Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008005.1 Hibiscus syriacus cultivar Beakdansim tig00110467_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: 1778185
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 7
Found at i:282682 original size:31 final size:30
Alignment explanation
Indices: 282591--282686 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
282581 AAAGATCCTC
* * *
282591 GGTAACTGTCCATAGGTCCCGAAGAACCTA
1 GGTAACTGTCCATATGTCTCGAAGAACATA
* **
282621 GGTAAACTATCCATATGT-TCCTTAGAACATA
1 GGT-AACTGTCCATATGTCT-CGAAGAACATA
282652 GGTATACTGTCCATATGTCTCGAA-AGACATA
1 GGTA-ACTGTCCATATGTCTCGAAGA-ACATA
282683 GGTA
1 GGTA
282687 GTTCTTTGAC
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
30 5 0.10
31 46 0.88
32 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (30 bp):
GGTAACTGTCCATATGTCTCGAAGAACATA
Found at i:283048 original size:2 final size:2
Alignment explanation
Indices: 283036--283072 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
283026 TACACAACTC
283036 AT AT A- 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
283073 TGTAACATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:283589 original size:19 final size:20
Alignment explanation
Indices: 283552--283589 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
283542 TTTTTCATTA
*
283552 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
283572 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
283590 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:287299 original size:30 final size:30
Alignment explanation
Indices: 287183--287282 Score: 191
Period size: 30 Copynumber: 3.3 Consensus size: 30
287173 GAAGGACCTA
287183 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
287213 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
287243 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
287273 TCCATAGGTC
1 TCCAGAGGTC
287283 CCGAAGAACC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 69 1.00
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:287299 original size:60 final size:60
Alignment explanation
Indices: 287183--287299 Score: 180
Period size: 60 Copynumber: 1.9 Consensus size: 60
287173 GAAGGACCTA
* * *
287183 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCACAAAGAACCTAGGTAACTG
* * *
287243 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCACAAAGAACCTAGGTAA
287300 ACTATCCATA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Consensus pattern (60 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCACAAAGAACCTAGGTAACTG
Found at i:287543 original size:4 final size:4
Alignment explanation
Indices: 287534--287558 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
287524 ATATAACCAT
287534 TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA T
287559 GTCATCCCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:291740 original size:15 final size:15
Alignment explanation
Indices: 291720--291749 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
291710 CATAAAAATA
291720 CAAATGCAAATATGC
1 CAAATGCAAATATGC
*
291735 CAAATGTAAATATGC
1 CAAATGCAAATATGC
291750 AATTGTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (15 bp):
CAAATGCAAATATGC
Found at i:291758 original size:14 final size:14
Alignment explanation
Indices: 291720--291773 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
291710 CATAAAAATA
*
291720 CAAATGCAAATATG
1 CAAATGTAAATATG
291734 CCAAATGTAAATATG
1 -CAAATGTAAATATG
* *
291749 CAATTGTAAAAATG
1 CAAATGTAAATATG
*
291763 TAAATGTAAAT
1 CAAATGTAAAT
291774 TATTTAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 20 0.61
15 13 0.39
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.28
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:293396 original size:23 final size:23
Alignment explanation
Indices: 293362--293409 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
293352 TTAATTCTTG
293362 AATATAATAAAATAAAAAATAAT
1 AATATAATAAAATAAAAAATAAT
* *
293385 AATAT-ATAAAAATAATAAGTAAT
1 AATATAAT-AAAATAAAAAATAAT
293408 AA
1 AA
293410 AGAATTTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (23 bp):
AATATAATAAAATAAAAAATAAT
Found at i:293410 original size:16 final size:16
Alignment explanation
Indices: 293365--293402 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
293355 ATTCTTGAAT
*
293365 ATAATAAAATA-AAAA
1 ATAATAATATATAAAA
293380 ATAATAATATATAAAA
1 ATAATAATATATAAAA
293396 ATAATAA
1 ATAATAA
293403 GTAATAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAATAATATATAAAA
Found at i:293929 original size:26 final size:27
Alignment explanation
Indices: 293895--293948 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
293885 ATTTCGAAAT
293895 TATAATTATAAA-AAAATATTAATTTA
1 TATAATTATAAATAAAATATTAATTTA
* *
293921 TATATTTATAAATAAAATATTTATTTA
1 TATAATTATAAATAAAATATTAATTTA
293948 T
1 T
293949 TTAAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
TATAATTATAAATAAAATATTAATTTA
Found at i:294136 original size:2 final size:2
Alignment explanation
Indices: 294131--294168 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
294121 TATTTAAAAA
* *
294131 AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
294169 TTATTTATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:294173 original size:12 final size:12
Alignment explanation
Indices: 294131--294176 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
294121 TATTTAAAAA
* *
294131 ATATATATATAA
1 ATATATTTATAT
*
294143 ATATATATATAT
1 ATATATTTATAT
294155 ATATATTTATAT
1 ATATATTTATAT
*
294167 ATTTATTTAT
1 ATATATTTAT
294177 GTGATTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
ATATATTTATAT
Found at i:294240 original size:16 final size:16
Alignment explanation
Indices: 294221--294253 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
294211 AATAACAAAT
294221 TAATA-TTATAAATAAA
1 TAATATTTA-AAATAAA
294237 TAATATTTAAAATAAA
1 TAATATTTAAAATAAA
294253 T
1 T
294254 TTAAAAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATATTTAAAATAAA
Found at i:322395 original size:17 final size:17
Alignment explanation
Indices: 322347--322396 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
322337 TTTTTCTAAT
322347 TTAATT-AATTTTAAAA
1 TTAATTAAATTTTAAAA
* * *
322363 CTCATTAAGTTTTAAAA
1 TTAATTAAATTTTAAAA
*
322380 TTAATTAAATTATAAAA
1 TTAATTAAATTTTAAAA
322397 AAAACTTAAG
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 4 0.15
17 22 0.85
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (17 bp):
TTAATTAAATTTTAAAA
Found at i:330818 original size:16 final size:16
Alignment explanation
Indices: 330797--330834 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
330787 ATTTCTATTC
330797 ACTTATATATATATAA
1 ACTTATATATATATAA
330813 ACTTATATATATATAA
1 ACTTATATATATATAA
330829 ACTTAT
1 ACTTAT
330835 TTTCATTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (16 bp):
ACTTATATATATATAA
Found at i:340988 original size:2 final size:2
Alignment explanation
Indices: 340981--341007 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
340971 ATTAAACATT
340981 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
341008 TCAGTAAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:341644 original size:18 final size:18
Alignment explanation
Indices: 341618--341665 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
341608 TTTATGAAAA
* * *
341618 CATCTAATGCATTTGATG
1 CATCGAATGCACTTCATG
341636 CATCGAATGCACTTCATG
1 CATCGAATGCACTTCATG
341654 CATCG-ATGCACT
1 CATCGAATGCACT
341666 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (18 bp):
CATCGAATGCACTTCATG
Found at i:343612 original size:21 final size:21
Alignment explanation
Indices: 343588--343627 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
343578 GAGAAATTGT
343588 TTTTAAAATAT-AAAAATGATA
1 TTTTAAAAT-TGAAAAATGATA
*
343609 TTTTGAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
343628 AAACAATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATA
Found at i:347449 original size:23 final size:22
Alignment explanation
Indices: 347391--347449 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
347381 ATCCCTTTGT
*
347391 ATGTGCATCGATACA-TCATGA
1 ATGTGCATCGATGCACTCATGA
347412 A-GATGCA-CGATGCACTCATTGA
1 ATG-TGCATCGATGCACTCA-TGA
347434 ATGTGCATCGATGCAC
1 ATGTGCATCGATGCAC
347450 AAAGCCATGC
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
20 7 0.22
21 8 0.25
22 8 0.25
23 9 0.28
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (22 bp):
ATGTGCATCGATGCACTCATGA
Found at i:350110 original size:64 final size:65
Alignment explanation
Indices: 349996--350116 Score: 183
Period size: 64 Copynumber: 1.9 Consensus size: 65
349986 AATGCATTAT
* * *
349996 ATGCATCGATGCACTCAGGATTTTATGAAATCATCGAATGCATTTGATGCATCGATGTACAAGAC
1 ATGCATCGATACACTCAGGATTTTATGAAATCATCGAATGCACTTCATGCATCGATGTACAAGAC
*
350061 ATGCATCGATACACTCAGGCTATTT-TGAAA-CATCGAATGCACTTCATGCATCGATG
1 ATGCATCGATACACTCAGGAT-TTTATGAAATCATCGAATGCACTTCATGCATCGATG
350117 CACTAAGGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
64 24 0.47
65 24 0.47
66 3 0.06
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (65 bp):
ATGCATCGATACACTCAGGATTTTATGAAATCATCGAATGCACTTCATGCATCGATGTACAAGAC
Found at i:350192 original size:21 final size:22
Alignment explanation
Indices: 350166--350261 Score: 130
Period size: 21 Copynumber: 4.5 Consensus size: 22
350156 TAATGTACCA
*
350166 ATGCACTAGAC-TTATGCATCG
1 ATGCACCAGACATTATGCATCG
350187 ATGCACCAG-CATTATGCATCG
1 ATGCACCAGACATTATGCATCG
350208 ATGCACCA-ACATTATGCATCG
1 ATGCACCAGACATTATGCATCG
*
350229 ATGCACC-GACCA-TATGCATTG
1 ATGCACCAGA-CATTATGCATCG
350250 ATGCACCAGACA
1 ATGCACCAGACA
350262 CTCCCAACTG
Statistics
Matches: 68, Mismatches: 2, Indels: 10
0.85 0.03 0.12
Matches are distributed among these distances:
20 1 0.01
21 63 0.93
22 4 0.06
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (22 bp):
ATGCACCAGACATTATGCATCG
Found at i:379109 original size:93 final size:93
Alignment explanation
Indices: 378861--379357 Score: 823
Period size: 93 Copynumber: 5.3 Consensus size: 93
378851 AATAAATTAA
*
378861 TTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCAAAATTTATTTGAAA
1 TTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAAA
*
378926 ATTATTAACCGAACCAAATCCACCGATTT
66 ATTATTAACCGAACCAAATCAACCGA-TT
* * * *
378955 TTTTTCTTTAACATTAATCGAACCAAAATTATTTCACTGTTAATCGAACCAAAATTTATTTGAAA
1 TTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAAA
*
379020 ATTATTAACCGAACCAAATCAACTGATT
66 ATTATTAACCGAACCAAATCAACCGATT
* * *
379048 TTTTTATTTAACATTAATTGAACCGAAATTATTTGATCGTTAATCGAACCGAAATTTATTTGAAA
1 TTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAAA
379113 ATTATTAACCGAACCAAATCAACCGATT
66 ATTATTAACCGAACCAAATCAACCGATT
* *
379141 TTTTTCTTTAACATTAATCGAACCGAAATTATTTGATCGTTAATCAAACCGAAATTTATTTGAAA
1 TTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAAA
*
379206 ATTATTAACCGAACCAAATCCACCGATT
66 ATTATTAACCGAACCAAATCAACCGATT
**
379234 TTTTTCTTTAACATTAATCGAAAAGAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAAA
1 TTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAAA
* *
379299 ATTATTAACCGAACCAAATTAACCAAATT
66 ATTATTAACCGAACCAAATCAACC-GATT
379328 TTTTTCTTTAACATTAATCGAACCGAAATT
1 TTTTTCTTTAACATTAATCGAACCGAAATT
379358 TTGGTTCGAT
Statistics
Matches: 376, Mismatches: 26, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
93 259 0.69
94 117 0.31
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (93 bp):
TTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAAA
ATTATTAACCGAACCAAATCAACCGATT
Found at i:379846 original size:30 final size:30
Alignment explanation
Indices: 379810--379866 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
379800 AGAATATATA
* *
379810 AATATTAAGGACCAAATGTATAATTATTCC
1 AATATTAAAGACCAAATATATAATTATTCC
* *
379840 AATATTAAAGATCAAATATGTAATTAT
1 AATATTAAAGACCAAATATATAATTAT
379867 GCCAGTTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (30 bp):
AATATTAAAGACCAAATATATAATTATTCC
Found at i:384958 original size:15 final size:15
Alignment explanation
Indices: 384938--384967 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
384928 AACATATTTT
*
384938 AAAATTAATTTTATC
1 AAAATTAATCTTATC
384953 AAAATTAATCTTATC
1 AAAATTAATCTTATC
384968 GAAAGATTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATTAATCTTATC
Found at i:402160 original size:18 final size:18
Alignment explanation
Indices: 402134--402175 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
402124 AATAAAAAAT
* *
402134 ATATTTTTTGAAAATTTA
1 ATATTTTTTTAAAATATA
402152 A-ATTTTTTTAAAATATA
1 ATATTTTTTTAAAATATA
402169 ATATTTT
1 ATATTTT
402176 AATGGATAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
ATATTTTTTTAAAATATA
Found at i:404082 original size:14 final size:14
Alignment explanation
Indices: 404059--404092 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
404049 TCTCTTAAGG
404059 AAATTTCAACAAA-
1 AAATTTCAACAAAC
404072 AAATCTTCAACAAAC
1 AAAT-TTCAACAAAC
404087 AAATTT
1 AAATTT
404093 TTACTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.21
14 11 0.58
15 4 0.21
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATTTCAACAAAC
Found at i:412131 original size:22 final size:23
Alignment explanation
Indices: 412101--412145 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
412091 AATTTATGTG
412101 TTTTCTTTTAAAAATATATATAC
1 TTTTCTTTTAAAAATATATATAC
* *
412124 TTTT-TTTTAAAATTTTATATAC
1 TTTTCTTTTAAAAATATATATAC
412146 AATTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTCTTTTAAAAATATATATAC
Found at i:412151 original size:22 final size:21
Alignment explanation
Indices: 412106--412160 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
412096 ATGTGTTTTC
* **
412106 TTTTAAAAATATATATACTTTT
1 TTTTAAAATTATATATAC-AAT
*
412128 TTTTAAAATTTTATATACAAT
1 TTTTAAAATTATATATACAAT
412149 TTTTAAAATTAT
1 TTTTAAAATTAT
412161 TAGATTGTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTAAAATTATATATACAAT
Found at i:413348 original size:2 final size:2
Alignment explanation
Indices: 413341--413397 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
413331 ATTAGAAAAT
413341 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
413383 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
413398 TACAATAATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:414643 original size:21 final size:21
Alignment explanation
Indices: 414600--414643 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
414590 CCAGAGTTAG
***
414600 ATTTTAATATCCGACTGTCAT
1 ATTTTAATATCCGACTAAAAT
414621 ATTTTAATATCCGACTAAAAT
1 ATTTTAATATCCGACTAAAAT
414642 AT
1 AT
414644 GATAGTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (21 bp):
ATTTTAATATCCGACTAAAAT
Found at i:415004 original size:27 final size:28
Alignment explanation
Indices: 414973--415027 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
414963 ATATATTTTA
*
414973 TCCAATAAAAAATATAATATTA-AAAAT
1 TCCAATAAAAAATATAATAATACAAAAT
415000 TCCAATAAAAAATATAATAATACAAAAT
1 TCCAATAAAAAATATAATAATACAAAAT
415028 CTGGAAGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (28 bp):
TCCAATAAAAAATATAATAATACAAAAT
Found at i:416194 original size:2 final size:2
Alignment explanation
Indices: 416189--416230 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
416179 TATATCATCA
416189 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
416231 TAAAAAATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:421575 original size:22 final size:23
Alignment explanation
Indices: 421522--421579 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
421512 AGTCTGTCTG
421522 TATGACACGTTTTACTTTGCCTT
1 TATGACACGTTTTACTTTGCCTT
421545 TATGACACGTTTT-CTTCTGCCTT
1 TATGACACGTTTTACTT-TGCCTT
421568 T-TGACACGTTTT
1 TATGACACGTTTT
421580 TTGATTGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
22 14 0.41
23 20 0.59
ACGTcount: A:0.16, C:0.22, G:0.14, T:0.48
Consensus pattern (23 bp):
TATGACACGTTTTACTTTGCCTT
Found at i:424645 original size:27 final size:25
Alignment explanation
Indices: 424607--424674 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 25
424597 AATAATTTTT
*
424607 TATTTTTTATATTAATTTTATATATAA
1 TATTTTATATATTAATTTTATA-A-AA
**
424634 TATTTTATATATTTGTTTTATAAAA
1 TATTTTATATATTAATTTTATAAAA
*
424659 TATTATATATA-TAATT
1 TATTTTATATATTAATT
424675 AATAAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
24 3 0.09
25 12 0.34
26 1 0.03
27 19 0.54
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (25 bp):
TATTTTATATATTAATTTTATAAAA
Found at i:426097 original size:19 final size:19
Alignment explanation
Indices: 426073--426116 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
426063 CATAGTCCTT
426073 GTCATCATCCTAGTTATAA
1 GTCATCATCCTAGTTATAA
426092 GTCATCATCCTAGTTATAA
1 GTCATCATCCTAGTTATAA
*
426111 CTCATC
1 GTCATC
426117 GTAATAGTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (19 bp):
GTCATCATCCTAGTTATAA
Found at i:430457 original size:6 final size:6
Alignment explanation
Indices: 430446--430491 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
430436 GAGACAGTGA
430446 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAA
430492 TTATAAGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (6 bp):
TGAAAG
Found at i:451520 original size:21 final size:20
Alignment explanation
Indices: 451495--451547 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
451485 AATTGTTATT
451495 TTTATAATTATTAATATTTAA
1 TTTATAATTATTAA-ATTTAA
* *
451516 TTTATTAATCAATAAATTTAA
1 TTTA-TAATTATTAAATTTAA
*
451537 TCTA-AATTATT
1 TTTATAATTATT
451548 TTATTCATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 5 0.19
21 13 0.50
22 8 0.31
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTATAATTATTAAATTTAA
Found at i:462120 original size:19 final size:20
Alignment explanation
Indices: 462074--462122 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
462064 TATATGAATC
462074 ATAAA-AATAAAAAGATAAA
1 ATAAATAATAAAAAGATAAA
462093 ATAAAATAATCAAAAA-AT-AA
1 AT-AAATAAT-AAAAAGATAAA
462113 ATAAATAATA
1 ATAAATAATA
462123 TTTTTTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 1 0.04
19 9 0.33
20 7 0.26
21 5 0.19
22 5 0.19
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (20 bp):
ATAAATAATAAAAAGATAAA
Found at i:470241 original size:18 final size:18
Alignment explanation
Indices: 470218--470258 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
470208 AGAACGATTA
*
470218 ATTTTAAT-AAATATTATT
1 ATTTTAATAAAATATCA-T
470236 ATTTT-ATAAAATATCAT
1 ATTTTAATAAAATATCAT
470253 ATTTTA
1 ATTTTA
470259 CCCCTAAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTAATAAAATATCAT
Found at i:470945 original size:66 final size:66
Alignment explanation
Indices: 470813--470950 Score: 154
Period size: 66 Copynumber: 2.1 Consensus size: 66
470803 GATGGGCCCT
* * * ** *
470813 ACGAAAGTTCCGTAGATTTGACACCCGACACATCGGAAGGCGGCTCATCAACACCCGTGGCTCCG
1 ACGAGAGTTCCGCAGATTTGACACCCGACACATCGGAAGGCGGCACATCAACACCCGAAGCCCCG
470878 G
66 G
* * * *
470879 ACGAGAGTTCCGCAGATTTGACACCCGACTCA-CTGGACGGCGTCACGTCAA-ATCCCGAAGCCC
1 ACGAGAGTTCCGCAGATTTGACACCCGACACATC-GGAAGGCGGCACATCAACA-CCCGAAGCCC
470942 CGG
64 CGG
470945 ACGAGA
1 ACGAGA
470951 CAGTAAATTC
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
65 2 0.03
66 58 0.97
ACGTcount: A:0.26, C:0.33, G:0.26, T:0.15
Consensus pattern (66 bp):
ACGAGAGTTCCGCAGATTTGACACCCGACACATCGGAAGGCGGCACATCAACACCCGAAGCCCCG
G
Found at i:479469 original size:21 final size:22
Alignment explanation
Indices: 479444--479494 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
479434 GTAGTGAGAG
*
479444 TGAGGAAGAGATTGCAGAGC-C
1 TGAGGAAGACATTGCAGAGCAC
479465 TGAGGAAGACATTGCAGAGCAC
1 TGAGGAAGACATTGCAGAGCAC
479487 -GAGGAAGA
1 TGAGGAAGA
479495 AAAACATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.37, C:0.14, G:0.37, T:0.12
Consensus pattern (22 bp):
TGAGGAAGACATTGCAGAGCAC
Found at i:491728 original size:21 final size:21
Alignment explanation
Indices: 491687--491728 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
491677 AATGGGGAAG
* *
491687 AAAAAATGTTAATTTTATTTA
1 AAAAAAAGTTAATTCTATTTA
491708 AAAAAAAGTTAACTTCT-TTTA
1 AAAAAAAGTTAA-TTCTATTTA
491729 TAACTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (21 bp):
AAAAAAAGTTAATTCTATTTA
Found at i:492652 original size:18 final size:20
Alignment explanation
Indices: 492623--492677 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 20
492613 GATTAAAAGT
* *
492623 ATAATATTATTTTACTAAT-
1 ATAATTTTATTTTAATAATG
492642 AT-ATTTTATTTTAATAATG
1 ATAATTTTATTTTAATAATG
*
492661 ATAATTTTGTTTTAATA
1 ATAATTTTATTTTAATA
492678 GTTTATGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 14 0.45
19 4 0.13
20 13 0.42
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
ATAATTTTATTTTAATAATG
Found at i:492673 original size:20 final size:18
Alignment explanation
Indices: 492629--492677 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
492619 AAGTATAATA
*
492629 TTATTTTACTAATATATT
1 TTATTTTAATAATATATT
492647 TTATTTTAATAATGATAATT
1 TTATTTTAATAAT-AT-ATT
*
492667 TTGTTTTAATA
1 TTATTTTAATA
492678 GTTTATGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 12 0.44
19 2 0.07
20 13 0.48
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (18 bp):
TTATTTTAATAATATATT
Found at i:505177 original size:12 final size:12
Alignment explanation
Indices: 505162--505200 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
505152 TTCGAATAAA
505162 TTATGTATTTTT
1 TTATGTATTTTT
*
505174 TTATATATTTTT
1 TTATGTATTTTT
*
505186 TTGTGTATATTTT
1 TTATGTAT-TTTT
505199 TT
1 TT
505201 TTATAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 17 0.74
13 6 0.26
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (12 bp):
TTATGTATTTTT
Found at i:506589 original size:23 final size:23
Alignment explanation
Indices: 506554--506723 Score: 195
Period size: 23 Copynumber: 7.5 Consensus size: 23
506544 AGATGAACAA
* * * *
506554 AAGAATAATAAATGGGTTTTTGG
1 AAGAAGAAGAAATGAGTTTATGG
506577 AAGAAGAAGAAATGAGTTTATGG
1 AAGAAGAAGAAATGAGTTTATGG
* *
506600 AAGAAGAAGAAACGAGTTTATGA
1 AAGAAGAAGAAATGAGTTTATGG
*
506623 AAGAAGAA-AAATGGGTTTATGG
1 AAGAAGAAGAAATGAGTTTATGG
* *
506645 AAGAAGAA-ACGATGAGTTAATGG
1 AAGAAGAAGA-AATGAGTTTATGG
506668 AAGAAGAAGAAA--ATGTTTATGG
1 AAGAAGAAGAAATGA-GTTTATGG
* *
506690 AAGAATAAGAAATGTGTTTATGG
1 AAGAAGAAGAAATGAGTTTATGG
506713 AAGAAGAAGAA
1 AAGAAGAAGAA
506724 TGATTCAAAC
Statistics
Matches: 125, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
21 1 0.01
22 38 0.30
23 85 0.68
24 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.28, T:0.22
Consensus pattern (23 bp):
AAGAAGAAGAAATGAGTTTATGG
Found at i:506644 original size:45 final size:44
Alignment explanation
Indices: 506554--506725 Score: 177
Period size: 45 Copynumber: 3.8 Consensus size: 44
506544 AGATGAACAA
* * * *
506554 AAGAATAATAAATGGGTTTTTGGAAGAAGAAGAAATGAGTTTATGG
1 AAGAAGAAGAAATGAGTTTATGGAAGAAGAA-AAATG-GTTTATGG
* *
506600 AAGAAGAAGAAACGAGTTTATGAAAGAAGAAAAATGGGTTTATGG
1 AAGAAGAAGAAATGAGTTTATGGAAGAAGAAAAAT-GGTTTATGG
* *
506645 AAGAAGAA-ACGATGAGTTAATGGAAGAAGAAGAAAAT-GTTTATGG
1 AAGAAGAAGA-AATGAGTTTATGGAAGAAG-A-AAAATGGTTTATGG
* * *
506690 AAGAATAAGAAATGTGTTTATGGAAGAAGAAGAATG
1 AAGAAGAAGAAATGAGTTTATGGAAGAAGAAAAATG
506726 ATTCAAACTG
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
43 4 0.04
44 2 0.02
45 66 0.63
46 28 0.27
47 5 0.05
ACGTcount: A:0.48, C:0.01, G:0.28, T:0.23
Consensus pattern (44 bp):
AAGAAGAAGAAATGAGTTTATGGAAGAAGAAAAATGGTTTATGG
Found at i:506672 original size:68 final size:68
Alignment explanation
Indices: 506553--506723 Score: 231
Period size: 68 Copynumber: 2.5 Consensus size: 68
506543 CAGATGAACA
* * *
506553 AAAGAATAATAAATGGGTTTTTGGAAGAAGAAGAAATGAGTTTATGGAAGAAGAAGAAACGA-GT
1 AAAGAATAAGAAATGGGTTTATGGAAGAAGAAGAAATGAGTTAATGGAAGAAGAAGAAA--ATGT
506617 TTATG
64 TTATG
* *
506622 AAAGAAGAA-AAATGGGTTTATGGAAGAAGAA-ACGATGAGTTAATGGAAGAAGAAGAAAATGTT
1 AAAGAATAAGAAATGGGTTTATGGAAGAAGAAGA-AATGAGTTAATGGAAGAAGAAGAAAATGTT
506685 TATG
65 TATG
* *
506689 GAAGAATAAGAAATGTGTTTATGGAAGAAGAAGAA
1 AAAGAATAAGAAATGGGTTTATGGAAGAAGAAGAA
506724 TGATTCAAAC
Statistics
Matches: 90, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
66 1 0.01
67 15 0.17
68 65 0.72
69 9 0.10
ACGTcount: A:0.49, C:0.01, G:0.28, T:0.22
Consensus pattern (68 bp):
AAAGAATAAGAAATGGGTTTATGGAAGAAGAAGAAATGAGTTAATGGAAGAAGAAGAAAATGTTT
ATG
Found at i:509678 original size:16 final size:17
Alignment explanation
Indices: 509643--509683 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
509633 ATGTAACAAT
509643 ATATTATAAAAATTTAAA
1 ATATTA-AAAAATTTAAA
509661 AT-TTAAAAAATATT-AA
1 ATATTAAAAAAT-TTAAA
509677 ATATTAA
1 ATATTAA
509684 TTTTATTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 10 0.48
17 9 0.43
18 2 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATTAAAAAATTTAAA
Found at i:510173 original size:21 final size:21
Alignment explanation
Indices: 510147--510197 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
510137 CGACCCGAAA
510147 TAATAAAAAATTATTTTTATT
1 TAATAAAAAATTATTTTTATT
510168 TAATAAAAAATTATTTTTATT
1 TAATAAAAAATTATTTTTATT
510189 TAATAAAAA
1 TAATAAAAA
510198 CAGTTAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAATAAAAAATTATTTTTATT
Found at i:510386 original size:267 final size:269
Alignment explanation
Indices: 509895--510444 Score: 781
Period size: 267 Copynumber: 2.0 Consensus size: 269
509885 CGGCCCGAAA
509895 TAATAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAATTATATATAGAGG
1 TAATAAAAAATTATTTTTATTCAATAAAAACAG-GA-TTAATTG-AAAAAAATTATATATAGAGG
* *
509960 AGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATTTTTTTTGGCCGGGTCGGGTA
63 AGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTT-G-CGGGTCGGGTA
* *
510025 TTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAAAAAAACCGACCTGACC
126 TTTTTCACCCTAAACCCGAACTCGACCCGACCCAAATATCACACTT-AAAAAAACCGACCCGACC
* * *
510090 CGACCAAAATAAAGTTTCACCCAACCCGAATATATGAATTAG-AA-ACCCGACCCGAAATAATAA
190 CAACCAAAATAAAGTTGCACCCAACCCGAATATATAAATTAGAAACACCCGACCCGAAATAATAA
*
510153 AAAATTATTTTTATT
255 AAAAATATTTTTATT
* * *
510168 TAATAAAAAATTATTTTTATTTAATAAAAACA-G-TTAATTG-AAAAAATTATGTATAGAGGGGT
1 TAATAAAAAATTATTTTTATTCAATAAAAACAGGATTAATTGAAAAAAATTATATATAGAGGAGT
* *
510230 ATTATTGTAATTATTCTTAAATATATAAGGTAAAATTATATATATTTT-CGGGTCTGGTATTTTT
66 ATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTGCGGGTCGGGTATTTTT
* *
510294 CACCCTAAACTCGAACTCGACCCGACCCAAATATCACACTT-AAAAAACCGACCCGACCCAATCA
131 CACCCTAAACCCGAACTCGACCCGACCCAAATATCACACTTAAAAAAACCGACCCGACCCAACCA
510358 AAATAAAGTTGCACCCGACCCGACCCGAATATATAAATTAGAAACCCGACCCGACCCGAAATAAT
196 AAATAAAGTTGCACCC-A----ACCCGAATATATAAATTAGAAA--C-ACCCGACCCGAAATAAT
510423 AAAAAAATATTTTTATT
253 AAAAAAATATTTTTATT
*
510440 CAATA
1 TAATA
510445 TATGAATAAG
Statistics
Matches: 251, Mismatches: 16, Indels: 21
0.87 0.06 0.07
Matches are distributed among these distances:
262 35 0.14
263 1 0.00
264 54 0.22
267 83 0.33
268 2 0.01
269 7 0.03
271 1 0.00
272 37 0.15
273 31 0.12
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (269 bp):
TAATAAAAAATTATTTTTATTCAATAAAAACAGGATTAATTGAAAAAAATTATATATAGAGGAGT
ATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTGCGGGTCGGGTATTTTT
CACCCTAAACCCGAACTCGACCCGACCCAAATATCACACTTAAAAAAACCGACCCGACCCAACCA
AAATAAAGTTGCACCCAACCCGAATATATAAATTAGAAACACCCGACCCGAAATAATAAAAAAAT
ATTTTTATT
Found at i:523472 original size:125 final size:125
Alignment explanation
Indices: 523250--523627 Score: 524
Period size: 125 Copynumber: 3.0 Consensus size: 125
523240 AATACCCACA
* * *
523250 TTGGGGCATGACTGAACCCCCATCATTTTGAAATGACAAGATCCAGACGAAGAAGGCATTGAGAA
1 TTGGGGCACGACTGAACCCCCATCATTTTGAAATGACAAGATTCAGACAAAGAAGGCATTGAGAA
* * * * **
523315 TAAGCCTTACAATTTGAGGTGTTGGGGTATTTTGAAGACCCGTACCTTTATAAGATAATG
66 TGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATG
* **
523375 TTGGGGCACGATTGAACCCCCATCATTTTGAAATGACAAGATTCAGACAAAGAAGGCATCAAGAA
1 TTGGGGCACGACTGAACCCCCATCATTTTGAAATGACAAGATTCAGACAAAGAAGGCATTGAGAA
*
523440 TGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATGAGATAATG
66 TGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATG
* * ** * *
523500 TTGGGGCGCGACTGAACCCACATCATGATGAAATTACAAGATTCAGACCAAGAAGGCATTGAGAA
1 TTGGGGCACGACTGAACCCCCATCATTTTGAAATGACAAGATTCAGACAAAGAAGGCATTGAGAA
* * * * *
523565 TGAGCCTTATAATTTGAGAT-ATTGAGGCATTTTGAAGGCCCGTACCAGAATAAAATAATG
66 TGAGCCTTACAATTTGAGGTGA-TGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATG
523625 TTG
1 TTG
523628 CGACATTAGT
Statistics
Matches: 224, Mismatches: 28, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
124 1 0.00
125 223 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.25
Consensus pattern (125 bp):
TTGGGGCACGACTGAACCCCCATCATTTTGAAATGACAAGATTCAGACAAAGAAGGCATTGAGAA
TGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATG
Found at i:524874 original size:36 final size:36
Alignment explanation
Indices: 524812--524965 Score: 222
Period size: 36 Copynumber: 4.3 Consensus size: 36
524802 AGTCAATCCT
524812 AAGCCTTCACCGGAG-ATAGTGAAGCAAACCATCTG
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
* *
524847 AAGCCTTCACCGGAGAATAGTGAAGCAATCAATCTG
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
524883 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCAT-
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATC-TG
* * * *
524919 AAGTCTTCACCAGAGAGTAGTGAAGCAAACCATCTT
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
*
524955 AAGTCTTCACC
1 AAGCCTTCACC
524966 AAAAAGTAGT
Statistics
Matches: 109, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
35 16 0.15
36 92 0.84
37 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (36 bp):
AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
Found at i:525261 original size:51 final size:51
Alignment explanation
Indices: 525184--525800 Score: 571
Period size: 51 Copynumber: 11.8 Consensus size: 51
525174 GTGAAGCAAA
* * *
525184 TGAAGATTATTTGAGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCCGTT
1 TGAAGA-TATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTT
* * *
525236 TGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAAGGAGCGAACCCGTG
1 TGAAGATATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTT
* * * *
525287 TGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
1 TGAAGATATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTT
* * * * *
525338 TGAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
1 TGAAGATATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTT
* * * * *
525389 TAAAGAGATGTCTGAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTG
1 TGAAGATAT-TC-GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTT
* * * *
525442 TGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
1 TGAAGATATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTT
* * *
525493 TGAAGATGTTCGAGTTCCATACTCCCT-GAAGAAAGAGGGAGCGAACCCGTAAGA
1 TGAAGATATTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGT---T
* *
525547 AGAAGATATTCGAGTTCTATACTCCCT-GAAGAAAGAGGGAGCGAGCCCGTTT
1 TGAAGATATTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCG-TT
* * *
525599 TCAGAAGATCATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCAAACCCGTT
1 T--GAAGAT-ATTCGAGTTCTATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTT
* * * * **
525654 TCCAAAAGATTATTCGAGTTCTATACTCCTTAAAGAAA-A---AGGGAATTCGCTT
1 T---GAAGA-TATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TT
* * * * *
525706 ACAGAAGATTATTCAAGTTCTATACTCCCTAGAGAAAGAGGGAGCAAACCTGTA
1 --TGAAGA-TATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTT
* * * * *
525760 AGAAGATGTTCGAGTTCCATAATCCCTAGAGAAATAGGGAG
1 TGAAGATATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAG
525801 TAGACCCGAT
Statistics
Matches: 477, Mismatches: 67, Indels: 43
0.81 0.11 0.07
Matches are distributed among these distances:
51 284 0.60
52 18 0.04
53 44 0.09
54 53 0.11
55 35 0.07
56 42 0.09
57 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (51 bp):
TGAAGATATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTT
Found at i:525476 original size:155 final size:155
Alignment explanation
Indices: 525196--525755 Score: 661
Period size: 155 Copynumber: 3.6 Consensus size: 155
525186 AAGATTATTT
* * * *
525196 GAGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCCGTTT-GA-AGATGTTCGAGTTCTATACT
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTAAAGAGATGTTCGAGTTCTATACT
525259 CCCTAGAGAAAGAAGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGAA
66 CCCTAGAGAAAGAAGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGAA
525324 GGAGCGAACCCGTTTGAAGATGTTC
131 GGAGCGAACCCGTTTGAAGATGTTC
* *
525349 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTAAAGAGATG-TCTGAGTTCCATAC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTAAAGAGATGTTC-GAGTTCTATAC
525413 TCCCTAGAGAAAGAAGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGA
65 TCCCTAGAGAAAGAAGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGA
525478 AGGAGCGAACCCGTTTGAAGATGTTC
130 AGGAGCGAACCCGTTTGAAGATGTTC
* * * *
525504 GAGTTCCATACTCCCTGAAGAAAGAGGGAGCGAACCCG-TAAGAAGAAGATATTCGAGTTCTATA
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTA-AAG-AGATGTTCGAGTTCTATA
* * * * *
525568 CTCCCT-GAAGAAAGAGGGAGCGAGCCCGTTTTCAGAAGATCATTCGAGTTCTATACTTCCTGAA
64 CTCCCTAG-AGAAAGAAGGAGCGAACCCG-TGT--GAAGAT-ATGCGAGTTCTATAC-TCCTTAA
* * * *
525632 AGAAAGAGGGAGCAAACCCGTTTCCAAAAGATTATTC
123 AGAAAGAAGGAGCGAACCCGTTT---GAAGA-TGTTC
* * ** * * * *
525669 GAGTTCTATACTCCTTAAAGAAA-AA-G-G-GAATTCGCTTACAGAAGATTATTCAAGTTCTATA
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTAAAG-AGA-TGTTCGAGTTCTATA
* *
525730 CTCCCTAGAGAAAGAGGGAGCAAACC
64 CTCCCTAGAGAAAGAAGGAGCGAACC
525756 TGTAAGAAGA
Statistics
Matches: 356, Mismatches: 32, Indels: 29
0.85 0.08 0.07
Matches are distributed among these distances:
153 37 0.10
154 5 0.01
155 145 0.41
156 37 0.10
157 4 0.01
159 6 0.02
160 14 0.04
161 38 0.11
162 39 0.11
163 2 0.01
164 5 0.01
165 24 0.07
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (155 bp):
GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTAAAGAGATGTTCGAGTTCTATACT
CCCTAGAGAAAGAAGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGAA
GGAGCGAACCCGTTTGAAGATGTTC
Found at i:525799 original size:102 final size:106
Alignment explanation
Indices: 525505--525799 Score: 262
Period size: 111 Copynumber: 2.8 Consensus size: 106
525495 AAGATGTTCG
* * *** *
525505 AGTTCCATACTCCCTG-AAGAAAGAGGGAGCGAACCCGTAAGAAGAAGA-TATTCGAGTTCTATA
1 AGTTCTATACTCCCTGAAAGAAAGAGGGAGCAAACCCGTGTCAA-AAGATTATTCGAGTTCCATA
* * * ** * * *
525568 CTCCCTGAAGAAAGAGGGAGCGAGCCCGTTTTCAGAAGATCATTCG
65 ATCCCTAAAGAAAAAGGGA---A-TTCGCTTACAGAAGATCATTCA
* * *
525614 AGTTCTATACTTCCTGAAAGAAAGAGGGAGCAAACCCGTTTCCAAAAGATTATTCGAGTTCTATA
1 AGTTCTATACTCCCTGAAAGAAAGAGGGAGCAAACCCGTGT-CAAAAGATTATTCGAGTTCCATA
* * *
525679 CTCCTTAAAGAAAAAGGGAATTCGCTTACAGAAGATTATTCA
65 ATCCCTAAAGAAAAAGGGAATTCGCTTACAGAAGATCATTCA
* *
525721 AGTTCTATACTCCCT-AGAGAAAGAGGGAGCAAA-CC-TGT-AAGAAGA-TGTTCGAGTTCCATA
1 AGTTCTATACTCCCTGAAAGAAAGAGGGAGCAAACCCGTGTCAA-AAGATTATTCGAGTTCCATA
* *
525781 ATCCCTAGAGAAATAGGGA
65 ATCCCTAAAGAAAAAGGGA
525800 GTAGACCCGA
Statistics
Matches: 158, Mismatches: 24, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
102 30 0.19
103 4 0.03
104 2 0.01
105 2 0.01
106 17 0.11
107 30 0.19
108 1 0.01
109 14 0.09
110 25 0.16
111 33 0.21
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (106 bp):
AGTTCTATACTCCCTGAAAGAAAGAGGGAGCAAACCCGTGTCAAAAGATTATTCGAGTTCCATAA
TCCCTAAAGAAAAAGGGAATTCGCTTACAGAAGATCATTCA
Found at i:525854 original size:55 final size:54
Alignment explanation
Indices: 525792--526395 Score: 481
Period size: 55 Copynumber: 11.2 Consensus size: 54
525782 TCCCTAGAGA
* * *
525792 AATAGGGAGTAGACCCGATTGTTGAAGTTTGTTCGAGTCTTATACTCTCTGAAAG
1 AATAGGGAGCAGACGCGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTG-AAG
* * * *
525847 AATAGGGAGCAGACACGATTGTTGAAGATTATTTGAGTCTCATACTCTCTGAAAG
1 AATAGGGAGCAGACGCGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTG-AAG
* * *
525902 AATAGGGAGTAGACACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGG
1 AATAGGGAGCAGACGCGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAA-G
* * * * *
525957 AATAGGGAGCATACACG-TT-TTCAAAAGATT-TTCGAGT-TCTATACTCCCTGGAG
1 AATAGGGAGCAGACGCGATTGTT--GAAGATTGTTCGAGTCT-TATACTCTCTGAAG
* * * *
526010 AAAGAGGGAAC-GAACCCGATTGTTGAAGATTG-T-GGGTCTTATACTCTCTGAAG
1 -AATAGGGAGCAG-ACGCGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAG
* * *
526063 AAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAG
1 -AATAGGGAGCAGACGCGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAG
* * * *
526118 AAATAGGG-GACAGATGCGATTGATGAAGATTG-T-GGGTCTTATACTCTCCGAAG
1 -AATAGGGAG-CAGACGCGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAG
* * * **
526171 AAAAAAGGGGGCAGACGCAATCATTGAAGATTGTTCG-GATCTTATACTCTCTGAAG
1 --AATAGGGAGCAGACGCGATTGTTGAAGATTGTTCGAG-TCTTATACTCTCTGAAG
* * * * *
526227 AAATAGGGGGCAGATGCGATTGATGAAGATT-AT-GGGTC---T-CTCTCTGAAG
1 -AATAGGGAGCAGACGCGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAG
* * *
526276 AATAGGG-GCAGAAGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAG
1 AATAGGGAGCAGACGCGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAG
* * ** * * * *
526329 AAATAGGGGGCATACAAGTTTGTTGAAGA-TGATTCAAGTCTTTATACCCTTTGAAG
1 -AATAGGGAGCAGACGCGATTGTTGAAGATTG-TTCGAGTC-TTATACTCTCTGAAG
526385 AAATAGGGAGC
1 -AATAGGGAGC
526396 GAACCCTAAG
Statistics
Matches: 452, Mismatches: 67, Indels: 59
0.78 0.12 0.10
Matches are distributed among these distances:
47 18 0.04
48 8 0.02
49 14 0.03
50 1 0.00
52 1 0.00
53 74 0.16
54 80 0.18
55 214 0.47
56 42 0.09
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (54 bp):
AATAGGGAGCAGACGCGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAG
Found at i:526147 original size:217 final size:216
Alignment explanation
Indices: 525762--526337 Score: 572
Period size: 217 Copynumber: 2.7 Consensus size: 216
525752 AACCTGTAAG
* * * * *
525762 AAGATGTTCGAGTTCCATAATCCCTAGAGAAATAGGGA-GTAGACCCGATTGTTGAAGTTTGTTC
1 AAGATTTTCGAGTTCTATACTCCCTGGAGAAATAGGGACG-AGACCCGATTGTTGAAGATTG-T-
* * * * * * * *
525826 GAGTCTTATACTCTCTGAA-AGAATAGGGAGCAGACACGATTGTTGAAGATTATTTGAGTCTCAT
63 GGGTCTTATACTCTCTGAAGA-AATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTAT
* * *
525890 ACTCTCTGAA-AGAATA-GGGAGTAGACACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTG
127 ACTCTCTGAAGA-AATAGGGGAGCAGACACGATTGATGAAGATTG-T-GAGTCTCATACTCTCCG
* * ***
525953 AAG-GAATAGGGAGCATACACGTTTTCA-A
189 AAGAAAAAAGGGAGC--ACACGCAATCATA
*
525981 AAGATTTTCGAGTTCTATACTCCCTGGAGAAAGAGGGAACGA-ACCCGATTGTTGAAGATTGTGG
1 AAGATTTTCGAGTTCTATACTCCCTGGAGAAATAGGG-ACGAGACCCGATTGTTGAAGATTGTGG
526045 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACT
65 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACT
** * *
526110 CTCTGAAGAAATAGGGGA-CAGATGCGATTGATGAAGATTGTGGGTCTTATACTCTCCGAAGAAA
130 CTCTGAAGAAATAGGGGAGCAGACACGATTGATGAAGATTGTGAGTCTCATACTCTCCGAAGAAA
* * *
526174 AAAGGGGGCAGACGCAATCATTG
195 AAAGGGAGCACACGCAATCA-TA
* * * * ** * *
526197 AAGATTGTTCG-GATCTTATACTCTCTGAAGAAATAGGG-GGCAGATGCGATTGATGAAGATTAT
1 AAGATT-TTCGAGTTC-TATACTCCCTGGAGAAATAGGGACG-AGACCCGATTGTTGAAGATTGT
*
526260 GGGTC---T-CTCTCTGAAG-AATA-GGGGCAGAAGCAATCGTTGAAGATTGTTCGAGTCTTATA
63 GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATA
526319 CTCTCTGAAGAAATAGGGG
128 CTCTCTGAAGAAATAGGGG
526338 GCATACAAGT
Statistics
Matches: 306, Mismatches: 39, Indels: 32
0.81 0.10 0.08
Matches are distributed among these distances:
211 57 0.19
212 4 0.01
213 10 0.03
214 8 0.03
215 18 0.06
216 19 0.06
217 130 0.42
218 7 0.02
219 50 0.16
220 2 0.01
221 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.28
Consensus pattern (216 bp):
AAGATTTTCGAGTTCTATACTCCCTGGAGAAATAGGGACGAGACCCGATTGTTGAAGATTGTGGG
TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACTC
TCTGAAGAAATAGGGGAGCAGACACGATTGATGAAGATTGTGAGTCTCATACTCTCCGAAGAAAA
AAGGGAGCACACGCAATCATA
Found at i:526221 original size:109 final size:108
Alignment explanation
Indices: 525828--526337 Score: 519
Period size: 109 Copynumber: 4.8 Consensus size: 108
525818 GTTTGTTCGA
* * * * * * *
525828 GTCTTATACTCTCTGAA-AGAATAGGGAGCAGACACGATTGTTGAAGATTATTTGAGTCTCATAC
1 GTCTTATACTCTCTGAAGA-AATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATAC
* ** * *
525892 TCTCTGAA-AGAATA-GGGAGTAGACACGATTGTTGAAGATTGTTCGA
65 TCTCTGAAGA-AATAGGGGA-CAGATGCGATTGATGAAGATTG-T-GG
* * * * * * * *
525938 GTCTCATACTCTCTGAAGGAATAGGGAGCATACAC-GT-TTTCAAAAGATT-TTCGAGT-TCTAT
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTT--GAAGATTGTTCGAGTCT-TAT
* * * * ** *
525999 ACTCCCTGGAGAAAGAGGGAAC-GAACCCGATTGTTGAAGATTGTGG
63 ACTCTCTGAAGAAATAGGGGACAG-ATGCGATTGATGAAGATTGTGG
526045 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACT
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACT
526110 CTCTGAAGAAATAGGGGACAGATGCGATTGATGAAGATTGTGG
66 CTCTGAAGAAATAGGGGACAGATGCGATTGATGAAGATTGTGG
* * *
526153 GTCTTATACTCTCCGAAGAAAAAAGGGGGCAGACGCAATCATTGAAGATTGTTCG-GATCTTATA
1 GTCTTATACTCTCTGAAG-AAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAG-TCTTATA
* *
526217 CTCTCTGAAGAAATAGGGGGCAGATGCGATTGATGAAGATTATGG
64 CTCTCTGAAGAAATAGGGGACAGATGCGATTGATGAAGATTGTGG
*
526262 GTC---T-CTCTCTGAAG-AATA-GGGGCAGAAGCAATCGTTGAAGATTGTTCGAGTCTTATACT
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACT
526321 CTCTGAAGAAATAGGGG
66 CTCTGAAGAAATAGGGG
526338 GCATACAAGT
Statistics
Matches: 346, Mismatches: 39, Indels: 38
0.82 0.09 0.09
Matches are distributed among these distances:
102 54 0.16
103 4 0.01
105 9 0.03
106 1 0.00
107 37 0.11
108 71 0.21
109 129 0.37
110 41 0.12
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.28
Consensus pattern (108 bp):
GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACT
CTCTGAAGAAATAGGGGACAGATGCGATTGATGAAGATTGTGG
Found at i:529034 original size:106 final size:108
Alignment explanation
Indices: 528919--529122 Score: 394
Period size: 106 Copynumber: 1.9 Consensus size: 108
528909 TTGTTCATAC
528919 GCACGTAGGTGTAGTTTATTTTTATGAGCATGTTTGAATTCGTTCAC-TTAATCGCATATTTAAT
1 GCACGTAGGTGTAGTTTATTTTTATGAGCATGTTTGAATTCGTTCACTTTAATCGCATATTTAAT
528983 TA-TTTTTGCATTAACATCACTTTGTATAATTTAATATTTTAT
66 TATTTTTTGCATTAACATCACTTTGTATAATTTAATATTTTAT
529025 GCACGTAGGTGTAGTTTATTTTTATGAGCATGTTTGAATTCGTTCACTTTAATCGCATATTTAAT
1 GCACGTAGGTGTAGTTTATTTTTATGAGCATGTTTGAATTCGTTCACTTTAATCGCATATTTAAT
529090 TATTTTTTGCATTAACATCACTTTGTATAATTT
66 TATTTTTTGCATTAACATCACTTTGTATAATTT
529123 TTGCATGATA
Statistics
Matches: 96, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
106 47 0.49
107 19 0.20
108 30 0.31
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (108 bp):
GCACGTAGGTGTAGTTTATTTTTATGAGCATGTTTGAATTCGTTCACTTTAATCGCATATTTAAT
TATTTTTTGCATTAACATCACTTTGTATAATTTAATATTTTAT
Found at i:531596 original size:2 final size:2
Alignment explanation
Indices: 531589--531629 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
531579 TGTAATTTAA
* *
531589 AT AT AT AT AT AT AT AT A- AT TT AT AT TT 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
531630 TATTGATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:531607 original size:23 final size:23
Alignment explanation
Indices: 531581--531628 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
531571 AAAATCTTTG
531581 TAATTTAAATATATATATATATA
1 TAATTTAAATATATATATATATA
* *
531604 TAATTTATATTTATATATATATA
1 TAATTTAAATATATATATATATA
531627 TA
1 TA
531629 TTATTGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATTTAAATATATATATATATA
Found at i:533621 original size:16 final size:16
Alignment explanation
Indices: 533588--533628 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
533578 GTTTACTTCA
533588 GAATGATT-AAACGTT
1 GAATGATTCAAACGTT
*
533603 GAATGATTCAAATGTT
1 GAATGATTCAAACGTT
533619 GAATGATTCA
1 GAATGATTCA
533629 GAGGCTCTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (16 bp):
GAATGATTCAAACGTT
Found at i:543818 original size:23 final size:23
Alignment explanation
Indices: 543792--543836 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
543782 CACCACAGCT
*
543792 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
543815 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
543837 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:544074 original size:149 final size:149
Alignment explanation
Indices: 543815--544118 Score: 554
Period size: 149 Copynumber: 2.0 Consensus size: 149
543805 CGAAGTGCCC
* *
543815 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
*
543880 CATATATATATGCTAGGGATCAAGTATATGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATATGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
543945 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
543964 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
* *
544029 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATATGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
*
544094 CATATGTCTCGAAGAACCG
131 CATATGTCCCGAAGAACCG
544113 CGTAGA
1 CGTAGA
544119 CCCTCGACTC
Statistics
Matches: 149, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 149 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATATGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:544770 original size:2 final size:2
Alignment explanation
Indices: 544763--544790 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
544753 TCTCTTAGAC
544763 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
544791 TCACATGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:545143 original size:18 final size:18
Alignment explanation
Indices: 545122--545156 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
545112 TCCCATCTAG
545122 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
545140 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
545157 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:545766 original size:21 final size:21
Alignment explanation
Indices: 545736--545780 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
545726 AATTTGTCGT
* *
545736 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
545757 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
545778 TTG
1 TTG
545781 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:549051 original size:21 final size:21
Alignment explanation
Indices: 549026--549067 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
549016 CCTAATATTG
549026 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
549047 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
549068 TAATATTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:551523 original size:2 final size:2
Alignment explanation
Indices: 551516--551540 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
551506 TTTTTAAGCA
551516 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
551541 ATCGATCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:554590 original size:312 final size:312
Alignment explanation
Indices: 554000--554599 Score: 722
Period size: 312 Copynumber: 1.9 Consensus size: 312
553990 TCTTTTTCTT
* * * ** * ** *
554000 AAGCTTCTTGGTAACTGGTTTTGTCGTTGACTTATCATTTCCTCGTTCAAGCACATTCAAGTCAG
1 AAGCTTCTTGCTAACTGATTTTCTCACTGACTTATCATTTCCTCCTTCAAGCACAACCAAATCAG
* * * *
554065 AAGGGCTATGGGAACCTTCATTTCCTGGCTTTCTTTCATCAAATGAAGGAACCTCAACATCTTGC
66 AAGGGCTATGAGAACCTTCATTTCCTGGCTTTCTATCATCAAATGAAGCAACCTCAACAACTTGC
* * * * * **
554130 TGCTTATTCTTCAGCTCATTGTGCTCTCCAACAACTTGTAATTGTTCTAAGCCGTATTCTTTGAT
131 TGCTTATTCTGCAGCACACTGTGCTCTCCAACAACTTGTAACTGTTCTAAGCCGTAATCTTCAAT
* * * *
554195 ATTTGATCTGCTTGCAGAGGTGGTCTCTCTTAATCCCTTGAAGGACATTTGGGGTGATTCCTCAC
196 ATTTGATCTGCTTGCAGAGGTGGACTCTCTTAATCCCGTGAAAGACATATGGGGTGATTCCTCAC
* *
554260 CAGCATTCTCACTTTGCATATCTGGCTTGTTCACCGGTTTTGTCAGTTTTGC
261 AAGCAATCTCACTTTGCATATCTGGCTTGTTCACCGGTTTTGTCAGTTTTGC
*
554312 AAGCTTCTTGCTAACTGATTTTCTCACTGACTTATCATTTCCTCCTTCAAGCACAACCAAATTAG
1 AAGCTTCTTGCTAACTGATTTTCTCACTGACTTATCATTTCCTCCTTCAAGCACAACCAAATCAG
** * * *
554377 AAGGGCTATGAGAATTTTCA-TTCC-GCAGTTTTCTATCATCAAGTGAAGCCACCTCAACAACTT
66 AAGGGCTATGAGAACCTTCATTTCCTG--GCTTTCTATCATCAAATGAAGCAACCTCAACAACTT
** * ** ** *
554440 GCTGCTTATTCTGCAGCACACCTG-GCTCTCCGCCCACTTGTGCCTGTTCTTGGCTGTAATCTTC
129 GCTGCTTATTCTGCAGCACA-CTGTGCTCTCCAACAACTTGTAACTGTTCTAAGCCGTAATCTTC
* * * *
554504 AATATTTGATCTGCTTGCTGGGGTGGACTCTCTTAATTCCGTGAAAGACATATGTGGTGACTT-C
193 AATATTTGATCTGCTTGCAGAGGTGGACTCTCTTAATCCCGTGAAAGACATATGGGGTGA-TTCC
* *
554568 TCATAAGCAATCTCATTTTGCATATCTGGCTT
257 TCACAAGCAATCTCACTTTGCATATCTGGCTT
554600 ACCTGCAAAG
Statistics
Matches: 238, Mismatches: 46, Indels: 8
0.82 0.16 0.03
Matches are distributed among these distances:
310 1 0.00
311 4 0.02
312 229 0.96
313 4 0.02
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.36
Consensus pattern (312 bp):
AAGCTTCTTGCTAACTGATTTTCTCACTGACTTATCATTTCCTCCTTCAAGCACAACCAAATCAG
AAGGGCTATGAGAACCTTCATTTCCTGGCTTTCTATCATCAAATGAAGCAACCTCAACAACTTGC
TGCTTATTCTGCAGCACACTGTGCTCTCCAACAACTTGTAACTGTTCTAAGCCGTAATCTTCAAT
ATTTGATCTGCTTGCAGAGGTGGACTCTCTTAATCCCGTGAAAGACATATGGGGTGATTCCTCAC
AAGCAATCTCACTTTGCATATCTGGCTTGTTCACCGGTTTTGTCAGTTTTGC
Found at i:559392 original size:18 final size:18
Alignment explanation
Indices: 559371--559411 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
559361 TAAATTTTAA
559371 ATTTTTCATTAAT-TATTT
1 ATTTTT-ATTAATATATTT
559389 A-TTTTATTAATAATATTT
1 ATTTTTATTAAT-ATATTT
559407 ATTTT
1 ATTTT
559412 AAAATTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 6 0.30
17 4 0.20
18 7 0.35
19 3 0.15
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTTATTAATATATTT
Found at i:559445 original size:41 final size:43
Alignment explanation
Indices: 559364--559449 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 43
559354 TTTATTTTAA
* * *
559364 ATTTTAAATTTTTCATTAATTATTTATTTTATTAATAATATTT
1 ATTTTAAAATTTTCATTAATTATTTATCTCATTAATAATATTT
*
559407 ATTTTAAAATTTT-ATTTA-TATTTATCTCATATAA-AATATTT
1 ATTTTAAAATTTTCATTAATTATTTATCTCAT-TAATAATATTT
559448 AT
1 AT
559450 GTTATATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
41 19 0.50
42 7 0.18
43 12 0.32
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (43 bp):
ATTTTAAAATTTTCATTAATTATTTATCTCATTAATAATATTT
Found at i:569492 original size:149 final size:151
Alignment explanation
Indices: 569260--569547 Score: 393
Period size: 149 Copynumber: 1.9 Consensus size: 151
569250 TGAACTTGAC
* * * * *
569260 AGATTTTGATCGCTTTTAATTCGTACTCTCTTCAAGACTTGTTTTCTAATCAATTTAGGGTTTGA
1 AGATTTTGATCGATTTTAATTCCTACTCTCATCAAGACTTGTTTTATAATCAATTTAGGGGTTGA
** *
569325 ATATGCTTCTTTTAAAACTATGTCATGGGCTTGTGATGAATCTCTTTTAGTAATGGTTAATTT-C
66 ATATGCTTCTACTAAAACTATGTCATGGGCTTGTGATGAATCTCTTTTAGTAATGGGTAATTTGC
569389 -TTTGAATTTTTTTCTTCAAT
131 GTTTGAATTTTTTTCTTCAAT
* *
569409 AGATTTTGATCTATTTTAATTCCT-CGTCTCATCAAGATTTGTTTTATAATCAATTTAGGGGTTG
1 AGATTTTGATCGATTTTAATTCCTAC-TCTCATCAAGACTTGTTTTATAATCAATTTAGGGGTTG
* * * * * * *
569473 AATCTGGTTCTACTGAAACTATGTTATGGGCTTGTGATGCATCTCTTTTTGTAATGGGTGATTTG
65 AATATGCTTCTACTAAAACTATGTCATGGGCTTGTGATGAATCTCTTTTAGTAATGGGTAATTTG
569538 CGTTTGAATT
130 CGTTTGAATT
569548 AGTATTTCTT
Statistics
Matches: 119, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
148 1 0.01
149 109 0.92
150 1 0.01
151 8 0.07
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (151 bp):
AGATTTTGATCGATTTTAATTCCTACTCTCATCAAGACTTGTTTTATAATCAATTTAGGGGTTGA
ATATGCTTCTACTAAAACTATGTCATGGGCTTGTGATGAATCTCTTTTAGTAATGGGTAATTTGC
GTTTGAATTTTTTTCTTCAAT
Found at i:570954 original size:149 final size:149
Alignment explanation
Indices: 570720--570991 Score: 411
Period size: 149 Copynumber: 1.8 Consensus size: 149
570710 ATTGAACTTG
* * * *
570720 ACAGATTTTGATCGCTTTTAATTCATACTCTCTTCAAGACTTGTTTTCTAATCAATTTAGGGTTT
1 ACAGATTTTGATCGATTTTAATTCATACTCTCATCAAGACTTGTTTTATAATCAATTTAGGGGTT
**
570785 GAATCTGCTTCTTTTAAAACTATGTCATGGGCTTGTGATGAATCTCTTTTTGTAATGGTTAATTT
66 GAATCTGCTTCTACTAAAACTATGTCATGGGCTTGTGATGAATCTCTTTTTGTAATGGTTAATTT
570850 CTTTGAATTTTTTTCTTCA
131 CTTTGAATTTTTTTCTTCA
* * * *
570869 ACAGATTTTGATCTATTTTAATTCCT-CATCTCATCAATATTTGTTTTATAATCAATTTAGGGGT
1 ACAGATTTTGATCGATTTTAATTCATAC-TCTCATCAAGACTTGTTTTATAATCAATTTAGGGGT
* * *
570933 TGAATCTGGTTCTACTGAAACTATGTCATGGGCTTGTGATGCATCTCTTTTTGTAATGG
65 TGAATCTGCTTCTACTAAAACTATGTCATGGGCTTGTGATGAATCTCTTTTTGTAATGG
570992 GTGTCATGGG
Statistics
Matches: 109, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
148 1 0.01
149 108 0.99
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (149 bp):
ACAGATTTTGATCGATTTTAATTCATACTCTCATCAAGACTTGTTTTATAATCAATTTAGGGGTT
GAATCTGCTTCTACTAAAACTATGTCATGGGCTTGTGATGAATCTCTTTTTGTAATGGTTAATTT
CTTTGAATTTTTTTCTTCA
Found at i:571006 original size:37 final size:37
Alignment explanation
Indices: 570956--571031 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
570946 ACTGAAACTA
570956 TGTCATGGGCTTGTGATGCATCTCTTTTTGTAATGGG
1 TGTCATGGGCTTGTGATGCATCTCTTTTTGTAATGGG
570993 TGTCATGGGCTTGTGATGCATCTCTTTTTGTAATGGG
1 TGTCATGGGCTTGTGATGCATCTCTTTTTGTAATGGG
571030 TG
1 TG
571032 ATTTGCGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.13, C:0.13, G:0.30, T:0.43
Consensus pattern (37 bp):
TGTCATGGGCTTGTGATGCATCTCTTTTTGTAATGGG
Found at i:572530 original size:238 final size:239
Alignment explanation
Indices: 572056--572530 Score: 681
Period size: 239 Copynumber: 2.0 Consensus size: 239
572046 GTTAACATGA
* * ** *
572056 AATTTCTTGGAATTTTTTTCTTTAAATAAGGGAGAAAGGATTAAAAGTGATGTGATGATCGAAAT
1 AATTTCTTCGAATTTTTTTCTTTAAATAAGGAAGAAAGGATTAAAAGCAATGTGATGATAGAAAT
*
572121 TCAATGGTCTCTCAATCCACTGATCTAATTTGATGTTACATTGAACTTGACAGATTTTGATCGCT
66 TCAATGGTCTCTCAATCCACTGATCTAATTTGATGTTACATTGAACTTGACAGATTATGATCGCT
* * * * *
572186 TTTAATTCCTACTCTCTTCAAGACTTGTTTTCTTATCAATTTAGGGTTTGAATCTACTTCTTTTA
131 TTTAATTACTACTCTCTTCAAGACTTGTTTTATAATCAATTTAGGGGTTGAATCTACTTCTCTTA
*
572251 AAATTATGTCATGGGCTTGTGATGAATCTCTTTTTGTAATGGTT
196 AAACTATGTCATGGGCTTGTGATGAATCTCTTTTTGTAATGGTT
* *
572295 AATTTCTTCGATTTTTTTTCTTTAAATATGGAAGAAAGGATTAAAAGCAATGTGATGATAGAAAT
1 AATTTCTTCGAATTTTTTTCTTTAAATAAGGAAGAAAGGATTAAAAGCAATGTGATGATAGAAAT
* * * * *
572360 TCAATGGTCTGTCAATCCACTGATCTAATTTGATGTTTCATTGAAGTTTCGACAGGTTATGATCT
66 TCAATGGTCTCTCAATCCACTGATCTAATTTGATGTTACATTGAA-CTT-GACAGATTATGATCG
* * *
572425 CTTTTATTTACTCCTCTCTTC-A-A-TTGTTTTATAATCAATTTAGGGGTTGAATC-AGGTTCTA
129 CTTTTAATTACTACTCTCTTCAAGACTTGTTTTATAATCAATTTAGGGGTTGAATCTA-CTTCT-
572486 CTT-AAACTATGTCATGGGCTTGTGATGAATCTCTTTTTGTAATGG
192 CTTAAAACTATGTCATGGGCTTGTGATGAATCTCTTTTTGTAATGG
572531 GTATTTTGTG
Statistics
Matches: 210, Mismatches: 22, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
237 1 0.00
238 72 0.34
239 104 0.50
240 3 0.01
241 30 0.14
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.42
Consensus pattern (239 bp):
AATTTCTTCGAATTTTTTTCTTTAAATAAGGAAGAAAGGATTAAAAGCAATGTGATGATAGAAAT
TCAATGGTCTCTCAATCCACTGATCTAATTTGATGTTACATTGAACTTGACAGATTATGATCGCT
TTTAATTACTACTCTCTTCAAGACTTGTTTTATAATCAATTTAGGGGTTGAATCTACTTCTCTTA
AAACTATGTCATGGGCTTGTGATGAATCTCTTTTTGTAATGGTT
Found at i:580230 original size:4 final size:4
Alignment explanation
Indices: 580223--580368 Score: 292
Period size: 4 Copynumber: 36.5 Consensus size: 4
580213 GCATGCATAC
580223 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
580271 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
580319 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
580367 AT
1 AT
580369 CCGCATTATG
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 142 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:581386 original size:13 final size:13
Alignment explanation
Indices: 581354--581388 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
581344 AAAAACATCT
581354 AAAACACCCAACC
1 AAAACACCCAACC
**
581367 ACCACACCCAACC
1 AAAACACCCAACC
581380 AAAACACCC
1 AAAACACCC
581389 CGACATTATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAACACCCAACC
Found at i:582822 original size:21 final size:20
Alignment explanation
Indices: 582794--582834 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
582784 ATTGTCATTA
582794 AGTTTCTACTATTACAGAAT
1 AGTTTCTACTATTACAGAAT
* *
582814 AGTTATCTACTTTTATAGAAT
1 AGTT-TCTACTATTACAGAAT
582835 TATTGTTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (20 bp):
AGTTTCTACTATTACAGAAT
Found at i:597228 original size:15 final size:15
Alignment explanation
Indices: 597204--597238 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
597194 GTATCATTAA
*
597204 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
*
597219 ATTAAATTATAAAGT
1 ATTAAATTATAAAAT
597234 ATTAA
1 ATTAA
597239 CCGTATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:597375 original size:24 final size:24
Alignment explanation
Indices: 597315--597381 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 24
597305 AAAAACTAAT
* *
597315 ATTTATAAATATTATATTTTAATTA
1 ATTTATAATTA-TATATTTTAACTA
* * * *
597340 AATTACATTTATATTTTTTAACTA
1 ATTTATAATTATATATTTTAACTA
*
597364 ATTTATAATTATACATTT
1 ATTTATAATTATATATTT
597382 AGTACTTTAT
Statistics
Matches: 31, Mismatches: 11, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
24 24 0.77
25 7 0.23
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTATAATTATATATTTTAACTA
Found at i:601774 original size:21 final size:21
Alignment explanation
Indices: 601741--601897 Score: 167
Period size: 21 Copynumber: 7.5 Consensus size: 21
601731 GTTTCTAGAT
* *
601741 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
*
601762 TCGTAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
601783 TCGCAATGCGAACTTAGACTA
1 TCGCAATGCGAACTTGGACTA
* * *
601804 TTGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* * * *
601824 TCGTAATGTGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
*
601845 TCGCAATGCAAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
601866 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
601887 TCGCAATGCGA
1 TCGCAATGCGA
601898 TAGTCGAAGT
Statistics
Matches: 110, Mismatches: 22, Indels: 8
0.79 0.16 0.06
Matches are distributed among these distances:
20 13 0.12
21 97 0.88
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:602550 original size:16 final size:16
Alignment explanation
Indices: 602525--602571 Score: 78
Period size: 16 Copynumber: 2.9 Consensus size: 16
602515 CGCCGTCCGT
602525 GTCG-GGTCGGGTCGG
1 GTCGTGGTCGGGTCGG
602540 GTCGTGGTCGGGTCGG
1 GTCGTGGTCGGGTCGG
602556 GTCGTGGTCGTGGTCG
1 GTCGTGGTCG-GGTCG
602572 TGGTAATACG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.13
16 21 0.70
17 5 0.17
ACGTcount: A:0.00, C:0.19, G:0.55, T:0.26
Consensus pattern (16 bp):
GTCGTGGTCGGGTCGG
Found at i:602575 original size:6 final size:5
Alignment explanation
Indices: 602525--602571 Score: 67
Period size: 5 Copynumber: 8.8 Consensus size: 5
602515 CGCCGTCCGT
602525 GTCGG GTCGG GTCGG GTCGTG GTCGG GTCGG GTCGTG GTCGTG GTCG
1 GTCGG GTCGG GTCGG GTCG-G GTCGG GTCGG GTCG-G GTCG-G GTCG
602572 TGGTAATACG
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
5 24 0.60
6 16 0.40
ACGTcount: A:0.00, C:0.19, G:0.55, T:0.26
Consensus pattern (5 bp):
GTCGG
Found at i:602624 original size:21 final size:21
Alignment explanation
Indices: 602600--602805 Score: 149
Period size: 21 Copynumber: 9.8 Consensus size: 21
602590 ACATGTCCGC
*
602600 ACGAATTTGGAATAAATCGCA
1 ACGAACTTGGAATAAATCGCA
*
602621 ACGAATTTGGAATAAATCGCA
1 ACGAACTTGGAATAAATCGCA
* *
602642 ACGCGAACTTCGACT--ATCGCA
1 A--CGAACTTGGAATAAATCGCA
602663 ACGAACTTGGAATAAATCGCA
1 ACGAACTTGGAATAAATCGCA
* * * *
602684 ACGCGAGCTTAGACT--ATCACA
1 A--CGAACTTGGAATAAATCGCA
* * *
602705 ACGAATTTGAAATAAATTGCA
1 ACGAACTTGGAATAAATCGCA
* *
602726 ACGCGAACTTCGACT--ATCGCA
1 A--CGAACTTGGAATAAATCGCA
602747 ACGAACTTGGAATAAATCGCA
1 ACGAACTTGGAATAAATCGCA
*
602768 ATGCGAACTTGGACT--ATCGCA
1 A--CGAACTTGGAATAAATCGCA
*
602789 ACGAATTTGGAATAAAT
1 ACGAACTTGGAATAAAT
602806 TACAACGCGA
Statistics
Matches: 143, Mismatches: 26, Indels: 32
0.71 0.13 0.16
Matches are distributed among these distances:
19 37 0.26
21 69 0.48
23 37 0.26
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.22
Consensus pattern (21 bp):
ACGAACTTGGAATAAATCGCA
Found at i:602674 original size:42 final size:42
Alignment explanation
Indices: 602615--602831 Score: 326
Period size: 42 Copynumber: 5.2 Consensus size: 42
602605 TTTGGAATAA
602615 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
* * *
602657 ATCGCAACGAACTTGGAATAAATCGCAACGCGAGCTTAGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
* * *
602699 ATCACAACGAATTTGAAATAAATTGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
* * *
602741 ATCGCAACGAACTTGGAATAAATCGCAATGCGAACTTGGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
** *
602783 ATCGCAACGAATTTGGAATAAATTACAACGCGAACTTGGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
602825 ATCGCAA
1 ATCGCAA
602832 TGCGAATATG
Statistics
Matches: 156, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 156 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (42 bp):
ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:610115 original size:18 final size:18
Alignment explanation
Indices: 610092--610127 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
610082 GTCGGTTAGT
610092 TAAATATATTAACAGTTC
1 TAAATATATTAACAGTTC
*
610110 TAAATATATTAAGAGTTC
1 TAAATATATTAACAGTTC
610128 AATAATGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.39
Consensus pattern (18 bp):
TAAATATATTAACAGTTC
Found at i:610131 original size:16 final size:16
Alignment explanation
Indices: 610089--610131 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
610079 AACGTCGGTT
*
610089 AGTTAAATATATTAAC
1 AGTTCAATATATTAAC
*
610105 AGTTCTAAATATATTAAG
1 AGTTC--AATATATTAAC
610123 AGTTCAATA
1 AGTTCAATA
610132 ATGTGTCACG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 8 0.35
18 15 0.65
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (16 bp):
AGTTCAATATATTAAC
Found at i:613096 original size:32 final size:33
Alignment explanation
Indices: 613059--613123 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
613049 TATTTGAAAA
613059 TTAAAAT-TATATAAACTAATTTTAAATT-AAAT
1 TTAAAATATATA-AAACTAATTTTAAATTCAAAT
* *
613091 TTAAAATATATAAAATTTATTTTAAATTCAAAT
1 TTAAAATATATAAAACTAATTTTAAATTCAAAT
613124 CTAACCAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 21 0.72
33 8 0.28
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (33 bp):
TTAAAATATATAAAACTAATTTTAAATTCAAAT
Found at i:614652 original size:6 final size:6
Alignment explanation
Indices: 614628--614670 Score: 59
Period size: 6 Copynumber: 7.0 Consensus size: 6
614618 TCATACAACT
* *
614628 TTTATA TTATAAA TATATA TTTATA TTTATA TTTATA TTTATA
1 TTTATA TT-TATA TTTATA TTTATA TTTATA TTTATA TTTATA
614671 GATCCGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 28 0.88
7 4 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (6 bp):
TTTATA
Found at i:616987 original size:34 final size:34
Alignment explanation
Indices: 616942--617018 Score: 136
Period size: 34 Copynumber: 2.3 Consensus size: 34
616932 AAATTAATAT
*
616942 GTGAATGTTCAAATTAGAATTAACCTATATTTAC
1 GTGAATATTCAAATTAGAATTAACCTATATTTAC
*
616976 GTGAATATTCAAATTATAATTAACCTATATTTAC
1 GTGAATATTCAAATTAGAATTAACCTATATTTAC
617010 GTGAATATT
1 GTGAATATT
617019 GATGTGTTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.40
Consensus pattern (34 bp):
GTGAATATTCAAATTAGAATTAACCTATATTTAC
Found at i:619726 original size:17 final size:17
Alignment explanation
Indices: 619704--619758 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
619694 CAACGTTATA
*
619704 ATAAATGTAAAGATTTG
1 ATAAATTTAAAGATTTG
* *
619721 ATAAATTTAACGA-TAG
1 ATAAATTTAAAGATTTG
*
619737 -TAAATTTAAAAATTTG
1 ATAAATTTAAAGATTTG
619753 ATAAAT
1 ATAAAT
619759 CTAACGACAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 10 0.33
16 4 0.13
17 16 0.53
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.36
Consensus pattern (17 bp):
ATAAATTTAAAGATTTG
Found at i:619752 original size:32 final size:32
Alignment explanation
Indices: 619705--619765 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
619695 AACGTTATAA
* *
619705 TAAATGTAAAGATTTGATAAATTTAACGATAG
1 TAAATGTAAAAATTTGATAAATCTAACGATAG
*
619737 TAAATTTAAAAATTTGATAAATCTAACGA
1 TAAATGTAAAAATTTGATAAATCTAACGA
619766 CAATTCTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.34
Consensus pattern (32 bp):
TAAATGTAAAAATTTGATAAATCTAACGATAG
Found at i:626174 original size:53 final size:53
Alignment explanation
Indices: 626115--626225 Score: 120
Period size: 53 Copynumber: 2.1 Consensus size: 53
626105 TTTTAATCAA
* ** *
626115 AATATTA-ATTATTAA-AATAT-TTAAAATATATTTATTAATATTTCTAATAATAT
1 AATATTATATTATTAATAATATAATAAAATA-ATCAATT-ATA-TTATAATAATAT
* *
626168 AATATTATATTTTTAATATTATAATAAAATAATCAATTATATTATAATAATAT
1 AATATTATATTATTAATAATATAATAAAATAATCAATTATATTATAATAATAT
626221 AATAT
1 AATAT
626226 AAGATATTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
53 23 0.47
54 10 0.20
55 9 0.18
56 7 0.14
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (53 bp):
AATATTATATTATTAATAATATAATAAAATAATCAATTATATTATAATAATAT
Found at i:626175 original size:26 final size:24
Alignment explanation
Indices: 626113--626175 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
626103 CATTTTAATC
626113 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
626137 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
626160 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
626176 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:626177 original size:22 final size:23
Alignment explanation
Indices: 626147--626193 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
626137 AAAATATATT
626147 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
626170 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
626192 TA
1 TA
626194 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:626232 original size:23 final size:23
Alignment explanation
Indices: 626183--626236 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
626173 TATATTTTTA
**
626183 ATATTATAATAAAATAATCAATT
1 ATATTATAATAAAATAATCAAAG
*
626206 ATATTATAATAATATAAT-ATAAG
1 ATATTATAATAAAATAATCA-AAG
626229 ATATTATA
1 ATATTATA
626237 TTATATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATTATAATAAAATAATCAAAG
Found at i:626299 original size:45 final size:45
Alignment explanation
Indices: 626207--626301 Score: 106
Period size: 45 Copynumber: 2.1 Consensus size: 45
626197 TAATCAATTA
* * *
626207 TATTATAATAATATAATATAAGATATTATATTATATTTTTATTTT
1 TATTATAATAATATAATATAAGATATTATATAAAATTTATATTTT
*
626252 TATTTTAATAATAT-ATAATAA-ATTATTA-ATAAAATTTATATTATT
1 TATTATAATAATATAAT-ATAAGA-TATTATATAAAATTTATATT-TT
626297 TATTA
1 TATTA
626302 ATTTCATAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
44 14 0.33
45 28 0.67
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (45 bp):
TATTATAATAATATAATATAAGATATTATATAAAATTTATATTTT
Found at i:626511 original size:27 final size:26
Alignment explanation
Indices: 626476--626527 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
626466 TATAATTTAT
626476 AATATTTTTATTTCAATAAAA-TATAAC
1 AATATTTTTA-TT-AATAAAACTATAAC
626503 AATATTTTTATTAATAAAACTATAA
1 AATATTTTTATTAATAAAACTATAA
626528 AAACAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 7 0.29
26 7 0.29
27 10 0.42
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (26 bp):
AATATTTTTATTAATAAAACTATAAC
Found at i:626730 original size:15 final size:14
Alignment explanation
Indices: 626692--626742 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
626682 CAAACATCGT
* *
626692 AAAACGTTTTACAG
1 AAAATGTTTTTCAG
626706 AAAATGTTTTTCAG
1 AAAATGTTTTTCAG
*
626720 AAAATATTTTTTCAG
1 AAAAT-GTTTTTCAG
626735 AAAATGTT
1 AAAATGTT
626743 GCTCTTTCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 19 0.59
15 13 0.41
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (14 bp):
AAAATGTTTTTCAG
Found at i:632839 original size:58 final size:59
Alignment explanation
Indices: 632740--632853 Score: 142
Period size: 58 Copynumber: 1.9 Consensus size: 59
632730 TAGCGTGATG
* *
632740 AATGATATAGAACATTTCAAAATTTAAGAACCAATTCAAAATGAG-TCATAATTTAAGA
1 AATGATATAGAACATTTCAAAAATTAAGAACCAATTCAAAATAAGATCATAATTTAAGA
* * * * *
632798 AATGATATAGAATATTTTAAAAATTATAG-ACTAGTTTAAAATAAGATCATAATTTA
1 AATGATATAGAACATTTCAAAAATTA-AGAACCAATTCAAAATAAGATCATAATTTA
632854 GGAACCTTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
58 35 0.74
59 12 0.26
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (59 bp):
AATGATATAGAACATTTCAAAAATTAAGAACCAATTCAAAATAAGATCATAATTTAAGA
Found at i:633945 original size:30 final size:30
Alignment explanation
Indices: 633889--633973 Score: 109
Period size: 30 Copynumber: 2.8 Consensus size: 30
633879 GTATATAACT
* **
633889 TAATTCGGAGCCAAAAC-ATCGTCGTTGTCG
1 TAATTCGGAGCC-AAACTGTCACCGTTGTCG
633919 TAATTCGGAGCCAAACTGTCACCGTTGTCG
1 TAATTCGGAGCCAAACTGTCACCGTTGTCG
* *
633949 GAATTTGGAGCCAAACTGTCACCGT
1 TAATTCGGAGCCAAACTGTCACCGT
633974 CATGACTCGG
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
29 4 0.08
30 45 0.92
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.26
Consensus pattern (30 bp):
TAATTCGGAGCCAAACTGTCACCGTTGTCG
Found at i:635282 original size:31 final size:32
Alignment explanation
Indices: 635247--635320 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
635237 GTTCCAACCA
* *
635247 AAGTCGCATGGCCCT-CCTCGCGTCCCAGCCG
1 AAGTCGCATGGCCCTCCCCCGCATCCCAGCCG
* * *
635278 AAGTCACACGGCCGTCCCCCGCATCCCAGCCG
1 AAGTCGCATGGCCCTCCCCCGCATCCCAGCCG
*
635310 AAGACGCATGG
1 AAGTCGCATGG
635321 TCTTCCATGC
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
31 12 0.35
32 22 0.65
ACGTcount: A:0.19, C:0.43, G:0.26, T:0.12
Consensus pattern (32 bp):
AAGTCGCATGGCCCTCCCCCGCATCCCAGCCG
Found at i:635493 original size:38 final size:39
Alignment explanation
Indices: 635448--635521 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 39
635438 TTTTCCCAAT
** *
635448 CCCCCAAAGATGCATTGAGAGCCATGC-TTTCTCCCCTA
1 CCCCCAAAGACACATTGAGAGCCATGCATCTCTCCCCTA
*
635486 CCCCCAAAGACACATTGGGAGCCATGCATCTCTCCC
1 CCCCCAAAGACACATTGAGAGCCATGCATCTCTCCC
635522 TTGCCATGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 24 0.77
39 7 0.23
ACGTcount: A:0.24, C:0.39, G:0.16, T:0.20
Consensus pattern (39 bp):
CCCCCAAAGACACATTGAGAGCCATGCATCTCTCCCCTA
Found at i:635656 original size:23 final size:21
Alignment explanation
Indices: 635617--635658 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
635607 CAATAACAAC
635617 TGCAAAATACAACAATAATGT
1 TGCAAAATACAACAATAATGT
*
635638 TGCAATAATAGCATCAATAAT
1 TGCAA-AATA-CAACAATAAT
635659 AAGGGTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 4 0.22
23 9 0.50
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (21 bp):
TGCAAAATACAACAATAATGT
Found at i:635786 original size:21 final size:19
Alignment explanation
Indices: 635753--635795 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
635743 GGGCATCGGA
*
635753 AAGAAGAAAGAAAGAAAGG
1 AAGAAGAAAGAAAGAAAAG
635772 AAGAAGAGGAAGAAAGAAAAG
1 AAGAAGA--AAGAAAGAAAAG
635793 AAG
1 AAG
635796 GATAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
21 14 0.67
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (19 bp):
AAGAAGAAAGAAAGAAAAG
Found at i:636079 original size:18 final size:18
Alignment explanation
Indices: 636026--636079 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 18
636016 AGCGATGATG
*
636026 TTATTATTATTTAATAAA
1 TTATTATTATTAAATAAA
* *
636044 ATATCATTATTTGAAAATAAA
1 TTATTATTA-TT--AAATAAA
636065 TTATTATTATTAAAT
1 TTATTATTATTAAAT
636080 TGTAGAAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
18 11 0.39
19 2 0.07
20 2 0.07
21 13 0.46
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
TTATTATTATTAAATAAA
Found at i:637116 original size:5 final size:5
Alignment explanation
Indices: 637035--637113 Score: 131
Period size: 5 Copynumber: 15.8 Consensus size: 5
637025 AGCAAAAATA
637035 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
* * *
637085 ATATG ATATG ATATA ATATA ATATA ATAT
1 ATATG ATATG ATATG ATATG ATATG ATAT
637114 AATTTATTTT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
5 73 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (5 bp):
ATATG
Found at i:637821 original size:21 final size:21
Alignment explanation
Indices: 637795--637895 Score: 84
Period size: 21 Copynumber: 4.9 Consensus size: 21
637785 AATTAGTTCC
637795 AAGAATCGCAACGCGATTATG
1 AAGAATCGCAACGCGATTATG
*
637816 AAGAATCGCAATGCGA-TA-G
1 AAGAATCGCAACGCGATTATG
** * *
637835 TACA-AATTCGCATTGCGATTTTC
1 -A-AGAA-TCGCAACGCGATTATG
* *
637858 CAGAATCGCAACGCGAATATG
1 AAGAATCGCAACGCGATTATG
637879 AA-AATCGCAACGCGATT
1 AAGAATCGCAACGCGATT
637896 CTGACTATCG
Statistics
Matches: 62, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
19 1 0.02
20 19 0.31
21 39 0.63
22 3 0.05
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (21 bp):
AAGAATCGCAACGCGATTATG
Found at i:637886 original size:20 final size:20
Alignment explanation
Indices: 637861--638116 Score: 214
Period size: 20 Copynumber: 12.7 Consensus size: 20
637851 GATTTTCCAG
** *
637861 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
* *
637881 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATCCGTA
* * *
637900 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATCCGT-A
*
637922 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
637942 AATCGCAACGAC-AATACATAA
1 AATCGCAACG-CGAATCCGT-A
* *
637963 AATCACAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
637983 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
638003 AATCGCAATGC-ATATCTGTA
1 AATCGCAACGCGA-ATCCGTA
* *
638023 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
638043 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
638063 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
*
638084 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
638104 AATCGCAACGCGA
1 AATCGCAACGCGA
638117 TCGATAATTC
Statistics
Matches: 187, Mismatches: 38, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.01
20 134 0.72
21 50 0.27
22 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:638024 original size:40 final size:41
Alignment explanation
Indices: 637861--638113 Score: 327
Period size: 41 Copynumber: 6.2 Consensus size: 41
637851 GATTTTCCAG
* * *
637861 AATCGCAACGCGAATATG-AAAATCGCAACGCG-ATTC-TGA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGT-A
* * *
637900 CTATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTA
1 -AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
* * *
637942 AATCGCAACGACAATACATAAAATCACAACGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
* * *
637983 AATCGCAACGAGAATACGT-AAATCGCAATGCATATCTGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
*
638023 AATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
*
638063 AATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
638104 AATCGCAACG
1 AATCGCAACG
638114 CGATCGATAA
Statistics
Matches: 187, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
40 86 0.46
41 96 0.51
42 4 0.02
43 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
Found at i:638214 original size:21 final size:21
Alignment explanation
Indices: 638185--638231 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
638175 ATTCTGACTA
638185 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
638206 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
638227 TCGCA
1 TCGCA
638232 ACGCGAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:638300 original size:82 final size:80
Alignment explanation
Indices: 638165--638314 Score: 180
Period size: 82 Copynumber: 1.8 Consensus size: 80
638155 GTTTCCAGAT
* * * **
638165 TCGCAACGCGATTCTGACTATCGCATTGCGATTTCCCAAATTCGCGTTGCGATTTTCCT-AATTC
1 TCGCAACGAGATTCTGACTATCGCAATACGATTT-CCAAATTCGCACTGCGA-TTT-CTGAATTC
638229 GCAACGCGAATACGTAAA
63 GCAACGCGAATACGTAAA
638247 TCGCAACGAGATTCTGACTATCGCAATACTGAATTT-CAAATTCGCAACT-CGATTTCTGAATTC
1 TCGCAACGAGATTCTGACTATCGCAATAC-G-ATTTCCAAATTCGC-ACTGCGATTTCTGAATTC
638310 GCAAC
63 GCAAC
638315 AGGTTTTAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
80 2 0.03
81 13 0.22
82 38 0.64
83 2 0.03
84 4 0.07
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (80 bp):
TCGCAACGAGATTCTGACTATCGCAATACGATTTCCAAATTCGCACTGCGATTTCTGAATTCGCA
ACGCGAATACGTAAA
Found at i:639140 original size:24 final size:24
Alignment explanation
Indices: 639113--639166 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
639103 GTATTCGAAA
639113 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* * *
639137 TTTGTTCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
639161 TTTGAT
1 TTTGAT
639167 GATTTTGCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:639375 original size:15 final size:14
Alignment explanation
Indices: 639357--639392 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
639347 GAAAAAGAAG
639357 AAGAATAAATCCCCA
1 AAGAA-AAATCCCCA
*
639372 AAGAAAAGTCCCCA
1 AAGAAAAATCCCCA
639386 AAGAAAA
1 AAGAAAA
639393 TGCCACGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.58, C:0.22, G:0.11, T:0.08
Consensus pattern (14 bp):
AAGAAAAATCCCCA
Found at i:641622 original size:20 final size:21
Alignment explanation
Indices: 641597--641705 Score: 129
Period size: 20 Copynumber: 5.4 Consensus size: 21
641587 CAACGCGGAA
641597 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAATATGACT
*
641617 ATCGCAACACGGAA-ATGACT
1 ATCGCAACGCGGAATATGACT
* *
641637 ATCTCAATGCGGAAT-TGACT
1 ATCGCAACGCGGAATATGACT
*
641657 ATCGTAACGCGGAA-ATGACT
1 ATCGCAACGCGGAATATGACT
* *
641677 ATCGAAACGC-GAAAATGACT
1 ATCGCAACGCGGAATATGACT
641697 ATCGCAACG
1 ATCGCAACG
641706 AGAATGCGAT
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
19 3 0.04
20 70 0.92
21 3 0.04
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGGAATATGACT
Found at i:641696 original size:40 final size:40
Alignment explanation
Indices: 641597--641705 Score: 146
Period size: 40 Copynumber: 2.7 Consensus size: 40
641587 CAACGCGGAA
* *
641597 ATCGCAACGCGAATATGACTATCGCAACACGGAAATGACT
1 ATCGCAACGCGAAAATGACTATCGCAACGCGGAAATGACT
* * * * *
641637 ATCTCAATGCGGAATTGACTATCGTAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACTATCGCAACGCGGAAATGACT
*
641677 ATCGAAACGCGAAAATGACTATCGCAACG
1 ATCGCAACGCGAAAATGACTATCGCAACG
641706 AGAATGCGAT
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (40 bp):
ATCGCAACGCGAAAATGACTATCGCAACGCGGAAATGACT
Found at i:641747 original size:19 final size:19
Alignment explanation
Indices: 641723--641854 Score: 131
Period size: 19 Copynumber: 7.4 Consensus size: 19
641713 GATTCACTCG
641723 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
641742 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
641756 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
641775 TTGCAATTTTTCATTTTGCA
1 TTGCGA-TTTTCATTTCGCA
*
641795 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
**
641809 TTGCGATAGTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
641828 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
641847 TTGCGATT
1 TTGCGATT
641855 CTCTCGTTGC
Statistics
Matches: 91, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
14 12 0.13
16 12 0.13
17 14 0.15
19 36 0.40
20 17 0.19
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Done.