Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397273.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_239.1, 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: 3496717
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 46782 characters in sequence are not A, C, G, or T
File 5 of 9
Found at i:1321169 original size:29 final size:29
Alignment explanation
Indices: 1321131--1321198 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 29
1321121 CACCTATTTA
1321131 TAATAGCTAAGATAAATCCTAATCAAATAG
1 TAAT-GCTAAGATAAATCCTAATCAAATAG
1321161 TAATGCTAAGATAAATCCTAATCAAATAG
1 TAATGCTAAGATAAATCCTAATCAAATAG
* *
1321190 GAATCCTAA
1 TAATGCTAA
1321199 TCCTAACTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 32 0.89
30 4 0.11
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.26
Consensus pattern (29 bp):
TAATGCTAAGATAAATCCTAATCAAATAG
Found at i:1326427 original size:24 final size:25
Alignment explanation
Indices: 1326399--1326457 Score: 66
Period size: 29 Copynumber: 2.2 Consensus size: 25
1326389 CACTATTTAT
*
1326399 AATAGT-TAAGATAAATCCTAATCA
1 AATAGTCTAAAATAAATCCTAATCA
1326423 AATAGTAATGCTAAAATAAATCCTAATCA
1 AATAG---T-CTAAAATAAATCCTAATCA
1326452 AATAGT
1 AATAGT
1326458 AATCCTAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
24 5 0.17
26 1 0.03
27 1 0.03
29 22 0.76
ACGTcount: A:0.51, C:0.12, G:0.08, T:0.29
Consensus pattern (25 bp):
AATAGTCTAAAATAAATCCTAATCA
Found at i:1326442 original size:29 final size:29
Alignment explanation
Indices: 1326409--1326465 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1326399 AATAGTTAAG
*
1326409 ATAAATCCTAATCAAATAGTAATGCTAAA
1 ATAAATCCTAATCAAATAGTAATCCTAAA
1326438 ATAAATCCTAATCAAATAGTAATCCTAA
1 ATAAATCCTAATCAAATAGTAATCCTAA
1326466 TCCTAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.51, C:0.16, G:0.05, T:0.28
Consensus pattern (29 bp):
ATAAATCCTAATCAAATAGTAATCCTAAA
Found at i:1326463 original size:17 final size:17
Alignment explanation
Indices: 1326412--1326467 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 17
1326402 AGTTAAGATA
1326412 AATCCTAATCAAATAGT
1 AATCCTAATCAAATAGT
*
1326429 AATGCT-A--AAATA--
1 AATCCTAATCAAATAGT
1326441 AATCCTAATCAAATAGT
1 AATCCTAATCAAATAGT
1326458 AATCCTAATC
1 AATCCTAATC
1326468 CTAAATAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
12 5 0.16
13 1 0.03
14 5 0.16
15 5 0.16
16 1 0.03
17 15 0.47
ACGTcount: A:0.48, C:0.18, G:0.05, T:0.29
Consensus pattern (17 bp):
AATCCTAATCAAATAGT
Found at i:1328805 original size:214 final size:214
Alignment explanation
Indices: 1328427--1329075 Score: 789
Period size: 214 Copynumber: 3.0 Consensus size: 214
1328417 TGATTATAAG
* * * * *
1328427 TATTATTTTATTATATATATGAAATTAATGACACAACTTATATTTTATAATATGTTGTATCAAAG
1 TATTATTTTATTATATATATAAAATTAATGATACAACTTATATGTTATAATGTTTTGTATCAAAG
* * * *
1328492 TATGTATAAATAATAACTGATTATAAATAATATGTTATAAAAACTAAAGTGATAAGTAATAAAGT
66 TTTGTATAAATAATAACTAATTATAAATAATATGTTATAAAATCTAAAGTGATAACTAATAAAGT
** * * * **
1328557 TATTAAGT-ATAAGCATATAAATAAAGTCTATTATAAGTTATAATAATGTTTATGCATAAATTAA
131 TATTAAGTGA-AATTATATAAATAAAGTCTATTATAAATTATAGTAATATTTATATATAAATTAA
*
1328621 ATACATCCATATATCTAATA
195 ATACATCCATATATATAATA
* * * *
1328641 TATTACTTTATTATATATATAAAATTAATTATATAACTTATATGTTATAATGTTTTATATCAAAG
1 TATTATTTTATTATATATATAAAATTAATGATACAACTTATATGTTATAATGTTTTGTATCAAAG
* * *
1328706 TTTGTAGAAATAATAACTAATTATAAATAATTTGTTATAAAATCTAAAGTGATAACTAATAAACT
66 TTTGTATAAATAATAACTAATTATAAATAATATGTTATAAAATCTAAAGTGATAACTAATAAAGT
* * *
1328771 TATTAAGTGAAATTATAGAAATAAA-ACTTATTATAAATTATAGTAATACTTACTTATTTATAAA
131 TATTAAGTGAAATTATATAAATAAAGTC-TATTATAAATTATAGTAATA--T--TTATATATAAA
* ** *
1328835 TTAAATATATGTATATGTATAATA
191 TTAAATACATCCATATATATAATA
*
1328859 TATTATTTTATTTTTTATATATATATGAAATTAATGATACAAATTATATGTTATAATGTTTTGTA
1 TATTATTTTA----TTATATATATA--AAATTAATGATACAACTTATATGTTATAATGTTTTGTA
* * * * *
1328924 TCAAAATTTGTTTAAATAATAACTAATTATAAACAATATGTTATAAAATCCAAGGTGATAACTAA
60 TCAAAGTTTGTATAAATAATAACTAATTATAAATAATATGTTATAAAATCTAAAGTGATAACTAA
* * *
1328989 TAAAGTTATTAAATGTAATTATATAAATAAAGTCTATTATAAATTATAGTAATACTTATATATAA
125 TAAAGTTATTAAGTGAAATTATATAAATAAAGTCTATTATAAATTATAGTAATATTTATATATAA
* **
1329054 ATTAAATATATGTATATATATA
190 ATTAAATACATCCATATATATA
1329076 TATGACTTAT
Statistics
Matches: 372, Mismatches: 50, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
213 1 0.00
214 151 0.41
215 1 0.00
216 1 0.00
218 37 0.10
220 30 0.08
222 11 0.03
224 139 0.37
225 1 0.00
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (214 bp):
TATTATTTTATTATATATATAAAATTAATGATACAACTTATATGTTATAATGTTTTGTATCAAAG
TTTGTATAAATAATAACTAATTATAAATAATATGTTATAAAATCTAAAGTGATAACTAATAAAGT
TATTAAGTGAAATTATATAAATAAAGTCTATTATAAATTATAGTAATATTTATATATAAATTAAA
TACATCCATATATATAATA
Found at i:1328818 original size:25 final size:25
Alignment explanation
Indices: 1328762--1328837 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 25
1328752 AAGTGATAAC
1328762 TAAT-AAACTTATTAAGTGAAATTATAG
1 TAATAAAACTTATT-A-T-AAATTATAG
*
1328789 AAATAAAACTTATTATAAATTATAG
1 TAATAAAACTTATTATAAATTATAG
**
1328814 TAATACTTACTTATTTATAAATTA
1 TAATA-AAACTTA-TTATAAATTA
1328838 AATATATGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
25 13 0.31
26 6 0.14
27 14 0.33
28 9 0.21
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (25 bp):
TAATAAAACTTATTATAAATTATAG
Found at i:1328950 original size:224 final size:222
Alignment explanation
Indices: 1328427--1329075 Score: 820
Period size: 224 Copynumber: 3.0 Consensus size: 222
1328417 TGATTATAAG
* * * *
1328427 TATTATTTTATTATATATATGAAATTAATGACACAACTTATATTTTATAATATGTTGTATCAAAG
1 TATT-TTTTA-TATATATATGAAATTAATGATACAACTTATATGTTATAATGTTTTGTATCAAAG
* * * *
1328492 TATGTATAAATAATAACTGATTATAAATAATATGTTATAAAAACTAAAGTGATAAGTAATAAAGT
64 TTTGTATAAATAATAACTAATTATAAATAATATGTTATAAAATCTAAAGTGATAACTAATAAAGT
** * * * *
1328557 TATTAAGT-ATAAGCATATAAATAAAGTCTATTATAAGTTATAATAAT--GT-TTATGCATAAAT
129 TATTAAGTGA-AATTATATAAATAAAGTCTATTATAAATTATAGTAATACTTATTAT-TATAAAT
* ** *
1328618 TAAATACATCCATATATCTAATATATTACTT
192 TAAATATATGTATATATATAATATATTACTT
* * *
1328649 TA----TTATATATATA--AAATTAATTATATAACTTATATGTTATAATGTTTTATATCAAAGTT
1 TATTTTTTATATATATATGAAATTAATGATACAACTTATATGTTATAATGTTTTGTATCAAAGTT
* * *
1328708 TGTAGAAATAATAACTAATTATAAATAATTTGTTATAAAATCTAAAGTGATAACTAATAAACTTA
66 TGTATAAATAATAACTAATTATAAATAATATGTTATAAAATCTAAAGTGATAACTAATAAAGTTA
* *
1328773 TTAAGTGAAATTATAGAAATAAA-ACTTATTATAAATTATAGTAATACTTACTTATTTATAAATT
131 TTAAGTGAAATTATATAAATAAAGTC-TATTATAAATTATAGTAATACTTA-TTA-TTATAAATT
* *
1328837 AAATATATGTATATGTATAATATATTATTT
193 AAATATATGTATATATATAATATATTACTT
* *
1328867 TATTTTTTATATATATATGAAATTAATGATACAAATTATATGTTATAATGTTTTGTATCAAAATT
1 TATTTTTTATATATATATGAAATTAATGATACAACTTATATGTTATAATGTTTTGTATCAAAGTT
* * * *
1328932 TGTTTAAATAATAACTAATTATAAACAATATGTTATAAAATCCAAGGTGATAACTAATAAAGTTA
66 TGTATAAATAATAACTAATTATAAATAATATGTTATAAAATCTAAAGTGATAACTAATAAAGTTA
* *
1328997 TTAAATGTAATTATATAAATAAAGTCTATTATAAATTATAGTAATACTTA-TA-TATAAATTAAA
131 TTAAGTGAAATTATATAAATAAAGTCTATTATAAATTATAGTAATACTTATTATTATAAATTAAA
1329060 TATATGTATATATATA
196 TATATGTATATATATA
1329076 TATGACTTAT
Statistics
Matches: 368, Mismatches: 45, Indels: 30
0.83 0.10 0.07
Matches are distributed among these distances:
213 1 0.00
214 132 0.36
215 1 0.00
216 9 0.02
217 3 0.01
218 36 0.10
219 1 0.00
220 26 0.07
222 15 0.04
224 143 0.39
225 1 0.00
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (222 bp):
TATTTTTTATATATATATGAAATTAATGATACAACTTATATGTTATAATGTTTTGTATCAAAGTT
TGTATAAATAATAACTAATTATAAATAATATGTTATAAAATCTAAAGTGATAACTAATAAAGTTA
TTAAGTGAAATTATATAAATAAAGTCTATTATAAATTATAGTAATACTTATTATTATAAATTAAA
TATATGTATATATATAATATATTACTT
Found at i:1332973 original size:2 final size:2
Alignment explanation
Indices: 1332966--1332996 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1332956 TTCAGAGTCG
*
1332966 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1332997 GTGTAACAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1334227 original size:251 final size:249
Alignment explanation
Indices: 1333757--1334972 Score: 905
Period size: 251 Copynumber: 4.9 Consensus size: 249
1333747 CATAATTTAT
* * * * ** * *
1333757 AAAATAATTATAGTGAAAAGTAGCTATTTATGAATCTTAAGGTAAATTTATAAAAATAAACGTAA
1 AAAATAATTATAGTGAAAATTA-CAATTTA-AAATCTTGACATAAATTTATAAGAATAAACATAA
* * * * * * * * * * * **
1333822 ACAATCATTAAGTTGAAACAAACATTATTTAAATATTAACATAAAT-TATTGAGAGTTCTCATAA
64 AAAATTATAAAGATGGAACAAGCATTGTTAAAATATTAACATAAATGT-GTAAGATTTAACATAA
* ** * * * *
1333886 AAAGTCAATTTAAAT-AAAATAAA-CATAATTTTTAAAAAAAATTAATCATTTACATCTATATTT
128 CAAGTCAA-TT-AATCAAAATAAATC-TAATTTTT-GTAAAAATTAAACATTTAAATTTATATTC
** * * *
1333949 TTTAGTTAAAAATATTTAA-TATTTACAAATTTTAATTTATAAACAAATAATAACAAGTATA
189 TCGAGCTAAAAATATTTAACAATTTACAAATTTTAATTTATAAA-AAATAATAACAAGGATA
* * * *
1334010 AAAATAGTTATAATGAAAAGTTACCATTTAAAATCTTGACATAAATTTATAAGAATAAATATAAA
1 AAAATAATTATAGTGAAAA-TTACAATTTAAAATCTTGACATAAATTTATAAGAATAAACATAAA
* ** * * * * *
1334075 AAATCATAAAGATAAAACAAGTATTATTAAAATATTTACATAAATGTGT-AGAGTTAACACAACA
65 AAATTATAAAGATGGAACAAGCATTGTTAAAATATTAACATAAATGTGTAAGATTTAACATAACA
* * **
1334139 AGTCAATTGAATCAAAATAAATCTAATTTTTTTAAAAATTAAATATTTAAATTTATATTCTTTAG
130 AGTCAATT-AATCAAAATAAATCTAATTTTTGTAAAAATTAAACATTTAAATTTATATTCTCGAG
* ** *
1334204 CTAAAAATGTTTAACAATTTACAAATTTTAATTTATAAAAGAGGAATAATAAGGATA
194 CTAAAAATATTTAACAATTTACAAATTTTAATTTATAAAA-AATAATAACAAGGATA
* * * * * * *
1334261 AAAATAATTATAGTGAAAATTAGTAATTGAAAACCTTAACGTAAA-TTA-ACGTA-AAACAT---
1 AAAATAATTATAGTGAAAATTA-CAATTTAAAATCTTGACATAAATTTATAAGAATAAACATAAA
* * * * *
1334320 ---TT-TAAATATGGAACAAGAATTGTTAAAATATTGACATAAATATGTAAGATTTAACGTAACA
65 AAATTATAAAGATGGAACAAGCATTGTTAAAATATTAACATAAATGTGTAAGATTTAACATAACA
* * * * *
1334381 ACTCAATTAATTCAAAACAAA-CTTAATTTTTTTGAAAATTAAACATTTAAATTTATATTCTCAA
130 AGTCAATTAA-TCAAAATAAATC-TAATTTTTGTAAAAATTAAACATTTAAATTTATATTCTCGA
* * * *
1334445 GCTAAAAATATTTGACAATTTATAAATTTTAATTTATAAAGAAATGATAACAAGAATA
193 GCTAAAAATATTTAACAATTTACAAATTTTAATTTATAAA-AAATAATAACAAGGATA
* * * * * **
1334503 AAAATAATTATATTTAAAA-TA-AA-TT---A-C--G--A-AACTATGTAAGAATTTACATAAAA
1 AAAATAATTATAGTGAAAATTACAATTTAAAATCTTGACATAAATTTATAAGAATAAACATAAAA
** * * *
1334556 AATTATAAAGAAAGATCATGCATTGTTAAAATATTAACATAAATGTGTGAGATTTAACATAACAA
66 AATTATAAAGATGGAACAAGCATTGTTAAAATATTAACATAAATGTGTAAGATTTAACATAACAA
* * * * *
1334621 ATTAATTAAGTCAAAATAAATTTAA-TTTTGTAAAAATTAAACATTTAAATTTATATTATCGAAC
131 GTCAATTAA-TCAAAATAAATCTAATTTTTGTAAAAATTAAACATTTAAATTTATATTCTCGAGC
** * * * * *
1334685 TAAAAATATTTATTAGTTTATACATTTTAATTTATAAATGAATAATAATAAGGATA
195 TAAAAATATTTAACAATTTACAAATTTTAATTTATAAA-AAATAATAACAAGGATA
* * *** * **
1334741 AAAATAATTATAGTGTAAATTAACAATTGAAAAATCTTGAC-TAACCCTATAAGAATTAATGTAA
1 AAAATAATTATAGTGAAAATT-ACAATT-TAAAATCTTGACATAAATTTATAAGAATAAACATAA
* * ** * **
1334805 AAAATTATAAA-AGTGGAACAAGTATTGTTAAAATATTGATGTAAATGTATAAGATTTAATGTAA
64 AAAATTATAAAGA-TGGAACAAGCATTGTTAAAATATTAACATAAATGTGTAAGATTTAACATAA
* * * * * * * * *
1334869 TAAGTCACTTAGGT-AAAATTAATATAA-CTTTGTGAAAATTAAACATTTAAGTTTATATTCCCG
128 CAAGTCAATTA-ATCAAAATAAATCTAATTTTTGTAAAAATTAAACATTTAAATTTATATTCTCG
*
1334932 AGCTAAAAATATTTAACAATTTACGAATTTTAATTTATAAA
192 AGCTAAAAATATTTAACAATTTACAAATTTTAATTTATAAA
1334973 TGAATAATTA
Statistics
Matches: 767, Mismatches: 158, Indels: 79
0.76 0.16 0.08
Matches are distributed among these distances:
229 2 0.00
230 1 0.00
231 3 0.00
232 4 0.01
234 1 0.00
235 1 0.00
238 99 0.13
239 72 0.09
240 1 0.00
241 43 0.06
242 132 0.17
243 1 0.00
246 1 0.00
247 1 0.00
248 5 0.01
249 4 0.01
250 128 0.17
251 175 0.23
252 67 0.09
253 24 0.03
254 2 0.00
ACGTcount: A:0.49, C:0.07, G:0.08, T:0.35
Consensus pattern (249 bp):
AAAATAATTATAGTGAAAATTACAATTTAAAATCTTGACATAAATTTATAAGAATAAACATAAAA
AATTATAAAGATGGAACAAGCATTGTTAAAATATTAACATAAATGTGTAAGATTTAACATAACAA
GTCAATTAATCAAAATAAATCTAATTTTTGTAAAAATTAAACATTTAAATTTATATTCTCGAGCT
AAAAATATTTAACAATTTACAAATTTTAATTTATAAAAAATAATAACAAGGATA
Found at i:1334437 original size:242 final size:240
Alignment explanation
Indices: 1333881--1335267 Score: 916
Period size: 251 Copynumber: 5.7 Consensus size: 240
1333871 TGAGAGTTCT
* * * * * *
1333881 CATAAAAAGTCAATTTAAAT-AAAATAAACATAATTTT-TAAAAAAAATTAATCATTTACATCTA
1 CATAACAAGTCAA-TTAAGTCAAAATAAATATAATTTTGT---AAAAATTAAACATTTAAATTTA
* ** * * * * *
1333944 TATTTTTTAGTTAAAAATATTTAA-TATTTACAAATTTTAATTTATAAACA-AATAATAACAAGT
62 TATTCTCGAGCTAAAAATATTTAACAATTTACAAATTTTAATTTATAAA-AGAAGAATAATAAGG
* * * * * ** * **
1334007 ATAAAAATAGTTATAATGAAAAGTTACCATTTAAAATCTTGACATAAATTTATAAGAATAAATAT
126 ATAAAAATAATTATAGTGAAAA-TTA-AATTGAAAA-C----C-TTAA--CGTAAGAATTAACGT
* ** * * *
1334072 AAAAAATCATAAAGATAAAACAAGTATTATTAAAATATTTACATAAATGTGT-AGAGTTAA
181 AAAAAATTATAAA-ATGGAACAAGTATTGTTAAAATATTGACATAAATGTGTAAGATTTAA
* * * *
1334132 CACAACAAGTCAATTGAA-TCAAAATAAATCTAATTTTTTTAAAAATTAAATATTTAAATTTATA
1 CATAACAAGTCAATT-AAGTCAAAATAAATATAA-TTTTGTAAAAATTAAACATTTAAATTTATA
** * *
1334196 TTCTTTAGCTAAAAATGTTTAACAATTTACAAATTTTAATTTATAAAAGAGGAATAATAAGGATA
64 TTCTCGAGCTAAAAATATTTAACAATTTACAAATTTTAATTTATAAAAGAAGAATAATAAGGATA
* *
1334261 AAAATAATTATAGTGAAAATTAGTAATTGAAAACCTTAACGT-A-AATTAACGTAAAACATTTTA
129 AAAATAATTATAGTGAAAATTA--AATTGAAAACCTTAACGTAAGAATTAACGTAAAAAATTATA
* *
1334324 AATATGGAACAAGAATTGTTAAAATATTGACATAAATATGTAAGATTTAA
192 AA-ATGGAACAAGTATTGTTAAAATATTGACATAAATGTGTAAGATTTAA
* * * * * *
1334374 CGTAACAACTCAATTAATTCAAAACAAACT-TAATTTTTTTGAAAATTAAACATTTAAATTTATA
1 CATAACAAGTCAATTAAGTCAAAATAAA-TATAA-TTTTGTAAAAATTAAACATTTAAATTTATA
* * * * *
1334438 TTCTCAAGCTAAAAATATTTGACAATTTATAAATTTTAATTTAT-AAAGAA-ATGATAACAAGAA
64 TTCTCGAGCTAAAAATATTTAACAATTTACAAATTTTAATTTATAAAAGAAGA--ATAATAAGGA
* * * * *
1334501 TAAAAATAATTATATTTAAAA-TAAATT-ACGAAA-C-T-ATGTAAGAATTTACATAAAAAATTA
127 TAAAAATAATTATAGTGAAAATTAAATTGA--AAACCTTAACGTAAGAATTAACGTAAAAAATTA
** * * * * *
1334561 TAAAGAAAGATCATGCATTGTTAAAATATTAACATAAATGTGTGAGATTTAA
190 TAAA-ATGGAACAAGTATTGTTAAAATATTGACATAAATGTGTAAGATTTAA
* * *
1334613 CATAACAAATTAATTAAGTCAAAATAAATTTAATTTTGTAAAAATTAAACATTTAAATTTATATT
1 CATAACAAGTCAATTAAGTCAAAATAAATATAATTTTGTAAAAATTAAACATTTAAATTTATATT
* * ** * * * * *
1334678 ATCGAACTAAAAATATTTATTAGTTTATACATTTTAATTTATAAATGAATAATAATAAGGATAAA
66 CTCGAGCTAAAAATATTTAACAATTTACAAATTTTAATTTATAAAAGAAGAATAATAAGGATAAA
* * * *
1334743 AATAATTATAGTGTAAATTAACAATTGAAAAATCTTGACTAACCCTATAAGAATTAATGTAAAAA
131 AATAATTATAGTGAAAATT-A-AATTG-AAAA-CCT---TAA--C-GTAAGAATTAACGTAAAAA
** *
1334808 ATTATAAAAGTGGAACAAGTATTGTTAAAATATTGATGTAAATGTATAAGATTTAA
186 ATTATAAAA-TGGAACAAGTATTGTTAAAATATTGACATAAATGTGTAAGATTTAA
** * * * * * * *
1334864 TGTAATAAGTCACTTAGGT-AAAATTAATATAACTTTGTGAAAATTAAACATTTAAGTTTATATT
1 CATAACAAGTCAATTAAGTCAAAATAAATATAATTTTGTAAAAATTAAACATTTAAATTTATATT
* * * * *
1334928 CCCGAGCTAAAAATATTTAACAATTTACGAATTTTAATTTATAAATGAATAATTAT-AGTGAATA
66 CTCGAGCTAAAAATATTTAACAATTTACAAATTTTAATTTATAAAAGAAGAATAATAAG-G-ATA
** * * * * * *
1334992 TTAACAA--CTA-CGAAACTTTAACTT--AAA-CTT---GTAAGAATTAATGTAAAAAATTATAA
129 AAAATAATTATAGTGAAA-ATTAAATTGAAAACCTTAACGTAAGAATTAACGTAAAAAATTATAA
* * * *
1335048 AAGTGGAACAAAG-ATGGTTAACATATTCACATAAATGAGTGAA-ATTTAA
193 AA-TGGAAC-AAGTATTGTTAAAATATTGACATAAATGTGT-AAGATTTAA
* * * * *
1335097 TATAATAAGTCAATTTAAGTCAAAATAAATATAACTTTTGTGAAAAGTAAAAATTTAAATTTATA
1 CATAACAAGTCAA-TTAAGTCAAAATAAATATAA-TTTTGTAAAAATTAAACATTTAAATTTATA
* * * * ** ** * * *
1335162 TTATCAAGC---CAGTATTTAACGGTTTGTAAATTTTAA-TTATTAATA-AATAATAGTAAGGAT
64 TTCTCGAGCTAAAAATATTTAACAATTTACAAATTTTAATTTA-TAAAAGAAGAATAATAAGGAT
* * *
1335222 AAAAATAATTGTATTGAAAATTAAAAATTGAAAAACCTTAATGTAA
128 AAAAATAATTATAGTGAAAATT--AAATTG-AAAACCTTAACGTAA
1335268 ACTTGTAAGA
Statistics
Matches: 906, Mismatches: 173, Indels: 123
0.75 0.14 0.10
Matches are distributed among these distances:
231 7 0.01
232 11 0.01
233 100 0.11
234 14 0.02
235 16 0.02
236 32 0.04
237 3 0.00
238 97 0.11
239 98 0.11
240 6 0.01
241 64 0.07
242 132 0.15
243 3 0.00
244 3 0.00
245 3 0.00
246 1 0.00
247 4 0.00
248 5 0.01
249 6 0.01
250 135 0.15
251 161 0.18
252 4 0.00
253 1 0.00
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (240 bp):
CATAACAAGTCAATTAAGTCAAAATAAATATAATTTTGTAAAAATTAAACATTTAAATTTATATT
CTCGAGCTAAAAATATTTAACAATTTACAAATTTTAATTTATAAAAGAAGAATAATAAGGATAAA
AATAATTATAGTGAAAATTAAATTGAAAACCTTAACGTAAGAATTAACGTAAAAAATTATAAAAT
GGAACAAGTATTGTTAAAATATTGACATAAATGTGTAAGATTTAA
Found at i:1334734 original size:480 final size:485
Alignment explanation
Indices: 1334070--1334972 Score: 1137
Period size: 480 Copynumber: 1.9 Consensus size: 485
1334060 AAGAATAAAT
* *
1334070 ATAAAAAATCATAAAGATAAAACAAGTATTATTAAAATATTTACATAAATGTGTAGAGTTAACAC
1 ATAAAAAATCATAAAGATAAAACAAGCATTATTAAAATATTAACATAAATGTGTAGAGTTAACAC
* * * *
1334135 AACAAGTCAATTGAATCAAAATAAATCTAATTTTTTTAAAAATTAAATATTTAAATTTATATTCT
66 AACAAATCAATTGAATCAAAATAAATCTAATTTTTGTAAAAATTAAACATTTAAATTTATATTAT
** * * *
1334200 TTAGCTAAAAATGTTTAACAATTTACAAATTTTAATTTATAAAAGAGGAATAATAAGGATAAAAA
131 CGAACTAAAAATATTTAACAATTTACAAATTTTAATTTATAAAAGAAGAATAATAAGGATAAAAA
** * * *
1334265 TAATTATAGTGAAAATTAGTAATTG-AAAA-CCT-TAA-C-GT-A-AATTAACGTAAAACATTTT
196 TAATTATAGTGAAAATTAACAATTGAAAAATCCTATAACCTATAAGAATTAACGTAAAAAATTAT
*
1334323 AAATA-TGGAACAAGAATTGTTAAAATATTGACATAAATATGTAAGATTTAACGTAACAACTCAA
261 AAA-AGTGGAACAAGAATTGTTAAAATATTGACATAAATATATAAGATTTAACGTAACAACTCAA
* * * *
1334387 TTAATTCAAAACAAACT-TAATTTTTTTGAAAATTAAACATTTAAATTTATATTCTCAAGCTAAA
325 TTAAGT-AAAACAAA-TATAA-CTTTGTGAAAATTAAACATTTAAATTTATATTCCCAAGCTAAA
* *
1334451 AATATTTGACAATTTATAAATTTTAATTTATAAAGAAATGATAACAAGAATAAAAATAATTATAT
387 AATATTTAACAATTTACAAATTTTAATTTATAAAGAAATGATAACAAGAATAAAAATAATTATAT
1334516 TTAAAATAAATTACGAAACTATGTAAGAATTTAC
452 TTAAAATAAATTACGAAACTATGTAAGAATTTAC
* * * * *
1334550 ATAAAAAATTATAAAGA-AAGATCATGCATTGTTAAAATATTAACATAAATGTGTGAGATTTAAC
1 ATAAAAAATCATAAAGATAA-AACAAGCATTATTAAAATATTAACATAAATGTGT-AGAGTTAAC
* * *
1334614 ATAACAAATTAATT-AAGTCAAAATAAATTTAA-TTTTGTAAAAATTAAACATTTAAATTTATAT
64 ACAACAAATCAATTGAA-TCAAAATAAATCTAATTTTTGTAAAAATTAAACATTTAAATTTATAT
** * * * * *
1334677 TATCGAACTAAAAATATTTATTAGTTTATACATTTTAATTTATAAATGAATAATAATAAGGATAA
128 TATCGAACTAAAAATATTTAACAATTTACAAATTTTAATTTATAAAAGAAGAATAATAAGGATAA
* * *
1334742 AAATAATTATAGTGTAAATTAACAATTGAAAAATCTTGACTAACCCTATAAGAATTAATGTAAAA
193 AAATAATTATAGTGAAAATTAACAATTGAAAAATCCT-A-TAA-CCTATAAGAATTAACGTAAAA
* ** * * *
1334807 AATTATAAAAGTGGAACAAGTATTGTTAAAATATTGATGTAAATGTATAAGATTTAATGTAATAA
255 AATTATAAAAGTGGAACAAGAATTGTTAAAATATTGACATAAATATATAAGATTTAACGTAACAA
* * * ** * *
1334872 GTCACTTAGGTAAAATTAATATAACTTTGTGAAAATTAAACATTTAAGTTTATATTCCCGAGCTA
320 CTCAATTAAGTAAAACAAATATAACTTTGTGAAAATTAAACATTTAAATTTATATTCCCAAGCTA
*
1334937 AAAATATTTAACAATTTACGAATTTTAATTTATAAA
385 AAAATATTTAACAATTTACAAATTTTAATTTATAAA
1334973 TGAATAATTA
Statistics
Matches: 353, Mismatches: 55, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
479 2 0.01
480 153 0.43
481 37 0.10
482 2 0.01
485 3 0.01
487 1 0.00
488 71 0.20
489 11 0.03
490 73 0.21
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (485 bp):
ATAAAAAATCATAAAGATAAAACAAGCATTATTAAAATATTAACATAAATGTGTAGAGTTAACAC
AACAAATCAATTGAATCAAAATAAATCTAATTTTTGTAAAAATTAAACATTTAAATTTATATTAT
CGAACTAAAAATATTTAACAATTTACAAATTTTAATTTATAAAAGAAGAATAATAAGGATAAAAA
TAATTATAGTGAAAATTAACAATTGAAAAATCCTATAACCTATAAGAATTAACGTAAAAAATTAT
AAAAGTGGAACAAGAATTGTTAAAATATTGACATAAATATATAAGATTTAACGTAACAACTCAAT
TAAGTAAAACAAATATAACTTTGTGAAAATTAAACATTTAAATTTATATTCCCAAGCTAAAAATA
TTTAACAATTTACAAATTTTAATTTATAAAGAAATGATAACAAGAATAAAAATAATTATATTTAA
AATAAATTACGAAACTATGTAAGAATTTAC
Found at i:1335197 original size:233 final size:230
Alignment explanation
Indices: 1334790--1335212 Score: 521
Period size: 233 Copynumber: 1.8 Consensus size: 230
1334780 ACTAACCCTA
* * **
1334790 TAAGAATTAATGTAAAAAATTATAAAAGTGGAACAAGTATTGTTAAAATATTGATGTAAATGTAT
1 TAAGAATTAATGTAAAAAATTATAAAAGTGGAACAAGTATGGTTAAAATATTCACATAAATGTAT
* * * * * *
1334855 AAGATTTAATGTAATAAGTCACTTAGGTAAAATTAATATAACTTTGTGAAAATTAAACATTTAAG
66 AAGATTTAATATAATAAGTCACTTAAGTAAAATAAATATAACTTTGTGAAAAGTAAAAATTTAAA
* * * *
1334920 TTTATATTCCCGAGCTAAAAATATTTAACAATTTACGAATTTTAATTTATAAATGAATAATTATA
131 TTTATATTACCAAGC--AAAATATTTAACAATTTACAAATTTTAA-TTATAAATAAATAATTATA
1334985 GTGAATATTAACAACTACGAAACTTTAACTTAAACTTG
193 GTGAATATTAACAACTACGAAACTTTAACTTAAACTTG
*
1335023 TAAGAATTAATGTAAAAAATTATAAAAGTGGAACAAAG-ATGGTTAACATATTCACATAAATG-A
1 TAAGAATTAATGTAAAAAATTATAAAAGTGGAAC-AAGTATGGTTAAAATATTCACATAAATGTA
*
1335086 GTGAA-ATTTAATATAATAAGTCAATTTAAGTCAAAATAAATATAACTTTTGTGAAAAGTAAAAA
65 -T-AAGATTTAATATAATAAGTC-ACTTAAGT-AAAATAAATATAAC-TTTGTGAAAAGTAAAAA
* * * ** ** *
1335150 TTTAAATTTATATTATCAAGC-CAGTATTTAACGGTTTGTAAATTTTAATTATTAATAAATAAT
125 TTTAAATTTATATTACCAAGCAAAATATTTAACAATTTACAAATTTTAATTATAAATAAATAAT
1335213 AGTAAGGATA
Statistics
Matches: 160, Mismatches: 24, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
232 14 0.09
233 90 0.56
234 11 0.07
235 13 0.08
236 32 0.20
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.36
Consensus pattern (230 bp):
TAAGAATTAATGTAAAAAATTATAAAAGTGGAACAAGTATGGTTAAAATATTCACATAAATGTAT
AAGATTTAATATAATAAGTCACTTAAGTAAAATAAATATAACTTTGTGAAAAGTAAAAATTTAAA
TTTATATTACCAAGCAAAATATTTAACAATTTACAAATTTTAATTATAAATAAATAATTATAGTG
AATATTAACAACTACGAAACTTTAACTTAAACTTG
Found at i:1335976 original size:16 final size:15
Alignment explanation
Indices: 1335955--1335995 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
1335945 ATTTATAAAT
1335955 AAATAATAATAAATAA
1 AAATAATAAT-AATAA
*
1335971 AAATAATTATAATAA
1 AAATAATAATAATAA
1335986 AAATTAATAA
1 AAA-TAATAA
1335996 CTGAAAATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATAATAATAATAA
Found at i:1348853 original size:29 final size:28
Alignment explanation
Indices: 1348821--1348898 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 28
1348811 GAAGGCTCAA
* *
1348821 AATGATGTCGTGCATATGTCTGGCACATG
1 AATGATATAGTGCATATGT-TGGCACATG
1348850 AATGATATAGTGCATATGTTCGGCACATG
1 AATGATATAGTGCATATGTT-GGCACATG
*
1348879 AATGATATAGTGCATTTGTT
1 AATGATATAGTGCATATGTT
1348899 TGGCTACTAG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 1 0.02
29 44 0.98
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (28 bp):
AATGATATAGTGCATATGTTGGCACATG
Found at i:1349400 original size:18 final size:20
Alignment explanation
Indices: 1349377--1349417 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1349367 TTTATGGGAA
1349377 ATATATG-A-AAATGTATTG
1 ATATATGTACAAATGTATTG
*
1349395 ATATATGTACAAATGTGTTG
1 ATATATGTACAAATGTATTG
1349415 ATA
1 ATA
1349418 CATACATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 1 0.05
20 12 0.60
ACGTcount: A:0.41, C:0.02, G:0.17, T:0.39
Consensus pattern (20 bp):
ATATATGTACAAATGTATTG
Found at i:1350423 original size:28 final size:28
Alignment explanation
Indices: 1350378--1350487 Score: 143
Period size: 28 Copynumber: 3.9 Consensus size: 28
1350368 TTTAATGCGA
*
1350378 TGCCTTTTAAAGGTTCAAGCATAACCAT
1 TGCCTTTTAAAGGATCAAGCATAACCAT
1350406 TGCCTTTTCAAA-GATCAAGCATAACCAT
1 TGCCTTTT-AAAGGATCAAGCATAACCAT
* *
1350434 TGCCTTTTTAAA-GATTAACCATAACCAT
1 TGCC-TTTTAAAGGATCAAGCATAACCAT
* *
1350462 TGCCTTTTAAAGGTTCAAGCACAACC
1 TGCCTTTTAAAGGATCAAGCATAACC
1350488 TTTAAACACT
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
27 7 0.10
28 58 0.81
29 7 0.10
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.31
Consensus pattern (28 bp):
TGCCTTTTAAAGGATCAAGCATAACCAT
Found at i:1351041 original size:20 final size:20
Alignment explanation
Indices: 1351001--1351069 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
1350991 ACATTCAATT
** *
1351001 CATTTTGAAACATATCCATA
1 CATTTTGAAATGTATCTATA
*
1351021 CATTTTGATATGTAT-TGATA
1 CATTTTGAAATGTATCT-ATA
1351041 CATTTTGGAAATGTATCTATA
1 CATTTT-GAAATGTATCTATA
*
1351062 AATTTTGA
1 CATTTTGA
1351070 GCAAAACTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
20 23 0.57
21 16 0.40
22 1 0.03
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (20 bp):
CATTTTGAAATGTATCTATA
Found at i:1351056 original size:21 final size:20
Alignment explanation
Indices: 1351018--1351069 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
1351008 AAACATATCC
*
1351018 ATACATTTTGATATGTATTG
1 ATACATTTTGAAATGTATTG
1351038 ATACATTTTGGAAATGTATCT-
1 ATACATTTT-GAAATGTAT-TG
*
1351059 ATAAATTTTGA
1 ATACATTTTGA
1351070 GCAAAACTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 11 0.39
21 16 0.57
22 1 0.04
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (20 bp):
ATACATTTTGAAATGTATTG
Found at i:1351206 original size:21 final size:21
Alignment explanation
Indices: 1351183--1351257 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
1351173 ACGATGGTTT
*
1351183 AAAACTAATTTAAACAAATTTA
1 AAAACT-ATTCAAACAAATTTA
* *
1351205 AAAACTATTCAAACAAGTTCA
1 AAAACTATTCAAACAAATTTA
* * * *
1351226 AAAGCCATTCAATC-AATTTC
1 AAAACTATTCAAACAAATTTA
1351246 AAAACTCATTCA
1 AAAACT-ATTCA
1351258 TGCAATTTTA
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
20 7 0.17
21 28 0.68
22 6 0.15
ACGTcount: A:0.51, C:0.19, G:0.03, T:0.28
Consensus pattern (21 bp):
AAAACTATTCAAACAAATTTA
Found at i:1351263 original size:21 final size:20
Alignment explanation
Indices: 1351199--1351272 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
1351189 AATTTAAACA
* *
1351199 AATTTAAAAACT-ATTCAAAC
1 AATTTCAAAACTCATTC-ATC
*
1351219 AAGTTCAAAAGC-CATTCAATC
1 AATTTCAAAA-CTCATTC-ATC
1351240 AATTTCAAAACTCATTCATGC
1 AATTTCAAAACTCATTCAT-C
*
1351261 AATTTTAAAACT
1 AATTTCAAAACT
1351273 TTCCACATGA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
20 11 0.24
21 34 0.76
ACGTcount: A:0.46, C:0.19, G:0.04, T:0.31
Consensus pattern (20 bp):
AATTTCAAAACTCATTCATC
Found at i:1351531 original size:21 final size:21
Alignment explanation
Indices: 1351491--1351554 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1351481 AAAAACATGA
* * *
1351491 TCAAACAACTTAAAAAATCAT
1 TCAAACAAGTTCAAAGATCAT
* *
1351512 TCAAACAAGTTCAAGGATCAC
1 TCAAACAAGTTCAAAGATCAT
*
1351533 TCAAACTAGTTCAAAGATCAT
1 TCAAACAAGTTCAAAGATCAT
1351554 T
1 T
1351555 AAAGCAATTT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.25
Consensus pattern (21 bp):
TCAAACAAGTTCAAAGATCAT
Found at i:1353511 original size:73 final size:73
Alignment explanation
Indices: 1353434--1353628 Score: 282
Period size: 73 Copynumber: 2.7 Consensus size: 73
1353424 AACTATGAGA
1353434 TTACTGCCAGAAACCAGGTTCAGAGACAGAAACGACTTAATCGACTAAGAAGCTTTATTAGTCGA
1 TTACTGCCAGAAACCAGGTTCAGAGACAGAAACGACTTAATCGACTAAGAAGCTTTATTAGTCGA
1353499 CTAAAAGG
66 CTAAAAGG
* * * *
1353507 TTACTGCCAGAAACCGGGTTCAAAGACAGAAATGACTTAATCGACTAAGAAGTTTTATTAGTCGA
1 TTACTGCCAGAAACCAGGTTCAGAGACAGAAACGACTTAATCGACTAAGAAGCTTTATTAGTCGA
*
1353572 CTAAGAGG
66 CTAAAAGG
* * * * * * *
1353580 CTACTACTAGAAACTAGGTTCAGAGACAGAGACGACTTATTCAACTAAG
1 TTACTGCCAGAAACCAGGTTCAGAGACAGAAACGACTTAATCGACTAAG
1353629 TAATAATGAT
Statistics
Matches: 107, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 107 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (73 bp):
TTACTGCCAGAAACCAGGTTCAGAGACAGAAACGACTTAATCGACTAAGAAGCTTTATTAGTCGA
CTAAAAGG
Found at i:1355199 original size:15 final size:16
Alignment explanation
Indices: 1355174--1355206 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
1355164 NNNATGGATG
1355174 ATGCAATTTGCTTTTA
1 ATGCAATTTGCTTTTA
1355190 ATGC-ATTTGCTTTTA
1 ATGCAATTTGCTTTTA
1355205 AT
1 AT
1355207 TTAGGAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.52
Consensus pattern (16 bp):
ATGCAATTTGCTTTTA
Found at i:1357278 original size:73 final size:73
Alignment explanation
Indices: 1357093--1357327 Score: 231
Period size: 73 Copynumber: 3.2 Consensus size: 73
1357083 AGAGACAGTA
* * ** * * * * *
1357093 TTAGTCGACTAAGAGATTAATGCCAAAAATCAGGTTCAGAGATAAAAACGACTTAATCGACTAAG
1 TTAGTCGACTAAGAGACTACTATCAGAAATCGGGTTCAGAGACAGAAATGACTTAATCGACTAAG
1357158 AAGTTTTG
66 AAGTTTTG
** * **
1357166 TTAGTCGACTAAGAGGTTACTATCAGAGATCGGAATCAGAGACAGAAATGACTTAATCGACTAAG
1 TTAGTCGACTAAGAGACTACTATCAGAAATCGGGTTCAGAGACAGAAATGACTTAATCGACTAAG
1357231 AAGTTTTG
66 AAGTTTTG
* * * * * *
1357239 TTAGTCGACTAAGAGACTACTGTTAGAAA-CTGGGTTCAGAGACAGAGATGACATAGTCAACTAA
1 TTAGTCGACTAAGAGACTACTATCAGAAATC-GGGTTCAGAGACAGAAATGACTTAATCGACTAA
**
1357303 GTAA-TAATG
65 G-AAGTTTTG
1357312 ATTAGTCGACTAAGAG
1 -TTAGTCGACTAAGAG
1357328 TATTCTATTT
Statistics
Matches: 134, Mismatches: 25, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
72 1 0.01
73 116 0.87
74 17 0.13
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.26
Consensus pattern (73 bp):
TTAGTCGACTAAGAGACTACTATCAGAAATCGGGTTCAGAGACAGAAATGACTTAATCGACTAAG
AAGTTTTG
Found at i:1368722 original size:34 final size:35
Alignment explanation
Indices: 1368684--1368759 Score: 102
Period size: 34 Copynumber: 2.2 Consensus size: 35
1368674 CATAAGAGCT
*
1368684 AGCACAATCTTCACAAT-ATCTTTT-ACAAGGATCA
1 AGCACAATCTTCACAATGCT-TTTTCACAAGGATCA
* *
1368718 AGCACAATTTTCATAATGCTTTTTCACAAGGATCA
1 AGCACAATCTTCACAATGCTTTTTCACAAGGATCA
1368753 AGCACAA
1 AGCACAA
1368760 CCTTTGTACC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
34 19 0.51
35 18 0.49
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (35 bp):
AGCACAATCTTCACAATGCTTTTTCACAAGGATCA
Found at i:1369423 original size:16 final size:16
Alignment explanation
Indices: 1369402--1369438 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1369392 GTAAAATAAT
1369402 AAATAAAATTAA-GATA
1 AAATAAAA-TAATGATA
1369418 AAATAAAATAATGATA
1 AAATAAAATAATGATA
1369434 AAATA
1 AAATA
1369439 TTAGAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24
Consensus pattern (16 bp):
AAATAAAATAATGATA
Found at i:1386225 original size:35 final size:35
Alignment explanation
Indices: 1386186--1386310 Score: 162
Period size: 35 Copynumber: 3.6 Consensus size: 35
1386176 AGGTTTATTC
*
1386186 ATGTGGTATTTTTACCCCCACAATGGGCTTTATGT
1 ATGTGGTATTCTTACCCCCACAATGGGCTTTATGT
* * * *
1386221 ATGTGGTATTCTTGCCCCCATAATGGGGTTAAT-T
1 ATGTGGTATTCTTACCCCCACAATGGGCTTTATGT
* * *
1386255 CATGTGGTATTTTTACCTCCACAATGGGCCTTATGT
1 -ATGTGGTATTCTTACCCCCACAATGGGCTTTATGT
1386291 ATGTGGTATTCTTACCCCCA
1 ATGTGGTATTCTTACCCCCA
1386311 TGATAGGCTT
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
34 1 0.01
35 72 0.97
36 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (35 bp):
ATGTGGTATTCTTACCCCCACAATGGGCTTTATGT
Found at i:1386269 original size:70 final size:70
Alignment explanation
Indices: 1386157--1386311 Score: 240
Period size: 70 Copynumber: 2.2 Consensus size: 70
1386147 TTTCAAGGTT
* * * * *
1386157 GTATTCTTACCCCTATAGT-AGGTTTATTCATGTGGTATTTTTACCCCCACAATGGGCTTTATGT
1 GTATTCTTACCCCCATAATGGGGTTAATTCATGTGGTATTTTTACCCCCACAATGGGCCTTATGT
1386221 ATGTG
66 ATGTG
* *
1386226 GTATTCTTGCCCCCATAATGGGGTTAATTCATGTGGTATTTTTACCTCCACAATGGGCCTTATGT
1 GTATTCTTACCCCCATAATGGGGTTAATTCATGTGGTATTTTTACCCCCACAATGGGCCTTATGT
1386291 ATGTG
66 ATGTG
1386296 GTATTCTTACCCCCAT
1 GTATTCTTACCCCCAT
1386312 GATAGGCTTG
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
69 16 0.21
70 61 0.79
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.40
Consensus pattern (70 bp):
GTATTCTTACCCCCATAATGGGGTTAATTCATGTGGTATTTTTACCCCCACAATGGGCCTTATGT
ATGTG
Found at i:1394115 original size:71 final size:72
Alignment explanation
Indices: 1393975--1394125 Score: 196
Period size: 71 Copynumber: 2.1 Consensus size: 72
1393965 CTATATCTCT
* * * * * * **
1393975 TCTGTAGTCAACTATGGCTATTCTTCACCTTGAATTTCTTGATCTTTTTGGAATAGGGTCGATTG
1 TCTGTAGTCAACTATGGCTATTCTTAAACTTCAATTTCTTGATCATTCTAGAATAGGGTCGATAA
1394040 TGCTTCC
66 TGCTTCC
* * *
1394047 TTTGTAGTCAACTATGGCTATTC-TAAACTTCATTTTCTTGATCATTCTAGAATAGGGTTGATAA
1 TCTGTAGTCAACTATGGCTATTCTTAAACTTCAATTTCTTGATCATTCTAGAATAGGGTCGATAA
1394111 TGCTTCC
66 TGCTTCC
1394118 TCTGTAGT
1 TCTGTAGT
1394126 TGACTAGGGC
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
71 45 0.67
72 22 0.33
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (72 bp):
TCTGTAGTCAACTATGGCTATTCTTAAACTTCAATTTCTTGATCATTCTAGAATAGGGTCGATAA
TGCTTCC
Found at i:1396733 original size:20 final size:19
Alignment explanation
Indices: 1396680--1396735 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 19
1396670 ATCCTAAAGG
*
1396680 GGATGAATTTTGAA-AATA
1 GGATGAATTTAGAAGAATA
* * *
1396698 GGATGAATCTAAAAGAGATT
1 GGATGAATTTAGAAGA-ATA
*
1396718 GGATGAATTTGGAAGAAT
1 GGATGAATTTAGAAGAAT
1396736 GAAAGATTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 11 0.38
19 3 0.10
20 15 0.52
ACGTcount: A:0.43, C:0.02, G:0.27, T:0.29
Consensus pattern (19 bp):
GGATGAATTTAGAAGAATA
Found at i:1400285 original size:52 final size:52
Alignment explanation
Indices: 1400190--1400334 Score: 154
Period size: 50 Copynumber: 2.8 Consensus size: 52
1400180 TTTGAGCGAA
* * * *
1400190 AAGTGATAACCCTCACATGATCGACAACGAGATTCTTGCTTTTTTTA-TAGGATC
1 AAGTGATAACCCTAACA--ATCCACAAAGGGATTCTTGCTTTTTTTACT-GGATC
* *
1400244 AAGTGATAACCCTTACAATCCACAAAGGGATTCTTAC--TTTTTACTGGATC
1 AAGTGATAACCCTAACAATCCACAAAGGGATTCTTGCTTTTTTTACTGGATC
* * *
1400294 AAGTGACAACCCAAACAATCTACAAA-GGATTCTTGCTTTTT
1 AAGTGATAACCCTAACAATCCACAAAGGGATTCTTGCTTTTT
1400335 GATAGAAAGT
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
49 9 0.12
50 33 0.42
51 4 0.05
52 16 0.21
54 16 0.21
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (52 bp):
AAGTGATAACCCTAACAATCCACAAAGGGATTCTTGCTTTTTTTACTGGATC
Found at i:1434481 original size:2 final size:2
Alignment explanation
Indices: 1434474--1434519 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
1434464 AATTCTTAGG
* * *
1434474 AT AT AT AT AT AT AT AT AT AT AT GT TT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1434516 AT AT
1 AT AT
1434520 GTTTATATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1434508 original size:24 final size:24
Alignment explanation
Indices: 1434475--1434531 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
1434465 ATTCTTAGGA
*
1434475 TATATATATATATATATATATGTT
1 TATATGTATATATATATATATGTT
1434499 TATATGTATATATATATATATGTT
1 TATATGTATATATATATATATGTT
1434523 TATATGTAT
1 TATATGTAT
1434532 GTATTTTGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (24 bp):
TATATGTATATATATATATATGTT
Found at i:1434526 original size:8 final size:8
Alignment explanation
Indices: 1434474--1434531 Score: 71
Period size: 8 Copynumber: 7.2 Consensus size: 8
1434464 AATTCTTAGG
*
1434474 ATATATAT
1 ATATATGT
*
1434482 ATATATAT
1 ATATATGT
1434490 ATATATGT
1 ATATATGT
*
1434498 TTATATGT
1 ATATATGT
*
1434506 ATATATAT
1 ATATATGT
1434514 ATATATGT
1 ATATATGT
*
1434522 TTATATGT
1 ATATATGT
1434530 AT
1 AT
1434532 GTATTTTGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 43 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (8 bp):
ATATATGT
Found at i:1436359 original size:18 final size:20
Alignment explanation
Indices: 1436322--1436359 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
1436312 AAATTATTTG
*
1436322 AAATATTTAATTTAATAAAA
1 AAATATTTAATTTAAGAAAA
1436342 AAATA-TTAA-TTAAGAAAA
1 AAATATTTAATTTAAGAAAA
1436360 GCTTATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 4 0.24
20 5 0.29
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
AAATATTTAATTTAAGAAAA
Found at i:1436489 original size:2 final size:2
Alignment explanation
Indices: 1436482--1436513 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1436472 TATCAAGAGG
1436482 AT 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 AT
1436514 CATTCACTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1436984 original size:18 final size:18
Alignment explanation
Indices: 1436952--1436986 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1436942 GGTAATTAAT
1436952 ATTAAAATAATGCAAAAA
1 ATTAAAATAATGCAAAAA
1436970 ATTAATAATAA-GCAAAA
1 ATTAA-AATAATGCAAAA
1436987 GGGAATGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.23
Consensus pattern (18 bp):
ATTAAAATAATGCAAAAA
Found at i:1443372 original size:23 final size:23
Alignment explanation
Indices: 1443353--1443440 Score: 104
Period size: 23 Copynumber: 3.8 Consensus size: 23
1443343 TGGCATTGTG
1443353 TGATTGGTTGATAGGTCATTGCA
1 TGATTGGTTGATAGGTCATTGCA
* * *
1443376 TTAGTAGTTGATAGGTCATTGCA
1 TGATTGGTTGATAGGTCATTGCA
* * * *
1443399 TTATTGGTTGATAGGTTATTACG
1 TGATTGGTTGATAGGTCATTGCA
1443422 TGATTGGTTGATAAGGTCA
1 TGATTGGTTGAT-AGGTCA
1443441 ATAGAACCAT
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 49 0.91
24 5 0.09
ACGTcount: A:0.24, C:0.07, G:0.28, T:0.41
Consensus pattern (23 bp):
TGATTGGTTGATAGGTCATTGCA
Found at i:1443798 original size:25 final size:25
Alignment explanation
Indices: 1443770--1443831 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
1443760 GATCGTTTTA
1443770 TGTAGGGCATTGCATAACTGTTATC
1 TGTAGGGCATTGCATAACTGTTATC
* * *
1443795 TGTAGGGTATTGCGTGACTGTTATC
1 TGTAGGGCATTGCATAACTGTTATC
*
1443820 TGTATGGCATTG
1 TGTAGGGCATTG
1443832 AGAGAATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.19, C:0.13, G:0.29, T:0.39
Consensus pattern (25 bp):
TGTAGGGCATTGCATAACTGTTATC
Found at i:1444554 original size:16 final size:16
Alignment explanation
Indices: 1444533--1444566 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1444523 TTTAAAGATG
1444533 TTCAAGAGAGAATAGT
1 TTCAAGAGAGAATAGT
*
1444549 TTCAAGAGAGGATAGT
1 TTCAAGAGAGAATAGT
1444565 TT
1 TT
1444567 TAACAAGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.29
Consensus pattern (16 bp):
TTCAAGAGAGAATAGT
Found at i:1446346 original size:29 final size:29
Alignment explanation
Indices: 1446264--1446416 Score: 170
Period size: 29 Copynumber: 5.3 Consensus size: 29
1446254 TCTTGTATTT
*
1446264 AATTAAGACAAAAATATTTTATCTTTTCTA
1 AATTAAGACAAAAATATTTT-TCTTGTCTA
*
1446294 AATTGAGAC--AAATATGTTTTCTTGTCTA
1 AATTAAGACAAAAATAT-TTTTCTTGTCTA
* * *
1446322 GATTAAGAAAAAAATATTTTTCTTGTTTTA
1 AATTAAGACAAAAATATTTTTCTTG-TCTA
*
1446352 AATTAAGACAAACATA-TTTTCTTGTCTA
1 AATTAAGACAAAAATATTTTTCTTGTCTA
* *
1446380 AATTAAGACTAAACAT-GTTTTCTTGTCTA
1 AATTAAGAC-AAAAATATTTTTCTTGTCTA
1446409 AATTAAGA
1 AATTAAGA
1446417 TAAACTTGTT
Statistics
Matches: 107, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
28 32 0.30
29 45 0.42
30 30 0.28
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (29 bp):
AATTAAGACAAAAATATTTTTCTTGTCTA
Found at i:1451357 original size:17 final size:17
Alignment explanation
Indices: 1451327--1451359 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1451317 TTCTCGATAA
1451327 AATAAAACTCCTTATTG
1 AATAAAACTCCTTATTG
1451344 AATAATAACT-CTTATT
1 AATAA-AACTCCTTATT
1451360 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAAAACTCCTTATTG
Found at i:1451635 original size:60 final size:58
Alignment explanation
Indices: 1451511--1451673 Score: 134
Period size: 60 Copynumber: 2.8 Consensus size: 58
1451501 TCTTGTCTTT
* * * *
1451511 AATTAAGACAAAAATATTTTATCTTTTCTAAATTGAGACAAATATGTTTTCTTGCATA
1 AATTAAGACAAAAATATTTTATCTTTTCTAAATTAAGACAAACATATTTTATTGCATA
** * * * *
1451569 GGTTAAGACAAAAAATATTTTTTTTTGTTTTAAATTAAGACAAACATATTTTATTATC-TA
1 AATTAAGAC-AAAAATATTTTATCTT-TTCTAAATTAAGACAAACATATTTTATT-GCATA
* * * * *
1451629 AATTAAGACCGAACAT-GTTT-TCTTGTCTAAATTAAGATAAACATA
1 AATTAAGA-CAAAAATATTTTATCTTTTCTAAATTAAGACAAACATA
1451674 GACATTTCAA
Statistics
Matches: 82, Mismatches: 19, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
57 18 0.22
58 10 0.12
59 17 0.21
60 35 0.43
61 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.40
Consensus pattern (58 bp):
AATTAAGACAAAAATATTTTATCTTTTCTAAATTAAGACAAACATATTTTATTGCATA
Found at i:1451644 original size:29 final size:28
Alignment explanation
Indices: 1451599--1451673 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 28
1451589 TTTTTTGTTT
1451599 TAAATTAAGACAAACATATTTTATTATC
1 TAAATTAAGACAAACATATTTTATTATC
* * * *
1451627 TAAATTAAGACCGAACATGTTTTCTTGTC
1 TAAATTAAGA-CAAACATATTTTATTATC
*
1451656 TAAATTAAGATAAACATA
1 TAAATTAAGACAAACATA
1451674 GACATTTCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 15 0.38
29 24 0.62
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (28 bp):
TAAATTAAGACAAACATATTTTATTATC
Found at i:1455942 original size:29 final size:28
Alignment explanation
Indices: 1455848--1456074 Score: 224
Period size: 29 Copynumber: 7.9 Consensus size: 28
1455838 TTTAAGACAA
* * *
1455848 TTCTTGTCTTTAATTAAGATAAAAATATTT
1 TTCTTGTC-TAAATTAAGACAAACATA-TT
* *
1455878 TGTCTTGTCTAAATTGAGACAAATC-TGTT
1 T-TCTTGTCTAAATTAAGACAAA-CATATT
* * *
1455907 TTCTTGTCTAGATTAAGATAAAAAGTATT
1 TTCTTGTCTAAATTAAGACAAACA-TATT
* *
1455936 TTCTTGTCTAAAATGAAGTCAAACATATT
1 TTCTTGTCT-AAATTAAGACAAACATATT
1455965 TTCTTGTCTAAATTAAGACCAAACATGA-T
1 TTCTTGTCTAAATTAAGA-CAAACAT-ATT
* * *
1455994 TTCTTGTCTATATTAAGACAAGCATGTT
1 TTCTTGTCTAAATTAAGACAAACATATT
* *
1456022 TTCTTGTCTAAATTAAAACATAACATGTT
1 TTCTTGTCTAAATTAAGACA-AACATATT
1456051 TTCTTGTCTAAATTAAGACAAACA
1 TTCTTGTCTAAATTAAGACAAACA
1456075 CGTTAAAGCT
Statistics
Matches: 164, Mismatches: 24, Indels: 20
0.79 0.12 0.10
Matches are distributed among these distances:
28 54 0.33
29 79 0.48
30 24 0.15
31 7 0.04
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.41
Consensus pattern (28 bp):
TTCTTGTCTAAATTAAGACAAACATATT
Found at i:1456024 original size:86 final size:86
Alignment explanation
Indices: 1455880--1456074 Score: 243
Period size: 86 Copynumber: 2.3 Consensus size: 86
1455870 AAATATTTTG
* * *
1455880 TCTTGTCTAAATTGAGACAAATC-TGTTTTCTTGTCTAGATTAAGATAAAAAGTATTTTCTTGTC
1 TCTTGTCTAAATTAAGACAAA-CATGATTTCTTGTCTAGATTAAGACAAAAAGTATTTTCTTGTC
**
1455944 TAAAATGAAGTCA-AACATATTT
65 T-AAATGAAAACATAACATATTT
* ** *
1455966 TCTTGTCTAAATTAAGACCAAACATGATTTCTTGTCTATATTAAGACAAGCA-TGTTTTCTTGTC
1 TCTTGTCTAAATTAAGA-CAAACATGATTTCTTGTCTAGATTAAGACAAAAAGTATTTTCTTGTC
* *
1456030 TAAATTAAAACATAACATGTTT
65 TAAATGAAAACATAACATATTT
1456052 TCTTGTCTAAATTAAGACAAACA
1 TCTTGTCTAAATTAAGACAAACA
1456075 CGTTAAAGCT
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
85 14 0.15
86 54 0.57
87 27 0.28
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (86 bp):
TCTTGTCTAAATTAAGACAAACATGATTTCTTGTCTAGATTAAGACAAAAAGTATTTTCTTGTCT
AAATGAAAACATAACATATTT
Found at i:1456037 original size:57 final size:56
Alignment explanation
Indices: 1455880--1456074 Score: 223
Period size: 57 Copynumber: 3.4 Consensus size: 56
1455870 AAATATTTTG
* * * *
1455880 TCTTGTCTAAATTGAGACAAATC-TGTTTTCTTGTCTAGATTAAGATAAA-AAGTATTT
1 TCTTGTCTAAATTAAGACAAA-CATGTTTTCTTGTCTAAATTAAGACAAACATG-A-TT
* * *
1455937 TCTTGTCTAAAATGAAGTCAAACATATTTTCTTGTCTAAATTAAGACCAAACATGATT
1 TCTTGTCT-AAATTAAGACAAACATGTTTTCTTGTCTAAATTAAGA-CAAACATGATT
* * * *
1455995 TCTTGTCTATATTAAGACAAGCATGTTTTCTTGTCTAAATTAAAACATAACATGTTT
1 TCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTAAATTAAGACA-AACATGATT
1456052 TCTTGTCTAAATTAAGACAAACA
1 TCTTGTCTAAATTAAGACAAACA
1456075 CGTTAAAGCT
Statistics
Matches: 117, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
56 2 0.02
57 69 0.59
58 40 0.34
59 4 0.03
60 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (56 bp):
TCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTAAATTAAGACAAACATGATT
Found at i:1467279 original size:16 final size:16
Alignment explanation
Indices: 1467258--1467289 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1467248 TCAAAATTCA
1467258 GACTTTGATTCTTTTG
1 GACTTTGATTCTTTTG
*
1467274 GACTTTGATTTTTTTG
1 GACTTTGATTCTTTTG
1467290 ATATTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.09, G:0.19, T:0.59
Consensus pattern (16 bp):
GACTTTGATTCTTTTG
Found at i:1467875 original size:223 final size:222
Alignment explanation
Indices: 1467473--1467906 Score: 502
Period size: 223 Copynumber: 1.9 Consensus size: 222
1467463 AATATATCAA
* ** * *
1467473 TACATGCTCATGATGTATCGATACATTTAGCCTCTAAAGGGTTGCCGATGAACATGTATTGATAC
1 TACATGCTCATGATGTAGCGATACATTTAGCCTAGAAAAGGTTGCCGATGAACATGTATCGATAC
* * * * *
1467538 ATGTTGATAATTTATCGATAAATTTTTCCTAGAACTAAATGTATCAATACATGACCTAATGTATC
66 ATGTTCATAATGTATCGATAAATTTTTCCCAGAACCAAATATATCAATACATGACCTAATGTATC
* * ** **
1467603 AATACATTCAGTTGATTTTAAAAAAGCAAAAAGGATAAAAATGTATTTTCACATCC-TGCCTTAT
131 AATACATTCAGTCGATTTCAAAAAA-CAAAAAGGATAAAAACATATTTTCACA-CCTTAACTTAT
*
1467667 AAATATACACCATTTTTTTTAAGTTTGGC
194 AAATATACACCACTTTTTTTAAGTTTGGC
* * *
1467696 TACATGGTCATGATGTAGCGATACATTTAGCCTAGAAAAGGTTTCTGATGAACATGTATCGATAC
1 TACATGCTCATGATGTAGCGATACATTTAGCCTAGAAAAGGTTGCCGATGAACATGTATCGATAC
* * * *
1467761 ATGTTCATAATGTATTGA-AACA-TTTTCCCAGGAACCAAATATATCGATACATGGCCTCATGTA
66 ATGTTCATAATGTATCGATAA-ATTTTTCCCA-GAACCAAATATATCAATACATGACCTAATGTA
** *
1467824 TTGATACATTTCA-TCGATTTCAAATAAA-TAAAAGG-TGCAAAAACATATTTTCACACCTTAAC
129 TCAATACA-TTCAGTCGATTTCAAA-AAACAAAAAGGAT--AAAAACATATTTTCACACCTTAAC
*
1467886 TTATAAATATACCCCACTTTT
190 TTATAAATATACACCACTTTT
1467907 AAAGTGTTGG
Statistics
Matches: 176, Mismatches: 28, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
221 1 0.01
222 17 0.10
223 151 0.86
224 7 0.04
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (222 bp):
TACATGCTCATGATGTAGCGATACATTTAGCCTAGAAAAGGTTGCCGATGAACATGTATCGATAC
ATGTTCATAATGTATCGATAAATTTTTCCCAGAACCAAATATATCAATACATGACCTAATGTATC
AATACATTCAGTCGATTTCAAAAAACAAAAAGGATAAAAACATATTTTCACACCTTAACTTATAA
ATATACACCACTTTTTTTAAGTTTGGC
Found at i:1469607 original size:21 final size:20
Alignment explanation
Indices: 1469581--1469632 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1469571 ATTACCAAAG
* *
1469581 GTATCGATAGATTCCTTGCAT
1 GTATCGATAGATT-CTAGAAT
*
1469602 GTATCGATACATTCTAGAAT
1 GTATCGATAGATTCTAGAAT
1469622 GTATCGATAGA
1 GTATCGATAGA
1469633 ATTGTTACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (20 bp):
GTATCGATAGATTCTAGAAT
Found at i:1473810 original size:59 final size:59
Alignment explanation
Indices: 1473718--1473835 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
1473708 TGACTTAACT
*
1473718 TCGTTTCCCCCTTCAAACACATCAGAACATCAAAATGTTAATTATTCCTAGCTTTCGAA
1 TCGTTTCCCCCTTCAAACACATCAGAACATCAAAATGTTAATTATTCCTAGATTTCGAA
1473777 TCGTTTCCCCCTTCAAACACATCAGAACATCAAAATGTTAATTATTCCTAGATTTCGAA
1 TCGTTTCCCCCTTCAAACACATCAGAACATCAAAATGTTAATTATTCCTAGATTTCGAA
1473836 AAATGTCAGC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.33, C:0.26, G:0.08, T:0.32
Consensus pattern (59 bp):
TCGTTTCCCCCTTCAAACACATCAGAACATCAAAATGTTAATTATTCCTAGATTTCGAA
Found at i:1485112 original size:20 final size:20
Alignment explanation
Indices: 1485087--1485145 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
1485077 GCATTCTATA
1485087 TGAAATGTATCTATACATTT
1 TGAAATGTATCTATACATTT
*
1485107 TGAAATGCATCTATACATTT
1 TGAAATGTATCTATACATTT
*
1485127 GGAAATGTAT-TGATACATT
1 TGAAATGTATCT-ATACATT
1485146 CACTAGGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 1 0.03
20 34 0.97
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.41
Consensus pattern (20 bp):
TGAAATGTATCTATACATTT
Found at i:1492047 original size:38 final size:38
Alignment explanation
Indices: 1492000--1492089 Score: 103
Period size: 38 Copynumber: 2.4 Consensus size: 38
1491990 CTTAAACGAC
* * * *
1492000 AATGACTTGTT-TAGCTTGTGCTTGATCCTGAAATAGGT
1 AATGACTTGTTAAAGCTTGTACTTGATCCT-AAAAAGGA
*
1492038 AATGACTTGTTAAAGGTTGTACTTGATCCTAAAAAGGA
1 AATGACTTGTTAAAGCTTGTACTTGATCCTAAAAAGGA
*
1492076 AATTACTTG-TAAAG
1 AATGACTTGTTAAAG
1492090 GTTATCCTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
37 5 0.11
38 25 0.56
39 15 0.33
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (38 bp):
AATGACTTGTTAAAGCTTGTACTTGATCCTAAAAAGGA
Found at i:1492100 original size:37 final size:39
Alignment explanation
Indices: 1492020--1492100 Score: 103
Period size: 37 Copynumber: 2.1 Consensus size: 39
1492010 TTAGCTTGTG
* * *
1492020 CTTGATCCTGAAATAGGTAATGACTTGTTAAAGGTTGTA
1 CTTGATCCTGAAAAAGGAAATGACTTGTTAAAGGTTATA
* *
1492059 CTTGATCCT-AAAAAGGAAATTACTTG-TAAAGGTTATC
1 CTTGATCCTGAAAAAGGAAATGACTTGTTAAAGGTTATA
1492096 CTTGA
1 CTTGA
1492101 ACTTGGTTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 14 0.38
38 14 0.38
39 9 0.24
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (39 bp):
CTTGATCCTGAAAAAGGAAATGACTTGTTAAAGGTTATA
Found at i:1497826 original size:21 final size:21
Alignment explanation
Indices: 1497800--1497864 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
1497790 CAAAGTCATT
1497800 ACCTTTTAAAGATCAAGCATA
1 ACCTTTTAAAGATCAAGCATA
* *
1497821 ACC-TTTACA-ACCAA-C-T-
1 ACCTTTTAAAGATCAAGCATA
* *
1497837 ACCTTTTAAGGATTAAGCATA
1 ACCTTTTAAAGATCAAGCATA
1497858 ACCTTTT
1 ACCTTTT
1497865 TACATTTTCC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
16 3 0.09
17 5 0.15
18 4 0.12
19 5 0.15
20 6 0.18
21 10 0.30
ACGTcount: A:0.37, C:0.23, G:0.08, T:0.32
Consensus pattern (21 bp):
ACCTTTTAAAGATCAAGCATA
Found at i:1498465 original size:22 final size:22
Alignment explanation
Indices: 1498440--1498493 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
1498430 TTCTTGATAA
1498440 TCAATTCTTCATTTTCAAGGTG
1 TCAATTCTTCATTTTCAAGGTG
1498462 TCAATTCTTCATTTTCAAGGTG
1 TCAATTCTTCATTTTCAAGGTG
*
1498484 TTAATTCTTC
1 TCAATTCTTC
1498494 TCAACTTGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.48
Consensus pattern (22 bp):
TCAATTCTTCATTTTCAAGGTG
Found at i:1513006 original size:19 final size:22
Alignment explanation
Indices: 1512982--1513025 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 22
1512972 GTAGTGAATT
*
1512982 TTTAGTTTTTG-TT-AA-TTAG
1 TTTAGTGTTTGATTGAATTTAG
1513001 TTTAGTGTTTGATTGAATTTAG
1 TTTAGTGTTTGATTGAATTTAG
1513023 TTT
1 TTT
1513026 TAATTGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.48
20 2 0.10
21 2 0.10
22 7 0.33
ACGTcount: A:0.20, C:0.00, G:0.18, T:0.61
Consensus pattern (22 bp):
TTTAGTGTTTGATTGAATTTAG
Found at i:1521306 original size:30 final size:29
Alignment explanation
Indices: 1521270--1521361 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 29
1521260 TATTGTGAAA
*
1521270 GTTTGTGGTAAGCCTATTAAAAAACCATGG
1 GTTTGTGGTAAGCCCATT-AAAAACCATGG
* * **
1521300 GTTTGTGGTGAGCCCATTGAAAAGTATGG
1 GTTTGTGGTAAGCCCATTAAAAACCATGG
*
1521329 GTTTATGGTTGAA-CCCATTAAAAACCATGG
1 GTTTGTGG-T-AAGCCCATTAAAAACCATGG
1521359 GTT
1 GTT
1521362 ATCACTTGAT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
29 15 0.30
30 34 0.68
31 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (29 bp):
GTTTGTGGTAAGCCCATTAAAAACCATGG
Found at i:1522276 original size:53 final size:52
Alignment explanation
Indices: 1522213--1522318 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 52
1522203 GGGCCTTTAG
*
1522213 AGTGTAAACAAACATGATTGTTATTTTTCTTTCAGTCAATGGTGGTTGGATCT
1 AGTGTAAACAAACATGATTGTTATTTTT-TTTCAGTCAATGGCGGTTGGATCT
*
1522266 AGTGTTAACAAACATGATTGTTATTTTTTTTCAGTCAATGGCGGTTGGATCT
1 AGTGTAAACAAACATGATTGTTATTTTTTTTCAGTCAATGGCGGTTGGATCT
1522318 A
1 A
1522319 TGAGGCAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 24 0.47
53 27 0.53
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (52 bp):
AGTGTAAACAAACATGATTGTTATTTTTTTTCAGTCAATGGCGGTTGGATCT
Found at i:1525844 original size:20 final size:21
Alignment explanation
Indices: 1525796--1525845 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1525786 TACTTTTAAA
*
1525796 TTAAATTAAAGCAAAATAGAG
1 TTAAATTAAAGCAAAATAGAC
*
1525817 TAAAATTAAA-CTAAAAT-GAC
1 TTAAATTAAAGC-AAAATAGAC
1525837 TTAAATTAA
1 TTAAATTAA
1525846 TTGCTCAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.28
Consensus pattern (21 bp):
TTAAATTAAAGCAAAATAGAC
Found at i:1527198 original size:16 final size:15
Alignment explanation
Indices: 1527177--1527207 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1527167 GCAAAATTTA
1527177 AATTTTGATTCTTTTT
1 AATTTTGATT-TTTTT
1527193 AATTTTGATTTTTTT
1 AATTTTGATTTTTTT
1527208 GATATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.71
Consensus pattern (15 bp):
AATTTTGATTTTTTT
Found at i:1528589 original size:68 final size:67
Alignment explanation
Indices: 1528451--1528672 Score: 232
Period size: 68 Copynumber: 3.3 Consensus size: 67
1528441 TACTGGTATG
* * * * * * * *
1528451 ATGATGCAAATTCCATATACCATATGAGATGATCAAATATGCATGATGT-ATACTATAAGATTCT
1 ATGATGTAAATTCCATATACCCTATGAGATGATTAAGTATGCATGAT-TAATGCCATAAGAATAT
1528515 GTAT
65 G-AT
* *
1528519 ATGATGTAAATTCCATATACCCTATGAGGTGATTAAGTATGCATGATTAATGCCATGAGAATATG
1 ATGATGTAAATTCCATATACCCTATGAGATGATTAAGTATGCATGATTAATGCCATAAGAATATG
1528584 CAT
66 -AT
* * * * * *
1528587 ATGACGTATATTCCATATACTGC-ATGAGATGATTAAGTACGCATGATTAATGCGATTAGAATAT
1 ATGATGTAAATTCCATATAC-CCTATGAGATGATTAAGTATGCATGATTAATGCCATAAGAATAT
*
1528651 GTT
65 GAT
*
1528654 ATGATGTATATTCCATATA
1 ATGATGTAAATTCCATATA
1528673 TTACTTGATA
Statistics
Matches: 132, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
67 20 0.15
68 111 0.84
69 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (67 bp):
ATGATGTAAATTCCATATACCCTATGAGATGATTAAGTATGCATGATTAATGCCATAAGAATATG
AT
Found at i:1532726 original size:9 final size:9
Alignment explanation
Indices: 1532712--1532797 Score: 54
Period size: 9 Copynumber: 9.0 Consensus size: 9
1532702 AATACTAAAC
1532712 CCTTTTTTT
1 CCTTTTTTT
1532721 CCTTTTTTCT
1 CCTTTTTT-T
1532731 CTCTTTTTTTT
1 C-C-TTTTTTT
1532742 CCTTCTTTTTT
1 CC-T-TTTTTT
1532753 CTCTTTCTTTT
1 C-CTTT-TTTT
1532764 -CTTTTTATT
1 CCTTTTT-TT
*
1532773 --TTCTTTT
1 CCTTTTTTT
1532780 -CTTCTTTTT
1 CCTT-TTTTT
1532789 CCTTTTTTT
1 CCTTTTTTT
1532798 TTCTCCTTTA
Statistics
Matches: 65, Mismatches: 2, Indels: 20
0.75 0.02 0.23
Matches are distributed among these distances:
7 2 0.03
8 8 0.12
9 23 0.35
10 10 0.15
11 15 0.23
12 7 0.11
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.77
Consensus pattern (9 bp):
CCTTTTTTT
Found at i:1532750 original size:22 final size:21
Alignment explanation
Indices: 1532714--1532769 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 21
1532704 TACTAAACCC
1532714 TTTTTTTCCTTTTTTCTCTCT
1 TTTTTTTCCTTTTTTCTCTCT
*
1532735 TTTTTTTCCTTCTTTTTTCTCT
1 TTTTTTTCCTT-TTTTCTCTCT
*
1532757 TTCTTTT-CTTTTT
1 TTTTTTTCCTTTTT
1532770 ATTTTCTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 3 0.09
21 14 0.44
22 15 0.47
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTTTTCCTTTTTTCTCTCT
Found at i:1532774 original size:11 final size:10
Alignment explanation
Indices: 1532714--1532779 Score: 60
Period size: 11 Copynumber: 6.3 Consensus size: 10
1532704 TACTAAACCC
*
1532714 TTTTTTTCCT
1 TTTTTTTTCT
*
1532724 TTTTTCTCTCT
1 TTTTT-TTTCT
*
1532735 TTTTTTTCCT
1 TTTTTTTTCT
*
1532745 TCTTTTTTCT
1 TTTTTTTTCT
*
1532755 CTTTCTTTTCT
1 -TTTTTTTTCT
1532766 TTTTATTTTCT
1 TTTT-TTTTCT
1532777 TTT
1 TTT
1532780 CTTCTTTTTC
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
10 19 0.43
11 25 0.57
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:1532774 original size:22 final size:21
Alignment explanation
Indices: 1532713--1532802 Score: 74
Period size: 22 Copynumber: 4.0 Consensus size: 21
1532703 ATACTAAACC
* *
1532713 CTTT-TTTTCCTTTTTTCTCT
1 CTTTCTTTTCTTTTTTTTTCT
* *
1532733 CTTTTTTTTCCTTCTTTTTTCT
1 CTTTCTTTT-CTTTTTTTTTCT
1532755 CTTTCTTTTCTTTTTATTTTCTT
1 CTTTCTTTTCTTTTT-TTTTC-T
*
1532778 TTCTTCTTTTTCCTTTTTTTTTCT
1 CT-TTC-TTTT-CTTTTTTTTTCT
1532802 C
1 C
1532803 CTTTATAAGT
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
20 4 0.07
21 9 0.16
22 22 0.39
23 2 0.04
24 4 0.07
25 9 0.16
26 6 0.11
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.77
Consensus pattern (21 bp):
CTTTCTTTTCTTTTTTTTTCT
Found at i:1532775 original size:16 final size:15
Alignment explanation
Indices: 1532723--1532799 Score: 61
Period size: 16 Copynumber: 5.1 Consensus size: 15
1532713 CTTTTTTTCC
*
1532723 TTTTTTC-TCTCTTT
1 TTTTTTCTTTTCTTT
*
1532737 TTTTTCCTTCTT-TTT
1 TTTTTTCTT-TTCTTT
*
1532752 TCTCTTTCTTTTCTTT
1 T-TTTTTCTTTTCTTT
*
1532768 TTATTTTCTTTTCTTC
1 TT-TTTTCTTTTCTTT
*
1532784 TTTTTCCTTTT-TTT
1 TTTTTTCTTTTCTTT
1532798 TT
1 TT
1532800 CTCCTTTATA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
14 10 0.20
15 16 0.32
16 24 0.48
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTCTTTTCTTT
Found at i:1532794 original size:20 final size:19
Alignment explanation
Indices: 1532712--1532798 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 19
1532702 AATACTAAAC
*
1532712 CCTTTTTTTCCTT-TTTTCT
1 CCTTTTTTTTCTTCTTTT-T
1532731 CTCTTTTTTTTCCTTCTTTTT
1 C-CTTTTTTTT-CTTCTTTTT
* * *
1532752 TCTCTTTCTT-TTCTTTTT
1 CCTTTTTTTTCTTCTTTTT
*
1532770 -ATTTTCTTTTCTTCTTTTT
1 CCTTTT-TTTTCTTCTTTTT
1532789 CCTTTTTTTT
1 CCTTTTTTTT
1532799 TCTCCTTTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
17 3 0.06
18 11 0.20
19 13 0.24
20 19 0.35
21 4 0.07
22 4 0.07
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.77
Consensus pattern (19 bp):
CCTTTTTTTTCTTCTTTTT
Found at i:1532798 original size:11 final size:11
Alignment explanation
Indices: 1532714--1532800 Score: 56
Period size: 11 Copynumber: 7.7 Consensus size: 11
1532704 TACTAAACCC
1532714 TTTTTTTCC-T
1 TTTTTTTCCTT
*
1532724 TTTTTCT-CTCT
1 TTTTTTTCCT-T
1532735 TTTTTTTCCTT
1 TTTTTTTCCTT
*
1532746 CTTTTTT-CTCT
1 TTTTTTTCCT-T
*
1532757 TTCTTTT-CTT
1 TTTTTTTCCTT
*
1532767 TTTATTTTCTTTT
1 TTT-TTTTC-CTT
1532780 CTTCTTTTTCCTT
1 -TT-TTTTTCCTT
1532793 TTTTTTTC
1 TTTTTTTC
1532801 TCCTTTATAA
Statistics
Matches: 60, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
9 1 0.02
10 11 0.18
11 32 0.53
12 4 0.07
13 4 0.07
14 7 0.12
15 1 0.02
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTTCCTT
Found at i:1532808 original size:37 final size:37
Alignment explanation
Indices: 1532734--1532808 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
1532724 TTTTTCTCTC
* *
1532734 TTTTTTTTCCTTCTTTTTTCTCTTTCTTTTCTTTTTA
1 TTTTTTTTCCTTCTTTTTCCTCTTTCTTTTCTCTTTA
*
1532771 TTTTCTTTT-CTTCTTTTTCCT-TTTTTTTTCTCCTTTA
1 TTTT-TTTTCCTTCTTTTTCCTCTTTCTTTTCT-CTTTA
1532808 T
1 T
1532809 AAGTATACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 9 0.27
37 20 0.61
38 4 0.12
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (37 bp):
TTTTTTTTCCTTCTTTTTCCTCTTTCTTTTCTCTTTA
Found at i:1538073 original size:68 final size:68
Alignment explanation
Indices: 1537810--1538073 Score: 221
Period size: 68 Copynumber: 3.9 Consensus size: 68
1537800 CATATACATG
* * * * * * * *
1537810 CTTACTCATCTCATA-AGCTATATGGAATTTACATCATATACATAATCTCATGACATT--T-ATA
1 CTTAATCACCTCATATAG-TATATGGAATATATATCATATACATATTCTTATGGCATTAATCATG
* *
1537871 CTTG
65 CATA
* * * * * * * *
1537875 CTTAATCATCTCATGTAATGTATAGAATAAACATCATATACATATTCTTATGGCATTAATTATGC
1 CTTAATCACCTCATATAGTATATGGAATATATATCATATACATATTCTTATGGCATTAATCATGC
1537940 ATA
66 ATA
* * * * *
1537943 CTTAATCATCTCATGTAGTATATGGAATATATATCATATACACATTCTCATGACATTAATCATGC
1 CTTAATCACCTCATATAGTATATGGAATATATATCATATACATATTCTTATGGCATTAATCATGC
1538008 ATA
66 ATA
* * * * * * *
1538011 GTTAATCACCTCATATGGTATATGGAATTTGTTTCATATACATAATCTTATGGCATTCATCAT
1 CTTAATCACCTCATATAGTATATGGAATATATATCATATACATATTCTTATGGCATTAATCAT
1538074 ACCAACATGC
Statistics
Matches: 161, Mismatches: 34, Indels: 5
0.81 0.17 0.03
Matches are distributed among these distances:
65 45 0.28
66 1 0.01
67 1 0.01
68 114 0.71
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (68 bp):
CTTAATCACCTCATATAGTATATGGAATATATATCATATACATATTCTTATGGCATTAATCATGC
ATA
Found at i:1539336 original size:15 final size:17
Alignment explanation
Indices: 1539304--1539340 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
1539294 GAATTCAATA
1539304 AAAATATCAAAAATATC
1 AAAATATCAAAAATATC
*
1539321 AAAAT-TCAAAGA-ATC
1 AAAATATCAAAAATATC
1539336 AAAAT
1 AAAAT
1539341 CTAAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 6 0.32
17 5 0.26
ACGTcount: A:0.65, C:0.11, G:0.03, T:0.22
Consensus pattern (17 bp):
AAAATATCAAAAATATC
Found at i:1547270 original size:17 final size:16
Alignment explanation
Indices: 1547228--1547261 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1547218 GAAAAAAAAA
1547228 TTTAGATTTTGATTCT
1 TTTAGATTTTGATTCT
1547244 TTTAGATTTTGATT-T
1 TTTAGATTTTGATTCT
1547259 TTT
1 TTT
1547262 TTATATTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.18, C:0.03, G:0.12, T:0.68
Consensus pattern (16 bp):
TTTAGATTTTGATTCT
Found at i:1551067 original size:20 final size:21
Alignment explanation
Indices: 1551023--1551071 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
1551013 ATTACCAAAG
* * *
1551023 GTATCGATAGATTCCTTACAT
1 GTATCGATACATTCCTAAAAT
1551044 GTATCGATACATT-CTAAAAT
1 GTATCGATACATTCCTAAAAT
1551064 GTATCGAT
1 GTATCGAT
1551072 TGATTTGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (21 bp):
GTATCGATACATTCCTAAAAT
Found at i:1561325 original size:26 final size:26
Alignment explanation
Indices: 1561289--1561386 Score: 92
Period size: 26 Copynumber: 3.8 Consensus size: 26
1561279 AACATATAAT
* *
1561289 TCCACATATGCCAGGGCATATACAAC
1 TCCAAATATGCCATGGCATATACAAC
* * * *
1561315 CCCAAATATGCTATGACATATAC--T
1 TCCAAATATGCCATGGCATATACAAC
* *
1561339 TCTAAATATGCCATTGCATATACAAC
1 TCCAAATATGCCATGGCATATACAAC
**
1561365 TCCAAATATGTTATGGCATATA
1 TCCAAATATGCCATGGCATATA
1561387 ATTCAAAATA
Statistics
Matches: 54, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
24 18 0.33
26 36 0.67
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (26 bp):
TCCAAATATGCCATGGCATATACAAC
Found at i:1561334 original size:50 final size:50
Alignment explanation
Indices: 1561266--1561399 Score: 160
Period size: 50 Copynumber: 2.7 Consensus size: 50
1561256 ATATATAATT
* ** * *
1561266 CCAAATATACTAAAACATATAATTCCACATATGCCAGGGCATATACAACC
1 CCAAATATGCTATGACATATAATTCAAAATATGCCAGGGCATATACAACC
* * ** *
1561316 CCAAATATGCTATGACATATACTTCTAAATATGCCATTGCATATACAACT
1 CCAAATATGCTATGACATATAATTCAAAATATGCCAGGGCATATACAACC
* *
1561366 CCAAATATGTTATGGCATATAATTCAAAATATGC
1 CCAAATATGCTATGACATATAATTCAAAATATGC
1561400 TAAATATGAT
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 71 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (50 bp):
CCAAATATGCTATGACATATAATTCAAAATATGCCAGGGCATATACAACC
Found at i:1567331 original size:15 final size:16
Alignment explanation
Indices: 1567300--1567333 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1567290 ATAATTTATT
*
1567300 AATTTTTAAAAATTAA
1 AATTATTAAAAATTAA
1567316 AATTATTAAAAA-TAA
1 AATTATTAAAAATTAA
1567331 AAT
1 AAT
1567334 CCACATAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTATTAAAAATTAA
Found at i:1567365 original size:21 final size:22
Alignment explanation
Indices: 1567323--1567365 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1567313 TAAAATTATT
**
1567323 AAAAATAAAATCCACATAACAA
1 AAAAATAAAAAACACATAACAA
*
1567345 AAAAATAAAAAAC-CATGACAA
1 AAAAATAAAAAACACATAACAA
1567366 GTAGGAGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.70, C:0.16, G:0.02, T:0.12
Consensus pattern (22 bp):
AAAAATAAAAAACACATAACAA
Found at i:1567596 original size:9 final size:9
Alignment explanation
Indices: 1567582--1567607 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1567572 ATGGATGGAG
1567582 AAATTTAAA
1 AAATTTAAA
1567591 AAATTTAAA
1 AAATTTAAA
1567600 AAATTTAA
1 AAATTTAA
1567608 GAATTTGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
AAATTTAAA
Found at i:1567664 original size:16 final size:17
Alignment explanation
Indices: 1567643--1567677 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1567633 TTGTAAAGTC
*
1567643 ATTTTATT-ATTTTTTA
1 ATTTTATTAATTATTTA
1567659 ATTTTATTAATTATTTA
1 ATTTTATTAATTATTTA
1567676 AT
1 AT
1567678 AAAAATTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTATTAATTATTTA
Found at i:1575367 original size:62 final size:62
Alignment explanation
Indices: 1575270--1575394 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
1575260 GATAAATACA
1575270 TTATCAAGTTAAAGAGCAATTGGGGACCATTCTAGATGCTATCTATAGATAGATTTACAAAT
1 TTATCAAGTTAAAGAGCAATTGGGGACCATTCTAGATGCTATCTATAGATAGATTTACAAAT
*
1575332 TTATCAAGTTAGAGAGCAATTGGGGACCATTCTAGATGCTATCTATAGATAGATTTACAAAT
1 TTATCAAGTTAAAGAGCAATTGGGGACCATTCTAGATGCTATCTATAGATAGATTTACAAAT
1575394 T
1 T
1575395 ATTGATAAAT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (62 bp):
TTATCAAGTTAAAGAGCAATTGGGGACCATTCTAGATGCTATCTATAGATAGATTTACAAAT
Found at i:1577034 original size:37 final size:37
Alignment explanation
Indices: 1576993--1577077 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 37
1576983 GCATCAAGTG
* * *
1576993 TGATTTGATTCTTCGAAGGATGCTTCGATTCTGAGCA
1 TGATTTGATTCTCCGAAGGATGCTTCAACTCTGAGCA
* *** *
1577030 TGATTTGAGTCTCCTTCGGATGCTTTAACTCTGAGCA
1 TGATTTGATTCTCCGAAGGATGCTTCAACTCTGAGCA
1577067 TGATTTGATTC
1 TGATTTGATTC
1577078 CTTATTGGTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (37 bp):
TGATTTGATTCTCCGAAGGATGCTTCAACTCTGAGCA
Found at i:1578421 original size:21 final size:20
Alignment explanation
Indices: 1578388--1578432 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
1578378 TGTTGAGTAG
1578388 TTAATTTAAGTTATTTTAGT
1 TTAATTTAAGTTATTTTAGT
* *
1578408 TTAATTTTATGTTATTTTATT
1 TTAA-TTTAAGTTATTTTAGT
1578429 TTAA
1 TTAA
1578433 ATTACTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (20 bp):
TTAATTTAAGTTATTTTAGT
Found at i:1584619 original size:69 final size:69
Alignment explanation
Indices: 1584504--1584660 Score: 199
Period size: 69 Copynumber: 2.3 Consensus size: 69
1584494 TAAATGTGAA
* * * *
1584504 GAGGAAGCATTCTTGATATAAGTAAGCTAAATGTAGGGATGCTCTTGATGTAAGTAAGCTGAATA
1 GAGGAAGCACTCTTGATGTAAGTAAGCTAAATGCAAGGATGCTCTTGATGTAAGTAAGCTGAATA
1584569 T-AG
66 TAAG
* * * * *
1584572 GAAGGAAGCACTCTTGATGTATGTAAGTTAAATGCAAGGATGTTCTTGATGTCAGTAAGCTTAAT
1 G-AGGAAGCACTCTTGATGTAAGTAAGCTAAATGCAAGGATGCTCTTGATGTAAGTAAGCTGAAT
*
1584637 GTAAG
65 ATAAG
*
1584642 GAGGAAGCACTTTTGATGT
1 GAGGAAGCACTCTTGATGT
1584661 CAATGAGGTG
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
68 1 0.01
69 72 0.95
70 3 0.04
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.31
Consensus pattern (69 bp):
GAGGAAGCACTCTTGATGTAAGTAAGCTAAATGCAAGGATGCTCTTGATGTAAGTAAGCTGAATA
TAAG
Found at i:1584630 original size:32 final size:32
Alignment explanation
Indices: 1584583--1584643 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1584573 AAGGAAGCAC
1584583 TCTTGATGTATGTAAG-TTAAATGCAAGGATGT
1 TCTTGATGTATGTAAGCTT-AATGCAAGGATGT
*
1584615 TCTTGATGTCA-GTAAGCTTAATGTAAGGA
1 TCTTGATGT-ATGTAAGCTTAATGCAAGGA
1584644 GGAAGCACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
32 23 0.88
33 3 0.12
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (32 bp):
TCTTGATGTATGTAAGCTTAATGCAAGGATGT
Found at i:1587510 original size:84 final size:84
Alignment explanation
Indices: 1587365--1587534 Score: 331
Period size: 84 Copynumber: 2.0 Consensus size: 84
1587355 ATGTAAGAAA
1587365 GTTTTGGATCACCTTTGTTAGTATTCTTGACCTCTACATTGAGTATGGGTTTACCAAGATCAAGG
1 GTTTTGGATCACCTTTGTTAGTATTCTTGACCTCTACATTGAGTATGGGTTTACCAAGATCAAGG
1587430 ACATAGAGACCATTTGAAT
66 ACATAGAGACCATTTGAAT
*
1587449 GTTTTGGATCACCTTTGTTAGTATTCTTGACCTCTACATTGAGTATGGGTTTACCAGGATCAAGG
1 GTTTTGGATCACCTTTGTTAGTATTCTTGACCTCTACATTGAGTATGGGTTTACCAAGATCAAGG
1587514 ACATAGAGACCATTTGAAT
66 ACATAGAGACCATTTGAAT
1587533 GT
1 GT
1587535 ATCTTTACAC
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (84 bp):
GTTTTGGATCACCTTTGTTAGTATTCTTGACCTCTACATTGAGTATGGGTTTACCAAGATCAAGG
ACATAGAGACCATTTGAAT
Found at i:1594640 original size:25 final size:25
Alignment explanation
Indices: 1594606--1594659 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
1594596 AGATCCTCAT
1594606 AGTTGACTCTCCACACTCCCTAGTC
1 AGTTGACTCTCCACACTCCCTAGTC
1594631 AGTTGACTCTCCACACTCCCTAGTC
1 AGTTGACTCTCCACACTCCCTAGTC
1594656 AGTT
1 AGTT
1594660 ATCACTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.20, C:0.37, G:0.13, T:0.30
Consensus pattern (25 bp):
AGTTGACTCTCCACACTCCCTAGTC
Found at i:1599446 original size:80 final size:80
Alignment explanation
Indices: 1599326--1599551 Score: 278
Period size: 80 Copynumber: 2.8 Consensus size: 80
1599316 TGTAATATGT
* * * * * *
1599326 ATGCCAAGAGATGCATGTGTTAAGCATA-TCATATACACTATGGACTTAGCATGTGAGTGATTTA
1 ATGCCATGAGATGTATATGTTGAG-ATAGTCATATACACTATGGGCTAAGCATGTGAGTGATTTA
* *
1599390 TGCA-GTTATGAAATGC
65 TG-AGGTTAGGAAATAC
* *
1599406 ATGCGATGAGATGTATATGTTGAGATATTCATATACACTATGGGCTAAGCATGTGAGTGATTTAT
1 ATGCCATGAGATGTATATGTTGAGATAGTCATATACACTATGGGCTAAGCATGTGAGTGATTTAT
1599471 GAGGTTAGGAAATAC
66 GAGGTTAGGAAATAC
* * * *
1599486 ATTCCATGAGATGTATGTTTTGAGATAGTCATATACACTATGGGCTAAACATGATGA-TGATTTA
1 ATGCCATGAGATGTATATGTTGAGATAGTCATATACACTATGGGCTAAGCATG-TGAGTGATTTA
1599550 TG
65 TG
1599552 GAAATGTTAA
Statistics
Matches: 128, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
79 4 0.03
80 121 0.95
81 3 0.02
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (80 bp):
ATGCCATGAGATGTATATGTTGAGATAGTCATATACACTATGGGCTAAGCATGTGAGTGATTTAT
GAGGTTAGGAAATAC
Found at i:1610603 original size:81 final size:80
Alignment explanation
Indices: 1610460--1610740 Score: 343
Period size: 80 Copynumber: 3.5 Consensus size: 80
1610450 AGCCCAAAGA
* * * * *
1610460 GTATATGACTATCTCCACATAAACATCTCATGGCATACATTTCATAACGTCAAAAATTACTTACA
1 GTATATGACTATCTCAACACATACATCTCATGGCATACATTTCATAACGTCATAAATCACTTACA
*
1610525 TCCTTAGCCTATAGT
66 TGCTTAGCCTATAGT
* * * *
1610540 GTATATGACTATCTCAACACATACACCATCATGGCATATAGTTCATAACCTCATAAATCACTTAC
1 GTATATGACTATCTCAACACATACATC-TCATGGCATACATTTCATAACGTCATAAATCACTTAC
* *
1610605 ATGCTTACCCTATCGT
65 ATGCTTAGCCTATAGT
*
1610621 -TCATATGACTATCTCAACACATACATCTAATGGCATACATTTCATAACGTCATAAATCACTTAC
1 GT-ATATGACTATCTCAACACATACATCTCATGGCATACATTTCATAACGTCATAAATCACTTAC
* *
1610685 GTGCTTAG-CTCATAAT
65 ATGCTTAGCCT-ATAGT
* * *
1610701 GCATATGA-TATACTTAACACATACATCTCATGGCGTACAT
1 GTATATGACTAT-CTCAACACATACATCTCATGGCATACAT
1610741 ATTACAATCT
Statistics
Matches: 171, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
79 5 0.03
80 97 0.57
81 69 0.40
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.32
Consensus pattern (80 bp):
GTATATGACTATCTCAACACATACATCTCATGGCATACATTTCATAACGTCATAAATCACTTACA
TGCTTAGCCTATAGT
Found at i:1624661 original size:12 final size:12
Alignment explanation
Indices: 1624646--1624681 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
1624636 AGAGATTTTT
1624646 GAGGCAGCAAGA
1 GAGGCAGCAAGA
1624658 GAGGCAGCAAG-
1 GAGGCAGCAAGA
1624669 GAGGGCAGCAAGA
1 GA-GGCAGCAAGA
1624682 AACTATTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.09
12 20 0.91
ACGTcount: A:0.39, C:0.17, G:0.44, T:0.00
Consensus pattern (12 bp):
GAGGCAGCAAGA
Found at i:1632058 original size:18 final size:18
Alignment explanation
Indices: 1632020--1632058 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1632010 AACAAAATTG
*
1632020 AAATAAAATAATTATATA
1 AAATAAAATAATTATAGA
1632038 AAATAAAATAATCT-TAGA
1 AAATAAAATAAT-TATAGA
1632056 AAA
1 AAA
1632059 ACATTATGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (18 bp):
AAATAAAATAATTATAGA
Found at i:1645974 original size:62 final size:61
Alignment explanation
Indices: 1645872--1645994 Score: 219
Period size: 62 Copynumber: 2.0 Consensus size: 61
1645862 TATGGTCTAA
1645872 ACATTATTTATTAAGAAATGCTTGAATGATTTAATGATAGTTCAAATTTATGTAAATGATAT
1 ACATTATTTATTAAGAAATGCTTGAATGATTTAATGATAGTTCAAATTTATGT-AATGATAT
* *
1645934 ACATTATTTATTAAGCAATGCTTGAATGATTTAATTATAGTTCAAATTTATGTAATGATAT
1 ACATTATTTATTAAGAAATGCTTGAATGATTTAATGATAGTTCAAATTTATGTAATGATAT
1645995 TGTATTTGGT
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
61 8 0.14
62 51 0.86
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (61 bp):
ACATTATTTATTAAGAAATGCTTGAATGATTTAATGATAGTTCAAATTTATGTAATGATAT
Found at i:1647187 original size:21 final size:20
Alignment explanation
Indices: 1647166--1647205 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1647156 CATTTTTTTC
1647166 TCTCTT-TCTTTT-TTCCTTT
1 TCTCTTCTCTTTTGTT-CTTT
1647185 TCTCTTCTCTTTTGTTCTTT
1 TCTCTTCTCTTTTGTTCTTT
1647205 T
1 T
1647206 ATTTTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 11 0.58
21 2 0.11
ACGTcount: A:0.00, C:0.25, G:0.03, T:0.72
Consensus pattern (20 bp):
TCTCTTCTCTTTTGTTCTTT
Found at i:1656511 original size:26 final size:27
Alignment explanation
Indices: 1656482--1656536 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
1656472 ACCTAATTAG
1656482 TTTTTATTTTATTGTA-TTTATTA-TCT
1 TTTTTA-TTTATTGTATTTTATTATTCT
*
1656508 TTTTTATTTATTTTATTTTATTATTCT
1 TTTTTATTTATTGTATTTTATTATTCT
1656535 TT
1 TT
1656537 GAAACAAACG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 8 0.31
26 13 0.50
27 5 0.19
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (27 bp):
TTTTTATTTATTGTATTTTATTATTCT
Found at i:1661526 original size:28 final size:28
Alignment explanation
Indices: 1661486--1661616 Score: 136
Period size: 28 Copynumber: 4.5 Consensus size: 28
1661476 CAGCTTTAAC
1661486 ATGTTTGTCTTAATTTAGACAAGAAAAT
1 ATGTTTGTCTTAATTTAGACAAGAAAAT
*
1661514 ATGTTTGTCTTAATTTCAAACAAGAAAAAT
1 ATGTTTGTCTTAATTT-AGACAAG-AAAAT
* **
1661544 ATTTTTTGTCTTAAGCTAGACAAGAAAAT
1 A-TGTTTGTCTTAATTTAGACAAGAAAAT
* * * *
1661573 ATATTTGTCTCAATTTAGACTAGATTAAGT
1 ATGTTTGTCTTAATTTAGACAAGA--AAAT
*
1661603 ATTTTTGTCTTAAT
1 ATGTTTGTCTTAAT
1661617 AAGATACAAG
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
28 34 0.40
29 12 0.14
30 27 0.32
31 12 0.14
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (28 bp):
ATGTTTGTCTTAATTTAGACAAGAAAAT
Found at i:1661606 original size:59 final size:58
Alignment explanation
Indices: 1661489--1661615 Score: 157
Period size: 59 Copynumber: 2.2 Consensus size: 58
1661479 CTTTAACATG
** * *
1661489 TTTGTCTTAATTTAGACAAGAAAATATGTTTGTCTTAATTTCAAACAAGAAAAATATTT
1 TTTGTCTTAAGCTAGACAAGAAAATATATTTGTCTCAATTTCAAACAAGAAAAATA-TT
* * * *
1661548 TTTGTCTTAAGCTAGACAAGAAAATATATTTGTCTCAATTT-AGACTAGATTAAGTATT
1 TTTGTCTTAAGCTAGACAAGAAAATATATTTGTCTCAATTTCAAACAAGA-AAAATATT
1661606 TTTGTCTTAA
1 TTTGTCTTAA
1661616 TAAGATACAA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
58 18 0.31
59 41 0.69
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (58 bp):
TTTGTCTTAAGCTAGACAAGAAAATATATTTGTCTCAATTTCAAACAAGAAAAATATT
Found at i:1667242 original size:52 final size:52
Alignment explanation
Indices: 1667185--1667283 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
1667175 TTTTGATTTA
* *
1667185 TTGCTTGCATTTAGCTTAGGAAAACT-TTTTACCTTTATTTATTATTTATGCT
1 TTGCTTGCATTTAGATTAGGAAAA-TATTTTACCTTGATTTATTATTTATGCT
*
1667237 TTGCTTGCATTTGGATTAGGAAAATATTTTACCTTGATTTATTATTT
1 TTGCTTGCATTTAGATTAGGAAAATATTTTACCTTGATTTATTATTT
1667284 GTTCTTTTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 1 0.02
52 42 0.98
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.52
Consensus pattern (52 bp):
TTGCTTGCATTTAGATTAGGAAAATATTTTACCTTGATTTATTATTTATGCT
Found at i:1673687 original size:20 final size:18
Alignment explanation
Indices: 1673662--1673698 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
1673652 GAAGATAGCT
1673662 AGGTCAATTGAAATAATTTC
1 AGGTCAA-TGAAA-AATTTC
1673682 AGGTCAATGAAAAATTT
1 AGGTCAATGAAAAATTT
1673699 AAAGCAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 5 0.29
20 7 0.41
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.32
Consensus pattern (18 bp):
AGGTCAATGAAAAATTTC
Found at i:1674884 original size:17 final size:17
Alignment explanation
Indices: 1674842--1674889 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
1674832 TTATCCAAAC
1674842 AAATAAACATAAATAATT
1 AAATAAAC-TAAATAATT
*
1674860 AATTAAACTAAA-AATT
1 AAATAAACTAAATAATT
1674876 AAATAAAACTAAAT
1 AAAT-AAACTAAAT
1674890 CACAATAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 7 0.27
17 12 0.46
18 7 0.27
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATAAACTAAATAATT
Found at i:1678394 original size:36 final size:37
Alignment explanation
Indices: 1678354--1678442 Score: 103
Period size: 36 Copynumber: 2.5 Consensus size: 37
1678344 GTGTGTGTGA
* * * *
1678354 TGTGGGAGTGCACATGAT-GGTAA-TGGTAGTGTGCGG
1 TGTGGGAGTGCACATGATAGATAACAGCTA-TGTGCAG
*
1678390 TGTGGTAGTGCACATG-TAGATAACAGCTATGTGCAG
1 TGTGGGAGTGCACATGATAGATAACAGCTATGTGCAG
1678426 TGTGGGAGTGCACATGA
1 TGTGGGAGTGCACATGA
1678443 CTTGTGTTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
35 1 0.02
36 40 0.91
37 3 0.07
ACGTcount: A:0.24, C:0.11, G:0.38, T:0.27
Consensus pattern (37 bp):
TGTGGGAGTGCACATGATAGATAACAGCTATGTGCAG
Found at i:1683886 original size:22 final size:22
Alignment explanation
Indices: 1683861--1683903 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1683851 TTATATCCTT
1683861 AAATATTGTTATGTTAATAATA
1 AAATATTGTTATGTTAATAATA
1683883 AAATATTGTTATGTTAATAAT
1 AAATATTGTTATGTTAATAAT
1683904 TTATATCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (22 bp):
AAATATTGTTATGTTAATAATA
Found at i:1684094 original size:2 final size:2
Alignment explanation
Indices: 1684087--1684112 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1684077 ATTTTCATTT
1684087 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
1684113 AAACTTTTAC
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):
TA
Found at i:1685050 original size:2 final size:2
Alignment explanation
Indices: 1685045--1685079 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1685035 TGTGTGTGTT
1685045 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1685080 GTGCATGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1686625 original size:36 final size:34
Alignment explanation
Indices: 1686518--1686680 Score: 125
Period size: 36 Copynumber: 4.7 Consensus size: 34
1686508 NNNNNNNNNA
* * *
1686518 ACTTAATTAAATAATTTAATTAATTAGGCATAATA
1 ACTTAATTAAATAATTTAATCAATAAGGC-TAATG
* * *
1686553 ATTTAATTAAATAATTTTAATCAATGAGGCCCAATG
1 ACTTAATTAAATAA-TTTAATCAATAAGG-CTAATG
*
1686589 ACTTAATTAAATAATTTCAATCAACTAAAGCTAATG
1 ACTTAATTAAATAATTT-AATCAA-TAAGGCTAATG
* ** * *
1686625 AATTAATTAAACGATTTAATTAATTAGG-TACA--
1 ACTTAATTAAATAATTTAATCAATAAGGCTA-ATG
*
1686657 ACTTAATTAAACAATTTTAATCAA
1 ACTTAATTAAATAA-TTTAATCAA
1686681 GTGCTTGAAA
Statistics
Matches: 104, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
32 12 0.12
33 10 0.10
34 4 0.04
35 21 0.20
36 53 0.51
37 4 0.04
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (34 bp):
ACTTAATTAAATAATTTAATCAATAAGGCTAATG
Found at i:1695313 original size:2 final size:2
Alignment explanation
Indices: 1695306--1695341 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1695296 TGTGATTAAC
*
1695306 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1695342 TACTAACATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1711389 original size:86 final size:87
Alignment explanation
Indices: 1711288--1711471 Score: 264
Period size: 87 Copynumber: 2.1 Consensus size: 87
1711278 TTTGGTACAA
* * * *
1711288 AAAAAAAATTACTCCCGTCAAACTTTTCAACGGAA-TTTCCAACGAAAAATAATCCGTTGGAAAT
1 AAAAAAATTTACTCCCATCAAACTTTCCAACGGAATTTTCCAACGAAAAATAATCCGTTAGAAAT
1711352 CCGTAGGAAAATTT-AAGGCCTC
66 CCGTAGGAAAATTTAAAGGCC-C
* * *
1711374 AAAAAAATTTACTCCCATCAAACTTTCCAACGGAATTTTCCAATGGACAATAATCCGTTAGAAAT
1 AAAAAAATTTACTCCCATCAAACTTTCCAACGGAATTTTCCAACGAAAAATAATCCGTTAGAAAT
* *
1711439 CCGTCGGAAAGTTTAAAGGCCC
66 CCGTAGGAAAATTTAAAGGCCC
1711461 AAAAAAATTTA
1 AAAAAAATTTA
1711472 AAACTTACTA
Statistics
Matches: 87, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
86 32 0.37
87 49 0.56
88 6 0.07
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25
Consensus pattern (87 bp):
AAAAAAATTTACTCCCATCAAACTTTCCAACGGAATTTTCCAACGAAAAATAATCCGTTAGAAAT
CCGTAGGAAAATTTAAAGGCCC
Found at i:1716972 original size:57 final size:56
Alignment explanation
Indices: 1716884--1717096 Score: 221
Period size: 57 Copynumber: 3.7 Consensus size: 56
1716874 CTCGCACGTG
* *
1716884 TAGCACCAAGCCTTCTTAGACAGATAACAAGCATGTGTCTCATGTAATACACATGTC
1 TAGCACCAAGCCTTC-TAGATAGATATCAAGCATGTGTCTCATGTAATACACATGTC
* * *
1716941 TAGCACCAAACCTTACTAGATAGGTATCAAGCATGTGTCTCATGTAATACACATGTT
1 TAGCACCAAGCCTT-CTAGATAGATATCAAGCATGTGTCTCATGTAATACACATGTC
* * * * *
1716998 TAGCACTAAGCCTTGCTAGATAGACATCAAGCATGTGTCTTCCT-CATTACACATGTC
1 TAGCACCAAGCCTT-CTAGATAGATATCAAGCATGTGTC-TCATGTAATACACATGTC
* * * * *
1717055 TAACATCAAGCCTTGTTATATAGACATCCCAAGCATGTGTCT
1 TAGCACCAAGCCTT-CTAGATAGATAT--CAAGCATGTGTCT
1717097 TACTCACTGC
Statistics
Matches: 133, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
57 116 0.87
58 5 0.04
59 12 0.09
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.29
Consensus pattern (56 bp):
TAGCACCAAGCCTTCTAGATAGATATCAAGCATGTGTCTCATGTAATACACATGTC
Found at i:1717471 original size:59 final size:59
Alignment explanation
Indices: 1717293--1717573 Score: 236
Period size: 59 Copynumber: 4.8 Consensus size: 59
1717283 ATGGAGCACA
* * * * *
1717293 ATGCTTGTGATGCATATCTAGCAAAGCTTAGTGCTAGATATGTGTAGTGA-GTAAGACAC
1 ATGCTTGTGATACCTATCTAGCAAGGCTTAGTGCTAGACATGTGTACT-ATGTAAGACAC
* ** * * * * *
1717352 ATGCTTGTGATGCCTATCTAGCAATTCCTAGTGCTAAACACGTGTAGT-TAATAATG-CAC
1 ATGCTTGTGATACCTATCTAGCAAGGCTTAGTGCTAGACATGTGTACTAT-GTAA-GACAC
* * *
1717411 ATGCTTGTGATACCTATCTAGTAAGGCTTAGTGCTAGACATTTGTACTATGTGAGACAC
1 ATGCTTGTGATACCTATCTAGCAAGGCTTAGTGCTAGACATGTGTACTATGTAAGACAC
* * * * * *
1717470 AT-ATT-TG-TCACATATATAGTAAGGCTTAGTGCTAGACATTTGTACTATGTGAGACAC
1 ATGCTTGTGAT-ACCTATCTAGCAAGGCTTAGTGCTAGACATGTGTACTATGTAAGACAC
* * * *
1717527 ATGC--CTGATACCTATTTAGCAAGGTTTGGTGCTAGACATGTGTACTA
1 ATGCTTGTGATACCTATCTAGCAAGGCTTAGTGCTAGACATGTGTACTA
1717574 CATGAGACTT
Statistics
Matches: 184, Mismatches: 29, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
56 1 0.01
57 84 0.46
58 4 0.02
59 93 0.51
60 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (59 bp):
ATGCTTGTGATACCTATCTAGCAAGGCTTAGTGCTAGACATGTGTACTATGTAAGACAC
Found at i:1717559 original size:57 final size:57
Alignment explanation
Indices: 1717307--1717627 Score: 227
Period size: 57 Copynumber: 5.6 Consensus size: 57
1717297 TTGTGATGCA
* * * * *
1717307 TATCTAGCAAAGCTTAGTGCTAGATATGTGTAGTGA-GTAAGACACATGCTTGTGATGCC
1 TATCTAGCAAGGCTTAGTGCTAGACATGTGTACT-ATGTGAGACACATG-TT-TGATACC
** * * * * * *
1717366 TATCTAGCAATTCCTAGTGCTAAACACGTGTAGT-TAATAATG-CACATGCTTGTGATACC
1 TATCTAGCAAGGCTTAGTGCTAGACATGTGTACTAT-GTGA-GACACATG-TT-TGATACC
* * * *
1717425 TATCTAGTAAGGCTTAGTGCTAGACATTTGTACTATGTGAGACACATATTTG-TCACA
1 TATCTAGCAAGGCTTAGTGCTAGACATGTGTACTATGTGAGACACATGTTTGAT-ACC
* * * **
1717482 TATATAGTAAGGCTTAGTGCTAGACATTTGTACTATGTGAGACACATGCCTGATACC
1 TATCTAGCAAGGCTTAGTGCTAGACATGTGTACTATGTGAGACACATGTTTGATACC
* * * ** ** * *
1717539 TATTTAGCAAGGTTTGGTGCTAGACATGTGTACTACATGAGACTTATGTTTGTTGCC
1 TATCTAGCAAGGCTTAGTGCTAGACATGTGTACTATGTGAGACACATGTTTGATACC
* * * *
1717596 TAACTAGCAAGGTTTGGTGCTAAACATGTGTA
1 TATCTAGCAAGGCTTAGTGCTAGACATGTGTA
1717628 GGGAGTGAGA
Statistics
Matches: 214, Mismatches: 41, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
56 1 0.00
57 127 0.59
58 4 0.02
59 80 0.37
60 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (57 bp):
TATCTAGCAAGGCTTAGTGCTAGACATGTGTACTATGTGAGACACATGTTTGATACC
Found at i:1730623 original size:21 final size:21
Alignment explanation
Indices: 1730588--1730661 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
1730578 CCAAGAAGAA
1730588 AAGAGAAAGGAGAAGAAAGAAGG
1 AAGAGAAA-G-GAAGAAAGAAGG
1730611 AAGAGAAAGGAAGAAAGGAAGG
1 AAGAGAAAGGAAGAAA-GAAGG
* *
1730633 -AGAGAAAAGAAG-AAGAA-A
1 AAGAGAAAGGAAGAAAGAAGG
1730651 AAG-GAAAGGAA
1 AAGAGAAAGGAA
1730662 AGATCGGTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
18 7 0.15
19 5 0.11
20 2 0.04
21 18 0.39
22 6 0.13
23 8 0.17
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (21 bp):
AAGAGAAAGGAAGAAAGAAGG
Found at i:1733925 original size:7 final size:7
Alignment explanation
Indices: 1733913--1733942 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1733903 GTTTAGCATA
1733913 GGCTATT
1 GGCTATT
1733920 GGCTATT
1 GGCTATT
1733927 GGCTATT
1 GGCTATT
1733934 GGCTATT
1 GGCTATT
1733941 GG
1 GG
1733943 AAGATTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.13, G:0.33, T:0.40
Consensus pattern (7 bp):
GGCTATT
Found at i:1744303 original size:99 final size:98
Alignment explanation
Indices: 1744183--1744362 Score: 225
Period size: 99 Copynumber: 1.8 Consensus size: 98
1744173 AGCATGTAAC
* * * * * * * *
1744183 TTGGTCTTTCTCTTTATATTTCATTAGGACATTAATTCTTAAAGTTAAAACACTTTAACCATGAT
1 TTGGTCTTTATCTTTATATTTCACTAGGACATAAACTCCTAAAGTT-AAACACCTCAACCATGAC
*
1744248 GTGTAACAATTTTTTTTTTCAACATGATGTGAAT
65 GTGTAACAACTTTTTTTTTCAACATGATGTGAAT
* * * * *
1744282 TTGGTCTTTATTTTTGTATTTCACTAGGACATAAACTCCTAATGTTAAACACCTCAAGCATGGCG
1 TTGGTCTTTATCTTTATATTTCACTAGGACATAAACTCCTAAAGTTAAACACCTCAACCATGACG
1744347 TGTAACAACTTTTTTT
66 TGTAACAACTTTTTTT
1744363 CAGCGTGGCG
Statistics
Matches: 67, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
98 29 0.43
99 38 0.57
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (98 bp):
TTGGTCTTTATCTTTATATTTCACTAGGACATAAACTCCTAAAGTTAAACACCTCAACCATGACG
TGTAACAACTTTTTTTTTCAACATGATGTGAAT
Found at i:1744551 original size:98 final size:99
Alignment explanation
Indices: 1744382--1744586 Score: 254
Period size: 98 Copynumber: 2.1 Consensus size: 99
1744372 GTATAATAAC
* * * ** *
1744382 TTTTTGTTTTCAACATGCTGTGTAACTTGATTTCTATGTTTGTATTTTGTTAGGACATAAACTAT
1 TTTTTTTTTTCAACATGCAGTGTAACTTGATCTCTATGTTTGTATTTACTTAGGAAATAAACTAT
* *
1744447 TGGAGTTAAGCA-CTTAAACATGGCATGTAACAA
66 TCGAGTTAAACACCTTAAACATGGCATGTAACAA
* *
1744480 TTTTTTTTTTCAACATGGAGTGTAACTTGGTCTCTAT-TTGTGTATTTCACTT-GGAAATAAACT
1 TTTTTTTTTTCAACATGCAGTGTAACTTGATCTCTATGTT-TGTATTT-ACTTAGGAAATAAACT
* **
1744543 CTTCGAGTTAAACACCTTAAACATGGTGTGTAACAA
64 ATTCGAGTTAAACACCTTAAACATGGCATGTAACAA
1744579 TTTTTTTT
1 TTTTTTTT
1744587 CAACACATGT
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
97 2 0.02
98 60 0.66
99 29 0.32
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.43
Consensus pattern (99 bp):
TTTTTTTTTTCAACATGCAGTGTAACTTGATCTCTATGTTTGTATTTACTTAGGAAATAAACTAT
TCGAGTTAAACACCTTAAACATGGCATGTAACAA
Found at i:1747477 original size:18 final size:18
Alignment explanation
Indices: 1747454--1747494 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1747444 AGACAATGGG
* *
1747454 AAAGGGAAGAGAGAAAAA
1 AAAGGGAAAAAAGAAAAA
1747472 AAAGGGAAAAAAGAAAAA
1 AAAGGGAAAAAAGAAAAA
*
1747490 GAAGG
1 AAAGG
1747495 ATAAATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (18 bp):
AAAGGGAAAAAAGAAAAA
Found at i:1756103 original size:2 final size:2
Alignment explanation
Indices: 1756063--1756091 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1756053 AACCTTTACG
1756063 TA TA TA T- 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
1756092 GCTTATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1757822 original size:16 final size:17
Alignment explanation
Indices: 1757782--1757825 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
1757772 TCACTAATAA
1757782 ATAAAATATTAATATTT
1 ATAAAATATTAATATTT
*
1757799 -TAATAATATT-TTATTT
1 ATAA-AATATTAATATTT
1757815 ATAAAATATTA
1 ATAAAATATTA
1757826 TTTTATTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATAAAATATTAATATTT
Found at i:1757847 original size:19 final size:19
Alignment explanation
Indices: 1757800--1757849 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1757790 TTAATATTTT
* *
1757800 AATAATATTTTATTTATAA
1 AATATTATTTTATTTACAA
1757819 AATATTATTTTATTT-CAA
1 AATATTATTTTATTTACAA
1757837 AATATTCATTTTA
1 AATATT-ATTTTA
1757850 CCTATCACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATTATTTTATTTACAA
Found at i:1766185 original size:25 final size:25
Alignment explanation
Indices: 1766151--1766199 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
1766141 CCAAAGATGT
1766151 ATTGGTTATTGGTGGAGATGTCCAA
1 ATTGGTTATTGGTGGAGATGTCCAA
1766176 ATTGGTTATTGGTGGAGATGTCCA
1 ATTGGTTATTGGTGGAGATGTCCA
1766200 CTTTTGGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.08, G:0.33, T:0.37
Consensus pattern (25 bp):
ATTGGTTATTGGTGGAGATGTCCAA
Found at i:1775516 original size:12 final size:13
Alignment explanation
Indices: 1775497--1775533 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
1775487 CAGAATAGTT
1775497 TCTTGCTGCCTCA
1 TCTTGCTGCCTCA
1775510 T-TTGCTGCCTC-
1 TCTTGCTGCCTCA
1775521 TCTTGCTGCCTCA
1 TCTTGCTGCCTCA
1775534 AAAATCTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 1 0.05
12 20 0.91
13 1 0.05
ACGTcount: A:0.05, C:0.38, G:0.16, T:0.41
Consensus pattern (13 bp):
TCTTGCTGCCTCA
Found at i:1776206 original size:21 final size:20
Alignment explanation
Indices: 1776182--1776226 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1776172 CTCTTAAAGT
*
1776182 AATTTAAAATAAAATACCTAA
1 AATTT-AAATAAAATAACTAA
* *
1776203 AATTTAACTAAAATAACTTA
1 AATTTAAATAAAATAACTAA
1776223 AATT
1 AATT
1776227 AATCACTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (20 bp):
AATTTAAATAAAATAACTAA
Done.