Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000121.1 Hibiscus syriacus cultivar Beakdansim tig00000218_pilon, 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: 2099483
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:187031 original size:21 final size:21
Alignment explanation
Indices: 186991--187050 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
186981 CCCCCTTTGA
186991 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATTCCCCCCAC
187012 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATTCCCCCCAC
* *
187033 AGGGGAATCGATACCCCC
1 AGGGGAACCGATTCCCCC
187051 TGGGGTTCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATTCCCCCCAC
Found at i:190645 original size:3 final size:3
Alignment explanation
Indices: 190637--190670 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
190627 GAATGCAAAA
190637 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
190671 ACGTTAAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:190833 original size:3 final size:3
Alignment explanation
Indices: 190825--190858 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
190815 AAATGCAAAA
190825 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
190859 ACGTTAAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:190857 original size:188 final size:188
Alignment explanation
Indices: 190480--191017 Score: 979
Period size: 188 Copynumber: 2.8 Consensus size: 188
190470 CTTACGTGAC
* *
190480 ACGTTAAACCAGTTGATTCAGCATGTTTGACTGATCCTTTGACTCTTCTTCTTCTTCAATATAAA
1 ACGTTAAACCAGTTGATTCAGTATGTTTGACCGATCCTTTGACTCTTCTTCTTCTTCAATATAAA
190545 TTACCACCCATGCAATTACCTAATGCCCATGCAAATAAATCATTAGGCAGATCCTCTATACGGGT
66 TTACCACCCATGCAATTACCTAATGCCCATGCAAATAAATCATTAGGCAGATCCTCTATACGGGT
190610 TGGTAATTAGAAAAATTGAATGCAAAATTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
131 TGGTAATTAGAAAAA---AATGCAAAATTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
* *
190671 ACGTTAAACCAGTTGATTCAGTATGTTTAACCGATTCTTTGACTCTTCTTCTTCTTCAATATAAA
1 ACGTTAAACCAGTTGATTCAGTATGTTTGACCGATCCTTTGACTCTTCTTCTTCTTCAATATAAA
190736 TTACCACCCATGCAATTACCTAATGCCCATGCAAATAAATCATTAGGCAGATCCTCTATACGGGT
66 TTACCACCCATGCAATTACCTAATGCCCATGCAAATAAATCATTAGGCAGATCCTCTATACGGGT
*
190801 TGGTAATTAGGAAAAAATGCAAAATTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
131 TGGTAATTAGAAAAAAATGCAAAATTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
190859 ACGTTAAACCAGTTGATTCA-TCATGTTTGACCGATCCTTTGACTCTTCTTCTTCTTCAATATAA
1 ACGTTAAACCAGTTGATTCAGT-ATGTTTGACCGATCCTTTGACTCTTCTTCTTCTTCAATATAA
190923 ATTACCACCCATGCAATTACCTAATGCCCATGCAAATAAATCATTAGGCAGATCCTCTATACGGG
65 ATTACCACCCATGCAATTACCTAATGCCCATGCAAATAAATCATTAGGCAGATCCTCTATACGGG
190988 TTGGTAATTAGCAAAAAAATGCAAAATTCT
130 TTGGTAATTAG-AAAAAAATGCAAAATTCT
191018 CCTCCTCTTC
Statistics
Matches: 337, Mismatches: 8, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
187 1 0.00
188 179 0.53
189 17 0.05
191 140 0.42
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (188 bp):
ACGTTAAACCAGTTGATTCAGTATGTTTGACCGATCCTTTGACTCTTCTTCTTCTTCAATATAAA
TTACCACCCATGCAATTACCTAATGCCCATGCAAATAAATCATTAGGCAGATCCTCTATACGGGT
TGGTAATTAGAAAAAAATGCAAAATTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT
Found at i:191022 original size:3 final size:3
Alignment explanation
Indices: 191016--191285 Score: 300
Period size: 3 Copynumber: 91.3 Consensus size: 3
191006 ATGCAAAATT
*
191016 CTC CTC CTC TTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
191064 CTC CTC CTC CTC CTC CTC CTC C-C CTC CTC CTC CTC CTC CTC CTC C-C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* * * * * * * * * * *
191110 TTT TTT TTT CTC CTT CTC CTC C-C CTT CTT CTC CTT CTT CTC CTTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C-TC
* * * * *
191155 CT- CTC CTC CTC CTC CTC CTC CTC CTC CTC C-C CTTT TTT TTT CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C-TC CTC CTC CTC
* * *
191199 CTT CTC CTC C-C CTT CTT CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
191246 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C
191286 ACCAAAATCT
Statistics
Matches: 239, Mismatches: 20, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
2 11 0.05
3 225 0.94
4 3 0.01
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (3 bp):
CTC
Found at i:191524 original size:116 final size:117
Alignment explanation
Indices: 191316--191553 Score: 460
Period size: 116 Copynumber: 2.0 Consensus size: 117
191306 ATAAAAAAAC
191316 AGGATTCAAGCTGACGATTTAAAACAAAGCCTAAATTCGGAGGAAAAAAAAGAGAAAGGAAGGCT
1 AGGATTCAAGCTGACGATTTAAAACAAAGCCTAAATTCGGAGGAAAAAAAAGAGAAAGGAAGGCT
191381 AATTAGCAATGCATGACATAACAATTATACTCAACAACAGCATCCCGGTTAT
66 AATTAGCAATGCATGACATAACAATTATACTCAACAACAGCATCCCGGTTAT
*
191433 TGGATTCAAGCTGACGATTTAAAACAAAGCCTAAATTCGGAGG-AAAAAAAGAGAAAGGAAGGCT
1 AGGATTCAAGCTGACGATTTAAAACAAAGCCTAAATTCGGAGGAAAAAAAAGAGAAAGGAAGGCT
191497 AATTAGCAATGCATGACATAACAATTATACTCAACAACAGCATCCCGGTTAT
66 AATTAGCAATGCATGACATAACAATTATACTCAACAACAGCATCCCGGTTAT
191549 AGGAT
1 AGGAT
191554 CAAAACGATG
Statistics
Matches: 119, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
116 77 0.65
117 42 0.35
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.20
Consensus pattern (117 bp):
AGGATTCAAGCTGACGATTTAAAACAAAGCCTAAATTCGGAGGAAAAAAAAGAGAAAGGAAGGCT
AATTAGCAATGCATGACATAACAATTATACTCAACAACAGCATCCCGGTTAT
Found at i:197342 original size:21 final size:23
Alignment explanation
Indices: 197318--197367 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
197308 AAAAGCATAA
197318 GAAAATGAT-TCAT-AA-GCAGAT
1 GAAAATG-TGTCATAAAGGCAGAT
*
197339 GAAAACGTGTCATAAAGGCAGAT
1 GAAAATGTGTCATAAAGGCAGAT
197362 GAAAAT
1 GAAAAT
197368 ACTCAACACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.04
21 10 0.42
22 2 0.08
23 11 0.46
ACGTcount: A:0.48, C:0.10, G:0.22, T:0.20
Consensus pattern (23 bp):
GAAAATGTGTCATAAAGGCAGAT
Found at i:198374 original size:29 final size:30
Alignment explanation
Indices: 198340--198397 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
198330 ATTACTCTGA
*
198340 TTATTAAATTT-TTAAAAGTTATAAAATGG
1 TTATTAAATTTATCAAAAGTTATAAAATGG
* *
198369 TTATTAAATTTATCAAACGTTGTAAAATG
1 TTATTAAATTTATCAAAAGTTATAAAATG
198398 ATCATTGTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.43
Consensus pattern (30 bp):
TTATTAAATTTATCAAAAGTTATAAAATGG
Found at i:205352 original size:15 final size:15
Alignment explanation
Indices: 205334--205373 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
205324 TCATTCTATT
205334 GTATCAATATAATGA
1 GTATCAATATAATGA
205349 GTATCAATATAATGA
1 GTATCAATATAATGA
205364 GTATCAATAT
1 GTATCAATAT
205374 TCTTTATTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.35
Consensus pattern (15 bp):
GTATCAATATAATGA
Found at i:209388 original size:36 final size:35
Alignment explanation
Indices: 209341--209409 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
209331 AAATTCAAGG
209341 GGTACCGATACCATGAA-GAACAGTATCGATACCAAA
1 GGTACCGATACC-TGAAGGAA-AGTATCGATACCAAA
* * *
209377 GGTACTGATACCTTAAGGAAGGTATCGATACCA
1 GGTACCGATACCTGAAGGAAAGTATCGATACCA
209410 TCTTTGAACG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 15 0.52
36 14 0.48
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (35 bp):
GGTACCGATACCTGAAGGAAAGTATCGATACCAAA
Found at i:210112 original size:18 final size:18
Alignment explanation
Indices: 210077--210112 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
210067 GAAGGATTAT
*
210077 TAGTGGTCCTGCGGGACA
1 TAGTGGTCCTGCGAGACA
*
210095 TAGTGGTCCTTCGAGACA
1 TAGTGGTCCTGCGAGACA
210113 AATATTCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.22, G:0.33, T:0.25
Consensus pattern (18 bp):
TAGTGGTCCTGCGAGACA
Found at i:228045 original size:31 final size:31
Alignment explanation
Indices: 228009--228068 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
227999 TTTGTAGTCA
228009 CTTTCGTTTCGTTTTAATTAAGATGTGGTAG
1 CTTTCGTTTCGTTTTAATTAAGATGTGGTAG
*
228040 CTTTCGTTTTGTTTTAATTAAGATGTGGT
1 CTTTCGTTTCGTTTTAATTAAGATGTGGT
228069 CACTTATCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.18, C:0.08, G:0.22, T:0.52
Consensus pattern (31 bp):
CTTTCGTTTCGTTTTAATTAAGATGTGGTAG
Found at i:237267 original size:30 final size:29
Alignment explanation
Indices: 237233--237327 Score: 145
Period size: 30 Copynumber: 3.2 Consensus size: 29
237223 TTTTTATTCC
237233 ACCATATTTTATTCAACATCCCATGCCACT
1 ACCAT-TTTTATTCAACATCCCATGCCACT
237263 ACCATTTTTTATTCAACATCCCATGCCACT
1 ACCA-TTTTTATTCAACATCCCATGCCACT
* *
237293 ACCATTTTATATTCAATATCCCATGCCACC
1 ACCATTTT-TATTCAACATCCCATGCCACT
237323 ACCAT
1 ACCAT
237328 GCCCCCACGT
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
29 4 0.07
30 56 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.34, G:0.03, T:0.34
Consensus pattern (29 bp):
ACCATTTTTATTCAACATCCCATGCCACT
Found at i:239102 original size:18 final size:18
Alignment explanation
Indices: 239081--239128 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
239071 AAACTCAGTA
239081 TTTTATTAAAATAAAATG
1 TTTTATTAAAATAAAATG
239099 TTTTATTAAAATAAAATG
1 TTTTATTAAAATAAAATG
239117 TTTTATTAAAAT
1 TTTTATTAAAAT
239129 CACTCAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (18 bp):
TTTTATTAAAATAAAATG
Found at i:240273 original size:45 final size:46
Alignment explanation
Indices: 240185--240275 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 46
240175 TGAAAAAAGT
* *
240185 CTGAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
240231 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
240276 TTCGATGTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 22 0.51
46 21 0.49
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:240323 original size:20 final size:20
Alignment explanation
Indices: 240295--240333 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
240285 CAAGAAATTA
240295 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
240315 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
240334 CCCTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:243117 original size:44 final size:44
Alignment explanation
Indices: 243021--243121 Score: 109
Period size: 44 Copynumber: 2.3 Consensus size: 44
243011 ATGCATCGAC
* * *
243021 ATGCATAGATGCACATTCAAGGCGTGCATCGGTGCATTAGCAAG
1 ATGCATCGATGCACATTCAAGGCGTGCATCGATGCACTAGCAAG
* *
243065 ATGAATCGATGCACATTCAAAGG-GATGCATCGATGCACT-GTTAAG
1 ATGCATCGATGCACATTC-AAGGCG-TGCATCGATGCACTAG-CAAG
243110 -TGCATCGATGCA
1 ATGCATCGATGCA
243122 TGAAGCACAA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
44 29 0.60
45 19 0.40
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.24
Consensus pattern (44 bp):
ATGCATCGATGCACATTCAAGGCGTGCATCGATGCACTAGCAAG
Found at i:249063 original size:20 final size:20
Alignment explanation
Indices: 249038--249075 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
249028 CAAGAAATTA
249038 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
*
249058 ATTGATGCATCGGTGCAT
1 ATTGATGCATCGATGCAT
249076 ACCCTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:250679 original size:20 final size:21
Alignment explanation
Indices: 250651--250696 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
250641 TACCTTTAAC
*
250651 TTAAAATTTTAAA-TTATAAT
1 TTAAAATTTAAAATTTATAAT
*
250671 TTAAGATTTAAAATTTTATAAT
1 TTAAAATTTAAAA-TTTATAAT
250693 TTAA
1 TTAA
250697 TGTTTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
22 11 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TTAAAATTTAAAATTTATAAT
Found at i:250706 original size:27 final size:26
Alignment explanation
Indices: 250645--250709 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 26
250635 ATATTTTACC
*
250645 TTTAACTTAAAATTTTAAATTATAAT
1 TTTAATTTAAAATTTTAAATTATAAT
*
250671 TTAAGATTTAAAATTTTATAATT-TAAT
1 TTTA-ATTTAAAATTTTA-AATTATAAT
250698 GTTTAATTTAAA
1 -TTTAATTTAAA
250710 GATAAGATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 3 0.09
27 23 0.70
28 7 0.21
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (26 bp):
TTTAATTTAAAATTTTAAATTATAAT
Found at i:252476 original size:30 final size:31
Alignment explanation
Indices: 252442--252544 Score: 90
Period size: 31 Copynumber: 3.4 Consensus size: 31
252432 TCACTGTTTA
252442 GGAAAA-AATAATGTAATAAATAGCATATTG
1 GGAAAAGAATAATGTAATAAATAGCATATTG
* *
252472 GGAAAAGAA-AATG-ACATTAAT-GTCATAATTT
1 GGAAAAGAATAATGTA-ATAAATAG-CAT-ATTG
* * *
252503 GGAAAA-ATATAATGTATTAAATAACATGTTG
1 GGAAAAGA-ATAATGTAATAAATAGCATATTG
252534 GGAAAAGAATA
1 GGAAAAGAATA
252545 TGACATTAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
29 2 0.04
30 19 0.33
31 23 0.40
32 12 0.21
33 1 0.02
ACGTcount: A:0.51, C:0.04, G:0.17, T:0.27
Consensus pattern (31 bp):
GGAAAAGAATAATGTAATAAATAGCATATTG
Found at i:255289 original size:30 final size:28
Alignment explanation
Indices: 255236--255306 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 28
255226 AAATATTTAA
255236 AATATTATTATTTTATATATTTAATATT
1 AATATTATTATTTTATATATTTAATATT
**
255264 AATA-TATTATTTTAGTATCATTTTAATAAA
1 AATATTATTATTTTA-TAT-A-TTTAATATT
255294 AATATTAATTATT
1 AATATT-ATTATT
255307 AAATTATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 10 0.28
28 7 0.19
29 1 0.03
30 11 0.31
31 1 0.03
32 6 0.17
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (28 bp):
AATATTATTATTTTATATATTTAATATT
Found at i:255391 original size:29 final size:29
Alignment explanation
Indices: 255348--255404 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
255338 AAGATTTTAT
255348 TGTTATAATTATATTATT-AGAATATATAG
1 TGTTATAATTATATT-TTAAGAATATATAG
* * *
255377 TGTTATACTTTTATTTTAATAATATATA
1 TGTTATAATTATATTTTAAGAATATATA
255405 ATAATTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.53
Consensus pattern (29 bp):
TGTTATAATTATATTTTAAGAATATATAG
Found at i:255412 original size:22 final size:20
Alignment explanation
Indices: 255387--255432 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
255377 TGTTATACTT
*
255387 TTATTTTAATAATATATAATA
1 TTATTTTAATAAAAT-TAATA
255408 --ATTATTAATAAAATTAATA
1 TTATT-TTAATAAAATTAATA
255427 TTATTT
1 TTATTT
255433 ATTAATTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 7
0.72 0.03 0.24
Matches are distributed among these distances:
19 8 0.38
20 10 0.48
21 3 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTATTTTAATAAAATTAATA
Found at i:255438 original size:29 final size:27
Alignment explanation
Indices: 255392--255455 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
255382 TACTTTTATT
*
255392 TTAATAATATATAATAATTATTAATAAAA
1 TTAATATTATATAATAA-T-TTAATAAAA
* * *
255421 TTAATATTATTTATTAATTTCATAAAA
1 TTAATATTATATAATAATTTAATAAAA
255448 -TAATATTA
1 TTAATATTA
255456 AGTTGTTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 8 0.26
27 8 0.26
28 1 0.03
29 14 0.45
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
TTAATATTATATAATAATTTAATAAAA
Found at i:255505 original size:14 final size:13
Alignment explanation
Indices: 255486--255548 Score: 58
Period size: 14 Copynumber: 4.8 Consensus size: 13
255476 AAATATAATA
255486 TAATATTCTTATTT
1 TAATATT-TTATTT
*
255500 TAATATTATATTTT
1 TAATATTTTA-TTT
* *
255514 TTATATTTTA--A
1 TAATATTTTATTT
255525 TAATATTATTATTT
1 TAATATT-TTATTT
255539 TAATATTTTA
1 TAATATTTTA
255549 AAAATAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
11 6 0.15
12 3 0.08
13 5 0.13
14 25 0.64
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (13 bp):
TAATATTTTATTT
Found at i:255539 original size:17 final size:17
Alignment explanation
Indices: 255485--255543 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
255475 TAAATATAAT
*
255485 ATAATATTCTTATTTTA
1 ATAATATTATTATTTTA
*
255502 ATATTATATTTTTTATATTTTA
1 ATA--ATA--TTAT-TATTTTA
255524 ATAATATTATTATTTTA
1 ATAATATTATTATTTTA
255541 ATA
1 ATA
255544 TTTTAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
17 13 0.37
18 3 0.09
19 3 0.09
20 3 0.09
21 3 0.09
22 10 0.29
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
ATAATATTATTATTTTA
Found at i:255539 original size:25 final size:25
Alignment explanation
Indices: 255495--255596 Score: 97
Period size: 25 Copynumber: 4.2 Consensus size: 25
255485 ATAATATTCT
*
255495 TATTTTAAT-ATTATA-T-TTTTTA
1 TATTTTAATAATAATATTATTTTTA
* *
255517 TATTTTAATAATATTATTATTTTAA
1 TATTTTAATAATAATATTATTTTTA
* *
255542 TATTTTAAAAATAATATTATTATT-
1 TATTTTAATAATAATATTATTTTTA
*
255566 T-TGTTAATAAATAATATTATTTATTA
1 TATTTTAAT-AATAATATTATTT-TTA
255592 TATTT
1 TATTT
255597 GATGTTTATA
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
22 9 0.15
23 9 0.15
24 14 0.23
25 27 0.44
26 1 0.02
27 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (25 bp):
TATTTTAATAATAATATTATTTTTA
Found at i:255548 original size:8 final size:8
Alignment explanation
Indices: 255495--255549 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
255485 ATAATATTCT
255495 TATTTTAA
1 TATTTTAA
*
255503 TATTAT-A
1 TATTTTAA
*
255510 T-TTTTTA
1 TATTTTAA
255517 TATTTTAA
1 TATTTTAA
* *
255525 TAATATTAT
1 T-ATTTTAA
255534 TATTTTAA
1 TATTTTAA
255542 TATTTTAA
1 TATTTTAA
255550 AAATAATATT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
6 3 0.08
7 4 0.11
8 24 0.65
9 6 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATTTTAA
Found at i:258060 original size:105 final size:105
Alignment explanation
Indices: 257878--258444 Score: 1089
Period size: 105 Copynumber: 5.4 Consensus size: 105
257868 TGTTGTTTTC
257878 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
257943 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
257983 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
258048 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
258088 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAGC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
258153 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
258193 GAGTCCAATATCCTTCGTTGCGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
258258 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
258298 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAGC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
258363 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
258403 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
258445 TAAAACCTGC
Statistics
Matches: 453, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 453 1.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:258639 original size:1 final size:1
Alignment explanation
Indices: 258633--258665 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
258623 ATGTTTGATG
258633 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
258666 GAAGATGCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:270580 original size:162 final size:163
Alignment explanation
Indices: 270313--270637 Score: 643
Period size: 162 Copynumber: 2.0 Consensus size: 163
270303 GAACACGCCG
270313 CCGTAAAATCCCAGAAAGGGCCACACGCCGCCTCGCCGGCCGCCGTTGGTCGGCGCCGGCCACCG
1 CCGTAAAATCCCAGAAAGGGCCACACGCCGCCTCGCCGGCCGCCGTTGGTCGGCGCCGGCCACCG
270378 ATCATCGGCGGCAAACCCAAAAAAAAAAAAAAAAAAAAAAATTGGTTTTTCTG-AAGCCTTTCTC
66 ATCATCGGCGGCAAACCCAAAAAAAAAAAAAAAAAAAAAAATTGGTTTTTCTGAAAGCCTTTCTC
270442 TCCCTCGACTCAATCTCAAATCCTTTTTTTGAA
131 TCCCTCGACTCAATCTCAAATCCTTTTTTTGAA
270475 CCGTAAAATCCCAGAAAGGGCCACACGCCGCCTCGCCGGCCGCCGTTGGTCGGCGCCGGCCACCG
1 CCGTAAAATCCCAGAAAGGGCCACACGCCGCCTCGCCGGCCGCCGTTGGTCGGCGCCGGCCACCG
270540 ATCATCGGCGGCAAACCCAAAAAAAAAAAAAAAAAAAAAAATTGGTTTTTCTGAAAGCCTTTCTC
66 ATCATCGGCGGCAAACCCAAAAAAAAAAAAAAAAAAAAAAATTGGTTTTTCTGAAAGCCTTTCTC
270605 TCCCTCGACTCAATCTCAAATCCTTTTTTTGAA
131 TCCCTCGACTCAATCTCAAATCCTTTTTTTGAA
270638 ATAGGCCTCG
Statistics
Matches: 162, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
162 118 0.73
163 44 0.27
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.20
Consensus pattern (163 bp):
CCGTAAAATCCCAGAAAGGGCCACACGCCGCCTCGCCGGCCGCCGTTGGTCGGCGCCGGCCACCG
ATCATCGGCGGCAAACCCAAAAAAAAAAAAAAAAAAAAAAATTGGTTTTTCTGAAAGCCTTTCTC
TCCCTCGACTCAATCTCAAATCCTTTTTTTGAA
Found at i:274435 original size:23 final size:23
Alignment explanation
Indices: 274404--274467 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
274394 ATAGGTAAAA
*
274404 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
274427 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
274450 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
274468 TTGTAAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:274932 original size:21 final size:23
Alignment explanation
Indices: 274883--274943 Score: 83
Period size: 21 Copynumber: 2.8 Consensus size: 23
274873 ATAGGTAAAA
*
274883 ATATGATGT-ATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
274905 ATATAATGTAATAGGTATCG-TT
1 ATATAATGTAATAGGTAGCGCTT
274927 -TATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
274944 TTGTAAAGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 16 0.46
22 10 0.29
23 9 0.26
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:275170 original size:481 final size:480
Alignment explanation
Indices: 273984--275814 Score: 3359
Period size: 475 Copynumber: 3.9 Consensus size: 480
273974 TAATCCAAAA
273984 AATAGGTAGTTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAA
1 AATAGGTAGTTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAA
274049 CATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAA
66 CATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAA
274114 TGATTTATTTTTTACGTTACG--ATATATATTATTATATTAAAAACAAT-AAC--ATATATTACA
131 TGATTTATTTTTTACGTTACGATATATATATTATTATATTAAAAACAATAAACATATATATTACA
274174 TATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATC
196 TATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATC
*
274239 AAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATA
261 AAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATG
*
274304 AAACACTATTAAAAAAAATTGAAACATAAATTAATAACTTTTAAAAAAGTGTCGATCCTTTTTAT
326 AAACACTATTAAAAAAAATTGAAACATAAATTAATAACTTTAAAAAAAGTGTCGATCCTTTTTAT
274369 AAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAAT
391 AAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAAT
274434 GTAATAGGTATCGTTTATATAATGT
456 GTAATAGGTATCGTTTATATAATGT
274459 AATAGGTAGTTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAA
1 AATAGGTAGTTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAA
274524 CATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAA
66 CATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAA
274589 TGATTTATTTTTTACGTTACGATATATATTATTATTATATTAAAAACAATAAACATATATATTAC
131 TGATTTATTTTTTACGTTACGATATATA-TATTATTATATTAAAAACAATAAACATATATATTAC
274654 ATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATAT
195 ATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATAT
*
274719 CAAAACAATCAAATAATTTTTTGTGTAAATAAAATTATTAAATTAATATTGTAGGTGGAAAACAT
260 CAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACAT
274784 GAAACACTATTAAAAAAAATTGAAACAT-AATTAATAACTTTAAAAAAAGTGTCGATCCTTTTTA
325 GAAACACTATTAAAAAAAATTGAAACATAAATTAATAACTTTAAAAAAAGTGTCGATCCTTTTTA
274848 TAAAAAGTATGGACACTTTCAATA-AATAGGTAAAAATATGATGT-ATAGGTAGCGCTTATATAA
390 TAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAA
274911 TGTAATAGGTATCG-TT-TATAATGT
455 TGTAATAGGTATCGTTTATATAATGT
274935 AATAGGTAGTTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAA
1 AATAGGTAGTTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAA
275000 CATTAA-TTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAA
66 CATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAA
275064 TGATTTATTTTTTACGTTACGATATATATTATTATTATATTAAAAACAATAAACATATATATTAC
131 TGATTTATTTTTTACGTTACGATATATA-TATTATTATATTAAAAACAATAAACATATATATTAC
275129 ATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATA-T-TTTTATAAAATAT
195 ATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATAT
275192 CAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATT-AATTAATATTGTAGGTGGAAAACAT
260 CAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACAT
275256 G-AACACTATTAAAAAAAATTGAAACATAAATTAATAACTTT-AAAAAAGTGTCGATCCTTTTTA
325 GAAACACTATTAAAAAAAATTGAAACATAAATTAATAACTTTAAAAAAAGTGTCGATCCTTTTTA
275319 TAAAAAGTATGGACACTTTCAATATAATAGGT-AAAATATGATGTAATAGGTAGCGCTTATAT-A
390 TAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAA
275382 TGTAATAGGTATCGTTTATATAATGT
455 TGTAATAGGTATCGTTTATATAATGT
275408 AATAGGTAGTTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAA
1 AATAGGTAGTTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAA
275473 CATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATA-TAA-TTAGTAATTATAGGCGTCTAA
66 CATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAA
* *
275536 TGATTTATTTTTTACGTTACGATATATATATTA--A-ATTAAAAAATAATAAAAATATATATTAC
131 TGATTTATTTTTTACGTTACGATATATATATTATTATATT-AAAAACAATAAACATATATATTAC
275598 ATATTTATTATTATCTTTGGTTAATATTGTTAAATTT-AATTCTAAATATTATTTTATAAAATAT
195 ATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATAT
* * **
275662 CAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTTGGTAAAAAACAT
260 CAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACAT
* *
275727 GAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAATTATCGATCCTTTTT
325 GAAACACTATTAAAAAAAATTGAAACATAAATTA-ATAACTTTAAAAAAAGTGTCGATCCTTTTT
275792 ATAAAAAGTATGGACACTTTCAA
389 ATAAAAAGTATGGACACTTTCAA
275815 CATATTATAA
Statistics
Matches: 1325, Mismatches: 12, Indels: 39
0.96 0.01 0.03
Matches are distributed among these distances:
468 14 0.01
469 61 0.05
470 51 0.04
471 127 0.10
472 146 0.11
473 141 0.11
474 75 0.06
475 323 0.24
476 79 0.06
477 7 0.01
478 54 0.04
479 23 0.02
480 59 0.04
481 165 0.12
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.41
Consensus pattern (480 bp):
AATAGGTAGTTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAA
CATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAA
TGATTTATTTTTTACGTTACGATATATATATTATTATATTAAAAACAATAAACATATATATTACA
TATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATC
AAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATG
AAACACTATTAAAAAAAATTGAAACATAAATTAATAACTTTAAAAAAAGTGTCGATCCTTTTTAT
AAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAAT
GTAATAGGTATCGTTTATATAATGT
Found at i:275387 original size:22 final size:23
Alignment explanation
Indices: 275354--275416 Score: 92
Period size: 22 Copynumber: 2.8 Consensus size: 23
275344 AATAGGTAAA
*
275354 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
275377 ATAT-ATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
275399 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
275417 TTGTAAAGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 20 0.56
23 16 0.44
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:276353 original size:21 final size:21
Alignment explanation
Indices: 276329--276368 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
276319 CTTATAATAT
276329 TTTACAATTAAGATAAAAAAG
1 TTTACAATTAAGATAAAAAAG
* *
276350 TTTATAGTTAAGATAAAAA
1 TTTACAATTAAGATAAAAA
276369 TAAAATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (21 bp):
TTTACAATTAAGATAAAAAAG
Found at i:276403 original size:30 final size:31
Alignment explanation
Indices: 276357--276426 Score: 106
Period size: 30 Copynumber: 2.3 Consensus size: 31
276347 AAGTTTATAG
*
276357 TTAAGATAAAAATAAAATATAT-TTCTTAAA
1 TTAAAATAAAAATAAAATATATATTCTTAAA
* *
276387 TTAAAATAAGAATAAAATATATATTTTTAAA
1 TTAAAATAAAAATAAAATATATATTCTTAAA
276418 TTAAAATAA
1 TTAAAATAA
276427 TATATATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 20 0.56
31 16 0.44
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (31 bp):
TTAAAATAAAAATAAAATATATATTCTTAAA
Found at i:276518 original size:16 final size:17
Alignment explanation
Indices: 276485--276527 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
276475 GTAAAAATAT
276485 AATATATTTAATAATTA
1 AATATATTTAATAATTA
276502 AATA-ATTT-ATAAGTTA
1 AATATATTTAATAA-TTA
276518 AGATATATTT
1 A-ATATATTT
276528 TTAGTCAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 4 0.17
16 8 0.35
17 7 0.30
18 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
AATATATTTAATAATTA
Found at i:287655 original size:21 final size:21
Alignment explanation
Indices: 287625--287672 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
287615 TAATTTTCAA
287625 ACATTATTGCACCTAATTTTG
1 ACATTATTGCACCTAATTTTG
*
287646 ACATTGTTGCACCTAATTTTG
1 ACATTATTGCACCTAATTTTG
287667 ACATTA
1 ACATTA
287673 CAATATTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (21 bp):
ACATTATTGCACCTAATTTTG
Found at i:295786 original size:22 final size:22
Alignment explanation
Indices: 295757--295801 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
295747 AAAAAATGTT
*
295757 GAAAAAAATAGCAGTTCGAAAAA
1 GAAAAAAA-AACAGTTCGAAAAA
*
295780 GAAAAAAAAACTGTTCGAAAAA
1 GAAAAAAAAACAGTTCGAAAAA
295802 AAAGACATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.62, C:0.09, G:0.16, T:0.13
Consensus pattern (22 bp):
GAAAAAAAAACAGTTCGAAAAA
Found at i:299677 original size:21 final size:21
Alignment explanation
Indices: 299620--299677 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
299610 TTTACCCATT
*
299620 TAATTTTCAAACATTATTGCACC
1 TAATTTT--AACATTGTTGCACC
299643 TAATTTTAACATTGTTGCACC
1 TAATTTTAACATTGTTGCACC
*
299664 TAATTTTGACATTG
1 TAATTTTAACATTG
299678 CAATATTAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 26 0.79
23 7 0.21
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (21 bp):
TAATTTTAACATTGTTGCACC
Found at i:300348 original size:17 final size:16
Alignment explanation
Indices: 300303--300348 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
300293 ACTATGAAAT
300303 AATAA-TAATA-TTTA
1 AATAATTAATATTTTA
*
300317 AATAAATTTATATTTTA
1 AAT-AATTAATATTTTA
300334 AATAATTAATCATTT
1 AATAATTAAT-ATTT
300349 AATTAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 3 0.12
15 2 0.08
16 10 0.38
17 11 0.42
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAATTAATATTTTA
Found at i:300349 original size:16 final size:15
Alignment explanation
Indices: 300303--300350 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
300293 ACTATGAAAT
300303 AATAA-TAATATTTA
1 AATAATTAATATTTA
*
300317 AATAAATTTATATTTTA
1 AAT-AATTAATA-TTTA
300334 AATAATTAATCATTTA
1 AATAATTAAT-ATTTA
300350 A
1 A
300351 TTAAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 3 0.11
15 2 0.07
16 15 0.54
17 8 0.29
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAATTAATATTTA
Found at i:302947 original size:2 final size:2
Alignment explanation
Indices: 302940--302982 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
302930 CTACCTCCCC
302940 AT AT AT AT AT 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 AT AT AT AT AT
302982 A
1 A
302983 GATTGTAGGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:305401 original size:46 final size:46
Alignment explanation
Indices: 305348--305442 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
305338 ACAAATAAAT
305348 CACTCGTTTTTAAGTTTTGTTACACATCTCCAATATCCTACTTTCA
1 CACTCGTTTTTAAGTTTTGTTACACATCTCCAATATCCTACTTTCA
305394 CACTCGTTTTTAAGTTTTGTTACACATCTCCAATATCCTACTTTCA
1 CACTCGTTTTTAAGTTTTGTTACACATCTCCAATATCCTACTTTCA
305440 CAC
1 CAC
305443 GTGTAGTTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.24, C:0.27, G:0.06, T:0.42
Consensus pattern (46 bp):
CACTCGTTTTTAAGTTTTGTTACACATCTCCAATATCCTACTTTCA
Found at i:305453 original size:46 final size:46
Alignment explanation
Indices: 305348--305453 Score: 160
Period size: 46 Copynumber: 2.3 Consensus size: 46
305338 ACAAATAAAT
**
305348 CACTCGTTTTTAAGTTTTGTTACACATCTCCAATATCCTACTTTCA
1 CACTCGTAGTTAAGTTTTGTTACACATCTCCAATATCCTACTTTCA
**
305394 CACTCGTTTTTAAGTTTTGTTACACATCTCCAATATCCTACTTTCA
1 CACTCGTAGTTAAGTTTTGTTACACATCTCCAATATCCTACTTTCA
305440 CACGT-GTAGTTAAG
1 CAC-TCGTAGTTAAG
305454 GGAACTTTAG
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
46 56 0.98
47 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.09, T:0.42
Consensus pattern (46 bp):
CACTCGTAGTTAAGTTTTGTTACACATCTCCAATATCCTACTTTCA
Found at i:307601 original size:13 final size:14
Alignment explanation
Indices: 307583--307615 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
307573 TATGCCCTTC
*
307583 CCCTAACTTA-AAA
1 CCCTAAATTATAAA
307596 CCCTAAATTATAAA
1 CCCTAAATTATAAA
307610 CCCTAA
1 CCCTAA
307616 GTTTGTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.24
Consensus pattern (14 bp):
CCCTAAATTATAAA
Found at i:311829 original size:29 final size:28
Alignment explanation
Indices: 311786--311912 Score: 87
Period size: 29 Copynumber: 4.4 Consensus size: 28
311776 CCAGTTACAT
*
311786 TTTTGGAAATT-TTTTAAAAATAGTGACA
1 TTTTGGTAATTATTTTAAAAA-AGTGACA
* * * *
311814 TTCTGGTAATTATTTTTAAAACGATAACA
1 TTTTGGTAATTATTTTAAAAAAG-TGACA
* * *
311843 TTTTGGGAATTATTTGT-AAAACGATGATA
1 TTTTGGTAATTATTT-TAAAAAAG-TGACA
* *
311872 TTTTGGTAATTATTTAAAAAAAAGGTGATA
1 TTTTGGTAATTATTT-TAAAAAA-GTGACA
*
311902 TTTTTGTAATT
1 TTTTGGTAATT
311913 TTCGAATGTG
Statistics
Matches: 80, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
28 10 0.12
29 49 0.61
30 20 0.25
31 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (28 bp):
TTTTGGTAATTATTTTAAAAAAGTGACA
Found at i:313511 original size:802 final size:801
Alignment explanation
Indices: 312070--313542 Score: 2757
Period size: 802 Copynumber: 1.8 Consensus size: 801
312060 ACCCGAAGGC
312070 CTCCAAATCATCAGTCAAACCCGTTGACTTTGATTTTGACCAAGAATTTGAATTTTCGAAAAGTC
1 CTCCAAATCATCAGTCAAACCCGTTGACTTTGATTTTGACCAAGAATTTGAATTTTCGAAAAGTC
*
312135 ATACTTTATGTTGTTCGACGCCCTGATTCCGGTTCCCACTCAATTTGGTAAAATTCAGACTCGAA
66 ATACTTTATGTTGTTCGACGCCCTGATTCCGATTCCCACTCAATTTGGTAAAATTCAGACTCGAA
* *
312200 AGCCTTCAAATTGATAGTCAAGCCCGGAAAATGCTTATATACTAAAGAGTTTAAGCTTTGAATGG
131 AGCCTTCAAATTGATAGTCAAGCCAGAAAAATGCTTATATACTAAAGAGTTTAAGCTTTGAATGG
312265 TTGAGTAAGACTTGCGACTGATAAATTATTAATGTTTGAAGGTACAAGAGACTCTCCTGACCGTT
196 TTGAGTAAGACTTGCGACTGATAAATTATTAATGTTTGAAGGTACAAGAGACTCTCCTGACCGTT
* * * *
312330 CGACAGCTCTACCTAGCTCATCTAGATTAGTTAAGCCGCGTGTGCTAGTATTCACCCGTAAGACC
261 CGACAGCTCGACCCAGCTCATCTAGATCAGTTAAGCCACGTGTGCTAGTATTCACCCGTAAGACC
*
312395 CGTAAATTTTATGATTTCAGAAATTAATTTTGTTACCCATTAGTAATATAATGTTATTATGGATT
326 CGTAAATTTTATGATTTCAGAAATTAATTTTGTTACCCATTAGTAATATAATATTATTATGGATT
*
312460 AGGTTCGAAAACAGTAGCAGAGCGTGGCGAGGCCAGCAATCACTAGATCTACTATTTAAACCTAT
391 AGGTTCGAAAACAGTAGCAGAGCGTGGCGAGGCCAACAATCACTAGATCTACTATTTAAACCTAT
312525 TGTCGAGGTGTGTTCCCTGTGTACTACTTGATTGTTTTATATGTTTTGAAATATGGTATATTGAA
456 TGTCGAGGTGTGTTCCCTGTGTACTACTTGATTGTTTTATATGTTTTGAAATATGGTATATTGAA
* *
312590 AGTTATGGTTTAATGTTTTATTAATCCACCTATTTACTGGTGATTGTTTATGGAATATGACTGAT
521 AGCTATGGTTTAATGTTTTATTAATCCACCTATTTACTGGTGATGGTTTATGGAATATGACTGAT
*
312655 ATATGATTATTGGTTTTCATTGGTATATGATAATATTAATTATGGAATTATGGAAATTATGCTTA
586 ATATGATTATTGATTTTCATTGGTATATGATAATATTAATTATGGAATTATGGAAATTATGCTTA
312720 CTGCATAAATAGTATTGTTGACCACTTTTGACCAGAACTTTGACTGGCTATTAAACAACCGTTAA
651 CTGCATAAATAGTATTGTTGACCACTTTTGACCAGAACTTTGACTGGCTATTAAACAACCGTTAA
312785 TCTTTTCCGAGAATACCTATCCTGATAGTTTTCGACGTTCCGAATCCGTTTTTGGGGTCGGTTTC
716 TCTTTTCCGAGAATACCTATCCTGATAGTTTTCGACGTTCCGAATCCGTTTTTGGGGTCGGTTTC
312850 ACAAAATTCAAAACCAAAAGT
781 ACAAAATTCAAAACCAAAAGT
* *
312871 CTCCGAATCGTCAGTCAAACCCGTTGACTTTGATTTTGACCAAGAATTTGAATTTTCGAAAAGTC
1 CTCCAAATCATCAGTCAAACCCGTTGACTTTGATTTTGACCAAGAATTTGAATTTTCGAAAAGTC
**
312936 ATACTTTATGTTGTTCGACGCCCTGATTCCGATTCCACACTCCGTTTGGTAAAATTCAGACTCGA
66 ATACTTTATGTTGTTCGACGCCCTGATTCCGATTCC-CACTCAATTTGGTAAAATTCAGACTCGA
313001 AAGCCTTCAAATTGATAGTCAAGCCAGAAAAATGCTTATATACTAAAGAGTTTAAGCTTTGAATG
130 AAGCCTTCAAATTGATAGTCAAGCCAGAAAAATGCTTATATACTAAAGAGTTTAAGCTTTGAATG
*
313066 GTTGAGTAAGACTTGGGACTGATAAATTATTAATGTTTGAAGGTACAAGAGACTCTCCTGACCGT
195 GTTGAGTAAGACTTGCGACTGATAAATTATTAATGTTTGAAGGTACAAGAGACTCTCCTGACCGT
*
313131 TCGACAGCTCGACCCAGCTCCTCTAGATCAGTTAAGCCACGTGTGCTAGTATTCACCCGTAAGAC
260 TCGACAGCTCGACCCAGCTCATCTAGATCAGTTAAGCCACGTGTGCTAGTATTCACCCGTAAGAC
*
313196 CCGTAAATTTTATGATTTCAGAAATTAATTTTGTTACCCATTAGTAATATAGTATTATTATGGAT
325 CCGTAAATTTTATGATTTCAGAAATTAATTTTGTTACCCATTAGTAATATAATATTATTATGGAT
313261 TAGGTTCGAAAACAGTAGCAGAGCGTGGCGAGGCCAACAATCACTAGATCTACTATTTAAACCTA
390 TAGGTTCGAAAACAGTAGCAGAGCGTGGCGAGGCCAACAATCACTAGATCTACTATTTAAACCTA
313326 TTGTCGAGGTGTGTTCCCTGTGTACTACTTGATTGTTTTATATGTTTTGAAATATGGTATATTGA
455 TTGTCGAGGTGTGTTCCCTGTGTACTACTTGATTGTTTTATATGTTTTGAAATATGGTATATTGA
313391 AAGCTATGGTTTAATGTTTTATTAATCCACCTATTTACTGGTGATGGTTTATGGAATATGACTGA
520 AAGCTATGGTTTAATGTTTTATTAATCCACCTATTTACTGGTGATGGTTTATGGAATATGACTGA
313456 TATATGATTATTGATTTTCATTGGTATATGATAATATTAATTATGGAATTATGGAAATTATGCTT
585 TATATGATTATTGATTTTCATTGGTATATGATAATATTAATTATGGAATTATGGAAATTATGCTT
*
313521 ACTGCATAAATAGTATTTTTGA
650 ACTGCATAAATAGTATTGTTGA
313543 AATACTAATT
Statistics
Matches: 651, Mismatches: 20, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
801 98 0.15
802 553 0.85
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35
Consensus pattern (801 bp):
CTCCAAATCATCAGTCAAACCCGTTGACTTTGATTTTGACCAAGAATTTGAATTTTCGAAAAGTC
ATACTTTATGTTGTTCGACGCCCTGATTCCGATTCCCACTCAATTTGGTAAAATTCAGACTCGAA
AGCCTTCAAATTGATAGTCAAGCCAGAAAAATGCTTATATACTAAAGAGTTTAAGCTTTGAATGG
TTGAGTAAGACTTGCGACTGATAAATTATTAATGTTTGAAGGTACAAGAGACTCTCCTGACCGTT
CGACAGCTCGACCCAGCTCATCTAGATCAGTTAAGCCACGTGTGCTAGTATTCACCCGTAAGACC
CGTAAATTTTATGATTTCAGAAATTAATTTTGTTACCCATTAGTAATATAATATTATTATGGATT
AGGTTCGAAAACAGTAGCAGAGCGTGGCGAGGCCAACAATCACTAGATCTACTATTTAAACCTAT
TGTCGAGGTGTGTTCCCTGTGTACTACTTGATTGTTTTATATGTTTTGAAATATGGTATATTGAA
AGCTATGGTTTAATGTTTTATTAATCCACCTATTTACTGGTGATGGTTTATGGAATATGACTGAT
ATATGATTATTGATTTTCATTGGTATATGATAATATTAATTATGGAATTATGGAAATTATGCTTA
CTGCATAAATAGTATTGTTGACCACTTTTGACCAGAACTTTGACTGGCTATTAAACAACCGTTAA
TCTTTTCCGAGAATACCTATCCTGATAGTTTTCGACGTTCCGAATCCGTTTTTGGGGTCGGTTTC
ACAAAATTCAAAACCAAAAGT
Found at i:336853 original size:55 final size:55
Alignment explanation
Indices: 336713--337293 Score: 802
Period size: 55 Copynumber: 10.7 Consensus size: 55
336703 CGTTTGATGG
*
336713 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATT-TATGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGT-TGA
* * *
336768 AGATTG-T-GGGTCTTATACTCTCTGAAGAAATAAGGGGCAGACGCGATCGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
* * *
336821 AGATTGTTCGGGTCTTATACTCTCTAAAGAAATAGGGGACAGACGCGATTGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
*
336876 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
* * * *
336931 AGATTGCTCGAGTCTTATACTTTCTGAAGAAATAGGGGGCATACGTGATT-TATGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGT-TGA
* * *
336986 AGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATTGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
*
337039 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGACAGACGCGATTGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
* *
337094 AGATTGTTTGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
* *
337149 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
* * ** **
337204 AGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACATGATTAATGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
* * * *
337257 AGATTGTCCCAGT-TCTATACTCTCTAAAGAAAGAGGG
1 AGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGG
337294 AGCGAACCCG
Statistics
Matches: 472, Mismatches: 44, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
53 137 0.29
54 9 0.02
55 326 0.69
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (55 bp):
AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
Found at i:337098 original size:218 final size:218
Alignment explanation
Indices: 336713--337293 Score: 975
Period size: 218 Copynumber: 2.7 Consensus size: 218
336703 CGTTTGATGG
*
336713 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATTTATGAAGATTGTGGG
1 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATTTATGAAGATTGTGGG
* * * *
336778 TCTTATACTCTCTGAAGAAATAAGGGGCAGACGCGATCGTTGAAGATTGTTCGGGTCTTATACTC
66 TCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTC
336843 TCTAAAGAAATAGGGGACAGACGCGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAA
131 TCTAAAGAAATAGGGGACAGACGCGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAA
336908 TAGGGGGCAGACACGATTGTTGA
196 TAGGGGGCAGACACGATTGTTGA
* *
336931 AGATTGCTCGAGTCTTATACTTTCTGAAGAAATAGGGGGCATACGTGATTTATGAAGATTGTGGG
1 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATTTATGAAGATTGTGGG
*
336996 TCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATTGTTGAAGATTGTTCGAGTCTTATACTC
66 TCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTC
* *
337061 TCTGAAGAAATAGGGGACAGACGCGATTGTTGAAGATTGTTTGAGTCTTATACTCTCTGAAGAAA
131 TCTAAAGAAATAGGGGACAGACGCGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAA
337126 TAGGGGGCAGACACGATTGTTGA
196 TAGGGGGCAGACACGATTGTTGA
* *
337149 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
1 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATTTATGAAGATTGTGGG
* * ** * *
337214 TCTTATACTCTCTGAAGAAATAGGGAGCAGACATGATTAATGAAGATTGTCCCAGT-TCTATACT
66 TCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCT-TATACT
*
337278 CTCTAAAGAAAGAGGG
130 CTCTAAAGAAATAGGG
337294 AGCGAACCCG
Statistics
Matches: 339, Mismatches: 23, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
217 1 0.00
218 338 1.00
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (218 bp):
AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATTTATGAAGATTGTGGG
TCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTC
TCTAAAGAAATAGGGGACAGACGCGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAA
TAGGGGGCAGACACGATTGTTGA
Found at i:337278 original size:163 final size:164
Alignment explanation
Indices: 336706--337293 Score: 796
Period size: 163 Copynumber: 3.6 Consensus size: 164
336696 TTCCCCACGT
* * * *
336706 TTGATGGAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATTTATGAAGA
1 TTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGA
* * *
336771 TTGT--GGGTCTTATACTCTCTGAAGAAATAAGGGGCAGACGCGATCGTTGAAGATTGTTCGGGT
66 TTGTCCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTG-TCGGGT
* *
336834 CTTATACTCTCTAAAGAAATAGGGGACAGACGCGA
130 CTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
* *
336869 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGA
1 TTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGA
* * *
336934 TTG-CTCGAGTCTTATACTTTCTGAAGAAATAGGGGGCATACGTGATT-TATGAAGATTGT-GGG
66 TTGTC-CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGT-TGAAGATTGTCGGG
* *
336996 TCTTATACTCTCTGAAGAAATAGGGGGCAGACACAA
129 TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
* * * *
337032 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGACAGACGCGATTGTTGAAGA
1 TTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGA
** * *
337097 TTGTTTGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGAAGATTGCTCGAGT
66 TTGTCCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTG-TCGGGT
337162 CTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
130 CTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
* * * *
337197 TTGATGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACATGATTAATGAAGA
1 TTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGA
* * *
337260 TTGTCCCAGT-TCTATACTCTCTAAAGAAAGAGGG
66 TTGTCCGAGTCT-TATACTCTCTGAAGAAATAGGG
337294 AGCGAACCCG
Statistics
Matches: 376, Mismatches: 40, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
162 1 0.00
163 278 0.74
164 5 0.01
165 92 0.24
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (164 bp):
TTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGA
TTGTCCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGAAGATTGTCGGGTC
TTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
Found at i:342999 original size:154 final size:154
Alignment explanation
Indices: 342714--343182 Score: 866
Period size: 154 Copynumber: 3.0 Consensus size: 154
342704 CCTGAAATTG
* *
342714 ATCACCCCTTCCACTGCCAACACCATTTGACTCTTTTGCCAAAGTTTCCTTATAGGAGTGGTATT
1 ATCATCCCTTCCACTGCCAACACCATTTGACTCTTCTGCCAAAGTTTCCTTATAGGAGTGGTATT
342779 TGCGATTTTTGTCATAGCGGTTCTGCAGGATTTGTTTATCATTGTGCTTCTTGAGCATTCGATCT
66 TGCGATTTTTGTCATAGCGGTTCTGCAGGATTTGTTTATCATTGTGCTTCTTGAGCATTCGATCT
*
342844 GCACGTGAACTGTGCTTTGCTTCA
131 GCACGTGAACTATGCTTTGCTTCA
*
342868 ATCATCCCTTCCACTGCCAACACCATTTGACTATTCTGCCAAAGTTTCCTTATAGGAGTGGTATT
1 ATCATCCCTTCCACTGCCAACACCATTTGACTCTTCTGCCAAAGTTTCCTTATAGGAGTGGTATT
342933 TGCGATTTTTGTCATAGCGGTTCTGCAGGATTTGTTTATCATTGTGCTTCTTGAGCATTCGATCT
66 TGCGATTTTTGTCATAGCGGTTCTGCAGGATTTGTTTATCATTGTGCTTCTTGAGCATTCGATCT
342998 GCACGTGAACTATGCTTTGCTTCA
131 GCACGTGAACTATGCTTTGCTTCA
*
343022 ATCATCCCTTCCACTGCCAACACCATTTGACTCCTCTGCCAAAGTTTCCTTATAGGAGTGGTATT
1 ATCATCCCTTCCACTGCCAACACCATTTGACTCTTCTGCCAAAGTTTCCTTATAGGAGTGGTATT
* * *
343087 TGCGATTTTTGTCATAGCGGTTCTGCAGGATTTATTTATCATTGTGCTTCTTGTGCATTTGATCT
66 TGCGATTTTTGTCATAGCGGTTCTGCAGGATTTGTTTATCATTGTGCTTCTTGAGCATTCGATCT
343152 GCACGTGAACTATGCTTTGCTTCA
131 GCACGTGAACTATGCTTTGCTTCA
343176 ATCATCC
1 ATCATCC
343183 ATTGCTGCAA
Statistics
Matches: 306, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
154 306 1.00
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.38
Consensus pattern (154 bp):
ATCATCCCTTCCACTGCCAACACCATTTGACTCTTCTGCCAAAGTTTCCTTATAGGAGTGGTATT
TGCGATTTTTGTCATAGCGGTTCTGCAGGATTTGTTTATCATTGTGCTTCTTGAGCATTCGATCT
GCACGTGAACTATGCTTTGCTTCA
Found at i:343597 original size:36 final size:36
Alignment explanation
Indices: 343547--343622 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
343537 TTATAGCAAA
* *
343547 AAAAATCGTCTTTATTCGAATTTTGCCAACAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
343583 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
343619 AAAA
1 AAAA
343623 TCCCGAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:346380 original size:36 final size:35
Alignment explanation
Indices: 346330--346407 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 35
346320 TATAGCAAAA
*
346330 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAG
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAG
346365 CAAAAATCGTATTTATTCGAATTTTGCCAAAAATAG
1 -AAAAATCGTATTTATTCGAATTTTGCCAAAAATAG
346401 AAAAATC
1 AAAAATC
346408 CCGAAAATCA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 7 0.17
36 34 0.83
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (35 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAG
Found at i:349167 original size:36 final size:36
Alignment explanation
Indices: 349117--349192 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
349107 TATAGCAAAA
*
349117 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
349153 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
349189 AAAA
1 AAAA
349193 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:351952 original size:36 final size:36
Alignment explanation
Indices: 351902--351974 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
351892 TATAGCAAAA
*
351902 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
351938 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
351974 A
1 A
351975 GAATCCCGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:354738 original size:36 final size:36
Alignment explanation
Indices: 354688--354763 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
354678 TATAGCAAAA
*
354688 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
354724 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
354760 AAAA
1 AAAA
354764 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:359357 original size:19 final size:20
Alignment explanation
Indices: 359333--359385 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
359323 AAAATCTTGA
359333 GTGCATCGATGCATGGTAT-
1 GTGCATCGATGCATGGTATG
*
359352 GTGCATCGATGCATGGTTTG
1 GTGCATCGATGCATGGTATG
*
359372 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
359386 CACTTTGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.17, C:0.17, G:0.34, T:0.32
Consensus pattern (20 bp):
GTGCATCGATGCATGGTATG
Found at i:361221 original size:19 final size:19
Alignment explanation
Indices: 361193--361244 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
361183 TTTAAGCAGG
361193 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
* *
361212 TGCATTGATGCACTGCTTA
1 TGCATCGATGCACTCCTTA
361231 TGCATCGATGCACT
1 TGCATCGATGCACT
361245 AATTGCATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:364422 original size:15 final size:15
Alignment explanation
Indices: 364404--364443 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
364394 CCGGTCTACT
364404 TATATTTACCATCCA
1 TATATTTACCATCCA
*
364419 TATATTTAACATCCA
1 TATATTTACCATCCA
364434 TATATTTACC
1 TATATTTACC
364444 TCATTTATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (15 bp):
TATATTTACCATCCA
Found at i:366736 original size:16 final size:18
Alignment explanation
Indices: 366705--366746 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
366695 ATAAAGTTTT
*
366705 AAAGTTGTTATGCATT-A
1 AAAGTTGATATGCATTGA
366722 AAAGTTGATAT-CATTGA
1 AAAGTTGATATGCATTGA
*
366739 AAATTTGA
1 AAAGTTGA
366747 AATCTATGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (18 bp):
AAAGTTGATATGCATTGA
Found at i:369029 original size:65 final size:64
Alignment explanation
Indices: 368896--369105 Score: 225
Period size: 65 Copynumber: 3.2 Consensus size: 64
368886 TGCACTAAGA
* * *
368896 GTGCATCGATGCATGAAATGCATTTC-ATGTTTCA-AAATAGCCAGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCA-TTCGATGTTTCATAAA-ATCCTGAGTGCATCGATGCATGG-T
368959 -T
63 AT
368960 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAATCCTGAGTGCATCGATGCATGGTAT
* * ** *
369025 GTGCATCGATGCATAAAATACATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGG-A
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCC-TGAGTGCATCGATGCATGGTA
369087 TT
64 -T
*
369089 GGTGCATCGGTGCATCA
1 -GTGCATCGATGCATCA
369106 CTTTGAACAA
Statistics
Matches: 128, Mismatches: 10, Indels: 15
0.84 0.07 0.10
Matches are distributed among these distances:
63 7 0.05
64 48 0.38
65 70 0.55
66 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCTGAGTGCATCGATGCATGGTAT
Found at i:369465 original size:21 final size:22
Alignment explanation
Indices: 369439--369490 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
369429 TTTGAAATTA
369439 CTCCCCCTTAC-TTTAACACTT
1 CTCCCCCTTACATTTAACACTT
* * *
369460 CTCCCCATAACATTTAACATTT
1 CTCCCCCTTACATTTAACACTT
369482 CTCCCCCTT
1 CTCCCCCTT
369491 TTTGTTAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (22 bp):
CTCCCCCTTACATTTAACACTT
Found at i:375355 original size:19 final size:18
Alignment explanation
Indices: 375333--375377 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
375323 TAATGGGTTA
*
375333 TTGTTAGCTTTTGTTAAGC
1 TTGTTAGCATTTGTT-AGC
375352 TTGTTAG-ATTTGTTAGC
1 TTGTTAGCATTTGTTAGC
375369 TT-TTAGCAT
1 TTGTTAGCAT
375378 CTACGTCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 4 0.17
17 7 0.29
18 6 0.25
19 7 0.29
ACGTcount: A:0.18, C:0.09, G:0.20, T:0.53
Consensus pattern (18 bp):
TTGTTAGCATTTGTTAGC
Found at i:387918 original size:16 final size:15
Alignment explanation
Indices: 387898--387945 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
387888 AAAATGTATA
387898 AAAAAAGAAATAATT
1 AAAAAAGAAATAATT
*
387913 ATAAAAGAAAATAA-T
1 AAAAAAG-AAATAATT
*
387928 AAAATAATAAATAATT
1 AAAA-AAGAAATAATT
387944 AA
1 AA
387946 TTAAAAATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (15 bp):
AAAAAAGAAATAATT
Found at i:388033 original size:17 final size:17
Alignment explanation
Indices: 388008--388041 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
387998 AATGAGATAA
*
388008 AAATTAAATAAACAAAT
1 AAATAAAATAAACAAAT
*
388025 AAATAAAATAAATAAAT
1 AAATAAAATAAACAAAT
388042 TGGGTTAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAACAAAT
Found at i:390452 original size:14 final size:14
Alignment explanation
Indices: 390433--390460 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
390423 ACCAAATCTA
390433 TTTTTTTTGCACTG
1 TTTTTTTTGCACTG
390447 TTTTTTTTGCACTG
1 TTTTTTTTGCACTG
390461 CACTGTTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.14, G:0.14, T:0.64
Consensus pattern (14 bp):
TTTTTTTTGCACTG
Found at i:394598 original size:86 final size:87
Alignment explanation
Indices: 394460--394635 Score: 300
Period size: 86 Copynumber: 2.0 Consensus size: 87
394450 CTCCCTCAAA
* *
394460 TTATCCATATGTGACTCTTCAATATACGCTTTGCGAAACTCAACTAATAAGTAATCCCATGTTTT
1 TTATCCATATGTGAATCTTCAATATACGCTTTGCGAAACTCAACCAATAAGTAATCCCATGTTTT
*
394525 TAACTCA-ACTACAACCTCATC
66 TAACTCAGACTACAACCGCATC
* *
394546 TTATCCATATGTGAATCTTCAATATACGTTTTGTGAAACTCAACCAATAAGTAATCCCATGTTTT
1 TTATCCATATGTGAATCTTCAATATACGCTTTGCGAAACTCAACCAATAAGTAATCCCATGTTTT
394611 TAACTCAGACTACAACCGCATC
66 TAACTCAGACTACAACCGCATC
394633 TTA
1 TTA
394636 ACAATGTCCC
Statistics
Matches: 84, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
86 68 0.81
87 16 0.19
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.34
Consensus pattern (87 bp):
TTATCCATATGTGAATCTTCAATATACGCTTTGCGAAACTCAACCAATAAGTAATCCCATGTTTT
TAACTCAGACTACAACCGCATC
Found at i:398464 original size:23 final size:23
Alignment explanation
Indices: 398420--398468 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
398410 ATAAAGAACC
*
398420 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
398443 AAAATAAAGTTAAAACAT-CCATT
1 AAAATAAACTT-AAACATACCATT
398466 AAA
1 AAA
398469 CCAACACCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:401797 original size:22 final size:22
Alignment explanation
Indices: 401727--401797 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 22
401717 AAGATGAGTA
*
401727 AAAGAGAGA-AAAAGTAAAAGTT
1 AAAGAAAGAGAAAAG-AAAAGTT
* *
401749 AACATGAAAGAGAAAA-AAATGAAT
1 AA-A-GAAAGAGAAAAGAAAAG-TT
401773 AAAGAAAGAGAAAAGAAAAGTT
1 AAAGAAAGAGAAAAGAAAAGTT
401795 AAA
1 AAA
401798 ATTTGGGAGG
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
22 17 0.44
23 10 0.26
24 8 0.21
25 4 0.10
ACGTcount: A:0.68, C:0.01, G:0.20, T:0.11
Consensus pattern (22 bp):
AAAGAAAGAGAAAAGAAAAGTT
Found at i:406108 original size:243 final size:238
Alignment explanation
Indices: 405659--406144 Score: 854
Period size: 243 Copynumber: 2.0 Consensus size: 238
405649 AAATTAGCTC
405659 CAAT-TGAACAAGGAATAATGAAGCTGCCCGGATCATTTCTCTTGGCGGCAACTTACTCAATGAA
1 CAATCTGAACAAGGAATAATGAAGCTGCCCGGATCATTTCTCTTGGCGGCAACTTACTCAATGAA
* *
405723 CCAAATTCTGTTGCCGTGCAACAGTCTCTACTTTCCTCTTCTTGGTACAATGTCCTTCAGAATTT
66 CAAAATTCTGTTACCGTGCAACAGTCTCTACTTTCCTCTTCTTGGTACAATGTCCTTCAGAATTT
405788 GGCATACATCGGCATCTGTTCAATAGCTTCCAAGAGAGGTATATTGATATGGAGCTGATCAAGAA
131 GGCATACATCGGCATCTGTTCAATAGCTTCCAAGAGAGGTATATTGATATGGAGCTGATCAAGAA
405853 TGTCTACGAACTTCTTGAACTGAACTTCATCATTGTGCTTCTT
196 TGTCTACGAACTTCTTGAACTGAACTTCATCATTGTGCTTCTT
405896 CAATCTGAACAAGGAATAATGAAGCTGCCCGGATCA-TTCTCTTTGGCGGCAACTTACTCAATGA
1 CAATCTGAACAAGGAATAATGAAGCTGCCCGGATCATTTCTC-TTGGCGGCAACTTACTCAAT--
405960 AGAACAAAATTTCTGTTACCGTGGCAACAGTCTCTACTTTCCTCTTCTTGGTACAGATGTCCTTC
63 -GAACAAAA-TTCTGTTACCGT-GCAACAGTCTCTACTTTCCTCTTCTTGGTACA-ATGTCCTTC
406025 AGAAATTTGGCATACATCGGCATCTGTTCAATAGCTTCCAAGAGAGGTATATTGATAT-G-GCTG
124 AG-AATTTGGCATACATCGGCATCTGTTCAATAGCTTCCAAGAGAGGTATATTGATATGGAGCTG
406088 ATCAAGAATGTCTACGAACTTCTTGAACTGAACTTCATCATTGTGCTTCTT
188 ATCAAGAATGTCTACGAACTTCTTGAACTGAACTTCATCATTGTGCTTCTT
406139 CAATCT
1 CAATCT
406145 TTGCGGGAAG
Statistics
Matches: 238, Mismatches: 2, Indels: 12
0.94 0.01 0.05
Matches are distributed among these distances:
237 9 0.04
238 51 0.21
241 7 0.03
242 11 0.05
243 93 0.39
244 12 0.05
245 55 0.23
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (238 bp):
CAATCTGAACAAGGAATAATGAAGCTGCCCGGATCATTTCTCTTGGCGGCAACTTACTCAATGAA
CAAAATTCTGTTACCGTGCAACAGTCTCTACTTTCCTCTTCTTGGTACAATGTCCTTCAGAATTT
GGCATACATCGGCATCTGTTCAATAGCTTCCAAGAGAGGTATATTGATATGGAGCTGATCAAGAA
TGTCTACGAACTTCTTGAACTGAACTTCATCATTGTGCTTCTT
Found at i:408858 original size:23 final size:23
Alignment explanation
Indices: 408814--408862 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
408804 ATAAAGAACC
*
408814 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
408837 AAAATAAAGTTAAAACAT-CCATT
1 AAAATAAACTT-AAACATACCATT
408860 AAA
1 AAA
408863 CCAACACCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:410747 original size:18 final size:18
Alignment explanation
Indices: 410721--410767 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
410711 CTTCTGGATT
*
410721 GTCGGAGCTGGCTCCTGG
1 GTCGAAGCTGGCTCCTGG
*
410739 GTCGAAGCTGGCTGCTGG
1 GTCGAAGCTGGCTCCTGG
*
410757 GTCAAAGCTGG
1 GTCGAAGCTGG
410768 AACTACATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.13, C:0.23, G:0.43, T:0.21
Consensus pattern (18 bp):
GTCGAAGCTGGCTCCTGG
Found at i:413597 original size:14 final size:14
Alignment explanation
Indices: 413578--413604 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
413568 AAAACCCTTG
413578 ATTTCTAAAAACTC
1 ATTTCTAAAAACTC
413592 ATTTCTAAAAACT
1 ATTTCTAAAAACT
413605 TAACCAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (14 bp):
ATTTCTAAAAACTC
Found at i:415816 original size:60 final size:60
Alignment explanation
Indices: 415708--415850 Score: 209
Period size: 60 Copynumber: 2.4 Consensus size: 60
415698 ATGCGGTTTA
* *
415708 ATTTTGGTCACCAAACTA-TTTTGTTTTCAAAATCATACATAAAGTTACATTTTGGTTAT
1 ATTTTGGTCACCAAACTATTTTTTTTTTCAAAATCATACATAAAGTTACAATTTGGTTAT
* *
415767 ATTTTGGTCACCTAACTATTTTTTTTTTCAAAATCATACATAACA-TTACAATTTGGTTCT
1 ATTTTGGTCACCAAACTATTTTTTTTTTCAAAATCATACATAA-AGTTACAATTTGGTTAT
* *
415827 ATTTTGGTCACCCAATTATTTTTT
1 ATTTTGGTCACCAAACTATTTTTT
415851 CGAAAACATA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
59 17 0.22
60 58 0.76
61 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (60 bp):
ATTTTGGTCACCAAACTATTTTTTTTTTCAAAATCATACATAAAGTTACAATTTGGTTAT
Found at i:419053 original size:22 final size:22
Alignment explanation
Indices: 419013--419063 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
419003 TTAAGTAAAT
* *
419013 TATTTTTATTATATTTATTTGAA
1 TATTTTAATTATATATATTT-AA
419036 TATTTTAATTA-ATATATTTAA
1 TATTTTAATTATATATATTTAA
*
419057 TAATTTA
1 TATTTTA
419064 TACTTTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 8 0.32
22 7 0.28
23 10 0.40
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TATTTTAATTATATATATTTAA
Found at i:435995 original size:16 final size:16
Alignment explanation
Indices: 435974--436008 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
435964 ATCAGAAACT
435974 AATCAAACTTATAAAA
1 AATCAAACTTATAAAA
435990 AATCAAACTTATAAAA
1 AATCAAACTTATAAAA
436006 AAT
1 AAT
436009 TACCAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (16 bp):
AATCAAACTTATAAAA
Found at i:440729 original size:39 final size:39
Alignment explanation
Indices: 440646--440900 Score: 160
Period size: 39 Copynumber: 6.6 Consensus size: 39
440636 ACAAGATCCC
* * * * **
440646 AAAA-AAATCCAATGACTTATTTCCTTTTTACAAAATAGG
1 AAAATAAATCCAACGATTTATTTCC-TTTAACAAAACAAA
*** *
440685 AAAATAAATATGACGATTTATTTCCTTTAACAAACCAAA
1 AAAATAAATCCAACGATTTATTTCCTTTAACAAAACAAA
* * * **
440724 AAAATAAATCCAATGATTAATTTCCTTTTACAAAACAGG
1 AAAATAAATCCAACGATTTATTTCCTTTAACAAAACAAA
* ** * **
440763 AAAATAAATCCAACGATTTATTTCCTTTTATGAATCAGG
1 AAAATAAATCCAACGATTTATTTCCTTTAACAAAACAAA
* * * **
440802 AAAAT-AAT-CAGACAATTTATTT--TTTTACAAAATAGG
1 AAAATAAATCCA-ACGATTTATTTCCTTTAACAAAACAAA
* * * * *
440838 AAAATAAATCTAACGATTTATTTCTTTTTACAAAATAGA
1 AAAATAAATCCAACGATTTATTTCCTTTAACAAAACAAA
* *
440877 AAAATAAATCAAACGATTTGTTTC
1 AAAATAAATCCAACGATTTATTTC
440901 GATTTTTTCC
Statistics
Matches: 176, Mismatches: 34, Indels: 12
0.79 0.15 0.05
Matches are distributed among these distances:
36 15 0.09
37 15 0.09
38 14 0.08
39 117 0.66
40 15 0.09
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.34
Consensus pattern (39 bp):
AAAATAAATCCAACGATTTATTTCCTTTAACAAAACAAA
Found at i:440770 original size:78 final size:77
Alignment explanation
Indices: 440646--441259 Score: 333
Period size: 78 Copynumber: 7.8 Consensus size: 77
440636 ACAAGATCCC
* *
440646 AAAA-AAATCCAATGACTTATTTCCTTTTTACAAAATAGGAAAATAAATATGACGATTTATTTCC
1 AAAATAAATCCAATGA-TTATTTCC-TTTTACAAAATAGGAAAATAAATCTAACGATTTATTTCC
* * *
440710 TTTAACAAACCAAA
64 TTTTACAAAACAGA
* *
440724 AAAATAAATCCAATGATTAATTTCCTTTTACAAAACAGGAAAATAAATCCAACGATTTATTTCCT
1 AAAATAAATCCAATGATT-ATTTCCTTTTACAAAATAGGAAAATAAATCTAACGATTTATTTCCT
** * *
440789 TTTATGAATCAGG
65 TTTACAAAACAGA
440802 AAAAT-AATCAGACAAT--TTATTT--TTTTACAAAATAGGAAAATAAATCTAACGATTTATTTC
1 AAAATAAATC---CAATGATTATTTCCTTTTACAAAATAGGAAAATAAATCTAACGATTTATTTC
* *
440862 TTTTTACAAAATAGA
63 CTTTTACAAAACAGA
* * * * * * * *
440877 AAAATAAATCAAACGATTTGTTTCGATTTTTTCCTTTTACGATATAAGAAACTAAATCCAACAAT
1 AAAATAAATC---C-A-----AT-GATTATTTCCTTTTACAAAATAGGAAAATAAATCTAACGAT
* * *
440942 TTATTTTCTTTATACAAAATAGG
56 TTATTTCCTTT-TACAAAACAGA
* * ** * * *
440965 AAAATAAATCAAAAT-ATTTACTTT-ATTTTACAAACCAGGAAACTAAAT-TCGATGATTTATTT
1 AAAATAAATC-CAATGA-TTA-TTTCCTTTTACAAAATAGGAAAATAAATCT-AACGATTTATTT
* *
441027 CATTCTT-CAAAATA-A
62 CCTT-TTACAAAACAGA
* * * * * * * * *
441042 CAAACTAAGTTCAACGATTTTTTCCCTTTTTCAAAATA-GAAACCTAAATCCAATGATTT-TTTC
1 -AAAATAAATCCAATGATTATTT-CCTTTTACAAAATAGGAAA-ATAAATCTAACGATTTATTTC
* * *
441105 TTTTTTCAAAATAGA
63 CTTTTACAAAACAGA
* * * *
441120 AAACT-AATCCAATGATTTTTTTCCTTTTTATAAAATAGGAAAATAAATCTAATGATTTATTTCC
1 AAAATAAATCCAATGA-TTATTTCC-TTTTACAAAATAGGAAAATAAATCTAACGATTTATTTCC
* *
441184 TTTTACAAACCAGG
64 TTTTACAAAACAGA
* * * * * *
441198 AAACTAAATTCTATGATTTATTTCCTCTTT-CAAAGTA-GAAAACTAAATCCAATGATTTATTT
1 AAAATAAATCCAATGA-TTATTTCCT-TTTACAAAATAGGAAAA-TAAATCTAACGATTTATTT
441260 TCTAATACAT
Statistics
Matches: 422, Mismatches: 77, Indels: 74
0.74 0.13 0.13
Matches are distributed among these distances:
75 50 0.12
76 21 0.05
77 70 0.17
78 142 0.34
79 68 0.16
80 9 0.02
82 1 0.00
85 6 0.01
86 1 0.00
87 34 0.08
88 20 0.05
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (77 bp):
AAAATAAATCCAATGATTATTTCCTTTTACAAAATAGGAAAATAAATCTAACGATTTATTTCCTT
TTACAAAACAGA
Found at i:440973 original size:40 final size:39
Alignment explanation
Indices: 440900--441262 Score: 174
Period size: 39 Copynumber: 9.3 Consensus size: 39
440890 CGATTTGTTT
* * * * *
440900 CGATTT-TTTCCTTTTACGATATAAGAAACTAAATCCAA
1 CGATTTATTTTCTTTTACAAAATAGGAAAATAAATCCAA
* *
440938 CAATTTATTTTCTTTATACAAAATAGGAAAATAAATCAAA
1 CGATTTATTTTCTTT-TACAAAATAGGAAAATAAATCCAA
** * * ** * * *
440978 ATATTTACTTTATTTTACAAACCAGGAAACTAAATTCGA
1 CGATTTATTTTCTTTTACAAAATAGGAAAATAAATCCAA
* ** * * *
441017 TGATTTA-TTTCATTCTT-CAAAATAACAAACTAAGTTCAA
1 CGATTTATTTTC-TT-TTACAAAATAGGAAAATAAATCCAA
* * *
441056 CGATTT-TTTCCCTTTTTCAAAATA-GAAACCTAAATCCAA
1 CGATTTATTT-TCTTTTACAAAATAGGAAA-ATAAATCCAA
* *
441095 TGA-TT-TTTTCTTTTTTCAAAATA-GAAAACT-AATCCAA
1 CGATTTATTTTC-TTTTACAAAATAGGAAAA-TAAATCCAA
* * *
441132 TGATTT-TTTTCCTTTTTATAAAATAGGAAAATAAATCTAA
1 CGATTTATTTT-C-TTTTACAAAATAGGAAAATAAATCCAA
* * ** * * *
441172 TGATTTATTTCCTTTTACAAACCAGGAAACTAAATTCTA
1 CGATTTATTTTCTTTTACAAAATAGGAAAATAAATCCAA
* * *
441211 TGATTTATTTCCTCTTT-CAAAGTA-GAAAACTAAATCCAA
1 CGATTTATTTTCT-TTTACAAAATAGGAAAA-TAAATCCAA
*
441250 TGATTTATTTTCT
1 CGATTTATTTTCT
441263 AATACATATC
Statistics
Matches: 257, Mismatches: 51, Indels: 33
0.75 0.15 0.10
Matches are distributed among these distances:
37 11 0.04
38 45 0.18
39 144 0.56
40 54 0.21
41 3 0.01
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (39 bp):
CGATTTATTTTCTTTTACAAAATAGGAAAATAAATCCAA
Found at i:441047 original size:39 final size:39
Alignment explanation
Indices: 441004--441259 Score: 254
Period size: 39 Copynumber: 6.6 Consensus size: 39
440994 ACAAACCAGG
* * *
441004 AAACTAAATTCGATGATTTATTTCATTCTTCAAAATA-A
1 AAACTAAATTCAATGATTTATTTCCTTTTTCAAAATAGA
* *
441042 CAAACTAAGTTCAACGATTT-TTTCCCTTTTTCAAAATAGA
1 -AAACTAAATTCAATGATTTATTT-CCTTTTTCAAAATAGA
* * *
441082 AACCTAAATCCAATGATTT-TTTCTTTTTTCAAAATAGA
1 AAACTAAATTCAATGATTTATTTCCTTTTTCAAAATAGA
* * *
441120 AAACT-AATCCAATGATTTTTTTCCTTTTTATAAAATAGGA
1 AAACTAAATTCAATGATTTATTTCCTTTTT-CAAAATA-GA
* ** *
441160 AAA-TAAA-TCTAATGATTTATTTCCTTTTACAAACCAGG
1 AAACTAAATTC-AATGATTTATTTCCTTTTTCAAAATAGA
* * *
441198 AAACTAAATTCTATGATTTATTTCCTCTTTCAAAGTAGA
1 AAACTAAATTCAATGATTTATTTCCTTTTTCAAAATAGA
*
441237 AAACTAAATCCAATGATTTATTT
1 AAACTAAATTCAATGATTTATTT
441260 TCTAATACAT
Statistics
Matches: 180, Mismatches: 28, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
37 13 0.07
38 35 0.19
39 105 0.58
40 27 0.15
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (39 bp):
AAACTAAATTCAATGATTTATTTCCTTTTTCAAAATAGA
Found at i:441060 original size:166 final size:161
Alignment explanation
Indices: 440744--441065 Score: 341
Period size: 166 Copynumber: 2.0 Consensus size: 161
440734 CAATGATTAA
* * **
440744 TTTCCTTTTACAAAACAGGAAAATAAATCCAACGATTTATTTCCTTTTATGAATCAGGAAAATAA
1 TTTCCTTTTACAAAACAAGAAAATAAATCCAACAATTTATTTCCTTTTAAAAATCAGGAAAATAA
* * *
440809 TCAGACAATTTATTTTTTTACAAAATAGGAAAATAAATCTAACGATTTATTTCTTTTTACAAAAT
66 TCAGAAAATTTATTTTTTTACAAAACAGGAAAATAAATCTAACGATTTATTTCTTCTTACAAAAT
440874 AGAAAAATAAATCAAACGATTTGTTTCGATTT
131 AGAAAAATAAATCAAACGATTT-TTTCGATTT
* * * * *
440906 TTTCCTTTTACGATATAAGAAACTAAATCCAACAATTTATTTTCTTTATACAAAAT-AGGAAAAT
1 TTTCCTTTTACAAAACAAGAAAATAAATCCAACAATTTATTTCCTTT-TA-AAAATCAGGAAAAT
* * * *
440970 AAATCA-AAATATTTACTTTATTTTACAAACCAGGAAACTAAAT-TCGATGATTTATTTCATTCT
64 -AATCAGAAA-ATTTA-TTT-TTTTACAAAACAGGAAAATAAATCT-AACGATTTATTTC-TTCT
* *
441033 T-CAAAATA-ACAAACTAAGTTC-AACGATTTTTTC
123 TACAAAATAGA-AAAATAA-ATCAAACGATTTTTTC
441066 CCTTTTTCAA
Statistics
Matches: 132, Mismatches: 18, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
162 40 0.30
163 12 0.09
164 13 0.10
165 9 0.07
166 52 0.39
167 6 0.05
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (161 bp):
TTTCCTTTTACAAAACAAGAAAATAAATCCAACAATTTATTTCCTTTTAAAAATCAGGAAAATAA
TCAGAAAATTTATTTTTTTACAAAACAGGAAAATAAATCTAACGATTTATTTCTTCTTACAAAAT
AGAAAAATAAATCAAACGATTTTTTCGATTT
Found at i:441528 original size:56 final size:58
Alignment explanation
Indices: 441462--441634 Score: 199
Period size: 58 Copynumber: 3.0 Consensus size: 58
441452 ATTTATTTCT
* * *
441462 TTATTCAAGATTCCCAATAAAATAAATTTAAT-ATTTATTTCCTTTAAC-AAATACAA
1 TTATTTAAGATTCTCAATAAAATAAATTTAATAATTTATTTCCTTTAACAAAATAAAA
* * * ** *
441518 TTATTTAAGATTTTCAAGAAAATAAATTTAATAATGTATTAACTTTTACAAAATAAAA
1 TTATTTAAGATTCTCAATAAAATAAATTTAATAATTTATTTCCTTTAACAAAATAAAA
* * * *
441576 TCATTTAAGATTCTAAATAAAATAAATTTAATAATTTATTTCTTTTTAA-AAGATAAAA
1 TTATTTAAGATTCTCAATAAAATAAATTTAATAATTTATTTC-CTTTAACAAAATAAAA
441634 T
1 T
441635 CATTCACTAT
Statistics
Matches: 95, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
56 28 0.29
57 12 0.13
58 51 0.54
59 4 0.04
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (58 bp):
TTATTTAAGATTCTCAATAAAATAAATTTAATAATTTATTTCCTTTAACAAAATAAAA
Found at i:441587 original size:58 final size:57
Alignment explanation
Indices: 441468--441726 Score: 197
Period size: 58 Copynumber: 4.5 Consensus size: 57
441458 TTCTTTATTC
* * * * * *
441468 AAGATTCCCAATAAAATAAATTTAAT-ATTTATTTCCTTTA-ACAAATACAATTATTT
1 AAGATTCTCAAGAAAATAAATTTAATAATTTATTACTTTTACA-AAATAAAATCATTT
* *
441524 AAGATTTTCAAGAAAATAAATTTAATAATGTATTAACTTTTACAAAATAAAATCATTT
1 AAGATTCTCAAGAAAATAAATTTAATAATTTATT-ACTTTTACAAAATAAAATCATTT
* * * *
441582 AAGATTCTAAATAAAATAAATTTAATAATTTATTTCTTTTTA-AAAGATAAAATCATTC
1 AAGATTCTCAAGAAAATAAATTTAATAATTTATTAC-TTTTACAAA-ATAAAATCATTT
** ** * * * ** *
441640 ACTATTCTCAAGAAAATCGATTTGACAATTTATT-TTTCTTACAAGTTATAATCATTT
1 AAGATTCTCAAGAAAATAAATTTAATAATTTATTACTT-TTACAAAATAAAATCATTT
* * *
441697 AAGAATTAT-AAGGAAATAAATTCAA-AATTT
1 AAG-ATTCTCAAGAAAATAAATTTAATAATTT
441727 TATTTTTCTT
Statistics
Matches: 160, Mismatches: 35, Indels: 16
0.76 0.17 0.08
Matches are distributed among these distances:
56 30 0.19
57 34 0.21
58 95 0.59
59 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (57 bp):
AAGATTCTCAAGAAAATAAATTTAATAATTTATTACTTTTACAAAATAAAATCATTT
Found at i:441958 original size:42 final size:45
Alignment explanation
Indices: 441900--442024 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 45
441890 TTTACTAACC
*
441900 CAATAATTAAAATGAACTAATCATTTGATTTTAATTTTCGC-A-A
1 CAATAATTAAAATGAACTAATCATTTGATTTTACTTTTCGCAACA
* *
441943 -AATAATTGAAATGAACTAATCATTTGATTTTACTTTTGGCAACA
1 CAATAATTAAAATGAACTAATCATTTGATTTTACTTTTCGCAACA
*
441987 CAATAATTAAAAGGAACTAATCATTTGATTTTACTTTT
1 CAATAATTAAAATGAACTAATCATTTGATTTTACTTTT
442025 GACAACCTAA
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
42 37 0.50
43 1 0.01
44 1 0.01
45 35 0.47
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (45 bp):
CAATAATTAAAATGAACTAATCATTTGATTTTACTTTTCGCAACA
Found at i:442007 original size:45 final size:45
Alignment explanation
Indices: 441900--442044 Score: 190
Period size: 45 Copynumber: 3.3 Consensus size: 45
441890 TTTACTAACC
* * *
441900 CAATAATTAAAATGAACTAATCATTTGATTTTAATTTTCGC-A-A
1 CAATAATTAAAAGGAACTAATCATTTGATTTTACTTTTGGCAACA
* *
441943 -AATAATTGAAATGAACTAATCATTTGATTTTACTTTTGGCAACA
1 CAATAATTAAAAGGAACTAATCATTTGATTTTACTTTTGGCAACA
*
441987 CAATAATTAAAAGGAACTAATCATTTGATTTTACTTTTGACAAC-
1 CAATAATTAAAAGGAACTAATCATTTGATTTTACTTTTGGCAACA
*
442031 CTAATAATCAAAAG
1 C-AATAATTAAAAG
442045 TCTTGGATTA
Statistics
Matches: 91, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
42 37 0.41
43 1 0.01
44 2 0.02
45 51 0.56
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (45 bp):
CAATAATTAAAAGGAACTAATCATTTGATTTTACTTTTGGCAACA
Found at i:442730 original size:3 final size:3
Alignment explanation
Indices: 442722--442765 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
442712 AGTCCAAAAT
442722 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
442766 CAAATATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:446351 original size:14 final size:15
Alignment explanation
Indices: 446315--446352 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
446305 TGGTCCATCA
446315 CCGAGTCAACTCGGT
1 CCGAGTCAACTCGGT
*
446330 CTGAGTCAACTC-GT
1 CCGAGTCAACTCGGT
446344 CCGAGTCAA
1 CCGAGTCAA
446353 ACCGTTGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.21
Consensus pattern (15 bp):
CCGAGTCAACTCGGT
Found at i:448866 original size:30 final size:30
Alignment explanation
Indices: 448832--448888 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
448822 TGAAAATTTG
*
448832 TTTTATGAGTTTACATGTATTCATAAACCA
1 TTTTATGAGTTTACATGTATTAATAAACCA
*
448862 TTTTATGAGTTTACATGTTTTAATAAA
1 TTTTATGAGTTTACATGTATTAATAAA
448889 AATTTTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (30 bp):
TTTTATGAGTTTACATGTATTAATAAACCA
Found at i:449389 original size:29 final size:28
Alignment explanation
Indices: 449333--449392 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 28
449323 GATGACGAAA
* *
449333 TTAGTATAGGACCTTATTTTTGTAAAAG
1 TTAGTATAGGAACTTACTTTTGTAAAAG
449361 TTAGTATAGGAACTGTACTTTTGTAAAAG
1 TTAGTATAGGAACT-TACTTTTGTAAAAG
449390 TTA
1 TTA
449393 CTTGAAGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (28 bp):
TTAGTATAGGAACTTACTTTTGTAAAAG
Found at i:450324 original size:14 final size:15
Alignment explanation
Indices: 450291--450325 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
450281 CCAGTCATAA
*
450291 AGTCAACTCGGTCTG
1 AGTCAACTCGGTCCG
450306 AGTCAACTC-GTCCG
1 AGTCAACTCGGTCCG
450320 AGTCAA
1 AGTCAA
450326 ACCGTTGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (15 bp):
AGTCAACTCGGTCCG
Found at i:451865 original size:15 final size:15
Alignment explanation
Indices: 451827--451862 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
451817 GTCCATCACA
*
451827 GAGTCAACTCGGTTT
1 GAGTCAACTCGGTCT
451842 GAGTCAACTC-GTCT
1 GAGTCAACTCGGTCT
451856 GAGTCAA
1 GAGTCAA
451863 ACTGTTGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (15 bp):
GAGTCAACTCGGTCT
Found at i:459303 original size:23 final size:23
Alignment explanation
Indices: 459272--459340 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
459262 AACCACAGCT
*
459272 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
459295 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
459318 CGTAGAATTACACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
459341 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:459528 original size:103 final size:104
Alignment explanation
Indices: 459356--459571 Score: 362
Period size: 103 Copynumber: 2.1 Consensus size: 104
459346 TAATGTCCAT
* * * *
459356 AAGGACCATATATCATTCCTTAAGAATTTATATACATATACTAGGGATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATTCATATACATATACCAAGGATCAAGTATGTGTCTCACC
*
459421 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 AGACTTCACACATATTCCAAAGAATACATATATGTCCCG
*
459460 AAGGACCACATATCATTCCTTAAGAA-TCATATACATATGCCAAGGATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATTCATATACATATACCAAGGATCAAGTATGTGTCTCACC
*
459524 AGACTTCACACATATTTCAAAGAATACATATATGTCCCG
66 AGACTTCACACATATTCCAAAGAATACATATATGTCCCG
459563 AAGGACCAC
1 AAGGACCAC
459572 GTAGACCCTC
Statistics
Matches: 105, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
103 80 0.76
104 25 0.24
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (104 bp):
AAGGACCACATATCATTCCTTAAGAATTCATATACATATACCAAGGATCAAGTATGTGTCTCACC
AGACTTCACACATATTCCAAAGAATACATATATGTCCCG
Found at i:460966 original size:22 final size:21
Alignment explanation
Indices: 460941--461000 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
460931 TTCGCTTGAG
*
460941 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
460963 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
460983 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
461001 CCCAGAAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 17 0.47
21 9 0.25
22 10 0.28
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:462455 original size:6 final size:6
Alignment explanation
Indices: 462444--462486 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
462434 AATTCCGTTA
*
462444 TATTTT TATTTTT TCGTTTT TATTTT TATTTT ATATTTT TATT
1 TATTTT TA-TTTT T-ATTTT TATTTT TATTTT -TATTTT TATT
462487 CGCTCAAGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 16 0.50
7 16 0.50
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.79
Consensus pattern (6 bp):
TATTTT
Found at i:462469 original size:13 final size:12
Alignment explanation
Indices: 462444--462486 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
462434 AATTCCGTTA
462444 TATTTTTATTTTT
1 TATTTTTA-TTTT
*
462457 TCGTTTTTATTTT
1 T-ATTTTTATTTT
462470 TATTTTATATTTT
1 TATTTT-TATTTT
462483 TATT
1 TATT
462487 CGCTCAAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 4 0.15
13 16 0.62
14 6 0.23
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.79
Consensus pattern (12 bp):
TATTTTTATTTT
Found at i:462483 original size:20 final size:20
Alignment explanation
Indices: 462444--462486 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
462434 AATTCCGTTA
* *
462444 TATTTTTATTTTTTCGTTTT
1 TATTTTTATTTTATAGTTTT
462464 TATTTTTATTTTATA-TTTT
1 TATTTTTATTTTATAGTTTT
462483 TATT
1 TATT
462487 CGCTCAAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.79
Consensus pattern (20 bp):
TATTTTTATTTTATAGTTTT
Found at i:467029 original size:70 final size:67
Alignment explanation
Indices: 466893--467029 Score: 238
Period size: 70 Copynumber: 2.0 Consensus size: 67
466883 CTAATTGTAT
466893 TGATACATGTGTAACACCCTCAACCAATCAAAAGGTGAATCTGATCAAAGATGTACATTGAACCA
1 TGATACATGTGTAACACCCTCAACCAATCAAAAGGTGAATCTGATCAAAGATGTACATTGAACCA
466958 CC
66 CC
*
466960 TGATACATGTGTAACACCCTCAAACCAAATCAAAAGTTGAATCTGATTCAAAGATGTACATTGAA
1 TGATACATGTGTAACACCCTC-AACC-AATCAAAAGGTGAATCTGA-TCAAAGATGTACATTGAA
467025 CCACC
63 CCACC
467030 AAAATGATAA
Statistics
Matches: 66, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
67 21 0.32
68 4 0.06
69 18 0.27
70 23 0.35
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.23
Consensus pattern (67 bp):
TGATACATGTGTAACACCCTCAACCAATCAAAAGGTGAATCTGATCAAAGATGTACATTGAACCA
CC
Found at i:478295 original size:18 final size:19
Alignment explanation
Indices: 478264--478318 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
478254 TAGTTTACCC
* *
478264 TTTTAAAATTTTTTAAGAA
1 TTTTAATATATTTTAAGAA
* *
478283 TTTT-TTATATTTTAAAAA
1 TTTTAATATATTTTAAGAA
*
478301 TTTTAATATTTTTTAAGA
1 TTTTAATATATTTTAAGA
478319 CTTATATAAG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
TTTTAATATATTTTAAGAA
Found at i:478309 original size:17 final size:18
Alignment explanation
Indices: 478274--478312 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
478264 TTTTAAAATT
* *
478274 TTTTAAGAATTTTTTATA
1 TTTTAAGAAATTTTAATA
478292 TTTTAA-AAATTTTAATA
1 TTTTAAGAAATTTTAATA
478309 TTTT
1 TTTT
478313 TTAAGACTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTAAGAAATTTTAATA
Found at i:478851 original size:14 final size:14
Alignment explanation
Indices: 478832--478859 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
478822 CTATATTTGT
478832 TGAAAAGTCAAGCA
1 TGAAAAGTCAAGCA
478846 TGAAAAGTCAAGCA
1 TGAAAAGTCAAGCA
478860 AATAGGCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.21, T:0.14
Consensus pattern (14 bp):
TGAAAAGTCAAGCA
Found at i:480411 original size:457 final size:466
Alignment explanation
Indices: 479320--480693 Score: 1884
Period size: 457 Copynumber: 3.0 Consensus size: 466
479310 ATTTTTTCGA
* * * *
479320 TTTTTCTGCGATGTTACTATTCACATAAATAGTGAATTTTGTGAATAGTAAAATTTAGTCGGCGA
1 TTTTTCTGTGAGGTTACTATTCACATGAATAGTGAATTTTGTGAATAGTAAAATTTGGTCGG-GA
* * *
479385 TACGAATTTATCGACGGAGGTGTTCTAATACACGGTGGTTCGCAGGAATTGTTAGAAACGATCC-
65 TACGAATTTGTCGACGGAGGTGTTCTAATACAC-GTGGTTCGCAGGAATTGTCAAAAACGATCCA
* * * *
479449 AAAGAAGCCAGATTCGAGTGGGAGC-GTGGCTTTGAGAAACGAAGAGGATGAGCTCAAGAGGGAG
129 AAAGAAGCCAAATTTGAGTGGGAGCAATGGCTTTGAGAAACGAAGTGGATGAGCTCAAGAGGGAG
* * *
479513 TTGCTCATATGAAAGGGAGCAATGAGTG---G-GGTGCGCTCAAGACCTTCTTAGAAGGACTTAG
194 CTGCTCATATGCAAGGGAGCAATGAGTGAATGAGGTGCGCTCAAGACCTTCTTGGAAGGACTTAG
* *
479574 ACTAGGGGCGATGCTCGGGGGAGAGCATGGTGATGCCCAGAGACTTTCGGAGGCCATAGCTGTAG
259 ACTAGGGGCGATGCTCGGGGGAGAGCAAGGTGATGCCCAGAGACTTTTGGAGGCCATAGCTGTAG
* * *
479639 ACGGGAAGCTAACTGAGCTTGCAAGTGACAAGCCAAGTAGCGATGTGTCGTCCAGGCCCATGCCC
324 -CCGAAAGCTGACTGAGCTTGCAAGTGACAAGCCAAGTAGC-A-GTGTCGTCCAGGCCCATGCCC
* * *
479704 AGAAATAGTGGCAATAGTGGGGGAGACTGGGAAAAGATACAACGGAGAGATGGTAGAGAAAGAGC
386 AGAGATAGTGGCAATAGTGGGGGAGACCGGGAAAAGGTAC-ACGGAGAGATGGTAGAGAAAGAGC
479769 TTTTGGTGTTGAATTTTTTCAGTTTT
450 TTTTGGTGTTG-----TTT-AG---T
** * *
479795 TTTTTCTGTGAGGTTACTATTCATGTGAATAGTGAA--TT-TAAATAGTAAAA-TTGGTCGGCA-
1 TTTTTCTGTGAGGTTACTATTCACATGAATAGTGAATTTTGTGAATAGTAAAATTTGGTCGGGAT
* * * * *
479855 ACGAATTTGTCGACGGAGGTGTTATAATACACGATGGTTCGCAAGAATTATC-AGAACGGTCCAA
66 ACGAATTTGTCGACGGAGGTGTTCTAATACACG-TGGTTCGCAGGAATTGTCAAAAACGATCCAA
479919 AAGAAGCCAAATTCT-AGTGGGAGCAATGGCTTTGAGAAACGAAGTGGATGAGCTCAAGAGGGAG
130 AAGAAGCCAAATT-TGAGTGGGAGCAATGGCTTTGAGAAACGAAGTGGATGAGCTCAAGAGGGAG
* * *
479983 CTGCCCATATGCAAGGTAGCAATGAGTGAATGAGG-GCGCTCAAGACCTTCTTGGAGGGACTTAG
194 CTGCTCATATGCAAGGGAGCAATGAGTGAATGAGGTGCGCTCAAGACCTTCTTGGAAGGACTTAG
* *
480047 ACTAGGGGCGATGCTCGGGGGAGAGCAAGGTGATTCCCAGAGACTTTTGGAGGCCATAGCTGTAT
259 ACTAGGGGCGATGCTCGGGGGAGAGCAAGGTGATGCCCAGAGACTTTTGGAGGCCATAGCTGTAG
* *
480112 CCAGAAAGCTGACTGAGCTTGTAAGTGACATGCCAAGTAGC-GTGTCGTCCAGG-CCATGCCCAG
324 CC-GAAAGCTGACTGAGCTTGCAAGTGACAAGCCAAGTAGCAGTGTCGTCCAGGCCCATGCCCAG
* *
480175 AGATAGTAGCAATAGTAGGGGAGACCGGGAAAAGGTACACTGGAGAGATGGTAGAGAAAGAGCTT
388 AGATAGTGGCAATAGTGGGGGAGACCGGGAAAAGGTACAC-GGAGAGATGGTAGAGAAAGAGCTT
480240 TT-G-G-TG-TT-G-
452 TTGGTGTTGTTTAGT
480249 TTTTT-T-T-AGGTTACTATTCACATGAATAGTGAATTTTGTGAATAGTAAAATTTGGTCGGTGA
1 TTTTTCTGTGAGGTTACTATTCACATGAATAGTGAATTTTGTGAATAGTAAAATTTGGTCGG-GA
*
480311 TACGAATTTGTCGACGGAGGTGTTCTAATATACGTGGTTCGCAGGAATTGTCAAAAACGATCCAA
65 TACGAATTTGTCGACGGAGGTGTTCTAATACACGTGGTTCGCAGGAATTGTCAAAAACGATCCAA
480376 AAGAAGCCAAATTTGAGTGGGAGCAATGGCTTTGAGAAACGAAGTGGATGAGCTCAAGAGGGAGC
130 AAGAAGCCAAATTTGAGTGGGAGCAATGGCTTTGAGAAACGAAGTGGATGAGCTCAAGAGGGAGC
*
480441 TGCTCATATGCAAGGGAGCAATGAGTGAATGAGGTGCGCTCAAGACCTTCTTGGAATGACTTAGA
195 TGCTCATATGCAAGGGAGCAATGAGTGAATGAGGTGCGCTCAAGACCTTCTTGGAAGGACTTAGA
* * **
480506 CCAGGGGCGATGCTCAGGGGAGAGCAAGGTGATGCCC--AGACTTTTGGAGGCCATAATTGTAGC
260 CTAGGGGCGATGCTCGGGGGAGAGCAAGGTGATGCCCAGAGACTTTTGGAGGCCATAGCTGTAGC
* * *
480569 CGAAAGCTGTCTAAGCTTGCAAGTGACAAGCCAAGTAGCGATGTGTCATCCAGGCCCATGCCCAG
325 CGAAAGCTGACTGAGCTTGCAAGTGACAAGCCAAGTAGC-A-GTGTCGTCCAGGCCCATGCCCAG
* * *
480634 AGATAGTGGTAATAGTGGGGGAGACCGGGAAAAGGTGCAGCGGAGAGATGTTAGAGAAAG
388 AGATAGTGGCAATAGTGGGGGAGACCGGGAAAAGGTACA-CGGAGAGATGGTAGAGAAAG
480694 GTCTTCTAGT
Statistics
Matches: 805, Mismatches: 70, Indels: 64
0.86 0.07 0.07
Matches are distributed among these distances:
451 24 0.03
452 1 0.00
453 3 0.00
454 16 0.02
455 42 0.05
456 42 0.05
457 136 0.17
458 74 0.09
459 63 0.08
460 3 0.00
466 2 0.00
467 1 0.00
468 11 0.01
469 136 0.17
470 74 0.09
471 7 0.01
472 12 0.01
473 125 0.16
474 2 0.00
475 31 0.04
ACGTcount: A:0.30, C:0.16, G:0.31, T:0.24
Consensus pattern (466 bp):
TTTTTCTGTGAGGTTACTATTCACATGAATAGTGAATTTTGTGAATAGTAAAATTTGGTCGGGAT
ACGAATTTGTCGACGGAGGTGTTCTAATACACGTGGTTCGCAGGAATTGTCAAAAACGATCCAAA
AGAAGCCAAATTTGAGTGGGAGCAATGGCTTTGAGAAACGAAGTGGATGAGCTCAAGAGGGAGCT
GCTCATATGCAAGGGAGCAATGAGTGAATGAGGTGCGCTCAAGACCTTCTTGGAAGGACTTAGAC
TAGGGGCGATGCTCGGGGGAGAGCAAGGTGATGCCCAGAGACTTTTGGAGGCCATAGCTGTAGCC
GAAAGCTGACTGAGCTTGCAAGTGACAAGCCAAGTAGCAGTGTCGTCCAGGCCCATGCCCAGAGA
TAGTGGCAATAGTGGGGGAGACCGGGAAAAGGTACACGGAGAGATGGTAGAGAAAGAGCTTTTGG
TGTTGTTTAGT
Found at i:484149 original size:48 final size:48
Alignment explanation
Indices: 484083--484187 Score: 201
Period size: 48 Copynumber: 2.2 Consensus size: 48
484073 TTTCAAATAT
*
484083 TAAAAAAAGATTCTAAATAGATATTATTCTTATAGTCACTTCGTATTA
1 TAAAAAAAAATTCTAAATAGATATTATTCTTATAGTCACTTCGTATTA
484131 TAAAAAAAAATTCTAAATAGATATTATTCTTATAGTCACTTCGTATTA
1 TAAAAAAAAATTCTAAATAGATATTATTCTTATAGTCACTTCGTATTA
484179 TAAAAAAAA
1 TAAAAAAAA
484188 GGAGTTACAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 56 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (48 bp):
TAAAAAAAAATTCTAAATAGATATTATTCTTATAGTCACTTCGTATTA
Found at i:486488 original size:242 final size:239
Alignment explanation
Indices: 486063--486544 Score: 871
Period size: 242 Copynumber: 2.0 Consensus size: 239
486053 AGTATATTTG
486063 GCATTGATGAACAGTTAATCTTCATCATCTATCGAATTTCCATATGAGACAATTCACCTATTTCT
1 GCATTGATGAACAGTTAATCTTCATCATCTATCGAATTTCCATATGAGACAATTCACCTATTTCT
486128 AAATTTTAGAAATTAACTTCCTAACATAAAATTCTACAGTCTCAAAGATTCTTTACGATATAACT
66 AAATTTTAGAAATTAACTTCCTAACATAAAATTCTACAGTCTCAAAGATTCTTTACGA-ATAACT
*
486193 TAGTTCATTATTTCGATTGGTGATTGCTTTGATTCGTTGTTGAGACCCATATCTAACTGAAGATA
130 TAGTTCATTATTTCGATTGGTGATTGCTTTGATTAGTTGTTGAGACCCATATCTAACTGAAGATA
486258 TTTTCCGCTTTGATCTGTAAGCTTCAACCATGAGTTTTATATCTTCA
195 TTTTCCGCTTTGATCTGT-AGCTTCAACCATGAG-TTTATATCTTCA
486305 GCATTGATGAAC-GTTAATCTTTCATCATCTATCGAAGTTTCCATATGAGACTAATTCACCTATT
1 GCATTGATGAACAGTTAATC-TTCATCATCTATCGAA-TTTCCATATGAGAC-AATTCACCTATT
486369 TCTAAATTTTAGAAAATTAACTTCCTAACAT-AAATTCTACAGTCTCAAAGATTCTTTACG-ATA
63 TCTAAATTTTAG-AAATTAACTTCCTAACATAAAATTCTACAGTCTCAAAGATTCTTTACGAATA
486432 ACTTAGTTCATTATTTCGATTGGTGATTGCTTTGATTAGTTGTTGAGACCCATATCTAACTGAAG
127 ACTTAGTTCATTATTTCGATTGGTGATTGCTTTGATTAGTTGTTGAGACCCATATCTAACTGAAG
486497 ATATTTTCCGCTTTGATCTGTAGCTTCAACCATGAGTTTATATCTTCA
192 ATATTTTCCGCTTTGATCTGTAGCTTCAACCATGAGTTTATATCTTCA
486545 TATTTTTTAT
Statistics
Matches: 235, Mismatches: 1, Indels: 10
0.96 0.00 0.04
Matches are distributed among these distances:
240 12 0.05
241 22 0.09
242 116 0.49
243 14 0.06
244 53 0.23
245 18 0.08
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (239 bp):
GCATTGATGAACAGTTAATCTTCATCATCTATCGAATTTCCATATGAGACAATTCACCTATTTCT
AAATTTTAGAAATTAACTTCCTAACATAAAATTCTACAGTCTCAAAGATTCTTTACGAATAACTT
AGTTCATTATTTCGATTGGTGATTGCTTTGATTAGTTGTTGAGACCCATATCTAACTGAAGATAT
TTTCCGCTTTGATCTGTAGCTTCAACCATGAGTTTATATCTTCA
Found at i:492282 original size:21 final size:21
Alignment explanation
Indices: 492240--492282 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
492230 TTTCTGGGCT
* *
492240 AGGGGAATCGATACCTATTCA
1 AGGGGAATCGATACCCACTCA
* *
492261 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
492282 A
1 A
492283 ACTAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:492948 original size:103 final size:103
Alignment explanation
Indices: 492723--492940 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
492713 GTAGAGGGTC
492723 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
* *
492788 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTATTAAGGAATGA
* *
492826 TATATGGTCATTCGAGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
492891 TTGATCCTTGGCATATGTATATGATTATTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTATTAAGGAATGA
492929 TATGTGGTCCTT
1 TATGTGGTCCTT
492941 ATGGACATTA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTATTAAGGAATGA
Found at i:492987 original size:23 final size:23
Alignment explanation
Indices: 492957--493008 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
492947 ATTATTATAT
492957 GGCACTCCGGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
*
492980 GGCACTCCGGTGCAATTCTACGT
1 GGCACTCCGGTGCAATTCTACGC
493003 GGCACT
1 GGCACT
493009 TAGGTACAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.17, C:0.33, G:0.27, T:0.23
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTCTACGC
Found at i:493018 original size:23 final size:23
Alignment explanation
Indices: 492957--493019 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
492947 ATTATTATAT
* *
492957 GGCACTCCGGTGCAATTCTACGC
1 GGCACTCAGGTACAATTCTACGC
* * *
492980 GGCACTCCGGTGCAATTCTACGT
1 GGCACTCAGGTACAATTCTACGC
*
493003 GGCACTTAGGTACAATT
1 GGCACTCAGGTACAATT
493020 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTCAGGTACAATTCTACGC
Found at i:495271 original size:37 final size:37
Alignment explanation
Indices: 495219--495365 Score: 258
Period size: 37 Copynumber: 4.0 Consensus size: 37
495209 AAACAAACAT
* *
495219 TAGAGTTTTACTATGATTCAAACACCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
*
495256 TAGAGTTTTATTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
*
495293 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
495330 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGG
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGG
495366 TTCCACAAGT
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 104 1.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.33
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
Found at i:496018 original size:25 final size:25
Alignment explanation
Indices: 495963--496022 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
495953 TGTTTTATTA
*
495963 ATTTTTA-TATATTTACTATTTTTT
1 ATTTTTATTATATATACTATTTTTT
* *
495987 ATATTTATTATATATATTA-TTTTT
1 ATTTTTATTATATATACTATTTTTT
496011 ACTTTTTATTAT
1 A-TTTTTATTAT
496023 TTATTGTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 12 0.40
25 18 0.60
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.68
Consensus pattern (25 bp):
ATTTTTATTATATATACTATTTTTT
Found at i:496024 original size:41 final size:40
Alignment explanation
Indices: 495974--496080 Score: 99
Period size: 41 Copynumber: 2.6 Consensus size: 40
495964 TTTTTATATA
*
495974 TTTACTATTTTTTATATTTATTATATATATTATTTTTACTT
1 TTTATTATTTTTTATATTTATTATATATATT-TTTTTACTT
* * * **
496015 TTTATTATTTATTGT-TTTATTTATATGTATTTTTTTTTTT
1 TTTATTATTTTTTATATTTA-TTATATATATTTTTTTACTT
* *
496055 TTTCTTTATTTTTTTATATTTTTTAT
1 TTT-ATTA-TTTTTTATATTTATTAT
496081 TTTACTTACT
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
40 14 0.27
41 25 0.48
42 10 0.19
43 3 0.06
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.75
Consensus pattern (40 bp):
TTTATTATTTTTTATATTTATTATATATATTTTTTTACTT
Found at i:496032 original size:16 final size:15
Alignment explanation
Indices: 495964--496050 Score: 52
Period size: 16 Copynumber: 5.3 Consensus size: 15
495954 GTTTTATTAA
495964 TTTTTATATATTTACTAT
1 TTTTTAT-TATTTA-T-T
495982 TTTTTA-TATTTATT
1 TTTTTATTATTTATT
* *
495996 ATATATATTATTT-TT
1 -TTTTTATTATTTATT
496011 ACTTTTTATTATTTATT
1 --TTTTTATTATTTATT
*
496028 GTTTTATTTATATGTATT
1 TTTTTA-TTAT-T-TATT
496046 TTTTT
1 TTTTT
496051 TTTTTTTCTT
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
14 1 0.02
15 12 0.22
16 25 0.45
17 3 0.05
18 14 0.25
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTTTATTATTTATT
Found at i:496037 original size:19 final size:19
Alignment explanation
Indices: 495979--496083 Score: 72
Period size: 19 Copynumber: 5.3 Consensus size: 19
495969 ATATATTTAC
495979 TATTTTTTATATTTATTATAT
1 TATTTTTT-TATTTATTAT-T
496000 ATATTATTTTTACTTTTTATTATT
1 -TATT-TTTTTA---TTTATTATT
* *
496024 TATTGTTTTATTTA-TATG
1 TATTTTTTTATTTATTATT
* * *
496042 TATTTTTTTTTTTTTTCTT
1 TATTTTTTTATTTATTATT
*
496061 TATTTTTTTA--TATTTTT
1 TATTTTTTTATTTATTATT
496078 TATTTT
1 TATTTT
496084 ACTTACTATT
Statistics
Matches: 68, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
17 11 0.16
18 14 0.21
19 15 0.22
22 11 0.16
23 8 0.12
24 1 0.01
25 8 0.12
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (19 bp):
TATTTTTTTATTTATTATT
Found at i:496054 original size:37 final size:37
Alignment explanation
Indices: 495994--496087 Score: 102
Period size: 37 Copynumber: 2.6 Consensus size: 37
495984 TTTATATTTA
495994 TTATATATATTATTTTTACTTTTTATTATTTATTGTT
1 TTATATATATTATTTTTACTTTTTATTATTTATTGTT
* * * * *
496031 TTATTTATATGTATTTTT-TTTTTTTTTCTTTATTTTT
1 TTATATATAT-TATTTTTACTTTTTATTATTTATTGTT
* *
496068 TTATATTTTTTA-TTTTACTT
1 TTATATATATTATTTTTACTT
496088 ACTATTTTAT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
35 4 0.09
36 4 0.09
37 31 0.67
38 7 0.15
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (37 bp):
TTATATATATTATTTTTACTTTTTATTATTTATTGTT
Found at i:496066 original size:17 final size:17
Alignment explanation
Indices: 495964--496083 Score: 59
Period size: 18 Copynumber: 6.6 Consensus size: 17
495954 GTTTTATTAA
* *
495964 TTTTTATATATTTACTAT
1 TTTTTATTTTTTTA-TAT
495982 TTTTTATATTTATTATATAT
1 TTTTTAT-TTT-TT-TATAT
496002 ATTATTT-TTACTTTTTATTAT
1 -TT-TTTATT--TTTTTA-TAT
* *
496023 TTATTGTTTTATTTATAT
1 TTTTTATTTT-TTTATAT
496041 GTATTTT-TTTTTTT-T-T
1 -T-TTTTATTTTTTTATAT
*
496057 TCTTTATTTTTTTATAT
1 TTTTTATTTTTTTATAT
496074 TTTTTATTTT
1 TTTTTATTTT
496084 ACTTACTATT
Statistics
Matches: 81, Mismatches: 6, Indels: 31
0.69 0.05 0.26
Matches are distributed among these distances:
14 3 0.04
15 8 0.10
16 2 0.02
17 11 0.14
18 15 0.19
19 12 0.15
20 15 0.19
21 10 0.12
22 5 0.06
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTTATTTTTTTATAT
Found at i:496142 original size:27 final size:27
Alignment explanation
Indices: 496112--496183 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
496102 GCTTTCTTTA
* *
496112 TCTTATCTTTTATCTAATTTGTTTTTT
1 TCTTATCTTTTATCTAATTTATTTATT
* *
496139 TCTTCAT-TTTAATTTAATTTATTTATT
1 TCTT-ATCTTTTATCTAATTTATTTATT
*
496166 TCTTACCTTTTTATCTAA
1 TCTTATC-TTTTATCTAA
496184 CACGTTCTTG
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
26 1 0.03
27 24 0.69
28 10 0.29
ACGTcount: A:0.21, C:0.12, G:0.01, T:0.65
Consensus pattern (27 bp):
TCTTATCTTTTATCTAATTTATTTATT
Found at i:502908 original size:22 final size:22
Alignment explanation
Indices: 502883--502940 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 22
502873 AGAATACAAC
* *
502883 TATCATACATAAACAT-TTCTCG
1 TATCATACATACACATCTT-TCA
502905 TATCAT--ATACACATCTTTCA
1 TATCATACATACACATCTTTCA
502925 TATCATACATACACAT
1 TATCATACATACACAT
502941 AATCCCGTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 15 0.48
21 2 0.06
22 14 0.45
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (22 bp):
TATCATACATACACATCTTTCA
Done.