Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 81 of 93
Found at i:31085898 original size:35 final size:35
Alignment explanation
Indices: 31085843--31085920 Score: 88
Period size: 35 Copynumber: 2.3 Consensus size: 35
31085833 GAAATAGTGC
* * *
31085843 TTCACTT-ATTTAGTTATTTTATGTGA-AGTAGTAT
1 TTCACTTGTTTTAGTTATTTTACGT-ACAATAGTAT
* *
31085877 TTCACTTGTTTTAGTTGTTTTACGTACAATAGTGT
1 TTCACTTGTTTTAGTTATTTTACGTACAATAGTAT
31085912 TTCACTTGT
1 TTCACTTGT
31085921 AATTGTTGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
34 8 0.22
35 29 0.78
ACGTcount: A:0.22, C:0.10, G:0.15, T:0.53
Consensus pattern (35 bp):
TTCACTTGTTTTAGTTATTTTACGTACAATAGTAT
Found at i:31113279 original size:12 final size:12
Alignment explanation
Indices: 31113262--31113299 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
31113252 ATTACAACAC
*
31113262 ATATATATATAT
1 ATATATATGTAT
31113274 ATATATATGTAT
1 ATATATATGTAT
*
31113286 ATGTATATGTAT
1 ATATATATGTAT
31113298 AT
1 AT
31113300 TTCTTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
ATATATATGTAT
Found at i:31127880 original size:18 final size:18
Alignment explanation
Indices: 31127843--31127886 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
31127833 AGGTTAAAAA
31127843 AATTAA-TAATTTTAATT
1 AATTAATTAATTTTAATT
*
31127860 AATTTATTAATTTT-ATAT
1 AATTAATTAATTTTAAT-T
31127878 AATTAATTA
1 AATTAATTA
31127887 TATAAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AATTAATTAATTTTAATT
Found at i:31127884 original size:14 final size:14
Alignment explanation
Indices: 31127865--31127898 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
31127855 TAATTAATTT
* *
31127865 ATTAATTTTATATA
1 ATTAATTATATAAA
31127879 ATTAATTATATAAA
1 ATTAATTATATAAA
31127893 ATTAAT
1 ATTAAT
31127899 AATTTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTAATTATATAAA
Found at i:31128022 original size:15 final size:17
Alignment explanation
Indices: 31127992--31128031 Score: 57
Period size: 15 Copynumber: 2.4 Consensus size: 17
31127982 GAATTAAATC
31127992 ATAAAATAATTTTATTA
1 ATAAAATAATTTTATTA
31128009 ATAAAA-AA-TTTATTA
1 ATAAAATAATTTTATTA
31128024 AGTAAAAT
1 A-TAAAAT
31128032 TATTAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 8 0.38
16 7 0.33
17 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
ATAAAATAATTTTATTA
Found at i:31132517 original size:2 final size:2
Alignment explanation
Indices: 31132510--31132546 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
31132500 GCACAAGTGC
* *
31132510 GT GT GT GT GT GT GT GT GT GT GT GT GT TT GT GT TT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
31132547 CAAAATGGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.46, T:0.54
Consensus pattern (2 bp):
GT
Found at i:31142528 original size:61 final size:60
Alignment explanation
Indices: 31142449--31142598 Score: 155
Period size: 61 Copynumber: 2.5 Consensus size: 60
31142439 TAAATTGAGG
* * * * *
31142449 AAATATATCAATACAAATTTTACGAAATGTCCCCTTTC-AC-AAATCTATCAATATATT-TGTT
1 AAATGTATCGATAAAAATTTTACAAAATGT---CTTTCAACTAAATCTATCAATACATTCT-TT
*
31142510 AAATGTATCGATAAAAATTTTACAAAATGTTTTTCAACTTAAATCTATCAATACATTCTTT
1 AAATGTATCGATAAAAATTTTACAAAATGTCTTTCAAC-TAAATCTATCAATACATTCTTT
* *
31142571 -TATGTATCGATAAAAATTCTACAAAATG
1 AAATGTATCGATAAAAATTTTACAAAATG
31142599 CCTCCTTATT
Statistics
Matches: 77, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
58 4 0.05
59 2 0.03
60 26 0.34
61 44 0.57
62 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (60 bp):
AAATGTATCGATAAAAATTTTACAAAATGTCTTTCAACTAAATCTATCAATACATTCTTT
Found at i:31142645 original size:20 final size:20
Alignment explanation
Indices: 31142620--31142657 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
31142610 TTCTTGTTAA
*
31142620 GAATGTATCGATACATTTAT
1 GAATGTATCGAGACATTTAT
31142640 GAATGTATCGAGACATTT
1 GAATGTATCGAGACATTT
31142658 TCTCTAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (20 bp):
GAATGTATCGAGACATTTAT
Found at i:31142839 original size:84 final size:84
Alignment explanation
Indices: 31142735--31142908 Score: 294
Period size: 84 Copynumber: 2.1 Consensus size: 84
31142725 CTGCTTAAAT
* *
31142735 CATACCTTAAATTTAACCATATATTCCACACTTTTCAATGTATATGTTTAGAACATAACTCAAAG
1 CATACATTAAATTTAACCATATATTCCACACTTTTCAATGTATATGTTCAGAACATAACTCAAAG
* * *
31142800 CTTCGATCAAAGTTCAAAC
66 CTTCAATCAAACTCCAAAC
*
31142819 CATACATTAAATTTAACCATATGTTCCACACTTTTCAATGTATATGTTCAGAACATAACTCAAAG
1 CATACATTAAATTTAACCATATATTCCACACTTTTCAATGTATATGTTCAGAACATAACTCAAAG
31142884 CTTCAATCAAACTCCAAAC
66 CTTCAATCAAACTCCAAAC
31142903 CATACA
1 CATACA
31142909 ATTTATTAAT
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.32
Consensus pattern (84 bp):
CATACATTAAATTTAACCATATATTCCACACTTTTCAATGTATATGTTCAGAACATAACTCAAAG
CTTCAATCAAACTCCAAAC
Found at i:31143323 original size:23 final size:23
Alignment explanation
Indices: 31143296--31143349 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
31143286 TGATTGGTCC
31143296 AATTAAATGCAAACCCTTATAAA
1 AATTAAATGCAAACCCTTATAAA
** *
31143319 AATTACGGTGCAAGCCCTTATAAA
1 AATTA-AATGCAAACCCTTATAAA
31143343 AATTAAA
1 AATTAAA
31143350 ATATGGGTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.26
Consensus pattern (23 bp):
AATTAAATGCAAACCCTTATAAA
Found at i:31149320 original size:60 final size:60
Alignment explanation
Indices: 31149209--31149363 Score: 195
Period size: 60 Copynumber: 2.6 Consensus size: 60
31149199 TTGACAGGTC
* * * * **
31149209 TATATTTGGTGGCATAAGGAGTTTCTATGAGTAGGTAAAGGGGAACCTAAAGCCTCGGTT
1 TATATTTGGTGGCATAGGGAGTTTCCATGAGTAGGCAAAGGAGAACCTAAAGCCTCAATT
* * *
31149269 TATATTTGGTGGCATGGGGAGTTTCCATGAGTCGGCAAA-GAGATACTTAAAGCCTCAATT
1 TATATTTGGTGGCATAGGGAGTTTCCATGAGTAGGCAAAGGAGA-ACCTAAAGCCTCAATT
* *
31149329 TATATTTGGTGGCATAGGGAGTTCCCACGAGTAGG
1 TATATTTGGTGGCATAGGGAGTTTCCATGAGTAGG
31149364 TGATAATTTT
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
59 3 0.04
60 78 0.96
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.30
Consensus pattern (60 bp):
TATATTTGGTGGCATAGGGAGTTTCCATGAGTAGGCAAAGGAGAACCTAAAGCCTCAATT
Found at i:31159491 original size:13 final size:13
Alignment explanation
Indices: 31159473--31159518 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
31159463 TTGTTTGTCT
31159473 TTAATGGATAGAA
1 TTAATGGATAGAA
31159486 TTAAT-GATTAGTAA
1 TTAATGGA-TAG-AA
*
31159500 TTAATGGAAAGAA
1 TTAATGGATAGAA
31159513 TTAATG
1 TTAATG
31159519 CAGTTGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
12 2 0.07
13 16 0.55
14 9 0.31
15 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.35
Consensus pattern (13 bp):
TTAATGGATAGAA
Found at i:31160034 original size:20 final size:20
Alignment explanation
Indices: 31160005--31160053 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
31159995 GCAACGGTTC
*
31160005 TGATCGCCGAACCGAATTTA
1 TGATCACCGAACCGAATTTA
31160025 TGATCACCGAACCGAATTTA
1 TGATCACCGAACCGAATTTA
31160045 TGATCACCG
1 TGATCACCG
31160054 TGGGATTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (20 bp):
TGATCACCGAACCGAATTTA
Found at i:31176601 original size:15 final size:15
Alignment explanation
Indices: 31176581--31176619 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
31176571 TTTACAATGC
*
31176581 AATGTGATTACAGGT
1 AATGTGATTACAAGT
*
31176596 AATGTGATTGCAAGT
1 AATGTGATTACAAGT
*
31176611 AAAGTGATT
1 AATGTGATT
31176620 GTAGAGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (15 bp):
AATGTGATTACAAGT
Found at i:31176929 original size:35 final size:33
Alignment explanation
Indices: 31176865--31176929 Score: 78
Period size: 35 Copynumber: 1.9 Consensus size: 33
31176855 TTTTATTATA
* *
31176865 ATATTATATATTTTATTTTCATTTCTTTTACCT
1 ATATTATATATTTTAATTTCATTTATTTTACCT
31176898 ATATTATATAAATTTTAATTTC-TTATATTTTA
1 ATATTATAT--ATTTTAATTTCATT-TATTTTA
31176930 TTTTATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 9 0.33
34 2 0.07
35 16 0.59
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (33 bp):
ATATTATATATTTTAATTTCATTTATTTTACCT
Found at i:31176935 original size:55 final size:52
Alignment explanation
Indices: 31176855--31176986 Score: 142
Period size: 55 Copynumber: 2.5 Consensus size: 52
31176845 TTATTTTTAT
* * * *
31176855 TTTTATTATAATATTATATATTTTATTTTCATTTCT-TTTACCTATATTATATAAA
1 TTTTATTTTAATATT-TTTATTTTATTTTAATTTCTAATT-CCTATATTATAT--A
* *
31176910 TTTTAATTTCTTATA-TTTTATTTTATTTTAATTTCTAATTCTTATATTATATA
1 TTTT-ATTT-TAATATTTTTATTTTATTTTAATTTCTAATTCCTATATTATATA
31176963 TTTTATTTTAATATTTTTATTTTA
1 TTTTATTTTAATATTTTTATTTTA
31176987 ATTATAACAT
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
51 4 0.06
52 14 0.21
53 5 0.08
55 33 0.50
56 6 0.09
57 4 0.06
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (52 bp):
TTTTATTTTAATATTTTTATTTTATTTTAATTTCTAATTCCTATATTATATA
Found at i:31176980 original size:14 final size:15
Alignment explanation
Indices: 31176958--31176988 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
31176948 TTCTTATATT
31176958 ATATATTTTATTTTA
1 ATATATTTTATTTTA
31176973 ATAT-TTTTATTTTA
1 ATATATTTTATTTTA
31176987 AT
1 AT
31176989 TATAACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATATATTTTATTTTA
Found at i:31178806 original size:18 final size:18
Alignment explanation
Indices: 31178783--31178817 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31178773 ACTTTTTATA
31178783 ATAATTT-TAATAAAAAAT
1 ATAATTTATAA-AAAAAAT
31178801 ATAATTTATAAAAAAAA
1 ATAATTTATAAAAAAAA
31178818 CTTACAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAATTTATAAAAAAAAT
Found at i:31187021 original size:20 final size:22
Alignment explanation
Indices: 31186993--31187038 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
31186983 TATTTCTATC
*
31186993 TAAACTTATAATAC-T-AAATA
1 TAAAATTATAATACATAAAATA
31187013 TAAAATTATAATACATAAAATA
1 TAAAATTATAATACATAAAATA
31187035 TAAA
1 TAAA
31187039 TAGTTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.57
21 1 0.04
22 9 0.39
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATTATAATACATAAAATA
Found at i:31189162 original size:14 final size:14
Alignment explanation
Indices: 31189143--31189170 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31189133 ATTTGATAAA
31189143 TTTTTTTTTAAGTT
1 TTTTTTTTTAAGTT
31189157 TTTTTTTTTAAGTT
1 TTTTTTTTTAAGTT
31189171 ATAATTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (14 bp):
TTTTTTTTTAAGTT
Found at i:31205526 original size:310 final size:310
Alignment explanation
Indices: 31204964--31206514 Score: 2958
Period size: 310 Copynumber: 5.0 Consensus size: 310
31204954 GGCACCCTCC
31204964 ATGATACGAGGACAAGAGTTAAAGCAGAATCAAAGTTTTGTGATCGATTACAGATAATTTGTTTC
1 ATGATACGAGGACAAGAGTTAAAGCAGAATCAAAGTTTTGTGATCGATTACAGATAATTTGTTTC
* *
31205029 GTCGACAACGATTCAAGGACTTGGAGGTGGGGGAAACGAGATTGAGCTTGTTCGGTTTCTTTCTC
66 GTCGACAAGGATTCAAGGACTTGGAGGTGGGGGAAACGAGATTGAGCCTGTTCGGTTTCTTTCTC
*
31205094 CATTTCATTTTGCGTACAGCACAAGGCCCAGTTTGTTATATATCTCTTTCACGATTTAGGCCCAA
131 CATTTCATTTTGCGTACAGCACAAGGCCCAATTTGTTATATATCTCTTTCACGATTTAGGCCCAA
*
31205159 TTGTGTTGCCATTAGTCTATTTTAAGTCTATAAAGAATCAACAAAAATTTCCAGTAAGACCCAAA
196 TTGTGTAGCCATTAGTCTATTTTAAGTCTATAAAGAATCAACAAAAATTTCCAGTAAGACCCAAA
31205224 GAAGAATGGAAACAACGAACAGGTTGAAGCTCAAATCAATGAGAAAACAA
261 GAAGAATGGAAACAACGAACAGGTTGAAGCTCAAATCAATGAGAAAACAA
31205274 ATGATACGAGGACAAGAGTTAAAGCAGAATCAAAGTTTTGTGATCGATTACAGATAATTTGTTTC
1 ATGATACGAGGACAAGAGTTAAAGCAGAATCAAAGTTTTGTGATCGATTACAGATAATTTGTTTC
31205339 GTCGACAAGGATTCAAGGACTTGGAGGTGGGGGAAACGAGATTGAGCCTGTTCGGTTTCTTTCTC
66 GTCGACAAGGATTCAAGGACTTGGAGGTGGGGGAAACGAGATTGAGCCTGTTCGGTTTCTTTCTC
* *
31205404 CCTTTCATTTTGCGTACAGCACAAGGCCCAATTTGTTATATATCTCTTTCACGATTTAGACCCAA
131 CATTTCATTTTGCGTACAGCACAAGGCCCAATTTGTTATATATCTCTTTCACGATTTAGGCCCAA
*
31205469 TTGTGTAGCCATTAGTCTATTTTAAGTCTATAAAAAATCAACAAAAATTTCCAGTAAGACCCAAA
196 TTGTGTAGCCATTAGTCTATTTTAAGTCTATAAAGAATCAACAAAAATTTCCAGTAAGACCCAAA
31205534 GAAGAATGGAAACAACGAACAGGTTGAAGCTCAAATCAATGAGAAAACAA
261 GAAGAATGGAAACAACGAACAGGTTGAAGCTCAAATCAATGAGAAAACAA
31205584 ATGATACGAGGACAAGAGTTAAAGCAGAATCAAAGTTTTGTGATCGATTACAGATAATTTGTTTC
1 ATGATACGAGGACAAGAGTTAAAGCAGAATCAAAGTTTTGTGATCGATTACAGATAATTTGTTTC
*
31205649 GTCGACAAGGATTCAAGGACTTGGAAGTGGGGGAAACGAGATTGAGCCTGTTCGGTTTCTTTCTC
66 GTCGACAAGGATTCAAGGACTTGGAGGTGGGGGAAACGAGATTGAGCCTGTTCGGTTTCTTTCTC
* *
31205714 CATTTCATTTTGCGTACAGCACAATGCCCAATTTGTTATATATCTCTTTCACGATTTAGGCCAAA
131 CATTTCATTTTGCGTACAGCACAAGGCCCAATTTGTTATATATCTCTTTCACGATTTAGGCCCAA
*
31205779 TTGTGTAGCCATTAGTCTATTTTAAGTCTATAAAGAATCAACAAAAATTTTCAGTAAGACCCAAA
196 TTGTGTAGCCATTAGTCTATTTTAAGTCTATAAAGAATCAACAAAAATTTCCAGTAAGACCCAAA
31205844 GAAGAATGGAAACAACGAACAGGTTGAAGCTCAAATCAATGAGAAAACAA
261 GAAGAATGGAAACAACGAACAGGTTGAAGCTCAAATCAATGAGAAAACAA
31205894 ATGATACGAGGACAAGAGTTAAAGCAGAATCAAAGTTTTGTGATCGATTACAGATAATTTGTTTC
1 ATGATACGAGGACAAGAGTTAAAGCAGAATCAAAGTTTTGTGATCGATTACAGATAATTTGTTTC
31205959 GTCGACAAGGATTCAAGGACTTGGAGGTGGGGGAAACGAGATTGAGCCTGTTCGGTTTCTTTCTC
66 GTCGACAAGGATTCAAGGACTTGGAGGTGGGGGAAACGAGATTGAGCCTGTTCGGTTTCTTTCTC
31206024 CATTTCATTTTGCGTACAGCACAAGGCCCAATTTGTTATATATCTCTTTCACGATTTAGGCCCAA
131 CATTTCATTTTGCGTACAGCACAAGGCCCAATTTGTTATATATCTCTTTCACGATTTAGGCCCAA
31206089 TTGTGTAGCCATTAGTCTATTTTAAGTCTATAAAGAATCAACAAAAATTTCCAGTAAGACCCAAA
196 TTGTGTAGCCATTAGTCTATTTTAAGTCTATAAAGAATCAACAAAAATTTCCAGTAAGACCCAAA
31206154 GAAGAATGGAAACAACGAACAGGTTGAAGCTCAAATCAATGAGAAAACAA
261 GAAGAATGGAAACAACGAACAGGTTGAAGCTCAAATCAATGAGAAAACAA
31206204 ATGATACGAGGACAAGAGTTAAAGCAGAATCAAAGTTTTGTGATCGATTACAGATAATTTGTTTC
1 ATGATACGAGGACAAGAGTTAAAGCAGAATCAAAGTTTTGTGATCGATTACAGATAATTTGTTTC
*
31206269 GTCGACAAGGATTCAAGGACTTGGAGGTGGGGGAAACGAGATTGAGCCTGTTCGATTTCTTTCTC
66 GTCGACAAGGATTCAAGGACTTGGAGGTGGGGGAAACGAGATTGAGCCTGTTCGGTTTCTTTCTC
31206334 CATTTCATTTTGCGTACAGCACAAGGCCCAATTTGTTATATATCTCTTTCACGATTTAGGCCCAA
131 CATTTCATTTTGCGTACAGCACAAGGCCCAATTTGTTATATATCTCTTTCACGATTTAGGCCCAA
* *
31206399 TTGTGTAGCCATTAATCTATTTTAAGTTTATAAAGAATCAACAAAAATTTCCAGTAAGACCCAAA
196 TTGTGTAGCCATTAGTCTATTTTAAGTCTATAAAGAATCAACAAAAATTTCCAGTAAGACCCAAA
* *
31206464 GAAGAATGGAAACAACGAACAAGTTGAAGCTCAAATAAATGAGAAAACAA
261 GAAGAATGGAAACAACGAACAGGTTGAAGCTCAAATCAATGAGAAAACAA
31206514 A
1 A
31206515 AGAGGTCCGA
Statistics
Matches: 1218, Mismatches: 23, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
310 1218 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (310 bp):
ATGATACGAGGACAAGAGTTAAAGCAGAATCAAAGTTTTGTGATCGATTACAGATAATTTGTTTC
GTCGACAAGGATTCAAGGACTTGGAGGTGGGGGAAACGAGATTGAGCCTGTTCGGTTTCTTTCTC
CATTTCATTTTGCGTACAGCACAAGGCCCAATTTGTTATATATCTCTTTCACGATTTAGGCCCAA
TTGTGTAGCCATTAGTCTATTTTAAGTCTATAAAGAATCAACAAAAATTTCCAGTAAGACCCAAA
GAAGAATGGAAACAACGAACAGGTTGAAGCTCAAATCAATGAGAAAACAA
Found at i:31209358 original size:310 final size:310
Alignment explanation
Indices: 31208796--31210279 Score: 2736
Period size: 310 Copynumber: 4.8 Consensus size: 310
31208786 AAAACAGTAN
31208796 ACAAGGATTCAAGGACTTGGAGGTGGGGGAAACGAGATTGAGCCTGTTCGGTTTCTTTCTCCATT
1 ACAAGGATTCAAGGACTTGGAGGTGGGGGAAACGAGATTGAGCCTGTTCGGTTTCTTTCTCCATT
* * *
31208861 TCATTTTGCGTACAGCACAAGGCCCAGTTTGTTATATATCTCTTTCACGATTTAGGCCCAATTGT
66 TCATTTTGCGTACAGCACAATGCCCAATTTGTTATATATCTCTTTCACGATTTAGACCCAATTGT
*
31208926 GTAGCCATTAATCTATTTTAAGTTTATAAAGAATCAACAAAAATTTCTAGTAAGACCCAAAGAAG
131 GTAGCCATTAATCTATTTTAAGTCTATAAAGAATCAACAAAAATTTCTAGTAAGACCCAAAGAAG
31208991 AATGGAAACAACGAACAGGTTGAAGCTCAAATCAATGAGAAAACAAATTATACGAGGACAAGAGT
196 AATGGAAACAACGAACAGGTTGAAGCTCAAATCAATGAGAAAACAAATTATACGAGGACAAGAGT
31209056 TAAAGCAGAATCAAAGTTTTGTGATCGATTACAGATAATTTGTTTCGTCG
261 TAAAGCAGAATCAAAGTTTTGTGATCGATTACAGATAATTTGTTTCGTCG
* *
31209106 ACAAGGATTCAAGGGCTTGGAGGTGGGGGAAACGAGATTGAGCTTGTTCGGTTTCTTTCTCCATT
1 ACAAGGATTCAAGGACTTGGAGGTGGGGGAAACGAGATTGAGCCTGTTCGGTTTCTTTCTCCATT
* * *
31209171 TCATTTTGCGTACAGCACAAGGCCCAGTTTGTTATATATCTCTTTCACGATTTAGGCCCAATTGT
66 TCATTTTGCGTACAGCACAATGCCCAATTTGTTATATATCTCTTTCACGATTTAGACCCAATTGT
*
31209236 GTAGCCATTAATCTATTTTAAGTTTATAAAGAATCAACAAAAATTTCTAGTAAGACCCAAAGAAG
131 GTAGCCATTAATCTATTTTAAGTCTATAAAGAATCAACAAAAATTTCTAGTAAGACCCAAAGAAG
31209301 AATGGAAACAACGAACAGGTTGAAGCTCAAATCAATGAGAAAACAAATTATACGAGGACAAGAGT
196 AATGGAAACAACGAACAGGTTGAAGCTCAAATCAATGAGAAAACAAATTATACGAGGACAAGAGT
31209366 TAAAGCAGAATCAAAGTTTTGTGATCGATTACAGATAATTTGTTTCGTCG
261 TAAAGCAGAATCAAAGTTTTGTGATCGATTACAGATAATTTGTTTCGTCG
* *
31209416 ACAAGGATTCAAGGACTTGGAAGTGGGGGAAACGAGATTGAGCCTGTTCGATTTCTTTCTCCATT
1 ACAAGGATTCAAGGACTTGGAGGTGGGGGAAACGAGATTGAGCCTGTTCGGTTTCTTTCTCCATT
31209481 TCATTTTGCGTACAGCACAATGCCCAATTTGTTATATATCTCTTTCACGATTTAGACCCAATTGT
66 TCATTTTGCGTACAGCACAATGCCCAATTTGTTATATATCTCTTTCACGATTTAGACCCAATTGT
* * *
31209546 GTAGCCATTAGTCTATTTTAAGTCTATAAAAAATCAACAAAAATTTCCAGTAAGACCCAAAGAAG
131 GTAGCCATTAATCTATTTTAAGTCTATAAAGAATCAACAAAAATTTCTAGTAAGACCCAAAGAAG
*
31209611 AATGGAAACAACGAACAGGTTGAAGCTCAAATCAATGAGAAAACAAATGATACGAGGACAAGAGT
196 AATGGAAACAACGAACAGGTTGAAGCTCAAATCAATGAGAAAACAAATTATACGAGGACAAGAGT
31209676 TAAAGCAGAATCAAAGTTTTGTGATCGATTACAGATAATTTGTTTCGTCG
261 TAAAGCAGAATCAAAGTTTTGTGATCGATTACAGATAATTTGTTTCGTCG
* *
31209726 ACAAGGATTCAAGGGCTTGGAGGTGGGGGAAACGAGATTGAGCTTGTTCGGTTTCTTTCTCCATT
1 ACAAGGATTCAAGGACTTGGAGGTGGGGGAAACGAGATTGAGCCTGTTCGGTTTCTTTCTCCATT
31209791 TCATTTTGCGTACAGCACAATGCCCAATTTGTTATATATCTCTTTCACGATTTAGACCCAATTGT
66 TCATTTTGCGTACAGCACAATGCCCAATTTGTTATATATCTCTTTCACGATTTAGACCCAATTGT
*
31209856 GTAGCCATTAGTCTATTTTAAGTCTATAAAGAATCAACAAAAATTT-TCAGTAAGACCCAAAGAA
131 GTAGCCATTAATCTATTTTAAGTCTATAAAGAATCAACAAAAATTTCT-AGTAAGACCCAAAGAA
31209920 GAATGGAAACAACGAACAGGTTGAAGCTCAAATCAATGAGAAAACAAATTATACGAGGACAAGAG
195 GAATGGAAACAACGAACAGGTTGAAGCTCAAATCAATGAGAAAACAAATTATACGAGGACAAGAG
31209985 TTAAAGCAGAATCAAAGTTTTGTGATCGATTACAGATAATTTGTTTCGTCG
260 TTAAAGCAGAATCAAAGTTTTGTGATCGATTACAGATAATTTGTTTCGTCG
* *
31210036 ACAAGGATTCAAGGACTTGGAAGTGGGGGAAACGAGATTGAGCCTGTTCGATTTCTTTCTCCATT
1 ACAAGGATTCAAGGACTTGGAGGTGGGGGAAACGAGATTGAGCCTGTTCGGTTTCTTTCTCCATT
31210101 TCATTTTGCGTACAGCACAATGCCCAATTTGTTATATATCTCTTTCACGATTTAGACCCAATTGT
66 TCATTTTGCGTACAGCACAATGCCCAATTTGTTATATATCTCTTTCACGATTTAGACCCAATTGT
*
31210166 GTAGCCATTAGAATCTATTTTAAGTCTATAAAGAATCAACAAAAATTTCCAGTAAGACCCAAAGA
131 GTAGCCATT--AATCTATTTTAAGTCTATAAAGAATCAACAAAAATTTCTAGTAAGACCCAAAGA
31210231 AGAATGGAAACAACGAACAGGTTGAAGCTCAAATCAATGAGAAAACAAA
194 AGAATGGAAACAACGAACAGGTTGAAGCTCAAATCAATGAGAAAACAAA
31210280 AGAGGTCCGA
Statistics
Matches: 1143, Mismatches: 27, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
310 1043 0.91
312 100 0.09
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.29
Consensus pattern (310 bp):
ACAAGGATTCAAGGACTTGGAGGTGGGGGAAACGAGATTGAGCCTGTTCGGTTTCTTTCTCCATT
TCATTTTGCGTACAGCACAATGCCCAATTTGTTATATATCTCTTTCACGATTTAGACCCAATTGT
GTAGCCATTAATCTATTTTAAGTCTATAAAGAATCAACAAAAATTTCTAGTAAGACCCAAAGAAG
AATGGAAACAACGAACAGGTTGAAGCTCAAATCAATGAGAAAACAAATTATACGAGGACAAGAGT
TAAAGCAGAATCAAAGTTTTGTGATCGATTACAGATAATTTGTTTCGTCG
Found at i:31217351 original size:22 final size:22
Alignment explanation
Indices: 31217325--31217367 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
31217315 ATCTATTGTT
31217325 AACTACTTTAATTGTACTAGAC
1 AACTACTTTAATTGTACTAGAC
31217347 AACTACTTTAATTGTACTAGA
1 AACTACTTTAATTGTACTAGA
31217368 TAACCAGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (22 bp):
AACTACTTTAATTGTACTAGAC
Found at i:31225183 original size:12 final size:12
Alignment explanation
Indices: 31225166--31225212 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
31225156 TCCACGACTG
31225166 CGGCTGCGGCTA
1 CGGCTGCGGCTA
*
31225178 CGGCTGCGACTA
1 CGGCTGCGGCTA
* *
31225190 CGGCTTCGGCTC
1 CGGCTGCGGCTA
*
31225202 CGGCTACGGCT
1 CGGCTGCGGCT
31225213 TCTTGAGAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.09, C:0.36, G:0.36, T:0.19
Consensus pattern (12 bp):
CGGCTGCGGCTA
Found at i:31225193 original size:24 final size:24
Alignment explanation
Indices: 31225160--31225206 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
31225150 GCTCCGTCCA
*
31225160 CGACTGCGGCTGCGGCTACGGCTG
1 CGACTACGGCTGCGGCTACGGCTG
* *
31225184 CGACTACGGCTTCGGCTCCGGCT
1 CGACTACGGCTGCGGCTACGGCT
31225207 ACGGCTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.36, T:0.19
Consensus pattern (24 bp):
CGACTACGGCTGCGGCTACGGCTG
Found at i:31225213 original size:18 final size:18
Alignment explanation
Indices: 31225166--31225214 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
31225156 TCCACGACTG
* * *
31225166 CGGCTGCGGCTACGGCTG
1 CGGCTACGGCTTCGGCTC
*
31225184 CGACTACGGCTTCGGCTC
1 CGGCTACGGCTTCGGCTC
31225202 CGGCTACGGCTTC
1 CGGCTACGGCTTC
31225215 TTGAGAGTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.08, C:0.37, G:0.35, T:0.20
Consensus pattern (18 bp):
CGGCTACGGCTTCGGCTC
Found at i:31230576 original size:55 final size:56
Alignment explanation
Indices: 31230469--31230577 Score: 148
Period size: 56 Copynumber: 2.0 Consensus size: 56
31230459 TAACATACAC
* ** * **
31230469 ACAATATGTATGTCTGATAAGAACATGATATGAATGAATGCACTAAAACAAAAAAT
1 ACAATATGAATGTCAAATAAGAACATAATATGAATGAATAAACTAAAACAAAAAAT
*
31230525 ACAATATGAATGTCAAATATGAACATAATAT-AATGAATAAACTAAAACAAAAA
1 ACAATATGAATGTCAAATAAGAACATAATATGAATGAATAAACTAAAACAAAAA
31230578 TGAAGAGAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
55 20 0.43
56 26 0.57
ACGTcount: A:0.55, C:0.10, G:0.11, T:0.24
Consensus pattern (56 bp):
ACAATATGAATGTCAAATAAGAACATAATATGAATGAATAAACTAAAACAAAAAAT
Found at i:31237656 original size:15 final size:15
Alignment explanation
Indices: 31237633--31237691 Score: 73
Period size: 15 Copynumber: 3.9 Consensus size: 15
31237623 ATTTAATACT
31237633 TTACAATGTAATGTGA
1 TTACAA-GTAATGTGA
*
31237649 TTACATGTAATGTGA
1 TTACAAGTAATGTGA
* *
31237664 TTGCAAGTAATATGA
1 TTACAAGTAATGTGA
*
31237679 ATACAAGTAATGT
1 TTACAAGTAATGT
31237692 AATTGCAAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
15 31 0.86
16 5 0.14
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.36
Consensus pattern (15 bp):
TTACAAGTAATGTGA
Found at i:31237689 original size:30 final size:30
Alignment explanation
Indices: 31237640--31237710 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
31237630 ACTTTACAAT
* * * *
31237640 GTAATGTGATTACATGTAATGTGATTGCAA
1 GTAATATGAATACAAGTAATGTAATTGCAA
31237670 GTAATATGAATACAAGTAATGTAATTGCAA
1 GTAATATGAATACAAGTAATGTAATTGCAA
*
31237700 GGAATAT-AATA
1 GTAATATGAATA
31237711 TTGCACTGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 4 0.11
30 32 0.89
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (30 bp):
GTAATATGAATACAAGTAATGTAATTGCAA
Found at i:31237700 original size:15 final size:15
Alignment explanation
Indices: 31237633--31237700 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
31237623 ATTTAATACT
*
31237633 TTACAATGTAATGTGA
1 TTACAA-GTAATGTAA
* *
31237649 TTACATGTAATGTGA
1 TTACAAGTAATGTAA
* *
31237664 TTGCAAGTAATATGAA
1 TTACAAGTAATGT-AA
31237680 -TACAAGTAATGTAA
1 TTACAAGTAATGTAA
*
31237694 TTGCAAG
1 TTACAAG
31237701 GAATATAATA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
14 2 0.05
15 34 0.81
16 6 0.14
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (15 bp):
TTACAAGTAATGTAA
Found at i:31237709 original size:15 final size:15
Alignment explanation
Indices: 31237663--31237709 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
31237653 ATGTAATGTG
31237663 ATTGCAAGTAATATGA
1 ATTGCAAGTAATAT-A
* *
31237679 A-TACAAGTAATGTA
1 ATTGCAAGTAATATA
*
31237693 ATTGCAAGGAATATA
1 ATTGCAAGTAATATA
31237708 AT
1 AT
31237710 ATTGCACTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 2 0.08
15 22 0.88
16 1 0.04
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.30
Consensus pattern (15 bp):
ATTGCAAGTAATATA
Found at i:31246189 original size:2 final size:2
Alignment explanation
Indices: 31246184--31246230 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
31246174 ACACACACAT
31246184 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31246225 TA TA TA
1 TA TA TA
31246231 ATCAACAGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31265556 original size:2 final size:2
Alignment explanation
Indices: 31265549--31265578 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31265539 ATACATATCC
31265549 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
31265579 TGTGTGACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31286885 original size:34 final size:34
Alignment explanation
Indices: 31286829--31286895 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
31286819 TTTGTTTTAT
* *
31286829 AAAAGTTGTTGGAAGTTATTGAAATATTGAATGC
1 AAAAGTTATTGGAAATTATTGAAATATTGAATGC
* *
31286863 AAAAGTTATTGTAAATTGTTGAAATATTGAATG
1 AAAAGTTATTGGAAATTATTGAAATATTGAATG
31286896 GATATAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.40, C:0.01, G:0.21, T:0.37
Consensus pattern (34 bp):
AAAAGTTATTGGAAATTATTGAAATATTGAATGC
Found at i:31302335 original size:14 final size:14
Alignment explanation
Indices: 31302316--31302342 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31302306 GTCATTATAT
31302316 TCTATTCTTTCTTC
1 TCTATTCTTTCTTC
31302330 TCTATTCTTTCTT
1 TCTATTCTTTCTT
31302343 TCCAATTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.26, G:0.00, T:0.67
Consensus pattern (14 bp):
TCTATTCTTTCTTC
Found at i:31306509 original size:2 final size:2
Alignment explanation
Indices: 31306498--31306592 Score: 135
Period size: 2 Copynumber: 49.5 Consensus size: 2
31306488 CATTTATTAT
*
31306498 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
31306539 TN TT TA TA T- TA T- TA T- 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
31306578 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
31306593 GTGTGTATTG
Statistics
Matches: 85, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
1 4 0.05
2 81 0.95
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (2 bp):
TA
Found at i:31320947 original size:31 final size:30
Alignment explanation
Indices: 31320888--31320958 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 30
31320878 GTTTGAACCA
* * *
31320888 CTGATACAAAGAATATTCAGTTTGCAATGT
1 CTGATATAAAGAATACTCAGATTGCAATGT
31320918 CTGATATAAAGAAATACTCAGATTGCAATGT
1 CTGATATAAAG-AATACTCAGATTGCAATGT
*
31320949 CTGCTATAAA
1 CTGATATAAA
31320959 TCCTTAAAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 10 0.28
31 26 0.72
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (30 bp):
CTGATATAAAGAATACTCAGATTGCAATGT
Found at i:31322178 original size:2 final size:2
Alignment explanation
Indices: 31322171--31322214 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
31322161 AGATAGATAG
31322171 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31322213 AT
1 AT
31322215 GGACACATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31331874 original size:27 final size:27
Alignment explanation
Indices: 31331837--31331889 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
31331827 GAAATGGAAT
*
31331837 AAAAAAAATAAAATAATTATT-TTATG
1 AAAAAAAATAAAATAATAATTATTATG
31331863 AAAATAAAATAAAATAATAATTATTAT
1 AAAA-AAAATAAAATAATAATTATTAT
31331890 ATAATTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 4 0.17
27 16 0.67
28 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (27 bp):
AAAAAAAATAAAATAATAATTATTATG
Found at i:31333390 original size:26 final size:26
Alignment explanation
Indices: 31333351--31333425 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
31333341 TTATTTGTAA
*
31333351 AATTTAAAATATTAAT-ATTTTATATAT
1 AATTT-AAATATTAATAATATTA-ATAT
*
31333378 AATTTAAATATTATTAATATTAATAT
1 AATTTAAATATTAATAATATTAATAT
* *
31333404 GATTAAAATATTAA-AATATTAA
1 AATTTAAATATTAATAATATTAA
31333426 AATATTAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 8 0.19
26 24 0.57
27 10 0.24
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (26 bp):
AATTTAAATATTAATAATATTAATAT
Found at i:31333418 original size:8 final size:8
Alignment explanation
Indices: 31333348--31333449 Score: 80
Period size: 8 Copynumber: 12.4 Consensus size: 8
31333338 AAATTATTTG
31333348 TAAAAT-T
1 TAAAATAT
31333355 TAAAATAT
1 TAAAATAT
* *
31333363 TAATATTT
1 TAAAATAT
*
31333371 TATATATAAT
1 TA-AAAT-AT
*
31333381 TTAAATAT
1 TAAAATAT
*
31333389 TATTAATAT
1 TA-AAATAT
*
31333398 TAATATGAT
1 TAAAAT-AT
31333407 TAAAATAT
1 TAAAATAT
31333415 TAAAATAT
1 TAAAATAT
31333423 TAAAATAT
1 TAAAATAT
* *
31333431 TAATATTT
1 TAAAATAT
*
31333439 TAAATTAT
1 TAAAATAT
31333447 TAA
1 TAA
31333450 TGTTTTATTT
Statistics
Matches: 75, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
7 6 0.08
8 46 0.61
9 21 0.28
10 2 0.03
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (8 bp):
TAAAATAT
Found at i:31333592 original size:17 final size:15
Alignment explanation
Indices: 31333545--31333618 Score: 59
Period size: 15 Copynumber: 5.2 Consensus size: 15
31333535 ATATTAAATT
*
31333545 ATAAATAAAATATTTA
1 ATAATTAAAATA-TTA
*
31333561 TTAATTAAAATATTA
1 ATAATTAAAATATTA
31333576 ATAATT--AA-ATT-
1 ATAATTAAAATATTA
*
31333587 AT-ATTAAAATATTG
1 ATAATTAAAATATTA
* *
31333601 ATATTTAAATTATTA
1 ATAATTAAAATATTA
31333616 ATA
1 ATA
31333619 TTTTAATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
10 3 0.06
11 2 0.04
12 5 0.11
13 5 0.11
14 2 0.04
15 20 0.43
16 10 0.21
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (15 bp):
ATAATTAAAATATTA
Found at i:31333597 original size:25 final size:25
Alignment explanation
Indices: 31333560--31333613 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
31333550 TAAAATATTT
31333560 ATTA-ATTAAAATATTAATAATTAA
1 ATTATATTAAAATATTAATAATTAA
* *
31333584 ATTATATTAAAATATTGATATTTAA
1 ATTATATTAAAATATTAATAATTAA
31333609 ATTAT
1 ATTAT
31333614 TAATATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 4 0.15
25 23 0.85
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
ATTATATTAAAATATTAATAATTAA
Found at i:31333631 original size:16 final size:15
Alignment explanation
Indices: 31333590--31333650 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
31333580 TTAAATTATA
* *
31333590 TTAAAATATTGATAT
1 TTAAATTATTAATAT
31333605 TTAAATTATTAATAT
1 TTAAATTATTAATAT
*
31333620 TTTAATTGA-T--TA-
1 TTAAATT-ATTAATAT
31333632 -TAAATTATTAATAT
1 TTAAATTATTAATAT
31333646 TTAAA
1 TTAAA
31333651 AAATAAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
10 1 0.03
11 6 0.17
13 4 0.11
15 24 0.67
16 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
TTAAATTATTAATAT
Found at i:31333639 original size:26 final size:27
Alignment explanation
Indices: 31333597--31333647 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
31333587 ATATTAAAAT
*
31333597 ATTGATATTTAAATTATTAATATTTTA
1 ATTGATATATAAATTATTAATATTTTA
31333624 ATTGAT-TATAAATTATTAATATTT
1 ATTGATATATAAATTATTAATATTT
31333648 AAAAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (27 bp):
ATTGATATATAAATTATTAATATTTTA
Found at i:31335273 original size:19 final size:19
Alignment explanation
Indices: 31335251--31335298 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
31335241 AATTATCATG
*
31335251 AATAATTATAATTATTTTA
1 AATAATTATAATTATATTA
* *
31335270 AATATTTTTAATTATATTA
1 AATAATTATAATTATATTA
*
31335289 AATAAATATA
1 AATAATTATA
31335299 TTAAAATTAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATAATTATAATTATATTA
Found at i:31338360 original size:39 final size:39
Alignment explanation
Indices: 31338317--31338394 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
31338307 GTTGTCAGAC
31338317 CAAAAGTTTGAACCTTGGAACCCTGCTTCTTTGAAAACT
1 CAAAAGTTTGAACCTTGGAACCCTGCTTCTTTGAAAACT
*
31338356 CAAAAGTTTGAACCTTGGAATCCTGCTTCTTTGAAAACT
1 CAAAAGTTTGAACCTTGGAACCCTGCTTCTTTGAAAACT
31338395 TTCTTTGATG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (39 bp):
CAAAAGTTTGAACCTTGGAACCCTGCTTCTTTGAAAACT
Found at i:31347191 original size:63 final size:65
Alignment explanation
Indices: 31347118--31347246 Score: 201
Period size: 63 Copynumber: 2.0 Consensus size: 65
31347108 GAACGATTGC
31347118 CCACTAAAATGATAATT-AATGGAACATGATTTATGTACACGAC-A-GCAATGGTGACTATGAAT
1 CCACTAAAATGATAATTAAAT-GAACATGATTTATGTACACGACTAGGCAATGGTGACTATGAAT
31347180 T
65 T
**
31347181 CCACTAAAATGATAATTAAATGAACATGATTTATGTACTTGACTATGGCAATGGTGACTATGAAT
1 CCACTAAAATGATAATTAAATGAACATGATTTATGTACACGACTA-GGCAATGGTGACTATGAAT
31347246 T
65 T
31347247 GATTAAGTAC
Statistics
Matches: 60, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
63 37 0.62
64 4 0.07
66 19 0.32
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (65 bp):
CCACTAAAATGATAATTAAATGAACATGATTTATGTACACGACTAGGCAATGGTGACTATGAATT
Found at i:31347852 original size:21 final size:21
Alignment explanation
Indices: 31347785--31347852 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
31347775 GAAAAATATA
*
31347785 GATACTTCCCCAAGAAGTATC
1 GATACTTCCCCTAGAAGTATC
** *
31347806 GATACCTATTGCCT--AAGCATC
1 GATA-CT-TCCCCTAGAAGTATC
*
31347827 AATACTTCCCCTAGAAGTATC
1 GATACTTCCCCTAGAAGTATC
31347848 GATAC
1 GATAC
31347853 CTATGACTTT
Statistics
Matches: 34, Mismatches: 9, Indels: 8
0.67 0.18 0.16
Matches are distributed among these distances:
19 4 0.12
20 2 0.06
21 23 0.68
22 2 0.06
23 3 0.09
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.26
Consensus pattern (21 bp):
GATACTTCCCCTAGAAGTATC
Found at i:31356110 original size:16 final size:15
Alignment explanation
Indices: 31356089--31356138 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
31356079 TCCTTAATAC
31356089 ATGTATACATATGTAT
1 ATGTATACATATGT-T
*
31356105 ATGTATATATATG-T
1 ATGTATACATATGTT
*
31356119 ATGTATGCATATGTGT
1 ATGTATACATATGT-T
31356135 ATGT
1 ATGT
31356139 CTATGTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 12 0.41
16 17 0.59
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.46
Consensus pattern (15 bp):
ATGTATACATATGTT
Found at i:31356299 original size:43 final size:43
Alignment explanation
Indices: 31356210--31356300 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
31356200 AAACATAGTT
*
31356210 TCCAACCACAACTTCCCATACCTTCCTACTTTTACCCCTCATA
1 TCCAACCACAACTTCCCATACCTTCCTACTTTTACCCCTCACA
* * *
31356253 TCCAACCGCAACTT-CCAGTACCTTCCTACTTTTACCCGTTACA
1 TCCAACCACAACTTCCCA-TACCTTCCTACTTTTACCCCTCACA
31356296 TCCAA
1 TCCAA
31356301 TTACTACTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 3 0.07
43 40 0.93
ACGTcount: A:0.25, C:0.42, G:0.03, T:0.30
Consensus pattern (43 bp):
TCCAACCACAACTTCCCATACCTTCCTACTTTTACCCCTCACA
Found at i:31358773 original size:3 final size:3
Alignment explanation
Indices: 31358765--31358791 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
31358755 GCCGGAGGCA
31358765 GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG
31358792 ATCAGAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:31372750 original size:23 final size:23
Alignment explanation
Indices: 31372707--31372755 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
31372697 TTATTCTTAA
*
31372707 AAATATTTATTTTAAAAAATTTT
1 AAATATTTATTTTAAAAAATTCT
* *
31372730 AAAT-TTTATTTTTATATAATTCT
1 AAATATTTA-TTTTAAAAAATTCT
31372753 AAA
1 AAA
31372756 GTGACACTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
AAATATTTATTTTAAAAAATTCT
Found at i:31373948 original size:19 final size:19
Alignment explanation
Indices: 31373924--31373985 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 19
31373914 ACGTTATTGT
31373924 TAAAATAAAATATATAATA
1 TAAAATAAAATATATAATA
31373943 TAAAATAAAATA-A-AATA
1 TAAAATAAAATATATAATA
31373960 TAAGAAATTAAAATTTATATAATA
1 T-A-AAA-TAAAA--TATATAATA
31373984 TA
1 TA
31373986 GGTAAAAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
17 5 0.14
18 2 0.06
19 15 0.42
20 5 0.14
22 2 0.06
23 2 0.06
24 5 0.14
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
TAAAATAAAATATATAATA
Found at i:31374305 original size:15 final size:15
Alignment explanation
Indices: 31374285--31374313 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31374275 TTATTTTCTA
31374285 TATAATCATATTACT
1 TATAATCATATTACT
31374300 TATAATCATATTAC
1 TATAATCATATTAC
31374314 ATTTTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (15 bp):
TATAATCATATTACT
Found at i:31374485 original size:1 final size:1
Alignment explanation
Indices: 31374481--31374522 Score: 75
Period size: 1 Copynumber: 42.0 Consensus size: 1
31374471 NCCCCCTCCA
*
31374481 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCTCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
31374523 AAAACCACCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.98, G:0.00, T:0.02
Consensus pattern (1 bp):
C
Found at i:31377181 original size:142 final size:143
Alignment explanation
Indices: 31376924--31377196 Score: 449
Period size: 142 Copynumber: 1.9 Consensus size: 143
31376914 TTGTAATTTT
* *
31376924 TCTTATGAAGGAAATTTTAGAATCATTGAACATGTTTTTTTGGATCTCTATGAAGGATTTATGGG
1 TCTTATGAAGGAAATTTTAGAATCATTGAACATGTTTTTTTGGATCTCTATGAAAGACTTATGGG
* *
31376989 TTGCCATTACAGAATGAAATATCTAAGAGATTGTGATGGTCCATATTGCTCTGAATCATGCAAGG
66 TTGCCATTACAGAATGAAATATCTAAGAGATTATGATGGTCCATACTGCTCTGAATCATGCAAGG
31377054 ATGAGCTAATCTA
131 ATGAGCTAATCTA
* *
31377067 TCTTATGAAGGAAATTTTAGGATGATTGAACATG-TTTTTTGGATCTCTATGAAAGACTTATGGG
1 TCTTATGAAGGAAATTTTAGAATCATTGAACATGTTTTTTTGGATCTCTATGAAAGACTTATGGG
* * * *
31377131 TTGCCATTACAGAATGAAATATCTTAGAGATTATGGTGTTCGATACTGCTCTGAATCATGCAAGG
66 TTGCCATTACAGAATGAAATATCTAAGAGATTATGATGGTCCATACTGCTCTGAATCATGCAAGG
31377196 A
131 A
31377197 CGCCACAAGA
Statistics
Matches: 120, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
142 88 0.73
143 32 0.27
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.36
Consensus pattern (143 bp):
TCTTATGAAGGAAATTTTAGAATCATTGAACATGTTTTTTTGGATCTCTATGAAAGACTTATGGG
TTGCCATTACAGAATGAAATATCTAAGAGATTATGATGGTCCATACTGCTCTGAATCATGCAAGG
ATGAGCTAATCTA
Found at i:31379286 original size:13 final size:13
Alignment explanation
Indices: 31379268--31379297 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
31379258 ATACATACAA
31379268 TGAAAATAAAAGT
1 TGAAAATAAAAGT
31379281 TGAAAATAAAAGT
1 TGAAAATAAAAGT
31379294 TGAA
1 TGAA
31379298 CAGATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (13 bp):
TGAAAATAAAAGT
Found at i:31381821 original size:21 final size:21
Alignment explanation
Indices: 31381779--31381822 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
31381769 AAAGATTTTG
*
31381779 AAAACACAATGCACTTATTTT
1 AAAACACAATGCACTTAGTTT
*
31381800 AAAA-ACAATGCAATTTAGTTT
1 AAAACACAATGC-ACTTAGTTT
31381821 AA
1 AA
31381823 TTTCTTGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.32
Consensus pattern (21 bp):
AAAACACAATGCACTTAGTTT
Found at i:31382119 original size:35 final size:35
Alignment explanation
Indices: 31382080--31382152 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
31382070 CATACTCAGC
31382080 TCATGTACACTCCCTACACGCACATTTCAATATCA
1 TCATGTACACTCCCTACACGCACATTTCAATATCA
* *
31382115 TCATGTGCTCTCCCTACACGCACATTTCAATATCA
1 TCATGTACACTCCCTACACGCACATTTCAATATCA
31382150 TCA
1 TCA
31382153 CACGCACTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.29, C:0.34, G:0.07, T:0.30
Consensus pattern (35 bp):
TCATGTACACTCCCTACACGCACATTTCAATATCA
Found at i:31382841 original size:2 final size:2
Alignment explanation
Indices: 31382834--31382861 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31382824 AGAAAGTTTA
31382834 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
31382862 AAAATGTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:31384047 original size:6 final size:6
Alignment explanation
Indices: 31384036--31384062 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31384026 CCTCAATACT
31384036 AAAGTA AAAGTA AAAGTA AAAGTA AAA
1 AAAGTA AAAGTA AAAGTA AAAGTA AAA
31384063 ACAACTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAGTA
Found at i:31386651 original size:4 final size:4
Alignment explanation
Indices: 31386644--31386682 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
31386634 AATAAAACAT
*
31386644 ATAA ATAA ATAA ATCAA ATAA ATCAA ATAA ATAA GTAA A
1 ATAA ATAA ATAA AT-AA ATAA AT-AA ATAA ATAA ATAA A
31386683 AAAAAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 23 0.74
5 8 0.26
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:31386662 original size:9 final size:9
Alignment explanation
Indices: 31386634--31386675 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
31386624 AAATATAATT
*
31386634 AATAAAACA
1 AATAAATCA
*
31386643 TATAAAT-A
1 AATAAATCA
31386651 AATAAATCA
1 AATAAATCA
31386660 AATAAATCA
1 AATAAATCA
31386669 AATAAAT
1 AATAAAT
31386676 AAGTAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 7 0.24
9 22 0.76
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (9 bp):
AATAAATCA
Found at i:31386662 original size:13 final size:13
Alignment explanation
Indices: 31386634--31386677 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
31386624 AAATATAATT
* *
31386634 AATAAAACATATA
1 AATAAATCAAATA
31386647 AATAAAT-AAATCA
1 AATAAATCAAAT-A
31386660 AATAAATCAAATA
1 AATAAATCAAATA
31386673 AATAA
1 AATAA
31386678 GTAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 3 0.11
13 20 0.74
14 4 0.15
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (13 bp):
AATAAATCAAATA
Found at i:31387556 original size:16 final size:17
Alignment explanation
Indices: 31387510--31387573 Score: 52
Period size: 15 Copynumber: 4.2 Consensus size: 17
31387500 GCTGAGGGCC
*
31387510 AAGAAAGAA-AGAAGA-
1 AAGAAAAAACAGAAGAG
*
31387525 AA-AAAAAACA-AGGAG
1 AAGAAAAAACAGAAGAG
31387540 AAGAAAAAA-AGAAGAG
1 AAGAAAAAACAGAAGAG
*
31387556 -AGAAAAAATAG-AGAG
1 AAGAAAAAACAGAAGAG
31387571 AAG
1 AAG
31387574 GGAGAGTATC
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
14 8 0.20
15 18 0.45
16 14 0.35
ACGTcount: A:0.72, C:0.02, G:0.25, T:0.02
Consensus pattern (17 bp):
AAGAAAAAACAGAAGAG
Found at i:31406790 original size:7 final size:7
Alignment explanation
Indices: 31406728--31406795 Score: 51
Period size: 7 Copynumber: 10.1 Consensus size: 7
31406718 TATTAAAAAT
31406728 TAAATTA
1 TAAATTA
31406735 TAAA-TA
1 TAAATTA
31406741 -AAA-TA
1 TAAATTA
31406746 TTAATATT-
1 -TAA-ATTA
31406754 TAAATTA
1 TAAATTA
31406761 TAAATTA
1 TAAATTA
31406768 TTAATATT-
1 -TAA-ATTA
31406776 TAAA--A
1 TAAATTA
31406781 TAAATTA
1 TAAATTA
31406788 TAAATTA
1 TAAATTA
31406795 T
1 T
31406796 TACTATTTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 20
0.72 0.00 0.28
Matches are distributed among these distances:
5 9 0.18
6 6 0.12
7 28 0.55
8 4 0.08
9 4 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAAATTA
Found at i:31406791 original size:27 final size:27
Alignment explanation
Indices: 31406716--31406929 Score: 127
Period size: 27 Copynumber: 7.6 Consensus size: 27
31406706 CTTCAAATAA
* *
31406716 AATATTAAAAATTAAATTATAAA-TA-A
1 AATATTTAAAA-TAAATTATAAATTATT
*
31406742 AATA-TTAATATTTAAATTATAAATTATT
1 AATATTTAA-A-ATAAATTATAAATTATT
31406770 AATATTTAAAATAAATTATAAATTATT
1 AATATTTAAAATAAATTATAAATTATT
* **
31406797 ACTATTTAAAAATAAA--ATAAATTAGA
1 AATATTT-AAAATAAATTATAAATTATT
* *
31406823 AATAAATAAGCATAATAACATT-TAAATTAGATAT
1 AAT-ATTTA--A-AATAA-ATTATAAATT--AT-T
* *
31406857 AAAATATTAATAATTAAATTATCAATTATT
1 AATAT-TTAA-AA-TAAATTATAAATTATT
*
31406887 AATATTTTAAATAAATTATCAAA-TATT
1 AATATTTAAAATAAATTAT-AAATTATT
31406914 AATATTTAAAAATAAA
1 AATATTT-AAAATAAA
31406930 ATAAAATAAA
Statistics
Matches: 147, Mismatches: 20, Indels: 40
0.71 0.10 0.19
Matches are distributed among these distances:
25 3 0.02
26 27 0.18
27 45 0.31
28 25 0.17
29 12 0.08
30 6 0.04
31 8 0.05
32 7 0.05
33 10 0.07
34 4 0.03
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (27 bp):
AATATTTAAAATAAATTATAAATTATT
Found at i:31406859 original size:117 final size:110
Alignment explanation
Indices: 31406735--31407028 Score: 345
Period size: 117 Copynumber: 2.7 Consensus size: 110
31406725 AATTAAATTA
*
31406735 TAAATAAAATATTAATATTTAAATTATAAATTATTAATATTTAAAATAAATTAT-AAATTATTAC
1 TAAATAAAATATTAATATTTAAATTATAAATTATTAATATTTAAAATAAATTATCAAA-TATTAA
31406799 TATTTAAAAATAAAATAAATTAGAAATAAATAAGCATAATAACATTTAAAT
65 TATTTAAAAATAAAATAAA--AGAAA-AAATAA--ATAATAACATTTAAAT
* * *
31406850 TAGATATAAAATATTAATAATTAAATTATCAATTATTAATATTTTAAATAAATTATCAAATATTA
1 TA-A-ATAAAATATTAATATTTAAATTATAAATTATTAATATTTAAAATAAATTATCAAATATTA
* * * *
31406915 ATATTTAAAAATAAAATAAAATAAAAAATTAATAATAATATTTATAT
64 ATATTTAAAAATAAAATAAAAGAAAAAATAAATAATAACATTTAAAT
*
31406962 TAAATAAAATATTAATATTTTAA-TAT--A-TATTAATGA-TTAAATTATAAA-TA--AAATATT
1 TAAATAAAATATTAATATTTAAATTATAAATTATTAAT-ATTTAAA--ATAAATTATCAAATATT
31407019 AATATTTAAA
63 AATATTTAAA
31407029 TTATCTATTA
Statistics
Matches: 162, Mismatches: 11, Indels: 22
0.83 0.06 0.11
Matches are distributed among these distances:
105 17 0.10
106 11 0.07
107 4 0.02
108 5 0.03
109 3 0.02
110 18 0.11
111 1 0.01
112 16 0.10
114 5 0.03
115 6 0.04
116 1 0.01
117 72 0.44
118 3 0.02
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (110 bp):
TAAATAAAATATTAATATTTAAATTATAAATTATTAATATTTAAAATAAATTATCAAATATTAAT
ATTTAAAAATAAAATAAAAGAAAAAATAAATAATAACATTTAAAT
Found at i:31406969 original size:30 final size:30
Alignment explanation
Indices: 31406933--31407105 Score: 109
Period size: 30 Copynumber: 5.5 Consensus size: 30
31406923 AAATAAAATA
*
31406933 AAATAAAAAATTAATAATAATATTTATATT
1 AAATAAAATATTAATAATAATATTTATATT
*
31406963 AAATAAAATATTAATATTTTAATA--TATATT
1 AAATAAAATATTAATA--ATAATATTTATATT
* * *
31406993 AATGATTAAATTATAAATAA-AATATTAATATTT
1 AA--A-TAAAATATTAATAATAATATTTATA-TT
* * * * * * * *
31407026 AAATTATCTATTATTAATATTTAAAAATAAAATA
1 AAA-TA--AAATATTAATA-ATAATATTTATATT
*
31407060 AAATAAAAAATTAATAATAATATTTATATT
1 AAATAAAATATTAATAATAATATTTATATT
31407090 AAATAAAATATTAATA
1 AAATAAAATATTAATA
31407106 TTTTAATATA
Statistics
Matches: 108, Mismatches: 23, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
30 50 0.46
31 12 0.11
32 9 0.08
33 26 0.24
34 4 0.04
35 7 0.06
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.41
Consensus pattern (30 bp):
AAATAAAATATTAATAATAATATTTATATT
Found at i:31406972 original size:18 final size:19
Alignment explanation
Indices: 31406945--31407462 Score: 99
Period size: 19 Copynumber: 25.9 Consensus size: 19
31406935 ATAAAAAATT
*
31406945 AATAATAATATTTATATTA
1 AATAATAATATTAATATTA
31406964 AATAA-AATATTAATATTTTA
1 AATAATAATATTAATA--TTA
31406984 ATATATATTAATGATTAA-ATTATA
1 A-ATA-A-TAAT-ATTAATA-T-TA
31407008 AATAA-AATATTAATATTTA
1 AATAATAATATTAATA-TTA
* *
31407027 AATTATCTATTATTAATATTTAAA
1 AA-TA-ATAATATTAATA-TT--A
* * *
31407051 AATAAAATAAAATAAAAAATT-
1 AAT--AATAATAT-TAATATTA
*
31407072 AATAATAATATTTATATTA
1 AATAATAATATTAATATTA
31407091 AATAA-AATATTAATATT-
1 AATAATAATATTAATATTA
*
31407108 -TTAATATATATTAATGATTA
1 AATAATA-ATATTAAT-ATTA
* *
31407128 AATTATAA-ATAAAATATT-
1 AATAATAATAT-TAATATTA
* *
31407146 AATATTTAA-ATTATCTATT-
1 AATA-ATAATATTA-ATATTA
* *
31407165 ATTAAT-AT-TTAA-AATA
1 AATAATAATATTAATATTA
31407181 AATAATCAATTATTAATATTTA
1 AATAAT-AA-TATTAATA-TTA
* *
31407203 AA-AATAAAATAAAATAATTGA
1 AATAATAATAT-TAAT-ATT-A
*
31407224 TCATAATAATATTTAA-ATTA
1 -AATAATAATA-TTAATATTA
*
31407244 AATAA-AAAATTAATATTTTA
1 AATAATAATATTAATA--TTA
* *
31407264 ACACATTAATGATTAA-ATTA
1 A-ATAATAAT-ATTAATATTA
31407284 TAATTAA-AATATTAATATTTA
1 -AA-TAATAATATTAATA-TTA
*
31407305 AATTATCAATTATTAATATTTTA
1 AATAAT-AA-TATTAATA--TTA
31407328 AATAAATTATCAATTATTAATATTTA
1 AAT--A--AT-AA-TATTAATA-TTA
*
31407354 AATAATAAAATATAATA-T-
1 AATAATAATAT-TAATATTA
31407372 AAT-ATAA-ATTAATCA-T-
1 AATAATAATATTAAT-ATTA
31407388 AATAAT-AT-TTAA-ATTA
1 AATAATAATATTAATATTA
*
31407404 AATAA-AATATTAGTATTTTAA
1 AATAATAATATTA--ATATT-A
*
31407425 AATAGTAAATATTAA-ATTGTA
1 AATAAT-AATATTAATA-T-TA
31407446 AATAA-AATATTAATATT
1 AATAATAATATTAATATT
31407463 TTAACTTATT
Statistics
Matches: 378, Mismatches: 46, Indels: 151
0.66 0.08 0.26
Matches are distributed among these distances:
14 1 0.00
15 7 0.02
16 27 0.07
17 18 0.05
18 46 0.12
19 71 0.19
20 47 0.12
21 47 0.12
22 33 0.09
23 33 0.09
24 18 0.05
25 9 0.02
26 7 0.02
27 14 0.04
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (19 bp):
AATAATAATATTAATATTA
Found at i:31407012 original size:44 final size:42
Alignment explanation
Indices: 31406962--31407201 Score: 199
Period size: 44 Copynumber: 5.5 Consensus size: 42
31406952 ATATTTATAT
31406962 TAAATAAAATATTAATATTTTAATATATATTAATGATTAAATTA
1 TAAATAAAATATTAATATTTTAATATATATTAAT-ATTAAA-TA
* *
31407006 TAAATAAAATATTAATATTTAAATTATCTATTATTAATATTTAAAAA
1 TAAATAAAATATTAATATTTTAA-TA--TA-TATTAATA-TTAAATA
** * *
31407053 TAAAATAAAATA--AA-AAATTAATA-ATAAT-AT-TTATAT-
1 T-AAATAAAATATTAATATTTTAATATATATTAATATTAAATA
31407089 TAAATAAAATATTAATATTTTAATATATATTAATGATTAAATTA
1 TAAATAAAATATTAATATTTTAATATATATTAAT-ATTAAA-TA
*
31407133 TAAATAAAATATTAATATTTAAATTATCTATTATTAATATTTAAA-A
1 TAAATAAAATATTAATATTTTAA-TA--TA-TATTAATA-TTAAATA
31407179 TAAATAATCAATTATTAATATTT
1 TAAATAA--AA-TATTAATATTT
31407202 AAAAATAAAA
Statistics
Matches: 160, Mismatches: 13, Indels: 41
0.75 0.06 0.19
Matches are distributed among these distances:
35 10 0.06
36 1 0.01
37 6 0.04
38 7 0.04
39 6 0.04
40 5 0.03
41 1 0.01
42 4 0.03
43 1 0.01
44 46 0.29
45 8 0.05
46 10 0.06
47 8 0.05
48 36 0.22
49 11 0.07
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (42 bp):
TAAATAAAATATTAATATTTTAATATATATTAATATTAAATA
Found at i:31407022 original size:68 final size:68
Alignment explanation
Indices: 31406945--31407158 Score: 257
Period size: 68 Copynumber: 3.3 Consensus size: 68
31406935 ATAAAAAATT
*
31406945 AATAATAATATTTATATTAAATAAAATATTAATATTTTAATATATATTAATGATTAAATTATAAA
1 AATAATAATATTTAAATTAAATAAAATATTAATATTTTAATATATATTAATGATTAAATTATAAA
31407010 TAA
66 TAA
* ** * * * * *
31407013 AATATTAATATTTAAATT--ATCTATTATTAATA-TTTAA-A-A-A-TAA-AATAAAATAAAAAA
1 AATAATAATATTTAAATTAAATAAAATATTAATATTTTAATATATATTAATGATTAAATTATAAA
*
31407070 T-T
66 TAA
*
31407072 AATAATAATATTTATATTAAATAAAATATTAATATTTTAATATATATTAATGATTAAATTATAAA
1 AATAATAATATTTAAATTAAATAAAATATTAATATTTTAATATATATTAATGATTAAATTATAAA
31407137 TAA
66 TAA
*
31407140 AATATTAATATTTAAATTA
1 AATAATAATATTTAAATTA
31407159 TCTATTATTA
Statistics
Matches: 115, Mismatches: 22, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
59 16 0.14
60 11 0.10
61 14 0.12
62 6 0.05
63 2 0.02
64 2 0.02
65 6 0.05
66 14 0.12
67 11 0.10
68 33 0.29
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (68 bp):
AATAATAATATTTAAATTAAATAAAATATTAATATTTTAATATATATTAATGATTAAATTATAAA
TAA
Found at i:31407046 original size:127 final size:127
Alignment explanation
Indices: 31406898--31407182 Score: 545
Period size: 127 Copynumber: 2.3 Consensus size: 127
31406888 ATATTTTAAA
* *
31406898 TAAATTATCAAATATTAATATTTAAAAATAAAATAAAATAAAAAATTAATAATAATATTTATATT
1 TAAATTATCTATTATTAATATTTAAAAATAAAATAAAATAAAAAATTAATAATAATATTTATATT
31406963 AAATAAAATATTAATATTTTAATATATATTAATGATTAAATTATAAATAAAATATTAATATT
66 AAATAAAATATTAATATTTTAATATATATTAATGATTAAATTATAAATAAAATATTAATATT
31407025 TAAATTATCTATTATTAATATTTAAAAATAAAATAAAATAAAAAATTAATAATAATATTTATATT
1 TAAATTATCTATTATTAATATTTAAAAATAAAATAAAATAAAAAATTAATAATAATATTTATATT
31407090 AAATAAAATATTAATATTTTAATATATATTAATGATTAAATTATAAATAAAATATTAATATT
66 AAATAAAATATTAATATTTTAATATATATTAATGATTAAATTATAAATAAAATATTAATATT
31407152 TAAATTATCTATTATTAATATTT-AAAATAAA
1 TAAATTATCTATTATTAATATTTAAAAATAAA
31407183 TAATCAATTA
Statistics
Matches: 156, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
126 8 0.05
127 148 0.95
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (127 bp):
TAAATTATCTATTATTAATATTTAAAAATAAAATAAAATAAAAAATTAATAATAATATTTATATT
AAATAAAATATTAATATTTTAATATATATTAATGATTAAATTATAAATAAAATATTAATATT
Found at i:31407192 original size:27 final size:28
Alignment explanation
Indices: 31407152--31407210 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 28
31407142 TATTAATATT
* *
31407152 TAAATTATCTATTATTAATATTT-AAAA
1 TAAATAATCAATTATTAATATTTAAAAA
31407179 TAAATAATCAATTATTAATATTTAAAAA
1 TAAATAATCAATTATTAATATTTAAAAA
31407207 TAAA
1 TAAA
31407211 ATAAAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 21 0.72
28 8 0.28
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (28 bp):
TAAATAATCAATTATTAATATTTAAAAA
Found at i:31407317 original size:151 final size:151
Alignment explanation
Indices: 31407025--31407486 Score: 629
Period size: 151 Copynumber: 3.0 Consensus size: 151
31407015 TATTAATATT
* ** * *
31407025 TAAATTATCTATTATTAATATTTAAAAATAAAATAAAATAAAAAATTAATAATAATATTTATATT
1 TAAATTATCAATTATTAATATTTAAAAATAAAATAAAATAATTAA-TCATAATAATATTTAAATT
31407090 AAATAAAATATTAATATTTTAATATATATTAATGATTAAATTATAAATAAAATATTAATATTTAA
65 AAATAAAATATTAATATTTTAA-A-ATATTAATGATTAAATTATAAATAAAATATTAATATTTAA
*
31407155 ATTATCTATTATTAATATTTAAAA
128 ATTATCAATTATTAATATTTAAAA
* *
31407179 TAAATAATCAATTATTAATATTTAAAAATAAAATAAAATAATTGATCATAATAATATTTAAATTA
1 TAAATTATCAATTATTAATATTTAAAAATAAAATAAAATAATTAATCATAATAATATTTAAATTA
* * * *
31407244 AATAAAAAATTAATATTTTAACACATTAATGATTAAATTATAATTAAAATATTAATATTTAAATT
66 AATAAAATATTAATATTTTAAAATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATT
*
31407309 ATCAATTATTAATATTTTAAA
131 ATCAATTATTAATATTTAAAA
31407330 TAAATTATCAATTATTAATATTTAAATAATAAAATATAATATAATATAAATTAATCATAATAATA
1 TAAATTATCAATTATTAATATTTAAA-AAT---A-A-AATA-AA-AT-AATTAATCATAATAATA
* * *
31407395 TTTAAATTAAATAAAATATTAGTATTTTAAAATAGTAAAT-ATTAAATTGTAAATAAAATATTAA
57 TTTAAATTAAATAAAATATTAATATTTTAAAATA-TTAATGATTAAATTATAAATAAAATATTAA
* *
31407459 TATTTTAACTTATTAATTATTAATATTT
121 TA-TTTAAATTATCAATTATTAATATTT
31407487 TAATTAATCT
Statistics
Matches: 273, Mismatches: 24, Indels: 15
0.88 0.08 0.05
Matches are distributed among these distances:
151 85 0.31
152 3 0.01
153 38 0.14
154 40 0.15
155 1 0.00
156 1 0.00
157 4 0.01
158 2 0.01
159 2 0.01
160 70 0.26
161 27 0.10
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (151 bp):
TAAATTATCAATTATTAATATTTAAAAATAAAATAAAATAATTAATCATAATAATATTTAAATTA
AATAAAATATTAATATTTTAAAATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATT
ATCAATTATTAATATTTAAAA
Found at i:31407333 original size:27 final size:26
Alignment explanation
Indices: 31407303--31407358 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 26
31407293 TATTAATATT
31407303 TAAATTATCAATTATTAATATTTTAAA
1 TAAATTATCAATTATTAATA-TTTAAA
31407330 TAAATTATCAATTATTAATATTTAAA
1 TAAATTATCAATTATTAATATTTAAA
31407356 TAA
1 TAA
31407359 TAAAATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 9 0.31
27 20 0.69
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (26 bp):
TAAATTATCAATTATTAATATTTAAA
Found at i:31407438 original size:23 final size:22
Alignment explanation
Indices: 31407243--31407489 Score: 95
Period size: 23 Copynumber: 11.0 Consensus size: 22
31407233 TATTTAAATT
*
31407243 AAATA-AAAAATTAATATTTTA
1 AAATATAAATATTAATATTTTA
* * * *
31407264 ACACATTAATGATTAA-ATTAT-
1 AAATATAAAT-ATTAATATTTTA
*
31407285 AATTA-AAATATTAATA-TTTA
1 AAATATAAATATTAATATTTTA
* *
31407305 AATTATCAATTATTAATATTTTAAA
1 AAATAT-AAATATTAATATTTT--A
* *
31407330 TAAATTATCAATTATTAATATTTAA
1 -AAA-TAT-AAATATTAATATTTTA
**
31407355 ATAATA-AAATA-TAATATAATA
1 A-AATATAAATATTAATATTTTA
*
31407376 TAAAT-TAATCATAATAATA-TTTA
1 -AAATATAA--ATATTAATATTTTA
* *
31407399 AATTAAATAAAATATTAGTATTTTA
1 AA--ATAT-AAATATTAATATTTTA
*
31407424 AAATAGTAAATATTAA-ATTGT-
1 AAATA-TAAATATTAATATTTTA
31407445 AAATA-AAATATTAATATTTTA
1 AAATATAAATATTAATATTTTA
** *
31407466 ACTTATTAATTATTAATATTTTA
1 AAATA-TAAATATTAATATTTTA
31407489 A
1 A
31407490 TTAATCTATT
Statistics
Matches: 170, Mismatches: 29, Indels: 52
0.68 0.12 0.21
Matches are distributed among these distances:
19 16 0.09
20 13 0.08
21 25 0.15
22 27 0.16
23 39 0.23
24 17 0.10
25 11 0.06
26 4 0.02
27 18 0.11
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
AAATATAAATATTAATATTTTA
Found at i:31407569 original size:15 final size:18
Alignment explanation
Indices: 31407549--31407584 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
31407539 ATAAAGGGTA
31407549 TTTTTA-TC-TTT-TTAT
1 TTTTTATTCATTTCTTAT
31407564 TTTTTATTCATTTCTTAT
1 TTTTTATTCATTTCTTAT
31407582 TTT
1 TTT
31407585 AAGGTTATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.33
16 2 0.11
17 3 0.17
18 7 0.39
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTATTCATTTCTTAT
Found at i:31407698 original size:16 final size:16
Alignment explanation
Indices: 31407677--31407707 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31407667 AATAACTATT
*
31407677 TTATTCTATTTTTACC
1 TTATTCTATTCTTACC
31407693 TTATTCTATTCTTAC
1 TTATTCTATTCTTAC
31407708 GTAATAACTA
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:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATTCTATTCTTACC
Found at i:31408492 original size:33 final size:33
Alignment explanation
Indices: 31408449--31408532 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
31408439 TTATGTTACA
* * *
31408449 TGATGTTAATATGACATGCTAACATGTCGTAAT
1 TGATGATAATATGACATGCTAACATATCATAAT
* ** *
31408482 TGATGATAATATAACATATTGACATATCATAAT
1 TGATGATAATATGACATGCTAACATATCATAAT
* *
31408515 TAATAATAATATGACATG
1 TGATGATAATATGACATG
31408533 TTAATGTAGT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.36
Consensus pattern (33 bp):
TGATGATAATATGACATGCTAACATATCATAAT
Found at i:31411358 original size:10 final size:10
Alignment explanation
Indices: 31411343--31411387 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
31411333 AAGTGAGTCT
31411343 TTTTTATTTA
1 TTTTTATTTA
31411353 TTTTTATTTA
1 TTTTTATTTA
*
31411363 TTTTT-TAT-
1 TTTTTATTTA
*
31411371 TTTTTATTTT
1 TTTTTATTTA
31411381 TTTTTAT
1 TTTTTAT
31411388 CTTTCACGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 5 0.16
9 4 0.13
10 22 0.71
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:31411371 original size:7 final size:7
Alignment explanation
Indices: 31411342--31411382 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
31411332 CAAGTGAGTC
31411342 TTTTTTA
1 TTTTTTA
31411349 TTTATTT-
1 TTT-TTTA
*
31411356 TTATTTA
1 TTTTTTA
31411363 TTTTTTA
1 TTTTTTA
31411370 TTTTTTA
1 TTTTTTA
31411377 TTTTTT
1 TTTTTT
31411383 TTTATCTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 3 0.10
7 24 0.80
8 3 0.10
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTA
Found at i:31411371 original size:17 final size:16
Alignment explanation
Indices: 31411342--31411387 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 16
31411332 CAAGTGAGTC
31411342 TTTTTTATTTATTTTTA
1 TTTTTT-TTTATTTTTA
31411359 TTTATTTTTTATTTTTTA
1 TTT-TTTTTTA-TTTTTA
31411377 TTTTTTTTTAT
1 TTTTTTTTTAT
31411388 CTTTCACGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 1 0.04
17 14 0.52
18 12 0.44
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTTTTTATTTTTA
Found at i:31412190 original size:140 final size:140
Alignment explanation
Indices: 31411940--31412309 Score: 431
Period size: 140 Copynumber: 2.6 Consensus size: 140
31411930 TAACTTCGGG
* * * *
31411940 TAAAGCAAGAAAGAAGTAGTAATAGTAATTTTCTTGGGCTCACGCAAAAGGTTCAAAATTTAACG
1 TAAAGCAAGAAAGAAGTAGTAATAGTAATTTTCTTGAGCTCACACAAGAGGTTCAAAATTTAACA
** * * *
31412005 TTACCCTGCTATTTAAGTAGACAACTTTTTAGGGCCTAGGGTCTGCCTTCTCATCGTTACGTACA
66 TTACCCTGCTATTTAAGTAGACAACTTTTTAGAACCTAGGCTCTGCCTTATCATCCTTACGTACA
*
31412070 AATCTTCGAA
131 AACCTTCGAA
* *
31412080 TAAAGCAAGAAAGAAGTAATAATAGTAATTTTCTTGAGCTCACACAAGTGGTTCAAAATTTAACA
1 TAAAGCAAGAAAGAAGTAGTAATAGTAATTTTCTTGAGCTCACACAAGAGGTTCAAAATTTAACA
* * * *
31412145 TTGCCGTG-TCATTTAAGTA-ATCAACTTTTTAGAACCTATGCTCTGCCTTATTATCCTTACGTA
66 TTACCCTGCT-ATTTAAGTAGA-CAACTTTTTAGAACCTAGGCTCTGCCTTATCATCCTTACGTA
** **
31412208 CTTACCTTCGGT
129 CAAACCTTCGAA
* * * * * **
31412220 TAAAGTAAGAAGGAAGTAGTAATACTAA-TTCCTTGAGCTCACACAAGAGGTTTAAAATTTAATG
1 TAAAGCAAGAAAGAAGTAGTAATAGTAATTTTCTTGAGCTCACACAAGAGGTTCAAAATTTAACA
***
31412284 TTACCCTTAAATTTAAGTAGACAACT
66 TTACCCTGCTATTTAAGTAGACAACT
31412310 ATTGAGAGCT
Statistics
Matches: 193, Mismatches: 33, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
139 52 0.27
140 141 0.73
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Consensus pattern (140 bp):
TAAAGCAAGAAAGAAGTAGTAATAGTAATTTTCTTGAGCTCACACAAGAGGTTCAAAATTTAACA
TTACCCTGCTATTTAAGTAGACAACTTTTTAGAACCTAGGCTCTGCCTTATCATCCTTACGTACA
AACCTTCGAA
Found at i:31413574 original size:34 final size:34
Alignment explanation
Indices: 31413530--31413598 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 34
31413520 TCAAAACTTC
31413530 ACCACGAGATGTTATATGTC-AAGATTAAAGCTTT
1 ACCACGAGATGTTATATG-CAAAGATTAAAGCTTT
* *
31413564 ACCACTAGATGTTATATGCAAAGGTTAAAGCTTT
1 ACCACGAGATGTTATATGCAAAGATTAAAGCTTT
31413598 A
1 A
31413599 TTAACATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 1 0.03
34 31 0.97
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.32
Consensus pattern (34 bp):
ACCACGAGATGTTATATGCAAAGATTAAAGCTTT
Found at i:31427788 original size:71 final size:71
Alignment explanation
Indices: 31427641--31427795 Score: 161
Period size: 71 Copynumber: 2.2 Consensus size: 71
31427631 TTATAAAATG
* * * *
31427641 CTATTTGTTTTCAATTATTTCTTTTATTTTCAATCAACTAACGGTAACATATATTTAAATATCTC
1 CTATTTTTTTTCAATTATTTCTTTTATTTCCAATCAACTAACAGTAAAATATATTTAAATATCTC
* *
31427706 CAATAG
66 CAACAA
* * * * *
31427712 TTATTTTTTTTCACTTATTTCTTTT-TTCTCCAATCAACTAATAGTAAAATGTATTT-AATAATT
1 CTATTTTTTTTCAATTATTTCTTTTATT-TCCAATCAACTAACAGTAAAATATATTTAAAT-ATC
*
31427775 TTCAACAA
64 TCCAACAA
31427783 CTATTTTATTTTC
1 CTATTTT-TTTTC
31427796 TATCCATAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
70 5 0.07
71 58 0.85
72 5 0.07
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.50
Consensus pattern (71 bp):
CTATTTTTTTTCAATTATTTCTTTTATTTCCAATCAACTAACAGTAAAATATATTTAAATATCTC
CAACAA
Found at i:31429286 original size:15 final size:17
Alignment explanation
Indices: 31429268--31429299 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31429258 TAATTTTACC
31429268 TAAT-AAATT-TTTTAT
1 TAATAAAATTATTTTAT
31429283 TAATAAAATTATTTTAT
1 TAATAAAATTATTTTAT
31429300 GATTTAATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 5 0.33
17 6 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATAAAATTATTTTAT
Found at i:31429372 original size:28 final size:28
Alignment explanation
Indices: 31429340--31429393 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
31429330 TGTTACAAAC
* *
31429340 AAATAAATTACACTCA-ATATAAATAAGT
1 AAATAAACTACA-TCAGACATAAATAAGT
31429368 AAATAAACTACATCAGACATAAATAA
1 AAATAAACTACATCAGACATAAATAA
31429394 AGTATTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 3 0.13
28 20 0.87
ACGTcount: A:0.59, C:0.13, G:0.04, T:0.24
Consensus pattern (28 bp):
AAATAAACTACATCAGACATAAATAAGT
Found at i:31432447 original size:11 final size:12
Alignment explanation
Indices: 31432431--31432473 Score: 54
Period size: 11 Copynumber: 3.6 Consensus size: 12
31432421 ATTCCAATTT
31432431 TTAATA-AAATA
1 TTAATATAAATA
31432442 TTAATATTAAATTA
1 TTAATA-TAAA-TA
31432456 TTAA-ATAAATA
1 TTAATATAAATA
31432467 TTAATAT
1 TTAATAT
31432474 TTAAATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
11 12 0.43
12 6 0.21
13 4 0.14
14 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAATATAAATA
Found at i:31432457 original size:14 final size:14
Alignment explanation
Indices: 31432435--31432483 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
31432425 CAATTTTTAA
*
31432435 TAAAATATTAATAT
1 TAAATTATTAATAT
31432449 TAAATTATTAA-A-
1 TAAATTATTAATAT
31432461 TAAA-TATTAATATT
1 TAAATTATTAATA-T
31432475 TAAATTATT
1 TAAATTATT
31432484 CAATTCTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 6 0.20
12 5 0.17
13 1 0.03
14 14 0.47
15 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAATTATTAATAT
Found at i:31442176 original size:18 final size:18
Alignment explanation
Indices: 31442155--31442189 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
31442145 AATTCATATA
31442155 ATTAATAAAATTATAATT
1 ATTAATAAAATTATAATT
*
31442173 ATTAATTAAATTATAAT
1 ATTAATAAAATTATAAT
31442190 ATCTTTTAAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTAATAAAATTATAATT
Found at i:31443078 original size:89 final size:89
Alignment explanation
Indices: 31442907--31443107 Score: 235
Period size: 89 Copynumber: 2.2 Consensus size: 89
31442897 GACCCCCAGC
* * * *
31442907 TCTCTCTCTCAACTCCTTCCTTTTCCAGCCGACGACAGAAGCCCGAAGCCCCAACTCTCTCTAGA
1 TCTCTCTCTC-GCTTCTTCCTTTTCCAGCCGACGACAAAAGCCCGAAGCCCCAACTCTCTCTAAA
* * *
31442972 ATTGGCGACACAGCAACCTAGATCT
65 ATCGACGACACAACAACCTAGATCT
* * * * * *
31442997 TGTCTCTCTCGCTTCTTCTTTTTTCAGCCGGCGACAAAAGCCCGAAAG-CCCAGCTCTCTTTAAA
1 TCTCTCTCTCGCTTCTTCCTTTTCCAGCCGACGACAAAAGCCCG-AAGCCCCAACTCTCTCTAAA
31443061 ATCGAC-AGCACAACAACCTAGATCT
65 ATCGACGA-CACAACAACCTAGATCT
*
31443086 TCTCTCTCTCGCTTTTTCCTTT
1 TCTCTCTCTCGCTTCTTCCTTT
31443108 CGCCGGCGGC
Statistics
Matches: 93, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
88 1 0.01
89 80 0.86
90 12 0.13
ACGTcount: A:0.22, C:0.35, G:0.13, T:0.29
Consensus pattern (89 bp):
TCTCTCTCTCGCTTCTTCCTTTTCCAGCCGACGACAAAAGCCCGAAGCCCCAACTCTCTCTAAAA
TCGACGACACAACAACCTAGATCT
Found at i:31443754 original size:16 final size:16
Alignment explanation
Indices: 31443729--31443760 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31443719 TGAAAATATG
*
31443729 CTTTCTAACGGAATTT
1 CTTTCCAACGGAATTT
31443745 CTTTCCAACGGAATTT
1 CTTTCCAACGGAATTT
31443761 TCGTTGGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (16 bp):
CTTTCCAACGGAATTT
Found at i:31453030 original size:2 final size:2
Alignment explanation
Indices: 31453023--31453053 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
31453013 TGAAGCAAAT
31453023 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
31453054 TGTCTATGTT
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:31456335 original size:14 final size:14
Alignment explanation
Indices: 31456316--31456342 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31456306 ACAATTCGTT
31456316 TTGATATTATTTAG
1 TTGATATTATTTAG
31456330 TTGATATTATTTA
1 TTGATATTATTTA
31456343 ATTTGATTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (14 bp):
TTGATATTATTTAG
Found at i:31461675 original size:57 final size:57
Alignment explanation
Indices: 31461606--31461716 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 57
31461596 GGATGATGAA
*
31461606 GAACTTTTTAATCTTGAAGTACCATACCTTAATACAATTGGAGCACTAATATATTTT
1 GAACTTTTTAATCTTAAAGTACCATACCTTAATACAATTGGAGCACTAATATATTTT
* * * *
31461663 GAACTTTTTAATCTTAAAGTATCATATCTTAATACAATTGGAGTATTAATATAT
1 GAACTTTTTAATCTTAAAGTACCATACCTTAATACAATTGGAGCACTAATATAT
31461717 CTATATAGTA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.41
Consensus pattern (57 bp):
GAACTTTTTAATCTTAAAGTACCATACCTTAATACAATTGGAGCACTAATATATTTT
Found at i:31464783 original size:20 final size:19
Alignment explanation
Indices: 31464755--31464793 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
31464745 AGGTATATAA
31464755 TATTCAAAAAAATTTTAAAT
1 TATTCAAAAAAA-TTTAAAT
*
31464775 TATTTAAAAAAATTTAAAT
1 TATTCAAAAAAATTTAAAT
31464794 AAGTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
TATTCAAAAAAATTTAAAT
Found at i:31464819 original size:29 final size:30
Alignment explanation
Indices: 31464786--31464860 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
31464776 ATTTAAAAAA
31464786 ATTTAAATAAGTTTTTATATTTTTATTAT-
1 ATTTAAATAAGTTTTTATATTTTTATTATG
* * * *
31464815 ATTTAATTAAATATTTATATTTTTATTTTG
1 ATTTAAATAAGTTTTTATATTTTTATTATG
*
31464845 AATTAAATAAGTTTTT
1 ATTTAAATAAGTTTTT
31464861 TTGACTAGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
29 25 0.68
30 12 0.32
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (30 bp):
ATTTAAATAAGTTTTTATATTTTTATTATG
Found at i:31466984 original size:19 final size:20
Alignment explanation
Indices: 31466960--31466998 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
31466950 ATCTTCTTAC
31466960 TCTTTTT-AAATTCTTTCTT
1 TCTTTTTAAAATTCTTTCTT
*
31466979 TCTTTTTAAAATTTTTTCTT
1 TCTTTTTAAAATTCTTTCTT
31466999 ATATTTCGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (20 bp):
TCTTTTTAAAATTCTTTCTT
Found at i:31483493 original size:29 final size:31
Alignment explanation
Indices: 31483461--31483528 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 31
31483451 TTTTAAAAAA
* *
31483461 TTTAAATAAAT-TCTTATTCTTT-TATTACG
1 TTTAAATAAATCTCTTATACTTTATATTAAG
* *
31483490 TTT-AATCAATCTCTTATACTTTATTTTAAG
1 TTTAAATAAATCTCTTATACTTTATATTAAG
31483520 -TTAAATAAA
1 TTTAAATAAA
31483529 CCCTTATCAC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 6 0.19
29 15 0.48
30 10 0.32
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.51
Consensus pattern (31 bp):
TTTAAATAAATCTCTTATACTTTATATTAAG
Found at i:31483694 original size:33 final size:33
Alignment explanation
Indices: 31483657--31483730 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
31483647 ATTATATCAA
* *
31483657 ATTAACATGTCA-TTTCATCATTAATTATAATTT
1 ATTAACATGTCACATT-ATCATTAATTATAATAT
* * *
31483690 ATTAATATGTCACATTATTATTAATTATGATAT
1 ATTAACATGTCACATTATCATTAATTATAATAT
31483723 ATTAACAT
1 ATTAACAT
31483731 ATAATGTTAG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
33 32 0.94
34 2 0.06
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.47
Consensus pattern (33 bp):
ATTAACATGTCACATTATCATTAATTATAATAT
Found at i:31494845 original size:45 final size:42
Alignment explanation
Indices: 31494754--31494842 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
31494744 CTTCCTGTTC
* *
31494754 CTTCTGTTGAAAATGATGATTGCAACGGTGAGTCTTCTTCTT
1 CTTCTGTTGAAAATGATGATTCCAACGGTGAATCTTCTTCTT
*** * *
31494796 CTTCTGTTGAAAATGATGATTCCGTTGGTGAATATCCTTCTT
1 CTTCTGTTGAAAATGATGATTCCAACGGTGAATCTTCTTCTT
31494838 CTTCT
1 CTTCT
31494843 TCTTCTTCTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.43
Consensus pattern (42 bp):
CTTCTGTTGAAAATGATGATTCCAACGGTGAATCTTCTTCTT
Found at i:31494932 original size:105 final size:105
Alignment explanation
Indices: 31494789--31494995 Score: 265
Period size: 105 Copynumber: 2.0 Consensus size: 105
31494779 CGGTGAGTCT
* * * * * * *
31494789 TCTTCTTCTTCTGTTGAAAATGATGATTCCGTTGGTGAATATCCTTCTTCTTCTTCTTCTTCTTC
1 TCTTCATCTTCTGTTGAAAATGATGATTCCGATGGTGAACATCCTTCATCTTCTTCCTCCTCCTC
* *
31494854 TGTTGAAAATGACGATCGCATTG-GTGAATATTCTTCTTCA
66 CGTTGAAAATGACGATCGCA-TGAGTGAACATTCTTCTTCA
* *
31494894 TCTTCATCTTCTGTTGAAAATGATGATTGC-ATGAGTGAACATTCTTCATCTTCTTCCTCCTCCT
1 TCTTCATCTTCTGTTGAAAATGATGATTCCGATG-GTGAACATCCTTCATCTTCTTCCTCCTCCT
* *
31494958 CCGTTGAAAATGATGATTGCATGAGTGAACATTCTTCT
65 CCGTTGAAAATGACGATCGCATGAGTGAACATTCTTCT
31494996 GATGATTCCA
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
104 4 0.05
105 83 0.95
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.43
Consensus pattern (105 bp):
TCTTCATCTTCTGTTGAAAATGATGATTCCGATGGTGAACATCCTTCATCTTCTTCCTCCTCCTC
CGTTGAAAATGACGATCGCATGAGTGAACATTCTTCTTCA
Found at i:31494976 original size:54 final size:52
Alignment explanation
Indices: 31494786--31494995 Score: 212
Period size: 54 Copynumber: 4.0 Consensus size: 52
31494776 CAACGGTGAG
* * * * *
31494786 TCTTCTTC-TTCT-TCTGTTGAAAATGATGATTCCGTTGGTGAATATCCTTCT
1 TCTTCTTCATCCTCTCTGTTGAAAATGATGATTGC-ATGGTGAACATTCTTCT
* * * * *
31494837 TCTTCTTCTTCTTCTTCTGTTGAAAATGACGATCGCATTGGTGAATATTCTTCT
1 TCTTCTTCATCCTC-TCTGTTGAAAATGATGATTGCA-TGGTGAACATTCTTCT
* *
31494891 TCATCTTCAT-CT-TCTGTTGAAAATGATGATTGCATGAGTGAACATTCTTCA
1 TCTTCTTCATCCTCTCTGTTGAAAATGATGATTGCATG-GTGAACATTCTTCT
* *
31494942 TCTTCTTCCTCCTCCTCCGTTGAAAATGATGATTGCATGAGTGAACATTCTTCT
1 TCTTCTTCATCCT-CTCTGTTGAAAATGATGATTGCATG-GTGAACATTCTTCT
31494996 GATGATTCCA
Statistics
Matches: 133, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
50 2 0.02
51 48 0.36
52 4 0.03
53 1 0.01
54 78 0.59
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.43
Consensus pattern (52 bp):
TCTTCTTCATCCTCTCTGTTGAAAATGATGATTGCATGGTGAACATTCTTCT
Found at i:31495007 original size:27 final size:27
Alignment explanation
Indices: 31494968--31495022 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
31494958 CCGTTGAAAA
*
31494968 TGATGATTGCATGAGTGAACATTCTTC
1 TGATGATTCCATGAGTGAACATTCTTC
31494995 TGATGATTCCATGAGTGAACATTCTTC
1 TGATGATTCCATGAGTGAACATTCTTC
31495022 T
1 T
31495023 TCTTCTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.38
Consensus pattern (27 bp):
TGATGATTCCATGAGTGAACATTCTTC
Found at i:31495013 original size:81 final size:81
Alignment explanation
Indices: 31494914--31495076 Score: 272
Period size: 81 Copynumber: 2.0 Consensus size: 81
31494904 CTGTTGAAAA
* *
31494914 TGATGATTGCATGAGTGAACATTCTTCATCTTCTTCCTCCTCCTCCGTTGAAAATGATGATTGCA
1 TGATGATTCCATGAGTGAACATTCTTCATCTTCTTCCTCCTCCTCCGCTGAAAATGATGATTGCA
31494979 TGAGTGAACATTCTTC
66 TGAGTGAACATTCTTC
* * *
31494995 TGATGATTCCATGAGTGAACATTCTTCTTCTTCTTCTTCCTCCTCTGCTGAAAATGATGATTGCA
1 TGATGATTCCATGAGTGAACATTCTTCATCTTCTTCCTCCTCCTCCGCTGAAAATGATGATTGCA
*
31495060 TGAGTGAATATTCTTC
66 TGAGTGAACATTCTTC
31495076 T
1 T
31495077 TCTTCTTCTT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 76 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (81 bp):
TGATGATTCCATGAGTGAACATTCTTCATCTTCTTCCTCCTCCTCCGCTGAAAATGATGATTGCA
TGAGTGAACATTCTTC
Found at i:31495076 original size:54 final size:54
Alignment explanation
Indices: 31494995--31495321 Score: 393
Period size: 54 Copynumber: 5.8 Consensus size: 54
31494985 AACATTCTTC
* * *
31494995 TGATGATTCCATGAGTGAACATTCTTCTTCTTCTTCTTCCTCCTCTGCTGAAAA
1 TGATGATTGCATGAGTGAATATTCTTCTTCTTCTTCTTCCTCCTCCGCTGAAAA
31495049 TGATGATTGCATGAGTGAATATTCTTCTTCTTCTTCTTCTTCTTCCTCTTCCTCCGCTGAAAA
1 TGATGATTGCATGAGTGAATA------TTCTTCTTCTTCTTCTT-C-C-TCCTCCGCTGAAAA
* * ** * *
31495112 TGATGAGTGCATAACAGAATATTCTTCTTCTTCTTGTTCTTCCTCCGCTGAAAA
1 TGATGATTGCATGAGTGAATATTCTTCTTCTTCTTCTTCCTCCTCCGCTGAAAA
*
31495166 TGATGATTGCATGATTGAATATTCTTCTTCTTCTTCTTCCTCTTCCTCCGCTGAAAA
1 TGATGATTGCATGAGTGAATATTCTTCTTCTTCTTCTT-C-C-TCCTCCGCTGAAAA
* *
31495223 TGATGATTGCCTGAGTGAATATTCTTCTTCTTCTTCTTCTTCCTCCTCCGCTGAAGA
1 TGATGATTGCATGAGTGAATA---TTCTTCTTCTTCTTCTTCCTCCTCCGCTGAAAA
* *
31495280 TGATGATTGCATGAGTGAATATCCTTCTTTTTCTTCTTCCTC
1 TGATGATTGCATGAGTGAATATTCTTCTTCTTCTTCTTCCTC
31495322 TTTCTCCTCC
Statistics
Matches: 237, Mismatches: 21, Indels: 30
0.82 0.07 0.10
Matches are distributed among these distances:
54 85 0.36
55 1 0.00
56 1 0.00
57 82 0.35
58 1 0.00
59 1 0.00
60 34 0.14
61 1 0.00
62 1 0.00
63 30 0.13
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (54 bp):
TGATGATTGCATGAGTGAATATTCTTCTTCTTCTTCTTCCTCCTCCGCTGAAAA
Found at i:31495078 original size:3 final size:3
Alignment explanation
Indices: 31495070--31495099 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
31495060 TGAGTGAATA
*
31495070 TTC TTC TTC TTC TTC TTC TTC TTC CTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
31495100 CTCCGCTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:31495137 original size:57 final size:57
Alignment explanation
Indices: 31494995--31495349 Score: 434
Period size: 57 Copynumber: 6.2 Consensus size: 57
31494985 AACATTCTTC
* * *
31494995 TGATGATTCCATGAGTGAACATTCTTCTTCTTCTTCTT-C-C-TCCTCTGCTGAAAA
1 TGATGATTGCATGAGTGAATATTCTTCTTCTTCTTCTTCCTCTTCCTCCGCTGAAAA
31495049 TGATGATTGCATGAGTGAATATTCTTCTTCTTCTTCTTCTTCTTCCTCTTCCTCCGCTGAAAA
1 TGATGATTGCATGAGTGAATA------TTCTTCTTCTTCTTCTTCCTCTTCCTCCGCTGAAAA
* * ** *
31495112 TGATGAGTGCATAACAGAATATTCTTCTTCTTCTT-GT--TCTTCCTCCGCTGAAAA
1 TGATGATTGCATGAGTGAATATTCTTCTTCTTCTTCTTCCTCTTCCTCCGCTGAAAA
*
31495166 TGATGATTGCATGATTGAATATTCTTCTTCTTCTTCTTCCTCTTCCTCCGCTGAAAA
1 TGATGATTGCATGAGTGAATATTCTTCTTCTTCTTCTTCCTCTTCCTCCGCTGAAAA
* * * *
31495223 TGATGATTGCCTGAGTGAATATTCTTCTTCTTCTTCTTCTTCCTCCTCCGCTGAAGA
1 TGATGATTGCATGAGTGAATATTCTTCTTCTTCTTCTTCCTCTTCCTCCGCTGAAAA
* * *
31495280 TGATGATTGCATGAGTGAATATCCTTCTTTTTCTTCTTCCTCTTTCTCCTCCGCTGTAAA
1 TGATGATTGCATGAGTGAATATTCTTCTTCTTCTTCTTCCTC--T-TCCTCCGCTGAAAA
*
31495340 TAATGATTGC
1 TGATGATTGC
31495350 TTTGGTGAAC
Statistics
Matches: 260, Mismatches: 26, Indels: 24
0.84 0.08 0.08
Matches are distributed among these distances:
54 67 0.26
55 1 0.00
56 1 0.00
57 121 0.47
60 38 0.15
61 1 0.00
62 1 0.00
63 30 0.12
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.43
Consensus pattern (57 bp):
TGATGATTGCATGAGTGAATATTCTTCTTCTTCTTCTTCCTCTTCCTCCGCTGAAAA
Found at i:31495346 original size:117 final size:117
Alignment explanation
Indices: 31495016--31495349 Score: 473
Period size: 117 Copynumber: 2.9 Consensus size: 117
31495006 TGAGTGAACA
*
31495016 TTCTTCTTCTTCTTCTTCCTCCTCTGCTGAAAATGATGATTGCATGAGTGAATATTCTTCTTCTT
1 TTCTTCTTCTTCTTCTTCCTCCTCCGCTGAAAATGATGATTGCATGAGTGAATATTCTTCTTCTT
* *
31495081 CTTCTTCTTCTTCCTCTTCCTCCGCTGAAAATGATGAGTGCATAACAGAATATTC
66 CTTCTTCCTCTT--TC-TCCTCCGCTGAAAATGATGATTGCATAACAGAATATTC
* *
31495136 TTCTTCTTCTTGTTC-T--TCCTCCGCTGAAAATGATGATTGCATGATTGAATATTCTTCTTCTT
1 TTCTTCTTCTTCTTCTTCCTCCTCCGCTGAAAATGATGATTGCATGAGTGAATATTCTTCTTCTT
* * **
31495198 CTTCTTCCTC--T-TCCTCCGCTGAAAATGATGATTGCCTGAGTGAATATTC
66 CTTCTTCCTCTTTCTCCTCCGCTGAAAATGATGATTGCATAACAGAATATTC
* * *
31495247 TTCTTCTTCTTCTTCTTCCTCCTCCGCTGAAGATGATGATTGCATGAGTGAATATCCTTCTTTTT
1 TTCTTCTTCTTCTTCTTCCTCCTCCGCTGAAAATGATGATTGCATGAGTGAATATTCTTCTTCTT
* *
31495312 CTTCTTCCTCTTTCTCCTCCGCTGTAAATAATGATTGC
66 CTTCTTCCTCTTTCTCCTCCGCTGAAAATGATGATTGC
31495350 TTTGGTGAAC
Statistics
Matches: 192, Mismatches: 16, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
111 47 0.24
112 1 0.01
113 1 0.01
114 52 0.27
116 1 0.01
117 75 0.39
119 1 0.01
120 14 0.07
ACGTcount: A:0.18, C:0.25, G:0.13, T:0.43
Consensus pattern (117 bp):
TTCTTCTTCTTCTTCTTCCTCCTCCGCTGAAAATGATGATTGCATGAGTGAATATTCTTCTTCTT
CTTCTTCCTCTTTCTCCTCCGCTGAAAATGATGATTGCATAACAGAATATTC
Found at i:31496565 original size:12 final size:12
Alignment explanation
Indices: 31496548--31496574 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
31496538 TCGATTCTTG
31496548 AAGAGAGGAAGA
1 AAGAGAGGAAGA
31496560 AAGAGAGGAAGA
1 AAGAGAGGAAGA
31496572 AAG
1 AAG
31496575 GAAGGTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (12 bp):
AAGAGAGGAAGA
Found at i:31497634 original size:18 final size:18
Alignment explanation
Indices: 31497607--31497669 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
31497597 AGACATCTCA
*
31497607 TCAGACTCATCTTCATCC
1 TCAGAATCATCTTCATCC
* * *
31497625 TCAGAATCATCGTCCTCA
1 TCAGAATCATCTTCATCC
*
31497643 TCAGAACCA-CTTTCATCC
1 TCAGAATCATC-TTCATCC
*
31497661 TGAGAATCA
1 TCAGAATCA
31497670 CTCTCATCGT
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
17 1 0.03
18 33 0.97
ACGTcount: A:0.29, C:0.33, G:0.10, T:0.29
Consensus pattern (18 bp):
TCAGAATCATCTTCATCC
Found at i:31504901 original size:23 final size:22
Alignment explanation
Indices: 31504849--31504902 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
31504839 CTATTTTTTT
31504849 ATAATCTTATAAATAGTTTCTA
1 ATAATCTTATAAATAGTTTCTA
* *
31504871 AGTGATCTTAATCAATAGTATTC-A
1 A-TAATCTT-ATAAATAGT-TTCTA
31504895 ATAATCTT
1 ATAATCTT
31504903 GTAAGATACA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 1 0.04
23 12 0.46
24 10 0.38
25 3 0.12
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (22 bp):
ATAATCTTATAAATAGTTTCTA
Found at i:31505177 original size:16 final size:17
Alignment explanation
Indices: 31505148--31505180 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31505138 TTGAAATTTT
*
31505148 AAATACTTAGTTACATA
1 AAATAATTAGTTACATA
31505165 AAATAATTA-TTACATA
1 AAATAATTAGTTACATA
31505181 TTTACTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (17 bp):
AAATAATTAGTTACATA
Found at i:31507203 original size:57 final size:57
Alignment explanation
Indices: 31507075--31507214 Score: 131
Period size: 57 Copynumber: 2.5 Consensus size: 57
31507065 GGAGAGAAGA
* * * * * * * *
31507075 TTTTCCTTTTCTTCCGACTTTGGTTCATAGAACTCTGTTTTTGTGTCATAGTAAGGC
1 TTTTCCTTTTCTTCTGACTTTGGTTTATACAACTATGATTTTCTGCCATACTAAGGC
* * *
31507132 TTTT-CTTCTCCTTCTGGCTTTGGTTTA-ACAACGTATGATTTTCTGCCATACTCAGGC
1 TTTTCCTT-TTCTTCTGACTTTGGTTTATACAAC-TATGATTTTCTGCCATACTAAGGC
* *
31507189 TTTTCCTTTTCTTCTGTCTTCGGTTT
1 TTTTCCTTTTCTTCTGACTTTGGTTT
31507215 GTAGAGGTAT
Statistics
Matches: 66, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
56 7 0.11
57 56 0.85
58 3 0.05
ACGTcount: A:0.13, C:0.22, G:0.16, T:0.49
Consensus pattern (57 bp):
TTTTCCTTTTCTTCTGACTTTGGTTTATACAACTATGATTTTCTGCCATACTAAGGC
Found at i:31507368 original size:57 final size:54
Alignment explanation
Indices: 31507299--31507461 Score: 164
Period size: 57 Copynumber: 2.9 Consensus size: 54
31507289 TGTAGTTGTC
*
31507299 TGGTTTTGTGCCATAGTAAGGCTTTTCTTCTCCTTCTGGCTTTGGTTTAGCAACGTA
1 TGGTTTTGTGCCATAATAAGGCTTTTCTT-TCCTTCTGGCTTTGGTTTAG--ACGTA
* * * * * * *
31507356 TGGTTTTCTGCCATACTCAGGCTTTTCCTTTTCTTCTGGTTTTGGCTTGTAGATGTT
1 TGGTTTTGTGCCATAATAAGGCTTTT-CTTTCCTTCTGGCTTTGG-TT-TAGACGTA
* * *
31507413 TTGTTTTGTGCAATAATTAGGCTTTTCTTTTCCTTCTGGCTTTGGTTTA
1 TGGTTTTGTGCCATAATAAGGCTTTTC-TTTCCTTCTGGCTTTGGTTTA
31507462 ACGACCTCCG
Statistics
Matches: 88, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
55 2 0.02
56 3 0.03
57 75 0.85
58 5 0.06
59 3 0.03
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.50
Consensus pattern (54 bp):
TGGTTTTGTGCCATAATAAGGCTTTTCTTTCCTTCTGGCTTTGGTTTAGACGTA
Found at i:31507475 original size:114 final size:114
Alignment explanation
Indices: 31507287--31507535 Score: 286
Period size: 114 Copynumber: 2.2 Consensus size: 114
31507277 CTGGCTTCTC
* * * *
31507287 CTTGTAGTTGTCTGGTTTTGTGCCATAGTAAGGCTTTTCTTCTCCTTCTGGCTTTGGTTTAGCAA
1 CTTGTAGATGTCTGGTTTTGTGCAATAATAAGGCTTTTCTTCTCCTTCTGGCTTTGGTTTAACAA
* * * * *
31507352 CGTATGGTTTTCTGCCATACTCAGGCTTTTCCTTTTCTTCTGGTTTTGG
66 CCTACGGTTTACTACCATAATCAGGCTTTTCCTTTTCTTCTGGTTTTGG
* * * * *
31507401 CTTGTAGATGTTTTGTTTTGTGCAATAATTAGGCTTTTCTTTTCCTTCTGGCTTTGGTTTAACGA
1 CTTGTAGATGTCTGGTTTTGTGCAATAATAAGGCTTTTCTTCTCCTTCTGGCTTTGGTTTAACAA
* * * * *
31507466 CCTCCGGTTTACTACCATAATCAGGCTTTT-CTTTGTCTACCGGCTTGGG
66 CCTACGGTTTACTACCATAATCAGGCTTTTCCTTT-TCTTCTGGTTTTGG
*
31507515 CTTGTA-ATAGTCTGGCTTTGT
1 CTTGTAGAT-GTCTGGTTTTGT
31507536 AGGCTTTTCT
Statistics
Matches: 111, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
113 6 0.05
114 105 0.95
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (114 bp):
CTTGTAGATGTCTGGTTTTGTGCAATAATAAGGCTTTTCTTCTCCTTCTGGCTTTGGTTTAACAA
CCTACGGTTTACTACCATAATCAGGCTTTTCCTTTTCTTCTGGTTTTGG
Found at i:31515466 original size:57 final size:54
Alignment explanation
Indices: 31515373--31515535 Score: 155
Period size: 57 Copynumber: 2.9 Consensus size: 54
31515363 TGTAGTTGTC
* * * *
31515373 TGGTTTTGTGCCATAGTAAGGCTTCTCTTCTCCTTCTGGCTTCGGTTTAGCAACGTA
1 TGGTTTTGTGCCATAATAAGGCTTTTCTT-TTCTTCTGGCTTTGGTTTAG--ACGTA
* * * * * *
31515430 TGGTTTTCTGCCATACTCAGGCTTTTCCTTTTCTTCTGGTTTTGGCTTGTAGATGTC
1 TGGTTTTGTGCCATAATAAGGCTTTT-CTTTTCTTCTGGCTTTGG-TT-TAGACGTA
* *
31515487 TTGTTTTGTGCCATAATTAGGCTTTTCTTTTCCTTCTGGCTTTGGTTTA
1 TGGTTTTGTGCCATAATAAGGCTTTTCTTTT-CTTCTGGCTTTGGTTTA
31515536 ACGACCTCGG
Statistics
Matches: 88, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
55 2 0.02
56 7 0.08
57 71 0.81
58 5 0.06
59 3 0.03
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.48
Consensus pattern (54 bp):
TGGTTTTGTGCCATAATAAGGCTTTTCTTTTCTTCTGGCTTTGGTTTAGACGTA
Found at i:31515549 original size:114 final size:114
Alignment explanation
Indices: 31515343--31515609 Score: 277
Period size: 114 Copynumber: 2.3 Consensus size: 114
31515333 CATACCCAGA
* *
31515343 CTTTTCCTCTGGCTTCGCCTTGTAGTTGTCTGGTTTTGTGCCATAGTAAGGCTTCTCTTCTCCTT
1 CTTTTCCTCTGGCTTCGCCTTGTAGATGTCTGGTTTTGTGCCATAATAAGGCTTCTCTTCTCCTT
* * * * * *
31515408 CTGGCTTCGGTTTAGCAACGTATGGTTTTCTGCCATACTCAGGCTTTTC
66 CTGGCTTCGGTTTAACAACCTAGGGTTTACTACCATAATCAGGCTTTTC
* * * * * * * *
31515457 CTTTTCTTCTGGTTTTGGCTTGTAGATGTCTTGTTTTGTGCCATAATTAGGCTTTTCTTTTCCTT
1 CTTTTCCTCTGGCTTCGCCTTGTAGATGTCTGGTTTTGTGCCATAATAAGGCTTCTCTTCTCCTT
* * * *
31515522 CTGGCTTTGGTTTAACGACCTCGGGTTTACTACCATAATCAGGCTCTT-
66 CTGGCTTCGGTTTAACAACCTAGGGTTTACTACCATAATCAGGCTTTTC
* * * * *
31515570 CTTTGTCCACCGGCTTGGGCTTGTA-ATAGTCTGGCTTTGT
1 CTTT-TCCTCTGGCTTCGCCTTGTAGAT-GTCTGGTTTTGT
31515610 AGGCTCTTCT
Statistics
Matches: 124, Mismatches: 27, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
113 6 0.05
114 118 0.95
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (114 bp):
CTTTTCCTCTGGCTTCGCCTTGTAGATGTCTGGTTTTGTGCCATAATAAGGCTTCTCTTCTCCTT
CTGGCTTCGGTTTAACAACCTAGGGTTTACTACCATAATCAGGCTTTTC
Done.