Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_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: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 78
Found at i:5359646 original size:55 final size:53
Alignment explanation
Indices: 5359496--5359652 Score: 133
Period size: 55 Copynumber: 2.8 Consensus size: 53
5359486 TTTAATATCT
* * *
5359496 TTATTAAAT-ATATTAAATATATAAATAATATTATTCATTATTAATATATAAATTT
1 TTATTATATAATATTAAA-A-ATAAATAATATTA-TAATTATTAATATATAAATTA
* *
5359551 TTATTATATATTATTAAAATAAAAATAATATCT-TATATTATT-ATA-ATATAATTGA
1 TTATTATATAATATTAAAA-ATAAATAATAT-TATA-ATTATTAATATATA-AATT-A
* *
5359606 TTATTTTTATAATATTAAAAATAATATAATATTATAATTATAAATAT
1 TTA-TTATATAATATTAAAAATAA-ATAATATTATAATTATTAATAT
5359653 TAATAAATAT
Statistics
Matches: 83, Mismatches: 9, Indels: 18
0.75 0.08 0.16
Matches are distributed among these distances:
53 3 0.04
54 8 0.10
55 38 0.46
56 34 0.41
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (53 bp):
TTATTATATAATATTAAAAATAAATAATATTATAATTATTAATATATAAATTA
Found at i:5359649 original size:25 final size:25
Alignment explanation
Indices: 5359612--5359663 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
5359602 TTGATTATTT
5359612 TTATAATATTAAA-AATAATATAATA
1 TTATAATATTAAATAATAATA-AATA
*
5359637 TTATAAT-TATAAATATTAATAAATA
1 TTATAATAT-TAAATAATAATAAATA
5359662 TT
1 TT
5359664 TTTAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 1 0.04
25 17 0.71
26 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TTATAATATTAAATAATAATAAATA
Found at i:5360638 original size:118 final size:116
Alignment explanation
Indices: 5360504--5360726 Score: 311
Period size: 118 Copynumber: 1.9 Consensus size: 116
5360494 ATTTACGGGT
* * * * *
5360504 TAGTTGAAATGATAAATAATTTAATATCGTTTAAATAAGTTTTAAATTTGAAGTTTTATGTATAC
1 TAGTTCAAATGATAAATAATTTAATATCATTTAAAAAAGTCTTAAATTTGAAGTCTTATG--TAC
* * * * * *
5360569 ATAAAATTTTTATTGGAAGATTTGTCTATTAAAATTAGATGTCTATTAACGGA
64 ATAAAATCTTTATTGAAAGACTCGTCCACTAAAATTAGATGTCTATTAACGGA
*
5360622 TAGTTCAAATGATAAATAATTTAATATCATTTAAAAAAGTCTTAAGTTTGAAGTCTTATGTACAT
1 TAGTTCAAATGATAAATAATTTAATATCATTTAAAAAAGTCTTAAATTTGAAGTCTTATGTACAT
*
5360687 AAAATCTTTGTTGAAAGACTCGTCCACTAAAATTAGATGT
66 AAAATCTTTATTGAAAGACTCGTCCACTAAAATTAGATGT
5360727 GTGACATCAA
Statistics
Matches: 92, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
116 38 0.41
118 54 0.59
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.40
Consensus pattern (116 bp):
TAGTTCAAATGATAAATAATTTAATATCATTTAAAAAAGTCTTAAATTTGAAGTCTTATGTACAT
AAAATCTTTATTGAAAGACTCGTCCACTAAAATTAGATGTCTATTAACGGA
Found at i:5363760 original size:22 final size:21
Alignment explanation
Indices: 5363721--5363761 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5363711 AGTAAAAAAA
**
5363721 CCGGATCGATTTTTATCCGAT
1 CCGGATCGATTTAAATCCGAT
5363742 CCGGATCGAATTTAAATCCG
1 CCGGATCG-ATTTAAATCCG
5363762 GCTATGTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (21 bp):
CCGGATCGATTTAAATCCGAT
Found at i:5367863 original size:49 final size:49
Alignment explanation
Indices: 5367772--5367865 Score: 134
Period size: 49 Copynumber: 1.9 Consensus size: 49
5367762 ATAAGCATAA
**
5367772 AGGGGCGGACCTCCATGCAGCCCGGGGTATCCCGGGCAACCCCTCATCC
1 AGGGGCGGACCTCCATGCAGCCCGGGGTATCCCAAGCAACCCCTCATCC
* ** *
5367821 AGGGGTGGACCTCCATGGTGCCCGGGGTATCCCAAGCCACCCCTC
1 AGGGGCGGACCTCCATGCAGCCCGGGGTATCCCAAGCAACCCCTC
5367866 CACAAGTGCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.16, C:0.39, G:0.31, T:0.14
Consensus pattern (49 bp):
AGGGGCGGACCTCCATGCAGCCCGGGGTATCCCAAGCAACCCCTCATCC
Found at i:5369757 original size:16 final size:15
Alignment explanation
Indices: 5369727--5369760 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
5369717 TAAAAAAGAA
5369727 AAATAAAATAATAAT
1 AAATAAAATAATAAT
*
5369742 AAATAATAATAGTAAT
1 AAATAA-AATAATAAT
5369758 AAA
1 AAA
5369761 GATAAAAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
AAATAAAATAATAAT
Found at i:5370602 original size:24 final size:25
Alignment explanation
Indices: 5370561--5370608 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
5370551 AAATCCTAAT
*
5370561 TAAAATACTAACATCTATT-TAAAC
1 TAAAATACTAACAACTATTATAAAC
5370585 TAAAATACCTAA-AACTATTATAAA
1 TAAAATA-CTAACAACTATTATAAA
5370609 ATATAATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (25 bp):
TAAAATACTAACAACTATTATAAAC
Found at i:5374412 original size:48 final size:49
Alignment explanation
Indices: 5374360--5374496 Score: 183
Period size: 48 Copynumber: 2.9 Consensus size: 49
5374350 TTGGCACTGA
* *
5374360 AATTGAAGAAACAA-ATGTGCAT-AGATCGGCCATAAATGATGGTGCAGG
1 AATTGAAGAAACAACACGTGCATGA-ATCGACCATAAATGATGGTGCAGG
*
5374408 AATTGAAG-AACAACACGTGCATGAATCGACCATAAATGATGGTGCATG
1 AATTGAAGAAACAACACGTGCATGAATCGACCATAAATGATGGTGCAGG
* * *
5374456 AATTGAAG-AACAACACGTGCGTGAGTCAACCATAAATGATG
1 AATTGAAGAAACAACACGTGCATGAATCGACCATAAATGATG
5374497 ATACAGAAAT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
47 5 0.06
48 75 0.93
49 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.20
Consensus pattern (49 bp):
AATTGAAGAAACAACACGTGCATGAATCGACCATAAATGATGGTGCAGG
Found at i:5390551 original size:59 final size:60
Alignment explanation
Indices: 5390455--5390570 Score: 166
Period size: 59 Copynumber: 1.9 Consensus size: 60
5390445 CATCATATGC
* *
5390455 CCCCAAACTATAACCTTCATTTTAAATTGTTCCTTAAACTTTTGAAGATTCTAATTTGAT
1 CCCCAAACTATAACCTTCATTCTAAATTGTTCCTTAAACTTTTGAACATTCTAATTTGAT
*
5390515 CCCCAAACTATAA-CTCTCA-TCTAAATTAG-TCCTTAAACTTTTGAACATTCTGATTT
1 CCCCAAACTATAACCT-TCATTCTAAATT-GTTCCTTAAACTTTTGAACATTCTAATTT
5390571 CATTCCTAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
59 34 0.67
60 17 0.33
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (60 bp):
CCCCAAACTATAACCTTCATTCTAAATTGTTCCTTAAACTTTTGAACATTCTAATTTGAT
Found at i:5390814 original size:60 final size:60
Alignment explanation
Indices: 5390717--5390862 Score: 150
Period size: 60 Copynumber: 2.4 Consensus size: 60
5390707 TATAGCTTGT
* * * * * * * * *
5390717 ATGAATTTGGAATGTTTAGAAAGTTTGGGGACCAATTTAGAATGA-AGGTTATAGTTTGGGG
1 ATGAAATTGAAATATTTA-AAAGTTTGAGAACCAATTTAGAATGATA-CTCATAGTTTAGAG
* * *
5390778 ATGAAATTGAAATATTTAAAAGTTTGAGAACTAATTTAGAATGATACTCATGGTTTATAG
1 ATGAAATTGAAATATTTAAAAGTTTGAGAACCAATTTAGAATGATACTCATAGTTTAGAG
*
5390838 ATGAAATTGAAACATTTAAAAGTTT
1 ATGAAATTGAAATATTTAAAAGTTT
5390863 ACAAACCCAC
Statistics
Matches: 71, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
60 55 0.77
61 16 0.23
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (60 bp):
ATGAAATTGAAATATTTAAAAGTTTGAGAACCAATTTAGAATGATACTCATAGTTTAGAG
Found at i:5396517 original size:13 final size:13
Alignment explanation
Indices: 5396445--5396549 Score: 52
Period size: 13 Copynumber: 7.5 Consensus size: 13
5396435 AAATATAATA
5396445 TATATAATATAAAT
1 TATAT-ATATAAAT
5396459 T-TATATATAAA-
1 TATATATATAAAT
*
5396470 CATATATTATAAACT
1 TATATA-TATAAA-T
*
5396485 ATATAATTATTATAAGT
1 -TAT-A-TA-TATAAAT
5396502 TATATATATAAAT
1 TATATATATAAAT
* * *
5396515 TATGTTTATATGAAC
1 TA--TATATATAAAT
* *
5396530 TATATATGTAAAC
1 TATATATATAAAT
5396543 TATATAT
1 TATATAT
5396550 GTATAAACTA
Statistics
Matches: 72, Mismatches: 10, Indels: 19
0.71 0.10 0.19
Matches are distributed among these distances:
12 11 0.15
13 32 0.44
14 3 0.04
15 11 0.15
16 5 0.07
17 2 0.03
18 8 0.11
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (13 bp):
TATATATATAAAT
Found at i:5396550 original size:13 final size:13
Alignment explanation
Indices: 5396527--5396552 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5396517 TGTTTATATG
5396527 AACTATATATGTA
1 AACTATATATGTA
5396540 AACTATATATGTA
1 AACTATATATGTA
5396553 TAAACTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
AACTATATATGTA
Found at i:5396556 original size:15 final size:14
Alignment explanation
Indices: 5396445--5396561 Score: 75
Period size: 15 Copynumber: 8.3 Consensus size: 14
5396435 AAATATAATA
*
5396445 TATATAATATAAA-
1 TATATATTATAAAC
*
5396458 TTTATA-TATAAAC
1 TATATATTATAAAC
5396471 -ATATATTATAAAC
1 TATATATTATAAAC
*
5396484 TATATAATTATTATAAG
1 TATAT-ATTA-TA-AAC
*
5396501 T-TATATATATAAAT
1 TATATAT-TATAAAC
*
5396515 TATGT-TTATATGAAC
1 TATATATTATA--AAC
*
5396530 TATATA-TGTAAAC
1 TATATATTATAAAC
5396543 TATATATGTATAAAC
1 TATATAT-TATAAAC
5396558 TATA
1 TATA
5396562 AAAAGTATAT
Statistics
Matches: 82, Mismatches: 9, Indels: 24
0.71 0.08 0.21
Matches are distributed among these distances:
12 10 0.12
13 25 0.30
14 8 0.10
15 29 0.35
16 7 0.09
17 3 0.04
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (14 bp):
TATATATTATAAAC
Found at i:5396711 original size:19 final size:20
Alignment explanation
Indices: 5396687--5396768 Score: 89
Period size: 19 Copynumber: 4.2 Consensus size: 20
5396677 TCTTATTTGG
5396687 GAATTTAGAGGGAAATTG-A
1 GAATTTAGAGGGAAATTGAA
* *
5396706 GAATTTAAAGGAAAATTGAA
1 GAATTTAGAGGGAAATTGAA
* *
5396726 AAATTTAGAGGG-AATAGAA
1 GAATTTAGAGGGAAATTGAA
* *
5396745 AAATTTGGAGGGAAATT-AA
1 GAATTTAGAGGGAAATTGAA
5396764 GAATT
1 GAATT
5396769 GAGTATGTGT
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
19 39 0.75
20 13 0.25
ACGTcount: A:0.49, C:0.00, G:0.26, T:0.26
Consensus pattern (20 bp):
GAATTTAGAGGGAAATTGAA
Found at i:5396781 original size:2 final size:2
Alignment explanation
Indices: 5396774--5396822 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
5396764 GAATTGAGTA
5396774 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
5396816 -G TG TG TG
1 TG TG TG TG
5396823 ATATATGAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
TG
Found at i:5397176 original size:21 final size:21
Alignment explanation
Indices: 5397152--5397194 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5397142 GTTAGAAGAT
5397152 AACTCGGGATCTTCAAGAGCC
1 AACTCGGGATCTTCAAGAGCC
5397173 AACTCGGGATCTTCAAGAGCC
1 AACTCGGGATCTTCAAGAGCC
5397194 A
1 A
5397195 TTAAGGACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (21 bp):
AACTCGGGATCTTCAAGAGCC
Found at i:5397858 original size:4 final size:4
Alignment explanation
Indices: 5397851--5400427 Score: 4759
Period size: 4 Copynumber: 656.5 Consensus size: 4
5397841 AAAATCACTA
5397851 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5397899 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5397947 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5397995 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5398043 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5398090 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
5398138 AGGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5398185 ATGT ATGT A--T ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5398230 ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5398277 ATGT ATGT ATGT ATGT -TGT ATGT ATGT ATGT ATGT ATGT AT-T ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5398323 ATGT ATGT ATGT ATGT -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5398370 A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5398417 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5398463 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5398510 ATGT ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5398557 ATGT ATGT ATGT ATGT AT-T ATGT ATGT ATGT ATGT ATGT A-GT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5398603 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5398651 ATGT ATGT ATGT ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5398698 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5398746 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5398794 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5398842 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5398889 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5398937 ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT -TGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5398983 ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5399030 ATGT ATG- ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG- ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5399076 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT A-GT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5399122 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5399170 ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A--T ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5399215 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AGTGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-TGT ATGT
5399264 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5399311 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT-T ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5399358 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5399406 ATGT ATGT ATGT ATGT ATG- ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5399453 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT-T ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5399500 ATGT ATGT ATGT -TGT ATGT ATGT ATGT ATGT ATGT A-GT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5399546 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5399594 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG- ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5399641 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5399689 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5399737 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5399785 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5399833 ATGT ATGT ATGT -TGT ATGT AT-T ATGT ATGT ATGT ATGT ATG- -TGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5399877 ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
5399924 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT ATGT ATGT ATGT GTGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5399971 AT-T ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5400018 ATGT ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5400064 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5400112 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
5400159 -TGT ATGT ATGT ATG- -TGT ATGT ATGT ATAT GTGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5400204 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5400252 ATGT ATGT ATGT ATGT ATGT -TGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5400299 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5400347 ATGT ATG- ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5400394 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
5400428 AAACCCTAAC
Statistics
Matches: 2515, Mismatches: 8, Indels: 100
0.96 0.00 0.04
Matches are distributed among these distances:
2 12 0.00
3 114 0.05
4 2385 0.95
5 4 0.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:5400535 original size:2 final size:2
Alignment explanation
Indices: 5400485--5400526 Score: 59
Period size: 2 Copynumber: 21.0 Consensus size: 2
5400475 ATAAACCATG
*
5400485 TA TA GTA TA CA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5400527 AACTATATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5400647 original size:7 final size:7
Alignment explanation
Indices: 5400610--5400643 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
5400600 TAATTTTATA
5400610 TAAACCC
1 TAAACCC
5400617 TAAACCC
1 TAAACCC
5400624 TAAACCC
1 TAAACCC
*
5400631 TAAACCT
1 TAAACCC
5400638 TAAACC
1 TAAACC
5400644 TTAATATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.18
Consensus pattern (7 bp):
TAAACCC
Found at i:5401124 original size:14 final size:14
Alignment explanation
Indices: 5401105--5401146 Score: 68
Period size: 14 Copynumber: 3.0 Consensus size: 14
5401095 AGTTTTATAG
5401105 AAACACTAAACCTT
1 AAACACTAAACCTT
5401119 AAACACTAAACCTT
1 AAACACTAAACCTT
5401133 AAATC-CTAAACCTT
1 AAA-CACTAAACCTT
5401147 TAGCCATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 26 0.96
15 1 0.04
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.24
Consensus pattern (14 bp):
AAACACTAAACCTT
Found at i:5401556 original size:11 final size:11
Alignment explanation
Indices: 5401542--5401590 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
5401532 CCATGTATAG
5401542 TATATATAAAC
1 TATATATAAAC
*
5401553 TATATATATA-
1 TATATATAAAC
5401563 TATATAT-AAC
1 TATATATAAAC
5401573 ATATATATAAAC
1 -TATATATAAAC
5401585 TATATA
1 TATATA
5401591 AAGTAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 1 0.03
10 7 0.21
11 22 0.67
12 3 0.09
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (11 bp):
TATATATAAAC
Found at i:5401682 original size:49 final size:49
Alignment explanation
Indices: 5401579--5401682 Score: 120
Period size: 48 Copynumber: 2.1 Consensus size: 49
5401569 TAACATATAT
* ** **
5401579 ATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACTATGC
1 ATAAACTATATAAAGTAAATAAAGTATATAGTTTATAGAAACACTAACC
* *
5401628 ATAAACTATATAAAGT-AATAAAGTATATATTTTATAGAAACCCTAAACC
1 ATAAACTATATAAAGTAAATAAAGTATATAGTTTATAGAAACACT-AACC
*
5401677 CTAAAC
1 ATAAAC
5401683 ATTAAACCAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 23 0.50
49 23 0.50
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (49 bp):
ATAAACTATATAAAGTAAATAAAGTATATAGTTTATAGAAACACTAACC
Found at i:5401978 original size:13 final size:13
Alignment explanation
Indices: 5401946--5401972 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5401936 TAATTTACAT
5401946 TTAAATAATTTTA
1 TTAAATAATTTTA
5401959 TTAAATAATTTTA
1 TTAAATAATTTTA
5401972 T
1 T
5401973 ATAATATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:5402008 original size:20 final size:19
Alignment explanation
Indices: 5401976--5402034 Score: 63
Period size: 17 Copynumber: 3.3 Consensus size: 19
5401966 ATTTTATATA
*
5401976 ATAT-GTATGTATAAACCAT
1 ATATAGTATATATAAACC-T
*
5401995 GTATAGTATATATAAA-CT
1 ATATAGTATATATAAACCT
5402013 ATATA-TATATATAAA-CT
1 ATATAGTATATATAAACCT
5402030 ATATA
1 ATATA
5402035 AAGTAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 17 0.47
18 5 0.14
19 4 0.11
20 10 0.28
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (19 bp):
ATATAGTATATATAAACCT
Found at i:5402015 original size:9 final size:9
Alignment explanation
Indices: 5402003--5402036 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
5401993 ATGTATAGTA
5402003 TATATAAAC
1 TATATAAAC
*
5402012 TATATATA-
1 TATATAAAC
5402020 TATATAAAC
1 TATATAAAC
5402029 TATATAAA
1 TATATAAA
5402037 GTAAATTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (9 bp):
TATATAAAC
Found at i:5402023 original size:17 final size:18
Alignment explanation
Indices: 5401996--5402034 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
5401986 ATAAACCATG
5401996 TATAGTATATATAAACTA
1 TATAGTATATATAAACTA
5402014 TATA-TATATATAAACTA
1 TATAGTATATATAAACTA
5402031 TATA
1 TATA
5402035 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (18 bp):
TATAGTATATATAAACTA
Found at i:5402118 original size:7 final size:7
Alignment explanation
Indices: 5402102--5402169 Score: 59
Period size: 7 Copynumber: 9.7 Consensus size: 7
5402092 AGTTTTATAG
*
5402102 AAACCCT
1 AAACCAT
*
5402109 AAACCTT
1 AAACCAT
*
5402116 AAACCCT
1 AAACCAT
*
5402123 AAACCCT
1 AAACCAT
5402130 AAACTC-T
1 AAAC-CAT
5402137 AAACCAT
1 AAACCAT
5402144 AAA-CACT
1 AAACCA-T
*
5402151 AAACAAT
1 AAACCAT
5402158 AAACCAT
1 AAACCAT
5402165 AAACC
1 AAACC
5402170 CTAATATAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
6 3 0.06
7 48 0.91
8 2 0.04
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.16
Consensus pattern (7 bp):
AAACCAT
Found at i:5402121 original size:14 final size:14
Alignment explanation
Indices: 5402102--5402169 Score: 82
Period size: 14 Copynumber: 4.9 Consensus size: 14
5402092 AGTTTTATAG
*
5402102 AAACCCTAAACCTT
1 AAACCCTAAACCAT
*
5402116 AAACCCTAAACCCT
1 AAACCCTAAACCAT
*
5402130 AAACTCTAAACCAT
1 AAACCCTAAACCAT
* *
5402144 AAACACTAAACAAT
1 AAACCCTAAACCAT
*
5402158 AAACCATAAACC
1 AAACCCTAAACC
5402170 CTAATATAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 46 1.00
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.16
Consensus pattern (14 bp):
AAACCCTAAACCAT
Found at i:5402128 original size:21 final size:21
Alignment explanation
Indices: 5402102--5402173 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
5402092 AGTTTTATAG
*
5402102 AAACCCTAAACCTTAAACCCT
1 AAACCCTAAACCTTAAACCAT
5402123 AAACCCTAAA-CTCTAAACCAT
1 AAACCCTAAACCT-TAAACCAT
* **
5402144 AAACACTAAACAATAAACCAT
1 AAACCCTAAACCTTAAACCAT
5402165 AAACCCTAA
1 AAACCCTAA
5402174 TATAAATGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
20 2 0.05
21 42 0.95
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.17
Consensus pattern (21 bp):
AAACCCTAAACCTTAAACCAT
Found at i:5402874 original size:14 final size:14
Alignment explanation
Indices: 5402855--5402924 Score: 61
Period size: 14 Copynumber: 5.7 Consensus size: 14
5402845 ATTTTTTCTT
5402855 TATATAAATTAAAC
1 TATATAAATTAAAC
5402869 TATAT-AATT----
1 TATATAAATTAAAC
5402878 TATATAAATTAAAC
1 TATATAAATTAAAC
5402892 TATAT-AATT----
1 TATATAAATTAAAC
5402901 TATATAAATTAAAC
1 TATATAAATTAAAC
*
5402915 TATATTAATT
1 TATATAAATT
5402925 TTCCTTTTCA
Statistics
Matches: 45, Mismatches: 1, Indels: 20
0.68 0.02 0.30
Matches are distributed among these distances:
9 10 0.22
10 8 0.18
13 8 0.18
14 19 0.42
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:5402880 original size:23 final size:23
Alignment explanation
Indices: 5402853--5402925 Score: 137
Period size: 23 Copynumber: 3.1 Consensus size: 23
5402843 TTATTTTTTC
5402853 TTTATATAAATTAAACTATATAA
1 TTTATATAAATTAAACTATATAA
5402876 TTTATATAAATTAAACTATATAA
1 TTTATATAAATTAAACTATATAA
5402899 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATA-TAA
5402923 TTT
1 TTT
5402926 TCCTTTTCAT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 43 0.88
24 6 0.12
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTATATAAATTAAACTATATAA
Found at i:5403209 original size:16 final size:16
Alignment explanation
Indices: 5403188--5403226 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
5403178 CGGATCATTT
5403188 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
*
5403204 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAA
*
5403220 ATAGGTC
1 ACAGGTC
5403227 GGGTAATACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.13, G:0.28, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:5403866 original size:133 final size:134
Alignment explanation
Indices: 5403621--5404196 Score: 807
Period size: 133 Copynumber: 4.3 Consensus size: 134
5403611 CGAGAATCGT
* * * * *
5403621 GATTTGCTTCGCTGCTCTTTAGGAAGACCAAATATGAAAAAAGAAGAATCTGCTCCACTACTATT
1 GATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTT
* *
5403686 TAGGGGAGATCAGACTTGAGAAAACTTTGATCCACTTCACTATTCTTCAAGAAAGATTGAATCAG
66 TAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTATTCTTCAAGGAAGATTGAATCAG
5403751 AATC
131 AATC
* * * *
5403755 GATTTACTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGCATCT-TTCCACTACTTTT
1 GATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTT
* * ** *
5403819 TAGGGGAGATCATACTCGAGAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCAG
66 TAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTATTCTTCAAGGAAGATTGAATCAG
5403884 AATC
131 AATC
*
5403888 GATTTGCTTCACTACTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTT
1 GATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTT
* * *
5403953 TAGGGGAGATAAGACTCGAGAAAACATTGATCCACTTCACTATTCTT-TAGGAAGATTGAATCAG
66 TAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTATTCTTCAAGGAAGATTGAATCAG
*
5404017 AATT
131 AATC
* * * *
5404021 GATTTGCTTCACTACTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATATGATCCATTACTCTT
1 GATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTT
* * *
5404086 TAGGGGAGATCAGACTTACTCGACAAAACTTTGATCCACTTCACTATTCTTCAA-GAATATTGAC
66 TAGGGGAGATCAG----ACTCGAGAAAACTTTGATCCACTTCACTATTCTTCAAGGAAGATTGAA
5404150 TCAGAATC
127 TCAGAATC
* * * *
5404158 GATTTGCTTCATTGCTCTTCACGAATATCAAATCTGAAA
1 GATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAA
5404197 TTAAACATTA
Statistics
Matches: 392, Mismatches: 44, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
133 213 0.54
134 97 0.25
137 81 0.21
138 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (134 bp):
GATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTT
TAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTATTCTTCAAGGAAGATTGAATCAG
AATC
Found at i:5404096 original size:267 final size:268
Alignment explanation
Indices: 5403621--5404196 Score: 825
Period size: 267 Copynumber: 2.1 Consensus size: 268
5403611 CGAGAATCGT
* * *
5403621 GATTTGCTTCGCTGCTCTTTAGGAAGACCAAATATGAAAAAAGAAGAATCTGCTCCACTACTATT
1 GATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAAAAGAAGAATCTGCTCCACTACTATT
* * *
5403686 TAGGGGAGATCAGACTTGAGAAAACTTTGATCCACTTCACTATTCTTCAAGAAAGATTGAATCAG
66 TAGGGGAGATAAGACTCGAGAAAACATTGATCCACTTCACTATTCTTCAAGAAAGATTGAATCAG
* * * *
5403751 AATCGATTTACTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGCATCTTTCCACTACT
131 AATCGATTTACTTCACTACTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATATATCCACTACT
* * * * *
5403816 TTTTAGGGGAGATC-A-TACTCGAGAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGA
196 CTTTAGGGGAGATCAACTACTCGACAAAACTTTGATCCACTTCACTACTCTTCA-AGAAGATTGA
5403879 ATCAGAATC
260 ATCAGAATC
* * *
5403888 GATTTGCTTCACTACTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTT
1 GATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAAAAGAAGAATCTGCTCCACTACTATT
* *
5403953 TAGGGGAGATAAGACTCGAGAAAACATTGATCCACTTCACTATTCTT-TAGGAAGATTGAATCAG
66 TAGGGGAGATAAGACTCGAGAAAACATTGATCCACTTCACTATTCTTCAAGAAAGATTGAATCAG
* * *
5404017 AATTGATTTGCTTCACTACTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATATGATCCATTAC
131 AATCGATTTACTTCACTACTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATAT-ATCCACTAC
* *
5404082 TCTTTAGGGGAGATCAGACTTACTCGACAAAACTTTGATCCACTTCACTATTCTTCAAGAATATT
195 TCTTTAGGGGAGATCA-AC-TACTCGACAAAACTTTGATCCACTTCACTACTCTTCAAGAAGATT
*
5404147 GACTCAGAATC
258 GAATCAGAATC
* * * *
5404158 GATTTGCTTCATTGCTCTTCACGAATATCAAATCTGAAA
1 GATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAA
5404197 TTAAACATTA
Statistics
Matches: 273, Mismatches: 31, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
266 65 0.24
267 124 0.45
269 1 0.00
270 50 0.18
271 33 0.12
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (268 bp):
GATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAAAAGAAGAATCTGCTCCACTACTATT
TAGGGGAGATAAGACTCGAGAAAACATTGATCCACTTCACTATTCTTCAAGAAAGATTGAATCAG
AATCGATTTACTTCACTACTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATATATCCACTACT
CTTTAGGGGAGATCAACTACTCGACAAAACTTTGATCCACTTCACTACTCTTCAAGAAGATTGAA
TCAGAATC
Found at i:5404543 original size:41 final size:41
Alignment explanation
Indices: 5404493--5404602 Score: 116
Period size: 42 Copynumber: 2.7 Consensus size: 41
5404483 GCCCGAAGGT
* * *
5404493 CTTATAGATGGCCCGAATAACTTATCATCT-TGCTCAAAAGA
1 CTTACAGATGACCCGAATGACTTATCAT-TATGCTCAAAAGA
* * *
5404534 -TTGACAGATGACCCGAAGGATTTAATCATTATGCTCGAAAGA
1 CTT-ACAGATGACCCGAATGACTT-ATCATTATGCTCAAAAGA
*
5404576 CTTACTGATGACCCGAATGACTTATCA
1 CTTACAGATGACCCGAATGACTTATCA
5404603 ATTTTGGAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
40 2 0.04
41 20 0.36
42 32 0.57
43 2 0.04
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (41 bp):
CTTACAGATGACCCGAATGACTTATCATTATGCTCAAAAGA
Found at i:5404933 original size:259 final size:259
Alignment explanation
Indices: 5404447--5405758 Score: 1962
Period size: 259 Copynumber: 5.1 Consensus size: 259
5404437 ATGAGAAGCT
* * * * **
5404447 TTTCTCATTTTTCGAAAAAACATGCGAAAACATCATGCCCGAAGGTCTTATAGATGGCCCGAATA
1 TTTCTCATTTTTC-AAAAATCATGTGGAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGG
* *
5404512 ACTTATCATCTTGCTCAAAAGATTGACAGATGACCCGAAGGATTTAATCATTATGCTCGAAAGAC
65 ACTTATCATCTTGCTCGAAAGATTGACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGAC
* * * * * *
5404577 TTACTGATGACCCGAATGACTTATCAATTTTGGAAATAGTTTACTTGATAATAATCTTTGGAAAT
130 TTACTGATGGCCCGAAGGACTTATCAATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAAT
* *
5404642 CGCTTTCTTACTTTTCAAAATTTTCATTTTCTGAAAATATTTAAATGAGAAACTTTGGAAATCGC
195 CACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATATTTAAATGAGAAACTTTGGAAATCGC
* * * * *
5404707 TTTCTCATTTTTCAAAAATCATATGTAAACATCCTGCTCGAAGGTCTTATAGATGGCCTGAATGA
1 TTTCTCATTTTTCAAAAATCATGTGGAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGGA
* * *
5404772 CTTATCATCTTGCTCTAAAGATTGACAGATGGCCCAAAGGATTTAATCATCATGCTCGAAAGACT
66 CTTATCATCTTGCTCGAAAGATTGACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACT
*
5404837 TATTGATGGCCCGAAGGACTTATCAATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATC
131 TACTGATGGCCCGAAGGACTTATCAATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATC
* *
5404902 ACTTTCTTACTTTTCAAAAATTACATTTTCTGAAAATATTTAAATGAGAAACTTTGGAAATCGT
196 ACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATATTTAAATGAGAAACTTTGGAAATCGC
* * * * **
5404966 TTTCTCATTTTTCGAAAATCATGTGGAAACATTCTGCACGAAGGTTTTATAGATGGTTCGAAGGA
1 TTTCTCATTTTTCAAAAATCATGTGGAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGGA
* * * *
5405031 CTTATCATCTTGCTCGAAAGACTGACAAATGACCCGAAGGATTTAATCATCATGCTTGAAAGACA
66 CTTATCATCTTGCTCGAAAGATTGACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACT
* * *
5405096 TACTGATAGCCCGAATGACTTATCAATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATT
131 TACTGATGGCCCGAAGGACTTATCAATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATC
5405161 ACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATATTTAAATGAGAAACTTTGGAAATCGC
196 ACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATATTTAAATGAGAAACTTTGGAAATCGC
* * * *
5405225 TTTCTCATTTTTCGAAAATCATTTGGAAACATCTTGCCTGAAGGTCTTATAGATGGCCCGAAGGA
1 TTTCTCATTTTTCAAAAATCATGTGGAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGGA
** * * *
5405290 CTTATCATCTTGCTCGAAAGGCTAACAGAAGAACCGAAGGATTTAATCATCATGCTCGAAAGACT
66 CTTATCATCTTGCTCGAAAGATTGACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACT
* * * * *
5405355 TACGGAAGGCCCGAAGGAATTATCTATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGAAAATC
131 TACTGATGGCCCGAAGGACTTATCAATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATC
* * *
5405420 GCTTTCTTACTTTTCAAAAATTTTATTTTCTGAAAATATTTAAATGAGAAACTTTGGAAATTGC
196 ACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATATTTAAATGAGAAACTTTGGAAATCGC
* * * *
5405484 TTTCTCATTTTTCGAAAATAATGTGGAAACATTCTGCCCGAAGGTCTTATAGATGGCCCGAAAGA
1 TTTCTCATTTTTCAAAAATCATGTGGAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGGA
* * * *
5405549 CTTATCATCTTGCTTGGAAGATTGACAGATGACCCGAAGGATTTAATCATCATGCTTGAAAGAAT
66 CTTATCATCTTGCTCGAAAGATTGACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACT
* * ** *
5405614 TACTGATGACCTGAAGGACTTATCAATTTTGGAAATAGTTTACAAGGTATGAAACTTTGGAAATC
131 TACTGATGGCCCGAAGGACTTATCAATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATC
5405679 GA-TTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATATTTAAATGAGAAACTTTGGAAATCGC
196 -ACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATATTTAAATGAGAAACTTTGGAAATCGC
5405743 TTTCTCA-TTTTCAAAA
1 TTTCTCATTTTTCAAAA
5405759 TAACTTAATG
Statistics
Matches: 950, Mismatches: 101, Indels: 4
0.90 0.10 0.00
Matches are distributed among these distances:
258 8 0.01
259 929 0.98
260 13 0.01
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (259 bp):
TTTCTCATTTTTCAAAAATCATGTGGAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGGA
CTTATCATCTTGCTCGAAAGATTGACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACT
TACTGATGGCCCGAAGGACTTATCAATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATC
ACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATATTTAAATGAGAAACTTTGGAAATCGC
Found at i:5405369 original size:42 final size:41
Alignment explanation
Indices: 5405279--5405378 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 41
5405269 TCTTATAGAT
* *
5405279 GGCCCGAAGGACTTATCATCTTGCTCGAAAGGCTAACAGAA
1 GGCCCGAAGGACTTATCATCATGCTCGAAAGACTAACAGAA
** * * *
5405320 GAACCGAAGGATTTAATCATCATGCTCGAAAGACTTACGGAA
1 GGCCCGAAGGACTT-ATCATCATGCTCGAAAGACTAACAGAA
*
5405362 GGCCCGAAGGAATTATC
1 GGCCCGAAGGACTTATC
5405379 TATTTTGGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
41 14 0.29
42 34 0.71
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (41 bp):
GGCCCGAAGGACTTATCATCATGCTCGAAAGACTAACAGAA
Found at i:5405605 original size:42 final size:41
Alignment explanation
Indices: 5405534--5405638 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 41
5405524 AAGGTCTTAT
* * * *
5405534 AGATGGCCCGAAAGACTTATCATCTTGCTTGGAAG-ATTGAC
1 AGATGACCCGAAGGACTTATCATCATGCTTGAAAGAATT-AC
*
5405575 AGATGACCCGAAGGATTTAATCATCATGCTTGAAAGAATTAC
1 AGATGACCCGAAGGACTT-ATCATCATGCTTGAAAGAATTAC
* *
5405617 TGATGACCTGAAGGACTTATCA
1 AGATGACCCGAAGGACTTATCA
5405639 ATTTTGGAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
41 19 0.35
42 32 0.59
43 3 0.06
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (41 bp):
AGATGACCCGAAGGACTTATCATCATGCTTGAAAGAATTAC
Found at i:5411219 original size:12 final size:12
Alignment explanation
Indices: 5411202--5411241 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
5411192 AGCATTTTAA
5411202 AAAATAAAACTT
1 AAAATAAAACTT
*
5411214 AAAATAAAA-TG
1 AAAATAAAACTT
5411225 AAAATGAAAACTT
1 AAAAT-AAAACTT
5411238 AAAA
1 AAAA
5411242 AGAGGAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 6 0.25
12 13 0.54
13 5 0.21
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (12 bp):
AAAATAAAACTT
Found at i:5413538 original size:24 final size:24
Alignment explanation
Indices: 5413511--5413617 Score: 108
Period size: 24 Copynumber: 4.5 Consensus size: 24
5413501 AAACGAATAT
5413511 ATCAGAAAAT-AAAACAGAATTCAG
1 ATCAG-AAATCAAAACAGAATTCAG
* * * *
5413535 ATCAGATATCAGAACAGAATCCGG
1 ATCAGAAATCAAAACAGAATTCAG
* *
5413559 ATCAGAAATCATAACAGAATTCAT
1 ATCAGAAATCAAAACAGAATTCAG
* * *
5413583 ATCAGAATTCAGAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
*
5413607 ATCGGAAATCA
1 ATCAGAAATCA
5413618 GATAAAACAT
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
23 3 0.04
24 65 0.96
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:5413540 original size:12 final size:12
Alignment explanation
Indices: 5413525--5413620 Score: 77
Period size: 12 Copynumber: 8.0 Consensus size: 12
5413515 GAAAATAAAA
5413525 CAGAATTCAGAT
1 CAGAATTCAGAT
*
5413537 CAG-ATATCAGAA
1 CAGAAT-TCAGAT
* *
5413549 CAGAATCCGGAT
1 CAGAATTCAGAT
* * *
5413561 CAGAAATCATAA
1 CAGAATTCAGAT
*
5413573 CAGAATTCATAT
1 CAGAATTCAGAT
*
5413585 CAGAATTCAGAA
1 CAGAATTCAGAT
*
5413597 CAGAATTCAAAT
1 CAGAATTCAGAT
* *
5413609 CGGAAATCAGAT
1 CAGAATTCAGAT
5413621 AAAACATTCA
Statistics
Matches: 64, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
11 2 0.03
12 60 0.94
13 2 0.03
ACGTcount: A:0.46, C:0.18, G:0.16, T:0.21
Consensus pattern (12 bp):
CAGAATTCAGAT
Found at i:5413618 original size:24 final size:24
Alignment explanation
Indices: 5413523--5413619 Score: 122
Period size: 24 Copynumber: 4.0 Consensus size: 24
5413513 CAGAAAATAA
*
5413523 AACAGAATTCAGATCAGATATCAG
1 AACAGAATTCAGATCAGAAATCAG
* * *
5413547 AACAGAATCCGGATCAGAAATCAT
1 AACAGAATTCAGATCAGAAATCAG
* *
5413571 AACAGAATTCATATCAGAATTCAG
1 AACAGAATTCAGATCAGAAATCAG
* *
5413595 AACAGAATTCAAATCGGAAATCAG
1 AACAGAATTCAGATCAGAAATCAG
5413619 A
1 A
5413620 TAAAACATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.20
Consensus pattern (24 bp):
AACAGAATTCAGATCAGAAATCAG
Found at i:5414780 original size:18 final size:18
Alignment explanation
Indices: 5414759--5414793 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5414749 CTCCATCTGG
*
5414759 TCTTATTATTTAATTTAA
1 TCTTATCATTTAATTTAA
*
5414777 TCTTATCATTTACTTTA
1 TCTTATCATTTAATTTA
5414794 GTCCTTTCAA
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:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (18 bp):
TCTTATCATTTAATTTAA
Found at i:5425347 original size:21 final size:21
Alignment explanation
Indices: 5425301--5425348 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
5425291 TCCCCTCTCA
*
5425301 TTTTCTCTTCTTTTCCTTTTC
1 TTTTTTCTTCTTTTCCTTTTC
* *
5425322 CTTTTTCTT-TTTTTCTCTTTC
1 TTTTTTCTTCTTTTCCT-TTTC
5425343 TTTTTT
1 TTTTTT
5425349 TCGTTTTGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTTTCTTCTTTTCCTTTTC
Found at i:5425849 original size:18 final size:18
Alignment explanation
Indices: 5425828--5425863 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5425818 TATGGGTTTA
5425828 CTGTTGATGATTATTTTT
1 CTGTTGATGATTATTTTT
**
5425846 CTGTTGATTTTTATTTTT
1 CTGTTGATGATTATTTTT
5425864 TCGATTTGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.06, G:0.14, T:0.67
Consensus pattern (18 bp):
CTGTTGATGATTATTTTT
Found at i:5426483 original size:160 final size:160
Alignment explanation
Indices: 5426219--5426539 Score: 642
Period size: 160 Copynumber: 2.0 Consensus size: 160
5426209 CGGACAAAAC
5426219 TAGTATATACAATCCTAAATCGAAATCTGGTTTTAGAGAAAGCCAAGGTATGATATCGACAAAGG
1 TAGTATATACAATCCTAAATCGAAATCTGGTTTTAGAGAAAGCCAAGGTATGATATCGACAAAGG
5426284 TGAAGGACAGCCAGTTTTACAAGACATCTTGAGAGAGTTTGTCTAGACAATTAAGCCCTTGTCTT
66 TGAAGGACAGCCAGTTTTACAAGACATCTTGAGAGAGTTTGTCTAGACAATTAAGCCCTTGTCTT
5426349 TTATCAAGGGATGCCTCACCGAGACGAGGT
131 TTATCAAGGGATGCCTCACCGAGACGAGGT
5426379 TAGTATATACAATCCTAAATCGAAATCTGGTTTTAGAGAAAGCCAAGGTATGATATCGACAAAGG
1 TAGTATATACAATCCTAAATCGAAATCTGGTTTTAGAGAAAGCCAAGGTATGATATCGACAAAGG
5426444 TGAAGGACAGCCAGTTTTACAAGACATCTTGAGAGAGTTTGTCTAGACAATTAAGCCCTTGTCTT
66 TGAAGGACAGCCAGTTTTACAAGACATCTTGAGAGAGTTTGTCTAGACAATTAAGCCCTTGTCTT
5426509 TTATCAAGGGATGCCTCACCGAGACGAGGT
131 TTATCAAGGGATGCCTCACCGAGACGAGGT
5426539 T
1 T
5426540 GTTCACATAC
Statistics
Matches: 161, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
160 161 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.27
Consensus pattern (160 bp):
TAGTATATACAATCCTAAATCGAAATCTGGTTTTAGAGAAAGCCAAGGTATGATATCGACAAAGG
TGAAGGACAGCCAGTTTTACAAGACATCTTGAGAGAGTTTGTCTAGACAATTAAGCCCTTGTCTT
TTATCAAGGGATGCCTCACCGAGACGAGGT
Found at i:5434584 original size:34 final size:32
Alignment explanation
Indices: 5434522--5434591 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
5434512 ACCTTACAAC
* *
5434522 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
5434554 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
5434588 TCCC
1 TCCC
5434592 CTTTACAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:5435123 original size:29 final size:31
Alignment explanation
Indices: 5435091--5435150 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
5435081 AAATTTTGAA
*
5435091 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
5435120 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
5435151 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:5437334 original size:25 final size:25
Alignment explanation
Indices: 5437276--5437335 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
5437266 TTCTTGGATA
* *
5437276 AACATAAATACGATGCTTTTGGACC
1 AACATAGATACAATGCTTTTGGACC
5437301 AAC-TAAGATACAATG-TTTATGGACC
1 AACAT-AGATACAATGCTTT-TGGACC
5437326 AACATAGATA
1 AACATAGATA
5437336 GTACTTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 4 0.13
25 25 0.83
26 1 0.03
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.27
Consensus pattern (25 bp):
AACATAGATACAATGCTTTTGGACC
Found at i:5441635 original size:23 final size:23
Alignment explanation
Indices: 5441603--5441658 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
5441593 CTATATGATC
*
5441603 TTGATAAATCACTTCCCGAATAA
1 TTGATGAATCACTTCCCGAATAA
5441626 TTGATGAATCACTTCCCGAATAA
1 TTGATGAATCACTTCCCGAATAA
*
5441649 CTGATGAATC
1 TTGATGAATC
5441659 CATTAGCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.30
Consensus pattern (23 bp):
TTGATGAATCACTTCCCGAATAA
Found at i:5443967 original size:26 final size:26
Alignment explanation
Indices: 5443935--5444010 Score: 118
Period size: 26 Copynumber: 2.9 Consensus size: 26
5443925 TATGGGCATG
5443935 TAATAATGTAATTATTAATTATTTAA
1 TAATAATGTAATTATTAATTATTTAA
5443961 TAATAATGTAATTATTAATTATTTAA
1 TAATAATGTAATTATTAATTATTTAA
**
5443987 TAATAATAAAAATTATT-ATTATTT
1 TAATAAT-GTAATTATTAATTATTT
5444011 GGGACAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
26 40 0.85
27 7 0.15
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (26 bp):
TAATAATGTAATTATTAATTATTTAA
Found at i:5448716 original size:18 final size:18
Alignment explanation
Indices: 5448692--5448738 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
5448682 AACCCGACCC
*
5448692 GACCCGACCCGACTTGTT
1 GACCCGACCCGACCTGTT
*
5448710 TACCCGACCCGACCTGTT
1 GACCCGACCCGACCTGTT
5448728 GACCCGACCCG
1 GACCCGACCCG
5448739 TTGACCCGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.17, C:0.45, G:0.21, T:0.17
Consensus pattern (18 bp):
GACCCGACCCGACCTGTT
Found at i:5448731 original size:13 final size:13
Alignment explanation
Indices: 5448715--5448746 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5448705 TTGTTTACCC
*
5448715 GACCCGACCTGTT
1 GACCCGACCCGTT
5448728 GACCCGACCCGTT
1 GACCCGACCCGTT
5448741 GACCCG
1 GACCCG
5448747 TTGACCGTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.44, G:0.25, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:5451388 original size:24 final size:24
Alignment explanation
Indices: 5451266--5451381 Score: 164
Period size: 24 Copynumber: 4.8 Consensus size: 24
5451256 TTCGATTTGA
5451266 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
5451290 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
*
5451314 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
5451338 ATTCTGATCTGTTACTTGACCT-G
1 ATTCTGATCTGATACTTGACATGG
*
5451361 ATTTCTGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
5451382 CTGATTTATG
Statistics
Matches: 84, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 80 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:5451404 original size:24 final size:24
Alignment explanation
Indices: 5451318--5451391 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
5451308 ACATGGATTC
* * *
5451318 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
5451342 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
5451366 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
5451390 TG
1 TG
5451392 TTTTGATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 42 0.95
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:5454256 original size:17 final size:17
Alignment explanation
Indices: 5454222--5454254 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5454212 TTTAATTATA
5454222 ATTATATAATTATATTT
1 ATTATATAATTATATTT
*
5454239 ATTATTTAA-TATATTT
1 ATTATATAATTATATTT
5454255 TACTCTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATATAATTATATTT
Found at i:5455041 original size:18 final size:18
Alignment explanation
Indices: 5455008--5455042 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5454998 AACATCCTCA
*
5455008 TCATCTTCAACTTCTTCC
1 TCATCTTCAACGTCTTCC
*
5455026 TCATCTTCATCGTCTTC
1 TCATCTTCAACGTCTTC
5455043 TTCTTCATTA
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:0.14, C:0.37, G:0.03, T:0.46
Consensus pattern (18 bp):
TCATCTTCAACGTCTTCC
Found at i:5456589 original size:18 final size:18
Alignment explanation
Indices: 5456558--5456601 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5456548 GTCACTTTCA
*
5456558 TCATTATCTACCTCTTCC
1 TCATCATCTACCTCTTCC
* *
5456576 TCCTCATCTTCCTCTTCC
1 TCATCATCTACCTCTTCC
5456594 TCATCATC
1 TCATCATC
5456602 GTCTACACCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.14, C:0.43, G:0.00, T:0.43
Consensus pattern (18 bp):
TCATCATCTACCTCTTCC
Found at i:5458664 original size:23 final size:24
Alignment explanation
Indices: 5458638--5458682 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5458628 TATAAAATAT
5458638 TTATAT-ATTTTCTTTAAAAAAAA
1 TTATATAATTTTCTTTAAAAAAAA
* *
5458661 TTATATAATTTTTTTTACAAAA
1 TTATATAATTTTCTTTAAAAAA
5458683 TTAAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
TTATATAATTTTCTTTAAAAAAAA
Found at i:5460401 original size:38 final size:38
Alignment explanation
Indices: 5460350--5460435 Score: 172
Period size: 38 Copynumber: 2.3 Consensus size: 38
5460340 CCCCGCCCCG
5460350 ATTATATATATATATAATATTTTATATTTTTTATATTA
1 ATTATATATATATATAATATTTTATATTTTTTATATTA
5460388 ATTATATATATATATAATATTTTATATTTTTTATATTA
1 ATTATATATATATATAATATTTTATATTTTTTATATTA
5460426 ATTATATATA
1 ATTATATATA
5460436 ATACAAACTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (38 bp):
ATTATATATATATATAATATTTTATATTTTTTATATTA
Found at i:5462159 original size:18 final size:18
Alignment explanation
Indices: 5462138--5462215 Score: 129
Period size: 18 Copynumber: 4.3 Consensus size: 18
5462128 GTAACTCTGC
*
5462138 TACCCAAAACGAGTCTGA
1 TACCCAAAACGAGTCTAA
*
5462156 TACCCAAAACGAGTGTAA
1 TACCCAAAACGAGTCTAA
*
5462174 TATCCAAAACGAGTCTAA
1 TACCCAAAACGAGTCTAA
5462192 TACCCAAAACGAGTCTAA
1 TACCCAAAACGAGTCTAA
5462210 TACCCA
1 TACCCA
5462216 TGAAACTTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.42, C:0.27, G:0.13, T:0.18
Consensus pattern (18 bp):
TACCCAAAACGAGTCTAA
Found at i:5465011 original size:22 final size:22
Alignment explanation
Indices: 5464986--5465029 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5464976 ATGTCCTTTG
*
5464986 AAGCATTTGGTTTCATGATTAT
1 AAGCATCTGGTTTCATGATTAT
5465008 AAGCATCTGGTTTCATGATTAT
1 AAGCATCTGGTTTCATGATTAT
5465030 TTTCATTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.43
Consensus pattern (22 bp):
AAGCATCTGGTTTCATGATTAT
Found at i:5466718 original size:16 final size:16
Alignment explanation
Indices: 5466683--5466722 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
5466673 TTCACATATG
5466683 AAAATTGATATTTTAAT
1 AAAATT-ATATTTTAAT
* *
5466700 AAAATTATTTTTTACT
1 AAAATTATATTTTAAT
5466716 AAAATTA
1 AAAATTA
5466723 CATGATTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
AAAATTATATTTTAAT
Found at i:5473729 original size:3 final size:3
Alignment explanation
Indices: 5473721--5473833 Score: 163
Period size: 3 Copynumber: 37.7 Consensus size: 3
5473711 TTTTTATCCA
* ** *
5473721 TAT TAT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
5473769 TAT TAT CAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5473817 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
5473834 ATTTATATTA
Statistics
Matches: 96, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 96 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:5473753 original size:27 final size:27
Alignment explanation
Indices: 5473722--5473833 Score: 197
Period size: 27 Copynumber: 4.1 Consensus size: 27
5473712 TTTTATCCAT
5473722 ATTATTATTATTAATATTATTATTATC
1 ATTATTATTATTAATATTATTATTATC
*
5473749 CTTATTATTATTAATATTATTATTATC
1 ATTATTATTATTAATATTATTATTATC
5473776 ATTATTATTATTAATATTATTATTATC
1 ATTATTATTATTAATATTATTATTATC
* *
5473803 ATTATTATTATTATTATTATTATTATT
1 ATTATTATTATTAATATTATTATTATC
5473830 ATTA
1 ATTA
5473834 ATTTATATTA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 81 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (27 bp):
ATTATTATTATTAATATTATTATTATC
Found at i:5475291 original size:20 final size:21
Alignment explanation
Indices: 5475254--5475294 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5475244 GATATTTTTA
**
5475254 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
5475275 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
5475295 ACATATAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:5486669 original size:1 final size:1
Alignment explanation
Indices: 5486663--5486703 Score: 55
Period size: 1 Copynumber: 41.0 Consensus size: 1
5486653 TTGAAGAGAG
* * *
5486663 AAAAAAAAAAAGAAAAAAAAAAGAAAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5486704 GAAAGGGGGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:5486680 original size:10 final size:10
Alignment explanation
Indices: 5486665--5486707 Score: 70
Period size: 10 Copynumber: 4.3 Consensus size: 10
5486655 GAAGAGAGAA
5486665 AAAAAAAAAG
1 AAAAAAAAAG
5486675 AAAAAAAAAAG
1 -AAAAAAAAAG
5486686 AAAAAAAAAG
1 AAAAAAAAAG
5486696 -AAAAAAAAG
1 AAAAAAAAAG
5486705 AAA
1 AAA
5486708 GGGGGTCAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.29
10 12 0.39
11 10 0.32
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:5486680 original size:11 final size:11
Alignment explanation
Indices: 5486664--5486703 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
5486654 TGAAGAGAGA
5486664 AAAAAAAAAAG
1 AAAAAAAAAAG
5486675 AAAAAAAAAAG
1 AAAAAAAAAAG
5486686 -AAAAAAAAAG
1 AAAAAAAAAAG
5486696 AAAAAAAA
1 AAAAAAAA
5486704 GAAAGGGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:5487926 original size:47 final size:48
Alignment explanation
Indices: 5487821--5487926 Score: 153
Period size: 52 Copynumber: 2.1 Consensus size: 48
5487811 GAATATGCCA
5487821 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA----GTTGGACAGAAC
5487873 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA-TTGGACAGAATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAGTTGGACAGAA-C
5487921 A-AGCAT
1 ATAGCAT
5487927 TGAATTTAGA
Statistics
Matches: 53, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
47 15 0.28
48 2 0.04
52 36 0.68
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (48 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAGTTGGACAGAAC
Found at i:5488042 original size:130 final size:130
Alignment explanation
Indices: 5487809--5488118 Score: 593
Period size: 130 Copynumber: 2.4 Consensus size: 130
5487799 ACTGGAACAA
*
5487809 ATGAATATGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
*
5487874 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTGGACAGAATCAAGCATTGAATTTAGAAT
66 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTGGACAAAATCAAGCATTGAATTTAGAAT
5487939 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
5488004 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTGGACAAAATCAAGCATTGAATTTAGAAT
66 TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTGGACAAAATCAAGCATTGAATTTAGAAT
*
5488069 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATC
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
5488119 CGAAGAAGTG
Statistics
Matches: 177, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 177 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (130 bp):
ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTGGACAAAATCAAGCATTGAATTTAGAAT
Found at i:5488056 original size:47 final size:48
Alignment explanation
Indices: 5487951--5488056 Score: 144
Period size: 52 Copynumber: 2.1 Consensus size: 48
5487941 GAATTTGCCA
*
5487951 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA----GTTGGACAAAAC
5488003 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA-TTGGACAAAATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAGTTGGACAAAA-C
5488051 A-AGCAT
1 ATAGCAT
5488057 TGAATTTAGA
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
47 14 0.27
48 2 0.04
52 36 0.69
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (48 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAGTTGGACAAAAC
Found at i:5488979 original size:113 final size:113
Alignment explanation
Indices: 5488676--5489563 Score: 1318
Period size: 113 Copynumber: 7.8 Consensus size: 113
5488666 AGCAAAGATT
* * *
5488676 TGAATCCATCATTTGATGGAACAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
*
5488741 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
* * *
5488789 TGAATCCGTCATTTGATGGATCAGCTTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TGAATCCATCATTTGATGGATCAAC-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * * ***
5488854 AGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTT
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
* * * * *
5488903 TAAATTCATCATTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
5488968 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
* * *
5489016 TGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
5489081 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
* * *
5489129 TGAATCCGTCATTTGATGGATCAGCTTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TGAATCCATCATTTGATGGATCAAC-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * * ***
5489194 AGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTT
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
* * * *
5489243 TAAATTCATCATTTGATGGATCAACATCTTTTCCAGAGAAGGTTCATAATGAGAAGAAATCATCT
1 TGAATCCATCATTTGATGGATC-A-A-CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
5489308 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
63 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
* *
5489359 TGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
5489424 GAA-G--GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
* * *
5489469 TGAATTCATCATTTGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGA
1 TGAATCCATCATTTGATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGA
*
5489533 AGAAGGAAG-AGAAAGGTCATAATGAGAAGAA
65 AGAAGGAAGAAG-AAGTTCATAATGAGAAGAA
5489564 CTCATCAAGA
Statistics
Matches: 700, Mismatches: 65, Indels: 20
0.89 0.08 0.03
Matches are distributed among these distances:
109 1 0.00
110 102 0.15
111 1 0.00
112 3 0.00
113 291 0.42
114 201 0.29
115 2 0.00
116 98 0.14
117 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
TGAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
Found at i:5489166 original size:227 final size:226
Alignment explanation
Indices: 5488676--5489563 Score: 1327
Period size: 227 Copynumber: 3.9 Consensus size: 226
5488666 AGCAAAGATT
* *
5488676 TGAATCCATCATTTGATGGAACAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
* *
5488741 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCGTCATTTGAT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGAT
* * *
5488806 GGATCAGCTTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTT
131 GGATCATC-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
* * ***
5488871 CATAATGAGAAGAACTTGTTCAACTTTTTGTT
195 CATAATGAGAAGAATTTGTTCAACCTTTTACC
* * * * * *
5488903 TAAATTCATCATTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
*
5488968 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGAT
*
5489033 GGATCATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
131 GGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
5489098 ATAATGAGAAGAATTTGTTCAACCTTTTACC
196 ATAATGAGAAGAATTTGTTCAACCTTTTACC
* *
5489129 TGAATCCGTCATTTGATGGATCAGCTTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TGAATCCATCATTTGATGGATCAGC-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * * *** * *
5489194 AGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGA
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGA
* *
5489259 TGGATCAACATCTTTTCCAGAGAAGGTTCATAATGAGAAGAAATCATCTGAAGAAGGAAGAAGAA
130 TGGAT---CATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
5489324 GTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
192 GTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
* *
5489359 TGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
*
5489424 GAA-G--GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCATTTGAT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGAT
* * * *
5489486 GGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AGAAAGG
131 GGATCATCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG-AAGT
5489549 TCATAATGAGAAGAA
194 TCATAATGAGAAGAA
5489564 CTCATCAAGA
Statistics
Matches: 603, Mismatches: 52, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
222 3 0.00
223 63 0.10
226 157 0.26
227 224 0.37
228 1 0.00
229 42 0.07
230 113 0.19
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (226 bp):
TGAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGAT
GGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
ATAATGAGAAGAATTTGTTCAACCTTTTACC
Found at i:5489321 original size:340 final size:339
Alignment explanation
Indices: 5488676--5489565 Score: 1540
Period size: 340 Copynumber: 2.6 Consensus size: 339
5488666 AGCAAAGATT
* * *
5488676 TGAATCCATCATTTGATGGAACAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
*
5488741 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCGTCATTTGAT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCGTCATTTGAT
5488806 GGATCAGCTTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTT
131 GGATCAGCTTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTT
5488871 CATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAG
196 CATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAG
*
5488936 AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
261 AGAAGGTTCATAATGAGAAGAAATCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAATTT
5489001 GTTCAACCTTTTACC
325 GTTCAACCTTTTACC
5489016 TGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
5489081 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCGTCATTTGAT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCGTCATTTGAT
5489146 GGATCAGCTTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTT
131 GGATCAGCTTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTT
*
5489211 CATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACATCTTTTC
196 CATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACA---TTGC
5489276 CAGAGAAGGTTCATAATGAGAAGAAATCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
258 CAGAGAAGGTTCATAATGAGAAGAAATCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAA
5489341 TTTGTTCAACCTTTTACC
322 TTTGTTCAACCTTTTACC
*
5489359 TGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
* *
5489424 GAA-G--GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCATTTGAT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCGTCATTTGAT
* * ** *
5489486 GGATCAAC-ATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AGAAAG
131 GGATCAGCTTTTTTCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAG-AAG
*
5489548 GTCATAATGAGAAGAACT
194 TTCATAATGAGAAGAACT
5489566 CATCAAGAGC
Statistics
Matches: 530, Mismatches: 15, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
338 3 0.01
339 62 0.12
340 312 0.59
342 1 0.00
343 152 0.29
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (339 bp):
TGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCGTCATTTGAT
GGATCAGCTTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTT
CATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAG
AGAAGGTTCATAATGAGAAGAAATCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAATTTG
TTCAACCTTTTACC
Found at i:5489821 original size:3 final size:3
Alignment explanation
Indices: 5489813--5489930 Score: 148
Period size: 3 Copynumber: 38.7 Consensus size: 3
5489803 TTTTTATCCA
* **
5489813 TAT TAT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAT TAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
* * *
5489859 TAT CAT TAT TAT TAA TA- TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5489906 TAT TAT TAT TATT TAT TATT TAT TA
1 TAT TAT TAT TA-T TAT TA-T TAT TA
5489931 ATTTATATTA
Statistics
Matches: 100, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
2 2 0.02
3 89 0.89
4 9 0.09
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:5491389 original size:20 final size:21
Alignment explanation
Indices: 5491352--5491392 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5491342 GATATTTTTA
**
5491352 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
5491373 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
5491393 ACATATAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:5493171 original size:21 final size:20
Alignment explanation
Indices: 5493131--5493170 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
5493121 TTGTTTTCTT
*
5493131 TTCCTTAACATGTTATTTTA
1 TTCCTTAACATATTATTTTA
5493151 TTCCTTTAACATTATTATTT
1 TTCC-TTAACA-TATTATTT
5493171 AGGTTTTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 6 0.35
22 7 0.41
ACGTcount: A:0.25, C:0.15, G:0.03, T:0.57
Consensus pattern (20 bp):
TTCCTTAACATATTATTTTA
Found at i:5494442 original size:24 final size:24
Alignment explanation
Indices: 5494402--5494461 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
5494392 TTGTTGGGGA
*
5494402 AAGGTAGTATCAATACT--GAT-AT
1 AAGG-AGTATCAATACTACTATAAT
*
5494424 AAGGGGTATCAATACTACTATAAT
1 AAGGAGTATCAATACTACTATAAT
*
5494448 AAGTAGTATCAATA
1 AAGGAGTATCAATA
5494462 TTGTGAATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 11 0.35
22 4 0.13
23 2 0.06
24 14 0.45
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (24 bp):
AAGGAGTATCAATACTACTATAAT
Found at i:5499763 original size:2 final size:2
Alignment explanation
Indices: 5499756--5499789 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5499746 GTTCAAAAAC
5499756 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
5499790 GTAAATAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5500369 original size:20 final size:21
Alignment explanation
Indices: 5500340--5500398 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 21
5500330 GAGGCTGCAT
*
5500340 GAACAATATCGGTACT-TGAA
1 GAACAATATCGGTACTATAAA
* *
5500360 GAATAATATCGATACTAACTAAA
1 GAACAATATCGGTACT-A-TAAA
5500383 GAACAATATCGGTACT
1 GAACAATATCGGTACT
5500399 GGATGAACAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 14 0.45
23 17 0.55
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (21 bp):
GAACAATATCGGTACTATAAA
Found at i:5503915 original size:17 final size:17
Alignment explanation
Indices: 5503893--5503927 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5503883 CCTACAAACA
5503893 TAGATTAATTTTTTATT
1 TAGATTAATTTTTTATT
5503910 TAGATTAATTTTTTATT
1 TAGATTAATTTTTTATT
5503927 T
1 T
5503928 TTGGTACCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (17 bp):
TAGATTAATTTTTTATT
Found at i:5506358 original size:21 final size:21
Alignment explanation
Indices: 5506332--5506371 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5506322 AACAAAAGGT
*
5506332 AGTATCGATACTACCATGAGA
1 AGTATCAATACTACCATGAGA
*
5506353 AGTATCAATACTACTATGA
1 AGTATCAATACTACCATGA
5506372 AAAATAGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (21 bp):
AGTATCAATACTACCATGAGA
Found at i:5507975 original size:29 final size:29
Alignment explanation
Indices: 5507942--5508009 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
5507932 CTTGAGAAAA
5507942 TGAAAACAAATGAGTACAAAAGTGTTCTT
1 TGAAAACAAATGAGTACAAAAGTGTTCTT
5507971 TGAAAACAAATGAGTACAAAAGTGTTCTT
1 TGAAAACAAATGAGTACAAAAGTGTTCTT
5508000 TGAAAACAAA
1 TGAAAACAAA
5508010 AGGAATGTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.25
Consensus pattern (29 bp):
TGAAAACAAATGAGTACAAAAGTGTTCTT
Found at i:5508415 original size:21 final size:21
Alignment explanation
Indices: 5508389--5508428 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5508379 AACAAAAGGT
*
5508389 AGTATCGATACTACCATGAGA
1 AGTATCAATACTACCATGAGA
*
5508410 AGTATCAATACTACTATGA
1 AGTATCAATACTACCATGA
5508429 AAAATAGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (21 bp):
AGTATCAATACTACCATGAGA
Found at i:5510572 original size:29 final size:29
Alignment explanation
Indices: 5510539--5510606 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 29
5510529 CTTGAGAAAA
*
5510539 TGAAAACAAATGAGTACAAAAGTGTTCTT
1 TGAAAACAAATGAGAACAAAAGTGTTCTT
5510568 TGAAAACAAATGAGAACAAAAGTGTTCTT
1 TGAAAACAAATGAGAACAAAAGTGTTCTT
5510597 TGAAAACAAA
1 TGAAAACAAA
5510607 AGGAATGTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.50, C:0.10, G:0.16, T:0.24
Consensus pattern (29 bp):
TGAAAACAAATGAGAACAAAAGTGTTCTT
Found at i:5513173 original size:29 final size:29
Alignment explanation
Indices: 5513140--5513207 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
5513130 CTTGAGAAAA
5513140 TGAAAACAAATGAGTACAAAAGTGTTCTT
1 TGAAAACAAATGAGTACAAAAGTGTTCTT
5513169 TGAAAACAAATGAGTACAAAAGTGTTCTT
1 TGAAAACAAATGAGTACAAAAGTGTTCTT
5513198 TGAAAACAAA
1 TGAAAACAAA
5513208 AGGAATGTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.25
Consensus pattern (29 bp):
TGAAAACAAATGAGTACAAAAGTGTTCTT
Found at i:5513613 original size:21 final size:21
Alignment explanation
Indices: 5513587--5513635 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5513577 AACAAAAGGT
*
5513587 AGTATCGATACTACCATGAGA
1 AGTATCAATACTACCATGAGA
* *
5513608 AGTATCAATACTACTATGAAA
1 AGTATCAATACTACCATGAGA
*
5513629 AATATCA
1 AGTATCA
5513636 GCACTGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (21 bp):
AGTATCAATACTACCATGAGA
Found at i:5515745 original size:27 final size:28
Alignment explanation
Indices: 5515702--5515766 Score: 114
Period size: 27 Copynumber: 2.3 Consensus size: 28
5515692 CTTGAGAAAA
5515702 TGAAAACAAATGAGTACAAAAGTGTTC-T
1 TGAAAAC-AATGAGTACAAAAGTGTTCTT
5515730 TGAAAACAATGAGTACAAAAGTGTTCTT
1 TGAAAACAATGAGTACAAAAGTGTTCTT
5515758 TGAAAACAA
1 TGAAAACAA
5515767 AAGGAATGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 19 0.53
28 17 0.47
ACGTcount: A:0.48, C:0.11, G:0.17, T:0.25
Consensus pattern (28 bp):
TGAAAACAATGAGTACAAAAGTGTTCTT
Found at i:5523041 original size:18 final size:18
Alignment explanation
Indices: 5523018--5523066 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 18
5523008 TATTCAGTTA
5523018 TATTATAATAATATATAT
1 TATTATAATAATATATAT
* *
5523036 TATTAT-ATACT-TATTT
1 TATTATAATAATATATAT
5523052 TA-TATAAT-ATATATA
1 TATTATAATAATATATA
5523067 ATAAATTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
15 4 0.16
16 11 0.44
17 4 0.16
18 6 0.24
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTATAATAATATATAT
Found at i:5523261 original size:16 final size:16
Alignment explanation
Indices: 5523227--5523265 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
5523217 TTTAATAATG
5523227 TAATACTATTATTTCAA
1 TAATA-TATTATTTCAA
5523244 TAATATATT-TTTCTAA
1 TAATATATTATTTC-AA
5523260 TAATAT
1 TAATAT
5523266 GATCAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.19
16 12 0.57
17 5 0.24
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATATATTATTTCAA
Found at i:5523327 original size:35 final size:37
Alignment explanation
Indices: 5523273--5523341 Score: 99
Period size: 35 Copynumber: 1.9 Consensus size: 37
5523263 TATGATCAAT
*
5523273 TATATTATAATATTATAATATT-TTTATT-TTAATGA
1 TATATAATAATATTATAATATTATTTATTATTAATGA
5523308 TATATAATAA-ATTATTAATATTATTTATTATTAA
1 TATATAATAATATTA-TAATATTATTTATTATTAA
5523342 AATATTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 4 0.13
35 16 0.53
36 6 0.20
37 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (37 bp):
TATATAATAATATTATAATATTATTTATTATTAATGA
Found at i:5523387 original size:22 final size:23
Alignment explanation
Indices: 5523336--5523394 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
5523326 TATTATTTAT
* * *
5523336 TATTAAAATATTTAAAATATATT
1 TATTAATATTTTTAAAATATATA
5523359 TATTAATCATTTTTAAAATATA-A
1 TATTAAT-ATTTTTAAAATATATA
5523382 TA-TAATATTTTTA
1 TATTAATATTTTTA
5523395 TGTTAATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 7 0.22
22 4 0.12
23 8 0.25
24 13 0.41
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTAATATTTTTAAAATATATA
Found at i:5523424 original size:22 final size:22
Alignment explanation
Indices: 5523367--5523426 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 22
5523357 TTTATTAATC
*
5523367 ATTTTTAA-AATATAATATAAT
1 ATTTTTAATAATATAATATTAT
*
5523388 ATTTTT-AT-GT-TAATATTAT
1 ATTTTTAATAATATAATATTAT
*
5523407 ATTTTTAATAATAAAATATT
1 ATTTTTAATAATATAATATT
5523427 TAATTTAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
19 14 0.45
20 4 0.13
21 7 0.23
22 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTTTTAATAATATAATATTAT
Found at i:5523539 original size:30 final size:31
Alignment explanation
Indices: 5523505--5523567 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
5523495 TAATTGATAC
5523505 TATTAATATT-A-TTTATTATTTAATAAAATA
1 TATTAATATTAATTTTATTATTT-ATAAAATA
* * *
5523535 TATTAATCTTAATTTTTTTATTTATAAATTA
1 TATTAATATTAATTTTATTATTTATAAAATA
5523566 TA
1 TA
5523568 AAATAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 9 0.32
31 10 0.36
32 9 0.32
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (31 bp):
TATTAATATTAATTTTATTATTTATAAAATA
Found at i:5523616 original size:27 final size:24
Alignment explanation
Indices: 5523555--5523624 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 24
5523545 AATTTTTTTA
5523555 TTTATAAATTA-TAAAAT-AATAT
1 TTTATAAATTATTAAAATAAATAT
5523577 TTTAATAATATTATTAAAATAAATAAT
1 TTT-ATAA-ATTATTAAAATAAAT-AT
*
5523604 GTTTATTAAATTATTACAATA
1 -TTTA-TAAATTATTAAAATA
5523625 TTGTTGAGAG
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 3 0.08
23 4 0.10
24 4 0.10
25 6 0.15
26 3 0.08
27 14 0.35
28 6 0.15
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (24 bp):
TTTATAAATTATTAAAATAAATAT
Found at i:5527540 original size:20 final size:20
Alignment explanation
Indices: 5527515--5527624 Score: 193
Period size: 20 Copynumber: 5.5 Consensus size: 20
5527505 AGGCTAAATA
*
5527515 GTATCGGTACCCCTCCTATG
1 GTATCGATACCCCTCCTATG
5527535 GTATCGATACCCCTCCTATG
1 GTATCGATACCCCTCCTATG
5527555 GTATCGATACCCCTCCTATG
1 GTATCGATACCCCTCCTATG
5527575 GTATCGATACCCCTCCTATG
1 GTATCGATACCCCTCCTATG
*
5527595 GTATCGATACCCCTCCTATA
1 GTATCGATACCCCTCCTATG
*
5527615 GTATCAATAC
1 GTATCGATAC
5527625 TTATATATTA
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 87 1.00
ACGTcount: A:0.22, C:0.34, G:0.15, T:0.30
Consensus pattern (20 bp):
GTATCGATACCCCTCCTATG
Found at i:5532077 original size:278 final size:278
Alignment explanation
Indices: 5531580--5532124 Score: 1018
Period size: 278 Copynumber: 2.0 Consensus size: 278
5531570 GTGTGAGCAT
*
5531580 TCAATGTCAAATGATTGAGAGTTATTTTTGAACAAATACTACTTTATATTTACCTCAAATTAATA
1 TCAATGTCAAATGATTGAGAGTTATTTTTGAACAAATACTACTTTATATTTACCCCAAATTAATA
5531645 AATAAAAGTTACTGATTAAGTTTGAGTTTTGGATTTAGTCCCTTTTTAAATTAAGGGTAAACTAT
66 AATAAAAGTTACTGATTAAGTTTGAGTTTTGGATTTAGTCCCTTTTTAAATTAAGGGTAAACTAT
*
5531710 AATTTTCATCACTCAACTTTGGTTTTATTTATGTTTTGATCATTAAACTTTAACAAAATCAATTT
131 AATTTTCATCACTCAACTTTGGTTTTATTTATGTTTTGATCATTAAACTTTAAAAAAATCAATTT
5531775 GATCGTTCAACTTTCAAATTACTTCGTTTTTATCATTCTACCGTTAAATGATAAATAGTATGATG
196 GATCGTTCAACTTTCAAATTACTTCGTTTTTATCATTCTACCGTTAAATGATAAATAGTATGATG
5531840 ACACGGTAGTCGTTTTTA
261 ACACGGTAGTCGTTTTTA
*
5531858 TCAATGTCAAATGATTGAGAGTTATTTTTGAATAAATACTACTTTATATTTACCCCAAATTAATA
1 TCAATGTCAAATGATTGAGAGTTATTTTTGAACAAATACTACTTTATATTTACCCCAAATTAATA
* **
5531923 AATAAATGTTACTGATTATTTTTGAGTTTTGGATTTAGTCCCTTTTTAAATTAAGGGTAAACTAT
66 AATAAAAGTTACTGATTAAGTTTGAGTTTTGGATTTAGTCCCTTTTTAAATTAAGGGTAAACTAT
* *
5531988 AATTTTCTTCACTCAACTTTGGTTTTATTTATGTTTTGATCATTAAACTTTAAAAAAATTAATTT
131 AATTTTCATCACTCAACTTTGGTTTTATTTATGTTTTGATCATTAAACTTTAAAAAAATCAATTT
5532053 GATCGTTCAACTTTCAAATTACTTCGTTTTTATCATTCTACCGTTAAATGATAAATAGTATGATG
196 GATCGTTCAACTTTCAAATTACTTCGTTTTTATCATTCTACCGTTAAATGATAAATAGTATGATG
5532118 ACACGGT
261 ACACGGT
5532125 GGTGGTTTAC
Statistics
Matches: 259, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
278 259 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (278 bp):
TCAATGTCAAATGATTGAGAGTTATTTTTGAACAAATACTACTTTATATTTACCCCAAATTAATA
AATAAAAGTTACTGATTAAGTTTGAGTTTTGGATTTAGTCCCTTTTTAAATTAAGGGTAAACTAT
AATTTTCATCACTCAACTTTGGTTTTATTTATGTTTTGATCATTAAACTTTAAAAAAATCAATTT
GATCGTTCAACTTTCAAATTACTTCGTTTTTATCATTCTACCGTTAAATGATAAATAGTATGATG
ACACGGTAGTCGTTTTTA
Found at i:5532241 original size:10 final size:11
Alignment explanation
Indices: 5532217--5532249 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
5532207 ATAAAATACA
*
5532217 TTTTTCTTTTC
1 TTTTTCTTCTC
5532228 TTTTTCTTCT-
1 TTTTTCTTCTC
5532238 TTTTTCTTCTC
1 TTTTTCTTCTC
5532249 T
1 T
5532250 CATTTTCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTCTTCTC
Found at i:5533795 original size:182 final size:181
Alignment explanation
Indices: 5533483--5533937 Score: 673
Period size: 182 Copynumber: 2.5 Consensus size: 181
5533473 ATTTTTTTAC
5533483 TACCGGTTTTGTCATTTCGAGACTC-ATTTTGTCATA-TTTTACCTGTTATATTGTTATGGATCG
1 TACC-GTTTTGTCATTTCGAGAC-CGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCG
* * * *
5533546 ATACATTTTTATAAAGTATCAACACTTTATTGGCGCTATACCTTCTTTTCTTTTAAATTCCAAAA
64 ATACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAA
* * *
5533611 GTGTCGATACTTATAATAAAGTATCGACACTTTCAACATA-TCTGGTAGCTCTT
129 GTGTCGATACTTATAATAAAATATCGACACTATCAACATATTC-GGTAGCGCTT
* *
5533664 TACCGATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTACATTGTTATGGATCGA
1 TACCG-TTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
* * *
5533729 TATATTTTTATAAAGTATCGACACTTTATTAGCGTTATAATTTCTTCTCTTTTAAATTCCAAAAG
65 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
*
5533794 TGTCGATACTTATAATAAAATATCGATACTATCAACATATTCGGTAGCGCTT
130 TGTCGATACTTATAATAAAATATCGACACTATCAACATATTCGGTAGCGCTT
* ** * *
5533846 TACCTGTTTTTTCATTTATAGATCGATTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGA
1 TACC-GTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
*
5533911 TACATTTTTATAAAATATCGACACTTT
65 TACATTTTTATAAAGTATCGACACTTT
5533938 CAATATATCC
Statistics
Matches: 247, Mismatches: 22, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
180 2 0.01
181 31 0.13
182 211 0.85
183 3 0.01
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (181 bp):
TACCGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGAT
ACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGT
GTCGATACTTATAATAAAATATCGACACTATCAACATATTCGGTAGCGCTT
Found at i:5534043 original size:111 final size:112
Alignment explanation
Indices: 5533808--5534270 Score: 732
Period size: 111 Copynumber: 4.1 Consensus size: 112
5533798 GATACTTATA
* * * * * * * *
5533808 ATAAAATATCGATACTATCAACATATTCGGTAGCGCTTTACCTGTTTTTTCATTTATAGATCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
5533873 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
5533920 ATAAAATATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
5533985 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* **
5534031 ATAAAGTATCGACACTTTTAATATATCTAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
5534096 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
5534142 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTATTTTTTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * * *
5534207 TTTGTCATTTTTTTTTATCTATTATATTGTTATGGATCAATATATTTTT
66 TTTGTCA--TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
5534256 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
5534271 AAACCGACAA
Statistics
Matches: 328, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
111 213 0.65
112 65 0.20
114 50 0.15
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:5540203 original size:20 final size:19
Alignment explanation
Indices: 5540158--5540204 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
5540148 CCCTATGAAC
5540158 AATATCGATACTGTTAATG
1 AATATCGATACTGTTAATG
*
5540177 AGGTATCGATACTGTAATAAT-
1 A-ATATCGATACTGT--TAATG
5540198 AATATCG
1 AATATCG
5540205 GTGCTTCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 1 0.04
20 17 0.74
21 1 0.04
22 4 0.17
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (19 bp):
AATATCGATACTGTTAATG
Found at i:5543352 original size:3 final size:3
Alignment explanation
Indices: 5543346--5543371 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5543336 TAATAATAAT
5543346 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
5543372 TAATAATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:5557578 original size:18 final size:17
Alignment explanation
Indices: 5557524--5557572 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
5557514 TTGGACCCTT
* *
5557524 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
5557542 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
5557560 AGTGCATTCGATG
1 AGTGCA-TCGATG
5557573 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:5557630 original size:64 final size:65
Alignment explanation
Indices: 5557524--5557706 Score: 223
Period size: 64 Copynumber: 2.8 Consensus size: 65
5557514 TTGGACCCTT
* * * *
5557524 AGTGCATCGGTGCACTA-AGAGTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCC
1 AGTGCATCGATGCA-TAGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAAACCA
5557587 G
65 G
* * * *
5557588 AGTGCATCGATGCATGGCTG-GTGCATCGATGCATCAAATGCATTCGATGTTT-AAATTAAATCA
1 AGTGCATCGATGCATAG-AGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAAACCA
5557651 G
65 G
*
5557652 AGTGCATCGATGCATAGAGAGTGCATCGGTGCAT-AGAATGCATTCGATGTTTCAA
1 AGTGCATCGATGCATAGAGAGTGCATCGATGCATCA-AATGCATTCGATGTTTCAA
5557707 TTTATCCATT
Statistics
Matches: 102, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
63 7 0.07
64 92 0.90
65 3 0.03
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (65 bp):
AGTGCATCGATGCATAGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAAACCAG
Found at i:5557674 original size:19 final size:19
Alignment explanation
Indices: 5557650--5557700 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
5557640 AAATTAAATC
5557650 AGAGTGCATCGATGCATAG
1 AGAGTGCATCGATGCATAG
*
5557669 AGAGTGCATCGGTGCATAG
1 AGAGTGCATCGATGCATAG
5557688 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
5557701 TTTCAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATAG
Found at i:5564778 original size:18 final size:17
Alignment explanation
Indices: 5564724--5564772 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
5564714 TTGGACCCTT
* *
5564724 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
5564742 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
5564760 AGTGCATTCGATG
1 AGTGCA-TCGATG
5564773 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:5564830 original size:64 final size:63
Alignment explanation
Indices: 5564724--5564907 Score: 214
Period size: 64 Copynumber: 2.9 Consensus size: 63
5564714 TTGGACCCTT
* * *
5564724 AGTGCATCGGTGCACTA-AGAGTGCATCGATGCATCAAGTGCATTCGATGTTTCAA-AATAGCCC
1 AGTGCATCGATGCA-TAGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAATAA-A-CCA
5564787 G
63 G
* * * *
5564788 AGTGCATCGATGCATGGCTG-GTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAG
1 AGTGCATCGATGCATAG-AGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAA-TAAACCAG
*
5564852 AGTGCATCGATGCATAGAGAGTGCATCGGTGCAT-AGAATGCATTCGATGTTTCAAT
1 AGTGCATCGATGCATAGAGAGTGCATCGATGCATCA-AATGCATTCGATGTTTCAAT
5564908 TTATCCATTG
Statistics
Matches: 103, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
63 4 0.04
64 95 0.92
65 2 0.02
66 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (63 bp):
AGTGCATCGATGCATAGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAATAAACCAG
Found at i:5564874 original size:19 final size:19
Alignment explanation
Indices: 5564850--5564900 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
5564840 TAATTAAATC
5564850 AGAGTGCATCGATGCATAG
1 AGAGTGCATCGATGCATAG
*
5564869 AGAGTGCATCGGTGCATAG
1 AGAGTGCATCGATGCATAG
5564888 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
5564901 TTTCAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATAG
Found at i:5565592 original size:22 final size:22
Alignment explanation
Indices: 5565566--5565614 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
5565556 CTAAACGATT
* *
5565566 GAAAACTTGGCATAAAAGTATA
1 GAAAACATGGCATAAAAGTAGA
* *
5565588 GAAAAGATGTCATAAAAGTAGA
1 GAAAACATGGCATAAAAGTAGA
5565610 GAAAA
1 GAAAA
5565615 ACAAACCATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.55, C:0.06, G:0.20, T:0.18
Consensus pattern (22 bp):
GAAAACATGGCATAAAAGTAGA
Found at i:5566807 original size:26 final size:24
Alignment explanation
Indices: 5566778--5566831 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 24
5566768 CAGAAGAGAT
* *
5566778 GAATTTATAAAATTTTAAAAGGTAAA
1 GAATTAATAAAA-TTTAAAAGAT-AA
*
5566804 GAATTAATATAATTTAAAAGATAA
1 GAATTAATAAAATTTAAAAGATAA
5566828 GAAT
1 GAAT
5566832 AAATTATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.24
25 9 0.36
26 10 0.40
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (24 bp):
GAATTAATAAAATTTAAAAGATAA
Found at i:5566881 original size:17 final size:18
Alignment explanation
Indices: 5566845--5566885 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
5566835 TTATTAATAA
5566845 TAAAATATATAAAAAATT
1 TAAAATATATAAAAAATT
* *
5566863 TAAAATATA-ATATAATT
1 TAAAATATATAAAAAATT
5566880 TAAAAT
1 TAAAAT
5566886 TTTCAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATATATAAAAAATT
Found at i:5570301 original size:15 final size:14
Alignment explanation
Indices: 5570267--5570300 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
5570257 AAAGGTAACA
5570267 TTTT-TCTTTTTTG
1 TTTTCTCTTTTTTG
5570280 TTTTCTCTTTTTTG
1 TTTTCTCTTTTTTG
5570294 -TTTCTCT
1 TTTTCTCT
5570301 CCGATTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (14 bp):
TTTTCTCTTTTTTG
Found at i:5570933 original size:3 final size:3
Alignment explanation
Indices: 5570925--5570953 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5570915 CCTGCAAATG
5570925 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5570954 TTTTTTAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5572424 original size:23 final size:21
Alignment explanation
Indices: 5572392--5572436 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
5572382 ATGTTAGTGT
5572392 AATAAATCATGTGAATTAATATA
1 AATAAATCATGTG-ATT-ATATA
*
5572415 AATAATTCATGTGATTATATA
1 AATAAATCATGTGATTATATA
5572436 A
1 A
5572437 GTTATATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 3 0.14
23 12 0.57
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (21 bp):
AATAAATCATGTGATTATATA
Found at i:5572548 original size:9 final size:9
Alignment explanation
Indices: 5572525--5572557 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
5572515 GGATATAAGA
5572525 GATATATGT
1 GATATATGT
5572534 G-T-TATGT
1 GATATATGT
5572541 GATATATGT
1 GATATATGT
5572550 GATATATG
1 GATATATG
5572558 GGAAACACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 6 0.27
8 2 0.09
9 14 0.64
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.45
Consensus pattern (9 bp):
GATATATGT
Found at i:5572768 original size:31 final size:31
Alignment explanation
Indices: 5572730--5572884 Score: 222
Period size: 31 Copynumber: 5.0 Consensus size: 31
5572720 GAGTCGAGGG
*
5572730 TTACCTATGTCCTTCAGGACATATGGACAGA
1 TTACCTATGTCCTTCGGGACATATGGACAGA
5572761 TTACCTATGTCCTTCGGGACATATGGACAGA
1 TTACCTATGTCCTTCGGGACATATGGACAGA
* *
5572792 TTACCTATGTCATTCGGGACATATGGACATA
1 TTACCTATGTCCTTCGGGACATATGGACAGA
*
5572823 TTACCTATGTCCTTCGGGATATATTGG-CAGGA
1 TTACCTATGTCCTTCGGGACATA-TGGACA-GA
* * *
5572855 TTACCTATGTCATTTGGGAGATATGGACAG
1 TTACCTATGTCCTTCGGGACATATGGACAG
5572885 GTCCTTCGGG
Statistics
Matches: 112, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
31 86 0.77
32 26 0.23
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (31 bp):
TTACCTATGTCCTTCGGGACATATGGACAGA
Found at i:5576235 original size:23 final size:21
Alignment explanation
Indices: 5576209--5576264 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
5576199 ACCTAGGCAT
5576209 AGTACCGATACCACAGATAGGG
1 AGTACCGATACCAC-GATAGGG
* *
5576231 AAGTATCGATACC-CTATAGGG
1 -AGTACCGATACCACGATAGGG
*
5576252 GGTACCGATACCA
1 AGTACCGATACCA
5576265 TTGTAAAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 10 0.36
21 6 0.21
22 1 0.04
23 11 0.39
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (21 bp):
AGTACCGATACCACGATAGGG
Found at i:5576692 original size:23 final size:21
Alignment explanation
Indices: 5576664--5576722 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 21
5576654 TGATTATATA
5576664 AGTTATATGATATGAACATATG
1 AGTTATATGATATGAAC-TATG
* *
5576686 AGATTATGTGAAATGAACTATG
1 AG-TTATATGATATGAACTATG
**
5576708 AGCCATATGATATGA
1 AGTTATATGATATGA
5576723 CATTGTGAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 9 0.30
22 8 0.27
23 13 0.43
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (21 bp):
AGTTATATGATATGAACTATG
Found at i:5576774 original size:16 final size:18
Alignment explanation
Indices: 5576753--5576794 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
5576743 GGATATAAGA
5576753 GATATATGTG-T-TATGT
1 GATATATGTGTTATATGT
5576769 GATATATGTGTTATATGT
1 GATATATGTGTTATATGT
5576787 GATATATG
1 GATATATG
5576795 GGAAAGACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 10 0.42
17 1 0.04
18 13 0.54
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.48
Consensus pattern (18 bp):
GATATATGTGTTATATGT
Done.