Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167849.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_12, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22966848
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 129000 characters in sequence are not A, C, G, or T
File 107 of 129
Found at i:17797159 original size:16 final size:17
Alignment explanation
Indices: 17797131--17797162 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17797121 ATTTAAGAAT
17797131 AAAAATAACTTTTTAAG
1 AAAAATAACTTTTTAAG
17797148 AAAAATAA-TTTTTAA
1 AAAAATAACTTTTTAA
17797163 AAATAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
AAAAATAACTTTTTAAG
Found at i:17798835 original size:21 final size:21
Alignment explanation
Indices: 17798811--17798850 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
17798801 GCATATTTAT
17798811 TAAATAATATAAATACCCAAA
1 TAAATAATATAAATACCCAAA
*
17798832 TAAATACTATAAATACCCA
1 TAAATAATATAAATACCCA
17798851 TAAATCAAAT
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:0.57, C:0.17, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAATAATATAAATACCCAAA
Found at i:17800015 original size:15 final size:15
Alignment explanation
Indices: 17799995--17800031 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
17799985 TTGGAATCGG
*
17799995 TTTGGATTGTATCAT
1 TTTGGATTGAATCAT
17800010 TTTGGATTGAATCAT
1 TTTGGATTGAATCAT
*
17800025 TTCGGAT
1 TTTGGAT
17800032 AAAAAATTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.49
Consensus pattern (15 bp):
TTTGGATTGAATCAT
Found at i:17800064 original size:11 final size:11
Alignment explanation
Indices: 17800048--17800080 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
17800038 TTAGATCATT
17800048 TCAAATTTAAA
1 TCAAATTTAAA
*
17800059 TCAAA-TCAAA
1 TCAAATTTAAA
17800069 TCAAATTTAAA
1 TCAAATTTAAA
17800080 T
1 T
17800081 AAAAAAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (11 bp):
TCAAATTTAAA
Found at i:17801453 original size:17 final size:18
Alignment explanation
Indices: 17801413--17801453 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
17801403 TGGATAGGAT
* *
17801413 AATTTATTTATTGATTAA
1 AATTTATTTATTCATCAA
17801431 AA-TTATTT-TTCATCAA
1 AATTTATTTATTCATCAA
17801447 AATTTAT
1 AATTTAT
17801454 ATAATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 8 0.40
17 10 0.50
18 2 0.10
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (18 bp):
AATTTATTTATTCATCAA
Found at i:17809956 original size:17 final size:17
Alignment explanation
Indices: 17809934--17809966 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17809924 TGCAACATCA
17809934 AGAAATAAAAAAAAATG
1 AGAAATAAAAAAAAATG
*
17809951 AGAAATTAAAAAAAAT
1 AGAAATAAAAAAAAAT
17809967 ACATTAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (17 bp):
AGAAATAAAAAAAAATG
Found at i:17815694 original size:12 final size:12
Alignment explanation
Indices: 17815677--17815727 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
17815667 ATTTCAAAAG
*
17815677 AAAAAAACCAGA
1 AAAAAAAACAGA
*
17815689 AAAAAAAAGAGA
1 AAAAAAAACAGA
*
17815701 AAAAAAAACTAGG
1 AAAAAAAAC-AGA
*
17815714 AAAATAAA-AGA
1 AAAAAAAACAGA
17815725 AAA
1 AAA
17815728 GAAATCGAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
11 5 0.16
12 18 0.56
13 9 0.28
ACGTcount: A:0.78, C:0.06, G:0.12, T:0.04
Consensus pattern (12 bp):
AAAAAAAACAGA
Found at i:17829451 original size:210 final size:211
Alignment explanation
Indices: 17829075--17829499 Score: 798
Period size: 210 Copynumber: 2.0 Consensus size: 211
17829065 TTGCATTCAA
17829075 AGAATGAGGCTTTGGAAAAATTCATCACTTTTAGCAAACAAATATAAAATGAAAAAGGTTATTCA
1 AGAATGAGGCTTTGGAAAAATTCATCACTTTTAGCAAACAAATATAAAATGAAAAAGGTTATTCA
* *
17829140 ATTACTAGTATTAGAAGTGATAATGGAAAGGAATTTAAAAATCTTGGTTTTAATGTATTTTGTAG
66 ATTACTAGTATTAGAAGTGATAATGGAAAAGAATTTAAAAATCTTGGCTTTAATGTATTTTGTAG
*
17829205 TGAAAATGGTATTAGCCATAATTTTTTTGCTCCTAGAACTCCTCAACAAAATGGGGTAGTAGAAA
131 TGAAAATGGTATTAGCCATAATTTTTTTGCTCCTAGAACTCCTCAACAAAATGGGGTAGTAAAAA
17829270 GGAGAAATAGAACTTT
196 GGAGAAATAGAACTTT
17829286 AGAATGAGGCTTT-GAAAAATTCATCACTTTTAGCAAACAAATATAAAATGAAAAAGGTTATTCA
1 AGAATGAGGCTTTGGAAAAATTCATCACTTTTAGCAAACAAATATAAAATGAAAAAGGTTATTCA
* *
17829350 ATTACTAGTATTAGAAGTGATCATGGAAAAGAATTTAAAAATTTTGGCTTTAATGTATTTTGTAG
66 ATTACTAGTATTAGAAGTGATAATGGAAAAGAATTTAAAAATCTTGGCTTTAATGTATTTTGTAG
17829415 TGAAAATGGTATTAGCCATAATTTTTTTGCTCCTAGAACTCCTCAACAAAATGGGGTAGTAAAAA
131 TGAAAATGGTATTAGCCATAATTTTTTTGCTCCTAGAACTCCTCAACAAAATGGGGTAGTAAAAA
17829480 GGAGAAATAGAACTTT
196 GGAGAAATAGAACTTT
17829496 AGAA
1 AGAA
17829500 GAAATGGCTA
Statistics
Matches: 209, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
210 196 0.94
211 13 0.06
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (211 bp):
AGAATGAGGCTTTGGAAAAATTCATCACTTTTAGCAAACAAATATAAAATGAAAAAGGTTATTCA
ATTACTAGTATTAGAAGTGATAATGGAAAAGAATTTAAAAATCTTGGCTTTAATGTATTTTGTAG
TGAAAATGGTATTAGCCATAATTTTTTTGCTCCTAGAACTCCTCAACAAAATGGGGTAGTAAAAA
GGAGAAATAGAACTTT
Found at i:17833988 original size:21 final size:22
Alignment explanation
Indices: 17833942--17833990 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
17833932 AAATTTATGA
17833942 GGAGTTATATTGTTATTCAGGG
1 GGAGTTATATTGTTATTCAGGG
17833964 GGAGTTATATTGTTATTCA-GG
1 GGAGTTATATTGTTATTCAGGG
17833985 GGAGTT
1 GGAGTT
17833991 TGTTTTTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.22, C:0.04, G:0.33, T:0.41
Consensus pattern (22 bp):
GGAGTTATATTGTTATTCAGGG
Found at i:17837893 original size:30 final size:29
Alignment explanation
Indices: 17837853--17837921 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
17837843 CTGAAATTAA
* * *
17837853 TAAAATATTATTTTTTAAATATAAATATT
1 TAAAATATTATTATATAAATATAAATAAT
*
17837882 TAAATATATTATTATATAAATATATATAAT
1 TAAA-ATATTATTATATAAATATAAATAAT
*
17837912 TAAAAAATTA
1 TAAAATATTA
17837922 AAAAATAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 9 0.26
30 25 0.74
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TAAAATATTATTATATAAATATAAATAAT
Found at i:17837901 original size:16 final size:16
Alignment explanation
Indices: 17837848--17837906 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
17837838 TTGACCTGAA
17837848 ATTA-ATAAA-ATATT
1 ATTATATAAATATATT
* *
17837862 ATTTTTTAAATATA--
1 ATTATATAAATATATT
* *
17837876 AATATTTAAATATATT
1 ATTATATAAATATATT
17837892 ATTATATAAATATAT
1 ATTATATAAATATAT
17837907 ATAATTAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 15 0.43
15 4 0.11
16 16 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTATATAAATATATT
Found at i:17837915 original size:14 final size:14
Alignment explanation
Indices: 17837867--17837915 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
17837857 ATATTATTTT
* *
17837867 TTAAATATAAATAT
1 TTAAATATATATAA
*
17837881 TTAAATATATTATTA
1 TTAAATATA-TATAA
17837896 TATAAATATATATAA
1 T-TAAATATATATAA
17837911 TTAAA
1 TTAAA
17837916 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 13 0.45
15 8 0.28
16 8 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAAATATATATAA
Found at i:17839271 original size:23 final size:22
Alignment explanation
Indices: 17839245--17839289 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
17839235 TTATAATTAT
17839245 TCATGCAAAAGTATCATAATAAA
1 TCATGCAAAA-TATCATAATAAA
* *
17839268 TCATGCTAAATATTATAATAAA
1 TCATGCAAAATATCATAATAAA
17839290 AATCCTACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (22 bp):
TCATGCAAAATATCATAATAAA
Found at i:17839287 original size:22 final size:23
Alignment explanation
Indices: 17839234--17839289 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
17839224 GTATCATGCA
* *
17839234 ATTATAATTATTCATGCAAAAGT
1 ATTATAATAAATCATGCAAAAGT
* *
17839257 ATCATAATAAATCATGCTAAA-T
1 ATTATAATAAATCATGCAAAAGT
17839279 ATTATAATAAA
1 ATTATAATAAA
17839290 AATCCTACCA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 11 0.39
23 17 0.61
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (23 bp):
ATTATAATAAATCATGCAAAAGT
Found at i:17839345 original size:28 final size:28
Alignment explanation
Indices: 17839299--17839352 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
17839289 AAATCCTACC
* **
17839299 AAAAATCATGCAAGGATATCATGCAAAA
1 AAAAATCATACAAAAATATCATGCAAAA
*
17839327 AAAAATCATACAAAAATATTATGCAA
1 AAAAATCATACAAAAATATCATGCAA
17839353 GCAAATCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.57, C:0.13, G:0.09, T:0.20
Consensus pattern (28 bp):
AAAAATCATACAAAAATATCATGCAAAA
Found at i:17839361 original size:41 final size:39
Alignment explanation
Indices: 17839287--17839369 Score: 94
Period size: 40 Copynumber: 2.1 Consensus size: 39
17839277 ATATTATAAT
* * * *
17839287 AAAAATCCTACCAAAAATCATGCAAGGATATCATGCAAAA
1 AAAAATCATACAAAAAATCATGCAAGCAAATCAT-CAAAA
* *
17839327 AAAAATCATACAAAAATATTATGCAAGCAAATCATTAAAA
1 AAAAATCATACAAAAA-ATCATGCAAGCAAATCATCAAAA
17839367 AAA
1 AAA
17839370 TCCATGCAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
40 21 0.58
41 15 0.42
ACGTcount: A:0.58, C:0.16, G:0.07, T:0.19
Consensus pattern (39 bp):
AAAAATCATACAAAAAATCATGCAAGCAAATCATCAAAA
Found at i:17840916 original size:25 final size:23
Alignment explanation
Indices: 17840878--17840932 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
17840868 ATTATTTATG
*
17840878 CAAAAATATCATAATAAATCATGC
1 CAAAAATATAATAA-AAATCATGC
* *
17840902 CAAATAATATAATAAAACTCTTGC
1 CAAA-AATATAATAAAAATCATGC
17840926 CAAAAAT
1 CAAAAAT
17840933 CATGTAAGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 3 0.11
24 15 0.56
25 9 0.33
ACGTcount: A:0.55, C:0.16, G:0.04, T:0.25
Consensus pattern (23 bp):
CAAAAATATAATAAAAATCATGC
Found at i:17840989 original size:38 final size:40
Alignment explanation
Indices: 17840927--17841007 Score: 103
Period size: 38 Copynumber: 2.1 Consensus size: 40
17840917 AACTCTTGCC
* **
17840927 AAAAATCATGTAAGGATATCATGCAAG-AAAT-ATAAAAA
1 AAAAATCATATAAAAATATCATGCAAGCAAATCATAAAAA
* *
17840965 AAAAATCATATAAAAATATTATGCAAGCAAATCATTAAAA
1 AAAAATCATATAAAAATATCATGCAAGCAAATCATAAAAA
17841005 AAA
1 AAA
17841008 TCCATGCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
38 23 0.64
39 4 0.11
40 9 0.25
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.22
Consensus pattern (40 bp):
AAAAATCATATAAAAATATCATGCAAGCAAATCATAAAAA
Found at i:17841014 original size:26 final size:26
Alignment explanation
Indices: 17840967--17841016 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
17840957 TATAAAAAAA
* *
17840967 AAATCATATAAAAATATTATGCAAGC
1 AAATCATATAAAAAAATCATGCAAGC
17840993 AAATCAT-TAAAAAAATCCATGCAA
1 AAATCATATAAAAAAAT-CATGCAA
17841017 AATATTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.24
Consensus pattern (26 bp):
AAATCATATAAAAAAATCATGCAAGC
Found at i:17841247 original size:18 final size:18
Alignment explanation
Indices: 17841227--17841277 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
17841217 TAAATAACAA
17841227 AAAAATC-AAATCAAATC
1 AAAAATCAAAATCAAATC
* **
17841244 AAAAGTCAAAAGAAAATC
1 AAAAATCAAAATCAAATC
17841262 AAAAATCAAAATCAAA
1 AAAAATCAAAATCAAA
17841278 AAGAAAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.69, C:0.14, G:0.04, T:0.14
Consensus pattern (18 bp):
AAAAATCAAAATCAAATC
Found at i:17841272 original size:6 final size:6
Alignment explanation
Indices: 17841228--17841278 Score: 54
Period size: 5 Copynumber: 8.7 Consensus size: 6
17841218 AAATAACAAA
*
17841228 AAAATC -AAATC -AAATC AAAAGTC AAAA-G AAAATC AAAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAA-TC AAAATC AAAATC -AAAATC AAAATC
17841275 AAAA
1 AAAA
17841279 AGAAAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 14 0.36
6 13 0.33
7 12 0.31
ACGTcount: A:0.69, C:0.14, G:0.04, T:0.14
Consensus pattern (6 bp):
AAAATC
Found at i:17841285 original size:13 final size:12
Alignment explanation
Indices: 17841251--17841284 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
17841241 ATCAAAAGTC
17841251 AAAAGAAAATCA
1 AAAAGAAAATCA
*
17841263 AAAATCAAAATCA
1 AAAA-GAAAATCA
17841276 AAAAGAAAA
1 AAAAGAAAA
17841285 AAAAGAAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.76, C:0.09, G:0.06, T:0.09
Consensus pattern (12 bp):
AAAAGAAAATCA
Found at i:17842352 original size:16 final size:17
Alignment explanation
Indices: 17842320--17842362 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
17842310 ACTTTTGAAT
17842320 AATAACAAA-ATAAT-AA
1 AATAA-AAATATAATAAA
*
17842336 AATAAAAATATACTAAA
1 AATAAAAATATAATAAA
17842353 AATAAAAATA
1 AATAAAAATA
17842363 AAATTTTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 3 0.12
16 9 0.38
17 12 0.50
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (17 bp):
AATAAAAATATAATAAA
Found at i:17844870 original size:18 final size:18
Alignment explanation
Indices: 17844849--17844885 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
17844839 AAAAAGGTGG
*
17844849 ACAAAAAGTGATGTTGAA
1 ACAAAAAGCGATGTTGAA
17844867 ACAAAAAGCGATGTTGAA
1 ACAAAAAGCGATGTTGAA
17844885 A
1 A
17844886 AAGAATAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.08, G:0.22, T:0.19
Consensus pattern (18 bp):
ACAAAAAGCGATGTTGAA
Found at i:17851233 original size:18 final size:18
Alignment explanation
Indices: 17851206--17851259 Score: 74
Period size: 18 Copynumber: 3.0 Consensus size: 18
17851196 TATTATTATT
*
17851206 AAATACAAAATACAAAAA
1 AAATATAAAATACAAAAA
*
17851224 AAATATAAAATACCAAAA
1 AAATATAAAATACAAAAA
17851242 AAATATAATAATA-AAAAA
1 AAATATAA-AATACAAAAA
17851260 TTAAATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 28 0.88
19 4 0.12
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (18 bp):
AAATATAAAATACAAAAA
Found at i:17851251 original size:16 final size:17
Alignment explanation
Indices: 17851213--17851272 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 17
17851203 ATTAAATACA
17851213 AAATACAAAAAAAATAT
1 AAATACAAAAAAAATAT
*
17851230 AAAATACCAAAAAAATAT
1 -AAATACAAAAAAAATAT
*
17851248 -AATA-ATAAAAAAT-T
1 AAATACAAAAAAAATAT
17851262 AAATA-AAAAAA
1 AAATACAAAAAA
17851273 TTGGGGATAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 1 0.03
15 16 0.43
16 4 0.11
18 16 0.43
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (17 bp):
AAATACAAAAAAAATAT
Found at i:17860299 original size:14 final size:15
Alignment explanation
Indices: 17860271--17860323 Score: 65
Period size: 14 Copynumber: 3.5 Consensus size: 15
17860261 TGTTTTCATC
17860271 TTCATTTTGCTTTCCA
1 TTCATTTT-CTTTCCA
17860287 TTC-TTTTCTTTCCA
1 TTCATTTTCTTTCCA
*
17860301 -TCATTTTCTTGCCA
1 TTCATTTTCTTTCCA
17860315 TTTCATTTT
1 -TTCATTTT
17860324 TGTGTGCTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 2 0.06
14 17 0.52
15 4 0.12
16 10 0.30
ACGTcount: A:0.11, C:0.25, G:0.04, T:0.60
Consensus pattern (15 bp):
TTCATTTTCTTTCCA
Found at i:17864784 original size:49 final size:49
Alignment explanation
Indices: 17864593--17865175 Score: 496
Period size: 49 Copynumber: 12.0 Consensus size: 49
17864583 TGAAAAACAT
* * *
17864593 ATGAGATTTTTAAAGTTATTGGGCCTCTGTTGAGAAGGA-C-TTTTCTAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAG-AGGAGCTTTTTC-AAG
* * * * *
17864642 ATAAGA-TTTTAAAGTTGTTAAGCCTCTACTGAGAGAAACTTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAG
* * *
17864690 AT-AGGA-TTTTAAAGTCGTTGAGCCTTTGCTGAGAGGAGGCCTTTTCAAG
1 ATGA-GATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGA-GCTTTTTCAAG
* * *
17864739 ATGAGATTTTTAAAGTTATTGAACCTCTGTTGAGAGGAGCTTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAG
* *
17864788 A-GATGGA-TTTTAAA-TTCGTTGAGCCTCTGCTAAGAAGAGCATTTTT-AAG
1 ATGA--GATTTTTAAAGTT-GTTGAGCCTCTGCTGAGAGGAGC-TTTTTCAAG
* **
17864837 ATG-GA-TTTTAAAGTTGTTGAGCCTTTATTGAGAGGAGCTTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAG
* *
17864884 AT-TGA-TTTTAAAGTTGTTGAGCCTTTGCTGAGAGGAGCTTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAG
* * * *
17864931 ATAAGATTTTTAAAGTTGTTGAGCCTCTGCTGAAAGGAGCCTATTTCATAT
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCA-AG
* * * * * *
17864982 TTTA-ATTTTTAAAGTTGTTAAGCCTCTGCTGAGAAGAACTTTTCCAA-
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAG
* * * * * *
17865029 ATGAAATTTTTAAAGTCGTTGAGCCTCTACTGATAGGAGCCCTGTT-AAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCAAG
* * * * * *
17865078 ATAAGATTTTTAAAGTTGTTGAGCATCTACTGAGATGAACCCTTTTCAAG
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGA-GGAGCTTTTTCAAG
* * * ** *
17865128 ATAAAATTTTTAATGTTGTTGAGCCTCTTTTGAGATGAGTCTTTTTCA
1 ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCA
17865176 GATTTTAAAT
Statistics
Matches: 437, Mismatches: 73, Indels: 47
0.78 0.13 0.08
Matches are distributed among these distances:
46 5 0.01
47 82 0.19
48 95 0.22
49 138 0.32
50 114 0.26
51 3 0.01
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.38
Consensus pattern (49 bp):
ATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAG
Found at i:17864857 original size:146 final size:146
Alignment explanation
Indices: 17864593--17864963 Score: 458
Period size: 146 Copynumber: 2.6 Consensus size: 146
17864583 TGAAAAACAT
* *
17864593 ATGAGATTTTTAAAGTTATTGGGCCTCTGTTGAGAAGGA-C-TTTTCTA-AGATAAGATTTTAAA
1 ATGAGATTTTTAAAGTTATTGAGCCTCTGTTGAG-AGGAGCTTTTTCAAGAGAT-AGATTTTAAA
* * *
17864655 GTTGTTAAGCCTCTACTGAGAGAAACTTTTTCAAGATAGGATTTTAAAGTCGTTGAGCCTTTGCT
64 GTTGTTGAGCCTCTGCTGAGAGAAACTTTTTCAAGATAGGATTTTAAAGTCGTTGAGCCTTTACT
17864720 GAGAGGAGGCCTTTTCAAG
129 GAGAGGA-GCCTTTTCAAG
* *
17864739 ATGAGATTTTTAAAGTTATTGAACCTCTGTTGAGAGGAGCTTTTTCAAGAGATGGATTTTAAA-T
1 ATGAGATTTTTAAAGTTATTGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAGATAGATTTTAAAGT
*
17864803 TCGTTGAGCCTCTGCT-A-AGAAGAGCATTTTT-AAGAT-GGATTTTAAAGTTGTTGAGCCTTTA
66 T-GTTGAGCCTCTGCTGAGAGAA-A-C-TTTTTCAAGATAGGATTTTAAAGTCGTTGAGCCTTTA
* *
17864864 TTGAGAGGAGCTTTTTCAAG
127 CTGAGAGGAGCCTTTTCAAG
* * * * *
17864884 AT-TGA-TTTTAAAGTTGTTGAGCCTTTGCTGAGAGGAGCTTTTTCAAGATA-AGATTTTTAAAG
1 ATGAGATTTTTAAAGTTATTGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAGATAGA-TTTTAAAG
17864946 TTGTTGAGCCTCTGCTGA
65 TTGTTGAGCCTCTGCTGA
17864964 AAGGAGCCTA
Statistics
Matches: 198, Mismatches: 17, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
142 2 0.01
143 61 0.31
144 5 0.03
145 20 0.10
146 68 0.34
147 33 0.17
148 9 0.05
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.37
Consensus pattern (146 bp):
ATGAGATTTTTAAAGTTATTGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAGATAGATTTTAAAGT
TGTTGAGCCTCTGCTGAGAGAAACTTTTTCAAGATAGGATTTTAAAGTCGTTGAGCCTTTACTGA
GAGGAGCCTTTTCAAG
Found at i:17864874 original size:96 final size:96
Alignment explanation
Indices: 17864623--17864958 Score: 380
Period size: 96 Copynumber: 3.5 Consensus size: 96
17864613 GGGCCTCTGT
* * * * *
17864623 TGAGAAGGA-CTTTTCTAAGATAAGA-TTTTAAAGTTGTTAAGCCTCTACTGAGAGAAACTTTTT
1 TGAG-AGGAGCTTTT-TAAGAT-GGATTTTTAAAGTTGTTGAGCCTCTATTGAGAGGAGCTTTTT
* *
17864686 CAAGATA-GGATTTTAAAGTCGTTGAGCCTTTGC
63 CAAGAGATGGATTTTAAATTCGTTGAGCCTTTGC
* * * *
17864719 TGAGAGGAGGCCTTTTCAAGATGAGATTTTTAAAGTTATTGAACCTCTGTTGAGAGGAGCTTTTT
1 TGAGAGGA-G-CTTTTTAAGATG-GATTTTTAAAGTTGTTGAGCCTCTATTGAGAGGAGCTTTTT
*
17864784 CAAGAGATGGATTTTAAATTCGTTGAGCCTCTGC
63 CAAGAGATGGATTTTAAATTCGTTGAGCCTTTGC
* * *
17864818 TAAGAAGAGCATTTTTAAGATGGA-TTTTAAAGTTGTTGAGCCTTTATTGAGAGGAGCTTTTTC-
1 TGAGAGGAGC-TTTTTAAGATGGATTTTTAAAGTTGTTGAGCCTCTATTGAGAGGAGCTTTTTCA
*
17864881 A-AGATTGATTTTAAAGTT-GTTGAGCCTTTGC
65 AGAGATGGATTTTAAA-TTCGTTGAGCCTTTGC
*
17864912 TGAGAGGAGCTTTTTCAAGATAAGATTTTTAAAGTTGTTGAGCCTCT
1 TGAGAGGAGCTTTTT-AAGAT-GGATTTTTAAAGTTGTTGAGCCTCT
17864959 GCTGAAAGGA
Statistics
Matches: 204, Mismatches: 25, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
93 5 0.02
94 38 0.19
95 9 0.04
96 59 0.29
97 10 0.05
98 53 0.26
99 30 0.15
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.37
Consensus pattern (96 bp):
TGAGAGGAGCTTTTTAAGATGGATTTTTAAAGTTGTTGAGCCTCTATTGAGAGGAGCTTTTTCAA
GAGATGGATTTTAAATTCGTTGAGCCTTTGC
Found at i:17865012 original size:99 final size:97
Alignment explanation
Indices: 17864598--17865179 Score: 492
Period size: 99 Copynumber: 6.0 Consensus size: 97
17864588 AACATATGAG
* * *
17864598 ATTTTTAAAGTTATTGGGCCTCTGTTGAGAAGGA-C-TTTTCTAAGATAAGA-TTTTAAAGTTGT
1 ATTTTTAAAGTTGTTGAGCCTCTGCTGAG-AGGAGCTTTTTC-AAGATAAGATTTTTAAAGTTGT
* * *
17864660 TAAGCCTCTACTGAGAGAAACTTTTTCAAGA-TA
64 TGAGCCTCTACTGAGAGGAGCTTTTTCAAGATTA
* * * * *
17864693 GGA-TTTTAAAGTCGTTGAGCCTTTGCTGAGAGGAGGCCTTTTCAAGATGAGATTTTTAAAGTTA
1 --ATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGA-GCTTTTTCAAGATAAGATTTTTAAAGTTG
* ** **
17864757 TTGAACCTCTGTTGAGAGGAGCTTTTTCAAGAGATGG
63 TTGAGCCTCTACTGAGAGGAGCTTTTTC-A-AGATTA
* * *
17864794 A-TTTTAAA-TTCGTTGAGCCTCTGCTAAGAAGAGCATTTTT-AAGAT-GGA-TTTTAAAGTTGT
1 ATTTTTAAAGTT-GTTGAGCCTCTGCTGAGAGGAGC-TTTTTCAAGATAAGATTTTTAAAGTTGT
* * *
17864854 TGAGCCTTTATTGAGAGGAGCTTTTTCAAGATTG
64 TGAGCCTCTACTGAGAGGAGCTTTTTCAAGATTA
*
17864888 A-TTTTAAAGTTGTTGAGCCTTTGCTGAGAGGAGCTTTTTCAAGATAAGATTTTTAAAGTTGTTG
1 ATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATAAGATTTTTAAAGTTGTTG
* * * **
17864952 AGCCTCTGCTGAAAGGAGCCTATTTCATATTTTA
66 AGCCTCTACTGAGAGGAG-CTTTTTCA-AGATTA
* * * * *
17864986 ATTTTTAAAGTTGTTAAGCCTCTGCTGAGAAGAACTTTTCCAA-ATGAA-ATTTTTAAAGTCGTT
1 ATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAT-AAGATTTTTAAAGTTGTT
* * * *
17865049 GAGCCTCTACTGATAGGAGCCCTGTT-AAGATAA
65 GAGCCTCTACTGAGAGGAG-CTTTTTCAAGATTA
* * * * * * *
17865082 GATTTTTAAAGTTGTTGAGCATCTACTGAGATGAACCCTTTTCAAGATAAAATTTTTAATGTTGT
1 -ATTTTTAAAGTTGTTGAGCCTCTGCTGAGA-GGAGCTTTTTCAAGATAAGATTTTTAAAGTTGT
** *
17865147 TGAGCCTCTTTTGAGATGAGTCTTTTTC-AGATT
64 TGAGCCTCTACTGAGAGGAG-CTTTTTCAAGATT
17865180 TTAAATTTTC
Statistics
Matches: 393, Mismatches: 70, Indels: 42
0.78 0.14 0.08
Matches are distributed among these distances:
93 5 0.01
94 38 0.10
95 9 0.02
96 88 0.22
97 47 0.12
98 96 0.24
99 107 0.27
100 3 0.01
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.38
Consensus pattern (97 bp):
ATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATAAGATTTTTAAAGTTGTTG
AGCCTCTACTGAGAGGAGCTTTTTCAAGATTA
Found at i:17868401 original size:19 final size:19
Alignment explanation
Indices: 17868351--17868405 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 19
17868341 ACTGAAAATA
17868351 TTTAAATTATATTATATATTT
1 TTTAAATT-T-TTATATATTT
17868372 TAATT-AATTTTTATATATTT
1 T--TTAAATTTTTATATATTT
17868392 TTTAAATTTTTATA
1 TTTAAATTTTTATA
17868406 AAATAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
18 2 0.06
19 10 0.32
20 11 0.35
21 2 0.06
22 4 0.13
23 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTAAATTTTTATATATTT
Found at i:17868831 original size:20 final size:19
Alignment explanation
Indices: 17868806--17868848 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
17868796 TTAAGGGGAG
17868806 GAAAAGGAAAGAAAAATAAA
1 GAAAAGGAAAG-AAAATAAA
* *
17868826 GAAAAGTAATGAAAATAAA
1 GAAAAGGAAAGAAAATAAA
17868845 -AAAA
1 GAAAA
17868849 AAAATTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 8 0.38
20 9 0.43
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.09
Consensus pattern (19 bp):
GAAAAGGAAAGAAAATAAA
Found at i:17868941 original size:17 final size:17
Alignment explanation
Indices: 17868903--17868935 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17868893 AGATTCAATA
17868903 AATTTTGATTTTTTTAT
1 AATTTTGATTTTTTTAT
*
17868920 AATTTTTATTTTTTTA
1 AATTTTGATTTTTTTA
17868936 ATATTTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (17 bp):
AATTTTGATTTTTTTAT
Found at i:17881180 original size:18 final size:18
Alignment explanation
Indices: 17881146--17881198 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
17881136 ATTTATATAT
17881146 AATTATTATTATTATTTTTA
1 AATTA-TATT-TTATTTTTA
17881166 AATTATATTTTATTTTTA
1 AATTATATTTTATTTTTA
*
17881184 TATTATATTTATATT
1 AATTATATTT-TATT
17881199 ATATTATCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 18 0.58
19 8 0.26
20 5 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
AATTATATTTTATTTTTA
Found at i:17881189 original size:11 final size:11
Alignment explanation
Indices: 17881155--17881203 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
17881145 TAATTATTAT
*
17881155 TATTATTTTTA
1 TATTATATTTA
*
17881166 AATTATATTT-
1 TATTATATTTA
17881176 TA-T-T-TTTA
1 TATTATATTTA
17881184 TATTATATTTA
1 TATTATATTTA
17881195 TATTATATT
1 TATTATATT
17881204 ATCTAACACA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
7 3 0.10
8 3 0.10
9 2 0.06
10 2 0.06
11 21 0.68
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTATATTTA
Found at i:17885956 original size:30 final size:30
Alignment explanation
Indices: 17885922--17885978 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
17885912 CAAATGATCT
17885922 ATATACTCATATAAAATTTAAAATTTAGTC
1 ATATACTCATATAAAATTTAAAATTTAGTC
*
17885952 ATATACTTATATAAAATTTAAAATTTA
1 ATATACTCATATAAAATTTAAAATTTA
17885979 ATCTTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (30 bp):
ATATACTCATATAAAATTTAAAATTTAGTC
Found at i:17886125 original size:14 final size:14
Alignment explanation
Indices: 17886108--17886204 Score: 64
Period size: 14 Copynumber: 7.2 Consensus size: 14
17886098 TTTATTATAT
17886108 ATAAT-TAATTATTA
1 ATAATATAA-TATTA
*
17886122 ATAATATCATATTA
1 ATAATATAATATTA
17886136 ATAATAT--TATT-
1 ATAATATAATATTA
** *
17886147 ATTGT-TTATATTA
1 ATAATATAATATTA
17886160 ATCAATATAATATTA
1 AT-AATATAATATTA
*
17886175 ATAATTTAA-ATTA
1 ATAATATAATATTA
*
17886188 AT-ATATCAATTTTA
1 ATAATAT-AATATTA
17886202 ATA
1 ATA
17886205 TTATTTTAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
10 1 0.02
11 3 0.05
12 11 0.17
13 10 0.15
14 29 0.45
15 11 0.17
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.48
Consensus pattern (14 bp):
ATAATATAATATTA
Found at i:17887141 original size:20 final size:18
Alignment explanation
Indices: 17887116--17887159 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 18
17887106 TTTTAAAAAA
17887116 AATTTATTAATTGTTTTATT
1 AATTTATTAATT-TTTT-TT
17887136 AATTTATTAATTTTTTTT
1 AATTTATTAATTTTTTTT
17887154 AATTTA
1 AATTTA
17887160 AATGTTGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 8 0.33
19 4 0.17
20 12 0.50
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
AATTTATTAATTTTTTTT
Found at i:17887542 original size:11 final size:11
Alignment explanation
Indices: 17887528--17887561 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
17887518 TTTTTTTTTC
*
17887528 TTTTTTATTAA
1 TTTTATATTAA
17887539 TTTTATATTAA
1 TTTTATATTAA
17887550 TTTTAT-TTAA
1 TTTTATATTAA
17887560 TT
1 TT
17887562 AAATTATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTATATTAA
Found at i:17887596 original size:7 final size:7
Alignment explanation
Indices: 17887586--17887615 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
17887576 TTTTTTACAT
17887586 TTTATTA
1 TTTATTA
17887593 TTTATTA
1 TTTATTA
17887600 TTTATTA
1 TTTATTA
*
17887607 ATTATTA
1 TTTATTA
17887614 TT
1 TT
17887616 ATAAAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTATTA
Found at i:17887723 original size:10 final size:10
Alignment explanation
Indices: 17887694--17887732 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
17887684 TTAAAATAAC
17887694 AAAAAAATATA
1 AAAAAAAT-TA
*
17887705 TATAAAAATTA
1 -AAAAAAATTA
17887716 AAAAAAATTA
1 AAAAAAATTA
17887726 AAAAAAA
1 AAAAAAA
17887733 ATTTTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 2 0.08
12 7 0.28
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAAAAATTA
Found at i:17887732 original size:21 final size:22
Alignment explanation
Indices: 17887694--17887735 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
17887684 TTAAAATAAC
* *
17887694 AAAAAAATATATATAAAAATTA
1 AAAAAAATATAAAAAAAAATTA
17887716 AAAAAAAT-TAAAAAAAAATT
1 AAAAAAATATAAAAAAAAATT
17887736 TTTTTTACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAAAAATATAAAAAAAAATTA
Found at i:17888700 original size:4 final size:4
Alignment explanation
Indices: 17888691--17888738 Score: 53
Period size: 4 Copynumber: 11.8 Consensus size: 4
17888681 AAATAAAAAT
* *
17888691 AAAG AAAG AAAG AAAG AGAG AAAAG AAAG AAA- AAATA AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG -AAAG AAAG AAAG AAA-G AAAG AAAG AAA
17888739 AAATAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
3 3 0.08
4 29 0.76
5 6 0.16
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:17888719 original size:25 final size:25
Alignment explanation
Indices: 17888686--17888755 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 25
17888676 ATAAGAAATA
* * *
17888686 AAAATAAAGAAAGAAA-GAAAGAGAG
1 AAAAGAAAGAAA-AAATAAAAGAAAG
17888711 AAAAGAAAGAAAAAATAAAAGAAAG
1 AAAAGAAAGAAAAAATAAAAGAAAG
17888736 AAAA-AATA-AAAATAATAAAA
1 AAAAGAA-AGAAAA-AATAAAA
17888756 TAATAATAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
24 9 0.23
25 30 0.77
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (25 bp):
AAAAGAAAGAAAAAATAAAAGAAAG
Found at i:17888740 original size:17 final size:16
Alignment explanation
Indices: 17888695--17888746 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
17888685 AAAAATAAAG
* *
17888695 AAAGAAAGAAAGAGAGA
1 AAAGAAAGAAA-AAATA
17888712 AAAGAAAGAAAAAATA
1 AAAGAAAGAAAAAATA
17888728 AAAGAAAGAAAAAATA
1 AAAGAAAGAAAAAATA
17888744 AAA
1 AAA
17888747 ATAATAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
16 22 0.67
17 11 0.33
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (16 bp):
AAAGAAAGAAAAAATA
Found at i:17888755 original size:14 final size:14
Alignment explanation
Indices: 17888738--17888777 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
17888728 AAAGAAAGAA
17888738 AAAATAAAAATAAT
1 AAAATAAAAATAAT
*
17888752 AAAATAATAATAAT
1 AAAATAAAAATAAT
17888766 AATAATGAAAAA
1 AA-AAT-AAAAA
17888778 AATGTTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 15 0.68
15 3 0.14
16 4 0.18
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (14 bp):
AAAATAAAAATAAT
Found at i:17888760 original size:17 final size:16
Alignment explanation
Indices: 17888720--17888770 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
17888710 GAAAAGAAAG
*
17888720 AAAAAATAAAAGA-AAG
1 AAAAAATAAAA-ATAAT
17888736 AAAAAATAAAAATAAT
1 AAAAAATAAAAATAAT
*
17888752 AAAATAATAATAATAAT
1 AAAA-AATAAAAATAAT
17888769 AA
1 AA
17888771 TGAAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
15 1 0.03
16 17 0.55
17 13 0.42
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (16 bp):
AAAAAATAAAAATAAT
Found at i:17888873 original size:20 final size:21
Alignment explanation
Indices: 17888843--17888894 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
17888833 ACTTGAAATT
17888843 AATATAGTAAAAATAT-ATTAA
1 AATATAGTAAAAAT-TCATTAA
17888864 AATA-AGTAAAAATTCATTAA
1 AATATAGTAAAAATTCATTAA
17888884 AA-ATAGTAAAA
1 AATATAGTAAAA
17888895 CTAAAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.07
20 23 0.79
21 4 0.14
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (21 bp):
AATATAGTAAAAATTCATTAA
Found at i:17888984 original size:22 final size:21
Alignment explanation
Indices: 17888938--17888985 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
17888928 AAATATTTGC
17888938 TAAAAATAATTTTAAAATTAAT
1 TAAAAATAATTTTAAAATT-AT
*
17888960 TAAAAATAAAATTTTTAAATT-T
1 TAAAAAT--AATTTTAAAATTAT
17888982 TAAA
1 TAAA
17888986 TTTTTGGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 12 0.52
24 11 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAAAATAATTTTAAAATTAT
Found at i:17890876 original size:30 final size:30
Alignment explanation
Indices: 17890841--17890899 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
17890831 CGTTTTCTAA
* *
17890841 AAAAATGAAGATCGAGTCA-AGATTTATTTT
1 AAAAAT-AAGACCAAGTCAGAGATTTATTTT
*
17890871 AAAAATAAGACCAAGTTAGAGATTTATTT
1 AAAAATAAGACCAAGTCAGAGATTTATTT
17890900 AAGGCATTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.32
Consensus pattern (30 bp):
AAAAATAAGACCAAGTCAGAGATTTATTTT
Found at i:17891017 original size:13 final size:13
Alignment explanation
Indices: 17891001--17891035 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
17890991 TTGGGTTTTC
17891001 TTTTTATTTAATT
1 TTTTTATTTAATT
*
17891014 TTTTTACTTTTATT
1 TTTTTA-TTTAATT
17891028 TTTTTATT
1 TTTTTATT
17891036 AAATAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATTTAATT
Found at i:17891458 original size:65 final size:63
Alignment explanation
Indices: 17891355--17891474 Score: 170
Period size: 65 Copynumber: 1.9 Consensus size: 63
17891345 ATTGAATGAA
* * * *
17891355 ATTATTGAAGGCGTTTTGGCTAAAAACGTCTTCAATAATTCATTCAAAAAATTTTGAAAATGG
1 ATTATTAAAGGCGTTTTGGCAAAAAACGTCTTCAATAATCCATACAAAAAATTTTGAAAATGG
17891418 ATTATTAAAGGCGTTTTCGGTCAAAAAACG-CTTTCAATAATCCATACAAAAAATTTT
1 ATTATTAAAGGCGTTTT-GG-CAAAAAACGTC-TTCAATAATCCATACAAAAAATTTT
17891475 TTGTATGAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
63 16 0.32
64 3 0.06
65 31 0.62
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (63 bp):
ATTATTAAAGGCGTTTTGGCAAAAAACGTCTTCAATAATCCATACAAAAAATTTTGAAAATGG
Found at i:17891818 original size:61 final size:62
Alignment explanation
Indices: 17891743--17891859 Score: 148
Period size: 63 Copynumber: 1.9 Consensus size: 62
17891733 TTTAGCCAAA
* * * *
17891743 AACGTCTTTAATAATCCAT-TCAAAAATTTG-GAGAGAGAATATTGAAGGTGTTTTCAGTCAT
1 AACGCCTTCAATAATCCATATAAAAAATTTGAGAGAG-GAATATTGAAGGTATTTTCAGTCAT
* *
17891804 AACGCCTTCAATAATCCATATAAAAAATTTTAGAGATGGATTATTGAAGGTATTTT
1 AACGCCTTCAATAATCCATATAAAAAATTTGAGAGA-GGAATATTGAAGGTATTTT
17891860 TGGCCAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
61 17 0.36
62 9 0.19
63 20 0.43
64 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (62 bp):
AACGCCTTCAATAATCCATATAAAAAATTTGAGAGAGGAATATTGAAGGTATTTTCAGTCAT
Found at i:17891895 original size:64 final size:63
Alignment explanation
Indices: 17891809--17892527 Score: 237
Period size: 64 Copynumber: 11.2 Consensus size: 63
17891799 GTCATAACGC
* *
17891809 CTTCAATAAT-CCATATAAAAAATTTTAGAGATGGATTATTGAAGGTATTTTTGGCCAAAAATAT
1 CTTCAATAATCCCTTAT-AAAAATTTTAGAGA-GGATTATTGAAGGTATTTTTGGTCAAAAATAT
* * * ***
17891873 CTTCAATAATCCCTTATAAAAATTCATTAAAGA-AATTATTGAAGGTTTTTTTTAACAAAAA-AT
1 CTTCAATAATCCCTTATAAAAATT--TTAGAGAGGATTATTGAAGGTATTTTTGGTCAAAAATAT
* * * ** * **
17891936 GCATTCAATAATCCTCTGA-AAAAA-TTTAAAAATTATTATTGAAGGCCCTTTTTTTTTTTTTTA
1 -C-TTCAATAATCC-CTTATAAAAATTTTAGAGAGGATTATTGAAGG---------TATTTTTGG
**
17891999 TCAAAAACGT
54 TCAAAAATAT
* * * * * * *
17892009 CTTTAATAATCCCTCATAAAAATTTATTGA-AGGGATTATTGAAAGCATTTTTTGTCAAAAACA-
1 CTTCAATAATCCCTTATAAAAATTT-TAGAGA-GGATTATTGAAGGTATTTTTGGTCAAAAATAT
* * **
17892072 CATTCAATAATCCC-TAGAAAAATTTTAGAG-GAGATTATTGAATGCGTTTTT-GTCCAAAAATA
1 C-TTCAATAATCCCTTATAAAAATTTTAGAGAG-GATTATTGAAGGTATTTTTGGT-CAAAAATA
*
17892134 C
63 T
* * *
17892135 CTTTAATAATCCCTCTCA-ATAAAA-TTTAGAAAGGATTATTGAAGGCGT-TTTTTGCT-AAAAA
1 CTTCAATAATCCCT-T-ATA-AAAATTTTAGAGAGGATTATTGAA-G-GTATTTTTGGTCAAAAA
**
17892196 TGC
61 TAT
** * * * * * * *
17892199 CTTCAATAATTTCTTGA-AAAAA-TTTGGAAAAGATTATTGAAAGTGTTTTT-GACAAAAAAAT
1 CTTCAATAATCCCTT-ATAAAAATTTTAGAGAGGATTATTGAAGGTATTTTTGGTCAAAAATAT
* * *
17892260 GCCTACAATAAT-CCTTCATAAAAATTCATTA-AG-GGAATTATTGAAGGTATTTTTGATTAAAA
1 --CTTCAATAATCCCTT-ATAAAAATT--TTAGAGAGG-ATTATTGAAGGTATTTTTGGTCAAAA
*
17892322 AT-G
60 ATAT
* * * *
17892325 CATTCAATAATCTCTCATAAAAACTTATTA-AGAGGATTATT-AATGGCATTTTTAGTCAAAAAT
1 C-TTCAATAATCCCTTATAAAAA-TT-TTAGAGAGGATTATTGAA-GGTATTTTTGGTCAAAAAT
**
17892388 GC
62 AT
* * * * ** * * * **
17892390 CTTTAATAATCTCTT-GAAAAATTTTATA-AGGGATTATTGAAAATGTTTTTGATAAAAAATGC
1 CTTCAATAATCCCTTATAAAAATTTTAGAGA-GGATTATTGAAGGTATTTTTGGTCAAAAATAT
* * * * * * * *
17892452 CTTTAATAATCCCTCATAAAAATTTATTGAGGGGATTAATAAAGGTATTTTTGGCCAAAAATTTT
1 CTTCAATAATCCCTTATAAAAATTT-TAGAGAGGATTATTGAAGGTATTTTTGGTCAAAAA-TAT
*
17892517 TTTCAATAATC
1 CTTCAATAATC
17892528 ATTCATAACA
Statistics
Matches: 501, Mismatches: 97, Indels: 113
0.70 0.14 0.16
Matches are distributed among these distances:
60 2 0.00
61 17 0.03
62 107 0.21
63 59 0.12
64 182 0.36
65 66 0.13
66 18 0.04
70 3 0.01
71 15 0.03
72 19 0.04
73 13 0.03
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.37
Consensus pattern (63 bp):
CTTCAATAATCCCTTATAAAAATTTTAGAGAGGATTATTGAAGGTATTTTTGGTCAAAAATAT
Found at i:17892130 original size:126 final size:125
Alignment explanation
Indices: 17892000--17892476 Score: 361
Period size: 126 Copynumber: 3.8 Consensus size: 125
17891990 TTTTTTTTAT
* *
17892000 CAAAAACGTCTTTAATAATCCCTCAT-AAAAATTTATTGAAGGGATTATTGAAAGCATTTTTTGT
1 CAAAAATGCCTTTAATAATCCCTCATAAAAAATTTATT-AAGGGATTATTGAAAGCATTTTTTGT
** *
17892064 CAAAAACACATTCAATAATCCCTAGAAAAATTTTAGAGGAGATTATTGAATGCGTTTTTGTC
65 CAAAAATGCATTCAATAATCTCTAGAAAAATTTTAGA-GAGATTATTGAATGCGTTTTTGTC
* * * * *
17892126 CAAAAATACCTTTAATAATCCCTC-TCAATAAAATTTA-GAAAGGATTATTGAAGGCGTTTTTTG
1 CAAAAATGCCTTTAATAATCCCTCAT-AA-AAAATTTATTAAGGGATTATTGAAAGCATTTTTTG
* * * * * * * * *
17892189 -CTAAAAATGCCTTCAATAATTTCTTGAAAAAATTTGGAAAAGATTATTGAAAGTGTTTTTGAC
64 TC-AAAAATGCATTCAATAATCTCTAGAAAAATTTTAG-AGAGATTATTGAATGCGTTTTTGTC
* ** * * * *
17892252 AAAAAAATGCCTACAATAATCCTTCAT-AAAAATTCATTAAGGGAATTATTGAAGGTA-TTTTTG
1 -CAAAAATGCCTTTAATAATCCCTCATAAAAAATTTATTAAGGG-ATTATTGAAAGCATTTTTTG
* * *
17892315 ATTAAAAATGCATTCAATAATCTCTCATAAAAACTTATTA-AGAGGATTATT-AATGGCATTTTT
64 -TCAAAAATGCATTCAATAATCTCT-AGAAAAA-TT-TTAGAGA-GATTATTGAAT-GCGTTTTT
17892378 AGT-
123 -GTC
* *
17892381 CAAAAATGCCTTTAATAAT--CTCTTGAAAAATTT-TATAAGGGATTATTGAAA--ATGTTTTTG
1 CAAAAATGCCTTTAATAATCCCTCATAAAAAATTTAT-TAAGGGATTATTGAAAGCAT-TTTTTG
* * * * *
17892441 ATAAAAAATGCCTTTAATAATCCCTCATAAAAATTT
64 -TCAAAAATGCATTCAATAATCTCT-AGAAAAATTT
17892477 ATTGAGGGGA
Statistics
Matches: 278, Mismatches: 52, Indels: 44
0.74 0.14 0.12
Matches are distributed among these distances:
124 2 0.01
125 11 0.04
126 149 0.54
127 65 0.23
128 34 0.12
129 14 0.05
130 3 0.01
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (125 bp):
CAAAAATGCCTTTAATAATCCCTCATAAAAAATTTATTAAGGGATTATTGAAAGCATTTTTTGTC
AAAAATGCATTCAATAATCTCTAGAAAAATTTTAGAGAGATTATTGAATGCGTTTTTGTC
Found at i:17892479 original size:126 final size:128
Alignment explanation
Indices: 17892254--17892513 Score: 310
Period size: 126 Copynumber: 2.0 Consensus size: 128
17892244 TTTTTGACAA
** *
17892254 AAAAATGCCTACAATAATCCTTCATAAAAATTCATTAAGGGAATTATTGAAGGTATTTTTGATTA
1 AAAAATGCCTACAATAATCCTTCATAAAAATTCATTAAGGGAATTATTGAAAATATTTTTGATAA
* * * *
17892319 AAAATGCATTCAATAATCTCTCATAAAAACTTATTAAGAGGATTATTAATGGCATTTTTAGTC
66 AAAATGCATTCAATAATCCCTCATAAAAACTTATTAAGAGGATTAATAAAGGCATTTTTAGCC
** * * * *
17892382 AAAAATGCCTTTAATAATCTCTTGA-AAAATTTTA-TAAGGG-ATTATTGAAAATGTTTTTGATA
1 AAAAATGCCTACAATAATC-CTTCATAAAAATTCATTAAGGGAATTATTGAAAATATTTTTGATA
* * * * * * *
17892444 AAAAATGCCTTTAATAATCCCTCATAAAAATTTATTGAGGGGATTAATAAAGGTATTTTTGGCC
65 AAAAATGCATTCAATAATCCCTCATAAAAACTTATTAAGAGGATTAATAAAGGCATTTTTAGCC
17892508 AAAAAT
1 AAAAAT
17892514 TTTTTTCAAT
Statistics
Matches: 111, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
126 77 0.69
127 6 0.05
128 24 0.22
129 4 0.04
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (128 bp):
AAAAATGCCTACAATAATCCTTCATAAAAATTCATTAAGGGAATTATTGAAAATATTTTTGATAA
AAAATGCATTCAATAATCCCTCATAAAAACTTATTAAGAGGATTAATAAAGGCATTTTTAGCC
Found at i:17892524 original size:191 final size:192
Alignment explanation
Indices: 17892166--17892589 Score: 464
Period size: 191 Copynumber: 2.2 Consensus size: 192
17892156 AAATTTAGAA
* * * *
17892166 AGGATTATTGAA-GGCGTTTTTTG-CTAAAAATGCCTTCAATAATTTCTTGAAAAAATTTGGAAA
1 AGGATTATTCAATGGCGTTTTTAGTC-AAAAATGCCTTCAATAATCTCTTGAAAAAATTTAGAAA
* *
17892229 AGATTATTGAAAGTGTTTTTGACAAAAAAATGCCTACAATAATCCTTCATAAAAATTCATTAAGG
65 AGATTATTGAAAATGTTTTTGACAAAAAAATGCCTACAATAATCCCTCATAAAAATTCATTAAGG
* * ** *
17892294 GAATTATTGAAGGTATTTTTGATTAAAAATGCATTCAATAATC-TCTCATAAAAACTTATTAAG
130 GAATTAATAAAGGTATTTTTGACCAAAAATGCATTCAATAATCAT-TCATAAAAACTTATTAAC
* * * * **
17892357 AGGATTATT-AATGGCATTTTTAGTCAAAAATGCCTTTAATAATCTCTTGAAAAATTTTATAAGG
1 AGGATTATTCAATGGCGTTTTTAGTCAAAAATGCCTTCAATAATCTCTTGAAAAAATTTAGAAAA
* ** * *
17892421 GATTATTGAAAATGTTTTTGA-TAAAAAATGCCTTTAATAATCCCTCATAAAAATTTATTGAGGG
66 GATTATTGAAAATGTTTTTGACAAAAAAATGCCTACAATAATCCCTCATAAAAATTCATTAAGGG
* * *** * * *
17892485 GATTAATAAAGGTATTTTTGGCCAAAAATTTTTTTCAATAATCATTCATAACAATTTATTGAC
131 AATTAATAAAGGTATTTTTGACCAAAAA-TGCATTCAATAATCATTCATAAAAACTTATTAAC
* * * * *
17892548 AGAATTATTCAAT-GCGTTTTTGGTTAAAAATACCTTGAATAA
1 AGGATTATTCAATGGCGTTTTTAGTCAAAAATGCCTTCAATAA
17892590 CCCAATTGAA
Statistics
Matches: 193, Mismatches: 35, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
190 61 0.32
191 127 0.66
192 5 0.03
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (192 bp):
AGGATTATTCAATGGCGTTTTTAGTCAAAAATGCCTTCAATAATCTCTTGAAAAAATTTAGAAAA
GATTATTGAAAATGTTTTTGACAAAAAAATGCCTACAATAATCCCTCATAAAAATTCATTAAGGG
AATTAATAAAGGTATTTTTGACCAAAAATGCATTCAATAATCATTCATAAAAACTTATTAAC
Found at i:17902127 original size:2 final size:2
Alignment explanation
Indices: 17902120--17902145 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17902110 ACATATGCAA
17902120 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
17902146 CATATGCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17904264 original size:2 final size:2
Alignment explanation
Indices: 17904257--17904301 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
17904247 ATTCATGCTA
*
17904257 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAA AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
17904299 AT A
1 AT A
17904302 ATACAATGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.95
3 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:17913457 original size:11 final size:11
Alignment explanation
Indices: 17913441--17913467 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
17913431 ATTTTAAATC
17913441 ATATTATTTTT
1 ATATTATTTTT
17913452 ATATTATTTTT
1 ATATTATTTTT
17913463 ATATT
1 ATATT
17913468 TTACATCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATATTATTTTT
Found at i:17914838 original size:18 final size:18
Alignment explanation
Indices: 17914817--17914857 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
17914807 AAGTATTTTA
17914817 TTTTAGTTTCATTATTTC
1 TTTTAGTTTCATTATTTC
17914835 TTTTAGTTTCATTATTTC
1 TTTTAGTTTCATTATTTC
17914853 TTTTA
1 TTTTA
17914858 TTATCCGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTAGTTTCATTATTTC
Found at i:17915126 original size:35 final size:35
Alignment explanation
Indices: 17915080--17915147 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
17915070 GATGCTTGGC
* *
17915080 GTGGATCGAACGGTTTAGGGTTGGCTCTGATACGT
1 GTGGATCGAACGATTTAGGGTTAGCTCTGATACGT
17915115 GTGGATCGAACGATTTAGGGTTAGCTCTGATAC
1 GTGGATCGAACGATTTAGGGTTAGCTCTGATAC
17915148 CACTTGTCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.21, C:0.15, G:0.34, T:0.31
Consensus pattern (35 bp):
GTGGATCGAACGATTTAGGGTTAGCTCTGATACGT
Found at i:17921378 original size:6 final size:6
Alignment explanation
Indices: 17921360--17921417 Score: 107
Period size: 6 Copynumber: 9.7 Consensus size: 6
17921350 CATAAACCCT
*
17921360 AAGGCA AAAGCA AAGGCA AAGGCA AAGGCA AAGGCA AAGGCA AAGGCA
1 AAGGCA AAGGCA AAGGCA AAGGCA AAGGCA AAGGCA AAGGCA AAGGCA
17921408 AAGGCA AAGG
1 AAGGCA AAGG
17921418 AATTATCTGG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.52, C:0.16, G:0.33, T:0.00
Consensus pattern (6 bp):
AAGGCA
Found at i:17921686 original size:21 final size:21
Alignment explanation
Indices: 17921660--17921774 Score: 71
Period size: 21 Copynumber: 5.5 Consensus size: 21
17921650 TATAATTTTG
17921660 ATTTTGATAATCTTTGATAAA
1 ATTTTGATAATCTTTGATAAA
* *
17921681 ATTTTGGTAAT-TTTAGATATA
1 ATTTTGATAATCTTT-GATAAA
*
17921702 ATTTT-AGTAA-CTTAT-AGTATA
1 ATTTTGA-TAATCTT-TGA-TAAA
* *
17921723 ATTTTGATAATC-ATGATACA
1 ATTTTGATAATCTTTGATAAA
* *
17921743 ATTTTGGTAAT-TTCTAATAAA
1 ATTTTGATAATCTT-TGATAAA
*
17921764 ATTTTAATAAT
1 ATTTTGATAAT
17921775 TTCTTGATGT
Statistics
Matches: 73, Mismatches: 11, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
20 18 0.25
21 52 0.71
22 3 0.04
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (21 bp):
ATTTTGATAATCTTTGATAAA
Found at i:17921767 original size:41 final size:42
Alignment explanation
Indices: 17921676--17921774 Score: 101
Period size: 41 Copynumber: 2.4 Consensus size: 42
17921666 ATAATCTTTG
* ** *
17921676 ATAAAATTTTGGTAATTTTAGATATAATTTTAGTAACTTATA
1 ATAAAATTTTGATAATCATAGATACAATTTTAGTAACTTATA
* * * * *
17921718 GTATAATTTTGATAATCAT-GATACAATTTTGGTAATTTCTA
1 ATAAAATTTTGATAATCATAGATACAATTTTAGTAACTTATA
*
17921759 ATAAAATTTTAATAAT
1 ATAAAATTTTGATAAT
17921775 TTCTTGATGT
Statistics
Matches: 45, Mismatches: 12, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
41 31 0.69
42 14 0.31
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.46
Consensus pattern (42 bp):
ATAAAATTTTGATAATCATAGATACAATTTTAGTAACTTATA
Found at i:17921791 original size:22 final size:22
Alignment explanation
Indices: 17921763--17921804 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
17921753 TTTCTAATAA
17921763 AATTTTAATAATTTCTTGATGT
1 AATTTTAATAATTTCTTGATGT
* *
17921785 AATTTTAGTAATTTTTTGAT
1 AATTTTAATAATTTCTTGAT
17921805 ACTTATGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (22 bp):
AATTTTAATAATTTCTTGATGT
Found at i:17922132 original size:22 final size:22
Alignment explanation
Indices: 17922107--17922850 Score: 223
Period size: 22 Copynumber: 33.8 Consensus size: 22
17922097 TATAATTGAG
* * *
17922107 TTATCATTAATTTATTATTATA
1 TTATCAATAATTTACTATTAAA
* *
17922129 TTATCAACAATTTACTATTAAT
1 TTATCAATAATTTACTATTAAA
* *
17922151 TTATCAATGATATACTATTAAA
1 TTATCAATAATTTACTATTAAA
* *
17922173 TTATCAATGATTTATTATTAAA
1 TTATCAATAATTTACTATTAAA
* * * **
17922195 TTAGCATTAATTTACTACTAGT
1 TTATCAATAATTTACTATTAAA
* * *
17922217 TTAT-AAGTTATTTACTACTAAG
1 TTATCAA-TAATTTACTATTAAA
* * * * *
17922239 TTATGATTGATTTATTACTAAA
1 TTATCAATAATTTACTATTAAA
* *
17922261 TTA-CTAATGATTTA-TA--AAG
1 TTATC-AATAATTTACTATTAAA
** *
17922280 TTAT-AACCGATTTACTATTAAT
1 TTATCAA-TAATTTACTATTAAA
* *
17922302 TTATCAATGATTTACTA-CAAA
1 TTATCAATAATTTACTATTAAA
*
17922323 GTTATCAATTATCAACTAATTAACTACTAAA
1 -TTATC-A--AT-AA-T--TTA-CTATTAAA
*
17922354 TTATCAATTATTTA-TATTAAA
1 TTATCAATAATTTACTATTAAA
* * * *
17922375 TTATTAGTAATTTACTACTAAC
1 TTATCAATAATTTACTATTAAA
17922397 TTATCAATAATTTA-TATCTAAA
1 TTATCAATAATTTACTAT-TAAA
* **
17922419 TTATCAATGATTTACTATTATG
1 TTATCAATAATTTACTATTAAA
* * * ** **
17922441 TTAT-TATGTAGTTACTACCATG
1 TTATCAAT-AATTTACTATTAAA
* * * *
17922463 TTATCATTGA-TTATTATTTAA
1 TTATCAATAATTTACTATTAAA
* ** * *
17922484 TTTTTGATTATTTACT-TCCAAA
1 TTATCAATAATTTACTAT-TAAA
* * **
17922506 TTAT-TATAAATTTATTACAAAA
1 TTATCAAT-AATTTACTATTAAA
* * * * * *
17922528 TTAACCATAATTCATTATCAAG
1 TTATCAATAATTTACTATTAAA
* *
17922550 CTATCATTAATTTA-TATTAAA
1 TTATCAATAATTTACTATTAAA
**
17922571 TTATCTGTAATTTACTATTAAA
1 TTATCAATAATTTACTATTAAA
* * * * *
17922593 TTATTATTGATTAACTATTAAG
1 TTATCAATAATTTACTATTAAA
* * *
17922615 TTAT-ATTAATTTATTCTTAAA
1 TTATCAATAATTTACTATTAAA
* ** *
17922636 TTTTCAACGATTAACTATTAAA
1 TTATCAATAATTTACTATTAAA
* * *
17922658 TTATCATTGATTTTCTATTAAA
1 TTATCAATAATTTACTATTAAA
** *
17922680 TTATTTATGATTTACTATTAAA
1 TTATCAATAATTTACTATTAAA
17922702 TTTATCAATTAA-TTACTATTAAA
1 -TTATCAA-TAATTTACTATTAAA
*
17922725 TTGA--AATAGA-TTATTATTAAA
1 TT-ATCAATA-ATTTACTATTAAA
* * *
17922746 TTATTACTAATTTACTATTAAG
1 TTATCAATAATTTACTATTAAA
* * *
17922768 CTATC-ATCAATTTATTATTAAG
1 TTATCAAT-AATTTACTATTAAA
* * * *
17922790 TTATCAATTATTAACTACTAAG
1 TTATCAATAATTTACTATTAAA
* * ** *
17922812 TTATCACTTATTTTTTATTAAC
1 TTATCAATAATTTACTATTAAA
* *
17922834 CTATCATTAATTTACTA
1 TTATCAATAATTTACTA
17922851 ATATGGTATT
Statistics
Matches: 533, Mismatches: 149, Indels: 80
0.70 0.20 0.10
Matches are distributed among these distances:
18 2 0.00
19 11 0.02
20 5 0.01
21 87 0.16
22 371 0.70
23 32 0.06
24 2 0.00
25 3 0.01
26 2 0.00
27 3 0.01
29 4 0.01
30 8 0.02
31 3 0.01
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.47
Consensus pattern (22 bp):
TTATCAATAATTTACTATTAAA
Found at i:17922358 original size:30 final size:29
Alignment explanation
Indices: 17922302--17922364 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
17922292 TACTATTAAT
* *
17922302 TTATCAATGATTTACTACAAAGTTATCAA
1 TTATCAATAATTAACTACAAAGTTATCAA
17922331 TTATCAACTAATTAACTACTAAA-TTATCAA
1 TTATCAA-TAATTAACTAC-AAAGTTATCAA
17922361 TTAT
1 TTAT
17922365 TTATATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 7 0.23
30 20 0.67
31 3 0.10
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (29 bp):
TTATCAATAATTAACTACAAAGTTATCAA
Found at i:17922392 original size:43 final size:44
Alignment explanation
Indices: 17922339--17922422 Score: 134
Period size: 43 Copynumber: 1.9 Consensus size: 44
17922329 AATTATCAAC
*
17922339 TAATTAACTACTAAATTATCAATTATTTATAT-TAAATTATTAG
1 TAATTAACTACTAAATTATCAATAATTTATATCTAAATTATTAG
* *
17922382 TAATTTACTACTAACTTATCAATAATTTATATCTAAATTAT
1 TAATTAACTACTAAATTATCAATAATTTATATCTAAATTAT
17922423 CAATGATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
43 29 0.78
44 8 0.22
ACGTcount: A:0.43, C:0.10, G:0.01, T:0.46
Consensus pattern (44 bp):
TAATTAACTACTAAATTATCAATAATTTATATCTAAATTATTAG
Found at i:17925357 original size:114 final size:114
Alignment explanation
Indices: 17925157--17925385 Score: 327
Period size: 114 Copynumber: 2.0 Consensus size: 114
17925147 TTGATTTACT
* * **
17925157 ACTAAATTAGCATAAAAAATTACTAACAGTATTTTAATCAATCAATTTTTAATATTTTTTGGAAT
1 ACTAAATTAGCATAAAAAATTACTAACAATATTTTAATCAATCAACTTTTAATATTTTTTAAAAT
* * *
17925222 TAAATTTATTAAGTGTTTAGTCAATAACTTTTAGCACTTTTTTAATCTA
66 TAAATTTATTAAATATTTAGTCAATAACTTTTAACACTTTTTTAATCTA
* *
17925271 ACTAAATTAGCATAAAAAATTACTAATAATATTTTAATTAATC-ACTTTTAATA-TTTTTAAAAT
1 ACTAAATTAGCATAAAAAATTACTAACAATATTTTAATCAATCAACTTTTAATATTTTTTAAAAT
* *
17925334 TAAATTTTTATTAAATATTTAGTCAATCACTTTTAACACTTTTTTAGTCTA
66 TAAA--TTTATTAAATATTTAGTCAATAACTTTTAACACTTTTTTAATCTA
17925385 A
1 A
17925386 TTATAAAAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
112 12 0.12
113 9 0.09
114 81 0.79
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (114 bp):
ACTAAATTAGCATAAAAAATTACTAACAATATTTTAATCAATCAACTTTTAATATTTTTTAAAAT
TAAATTTATTAAATATTTAGTCAATAACTTTTAACACTTTTTTAATCTA
Found at i:17929175 original size:4 final size:4
Alignment explanation
Indices: 17929161--17929203 Score: 70
Period size: 4 Copynumber: 10.8 Consensus size: 4
17929151 ATTTGATTGT
17929161 TTAA TTAAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA -TAA TTA
1 TTAA TT-AA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
17929204 TCATTATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 3 0.08
4 30 0.81
5 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (4 bp):
TTAA
Found at i:17942421 original size:17 final size:17
Alignment explanation
Indices: 17942395--17942427 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17942385 TTACTCTGAC
*
17942395 TTTTTTCTTTTTTTTTA
1 TTTTTGCTTTTTTTTTA
17942412 TTTTTGCTTTTTTTTT
1 TTTTTGCTTTTTTTTT
17942428 TTTAGCTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.06, G:0.03, T:0.88
Consensus pattern (17 bp):
TTTTTGCTTTTTTTTTA
Found at i:17942422 original size:15 final size:15
Alignment explanation
Indices: 17942403--17942436 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
17942393 ACTTTTTTCT
*
17942403 TTTTTTTTATTTTTGC
1 TTTTTTTT-TTTTAGC
17942419 TTTTTTTTTTTTAGC
1 TTTTTTTTTTTTAGC
17942434 TTT
1 TTT
17942437 CTCTAGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTTTTAGC
Found at i:17949165 original size:15 final size:15
Alignment explanation
Indices: 17949140--17949181 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
17949130 CGTTGGATAA
17949140 AATTTTT-TTATTAT
1 AATTTTTATTATTAT
* *
17949154 ATTTTTTATTATTTT
1 AATTTTTATTATTAT
*
17949169 AATTATTATTATT
1 AATTTTTATTATT
17949182 TTATAAGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
AATTTTTATTATTAT
Found at i:17950404 original size:21 final size:20
Alignment explanation
Indices: 17950380--17950419 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
17950370 GTAATTAATT
17950380 ATAAATTAGTATTACTAAAAA
1 ATAAATTAGTA-TACTAAAAA
* *
17950401 ATAACTTATTATACTAAAA
1 ATAAATTAGTATACTAAAA
17950420 TCTAGTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (20 bp):
ATAAATTAGTATACTAAAAA
Found at i:17950599 original size:17 final size:17
Alignment explanation
Indices: 17950563--17950601 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
17950553 TGGTAATATA
**
17950563 ATTATCAAAATAATTTT
1 ATTATCAAAATAATCAT
*
17950580 ATTATCAAGATAATCAT
1 ATTATCAAAATAATCAT
17950597 ATTAT
1 ATTAT
17950602 TTGTGATTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (17 bp):
ATTATCAAAATAATCAT
Found at i:17950788 original size:17 final size:16
Alignment explanation
Indices: 17950759--17950790 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
17950749 TTTAATGTTG
17950759 TTTAAAAATAATAATT
1 TTTAAAAATAATAATT
17950775 TTTAAAATATAATAAT
1 TTTAAAA-ATAATAAT
17950791 GTTTGTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTAAAAATAATAATT
Found at i:17951242 original size:31 final size:31
Alignment explanation
Indices: 17951204--17951265 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
17951194 AAAGACGGAG
17951204 TATATTATATATAAAACATTAAAAAAATACA
1 TATATTATATATAAAACATTAAAAAAATACA
17951235 TATATTATATATAAAACATTAAAAAAATACA
1 TATATTATATATAAAACATTAAAAAAATACA
17951266 CAAATAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (31 bp):
TATATTATATATAAAACATTAAAAAAATACA
Found at i:17951300 original size:12 final size:12
Alignment explanation
Indices: 17951280--17951310 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
17951270 TAAAAGATTA
17951280 TGAAAATTAATT
1 TGAAAATTAATT
*
17951292 TGAACATTAATT
1 TGAAAATTAATT
17951304 TGAAAAT
1 TGAAAAT
17951311 ATAAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (12 bp):
TGAAAATTAATT
Found at i:17951564 original size:2 final size:2
Alignment explanation
Indices: 17951551--17951593 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
17951541 AATGATTATT
*
17951551 TA TA TT 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 TA TA
17951593 T
1 T
17951594 TGAAGCCCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:17952988 original size:16 final size:16
Alignment explanation
Indices: 17952964--17952998 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
17952954 ATATAATTTT
*
17952964 TTATTTTATATTTAAA
1 TTATATTATATTTAAA
*
17952980 TTATATTATATTTCAA
1 TTATATTATATTTAAA
17952996 TTA
1 TTA
17952999 AAATTTCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATATTATATTTAAA
Found at i:17953580 original size:15 final size:18
Alignment explanation
Indices: 17953560--17953595 Score: 51
Period size: 15 Copynumber: 2.2 Consensus size: 18
17953550 GTAATTTATG
17953560 TATTCC-TA-TAAAAT-C
1 TATTCCGTACTAAAATAC
17953575 TATTCCGTACTAAAATAC
1 TATTCCGTACTAAAATAC
17953593 TAT
1 TAT
17953596 ATATAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.33
16 2 0.11
17 6 0.33
18 4 0.22
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (18 bp):
TATTCCGTACTAAAATAC
Found at i:17962996 original size:2 final size:2
Alignment explanation
Indices: 17962989--17963018 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17962979 ACAACTCAAA
17962989 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
17963019 GAAGCTTGAT
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17965845 original size:29 final size:31
Alignment explanation
Indices: 17965778--17965846 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 31
17965768 AATATTTTTA
17965778 TATTTTTTTAAAATAATATATTTAATAAATT
1 TATTTTTTTAAAATAATATATTTAATAAATT
** *
17965809 TA-AATTTTAAATATCA-ATATTT-AT-AATT
1 TATTTTTTTAAA-ATAATATATTTAATAAATT
17965837 TATTTTTTTA
1 TATTTTTTTA
17965847 TTTTTAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
28 6 0.19
29 7 0.23
30 13 0.42
31 5 0.16
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (31 bp):
TATTTTTTTAAAATAATATATTTAATAAATT
Found at i:17969640 original size:21 final size:21
Alignment explanation
Indices: 17969616--17969662 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
17969606 AAATAGATTT
17969616 TGAAACATTTCAAAATAGGTA
1 TGAAACATTTCAAAATAGGTA
**
17969637 TGAAATTTTTCAAAATAGGTA
1 TGAAACATTTCAAAATAGGTA
17969658 TGAAA
1 TGAAA
17969663 TTTTAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (21 bp):
TGAAACATTTCAAAATAGGTA
Found at i:17969663 original size:21 final size:21
Alignment explanation
Indices: 17969623--17969666 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
17969613 TTTTGAAACA
17969623 TTTCAAAATAGGTATGAAATT
1 TTTCAAAATAGGTATGAAATT
17969644 TTTCAAAATAGGTATGAAATT
1 TTTCAAAATAGGTATGAAATT
17969665 TT
1 TT
17969667 AGAAAAAGAA
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:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (21 bp):
TTTCAAAATAGGTATGAAATT
Found at i:17969672 original size:21 final size:21
Alignment explanation
Indices: 17969626--17969672 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
17969616 TGAAACATTT
*
17969626 CAAAATAGGTATGAAATTTTT
1 CAAAATAGGTATGAAATTTTA
17969647 CAAAATAGGTATGAAATTTTA
1 CAAAATAGGTATGAAATTTTA
*
17969668 GAAAA
1 CAAAA
17969673 AGAAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.32
Consensus pattern (21 bp):
CAAAATAGGTATGAAATTTTA
Found at i:17970630 original size:16 final size:16
Alignment explanation
Indices: 17970611--17970647 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
17970601 ATTTGACCTT
*
17970611 AATGCTTGTGGTTTAA
1 AATGCTTGTAGTTTAA
17970627 AATGCTTGTAGTTTAA
1 AATGCTTGTAGTTTAA
17970643 AATGC
1 AATGC
17970648 CTGAATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.41
Consensus pattern (16 bp):
AATGCTTGTAGTTTAA
Found at i:17976942 original size:101 final size:100
Alignment explanation
Indices: 17976755--17976946 Score: 305
Period size: 101 Copynumber: 1.9 Consensus size: 100
17976745 GCTTTACATA
* *
17976755 CATATTATATAGTCAAATTATATATCTTAGATCTTTTAAAATAAAAATAAATGCATTTACTCATA
1 CATATTATATAGTCAAATTATATATCTCAAATCTTTTAAAATAAAAATAAATGCATTTACTCATA
* * *
17976820 GATAAGGTTTGTACCTGGTTGAATGCTTTACTTCG
66 GATAAGATTTATACCTAGTTGAATGCTTTACTTCG
*
17976855 CATATTATATAGTCAAAATTATATATCTCAAATCTTTTAAAATAAAAATAAATGCATTTACTCCT
1 CATATTATATAGTC-AAATTATATATCTCAAATCTTTTAAAATAAAAATAAATGCATTTACTCAT
17976920 AGATAAGATTTATAACC-AGTTGAATGC
65 AGATAAGATTTAT-ACCTAGTTGAATGC
17976947 AATACCAATT
Statistics
Matches: 84, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
100 14 0.17
101 67 0.80
102 3 0.04
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (100 bp):
CATATTATATAGTCAAATTATATATCTCAAATCTTTTAAAATAAAAATAAATGCATTTACTCATA
GATAAGATTTATACCTAGTTGAATGCTTTACTTCG
Found at i:17977665 original size:6 final size:7
Alignment explanation
Indices: 17977640--17977664 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17977630 TAAGGATGAA
17977640 AAAAATT
1 AAAAATT
17977647 AAAAATT
1 AAAAATT
17977654 AAAAATT
1 AAAAATT
17977661 AAAA
1 AAAA
17977665 TACATTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAAATT
Found at i:17979022 original size:11 final size:11
Alignment explanation
Indices: 17979006--17979032 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
17978996 TGAGTAATAG
17979006 AAATATAAAAT
1 AAATATAAAAT
17979017 AAATATAAAAT
1 AAATATAAAAT
17979028 AAATA
1 AAATA
17979033 ATTAAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AAATATAAAAT
Found at i:17983212 original size:19 final size:19
Alignment explanation
Indices: 17983188--17983250 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
17983178 AAATATCAAC
17983188 AATCATGCAATAAATATTA
1 AATCATGCAATAAATATTA
*
17983207 AATCATACAATGCAAA-AGTT-
1 AATCATGCAAT--AAATA-TTA
*
17983227 -ATCATGCAATAAATATAA
1 AATCATGCAATAAATATTA
17983245 AATCAT
1 AATCAT
17983251 ATCATGTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
17 4 0.11
18 1 0.03
19 24 0.69
20 1 0.03
21 5 0.14
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (19 bp):
AATCATGCAATAAATATTA
Found at i:17983240 original size:38 final size:36
Alignment explanation
Indices: 17983188--17983350 Score: 165
Period size: 34 Copynumber: 4.5 Consensus size: 36
17983178 AAATATCAAC
* *
17983188 AATCATGCAATAAATATTAAATCATACAATGCAA-A
1 AATCATGCAATAAATATAAAATCATACCATGCAATA
* *
17983223 AGTTATCATGCAATAAATATAAAATCATATCATGTAATA
1 A---ATCATGCAATAAATATAAAATCATACCATGCAATA
* *
17983262 AATTATGCAAT-AA-ATAAAATCATACCATACAATA
1 AATCATGCAATAAATATAAAATCATACCATGCAATA
* * *
17983296 AATAATGCAAT-AATATAAAATCATACCATGTAAAA
1 AATCATGCAATAAATATAAAATCATACCATGCAATA
17983331 ATTATCATGCAAT-AATATAA
1 A--ATCATGCAATAAATATAA
17983351 TACCATAAAA
Statistics
Matches: 108, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
34 30 0.28
35 22 0.20
36 9 0.08
37 16 0.15
38 29 0.27
39 2 0.02
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (36 bp):
AATCATGCAATAAATATAAAATCATACCATGCAATA
Found at i:17983281 original size:17 final size:17
Alignment explanation
Indices: 17983261--17983316 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
17983251 ATCATGTAAT
*
17983261 AAATTATGCAATAAATA
1 AAATAATGCAATAAATA
* * *
17983278 AAATCATACCATACAAT-
1 AAATAATGCAATA-AATA
17983295 AAATAATGCAATAATATA
1 AAATAATGCAATAA-ATA
17983313 AAAT
1 AAAT
17983317 CATACCATGT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
16 1 0.03
17 22 0.73
18 7 0.23
ACGTcount: A:0.59, C:0.11, G:0.04, T:0.27
Consensus pattern (17 bp):
AAATAATGCAATAAATA
Found at i:17983428 original size:24 final size:24
Alignment explanation
Indices: 17983398--17983464 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
17983388 GCAATCAAAT
*
17983398 ATAATCACATAAATAAATATATTA
1 ATAATCACACAAATAAATATATTA
** *
17983422 ATAATCATGCAATTAAATATATTA
1 ATAATCACACAAATAAATATATTA
* *
17983446 ATAATCATACAATTAAATA
1 ATAATCACACAAATAAATA
17983465 AATCATGCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.55, C:0.09, G:0.01, T:0.34
Consensus pattern (24 bp):
ATAATCACACAAATAAATATATTA
Found at i:17983439 original size:28 final size:27
Alignment explanation
Indices: 17983406--17983467 Score: 85
Period size: 24 Copynumber: 2.4 Consensus size: 27
17983396 ATATAATCAC
*
17983406 ATAAATAAATATATTAATAATCATGCA
1 ATAAATAAATATATTAATAATCATACA
17983433 AT---TAAATATATTAATAATCATACA
1 ATAAATAAATATATTAATAATCATACA
17983457 ATTAAATAAAT
1 A-TAAATAAAT
17983468 CATGCAAGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
24 22 0.73
25 1 0.03
27 2 0.07
28 5 0.17
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.35
Consensus pattern (27 bp):
ATAAATAAATATATTAATAATCATACA
Found at i:17984152 original size:21 final size:22
Alignment explanation
Indices: 17984122--17984165 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
17984112 CTTCTTTTTT
17984122 TTTTTATTTTACCAATTGACTA
1 TTTTTATTTTACCAATTGACTA
17984144 TTTTT-TTTTACCAATTGACTA
1 TTTTTATTTTACCAATTGACTA
17984165 T
1 T
17984166 GACTCTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.25, C:0.14, G:0.05, T:0.57
Consensus pattern (22 bp):
TTTTTATTTTACCAATTGACTA
Found at i:17986580 original size:6 final size:6
Alignment explanation
Indices: 17986569--17986611 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
17986559 AAAGTATTAA
* * *
17986569 AATTTT AATTTT AGTTTT AGTTTT AATTTT AATTTT GATTTT A
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT A
17986612 GTGTTTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (6 bp):
AATTTT
Found at i:17986600 original size:24 final size:25
Alignment explanation
Indices: 17986569--17986622 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
17986559 AAAGTATTAA
17986569 AATTTTAATTTT-AGTTTTA-GTTTT
1 AATTTTAATTTTGA-TTTTAGGTTTT
17986593 AATTTTAATTTTGATTTTAGTGTTTT
1 AATTTTAATTTTGATTTTAG-GTTTT
17986619 AATT
1 AATT
17986623 AGTAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 17 0.63
25 1 0.04
26 9 0.33
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (25 bp):
AATTTTAATTTTGATTTTAGGTTTT
Found at i:17990476 original size:13 final size:13
Alignment explanation
Indices: 17990460--17990484 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17990450 GTGCAAATAA
17990460 AAAAAAAAAAAGT
1 AAAAAAAAAAAGT
17990473 AAAAAAAAAAAG
1 AAAAAAAAAAAG
17990485 AAGACTAAAA
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:0.88, C:0.00, G:0.08, T:0.04
Consensus pattern (13 bp):
AAAAAAAAAAAGT
Found at i:17991560 original size:22 final size:22
Alignment explanation
Indices: 17991529--17991577 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
17991519 CTCTAATATT
* *
17991529 TTTTTAATGTAAATTTTTAAAA
1 TTTTTAATGTAAATCTCTAAAA
* *
17991551 TTTTTGATGTGAATCTCTAAAA
1 TTTTTAATGTAAATCTCTAAAA
17991573 TTTTT
1 TTTTT
17991578 TGAATTTGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.55
Consensus pattern (22 bp):
TTTTTAATGTAAATCTCTAAAA
Found at i:17991598 original size:46 final size:47
Alignment explanation
Indices: 17991501--17991627 Score: 143
Period size: 46 Copynumber: 2.8 Consensus size: 47
17991491 TTTGATTTTT
* * * *
17991501 GAAATTTTAGGTGTGAATCTCTAATATTTTTTTAATGTAAATTTTTA
1 GAAATTTTAGATGTGAATCTCTAAAATTTTTTGAATGTAAATTATTA
* * *
17991548 -AAATTTTTGATGTGAATCTCTAAAATTTTTTGAATTTGAA-TATTA
1 GAAATTTTAGATGTGAATCTCTAAAATTTTTTGAATGTAAATTATTA
* * *
17991593 GAAATTTTGGATATGAATC-CTTAAATTTTTTGAAT
1 GAAATTTTAGATGTGAATCTCTAAAATTTTTTGAAT
17991628 AAAAATCTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
45 19 0.28
46 50 0.72
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.49
Consensus pattern (47 bp):
GAAATTTTAGATGTGAATCTCTAAAATTTTTTGAATGTAAATTATTA
Found at i:17991622 original size:22 final size:22
Alignment explanation
Indices: 17991548--17991622 Score: 55
Period size: 22 Copynumber: 3.4 Consensus size: 22
17991538 TAAATTTTTA
* *
17991548 AAATTTTT-GATGTGAATCTCTA
1 AAATTTTTGGATATGAATC-CTT
* * *
17991570 AAATTTTTTGAATTTGAAT-ATT
1 AAA-TTTTTGGATATGAATCCTT
*
17991592 AGAAATTTTGGATATGAATCCTT
1 A-AATTTTTGGATATGAATCCTT
17991615 AAATTTTT
1 AAATTTTT
17991623 TGAATAAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
22 23 0.57
23 10 0.25
24 7 0.17
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.48
Consensus pattern (22 bp):
AAATTTTTGGATATGAATCCTT
Found at i:17992008 original size:35 final size:35
Alignment explanation
Indices: 17991969--17992036 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
17991959 AAATCTTCCA
*
17991969 TTTTTACGAAACTGAAACTCTTACGAATTTGAAAG
1 TTTTTACGAAACTAAAACTCTTACGAATTTGAAAG
* ** * *
17992004 TTTTTATGAGTCTAAAATTCTTATGAATTTGAA
1 TTTTTACGAAACTAAAACTCTTACGAATTTGAA
17992037 GTTCTTGTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.41
Consensus pattern (35 bp):
TTTTTACGAAACTAAAACTCTTACGAATTTGAAAG
Found at i:17992041 original size:17 final size:17
Alignment explanation
Indices: 17991987--17992053 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 17
17991977 AAACTGAAAC
*
17991987 TCTTACGAATTTGAAAGT
1 TCTTATGAATTTG-AAGT
* * * * *
17992005 TTTTATGAGTCTAAAAT
1 TCTTATGAATTTGAAGT
17992022 TCTTATGAATTTGAAGT
1 TCTTATGAATTTGAAGT
* *
17992039 TCTTGTGAATATGAA
1 TCTTATGAATTTGAA
17992054 ATTATTGAAA
Statistics
Matches: 36, Mismatches: 13, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
17 28 0.78
18 8 0.22
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.43
Consensus pattern (17 bp):
TCTTATGAATTTGAAGT
Found at i:17992086 original size:17 final size:17
Alignment explanation
Indices: 17992007--17992105 Score: 65
Period size: 17 Copynumber: 5.8 Consensus size: 17
17991997 TTGAAAGTTT
*
17992007 TTATGAGTCTAAAATTC
1 TTATGAATCTAAAATTC
* * *
17992024 TTATGAATTTGAAGTTC
1 TTATGAATCTAAAATTC
* * * *
17992041 TTGTGAATATGAAATTA
1 TTATGAATCTAAAATTC
* *
17992058 TTGA-AAACCTAAAATTC
1 TT-ATGAATCTAAAATTC
17992075 TTATGAATCTAAAAATTC
1 TTATGAATCT-AAAATTC
* *
17992093 TTGTGAATATAAA
1 TTATGAATCTAAA
17992106 CTCTTGTAAA
Statistics
Matches: 61, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
16 1 0.02
17 45 0.74
18 15 0.25
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.39
Consensus pattern (17 bp):
TTATGAATCTAAAATTC
Found at i:17992091 original size:18 final size:18
Alignment explanation
Indices: 17992068--17992105 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17992058 TTGAAAACCT
*
17992068 AAAATTCTTATGAATCTA
1 AAAATTCTTATGAATATA
*
17992086 AAAATTCTTGTGAATATA
1 AAAATTCTTATGAATATA
17992104 AA
1 AA
17992106 CTCTTGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (18 bp):
AAAATTCTTATGAATATA
Found at i:17992185 original size:33 final size:32
Alignment explanation
Indices: 17992119--17992185 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
17992109 TTGTAAATCT
* *
17992119 TTGAATTCTTGTAAAATTAAAATTTTTATGAA
1 TTGAATTCTTGTAAAATTAAAACTTTTAGGAA
*
17992151 TTGAATTCTTGCT-AATTTGAAAACTTTTAGGAA
1 TTGAATTCTTG-TAAAATT-AAAACTTTTAGGAA
17992184 TT
1 TT
17992186 TAAAACATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46
Consensus pattern (32 bp):
TTGAATTCTTGTAAAATTAAAACTTTTAGGAA
Found at i:17992274 original size:35 final size:35
Alignment explanation
Indices: 17992188--17992311 Score: 182
Period size: 35 Copynumber: 3.6 Consensus size: 35
17992178 TAGGAATTTA
* *
17992188 AAACATTTGTGAATCTGAAA-CTTC-TGCAAAACTTG
1 AAACCTTTGTGAATCTGAAATCTCCAT--AAAACTTG
*
17992223 GAACC-TTGTGAATCTGAAATCTCCATAAAACTTG
1 AAACCTTTGTGAATCTGAAATCTCCATAAAACTTG
17992257 AAACCTTTGTGAATCTGAAATCTCCATAAAACTTG
1 AAACCTTTGTGAATCTGAAATCTCCATAAAACTTG
17992292 AAACCTTTGTGAATCTGAAA
1 AAACCTTTGTGAATCTGAAA
17992312 CCATTGCGAA
Statistics
Matches: 82, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
34 26 0.32
35 55 0.67
36 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.31
Consensus pattern (35 bp):
AAACCTTTGTGAATCTGAAATCTCCATAAAACTTG
Found at i:17992312 original size:17 final size:17
Alignment explanation
Indices: 17992255--17992313 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
17992245 CCATAAAACT
17992255 TGAAACCTTTGTGAATC
1 TGAAACCTTTGTGAATC
* *** * *
17992272 TGAAATCTCCATAAAAC
1 TGAAACCTTTGTGAATC
17992289 TTGAAACCTTTGTGAATC
1 -TGAAACCTTTGTGAATC
17992307 TGAAACC
1 TGAAACC
17992314 ATTGCGAAAC
Statistics
Matches: 29, Mismatches: 12, Indels: 2
0.67 0.28 0.05
Matches are distributed among these distances:
17 18 0.62
18 11 0.38
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.31
Consensus pattern (17 bp):
TGAAACCTTTGTGAATC
Found at i:17992351 original size:27 final size:28
Alignment explanation
Indices: 17992319--17992372 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
17992309 AAACCATTGC
*
17992319 GAAACTTGGAATTCTTACAAA-CTTTAA
1 GAAACTTAGAATTCTTACAAACCTTTAA
17992346 GAAACTTAGAATTCTTACAAACCTTTA
1 GAAACTTAGAATTCTTACAAACCTTTA
17992373 CGAATATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (28 bp):
GAAACTTAGAATTCTTACAAACCTTTAA
Found at i:17992822 original size:5 final size:6
Alignment explanation
Indices: 17992807--17992852 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
17992797 TTGGTTTGAG
* *
17992807 TTTTAG TTTTAA -TTTAA TTTTAA TTTTAA TTTTAA TTTTGA TTTTA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTA
17992853 GTGTTTTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
5 5 0.14
6 31 0.86
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:17992827 original size:11 final size:11
Alignment explanation
Indices: 17992808--17992844 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
17992798 TGGTTTGAGT
*
17992808 TTTAGTTTTAA
1 TTTAATTTTAA
17992819 TTTAATTTTAA
1 TTTAATTTTAA
17992830 TTTTAATTTTAA
1 -TTTAATTTTAA
17992842 TTT
1 TTT
17992845 TGATTTTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (11 bp):
TTTAATTTTAA
Found at i:17992839 original size:29 final size:29
Alignment explanation
Indices: 17992788--17992850 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
17992778 AAAGTCTGAC
** * *
17992788 AATTTAATTTTGGTTTGAGTTTTAGTTTT
1 AATTTAATTTTAATTTGAATTTTAATTTT
*
17992817 AATTTAATTTTAATTTTAATTTTAATTTT
1 AATTTAATTTTAATTTGAATTTTAATTTT
*
17992846 GATTT
1 AATTT
17992851 TAGTGTTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (29 bp):
AATTTAATTTTAATTTGAATTTTAATTTT
Found at i:18009316 original size:2 final size:2
Alignment explanation
Indices: 18009309--18009352 Score: 70
Period size: 2 Copynumber: 21.0 Consensus size: 2
18009299 AAGAGATTTA
18009309 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AGT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T A-T AT AT AT
18009353 CAAAGTAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
2 36 0.90
3 4 0.10
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18017128 original size:12 final size:12
Alignment explanation
Indices: 18017095--18017128 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
18017085 AAGAAAAGCT
18017095 AAATATTTTTAA
1 AAATATTTTTAA
*
18017107 AAGATTTTTTTAA
1 AA-ATATTTTTAA
18017120 AAATATTTT
1 AAATATTTT
18017129 AGCCTTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (12 bp):
AAATATTTTTAA
Found at i:18019379 original size:15 final size:16
Alignment explanation
Indices: 18019359--18019390 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
18019349 GAGACAGCCT
18019359 AAAAAAAAGACA-AAA
1 AAAAAAAAGACATAAA
18019374 AAAAAAAAGACATAAA
1 AAAAAAAAGACATAAA
18019390 A
1 A
18019391 CGTAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.84, C:0.06, G:0.06, T:0.03
Consensus pattern (16 bp):
AAAAAAAAGACATAAA
Found at i:18021974 original size:2 final size:2
Alignment explanation
Indices: 18021967--18021999 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18021957 TCTCAATTTA
18021967 AT AT AT AT 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 AT AT AT AT A
18022000 ATGGGTATCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18023217 original size:23 final size:24
Alignment explanation
Indices: 18023191--18023247 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 24
18023181 AAATTTTGAG
18023191 TTTTAAAATTTTCAA-AATATATT-
1 TTTTAAAATTTT-AATAATATATTA
18023214 TTTTAAAATTTTAATTGAATATATTA
1 TTTTAAAATTTTAA-T-AATATATTA
18023240 TTTTAAAA
1 TTTTAAAA
18023248 ATAAAAGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 2 0.07
23 12 0.40
25 8 0.27
26 8 0.27
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTTAAAATTTTAATAATATATTA
Done.