Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007957.1 Hibiscus syriacus cultivar Beakdansim tig00110384_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: 8646418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 28 of 43
Found at i:5665318 original size:22 final size:22
Alignment explanation
Indices: 5665287--5665336 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
5665277 ATAATGCATA
*
5665287 TATATTATAT-ATTTTCAAAAAC
1 TATATAATATGATTTT-AAAAAC
* *
5665309 TATATAATATGCTTTTAAAAAT
1 TATATAATATGATTTTAAAAAC
5665331 TATATA
1 TATATA
5665337 TATTATCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (22 bp):
TATATAATATGATTTTAAAAAC
Found at i:5665338 original size:26 final size:26
Alignment explanation
Indices: 5665309--5665386 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 26
5665299 TTTCAAAAAC
5665309 TATATAATATGCTTTTAAAAATTATA
1 TATATAATATGCTTTTAAAAATTATA
** *
5665335 TATAT--TAT-CAATAAAAAATTATA
1 TATATAATATGCTTTTAAAAATTATA
5665358 TAT-TATATATG-TTTTCAAAAATTATA
1 TATATA-ATATGCTTTT-AAAAATTATA
5665384 TAT
1 TAT
5665387 TTTAAAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
22 1 0.02
23 15 0.37
24 3 0.07
25 4 0.10
26 18 0.44
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (26 bp):
TATATAATATGCTTTTAAAAATTATA
Found at i:5665383 original size:19 final size:19
Alignment explanation
Indices: 5665359--5665446 Score: 72
Period size: 19 Copynumber: 4.5 Consensus size: 19
5665349 AAAATTATAT
*
5665359 ATTATATATGTTTTCAAAA
1 ATTATATATATTTTCAAAA
*
5665378 A-T-TATATATTTTAAAAA
1 ATTATATATATTTTCAAAA
* *
5665395 ATAATATATATATTCAAAA
1 ATTATATATATTTTCAAAA
*
5665414 CCTATATATCATATATTTTCTAAA
1 ---AT-TAT-ATATATTTTCAAAA
5665438 ATTATATAT
1 ATTATATAT
5665447 TATATATATT
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
17 14 0.26
18 1 0.02
19 18 0.33
20 3 0.06
21 2 0.04
22 2 0.04
23 2 0.04
24 12 0.22
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (19 bp):
ATTATATATATTTTCAAAA
Found at i:5665387 original size:47 final size:49
Alignment explanation
Indices: 5665315--5665408 Score: 126
Period size: 49 Copynumber: 2.0 Consensus size: 49
5665305 AAACTATATA
5665315 ATATGCTTTTAAAAATTATATATATTATCAATAAAA-AAT-TATATATTAT
1 ATATGCTTTTAAAAATTATATATATT-TCAA-AAAATAATATATATATTAT
5665364 ATATG-TTTTCAAAAATTATATAT-TTT-AAAAAATAATATATATATT
1 ATATGCTTTT-AAAAATTATATATATTTCAAAAAATAATATATATATT
5665409 CAAAACCTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
45 4 0.10
46 5 0.12
47 9 0.21
48 6 0.14
49 18 0.43
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (49 bp):
ATATGCTTTTAAAAATTATATATATTTCAAAAAATAATATATATATTAT
Found at i:5665389 original size:17 final size:18
Alignment explanation
Indices: 5665361--5665413 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
5665351 AATTATATAT
*
5665361 TATATATGTTTTCAAAAA
1 TATATATATTTTCAAAAA
*
5665379 T-TATATATTTTAAAAAA
1 TATATATATTTTCAAAAA
*
5665396 TAATATATATATTCAAAA
1 T-ATATATATTTTCAAAA
5665414 CCTATATATC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 15 0.52
18 1 0.03
19 13 0.45
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
TATATATATTTTCAAAAA
Found at i:5665428 original size:26 final size:24
Alignment explanation
Indices: 5665398--5665481 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 24
5665388 TTAAAAAATA
5665398 ATATATATATTCAAAACCTATATATC
1 ATATATAT-TTCAAAA-CTATATATC
* *
5665424 ATATAT-TTTCTAAAATTATATATT
1 ATATATATTTC-AAAACTATATATC
* *
5665448 ATATATATTTTCAAAAATTTATATAC
1 ATATATA-TTTCAAAACTATATAT-C
5665474 AT-TATATT
1 ATATATATT
5665482 ATATAAATAC
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
24 18 0.37
25 19 0.39
26 12 0.24
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATATATTTCAAAACTATATATC
Found at i:5665429 original size:24 final size:24
Alignment explanation
Indices: 5665380--5665456 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
5665370 TTTCAAAAAT
* *
5665380 TATATATTTTAAAA-AATA-AT-A
1 TATATATTCTAAAACTATATATCA
5665401 TATATATTC-AAAACCTATATATCA
1 TATATATTCTAAAA-CTATATATCA
* * *
5665425 TATATTTTCTAAAATTATATATTA
1 TATATATTCTAAAACTATATATCA
5665449 TATATATT
1 TATATATT
5665457 TTCAAAAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 4 0.09
21 8 0.18
22 3 0.07
23 2 0.04
24 24 0.53
25 4 0.09
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (24 bp):
TATATATTCTAAAACTATATATCA
Found at i:5665479 original size:27 final size:26
Alignment explanation
Indices: 5665395--5665480 Score: 74
Period size: 26 Copynumber: 3.4 Consensus size: 26
5665385 ATTTTAAAAA
**
5665395 ATAATATATATA--TTCAAAACCTAT
1 ATAATATATATATTTTCAAAAATTAT
* *
5665419 AT-AT-CATATATTTTCTAAAATTAT
1 ATAATATATATATTTTCAAAAATTAT
*
5665443 ATATTATATATATTTTCAAAAATTTAT
1 ATAATATATATATTTTCAAAAA-TTAT
5665470 ATACAT-TATAT
1 ATA-ATATATAT
5665481 TATATAAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
22 5 0.10
23 2 0.04
24 13 0.27
25 1 0.02
26 14 0.29
27 12 0.25
28 1 0.02
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (26 bp):
ATAATATATATATTTTCAAAAATTAT
Found at i:5666988 original size:21 final size:21
Alignment explanation
Indices: 5666950--5666999 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
5666940 AAAAAATTCA
* * *
5666950 GATATCCAAAAATTCGGATCG
1 GATATCCGAAAATCCGGATCC
*
5666971 GATATCCGAATATCCGGATCC
1 GATATCCGAAAATCCGGATCC
5666992 GA-ATCCGA
1 GATATCCGA
5667000 TTTTTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (21 bp):
GATATCCGAAAATCCGGATCC
Found at i:5667100 original size:21 final size:21
Alignment explanation
Indices: 5667055--5667100 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
5667045 TTAATCAACA
*
5667055 TAAAATTAAAAGTTTAAGTAT
1 TAAAATTAAAAGTTTAAGTAC
5667076 TAAAATTAATAA-TTT-AGATAC
1 TAAAATTAA-AAGTTTAAG-TAC
5667097 TAAA
1 TAAA
5667101 TGCGTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 2 0.09
21 18 0.82
22 2 0.09
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (21 bp):
TAAAATTAAAAGTTTAAGTAC
Found at i:5668881 original size:14 final size:14
Alignment explanation
Indices: 5668848--5668886 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
5668838 ATCCGAATTT
5668848 TCGGATCGGA-TCA
1 TCGGATCGGATTCA
* *
5668861 ACGGATCGGATTGA
1 TCGGATCGGATTCA
5668875 TCGGATCGGATT
1 TCGGATCGGATT
5668887 TTTTTGCACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (14 bp):
TCGGATCGGATTCA
Found at i:5669122 original size:7 final size:7
Alignment explanation
Indices: 5669110--5669135 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5669100 CGGGTTACCC
5669110 TTAATAT
1 TTAATAT
5669117 TTAATAT
1 TTAATAT
5669124 TTAATAT
1 TTAATAT
5669131 TTAAT
1 TTAAT
5669136 TTTTCAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTAATAT
Found at i:5670282 original size:23 final size:23
Alignment explanation
Indices: 5670241--5670302 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
5670231 TATATATTAA
*
5670241 TTTTGTAGTAATTTAATTTTT-AT
1 TTTTGTA-TATTTTAATTTTTCAT
*
5670264 TTTTAGTAT-TTTTATATTTTTCCT
1 TTTT-GTATATTTTA-ATTTTTCAT
5670288 TTTTGTATATTTTAA
1 TTTTGTATATTTTAA
5670303 ATAATTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
22 4 0.12
23 16 0.48
24 13 0.39
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.68
Consensus pattern (23 bp):
TTTTGTATATTTTAATTTTTCAT
Found at i:5670477 original size:21 final size:21
Alignment explanation
Indices: 5670418--5670477 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
5670408 ATTGTAGATC
* *
5670418 ATTACATTAATATCGTAAATT
1 ATTACATTAATATCATAAAAT
*
5670439 ATTGCATTAATA-CTATAAAAT
1 ATTACATTAATATC-ATAAAAT
*
5670460 ATTACGTTAATATCATAA
1 ATTACATTAATATCATAA
5670478 TGGTCAACGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (21 bp):
ATTACATTAATATCATAAAAT
Found at i:5670794 original size:8 final size:8
Alignment explanation
Indices: 5670777--5670810 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
5670767 TTAACTTTCC
*
5670777 TCTCTGTT
1 TCTCTATT
5670785 TCTCTATT
1 TCTCTATT
5670793 TCTCTATT
1 TCTCTATT
5670801 TCTCTATT
1 TCTCTATT
5670809 TC
1 TC
5670811 ATCCTTAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.09, C:0.26, G:0.03, T:0.62
Consensus pattern (8 bp):
TCTCTATT
Found at i:5680587 original size:33 final size:33
Alignment explanation
Indices: 5680539--5680601 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
5680529 AAAGTCTAGT
* *
5680539 TACTAATTTGTTAATAGATAATAAGAAAATTAC
1 TACTAATTTGTTAATAAATAACAAGAAAATTAC
* *
5680572 TACTTATTTTTTAATAAATAACAAGAAAAT
1 TACTAATTTGTTAATAAATAACAAGAAAAT
5680602 ATTAAATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (33 bp):
TACTAATTTGTTAATAAATAACAAGAAAATTAC
Found at i:5687239 original size:25 final size:26
Alignment explanation
Indices: 5687198--5687246 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
5687188 AACATATAAG
*
5687198 TTCACACATCCATAAATCCAAACAAA
1 TTCACACATCCACAAATCCAAACAAA
*
5687224 TTCACA-ATCCACAAATTCAAACA
1 TTCACACATCCACAAATCCAAACA
5687247 TTCCAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (26 bp):
TTCACACATCCACAAATCCAAACAAA
Found at i:5695469 original size:22 final size:22
Alignment explanation
Indices: 5695444--5695485 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5695434 TACGTTTCAG
5695444 CTAGGGTAAGACCTTATGGACC
1 CTAGGGTAAGACCTTATGGACC
*
5695466 CTAGGGTAAGTCCTTATGGA
1 CTAGGGTAAGACCTTATGGA
5695486 TGCAGTTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (22 bp):
CTAGGGTAAGACCTTATGGACC
Found at i:5697211 original size:2 final size:2
Alignment explanation
Indices: 5697204--5697255 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
5697194 TATGTTATGA
5697204 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
5697246 AT AT AT AT AT
1 AT AT AT AT AT
5697256 TATGTGAAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5697724 original size:23 final size:23
Alignment explanation
Indices: 5697698--5697800 Score: 107
Period size: 23 Copynumber: 4.4 Consensus size: 23
5697688 GAGTCGAAGG
*
5697698 TTCTATGCGGTCCTTCGGGACAA
1 TTCTATGTGGTCCTTCGGGACAA
5697721 TTCTATGTGGTCCTTCGGGACAAA
1 TTCTATGTGGTCCTTCGGGAC-AA
* * * *
5697745 TTCTACGTGGTCCTTTGGGATAT
1 TTCTATGTGGTCCTTCGGGACAA
* *** *
5697768 TTTTACAAGGTCCTTCGGGACAT
1 TTCTATGTGGTCCTTCGGGACAA
5697791 TTCTATGTGG
1 TTCTATGTGG
5697801 CACTTCAATG
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
23 45 0.69
24 20 0.31
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.37
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCGGGACAA
Found at i:5702598 original size:18 final size:18
Alignment explanation
Indices: 5702572--5702606 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5702562 TCGAAAGGAC
*
5702572 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
5702590 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
5702607 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:5706274 original size:2 final size:2
Alignment explanation
Indices: 5706267--5706295 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5706257 ATGGGTAGAT
5706267 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5706296 CCACTTAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5707405 original size:24 final size:24
Alignment explanation
Indices: 5707373--5707421 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
5707363 GACATTCTAC
5707373 TTTGACCATGACTTTATGATTATG
1 TTTGACCATGACTTTATGATTATG
5707397 TTTGACCATGACTTTATGATTATG
1 TTTGACCATGACTTTATGATTATG
5707421 T
1 T
5707422 CAATAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.47
Consensus pattern (24 bp):
TTTGACCATGACTTTATGATTATG
Found at i:5712009 original size:70 final size:70
Alignment explanation
Indices: 5711876--5712008 Score: 169
Period size: 70 Copynumber: 1.9 Consensus size: 70
5711866 AAATGACCAT
* * * **
5711876 AAACATTATTAGGCACTACCGATTTTATTATTATTGGGCGTTTTAACCGGATTTTTAAAAAAATA
1 AAACATTATTAGGCACTACCGATTTTATTATTATTGGACCTTTTAACCGGAATGCTAAAAAAATA
5711941 ATCGG
66 ATCGG
* * *
5711946 AAACATTATTAGGCGCTACCGATTTTATTATTCTTGGACACTTTT-ATCGGAAATGCTAAAAAA
1 AAACATTATTAGGCACTACCGATTTTATTATTATTGGAC-CTTTTAACCGG-AATGCTAAAAAA
5712009 TGATGTTTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
70 40 0.75
71 13 0.25
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (70 bp):
AAACATTATTAGGCACTACCGATTTTATTATTATTGGACCTTTTAACCGGAATGCTAAAAAAATA
ATCGG
Found at i:5713024 original size:91 final size:91
Alignment explanation
Indices: 5712869--5713253 Score: 519
Period size: 91 Copynumber: 4.2 Consensus size: 91
5712859 ATACCTTAAC
* * **
5712869 TCATAATGAGAAGAACTTGTTCAACCTCAACTCAGCATTTCCAACGGAGAGTTCATAATGAGAAG
1 TCATAATGAGAAGAACTTGTTCAACCTTAGCTCAGCATTTCCAGTGGAGAGTTCATAATGAGAAG
* *
5712934 AACTCGTCCAACGAGAGAGAAGAAGT
66 AACTCATCCAACGAGAGAGAAAAAGT
* * * *
5712960 TCATAATAAGAAGAACTTGTTCAACCTTGGTTCAAG-ATTTCCAGTGGAGAATTCATAATGAGAA
1 TCATAATGAGAAGAACTTGTTCAACCTTAGCTC-AGCATTTCCAGTGGAGAGTTCATAATGAGAA
5713024 GAACTCATCCAACGAG-GA-AGAAAAGT
65 GAACTCATCCAACGAGAGAGA-AAAAGT
* *
5713050 TCATAATGAGAAGAAATTGTTCAATCTTAGCTCAGCATTTCCAGTGGAGAGTTCATAATGAGAAG
1 TCATAATGAGAAGAACTTGTTCAACCTTAGCTCAGCATTTCCAGTGGAGAGTTCATAATGAGAAG
* *
5713115 AACTCATCCAACGAGGGAGAAAAAAT
66 AACTCATCCAACGAGAGAGAAAAAGT
* **
5713141 TCATAATGAGAAGAATTTGTTCAACCTTAGCTCAGCATTTCCA-ACGATGAGTTCATAATGAGAA
1 TCATAATGAGAAGAACTTGTTCAACCTTAGCTCAGCATTTCCAGTGGA-GAGTTCATAATGAGAA
*
5713205 GAACTCGTCCAACGA-AGGAGAAAAAGT
65 GAACTCATCCAACGAGA-GAGAAAAAGT
* *
5713232 TAATAATGAGAAGAATTTGTTC
1 TCATAATGAGAAGAACTTGTTC
5713254 CTTCTGGCTC
Statistics
Matches: 262, Mismatches: 25, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
89 3 0.01
90 80 0.31
91 176 0.67
92 3 0.01
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.24
Consensus pattern (91 bp):
TCATAATGAGAAGAACTTGTTCAACCTTAGCTCAGCATTTCCAGTGGAGAGTTCATAATGAGAAG
AACTCATCCAACGAGAGAGAAAAAGT
Found at i:5713183 original size:181 final size:182
Alignment explanation
Indices: 5712869--5713253 Score: 535
Period size: 181 Copynumber: 2.1 Consensus size: 182
5712859 ATACCTTAAC
*
5712869 TCATAATGAGAAGAACTTGTTCAACCTCAACTCAGCATTTCCAACGGAGAGTTCATAATGAGAAG
1 TCATAATGAGAAGAAATTGTTCAACCTCAACTCAGCATTTCCAACGGAGAGTTCATAATGAGAAG
* * * * *
5712934 AACTCGTCCAACGAGAGAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTGGTTCAAGATT
66 AACTCATCCAACGAGAGAGAAAAAATTCATAATAAGAAGAACTTGTTCAACCTTAGCTCAAGATT
**
5712999 TCCAGTGGA-GAATTCATAATGAGAAGAACTCATCCAACG-AGGA-AGAAAAGT
131 TCCA-ACGATGAATTCATAATGAGAAGAACTCATCCAACGAAGGAGA-AAAAGT
* * * **
5713050 TCATAATGAGAAGAAATTGTTCAATCTTAGCTCAGCATTTCCAGTGGAGAGTTCATAATGAGAAG
1 TCATAATGAGAAGAAATTGTTCAACCTCAACTCAGCATTTCCAACGGAGAGTTCATAATGAGAAG
* * *
5713115 AACTCATCCAACGAGGGAGAAAAAATTCATAATGAGAAGAATTTGTTCAACCTTAGCTC-AGCAT
66 AACTCATCCAACGAGAGAGAAAAAATTCATAATAAGAAGAACTTGTTCAACCTTAGCTCAAG-AT
* *
5713179 TTCCAACGATGAGTTCATAATGAGAAGAACTCGTCCAACGAAGGAGAAAAAGT
130 TTCCAACGATGAATTCATAATGAGAAGAACTCATCCAACGAAGGAGAAAAAGT
* *
5713232 TAATAATGAGAAGAATTTGTTC
1 TCATAATGAGAAGAAATTGTTC
5713254 CTTCTGGCTC
Statistics
Matches: 180, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
180 4 0.02
181 145 0.81
182 30 0.17
183 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.24
Consensus pattern (182 bp):
TCATAATGAGAAGAAATTGTTCAACCTCAACTCAGCATTTCCAACGGAGAGTTCATAATGAGAAG
AACTCATCCAACGAGAGAGAAAAAATTCATAATAAGAAGAACTTGTTCAACCTTAGCTCAAGATT
TCCAACGATGAATTCATAATGAGAAGAACTCATCCAACGAAGGAGAAAAAGT
Found at i:5713430 original size:98 final size:96
Alignment explanation
Indices: 5713260--5713510 Score: 339
Period size: 98 Copynumber: 2.6 Consensus size: 96
5713250 GTTCCTTCTG
* *
5713260 GCTCATCCATCGCATACAGAGTTGGATC-A-A-CATC-ACAGTGTCATTCTTTCTCGATTCCATC
1 GCTCATCCATCGCATACAGAGTTGGATCAACATCATCAACATTGTCATTCTTGCTCGATTCCATC
* * * *
5713321 ACATACGGAGTTGGAACAGCACCAATGCTTC
66 ACATACAGAGTTGGAACAACACCAATACATC
* * *
5713352 GCTCAAATCCATCACATACGGAGTTGGATCAACATCATCAACATTGTCATTCTTGCTCAATTCCA
1 GCTC--ATCCATCGCATACAGAGTTGGATCAACATCATCAACATTGTCATTCTTGCTCGATTCCA
*
5713417 TCACATACAGAGTTGGAACAACACCAATACATG
64 TCACATACAGAGTTGGAACAACACCAATACATC
* * *
5713450 GCTCATCCATCGCATACTGAGTTGGATCAACGTCATCAACATTGTCATTCTCGCTCGATTC
1 GCTCATCCATCGCATACAGAGTTGGATCAACATCATCAACATTGTCATTCTTGCTCGATTC
5713511 ATCGCTTATG
Statistics
Matches: 138, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
92 4 0.03
94 22 0.16
95 1 0.01
96 53 0.38
97 4 0.03
98 54 0.39
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (96 bp):
GCTCATCCATCGCATACAGAGTTGGATCAACATCATCAACATTGTCATTCTTGCTCGATTCCATC
ACATACAGAGTTGGAACAACACCAATACATC
Found at i:5720070 original size:88 final size:88
Alignment explanation
Indices: 5719971--5720137 Score: 298
Period size: 88 Copynumber: 1.9 Consensus size: 88
5719961 AACATTAAAA
* *
5719971 AATAAAATGCATACATGTATTTGATAATAAATGAGTTATAATTTTAAAATAATTATATACAGATT
1 AATAAAATGCATACATGTATTTGATAATAAATGAGTTATAAATTTAAAATAATTATATAAAGATT
5720036 ATTTAATTAAAAAATAAAGACAT
66 ATTTAATTAAAAAATAAAGACAT
* *
5720059 AATAAAGTGCATACATGTATTTGATAATAAATGAGTTATAAATTTAAAATAATTATATAAAGGTT
1 AATAAAATGCATACATGTATTTGATAATAAATGAGTTATAAATTTAAAATAATTATATAAAGATT
5720124 ATTTAATTAAAAAA
66 ATTTAATTAAAAAA
5720138 ATTATTATAA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 75 1.00
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.37
Consensus pattern (88 bp):
AATAAAATGCATACATGTATTTGATAATAAATGAGTTATAAATTTAAAATAATTATATAAAGATT
ATTTAATTAAAAAATAAAGACAT
Found at i:5720125 original size:28 final size:29
Alignment explanation
Indices: 5720093--5720147 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
5720083 TAATAAATGA
*
5720093 GTTA-TAAATTTAAAATAATTA-TATAAAG
1 GTTATTAAA-TTAAAAAAATTATTATAAAG
*
5720121 GTTATTTAATTAAAAAAATTATTATAA
1 GTTATTAAATTAAAAAAATTATTATAA
5720148 GTTATAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (29 bp):
GTTATTAAATTAAAAAAATTATTATAAAG
Found at i:5721923 original size:21 final size:21
Alignment explanation
Indices: 5721861--5721911 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
5721851 AACATCATGG
5721861 AAGTTTCGAAACTATGACCCA
1 AAGTTTCGAAACTATGACCCA
5721882 AAGTTTCGAAACTATGACCCA
1 AAGTTTCGAAACTATGACCCA
5721903 AAGTTTCGA
1 AAGTTTCGA
5721912 TACTCTTGCC
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:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (21 bp):
AAGTTTCGAAACTATGACCCA
Found at i:5729252 original size:21 final size:23
Alignment explanation
Indices: 5729220--5729261 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
5729210 CTTCAACTTG
5729220 AAGATGGGAGAAGAA-ATGAGAA
1 AAGATGGGAGAAGAAGATGAGAA
5729242 AAGAT-GGAGAAGAAGATGAG
1 AAGATGGGAGAAGAAGATGAG
5729262 TTTTTGGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.52, C:0.00, G:0.38, T:0.10
Consensus pattern (23 bp):
AAGATGGGAGAAGAAGATGAGAA
Found at i:5729257 original size:12 final size:12
Alignment explanation
Indices: 5729219--5729259 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
5729209 CCTTCAACTT
5729219 GAAGATGGGAGAA
1 GAAGAT-GGAGAA
5729232 GAA-AT-GAGAA
1 GAAGATGGAGAA
5729242 -AAGATGGAGAA
1 GAAGATGGAGAA
5729253 GAAGATG
1 GAAGATG
5729260 AGTTTTTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
9 2 0.08
10 7 0.28
11 5 0.20
12 8 0.32
13 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.39, T:0.10
Consensus pattern (12 bp):
GAAGATGGAGAA
Found at i:5729641 original size:16 final size:15
Alignment explanation
Indices: 5729607--5729644 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
5729597 AAATTTACCA
*
5729607 AATTTT-ATTAAATT
1 AATTTTAATTAAAAT
5729621 AATTTTAATTCAAAAT
1 AATTTTAATT-AAAAT
5729637 AATTTTAA
1 AATTTTAA
5729645 AAATTTAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 3 0.14
16 12 0.57
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTTTAATTAAAAT
Found at i:5729996 original size:13 final size:14
Alignment explanation
Indices: 5729976--5730009 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5729966 CATTATTTTA
5729976 TATAATA-TTTATT
1 TATAATATTTTATT
*
5729989 TTTAATATTTTATT
1 TATAATATTTTATT
5730003 TATAATA
1 TATAATA
5730010 ATATTTTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATAATATTTTATT
Found at i:5730011 original size:17 final size:16
Alignment explanation
Indices: 5729972--5730017 Score: 62
Period size: 17 Copynumber: 3.0 Consensus size: 16
5729962 ACGTCATTAT
5729972 TTTATATAATA-TTTA
1 TTTATATAATATTTTA
5729987 TTT-T-TAATATTTTA
1 TTTATATAATATTTTA
5730001 TTTATAATAATATTTTA
1 TTTAT-ATAATATTTTA
5730018 ACTAAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 5 0.19
14 8 0.30
15 4 0.15
17 10 0.37
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTATATAATATTTTA
Found at i:5734820 original size:76 final size:76
Alignment explanation
Indices: 5734300--5735065 Score: 1281
Period size: 75 Copynumber: 10.4 Consensus size: 76
5734290 AGGTCTTAAC
* * *
5734300 AAACATCATGCACTGAAGG-CTTACAGATGA-CCGAAGG-TTTGAAAA-ATCAAAACGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
5734361 AGGCTTTTTGA
66 AGGCTTTTTGG
5734372 AAACATCATGCACTGTAGGACTTACAGATGA-CCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
5734436 AGGCTTTTTGG
66 AGGCTTTTTGG
*
5734447 AAACATCATGCACTGTAGG---T--AGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
5734507 AGGCTTTTTGG
66 AGGCTTTTTGG
*
5734518 AAACATCATGCACTGTAGGACTTACAGATGGCCCTAAGGCTTTGAAAACATCAAAAA--TCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
5734581 AGGC-TTTTGG
66 AGGCTTTTTGG
5734591 -AACATCATGCA-TGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT--CGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
5734652 AGGCTTTTTGG
66 AGGCTTTTTGG
5734663 -AACATCATGCACTGTAGGACTTAC--ATGACCCTAAGGCTTTGAAAACATCAAAAAGCT-CCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
5734724 AGGCTTTTTGG
66 AGGCTTTTTGG
*
5734735 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCGAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
5734800 AGGCTTTTTGG
66 AGGCTTTTTGG
*
5734811 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCGAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
5734876 AGGCTTTTTGG
66 AGGCTTTTTGG
5734887 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGG-TTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
5734951 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
5734962 AAACATCATGCACTGTAGGACTTACAGATGGCCCTAAGGCTTTGAAAACATCAAAAATCT-CCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
5735026 AGGCTTTTTGG
66 AGGCTTTTTGG
5735037 AAACATCATGCACTGTAGGACTTACAGAT
1 AAACATCATGCACTGTAGGACTTACAGAT
5735066 TTGGAAACAT
Statistics
Matches: 663, Mismatches: 12, Indels: 35
0.93 0.02 0.05
Matches are distributed among these distances:
70 6 0.01
71 145 0.22
72 61 0.09
73 60 0.09
74 19 0.03
75 193 0.29
76 179 0.27
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:5735072 original size:33 final size:33
Alignment explanation
Indices: 5735032--5735095 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
5735022 CCGAAGGCTT
5735032 TTTGGAAACATCATGCACTGTAGGACTTACAGA
1 TTTGGAAACATCATGCACTGTAGGACTTACAGA
5735065 TTTGGAAACATCATGCACTGTAGGACTTACA
1 TTTGGAAACATCATGCACTGTAGGACTTACA
5735096 TATGACCCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (33 bp):
TTTGGAAACATCATGCACTGTAGGACTTACAGA
Found at i:5735190 original size:184 final size:184
Alignment explanation
Indices: 5734882--5735250 Score: 686
Period size: 184 Copynumber: 2.0 Consensus size: 184
5734872 CCGAAGGCTT
5734882 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTGAAAACATCAAAAAGCTC
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTGAAAACATCAAAAAGCTC
*
5734947 CCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGGCCCTAAGGCTTTGAAAACA
66 CCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACA
*
5735012 TCAAAAATCT-CCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
131 TCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
*
5735065 TTTGGAAACATCATGCACTGTAGGACTTACATATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGG-TTTGAAAACATCAAAAAGCT
5735130 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
65 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
*
5735195 ATCGAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
130 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
5735250 T
1 T
5735251 GACCCTAAGG
Statistics
Matches: 180, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
183 43 0.24
184 93 0.52
185 44 0.24
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (184 bp):
TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTGAAAACATCAAAAAGCTC
CCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACA
TCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
Found at i:5735314 original size:75 final size:76
Alignment explanation
Indices: 5735065--5735326 Score: 499
Period size: 76 Copynumber: 3.5 Consensus size: 76
5735055 GACTTACAGA
*
5735065 TTTGGAAACATCATGCACTGTAGGACTTACATATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
5735130 CCCGAAGGCTT
66 CCCGAAGGCTT
*
5735141 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCGAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
5735206 CCCGAAGGCTT
66 CCCGAAGGCTT
5735217 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTG-AAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
5735281 CCCGAAGGCTT
66 CCCGAAGGCTT
5735292 TTTGGAAACATCATGCACTGTAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATG
5735327 TGGGAAATAG
Statistics
Matches: 183, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
75 60 0.33
76 123 0.67
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:5735973 original size:22 final size:22
Alignment explanation
Indices: 5735948--5736002 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
5735938 AATAAAGCTT
5735948 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
5735970 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
5735992 TCATCTTTGAA
1 TCATCTTTGAA
5736003 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:5740712 original size:11 final size:10
Alignment explanation
Indices: 5740696--5740799 Score: 75
Period size: 11 Copynumber: 9.4 Consensus size: 10
5740686 ATTTCTCCCC
*
5740696 TTTTTTTTCA
1 TTTTTTTTCT
5740706 TTTTTTTTCT
1 TTTTTTTTCT
5740716 TTTTCTTTTCT
1 TTTT-TTTTCT
5740727 TTTTTCTTT-T
1 TTTTT-TTTCT
*
5740737 TTCGTTTTTCGT
1 TT-TTTTTTC-T
*
5740749 TTTTCTCTTTTT
1 TTTT-T-TTTCT
5740761 TCTTTTTTTCTT
1 T-TTTTTTTC-T
5740773 TTTTTCTTTCTT
1 TTTTT-TTTC-T
5740785 TCTTTTTTTCT
1 T-TTTTTTTCT
5740796 TTTT
1 TTTT
5740800 CCTTCTTCTT
Statistics
Matches: 78, Mismatches: 5, Indels: 22
0.74 0.05 0.21
Matches are distributed among these distances:
10 23 0.29
11 25 0.32
12 20 0.26
13 10 0.13
ACGTcount: A:0.01, C:0.14, G:0.02, T:0.83
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:5740718 original size:7 final size:7
Alignment explanation
Indices: 5740708--5740799 Score: 100
Period size: 8 Copynumber: 12.7 Consensus size: 7
5740698 TTTTTTCATT
5740708 TTTTTTC
1 TTTTTTC
5740715 -TTTTTC
1 TTTTTTC
5740721 --TTTTC
1 TTTTTTC
5740726 TTTTTTC
1 TTTTTTC
5740733 TTTTTTC
1 TTTTTTC
*
5740740 GTTTTTC
1 TTTTTTC
5740747 GTTTTTCTC
1 -TTTTT-TC
5740756 TTTTTTC
1 TTTTTTC
5740763 TTTTTTTC
1 -TTTTTTC
5740771 TTTTTTTC
1 -TTTTTTC
5740779 TTTCTTTC
1 TTT-TTTC
5740787 TTTTTTTC
1 -TTTTTTC
5740795 TTTTT
1 TTTTT
5740800 CCTTCTTCTT
Statistics
Matches: 76, Mismatches: 2, Indels: 14
0.83 0.02 0.15
Matches are distributed among these distances:
5 5 0.07
6 6 0.08
7 28 0.37
8 32 0.42
9 5 0.07
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (7 bp):
TTTTTTC
Found at i:5740720 original size:16 final size:15
Alignment explanation
Indices: 5740699--5740814 Score: 85
Period size: 16 Copynumber: 7.2 Consensus size: 15
5740689 TCTCCCCTTT
5740699 TTTTTCATTTTTTTTC
1 TTTTTC-TTTTTTTTC
5740715 TTTTTCTTTTCTTTT-
1 TTTTTCTTTT-TTTTC
5740730 TTCTTT-TTTCGTTTTTC
1 TT-TTTCTTT--TTTTTC
*
5740747 GTTTTTCTCTTTTTTC
1 -TTTTTCTTTTTTTTC
*
5740763 TTTTTTTCTTTTTTTC
1 TTTTTCT-TTTTTTTC
5740779 TTTCTT-TCTTTTTTTC
1 TTT-TTCT-TTTTTTTC
*
5740795 TTTTTCCTTCTTCTTTC
1 TTTTT-CTT-TTTTTTC
5740812 TTT
1 TTT
5740815 GCTGGATGAG
Statistics
Matches: 84, Mismatches: 4, Indels: 23
0.76 0.04 0.21
Matches are distributed among these distances:
15 17 0.20
16 47 0.56
17 16 0.19
18 4 0.05
ACGTcount: A:0.01, C:0.17, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTTCTTTTTTTTC
Found at i:5746108 original size:20 final size:20
Alignment explanation
Indices: 5746061--5746121 Score: 52
Period size: 20 Copynumber: 2.9 Consensus size: 20
5746051 CAAACCTCTG
5746061 AAAAATAATTAAAATAATGAAAAC
1 AAAAAT-ATT-AAA-AAT-AAAAC
* *
5746085 -AAAATACTTGAAAATAAAAT
1 AAAAATA-TTAAAAATAAAAC
5746105 AAAAATATTAAAAATAA
1 AAAAATATTAAAAATAA
5746122 TATACATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
20 13 0.41
21 9 0.28
22 3 0.09
23 7 0.22
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (20 bp):
AAAAATATTAAAAATAAAAC
Found at i:5746155 original size:24 final size:23
Alignment explanation
Indices: 5746093--5746155 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 23
5746083 ACAAAATACT
*
5746093 TGAAAATAA-AATAAAAATATTA
1 TGAAAATAATAATATAAATATTA
5746115 --AAAATAATATACATATAAATATTA
1 TGAAAAT-A-ATA-ATATAAATATTA
5746139 TGAAAATAATAAGTATA
1 TGAAAATAATAA-TATA
5746156 TGTAAAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
20 5 0.15
21 1 0.03
22 1 0.03
23 2 0.06
24 18 0.55
25 1 0.03
26 5 0.15
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (23 bp):
TGAAAATAATAATATAAATATTA
Found at i:5746156 original size:26 final size:25
Alignment explanation
Indices: 5746093--5746156 Score: 66
Period size: 26 Copynumber: 2.7 Consensus size: 25
5746083 ACAAAATACT
5746093 TGAAAATAA-AATA-A-AAATATTA
1 TGAAAATAATAATATATAAATATTA
*
5746115 --AAAATAATATACATATAAATATTA
1 TGAAAATAATA-ATATATAAATATTA
5746139 TGAAAATAATAAGTATAT
1 TGAAAATAATAA-TATAT
5746157 GTAAAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
20 7 0.21
21 1 0.03
22 2 0.06
23 1 0.03
24 8 0.24
25 1 0.03
26 13 0.39
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (25 bp):
TGAAAATAATAATATATAAATATTA
Found at i:5748399 original size:3 final size:3
Alignment explanation
Indices: 5748393--5748462 Score: 74
Period size: 3 Copynumber: 24.0 Consensus size: 3
5748383 AATAATTATT
* *
5748393 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TAA TAT TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
**
5748436 TAA TAA TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
5748463 ATTAAGTAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
2 6 0.11
3 46 0.84
4 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:5748438 original size:18 final size:18
Alignment explanation
Indices: 5748382--5748462 Score: 94
Period size: 18 Copynumber: 4.3 Consensus size: 18
5748372 TCTGGGCTTG
5748382 TAATAATTATTTAATAATAA
1 TAATAA-TATTT-ATAATAA
*
5748402 T-ATAATATATATAATATAA
1 TAATAATATTTAT-A-ATAA
5748421 TAATAATATTTATAATAA
1 TAATAATATTTATAATAA
5748439 TAATAATAATTT-TAATAA
1 TAATAAT-ATTTATAATAA
5748457 TAATAA
1 TAATAA
5748463 ATTAAGTAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
17 2 0.04
18 28 0.51
19 14 0.25
20 11 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAATATTTATAATAA
Found at i:5750685 original size:29 final size:29
Alignment explanation
Indices: 5750648--5750719 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
5750638 AAAAATTGTT
*
5750648 TTCGCTCCCCTAAAATTTTATAAATTCAAA
1 TTCG-TCCCCTAAAATTTTATAAATCCAAA
* * * *
5750678 TTCGTCCCCCTGAATTTTTATAAGTCCAAG
1 TTCGT-CCCCTAAAATTTTATAAATCCAAA
*
5750708 TTCGTCTCCTAA
1 TTCGTCCCCTAA
5750720 CTTAAAATCA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
29 6 0.18
30 28 0.82
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (29 bp):
TTCGTCCCCTAAAATTTTATAAATCCAAA
Found at i:5750712 original size:30 final size:30
Alignment explanation
Indices: 5750654--5750713 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
5750644 TGTTTTCGCT
*
5750654 CCCCTAAAATTTTATAAATTCAAATTCGTC
1 CCCCTAAAATTTTATAAATCCAAATTCGTC
* * * *
5750684 CCCCTGAATTTTTATAAGTCCAAGTTCGTC
1 CCCCTAAAATTTTATAAATCCAAATTCGTC
5750714 TCCTAACTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
CCCCTAAAATTTTATAAATCCAAATTCGTC
Found at i:5752816 original size:38 final size:37
Alignment explanation
Indices: 5752723--5753039 Score: 304
Period size: 37 Copynumber: 8.7 Consensus size: 37
5752713 GAATGATTAG
5752723 AAAA-GTTTTTAAAACTATATATTATAT-AGTTTTC-
1 AAAATGTTTTTAAAACTATATATTATATAAGTTTTCA
*
5752757 AAAACG-TTTT-AAA--A-ATATTATATAAGTTTTCAA
1 AAAATGTTTTTAAAACTATATATTATATAAGTTTTC-A
* * *
5752790 AAAATGTTTTTAAAATTATATATTATATAATTTTTTA
1 AAAATGTTTTTAAAACTATATATTATATAAGTTTTCA
*
5752827 AAAATGTTTTTAAAAC--TATA-TATATAATTTTTCA
1 AAAATGTTTTTAAAACTATATATTATATAAGTTTTCA
* *
5752861 AAAATGTTTTAAAAAACTATATACTATATAAGTTTTC-
1 AAAATGTTTT-TAAAACTATATATTATATAAGTTTTCA
* *
5752898 AAAATGTTTTAAAAACTATATAATATATAAATGTTTTC-
1 AAAATGTTTTTAAAACTATATATTATAT-AA-GTTTTCA
*
5752936 AAAATGTTTTAAAAAACTATATATTATATATA-TTTT-A
1 AAAATGTTTT-TAAAACTATATATTATATA-AGTTTTCA
* * * *
5752973 AAAATGTTTTCAAAAACTATATAATATATAAATTTTCG
1 AAAATGTTTT-TAAAACTATATATTATATAAGTTTTCA
*
5753011 AAAATCGTTTTCTAAAAATTATATATTAT
1 AAAAT-GTTTT-T-AAAACTATATATTAT
5753040 TTTTTGTCAA
Statistics
Matches: 246, Mismatches: 15, Indels: 38
0.82 0.05 0.13
Matches are distributed among these distances:
30 9 0.04
31 8 0.03
33 8 0.03
34 35 0.14
35 13 0.05
36 18 0.07
37 69 0.28
38 49 0.20
39 24 0.10
40 13 0.05
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.44
Consensus pattern (37 bp):
AAAATGTTTTTAAAACTATATATTATATAAGTTTTCA
Found at i:5754789 original size:37 final size:37
Alignment explanation
Indices: 5754739--5754813 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
5754729 TCTGATGGAA
5754739 ACTGAATTCCTTGGTGAGTGGGACACCGAGTTCAGCC
1 ACTGAATTCCTTGGTGAGTGGGACACCGAGTTCAGCC
5754776 ACTGAATTCCTTGGTGAGTGGGACACCGAGTTCAGCC
1 ACTGAATTCCTTGGTGAGTGGGACACCGAGTTCAGCC
5754813 A
1 A
5754814 TACAAGCTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (37 bp):
ACTGAATTCCTTGGTGAGTGGGACACCGAGTTCAGCC
Found at i:5755665 original size:12 final size:13
Alignment explanation
Indices: 5755647--5755691 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
5755637 TGGTCCTGCA
5755647 AAATAATTAAAAT
1 AAATAATTAAAAT
5755660 -AATAA-TAATAAT
1 AAATAATTAA-AAT
*
5755672 AAATAAAT-AAAT
1 AAATAATTAAAAT
5755684 AAATAATT
1 AAATAATT
5755692 TTTTAAAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
11 3 0.11
12 18 0.64
13 6 0.21
14 1 0.04
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATAATTAAAAT
Found at i:5756232 original size:67 final size:65
Alignment explanation
Indices: 5756104--5756232 Score: 154
Period size: 67 Copynumber: 2.0 Consensus size: 65
5756094 GAAGGTTTGG
* * * *
5756104 TGTTTCAAGAGAAACATTTTCAATGGTTTTTTTCAAGAGAAACTGTCTCAAGGGAGGCAAAATTT
1 TGTTTCAAGAGAAACATTTTCAAAGATTTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* *
5756169 TGTTTCAAGAGAAAC-TTATTCAAAGATTGGTGTTTT-AAGAGAATCTGTCTCAAGATAGACAAA
1 TGTTTCAAGAGAAACATT-TTCAAAGATT--T-TTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
5756232 A
62 A
5756233 CTTAGTTCCG
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
64 2 0.04
65 23 0.43
67 25 0.46
68 4 0.07
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (65 bp):
TGTTTCAAGAGAAACATTTTCAAAGATTTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:5756333 original size:102 final size:104
Alignment explanation
Indices: 5756141--5756387 Score: 263
Period size: 101 Copynumber: 2.4 Consensus size: 104
5756131 TTTTTTCAAG
* * * *
5756141 AGAAACTGTCTCAAGGGAGGCAAAATTTTGTTTCAAGAGAAACTTATTCAAAGATTGGTGTTTTA
1 AGAAACTATCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACATATTCAAAGATTGGTGTTTCA
* *
5756206 AGAGAATCTGTCTCAAGATAGACAAAACTTAGTTCCGAA
66 AGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCGAA
** * * *
5756245 AGAAACTATCTCAAGGGAGACGGAA-TTTGTTTTAAG-GAAAACATATTCAAATATT-TTGTTTC
1 AGAAACTATCTCAAGGGAGACAAAATTTTGTTTCAAGAG-AAACATATTCAAAGATTGGTGTTTC
* * *
5756307 AAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTC-AA
65 AAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCGAA
* * * * *
5756345 GGGAAATTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAAC
1 -AGAAACTATCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAAC
5756388 TGTCTTAAGA
Statistics
Matches: 119, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
100 2 0.02
101 39 0.33
102 32 0.27
103 25 0.21
104 21 0.18
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (104 bp):
AGAAACTATCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACATATTCAAAGATTGGTGTTTCA
AGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCGAA
Found at i:5756346 original size:36 final size:36
Alignment explanation
Indices: 5756299--5756443 Score: 236
Period size: 36 Copynumber: 4.0 Consensus size: 36
5756289 ATTCAAATAT
*
5756299 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAA
* *
5756335 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAA
*
5756371 TTTGTTTCAAGGGAAACTGTCTTAAGAGAGAAAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAA
* *
5756407 TTTGTTTCAAGAGAAACTATCTCAAGAGAGAAAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAA
5756443 T
1 T
5756444 AACCCTTATT
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 102 1.00
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAA
Found at i:5756380 original size:21 final size:20
Alignment explanation
Indices: 5756320--5756420 Score: 71
Period size: 21 Copynumber: 5.4 Consensus size: 20
5756310 GGAAACTGTC
5756320 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGA-AAAATTTGTT
*
5756341 TCAAG-G-G--AAA-TTGTC
1 TCAAGAGAGAAAAATTTGTT
5756356 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGA-AAAATTTGTT
*
5756377 TCAAG-G-G--AAA-CTGTCT
1 TCAAGAGAGAAAAATTTGT-T
5756393 T-AAGAGAGAAAAAATTTGTT
1 TCAAGAGAG-AAAAATTTGTT
5756413 TCAAGAGA
1 TCAAGAGA
5756421 AACTATCTCA
Statistics
Matches: 62, Mismatches: 4, Indels: 28
0.66 0.04 0.30
Matches are distributed among these distances:
15 15 0.24
16 10 0.16
17 2 0.03
19 2 0.03
20 10 0.16
21 23 0.37
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.27
Consensus pattern (20 bp):
TCAAGAGAGAAAAATTTGTT
Found at i:5756646 original size:67 final size:66
Alignment explanation
Indices: 5756517--5756646 Score: 156
Period size: 67 Copynumber: 2.0 Consensus size: 66
5756507 GAAGGTTTGG
* * * * *
5756517 TGTTTCAAGAGAAACATTTTCAATGGTTTTTTTTCAAGAGAAACTGTCTCAAGGGAGGCAAAATT
1 TGTTTCAAGAGAAACATTTTCAAAGATTTGTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
5756582 T
66 T
* *
5756583 TGTTTCAAGAGAAAC-TTATTCAAAGATTGGTGTTTT-AAGAGAATCTGTCTCAAGATAGACAAA
1 TGTTTCAAGAGAAACATT-TTCAAAGATT--TGTTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
5756646 A
63 A
5756647 CTTAGTTCCG
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
65 2 0.04
66 23 0.43
67 24 0.44
68 5 0.09
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (66 bp):
TGTTTCAAGAGAAACATTTTCAAAGATTTGTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
T
Found at i:5756760 original size:36 final size:36
Alignment explanation
Indices: 5756713--5756857 Score: 254
Period size: 36 Copynumber: 4.0 Consensus size: 36
5756703 ATTCAAATAT
5756713 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
5756749 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
5756785 TTTGTTTTAAGGGAAACTGTCTCAAGAGAGAAAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
5756821 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
5756857 T
1 T
5756858 AACCCTTATT
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 103 1.00
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:5756800 original size:102 final size:104
Alignment explanation
Indices: 5756548--5756800 Score: 282
Period size: 102 Copynumber: 2.5 Consensus size: 104
5756538 AATGGTTTTT
* * *
5756548 TTTCAAGAGAAACTGTCTCAAGGGAGGCAAAATTTTGTTTCAAGAG-AAACTTATTCAAAGATTG
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAAACATATTCAAAGATTG
* * *
5756612 GTGTTTTAAGAGAATCTGTCTCAAGATAGACAAAACTTAG
65 GTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAG
* * * ** * *
5756652 TTCCGAA-ATAAACTATCTCAAGGGAGACGGATTTTGTTTCAA-GGAAAACATATTCAAATATT-
1 TTTC-AAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAACATATTCAAAGATTG
* * *
5756714 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTG
65 GTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAG
* * *
5756753 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAA
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAA
5756801 CTGTCTCAAG
Statistics
Matches: 120, Mismatches: 25, Indels: 10
0.77 0.16 0.06
Matches are distributed among these distances:
100 2 0.02
101 33 0.28
102 36 0.30
103 25 0.21
104 22 0.18
105 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (104 bp):
TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAACATATTCAAAGATTGG
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAG
Found at i:5757176 original size:36 final size:36
Alignment explanation
Indices: 5757129--5757322 Score: 262
Period size: 36 Copynumber: 5.2 Consensus size: 36
5757119 ATTCAAATAT
*
5757129 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
5757165 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
5757201 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTC-A-AGAG----AGACAAAA
*
5757243 TTTGTTTCAAGAGAAACTGTCACAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
5757279 TTTGTTTAAAGAGAAATTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
5757315 CTTTGTTT
1 -TTTGTTT
5757323 TGAGTAAATT
Statistics
Matches: 142, Mismatches: 9, Indels: 13
0.87 0.05 0.08
Matches are distributed among these distances:
36 97 0.68
37 8 0.06
38 4 0.03
40 4 0.03
41 1 0.01
42 28 0.20
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:5757178 original size:416 final size:414
Alignment explanation
Indices: 5756027--5757279 Score: 2231
Period size: 414 Copynumber: 3.0 Consensus size: 414
5756017 TTTGGTTGGC
*
5756027 AAATAACCCTTAATGCCTTGAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAAC
1 AAATAACCCTTATTGCCTTGAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAAC
5756092 TCGAAGGTTTGGTGTTTCAAGAGAAACATTTTCAATGG-TTTTTTTCAAGAGAAACTGTCTCAAG
66 TCGAAGGTTTGGTGTTTCAAGAGAAACATTTTCAATGGTTTTTTTTCAAGAGAAACTGTCTCAAG
5756156 GGAGGCAAAATTTTGTTTCAAGAGAAACTTATTCAAAGATTGGTGTTTTAAGAGAATCTGTCTCA
131 GGAGGCAAAATTTTGTTTCAAGAGAAACTTATTCAAAGATTGGTGTTTTAAGAGAATCTGTCTCA
*
5756221 AGATAGACAAAACTTAGTTCCGAAAGAAACTATCTCAAGGGAGACGGAATTTGTTTTAAGGAAAA
196 AGATAGACAAAACTTAGTTCCGAAAGAAACTATCTCAAGGGAGACGGAATTTGTTTCAAGGAAAA
5756286 CATATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
261 CATATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
* *
5756351 TTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTTAAGAGAGAAAAAATTTGTTTCA
326 CTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAATTTGTTTCA
*
5756416 AGAGAAACTATCTCAAGAGAGAAA
391 AGAGAAACTATCTCAAGAGAGACA
*
5756440 AAATAACCCTTATTTCCTTGAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAAC
1 AAATAACCCTTATTGCCTTGAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAAC
*
5756505 TTGAAGGTTTGGTGTTTCAAGAGAAACATTTTCAATGGTTTTTTTTCAAGAGAAACTGTCTCAAG
66 TCGAAGGTTTGGTGTTTCAAGAGAAACATTTTCAATGGTTTTTTTTCAAGAGAAACTGTCTCAAG
5756570 GGAGGCAAAATTTTGTTTCAAGAGAAACTTATTCAAAGATTGGTGTTTTAAGAGAATCTGTCTCA
131 GGAGGCAAAATTTTGTTTCAAGAGAAACTTATTCAAAGATTGGTGTTTTAAGAGAATCTGTCTCA
* *
5756635 AGATAGACAAAACTTAGTTCCGAAATAAACTATCTCAAGGGAGACGGATTTTGTTTCAAGGAAAA
196 AGATAGACAAAACTTAGTTCCGAAAGAAACTATCTCAAGGGAGACGGAATTTGTTTCAAGGAAAA
5756700 CATATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
261 CATATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
*
5756765 CTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAACTGTCTCAAGAGAGAAAAAATTTGTTTCA
326 CTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAATTTGTTTCA
5756830 AGAGAAACTATCTCAAGAGAGACA
391 AGAGAAACTATCTCAAGAGAGACA
*
5756854 AAATAACCCTTATTGCCTTGAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGTGTAATTGAAC
1 AAATAACCCTTATTGCCTTGAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAAC
* *
5756919 TCGAAGGTTTGGTGTTTCAAGAGAAACATTTTCAATGGTTTTTTTTTTCAAGAGAAACTTTCTCG
66 TCGAAGGTTTGGTGTTTCAAGAGAAACATTTTCAATGG--TTTTTTTTCAAGAGAAACTGTCTCA
5756984 AGGGAGGCAAAATTTTGTTTCAAGAGAAACTTATTCAAAGATTGG-GTTTTTAAGAGAATCTGTC
129 AGGGAGGCAAAATTTTGTTTCAAGAGAAACTTATTCAAAGATTGGTG-TTTTAAGAGAATCTGTC
* *
5757048 TCAAGATAGACAAAACTTATTTCCGAAAGAAACTATCTCAAGGGAGACAGAATTTGTTTCAAGGA
193 TCAAGATAGACAAAACTTAGTTCCGAAAGAAACTATCTCAAGGGAGACGGAATTTGTTTCAAGGA
5757113 AAACATATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGG
258 AAACATATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGG
* * *
5757178 AAACTGTCTCAAGAGAGAAAAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAGACAAAA
323 AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAG----A-A-AAAA
* *
5757243 TTTGTTTCAAGAGAAACTGTCACAAGAGAGACA
382 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACA
5757276 AAAT
1 AAAT
5757280 TTGTTTAAAG
Statistics
Matches: 805, Mismatches: 25, Indels: 11
0.96 0.03 0.01
Matches are distributed among these distances:
413 100 0.12
414 403 0.50
415 1 0.00
416 260 0.32
420 1 0.00
421 1 0.00
422 39 0.05
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (414 bp):
AAATAACCCTTATTGCCTTGAGTTATGTTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAAC
TCGAAGGTTTGGTGTTTCAAGAGAAACATTTTCAATGGTTTTTTTTCAAGAGAAACTGTCTCAAG
GGAGGCAAAATTTTGTTTCAAGAGAAACTTATTCAAAGATTGGTGTTTTAAGAGAATCTGTCTCA
AGATAGACAAAACTTAGTTCCGAAAGAAACTATCTCAAGGGAGACGGAATTTGTTTCAAGGAAAA
CATATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
CTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAATTTGTTTCA
AGAGAAACTATCTCAAGAGAGACA
Found at i:5757212 original size:21 final size:20
Alignment explanation
Indices: 5757150--5757214 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
5757140 GGAAACTGTC
5757150 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGA-AAAATTTGTT
* *
5757171 TCAAG-G-G--AAA-CTGTC
1 TCAAGAGAGAAAAATTTGTT
5757186 TCAAGAGAGAAAAAATTTGTT
1 TCAAGAGAG-AAAAATTTGTT
5757207 TCAAGAGA
1 TCAAGAGA
5757215 AACTATCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 8 0.24
16 4 0.12
17 1 0.03
19 1 0.03
20 4 0.12
21 16 0.47
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.25
Consensus pattern (20 bp):
TCAAGAGAGAAAAATTTGTT
Found at i:5757269 original size:78 final size:78
Alignment explanation
Indices: 5757157--5757313 Score: 260
Period size: 78 Copynumber: 2.0 Consensus size: 78
5757147 GTCTCAAGAG
* * *
5757157 AGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAATTTGTTTCAAGAGAAACTATC
1 AGACAAAATTTGTTTCAAGAGAAACTGTCACAAGAGAGAAAAAATTTGTTTAAAGAGAAACTATC
5757222 TCAAGAGAGACAA
66 TCAAGAGAGACAA
* * *
5757235 AGACAAAATTTGTTTCAAGAGAAACTGTCACAAGAGAGACAAAATTTGTTTAAAGAGAAATTGTC
1 AGACAAAATTTGTTTCAAGAGAAACTGTCACAAGAGAGAAAAAATTTGTTTAAAGAGAAACTATC
5757300 TCAAGAGAGACAA
66 TCAAGAGAGACAA
5757313 A
1 A
5757314 ACTTTGTTTT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 73 1.00
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.23
Consensus pattern (78 bp):
AGACAAAATTTGTTTCAAGAGAAACTGTCACAAGAGAGAAAAAATTTGTTTAAAGAGAAACTATC
TCAAGAGAGACAA
Found at i:5757810 original size:116 final size:116
Alignment explanation
Indices: 5757539--5757764 Score: 364
Period size: 116 Copynumber: 1.9 Consensus size: 116
5757529 AAGATGAATG
* * *
5757539 TTACTGGTGAGCACAATTCCCTTCATCGTGAAGTTGAAACCGTGGATGGCCTCTTCGTCATGAAG
1 TTACTGGTGAGCACAATTCCCTTCACCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTCATGAAG
* *
5757604 TTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATTAATA
66 TTGAGCCTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCCAATTAATA
* *
5757655 TTACTGGTGAGCACGATTCCCTTCACCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAG
1 TTACTGGTGAGCACAATTCCCTTCACCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTCATGAAG
*
5757720 TTGAGCCTT-AACTTGAATATCCTTCGTTGTGAAGTTGAAATCCAA
66 TTGAGCCTTGAA-TTGAATATCCTTCGTCGTGAAGTTGAAATCCAA
5757765 GCTTGTATTG
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
115 2 0.02
116 99 0.98
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (116 bp):
TTACTGGTGAGCACAATTCCCTTCACCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTCATGAAG
TTGAGCCTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCCAATTAATA
Found at i:5763175 original size:30 final size:30
Alignment explanation
Indices: 5763111--5763187 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
5763101 ACAAAACCGG
* * *
5763111 TAAAAAATGATCGGAAACATTATCAGGCGC
1 TAAAAAATGACCGAAAACATTATCAAGCGC
*
5763141 TAAAAAATGACCGAAAACATTA-CTAAGCGT
1 TAAAAAATGACCGAAAACATTATC-AAGCGC
*
5763171 TAAAATATGACCGAAAA
1 TAAAAAATGACCGAAAA
5763188 TGTTAAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
29 1 0.02
30 40 0.98
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (30 bp):
TAAAAAATGACCGAAAACATTATCAAGCGC
Found at i:5764219 original size:31 final size:30
Alignment explanation
Indices: 5764132--5764235 Score: 93
Period size: 31 Copynumber: 3.4 Consensus size: 30
5764122 AAACATGTAA
* * * *
5764132 ATATAAAATTAAACTGAAAATTTAATTTCAT
1 ATATCAAATTAAAC-AAAAAATTAAATTCAT
* *
5764163 ATATC-ATTTAAACAAAAAATCAAATTCAT
1 ATATCAAATTAAACAAAAAATTAAATTCAT
* * *
5764192 ATATCAAATTGAACAATAAAATTAAATTTAA
1 ATATCAAATTAAACAA-AAAATTAAATTCAT
*
5764223 ATATCAAAATAAA
1 ATATCAAATTAAA
5764236 TATTTACCAA
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
29 17 0.29
30 15 0.26
31 26 0.45
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.33
Consensus pattern (30 bp):
ATATCAAATTAAACAAAAAATTAAATTCAT
Found at i:5765563 original size:39 final size:37
Alignment explanation
Indices: 5765520--5765632 Score: 124
Period size: 37 Copynumber: 3.0 Consensus size: 37
5765510 ACATATATAC
*
5765520 ACATATATATTATATAGTTTGCAAATTATTTTTGAAAAT
1 ACATATATATTATATAGTTT--AAAATATTTTTGAAAAT
* *
5765559 ACATATATAATATATAGTTTAAAACATTTTTTG-AAAT
1 ACATATATATTATATAGTTTAAAATA-TTTTTGAAAAT
*
5765596 --ATGTATATTATATAGTTTTTAAAATATTTTTGAAAAT
1 ACATATATATTATATAG--TTTAAAATATTTTTGAAAAT
5765633 TATAATATAG
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
35 13 0.20
36 6 0.09
37 20 0.31
38 6 0.09
39 19 0.30
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (37 bp):
ACATATATATTATATAGTTTAAAATATTTTTGAAAAT
Found at i:5765646 original size:32 final size:33
Alignment explanation
Indices: 5765561--5765685 Score: 121
Period size: 32 Copynumber: 3.7 Consensus size: 33
5765551 TTGAAAATAC
*
5765561 ATATATAATATA-TAGTTTAAAACATTTTTTGAAA
1 ATATATAATATAGT-TTTTAAAACA-TTTTTGAAA
* *
5765595 TATGTATATTATATAGTTTTTAAAATATTTTTGAAA
1 -A--TATATAATATAGTTTTTAAAACATTTTTGAAA
*
5765631 AT-TATAATATAGTTTTTGAAAACGTTTTT-AAA
1 ATATATAATATAGTTTTT-AAAACATTTTTGAAA
* *
5765663 ATATATAATATACTTTTGAAAAC
1 ATATATAATATAGTTTTTAAAAC
5765686 GTTATGAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
32 24 0.31
33 23 0.30
35 2 0.03
36 9 0.12
37 18 0.23
38 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.46
Consensus pattern (33 bp):
ATATATAATATAGTTTTTAAAACATTTTTGAAA
Found at i:5765686 original size:32 final size:31
Alignment explanation
Indices: 5765599--5765811 Score: 106
Period size: 32 Copynumber: 6.8 Consensus size: 31
5765589 TTGAAATATG
* * **
5765599 TATATTATATAGTTTTTAAAATATTTTTGAAAA
1 TATATAATATA-TTTTGAAAACGTTTTT-AAAA
5765632 T-TATAATATAGTTTTTGAAAACGTTTTTAAAA
1 TATATAATATA--TTTTGAAAACGTTTTTAAAA
**
5765664 TATATAATATACTTTTGAAAACGTTATGAAAACA
1 TATATAATATA-TTTTGAAAACGTT-TTTAAA-A
* ** *
5765698 TTTATATAATATATAATTTTTAAAAACCATTTTGAAA
1 --TATAT-A-ATAT-A-TTTTGAAAACGTTTTTAAAA
* *
5765735 -ATAT-AT-T-TTTTGAAAA---TTATATAA
1 TATATAATATATTTTGAAAACGTTTTTAAAA
*
5765759 TATAT-A-GT-TTTTGAAAACGTTTTTAAAA
1 TATATAATATATTTTGAAAACGTTTTTAAAA
5765787 TATATAATATACTTTTGAAAACGTT
1 TATATAATATA-TTTTGAAAACGTT
5765812 ATGAAAACAT
Statistics
Matches: 140, Mismatches: 22, Indels: 37
0.70 0.11 0.19
Matches are distributed among these distances:
24 5 0.04
25 15 0.11
27 8 0.06
28 11 0.08
29 1 0.01
30 2 0.01
31 2 0.01
32 39 0.28
33 27 0.19
34 5 0.04
36 5 0.04
37 2 0.01
38 7 0.05
39 11 0.08
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (31 bp):
TATATAATATATTTTGAAAACGTTTTTAAAA
Found at i:5765709 original size:43 final size:42
Alignment explanation
Indices: 5765647--5765835 Score: 124
Period size: 43 Copynumber: 4.5 Consensus size: 42
5765637 ATATAGTTTT
* *
5765647 TGAAAACGTTTTTAAAATATATAATATACTTTTGAAAACGTTA
1 TGAAAACATTTTTATAATATATAATATA-TTTTGAAAACGTTA
* * * *
5765690 TGAAAACATTTATATAATATAT-A-AT-TTTTAAAAACCATTT
1 TGAAAACATTTTTATAATATATAATATATTTTGAAAA-CGTTA
* * * * * * *
5765730 TGAAAATATATTTTTTGAA-A-ATTATATAATAT--ATA-GTTTT
1 TGAAAACAT-TTTTAT-AATATATAATATATTTTGAAAACG-TTA
* *
5765770 TGAAAACGTTTTTAAAATATATAATATACTTTTGAAAACGTTA
1 TGAAAACATTTTTATAATATATAATATA-TTTTGAAAACGTTA
*
5765813 TGAAAACATTTATATAATATATA
1 TGAAAACATTTTTATAATATATA
5765836 TTTTTAAAAA
Statistics
Matches: 108, Mismatches: 25, Indels: 26
0.68 0.16 0.16
Matches are distributed among these distances:
38 2 0.02
39 13 0.12
40 30 0.28
41 12 0.11
42 5 0.05
43 45 0.42
44 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (42 bp):
TGAAAACATTTTTATAATATATAATATATTTTGAAAACGTTA
Found at i:5765747 original size:15 final size:16
Alignment explanation
Indices: 5765727--5765756 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5765717 TTAAAAACCA
5765727 TTTTGAAAA-TATATT
1 TTTTGAAAATTATATT
5765742 TTTTGAAAATTATAT
1 TTTTGAAAATTATAT
5765757 AATATATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (16 bp):
TTTTGAAAATTATATT
Found at i:5765763 original size:25 final size:25
Alignment explanation
Indices: 5765699--5765775 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
5765689 ATGAAAACAT
*
5765699 TTATATAATATATAATTTTTAAAAA
1 TTATATAATATATAATTTTTGAAAA
** * * *
5765724 CCATTTTGAAAATATATTTTTTGAAAA
1 TTA-TAT-AATATATAATTTTTGAAAA
*
5765751 TTATATAATATATAGTTTTTGAAAA
1 TTATATAATATATAATTTTTGAAAA
5765776 CGTTTTTAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
25 18 0.46
26 4 0.10
27 17 0.44
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (25 bp):
TTATATAATATATAATTTTTGAAAA
Found at i:5765774 original size:123 final size:118
Alignment explanation
Indices: 5765622--5765862 Score: 437
Period size: 123 Copynumber: 2.0 Consensus size: 118
5765612 TTTTAAAATA
5765622 TTTTTGAAAATTATAATATAGTTTTTGAAAACGTTTTTAAAATATATAATATACTTTTGAAAACG
1 TTTTTGAAAATTATAATATAGTTTTTGAAAACGTTTTTAAAATATATAATATACTTTTGAAAACG
5765687 TTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATATAT
66 TTATGAAAACATTTATATAATATAT-ATTTTTAAAAACCATTTTGAAAATATAT
5765741 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATAATATACTTTTGAA
1 TTTTTGAAAA-T-TAT-A-ATATAGTTTTTGAAAACGTTTTTAAAATATATAATATACTTTTGAA
5765806 AACGTTATGAAAACATTTATATAATATATATTTTTAAAAACCATTTTGAAAATATAT
62 AACGTTATGAAAACATTTATATAATATATATTTTTAAAAACCATTTTGAAAATATAT
5765863 AATATAGTTT
Statistics
Matches: 118, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
119 10 0.08
120 1 0.01
121 3 0.03
122 29 0.25
123 75 0.64
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (118 bp):
TTTTTGAAAATTATAATATAGTTTTTGAAAACGTTTTTAAAATATATAATATACTTTTGAAAACG
TTATGAAAACATTTATATAATATATATTTTTAAAAACCATTTTGAAAATATAT
Found at i:5765791 original size:35 final size:34
Alignment explanation
Indices: 5765742--5765920 Score: 141
Period size: 33 Copynumber: 5.1 Consensus size: 34
5765732 AAAATATATT
*
5765742 TTTTGAAAATTATATAATATATAGTTTTTGAAAACG
1 TTTT-AAAAATATAT-ATATATAGTTTTTGAAAACG
* *
5765778 TTTTTAAAATATATA-ATATA-CTTTTGAAAACG
1 TTTTAAAAATATATATATATAGTTTTTGAAAACG
* * *
5765810 TTATGAAAACATTTATATAATATATA-TTTTTAAAAACCA
1 TT-TTAAAA-A--TATAT-ATATATAGTTTTTGAAAA-CG
* ** *
5765849 TTTTGAAAATATATA-ATATAGTTTTTTCAAACA
1 TTTTAAAAATATATATATATAGTTTTTGAAAACG
*
5765882 TTTTAAAAATTTATATATTATATGTTTTTGAAAACG
1 TTTTAAAAATATATATA-TATA-GTTTTTGAAAACG
5765918 TTT
1 TTT
5765921 ATATATAATA
Statistics
Matches: 115, Mismatches: 17, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
32 13 0.11
33 29 0.25
34 12 0.10
35 17 0.15
36 22 0.19
37 2 0.02
38 17 0.15
39 3 0.03
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (34 bp):
TTTTAAAAATATATATATATAGTTTTTGAAAACG
Found at i:5765858 original size:71 final size:70
Alignment explanation
Indices: 5765743--5765916 Score: 203
Period size: 71 Copynumber: 2.5 Consensus size: 70
5765733 AAATATATTT
* *
5765743 TTTG-AAAA-TTATATAATATATAGTTTTTGAAAA-CGTTTTTAAAATATATAATATA-CTTTTG
1 TTTGAAAAATTTATATAATATATA-TTTTTGAAAACCATTTTGAAAATATATAATATAGCTTTTG
*
5765804 AAAACG
65 AAAACA
* *
5765810 TTATGAAAACATTTATATAATATATATTTTTAAAAACCATTTTGAAAATATATAATATAGTTTTT
1 TT-TGAAAA-ATTTATATAATATATATTTTTGAAAACCATTTTGAAAATATATAATATAGCTTTT
**
5765875 TCAAACA
64 GAAAACA
* * *
5765882 TTTTAAAAATTTATATATTATATGTTTTTGAAAAC
1 TTTGAAAAATTTATATAATATATATTTTTGAAAAC
5765917 GTTTATATAT
Statistics
Matches: 90, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
67 2 0.02
68 2 0.02
69 3 0.03
70 34 0.38
71 39 0.43
72 10 0.11
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (70 bp):
TTTGAAAAATTTATATAATATATATTTTTGAAAACCATTTTGAAAATATATAATATAGCTTTTGA
AAACA
Found at i:5765884 original size:155 final size:153
Alignment explanation
Indices: 5765584--5765891 Score: 321
Period size: 155 Copynumber: 2.0 Consensus size: 153
5765574 AGTTTAAAAC
* *
5765584 ATTTTTTGAAATATGTATATTATATAGTTTTTAAAATATTTTTGAAAATTATAATATAGTTTTTG
1 ATTTTTTGAAATATGTATATTATATAGTTTTTAAAACATTTTTGAAAATTATAATATAGCTTTTG
** * *
5765649 AAAACGTTTTTAAAATATATAATATACTTTTGAAAACGTTATGAAAACATTTATATAATATATAA
66 AAAACGTTTGAAAAATATATAATATACTTTTAAAAACATTATGAAAACA-TTATATAATATAT-A
*
5765714 TTTTTAAAAACCATTTTGAAAATAT
129 TTTTTAAAAACCATTTTAAAAATAT
*
5765739 ATTTTTTGAAA-AT-TATATAATATATAGTTTTTGAAAACGTTTTT-AAAATATATAATATA-CT
1 ATTTTTTGAAATATGTATAT--TATATAGTTTTT-AAAACATTTTTGAAAAT-TATAATATAGCT
* *
5765800 TTTGAAAACGTTATGAAAACATTTATATAATATATATTTTTAAAAACCATTTTG-AAA-A-TATA
62 TTTGAAAACGTT-TGAAAA-A--TATAT-A-ATATACTTTTAAAAA-CATTATGAAAACATTATA
*
5765862 TAATATAGT-TTTTT-CAAA-CATTTTAAAAAT
120 TAATATA-TATTTTTAAAAACCATTTTAAAAAT
5765892 TTATATATTA
Statistics
Matches: 130, Mismatches: 11, Indels: 24
0.79 0.07 0.15
Matches are distributed among these distances:
153 5 0.04
154 2 0.02
155 52 0.40
156 25 0.19
157 6 0.05
158 11 0.08
159 6 0.05
160 2 0.02
161 16 0.12
162 5 0.04
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (153 bp):
ATTTTTTGAAATATGTATATTATATAGTTTTTAAAACATTTTTGAAAATTATAATATAGCTTTTG
AAAACGTTTGAAAAATATATAATATACTTTTAAAAACATTATGAAAACATTATATAATATATATT
TTTAAAAACCATTTTAAAAATAT
Found at i:5765910 original size:25 final size:27
Alignment explanation
Indices: 5765882--5765931 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
5765872 TTTTCAAACA
*
5765882 TTTT-AAAA-ATTTATATATTATATGT
1 TTTTGAAAACATTTATATATAATATGT
*
5765907 TTTTGAAAACGTTTATATATAATAT
1 TTTTGAAAACATTTATATATAATAT
5765932 TATATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 4 0.19
27 13 0.62
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (27 bp):
TTTTGAAAACATTTATATATAATATGT
Found at i:5766939 original size:2 final size:2
Alignment explanation
Indices: 5766932--5766968 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5766922 GTTTTGGTCC
5766932 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5766969 TCCGAATTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5771490 original size:17 final size:18
Alignment explanation
Indices: 5771462--5771496 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
5771452 GTCATTTTGT
5771462 CCGCACTCAATTGAATGC
1 CCGCACTCAATTGAATGC
5771480 CCGCA-TCAATTGAATGC
1 CCGCACTCAATTGAATGC
5771497 AAAGCATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (18 bp):
CCGCACTCAATTGAATGC
Found at i:5772588 original size:164 final size:165
Alignment explanation
Indices: 5772311--5773475 Score: 1333
Period size: 164 Copynumber: 7.1 Consensus size: 165
5772301 AGCTTAGCTT
* * ** * *
5772311 AAGGCCAGAAGGGCTATCTGCCCAC-CAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
1 AAGGCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
* * * * **
5772375 ATCATTTGCAGTACAGCTTAAGTTGAGAAGAGCTATCTGCCAAAGACCCTTAAGTTCGATTACAC
66 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACAC
*
5772440 TCAGCTTCAAGGGCATAACATTTACAGCATAACTC
131 TCAGCTTCAAGGGCATATCATTTACAGCATAACTC
* * *
5772475 AAGGCTAGAAGGGTTATCTGTTAGC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
1 AAGGCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
* **
5772539 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGT
66 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACAC
* * * *
5772604 TCAGCTTCGAA-GGCACATCATTTGCAGTATAACTT
131 TCAGCTTC-AAGGGCATATCATTTACAGCATAACTC
* *
5772639 AAGTCAAGAAGGATTATCTGCTAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
1 AAGGCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
* **
5772704 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCC-AAGA-CC-CGAGTTCGACTACGT
66 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACAC
* * *
5772766 TCAGCTTCGAA-GGC--ATCATTTGCAGTAT-ACTT
131 TCAGCTTC-AAGGGCATATCATTTACAGCATAACTC
* *
5772798 AAGTCAAGAAGGATTATCTGCTAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG--C
1 AAGGCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
* * * ** * **
5772861 A-CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATGCCAACTAAAGACCCTTAAGTTCGATTAC
66 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTAT--CTGCCAAAGACCCTCGAGTTCGATTAC
5772925 ACTCAGCTTCAAGGGCATATCATTTACAGCATAACTC
129 ACTCAGCTTCAAGGGCATATCATTTACAGCATAACTC
* * *
5772962 AAGGCTAGAAGGGTTATCTG-TCACCAAAGACCTTTGAGTTCGACTACGCTCAG--CCAAGGCAC
1 AAGGCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
* * **
5773024 ATCATTTACAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGT
66 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACAC
* ** * *
5773089 TCAGCTTCGAA-GGCACATCATTTGTAGTATAACTT
131 TCAGCTTC-AAGGGCATATCATTTACAGCATAACTC
* * * * * * * *
5773124 AAGTCAAGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCA
1 AAGGCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCA
* * * * * * * *
5773189 TATCATTTGCGGCACAGCTTAAGTCTAGAAGGGCTGTCTGCCAACAAAAGACCTTCGAGTTTGAT
65 CATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AAAGACCCTCGAGTTCGAT
* ** *
5773254 TATACTCAGCTTCGGGGGCACATCATTTACAGCATAACTC
126 TACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTC
* *
5773294 AAGGCTAGAAGGGTTATCTG-TGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCA
1 AAGGCAAGAAGGGTTATCTGCT-AACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCA
* *
5773358 CATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACTCC-CGAGTTCGATTAC
65 CATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC-CCTCGAGTTCGATTAC
* * * *
5773422 ACTCAACTTCGAGGTCATATCATTTACAACATAACTC
129 ACTCAGCTTCAAGGGCATATCATTTACAGCATAACTC
* * *
5773459 ATGGCGAGAAAGGTTAT
1 AAGGCAAGAAGGGTTAT
5773476 TTGTCAATAA
Statistics
Matches: 856, Mismatches: 119, Indels: 51
0.83 0.12 0.05
Matches are distributed among these distances:
156 31 0.04
157 2 0.00
158 2 0.00
159 70 0.08
160 18 0.02
161 27 0.03
162 95 0.11
163 75 0.09
164 213 0.25
165 148 0.17
166 39 0.05
167 1 0.00
168 1 0.00
169 39 0.05
170 95 0.11
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (165 bp):
AAGGCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACAC
TCAGCTTCAAGGGCATATCATTTACAGCATAACTC
Found at i:5772649 original size:81 final size:81
Alignment explanation
Indices: 5772295--5773457 Score: 952
Period size: 81 Copynumber: 14.2 Consensus size: 81
5772285 TAAACAAACT
* * * *
5772295 ATTTGCAGCTTAGCTTAAGGCCAGAAGGGCTATCTGCCCACCAAGA-CCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG-CCA--AAGACCCTT-GAGTTCGACTACG
5772359 CTCAGC-TCCAAGGCACATC
62 CTCAGCTTCCAAGGCACATC
* * * * * * * *
5772378 ATTTGCAGTACAGCTTAAGTTGAGAAGAGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTTCGACTACGCTCA
* *
5772443 GCTT-CAAGGGCATAAC
66 GCTTCCAA-GGCACATC
* * * * * * *
5772459 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCTTGAGTTCGACTACGC
5772524 TCAGC-TCCAAGGCACATC
63 TCAGCTTCCAAGGCACATC
* * * *
5772542 ATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGTTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTTCGACTACGCTCA
*
5772607 GCTTCGAAGGCACATC
66 GCTTCCAAGGCACATC
* * ** *
5772623 ATTTGCAGTATAACTTAAGTCAAGAAGGATTATCTGCTAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGC---C-AAAGACCCTTGAGTTCGACTACG
5772688 CTCAGC-TCCAAGGCACATC
62 CTCAGCTTCCAAGGCACATC
* * *
5772707 ATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCC-AAGACCC--GAGTTCGACTACGTTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTTCGACTACGCTCA
*
5772769 GCTTCGAAGG--CATC
66 GCTTCCAAGGCACATC
* * ** *
5772783 ATTTGCAGTAT-ACTTAAGTCAAGAAGGATTATCTGCTAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGC---C-AAAGACCCTTGAGTTCGACTACG
5772847 CTCAGC-TCCAAGG--CA-C
62 CTCAGCTTCCAAGGCACATC
* ** * * * *
5772863 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATGCCAACTAAAGACCCTTAAGTTCGATTACACT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTAT--CTGCCAAAGACCCTTGAGTTCGACTACGCT
*
5772928 CAGCTT-CAAGGGCATATC
64 CAGCTTCCAA-GGCACATC
* * * * * *
5772946 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCTTGAGTTCGACTACGC
5773011 TCAG---CCAAGGCACATC
63 TCAGCTTCCAAGGCACATC
* * * * *
5773027 ATTTACAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGTTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTTCGACTACGCTCA
*
5773092 GCTTCGAAGGCACATC
66 GCTTCCAAGGCACATC
* * * * * * *
5773108 ATTTGTAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG-C--C-AAAGACCCTTGAGTTCGACTACG
*
5773173 CTCAGCTT-CAAGGGCATATC
62 CTCAGCTTCCAA-GGCACATC
* * * * * * * *
5773193 ATTTGCGGCACAGCTTAAGTCTAGAAGGGCTGTCTGCCAACAAAAGA-CCTTCGAGTTTGATTAT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG-C--C-AAAGACCCTT-GAGTTCGACTAC
* ***
5773257 ACTCAGCTTCGGGGGCACATC
61 GCTCAGCTTCCAAGGCACATC
* * * * * *
5773278 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGACCCTTGAGTTCGACTACG
5773343 CTCAGC-TCCAAGGCACATC
62 CTCAGCTTCCAAGGCACATC
* * * * *
5773362 ATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACTCC-CGAGTTCGATTACACTC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGAC-CCTTGAGTTCGACTACGCTC
* * *
5773426 AACTT-CGAGGTCATATC
65 AGCTTCCAAGG-CACATC
* *
5773443 ATTTACAACATAACT
1 ATTTGCAGCATAACT
5773458 CATGGCGAGA
Statistics
Matches: 869, Mismatches: 163, Indels: 98
0.77 0.14 0.09
Matches are distributed among these distances:
75 21 0.02
76 14 0.02
77 18 0.02
78 34 0.04
79 34 0.04
80 96 0.11
81 208 0.24
82 28 0.03
83 97 0.11
84 143 0.16
85 170 0.20
86 3 0.00
87 3 0.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (81 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTTCGACTACGCTCA
GCTTCCAAGGCACATC
Found at i:5774085 original size:36 final size:34
Alignment explanation
Indices: 5774040--5774164 Score: 135
Period size: 36 Copynumber: 3.5 Consensus size: 34
5774030 ACATATATAC
*
5774040 ACATATATATATAGTTTGCAAATTATTTTTGAAAAT
1 ACATATATATATAGTTT--AAAATATTTTTGAAAAT
*
5774076 ACATATATATATAGTTTAAAACATTTTTTGAAAAT
1 ACATATATATATAGTTTAAAATA-TTTTTGAAAAT
**
5774111 ATGTATATTATATAGTTTTTAAAATATTTTTGAAAAT
1 ACATATA-TATATAG--TTTAAAATATTTTTGAAAAT
*
5774148 -TATATAATATATAGTTT
1 ACATAT-ATATATAGTTT
5774165 TGAAAACGTT
Statistics
Matches: 78, Mismatches: 6, Indels: 12
0.81 0.06 0.12
Matches are distributed among these distances:
34 7 0.09
35 16 0.21
36 35 0.45
37 12 0.15
38 8 0.10
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (34 bp):
ACATATATATATAGTTTAAAATATTTTTGAAAAT
Found at i:5774183 original size:24 final size:21
Alignment explanation
Indices: 5774127--5774185 Score: 57
Period size: 24 Copynumber: 2.6 Consensus size: 21
5774117 ATTATATAGT
5774127 TTTTAAAATAT-TTTTGAAAA
1 TTTTAAAATATATTTTGAAAA
*
5774147 TTATATAATATATAGTTTTGAAAA
1 TT-T-TAAAATATA-TTTTGAAAA
5774171 CGTTTTAAAATATAT
1 --TTTTAAAATATAT
5774186 ATAATATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
20 2 0.06
21 1 0.03
22 7 0.23
23 1 0.03
24 17 0.55
25 1 0.03
26 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (21 bp):
TTTTAAAATATATTTTGAAAA
Found at i:5774193 original size:35 final size:36
Alignment explanation
Indices: 5774066--5774433 Score: 258
Period size: 35 Copynumber: 10.1 Consensus size: 36
5774056 TGCAAATTAT
* *
5774066 TTTTGAAAATACATAT-ATATATAG-TTT-AAAACATT
1 TTTTGAAAATATATATAATATATAGTTTTGAAAAC--G
* * * **
5774101 TTTTGAAAATATGTATATTATATAGTTTTTAAAATAT
1 TTTTGAAAATATATATAATATATAGTTTTGAAAA-CG
5774138 TTTTGAAAAT-TATATAATATATAGTTTTGAAAACG
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACG
*
5774173 TTTT-AAAATATATATAATATATACTTTTGAAAACG
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACG
* * * * *
5774208 TTATGAAAACATTTATATAATATATAATTTTTAAAAACCA
1 TTTTG-AAA-ATATATATAATATAT-AGTTTTGAAAA-CG
*
5774248 TTTTGAAAATATTTTGAAAATTATATAATATAGTTTTTGAAAACG
1 TTTTGAAAATA---T--ATA-TA-AT-ATATAG-TTTTGAAAACG
* *
5774293 TTTT-TAAA-ATATATAATATATACTTTTGAAAACG
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACG
* * * *
5774327 TTATGAAAACATTTATATAATATAT--TTTTAAAAACCA
1 TTTTG-AAA-ATATATATAATATATAGTTTTGAAAA-CG
* * *
5774364 TTTTGAAAAAATATATAATATATAGTTTTTAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACG
*
5774400 TTTT-AAAA-ATTTAT-ATATAT-GTTTTGAAAACG
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACG
5774432 TT
1 TT
5774434 ATATATATAA
Statistics
Matches: 271, Mismatches: 36, Indels: 55
0.75 0.10 0.15
Matches are distributed among these distances:
32 12 0.04
33 6 0.02
34 24 0.09
35 67 0.25
36 48 0.18
37 33 0.12
38 34 0.13
39 12 0.04
40 6 0.02
41 1 0.00
43 3 0.01
44 5 0.02
45 8 0.03
46 12 0.04
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (36 bp):
TTTTGAAAATATATATAATATATAGTTTTGAAAACG
Found at i:5774330 original size:119 final size:118
Alignment explanation
Indices: 5774126--5774372 Score: 410
Period size: 119 Copynumber: 2.1 Consensus size: 118
5774116 TATTATATAG
*
5774126 TTTTTAAAATATTTTTGAAAATTATATAATATATAGTTTTGAAAACGTTTTAAAATATATATAAT
1 TTTTGAAAATATTTTTGAAAATTATATAATATATA-TTTTGAAAACGTTTTAAAATATATATAAT
5774191 ATATACTTTTGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCA
65 ATATACTTTTGAAAACGTTATGAAAACATTTATAT-A-ATAT-ATTTTTAAAAACCA
*
5774248 TTTTGAAAATA-TTTTGAAAATTATATAATATAGT-TTTTGAAAACGTTTTTAAA-ATATATAAT
1 TTTTGAAAATATTTTTGAAAATTATATAATATA-TATTTTGAAAACGTTTTAAAATATATATAAT
5774310 ATATACTTTTGAAAACGTTATGAAAACATTTATATAATATATTTTTAAAAACCA
65 ATATACTTTTGAAAACGTTATGAAAACATTTATATAATATATTTTTAAAAACCA
5774364 TTTTGAAAA
1 TTTTGAAAA
5774373 AATATATAAT
Statistics
Matches: 122, Mismatches: 2, Indels: 8
0.92 0.02 0.06
Matches are distributed among these distances:
116 23 0.19
117 4 0.03
118 1 0.01
119 44 0.36
120 18 0.15
121 21 0.17
122 11 0.09
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.43
Consensus pattern (118 bp):
TTTTGAAAATATTTTTGAAAATTATATAATATATATTTTGAAAACGTTTTAAAATATATATAATA
TATACTTTTGAAAACGTTATGAAAACATTTATATAATATATTTTTAAAAACCA
Found at i:5774378 original size:71 final size:70
Alignment explanation
Indices: 5774248--5774429 Score: 194
Period size: 73 Copynumber: 2.6 Consensus size: 70
5774238 TTAAAAACCA
* * * *
5774248 TTTTGAAAATATTTTG-AAAA-TTATATAATATAGTTTTTGAAAACGTTTT--TAAAATATATAA
1 TTTTGAAAACA-TTTGAAAAATTTATATAATATA-TTTTTAAAAACATTTTGAAAAAATATATAA
5774309 TATATAC
64 TATATAC
*
5774316 TTTTGAAAACGTTATGAAAACATTTATATAATATATTTTTAAAAACCATTTTGAAAAAATATATA
1 TTTTGAAAACATT-TGAAAA-ATTTATATAATATATTTTTAAAAA-CATTTTGAAAAAATATATA
*
5774381 ATATATAG
63 ATATATAC
* * * *
5774389 TTTTTAAAACATTTTAAAAATTTATAT-ATATGTTTTGAAAA
1 TTTTGAAAACATTTGAAAAATTTATATAATATATTTTTAAAA
5774430 CGTTATATAT
Statistics
Matches: 96, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
67 2 0.02
68 11 0.11
69 3 0.03
70 22 0.23
71 25 0.26
72 5 0.05
73 28 0.29
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.44
Consensus pattern (70 bp):
TTTTGAAAACATTTGAAAAATTTATATAATATATTTTTAAAAACATTTTGAAAAAATATATAATA
TATAC
Found at i:5775463 original size:2 final size:2
Alignment explanation
Indices: 5775451--5775486 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5775441 GTTTTGGTCC
5775451 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5775487 TCCGAATTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5778867 original size:21 final size:19
Alignment explanation
Indices: 5778815--5778868 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 19
5778805 TTAAATTTTG
5778815 TAAAAAAATATATAAATTT
1 TAAAAAAATATATAAATTT
*
5778834 T--ATAAAT-T-TAAATTT
1 TAAAAAAATATATAAATTT
5778849 AATAAAAAAATATATAAATT
1 --TAAAAAAATATATAAATT
5778869 GAAAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
15 7 0.26
16 1 0.04
17 6 0.22
19 6 0.22
20 1 0.04
21 6 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAAAAAATATATAAATTT
Found at i:5778886 original size:26 final size:27
Alignment explanation
Indices: 5778834--5778889 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
5778824 ATATAAATTT
* *
5778834 TATAAATTTAAATTTAATAAAAAAATA
1 TATAAATTGAAATATAATAAAAAAATA
* *
5778861 TATAAATTGAAA-ATAATACAATAATA
1 TATAAATTGAAATATAATAAAAAAATA
5778887 TAT
1 TAT
5778890 TTTCTATGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (27 bp):
TATAAATTGAAATATAATAAAAAAATA
Found at i:5790465 original size:19 final size:19
Alignment explanation
Indices: 5790441--5790479 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
5790431 ATATATTTTT
* *
5790441 TAAATTTTTTAAAAATATA
1 TAAATTGTTGAAAAATATA
*
5790460 TAAATTGTTGAAAAGTATA
1 TAAATTGTTGAAAAATATA
5790479 T
1 T
5790480 TTTTAATAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (19 bp):
TAAATTGTTGAAAAATATA
Found at i:5791705 original size:21 final size:20
Alignment explanation
Indices: 5791666--5791705 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5791656 TAATATATCG
5791666 AATATAATCTAAAATTATAA
1 AATATAATCTAAAATTATAA
* *
5791686 AATATATTCATAATATTATA
1 AATATAATC-TAAAATTATA
5791706 TTTTAAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
AATATAATCTAAAATTATAA
Found at i:5791735 original size:16 final size:17
Alignment explanation
Indices: 5791714--5791752 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
5791704 TATTTTAAAG
*
5791714 AAAATATT-TTGAGAGT
1 AAAATATTAATGAGAGT
5791730 AAAATATTAATGAGAGT
1 AAAATATTAATGAGAGT
5791747 ATAAAT
1 A-AAAT
5791753 GAGTCAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 8 0.40
18 4 0.20
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.33
Consensus pattern (17 bp):
AAAATATTAATGAGAGT
Found at i:5795561 original size:312 final size:315
Alignment explanation
Indices: 5794943--5795573 Score: 766
Period size: 312 Copynumber: 2.0 Consensus size: 315
5794933 GATTCAAAAC
* * * *
5794943 AGTATTGTAACACCATTATGAACACACATATATTGATCTGAGAAGTCTGGTAGGTTAGCCTAGCA
1 AGTATTGTAACACCATTAGGAACACACATATATAGATCTAAGAAGTCTGGTAGGTTAACCTAGCA
* * * * *
5795008 CTGTGACTGCCTATCACAGTCACGACATTGTTAGATCATACGAATCGGAAGAACTATATCAAAAT
66 CTGAGACTACCTATCACAGTCACGACAGTGCTAGATCATACGAATCGAAAGAACTATATCAAAAT
*
5795073 CCTAATATAATAAATAATAAATTATACTTAAACAATTTAAAGAAACCTACGAGTAGCTCTTGAAG
131 CCTAATATAATAAATAATAAAATATACTTAAACAATTTAAAGAAACCTACGAGTAGCTCTTGAAG
* * * * * * *
5795138 AATGTAAATCATACGAATCTGCTGAATGGAGAGCACTGAATCTAGTCAACCCTCAGTCAGGAGAA
196 AACGTAAATCATACAAATATGCTGAACGGAAAGCACCGAACCTAGTCAACCCTCAGTCAGGAGAA
* * *
5795203 ACGTGAAGACCTTCATAAGAATATAATCCCAAATCAATATTATATTCAATACCCA
261 ACGTGAAGACATTCATAAAAATATAATCCCAAATCAATACTATATTCAATACCCA
* *
5795258 AGTATTGTAACACCATTAGGAACACACGTGTATCAG-TCTAAGAAGTCTAGGTAAGG-TAACCTA
1 AGTATTGTAACACCATTAGGAACACACATATAT-AGATCTAAGAAGTCT-GGT-AGGTTAACCTA
* * *
5795321 CTGC-C-GAGACTACCTATCACGGTCAACGACAGTGCTAGATCCTACGAATCGAAAGAACTGTAT
63 --GCACTGAGACTACCTATCACAGTC-ACGACAGTGCTAGATCATACGAATCGAAAGAACTATAT
* * *
5795384 CAAAATCCTAATATAATAAATAATAAAATGTACTT-AA-AA-TTAACA-AAATC-A-GAGTAGTT
125 CAAAATCCTAATATAATAAATAATAAAATATACTTAAACAATTTAA-AGAAACCTACGAGTAGCT
* * * * *
5795443 TTTGAAGAACGTGAATCATACAAATATGTTGAACGGAAAGCACCGAACCTAGTCGACCCT-TGAT
189 CTTGAAGAACGTAAATCATACAAATATGCTGAACGGAAAGCACCGAACCTAGTCAACCCTCAG-T
* *
5795507 CAGG-GAAAACGTG-AGTACATTCATAAAAATATAATCTCAAATCAATACTATATTCAATGCCCA
253 CAGGAG-AAACGTGAAG-ACATTCATAAAAATATAATCCCAAATCAATACTATATTCAATACCCA
5795570 AGTA
1 AGTA
5795574 ATCATGCAAA
Statistics
Matches: 271, Mismatches: 35, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
311 4 0.01
312 114 0.42
313 1 0.00
314 8 0.03
315 44 0.16
316 28 0.10
317 70 0.26
318 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.26
Consensus pattern (315 bp):
AGTATTGTAACACCATTAGGAACACACATATATAGATCTAAGAAGTCTGGTAGGTTAACCTAGCA
CTGAGACTACCTATCACAGTCACGACAGTGCTAGATCATACGAATCGAAAGAACTATATCAAAAT
CCTAATATAATAAATAATAAAATATACTTAAACAATTTAAAGAAACCTACGAGTAGCTCTTGAAG
AACGTAAATCATACAAATATGCTGAACGGAAAGCACCGAACCTAGTCAACCCTCAGTCAGGAGAA
ACGTGAAGACATTCATAAAAATATAATCCCAAATCAATACTATATTCAATACCCA
Found at i:5804340 original size:18 final size:18
Alignment explanation
Indices: 5804317--5804369 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
5804307 GAGGGTTATA
*
5804317 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
*
5804335 AGTGGTCCTTCGGGAAAT
1 AGTGGTCCTTCGGGACAT
5804353 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
5804370 AATTTTAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:5806232 original size:220 final size:221
Alignment explanation
Indices: 5805844--5806272 Score: 603
Period size: 220 Copynumber: 1.9 Consensus size: 221
5805834 GATGATATCG
* * *
5805844 CCTCAACATAGATACATAGAAAATCTCATGAATACAACTACATGGGGGAGGCAACTCAAGCTAAT
1 CCTCAACATAGATACATAGAAAACCTCATGAATACAACTAAATGGGGGAGGCAACTCAAGCAAAT
* * ** * * *
5805909 AACCAATAGGTCCGACTCTCTTTAGAATATGGTATGACCTAGTAAATCTCAGACTTATCTTACCC
66 AAACAATAGGTCCAACTCTCTTTAGAATATAATATGACCTAATAAATCTCAGACTCAGCTTACCC
* * * *
5805974 TTACGTCCAAATCTTAGTGTCTTCTTCCACAAAGATACAAACCTTATTC-CCAACCTCTAACTCG
131 TTACGTCCAAATCCTAGTGTATTCTTCCACAAAGATACAAAACTTATTCTCCAACCTCCAACTCG
*
5806038 ATATCTTTCCTCATCTGATCAGCATA
196 ATATATTTCCTCATCTGATCAGCATA
* *
5806064 CCTCAGCATAGATACATAGAAAACCTCATGAATACAACTAAACT-GGGGAGGCAACTTAAGCAAA
1 CCTCAACATAGATACATAGAAAACCTCATGAATACAACTAAA-TGGGGGAGGCAACTCAAGCAAA
* * *
5806128 TAAACAATAGGTCTAACTCTCTTTAGAATATAATAT-AGCCTAATAAATCTCATACTCAGCTTAT
65 TAAACAATAGGTCCAACTCTCTTTAGAATATAATATGA-CCTAATAAATCTCAGACTCAGCTTAC
* **
5806192 CCTTACGTCCAAATCCTAGTGTATTCTTCCACGAAGATACAAAACTTATTCTTTAACCTCCAACT
129 CCTTACGTCCAAATCCTAGTGTATTCTTCCACAAAGATACAAAACTTATTCTCCAACCTCCAACT
*
5806257 TGATATATTTCCTCAT
194 CGATATATTTCCTCAT
5806273 ATGTTCAACA
Statistics
Matches: 182, Mismatches: 24, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
219 1 0.01
220 156 0.86
221 25 0.14
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.29
Consensus pattern (221 bp):
CCTCAACATAGATACATAGAAAACCTCATGAATACAACTAAATGGGGGAGGCAACTCAAGCAAAT
AAACAATAGGTCCAACTCTCTTTAGAATATAATATGACCTAATAAATCTCAGACTCAGCTTACCC
TTACGTCCAAATCCTAGTGTATTCTTCCACAAAGATACAAAACTTATTCTCCAACCTCCAACTCG
ATATATTTCCTCATCTGATCAGCATA
Found at i:5818746 original size:10 final size:10
Alignment explanation
Indices: 5818733--5818769 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
5818723 CATTTAAATG
5818733 ATAAACGAAC
1 ATAAACGAAC
5818743 ATAAACGAAC
1 ATAAACGAAC
*
5818753 GTAAACGAAC
1 ATAAACGAAC
5818763 ATAAACG
1 ATAAACG
5818770 GACAACACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.57, C:0.19, G:0.14, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:5819072 original size:14 final size:14
Alignment explanation
Indices: 5819055--5819089 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5819045 ATGAACGAAC
*
5819055 ATGAATGGACATAA
1 ATGAACGGACATAA
5819069 ATGAACGGACATAA
1 ATGAACGGACATAA
*
5819083 ACGAACG
1 ATGAACG
5819090 TAAAATCGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.49, C:0.14, G:0.23, T:0.14
Consensus pattern (14 bp):
ATGAACGGACATAA
Found at i:5819093 original size:24 final size:24
Alignment explanation
Indices: 5819036--5819093 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
5819026 GCCCTCTGTT
* *
5819036 CGAATATAAATGAACGAACATGAA
1 CGAACATAAATGAACGAACATAAA
* * *
5819060 TGGACATAAATGAACGGACATAAA
1 CGAACATAAATGAACGAACATAAA
*
5819084 CGAACGTAAA
1 CGAACATAAA
5819094 ATCGAACGTT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.14, G:0.19, T:0.16
Consensus pattern (24 bp):
CGAACATAAATGAACGAACATAAA
Found at i:5819555 original size:31 final size:31
Alignment explanation
Indices: 5819518--5819621 Score: 163
Period size: 31 Copynumber: 3.4 Consensus size: 31
5819508 TTTAATCACC
* *
5819518 AATTTAAAATGAGAGTTATAGTTTGAGTACT
1 AATTTAAAATGAGGGTTATAGTTTGAGCACT
*
5819549 AATTTAAAATGAGGGTTATAGTTTGAGCATT
1 AATTTAAAATGAGGGTTATAGTTTGAGCACT
* *
5819580 AATTTAAAATGAGGGTTATAATTTGAGCACC
1 AATTTAAAATGAGGGTTATAGTTTGAGCACT
5819611 AATTTAAAATG
1 AATTTAAAATG
5819622 GGTTCTTTTG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 67 1.00
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.37
Consensus pattern (31 bp):
AATTTAAAATGAGGGTTATAGTTTGAGCACT
Found at i:5822051 original size:3 final size:3
Alignment explanation
Indices: 5822043--5822073 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5822033 TTACATAAAC
5822043 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5822074 TAAATAGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5828073 original size:2 final size:2
Alignment explanation
Indices: 5828066--5828092 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5828056 ATCGAGTAGT
5828066 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
5828093 TTTAACATAT
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:5829621 original size:20 final size:20
Alignment explanation
Indices: 5829589--5829626 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5829579 CACTAACTTA
*
5829589 TTTCTTTTGATTGTATCATC
1 TTTCTTTTGATTGCATCATC
5829609 TTTC-TTTGCATTGCATCA
1 TTTCTTTTG-ATTGCATCA
5829627 ACATAACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.16, C:0.18, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTCTTTTGATTGCATCATC
Found at i:5830145 original size:27 final size:26
Alignment explanation
Indices: 5830101--5830155 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
5830091 ATCAACATTT
*
5830101 TTTGCATATGCATTTGTATTTGCATC
1 TTTGCATATGCATATGTATTTGCATC
* *
5830127 TTTGCATTTTGCATATGTATTTGTATC
1 TTTGCA-TATGCATATGTATTTGCATC
5830154 TT
1 TT
5830156 CACATTCTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.18, C:0.13, G:0.15, T:0.55
Consensus pattern (26 bp):
TTTGCATATGCATATGTATTTGCATC
Found at i:5830161 original size:27 final size:27
Alignment explanation
Indices: 5830109--5830183 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
5830099 TTTTTGCATA
* ** *
5830109 TGCATTTGTATTTGCATCTTTGCATTT
1 TGCATATGTATTTGCATCTTCACATTC
*
5830136 TGCATATGTATTTGTATCTTCACATTC
1 TGCATATGTATTTGCATCTTCACATTC
*
5830163 TGCATGATGCA-TTGCAT-TTCA
1 TGCAT-ATGTATTTGCATCTTCA
5830184 GAGGATCATC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
26 4 0.10
27 32 0.80
28 4 0.10
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.48
Consensus pattern (27 bp):
TGCATATGTATTTGCATCTTCACATTC
Found at i:5830203 original size:63 final size:63
Alignment explanation
Indices: 5830132--5830296 Score: 233
Period size: 63 Copynumber: 2.6 Consensus size: 63
5830122 GCATCTTTGC
* * *
5830132 ATTTTGCATATGTATTTGTATCTTCACATTCTGCATGATGCATTGCATTTCAGAGGATCATCA
1 ATTTTGCATCTGCATTTGTATCTTCGCATTCTGCATGATGCATTGCATTTCAGAGGATCATCA
* * * * *
5830195 ATTTTGCATCTACATTTGCATCTTCGCATTCTGCATGATGTATTGTATTTCATAGGATCATCA
1 ATTTTGCATCTGCATTTGTATCTTCGCATTCTGCATGATGCATTGCATTTCAGAGGATCATCA
*
5830258 ATTTTGCATCTGCATTTGCT-TCTTCGCATTTTGCATGAT
1 ATTTTGCATCTGCATTTG-TATCTTCGCATTCTGCATGAT
5830297 CATCATAAAT
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 90 1.00
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (63 bp):
ATTTTGCATCTGCATTTGTATCTTCGCATTCTGCATGATGCATTGCATTTCAGAGGATCATCA
Found at i:5832394 original size:8 final size:8
Alignment explanation
Indices: 5832368--5832444 Score: 54
Period size: 8 Copynumber: 10.0 Consensus size: 8
5832358 AGATCCAATC
*
5832368 AGAACAAA
1 AGAAAAAA
*
5832376 A-AAAGAA
1 AGAAAAAA
5832383 AGAAAAAA
1 AGAAAAAA
*
5832391 AG-AAAAG
1 AGAAAAAA
* *
5832398 AGCAACAA
1 AGAAAAAA
*
5832406 AGAGCAAAA
1 AGA-AAAAA
5832415 AG--AAAA
1 AGAAAAAA
*
5832421 AGAAACAA
1 AGAAAAAA
5832429 AGAAAAAA
1 AGAAAAAA
5832437 AGAAAAAA
1 AGAAAAAA
5832445 CAAAGAAAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
6 6 0.11
7 11 0.21
8 31 0.58
9 5 0.09
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:5832394 original size:23 final size:22
Alignment explanation
Indices: 5832368--5832444 Score: 82
Period size: 23 Copynumber: 3.4 Consensus size: 22
5832358 AGATCCAATC
*
5832368 AGAACAAAAAAAGAAAGAAAAAA
1 AGAA-AAAAAAACAAAGAAAAAA
** *
5832391 AGAAAAGAGCAACAAAGAGCAAAA
1 AGAAAA-AAAAACAAAGA-AAAAA
*
5832415 AGAAAAAGAAACAAAGAAAAAA
1 AGAAAAAAAAACAAAGAAAAAA
5832437 AGAAAAAA
1 AGAAAAAA
5832445 CAAAGAAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
22 13 0.29
23 22 0.49
24 10 0.22
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (22 bp):
AGAAAAAAAAACAAAGAAAAAA
Found at i:5832454 original size:19 final size:20
Alignment explanation
Indices: 5832381--5832454 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 20
5832371 ACAAAAAAAG
5832381 AAAGAAAAAAAGAAAAGAGCAAC
1 AAAGAAAAAAAG-AAAGA--AAC
*
5832404 AAAGAGCAAAAAGAAAAAGAAAC
1 AAAGA--AAAAA-AGAAAGAAAC
5832427 AAAGAAAAAAAGAAA-AAAC
1 AAAGAAAAAAAGAAAGAAAC
5832446 AAAGAAAAA
1 AAAGAAAAA
5832455 GGGACGAGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
19 13 0.28
20 4 0.09
21 5 0.11
23 13 0.28
25 10 0.22
26 1 0.02
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAAAGAAAGAAAC
Found at i:5833501 original size:32 final size:32
Alignment explanation
Indices: 5833464--5833547 Score: 123
Period size: 32 Copynumber: 2.6 Consensus size: 32
5833454 TAATGAGGGA
* *
5833464 ATCTTTGAAGATTCAACATCAAATGTTGGGGC
1 ATCTTTGGAGATTCAACATCAAATATTGGGGC
* *
5833496 ATCTTTGGAGATTCAACATCGAATATTGGGGT
1 ATCTTTGGAGATTCAACATCAAATATTGGGGC
*
5833528 ATCTTTGGGGATTCAACATC
1 ATCTTTGGAGATTCAACATC
5833548 CTGATGTGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (32 bp):
ATCTTTGGAGATTCAACATCAAATATTGGGGC
Found at i:5833812 original size:22 final size:22
Alignment explanation
Indices: 5833787--5833837 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
5833777 AATCTTTGAG
*
5833787 TTTGTTTCTTTGAAAACAAAAT
1 TTTGTCTCTTTGAAAACAAAAT
5833809 TTTGTCTCTTTGAAAACAAAAT
1 TTTGTCTCTTTGAAAACAAAAT
5833831 TTTGTCT
1 TTTGTCT
5833838 ATTTTGAGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (22 bp):
TTTGTCTCTTTGAAAACAAAAT
Found at i:5834022 original size:42 final size:41
Alignment explanation
Indices: 5833976--5834094 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 41
5833966 TGTAGGAGCT
5833976 GTATCAACCCAGATAACCAGTCGTCCTCATCACGTATGAACC
1 GTATCAACCCAGATAACCAGTCGTCCTCATCACGTA-GAACC
* * * *
5834018 GTATCATCACCC-G---ACCAGAT-TTCCTCATTATGTAGAAGCT
1 GTATCA--ACCCAGATAACCAG-TCGTCCTCATCACGTAGAA-CC
* *
5834058 GTGTCAACCCAGATAACCAGCCGTCCTCATCACGTAG
1 GTATCAACCCAGATAACCAGTCGTCCTCATCACGTAG
5834095 GAACTGTGTT
Statistics
Matches: 59, Mismatches: 9, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
38 4 0.07
39 4 0.07
40 22 0.37
41 1 0.02
42 23 0.39
43 1 0.02
44 4 0.07
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.24
Consensus pattern (41 bp):
GTATCAACCCAGATAACCAGTCGTCCTCATCACGTAGAACC
Found at i:5834059 original size:82 final size:82
Alignment explanation
Indices: 5833922--5834098 Score: 248
Period size: 82 Copynumber: 2.2 Consensus size: 82
5833912 AGAACTCTTT
* * * *
5833922 ATCACGTATGAGCCATGTCATCCACCGACCAGATCTCTTCATCATGTAGGAGCTGTATCAACCCA
1 ATCACGTATGAACCATATCATCCACCGACCAGATCTCCTCATCATGTAGAAGCTGTATCAACCCA
*
5833987 GATAACCAGTCGTCCTC
66 GATAACCAGCCGTCCTC
* * * *
5834004 ATCACGTATGAACCGTATCAT-CACCCGACCAGATTTCCTCATTATGTAGAAGCTGTGTCAACCC
1 ATCACGTATGAACCATATCATCCA-CCGACCAGATCTCCTCATCATGTAGAAGCTGTATCAACCC
5834068 AGATAACCAGCCGTCCTC
65 AGATAACCAGCCGTCCTC
*
5834086 ATCACGTAGGAAC
1 ATCACGTATGAAC
5834099 TGTGTTATCA
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
81 2 0.02
82 82 0.98
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (82 bp):
ATCACGTATGAACCATATCATCCACCGACCAGATCTCCTCATCATGTAGAAGCTGTATCAACCCA
GATAACCAGCCGTCCTC
Found at i:5834131 original size:46 final size:45
Alignment explanation
Indices: 5834079--5834411 Score: 243
Period size: 46 Copynumber: 7.6 Consensus size: 45
5834069 GATAACCAGC
** * **
5834079 CGTCCTCATCACGTAGGAACTGTGTTATCACCCTTAGATGGTCTGT
1 CGTCCTCATCACGTAGGAACCATGTCATCACCCTTAGAT-ACCTGT
*
5834125 CGTCCTCATCGCGTAGGAACCATGTCATCACCC---G--ACCTGAT
1 CGTCCTCATCACGTAGGAACCATGTCATCACCCTTAGATACCTG-T
* * * *
5834166 -TTCCTCATCACGTAGGAACCATGTCA--ACCC-CAGATAACCAGC
1 CGTCCTCATCACGTAGGAACCATGTCATCACCCTTAGAT-ACCTGT
* * * * * * *
5834208 CGTCCTCATCACATAGGAATCGTGTTATCACCTTTAGATGATCTAT
1 CGTCCTCATCACGTAGGAACCATGTCATCACCCTTAGAT-ACCTGT
5834254 CGTCCTCATCACGTAGGAACCATGTCATCA-CC-T-G--ACCTGAT
1 CGTCCTCATCACGTAGGAACCATGTCATCACCCTTAGATACCTG-T
* * * *
5834295 C-TCCTCATCACGTAGGAGCCGTGTCA-C-CCCTTTGATAACCAGT
1 CGTCCTCATCACGTAGGAACCATGTCATCACCCTTAGAT-ACCTGT
* * * *
5834338 CGTCCTCATCACGTAGGAACAATGTTATCACCCTTAGATGACATGC
1 CGTCCTCATCACGTAGGAACCATGTCATCACCCTTAGAT-ACCTGT
5834384 CGTCCTCAT-AGCGTAGGAACCATGTCAT
1 CGTCCTCATCA-CGTAGGAACCATGTCAT
5834412 TACTCGACCA
Statistics
Matches: 223, Mismatches: 43, Indels: 42
0.72 0.14 0.14
Matches are distributed among these distances:
38 4 0.02
39 3 0.01
40 55 0.25
41 4 0.02
43 29 0.13
44 26 0.12
45 6 0.03
46 96 0.43
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (45 bp):
CGTCCTCATCACGTAGGAACCATGTCATCACCCTTAGATACCTGT
Found at i:5834182 original size:40 final size:40
Alignment explanation
Indices: 5834127--5834320 Score: 129
Period size: 40 Copynumber: 4.6 Consensus size: 40
5834117 TGGTCTGTCG
*
5834127 TCCTCATCGCGTAGGAACCATGTCATCACCCGACCTGATT
1 TCCTCATCACGTAGGAACCATGTCATCACCCGACCTGATT
* * ***
5834167 TCCTCATCACGTAGGAACCATGTCAAC-CCCAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCATGTCATCACCC-G---ACCTGATT
* * * * ** **
5834210 TCCTCATCACATAGGAATCGTGTTATCACCTTTAGATGATCTAT
1 TCCTCATCACGTAGGAACCATGTCATCACC-CGACCTGA--T-T
* *
5834254 CGTCCTCATCACGTAGGAACCATGTCATCACCTGACCTGATC
1 --TCCTCATCACGTAGGAACCATGTCATCACCCGACCTGATT
* *
5834296 TCCTCATCACGTAGGAGCCGTGTCA
1 TCCTCATCACGTAGGAACCATGTCA
5834321 CCCCTTTGAT
Statistics
Matches: 114, Mismatches: 29, Indels: 22
0.69 0.18 0.13
Matches are distributed among these distances:
39 3 0.03
40 49 0.43
41 2 0.02
43 27 0.24
44 2 0.02
45 5 0.04
46 26 0.23
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.25
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCATGTCATCACCCGACCTGATT
Found at i:5834247 original size:129 final size:129
Alignment explanation
Indices: 5833995--5834454 Score: 556
Period size: 129 Copynumber: 3.6 Consensus size: 129
5833985 CAGATAACCA
* * * * * * *
5833995 GTCGTCCTCATCACGTATGAACCGTATCATCACCCGACCAGATTTCCTCATTATGTA-GAAGCTG
1 GTCGTCCTCATCACGTAGGAACCATGTCATCACCCGACCAGATCTCCTCATCACGTAGGAA-CCG
*
5834059 TGTCAA-CCCAGATAACCAGCCGTCCTCATCACGTAGGAACTGTGTTATCACCCTTAGATGGTCT
65 TGTCAACCCCAGATAACCAGCCGTCCTCATCACGTAGGAACAGTGTTATCACCCTTAGATGGTCT
* * * *
5834123 GTCGTCCTCATCGCGTAGGAACCATGTCATCACCCGACCTGATTTCCTCATCACGTAGGAACCAT
1 GTCGTCCTCATCACGTAGGAACCATGTCATCACCCGACCAGATCTCCTCATCACGTAGGAACCGT
* * *
5834188 GTCAACCCCAGATAACCAGCCGTCCTCATCACATAGGAATC-GTGTTATCACCTTTAGATGATCT
66 GTCAACCCCAGATAACCAGCCGTCCTCATCACGTAGGAA-CAGTGTTATCACCCTTAGATGGTCT
* * * *
5834252 ATCGTCCTCATCACGTAGGAACCATGTCATCACCTGACCTGATCTCCTCATCACGTAGGAGCCGT
1 GTCGTCCTCATCACGTAGGAACCATGTCATCACCCGACCAGATCTCCTCATCACGTAGGAACCGT
* * * *
5834317 GTC-ACCCCTTTGATAACCAGTCGTCCTCATCACGTAGGAACAATGTTATCACCCTTAGAT-GAC
66 GTCAACCCC--AGATAACCAGCCGTCCTCATCACGTAGGAACAGTGTTATCACCCTTAGATGGTC
5834380 AT
129 -T
* * * * **
5834382 GCCGTCCTCAT-AGCGTAGGAACCATGTCATTACTCGACCAGATCTCCTCATCACATAGGAGTCG
1 GTCGTCCTCATCA-CGTAGGAACCATGTCATCACCCGACCAGATCTCCTCATCACGTAGGAACCG
5834446 TGTC-ACCCC
65 TGTCAACCCC
5834455 TTTGATAGCT
Statistics
Matches: 291, Mismatches: 33, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
128 62 0.21
129 121 0.42
130 108 0.37
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.26
Consensus pattern (129 bp):
GTCGTCCTCATCACGTAGGAACCATGTCATCACCCGACCAGATCTCCTCATCACGTAGGAACCGT
GTCAACCCCAGATAACCAGCCGTCCTCATCACGTAGGAACAGTGTTATCACCCTTAGATGGTCT
Found at i:5834392 original size:130 final size:127
Alignment explanation
Indices: 5833997--5834502 Score: 547
Period size: 130 Copynumber: 3.9 Consensus size: 127
5833987 GATAACCAGT
* * * * * * * *
5833997 CGTCCTCATCACGTATGAACCGTATCATCACCCGACCAGATTTCCTCATTATGTAGAAGCTGTGT
1 CGTCCTCATCACGTAGGAACCATGTCATCACCCGACCAGATCTCCTCATCACGTAGGAGCCGTGT
* * *
5834062 CAACCCAGATAACCAGCCGTCCTCATCACGTAGGAA-CTGTGTTATCACCCTTAGATGGTC-TG
66 CACCCCAGATAACCAGCCGTCCTCATCACGTAGGAATC-ATGTTATCACCCTTAGAT-GACATG
* * * * *
5834124 TCGTCCTCATCGCGTAGGAACCATGTCATCACCCGACCTGATTTCCTCATCACGTAGGAACCATG
1 -CGTCCTCATCACGTAGGAACCATGTCATCACCCGACCAGATCTCCTCATCACGTAGGAGCCGTG
* * *
5834189 TCAACCCCAGATAACCAGCCGTCCTCATCACATAGGAATCGTGTTATCACCTTTAGATGATCTAT
65 TC-ACCCCAGATAACCAGCCGTCCTCATCACGTAGGAATCATGTTATCACCCTTAGATGA-C-AT
5834254 -
127 G
* *
5834254 CGTCCTCATCACGTAGGAACCATGTCATCACCTGACCTGATCTCCTCATCACGTAGGAGCCGTGT
1 CGTCCTCATCACGTAGGAACCATGTCATCACCCGACCAGATCTCCTCATCACGTAGGAGCCGTGT
* *
5834319 CACCCCTTTGATAACCAGTCGTCCTCATCACGTAGGAA-CAATGTTATCACCCTTAGATGACATG
66 CACCCC--AGATAACCAGCCGTCCTCATCACGTAGGAATC-ATGTTATCACCCTTAGATGACATG
* * * *
5834383 CCGTCCTCAT-AGCGTAGGAACCATGTCATTACTCGACCAGATCTCCTCATCACATAGGAGTCGT
1 -CGTCCTCATCA-CGTAGGAACCATGTCATCACCCGACCAGATCTCCTCATCACGTAGGAGCCGT
* * * ** *
5834447 GTCACCCCTTTGATAGCTAGTTGTCCTCATCGCGTAGGAATCGA-GTTATCACCCTT
64 GTCACCCC--AGATAACCAGCCGTCCTCATCACGTAGGAATC-ATGTTATCACCCTT
5834503 CGTAAAGATA
Statistics
Matches: 330, Mismatches: 36, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
128 63 0.19
129 115 0.35
130 149 0.45
131 3 0.01
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.27
Consensus pattern (127 bp):
CGTCCTCATCACGTAGGAACCATGTCATCACCCGACCAGATCTCCTCATCACGTAGGAGCCGTGT
CACCCCAGATAACCAGCCGTCCTCATCACGTAGGAATCATGTTATCACCCTTAGATGACATG
Found at i:5835862 original size:2 final size:2
Alignment explanation
Indices: 5835855--5835912 Score: 52
Period size: 2 Copynumber: 30.5 Consensus size: 2
5835845 ATCGAGTAGT
* * *
5835855 TA TA TA TA TA TA TA TA TA TA TA -A TA T- TT TA -A TT TT TA TGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
5835895 T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
5835913 TATTTTAACA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
1 4 0.08
2 42 0.88
3 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (2 bp):
TA
Found at i:5837711 original size:16 final size:16
Alignment explanation
Indices: 5837671--5837792 Score: 72
Period size: 16 Copynumber: 7.5 Consensus size: 16
5837661 GATCAAAGAC
*
5837671 AAATATAAAAATAATA
1 AAATAAAAAAATAATA
*
5837687 AACTAAAAAAATAATA
1 AAATAAAAAAATAATA
* *
5837703 AAATCAAAAGAGAAGAAAA
1 AAAT-AAAA-A-AATAATA
*
5837722 AAATAAATAAAT-A-A
1 AAATAAAAAAATAATA
* * *
5837736 AAATAGAGAAA-AATC
1 AAATAAAAAAATAATA
* *
5837751 GAAGAAATAAAATGAGATA
1 AAATAAA-AAAAT-A-ATA
5837770 AAATAAAAAAATAA-A
1 AAATAAAAAAATAATA
5837785 AAATAAAA
1 AAATAAAA
5837793 TACATGAAAA
Statistics
Matches: 80, Mismatches: 17, Indels: 19
0.69 0.15 0.16
Matches are distributed among these distances:
14 11 0.14
15 14 0.17
16 23 0.29
17 6 0.08
18 10 0.12
19 16 0.20
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (16 bp):
AAATAAAAAAATAATA
Found at i:5837745 original size:26 final size:27
Alignment explanation
Indices: 5837691--5837748 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
5837681 ATAATAAACT
*
5837691 AAAAAAATAATAAAATCAAAAGAGAAG
1 AAAAAAATAATAAAATAAAAAGAGAAG
*
5837718 AAAAAAATAA-ATAAATAAAAATAG-AG
1 AAAAAAATAATA-AAATAAAAAGAGAAG
5837744 AAAAA
1 AAAAA
5837749 TCGAAGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.78, C:0.02, G:0.09, T:0.12
Consensus pattern (27 bp):
AAAAAAATAATAAAATAAAAAGAGAAG
Done.