Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, 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: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 26 of 32
Found at i:12849771 original size:66 final size:66
Alignment explanation
Indices: 12849690--12849824 Score: 270
Period size: 66 Copynumber: 2.0 Consensus size: 66
12849680 TCTTTGAGGA
12849690 TTTCTACTTGAGCAAACGACATTTGAATTTAAATTGGTCAAGTTTTTTACATTCAAAGCACATCG
1 TTTCTACTTGAGCAAACGACATTTGAATTTAAATTGGTCAAGTTTTTTACATTCAAAGCACATCG
12849755 C
66 C
12849756 TTTCTACTTGAGCAAACGACATTTGAATTTAAATTGGTCAAGTTTTTTACATTCAAAGCACATCG
1 TTTCTACTTGAGCAAACGACATTTGAATTTAAATTGGTCAAGTTTTTTACATTCAAAGCACATCG
12849821 C
66 C
12849822 TTT
1 TTT
12849825 ATCTTTTTTG
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:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (66 bp):
TTTCTACTTGAGCAAACGACATTTGAATTTAAATTGGTCAAGTTTTTTACATTCAAAGCACATCG
C
Found at i:12852814 original size:24 final size:24
Alignment explanation
Indices: 12852787--12852836 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
12852777 AATAATTATA
*
12852787 TTGGGAAATAGACAATTGTGTTTG
1 TTGGGAAACAGACAATTGTGTTTG
* *
12852811 TT-GGCAACAGAGAATTGTGTTTG
1 TTGGGAAACAGACAATTGTGTTTG
12852834 TTG
1 TTG
12852837 TGAAGAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.26, C:0.06, G:0.30, T:0.38
Consensus pattern (24 bp):
TTGGGAAACAGACAATTGTGTTTG
Found at i:12854256 original size:22 final size:23
Alignment explanation
Indices: 12854224--12854266 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
12854214 CAAATTGTGA
12854224 AACACAAGAAGAGA-AGAAAAGGC
1 AACACAAGAAGA-ACAGAAAAGGC
12854247 AACA-AAGAAGAACAGAAAAG
1 AACACAAGAAGAACAGAAAAG
12854267 AAGCAGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 1 0.05
22 14 0.74
23 4 0.21
ACGTcount: A:0.65, C:0.12, G:0.23, T:0.00
Consensus pattern (23 bp):
AACACAAGAAGAACAGAAAAGGC
Found at i:12867323 original size:234 final size:230
Alignment explanation
Indices: 12866855--12867720 Score: 577
Period size: 231 Copynumber: 3.7 Consensus size: 230
12866845 ATTTTAGTTC
*
12866855 TTAAGCAATTAATTAAATTAGTAATATTATTTAATTTAAAAATATTTAAATTAATTAAGGTGTGA
1 TTAAGCAATTAATTAAATTAGTAATATTATTTAATTTAAAAATATTTAAATTAATTAAGGTTTGA
* *
12866920 GGGAACTAATTATATAATTTAACTAATTAAAAAGAATCATGTATTAGTAATTAAGAAAGTAATTA
66 GGGAACTAATTAAATAATTTAACTAATTAAAAAGAATCATGTATAAGTAATTAAGAAAGTAATTA
* **
12866985 AACTATTAAATTTAGTAAAATTTAAAATTATTTAAATTAATCAAAGATTTATTAAATTAATTAAA
131 AACTATTAAATTTAGTAAAATTTAAAATTATTTAAATTAATCAAAGATTGAGGAAATTAATTAAA
* *
12867050 TAATTTAACTAATCCAATGAAAAAATATTTTACTAA
196 TAATTTAACTAATCCAA-GAAAAAATATTCTAATAA
* *
12867086 TTAAGCAATTAATTAAATCAGTAATATTATTTAATTTATAAAATATTCAAATTAATTAAGGTTTG
1 TTAAGCAATTAATTAAATTAGTAATATTATTTAATTTA-AAAATATTTAAATTAATTAAGGTTTG
* ** ** * * * * *
12867151 A-TGAGTTAATTAAATAATTTAGTTAATTAGGTAATGTAAT-GTGTTATAAGTAATTAAGCAATT
65 AGGGAACTAATTAAATAATTTAACTAATTA--AAAAG-AATCATG-TATAAGTAATTAAGAAAGT
* * * * * *
12867214 AATTAAA-TCATT-AATATTATGTAATATTT-TATTTATTTAAA-TAAGT-TAAGGTTGGAGGCA
126 AATTAAACT-ATTAAAT-TTA-GTAAAATTTAAAATTATTTAAATTAA-TCAAAGATT-GAGGAA
* * *
12867274 ATTAATTACATAATTTAACTAAT-TAA-AAAGAATCATGTACTAATAA
186 ATTAATTAAATAATTTAACTAATCCAAGAAAAAAT-AT-T-CTAATAA
* *
12867320 TTAATCAATTAATTAAATTAGTAA-ATT-TTGTAAAATTTAAAATTATTTAAATTAATTAAGGTT
1 TTAAGCAATTAATTAAATTAGTAATATTATT-T--AATTTAAAAATATTTAAATTAATTAAGGTT
*** * * * ** ** * * *
12867383 CT-ATTAAATTAATTCAATAATTTAACTAA-TCAACTGAAAAATGTTTAAGTAATTAAGCAATTA
63 -TGAGGGAACTAATTAAATAATTTAACTAATTAAAAAGAATCATGTATAAGTAATTAAGAAAGTA
* *** * * * * * * *
12867446 ATTAAACTA-GAAATATTA-TTTCATTATATAA-TATTTAAATTAATTAAGGTTTAATG-AGTTA
127 ATTAAACTATTAAAT-TTAGTAAAATT-TAAAATTATTTAAATTAATCAAAGATTGAGGAAATTA
* *** * ** * * *
12867507 ATCAAATAATTTGGTTAAT-TAAGTAATGTAATGTGTTATAAGTGA
190 ATTAAATAATTTAACTAATCCAAG-AA---AAAATATTCTAA-TAA
* * * ** * ** * *
12867552 TTAAGTAATTAATTAAATCATTAATATTACAT-ATTT-TATTTATTTCAATTAATTGAGGTTTGA
1 TTAAGCAATTAATTAAATTAGTAATATTATTTAATTTAAAAATATTTAAATTAATTAAGGTTTGA
* * * * * ** *
12867615 GGG-ACTTAATTACATAATATAAATAATTAAAAAGAATAATGTATTAGTAATTAATCAATTAATT
66 GGGAAC-TAATTAAATAATTTAACTAATTAAAAAGAATCATGTATAAGTAATTAAGAAAGTAATT
* * *
12867679 AAATTAGTAAATTTAATAAAATTTAAAATTATTTAAATTAAT
130 AAACTATTAAATTTAGTAAAATTTAAAATTATTTAAATTAAT
12867721 TAAGATTTTA
Statistics
Matches: 499, Mismatches: 97, Indels: 78
0.74 0.14 0.12
Matches are distributed among these distances:
228 2 0.00
229 62 0.12
230 58 0.12
231 135 0.27
232 58 0.12
233 29 0.06
234 120 0.24
235 35 0.07
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (230 bp):
TTAAGCAATTAATTAAATTAGTAATATTATTTAATTTAAAAATATTTAAATTAATTAAGGTTTGA
GGGAACTAATTAAATAATTTAACTAATTAAAAAGAATCATGTATAAGTAATTAAGAAAGTAATTA
AACTATTAAATTTAGTAAAATTTAAAATTATTTAAATTAATCAAAGATTGAGGAAATTAATTAAA
TAATTTAACTAATCCAAGAAAAAATATTCTAATAA
Found at i:12867691 original size:17 final size:17
Alignment explanation
Indices: 12867671--12867718 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
12867661 GTAATTAATC
12867671 AATTAATTAAATTAGTAA
1 AATTAATTAAATTA-TAA
* *
12867689 ATTTAATAAAATT-TAA
1 AATTAATTAAATTATAA
*
12867705 AATTATTTAAATTA
1 AATTAATTAAATTA
12867719 ATTAAGATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
16 13 0.54
18 11 0.46
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
AATTAATTAAATTATAA
Found at i:12867708 original size:345 final size:346
Alignment explanation
Indices: 12866855--12867744 Score: 1236
Period size: 345 Copynumber: 2.6 Consensus size: 346
12866845 ATTTTAGTTC
* * ** ** *
12866855 TTAAGCAATTAATTAAATTAGTAATATTATTTAAT-TTAAAAATATTTAAATTAATTAAGGTGTG
1 TTAAGCAATTAATTAAATCATTAATATTA--TAATATTTTATTTATTT-AATTAATTAAGGTTTG
* ** *
12866919 AGGGAAC-TAATTATATAATTTAACTAATTAAAAAGAATCATGTATTAGTAATTAAGAAAGTAAT
63 AGGG-ACTTAATTACATAATTTAACTAATTAAAAAGAATCATGTATTAGTAATTAATCAATTAAT
* * *
12866983 TAAACTATTAAATTTAGTAAAATTTAAAATTATTTAAATTAATCAAAGATTTATTAAATTAATTA
127 TAAATTAGTAAATTTAGTAAAATTTAAAATTATTTAAATTAAT-TAAGATTTATTAAATTAATTA
* *
12867048 AATAATTTAACTAATCCAATGAAAAAATATTTTACTAATTAAGCAATTAATTAAATCAGTAATAT
191 AATAATTTAACTAATCCAATGAAAAAATATTTAACTAATTAAGCAATTAATTAAATCAGAAATAT
* *
12867113 TATTTAATTTATAAAATATTCAAATTAATTAAGGTTTGATGAGTTAATTAAATAATTTAGTTAAT
256 TATTTAATTTATAAAATATTCAAATTAATTAAGGTTTAATGAGTTAATCAAATAATTTAGTTAAT
*
12867178 TAGGTAATGTAATGTGTTATAAGTAA
321 TAAGTAATGTAATGTGTTATAAGTAA
* *
12867204 TTAAGCAATTAATTAAATCATTAATATTATGTAATATTTTATTTATTTAAATAAGTTAAGGTTGG
1 TTAAGCAATTAATTAAATCATTAATATTA--TAATATTTTATTTATTTAATTAA-TTAAGGTTTG
* * * *
12867269 AGGCAATTAATTACATAATTTAACTAATTAAAAAGAATCATGTACTAATAATTAATCAATTAATT
63 AGGGACTTAATTACATAATTTAACTAATTAAAAAGAATCATGTATTAGTAATTAATCAATTAATT
* * *
12867334 AAATTAGTAAATTTTGTAAAATTTAAAATTATTTAAATTAATTAAGGTTCTATTAAATTAATTCA
128 AAATTAGTAAATTTAGTAAAATTTAAAATTATTTAAATTAATTAAGATT-TATTAAATTAATTAA
* *
12867399 ATAATTTAACTAAT-CAACTG-AAAAATGTTTAAGTAATTAAGCAATTAATTAAA-CTAGAAATA
192 ATAATTTAACTAATCCAA-TGAAAAAATATTTAACTAATTAAGCAATTAATTAAATC-AGAAATA
* * * *
12867461 TTATTTCA-TTATATAATATTTAAATTAATTAAGGTTTAATGAGTTAATCAAATAATTTGGTTAA
255 TTATTTAATTTATAAAATATTCAAATTAATTAAGGTTTAATGAGTTAATCAAATAATTTAGTTAA
*
12867525 TTAAGTAATGTAATGTGTTATAAGTGA
320 TTAAGTAATGTAATGTGTTATAAGTAA
* * *
12867552 TTAAGTAATTAATTAAATCATTAATATTA-CATATTTTATTTATTTCAATTAATTGAGGTTTGAG
1 TTAAGCAATTAATTAAATCATTAATATTATAATATTTTATTTATTT-AATTAATTAAGGTTTGAG
* * *
12867616 GGACTTAATTACATAATATAAATAATTAAAAAGAATAATGTATTAGTAATTAATCAATTAATTAA
65 GGACTTAATTACATAATTTAACTAATTAAAAAGAATCATGTATTAGTAATTAATCAATTAATTAA
*
12867681 ATTAGTAAATTTAATAAAATTTAAAATTATTTAAATTAATTAAGATTTTATTAAATTAATTAAA
130 ATTAGTAAATTTAGTAAAATTTAAAATTATTTAAATTAATTAAGA-TTTATTAAATTAATTAAA
12867745 AAATATTATA
Statistics
Matches: 481, Mismatches: 52, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
345 140 0.29
346 7 0.01
348 105 0.22
349 89 0.19
350 140 0.29
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (346 bp):
TTAAGCAATTAATTAAATCATTAATATTATAATATTTTATTTATTTAATTAATTAAGGTTTGAGG
GACTTAATTACATAATTTAACTAATTAAAAAGAATCATGTATTAGTAATTAATCAATTAATTAAA
TTAGTAAATTTAGTAAAATTTAAAATTATTTAAATTAATTAAGATTTATTAAATTAATTAAATAA
TTTAACTAATCCAATGAAAAAATATTTAACTAATTAAGCAATTAATTAAATCAGAAATATTATTT
AATTTATAAAATATTCAAATTAATTAAGGTTTAATGAGTTAATCAAATAATTTAGTTAATTAAGT
AATGTAATGTGTTATAAGTAA
Found at i:12867721 original size:20 final size:20
Alignment explanation
Indices: 12867698--12867751 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
12867688 AATTTAATAA
12867698 AATTTAAAATTATTTAAATT
1 AATTTAAAATTATTTAAATT
* *
12867718 AA-TTAAGATTTTATTAAATT
1 AATTTAAAATTAT-TTAAATT
* *
12867738 AATTAAAAAATATT
1 AATTTAAAATTATT
12867752 ATATACTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
19 8 0.31
20 12 0.46
21 6 0.23
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
AATTTAAAATTATTTAAATT
Found at i:12867750 original size:116 final size:116
Alignment explanation
Indices: 12866855--12867744 Score: 630
Period size: 116 Copynumber: 7.7 Consensus size: 116
12866845 ATTTTAGTTC
** * *
12866855 TTAAGCAATTAATTAAATTAGT-AATATT-ATTTAATTTAAAAATATTTAAATTAATTAAGGTGT
1 TTAAGCAATTAATTAAATTAGTAAATATTAATAAAATTTAAAATTATTTAAATTAATTAAGGTTT
* * *
12866918 GAGGGAACTAATTATATAATTTAACTAATTAAAAAGAATCATGTATTAGTAA
66 GAGTGAATTAATTAAATAATTTAACTAATTAAAAAGAAT-ATGTATTAGTAA
* * * * * * *
12866970 TTAAGAAAGTAATTAAACTATTAAAT-TTAGTAAAATTTAAAATTATTTAAATTAATCAAAGATT
1 TTAAGCAATTAATTAAATTAGTAAATATTAATAAAATTTAAAATTATTTAAATTAAT-TAAGGTT
* * * * *
12867034 T-ATTAAATTAATTAAATAATTTAACTAATCCAATGAAAAAATAT-T-TTACTAA
65 TGAGTGAATTAATTAAATAATTTAACTAAT-TAA--AAAGAATATGTATTAGTAA
* ** * *
12867086 TTAAGCAATTAATTAAATCAGT-AATATT-ATTTAATTTATAAAATATTCAAATTAATTAAGGTT
1 TTAAGCAATTAATTAAATTAGTAAATATTAATAAAATTTA-AAATTATTTAAATTAATTAAGGTT
* ** * * * *
12867149 TGA-TGAGTTAATTAAATAATTTAGTTAATTAGGTAATGTAATGTGTTATAAGTAA
65 TGAGTGAATTAATTAAATAATTTAACTAATTA--AAAAG-AATATG-TATTAGTAA
* * * * * *
12867204 TTAAGCAATTAATTAAATCA-TTAATATTATGTAATATTT-TATTTATTTAAA-TAAGTTAAGGT
1 TTAAGCAATTAATTAAATTAGTAAATATTA-ATAAAATTTAAAATTATTTAAATTAA-TTAAGGT
* * * *
12867266 TGGAG-GCAATTAATTACATAATTTAACTAATTAAAAAGAATCATGTACTAATAA
64 TTGAGTG-AATTAATTAAATAATTTAACTAATTAAAAAGAAT-ATGTATTAGTAA
* **
12867320 TTAATCAATTAATTAAATTAGTAAAT-TTTGTAAAATTTAAAATTATTTAAATTAATTAAGGTTC
1 TTAAGCAATTAATTAAATTAGTAAATATTAATAAAATTTAAAATTATTTAAATTAATTAAGGTT-
* * * * *
12867384 T-ATTAAATTAATTCAATAATTTAACTAATCAACTGAA-AA-ATGT-TTAAGTAA
65 TGAGTGAATTAATTAAATAATTTAACTAATTAA--AAAGAATATGTATT-AGTAA
* *** *
12867435 TTAAGCAATTAATTAAACTAG-AAATATT-ATTTCATTATATAA-TATTTAAATTAATTAAGGTT
1 TTAAGCAATTAATTAAATTAGTAAATATTAATAAAATT-TAAAATTATTTAAATTAATTAAGGTT
* * * *** * * * *
12867497 T-AATGAGTTAATCAAATAATTTGGTTAATTAAGTAATGTAATGTGTTATAAGTGA
65 TGAGTGAATTAATTAAATAATTTAACTAATTAA--AAAG-AATATG-TATTAGTAA
* * * * * * *
12867552 TTAAGTAATTAATTAAATCA-TTAATATTACAT---ATTT-TATTTATTTCAATTAATTGAGGTT
1 TTAAGCAATTAATTAAATTAGTAAATATTA-ATAAAATTTAAAATTATTTAAATTAATTAAGGTT
* * * * *
12867612 TGAGGGACTTAATTACATAATATAAATAATTAAAAAGAATAATGTATTAGTAA
65 TGAGTGAATTAATTAAATAATTTAACTAATTAAAAAGAAT-ATGTATTAGTAA
* *
12867665 TTAATCAATTAATTAAATTAGTAAAT-TTAATAAAATTTAAAATTATTTAAATTAATTAAGATTT
1 TTAAGCAATTAATTAAATTAGTAAATATTAATAAAATTTAAAATTATTTAAATTAATTAAGGTTT
* * *
12867729 TATTAAATTAATTAAA
66 GAGTGAATTAATTAAA
12867745 AAATATTATA
Statistics
Matches: 593, Mismatches: 134, Indels: 95
0.72 0.16 0.12
Matches are distributed among these distances:
112 2 0.00
113 55 0.09
114 43 0.07
115 129 0.22
116 219 0.37
117 55 0.09
118 55 0.09
119 30 0.05
120 5 0.01
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (116 bp):
TTAAGCAATTAATTAAATTAGTAAATATTAATAAAATTTAAAATTATTTAAATTAATTAAGGTTT
GAGTGAATTAATTAAATAATTTAACTAATTAAAAAGAATATGTATTAGTAA
Found at i:12872037 original size:13 final size:14
Alignment explanation
Indices: 12872009--12872037 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12871999 ACATAACATA
12872009 TACTTAAAATCAAT
1 TACTTAAAATCAAT
12872023 TACTTAAAA-CAAT
1 TACTTAAAATCAAT
12872036 TA
1 TA
12872038 AAATAAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (14 bp):
TACTTAAAATCAAT
Found at i:12889626 original size:21 final size:21
Alignment explanation
Indices: 12889577--12889618 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 21
12889567 TTTAATATTA
12889577 AATATATTATAAATATTTTTTAT
1 AATATA-TA-AAATATTTTTTAT
12889600 AATATATAAAATATTTTTT
1 AATATATAAAATATTTTTT
12889619 TATTTATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.58
22 2 0.11
23 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AATATATAAAATATTTTTTAT
Found at i:12890391 original size:6 final size:6
Alignment explanation
Indices: 12890380--12890404 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12890370 CACCATGATC
12890380 TATAAA TATAAA TATAAA TATAAA T
1 TATAAA TATAAA TATAAA TATAAA T
12890405 TCTTAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TATAAA
Found at i:12906816 original size:18 final size:18
Alignment explanation
Indices: 12906793--12906835 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
12906783 CAGCAGGTTG
12906793 GCAATTGAAGGGAACGCT
1 GCAATTGAAGGGAACGCT
12906811 GCAATTGAAGGGAACGCT
1 GCAATTGAAGGGAACGCT
12906829 GCAATTG
1 GCAATTG
12906836 CCAACCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.33, T:0.19
Consensus pattern (18 bp):
GCAATTGAAGGGAACGCT
Found at i:12912894 original size:14 final size:13
Alignment explanation
Indices: 12912869--12912906 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
12912859 GATATGAAAT
12912869 ATAATTTAAAAAA
1 ATAATTTAAAAAA
12912882 ATAATTATAAAAAA
1 ATAATT-TAAAAAA
12912896 A-ATATTTAAAA
1 ATA-ATTTAAAA
12912907 GATGAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAATTTAAAAAA
Found at i:12917289 original size:17 final size:17
Alignment explanation
Indices: 12917267--12917301 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12917257 CAGCTTTTAT
12917267 TCTTTAAAATATCTTCA
1 TCTTTAAAATATCTTCA
12917284 TCTTTAAAATATCTTCA
1 TCTTTAAAATATCTTCA
12917301 T
1 T
12917302 TCTCTTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (17 bp):
TCTTTAAAATATCTTCA
Found at i:12928372 original size:201 final size:202
Alignment explanation
Indices: 12928025--12928536 Score: 710
Period size: 203 Copynumber: 2.5 Consensus size: 202
12928015 ACACATTCAT
* * *
12928025 GCAGTGCTCAAAAACTACTGAACAAAAACCTCAAAATAAGAGATGAATTG--CAAGTCACGCACC
1 GCAGTGCT-AAAAACTAGTGAACAAAAACCTCAAAACAAGAGATGAATTGCACAAGTCACGCACT
* * *
12928088 GCCAGTCTCGCAATACCTAATAATGAGTCACCCAATGCGTAATATCCACTCATATTATGCCAACA
65 GCCAGTCTCGCAATACCTAATAATAAGTCACTCAATGCGTAATATCCACTCACATTATGCCAACA
* *
12928153 TAACCAGTCACATAACGG-CCAATGTCATGCAAAA-ATAACAACAGATCACGCAATACATAAAAA
130 TAACCAATCACATAACGGCCCAATGTCACGCAAAACATAACAACAGATCACGCAATACATAAAAA
12928216 TCAGTCAC
195 TCAGTCAC
* *
12928224 GCAGTGCCTAAAAACTAGTGAACAAAAACCTCAAAACAAGAGATGAATTGCACAAATCATGCACT
1 GCAGTG-CTAAAAACTAGTGAACAAAAACCTCAAAACAAGAGATGAATTGCACAAGTCACGCACT
* * *
12928289 GCTAGTCTTGCAATACCTAATAATAAGTCACTCAATGTGTAATATCCACTCACATTATGCCAACA
65 GCCAGTCTCGCAATACCTAATAATAAGTCACTCAATGCGTAATATCCACTCACATTATGCCAACA
** * *
12928354 TAACCAATCATGTAACGGCCCAATGTCACGCAAAACATAACAACAGGTTACGCAATACATAAAAA
130 TAACCAATCACATAACGGCCCAATGTCACGCAAAACATAACAACAGATCACGCAATACATAAAAA
*
12928419 TTAGTCAC
195 TCAGTCAC
* * * * *
12928427 TCAATGTCTACAAACTAGTGAAAAAAAACCTCAAAACAAGGGATGAATTGCACAAGTCACGCACC
1 GCAGTG-CTAAAAACTAGTGAACAAAAACCTCAAAACAAGAGATGAATTGCACAAGTCACGCA-C
* * * *
12928492 T-CCAATCTCGTAATACCTAATAATAACTCTCTCAATGCGTAATAT
64 TGCCAGTCTCGCAATACCTAATAATAAGTCACTCAATGCGTAATAT
12928537 GGAGAGGCTT
Statistics
Matches: 274, Mismatches: 33, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
199 45 0.16
200 2 0.01
201 84 0.31
202 15 0.05
203 126 0.46
204 2 0.01
ACGTcount: A:0.42, C:0.25, G:0.13, T:0.21
Consensus pattern (202 bp):
GCAGTGCTAAAAACTAGTGAACAAAAACCTCAAAACAAGAGATGAATTGCACAAGTCACGCACTG
CCAGTCTCGCAATACCTAATAATAAGTCACTCAATGCGTAATATCCACTCACATTATGCCAACAT
AACCAATCACATAACGGCCCAATGTCACGCAAAACATAACAACAGATCACGCAATACATAAAAAT
CAGTCAC
Found at i:12929526 original size:28 final size:28
Alignment explanation
Indices: 12929493--12929577 Score: 143
Period size: 28 Copynumber: 3.0 Consensus size: 28
12929483 AATGTCGATA
*
12929493 TAAGTGCAATTAAGGGGGTTGAATTGGT
1 TAAGTGCAATTAAGGGGGCTGAATTGGT
12929521 TAAGTGCAATTAAGGGGGCTGAATTGGT
1 TAAGTGCAATTAAGGGGGCTGAATTGGT
* *
12929549 TCAGTGCAATTAAAGGGGCTGAATTGGT
1 TAAGTGCAATTAAGGGGGCTGAATTGGT
12929577 T
1 T
12929578 GTTAAGCATT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.28, C:0.07, G:0.34, T:0.31
Consensus pattern (28 bp):
TAAGTGCAATTAAGGGGGCTGAATTGGT
Found at i:12929635 original size:63 final size:62
Alignment explanation
Indices: 12929559--12929761 Score: 255
Period size: 63 Copynumber: 3.2 Consensus size: 62
12929549 TCAGTGCAAT
* * * *
12929559 TAAAGGGGCTGAATTGGTTGTTAAGCATTTCCAATTCTCTAATAATTTTACAGAATTTGTTA-
1 TAAAGGGGCTGAATTGGTTATTAAGTA-TTCCAATTCTCTTATAATTTTACAAAATTTGTTAG
* * * * *
12929621 TAAAGGGGGTTGAATTGTTTATTAAGTATTCTTAATTCTCTTATAATTTTACATAATTTGTTAT
1 TAAA-GGGGCTGAATTGGTTATTAAGTATTC-CAATTCTCTTATAATTTTACAAAATTTGTTAG
* * *
12929685 TAAAAGGGCTGAATTGGTTATTAAGTATTCCTAATTCTCTTCTAACTTTACAAAATTTGTTAG
1 TAAAGGGGCTGAATTGGTTATTAAGTATTCC-AATTCTCTTATAATTTTACAAAATTTGTTAG
12929748 TAAAGGGGCTGAAT
1 TAAAGGGGCTGAAT
12929762 AAGTACATAA
Statistics
Matches: 121, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
62 7 0.06
63 110 0.91
64 4 0.03
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (62 bp):
TAAAGGGGCTGAATTGGTTATTAAGTATTCCAATTCTCTTATAATTTTACAAAATTTGTTAG
Found at i:12929857 original size:15 final size:15
Alignment explanation
Indices: 12929837--12929870 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
12929827 ATGCTAAAAA
12929837 AATATTCAGTCACAT
1 AATATTCAGTCACAT
*
12929852 AATATTCAGTCACGT
1 AATATTCAGTCACAT
12929867 AATA
1 AATA
12929871 CCAAATAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (15 bp):
AATATTCAGTCACAT
Found at i:12930443 original size:19 final size:19
Alignment explanation
Indices: 12930415--12930504 Score: 76
Period size: 21 Copynumber: 4.6 Consensus size: 19
12930405 TTCTCACAAT
*
12930415 TTTTTCATTTTTAAAATATA
1 TTTTTAATTTTTAAAA-ATA
12930435 TTTTT-ATTTTTAAAAA-A
1 TTTTTAATTTTTAAAAATA
*
12930452 TTTTATAATTTTTATAACATA
1 TTTT-TAATTTTTA-AAAATA
* *
12930473 TTTTTATTTTTTTAAAAAAAA
1 TTTTTA-ATTTTT-AAAAATA
*
12930494 TTTATAATTTT
1 TTTTTAATTTT
12930505 ATCTTAATAA
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
17 5 0.09
18 2 0.03
19 17 0.29
20 14 0.24
21 19 0.33
22 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTTAATTTTTAAAAATA
Found at i:12930506 original size:40 final size:38
Alignment explanation
Indices: 12930421--12930504 Score: 114
Period size: 38 Copynumber: 2.1 Consensus size: 38
12930411 CAATTTTTTC
* * *
12930421 ATTTTTAAAATATATTTTTATTTTTAAAAAATTTTATA
1 ATTTTTATAACATATTTTTATTTTTAAAAAAATTTATA
12930459 ATTTTTATAACATATTTTTATTTTTTTAAAAAAAATTTATA
1 ATTTTTATAACATATTTTTA--TTTTT-AAAAAAATTTATA
12930500 ATTTT
1 ATTTT
12930505 ATCTTAATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
38 18 0.45
40 5 0.12
41 17 0.43
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (38 bp):
ATTTTTATAACATATTTTTATTTTTAAAAAAATTTATA
Found at i:12937604 original size:35 final size:35
Alignment explanation
Indices: 12937533--12937613 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 35
12937523 AATGTCTTGA
* * *
12937533 TAAAGGTTATGCCTGATTATGCAAAATGCATGTTG
1 TAAAGATTATGCCTGATCATGCAAAATGCATATTG
* * *
12937568 TAGAGATTATGCCTGATCCTGC-AAATAGTATATTG
1 TAAAGATTATGCCTGATCATGCAAAAT-GCATATTG
*
12937603 TAAAGGTTATG
1 TAAAGATTATG
12937614 TCTAACCTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
34 4 0.11
35 33 0.89
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.35
Consensus pattern (35 bp):
TAAAGATTATGCCTGATCATGCAAAATGCATATTG
Found at i:12939339 original size:108 final size:109
Alignment explanation
Indices: 12939150--12939355 Score: 333
Period size: 108 Copynumber: 1.9 Consensus size: 109
12939140 TCCTCACGTG
* *
12939150 AGAGGAACCTTGAGAAGTTGTGAGTGACTACTATTGTTGGCTTGAGGGTTTCAAAGACGTTTTCT
1 AGAGGAACCTTGAGAAGTTGTGAGTGACTACTATTGTTGGCTTGAGGGCTTCAAAGACGTGTTCT
12939215 TATGCATCAATCATGGCTGTTGTTAT-GTTCTTGCTCCCATGTA
66 TATGCATCAATCATGGCTGTTGTTATAGTTCTTGCTCCCATGTA
* * * * * *
12939258 AGAGGAACCTTGAGAAGTTGTGATTGGCTACTATTTTTGGTTTGAGGGCTTCGAAGCCGTGTTCT
1 AGAGGAACCTTGAGAAGTTGTGAGTGACTACTATTGTTGGCTTGAGGGCTTCAAAGACGTGTTCT
12939323 TATGCATCAATCATGGCTGTTGTTATAGTTCTT
66 TATGCATCAATCATGGCTGTTGTTATAGTTCTT
12939356 TCCCCCACTA
Statistics
Matches: 89, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
108 83 0.93
109 6 0.07
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (109 bp):
AGAGGAACCTTGAGAAGTTGTGAGTGACTACTATTGTTGGCTTGAGGGCTTCAAAGACGTGTTCT
TATGCATCAATCATGGCTGTTGTTATAGTTCTTGCTCCCATGTA
Found at i:12945897 original size:3 final size:3
Alignment explanation
Indices: 12945889--12945916 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12945879 TAACATATGC
12945889 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
12945917 TAAGCCAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:12946704 original size:11 final size:11
Alignment explanation
Indices: 12946690--12946723 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
12946680 ACCCATTAAA
12946690 AAAAAAGAAAT
1 AAAAAAGAAAT
*
12946701 AAAAAAGAAAG
1 AAAAAAGAAAT
12946712 AAAGAAAGAAAT
1 AAA-AAAGAAAT
12946724 TAAGGGTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (11 bp):
AAAAAAGAAAT
Found at i:12949986 original size:4 final size:4
Alignment explanation
Indices: 12949979--12950003 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
12949969 TATATATATA
12949979 TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG T
12950004 CAAAAGAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:12957945 original size:27 final size:26
Alignment explanation
Indices: 12957913--12957966 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 26
12957903 CTTCAACATC
12957913 ACCCATCCAATGCATATATAAATTGAA
1 ACCCATCCAATGCATATATAAA-TGAA
*
12957940 ACCCATCCAATGCATATATTAATGAA
1 ACCCATCCAATGCATATATAAATGAA
12957966 A
1 A
12957967 GTTGCGACTC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.26
Consensus pattern (26 bp):
ACCCATCCAATGCATATATAAATGAA
Found at i:12958270 original size:2 final size:2
Alignment explanation
Indices: 12958263--12958327 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
12958253 CTTCCTCTTT
*
12958263 AC AC AC AC AC AC AC AC TC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
12958305 AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC A
12958328 TATATATATA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.49, G:0.00, T:0.02
Consensus pattern (2 bp):
AC
Found at i:12958332 original size:2 final size:2
Alignment explanation
Indices: 12958327--12958353 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12958317 ACACACACAC
12958327 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
12958354 CTGACTGCTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12963066 original size:32 final size:32
Alignment explanation
Indices: 12963025--12963088 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
12963015 GTTCGAGACA
12963025 ATCAGCATAACTTGGCATAATTCATCATGTGC
1 ATCAGCATAACTTGGCATAATTCATCATGTGC
12963057 ATCAGCATAACTTGGCATAATTCATCATGTGC
1 ATCAGCATAACTTGGCATAATTCATCATGTGC
12963089 TTAGAATTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (32 bp):
ATCAGCATAACTTGGCATAATTCATCATGTGC
Found at i:12967379 original size:16 final size:16
Alignment explanation
Indices: 12967358--12967407 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
12967348 TTACAAATAA
12967358 ATAAATTACACCAAAC
1 ATAAATTACACCAAAC
*
12967374 ATAAA-TA-AGC-AA-
1 ATAAATTACACCAAAC
*
12967386 GTAAATTACACCAAAC
1 ATAAATTACACCAAAC
12967402 ATAAAT
1 ATAAAT
12967408 AAAGTTTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
12 4 0.15
13 4 0.15
14 4 0.15
15 4 0.15
16 10 0.38
ACGTcount: A:0.58, C:0.18, G:0.04, T:0.20
Consensus pattern (16 bp):
ATAAATTACACCAAAC
Found at i:12979129 original size:2 final size:2
Alignment explanation
Indices: 12979122--12979188 Score: 118
Period size: 2 Copynumber: 34.0 Consensus size: 2
12979112 AAAGATACTA
*
12979122 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12979164 CT CT CT CT -T CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
12979189 ATATATATAT
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:12979193 original size:2 final size:2
Alignment explanation
Indices: 12979188--12979217 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12979178 TCTCTCTCTC
12979188 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12979218 GCATTATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12984764 original size:60 final size:60
Alignment explanation
Indices: 12984691--12984814 Score: 239
Period size: 60 Copynumber: 2.1 Consensus size: 60
12984681 AGAGAAATCT
*
12984691 TTAAAGACCACAATAAAGGAGTGCATATAACATAGTAAACAGACTAGCAGGAAACTCTGC
1 TTAAAGACCACAATAAAGAAGTGCATATAACATAGTAAACAGACTAGCAGGAAACTCTGC
12984751 TTAAAGACCACAATAAAGAAGTGCATATAACATAGTAAACAGACTAGCAGGAAACTCTGC
1 TTAAAGACCACAATAAAGAAGTGCATATAACATAGTAAACAGACTAGCAGGAAACTCTGC
12984811 TTAA
1 TTAA
12984815 CTTTCCCAAA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.46, C:0.18, G:0.17, T:0.19
Consensus pattern (60 bp):
TTAAAGACCACAATAAAGAAGTGCATATAACATAGTAAACAGACTAGCAGGAAACTCTGC
Found at i:12996910 original size:32 final size:31
Alignment explanation
Indices: 12996874--12996963 Score: 92
Period size: 31 Copynumber: 2.9 Consensus size: 31
12996864 ATTTTCAAAA
* * *
12996874 AAAAATTTATACTATAAGAAACTAAATTAAAT
1 AAAAATATATAATATAAG-AACTAAATTAAAC
*
12996906 AAAAATATATAATATAAGAATTAAATTAAAC
1 AAAAATATATAATATAAGAACTAAATTAAAC
* * *
12996937 AAAACTGAGATATTA-AAGAACTAAATT
1 AAAAAT-ATATAATATAAGAACTAAATT
12996964 GAAAACATAT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
31 27 0.55
32 22 0.45
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.29
Consensus pattern (31 bp):
AAAAATATATAATATAAGAACTAAATTAAAC
Found at i:12996934 original size:31 final size:32
Alignment explanation
Indices: 12996874--12996940 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
12996864 ATTTTCAAAA
* * *
12996874 AAAAATTTATACTATAAGAAACTAAATTAAAT
1 AAAAATATATAATATAAGAAACTAAATTAAAC
*
12996906 AAAAATATATAATATAAG-AATTAAATTAAAC
1 AAAAATATATAATATAAGAAACTAAATTAAAC
12996937 AAAA
1 AAAA
12996941 CTGAGATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 15 0.48
32 16 0.52
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.28
Consensus pattern (32 bp):
AAAAATATATAATATAAGAAACTAAATTAAAC
Found at i:12997227 original size:10 final size:9
Alignment explanation
Indices: 12997199--12997236 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
12997189 CTAATTTTTT
*
12997199 ATATATATG
1 ATATATATA
12997208 ATATATAT-
1 ATATATATA
12997216 ATATAT-TA
1 ATATATATA
12997224 ATATATATA
1 ATATATATA
12997233 ATAT
1 ATAT
12997237 TTTATACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 1 0.04
8 12 0.44
9 14 0.52
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (9 bp):
ATATATATA
Found at i:12997281 original size:16 final size:16
Alignment explanation
Indices: 12997257--12997290 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12997247 TATTAAGAAA
*
12997257 AATTGATAATAAACTT
1 AATTAATAATAAACTT
*
12997273 AATTAATAATATACTT
1 AATTAATAATAAACTT
12997289 AA
1 AA
12997291 AATATATTAA
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:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (16 bp):
AATTAATAATAAACTT
Found at i:13001283 original size:70 final size:71
Alignment explanation
Indices: 13001140--13001326 Score: 220
Period size: 70 Copynumber: 2.6 Consensus size: 71
13001130 TGTTTTTAAC
* * * * * *
13001140 AAATGAAAAATATTTGGAATTTATTTAAAATATTAAAAATTCAAATTCAAATTAGAAGTCAAATG
1 AAATAAAAAATA-TTAGAATTTATTTAAAATATTGAAAACTCAAATTCAAATTAAAAGTCAAAGG
*
13001205 TGGATAT
65 TAGATAT
* *
13001212 AAATAAAAAATA-TATGAATTTATTT-AAATAATTGAAAACTCAAATT-GAATTAAAAGTCAAGG
1 AAATAAAAAATATTA-GAATTTATTTAAAAT-ATTGAAAACTCAAATTCAAATTAAAAGTCAAAG
13001274 GTAGATAT
64 GTAGATAT
*
13001282 AAATAAAAAA-ATTCAAAATTTATTTAAAATATTGAAAACTCAAAT
1 AAATAAAAAATATT-AGAATTTATTTAAAATATTGAAAACTCAAAT
13001327 GTATATAAAA
Statistics
Matches: 100, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
69 1 0.01
70 59 0.59
71 29 0.29
72 11 0.11
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (71 bp):
AAATAAAAAATATTAGAATTTATTTAAAATATTGAAAACTCAAATTCAAATTAAAAGTCAAAGGT
AGATAT
Found at i:13001326 original size:26 final size:26
Alignment explanation
Indices: 13001297--13001383 Score: 66
Period size: 28 Copynumber: 3.2 Consensus size: 26
13001287 AAAAAATTCA
13001297 AAATTTATTTAAAATATTGAAAACTC
1 AAATTTATTTAAAATATTGAAAACTC
** *** * *
13001323 AAATGTATATAAAAAATAAAAAAATATTT
1 AAAT-T-TATTTAAAATATTGAAA-ACTC
*
13001352 AGAATTTATTTAAAATGTTGAAAACTC
1 A-AATTTATTTAAAATATTGAAAACTC
13001379 AAATT
1 AAATT
13001384 GAAGTTAGTG
Statistics
Matches: 42, Mismatches: 15, Indels: 8
0.65 0.23 0.12
Matches are distributed among these distances:
26 8 0.19
27 4 0.10
28 23 0.55
29 4 0.10
30 3 0.07
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.36
Consensus pattern (26 bp):
AAATTTATTTAAAATATTGAAAACTC
Found at i:13001693 original size:14 final size:14
Alignment explanation
Indices: 13001674--13001723 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
13001664 ATGTTACAAA
13001674 TAAATAAATTATAT
1 TAAATAAATTATAT
*
13001688 TAAATATAAATA-AGT
1 TAAATA-AATTATA-T
13001703 T-AATAAATTATAT
1 TAAATAAATTATAT
*
13001716 CAAATAAA
1 TAAATAAA
13001724 AGTAAACTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
13 5 0.17
14 18 0.62
15 6 0.21
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (14 bp):
TAAATAAATTATAT
Found at i:13002050 original size:22 final size:22
Alignment explanation
Indices: 13002024--13002093 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
13002014 CAATACCATT
13002024 AATAATTAAATTATTAATTTTA
1 AATAATTAAATTATTAATTTTA
* *
13002046 TATAATTAAATATATAAAATTATTA
1 AATAATTAAAT-TAT-TAATT-TTA
*
13002071 AATTAACTAAATTAATTAATTTT
1 AA-TAATTAAATT-ATTAATTTT
13002094 TTTTGATCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
22 10 0.26
23 3 0.08
24 6 0.16
25 9 0.24
26 10 0.26
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (22 bp):
AATAATTAAATTATTAATTTTA
Found at i:13009827 original size:18 final size:19
Alignment explanation
Indices: 13009804--13009840 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
13009794 CTTCTTACTC
13009804 CCTTTAAATACTT-TTTTT
1 CCTTTAAATACTTATTTTT
13009822 CCTTTAAATACTTATTTTT
1 CCTTTAAATACTTATTTTT
13009841 ATATTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.59
Consensus pattern (19 bp):
CCTTTAAATACTTATTTTT
Found at i:13014107 original size:28 final size:28
Alignment explanation
Indices: 13014074--13014127 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
13014064 GATTGAAACT
13014074 TTATTTATGTTTAATGTAATTTATTTTC
1 TTATTTATGTTTAATGTAATTTATTTTC
**
13014102 TTATTTATGTTTGGTGTAATTTATTT
1 TTATTTATGTTTAATGTAATTTATTT
13014128 ATTTTAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.22, C:0.02, G:0.11, T:0.65
Consensus pattern (28 bp):
TTATTTATGTTTAATGTAATTTATTTTC
Found at i:13015572 original size:57 final size:58
Alignment explanation
Indices: 13015472--13015582 Score: 129
Period size: 57 Copynumber: 1.9 Consensus size: 58
13015462 TTTAAAGATT
* * * * *
13015472 ATATATTCAAAATAATTTCCTTTCAACTAAATATAAAATATAAAATAT-ATATAAAAG
1 ATATATTCAAAATAAATTCCTCTCAACTAAACAGAAAATATAAAAAATGATATAAAAG
*
13015529 ATATATTCAAAATAAATTCCTCTC-ACATAAACAG-AATTAATAAAAAATGATATA
1 ATATATTCAAAATAAATTCCTCTCAAC-TAAACAGAAAAT-ATAAAAAATGATATA
13015583 TTAATGAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
56 5 0.11
57 35 0.78
58 5 0.11
ACGTcount: A:0.54, C:0.11, G:0.03, T:0.32
Consensus pattern (58 bp):
ATATATTCAAAATAAATTCCTCTCAACTAAACAGAAAATATAAAAAATGATATAAAAG
Found at i:13015844 original size:18 final size:18
Alignment explanation
Indices: 13015821--13015858 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
13015811 AGTATAAACA
13015821 AATATAAA-TAAAAATAAT
1 AATATAAATTAAAAA-AAT
13015839 AATATAAATTAAAAAAAT
1 AATATAAATTAAAAAAAT
13015857 AA
1 AA
13015859 AAAAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AATATAAATTAAAAAAAT
Found at i:13015868 original size:18 final size:19
Alignment explanation
Indices: 13015829--13015871 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
13015819 CAAATATAAA
*
13015829 TAAAAATAATAATATAAAT
1 TAAAAATAATAATAAAAAT
13015848 TAAAAA-AATAA-AAAAAT
1 TAAAAATAATAATAAAAAT
*
13015865 TTAAAAT
1 TAAAAAT
13015872 TAAGTGAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 10 0.48
18 5 0.24
19 6 0.29
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAAATAATAATAAAAAT
Found at i:13023977 original size:35 final size:35
Alignment explanation
Indices: 13023931--13024099 Score: 169
Period size: 35 Copynumber: 4.8 Consensus size: 35
13023921 NNNNNNNNNN
13023931 CAATAACTTAATTAAATAATTTAATTAATTAAGCT
1 CAATAACTTAATTAAATAATTTAATTAATTAAGCT
* * * *
13023966 CAACAATTTAATTAAATAATTTTAATCAATT-AGGT
1 CAATAACTTAATTAAATAA-TTTAATTAATTAAGCT
*** * *
13024001 CTAATAACTTAATTGTTTAATTTAATTAATTAGGTT
1 C-AATAACTTAATTAAATAATTTAATTAATTAAGCT
* * *
13024037 CAATGACTTAATTAAATAATTTAATTAATTAGGCC
1 CAATAACTTAATTAAATAATTTAATTAATTAAGCT
*** *
13024072 CAATGGTTTAATTAAACAATTTAATTAA
1 CAATAACTTAATTAAATAATTTAATTAA
13024100 GCAATTTTAA
Statistics
Matches: 110, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
35 84 0.76
36 26 0.24
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (35 bp):
CAATAACTTAATTAAATAATTTAATTAATTAAGCT
Found at i:13029097 original size:15 final size:14
Alignment explanation
Indices: 13029063--13029093 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13029053 ACAGTTTATC
*
13029063 TATAAAAAAGAATT
1 TATAAAAAAAAATT
13029077 TATAAAAAAAAATT
1 TATAAAAAAAAATT
13029091 TAT
1 TAT
13029094 TAAATAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (14 bp):
TATAAAAAAAAATT
Found at i:13035450 original size:24 final size:24
Alignment explanation
Indices: 13035418--13035467 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
13035408 AAGAACATGC
13035418 AATACATGATAATTTATTAGATTG
1 AATACATGATAATTTATTAGATTG
13035442 AATACATGATAATTTATTAGATTG
1 AATACATGATAATTTATTAGATTG
13035466 AA
1 AA
13035468 AAATGTTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (24 bp):
AATACATGATAATTTATTAGATTG
Found at i:13041546 original size:19 final size:19
Alignment explanation
Indices: 13041508--13041546 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
13041498 TCATCCTGAG
*
13041508 ACCTTCTAAGTGACCCAAA
1 ACCTTCTAAGTGACCAAAA
*
13041527 ACCTTCTAAGTGACTAAAA
1 ACCTTCTAAGTGACCAAAA
13041546 A
1 A
13041547 GGTTGGTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.23
Consensus pattern (19 bp):
ACCTTCTAAGTGACCAAAA
Found at i:13046017 original size:15 final size:16
Alignment explanation
Indices: 13045983--13046020 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
13045973 TCCTTAAAGT
* *
13045983 ATAACTAAAGTAAAAG
1 ATAATTAAAGTAAAAA
13045999 ATAATTAAAG-AAAAA
1 ATAATTAAAGTAAAAA
13046014 ATAATTA
1 ATAATTA
13046021 TAAAAATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.24
Consensus pattern (16 bp):
ATAATTAAAGTAAAAA
Found at i:13047528 original size:21 final size:20
Alignment explanation
Indices: 13047459--13047528 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 20
13047449 AGATTTAACA
*
13047459 ACATTTATCGATAGATGATC
1 ACATTTATCGATAGATGAGC
*
13047479 ATCATCTT-TTGATAGAT-AGGC
1 A-CAT-TTATCGATAGATGA-GC
13047500 -CTATTTATCGATAGATCGAGC
1 AC-ATTTATCGATAGAT-GAGC
13047521 ACATTTAT
1 ACATTTAT
13047529 TGATTGATAG
Statistics
Matches: 39, Mismatches: 3, Indels: 15
0.68 0.05 0.26
Matches are distributed among these distances:
19 3 0.08
20 12 0.31
21 20 0.51
22 4 0.10
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (20 bp):
ACATTTATCGATAGATGAGC
Found at i:13047532 original size:41 final size:41
Alignment explanation
Indices: 13047461--13047538 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
13047451 ATTTAACAAC
*
13047461 ATTTATCGATAGATGATCATCATCTTTTGATAGATAGGCCT
1 ATTTATCGATAGATGAGCATCATCTTTTGATAGATAGGCCT
*
13047502 ATTTATCGATAGATCGAGCA-CAT-TTATTGATTGATAG
1 ATTTATCGATAGAT-GAGCATCATCTT-TTGATAGATAG
13047539 CAACCCGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 2 0.06
41 27 0.82
42 4 0.12
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (41 bp):
ATTTATCGATAGATGAGCATCATCTTTTGATAGATAGGCCT
Found at i:13053845 original size:16 final size:17
Alignment explanation
Indices: 13053812--13053853 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
13053802 AATACCTTTA
*
13053812 CTTTTCTTTTCCTAATT
1 CTTTTCTTTCCCTAATT
13053829 CTTTTCTTTCCCT-ATT
1 CTTTTCTTTCCCTAATT
13053845 CTTTT-TTTC
1 CTTTTCTTTC
13053854 TTTCTCTGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 4 0.17
16 8 0.33
17 12 0.50
ACGTcount: A:0.07, C:0.26, G:0.00, T:0.67
Consensus pattern (17 bp):
CTTTTCTTTCCCTAATT
Found at i:13054101 original size:17 final size:16
Alignment explanation
Indices: 13054081--13054119 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
13054071 TATTTATCTC
13054081 TTTTTTTTATTTTTTGA
1 TTTTTTTTATTTTTT-A
*
13054098 TTTTTATTATTTTTTA
1 TTTTTTTTATTTTTTA
13054114 TTTTTT
1 TTTTTT
13054120 CAAATTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.85
Consensus pattern (16 bp):
TTTTTTTTATTTTTTA
Found at i:13054103 original size:27 final size:24
Alignment explanation
Indices: 13054059--13054126 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 24
13054049 GAACATATCC
*
13054059 TTATCTTTTTCATATTTATCTCTTTTTT
1 TTAT-TTTTTCATATTTA--T-TATTTT
* *
13054087 TTATTTTTTGATTTTTATTATTTT
1 TTATTTTTTCATATTTATTATTTT
*
13054111 TTATTTTTTCAAATTT
1 TTATTTTTTCATATTT
13054127 CAATAGATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
24 18 0.53
25 1 0.03
27 11 0.32
28 4 0.12
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.74
Consensus pattern (24 bp):
TTATTTTTTCATATTTATTATTTT
Found at i:13055360 original size:36 final size:36
Alignment explanation
Indices: 13055319--13055400 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
13055309 AAGGTAGTGT
* *
13055319 GGTTGTACTTGATCC-TTAGAAGGTATTGTGTTGTAAA
1 GGTTGTACTTGATCCATAAG-AGGTAGTGT-TTGTAAA
*
13055356 -GTTGTGCTTGATCCATAAGAGGTAGTGTTTGTAAA
1 GGTTGTACTTGATCCATAAGAGGTAGTGTTTGTAAA
*
13055391 GGTTATACTT
1 GGTTGTACTT
13055401 AAGCCTTTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
35 7 0.18
36 28 0.74
37 3 0.08
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.40
Consensus pattern (36 bp):
GGTTGTACTTGATCCATAAGAGGTAGTGTTTGTAAA
Found at i:13061590 original size:18 final size:18
Alignment explanation
Indices: 13061569--13061604 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
13061559 AAGAAGATTG
13061569 GAAAAAGAGAGAAAAGAA
1 GAAAAAGAGAGAAAAGAA
* *
13061587 GAAAGAGAGAGGAAAGAA
1 GAAAAAGAGAGAAAAGAA
13061605 AAAGACAAAT
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
GAAAAAGAGAGAAAAGAA
Found at i:13061593 original size:16 final size:16
Alignment explanation
Indices: 13061569--13061609 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
13061559 AAGAAGATTG
13061569 GAAAAAGAGAGA-AAA
1 GAAAAAGAGAGAGAAA
13061584 GAAGAAAGAGAGAGGAAA
1 GAA-AAAGAGAGA-GAAA
13061602 GAAAAAGA
1 GAAAAAGA
13061610 CAAATCTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 3 0.13
16 9 0.39
17 5 0.22
18 6 0.26
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (16 bp):
GAAAAAGAGAGAGAAA
Found at i:13067832 original size:323 final size:321
Alignment explanation
Indices: 13067220--13067810 Score: 934
Period size: 323 Copynumber: 1.8 Consensus size: 321
13067210 TAGGAGCAAT
*
13067220 AAAGCCTCCTTAACTCTTTTTTTCCTCAAAGAATCCTTTTGGAGAAAAACCCCTCCTTAAACAAG
1 AAAGCCTCCTTAACTCTTTTTTCCCTCAAAGAATCCTTTTGGAGAAAAACCCCTCCTTAAACAAG
*
13067285 CATTGGTGACCCAAGTCGTGGCACAAAAAACATAACATTAAGAAAAGAGAGGCAAAAAAGTTACT
66 CATTGGTGACCCAAGTCGTGGCACAAAAAACATAACACTAAGAAAAGAGAGGCAAAAAAGTTACT
* * *
13067350 GTGTCACCAAAAAGACAATCTCTAGAGAAAACAACATGGAACAAAGCAACCTTTCTCCAAGGAAA
131 GTGTCACAAAAAAGACAATCTCCAAAGAAAACAACATGGAACAAAGCAACCTTTCTCCAAGGAAA
* * *
13067415 GCGGACCTCAAGCTCCATGAGCCCTCCTTGTTCCATCAGCACACCACTCACAATCCTATGAACAT
196 GAGGACCTCAAGCTCCATGAACCCTCCTTGTTCCATCAGCACACCACTCACAATCCTAAGAACAT
13067480 ATGACCACCACCCTCTTGCCTTAAAGAAGCAACACCTTTTCCCTTCAACCCTTATACCGAC
261 ATGACCACCACCCTCTTGCCTTAAAGAAGCAACACCTTTTCCCTTCAACCCTTATACCGAC
*
13067541 AAAGCCTCCTTAACTCTTTTTTCCCTCAAAGAATCC-TTTGGAGAAGAA-CCCTCCTTAAACAAG
1 AAAGCCTCCTTAACTCTTTTTTCCCTCAAAGAATCCTTTTGGAGAAAAACCCCTCCTTAAACAAG
* * * **
13067604 CATTGGTGACCTAAGTCGTGGCACAAAAAACATAACACTAAGAAAAGTGAGGCAAAGAAGTTGTT
66 CATTGGTGACCCAAGTCGTGGCACAAAAAACATAACACTAAGAAAAGAGAGGCAAAAAAGTTACT
*
13067669 GTGTCACAAAAAAGATAATCTCCAAAGAAACTCAACAACATGGAACAAAGCAACCTTTCTCCAAG
131 GTGTCACAAAAAAGACAATCTCCAAAG-AA---AACAACATGGAACAAAGCAACCTTTCTCCAAG
* * * * ** *
13067734 GGAAGAGGACCTCAAGCTTCATGAACCTTCTTTGTTCCATCAGCACACTGCTCATAATCCTAAGA
192 GAAAGAGGACCTCAAGCTCCATGAACCCTCCTTGTTCCATCAGCACACCACTCACAATCCTAAGA
13067799 ACATATGACCAC
257 ACATATGACCAC
13067811 TTCTTTTTTG
Statistics
Matches: 244, Mismatches: 22, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
319 97 0.40
320 13 0.05
321 35 0.14
323 99 0.41
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.22
Consensus pattern (321 bp):
AAAGCCTCCTTAACTCTTTTTTCCCTCAAAGAATCCTTTTGGAGAAAAACCCCTCCTTAAACAAG
CATTGGTGACCCAAGTCGTGGCACAAAAAACATAACACTAAGAAAAGAGAGGCAAAAAAGTTACT
GTGTCACAAAAAAGACAATCTCCAAAGAAAACAACATGGAACAAAGCAACCTTTCTCCAAGGAAA
GAGGACCTCAAGCTCCATGAACCCTCCTTGTTCCATCAGCACACCACTCACAATCCTAAGAACAT
ATGACCACCACCCTCTTGCCTTAAAGAAGCAACACCTTTTCCCTTCAACCCTTATACCGAC
Found at i:13076499 original size:165 final size:165
Alignment explanation
Indices: 13076227--13076560 Score: 483
Period size: 165 Copynumber: 2.0 Consensus size: 165
13076217 CCGTGATAAT
*
13076227 TGTTATGAGATTGTTGGTTACCCAACAGATTGGAAAAGAAAATTGAATGCTGGAGGAGACCAAAC
1 TGTTATGAGATTGTTGGTTACCCAACAGATTGGAAAAGAAAATTGAAAGCTGGAGGAGACCAAAC
*
13076292 ACGTGTACGCAATGGTAGAGGGCCAAGAACTTTAGCAACGTTGACTGGCACGAAAGCTCATGATT
66 ACGTGTACGCAATGGTAGAGGGCCAAGAACTTGAGCAACGTTGACTGGCACGAAAGCTCATGATT
* * *
13076357 TCCTGACTGAGACAGAAACAGGCACGCTTCAGGAG
131 TCCTGACTGAGACAGAAACAGGCACACCTCAAGAG
* * *
13076392 TGTTATGAGATTGTTGGTTACCCAATAGATTGGCAAAGAAAATTGAAAGCTGGAGGAGACCAAGC
1 TGTTATGAGATTGTTGGTTACCCAACAGATTGGAAAAGAAAATTGAAAGCTGGAGGAGACCAAAC
* * ** *
13076457 ACGTGTACGTAGTGGTAG-GGGCCCAAGAACTTCGA-CAACGTTGACTGGCACGAAAGCTTGTGT
66 ACGTGTACGCAATGGTAGAGGG-CCAAGAACTT-GAGCAACGTTGACTGGCACGAAAGCTCATGA
* ** *
13076520 TTTCTTGGTTGAGACAGAGACAGGCACACCTCAAGAG
129 TTTCCTGACTGAGACAGAAACAGGCACACCTCAAGAG
13076557 TGTT
1 TGTT
13076561 CTTCACTTGT
Statistics
Matches: 150, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
164 3 0.02
165 146 0.97
166 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (165 bp):
TGTTATGAGATTGTTGGTTACCCAACAGATTGGAAAAGAAAATTGAAAGCTGGAGGAGACCAAAC
ACGTGTACGCAATGGTAGAGGGCCAAGAACTTGAGCAACGTTGACTGGCACGAAAGCTCATGATT
TCCTGACTGAGACAGAAACAGGCACACCTCAAGAG
Found at i:13084084 original size:16 final size:18
Alignment explanation
Indices: 13084059--13084096 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
13084049 ATACATCTTC
13084059 ATTCTCTCTCTTGCCTTT
1 ATTCTCTCTCTTGCCTTT
13084077 ATTCTCTCTCTTGCCTTT
1 ATTCTCTCTCTTGCCTTT
13084095 AT
1 AT
13084097 AGTCTTCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.08, C:0.32, G:0.05, T:0.55
Consensus pattern (18 bp):
ATTCTCTCTCTTGCCTTT
Found at i:13092362 original size:25 final size:25
Alignment explanation
Indices: 13092334--13092390 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
13092324 GAAATATTGT
*
13092334 TTGTTATTAAA-TTTAATTTTTTTTA
1 TTGTT-TTAAATTTTAATATTTTTTA
13092359 TTGTTTTAAATTTTAATATTTTTTA
1 TTGTTTTAAATTTTAATATTTTTTA
*
13092384 TTTTTTT
1 TTGTTTT
13092391 TTATTAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 5 0.17
25 24 0.83
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.72
Consensus pattern (25 bp):
TTGTTTTAAATTTTAATATTTTTTA
Found at i:13092990 original size:19 final size:20
Alignment explanation
Indices: 13092963--13093000 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
13092953 TTGAACTAAA
13092963 TTTTATATTTT-ATTTAATG
1 TTTTATATTTTGATTTAATG
*
13092982 TTTTCTATTTTGATTTAAT
1 TTTTATATTTTGATTTAAT
13093001 TTTATTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTATATTTTGATTTAATG
Found at i:13093281 original size:17 final size:17
Alignment explanation
Indices: 13093259--13093291 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13093249 TTATATTTGA
*
13093259 TGTTATTATTATTTTTT
1 TGTTATAATTATTTTTT
13093276 TGTTATAATTATTTTT
1 TGTTATAATTATTTTT
13093292 ATAATTATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (17 bp):
TGTTATAATTATTTTTT
Found at i:13100109 original size:22 final size:22
Alignment explanation
Indices: 13100084--13100130 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
13100074 CACAAGTAAC
13100084 TTTCCAAACAATATAACATCCT
1 TTTCCAAACAATATAACATCCT
* * *
13100106 TTT-CTAACCATATAATATCCT
1 TTTCCAAACAATATAACATCCT
13100127 TTTC
1 TTTC
13100131 TGATTCTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTCCAAACAATATAACATCCT
Found at i:13100922 original size:17 final size:17
Alignment explanation
Indices: 13100900--13100935 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
13100890 AGGCATAAAG
13100900 CTTCATCCATGAAATCA
1 CTTCATCCATGAAATCA
13100917 CTTCATCCATGAAATCA
1 CTTCATCCATGAAATCA
13100934 CT
1 CT
13100936 AACTTTGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.31, G:0.06, T:0.31
Consensus pattern (17 bp):
CTTCATCCATGAAATCA
Found at i:13103860 original size:2 final size:2
Alignment explanation
Indices: 13103853--13103886 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
13103843 AAACCCGCGG
* *
13103853 AT AT AT AT AT AT AT AT TT AT TT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13103887 GTTCCTTGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:13105128 original size:2 final size:2
Alignment explanation
Indices: 13105121--13105146 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13105111 ACTGAAAGTG
13105121 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
13105147 GCAGTACTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13108570 original size:12 final size:12
Alignment explanation
Indices: 13108553--13108617 Score: 62
Period size: 12 Copynumber: 5.4 Consensus size: 12
13108543 CCTTAATTAG
13108553 AAATTTTCAAGA
1 AAATTTTCAAGA
* *
13108565 AAATTTCCTTAG-
1 AAATTTTC-AAGA
13108577 AAATTTTCAAGA
1 AAATTTTCAAGA
* *
13108589 AAATTTCCTTAG-
1 AAATTTTC-AAGA
13108601 AAATTTTCAAGA
1 AAATTTTCAAGA
13108613 AAATT
1 AAATT
13108618 ATCCCTTCTA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
11 4 0.10
12 33 0.80
13 4 0.10
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.37
Consensus pattern (12 bp):
AAATTTTCAAGA
Found at i:13108571 original size:11 final size:11
Alignment explanation
Indices: 13108551--13108617 Score: 53
Period size: 11 Copynumber: 5.7 Consensus size: 11
13108541 TTCCTTAATT
*
13108551 AGAAATTTTCA
1 AGAAAATTTCA
*
13108562 AGAAAATTTCCTT
1 AGAAAATTT-C-A
*
13108575 AGAAATTTTCA
1 AGAAAATTTCA
*
13108586 AGAAAATTTCCTT
1 AGAAAATTT-C-A
*
13108599 AGAAATTTTCA
1 AGAAAATTTCA
13108610 AGAAAATT
1 AGAAAATT
13108618 ATCCCTTCTA
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
11 23 0.53
12 4 0.09
13 16 0.37
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36
Consensus pattern (11 bp):
AGAAAATTTCA
Found at i:13108577 original size:24 final size:24
Alignment explanation
Indices: 13108549--13108617 Score: 138
Period size: 24 Copynumber: 2.9 Consensus size: 24
13108539 ATTTCCTTAA
13108549 TTAGAAATTTTCAAGAAAATTTCC
1 TTAGAAATTTTCAAGAAAATTTCC
13108573 TTAGAAATTTTCAAGAAAATTTCC
1 TTAGAAATTTTCAAGAAAATTTCC
13108597 TTAGAAATTTTCAAGAAAATT
1 TTAGAAATTTTCAAGAAAATT
13108618 ATCCCTTCTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (24 bp):
TTAGAAATTTTCAAGAAAATTTCC
Found at i:13108584 original size:13 final size:13
Alignment explanation
Indices: 13108549--13108608 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
13108539 ATTTCCTTAA
13108549 TTAGAAATTTT-C
1 TTAGAAATTTTCC
* *
13108561 -AAGAAAATTTCC
1 TTAGAAATTTTCC
13108573 TTAGAAATTTT-C
1 TTAGAAATTTTCC
* *
13108585 -AAGAAAATTTCC
1 TTAGAAATTTTCC
13108597 TTAGAAATTTTC
1 TTAGAAATTTTC
13108609 AAGAAAATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
11 16 0.44
12 3 0.08
13 17 0.47
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (13 bp):
TTAGAAATTTTCC
Found at i:13108731 original size:20 final size:20
Alignment explanation
Indices: 13108672--13108731 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
13108662 ACTTATTTTT
* *
13108672 TTTATTTATTTATATTAAAA
1 TTTATTTTTTTATTTTAAAA
* * * *
13108692 -TTATCTTATTAATTTCAAA
1 TTTATTTTTTTATTTTAAAA
13108711 TTTATTTTTTTATTTTAAAA
1 TTTATTTTTTTATTTTAAAA
13108731 T
1 T
13108732 CAAAATCTGA
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATTTTTTTATTTTAAAA
Found at i:13109416 original size:20 final size:23
Alignment explanation
Indices: 13109393--13109439 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 23
13109383 ATACTAGAAG
13109393 TAAAAT-AATAAT-AAAATAA-A
1 TAAAATAAATAATAAAAATAATA
13109413 T-AAATAAATAATAAAAATAATA
1 TAAAATAAATAATAAAAATAATA
13109435 TAAAA
1 TAAAA
13109440 CACCAAGCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 4 0.17
20 7 0.30
21 7 0.30
22 2 0.09
23 3 0.13
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (23 bp):
TAAAATAAATAATAAAAATAATA
Found at i:13110516 original size:47 final size:48
Alignment explanation
Indices: 13110459--13110888 Score: 297
Period size: 47 Copynumber: 9.0 Consensus size: 48
13110449 ATCTGGCTAC
* ** *
13110459 ACAACATAAAATGATTGGAAAAGCTTTTTATCTCTAAATGAGGCTATG
1 ACAACTTAAAATGATTGGAAAAGCTCCTTATCTCTAAACGAGGCTATG
* * * * *
13110507 AC-ACTTAAAATGATTGGAAAAGCTCATCAACTCTAAATGAGACTATG
1 ACAACTTAAAATGATTGGAAAAGCTCCTTATCTCTAAACGAGGCTATG
* * * * * * *
13110554 -CAAATTAAAATAATTGGAAAAACT-CTTCATCTTTAAACAAAGCTA-C
1 ACAACTTAAAATGATTGGAAAAGCTCCTT-ATCTCTAAACGAGGCTATG
* * * * * * *
13110600 CCAACTTAAAAATGGTTGAAAAAAG-TCCTCATCTTTAAACGAGACTTTG
1 ACAACTT-AAAATGATTG-GAAAAGCTCCTTATCTCTAAACGAGGCTATG
* * * * *
13110649 -CAACTTGGATTTTCAATGATTTG-AAAGCTCTTTATCTCTAAAGGAGGCTA-C
1 ACAACTT--A----AAATGATTGGAAAAGCTCCTTATCTCTAAACGAGGCTATG
* * *
13110700 ACAACTTAAAATGATTTGAAAAGCTCCTTATCTCTAAAGGAGGCTA-C
1 ACAACTTAAAATGATTGGAAAAGCTCCTTATCTCTAAACGAGGCTATG
* * *
13110747 ACAACTTAAAATGATTTGAAAAGCTCCTTATCTCTAAAGGAGGCTA-C
1 ACAACTTAAAATGATTGGAAAAGCTCCTTATCTCTAAACGAGGCTATG
* * ** * *
13110794 ACAACTTAAAATGATTGAAAAATCTGTTTATCTCTAAATGAGGTTATG
1 ACAACTTAAAATGATTGGAAAAGCTCCTTATCTCTAAACGAGGCTATG
* * * * *
13110842 -CAACTTAAAGTGATTGAAAAAGCTGCTCATCTTTAAACGAGGCTATG
1 ACAACTTAAAATGATTGGAAAAGCTCCTTATCTCTAAACGAGGCTATG
13110889 TAACTTTAAA
Statistics
Matches: 308, Mismatches: 58, Indels: 33
0.77 0.15 0.08
Matches are distributed among these distances:
46 11 0.04
47 227 0.74
48 30 0.10
49 7 0.02
50 1 0.00
51 4 0.01
52 22 0.07
53 6 0.02
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (48 bp):
ACAACTTAAAATGATTGGAAAAGCTCCTTATCTCTAAACGAGGCTATG
Found at i:13110788 original size:94 final size:95
Alignment explanation
Indices: 13110460--13110886 Score: 332
Period size: 94 Copynumber: 4.5 Consensus size: 95
13110450 TCTGGCTACA
* * ** * *
13110460 CAACATAAAATGATTGGAAAAGCTTTTTATCTCTAAATGAGGCTATGAC-ACTTAAAATGA-TTG
1 CAACTTAAAATGATTTGAAAAGCTCCTTATCTCTAAACGAGGCTA-CACAACTTAAAATGATTTG
* * * *
13110523 GAAAAGCTCATCAACTCTAAATGAGACTATG
65 AAAAAGCTCCTCATCTCTAAATGAGGCTATG
* * * * * * * * *
13110554 CAAATTAAAATAATTGGAAAAACT-CTTCATCTTTAAACAAAGCTACCCAACTTAAAAATG-GTT
1 CAACTTAAAATGATTTGAAAAGCTCCTT-ATCTCTAAACGAGGCTACACAACTT-AAAATGATTT
* * * *
13110617 GAAAAAAG-TCCTCATCTTTAAACGAGACTTTG
64 G-AAAAAGCTCCTCATCTCTAAATGAGGCTATG
* * *
13110649 CAACTTGGATTTTCAATGATTTG-AAAGCTCTTTATCTCTAAAGGAGGCTACACAACTTAAAATG
1 CAACTT--A----AAATGATTTGAAAAGCTCCTTATCTCTAAACGAGGCTACACAACTTAAAATG
* * **
13110713 ATTTG-AAAAGCTCCTTATCTCTAAAGGAGGCTACA
60 ATTTGAAAAAGCTCCTCATCTCTAAATGAGGCTATG
*
13110748 CAACTTAAAATGATTTGAAAAGCTCCTTATCTCTAAAGGAGGCTACACAACTTAAAATGA-TTGA
1 CAACTTAAAATGATTTGAAAAGCTCCTTATCTCTAAACGAGGCTACACAACTTAAAATGATTTGA
* ** * *
13110812 AAAATCTGTTTATCTCTAAATGAGGTTATG
66 AAAAGCTCCTCATCTCTAAATGAGGCTATG
* * * *
13110842 CAACTTAAAGTGA-TTGAAAAAGCTGCTCATCTTTAAACGAGGCTA
1 CAACTTAAAATGATTTG-AAAAGCTCCTTATCTCTAAACGAGGCTA
13110887 TGTAACTTTA
Statistics
Matches: 266, Mismatches: 50, Indels: 34
0.76 0.14 0.10
Matches are distributed among these distances:
93 18 0.07
94 137 0.52
95 33 0.12
96 5 0.02
97 2 0.01
98 5 0.02
99 29 0.11
100 28 0.11
101 9 0.03
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (95 bp):
CAACTTAAAATGATTTGAAAAGCTCCTTATCTCTAAACGAGGCTACACAACTTAAAATGATTTGA
AAAAGCTCCTCATCTCTAAATGAGGCTATG
Found at i:13119125 original size:73 final size:73
Alignment explanation
Indices: 13119006--13119147 Score: 230
Period size: 73 Copynumber: 1.9 Consensus size: 73
13118996 AAACATGAAA
* *
13119006 TGTAGCAAAATCATTAGAACAATGCCTAGAGTTGTTACACACCATGCACGTAACATCTCTAATGC
1 TGTAGCAAAATCATTAGAACAATACCCAGAGTTGTTACACACCATGCACGTAACATCTCTAATGC
13119071 ACATTGCG
66 ACATTGCG
* ** *
13119079 TGTAGCAAAATCATTAGAACATTACCCAGAGTTGTTACATGCCATGCATGTAACATCTCTAATGC
1 TGTAGCAAAATCATTAGAACAATACCCAGAGTTGTTACACACCATGCACGTAACATCTCTAATGC
13119144 ACAT
66 ACAT
13119148 GACATGTAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 63 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (73 bp):
TGTAGCAAAATCATTAGAACAATACCCAGAGTTGTTACACACCATGCACGTAACATCTCTAATGC
ACATTGCG
Found at i:13119215 original size:23 final size:23
Alignment explanation
Indices: 13119183--13119269 Score: 102
Period size: 23 Copynumber: 3.7 Consensus size: 23
13119173 ACATGTTTAA
13119183 GAACATGGCATGTAACATTTTTT
1 GAACATGGCATGTAACATTTTTT
* * * *
13119206 GAACACGGCATTTAACATGTTGT
1 GAACATGGCATGTAACATTTTTT
*
13119229 CAACATGGCATGTAACAATTTTTT
1 GAACATGGCATGTAAC-ATTTTTT
* *
13119253 GAACATGACATATAACA
1 GAACATGGCATGTAACA
13119270 AAATTTTTTA
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
23 33 0.65
24 18 0.35
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (23 bp):
GAACATGGCATGTAACATTTTTT
Found at i:13124164 original size:13 final size:13
Alignment explanation
Indices: 13124146--13124171 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13124136 ATTTAAACAT
13124146 CTTGTTATTCTAG
1 CTTGTTATTCTAG
13124159 CTTGTTATTCTAG
1 CTTGTTATTCTAG
13124172 TTTATAATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (13 bp):
CTTGTTATTCTAG
Found at i:13124878 original size:76 final size:76
Alignment explanation
Indices: 13124771--13125405 Score: 436
Period size: 76 Copynumber: 8.5 Consensus size: 76
13124761 CACGTCACAT
** * * *
13124771 TTGTTAGATGTCGTTTACATCTTGTCATGACACACCGTGTCATTGACGTATTATATTGTTACACG
1 TTGTTAGATGTCGTTTACATCTTGTGGTGACACGCCATGTCATTGACGTATTATATGGTTACACG
*
13124836 CCACGCTCAAA
66 CCACGCTCCAA
* ** *
13124847 TTGTTAGATGTCGTTTACATCTTGTGGTGACATGCCATGTTGTT-ACAGTATTATAAGGTTACAC
1 TTGTTAGATGTCGTTTACATCTTGTGGTGACACGCCATGTCATTGAC-GTATTATATGGTTACAC
* * **
13124911 GTCATGCTTGAA
65 GCCACGCTCCAA
* * * * * * * *
13124923 TTGTTAAATATTGTTTACA--------AGACACTCTATGTCATTG-CATTATTATAGGGTTACAC
1 TTGTTAGATGTCGTTTACATCTTGTGGTGACACGCCATGTCATTGAC-GTATTATATGGTTACAC
*
13124979 ACCACGCTCCAA
65 GCCACGCTCCAA
* * * * *
13124991 TTGTTAGATGTCATTTACATCTTGTGGTGACACACCATGTCATTGTA-GGATTATATTGTTACAG
1 TTGTTAGATGTCGTTTACATCTTGTGGTGACACGCCATGTCATTG-ACGTATTATATGGTTACAC
13125055 GCCACGCTCCAA
65 GCCACGCTCCAA
* * *** * * * *
13125067 TTGTTAGATGTCATTTACATCTTGTTGTGACACATTGA-GTCA-TCACAGTATTGTAGGGTGACA
1 TTGTTAGATGTCGTTTACATCTTGTGGTGACAC-GCCATGTCATTGAC-GTATTATATGGTTACA
*
13125130 CGCCACTCTCCAA
64 CGCCACGCTCCAA
* * * * ** * * *
13125143 TTGTTAGATGTTGTTTACATCTTGTGATGATATGCCATGTTGTTGACATATTATATTGTTACACA
1 TTGTTAGATGTCGTTTACATCTTGTGGTGACACGCCATGTCATTGACGTATTATATGGTTACACG
* *
13125208 CCACGTTTCAA
66 CCACGCTCCAA
* * * * * * * *
13125219 TTGTTAAATGTTGTTTACATCTTTTGGTGGCATGCCATGTCATTCTA-GTATTATAAGGTTAAAC
1 TTGTTAGATGTCGTTTACATCTTGTGGTGACACGCCATGTCATT-GACGTATTATATGGTTACAC
* *
13125283 GTCACGCTCTAA
65 GCCACGCTCCAA
* * * * * * * *
13125295 TTGTTAGATGTCATTTATATTTTATGGTGACACGTCATGGT-GTTGACGTATTATATTGTTACAT
1 TTGTTAGATGTCGTTTACATCTTGTGGTGACACGCCAT-GTCATTGACGTATTATATGGTTACAC
* * *
13125359 ACCATGCTCAAA
65 GCCACGCTCCAA
* * **
13125371 TTGTTAGATGTTGTTTATATCTTGTTATGACACGC
1 TTGTTAGATGTCGTTTACATCTTGTGGTGACACGC
13125406 TGAGTCGTTA
Statistics
Matches: 421, Mismatches: 118, Indels: 40
0.73 0.20 0.07
Matches are distributed among these distances:
68 50 0.12
74 1 0.00
75 5 0.01
76 358 0.85
77 7 0.02
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.39
Consensus pattern (76 bp):
TTGTTAGATGTCGTTTACATCTTGTGGTGACACGCCATGTCATTGACGTATTATATGGTTACACG
CCACGCTCCAA
Found at i:13125084 original size:144 final size:144
Alignment explanation
Indices: 13124819--13125085 Score: 327
Period size: 144 Copynumber: 1.9 Consensus size: 144
13124809 GTCATTGACG
** * * **
13124819 TATTATATTGTTACACGCCACGCTCAAATTGTTAGATGTCGTTTACATCTTGTGGTGACATGCCA
1 TATTATAGGGTTACACACCACGCTCAAATTGTTAGATGTCATTTACATCTTGTGGTGACACACCA
** * * * ** **
13124884 TGTTGTTACAGTATTATAAGGTTACACGTCATGCTTGAATTGTTAAATATTGTTTACAAGACACT
66 TGTCATTACAGGATTATAAGGTTACACGCCACGCTCCAATTGTTAAATATCATTTACAAGACACT
13124949 CTATGTCATTGCAT
131 CTATGTCATTGCAT
*
13124963 TATTATAGGGTTACACACCACGCTCCAATTGTTAGATGTCATTTACATCTTGTGGTGACACACCA
1 TATTATAGGGTTACACACCACGCTCAAATTGTTAGATGTCATTTACATCTTGTGGTGACACACCA
** ** * * *
13125028 TGTCATTGTAGGATTATATTGTTACAGGCCACGCTCCAATTGTTAGATGTCATTTACA
66 TGTCATTACAGGATTATAAGGTTACACGCCACGCTCCAATTGTTAAATATCATTTACA
13125086 TCTTGTTGTG
Statistics
Matches: 100, Mismatches: 23, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
144 100 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (144 bp):
TATTATAGGGTTACACACCACGCTCAAATTGTTAGATGTCATTTACATCTTGTGGTGACACACCA
TGTCATTACAGGATTATAAGGTTACACGCCACGCTCCAATTGTTAAATATCATTTACAAGACACT
CTATGTCATTGCAT
Found at i:13125375 original size:228 final size:228
Alignment explanation
Indices: 13124963--13125400 Score: 504
Period size: 228 Copynumber: 1.9 Consensus size: 228
13124953 GTCATTGCAT
*
13124963 TATTATAGGGTTACACACCACGCTCCAATTGTTAGATGTCATTTACATCTTGTGGTGACACACCA
1 TATTATAGGGTTACACACCACGCTCCAATTGTTAAATGTCATTTACATCTTGTGGTGACACACCA
* ** * * * *
13125028 TGTCATTGTAGGATTATATTGTTACAGGCCACGCTCCAATTGTTAGATGTCATTTACATCTTGTT
66 TGTCATTCTAGGATTATAAGGTTAAACGCCACGCTCCAATTGTTAGATGTCATTTACATCTTATG
* * *
13125093 GTGACACATTGAGTCATCACAGTATTGTAGGGTGACACGCCACTCTCCAATTGTTAGATGTTGTT
131 GTGACACATTGAGTCATCACAGTATTATAGGGTGACACACCACTCTCAAATTGTTAGATGTTGTT
13125158 TACATCTTGTGATGATATGCCATGTTGTTGACA
196 TACATCTTGTGATGATATGCCATGTTGTTGACA
** * * ** * * **
13125191 TATTATATTGTTACACACCACGTTTCAATTGTTAAATGTTGTTTACATCTTTTGGTGGCATGCCA
1 TATTATAGGGTTACACACCACGCTCCAATTGTTAAATGTCATTTACATCTTGTGGTGACACACCA
* * * * *
13125256 TGTCATTCTAGTATTATAAGGTTAAACGTCACGCTCTAATTGTTAGATGTCATTTATATTTTATG
66 TGTCATTCTAGGATTATAAGGTTAAACGCCACGCTCCAATTGTTAGATGTCATTTACATCTTATG
* ** * ** * *
13125321 GTGACACGTCATG-GTGTTGAC-GTATTATATTGTTACATACCA-TGCTCAAATTGTTAGATGTT
131 GTGACACAT--TGAGTCATCACAGTATTATAGGGTGACACACCACT-CTCAAATTGTTAGATGTT
* *
13125383 GTTTATATCTTGTTATGA
193 GTTTACATCTTGTGATGA
13125401 CACGCTGAGT
Statistics
Matches: 171, Mismatches: 36, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
227 1 0.01
228 163 0.95
229 5 0.03
230 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.39
Consensus pattern (228 bp):
TATTATAGGGTTACACACCACGCTCCAATTGTTAAATGTCATTTACATCTTGTGGTGACACACCA
TGTCATTCTAGGATTATAAGGTTAAACGCCACGCTCCAATTGTTAGATGTCATTTACATCTTATG
GTGACACATTGAGTCATCACAGTATTATAGGGTGACACACCACTCTCAAATTGTTAGATGTTGTT
TACATCTTGTGATGATATGCCATGTTGTTGACA
Found at i:13130004 original size:46 final size:43
Alignment explanation
Indices: 13129954--13130102 Score: 109
Period size: 46 Copynumber: 3.3 Consensus size: 43
13129944 ATCGATGGCA
13129954 TGTCACATATTTCCTCTATGTCATCACATATATTCTCACCATGTTG
1 TGTCACATATTTCCTCTATG-CAT--CATATATTCTCACCATGTTG
* * * *
13130000 TGTCACATATTCTCACTCTAACGCATCAGATATTCTCATCATGTCG
1 TGTCACATATT-TC-CTCT-ATGCATCATATATTCTCACCATGTTG
* * * * * * **
13130046 TCTCACATATTCCCTCCATGGCATGTTATATATTCTTACCTTACTG
1 TGTCACATATTTCCTCTAT-GCA--TCATATATTCTCACCATGTTG
13130092 TGTCACATATT
1 TGTCACATATT
13130103 CAATCCATGG
Statistics
Matches: 80, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
43 1 0.01
44 6 0.08
45 1 0.01
46 61 0.76
47 2 0.03
48 7 0.09
49 2 0.03
ACGTcount: A:0.24, C:0.27, G:0.09, T:0.40
Consensus pattern (43 bp):
TGTCACATATTTCCTCTATGCATCATATATTCTCACCATGTTG
Found at i:13130009 original size:23 final size:23
Alignment explanation
Indices: 13129983--13130605 Score: 319
Period size: 23 Copynumber: 27.0 Consensus size: 23
13129973 GTCATCACAT
**
13129983 ATATTCTCACCATGTTGTGTCAC
1 ATATTCTCACCATGCCGTGTCAC
** ** *
13130006 ATATTCTCACTC-TAACGCATCAG
1 ATATTCTCAC-CATGCCGTGTCAC
* * *
13130029 ATATTCTCATCATGTCGTCTCAC
1 ATATTCTCACCATGCCGTGTCAC
* * * * * *
13130052 ATATTCCCTCCATGGCATGTTAT
1 ATATTCTCACCATGCCGTGTCAC
* * * *
13130075 ATATTCTTACCTTACTGTGTCAC
1 ATATTCTCACCATGCCGTGTCAC
* *
13130098 ATATTC-AATCCATGGCGTGTCAC
1 ATATTCTCA-CCATGCCGTGTCAC
* ** *
13130121 ATATT-TCCTCCATGTAGTCTCAC
1 ATATTCT-CACCATGCCGTGTCAC
*
13130144 ATATTCTCACCATGCCATGTCAC
1 ATATTCTCACCATGCCGTGTCAC
* * * *
13130167 ATATTCTCACCCTGGCATGTTAC
1 ATATTCTCACCATGCCGTGTCAC
* * * *
13130190 ATATTCTCACCCTACCATGTTAC
1 ATATTCTCACCATGCCGTGTCAC
* *
13130213 ATATTCTCACCCTACCGTGTCAC
1 ATATTCTCACCATGCCGTGTCAC
** *
13130236 ATATTCTCACCATGATGTCTCAC
1 ATATTCTCACCATGCCGTGTCAC
* * * * *
13130259 ATACTCTCACAATGTCATCTCAC
1 ATATTCTCACCATGCCGTGTCAC
*
13130282 ATACTCTCACCAT-CTCGTGTCAC
1 ATATTCTCACCATGC-CGTGTCAC
*
13130305 ACATTCTCACCATGCCGTGTCAC
1 ATATTCTCACCATGCCGTGTCAC
* *
13130328 ATAGTCTCACCATGCCGTGTAAC
1 ATATTCTCACCATGCCGTGTCAC
* * * ** *
13130351 ATATTCCCTCCTTATCGTATCAC
1 ATATTCTCACCATGCCGTGTCAC
*
13130374 ATACTCTCACCATGCCGTGTCAC
1 ATATTCTCACCATGCCGTGTCAC
* * * * *
13130397 ATATTCCCTCCATGGCATGTCAT
1 ATATTCTCACCATGCCGTGTCAC
* * ***
13130420 ATATTCCCACCCTATTGTGTCAC
1 ATATTCTCACCATGCCGTGTCAC
* *
13130443 ATATTCTCACCCTGCCATAG-CAC
1 ATATTCTCACCATGCCGT-GTCAC
** * * *
13130466 ATATTCTTTCCATTCCATGTTAC
1 ATATTCTCACCATGCCGTGTCAC
* *
13130489 ATATTCCCACCATGGCGTGTCAC
1 ATATTCTCACCATGCCGTGTCAC
* * * * *
13130512 AAACCTTAAATC-CTAT--CGTGCCAT
1 ATA--TT--CTCACCATGCCGTGTCAC
* *
13130536 ATATTCTCATCATGTCGTGTCAC
1 ATATTCTCACCATGCCGTGTCAC
* *
13130559 ATATTC-CTTCCATGCCGTATCAC
1 ATATTCTC-ACCATGCCGTGTCAC
* *
13130582 ATATTCTCACCATGGCATGTCAC
1 ATATTCTCACCATGCCGTGTCAC
13130605 A
1 A
13130606 AACCCTATAC
Statistics
Matches: 445, Mismatches: 136, Indels: 38
0.72 0.22 0.06
Matches are distributed among these distances:
20 2 0.00
21 2 0.00
22 6 0.01
23 416 0.93
24 13 0.03
25 2 0.00
26 3 0.01
27 1 0.00
ACGTcount: A:0.24, C:0.32, G:0.10, T:0.34
Consensus pattern (23 bp):
ATATTCTCACCATGCCGTGTCAC
Found at i:13130192 original size:46 final size:46
Alignment explanation
Indices: 13130140--13130678 Score: 275
Period size: 46 Copynumber: 11.7 Consensus size: 46
13130130 CCATGTAGTC
* *
13130140 TCACATATTCTCACCATGCCATGTCACATATTCTCACCCTGGCATG
1 TCACATATTCTCACCATGCCATGTCACATATTCTCACCATGCCATG
* * * * * * *
13130186 TTACATATTCTCACCCTACCATGTTACATATTCTCACCCTACCGTG
1 TCACATATTCTCACCATGCCATGTCACATATTCTCACCATGCCATG
* * * *
13130232 TCACATATTCTCACCATG--ATGTCTCACATACTCTCACAATGTCATC
1 TCACATATTCTCACCATGCCATG--TCACATATTCTCACCATGCCATG
* * * *
13130278 TCACATACTCTCACCAT-CTCGTGTCACACATTCTCACCATGCCGTG
1 TCACATATTCTCACCATGC-CATGTCACATATTCTCACCATGCCATG
* * * * * * ** * *
13130324 TCACATAGTCTCACCATGCCGTGTAACATATTCCCTCCTTATCGTA
1 TCACATATTCTCACCATGCCATGTCACATATTCTCACCATGCCATG
* * * * *
13130370 TCACATACTCTCACCATGCCGTGTCACATATTCCCTCCATGGCATG
1 TCACATATTCTCACCATGCCATGTCACATATTCTCACCATGCCATG
* * * **** *
13130416 TCATATATTCCCACCCTATTGTGTCACATATTCTCACCCTGCCATAG
1 TCACATATTCTCACCATGCCATGTCACATATTCTCACCATGCCAT-G
** * * * * *
13130463 -CACATATTCTTTCCATTCCATGTTACATATTCCCACCATGGCGTG
1 TCACATATTCTCACCATGCCATGTCACATATTCTCACCATGCCATG
** * * * * * *
13130508 TCACA-AACCTTA-AAT-CCTATCGTGCCATATATTCTCATCATGTCGTG
1 TCACATATTCTCACCATGCC-AT-GT--CACATATTCTCACCATGCCATG
* * * *
13130555 TCACATATTC-CTTCCATGCCGTATCACATATTCTCACCATGGCATG
1 TCACATATTCTC-ACCATGCCATGTCACATATTCTCACCATGCCATG
* ** * * * * * * * * *
13130601 TCACAAACCCTATACCCTACCATGTCACATTTTCCCTCTATGTCATC
1 TCACATATTCT-CACCATGCCATGTCACATATTCTCACCATGCCATG
* *
13130648 TCACATATTCTCACCATGTCATGTCAAATAT
1 TCACATATTCTCACCATGCCATGTCACATAT
13130679 AGTTCTCACA
Statistics
Matches: 364, Mismatches: 111, Indels: 36
0.71 0.22 0.07
Matches are distributed among these distances:
43 2 0.01
44 7 0.02
45 7 0.02
46 283 0.78
47 55 0.15
48 5 0.01
49 3 0.01
50 2 0.01
ACGTcount: A:0.25, C:0.34, G:0.09, T:0.32
Consensus pattern (46 bp):
TCACATATTCTCACCATGCCATGTCACATATTCTCACCATGCCATG
Found at i:13130644 original size:93 final size:93
Alignment explanation
Indices: 13130440--13130657 Score: 213
Period size: 93 Copynumber: 2.3 Consensus size: 93
13130430 CCTATTGTGT
* * * ** * * * *
13130440 CACATATTCTCACCCTGCCATAGCACATATTCTTTCCATTCCATGTTACATATTCCCACCATGGC
1 CACATATTCTCATCATGTCATCTCACATATTCCTTCCATGCCATATCACATATTCCCACCATGGC
* * * * *
13130505 GTGTCACAAACCTTAAATCCTATCGTGC
66 ATGTCACAAACCCTAAACCCTACCATGC
* * * * *
13130533 CATATATTCTCATCATGTCGTGTCACATATTCCTTCCATGCCGTATCACATATTCTCACCATGGC
1 CACATATTCTCATCATGTCATCTCACATATTCCTTCCATGCCATATCACATATTCCCACCATGGC
* *
13130598 ATGTCACAAACCCTATACCCTACCATGT
66 ATGTCACAAACCCTAAACCCTACCATGC
* *
13130626 CACATTTTC-CCTCTATGTCATCTCACATATTC
1 CACATATTCTCATC-ATGTCATCTCACATATTC
13130658 TCACCATGTC
Statistics
Matches: 99, Mismatches: 25, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
92 3 0.03
93 96 0.97
ACGTcount: A:0.25, C:0.33, G:0.09, T:0.33
Consensus pattern (93 bp):
CACATATTCTCATCATGTCATCTCACATATTCCTTCCATGCCATATCACATATTCCCACCATGGC
ATGTCACAAACCCTAAACCCTACCATGC
Found at i:13130665 original size:93 final size:93
Alignment explanation
Indices: 13130382--13130665 Score: 200
Period size: 93 Copynumber: 3.1 Consensus size: 93
13130372 ACATACTCTC
* * * * *** *
13130382 ACCATGCCGTGTCACATATTCCCTCCATGGCATGTCATATATTCCC---ACCCTATTGTGTCACA
1 ACCATGCCGTATCACATATTCCCACCATGGCATGTCACA-A-ACCCTAAACCCTACCATGCCACA
* * * ** *
13130444 TATTCTCACCCTGCCATAGCACATATTCTT
64 TATTCTCATCATGTCATCTCACATATTCCT
* * * * * * * * * * *
13130474 TCCATTCCATGTTACATATTCCCACCATGGCGTGTCACAAACCTTAAATCCTATCGTGCCATATA
1 ACCATGCCGTATCACATATTCCCACCATGGCATGTCACAAACCCTAAACCCTACCATGCCACATA
* *
13130539 TTCTCATCATGTCGTGTCACATATTCCT
66 TTCTCATCATGTCATCTCACATATTCCT
* * * * *
13130567 TCCATGCCGTATCACATATTCTCACCATGGCATGTCACAAACCCTATACCCTACCATGTCACATT
1 ACCATGCCGTATCACATATTCCCACCATGGCATGTCACAAACCCTAAACCCTACCATGCCACATA
*
13130632 TTC-CCTCTATGTCATCTCACATATT-CT
66 TTCTCATC-ATGTCATCTCACATATTCCT
13130659 CACCATG
1 -ACCATG
13130666 TCATGTCAAA
Statistics
Matches: 149, Mismatches: 38, Indels: 9
0.76 0.19 0.05
Matches are distributed among these distances:
90 2 0.01
91 1 0.01
92 37 0.25
93 109 0.73
ACGTcount: A:0.24, C:0.33, G:0.10, T:0.33
Consensus pattern (93 bp):
ACCATGCCGTATCACATATTCCCACCATGGCATGTCACAAACCCTAAACCCTACCATGCCACATA
TTCTCATCATGTCATCTCACATATTCCT
Found at i:13133213 original size:6 final size:6
Alignment explanation
Indices: 13133202--13133226 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
13133192 TCCATGAAGA
13133202 ATTTAT ATTTAT ATTTAT ATTTAT A
1 ATTTAT ATTTAT ATTTAT ATTTAT A
13133227 GATCATGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATTTAT
Found at i:13135961 original size:75 final size:72
Alignment explanation
Indices: 13135851--13135997 Score: 213
Period size: 75 Copynumber: 2.0 Consensus size: 72
13135841 ATTTGAAATA
* * *
13135851 TAATTTTTTATGATATATAAATACATATTTTATACCGTTAGAAAGCTAATAAAAAATATAAACAT
1 TAATTTTTTATGATATATAAATAAATATTTTATACCATTACAAAGCTAATAAAAAATA-AAACAT
13135916 ATCTATTG
65 ATCTATTG
* *
13135924 TAATTTTTTATGATATATATATAAATATATATTATACCATTACAAAGCTAATAAAAAATAAAATA
1 TAATTTTTTATGATATATAAATAAATAT-T-TTATACCATTACAAAGCTAATAAAAAATAAAACA
*
13135989 TATTTATTG
64 TATCTATTG
13135998 CATATTTATA
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
73 26 0.39
74 13 0.20
75 27 0.41
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (72 bp):
TAATTTTTTATGATATATAAATAAATATTTTATACCATTACAAAGCTAATAAAAAATAAAACATA
TCTATTG
Found at i:13136123 original size:77 final size:77
Alignment explanation
Indices: 13136014--13136164 Score: 196
Period size: 77 Copynumber: 2.0 Consensus size: 77
13136004 TATACATAAT
* * * *
13136014 AATCATAAACTAGCAATTTAAATAAAACAAAATCATGATTAAAACA-TGTTTTTAAAATATGCAT
1 AATCATAAACTAGCAATTTAAATAAAACAAAATCATGATCAAAACACAG-TTTCAAAATATACAT
13136078 GAATTAAAAGTTA
65 GAATTAAAAGTTA
* * * * * *
13136091 AATCATAAATTTGTAATTTAAATTAAATAAAATCATGATCAAAACACAGTTTCAAAATGTACATG
1 AATCATAAACTAGCAATTTAAATAAAACAAAATCATGATCAAAACACAGTTTCAAAATATACATG
13136156 AATTAAAAG
66 AATTAAAAG
13136165 GATGAAAGTA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
77 62 0.98
78 1 0.02
ACGTcount: A:0.52, C:0.09, G:0.08, T:0.31
Consensus pattern (77 bp):
AATCATAAACTAGCAATTTAAATAAAACAAAATCATGATCAAAACACAGTTTCAAAATATACATG
AATTAAAAGTTA
Found at i:13136665 original size:15 final size:15
Alignment explanation
Indices: 13136645--13136674 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13136635 AACAATATTC
13136645 AATATTAATTAATTA
1 AATATTAATTAATTA
*
13136660 AATATTTATTAATTA
1 AATATTAATTAATTA
13136675 TTCACAAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATATTAATTAATTA
Found at i:13141114 original size:25 final size:25
Alignment explanation
Indices: 13141072--13141176 Score: 99
Period size: 25 Copynumber: 4.2 Consensus size: 25
13141062 ACAAAATGTT
* *
13141072 ATGTT-AAAAAAATTTTGTTATATGTC
1 ATGTTCAAAAAAA--TTGTTACATGCC
13141098 ATGTTCAAAAAAATTGTTACATGCC
1 ATGTTCAAAAAAATTGTTACATGCC
* * * *
13141123 ATGTT-GACAACA-TGTTAAATGCC
1 ATGTTCAAAAAAATTGTTACATGCC
* *
13141146 GTGTTCAAAAAAAATGTTACATGCC
1 ATGTTCAAAAAAATTGTTACATGCC
13141171 ATGTTC
1 ATGTTC
13141177 TTAAACATGT
Statistics
Matches: 64, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
23 14 0.22
24 8 0.12
25 30 0.47
26 5 0.08
27 7 0.11
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35
Consensus pattern (25 bp):
ATGTTCAAAAAAATTGTTACATGCC
Found at i:13141361 original size:73 final size:73
Alignment explanation
Indices: 13141204--13141361 Score: 253
Period size: 73 Copynumber: 2.2 Consensus size: 73
13141194 ATATATTTTT
* *
13141204 TACATGTCATGTGCATTAGAGATGTTACATGCATGGCATGTAACAACTCTGGGTAATGTTCTAAT
1 TACATGTCATGTGCATTAGAGATGTTACATGCATGGCATGTAACAACTCTAGGCAATGTTCTAAT
13141269 GATTTTGC
66 GATTTTGC
* * * **
13141277 TACACGCCATGTGCATTAGAGATGTTACGTGCATGGTGTGTAACAACTCTAGGCAATGTTCTAAT
1 TACATGTCATGTGCATTAGAGATGTTACATGCATGGCATGTAACAACTCTAGGCAATGTTCTAAT
13141342 GATTTTGC
66 GATTTTGC
13141350 TACATGTCATGT
1 TACATGTCATGT
13141362 TTACTACACT
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (73 bp):
TACATGTCATGTGCATTAGAGATGTTACATGCATGGCATGTAACAACTCTAGGCAATGTTCTAAT
GATTTTGC
Found at i:13143775 original size:2 final size:2
Alignment explanation
Indices: 13143770--13143812 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
13143760 ATAAAAAATT
* * *
13143770 TG TG TG TG TG TG TG TG CG TG TG CG TG TG TC TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
13143812 T
1 T
13143813 TGTTGAGACA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.07, G:0.47, T:0.47
Consensus pattern (2 bp):
TG
Found at i:13144328 original size:21 final size:21
Alignment explanation
Indices: 13144288--13144328 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
13144278 TAATCTTTCT
*
13144288 TAAGATATTGTTGATCTTAAA
1 TAAGATATTGTTAATCTTAAA
* *
13144309 TAAGATTTTGTTAATTTTAA
1 TAAGATATTGTTAATCTTAA
13144329 TTTTGAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (21 bp):
TAAGATATTGTTAATCTTAAA
Found at i:13144698 original size:2 final size:2
Alignment explanation
Indices: 13144693--13144743 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
13144683 AGTTGATCTA
*
13144693 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT 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
13144735 AT AT AT AT A
1 AT AT AT AT A
13144744 AAGTAATCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13150915 original size:31 final size:31
Alignment explanation
Indices: 13150869--13150931 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
13150859 TCTTTTAAAA
* * *
13150869 TAACCTTATAGAATATTTTCTCTTGATTTTT
1 TAACATTATAAAATATTTTATCTTGATTTTT
*
13150900 TAACATTATAAAATATTTTATTTTGATTTTT
1 TAACATTATAAAATATTTTATCTTGATTTTT
13150931 T
1 T
13150932 CCTTGATTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.57
Consensus pattern (31 bp):
TAACATTATAAAATATTTTATCTTGATTTTT
Found at i:13153089 original size:17 final size:18
Alignment explanation
Indices: 13153058--13153092 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
13153048 AATTTCACCA
13153058 TTTATATTGTCAAATAAT
1 TTTATATTGTCAAATAAT
*
13153076 TTTATATT-TTAAATAAT
1 TTTATATTGTCAAATAAT
13153093 GTGAACAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTATATTGTCAAATAAT
Found at i:13155240 original size:2 final size:2
Alignment explanation
Indices: 13155228--13155258 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
13155218 AAACGCACAT
*
13155228 TC TC TC AC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
13155259 GAAACCTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.48, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:13162152 original size:21 final size:21
Alignment explanation
Indices: 13162128--13162177 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
13162118 ATCATTGTCA
13162128 TCATCATCACTATCATAATCT-
1 TCATCATCACTATCATAA-CTG
***
13162149 TCATCATTGTTATCATAACTG
1 TCATCATCACTATCATAACTG
13162170 TCATCATC
1 TCATCATC
13162178 CCCACCATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.40
Consensus pattern (21 bp):
TCATCATCACTATCATAACTG
Found at i:13163408 original size:82 final size:82
Alignment explanation
Indices: 13163267--13163426 Score: 248
Period size: 82 Copynumber: 2.0 Consensus size: 82
13163257 GTTAACAGAA
* * * * *
13163267 AAAAAGTGGGGTTAATAAGTCTTAAAAGACTATGCTCCTATCACCTGATCTTCAGGTGTTAGTCT
1 AAAAAGTGGGGTTAATAAATCTTAAAAGACTATACTCCCATCACCTGATCTTCAAGTGTTAATCT
13163332 TATCGCTAACCACAGGG
66 TATCGCTAACCACAGGG
* *
13163349 AAAAAGTGGGGTTAATAAATCTTAAAGGACTATACTCCCATCACTTGATCTTCAAGTGTTAATCT
1 AAAAAGTGGGGTTAATAAATCTTAAAAGACTATACTCCCATCACCTGATCTTCAAGTGTTAATCT
*
13163414 TATTGCTAACCAC
66 TATCGCTAACCAC
13163427 TAATATCCAC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 70 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (82 bp):
AAAAAGTGGGGTTAATAAATCTTAAAAGACTATACTCCCATCACCTGATCTTCAAGTGTTAATCT
TATCGCTAACCACAGGG
Found at i:13167839 original size:2 final size:2
Alignment explanation
Indices: 13167832--13167861 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13167822 TTCACAACGG
13167832 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13167862 GGGTTCAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13176867 original size:9 final size:9
Alignment explanation
Indices: 13176830--13176896 Score: 53
Period size: 9 Copynumber: 7.2 Consensus size: 9
13176820 AAAATAAATG
*
13176830 CTCAACTAT
1 CTCAACTCT
* *
13176839 TTCAACTCG
1 CTCAACTCT
13176848 CTCAACTCTCT
1 CTCAA--CTCT
13176859 CTCAACTCT
1 CTCAACTCT
* *
13176868 CTGAACTGT
1 CTCAACTCT
*
13176877 ATCAACTCT
1 CTCAACTCT
*
13176886 ATCAACTCT
1 CTCAACTCT
13176895 CT
1 CT
13176897 ATTGAGAACC
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
9 37 0.82
11 8 0.18
ACGTcount: A:0.25, C:0.36, G:0.04, T:0.34
Consensus pattern (9 bp):
CTCAACTCT
Found at i:13176978 original size:63 final size:63
Alignment explanation
Indices: 13176855--13176978 Score: 149
Period size: 63 Copynumber: 2.0 Consensus size: 63
13176845 TCGCTCAACT
* * *
13176855 CTCTCTCAACTCTCTGAACTGTATCAACTCTATCAACTCTCTATTGAGAACCATCATCATCAG
1 CTCTCTCAACTCTCTAAACTGTATCAACTCTATCAACTCTCTATTAAGAACAATCATCATCAG
* * * * * * * *
13176918 CTCTCTTAGCTCTCTAAACTGTATCAGCTCTGTCAACTTTCTGTTAAGTACAATCGTCATC
1 CTCTCTCAACTCTCTAAACTGTATCAACTCTATCAACTCTCTATTAAGAACAATCATCATC
13176979 GTGTTGTAAT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
63 50 1.00
ACGTcount: A:0.26, C:0.30, G:0.10, T:0.35
Consensus pattern (63 bp):
CTCTCTCAACTCTCTAAACTGTATCAACTCTATCAACTCTCTATTAAGAACAATCATCATCAG
Found at i:13177280 original size:23 final size:23
Alignment explanation
Indices: 13177230--13177339 Score: 77
Period size: 23 Copynumber: 4.9 Consensus size: 23
13177220 AAGATTTTTG
13177230 TTGAACATGGCA-TGTAAC-ATGTT
1 TTGAACATGG-AGTGTAACAAT-TT
*
13177253 GTGAACATGGAGTGTAACAATTT
1 TTGAACATGGAGTGTAACAATTT
* * *
13177276 TTGAACTTGCA-TGTGAC-ATTT
1 TTGAACATGGAGTGTAACAATTT
* * *
13177297 TTGAATAT-AACGTGTAACATTTT
1 TTGAACATGGA-GTGTAACAATTT
* *
13177320 TTGAATATGGCGTGTAACAA
1 TTGAACATGGAGTGTAACAA
13177340 CATGACTAAC
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
20 1 0.01
21 10 0.15
22 11 0.16
23 44 0.65
24 2 0.03
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (23 bp):
TTGAACATGGAGTGTAACAATTT
Found at i:13181372 original size:31 final size:31
Alignment explanation
Indices: 13181336--13181404 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
13181326 GACATCTTAT
*
13181336 GGTGACACACTGCA-TAGTTGTAGTATTATGG
1 GGTGACACACTG-AGTAGTTGCAGTATTATGG
* *
13181367 GGTGACACGCTGAGTGGTTGCAGTATTATGG
1 GGTGACACACTGAGTAGTTGCAGTATTATGG
13181398 GGTGACA
1 GGTGACA
13181405 TGCCATGCCC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 1 0.03
31 33 0.97
ACGTcount: A:0.23, C:0.13, G:0.35, T:0.29
Consensus pattern (31 bp):
GGTGACACACTGAGTAGTTGCAGTATTATGG
Found at i:13181481 original size:31 final size:31
Alignment explanation
Indices: 13181443--13181511 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
13181433 GACATCTCGT
*
13181443 GGTGACACGCTAAGTGGTTACAGTATTATGG
1 GGTGACACACTAAGTGGTTACAGTATTATGG
* * **
13181474 GGTGACACATTGAGTGGTTGTAGTATTATGG
1 GGTGACACACTAAGTGGTTACAGTATTATGG
13181505 GGTGACA
1 GGTGACA
13181512 TACCATGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.10, G:0.35, T:0.30
Consensus pattern (31 bp):
GGTGACACACTAAGTGGTTACAGTATTATGG
Found at i:13184107 original size:151 final size:152
Alignment explanation
Indices: 13183853--13184181 Score: 416
Period size: 151 Copynumber: 2.2 Consensus size: 152
13183843 AAACAGGACC
* * ** *
13183853 GATTAGTGGTTGAGGAGCTATCGTCGCCTTTATTAACTGTAATAACAAAAATTACTGTGTTATTC
1 GATTGGTGGTTGAGGAGCTATTGTCGCCTCCATCAACTGTAATAACAAAAATTACTGTGTTATTC
** * * *
13183918 GATAAACATATGTGGAACTGTTGAACACAAATTATTAAAACCATTTTTACTAG-TGGCTTGTTAG
66 GATAAACATATGTGGAAAAGTAGAACACAAATTATTAAAACCATTATTAC-AGATGGCTCGTTAG
13183982 CACTGTGCGGT-TAAGCAAAA-CT
130 CACTGTG-GGTCTAAGCAAAACCT
* * * *
13184004 GATTGGTGGTTGAGGAGCTATTGTCGCCTCCATCAATTGTAATAATAAAAATTTCTGTGTTATTT
1 GATTGGTGGTTGAGGAGCTATTGTCGCCTCCATCAACTGTAATAACAAAAATTACTGTGTTATTC
* * *
13184069 GATAAACATATGTGGAAAAGTAGAACATAAA-TAGTTAAAACCATTATTACCGATGGCTCGTTAT
66 GATAAACATATGTGGAAAAGTAGAACACAAATTA-TTAAAACCATTATTACAGATGGCTCGTTAG
*
13184133 CACTGTGTGTCTAAGCAAAACCT
130 CACTGTGGGTCTAAGCAAAACCT
* *
13184156 -ATCGGTGGTTGAGAAGCTATTGTCGC
1 GATTGGTGGTTGAGGAGCTATTGTCGC
13184182 ATGGTTCAAT
Statistics
Matches: 154, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
150 5 0.03
151 147 0.95
152 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (152 bp):
GATTGGTGGTTGAGGAGCTATTGTCGCCTCCATCAACTGTAATAACAAAAATTACTGTGTTATTC
GATAAACATATGTGGAAAAGTAGAACACAAATTATTAAAACCATTATTACAGATGGCTCGTTAGC
ACTGTGGGTCTAAGCAAAACCT
Found at i:13184218 original size:151 final size:151
Alignment explanation
Indices: 13183893--13184251 Score: 334
Period size: 151 Copynumber: 2.4 Consensus size: 151
13183883 TATTAACTGT
* * * ** *
13183893 AATAACAAAAATTACTGTGTTATTCGATAAACATATGTGGAACTGTTGAACACAAATTATTAAAA
1 AATAACAAAAATTGCTATATTATTCGATAAACATATGTGGAAAAGTAGAACACAAATTATTAAAA
* * * * *
13183958 CCATTTTTACTAGTGGCTTGTTAGCACTGTGCGGTTAAGCAAAACTGATTGGTGGTTGAGGAGCT
66 CCATTATTACGAGTGGCTCGTTAGCACTGTGCGGTTAAGCAAAACTGATCGGTGGTTGAGAAGCT
* **
13184023 ATTGTCGCCTCCATCAATTGT
131 ATTGTCGCATCCATCAATTAC
* * * * * *
13184044 AATAATAAAAATTTCTGTGTTATTTGATAAACATATGTGGAAAAGTAGAACATAAA-TAGTTAAA
1 AATAACAAAAATTGCTATATTATTCGATAAACATATGTGGAAAAGTAGAACACAAATTA-TTAAA
* *
13184108 ACCATTATTACCGA-TGGCTCGTTATCACTGTG-TGTCTAAGCAAAACCT-ATCGGTGGTTGAGA
65 ACCATTATTA-CGAGTGGCTCGTTAGCACTGTGCGGT-TAAGCAAAA-CTGATCGGTGGTTGAGA
***
13184170 AGCTATTGTCGCATGGTTCAATTAC
127 AGCTATTGTCGCATCCATCAATTAC
* * * * * ** *
13184195 AA-ACACAGATATTGCTATATTATTC-ATAATCACATATGGAAGTGTTGAACACAAATT
1 AATA-ACAAAAATTGCTATATTATTCGATAAACATATGTGGAAAAGTAGAACACAAATT
13184252 GTTGGAATCA
Statistics
Matches: 168, Mismatches: 34, Indels: 12
0.79 0.16 0.06
Matches are distributed among these distances:
150 28 0.17
151 136 0.81
152 4 0.02
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (151 bp):
AATAACAAAAATTGCTATATTATTCGATAAACATATGTGGAAAAGTAGAACACAAATTATTAAAA
CCATTATTACGAGTGGCTCGTTAGCACTGTGCGGTTAAGCAAAACTGATCGGTGGTTGAGAAGCT
ATTGTCGCATCCATCAATTAC
Found at i:13187436 original size:23 final size:23
Alignment explanation
Indices: 13187406--13187493 Score: 79
Period size: 23 Copynumber: 3.8 Consensus size: 23
13187396 CACATAAATG
*
13187406 CTCACCATGCCGTGTCACAGATT
1 CTCACCATGCCATGTCACAGATT
* * *
13187429 CTCACCATGCCATCTCATACGGTT
1 CTCACCATGCCATGTCACA-GATT
* * **
13187453 TTGA-CATGCTTTGTCACAGATT
1 CTCACCATGCCATGTCACAGATT
*
13187475 CTCACCATGGCATGTCACA
1 CTCACCATGCCATGTCACA
13187494 AACTCTAAAT
Statistics
Matches: 47, Mismatches: 16, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
22 5 0.11
23 37 0.79
24 5 0.11
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.30
Consensus pattern (23 bp):
CTCACCATGCCATGTCACAGATT
Found at i:13187638 original size:23 final size:23
Alignment explanation
Indices: 13187599--13187677 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 23
13187589 CTCTAATTGC
* * * *
13187599 CGTATCGCATATGCTCACCATGT
1 CGTATCACATATTCTCACAATGG
* *
13187622 CGTCTTACATATTCTCACAATGG
1 CGTATCACATATTCTCACAATGG
* *
13187645 CGTATCACATATTCACACTATGG
1 CGTATCACATATTCTCACAATGG
* *
13187668 CATGTCACAT
1 CGTATCACAT
13187678 TCTCATGCTG
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.32
Consensus pattern (23 bp):
CGTATCACATATTCTCACAATGG
Found at i:13187763 original size:23 final size:23
Alignment explanation
Indices: 13187691--13187772 Score: 73
Period size: 23 Copynumber: 3.6 Consensus size: 23
13187681 CATGCTGGTG
13187691 TGTCACATATTCTTACCATGTC-A
1 TGTCACATATTCTTACCAT-TCTA
*
13187714 TCTCACATATTCCTT-CCAAGTT-T-
1 TGTCACATATT-CTTACC-A-TTCTA
*
13187737 TGTCACATATTCTTACCCTTCTA
1 TGTCACATATTCTTACCATTCTA
*
13187760 TGTCATATATTCT
1 TGTCACATATTCT
13187773 CTCCATGATG
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
21 2 0.04
22 4 0.08
23 36 0.75
24 5 0.10
25 1 0.02
ACGTcount: A:0.23, C:0.27, G:0.06, T:0.44
Consensus pattern (23 bp):
TGTCACATATTCTTACCATTCTA
Found at i:13187787 original size:46 final size:46
Alignment explanation
Indices: 13187689--13187789 Score: 116
Period size: 46 Copynumber: 2.2 Consensus size: 46
13187679 CTCATGCTGG
*
13187689 TGTGTCACATATTCTTACCATGTCATCTCACATATTCCTTCCAAGT
1 TGTGTCACATATTCTTACCATGTCATCTCACATATTCCTTCCAAGA
* * * * *
13187735 TTTGTCACATATTCTTACCCT-TCTATGTCATATATT-CTCTCCATGA
1 TGTGTCACATATTCTTACCATGTC-ATCTCACATATTCCT-TCCAAGA
13187781 TGTGTCACA
1 TGTGTCACA
13187790 AACTCTAAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
45 4 0.09
46 42 0.91
ACGTcount: A:0.23, C:0.27, G:0.09, T:0.42
Consensus pattern (46 bp):
TGTGTCACATATTCTTACCATGTCATCTCACATATTCCTTCCAAGA
Found at i:13187841 original size:23 final size:23
Alignment explanation
Indices: 13187807--13187882 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
13187797 AACCCTATTG
*
13187807 TGTCACATATTCTCACCATGACC-
1 TGTCACACATTC-CACCATGACCA
*
13187830 TGTCACACATTCCTACTAT-ACCA
1 TGTCACACATTCC-ACCATGACCA
*
13187853 TATCACACATTCCCACCATGA-CA
1 TGTCACACATT-CCACCATGACCA
*
13187876 TTTCACA
1 TGTCACA
13187883 AACTCTAAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
22 4 0.09
23 37 0.84
24 3 0.07
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (23 bp):
TGTCACACATTCCACCATGACCA
Found at i:13190280 original size:44 final size:44
Alignment explanation
Indices: 13190230--13190319 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
13190220 TCCTAATTAT
13190230 TTGATTAATGTAGTTTTCATCACAAATGTAGACATTCCATTTTG
1 TTGATTAATGTAGTTTTCATCACAAATGTAGACATTCCATTTTG
13190274 TTGATTAATGTAGTTTTCATCACAAATGTAGACATTCCATTTTG
1 TTGATTAATGTAGTTTTCATCACAAATGTAGACATTCCATTTTG
13190318 TT
1 TT
13190320 TGAGGGTCTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.44
Consensus pattern (44 bp):
TTGATTAATGTAGTTTTCATCACAAATGTAGACATTCCATTTTG
Found at i:13190385 original size:17 final size:17
Alignment explanation
Indices: 13190365--13190402 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
13190355 TAAAATTGAA
13190365 AAAAATAAAGAAAA-AAG
1 AAAAAT-AAGAAAAGAAG
*
13190382 AAAAATAGGAAAAGAAG
1 AAAAATAAGAAAAGAAG
13190399 AAAA
1 AAAA
13190403 CTCAGGTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (17 bp):
AAAAATAAGAAAAGAAG
Found at i:13195583 original size:36 final size:37
Alignment explanation
Indices: 13195543--13195689 Score: 133
Period size: 36 Copynumber: 4.1 Consensus size: 37
13195533 GGTGCATGTC
* *
13195543 CCACTAGATTATTTGCCAATGAGTGGGGCAGAA-GTA
1 CCACTAGATTATTTGCCAATAAGTGGGGCAGAACATA
* * * **
13195579 CCACTAAATTATTTGCCAATAAGTGAGG-TGAATGTA
1 CCACTAGATTATTTGCCAATAAGTGGGGCAGAACATA
* * * * *
13195615 CCTCTAGCTTATTTGCCAATGAGT--AGCAAAACATA
1 CCACTAGATTATTTGCCAATAAGTGGGGCAGAACATA
* *
13195650 CCATTAGATTGTTTGCCAATAAGTGGGGCAGAA-ATA
1 CCACTAGATTATTTGCCAATAAGTGGGGCAGAACATA
13195686 CCAC
1 CCAC
13195690 CATCATATAG
Statistics
Matches: 86, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
34 1 0.01
35 26 0.30
36 54 0.63
37 5 0.06
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (37 bp):
CCACTAGATTATTTGCCAATAAGTGGGGCAGAACATA
Found at i:13196972 original size:21 final size:21
Alignment explanation
Indices: 13196946--13197017 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
13196936 GGCACAATTC
13196946 TTTTTGTAACTAAAGTTTATA
1 TTTTTGTAACTAAAGTTTATA
* * * *
13196967 TTTTTGTAAGTGAAGTTGATC
1 TTTTTGTAACTAAAGTTTATA
**
13196988 TTTTCATAACTAAAGTTTATA
1 TTTTTGTAACTAAAGTTTATA
13197009 TTTTTGTAA
1 TTTTTGTAA
13197018 TTAGTTTGGA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.51
Consensus pattern (21 bp):
TTTTTGTAACTAAAGTTTATA
Found at i:13202849 original size:154 final size:155
Alignment explanation
Indices: 13202558--13202858 Score: 401
Period size: 154 Copynumber: 1.9 Consensus size: 155
13202548 TTTTTCATAG
* * * * * * *
13202558 GTCTTCTAGCTCTAGAGTTTTTCTTTATGAAATTGTTAAATTTTCTTGCTAACATGGGCAAATCC
1 GTCTTATAGCTCTAGAGTTTCTCTTTATGAAATTATGAAATTTTCGTGCGAACATGGCCAAATCC
* * * * *
13202623 TTTTCCTTTTCACTCTCAATTGTAATGTTTTTCTTATCTCCTCGACTAAAGATTTAAGGACTAAA
66 TCTTCATTTTCACTATCAATTGTAATGGTTTTCTTATCTCCTCAACTAAAGATTTAAGGACTAAA
13202688 CCTTTTTT-TTTGGCCTCTTCACTA
131 CCTTTTTTGTTTGGCCTCTTCACTA
* *
13202712 GTCTTATAGCTTTAGAG-TTCTCTTTTATGAACTTATGAAATTTTCGTGCGAACATGGCCAAATC
1 GTCTTATAGCTCTAGAGTTTCTC-TTTATGAAATTATGAAATTTTCGTGCGAACATGGCCAAATC
* * * *
13202776 CTCTTCATTTTCACTATCACTTTTGATGGTTTTCTTATCCTCCTCAACTAAAGATTTAGGGACTA
65 CTCTTCATTTTCACTATCAATTGTAATGGTTTTCTTAT-CTCCTCAACTAAAGATTTAAGGACTA
13202841 AACC-TTTTTGTTTGGCCT
129 AACCTTTTTTGTTTGGCCT
13202859 TTTCCTTCTT
Statistics
Matches: 126, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
153 4 0.03
154 86 0.68
155 36 0.29
ACGTcount: A:0.23, C:0.20, G:0.13, T:0.44
Consensus pattern (155 bp):
GTCTTATAGCTCTAGAGTTTCTCTTTATGAAATTATGAAATTTTCGTGCGAACATGGCCAAATCC
TCTTCATTTTCACTATCAATTGTAATGGTTTTCTTATCTCCTCAACTAAAGATTTAAGGACTAAA
CCTTTTTTGTTTGGCCTCTTCACTA
Done.