Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr9
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: 70906002
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.33
Warning! 1642329 characters in sequence are not A, C, G, or T
File 95 of 221
Found at i:28190823 original size:18 final size:18
Alignment explanation
Indices: 28190800--28190838 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
28190790 TTTACCAACT
28190800 TTATGGATAATAATTTAA
1 TTATGGATAATAATTTAA
28190818 TTATGGATAATAATTTAA
1 TTATGGATAATAATTTAA
28190836 TTA
1 TTA
28190839 AAGATACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (18 bp):
TTATGGATAATAATTTAA
Found at i:28190844 original size:18 final size:18
Alignment explanation
Indices: 28190805--28190844 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
28190795 CAACTTTATG
**
28190805 GATAATAATTTAATTATG
1 GATAATAATTTAATTAAA
28190823 GATAATAATTTAATTAAA
1 GATAATAATTTAATTAAA
28190841 GATA
1 GATA
28190845 CAACATAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (18 bp):
GATAATAATTTAATTAAA
Found at i:28191929 original size:27 final size:27
Alignment explanation
Indices: 28191864--28191933 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
28191854 CAGATTTTAG
* *
28191864 ATTGTTGGATTTTGATATATGTCTTGA
1 ATTGTTGGATATTGATATATGTCTTAA
* *
28191891 ATTGGTTAGATATTGAT-TATGTTTTAA
1 ATT-GTTGGATATTGATATATGTCTTAA
28191918 CATTGTTGGATATTGA
1 -ATTGTTGGATATTGA
28191934 ATTGATTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.50
Consensus pattern (27 bp):
ATTGTTGGATATTGATATATGTCTTAA
Found at i:28191938 original size:32 final size:33
Alignment explanation
Indices: 28191902--28191969 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 33
28191892 TTGGTTAGAT
28191902 ATTG-ATTATGTTTTAA-CATTGTTGGATATTGA
1 ATTGTATTATGTTTTAAGC-TTGTTGGATATTGA
28191934 ATTGATTATTATGTTTTAAGCTTGTTGGATATTGA
1 ATTG--TATTATGTTTTAAGCTTGTTGGATATTGA
28191969 A
1 A
28191970 ATTATTGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
32 4 0.12
35 27 0.84
36 1 0.03
ACGTcount: A:0.28, C:0.03, G:0.19, T:0.50
Consensus pattern (33 bp):
ATTGTATTATGTTTTAAGCTTGTTGGATATTGA
Found at i:28193036 original size:72 final size:72
Alignment explanation
Indices: 28192919--28193062 Score: 270
Period size: 72 Copynumber: 2.0 Consensus size: 72
28192909 TTGATACATT
*
28192919 TATGTGGTGTAATATTATGTACTTGGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
1 TATGTGGTGTAATATTATGCACTTGGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
28192984 TTGGATA
66 TTGGATA
*
28192991 TATGTGGTGTAATATTATGCACTTGGACAATGTTGTTACTATGTGGTGTACCATTAATTATGTAT
1 TATGTGGTGTAATATTATGCACTTGGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
28193056 TTGGATA
66 TTGGATA
28193063 ATATTATTAT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (72 bp):
TATGTGGTGTAATATTATGCACTTGGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
TTGGATA
Found at i:28193300 original size:12 final size:12
Alignment explanation
Indices: 28193229--28193300 Score: 51
Period size: 12 Copynumber: 6.2 Consensus size: 12
28193219 AAATCATTGC
28193229 AATATATGTAAA
1 AATATATGTAAA
* * **
28193241 AACA-ATTTATT
1 AATATATGTAAA
28193252 AATATAT-TAATA
1 AATATATGTAA-A
* **
28193264 AATATATATATT
1 AATATATGTAAA
28193276 AATATATGT-AA
1 AATATATGTAAA
28193287 AATATATGTAAA
1 AATATATGTAAA
28193299 AA
1 AA
28193301 CAACTTTTCC
Statistics
Matches: 44, Mismatches: 12, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
11 18 0.41
12 24 0.55
13 2 0.05
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (12 bp):
AATATATGTAAA
Found at i:28193353 original size:32 final size:33
Alignment explanation
Indices: 28193312--28193396 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 33
28193302 AACTTTTCCG
* * *
28193312 GAAAATATTTT-CAGGAAATCTGCCAAACAGCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
28193344 GAAAATATTTTACA-CAGATTTACCAAACACCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
28193376 GAAAATATTTTCCAGTAAATC
1 GAAAATATTTTACAGCAAATC
28193397 ATTTTACAGA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
32 37 0.88
33 5 0.12
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (33 bp):
GAAAATATTTTACAGCAAATCTACCAAACACCA
Found at i:28193414 original size:20 final size:20
Alignment explanation
Indices: 28193389--28193428 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28193379 AATATTTTCC
*
28193389 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
28193409 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
28193429 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:28193434 original size:34 final size:35
Alignment explanation
Indices: 28193377--28193443 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
28193367 CAAACACCAG
*
28193377 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
28193412 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
28193444 TAACATTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:28196798 original size:39 final size:39
Alignment explanation
Indices: 28196706--28196954 Score: 254
Period size: 39 Copynumber: 6.4 Consensus size: 39
28196696 GGATCTTCGT
* * * **
28196706 TGATACACAAGTTATCCATAAGCTCACAGAGGAGCTTCCC
1 TGATACACAACTTATCC-TTAGCTCACGGAGGAGCTTTGC
* * * *
28196746 TGATA-ACACCTTATCCTTCGCTCACGCATGAGCTTTGC
1 TGATACACAACTTATCCTTAGCTCACGGAGGAGCTTTGC
* * * *
28196784 TGATACACAGCTTATTCATAAGCTCACAGG-GGAGATTTGC
1 TGATACACAACTTA-TCCTTAGCTCAC-GGAGGAGCTTTGC
*
28196824 TGATACACAACTTGTCCTTAGCTCACGGA-GAGCTTTGC
1 TGATACACAACTTATCCTTAGCTCACGGAGGAGCTTTGC
* * * *
28196862 TGATACACAACTTATCCATAAGCTTAAGG-GTAGCTTTGC
1 TGATACACAACTTATCC-TTAGCTCACGGAGGAGCTTTGC
* *
28196901 TGATACACAACTTCTCCTTAGCTCATGGAGGAGCTTTGC
1 TGATACACAACTTATCCTTAGCTCACGGAGGAGCTTTGC
28196940 TGATACACAACTTAT
1 TGATACACAACTTAT
28196955 AAAGCCGTTC
Statistics
Matches: 170, Mismatches: 32, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
38 54 0.32
39 81 0.48
40 34 0.20
41 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (39 bp):
TGATACACAACTTATCCTTAGCTCACGGAGGAGCTTTGC
Found at i:28196804 original size:78 final size:77
Alignment explanation
Indices: 28196652--28196954 Score: 324
Period size: 78 Copynumber: 3.8 Consensus size: 77
28196642 AAGCTTGCAT
* * * * * *
28196652 AGGGAGCTTTGCTGGTACACAAGTTCATCACTTAAGCTCATATGG-GATCTTCGTTGATACACAA
1 AGGGAGCTTTGCTGATACACAACTT-ATC-CTT-AGCTC--ACGGAGAGCTTTGCTGATACACAA
*
28196716 GTTATCCATAAGCTCAC
61 CTTATCCATAAGCTCAC
** * * * *
28196733 AGAGGAGCTTCCCTGATA-ACACCTTATCCTTCGCTCACGCATGAGCTTTGCTGATACACAGCTT
1 AG-GGAGCTTTGCTGATACACAACTTATCCTTAGCTCACGGA-GAGCTTTGCTGATACACAACTT
*
28196797 ATTCATAAGCTCAC
64 ATCCATAAGCTCAC
* *
28196811 AGGGGAGATTTGCTGATACACAACTTGTCCTTAGCTCACGGAGAGCTTTGCTGATACACAACTTA
1 A-GGGAGCTTTGCTGATACACAACTTATCCTTAGCTCACGGAGAGCTTTGCTGATACACAACTTA
*
28196876 TCCATAAGCTTA-
65 TCCATAAGCTCAC
* *
28196888 AGGGTAGCTTTGCTGATACACAACTTCTCCTTAGCTCATGGAGGAGCTTTGCTGATACACAACTT
1 AGGG-AGCTTTGCTGATACACAACTTATCCTTAGCTCACGGA-GAGCTTTGCTGATACACAACTT
28196953 AT
64 AT
28196955 AAAGCCGTTC
Statistics
Matches: 188, Mismatches: 27, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
76 5 0.03
77 35 0.19
78 103 0.55
79 23 0.12
80 3 0.02
81 7 0.04
82 12 0.06
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (77 bp):
AGGGAGCTTTGCTGATACACAACTTATCCTTAGCTCACGGAGAGCTTTGCTGATACACAACTTAT
CCATAAGCTCAC
Found at i:28222031 original size:35 final size:35
Alignment explanation
Indices: 28221987--28222071 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 35
28221977 ACCTACTTTT
*
28221987 AAAGAGTTGGGATAGAC-CACTCTATGCCAACCTTAA
1 AAAG-GTTGGGATAGACTCA-TCTAAGCCAACCTTAA
* * *
28222023 AAAGGTTGGGATTGACTCATCTAAGGCAACTTTAA
1 AAAGGTTGGGATAGACTCATCTAAGCCAACCTTAA
*
28222058 ACAGGTTGGGATAG
1 AAAGGTTGGGATAG
28222072 GCCTTACCTG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
35 36 0.86
36 6 0.14
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (35 bp):
AAAGGTTGGGATAGACTCATCTAAGCCAACCTTAA
Found at i:28226156 original size:82 final size:82
Alignment explanation
Indices: 28226012--28226380 Score: 614
Period size: 82 Copynumber: 4.5 Consensus size: 82
28226002 NNNNNNNNNN
* *
28226012 GATGTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTGTCTGCTCCGCTACTGC
1 GATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTGTCTGCTCCACTACTGC
28226077 TTAGGGAGATAAGACTT
66 TTAGGGAGATAAGACTT
*
28226094 GATGCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTTTGTCTGCTCCACTACTGC
1 GATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTGTCTGCTCCACTACTGC
28226159 TTAGGGAGATAAGACTT
66 TTAGGGAGATAAGACTT
* * * * *
28226176 GATGCGATCTGCTCCACTATTACTTAGAGAGATAAGATCTGTGGTTTTGTCCGCTCCGCTACTGC
1 GATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTGTCTGCTCCACTACTGC
28226241 TTAGGGAGATAAGACTT
66 TTAGGGAGATAAGACTT
* * * *
28226258 AATGCGATCTACTCCACTACTGCTTAGAGAGATAAGATCTGTGGTTTTGTCTGCTCCACTACTAC
1 GATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTGTCTGCTCCACTACTGC
*
28226323 TTAGGGAGATAAGACTG
66 TTAGGGAGATAAGACTT
28226340 GATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGA-CTGT
1 GATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
28226381 AATCTTCGAT
Statistics
Matches: 269, Mismatches: 18, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
81 4 0.01
82 265 0.99
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.31
Consensus pattern (82 bp):
GATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTGTCTGCTCCACTACTGC
TTAGGGAGATAAGACTT
Found at i:28226617 original size:134 final size:133
Alignment explanation
Indices: 28226425--28227064 Score: 869
Period size: 134 Copynumber: 4.8 Consensus size: 133
28226415 TAAGATTACT
* * *
28226425 GGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATATTCGATCTGCTTCTCTG
1 GGCTTCAATGTACTCCACTGT-A-GTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCTCTG
* * *
28226490 CCAAATATAGGAAGGCAAAATCTGTAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGA
64 CCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCC-AATACAGGGAGATAGA
28226555 GTTATC
128 GTTATC
* * * *
28226561 GGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCATCAATCTGCTTCTTTACC
1 GGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCTCTGCC
* *
28226626 AAATACAGGAAGGCAAGATCTGCAATCTTTAATCTATTCCACTGCCAA-CCAGGGAGATAGAGTT
66 AAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAATACAGGGAGATAGAGTT
28226690 ATC
131 ATC
* * * *
28226693 GGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGTCATCTTCGATCTACTCCACT-
1 GGCTTCAATGTACTCCACTGTAGT--CAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCTCTG
* *** * * ** * ** *
28226757 ACTGCT-TAGGGAGATAAGATCTGTAATCTTC-ATCCTATTCCACTG-CTGT-CTAGGGAGACAG
64 CCAAATACAGGAAGGCAAGATCTGCAATCTTCAAT-CTATTCCACTGCCAATAC-AGGGAGATAG
28226818 AGTTATC
127 AGTTATC
28226825 GGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCTCTGCC
1 GGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCTCTGCC
*
28226890 AAATACAGGAAGGCAAGATCTGCAATCTTCAATTTATTCCACTGCCAAATACAGGGAGATAGAGT
66 AAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCC-AATACAGGGAGATAGAGT
28226955 TATC
130 TATC
* *
28226959 GGCTTCAATGTACTCCACTATAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCC
1 GGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCTCTGCC
*
28227024 AAATACAGGAAGGTAAGATCTGCAATCTTCAATCTACTTCC
66 AAATACAGGAAGGCAAGATCTGCAATCTTCAATCTA-TTCC
28227065 TACCAATATA
Statistics
Matches: 439, Mismatches: 53, Indels: 25
0.85 0.10 0.05
Matches are distributed among these distances:
130 34 0.08
131 6 0.01
132 142 0.32
133 7 0.02
134 223 0.51
135 6 0.01
136 21 0.05
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (133 bp):
GGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCTCTGCC
AAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAATACAGGGAGATAGAGTT
ATC
Found at i:28226768 original size:44 final size:44
Alignment explanation
Indices: 28226720--28226814 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 44
28226710 CTGTAGTCAC
* *
28226720 AGGGAGGTAAAATCTGTCATCTTCGAT-CTACTCCACTACTG-CTT
1 AGGGAGATAAAATCTGTAATCTTC-ATCCTACTCCACTACTGTC-T
* * *
28226764 AGGGAGATAAGATCTGTAATCTTCATCCTATTCCACTGCTGTCT
1 AGGGAGATAAAATCTGTAATCTTCATCCTACTCCACTACTGTCT
28226808 AGGGAGA
1 AGGGAGA
28226815 CAGAGTTATC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
43 2 0.05
44 41 0.93
45 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (44 bp):
AGGGAGATAAAATCTGTAATCTTCATCCTACTCCACTACTGTCT
Found at i:28226881 original size:264 final size:269
Alignment explanation
Indices: 28226425--28227064 Score: 857
Period size: 264 Copynumber: 2.4 Consensus size: 269
28226415 TAAGATTACT
* * * * * *
28226425 GGCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATATTCGATCTGCTTCTCTG
1 GGCTTCAATGTACTCCACTGTAGTC-CAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTG
* * *
28226490 CCAAATATAGGAAGGCAAAATCTGTAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGA
65 ACAAATATAGGAAGACAAAATCTGTAATCTTCAATCTATTCCACTGCCAAATACAGGGAGACAGA
28226555 GTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCATCAATCTGCTTC
130 GTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCATCAATCTGCTTC
* * *
28226620 TTTACCAAATACAGGAAGGCAAGATCTGCAATCTTTAATCTATTCCACTGCC-AA-CCAGGGAGA
195 TCTACCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGA
28226683 TAGAGTTATC
260 TAGAGTTATC
*
28226693 GGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGTCATCTTCGATCTACTCCACT-
1 GGCTTCAATGTACTCCACTGTAGTC-CAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTG
*** * * * **
28226757 ACTGCT-TAGGGAGATAAGATCTGTAATCTTC-ATCCTATTCCACTG-C-TGT-CTAGGGAGACA
65 ACAAATATAGGAAGACAAAATCTGTAATCTTCAAT-CTATTCCACTGCCAAATAC-AGGGAGACA
* *
28226817 GAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCT
128 GAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCATCAATCTGCT
* *
28226882 TCTCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATTTATTCCACTGCCAAATACAGGGA
193 TCTCTACCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGA
28226947 GATAGAGTTATC
258 GATAGAGTTATC
* * * * *
28226959 GGCTTCAATGTACTCCACTATAGT-CAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGC
1 GGCTTCAATGTACTCCACTGTAGTCCAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTGA
* ** * *
28227023 CAAATACAGGAAGGTAAGATCTGCAATCTTCAATCTACTTCC
66 CAAATATAGGAAGACAAAATCTGTAATCTTCAATCTA-TTCC
28227065 TACCAATATA
Statistics
Matches: 325, Mismatches: 39, Indels: 17
0.85 0.10 0.04
Matches are distributed among these distances:
263 1 0.00
264 156 0.48
265 7 0.02
266 97 0.30
267 8 0.02
268 56 0.17
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (269 bp):
GGCTTCAATGTACTCCACTGTAGTCCAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTGA
CAAATATAGGAAGACAAAATCTGTAATCTTCAATCTATTCCACTGCCAAATACAGGGAGACAGAG
TTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCATCAATCTGCTTCT
CTACCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGAT
AGAGTTATC
Found at i:28227096 original size:44 final size:45
Alignment explanation
Indices: 28226997--28227267 Score: 219
Period size: 44 Copynumber: 6.1 Consensus size: 45
28226987 GAGGTAAAAT
* * * * * ** *
28226997 CTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGTAAGAT
1 CTGCTATCTTCGATCTACTTCACTACC-AATATAGGAAGACAAGAC
* * *
28227043 CTGCAATCTTCAATCTACTTC-CTACCAATATAGGAAGACAGGAC
1 CTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAGAC
* * * *
28227087 CTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGAT
1 CTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAGAC
* * * * *
28227131 CTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGAT
1 CTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAGAC
* * * **
28227176 CTGC-ATCGTCGATCCACTTC-CTACCAATATAGGAAAACCGGAC
1 CTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAGAC
* * * * * *
28227219 CTGTTATCTTTGATCTACTTCAC-GCCAATACATGAAGACAAGAT
1 CTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAGAC
28227263 CTGCT
1 CTGCT
28227268 TTAATGACTT
Statistics
Matches: 178, Mismatches: 43, Indels: 10
0.77 0.19 0.04
Matches are distributed among these distances:
43 20 0.11
44 113 0.63
45 27 0.15
46 18 0.10
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (45 bp):
CTGCTATCTTCGATCTACTTCACTACCAATATAGGAAGACAAGAC
Found at i:28228765 original size:22 final size:21
Alignment explanation
Indices: 28228736--28228805 Score: 79
Period size: 21 Copynumber: 3.2 Consensus size: 21
28228726 AGTAGAGGTC
28228736 TTTTCTTTTATTTTTGGTTTT
1 TTTTCTTTTATTTTTGGTTTT
*
28228757 TTTTGCTTTTTATTTTCTAGTTTT
1 TTTT-C-TTTTATTTT-TGGTTTT
*
28228781 TTTT-TTTTATTTTTGCTCTTT
1 TTTTCTTTTATTTTTGGT-TTT
28228802 TTTT
1 TTTT
28228806 TCCTCCACTG
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
20 2 0.05
21 20 0.48
22 1 0.02
23 9 0.21
24 10 0.24
ACGTcount: A:0.06, C:0.07, G:0.07, T:0.80
Consensus pattern (21 bp):
TTTTCTTTTATTTTTGGTTTT
Found at i:28230244 original size:62 final size:62
Alignment explanation
Indices: 28230086--28230267 Score: 284
Period size: 62 Copynumber: 3.0 Consensus size: 62
28230076 CTAAACTCGA
* **
28230086 CGTACTTTTGGATTTTAGGAAATTTATTATATAAAATGAAATGTAATGTTGATGCATGAATG
1 CGTATTTTTGGATTTTAGGAAATTTATTATATGCAATGAAATGTAATGTTGATGCATGAATG
*
28230148 CGTATTTTTGAATTTTAGGAAATTTATTATATGCAATGAAATGTAATGTTGATGCATGAATG
1 CGTATTTTTGGATTTTAGGAAATTTATTATATGCAATGAAATGTAATGTTGATGCATGAATG
*
28230210 CGTATTTTTGGATTTTAGGAAA--T-TTAT-TGC-ATGCAATGTAATGTTGATGCATGAATG
1 CGTATTTTTGGATTTTAGGAAATTTATTATATGCAATGAAATGTAATGTTGATGCATGAATG
28230267 C
1 C
28230268 AAAAAAGAGA
Statistics
Matches: 114, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
57 27 0.24
58 3 0.03
59 4 0.04
60 1 0.01
62 79 0.69
ACGTcount: A:0.32, C:0.06, G:0.20, T:0.41
Consensus pattern (62 bp):
CGTATTTTTGGATTTTAGGAAATTTATTATATGCAATGAAATGTAATGTTGATGCATGAATG
Found at i:28232609 original size:16 final size:16
Alignment explanation
Indices: 28232585--28232615 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28232575 TATGTACCGA
*
28232585 AAATTTAAATAAATAT
1 AAATATAAATAAATAT
28232601 AAATATAAATAAATA
1 AAATATAAATAAATA
28232616 GATAACAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATATAAATAAATAT
Found at i:28237511 original size:15 final size:15
Alignment explanation
Indices: 28237491--28237523 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
28237481 AATCATTGGG
28237491 TTGAGCCTGAAAAGT
1 TTGAGCCTGAAAAGT
*
28237506 TTGAGCCTGAAAGGT
1 TTGAGCCTGAAAAGT
28237521 TTG
1 TTG
28237524 TCAACAGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.30
Consensus pattern (15 bp):
TTGAGCCTGAAAAGT
Found at i:28243147 original size:19 final size:19
Alignment explanation
Indices: 28243119--28243160 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
28243109 CATGTATAAA
28243119 TTTTAGTTTTTTATTTCAT
1 TTTTAGTTTTTTATTTCAT
* *
28243138 TTTTATTTTTTTATTTTAT
1 TTTTAGTTTTTTATTTCAT
28243157 TTTT
1 TTTT
28243161 CTTATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTTAGTTTTTTATTTCAT
Found at i:28243520 original size:7 final size:7
Alignment explanation
Indices: 28243508--28243605 Score: 63
Period size: 7 Copynumber: 13.4 Consensus size: 7
28243498 CTGACCCTTG
28243508 AAACCCT
1 AAACCCT
28243515 AAACCCT
1 AAACCCT
28243522 AAATCCCT
1 AAA-CCCT
*
28243530 AACCCCT
1 AAACCCT
*
28243537 AACCCCT
1 AAACCCT
28243544 AAATCCCCCT
1 AAA---CCCT
28243554 -AACCCTT
1 AAACCC-T
* *
28243561 AAAGCAT
1 AAACCCT
*
28243568 AACCCCT
1 AAACCCT
*
28243575 AACCCCT
1 AAACCCT
* *
28243582 AAATCTT
1 AAACCCT
*
28243589 AAATCCT
1 AAACCCT
28243596 AAACCCT
1 AAACCCT
28243603 AAA
1 AAA
28243606 TCCATACCCC
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
6 3 0.04
7 55 0.75
8 9 0.12
9 2 0.03
10 4 0.05
ACGTcount: A:0.39, C:0.41, G:0.01, T:0.19
Consensus pattern (7 bp):
AAACCCT
Found at i:28243533 original size:21 final size:21
Alignment explanation
Indices: 28243509--28243605 Score: 72
Period size: 21 Copynumber: 4.4 Consensus size: 21
28243499 TGACCCTTGA
28243509 AACCCTAAACCCTAAATCCCT
1 AACCCTAAACCCTAAATCCCT
*
28243530 AACCCCTAACCCCTAAATCCCCCT
1 AA-CCCTAAACCCTAAAT--CCCT
* * *
28243554 AACCCTTAAAGCAT-AACCCCT
1 AACCC-TAAACCCTAAATCCCT
* *
28243575 AACCCCTAAATCTTAAAT-CCT
1 AA-CCCTAAACCCTAAATCCCT
28243596 AAACCCTAAA
1 -AACCCTAAA
28243606 TCCATACCCC
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
21 24 0.39
22 21 0.34
23 5 0.08
24 11 0.18
ACGTcount: A:0.38, C:0.41, G:0.01, T:0.20
Consensus pattern (21 bp):
AACCCTAAACCCTAAATCCCT
Found at i:28244172 original size:41 final size:41
Alignment explanation
Indices: 28244127--28244280 Score: 195
Period size: 41 Copynumber: 3.8 Consensus size: 41
28244117 TTTTATTATT
* *
28244127 ATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGGCTCGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
* ** *
28244168 ATTAGCGACGCTACTTC-AAAACGCCGCTAAAGCCCCGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
* *
28244208 ATTAGCGGCACTTTTTCAAAAACACCGCTAAA-GCCCTGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCC-GAGC
* *
28244249 AGTAGCAGCGCTTTTTCAAAAACGCCGCTAAA
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAA
28244281 AGCCTATTTT
Statistics
Matches: 95, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
40 36 0.38
41 59 0.62
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.21
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
Found at i:28244267 original size:81 final size:82
Alignment explanation
Indices: 28244127--28244280 Score: 206
Period size: 81 Copynumber: 1.9 Consensus size: 82
28244117 TTTTATTATT
* ** * *
28244127 ATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGGCTCGAGCATTAGCGACGCTACTTC-AAAACG
1 ATTAGCGGCACTTTTTCAAAAACACCGCTAAAGCCTCGAGCAGTAGCGACGCTACTTCAAAAACG
28244191 CCGCTAAAGCCCCGAGC
66 CCGCTAAAGCCCCGAGC
**
28244208 ATTAGCGGCACTTTTTCAAAAACACCGCTAAAGCC-CTGAGCAGTAGC-AGCGCTTTTTCAAAAA
1 ATTAGCGGCACTTTTTCAAAAACACCGCTAAAGCCTC-GAGCAGTAGCGA-CGCTACTTCAAAAA
28244271 CGCCGCTAAA
64 CGCCGCTAAA
28244281 AGCCTATTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
80 2 0.03
81 47 0.75
82 14 0.22
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.21
Consensus pattern (82 bp):
ATTAGCGGCACTTTTTCAAAAACACCGCTAAAGCCTCGAGCAGTAGCGACGCTACTTCAAAAACG
CCGCTAAAGCCCCGAGC
Found at i:28245540 original size:37 final size:37
Alignment explanation
Indices: 28245490--28245574 Score: 152
Period size: 37 Copynumber: 2.3 Consensus size: 37
28245480 TTGAAGCCTA
28245490 TGGAGAGAGGAATGGCAAATCTGAATATTTACGATGG
1 TGGAGAGAGGAATGGCAAATCTGAATATTTACGATGG
28245527 TGGAGAGAGGAATGGCAAATCTGAATATTTACGATGG
1 TGGAGAGAGGAATGGCAAATCTGAATATTTACGATGG
*
28245564 TGAAGATGAGG
1 TGGAGA-GAGG
28245575 CTTGGAGCCT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 42 0.91
38 4 0.09
ACGTcount: A:0.35, C:0.07, G:0.34, T:0.24
Consensus pattern (37 bp):
TGGAGAGAGGAATGGCAAATCTGAATATTTACGATGG
Found at i:28246883 original size:3 final size:3
Alignment explanation
Indices: 28246875--28246915 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
28246865 AATATACCAC
28246875 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
28246916 AGTAATTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:28267703 original size:50 final size:50
Alignment explanation
Indices: 28267626--28267766 Score: 194
Period size: 50 Copynumber: 2.8 Consensus size: 50
28267616 TTGACGCTAA
* * * **
28267626 TAGATTGAAGCCACAACGGCGAGTCTTACTTCCCTGGCATTGTAGTGGAG
1 TAGATTGAAGCCACAACGGTGAATCTTACTTCCCTAGCATTGTAGCAGAG
**
28267676 TAGATTGAAGCCACAACGGTGAATCTTACTTCCCTAGTGTTGTAGCAGAG
1 TAGATTGAAGCCACAACGGTGAATCTTACTTCCCTAGCATTGTAGCAGAG
*
28267726 TAGATTGAAGCCACGACGGTGAATCTTA-TCTCCCTAGCATT
1 TAGATTGAAGCCACAACGGTGAATCTTACT-TCCCTAGCATT
28267767 AAGGCTTGGA
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
49 1 0.01
50 79 0.99
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (50 bp):
TAGATTGAAGCCACAACGGTGAATCTTACTTCCCTAGCATTGTAGCAGAG
Found at i:28267892 original size:50 final size:50
Alignment explanation
Indices: 28267838--28268117 Score: 165
Period size: 50 Copynumber: 5.6 Consensus size: 50
28267828 GGTATTACAA
*
28267838 TGGAATAGATTGAAGCCACAACAGTGAATCTTACTTCTCTGACGGTGTAG
1 TGGAATAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGACGGTGTAG
* ** * * *** **
28267888 TGGAACAGATTGAAGTTACGACGGTGAATCTGT--TTCCCTGATATTACAG
1 TGGAATAGATTGAAGCCACAACAGTGAATCT-TACTTCCCTGACGGTGTAG
**
28267937 TGGAATAGATTGAAGCCACAAC-GACAAATCTTACTTCCCT-AGCGGTGTAG
1 TGGAATAGATTGAAGCCACAACAG-TGAATCTTACTTCCCTGA-CGGTGTAG
* * * *** * ** * *
28267987 TGGAATAGATTGAAGCTACGATAGTGAATCTGGTTTCCCCGACATTGCAA
1 TGGAATAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGACGGTGTAG
** * ** * * * *
28268037 TTAAAAAGATTGAAGCCACAATGGTGAATCTTACCTCCCTGGCGATGCA-
1 TGGAATAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGACGGTGTAG
* * * *
28268086 TGGAATAGATTAAAGTCACAACGGCGAATCTT
1 TGGAATAGATTGAAGCCACAACAGTGAATCTT
28268118 GTTTCCCCTA
Statistics
Matches: 167, Mismatches: 56, Indels: 15
0.70 0.24 0.06
Matches are distributed among these distances:
48 2 0.01
49 59 0.35
50 103 0.62
51 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (50 bp):
TGGAATAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGACGGTGTAG
Found at i:28268131 original size:99 final size:100
Alignment explanation
Indices: 28267844--28268150 Score: 318
Period size: 99 Copynumber: 3.1 Consensus size: 100
28267834 ACAATGGAAT
* * * * *
28267844 AGATTGAAGCCACAACAGTGAATCTTACTTCTCTGACGGTGTAGTGGAACAGATTGAAGTTACGA
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGTCACGA
* * ** *
28267909 CGGTGAATC-TGTTT-CCCTGATATTACAGTGGAAT
66 CGGTGAATCTTGTTTCCCCT-ACATTGCAGTTAAAA
*** *
28267943 AGATTGAAGCCACAACGACAAATCTTACTTCCCTAGCGGTGTAGTGGAATAGATTGAAG-CTACG
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGTC-ACG
** * * *
28268007 ATAGTGAATCTGGTTTCCCCGACATTGCAATTAAAA
65 ACGGTGAATCTTGTTTCCCCTACATTGCAGTTAAAA
* * * * * *
28268043 AGATTGAAGCCACAATGGTGAATCTTACCTCCCTGGCGATGCA-TGGAATAGATTAAAGTCACAA
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGTCACGA
*
28268107 CGGCGAATCTTGTTTCCCCTACATTGCAGTTAAACA
66 CGGTGAATCTTGTTTCCCCTACATTGCAGTTAAA-A
28268143 A-ATTGAAG
1 AGATTGAAG
28268151 AAAACAATCC
Statistics
Matches: 168, Mismatches: 35, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
99 114 0.68
100 51 0.30
101 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (100 bp):
AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGTCACGA
CGGTGAATCTTGTTTCCCCTACATTGCAGTTAAAA
Found at i:28268215 original size:42 final size:42
Alignment explanation
Indices: 28268161--28268462 Score: 194
Period size: 44 Copynumber: 7.1 Consensus size: 42
28268151 AAAACAATCC
*
28268161 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCAGATCT
** * *** ***
28268203 TATCTCTTTGAAGTTGTAGAATAGCAGA-TCGCATCCAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAT-CAGATCT
*
28268244 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAAAT-A-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT----AAAATCAGATCT
* *
28268288 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATCAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCAGATCT
* ** ** *
28268330 TATCTCTCTGAAGTTGC-GAAGAGCAGA-CCACATACAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAT-CAGATCT
* *
28268370 TATCTTCCTGAAGTTGCAGTGGAATAGACAGA--AGAAATCA-ATCC
1 TATCTCCCTGAAGTTGCAGTGG---AG-CAGATTA-AAATCAGATCT
* **
28268414 TATCTCCCTGAAGTTTCAGTGGAGTGGATTAAAAAAT-AGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT--AAAATCAGATCT
28268457 TATCTC
1 TATCTC
28268463 TATAAATTAT
Statistics
Matches: 197, Mismatches: 41, Indels: 43
0.70 0.15 0.15
Matches are distributed among these distances:
40 28 0.14
41 43 0.22
42 45 0.23
43 13 0.07
44 59 0.30
45 7 0.04
46 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (42 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCAGATCT
Found at i:28268428 original size:126 final size:127
Alignment explanation
Indices: 28268147--28268463 Score: 451
Period size: 126 Copynumber: 2.5 Consensus size: 127
28268137 TAAACAAATT
* *
28268147 GAAGAAAACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTTT
1 GAAGAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCT
* * * * * **
28268212 GAAGTTGTAGAATAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
66 GAAGTTGTAGAAGAGCAGACCACATACAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACA
*
28268274 GAAGAAAAT-AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAACATCAGATCTTATCTCTC
1 GAAG-AAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTC
* * *
28268338 TGAAGTTG-CGAAGAGCAGACCACATACAGTCTTATCTTCCTGAAGTTGCAGTGGAATAGACA
65 TGAAGTTGTAGAAGAGCAGACCACATACAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACA
* *
28268400 GAAGAAATCAATCCTATCTCCCTGAAGTTTCAGTGGAGTGGATTAAAAAAT-AGATCTTATCTCT
1 GAAGAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATT--AAAATCAGATCTTATCTCT
28268464 ATAAATTATA
Statistics
Matches: 170, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
125 4 0.02
126 81 0.48
127 78 0.46
128 7 0.04
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (127 bp):
GAAGAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCT
GAAGTTGTAGAAGAGCAGACCACATACAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACA
Found at i:28270060 original size:25 final size:24
Alignment explanation
Indices: 28270014--28270060 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
28270004 AGTTACAATT
*
28270014 ATTATTATTGTATTATATATCACC
1 ATTATTATTGTATTATAGATCACC
* *
28270038 ATTATTTTTAGTATTATCGATCA
1 ATTATTATT-GTATTATAGATCA
28270061 TTGTTATGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (24 bp):
ATTATTATTGTATTATAGATCACC
Found at i:28275917 original size:17 final size:18
Alignment explanation
Indices: 28275895--28275929 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28275885 GGTTCATGGC
*
28275895 AACGATA-CATCAAGTTT
1 AACGATACCATAAAGTTT
28275912 AACGATACCATAAAGTTT
1 AACGATACCATAAAGTTT
28275930 TTTGGCTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (18 bp):
AACGATACCATAAAGTTT
Found at i:28277843 original size:21 final size:20
Alignment explanation
Indices: 28277791--28277833 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
28277781 ACGGGTTAGT
28277791 TTGACTATAATAGTTAATAAA
1 TTGA-TATAATAGTTAATAAA
*
28277812 TTGATCATAATAGTTCATAAA
1 TTGAT-ATAATAGTTAATAAA
28277833 T
1 T
28277834 AATATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (20 bp):
TTGATATAATAGTTAATAAA
Found at i:28283628 original size:3 final size:3
Alignment explanation
Indices: 28283620--28283645 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28283610 AGTGGCCGGT
28283620 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
28283646 TCCTTCTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:28286893 original size:36 final size:37
Alignment explanation
Indices: 28286853--28286925 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 37
28286843 ACTTTACTGC
* *
28286853 TTTCGATTAGAA-TGAGGGAAAATTCTGGCTTACTAT
1 TTTCGATTAGAATTCAGGGAAAATTCTGGATTACTAT
28286889 TTTCGATTAGAATTTTCAGGGAAAATTCTGGATTACT
1 TTTCGATTAGAA--TTCAGGGAAAATTCTGGATTACT
28286926 GCTTTGCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 12 0.38
39 20 0.62
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (37 bp):
TTTCGATTAGAATTCAGGGAAAATTCTGGATTACTAT
Found at i:28295027 original size:7 final size:7
Alignment explanation
Indices: 28295017--28295041 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28295007 GTTTTAGTAA
28295017 TTAGATT
1 TTAGATT
28295024 TTAGATT
1 TTAGATT
28295031 TTAGATT
1 TTAGATT
28295038 TTAG
1 TTAG
28295042 TTAGATAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (7 bp):
TTAGATT
Found at i:28296649 original size:49 final size:48
Alignment explanation
Indices: 28296551--28296647 Score: 119
Period size: 50 Copynumber: 2.0 Consensus size: 48
28296541 TATAAAATAT
*
28296551 ATAAATATAAATATAAAAAAATTCAGAAACATATATATAATCTAGAAA
1 ATAAATATAAATATAAAAAAATTCAGAAACATATATATAATCTAAAAA
* *
28296599 ATAACATATAAATTATAAAAAAATTTATAAA-A-ATATGATAAT-TAAAAA
1 ATAA-ATATAAA-TATAAAAAAATTCAGAAACATATAT-ATAATCTAAAAA
28296647 A
1 A
28296648 ATTAGTTGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
48 14 0.33
49 13 0.30
50 16 0.37
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (48 bp):
ATAAATATAAATATAAAAAAATTCAGAAACATATATATAATCTAAAAA
Found at i:28297168 original size:20 final size:21
Alignment explanation
Indices: 28297145--28297186 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28297135 TATCATTAGA
28297145 AATTT-TAAAAAATCAAAAAT
1 AATTTATAAAAAATCAAAAAT
* *
28297165 AATTTATAAAAATTGAAAAAT
1 AATTTATAAAAAATCAAAAAT
28297186 A
1 A
28297187 CTAAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
AATTTATAAAAAATCAAAAAT
Found at i:28300115 original size:18 final size:18
Alignment explanation
Indices: 28300089--28300133 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
28300079 ATGTGAGAAT
*
28300089 TGATGTTCACATTTTAAA
1 TGATGTTCACATTTCAAA
*
28300107 TGATATTCACATTTCAAA
1 TGATGTTCACATTTCAAA
28300125 TGATGTTCA
1 TGATGTTCA
28300134 AATTGATGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (18 bp):
TGATGTTCACATTTCAAA
Found at i:28300662 original size:72 final size:72
Alignment explanation
Indices: 28300557--28300728 Score: 233
Period size: 72 Copynumber: 2.4 Consensus size: 72
28300547 AACAACAATG
* * * * *
28300557 CTAAA-CTAGTTTTATCAATAGTTATTTACGTTTGGTTTTTGGATATTGAATTTATGTTCTACTT
1 CTAAATCTAGTTTTATCAATAGTTGTTTATGTTTGGTATTTGGATATTAAATTTATGTTCTACTG
28300621 ATTTAT-
66 ATTTATA
* * *
28300627 GTGTAATCTAGTTTTATTAATAGTTGTTTATGTTTGGTATTTGGATATTAAATTTATGTTCTACT
1 CT-AAATCTAGTTTTATCAATAGTTGTTTATGTTTGGTATTTGGATATTAAATTTATGTTCTACT
28300692 GATTTATA
65 GATTTATA
*
28300700 CTAAAT-TAATTTTATCAATAGTTGTTTAT
1 CTAAATCTAGTTTTATCAATAGTTGTTTAT
28300729 ATATGATTTT
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
70 1 0.01
71 23 0.26
72 62 0.71
73 1 0.01
ACGTcount: A:0.27, C:0.06, G:0.13, T:0.53
Consensus pattern (72 bp):
CTAAATCTAGTTTTATCAATAGTTGTTTATGTTTGGTATTTGGATATTAAATTTATGTTCTACTG
ATTTATA
Found at i:28300751 original size:71 final size:72
Alignment explanation
Indices: 28300566--28300752 Score: 191
Period size: 72 Copynumber: 2.6 Consensus size: 72
28300556 GCTAAACTAG
* ** * * * * * * *
28300566 TTTTATCAATAGTTATTTACGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
1 TTTTATCAATAGTTGTTTATATATGATATTTGGATATTAAATTTATGTTCTACTGATTTATCTGA
*
28300631 AATCTAG
66 AATCTAA
* * * *
28300638 TTTTATTAATAGTTGTTTATGTTTGGTATTTGGATATTAAATTTATGTTCTACTGATTTATACT-
1 TTTTATCAATAGTTGTTTATATATGATATTTGGATATTAAATTTATGTTCTACTGATTTAT-CTG
28300702 AAAT-TAA
65 AAATCTAA
*
28300709 TTTTATCAATAGTTGTTTATATATGAT-TTTGGATGTTCAAATTT
1 TTTTATCAATAGTTGTTTATATATGATATTTGGATATT-AAATTT
28300753 TTTCATAGGT
Statistics
Matches: 99, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
70 9 0.09
71 31 0.31
72 58 0.59
73 1 0.01
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.54
Consensus pattern (72 bp):
TTTTATCAATAGTTGTTTATATATGATATTTGGATATTAAATTTATGTTCTACTGATTTATCTGA
AATCTAA
Found at i:28302118 original size:15 final size:15
Alignment explanation
Indices: 28302098--28302129 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28302088 AGAAGGTGAT
28302098 GATGATGACGACGAC
1 GATGATGACGACGAC
*
28302113 GATGATGATGACGAC
1 GATGATGACGACGAC
28302128 GA
1 GA
28302130 CGATAATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.34, T:0.16
Consensus pattern (15 bp):
GATGATGACGACGAC
Found at i:28302118 original size:18 final size:18
Alignment explanation
Indices: 28302095--28302140 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
28302085 TCGAGAAGGT
28302095 GATGATGATGACGACGAC
1 GATGATGATGACGACGAC
28302113 GATGATGATGACGACGAC
1 GATGATGATGACGACGAC
*
28302131 GATAATGATG
1 GATGATGATG
28302141 GTGATGATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.35, C:0.13, G:0.33, T:0.20
Consensus pattern (18 bp):
GATGATGATGACGACGAC
Found at i:28302120 original size:21 final size:21
Alignment explanation
Indices: 28302094--28302152 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
28302084 GTCGAGAAGG
*
28302094 TGATGATGATGACGACGACGA
1 TGATGATGATGACGACGACAA
* *
28302115 TGATGATGACGACGACGATAA
1 TGATGATGATGACGACGACAA
* *
28302136 TGATGGTGATGATGACG
1 TGATGATGATGACGACG
28302153 GTGAATCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.32, C:0.12, G:0.34, T:0.22
Consensus pattern (21 bp):
TGATGATGATGACGACGACAA
Found at i:28307066 original size:40 final size:40
Alignment explanation
Indices: 28307029--28307253 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
28307019 GCTACTCGTT
* *
28307029 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
28307069 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
28307109 CAAATGCCTTCGGGCCTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
28307149 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
28307188 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
28307229 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
28307254 CATCATTCAA
Statistics
Matches: 166, Mismatches: 14, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
38 2 0.01
39 33 0.20
40 118 0.71
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:28307213 original size:119 final size:120
Alignment explanation
Indices: 28307029--28307253 Score: 296
Period size: 119 Copynumber: 1.9 Consensus size: 120
28307019 GCTACTCGTT
*
28307029 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* * *
28307094 ATTTAGTAAC-TCGCACAAATGCCTTCGGGCCTTAACCCGGATTTAGTAACTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * **
28307149 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* * *
28307211 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
28307254 CATCATTCAA
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
118 4 0.04
119 65 0.71
120 22 0.24
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:28315142 original size:79 final size:81
Alignment explanation
Indices: 28315040--28315224 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
28315030 GCTCCTCGTT
* *
28315040 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
28315103 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* **
28315120 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
28315184 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
28315200 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28315225 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:28315224 original size:40 final size:40
Alignment explanation
Indices: 28315040--28315224 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
28315030 GCTCCTCGTT
* *
28315040 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
28315080 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
28315120 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
28315159 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
28315200 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28315225 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.25
40 80 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:28317120 original size:42 final size:40
Alignment explanation
Indices: 28317069--28317164 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
28317059 CTAAATCATG
*
28317069 TCCACATCAGCGCGATGTCAAG-GGACGTGTCAGCAAATCGCA
1 TCCACATCAGCGCGAT-T--AGCGGACGTGGCAGCAAATCGCA
* *
28317111 TCCACATCAGCGCGATTTGCTGACGTGGCAGCAAATCGCA
1 TCCACATCAGCGCGATTAGCGGACGTGGCAGCAAATCGCA
* *
28317151 TCCACGTAAGCGCG
1 TCCACATCAGCGCG
28317165 CTTTGTGGTC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
39 1 0.02
40 30 0.62
41 1 0.02
42 16 0.33
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.18
Consensus pattern (40 bp):
TCCACATCAGCGCGATTAGCGGACGTGGCAGCAAATCGCA
Found at i:28317147 original size:40 final size:40
Alignment explanation
Indices: 28317092--28317169 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
28317082 GATGTCAAGG
* *
28317092 GACGTGTCAGCAAATCGCATCCACATCAGCGCGATTTGCT
1 GACGTGGCAGCAAATCGCATCCACATAAGCGCGATTTGCT
* *
28317132 GACGTGGCAGCAAATCGCATCCACGTAAGCGCGCTTTG
1 GACGTGGCAGCAAATCGCATCCACATAAGCGCGATTTG
28317170 TGGTCATGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.24, C:0.29, G:0.26, T:0.21
Consensus pattern (40 bp):
GACGTGGCAGCAAATCGCATCCACATAAGCGCGATTTGCT
Found at i:28317183 original size:40 final size:40
Alignment explanation
Indices: 28317096--28317185 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
28317086 TCAAGGGACG
* *
28317096 TGTCAGCAAATCGCATCCACATCAGCGCGATTTGCTGACG
1 TGTCAGCAAATCGCATCCACATAAGCGCGATTTGCTGACA
* * * *
28317136 TGGCAGCAAATCGCATCCACGTAAGCGCGCTTTG-TGGTCA
1 TGTCAGCAAATCGCATCCACATAAGCGCGATTTGCT-GACA
28317176 TGTCAGCAAA
1 TGTCAGCAAA
28317186 GCGCGCTGAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.02
40 41 0.98
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (40 bp):
TGTCAGCAAATCGCATCCACATAAGCGCGATTTGCTGACA
Found at i:28317683 original size:127 final size:124
Alignment explanation
Indices: 28317402--28317967 Score: 672
Period size: 124 Copynumber: 4.5 Consensus size: 124
28317392 GATAAAATCA
* * * * * * * * * *
28317402 AAGCAGGATGATTTATCA-AAGGATTTTTGAAGTCACTCCCACGTGTACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACACGCTTTTGCTACAGT
* * *
28317466 AGATCCTGGAAAAATAATTTTGAGTTAACGTTTCTAAGCAAATAGTTTAAAAAAA-GCTTC
66 AGGTCCTGGAAAAATAATTTCGAGTTAACGTTTCTGAGCAAATAG--TAAAAAAACGCTTC
*
28317526 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGAGCCCTCGTGGACACGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACACGCTTTTGCTACAGT
* * *
28317591 TGGTCTTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
66 AGGTCCTGGAA-AAATAATTTCGAGTTAACGTTTCTGAGCAAATAG--TAAAAAAACGCTTC
* *
28317653 AAGCAGGATGCTTTATGAGAAGAAATTGTGAAATCGCGCTCAT-GTGGACACGCTTTTGCTACAG
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGC-CCTCGTGGACACGCTTTTGCTACAG
* * * *
28317717 TAGGTCCTGAAAAAATAATTTCGAGTTAACGTTTTTGAGCAAATAGTATAAAAACGCTGC
65 TAGGTCCTGGAAAAATAATTTCGAGTTAACGTTTCTGAGCAAATAGTAAAAAAACGCTTC
* *
28317777 AAGTAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACACGCTTTTGCTACAG
* * * * * * *
28317841 TAAGTTCTGGAAAAATAATTTCGACTTGACATTTCTGAGCAAATAGTATAAAATCGCTTC
65 TAGGTCCTGGAAAAATAATTTCGAGTTAACGTTTCTGAGCAAATAGTAAAAAAACGCTTC
* * * * * * * **
28317901 TAGTAGGATTCTTTATGAGAAGAATTTGTGAAATCGCACCCACATGGACGCATTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACACGCTTTTGCTACAGT
28317966 AG
66 AG
28317968 CATGTTTGGG
Statistics
Matches: 387, Mismatches: 48, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
123 4 0.01
124 189 0.49
125 47 0.12
126 73 0.19
127 72 0.19
128 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (124 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACACGCTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTCGAGTTAACGTTTCTGAGCAAATAGTAAAAAAACGCTTC
Found at i:28321153 original size:21 final size:21
Alignment explanation
Indices: 28321127--28321287 Score: 198
Period size: 21 Copynumber: 7.6 Consensus size: 21
28321117 TCAAATTATA
28321127 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
28321148 TTTAAGTTAAGTGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* * * *
28321169 TTTTATTTAAGGGTTACGATT
1 TTTAAGTTAAGGGTTAGGGTT
* *
28321190 TTAAAGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* * *
28321212 CTTAATTTAAGGGTTACGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
28321233 TTAAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
28321255 TTTAAGTTAAGGGTTAGGG-T
1 TTTAAGTTAAGGGTTAGGGTT
28321275 TTTAAGTTAAGGG
1 TTTAAGTTAAGGG
28321288 GTTATGTAAT
Statistics
Matches: 118, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
20 14 0.12
21 69 0.58
22 35 0.30
ACGTcount: A:0.25, C:0.02, G:0.29, T:0.44
Consensus pattern (21 bp):
TTTAAGTTAAGGGTTAGGGTT
Found at i:28321282 original size:85 final size:85
Alignment explanation
Indices: 28321128--28321293 Score: 235
Period size: 85 Copynumber: 2.0 Consensus size: 85
28321118 CAAATTATAT
* * * * *
28321128 TTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGTGTTAGGGTTTTTTATTTAAGGGTTACGATTTTA
1 TTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTACGATTTTA
*
28321193 AAGTTAAGGGTTTATGGTTC
66 AAGTTAAGGGGTTATGGTTC
* * *
28321213 TTAATTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTT
1 TTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTACGATTTT
28321278 -AAGTTAAGGGGTTATG
65 AAAGTTAAGGGGTTATG
28321294 TAATAGCCTG
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
85 44 0.62
86 27 0.38
ACGTcount: A:0.25, C:0.02, G:0.29, T:0.44
Consensus pattern (85 bp):
TTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTACGATTTTA
AAGTTAAGGGGTTATGGTTC
Found at i:28321290 original size:43 final size:43
Alignment explanation
Indices: 28321127--28321287 Score: 218
Period size: 43 Copynumber: 3.8 Consensus size: 43
28321117 TCAAATTATA
* * *
28321127 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGTG-TTAGGGTT
1 TTTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTT
* * * *
28321169 TTTTATTTAAGGGTTACGATTTTAAAGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTT
* *
28321212 CTTAATTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTT
*
28321255 TTTAAGTTAAGGGTTAGGGTTTT-AAGTTAAGGG
1 TTTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGG
28321288 GTTATGTAAT
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
42 38 0.37
43 66 0.63
ACGTcount: A:0.25, C:0.02, G:0.29, T:0.44
Consensus pattern (43 bp):
TTTAAGTTAAGGGTTACGGTTTTAAAGTTAAGGGTTTAGGGTT
Found at i:28323680 original size:46 final size:46
Alignment explanation
Indices: 28323605--28323697 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
28323595 TATGGCAAAG
*
28323605 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
*
28323651 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
28323697 T
1 T
28323698 ATAGCAATGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:28324075 original size:22 final size:22
Alignment explanation
Indices: 28324050--28324448 Score: 415
Period size: 22 Copynumber: 18.5 Consensus size: 22
28324040 GGGTGTTACA
*
28324050 GGTTAGGGTCTTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
28324072 GGTTAGGGTTTTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
28324094 GGTTAGGGTTTTTAAGTTAA-G
1 GGTTAGGGTTTTTAAGTTAAGG
* *
28324115 GGTTAGGATTTTTAGGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
* *
28324137 GTTTATGGTTTTTAAGTTAA-G
1 GGTTAGGGTTTTTAAGTTAAGG
28324158 GGTTAGGGTTTTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
*
28324180 GTTTAGGGTTTTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
* ** *
28324202 GATTAAAGTTTTTAAGTTAAAG
1 GGTTAGGGTTTTTAAGTTAAGG
* *
28324224 GTTTAGGGTTTTTAAGTTAAAG
1 GGTTAGGGTTTTTAAGTTAAGG
*
28324246 GTTTAGGG--TTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
28324266 GG-TAGGG--TTTAAGTTAA-G
1 GGTTAGGGTTTTTAAGTTAAGG
* *
28324284 GGTTCAGAGTTTTTAATTTAAGG
1 GGTT-AGGGTTTTTAAGTTAAGG
* *
28324307 GTTTAAGGTTTTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
* * *
28324329 AGTTAGGGTTTTTAGGTTAAGA
1 GGTTAGGGTTTTTAAGTTAAGG
* * *
28324351 GTTTATGATTTTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
* * *
28324373 GTTTAAGGTTTTTAATTTAA-G
1 GGTTAGGGTTTTTAAGTTAAGG
* *
28324394 AGTTAGGAG-TTTTAAGGTTTA-G
1 GGTTAGG-GTTTTTAA-GTTAAGG
*
28324416 GGTTAGGGTTTTTAGGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
* *
28324438 GTTTAAGGTTT
1 GGTTAGGGTTT
28324449 GTCAATTAAA
Statistics
Matches: 317, Mismatches: 49, Indels: 22
0.82 0.13 0.06
Matches are distributed among these distances:
18 3 0.01
19 16 0.05
20 15 0.05
21 54 0.17
22 225 0.71
23 4 0.01
ACGTcount: A:0.26, C:0.01, G:0.31, T:0.43
Consensus pattern (22 bp):
GGTTAGGGTTTTTAAGTTAAGG
Found at i:28324134 original size:43 final size:43
Alignment explanation
Indices: 28324052--28324448 Score: 466
Period size: 44 Copynumber: 9.2 Consensus size: 43
28324042 GTGTTACAGG
* *
28324052 TTAGGGTCTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGG
1 TTAGGGTTTTTAAGTTAA-GGGTTAGGGTTTTTAAGTTAAGGGT
* *
28324096 TTAGGGTTTTTAAGTTAAGGGTTAGGATTTTTAGGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGT
*
28324139 TTATGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGT
** *
28324182 TTAGGGTTTTTAAGTTAAGGGATTAAAGTTTTTAAGTTAAAGGT
1 TTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGT
*
28324226 TTAGGGTTTTTAAGTTAAAGGTTTAGGG--TTTAAGTTAAGGG-
1 TTAGGGTTTTTAAGTT-AAGGGTTAGGGTTTTTAAGTTAAGGGT
* * *
28324267 GTAGGG--TTTAAGTTAAGGGTTCAGAGTTTTTAATTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGTT-AGGGTTTTTAAGTTAAGGGT
* * *
28324309 TTAAGGTTTTTAAGTTAAGGAGTTAGGGTTTTTAGGTTAAGAGT
1 TTAGGGTTTTTAAGTTAAGG-GTTAGGGTTTTTAAGTTAAGGGT
* * * * *
28324353 TTATGATTTTTAAGTTAAGGGTTTAAGGTTTTTAATTTAAGAG-
1 TTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGT
* *
28324396 TTAGGAG-TTTTAAGGTTTAGGGTTAGGGTTTTTAGGTTAAGGGT
1 TTAGG-GTTTTTAA-GTTAAGGGTTAGGGTTTTTAAGTTAAGGGT
*
28324440 TTAAGGTTT
1 TTAGGGTTT
28324449 GTCAATTAAA
Statistics
Matches: 301, Mismatches: 38, Indels: 28
0.82 0.10 0.08
Matches are distributed among these distances:
38 6 0.02
39 11 0.04
41 17 0.06
42 16 0.05
43 111 0.37
44 133 0.44
45 7 0.02
ACGTcount: A:0.26, C:0.01, G:0.30, T:0.44
Consensus pattern (43 bp):
TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGT
Found at i:28324993 original size:18 final size:18
Alignment explanation
Indices: 28324966--28325000 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28324956 GGAAAAGGAA
* *
28324966 ACATATAAGGGTTAAGAT
1 ACATAAAAGGGCTAAGAT
28324984 ACATAAAAGGGCTAAGA
1 ACATAAAAGGGCTAAGA
28325001 AACGCACCTG
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:0.49, C:0.09, G:0.23, T:0.20
Consensus pattern (18 bp):
ACATAAAAGGGCTAAGAT
Found at i:28325661 original size:7 final size:7
Alignment explanation
Indices: 28325651--28325676 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28325641 TTATATACAT
28325651 AATACTA
1 AATACTA
28325658 AATACTA
1 AATACTA
28325665 AATACTA
1 AATACTA
28325672 AATAC
1 AATAC
28325677 CAATAGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:28326662 original size:11 final size:11
Alignment explanation
Indices: 28326648--28326699 Score: 77
Period size: 11 Copynumber: 4.6 Consensus size: 11
28326638 TGGAAAGAAT
*
28326648 TTGAGAGCAAA
1 TTGAGAGGAAA
28326659 TTGAGAGGAAA
1 TTGAGAGGAAA
*
28326670 TTTAGAGGAAA
1 TTGAGAGGAAA
28326681 TTGAGAGGAAA
1 TTGAGAGGAAA
28326692 TTTGAGAG
1 -TTGAGAG
28326700 AGGATTAGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
11 30 0.81
12 7 0.19
ACGTcount: A:0.42, C:0.02, G:0.33, T:0.23
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:28326681 original size:22 final size:23
Alignment explanation
Indices: 28326645--28326699 Score: 94
Period size: 22 Copynumber: 2.4 Consensus size: 23
28326635 ATTTGGAAAG
28326645 AATTTGAGAGCAAATTGAGAGGA
1 AATTTGAGAGCAAATTGAGAGGA
*
28326668 AATTT-AGAGGAAATTGAGAGGA
1 AATTTGAGAGCAAATTGAGAGGA
28326690 AATTTGAGAG
1 AATTTGAGAG
28326700 AGGATTAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 21 0.70
23 9 0.30
ACGTcount: A:0.44, C:0.02, G:0.31, T:0.24
Consensus pattern (23 bp):
AATTTGAGAGCAAATTGAGAGGA
Found at i:28326941 original size:40 final size:42
Alignment explanation
Indices: 28326886--28326987 Score: 118
Period size: 40 Copynumber: 2.5 Consensus size: 42
28326876 CACAAAGCAT
* * *
28326886 GCTGACATGGACGCGATTTACTGCCACGTCAGCT-A-ACCGC
1 GCTGACGTGGACGCGATTTACTGACACGTCACCTGACACCGC
* * *
28326926 GCTGACGTGGACGCGATTTGCTGACACGTCCCCTGACATCGC
1 GCTGACGTGGACGCGATTTACTGACACGTCACCTGACACCGC
* *
28326968 GCTGACGTGAACGCAATTTA
1 GCTGACGTGGACGCGATTTA
28326988 AAGGAAAATG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 29 0.57
41 1 0.02
42 21 0.41
ACGTcount: A:0.22, C:0.30, G:0.26, T:0.22
Consensus pattern (42 bp):
GCTGACGTGGACGCGATTTACTGACACGTCACCTGACACCGC
Found at i:28332306 original size:21 final size:21
Alignment explanation
Indices: 28332280--28332320 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28332270 AAACAATGAT
28332280 AAAAAGTATCAATACATTTTC
1 AAAAAGTATCAATACATTTTC
* *
28332301 AAAAAGTATCTATACCTTTT
1 AAAAAGTATCAATACATTTT
28332321 ACCAAGTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.37
Consensus pattern (21 bp):
AAAAAGTATCAATACATTTTC
Found at i:28333084 original size:27 final size:27
Alignment explanation
Indices: 28333034--28333085 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
28333024 ACTAACATAT
*
28333034 ATATAATTATTATTTAATATATAATTA
1 ATATAATTATTATTTAATAAATAATTA
*
28333061 ATATAATTATT-TTTTATAAAATAAT
1 ATATAATTATTATTTAAT-AAATAAT
28333086 ATTTTTGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
ATATAATTATTATTTAATAAATAATTA
Found at i:28337538 original size:18 final size:18
Alignment explanation
Indices: 28337507--28337554 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
28337497 ATATAATTTT
*
28337507 AAATAATTTTTAAAATTCA
1 AAAT-ATTTATAAAATTCA
*
28337526 AAATATTTATAAAAATTCT
1 AAATATTTAT-AAAATTCA
28337545 AAA-ATTTATA
1 AAATATTTATA
28337555 TTTTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 11 0.42
19 14 0.54
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATTTATAAAATTCA
Found at i:28337598 original size:12 final size:10
Alignment explanation
Indices: 28337561--28337600 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
28337551 TATATTTTTT
28337561 AAAAATTATA
1 AAAAATTATA
*
28337571 AAAAATTCTA
1 AAAAATTATA
28337581 AAAAATATATA
1 AAAAAT-TATA
28337592 AAGAAATTA
1 AA-AAATTA
28337601 AAACATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 15 0.58
11 7 0.27
12 4 0.15
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (10 bp):
AAAAATTATA
Found at i:28337603 original size:19 final size:18
Alignment explanation
Indices: 28337558--28337612 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 18
28337548 ATTTATATTT
28337558 TTTAAAAATTATAAAAAA
1 TTTAAAAATTATAAAAAA
28337576 TTCTAAAAAATATATAAAGAAA
1 TT-T-AAAAAT-TATAAA-AAA
28337598 -TTAAAACATTA-AAAA
1 TTTAAAA-ATTATAAAA
28337613 TTTTCTAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
17 1 0.03
18 5 0.16
19 7 0.22
20 9 0.28
21 7 0.22
22 3 0.09
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (18 bp):
TTTAAAAATTATAAAAAA
Found at i:28347799 original size:26 final size:24
Alignment explanation
Indices: 28347750--28347826 Score: 66
Period size: 27 Copynumber: 3.0 Consensus size: 24
28347740 TTAATTAATT
* *
28347750 TTTAAAAATTAAAATGATAAAAAATA
1 TTTAAAAA-TAAAATTAT-TAAAATA
28347776 TTGTAAAAATAAAAATTATTAAAATTA
1 TT-TAAAAAT-AAAATTATTAAAA-TA
*
28347803 TTTAGAAAATATAA-TATTAAAATA
1 TTTA-AAAATAAAATTATTAAAATA
28347827 ATTTTTTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
24 2 0.05
25 8 0.18
26 12 0.27
27 22 0.50
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (24 bp):
TTTAAAAATAAAATTATTAAAATA
Found at i:28347799 original size:27 final size:26
Alignment explanation
Indices: 28347750--28347813 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
28347740 TTAATTAATT
*
28347750 TTTAAAAATTAAAATGATAAAAAATA
1 TTTAAAAATAAAAATGATAAAAAATA
* * *
28347776 TTGTAAAAATAAAAATTATTAAAATTA
1 TT-TAAAAATAAAAATGATAAAAAATA
28347803 TTTAGAAAATA
1 TTTA-AAAATA
28347814 TAATATTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 4 0.12
27 28 0.88
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (26 bp):
TTTAAAAATAAAAATGATAAAAAATA
Found at i:28348735 original size:41 final size:40
Alignment explanation
Indices: 28348639--28348796 Score: 199
Period size: 40 Copynumber: 3.9 Consensus size: 40
28348629 TTTGGATAGA
* * * * *
28348639 AAACGCCGTAAAAGGTAAAGCATTAGCAGCGTTTTTGCGT
1 AAACGCCGTAAAAGGTAAAGCAATAGCGGCATTTTTTCAT
* *
28348679 AAACGCCGTAAAAGGTAAAGTAATAGTGGCATTTTTCTCAT
1 AAACGCCGTAAAAGGTAAAGCAATAGCGGCATTTTT-TCAT
* *
28348720 AAACGCCGCAAAAGGTAAAGCAACAGCGGCATTTTTTCAT
1 AAACGCCGTAAAAGGTAAAGCAATAGCGGCATTTTTTCAT
* * *
28348760 AAACGCCGTTAAAGGTAAAGCAATAGCAGCGTTTTTT
1 AAACGCCGTAAAAGGTAAAGCAATAGCGGCATTTTTT
28348797 TCCACAAAAG
Statistics
Matches: 101, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 67 0.66
41 34 0.34
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (40 bp):
AAACGCCGTAAAAGGTAAAGCAATAGCGGCATTTTTTCAT
Found at i:28348795 original size:81 final size:82
Alignment explanation
Indices: 28348639--28348813 Score: 208
Period size: 81 Copynumber: 2.1 Consensus size: 82
28348629 TTTGGATAGA
* ** * * *
28348639 AAACGCCGTAAAAGGTAAAGCATTAGCAGCGTTTTTGCGTAAACGCCGTAAAAGGTAAAGTAATA
1 AAACGCCGCAAAAGGTAAAGCAACAGCAGCATTTTTGCATAAACGCCGTAAAAGGTAAAGCAATA
** *
28348704 GTGGCATTTTTCT-CAT
66 GCAGCATTTTTCTCCAC
* * *
28348720 AAACGCCGCAAAAGGTAAAGCAACAGCGGCATTTTTTCATAAACGCCGTTAAAGGTAAAGCAATA
1 AAACGCCGCAAAAGGTAAAGCAACAGCAGCATTTTTGCATAAACGCCGTAAAAGGTAAAGCAATA
* *
28348785 GCAGCGTTTTTTTCCAC
66 GCAGCATTTTTCTCCAC
*
28348802 AAAAGCCGCAAA
1 AAACGCCGCAAA
28348814 TATTTTTTAT
Statistics
Matches: 78, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
81 65 0.83
82 13 0.17
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (82 bp):
AAACGCCGCAAAAGGTAAAGCAACAGCAGCATTTTTGCATAAACGCCGTAAAAGGTAAAGCAATA
GCAGCATTTTTCTCCAC
Found at i:28349165 original size:20 final size:20
Alignment explanation
Indices: 28349128--28349166 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28349118 AAACTCTATC
*
28349128 TATTTTGGTTTTACATGAAG
1 TATTTTGGTTCTACATGAAG
*
28349148 TATTTTGGTTCTATATGAA
1 TATTTTGGTTCTACATGAA
28349167 ATGAATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.51
Consensus pattern (20 bp):
TATTTTGGTTCTACATGAAG
Found at i:28355395 original size:29 final size:29
Alignment explanation
Indices: 28355362--28355420 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
28355352 CATCTCTTGG
28355362 TAAGCATTTAATTTCACTACCTCTTTTAC
1 TAAGCATTTAATTTCACTACCTCTTTTAC
28355391 TAAGCATTTAATTTCACTACCTCTTTTAC
1 TAAGCATTTAATTTCACTACCTCTTTTAC
28355420 T
1 T
28355421 TTCTGGTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.24, G:0.03, T:0.46
Consensus pattern (29 bp):
TAAGCATTTAATTTCACTACCTCTTTTAC
Found at i:28355607 original size:66 final size:66
Alignment explanation
Indices: 28355501--28355637 Score: 249
Period size: 66 Copynumber: 2.1 Consensus size: 66
28355491 GCTTAAAGTT
*
28355501 TATATGTTGTGGGTGTTACATAAAATACTTATTTTACTTTGATTATCGGGAATTATACACCTTTC
1 TATACGTTGTGGGTGTTACATAAAATACTTATTTTACTTTGATTATC-GGAATTATACACCTTTC
28355566 AC
65 AC
28355568 TATACGTTGTGGGTGTTACAT-AAATACTTATTTTACTTTGATTATCGGAATTATACACCTTTCA
1 TATACGTTGTGGGTGTTACATAAAATACTTATTTTACTTTGATTATCGGAATTATACACCTTTCA
28355632 C
66 C
28355633 TATAC
1 TATAC
28355638 TTAAATCTGC
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
65 24 0.35
66 25 0.36
67 20 0.29
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (66 bp):
TATACGTTGTGGGTGTTACATAAAATACTTATTTTACTTTGATTATCGGAATTATACACCTTTCA
C
Found at i:28356238 original size:161 final size:164
Alignment explanation
Indices: 28356038--28357152 Score: 930
Period size: 164 Copynumber: 6.9 Consensus size: 164
28356028 ATTTCATGGA
* *
28356038 TGTTATATAAATGCTTATTTTTCTTTGGTTATCGGAATCATACACCTTTCACTATACCTAAACCT
1 TGTTATATAAATGCTTATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAACCT
* *
28356103 CTATTTTA-T-T-ATGCTTATTTTGTTTTTGTTTCAATAAGT-AAATAGGTTTTCAAATTAGATA
66 CTATTTTATTATAATGCTTATTTTGTTTTTGTTTTAATAAGTAAAAT-GGTTTTCAAATTATATA
**
28356164 TCTTTTAACGATACTTAAAGTTTATATTTTA-CGAG
130 TCTTTTAACGATACTTAAAGTTTATATTCCATC-AG
* * * * *
28356199 TGTTATATAAATACTTATTTTGCTTTGGTTATAGGAATCATACACCTTCCGCTATACCTAAACCT
1 TGTTATATAAATGCTTATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAACCT
* * * * * *
28356264 TTATTTTATTATAAATGCTTATTTTGTTTCTATTTTAATAAGTAAGACGGTTTTCGAATTATATA
66 CTATTTTATTAT-AATGCTTATTTTGTTTTTGTTTTAATAAGTAAAATGGTTTTCAAATTATATA
* *
28356329 TCTTTTAACGATACTAATTAAAGTTTATATTTCAT-TG
130 TCTTTTAACGATAC---TTAAAGTTTATATTCCATCAG
*
28356366 TG-TACTATAAATG-TTAATTTTGCTTTCGTTATCGGAATCATCCACCTTTCACTATACCTAAAC
1 TGTTA-TATAAATGCTT-ATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAAC
* * *
28356429 CTCTATTTTATTATAGATGCTTACTTTTGTTTTTATTTTAATAAGTATAATGATTTTTGAATTAT
64 CTCTATTTTATTATA-ATGCTTA-TTTTGTTTTTGTTTTAATAAGTA-AA--A----TG-GTTTT
* * *
28356494 AATGAATTATATATCTTTTAACGATATTTAAAGTTTATATTTCATC-G
119 CA--AATTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCAG
* * * * **
28356541 TACG-T-TATAAATGCTTATTTTAC-TTC-TT-T---TA-CA-ATACC--T-A--A-ACTTGTA-
1 T--GTTATATAAATGCTTATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAAC
* * * * * ** * *
28356589 TTTTATTATA-AATGAT--TAT-TTT-GTTCCTGTTTTAATAGGCAAAATGG-TTTCAAATTATA
64 CTCTATTTTATTATAATGCT-TATTTTGTTTTTGTTTTAATAAGTAAAATGGTTTTCAAATTATA
* *
28356648 TATCTTTTAACGATACCTAAAGTTTATATTCCAT-TG
128 TATCTTTTAACGATACTTAAAGTTTATATTCCATCAG
* * * * ** *
28356684 TGTTCTATAAATACTTATTTTGCTTTCGTTATCGGAATCGTACACTTTTTTCTATACCTAAACTT
1 TGTTATATAAATGCTTATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAACCT
* *
28356749 ATATTTTATTATAAATGCTTATTTTGTTTTTGTTTTAATAAGTAAAATGGTTTTCAATTTATATA
66 CTATTTTATTAT-AATGCTTATTTTGTTTTTGTTTTAATAAGTAAAATGGTTTTCAAATTATATA
28356814 TCTTTTAACGATACTTAAAGTTTATATTCCATC-G
130 TCTTTTAACGATACTTAAAGTTTATATTCCATCAG
* * * * * * * * *
28356848 TGTTTTATAAATTCTTATTTCGCTTTCGTTATCGGAATCAGACATCTTTTATTATACTTAAACTT
1 TGTTATATAAATGCTTATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAACCT
* * * *
28356913 GTATTTTATTATAAATGCTTATTTTG-TTTT-TATTATTAAGTAAGATGGTTTTCAAATTATATA
66 CTATTTTATTAT-AATGCTTATTTTGTTTTTGTTTTAATAAGTAAAATGGTTTTCAAATTATATA
* *
28356976 TCTTTTAACGATGAC-TAAA-TCTATACTCCATC-G
130 TCTTTTAACGAT-ACTTAAAGTTTATATTCCATCAG
* * * * * *
28357009 TGTCT-TATAAATGCTTATTTT-CTTTGGTTATTGAAATCATATACCTTTTACTATACCCAAACC
1 TGT-TATATAAATGCTTATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAACC
* * * * * * * *
28357072 -CGTATTTTATTATAAATACTTATTTTGTATTTATTTTAATATGCAGATTGGTTTTCAAATTATG
65 TC-TATTTTATTAT-AATGCTTATTTTGTTTTTGTTTTAATAAGTAAAATGGTTTTCAAATTATA
*
28357136 TATCTTTT-ACAATACTT
128 TATCTTTTAACGATACTT
28357153 GTAATTTATG
Statistics
Matches: 780, Mismatches: 114, Indels: 120
0.77 0.11 0.12
Matches are distributed among these distances:
141 1 0.00
142 1 0.00
143 56 0.07
144 3 0.00
145 5 0.01
146 1 0.00
147 2 0.00
149 1 0.00
150 1 0.00
151 4 0.01
153 3 0.00
154 14 0.02
155 3 0.00
156 2 0.00
157 5 0.01
158 10 0.01
159 4 0.01
160 67 0.09
161 109 0.14
162 83 0.11
163 28 0.04
164 126 0.16
165 56 0.07
166 7 0.01
167 75 0.10
168 40 0.05
169 2 0.00
171 1 0.00
172 1 0.00
173 2 0.00
174 3 0.00
175 35 0.04
176 5 0.01
177 2 0.00
178 22 0.03
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.48
Consensus pattern (164 bp):
TGTTATATAAATGCTTATTTTGCTTTCGTTATCGGAATCATACACCTTTCACTATACCTAAACCT
CTATTTTATTATAATGCTTATTTTGTTTTTGTTTTAATAAGTAAAATGGTTTTCAAATTATATAT
CTTTTAACGATACTTAAAGTTTATATTCCATCAG
Found at i:28356719 original size:318 final size:310
Alignment explanation
Indices: 28355702--28357152 Score: 1001
Period size: 324 Copynumber: 4.5 Consensus size: 310
28355692 CAACTATGCT
** * * * *
28355702 TAAAGTTTATATTTTATGAGTGTTATATAAATGCTTGTTTTGCTTTGGTTATCGGAATCATACAC
1 TAAAGTTTATATTCCAT-TGTGTTCTATAAAT-CTTATTTTGCTTTCGTTATCGGAATCATACAC
* * * * * * *
28355767 CTTTCACCATACCTATACCTCTATTTTATTATAAATGCGTACTTT-ATTTT-TTTTAATAAGTAG
64 CTTTTACTATACCTAAACCTCTATTTTATTATAAATGCTTATTTTGTTTTTATTTTAATAAGTAA
* * * * ** **
28355830 AACGATTTTCGAA-TTATATATCTTTTAACGATACTTAAAATTTATATTTCATTATATATTATAA
129 AATGGTTTTC-AATTTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCGTACGTTATAA
* * * * * * *
28355894 ATGCTTATTTTGCTTTGGTTATCGGAATCATACACCTTTCACCATATCTATACCTCTATTTTGTT
193 ATGCTTA-TTT-C-----TTATC---AT-AT----CTTTTACAATACCTAAACTTGTATTTTATT
* * * * * * *
28355959 ATAAATGCGTAATTTGCTTTTGTTTTAATAAGTAAAACGATTTTCGAATTATATATCTTTTAACG
243 ATAAATGCTTATTTTG-TTCT-TTTTAATAAGTAAGATGGTTTTCAAATTATATATCTTTTAACG
28356024 --A--
306 ATACC
* * * *
28356025 T--A---TAT-TT-CATGGATGTTATATAAATGCTTATTTTTCTTTGGTTATCGGAATCATACAC
1 TAAAGTTTATATTCCATTG-TGTTCTATAAAT-CTTATTTTGCTTTCGTTATCGGAATCATACAC
* * *
28356083 CTTTCACTATACCTAAACCTCTATTTTA-T-T--ATGCTTATTTTGTTTTTGTTTCAATAAGT-A
64 CTTTTACTATACCTAAACCTCTATTTTATTATAAATGCTTATTTTGTTTTTATTTTAATAAGTAA
* * ** *
28356143 AATAGGTTTTCAAATTAGATATCTTTTAACGATACTTAAAGTTTATATTTTA-CG-AGTGTTATA
129 AAT-GGTTTTCAATTTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCGTA-CG-T-TA
* * *** *
28356206 TAAATACTTATTTTGCTTTGGTTATAGGAATCATACACCTTCCGCTATACCTAAACCTT-TATTT
190 TAAATGCTTA-TTT-C------T-T----ATCAT--ATCTTTTACAATACCTAAA-CTTGTATTT
* *
28356270 TATTATAAATGCTTATTTTGTTTCTATTTTAATAAGTAAGACGGTTTTCGAATTATATATCTTTT
239 TATTATAAATGCTTATTTTG-TTCT-TTTTAATAAGTAAGATGGTTTTCAAATTATATATCTTTT
*
28356335 AACGATACTAAT
302 AACGATAC---C
* * * *
28356347 TAAAGTTTATATTTCATTGTGTACTATAAATGTTAATTTTGCTTTCGTTATCGGAATCATCCACC
1 TAAAGTTTATATTCCATTGTGTTCTATAAATCTT-ATTTTGCTTTCGTTATCGGAATCATACACC
* *
28356412 TTTCACTATACCTAAACCTCTATTTTATTATAGATGCTTACTTTTGTTTTTATTTTAATAAGTAT
65 TTTTACTATACCTAAACCTCTATTTTATTATAAATGCTTA-TTTTGTTTTTATTTTAATAAGTA-
** * * *
28356477 AATGATTTTTGAATTATAATGAATTATATATCTTTTAACGATATTTAAAGTTTATATTTCATCGT
128 AA--ATGGTT---TT-CAAT---TTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCGT
28356542 ACGTTATAAATGCTTA-TT-TTA-C-T-TCTTTTACAATACCTAAACTTGTATTTTATTATAAAT
184 ACGTTATAAATGCTTATTTCTTATCATATCTTTTACAATACCTAAACTTGTATTTTATTATAAAT
* * * *
28356602 GATTATTTTGTTCCTGTTTTAATAGGCAAAATGG-TTTCAAATTATATATCTTTTAACGATACC
249 GCTTATTTTGTT-CT-TTTTAATAAGTAAGATGGTTTTCAAATTATATATCTTTTAACGATACC
* *
28356665 TAAAGTTTATATTCCATTGTGTTCTATAAATACTTATTTTGCTTTCGTTATCGGAATCGTACACT
1 TAAAGTTTATATTCCATTGTGTTCTATAAAT-CTTATTTTGCTTTCGTTATCGGAATCATACACC
* * * *
28356730 TTTTTCTATACCTAAACTTATATTTTATTATAAATGCTTATTTTGTTTTTGTTTTAATAAGTAAA
65 TTTTACTATACCTAAACCTCTATTTTATTATAAATGCTTATTTTGTTTTTATTTTAATAAGTAAA
***
28356795 ATGGTTTTCAATTTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCGTGTTTTATAAAT
130 ATGGTTTTCAATTTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCGTACGTTATAAAT
* ** *
28356860 TCTTATTTCGCTTTCGTTATCGGAATCAGACATCTTTTATTATACTTAAACTTGTATTTTATTAT
195 GCTTA------TTTC-TTATC---AT-----ATCTTTTACAATACCTAAACTTGTATTTTATTAT
*
28356925 AAATGCTTATTTTGTT-TTTATTATTAAGTAAGATGGTTTTCAAATTATATATCTTTTAACGATG
245 AAATGCTTATTTTGTTCTTT-TTAATAAGTAAGATGGTTTTCAAATTATATATCTTTTAACGAT-
28356989 A-C
308 ACC
* * * * * * *
28356991 TAAA-TCTATACTCCATCGTG-TCTTATAAATGCTTATTTT-CTTTGGTTATTGAAATCATATAC
1 TAAAGTTTATATTCCATTGTGTTC-TATAAAT-CTTATTTTGCTTTCGTTATCGGAATCATACAC
* * * * *
28357053 CTTTTACTATACCCAAACC-CGTATTTTATTATAAATACTTATTTTGTATTTATTTTAATATGCA
64 CTTTTACTATACCTAAACCTC-TATTTTATTATAAATGCTTATTTTGTTTTTATTTTAATAAGTA
* * * * *
28357117 GATTGGTTTTCAAATTATGTATCTTTT-ACAATACTT
128 AAATGGTTTTCAATTTATATATCTTTTAACGATACTT
28357153 GTAATTTATG
Statistics
Matches: 930, Mismatches: 121, Indels: 154
0.77 0.10 0.13
Matches are distributed among these distances:
307 52 0.06
310 3 0.00
311 2 0.00
312 10 0.01
313 9 0.01
314 59 0.06
315 97 0.10
316 82 0.09
317 27 0.03
318 96 0.10
319 4 0.00
321 37 0.04
322 54 0.06
323 9 0.01
324 99 0.11
325 42 0.05
326 32 0.03
327 52 0.06
328 66 0.07
329 5 0.01
330 1 0.00
331 1 0.00
332 8 0.01
333 20 0.02
335 2 0.00
336 2 0.00
337 2 0.00
339 2 0.00
340 4 0.00
342 11 0.01
343 36 0.04
344 3 0.00
345 1 0.00
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.48
Consensus pattern (310 bp):
TAAAGTTTATATTCCATTGTGTTCTATAAATCTTATTTTGCTTTCGTTATCGGAATCATACACCT
TTTACTATACCTAAACCTCTATTTTATTATAAATGCTTATTTTGTTTTTATTTTAATAAGTAAAA
TGGTTTTCAATTTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCGTACGTTATAAATG
CTTATTTCTTATCATATCTTTTACAATACCTAAACTTGTATTTTATTATAAATGCTTATTTTGTT
CTTTTTAATAAGTAAGATGGTTTTCAAATTATATATCTTTTAACGATACC
Found at i:28360306 original size:87 final size:87
Alignment explanation
Indices: 28360160--28360362 Score: 397
Period size: 87 Copynumber: 2.3 Consensus size: 87
28360150 AAAAACCTTG
28360160 ATCCATCTCCATCCACAAGGTTCTAGCAATGTTGGGCTAAGAAAATGTTTATTAATAGATAAAAA
1 ATCCATCTCCATCCACAAGGTTCTAGCAATGTTGGGCTAAGAAAATGTTTATTAATAGATAAAAA
28360225 TAGGATGGTGAACGGGAGTTTA
66 TAGGATGGTGAACGGGAGTTTA
28360247 ATCCATCTCCATCCACAAGGTTCTAGCAATGTTGGGCTAAGAAAATGTTTATTAATAGATAAAAA
1 ATCCATCTCCATCCACAAGGTTCTAGCAATGTTGGGCTAAGAAAATGTTTATTAATAGATAAAAA
28360312 TAGGATGGTGAACGGGAGTTTA
66 TAGGATGGTGAACGGGAGTTTA
*
28360334 ATCCATCTCCATCCACAAGGTTTTAGCAA
1 ATCCATCTCCATCCACAAGGTTCTAGCAA
28360363 GAATGAAGAA
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 115 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (87 bp):
ATCCATCTCCATCCACAAGGTTCTAGCAATGTTGGGCTAAGAAAATGTTTATTAATAGATAAAAA
TAGGATGGTGAACGGGAGTTTA
Found at i:28360399 original size:87 final size:87
Alignment explanation
Indices: 28360160--28360400 Score: 229
Period size: 87 Copynumber: 2.8 Consensus size: 87
28360150 AAAAACCTTG
* * * * ** * * * *
28360160 ATCCATCTCCATCCACAAGGTTCTAGCAATGTTGGGCTAAGAAAATGTTTATTAATAGATAAAAA
1 ATCCATCTCCATCCACAAGGTTCTAGCAATGATGAGCAAAAAAAATGACTATCAACAAAAAAAAA
28360225 TAGGATGGTGAACGGGAGTTTA
66 TAGGATGGTGAACGGGAGTTTA
* * * * ** * * * *
28360247 ATCCATCTCCATCCACAAGGTTCTAGCAATGTTGGGCTAAGAAAATGTTTATTAATAGATAAAAA
1 ATCCATCTCCATCCACAAGGTTCTAGCAATGATGAGCAAAAAAAATGACTATCAACAAAAAAAAA
28360312 TAGGATGGTGAACGGGAGTTTA
66 TAGGATGGTGAACGGGAGTTTA
*
28360334 ATCCATCTCCATCCACAAGGTTTTAGCAA-GAATGAAG-AAACAAAAAT-ACTA-CAACAAAAAG
1 ATCCATCTCCATCCACAAGGTTCTAGCAATG-ATG-AGCAAA-AAAAATGACTATCAACAAAAA-
28360395 AAAATA
62 AAAATA
28360401 AAAAGAAGAG
Statistics
Matches: 139, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
86 6 0.04
87 127 0.91
88 6 0.04
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (87 bp):
ATCCATCTCCATCCACAAGGTTCTAGCAATGATGAGCAAAAAAAATGACTATCAACAAAAAAAAA
TAGGATGGTGAACGGGAGTTTA
Found at i:28361919 original size:17 final size:17
Alignment explanation
Indices: 28361896--28361963 Score: 64
Period size: 17 Copynumber: 4.0 Consensus size: 17
28361886 AGCTCTAGTA
28361896 CTGGCGAACTCCTATGT
1 CTGGCGAACTCCTATGT
* * *
28361913 TTGGCGAACTCTTATGC
1 CTGGCGAACTCCTATGT
* * *
28361930 CCGGCAAACCCCTATGT
1 CTGGCGAACTCCTATGT
**
28361947 CTAACGAACTCCTATGT
1 CTGGCGAACTCCTATGT
28361964 TTGACAAACA
Statistics
Matches: 37, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (17 bp):
CTGGCGAACTCCTATGT
Found at i:28362077 original size:13 final size:13
Alignment explanation
Indices: 28362055--28362107 Score: 61
Period size: 13 Copynumber: 3.9 Consensus size: 13
28362045 GGCAAACTCA
*
28362055 CCTATGGTGAACC
1 CCTATCGTGAACC
28362068 CCTATCGTGAACTC
1 CCTATCGTGAAC-C
* *
28362082 ACCTATGGCGAACC
1 -CCTATCGTGAACC
28362096 CCTATCGTGAAC
1 CCTATCGTGAAC
28362108 TGCCTTAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
13 21 0.64
14 2 0.06
15 10 0.30
ACGTcount: A:0.25, C:0.34, G:0.19, T:0.23
Consensus pattern (13 bp):
CCTATCGTGAACC
Found at i:28362080 original size:28 final size:28
Alignment explanation
Indices: 28362049--28362108 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
28362039 CCTTATGGCA
*
28362049 AACTCACCTATGGTGAACCCCTATCGTG
1 AACTCACCTATGGCGAACCCCTATCGTG
28362077 AACTCACCTATGGCGAACCCCTATCGTG
1 AACTCACCTATGGCGAACCCCTATCGTG
28362105 AACT
1 AACT
28362109 GCCTTAATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.23
Consensus pattern (28 bp):
AACTCACCTATGGCGAACCCCTATCGTG
Found at i:28362094 original size:15 final size:15
Alignment explanation
Indices: 28362042--28362094 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
28362032 GAGTAACCCT
*
28362042 TATGGCAAACTCACC
1 TATGGCGAACTCACC
*
28362057 TATGGTGAAC-C-CC
1 TATGGCGAACTCACC
* *
28362070 TATCGTGAACTCACC
1 TATGGCGAACTCACC
28362085 TATGGCGAAC
1 TATGGCGAAC
28362095 CCCTATCGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
13 11 0.35
14 2 0.06
15 18 0.58
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (15 bp):
TATGGCGAACTCACC
Found at i:28367353 original size:10 final size:10
Alignment explanation
Indices: 28367329--28367370 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
28367319 TTTTTAAAAA
28367329 TTAAAATTA-
1 TTAAAATTAT
*
28367338 TTAAAACTAT
1 TTAAAATTAT
28367348 TTAAAATATAT
1 TTAAAAT-TAT
28367359 TTAAAATTAT
1 TTAAAATTAT
28367369 TT
1 TT
28367371 TTTTTAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 8 0.28
10 11 0.38
11 10 0.34
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (10 bp):
TTAAAATTAT
Found at i:28368543 original size:41 final size:40
Alignment explanation
Indices: 28368427--28368543 Score: 162
Period size: 40 Copynumber: 2.9 Consensus size: 40
28368417 TTTGGATAGA
* * *
28368427 AAACGCCGTAAAAGGTAAAGCATTAGCAGCGTTTTTGCGT
1 AAACGCCGTAAAAGGTAAAGCAATAGCAGCGTTTTTTCAT
* ** *
28368467 AAACGCCGTAAAAGGTAAAGTAATAGTGGCATTTTTTCAT
1 AAACGCCGTAAAAGGTAAAGCAATAGCAGCGTTTTTTCAT
*
28368507 AAACGCCGTTAAAGGTAAAGCAATAGCAGCGTTTTTT
1 AAACGCCGTAAAAGGTAAAGCAATAGCAGCGTTTTTT
28368544 TCCACAAAAG
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.27
Consensus pattern (40 bp):
AAACGCCGTAAAAGGTAAAGCAATAGCAGCGTTTTTTCAT
Found at i:28368913 original size:20 final size:20
Alignment explanation
Indices: 28368876--28368914 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28368866 AAACTCTATC
*
28368876 TATTTTGGTTTTACATGAAG
1 TATTTTGGTTCTACATGAAG
*
28368896 TATTTTGGTTCTATATGAA
1 TATTTTGGTTCTACATGAA
28368915 ATGAATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.51
Consensus pattern (20 bp):
TATTTTGGTTCTACATGAAG
Found at i:28375143 original size:29 final size:29
Alignment explanation
Indices: 28375110--28375168 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
28375100 CATCTCTTGG
28375110 TAAGCATTTAATTTCACTACCTCTTTTAC
1 TAAGCATTTAATTTCACTACCTCTTTTAC
28375139 TAAGCATTTAATTTCACTACCTCTTTTAC
1 TAAGCATTTAATTTCACTACCTCTTTTAC
28375168 T
1 T
28375169 TTCTGGTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.24, G:0.03, T:0.46
Consensus pattern (29 bp):
TAAGCATTTAATTTCACTACCTCTTTTAC
Found at i:28375355 original size:66 final size:66
Alignment explanation
Indices: 28375249--28375385 Score: 249
Period size: 66 Copynumber: 2.1 Consensus size: 66
28375239 GCTTAAAGTT
*
28375249 TATATGTTGTGGGTGTTACATAAAATACTTATTTTACTTTGATTATCGGGAATTATACACCTTTC
1 TATACGTTGTGGGTGTTACATAAAATACTTATTTTACTTTGATTATC-GGAATTATACACCTTTC
28375314 AC
65 AC
28375316 TATACGTTGTGGGTGTTACAT-AAATACTTATTTTACTTTGATTATCGGAATTATACACCTTTCA
1 TATACGTTGTGGGTGTTACATAAAATACTTATTTTACTTTGATTATCGGAATTATACACCTTTCA
28375380 C
66 C
28375381 TATAC
1 TATAC
28375386 TTAAATCTGC
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
65 24 0.35
66 25 0.36
67 20 0.29
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (66 bp):
TATACGTTGTGGGTGTTACATAAAATACTTATTTTACTTTGATTATCGGAATTATACACCTTTCA
C
Found at i:28376467 original size:318 final size:309
Alignment explanation
Indices: 28375450--28376899 Score: 988
Period size: 323 Copynumber: 4.5 Consensus size: 309
28375440 CAACTATGCT
** * * * *
28375450 TAAAGTTTATATTTTATGAGTGTTATATAAATGCTTGTTTTGCTTTGGTTATCGGAATCATACAC
1 TAAAGTTTATATTCCAT-TGTGTTCTATAAAT-CTTATTTTGCTTTCGTTATCGGAATCATACAC
* * * * * * *
28375515 CTTTCACCATACCTATACCTCTATTTTATTATAAATGCGTACTTT-ATTTT-TTTTAATAAGTAG
64 CTTTTACTATACCTAAACCTCTATTTTATTATAAATGCTTATTTTGTTTTTATTTTAATAAGTAA
* * * * ** **
28375578 AACGATTTTCGAA-TTATATATCTTTTAACGATACTTAAAATTTATATTTCATTATATATTATAA
129 AATGGTTTTC-AATTTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCGTACGTTATAA
* * * * * * *
28375642 ATGCTTATTTTGCTTTGGTTATCGGAATCATACACCTTTCACCATATCTATACCTCTATTTTGTT
193 ATGCTTA-TTT-C-----TTATC---AT-AT----CTTTTACAATACCTAAACTTGTATTTTATT
* * * * * * *
28375707 ATAAATGCGTAATTTGCTTTTGTTTTAATAAGTAAAACGATTTTCGAATTATATATCTTTTAACG
243 ATAAATGCTTATTTTG-TTCT-TTTTAATAAGTAAGATG-GTTTCAAATTATATATCTTTTAACG
28375772 --A--
305 ATACC
* * * *
28375773 T--A---TAT-TT-CATGGATGTTATATAAATGCTTATTTTTCTTTGGTTATCGGAATCATACAC
1 TAAAGTTTATATTCCATTG-TGTTCTATAAAT-CTTATTTTGCTTTCGTTATCGGAATCATACAC
* * *
28375831 CTTTCACTATACCTAAACCTCTATTTTA-T-T--ATGCTTATTTTGTTTTTGTTTCAATAAGT-A
64 CTTTTACTATACCTAAACCTCTATTTTATTATAAATGCTTATTTTGTTTTTATTTTAATAAGTAA
* * ** *
28375891 AATAGGTTTTCAAATTAGATATCTTTTAACGATACTTAAAGTTTATATTTTA-CG-AGTGTTATA
129 AAT-GGTTTTCAATTTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCGTA-CG-T-TA
* * *** *
28375954 TAAATACTTATTTTGCTTTGGTTATAGGAATCATACACCTTCCGCTATACCTAAACCTT-TATTT
190 TAAATGCTTA-TTT-C------T-T----ATCAT--ATCTTTTACAATACCTAAA-CTTGTATTT
* *
28376018 TATTATAAATGCTTATTTTGTTTCTATTTTAATAAGTAAGACGGTTTTCGAATTATATATCTTTT
239 TATTATAAATGCTTATTTTG-TTCT-TTTTAATAAGTAAGATGG-TTTCAAATTATATATCTTTT
*
28376083 AACGATACTAAT
301 AACGATAC---C
* * * *
28376095 TAAAGTTTATATTTCATTGTGTACTATAAATGTTAATTTTGCTTTCGTTATCGGAATCATCCACC
1 TAAAGTTTATATTCCATTGTGTTCTATAAATCTT-ATTTTGCTTTCGTTATCGGAATCATACACC
* *
28376160 TTTCACTATACCTAAACCTCTATTTTATTATAGATGCTTACTTTTGTTTTTATTTTAATAAGTAT
65 TTTTACTATACCTAAACCTCTATTTTATTATAAATGCTTA-TTTTGTTTTTATTTTAATAAGTA-
** * * *
28376225 AATGATTTTTGAATTATAATGAATTATATATCTTTTAACGATATTTAAAGTTTATATTTCATCGT
128 AA--ATGGTT---TT-CAAT---TTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCGT
28376290 ACGTTATAAATGCTTA-TT-TTA-C-T-TCTTTTACAATACCTAAACTTGTATTTTATTATAAAT
184 ACGTTATAAATGCTTATTTCTTATCATATCTTTTACAATACCTAAACTTGTATTTTATTATAAAT
* * * *
28376350 GATTATTTTGTTCCTGTTTTAATAGGCAAAATGGTTTCAAATTATATATCTTTTAACGATACC
249 GCTTATTTTGTT-CT-TTTTAATAAGTAAGATGGTTTCAAATTATATATCTTTTAACGATACC
* *
28376413 TAAAGTTTATATTCCATTGTGTTCTATAAATACTTATTTTGCTTTCGTTATCGGAATCGTACACT
1 TAAAGTTTATATTCCATTGTGTTCTATAAAT-CTTATTTTGCTTTCGTTATCGGAATCATACACC
* * * *
28376478 TTTTTCTATACCTAAACTTATATTTTATTATAAATGCTTATTTTGTTTTTGTTTTAATAAGTAAA
65 TTTTACTATACCTAAACCTCTATTTTATTATAAATGCTTATTTTGTTTTTATTTTAATAAGTAAA
***
28376543 ATGGTTTTCAATTTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCGTGTTTTATAAAT
130 ATGGTTTTCAATTTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCGTACGTTATAAAT
* ** *
28376608 TCTTATTTCGCTTTCGTTATCGGAATCAGACATCTTTTATTATACTTAAACTTGTATTTTATTAT
195 GCTTA------TTTC-TTATC---AT-----ATCTTTTACAATACCTAAACTTGTATTTTATTAT
*
28376673 AAATGCTTATTTTGTT-TTTATTATTAAGTAAGATGGTTTCAAATTATATATCTTTTAACGATGA
245 AAATGCTTATTTTGTTCTTT-TTAATAAGTAAGATGGTTTCAAATTATATATCTTTTAACGAT-A
28376737 -C
308 CC
* * ** * * * *
28376738 TAAA-TCTATACTCCATCAT-ATCTTATAAATGCTTATTTT-CTTTGGTTATTGAAATCATACAC
1 TAAAGTTTATATTCCATTGTGTTC-TATAAAT-CTTATTTTGCTTTCGTTATCGGAATCATACAC
* * * *
28376800 CTTTTACTATACCTAAACC-CGTATTTTATTATAAATCCTTATTTTGTATTTATTTTAATATGCA
64 CTTTTACTATACCTAAACCTC-TATTTTATTATAAATGCTTATTTTGTTTTTATTTTAATAAGTA
* * ** *
28376864 AATTGGTTTTCAAATTAGGTATCTTTT-ACAATACTT
128 AAATGGTTTTCAATTTATATATCTTTTAACGATACTT
28376900 GTAATTTATG
Statistics
Matches: 929, Mismatches: 121, Indels: 155
0.77 0.10 0.13
Matches are distributed among these distances:
307 52 0.06
310 3 0.00
311 2 0.00
312 10 0.01
313 9 0.01
314 59 0.06
315 96 0.10
316 82 0.09
317 27 0.03
318 96 0.10
319 4 0.00
321 37 0.04
322 62 0.07
323 99 0.11
324 29 0.03
325 45 0.05
326 2 0.00
327 51 0.05
328 66 0.07
329 5 0.01
330 1 0.00
331 1 0.00
332 8 0.01
333 20 0.02
335 2 0.00
336 2 0.00
337 2 0.00
339 2 0.00
340 4 0.00
342 11 0.01
343 36 0.04
344 3 0.00
345 1 0.00
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.48
Consensus pattern (309 bp):
TAAAGTTTATATTCCATTGTGTTCTATAAATCTTATTTTGCTTTCGTTATCGGAATCATACACCT
TTTACTATACCTAAACCTCTATTTTATTATAAATGCTTATTTTGTTTTTATTTTAATAAGTAAAA
TGGTTTTCAATTTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCGTACGTTATAAATG
CTTATTTCTTATCATATCTTTTACAATACCTAAACTTGTATTTTATTATAAATGCTTATTTTGTT
CTTTTTAATAAGTAAGATGGTTTCAAATTATATATCTTTTAACGATACC
Found at i:28376504 original size:163 final size:163
Alignment explanation
Indices: 28376322--28376891 Score: 690
Period size: 164 Copynumber: 3.5 Consensus size: 163
28376312 TTCTTTTACA
* * *
28376322 ATACCTAAACTTGTATTTTATTATAAATGATTATTTTGTTCCTGTTTTAATAGGCAAAATGG-TT
1 ATACCTAAACTTGTATTTTATTATAAATGCTTATTTTGTT-TTGTTTTAATAAGCAAAATGGTTT
*
28376386 TCAAATTATATATCTTTTAACGATACCTAAAGTTTATATTCCATTGTGTTCTATAAATACTTATT
65 TCAAATTATATATCTTTTAACGATACCTAAAGTTTATATTCCATCGTGTTCTATAAATACTTATT
28376451 TTGCTTTCGTTATCGGAATCGTACACTTTTTTCT
130 TTGCTTTCGTTATCGGAATCGTACACTTTTTTCT
* *
28376485 ATACCTAAACTTATATTTTATTATAAATGCTTATTTTGTTTTTGTTTTAATAAGTAAAATGGTTT
1 ATACCTAAACTTGTATTTTATTATAAATGCTTATTTTG-TTTTGTTTTAATAAGCAAAATGGTTT
* * * *
28376550 TCAATTTATATATCTTTTAACGATACTTAAAGTTTATATTCCATCGTGTTTTATAAATTCTTATT
65 TCAAATTATATATCTTTTAACGATACCTAAAGTTTATATTCCATCGTGTTCTATAAATACTTATT
* *
28376615 TCGCTTTCGTTATCGGAATCAG-ACATCTTTTAT-T
130 TTGCTTTCGTTATCGGAATC-GTACA-CTTTTTTCT
* * * * *
28376649 ATACTTAAACTTGTATTTTATTATAAATGCTTATTTTGTTTT-TATTATTAAGTAAGATGG-TTT
1 ATACCTAAACTTGTATTTTATTATAAATGCTTATTTTGTTTTGTTTTAATAAGCAAAATGGTTTT
* * * * *
28376712 CAAATTATATATCTTTTAACGATGA-CTAAA-TCTATACTCCATCAT-ATCTTATAAATGCTTAT
66 CAAATTATATATCTTTTAACGAT-ACCTAAAGTTTATATTCCATCGTGTTC-TATAAATACTTAT
* * * * * *
28376774 TTT-CTTTGGTTATTGAAATCATACACCTTTTACT
129 TTTGCTTTCGTTATCGGAATCGTACACTTTTTTCT
** * * * *
28376808 ATACCTAAACCCGTATTTTATTATAAATCCTTATTTTGTATTTATTTTAATATGCAAATTGGTTT
1 ATACCTAAACTTGTATTTTATTATAAATGCTTATTTTGT-TTTGTTTTAATAAGCAAAATGGTTT
**
28376873 TCAAATTAGGTATCTTTTA
65 TCAAATTATATATCTTTTA
28376892 CAATACTTGT
Statistics
Matches: 351, Mismatches: 45, Indels: 23
0.84 0.11 0.05
Matches are distributed among these distances:
158 4 0.01
159 54 0.15
160 29 0.08
161 41 0.12
162 35 0.10
163 58 0.17
164 123 0.35
165 7 0.02
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (163 bp):
ATACCTAAACTTGTATTTTATTATAAATGCTTATTTTGTTTTGTTTTAATAAGCAAAATGGTTTT
CAAATTATATATCTTTTAACGATACCTAAAGTTTATATTCCATCGTGTTCTATAAATACTTATTT
TGCTTTCGTTATCGGAATCGTACACTTTTTTCT
Found at i:28381601 original size:15 final size:15
Alignment explanation
Indices: 28381581--28381673 Score: 72
Period size: 13 Copynumber: 6.6 Consensus size: 15
28381571 CTCCTATGTC
*
28381581 TGGTGAACTCACATA
1 TGGTGAACTCACCTA
*
28381596 TGGTGAAC-C-CTTA
1 TGGTGAACTCACCTA
**
28381609 TGGCAAACTCACCTA
1 TGGTGAACTCACCTA
*
28381624 TGGTGAAC-C-CTTA
1 TGGTGAACTCACCTA
*
28381637 TCGTGAACTCACCTA
1 TGGTGAACTCACCTA
*
28381652 TGGCGAAC-C-CCTA
1 TGGTGAACTCACCTA
*
28381665 TCGTGAACT
1 TGGTGAACT
28381674 GCCTTAATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 11
0.71 0.15 0.13
Matches are distributed among these distances:
13 29 0.48
14 5 0.08
15 26 0.43
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (15 bp):
TGGTGAACTCACCTA
Found at i:28381668 original size:28 final size:28
Alignment explanation
Indices: 28381583--28381673 Score: 128
Period size: 28 Copynumber: 3.2 Consensus size: 28
28381573 CCTATGTCTG
* *
28381583 GTGAACTCACATATGGTGAACCCTTATG
1 GTGAACTCACCTATGGTGAACCCTTATC
**
28381611 GCAAACTCACCTATGGTGAACCCTTATC
1 GTGAACTCACCTATGGTGAACCCTTATC
* *
28381639 GTGAACTCACCTATGGCGAACCCCTATC
1 GTGAACTCACCTATGGTGAACCCTTATC
28381667 GTGAACT
1 GTGAACT
28381674 GCCTTAATTC
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (28 bp):
GTGAACTCACCTATGGTGAACCCTTATC
Found at i:28387091 original size:15 final size:16
Alignment explanation
Indices: 28387073--28387154 Score: 59
Period size: 16 Copynumber: 5.2 Consensus size: 16
28387063 TAATAAATTT
*
28387073 TTTAAATTTA-AAAAA
1 TTTAAATATATAAAAA
28387088 TTTAAATATATAAAAA
1 TTTAAATATATAAAAA
*
28387104 -TT--ATATCTAAAAA
1 TTTAAATATATAAAAA
*
28387117 TTAAAAT-TATTAAAACTA
1 TTTAAATATA-TAAAA--A
28387135 TTTAAA-ATATATAAAA
1 TTTAAATATATA-AAAA
28387151 TTTA
1 TTTA
28387155 TTTTTTTAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 17
0.71 0.07 0.23
Matches are distributed among these distances:
13 10 0.19
14 1 0.02
15 12 0.23
16 17 0.32
17 2 0.04
18 11 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
TTTAAATATATAAAAA
Found at i:28387131 original size:28 final size:26
Alignment explanation
Indices: 28387078--28387152 Score: 69
Period size: 28 Copynumber: 2.7 Consensus size: 26
28387068 AATTTTTTAA
* *
28387078 ATTTAAAAAATTTAAATATATAAAAATT
1 ATTT-AAAAATTAAAAT-TATAAAAACT
*
28387106 ATATCTAAAAATTAAAATTATTAAAACT
1 AT-T-TAAAAATTAAAATTATAAAAACT
28387134 ATTTAAAATATATAAAATT
1 ATTTAAAA-AT-TAAAATT
28387153 TATTTTTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
26 5 0.12
27 3 0.08
28 19 0.47
29 12 0.30
30 1 0.03
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.39
Consensus pattern (26 bp):
ATTTAAAAATTAAAATTATAAAAACT
Found at i:28387581 original size:12 final size:11
Alignment explanation
Indices: 28387550--28387575 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28387540 ATTATTTTAA
28387550 TTTTAAAATAC
1 TTTTAAAATAC
28387561 TTTTAAAATAC
1 TTTTAAAATAC
28387572 TTTT
1 TTTT
28387576 TTAAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:28387593 original size:8 final size:9
Alignment explanation
Indices: 28387572--28387611 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
28387562 TTTAAAATAC
28387572 TTTTTTAAA
1 TTTTTTAAA
28387581 TTTTTTAAA
1 TTTTTTAAA
28387590 TTTTTTAAA
1 TTTTTTAAA
28387599 --TTTTAAA
1 TTTTTTAAA
28387606 TTTTTT
1 TTTTTT
28387612 TTAAAATACG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.24
9 22 0.76
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:28387616 original size:18 final size:17
Alignment explanation
Indices: 28387572--28387611 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
28387562 TTTAAAATAC
28387572 TTTTTTAAATTTTTTAAA
1 TTTTTTAAA-TTTTTAAA
28387590 TTTTTTAAA-TTTTAAA
1 TTTTTTAAATTTTTAAA
28387606 TTTTTT
1 TTTTTT
28387612 TTAAAATACG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 13 0.59
18 9 0.41
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTTAAATTTTTAAA
Found at i:28387634 original size:48 final size:48
Alignment explanation
Indices: 28387544--28387641 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 48
28387534 ATTTTTATTA
*
28387544 TTTTAATTTTAAAATACTTTTAAAATACTTTTTTAAATTTTTTAAATT
1 TTTTAATTTTAAAATACTTTTAAAATACGTTTTTAAATTTTTTAAATT
* ** *
28387592 TTTTAAATTTTAAATTTTTTTTAAAATACGTTTTT-AATTTTTTTAATT
1 TTTT-AATTTTAAAATACTTTTAAAATACGTTTTTAAATTTTTTAAATT
28387640 TT
1 TT
28387642 AAAATATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
48 18 0.41
49 26 0.59
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (48 bp):
TTTTAATTTTAAAATACTTTTAAAATACGTTTTTAAATTTTTTAAATT
Found at i:28387642 original size:39 final size:40
Alignment explanation
Indices: 28387561--28387697 Score: 138
Period size: 39 Copynumber: 3.4 Consensus size: 40
28387551 TTTAAAATAC
* * *
28387561 TTTTAAAATACTTTTTTAAAT--T-TTTTAAATTTTTTAAA
1 TTTTAAAATA-TTTTTAAAATACTGTTTTTAATTTTTTTAA
* *
28387599 TTTTAAATTTTTTTTAAAATAC-GTTTTTAATTTTTTTAA
1 TTTTAAAATATTTTTAAAATACTGTTTTTAATTTTTTTAA
*
28387638 TTTTAAAATATTTTTAAAATACTTTTTTTTAATTTTTTTTTAA
1 TTTTAAAATATTTTTAAAATAC-TGTTTTTAA--TTTTTTTAA
28387681 TTTTTAAAATAATTTTT
1 -TTTTAAAAT-ATTTTT
28387698 TAGTATTTAT
Statistics
Matches: 82, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
37 9 0.11
38 8 0.10
39 34 0.41
41 7 0.09
43 9 0.11
44 9 0.11
45 6 0.07
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.64
Consensus pattern (40 bp):
TTTTAAAATATTTTTAAAATACTGTTTTTAATTTTTTTAA
Found at i:28387675 original size:10 final size:11
Alignment explanation
Indices: 28387660--28387685 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28387650 TTTAAAATAC
28387660 TTTTTTTTAAT
1 TTTTTTTTAAT
28387671 TTTTTTTTAAT
1 TTTTTTTTAAT
28387682 TTTT
1 TTTT
28387686 AAAATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTAAT
Found at i:28388350 original size:17 final size:18
Alignment explanation
Indices: 28388316--28388350 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28388306 TTTTCAAAAT
*
28388316 TTTAAAATAATTTTTAAA
1 TTTAAAATAATTTATAAA
28388334 TTTAAAAT-ATTTATAAA
1 TTTAAAATAATTTATAAA
28388351 ATTCTCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAAAATAATTTATAAA
Found at i:28388352 original size:18 final size:18
Alignment explanation
Indices: 28388304--28388353 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
28388294 ATTTCAACAG
28388304 AATTTTCAAAATTTTAAAAT
1 AATTTT-AAAA-TTTAAAAT
*
28388324 AATTTTTAAATTTAAAAT
1 AATTTTAAAATTTAAAAT
28388342 -ATTTATAAAATT
1 AATTT-TAAAATT
28388354 CTCAAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 4 0.15
18 14 0.52
19 3 0.11
20 6 0.22
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
AATTTTAAAATTTAAAAT
Found at i:28391745 original size:11 final size:11
Alignment explanation
Indices: 28391723--28391762 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
28391713 AACTAATCCT
28391723 CTCTCAAATTTC
1 CTCTC-AATTTC
28391735 CTCTCAATTTC
1 CTCTCAATTTC
28391746 CTCTCAATTTC
1 CTCTCAATTTC
28391757 CT-TCAA
1 CTCTCAA
28391763 AAATTCTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 4 0.14
11 19 0.68
12 5 0.18
ACGTcount: A:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:28393304 original size:18 final size:18
Alignment explanation
Indices: 28393277--28393314 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
28393267 TAGGTGCGTT
*
28393277 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
28393295 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
28393313 TC
1 TC
28393315 ATTTTTCGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.29, G:0.08, T:0.39
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:28393857 original size:43 final size:43
Alignment explanation
Indices: 28393770--28393857 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 43
28393760 AATAAGGAGT
** * *
28393770 TTATTTGATGTAATAAAATAGATTTTTTTTAGTTATTTTGATA
1 TTATTTGATGTAATAAAATAGAAATTTTTGAGATATTTTGATA
28393813 TTATTTGATGTAATAAAATAGAAATTTTTGA-ATATTTTGAATA
1 TTATTTGATGTAATAAAATAGAAATTTTTGAGATATTTTG-ATA
28393856 TT
1 TT
28393858 TTGATATTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 7 0.17
43 33 0.82
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.52
Consensus pattern (43 bp):
TTATTTGATGTAATAAAATAGAAATTTTTGAGATATTTTGATA
Found at i:28393922 original size:23 final size:23
Alignment explanation
Indices: 28393896--28394404 Score: 624
Period size: 23 Copynumber: 22.9 Consensus size: 23
28393886 ATTAATACCC
*
28393896 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
* **
28393919 TTAAATTAAAACCCCTAACC-CC
1 TTAAATTAAAAACCCTAACCTAA
* *
28393941 TTAACTTAAAAATCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
* *
28393964 TTAAATTAAAAACCCTAGCC--C
1 TTAAATTAAAAACCCTAACCTAA
28393985 TTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
*
28394008 TTAAATTAAAAACCCTAACC--C
1 TTAAATTAAAAACCCTAACCTAA
*
28394029 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
28394052 TTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
*
28394075 TTAAATTAAAAACCCTAACC--C
1 TTAAATTAAAAACCCTAACCTAA
*
28394096 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
28394119 TTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
*
28394142 TTAAATTAAAAACCCTAACC--C
1 TTAAATTAAAAACCCTAACCTAA
*
28394163 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
28394186 TTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
*
28394209 TTAAATTAAAAACCCTAACC-CA
1 TTAAATTAAAAACCCTAACCTAA
* *
28394231 -TAACTTAAAAACCCTAACCTGA
1 TTAAATTAAAAACCCTAACCTAA
*
28394253 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
* *
28394276 TTAAATTAAAAATCCTAACCTAT
1 TTAAATTAAAAACCCTAACCTAA
*
28394299 TTAAATT-AAAACCCTAACC--C
1 TTAAATTAAAAACCCTAACCTAA
*
28394319 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAA
*
28394342 TTTAATTAAAAACCCTAAACCCT-A
1 TTAAATTAAAAACCCT-AA-CCTAA
* * *
28394366 --AACTTAAAAACTCTAACC-CA
1 TTAAATTAAAAACCCTAACCTAA
*
28394386 TT-ACTTAAAAACCCTAACC
1 TTAAATTAAAAACCCTAACC
28394405 CCCTAACCTA
Statistics
Matches: 423, Mismatches: 44, Indels: 40
0.83 0.09 0.08
Matches are distributed among these distances:
20 9 0.02
21 124 0.29
22 41 0.10
23 243 0.57
24 3 0.01
25 3 0.01
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (23 bp):
TTAAATTAAAAACCCTAACCTAA
Found at i:28394002 original size:44 final size:45
Alignment explanation
Indices: 28393896--28394404 Score: 623
Period size: 44 Copynumber: 11.4 Consensus size: 45
28393886 ATTAATACCC
* * **
28393896 TTAACTTAAAAACCCTAACCTAATTAAATTAAAACCCCTAACCCC
1 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTA
* * * *
28393941 TTAACTTAAAAATCCTAACCTAATTAAATTAAAAACCCTAGCC-C
1 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTA
*
28393985 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACC-C
1 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTA
*
28394029 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCT-A
* *
28394075 TTAAATTAAAAACCCTAACC--CTTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCT-A
*
28394119 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACC-C
1 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTA
*
28394163 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCT-A
* *
28394209 TTAAATTAAAAACCCTAACC-CA-TAACTTAAAAACCCTAACCTGA
1 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCT-A
* *
28394253 TTAACTTAAAAACCCTAACCTAATTAAATTAAAAATCCTAACCTA
1 TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTA
* *
28394298 TTTAAATT-AAAACCCTAACC--CTTAACTTAAAAACCCTAACCTAA
1 -TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCT-A
* * * *
28394342 TTTAATTAAAAACCCTAAACCCT-A--AACTTAAAAACTCTAACCCA
1 TTAAATTAAAAACCCT-AA-CCTAATTAAATTAAAAACCCTAACCTA
*
28394386 TT-ACTTAAAAACCCTAACC
1 TTAAATTAAAAACCCTAACC
28394405 CCCTAACCTA
Statistics
Matches: 417, Mismatches: 33, Indels: 32
0.87 0.07 0.07
Matches are distributed among these distances:
41 2 0.00
42 2 0.00
43 37 0.09
44 219 0.53
45 74 0.18
46 83 0.20
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (45 bp):
TTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTA
Found at i:28394025 original size:67 final size:66
Alignment explanation
Indices: 28393892--28394404 Score: 712
Period size: 67 Copynumber: 7.7 Consensus size: 66
28393882 AACCATTAAT
* ** * *
28393892 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAACCCCTAACC-CCTTAACTTAAAAATCC
1 ACCCTTAACTTAAAAACCCTAACCT-ATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCC
28393956 TA
65 TA
* * * *
28393958 ACCTAATTAAATTAAAAACCCTAGCC-CTTAAATTAAAAACCCTAACCTAATTAAATTAAAAACC
1 ACC--CTTAACTTAAAAACCCTAACCTATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACC
28394022 CTA
64 CTA
28394025 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCC
1 ACCCTTAACTTAAAAACCCTAACCT-ATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCC
28394090 TA
65 TA
28394092 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCC
1 ACCCTTAACTTAAAAACCCTAACCT-ATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCC
28394157 TA
65 TA
28394159 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCC
1 ACCCTTAACTTAAAAACCCTAACCT-ATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCC
28394224 TA
65 TA
* * *
28394226 ACCCATAACTTAAAAACCCTAACCTGATTAACTTAAAAACCCTAACCTAATTAAATTAAAAATCC
1 ACCCTTAACTTAAAAACCCTAACCT-ATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCC
28394291 TA
65 TA
* * * * *
28394293 ACCTATTTAAATT-AAAACCCTAACC-CTTAACTTAAAAACCCTAACCTAATTTAATTAAAAACC
1 ACC--CTTAACTTAAAAACCCTAACCTATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACC
28394356 CTAA
64 CT-A
* * * *
28394360 ACCCTAAACTTAAAAACTCTAACCCATT-ACTTAAAAACCCTAACC
1 ACCCTTAACTTAAAAACCCTAACCTATTAAATTAAAAACCCTAACC
28394405 CCCTAACCTA
Statistics
Matches: 409, Mismatches: 28, Indels: 20
0.89 0.06 0.04
Matches are distributed among these distances:
65 23 0.06
66 87 0.21
67 264 0.65
68 30 0.07
69 5 0.01
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.26
Consensus pattern (66 bp):
ACCCTTAACTTAAAAACCCTAACCTATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCT
A
Found at i:28394519 original size:17 final size:17
Alignment explanation
Indices: 28394497--28394566 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
28394487 ACTGGTACTA
28394497 ATAATTAATAATTTTAT
1 ATAATTAATAATTTTAT
*
28394514 ATAATTTGATAATTTTACT
1 ATAA-TTAATAATTTTA-T
* *
28394533 AATCATTAATACAATTTAT
1 -ATAATTAATA-ATTTTAT
*
28394552 -CAATTAATAATTTTA
1 ATAATTAATAATTTTA
28394567 CATTCACATA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
16 5 0.12
17 11 0.26
18 11 0.26
19 7 0.17
20 8 0.19
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (17 bp):
ATAATTAATAATTTTAT
Found at i:28394640 original size:115 final size:115
Alignment explanation
Indices: 28394438--28394680 Score: 391
Period size: 115 Copynumber: 2.1 Consensus size: 115
28394428 CCCTAAACGA
* *
28394438 AATTAATAATTTTACTTTCACATAAGGTTAGATTTGGAAAAAAAATTTTACTGGTACTAATAATT
1 AATTAATAATTTTACATTCACATAAGGTTAGATTT-GAAAAAAAATTTTACTGGTACTAACAATT
*
28394503 AATAATTTTATATAATTTGATAA-TTTTACTAATCATTAATACAATTTATC
65 AATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
* **
28394553 AATTAATAATTTTACATTCACATAATGTTAGATTT-ATAAAAATGTTTTGACTGGTACTAACAAT
1 AATTAATAATTTTACATTCACATAAGGTTAGATTTGA-AAAAAAATTTT-ACTGGTACTAACAAT
28394617 TAATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
64 TAATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
28394669 AATTAATAATTT
1 AATTAATAATTT
28394681 CACAAACTTA
Statistics
Matches: 119, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
113 1 0.01
114 9 0.08
115 71 0.60
116 38 0.32
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (115 bp):
AATTAATAATTTTACATTCACATAAGGTTAGATTTGAAAAAAAATTTTACTGGTACTAACAATTA
ATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
Found at i:28397842 original size:17 final size:18
Alignment explanation
Indices: 28397809--28397842 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28397799 TGTTAACACT
*
28397809 TAAAATAATATTATATAG
1 TAAAATAATAGTATATAG
28397827 TAAAATAAT-GTATATA
1 TAAAATAATAGTATATA
28397843 CAAAAAATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
TAAAATAATAGTATATAG
Found at i:28401454 original size:59 final size:61
Alignment explanation
Indices: 28401305--28401454 Score: 171
Period size: 60 Copynumber: 2.5 Consensus size: 61
28401295 AATTTGATAT
* *
28401305 TTTTTTCTTAATTTGGTACCTAAAC-TTTTTGTTGCCCAATTCGATACCTAAAATCGACAC
1 TTTTTTCATAATTTGGTACCTAAACTTTTTTGTGGCCCAATTCGATACCTAAAATCGACAC
* * * * * * * *
28401365 TTTTTTTATAATTTGGTACCTAAACTTTTTTG-GGCCCAATTTGGTACTTGAACTTGGCA-
1 TTTTTTCATAATTTGGTACCTAAACTTTTTTGTGGCCCAATTCGATACCTAAAATCGACAC
* *
28401424 TTTTTTCCTAATTTGGTACCTAAGCTTTTTT
1 TTTTTTCATAATTTGGTACCTAAACTTTTTT
28401455 TTAGGTTCAA
Statistics
Matches: 76, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
59 28 0.37
60 42 0.55
61 6 0.08
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.47
Consensus pattern (61 bp):
TTTTTTCATAATTTGGTACCTAAACTTTTTTGTGGCCCAATTCGATACCTAAAATCGACAC
Found at i:28401968 original size:31 final size:30
Alignment explanation
Indices: 28401915--28402030 Score: 123
Period size: 31 Copynumber: 3.9 Consensus size: 30
28401905 CCCCAAAAAG
* * *
28401915 TTTAATTACCAACTTAAGAAAAAGTGTCAAA
1 TTTAAATACCAAATT-AGAAAAAATGTCAAA
*
28401946 TTTAAATATCAAATTAGAAAAAAATGTCAAA
1 TTTAAATACCAAATTAG-AAAAAATGTCAAA
* *
28401977 TTTAGATACCAAATTAGACCAAAA--T-AAA
1 TTTAAATACCAAATTAGA-AAAAATGTCAAA
28402005 TTTAAATACCAAATTA-AAAAAATGTC
1 TTTAAATACCAAATTAGAAAAAATGTC
28402031 GGTTTCAAAT
Statistics
Matches: 71, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
26 4 0.06
27 1 0.01
28 19 0.27
29 1 0.01
30 3 0.04
31 43 0.61
ACGTcount: A:0.53, C:0.11, G:0.07, T:0.28
Consensus pattern (30 bp):
TTTAAATACCAAATTAGAAAAAATGTCAAA
Found at i:28402646 original size:14 final size:15
Alignment explanation
Indices: 28402629--28402665 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
28402619 ATATAATTAT
28402629 TATTATTTAATAT-A
1 TATTATTTAATATAA
28402643 TATTA-TTAATATAA
1 TATTATTTAATATAA
*
28402657 TATTTTTTA
1 TATTATTTA
28402666 TAACATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 7 0.35
14 10 0.50
15 3 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTATTTAATATAA
Found at i:28403037 original size:71 final size:71
Alignment explanation
Indices: 28402929--28403087 Score: 318
Period size: 71 Copynumber: 2.2 Consensus size: 71
28402919 AATTAATCGG
28402929 TCGGTTAATTCGGTTAATTTTTTTATATGTTTTATACTTGTTTTAACCAAAAATCAAAAAACATA
1 TCGGTTAATTCGGTTAATTTTTTTATATGTTTTATACTTGTTTTAACCAAAAATCAAAAAACATA
28402994 TAAATT
66 TAAATT
28403000 TCGGTTAATTCGGTTAATTTTTTTATATGTTTTATACTTGTTTTAACCAAAAATCAAAAAACATA
1 TCGGTTAATTCGGTTAATTTTTTTATATGTTTTATACTTGTTTTAACCAAAAATCAAAAAACATA
28403065 TAAATT
66 TAAATT
28403071 TCGGTTAATTCGGTTAA
1 TCGGTTAATTCGGTTAA
28403088 CTAACCGAAT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 88 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (71 bp):
TCGGTTAATTCGGTTAATTTTTTTATATGTTTTATACTTGTTTTAACCAAAAATCAAAAAACATA
TAAATT
Found at i:28410101 original size:21 final size:21
Alignment explanation
Indices: 28410077--28410116 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28410067 TTCTTTTGAA
*
28410077 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
28410098 CCTCTGCTTCCCTCGCTGC
1 CCTCTGCTTCCCTCGCTGC
28410117 TGCATCTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.03, C:0.47, G:0.17, T:0.33
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:28410180 original size:87 final size:87
Alignment explanation
Indices: 28410012--28410171 Score: 223
Period size: 87 Copynumber: 1.8 Consensus size: 87
28410002 TTCTGCTCTG
* * * * * *
28410012 CTCTGCTTCTCTTGCTGTAGCCTCTGCTTTAAGTTGTAGCTGCAGTTCTTCATATTTCTTTTGAA
1 CTCTGCTTCCCTCGCTGTAGCATCTACTTTAAGTTGTAGCTGAAGTTCTTCATATTTCCTTTGAA
** *
28410077 CCTCTGCTTCTCTCGCTGCAGC
66 CCTCAACTTCGCTCGCTGCAGC
28410099 CTCTGCTTCCCTCGCTGCT-GCATCTACTTTAAGTTGTAGCTGAAGTTCTTCATATTTCCTTTGA
1 CTCTGCTTCCCTCGCTG-TAGCATCTACTTTAAGTTGTAGCTGAAGTTCTTCATATTTCCTTTGA
28410163 ACCTCAACT
65 ACCTCAACT
28410172 GTGGTCGCTT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
87 63 0.98
88 1 0.02
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (87 bp):
CTCTGCTTCCCTCGCTGTAGCATCTACTTTAAGTTGTAGCTGAAGTTCTTCATATTTCCTTTGAA
CCTCAACTTCGCTCGCTGCAGC
Done.