Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168037.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_29, 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: 14313602
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 50000 characters in sequence are not A, C, G, or T
File 65 of 74
Found at i:12848998 original size:20 final size:21
Alignment explanation
Indices: 12848951--12849001 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
12848941 TTCCAACTTA
**
12848951 AAATTCAAAGGTTCACAATTT
1 AAATTCAAAAATTCACAATTT
*
12848972 GAATTCAAAAATTCACAA-TT
1 AAATTCAAAAATTCACAATTT
12848992 AAATTCAAAA
1 AAATTCAAAA
12849002 GTTTGCAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (21 bp):
AAATTCAAAAATTCACAATTT
Found at i:12849099 original size:19 final size:18
Alignment explanation
Indices: 12849071--12849106 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12849061 ATCCAAAAAT
12849071 TCACAAGATTTCAAAGAC
1 TCACAAGATTTCAAAGAC
*
12849089 TCACAAAGATTTGAAAGA
1 TCAC-AAGATTTCAAAGA
12849107 GATTTAAAGG
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:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (18 bp):
TCACAAGATTTCAAAGAC
Found at i:12849115 original size:19 final size:19
Alignment explanation
Indices: 12849093--12849295 Score: 62
Period size: 19 Copynumber: 10.9 Consensus size: 19
12849083 AAAGACTCAC
12849093 AAAGATTTG-AAAGAGATTT
1 AAAGATTTGTAAA-AGATTT
*
12849112 AAAGGTTTGTAAAAGATTT
1 AAAGATTTGTAAAAGATTT
* *** *
12849131 CAA-ATTCACAAAA-ATTC
1 AAAGATTTGTAAAAGATTT
* * * *
12849148 AAACATTCGTAAAAAATTC
1 AAAGATTTGTAAAAGATTT
** **
12849167 AAAGGCTTACAAAAGATTT
1 AAAGATTTGTAAAAGATTT
12849186 AAAGATTCT-TAAAAGA-TT
1 AAAGATT-TGTAAAAGATTT
* * *** *
12849204 CAATATTCACAAAAGATTC
1 AAAGATTTGTAAAAGATTT
*
12849223 AAA-A-TT-TACCAAGATTT
1 AAAGATTTGTA-AAAGATTT
**
12849240 AAAGATTTGTAAAAGATAC
1 AAAGATTTGTAAAAGATTT
* * * *
12849259 AAAGGTTGGCAAAAGATTC
1 AAAGATTTGTAAAAGATTT
* *
12849278 AAAAATTCGTAAAAGATT
1 AAAGATTTGTAAAAGATT
12849296 CATAATTCAC
Statistics
Matches: 132, Mismatches: 42, Indels: 20
0.68 0.22 0.10
Matches are distributed among these distances:
16 1 0.01
17 15 0.11
18 29 0.22
19 81 0.61
20 6 0.05
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.29
Consensus pattern (19 bp):
AAAGATTTGTAAAAGATTT
Found at i:12849155 original size:18 final size:19
Alignment explanation
Indices: 12849122--12849349 Score: 91
Period size: 19 Copynumber: 12.4 Consensus size: 19
12849112 AAAGGTTTGT
12849122 AAAAGATTTC-AA-ATTCAC
1 AAAAGA-TTCAAACATTCAC
**
12849140 AAAA-ATTCAAACATTCGT
1 AAAAGATTCAAACATTCAC
*
12849158 AAAAAATTCAAAGGC-TT-AC
1 AAAAGATTCAAA--CATTCAC
* * **
12849177 AAAAGATTTAAAGATTCTT
1 AAAAGATTCAAACATTCAC
*
12849196 AAAAGATTC-AATATTCAC
1 AAAAGATTCAAACATTCAC
*
12849214 AAAAGATTCAAA-ATTTAC
1 AAAAGATTCAAACATTCAC
* * * ***
12849232 -CAAGATTTAAAGATTTGT
1 AAAAGATTCAAACATTCAC
* ** **
12849250 AAAAGATACAAAGGTTGGC
1 AAAAGATTCAAACATTCAC
* **
12849269 AAAAGATTCAAAAATTCGT
1 AAAAGATTCAAACATTCAC
*
12849288 AAAAGATTCATA-ATTCAC
1 AAAAGATTCAAACATTCAC
* *
12849306 AAAAGATTC-AAGATTTAC
1 AAAAGATTCAAACATTCAC
* * *
12849324 -AAATATTCAAAGATTCGC
1 AAAAGATTCAAACATTCAC
12849342 AAAAGATT
1 AAAAGATT
12849350 TAAGATTCGC
Statistics
Matches: 159, Mismatches: 38, Indels: 25
0.72 0.17 0.11
Matches are distributed among these distances:
16 3 0.02
17 20 0.13
18 63 0.40
19 70 0.44
20 2 0.01
21 1 0.01
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.28
Consensus pattern (19 bp):
AAAAGATTCAAACATTCAC
Found at i:12849205 original size:38 final size:36
Alignment explanation
Indices: 12849106--12849221 Score: 112
Period size: 38 Copynumber: 3.1 Consensus size: 36
12849096 GATTTGAAAG
*
12849106 AGATTTAAAGGTT-TGTAAAAGATTTCAAATTCACAAA
1 AGATTTAAAGATTCT-TAAAAGA-TTCAAATTCACAAA
* * * *
12849143 A-ATTCAAACATTCGTAAAAAATTCAAAGGCTT-ACAAA
1 AGATTTAAAGATTCTTAAAAGATTCAAA---TTCACAAA
12849180 AGATTTAAAGATTCTTAAAAGATTCAATATTCACAAA
1 AGATTTAAAGATTCTTAAAAGATTCAA-ATTCACAAA
12849217 AGATT
1 AGATT
12849222 CAAAATTTAC
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
35 6 0.10
36 16 0.25
37 17 0.27
38 23 0.37
39 1 0.02
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.30
Consensus pattern (36 bp):
AGATTTAAAGATTCTTAAAAGATTCAAATTCACAAA
Found at i:12849346 original size:92 final size:91
Alignment explanation
Indices: 12849122--12849348 Score: 269
Period size: 92 Copynumber: 2.5 Consensus size: 91
12849112 AAAGGTTTGT
* * * * *
12849122 AAAAGATTTCAAATTCACAAAAATTCAAACATTCGTAAAAAATTCAAAGGCTTACAAAAGATTTA
1 AAAAGA-TTCAAATTTACAAAAATTCAAAGATTCGTAAAAGATACAAAGGCTTACAAAAGATTCA
* *
12849187 AAGATTCTTAAAAGATTCAATATTCAC
65 AAAATTCGTAAAAGATTCAATATTCAC
* * * * *
12849214 AAAAGATTCAAAATTTACCAAGATTTAAAGATTTGTAAAAGATACAAAGG-TTGGCAAAAGATTC
1 AAAAGATTC-AAATTTACAAAAATTCAAAGATTCGTAAAAGATACAAAGGCTT-ACAAAAGATTC
12849278 AAAAATTCGTAAAAGATTC-ATAATTCAC
64 AAAAATTCGTAAAAGATTCAAT-ATTCAC
* *
12849306 AAAAGATTCAAGATTTACAAATATTCAAAGATTCGCAAAAGAT
1 AAAAGATTCAA-ATTTACAAAAATTCAAAGATTCGTAAAAGAT
12849349 TTAAGATTCG
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
91 9 0.08
92 105 0.92
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.27
Consensus pattern (91 bp):
AAAAGATTCAAATTTACAAAAATTCAAAGATTCGTAAAAGATACAAAGGCTTACAAAAGATTCAA
AAATTCGTAAAAGATTCAATATTCAC
Found at i:12849354 original size:18 final size:18
Alignment explanation
Indices: 12849176--12849361 Score: 99
Period size: 18 Copynumber: 10.2 Consensus size: 18
12849166 CAAAGGCTTA
* *
12849176 CAAAAGATTTAAAGATTCT
1 CAAAAGA-TTCAAGATTCG
* * *
12849195 TAAAAGATTCAATATTCA
1 CAAAAGATTCAAGATTCG
* **
12849213 CAAAAGATTCAAAATTTA
1 CAAAAGATTCAAGATTCG
* * *
12849231 C-CAAGATTTAAAGATTTG
1 CAAAAGA-TTCAAGATTCG
* * * *
12849249 TAAAAGATACAAAGGTTGG
1 CAAAAGATTC-AAGATTCG
*
12849268 CAAAAGATTCAAAAATTCG
1 CAAAAGATTC-AAGATTCG
* *
12849287 TAAAAGATTCATA-ATTCA
1 CAAAAGATTCA-AGATTCG
**
12849305 CAAAAGATTCAAGATTTA
1 CAAAAGATTCAAGATTCG
*
12849323 C-AAATATTCAAAGATTCG
1 CAAAAGATTC-AAGATTCG
*
12849341 CAAAAGATTTAAGATTCG
1 CAAAAGATTCAAGATTCG
12849359 CAA
1 CAA
12849362 TGTCATAACC
Statistics
Matches: 129, Mismatches: 31, Indels: 15
0.74 0.18 0.09
Matches are distributed among these distances:
17 12 0.09
18 71 0.55
19 46 0.36
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (18 bp):
CAAAAGATTCAAGATTCG
Found at i:12850633 original size:58 final size:58
Alignment explanation
Indices: 12850461--12850709 Score: 211
Period size: 58 Copynumber: 4.3 Consensus size: 58
12850451 GTAAGAGTTA
* * * *
12850461 TAGGGCTTGAATTTTAAGGTTTGGAAA-GTTTAGGGTTTTGA-TTTAGGCTTTAG-GGTT
1 TAGGGTTTTAATTTTAAGGTTT-GAAAGGTTTAGGG-TTTAATTTTAGGGTTTAGAGGTT
** * * * *
12850518 TAGATTTTTTATTTTAAGGTTT-AAAGGGTTTAAGGTTTTAGTTTTAGGGTTCAGAGGTT
1 TAGGGTTTTAATTTTAAGGTTTGAAA-GGTTT-AGGGTTTAATTTTAGGGTTTAGAGGTT
* * * * *
12850577 TGGGGTTTTAATTTTAAGGTTTGGAGGGTCTAGGGTTTAATTTTAGGGTTTGGAGGTT
1 TAGGGTTTTAATTTTAAGGTTTGAAAGGTTTAGGGTTTAATTTTAGGGTTTAGAGGTT
* * * * *
12850635 TAGGG-TTTCATTTTTAGAGTTTGAAAGGTTTAGGGTTTAATTTTAAGGTTTGAAAGTTT
1 TAGGGTTTTAATTTTAAG-GTTTGAAAGGTTTAGGGTTTAATTTTAGGGTTT-AGAGGTT
*
12850694 TAGGGATTTTATTTTT
1 TAGGG-TTTTAATTTT
12850710 TAATTTTAAA
Statistics
Matches: 149, Mismatches: 33, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
55 3 0.02
57 34 0.23
58 69 0.46
59 35 0.23
60 1 0.01
61 7 0.05
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.47
Consensus pattern (58 bp):
TAGGGTTTTAATTTTAAGGTTTGAAAGGTTTAGGGTTTAATTTTAGGGTTTAGAGGTT
Found at i:12850688 original size:29 final size:29
Alignment explanation
Indices: 12850461--12850708 Score: 161
Period size: 29 Copynumber: 8.5 Consensus size: 29
12850451 GTAAGAGTTA
*
12850461 TAGGGCTTGAATTTTAAGGTTTGGAAA-GTT
1 TAGGG-TTTAATTTTAAGGTTT-GAAAGGTT
* *
12850491 TAGGGTTTTGA-TTT-AGGCTTT--AGGGTT
1 TAGGG-TTTAATTTTAAGG-TTTGAAAGGTT
** *
12850518 TAGATTTTTTATTTTAAGGTTT-AAAGGGTT
1 TAG-GGTTTAATTTTAAGGTTTGAAA-GGTT
* * * * *
12850548 TAAGGTTTTAGTTTT-AGGGTTCAGAGGTT
1 T-AGGGTTTAATTTTAAGGTTTGAAAGGTT
* * * *
12850577 TGGGGTTTTAATTTTAAGGTTTGGAGGGTC
1 TAGGG-TTTAATTTTAAGGTTTGAAAGGTT
* *
12850607 TAGGGTTTAATTTTAGGGTTTG-GAGGTT
1 TAGGGTTTAATTTTAAGGTTTGAAAGGTT
* *
12850635 TAGGGTTTCATTTTTAGAGTTTGAAAGGTT
1 TAGGGTTTAATTTTAAG-GTTTGAAAGGTT
*
12850665 TAGGGTTTAATTTTAAGGTTTGAAAGTTT
1 TAGGGTTTAATTTTAAGGTTTGAAAGGTT
*
12850694 TAGGGATTTTATTTT
1 TAGGG-TTTAATTTT
12850709 TTAATTTTAA
Statistics
Matches: 169, Mismatches: 35, Indels: 28
0.73 0.15 0.12
Matches are distributed among these distances:
26 1 0.01
27 10 0.06
28 28 0.17
29 65 0.38
30 63 0.37
31 2 0.01
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.47
Consensus pattern (29 bp):
TAGGGTTTAATTTTAAGGTTTGAAAGGTT
Found at i:12850999 original size:22 final size:22
Alignment explanation
Indices: 12850967--12851044 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 22
12850957 TATTCTATTC
*
12850967 TTATTATTATTTTTTTAGATTA
1 TTATTACTATTTTTTTAGATTA
** *
12850989 TTATTACTATTTTTCAAGCATTT
1 TTATTACTATTTTTTTAG-ATTA
*
12851012 TTAATA-TATATTTTTTAG-TTA
1 TTATTACTAT-TTTTTTAGATTA
*
12851033 TTA-TCCTATTTT
1 TTATTACTATTTT
12851045 GTTTTCATTT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
20 4 0.09
21 8 0.18
22 18 0.41
23 14 0.32
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63
Consensus pattern (22 bp):
TTATTACTATTTTTTTAGATTA
Found at i:12851151 original size:30 final size:29
Alignment explanation
Indices: 12851117--12851177 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
12851107 TATCATGCAT
* * *
12851117 AAATATTAAAAATAAAACTCAAAATAACAA
1 AAATAATAAAAATAAAAATAAAAATAA-AA
*
12851147 AAATAATAAAATTAAAAATAAAAATAAAA
1 AAATAATAAAAATAAAAATAAAAATAAAA
12851176 AA
1 AA
12851178 TATGAACTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (29 bp):
AAATAATAAAAATAAAAATAAAAATAAAA
Found at i:12851168 original size:6 final size:6
Alignment explanation
Indices: 12851123--12851176 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
12851113 GCATAAATAT
* * * *
12851123 TAAAAA TAAAAC TCAAAA TAACAAA -AATAA TAAAAT TAAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAA-AAA TAAAAA TAAAAA TAAAAA TAAAAA
12851171 TAAAAA
1 TAAAAA
12851177 ATATGAACTG
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
5 2 0.05
6 33 0.87
7 3 0.08
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:12852830 original size:45 final size:44
Alignment explanation
Indices: 12852581--12852861 Score: 202
Period size: 44 Copynumber: 6.3 Consensus size: 44
12852571 TTCATGTTTA
* * * *
12852581 AAATTTCAAAGATTCACATTAAAAAATATTAGAAATTTACATCC
1 AAATTTCAAAGATTCACATTTAAAAATTTTAGAGATTCACATCC
* * * *
12852625 AAGATTT-AAAGTTTCACATTTGAAAATCTTAGAGATTCATATCC
1 AA-ATTTCAAAGATTCACATTTAAAAATTTTAGAGATTCACATCC
* * *
12852669 AAGA-TTCAAATG-TTCATATTTGAAAATTTTAGAGATTCACATACA
1 AA-ATTTCAAA-GATTCACATTTAAAAATTTTAGAGATTCACAT-CC
* * * * *
12852714 AAAATTCAAAGATT--CTTTTAAAAAAATTTAGGGATTCATAT-C
1 AAATTTCAAAGATTCACATTT-AAAAATTTTAGAGATTCACATCC
* * * *
12852756 AAATTTTTAAAAATTCACATTTAAAAAATTTTGGAAATTCACATCC
1 AAA-TTTCAAAGATTCACATTT-AAAAATTTTAGAGATTCACATCC
* *
12852802 GAAATTTCAAA-AGTTCACATTTAAAAATTTTAG-GCAGTCACATCT
1 -AAATTTCAAAGA-TTCACATTTAAAAATTTTAGAG-ATTCACATCC
12852847 AACATTT-AAAGATTC
1 AA-ATTTCAAAGATTC
12852862 GGATTTGAAA
Statistics
Matches: 189, Mismatches: 32, Indels: 32
0.75 0.13 0.13
Matches are distributed among these distances:
42 3 0.02
43 13 0.07
44 93 0.49
45 61 0.32
46 16 0.08
47 3 0.02
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.35
Consensus pattern (44 bp):
AAATTTCAAAGATTCACATTTAAAAATTTTAGAGATTCACATCC
Found at i:12852964 original size:68 final size:67
Alignment explanation
Indices: 12852869--12853101 Score: 227
Period size: 68 Copynumber: 3.5 Consensus size: 67
12852859 TTCGGATTTG
* * * **
12852869 AAATTCAAAGATTCTTATTTAAAAATTTTAGAGATTCACATCCAAAATGTTAAAGATTTGCATTT
1 AAATTCAAAGATTCTTATTTGAAAATTTTAGAGATTCTCATCCAAAAT-TTAAACATTCACATTT
12852934 CAA
65 CAA
* * * * * *
12852937 AAATTCAAATATGCTTATTTGGAAATTTTTAAAAATTCTCATCCAAAATTTCAACATTCACATTT
1 AAATTCAAAGATTCTTATTT-GAAAATTTTAGAGATTCTCATCCAAAATTTAAACATTCACATTT
*
12853002 GAA
65 CAA
* * * * ***
12853005 AAGTTCAAGGATTCTTATTTGAAAATTTTAGAGATTCTCATCCAAAA-TTCAAGATTTGTATTT-
1 AAATTCAAAGATTCTTATTTGAAAATTTTAGAGATTCTCATCCAAAATTTAAACATTCACATTTC
*
12853068 GA
66 AA
* * *
12853070 AAGTTCAAAGATTCTCATTTCAAAATTTTAGA
1 AAATTCAAAGATTCTTATTTGAAAATTTTAGA
12853102 TCCAAAATTC
Statistics
Matches: 137, Mismatches: 27, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
65 30 0.22
66 12 0.09
67 24 0.18
68 48 0.35
69 23 0.17
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.38
Consensus pattern (67 bp):
AAATTCAAAGATTCTTATTTGAAAATTTTAGAGATTCTCATCCAAAATTTAAACATTCACATTTC
AA
Found at i:12853089 original size:22 final size:23
Alignment explanation
Indices: 12852992--12853094 Score: 72
Period size: 23 Copynumber: 4.7 Consensus size: 23
12852982 AAATTTCAAC
* *
12852992 ATTCACATTTGAAAAGTTCAAGG
1 ATTCTCATTTGAAAAGTTCAAAG
* * * *
12853015 ATTCTTATTTGAAAATTTTAGAG
1 ATTCTCATTTGAAAAGTTCAAAG
**
12853038 ATTCTCA-TCCAAAA-TTC-AAG
1 ATTCTCATTTGAAAAGTTCAAAG
*
12853058 ATT-TGTATTTG-AAAGTTCAAAG
1 ATTCT-CATTTGAAAAGTTCAAAG
*
12853080 ATTCTCATTTCAAAA
1 ATTCTCATTTGAAAA
12853095 TTTTAGATCC
Statistics
Matches: 58, Mismatches: 16, Indels: 12
0.67 0.19 0.14
Matches are distributed among these distances:
19 1 0.02
20 9 0.16
21 6 0.10
22 15 0.26
23 27 0.47
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.38
Consensus pattern (23 bp):
ATTCTCATTTGAAAAGTTCAAAG
Found at i:12854595 original size:29 final size:30
Alignment explanation
Indices: 12854533--12854595 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 30
12854523 TCTTTCAACA
*
12854533 ATTTTCTCTTCTCTTTTCTTCATTTCTTTT
1 ATTTTCTCTTCTATTTTCTTCATTTCTTTT
* *
12854563 -TTTT-TCTTCATATTTTC-TCCTTTTTTTT
1 ATTTTCTCTTC-TATTTTCTTCATTTCTTTT
12854591 ATTTT
1 ATTTT
12854596 GCATTTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (30 bp):
ATTTTCTCTTCTATTTTCTTCATTTCTTTT
Found at i:12858171 original size:18 final size:18
Alignment explanation
Indices: 12858136--12858171 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12858126 TGCTTTTTTG
*
12858136 CTACTATCTTACTTATGA
1 CTACTATCTTACTAATGA
*
12858154 CTACTATCTTGCTAATGA
1 CTACTATCTTACTAATGA
12858172 TCAATTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
CTACTATCTTACTAATGA
Found at i:12860878 original size:10 final size:11
Alignment explanation
Indices: 12860862--12860916 Score: 53
Period size: 10 Copynumber: 5.2 Consensus size: 11
12860852 TAAATTTTAA
12860862 AATTTT-ATAT
1 AATTTTAATAT
*
12860872 TATTTTAATAT
1 AATTTTAATAT
12860883 AATTTTTAATAT
1 AA-TTTTAATAT
*
12860895 -ATTTCAATA-
1 AATTTTAATAT
*
12860904 AATTTAAATAT
1 AATTTTAATAT
12860915 AA
1 AA
12860917 AATAATTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
10 20 0.54
11 8 0.22
12 9 0.24
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
AATTTTAATAT
Found at i:12860907 original size:21 final size:21
Alignment explanation
Indices: 12860859--12860908 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
12860849 TTTTAAATTT
* *
12860859 TAAAATTTTATATTATTTTAA
1 TAAATTTTTATATTATTTCAA
12860880 TATAATTTTTA-ATATATTTCAA
1 TA-AATTTTTATAT-TATTTCAA
12860902 TAAATTT
1 TAAATTT
12860909 AAATATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TAAATTTTTATATTATTTCAA
Found at i:12861067 original size:2 final size:2
Alignment explanation
Indices: 12861060--12861097 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
12861050 ATTCAGCATT
* *
12861060 TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12861098 ATTAGTCTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:12861868 original size:12 final size:12
Alignment explanation
Indices: 12861851--12861875 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12861841 ATTTATAATA
12861851 TATAAACAAAAT
1 TATAAACAAAAT
12861863 TATAAACAAAAT
1 TATAAACAAAAT
12861875 T
1 T
12861876 TTGAAACGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (12 bp):
TATAAACAAAAT
Found at i:12865968 original size:9 final size:9
Alignment explanation
Indices: 12865929--12865979 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
12865919 AATTTAATTT
12865929 AATTTAAAA
1 AATTTAAAA
**
12865938 TTTTTAAAA
1 AATTTAAAA
12865947 AATTATAAATA
1 AATT-TAAA-A
12865958 AATTTAATAA
1 AATTTAA-AA
12865968 AA-TTAAAA
1 AATTTAAAA
12865976 AATT
1 AATT
12865980 ATATATAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
8 4 0.12
9 14 0.41
10 10 0.29
11 6 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
AATTTAAAA
Found at i:12871829 original size:16 final size:16
Alignment explanation
Indices: 12871808--12871841 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12871798 ATAGCTGTCA
12871808 CTAGATTTCATCAACT
1 CTAGATTTCATCAACT
* *
12871824 CTAGATTTTATTAACT
1 CTAGATTTCATCAACT
12871840 CT
1 CT
12871842 TTTCACTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (16 bp):
CTAGATTTCATCAACT
Found at i:12872679 original size:32 final size:33
Alignment explanation
Indices: 12872611--12872716 Score: 92
Period size: 32 Copynumber: 3.3 Consensus size: 33
12872601 ATTATTTTAT
* * *
12872611 ATAAAAAAAATGAATTTTATCATATTATAAATA
1 ATAAAAAAAATGAACTTTATCACATTATAAAAA
* *
12872644 ATAAAATAAATGAACTTTATC-CGTTATAAAAA
1 ATAAAAAAAATGAACTTTATCACATTATAAAAA
** * * *
12872676 ATAAAGCAAATGAA-TTTCATCTCATTATGATAA
1 ATAAAAAAAATGAACTTT-ATCACATTATAAAAA
12872709 A-AAAAAAA
1 ATAAAAAAA
12872717 TTTTTTAAAT
Statistics
Matches: 59, Mismatches: 12, Indels: 5
0.78 0.16 0.07
Matches are distributed among these distances:
31 3 0.05
32 28 0.47
33 28 0.47
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.31
Consensus pattern (33 bp):
ATAAAAAAAATGAACTTTATCACATTATAAAAA
Found at i:12873090 original size:16 final size:16
Alignment explanation
Indices: 12873071--12873103 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12873061 AGCAAGTATA
12873071 AATTTATTAAAAA-AAT
1 AATTT-TTAAAAACAAT
12873087 AATTTTTAAAAACAAT
1 AATTTTTAAAAACAAT
12873103 A
1 A
12873104 GATGATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
AATTTTTAAAAACAAT
Found at i:12881933 original size:50 final size:50
Alignment explanation
Indices: 12881856--12881956 Score: 148
Period size: 50 Copynumber: 2.0 Consensus size: 50
12881846 TTATGCTAAA
* * *
12881856 ACTAAAACCTAAGTTTAATGGCTATCTTACCATGACAAAAAGTAAAGGAG
1 ACTAAAACCTAAGTTTAAAGGCCATCTTACCATCACAAAAAGTAAAGGAG
* **
12881906 ACTAAAACCTAAGTTTAAAGGCCATCTTACTATCATGAAAAGTAAAGGAG
1 ACTAAAACCTAAGTTTAAAGGCCATCTTACCATCACAAAAAGTAAAGGAG
12881956 A
1 A
12881957 ACTGCTCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.24
Consensus pattern (50 bp):
ACTAAAACCTAAGTTTAAAGGCCATCTTACCATCACAAAAAGTAAAGGAG
Found at i:12890342 original size:8 final size:8
Alignment explanation
Indices: 12890317--12890352 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
12890307 TTAAAACGAT
*
12890317 ATATTAAA
1 ATATAAAA
12890325 ATATATAAA
1 ATATA-AAA
12890334 ATATAAAA
1 ATATAAAA
12890342 ATATAAAA
1 ATATAAAA
12890350 ATA
1 ATA
12890353 ATATGATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 18 0.69
9 8 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
ATATAAAA
Found at i:12890342 original size:17 final size:16
Alignment explanation
Indices: 12890317--12890352 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
12890307 TTAAAACGAT
*
12890317 ATATTAAAATATATAAA
1 ATATAAAAATATA-AAA
12890334 ATATAAAAATATAAAA
1 ATATAAAAATATAAAA
12890350 ATA
1 ATA
12890353 ATATGATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATATAAAAATATAAAA
Found at i:12894384 original size:13 final size:13
Alignment explanation
Indices: 12894366--12894390 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12894356 TTAATTACAT
12894366 TTATTTTTTATTA
1 TTATTTTTTATTA
12894379 TTATTTTTTATT
1 TTATTTTTTATT
12894391 TTAAATCACT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTTTATTA
Found at i:12897859 original size:17 final size:18
Alignment explanation
Indices: 12897822--12897862 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12897812 CCAAAAATAC
*
12897822 AAAAATAAAAAGTTAACA
1 AAAAATAAAAAGTGAACA
*
12897840 AAAAATAAAAA-TGAAGA
1 AAAAATAAAAAGTGAACA
12897857 AAAAAT
1 AAAAAT
12897863 TAGAAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (18 bp):
AAAAATAAAAAGTGAACA
Found at i:12903094 original size:6 final size:6
Alignment explanation
Indices: 12903083--12903142 Score: 70
Period size: 6 Copynumber: 10.2 Consensus size: 6
12903073 GGGTTTCGAC
* *
12903083 TAGGGT TAGGGTT TAGGG- TATGTT TAGGGT TAGGGT TAGGGT TAGGGT
1 TAGGGT TAGGG-T TAGGGT TAGGGT TAGGGT TAGGGT TAGGGT TAGGGT
*
12903131 TA-GTT TAGGGT T
1 TAGGGT TAGGGT T
12903143 TTGGCTAGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
5 7 0.16
6 32 0.71
7 6 0.13
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (6 bp):
TAGGGT
Found at i:12903095 original size:29 final size:29
Alignment explanation
Indices: 12903046--12903101 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
12903036 TAGGTTTAGA
12903046 GTTTCAACTAAGGGTAAGGTTTAGGGTGG
1 GTTTCAACTAAGGGTAAGGTTTAGGGTGG
* *
12903075 GTTTCGACT-AGGGTTAGGGTTTAGGGT
1 GTTTCAACTAAGGG-TAAGGTTTAGGGT
12903102 ATGTTTAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.20, C:0.07, G:0.39, T:0.34
Consensus pattern (29 bp):
GTTTCAACTAAGGGTAAGGTTTAGGGTGG
Found at i:12903107 original size:29 final size:29
Alignment explanation
Indices: 12903046--12903130 Score: 75
Period size: 29 Copynumber: 2.9 Consensus size: 29
12903036 TAGGTTTAGA
* * *
12903046 GTTTCAACTAAGGG-TAAGGTTTAGGGTGG
1 GTTTCGACT-AGGGTTAGGGTTTAGGGTAG
*
12903075 GTTTCGACTAGGGTTAGGGTTTAGGGTAT
1 GTTTCGACTAGGGTTAGGGTTTAGGGTAG
* **
12903104 GTTTAGGGTTAGGGTTAGGG-TTAGGGT
1 GTTT-CGACTAGGGTTAGGGTTTAGGGT
12903131 TAGTTTAGGG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 4 0.09
29 31 0.66
30 12 0.26
ACGTcount: A:0.19, C:0.05, G:0.41, T:0.35
Consensus pattern (29 bp):
GTTTCGACTAGGGTTAGGGTTTAGGGTAG
Found at i:12905264 original size:67 final size:67
Alignment explanation
Indices: 12905156--12905291 Score: 254
Period size: 67 Copynumber: 2.0 Consensus size: 67
12905146 AGATAGTCAA
* *
12905156 TTGCTTTTTGGTTAAGTTTTGTATCTGGACTTTAGTACCTTTCTAGAATGCATAGAAGTATACTC
1 TTGCTTTTTGGTTAAGTTTTGTATCTAGACTTTAGTACCTTTCTAGAATGCATAGAACTATACTC
12905221 TT
66 TT
12905223 TTGCTTTTTGGTTAAGTTTTGTATCTAGACTTTAGTACCTTTCTAGAATGCATAGAACTATACTC
1 TTGCTTTTTGGTTAAGTTTTGTATCTAGACTTTAGTACCTTTCTAGAATGCATAGAACTATACTC
12905288 TT
66 TT
12905290 TT
1 TT
12905292 ATCATAGGTA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (67 bp):
TTGCTTTTTGGTTAAGTTTTGTATCTAGACTTTAGTACCTTTCTAGAATGCATAGAACTATACTC
TT
Found at i:12908194 original size:15 final size:16
Alignment explanation
Indices: 12908174--12908203 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12908164 ATATTAAAAC
12908174 ATATAAAAA-ATAAAT
1 ATATAAAAATATAAAT
12908189 ATATAAAAATATAAA
1 ATATAAAAATATAAA
12908204 AATCATATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
ATATAAAAATATAAAT
Found at i:12908200 original size:8 final size:8
Alignment explanation
Indices: 12908168--12908206 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
12908158 AACTATATAT
12908168 TAAAACATA
1 TAAAA-ATA
12908177 TAAAAA-A
1 TAAAAATA
*
12908184 TAAATATA
1 TAAAAATA
12908192 TAAAAATA
1 TAAAAATA
12908200 TAAAAAT
1 TAAAAAT
12908207 CATATGATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
7 6 0.22
8 16 0.59
9 5 0.19
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (8 bp):
TAAAAATA
Found at i:12914378 original size:24 final size:24
Alignment explanation
Indices: 12914340--12914385 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
12914330 GGGAATAAAC
*
12914340 TATTAGTATTTAAAATTTTTATTT
1 TATTAGTATTTAAAATTATTATTT
12914364 TATTA-TATTTAAAAATTATTAT
1 TATTAGTATTT-AAAATTATTAT
12914386 AAAATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TATTAGTATTTAAAATTATTATTT
Found at i:12917769 original size:17 final size:18
Alignment explanation
Indices: 12917742--12917783 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
12917732 CATGTTTTTG
12917742 CTTTTTCAAAATCAAAAT
1 CTTTTTCAAAATCAAAAT
12917760 CTTTTT-AAAATCAAAAT
1 CTTTTTCAAAATCAAAAT
*
12917777 CTCTTTC
1 CTTTTTC
12917784 TCCAATCAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.43
Consensus pattern (18 bp):
CTTTTTCAAAATCAAAAT
Found at i:12920149 original size:165 final size:165
Alignment explanation
Indices: 12919877--12920210 Score: 605
Period size: 165 Copynumber: 2.0 Consensus size: 165
12919867 TTGATTTTTT
* *
12919877 AAAACTAATTTACATGTCCTTATATATGGTTTCAAATGAAGTTATATTTGAAGTCTCTTAGACAA
1 AAAACTAATTTACATGTCCTTATATATGGTTTCAAAGGAAGTTATATTTGAAATCTCTTAGACAA
*
12919942 ATAATTGATTTTTTCTTATAGCTTTAGTTGAGTAATAGTTATTATAAATTCCTAGGCTAATAACA
66 ATAATTGATTTTCTCTTATAGCTTTAGTTGAGTAATAGTTATTATAAATTCCTAGGCTAATAACA
*
12920007 AATTTTCTTTCAAAACTCATTAATTTTATTTAATA
131 AATTTTCTTTCAAAACTCATTAATTTTATTTAACA
12920042 AAAACTAATTTACATGTCCTTATATATGGTTTCAAAGGAAGTTATATTTGAAATCTCTTAGACAA
1 AAAACTAATTTACATGTCCTTATATATGGTTTCAAAGGAAGTTATATTTGAAATCTCTTAGACAA
**
12920107 ATAATTGATTTTCTCTTATAGCTTTAGTTGAGTAATAGTTATTATAAATTGTTAGGCTAATAACA
66 ATAATTGATTTTCTCTTATAGCTTTAGTTGAGTAATAGTTATTATAAATTCCTAGGCTAATAACA
*
12920172 AATTTTCTTTTAAAACTCATTAATTTTATTTAACA
131 AATTTTCTTTCAAAACTCATTAATTTTATTTAACA
12920207 AAAA
1 AAAA
12920211 TTGTTTATAC
Statistics
Matches: 162, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
165 162 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (165 bp):
AAAACTAATTTACATGTCCTTATATATGGTTTCAAAGGAAGTTATATTTGAAATCTCTTAGACAA
ATAATTGATTTTCTCTTATAGCTTTAGTTGAGTAATAGTTATTATAAATTCCTAGGCTAATAACA
AATTTTCTTTCAAAACTCATTAATTTTATTTAACA
Found at i:12921287 original size:29 final size:29
Alignment explanation
Indices: 12921250--12921307 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
12921240 TAGAGTTTCA
*
12921250 ACTAGGGTTAAGG-TTTAAGGTAGGTTTAG
1 ACTAAGGTT-AGGATTTAAGGTAGGTTTAG
* *
12921279 ACTAAGGTTAGGATTTAGGGTATGTTTAG
1 ACTAAGGTTAGGATTTAAGGTAGGTTTAG
12921308 GGTTAAGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.28, C:0.03, G:0.33, T:0.36
Consensus pattern (29 bp):
ACTAAGGTTAGGATTTAAGGTAGGTTTAG
Found at i:12926175 original size:22 final size:22
Alignment explanation
Indices: 12926150--12926195 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
12926140 AGACATGAAT
*
12926150 AAAATAAAAG-AGTAAAAGAAAA
1 AAAATAAAAGAAATAAAA-AAAA
*
12926172 AAAATACAAGAAATAAAAAAAA
1 AAAATAAAAGAAATAAAAAAAA
12926194 AA
1 AA
12926196 TTGAGAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.80, C:0.02, G:0.09, T:0.09
Consensus pattern (22 bp):
AAAATAAAAGAAATAAAAAAAA
Found at i:12929807 original size:18 final size:17
Alignment explanation
Indices: 12929786--12929834 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
12929776 TGGTTTAGGG
12929786 TAAGATTAGAGTTTAAA
1 TAAGATTAGAGTTTAAA
*
12929803 CTAAGATTAG-GTTTTAA
1 -TAAGATTAGAGTTTAAA
*
12929820 TGAGGATTAGAGTTT
1 T-AAGATTAGAGTTT
12929835 CATATAGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 1 0.04
17 13 0.48
18 13 0.48
ACGTcount: A:0.37, C:0.02, G:0.22, T:0.39
Consensus pattern (17 bp):
TAAGATTAGAGTTTAAA
Found at i:12929930 original size:18 final size:18
Alignment explanation
Indices: 12929883--12929931 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
12929873 TTAAGGTTAA
12929883 GGTTTGGGTTTAGGATAT
1 GGTTTGGGTTTAGGATAT
* *
12929901 -GTTTAGGTTTTAGGCTAT
1 GGTTT-GGGTTTAGGATAT
12929919 GGTTTGGGTTTAG
1 GGTTTGGGTTTAG
12929932 AGGGGTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 4 0.15
18 18 0.69
19 4 0.15
ACGTcount: A:0.14, C:0.02, G:0.37, T:0.47
Consensus pattern (18 bp):
GGTTTGGGTTTAGGATAT
Found at i:12929945 original size:36 final size:34
Alignment explanation
Indices: 12929882--12929983 Score: 91
Period size: 34 Copynumber: 2.9 Consensus size: 34
12929872 TTTAAGGTTA
* * *
12929882 AGGTTTGGGTTTAGGATATGTTT-AGGTTTTAGGCT
1 AGGTTTGGGTTTA-GAGAGGTTTAAGGTTTT-GACT
*
12929917 ATGGTTTGGGTTTAGAGGGGTTTAAGGTTTTGACT
1 A-GGTTTGGGTTTAGAGAGGTTTAAGGTTTTGACT
* * *
12929952 AGGTTAGGGTTTAAAGTGG-TTAAGGGTTTTGA
1 AGGTTTGGGTTTAGAGAGGTTTAA-GGTTTTGA
12929984 TTTAGGGTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
33 4 0.07
34 23 0.40
35 11 0.19
36 19 0.33
ACGTcount: A:0.20, C:0.02, G:0.36, T:0.42
Consensus pattern (34 bp):
AGGTTTGGGTTTAGAGAGGTTTAAGGTTTTGACT
Found at i:12929980 original size:34 final size:36
Alignment explanation
Indices: 12929919--12929997 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 36
12929909 TTTAGGCTAT
* *
12929919 GGTTTGGGTTTAGAGGGGTTTAAGGTTTTGA-CTA-
1 GGTTAGGGTTTAAAGGGGTTTAAGGTTTTGATCTAG
* *
12929953 GGTTAGGGTTTAAAGTGG-TTAAGGGTTTTGATTTAG
1 GGTTAGGGTTTAAAGGGGTTTAA-GGTTTTGATCTAG
12929989 GGTTAGGGT
1 GGTTAGGGT
12929998 AGGTTTATGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
33 4 0.11
34 23 0.61
35 2 0.05
36 9 0.24
ACGTcount: A:0.19, C:0.01, G:0.39, T:0.41
Consensus pattern (36 bp):
GGTTAGGGTTTAAAGGGGTTTAAGGTTTTGATCTAG
Found at i:12930231 original size:23 final size:21
Alignment explanation
Indices: 12930197--12930238 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
12930187 TGTTCAGGGT
12930197 TTTAGCTAGGTTAAGGTTTCA
1 TTTAGCTAGGTTAAGGTTTCA
12930218 TTTAGGCTAAGGTTAAGGTTT
1 TTTA-GCT-AGGTTAAGGTTT
12930239 AGCCTAGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 3 0.16
23 12 0.63
ACGTcount: A:0.24, C:0.07, G:0.26, T:0.43
Consensus pattern (21 bp):
TTTAGCTAGGTTAAGGTTTCA
Found at i:12932412 original size:130 final size:128
Alignment explanation
Indices: 12931991--12933105 Score: 707
Period size: 129 Copynumber: 8.7 Consensus size: 128
12931981 AAAAAATTAC
* * * * *
12931991 TGCAAAAACTTGTTTTATTTGTAACAATTTTTCAATGTCGTTGCTTAAGTTA-TTTTTAATATTT
1 TGCAAAAACTTGTTTTATTTGCAACAATTTTTCAATGTTGTTACTTAATTTATTTTTTAAAATTT
** * * **
12932055 TATGA-AATGCAAAAAAAGTTGTTATGCTAGTTTTTATCATATTTGAAATGATAAAATATTATCA
66 TAT-ACAA--CAAAAAAAGTTGTTATGAAAATTTTTATCATATTTGTAATGATAAAATATTATTG
12932119 T
128 T
** * * ** * * *
12932120 TATAAAAACTTATTTTATTTGCAACGATTTTTCAATGTCATTGCTTAAGTTATTTTTTTAATATT
1 TGCAAAAACTTGTTTTATTTGCAACAATTTTTCAATGTTGTTACTTAATTTA-TTTTTTAA-AAT
* *
12932185 TTCTACAACAACAAAAAAAGTTGTTATGAAAATTTTTATCATATTTGTAATGATAAAAAATTATT
64 TT-TA-TACAACAAAAAAAGTTGTTATGAAAATTTTTATCATATTTGTAATGATAAAATATTATT
12932250 GT
127 GT
* * * * *
12932252 TGCAAAAATTTCTTTTATTTGCAATAATTTTTTAATGTTGTTACTTAATTTATTTGTTTAATATT
1 TGCAAAAACTTGTTTTATTTGCAACAATTTTTCAATGTTGTTACTTAATTTATTT-TTTAAAATT
* * ** *
12932317 TTATACAACAAAAAAAGTTGTTATGAAAATTTTTTATTACATTTGTAACAATAAAAAATTATTGT
65 TTATACAACAAAAAAAGTTGTTATGAAAA-TTTTTATCATATTTGTAATGATAAAATATTATTGT
* * ** * * * *
12932382 TGCGAAAACTTGTTTTATTTACAATGATTTTTCAATATAT-TT--TTAA--TAGTTTAT-ACA--
1 TGCAAAAACTTGTTTTATTTGCAACAATTTTTCAATGT-TGTTACTTAATTTATTTTTTAAAATT
* * * ** *
12932439 --AT--AACAAAAAAA-TTATTA-CAAAATTTTTTATCATATTTATAACAATAAAA-ATTATTAT
65 TTATACAACAAAAAAAGTTGTTATGAAAA-TTTTTATCATATTTGTAATGATAAAATATTATTGT
* * * ** * * * *
12932497 AGCGAAAATTTGTTTTATTTATAATAATTTTTTAATGTTGTTACTTAATTTATTTTTAAAAACTT
1 TGCAAAAACTTGTTTTATTTGCAACAATTTTTCAATGTTGTTACTTAATTTATTTTTTAAAATTT
* * * * *
12932562 TATACAACGATAAAAAGGTTGTTATAAAAAATTTTATCATATTTGTAATGATAACATATTAGTGT
66 TATACAAC-A-AAAAAAGTTGTTATGAAAATTTTTATCATATTTGTAATGATAAAATATTATTGT
* * * ** ** * * * *
12932627 TACTAAAACTTATTTTATTTATAATGATTTTTTAAT-TTCATTAGTTAGTTTATTTTTTAAAAAT
1 TGCAAAAACTTGTTTTATTTGCAACAATTTTTCAATGTT-GTTACTTAATTTATTTTTT-AAAAT
* * * ** * * * *
12932691 TTTTTACAACGACAAAAAATTTGTTACGAAAATTTGCATTACATTTGTAATAATGAAATATTATT
64 TTTATACAAC-A-AAAAAAGTTGTTATGAAAATTTTTATCATATTTGTAATGATAAAATATTATT
12932756 GT
127 GT
* * * *
12932758 TGTAAAAACTTGCTTTATTTGTAACAATTTTTCAATATTGTTACTTAATTTATTTTTTAAAAATT
1 TGCAAAAACTTGTTTTATTTGCAACAATTTTTCAATGTTGTTACTTAATTTATTTTTT-AAAATT
* * * * * * * * *
12932823 CTT-TACAATGACAAAAAGTTATTACGAAAA-TTTTATCACATTTATAACGATAAAATATTAGTA
65 -TTATACAA-CAAAAAAAGTTGTTATGAAAATTTTTATCATATTTGTAATGATAAAATATTATTG
12932886 T
128 T
* * * ****
12932887 TGTAAAACCTTATTTTATTTGCAACAAATTTTT-AACACCGTTACTTAATTTATTTTTTAAAAAT
1 TGCAAAAACTTGTTTTATTTGCAAC-AATTTTTCAATGTTGTTACTTAATTTATTTTTT-AAAAT
** * * * * *
12932951 TTTATACGATGACAAAAA-TT-TTATTACAAAAATTTTATCATATTTAG-AATGAAAAAAAATT-
64 TTTATAC-AACAAAAAAAGTTGTTA-T-GAAAATTTTTATCATATTT-GTAATGATAAAATATTA
12933012 TTGT
125 TTGT
* * * ** ** * * * *
12933016 TACGAAAATTTGTTTTATTTATAACGAA-TTTTCTTTGTCGTTGCTTAAATTATTTTTTAACATT
1 TGCAAAAACTTGTTTTATTTGCAAC-AATTTTTCAATGTTGTTACTTAATTTATTTTTTAAAATT
*
12933080 TTAATATAACAATATAAAAGTTGTTA
65 TT-ATACAACAA-A-AAAAGTTGTTA
12933106 CAAATTTTGT
Statistics
Matches: 783, Mismatches: 159, Indels: 85
0.76 0.15 0.08
Matches are distributed among these distances:
114 1 0.00
115 41 0.05
116 28 0.04
117 9 0.01
118 10 0.01
119 5 0.01
120 4 0.01
124 4 0.01
125 2 0.00
126 7 0.01
127 4 0.01
128 26 0.03
129 232 0.30
130 172 0.22
131 128 0.16
132 105 0.13
133 3 0.00
134 2 0.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (128 bp):
TGCAAAAACTTGTTTTATTTGCAACAATTTTTCAATGTTGTTACTTAATTTATTTTTTAAAATTT
TATACAACAAAAAAAGTTGTTATGAAAATTTTTATCATATTTGTAATGATAAAATATTATTGT
Found at i:12932488 original size:116 final size:114
Alignment explanation
Indices: 12932308--12932528 Score: 293
Period size: 115 Copynumber: 1.9 Consensus size: 114
12932298 AATTTATTTG
* * * * *
12932308 TTTAATATTTTATACAACAAAAAAAGTTGTTATGAAAATTTTTTATTACATTTGTAACAATAAAA
1 TTTAATAGTTTATACAACAAAAAAAGTTATTATCAAAATTTTTTATCACATTTATAACAAT-AAA
* * *
12932373 AATTATTGTTGCGAAAACTTGTTTTATTTACAATGATTTTTCAATATATT
65 AATTATTATAGCGAAAACTTGTTTTATTTACAATAATTTTTCAATATATT
*
12932423 TTTAATAGTTTATACAATAACAAAAAAA-TTATTA-CAAAATTTTTTATCATATTTATAACAATA
1 TTTAATAGTTTATAC---AACAAAAAAAGTTATTATCAAAATTTTTTATCACATTTATAACAATA
* *
12932486 AAAATTATTATAGCGAAAATTTGTTTTATTTATAATAATTTTT
63 AAAATTATTATAGCGAAAACTTGTTTTATTTACAATAATTTTT
12932529 TAATGTTGTT
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
115 53 0.58
116 24 0.26
117 5 0.05
118 10 0.11
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (114 bp):
TTTAATAGTTTATACAACAAAAAAAGTTATTATCAAAATTTTTTATCACATTTATAACAATAAAA
ATTATTATAGCGAAAACTTGTTTTATTTACAATAATTTTTCAATATATT
Found at i:12932608 original size:245 final size:247
Alignment explanation
Indices: 12932174--12932658 Score: 629
Period size: 245 Copynumber: 2.0 Consensus size: 247
12932164 TTAAGTTATT
* * * * * **
12932174 TTTTTAATATTTTCTACAACAACAAAAAAAGTTGTTATGAAAATTTTTATCATATTTGTAATGAT
1 TTTTTAATAGTTTATACAACAACAAAAAAAGTTATTATCAAAATTTTTATCATATTTATAACAAT
* * *
12932239 AAAAAATTATTGTTGCAAAAATTTCTTTTATTTGCAATAATTTTTTAATGTTGTTACTTAATTTA
66 AAAAAATTATTATAGCAAAAATTTCTTTTATTTACAATAATTTTTTAATGTTGTTACTTAATTTA
* * * ** *
12932304 TTTGTTTAATATTTTATACAACAAAAAAAGTTGTTATGAAAATTTTTTATTACATTTGTAACAAT
131 TTTGTTAAAAACTTTATACAACAAAAAAAGTTGTTATGAAAAAATTTTATCACATTTGTAACAAT
* * *
12932369 AAAAAATTATTGTTGCGAAAACTTGTTTTATTTACAATGATTTTTCAATATA
196 AAAAAATTAGTGTTACGAAAACTTATTTTATTTACAATGATTTTTCAATATA
*
12932421 TTTTTAATAGTTTATACAATAACAAAAAAA-TTATTA-CAAAATTTTTTATCATATTTATAACAA
1 TTTTTAATAGTTTATACAACAACAAAAAAAGTTATTATCAAAA-TTTTTATCATATTTATAACAA
* * *
12932484 T-AAAAATTATTATAGCGAAAATTTGTTTTATTTATAATAATTTTTTAATGTTGTTACTTAATTT
65 TAAAAAATTATTATAGCAAAAATTTCTTTTATTTACAATAATTTTTTAATGTTGTTACTTAATTT
* * *
12932548 ATTT-TTAAAAACTTTATACAACGATAAAAAGGTTGTTAT-AAAAAATTTTATCATATTTGTAAT
130 ATTTGTTAAAAACTTTATACAAC-A-AAAAAAGTTGTTATGAAAAAATTTTATCACATTTGTAAC
* * * * *
12932611 GATAACATATTAGTGTTACTAAAACTTATTTTATTTATAATGATTTTT
193 AATAAAAAATTAGTGTTACGAAAACTTATTTTATTTACAATGATTTTT
12932659 TAATTTCATT
Statistics
Matches: 204, Mismatches: 31, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
244 15 0.07
245 125 0.61
246 37 0.18
247 27 0.13
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (247 bp):
TTTTTAATAGTTTATACAACAACAAAAAAAGTTATTATCAAAATTTTTATCATATTTATAACAAT
AAAAAATTATTATAGCAAAAATTTCTTTTATTTACAATAATTTTTTAATGTTGTTACTTAATTTA
TTTGTTAAAAACTTTATACAACAAAAAAAGTTGTTATGAAAAAATTTTATCACATTTGTAACAAT
AAAAAATTAGTGTTACGAAAACTTATTTTATTTACAATGATTTTTCAATATA
Found at i:12932708 original size:131 final size:128
Alignment explanation
Indices: 12932509--12933047 Score: 467
Period size: 131 Copynumber: 4.1 Consensus size: 128
12932499 CGAAAATTTG
* * * *
12932509 TTTTATTTATAATAATTTTTTAATGTTGTTACTTAATTTA-TTTTTAAAAACTTTATACAACGAT
1 TTTTATTTATAACAATTTTTTAATATTGTTACTTAATTTATTTTTTAAAAATTTTATACAACGAC
* *
12932573 AAAAAGGTTGTTATAAAAAATTTTATCATATTTGTAATGATAACATATTAGTGTTACTAAAACTT
66 AAAAA-GTTGTTA-AAAAAATTTTATCACATTTGTAATGATAAAATATTAGTGTT-CTAAAACTT
12932638 A
128 A
** * * * *
12932639 TTTTATTTATAATGATTTTTTAAT-TTCATTAGTTAGTTTATTTTTTAAAAATTTTTTACAACGA
1 TTTTATTTATAACAATTTTTTAATATT-GTTACTTAATTTATTTTTTAAAAATTTTATACAACGA
* ** * * * * * *
12932703 CAAAAAATTTGTTACGAAAATTTGCATTACATTTGTAATAATGAAATATTATTGTTGTAAAAACT
65 C-AAAAAGTTGTTAAAAAAATTT-TATCACATTTGTAATGATAAAATATTAGTGTTCT-AAAACT
*
12932768 TG
127 TA
* * * *
12932770 CTTTATTTGTAACAATTTTTCAATATTGTTACTTAATTTATTTTTTAAAAATTCTT-TACAATGA
1 TTTTATTTATAACAATTTTTTAATATTGTTACTTAATTTATTTTTTAAAAATT-TTATACAACGA
* ** * * * *
12932834 CAAAAAGTTATTACGAAAATTTTATCACATTTATAACGATAAAATATTAGTATTGTAAAACCTTA
65 CAAAAAGTTGTTAAAAAAATTTTATCACATTTGTAATGATAAAATATTAGTGTTCTAAAA-CTTA
** * * ** * *
12932899 TTTTATTTGCAACAAATTTTTAACACCGTTACTTAATTTATTTTTTAAAAATTTTATACGATGAC
1 TTTTATTTATAACAATTTTTTAATATTGTTACTTAATTTATTTTTTAAAAATTTTATACAACGAC
* * * * * * * * *
12932964 AAAAATTTTATTACAAAAATTTTATCATATTTAG-AATGAAAAAAAATT-TTGTTACGAAAATTT
66 AAAAA-GTTGTTAAAAAAATTTTATCACATTT-GTAATGATAAAATATTAGTGTT-CTAAAACTT
*
12933027 G
128 A
12933028 TTTTATTTATAACGAATTTT
1 TTTTATTTATAAC-AATTTT
12933048 CTTTGTCGTT
Statistics
Matches: 333, Mismatches: 63, Indels: 26
0.79 0.15 0.06
Matches are distributed among these distances:
128 6 0.02
129 106 0.32
130 103 0.31
131 109 0.33
132 9 0.03
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (128 bp):
TTTTATTTATAACAATTTTTTAATATTGTTACTTAATTTATTTTTTAAAAATTTTATACAACGAC
AAAAAGTTGTTAAAAAAATTTTATCACATTTGTAATGATAAAATATTAGTGTTCTAAAACTTA
Found at i:12932967 original size:260 final size:261
Alignment explanation
Indices: 12932501--12932985 Score: 600
Period size: 260 Copynumber: 1.9 Consensus size: 261
12932491 TATTATAGCG
* * * * *
12932501 AAAATTTGTTTTATTTATAATAATTTTTTAATGTTGTTACTTAATTTATTTTTAAAAACTTTATA
1 AAAACTTGCTTTATTTATAACAATTTTTCAATATTGTTACTTAATTTATTTTTAAAAACTTTATA
* * * * * * *
12932566 CAACGATAAAAAGGTTGTTATAAAAAATTTTATCATATTTGTAATGATAACATATTAGTGTTACT
66 CAACGACAAAAAGGTTATTATAAAAAATTTTATCACATTTATAACGATAAAATATTAGTATTACT
* ** * *** * * *
12932631 AAAACTTATTTTATTTATAATGATTTTTTAATTTCATTAGTTAGTTTATTTTTTAAAAATTTTTT
131 AAAACTTATTTTATTTACAACAAATTTTTAACACCATTACTTAATTTATTTTTTAAAAATTTTAT
* *
12932696 ACAACGACAAAAAATTTGTTACGAAAATTTGCATTACATTTGTAATAATGAAATATTATTGTTGT
196 ACAACGACAAAAAATTTATTACAAAAATTTGCATTACATTTGTAATAATGAAATATTATTGTTGT
12932761 A
261 A
* *
12932762 AAAACTTGCTTTATTTGTAACAATTTTTCAATATTGTTACTTAATTTATTTTTTAAAAA-TTCTT
1 AAAACTTGCTTTATTTATAACAATTTTTCAATATTGTTACTTAATTTA-TTTTTAAAAACTT-TA
* **
12932826 TACAATGACAAAAA-GTTATTA-CGAAAATTTTATCACATTTATAACGATAAAATATTAGTATT-
64 TACAACGACAAAAAGGTTATTATAAAAAATTTTATCACATTTATAACGATAAAATATTAGTATTA
* * *
12932888 GTAAAACCTTATTTTATTTGCAACAAATTTTTAACACCGTTACTTAATTTATTTTTTAAAAATTT
129 CTAAAA-CTTATTTTATTTACAACAAATTTTTAACACCATTACTTAATTTATTTTTTAAAAATTT
* * *
12932953 TATACGATGACAAAAATTTTATTACAAAAATTT
193 TATACAACGACAAAAAATTTATTACAAAAATTT
12932986 TATCATATTT
Statistics
Matches: 186, Mismatches: 35, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
259 5 0.03
260 108 0.58
261 50 0.27
262 23 0.12
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (261 bp):
AAAACTTGCTTTATTTATAACAATTTTTCAATATTGTTACTTAATTTATTTTTAAAAACTTTATA
CAACGACAAAAAGGTTATTATAAAAAATTTTATCACATTTATAACGATAAAATATTAGTATTACT
AAAACTTATTTTATTTACAACAAATTTTTAACACCATTACTTAATTTATTTTTTAAAAATTTTAT
ACAACGACAAAAAATTTATTACAAAAATTTGCATTACATTTGTAATAATGAAATATTATTGTTGT
A
Found at i:12932981 original size:14 final size:14
Alignment explanation
Indices: 12932962--12932988 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12932952 TTATACGATG
12932962 ACAAAAATTTTATT
1 ACAAAAATTTTATT
12932976 ACAAAAATTTTAT
1 ACAAAAATTTTAT
12932989 CATATTTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
ACAAAAATTTTATT
Found at i:12933531 original size:66 final size:66
Alignment explanation
Indices: 12933425--12933559 Score: 270
Period size: 66 Copynumber: 2.0 Consensus size: 66
12933415 GATGACATCC
12933425 AATATTAATTTCAATTAAACAAGATAAAATCATATAAGATTGCTAAGTACAGTATTAAATAAGTT
1 AATATTAATTTCAATTAAACAAGATAAAATCATATAAGATTGCTAAGTACAGTATTAAATAAGTT
12933490 A
66 A
12933491 AATATTAATTTCAATTAAACAAGATAAAATCATATAAGATTGCTAAGTACAGTATTAAATAAGTT
1 AATATTAATTTCAATTAAACAAGATAAAATCATATAAGATTGCTAAGTACAGTATTAAATAAGTT
12933556 A
66 A
12933557 AAT
1 AAT
12933560 TATTGAGAAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 69 1.00
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.33
Consensus pattern (66 bp):
AATATTAATTTCAATTAAACAAGATAAAATCATATAAGATTGCTAAGTACAGTATTAAATAAGTT
A
Found at i:12933896 original size:9 final size:9
Alignment explanation
Indices: 12933882--12933924 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
12933872 TAAAAATTGA
12933882 AATAAAAAC
1 AATAAAAAC
12933891 AATAAAAAC
1 AATAAAAAC
*
12933900 AAATAAAAAT
1 -AATAAAAAC
* *
12933910 AAAAAAAAT
1 AATAAAAAC
12933919 AATAAA
1 AATAAA
12933925 TAAAATACCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
9 22 0.73
10 8 0.27
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (9 bp):
AATAAAAAC
Found at i:12933904 original size:10 final size:10
Alignment explanation
Indices: 12933881--12933917 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
12933871 ATAAAAATTG
12933881 AAATAAAAAC
1 AAATAAAAAC
12933891 -AATAAAAAC
1 AAATAAAAAC
*
12933900 AAATAAAAAT
1 AAATAAAAAC
12933910 AAA-AAAAA
1 AAATAAAAA
12933918 TAATAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 14 0.56
10 11 0.44
ACGTcount: A:0.84, C:0.05, G:0.00, T:0.11
Consensus pattern (10 bp):
AAATAAAAAC
Found at i:12933912 original size:16 final size:16
Alignment explanation
Indices: 12933891--12933929 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
12933881 AAATAAAAAC
12933891 AATAAAAACAAATAA-A
1 AATAAAAA-AAATAATA
12933907 AATAAAAAAAATAATA
1 AATAAAAAAAATAATA
12933923 AATAAAA
1 AATAAAA
12933930 TACCTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (16 bp):
AATAAAAAAAATAATA
Found at i:12933916 original size:19 final size:19
Alignment explanation
Indices: 12933881--12933917 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12933871 ATAAAAATTG
*
12933881 AAATAAAAACAATAAAAAC
1 AAATAAAAACAAAAAAAAC
*
12933900 AAATAAAAATAAAAAAAA
1 AAATAAAAACAAAAAAAA
12933918 TAATAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.84, C:0.05, G:0.00, T:0.11
Consensus pattern (19 bp):
AAATAAAAACAAAAAAAAC
Found at i:12940155 original size:18 final size:19
Alignment explanation
Indices: 12940129--12940181 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
12940119 TTTAAATAAA
*
12940129 AATATTTTAATAATTTT-T
1 AATAATTTAATAATTTTAT
*
12940147 AATAATTTATTAATTTTAT
1 AATAATTTAATAATTTTAT
*
12940166 AA-ATATTAAATAATTT
1 AATA-ATTTAATAATTT
12940182 AAATTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 16 0.55
19 13 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATAATTTAATAATTTTAT
Found at i:12940723 original size:2 final size:2
Alignment explanation
Indices: 12940716--12940742 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12940706 ATTAATAAAG
12940716 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
12940743 GAACAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12944729 original size:12 final size:12
Alignment explanation
Indices: 12944702--12944746 Score: 51
Period size: 10 Copynumber: 4.0 Consensus size: 12
12944692 AAGGTTGGAA
12944702 AATTAAAAAATT
1 AATTAAAAAATT
12944714 --TTAAAAAATT
1 AATTAAAAAATT
*
12944724 AATT-AAAAATA
1 AATTAAAAAATT
*
12944735 AAATAAAAAATT
1 AATTAAAAAATT
12944747 TTCTTTCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
10 10 0.37
11 9 0.33
12 8 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATTAAAAAATT
Found at i:12945073 original size:8 final size:8
Alignment explanation
Indices: 12945062--12945178 Score: 55
Period size: 8 Copynumber: 14.2 Consensus size: 8
12945052 AAAAATTTTG
12945062 AAACCCTA
1 AAACCCTA
*
12945070 AAACCTTTA
1 AAACC-CTA
* * *
12945079 AAATCTTG
1 AAACCCTA
*
12945087 AAACTCT-
1 AAACCCTA
12945094 AAACCCTA
1 AAACCCTA
*
12945102 AAA-CTTCA
1 AAACCCT-A
12945110 AAACCCTA
1 AAACCCTA
*
12945118 AAACCCTTCG
1 AAACCC-T-A
12945128 AAA-CCTA
1 AAACCCTA
12945135 AAACCTTCTA
1 AAACC--CTA
*
12945145 AAA--TTA
1 AAACCCTA
12945151 TAAACCCTA
1 -AAACCCTA
12945160 AAACCCTAA
1 AAACCCT-A
12945169 AAACCCTA
1 AAACCCTA
12945177 AA
1 AA
12945179 CCCAAAAATT
Statistics
Matches: 83, Mismatches: 13, Indels: 26
0.68 0.11 0.21
Matches are distributed among these distances:
6 2 0.02
7 14 0.17
8 37 0.45
9 21 0.25
10 9 0.11
ACGTcount: A:0.48, C:0.29, G:0.02, T:0.21
Consensus pattern (8 bp):
AAACCCTA
Found at i:12945081 original size:25 final size:24
Alignment explanation
Indices: 12945053--12945170 Score: 74
Period size: 25 Copynumber: 5.2 Consensus size: 24
12945043 AGTAAATAAA
*
12945053 AAAATTTTGAAACCCTAAAACCTTT
1 AAAATTTTGAAACCCTAAAACC-CT
* *
12945078 AAAATCTTGAAACTCT-AAACCCT
1 AAAATTTTGAAACCCTAAAACCCT
* **
12945101 AAAACTTCAAAACCCTAAAACCC-
1 AAAATTTTGAAACCCTAAAACCCT
*
12945124 -----TTCGAAA-CCTAAAACCTTCT
1 AAAATTTTGAAACCCTAAAACC--CT
*
12945144 AAAATTAT-AAACCCTAAAACCCT
1 AAAATTTTGAAACCCTAAAACCCT
12945167 AAAA
1 AAAA
12945171 ACCCTAAACC
Statistics
Matches: 72, Mismatches: 11, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
17 9 0.12
18 6 0.08
19 1 0.01
23 18 0.25
24 14 0.19
25 24 0.33
ACGTcount: A:0.47, C:0.26, G:0.03, T:0.24
Consensus pattern (24 bp):
AAAATTTTGAAACCCTAAAACCCT
Found at i:12945113 original size:16 final size:16
Alignment explanation
Indices: 12945062--12945227 Score: 65
Period size: 15 Copynumber: 10.4 Consensus size: 16
12945052 AAAAATTTTG
*
12945062 AAACCCTAAAACCTTTA
1 AAACCCTAAAA-CTTCA
* * * *
12945079 AAATCTTGAAAC-TCT
1 AAACCCTAAAACTTCA
12945094 AAACCCTAAAACTTCA
1 AAACCCTAAAACTTCA
*
12945110 AAACCCTAAAACCCTTCG
1 AAACCCTAAAA--CTTCA
12945128 AAA-CCTAAAACCTTCTA
1 AAACCCTAAAA-CTTC-A
*** * *
12945145 AAATTATAAACCCT-A
1 AAACCCTAAAACTTCA
* *
12945160 AAACCCTAAAAAC-CCT
1 AAACCCT-AAAACTTCA
* *
12945176 AAACCCAAAAATTTCA
1 AAACCCTAAAACTTCA
* *
12945192 AAACCCT-AAATTTTA
1 AAACCCTAAAACTTCA
* *
12945207 AAATCCT-AAATTTCA
1 AAACCCTAAAACTTCA
12945222 AAACCC
1 AAACCC
12945228 CAGATCTCGA
Statistics
Matches: 111, Mismatches: 30, Indels: 18
0.70 0.19 0.11
Matches are distributed among these distances:
15 44 0.40
16 36 0.32
17 20 0.18
18 11 0.10
ACGTcount: A:0.48, C:0.28, G:0.01, T:0.23
Consensus pattern (16 bp):
AAACCCTAAAACTTCA
Found at i:12945172 original size:17 final size:15
Alignment explanation
Indices: 12945152--12945186 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
12945142 CTAAAATTAT
12945152 AAACCCTAAAACCCTAA
1 AAACCCT-AAACCC-AA
12945169 AAACCCTAAACCCAA
1 AAACCCTAAACCCAA
12945184 AAA
1 AAA
12945187 TTTCAAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 6 0.33
17 7 0.39
ACGTcount: A:0.57, C:0.34, G:0.00, T:0.09
Consensus pattern (15 bp):
AAACCCTAAACCCAA
Found at i:12945202 original size:15 final size:15
Alignment explanation
Indices: 12945184--12945227 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
12945174 CTAAACCCAA
12945184 AAATTTCAAAACCCT
1 AAATTTCAAAACCCT
* *
12945199 AAATTTTAAAATCCT
1 AAATTTCAAAACCCT
12945214 AAATTTCAAAACCC
1 AAATTTCAAAACCC
12945228 CAGATCTCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATTTCAAAACCCT
Found at i:12945241 original size:30 final size:30
Alignment explanation
Indices: 12945184--12945246 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
12945174 CTAAACCCAA
* * *
12945184 AAATTTCAAAACCCTAAATTTTAAAATCCT
1 AAATTTCAAAACCCCAAATCTCAAAATCCT
* *
12945214 AAATTTCAAAACCCCAGATCTCGAAATCCT
1 AAATTTCAAAACCCCAAATCTCAAAATCCT
12945244 AAA
1 AAA
12945247 CACAAAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.46, C:0.24, G:0.03, T:0.27
Consensus pattern (30 bp):
AAATTTCAAAACCCCAAATCTCAAAATCCT
Found at i:12952276 original size:21 final size:20
Alignment explanation
Indices: 12952250--12952299 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
12952240 GTTATAACTC
12952250 TTTGACTTTTGACTTTTAATT
1 TTTGACTTTTGACTTTTAA-T
* * *
12952271 TTTGACCTTTGATTTTTTAT
1 TTTGACTTTTGACTTTTAAT
12952291 TTTGACTTT
1 TTTGACTTT
12952300 AACCTTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.16, C:0.10, G:0.10, T:0.64
Consensus pattern (20 bp):
TTTGACTTTTGACTTTTAAT
Found at i:12956080 original size:21 final size:21
Alignment explanation
Indices: 12956056--12956128 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
12956046 CAGCTTGACC
*
12956056 TGATTGATCCCTTAAGGGATA
1 TGATTAATCCCTTAAGGGATA
* **** *
12956077 TGATTAATCCCCTGCTTGACA
1 TGATTAATCCCTTAAGGGATA
**
12956098 TGATCGATCCCTTAAGGGATA
1 TGATTAATCCCTTAAGGGATA
12956119 TGATTAATCC
1 TGATTAATCC
12956129 TCTGCTTGAC
Statistics
Matches: 35, Mismatches: 17, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (21 bp):
TGATTAATCCCTTAAGGGATA
Found at i:12956107 original size:42 final size:42
Alignment explanation
Indices: 12956048--12956148 Score: 175
Period size: 42 Copynumber: 2.4 Consensus size: 42
12956038 CAACTATCCA
* *
12956048 GCTTGACCTGATTGATCCCTTAAGGGATATGATTAATCCCCT
1 GCTTGACATGATCGATCCCTTAAGGGATATGATTAATCCCCT
*
12956090 GCTTGACATGATCGATCCCTTAAGGGATATGATTAATCCTCT
1 GCTTGACATGATCGATCCCTTAAGGGATATGATTAATCCCCT
12956132 GCTTGACATGATCGATC
1 GCTTGACATGATCGATC
12956149 TCTCTTGTGT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (42 bp):
GCTTGACATGATCGATCCCTTAAGGGATATGATTAATCCCCT
Found at i:12959548 original size:20 final size:20
Alignment explanation
Indices: 12959510--12959549 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12959500 TACTTATTCT
* *
12959510 TTTATATATGTTTTTTTTTC
1 TTTATATATGTATTGTTTTC
*
12959530 TTTATTTATGTATTGTTTTC
1 TTTATATATGTATTGTTTTC
12959550 AATGACATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.07, T:0.72
Consensus pattern (20 bp):
TTTATATATGTATTGTTTTC
Found at i:12960456 original size:30 final size:30
Alignment explanation
Indices: 12960420--12960506 Score: 129
Period size: 31 Copynumber: 2.9 Consensus size: 30
12960410 GATCAAAAAC
*
12960420 TTAATTAAGTAAAAATAAATATTTAATAAT
1 TTAATTAAATAAAAATAAATATTTAATAAT
* **
12960450 TTAATTAAATAAAAATAAAAATTTTAATTGT
1 TTAATTAAATAAAAATAAATA-TTTAATAAT
12960481 TTAATTAAATAAAAATAAATATTTAA
1 TTAATTAAATAAAAATAAATATTTAA
12960507 AAACTCATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
30 24 0.47
31 27 0.53
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (30 bp):
TTAATTAAATAAAAATAAATATTTAATAAT
Found at i:12962904 original size:2 final size:2
Alignment explanation
Indices: 12962897--12962933 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
12962887 ACTGAAAAGC
*
12962897 AT AT AT AT AT AT AT A- AT AT AT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12962934 TTCTGTATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12975650 original size:18 final size:18
Alignment explanation
Indices: 12975627--12975661 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12975617 TTAATTATTT
12975627 TTTTATAATTTTTTAAAG
1 TTTTATAATTTTTTAAAG
*
12975645 TTTTATGATTTTTTAAA
1 TTTTATAATTTTTTAAA
12975662 ATTAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
TTTTATAATTTTTTAAAG
Found at i:12975696 original size:20 final size:20
Alignment explanation
Indices: 12975667--12975716 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
12975657 TTAAAATTAA
* *
12975667 ATTTTCAAAAAATCATATA-
1 ATTTTTAAAAAATCATAAAT
*
12975686 ATTTTTAAAAAATTATAAAT
1 ATTTTTAAAAAATCATAAAT
12975706 ATTTTTAAAAA
1 ATTTTTAAAAA
12975717 TTTAACTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTTTTAAAAAATCATAAAT
Found at i:12975781 original size:18 final size:19
Alignment explanation
Indices: 12975753--12975788 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
12975743 TAAAAAACGA
*
12975753 ATTTTTGAAAAATTTTATG
1 ATTTTTGAAAAAATTTATG
12975772 ATTTTT-AAAAAATTTAT
1 ATTTTTGAAAAAATTTAT
12975789 TTTCTAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
ATTTTTGAAAAAATTTATG
Found at i:12976419 original size:28 final size:27
Alignment explanation
Indices: 12976354--12976422 Score: 111
Period size: 27 Copynumber: 2.5 Consensus size: 27
12976344 ATTCGATAAT
*
12976354 AATCAAATCGAGTATAAATTTTTTTAA
1 AATCAAATCGAATATAAATTTTTTTAA
*
12976381 AATCAAATCGAATATAAATTTTTTTCA
1 AATCAAATCGAATATAAATTTTTTTAA
12976408 AATCAAATTCGAATA
1 AATCAAA-TCGAATA
12976423 ATTTAAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 32 0.82
28 7 0.18
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (27 bp):
AATCAAATCGAATATAAATTTTTTTAA
Found at i:12982261 original size:2 final size:2
Alignment explanation
Indices: 12982254--12982298 Score: 56
Period size: 2 Copynumber: 22.0 Consensus size: 2
12982244 ATCACTCCTT
*
12982254 TA TA TA TA TA T- TA TA TA TA TA TA TA CCA TA TA TA CTA 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
12982297 TA
1 TA
12982299 AGAAGTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 1 0.03
2 34 0.89
3 3 0.08
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:12982269 original size:11 final size:11
Alignment explanation
Indices: 12982253--12982298 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
12982243 GATCACTCCT
12982253 TTATATATATA
1 TTATATATATA
12982264 TTATATATATA
1 TTATATATATA
*
12982275 TATACCATATATA
1 T-TA-TATATATA
*
12982288 CTATATATATA
1 TTATATATATA
12982299 AGAAGTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 19 0.63
12 4 0.13
13 7 0.23
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (11 bp):
TTATATATATA
Found at i:12982272 original size:13 final size:12
Alignment explanation
Indices: 12982254--12982298 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
12982244 ATCACTCCTT
12982254 TATATATATAT-
1 TATATATATATA
12982265 TATATATATATA
1 TATATATATATA
*
12982277 TACCATATATACTA
1 TA-TATATATA-TA
12982291 TATATATA
1 TATATATA
12982299 AGAAGTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 11 0.38
12 2 0.07
13 12 0.41
14 4 0.14
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (12 bp):
TATATATATATA
Found at i:12986173 original size:23 final size:23
Alignment explanation
Indices: 12986138--12986182 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
12986128 TATTGGCTAA
*
12986138 AATAAATAAATAACTAAAAATTG
1 AATAAATAAATAAATAAAAATTG
** *
12986161 AATAAATGCATAAATAATAATT
1 AATAAATAAATAAATAAAAATT
12986183 AAGTTATTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (23 bp):
AATAAATAAATAAATAAAAATTG
Found at i:12986520 original size:18 final size:18
Alignment explanation
Indices: 12986497--12986531 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12986487 TTAATTATTT
12986497 TTTTATAATTTTTTAAAG
1 TTTTATAATTTTTTAAAG
*
12986515 TTTTATGATTTTTTAAA
1 TTTTATAATTTTTTAAA
12986532 ATTAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
TTTTATAATTTTTTAAAG
Found at i:12986588 original size:19 final size:19
Alignment explanation
Indices: 12986535--12986586 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
12986525 TTTTAAAATT
* *
12986535 AAATTTTCAAAAAATCATA
1 AAATTTTTAAAAAATTATA
12986554 AAATTTTTAAAAAATTATA
1 AAATTTTTAAAAAATTATA
12986573 AATATTTTTAAAAA
1 AA-ATTTTTAAAAA
12986587 TTTAACTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 19 0.63
20 11 0.37
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTTTTAAAAAATTATA
Found at i:12986651 original size:18 final size:19
Alignment explanation
Indices: 12986623--12986658 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
12986613 TAAAAAACGA
*
12986623 ATTTTTGAAAAATTTTATG
1 ATTTTTGAAAAAATTTATG
12986642 ATTTTT-AAAAAATTTAT
1 ATTTTTGAAAAAATTTAT
12986659 TTTCTAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
ATTTTTGAAAAAATTTATG
Found at i:12987289 original size:28 final size:27
Alignment explanation
Indices: 12987224--12987292 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
12987214 ACTCGATAAT
* * *
12987224 AATCGAATCGAGTATGAATTTTTTTAA
1 AATCAAATCGAATATAAATTTTTTTAA
*
12987251 AATCAAATCGAATATAAATTTTTTTCA
1 AATCAAATCGAATATAAATTTTTTTAA
12987278 AATCAAATTCGAATA
1 AATCAAA-TCGAATA
12987293 ATTTAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 30 0.81
28 7 0.19
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (27 bp):
AATCAAATCGAATATAAATTTTTTTAA
Found at i:12993136 original size:2 final size:2
Alignment explanation
Indices: 12993129--12993168 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
12993119 ATCACTCCTT
*
12993129 TA TA TA TA TA TA TA TA TA TA TA CA 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
12993169 AAGAAGTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:12996626 original size:12 final size:12
Alignment explanation
Indices: 12996609--12996634 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12996599 TAATTTAAAT
12996609 ATACAAAATCAA
1 ATACAAAATCAA
12996621 ATACAAAATCAA
1 ATACAAAATCAA
12996633 AT
1 AT
12996635 TTATAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.19
Consensus pattern (12 bp):
ATACAAAATCAA
Found at i:12997002 original size:15 final size:16
Alignment explanation
Indices: 12996982--12997011 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12996972 AATTAAAACC
12996982 ATATAC-TAAAATAAA
1 ATATACATAAAATAAA
12996997 ATATACATAAAATAA
1 ATATACATAAAATAA
12997012 TAAACTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (16 bp):
ATATACATAAAATAAA
Found at i:13007566 original size:29 final size:27
Alignment explanation
Indices: 13007526--13007598 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 27
13007516 TAAATTAAAT
*
13007526 AAAATATT-TAATATAGTATTCAAAGTTTA
1 AAAAT-TTATAATATAATATTCAAA--TTA
*
13007555 AAAATTTATAATATAATATTTAAATTA
1 AAAATTTATAATATAATATTCAAATTA
*
13007582 TAAATTTATTAAT-TAAT
1 AAAATTTA-TAATATAAT
13007599 TTAATATTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
27 14 0.36
28 6 0.15
29 19 0.49
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (27 bp):
AAAATTTATAATATAATATTCAAATTA
Found at i:13007722 original size:29 final size:29
Alignment explanation
Indices: 13007689--13007744 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
13007679 AATAAAATCA
13007689 AAATTCAAAT-ATCATATTAAAAATTTTTT
1 AAATT-AAATCATCATATTAAAAATTTTTT
* * *
13007718 AAATTTAATCATTATATTAAATATTTT
1 AAATTAAATCATCATATTAAAAATTTT
13007745 ATTATATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.13
29 20 0.87
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.48
Consensus pattern (29 bp):
AAATTAAATCATCATATTAAAAATTTTTT
Found at i:13009995 original size:45 final size:45
Alignment explanation
Indices: 13009942--13010038 Score: 176
Period size: 45 Copynumber: 2.2 Consensus size: 45
13009932 TTAGCTGGCT
* *
13009942 TTAAACTTCTGCTCACCAATAATCTCATGCTTAAAGATAAGTAAG
1 TTAAACTTCTGCTCACCAACAATCTCATGCCTAAAGATAAGTAAG
13009987 TTAAACTTCTGCTCACCAACAATCTCATGCCTAAAGATAAGTAAG
1 TTAAACTTCTGCTCACCAACAATCTCATGCCTAAAGATAAGTAAG
13010032 TTAAACT
1 TTAAACT
13010039 GCCACTTAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.30
Consensus pattern (45 bp):
TTAAACTTCTGCTCACCAACAATCTCATGCCTAAAGATAAGTAAG
Found at i:13014734 original size:13 final size:14
Alignment explanation
Indices: 13014694--13014736 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
13014684 ATCAATGTAA
*
13014694 AACTTTTTAATTTT
1 AACTTTTTGATTTT
13014708 ATACTTTTTG-TTTT
1 A-ACTTTTTGATTTT
13014722 AAC-TTTTGATTTT
1 AACTTTTTGATTTT
13014735 AA
1 AA
13014737 TAAATCTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 5 0.19
13 8 0.31
14 6 0.23
15 7 0.27
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.63
Consensus pattern (14 bp):
AACTTTTTGATTTT
Found at i:13015130 original size:9 final size:9
Alignment explanation
Indices: 13015116--13015158 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
13015106 GTAACTTCAT
13015116 ATATATATA
1 ATATATATA
13015125 ATATATAT-
1 ATATATATA
13015133 A-ATATATA
1 ATATATATA
13015141 ATATATAT-
1 ATATATATA
13015149 ATATATATA
1 ATATATATA
13015158 A
1 A
13015159 AAGAATCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 6 0.19
8 10 0.32
9 15 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
ATATATATA
Found at i:13015177 original size:2 final size:2
Alignment explanation
Indices: 13015114--13015157 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
13015104 ATGTAACTTC
13015114 AT AT AT AT AT A- AT AT AT AT A- AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13015153 AT AT A
1 AT AT A
13015158 AAAGAATCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:13015314 original size:38 final size:38
Alignment explanation
Indices: 13015271--13015349 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
13015261 TTAAAATCCT
13015271 ACATAAAGTTGCGTAAGAGGAATCAATTTATATACACC
1 ACATAAAGTTGCGTAAGAGGAATCAATTTATATACACC
*
13015309 ACATAAAGTTGCGTAAGATGAATCAATTTATATACACC
1 ACATAAAGTTGCGTAAGAGGAATCAATTTATATACACC
13015347 ACA
1 ACA
13015350 GAGGTTTAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (38 bp):
ACATAAAGTTGCGTAAGAGGAATCAATTTATATACACC
Found at i:13015624 original size:21 final size:21
Alignment explanation
Indices: 13015600--13015644 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
13015590 TTAAAATTAG
* *
13015600 ATTATTTGA-TAAACAACTAAA
1 ATTATTT-ATTAAAAAAATAAA
13015621 ATTATTTATTAAAAAAATAAA
1 ATTATTTATTAAAAAAATAAA
13015642 ATT
1 ATT
13015645 CATATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (21 bp):
ATTATTTATTAAAAAAATAAA
Found at i:13020598 original size:35 final size:35
Alignment explanation
Indices: 13020547--13020616 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
13020537 ATGGAGATGT
*
13020547 GTATGATTTTAAATTTTTATTAAGTATGGGAATGA
1 GTATAATTTTAAATTTTTATTAAGTATGGGAATGA
13020582 GTATAATTTTAAATTTTTATTAAGTATGGGAATGA
1 GTATAATTTTAAATTTTTATTAAGTATGGGAATGA
13020617 AAACGGGTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.46
Consensus pattern (35 bp):
GTATAATTTTAAATTTTTATTAAGTATGGGAATGA
Found at i:13023148 original size:12 final size:12
Alignment explanation
Indices: 13023131--13023166 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
13023121 TGCAATTCAA
13023131 ATATATATATGT
1 ATATATATATGT
*
13023143 ATATATATATTT
1 ATATATATATGT
*
13023155 ATTTATATATGT
1 ATATATATATGT
13023167 TGCATTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (12 bp):
ATATATATATGT
Found at i:13029521 original size:55 final size:55
Alignment explanation
Indices: 13029431--13029537 Score: 171
Period size: 55 Copynumber: 1.9 Consensus size: 55
13029421 ACGATTCTTT
*
13029431 TTTGGGTTCAAATATGTTTCCTTATTAATATTATTTGTTTGTTATGTAATTGTAAA
1 TTTGGGTTC-AATATGTTTCCTTATTAATATTATTTGTTTATTATGTAATTGTAAA
*
13029487 TTTGGGTTC-ATATGTTTCCTTTTTTAATATTATTTGTTTATTATGTAATTG
1 TTTGGGTTCAATATGTTTCC-TTATTAATATTATTTGTTTATTATGTAATTG
13029538 ATGTTATTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
54 10 0.21
55 29 0.60
56 9 0.19
ACGTcount: A:0.23, C:0.06, G:0.14, T:0.57
Consensus pattern (55 bp):
TTTGGGTTCAATATGTTTCCTTATTAATATTATTTGTTTATTATGTAATTGTAAA
Found at i:13030528 original size:35 final size:36
Alignment explanation
Indices: 13030447--13030529 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 36
13030437 TTTCATGTTT
** * *
13030447 GTTTTATCGTGTGTATATTTTTCTACTAATGCATTG
1 GTTTTATTATGTGTATATTTTTCTACTAATACATAG
* *
13030483 TTTTTATTATGTGTATA-TTTTCTACTAATACGGTAG
1 GTTTTATTATGTGTATATTTTTCTACTAATAC-ATAG
13030519 GTTTT-TTATGT
1 GTTTTATTATGT
13030530 TTTCTGTATC
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
35 19 0.49
36 20 0.51
ACGTcount: A:0.20, C:0.08, G:0.16, T:0.55
Consensus pattern (36 bp):
GTTTTATTATGTGTATATTTTTCTACTAATACATAG
Found at i:13041809 original size:27 final size:27
Alignment explanation
Indices: 13041750--13041803 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
13041740 ACTCAAACCT
*
13041750 TAGTTCCTCACAACCACTTCAAAATAC
1 TAGTTCCTCACAACCACTCCAAAATAC
* *
13041777 TAGTTCCTTACAGCCACTCCAAAATAC
1 TAGTTCCTCACAACCACTCCAAAATAC
13041804 ATGTTCTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.35, C:0.33, G:0.06, T:0.26
Consensus pattern (27 bp):
TAGTTCCTCACAACCACTCCAAAATAC
Found at i:13048732 original size:19 final size:20
Alignment explanation
Indices: 13048693--13048736 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
13048683 TTGAACCGAA
* *
13048693 TTATATATTTTTCTTAATTT
1 TTATATATATTTCTAAATTT
13048713 TTATATATATTT-TAAATTT
1 TTATATATATTTCTAAATTT
13048732 TTATA
1 TTATA
13048737 AAATAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATATATATTTCTAAATTT
Found at i:13048831 original size:6 final size:7
Alignment explanation
Indices: 13048814--13048840 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
13048804 ATAAACATTA
13048814 AAAAATT
1 AAAAATT
13048821 AAAAATT
1 AAAAATT
13048828 AAAAATT
1 AAAAATT
13048835 AAAAAT
1 AAAAAT
13048841 CGATAAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAAATT
Found at i:13049057 original size:303 final size:292
Alignment explanation
Indices: 13048674--13049279 Score: 926
Period size: 303 Copynumber: 2.0 Consensus size: 292
13048664 AAAATTGAAA
** **
13048674 AAAAAAAAATTGAACCGAATTATATATTTTTCTTAATTTTTATATATATTTTAAATTTTTATAAA
1 AAAAAAAAATCAAACCGAATTATATATTTTTCTTAATTTTTATATATATTTTAAATTTACATAAA
13048739 ATAAAAATAATAATTTTATATCAAAATTTACTTAAATATATTAAAATTTTATATTAAAATAATAT
66 ATAAAAATAATAATTTTATATCAAAATTTACTTAAATATATTAAAATTTTATATTAAAATAATAT
13048804 ATAAACATTAAAAAATTAAAAATTAAAAATTAAAAATCGATAAATCAAACGAATTGGTAAAATTC
131 ATAAACATT-----A--AAAAATTAAAAATTAAAAATCGATAAATCAAACGAATTGGTAAAATTC
* * * *
13048869 AATTCGATTCGATATATATCAAATAAAAATTTGGTTCGAATTCAAATTGAATTTTAAATTTTTAT
189 AATTCGATTCGATATAGATCAAATAAAAATTTAG-T-AAATTCAAATTAAATTTTAAATTTTTAT
* *
13048934 AATATTATGTAATATCTGAAAAAATCGAATCAAATTTAATT
252 AATATTATATAATATCTGAAAAAATCGAATCAAATTCAATT
*
13048975 AAAAAAAAATCAAATCGAATTATATATATTTT-TTAATTTTTATATATATATTTTAAATTTACAT
1 AAAAAAAAATCAAACCGAATTATATAT-TTTTCTTAA-TTTT-TATATATATTTTAAATTTACAT
* *
13049039 AACATAAAAATAATAATTTTATATTAAAATTTACTTAAATATATTAAAATTTTATATTAAAATAA
63 AAAATAAAAATAATAATTTTATATCAAAATTTACTTAAATATATTAAAATTTTATATTAAAATAA
** *
13049104 TATATAAACATTAAAAAATTAAAAATTAAAAATCGATAAATTGAACGAATTGGTAAAATTCAGTT
128 TATATAAACATTAAAAAATTAAAAATTAAAAATCGATAAATCAAACGAATTGGTAAAATTCAATT
*
13049169 CGGTTCGATATAGATCAAATAAAAATTTAGTAAATTCAAATTAAATTTTAAATTTTTATAATATT
193 CGATTCGATATAGATCAAATAAAAATTTAGTAAATTCAAATTAAATTTTAAATTTTTATAATATT
13049234 ATATAATATCTGAAAAAATCGAATCAAATTCAATT
258 ATATAATATCTGAAAAAATCGAATCAAATTCAATT
* *
13049269 CAAACAAAATC
1 AAAAAAAAATC
13049280 GTTATTATCC
Statistics
Matches: 283, Mismatches: 19, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
294 74 0.26
295 1 0.00
296 76 0.27
298 1 0.00
301 28 0.10
302 8 0.03
303 95 0.34
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (292 bp):
AAAAAAAAATCAAACCGAATTATATATTTTTCTTAATTTTTATATATATTTTAAATTTACATAAA
ATAAAAATAATAATTTTATATCAAAATTTACTTAAATATATTAAAATTTTATATTAAAATAATAT
ATAAACATTAAAAAATTAAAAATTAAAAATCGATAAATCAAACGAATTGGTAAAATTCAATTCGA
TTCGATATAGATCAAATAAAAATTTAGTAAATTCAAATTAAATTTTAAATTTTTATAATATTATA
TAATATCTGAAAAAATCGAATCAAATTCAATT
Found at i:13050654 original size:24 final size:25
Alignment explanation
Indices: 13050622--13050668 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
13050612 AATCTATTCT
13050622 AACTATCAACAAA-TTTTAGAATCG
1 AACTATCAACAAATTTTTAGAATCG
13050646 AACTATCAACAAATTTTTAGAAT
1 AACTATCAACAAATTTTTAGAAT
13050669 TTTAGGTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (25 bp):
AACTATCAACAAATTTTTAGAATCG
Found at i:13055407 original size:3 final size:3
Alignment explanation
Indices: 13055395--13055429 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
13055385 TGCTGCTGCT
* *
13055395 GCC GCA GCC GCC GCC GCC GCC GCC GCT GCC GCC GC
1 GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GCC GC
13055430 TTTGTTCGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.60, G:0.34, T:0.03
Consensus pattern (3 bp):
GCC
Found at i:13055430 original size:9 final size:9
Alignment explanation
Indices: 13055380--13055430 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 9
13055370 AACCGTCTTA
*
13055380 GCCGCTGCT
1 GCCGCTGCC
*
13055389 GCTGCTGCC
1 GCCGCTGCC
* *
13055398 GCAGCCGCC
1 GCCGCTGCC
*
13055407 GCCGCCGCC
1 GCCGCTGCC
13055416 GCCGCTGCC
1 GCCGCTGCC
13055425 GCCGCT
1 GCCGCT
13055431 TTGTTCGACC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.02, C:0.53, G:0.33, T:0.12
Consensus pattern (9 bp):
GCCGCTGCC
Found at i:13060398 original size:339 final size:339
Alignment explanation
Indices: 13059773--13062829 Score: 5308
Period size: 339 Copynumber: 9.0 Consensus size: 339
13059763 GTATTTGCAG
*
13059773 GTTTCCATGCGAGCTTCCTAGTTTCCTTCAAAAGATCCATCACATATTTCTATTGTGAGATGAAA
1 GTTTACATGCGAGCTTCCTAGTTTCCTTCAAAAGATCCATCACATATTTCTATTGTGAGATGAAA
*
13059838 ATACCATAATGTGAGTGAGCTACTTCAATTCGTAGGAAGTTCTTCAATCTCCCTTGCTCTTTTAT
66 ATACCATAATGTGAGTGAGCTACTTCAATTCCTAGGAAGTTCTTCAATCTCCCTTGCTCTTTTAT
*
13059903 CTCAAATTCTCTAGTCAAACACTGCTTTAAAGATTCTGTCTCTTTTTCATCATCTTCGGTTACAA
131 CTCAAATTCTCTAGTCAAACACTGCTTTAGAGATTCTGTCTCTTTTTCATCATCTTCGGTTACAA
13059968 TTATATCATCAACATACACTAATAGAACTATGACTCTTCCTGAATTAAAGTGCTTGATAAACAAT
196 TTATATCATCAACATACACTAATAGAACTATGACTCTTCCTGAATTAAAGTGCTTGATAAACAAT
13060033 GTGTGATCTCCTTGACTCTGCTTATATCCCATTGCTAGCATCACTTTGGCAAATCTCCCGAACCA
261 GTGTGATCTCCTTGACTCTGCTTATATCCCATTGCTAGCATCACTTTGGCAAATCTCCCGAACCA
13060098 AGCCCTAGGAGACT
326 AGCCCTAGGAGACT
13060112 GTTTACATGCGAGCTTCCTAGTTTCCTTCAAAAGATCCATCACATATTTCTATTGTGAGATGAAA
1 GTTTACATGCGAGCTTCCTAGTTTCCTTCAAAAGATCCATCACATATTTCTATTGTGAGATGAAA
13060177 ATACCATAATGTGAGTGAGCTACTTCAATTCCTAGGAAGTTCTTCAATCTCCCTTGCTCTTTTAT
66 ATACCATAATGTGAGTGAGCTACTTCAATTCCTAGGAAGTTCTTCAATCTCCCTTGCTCTTTTAT
* *
13060242 CTCAAATACTTTAGTCAAACACTGCTTTAGAGATTCTGTCTCTTTTTCATCATCTTCGGTTACAA
131 CTCAAATTCTCTAGTCAAACACTGCTTTAGAGATTCTGTCTCTTTTTCATCATCTTCGGTTACAA
* * *
13060307 TTATATCATCAACATACACTAATAGAACTATGACTATTCTTGAATTAAAGTGCTTGATAAACAAC
196 TTATATCATCAACATACACTAATAGAACTATGACTCTTCCTGAATTAAAGTGCTTGATAAACAAT
* * * **
13060372 GTGTGATCTCGTTGACTCTGCTTATATCCTATTGCTAGCATCACTTTGGCAAATTTTTCGAACCA
261 GTGTGATCTCCTTGACTCTGCTTATATCCCATTGCTAGCATCACTTTGGCAAATCTCCCGAACCA
*
13060437 AGCCCTAGGAAACT
326 AGCCCTAGGAGACT
*
13060451 GTTTACATGCGAGCTTCCTAGTTTCGTTCAAAAGATCCATCACATATTTCTATTGTGAGATGAAA
1 GTTTACATGCGAGCTTCCTAGTTTCCTTCAAAAGATCCATCACATATTTCTATTGTGAGATGAAA
*
13060516 ATACCATAATGTGAGCGAGCTACTTCAATTCCTAGGAAG-TCTTTCAATCTCCCTTGCTCTTTTA
66 ATACCATAATGTGAGTGAGCTACTTCAATTCCTAGGAAGTTC-TTCAATCTCCCTTGCTCTTTTA
*
13060580 TCTCAAATTCTCTAGTCAAACACTACTTTAGAGATTCTGTCTCTTTTTCATCATCTTCGGTTACA
130 TCTCAAATTCTCTAGTCAAACACTGCTTTAGAGATTCTGTCTCTTTTTCATCATCTTCGGTTACA
13060645 ATTATATCATCAACATACACTAATAGAACTATGACTCTTCCTGAATTAAAGTGCTTGATAAACAA
195 ATTATATCATCAACATACACTAATAGAACTATGACTCTTCCTGAATTAAAGTGCTTGATAAACAA
* * * ** *
13060710 TGTGTGATCGCCTTGACTCTGCTTATATCCCATCGCTAGCACCGGTTTGGCAAATCTCTCGAACC
260 TGTGTGATCTCCTTGACTCTGCTTATATCCCATTGCTAGCATCACTTTGGCAAATCTCCCGAACC
* *
13060775 AAGCACTCGGAGACT
325 AAGCCCTAGGAGACT
*
13060790 GTTTACATGCGAGCTTCCTAGTTTCCTTCAAAAGATCCTTCACATATTTCTATTGTGAGATGAAA
1 GTTTACATGCGAGCTTCCTAGTTTCCTTCAAAAGATCCATCACATATTTCTATTGTGAGATGAAA
*
13060855 ATACCATAATGTGAGTGAGCCACTTCAATTCCTAGGAAGTTCTTCAATCTCCCTTGCTCTTTTAT
66 ATACCATAATGTGAGTGAGCTACTTCAATTCCTAGGAAGTTCTTCAATCTCCCTTGCTCTTTTAT
* * * * *
13060920 TTCAAATTCTCTAGTCAAACACTGCTTTAGAGATTCTGTCTCTTTTTCATCATATTTGGTTATAG
131 CTCAAATTCTCTAGTCAAACACTGCTTTAGAGATTCTGTCTCTTTTTCATCATCTTCGGTTACAA
*
13060985 TTATATTATCAACATACACTAATAGAACTATGACTCTTCCTGAATTAAAGTGCTTGATAAACAAT
196 TTATATCATCAACATACACTAATAGAACTATGACTCTTCCTGAATTAAAGTGCTTGATAAACAAT
*
13061050 GTGTGATCTCCTTGACTTTGCTTATATCCCATTGCTAGCATCACTTTGGCAAATCTCCCGAACCA
261 GTGTGATCTCCTTGACTCTGCTTATATCCCATTGCTAGCATCACTTTGGCAAATCTCCCGAACCA
13061115 AGCCCTAGGAGACT
326 AGCCCTAGGAGACT
*
13061129 GTTTTGCATGCGAGCTTCCTAGTTTCCTTCAAAAGATCCATCACATATTTCTATTGTGAGATGAA
1 G-TTTACATGCGAGCTTCCTAGTTTCCTTCAAAAGATCCATCACATATTTCTATTGTGAGATGAA
* *
13061194 AATACCATAATGTGAGTGAGCTACTTCAATTCCTAGGAATTTCTTCAATCTCCCCTGCTCTTTTA
65 AATACCATAATGTGAGTGAGCTACTTCAATTCCTAGGAAGTTCTTCAATCTCCCTTGCTCTTTTA
* *
13061259 TCTCAAATTCTCTAGTCAAACATTGCTTTAGAGATTCTGTCTCTTTTTCATCATCTTCGGTTGCA
130 TCTCAAATTCTCTAGTCAAACACTGCTTTAGAGATTCTGTCTCTTTTTCATCATCTTCGGTTACA
* *
13061324 GTGATATCATCAACATACACTAATAGAACTATGACTCTTCCTGAATTAAAGTGCTTGATAAACAA
195 ATTATATCATCAACATACACTAATAGAACTATGACTCTTCCTGAATTAAAGTGCTTGATAAACAA
* * *
13061389 TGTGTGATCTACTTGACTTTGCTTATATTCCATTGCTAGCATCACTTTGGCAAATCTCCCGAACC
260 TGTGTGATCTCCTTGACTCTGCTTATATCCCATTGCTAGCATCACTTTGGCAAATCTCCCGAACC
13061454 AAGCCCTAGGAGACT
325 AAGCCCTAGGAGACT
* *
13061469 GTTTACATGCGAGCTTCCTAGTTTCGTTCAAAAGATCCATCACATATTTCTGTTGTGAGATGAAA
1 GTTTACATGCGAGCTTCCTAGTTTCCTTCAAAAGATCCATCACATATTTCTATTGTGAGATGAAA
*
13061534 ATACCATAATGTGAGTGAGCTACTTCAATTCCTAGGAAGTTCTTCAATCTCCCTTACTCTTTTAT
66 ATACCATAATGTGAGTGAGCTACTTCAATTCCTAGGAAGTTCTTCAATCTCCCTTGCTCTTTTAT
* *
13061599 CTCAAATTCTCTAGTCAAACATTACTTTAGAGATTCTGTCTCTTTTTCATCATCTTCGGTTACAA
131 CTCAAATTCTCTAGTCAAACACTGCTTTAGAGATTCTGTCTCTTTTTCATCATCTTCGGTTACAA
*
13061664 TTATATCATCAACATACACTAATAGAACTATGACTCTTCCTGAATTAAAGTGTTTGATAAACAAT
196 TTATATCATCAACATACACTAATAGAACTATGACTCTTCCTGAATTAAAGTGCTTGATAAACAAT
* * *
13061729 GTGTGATCTCTTTGACTCTGCTTATATTCCATTGCTAGCATCACATTGGCAAATCTCCCGAACCA
261 GTGTGATCTCCTTGACTCTGCTTATATCCCATTGCTAGCATCACTTTGGCAAATCTCCCGAACCA
13061794 AGCCCTAGGAGACT
326 AGCCCTAGGAGACT
** *
13061808 GTTTACATGCGAGCTTCCTAGTTTCCTTCAAAAGATTTATCACATATTTCTATTGTGAGATGAAG
1 GTTTACATGCGAGCTTCCTAGTTTCCTTCAAAAGATCCATCACATATTTCTATTGTGAGATGAAA
**
13061873 ATACCATAATGTGAGTGAGCTACTTCAATTCCTAGGAAGTTCCCCAATCTCCCTTGCTCTTTTAT
66 ATACCATAATGTGAGTGAGCTACTTCAATTCCTAGGAAGTTCTTCAATCTCCCTTGCTCTTTTAT
*
13061938 CTCAAATTCTCTAGTCAAACACTGCTTTAGAGATTCTGTCTCTTTTTCATAATCTTCGGTTACAA
131 CTCAAATTCTCTAGTCAAACACTGCTTTAGAGATTCTGTCTCTTTTTCATCATCTTCGGTTACAA
13062003 TTATATCATCAACATACACTAATAGAACTATGACTCTTCCTGAATTAAAGTGCTTGATAAACAAT
196 TTATATCATCAACATACACTAATAGAACTATGACTCTTCCTGAATTAAAGTGCTTGATAAACAAT
* ** *
13062068 GTGTGATCTCCTTGACTCTGTTTATATCCCATTGCTAGTGTCACTTTGGCAAATCTCCCAAACCA
261 GTGTGATCTCCTTGACTCTGCTTATATCCCATTGCTAGCATCACTTTGGCAAATCTCCCGAACCA
13062133 AGCCCTAGGAGACT
326 AGCCCTAGGAGACT
*
13062147 GTTTACATGCGAGCTTCCTAGTTTCGTTCAAAAGATCCATCACATATTTCTATTGTGAGATGAAA
1 GTTTACATGCGAGCTTCCTAGTTTCCTTCAAAAGATCCATCACATATTTCTATTGTGAGATGAAA
13062212 ATACCATAATGTGAGTGAGCTACTTCAATTCCTAGGAAGTTCTTCAATCTCCCTTGCTCTTTTAT
66 ATACCATAATGTGAGTGAGCTACTTCAATTCCTAGGAAGTTCTTCAATCTCCCTTGCTCTTTTAT
* * *
13062277 CTCAAATTCTCTAGTCAAACACTGCTTTAGAGATTCTGTCTCTTTTTCATCATATTCGGTTATAG
131 CTCAAATTCTCTAGTCAAACACTGCTTTAGAGATTCTGTCTCTTTTTCATCATCTTCGGTTACAA
* * * * *
13062342 TTTTATTATCAACATACACTAATAGAACTACGACTCTTGCTGAATTAAAGTGCTTTATAAACAAT
196 TTATATCATCAACATACACTAATAGAACTATGACTCTTCCTGAATTAAAGTGCTTGATAAACAAT
*
13062407 GTGTGATCTCCTTGACTCTGCATATATCCCAATT-CTAGCATCACTTTGGCAAATCTCCCGAACC
261 GTGTGATCTCCTTGACTCTGCTTATATCCC-ATTGCTAGCATCACTTTGGCAAATCTCCCGAACC
13062471 AAGCCCTAGGAGACT
325 AAGCCCTAGGAGACT
*
13062486 GTATACATGCGAGCTTCCTAGTTTCCTTCAAAAGATCCATCACATATTTCTATTGTGAGATGAAA
1 GTTTACATGCGAGCTTCCTAGTTTCCTTCAAAAGATCCATCACATATTTCTATTGTGAGATGAAA
13062551 ATACCATAATGTGAGTGAGCTACTTCAATTCCTAGGAAGTTCTTCAATCTCCCTTGCTCTTTTAT
66 ATACCATAATGTGAGTGAGCTACTTCAATTCCTAGGAAGTTCTTCAATCTCCCTTGCTCTTTTAT
* * *
13062616 CTCAAATTCTCTAGTCAAACACTGCTTTAGAGATTCTGTCTCTTTTTCATCATTTTCAGTTACAG
131 CTCAAATTCTCTAGTCAAACACTGCTTTAGAGATTCTGTCTCTTTTTCATCATCTTCGGTTACAA
*
13062681 TTATATCATCAACATACAGTAATAGAACTATGACTCTTCCTGAATTAAAGTGCTTGATAAACAAT
196 TTATATCATCAACATACACTAATAGAACTATGACTCTTCCTGAATTAAAGTGCTTGATAAACAAT
* * * * **
13062746 GTGTGATCTCTTTGACTCTGTTTATATTCCATTGCTAGCATCACTTTGGTAAATCTCCTTAACCA
261 GTGTGATCTCCTTGACTCTGCTTATATCCCATTGCTAGCATCACTTTGGCAAATCTCCCGAACCA
*
13062811 AGCGCTAGGAGACT
326 AGCCCTAGGAGACT
13062825 GTTTA
1 GTTTA
13062830 AAGTCATATA
Statistics
Matches: 2570, Mismatches: 143, Indels: 10
0.94 0.05 0.00
Matches are distributed among these distances:
338 5 0.00
339 2236 0.87
340 329 0.13
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (339 bp):
GTTTACATGCGAGCTTCCTAGTTTCCTTCAAAAGATCCATCACATATTTCTATTGTGAGATGAAA
ATACCATAATGTGAGTGAGCTACTTCAATTCCTAGGAAGTTCTTCAATCTCCCTTGCTCTTTTAT
CTCAAATTCTCTAGTCAAACACTGCTTTAGAGATTCTGTCTCTTTTTCATCATCTTCGGTTACAA
TTATATCATCAACATACACTAATAGAACTATGACTCTTCCTGAATTAAAGTGCTTGATAAACAAT
GTGTGATCTCCTTGACTCTGCTTATATCCCATTGCTAGCATCACTTTGGCAAATCTCCCGAACCA
AGCCCTAGGAGACT
Found at i:13065548 original size:22 final size:23
Alignment explanation
Indices: 13065509--13065552 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
13065499 ATACCATGTA
13065509 GAAAAACTAAGAAATAAAACTAT
1 GAAAAACTAAGAAATAAAACTAT
*
13065532 GAAAAACTAAG-AGTAAAACTA
1 GAAAAACTAAGAAATAAAACTA
13065553 AATGTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.64, C:0.09, G:0.11, T:0.16
Consensus pattern (23 bp):
GAAAAACTAAGAAATAAAACTAT
Found at i:13071237 original size:21 final size:19
Alignment explanation
Indices: 13071208--13071253 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 19
13071198 AATATGATTT
*
13071208 AAAATTTTAATAAAATTATA
1 AAAAATTTAATAAAATTA-A
13071228 AATAAATTTAATAAAATTAA
1 AA-AAATTTAATAAAATTAA
13071248 AAAAAT
1 AAAAAT
13071254 ATATTTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 4 0.17
20 5 0.21
21 15 0.62
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATTTAATAAAATTAA
Found at i:13072606 original size:14 final size:13
Alignment explanation
Indices: 13072570--13072608 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
13072560 TGAGAAAATT
13072570 ATAAAAATATTTA
1 ATAAAAATATTTA
*
13072583 A-AAGAATATTGTA
1 ATAAAAATATT-TA
13072596 ATAAAAATATTTA
1 ATAAAAATATTTA
13072609 TGTTTTTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 8 0.36
13 6 0.27
14 8 0.36
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (13 bp):
ATAAAAATATTTA
Found at i:13072809 original size:10 final size:10
Alignment explanation
Indices: 13072794--13072818 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
13072784 GCCAAATAGC
13072794 TTTTTTTATT
1 TTTTTTTATT
13072804 TTTTTTTATT
1 TTTTTTTATT
13072814 TTTTT
1 TTTTT
13072819 AGGGAGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:13079654 original size:13 final size:15
Alignment explanation
Indices: 13079622--13079657 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
13079612 TTAGGATGAC
13079622 AAATCAA-AGAATTA
1 AAATCAACAGAATTA
13079636 AAATCAACA-AATT-
1 AAATCAACAGAATTA
13079649 AAATCAACA
1 AAATCAACA
13079658 TTAATATTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.43
14 11 0.52
15 1 0.05
ACGTcount: A:0.64, C:0.14, G:0.03, T:0.19
Consensus pattern (15 bp):
AAATCAACAGAATTA
Found at i:13079932 original size:3 final size:3
Alignment explanation
Indices: 13079924--13079977 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
13079914 AAAGGATCAG
13079924 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
13079972 ATA ATA
1 ATA ATA
13079978 TAGAGTGAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:13086237 original size:22 final size:21
Alignment explanation
Indices: 13086186--13086237 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
13086176 TGGGTAATTA
* * *
13086186 TTTATTTATTTGTTTTTTTGT
1 TTTATTTATTTATATTTATGT
13086207 TTTATTTTATTTATATTTATGTT
1 TTTA-TTTATTTATATTTATG-T
13086230 TTTATTTA
1 TTTATTTA
13086238 GTATATGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 17 0.65
23 5 0.19
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (21 bp):
TTTATTTATTTATATTTATGT
Found at i:13089716 original size:16 final size:17
Alignment explanation
Indices: 13089687--13089733 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
13089677 AAAAAATTTT
13089687 AAAAAATAAAAAACCCA
1 AAAAAATAAAAAACCCA
**
13089704 AAAAAAT-AAAAACTGA
1 AAAAAATAAAAAACCCA
13089720 AAAAAATGAAAAAA
1 AAAAAAT-AAAAAA
13089734 AAAAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 14 0.54
17 7 0.27
18 5 0.19
ACGTcount: A:0.79, C:0.09, G:0.04, T:0.09
Consensus pattern (17 bp):
AAAAAATAAAAAACCCA
Found at i:13090220 original size:9 final size:10
Alignment explanation
Indices: 13090203--13090281 Score: 60
Period size: 9 Copynumber: 8.2 Consensus size: 10
13090193 TATAATTGTA
13090203 AATATATATTT
1 AATATATA-TT
13090214 AATATATATT
1 AATATATATT
* *
13090224 AA-AAATCTT
1 AATATATATT
*
13090233 AATTACATATT
1 AA-TATATATT
*
13090244 -TTA-AT-TT
1 AATATATATT
*
13090251 AATATATATA
1 AATATATATT
13090261 AATATAT-TT
1 AATATATATT
13090270 AATATATATT
1 AATATATATT
13090280 AA
1 AA
13090282 AAAACTTAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
7 2 0.04
8 4 0.07
9 19 0.35
10 16 0.30
11 13 0.24
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (10 bp):
AATATATATT
Found at i:13090222 original size:13 final size:12
Alignment explanation
Indices: 13090152--13090223 Score: 66
Period size: 11 Copynumber: 6.2 Consensus size: 12
13090142 AGTGCATTAC
13090152 ATTTAAAT-TA-
1 ATTTAAATATAT
*
13090162 ATATAAATATAT
1 ATTTAAATATAT
13090174 ATTT-AATATA-
1 ATTTAAATATAT
13090184 ATTTTAAAT-TAT
1 A-TTTAAATATAT
13090196 AATTGTAAATATAT
1 -ATT-TAAATATAT
13090210 ATTT-AATATAT
1 ATTTAAATATAT
13090221 ATT
1 ATT
13090224 AAAAATCTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
10 8 0.15
11 23 0.44
12 9 0.17
13 9 0.17
14 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (12 bp):
ATTTAAATATAT
Found at i:13090290 original size:19 final size:19
Alignment explanation
Indices: 13090212--13090291 Score: 58
Period size: 19 Copynumber: 4.3 Consensus size: 19
13090202 AAATATATAT
*
13090212 TTAATATATATTAAAAATC
1 TTAATATATATTAAAAAAC
* ** *
13090231 TTAATTACATATT--TTAAT
1 TTAA-TATATATTAAAAAAC
* *
13090249 TTAATATATA-TAAATATAT
1 TTAATATATATTAAA-AAAC
13090268 TTAATATATATTAAAAAAC
1 TTAATATATATTAAAAAAC
13090287 TTAAT
1 TTAAT
13090292 TAAAAAGTAT
Statistics
Matches: 45, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
16 1 0.02
17 5 0.11
18 5 0.11
19 23 0.51
20 11 0.24
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAATATATATTAAAAAAC
Found at i:13090694 original size:23 final size:24
Alignment explanation
Indices: 13090658--13090704 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
13090648 CACTGCCATC
13090658 ATCACCACTCCTACACCC-CCACT
1 ATCACCACTCCTACACCCACCACT
*
13090681 ATCACCA-TCACTACTCCCACCACT
1 ATCACCACTC-CTACACCCACCACT
13090705 GCCCTTATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 2 0.10
23 14 0.67
24 5 0.24
ACGTcount: A:0.28, C:0.53, G:0.00, T:0.19
Consensus pattern (24 bp):
ATCACCACTCCTACACCCACCACT
Found at i:13093524 original size:12 final size:12
Alignment explanation
Indices: 13093507--13093542 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
13093497 AGAGAAGAGG
13093507 AGGAGAGGGAGA
1 AGGAGAGGGAGA
13093519 AGGAGAGGGAGA
1 AGGAGAGGGAGA
*
13093531 AGGACAGGGAGA
1 AGGAGAGGGAGA
13093543 GAGAAGAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.03, G:0.56, T:0.00
Consensus pattern (12 bp):
AGGAGAGGGAGA
Done.