Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008027.1 Hibiscus syriacus cultivar Beakdansim tig00110503_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: 7662336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 38
Found at i:5179099 original size:13 final size:13
Alignment explanation
Indices: 5179078--5179110 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
5179068 CCCTCGTTTG
*
5179078 CTCGACTCTTACC
1 CTCGGCTCTTACC
5179091 CTCGGCTCTTACC
1 CTCGGCTCTTACC
5179104 CTCGGCT
1 CTCGGCT
5179111 TAGCATCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.09, C:0.45, G:0.15, T:0.30
Consensus pattern (13 bp):
CTCGGCTCTTACC
Found at i:5181708 original size:24 final size:22
Alignment explanation
Indices: 5181687--5181756 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
5181677 CTTAAAGGGG
5181687 CACTGAATATTTGTCCCGAAGGAC
1 CACTGAATA--TGTCCCGAAGGAC
* *
5181711 CACTGGATATGTCCCGAAGGAT
1 CACTGAATATGTCCCGAAGGAC
* *
5181733 CACTGGATATGTCTCGAAGGAC
1 CACTGAATATGTCCCGAAGGAC
5181755 CA
1 CA
5181757 ATGTAACCCT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 34 0.81
24 8 0.19
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (22 bp):
CACTGAATATGTCCCGAAGGAC
Found at i:5181726 original size:22 final size:22
Alignment explanation
Indices: 5181698--5181756 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
5181688 ACTGAATATT
5181698 TGTCCCGAAGGACCACTGGATA
1 TGTCCCGAAGGACCACTGGATA
*
5181720 TGTCCCGAAGGATCACTGGATA
1 TGTCCCGAAGGACCACTGGATA
*
5181742 TGTCTCGAAGGACCA
1 TGTCCCGAAGGACCA
5181757 ATGTAACCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.20
Consensus pattern (22 bp):
TGTCCCGAAGGACCACTGGATA
Found at i:5188373 original size:21 final size:20
Alignment explanation
Indices: 5188334--5188373 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5188324 TGATCATGAC
*
5188334 ATTTCAATATACATGTATAT
1 ATTTCAATATACATATATAT
*
5188354 ATTTCACTATAACATATATA
1 ATTTCAATAT-ACATATATA
5188374 ATCATGTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (20 bp):
ATTTCAATATACATATATAT
Found at i:5188590 original size:22 final size:22
Alignment explanation
Indices: 5188560--5188642 Score: 148
Period size: 22 Copynumber: 3.8 Consensus size: 22
5188550 TGACGACTAC
* *
5188560 GTCCTGAAGGACCATTGGATAT
1 GTCCCGAAGGACCACTGGATAT
5188582 GTCCCGAAGGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAT
5188604 GTCCCGAAGGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAT
5188626 GTCCCGAAGGACCACTG
1 GTCCCGAAGGACCACTG
5188643 TAACCCTCGA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 59 1.00
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAT
Found at i:5189279 original size:64 final size:64
Alignment explanation
Indices: 5189211--5189333 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 64
5189201 ACATAAATCC
** *
5189211 CATTCGATGTTTGTATTTTAAACGG-GTGCATCGATGTACTACTTGTGCATCGATACACTGATGG
1 CATTCGATGTTTGTATTTTAAA-GGAGTGCATCGATACACTACATGTGCATCGATACACTGATGG
* * * *
5189275 CATTCGATGTTTTTATTTTAAAGGAGTGCGTCGTTACACTTCATGTGCATCGATACACT
1 CATTCGATGTTTGTATTTTAAAGGAGTGCATCGATACACTACATGTGCATCGATACACT
5189334 TCATGTGCAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 2 0.04
64 49 0.96
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (64 bp):
CATTCGATGTTTGTATTTTAAAGGAGTGCATCGATACACTACATGTGCATCGATACACTGATGG
Found at i:5189331 original size:19 final size:19
Alignment explanation
Indices: 5189309--5189351 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
5189299 AGTGCGTCGT
5189309 TACACTTCATGTGCATCGA
1 TACACTTCATGTGCATCGA
5189328 TACACTTCATGTGCATCGA
1 TACACTTCATGTGCATCGA
5189347 TACAC
1 TACAC
5189352 CTTGAACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (19 bp):
TACACTTCATGTGCATCGA
Found at i:5191741 original size:14 final size:13
Alignment explanation
Indices: 5191722--5191787 Score: 54
Period size: 14 Copynumber: 5.3 Consensus size: 13
5191712 CGTAAAATTA
5191722 TATGTTTGTTCATT
1 TATG-TTGTTCATT
5191736 TATG-T-TT-ATT
1 TATGTTGTTCATT
5191746 TATGTCTGTTCATT
1 TATGT-TGTTCATT
*
5191760 TA---TATTCATT
1 TATGTTGTTCATT
5191770 TATGTCTGTTCATT
1 TATGT-TGTTCATT
5191784 TATG
1 TATG
5191788 CTCGAACAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 16
0.70 0.03 0.27
Matches are distributed among these distances:
10 16 0.38
11 2 0.05
12 2 0.05
13 2 0.05
14 20 0.48
ACGTcount: A:0.18, C:0.09, G:0.12, T:0.61
Consensus pattern (13 bp):
TATGTTGTTCATT
Found at i:5191755 original size:24 final size:24
Alignment explanation
Indices: 5191722--5191787 Score: 105
Period size: 24 Copynumber: 2.8 Consensus size: 24
5191712 CGTAAAATTA
* *
5191722 TATGTTTGTTCATTTATGTTTATT
1 TATGTCTGTTCATTTATGTTCATT
*
5191746 TATGTCTGTTCATTTATATTCATT
1 TATGTCTGTTCATTTATGTTCATT
5191770 TATGTCTGTTCATTTATG
1 TATGTCTGTTCATTTATG
5191788 CTCGAACAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.18, C:0.09, G:0.12, T:0.61
Consensus pattern (24 bp):
TATGTCTGTTCATTTATGTTCATT
Found at i:5192144 original size:40 final size:40
Alignment explanation
Indices: 5192080--5192191 Score: 163
Period size: 40 Copynumber: 2.8 Consensus size: 40
5192070 CGTTTATGTT
* * **
5192080 CGTTTATTT-ATTAAATGAATGAACATGAACAAGATTTTA
1 CGTTCATTTAATTAAATGAACGAACACAAACAAGATTTTA
*
5192119 CGTTCATTTAATTAAATGAACGAACACAAACAAGATTTTG
1 CGTTCATTTAATTAAATGAACGAACACAAACAAGATTTTA
*
5192159 CGTTCATTTAATTAAATTAACGAACACAAACAA
1 CGTTCATTTAATTAAATGAACGAACACAAACAA
5192192 AGGGCTCGTT
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
39 8 0.12
40 58 0.88
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32
Consensus pattern (40 bp):
CGTTCATTTAATTAAATGAACGAACACAAACAAGATTTTA
Found at i:5192545 original size:10 final size:10
Alignment explanation
Indices: 5192527--5192577 Score: 75
Period size: 10 Copynumber: 5.1 Consensus size: 10
5192517 GTGTTTGTGT
*
5192527 TGTTTGTTTA
1 TGTTCGTTTA
5192537 TGTTCGTTTA
1 TGTTCGTTTA
* *
5192547 CGTTCGTTTG
1 TGTTCGTTTA
5192557 TGTTCGTTTA
1 TGTTCGTTTA
5192567 TGTTCGTTTA
1 TGTTCGTTTA
5192577 T
1 T
5192578 CATTTAAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.08, C:0.10, G:0.22, T:0.61
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:5192834 original size:20 final size:20
Alignment explanation
Indices: 5192806--5192845 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5192796 TTATTATGTT
* *
5192806 CGTTCGTTTGTGTTTGTTTA
1 CGTTCGTTTATGTTCGTTTA
*
5192826 CGTTTGTTTATGTTCGTTTA
1 CGTTCGTTTATGTTCGTTTA
5192846 TCATTTAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.07, C:0.10, G:0.23, T:0.60
Consensus pattern (20 bp):
CGTTCGTTTATGTTCGTTTA
Found at i:5193609 original size:21 final size:21
Alignment explanation
Indices: 5193576--5193622 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
5193566 ATACCCTAAA
*
5193576 CCTAAACTCTAAA-TCTTATAC
1 CCTAAACTCTAAACTATTA-AC
5193597 CCTAAAC-CTTAAACTATTAAC
1 CCTAAACTC-TAAACTATTAAC
5193618 CCTAA
1 CCTAA
5193623 GCCCTAAGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 1 0.04
21 18 0.78
22 4 0.17
ACGTcount: A:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (21 bp):
CCTAAACTCTAAACTATTAAC
Found at i:5196130 original size:16 final size:15
Alignment explanation
Indices: 5196109--5196160 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
5196099 AAATCGTCGA
5196109 CCGGAAGTTCGGGTAC
1 CCGGAA-TTCGGGTAC
*
5196125 CCGGAAATCGGGTAC
1 CCGGAATTCGGGTAC
* *
5196140 CCGAAAATCCGGGTAC
1 CCG-GAATTCGGGTAC
5196156 CCGGA
1 CCGGA
5196161 TTTGCACACC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 12 0.40
16 18 0.60
ACGTcount: A:0.25, C:0.29, G:0.33, T:0.13
Consensus pattern (15 bp):
CCGGAATTCGGGTAC
Found at i:5196137 original size:15 final size:15
Alignment explanation
Indices: 5196117--5196160 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
5196107 GACCGGAAGT
5196117 TCGGGTACCCGGAAA
1 TCGGGTACCCGGAAA
*
5196132 TCGGGTACCCGAAAA
1 TCGGGTACCCGGAAA
5196147 TCCGGGTACCCGGA
1 T-CGGGTACCCGGA
5196161 TTTGCACACC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.25, C:0.30, G:0.32, T:0.14
Consensus pattern (15 bp):
TCGGGTACCCGGAAA
Found at i:5196460 original size:30 final size:30
Alignment explanation
Indices: 5196424--5196492 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
5196414 GGAACTTAAT
*
5196424 TTGACATGTTGCAATCTTTTGTAGGTAAAC
1 TTGACATGTTGCAATCTTTTGTAAGTAAAC
5196454 TTGACATGTTGCAATCTTTTGTAAGTAAAC
1 TTGACATGTTGCAATCTTTTGTAAGTAAAC
5196484 TTGACATGT
1 TTGACATGT
5196493 GTTGTCATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.41
Consensus pattern (30 bp):
TTGACATGTTGCAATCTTTTGTAAGTAAAC
Found at i:5196644 original size:36 final size:35
Alignment explanation
Indices: 5196590--5196661 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 35
5196580 AAGGAAATAA
* *
5196590 TGTCATCTTGTATAAATTTGGATATGTTGTCATAT
1 TGTCATCTTGTATAAATTTAGATATGTTATCATAT
* *
5196625 TGTCATCTTTTTATAAATTTAGATGTGTTATCATAT
1 TGTCATC-TTGTATAAATTTAGATATGTTATCATAT
5196661 T
1 T
5196662 TGTAAACTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 7 0.22
36 25 0.78
ACGTcount: A:0.26, C:0.08, G:0.14, T:0.51
Consensus pattern (35 bp):
TGTCATCTTGTATAAATTTAGATATGTTATCATAT
Found at i:5196866 original size:11 final size:11
Alignment explanation
Indices: 5196850--5196937 Score: 86
Period size: 11 Copynumber: 7.7 Consensus size: 11
5196840 AGGTTCAAAT
*
5196850 TCGAGCTTGAA
1 TCGAGCTTAAA
*
5196861 TCGAGCTCAAAA
1 TCGAGCT-TAAA
*
5196873 TCGAGCTTGAA
1 TCGAGCTTAAA
*
5196884 TCGAGCTCAAAA
1 TCGAGCT-TAAA
*
5196896 TCGAGCTTCAA
1 TCGAGCTTAAA
*
5196907 TCGAGCTCAAAA
1 TCGAGCT-TAAA
*
5196919 TCGAGCTTCAA
1 TCGAGCTTAAA
5196930 TCGAGCTT
1 TCGAGCTT
5196938 GAGTCTCGAG
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
11 35 0.56
12 27 0.44
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (11 bp):
TCGAGCTTAAA
Found at i:5196876 original size:12 final size:12
Alignment explanation
Indices: 5196859--5196925 Score: 86
Period size: 12 Copynumber: 5.8 Consensus size: 12
5196849 TTCGAGCTTG
5196859 AATCGAGCTCAA
1 AATCGAGCTCAA
**
5196871 AATCGAGCT-TG
1 AATCGAGCTCAA
5196882 AATCGAGCTCAA
1 AATCGAGCTCAA
5196894 AATCGAGCTTC--
1 AATCGAGC-TCAA
5196905 AATCGAGCTCAA
1 AATCGAGCTCAA
5196917 AATCGAGCT
1 AATCGAGCT
5196926 TCAATCGAGC
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
10 2 0.04
11 17 0.36
12 26 0.55
13 2 0.04
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (12 bp):
AATCGAGCTCAA
Found at i:5196876 original size:23 final size:23
Alignment explanation
Indices: 5196844--5196936 Score: 159
Period size: 23 Copynumber: 4.0 Consensus size: 23
5196834 TTTTGTAGGT
* *
5196844 TCAAATTCGAGCTTGAATCGAGC
1 TCAAAATCGAGCTTCAATCGAGC
*
5196867 TCAAAATCGAGCTTGAATCGAGC
1 TCAAAATCGAGCTTCAATCGAGC
5196890 TCAAAATCGAGCTTCAATCGAGC
1 TCAAAATCGAGCTTCAATCGAGC
5196913 TCAAAATCGAGCTTCAATCGAGC
1 TCAAAATCGAGCTTCAATCGAGC
5196936 T
1 T
5196937 TGAGTCTCGA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 68 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (23 bp):
TCAAAATCGAGCTTCAATCGAGC
Found at i:5199779 original size:22 final size:22
Alignment explanation
Indices: 5199754--5199800 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
5199744 CTCAGATAAA
5199754 AGTAAGTTTTTAGAATAGCTTC
1 AGTAAGTTTTTAGAATAGCTTC
5199776 AGTAAGTTTTTAGAATAGCTTC
1 AGTAAGTTTTTAGAATAGCTTC
5199798 AGT
1 AGT
5199801 GATAGAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (22 bp):
AGTAAGTTTTTAGAATAGCTTC
Found at i:5203496 original size:4 final size:4
Alignment explanation
Indices: 5203487--5203513 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5203477 CAATGCATGT
5203487 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
5203514 CATAGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:5213396 original size:2 final size:2
Alignment explanation
Indices: 5213383--5213466 Score: 145
Period size: 2 Copynumber: 43.0 Consensus size: 2
5213373 TACTCAAGTG
*
5213383 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5213424 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5213465 AT
1 AT
5213467 GTGTGTGTGT
Statistics
Matches: 78, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
1 2 0.03
2 76 0.97
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5213824 original size:27 final size:29
Alignment explanation
Indices: 5213780--5213842 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
5213770 GAGTTTCTAA
*
5213780 AAATATTAGAGGGGCTAAATTAT-TTTTTT
1 AAAT-TTAGAGGGGCTAAATTATAATTTTT
*
5213809 AAATTTA-AGGGTCTAAATTATAATTTTT
1 AAATTTAGAGGGGCTAAATTATAATTTTT
5213837 AAATTT
1 AAATTT
5213843 TAACGGGGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 13 0.42
28 14 0.45
29 4 0.13
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (29 bp):
AAATTTAGAGGGGCTAAATTATAATTTTT
Found at i:5217335 original size:32 final size:31
Alignment explanation
Indices: 5217257--5217336 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 31
5217247 ATTGAAGTTT
*
5217257 ATTTTTTTTAATTTAATTACTTAACTTTCAA
1 ATTTTTTTTAATTTAATCACTTAACTTTCAA
* ** **
5217288 AATACTCCTAATTTAATCACTCTAACTTTCAA
1 ATTTTTTTTAATTTAATCACT-TAACTTTCAA
*
5217320 ATTTTTTTTATTTTAAT
1 ATTTTTTTTAATTTAAT
5217337 TATCTATTAA
Statistics
Matches: 36, Mismatches: 12, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
31 15 0.42
32 21 0.58
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.54
Consensus pattern (31 bp):
ATTTTTTTTAATTTAATCACTTAACTTTCAA
Found at i:5225116 original size:142 final size:142
Alignment explanation
Indices: 5224855--5225119 Score: 503
Period size: 142 Copynumber: 1.9 Consensus size: 142
5224845 TTGTGTATAC
*
5224855 ATTCGTATTCAAAATTTACTTACAAACTGAAGTAAGATCTTAATGAGAAAGCTGTAATCAATAGG
1 ATTCGTATTCAAAATTTACTTACAAACTGAAGTAAGATCTTAATAAGAAAGCTGTAATCAATAGG
*
5224920 ATTTTCCTAATCCTCCTGGAAAGGAAGAAGGTGAAATTCTTTTTCCTTTTCACAGGGATTAGGAG
66 ATTTTCCTAATCCTCCTGGAAAGGAAGAAGGTGAAATTCTTTTTCCTTTCCACAGGGATTAGGAG
5224985 GAAGGACATGAA
131 GAAGGACATGAA
*
5224997 ATTCGTATTCAAAATTTACTTACAAACTGAATTAAGATCTTAATAAGAAAGCTGTAATCAATAGG
1 ATTCGTATTCAAAATTTACTTACAAACTGAAGTAAGATCTTAATAAGAAAGCTGTAATCAATAGG
5225062 ATTTTCCTAATCCTCCTGGAAAGGAAGAAGGTGAAATTCTTTTTCCTTTCCACAGGGA
66 ATTTTCCTAATCCTCCTGGAAAGGAAGAAGGTGAAATTCTTTTTCCTTTCCACAGGGA
5225120 CCAGGAGACC
Statistics
Matches: 120, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
142 120 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (142 bp):
ATTCGTATTCAAAATTTACTTACAAACTGAAGTAAGATCTTAATAAGAAAGCTGTAATCAATAGG
ATTTTCCTAATCCTCCTGGAAAGGAAGAAGGTGAAATTCTTTTTCCTTTCCACAGGGATTAGGAG
GAAGGACATGAA
Found at i:5227622 original size:31 final size:31
Alignment explanation
Indices: 5227587--5227652 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
5227577 ATCACACACC
* *
5227587 TTAAATAGGGGTGTTTAATCCGTCGGTTTGG
1 TTAAATAAGGGTGTTTAATCCATCGGTTTGG
* *
5227618 TTAAATAAGTGTGTTTAATCCATCGTTTTGG
1 TTAAATAAGGGTGTTTAATCCATCGGTTTGG
5227649 TTAA
1 TTAA
5227653 TCACACACCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.42
Consensus pattern (31 bp):
TTAAATAAGGGTGTTTAATCCATCGGTTTGG
Found at i:5228087 original size:20 final size:19
Alignment explanation
Indices: 5228054--5228090 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
5228044 TTAGACAGGT
5228054 TTTTCTTAAGATTTTTTTA
1 TTTTCTTAAGATTTTTTTA
5228073 TTTTCTTAA-ATATTTTTT
1 TTTTCTTAAGAT-TTTTTT
5228091 CTAGAATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.70
Consensus pattern (19 bp):
TTTTCTTAAGATTTTTTTA
Found at i:5228687 original size:22 final size:22
Alignment explanation
Indices: 5228647--5228688 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5228637 TTAGACAGAT
* *
5228647 TTTTCTTTAAGATTTTTTTTTC
1 TTTTCTTAAAGATTGTTTTTTC
*
5228669 TTTTCTTAAATATTGTTTTT
1 TTTTCTTAAAGATTGTTTTT
5228689 ACGGCTAAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.71
Consensus pattern (22 bp):
TTTTCTTAAAGATTGTTTTTTC
Found at i:5234280 original size:60 final size:60
Alignment explanation
Indices: 5234187--5234311 Score: 250
Period size: 60 Copynumber: 2.1 Consensus size: 60
5234177 TAATGAAATT
5234187 AAAATTATAGATAAAGTATTTAACATGCATTTACATAATATTTTTATTGAAAAAATAAAA
1 AAAATTATAGATAAAGTATTTAACATGCATTTACATAATATTTTTATTGAAAAAATAAAA
5234247 AAAATTATAGATAAAGTATTTAACATGCATTTACATAATATTTTTATTGAAAAAATAAAA
1 AAAATTATAGATAAAGTATTTAACATGCATTTACATAATATTTTTATTGAAAAAATAAAA
5234307 AAAAT
1 AAAAT
5234312 AAGTATTATT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.53, C:0.05, G:0.06, T:0.36
Consensus pattern (60 bp):
AAAATTATAGATAAAGTATTTAACATGCATTTACATAATATTTTTATTGAAAAAATAAAA
Found at i:5236794 original size:37 final size:37
Alignment explanation
Indices: 5236744--5236815 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
5236734 GGATATTCAA
*
5236744 TGTTAGTTTTGAACCAAAACTATCTAATTTTCTTTAG
1 TGTTAGTTTTGAACCAAAACCATCTAATTTTCTTTAG
5236781 TGTTAGTTTTGAACCAAAACCATCTAATTTTCTTT
1 TGTTAGTTTTGAACCAAAACCATCTAATTTTCTTT
5236816 CTTTCTTCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (37 bp):
TGTTAGTTTTGAACCAAAACCATCTAATTTTCTTTAG
Found at i:5250112 original size:16 final size:17
Alignment explanation
Indices: 5250085--5250118 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5250075 TTACTCACTA
5250085 TTTTATAAAAGTAAATG
1 TTTTATAAAAGTAAATG
*
5250102 TTTTA-AAAAGTCAATG
1 TTTTATAAAAGTAAATG
5250118 T
1 T
5250119 GACACGTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.41
Consensus pattern (17 bp):
TTTTATAAAAGTAAATG
Found at i:5252814 original size:21 final size:20
Alignment explanation
Indices: 5252789--5252827 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5252779 GATCAAGGCC
*
5252789 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCAT-AAATCT
*
5252810 TTTGTCGAGGCCATAAAT
1 TTTGTCGAAGCCATAAAT
5252828 TATTGCAGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (20 bp):
TTTGTCGAAGCCATAAATCT
Found at i:5253967 original size:16 final size:16
Alignment explanation
Indices: 5253946--5253978 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5253936 ACCGCGATAT
5253946 CAAGATCTACCTGATC
1 CAAGATCTACCTGATC
*
5253962 CAAGATCTGCCTGATC
1 CAAGATCTACCTGATC
5253978 C
1 C
5253979 TCCATAGGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.24
Consensus pattern (16 bp):
CAAGATCTACCTGATC
Found at i:5256314 original size:2 final size:2
Alignment explanation
Indices: 5256307--5256345 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5256297 TATTCCGAAT
5256307 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5256346 CAATTAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5260371 original size:23 final size:23
Alignment explanation
Indices: 5260345--5260394 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
5260335 AAATACACCG
*
5260345 AAGTGCCACGTAGAATTGAACCA
1 AAGTGCCACGTAGAAATGAACCA
* *
5260368 AAGTGCCGCGTAGAAATGCACCA
1 AAGTGCCACGTAGAAATGAACCA
5260391 AAGT
1 AAGT
5260395 TCCATATAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (23 bp):
AAGTGCCACGTAGAAATGAACCA
Found at i:5267252 original size:23 final size:23
Alignment explanation
Indices: 5267216--5267280 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
5267206 CACCACAGCT
* *
5267216 CGTATAAATACACCAAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
* * *
5267239 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCAAAGTGCCA
5267262 CGTAGAAATGCACCAAAGT
1 CGTAGAAATGCACCAAAGT
5267281 ACCATATAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCAAAGTGCCA
Found at i:5270008 original size:15 final size:15
Alignment explanation
Indices: 5269988--5270017 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5269978 AGGTGTTCCC
5269988 TTAGATTGGAACCTA
1 TTAGATTGGAACCTA
5270003 TTAGATTGGAACCTA
1 TTAGATTGGAACCTA
5270018 AGCCAATAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (15 bp):
TTAGATTGGAACCTA
Found at i:5275259 original size:2 final size:2
Alignment explanation
Indices: 5275252--5275283 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5275242 TAGTAACTAA
5275252 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
5275284 TAAAAGAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5289034 original size:55 final size:56
Alignment explanation
Indices: 5288931--5289035 Score: 149
Period size: 56 Copynumber: 1.9 Consensus size: 56
5288921 AAAGGGCTAT
* * * * *
5288931 GGAGGGAGGGAGTGTGATCTAGTTATATAATGTAAAATTAAAAAGTTTTGAGGGAG
1 GGAGGGAGGGAGTATGATCTACTTACACAATATAAAATTAAAAAGTTTTGAGGGAG
*
5288987 GGAGGGAGTGAGTATGATCTACTTACACAATAT-AAATTAAAAAGTTTTG
1 GGAGGGAGGGAGTATGATCTACTTACACAATATAAAATTAAAAAGTTTTG
5289036 CACTAATTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
55 16 0.37
56 27 0.63
ACGTcount: A:0.37, C:0.05, G:0.29, T:0.30
Consensus pattern (56 bp):
GGAGGGAGGGAGTATGATCTACTTACACAATATAAAATTAAAAAGTTTTGAGGGAG
Found at i:5307732 original size:18 final size:18
Alignment explanation
Indices: 5307693--5307732 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5307683 TATAAATACT
* *
5307693 AATAATAATTAATCATAT
1 AATAATAATTAATAATAA
*
5307711 AATAATTATTAATAATAA
1 AATAATAATTAATAATAA
5307729 AATA
1 AATA
5307733 TTAAAATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
AATAATAATTAATAATAA
Found at i:5309157 original size:19 final size:19
Alignment explanation
Indices: 5309133--5309184 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 19
5309123 CACCTTTAAA
5309133 ATTTTATAATTTAATCCTT
1 ATTTTATAATTTAATCCTT
* * * *
5309152 ATTTTAGAATATAAACTTT
1 ATTTTATAATTTAATCCTT
*
5309171 A-GTTATAATTTAAT
1 ATTTTATAATTTAAT
5309185 TTAATCTAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (19 bp):
ATTTTATAATTTAATCCTT
Found at i:5324473 original size:21 final size:21
Alignment explanation
Indices: 5324390--5324482 Score: 71
Period size: 21 Copynumber: 4.4 Consensus size: 21
5324380 AGAGTTCTAC
* * *
5324390 GTGGTCCTTCGGGATATATAT
1 GTGGTCCTTTGGAACATATAT
**
5324411 GTAATCCTTTGGAACATATAT
1 GTGGTCCTTTGGAACATATAT
* * *
5324432 GCGGT-TTTTCGGAACACATAT
1 GTGGTCCTTT-GGAACATATAT
* *
5324453 TTGGTCCTTTGGAATATATAT
1 GTGGTCCTTTGGAACATATAT
*
5324474 GTGATCCTT
1 GTGGTCCTT
5324483 AAGGAGTGGT
Statistics
Matches: 53, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
20 3 0.06
21 47 0.89
22 3 0.06
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.40
Consensus pattern (21 bp):
GTGGTCCTTTGGAACATATAT
Found at i:5324514 original size:21 final size:21
Alignment explanation
Indices: 5324488--5324546 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
5324478 TCCTTAAGGA
*
5324488 GTGGTCCTTCGAGACATCTAT
1 GTGGTCTTTCGAGACATCTAT
5324509 GTGGTCTTTCGAGACATCTAT
1 GTGGTCTTTCGAGACATCTAT
*
5324530 GTGGTTTTTCGAGACAT
1 GTGGTCTTTCGAGACAT
5324547 TTATACGCAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (21 bp):
GTGGTCTTTCGAGACATCTAT
Found at i:5326091 original size:31 final size:31
Alignment explanation
Indices: 5326020--5326094 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
5326010 TTACGTCAGT
*
5326020 GACCATATTACAAACGGACTAAATGTTGGGG
1 GACCATATTGCAAACGGACTAAATGTTGGGG
5326051 GACCATATTGCAAACGGACTAAATGTTGGGG
1 GACCATATTGCAAACGGACTAAATGTTGGGG
**
5326082 GACTGTATTGCAA
1 GACCATATTGCAA
5326095 GTTTTAAAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (31 bp):
GACCATATTGCAAACGGACTAAATGTTGGGG
Found at i:5328165 original size:14 final size:14
Alignment explanation
Indices: 5328143--5328202 Score: 111
Period size: 14 Copynumber: 4.3 Consensus size: 14
5328133 CGTTGGGCAT
*
5328143 CCGAAGGCATCCGA
1 CCGAGGGCATCCGA
5328157 CCGAGGGCATCCGA
1 CCGAGGGCATCCGA
5328171 CCGAGGGCATCCGA
1 CCGAGGGCATCCGA
5328185 CCGAGGGCATCCGA
1 CCGAGGGCATCCGA
5328199 CCGA
1 CCGA
5328203 TGCCATTCGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
14 45 1.00
ACGTcount: A:0.23, C:0.37, G:0.33, T:0.07
Consensus pattern (14 bp):
CCGAGGGCATCCGA
Found at i:5328217 original size:28 final size:28
Alignment explanation
Indices: 5328150--5328217 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
5328140 CATCCGAAGG
*
5328150 CATCCGACCGAGGGCATCCGACCGAGGG
1 CATCCGACCGAGGGCATCCGACCGAGGC
*
5328178 CATCCGACCGAGGGCATCCGACCGATGC
1 CATCCGACCGAGGGCATCCGACCGAGGC
* *
5328206 CATTCGAGCGAG
1 CATCCGACCGAG
5328218 CTATGCGAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.22, C:0.35, G:0.32, T:0.10
Consensus pattern (28 bp):
CATCCGACCGAGGGCATCCGACCGAGGC
Found at i:5328982 original size:31 final size:31
Alignment explanation
Indices: 5328908--5328982 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
5328898 TTGCGTCAGT
*
5328908 GACCGTATTGCAAACGGACTAAATGTTGGGG
1 GACCGTATTGCAAACGGACTAAATGTTGGGA
* * *
5328939 GACCATACTGCAAACGGATTAAATGTTGGGA
1 GACCGTATTGCAAACGGACTAAATGTTGGGA
*
5328970 GACTGTATTGCAA
1 GACCGTATTGCAA
5328983 GTTTTAAAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (31 bp):
GACCGTATTGCAAACGGACTAAATGTTGGGA
Found at i:5330989 original size:17 final size:17
Alignment explanation
Indices: 5330963--5331004 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
5330953 ATTATATGGA
*
5330963 TATT-TTATTCATTTAT
1 TATTATTATTCATGTAT
*
5330979 TTTTATTATTCATGTAT
1 TATTATTATTCATGTAT
5330996 TATTATTAT
1 TATTATTAT
5331005 ATATATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATGTAT
Found at i:5334597 original size:22 final size:22
Alignment explanation
Indices: 5334572--5334629 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 22
5334562 AACAAAAAGG
5334572 GCAAAAAGAAAAAAGAAAAGAA
1 GCAAAAAGAAAAAAGAAAAGAA
* *
5334594 GCAAAAAAGGAAAAA-ACAAGAA
1 GC-AAAAAGAAAAAAGAAAAGAA
*
5334616 -CAAAAATAAAAAAG
1 GCAAAAAGAAAAAAG
5334630 GGAACAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 10 0.33
21 1 0.03
22 8 0.27
23 11 0.37
ACGTcount: A:0.76, C:0.07, G:0.16, T:0.02
Consensus pattern (22 bp):
GCAAAAAGAAAAAAGAAAAGAA
Found at i:5335270 original size:22 final size:22
Alignment explanation
Indices: 5335242--5335292 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
5335232 CCCCATCAAT
5335242 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
5335264 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
5335286 CCTTTGA
1 CCTTTGA
5335293 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:5335730 original size:18 final size:18
Alignment explanation
Indices: 5335707--5335742 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5335697 TCAACATCAA
* *
5335707 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
5335725 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
5335743 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:5336266 original size:36 final size:36
Alignment explanation
Indices: 5336223--5336366 Score: 252
Period size: 36 Copynumber: 4.0 Consensus size: 36
5336213 ACTAGAAGAG
5336223 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
5336259 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
5336295 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
5336331 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
5336367 ATATTTGAAT
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 100 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:5336266 original size:71 final size:72
Alignment explanation
Indices: 5336181--5336366 Score: 227
Period size: 72 Copynumber: 2.6 Consensus size: 72
5336171 GTTTTTCTTA
* * * * *
5336181 AAACAAGA-TTTGTCTCGCTTGAGATC-GTTTTCACTAG-AA-GAGTTTTGTCTCTCTTGAGACA
1 AAACAA-ATTTTGTCTCTCTTGAGA-CAG-TTTCACTAGAAACAAATTTCGTCTATCTTGAGACA
5336242 GTTTCCCTTG
63 GTTTCCCTTG
* *
5336252 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGTT
5336317 TCCCTTG
66 TCCCTTG
* * *
5336324 AAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCACTAGAAACAAA
5336367 ATATTTGAAT
Statistics
Matches: 102, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
70 9 0.09
71 24 0.24
72 69 0.68
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (72 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGTT
TCCCTTG
Found at i:5336324 original size:72 final size:71
Alignment explanation
Indices: 5336224--5336504 Score: 281
Period size: 72 Copynumber: 4.0 Consensus size: 71
5336214 CTAGAAGAGT
* *
5336224 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGA
1 TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
5336289 AACAAA
66 AACAAA
*
5336295 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 TTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
5336360 AAACAAA
65 AAACAAA
* * * * **** * * **
5336367 -----ATAT-TTGA-ATATGTTTTCTTTGAAACAAATACCATTTCCCTTGAGACAGTTTCTTTTG
1 TTTGTCTATCTTGAGACA-GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
5336425 GAACTAAGT
65 AAAC-AA-A
* * *
5336434 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG
1 TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTT-GTCTCTCTTGAGACAGTTTCCCTTG
5336498 AAACAAA
65 AAACAAA
5336505 ATCTTTGAAT
Statistics
Matches: 163, Mismatches: 35, Indels: 24
0.73 0.16 0.11
Matches are distributed among these distances:
64 2 0.01
65 42 0.26
66 5 0.03
71 3 0.02
72 72 0.44
73 37 0.23
74 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.40
Consensus pattern (71 bp):
TTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
AACAAA
Found at i:5336489 original size:36 final size:36
Alignment explanation
Indices: 5336406--5336503 Score: 135
Period size: 36 Copynumber: 2.7 Consensus size: 36
5336396 TACCATTTCC
* * *
5336406 CTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCT
1 CTTGAGACAGTTTCTCTTGAAAC-AAGTTTTGTCTAT
5336443 CTTGAGACAGTTTCTCTTGAAACAA-TTTTCGTCTAT
1 CTTGAGACAGTTTCTCTTGAAACAAGTTTT-GTCTAT
*
5336479 CTTGAGACAGTTTCCCTTGAAACAA
1 CTTGAGACAGTTTCTCTTGAAACAA
5336504 AATCTTTGAA
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
35 4 0.07
36 31 0.55
37 21 0.38
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.40
Consensus pattern (36 bp):
CTTGAGACAGTTTCTCTTGAAACAAGTTTTGTCTAT
Found at i:5336531 original size:138 final size:136
Alignment explanation
Indices: 5336264--5336566 Score: 385
Period size: 138 Copynumber: 2.2 Consensus size: 136
5336254 ACAAATTTTG
*
5336264 TCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATA
1 TCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATA
* * * ** *
5336329 AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCTTTGAAACA
66 AATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATATTTCCCCTAAAACA
5336394 AATACCAT
131 AA-A-CAT
* * * * * *
5336402 T-TCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA-
1 TCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAAT
* * *
5336465 CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTAAAA
65 AAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATATTTCCCCTAAAA
**
5336530 CAAAATTT
129 CAAAACAT
*
5336538 TCTCCCTTGAGACAGTTACTCTTGAAACA
1 TCTCCCTTGAGACAGTTTCTCTTGAAACA
5336567 CAAAATCTTC
Statistics
Matches: 141, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
136 3 0.02
137 53 0.38
138 85 0.60
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (136 bp):
TCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATA
AATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATATTTCCCCTAAAACA
AAACAT
Found at i:5336588 original size:66 final size:68
Alignment explanation
Indices: 5336479--5336634 Score: 203
Period size: 66 Copynumber: 2.4 Consensus size: 68
5336469 TTTCGTCTAT
* **
5336479 CTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCCCTAAAACA-AAATTT-TC
1 CTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCCTAAAACATAAATTTGTC
5336540 TCC
66 TCC
* * * *
5336543 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTT
1 CTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCCTAAAACATAAATTTGTC
5336608 TCC
66 TCC
* *
5336611 CTTGAGACCGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
5336635 ACAGATATCT
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
64 17 0.22
65 2 0.03
66 29 0.37
67 5 0.06
68 25 0.32
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (68 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCCTAAAACATAAATTTGTC
TCC
Found at i:5336819 original size:29 final size:29
Alignment explanation
Indices: 5336786--5336852 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
5336776 GAATGTGCAC
* *
5336786 ATCAGATTTGAACATTTGAAGAATTCAAG-
1 ATCAGATTTCAAAATTTGAAG-ATTCAAGA
**
5336815 ATCAGAGATCAAAATTTGAAGATTCAAGA
1 ATCAGATTTCAAAATTTGAAGATTCAAGA
5336844 ATCAAGATT
1 ATC-AGATT
5336853 CCAGACAGGC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 7 0.23
29 20 0.67
30 3 0.10
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.28
Consensus pattern (29 bp):
ATCAGATTTCAAAATTTGAAGATTCAAGA
Found at i:5337460 original size:105 final size:105
Alignment explanation
Indices: 5337278--5338001 Score: 1149
Period size: 105 Copynumber: 7.0 Consensus size: 105
5337268 GCACTCGAGG
* * ** * *
5337278 CAACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAATAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAACAACTTCTCAATTTCAG
5337343 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
5337384 CAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
5337449 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
5337489 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGT---CAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* * *
5337551 ACCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
5337591 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
5337656 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* **
5337696 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCGCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
5337761 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * *
5337801 CAATGCAAGTTCAACTTCACGATGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
5337866 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
5337906 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** * *
5337966 TTCAATTTCAACTTCACGACGGAGGATATTGGACTC
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTC
5338002 TGAACAATGC
Statistics
Matches: 587, Mismatches: 28, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
100 37 0.06
101 1 0.00
102 101 0.17
103 2 0.00
104 2 0.00
105 405 0.69
106 39 0.07
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.23
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:5337642 original size:207 final size:207
Alignment explanation
Indices: 5337278--5338001 Score: 1130
Period size: 207 Copynumber: 3.5 Consensus size: 207
5337268 GCACTCGAGG
* * ** *
5337278 CAACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAATAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTC----AACAACTTCTCAATTTCAG
*
5337343 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACG
62 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
5337408 AAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAG
127 AAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
5337473 GATATTGGACTTCAGA
192 GATATTGGACTTCAGA
* *
5337489 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACTTCTCAATTTCAGAACC
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACTTCTCAATTTCAGAGCC
* *
5337554 AATTTCAACTTCACAATGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGG
66 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
5337619 GACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
131 GACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
5337684 TTGGACTTCAGA
196 TTGGACTTCAGA
* **
5337696 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCGCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGT---CAACAACTTCTCAATTTCAGA
* *
5337761 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGATGA
63 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* *
5337826 AGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGG
128 AGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
*
5337891 ATATTGGACTCCAGA
193 ATATTGGACTTCAGA
* **
5337906 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATT-TC-A-TTCAGATT
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACTTCTCAATTTCAGAGC
* *
5337968 CAATTTCAACTTCACGACGGAGGATATTGGACTC
65 CAATTTCAACTTCACAACGAAGGATATTGGACTC
5338002 TGAACAATGC
Statistics
Matches: 477, Mismatches: 32, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
205 36 0.08
206 1 0.00
207 204 0.43
208 4 0.01
210 196 0.41
211 36 0.08
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.23
Consensus pattern (207 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACTTCTCAATTTCAGAGCC
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
TTGGACTTCAGA
Found at i:5339178 original size:17 final size:17
Alignment explanation
Indices: 5339152--5339190 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
5339142 ATTATATGGA
*
5339152 TATT-TTATTCATTTAT
1 TATTATTATTCATGTAT
*
5339168 TTTTATTATTCATGTAT
1 TATTATTATTCATGTAT
5339185 TATTAT
1 TATTAT
5339191 ATGTATATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATGTAT
Found at i:5339203 original size:48 final size:49
Alignment explanation
Indices: 5339136--5339254 Score: 115
Period size: 53 Copynumber: 2.4 Consensus size: 49
5339126 ATTAGTCCCT
5339136 TTATT-TATTATATGGATATT-TTA-TTCATTT-ATTTTTA-T-TATTCATGTA
1 TTATTATATTATAT--ATATTATTATTTCATTTGATTTTTACTATATT--T-TA
5339184 TTATTATATGTATATATATTAAATTATTTTCATTTGATTTTTACTATATTTTA
1 TTATTATAT-TATATATATT--ATTA-TTTCATTTGATTTTTACTATATTTTA
5339237 TTATTATATTATATATAT
1 TTATTATATTATATATAT
5339255 ATTTCTTTAA
Statistics
Matches: 61, Mismatches: 0, Indels: 16
0.79 0.00 0.21
Matches are distributed among these distances:
48 10 0.16
49 3 0.05
50 5 0.08
51 3 0.05
52 9 0.15
53 18 0.30
54 8 0.13
55 1 0.02
56 4 0.07
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.61
Consensus pattern (49 bp):
TTATTATATTATATATATTATTATTTCATTTGATTTTTACTATATTTTA
Found at i:5341783 original size:24 final size:23
Alignment explanation
Indices: 5341739--5341783 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
5341729 GTACTCAACG
**
5341739 TATAATTATATTTTAGTTAAAGA
1 TATAATTATATTTTAAATAAAGA
*
5341762 TATAATTGTAATTTTAAATAAA
1 TATAATTAT-ATTTTAAATAAA
5341784 TCATAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (23 bp):
TATAATTATATTTTAAATAAAGA
Found at i:5346490 original size:18 final size:17
Alignment explanation
Indices: 5346436--5346484 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
5346426 TTGAATCCTT
* *
5346436 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
5346454 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
5346472 AGTGCATTCGATG
1 AGTGCA-TCGATG
5346485 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:5353595 original size:18 final size:17
Alignment explanation
Indices: 5353541--5353589 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
5353531 TTGGATCCTT
* *
5353541 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
5353559 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
5353577 AGTGCATTCGATG
1 AGTGCA-TCGATG
5353590 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:5366683 original size:25 final size:25
Alignment explanation
Indices: 5366655--5366702 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
5366645 ATAACATTTT
*
5366655 TTATTATAATGACGAAAAATAATAC
1 TTATTATAATGACAAAAAATAATAC
*
5366680 TTATTATAATGATAAAAAATAAT
1 TTATTATAATGACAAAAAATAAT
5366703 GACACTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.35
Consensus pattern (25 bp):
TTATTATAATGACAAAAAATAATAC
Found at i:5366860 original size:27 final size:27
Alignment explanation
Indices: 5366799--5366877 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 27
5366789 TGTTGACGCT
*
5366799 ATATTTTAATGAATGTGATTAATATCA
1 ATATTTGAATGAATGTGATTAATATCA
* * *
5366826 GT-TGTTGAATTAATATGATTAATATCA
1 ATAT-TTGAATGAATGTGATTAATATCA
*
5366853 ATATTTGAATGAATGTGATGAATAT
1 ATATTTGAATGAATGTGATTAATAT
5366878 TAATTCAACT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
26 1 0.02
27 40 0.95
28 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.43
Consensus pattern (27 bp):
ATATTTGAATGAATGTGATTAATATCA
Found at i:5367513 original size:96 final size:102
Alignment explanation
Indices: 5367333--5367547 Score: 280
Period size: 96 Copynumber: 2.2 Consensus size: 102
5367323 TTAAACAAAA
* * *
5367333 AATATGTTAAATCAAAATAAATAGTCTAATTAATTTATATTTACAATAAAAAATAAAACATTAAA
1 AATATGTAAAATCAAAATAAATAGTCCAATTAATTTATATTTAC-ACAAAAAATAAAACATTAAA
* *
5367398 ATTTAAACTAAACTTACCAAACCACTCAAATACGATTT
65 ATTTAAACTAAACTTACCAAACCACTCAAATACAACTT
* * * *
5367436 AATCTGTAAAATCAAAATAAATAGTCCAA-TAATTTATA-TTAC-CCAATAA-AAAA-A-TATAA
1 AATATGTAAAATCAAAATAAATAGTCCAATTAATTTATATTTACACAAAAAATAAAACATTAAAA
*
5367495 TTTAAACTAAACTTACCAAACTACTCAAATACAACTT
66 TTTAAACTAAACTTACCAAACCACTCAAATACAACTT
*
5367532 AATATGTATAATCAAA
1 AATATGTAAAATCAAA
5367548 TGGGGAAAAT
Statistics
Matches: 100, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
96 52 0.52
97 1 0.01
98 4 0.04
99 4 0.04
101 4 0.04
102 9 0.09
103 26 0.26
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.31
Consensus pattern (102 bp):
AATATGTAAAATCAAAATAAATAGTCCAATTAATTTATATTTACACAAAAAATAAAACATTAAAA
TTTAAACTAAACTTACCAAACCACTCAAATACAACTT
Found at i:5371437 original size:33 final size:31
Alignment explanation
Indices: 5371400--5371464 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 31
5371390 AGTTCTCACC
*
5371400 ATCCATAAATCCAAACAAATT-CAAAATCAATCA
1 ATCCACAAATCCAAAC--ATTCCAAAAT-AATCA
*
5371433 ATCCACAAATTCAAACATTCCAAAATAATCA
1 ATCCACAAATCCAAACATTCCAAAATAATCA
5371464 A
1 A
5371465 AATGTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 9 0.31
32 6 0.21
33 14 0.48
ACGTcount: A:0.54, C:0.25, G:0.00, T:0.22
Consensus pattern (31 bp):
ATCCACAAATCCAAACATTCCAAAATAATCA
Found at i:5371785 original size:12 final size:12
Alignment explanation
Indices: 5371768--5371796 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
5371758 TTGTTGTGCT
5371768 TGCTCCTCGGGC
1 TGCTCCTCGGGC
5371780 TGCTCCTCGGGC
1 TGCTCCTCGGGC
5371792 TGCTC
1 TGCTC
5371797 AGGCTCATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.41, G:0.31, T:0.28
Consensus pattern (12 bp):
TGCTCCTCGGGC
Found at i:5373460 original size:23 final size:23
Alignment explanation
Indices: 5373427--5373512 Score: 145
Period size: 23 Copynumber: 3.7 Consensus size: 23
5373417 CCAGAACCCC
* *
5373427 AGGGGGTATCGATTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
5373450 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
5373473 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
*
5373496 AGGAGGAATCGGTTCCC
1 AGGGGGAATCGGTTCCC
5373513 TCATGGGGGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:5386377 original size:23 final size:21
Alignment explanation
Indices: 5386334--5386374 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
5386324 GAGTTTATTT
*
5386334 TCATTTTTTAATTTTGAAACA
1 TCATTTTTTAATTTTAAAACA
5386355 TCATTTTTTATATTTTAAAA
1 TCATTTTTTA-ATTTTAAAA
5386375 ACAATTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.56
Consensus pattern (21 bp):
TCATTTTTTAATTTTAAAACA
Found at i:5389014 original size:15 final size:15
Alignment explanation
Indices: 5388994--5389023 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5388984 CAAAATTGAT
5388994 AGTTTAAATACTAAA
1 AGTTTAAATACTAAA
*
5389009 AGTTTAGATACTAAA
1 AGTTTAAATACTAAA
5389024 CATGTTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (15 bp):
AGTTTAAATACTAAA
Found at i:5389274 original size:3 final size:3
Alignment explanation
Indices: 5389266--5389317 Score: 95
Period size: 3 Copynumber: 17.0 Consensus size: 3
5389256 TAATTTTGAT
5389266 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
5389312 ATA ATA
1 ATA ATA
5389318 CGTGTTAAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5390815 original size:16 final size:16
Alignment explanation
Indices: 5390777--5390808 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5390767 AACACAATAA
5390777 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
5390793 ACAAACATAAACGAAC
1 ACGAACATAAACGAAC
5390809 CTGAACAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.25, G:0.09, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:5390863 original size:23 final size:23
Alignment explanation
Indices: 5390760--5390864 Score: 63
Period size: 23 Copynumber: 4.4 Consensus size: 23
5390750 ACGAACGGAT
* **
5390760 GTAAATGAACACAATAAACGAAC
1 GTAAACGAACACAATAAATAAAC
* *
5390783 ATAAACGAACACAA-ACATAAAC
1 GTAAACGAACACAATAAATAAAC
* * *
5390805 G-AACCTGAACA-AATATAAAAAAT
1 GTAAAC-GAACACAATA-AATAAAC
5390828 GAATATAATCGAACACAATAAATAAAC
1 G--TA-AA-CGAACACAATAAATAAAC
5390855 GTAAACGAAC
1 GTAAACGAAC
5390865 TTAAACAACA
Statistics
Matches: 60, Mismatches: 13, Indels: 18
0.66 0.14 0.20
Matches are distributed among these distances:
21 5 0.08
22 11 0.18
23 22 0.37
24 2 0.03
25 2 0.03
26 1 0.02
27 12 0.20
28 5 0.08
ACGTcount: A:0.59, C:0.17, G:0.10, T:0.14
Consensus pattern (23 bp):
GTAAACGAACACAATAAATAAAC
Found at i:5390911 original size:25 final size:25
Alignment explanation
Indices: 5390874--5390932 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
5390864 CTTAAACAAC
*
5390874 ATCAATAACCACATAAAATTCATTA
1 ATCAATAATCACATAAAATTCATTA
5390899 ATCAATAATCACATAAAATTCATTA
1 ATCAATAATCACATAAAATTCATTA
*
5390924 TTCAATAAT
1 ATCAATAAT
5390933 GTAACCCACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (25 bp):
ATCAATAATCACATAAAATTCATTA
Found at i:5391026 original size:16 final size:18
Alignment explanation
Indices: 5390997--5391033 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5390987 TATTTTCTTT
*
5390997 AATTGATTTCAG-TTTAA
1 AATTGATTTAAGTTTTAA
5391014 AATT-ATTTAAGTTTTAA
1 AATTGATTTAAGTTTTAA
5391031 AAT
1 AAT
5391034 ATTAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (18 bp):
AATTGATTTAAGTTTTAA
Found at i:5391104 original size:14 final size:14
Alignment explanation
Indices: 5391085--5391111 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5391075 TAGACTGAAT
5391085 ATAAACGAACATAC
1 ATAAACGAACATAC
5391099 ATAAACGAACATA
1 ATAAACGAACATA
5391112 TACGTACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.19, G:0.07, T:0.15
Consensus pattern (14 bp):
ATAAACGAACATAC
Found at i:5391136 original size:14 final size:14
Alignment explanation
Indices: 5391117--5391156 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
5391107 ACATATACGT
*
5391117 ACATAAACGAGCGA
1 ACATAAACGAACGA
*
5391131 ACATAAATGAACGA
1 ACATAAACGAACGA
*
5391145 ACATAAGCGAAC
1 ACATAAACGAAC
5391157 ATACACAGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.53, C:0.20, G:0.17, T:0.10
Consensus pattern (14 bp):
ACATAAACGAACGA
Found at i:5391170 original size:20 final size:22
Alignment explanation
Indices: 5391145--5391194 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
5391135 AAATGAACGA
*
5391145 ACATAA-G-CGAACATACACAG
1 ACATAATGACGAACATAAACAG
5391165 ACATAAATGAACGAACATAAACAG
1 ACAT-AATG-ACGAACATAAACAG
5391189 ACATAA
1 ACATAA
5391195 ATGAACGGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 4 0.16
21 2 0.08
22 1 0.04
23 2 0.08
24 16 0.64
ACGTcount: A:0.56, C:0.20, G:0.12, T:0.12
Consensus pattern (22 bp):
ACATAATGACGAACATAAACAG
Found at i:5391179 original size:24 final size:24
Alignment explanation
Indices: 5391152--5391201 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
5391142 CGAACATAAG
*
5391152 CGAACATACACAGACATAAATGAA
1 CGAACATAAACAGACATAAATGAA
5391176 CGAACATAAACAGACATAAATGAA
1 CGAACATAAACAGACATAAATGAA
5391200 CG
1 CG
5391202 GATTACCGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.20, G:0.14, T:0.12
Consensus pattern (24 bp):
CGAACATAAACAGACATAAATGAA
Found at i:5391744 original size:15 final size:15
Alignment explanation
Indices: 5391724--5391766 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
5391714 ATAAGGTTAT
5391724 TTATTTTAAAATAAA
1 TTATTTTAAAATAAA
5391739 TTATTTTAAAATAAA
1 TTATTTTAAAATAAA
*
5391754 TTATTATAAAATA
1 TTATTTTAAAATA
5391767 TGAATTGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATTTTAAAATAAA
Found at i:5391788 original size:52 final size:45
Alignment explanation
Indices: 5391722--5391831 Score: 141
Period size: 45 Copynumber: 2.3 Consensus size: 45
5391712 TAATAAGGTT
5391722 ATTTATTTTAAAATAAATTATTTTAAAATAAATTATTA-TAAAATATGAATTG
1 ATTTATTTTAAAAT-AATTATTTT-AAAT-AATTATTAGT---ATA--AATTG
5391774 ATTTATTTTAAAATAATTATTTTAAATAATTATTAGTATAAATTG
1 ATTTATTTTAAAATAATTATTTTAAATAATTATTAGTATAAATTG
5391819 ATTTATTTTAAAA
1 ATTTATTTTAAAA
5391832 ATGGATGATT
Statistics
Matches: 57, Mismatches: 0, Indels: 9
0.86 0.00 0.14
Matches are distributed among these distances:
45 18 0.32
47 3 0.05
49 8 0.14
50 5 0.09
51 9 0.16
52 14 0.25
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (45 bp):
ATTTATTTTAAAATAATTATTTTAAATAATTATTAGTATAAATTG
Found at i:5391802 original size:13 final size:14
Alignment explanation
Indices: 5391724--5391807 Score: 65
Period size: 15 Copynumber: 6.4 Consensus size: 14
5391714 ATAAGGTTAT
5391724 TTATTTTAAAATAAA
1 TTATTTTAAAAT-AA
5391739 TTATTTTAAAATAAA
1 TTATTTTAAAAT-AA
*
5391754 TTATTATAAAAT-A
1 TTATTTTAAAATAA
* * *
5391767 TGA-ATT--GAT--
1 TTATTTTAAAATAA
5391776 TTATTTTAAAATAA
1 TTATTTTAAAATAA
5391790 TTATTTT-AAATAA
1 TTATTTTAAAATAA
5391803 TTATT
1 TTATT
5391808 AGTATAAATT
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
9 2 0.04
10 4 0.07
12 3 0.05
13 14 0.25
14 7 0.12
15 26 0.46
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TTATTTTAAAATAA
Found at i:5391816 original size:16 final size:13
Alignment explanation
Indices: 5391776--5391807 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
5391766 ATGAATTGAT
5391776 TTATTTTAAAATAA
1 TTATTTT-AAATAA
5391790 TTATTTTAAATAA
1 TTATTTTAAATAA
5391803 TTATT
1 TTATT
5391808 AGTATAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATTTTAAATAA
Found at i:5391880 original size:31 final size:32
Alignment explanation
Indices: 5391845--5391905 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
5391835 GATGATTTAT
*
5391845 ATTTAGTT-GTATAGATTGA-TTATTTTAAATA
1 ATTTA-TTAGTATAGATTGATTTACTTTAAATA
*
5391876 ATTTATTAGTATGGATTGATTTACTTTAAA
1 ATTTATTAGTATAGATTGATTTACTTTAAA
5391906 ATATGGATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 2 0.08
31 15 0.58
32 9 0.35
ACGTcount: A:0.34, C:0.02, G:0.13, T:0.51
Consensus pattern (32 bp):
ATTTATTAGTATAGATTGATTTACTTTAAATA
Found at i:5391929 original size:22 final size:22
Alignment explanation
Indices: 5391885--5391927 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5391875 AATTTATTAG
5391885 TATGGATTGATTTACTTTAAAA
1 TATGGATTGATTTACTTTAAAA
5391907 TATGGATTGATTTA-TTTAAAA
1 TATGGATTGATTTACTTTAAAA
5391928 ATTTATTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (22 bp):
TATGGATTGATTTACTTTAAAA
Found at i:5391940 original size:52 final size:54
Alignment explanation
Indices: 5391858--5392150 Score: 316
Period size: 52 Copynumber: 5.5 Consensus size: 54
5391848 TAGTTGTATA
*
5391858 GATTGA-TTATTTTAAATAATTTATTAGTATGGATTGATTTACTTTAAAATATG
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
*
5391911 GATTGATTTA-TTTAAA-AATTTATTAGTATGTATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
5391963 GA-TGATTTATTTTAAATAA-TTATTAGTATGGATTGATTTATTTTAAATAATTATTTG
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA-TA--TG
* * * * ** * * * * * * *** *
5392020 TATGGATTGA-TTGATTTATTTTA-AAATATTGTTTGA-TTATTGTAGTGTATA
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
5392071 GATTGA-TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
5392124 GATTGATTTATTTTAAATAATTTATTA
1 GATTGATTTATTTTAAATAATTTATTA
5392151 TTTTAATTGT
Statistics
Matches: 191, Mismatches: 35, Indels: 27
0.75 0.14 0.11
Matches are distributed among these distances:
50 2 0.01
51 21 0.11
52 75 0.39
53 34 0.18
54 25 0.13
55 3 0.02
56 6 0.03
57 17 0.09
58 8 0.04
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (54 bp):
GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
Found at i:5392002 original size:31 final size:31
Alignment explanation
Indices: 5391959--5392118 Score: 133
Period size: 31 Copynumber: 4.7 Consensus size: 31
5391949 TATTTTAAAA
5391959 TATGGA-TGATTTATTTTAAATAATTATTAG
1 TATGGATTGATTTATTTTAAATAATTATTAG
*
5391989 TATGGATTGATTTATTTTAAATAATTATTTG
1 TATGGATTGATTTATTTTAAATAATTATTAG
*
5392020 TATGGATTGATTGATTTATTTTAAAATATTGTTTGATTATTG
1 TAT-G---GATTGATTTATTTT-AAATA---ATT-ATTA--G
* *
5392062 TAGTGTATAGATTGATTATTTTAAATAATTTATTAG
1 TA-TGGATTGATT--T-ATTTTAAATAA-TTATTAG
5392098 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
5392119 ATATGGATTG
Statistics
Matches: 105, Mismatches: 8, Indels: 32
0.72 0.06 0.22
Matches are distributed among these distances:
30 6 0.06
31 26 0.25
32 9 0.09
33 1 0.01
35 22 0.21
36 8 0.08
38 4 0.04
39 10 0.10
40 3 0.03
41 6 0.06
42 9 0.09
43 1 0.01
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (31 bp):
TATGGATTGATTTATTTTAAATAATTATTAG
Found at i:5392121 original size:74 final size:76
Alignment explanation
Indices: 5391988--5392131 Score: 204
Period size: 74 Copynumber: 1.9 Consensus size: 76
5391978 ATAATTATTA
* * * *
5391988 GTATGGATTGATTTATTTTAAATAATTATTTGTATGGATTGATTGATTTATTTTAAAATATTGTT
1 GTATAGATTGATTTATTTTAAATAATTATTAGTATGG--TGATTGATTTATTTTAAAATATGGAT
5392053 TGATTATTGTAGT
64 TGATTATTGTAGT
5392066 GTATAGATTGA-TTATTTTAAATAATTTATTAGTAT-G-GATTGATTTATTTTAAAATATGGATT
1 GTATAGATTGATTTATTTTAAATAA-TTATTAGTATGGTGATTGATTTATTTTAAAATATGGATT
5392128 GATT
65 GATT
5392132 TATTTTAAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
74 28 0.46
77 14 0.23
78 19 0.31
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (76 bp):
GTATAGATTGATTTATTTTAAATAATTATTAGTATGGTGATTGATTTATTTTAAAATATGGATTG
ATTATTGTAGT
Found at i:5392153 original size:21 final size:22
Alignment explanation
Indices: 5392098--5392140 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
5392088 AATTTATTAG
5392098 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
5392120 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
5392141 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:5392200 original size:31 final size:31
Alignment explanation
Indices: 5392165--5392223 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
5392155 AATTGTATGG
* *
5392165 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
5392196 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
5392224 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:5397365 original size:60 final size:60
Alignment explanation
Indices: 5397291--5397464 Score: 197
Period size: 61 Copynumber: 2.9 Consensus size: 60
5397281 GTCTCTAAAT
* * * *
5397291 TATGACTCTCATTCTAAATTGATCTTTAAACTTTTGAATATTCTAATTTCATCCTCAAAC
1 TATGACACTCATTCTAAATTGATCCTTAAACTTTTGAACATTCCAATTTCATCCTCAAAC
* * * *
5397351 TATGATACTCATTCTAAATT-AGTCCTTAAAATTCATGAACATCCCAATTTCATCCTCAAAC
1 TATGACACTCATTCTAAATTGA-TCCTTAAACTT-TTGAACATTCCAATTTCATCCTCAAAC
* * * * * *
5397412 TATGACCCTTATTCTAAGTTGGTCCCTAAACTTTTAAACATTCCAATTTCATC
1 TATGACACTCATTCTAAATTGATCCTTAAACTTTTGAACATTCCAATTTCATC
5397465 ACCAAATTTA
Statistics
Matches: 93, Mismatches: 18, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
59 1 0.01
60 44 0.47
61 48 0.52
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (60 bp):
TATGACACTCATTCTAAATTGATCCTTAAACTTTTGAACATTCCAATTTCATCCTCAAAC
Found at i:5402555 original size:45 final size:46
Alignment explanation
Indices: 5402506--5402593 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
5402496 AAACATCGAA
*
5402506 TGCATTTTATGCATCGATGAAC-ATACCATGCATCGATGCACTTAG
1 TGCATTTGATGCATCGATGAACAATACCATGCATCGATGCACTTAG
* *
5402551 TGCATTTGATGCATCGATGCACAATATCATGCATCGATGCACT
1 TGCATTTGATGCATCGATGAACAATACCATGCATCGATGCACT
5402594 CAGGTTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 20 0.51
46 19 0.49
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGAACAATACCATGCATCGATGCACTTAG
Found at i:5408363 original size:42 final size:44
Alignment explanation
Indices: 5408316--5408407 Score: 109
Period size: 44 Copynumber: 2.1 Consensus size: 44
5408306 TTGTGCTTCA
* *
5408316 TGCATCAATACACC-T-AACAGTGCATCGATGCA-TCCTTGAATG
1 TGCATCAATACACCATGAA-AGTGCACCGATGCACGCCTTGAATG
* * *
5408358 TGCATCGATACACCATGAAGGTGCACCGATGCACGCCTTGAATT
1 TGCATCAATACACCATGAAAGTGCACCGATGCACGCCTTGAATG
5408402 TGCATC
1 TGCATC
5408408 GATTCACAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
42 13 0.31
43 13 0.31
44 16 0.38
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (44 bp):
TGCATCAATACACCATGAAAGTGCACCGATGCACGCCTTGAATG
Found at i:5408381 original size:21 final size:22
Alignment explanation
Indices: 5408335--5408387 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
5408325 ACACCTAACA
* * *
5408335 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATACATCCATGAAG
5408357 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATACATCCATGAAG
*
5408378 GTGCACCGAT
1 GTGCATCGAT
5408388 GCACGCCTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
GTGCATCGATACATCCATGAAG
Found at i:5408431 original size:43 final size:42
Alignment explanation
Indices: 5408334--5408433 Score: 103
Period size: 43 Copynumber: 2.3 Consensus size: 42
5408324 TACACCTAAC
* * *
5408334 AGTGCATCGATGCATCCTTGAATGTGCATCGATACACCATGA
1 AGTGCATCGATGCAGCCTTGAATGTGCATCGATACACAAGGA
* * * *
5408376 AGGTGCACCGATGCACGCCTTGAATTTGCATCGATTCACAAGGCC
1 A-GTGCATCGATGCA-GCCTTGAATGTGCATCGATACACAAGG-A
5408421 A-TGCATCGATGCA
1 AGTGCATCGATGCA
5408434 TCCGTCGGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
42 1 0.02
43 23 0.49
44 22 0.47
45 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (42 bp):
AGTGCATCGATGCAGCCTTGAATGTGCATCGATACACAAGGA
Found at i:5411049 original size:20 final size:20
Alignment explanation
Indices: 5411020--5411058 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5411010 TTTAAGAGTG
5411020 ATGCACCGATGCACCAATTC
1 ATGCACCGATGCACCAATTC
*
5411040 ATGCATCGATGCACCAATT
1 ATGCACCGATGCACCAATT
5411059 AATTTTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (20 bp):
ATGCACCGATGCACCAATTC
Found at i:5411089 original size:45 final size:45
Alignment explanation
Indices: 5411040--5411145 Score: 144
Period size: 45 Copynumber: 2.4 Consensus size: 45
5411030 GCACCAATTC
*
5411040 ATGCATCGATGCAC-CAATTAATTTTTC-AAACATCGAATGCATTTT
1 ATGCATCGATGCACTC-A-GAATTTTTCAAAACATCGAATGCATTTT
* **
5411085 ATGCATCGATGAACTCAGGCTTTTTCAAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGAATTTTTCAAAACATCGAATGCATTTT
5411130 ATGCATCGATGCACTC
1 ATGCATCGATGCACTC
5411146 TTAGTGCACC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
44 6 0.11
45 47 0.87
46 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGAATTTTTCAAAACATCGAATGCATTTT
Found at i:5411901 original size:22 final size:22
Alignment explanation
Indices: 5411858--5411906 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
5411848 ATTATTAATT
5411858 GATTAAAAAAATTATTCTAGAC
1 GATTAAAAAAATTATTCTAGAC
*
5411880 TATTAAAAATAA-TATT-TGAGAC
1 GATTAAAAA-AATTATTCT-AGAC
5411902 GATTA
1 GATTA
5411907 TATTAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 1 0.04
22 20 0.87
23 2 0.09
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.35
Consensus pattern (22 bp):
GATTAAAAAAATTATTCTAGAC
Found at i:5420778 original size:13 final size:13
Alignment explanation
Indices: 5420760--5420786 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5420750 TTTTAATAAA
5420760 ATATACAAGTTCT
1 ATATACAAGTTCT
5420773 ATATACAAGTTCT
1 ATATACAAGTTCT
5420786 A
1 A
5420787 AGGATTAAAT
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:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (13 bp):
ATATACAAGTTCT
Found at i:5423609 original size:29 final size:29
Alignment explanation
Indices: 5423575--5423757 Score: 156
Period size: 29 Copynumber: 6.6 Consensus size: 29
5423565 CGGTTGACCG
5423575 GGTGATATTTTAGTAATTATTTTGAAAAT
1 GGTGATATTTTAGTAATTATTTTGAAAAT
*
5423604 GGTGATATTTTGGTAATTATTTTGAAAAT
1 GGTGATATTTTAGTAATTATTTTGAAAAT
*
5423633 GGTGCTATTTT-G------TTTT-AAAA-
1 GGTGATATTTTAGTAATTATTTTGAAAAT
* * *
5423653 GAGTGATAATTTCGTAATT-TTTTTAAAGA-
1 G-GTGATATTTTAGTAATTATTTTGAAA-AT
*
5423682 GGTGATATTTTAGTAATTATTTTGGAAAT
1 GGTGATATTTTAGTAATTATTTTGAAAAT
* *
5423711 GGTGCTATTTTGGTAATTGATTTT-AAAAT
1 GGTGATATTTTAGTAATT-ATTTTGAAAAT
* * *
5423740 GATGCTATTTTCGTAATT
1 GGTGATATTTTAGTAATT
5423758 TGTTTTTAAA
Statistics
Matches: 129, Mismatches: 13, Indels: 24
0.78 0.08 0.14
Matches are distributed among these distances:
20 1 0.01
21 12 0.09
22 5 0.04
27 4 0.03
28 20 0.16
29 82 0.64
30 5 0.04
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.48
Consensus pattern (29 bp):
GGTGATATTTTAGTAATTATTTTGAAAAT
Found at i:5423680 original size:27 final size:28
Alignment explanation
Indices: 5423645--5423704 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
5423635 TGCTATTTTG
* *
5423645 TTTTAAAAGA-GTGATAATTTCGTAATT
1 TTTTTAAAGAGGTGATAATTTAGTAATT
*
5423672 TTTTTAAAGAGGTGATATTTTAGTAATT
1 TTTTTAAAGAGGTGATAATTTAGTAATT
*
5423700 ATTTT
1 TTTTT
5423705 GGAAATGGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 9 0.32
28 19 0.68
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.50
Consensus pattern (28 bp):
TTTTTAAAGAGGTGATAATTTAGTAATT
Found at i:5423711 original size:78 final size:79
Alignment explanation
Indices: 5423576--5423722 Score: 226
Period size: 78 Copynumber: 1.9 Consensus size: 79
5423566 GGTTGACCGG
* *
5423576 GTGATATTTTAGTAATTATTTTGAAAATGGTGATATTTTGGTAATTATTTTGAAAATGGTGCTAT
1 GTGATAATTTAGTAATTATTTTGAAAATGGTGATATTTTAGTAATTATTTTGAAAATGGTGCTAT
5423641 TTTGTTTTAAAAGA
66 TTTGTTTTAAAAGA
* * *
5423655 GTGATAATTTCGTAATT-TTTTTAAAGA-GGTGATATTTTAGTAATTATTTTGGAAATGGTGCTA
1 GTGATAATTTAGTAATTATTTTGAAA-ATGGTGATATTTTAGTAATTATTTTGAAAATGGTGCTA
5423718 TTTTG
65 TTTTG
5423723 GTAATTGATT
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
78 46 0.74
79 16 0.26
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (79 bp):
GTGATAATTTAGTAATTATTTTGAAAATGGTGATATTTTAGTAATTATTTTGAAAATGGTGCTAT
TTTGTTTTAAAAGA
Found at i:5424626 original size:62 final size:62
Alignment explanation
Indices: 5424436--5424839 Score: 429
Period size: 62 Copynumber: 6.5 Consensus size: 62
5424426 AACTTCGACT
* *
5424436 ATCGCAATGCGAACTTGGACTATCGCAATGCGAA--TATGTA-AATCGCAATACG-ATA-GTCGA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTA-G-ACTATCGCAATGCGAATATGT--A
*
5424496 CT
62 -A
* *
5424498 ATCACAATGCGAACTTGGACTATCGCAATGCGAA--TATGTA-AATCGCAATGCG-ATA-GTCGA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTA-G-ACTATCGCAATGCGAATATGT--A
*
5424558 CT
62 -A
5424560 ATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTAGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTAGACTATCGCAATGCGAATATGTAA
* * *
5424622 ATCGCAATGCGATA-GTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGAACTTAGACTATCGCAATGCGAATATGTAA
* * * * * *
5424684 ATCGCAATGCGATA-GTCGACTATCGCAATACGAACTTGGACTATCGTAATACGAATATGTAA
1 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGAACTTAGACTATCGCAATGCGAATATGTAA
* * *
5424746 ATCGCAATGCGATA-GTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGAACTTAGACTATCGCAATGCGAATATGTAA
*
5424808 ATCGCAATGCGAACTTGGACTATCGCATTGCG
1 ATCGCAATGCGAACTTGGACTATCGCAATGCG
5424840 GTTTACATAT
Statistics
Matches: 318, Mismatches: 17, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
61 1 0.00
62 296 0.93
63 14 0.04
64 5 0.02
65 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (62 bp):
ATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTAGACTATCGCAATGCGAATATGTAA
Found at i:5424643 original size:124 final size:124
Alignment explanation
Indices: 5424436--5424839 Score: 497
Period size: 124 Copynumber: 3.3 Consensus size: 124
5424426 AACTTCGACT
*
5424436 ATCGCAATGCGAACTTGGACTATCGCAATGCGAA--TATGTA-AATCGCAATACG-ATA-GTCGA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTA-G-ACTATCGCAATACGAATATGT--A
* * * * * *
5424496 CTATCACAATGCGA-ACTTGGACTATCGCAATGCGAA-TATGTA-AATCGCAATGCG-ATA-GTC
62 -AATCGCAATGCGATA-GTCGACTATCGCAATGCGAACT-TGGACTATCGCAATGCGAATATGT-
*
5424556 GACT
123 -A-A
*
5424560 ATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTAGACTATCGCAATGCGAATATGTAAATC
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTAGACTATCGCAATACGAATATGTAAATC
5424625 GCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
66 GCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
* * * * *
5424684 ATCGCAATGCGATA-GTCGACTATCGCAATACGAACTTGGACTATCGTAATACGAATATGTAAAT
1 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGAACTTAGACTATCGCAATACGAATATGTAAAT
5424748 CGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
65 CGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
*
5424808 ATCGCAATGCGAACTTGGACTATCGCATTGCG
1 ATCGCAATGCGAACTTGGACTATCGCAATGCG
5424840 GTTTACATAT
Statistics
Matches: 249, Mismatches: 19, Indels: 24
0.85 0.07 0.08
Matches are distributed among these distances:
123 1 0.00
124 209 0.84
125 27 0.11
126 8 0.03
127 4 0.02
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (124 bp):
ATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTAGACTATCGCAATACGAATATGTAAATC
GCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
Found at i:5424679 original size:145 final size:145
Alignment explanation
Indices: 5424416--5424738 Score: 574
Period size: 145 Copynumber: 2.2 Consensus size: 145
5424406 GTTTCCAGAT
* * *
5424416 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTAGACTATCGCAATGCGAATATGTAAATCG
5424481 CAATACGATAGTCGACTATCACAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAA
66 CAATACGATAGTCGACTATCACAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAA
5424546 TGCGATAGTCGACTA
131 TGCGATAGTCGACTA
5424561 TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTAGACTATCGCAATGCGAATATGTAAATCG
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTAGACTATCGCAATGCGAATATGTAAATCG
* *
5424626 CAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAA
66 CAATACGATAGTCGACTATCACAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAA
5424691 TGCGATAGTCGACTA
131 TGCGATAGTCGACTA
* * *
5424706 TCGCAATACGAACTTGGACTATCGTAATACGAA
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAA
5424739 TATGTAAATC
Statistics
Matches: 170, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
145 170 1.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (145 bp):
TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTAGACTATCGCAATGCGAATATGTAAATCG
CAATACGATAGTCGACTATCACAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAA
TGCGATAGTCGACTA
Found at i:5424860 original size:41 final size:41
Alignment explanation
Indices: 5424436--5424839 Score: 277
Period size: 41 Copynumber: 9.8 Consensus size: 41
5424426 AACTTCGACT
5424436 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
* * * * * *
5424477 ATCGCAATACGATA-GTCGACTATCACAATGCGAACT-TGGACT
1 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGAA-TATGTA-A
* * *
5424519 ATCGCAATGCGAA-TATGTA-AATCGCAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAACT-TGGACTATCGCAATGCGAATATGT--A-A
*
5424560 ATCGCAATGCGAACTTGGACTATCGCAATGCGAACT-TAG-ACT
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAA-TAT-GTA-A
* * *
5424602 ATCGCAATGCGAA-TATGTA-AATCGCAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAACT-TGGACTATCGCAATGCGAATATGT--A-A
5424643 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
* * * * *
5424684 ATCGCAATGCGATA-GTCGACTATCGCAATACGAACT-TGGACT
1 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGAA-TATGTA-A
* * * * *
5424726 ATCGTAATACGAA-TATGTA-AATCGCAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAACT-TGGACTATCGCAATGCGAATATGT--A-A
5424767 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
*
5424808 ATCGCAATGCGAACTTGGACTATCGCATTGCG
1 ATCGCAATGCGAACTTGGACTATCGCAATGCG
5424840 GTTTACATAT
Statistics
Matches: 291, Mismatches: 39, Indels: 66
0.73 0.10 0.17
Matches are distributed among these distances:
38 1 0.00
39 5 0.02
40 3 0.01
41 183 0.63
42 86 0.30
43 7 0.02
44 5 0.02
45 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (41 bp):
ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
Found at i:5424875 original size:21 final size:21
Alignment explanation
Indices: 5424849--5424889 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
5424839 GGTTTACATA
5424849 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
5424870 TTCGCATTGCGATAGTCCAA
1 TTCGCATTGCGATAGTCCAA
5424890 AATCACAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:5425637 original size:21 final size:21
Alignment explanation
Indices: 5425611--5425684 Score: 121
Period size: 21 Copynumber: 3.4 Consensus size: 21
5425601 ATTTTGGACT
5425611 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
*
5425632 ATCGCAACGTGAACTTGGAATAA
1 ATCGCAAC--GAATTTGGAATAA
5425655 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
5425676 ATCGCAACG
1 ATCGCAACG
5425685 CGAACTTCGA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
21 29 0.59
23 20 0.41
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:5425710 original size:44 final size:42
Alignment explanation
Indices: 5425607--5425703 Score: 149
Period size: 44 Copynumber: 2.3 Consensus size: 42
5425597 TGCGATTTTG
* *
5425607 GACTATCGCAACGAATTTGGAATAAATCGCAACGTGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
5425649 GAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
5425693 GACTATCGCAA
1 GACTATCGCAA
5425704 TGCGAATATG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
42 10 0.20
44 39 0.80
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:5426382 original size:42 final size:41
Alignment explanation
Indices: 5426323--5426484 Score: 252
Period size: 42 Copynumber: 3.9 Consensus size: 41
5426313 GAAGTATTAT
*
5426323 CAGGTCCCTTTGCTGTGTGCGAATGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTCC
*
5426365 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCT
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTCC
5426407 CAGGTCCCTTTGCTGTGTGCAAGGATAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAGTTTCC
* *
5426449 CATGTCCCTTTGCTGTGTGCAAGGGTAAACCTTACA
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACA
5426485 ATTTTCCTAG
Statistics
Matches: 112, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
41 4 0.04
42 106 0.95
43 2 0.02
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (41 bp):
CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTCC
Found at i:5426463 original size:84 final size:84
Alignment explanation
Indices: 5426322--5426484 Score: 283
Period size: 84 Copynumber: 1.9 Consensus size: 84
5426312 GGAAGTATTA
*
5426322 TCAGGTCCCTTTGCTGTGTGCGAATGTAAGCCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCAA
1 TCAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCAA
*
5426387 GGGTAAGCCTTACAGTTTC
66 GGGTAAACCTTACAGTTTC
*
5426406 TCAGGTCCCTTTGCTGTGTGC-AAGGATAAGCCTTACAGTTTCCCATGTCCCTTTGCTGTGTGCA
1 TCAGGTCCCTTTGCTGTGTGCGAAGG-TAAGCCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCA
5426470 AGGGTAAACCTTACA
65 AGGGTAAACCTTACA
5426485 ATTTTCCTAG
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
83 3 0.04
84 72 0.96
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.33
Consensus pattern (84 bp):
TCAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCAA
GGGTAAACCTTACAGTTTC
Found at i:5428474 original size:20 final size:20
Alignment explanation
Indices: 5428446--5428485 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5428436 AAATGAATTT
*
5428446 ATTTAGTGACCAAATTATAA
1 ATTTAGTGACCAAAGTATAA
*
5428466 ATTTGGTGACCAAAGTATAA
1 ATTTAGTGACCAAAGTATAA
5428486 GTTTTGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (20 bp):
ATTTAGTGACCAAAGTATAA
Found at i:5429735 original size:24 final size:24
Alignment explanation
Indices: 5429703--5429748 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
5429693 GCATGATATG
5429703 GTACATAGATGTTTTATACATCGT
1 GTACATAGATGTTTTATACATCGT
5429727 GTACATAGATGTTTTATACATC
1 GTACATAGATGTTTTATACATC
5429749 ATCTGGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (24 bp):
GTACATAGATGTTTTATACATCGT
Found at i:5432149 original size:60 final size:59
Alignment explanation
Indices: 5432039--5432200 Score: 184
Period size: 60 Copynumber: 2.7 Consensus size: 59
5432029 TATATCATAT
* * * *
5432039 ATCCCAAAACGATGAACCTCATT-TCAAGTTAGTCCTTAAAGTTTTAAACATTTCAATTAC
1 ATCCC-AAACTATGAATCTCATTCT-AAATTAGTCCTTAAACTTTTAAACATTTCAATTAC
* * * * *
5432099 ATCCTCAAATTATGACTCTCATTCTAAATTAGTCTTTAAACTTTTGAACATTTCAATTTC
1 ATCC-CAAACTATGAATCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTTCAATTAC
*
5432159 ATCCCAAACTATGAATCTCATTCTAAATT-GATCCCTAAACTT
1 ATCCCAAACTATGAATCTCATTCTAAATTAG-TCCTTAAACTT
5432201 GTATATCTTA
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
58 1 0.01
59 32 0.37
60 51 0.59
61 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (59 bp):
ATCCCAAACTATGAATCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTTCAATTAC
Found at i:5438032 original size:22 final size:20
Alignment explanation
Indices: 5437992--5438039 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
5437982 CTTTAGTTTT
5437992 TTAAAATTTTTAATTAAAAA
1 TTAAAATTTTTAATTAAAAA
*
5438012 TTAATATTTTTATTATTAAAAA
1 TTAAAATTTTTA--ATTAAAAA
*
5438034 ATAAAA
1 TTAAAA
5438040 AAATAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 11 0.48
22 12 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAAAATTTTTAATTAAAAA
Found at i:5439803 original size:20 final size:20
Alignment explanation
Indices: 5439780--5439820 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
5439770 AATATCAAGT
*
5439780 AGAAGCAAGCAATATAAAAC
1 AGAAGCAAACAATATAAAAC
5439800 AGAAGCAAACAATATAAAAC
1 AGAAGCAAACAATATAAAAC
5439820 A
1 A
5439821 TAATAAAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.63, C:0.15, G:0.12, T:0.10
Consensus pattern (20 bp):
AGAAGCAAACAATATAAAAC
Done.