Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 123 of 141
Found at i:39249818 original size:6 final size:6
Alignment explanation
Indices: 39249807--39249838 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
39249797 TTAAAGTGAT
39249807 TTTTTA TTTTTA TTTTTA -TTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
39249839 GATCACACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:39249828 original size:11 final size:11
Alignment explanation
Indices: 39249807--39249838 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
39249797 TTAAAGTGAT
39249807 TTTTTATTTTTA
1 TTTTTA-TTTTA
39249819 TTTTTATTTTA
1 TTTTTATTTTA
39249830 TTTTTATTT
1 TTTTTATTT
39249839 GATCACACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:39250377 original size:14 final size:14
Alignment explanation
Indices: 39250355--39250387 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
39250345 TTTTTTTTAG
39250355 AAAAA-TAAATGAA
1 AAAAATTAAATGAA
*
39250368 AAAAATTAAATTAA
1 AAAAATTAAATGAA
39250382 AAAAAT
1 AAAAAT
39250388 CAGTGTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
AAAAATTAAATGAA
Found at i:39258161 original size:4 final size:4
Alignment explanation
Indices: 39258152--39258211 Score: 120
Period size: 4 Copynumber: 15.0 Consensus size: 4
39258142 ACATATGTTC
39258152 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
39258200 ATGT ATGT ATGT
1 ATGT ATGT ATGT
39258212 GATCACATGG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:39261991 original size:4 final size:4
Alignment explanation
Indices: 39261982--39262021 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
39261972 AGTAAAAGAT
39261982 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
39262022 TCTGAAAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:39280024 original size:31 final size:31
Alignment explanation
Indices: 39279957--39280024 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
39279947 TCTTTTTATT
*
39279957 AATATATGAATATTATGTTTGTTAATATATG
1 AATATATGAATATTATGTTTGATAATATATG
39279988 AATATATGAATATTATGTTTGGAT-AT-TATG
1 AATATATGAATATTATGTTT-GATAATATATG
39280018 ACATATA
1 A-ATATA
39280025 AACTAATGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
30 5 0.15
31 27 0.79
32 2 0.06
ACGTcount: A:0.40, C:0.01, G:0.13, T:0.46
Consensus pattern (31 bp):
AATATATGAATATTATGTTTGATAATATATG
Found at i:39280332 original size:45 final size:44
Alignment explanation
Indices: 39280243--39280335 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 44
39280233 ATTACAACAT
39280243 CATTCCATTCAACCAAACACAATAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAATAATACTATTACAGTTCTATTC
* *
39280287 CATTCCATTCAACCAAACA-ATTGAATTACTATTACAGTTTTATTC
1 CATTCCATTCAACCAAACACAAT-AA-TACTATTACAGTTCTATTC
39280332 CATT
1 CATT
39280336 ACACATCTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 2 0.04
44 21 0.47
45 22 0.49
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAATAATACTATTACAGTTCTATTC
Found at i:39280338 original size:16 final size:16
Alignment explanation
Indices: 39280317--39280355 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
39280307 TTGAATTACT
* *
39280317 ATTACAGTTTTATTCC
1 ATTACAGATCTATTCC
*
39280333 ATTACACATCTATTCC
1 ATTACAGATCTATTCC
39280349 ATTACAG
1 ATTACAG
39280356 CGAAGCAAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (16 bp):
ATTACAGATCTATTCC
Found at i:39280688 original size:19 final size:19
Alignment explanation
Indices: 39280653--39280699 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
39280643 TATTCTTAAA
*
39280653 ATTAAAAATCATTAAAACT
1 ATTAAAAATCATAAAAACT
*
39280672 ATTAAAAAGT-ATAAAAATT
1 ATTAAAAA-TCATAAAAACT
39280691 ATTTAAAAA
1 A-TTAAAAA
39280700 AATAATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (19 bp):
ATTAAAAATCATAAAAACT
Found at i:39289158 original size:29 final size:30
Alignment explanation
Indices: 39289094--39289164 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 30
39289084 TTAAAAAAGA
*
39289094 TTAAAATTATTTTAGATATTTTTATACTTT
1 TTAAAATAATTTTAGATATTTTTATACTTT
*
39289124 TT-AAATGATTTTA-ATGATTTTTA-A-TTT
1 TTAAAATAATTTTAGAT-ATTTTTATACTTT
39289151 TTAAAAATAATTTT
1 TT-AAAATAATTTT
39289165 TATAACTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
27 5 0.14
28 3 0.08
29 26 0.72
30 2 0.06
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (30 bp):
TTAAAATAATTTTAGATATTTTTATACTTT
Found at i:39293276 original size:3 final size:3
Alignment explanation
Indices: 39293264--39293337 Score: 86
Period size: 3 Copynumber: 26.3 Consensus size: 3
39293254 CATGTATGTT
39293264 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
39293310 ATA GT- ATA A-C ATA ATA A-A AAA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
39293338 AACAGTGTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
2 8 0.13
3 53 0.87
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:39293294 original size:21 final size:20
Alignment explanation
Indices: 39293264--39293337 Score: 98
Period size: 21 Copynumber: 3.8 Consensus size: 20
39293254 CATGTATGTT
39293264 ATAAAATAATAATAATAATA
1 ATAAAATAATAATAATAATA
39293284 ATAATAATAATAATAATAATA
1 ATAA-AATAATAATAATAATA
* *
39293305 ATAAAATAGT-ATAA-CATA
1 ATAAAATAATAATAATAATA
*
39293323 ATAAAAAAATAATAA
1 ATAAAATAATAATAA
39293338 AACAGTGTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
18 11 0.23
19 8 0.17
20 9 0.19
21 20 0.42
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (20 bp):
ATAAAATAATAATAATAATA
Found at i:39298436 original size:17 final size:19
Alignment explanation
Indices: 39298402--39298440 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
39298392 CACGAACTAA
*
39298402 TTTCAATAAGAATTTTATT
1 TTTCAATAAGAATATTATT
39298421 TTTCAATAA-AA-ATTATT
1 TTTCAATAAGAATATTATT
39298438 TTT
1 TTT
39298441 GAAGCAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 2 0.11
19 9 0.47
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (19 bp):
TTTCAATAAGAATATTATT
Found at i:39303118 original size:25 final size:25
Alignment explanation
Indices: 39303059--39303108 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
39303049 CAGGTAAGGC
*
39303059 TCCTTCTCCTTCATTCGTTCTTCAT
1 TCCTTCTTCTTCATTCGTTCTTCAT
* *
39303084 TCCTTTTTCTTCTTTCGTTCTTCAT
1 TCCTTCTTCTTCATTCGTTCTTCAT
39303109 GTTCTCTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.06, C:0.32, G:0.04, T:0.58
Consensus pattern (25 bp):
TCCTTCTTCTTCATTCGTTCTTCAT
Found at i:39306900 original size:21 final size:21
Alignment explanation
Indices: 39306849--39306903 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
39306839 ACCGCTGTTT
* *
39306849 CTAATCTCACTGCTACAGTAG
1 CTAATCTCACCGCTACAGTAA
* *
39306870 CAAATATCACCGCTACAGTAA
1 CTAATCTCACCGCTACAGTAA
39306891 CTAATCTCACCGC
1 CTAATCTCACCGC
39306904 CACCGCTGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.33, G:0.11, T:0.24
Consensus pattern (21 bp):
CTAATCTCACCGCTACAGTAA
Found at i:39313690 original size:12 final size:12
Alignment explanation
Indices: 39313673--39313697 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39313663 CTCTGCCCTC
39313673 CAACACATGTCT
1 CAACACATGTCT
39313685 CAACACATGTCT
1 CAACACATGTCT
39313697 C
1 C
39313698 CCTAGCCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.36, G:0.08, T:0.24
Consensus pattern (12 bp):
CAACACATGTCT
Found at i:39324441 original size:64 final size:65
Alignment explanation
Indices: 39324321--39324443 Score: 149
Period size: 64 Copynumber: 1.9 Consensus size: 65
39324311 TCCAAATGTG
* * *
39324321 AGCATAGTGGAGGGATCAAAAACTAAAATTTGACTATGATATTATAATAACTAAAAAAGCACATT
1 AGCATAGTAGAGGGATCAAAAACTAAAATTTGACCATGATATTATAATAACCAAAAAAGCACATT
* ** * * * *
39324386 AGCATAGTAGAGGGATCAAACA-TGTAGTTTGACCATTATATTATAGTGACCAAAAAAG
1 AGCATAGTAGAGGGATCAAAAACTAAAATTTGACCATGATATTATAATAACCAAAAAAG
39324444 AGGAAAGGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
64 28 0.58
65 20 0.42
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (65 bp):
AGCATAGTAGAGGGATCAAAAACTAAAATTTGACCATGATATTATAATAACCAAAAAAGCACATT
Found at i:39325724 original size:2 final size:2
Alignment explanation
Indices: 39325717--39325742 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39325707 TTCTTCCATT
39325717 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
39325743 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39330079 original size:2 final size:2
Alignment explanation
Indices: 39330072--39330107 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
39330062 GTATTTACAA
39330072 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39330108 AGAATGCATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39339462 original size:2 final size:2
Alignment explanation
Indices: 39339457--39339489 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39339447 ATATATATAT
39339457 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
39339490 ATCAGCTGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39340188 original size:3 final size:3
Alignment explanation
Indices: 39340182--39340213 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
39340172 CTTTGATGAT
39340182 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC AC
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC AC
39340214 TAGATGTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:39353354 original size:14 final size:14
Alignment explanation
Indices: 39353319--39353351 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
39353309 CATCATTTGT
39353319 CTATAACCAAAACC
1 CTATAACCAAAACC
39353333 CTATAACCAAAACC
1 CTATAACCAAAACC
39353347 C-ATAA
1 CTATAA
39353352 ACCCATACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.15
Consensus pattern (14 bp):
CTATAACCAAAACC
Found at i:39353465 original size:10 final size:10
Alignment explanation
Indices: 39353450--39353484 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
39353440 AAAAGAGAAT
39353450 GAAAAAAAAA
1 GAAAAAAAAA
39353460 GAAAAAAAAA
1 GAAAAAAAAA
*
39353470 AAAAAAAAGAA
1 GAAAAAAA-AA
39353481 GAAA
1 GAAA
39353485 GTTAAAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:39357337 original size:21 final size:21
Alignment explanation
Indices: 39357293--39357337 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
39357283 AAATACCCTA
* * *
39357293 CCGGAGGAACCAGAATCCCAG
1 CCGGAGCAACCACAACCCCAG
*
39357314 CCGGAGCAACCACAACCCCCG
1 CCGGAGCAACCACAACCCCAG
39357335 CCG
1 CCG
39357338 AAAGCTGAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.44, G:0.24, T:0.02
Consensus pattern (21 bp):
CCGGAGCAACCACAACCCCAG
Found at i:39357730 original size:48 final size:48
Alignment explanation
Indices: 39357604--39357723 Score: 154
Period size: 47 Copynumber: 2.5 Consensus size: 48
39357594 TTACTTTAAT
* * *
39357604 ATTTTTAATATAATTGAAATTCTTTACAATAACGTTTTAAATAAGGCA
1 ATTTTTAATATAATAGAAATTCTTTACAATAAAGTTTTAAATAAGACA
* * * *
39357652 GTTTTT-TTATAATCA-AAATTCTTTATAATAAATTTTTAAATAAGACA
1 ATTTTTAATATAAT-AGAAATTCTTTACAATAAAGTTTTAAATAAGACA
39357699 ATTTTTAATATAATAGAAATTCTTT
1 ATTTTTAATATAATAGAAATTCTTT
39357724 TAAATAAGGC
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
47 40 0.67
48 20 0.33
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.46
Consensus pattern (48 bp):
ATTTTTAATATAATAGAAATTCTTTACAATAAAGTTTTAAATAAGACA
Found at i:39357953 original size:95 final size:94
Alignment explanation
Indices: 39357783--39358004 Score: 257
Period size: 95 Copynumber: 2.4 Consensus size: 94
39357773 ATAAATATAT
* * ** * *
39357783 AATTAATTTACTCAAGTAACCCTGAACCCTAATTTATTTGATTTTTCCTTAAAAACCCTTAACTC
1 AATTAATTTACTCAAGTAACCCTAAACCCTAATTTAATTGATTTTTCCTTAAAAACAATAAACAC
* * * *
39357848 TAAATCCTAATCTGATTTTTAAATTTTTTA
66 GAAATACTAATC-CAATTTTAAATTTTTTA
* * *
39357878 AATTAAATTACTCAAGTAACCCTAAACCCTAATTTAATTGATTTTTTCTTAAAAAATAATAAACA
1 AATTAATTTACTCAAGTAACCCTAAACCCTAATTTAATTGATTTTTCCTT-AAAAACAATAAACA
*
39357943 CGAAA-ACTAATCCAATTTTAAATTTTTTT
65 CGAAATACTAATCCAATTTTAAATTTTTTA
** **
39357972 AATTAATTTACTTGACAAACCCTAAACCCTAAT
1 AATTAATTTACTCAAGTAACCCTAAACCCTAAT
39358005 CCCTTATTTA
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
94 42 0.39
95 52 0.49
96 13 0.12
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.39
Consensus pattern (94 bp):
AATTAATTTACTCAAGTAACCCTAAACCCTAATTTAATTGATTTTTCCTTAAAAACAATAAACAC
GAAATACTAATCCAATTTTAAATTTTTTA
Found at i:39362595 original size:16 final size:15
Alignment explanation
Indices: 39362570--39362603 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
39362560 CACATTTGGT
39362570 ATATTATAATTTTCAA
1 ATATTATAATTTT-AA
*
39362586 ATATTTTAATTTTAA
1 ATATTATAATTTTAA
39362601 ATA
1 ATA
39362604 AAATTAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTATAATTTTAA
Found at i:39367963 original size:21 final size:21
Alignment explanation
Indices: 39367939--39367978 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39367929 CAAATATCTT
* *
39367939 TTTAAAATTAAAATAATAAGA
1 TTTAAAAATAAAAAAATAAGA
39367960 TTTAAAAATAAAAAAATAA
1 TTTAAAAATAAAAAAATAA
39367979 AGGCAAGCTC
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:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (21 bp):
TTTAAAAATAAAAAAATAAGA
Found at i:39369558 original size:6 final size:6
Alignment explanation
Indices: 39369549--39369579 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
39369539 TTTATTTTAT
39369549 TTAATA TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA TTAATA T
39369580 AAAAATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:39369622 original size:26 final size:27
Alignment explanation
Indices: 39369587--39369652 Score: 100
Period size: 26 Copynumber: 2.5 Consensus size: 27
39369577 TATAAAAATT
39369587 TAAATTTATTATTATA-TTTTTGAAAA
1 TAAATTTATTATTATATTTTTTGAAAA
39369613 TAAATTTATTATTATATTTTTTGAAAA
1 TAAATTTATTATTATATTTTTTGAAAA
*
39369640 -ATATTTATGTATT
1 TAAATTTAT-TATT
39369653 TTTATATATT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
26 23 0.62
27 14 0.38
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (27 bp):
TAAATTTATTATTATATTTTTTGAAAA
Found at i:39370593 original size:16 final size:17
Alignment explanation
Indices: 39370572--39370604 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
39370562 TTTAATGAGA
39370572 AATTTAA-AAAATTTTG
1 AATTTAATAAAATTTTG
39370588 AATTTAATTAAAATTTT
1 AATTTAA-TAAAATTTT
39370605 CAAAAACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
AATTTAATAAAATTTTG
Found at i:39372995 original size:23 final size:23
Alignment explanation
Indices: 39372969--39373016 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
39372959 TAATTTAATT
39372969 AAAT-AAATTATTAAAAATAAAAA
1 AAATAAAATT-TTAAAAATAAAAA
*
39372992 AAATAAAAATTTTAAAAGTAAAAA
1 AAAT-AAAATTTTAAAAATAAAAA
39373016 A
1 A
39373017 CCAGGTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 4 0.18
24 13 0.59
25 5 0.23
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (23 bp):
AAATAAAATTTTAAAAATAAAAA
Found at i:39379917 original size:26 final size:25
Alignment explanation
Indices: 39379885--39379940 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
39379875 GTAGTGACTG
*
39379885 GTTTAACCAACTAGTTCTATTAACT
1 GTTTAACCAAATAGTTCTATTAACT
* *
39379910 GATTTAACTAAATGGTTCTATTAACT
1 G-TTTAACCAAATAGTTCTATTAACT
39379936 GTTTA
1 GTTTA
39379941 TTTAAAAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (25 bp):
GTTTAACCAAATAGTTCTATTAACT
Found at i:39380229 original size:30 final size:29
Alignment explanation
Indices: 39380171--39380237 Score: 89
Period size: 30 Copynumber: 2.3 Consensus size: 29
39380161 TTTTTAATCG
*
39380171 TTAACCGAACCGAAATTTTTTCAAAAAAAA
1 TTAACCGAACCGAAATTTTTGC-AAAAAAA
***
39380201 TTAACCGAACCGAAATTTTTGGTTAAAAA
1 TTAACCGAACCGAAATTTTTGCAAAAAAA
39380230 TTAACCGA
1 TTAACCGA
39380238 GTTAACCGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 13 0.39
30 20 0.61
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.28
Consensus pattern (29 bp):
TTAACCGAACCGAAATTTTTGCAAAAAAA
Found at i:39380244 original size:9 final size:9
Alignment explanation
Indices: 39380228--39380276 Score: 73
Period size: 9 Copynumber: 5.4 Consensus size: 9
39380218 TTTGGTTAAA
39380228 AATTAACCG
1 AATTAACCG
*
39380237 AGTTAACCG
1 AATTAACCG
39380246 AATT-ACCTG
1 AATTAACC-G
39380255 AATTAACCG
1 AATTAACCG
39380264 AATTAACCG
1 AATTAACCG
39380273 AATT
1 AATT
39380277 GAATCAGTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
8 3 0.08
9 30 0.83
10 3 0.08
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:39381378 original size:31 final size:30
Alignment explanation
Indices: 39381343--39381510 Score: 108
Period size: 31 Copynumber: 5.5 Consensus size: 30
39381333 TAATCACATT
*
39381343 AATATTAAATTAATAAAATGTAATCTAGATA
1 AATATTAAATTAATAAAATCT-ATCTAGATA
* *** * * * *
39381374 AATATTAAGTTAAATTTGATATA-CCATATT
1 AATATTAAATT-AATAAAATCTATCTAGATA
* *
39381404 AATATTAAATTAATAAAATACTATTTAGACA
1 AATATTAAATTAATAAAAT-CTATCTAGATA
** * *
39381435 AATATTAAATTAAATTTAA--TATCTCATATT
1 AATATTAAATT-AATAAAATCTATCT-AGATA
*
39381465 AATATTAAATTAATAAAATACTATTTAGATA
1 AATATTAAATTAATAAAAT-CTATCTAGATA
*
39381496 AATATTAAAATAATA
1 AATATTAAATTAATA
39381511 TTATCTTTGG
Statistics
Matches: 99, Mismatches: 30, Indels: 16
0.68 0.21 0.11
Matches are distributed among these distances:
29 14 0.14
30 29 0.29
31 41 0.41
32 15 0.15
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (30 bp):
AATATTAAATTAATAAAATCTATCTAGATA
Found at i:39381438 original size:61 final size:61
Alignment explanation
Indices: 39381340--39381504 Score: 253
Period size: 61 Copynumber: 2.7 Consensus size: 61
39381330 AATTAATCAC
* * * *
39381340 ATTAATATTAAATTAATAAAAT-GTAATCTAGATAAATATTAAGTTAAATTTGATATAC-CAT
1 ATTAATATTAAATTAATAAAATACT-ATTTAGATAAATATTAAATTAAATTTAATAT-CTCAT
*
39381401 ATTAATATTAAATTAATAAAATACTATTTAGACAAATATTAAATTAAATTTAATATCTCAT
1 ATTAATATTAAATTAATAAAATACTATTTAGATAAATATTAAATTAAATTTAATATCTCAT
39381462 ATTAATATTAAATTAATAAAATACTATTTAGATAAATATTAAA
1 ATTAATATTAAATTAATAAAATACTATTTAGATAAATATTAAA
39381505 ATAATATTAT
Statistics
Matches: 96, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
60 1 0.01
61 94 0.98
62 1 0.01
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.40
Consensus pattern (61 bp):
ATTAATATTAAATTAATAAAATACTATTTAGATAAATATTAAATTAAATTTAATATCTCAT
Found at i:39381469 original size:30 final size:31
Alignment explanation
Indices: 39381374--39381477 Score: 97
Period size: 30 Copynumber: 3.4 Consensus size: 31
39381364 AATCTAGATA
* *
39381374 AATATTAAGTTAAATTTGATATAC-CATATT
1 AATATTAAATTAAATTTAATATACTCATATT
** * * * **
39381404 AATATTAAATT-AATAAAATACTATTTAGACA
1 AATATTAAATTAAATTTAATA-TACTCATATT
39381435 AATATTAAATTAAATTTAATAT-CTCATATT
1 AATATTAAATTAAATTTAATATACTCATATT
39381465 AATATTAAATTAA
1 AATATTAAATTAA
39381478 TAAAATACTA
Statistics
Matches: 55, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
29 6 0.11
30 28 0.51
31 14 0.25
32 7 0.13
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (31 bp):
AATATTAAATTAAATTTAATATACTCATATT
Found at i:39398005 original size:172 final size:173
Alignment explanation
Indices: 39397712--39398198 Score: 529
Period size: 172 Copynumber: 2.8 Consensus size: 173
39397702 TAAATTTGGA
* * * * * *
39397712 ATCTACAATTAAAATGAACTTCCGAGAAATCATGAACCGATTGCTTTTGATTTATTATGAA-CAG
1 ATCTACAATTGAAATGAACTTCAGAGAATTCATAAACCGATT-CCTTTGGTTTATTATGAATCAG
* ** * * ** *
39397776 CTTGATCTTTAAGATTGTGAAATGGATACTGTAATTTATTTGAATTTCTGTTGAATTATGTGCTG
65 -TTGAACTTTAAGATTGTGAAACAGATAATGTAATTGATTTGAATTTCTAATGAATTATGTGCAG
* * * * *
39397841 GTGAAGCTTTGTTCATTTCAATTTGTCCGGAGTTTTATTTAACGT
129 GTAAAGCTTTGTTCATTTCAATTTATCAGGAGTTTTAATTAACGC
*
39397886 ATCTACAATTGAAATGAACTTCTGAGAATTCATAAACCGATTCCTTTGGTTTATTATGAATC-GT
1 ATCTACAATTGAAATGAACTTCAGAGAATTCATAAACCGATTCCTTTGGTTTATTATGAATCAGT
* *
39397950 TGAACTTTAAGATTGTTAAACAGATAATGTAATTGCTTTGAATTGT-TAATGAATTATGTGCAGG
66 TGAACTTTAAGATTGTGAAACAGATAATGTAATTGATTTGAATT-TCTAATGAATTATGTGCAGG
* *
39398014 TAAAGCTTTGTTTATTTCAATTTATCAGGAGTTTTAATTATCGC
130 TAAAGCTTTGTTCATTTCAATTTATCAGGAGTTTTAATTAACGC
* * * * * *
39398058 ATCT-CTAATGGAAATAAACTTCAGAGAATTCATAAACCGGTTGCTTTGGTTTTGTTATGAATCT
1 ATCTAC-AATTGAAATGAACTTCAGAGAATTCATAAACCGATTCCTTTGG-TTTATTATGAATCA
* * * * * *
39398122 CTTGAAC-TTAAGATTGTGAAGCAGATGATGTAATTGATTCAGATTGTTCT--CGAAATTATGTG
64 GTTGAACTTTAAGATTGTGAAACAGATAATGTAATTGATT-TGAAT-TTCTAATG-AATTATGTG
39398184 CAGGTAAAGCTTTGT
126 CAGGTAAAGCTTTGT
39398199 GCTTAGCTTT
Statistics
Matches: 267, Mismatches: 37, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
171 1 0.00
172 132 0.49
173 59 0.22
174 73 0.27
175 2 0.01
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (173 bp):
ATCTACAATTGAAATGAACTTCAGAGAATTCATAAACCGATTCCTTTGGTTTATTATGAATCAGT
TGAACTTTAAGATTGTGAAACAGATAATGTAATTGATTTGAATTTCTAATGAATTATGTGCAGGT
AAAGCTTTGTTCATTTCAATTTATCAGGAGTTTTAATTAACGC
Found at i:39402757 original size:48 final size:48
Alignment explanation
Indices: 39402686--39402780 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
39402676 CCAAGGTGCT
*
39402686 ATCCCAAATTTAGATATTGTTTTCCCTATGCAGCAAGAAGTTAGCACA
1 ATCCCAAATTTAGATACTGTTTTCCCTATGCAGCAAGAAGTTAGCACA
* * *
39402734 ATCCCAGATTTAGATACTGTTTTCCCTGTGTAGCAAGAAGTTAGCAC
1 ATCCCAAATTTAGATACTGTTTTCCCTATGCAGCAAGAAGTTAGCAC
39402781 GGTCCTTCCC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (48 bp):
ATCCCAAATTTAGATACTGTTTTCCCTATGCAGCAAGAAGTTAGCACA
Found at i:39410606 original size:24 final size:24
Alignment explanation
Indices: 39410579--39410624 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
39410569 CTCTTTGCCA
*
39410579 TCATCCTCTCTTTTTTCTTCTTTT
1 TCATCCTCTCTATTTTCTTCTTTT
*
39410603 TCATCTTCTCTATTTTCTTCTT
1 TCATCCTCTCTATTTTCTTCTT
39410625 CCCTTTCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.07, C:0.28, G:0.00, T:0.65
Consensus pattern (24 bp):
TCATCCTCTCTATTTTCTTCTTTT
Found at i:39410625 original size:27 final size:26
Alignment explanation
Indices: 39410584--39410639 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
39410574 TGCCATCATC
* **
39410584 CTCTCTTTTTTCTTCTTTTTCATCTT
1 CTCTATTTTTTCTTCCCTTTCATCTT
39410610 CTCTATTTTCTTCTTCCCTTTCATCTT
1 CTCTATTTT-TTCTTCCCTTTCATCTT
39410637 CTC
1 CTC
39410640 CTCCTTTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.05, C:0.32, G:0.00, T:0.62
Consensus pattern (26 bp):
CTCTATTTTTTCTTCCCTTTCATCTT
Found at i:39413489 original size:17 final size:19
Alignment explanation
Indices: 39413457--39413492 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
39413447 TATTTTAAAT
39413457 TATGCATTATGTAAATTTA
1 TATGCATTATGTAAATTTA
39413476 TATG-ATTATG-AAATTTA
1 TATGCATTATGTAAATTTA
39413493 AATAGGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 6 0.35
19 4 0.24
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (19 bp):
TATGCATTATGTAAATTTA
Found at i:39414040 original size:8 final size:8
Alignment explanation
Indices: 39414022--39414065 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
39414012 AATAAATATA
39414022 TTTTTTA-
1 TTTTTTAT
39414029 TTTTTTAT
1 TTTTTTAT
**
39414037 TTTTAAAAT
1 TTTT-TTAT
39414046 TTTTTTAT
1 TTTTTTAT
39414054 TTTTTTAT
1 TTTTTTAT
39414062 TTTT
1 TTTT
39414066 AAAATAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
7 7 0.23
8 18 0.58
9 6 0.19
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTAT
Found at i:39414053 original size:24 final size:25
Alignment explanation
Indices: 39414022--39414070 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
39414012 AATAAATATA
39414022 TTTTTTA-TTTTTTATTTTTAAAAT
1 TTTTTTATTTTTTTATTTTTAAAAT
39414046 TTTTTTATTTTTTTATTTTTAAAAT
1 TTTTTTATTTTTTTATTTTTAAAAT
39414071 AAATTTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (25 bp):
TTTTTTATTTTTTTATTTTTAAAAT
Found at i:39414367 original size:15 final size:15
Alignment explanation
Indices: 39414349--39414380 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
39414339 AAGTGTTTTT
39414349 CAATAAAGTCTTGAA
1 CAATAAAGTCTTGAA
39414364 CAATAAAGTCTTGAA
1 CAATAAAGTCTTGAA
39414379 CA
1 CA
39414381 TAAGATAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (15 bp):
CAATAAAGTCTTGAA
Found at i:39421223 original size:69 final size:69
Alignment explanation
Indices: 39421112--39421250 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
39421102 ACCACAGATA
39421112 TTCTAACTGAAGGCTTTCATTGTGACTGGTTGACCTACTTATTAGCGATCGTCGATAATTCATAA
1 TTCTAACTGAAGGCTTTCATTGTGACTGGTTGACCTACTTATTAGCGATCGTCGATAATTCATAA
39421177 TTTG
66 TTTG
39421181 TTCTAACTGAAGGCTTTCATTGTGACTGGTTGACCTACTTATTAGCGATCGTCGATAATTCATAA
1 TTCTAACTGAAGGCTTTCATTGTGACTGGTTGACCTACTTATTAGCGATCGTCGATAATTCATAA
39421246 TTTG
66 TTTG
39421250 T
1 T
39421251 CTCCATATTC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (69 bp):
TTCTAACTGAAGGCTTTCATTGTGACTGGTTGACCTACTTATTAGCGATCGTCGATAATTCATAA
TTTG
Found at i:39422341 original size:32 final size:33
Alignment explanation
Indices: 39422280--39422343 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
39422270 CCTTCAAAAC
*
39422280 GTGCCACTTATAGGCAAACGATAGAACTTGGGG
1 GTGCCACTTATAGGCAAACGAAAGAACTTGGGG
* *
39422313 GTGCCAC-TATCGGCAGACGAAAGAACTTGGG
1 GTGCCACTTATAGGCAAACGAAAGAACTTGGG
39422344 CACACCACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 21 0.75
33 7 0.25
ACGTcount: A:0.30, C:0.20, G:0.31, T:0.19
Consensus pattern (33 bp):
GTGCCACTTATAGGCAAACGAAAGAACTTGGGG
Found at i:39424098 original size:30 final size:30
Alignment explanation
Indices: 39424045--39424142 Score: 115
Period size: 30 Copynumber: 3.3 Consensus size: 30
39424035 GAGCAAAGTT
* * ** *
39424045 AATAATAAAACAATAATTATATAATAGTAA
1 AATAACAAAATAATAACAATATAATAATAA
* * *
39424075 AACAACAAAATAATAGCAATATAATACTAA
1 AATAACAAAATAATAACAATATAATAATAA
*
39424105 AATAACAAAATAATAACAAAATAATAATAA
1 AATAACAAAATAATAACAATATAATAATAA
39424135 AATAACAA
1 AATAACAA
39424143 TAAAGCAACA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.67, C:0.08, G:0.02, T:0.22
Consensus pattern (30 bp):
AATAACAAAATAATAACAATATAATAATAA
Found at i:39424125 original size:19 final size:19
Alignment explanation
Indices: 39424103--39424142 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
39424093 ATATAATACT
39424103 AAAATAACAA-AATAATAAC
1 AAAATAACAATAA-AATAAC
*
39424122 AAAATAATAATAAAATAAC
1 AAAATAACAATAAAATAAC
39424141 AA
1 AA
39424143 TAAAGCAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAATAACAATAAAATAAC
Found at i:39424131 original size:11 final size:11
Alignment explanation
Indices: 39424078--39424139 Score: 67
Period size: 11 Copynumber: 5.9 Consensus size: 11
39424068 ATAGTAAAAC
39424078 AACAAAATAAT
1 AACAAAATAAT
* *
39424089 AGCAATATAAT
1 AACAAAATAAT
*
39424100 -AC-TAA-AAT
1 AACAAAATAAT
39424108 AACAAAATAAT
1 AACAAAATAAT
39424119 AACAAAATAAT
1 AACAAAATAAT
*
39424130 AATAAAATAA
1 AACAAAATAA
39424140 CAATAAAGCA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
8 3 0.07
9 3 0.07
10 3 0.07
11 32 0.78
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.21
Consensus pattern (11 bp):
AACAAAATAAT
Found at i:39424144 original size:11 final size:11
Alignment explanation
Indices: 39424105--39424146 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
39424095 ATAATACTAA
*
39424105 AATAACAAAAT
1 AATAATAAAAT
*
39424116 AATAACAAAAT
1 AATAATAAAAT
39424127 AATAATAAAAT
1 AATAATAAAAT
*
39424138 AACAATAAA
1 AATAATAAA
39424147 GCAACATCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:39435881 original size:17 final size:17
Alignment explanation
Indices: 39435859--39435928 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 17
39435849 GCAATTAATT
39435859 AATTTTTTAAAATTTAA
1 AATTTTTTAAAATTTAA
** *
39435876 AATTTTCAAAAAGTATAA
1 AATTTTTTAAAA-TTTAA
***
39435894 AAAAATTTAAAA-TTAA
1 AATTTTTTAAAATTTAA
* *
39435910 AATTGTTTAAAAATTAA
1 AATTTTTTAAAATTTAA
39435927 AA
1 AA
39435929 ATATAATTTT
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
16 12 0.31
17 16 0.41
18 11 0.28
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (17 bp):
AATTTTTTAAAATTTAA
Found at i:39435921 original size:24 final size:25
Alignment explanation
Indices: 39435894--39435947 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
39435884 AAAAGTATAA
*
39435894 AAAAATTTAAAATTA-AAATTGTTT
1 AAAAATTTAAAAATATAAATTGTTT
* *
39435918 AAAAA-TTAAAAATATAATTTTTTT
1 AAAAATTTAAAAATATAAATTGTTT
39435942 AAAAAT
1 AAAAAT
39435948 ATTTTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
AAAAATTTAAAAATATAAATTGTTT
Found at i:39435922 original size:35 final size:33
Alignment explanation
Indices: 39435864--39435929 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 33
39435854 TAATTAATTT
39435864 TTTAAAATTTAAAATTTTCAAAAAGTATAAAAAAA
1 TTTAAAATTTAAAATTTTCAAAAA-T-TAAAAAAA
*
39435899 TTTAAAA-TTAAAATTGTTTAAAAATTAAAAA
1 TTTAAAATTTAAAATT-TTCAAAAATTAAAAA
39435930 TATAATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 6 0.21
34 9 0.31
35 14 0.48
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (33 bp):
TTTAAAATTTAAAATTTTCAAAAATTAAAAAAA
Found at i:39435958 original size:16 final size:16
Alignment explanation
Indices: 39435923--39435962 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
39435913 TGTTTAAAAA
39435923 TTAAAAATATAATTTTT
1 TTAAAAATAT-ATTTTT
39435940 TTAAAAATAT-TTTTAT
1 TTAAAAATATATTTT-T
39435956 TTAAAAA
1 TTAAAAA
39435963 ATTAGTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.18
16 8 0.36
17 10 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAAAATATATTTTT
Found at i:39438825 original size:21 final size:21
Alignment explanation
Indices: 39438799--39438854 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
39438789 AACAGCGGTG
*
39438799 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
39438820 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
39438841 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
39438855 AACAATGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:39445350 original size:11 final size:11
Alignment explanation
Indices: 39445334--39445359 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39445324 TGTACCTGCA
39445334 AAAAAAAAAAT
1 AAAAAAAAAAT
39445345 AAAAAAAAAAT
1 AAAAAAAAAAT
39445356 AAAA
1 AAAA
39445360 TGTTTGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAAAAAAT
Found at i:39452466 original size:18 final size:17
Alignment explanation
Indices: 39452424--39452457 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39452414 TTGGTATCTG
*
39452424 AACTTGACAACTTTCTT
1 AACTTGGCAACTTTCTT
39452441 AACTTGGCAACTTTCTT
1 AACTTGGCAACTTTCTT
39452458 TAATTTGGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (17 bp):
AACTTGGCAACTTTCTT
Found at i:39463353 original size:29 final size:29
Alignment explanation
Indices: 39463325--39463380 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
39463315 GTCAAATTTG
39463325 GGGATTTTGGGTAAGGG-TTTTGATTTTT
1 GGGATTTTGGGTAAGGGTTTTTGATTTTT
* * *
39463353 GGGATTTTTGTTTAGGGTTTTTGATTTT
1 GGGATTTTGGGTAAGGGTTTTTGATTTT
39463381 AGAGGTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.12, C:0.00, G:0.32, T:0.55
Consensus pattern (29 bp):
GGGATTTTGGGTAAGGGTTTTTGATTTTT
Found at i:39463936 original size:21 final size:21
Alignment explanation
Indices: 39463912--39463951 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39463902 ATCTATTTTG
* *
39463912 ATAATTTTATATTTTAAAAAA
1 ATAATTTAATAATTTAAAAAA
39463933 ATAATTTAATAATTTAAAA
1 ATAATTTAATAATTTAAAA
39463952 TTATTTGCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAATTTAATAATTTAAAAAA
Found at i:39466697 original size:16 final size:15
Alignment explanation
Indices: 39466657--39466697 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
39466647 ATTAATACTA
* *
39466657 TTATTTATCAAAATT
1 TTATTTATAAAAATC
39466672 TTATTTATAAAAATC
1 TTATTTATAAAAATC
39466687 TTATATTATAA
1 TTAT-TTATAA
39466698 TTGTGTCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (15 bp):
TTATTTATAAAAATC
Found at i:39468405 original size:24 final size:23
Alignment explanation
Indices: 39468361--39468405 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
39468351 GTCAAAACTA
*
39468361 AAATATAGAATCAAATTTAAACG
1 AAATATAGAATCAAATCTAAACG
39468384 AAATATAAGAATCACAA-CTAAA
1 AAATAT-AGAATCA-AATCTAAA
39468406 ATTTAACCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 6 0.32
24 11 0.58
25 2 0.11
ACGTcount: A:0.60, C:0.11, G:0.07, T:0.22
Consensus pattern (23 bp):
AAATATAGAATCAAATCTAAACG
Found at i:39471082 original size:12 final size:14
Alignment explanation
Indices: 39471064--39471103 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
39471054 ATAATAGGTT
39471064 TTTAATTAAAT-AA
1 TTTAATTAAATAAA
39471077 -TTAATTAAATAAA
1 TTTAATTAAATAAA
*
39471090 TTTAATTAATTAAA
1 TTTAATTAAATAAA
39471104 AAATTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 10 0.42
13 2 0.08
14 12 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:39471097 original size:18 final size:17
Alignment explanation
Indices: 39471074--39471119 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 17
39471064 TTTAATTAAA
39471074 TAATTAATTAAATAAATT
1 TAATTAATTAAA-AAATT
39471092 TAATTAATTAAAAAATT
1 TAATTAATTAAAAAATT
39471109 TAAATTAATTA
1 T-AATTAATTA
39471120 CACCTTGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATTAATTAAAAAATT
Found at i:39471429 original size:10 final size:11
Alignment explanation
Indices: 39471398--39471426 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
39471388 CCTCTCTTAT
39471398 ATTTCCTTTCA
1 ATTTCCTTTCA
39471409 A-TTCCTTTCA
1 ATTTCCTTTCA
39471419 ATTTCCTT
1 ATTTCCTT
39471427 CAAAAATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTTCCTTTCA
Found at i:39472525 original size:7 final size:7
Alignment explanation
Indices: 39472515--39472546 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
39472505 ATTCGATTGA
39472515 TATTTAG
1 TATTTAG
39472522 TATTTAG
1 TATTTAG
39472529 TATTTAG
1 TATTTAG
39472536 TATTTAG
1 TATTTAG
39472543 TATT
1 TATT
39472547 ATGTATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.59
Consensus pattern (7 bp):
TATTTAG
Found at i:39473221 original size:18 final size:18
Alignment explanation
Indices: 39473195--39473229 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39473185 AGGTGCGTTT
*
39473195 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
39473213 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
39473230 TCCTTTTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:39473700 original size:44 final size:45
Alignment explanation
Indices: 39473651--39473737 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 45
39473641 ATATTTTGAA
*
39473651 TATTTTGATATTATTTTATGTAAAAAAATAGAAATTT-TTTGAGT
1 TATTTTGATATTATTTGATGTAAAAAAATAGAAATTTATTTGAGT
* *
39473695 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGA
1 TATTTTGATATTATTTGATGTAAAAAAATAGAAATTTATTTGA
39473738 TGTAATAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 34 0.87
45 5 0.13
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (45 bp):
TATTTTGATATTATTTGATGTAAAAAAATAGAAATTTATTTGAGT
Found at i:39473825 original size:26 final size:25
Alignment explanation
Indices: 39473705--39473823 Score: 211
Period size: 25 Copynumber: 4.7 Consensus size: 25
39473695 TATTTTGATA
39473705 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
39473730 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
39473755 TCATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
39473780 TTATTTAATGTAATAAAAATAGAAGT
1 TTATTTGATGTAAT-AAAATAGAAGT
39473806 TTATTTGATGTAATAAAA
1 TTATTTGATGTAATAAAA
39473824 ATCCTAACCT
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
25 65 0.73
26 24 0.27
ACGTcount: A:0.45, C:0.01, G:0.14, T:0.39
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:39473950 original size:29 final size:29
Alignment explanation
Indices: 39473908--39473964 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
39473898 NNNNNNNNNN
39473908 AACCCTAACCTAATTTAATTAAAAACCCC
1 AACCCTAACCTAATTTAATTAAAAACCCC
39473937 AACCCTAACCTAATTTAATTAAAAACCC
1 AACCCTAACCTAATTTAATTAAAAACCC
39473965 TAAACCCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.25
Consensus pattern (29 bp):
AACCCTAACCTAATTTAATTAAAAACCCC
Found at i:39473983 original size:22 final size:20
Alignment explanation
Indices: 39473951--39473996 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
39473941 CTAACCTAAT
39473951 TTAA-TTAAAAACCCTAAACCC
1 TTAACTTAAAAACCCT-AA-CC
39473972 TTAACTTAAAAACCCTAACC
1 TTAACTTAAAAACCCTAACC
39473992 TTAAC
1 TTAAC
39473997 CTAATTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 7 0.29
21 6 0.25
22 11 0.46
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (20 bp):
TTAACTTAAAAACCCTAACC
Found at i:39474176 original size:72 final size:72
Alignment explanation
Indices: 39474015--39474712 Score: 1342
Period size: 72 Copynumber: 9.7 Consensus size: 72
39474005 ATTAAAAACT
* * * * *
39474015 CTAACCTAATTTAATTGAAAACCCTAACCTAATTTACTTAAAAACCCTAAACCCTTAATTAAAAA
1 CTAACCTAAATTAATTAAAAACTCTAACATAATTTAATTAAAAACCCTAAA-CCTTAATTAAAAA
39474080 CGCTAACC
65 CGCTAACC
39474088 CTAACCTAAATTAATTAAAAACTCTAACATAATTTAATTAAAAACCCTAAACCTTAATTAAAAAC
1 CTAACCTAAATTAATTAAAAACTCTAACATAATTTAATTAAAAACCCTAAACCTTAATTAAAAAC
39474153 GCTAACC
66 GCTAACC
39474160 CTAACCTAAATTAATTAAAAACTCTAACATAATTTAATTAAAAACCCTAAACCTTAATTAAAAAC
1 CTAACCTAAATTAATTAAAAACTCTAACATAATTTAATTAAAAACCCTAAACCTTAATTAAAAAC
39474225 GCTAACC
66 GCTAACC
39474232 CTAACCTAAATTAATTAAAAACTCTAACATAATTTAATTAAAAACCCTAAACCTTAATTAAAAAC
1 CTAACCTAAATTAATTAAAAACTCTAACATAATTTAATTAAAAACCCTAAACCTTAATTAAAAAC
39474297 GCTAACC
66 GCTAACC
39474304 CTAACCTAAATTAATTAAAAACTCTAACATAATTTAATTAAAAACCCTAAACCTTAATTAAAAAC
1 CTAACCTAAATTAATTAAAAACTCTAACATAATTTAATTAAAAACCCTAAACCTTAATTAAAAAC
39474369 GCTAACC
66 GCTAACC
39474376 CTAACCTAAATTAATTAAAAACTCTAACATAATTTAATTAAAAACCCTAAACCTTAATTAAAAAC
1 CTAACCTAAATTAATTAAAAACTCTAACATAATTTAATTAAAAACCCTAAACCTTAATTAAAAAC
39474441 GCTAACC
66 GCTAACC
39474448 CTAACCTAAATTAATTAAAAACTCTAACATAATTTAATTAAAAACCCTAAACCTTAATTAAAAAC
1 CTAACCTAAATTAATTAAAAACTCTAACATAATTTAATTAAAAACCCTAAACCTTAATTAAAAAC
39474513 GCTAACC
66 GCTAACC
39474520 CTAACCTAAATTAATTAAAAACTCTAACATAATTTAATTAAAAACCCTAAACCTTAATTAAAAAC
1 CTAACCTAAATTAATTAAAAACTCTAACATAATTTAATTAAAAACCCTAAACCTTAATTAAAAAC
39474585 GCTAACC
66 GCTAACC
39474592 CTAACCTAAATTAATTAAAAACTCTAACATAATTTAATTAAAAACCCTAAACCTTAATTAAAAAC
1 CTAACCTAAATTAATTAAAAACTCTAACATAATTTAATTAAAAACCCTAAACCTTAATTAAAAAC
39474657 GCTAACC
66 GCTAACC
39474664 CTAACCTAAATTAATTAAAAACTCTAACATAATTTAATTAAAAACCCTA
1 CTAACCTAAATTAATTAAAAACTCTAACATAATTTAATTAAAAACCCTA
39474713 TGGGAAAAAC
Statistics
Matches: 620, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
72 574 0.93
73 46 0.07
ACGTcount: A:0.49, C:0.21, G:0.01, T:0.28
Consensus pattern (72 bp):
CTAACCTAAATTAATTAAAAACTCTAACATAATTTAATTAAAAACCCTAAACCTTAATTAAAAAC
GCTAACC
Found at i:39474988 original size:23 final size:23
Alignment explanation
Indices: 39474962--39475078 Score: 132
Period size: 23 Copynumber: 4.9 Consensus size: 23
39474952 TGGTAAATTG
39474962 CCTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAA
39474985 CCTAATTTAATTAAAAACCCTAAA
1 CCTAATTTAATTAAAAACCCT-AA
*
39475009 CC---CTTAACTTAAAAACCCTAA
1 CCTAATTTAA-TTAAAAACCCTAA
39475030 CCTTAACCTCATTTAATTAAAAACCCTAA
1 CC-T-A----ATTTAATTAAAAACCCTAA
39475059 CCTAATTTAATTAAAAACCC
1 CCTAATTTAATTAAAAACCC
39475079 ATCTTCTTCA
Statistics
Matches: 81, Mismatches: 2, Indels: 22
0.77 0.02 0.21
Matches are distributed among these distances:
21 8 0.10
22 11 0.14
23 37 0.46
24 4 0.05
27 1 0.01
28 1 0.01
29 15 0.19
30 4 0.05
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (23 bp):
CCTAATTTAATTAAAAACCCTAA
Found at i:39477685 original size:21 final size:23
Alignment explanation
Indices: 39477629--39477685 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 23
39477619 CTCTTTATTT
*
39477629 TCCATTCTCTTCTCCTTCTCCTTC
1 TCCATT-TCTTTTCCTTCTCCTTC
* * *
39477653 TCCCTATGTTTTCC-TC-CCTTC
1 TCCATTTCTTTTCCTTCTCCTTC
39477674 TCCATTTCTTTT
1 TCCATTTCTTTT
39477686 AACGTAATTT
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
21 14 0.54
22 2 0.08
23 6 0.23
24 4 0.15
ACGTcount: A:0.05, C:0.40, G:0.02, T:0.53
Consensus pattern (23 bp):
TCCATTTCTTTTCCTTCTCCTTC
Found at i:39480612 original size:2 final size:2
Alignment explanation
Indices: 39480605--39480633 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
39480595 GAAATTCTTT
39480605 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39480634 GTAATGCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39488892 original size:31 final size:29
Alignment explanation
Indices: 39488844--39488913 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
39488834 ATCCCAAAAC
* *
39488844 TATACATGAAGTATGATTTAATGTGTAATTG
1 TATACATGAACTATGA-TT-ATCTGTAATTG
* * *
39488875 TATACATGAACTTTGATTCTCTGTAATTT
1 TATACATGAACTATGATTATCTGTAATTG
39488904 TATACATGAA
1 TATACATGAA
39488914 ATTTTTCAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 18 0.53
30 2 0.06
31 14 0.41
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (29 bp):
TATACATGAACTATGATTATCTGTAATTG
Found at i:39502873 original size:507 final size:508
Alignment explanation
Indices: 39501910--39502924 Score: 2023
Period size: 507 Copynumber: 2.0 Consensus size: 508
39501900 ATTATTGAAT
39501910 TGAGAATAGAATCAATTAAATTAAAAATTAATTAATTAATTAATTACATCATAATCCGATTTTCA
1 TGAGAATAGAATCAATTAAATTAAAAATTAATTAATTAATTAATTACATCATAATCCGATTTTCA
39501975 AAACATTAATTATAATTGTGAAAGCCTAATGAAACCCATTCTAACAAAATCATGTAGTGGTGGCC
66 AAACATTAATTATAATTGTGAAAGCCTAATGAAACCCATTCTAACAAAATCATGTAGTGGTGGCC
39502040 AGGCTAGTTCTAGCCTTGGCTTTCCAATTTTTCTTTTCCCTCTTTTACCTCAAAAAAAGAAGGAA
131 AGGCTAGTTCTAGCCTTGGCTTTCCAATTTTTCTTTTCCCTCTTTTACCTCAAAAAAAGAAGGAA
39502105 AAAGAAAAAGATGTTCCAAAGCCAAACTACCAAGTATGACCCATTTGAATTTAATTGCTCCACTT
196 AAAGAAAAAGATGTTCCAAAGCCAAACTACCAAGTATGACCCATTTGAATTTAATTGCTCCACTT
39502170 TATGTAGATTTAGTAATAATATCTCATTAAAAACTTTTAAAATGTAAAAAAAAAAATCCTTTTTT
261 TATGTAGATTTAGTAATAATATCTCATTAAAAACTTTTAAAATGTAAAAAAAAAAATCCTTTTTT
39502235 AACTCAAAAATTAGAATTTTCTAATATAACTCGTCATTATTACCTTAAATGTATATGTCAAGACA
326 AACTCAAAAATTAGAATTTTCTAATATAACTCGTCATTATTACCTTAAATGTATATGTCAAGACA
39502300 AGTTACAAAGTAAAATTTTGAGTGATACTTGGTAGTGTTCATTATAATCCATTATTATAACATTG
391 AGTTACAAAGTAAAATTTTGAGTGATACTTGGTAGTGTTCATTATAATCCATTATTATAACATTG
39502365 AAGCAAAACTTGTCATATTTGTGTTGGCAAATTAATGAAACGAAATCTTTAAG
456 AAGCAAAACTTGTCATATTTGTGTTGGCAAATTAATGAAACGAAATCTTTAAG
39502418 TGAGAATAG-ATCAATTAAATTAAAAATTAATTAATTAATTAATTACATCATAATCCGATTTTCA
1 TGAGAATAGAATCAATTAAATTAAAAATTAATTAATTAATTAATTACATCATAATCCGATTTTCA
39502482 AAACATTAATTATAATTGTGAAAGCCTAATGAAACCCATTCTAACAAAATCATGTAGTGGTGGCC
66 AAACATTAATTATAATTGTGAAAGCCTAATGAAACCCATTCTAACAAAATCATGTAGTGGTGGCC
39502547 AGGCTAGTTCTAGCCTTGGCTTTCCAATTTTTCTTTTCCCTCTTTTACCTCAAAAAAAGAAGGAA
131 AGGCTAGTTCTAGCCTTGGCTTTCCAATTTTTCTTTTCCCTCTTTTACCTCAAAAAAAGAAGGAA
39502612 AAAGAAAAAGATGTTCCAAAGCCAAACTACCAAGTATGACCCATTTGAATTTAATTGCTCCACTT
196 AAAGAAAAAGATGTTCCAAAGCCAAACTACCAAGTATGACCCATTTGAATTTAATTGCTCCACTT
39502677 TATGTAGATTTAGTAATAATATCTCATTAAAAACTTTTAAAATGTAAAAAAAAAAATCCTTTTTT
261 TATGTAGATTTAGTAATAATATCTCATTAAAAACTTTTAAAATGTAAAAAAAAAAATCCTTTTTT
39502742 AACTCAAAAATTAGAATTTTCTAATATAACTCGTCATTATTACCTTAAATGTATATGTCAAGACA
326 AACTCAAAAATTAGAATTTTCTAATATAACTCGTCATTATTACCTTAAATGTATATGTCAAGACA
39502807 AGTTACAAAGTAAAATTTTGAGTGATACTTGGTAGTGTTCATTATAATCCATTATTATAACATTG
391 AGTTACAAAGTAAAATTTTGAGTGATACTTGGTAGTGTTCATTATAATCCATTATTATAACATTG
39502872 AAGCAAAACTTGTCATATTTGTGTTGGCAAATTAATGAAACGAAATCTTTAAG
456 AAGCAAAACTTGTCATATTTGTGTTGGCAAATTAATGAAACGAAATCTTTAAG
39502925 CTATTAACTT
Statistics
Matches: 507, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
507 498 0.98
508 9 0.02
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (508 bp):
TGAGAATAGAATCAATTAAATTAAAAATTAATTAATTAATTAATTACATCATAATCCGATTTTCA
AAACATTAATTATAATTGTGAAAGCCTAATGAAACCCATTCTAACAAAATCATGTAGTGGTGGCC
AGGCTAGTTCTAGCCTTGGCTTTCCAATTTTTCTTTTCCCTCTTTTACCTCAAAAAAAGAAGGAA
AAAGAAAAAGATGTTCCAAAGCCAAACTACCAAGTATGACCCATTTGAATTTAATTGCTCCACTT
TATGTAGATTTAGTAATAATATCTCATTAAAAACTTTTAAAATGTAAAAAAAAAAATCCTTTTTT
AACTCAAAAATTAGAATTTTCTAATATAACTCGTCATTATTACCTTAAATGTATATGTCAAGACA
AGTTACAAAGTAAAATTTTGAGTGATACTTGGTAGTGTTCATTATAATCCATTATTATAACATTG
AAGCAAAACTTGTCATATTTGTGTTGGCAAATTAATGAAACGAAATCTTTAAG
Found at i:39513485 original size:18 final size:18
Alignment explanation
Indices: 39513464--39513503 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
39513454 TGTAGAGGCT
* *
39513464 AAATATTAATAACTAATA
1 AAATATTAAGAAATAATA
*
39513482 AAATATTACGAAATAATA
1 AAATATTAAGAAATAATA
39513500 AAAT
1 AAAT
39513504 TGATATTAAA
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:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (18 bp):
AAATATTAAGAAATAATA
Found at i:39523925 original size:16 final size:16
Alignment explanation
Indices: 39523893--39523936 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
39523883 GCTAATATTA
39523893 AATTTTAGGTTTAAGGT
1 AATTTTA-GTTTAAGGT
*
39523910 AATTTTAGTTTCAGGT
1 AATTTTAGTTTAAGGT
*
39523926 TATTTTGAGTT
1 AATTTT-AGTT
39523937 GAAGTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.25, C:0.02, G:0.20, T:0.52
Consensus pattern (16 bp):
AATTTTAGTTTAAGGT
Found at i:39530292 original size:15 final size:15
Alignment explanation
Indices: 39530269--39530302 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
39530259 AAACATATTT
*
39530269 TAAATTATTAAAAAA
1 TAAAATATTAAAAAA
*
39530284 TAAAATATTAAGAAA
1 TAAAATATTAAAAAA
39530299 TAAA
1 TAAA
39530303 TAAACTCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (15 bp):
TAAAATATTAAAAAA
Found at i:39531548 original size:21 final size:21
Alignment explanation
Indices: 39531522--39531568 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
39531512 CGCAAAGGAT
39531522 GTGGACAACTTCTTGTGGGAA
1 GTGGACAACTTCTTGTGGGAA
*
39531543 GTGGACAATTTCTTGTGGGAA
1 GTGGACAACTTCTTGTGGGAA
39531564 GTGGA
1 GTGGA
39531569 GCAATACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.11, G:0.36, T:0.30
Consensus pattern (21 bp):
GTGGACAACTTCTTGTGGGAA
Found at i:39535600 original size:3 final size:3
Alignment explanation
Indices: 39535592--39535638 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
39535582 TATGTATTAA
*
39535592 AAT AAT AAT AAGT AAT -AT AAT AAT AAT AGT AAT ATAT AAT -AT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
39535637 AA
1 AA
39535639 CAAAGATAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 4 0.11
3 28 0.74
4 6 0.16
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:39535613 original size:15 final size:16
Alignment explanation
Indices: 39535593--39535634 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
39535583 ATGTATTAAA
39535593 ATAATAATA-AGTAAT
1 ATAATAATATAGTAAT
39535608 ATAATAATAATAGTAAT
1 ATAATAAT-ATAGTAAT
39535625 AT-ATAATATA
1 ATAATAATATA
39535635 ATAACAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 11 0.44
16 6 0.24
17 8 0.32
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (16 bp):
ATAATAATATAGTAAT
Found at i:39535618 original size:21 final size:19
Alignment explanation
Indices: 39535592--39535638 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
39535582 TATGTATTAA
39535592 AATAATAATAAGTAATATAAT
1 AATAATAATAA-T-ATATAAT
*
39535613 AATAATAGTAATATATAAT
1 AATAATAATAATATATAAT
39535632 -ATAATAA
1 AATAATAA
39535639 CAAAGATAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 6 0.25
19 7 0.29
20 1 0.04
21 10 0.42
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (19 bp):
AATAATAATAATATATAAT
Found at i:39535624 original size:24 final size:24
Alignment explanation
Indices: 39535592--39535638 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
39535582 TATGTATTAA
39535592 AATAATAATA-AGTAATATAATAAT
1 AATAATAATATA-TAATATAATAAT
*
39535616 AATAGTAATATATAATATAATAA
1 AATAATAATATATAATATAATAA
39535639 CAAAGATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (24 bp):
AATAATAATATATAATATAATAAT
Found at i:39536891 original size:5 final size:5
Alignment explanation
Indices: 39536881--39536922 Score: 68
Period size: 5 Copynumber: 8.6 Consensus size: 5
39536871 CCCCATTTTC
*
39536881 AAAA- AAAAA AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
39536923 GAATGTGCCC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
4 4 0.11
5 32 0.89
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:39537030 original size:18 final size:18
Alignment explanation
Indices: 39536994--39537031 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
39536984 ATATTGAAAT
*
39536994 TATGCTTAGTTAAATAAA
1 TATGCTTAGCTAAATAAA
39537012 TATGCTTAGACTAAA-AAA
1 TATGCTTAG-CTAAATAAA
39537030 TA
1 TA
39537032 AAGCTTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (18 bp):
TATGCTTAGCTAAATAAA
Found at i:39545786 original size:8 final size:8
Alignment explanation
Indices: 39545773--39545797 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
39545763 GTGATGTTCT
39545773 TGTTGCTG
1 TGTTGCTG
39545781 TGTTGCTG
1 TGTTGCTG
39545789 TGTTGCTG
1 TGTTGCTG
39545797 T
1 T
39545798 ATGATGTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.36, T:0.52
Consensus pattern (8 bp):
TGTTGCTG
Found at i:39549126 original size:37 final size:37
Alignment explanation
Indices: 39549077--39549160 Score: 152
Period size: 37 Copynumber: 2.3 Consensus size: 37
39549067 GAGGAAAAGA
*
39549077 TTATA-TTTGATATGAATCAAAAGAGGATTGAGTTAT
1 TTATATTTTGATATGAATCAAAAGAGGATTGAATTAT
39549113 TTATATTTTGATATGAATCAAAAGAGGATTGAATTAT
1 TTATATTTTGATATGAATCAAAAGAGGATTGAATTAT
39549150 TTATATTTTGA
1 TTATATTTTGA
39549161 ATTGAACTCG
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
36 5 0.11
37 41 0.89
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (37 bp):
TTATATTTTGATATGAATCAAAAGAGGATTGAATTAT
Found at i:39550571 original size:41 final size:41
Alignment explanation
Indices: 39550508--39550716 Score: 265
Period size: 41 Copynumber: 5.1 Consensus size: 41
39550498 CTTTCGGGGC
* * * * * * *
39550508 TTTAGAGGCGTTTTTAATAAAGCGCCACTAGTGCTTAGGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGA
* * * *
39550549 TTTAGTGGCGTCTTTGAGAAAGCGCCTCTAATGCTCAGGGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGA
* *
39550590 TTTAGCGGCGTTTTTGAGAAAGCACCGCTAATGCTCAGTGA
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGA
* * *
39550631 TTTGGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTCAGTGA
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGA
*
39550672 TTTAGTGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGA
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGA
39550713 TTTA
1 TTTA
39550717 AAATAATTTA
Statistics
Matches: 148, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 148 1.00
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGA
Found at i:39554851 original size:43 final size:43
Alignment explanation
Indices: 39554776--39554888 Score: 163
Period size: 43 Copynumber: 2.6 Consensus size: 43
39554766 AAATATTTTT
* * * *
39554776 TAAATGTCTTGTTCTTTAGCGGAGTTTGTGGGAAAAGCGCTGC
1 TAAAGGTCTTGTTCTTTAGCGGCGTTTATGGGAAAAGCGCCGC
*
39554819 TAAAGGTCTTGTTTTTTAGCGGCGTTTATGGGAAAAGCGCCGC
1 TAAAGGTCTTGTTCTTTAGCGGCGTTTATGGGAAAAGCGCCGC
* *
39554862 TAAAGGTCTTGTTCTATAACGGCGTTT
1 TAAAGGTCTTGTTCTTTAGCGGCGTTT
39554889 GTATCATTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 62 1.00
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.35
Consensus pattern (43 bp):
TAAAGGTCTTGTTCTTTAGCGGCGTTTATGGGAAAAGCGCCGC
Found at i:39554980 original size:43 final size:43
Alignment explanation
Indices: 39554907--39555175 Score: 367
Period size: 43 Copynumber: 6.3 Consensus size: 43
39554897 TAGCGGCGTT
* *
39554907 TAGCAGCGTTTGTGGGAAAAGCGCCACTAAAGGTCTTGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGTTCTA
* ** * * * *
39554950 TAGCGGCGTTTGTGGGAAAAGTGATGCTAAATGTCATGATCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGTTCTA
*
39554993 TAGCGACGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGTTCTA
* **
39555036 TAGCGGCGTTTGTGTGAAAAATGCCGCTAAAGGTCTTGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGTTCTA
* **
39555079 TAGCGGCGTTTGTGTGAAAAATGCCGCTAAAGGTCTTGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGTTCTA
* *
39555122 TAGCGGCGTTTGTGTGAAAAGCGCTGCTAAAGGTCTTGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGTTCTA
*
39555165 TAGCAGCGTTT
1 TAGCGGCGTTT
39555176 ATTTCTAAAA
Statistics
Matches: 201, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 201 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.31
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGTTCTA
Found at i:39555003 original size:115 final size:115
Alignment explanation
Indices: 39554790--39555005 Score: 288
Period size: 115 Copynumber: 1.9 Consensus size: 115
39554780 TGTCTTGTTC
* ** * *
39554790 TTTAGCGGAGTTTGTGGGAAAAGCGCTGCTAAAGGTCTTGTTTTTTAGCGGCGTTTATGGGAAAA
1 TTTAGCAGAGTTTGTGGGAAAAGCGCCACTAAAGGTCTTGTTCTATAGCGGCGTTTATGGGAAAA
* * * *
39554855 GCGCCGCTAAAGGTCTTGTTCTATAACGGCGTTTGTATCATTTAGCGGCG
66 GCGACGCTAAAGGTCATGATCTATAACGACGTTTGTATCATTTAGCGGCG
* *
39554905 TTTAGCAGCGTTTGTGGGAAAAGCGCCACTAAAGGTCTTGTTCTATAGCGGCGTTTGTGGGAAAA
1 TTTAGCAGAGTTTGTGGGAAAAGCGCCACTAAAGGTCTTGTTCTATAGCGGCGTTTATGGGAAAA
* * * * *
39554970 GTGATGCTAAATGTCATGATCTTTAGCGACGTTTGT
66 GCGACGCTAAAGGTCATGATCTATAACGACGTTTGT
39555006 GGGAAAAGCG
Statistics
Matches: 85, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
115 85 1.00
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (115 bp):
TTTAGCAGAGTTTGTGGGAAAAGCGCCACTAAAGGTCTTGTTCTATAGCGGCGTTTATGGGAAAA
GCGACGCTAAAGGTCATGATCTATAACGACGTTTGTATCATTTAGCGGCG
Found at i:39558448 original size:18 final size:19
Alignment explanation
Indices: 39558420--39558455 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
39558410 AGTACCTGAT
39558420 TAGTAATCAGTAACAGTAG
1 TAGTAATCAGTAACAGTAG
39558439 TAGTAA-CAGTAACAGTA
1 TAGTAATCAGTAACAGTA
39558456 TTCAACACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.25
Consensus pattern (19 bp):
TAGTAATCAGTAACAGTAG
Found at i:39558509 original size:45 final size:45
Alignment explanation
Indices: 39558447--39558653 Score: 326
Period size: 45 Copynumber: 4.6 Consensus size: 45
39558437 AGTAGTAACA
** *
39558447 GTAACAGTATTCAACACACAAAGTGCTGAATCT-GTAACAGTAATG
1 GTAACAGTATTTGACACACAAAGTGCCGAAT-TGGTAACAGTAATG
39558492 GTAACAGTATTTGACACACAAAGTGCCGAATTGGTAACAGTAATG
1 GTAACAGTATTTGACACACAAAGTGCCGAATTGGTAACAGTAATG
39558537 GTAACAGTATTTGACACACAAAGTGCCGAATTGGTAACAGTAATG
1 GTAACAGTATTTGACACACAAAGTGCCGAATTGGTAACAGTAATG
* **
39558582 GTAACAGTATTTGACACACAAAGTGCCGAATCGGTAACAGTAACA
1 GTAACAGTATTTGACACACAAAGTGCCGAATTGGTAACAGTAATG
* *
39558627 GTAACAATATTCGACACACAAAGTGCC
1 GTAACAGTATTTGACACACAAAGTGCC
39558654 AAATCGATAA
Statistics
Matches: 153, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
44 1 0.01
45 152 0.99
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (45 bp):
GTAACAGTATTTGACACACAAAGTGCCGAATTGGTAACAGTAATG
Found at i:39558659 original size:45 final size:45
Alignment explanation
Indices: 39558440--39558674 Score: 317
Period size: 45 Copynumber: 5.2 Consensus size: 45
39558430 TAACAGTAGT
** * *
39558440 AGTAACAGTAACAGTATTCAACACACAAAGTGCTGAATCTGTAAC
1 AGTAACAGTAACAGTATTTGACACACAAAGTGCCGAATCGGTAAC
** *
39558485 AGTAATGGTAACAGTATTTGACACACAAAGTGCCGAATTGGTAAC
1 AGTAACAGTAACAGTATTTGACACACAAAGTGCCGAATCGGTAAC
** *
39558530 AGTAATGGTAACAGTATTTGACACACAAAGTGCCGAATTGGTAAC
1 AGTAACAGTAACAGTATTTGACACACAAAGTGCCGAATCGGTAAC
**
39558575 AGTAATGGTAACAGTATTTGACACACAAAGTGCCGAATCGGTAAC
1 AGTAACAGTAACAGTATTTGACACACAAAGTGCCGAATCGGTAAC
* * * * *
39558620 AGTAACAGTAACAATATTCGACACACAAAGTGCCAAATCGATAAT
1 AGTAACAGTAACAGTATTTGACACACAAAGTGCCGAATCGGTAAC
39558665 AGTAACAGTA
1 AGTAACAGTA
39558675 GTCGGCATAT
Statistics
Matches: 175, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 175 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (45 bp):
AGTAACAGTAACAGTATTTGACACACAAAGTGCCGAATCGGTAAC
Found at i:39562351 original size:23 final size:23
Alignment explanation
Indices: 39562318--39562364 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
39562308 GAATAAACTT
39562318 TTTTTTAAAATTTTATTAAGATTA
1 TTTTTTAAAATTTTATTAA-ATTA
39562342 TTTTTT-AAATTTTATTAAATTA
1 TTTTTTAAAATTTTATTAAATTA
39562364 T
1 T
39562365 ATATAGCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 5 0.22
23 12 0.52
24 6 0.26
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTTTTAAAATTTTATTAAATTA
Found at i:39582125 original size:29 final size:29
Alignment explanation
Indices: 39582087--39582150 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
39582077 AATTTTTTGG
*
39582087 ATTAATGATAACAACTTAATTGAGTGTGA
1 ATTAAGGATAACAACTTAATTGAGTGTGA
39582116 ATTAAGGATAACAACTTAATTGAGTGTGA
1 ATTAAGGATAACAACTTAATTGAGTGTGA
39582145 ATTAAG
1 ATTAAG
39582151 TTGAAGGGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (29 bp):
ATTAAGGATAACAACTTAATTGAGTGTGA
Found at i:39583894 original size:20 final size:20
Alignment explanation
Indices: 39583846--39583897 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
39583836 TTTTCTAATT
*
39583846 TATGCATTTTTATAATTCTTG
1 TATG-ATTTTTATAATTCTTA
* * *
39583867 TATAATTTTTATACTTTTTA
1 TATGATTTTTATAATTCTTA
39583887 TATGATTTTTA
1 TATGATTTTTA
39583898 ATAAAAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.62
Consensus pattern (20 bp):
TATGATTTTTATAATTCTTA
Found at i:39584231 original size:31 final size:29
Alignment explanation
Indices: 39584137--39584234 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 29
39584127 TACACCGTGC
* *
39584137 CTTAATTGATTGAAATTTTAACTACAACA
1 CTTAATTGATTGAAATTTTAACTTCAAGA
* * *
39584166 ATTAACTG-TT--AACTTTAACTATCAAAGA
1 CTTAATTGATTGAAATTTTAACT-TC-AAGA
39584194 GCTTAATTGATTGAAATTTTAACATTCAAGGA
1 -CTTAATTGATTGAAATTTTAAC-TTCAA-GA
39584226 CTTAATTGA
1 CTTAATTGA
39584235 ATTTTTTTGA
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
26 9 0.17
27 1 0.02
28 5 0.09
29 12 0.23
30 2 0.04
31 11 0.21
32 12 0.23
33 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (29 bp):
CTTAATTGATTGAAATTTTAACTTCAAGA
Found at i:39594025 original size:3 final size:3
Alignment explanation
Indices: 39594017--39594061 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
39594007 CGAGTATATG
39594017 TAT TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39594062 GTTTATCTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 1 0.03
3 38 0.95
4 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:39597159 original size:11 final size:11
Alignment explanation
Indices: 39597140--39597183 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
39597130 ATGAAGAAAT
*
39597140 TTTTTTTAAAA
1 TTTTATTAAAA
39597151 TTTTATTAAGAAA
1 TTTTATT-A-AAA
39597164 TTTT-TTAAAA
1 TTTTATTAAAA
39597174 TTTTATTAAA
1 TTTTATTAAA
39597184 TTATATATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
10 7 0.24
11 12 0.41
12 3 0.10
13 7 0.24
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTTATTAAAA
Found at i:39597185 original size:10 final size:10
Alignment explanation
Indices: 39597141--39597183 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 10
39597131 TGAAGAAATT
39597141 TTTTTTAAAA
1 TTTTTTAAAA
39597151 TTTTATTAAGAAA
1 TTTT-TT-A-AAA
39597164 TTTTTTAAAA
1 TTTTTTAAAA
39597174 TTTTATTAAA
1 TTTT-TTAAA
39597184 TTATATATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 11 0.38
11 8 0.28
12 3 0.10
13 7 0.24
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (10 bp):
TTTTTTAAAA
Found at i:39598443 original size:126 final size:126
Alignment explanation
Indices: 39598195--39598436 Score: 439
Period size: 126 Copynumber: 1.9 Consensus size: 126
39598185 GATGAGAAAT
* * *
39598195 AGTGTAGAGAAAGAAAATAAGGGTGTTATAAACATGGTAATAAACATCCTGTATTAAAACAGTTT
1 AGTGTAAAGAAAGAAAATAAGGGTGTTATAAACATGGTAATAAACATACTGTACTAAAACAGTTT
*
39598260 TTGACAGCAACAGTAGGCTCACTTTGAAAAATCACCATAAATTATGAAAATAAAATTACAC
66 TGGACAGCAACAGTAGGCTCACTTTGAAAAATCACCATAAATTATGAAAATAAAATTACAC
*
39598321 AGTGTAAAGAAAGAAAATAAGGGTGTTATAAACATGGTAATAAACATATTGTACTAAAACAGTTT
1 AGTGTAAAGAAAGAAAATAAGGGTGTTATAAACATGGTAATAAACATACTGTACTAAAACAGTTT
39598386 TGGACAGCAACAGTAGGCTCACTTTGAAAAATCACCATAAATTATGAAAAT
66 TGGACAGCAACAGTAGGCTCACTTTGAAAAATCACCATAAATTATGAAAAT
39598437 CGAATTAGAG
Statistics
Matches: 111, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
126 111 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (126 bp):
AGTGTAAAGAAAGAAAATAAGGGTGTTATAAACATGGTAATAAACATACTGTACTAAAACAGTTT
TGGACAGCAACAGTAGGCTCACTTTGAAAAATCACCATAAATTATGAAAATAAAATTACAC
Found at i:39603068 original size:46 final size:46
Alignment explanation
Indices: 39602997--39603085 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
39602987 NNNNNNNNNN
* *
39602997 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTAAG
1 TTGTGAAAAGTAGGTATGGTATTTCAAGGAAGAAAACCATACTAAG
39603043 TTGTGAAAAGTAGGTATGGTATTTCAAGGAAGAAAACCATACT
1 TTGTGAAAAGTAGGTATGGTATTTCAAGGAAGAAAACCATACT
39603086 GAATTATAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.28
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTATTTCAAGGAAGAAAACCATACTAAG
Found at i:39605377 original size:13 final size:13
Alignment explanation
Indices: 39605361--39605385 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39605351 TGCTGTGGAA
39605361 AAGTACTTTTGAG
1 AAGTACTTTTGAG
39605374 AAGTACTTTTGA
1 AAGTACTTTTGA
39605386 AAATTTTGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
AAGTACTTTTGAG
Found at i:39606967 original size:43 final size:43
Alignment explanation
Indices: 39606919--39607074 Score: 177
Period size: 43 Copynumber: 3.6 Consensus size: 43
39606909 TTATGTGAAA
* * ** *
39606919 AAACGCCGCTAATGATCATGGCCTTTAGTGGCACTTCTATCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGTAACACTTCTACCAC
* * *
39606962 AAACGCCGCTAAAGATTATGACGTTTAGTAACGCTTCTACCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGTAACACTTCTACCAC
** ** *
39607005 AAACGCCGCTAAAGATCATGACCTTTAGCGATGCTTCTACCAA
1 AAACGCCGCTAAAGATCATGACCTTTAGTAACACTTCTACCAC
* *
39607048 AAATGCCGCTAAAGACCATGACCTTTA
1 AAACGCCGCTAAAGATCATGACCTTTA
39607075 ACTGCGCTTC
Statistics
Matches: 97, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 97 1.00
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGACCTTTAGTAACACTTCTACCAC
Found at i:39607069 original size:86 final size:86
Alignment explanation
Indices: 39606919--39607094 Score: 210
Period size: 86 Copynumber: 2.0 Consensus size: 86
39606909 TTATGTGAAA
* * * * * * **
39606919 AAACGCCGCTAATGATCATGGCCTTTAGTGGCACTTCTATCACAAACGCCGCTAAAGATTATGAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGACACTTCTACCAAAAACGCCGCTAAAGACCATGAC
* *
39606984 GTTT-AGTAACGCTTCTACCAC
66 CTTTAACT-ACGCTTCTACCAC
** *
39607005 AAACGCCGCTAAAGATCATGACCTTTAGCGATGCTTCTACCAAAAATGCCGCTAAAGACCATGAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGACACTTCTACCAAAAACGCCGCTAAAGACCATGAC
*
39607070 CTTTAACTGCGCTTCTACCAC
66 CTTTAACTACGCTTCTACCAC
39607091 AAAC
1 AAAC
39607095 ATCGCTATAA
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
86 73 0.97
87 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.24
Consensus pattern (86 bp):
AAACGCCGCTAAAGATCATGACCTTTAGCGACACTTCTACCAAAAACGCCGCTAAAGACCATGAC
CTTTAACTACGCTTCTACCAC
Found at i:39607084 original size:43 final size:43
Alignment explanation
Indices: 39606917--39607094 Score: 151
Period size: 43 Copynumber: 4.1 Consensus size: 43
39606907 GTTTATGTGA
* * * ** * * *
39606917 AAAAACGCCGCTAATGATCATGGCCTTTAGTGGCACTTCTATC
1 AAAAACGCCGCTAAAGACCATGACCTTTAACGACGCTTCTACC
* ** * ***
39606960 ACAAACGCCGCTAAAGATTATGACGTTTAGTAACGCTTCTACC
1 AAAAACGCCGCTAAAGACCATGACCTTTAACGACGCTTCTACC
* * * *
39607003 ACAAACGCCGCTAAAGATCATGACCTTTAGCGATGCTTCTACC
1 AAAAACGCCGCTAAAGACCATGACCTTTAACGACGCTTCTACC
*
39607046 AAAAATGCCGCTAAAGACCATGACCTTTAACTG-CGCTTCTACC
1 AAAAACGCCGCTAAAGACCATGACCTTTAAC-GACGCTTCTACC
*
39607089 ACAAAC
1 AAAAAC
39607095 ATCGCTATAA
Statistics
Matches: 113, Mismatches: 21, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
43 112 0.99
44 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGACCATGACCTTTAACGACGCTTCTACC
Found at i:39613139 original size:14 final size:14
Alignment explanation
Indices: 39613122--39613173 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
39613112 AAACCCCAAC
39613122 CCCTAAACCATAAT
1 CCCTAAACCATAAT
*
39613136 CCCTAATCCATAAT
1 CCCTAAACCATAAT
* *
39613150 TCCTAAATCCATACT
1 CCCTAAA-CCATAAT
39613165 CCCTAAACC
1 CCCTAAACC
39613174 TTAAAATAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.37, C:0.38, G:0.00, T:0.25
Consensus pattern (14 bp):
CCCTAAACCATAAT
Found at i:39613160 original size:15 final size:15
Alignment explanation
Indices: 39613122--39613171 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
39613112 AAACCCCAAC
39613122 CCCTAAA-CCATAAT
1 CCCTAAATCCATAAT
39613136 CCCT-AATCCATAAT
1 CCCTAAATCCATAAT
* *
39613150 TCCTAAATCCATACT
1 CCCTAAATCCATAAT
39613165 CCCTAAA
1 CCCTAAA
39613172 CCTTAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 2 0.06
14 14 0.45
15 15 0.48
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.26
Consensus pattern (15 bp):
CCCTAAATCCATAAT
Found at i:39613583 original size:40 final size:42
Alignment explanation
Indices: 39613515--39613627 Score: 135
Period size: 40 Copynumber: 2.8 Consensus size: 42
39613505 TAAAATGTTT
* * * * *
39613515 TTAGCCGCGCTTTTTCAAAAACGCCGCTAAAGGC-CCTAGCA
1 TTAGCGGCGCATTTTAAAAAACGCCGCTAAAGACACCGAGCA
39613556 TTAGCGGCGC-TTTTAAAAAACGCCGCTAAA-ACACCGAGCA
1 TTAGCGGCGCATTTTAAAAAACGCCGCTAAAGACACCGAGCA
*
39613596 TTAGCGACGCATTTTCAAAAAAC-CCGCTAAAG
1 TTAGCGGCGCATTTT-AAAAAACGCCGCTAAAG
39613628 CCCCGAAAGG
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
39 1 0.02
40 34 0.54
41 21 0.33
42 7 0.11
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (42 bp):
TTAGCGGCGCATTTTAAAAAACGCCGCTAAAGACACCGAGCA
Found at i:39614170 original size:72 final size:72
Alignment explanation
Indices: 39614037--39614275 Score: 376
Period size: 72 Copynumber: 3.3 Consensus size: 72
39614027 AAAATCATAT
39614037 ATAAACAACTATTGATAAAACTA-ATT-TAGTATAAATAAGTAGAACATAAATTCAATATCCAAA
1 ATAAACAACTATTGATAAAACTAGATTATA-TATAAATAAGTAGAACATAAATTCAATATCCAAA
*
39614100 GACCAAAC
65 AACCAAAC
* *
39614108 ATAAACAACTATTAATAAAACTAGATTATACCATAAATAAG-AGAACATAAATTCAATATCCAAA
1 ATAAACAACTATTGATAAAACTAGATTATA-TATAAATAAGTAGAACATAAATTCAATATCCAAA
39614172 AACCAAAC
65 AACCAAAC
* * *
39614180 ATAAACGACCATTGATAAAACTAGATTACATATAAATAAGTAGAACATAAATTCAATATCCAAAA
1 ATAAACAACTATTGATAAAACTAGATTATATATAAATAAGTAGAACATAAATTCAATATCCAAAA
39614245 ACCAAAC
66 ACCAAAC
*
39614252 ATAAATAACTATTGATAAAACTAG
1 ATAAACAACTATTGATAAAACTAG
39614276 TTTAGCATTG
Statistics
Matches: 153, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
71 31 0.20
72 111 0.73
73 11 0.07
ACGTcount: A:0.55, C:0.15, G:0.06, T:0.24
Consensus pattern (72 bp):
ATAAACAACTATTGATAAAACTAGATTATATATAAATAAGTAGAACATAAATTCAATATCCAAAA
ACCAAAC
Found at i:39615903 original size:3 final size:3
Alignment explanation
Indices: 39615895--39615944 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
39615885 TCATTTTACA
* * * *
39615895 TAT TAT TAT TAC TAT TA- TAT TA- TAT TAT TAT AAA TAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39615941 TAT T
1 TAT T
39615945 TACTCAACTA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:39620588 original size:11 final size:12
Alignment explanation
Indices: 39620566--39620610 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
39620556 AGAATGTTAA
39620566 AAAAAAGAAAAG
1 AAAAAAGAAAAG
39620578 AAAAAAG-AAAG
1 AAAAAAGAAAAG
*
39620589 GAAAAAGAAAAG
1 AAAAAAGAAAAG
39620601 AAAAGAAGAA
1 AAAA-AAGAA
39620611 TGAGAGGCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 10 0.34
12 14 0.48
13 5 0.17
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:39621090 original size:107 final size:107
Alignment explanation
Indices: 39620873--39621092 Score: 300
Period size: 107 Copynumber: 2.1 Consensus size: 107
39620863 GGGGCACCTG
* * *
39620873 TTTTCATCTTATTCATTTCGTATCTTAGAAAAATTTGCTATCTTGATTATTTATTTATTTCGAGC
1 TTTTCATCTTATTCATTTCGAATCTTAGAAAAATTTGCTATCCTGATTATTTATTTATTTAGAGC
* **
39620938 TTTGTTCTCAATAAAATTCCATCTTATCCATTGTAATAATCC
66 TCTACTCTCAATAAAATTCCATCTTATCCATTGTAATAATCC
* * * *
39620980 TTTTCATCTTATTCATTTTGAATCTTAGCAAAATTTTCTATCCTGATTAATTTATTTGTTTAGAG
1 TTTTCATCTTATTCATTTCGAATCTTAGAAAAATTTGCTATCCTGATT-ATTTATTTATTTAGAG
* *
39621045 CTCTACTCTCAATAAAATTTCATCTT-TCCCATTGTGATAAT-C
65 CTCTACTCTCAATAAAATTCCATCTTAT-CCATTGTAATAATCC
39621087 TTTTCA
1 TTTTCA
39621093 AGCATTTTCC
Statistics
Matches: 99, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
107 51 0.52
108 48 0.48
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.49
Consensus pattern (107 bp):
TTTTCATCTTATTCATTTCGAATCTTAGAAAAATTTGCTATCCTGATTATTTATTTATTTAGAGC
TCTACTCTCAATAAAATTCCATCTTATCCATTGTAATAATCC
Found at i:39622136 original size:44 final size:44
Alignment explanation
Indices: 39622086--39622220 Score: 105
Period size: 44 Copynumber: 3.0 Consensus size: 44
39622076 TAGATCTCAT
39622086 CTTCCTGTACTGGCAGCGAAGCAGATTGAAGACACAAGCCTAAC
1 CTTCCTGTACTGGCAGCGAAGCAGATTGAAGACACAAGCCTAAC
* * * * * * ***
39622130 CTTCCTG-AGTTTGCAGCGGAGCAGACT-AAAAGCAGC-AGATCTCGT
1 CTTCCTGTA-CTGGCAGCGAAGCAGATTGAAGA-CA-CAAG-CCTAAC
* * *
39622175 CTTCCTGTACTGGCAGTGAAGCAGATCGAAGACACAAGCCTGAC
1 CTTCCTGTACTGGCAGCGAAGCAGATTGAAGACACAAGCCTAAC
39622219 CT
1 CT
39622221 CTCTGAGTTT
Statistics
Matches: 64, Mismatches: 20, Indels: 14
0.65 0.20 0.14
Matches are distributed among these distances:
43 4 0.06
44 30 0.47
45 26 0.41
46 4 0.06
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (44 bp):
CTTCCTGTACTGGCAGCGAAGCAGATTGAAGACACAAGCCTAAC
Found at i:39622304 original size:89 final size:89
Alignment explanation
Indices: 39621975--39622293 Score: 460
Period size: 89 Copynumber: 3.6 Consensus size: 89
39621965 CAGAGGAATG
* * * *
39621975 GACTAAAAGCAGCAGATCTCGTCTTTCTGTACCGACAGCGAAGCAGATCGAAAACACAAGCCTGA
1 GACTAAAAGCAGCAGATCTCGTCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACAAGCCTGA
* * *
39622040 CCTCCCTGAGTTTGCAGCAGAACA
66 CCTCTCTGAGTTTGCAGCGGAGCA
* * * * *
39622064 AACTAAAAGCAGTAGATCTCATCTTCCTGTACTGGCAGCGAAGCAGATTGAAGACACAAGCCTAA
1 GACTAAAAGCAGCAGATCTCGTCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACAAGCCTGA
39622129 CCT-TCCTGAGTTTGCAGCGGAGCA
66 CCTCT-CTGAGTTTGCAGCGGAGCA
*
39622153 GACTAAAAGCAGCAGATCTCGTCTTCCTGTACTGGCAGTGAAGCAGATCGAAGACACAAGCCTGA
1 GACTAAAAGCAGCAGATCTCGTCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACAAGCCTGA
*
39622218 CCTCTCTGAGTTTGCAGCGGAGTA
66 CCTCTCTGAGTTTGCAGCGGAGCA
* * * *
39622242 GACTAAGAGTAGCAGATCTCGTCTTTCTGTACTGGCAGTGAAGCAGATCGAA
1 GACTAAAAGCAGCAGATCTCGTCTTCCTGTACTGGCAGCGAAGCAGATCGAA
39622294 AGCACTAGCC
Statistics
Matches: 206, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
89 205 1.00
90 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.24, T:0.21
Consensus pattern (89 bp):
GACTAAAAGCAGCAGATCTCGTCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACAAGCCTGA
CCTCTCTGAGTTTGCAGCGGAGCA
Found at i:39622829 original size:44 final size:44
Alignment explanation
Indices: 39622755--39622844 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
39622745 TGGAAGCTAT
* * * * *
39622755 AAATTACAAACCCTGTCTCTCTGAAGTTGCAGTAGAGTAGATTG
1 AAATAACAAACCCTATCTCTCTAAAATTGCAGTAGAGCAGATTG
* *
39622799 AAATAACAAACCTTATCTCTCTAAAATTGCAGTAGAGCAGGTTG
1 AAATAACAAACCCTATCTCTCTAAAATTGCAGTAGAGCAGATTG
39622843 AA
1 AA
39622845 GTTACTAACA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.28
Consensus pattern (44 bp):
AAATAACAAACCCTATCTCTCTAAAATTGCAGTAGAGCAGATTG
Done.