTCAAGGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAAGGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
61279295 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
61279323 GAACTCGGACTCAACTCAAGGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAAGGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
61279388 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
61279416 GAACTCGGACTCAACTCAAGGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAAGGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
61279481 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
61279509 GAACTCGGACTCAACTCAAGGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAAGGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
61279574 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
61279602 GAACTCGGACTCAACTCAAGGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAAGGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
61279667 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
61279695 GAACTCGGACTCAACTCAAGGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAAGGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
61279760 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
61279788 GAACTCGGACTCAACTCAAGGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAAGGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
61279853 CGAGTTCGGATGC
66 CGAGTTCGGATGC
61279866 TCAACCATCC
Statistics
Matches: 631, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 43 0.07
93 588 0.93
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAAGGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:61282047 original size:20 final size:21
Alignment explanation
Indices: 61282016--61282058 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
61282006 TAAACATAAA
61282016 AATAGAAATAAAACTAAAAAT
1 AATAGAAATAAAACTAAAAAT
*
61282037 AATAG-AATAAAATTAAAAAT
1 AATAGAAATAAAACTAAAAAT
61282057 AA
1 AA
61282059 AAATAAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (21 bp):
AATAGAAATAAAACTAAAAAT
Found at i:61282061 original size:7 final size:6
Alignment explanation
Indices: 61281999--61282065 Score: 71
Period size: 6 Copynumber: 10.8 Consensus size: 6
61281989 GTCTAAAATC
* * * *
61281999 ATAACA ATAAAC ATAAAA ATAGAA ATAAAA CTAAAA ATAATAGA ATAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAA-A-A ATAAAA
*
61282049 TTAAAA ATAAAA ATAAA
1 ATAAAA ATAAAA ATAAA
61282066 TGATAAATGG
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
6 43 0.86
7 2 0.04
8 5 0.10
ACGTcount: A:0.73, C:0.04, G:0.03, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:61283511 original size:19 final size:20
Alignment explanation
Indices: 61283477--61283515 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
61283467 ATGACAGATG
*
61283477 TAATATAAGAATAATAACAA
1 TAATATAAGAAAAATAACAA
61283497 TAATA-AAGAAAAATAACAA
1 TAATATAAGAAAAATAACAA
61283516 GTAACTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (20 bp):
TAATATAAGAAAAATAACAA
Found at i:61283716 original size:18 final size:19
Alignment explanation
Indices: 61283685--61283739 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
61283675 AAGAAAAGAA
* *
61283685 AAATAATTAATAATACTAG
1 AAATAAATAATAATAATAG
61283704 TAAA-AAA-AATAATAATAG
1 -AAATAAATAATAATAATAG
61283722 AAATAAATAATAATAATA
1 AAATAAATAATAATAATA
61283740 AAGCAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 3 0.10
18 13 0.42
19 12 0.39
20 3 0.10
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (19 bp):
AAATAAATAATAATAATAG
Found at i:61283751 original size:22 final size:22
Alignment explanation
Indices: 61283704--61283753 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
61283694 ATAATACTAG
61283704 TAAAA-AAAATAATAATAGAAA
1 TAAAATAAAATAATAATAGAAA
*
61283725 T-AAATAATAATAATAA-AGCAA
1 TAAAATAA-AATAATAATAGAAA
61283746 TAAAATAA
1 TAAAATAA
61283754 CCGACAGTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 8 0.32
22 14 0.56
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.22
Consensus pattern (22 bp):
TAAAATAAAATAATAATAGAAA
Found at i:61284079 original size:24 final size:25
Alignment explanation
Indices: 61284026--61284087 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
61284016 TCCTTATTTC
61284026 ATTAAAT-AAAAAATTTGAAAATAT
1 ATTAAATCAAAAAATTTGAAAATAT
* *
61284050 AATAAATCAAATACATTT-AAAA-AT
1 ATTAAATCAAA-AAATTTGAAAATAT
*
61284074 ATTAAAACAAAAAA
1 ATTAAATCAAAAAA
61284088 CAAATAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 2 0.06
24 17 0.55
25 7 0.23
26 5 0.16
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (25 bp):
ATTAAATCAAAAAATTTGAAAATAT
Found at i:61284179 original size:26 final size:25
Alignment explanation
Indices: 61284122--61284181 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
61284112 TTGATAATTT
61284122 TTTTATATTTTTAGATATTTTACATA
1 TTTT-TATTTTTAGATATTTTACATA
* * *
61284148 TATTTTATTTTTATATATTTATCCCTA
1 T-TTTTATTTTTAGATATTT-TACATA
61284175 TTTTTAT
1 TTTTTAT
61284182 AAACTTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 21 0.72
27 8 0.28
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.65
Consensus pattern (25 bp):
TTTTTATTTTTAGATATTTTACATA
Found at i:61284786 original size:11 final size:11
Alignment explanation
Indices: 61284770--61284839 Score: 70
Period size: 11 Copynumber: 6.4 Consensus size: 11
61284760 CCACAAAAGT
61284770 AGCACCAAAAC
1 AGCACCAAAAC
61284781 AGCACCAAAAC
1 AGCACCAAAAC
* *
61284792 AACATCAAAAC
1 AGCACCAAAAC
*
61284803 AGCTCCAAAAC
1 AGCACCAAAAC
* * *
61284814 ATCACAAAAAAA
1 AGCAC-CAAAAC
61284826 AGCACC-AAAC
1 AGCACCAAAAC
61284836 AGCA
1 AGCA
61284840 GCAGTGAGAA
Statistics
Matches: 46, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
10 7 0.15
11 31 0.67
12 8 0.17
ACGTcount: A:0.57, C:0.31, G:0.07, T:0.04
Consensus pattern (11 bp):
AGCACCAAAAC
Found at i:61288221 original size:20 final size:20
Alignment explanation
Indices: 61288196--61288242 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
61288186 AACCTGCAAA
* *
61288196 AAGAAGATGCAGTAGTGAAG
1 AAGAAGATGCAGCAGTAAAG
*
61288216 AAGAAGATGTAGCAGTAAAG
1 AAGAAGATGCAGCAGTAAAG
61288236 AAGAAGA
1 AAGAAGA
61288243 AGAAGAAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.51, C:0.04, G:0.32, T:0.13
Consensus pattern (20 bp):
AAGAAGATGCAGCAGTAAAG
Found at i:61294874 original size:26 final size:27
Alignment explanation
Indices: 61294845--61294898 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
61294835 TCACACAAGT
*
61294845 TAGTCATTT-ACGCACGAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
* *
61294871 TAGTCATTTAACACCCTAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
61294898 T
1 T
61294899 GGTAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (27 bp):
TAGTCATTTAACACACGAGGGGCAAAA
Found at i:61294961 original size:27 final size:27
Alignment explanation
Indices: 61294928--61295094 Score: 167
Period size: 27 Copynumber: 6.2 Consensus size: 27
61294918 GGTATCTCGA
* *
61294928 TAATTCTACCCTACAGGGGGATTTTAG
1 TAATTCTACCTTACAGGGGTATTTTAG
* * *
61294955 TATTTCTACCCTACAAGGGTATTTT-G
1 TAATTCTACCTTACAGGGGTATTTTAG
*
61294981 CTAATTCTACCTTACAGGGATATTTTAG
1 -TAATTCTACCTTACAGGGGTATTTTAG
* **
61295009 TAAATCTACCTTACAGGGGTATTTCGG
1 TAATTCTACCTTACAGGGGTATTTTAG
* *
61295036 TAATTCTACTTTACAGGGGTATTTCAG
1 TAATTCTACCTTACAGGGGTATTTTAG
* ** *
61295063 TAATTTTA-CAAATCAGGGGTATTTTGG
1 TAATTCTACCTTA-CAGGGGTATTTTAG
61295090 TAATT
1 TAATT
61295095 TTGCTAATCG
Statistics
Matches: 117, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
26 2 0.02
27 114 0.97
28 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.39
Consensus pattern (27 bp):
TAATTCTACCTTACAGGGGTATTTTAG
Found at i:61295065 original size:54 final size:54
Alignment explanation
Indices: 61294907--61295065 Score: 183
Period size: 54 Copynumber: 2.9 Consensus size: 54
61294897 ATGGTAATTT
* * * * * **
61294907 TACCCCACAAAGGTATCTCGATAATTCTACCCTACAGGGGGATTTTAGTATTTC
1 TACCCTACAAGGGTATTTCGATAATTCTACCTTACAGGGGTATTTTAGTAAATC
* * *
61294961 TACCCTACAAGGGTATTTTGCTAATTCTACCTTACAGGGATATTTTAGTAAATC
1 TACCCTACAAGGGTATTTCGATAATTCTACCTTACAGGGGTATTTTAGTAAATC
* * * * *
61295015 TACCTTACAGGGGTATTTCGGTAATTCTACTTTACAGGGGTATTTCAGTAA
1 TACCCTACAAGGGTATTTCGATAATTCTACCTTACAGGGGTATTTTAGTAA
61295066 TTTTACAAAT
Statistics
Matches: 88, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 88 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (54 bp):
TACCCTACAAGGGTATTTCGATAATTCTACCTTACAGGGGTATTTTAGTAAATC
Found at i:61295095 original size:27 final size:27
Alignment explanation
Indices: 61295022--61295148 Score: 107
Period size: 27 Copynumber: 4.7 Consensus size: 27
61295012 ATCTACCTTA
* * **
61295022 CAGGGGTATTTCGGTAATTCTAC-TTT
1 CAGGGGTATTTTGGTAATTTTACAAAT
**
61295048 ACAGGGGTATTTCAGTAATTTTACAAAT
1 -CAGGGGTATTTTGGTAATTTTACAAAT
* *
61295076 CAGGGGTATTTTGGTAATTTTGCTAAT
1 CAGGGGTATTTTGGTAATTTTACAAAT
* * *
61295103 C-GAGGGTATTTTGGCAATTTCACAAAC
1 CAG-GGGTATTTTGGTAATTTTACAAAT
*
61295130 CA-GAGTATTTTGGTAATTT
1 CAGGGGTATTTTGGTAATTT
61295149 GGTAAACTAA
Statistics
Matches: 82, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
26 16 0.20
27 65 0.79
28 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (27 bp):
CAGGGGTATTTTGGTAATTTTACAAAT
Found at i:61295155 original size:26 final size:26
Alignment explanation
Indices: 61295081--61295164 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
61295071 CAAATCAGGG
* * * *
61295081 GTATTTTGGTAATTTTGCTAATCGAGG
1 GTATTTTGGTAA-TTTGATAAACCAGA
* * *
61295108 GTATTTTGGCAATTTCACAAACCAGA
1 GTATTTTGGTAATTTGATAAACCAGA
* * *
61295134 GTATTTTGGTAATTTGGTAAACTAAA
1 GTATTTTGGTAATTTGATAAACCAGA
61295160 GTATT
1 GTATT
61295165 CTAAACAGGG
Statistics
Matches: 44, Mismatches: 13, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
26 33 0.75
27 11 0.25
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (26 bp):
GTATTTTGGTAATTTGATAAACCAGA
Found at i:61297378 original size:69 final size:69
Alignment explanation
Indices: 61297280--61297461 Score: 292
Period size: 69 Copynumber: 2.6 Consensus size: 69
61297270 ACAGATATAT
* * *
61297280 ATATATATGTGGCAAAGCCACCAGATTGCAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAAA
1 ATATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCTGCCAGATATTGTAACGAAGTCACCAAA
61297345 ACAG
66 ACAG
* * * *
61297349 ATATATATGTGGCGAGGCCACCAGGTTGCAGCGAGGTTGCCAGATATTGTAACGGAGTCACCAGA
1 ATATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCTGCCAGATATTGTAACGAAGTCACCAAA
61297414 ACAG
66 ACAG
*
61297418 ATATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCTACCAGA
1 ATATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCTGCCAGA
61297462 ACGCTTCCTC
Statistics
Matches: 103, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 103 1.00
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.19
Consensus pattern (69 bp):
ATATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCTGCCAGATATTGTAACGAAGTCACCAAA
ACAG
Found at i:61298124 original size:27 final size:27
Alignment explanation
Indices: 61298108--61298254 Score: 204
Period size: 27 Copynumber: 5.4 Consensus size: 27
61298098 ATTTCATCCC
*
61298108 ACAAGGGTATCTCGGTAATTCTACCCT
1 ACAAGGGTATTTCGGTAATTCTACCCT
* *
61298135 ACAGGGGTATTTTGGTAATTCTACCCT
1 ACAAGGGTATTTCGGTAATTCTACCCT
61298162 ACAAGGGTATTTCGGTAATTCTACCCT
1 ACAAGGGTATTTCGGTAATTCTACCCT
* * *
61298189 ACAGGGGTATTTCAGTAAATCTACCCT
1 ACAAGGGTATTTCGGTAATTCTACCCT
* *
61298216 ACAAGGGTATTTCTGTAATTCTACCAT
1 ACAAGGGTATTTCGGTAATTCTACCCT
* *
61298243 ATAGGGGTATTT
1 ACAAGGGTATTT
61298255 TAGTAATTTT
Statistics
Matches: 106, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 106 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (27 bp):
ACAAGGGTATTTCGGTAATTCTACCCT
Found at i:61298260 original size:27 final size:27
Alignment explanation
Indices: 61298112--61298289 Score: 198
Period size: 27 Copynumber: 6.6 Consensus size: 27
61298102 CATCCCACAA
* *
61298112 GGGTATCTCGGTAATTCTACCCTACAG
1 GGGTATTTTGGTAATTCTACCCTACAG
*
61298139 GGGTATTTTGGTAATTCTACCCTACAA
1 GGGTATTTTGGTAATTCTACCCTACAG
*
61298166 GGGTATTTCGGTAATTCTACCCTACAG
1 GGGTATTTTGGTAATTCTACCCTACAG
** * *
61298193 GGGTATTTCAGTAAATCTACCCTACAA
1 GGGTATTTTGGTAATTCTACCCTACAG
* *
61298220 GGGTATTTCT-GTAATTCTACCATATAG
1 GGGTATTT-TGGTAATTCTACCCTACAG
* * **
61298247 GGGTATTTTAGTAATTTTA-CAAATCAG
1 GGGTATTTTGGTAATTCTACCCTA-CAG
61298274 GGGTATTTTGGTAATT
1 GGGTATTTTGGTAATT
61298290 TGTTGAACTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.03
27 127 0.97
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (27 bp):
GGGTATTTTGGTAATTCTACCCTACAG
Found at i:61298289 original size:54 final size:54
Alignment explanation
Indices: 61298108--61298262 Score: 247
Period size: 54 Copynumber: 2.9 Consensus size: 54
61298098 ATTTCATCCC
* *
61298108 ACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTTGGTAATTCTACCCT
1 ACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCT
* *
61298162 ACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAAATCTACCCT
1 ACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCT
* * *
61298216 ACAAGGGTATTTCTGTAATTCTACCATATAGGGGTATTTTAGTAATT
1 ACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTTAGTAATT
61298263 TTACAAATCA
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 92 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (54 bp):
ACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCT
Found at i:61305324 original size:13 final size:13
Alignment explanation
Indices: 61305306--61305331 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61305296 ACGAGGGCTC
61305306 CTTCGTTCCTTTG
1 CTTCGTTCCTTTG
61305319 CTTCGTTCCTTTG
1 CTTCGTTCCTTTG
61305332 TGGCTCTCCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.31, G:0.15, T:0.54
Consensus pattern (13 bp):
CTTCGTTCCTTTG
Found at i:61317160 original size:86 final size:86
Alignment explanation
Indices: 61317011--61317172 Score: 193
Period size: 86 Copynumber: 1.9 Consensus size: 86
61317001 TTATTTGTAT
* *
61317011 TGTAACACCCCTAACCCGTATCCGTCGTCAAAACAGGGTTTCAGAGCATTACCAAAACTTTCAGA
1 TGTAACACCCCTAACCCATATCCGTCGTCAAAACAGGGTTTCAGAGCATTACCAAAACATTCAG-
61317076 AACA-TTTACAAGTAAATCATG
65 AACATTTTACAAGTAAATCATG
* * * * ** ***
61317097 TGTAACACCCCTAACTCATATTCGTCG-CTAAAATAGGGTTTCGGAGTGTTACTGGAACATTCAG
1 TGTAACACCCCTAACCCATATCCGTCGTC-AAAACAGGGTTTCAGAGCATTACCAAAACATTCAG
61317161 AACATTTTACAA
65 AACATTTTACAA
61317173 TCAATTCATG
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
85 5 0.08
86 58 0.92
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.27
Consensus pattern (86 bp):
TGTAACACCCCTAACCCATATCCGTCGTCAAAACAGGGTTTCAGAGCATTACCAAAACATTCAGA
ACATTTTACAAGTAAATCATG
Found at i:61317707 original size:40 final size:40
Alignment explanation
Indices: 61317306--61317688 Score: 748
Period size: 40 Copynumber: 9.6 Consensus size: 40
61317296 GGTATCAGAG
61317306 CATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAT
1 CATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAT
61317346 CATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAT
1 CATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAT
61317386 CATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAT
1 CATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAT
61317426 CATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAT
1 CATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAT
61317466 CATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAT
1 CATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAT
61317506 CATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAT
1 CATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAT
61317546 CATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAT
1 CATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAT
61317586 CATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAT
1 CATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAT
*
61317626 CATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAG
1 CATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAT
*
61317666 CATTCGTGCTAGTGATATATCCG
1 CATTCGTGCTAGTGATGTATCCG
61317689 TGCCAAATCC
Statistics
Matches: 341, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 341 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.30
Consensus pattern (40 bp):
CATTCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAT
Found at i:61322298 original size:12 final size:12
Alignment explanation
Indices: 61322281--61322313 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
61322271 CTAGACACAA
61322281 GCCCGTGTGTCT
1 GCCCGTGTGTCT
61322293 GCCCGTGTGTCT
1 GCCCGTGTGTCT
*
61322305 GCCCATGTG
1 GCCCGTGTG
61322314 GACAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.03, C:0.33, G:0.33, T:0.30
Consensus pattern (12 bp):
GCCCGTGTGTCT
Found at i:61324405 original size:47 final size:47
Alignment explanation
Indices: 61324335--61324454 Score: 170
Period size: 47 Copynumber: 2.6 Consensus size: 47
61324325 CCCTTCGGGA
* * *
61324335 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGC
* *
61324382 CTTATCACATATACACAGC-TTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACA-CTTTCACATCCATCACATCGGCCATTAGGC
*
61324429 CTTATCTCATATATACACTTTCACAT
1 CTTATCACATATATACACTTTCACAT
61324455 TAATCAGGAT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
46 1 0.02
47 62 0.97
48 1 0.02
ACGTcount: A:0.28, C:0.31, G:0.07, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGC
Found at i:61324588 original size:22 final size:22
Alignment explanation
Indices: 61324560--61324682 Score: 70
Period size: 22 Copynumber: 5.3 Consensus size: 22
61324550 TTTCACATCC
61324560 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
61324582 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
61324606 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
** * * *
61324629 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
61324653 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
61324676 ATCACAT
1 ATCACAT
61324683 ATATACACTT
Statistics
Matches: 71, Mismatches: 20, Indels: 20
0.64 0.18 0.18
Matches are distributed among these distances:
22 29 0.41
23 10 0.14
24 10 0.14
25 22 0.31
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:61324589 original size:197 final size:197
Alignment explanation
Indices: 61324254--61324657 Score: 720
Period size: 197 Copynumber: 2.1 Consensus size: 197
61324244 AAGCCTACGG
*
61324254 ACATTAATTAGGATAATATTCTCGCATAAAGCCTGCGGGGTTTTAACCCGGATATAGTACTGACA
1 ACATTAATCAGGATAATATTCTCGCATAAAGCCTGCGGGGTTTTAACCCGGATATAGTACTGACA
61324319 CAAATGCCCTTCGGGACTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGCCT
66 CAAATGCCCTTCGGGACTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGCCT
* *
61324384 TATCACATATACACAGC-TTCACATCCATCACATCGGCCATTAGGTCTTATCTCATATATACACT
131 TATCACATATACACA-CTTTCACATCCATCACATCGGCCATTAGGCCTTATCACATATATACACT
61324448 TTC
195 TTC
61324451 ACATTAATCAGGATAATATTCTCGCATAAAGCCTGCGGGGTTTTAACCCGGATATAGTACTGACA
1 ACATTAATCAGGATAATATTCTCGCATAAAGCCTGCGGGGTTTTAACCCGGATATAGTACTGACA
61324516 CAAATGCCCTTCGGGACTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGCCT
66 CAAATGCCCTTCGGGACTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGCCT
* * * *
61324581 TATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTT
131 TATCACATATACACACTTTCACATCCATCACATCGGCCATTAGGCCTTATCACATATATACACTT
61324646 TC
196 TC
*
61324648 ACATTCATCA
1 ACATTAATCA
61324658 CATTGGCCAT
Statistics
Matches: 198, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
196 1 0.01
197 197 0.99
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (197 bp):
ACATTAATCAGGATAATATTCTCGCATAAAGCCTGCGGGGTTTTAACCCGGATATAGTACTGACA
CAAATGCCCTTCGGGACTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGCCT
TATCACATATACACACTTTCACATCCATCACATCGGCCATTAGGCCTTATCACATATATACACTT
TC
Found at i:61324595 original size:47 final size:47
Alignment explanation
Indices: 61324532--61324756 Score: 405
Period size: 47 Copynumber: 4.7 Consensus size: 47
61324522 CCCTTCGGGA
* *
61324532 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
61324579 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
61324626 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
61324673 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
61324720 CTTATCACATATATATACACTTTCACATTCATCACAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACAT
61324757 NNNNNNNNNN
Statistics
Matches: 173, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
47 146 0.84
49 27 0.16
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.35
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:61338130 original size:16 final size:16
Alignment explanation
Indices: 61338100--61338135 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
61338090 GAATCGAGAT
61338100 TAACTAGATAAATTACC
1 TAACTAGATAAATTA-C
61338117 TAACTAGA-AAATTAC
1 TAACTAGATAAATTAC
61338132 TAAC
1 TAAC
61338136 ATCAATTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 6 0.32
17 8 0.42
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.28
Consensus pattern (16 bp):
TAACTAGATAAATTAC
Found at i:61350256 original size:15 final size:16
Alignment explanation
Indices: 61350225--61350270 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
61350215 ATGAAGGAAG
* *
61350225 AAGAAAGAGAAATAAT
1 AAGAAAAAGAAAGAAT
*
61350241 AAG-GAAAGAAAGAAT
1 AAGAAAAAGAAAGAAT
61350256 AAGAAAAAGAAAGAA
1 AAGAAAAAGAAAGAA
61350271 GGAAAAGGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.07
Consensus pattern (16 bp):
AAGAAAAAGAAAGAAT
Found at i:61355684 original size:22 final size:23
Alignment explanation
Indices: 61355645--61355687 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
61355635 GAAGTCCTGC
*
61355645 CCGTCCATCCTCTACACTCCACT
1 CCGTCCAGCCTCTACACTCCACT
61355668 CCGTCCAGCC-CTACACTCCA
1 CCGTCCAGCCTCTACACTCCA
61355688 TGTGGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.19, C:0.53, G:0.07, T:0.21
Consensus pattern (23 bp):
CCGTCCAGCCTCTACACTCCACT
Found at i:61371082 original size:12 final size:12
Alignment explanation
Indices: 61371067--61371113 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
61371057 AATAAAATTT
61371067 AAATGAAAATAA
1 AAATGAAAATAA
*
61371079 AAATCAAAATAA
1 AAATGAAAATAA
*
61371091 AAATAAAAAT-A
1 AAATGAAAATAA
*
61371102 AAATGAGAATAA
1 AAATGAAAATAA
61371114 GAATAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.17
Consensus pattern (12 bp):
AAATGAAAATAA
Found at i:61371106 original size:35 final size:37
Alignment explanation
Indices: 61371045--61371113 Score: 97
Period size: 35 Copynumber: 1.9 Consensus size: 37
61371035 GATATGTCTT
* *
61371045 TCAAAATAAAATAATAAAATTTAAATGAAAATAAAAA
1 TCAAAATAAAATAATAAAAATAAAATGAAAATAAAAA
*
61371082 TCAAAAT-AAA-AATAAAAATAAAATGAGAATAA
1 TCAAAATAAAATAATAAAAATAAAATGAAAATAA
61371114 GAATAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 19 0.66
36 3 0.10
37 7 0.24
ACGTcount: A:0.71, C:0.03, G:0.04, T:0.22
Consensus pattern (37 bp):
TCAAAATAAAATAATAAAAATAAAATGAAAATAAAAA
Found at i:61371118 original size:17 final size:17
Alignment explanation
Indices: 61371057--61371120 Score: 74
Period size: 17 Copynumber: 3.7 Consensus size: 17
61371047 AAAATAAAAT
* *
61371057 AATAAAATTTAAATGAA
1 AATAAAAATAAAATGAA
*
61371074 AATAAAAATCAAAATAAA
1 AATAAAAAT-AAAATGAA
*
61371092 AATAAAAATAAAATGAG
1 AATAAAAATAAAATGAA
*
61371109 AATAAGAATAAA
1 AATAAAAATAAA
61371121 TAAATCAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
17 25 0.62
18 15 0.38
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (17 bp):
AATAAAAATAAAATGAA
Found at i:61371119 original size:6 final size:6
Alignment explanation
Indices: 61371067--61371104 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
61371057 AATAAAATTT
* *
61371067 AAATGA AAATAA AAATCA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AA
61371105 TGAGAATAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:61375099 original size:49 final size:49
Alignment explanation
Indices: 61375045--61375276 Score: 232
Period size: 49 Copynumber: 4.7 Consensus size: 49
61375035 CTGGTACGCA
* *
61375045 TAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACG
* * * *
61375094 TAGTAGCCTGTACTTAATACTACACACGTGACCAATTATCCTGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACG
* * ** ** *
61375143 TAGTAGCCTGTACTTAGTACTACACACGTGACCTAACCATTTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACC-AATTATCCGGTACACG
* * ** *
61375193 TAGTAGCCTGCACTTAGTACTACACACGTC-ATCACAATTTTCGGGTATGCA
1 TAGTAGCCTGCACTTAGTACTACACACG-CGA-C-CAATTATCCGGTACACG
* * *
61375244 TAGTAGCATGCACTTAGTACTGCACATGCGACC
1 TAGTAGCCTGCACTTAGTACTACACACGCGACC
61375277 TCACAATAGA
Statistics
Matches: 151, Mismatches: 27, Indels: 10
0.80 0.14 0.05
Matches are distributed among these distances:
49 76 0.50
50 40 0.26
51 34 0.23
52 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACG
Found at i:61377652 original size:36 final size:36
Alignment explanation
Indices: 61377610--61377684 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
61377600 AAGCAAAGAG
*
61377610 AAAATTTGGAAAAAGACTTGAAGAAAAGCAATTGAT
1 AAAATTTGGAAAAAGACTTGAAGAAAAGAAATTGAT
*
61377646 AAAATTTGGAAAAAGACTTGAAGAATAGAAATTGAT
1 AAAATTTGGAAAAAGACTTGAAGAAAAGAAATTGAT
61377682 AAA
1 AAA
61377685 GACGACACCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.55, C:0.04, G:0.19, T:0.23
Consensus pattern (36 bp):
AAAATTTGGAAAAAGACTTGAAGAAAAGAAATTGAT
Found at i:61378316 original size:119 final size:119
Alignment explanation
Indices: 61378105--61378341 Score: 456
Period size: 119 Copynumber: 2.0 Consensus size: 119
61378095 ATACATTTCA
*
61378105 AATAATAATAACAAGATCCATCATAGGTTTTATCCCTCTTAGGTATCTAAGGGGTTTAGTTCATA
1 AATAATAATAACAAGATCCATCATAGGTTTTATCCCTCTTAGGTATCTAAGGGATTTAGTTCATA
61378170 ATAAAATAAGAGTACATCTCAAAAGTATGAAAATAACAAAACATAAAGAAAACT
66 ATAAAATAAGAGTACATCTCAAAAGTATGAAAATAACAAAACATAAAGAAAACT
*
61378224 AATAATAATAACAAGATCCATCGTAGGTTTTATCCCTCTTAGGTATCTAAGGGATTTAGTTCATA
1 AATAATAATAACAAGATCCATCATAGGTTTTATCCCTCTTAGGTATCTAAGGGATTTAGTTCATA
61378289 ATAAAATAAGAGTACATCTCAAAAGTATGAAAATAACAAAACATAAAGAAAAC
66 ATAAAATAAGAGTACATCTCAAAAGTATGAAAATAACAAAACATAAAGAAAAC
61378342 CTTAAAACCC
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
119 116 1.00
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (119 bp):
AATAATAATAACAAGATCCATCATAGGTTTTATCCCTCTTAGGTATCTAAGGGATTTAGTTCATA
ATAAAATAAGAGTACATCTCAAAAGTATGAAAATAACAAAACATAAAGAAAACT
Found at i:61384731 original size:37 final size:38
Alignment explanation
Indices: 61384676--61384750 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 38
61384666 GATAGTTCAA
* *
61384676 ATTAATTGGTGGAGAGATTGGAATAGAGG-TTAAGGAG
1 ATTAATTGGTGGAGAGATTAGAAGAGAGGTTTAAGGAG
* *
61384713 ATTAGTTGGTGGAGAGATTAGAGGAGAGGTTTAAGGAG
1 ATTAATTGGTGGAGAGATTAGAAGAGAGGTTTAAGGAG
61384751 TGGATTATGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
37 25 0.76
38 8 0.24
ACGTcount: A:0.33, C:0.00, G:0.40, T:0.27
Consensus pattern (38 bp):
ATTAATTGGTGGAGAGATTAGAAGAGAGGTTTAAGGAG
Found at i:61388529 original size:40 final size:40
Alignment explanation
Indices: 61388431--61388693 Score: 309
Period size: 40 Copynumber: 6.6 Consensus size: 40
61388421 TCCTCGTTCA
* * * ** *
61388431 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
61388470 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
61388510 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
61388550 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
61388590 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
61388630 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
61388670 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
61388694 CAGCATTCAA
Statistics
Matches: 199, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
39 37 0.19
40 154 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:61397605 original size:40 final size:40
Alignment explanation
Indices: 61397507--61397769 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
61397497 TCCTCGTTCA
* * * * *
61397507 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
61397546 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
61397586 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
61397626 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
61397666 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
61397706 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
61397746 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
61397770 CAGCATTCAA
Statistics
Matches: 202, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 38 0.19
40 156 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:61397778 original size:41 final size:41
Alignment explanation
Indices: 61397701--61397778 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
61397691 TTAGTATCTC
* * *
61397701 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
61397742 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
61397779 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:61407539 original size:43 final size:43
Alignment explanation
Indices: 61407436--61407543 Score: 155
Period size: 43 Copynumber: 2.5 Consensus size: 43
61407426 TAGCTTAGCT
* *
61407436 ATGGTCTTACTCGA-AATCAAATAATGATGCCAATATCCTAGAC
1 ATGGTCTTACAC-ATAATCACATAATGATGCCAATATCCTAGAC
* * *
61407479 ATGGTCTTACACGTAATCACATAATGATGTCAATGTCCTAGAC
1 ATGGTCTTACACATAATCACATAATGATGCCAATATCCTAGAC
61407522 ATGGTCTTACACATAATCACAT
1 ATGGTCTTACACATAATCACAT
61407544 CTCATTAATC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (43 bp):
ATGGTCTTACACATAATCACATAATGATGCCAATATCCTAGAC
Found at i:61412422 original size:43 final size:43
Alignment explanation
Indices: 61412365--61412480 Score: 119
Period size: 43 Copynumber: 2.7 Consensus size: 43
61412355 TGTGATTACA
* * * *
61412365 TGTAAGACCTTGTGTGGGACAGTGGCATTGTATTAT-GA-TTATG
1 TGTAAGACCATGTGTGGGACAGTGGCATCGT-TAATCGACTT-CG
* * *
61412408 TGTAAGATCATGTGTGGAACATTGGCATCGTTAATCGACTTCG
1 TGTAAGACCATGTGTGGGACAGTGGCATCGTTAATCGACTTCG
* *
61412451 TGTAACACCCTGTGTGGGACAGTGGCATCG
1 TGTAAGACCATGTGTGGGACAGTGGCATCG
61412481 ATACGTGTTA
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
42 3 0.05
43 54 0.92
44 2 0.03
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAAGACCATGTGTGGGACAGTGGCATCGTTAATCGACTTCG
Found at i:61427394 original size:30 final size:30
Alignment explanation
Indices: 61427360--61427420 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
61427350 TCCTTAACTC
61427360 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
61427390 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
61427420 A
1 A
61427421 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:61438410 original size:43 final size:41
Alignment explanation
Indices: 61438330--61438410 Score: 108
Period size: 43 Copynumber: 1.9 Consensus size: 41
61438320 TAAATCCAAT
* * * *
61438330 AACCTAAGTTTATCTTCTCCTTTTTAAATTTTTTTTTCAAC
1 AACCCAAGATTATCTTCTCCTTTTTAAATTCTATTTTCAAC
61438371 AACCCAAGATTATCTTCTCCTCTTTTTAAATTCTATTTTC
1 AACCCAAGATTATCTTCT-C-CTTTTTAAATTCTATTTTC
61438411 TAGGATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 16 0.47
42 1 0.03
43 17 0.50
ACGTcount: A:0.25, C:0.22, G:0.02, T:0.51
Consensus pattern (41 bp):
AACCCAAGATTATCTTCTCCTTTTTAAATTCTATTTTCAAC
Found at i:61439747 original size:19 final size:19
Alignment explanation
Indices: 61439723--61439772 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
61439713 AAAGCCCATA
61439723 ACACGACCCATGTTAGCCC
1 ACACGACCCATGTTAGCCC
* *
61439742 ATACGACCCATGTTGGCCC
1 ACACGACCCATGTTAGCCC
61439761 ACACGA-CCATGT
1 ACACGACCCATGT
61439773 GGCCTAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.26, C:0.38, G:0.18, T:0.18
Consensus pattern (19 bp):
ACACGACCCATGTTAGCCC
Found at i:61441063 original size:12 final size:12
Alignment explanation
Indices: 61441048--61441077 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
61441038 CATTGATCCA
61441048 CTCCTCAAATCT
1 CTCCTCAAATCT
*
61441060 CTCCCCAAATCT
1 CTCCTCAAATCT
61441072 CTCCTC
1 CTCCTC
61441078 TCATCCCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.20, C:0.50, G:0.00, T:0.30
Consensus pattern (12 bp):
CTCCTCAAATCT
Found at i:61447582 original size:19 final size:19
Alignment explanation
Indices: 61447558--61447607 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
61447548 AAAGCCCATA
61447558 ACACGACCCATGTTAGCCC
1 ACACGACCCATGTTAGCCC
* *
61447577 ATACGACCCATGTTGGCCC
1 ACACGACCCATGTTAGCCC
61447596 ACACGA-CCATGT
1 ACACGACCCATGT
61447608 GGCCTAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.26, C:0.38, G:0.18, T:0.18
Consensus pattern (19 bp):
ACACGACCCATGTTAGCCC
Found at i:61448293 original size:28 final size:28
Alignment explanation
Indices: 61448253--61448312 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
61448243 TTACCTCTTA
*
61448253 GGGTTGTAACAGTCATTTCATCAATACG
1 GGGTTATAACAGTCATTTCATCAATACG
61448281 GGGTTATAACAGTCATTTCATCAATACG
1 GGGTTATAACAGTCATTTCATCAATACG
61448309 GGGT
1 GGGT
61448313 CTAAAAGTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (28 bp):
GGGTTATAACAGTCATTTCATCAATACG
Found at i:61449698 original size:12 final size:12
Alignment explanation
Indices: 61449683--61449712 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
61449673 CCTTGATCCA
61449683 CTCCTCAAATCT
1 CTCCTCAAATCT
*
61449695 CTCCCCAAATCT
1 CTCCTCAAATCT
61449707 CTCCTC
1 CTCCTC
61449713 TCATCCCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.20, C:0.50, G:0.00, T:0.30
Consensus pattern (12 bp):
CTCCTCAAATCT
Found at i:61453245 original size:277 final size:275
Alignment explanation
Indices: 61452753--61453446 Score: 1041
Period size: 277 Copynumber: 2.5 Consensus size: 275
61452743 ACATAGATAA
*
61452753 AATTAATATACGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTAAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTAAATTTATTAATA
* * *
61452818 TAAACAGTTATATTAATTAATTTCAGTCAAAATATAAAAGACACGGAAAGTAATATTCTTTTGGA
66 TAAACAGTTATATTAATTAATTTCAGTCAAAATATAAAAGACATGGAAATTAATATTCTTTCGGA
* *
61452883 AAAATATAATTAATCTATGAATTTGATTCATACAACATATTAATTGTATATATTTTACCAAATTT
131 AAAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTT
* *
61452948 ATTAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATAAAAATTAATATTC
196 ATTAATATAAACAATTATATTAACTAATTTCGATCAAAATATAAAAGACATAAAAATTAATATTC
61453013 TTTTGGAAAGAATAT
261 TTTTGGAAAGAATAT
* * * *
61453028 AATTAATACATGAATTTGGTTCATACAAAATATTAATTGTATATTTATTTACTGAATTTATTAAT
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATAT-TTTACTAAATTTATTAAT
* * *
61453093 ATAAACAGTTAGATTAATTAATTTCAATCAAAATATAAAAGACATGAAAATTAATATTCTTTCGG
65 ATAAACAGTTATATTAATTAATTTCAGTCAAAATATAAAAGACATGGAAATTAATATTCTTTCGG
* * * * *
61453158 AAGGAATGTAATTAATATATGAATTTGATTCATATAAAATGTTATTTGTATATATTTTA-CAGAA
130 AA-AAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCA-AA
* * **
61453222 TTTATTAATATAAACAGTTATATTAACTAATTTCGATCAAAATATATAAGACATGGAAATTAATA
193 TTTATTAATATAAACAATTATATTAACTAATTTCGATCAAAATATAAAAGACATAAAAATTAATA
61453287 TTCTTTTGGAAAGAATAT
258 TTCTTTTGGAAAGAATAT
* * * *
61453305 AATTAGTATATGAATTTGATTCATACAAGATATTAGTTGTATATATTTTACCAAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTAAATTTATTAATA
* * * *
61453370 TAAGCAGTTATATTAATTAATTTCGGTCAAAATATATAAGACATGGAAATTAATATTCCTTT-GA
66 TAAACAGTTATATTAATTAATTTCAGTCAAAATATAAAAGACATGGAAATTAATATT-CTTTCGG
61453434 AAAGAATATAATT
130 AAA-AATATAATT
61453447 CTCTTTTCTA
Statistics
Matches: 373, Mismatches: 41, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
275 42 0.11
276 159 0.43
277 172 0.46
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (275 bp):
AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTAAATTTATTAATA
TAAACAGTTATATTAATTAATTTCAGTCAAAATATAAAAGACATGGAAATTAATATTCTTTCGGA
AAAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTT
ATTAATATAAACAATTATATTAACTAATTTCGATCAAAATATAAAAGACATAAAAATTAATATTC
TTTTGGAAAGAATAT
Found at i:61453276 original size:138 final size:137
Alignment explanation
Indices: 61452753--61453446 Score: 1023
Period size: 138 Copynumber: 5.0 Consensus size: 137
61452743 ACATAGATAA
*
61452753 AATTAATATACGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTAAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTAC-AAATTTATTAATA
* *
61452818 TAAACAGTTATATTAATTAATTTC-AGTCAAAATATAAAAGACACGGAAAGTAATATTCTTTTGG
65 TAAACAGTTATATTAATTAATTTCGA-TCAAAATATAAAAGACATGGAAATTAATATTCTTTTGG
61452882 AAA-AATAT
129 AAAGAATAT
* *
61452890 AATTAATCTATGAATTTGATTCATACAACATATTAATTGTATATATTTTACCAAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTA-CAAATTTATTAATA
* * **
61452955 TAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATAAAAATTAATATTCTTTTGGA
65 TAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
61453020 AAGAATAT
130 AAGAATAT
* * * *
61453028 AATTAATACATGAATTTGGTTCATACAAAATATTAATTGTATATTTATTTACTGAATTTATTAAT
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATAT-TTTAC-AAATTTATTAAT
* * * *
61453093 ATAAACAGTTAGATTAATTAATTTCAATCAAAATATAAAAGACATGAAAATTAATATTCTTTCGG
64 ATAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGGAAATTAATATTCTTTTGG
* *
61453158 AAGGAATGT
129 AAAGAATAT
* * *
61453167 AATTAATATATGAATTTGATTCATATAAAATGTTATTTGTATATATTTTACAGAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACA-AATTTATTAATA
* *
61453232 TAAACAGTTATATTAACTAATTTCGATCAAAATATATAAGACATGGAAATTAATATTCTTTTGGA
65 TAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
61453297 AAGAATAT
130 AAGAATAT
* * *
61453305 AATTAGTATATGAATTTGATTCATACAAGATATTAGTTGTATATATTTTACCAAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTA-CAAATTTATTAATA
* * * * *
61453370 TAAGCAGTTATATTAATTAATTTCGGTCAAAATATATAAGACATGGAAATTAATATTCCTTTGAA
65 TAAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
61453435 AAGAATAT
130 AAGAATAT
61453443 AATT
1 AATT
61453447 CTCTTTTCTA
Statistics
Matches: 502, Mismatches: 48, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
137 120 0.24
138 259 0.52
139 123 0.25
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (137 bp):
AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACAAATTTATTAATAT
AAACAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAA
AGAATAT
Found at i:61453515 original size:75 final size:75
Alignment explanation
Indices: 61453422--61453571 Score: 248
Period size: 75 Copynumber: 2.0 Consensus size: 75
61453412 ATGGAAATTA
61453422 ATATTCCTTTGAAAAGAATATAATTC-TCTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAG
1 ATATTCCTTTGAAAAGAATATAATTCAT-TTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAG
61453486 AGAATAATCAT
65 AGAATAATCAT
* * * *
61453497 ATATTCTTTTGGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTTATAAGG
1 ATATTCCTTTGAAAAGAATATAATTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGA
61453562 GAATAATCAT
66 GAATAATCAT
61453572 GGTTTTCCTT
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
75 69 0.99
76 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.45
Consensus pattern (75 bp):
ATATTCCTTTGAAAAGAATATAATTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGA
GAATAATCAT
Found at i:61457204 original size:28 final size:28
Alignment explanation
Indices: 61457154--61457208 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
61457144 TTTTCCTAAT
*
61457154 GGTAACCATCCACGATACGACTCTTAAG
1 GGTAACCATCCACGATACAACTCTTAAG
* * *
61457182 GGTAACCATCTATGATTCAACTCTTAA
1 GGTAACCATCCACGATACAACTCTTAA
61457209 AGTTAAACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (28 bp):
GGTAACCATCCACGATACAACTCTTAAG
Found at i:61457762 original size:17 final size:17
Alignment explanation
Indices: 61457740--61457774 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
61457730 TTTTAATAGA
61457740 TTTATGTCTATATTTAG
1 TTTATGTCTATATTTAG
61457757 TTTATGTCTATATTTAG
1 TTTATGTCTATATTTAG
61457774 T
1 T
61457775 GCATATTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.60
Consensus pattern (17 bp):
TTTATGTCTATATTTAG
Found at i:61457988 original size:228 final size:229
Alignment explanation
Indices: 61457574--61458020 Score: 815
Period size: 228 Copynumber: 2.0 Consensus size: 229
61457564 AGCTGGTTAA
* *
61457574 TTGAGTAAGTATAGTATTTTTTTTATTGAGTGGCGTACTCTGTTGGATTCACCTTCTGGTGAATT
1 TTGAGTAAGTACAGTATTTTTTTTATTGAGTGGCGTACTCTGTTGGATTCACCTTCTGGCGAATT
* *
61457639 CCAAGTTTTAACGAACTCTAGGGTTTATGGGGCTCTTCTATTAAATATCCGCCCACCCCAGATGT
66 CCAAGTTTTAACGAACTCTAGGGTTTAGGGGGCTATTCTATTAAATATCCGCCCACCCCAGATGT
61457704 TTTGAGCAAACTCGTTAAGTTCGCAATTTTAATAGATTTATGTCTATATTTAGTTTATGTCTATA
131 TTTGAGCAAACTCGTTAAGTTCGCAATTTTAATAGATTTATGTCTATATTTAGTTTATGTCTATA
61457769 TTTAGTGCATATTATGATAACTTATGTCTATATT
196 TTTAGTGCATATTATGATAACTTATGTCTATATT
61457803 TTGAGTAAGTACAGTA-TTTTTTTATTGAGTGGCGTACTCTGTTGGATTCACCTTCTGGCGAATT
1 TTGAGTAAGTACAGTATTTTTTTTATTGAGTGGCGTACTCTGTTGGATTCACCTTCTGGCGAATT
*
61457867 CCAAGTTTTAACGAACTCTAGGGTTTAGGGGGCTATTTTATTAAATATCCGCCCACCCCAGATGT
66 CCAAGTTTTAACGAACTCTAGGGTTTAGGGGGCTATTCTATTAAATATCCGCCCACCCCAGATGT
**
61457932 TTTGAGTGAACTCGTTAAGTTCGCAATTTTAATAGATTTATGTCTATATTTAGTTTATGTCTATA
131 TTTGAGCAAACTCGTTAAGTTCGCAATTTTAATAGATTTATGTCTATATTTAGTTTATGTCTATA
*
61457997 TTTAGTGCATATTATGATGACTTA
196 TTTAGTGCATATTATGATAACTTA
61458021 GTTAGTCATG
Statistics
Matches: 210, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
228 195 0.93
229 15 0.07
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (229 bp):
TTGAGTAAGTACAGTATTTTTTTTATTGAGTGGCGTACTCTGTTGGATTCACCTTCTGGCGAATT
CCAAGTTTTAACGAACTCTAGGGTTTAGGGGGCTATTCTATTAAATATCCGCCCACCCCAGATGT
TTTGAGCAAACTCGTTAAGTTCGCAATTTTAATAGATTTATGTCTATATTTAGTTTATGTCTATA
TTTAGTGCATATTATGATAACTTATGTCTATATT
Found at i:61457990 original size:17 final size:17
Alignment explanation
Indices: 61457968--61458002 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
61457958 TTTTAATAGA
61457968 TTTATGTCTATATTTAG
1 TTTATGTCTATATTTAG
61457985 TTTATGTCTATATTTAG
1 TTTATGTCTATATTTAG
61458002 T
1 T
61458003 GCATATTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.60
Consensus pattern (17 bp):
TTTATGTCTATATTTAG
Found at i:61464258 original size:16 final size:16
Alignment explanation
Indices: 61464237--61464293 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
61464227 TTTGGTTCGC
*
61464237 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
61464253 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
61464269 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
61464285 TGTAATGGA
1 TGTAATGGA
61464294 AAAGCTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:61464560 original size:18 final size:17
Alignment explanation
Indices: 61464539--61464573 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
61464529 TTATTATTAA
*
61464539 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
61464557 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
61464574 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:61464581 original size:79 final size:79
Alignment explanation
Indices: 61464498--61464741 Score: 220
Period size: 79 Copynumber: 3.1 Consensus size: 79
61464488 TTATTATCAA
61464498 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
1 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
61464563 TTTAATAAAATTCT
66 TTTAATAAAATTCT
* * * * **** * * *
61464577 TAATAATTAGCA-TAAAT-TTGTTTTGGTA-AATTATTATT--GT-TATTGTT-ATTTAAAT-TT
1 TAATAAATA--ATTTAATCATATTTAAACATAATTATTATTAAATATATT-TTAATTAAAATATA
* * *
61464634 TAA--TAAGATTAATATCAA
63 TAATTTAATA-AAAT-TC-T
*
61464652 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
1 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
61464717 TTTAATAAAATTCT
66 TTTAATAAAATTCT
*
61464731 TAATAATTAAT
1 TAATAAATAAT
61464742 ATTCTTATAT
Statistics
Matches: 119, Mismatches: 30, Indels: 32
0.66 0.17 0.18
Matches are distributed among these distances:
72 4 0.03
73 4 0.03
74 10 0.08
75 24 0.20
76 13 0.11
78 12 0.10
79 34 0.29
80 10 0.08
81 4 0.03
82 4 0.03
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (79 bp):
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
TTTAATAAAATTCT
Found at i:61464710 original size:16 final size:16
Alignment explanation
Indices: 61464673--61464714 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
61464663 TTAATCATAT
*
61464673 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
61464689 TT-AAATATATTATAA
1 TTAAAATATATTATAA
61464704 TTAAAATATAT
1 TTAAAATATAT
61464715 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:61464712 original size:154 final size:156
Alignment explanation
Indices: 61464426--61464739 Score: 578
Period size: 154 Copynumber: 2.0 Consensus size: 156
61464416 TAGAATACCC
61464426 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-TA
*
61464491 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
65 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
61464556 TATATAATTTAATAAAATTCTTAATAA
130 TATATAATTTAATAAAATTCTTAATAA
* *
61464583 TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-A-
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATAT
61464646 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
66 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
61464711 ATATAATTTAATAAAATTCTTAATAA
131 ATATAATTTAATAAAATTCTTAATAA
61464737 TTA
1 TTA
61464740 ATATTCTTAT
Statistics
Matches: 154, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
154 93 0.60
155 1 0.01
157 60 0.39
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (156 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATAT
TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
ATATAATTTAATAAAATTCTTAATAA
Found at i:61464721 original size:14 final size:15
Alignment explanation
Indices: 61464682--61464723 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
61464672 TTTAAACATA
*
61464682 ATTATTATTAAATAT
1 ATTATAATTAAATAT
61464697 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
61464711 A-TATAATTTAATA
1 ATTATAATTAAATA
61464724 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:61464790 original size:17 final size:16
Alignment explanation
Indices: 61464768--61464814 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
61464758 ACTCAAATCA
61464768 TAATATATGATTATAAC
1 TAATATATGATT-TAAC
*
61464785 T-A-ATATGATTTAAT
1 TAATATATGATTTAAC
61464799 TAAATATATGATTTAA
1 T-AATATATGATTTAA
61464815 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 2 0.08
17 12 0.46
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATATATGATTTAAC
Found at i:61464815 original size:17 final size:17
Alignment explanation
Indices: 61464787--61464820 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
61464777 ATTATAACTA
*
61464787 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
61464804 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
61464821 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:61464963 original size:93 final size:92
Alignment explanation
Indices: 61464853--61465047 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
61464843 GATTATAGTT
* * *
61464853 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTAT-ATAATAATATATAATTTC
* *
61464916 ATAAAATTCTTGATAATAAAAATTTTCTTA
64 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
61464946 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAGTGATATATAATTTCAT
1 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
61465011 AAAATTCTTAATAATAAAATGTTCTTA
66 AAAATTCTTAATAATAAAATGTTCTTA
61465038 TATGAATTTA
1 TATGAATTTA
61465048 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 21 0.23
93 68 0.73
94 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
AAAATTCTTAATAATAAAATGTTCTTA
Found at i:61470352 original size:40 final size:40
Alignment explanation
Indices: 61470301--61470405 Score: 201
Period size: 40 Copynumber: 2.6 Consensus size: 40
61470291 GAGCTACTCA
61470301 TGGGCCTGCTCACACAAGCTGACAGTCAGGACGTAACTACT
1 TGGG-CTGCTCACACAAGCTGACAGTCAGGACGTAACTACT
61470342 TGGGCTGCTCACACAAGCTGACAGTCAGGACGTAACTACT
1 TGGGCTGCTCACACAAGCTGACAGTCAGGACGTAACTACT
61470382 TGGGCTGCTCACACAAGCTGACAG
1 TGGGCTGCTCACACAAGCTGACAG
61470406 GTACCCGCAA
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 60 0.94
41 4 0.06
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.19
Consensus pattern (40 bp):
TGGGCTGCTCACACAAGCTGACAGTCAGGACGTAACTACT
Found at i:61477401 original size:33 final size:34
Alignment explanation
Indices: 61477364--61477445 Score: 112
Period size: 34 Copynumber: 2.4 Consensus size: 34
61477354 CTGACATTGT
* *
61477364 AATGGGCTTAGGCCC-CACTAATACTGTTACTGA
1 AATGGGCTAAGGCCCACACTAATACTATTACTGA
* * *
61477397 AATGGGCTCAGGCCCAGACTACTACTATTACTGA
1 AATGGGCTAAGGCCCACACTAATACTATTACTGA
61477431 AATGGGCTAAGGCCC
1 AATGGGCTAAGGCCC
61477446 TAACTGAAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 14 0.33
34 29 0.67
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (34 bp):
AATGGGCTAAGGCCCACACTAATACTATTACTGA
Found at i:61493237 original size:17 final size:15
Alignment explanation
Indices: 61493190--61493251 Score: 79
Period size: 15 Copynumber: 4.0 Consensus size: 15
61493180 AGAAAACCCA
*
61493190 ATAAAGAAGTCCAAG
1 ATAAAGAAATCCAAG
*
61493205 ATAGAGAAATCCAAG
1 ATAAAGAAATCCAAG
61493220 ATAAAGAAACTCCCAAG
1 ATAAAGAAA-T-CCAAG
*
61493237 ATTAAGAAATCCAAG
1 ATAAAGAAATCCAAG
61493252 TTACAAAACC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
15 26 0.63
16 2 0.05
17 13 0.32
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.15
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:61501854 original size:15 final size:15
Alignment explanation
Indices: 61501817--61501878 Score: 52
Period size: 15 Copynumber: 4.0 Consensus size: 15
61501807 ATAAAACCCA
* *
61501817 ATAAAGAAGTCCGAG
1 ATAAAGAAATCCAAG
* *
61501832 ACAGAGAAATCCAAG
1 ATAAAGAAATCCAAG
61501847 ATAAAGAAACTCTCAAG
1 ATAAAGAAA-TC-CAAG
**
61501864 ATTCAGAAATCCAAG
1 ATAAAGAAATCCAAG
61501879 TTACAATACC
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
15 22 0.59
16 4 0.11
17 11 0.30
ACGTcount: A:0.50, C:0.18, G:0.18, T:0.15
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:61512384 original size:37 final size:36
Alignment explanation
Indices: 61512343--61512419 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 36
61512333 GTTTACCTAG
**
61512343 AGGACGCTAGATGAAAGGGAGGAGTGTTGGAGTCGAA
1 AGGACGCTAGATGAAAGGGAGGAGTGTCAGAGTC-AA
*
61512380 AGGACGCTAGATGAAGGGGAGGAGTGTCAGAGTCAA
1 AGGACGCTAGATGAAAGGGAGGAGTGTCAGAGTCAA
61512416 AGGA
1 AGGA
61512420 AGCGAGGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
36 6 0.16
37 31 0.84
ACGTcount: A:0.34, C:0.09, G:0.43, T:0.14
Consensus pattern (36 bp):
AGGACGCTAGATGAAAGGGAGGAGTGTCAGAGTCAA
Found at i:61518987 original size:38 final size:38
Alignment explanation
Indices: 61518896--61519082 Score: 191
Period size: 38 Copynumber: 4.8 Consensus size: 38
61518886 TCCAGTTACT
* * * *
61518896 AGCACTAAGCCTGCGGGACTTTAAGCTCAGATATAATACC
1 AGCACGAAGCCTGCGGGA-TTTAA-CCCGGATATAATTCC
* *
61518936 AGCAC-TAGACCTGCGGGATTTAACCCGGACATAATTCC
1 AGCACGAAG-CCTGCGGGATTTAACCCGGATATAATTCC
** *
61518974 AGCACGAAGCCTGCTAGATTTAACCCAGATAT-ATTACC
1 AGCACGAAGCCTGCGGGATTTAACCCGGATATAATT-CC
61519012 AGCACGAAGCCTGCGGGATTTAACCCGGATATAATTCC
1 AGCACGAAGCCTGCGGGATTTAACCCGGATATAATTCC
* *
61519050 AGCA-TATAGCCTGCGGGTCTTTAAGCCCGGATA
1 AGCACGA-AGCCTGCGGG-ATTTAA-CCCGGATA
61519083 CACATCAAAT
Statistics
Matches: 125, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
37 4 0.03
38 82 0.66
39 17 0.14
40 22 0.18
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.22
Consensus pattern (38 bp):
AGCACGAAGCCTGCGGGATTTAACCCGGATATAATTCC
Found at i:61519012 original size:76 final size:78
Alignment explanation
Indices: 61518896--61519082 Score: 229
Period size: 76 Copynumber: 2.4 Consensus size: 78
61518886 TCCAGTTACT
* * * *
61518896 AGCACTAAGCCTGCGGGACTTTAAGCTCAGATATAATACCAGCAC-TAGACCTGCGGGATTTAAC
1 AGCACGAAGCCTGCGAGACTTTAAGCCCAGATATAATACCAGCACGAAG-CCTGCGGGATTTAAC
61518960 CCGGACATAATTCC
65 CCGGACATAATTCC
* *
61518974 AGCACGAAGCCTGCTAGA-TTTAA-CCCAGATATATTACCAGCACGAAGCCTGCGGGATTTAACC
1 AGCACGAAGCCTGCGAGACTTTAAGCCCAGATATAATACCAGCACGAAGCCTGCGGGATTTAACC
*
61519037 CGGATATAATTCC
66 CGGACATAATTCC
* * * *
61519050 AGCA-TATAGCCTGCGGGTCTTTAAGCCCGGATA
1 AGCACGA-AGCCTGCGAGACTTTAAGCCCAGATA
61519083 CACATCAAAT
Statistics
Matches: 93, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
75 1 0.01
76 58 0.62
77 12 0.13
78 22 0.24
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.22
Consensus pattern (78 bp):
AGCACGAAGCCTGCGAGACTTTAAGCCCAGATATAATACCAGCACGAAGCCTGCGGGATTTAACC
CGGACATAATTCC
Found at i:61530372 original size:20 final size:21
Alignment explanation
Indices: 61530349--61530390 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
61530339 AATAATTCAT
*
61530349 AAAAAATTTAAAAAATA-AAA
1 AAAAAATTAAAAAAATATAAA
*
61530369 AAAATATTAAAAAAATATAAA
1 AAAAAATTAAAAAAATATAAA
61530390 A
1 A
61530391 CACGATTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (21 bp):
AAAAAATTAAAAAAATATAAA
Found at i:61530384 original size:11 final size:11
Alignment explanation
Indices: 61530322--61530390 Score: 53
Period size: 11 Copynumber: 6.7 Consensus size: 11
61530312 TTTCAGTTTC
61530322 TATTAAAAAAA
1 TATTAAAAAAA
*
61530333 TTATT-AAATAA
1 -TATTAAAAAAA
*
61530344 T-TCATAAAAAA
1 TATTA-AAAAAA
61530355 T-TT-AAAAAA
1 TATTAAAAAAA
61530364 TA--AAAAAAA
1 TATTAAAAAAA
61530373 TATTAAAAAAA
1 TATTAAAAAAA
61530384 TA-TAAAA
1 TATTAAAA
61530391 CACGATTCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
9 16 0.34
10 6 0.13
11 21 0.45
12 4 0.09
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (11 bp):
TATTAAAAAAA
Found at i:61530390 original size:9 final size:9
Alignment explanation
Indices: 61530347--61530390 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
61530337 TAAATAATTC
61530347 ATAAAAAAT
1 ATAAAAAAT
*
61530356 TTAAAAAAT
1 ATAAAAAAT
*
61530365 AAAAAAAAT
1 ATAAAAAAT
61530374 ATTAAAAAAAT
1 A-T-AAAAAAT
61530385 ATAAAA
1 ATAAAA
61530391 CACGATTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 20 0.69
10 1 0.03
11 8 0.28
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:61536661 original size:21 final size:21
Alignment explanation
Indices: 61536632--61536672 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
61536622 TGATACATAA
*
61536632 TTGTTAATT-TTCAAACTTTAG
1 TTGTCAATTCTTCAAA-TTTAG
61536653 TTGTCAATTCTTCAAATTTA
1 TTGTCAATTCTTCAAATTTA
61536673 TTATAGTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.29, C:0.12, G:0.07, T:0.51
Consensus pattern (21 bp):
TTGTCAATTCTTCAAATTTAG
Found at i:61538490 original size:19 final size:21
Alignment explanation
Indices: 61538451--61538490 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
61538441 AAATCAAAGT
*
61538451 ATTTTTCAAAATTTGAAAATA
1 ATTTTTCAAAATTTCAAAATA
61538472 ATTTTT-AAAA-TTCAAAATA
1 ATTTTTCAAAATTTCAAAATA
61538491 TTTATAGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 4 0.22
21 6 0.33
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (21 bp):
ATTTTTCAAAATTTCAAAATA
Found at i:61538550 original size:9 final size:9
Alignment explanation
Indices: 61538538--61538574 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
61538528 TAAAAATTTT
61538538 AAAAAATAA
1 AAAAAATAA
*
61538547 AAAAAATAT
1 AAAAAATAA
61538556 AAAAAATAA
1 AAAAAATAA
61538565 AAAATAATAA
1 AAAA-AATAA
61538575 TTTTGGAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 20 0.80
10 5 0.20
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAAAATAA
Found at i:61538550 original size:18 final size:18
Alignment explanation
Indices: 61538514--61538568 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
61538504 TAAAATTTAT
61538514 ATTTTAAAAAA-AATTAAAA
1 ATTTTAAAAAATAA--AAAA
61538533 ATTTTAAAAAATAAAAAA
1 ATTTTAAAAAATAAAAAA
* *
61538551 AATATAAAAAATAAAAAA
1 ATTTTAAAAAATAAAAAA
61538569 TAATAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 20 0.61
19 11 0.33
20 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
ATTTTAAAAAATAAAAAA
Found at i:61538551 original size:19 final size:19
Alignment explanation
Indices: 61538514--61538568 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
61538504 TAAAATTTAT
*
61538514 ATTTTAAAAAA-AATTAAAA
1 ATTTTAAAAAATAA-AAAAA
61538533 ATTTTAAAAAATAAAAAAA
1 ATTTTAAAAAATAAAAAAA
*
61538552 A-TATAAAAAATAAAAAA
1 ATTTTAAAAAATAAAAAA
61538569 TAATAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 15 0.45
19 16 0.48
20 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (19 bp):
ATTTTAAAAAATAAAAAAA
Found at i:61538574 original size:17 final size:17
Alignment explanation
Indices: 61538521--61538574 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
61538511 TATATTTTAA
* **
61538521 AAAAAATTAAAAATTTT
1 AAAAAATAAAAAATAAT
*
61538538 AAAAAATAAAAAAAATAT
1 AAAAAATAAAAAATA-AT
61538556 AAAAAATAAAAAATAAT
1 AAAAAATAAAAAATAAT
61538573 AA
1 AA
61538575 TTTTGGAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAAAATAAAAAATAAT
Found at i:61538893 original size:21 final size:21
Alignment explanation
Indices: 61538869--61538908 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
61538859 ACATTTTTTA
*
61538869 AAGTTAAAAGTCAAAACTATC
1 AAGTTAAAAGGCAAAACTATC
*
61538890 AAGTTAAAAGGCCAAACTA
1 AAGTTAAAAGGCAAAACTA
61538909 CGTTATTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.15, G:0.12, T:0.20
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACTATC
Found at i:61540705 original size:3 final size:3
Alignment explanation
Indices: 61540699--61540724 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
61540689 CAACAACAAC
61540699 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
61540725 GCTGTTATCA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:61547538 original size:78 final size:78
Alignment explanation
Indices: 61547436--61547588 Score: 252
Period size: 78 Copynumber: 2.0 Consensus size: 78
61547426 TGTGTAGGCC
61547436 CCACGAGCATATGGGCCCACACGGGTAAACCACATAGACGTGTAGAGAAGATTGGGCCAGAATGT
1 CCACGAGCATATGGGCCCACACGGGTAAACCACATAGACGTGTAGAGAAGATTGGGCCAGAATGT
61547501 GTAGTTCACACGA
66 GTAGTTCACACGA
* * * * **
61547514 CCACGGGCATGTGGGCCTACACGGGTAAACCACATAGACGTGTGGAGAAGATTGGGCCAGGCTGT
1 CCACGAGCATATGGGCCCACACGGGTAAACCACATAGACGTGTAGAGAAGATTGGGCCAGAATGT
61547579 GTAGTTCACA
66 GTAGTTCACA
61547589 TGGCTAAGGC
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 69 1.00
ACGTcount: A:0.29, C:0.23, G:0.31, T:0.18
Consensus pattern (78 bp):
CCACGAGCATATGGGCCCACACGGGTAAACCACATAGACGTGTAGAGAAGATTGGGCCAGAATGT
GTAGTTCACACGA
Found at i:61554041 original size:52 final size:53
Alignment explanation
Indices: 61553950--61554049 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 53
61553940 ATGTAAGTCC
* *
61553950 ATATCATATATATGGCTTTGGAGATAGGAATGAGCCATGTAAGCCCATATTAT
1 ATATCATATATATGGCATTGGAGATAGGAATAAGCCATGTAAGCCCATATTAT
** *
61554003 ATAT-ATATATATGGCATTGGAGATAGGAATAATTCATGTAAGTCCAT
1 ATATCATATATATGGCATTGGAGATAGGAATAAGCCATGTAAGCCCAT
61554050 GTCGAAGACA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 38 0.90
53 4 0.10
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (53 bp):
ATATCATATATATGGCATTGGAGATAGGAATAAGCCATGTAAGCCCATATTAT
Found at i:61558166 original size:40 final size:40
Alignment explanation
Indices: 61558108--61558186 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
61558098 ACACACCATG
* * *
61558108 TGGGGATACAATCGACCCACCCAGCCCTACATACCAAGTA
1 TGGGGATAAAATCAACCCACCCAGCCCTACACACCAAGTA
* * *
61558148 TGGGGATAAAATCAACCCATCTAGCCTTACACACCAAGT
1 TGGGGATAAAATCAACCCACCCAGCCCTACACACCAAGT
61558187 GGTACTGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (40 bp):
TGGGGATAAAATCAACCCACCCAGCCCTACACACCAAGTA
Found at i:61564966 original size:25 final size:25
Alignment explanation
Indices: 61564925--61565007 Score: 87
Period size: 25 Copynumber: 3.4 Consensus size: 25
61564915 CTGGAGGCCT
* * *
61564925 AGCCTCTTTTAAT-AACTGGGGTAA
1 AGCCTTTTTTGATAAACTGGGGCAA
61564949 AGCCTTTTTTGATAAACTGGGGCAA
1 AGCCTTTTTTGATAAACTGGGGCAA
* * * *
61564974 AGCCCTTTTCGGTAAACTGGGGCAT
1 AGCCTTTTTTGATAAACTGGGGCAA
*
61564999 AGCCCTTTT
1 AGCCTTTTT
61565008 AGCACTTCCT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
24 11 0.22
25 40 0.78
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (25 bp):
AGCCTTTTTTGATAAACTGGGGCAA
Found at i:61565241 original size:27 final size:27
Alignment explanation
Indices: 61565211--61565396 Score: 282
Period size: 27 Copynumber: 6.9 Consensus size: 27
61565201 GGGCAAAATA
* * * *
61565211 GTAATTTTACCCCACAAGGGTATCTCG
1 GTAATTCTACCCTACAGGGGTATTTCG
*
61565238 GTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCG
* *
61565265 GTAATTCTACCCTACAAGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCG
*
61565292 GTAATTCTACCCTACAAGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCG
61565319 GTAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCG
*
61565346 ATAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCG
*
61565373 GTAGTTCTACCCTACAGGGGTATT
1 GTAATTCTACCCTACAGGGGTATT
61565397 CAATAATTTT
Statistics
Matches: 148, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 148 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTCG
Found at i:61565472 original size:27 final size:28
Alignment explanation
Indices: 61565436--61565811 Score: 132
Period size: 27 Copynumber: 13.9 Consensus size: 28
61565426 GTAATTCTGT
* *
61565436 AAATCGAAGGTACTTTGGTAATTTTTAC
1 AAATCGAAGGTATTTTAGTAATTTTTAC
*
61565464 AAGTC-AAGGGTATTTTAGTAA-TTTTAC
1 AAATCGAA-GGTATTTTAGTAATTTTTAC
* *
61565491 AAATCGAGGGTATTTTAGTAA-TTTTGC
1 AAATCGAAGGTATTTTAGTAATTTTTAC
* ** *
61565518 AAA-CTGAGGGTATTTCGGTAA-TTTCAC
1 AAATC-GAAGGTATTTTAGTAATTTTTAC
* * *
61565545 AAATC-AGGGGCATTTTGGTAA-TTTTAC
1 AAATCGA-AGGTATTTTAGTAATTTTTAC
* * *
61565572 AAA-CTAGGGGTATTTTGGTAATTTTGT--
1 AAATCGA-AGGTATTTTAGTAATTTT-TAC
* *
61565599 AAA-CCAAGGGTATTTTGGTAA-TTTTAC
1 AAATCGAA-GGTATTTTAGTAATTTTTAC
* *
61565626 AAGTC-AAGGGTATTTTAGTAA-TTTCAC
1 AAATCGAA-GGTATTTTAGTAATTTTTAC
* * * *
61565653 AAAT-TAGGGGTATTTTGGTAA-TTTTAT
1 AAATCGA-AGGTATTTTAGTAATTTTTAC
* * * *
61565680 AAGTCGAGGGTATTTCAGTAA-TTTCAC
1 AAATCGAAGGTATTTTAGTAATTTTTAC
* * * *
61565707 AAAT-TAGGGGTATTTTGGTAA-TTTCAC
1 AAATCGA-AGGTATTTTAGTAATTTTTAC
* * * *
61565734 -AACCCAGGGGTATTTTGGTAA-TTTTAC
1 AAATCGA-AGGTATTTTAGTAATTTTTAC
* *
61565761 AAA-CCAGGGGTATTTTAGTAA-TTTTAC
1 AAATCGA-AGGTATTTTAGTAATTTTTAC
* * *
61565788 AAATTGAGGGCATTTTAGTAATTT
1 AAATCGAAGGTATTTTAGTAATTT
61565812 GGTAAACTAA
Statistics
Matches: 287, Mismatches: 41, Indels: 40
0.78 0.11 0.11
Matches are distributed among these distances:
25 1 0.00
26 9 0.03
27 249 0.87
28 27 0.09
29 1 0.00
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (28 bp):
AAATCGAAGGTATTTTAGTAATTTTTAC
Done.