Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008489.1 Hibiscus syriacus cultivar Beakdansim tig00111331_pilon, whole genome shotgun sequence
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: 1108073
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:306135 original size:64 final size:64
Alignment explanation
Indices: 306053--306273 Score: 284
Period size: 64 Copynumber: 3.5 Consensus size: 64
306043 TTGAAGGTGT
* * * **
306053 ATCGATGCACAGGAAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTCGTG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTCGTG
306116 C
64 C
* *
306117 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTCGTGT
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCGTGC
* * * **
306181 ATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCGTGC
* *
306245 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
306274 ACCTTCATTA
Statistics
Matches: 139, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
64 133 0.96
65 6 0.04
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCGTGC
Found at i:307235 original size:103 final size:103
Alignment explanation
Indices: 307010--307226 Score: 389
Period size: 103 Copynumber: 2.1 Consensus size: 103
307000 GTCGAGGGTC
307010 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
* *
307075 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
307113 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATTTGTGAAGTCTAGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
*
307178 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
307216 TCTGTGGTCCT
1 TATGTGGTCCT
307227 CATGGACATT
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:307310 original size:23 final size:23
Alignment explanation
Indices: 307234--307311 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
307224 CCTCATGGAC
*
307234 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
307258 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
307281 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
307304 ATTATATG
1 ATTATATG
307312 AGCTGTGGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 42 0.93
24 3 0.07
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:311476 original size:64 final size:64
Alignment explanation
Indices: 311408--311588 Score: 222
Period size: 64 Copynumber: 2.8 Consensus size: 64
311398 AAGGTGTATC
* * **
311408 GATGCACAGGAAGTGCATTGATACA-CTCTTTTAA-AATAAATACATCGAATGCAATTCGTGCAT
1 GATGCACAAGAAGTGCATCGATACATC-CCATTAATAATAAA-ACATCGAATGCAATTCGTGCAT
311471 T
64 T
* * * *
311472 GATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTCGTGCATT
1 GATGCACAAGAAGTGCATCGATACATCCCATTAATAATAAAACATCGAATGCAATTCGTGCATT
* * * *
311536 GATGCATAAGTAGTGCATCGATGCATCCCATTAATAATACAACATCGAATGCA
1 GATGCACAAGAAGTGCATCGATACATCCCATTAATAATAAAACATCGAATGCA
311589 TTTTATGCAC
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
64 99 0.94
65 6 0.06
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (64 bp):
GATGCACAAGAAGTGCATCGATACATCCCATTAATAATAAAACATCGAATGCAATTCGTGCATT
Found at i:311604 original size:64 final size:64
Alignment explanation
Indices: 311449--311625 Score: 284
Period size: 64 Copynumber: 2.8 Consensus size: 64
311439 TAAAATAAAT
311449 ACATCGAATGCAATTCGTGCATTGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAA
1 ACATCGAATGCAATTCGTGCATTGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAA
311513 ACATCGAATGCAATTCGTGCATTGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAT-ACA
1 ACATCGAATGCAATTCGTGCATTGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGA-A
* ** ** *
311577 ACATCGAATGCATTTTATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 ACATCGAATGCAATTCGTGCATTGATGCATAAGTAGTGCATCGATGCAT
311626 ACCTTCATTA
Statistics
Matches: 106, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
63 1 0.01
64 105 0.99
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (64 bp):
ACATCGAATGCAATTCGTGCATTGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAA
Found at i:312587 original size:103 final size:103
Alignment explanation
Indices: 312362--312579 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
312352 GTCGAGGGTC
312362 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
312427 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
312465 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
312530 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
312568 TATGTGGTCCTT
1 TATGTGGTCCTT
312580 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:312662 original size:23 final size:23
Alignment explanation
Indices: 312586--312663 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
312576 CCTTATGGAC
*
312586 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
312610 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
312633 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
312656 ATTATATG
1 ATTATATG
312664 AGCTATGGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 42 0.93
24 3 0.07
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:316444 original size:16 final size:16
Alignment explanation
Indices: 316425--316478 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
316415 GTAGAAAGAG
*
316425 AAAAATAAAAAATAAA
1 AAAAATAGAAAATAAA
*
316441 AAAAATTGAAAATGAAA
1 AAAAATAGAAAAT-AAA
316458 AAAAA-ATGAAAATAAA
1 AAAAATA-GAAAATAAA
316474 AAAAA
1 AAAAA
316479 GAATGAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 19 0.58
17 14 0.42
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.13
Consensus pattern (16 bp):
AAAAATAGAAAATAAA
Found at i:316486 original size:18 final size:16
Alignment explanation
Indices: 316433--316478 Score: 74
Period size: 17 Copynumber: 2.8 Consensus size: 16
316423 AGAAAAATAA
*
316433 AAAATAAAAAAAATTG
1 AAAATAAAAAAAAATG
316449 AAAATGAAAAAAAAATG
1 AAAAT-AAAAAAAAATG
316466 AAAATAAAAAAAA
1 AAAATAAAAAAAA
316479 GAATGAAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (16 bp):
AAAATAAAAAAAAATG
Found at i:316491 original size:17 final size:17
Alignment explanation
Indices: 316425--316491 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
316415 GTAGAAAGAG
316425 AAAAAT-AAAA-AATAAA
1 AAAAATGAAAAGAA-AAA
316441 AAAAATTGAAAATG-AAAA
1 AAAAA-TGAAAA-GAAAAA
*
316459 AAAAATGAAAATAAAAA
1 AAAAATGAAAAGAAAAA
316476 AAAGAATG-AAAGAAAA
1 AAA-AATGAAAAGAAAA
316492 TTCACCCAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
16 5 0.12
17 21 0.49
18 16 0.37
19 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (17 bp):
AAAAATGAAAAGAAAAA
Found at i:317887 original size:113 final size:114
Alignment explanation
Indices: 317689--317986 Score: 445
Period size: 113 Copynumber: 2.6 Consensus size: 114
317679 AAGTTAGGAT
* *
317689 ATGTTAGGGCACGACTTAACCCCTATCATATTGAGATGACAAGACCCAGACCAAGAAGGCATTGA
1 ATGTTGGGGCACGACTGAACCCCTATCATATTGAGATGACAAGACCCAGACCAAGAAGGCATTGA
*
317754 GAATGAGCCTTACAATTTGAGGTGTT-GGGCATTCTGAAGGCTCGTACC
66 GAATGAGCCTTACAATTTGAGGTGTTAGGGCATTCTGAAGGCCCGTACC
*
317802 ATGTTGGGGCACGACTGAACCCCTATCATGTTGAGATGACAAGACCCAGACCAAGAAGGCATTGA
1 ATGTTGGGGCACGACTGAACCCCTATCATATTGAGATGACAAGACCCAGACCAAGAAGGCATTGA
*
317867 GAATGAGCCTTATAATTTGAGGTGTTAGGGCATTCTGAAGGCCCGTACC
66 GAATGAGCCTTACAATTTGAGGTGTTAGGGCATTCTGAAGGCCCGTACC
* * * * * ** * * **
317916 ATATTGGGGTACGACTGAACCCATAACATTTTGAGATGACAAGATTCAGACTAAAAAGTTATTGA
1 ATGTTGGGGCACGACTGAACCCCTATCATATTGAGATGACAAGACCCAGACCAAGAAGGCATTGA
317981 GAATGA
66 GAATGA
317987 ATCTCGCAAC
Statistics
Matches: 168, Mismatches: 16, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
113 87 0.52
114 81 0.48
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (114 bp):
ATGTTGGGGCACGACTGAACCCCTATCATATTGAGATGACAAGACCCAGACCAAGAAGGCATTGA
GAATGAGCCTTACAATTTGAGGTGTTAGGGCATTCTGAAGGCCCGTACC
Found at i:318776 original size:70 final size:73
Alignment explanation
Indices: 318687--318870 Score: 275
Period size: 70 Copynumber: 2.6 Consensus size: 73
318677 TGAGATTGGG
* *
318687 GCAAGTCAATCTTAAGCCTTCACCGGAGAGTAGTGAATCAATC-ATCTTAA-CCTTCACCGAAGA
1 GCAAGTCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATCAATCTTAAGCCTTCACCGAAGA
318750 GGAGTGAA
66 GGAGTGAA
* * * *
318758 GC-AGTCATTCTTAAGCCTTCACCGAAGAGGAGTGAAGCAGTCAATCTTAAGCCTTTACCGAAGA
1 GCAAGTCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATCAATCTTAAGCCTTCACCGAAGA
*
318822 GTAGTGAA
66 GGAGTGAA
*
318830 GCAACTCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAA
1 GCAAGTCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAA
318871 ATCCATCCGT
Statistics
Matches: 99, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
70 35 0.35
71 9 0.09
72 21 0.21
73 34 0.34
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (73 bp):
GCAAGTCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATCAATCTTAAGCCTTCACCGAAGA
GGAGTGAA
Found at i:318848 original size:37 final size:37
Alignment explanation
Indices: 318687--318870 Score: 270
Period size: 36 Copynumber: 5.1 Consensus size: 37
318677 TGAGATTGGG
*
318687 GCAAGTCAATCTTAAGCCTTCACCGGAGAGTAGTGAA
1 GCAAGTCAATCTTAAGCCTTCACCGAAGAGTAGTGAA
* *
318724 TCAA-TC-ATCTTAA-CCTTCACCGAAGAGGAGTGAA
1 GCAAGTCAATCTTAAGCCTTCACCGAAGAGTAGTGAA
* *
318758 GC-AGTCATTCTTAAGCCTTCACCGAAGAGGAGTGAA
1 GCAAGTCAATCTTAAGCCTTCACCGAAGAGTAGTGAA
*
318794 GC-AGTCAATCTTAAGCCTTTACCGAAGAGTAGTGAA
1 GCAAGTCAATCTTAAGCCTTCACCGAAGAGTAGTGAA
*
318830 GCAACTCAATCTTAAGCCTTCACCGAAGAGTAGTGAA
1 GCAAGTCAATCTTAAGCCTTCACCGAAGAGTAGTGAA
318867 GCAA
1 GCAA
318871 ATCCATCCGT
Statistics
Matches: 133, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
33 1 0.01
34 22 0.17
35 13 0.10
36 58 0.44
37 39 0.29
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (37 bp):
GCAAGTCAATCTTAAGCCTTCACCGAAGAGTAGTGAA
Found at i:319066 original size:42 final size:42
Alignment explanation
Indices: 318995--319092 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
318985 AATTTATAAG
* * * *
318995 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCGGGCCATCAGAAAGCCTTCCGAGCATGATGATTAAA
* *
319037 TCCTTCGGGTCATCAGAAAGCCTTCCGAGCATGATGATTAAG
1 TCCTTCGGGCCATCAGAAAGCCTTCCGAGCATGATGATTAAA
*
319079 TCCTTCGAGCCATC
1 TCCTTCGGGCCATC
319093 CATAAAACCT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (42 bp):
TCCTTCGGGCCATCAGAAAGCCTTCCGAGCATGATGATTAAA
Found at i:319088 original size:22 final size:22
Alignment explanation
Indices: 319011--319088 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
319001 GGGCCATCAG
* *
319011 TAAGTCTTTCGAGCATGATGCT
1 TAAGTCCTTCGAGCATGATGAT
* * *
319033 TAAATCCTTCGGGTCATCA-GA-
1 TAAGTCCTTCGAG-CATGATGAT
319054 -AAG-CCTTCCGAGCATGATGAT
1 TAAGTCCTT-CGAGCATGATGAT
319075 TAAGTCCTTCGAGC
1 TAAGTCCTTCGAGC
319089 CATCCATAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
19 8 0.19
20 7 0.17
22 19 0.45
23 8 0.19
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (22 bp):
TAAGTCCTTCGAGCATGATGAT
Found at i:319262 original size:42 final size:41
Alignment explanation
Indices: 319196--319297 Score: 132
Period size: 42 Copynumber: 2.5 Consensus size: 41
319186 TTCACAATTT
* * *
319196 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATG
* * *
319237 CTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATG
*
319279 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTTCGGGCCATC
319298 CATAAAACCT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
41 16 0.31
42 35 0.69
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATG
Found at i:319641 original size:20 final size:20
Alignment explanation
Indices: 319616--319683 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
319606 TCACAATTTA
319616 TAAGTCCTTCGGGTCATCAG
1 TAAGTCCTTCGGGTCATCAG
* * *
319636 TAAGTCTTTCGAG-CATGATG
1 TAAGTCCTTCGGGTCATCA-G
*
319656 CTTAAATCCTTCGGGTCATCAG
1 --TAAGTCCTTCGGGTCATCAG
*
319678 CAAGTC
1 TAAGTC
319684 TTCCAAGCAT
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
19 4 0.11
20 16 0.46
22 11 0.31
23 4 0.11
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (20 bp):
TAAGTCCTTCGGGTCATCAG
Found at i:319683 original size:42 final size:42
Alignment explanation
Indices: 319620--319710 Score: 137
Period size: 42 Copynumber: 2.2 Consensus size: 42
319610 AATTTATAAG
* * * *
319620 TCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCGGGTCATCAGCAAGTCTTCCAAGCATGATGATTAAA
*
319662 TCCTTCGGGTCATCAGCAAGTCTTCCAAGCATGATGATTAAG
1 TCCTTCGGGTCATCAGCAAGTCTTCCAAGCATGATGATTAAA
319704 TCCTTCG
1 TCCTTCG
319711 AGCCATCCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (42 bp):
TCCTTCGGGTCATCAGCAAGTCTTCCAAGCATGATGATTAAA
Found at i:319842 original size:206 final size:205
Alignment explanation
Indices: 318938--320368 Score: 2120
Period size: 205 Copynumber: 6.9 Consensus size: 205
318928 GATGTTTTAA
*
318938 GATGATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
1 GATGATGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
* * * **
319003 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCAGAAAGCCTTCCGAGCA
66 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCA
*
319068 TGATGATTAAGTCCTTCGAGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAA
131 TGATGA-TAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAA
319133 AATGAAAAAAT
195 AATGAAAAAAT
319144 GATGATGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
1 GATGATGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
319209 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCA
66 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCA
* * * *
319274 AGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGTGTCGGATGTTTTCACATGAATTTGAGA
131 TGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAA
319339 ATGAAAAAAT
196 ATGAAAAAAT
* * *
319349 GATGTTGGAATTTTTGAAAATGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCATTCGG
1 GATGATGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
* * *
319414 GTCATCAGTAAGTCTTTCGAGCATGATGCGTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGTA
66 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCA
* * *
319479 AGATGATAAGTCCTTTGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCA-TTGAATTTGAAA
131 TGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAA
319543 AT-AAGAAAAT
196 ATGAA-AAAAT
319553 GATGTTTTAAGATGATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATA
1 GA-----T--GATG--G-AATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATA
* * *
319618 AGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCAGCAAGT
56 AGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGT
* *
319683 CTTCCA-AGCATGATGATTAAGTCCTTCGAGCCATCCATAAAACCTTCGGGTAGGATGTTTTCAC
121 CTT-TAGAGCATGATGA-TAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCAC
319747 ATGAATTTGAAAATGAAAAAAT
184 ATGAATTTGAAAATGAAAAAAT
319769 GATGATGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
1 GATGATGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
319834 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCA
66 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCA
*
319899 AGATGATAAGAT-CTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAA
131 TGATGATAAG-TCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAA
319963 AATGAAAAAAT
195 AATGAAAAAAT
* *
319974 GATGATTGAATTTTTGAAAACGAAGAATGTGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
1 GATGATGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
* * *
320039 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATTCTTAGGGTCATCTGTAAGCCTTTAGAGCA
66 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGC-
* * * *
320104 AT-ATGATAAGTCCTTCGGACCATCCGTAAGACCTTCGGGTAGGATGTTTTCA-TTGAATTTGAA
130 ATGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAA
320167 AAT-AAGAAAAT
195 AATGAA-AAAAT
* *
320178 GATGTTTTAAGATAATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAACTTTCACAATTTATA
1 GA-----T--G---ATGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATA
* * * **
320243 AGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCCCTCGGGCCATCAATAAGT
56 AGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGT
* * * * * **
320308 CTTTTGAGAATGATGCTTAAATCCTTCGGGTCATCCATAAGGCCTTCGGGTAGGATGTTTT
121 CTTTAGAGCATGATG-ATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTT
320369 TCACCAAGAT
Statistics
Matches: 1123, Mismatches: 70, Indels: 55
0.90 0.06 0.04
Matches are distributed among these distances:
203 4 0.00
204 40 0.04
205 474 0.42
206 252 0.22
207 1 0.00
209 6 0.01
211 5 0.00
213 3 0.00
214 232 0.21
215 84 0.07
216 20 0.02
217 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (205 bp):
GATGATGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCA
TGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAA
ATGAAAAAAT
Found at i:320085 original size:625 final size:625
Alignment explanation
Indices: 318873--320368 Score: 2620
Period size: 625 Copynumber: 2.4 Consensus size: 625
318863 TGAAGCAAAT
*
318873 CCATCCGTAAGACCTTCAGGTAGGATGTTTTCATTGAATTTGAAAATAAGAAAATGATGTTTTAA
1 CCATCCGTAAGACCTTCGGGTAGGATGTTTTCATTGAATTTGAAAATAAGAAAATGATGTTTTAA
318938 GATGATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
66 GATGATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
*
319003 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCAGAAAGCCTTCCGAGCA
131 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCAGAAAGTCTTCCGAGCA
319068 TGATGATTAAGTCCTTCGAGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAA
196 TGATGATTAAGTCCTTCGAGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAA
319133 AATGAAAAAATGATGATGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTAT
261 AATGAAAAAATGATGATGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTAT
319198 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAG
326 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAG
* *
319263 TCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGTGTCGGATGTTTTCACA
391 TCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACA
* *
319328 TGAATTTGAGAATGAAAAAATGATGTTGGAATTTTTGAAAATGAAGAATGCGAGTTTCAAAATTT
456 TGAATTTGAAAATGAAAAAATGATGTTGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTT
* *
319393 CACAATTTATAAGTCATTCGGGTCATCAGTAAGTCTTTCGAGCATGATGCGTAAATCCTTCGGGT
521 CACAATTTATAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCGTAAATCCTTAGGGT
* * * *
319458 CATCTGTAAGTCTTTAGAGTAAGATGATAAGTCCTTTGGG
586 CATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGA
* *
319498 CCATCCATAAAACCTTCGGGTAGGATGTTTTCATTGAATTTGAAAATAAGAAAATGATGTTTTAA
1 CCATCCGTAAGACCTTCGGGTAGGATGTTTTCATTGAATTTGAAAATAAGAAAATGATGTTTTAA
319563 GATGATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
66 GATGATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
* * *
319628 GTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCAGCAAGTCTTCCAAGCA
131 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCAGAAAGTCTTCCGAGCA
319693 TGATGATTAAGTCCTTCGAGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAA
196 TGATGATTAAGTCCTTCGAGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAA
319758 AATGAAAAAATGATGATGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTAT
261 AATGAAAAAATGATGATGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTAT
319823 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAG
326 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAG
319888 TCTTTAGAGCAAGATGATAAGAT-CTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCAC
391 TCTTTAGAGCAAGATGATAAG-TCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCAC
*
319952 ATGAATTTGAAAATGAAAAAATGATGATT-GAATTTTTGAAAACGAAGAATGTGAGTTTCAAAAT
455 ATGAATTTGAAAATGAAAAAATGATG-TTGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAAT
* * *
320016 TTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATTCTTAGG
519 TTCACAATTTATAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCGTAAATCCTTAGG
*
320081 GTCATCTGTAAGCCTTTAGAGCAATATGATAAGTCCTTCGGA
584 GTCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGA
320123 CCATCCGTAAGACCTTCGGGTAGGATGTTTTCATTGAATTTGAAAATAAGAAAATGATGTTTTAA
1 CCATCCGTAAGACCTTCGGGTAGGATGTTTTCATTGAATTTGAAAATAAGAAAATGATGTTTTAA
* *
320188 GATAATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAACTTTCACAATTTATAAGTCCTTCGG
66 GATGATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
* * * ** *
320253 GCCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCCCTCGGGCCATCA-ATAAGTCTTTTGAGA
131 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCAGA-AAGTCTTCCGAGC
* * * * **
320317 ATGATGCTTAAATCCTTCGGGTCATCCATAAGGCCTTCGGGTAGGATGTTTT
195 ATGATGATTAAGTCCTTCGAGCCATCCATAAAACCTTCGGGTAGGATGTTTT
320369 TCACCAAGAT
Statistics
Matches: 827, Mismatches: 41, Indels: 6
0.95 0.05 0.01
Matches are distributed among these distances:
625 824 1.00
626 3 0.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (625 bp):
CCATCCGTAAGACCTTCGGGTAGGATGTTTTCATTGAATTTGAAAATAAGAAAATGATGTTTTAA
GATGATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCAGAAAGTCTTCCGAGCA
TGATGATTAAGTCCTTCGAGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAA
AATGAAAAAATGATGATGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTAT
AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAG
TCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACA
TGAATTTGAAAATGAAAAAATGATGTTGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTT
CACAATTTATAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCGTAAATCCTTAGGGT
CATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGA
Found at i:320308 original size:42 final size:42
Alignment explanation
Indices: 320249--320348 Score: 155
Period size: 42 Copynumber: 2.4 Consensus size: 42
320239 TATAAGTCCT
* *
320249 TCGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCCC
1 TCGGGCCATCAATAAGTCTTTTGAGAATGATGCTTAAATCCC
*
320291 TCGGGCCATCAATAAGTCTTTTGAGAATGATGCTTAAATCCT
1 TCGGGCCATCAATAAGTCTTTTGAGAATGATGCTTAAATCCC
* *
320333 TCGGGTCATCCATAAG
1 TCGGGCCATCAATAAG
320349 GCCTTCGGGT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (42 bp):
TCGGGCCATCAATAAGTCTTTTGAGAATGATGCTTAAATCCC
Found at i:325398 original size:21 final size:20
Alignment explanation
Indices: 325312--325469 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
325302 AAATGACCAA
**
325312 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
325331 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
325351 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
325371 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* ** * *
325392 GAAAATCGCAATACGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
325413 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
325433 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
325454 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
325470 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:325498 original size:20 final size:20
Alignment explanation
Indices: 325437--325646 Score: 192
Period size: 20 Copynumber: 10.5 Consensus size: 20
325427 GATTTTCAAG
* ** *
325437 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
325457 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
325477 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
325497 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
325517 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* **
325537 AATCGTAATACGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
325557 TATCGCAACACGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
325577 AATCGCAACG-ATAATCTGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
325597 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
325617 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
325637 AATCGCAACG
1 AATCGCAACG
325647 AGAATCTGTA
Statistics
Matches: 157, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
19 2 0.01
20 153 0.97
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:326402 original size:24 final size:24
Alignment explanation
Indices: 326358--326404 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
326348 AAATTTGGTC
*
326358 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGAACTTTGATA
*
326382 TTGGTCAATA-CACGAATTTTGAT
1 TTGGTCAATATC-CGAACTTTGAT
326405 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGAACTTTGATA
Found at i:326596 original size:12 final size:12
Alignment explanation
Indices: 326579--326603 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
326569 ATATAATCCT
326579 GAAGAAGAAAAA
1 GAAGAAGAAAAA
326591 GAAGAAGAAAAA
1 GAAGAAGAAAAA
326603 G
1 G
326604 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:328994 original size:72 final size:72
Alignment explanation
Indices: 328902--329105 Score: 290
Period size: 72 Copynumber: 2.8 Consensus size: 72
328892 GCAACGAGAG
328902 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
328967 AAATGAA
66 AAATGAA
* *
328974 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAAAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGC
329038 GAAATGAA
65 GAAATGAA
* * * * *
329046 AATCGCAACGAGAGAATCG-CAATGCGAA-ATGAAAATCGCAATGC-GAAATGAAAATCGCAA
1 AATCGCAATGCGA-AAT-GAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAA
329106 CGAGAGAATC
Statistics
Matches: 119, Mismatches: 9, Indels: 9
0.87 0.07 0.07
Matches are distributed among these distances:
71 17 0.14
72 92 0.77
73 9 0.08
74 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:329016 original size:105 final size:101
Alignment explanation
Indices: 328888--329157 Score: 364
Period size: 105 Copynumber: 2.6 Consensus size: 101
328878 TGGAAATTAC
328888 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA-C-ATGAAAATCGCAATGCGGAAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAGCAATGAAAATCGCAA--C-G--A
328951 TGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
61 -GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
328993 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA-GC--AATGAAAATCGCAACGAG
*
329058 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
62 AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
329098 AATCGCAACGAGAGAATCGCAATGTGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAACGAGAGAATCGCAATG-CGAAATGAAAATCCCAA-GC--AATGAAAATCGCA
329158 TTGCGATTTT
Statistics
Matches: 155, Mismatches: 3, Indels: 14
0.90 0.02 0.08
Matches are distributed among these distances:
105 123 0.79
106 16 0.10
108 2 0.01
109 1 0.01
111 13 0.08
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (101 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAGCAATGAAAATCGCAACGAGAAAA
TCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:329023 original size:53 final size:52
Alignment explanation
Indices: 328888--329157 Score: 406
Period size: 53 Copynumber: 5.1 Consensus size: 52
328878 TGGAAATTAC
*
328888 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
328935 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
328993 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
329046 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
329098 AATCGCAACGAGAGAATCGCAATGTGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATG-CGAAATGAAAATCGCAATGCGAAATGAA
329151 AATCGCA
1 AATCGCA
329158 TTGCGATTTT
Statistics
Matches: 206, Mismatches: 4, Indels: 20
0.90 0.02 0.09
Matches are distributed among these distances:
47 8 0.04
49 1 0.00
50 1 0.00
52 65 0.32
53 115 0.56
55 2 0.01
56 1 0.00
58 13 0.06
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:329163 original size:72 final size:68
Alignment explanation
Indices: 328879--329162 Score: 265
Period size: 72 Copynumber: 4.0 Consensus size: 68
328869 ATCGCAACAT
* * *
328879 GGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAA
1 GGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGATGAAAATCGCAA
328943 TGC
66 TGC
* *
328946 GGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGA-GAGAAT
1 GGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAACGATGAAAAT
329010 CGCAATGC
61 CGCAATGC
* * * * *
329018 GGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAAA
1 GGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAA--CG--ATGAAA
329080 ATCGCAATGC
59 ATCGCAATGC
*
329090 -GAAATGAAAATCGCAACGAGAGAATCGCAATGTGGAAATGAAAATCGCAATGCGAAATGAAAAT
1 GGAAATGAAAATCGCAACGAGAGAATCGCAATG-CGAAATGAAAATCGCAA--CG--ATGAAAAT
*
329154 CGCATTGC
61 CGCAATGC
329162 G
1 G
329163 ATTTTCATTT
Statistics
Matches: 180, Mismatches: 18, Indels: 32
0.78 0.08 0.14
Matches are distributed among these distances:
65 7 0.04
66 7 0.04
67 25 0.14
69 4 0.02
70 1 0.01
71 21 0.12
72 107 0.59
73 3 0.02
74 5 0.03
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (68 bp):
GGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGATGAAAATCGCAA
TGC
Found at i:329263 original size:19 final size:19
Alignment explanation
Indices: 329153--329255 Score: 153
Period size: 19 Copynumber: 5.6 Consensus size: 19
329143 GAAATGAAAA
329153 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
329172 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
*
329192 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
329208 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
329225 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
329244 TCGCATTGCGAT
1 TCGCATTGCGAT
329256 AGTCATTTTT
Statistics
Matches: 76, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 37 0.49
20 19 0.25
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:329381 original size:14 final size:14
Alignment explanation
Indices: 329362--329398 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
329352 CATCAATTAC
329362 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
329376 ACAAATCATCTTTT
1 ACAAATCAACTTTT
329390 ACAAATCAA
1 ACAAATCAA
329399 TTAAATAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:330078 original size:19 final size:19
Alignment explanation
Indices: 330036--330213 Score: 177
Period size: 19 Copynumber: 9.6 Consensus size: 19
330026 TAGTTTACTT
* *
330036 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TCAAAA
* *
330056 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATCAAAA
* * *
330075 TCGCAATGAGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
330094 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
330113 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
330132 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
330151 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAATCAAAA
* *
330165 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
330184 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
330203 TCGCAATGCGA
1 TCGCAACGCGA
330214 TTTTGGTTTC
Statistics
Matches: 135, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
14 9 0.07
15 1 0.01
16 2 0.01
17 2 0.01
18 1 0.01
19 108 0.80
20 12 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATCAAAA
Found at i:330185 original size:52 final size:55
Alignment explanation
Indices: 330052--330208 Score: 194
Period size: 52 Copynumber: 2.9 Consensus size: 55
330042 CACGAAACTT
* * * **
330052 AAAATCGCAACGCGAAATGAGAATCGCAATGAGAAACCAAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAAC-CG-AACC
**
330109 AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAA-CG-A-C
1 AAAATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACCGAACC
* *
330161 AGAATCGCAATGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAA
1 AAAATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAA
330209 TGCGATTTTG
Statistics
Matches: 89, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
52 45 0.51
53 1 0.01
55 2 0.02
57 41 0.46
ACGTcount: A:0.48, C:0.24, G:0.19, T:0.10
Consensus pattern (55 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACCGAACC
Found at i:330225 original size:19 final size:19
Alignment explanation
Indices: 330203--330267 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
330193 GAAATGAAAA
*
330203 TCGCAATGCGATTTTGGTT
1 TCGCATTGCGATTTTGGTT
*
330222 TCGCGTTGCGATTTT-G--
1 TCGCATTGCGATTTTGGTT
330238 TCG--TTGCGATTTTGGTT
1 TCGCATTGCGATTTTGGTT
330255 TCGCATTGCGATT
1 TCGCATTGCGATT
330268 CTGTCGTTGC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 3 0.08
17 3 0.08
18 1 0.03
19 21 0.54
ACGTcount: A:0.11, C:0.17, G:0.28, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTGGTT
Found at i:330244 original size:14 final size:14
Alignment explanation
Indices: 330225--330283 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
330215 TTTGGTTTCG
330225 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
330239 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
330256 CGCATTGCGATTCTGT
1 CG--TTGCGATTTTGT
330272 CGTTGCGATTTT
1 CGTTGCGATTTT
330284 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 21 0.55
15 1 0.03
16 3 0.08
17 3 0.08
18 1 0.03
19 9 0.24
ACGTcount: A:0.08, C:0.17, G:0.27, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:330251 original size:33 final size:33
Alignment explanation
Indices: 330209--330332 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
330199 AAAATCGCAA
*
330209 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
*
330242 TGCGATTTTGGTTTCGCATTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
330275 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
330308 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
330333 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 69 0.85
34 12 0.15
ACGTcount: A:0.10, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:330589 original size:93 final size:93
Alignment explanation
Indices: 330430--330838 Score: 791
Period size: 93 Copynumber: 4.4 Consensus size: 93
330420 TCAGGGTATT
330430 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
330495 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
330523 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
330588 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
330616 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
* *
330681 CACTATTTCACAGTGTAAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
330709 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
330774 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
330802 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
330839 AAGCAATCTA
Statistics
Matches: 311, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 311 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:332556 original size:20 final size:20
Alignment explanation
Indices: 332525--332621 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
332515 TTTTGGTTGA
332525 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
332545 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
332565 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
332584 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
332599 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
332619 AAT
1 AAT
332622 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:332577 original size:21 final size:21
Alignment explanation
Indices: 332523--332587 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
332513 TCTTTTGGTT
332523 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
332544 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
332564 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
332585 GAA
1 GAA
332588 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:332591 original size:14 final size:14
Alignment explanation
Indices: 332572--332628 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
332562 GAGAAATGAA
332572 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
332586 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
332605 AATCGCAACGAGAG
1 AATCGCAACGAGAG
332619 AATCGCAACG
1 AATCGCAACG
332629 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:332604 original size:33 final size:33
Alignment explanation
Indices: 332523--332645 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
332513 TCTTTTGGTT
*
332523 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
332564 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
332597 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
332630 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
332646 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:332681 original size:14 final size:14
Alignment explanation
Indices: 332662--332718 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
332652 TTTGGTTTCG
332662 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
332676 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
332695 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
332709 CGTTGCGATT
1 CGTTGCGATT
332719 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:332694 original size:33 final size:33
Alignment explanation
Indices: 332646--332725 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
332636 AAAATCGCAA
**
332646 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
332679 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
332712 TGCGATTTTCATTT
1 TGCGATTTTCATTT
332726 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:332731 original size:21 final size:21
Alignment explanation
Indices: 332706--332779 Score: 89
Period size: 21 Copynumber: 3.5 Consensus size: 21
332696 GTTGCGATTC
332706 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
*
332727 TCTCGTTGC-ATATAGTCA-TTT
1 TCTCGTTGCGAT-T-TTCATTTT
* *
332748 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
332769 TCTCGTTGCGA
1 TCTCGTTGCGA
332780 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
20 5 0.11
21 34 0.77
22 5 0.11
ACGTcount: A:0.15, C:0.20, G:0.16, T:0.49
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:332901 original size:33 final size:33
Alignment explanation
Indices: 332859--332929 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
332849 AATACTAACT
332859 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
332892 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
332925 TGAAA
1 TGAAA
332930 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:333334 original size:20 final size:20
Alignment explanation
Indices: 333309--333502 Score: 239
Period size: 20 Copynumber: 9.7 Consensus size: 20
333299 CTTTAAAAAT
333309 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
333329 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
333349 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* *
333370 CGCGTTGTGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
333390 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
333410 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
333430 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
333450 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
333470 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
333490 CGCGTTGCGATTT
1 CGCGTTGCGATTT
333503 TGGAAACTGA
Statistics
Matches: 151, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
20 133 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:333832 original size:22 final size:23
Alignment explanation
Indices: 333787--333835 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
333777 ACCCAGATCG
*
333787 TTGACTTTGACCTTGGGTTAACT
1 TTGACTTTGACCTAGGGTTAACT
* *
333810 TTGACTTTGATC-AGGGTTGACT
1 TTGACTTTGACCTAGGGTTAACT
333832 TTGA
1 TTGA
333836 TAAAAAAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.18, C:0.14, G:0.24, T:0.43
Consensus pattern (23 bp):
TTGACTTTGACCTAGGGTTAACT
Found at i:334655 original size:22 final size:22
Alignment explanation
Indices: 334626--334678 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
334616 TCGAATCGTA
* *
334626 AGCCTCTACGAAAACGCGTCTC
1 AGCCTCTACGAAAACACGTATC
*
334648 GGCCTCTACGAAAACACGTATC
1 AGCCTCTACGAAAACACGTATC
334670 AGCCTCTAC
1 AGCCTCTAC
334679 TTAGTTCACC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.28, C:0.36, G:0.17, T:0.19
Consensus pattern (22 bp):
AGCCTCTACGAAAACACGTATC
Found at i:341374 original size:84 final size:83
Alignment explanation
Indices: 341245--341963 Score: 687
Period size: 84 Copynumber: 8.7 Consensus size: 83
341235 AACTCATCAT
* * *
341245 GTCTTTGGTTGGCAGATAGTCCTTCTCGACTTAAGATATGCTGCAAATGATGTGCCTCAGAGCTG
1 GTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTC-GAGCTG
*
341310 AGCGTAGTCAAACTCGAAG
65 AGCGTAGTCGAACTCGAAG
* * * * ** * *
341329 GTCTTTGGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTACCTTGGAGCTG
1 GTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC-TCGAGCTG
* *
341394 GGCGTAGTCGAACTCAAAG
65 AGCGTAGTCGAACTCGAAG
* *
341413 GTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCT
1 GTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG-CCTCG-AGCT
* * * *
341478 GAGTGTAATCAAACTCGAGG
64 GAGCGTAGTCGAACTCGAAG
*
341498 GTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCTG
1 GTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC-TCGAGCTG
*
341559 AGCGTAGTCGAACTCAAAG
65 AGCGTAGTCGAACTCGAAG
* * * * * * * * * *
341578 GTATTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTTCCCTCGAAGC
1 GT-CTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATG-TGCCTCG-AGC
* * **
341642 TGAGTGTAATCGAACTCGGGG
63 TGAGCGTAGTCGAACTCGAAG
* * *
341663 GTC--T--TCGGCAGATAGCCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCTTGGAGCTG
1 GTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC-TCGAGCTG
341724 AGCGTAGTCGAACTCGAAG
65 AGCGTAGTCGAACTCGAAG
* * * * * * * * * *
341743 GTATTTTGG-CGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGC
1 GT-CTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG-CCTCG-AGC
* * *
341807 TGAGTGTAATCGAACTCGAGG
63 TGAGCGTAGTCGAACTCGAAG
*
341828 GTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTG
1 GTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC-TCGAGCTG
341889 AGCGTAGTCGAACTCGAAG
65 AGCGTAGTCGAACTCGAAG
* * * * *
341908 GTCTTTGGTTGGCAAATAGCCCTTCTTGTCTTGAGCTATATTGCAAATG-T-TGCCTC
1 GTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTC
341964 AAAAAATGGC
Statistics
Matches: 510, Mismatches: 99, Indels: 55
0.77 0.15 0.08
Matches are distributed among these distances:
80 74 0.15
81 122 0.24
82 7 0.01
83 4 0.01
84 230 0.45
85 73 0.14
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (83 bp):
GTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTCGAGCTGA
GCGTAGTCGAACTCGAAG
Found at i:341933 original size:165 final size:165
Alignment explanation
Indices: 341245--341956 Score: 937
Period size: 165 Copynumber: 4.3 Consensus size: 165
341235 AACTCATCAT
** * * *
341245 GTCTTTGGTTGGCAGATAGTCCTTCTCGACTTAAGATATGCTGCAAATGATGTG-CCTC-AGAGC
1 GTCTTTGGTTGGCAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGATGTGCCCTCGA-AGC
* * * * * * * **
341308 TGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGC
65 TGAGTGTAATCAAACTCGAGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGC
* *
341373 AAATGATGTACCTTGGAGCTGGGCGTAGTCGAACTCAAAG
126 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
* * *
341413 GTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCT
1 GTCTTTGGTTGGCAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCT
341478 GAGTGTAATCAAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATG
66 GAGTGTAATCAAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATG
*
341543 ATGTGCCTTAGAGCTGAGCGTAGTCGAACTCAAAG
131 ATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
* * * * *
341578 GTATTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTTCCCTCGAAGC
1 GT-CTTTGGTTGGCAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGC
* * * *
341642 TGAGTGTAATCGAACTCGGGGGTCTTCGGCAGATAGCCCTTCTCGACTTAAGTTATACTGCAAAT
65 TGAGTGTAATCAAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAAT
*
341707 GATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
130 GATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
* * * * *
341743 GTATTTTGG-CGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGC
1 GT-CTTTGGTTGGCAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGC
*
341807 TGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAAT
65 TGAGTGTAATCAAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAAT
*
341872 GATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
130 GATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
* * * * * **
341908 GTCTTTGGTTGGCAAATAGCCCTTCTTGTCTTGAGCTATATTGCAAATG
1 GTCTTTGGTTGGCAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATG
341957 TTGCCTCAAA
Statistics
Matches: 494, Mismatches: 46, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
164 5 0.01
165 404 0.82
166 5 0.01
167 1 0.00
168 50 0.10
169 28 0.06
170 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (165 bp):
GTCTTTGGTTGGCAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCT
GAGTGTAATCAAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATG
ATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
Found at i:345748 original size:6 final size:6
Alignment explanation
Indices: 345737--345771 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
345727 TTAATTACGA
345737 AAATTT AAATTT AAATTT AAATTT AAATTT AAATT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATT
345772 ATTCGATCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
AAATTT
Found at i:349196 original size:18 final size:17
Alignment explanation
Indices: 349173--349206 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
349163 ATTCCTATTT
349173 ATTTTTATTATAATTATA
1 ATTTTTATTAT-ATTATA
*
349191 ATTTTTTTTATATTAT
1 ATTTTTATTATATTAT
349207 TACTTTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTTATTATATTATA
Found at i:359187 original size:20 final size:19
Alignment explanation
Indices: 359157--359210 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
359147 CCTAAATTGA
*
359157 AAAAAAGAAAAGAGAAAAG
1 AAAAAAGAAAAGAAAAAAG
*
359176 AGAAAAATAAAA-AATAAAAG
1 A-AAAAAGAAAAGAA-AAAAG
359196 -AAAAAGAAAAGAAAA
1 AAAAAAGAAAAGAAAA
359211 TAAGGTAGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
18 11 0.38
19 4 0.14
20 14 0.48
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (19 bp):
AAAAAAGAAAAGAAAAAAG
Found at i:359200 original size:6 final size:6
Alignment explanation
Indices: 359158--359210 Score: 56
Period size: 6 Copynumber: 8.7 Consensus size: 6
359148 CTAAATTGAA
*
359158 AAAAAG AAAAGAG AAAAGAG AAAAAT AAAAA- ATAAAAG AAAAAG -AAAAG
1 AAAAAG AAAA-AG AAAA-AG AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG
359207 AAAA
1 AAAA
359211 TAAGGTAGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
5 6 0.14
6 22 0.52
7 14 0.33
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:360451 original size:106 final size:103
Alignment explanation
Indices: 360264--360600 Score: 363
Period size: 106 Copynumber: 3.3 Consensus size: 103
360254 ACAACCTGCG
* *
360264 ATTTCAACTTCACGACGAAGGGA-ATCGTGCACACAAGACAGCACAAGCTTC-ACTTCACGACGA
1 ATTTCAACTTCACAACGAA-GGATAT--TGGACACAAGACAGCACAAGC-TCAACTTCACGACGA
*
360327 AGGGGCAGCTGACTGTCAACAAACAATTTCCCAGTTTCAGAGTCA
62 AGGGGCGGCTGACTGTCAACAAACAATTTCCCAG-TTCAGA--CA
* *
360372 ATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACACAAGACAGCACAAGCTCAACTTCACGACGAAGGG
*
360437 GCGGCTGATTGTCAACAAACAA-TT-CC----C---CA
66 GCGGCTGACTGTCAACAAACAATTTCCCAGTTCAGACA
* * * **
360466 ATTTCAACTTCACAGCGAAGGATATTGGACCCAAGATAGCACAAGCTCAACTTCACGGTGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACACAAGACAGCACAAGCTCAACTTCACGACGAAGGG
* *
360531 GCGGCTGACTGTCAACAAATAATCTCCCAGTTCCAGAACCA
66 GCGGCTGACTGTCAACAAACAATTTCCCAGTT-CAG-A-CA
** *
360572 ATTTCAACTTCACGGCGGAGGATATTGGA
1 ATTTCAACTTCACAACGAAGGATATTGGA
360601 TTCGGAACAA
Statistics
Matches: 198, Mismatches: 17, Indels: 30
0.81 0.07 0.12
Matches are distributed among these distances:
94 81 0.41
95 1 0.01
96 2 0.01
99 1 0.01
101 1 0.01
104 2 0.01
105 4 0.02
106 83 0.42
107 3 0.02
108 20 0.10
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (103 bp):
ATTTCAACTTCACAACGAAGGATATTGGACACAAGACAGCACAAGCTCAACTTCACGACGAAGGG
GCGGCTGACTGTCAACAAACAATTTCCCAGTTCAGACA
Found at i:360531 original size:94 final size:95
Alignment explanation
Indices: 360370--360558 Score: 299
Period size: 94 Copynumber: 2.0 Consensus size: 95
360360 GTTTCAGAGT
* *
360370 CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCATGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACGACGAAG
*
360435 GGGCGGCTGATTGTCAACAAACAAT-TCCC
66 GGGCGGCTGACTGTCAACAAACAATCTCCC
* * **
360464 CAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGATAGCACAAGCTCAACTTCACGGTGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACGACGAAG
*
360529 GGGCGGCTGACTGTCAACAAATAATCTCCC
66 GGGCGGCTGACTGTCAACAAACAATCTCCC
360559 AGTTCCAGAA
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
94 82 0.95
95 4 0.05
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (95 bp):
CAATTTCAACTTCACAACGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACGACGAAG
GGGCGGCTGACTGTCAACAAACAATCTCCC
Found at i:362701 original size:2 final size:2
Alignment explanation
Indices: 362694--362749 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
362684 TTATTTCTTC
362694 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
362736 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
362750 TACTATAACT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:368965 original size:102 final size:102
Alignment explanation
Indices: 368789--368992 Score: 408
Period size: 102 Copynumber: 2.0 Consensus size: 102
368779 GTTTCCTTGC
368789 CTTCCTCATGAAATTAATGTCTTAGAACACTAAGGGGTTTAATGACCCCCTTAAATAGTGTGGTG
1 CTTCCTCATGAAATTAATGTCTTAGAACACTAAGGGGTTTAATGACCCCCTTAAATAGTGTGGTG
368854 TTGTTTTCAAGAATAGAAAGTTAAATATTGATTGTGT
66 TTGTTTTCAAGAATAGAAAGTTAAATATTGATTGTGT
368891 CTTCCTCATGAAATTAATGTCTTAGAACACTAAGGGGTTTAATGACCCCCTTAAATAGTGTGGTG
1 CTTCCTCATGAAATTAATGTCTTAGAACACTAAGGGGTTTAATGACCCCCTTAAATAGTGTGGTG
368956 TTGTTTTCAAGAATAGAAAGTTAAATATTGATTGTGT
66 TTGTTTTCAAGAATAGAAAGTTAAATATTGATTGTGT
368993 TTGTCTGCTT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 102 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (102 bp):
CTTCCTCATGAAATTAATGTCTTAGAACACTAAGGGGTTTAATGACCCCCTTAAATAGTGTGGTG
TTGTTTTCAAGAATAGAAAGTTAAATATTGATTGTGT
Found at i:379331 original size:160 final size:157
Alignment explanation
Indices: 378945--379424 Score: 573
Period size: 160 Copynumber: 3.1 Consensus size: 157
378935 GAACTTAAAG
* * *
378945 TAAGGAAATTATAAAAAAAATGAGGGATTAAATTGAAAAATA-AAAATTTGTTATCAAAAAGAGA
1 TAAGGAAATTAT-AAAAAATTGAGGGACTAAATTGAAAAATAGAAAATTTGTTATCAAAAAGAGG
* * * * * *
379009 AATTGAAAGTACATATGTATTATACGATGGTTTAGGAACACGTGGTTCAAATTTGGTAAAAACAT
65 AATTGAAAGTACATATGTATTCTTCAATGGTTTAGGAGCATGTGGTTCAAATTTGGTAAAAAAAT
*
379074 -ACT----TAAAGGATGAATTGAAGAAA
130 GACTAAAATAAAAGATGAATTGAAGAAA
* * * *
379097 TAAAGAAATTATATATAAATTGAGGGACTAAATTAAAAAATAGAAAATTTGTTATAAAAAAGAGG
1 TAAGGAAATTATA-AAAAATTGAGGGACTAAATTGAAAAATAGAAAATTTGTTATCAAAAAGAGG
* * * * *
379162 AACTGAAAGTGCATACGTATTCTTCCATGGTTTAGGAGTATGTGGTTCAAATTTGGTAAAACAAA
65 AATTGAAAGTACATATGTATTCTTCAATGGTTTAGGAGCATGTGGTTCAAATTTGGTAAAA-AAA
*
379227 TGGACATAAAATAAAAGAGGAATTGAAGAAA
129 T-GAC-TAAAATAAAAGATGAATTGAAGAAA
*
379258 TAAGGAAATTATAAAAAATTGAGGGACTAAATTGAAAAATAGAAAATTTTTTATCAAAAAGAGGA
1 TAAGGAAATTATAAAAAATTGAGGGACTAAATTGAAAAATAGAAAATTTGTTATCAAAAAGAGGA
* * * *
379323 ATTGAAAGTATATATGTATTCTAT-AATAGTTTAGGAGCATGTGGTTCAATTTTGGT-AAAAAAC
66 ATTGAAAGTACATATGTATTCT-TCAATGGTTTAGGAGCATGTGGTTCAAATTTGGTAAAAAAAT
*
379386 GAACTTAAAAT-AAAGAATGAATTGAAGGAA
130 G-AC-TAAAATAAAAG-ATGAATTGAAGAAA
*
379416 TAATGAAAT
1 TAAGGAAAT
379425 CAGGGATTTA
Statistics
Matches: 278, Mismatches: 37, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
151 1 0.00
152 35 0.13
153 72 0.26
154 3 0.01
156 2 0.01
157 6 0.02
158 31 0.11
159 3 0.01
160 94 0.34
161 31 0.11
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.28
Consensus pattern (157 bp):
TAAGGAAATTATAAAAAATTGAGGGACTAAATTGAAAAATAGAAAATTTGTTATCAAAAAGAGGA
ATTGAAAGTACATATGTATTCTTCAATGGTTTAGGAGCATGTGGTTCAAATTTGGTAAAAAAATG
ACTAAAATAAAAGATGAATTGAAGAAA
Found at i:380000 original size:59 final size:59
Alignment explanation
Indices: 379882--380003 Score: 140
Period size: 59 Copynumber: 2.1 Consensus size: 59
379872 GTCGGGTGAA
* *
379882 CATTTTGTAACTTTTAATAGTCGAGAGACTAAAAAAGTAACGTCCTATAATTGATGGAC
1 CATTTTGTAACTTTTAATAGTCGAGAGACTAAAAAAGTAACGCCCTATAATTGAGGGAC
* * * ** *
379941 CATTTTGTACCTTTTAATAGTC-AGTGACTTAACAAAGTAGTGCCCTATAGTT-AGGGGAC
1 CATTTTGTAACTTTTAATAGTCGAGAGAC-TAAAAAAGTAACGCCCTATAATTGA-GGGAC
380000 CATT
1 CATT
380004 AGTGTACTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
58 6 0.11
59 47 0.89
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Consensus pattern (59 bp):
CATTTTGTAACTTTTAATAGTCGAGAGACTAAAAAAGTAACGCCCTATAATTGAGGGAC
Found at i:393269 original size:18 final size:18
Alignment explanation
Indices: 393246--393280 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
393236 CCAACATTTT
*
393246 CCCAAATCTTAGAAAATC
1 CCCAAAACTTAGAAAATC
*
393264 CCCAAAACTTTGAAAAT
1 CCCAAAACTTAGAAAAT
393281 TTTAATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.26, G:0.06, T:0.23
Consensus pattern (18 bp):
CCCAAAACTTAGAAAATC
Found at i:395188 original size:20 final size:19
Alignment explanation
Indices: 395165--395211 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
395155 CGATATACCA
395165 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
395185 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
395205 GGTAAAA
1 GGTAAAA
395212 TGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:395307 original size:181 final size:182
Alignment explanation
Indices: 394953--395425 Score: 678
Period size: 181 Copynumber: 2.6 Consensus size: 182
394943 GATCCAAATT
* * * **
394953 AAAAATATGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
** * * * *
395018 AAACCGGTAAAGCGCTATCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAATGATACCGGATACATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* *
395083 GTGAATTTAAAAGAGAAGCAGTTCTAAATCCTATAAAGTGTCGATACTTTTA
131 GTGAATTTAAAAGAGAAGCAGTTCTAAAGCCTATAAAGTGTCGATACTTTAA
* * *
395135 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * *
395200 AAACCGGTAAAATGTTACCGGATACATTGAAAGTGTCGATACTTT-ATATAATGATCGACACTTT
66 AAACCGGTAAAATGATACCGGATACATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* * ** *
395264 GTGAATTTAAAAGAGAAGCATTTTTAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTCTAAAGCCTATAAAGTGTCGATACTTTAA
*
395316 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * *
395381 AAACTGATAAAATCATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAATGATACCGGATACATTGAAAGTGTCGATACTTT
395426 CGTAAGTACG
Statistics
Matches: 259, Mismatches: 32, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
181 163 0.63
182 96 0.37
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAATGATACCGGATACATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTCTAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:395369 original size:20 final size:20
Alignment explanation
Indices: 395346--395384 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
395336 CGATATAACA
395346 GGTA-AAAATATGATAAAACC
1 GGTATAAAA-ATGATAAAACC
*
395366 GGTATCAAAATGATAAAAC
1 GGTATAAAAATGATAAAAC
395385 TGATAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.54, C:0.10, G:0.15, T:0.21
Consensus pattern (20 bp):
GGTATAAAAATGATAAAACC
Found at i:397528 original size:15 final size:15
Alignment explanation
Indices: 397508--397536 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
397498 GTTGTATTGG
397508 GGGATGACGGTGAGT
1 GGGATGACGGTGAGT
397523 GGGATGACGGTGAG
1 GGGATGACGGTGAG
397537 GGAAAACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.55, T:0.17
Consensus pattern (15 bp):
GGGATGACGGTGAGT
Found at i:397680 original size:21 final size:21
Alignment explanation
Indices: 397621--397685 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
397611 AAGACAATCA
* *
397621 AGAGTCGAAGAGAAACTAGAT
1 AGAGTCGAAGAGAAACTTGAG
*
397642 AGAGTCGAGGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
397663 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
397684 AG
1 AG
397686 GCATAAGGGG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.42, C:0.11, G:0.32, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:397761 original size:33 final size:33
Alignment explanation
Indices: 397719--397784 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
397709 AAATAGATGG
*
397719 AGTGGTGAAAGAAGTAGAGGTATTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTATTAAGGGGTGA
* * *
397752 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTATTAAGGGGTGA
397785 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTATTAAGGGGTGA
Found at i:399603 original size:19 final size:19
Alignment explanation
Indices: 399579--399627 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
399569 AATGTAGGGT
399579 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
399598 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
399617 TAATTTTGTAT
1 TAATTTTGTAT
399628 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:400724 original size:389 final size:391
Alignment explanation
Indices: 399740--400818 Score: 1642
Period size: 396 Copynumber: 2.8 Consensus size: 391
399730 AATTTACAAT
* *
399740 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCTATATATAAAAAGTGTCGATTCCAAAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGA-TCCCAAAACAT
* * * *
399805 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTGCAAGTATACCAGTTTT
65 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * * *
399870 TTGAGATAATAGGTCTAAATAATATATCGAAACTTTTGTAGTTTGTGTCGATATTTCTGGTCCAA
130 ATGAGATAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTCTGGTCCAG
*
399935 AATGAATGGCAAACAGGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAA
195 AATGAATGGCAAACAGGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
* * *
400000 AACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTGCAAGTATACCG
260 AACATCGAAACCCAAAAGTATAATGTAATATGT-A------AATCTAACCGGTACAAGTATACCG
*
400065 GTTTATGAGAGAAGAATAGGTAATAATGTATCGACACTTTTGTAGTTTATGTCGATATTTCTGGT
318 GTTTATGAGAGAAGAATAGCTAATAATGTATCGACACTTTTGTAGTTTATGTCGATATTTCTGGT
400130 CCAGAATGA
383 CCAGAATGA
* *
400139 ATGGCAAACAGGCTGCAACCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATTCCC-CAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGA-TCCCAAAACAT
**
400201 CGAAAATCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
65 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
400266 ATGAGATAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTCTGGTCTAG
130 ATGAGATAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTCTGGTCCAG
400331 AATGAATGGCAAACAGGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
195 AATGAATGGCAAACAGGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
*
400396 AACATCGAAAACCAAAAGTATAATGTAATATGTAAATCTAACCGGTACAAGTATACCGGTTTTAT
260 AACATCGAAACCCAAAAGTATAATGTAATATGTAAATCTAACCGGTACAAGTATACCGG-TTTAT
* * * *
400461 GAGAGAA-TAT-GTCTAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGA
324 GAGAGAAGAATAG-CTAATAATGTATCGACACTTTTGTAGTTTATGTCGATATTTCTGGTCCAGA
400524 ATGA
388 ATGA
*
400528 ATGGCAAACAGGGTGCAACCATAGAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCA-AAACAT
400593 CGAAACCCAAAAGTA-AATGTAATATGTAA-TTTTCAATCTAACCGGTACAAGTATA-CGGTTTT
65 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
400655 ATGAGATAATAGGTCTAAATAATGT-GCG-CACTTTTTTTTGTTTGTGTGTCGATATTT-TGGTC
130 ATGAGATAATAGGTCTAAATAATGTATCGACAC-TTTTGTAG-TT-TGTGTCGATATTTCTGGTC
* * *
400717 CAGAATGAATGGAAAACAGGGTGC-ACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC
192 CAGAATGAATGGCAAACAGGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC
*
400781 ATAAACATCGAAACCCATAAGTATAATGTAATATGTAA
257 ATAAACATCGAAACCCAAAAGTATAATGTAATATGTAA
400819 TTTTTCAATC
Statistics
Matches: 632, Mismatches: 39, Indels: 29
0.90 0.06 0.04
Matches are distributed among these distances:
387 3 0.00
388 84 0.13
389 169 0.27
390 55 0.09
391 30 0.05
392 18 0.03
395 1 0.00
396 219 0.35
397 20 0.03
399 33 0.05
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (391 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAACATC
GAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTA
TGAGATAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTCTGGTCCAGA
ATGAATGGCAAACAGGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAA
ACATCGAAACCCAAAAGTATAATGTAATATGTAAATCTAACCGGTACAAGTATACCGGTTTATGA
GAGAAGAATAGCTAATAATGTATCGACACTTTTGTAGTTTATGTCGATATTTCTGGTCCAGAATG
A
Found at i:400905 original size:197 final size:200
Alignment explanation
Indices: 399740--400886 Score: 1707
Period size: 197 Copynumber: 5.8 Consensus size: 200
399730 AATTTACAAT
* * * *
399740 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCTATATATAAAAAGTGTCGATTCCAAAAACAT
1 ATGGCAAACAGGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * * *
399805 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTGCAAGTATACCAGTTTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * * *
399870 TTGAGATAATAGGTCTAAATAATATATCGAAACTTTTGTAGTTTGTGTCGATATTTCTGGTCCAA
131 ATGAGATAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTCTGGTCCAG
399935 AATGA
196 AATGA
*
399940 ATGGCAAACAGGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGCAAACAGGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * *
400005 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTGCAAGTATACCGG-TTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
400069 ATGAGAGAAGAATAGG--T-AATAATGTATCGACACTTTTGTAGTTTATGTCGATATTTCTGGTC
131 AT--GAG-ATAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTCTGGTC
400131 CAGAATGA
193 CAGAATGA
*
400139 ATGGCAAACAGGCTGCAACCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATTCCC--CAACA
1 ATGGCAAACAGGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGA-TCCCATAAACA
**
400200 TCGAAAATCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
65 TCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
*
400265 TATGAGATAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTCTGGTCTA
130 TATGAGATAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTCTGGTCCA
400330 GAATGA
195 GAATGA
400336 ATGGCAAACAGGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
400401 CGAAAACCAAAAGTATAATGTAATATGT-A------AATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * * *
400459 ATGAGAGAATATGTCT-AATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGATAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTCTGGTCCAG
400523 AATGA
196 AATGA
* *
400528 ATGGCAAACAGGGTGCAACCATAGAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
400593 CGAAACCCAAAAGTA-AATGTAATATGTAA-TTTTCAATCTAACCGGTACAAGTATA-CGGTTTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
400655 ATGAGATAATAGGTCTAAATAATGT-GCG-CACTTTTTTTTGTTTGTGTGTCGATATTT-TGGTC
131 ATGAGATAATAGGTCTAAATAATGTATCGACAC-TTTTGTAG-TT-TGTGTCGATATTTCTGGTC
400717 CAGAATGA
193 CAGAATGA
* * *
400725 ATGGAAAACAGGGTGC-ACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
400789 CGAAACCCATAAGTATAATGTAATATGTAATTTTTCAATCTAA-CGGTACAAGTATA-CGG-TTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
400851 ATGAGATAATAGGTCTAAATAATATGTATCGACACT
131 ATGAGATAATAGGTCTAAAT-A-ATGTATCGACACT
400887 GTTTAATGTT
Statistics
Matches: 880, Mismatches: 39, Indels: 57
0.90 0.04 0.06
Matches are distributed among these distances:
191 12 0.01
192 128 0.15
193 43 0.05
194 7 0.01
195 6 0.01
196 174 0.20
197 197 0.22
198 37 0.04
199 108 0.12
200 158 0.18
201 3 0.00
202 7 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (200 bp):
ATGGCAAACAGGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGATAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTCTGGTCCAG
AATGA
Found at i:401024 original size:267 final size:272
Alignment explanation
Indices: 400685--401224 Score: 995
Period size: 267 Copynumber: 2.0 Consensus size: 272
400675 AATGTGCGCA
*
400685 CTTTTTTTTGTTTGTGTGTCGATATTTTGGTCCAGAATGAATGGAAAACAGGGTGCACAATAAAG
1 CTTTTTTTAGTTTGTGTGTCGATATTTTGGTCCAGAATGAATGGAAAACAGGGTGCACAATAAAG
400750 TGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAT
66 TGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAT
400815 GTAATTTTTCAATCTAA-CGGTACAAGTATA-CGG-TTTATGAGATAATAGGTCTAAATAATATG
131 GTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGATAATAGGTCTAAATAATATG
400877 TATCGACACTGTTTAATGTTTTGTCGATACTAATTTAAATATCAAGTGTTTT-CACCGTTCACTA
196 TATCGACACTGTTTAATGTTTTGTCGATACTAATTTAAATATCAAGTGTTTTCCACCGTTCACTA
400941 TATATAGTACTC
261 TATATAGTACTC
400953 CTTTTTTTAG-TT-TGTGTCGATATTTTGGTCCAGAA-GAATGGAAAACAGGGTGCAAACAATAA
1 CTTTTTTTAGTTTGTGTGTCGATATTTTGGTCCAGAATGAATGGAAAACAGGGTGC--ACAATAA
401015 AGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAAT
64 AGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAAT
401080 ATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGATAATAGGTCTAAATAATA
129 ATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGATAATAGGTCTAAATAATA
401145 TGTATCGACACTGTTTAATGTTTTGTCGATACTAATTTAAATATCAAGTGTTTTCCCACCGTTCA
194 TGTATCGACACTGTTTAATGTTTTGTCGATACTAATTTAAATATCAAGTGTTTT-CCACCGTTCA
401210 CTATATATAGTACTC
258 CTATATATAGTACTC
401225 TAAATCGAAA
Statistics
Matches: 264, Mismatches: 1, Indels: 10
0.96 0.00 0.04
Matches are distributed among these distances:
265 18 0.07
266 23 0.09
267 93 0.35
268 22 0.08
269 3 0.01
270 81 0.31
272 24 0.09
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (272 bp):
CTTTTTTTAGTTTGTGTGTCGATATTTTGGTCCAGAATGAATGGAAAACAGGGTGCACAATAAAG
TGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAT
GTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGATAATAGGTCTAAATAATATG
TATCGACACTGTTTAATGTTTTGTCGATACTAATTTAAATATCAAGTGTTTTCCACCGTTCACTA
TATATAGTACTC
Found at i:402518 original size:18 final size:18
Alignment explanation
Indices: 402497--402620 Score: 122
Period size: 18 Copynumber: 6.9 Consensus size: 18
402487 CAAGCGCTCA
*
402497 ATGAAGATGAAGCTGACG
1 ATGAAGATGAAGATGACG
* *
402515 ATGAAGATGACGATGAAG
1 ATGAAGATGAAGATGACG
* *
402533 ATGACGATGATGATGACG
1 ATGAAGATGAAGATGACG
* * *
402551 ATGATGATGACGATGAAG
1 ATGAAGATGAAGATGACG
* *
402569 CTGACGATGAAGATGACG
1 ATGAAGATGAAGATGACG
* *
402587 ATGAAGATGATGACGACG
1 ATGAAGATGAAGATGACG
* *
402605 ATGATGATGATGATGA
1 ATGAAGATGAAGATGA
402621 TCCAAACAAG
Statistics
Matches: 87, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 87 1.00
ACGTcount: A:0.38, C:0.09, G:0.33, T:0.20
Consensus pattern (18 bp):
ATGAAGATGAAGATGACG
Found at i:402621 original size:6 final size:6
Alignment explanation
Indices: 402510--402620 Score: 114
Period size: 6 Copynumber: 18.5 Consensus size: 6
402500 AAGATGAAGC
* * * *
402510 TGACGA TGAAGA TGACGA TGAAGA TGACGA TGATGA TGACGA TGATGA
1 TGACGA TGACGA TGACGA TGACGA TGACGA TGACGA TGACGA TGACGA
* * * * * *
402558 TGACGA TGAAGC TGACGA TGAAGA TGACGA TGAAGA TGATGA CGACGA
1 TGACGA TGACGA TGACGA TGACGA TGACGA TGACGA TGACGA TGACGA
* *
402606 TGATGA TGATGA TGA
1 TGACGA TGACGA TGA
402621 TCCAAACAAG
Statistics
Matches: 85, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 85 1.00
ACGTcount: A:0.37, C:0.09, G:0.33, T:0.21
Consensus pattern (6 bp):
TGACGA
Found at i:402621 original size:12 final size:12
Alignment explanation
Indices: 402497--402620 Score: 158
Period size: 12 Copynumber: 10.3 Consensus size: 12
402487 CAAGCGCTCA
*
402497 ATGAAGATGAAG
1 ATGACGATGAAG
*
402509 CTGACGATGAAG
1 ATGACGATGAAG
402521 ATGACGATGAAG
1 ATGACGATGAAG
*
402533 ATGACGATGATG
1 ATGACGATGAAG
*
402545 ATGACGATGATG
1 ATGACGATGAAG
402557 ATGACGATGAAG
1 ATGACGATGAAG
*
402569 CTGACGATGAAG
1 ATGACGATGAAG
402581 ATGACGATGAAG
1 ATGACGATGAAG
* * *
402593 ATGATGACGACG
1 ATGACGATGAAG
* *
402605 ATGATGATGATG
1 ATGACGATGAAG
402617 ATGA
1 ATGA
402621 TCCAAACAAG
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 100 1.00
ACGTcount: A:0.38, C:0.09, G:0.33, T:0.20
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:404234 original size:183 final size:183
Alignment explanation
Indices: 403824--404930 Score: 1856
Period size: 183 Copynumber: 6.1 Consensus size: 183
403814 CAAAGTTTTC
* *
403824 ACACTTTTTAATATTGTGTCTGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCATT-
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACC-TTG
* *** *
403888 TCAAAAAGTGTCGATTGAAAAAAACATCGGAACCCAGAA-T-TAATGTAATAGATAATTTTGTAA
65 TCAAAAAGTGTCGA--CATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAA
403951 TATAACCGGTAT-AA-ATA-CGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
128 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
404004 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGAAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
404069 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
* *
404134 AACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
404187 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTAT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
*
404252 CAAAAAGTGTCGACATTTGCACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
404317 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* *
404370 ACACTTTTTAATATTGTGTCGGTATTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTAT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
*
404435 CAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
* *
404500 AACTGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACATATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
404553 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
*
404618 CAAAAAGTGTCGACATTTACACATCGGAACCCAAAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
404683 AACC-GTATAAATATACCGGTTTT-TGAGCGAATAGG--TACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
404732 ACACTTTTTAATATTGTGTCGGTACTTTATGCCCAGATTGGAAG-AAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
*
404796 CAAAAAGTGTC-A-ATTTTACACATCGAAACCCAG-ATTATAATGTAATAGAT-A-TTTGTAATA
66 CAAAAAGTGTCGACA-TTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
*
404856 TAACCGGTAT-AATATACC-GTTTT-TGAGCGAATAGGTCTACAACCTATATCA
130 TAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
404907 ACACTTTTTAATATTGTGTCGGTA
1 ACACTTTTTAATATTGTGTCGGTA
404931 ATTTTAAGTA
Statistics
Matches: 888, Mismatches: 29, Indels: 25
0.94 0.03 0.03
Matches are distributed among these distances:
173 17 0.02
174 22 0.02
175 42 0.05
176 18 0.02
177 18 0.02
178 49 0.06
179 59 0.07
180 107 0.12
181 14 0.02
182 22 0.02
183 520 0.59
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:407714 original size:23 final size:23
Alignment explanation
Indices: 407683--407755 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
407673 ATAGGTAAAA
* *
407683 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGTGCTT
* *
407706 ATATAATGTAATATGTAGTGTTT
1 ATATAATGTAATAGGTAGTGCTT
*
407729 ATATAATGTAATAGATAGTGCTT
1 ATATAATGTAATAGGTAGTGCTT
407752 ATAT
1 ATAT
407756 TATAAAGTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:410388 original size:3 final size:3
Alignment explanation
Indices: 410380--410442 Score: 99
Period size: 3 Copynumber: 21.0 Consensus size: 3
410370 TATCTGCTCT
* * *
410380 TGA TGA TGA TGA TCA TGA TAA TGA TGA TGA TGA TGA TGA TTA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
410428 TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA
410443 GAGTGAGGAT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:417509 original size:14 final size:14
Alignment explanation
Indices: 417489--417522 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
417479 TTCTTTAAAC
417489 TTTTCTTTT-TTAT
1 TTTTCTTTTGTTAT
417502 TGTTTCTTTTGTTAT
1 T-TTTCTTTTGTTAT
417517 TTTTCT
1 TTTTCT
417523 CTTCTTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 13 0.68
15 5 0.26
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.79
Consensus pattern (14 bp):
TTTTCTTTTGTTAT
Found at i:419915 original size:159 final size:159
Alignment explanation
Indices: 419626--419944 Score: 638
Period size: 159 Copynumber: 2.0 Consensus size: 159
419616 TAAGGGCAGT
419626 ATCAGTACTGCAATTTAGATTATCAATACTACTATTAAAAGTTGTAGTGGTACGGAAATAGTATC
1 ATCAGTACTGCAATTTAGATTATCAATACTACTATTAAAAGTTGTAGTGGTACGGAAATAGTATC
419691 AGTACCAAAATAGTTTACTTGAATTTGTAAAACGAAAGGAGTATCGATATTACCTTAAATAGTAT
66 AGTACCAAAATAGTTTACTTGAATTTGTAAAACGAAAGGAGTATCGATATTACCTTAAATAGTAT
419756 CAGTGTTGTTGTGTACTTTTAAAGCATCA
131 CAGTGTTGTTGTGTACTTTTAAAGCATCA
419785 ATCAGTACTGCAATTTAGATTATCAATACTACTATTAAAAGTTGTAGTGGTACGGAAATAGTATC
1 ATCAGTACTGCAATTTAGATTATCAATACTACTATTAAAAGTTGTAGTGGTACGGAAATAGTATC
419850 AGTACCAAAATAGTTTACTTGAATTTGTAAAACGAAAGGAGTATCGATATTACCTTAAATAGTAT
66 AGTACCAAAATAGTTTACTTGAATTTGTAAAACGAAAGGAGTATCGATATTACCTTAAATAGTAT
419915 CAGTGTTGTTGTGTACTTTTAAAGCATCA
131 CAGTGTTGTTGTGTACTTTTAAAGCATCA
419944 A
1 A
419945 CACCAGTAAT
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 160 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (159 bp):
ATCAGTACTGCAATTTAGATTATCAATACTACTATTAAAAGTTGTAGTGGTACGGAAATAGTATC
AGTACCAAAATAGTTTACTTGAATTTGTAAAACGAAAGGAGTATCGATATTACCTTAAATAGTAT
CAGTGTTGTTGTGTACTTTTAAAGCATCA
Found at i:421985 original size:2 final size:2
Alignment explanation
Indices: 421978--422021 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
421968 AATAATAAAC
* * *
421978 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
422020 TA
1 TA
422022 ACAGAAACAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
TA
Found at i:426615 original size:20 final size:20
Alignment explanation
Indices: 426590--426629 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
426580 TTTTAATTGA
* *
426590 TTATTATTATTATTATTATT
1 TTATTAATAATATTATTATT
*
426610 TTATTAATAATATTTTTATT
1 TTATTAATAATATTATTATT
426630 GTTTTCTTAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTAATAATATTATTATT
Found at i:431571 original size:61 final size:61
Alignment explanation
Indices: 431476--431598 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
431466 AATAATTGGC
431476 GATCTCAAAGGATGTCAAGAACAATACGAAGGCGTCTATCATGTTATTCCTCATATCGTGA
1 GATCTCAAAGGATGTCAAGAACAATACGAAGGCGTCTATCATGTTATTCCTCATATCGTGA
431537 GATCTCAAAGGATGTCAAGAACAATACGAAGGCGTCTATCATGTTATTCCTCATATCGTGA
1 GATCTCAAAGGATGTCAAGAACAATACGAAGGCGTCTATCATGTTATTCCTCATATCGTGA
431598 G
1 G
431599 TACACGAGGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (61 bp):
GATCTCAAAGGATGTCAAGAACAATACGAAGGCGTCTATCATGTTATTCCTCATATCGTGA
Found at i:440175 original size:7 final size:7
Alignment explanation
Indices: 440163--440192 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
440153 TTCTCCAGAG
440163 CTTTCTT
1 CTTTCTT
440170 CTTTCTT
1 CTTTCTT
440177 CTTTCTT
1 CTTTCTT
440184 C-TTCTT
1 CTTTCTT
440190 CTT
1 CTT
440193 CATACGTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (7 bp):
CTTTCTT
Found at i:441617 original size:30 final size:30
Alignment explanation
Indices: 441577--441649 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
441567 GGTTCTTCGG
*
441577 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
441607 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
441637 GACCTCTGGATAG
1 GACCTCTGGATAG
441650 GTCCTTCGGG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:441807 original size:19 final size:19
Alignment explanation
Indices: 441780--441828 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
441770 ACTGGATATG
*
441780 ATGATATGTTTGTTTCCTT
1 ATGAAATGTTTGTTTCCTT
*
441799 ATGAAATGTTTTTTTTCCTT
1 ATGAAATG-TTTGTTTCCTT
441819 ATGAAATGTT
1 ATGAAATGTT
441829 ATGTGTGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.22, C:0.08, G:0.14, T:0.55
Consensus pattern (19 bp):
ATGAAATGTTTGTTTCCTT
Found at i:444719 original size:20 final size:20
Alignment explanation
Indices: 444694--444732 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
444684 AAGTGCAACT
444694 GAAGCATCAGAA-TGTTGTTA
1 GAAGCA-CAGAAGTGTTGTTA
*
444714 GAAGCACTGAAGTGTTGTT
1 GAAGCACAGAAGTGTTGTT
444733 TGTACCCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.31, C:0.10, G:0.28, T:0.31
Consensus pattern (20 bp):
GAAGCACAGAAGTGTTGTTA
Found at i:445677 original size:3 final size:3
Alignment explanation
Indices: 445671--445733 Score: 85
Period size: 3 Copynumber: 21.7 Consensus size: 3
445661 TCCAATAATA
* * *
445671 TAT TAT TAT TAT TAT TAT TAT TA- TAT TAC AAT TAT TAT TAT CA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
445717 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
445734 CAAATATTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 3 0.06
3 49 0.94
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:445704 original size:20 final size:20
Alignment explanation
Indices: 445681--445733 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
445671 TATTATTATT
445681 ATTATTATTATTATATTACA
1 ATTATTATTATTATATTACA
* **
445701 ATTATTATTATCATATTATT
1 ATTATTATTATTATATTACA
445721 ATTATTATTATTA
1 ATTATTATTATTA
445734 CAAATATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTATTATTATTATATTACA
Found at i:446172 original size:18 final size:18
Alignment explanation
Indices: 446149--446186 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
446139 TTCCCTACAA
446149 AAAAAGGA-ACACAACGGG
1 AAAAAGGAGA-ACAACGGG
446167 AAAAAGGAGAACAACGGG
1 AAAAAGGAGAACAACGGG
446185 AA
1 AA
446187 GAACGGGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.58, C:0.13, G:0.29, T:0.00
Consensus pattern (18 bp):
AAAAAGGAGAACAACGGG
Found at i:447647 original size:9 final size:9
Alignment explanation
Indices: 447633--447665 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
447623 TATCTTATGC
447633 TAATTAATT
1 TAATTAATT
447642 TAATTAATT
1 TAATTAATT
*
447651 TTA-TAATT
1 TAATTAATT
447659 TAATTAA
1 TAATTAA
447666 AGAATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TAATTAATT
Found at i:449554 original size:15 final size:15
Alignment explanation
Indices: 449534--449569 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
449524 CCGAACAAAA
449534 CATGAAACTAGAAAG
1 CATGAAACTAGAAAG
**
449549 CATGAAGTTAGAAAG
1 CATGAAACTAGAAAG
449564 CATGAA
1 CATGAA
449570 GTTATGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.11, G:0.22, T:0.17
Consensus pattern (15 bp):
CATGAAACTAGAAAG
Found at i:449570 original size:15 final size:15
Alignment explanation
Indices: 449542--449573 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
449532 AACATGAAAC
449542 TAGAAAGCATGAAGT
1 TAGAAAGCATGAAGT
449557 TAGAAAGCATGAAGT
1 TAGAAAGCATGAAGT
449572 TA
1 TA
449574 TGATTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.25, T:0.22
Consensus pattern (15 bp):
TAGAAAGCATGAAGT
Found at i:456628 original size:46 final size:46
Alignment explanation
Indices: 456578--456914 Score: 485
Period size: 46 Copynumber: 7.3 Consensus size: 46
456568 TATGGCCTAT
* * * * * *
456578 TTTCATGCCTTAATACACCCGTTCATACATTTTTGTTACGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGACATCC
* * * **
456624 TTTCATTCCTTAATCCATCCGTTCATGCATTTTGGTTATGGTATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGACATCC
* * *
456670 TTTCATGCCTTAATGCATTCTTTCATGCATTTTAGTTATGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGACATCC
* *
456716 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGATATGACATCA
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGACATCC
* * *
456762 TTTCATTCCTTAATGCATTCATTCATGCATTTTAGTTATGACATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGACATCC
*
456808 TTTCATTCCTTAATGCATCCGTTCATGCATTTTAGTTATGACATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGACATCC
*
456854 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGTCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGACATCC
456900 TTTCATGCCTTAATG
1 TTTCATGCCTTAATG
456915 ATAACATAGT
Statistics
Matches: 264, Mismatches: 27, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 264 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.43
Consensus pattern (46 bp):
TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGACATCC
Found at i:456694 original size:20 final size:20
Alignment explanation
Indices: 456666--456914 Score: 102
Period size: 26 Copynumber: 10.9 Consensus size: 20
456656 TGGTTATGGT
456666 ATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCCTTAATGC
* *
456686 ATTCTTTCATGCATTTTAGTTATGGC
1 ATCCTTTCATGC--CTTA---AT-GC
456712 ATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCCTTAATGC
* *
456732 ATCCGTTCATGCATTTTAGATATGAC
1 ATCCTTTCATGC--CTT--A-ATG-C
* *
456758 ATCATTTCATTCCTTAATGC
1 ATCCTTTCATGCCTTAATGC
* * *
456778 ATTCATTCATGCATTTTAGTTATGAC
1 ATCCTTTCATGC--CTTA---ATG-C
*
456804 ATCCTTTCATTCCTTAATGC
1 ATCCTTTCATGCCTTAATGC
* *
456824 ATCCGTTCATGCATTTTAGTTATGAC
1 ATCCTTTCATGC--CTTA---ATG-C
456850 ATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCCTTAATGC
* *
456870 ATCCGTTCATGCATTTTAGTTATGTC
1 ATCCTTTCATGC--CTTA---ATG-C
456896 ATCCTTTCATGCCTTAATG
1 ATCCTTTCATGCCTTAATG
456915 ATAACATAGT
Statistics
Matches: 171, Mismatches: 28, Indels: 59
0.66 0.11 0.23
Matches are distributed among these distances:
20 56 0.33
21 14 0.08
22 15 0.09
24 15 0.09
25 14 0.08
26 57 0.33
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (20 bp):
ATCCTTTCATGCCTTAATGC
Found at i:460677 original size:21 final size:21
Alignment explanation
Indices: 460651--460706 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
460641 ATAGACTTTG
* *
460651 TCCCGAAGGACCACATATATA
1 TCCCGAATGACCACATAAATA
*
460672 TCCCGAATGACCACATAAATG
1 TCCCGAATGACCACATAAATA
*
460693 TCCCAAATGACCAC
1 TCCCGAATGACCAC
460707 TCCTTAAGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.38, C:0.32, G:0.12, T:0.18
Consensus pattern (21 bp):
TCCCGAATGACCACATAAATA
Found at i:467009 original size:21 final size:21
Alignment explanation
Indices: 466979--467060 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 21
466969 ACATAGACTT
*
466979 TGTCCTGAAGGACCACATATA
1 TGTCCCGAAGGACCACATATA
* *
467000 TGTCCCGAAGAACCGCATATA
1 TGTCCCGAAGGACCACATATA
* * * **
467021 TGTTCCAAATGAATACATATA
1 TGTCCCGAAGGACCACATATA
* *
467042 TATCTCGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
467061 GAACCCTCGA
Statistics
Matches: 44, Mismatches: 17, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATATA
Found at i:470242 original size:44 final size:44
Alignment explanation
Indices: 470193--470305 Score: 165
Period size: 44 Copynumber: 2.6 Consensus size: 44
470183 CATTTGCTCA
* * * *
470193 TCCATCACAGAATGAGTTAGATCAGA-ATCATCGTTTCGCTTAAT
1 TCCATCACAGAAGGAGTTGGATCA-ATATCATCGTTTCACTCAAT
*
470237 TCCATCACAGAAGGAGTTGGATCAATATCATCGTTTCACTCGAT
1 TCCATCACAGAAGGAGTTGGATCAATATCATCGTTTCACTCAAT
470281 TCCATCACAGAAGGAGTTGGATCAA
1 TCCATCACAGAAGGAGTTGGATCAA
470306 CATGTTCAGT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
43 1 0.02
44 62 0.98
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (44 bp):
TCCATCACAGAAGGAGTTGGATCAATATCATCGTTTCACTCAAT
Found at i:476720 original size:19 final size:19
Alignment explanation
Indices: 476696--476733 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
476686 TTGTCAAAGG
476696 CTTTCAACAAAAGGAATGT
1 CTTTCAACAAAAGGAATGT
476715 CTTTCAACAAAAGGAATGT
1 CTTTCAACAAAAGGAATGT
476734 ATTGACTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (19 bp):
CTTTCAACAAAAGGAATGT
Found at i:479635 original size:33 final size:33
Alignment explanation
Indices: 479575--479638 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
479565 CCTTGCTATT
* *
479575 AAGTTTCTCGAACCATACCCTATTACCCTGATC
1 AAGTTGCTCGAACCATACCCTACTACCCTGATC
* * *
479608 AAGTTGCTCGAACCATGCTCTGCTACCCTGA
1 AAGTTGCTCGAACCATACCCTACTACCCTGA
479639 CACTACAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.25, C:0.33, G:0.14, T:0.28
Consensus pattern (33 bp):
AAGTTGCTCGAACCATACCCTACTACCCTGATC
Found at i:482138 original size:3 final size:3
Alignment explanation
Indices: 482130--482154 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
482120 GATTAGACAA
482130 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
482155 TATTAAGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:487340 original size:2 final size:2
Alignment explanation
Indices: 487333--487384 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
487323 ATTTAAACAA
487333 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
487375 AT AT TT AT AT
1 AT AT AT AT AT
487385 GACTAAGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:488892 original size:3 final size:3
Alignment explanation
Indices: 488867--488931 Score: 64
Period size: 3 Copynumber: 21.3 Consensus size: 3
488857 AAATGGGCCT
*
488867 ATA AT- ATA ATA A-A ATTA AAA ATA ATAA ATA ATA ATA ATA ATTA ATA
1 ATA ATA ATA ATA ATA A-TA ATA ATA AT-A ATA ATA ATA ATA A-TA ATA
488913 A-A ATAA ATA ATA ATA ATA A
1 ATA AT-A ATA ATA ATA ATA A
488932 AAAATCAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
2 6 0.11
3 36 0.68
4 11 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:488903 original size:28 final size:27
Alignment explanation
Indices: 488867--488933 Score: 95
Period size: 25 Copynumber: 2.6 Consensus size: 27
488857 AAATGGGCCT
488867 ATAAT-ATAATAAAATTAAAAATAATAA
1 ATAATAATAATAAAATTAAAAA-AATAA
*
488894 ATAATAATAAT--AATTAATAAAATAA
1 ATAATAATAATAAAATTAAAAAAATAA
488919 ATAATAATAATAAAA
1 ATAATAATAATAAAA
488934 AATCAAATGG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
25 16 0.44
26 8 0.22
27 7 0.19
28 5 0.14
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (27 bp):
ATAATAATAATAAAATTAAAAAAATAA
Found at i:488917 original size:25 final size:26
Alignment explanation
Indices: 488872--488931 Score: 97
Period size: 25 Copynumber: 2.4 Consensus size: 26
488862 GGCCTATAAT
488872 ATAATAA-AATTAAAAATAATAAATA
1 ATAATAATAATTAAAAATAATAAATA
*
488897 ATAATAATAATTAATAA-AATAAATA
1 ATAATAATAATTAAAAATAATAAATA
488922 ATAATAATAA
1 ATAATAATAA
488932 AAAATCAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
25 25 0.76
26 8 0.24
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (26 bp):
ATAATAATAATTAAAAATAATAAATA
Found at i:488941 original size:25 final size:24
Alignment explanation
Indices: 488867--488941 Score: 82
Period size: 25 Copynumber: 3.1 Consensus size: 24
488857 AAATGGGCCT
*
488867 ATAATATAATAA-AATTAAAAAT-A
1 ATAA-ATAATAATAATAAAAAATAA
**
488890 ATAAATAATAATAATAATTAATAAA
1 ATAAATAATAATAATAAAAAAT-AA
488915 ATAAATAATAATAATAAAAAATCAA
1 ATAAATAATAATAATAAAAAAT-AA
488940 AT
1 AT
488942 GGAAAAAAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
22 7 0.16
23 11 0.26
25 25 0.58
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.29
Consensus pattern (24 bp):
ATAAATAATAATAATAAAAAATAA
Found at i:489322 original size:138 final size:139
Alignment explanation
Indices: 489156--489515 Score: 451
Period size: 138 Copynumber: 2.6 Consensus size: 139
489146 CTAGCAAAAA
* * * * *
489156 GTTGAACAAATTCTTCTCATTATAAACTTCTTATTCTTTTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATGAGTTCTTCTCATTATGAA
* * * * ** *
489221 CTCCTTCTGGAAATGTTGATCTTCAAAAGAGG-GGTT-GTTGATTCAGCTTTATATGTGATGAAT
66 CTCCTTCTGGAAATGTTGATCCTCAAAAGAGGTGCTTCGTTCATTCAACTCCATAGGTGATGAA-
489284 TTAAGGC-AAG
130 TTAA-GCTAAG
489294 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATGAGTTCTTCTCATTATGAA
* * * *
489359 CTTCC-TCTGAAAATGTTGATCCTCAAGAGAGGTTCTTCTTTCATTCAACTCCATAGGTGATGAA
66 C-TCCTTCTGGAAATGTTGATCCTCAAAAGAGGTGCTTCGTTCATTCAACTCCATAGGTGATGAA
489423 TTAAGCTAAG
130 TTAAGCTAAG
* * * * *
489433 GTCGAACAAGTTATTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTATCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATGAGTTCTTCTCATTATGAA
*
489498 CT-TTATCTGGAAATGTTG
66 CTCCT-TCTGGAAATGTTG
489516 GTGTTTATCT
Statistics
Matches: 193, Mismatches: 23, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
138 88 0.46
139 85 0.44
140 20 0.10
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (139 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATGAGTTCTTCTCATTATGAA
CTCCTTCTGGAAATGTTGATCCTCAAAAGAGGTGCTTCGTTCATTCAACTCCATAGGTGATGAAT
TAAGCTAAG
Found at i:489470 original size:139 final size:138
Alignment explanation
Indices: 489159--489515 Score: 450
Period size: 139 Copynumber: 2.6 Consensus size: 138
489149 GCAAAAAGTT
* * * * *
489159 GAACAAATTCTTCTCATTATAAACTTCTTATTCTTTTTCAGATGAGTTCTTCTCATTATGAAC-T
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATGAGTTCTTCTCATTATGAACTT
* * * * ** *
489223 CCTTCTGGAAATGTTGATCTTCAAAAGAGGGGTTGTTGATTCAGCTTTATATGTGATGAATTTAA
66 CC-TCTGGAAATGTTGATCCTCAAAAGAGGGCTTGTTCATTCAACTCCATAGGTGATGAATTTAA
*
489288 GGCAAGGTT
130 GGCAAGGTC
489297 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATGAGTTCTTCTCATTATGAACTT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATGAGTTCTTCTCATTATGAACTT
* * * *
489362 CCTCTGAAAATGTTGATCCTCAAGAGAGGTTCTTCTTTCATTCAACTCCATAGGTGATGAA-TTA
66 CCTCTGGAAATGTTGATCCTCAAAAGAGG-GCTT-GTTCATTCAACTCCATAGGTGATGAATTTA
489426 A-GCTAAGGTC
129 AGGC-AAGGTC
* * * *
489436 GAACAAGTTATTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTATCATTATGAACTT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATGAGTTCTTCTCATTATGAACTT
**
489501 TATCTGGAAATGTTG
66 CCTCTGGAAATGTTG
489516 GTGTTTATCT
Statistics
Matches: 191, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
138 84 0.44
139 87 0.46
140 20 0.10
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (138 bp):
GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATGAGTTCTTCTCATTATGAACTT
CCTCTGGAAATGTTGATCCTCAAAAGAGGGCTTGTTCATTCAACTCCATAGGTGATGAATTTAAG
GCAAGGTC
Found at i:489755 original size:112 final size:112
Alignment explanation
Indices: 489545--489761 Score: 328
Period size: 112 Copynumber: 1.9 Consensus size: 112
489535 TGTGATAGAG
* * * *
489545 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTCTTCAGATGAGTTCTT
1 TCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATGAGTTATT
* *
489610 CTCATTATGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAAT
66 CTCATTATGAACTTCATCTGGAAAAGTTCATCCATCGAGTGATGAAT
*
489657 TCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTATTCTTCCTTCTTCAGATGAGTTAT
1 TCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCC-TCTTCAGATGAGTTAT
* * *
489722 TCTCATTATGAACTTTATCT-GAAATGTTCATCCATTGAGT
65 TCTCATTATGAACTTCATCTGGAAAAGTTCATCCATCGAGT
489762 AATGGATTAA
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
112 61 0.65
113 33 0.35
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (112 bp):
TCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTCTTCAGATGAGTTATT
CTCATTATGAACTTCATCTGGAAAAGTTCATCCATCGAGTGATGAAT
Found at i:506185 original size:23 final size:26
Alignment explanation
Indices: 506159--506271 Score: 69
Period size: 27 Copynumber: 4.3 Consensus size: 26
506149 GAAAATGTCT
506159 AAATAAA-AAAA-AAGAAAAA-AATA
1 AAATAAACAAAACAAGAAAAATAATA
506182 AAATGATAA-AAGAA-AA-AAAAAGTAATA
1 AAAT-A-AACAA-AACAAGAAAAA-TAATA
* *
506209 AGATAAATAAAATCAAGATAAAAATAA-A
1 AAATAAACAAAA-CAAG--AAAAATAATA
*
506237 GAATAAAACAAAACAAGATAAAATAATA
1 AAAT-AAACAAAACAAGA-AAAATAATA
506265 AAATAAA
1 AAATAAA
506272 TAAAGATGAA
Statistics
Matches: 71, Mismatches: 5, Indels: 24
0.71 0.05 0.24
Matches are distributed among these distances:
23 4 0.06
24 1 0.01
25 13 0.18
26 8 0.11
27 19 0.27
28 11 0.15
29 10 0.14
30 5 0.07
ACGTcount: A:0.76, C:0.03, G:0.07, T:0.14
Consensus pattern (26 bp):
AAATAAACAAAACAAGAAAAATAATA
Found at i:506242 original size:28 final size:29
Alignment explanation
Indices: 506198--506288 Score: 91
Period size: 28 Copynumber: 3.2 Consensus size: 29
506188 TAAAAGAAAA
*
506198 AAAAAGTAATAAGATAAATAAAATCAAGAT
1 AAAAA-TAATAAAATAAATAAAATCAAGAT
* *
506228 AAAAATAA-AGAATAAA-ACAAAACAAGAT
1 AAAAATAATAAAATAAATA-AAATCAAGAT
*
506256 -AAAATAATAAAATAAATAAAGATGAA-AT
1 AAAAATAATAAAATAAATAAA-ATCAAGAT
506284 AAAAA
1 AAAAA
506289 AATGAACAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
27 8 0.16
28 26 0.52
29 11 0.22
30 5 0.10
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (29 bp):
AAAAATAATAAAATAAATAAAATCAAGAT
Found at i:506267 original size:8 final size:9
Alignment explanation
Indices: 506158--506291 Score: 55
Period size: 8 Copynumber: 14.6 Consensus size: 9
506148 AGAAAATGTC
506158 TAAATAAAA
1 TAAATAAAA
*
506167 -AAAAAGAAA
1 TAAATA-AAA
*
506176 AAAATAAAA
1 TAAATAAAA
*
506185 T-GATAAAA
1 TAAATAAAA
*
506193 GAAA-AAAA
1 TAAATAAAA
* *
506201 AAGTAATAAGA
1 TA--AATAAAA
506212 TAAATAAAA
1 TAAATAAAA
506221 TCAAGATAAAAA
1 T-AA-AT-AAAA
* *
506233 TAAAGAATA
1 TAAATAAAA
*
506242 -AAACAAAA
1 TAAATAAAA
*
506250 CAAGATAAAA
1 TAA-ATAAAA
506260 T-AATAAAA
1 TAAATAAAA
506268 TAAATAAAGA
1 TAAATAAA-A
506278 TGAAATAAAA
1 T-AAATAAAA
506288 -AAAT
1 TAAAT
506292 GAACAAAATT
Statistics
Matches: 95, Mismatches: 16, Indels: 29
0.68 0.11 0.21
Matches are distributed among these distances:
8 32 0.34
9 26 0.27
10 17 0.18
11 15 0.16
12 5 0.05
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (9 bp):
TAAATAAAA
Found at i:506277 original size:23 final size:22
Alignment explanation
Indices: 506214--506291 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 22
506204 TAATAAGATA
* *
506214 AATAAAATCAAGATAAAAATAAAG
1 AATAAAAT-AA-ATAAAGATAAAT
*
506238 AATAAAACAAA-ACAAGATAAAAT
1 AATAAAATAAATA-AAGAT-AAAT
506261 AATAAAATAAATAAAGATGAAAT
1 AATAAAATAAATAAAGAT-AAAT
*
506284 AAAAAAAT
1 AATAAAAT
506292 GAACAAAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
21 1 0.02
22 5 0.11
23 31 0.69
24 8 0.18
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.17
Consensus pattern (22 bp):
AATAAAATAAATAAAGATAAAT
Found at i:506320 original size:15 final size:15
Alignment explanation
Indices: 506293--506342 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
506283 TAAAAAAATG
*
506293 AACA-AAATTAATAA
1 AACAGAAATAAATAA
506307 AACAGAAATAAATAA
1 AACAGAAATAAATAA
* *
506322 ATCAAAAATAAA-AA
1 AACAGAAATAAATAA
506336 AAC-GAAA
1 AACAGAAA
506343 GGAAAGGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 3 0.10
14 8 0.27
15 19 0.63
ACGTcount: A:0.74, C:0.08, G:0.04, T:0.14
Consensus pattern (15 bp):
AACAGAAATAAATAA
Found at i:506478 original size:2 final size:2
Alignment explanation
Indices: 506471--506515 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
506461 ACAAAAATAG
506471 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
506513 AT A
1 AT A
506516 ATGCTAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:507593 original size:18 final size:16
Alignment explanation
Indices: 507570--507610 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 16
507560 ATATGTAATG
507570 ATATAATATATACGCATT
1 ATATAATATATA--CATT
507588 ATATAATATATACATT
1 ATATAATATATACATT
507604 ATATAAT
1 ATATAAT
507611 TGACGAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 11 0.48
18 12 0.52
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (16 bp):
ATATAATATATACATT
Found at i:507596 original size:16 final size:16
Alignment explanation
Indices: 507577--507610 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
507567 ATGATATAAT
*
507577 ATATACGCATTATATA
1 ATATACACATTATATA
*
507593 ATATATACATTATATA
1 ATATACACATTATATA
507609 AT
1 AT
507611 TGACGAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (16 bp):
ATATACACATTATATA
Found at i:512461 original size:18 final size:17
Alignment explanation
Indices: 512438--512472 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
512428 CAACCCACAC
*
512438 ACCATATGAGTGAGGTCT
1 ACCATAAGAGTG-GGTCT
512456 ACCATAAGAGTGGGTCT
1 ACCATAAGAGTGGGTCT
512473 CCTCTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (17 bp):
ACCATAAGAGTGGGTCT
Found at i:514377 original size:15 final size:15
Alignment explanation
Indices: 514357--514405 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
514347 TGATCTGATT
514357 TGAATAACACATATC
1 TGAATAACACATATC
514372 TGAAT-ACACATATAC
1 TGAATAACACATAT-C
* *
514387 -GAATATCATATATC
1 TGAATAACACATATC
514401 TGAAT
1 TGAAT
514406 TCCAATCTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 13 0.45
15 16 0.55
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (15 bp):
TGAATAACACATATC
Found at i:518824 original size:32 final size:32
Alignment explanation
Indices: 518754--518827 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
518744 CCTAAGGTGA
* *
518754 CCCTTGGGTAGGCTCTGAGGCCCCGAGAAACT
1 CCCTTGGGTAGGCTCTCAGGCCCCAAGAAACT
** **
518786 TTCTTGGGTAGGCTCTCAGGCCCCAAGGCACT
1 CCCTTGGGTAGGCTCTCAGGCCCCAAGAAACT
518818 CCCTTGGGTA
1 CCCTTGGGTA
518828 AATCATGGGA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.16, C:0.31, G:0.30, T:0.23
Consensus pattern (32 bp):
CCCTTGGGTAGGCTCTCAGGCCCCAAGAAACT
Found at i:520533 original size:39 final size:39
Alignment explanation
Indices: 520490--520564 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
520480 GAGTAAAATA
* *
520490 AAGGCGATAACACCTAAGGTGAGGATGTTGAGTGCAATG
1 AAGGCAATAACACCTAAGGTGAGGATGTCGAGTGCAATG
** *
520529 AAGGCAATAATGCCTAGGGTGAGGATGTCGAGTGCA
1 AAGGCAATAACACCTAAGGTGAGGATGTCGAGTGCA
520565 GTAAAGATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.20
Consensus pattern (39 bp):
AAGGCAATAACACCTAAGGTGAGGATGTCGAGTGCAATG
Done.