Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 69 of 349
Found at i:20334349 original size:75 final size:75
Alignment explanation
Indices: 20334226--20334375 Score: 291
Period size: 75 Copynumber: 2.0 Consensus size: 75
20334216 AATTAGTTGT
*
20334226 GTAGTTAATTAGATTTCGGTTAAGTGAATTTGCATGAATTAAGAATTGTTATTGTATAAGGACTA
1 GTAGTTAATTAGATTTCGGTTAAGTGAATTTGCATGAATTAAGAATTGTTATTGTATAAGAACTA
20334291 AACCGTGTAC
66 AACCGTGTAC
20334301 GTAGTTAATTAGATTTCGGTTAAGTGAATTTGCATGAATTAAGAATTGTTATTGTATAAGAACTA
1 GTAGTTAATTAGATTTCGGTTAAGTGAATTTGCATGAATTAAGAATTGTTATTGTATAAGAACTA
20334366 AACCGTGTAC
66 AACCGTGTAC
20334376 AGGATAAAAG
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (75 bp):
GTAGTTAATTAGATTTCGGTTAAGTGAATTTGCATGAATTAAGAATTGTTATTGTATAAGAACTA
AACCGTGTAC
Found at i:20334641 original size:15 final size:15
Alignment explanation
Indices: 20334616--20334650 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
20334606 ATTAAATAGG
20334616 AAAGA-AAAGAAAGA
1 AAAGAGAAAGAAAGA
*
20334630 AAAGAGAAAGAAATA
1 AAAGAGAAAGAAAGA
20334645 AAAGAG
1 AAAGAG
20334651 GAGAAAGACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (15 bp):
AAAGAGAAAGAAAGA
Found at i:20336256 original size:21 final size:21
Alignment explanation
Indices: 20336232--20336275 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
20336222 AAATGTGGTG
20336232 ATGTTTACCTTTTGTGACGGC
1 ATGTTTACCTTTTGTGACGGC
20336253 ATGTTTACCTTTTGTGACGGC
1 ATGTTTACCTTTTGTGACGGC
20336274 AT
1 AT
20336276 ATATGAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.43
Consensus pattern (21 bp):
ATGTTTACCTTTTGTGACGGC
Found at i:20341568 original size:39 final size:39
Alignment explanation
Indices: 20341521--20341652 Score: 210
Period size: 39 Copynumber: 3.4 Consensus size: 39
20341511 TATATAAGAT
20341521 TGGAAATATATCCGGACATGAGGTCCGCAGGCTATATGC
1 TGGAAATATATCCGGACATGAGGTCCGCAGGCTATATGC
20341560 TGGAAATATATCCGGACATGAGGTCCGCAGGCTATATGC
1 TGGAAATATATCCGGACATGAGGTCCGCAGGCTATATGC
* * * **
20341599 TGGAAATATATCCGGACTTGAAGTCCACAGGCTACGTGC
1 TGGAAATATATCCGGACATGAGGTCCGCAGGCTATATGC
*
20341638 TGGAAAAATATCCGG
1 TGGAAATATATCCGG
20341653 GTTAAAGACC
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 87 1.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (39 bp):
TGGAAATATATCCGGACATGAGGTCCGCAGGCTATATGC
Found at i:20341666 original size:78 final size:78
Alignment explanation
Indices: 20341521--20341670 Score: 185
Period size: 78 Copynumber: 1.9 Consensus size: 78
20341511 TATATAAGAT
* * * * * **
20341521 TGGAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTGGAAATATATCCGGACATGAGGTCC
1 TGGAAATATATCCGGACATGAAGTCCACAGGCTACATGCTGGAAAAATATCCGGACATAAGACCC
20341586 GCAGGCTATATGC
66 GCAGGCTATATGC
* * **
20341599 TGGAAATATATCCGGACTTGAAGTCCACAGGCTACGTGCTGGAAAAATATCCGG-GTTAAAGACC
1 TGGAAATATATCCGGACATGAAGTCCACAGGCTACATGCTGGAAAAATATCCGGACAT-AAGACC
20341663 CGCAGGCT
65 CGCAGGCT
20341671 TACGCTAGTA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
77 1 0.02
78 59 0.98
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.22
Consensus pattern (78 bp):
TGGAAATATATCCGGACATGAAGTCCACAGGCTACATGCTGGAAAAATATCCGGACATAAGACCC
GCAGGCTATATGC
Found at i:20341669 original size:39 final size:39
Alignment explanation
Indices: 20341521--20341670 Score: 122
Period size: 39 Copynumber: 3.8 Consensus size: 39
20341511 TATATAAGAT
* * * * * *
20341521 TGGAAATATATCCGGACATGAGGTCCGCAGGCTATATGC
1 TGGAAAAATATCCGGACTTAAAGCCCGCAGGCTACATGC
* * * * * *
20341560 TGGAAATATATCCGGACATGAGGTCCGCAGGCTATATGC
1 TGGAAAAATATCCGGACTTAAAGCCCGCAGGCTACATGC
* * * * *
20341599 TGGAAATATATCCGGACTTGAAGTCCACAGGCTACGTGC
1 TGGAAAAATATCCGGACTTAAAGCCCGCAGGCTACATGC
*
20341638 TGGAAAAATATCCGG-GTTAAAGACCCGCAGGCT
1 TGGAAAAATATCCGGACTTAAAG-CCCGCAGGCT
20341671 TACGCTAGTA
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
38 5 0.05
39 95 0.95
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.22
Consensus pattern (39 bp):
TGGAAAAATATCCGGACTTAAAGCCCGCAGGCTACATGC
Found at i:20345335 original size:11 final size:11
Alignment explanation
Indices: 20345319--20345361 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
20345309 ACCTCGTGAA
20345319 AATATATTAAT
1 AATATATTAAT
*
20345330 AATATATAAAT
1 AATATATTAAT
20345341 -A-ATATTAAT
1 AATATATTAAT
*
20345350 AATATAATAAT
1 AATATATTAAT
20345361 A
1 A
20345362 TAGAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
11 18 0.67
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATATTAAT
Found at i:20345361 original size:20 final size:20
Alignment explanation
Indices: 20345318--20345355 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20345308 AACCTCGTGA
20345318 AAAT-ATATTAATAATATAT
1 AAATAATATTAATAATATAT
20345337 AAATAATATTAATAATATA
1 AAATAATATTAATAATATA
20345356 ATAATATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATAATATTAATAATATAT
Found at i:20352990 original size:25 final size:25
Alignment explanation
Indices: 20352961--20353013 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
20352951 TACCAATTAG
*
20352961 ACCGAAACCATCTACATTTAAAACT
1 ACCGAAACCAACTACATTTAAAACT
20352986 ACCGAAACCAACTACATTTAAAACT
1 ACCGAAACCAACTACATTTAAAACT
20353011 ACC
1 ACC
20353014 ATACCATTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.45, C:0.30, G:0.04, T:0.21
Consensus pattern (25 bp):
ACCGAAACCAACTACATTTAAAACT
Found at i:20361980 original size:16 final size:16
Alignment explanation
Indices: 20361959--20361991 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20361949 CTATATAATC
20361959 AAATTTAGTTC-ATTCA
1 AAATTTA-TTCTATTCA
20361975 AAATTTATTCTATTCA
1 AAATTTATTCTATTCA
20361991 A
1 A
20361992 TTTAATCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.45
Consensus pattern (16 bp):
AAATTTATTCTATTCA
Found at i:20367200 original size:37 final size:37
Alignment explanation
Indices: 20367141--20367233 Score: 159
Period size: 37 Copynumber: 2.5 Consensus size: 37
20367131 TATTACAATT
20367141 CCGATGAGTGTTGGGCACACATTTTATTTTGGTTATG
1 CCGATGAGTGTTGGGCACACATTTTATTTTGGTTATG
* *
20367178 CCGGTGAGTGTTGGGCAGACATTTTATTTTGGTTATG
1 CCGATGAGTGTTGGGCACACATTTTATTTTGGTTATG
*
20367215 CCGATGAGCGTTGGGCACA
1 CCGATGAGTGTTGGGCACA
20367234 AGTTATACTT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.18, C:0.15, G:0.31, T:0.35
Consensus pattern (37 bp):
CCGATGAGTGTTGGGCACACATTTTATTTTGGTTATG
Found at i:20375348 original size:15 final size:15
Alignment explanation
Indices: 20375328--20375356 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20375318 ATTATTAGAT
20375328 CTATTTTTGTTTGGC
1 CTATTTTTGTTTGGC
20375343 CTATTTTTGTTTGG
1 CTATTTTTGTTTGG
20375357 ACATAGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.10, G:0.21, T:0.62
Consensus pattern (15 bp):
CTATTTTTGTTTGGC
Found at i:20379415 original size:25 final size:25
Alignment explanation
Indices: 20379381--20379431 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
20379371 TTCCTTATAA
**
20379381 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
20379406 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
20379431 A
1 A
20379432 TTTTCCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:20379430 original size:12 final size:12
Alignment explanation
Indices: 20379384--20379431 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
20379374 CTTATAAACT
20379384 TTAAATTAGGAA
1 TTAAATTAGGAA
** *
20379396 TTCTATTAGGACT
1 TTAAATTAGGA-A
20379409 TTAAATTAGGAA
1 TTAAATTAGGAA
*
20379421 TTAGATTAGGA
1 TTAAATTAGGA
20379432 TTTTCCTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (12 bp):
TTAAATTAGGAA
Found at i:20382514 original size:13 final size:13
Alignment explanation
Indices: 20382498--20382548 Score: 54
Period size: 12 Copynumber: 4.1 Consensus size: 13
20382488 TTCCTTATAA
20382498 AATTTAAATTAGG
1 AATTTAAATTAGG
20382511 AATTCT--ATTAGG
1 AATT-TAAATTAGG
*
20382523 ACTTTAAATTAGG
1 AATTTAAATTAGG
*
20382536 AA-TTAGATTAGG
1 AATTTAAATTAGG
20382548 A
1 A
20382549 TTTTCCTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 1 0.03
12 19 0.59
13 11 0.34
14 1 0.03
ACGTcount: A:0.41, C:0.04, G:0.18, T:0.37
Consensus pattern (13 bp):
AATTTAAATTAGG
Found at i:20382534 original size:25 final size:25
Alignment explanation
Indices: 20382500--20382548 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
20382490 CCTTATAAAA
**
20382500 TTTAAATTAGGAATTCTATTAGGAC
1 TTTAAATTAGGAATTAGATTAGGAC
20382525 TTTAAATTAGGAATTAGATTAGGA
1 TTTAAATTAGGAATTAGATTAGGA
20382549 TTTTCCTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39
Consensus pattern (25 bp):
TTTAAATTAGGAATTAGATTAGGAC
Found at i:20385175 original size:38 final size:38
Alignment explanation
Indices: 20385120--20385199 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 38
20385110 TAGTTACAAA
*
20385120 AAATTTTAAATAATTATATGTAGGATGATAAAAGAAAT
1 AAATTATAAATAATTATATGTAGGATGATAAAAGAAAT
*
20385158 AAATTATAAATAGTTATATGTAGGATGATAAAAGAAAT
1 AAATTATAAATAATTATATGTAGGATGATAAAAGAAAT
20385196 AAAT
1 AAAT
20385200 GATTCAATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.33
Consensus pattern (38 bp):
AAATTATAAATAATTATATGTAGGATGATAAAAGAAAT
Found at i:20390170 original size:23 final size:22
Alignment explanation
Indices: 20390123--20390170 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
20390113 AGCGTTTACA
* *
20390123 TTTTTTTCTATCAATTTGGTTT
1 TTTTTTTCTATCAATTTGATAT
20390145 TTTTTTTCT-TCTAAATTTGATAT
1 TTTTTTTCTATC--AATTTGATAT
20390168 TTT
1 TTT
20390171 AACCTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 9 0.41
23 11 0.50
ACGTcount: A:0.17, C:0.08, G:0.06, T:0.69
Consensus pattern (22 bp):
TTTTTTTCTATCAATTTGATAT
Found at i:20397072 original size:18 final size:18
Alignment explanation
Indices: 20397049--20397091 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
20397039 AAATAATTAC
20397049 GTAAGC-AATGAATGCTTA
1 GTAAGCTAA-GAATGCTTA
*
20397067 GTAAGCTCAGAATGCTTA
1 GTAAGCTAAGAATGCTTA
20397085 GTAAGCT
1 GTAAGCT
20397092 CATATAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (18 bp):
GTAAGCTAAGAATGCTTA
Found at i:20397092 original size:18 final size:18
Alignment explanation
Indices: 20397058--20397093 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
20397048 CGTAAGCAAT
20397058 GAATGCTTAGTAAGCTCA
1 GAATGCTTAGTAAGCTCA
20397076 GAATGCTTAGTAAGCTCA
1 GAATGCTTAGTAAGCTCA
20397094 TATAAACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (18 bp):
GAATGCTTAGTAAGCTCA
Found at i:20397799 original size:35 final size:35
Alignment explanation
Indices: 20397737--20397818 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 35
20397727 AATCTAACTG
*
20397737 AAACACATCAGATGCTCATAAGAGCTAATCCATCCC
1 AAACACACCA-ATGCTCATAAGAGCTAATCCATCCC
* **
20397773 AAACACACCAATGCTCATAAGGGCTAATCCATCTG
1 AAACACACCAATGCTCATAAGAGCTAATCCATCCC
20397808 AAACACACCAA
1 AAACACACCAA
20397819 AACATAGAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 33 0.79
36 9 0.21
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.17
Consensus pattern (35 bp):
AAACACACCAATGCTCATAAGAGCTAATCCATCCC
Found at i:20401953 original size:12 final size:12
Alignment explanation
Indices: 20401936--20401967 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
20401926 ATATAACTTT
20401936 AATATTTATTAA
1 AATATTTATTAA
*
20401948 AATATTTATTAC
1 AATATTTATTAA
20401960 AATATTTA
1 AATATTTA
20401968 CACCATTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (12 bp):
AATATTTATTAA
Found at i:20404132 original size:16 final size:17
Alignment explanation
Indices: 20404111--20404180 Score: 76
Period size: 16 Copynumber: 4.4 Consensus size: 17
20404101 TTTGGTTCAC
*
20404111 TGTAATGGAATAAG-GT
1 TGTAATTGAATAAGAGT
20404127 TGTAATTGAAT-AGAGT
1 TGTAATTGAATAAGAGT
*
20404143 TGTAATTGAAT-AGAGC
1 TGTAATTGAATAAGAGT
* *
20404159 TGTAATAGAAT-AGAGC
1 TGTAATTGAATAAGAGT
20404175 TGTAAT
1 TGTAAT
20404181 AAGTAATTCA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
15 2 0.04
16 48 0.96
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.33
Consensus pattern (17 bp):
TGTAATTGAATAAGAGT
Found at i:20404154 original size:32 final size:32
Alignment explanation
Indices: 20404110--20404180 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
20404100 GTTTGGTTCA
* *
20404110 CTGTAATGGAATA-AGGTTGTAATTGAATAGAG
1 CTGTAATGGAATAGA-GCTGTAATAGAATAGAG
* *
20404142 TTGTAATTGAATAGAGCTGTAATAGAATAGAG
1 CTGTAATGGAATAGAGCTGTAATAGAATAGAG
20404174 CTGTAAT
1 CTGTAAT
20404181 AAGTAATTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
32 32 0.97
33 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.32
Consensus pattern (32 bp):
CTGTAATGGAATAGAGCTGTAATAGAATAGAG
Found at i:20404181 original size:16 final size:16
Alignment explanation
Indices: 20404127--20404181 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
20404117 GGAATAAGGT
* *
20404127 TGTAATTGAATAGAGT
1 TGTAATAGAATAGAGC
*
20404143 TGTAATTGAATAGAGC
1 TGTAATAGAATAGAGC
20404159 TGTAATAGAATAGAGC
1 TGTAATAGAATAGAGC
20404175 TGTAATA
1 TGTAATA
20404182 AGTAATTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.33
Consensus pattern (16 bp):
TGTAATAGAATAGAGC
Found at i:20404251 original size:44 final size:46
Alignment explanation
Indices: 20404166--20404255 Score: 130
Period size: 44 Copynumber: 2.0 Consensus size: 46
20404156 AGCTGTAATA
*
20404166 GAATAGAGCTGTAATAAGTAATTCAACTGTTTGGTTGAATGGAATG
1 GAATAGAACTGTAATAAGTAATTCAACTGTTTGGTTGAATGGAATG
***
20404212 GAATAGAACTGTAAT-AGT-ATTCTTGTGTTTGGTTGAATGGAATG
1 GAATAGAACTGTAATAAGTAATTCAACTGTTTGGTTGAATGGAATG
20404256 ATGTTGTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 23 0.57
45 3 0.08
46 14 0.35
ACGTcount: A:0.32, C:0.06, G:0.27, T:0.36
Consensus pattern (46 bp):
GAATAGAACTGTAATAAGTAATTCAACTGTTTGGTTGAATGGAATG
Found at i:20404864 original size:18 final size:18
Alignment explanation
Indices: 20404841--20404876 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
20404831 ACGTGGTAGT
20404841 CCAACTAGATTTTAAGTA
1 CCAACTAGATTTTAAGTA
20404859 CCAACTAGATTTTAAGTA
1 CCAACTAGATTTTAAGTA
20404877 TATCTGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (18 bp):
CCAACTAGATTTTAAGTA
Found at i:20404938 original size:40 final size:40
Alignment explanation
Indices: 20404883--20404960 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
20404873 AGTATATCTG
* *
20404883 TTAATACATACTTCATCCGGTTAAATTATACAGTTTTCTA
1 TTAATACATACTTCATCCGGCTAAATTATACAATTTTCTA
20404923 TTAATACATACTTCATCCGGCTAAATTATACAATTTTC
1 TTAATACATACTTCATCCGGCTAAATTATACAATTTTC
20404961 ACGCAAATGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.41
Consensus pattern (40 bp):
TTAATACATACTTCATCCGGCTAAATTATACAATTTTCTA
Found at i:20405084 original size:11 final size:10
Alignment explanation
Indices: 20405064--20405089 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
20405054 ATCAAGAATC
20405064 AAACAAAAAA
1 AAACAAAAAA
20405074 AAACAAAAAA
1 AAACAAAAAA
20405084 AAACAA
1 AAACAA
20405090 CAGGTGCGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (10 bp):
AAACAAAAAA
Found at i:20406867 original size:17 final size:17
Alignment explanation
Indices: 20406847--20406904 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
20406837 ATATTTAATG
20406847 ATATAATATATAAAAAT
1 ATATAATATATAAAAAT
*
20406864 ATAT--T-TATAAGAAT
1 ATATAATATATAAAAAT
20406878 A-ATAATTATATAAAAAT
1 ATATAA-TATATAAAAAT
*
20406895 ATAAAATATA
1 ATATAATATA
20406905 ATGGTTTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
13 2 0.06
14 9 0.27
15 1 0.03
16 1 0.03
17 17 0.52
18 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
ATATAATATATAAAAAT
Found at i:20407213 original size:18 final size:19
Alignment explanation
Indices: 20407186--20407294 Score: 100
Period size: 20 Copynumber: 5.6 Consensus size: 19
20407176 ATTTAATGAC
20407186 ATAATAATATAAAATAA-AT
1 ATAAT-ATATAAAATAATAT
*
20407205 ATAATATATAATATGAA-AGT
1 ATAATATATAAAAT-AATA-T
* *
20407225 AT-GTATGTGAAAATAATAT
1 ATAATATAT-AAAATAATAT
20407244 ATAATATAT-AAATAATAT
1 ATAATATATAAAATAATAT
20407262 GAGTAATATATAAAATAATCAT
1 -A-TAATATATAAAATAAT-AT
20407284 ATAATATATAA
1 ATAATATATAA
20407295 TTTAAAAAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
18 17 0.23
19 18 0.24
20 30 0.40
21 8 0.11
22 2 0.03
ACGTcount: A:0.58, C:0.01, G:0.06, T:0.35
Consensus pattern (19 bp):
ATAATATATAAAATAATAT
Found at i:20407249 original size:7 final size:7
Alignment explanation
Indices: 20407237--20407295 Score: 56
Period size: 7 Copynumber: 8.7 Consensus size: 7
20407227 GTATGTGAAA
20407237 ATAATAT
1 ATAATAT
20407244 ATAATAT
1 ATAATAT
20407251 AT-A-A-
1 ATAATAT
20407255 ATAATAT
1 ATAATAT
20407262 GAGTAATAT
1 -A-TAATAT
20407271 ATAA-A-
1 ATAATAT
20407276 ATAATCAT
1 ATAAT-AT
20407284 ATAATAT
1 ATAATAT
20407291 ATAAT
1 ATAAT
20407296 TTAAAAAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
4 2 0.05
5 6 0.14
6 3 0.07
7 20 0.45
8 7 0.16
9 6 0.14
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (7 bp):
ATAATAT
Found at i:20407295 original size:27 final size:27
Alignment explanation
Indices: 20407237--20407310 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
20407227 GTATGTGAAA
*
20407237 ATAATATATAATAT-ATAAATAATATG
1 ATAATATATAAAATAATAAATAATATG
*
20407263 AGTAATATATAAAATAATCATATAATAT-
1 A-TAATATATAAAATAAT-AAATAATATG
* *
20407291 ATAATTTAAAAAATAA-AAAT
1 ATAATATATAAAATAATAAAT
20407311 GAAGCAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
25 3 0.08
26 1 0.03
27 25 0.62
28 3 0.08
29 8 0.20
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (27 bp):
ATAATATATAAAATAATAAATAATATG
Found at i:20414839 original size:17 final size:19
Alignment explanation
Indices: 20414817--20414862 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
20414807 TAATTACAAC
20414817 ATAATTTAATAA-A-TAAA
1 ATAATTTAATAACATTAAA
*
20414834 ATAA-TTACATAACATTAAT
1 ATAATTTA-ATAACATTAAA
20414853 ATAATTTAAT
1 ATAATTTAAT
20414863 GATTTGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
16 3 0.12
17 8 0.33
18 1 0.04
19 9 0.38
20 3 0.12
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAATTTAATAACATTAAA
Found at i:20431664 original size:16 final size:17
Alignment explanation
Indices: 20431632--20431664 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20431622 TTTATAAGTA
*
20431632 TATATCAATCGTTTCAT
1 TATATCAATCATTTCAT
20431649 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
20431665 GTTTCATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:20432107 original size:92 final size:92
Alignment explanation
Indices: 20431960--20432170 Score: 350
Period size: 92 Copynumber: 2.3 Consensus size: 92
20431950 TGCCATAGTG
* * *
20431960 TCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
1 TCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
* *
20432025 TTCTTTTCATGTCACGTTGCCACGGTA
66 TTCGTTTCATATCACGTTGCCACGGTA
*
20432052 TCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
1 TCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
*
20432117 TTCGTTTCATATCACGTTGCCATGGTA
66 TTCGTTTCATATCACGTTGCCACGGTA
*
20432144 TCTTTCAACCATGGTCTTACACATTTC
1 TCTTTCAACCATGGTCTTACTCATTTC
20432171 ATATCAGATA
Statistics
Matches: 110, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
92 110 1.00
ACGTcount: A:0.18, C:0.25, G:0.14, T:0.42
Consensus pattern (92 bp):
TCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
TTCGTTTCATATCACGTTGCCACGGTA
Found at i:20432176 original size:46 final size:46
Alignment explanation
Indices: 20431950--20432172 Score: 304
Period size: 46 Copynumber: 4.8 Consensus size: 46
20431940 TTTGACATGA
* * * * *
20431950 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATGTCACGT
*
20431996 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
* ** *
20432042 TGCCACGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
* *
20432088 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
**
20432134 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT
20432173 ATCAGATAGC
Statistics
Matches: 156, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 4 0.03
46 152 0.97
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.42
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
Found at i:20438153 original size:13 final size:13
Alignment explanation
Indices: 20438135--20438171 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
20438125 TGGGGTCACA
20438135 CGGGCGTGTGTCT
1 CGGGCGTGTGTCT
20438148 CGGGCGTGTGTCT
1 CGGGCGTGTGTCT
* *
20438161 CAGCCGTGTGT
1 CGGGCGTGTGT
20438172 GACACAAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.03, C:0.24, G:0.43, T:0.30
Consensus pattern (13 bp):
CGGGCGTGTGTCT
Found at i:20439634 original size:13 final size:14
Alignment explanation
Indices: 20439616--20439651 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
20439606 AACCCGCTTT
20439616 ATAATAATA-AATA
1 ATAATAATATAATA
20439629 ATAATAATATAATA
1 ATAATAATATAATA
20439643 ATAA-AATAT
1 ATAATAATAT
20439652 TTTTTTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATAATATAATA
Found at i:20443413 original size:26 final size:25
Alignment explanation
Indices: 20443332--20443413 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 25
20443322 CAACTACCTA
* *
20443332 TAAATAATTCAAATAAAAT-TATATT
1 TAAAAAATTAAAATAAAATCTA-ATT
*
20443357 TAGAAAATTAAAAT--AATCTAACTT
1 TAAAAAATTAAAATAAAATCTAA-TT
*
20443381 CCTAAAAGATTAAAATAAAATCTAATT
1 --TAAAAAATTAAAATAAAATCTAATT
20443408 TAAAAA
1 TAAAAA
20443414 TAAATATTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
23 4 0.09
24 4 0.09
25 16 0.36
26 12 0.27
27 2 0.04
28 7 0.16
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (25 bp):
TAAAAAATTAAAATAAAATCTAATT
Found at i:20444129 original size:29 final size:30
Alignment explanation
Indices: 20444087--20444145 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
20444077 ACTTAACAAG
20444087 CAAATGCCTCTAAAATAATAA-AAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
20444116 CAAATTCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
20444146 TAATAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:20445307 original size:64 final size:64
Alignment explanation
Indices: 20445229--20445354 Score: 180
Period size: 64 Copynumber: 2.0 Consensus size: 64
20445219 GGATAACTTT
** ** *
20445229 AGTCAAAAGTATAAAATGGCATGTATCAATTATTCAATAGATTAATGTGCCACATCAATAATAG
1 AGTCAAAAGTATAAAATGGCACATATCAAAAATTCAATAAATTAATGTGCCACATCAATAATAG
* * *
20445293 AGTCAAAAGTATAAAATGGCACATGTCAAAAATTCAATAAATTAATGTGTCACATCAGTAAT
1 AGTCAAAAGTATAAAATGGCACATATCAAAAATTCAATAAATTAATGTGCCACATCAATAAT
20445355 CTATTGGTGG
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (64 bp):
AGTCAAAAGTATAAAATGGCACATATCAAAAATTCAATAAATTAATGTGCCACATCAATAATAG
Found at i:20447113 original size:60 final size:60
Alignment explanation
Indices: 20446999--20447114 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
20446989 TTTATCCTGT
* * * ** *
20446999 TTCATTTTCAAAAGTTTTGGTTCAATCCAGTAAGTATTTTTGAAAGTTTGGTTCCGCAAG
1 TTCATTTTCAAAAGTTCTAGTTCAATCCAGTAAGTATTTTAGAAAGACTAGTTCCGCAAG
*
20447059 TTCATTTTCAAAAGTTCTAGTTCCA-CCTAGT-AGATATTTTAGAAAGACTAGTTCCG
1 TTCATTTTCAAAAGTTCTAGTTCAATCC-AGTAAG-TATTTTAGAAAGACTAGTTCCG
20447115 TCTAGGTTTG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
59 4 0.09
60 43 0.91
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (60 bp):
TTCATTTTCAAAAGTTCTAGTTCAATCCAGTAAGTATTTTAGAAAGACTAGTTCCGCAAG
Found at i:20453385 original size:71 final size:71
Alignment explanation
Indices: 20453266--20453398 Score: 221
Period size: 71 Copynumber: 1.9 Consensus size: 71
20453256 ATATTGGGAG
*
20453266 AATGGATATTATCCAAAAGAGATTAAGCATATCTTACGAGAGTAACTCATTTATAACAAGGTCAG
1 AATGGATATTATCCAAAAGAGATTAAGCATATCCTACGAGAGTAACTCATTTATAACAAGGTCAG
20453331 TGGACA
66 TGGACA
* * * *
20453337 AATGGATATTATCCCAAAGAGATTAAGCTTATCCTATGAGAGTCACTCATTTATAACAAGGT
1 AATGGATATTATCCAAAAGAGATTAAGCATATCCTACGAGAGTAACTCATTTATAACAAGGT
20453399 TATTAGACAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 57 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (71 bp):
AATGGATATTATCCAAAAGAGATTAAGCATATCCTACGAGAGTAACTCATTTATAACAAGGTCAG
TGGACA
Found at i:20453702 original size:6 final size:6
Alignment explanation
Indices: 20453691--20453725 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
20453681 GGTTTTCTCC
20453691 AAAATG AAAATG AAAATG AAAATGG AGAAATG AAA
1 AAAATG AAAATG AAAATG AAAAT-G A-AAATG AAA
20453726 TCATTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.70
7 4 0.15
8 4 0.15
ACGTcount: A:0.66, C:0.00, G:0.20, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:20453749 original size:63 final size:63
Alignment explanation
Indices: 20453646--20453776 Score: 178
Period size: 63 Copynumber: 2.1 Consensus size: 63
20453636 AGAATTGGTG
* * *
20453646 AAATGGAGAAATAGGAAACATTTGAAAATGATTAAGGTTTTCTCCAAAATGAAAATGAAAATGA
1 AAATGGAGAAATA-GAAACATTTAAAAATGATTAAGGTTTTCTCCAAAATAAAAATAAAAATGA
20453710 AAATGGAGAAAT-GAAATCATTTAAAAATGAATGT-A-GTTTTCTCCAAAATAAAAATAAAAATG
1 AAATGGAGAAATAGAAA-CATTTAAAAATG-AT-TAAGGTTTTCTCCAAAATAAAAATAAAAATG
20453772 A
63 A
20453773 AAAT
1 AAAT
20453777 AAAAAATGAA
Statistics
Matches: 61, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
62 4 0.07
63 41 0.67
64 15 0.25
65 1 0.02
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (63 bp):
AAATGGAGAAATAGAAACATTTAAAAATGATTAAGGTTTTCTCCAAAATAAAAATAAAAATGA
Found at i:20453775 original size:12 final size:13
Alignment explanation
Indices: 20453754--20453789 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
20453744 AGTTTTCTCC
*
20453754 AAAATAAAAAT-A
1 AAAATGAAAATAA
20453766 AAAATGAAAATAA
1 AAAATGAAAATAA
20453779 AAAATGAAAAT
1 AAAATGAAAAT
20453790 GTCCTGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (13 bp):
AAAATGAAAATAA
Found at i:20456596 original size:12 final size:12
Alignment explanation
Indices: 20456559--20456606 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
20456549 TATTTAAATT
*
20456559 TTTTATTAATTA
1 TTTTATTAATAA
* *
20456571 TTGTATT--TAC
1 TTTTATTAATAA
20456581 TTTTATTAATAA
1 TTTTATTAATAA
20456593 TTTTATTAATAA
1 TTTTATTAATAA
20456605 TT
1 TT
20456607 AAGATGTTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
10 7 0.24
12 22 0.76
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (12 bp):
TTTTATTAATAA
Found at i:20457122 original size:59 final size:59
Alignment explanation
Indices: 20457059--20457183 Score: 187
Period size: 59 Copynumber: 2.1 Consensus size: 59
20457049 GGGTTTGAAT
*
20457059 TTTTTTTTATCCAAGTTACACCTTGAAATTGAAAATTGTTCTCACATTGGAGCCTAAAC
1 TTTTTTTTATCCAAGTTACACCTTGAAATTGAAAATTGTTCCCACATTGGAGCCTAAAC
* * ** * *
20457118 TTTTTTTTGTCTAAGTTAGGCCTTGAACTTGAAAATTGTTCCCACATTGGAGCTTAAAC
1 TTTTTTTTATCCAAGTTACACCTTGAAATTGAAAATTGTTCCCACATTGGAGCCTAAAC
20457177 TTTTTTT
1 TTTTTTT
20457184 CATGTCCAAG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (59 bp):
TTTTTTTTATCCAAGTTACACCTTGAAATTGAAAATTGTTCCCACATTGGAGCCTAAAC
Found at i:20460426 original size:12 final size:12
Alignment explanation
Indices: 20460400--20460443 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
20460390 ACTTAGACCT
*
20460400 TATA-ATATATA
1 TATATATATGTA
* *
20460411 TATATGTGTGTA
1 TATATATATGTA
20460423 TATATATATGTA
1 TATATATATGTA
20460435 TATATATAT
1 TATATATAT
20460444 AAATGCAAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 4 0.15
12 23 0.85
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (12 bp):
TATATATATGTA
Found at i:20460426 original size:14 final size:14
Alignment explanation
Indices: 20460405--20460444 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
20460395 GACCTTATAA
*
20460405 TATATATATATGTG
1 TATATATATATATG
*
20460419 TGTATATATATATG
1 TATATATATATATG
20460433 TATATATATATA
1 TATATATATATA
20460445 AATGCAAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (14 bp):
TATATATATATATG
Found at i:20460426 original size:16 final size:16
Alignment explanation
Indices: 20460404--20460444 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
20460394 AGACCTTATA
*
20460404 ATATATATATATGTGT
1 ATATATATATATGTAT
*
20460420 GTATATATATATGTAT
1 ATATATATATATGTAT
20460436 ATATATATA
1 ATATATATA
20460445 AATGCAAGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (16 bp):
ATATATATATATGTAT
Found at i:20461392 original size:21 final size:21
Alignment explanation
Indices: 20461361--20461403 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 21
20461351 ATTTTCTTTT
20461361 ATTTTTTC-TTTTTAG-AAAA
1 ATTTTTTCTTTTTTAGTAAAA
20461380 ATTTTTTAGCTTTTTTAGTAAAA
1 ATTTTTT--CTTTTTTAGTAAAA
20461403 A
1 A
20461404 GGGAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 7 0.35
21 1 0.05
22 7 0.35
23 5 0.25
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.56
Consensus pattern (21 bp):
ATTTTTTCTTTTTTAGTAAAA
Found at i:20464612 original size:21 final size:21
Alignment explanation
Indices: 20464586--20464625 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
20464576 CATTTGGGTG
*
20464586 TTCGATGCTTTTGAGAAAACT
1 TTCGATGCTTTTGAAAAAACT
20464607 TTCGATGCTTTTGAAAAAA
1 TTCGATGCTTTTGAAAAAA
20464626 GTCTAATATC
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:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (21 bp):
TTCGATGCTTTTGAAAAAACT
Found at i:20469292 original size:44 final size:44
Alignment explanation
Indices: 20469204--20469294 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
20469194 GTAGGTCAAA
* **
20469204 TAATATTAAAATAACCTACACTAATAAGAGTTTAGGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATAAGAGTTTAAGTGAAAAAC
*
20469248 TAATATTAAAATAATCTACACTAATCAA-AGTTTAAGTGAAAAAC
1 TAATATTAAAATAACCTACACTAAT-AAGAGTTTAAGTGAAAAAC
20469292 TAA
1 TAA
20469295 AAACAGAGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 40 0.95
45 2 0.05
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATAAGAGTTTAAGTGAAAAAC
Found at i:20470468 original size:102 final size:103
Alignment explanation
Indices: 20470298--20470485 Score: 229
Period size: 102 Copynumber: 1.8 Consensus size: 103
20470288 TATCAATACA
* * * * * **
20470298 GTATCGATACTTTGTAGGTTTTGTGAGAAACATAATGCTATTTTGATATTGCTTTTAAGAAGGGG
1 GTATCGATACTTTGTAGGGTTTGTGAGAAACAAAATGCCACTTTGATATCGCTTTTAAGAAAAGG
20470363 TATCGA-AATTTCAAAAAATATTGACACTTAATCAAAAG
66 TATCGATAA-TTCAAAAAATATTGACACTTAATCAAAAG
* * * *
20470401 GTATCGATACTTAT-TAGGGTTTGTGA-AAACAAAATTCCACTTTGGTATCGTTTTTAAGAAAAT
1 GTATCGATACTT-TGTAGGGTTTGTGAGAAACAAAATGCCACTTTGATATCGCTTTTAAGAAAAG
*
20470464 GTATCGATAATTCAGAAAATAT
65 GTATCGATAATTCAAAAAATAT
20470486 CAATACTTGG
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
102 45 0.63
103 25 0.35
104 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (103 bp):
GTATCGATACTTTGTAGGGTTTGTGAGAAACAAAATGCCACTTTGATATCGCTTTTAAGAAAAGG
TATCGATAATTCAAAAAATATTGACACTTAATCAAAAG
Found at i:20472878 original size:37 final size:37
Alignment explanation
Indices: 20472835--20472910 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
20472825 AAAGAACCAT
20472835 TTTACATAGTTTAGAAATACAAAAAAAGGGCCTCTCA
1 TTTACATAGTTTAGAAATACAAAAAAAGGGCCTCTCA
20472872 TTTACATAGTTTAGAAATACAAAAAAAGGGCCTCTCA
1 TTTACATAGTTTAGAAATACAAAAAAAGGGCCTCTCA
20472909 TT
1 TT
20472911 AAATCATTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (37 bp):
TTTACATAGTTTAGAAATACAAAAAAAGGGCCTCTCA
Found at i:20480149 original size:154 final size:154
Alignment explanation
Indices: 20479717--20480127 Score: 734
Period size: 154 Copynumber: 2.7 Consensus size: 154
20479707 CCCTCCTTTC
*
20479717 TCAACTGCGCAGCCATACCCTTTGAAGGTGGTGGCTTGGATTAGGCTTCCTGAATTGCTTAGAGA
1 TCAACTGTGCAGCCATACCCTTTGAAGGTGGTGGCTTGGATTAGGCTTCCTGAATTGCTTAGAGA
20479782 AATGTATAAGCGTAGTATCCTGCATGCAATTGGCGAAATGATGGGAAAAATAATCAAGGTCGACT
66 AATGTATAAGCGTAGTATCCTGCATGCAATTGGCGAAATGATGGGAAAAATAATCAAGGTCGACT
20479847 ACATGTCTGAAGATGGTTTGAAAG
131 ACATGTCTGAAGATGGTTTGAAAG
20479871 TCAACTGTGCAGCCATACCCTTTGAAGGTGGTGGCTTGGATTAGGCTTCCTGAATTGCTTAGAGA
1 TCAACTGTGCAGCCATACCCTTTGAAGGTGGTGGCTTGGATTAGGCTTCCTGAATTGCTTAGAGA
20479936 AATGTATAAGCGTAGTATCCTGCATGCAATTGGCGAAATGATGGGAAAAATAATCAAGGTCGACT
66 AATGTATAAGCGTAGTATCCTGCATGCAATTGGCGAAATGATGGGAAAAATAATCAAGGTCGACT
20480001 ACATGTCTGAAGATGGTTTGAAAG
131 ACATGTCTGAAGATGGTTTGAAAG
* *
20480025 TCAACTGTGCAGCCATACCCTTTGAAGGTGGTGGCTTGGATTAGGCTTCCT-AGATTGCCTAGTG
1 TCAACTGTGCAGCCATACCCTTTGAAGGTGGTGGCTTGGATTAGGCTTCCTGA-ATTGCTTAGAG
* * ** *
20480089 AAATGCATAAGCATAGTATTTTGCATGCAATTGGTGAAA
65 AAATGTATAAGCGTAGTATCCTGCATGCAATTGGCGAAA
20480128 CGACAATGAA
Statistics
Matches: 248, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
153 1 0.00
154 247 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (154 bp):
TCAACTGTGCAGCCATACCCTTTGAAGGTGGTGGCTTGGATTAGGCTTCCTGAATTGCTTAGAGA
AATGTATAAGCGTAGTATCCTGCATGCAATTGGCGAAATGATGGGAAAAATAATCAAGGTCGACT
ACATGTCTGAAGATGGTTTGAAAG
Found at i:20483228 original size:25 final size:25
Alignment explanation
Indices: 20483197--20483246 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
20483187 CAGCATTGAG
**
20483197 AAAATCTGGGAAAGCATTGAGAAAA
1 AAAATCTAAGAAAGCATTGAGAAAA
20483222 AAAATCTAAGAAAGCATTGAGAAAA
1 AAAATCTAAGAAAGCATTGAGAAAA
20483247 TTTTTTTGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.56, C:0.08, G:0.20, T:0.16
Consensus pattern (25 bp):
AAAATCTAAGAAAGCATTGAGAAAA
Found at i:20483246 original size:21 final size:21
Alignment explanation
Indices: 20483188--20483247 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 21
20483178 CTCCAAATTC
**
20483188 AGCATTGAGAAAATCTGGGAA
1 AGCATTGAGAAAATCTAAGAA
20483209 AGCATTGAGAAAAAAAATCTAAGAA
1 AGCATTGAG----AAAATCTAAGAA
20483234 AGCATTGAGAAAAT
1 AGCATTGAGAAAAT
20483248 TTTTTTGGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
21 14 0.42
25 19 0.58
ACGTcount: A:0.52, C:0.08, G:0.22, T:0.18
Consensus pattern (21 bp):
AGCATTGAGAAAATCTAAGAA
Found at i:20484869 original size:38 final size:37
Alignment explanation
Indices: 20484787--20484892 Score: 115
Period size: 38 Copynumber: 2.8 Consensus size: 37
20484777 ACAATACATA
20484787 AACAGTAGACATGCTTAACATGTATTCAGTCTAACAG
1 AACAGTAGACATGCTTAACATGTATTCAGTCTAACAG
* * *
20484824 AGGCAGTAGACATGCTTAATATGTATTCAAT-TCAACAG
1 A-ACAGTAGACATGCTTAACATGTATTCAGTCT-AACAG
* * * *
20484862 TAACAGTAGGCATGCTGAGCATGTAATCAGT
1 -AACAGTAGACATGCTTAACATGTATTCAGT
20484893 AATACAGTGG
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
37 2 0.04
38 53 0.95
39 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (37 bp):
AACAGTAGACATGCTTAACATGTATTCAGTCTAACAG
Found at i:20489403 original size:26 final size:26
Alignment explanation
Indices: 20489372--20489426 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
20489362 CTTTCATTTT
*
20489372 CATGTTGAACATCTCTCTGCCTTCAA
1 CATGTTGAACATCTCTCTACCTTCAA
20489398 CATGTTGAACATCTCTCTACCTTCAA
1 CATGTTGAACATCTCTCTACCTTCAA
20489424 CAT
1 CAT
20489427 CTCTAATCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.25, C:0.31, G:0.09, T:0.35
Consensus pattern (26 bp):
CATGTTGAACATCTCTCTACCTTCAA
Found at i:20511260 original size:19 final size:20
Alignment explanation
Indices: 20511236--20511292 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
20511226 CAATGACTAA
20511236 AATGGAAATGAGAAA-AATT
1 AATGGAAATGAGAAATAATT
*
20511255 AATGG--ATGATAAATAATT
1 AATGGAAATGAGAAATAATT
*
20511273 AATAGGAAAT-AAAAATAATT
1 AAT-GGAAATGAGAAATAATT
20511293 TTATGTCATC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
17 7 0.22
18 7 0.22
19 7 0.22
20 9 0.28
21 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.26
Consensus pattern (20 bp):
AATGGAAATGAGAAATAATT
Found at i:20513987 original size:20 final size:20
Alignment explanation
Indices: 20513964--20514104 Score: 66
Period size: 20 Copynumber: 7.0 Consensus size: 20
20513954 AAGACATCAA
*
20513964 TAATGCAGACAAGCTGCTAG
1 TAATGCAGACAAGCTGCCAG
*** * ** *
20513984 TAATTTGGTCAAGCCACTAG
1 TAATGCAGACAAGCTGCCAG
* **
20514004 TAATGCAGATAAATTGCCAG
1 TAATGCAGACAAGCTGCCAG
** * *
20514024 TGGTACAGACAAGCTACCAG
1 TAATGCAGACAAGCTGCCAG
* * * *
20514044 TAATGCAAATAAACTGCTAG
1 TAATGCAGACAAGCTGCCAG
* *
20514064 TAGTGCAGAAAAGCTGCCAG
1 TAATGCAGACAAGCTGCCAG
* * *
20514084 AAATGCAGATAAACTGCCAG
1 TAATGCAGACAAGCTGCCAG
20514104 T
1 T
20514105 GATGTAAAAA
Statistics
Matches: 80, Mismatches: 41, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
20 80 1.00
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (20 bp):
TAATGCAGACAAGCTGCCAG
Found at i:20514037 original size:40 final size:40
Alignment explanation
Indices: 20513993--20514105 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 40
20513983 GTAATTTGGT
* * *
20513993 CAAGCCACTAGTAATGCAGATAAATTGCCAGTGGTACAGA
1 CAAGCTACCAGTAATGCAGATAAACTGCCAGTGGTACAGA
* * * *
20514033 CAAGCTACCAGTAATGCAAATAAACTGCTAGTAGTGCAGA
1 CAAGCTACCAGTAATGCAGATAAACTGCCAGTGGTACAGA
* * *
20514073 AAAGCTGCCAGAAATGCAGATAAACTGCCAGTG
1 CAAGCTACCAGTAATGCAGATAAACTGCCAGTG
20514106 ATGTAAAAAG
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (40 bp):
CAAGCTACCAGTAATGCAGATAAACTGCCAGTGGTACAGA
Found at i:20531495 original size:43 final size:43
Alignment explanation
Indices: 20531448--20531529 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
20531438 TGTGATTACA
* *
20531448 TGTAAGACGATGTCT-GAGACATTGGCATTG-TATTATGATTTCG
1 TGTAAGACCATGTCTAG-GACAGTGGCATTGATA-TATGATTTCG
*
20531491 TGTAAGACCTTGTCTAGGACAGTGGCATTGATATATGAT
1 TGTAAGACCATGTCTAGGACAGTGGCATTGATATATGAT
20531530 AACATGAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
43 31 0.91
44 3 0.09
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.35
Consensus pattern (43 bp):
TGTAAGACCATGTCTAGGACAGTGGCATTGATATATGATTTCG
Found at i:20533976 original size:45 final size:45
Alignment explanation
Indices: 20533912--20534002 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
20533902 TGCCCGAGAG
*
20533912 TATGTGTCTACTGAGGAGATCATGTGTAAACGATTCGTTGATAGA
1 TATGTGTCTACTGAGGAGATCATGTGTAAACGATTCGTTGACAGA
20533957 TATGTGTCTACTGAGGAGATCATGTGTAAACGATTCGTTGACAGA
1 TATGTGTCTACTGAGGAGATCATGTGTAAACGATTCGTTGACAGA
20534002 T
1 T
20534003 TGAATGAAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (45 bp):
TATGTGTCTACTGAGGAGATCATGTGTAAACGATTCGTTGACAGA
Found at i:20536572 original size:25 final size:25
Alignment explanation
Indices: 20536544--20536593 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
20536534 CCTTATAATA
* *
20536544 TAAAAATGACCGTTTTGCCCCTAGG
1 TAAAAATGACCGTTATACCCCTAGG
*
20536569 TAAAAATGATCGTTATACCCCTAGG
1 TAAAAATGACCGTTATACCCCTAGG
20536594 GTTTAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (25 bp):
TAAAAATGACCGTTATACCCCTAGG
Found at i:20536660 original size:20 final size:20
Alignment explanation
Indices: 20536637--20536695 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
20536627 TAAACATGGT
20536637 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
20536657 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
*
20536677 AAGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
20536696 TGTATTCATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:20536831 original size:24 final size:24
Alignment explanation
Indices: 20536745--20536890 Score: 188
Period size: 25 Copynumber: 6.0 Consensus size: 24
20536735 GGAGGAAGTG
20536745 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
* *
20536769 GATAAAGGGCTTATGCCTCAGTTAT
1 TA-AAAGGGCTTATGCCCCAGTTAT
* *
20536794 GATATAGGGCTTATGCCCCAGTTAT
1 TA-AAAGGGCTTATGCCCCAGTTAT
*
20536819 TAAAAGGGCTTATGCCCTAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
20536843 TAAAAGGGCTT-TGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
20536866 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 TAAAAG-GGCTTATGCC-CCAGTTAT
20536891 ATGATAAAGC
Statistics
Matches: 109, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
23 18 0.17
24 38 0.35
25 53 0.49
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:20536842 original size:49 final size:48
Alignment explanation
Indices: 20536746--20536890 Score: 188
Period size: 47 Copynumber: 3.0 Consensus size: 48
20536736 GAGGAAGTGT
*
20536746 AAAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCTCAGTTATG
1 AAAAGGGCTTATGCCCCAGTTATTA-AAAGGGCTTATGCCTCAGTTATG
* *
20536795 ATATAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCC-CTAGTTATT
1 A-AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCTC-AGTTATG
*
20536844 AAAAGGGCTT-TGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATTAAAAG-GGCTTATGCCT-CAGTTAT
20536891 ATGATAAAGC
Statistics
Matches: 86, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
47 23 0.27
48 18 0.21
49 23 0.27
50 22 0.26
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCTCAGTTATG
Found at i:20544882 original size:33 final size:34
Alignment explanation
Indices: 20544826--20544893 Score: 120
Period size: 33 Copynumber: 2.0 Consensus size: 34
20544816 TGGTTAGATT
20544826 AAGTTAACTTTAATATATAAAATGATAAATAAAA
1 AAGTTAACTTTAATATATAAAATGATAAATAAAA
*
20544860 AAGTTAACTTTCA-ATATAAAATGATAAATAAAA
1 AAGTTAACTTTAATATATAAAATGATAAATAAAA
20544893 A
1 A
20544894 TTAAAGTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 21 0.64
34 12 0.36
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (34 bp):
AAGTTAACTTTAATATATAAAATGATAAATAAAA
Found at i:20547618 original size:21 final size:21
Alignment explanation
Indices: 20547592--20547637 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
20547582 TGTTACATAG
* *
20547592 TGACTGTTTGAAAGCTGTTTC
1 TGACTGGTTGAAAGATGTTTC
20547613 TGACTGGTTGAAAGATGTTTC
1 TGACTGGTTGAAAGATGTTTC
20547634 TGAC
1 TGAC
20547638 CGTCAGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.13, G:0.26, T:0.39
Consensus pattern (21 bp):
TGACTGGTTGAAAGATGTTTC
Found at i:20552264 original size:79 final size:82
Alignment explanation
Indices: 20552153--20552337 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
20552143 GCTCCTCGTT
* *
20552153 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
20552216 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
20552233 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
20552296 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
20552313 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
20552338 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 (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:20552337 original size:40 final size:40
Alignment explanation
Indices: 20552153--20552337 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
20552143 GCTCCTCGTT
* *
20552153 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
20552193 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
20552233 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
20552272 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
20552313 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
20552338 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:20558995 original size:40 final size:40
Alignment explanation
Indices: 20558951--20559135 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
20558941 GCTCCTCGTT
* *
20558951 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
20558991 CAAATGCCTTCGAGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
20559031 CAAATGCCTTCGGG-CTTAGCCC-GAAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
20559070 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
20559111 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
20559136 CATCATTCAA
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
38 4 0.03
39 29 0.24
40 75 0.61
41 14 0.11
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:20559062 original size:79 final size:81
Alignment explanation
Indices: 20558951--20559133 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
20558941 GCTCCTCGTT
* **
20558951 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGAGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCG-GATCTTAACCCG
* *
20559015 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
20559031 CAAATGCCTTCGGG-CTTAGCCCGAA-ATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGAATA-TAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
20559094 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
20559111 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
20559134 GACATCATTC
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.62
80 31 0.35
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:20567095 original size:10 final size:10
Alignment explanation
Indices: 20567080--20567112 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
20567070 TATGGGCTTA
20567080 GGCCGTGTTG
1 GGCCGTGTTG
20567090 GGCCGTGTTG
1 GGCCGTGTTG
*
20567100 GGCCATGTTG
1 GGCCGTGTTG
20567110 GGC
1 GGC
20567113 TGAAATCGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.03, C:0.21, G:0.48, T:0.27
Consensus pattern (10 bp):
GGCCGTGTTG
Found at i:20579720 original size:14 final size:14
Alignment explanation
Indices: 20579701--20579727 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20579691 CTGTTTTTAT
20579701 TATGTGTGAAATTC
1 TATGTGTGAAATTC
20579715 TATGTGTGAAATT
1 TATGTGTGAAATT
20579728 TTCGTGATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.44
Consensus pattern (14 bp):
TATGTGTGAAATTC
Found at i:20582230 original size:3 final size:3
Alignment explanation
Indices: 20582222--20582256 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
20582212 ACATACCTCA
* *
20582222 TTC TTC TTC TTT TTC TTC TTC TTC TTC TTT TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
20582257 TGAGGAACAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (3 bp):
TTC
Found at i:20585672 original size:24 final size:22
Alignment explanation
Indices: 20585636--20585681 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
20585626 TGTATAAGAT
**
20585636 TTTTAAATAAATTTGTTTAAAA
1 TTTTAAATAAATTAATTTAAAA
20585658 TTTTAATATTAAATTAATTTAAAA
1 TTTTAA-A-TAAATTAATTTAAAA
20585682 ATATAAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 1 0.05
24 13 0.65
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTTAAATAAATTAATTTAAAA
Found at i:20585709 original size:22 final size:23
Alignment explanation
Indices: 20585675--20585719 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
20585665 ATTAAATTAA
*
20585675 TTTAAAAATATAAACATA-ATTT
1 TTTAAAAATATAAAAATATATTT
20585697 TTTATAAAA-ATAAAAATATATTT
1 TTTA-AAAATATAAAAATATATTT
20585720 AAAAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TTTAAAAATATAAAAATATATTT
Found at i:20585739 original size:20 final size:21
Alignment explanation
Indices: 20585702--20585741 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20585692 AATTTTTTAT
*
20585702 AAAAATAAAAATATATTTAAA
1 AAAAATAAAAACATATTTAAA
*
20585723 AAAAATTAAAACA-ATTTAA
1 AAAAATAAAAACATATTTAA
20585742 CAAGCATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAAATAAAAACATATTTAAA
Found at i:20587809 original size:12 final size:12
Alignment explanation
Indices: 20587787--20587823 Score: 65
Period size: 12 Copynumber: 3.0 Consensus size: 12
20587777 AATAATTAAT
20587787 TAAGTTCAAGTGG
1 TAAG-TCAAGTGG
20587800 TAAGTCAAGTGG
1 TAAGTCAAGTGG
20587812 TAAGTCAAGTGG
1 TAAGTCAAGTGG
20587824 CTTTTACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.32, C:0.08, G:0.32, T:0.27
Consensus pattern (12 bp):
TAAGTCAAGTGG
Found at i:20596669 original size:19 final size:19
Alignment explanation
Indices: 20596645--20596682 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
20596635 AATTTGTCAC
20596645 TGTTATTGGAGTATGCTAA
1 TGTTATTGGAGTATGCTAA
20596664 TGTTATTGGAGTATGCTAA
1 TGTTATTGGAGTATGCTAA
20596683 GGGCTTAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.42
Consensus pattern (19 bp):
TGTTATTGGAGTATGCTAA
Found at i:20597018 original size:131 final size:131
Alignment explanation
Indices: 20596784--20597046 Score: 490
Period size: 131 Copynumber: 2.0 Consensus size: 131
20596774 AGGCACTTTT
*
20596784 CAATCAGCTGAAGTTGGTGAGATGGTTATAATTTGTAGTAGGTTTTAAGCTGAAAAATGACGTCA
1 CAATCAGCTGAAGTTGGAGAGATGGTTATAATTTGTAGTAGGTTTTAAGCTGAAAAATGACGTCA
*
20596849 GGACCGTCAGGTAGAGCTTTAGGTTGAAAAGTTTGGGCATTGAGATGGACCATAGAAGTGTTTTG
66 GGACCGTCAGGTAAAGCTTTAGGTTGAAAAGTTTGGGCATTGAGATGGACCATAGAAGTGTTTTG
20596914 G
131 G
*
20596915 CAATCAGCTGAAGTTGGAGAGATGGTTATAATTTGTAGTAGGTTTTAAGCTGAAAAATGAGGTCA
1 CAATCAGCTGAAGTTGGAGAGATGGTTATAATTTGTAGTAGGTTTTAAGCTGAAAAATGACGTCA
*
20596980 GGACTGTCAGGTAAAGCTTTAGGTTGAAAAGTTTGGGCATTGAGATGGACCATAGAAGTGTTTTG
66 GGACCGTCAGGTAAAGCTTTAGGTTGAAAAGTTTGGGCATTGAGATGGACCATAGAAGTGTTTTG
20597045 G
131 G
20597046 C
1 C
20597047 CTCATACATA
Statistics
Matches: 128, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
131 128 1.00
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (131 bp):
CAATCAGCTGAAGTTGGAGAGATGGTTATAATTTGTAGTAGGTTTTAAGCTGAAAAATGACGTCA
GGACCGTCAGGTAAAGCTTTAGGTTGAAAAGTTTGGGCATTGAGATGGACCATAGAAGTGTTTTG
G
Found at i:20602024 original size:12 final size:12
Alignment explanation
Indices: 20602007--20602058 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
20601997 CTGTTATGAG
20602007 TAGCAA-TTCTGT
1 TAGCAAGTT-TGT
20602019 TAGCAAGTTTGT
1 TAGCAAGTTTGT
*
20602031 TAGCTAAGCTTGT
1 TAGC-AAGTTTGT
*
20602044 TAGCTAAGTCTGT
1 TAGC-AAGTTTGT
20602057 TA
1 TA
20602059 ACTAAGTCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
12 13 0.37
13 22 0.63
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.40
Consensus pattern (12 bp):
TAGCAAGTTTGT
Found at i:20602066 original size:13 final size:13
Alignment explanation
Indices: 20602014--20602067 Score: 67
Period size: 13 Copynumber: 4.2 Consensus size: 13
20602004 GAGTAGCAAT
20602014 TCTGTTAGC-AAG
1 TCTGTTAGCTAAG
*
20602026 TTTGTTAGCTAAG
1 TCTGTTAGCTAAG
20602039 -CTTGTTAGCTAAG
1 TC-TGTTAGCTAAG
*
20602052 TCTGTTAACTAAG
1 TCTGTTAGCTAAG
20602065 TCT
1 TCT
20602068 ATAAATACTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
12 8 0.22
13 27 0.75
14 1 0.03
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (13 bp):
TCTGTTAGCTAAG
Found at i:20605728 original size:25 final size:26
Alignment explanation
Indices: 20605700--20605761 Score: 90
Period size: 25 Copynumber: 2.4 Consensus size: 26
20605690 TTGTTATGAG
*
20605700 TAGCTAAGTCTGTTAGC-AAGTTTGT
1 TAGCTAAGTCTGTTAGCTAAGTCTGT
*
20605725 TAGCTAAGTTTGTTAGCTAAGTCTGT
1 TAGCTAAGTCTGTTAGCTAAGTCTGT
*
20605751 TAACTAAGTCT
1 TAGCTAAGTCT
20605762 ATAAATACTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 16 0.50
26 16 0.50
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (26 bp):
TAGCTAAGTCTGTTAGCTAAGTCTGT
Found at i:20605733 original size:13 final size:13
Alignment explanation
Indices: 20605700--20605761 Score: 90
Period size: 13 Copynumber: 4.8 Consensus size: 13
20605690 TTGTTATGAG
20605700 TAGCTAAGTCTGT
1 TAGCTAAGTCTGT
*
20605713 TAGC-AAGTTTGT
1 TAGCTAAGTCTGT
*
20605725 TAGCTAAGTTTGT
1 TAGCTAAGTCTGT
20605738 TAGCTAAGTCTGT
1 TAGCTAAGTCTGT
*
20605751 TAACTAAGTCT
1 TAGCTAAGTCT
20605762 ATAAATACTA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
12 11 0.24
13 34 0.76
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (13 bp):
TAGCTAAGTCTGT
Found at i:20607783 original size:13 final size:13
Alignment explanation
Indices: 20607726--20607781 Score: 87
Period size: 13 Copynumber: 4.4 Consensus size: 13
20607716 TATGAGTAGT
20607726 TAAGTTTGTTAGC
1 TAAGTTTGTTAGC
20607739 -AAGTTTGTTAGC
1 TAAGTTTGTTAGC
20607751 TAAGTTTGTTAGC
1 TAAGTTTGTTAGC
* *
20607764 TAAGTCTGTTAAC
1 TAAGTTTGTTAGC
20607777 TAAGT
1 TAAGT
20607782 CTATAAATAC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.30
13 28 0.70
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.43
Consensus pattern (13 bp):
TAAGTTTGTTAGC
Found at i:20613237 original size:18 final size:18
Alignment explanation
Indices: 20613198--20613240 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
20613188 ATATTTTTAA
*
20613198 AAAAATATTAATTACCAT
1 AAAAATATTAAGTACCAT
*
20613216 AAAAATATT-AGTACGAT
1 AAAAATATTAAGTACCAT
20613233 GAAAAATA
1 -AAAAATA
20613241 ATTTCTAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.28
Consensus pattern (18 bp):
AAAAATATTAAGTACCAT
Found at i:20614483 original size:14 final size:13
Alignment explanation
Indices: 20614465--20614498 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
20614455 CTTTTCTTCT
20614465 TTCTTTTTTTTTG
1 TTCTTTTTTTTTG
*
20614478 TCTCTTTCTTTTTG
1 T-TCTTTTTTTTTG
20614492 TTCTTTT
1 TTCTTTT
20614499 CCCTTCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (13 bp):
TTCTTTTTTTTTG
Found at i:20618601 original size:30 final size:30
Alignment explanation
Indices: 20618567--20618626 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
20618557 ACTTAACAAG
*
20618567 CAAATACCTCTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
** *
20618597 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
20618627 TAATAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:20622676 original size:15 final size:15
Alignment explanation
Indices: 20622646--20622676 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20622636 TAATTGTAAT
20622646 AAATATTTATTATGA
1 AAATATTTATTATGA
*
20622661 AAATATTTATTTTGA
1 AAATATTTATTATGA
20622676 A
1 A
20622677 TATTTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (15 bp):
AAATATTTATTATGA
Found at i:20623660 original size:24 final size:24
Alignment explanation
Indices: 20623628--20623677 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
20623618 TCATAATCAA
* * *
20623628 ATACAAATGCATATACAGATTTAG
1 ATACAAATGCAGACACAGATATAG
20623652 ATACAAATGCAGACACAGATATAG
1 ATACAAATGCAGACACAGATATAG
20623676 AT
1 AT
20623678 GTAGTCATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (24 bp):
ATACAAATGCAGACACAGATATAG
Found at i:20626579 original size:18 final size:18
Alignment explanation
Indices: 20626556--20626591 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20626546 AATAAAGTTC
*
20626556 ATCATTTAAATTAATTAA
1 ATCATTTAAATCAATTAA
20626574 ATCATTTAAATCAATTAA
1 ATCATTTAAATCAATTAA
20626592 TAATATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (18 bp):
ATCATTTAAATCAATTAA
Found at i:20628840 original size:21 final size:21
Alignment explanation
Indices: 20628809--20628858 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
20628799 TGAAATACAT
20628809 AACAT-AT-ATATAAAAAAAA
1 AACATAATAATATAAAAAAAA
*
20628828 CAACA-AATAATATAAAAATAA
1 -AACATAATAATATAAAAAAAA
20628849 AACATAATAA
1 AACATAATAA
20628859 AGATTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (21 bp):
AACATAATAATATAAAAAAAA
Found at i:20628931 original size:26 final size:25
Alignment explanation
Indices: 20628878--20628963 Score: 90
Period size: 26 Copynumber: 3.5 Consensus size: 25
20628868 AATAAAATGT
* *
20628878 AATATAAACATATAAG-AAAATAATA
1 AATAT-AATATATAAGTAATATAATA
*
20628903 AATATAATATA-AAGTAACGTATAAAA
1 AATATAATATATAAGTAA--TATAATA
20628929 AATAT-ATATATAAGTAAT-TAATA
1 AATATAATATATAAGTAATATAATA
20628952 AATATAATATAT
1 AATATAATATAT
20628964 GTGAAAATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
23 12 0.23
24 14 0.27
25 10 0.19
26 16 0.31
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (25 bp):
AATATAATATATAAGTAATATAATA
Found at i:20628971 original size:17 final size:18
Alignment explanation
Indices: 20628951--20628987 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
20628941 AGTAATTAAT
*
20628951 AAATATAAT-ATATGTGA
1 AAATATAATAATATATGA
20628968 AAATATAATAATATATGA
1 AAATATAATAATATATGA
20628986 AA
1 AA
20628988 GAGATGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (18 bp):
AAATATAATAATATATGA
Found at i:20628975 original size:49 final size:48
Alignment explanation
Indices: 20628887--20628983 Score: 115
Period size: 49 Copynumber: 2.0 Consensus size: 48
20628877 TAATATAAAC
**
20628887 ATATAAGAAAATAATAAATATAATATAAAGTAACGTATAAAAAATATAT
1 ATATAAGAAAATAATAAATATAATATAAAGTAAAATAT-AAAAATATAT
* * * *
20628936 ATATAAGTAATTAATAAATATAATAT-ATGTGAAAATATAATAATATAT
1 ATATAAGAAAATAATAAATATAATATAAAGT-AAAATATAAAAATATAT
20628984 GAAAGAGATG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
48 12 0.29
49 29 0.71
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (48 bp):
ATATAAGAAAATAATAAATATAATATAAAGTAAAATATAAAAATATAT
Found at i:20628976 original size:26 final size:25
Alignment explanation
Indices: 20628846--20628983 Score: 87
Period size: 26 Copynumber: 5.7 Consensus size: 25
20628836 AATATAAAAA
* * *
20628846 TAAAACATAATAAAGATTATATAA-
1 TAAAATATAATAAATATAATATAAG
* *
20628870 TAAAATGTAATATAA-A-CATATAAG
1 TAAAATATAATA-AATATAATATAAG
20628894 --AAA-ATAATAAATATAATATAAAG
1 TAAAATATAATAAATATAATAT-AAG
** *
20628917 TAACGTATAAAAAATATATATATAAG
1 TAAAATATAATAAATATA-ATATAAG
*
20628943 T--AAT-TAATAAATATAATATATG
1 TAAAATATAATAAATATAATATAAG
20628965 TGAAAATATAATAATATAT
1 T-AAAATATAATAA-ATAT
20628984 GAAAGAGATG
Statistics
Matches: 88, Mismatches: 12, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
20 2 0.02
21 6 0.07
22 14 0.16
23 19 0.22
24 12 0.14
25 6 0.07
26 21 0.24
27 8 0.09
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (25 bp):
TAAAATATAATAAATATAATATAAG
Found at i:20631055 original size:83 final size:83
Alignment explanation
Indices: 20630916--20631447 Score: 735
Period size: 83 Copynumber: 6.2 Consensus size: 83
20630906 TTCGATTTGT
* *
20630916 AAGGATGTCAAATCATCTTGAATCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
1 AAGGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
20630981 TTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
*
20630999 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
1 AAGGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
20631064 TTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
*
20631082 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
1 AAGGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
20631147 TTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
* *
20631165 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGA
1 AAGGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
20631230 TTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
20631248 AAGGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAACATTTGAGAGTCATATCTGCA
1 AAGGATGCCAAATCATCTTGAGTC----T--G----TTTGAGAACATTTGAGAGTCATATCTGCA
* *
20631313 ACGTCCTCGATTTGTTCTTTGTAAGCAC
56 ATGTCCTCGATTTGTTCCTTGTAAGCAC
* * * * * * *
20631341 AAGGATACCAAATCATCTT-AGATCTGCTTCAGTATAAACATCTGA-AGGTTAGATCTGCTATGT
1 AAGGATGCCAAATCATCTTGAG-TCTG-TT-TG-A-GAACATTTGAGA-GTCATATCTGCAATGT
* *
20631404 CCTCGATTTGTTTCTTGTAAACAC
60 CCTCGATTTGTTCCTTGTAAGCAC
* *
20631428 AAGAATACCAAATCATCTTG
1 AAGGATGCCAAATCATCTTG
20631448 GATCTGCTTC
Statistics
Matches: 414, Mismatches: 19, Indels: 27
0.90 0.04 0.06
Matches are distributed among these distances:
83 268 0.65
84 2 0.00
85 1 0.00
86 2 0.00
87 61 0.15
89 2 0.00
92 2 0.00
93 76 0.18
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (83 bp):
AAGGATGCCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
TTTGTTCCTTGTAAGCAC
Found at i:20631287 original size:10 final size:10
Alignment explanation
Indices: 20631274--20631300 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
20631264 CTTGAGTCTG
20631274 TTTGAGAACA
1 TTTGAGAACA
20631284 TTTGAGAACA
1 TTTGAGAACA
20631294 TTTGAGA
1 TTTGAGA
20631301 GTCATATCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.33
Consensus pattern (10 bp):
TTTGAGAACA
Found at i:20631326 original size:176 final size:180
Alignment explanation
Indices: 20631108--20631447 Score: 485
Period size: 176 Copynumber: 1.9 Consensus size: 180
20631098 CTTGAGTCTG
* *
20631108 TTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
1 TTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCACAAGGATAC
* * * *
20631173 CAAACCATCTT-GAGTCTG-TT-TG-A-GAACATTTG-AGAGTCATATCTGCAACGTCCTCGATT
66 CAAACCATCTTAGA-TCTGCTTCAGTATAAACATCTGAAG-GTCAGATCTGCAACGTCCTCGATT
* * *
20631232 TGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGAGTCTGTTTGAGAACA
129 TGTTCCTTGTAAACACAAGAATACCAAATCATCTTGAGTCTGTTTGAGAACA
*
20631284 TTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCTTTGTAAGCACAAGGATAC
1 TTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCACAAGGATAC
* * * *
20631349 CAAATCATCTTAGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTCCTCGATTTG
66 CAAACCATCTTAGATCTGCTTCAGTATAAACATCTGAAGGTCAGATCTGCAACGTCCTCGATTTG
*
20631414 TTTCTTGTAAACACAAGAATACCAAATCATCTTG
131 TTCCTTGTAAACACAAGAATACCAAATCATCTTG
20631448 GATCTGCTTC
Statistics
Matches: 143, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
176 76 0.53
177 4 0.03
178 1 0.01
179 1 0.01
180 59 0.41
181 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (180 bp):
TTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCACAAGGATAC
CAAACCATCTTAGATCTGCTTCAGTATAAACATCTGAAGGTCAGATCTGCAACGTCCTCGATTTG
TTCCTTGTAAACACAAGAATACCAAATCATCTTGAGTCTGTTTGAGAACA
Found at i:20631341 original size:93 final size:93
Alignment explanation
Indices: 20631191--20631447 Score: 323
Period size: 93 Copynumber: 2.8 Consensus size: 93
20631181 CTTGAGTCTG
*
20631191 TTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
1 TTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCACAAGGATAC
20631256 CAAATCATCTTGAGTCTGTTTGAGAACA
66 CAAATCATCTTGAGTCTGTTTGAGAACA
*
20631284 TTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCTTTGTAAGCACAAGGATAC
1 TTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCACAAGGATAC
* *
20631349 CAAATCATCTT-AGATCTGCTTCAG----
66 CAAATCATCTTGAG-TCTGTTTGAGAACA
* * * * * * * * *
20631373 TAT-A-AACATCTGA-AGGTTAGATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATA
1 TTTGAGAACATTTGAGA-GTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCACAAGGATA
20631435 CCAAATCATCTTG
65 CCAAATCATCTTG
20631448 GATCTGCTTC
Statistics
Matches: 147, Mismatches: 14, Indels: 11
0.85 0.08 0.06
Matches are distributed among these distances:
86 1 0.01
87 59 0.40
88 1 0.01
89 2 0.01
92 2 0.01
93 82 0.56
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (93 bp):
TTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCACAAGGATAC
CAAATCATCTTGAGTCTGTTTGAGAACA
Found at i:20643374 original size:20 final size:21
Alignment explanation
Indices: 20643342--20643390 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
20643332 TGATATACAT
20643342 AACAT-AT-ATATAAAAA-AA
1 AACATAATAATATAAAAATAA
20643360 CAACA-AATAATATAAAAATAA
1 -AACATAATAATATAAAAATAA
20643381 AACATAATAA
1 AACATAATAA
20643391 AGATTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 6 0.23
20 13 0.50
21 7 0.27
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.20
Consensus pattern (21 bp):
AACATAATAATATAAAAATAA
Found at i:20643509 original size:17 final size:18
Alignment explanation
Indices: 20643489--20643525 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
20643479 AGTAATTAAT
*
20643489 AAATATAAT-ATATGTGA
1 AAATATAATAATATATGA
20643506 AAATATAATAATATATGA
1 AAATATAATAATATATGA
20643524 AA
1 AA
20643526 GAGATGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (18 bp):
AAATATAATAATATATGA
Found at i:20648973 original size:29 final size:32
Alignment explanation
Indices: 20648941--20649008 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 32
20648931 TTAATTAAAA
20648941 TTTTAAAAAATA-TTTTTA-AAATTTTT-AAT
1 TTTTAAAAAATAGTTTTTATAAATTTTTGAAT
**
20648970 TTTT-AAAAATAGTTTTTATATTTTTTTGAAT
1 TTTTAAAAAATAGTTTTTATAAATTTTTGAAT
20649001 TTTTAAAA
1 TTTTAAAA
20649009 TTTTAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 7 0.21
29 10 0.30
30 6 0.18
31 7 0.21
32 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (32 bp):
TTTTAAAAAATAGTTTTTATAAATTTTTGAAT
Found at i:20648992 original size:28 final size:30
Alignment explanation
Indices: 20648939--20649008 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 30
20648929 AATTAATTAA
*
20648939 AATTTTAAAAAATATTTTTAAAA-TTTTT-
1 AATTTTTAAAAATATTTTTAAAATTTTTTG
* *
20648967 AATTTTTAAAAATAGTTTTTATATTTTTTTG
1 AATTTTTAAAAATA-TTTTTAAAATTTTTTG
20648998 AATTTTTAAAA
1 AATTTTTAAAA
20649009 TTTTAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 13 0.36
29 7 0.19
30 5 0.14
31 11 0.31
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (30 bp):
AATTTTTAAAAATATTTTTAAAATTTTTTG
Found at i:20650427 original size:35 final size:34
Alignment explanation
Indices: 20650388--20650453 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
20650378 AAATAATTTT
* * * *
20650388 TAAAATTCTAAATATTTATAGAAATTCTAAAATTC
1 TAAAATTATAAAT-TTTAAAAAAAATCTAAAATTC
20650423 TAAAATTATAAATTTTAAAAAAAATCTAAAA
1 TAAAATTATAAATTTTAAAAAAAATCTAAAA
20650454 AAATTTATAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 15 0.56
35 12 0.44
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (34 bp):
TAAAATTATAAATTTTAAAAAAAATCTAAAATTC
Found at i:20650443 original size:16 final size:16
Alignment explanation
Indices: 20650382--20650443 Score: 54
Period size: 16 Copynumber: 3.7 Consensus size: 16
20650372 TTTTGAAAAT
*
20650382 AATTTTTAAAATTCTA
1 AATTTTAAAAATTCTA
20650398 AATATTTATAGAAATTCTAA
1 AAT-TTTA-A-AAATTCT-A
* *
20650418 AATTCT-AAAATTATA
1 AATTTTAAAAATTCTA
20650433 AATTTTAAAAA
1 AATTTTAAAAA
20650444 AAATCTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
15 6 0.16
16 13 0.35
17 4 0.11
18 1 0.03
19 9 0.24
20 4 0.11
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (16 bp):
AATTTTAAAAATTCTA
Found at i:20652178 original size:22 final size:22
Alignment explanation
Indices: 20652135--20652179 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
20652125 GGCCTATTAT
* *
20652135 AAACCAAAGATAATAAATATAA
1 AAACCAAAGATAAAAAAAATAA
20652157 AAACCAAA-ATAAAAAACAATAA
1 AAACCAAAGATAAAAAA-AATAA
20652179 A
1 A
20652180 CGACCCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.73, C:0.11, G:0.02, T:0.13
Consensus pattern (22 bp):
AAACCAAAGATAAAAAAAATAA
Found at i:20655582 original size:132 final size:132
Alignment explanation
Indices: 20655408--20655652 Score: 400
Period size: 132 Copynumber: 1.9 Consensus size: 132
20655398 CATTCAAAAA
* * * *
20655408 TTCTTCAAAACGAAGATGAGATTCGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGG
1 TTCTTCAAAACGAAGACGAGATTCGATATTTAGCAATTCGCGGAATCGTGCCATAACGTGTTGGG
*
20655473 TTGAAATTTCGCGTTTGCTCAAAATAATCGAATATTACTTCAAAATTTTCACTCATGTCTTTTAA
66 TTGAAATTTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTTCACTCATGTCTTTTAA
20655538 AG
131 AG
* *
20655540 TTCTTCAAAATGAAGACGAGATTCGATATTTAGCAATTCGCGGAATTGTGCCATAACGTGTTGGG
1 TTCTTCAAAACGAAGACGAGATTCGATATTTAGCAATTCGCGGAATCGTGCCATAACGTGTTGGG
* * *
20655605 TTGCAATTTCGCGTTTGCTCAAAATAATCGAGTATCCCTTCAAAATTT
66 TTGAAATTTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTT
20655653 CATTCATATT
Statistics
Matches: 103, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
132 103 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (132 bp):
TTCTTCAAAACGAAGACGAGATTCGATATTTAGCAATTCGCGGAATCGTGCCATAACGTGTTGGG
TTGAAATTTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTTCACTCATGTCTTTTAA
AG
Found at i:20655696 original size:132 final size:132
Alignment explanation
Indices: 20655404--20655696 Score: 374
Period size: 132 Copynumber: 2.2 Consensus size: 132
20655394 CATTCATTCA
* ** * * *
20655404 AAAATTCTTCAAAACGAAGATGAGATTCGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGT
1 AAAATTATTCAAAACGAAGACAAGATTCGATATTTAGCAATTCGCGGAATCGTGCCATAACGTGT
* *
20655469 TGGGTTGAAATTTCGCGTTTGCTCAAAATAATCGAATATTACTTCAAAATTTTCACTCATGTCTT
66 TGGGTTGAAATTTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTTCACTCATATCTT
20655534 TT
131 TT
* * * * *
20655536 AAAGTTCTTCAAAATGAAGACGAGATTCGATATTTAGCAATTCGCGGAATTGTGCCATAACGTGT
1 AAAATTATTCAAAACGAAGACAAGATTCGATATTTAGCAATTCGCGGAATCGTGCCATAACGTGT
* * * *
20655601 TGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAGTATCCCTTCAAAA-TTTCATTCATAT-TT
66 TGGGTTGAAATTTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTTCACTCATATCTT
20655664 TCT
131 T-T
* * *
20655667 AAAAATTATTTAAAACGAAGGCAATATTCG
1 -AAAATTATTCAAAACGAAGACAAGATTCG
20655697 GCGTTTGACA
Statistics
Matches: 139, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
130 3 0.02
131 11 0.08
132 125 0.90
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (132 bp):
AAAATTATTCAAAACGAAGACAAGATTCGATATTTAGCAATTCGCGGAATCGTGCCATAACGTGT
TGGGTTGAAATTTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTTCACTCATATCTT
TT
Found at i:20655709 original size:132 final size:132
Alignment explanation
Indices: 20655404--20655759 Score: 369
Period size: 132 Copynumber: 2.7 Consensus size: 132
20655394 CATTCATTCA
* ** * * *
20655404 AAAATTCTTCAAAACGAAGATGAGATTCGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGT
1 AAAATTATTCAAAACGAAGACAAGATTCGACGTTTGACAATTCGCGGAATCGTGCCATAACGTGT
* *
20655469 TGGGTTGAAATTTCGCGTTTGCTCAAAATAATCGAATATTACTTCAAAATTTTCACTCATGTCTT
66 TGGGTTGAAATTTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTTCACTCATATCTT
20655534 TT
131 TT
* * * * ** *
20655536 AAAGTTCTTCAAAATGAAGACGAGATTCGATATTT-AGCAATTCGCGGAATTGTGCCATAACGTG
1 AAAATTATTCAAAACGAAGACAAGATTCGACGTTTGA-CAATTCGCGGAATCGTGCCATAACGTG
* * * *
20655600 TTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAGTATCCCTTCAAAA-TTTCATTCATAT-T
65 TTGGGTTGAAATTTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTTCACTCATATCT
20655663 TTCT
130 TT-T
* * * * * * * *
20655667 AAAAATTATTTAAAACGAAGGCAATATTCGGCGTTTGACAATTCG-AGAATCATGCCCTATCGTG
1 -AAAATTATTCAAAACGAAGACAAGATTCGACGTTTGACAATTCGCGGAATCGTGCCATAACGTG
* * ** *
20655731 CTGGGTCGTGATTTCTCGTTTGCTCAAAA
65 TTGGGTTGAAATTTCGCGTTTGCTCAAAA
20655760 CGATCGAACA
Statistics
Matches: 187, Mismatches: 33, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
130 3 0.02
131 49 0.26
132 134 0.72
133 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (132 bp):
AAAATTATTCAAAACGAAGACAAGATTCGACGTTTGACAATTCGCGGAATCGTGCCATAACGTGT
TGGGTTGAAATTTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTTCACTCATATCTT
TT
Found at i:20656055 original size:130 final size:130
Alignment explanation
Indices: 20655809--20656056 Score: 327
Period size: 130 Copynumber: 1.9 Consensus size: 130
20655799 AAAAAACTTA
* * *
20655809 AAAACGAAGACGATGTTCAATGTTTGGCGATTTGAGAATCGTGCCCTATCGTGCTGGGTTGCGCT
1 AAAACGAAGACGATGTTCAATGTTTGACGATTTGAGAATCGAGCCCTATCGTGCTGGGTTGCACT
* * * *
20655874 TTTTCATTGGTTCGAAACAATTGAAGATCCCTTCAGAATTTCACTCATATTTTCTAAAATCTTTC
66 TTTTCATTGGTCCAAAACAATCGAAGATCCCTTCAGAATTTCACACATATTTTCTAAAATCTTTC
* * * *
20655939 AAAATGAAGGCGATGTTCGATGTTTGACGGTTTGAGAATCGAGCCCTATCGTGCTGGGTTGCACT
1 AAAACGAAGACGATGTTCAATGTTTGACGATTTGAGAATCGAGCCCTATCGTGCTGGGTTGCACT
* * * * * *
20656004 TTTTCATTTGTCCAAAATAATCGAATATCTCC-TCGGGATTTCACACGTATTTT
66 TTTTCATTGGTCCAAAACAATCGAAGATC-CCTTCAGAATTTCACACATATTTT
20656057 ATAAGGTTAG
Statistics
Matches: 100, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
130 98 0.98
131 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (130 bp):
AAAACGAAGACGATGTTCAATGTTTGACGATTTGAGAATCGAGCCCTATCGTGCTGGGTTGCACT
TTTTCATTGGTCCAAAACAATCGAAGATCCCTTCAGAATTTCACACATATTTTCTAAAATCTTTC
Found at i:20659516 original size:41 final size:41
Alignment explanation
Indices: 20659259--20659521 Score: 352
Period size: 41 Copynumber: 6.4 Consensus size: 41
20659249 CGTTCCAAAA
* * * * *
20659259 AAAACACCGGTAAAAA-CAGAGCATTCGCGGCGTTTTTTA-CT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCG--CTTTAGGT
* *
20659300 AAAACGCCGCTAAAAA-TAAAGCATTAGCGGCGCTTTAGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGT
* *
20659340 AAAACACCGCTAAAAACCAGAGCATTAGTGGCGCTTTAGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGT
*
20659381 AAAACGCCGCTAATAACCAGAGCATTAGCGGCGCTTTAGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGT
** *
20659422 AAAACGCCGCTAAAAACCAGAGCATTAGCCACGCTTTATGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGT
20659463 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGT
* *
20659504 AAAATGCTGCTAAAAACC
1 AAAACGCCGCTAAAAACC
20659522 CCATAACCCC
Statistics
Matches: 197, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 4 0.02
40 16 0.08
41 177 0.90
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGT
Found at i:20660575 original size:15 final size:15
Alignment explanation
Indices: 20660555--20660586 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20660545 TTTAATTTAG
*
20660555 AAGATAAATGTATAT
1 AAGATAAATATATAT
20660570 AAGATAAATATATAT
1 AAGATAAATATATAT
20660585 AA
1 AA
20660587 AATATTATTT
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:0.59, C:0.00, G:0.09, T:0.31
Consensus pattern (15 bp):
AAGATAAATATATAT
Found at i:20663513 original size:133 final size:134
Alignment explanation
Indices: 20663355--20663607 Score: 472
Period size: 134 Copynumber: 1.9 Consensus size: 134
20663345 TGGTGATTCC
20663355 ATTTTGGTTATTTAGATGTTATTTTGGTCTG-TTTTCATGCTTCTATCCAACTTATGTGTTTAGT
1 ATTTTGGTTATTTAGATGTTATTTTGGTCTGTTTTTCATGCTTCTATCCAACTTATGTGTTTAGT
20663419 GTGGACTTAGATTGATTTAAGAGTTTATTGCTGTCTTGTTGCTCACGTTTTATATAATAAAATTG
66 GTGGACTTAGATTGATTTAAGAGTTTATTGCTGTCTTGTTGCTCACGTTTTATATAATAAAATTG
20663484 TTAT
131 TTAT
* *
20663488 ATTTTGGTTATTTAGATGTTCTTTTGGTCTGTTTTTCATGTTTCTATCCAACTTATGTGTTTAGT
1 ATTTTGGTTATTTAGATGTTATTTTGGTCTGTTTTTCATGCTTCTATCCAACTTATGTGTTTAGT
*
20663553 GTGGACTTAGATTGATTTAAGAGTTTATTGCTGTCTTGTTGCTTACGTTTTATAT
66 GTGGACTTAGATTGATTTAAGAGTTTATTGCTGTCTTGTTGCTCACGTTTTATAT
20663608 TGTTGAATTC
Statistics
Matches: 116, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
133 30 0.26
134 86 0.74
ACGTcount: A:0.20, C:0.10, G:0.19, T:0.52
Consensus pattern (134 bp):
ATTTTGGTTATTTAGATGTTATTTTGGTCTGTTTTTCATGCTTCTATCCAACTTATGTGTTTAGT
GTGGACTTAGATTGATTTAAGAGTTTATTGCTGTCTTGTTGCTCACGTTTTATATAATAAAATTG
TTAT
Done.