Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 33 of 45
Found at i:5829155 original size:16 final size:16
Alignment explanation
Indices: 5829134--5829179 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
5829124 TTATGAATTT
5829134 TTTTAAATTTAGATTA
1 TTTTAAATTTAGATTA
*
5829150 TTTTAAATTTTGATTA
1 TTTTAAATTTAGATTA
* *
5829166 GTTCAAATTTAGAT
1 TTTTAAATTTAGAT
5829180 GAGTTTTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.54
Consensus pattern (16 bp):
TTTTAAATTTAGATTA
Found at i:5829184 original size:16 final size:16
Alignment explanation
Indices: 5829138--5829184 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
5829128 GAATTTTTTT
* *
5829138 AAATTTAGATTATTTT
1 AAATTTAGATTAGTTC
*
5829154 AAATTTTGATTAGTTC
1 AAATTTAGATTAGTTC
*
5829170 AAATTTAGATGAGTT
1 AAATTTAGATTAGTT
5829185 TTGAAGAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (16 bp):
AAATTTAGATTAGTTC
Found at i:5830230 original size:125 final size:127
Alignment explanation
Indices: 5830097--5830341 Score: 307
Period size: 125 Copynumber: 1.9 Consensus size: 127
5830087 TTATTTATGT
* * ** * *
5830097 ATATTATTAATATTTAATTTTATGTAG-TCATTATATACTTCATGTTACTATATTGCTATATAAA
1 ATATTATTAATATTTAAGTTTAT-AAGATCACCATATACTTCATGCTACTATATTACTATATAAA
* * * *
5830161 TATTAATT-TT-TATTATTAAATTATAATGGTAATATATTTAGTCCATATTTAGTACATGCAG
65 TATTAATTGTTATATTACTAAATTATAATAGTAATAAATTTACTCCATATTTAGTACATGCAG
* * * * *
5830222 ATATTATTAATATTTAAGTTTATAAGATTACCATATACTTCGTGCTATTATATTATTGTATAAAT
1 ATATTATTAATATTTAAGTTTATAAGATCACCATATACTTCATGCTACTATATTACTATATAAAT
* *
5830287 ATTAATTGTTATATTACTAAATTATACTATTAATAAATTTACTCCATATTTAGTA
66 ATTAATTGTTATATTACTAAATTATAATAGTAATAAATTTACTCCATATTTAGTA
5830342 TATGTAACAC
Statistics
Matches: 100, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
124 2 0.02
125 58 0.58
126 2 0.02
127 38 0.38
ACGTcount: A:0.37, C:0.08, G:0.07, T:0.48
Consensus pattern (127 bp):
ATATTATTAATATTTAAGTTTATAAGATCACCATATACTTCATGCTACTATATTACTATATAAAT
ATTAATTGTTATATTACTAAATTATAATAGTAATAAATTTACTCCATATTTAGTACATGCAG
Found at i:5830591 original size:20 final size:20
Alignment explanation
Indices: 5830568--5830606 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5830558 CATTTAACAC
*
5830568 AATATTATAATATAAAATAT
1 AATATGATAATATAAAATAT
*
5830588 AATATGATAATATTAAATA
1 AATATGATAATATAAAATA
5830607 AAGTATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
AATATGATAATATAAAATAT
Found at i:5830784 original size:14 final size:15
Alignment explanation
Indices: 5830759--5830792 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5830749 GTGTAAAAAG
5830759 AAAATTGAAAAGATA
1 AAAATTGAAAAGATA
*
5830774 AAAATTG-AAAGATG
1 AAAATTGAAAAGATA
5830788 AAAAT
1 AAAAT
5830793 AGTGAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.21
Consensus pattern (15 bp):
AAAATTGAAAAGATA
Found at i:5836104 original size:19 final size:19
Alignment explanation
Indices: 5836064--5836125 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
5836054 ATAATAATTA
*
5836064 TAAATATATT-TTCATAAAT
1 TAAATAT-TTATTTATAAAT
*
5836083 T-AATATTTTATTTATAATT
1 TAAATA-TTTATTTATAAAT
5836102 TAAATATTTATTT-TAAAT
1 TAAATATTTATTTATAAAT
*
5836120 AAAATA
1 TAAATA
5836126 ATATAATTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
18 15 0.42
19 17 0.47
20 4 0.11
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TAAATATTTATTTATAAAT
Found at i:5836109 original size:20 final size:20
Alignment explanation
Indices: 5836057--5836114 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
5836047 TAATTGTATA
* *
5836057 ATAATTATAAATATATT-TTC
1 ATAATT-TAAATATTTTATTT
*
5836077 ATAAATT-AATATTTTATTT
1 ATAATTTAAATATTTTATTT
5836096 ATAATTTAAATA-TTTATTT
1 ATAATTTAAATATTTTATTT
5836115 TAAATAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 7 0.22
19 16 0.50
20 9 0.28
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
ATAATTTAAATATTTTATTT
Found at i:5836116 original size:20 final size:20
Alignment explanation
Indices: 5836057--5836116 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
5836047 TAATTGTATA
5836057 ATAATTATAAATA--TATTTT
1 ATAATT-TAAATATTTATTTT
*
5836076 CATAAATT-AATATTT-TATTT
1 -ATAATTTAAATATTTAT-TTT
5836096 ATAATTTAAATATTTATTTT
1 ATAATTTAAATATTTATTTT
5836116 A
1 A
5836117 AATAAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
18 4 0.12
19 8 0.24
20 20 0.61
21 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
ATAATTTAAATATTTATTTT
Found at i:5836410 original size:69 final size:69
Alignment explanation
Indices: 5836335--5836464 Score: 172
Period size: 69 Copynumber: 1.9 Consensus size: 69
5836325 CTTTTGATTT
* * *
5836335 TTTAAGTCATTTAGAT-TGAATCAAATTCGATTTTAAATCAGCTCAAGAAGACTTTCAAGTTCGA
1 TTTAAGTCATTCAGATCAG-ATCAAATTCGATCTTAAATCAGCTCAAGAAGACTTTCAAGTTCGA
5836399 GCTAC
65 GCTAC
* * * * *
5836404 TTTAAGTCATTCAGATCAGATCAAATTTGATCTTAGATCGGTTCAAGAAGGCTTTCAAGTT
1 TTTAAGTCATTCAGATCAGATCAAATTCGATCTTAAATCAGCTCAAGAAGACTTTCAAGTT
5836465 TAGGCTTACT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
69 51 0.98
70 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (69 bp):
TTTAAGTCATTCAGATCAGATCAAATTCGATCTTAAATCAGCTCAAGAAGACTTTCAAGTTCGAG
CTAC
Found at i:5836583 original size:29 final size:29
Alignment explanation
Indices: 5836520--5836584 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
5836510 AGTTCTGTTA
* * *
5836520 ATTTTTAAATAAATTATCAAAATAATATT
1 ATTTTAAAATAAATTACCAAAATAATACT
* *
5836549 AATTTAAAATAAATTACCAAAATATTACT
1 ATTTTAAAATAAATTACCAAAATAATACT
5836578 ATTTTAA
1 ATTTTAA
5836585 TACGCAAGGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (29 bp):
ATTTTAAAATAAATTACCAAAATAATACT
Found at i:5838124 original size:30 final size:31
Alignment explanation
Indices: 5838070--5838128 Score: 77
Period size: 29 Copynumber: 1.9 Consensus size: 31
5838060 TTTCGGTAAA
*
5838070 ATAATTATTTTACTATAGTTATTTTTATTTTTT
1 ATAATTA-TTTACTATAATTA-TTTTATTTTTT
5838103 ATAATTA-TTAC-ATAATTATTTTATTT
1 ATAATTATTTACTATAATTATTTTATTT
5838129 AAACAAGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 8 0.32
30 6 0.24
31 4 0.16
33 7 0.28
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (31 bp):
ATAATTATTTACTATAATTATTTTATTTTTT
Found at i:5840102 original size:2 final size:2
Alignment explanation
Indices: 5840097--5840127 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5840087 CGTGTGTGTG
*
5840097 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5840128 CCAACTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:5843568 original size:25 final size:25
Alignment explanation
Indices: 5843540--5843591 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
5843530 AAAATCAAAT
*
5843540 AATTTT-TTATTTAATATAATTAATA
1 AATTTTATTATATAATA-AATTAATA
*
5843565 AATTTTATTATATAATAAATTAGTA
1 AATTTTATTATATAATAAATTAATA
5843590 AA
1 AA
5843592 CATATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
AATTTTATTATATAATAAATTAATA
Found at i:5843807 original size:26 final size:26
Alignment explanation
Indices: 5843763--5843823 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
5843753 TTTTAATATG
*
5843763 TATTTT-AGTATTTAATATA-A-ATA
1 TATTTTAATTATTTAATATATACATA
*
5843786 TAATTTTTAATTATTTATTATATACATA
1 T-A-TTTTAATTATTTAATATATACATA
5843814 TATTTTAATT
1 TATTTTAATT
5843824 TAATATCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
23 1 0.03
24 1 0.03
25 4 0.13
26 19 0.61
27 2 0.06
28 4 0.13
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (26 bp):
TATTTTAATTATTTAATATATACATA
Found at i:5845427 original size:2 final size:2
Alignment explanation
Indices: 5845420--5845454 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5845410 CTTTGGTCCC
*
5845420 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5845455 GAGGATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5845840 original size:14 final size:14
Alignment explanation
Indices: 5845821--5845870 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
5845811 AGTTAATATT
*
5845821 TAAAAAGATTTAAA
1 TAAAAATATTTAAA
5845835 TAAAAATA-TTAAA
1 TAAAAATATTTAAA
5845848 TTAAAAATATATTTAAA
1 -T-AAAA-ATATTTAAA
5845865 TAAAAA
1 TAAAAA
5845871 ATAAAAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
13 5 0.16
14 9 0.29
15 8 0.26
16 4 0.13
17 5 0.16
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (14 bp):
TAAAAATATTTAAA
Found at i:5845865 original size:17 final size:17
Alignment explanation
Indices: 5845828--5845873 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
5845818 ATTTAAAAAG
5845828 ATTTAAA-T-AAAA-AT
1 ATTTAAATTAAAAATAT
5845842 A-TTAAATTAAAAATAT
1 ATTTAAATTAAAAATAT
*
5845858 ATTTAAATAAAAAATA
1 ATTTAAATTAAAAATA
5845874 AAAATTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.19
14 2 0.07
15 4 0.15
16 3 0.11
17 13 0.48
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAATTAAAAATAT
Found at i:5845865 original size:24 final size:22
Alignment explanation
Indices: 5845838--5845898 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
5845828 ATTTAAATAA
5845838 AAATATTAAATTAAAAATATATTT
1 AAATA-TAAATTAAAAAT-TATTT
* *
5845862 AAATAAAAAATAAAAATTATTT
1 AAATATAAATTAAAAATTATTT
*
5845884 AAAAAATAAATTAAA
1 -AAATATAAATTAAA
5845899 CTTTAATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 5 0.16
23 21 0.68
24 5 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATATAAATTAAAAATTATTT
Found at i:5845868 original size:16 final size:15
Alignment explanation
Indices: 5845822--5845873 Score: 63
Period size: 16 Copynumber: 3.5 Consensus size: 15
5845812 GTTAATATTT
*
5845822 AAAAAGATTTAAAT-
1 AAAAATATTTAAATA
5845836 AAAAATA-TTAAATTA
1 AAAAATATTTAAA-TA
5845851 AAAATATATTTAAATA
1 AAAA-ATATTTAAATA
5845867 AAAAATA
1 AAAAATA
5845874 AAAATTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
13 5 0.15
14 7 0.21
15 7 0.21
16 9 0.27
17 5 0.15
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (15 bp):
AAAAATATTTAAATA
Found at i:5845882 original size:22 final size:23
Alignment explanation
Indices: 5845835--5845894 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 23
5845825 AAGATTTAAA
5845835 TAAAAATATTAAATTAAAAATATATT
1 TAAAAA-A-TAAA-TAAAAATATATT
5845861 TAAATAAA-AAATAAAAAT-TATT
1 TAAA-AAATAAATAAAAATATATT
5845883 TAAAAAATAAAT
1 TAAAAAATAAAT
5845895 TAAACTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
21 3 0.09
22 12 0.38
23 7 0.22
24 3 0.09
26 5 0.16
27 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
TAAAAAATAAATAAAAATATATT
Found at i:5848466 original size:21 final size:19
Alignment explanation
Indices: 5848442--5848495 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
5848432 GCTCGGTTTA
*
5848442 ATTTTTTCAGTTAGAAATAAT
1 ATTTTTT-AATTA-AAATAAT
5848463 A-TTTTTAATTAAAATAAT
1 ATTTTTTAATTAAAATAAT
*
5848481 ATATTTTTATTTAAA
1 AT-TTTTTAATTAAA
5848496 TTTAATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 8 0.28
19 4 0.14
20 16 0.55
21 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (19 bp):
ATTTTTTAATTAAAATAAT
Found at i:5848467 original size:19 final size:18
Alignment explanation
Indices: 5848440--5848482 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
5848430 TGGCTCGGTT
* *
5848440 TAATTTTTTCAGTTAGAAA
1 TAATATTTTCAATTA-AAA
*
5848459 TAATATTTTTAATTAAAA
1 TAATATTTTCAATTAAAA
5848477 TAATAT
1 TAATAT
5848483 ATTTTTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (18 bp):
TAATATTTTCAATTAAAA
Found at i:5851252 original size:2 final size:2
Alignment explanation
Indices: 5851245--5851291 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
5851235 GAAAAGGTAT
5851245 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5851287 TC TC T
1 TC TC T
5851292 ATGTATATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5852822 original size:2 final size:2
Alignment explanation
Indices: 5852815--5852854 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5852805 TTTCTTCTCT
5852815 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5852855 AAAATCTACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5855194 original size:2 final size:2
Alignment explanation
Indices: 5855189--5855239 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
5855179 ATATATATAT
*
5855189 AG AG AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5855231 AG AG AG AG A
1 AG AG AG AG A
5855240 AAGCGAACAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5855448 original size:12 final size:12
Alignment explanation
Indices: 5855425--5855459 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5855415 TTATGGTGGA
*
5855425 GGATGTGCTGCT
1 GGATGTGGTGCT
*
5855437 GGCTGTGGTGCT
1 GGATGTGGTGCT
5855449 GGATGTGGTGC
1 GGATGTGGTGC
5855460 AGGTTGCGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.14, G:0.49, T:0.31
Consensus pattern (12 bp):
GGATGTGGTGCT
Found at i:5855470 original size:24 final size:24
Alignment explanation
Indices: 5855425--5855470 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
5855415 TTATGGTGGA
* *
5855425 GGATGTGCTGCTGGCTGTGGTGCT
1 GGATGTGCTGCAGGCTGCGGTGCT
* *
5855449 GGATGTGGTGCAGGTTGCGGTG
1 GGATGTGCTGCAGGCTGCGGTG
5855471 GATAACTCCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.07, C:0.13, G:0.50, T:0.30
Consensus pattern (24 bp):
GGATGTGCTGCAGGCTGCGGTGCT
Found at i:5858415 original size:3 final size:3
Alignment explanation
Indices: 5858407--5858442 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
5858397 GAAACGCAAC
*
5858407 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG ATG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
5858443 CATAAAGACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:5858855 original size:24 final size:24
Alignment explanation
Indices: 5858827--5858873 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5858817 AATAATTAAA
*
5858827 TTAATT-TTTATATTTTATTATATT
1 TTAATTATTTAT-TTATATTATATT
*
5858851 TTAATTATTTCTTTATATTATAT
1 TTAATTATTTATTTATATTATAT
5858874 AAATGTGTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (24 bp):
TTAATTATTTATTTATATTATATT
Found at i:5861677 original size:27 final size:28
Alignment explanation
Indices: 5861639--5861691 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
5861629 TTTGAAACCC
5861639 AAACAAATTAAATTAAA-AGTTTAAATT
1 AAACAAATTAAATTAAATAGTTTAAATT
*
5861666 AAACAAATTAAATTAAATATTTTAAA
1 AAACAAATTAAATTAAATAGTTTAAA
5861692 ATAATTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (28 bp):
AAACAAATTAAATTAAATAGTTTAAATT
Found at i:5861678 original size:14 final size:14
Alignment explanation
Indices: 5861639--5861682 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
5861629 TTTGAAACCC
5861639 AAACAAATTAAATT
1 AAACAAATTAAATT
**
5861653 AAA-AGTTTAAATT
1 AAACAAATTAAATT
5861666 AAACAAATTAAATT
1 AAACAAATTAAATT
5861680 AAA
1 AAA
5861683 TATTTTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (14 bp):
AAACAAATTAAATT
Found at i:5861786 original size:27 final size:26
Alignment explanation
Indices: 5861756--5861811 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
5861746 AAAATAATTT
5861756 TTTACAATAATAAAAACTATTATTATA
1 TTTACAATAATAAAAACTATTATTA-A
* * * *
5861783 TTTATAATAATATAATCTTTTATTAA
1 TTTACAATAATAAAAACTATTATTAA
5861809 TTT
1 TTT
5861812 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTACAATAATAAAAACTATTATTAA
Found at i:5863158 original size:2 final size:2
Alignment explanation
Indices: 5863147--5863182 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
5863137 AGAAAAAAGC
* *
5863147 CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CC CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5863183 TCCCCTTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (2 bp):
CT
Found at i:5863339 original size:2 final size:2
Alignment explanation
Indices: 5863334--5863364 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5863324 AATATATATT
5863334 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5863365 ACATATTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5864621 original size:2 final size:2
Alignment explanation
Indices: 5864614--5864647 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5864604 AATAAAACAG
5864614 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5864648 GTATTCTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5875137 original size:21 final size:21
Alignment explanation
Indices: 5875112--5875153 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5875102 AATTTGAATT
5875112 ATTATTAATAAATTAATAAAA
1 ATTATTAATAAATTAATAAAA
** *
5875133 ATTATTTTTATATTAATAAAA
1 ATTATTAATAAATTAATAAAA
5875154 TAAATATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTATTAATAAATTAATAAAA
Found at i:5875165 original size:23 final size:21
Alignment explanation
Indices: 5875123--5875165 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
5875113 TTATTAATAA
*
5875123 ATTAATAAAAATTATTTTTAT
1 ATTAATAAAAAATATTTTTAT
5875144 ATTAATAAAATAAATATTTTTA
1 ATTAAT-AAA-AAATATTTTTA
5875166 AATATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 3 0.16
23 10 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTAATAAAAAATATTTTTAT
Found at i:5876476 original size:18 final size:18
Alignment explanation
Indices: 5876449--5876490 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
5876439 TATAAATTTT
*
5876449 AAAAAT-AAATTTAATTA
1 AAAAATAAAATATAATTA
*
5876466 AAAAATAAAATATATTTA
1 AAAAATAAAATATAATTA
5876484 AAAAATA
1 AAAAATA
5876491 CGTTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAATAAAATATAATTA
Found at i:5876579 original size:19 final size:19
Alignment explanation
Indices: 5876552--5876601 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
5876542 TTTTTTTTAA
*
5876552 TTATTAATATATGTTATA-C
1 TTATAAATATAT-TTATATC
5876571 TTATAAATATAATTTATATC
1 TTATAAATAT-ATTTATATC
*
5876591 ATATAAATATA
1 TTATAAATATA
5876602 AATAATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (19 bp):
TTATAAATATATTTATATC
Found at i:5876609 original size:20 final size:20
Alignment explanation
Indices: 5876572--5876609 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5876562 ATGTTATACT
* *
5876572 TATAAATATAATTTATATCA
1 TATAAATATAAATAATATCA
5876592 TATAAATATAAATAATAT
1 TATAAATATAAATAATAT
5876610 TATGATATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TATAAATATAAATAATATCA
Found at i:5880310 original size:5 final size:5
Alignment explanation
Indices: 5880300--5880326 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5880290 GGCACTTGCT
5880300 TAGCC TAGCC TAGCC TAGCC TAGCC TA
1 TAGCC TAGCC TAGCC TAGCC TAGCC TA
5880327 ATCTCCTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (5 bp):
TAGCC
Found at i:5881421 original size:2 final size:2
Alignment explanation
Indices: 5881414--5881445 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5881404 GGGAACTGAA
5881414 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
5881446 GATTGTATGT
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:5887163 original size:12 final size:12
Alignment explanation
Indices: 5887146--5887209 Score: 69
Period size: 12 Copynumber: 5.3 Consensus size: 12
5887136 TAAAAATATG
5887146 AATATAAAATAA
1 AATATAAAATAA
*
5887158 AATAT-AATTAA
1 AATATAAAATAA
*
5887169 TATATAAAATAA
1 AATATAAAATAA
*
5887181 AATATAATATAA
1 AATATAAAATAA
5887193 AA-ATAATAATATA
1 AATATAA-AATA-A
5887206 AATA
1 AATA
5887210 ATATCAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
11 13 0.31
12 25 0.60
13 3 0.07
14 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATATAAAATAA
Found at i:5887198 original size:23 final size:23
Alignment explanation
Indices: 5887140--5887219 Score: 83
Period size: 23 Copynumber: 3.5 Consensus size: 23
5887130 GCGAGTTAAA
* *
5887140 AATATGAATATAAAATAAAATAT
1 AATATAAAAATAAAATAAAATAT
*
5887163 AAT-TAATATATAAAATAAAATAT
1 AATATAA-AAATAAAATAAAATAT
*
5887186 AATATAAAAATAATAATATAA-AT
1 AATATAAAAATAA-AATAAAATAT
*
5887209 AATATCAAAAT
1 AATATAAAAAT
5887220 TTAAGTGATA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
22 2 0.04
23 39 0.78
24 9 0.18
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (23 bp):
AATATAAAAATAAAATAAAATAT
Found at i:5887210 original size:18 final size:18
Alignment explanation
Indices: 5887136--5887210 Score: 84
Period size: 18 Copynumber: 4.2 Consensus size: 18
5887126 TTATGCGAGT
*
5887136 TAAAAATATGAATATAAAA
1 TAAAAATAT-AATATAATA
5887155 T-AAAATATAAT-TAATA
1 TAAAAATATAATATAATA
*
5887171 TATAAAATAAAATATAATA
1 TA-AAAATATAATATAATA
5887190 TAAAAATAATAATATAA-A
1 TAAAAAT-ATAATATAATA
5887208 TAA
1 TAA
5887211 TATCAAAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
16 5 0.10
17 3 0.06
18 25 0.51
19 16 0.33
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (18 bp):
TAAAAATATAATATAATA
Found at i:5887613 original size:13 final size:13
Alignment explanation
Indices: 5887595--5887638 Score: 58
Period size: 12 Copynumber: 3.6 Consensus size: 13
5887585 AAAAATAATT
5887595 ATAATATAAAAAG
1 ATAATATAAAAAG
5887608 ATAATAT-AAAA-
1 ATAATATAAAAAG
*
5887619 ATAATATAAATAG
1 ATAATATAAAAAG
5887632 AT-ATATA
1 ATAATATA
5887639 GTTAAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 7 0.25
12 12 0.43
13 9 0.32
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (13 bp):
ATAATATAAAAAG
Found at i:5887622 original size:11 final size:12
Alignment explanation
Indices: 5887595--5887638 Score: 56
Period size: 11 Copynumber: 3.7 Consensus size: 12
5887585 AAAAATAATT
5887595 ATAATATAAAAAG
1 ATAATAT-AAAAG
5887608 ATAATATAAAA-
1 ATAATATAAAAG
5887619 ATAATATAAATAG
1 ATAATATAAA-AG
5887632 AT-ATATA
1 ATAATATA
5887639 GTTAAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 10 0.34
12 10 0.34
13 9 0.31
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (12 bp):
ATAATATAAAAG
Found at i:5889843 original size:16 final size:16
Alignment explanation
Indices: 5889824--5889854 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5889814 TAGCTCATGA
*
5889824 TTTATTAAGATTATAT
1 TTTAATAAGATTATAT
5889840 TTTAATAAGATTATA
1 TTTAATAAGATTATA
5889855 AAACACTCTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
TTTAATAAGATTATAT
Found at i:5902593 original size:21 final size:21
Alignment explanation
Indices: 5902552--5902594 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5902542 GCTTTCAATC
* *
5902552 TTCTAGTGACATGATTTTATT
1 TTCTAGTGACATAATTGTATT
5902573 TTCTA-TGACATTAATTGTATT
1 TTCTAGTGACA-TAATTGTATT
5902594 T
1 T
5902595 CATTTAATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.26, C:0.09, G:0.12, T:0.53
Consensus pattern (21 bp):
TTCTAGTGACATAATTGTATT
Found at i:5902862 original size:22 final size:21
Alignment explanation
Indices: 5902827--5902869 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
5902817 TATTTTTGTG
*
5902827 AAATTTATTCATAAATTATAA
1 AAATTTATTCATAAATAATAA
*
5902848 AAATTATATTTATAAATAATAA
1 AAATT-TATTCATAAATAATAA
5902870 TTAAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATTTATTCATAAATAATAA
Found at i:5903792 original size:21 final size:20
Alignment explanation
Indices: 5903726--5903792 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
5903716 AATAACGTCC
* *
5903726 AATTTTATTATTATATTAATT
1 AATTTTAATATTAT-TAAATT
*
5903747 AATTTTACTATTATT--ATT
1 AATTTTAATATTATTAAATT
5903765 -ATGTTTAATATTATTAAAATT
1 AAT-TTTAATATTATT-AAATT
5903786 AATTTTA
1 AATTTTA
5903793 CTGTTATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 2 0.05
18 14 0.36
20 1 0.03
21 20 0.51
22 2 0.05
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (20 bp):
AATTTTAATATTATTAAATT
Found at i:5904534 original size:20 final size:21
Alignment explanation
Indices: 5904511--5904551 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
5904501 CATCATTAAT
5904511 TTTAATATTATTATTA-AATA
1 TTTAATATTATTATTACAATA
*
5904531 TTTAATTTTATTATTACAATA
1 TTTAATATTATTATTACAATA
5904552 ACTAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTAATATTATTATTACAATA
Found at i:5904839 original size:23 final size:23
Alignment explanation
Indices: 5904787--5904839 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
5904777 ATTTATTTGT
*
5904787 ATTTAAAATTATTTATAATATTA
1 ATTTAAAATAATTTATAATATTA
* *
5904810 ATATAAAATAATTTTTAATATTA
1 ATTTAAAATAATTTATAATATTA
*
5904833 TTTTAAA
1 ATTTAAA
5904840 TAGTGATCCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTTAAAATAATTTATAATATTA
Found at i:5907075 original size:18 final size:18
Alignment explanation
Indices: 5907052--5907088 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5907042 AAGTTTCAAA
5907052 CAAAAATATAATTGATGT
1 CAAAAATATAATTGATGT
5907070 CAAAAATATAATTGATGT
1 CAAAAATATAATTGATGT
5907088 C
1 C
5907089 TAAAGGGACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (18 bp):
CAAAAATATAATTGATGT
Found at i:5913034 original size:20 final size:20
Alignment explanation
Indices: 5912991--5913050 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
5912981 CACATGGTCC
***
5912991 TGTATCGATACATTTCAGACA
1 TGTATCGATACA-TTCACTTA
5913012 TGTATCGATACATTCACTTA
1 TGTATCGATACATTCACTTA
*
5913032 TGTATCGATATATTCACTT
1 TGTATCGATACATTCACTT
5913051 GTTATGTCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
20 23 0.66
21 12 0.34
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTCACTTA
Found at i:5917512 original size:13 final size:13
Alignment explanation
Indices: 5917494--5917518 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5917484 ACAAATAGTA
5917494 AATGTATCGATAT
1 AATGTATCGATAT
5917507 AATGTATCGATA
1 AATGTATCGATA
5917519 CATGCCTAAA
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:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
AATGTATCGATAT
Found at i:5917576 original size:20 final size:20
Alignment explanation
Indices: 5917548--5917588 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
5917538 TACATACTAC
*
5917548 TAAGGAAATGTATCGATACA
1 TAAGCAAATGTATCGATACA
5917568 TAAGCAAATGTATCGATACA
1 TAAGCAAATGTATCGATACA
5917588 T
1 T
5917589 TTACTGTTTG
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:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (20 bp):
TAAGCAAATGTATCGATACA
Found at i:5917621 original size:20 final size:21
Alignment explanation
Indices: 5917576--5917630 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
5917566 CATAAGCAAA
**
5917576 TGTATCGATACATTTACTGTT
1 TGTATCGATACATTTACTCAT
*
5917597 TGTATCGATACATTT-TTCAT
1 TGTATCGATACATTTACTCAT
5917617 TGTATCGATACATT
1 TGTATCGATACATT
5917631 CTGGGTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47
Consensus pattern (21 bp):
TGTATCGATACATTTACTCAT
Found at i:5920195 original size:79 final size:79
Alignment explanation
Indices: 5920049--5920595 Score: 554
Period size: 79 Copynumber: 6.9 Consensus size: 79
5920039 TCATTAATGT
* * * * * **
5920049 TTTTATTTCCAAAATATCAATTTTTCACCATC-GAGGATACTCCAACCTCGTTATTTTTGAGAAG
1 TTTTATTTCTAAAACACCGATTTTTCACCATCGGA-GATACTCCAACCTCGTTATTTTCGAGGGG
5920113 ATACTCCAACCCTGG
65 ATACTCCAACCCTGG
* * * * *
5920128 CTTTATTTATAAAATATCGATTTTTCACCATCGGAGATACTCCAACCTCGTTAGTTTCGAGGGGA
1 TTTTATTTCTAAAACACCGATTTTTCACCATCGGAGATACTCCAACCTCGTTATTTTCGAGGGGA
* *
5920193 TACTCTAA-CCTCGA
66 TACTCCAACCCT-GG
* * * * *
5920207 TTTTATTTCTAAAATACCGATTTTCCATCATCAGGA-ATACTCCAACCCCATTATTTTCGAGGGG
1 TTTTATTTCTAAAACACCGATTTTTCACCATC-GGAGATACTCCAACCTCGTTATTTTCGAGGGG
5920271 ATACTCCAA-CCTGGG
65 ATACTCCAACCCT-GG
* * * *
5920286 TTTTATTTCTAAAACACCGATTTTTCACCATCGAAGATACTCAAACCCCATTATTTTCGAGGGGA
1 TTTTATTTCTAAAACACCGATTTTTCACCATCGGAGATACTCCAACCTCGTTATTTTCGAGGGGA
* *
5920351 TACTTCAACCCTAG
66 TACTCCAACCCTGG
* * * * ** * *
5920365 TTTTATTTCTAAAACACTGATTTTCCACCATTGGGGATTTTCTAATCC-CGTTA-TTTCTGAGAG
1 TTTTATTTCTAAAACACCGATTTTTCACCATCGGAGATACTCCAA-CCTCGTTATTTTC-GAGGG
**
5920428 GATACTCCAACCCCAG
64 GATACTCCAACCCTGG
* * * * *
5920444 TTTTTTTTCTAAAACACTGATTTTTCACCATCGG-GATACTCTAACC-CTTTTATTTTGGAGGGG
1 TTTTATTTCTAAAACACCGATTTTTCACCATCGGAGATACTCCAACCTC-GTTATTTTCGAGGGG
* *
5920507 ATACTCCAACTCTGA
65 ATACTCCAACCCTGG
* * * *
5920522 TTTTATTTCTAAAACACCGA-TTTTCACCATCGGAAATACTCTAACCTTGTTATTTCCGAGGGGA
1 TTTTATTTCTAAAACACCGATTTTTCACCATCGGAGATACTCCAACCTCGTTATTTTCGAGGGGA
5920586 TACTCCAACC
66 TACTCCAACC
5920596 TTATTTTTAA
Statistics
Matches: 397, Mismatches: 60, Indels: 23
0.83 0.12 0.05
Matches are distributed among these distances:
77 16 0.04
78 87 0.22
79 284 0.72
80 10 0.03
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (79 bp):
TTTTATTTCTAAAACACCGATTTTTCACCATCGGAGATACTCCAACCTCGTTATTTTCGAGGGGA
TACTCCAACCCTGG
Found at i:5928539 original size:16 final size:16
Alignment explanation
Indices: 5928516--5928567 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
5928506 ATGAAAACCC
5928516 AAAA-AGGAAAAAAAA
1 AAAAGAGGAAAAAAAA
*
5928531 AAAAGAGGAAAGAAAA
1 AAAAGAGGAAAAAAAA
**
5928547 AAAAGAACAAAAAAAA
1 AAAAGAGGAAAAAAAA
5928563 GAAAA
1 -AAAA
5928568 AAGAAAAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 4 0.13
16 23 0.74
17 4 0.13
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAGAGGAAAAAAAA
Found at i:5928558 original size:12 final size:12
Alignment explanation
Indices: 5928525--5928586 Score: 61
Period size: 12 Copynumber: 4.7 Consensus size: 12
5928515 CAAAAAGGAA
5928525 AAAAAAAAAAGAGG
1 AAAAAAAAAA-A-G
5928539 AAAGAAAAAAAAG
1 AAA-AAAAAAAAG
*
5928552 AACAAAAAAAAG
1 AAAAAAAAAAAG
5928564 AAAAAAGAAAAAGG
1 AAAAAA-AAAAA-G
5928578 AGAAAAAAA
1 A-AAAAAAA
5928587 CCTGCTTAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
12 14 0.33
13 8 0.19
14 8 0.19
15 12 0.29
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:5928574 original size:16 final size:15
Alignment explanation
Indices: 5928516--5928575 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 15
5928506 ATGAAAACCC
*
5928516 AAAAAGGAAAAAAAA
1 AAAAAAGAAAAAAAA
*
5928531 AAAAGAGGAAAGAAAAA
1 AAAA-AAGAAA-AAAAA
* *
5928548 AAAGAACAAAAAAAA
1 AAAAAAGAAAAAAAA
5928563 GAAAAAAGAAAAA
1 -AAAAAAGAAAAA
5928576 GGAGAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
15 9 0.24
16 20 0.54
17 8 0.22
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAA
Found at i:5928581 original size:28 final size:27
Alignment explanation
Indices: 5928516--5928586 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 27
5928506 ATGAAAACCC
* **
5928516 AAAAAGGAAAAAAAAAAAAGAGGAAAG
1 AAAAAGGAGAAAAAAAAAAGAAAAAAG
**
5928543 AAAAAAAAGAACAAAAAAAAGAAAAAAG
1 AAAAAGGAGAA-AAAAAAAAGAAAAAAG
5928571 AAAAAGGAGAAAAAAA
1 AAAAAGGAGAAAAAAA
5928587 CCTGCTTAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 13 0.36
28 23 0.64
ACGTcount: A:0.82, C:0.01, G:0.17, T:0.00
Consensus pattern (27 bp):
AAAAAGGAGAAAAAAAAAAGAAAAAAG
Found at i:5929714 original size:59 final size:59
Alignment explanation
Indices: 5929526--5930028 Score: 461
Period size: 59 Copynumber: 8.4 Consensus size: 59
5929516 CCTTTTATCT
* * *
5929526 TTTTAGTCCTTAAAGAGCAAGATGC-CTTTTCCTTTTAAAGCCCACACCAGTTGGTGGCACC
1 TTTTAGTCCTCAAAGAGCAGGA--CAC-TTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * *
5929587 TTTTAGTCCTTAAAGAGCAGGGCCCTTTCTTTTTTAAAGCCCACAAAAGTTGGTGGCACC
1 TTTTAGTCCTCAAAGAGCAGGACACTTTC-CTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * *
5929647 TTTTAGTCCTCAAAGAGTAAGATACTTTCCTTTTAAAGCCCATACAAGTTGGTGGCACC
1 TTTTAGTCCTCAAAGAGCAGGACACTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
** * * *
5929706 TTCCAGTCCTCAAAGAGTAGGACACTTTCCTTTCAAAGCCCATACAAGTTGGTGGCACC
1 TTTTAGTCCTCAAAGAGCAGGACACTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
** * * * * * * ** * *
5929765 TTCCAATCTTTAAAGAACATGATACCTTCTCCTTGCAAAGCCCACACAAGTTGGCGACACC
1 TTTTAGTCCTCAAAGAGCAGGACA-CTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * ** * * ** *
5929826 TTTTAGCCCTCAAAAAGTTGGACGCTTTCCTTTCAAAGCCCACACAAGTTGGCAGCATC
1 TTTTAGTCCTCAAAGAGCAGGACACTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * * *
5929885 TTTCAGTCCTCAAAAAGTAGGACGCCTTCTCTTTAGAAAGCCCACACAAGTTGGTGGCACC
1 TTTTAGTCCTCAAAGAGCAGGACACTTTC-CTTT-TAAAGCCCACACAAGTTGGTGGCACC
* * * *
5929946 TTCTAGTCCTCAAAGAGCAGGACACATCTT-TTTTTAAAAGCCTACACAAGCTGGTGGCACC
1 TTTTAGTCCTCAAAGAGCAGGACAC-T-TTCCTTTT-AAAGCCCACACAAGTTGGTGGCACC
5930007 TTTTAGTCCTCAAAGAGCAGGA
1 TTTTAGTCCTCAAAGAGCAGGA
5930029 TGCCTCTCTC
Statistics
Matches: 367, Mismatches: 66, Indels: 18
0.81 0.15 0.04
Matches are distributed among these distances:
59 156 0.43
60 61 0.17
61 148 0.40
63 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (59 bp):
TTTTAGTCCTCAAAGAGCAGGACACTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
Found at i:5929838 original size:120 final size:120
Alignment explanation
Indices: 5929530--5930022 Score: 472
Period size: 120 Copynumber: 4.1 Consensus size: 120
5929520 TTATCTTTTT
* * * * * * *
5929530 AGTCCTTAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACCAGTTGGTGGCACCTTTTAGTC
1 AGTCCTCAAAGAACAAGATACCTTCTCCTTGTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTC
* * * * * * *
5929595 CTTAAAGAGCAGGGCCCTTTCTTTTTTAAAGCCCACAAAAGTTGGTGGCACCTTTT
66 CTCAAAGAGCAGGACACTTTC-CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
** * * *
5929651 AGTCCTCAAAGAGTAAGATA-CTT-TCCTTTTAAAGCCCATACAAGTTGGTGGCACCTTCCAGTC
1 AGTCCTCAAAGAACAAGATACCTTCTCCTTGTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTC
* * *
5929714 CTCAAAGAGTAGGACACTTTCCTTTCAAAGCCCATACAAGTTGGTGGCACCTTCC
66 CTCAAAGAGCAGGACACTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * * * * * * *
5929769 AATCTTTAAAGAACATGATACCTTCTCCTTGCAAAGCCCACACAAGTTGGCGACACCTTTTAGCC
1 AGTCCTCAAAGAACAAGATACCTTCTCCTTGTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTC
* ** * ** *
5929834 CTCAAAAAGTTGGACGCTTTCCTTTCAAAGCCCACACAAGTTGGCAGCATCTTTC
66 CTCAAAGAGCAGGACACTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * ** *
5929889 AGTCCTCAAA-AAGTAGGACGCCTTCTCTTTAG-AAAGCCCACACAAGTTGGTGGCACCTTCTAG
1 AGTCCTCAAAGAA-CAAGATACCTTCTCCTT-GTAAAGCCCACACAAGTTGGTGGCACCTTCTAG
** * * * *
5929952 TCCTCAAAGAGCAGGACACATCTTTTTTTAAAAGCCTACACAAGCTGGTGGCACCTTTT
64 TCCTCAAAGAGCAGGACAC-T-TTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
5930011 AGTCCTCAAAGA
1 AGTCCTCAAAGA
5930023 GCAGGATGCC
Statistics
Matches: 301, Mismatches: 64, Indels: 12
0.80 0.17 0.03
Matches are distributed among these distances:
118 42 0.14
119 58 0.19
120 143 0.48
121 19 0.06
122 38 0.13
123 1 0.00
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.28
Consensus pattern (120 bp):
AGTCCTCAAAGAACAAGATACCTTCTCCTTGTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTC
CTCAAAGAGCAGGACACTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:5929856 original size:179 final size:181
Alignment explanation
Indices: 5929622--5929948 Score: 460
Period size: 179 Copynumber: 1.8 Consensus size: 181
5929612 TTTCTTTTTT
* * * * * *
5929622 AAAGCCCACAAAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAAGATACTTTCCTTTTAAAGCC
1 AAAGCCCACAAAAGTTGGCGACACCTTTTAGCCCTCAAAAAGTAAGACACTTTCCTTTCAAAGCC
* ** * * *
5929687 CATACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGTAGGACACTTTC-CTTT-CAAAGCCCATA
66 CACACAAGTTGGCAGCACCTTCCAGTCCTCAAAAAGTAGGACACCTTCTCTTTACAAAGCCCACA
5929750 CAAGTTGGTGGCACCTTCCAATCTTTAAAGAACATGATACCTTCTCCTTGC
131 CAAGTTGGTGGCACCTTCCAATCTTTAAAGAACATGATACCTTCTCCTTGC
* ** *
5929801 AAAGCCCACACAAGTTGGCGACACCTTTTAGCCCTCAAAAAGTTGGACGCTTTCCTTTCAAAGCC
1 AAAGCCCACAAAAGTTGGCGACACCTTTTAGCCCTCAAAAAGTAAGACACTTTCCTTTCAAAGCC
* * * *
5929866 CACACAAGTTGGCAGCATCTTTCAGTCCTCAAAAAGTAGGACGCCTTCTCTTTAGAAAGCCCACA
66 CACACAAGTTGGCAGCACCTTCCAGTCCTCAAAAAGTAGGACACCTTCTCTTTACAAAGCCCACA
5929931 CAAGTTGGTGGCACCTTC
131 CAAGTTGGTGGCACCTTC
5929949 TAGTCCTCAA
Statistics
Matches: 126, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
179 95 0.75
180 4 0.03
181 27 0.21
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (181 bp):
AAAGCCCACAAAAGTTGGCGACACCTTTTAGCCCTCAAAAAGTAAGACACTTTCCTTTCAAAGCC
CACACAAGTTGGCAGCACCTTCCAGTCCTCAAAAAGTAGGACACCTTCTCTTTACAAAGCCCACA
CAAGTTGGTGGCACCTTCCAATCTTTAAAGAACATGATACCTTCTCCTTGC
Found at i:5930705 original size:21 final size:20
Alignment explanation
Indices: 5930679--5930727 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
5930669 TAAATGAATT
5930679 GATACATTTACT-ATTTGTATC
1 GATACATTT-CTCA-TTGTATC
*
5930700 GATACATTTTTCATTGTATC
1 GATACATTTCTCATTGTATC
5930720 GATACATT
1 GATACATT
5930728 CTGGGTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.47
Consensus pattern (20 bp):
GATACATTTCTCATTGTATC
Found at i:5935799 original size:52 final size:51
Alignment explanation
Indices: 5935721--5935869 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 51
5935711 CGAAATATGA
*
5935721 AAATTTGCCTGCATGCATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTT-ATAGTGTATCGATACATCTGGGC
*
5935773 AAATTTGCCTGTATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTTATAGTGTATCGATACATCTGGGC
* * **
5935825 AAATTTACCTGCATGTATCGATATAAATATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTTAT-AGTGTATCGATACA
5935870 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 3 0.03
52 82 0.93
53 3 0.03
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTTATAGTGTATCGATACATCTGGGC
Found at i:5935876 original size:13 final size:13
Alignment explanation
Indices: 5935858--5935882 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5935848 TAAATATCAG
5935858 TGTATCGATACAA
1 TGTATCGATACAA
5935871 TGTATCGATACA
1 TGTATCGATACA
5935883 TTTGGGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5936846 original size:50 final size:50
Alignment explanation
Indices: 5936762--5936911 Score: 158
Period size: 50 Copynumber: 3.0 Consensus size: 50
5936752 CAACTCTAGC
* * *
5936762 TTTATTTTTATAACACCGATTTTCCACCATCGGAGATACTCCAACCTCGGT
1 TTTATTTATA-AACACCAATTTTCCACCATCGGAGATACTCCAACCTCGAT
* * * * *
5936813 TTTATTTCTAAACACTAATTTTTCATCATCGGAGATACTCCAACCTTGAT
1 TTTATTTATAAACACCAATTTTCCACCATCGGAGATACTCCAACCTCGAT
* ** *
5936863 TTTATTTATAAAATACCAATTTTCTGCCATCAGG-GATACTCTAACCTCG
1 TTTATTTAT-AAACACCAATTTTCCACCATC-GGAGATACTCCAACCTCG
5936912 TTATTTTCGA
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
50 42 0.52
51 37 0.46
52 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (50 bp):
TTTATTTATAAACACCAATTTTCCACCATCGGAGATACTCCAACCTCGAT
Found at i:5936935 original size:79 final size:77
Alignment explanation
Indices: 5936846--5937267 Score: 373
Period size: 79 Copynumber: 5.4 Consensus size: 77
5936836 CATCATCGGA
** * * * *
5936846 GATACTCCAACCTTGATTTTATTTATAAAATACCAATTTTCTGCCATC-AGGGATACTCTAACCT
1 GATACTCCAACC-CCATTTTATTTCTAAAACACCGATTTT-TACCATCGA-GGATACTCTAACCT
*
5936910 CGTTATTTTCGACGG
63 CGTTATTTTCGAGGG
* ** *
5936925 CATACTCCAACCCCCATTTTATTTCTAAAACATTGATTTTCTACTATCGAGGATACTCTAACCAT
1 GATACTCCAA-CCCCATTTTATTTCTAAAACACCGATTTT-TACCATCGAGGATACTCTAACC-T
*
5936990 -ATTATTTTCGAGGG
63 CGTTATTTTCGAGGG
* * * * * * *
5937004 GATACTTCAACCCCAGTTTTATTTCTAAAACATCAATTTTTCACAATTGAGGATACTCGAATCTC
1 GATACTCCAACCCCA-TTTTATTTCTAAAACACCGATTTTT-ACCATCGAGGATACTCTAACCTC
*
5937069 GTTATTTTTGAGGG
64 GTTATTTTCGAGGG
* ** ** * * * * *
5937083 GATACTTCAACCCGGTTTTATTTCTAAAATGCTGATTTTTCACCATCGGGGATAGTCCAATCTCG
1 GATACTCCAACCCCATTTTATTTCTAAAACACCGATTTTT-ACCATCGAGGATACTCTAACCTCG
* *
5937148 TTATTTTTGAAGG
65 TTATTTTCGAGGG
* *
5937161 GATACTCCAACCCCAGTTT-TTTCTAAAACACCGATTTTTCGCCATCGAGGATACTCTAACCTCG
1 GATACTCCAACCCCATTTTATTTCTAAAACACCGATTTTT-ACCATCGAGGATACTCTAACCTCG
* *
5937225 TTATTTCCAAGGG
65 TTATTTTCGAGGG
** *
5937238 GATACTCCAATCCCGTTTTTATCTCTAAAA
1 GATACTCCAA-CCCCATTTTATTTCTAAAA
5937268 TATTAAATTT
Statistics
Matches: 280, Mismatches: 55, Indels: 16
0.80 0.16 0.05
Matches are distributed among these distances:
77 56 0.20
78 80 0.29
79 140 0.50
80 4 0.01
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.36
Consensus pattern (77 bp):
GATACTCCAACCCCATTTTATTTCTAAAACACCGATTTTTACCATCGAGGATACTCTAACCTCGT
TATTTTCGAGGG
Found at i:5938599 original size:12 final size:12
Alignment explanation
Indices: 5938582--5938607 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5938572 AGTAATAGGG
5938582 AAAAGAAGAAAA
1 AAAAGAAGAAAA
5938594 AAAAGAAGAAAA
1 AAAAGAAGAAAA
5938606 AA
1 AA
5938608 GAAAACAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAGAAGAAAA
Found at i:5938634 original size:17 final size:16
Alignment explanation
Indices: 5938584--5938623 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
5938574 TAATAGGGAA
*
5938584 AAGAAGAAA-AAAAAG
1 AAGAAAAAAGAAAAAG
5938599 AAGAAAAAAGAAAACAG
1 AAGAAAAAAGAAAA-AG
5938616 AAGAAAAA
1 AAGAAAAA
5938624 TAGGATAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 4 0.18
17 10 0.45
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAGAAAAAG
Found at i:5938892 original size:20 final size:21
Alignment explanation
Indices: 5938846--5938892 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
5938836 GAACTCAAAA
5938846 GAAT-AACCCAAGTCAAACTC
1 GAATCAACCCAAGTCAAACTC
* *
5938866 GAA-CAACCCAGGTCAAA-TT
1 GAATCAACCCAAGTCAAACTC
5938885 GAATCAAC
1 GAATCAAC
5938893 ACAAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.45, C:0.28, G:0.13, T:0.15
Consensus pattern (21 bp):
GAATCAACCCAAGTCAAACTC
Found at i:5938957 original size:20 final size:19
Alignment explanation
Indices: 5938929--5938971 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5938919 CAAAAAGGTT
**
5938929 AAATGGATATAATTAAGTCA
1 AAATGGATA-AAAAAAGTCA
*
5938949 AAATTGATAAAAAAAGTCA
1 AAATGGATAAAAAAAGTCA
5938968 AAAT
1 AAAT
5938972 CAAAATGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.58, C:0.05, G:0.12, T:0.26
Consensus pattern (19 bp):
AAATGGATAAAAAAAGTCA
Found at i:5939053 original size:28 final size:29
Alignment explanation
Indices: 5938992--5939054 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
5938982 TGGTAAAAAT
* * *
5938992 AAAAAGTCAACTTTAATAAAAATGGATTG
1 AAAAATTCAACTTTAATAAAAATAGATTA
* *
5939021 AAAAATTCAACTTTAATGAAATTAG-TTA
1 AAAAATTCAACTTTAATAAAAATAGATTA
5939049 AAAAAT
1 AAAAAT
5939055 GTAATGCCCA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.54, C:0.06, G:0.10, T:0.30
Consensus pattern (29 bp):
AAAAATTCAACTTTAATAAAAATAGATTA
Found at i:5939133 original size:22 final size:24
Alignment explanation
Indices: 5939084--5939139 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
5939074 CATGTAGGAG
*
5939084 TTTAATTAGATTTTTTATTAGAAAT
1 TTTAATTA-ATTTTCTATTAGAAAT
*
5939109 TTTAATTAATTTTCT-TTAG-ACT
1 TTTAATTAATTTTCTATTAGAAAT
5939131 TTTAATTAA
1 TTTAATTAA
5939140 AAGTTTACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 11 0.38
23 4 0.14
24 6 0.21
25 8 0.28
ACGTcount: A:0.34, C:0.04, G:0.05, T:0.57
Consensus pattern (24 bp):
TTTAATTAATTTTCTATTAGAAAT
Found at i:5939313 original size:29 final size:28
Alignment explanation
Indices: 5939280--5939342 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 28
5939270 TTGATAAAAA
5939280 TAAAAAGTCAACTT-TAATCAAAATTAAT
1 TAAAAAGTCAACTTCTAATC-AAATTAAT
5939308 TGAAAAAGTCAACTTCTAATCAAATTAAT
1 T-AAAAAGTCAACTTCTAATCAAATTAAT
5939337 TAAAAA
1 TAAAAA
5939343 TCTAAGGCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
28 6 0.18
29 22 0.67
30 5 0.15
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (28 bp):
TAAAAAGTCAACTTCTAATCAAATTAAT
Found at i:5939690 original size:17 final size:17
Alignment explanation
Indices: 5939668--5939700 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5939658 ACCTATCATA
5939668 TATAGAAGTTT-TAGTTG
1 TATAGAA-TTTCTAGTTG
5939685 TATAGAATTTCTAGTT
1 TATAGAATTTCTAGTT
5939701 AAACTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.30, C:0.03, G:0.18, T:0.48
Consensus pattern (17 bp):
TATAGAATTTCTAGTTG
Found at i:5939713 original size:2 final size:2
Alignment explanation
Indices: 5939706--5939747 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5939696 TAGTTAAACT
5939706 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5939748 GAATTTTCAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5939814 original size:28 final size:29
Alignment explanation
Indices: 5939783--5939855 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 29
5939773 AATTAAAATG
*
5939783 TTTACATGTAGTA-TTTTTAACTAAACCT
1 TTTACATGTAGAATTTTTTAACTAAACCT
* * * *
5939811 TTTATATATTGAATTTTTTAATTAAACCT
1 TTTACATGTAGAATTTTTTAACTAAACCT
5939840 TTATACATG-A-AATTTT
1 TT-TACATGTAGAATTTT
5939856 CATTTAAACT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
28 15 0.43
29 16 0.46
30 4 0.11
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (29 bp):
TTTACATGTAGAATTTTTTAACTAAACCT
Found at i:5939850 original size:27 final size:27
Alignment explanation
Indices: 5939795--5939918 Score: 81
Period size: 27 Copynumber: 4.5 Consensus size: 27
5939785 TACATGTAGT
* *
5939795 ATTTTTAACTAAACCTTTTATATATTGAA
1 ATTTTTAATTAAACC-TTTATACA-TGAA
*
5939824 TTTTTTAATTAAACCTTTATACATGAA
1 ATTTTTAATTAAACCTTTATACATGAA
* * * * * *
5939851 ATTTTCATTTAAACTTTTACATATGGA
1 ATTTTTAATTAAACCTTTATACATGAA
** *
5939878 ATTTCCAATTAAA-CTTT-TCACATATAGA
1 ATTTTTAATTAAACCTTTAT-ACAT-GA-A
5939906 ATTTTTAATTAAA
1 ATTTTTAATTAAA
5939919 AATTTTTTTG
Statistics
Matches: 73, Mismatches: 19, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
26 6 0.08
27 35 0.48
28 19 0.26
29 13 0.18
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (27 bp):
ATTTTTAATTAAACCTTTATACATGAA
Found at i:5939908 original size:28 final size:27
Alignment explanation
Indices: 5939760--5939918 Score: 115
Period size: 28 Copynumber: 5.7 Consensus size: 27
5939750 ATTTTCAGTT
* * *
5939760 ATATTGAAATTTCAATTAAAATGTTTAC
1 ATATAGAATTTTCAATTAAACT-TTTAC
* * * * *
5939788 ATGTAGTATTTTTAACTAAACCTTTTAT
1 ATATAGAATTTTCAATTAAA-CTTTTAC
* *
5939816 ATATTGAATTTTTTAATTAAACCTTTATAC
1 ATATAGAA-TTTTCAATTAAA-CTTT-TAC
* *
5939846 AT-GA-AATTTTCATTTAAACTTTTAC
1 ATATAGAATTTTCAATTAAACTTTTAC
* *
5939871 ATATGGAATTTCCAATTAAACTTTTCAC
1 ATATAGAATTTTCAATTAAACTTTT-AC
*
5939899 ATATAGAATTTTTAATTAAA
1 ATATAGAATTTTCAATTAAA
5939919 AATTTTTTTG
Statistics
Matches: 101, Mismatches: 24, Indels: 12
0.74 0.18 0.09
Matches are distributed among these distances:
25 5 0.05
26 4 0.04
27 27 0.27
28 44 0.44
29 17 0.17
30 4 0.04
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (27 bp):
ATATAGAATTTTCAATTAAACTTTTAC
Found at i:5940054 original size:29 final size:28
Alignment explanation
Indices: 5940004--5940072 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 28
5939994 CATATATGGA
* * *
5940004 ATTTTCAATT-AAACTTTATACATTTAGG
1 ATTTTTAATTAAAAATTTATACATATA-G
5940032 ATTTTTTAATTAAAAATTT-TACATATAG
1 A-TTTTTAATTAAAAATTTATACATATAG
*
5940060 AATTTTAATTAAA
1 ATTTTTAATTAAA
5940073 CCTTTTAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 11 0.31
28 3 0.09
29 15 0.43
30 6 0.17
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (28 bp):
ATTTTTAATTAAAAATTTATACATATAG
Found at i:5940078 original size:27 final size:26
Alignment explanation
Indices: 5939947--5940079 Score: 104
Period size: 27 Copynumber: 4.8 Consensus size: 26
5939937 TTTCACTTAA
* **
5939947 AGAATTTTTAATTAAACTATTACAGCT
1 AGAA-TTTTAATTAAACTTTTACATAT
* * *
5939974 AGAATTTTTAACTAAACTTTCATATAT
1 AGAA-TTTTAATTAAACTTTTACATAT
* *
5940001 GGAATTTTCAATTAAACTTTATACATTT
1 AGAATTTT-AATTAAACTTT-TACATAT
* *
5940029 AGGATTTTTTAATTAAAAATTTTACATAT
1 A-GA-ATTTTAATT-AAACTTTTACATAT
5940058 AGAATTTTAATTAAACCTTTTA
1 AGAATTTTAATTAAA-CTTTTA
5940080 ATTAAATTCT
Statistics
Matches: 83, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
26 7 0.08
27 47 0.57
28 6 0.07
29 13 0.16
30 10 0.12
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (26 bp):
AGAATTTTAATTAAACTTTTACATAT
Found at i:5943744 original size:29 final size:29
Alignment explanation
Indices: 5943712--5943777 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
5943702 TTTATCAATC
5943712 TATGAACAAGAAAATGCCAAGGAAAATAG
1 TATGAACAAGAAAATGCCAAGGAAAATAG
*
5943741 TATGAATAAGAAAATGCCAAGGAAAATAG
1 TATGAACAAGAAAATGCCAAGGAAAATAG
5943770 TATGAACA
1 TATGAACA
5943778 TGGATATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.55, C:0.09, G:0.20, T:0.17
Consensus pattern (29 bp):
TATGAACAAGAAAATGCCAAGGAAAATAG
Found at i:5946309 original size:66 final size:66
Alignment explanation
Indices: 5945951--5946438 Score: 240
Period size: 66 Copynumber: 7.5 Consensus size: 66
5945941 CACTAGAGTG
* *** * **
5945951 AAACCTAAGTCT-AAAAAA-GTTGACCAAGATGAAACTGATAAAGTCAACTAAATGTGATTAGGG
1 AAACCTAAGT-TGAAAAAAGGTTGACTAAGGCAAAACTAATAAAGTCAACTAAATGTGACAAGGG
5946014 TA
65 TA
* * ** * * * * * * * **
5946016 AAACCTAAATCGAAAATGGGTTAAGTAGGGTAAAA-TCGATAAAGTCAACTATAGGTGATTAGGG
1 AAACCTAAGTTGAAAAAAGGTTGACTAAGGCAAAACT-AATAAAGTCAACTAAATGTGACAAGGG
5946080 TA
65 TA
* * * * ** * * * **
5946082 GAACTTAAG-TAAAAAAATGGTTGACCAAGATAAAATTGATAAAATCAACT-GGT-TGACAAGGG
1 AAACCTAAGTTGAAAAAA-GGTTGACTAAGGCAAAACTAATAAAGTCAACTAAATGTGACAAGGG
5946144 TA
65 TA
* * * * * * * *
5946146 GAACCT-AGTCGAAAAAAGGTTGACTAGGGAAAAACTAATAAA-TTAAC-AAGTTTAACTAA-GG
1 AAACCTAAGTTGAAAAAAGGTTGACTAAGGCAAAACTAATAAAGTCAACTAAATGTGAC-AAGGG
5946207 TA
65 TA
* * * *
5946209 AAAACTAAATTGAAAAAGGGTT-AGC-AAGGACAAAACTAATAAAGTCAACTAAAAGTGACAAGG
1 AAACCTAAGTTGAAAAAAGGTTGA-CTAAGG-CAAAACTAATAAAGTCAACTAAATGTGACAAGG
5946272 GTA
64 GTA
* * *
5946275 GAACCTAAGTTGAAAAAAGGTTGACTAAGGCAAAACTAATAAA-TCAAC-AAGTTTGACCAA-GG
1 AAACCTAAGTTGAAAAAAGGTTGACTAAGGCAAAACTAATAAAGTCAACTAAATGTGA-CAAGGG
5946337 TA
65 TA
* * * * ** *
5946339 AAAACTAAG-TCAAAAAAGGTTGAC-CAGGACAAAACTAATAAAGTCAACCAAGGGTGA-AAAGG
1 AAACCTAAGTTGAAAAAAGGTTGACTAAGG-CAAAACTAATAAAGTCAACTAAATGTGACAAGGG
*
5946401 TC
65 TA
* * * *
5946403 AAACTTAAATCT-AAAAGAGGTTGACTAGGGCAAAAC
1 AAACCTAAGT-TGAAAAAAGGTTGACTAAGGCAAAAC
5946439 CGATAAATCG
Statistics
Matches: 324, Mismatches: 74, Indels: 50
0.72 0.17 0.11
Matches are distributed among these distances:
62 9 0.03
63 65 0.20
64 77 0.24
65 56 0.17
66 111 0.34
67 6 0.02
ACGTcount: A:0.48, C:0.12, G:0.20, T:0.20
Consensus pattern (66 bp):
AAACCTAAGTTGAAAAAAGGTTGACTAAGGCAAAACTAATAAAGTCAACTAAATGTGACAAGGGT
A
Found at i:5946317 original size:130 final size:128
Alignment explanation
Indices: 5946135--5946386 Score: 380
Period size: 130 Copynumber: 2.0 Consensus size: 128
5946125 ATCAACTGGT
* *
5946135 TGACAAGGGTAGAACCTAGTCGAAAAAAGGTTGACTAGGGAAAAACTAATAAATTAACAAGTTTA
1 TGACAAGGGTAGAACCTAGTCGAAAAAAGGTTGACTAAGGAAAAACTAATAAATCAACAAGTTTA
* * * *
5946200 ACTAAGGTAAAAACTAAATTGAAAAAGGGTT-AGCAAGGACAAAACTAATAAAGTCAACTAAAAG
66 ACCAAGGTAAAAACT-AAGTCAAAAAAGGTTGA-CAAGGACAAAACTAATAAAGTCAACTAAAAG
* *
5946264 TGACAAGGGTAGAACCTAAGTTGAAAAAAGGTTGACTAAGGCAAAACTAATAAATCAACAAGTTT
1 TGACAAGGGTAGAACCT-AGTCGAAAAAAGGTTGACTAAGGAAAAACTAATAAATCAACAAGTTT
* *
5946329 GACCAAGGTAAAAACTAAGTCAAAAAAGGTTGACCAGGACAAAACTAATAAAGTCAAC
65 AACCAAGGTAAAAACTAAGTCAAAAAAGGTTGACAAGGACAAAACTAATAAAGTCAAC
5946387 CAAGGGTGAA
Statistics
Matches: 111, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
129 53 0.48
130 58 0.52
ACGTcount: A:0.50, C:0.13, G:0.19, T:0.19
Consensus pattern (128 bp):
TGACAAGGGTAGAACCTAGTCGAAAAAAGGTTGACTAAGGAAAAACTAATAAATCAACAAGTTTA
ACCAAGGTAAAAACTAAGTCAAAAAAGGTTGACAAGGACAAAACTAATAAAGTCAACTAAAAG
Found at i:5946401 original size:64 final size:63
Alignment explanation
Indices: 5946087--5946453 Score: 219
Period size: 63 Copynumber: 5.7 Consensus size: 63
5946077 GGGTAGAACT
* * * * * * * * *
5946087 TAAGTAAAAAAATGGTTGACCAA-GATAAAATTGATAAAATCAAC-TGGTTGACAAGGGTAGAAC
1 TAAGTCAAAAAA-GGTTGA-CAAGGACAAAACTAAT-AAATCAACAAGGGTGACAAAGGTAAAAA
5946150 C
63 C
* * ** * *
5946151 T-AGTCGAAAAAAGGTTGACTAGGGA-AAAACTAATAAATTAACAAGTTTAACTAAGGTAAAAAC
1 TAAGTC-AAAAAAGGTTGAC-AAGGACAAAACTAATAAATCAACAAGGGTGACAAAGGTAAAAAC
* * * ** * *
5946214 TAAATTGAAAAAGGGTT-AGCAAGGACAAAACTAATAAAGTCAACTAAAAGTGACAAGGGTAGAA
1 T-AAGTCAAAAAAGGTTGA-CAAGGACAAAACTAATAAA-TCAAC-AAGGGTGACAAAGGTAAAA
*
5946278 CC
62 AC
* ** *
5946280 TAAGTTGAAAAAAGGTTGACTAAGG-CAAAACTAATAAATCAACAAGTTTGACCAAGGTAAAAAC
1 TAAG-TCAAAAAAGGTTGAC-AAGGACAAAACTAATAAATCAACAAGGGTGACAAAGGTAAAAAC
* *
5946344 TAAGTCAAAAAAGGTTGACCAGGACAAAACTAATAAAGTCAACCAAGGGTGA-AAAGGT-CAAAC
1 TAAGTCAAAAAAGGTTGACAAGGACAAAACTAATAAA-TCAA-CAAGGGTGACAAAGGTAAAAAC
* * * * ** *
5946407 TTAAATCTAAAAGAGGTTGACTAGGGCAAAACCGATAAATCGACAAG
1 -TAAGTC-AAAAAAGGTTGACAAGGACAAAACTAATAAATCAACAAG
5946454 TTTAAAGGGT
Statistics
Matches: 238, Mismatches: 47, Indels: 37
0.74 0.15 0.11
Matches are distributed among these distances:
62 11 0.05
63 71 0.30
64 66 0.28
65 46 0.19
66 39 0.16
67 5 0.02
ACGTcount: A:0.49, C:0.13, G:0.20, T:0.19
Consensus pattern (63 bp):
TAAGTCAAAAAAGGTTGACAAGGACAAAACTAATAAATCAACAAGGGTGACAAAGGTAAAAAC
Found at i:5946475 original size:129 final size:128
Alignment explanation
Indices: 5946135--5946456 Score: 348
Period size: 129 Copynumber: 2.5 Consensus size: 128
5946125 ATCAACTGGT
* * * * * * *
5946135 TGACAAGGGTAGAACCT-AGTCGAAAAAAGGTTGACTAGGGAAAAACTAATAAATTAACAAGTTT
1 TGACAAAGGTAGAACCTAAATTGAAAAAAGGTTGACTAAGGCAAAACCAATAAATCAACAAGTTT
* * * * * *
5946199 AACTAAGGTAAAAACTAAATTGAAAAAGGGTT-AGCAAGGACAAAACTAATAAAGTCAACTAAAA
66 GAC-AAGGTAAAAACT-AAGTCAAAAAAGGTTGA-CCAGGACAAAACTAATAAAGTCAACCAAAA
5946263 G
128 G
* * *
5946264 TGACAAGGGTAGAACCTAAGTTGAAAAAAGGTTGACTAAGGCAAAACTAATAAATCAACAAGTTT
1 TGACAAAGGTAGAACCTAAATTGAAAAAAGGTTGACTAAGGCAAAACCAATAAATCAACAAGTTT
**
5946329 GACCAAGGTAAAAACTAAGTCAAAAAAGGTTGACCAGGACAAAACTAATAAAGTCAACCAAGGG
66 GA-CAAGGTAAAAACTAAGTCAAAAAAGGTTGACCAGGACAAAACTAATAAAGTCAACCAAAAG
* * * * *
5946393 TGA-AAAGGTCA-AACTTAAATCT-AAAAGAGGTTGACTAGGGCAAAACCGATAAATCGACAAGT
1 TGACAAAGGT-AGAACCTAAAT-TGAAAAAAGGTTGACTAAGGCAAAACCAATAAATCAACAAGT
5946455 TT
64 TT
5946457 AAAGGGTGAC
Statistics
Matches: 168, Mismatches: 20, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
128 49 0.29
129 61 0.36
130 57 0.34
131 1 0.01
ACGTcount: A:0.48, C:0.13, G:0.20, T:0.19
Consensus pattern (128 bp):
TGACAAAGGTAGAACCTAAATTGAAAAAAGGTTGACTAAGGCAAAACCAATAAATCAACAAGTTT
GACAAGGTAAAAACTAAGTCAAAAAAGGTTGACCAGGACAAAACTAATAAAGTCAACCAAAAG
Found at i:5946798 original size:118 final size:118
Alignment explanation
Indices: 5946590--5946818 Score: 440
Period size: 118 Copynumber: 1.9 Consensus size: 118
5946580 ATTGACAAAC
5946590 CAACAAATTAAAAGGATAAAATAACATTTGACACTTGATCAATTGACGGATAAAGGATTTTACAT
1 CAACAAATTAAAAGGATAAAATAACATTTGACACTTGATCAATTGACGGATAAAGGATTTTACAT
*
5946655 TTGATTTTAAAGGAATAAGCATGATCATCACTTTATTCTAATGTCACGCTAAT
66 TTGATTTTAAAGGAATAAGCATGATCATCACTTTATTCCAATGTCACGCTAAT
5946708 CAACAAATTAAAAGGATAAAATAACATTTGACACTTGATCAATTGACGGATAAAGGATTTTACAT
1 CAACAAATTAAAAGGATAAAATAACATTTGACACTTGATCAATTGACGGATAAAGGATTTTACAT
*
5946773 TTGATTTTAAAGGAATAAGCATGATCATCACTTTCTTCCAATGTCA
66 TTGATTTTAAAGGAATAAGCATGATCATCACTTTATTCCAATGTCA
5946819 TGCTTAACTC
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
118 109 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (118 bp):
CAACAAATTAAAAGGATAAAATAACATTTGACACTTGATCAATTGACGGATAAAGGATTTTACAT
TTGATTTTAAAGGAATAAGCATGATCATCACTTTATTCCAATGTCACGCTAAT
Found at i:5948078 original size:21 final size:22
Alignment explanation
Indices: 5948054--5948100 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
5948044 CTTTTTTAGG
5948054 TTTTCATCTGATTTTTT-T-CTT
1 TTTTCATCT-ATTTTTTATCCTT
* *
5948075 TTTTGATCTTTTTTTTATCCTT
1 TTTTCATCTATTTTTTATCCTT
5948097 TTTT
1 TTTT
5948101 TTACCTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 6 0.27
21 9 0.41
22 7 0.32
ACGTcount: A:0.09, C:0.13, G:0.04, T:0.74
Consensus pattern (22 bp):
TTTTCATCTATTTTTTATCCTT
Found at i:5949975 original size:17 final size:17
Alignment explanation
Indices: 5949953--5950004 Score: 104
Period size: 17 Copynumber: 3.1 Consensus size: 17
5949943 CTTATCTAGA
5949953 TCAATTTCAATCTTTTT
1 TCAATTTCAATCTTTTT
5949970 TCAATTTCAATCTTTTT
1 TCAATTTCAATCTTTTT
5949987 TCAATTTCAATCTTTTT
1 TCAATTTCAATCTTTTT
5950004 T
1 T
5950005 TCACTCACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (17 bp):
TCAATTTCAATCTTTTT
Found at i:5955950 original size:20 final size:21
Alignment explanation
Indices: 5955925--5955964 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5955915 GCATCAATAT
*
5955925 ATTCACTTA-TGTATCGATAA
1 ATTCACTAATTGTATCGATAA
5955945 ATTCACTAATTGTATCGATA
1 ATTCACTAATTGTATCGATA
5955965 TAAATTGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (21 bp):
ATTCACTAATTGTATCGATAA
Found at i:5960402 original size:155 final size:152
Alignment explanation
Indices: 5960101--5960526 Score: 376
Period size: 155 Copynumber: 2.8 Consensus size: 152
5960091 AATATGTACG
* * * * *
5960101 CCTTTGGCATAAAAGCGACTTGGTGACTATCTAGGACTCA-TTCTAGGGAAATTAACAAAATGCC
1 CCTTTGGCATAAAAGCGACCTAGTGACTAACTAGGACTCAGTTCTA-AGAAATTACCAAAATGCC
* * * * * * *
5960165 TTAGAGTATACCTTCGACATGAAAGTATCTCGATAACCTTAAATGACATGAAAAGTTAAGCAAAA
65 TTAAAGTATACTTTC-ACATGAAAGTATCTAGGTAACCCTAAAAGACATGAAAAGATAAGCAAAA
* * * *
5960230 GGTTTAAATTATCCTAAATATACA
129 GGATGAAACTATCCTAAATACACA
** *
5960254 TTTTTGGCATAAAAGCGACCTAGTGACTAACTAGGACTCAGTTTTAATGAAATTACCAAAATGCC
1 CCTTTGGCATAAAAGCGACCTAGTGACTAACTAGGACTCAGTTCTAA-GAAATTACCAAAATGCC
* * * * *
5960319 TCTAAAGTATAGCTTTCATC-TAAAAGTATCTAGGTAACCCTAAAGGACACGAAATGAT-ATCAA
65 T-TAAAGTATA-CTTTCA-CATGAAAGTATCTAGGTAACCCTAAAAGACATGAAAAGATAAGC-A
* * *
5960382 AAATGATGAACCTATCCTAAATGCACA
126 AAAGGATGAAACTATCCTAAATACACA
* * * * * * ** * *
5960409 CCTTTAGCATAAAAGCAACC-CGATAACTACCCACAACTCGGTTCTAAAAAATTACC-AAATGCC
1 CCTTTGGCATAAAAGCGACCTAG-TGACTAACTAGGACTCAGTTCTAAGAAATTACCAAAATGCC
* *
5960472 TATAAAGTATACCTTTGACATGAAAGTATCTTGGTAACCCTAAAAGACATGAAAA
65 T-TAAAGTATA-CTTTCACATGAAAGTATCTAGGTAACCCTAAAAGACATGAAAA
5960527 TGAAATAAAA
Statistics
Matches: 218, Mismatches: 47, Indels: 16
0.78 0.17 0.06
Matches are distributed among these distances:
152 1 0.00
153 87 0.40
154 32 0.15
155 93 0.43
156 5 0.02
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27
Consensus pattern (152 bp):
CCTTTGGCATAAAAGCGACCTAGTGACTAACTAGGACTCAGTTCTAAGAAATTACCAAAATGCCT
TAAAGTATACTTTCACATGAAAGTATCTAGGTAACCCTAAAAGACATGAAAAGATAAGCAAAAGG
ATGAAACTATCCTAAATACACA
Found at i:5962517 original size:12 final size:12
Alignment explanation
Indices: 5962502--5962527 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5962492 ACTATTTATG
5962502 ATGTATCGATAC
1 ATGTATCGATAC
5962514 ATGTATCGATAC
1 ATGTATCGATAC
5962526 AT
1 AT
5962528 ATTTTGTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:5962573 original size:53 final size:53
Alignment explanation
Indices: 5962515--5962651 Score: 220
Period size: 53 Copynumber: 2.6 Consensus size: 53
5962505 TATCGATACA
* *
5962515 TGTATCGATACATATTTTGTGTATCGATACGAATTTGGCTATTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
5962568 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
*
5962621 TGTATAGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
5962652 TATGCAATCT
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
53 64 0.83
54 13 0.17
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:5962684 original size:20 final size:20
Alignment explanation
Indices: 5962639--5962692 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
5962629 TACATATTTG
*
5962639 TGTGTATCGATACTATGCAA
1 TGTGTATCGATACTATGAAA
* *
5962659 TCTGTATCGATAC-ATTTAAA
1 TGTGTATCGATACTA-TGAAA
5962679 TGTGTATCGATACT
1 TGTGTATCGATACT
5962693 TTTCAGGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTGTATCGATACTATGAAA
Found at i:5962757 original size:21 final size:21
Alignment explanation
Indices: 5962731--5962771 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5962721 GTCAACCTTG
5962731 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
5962752 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
5962772 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:5965643 original size:13 final size:13
Alignment explanation
Indices: 5965617--5965671 Score: 69
Period size: 13 Copynumber: 4.2 Consensus size: 13
5965607 AAGAAAATAA
5965617 AAAAAAAAGAAAG
1 AAAAAAAAGAAAG
5965630 AAAGAAAAAG-AAG
1 AAA-AAAAAGAAAG
*
5965643 AAAAAGAAGAAAG
1 AAAAAAAAGAAAG
5965656 AAAAAAGAA-AAAG
1 AAAAAA-AAGAAAG
5965669 AAA
1 AAA
5965672 GTTTATTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
12 5 0.14
13 24 0.65
14 8 0.22
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAG
Found at i:5965645 original size:9 final size:9
Alignment explanation
Indices: 5965617--5965670 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
5965607 AAGAAAATAA
*
5965617 AAAAAAAAG
1 AAAAAGAAG
*
5965626 AAAGA-AAG
1 AAAAAGAAG
5965634 AAAAAGAAG
1 AAAAAGAAG
5965643 AAAAAGAAG
1 AAAAAGAAG
*
5965652 AAAGAAAAAAG
1 -AA-AAAGAAG
5965663 AAAAAGAA
1 AAAAAGAA
5965671 AGTTTATTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
8 7 0.18
9 21 0.55
10 4 0.11
11 6 0.16
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:5965650 original size:23 final size:21
Alignment explanation
Indices: 5965607--5965672 Score: 84
Period size: 20 Copynumber: 3.1 Consensus size: 21
5965597 AAGCTCCACT
5965607 AAGAAA-ATAAAAA-AAAAAGA
1 AAGAAAGA-AAAAAGAAAAAGA
5965627 AAGAAAGAAAAAGAAGAAAAAG-
1 AAGAAAG-AAAA-AAGAAAAAGA
5965649 AAGAAAGAAAAAAGAAAAAGA
1 AAGAAAGAAAAAAGAAAAAGA
5965670 AAG
1 AAG
5965673 TTTATTCTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
20 15 0.37
21 10 0.24
22 10 0.24
23 6 0.15
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (21 bp):
AAGAAAGAAAAAAGAAAAAGA
Found at i:5965653 original size:26 final size:26
Alignment explanation
Indices: 5965617--5965671 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
5965607 AAGAAAATAA
*
5965617 AAAAAAAAGAAAGAAAGAAA-AAGAAG
1 AAAAAAAAGAAAGAAA-AAAGAAAAAG
*
5965643 AAAAAGAAGAAAGAAAAAAGAAAAAG
1 AAAAAAAAGAAAGAAAAAAGAAAAAG
5965669 AAA
1 AAA
5965672 GTTTATTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 3 0.12
26 23 0.88
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (26 bp):
AAAAAAAAGAAAGAAAAAAGAAAAAG
Found at i:5965663 original size:29 final size:28
Alignment explanation
Indices: 5965615--5965670 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
5965605 CTAAGAAAAT
5965615 AAAAAAAAAAGAAAGAAAGAAAAAGAAG
1 AAAAAAAAAAGAAAGAAAGAAAAAGAAG
5965643 AAAAAGAAGAAAGAAA-AAAGAAAAAGAA
1 AAAAA-AA-AAAGAAAGAAAGAAAAAGAA
5965671 AGTTTATTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 5 0.19
29 14 0.54
30 7 0.27
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (28 bp):
AAAAAAAAAAGAAAGAAAGAAAAAGAAG
Found at i:5966097 original size:21 final size:21
Alignment explanation
Indices: 5966073--5966122 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
5966063 TGTTCATGTT
5966073 ATTATGTTTA-ATTTAGTTTCC
1 ATTATGTTTATATTTAGTTT-C
*
5966094 ATTAT-TGTTATGTTTAGTTTC
1 ATTATGT-TTATATTTAGTTTC
5966115 ATTATGTT
1 ATTATGTT
5966123 ACTTTAAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 1 0.04
21 15 0.60
22 9 0.36
ACGTcount: A:0.22, C:0.06, G:0.12, T:0.60
Consensus pattern (21 bp):
ATTATGTTTATATTTAGTTTC
Found at i:5966109 original size:22 final size:20
Alignment explanation
Indices: 5966084--5966123 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
5966074 TTATGTTTAA
5966084 TTTAGTTTCCATTATTGTTATG
1 TTTAGTTT-CATTA-TGTTATG
5966106 TTTAGTTTCATTATGTTA
1 TTTAGTTTCATTATGTTA
5966124 CTTTAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.20, C:0.07, G:0.12, T:0.60
Consensus pattern (20 bp):
TTTAGTTTCATTATGTTATG
Found at i:5969653 original size:13 final size:13
Alignment explanation
Indices: 5969635--5969663 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5969625 ATCTTTTAAA
5969635 ATAATATATGGAT
1 ATAATATATGGAT
5969648 ATAATATATGGAT
1 ATAATATATGGAT
5969661 ATA
1 ATA
5969664 TTTTGATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (13 bp):
ATAATATATGGAT
Found at i:5970055 original size:34 final size:34
Alignment explanation
Indices: 5970008--5970126 Score: 145
Period size: 34 Copynumber: 3.5 Consensus size: 34
5969998 GGTAAAAACC
*
5970008 ACCATTTAATCAACAATGGCAACCTACCAAATCT
1 ACCATTTAATCAACAATGGTAACCTACCAAATCT
*
5970042 ACCATTTAGTCAACAATGGTAAGCC-ACCAAATC-
1 ACCATTTAATCAACAATGGTAA-CCTACCAAATCT
* *
5970075 ACCCATTTAATCAATAATGGTAAGCTACCAAAT-T
1 A-CCATTTAATCAACAATGGTAACCTACCAAATCT
*
5970109 TCTCATTTAATCAACAAT
1 AC-CATTTAATCAACAAT
5970127 TCTCCCACTT
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
33 3 0.04
34 68 0.93
35 2 0.03
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.27
Consensus pattern (34 bp):
ACCATTTAATCAACAATGGTAACCTACCAAATCT
Found at i:5974600 original size:34 final size:34
Alignment explanation
Indices: 5974534--5974652 Score: 111
Period size: 34 Copynumber: 3.5 Consensus size: 34
5974524 GGTAAAAACC
* *
5974534 ACCATTTAATCAACAAT-G-ACATCCTACCAAATCT
1 ACCATTTAATCAACAATGGTA-AGCC-ACAAAATCT
*
5974568 ACCATTTAGTCAACAATGGTAAGCCACAAAATC-
1 ACCATTTAATCAACAATGGTAAGCCACAAAATCT
* * *
5974601 ACCTATTTAATCAATAATGGTAAGCTACCAAAT-T
1 ACC-ATTTAATCAACAATGGTAAGCCACAAAATCT
*
5974635 TCTCATTTAATCAACAAT
1 AC-CATTTAATCAACAAT
5974653 TCTCCCACTT
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
33 3 0.04
34 62 0.87
35 5 0.07
36 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.29
Consensus pattern (34 bp):
ACCATTTAATCAACAATGGTAAGCCACAAAATCT
Found at i:5979422 original size:21 final size:21
Alignment explanation
Indices: 5979376--5979424 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
5979366 AAAAGATATA
5979376 TTTGGATGAAATGATGCATTG
1 TTTGGATGAAATGATGCATTG
* *
5979397 GTTGGATGAAA-GAATGCATTT
1 TTTGGATGAAATG-ATGCATTG
5979418 TTTGGAT
1 TTTGGAT
5979425 TAAAAATTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.39
Consensus pattern (21 bp):
TTTGGATGAAATGATGCATTG
Found at i:5984448 original size:21 final size:21
Alignment explanation
Indices: 5984422--5984479 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
5984412 AAAGATATAT
5984422 TTGGATGAAATG-ATGCATTGG
1 TTGGATGAAA-GAATGCATTGG
**
5984443 TTGGATGAAAGAATGCATTTT
1 TTGGATGAAAGAATGCATTGG
*
5984464 TTAGATGAAA-AATGCA
1 TTGGATGAAAGAATGCA
5984480 ACTTTTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 26 0.79
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (21 bp):
TTGGATGAAAGAATGCATTGG
Found at i:5984485 original size:20 final size:21
Alignment explanation
Indices: 5984446--5984486 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5984436 GCATTGGTTG
**
5984446 GATGAAAGAATGCATTTTTTA
1 GATGAAAGAATGCAACTTTTA
5984467 GATGAAA-AATGCAACTTTTA
1 GATGAAAGAATGCAACTTTTA
5984487 ATAACCAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (21 bp):
GATGAAAGAATGCAACTTTTA
Found at i:5984485 original size:21 final size:21
Alignment explanation
Indices: 5984446--5984485 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5984436 GCATTGGTTG
*
5984446 GATGAAAGAATGCATTTTTTA
1 GATGAAAGAATGCACTTTTTA
5984467 GATGAAA-AATGCAACTTTT
1 GATGAAAGAATGC-ACTTTT
5984486 AATAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.35
Consensus pattern (21 bp):
GATGAAAGAATGCACTTTTTA
Found at i:5988691 original size:24 final size:25
Alignment explanation
Indices: 5988632--5988691 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
5988622 ACTTAAGGAA
* * *
5988632 AGCTAAGTATTTAAAATACTAGTAT
1 AGCTAGGTATTTAAAACACTAATAT
*
5988657 AGCTAGGTATTTAAAGCACTAATAT
1 AGCTAGGTATTTAAAACACTAATAT
5988682 A-CTAGGTATT
1 AGCTAGGTATT
5988692 ATAACCGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 9 0.29
25 22 0.71
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (25 bp):
AGCTAGGTATTTAAAACACTAATAT
Found at i:5988909 original size:26 final size:26
Alignment explanation
Indices: 5988879--5988933 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
5988869 TAAACTAATT
* *
5988879 TTAATAATTAAATAATATTATCAGGA
1 TTAATAATTAAATAACATTATCAAGA
*
5988905 TTAATAATTAAATTACATTATCAAGA
1 TTAATAATTAAATAACATTATCAAGA
5988931 TTA
1 TTA
5988934 GTGAAATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.40
Consensus pattern (26 bp):
TTAATAATTAAATAACATTATCAAGA
Found at i:5990236 original size:51 final size:51
Alignment explanation
Indices: 5990099--5990249 Score: 145
Period size: 47 Copynumber: 3.0 Consensus size: 51
5990089 TGAATGGGAA
* * *
5990099 AGAGGAAATGTATACATTTAATTTAATAAATTAATTTGATTCATGCATGGAG
1 AGAGGAAAT-AATACATTTAATTTAATAAACTAATTTGATTCATGTATGGAG
* * *
5990151 AGAGGAAATAA-ACA-CT-A-TTAA-CAAGTCAATTTGATTCATGTATGG-G
1 AGAGGAAATAATACATTTAATTTAATAAACT-AATTTGATTCATGTATGGAG
* *
5990197 AG-GAGACATAAATACATTTAATTTAATAAACTAATTTGATTCATGTGTGGAG
1 AGAG-GAAAT-AATACATTTAATTTAATAAACTAATTTGATTCATGTATGGAG
5990249 A
1 A
5990250 ATGGAGATGA
Statistics
Matches: 80, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
45 1 0.01
46 10 0.12
47 23 0.29
48 4 0.05
49 2 0.03
50 4 0.05
51 22 0.28
52 14 0.17
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (51 bp):
AGAGGAAATAATACATTTAATTTAATAAACTAATTTGATTCATGTATGGAG
Found at i:5990969 original size:47 final size:49
Alignment explanation
Indices: 5990915--5991020 Score: 126
Period size: 48 Copynumber: 2.2 Consensus size: 49
5990905 ATGTATAAAA
* * * * *
5990915 AGAGGAGATGAATTTTATAT-CTAAAGTAATTTGATTTATATA-GGGAG
1 AGAGGAGATGAATATAATATAATAAAATAATTTGATTCATATATGGGAG
* *
5990962 AGTGGAGATGAATATAATTTAATAAAATAATTTGATTCATATATGGGAG
1 AGAGGAGATGAATATAATATAATAAAATAATTTGATTCATATATGGGAG
*
5991011 TGAGGAGATG
1 AGAGGAGATG
5991021 TGTGTATTTG
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
47 16 0.33
48 19 0.40
49 13 0.27
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.34
Consensus pattern (49 bp):
AGAGGAGATGAATATAATATAATAAAATAATTTGATTCATATATGGGAG
Found at i:5991365 original size:13 final size:13
Alignment explanation
Indices: 5991347--5991371 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5991337 TCATAAAATA
5991347 TTTTTTATTTTCC
1 TTTTTTATTTTCC
5991360 TTTTTTATTTTC
1 TTTTTTATTTTC
5991372 ATTTGTTAAA
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:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTATTTTCC
Found at i:5992219 original size:19 final size:19
Alignment explanation
Indices: 5992195--5992231 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
5992185 ATTTAAAATA
5992195 AAATTATTTTTATTCAAAC
1 AAATTATTTTTATTCAAAC
5992214 AAATTATTTTTATTCAAA
1 AAATTATTTTTATTCAAA
5992232 AATATTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATTATTTTTATTCAAAC
Found at i:5992677 original size:21 final size:22
Alignment explanation
Indices: 5992653--5992701 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
5992643 ACATCATATT
* *
5992653 TTAATCTT-ATTGTTATAGTAC
1 TTAATCTTCATCGGTATAGTAC
*
5992674 TTAAT-TTCATCGGTATAGTAG
1 TTAATCTTCATCGGTATAGTAC
5992695 TTAATCT
1 TTAATCT
5992702 CACGGTTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 20 0.87
22 1 0.04
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (22 bp):
TTAATCTTCATCGGTATAGTAC
Done.