Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 62 of 378
Found at i:15899030 original size:51 final size:52
Alignment explanation
Indices: 15898954--15899071 Score: 159
Period size: 51 Copynumber: 2.2 Consensus size: 52
15898944 ATGTGTCGAC
*
15898954 TACTGTGACTGTTCCAGATTCGTTCCGAAGAGGTAC-TCTGTACCAG-ACTGT
1 TACTGTTACTGTTCCAGATTCGTTCCGAAGAGGTACTTCTGTACC-GCACTGT
* * *
15899005 TACTGTTACTGTTCCAGATTTGTTCCGATGAGGTACTTTGTGTACCGCTACTGT
1 TACTGTTACTGTTCCAGATTCGTTCCGAAGAGGTAC-TTCTGTACCGC-ACTGT
15899059 TACTGTTACTGTT
1 TACTGTTACTGTT
15899072 ATTGTTACCC
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
51 33 0.56
52 1 0.02
53 7 0.12
54 18 0.31
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (52 bp):
TACTGTTACTGTTCCAGATTCGTTCCGAAGAGGTACTTCTGTACCGCACTGT
Found at i:15903602 original size:60 final size:60
Alignment explanation
Indices: 15903528--15903662 Score: 157
Period size: 60 Copynumber: 2.2 Consensus size: 60
15903518 GAGTTATCTA
* *
15903528 GGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCC-CTTACAATATC-AGAGTATACTG
1 GGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAA-ATCAAGA-TATACTG
* * * * *
15903589 GGCCTAGCCCATATCAGTATCAATCTGGGTCGTAGCCCTATTACAAGTCAAGATATATTG
1 GGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAATCAAGATATACTG
*
15903649 GGCCTTGCCCATAT
1 GGCCTAGCCCATAT
15903663 TAACATAGTT
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
60 51 0.80
61 13 0.20
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (60 bp):
GGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAATCAAGATATACTG
Found at i:15906459 original size:40 final size:39
Alignment explanation
Indices: 15906291--15906461 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
15906281 AGAAATTGAA
* *
15906291 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
15906331 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
15906371 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
15906411 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
15906451 TGATATCCGGG
1 TGATATCCGGG
15906462 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:15913986 original size:40 final size:39
Alignment explanation
Indices: 15913818--15913988 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
15913808 AGAAATTGAA
* *
15913818 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
15913858 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
15913898 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
15913938 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
15913978 TGATATCCGGG
1 TGATATCCGGG
15913989 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:15916436 original size:15 final size:15
Alignment explanation
Indices: 15916416--15916445 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
15916406 TAGACATACG
15916416 AAATAATAATAATAA
1 AAATAATAATAATAA
15916431 AAATAATAATAATAA
1 AAATAATAATAATAA
15916446 CATCCAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATAATAATAATAA
Found at i:15918122 original size:39 final size:39
Alignment explanation
Indices: 15918079--15918268 Score: 274
Period size: 39 Copynumber: 4.9 Consensus size: 39
15918069 GTGCGAATTG
*
15918079 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCTAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
** *
15918118 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
*
15918157 TGATATCCGGGCTAAGCCCGAAGGCAATTGTACGAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
* *
15918196 TGATAT-CGGGCTAAGCCCGAAGGCAATTGTGCGAGTTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
* **
15918234 TGATATCCGGGTTAAGTCCCGAAGGCGTTTGTGCG
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCG
15918269 GGTTACCATA
Statistics
Matches: 135, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
38 35 0.26
39 84 0.62
40 16 0.12
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
Found at i:15918197 original size:78 final size:77
Alignment explanation
Indices: 15918068--15918259 Score: 330
Period size: 78 Copynumber: 2.5 Consensus size: 77
15918058 TGTGCATGAA
* *
15918068 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCTAGCTATGATATCCGGGCTAA
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTACGAGCTATGATAT-CGGGCTAA
15918133 GCCCGAAGGCAAT
65 GCCCGAAGGCAAT
15918146 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTACGAGCTATGATATCGGGCTAAG
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTACGAGCTATGATATCGGGCTAAG
15918211 CCCGAAGGCAAT
66 CCCGAAGGCAAT
* *
15918223 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGC
1 TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGC
15918260 GTTTGTGCGG
Statistics
Matches: 109, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
77 46 0.42
78 63 0.58
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (77 bp):
TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTACGAGCTATGATATCGGGCTAAG
CCCGAAGGCAAT
Found at i:15921878 original size:33 final size:33
Alignment explanation
Indices: 15921841--15921909 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
15921831 AGAAGGGGAA
15921841 AGAGAAAGTGGACGAGGATATCGAGTAAACTCG
1 AGAGAAAGTGGACGAGGATATCGAGTAAACTCG
15921874 AGAGAAAGTGGACGAGGATATCGAGTAAACTCG
1 AGAGAAAGTGGACGAGGATATCGAGTAAACTCG
15921907 AGA
1 AGA
15921910 ATTACGGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.41, C:0.12, G:0.33, T:0.14
Consensus pattern (33 bp):
AGAGAAAGTGGACGAGGATATCGAGTAAACTCG
Found at i:15922443 original size:6 final size:6
Alignment explanation
Indices: 15922432--15922458 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
15922422 TGTGTACCGC
15922432 TACTGT TACTGT TACTGT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TAC
15922459 ACTTACAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:15927689 original size:13 final size:13
Alignment explanation
Indices: 15927671--15927695 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15927661 TAAAATAAAA
15927671 GAAATAAAGAAAT
1 GAAATAAAGAAAT
15927684 GAAATAAAGAAA
1 GAAATAAAGAAA
15927696 AGGAAAAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (13 bp):
GAAATAAAGAAAT
Found at i:15929938 original size:26 final size:26
Alignment explanation
Indices: 15929902--15930011 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
15929892 TGATACAAAT
15929902 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
15929928 TGATAATAGGTTAGGTAAATATTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
15929954 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
15929980 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
15930006 TGATAA
1 TGATAA
15930012 GAATTTCATG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:15934887 original size:33 final size:33
Alignment explanation
Indices: 15934850--15934919 Score: 83
Period size: 33 Copynumber: 2.1 Consensus size: 33
15934840 TATTTATACA
15934850 ATTATAATATT-TTATT-TAAATT-AGTAGATATTT
1 ATTAT-ATATTATTATTAT-AATTAAG-AGATATTT
*
15934883 ATTATTTATTATTATTATAATTAAGAGATATTT
1 ATTATATATTATTATTATAATTAAGAGATATTT
15934916 ATTA
1 ATTA
15934920 ATTAAATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
32 4 0.12
33 26 0.79
34 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (33 bp):
ATTATATATTATTATTATAATTAAGAGATATTT
Found at i:15951204 original size:3 final size:3
Alignment explanation
Indices: 15951192--15951221 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
15951182 AGAAGAAGAA
*
15951192 GAG GAA GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
15951222 AAGAAGAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:15951244 original size:9 final size:9
Alignment explanation
Indices: 15951185--15951245 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 9
15951175 AAATAATAGA
15951185 AGAAGAA-G
1 AGAAGAAGG
15951193 AGGAAG-AGG
1 A-GAAGAAGG
* *
15951202 AGGAGGAGG
1 AGAAGAAGG
* *
15951211 AGGAGGAGG
1 AGAAGAAGG
*
15951220 AGAAGAAGA
1 AGAAGAAGG
15951229 AGAAGAAGG
1 AGAAGAAGG
15951238 AGAAGAAG
1 AGAAGAAG
15951246 AAAAATAGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
8 5 0.11
9 40 0.89
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (9 bp):
AGAAGAAGG
Found at i:15953282 original size:37 final size:38
Alignment explanation
Indices: 15953223--15953310 Score: 142
Period size: 38 Copynumber: 2.3 Consensus size: 38
15953213 CATTGTGAAC
* *
15953223 AGCCTCACTAACAATGATACACACA-CCCAAAAAAAAT
1 AGCCCCACCAACAATGATACACACACCCCAAAAAAAAT
*
15953260 AGCCCCACCAACAATGATACACACACCCCTAAAAAAAT
1 AGCCCCACCAACAATGATACACACACCCCAAAAAAAAT
15953298 AGCCCCACCAACA
1 AGCCCCACCAACA
15953311 TACATATTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
37 23 0.49
38 24 0.51
ACGTcount: A:0.48, C:0.36, G:0.06, T:0.10
Consensus pattern (38 bp):
AGCCCCACCAACAATGATACACACACCCCAAAAAAAAT
Found at i:15953386 original size:39 final size:40
Alignment explanation
Indices: 15953332--15953432 Score: 150
Period size: 40 Copynumber: 2.5 Consensus size: 40
15953322 AAAAAAATAC
*
15953332 TCACTGCATGTATATTAAAAAA-AGGCAACACACCGACAA
1 TCACTGCATGTATATTAAAAAATAGGCAACACACCAACAA
* * *
15953371 TCACTGCATGCATATTAAAAAATAGTCAACACACCAATAA
1 TCACTGCATGTATATTAAAAAATAGGCAACACACCAACAA
*
15953411 TCAATGCATGTATATTAAAAAA
1 TCACTGCATGTATATTAAAAAA
15953433 CATTCACTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
39 21 0.38
40 34 0.62
ACGTcount: A:0.48, C:0.20, G:0.10, T:0.23
Consensus pattern (40 bp):
TCACTGCATGTATATTAAAAAATAGGCAACACACCAACAA
Found at i:15953845 original size:26 final size:26
Alignment explanation
Indices: 15953816--15953869 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
15953806 GACCAGTGAG
15953816 TAGGGCTCTTTTCCTTCAACCAATCA
1 TAGGGCTCTTTTCCTTCAACCAATCA
*
15953842 TAGGGTTCTTTTCCTTCAACCAATCA
1 TAGGGCTCTTTTCCTTCAACCAATCA
15953868 TA
1 TA
15953870 ATCATGCTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.24, C:0.28, G:0.11, T:0.37
Consensus pattern (26 bp):
TAGGGCTCTTTTCCTTCAACCAATCA
Found at i:15955576 original size:48 final size:48
Alignment explanation
Indices: 15955460--15955568 Score: 191
Period size: 48 Copynumber: 2.3 Consensus size: 48
15955450 TTGGATACAA
* *
15955460 ACAATGGCAGATATACACAATAAACATCAGTTTGATACCGGTATTCAT
1 ACAATGGCAGATATACACAATAAACATCAGTTTGATAACGGCATTCAT
*
15955508 ACAATGGCAGATATACACAATAAACATCAGTTTGATAATGGCATTCAT
1 ACAATGGCAGATATACACAATAAACATCAGTTTGATAACGGCATTCAT
15955556 ACAATGGCAGATA
1 ACAATGGCAGATA
15955569 CAAACAATGG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (48 bp):
ACAATGGCAGATATACACAATAAACATCAGTTTGATAACGGCATTCAT
Found at i:15955576 original size:64 final size:64
Alignment explanation
Indices: 15955508--15955640 Score: 221
Period size: 64 Copynumber: 2.1 Consensus size: 64
15955498 CGGTATTCAT
* * * *
15955508 ACAATGGCAGATATACACAATAAACATCAGTTTGATAATGGCATTCATACAATGGCAGATACAA
1 ACAATGGCAAATATACAAAATAAACATCAGTTTGATAATAGCATTCATACAATGGCAAATACAA
*
15955572 ACAATGGCAAATATACAAAATAAACATCAGTTTGATAATAGCATTCGTACAATGGCAAATACAA
1 ACAATGGCAAATATACAAAATAAACATCAGTTTGATAATAGCATTCATACAATGGCAAATACAA
15955636 ACAAT
1 ACAAT
15955641 AAACACCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.23
Consensus pattern (64 bp):
ACAATGGCAAATATACAAAATAAACATCAGTTTGATAATAGCATTCATACAATGGCAAATACAA
Found at i:15955810 original size:18 final size:18
Alignment explanation
Indices: 15955753--15955911 Score: 88
Period size: 18 Copynumber: 8.5 Consensus size: 18
15955743 AAATAACCCT
15955753 AAATTGAAATCAAAATCA
1 AAATTGAAATCAAAATCA
* * *
15955771 AAATT-AAATTCTAATTCC
1 AAATTGAAA-TCAAAATCA
* *
15955789 AAATTGAGATCAAAATCG
1 AAATTGAAATCAAAATCA
*
15955807 AAATTGAAATCAAAATCT
1 AAATTGAAATCAAAATCA
* **
15955825 AAA-TCAGAATCAGTGAGTGTTTCA
1 AAATTGA-AATCA---A---AATCA
* *
15955849 AAATTAAAATCAAAATTA
1 AAATTGAAATCAAAATCA
*
15955867 AAATAGAAATCAAAATCA
1 AAATTGAAATCAAAATCA
** * *
15955885 AAATCAAAATCGAAATTA
1 AAATTGAAATCAAAATCA
15955903 AAATTGAAA
1 AAATTGAAA
15955912 CCGAAACAAC
Statistics
Matches: 105, Mismatches: 26, Indels: 20
0.70 0.17 0.13
Matches are distributed among these distances:
17 5 0.05
18 84 0.80
19 2 0.02
21 2 0.02
24 10 0.10
25 2 0.02
ACGTcount: A:0.55, C:0.11, G:0.08, T:0.26
Consensus pattern (18 bp):
AAATTGAAATCAAAATCA
Found at i:15955863 original size:12 final size:12
Alignment explanation
Indices: 15955846--15955906 Score: 79
Period size: 12 Copynumber: 5.1 Consensus size: 12
15955836 AGTGAGTGTT
15955846 TCAAAATTAAAA
1 TCAAAATTAAAA
15955858 TCAAAATTAAAA
1 TCAAAATTAAAA
*
15955870 T-AGAAATCAAAA
1 TCA-AAATTAAAA
*
15955882 TCAAAATCAAAA
1 TCAAAATTAAAA
*
15955894 TCGAAATTAAAA
1 TCAAAATTAAAA
15955906 T
1 T
15955907 TGAAACCGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
11 1 0.02
12 42 0.95
13 1 0.02
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.23
Consensus pattern (12 bp):
TCAAAATTAAAA
Found at i:15955907 original size:6 final size:6
Alignment explanation
Indices: 15955846--15955906 Score: 70
Period size: 6 Copynumber: 10.2 Consensus size: 6
15955836 AGTGAGTGTT
* *
15955846 TCAAAA TTAAAA TCAAAA TTAAAA T-AGAAA TCAAAA TCAAAA TCAAAA
1 TCAAAA TCAAAA TCAAAA TCAAAA TCA-AAA TCAAAA TCAAAA TCAAAA
* *
15955894 TCGAAA TTAAAA T
1 TCAAAA TCAAAA T
15955907 TGAAACCGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
5 1 0.02
6 45 0.96
7 1 0.02
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.23
Consensus pattern (6 bp):
TCAAAA
Found at i:15956496 original size:31 final size:30
Alignment explanation
Indices: 15956453--15956513 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
15956443 TTAGTAACTA
*
15956453 TTTTGTTACTTTTTTATAACGTTG-GTGACTG
1 TTTTGTTACTTTTTGA-AA-GTTGAGTGACTG
15956484 TTTTG-TAGCTTTTTGAAAGTTGAGTGACTG
1 TTTTGTTA-CTTTTTGAAAGTTGAGTGACTG
15956514 AAATGAAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 4 0.15
30 11 0.41
31 12 0.44
ACGTcount: A:0.18, C:0.08, G:0.23, T:0.51
Consensus pattern (30 bp):
TTTTGTTACTTTTTGAAAGTTGAGTGACTG
Found at i:15968097 original size:44 final size:44
Alignment explanation
Indices: 15968032--15968619 Score: 206
Period size: 44 Copynumber: 12.9 Consensus size: 44
15968022 AGGACTTGTT
* * * * *
15968032 GCTTTAATCAGCTCCATTGCAACTTCATGGAGATAAGATTAGTA
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGCA
* *
15968076 GCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTGGCA
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGCA
* * * * *
15968120 TCTTCAGTCTGCTCCACTGTATCTTCAGGGAGATAAGACTTGTAGTGGTA
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA--T-TA---GCA
* ** * * * * * *
15968170 GATTTGATCTGATCTACTGCAACTTCAGAGG-TATAGGACTAATC-
1 GCTTCAATCTGCTCCACTGCAACTTCAG-GGAGATAAGA-TTAGCA
* * * * *
15968214 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAGCT
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGCA
* *
15968258 GTCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTT-G-A
1 G-CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAGCA
* * * * * * *
15968302 ACTTCAACCTGTTCTACTGCTACTTCAGGGAGATAAGGTTTGTGATTTGTA
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA-------GATTAGCA
* *
15968353 GCTTCAATCTGGC-CCACTGTAACTTCAGGGAGATAAGATTCGCGATGGTA
1 GCTTCAATCT-GCTCCACTGCAACTTCAGGGAGATAAGATT----A--GCA
* ** * * * *
15968403 GATTTGATCTGAC-CCACTACAACTTCAGAGG-TATAGGATTCA-TA
1 GCTTCAATCTG-CTCCACTGCAACTTCAG-GGAGATAAGATT-AGCA
* * * * * *
15968447 GCTTTAATCTACACTACTGCAACTTCAGAGAGATAAGATTTGCTA
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGC-A
* * * * * * ** *
15968492 TCTTTAGTCTGCTCTACTACAAATTTGGGGAGATAAGACTT-GGA
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAGCA
* ** * * *
15968536 ACGGCAACCTGCTCCACTACAACTTCAGGGAGATAAGACTT-GGA
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAGCA
* * * * *
15968580 ACTGCAACCTGCTCCACTGCAACTTTAGAGAGATAAGATT
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
15968620 CATCATTTTC
Statistics
Matches: 410, Mismatches: 100, Indels: 69
0.71 0.17 0.12
Matches are distributed among these distances:
43 38 0.09
44 203 0.50
45 63 0.15
46 5 0.01
47 2 0.00
48 1 0.00
49 4 0.01
50 60 0.15
51 33 0.08
52 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (44 bp):
GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGCA
Found at i:15968330 original size:182 final size:182
Alignment explanation
Indices: 15968008--15968338 Score: 445
Period size: 182 Copynumber: 1.8 Consensus size: 182
15967998 GACTTACTAA
* ** * * *
15968008 AACTTTAGAGGTATAGGACTTGTTGCTTTAATCAGCTCCATTGCAACTTCATGGAGATAAGATTA
1 AACTTCAGAGGTATAGGACTAATCGCTTTAATCAGCTCCACTGCAACTTCAGGGAGATAAGATTA
* * * **
15968073 GTAGCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGATTGGCATCTTCAGTCTGCTCCACT
66 GTAGCTTCAATCTGCTCCACTACAACTTCAGGGAGATAAGATTGGCAACTTCAACCTGCTCCACT
15968138 GTATCTTCAGGGAGATAAGACTTGTAGTGGTAGATTTGATCTGATCTACTGC
131 GTATCTTCAGGGAGATAAGACTTGTAGTGGTAGATTTGATCTGATCTACTGC
* * *
15968190 AACTTCAGAGGTATAGGACTAATCGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTA
1 AACTTCAGAGGTATAGGACTAATCGCTTTAATCAGCTCCACTGCAACTTCAGGGAGATAAGATTA
* * *
15968255 GCT-GTCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTT-G-AACTTCAACCTGTTCT
66 G-TAG-CTTCAATCTGCTCCACTACAACTTCAGGGAGATAAGA-TTGGCAACTTCAACCTGCTCC
15968317 ACTGCTA-CTTCAGGGAGATAAG
128 ACTG-TATCTTCAGGGAGATAAG
15968339 GTTTGTGATT
Statistics
Matches: 128, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
182 88 0.69
183 38 0.30
184 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (182 bp):
AACTTCAGAGGTATAGGACTAATCGCTTTAATCAGCTCCACTGCAACTTCAGGGAGATAAGATTA
GTAGCTTCAATCTGCTCCACTACAACTTCAGGGAGATAAGATTGGCAACTTCAACCTGCTCCACT
GTATCTTCAGGGAGATAAGACTTGTAGTGGTAGATTTGATCTGATCTACTGC
Found at i:15968404 original size:233 final size:234
Alignment explanation
Indices: 15968133--15968572 Score: 589
Period size: 233 Copynumber: 1.9 Consensus size: 234
15968123 TCAGTCTGCT
* * * * *
15968133 CCACTGTATCTTCAGGGAGATAAGACTTGTAGTGGTAGATTTGATCTGATCTACTGCAACTTCAG
1 CCACTGTAACTTCAGGGAGATAAGACTTGGAGTGGTAGATTTGATCTGACCCACTACAACTTCAG
* * * * * * *
15968198 AGGTATAGGACTAATCGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAGCTGTCTT
66 AGGTATAGGACTAATAGCTTTAATCCACACCACTGCAACTTCAGAGAGATAAGATTAGCTATCTT
* ** * * * *
15968263 CAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTT-GAACTTCAACCTGTTCTACTGCTACTT
131 CAGTCTGCTCCACTACAAATTCAGGGAGATAAGACTTGGAACGGCAACCTGCTCCACTACAACTT
15968327 CAGGGAGATAAGGTTTGTGATTTGTAGCTTCAATCTGGC
196 CAGGGAGATAAGGTTTGTGATTTGTAGCTTCAATCTGGC
15968366 CCACTGTAACTTCAGGGAGATAAGA-TTCGCGA-TGGTAGATTTGATCTGACCCACTACAACTTC
1 CCACTGTAACTTCAGGGAGATAAGACTT-G-GAGTGGTAGATTTGATCTGACCCACTACAACTTC
* * * * *
15968429 AGAGGTATAGGATTCATAGCTTTAATCTACACTACTGCAACTTCAGAGAGATAAGATTTGCTATC
64 AGAGGTATAGGACTAATAGCTTTAATCCACACCACTGCAACTTCAGAGAGATAAGATTAGCTATC
* * **
15968494 TTTAGTCTGCTCTACTACAAATTTGGGGAGATAAGACTTGGAACGGCAACCTGCTCCACTACAAC
129 TTCAGTCTGCTCCACTACAAATTCAGGGAGATAAGACTTGGAACGGCAACCTGCTCCACTACAAC
15968559 TTCAGGGAGATAAG
194 TTCAGGGAGATAAG
15968573 ACTTGGAACT
Statistics
Matches: 176, Mismatches: 28, Indels: 5
0.84 0.13 0.02
Matches are distributed among these distances:
232 2 0.01
233 140 0.80
234 34 0.19
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.30
Consensus pattern (234 bp):
CCACTGTAACTTCAGGGAGATAAGACTTGGAGTGGTAGATTTGATCTGACCCACTACAACTTCAG
AGGTATAGGACTAATAGCTTTAATCCACACCACTGCAACTTCAGAGAGATAAGATTAGCTATCTT
CAGTCTGCTCCACTACAAATTCAGGGAGATAAGACTTGGAACGGCAACCTGCTCCACTACAACTT
CAGGGAGATAAGGTTTGTGATTTGTAGCTTCAATCTGGC
Found at i:15968427 original size:50 final size:51
Alignment explanation
Indices: 15968323--15968430 Score: 119
Period size: 50 Copynumber: 2.1 Consensus size: 51
15968313 TTCTACTGCT
* * * * * * **
15968323 ACTTCAGGGAGATAAGGTTTGTGATTTGTAGCTTCAATCTGGCCCACTGTA
1 ACTTCAGGGAGATAAGATTCGCGATTGGTAGATTCAATCTGACCCACTACA
**
15968374 ACTTCAGGGAGATAAGATTCGCGA-TGGTAGATTTGATCTGACCCACTACA
1 ACTTCAGGGAGATAAGATTCGCGATTGGTAGATTCAATCTGACCCACTACA
15968424 ACTTCAG
1 ACTTCAG
15968431 AGGTATAGGA
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
50 26 0.55
51 21 0.45
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (51 bp):
ACTTCAGGGAGATAAGATTCGCGATTGGTAGATTCAATCTGACCCACTACA
Found at i:15969256 original size:25 final size:24
Alignment explanation
Indices: 15969222--15969274 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
15969212 ATGATCCCCT
15969222 TTTACACTTGGGTTAACATTACTC
1 TTTACACTTGGGTTAACATTACTC
* *
15969246 GTTTACACTTGGGTTGACATTGCTC
1 -TTTACACTTGGGTTAACATTACTC
15969271 TTTA
1 TTTA
15969275 TTTGTCGAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 4 0.15
25 22 0.85
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (24 bp):
TTTACACTTGGGTTAACATTACTC
Found at i:15979350 original size:54 final size:54
Alignment explanation
Indices: 15979268--15979467 Score: 303
Period size: 54 Copynumber: 3.7 Consensus size: 54
15979258 AACATGAGAT
* *
15979268 ATGTGATTTTCGTATAAGACCATAGCTGGGCTATGGCATCGGGGTGATGTGATC
1 ATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGAGTGATGTGATC
* *
15979322 ATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATAGGTGTGATGTGATC
1 ATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGAGTGATGTGATC
** *
15979376 ATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGAGACATGTGATT
1 ATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGAGTGATGTGATC
* * *
15979430 ATGTG-CTTCCGTATAAGACCATATCTGGGATATGGCAT
1 ATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCAT
15979468 TAGTGTGATA
Statistics
Matches: 135, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
53 30 0.22
54 105 0.78
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.31
Consensus pattern (54 bp):
ATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGAGTGATGTGATC
Found at i:15979493 original size:47 final size:47
Alignment explanation
Indices: 15979331--15979528 Score: 189
Period size: 47 Copynumber: 3.9 Consensus size: 47
15979321 CATGTGATTT
* * * * *
15979331 CCGTATAAGACCATAGCTGGGCTATGGCATAGGTGTGATGTGATCATGTGATTT
1 CCGTATAAGACCATATCTGGGATATGGCAT---T-AG-TGTGAT-ATGTG-CTA
* * * *
15979385 CCGTATAAGACCATAGCTGGGCTATGGCATCGGAGACATGTGATTATGTGCTT
1 CCGTATAAGACCATATCTGGGATATGGCAT--TAG---TGTGA-TATGTGCTA
15979438 CCGTATAAGACCATATCTGGGATATGGCATTAGTGTGATATGTGCTA
1 CCGTATAAGACCATATCTGGGATATGGCATTAGTGTGATATGTGCTA
*
15979485 CTGTATAAGACCATATCTGGGATATGGCATTAGTGTGATATGTG
1 CCGTATAAGACCATATCTGGGATATGGCATTAGTGTGATATGTG
15979529 GTCCATGTAA
Statistics
Matches: 132, Mismatches: 9, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
47 51 0.39
48 5 0.04
51 2 0.02
52 1 0.01
53 31 0.23
54 41 0.31
55 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (47 bp):
CCGTATAAGACCATATCTGGGATATGGCATTAGTGTGATATGTGCTA
Found at i:15979557 original size:46 final size:46
Alignment explanation
Indices: 15979423--15979558 Score: 139
Period size: 47 Copynumber: 2.9 Consensus size: 46
15979413 ATCGGAGACA
* * * *
15979423 TGTGATTATGTGCTTCCGTATAAGACCATATCTGGGATATGGCATTAG
1 TGTGA-TATGTGCTACTG-ATAAGACCATAGCTAGGATATGGCATTAG
* *
15979471 TGTGATATGTGCTACTGTATAAGACCATATCTGGGATATGGCATTAG
1 TGTGATATGTGCTACTG-ATAAGACCATAGCTAGGATATGGCATTAG
* * * *
15979518 TGTGATATGTGGTCCATG-TAAGACCATGGCTAGGCTATGGC
1 TGTGATATGTGCTAC-TGATAAGACCATAGCTAGGATATGGC
15979559 TTCGGTGTGT
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
46 19 0.24
47 53 0.67
48 7 0.09
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (46 bp):
TGTGATATGTGCTACTGATAAGACCATAGCTAGGATATGGCATTAG
Found at i:15983731 original size:19 final size:19
Alignment explanation
Indices: 15983685--15983732 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
15983675 GTATATATTT
15983685 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
15983703 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
15983722 TAAATTTTATT
1 TAAATTTTATT
15983733 CATATTCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:15985135 original size:40 final size:40
Alignment explanation
Indices: 15985064--15985169 Score: 144
Period size: 40 Copynumber: 2.7 Consensus size: 40
15985054 TACTAGCTCG
* * *
15985064 TAGCCTGCGGGTCTCT-AGCCCGGATAGCATTCTAGCACGA
1 TAGCCTGCGGGTCTTTAAGCCCGGATAACATTCCAGCA-GA
* *
15985104 -AGCTTGCGGGTCTTTAAGCCCGGATAACATTCCAGCATA
1 TAGCCTGCGGGTCTTTAAGCCCGGATAACATTCCAGCAGA
15985143 TAGCCTGCGGGTCTTTAAGCCCGGATA
1 TAGCCTGCGGGTCTTTAAGCCCGGATA
15985170 CAATTCCTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
39 14 0.24
40 44 0.76
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.25
Consensus pattern (40 bp):
TAGCCTGCGGGTCTTTAAGCCCGGATAACATTCCAGCAGA
Found at i:15986295 original size:2 final size:2
Alignment explanation
Indices: 15986288--15986312 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15986278 CCGAATGTAC
15986288 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
15986313 AACTCAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15995117 original size:29 final size:30
Alignment explanation
Indices: 15995066--15995122 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
15995056 CACCCTTAAA
* * *
15995066 ATATTTGCACTATAGTCCTTC-AACTTTTC
1 ATATTTACACTATAATCCCTCAAACTTTTC
*
15995095 ATATTTACACTTTAATCCCTCAAACTTT
1 ATATTTACACTATAATCCCTCAAACTTT
15995123 GAGTATTTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 17 0.74
30 6 0.26
ACGTcount: A:0.28, C:0.25, G:0.04, T:0.44
Consensus pattern (30 bp):
ATATTTACACTATAATCCCTCAAACTTTTC
Found at i:16002332 original size:45 final size:43
Alignment explanation
Indices: 16002216--16002335 Score: 134
Period size: 43 Copynumber: 2.7 Consensus size: 43
16002206 GCTACAAGTT
* *
16002216 ACAATCCTTATCTCCTTGAAGTTGCAGTGGAGCAGGAAAGTAC
1 ACAAACCTTATCTCCTTGAAGTTGCAGTAGAGCAGGAAAGTAC
* * *
16002259 ACAAACCTTATCTCCCTGAAATTGCAGTAGAGCAGGTTGAAATTAC
1 ACAAACCTTATCTCCTTGAAGTTGCAGTAGAGCA-G--GAAAGTAC
* * *
16002305 -CAAATCTTATCTCCTTTAAGTTCCAGTAGAG
1 ACAAACCTTATCTCCTTGAAGTTGCAGTAGAG
16002336 TAGATCAAAG
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
43 30 0.47
44 1 0.02
45 26 0.41
46 7 0.11
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (43 bp):
ACAAACCTTATCTCCTTGAAGTTGCAGTAGAGCAGGAAAGTAC
Found at i:16002720 original size:19 final size:18
Alignment explanation
Indices: 16002696--16002731 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
16002686 GCGGCCCAAT
16002696 TACCCTAACCCAACTAAAC
1 TACCCTAACCCAA-TAAAC
*
16002715 TACCCTAGCCCAATAAA
1 TACCCTAACCCAATAAA
16002732 GCCCAACCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.42, C:0.39, G:0.03, T:0.17
Consensus pattern (18 bp):
TACCCTAACCCAATAAAC
Found at i:16003770 original size:13 final size:12
Alignment explanation
Indices: 16003749--16003779 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
16003739 GTTTTGTTTG
16003749 TTATTTTTTTAT
1 TTATTTTTTTAT
16003761 TTATTCTTTTTAT
1 TTATT-TTTTTAT
16003774 TTATTT
1 TTATTT
16003780 AGTCCTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (12 bp):
TTATTTTTTTAT
Found at i:16017165 original size:11 final size:11
Alignment explanation
Indices: 16017159--16017184 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16017149 TGAAATTTTC
16017159 TCAAAATTCTA
1 TCAAAATTCTA
16017170 TCAAAATTCTA
1 TCAAAATTCTA
16017181 TCAA
1 TCAA
16017185 TTTTATTTGT
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:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (11 bp):
TCAAAATTCTA
Found at i:16017375 original size:48 final size:46
Alignment explanation
Indices: 16017323--16017433 Score: 132
Period size: 48 Copynumber: 2.3 Consensus size: 46
16017313 AGTAATAATT
*
16017323 TTAAATTTTGAATACTATTCAATATTTTCTTAATTTTTGCAAATTTAA
1 TTAAA-TTTGAATACTATTCAATATTTTCTTAATTTATGC-AATTTAA
** * *
16017371 TTAAATTTGCAATACTATTTGATATTTTTTTCATTTATGCAATTTAA
1 TTAAATTTG-AATACTATTCAATATTTTCTTAATTTATGCAATTTAA
*
16017418 TTAAAATTTCAATACT
1 TT-AAATTTGAATACT
16017434 GCTTGATTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
47 19 0.35
48 36 0.65
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (46 bp):
TTAAATTTGAATACTATTCAATATTTTCTTAATTTATGCAATTTAA
Found at i:16017433 original size:47 final size:48
Alignment explanation
Indices: 16017323--16017456 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 48
16017313 AGTAATAATT
* * ** * * *
16017323 TTAAATTTTGAATACTATTCAATATTTTCTTAATTTTTGCAAATTTAA
1 TTAAAATTTCAATACTATTTGATATTTTTTTCATTTATGCAAATTTAA
16017371 TT-AAATTTGCAATACTATTTGATATTTTTTTCATTTATGC-AATTTAA
1 TTAAAATTT-CAATACTATTTGATATTTTTTTCATTTATGCAAATTTAA
** *
16017418 TTAAAATTTCAATACTGCTTGATTTTTTTTTCATTTATG
1 TTAAAATTTCAATACTATTTGATATTTTTTTCATTTATG
16017457 ATATTTGCAT
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
47 41 0.55
48 33 0.45
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (48 bp):
TTAAAATTTCAATACTATTTGATATTTTTTTCATTTATGCAAATTTAA
Found at i:16018457 original size:7 final size:7
Alignment explanation
Indices: 16018447--16018506 Score: 111
Period size: 7 Copynumber: 8.6 Consensus size: 7
16018437 TTAGTATTTA
16018447 GTATTAT
1 GTATTAT
16018454 GTATTAT
1 GTATTAT
16018461 GTATTAT
1 GTATTAT
*
16018468 GTATAAT
1 GTATTAT
16018475 GTATTAT
1 GTATTAT
16018482 GTATTAT
1 GTATTAT
16018489 GTATTAT
1 GTATTAT
16018496 GTATTAT
1 GTATTAT
16018503 GTAT
1 GTAT
16018507 ATAAATAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 51 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (7 bp):
GTATTAT
Found at i:16018936 original size:7 final size:7
Alignment explanation
Indices: 16018926--16018964 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
16018916 TTAGTATTTA
16018926 GTATTAT
1 GTATTAT
16018933 GTATTAT
1 GTATTAT
16018940 GTATTAT
1 GTATTAT
16018947 GTATTAT
1 GTATTAT
16018954 GTATTAT
1 GTATTAT
16018961 GTAT
1 GTAT
16018965 ATAAATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.56
Consensus pattern (7 bp):
GTATTAT
Found at i:16018936 original size:14 final size:15
Alignment explanation
Indices: 16018919--16018964 Score: 71
Period size: 14 Copynumber: 3.3 Consensus size: 15
16018909 TTAATATTTA
16018919 GTATTTA-GTATTAT
1 GTATTTATGTATTAT
16018933 GTA-TTATGTATTAT
1 GTATTTATGTATTAT
16018947 GTA-TTATGTATTAT
1 GTATTTATGTATTAT
16018961 GTAT
1 GTAT
16018965 ATAAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 3 0.10
14 27 0.90
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (15 bp):
GTATTTATGTATTAT
Found at i:16019330 original size:458 final size:458
Alignment explanation
Indices: 16018468--16019369 Score: 1538
Period size: 458 Copynumber: 2.0 Consensus size: 458
16018458 TATGTATTAT
16018468 GTATAATGTATTATGTATTATGTATTATGTATTATGTATATAAATAATATTTTTATCATGTTCAT
1 GTATAATGTATTATGTATTATGTATTATGTATTATGTATATAAATAATATTTTTATCATGTTCAT
* *
16018533 ATAGTTTCAATGGACACCATACGAGGATCCGGCAATTCGGGCAGTAATTCCAGATGAATTCTTTC
66 ATAGTGTCAATAGACACCATACGAGGATCCGGCAATTCGGGCAGTAATTCCAGATGAATTCTTTC
* *
16018598 AAAATCTAAACGCTTGGCATGTGAAGGTTGCATTGGTGAACTATGCTACCGTGGAGATGCACCAG
131 AAAATCCAAACGCTTGGCATGTGAAGGTCGCATTGGTGAACTATGCTACCGTGGAGATGCACCAG
16018663 TCAGATAGAGTATTGAGGCAATTTGAATTCAGACAACCAATTCCCGTGGCACCTGAGGTGTTTGA
196 TCAGATAGAGTATTGAGGCAATTTGAATTCAGACAACCAATTCCCGTGGCACCTGAGGTGTTTGA
* * *
16018728 TGATGAGCACAAAGTCGACTTACGGCAACTGCATACGGATTGGCCGAGATTCTGGTCACACTATA
261 TAATGAGCACAAAGTCGACTTACAGCAACTACATACGGATTGGCCGAGATTCTGGTCACACTATA
* *
16018793 TCAAAATGTGGAAAAATCGGTATGATTATATCTCAACTCGAGAACCGATCATTGTTCCAGAGTTA
326 TCAAAATATGGAAAAATCGGTATGATTATATCTCAACTCGAGAACCGATCATCGTTCCAGAGTTA
* *
16018858 ACGTGCGTACCGGAATACATGTCATGGTTTAGGATCCA-AGGTAAGCCATATTTAATATTTAGTA
391 ACGTGCGTACCGGAATACATGCCATGGTTTAGGATCCATA-GCAAGCCATATTTAATATTTAGTA
16018922 TTTA
455 TTTA
* *
16018926 GTATTATGTATTATGTATTATGTATTATGTATTATGTATATAAATAATATTTTTATCATGTTTAT
1 GTATAATGTATTATGTATTATGTATTATGTATTATGTATATAAATAATATTTTTATCATGTTCAT
* *
16018991 ATAGTGTCAATAGACACCATACGAGGATCTGGCAATTCGGGCAGTAATTCCGGATGAATTCTTTC
66 ATAGTGTCAATAGACACCATACGAGGATCCGGCAATTCGGGCAGTAATTCCAGATGAATTCTTTC
16019056 AAAATCCAAACGCTTGGCATGTGAAGGTCGCATTGGTGAACTATGCTACCGTGGAGATGCACCAG
131 AAAATCCAAACGCTTGGCATGTGAAGGTCGCATTGGTGAACTATGCTACCGTGGAGATGCACCAG
* *
16019121 TCAGATAGAGTATTGAGGCAATTTGGATTCAGACAACCGATTCCCGTGGCACCTGAGGTGTTTGA
196 TCAGATAGAGTATTGAGGCAATTTGAATTCAGACAACCAATTCCCGTGGCACCTGAGGTGTTTGA
* * *
16019186 TAATGAGCACAAAGTCGACTTACAGTAACTACATACGGATTGGCTGATATTCTGGTCACACTATA
261 TAATGAGCACAAAGTCGACTTACAGCAACTACATACGGATTGGCCGAGATTCTGGTCACACTATA
** * * *
16019251 TTGAAATATGGGAAAATCGGTATGATTATATAC-CAACTCGGGAACCGATCATCGTTTCAGAGTT
326 TCAAAATATGGAAAAATCGGTATGATTATAT-CTCAACTCGAGAACCGATCATCGTTCCAGAGTT
*
16019315 AGCGTGCGTACCGGAATACATGCCATGGTTTAGGATCCATAGCAAGCCATATTTA
390 AACGTGCGTACCGGAATACATGCCATGGTTTAGGATCCATAGCAAGCCATATTTA
16019370 TTATCGGAAG
Statistics
Matches: 416, Mismatches: 26, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
458 414 1.00
459 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (458 bp):
GTATAATGTATTATGTATTATGTATTATGTATTATGTATATAAATAATATTTTTATCATGTTCAT
ATAGTGTCAATAGACACCATACGAGGATCCGGCAATTCGGGCAGTAATTCCAGATGAATTCTTTC
AAAATCCAAACGCTTGGCATGTGAAGGTCGCATTGGTGAACTATGCTACCGTGGAGATGCACCAG
TCAGATAGAGTATTGAGGCAATTTGAATTCAGACAACCAATTCCCGTGGCACCTGAGGTGTTTGA
TAATGAGCACAAAGTCGACTTACAGCAACTACATACGGATTGGCCGAGATTCTGGTCACACTATA
TCAAAATATGGAAAAATCGGTATGATTATATCTCAACTCGAGAACCGATCATCGTTCCAGAGTTA
ACGTGCGTACCGGAATACATGCCATGGTTTAGGATCCATAGCAAGCCATATTTAATATTTAGTAT
TTA
Found at i:16019569 original size:18 final size:18
Alignment explanation
Indices: 16019546--16019588 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
16019536 CGCGAGATGC
*
16019546 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
16019564 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
16019582 GTTTCCT
1 GTATCCT
16019589 TTTTCTAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.09, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:16023302 original size:126 final size:124
Alignment explanation
Indices: 16023059--16023434 Score: 497
Period size: 126 Copynumber: 3.0 Consensus size: 124
16023049 GCTCATTTGT
* * *
16023059 AGGCTCATTTTTCTGCGATCTACTGTAGCAAAAGAGCGTCCACGTGGGATCTTTTTTCAGAATTT
1 AGGCTCATTTTTCTGCGAACTACTGTAGCAAAAGAGCGTCCACGT-GGAGCTTTTTTCAGAA--A
*
16023124 TTTTCCGACAGTGCATCCTACTTGAAGCGTTTTCAACACTATTTGTTCAGAAATGTCTACTC
63 TTTTCTGACAGTGCATCCTACTTGAAGCGTTTTCAACACTATTTGTTCAGAAATGTCTACTC
* *
16023186 AGGCTCATTTTCCTGCGAACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTTTTTCAGAACTT
1 AGGCTCATTTTTCTGCGAACTACTGTAGCAAAAGAGCGTCCACGTGG-AGCTTTTTTCAGAAATT
* * * * *
16023251 TTGCTGACAGTGCATCCTGCTTGAAGCGTTTTCGACACTATCTATTCAGAAACGTCTACTC
65 TT-CTGACAGTGCATCCTACTTGAAGCGTTTTCAACACTATTTGTTCAGAAATGTCTACTC
** * * * *
16023312 AGATTTATTTTTCTACAAAC-ACTGTAGCAAAAGAGCGTCCACGT-GAG-TTTTTTCCAAAAATT
1 AGGCTCATTTTTCTGCGAACTACTGTAGCAAAAGAGCGTCCACGTGGAGCTTTTTT-CAGAAATT
* * *
16023374 TTCTGACACTGCATCCTACTTAAAGCGTTTTCAACATTATTTGTTCAGAAATGTCTACTC
65 TTCTGACAGTGCATCCTACTTGAAGCGTTTTCAACACTATTTGTTCAGAAATGTCTACTC
16023434 A
1 A
16023435 AAATTATTCT
Statistics
Matches: 220, Mismatches: 26, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
122 57 0.26
123 10 0.05
124 1 0.00
125 28 0.13
126 68 0.31
127 56 0.25
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (124 bp):
AGGCTCATTTTTCTGCGAACTACTGTAGCAAAAGAGCGTCCACGTGGAGCTTTTTTCAGAAATTT
TCTGACAGTGCATCCTACTTGAAGCGTTTTCAACACTATTTGTTCAGAAATGTCTACTC
Found at i:16024124 original size:23 final size:23
Alignment explanation
Indices: 16024085--16024149 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 23
16024075 TTTTTTTTAT
16024085 AAACCCTAAAACCCTAAAACATAAA
1 AAACCCT--AACCCTAAAACATAAA
**
16024110 AAACCCTAACCCTAAATTATAAA
1 AAACCCTAACCCTAAAACATAAA
*
16024133 AAACCCTAACCTTAAAA
1 AAACCCTAACCCTAAAA
16024150 ATCCTAACGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 29 0.81
25 7 0.19
ACGTcount: A:0.55, C:0.28, G:0.00, T:0.17
Consensus pattern (23 bp):
AAACCCTAACCCTAAAACATAAA
Found at i:16024502 original size:24 final size:24
Alignment explanation
Indices: 16024475--16024523 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
16024465 GCCAGATTTT
16024475 ATACGGGGTGGAACCAAGTCAAGC
1 ATACGGGGTGGAACCAAGTCAAGC
16024499 ATACGGGGTGGAACCAAGTCAAGC
1 ATACGGGGTGGAACCAAGTCAAGC
16024523 A
1 A
16024524 ACGTTTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.33, T:0.12
Consensus pattern (24 bp):
ATACGGGGTGGAACCAAGTCAAGC
Found at i:16027318 original size:20 final size:19
Alignment explanation
Indices: 16027286--16027324 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
16027276 TAAATTAAAG
16027286 TTTTAGTGTTTTATTTAATT
1 TTTTAGTGTTTTA-TTAATT
16027306 TTTTAAGTG-TTTATTAATT
1 TTTT-AGTGTTTTATTAATT
16027325 AGTGTTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 8 0.44
21 4 0.22
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (19 bp):
TTTTAGTGTTTTATTAATT
Found at i:16027682 original size:20 final size:20
Alignment explanation
Indices: 16027657--16027702 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
16027647 AAAAAATTTA
*
16027657 TTTTATGTAAAAACTTA-AAC
1 TTTTATATAAAAA-TTATAAC
*
16027677 TTTTATATAAAAATTATAAT
1 TTTTATATAAAAATTATAAC
16027697 TTTTAT
1 TTTTAT
16027703 TTTCTATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTTATATAAAAATTATAAC
Found at i:16028368 original size:24 final size:22
Alignment explanation
Indices: 16028341--16028407 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 22
16028331 AAAAACCTTT
16028341 TATTTTTATATATTTAAAAAAACA
1 TATTTTTATAT-TTTAAAAAAA-A
*
16028365 TATTTTCATACTTTTCAATAAAAAA
1 TATTTTTATA-TTTT-AA-AAAAAA
*
16028390 TA-TTTTATATTTTTAAAA
1 TATTTTTATATTTTAAAAA
16028408 TTTTAATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.08
22 1 0.03
23 4 0.11
24 18 0.49
25 6 0.16
26 5 0.14
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTTTTATATTTTAAAAAAAA
Found at i:16028514 original size:16 final size:16
Alignment explanation
Indices: 16028493--16028533 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
16028483 AATGTGTCAA
16028493 GTATTAAATTTATCAC
1 GTATTAAATTTATCAC
16028509 GTATTAAATTTATCAC
1 GTATTAAATTTATCAC
*
16028525 GTGTTAAAT
1 GTATTAAAT
16028534 ATTCATTAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.44
Consensus pattern (16 bp):
GTATTAAATTTATCAC
Found at i:16038995 original size:17 final size:17
Alignment explanation
Indices: 16038975--16039008 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16038965 AGGTTTAGGT
16038975 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
**
16038992 TTAAATTTTTTAATTAA
1 TTAAAAATTTTAATTAA
16039009 AAATCTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:16039019 original size:17 final size:16
Alignment explanation
Indices: 16038981--16039031 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
16038971 AGGTTTAAAA
16038981 ATTTTAATTAATTAAATT
1 ATTTTAATTAA--AAATT
16038999 -TTTTAATTAAAAATCT
1 ATTTTAATTAAAAAT-T
*
16039015 ATTTTCATCTAAAAATT
1 ATTTTAAT-TAAAAATT
16039032 CAAGTTGGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 4 0.14
16 1 0.03
17 17 0.59
18 7 0.24
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTTAATTAAAAATT
Found at i:16039154 original size:31 final size:29
Alignment explanation
Indices: 16039119--16039182 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
16039109 GATCACTTCG
*
16039119 TAACAAAATAATAATATAAGTGACTAAAATA
1 TAAC-AAATAA-AACATAAGTGACTAAAATA
** *
16039150 TAACATTTCAAACATAAGTGACTAAAATA
1 TAACAAATAAAACATAAGTGACTAAAATA
16039179 TAAC
1 TAAC
16039183 CTGGGACAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 22 0.76
30 3 0.10
31 4 0.14
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.27
Consensus pattern (29 bp):
TAACAAATAAAACATAAGTGACTAAAATA
Found at i:16039877 original size:13 final size:14
Alignment explanation
Indices: 16039858--16039898 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
16039848 ATTTCAATTT
16039858 TATTTTAATAATAA
1 TATTTTAATAATAA
16039872 -ATTTTAA-AATAA
1 TATTTTAATAATAA
16039884 TAGTTTTAAATAATA
1 TA-TTTT-AATAATA
16039899 TGATTCACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 5 0.22
13 8 0.35
14 4 0.17
15 2 0.09
16 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (14 bp):
TATTTTAATAATAA
Found at i:16039951 original size:15 final size:15
Alignment explanation
Indices: 16039931--16039987 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
16039921 ATTCAATATT
16039931 AATATTTTAATAATA
1 AATATTTTAATAATA
*
16039946 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
16039965 AATATATTAATAATA
1 AATATTTTAATAATA
*
16039980 AATGTTTT
1 AATATTTT
16039988 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:16040466 original size:14 final size:14
Alignment explanation
Indices: 16040447--16040484 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
16040437 CCAGAAAAGT
16040447 AATCATTTTCC-ATA
1 AATCATTTTCCGA-A
16040461 AATCATTTTCCGAA
1 AATCATTTTCCGAA
*
16040475 AGTCATTTTC
1 AATCATTTTC
16040485 AGTGAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 21 0.95
15 1 0.05
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.42
Consensus pattern (14 bp):
AATCATTTTCCGAA
Found at i:16044132 original size:15 final size:14
Alignment explanation
Indices: 16044108--16044137 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
16044098 TGTCTACCCT
16044108 CATCAAGTAATTAC
1 CATCAAGTAATTAC
16044122 CATCTAAGTAATTAC
1 CATC-AAGTAATTAC
16044137 C
1 C
16044138 TTTGATTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (14 bp):
CATCAAGTAATTAC
Found at i:16061999 original size:34 final size:34
Alignment explanation
Indices: 16061952--16062018 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
16061942 CACATCTGGC
*
16061952 ACTGAAACTGAAATGGACTAAGGCCCAAACTACT
1 ACTGAAACCGAAATGGACTAAGGCCCAAACTACT
* * *
16061986 ACTGAAACCGAAATGGGCTTAGGCCCAGACTAC
1 ACTGAAACCGAAATGGACTAAGGCCCAAACTAC
16062019 ATTTGACTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.16
Consensus pattern (34 bp):
ACTGAAACCGAAATGGACTAAGGCCCAAACTACT
Found at i:16071867 original size:13 final size:13
Alignment explanation
Indices: 16071849--16071887 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
16071839 AAGTAATCGA
*
16071849 ACACGAGCATGTT
1 ACACGAGCATGTC
*
16071862 ACACGAGCGTGTC
1 ACACGAGCATGTC
16071875 ACACGAGCATGTC
1 ACACGAGCATGTC
16071888 CCTACCAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (13 bp):
ACACGAGCATGTC
Found at i:16081173 original size:26 final size:25
Alignment explanation
Indices: 16081137--16081187 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 25
16081127 GTCGAACCCA
16081137 AAGGAACTAAAAGTACTAGTAATGAC
1 AAGGAACTAAAAGTACTAG-AATGAC
16081163 AAGGAACTAAAAGTACTAGAATGAC
1 AAGGAACTAAAAGTACTAGAATGAC
16081188 TGTCCTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.51, C:0.12, G:0.20, T:0.18
Consensus pattern (25 bp):
AAGGAACTAAAAGTACTAGAATGAC
Found at i:16083883 original size:17 final size:17
Alignment explanation
Indices: 16083861--16083899 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
16083851 TTTTAAAAGG
*
16083861 AAAACAAATGAATCTTC
1 AAAACAAATGAATCTTA
16083878 AAAACAAATGAATCTTA
1 AAAACAAATGAATCTTA
16083895 AAAAC
1 AAAAC
16083900 TTAATGACAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.15, G:0.05, T:0.21
Consensus pattern (17 bp):
AAAACAAATGAATCTTA
Found at i:16087760 original size:42 final size:42
Alignment explanation
Indices: 16087708--16087795 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
16087698 CCTTAGGCCT
* * ** *
16087708 ATTTCAATATCACATGTAATGTCAATGGATGTATGCAAGCCC
1 ATTTAAATATCACATGAAATACCAATGAATGTATGCAAGCCC
*
16087750 ATTTAAATATCACATGAAATACCAATGAATGTATGTAAGCCC
1 ATTTAAATATCACATGAAATACCAATGAATGTATGCAAGCCC
16087792 ATTT
1 ATTT
16087796 GGGGAGACTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.32
Consensus pattern (42 bp):
ATTTAAATATCACATGAAATACCAATGAATGTATGCAAGCCC
Found at i:16088010 original size:26 final size:26
Alignment explanation
Indices: 16087934--16088114 Score: 278
Period size: 26 Copynumber: 7.1 Consensus size: 26
16087924 GCCTAGCCTC
*
16087934 TTCAAT-AACTAGGGCA-AAGCCCTT
1 TTCAATAAACTGGGGCATAAGCCCTT
** * *
16087958 TTCGGTAAACTAGGG-AAAAGCCCTT
1 TTCAATAAACTGGGGCATAAGCCCTT
16087983 TTCAATAAACTGGGGCATAAGCCCTT
1 TTCAATAAACTGGGGCATAAGCCCTT
*
16088009 TTCGATAAACTGGGGCATAAGCCCTT
1 TTCAATAAACTGGGGCATAAGCCCTT
16088035 TTCAATAAACTGGGGCATAAGCCCTT
1 TTCAATAAACTGGGGCATAAGCCCTT
*
16088061 TTCGATAAACTGGGGCATAAGCCCTT
1 TTCAATAAACTGGGGCATAAGCCCTT
16088087 TTCAATAAACTGGGGCATAAGCCCTT
1 TTCAATAAACTGGGGCATAAGCCCTT
16088113 TT
1 TT
16088115 GCACTTCCTC
Statistics
Matches: 144, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
24 5 0.03
25 28 0.19
26 111 0.77
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (26 bp):
TTCAATAAACTGGGGCATAAGCCCTT
Found at i:16089007 original size:27 final size:27
Alignment explanation
Indices: 16088916--16088999 Score: 134
Period size: 27 Copynumber: 3.1 Consensus size: 27
16088906 GGGCATATTC
* *
16088916 GTCATTTTACCATACAGGGG-TATTACG
1 GTCACTTTACCCTACAGGGGCT-TTACG
16088943 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCCTACAGGGGCTTTACG
16088970 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCCTACAGGGGCTTTACG
16088997 GTC
1 GTC
16089000 TTTTTACCTA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
27 53 0.98
28 1 0.02
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (27 bp):
GTCACTTTACCCTACAGGGGCTTTACG
Found at i:16089091 original size:27 final size:27
Alignment explanation
Indices: 16089061--16089396 Score: 119
Period size: 27 Copynumber: 12.4 Consensus size: 27
16089051 GTAAATCTAC
*
16089061 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* *
16089088 AAACCAATGGTATTTCTA-TAATTTTTAG
1 AAACCAAGGGTATTTC-AGTAA-TTTTAT
* * * * *
16089116 AAAGTCAACGGTATTTCTGTAACTTTGT
1 AAA-CCAAGGGTATTTCAGTAATTTTAT
* * ** *
16089144 AAATCAGGGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
*** * * *
16089171 AAATTGAGAGTATTTC-GATAATTTCAC
1 AAACCAAGGGTATTTCAG-TAATTTTAT
*
16089198 AAACC-AGTGGTATTTTC-GTAATTTTAC
1 AAACCAAG-GGTA-TTTCAGTAATTTTAT
* * ** *
16089225 AAACTAGGGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
* * *
16089252 AAACC-AGGGTATTTTAGCAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
* * **
16089278 AGA-CTAGGGTATTTTGGTAATTTTACT
1 AAACCAAGGGTATTTCAGTAATTTTA-T
* * * ** *
16089305 -GATCGAGGGTATTTTGGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* * *
16089331 AAACCAATGGTATTTTAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* * *** * *
16089358 AAATCGAGGGTAAAACAGTAATTCTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
*
16089385 AAATCAAGGGTA
1 AAACCAAGGGTA
16089397 AAATAGTAAT
Statistics
Matches: 243, Mismatches: 53, Indels: 26
0.75 0.16 0.08
Matches are distributed among these distances:
25 1 0.00
26 47 0.19
27 161 0.66
28 20 0.08
29 14 0.06
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTAT
Found at i:16089212 original size:54 final size:53
Alignment explanation
Indices: 16089151--16089328 Score: 171
Period size: 53 Copynumber: 3.3 Consensus size: 53
16089141 TGTAAATCAG
* *
16089151 GGGTATTTTGGTAATTTTACAAA-TTGAGAGTATTTCGATAATTTCACAAACCA
1 GGGTATTTTAGTAATTTTACAAACTAG-GAGTATTTCGATAATTTCACAAACCA
* * * * *
16089204 GTGGTATTTTCGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCA
1 G-GGTATTTTAGTAATTTTACAAACTAGGAGTATTTCGATAATTTCACAAACCA
* * * * * * * *
16089258 GGGTATTTTAGCAATTTTACAGACTAGG-GTATTTTGGTAATTTTACTGATCGA
1 GGGTATTTTAGTAATTTTACAAACTAGGAGTATTTCGATAATTTCAC-AAACCA
*
16089311 GGGTATTTTGGTAATTTT
1 GGGTATTTTAGTAATTTT
16089329 GTAAACCAAT
Statistics
Matches: 108, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
52 18 0.17
53 44 0.41
54 44 0.41
55 2 0.02
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.42
Consensus pattern (53 bp):
GGGTATTTTAGTAATTTTACAAACTAGGAGTATTTCGATAATTTCACAAACCA
Found at i:16089273 original size:26 final size:26
Alignment explanation
Indices: 16089151--16089355 Score: 194
Period size: 27 Copynumber: 7.7 Consensus size: 26
16089141 TGTAAATCAG
**
16089151 GGGTATTTTGGTAATTTTACAAATTGA
1 GGGTATTTTGGTAATTTTACAAA-CCA
* * * *
16089178 GAGTATTTCGATAATTTCACAAACCA
1 GGGTATTTTGGTAATTTTACAAACCA
* *
16089204 GTGGTATTTTCGTAATTTTACAAACTA
1 G-GGTATTTTGGTAATTTTACAAACCA
16089231 GGGGTATTTTGGTAATTTTACAAACCA
1 -GGGTATTTTGGTAATTTTACAAACCA
* * * *
16089258 GGGTATTTTAGCAATTTTACAGACTA
1 GGGTATTTTGGTAATTTTACAAACCA
* * *
16089284 GGGTATTTTGGTAATTTTACTGATCGA
1 GGGTATTTTGGTAATTTTAC-AAACCA
**
16089311 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACC-A
* *
16089338 TGGTATTTTAGTAATTTT
1 GGGTATTTTGGTAATTTT
16089356 GTAAATCGAG
Statistics
Matches: 143, Mismatches: 31, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
26 44 0.31
27 98 0.69
28 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (26 bp):
GGGTATTTTGGTAATTTTACAAACCA
Found at i:16089379 original size:54 final size:54
Alignment explanation
Indices: 16089321--16089504 Score: 179
Period size: 54 Copynumber: 3.4 Consensus size: 54
16089311 GGGTATTTTG
* * *** * *
16089321 GTAATTTTGTAAACCAATGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAACCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
* **
16089375 GTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAACCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
* * ** * * **
16089429 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAGTTGAGGGTAAAATG
1 GTAATTCTGTAAACCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
* * *
16089483 GTAATTCTATAAATCGAGGGTA
1 GTAATTCTGTAAACCAAGGGTA
16089505 CTTTGGTAAT
Statistics
Matches: 114, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 114 1.00
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.32
Consensus pattern (54 bp):
GTAATTCTGTAAACCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
Found at i:16089512 original size:81 final size:81
Alignment explanation
Indices: 16089339--16089515 Score: 246
Period size: 81 Copynumber: 2.2 Consensus size: 81
16089329 GTAAACCAAT
* * * *
16089339 GGTATTTTAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAATAGT
1 GGTAATTTGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAATAGT
16089404 AATTCTATAAATCGAG
66 AATTCTATAAATCGAG
** * * ** *
16089420 GGTAAAATGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAGTTGAGGGTAAAATGGT
1 GGTAATTTGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAATAGT
16089485 AATTCTATAAATCGAG
66 AATTCTATAAATCGAG
*
16089501 GGTACTTTGGTAATT
1 GGTAATTTGGTAATT
16089516 TTACAATTTG
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (81 bp):
GGTAATTTGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAATAGT
AATTCTATAAATCGAG
Found at i:16089515 original size:27 final size:27
Alignment explanation
Indices: 16089348--16089504 Score: 215
Period size: 27 Copynumber: 5.8 Consensus size: 27
16089338 TGGTATTTTA
* * **
16089348 GTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTATAAATCGAGGGTAAAATG
* * *
16089375 GTAATTCTGTAAATCAAGGGTAAAATA
1 GTAATTCTATAAATCGAGGGTAAAATG
16089402 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
* *
16089429 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
* *
16089456 GTAATTCTATAAGTTGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
16089483 GTAATTCTATAAATCGAGGGTA
1 GTAATTCTATAAATCGAGGGTA
16089505 CTTTGGTAAT
Statistics
Matches: 116, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 116 1.00
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (27 bp):
GTAATTCTATAAATCGAGGGTAAAATG
Found at i:16089529 original size:81 final size:81
Alignment explanation
Indices: 16089348--16089504 Score: 251
Period size: 81 Copynumber: 1.9 Consensus size: 81
16089338 TGGTATTTTA
* *
16089348 GTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATA
1 GTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAATAGTAATTCTATA
16089413 AATCGAGGGTAAAATG
66 AATCGAGGGTAAAATG
* * ** *
16089429 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAGTTGAGGGTAAAATGGTAATTCTATA
1 GTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAATAGTAATTCTATA
16089494 AATCGAGGGTA
66 AATCGAGGGTA
16089505 CTTTGGTAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 69 1.00
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (81 bp):
GTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAATAGTAATTCTATA
AATCGAGGGTAAAATG
Found at i:16092082 original size:18 final size:20
Alignment explanation
Indices: 16092044--16092082 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
16092034 GATTTCGTAA
*
16092044 TTTGGCCCATTTTCTTCGTT
1 TTTGGCCCAGTTTCTTCGTT
16092064 TTTGGCCC-GTTTC-TCGTT
1 TTTGGCCCAGTTTCTTCGTT
16092082 T
1 T
16092083 ATTTCGCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.03, C:0.26, G:0.18, T:0.54
Consensus pattern (20 bp):
TTTGGCCCAGTTTCTTCGTT
Found at i:16097528 original size:28 final size:28
Alignment explanation
Indices: 16097496--16097564 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
16097486 GCGTAGATCA
16097496 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
16097524 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
16097552 CGATA-TACCCCTA
1 CGAAATTACCCCTA
16097565 GGGTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:16103823 original size:20 final size:20
Alignment explanation
Indices: 16103798--16103835 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16103788 GTTTATTCGC
*
16103798 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
16103818 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
16103836 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:16105493 original size:28 final size:27
Alignment explanation
Indices: 16105461--16105528 Score: 111
Period size: 28 Copynumber: 2.5 Consensus size: 27
16105451 GCGTAGATCA
16105461 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAG-AAAATTAC
16105489 CGAAATTACCCCTAAAGAGAAAATTAC
1 CGAAATTACCCCTAAAGAGAAAATTAC
*
16105516 CGATA-TACCCCTA
1 CGAAATTACCCCTA
16105529 GGGTTTTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 8 0.21
27 12 0.31
28 19 0.49
ACGTcount: A:0.44, C:0.26, G:0.10, T:0.19
Consensus pattern (27 bp):
CGAAATTACCCCTAAAGAGAAAATTAC
Found at i:16108360 original size:28 final size:28
Alignment explanation
Indices: 16108328--16108396 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
16108318 GCGTAGATCA
16108328 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
16108356 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
16108384 CGATA-TACCCCTA
1 CGAAATTACCCCTA
16108397 GGGTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:16110150 original size:89 final size:89
Alignment explanation
Indices: 16109999--16110177 Score: 322
Period size: 89 Copynumber: 2.0 Consensus size: 89
16109989 TAAATCTAAT
*
16109999 TCCATGTTAACTAAACATGCAAGGGACCTTAAAACTACTCTCATTTATCATCATTTCACAATAGA
1 TCCATGTTAACCAAACATGCAAGGGACCTTAAAACTACTCTCATTTATCATCATTTCACAATAGA
*
16110064 TCCCTAGAATTTATACCTTTACAA
66 TCCCTAAAATTTATACCTTTACAA
* *
16110088 TCCATGTTAACCAAACATGCAAGGGACCTTGAAACTACTCTCATTTATCATCATTTTACAATAGA
1 TCCATGTTAACCAAACATGCAAGGGACCTTAAAACTACTCTCATTTATCATCATTTCACAATAGA
16110153 TCCCTAAAATTTATACCTTTACAA
66 TCCCTAAAATTTATACCTTTACAA
16110177 T
1 T
16110178 TTAGTCCCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 86 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (89 bp):
TCCATGTTAACCAAACATGCAAGGGACCTTAAAACTACTCTCATTTATCATCATTTCACAATAGA
TCCCTAAAATTTATACCTTTACAA
Found at i:16114958 original size:40 final size:40
Alignment explanation
Indices: 16114902--16115109 Score: 269
Period size: 40 Copynumber: 5.2 Consensus size: 40
16114892 TGAATGATAC
* *
16114902 CCGGGCTAAGCCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTG-TTATAT
* *
16114942 TCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT
16114982 CCGGGCTAAGACCCGAAGGCATTTGTG-TGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCT-AGTTGTTATAT
* * *
16115022 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGCTATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT
* * * * *
16115062 CCAGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT
16115102 CC-GGCTAA
1 CCGGGCTAA
16115110 ATTCCGAAGA
Statistics
Matches: 147, Mismatches: 18, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
39 5 0.03
40 140 0.95
41 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT
Found at i:16117470 original size:21 final size:22
Alignment explanation
Indices: 16117424--16117476 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
16117414 GAGTTCGGAG
* *
16117424 TTCTATTGATATAACTCTGGGC
1 TTCTATCGATACAACTCTGGGC
* *
16117446 -TCTATGGATACAAC-CTGGTC
1 TTCTATCGATACAACTCTGGGC
16117466 TTCTATCGATA
1 TTCTATCGATA
16117477 AAACACCCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (22 bp):
TTCTATCGATACAACTCTGGGC
Found at i:16121876 original size:78 final size:78
Alignment explanation
Indices: 16121747--16121902 Score: 258
Period size: 78 Copynumber: 2.0 Consensus size: 78
16121737 TAATGACTAT
* *
16121747 GCAAGAAGATTAAATCAATTTGAAAGAAATCAAGAATGAAATTTAGTTGATAGGCTTAGTAACCA
1 GCAAGAAGATTAAATCAATTTGAAAGAAATCAAGAACGAAATTTAGTTGATAGGCCTAGTAACCA
16121812 TCCAACTATAGGA
66 TCCAACTATAGGA
* * * *
16121825 GCAAGAGGATTAAATCAATTTGAAAGAAATCAAGTACGGAATTTAGTTGATAGGCCTAGTGACCA
1 GCAAGAAGATTAAATCAATTTGAAAGAAATCAAGAACGAAATTTAGTTGATAGGCCTAGTAACCA
16121890 TCCAACTATAGGA
66 TCCAACTATAGGA
16121903 ACTAAATGGG
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (78 bp):
GCAAGAAGATTAAATCAATTTGAAAGAAATCAAGAACGAAATTTAGTTGATAGGCCTAGTAACCA
TCCAACTATAGGA
Found at i:16123185 original size:20 final size:21
Alignment explanation
Indices: 16123162--16123202 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16123152 ATCACTTTAA
*
16123162 TATTAA-ATTAATATAATATT
1 TATTAAGATAAATATAATATT
*
16123182 TATTAAGATAAATATATTATT
1 TATTAAGATAAATATAATATT
16123203 AAAATTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
TATTAAGATAAATATAATATT
Found at i:16123474 original size:17 final size:18
Alignment explanation
Indices: 16123443--16123477 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
16123433 TTAACTTTAA
16123443 TTAAATTATTAAAAAAAT
1 TTAAATTATTAAAAAAAT
16123461 TTAAATT-TTGAAAAAAA
1 TTAAATTATT-AAAAAAA
16123478 AAGAAGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
TTAAATTATTAAAAAAAT
Found at i:16123985 original size:8 final size:8
Alignment explanation
Indices: 16123974--16124024 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
16123964 TAATTTTTTA
16123974 AAAATTAT
1 AAAATTAT
16123982 AAAATTA-
1 AAAATTAT
*
16123989 AAAACTATT
1 AAAATTA-T
*
16123998 AAAATAAT
1 AAAATTAT
*
16124006 AAACTTAT
1 AAAATTAT
*
16124014 AAAAATAT
1 AAAATTAT
16124022 AAA
1 AAA
16124025 TTTAATTTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
7 6 0.18
8 23 0.68
9 5 0.15
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (8 bp):
AAAATTAT
Found at i:16124024 original size:24 final size:24
Alignment explanation
Indices: 16123974--16124021 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
16123964 TAATTTTTTA
* *
16123974 AAAATTATAAAATTAAAAACTATT
1 AAAATAATAAAATTAAAAAATATT
*
16123998 AAAATAATAAACTTATAAAAATAT
1 AAAATAATAAAATTA-AAAAATAT
16124022 AAATTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (24 bp):
AAAATAATAAAATTAAAAAATATT
Found at i:16126024 original size:53 final size:53
Alignment explanation
Indices: 16125830--16126036 Score: 200
Period size: 53 Copynumber: 3.8 Consensus size: 53
16125820 ATTAGGGTTT
* * * * *
16125830 AAGGATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCTACAAGGC
1 AAGGAAACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT-TATAAGGC
* * * * * *
16125884 AAGGAAATCATGTAAGACCATGTCAAGACATGG-GATCGATAAACTAATATAAGGC
1 AAGGAAACCATGTAAGACCATGCCAAGACATGGCAAT-GGT-AAGT-TTATAAGGC
* ** * *
16125939 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTTATAAGGC
1 AAGGAAACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTTATAAGGC
* * *
16125992 AAGGAAACCACGTAAGATCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGAAACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
16126037 AAAAAGGAAT
Statistics
Matches: 119, Mismatches: 30, Indels: 9
0.75 0.19 0.06
Matches are distributed among these distances:
53 46 0.39
54 32 0.27
55 39 0.33
56 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (53 bp):
AAGGAAACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTTATAAGGC
Found at i:16140967 original size:24 final size:24
Alignment explanation
Indices: 16140922--16140967 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
16140912 TGCATTATGG
**
16140922 AAGGAAAATAAAGAAATGAAAAAA
1 AAGGAAAATAAAGAAAAAAAAAAA
* *
16140946 AAGGAAAATGATGAAAAAAAAA
1 AAGGAAAATAAAGAAAAAAAAA
16140968 GAGTGTGGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGGAAAATAAAGAAAAAAAAAAA
Found at i:16142289 original size:29 final size:29
Alignment explanation
Indices: 16142256--16142444 Score: 229
Period size: 29 Copynumber: 6.5 Consensus size: 29
16142246 GTGACGAGAT
16142256 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
16142285 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
16142314 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
16142343 TGGCACTAAGTGTGCATGTTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
16142372 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
16142401 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
16142430 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
16142445 GAAATCGAGT
Statistics
Matches: 138, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
28 2 0.01
29 135 0.98
30 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:16174036 original size:40 final size:40
Alignment explanation
Indices: 16173972--16174138 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
16173962 ACCTTGGGAT
** *
16173972 TTAA-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAACCCGGATATAATAACTAGCACAATTGCCTTCGGGTC
* * * *
16174011 TTAACCCGGATTTAGTGACTTGCAC-ATTGCCTTCGGGTC
1 TTAACCCGGATATAATAACTAGCACAATTGCCTTCGGGTC
* *
16174050 TTAACCCGGATATAACAACTCGCACGAA-TGCCTTCGGGTC
1 TTAACCCGGATATAATAACTAGCAC-AATTGCCTTCGGGTC
* * * * *
16174090 TTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGAC
1 TTAACCCGGATATAATAACTAGCACAATTGCCTTCGGGTC
*
16174130 TTAGCCCGG
1 TTAACCCGG
16174139 GTATCATTCA
Statistics
Matches: 107, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
39 40 0.37
40 66 0.62
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
TTAACCCGGATATAATAACTAGCACAATTGCCTTCGGGTC
Found at i:16190428 original size:2 final size:2
Alignment explanation
Indices: 16190421--16190458 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
16190411 TTAAATTACC
16190421 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16190459 ATTTATATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16194279 original size:2 final size:2
Alignment explanation
Indices: 16194272--16194301 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16194262 GCCTCAGAAA
16194272 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
16194302 GTGTATGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:16197727 original size:18 final size:19
Alignment explanation
Indices: 16197686--16197727 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
16197676 TTAATAAAAA
*
16197686 ATTATACATGAAATTTAAT
1 ATTATACATGAAATATAAT
* *
16197705 TTTATGCATG-AATATAAT
1 ATTATACATGAAATATAAT
16197723 ATTAT
1 ATTAT
16197728 TTAATTCAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (19 bp):
ATTATACATGAAATATAAT
Found at i:16199347 original size:20 final size:20
Alignment explanation
Indices: 16199324--16199385 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
16199314 TAATCAAAGA
16199324 AACATATTAGAACAAAATAT
1 AACATATTAGAACAAAATAT
* **
16199344 AACAAATT--TCCAAACATA-
1 AACATATTAGAACAAA-ATAT
*
16199362 GACATATTAGAACAAAATAT
1 AACATATTAGAACAAAATAT
16199382 AACA
1 AACA
16199386 AATTTCTAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 8
0.65 0.17 0.17
Matches are distributed among these distances:
18 10 0.33
19 6 0.20
20 14 0.47
ACGTcount: A:0.58, C:0.15, G:0.05, T:0.23
Consensus pattern (20 bp):
AACATATTAGAACAAAATAT
Found at i:16199376 original size:38 final size:38
Alignment explanation
Indices: 16199325--16199401 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
16199315 AATCAAAGAA
16199325 ACATATTAGAACAAAATATAACAAATTTCCAAACATAG
1 ACATATTAGAACAAAATATAACAAATTTCCAAACATAG
*
16199363 ACATATTAGAACAAAATATAACAAATTTCTAAACATAG
1 ACATATTAGAACAAAATATAACAAATTTCCAAACATAG
16199401 A
1 A
16199402 TAAATAACAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.56, C:0.14, G:0.05, T:0.25
Consensus pattern (38 bp):
ACATATTAGAACAAAATATAACAAATTTCCAAACATAG
Found at i:16200049 original size:3 final size:3
Alignment explanation
Indices: 16200041--16200192 Score: 51
Period size: 3 Copynumber: 49.7 Consensus size: 3
16200031 GAATTAAAAT
* * * * **
16200041 TAA TAA TAA CAA AAA TAA TAA TAA TAA TAG TAA TAA -AA AAA TGC TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * * *
16200088 TAG TGA TAT TAG TGA TAG TAA TAA TAGA AAA TAA TAA T-A TACA TAC
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA-A TAA
* * *
16200134 TAA TAA CAA CAA TAA T-A TGA TAAA TAGGA -AA TAA TAA TACA CTAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TA--A TAA TAA TAA TA-A -TAA
*
16200179 TAA GAA TAA TAA TA
1 TAA TAA TAA TAA TA
16200193 GATTACTAAT
Statistics
Matches: 108, Mismatches: 30, Indels: 22
0.68 0.19 0.14
Matches are distributed among these distances:
2 7 0.06
3 88 0.81
4 10 0.09
5 3 0.03
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:16201601 original size:16 final size:17
Alignment explanation
Indices: 16201571--16201603 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16201561 TTTAATATTA
*
16201571 TTGTTTTATTAATGTAT
1 TTGTATTATTAATGTAT
16201588 TTGTATTATT-ATGTAT
1 TTGTATTATTAATGTAT
16201604 GTATATACAT
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:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (17 bp):
TTGTATTATTAATGTAT
Found at i:16201703 original size:18 final size:19
Alignment explanation
Indices: 16201666--16201714 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
16201656 TATTTGTTCC
*
16201666 TTTTAAGTATTATATATATA
1 TTTTATGTA-TATATATATA
16201686 TTTTATGTATAT-TATATA
1 TTTTATGTATATATATATA
*
16201704 TTATATGTATA
1 TTTTATGTATA
16201715 CTTTATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 16 0.59
19 3 0.11
20 8 0.30
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (19 bp):
TTTTATGTATATATATATA
Found at i:16201714 original size:11 final size:11
Alignment explanation
Indices: 16201673--16201729 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
16201663 TCCTTTTAAG
16201673 TATTATATATA
1 TATTATATATA
* *
16201684 TATTTTATGTA
1 TATTATATATA
16201695 TATTATATATTA
1 TATTATATA-TA
*
16201707 TATGTATACTTTA
1 TAT-TATA-TATA
*
16201720 TTTTATATAT
1 TATTATATAT
16201730 TACGTATATA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
11 18 0.50
12 9 0.25
13 8 0.22
14 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (11 bp):
TATTATATATA
Found at i:16201725 original size:18 final size:18
Alignment explanation
Indices: 16201676--16201727 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
16201666 TTTTAAGTAT
*
16201676 TATA-TATATATTTTATG
1 TATATTATATATTATATG
16201693 TATATTATATATTATATG
1 TATATTATATATTATATG
*
16201711 TATACTT-TATTTTATAT
1 TATA-TTATATATTATAT
16201728 ATTACGTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 4 0.13
18 25 0.81
19 2 0.06
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (18 bp):
TATATTATATATTATATG
Found at i:16201738 original size:34 final size:33
Alignment explanation
Indices: 16201684--16201749 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 33
16201674 ATTATATATA
16201684 TATTTTATGTATATTATATATTA-TATGTATACTT
1 TATTTTA-GTATATTATATA-TACTATGTATACTT
16201718 TATTTTA-TATATTACGTATATACTATGTATAC
1 TATTTTAGTATATTA--TATATACTATGTATAC
16201750 GCTTTTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
32 7 0.24
33 2 0.07
34 20 0.69
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (33 bp):
TATTTTAGTATATTATATATACTATGTATACTT
Found at i:16202987 original size:3 final size:3
Alignment explanation
Indices: 16202979--16203035 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
16202969 TGGTTACGAC
16202979 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16203027 AAT AA- AAT A
1 AAT AAT AAT A
16203036 GAAAAGACTA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16204224 original size:12 final size:12
Alignment explanation
Indices: 16204193--16204224 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
16204183 GTGGCTAGGG
16204193 TTTTTTTTCTTT
1 TTTTTTTTCTTT
*
16204205 TTTCTTTTCTTT
1 TTTTTTTTCTTT
16204217 TTTTTTTT
1 TTTTTTTT
16204225 ATTATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (12 bp):
TTTTTTTTCTTT
Found at i:16205849 original size:3 final size:3
Alignment explanation
Indices: 16205841--16205892 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
16205831 GGTCTGAAAC
16205841 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
16205889 TAA T
1 TAA T
16205893 GTATACATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:16206648 original size:16 final size:17
Alignment explanation
Indices: 16206627--16206661 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
16206617 TCAAATGTAA
16206627 AAAAAAAAGAAA-AAAG
1 AAAAAAAAGAAAGAAAG
16206643 AAAAAAAAGAAAGAAAG
1 AAAAAAAAGAAAGAAAG
16206660 AA
1 AA
16206662 TCAAAGGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAAAGAAAG
Found at i:16208715 original size:2 final size:2
Alignment explanation
Indices: 16208710--16208737 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16208700 TCTGTCTCTT
16208710 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16208738 AGTTTAATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16209762 original size:15 final size:15
Alignment explanation
Indices: 16209727--16209773 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
16209717 TTTTTTTTAT
*
16209727 TTTTCGAGTTTTAGG
1 TTTTCAAGTTTTAGG
*
16209742 -TTTCAAGTTTTGGG
1 TTTTCAAGTTTTAGG
*
16209756 TTTTCAA-TTTGAGG
1 TTTTCAAGTTTTAGG
16209770 TTTT
1 TTTT
16209774 GGTTTTTAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 21 0.78
15 6 0.22
ACGTcount: A:0.15, C:0.06, G:0.23, T:0.55
Consensus pattern (15 bp):
TTTTCAAGTTTTAGG
Found at i:16212142 original size:25 final size:25
Alignment explanation
Indices: 16212114--16212164 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
16212104 TATAAATACT
16212114 AAAATAATTAACAGTGAAAGTATAG
1 AAAATAATTAACAGTGAAAGTATAG
16212139 AAAATAATTAACAGTGAAAGTATAG
1 AAAATAATTAACAGTGAAAGTATAG
16212164 A
1 A
16212165 GTAATGAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.57, C:0.04, G:0.16, T:0.24
Consensus pattern (25 bp):
AAAATAATTAACAGTGAAAGTATAG
Found at i:16212337 original size:19 final size:19
Alignment explanation
Indices: 16212310--16212353 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
16212300 TTATTTTTTT
*
16212310 AGTTGAGATGGTGTCAATG
1 AGTTAAGATGGTGTCAATG
16212329 AGTTAAGATGGTGTCAATG
1 AGTTAAGATGGTGTCAATG
16212348 AGTTAA
1 AGTTAA
16212354 CTTACACCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.32
Consensus pattern (19 bp):
AGTTAAGATGGTGTCAATG
Found at i:16212638 original size:19 final size:18
Alignment explanation
Indices: 16212616--16212674 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
16212606 AAGTTTTTTT
16212616 ATAATTTATATACTTTTAA
1 ATAATTTATATA-TTTTAA
*
16212635 ATAATTTAAATAATTTTAA
1 ATAATTTATAT-ATTTTAA
16212654 AT--TTT-TATATTTTAA
1 ATAATTTATATATTTTAA
*
16212669 AAAATT
1 ATAATT
16212675 AATTAATTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
15 8 0.24
16 2 0.06
17 5 0.15
19 18 0.53
20 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
ATAATTTATATATTTTAA
Found at i:16214800 original size:3 final size:3
Alignment explanation
Indices: 16214794--16214840 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
16214784 TTCACATTTC
16214794 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
16214841 GAATTTCAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:16215496 original size:25 final size:25
Alignment explanation
Indices: 16215467--16215519 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
16215457 AATGTATCGA
16215467 ATTTGTTTTTGTATTATTAAAAAGT
1 ATTTGTTTTTGTATTATTAAAAAGT
16215492 ATTTGTTTTTGTATTATTAAAAAGT
1 ATTTGTTTTTGTATTATTAAAAAGT
16215517 ATT
1 ATT
16215520 AAATAAGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (25 bp):
ATTTGTTTTTGTATTATTAAAAAGT
Found at i:16215757 original size:24 final size:25
Alignment explanation
Indices: 16215721--16215775 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
16215711 TTTAATTCTT
*
16215721 TTTAATTATATAA-AAATAAAATTAA
1 TTTATTTATATAATAAA-AAAATTAA
*
16215746 TTTATTTA-ATAATAAAAAGATTAA
1 TTTATTTATATAATAAAAAAATTAA
16215770 TTTATT
1 TTTATT
16215776 CCAATTCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 17 0.63
25 10 0.37
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
TTTATTTATATAATAAAAAAATTAA
Found at i:16215759 original size:21 final size:20
Alignment explanation
Indices: 16215722--16215762 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
16215712 TTAATTCTTT
16215722 TTAATTATATAAAAATAAAA
1 TTAATTATATAAAAATAAAA
* *
16215742 TTAATTTATTTAATAATAAAA
1 TTAA-TTATATAAAAATAAAA
16215763 AGATTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAATTATATAAAAATAAAA
Found at i:16217450 original size:46 final size:46
Alignment explanation
Indices: 16217383--16217474 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
16217373 TTTGTGTTAA
16217383 GTTTTTAGAAGGGTTGGGCATTATCTTGTTTGATACAGAAAGAGAG
1 GTTTTTAGAAGGGTTGGGCATTATCTTGTTTGATACAGAAAGAGAG
* *
16217429 GTTTTTAGAAGGGTTGGGCATTATCTTGTTTGATAGAGAGAGAGAG
1 GTTTTTAGAAGGGTTGGGCATTATCTTGTTTGATACAGAAAGAGAG
16217475 CTATTCAGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.27, C:0.05, G:0.33, T:0.35
Consensus pattern (46 bp):
GTTTTTAGAAGGGTTGGGCATTATCTTGTTTGATACAGAAAGAGAG
Found at i:16219301 original size:13 final size:13
Alignment explanation
Indices: 16219283--16219317 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
16219273 GTGGCCAAAT
16219283 AAATAGGAGTGCA
1 AAATAGGAGTGCA
16219296 AAATAGGAGTGCA
1 AAATAGGAGTGCA
16219309 AAATAGGAG
1 AAATAGGAG
16219318 GATTTGCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.49, C:0.06, G:0.31, T:0.14
Consensus pattern (13 bp):
AAATAGGAGTGCA
Found at i:16219464 original size:26 final size:26
Alignment explanation
Indices: 16219425--16219531 Score: 162
Period size: 26 Copynumber: 4.2 Consensus size: 26
16219415 TTATACAAAT
16219425 TGATAATGGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
* *
16219451 TGACAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
*
16219477 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
* *
16219503 TGATAATAGTTTAGGTAAAT-TTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
16219528 TGAT
1 TGAT
16219532 GGAATTTCAT
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
25 9 0.12
26 65 0.88
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATATTCCA
Found at i:16226481 original size:26 final size:26
Alignment explanation
Indices: 16226447--16226554 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
16226437 TTATACAAAT
16226447 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
16226473 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
16226499 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
16226525 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
16226551 TGAT
1 TGAT
16226555 GGAATTTCAT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:16230664 original size:27 final size:27
Alignment explanation
Indices: 16230634--16230695 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
16230624 GGGCAAAATG
16230634 GTAATTTTACCCCACAAGGGTATTTCA
1 GTAATTTTACCCCACAAGGGTATTTCA
* * *
16230661 GTAATTTTACCCTACAGGGGTATTTTA
1 GTAATTTTACCCCACAAGGGTATTTCA
16230688 GTAATTTT
1 GTAATTTT
16230696 TCAAACCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (27 bp):
GTAATTTTACCCCACAAGGGTATTTCA
Done.