Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 142 of 410
Found at i:43140646 original size:29 final size:29
Alignment explanation
Indices: 43140555--43140653 Score: 112
Period size: 29 Copynumber: 3.4 Consensus size: 29
43140545 TACCGATCTC
*
43140555 GCACACATAGTGCTCAGTTAAAGGAATTT
1 GCACACACAGTGCTCAGTTAAAGGAATTT
* * ** *
43140584 GCACACACAGTCCTCAATT-ACCG-ATCTC
1 GCACACACAGTGCTCAGTTAAAGGAAT-TT
*
43140612 GCACACATAGTGCTCAGTTAAAGGAATTT
1 GCACACACAGTGCTCAGTTAAAGGAATTT
43140641 GCACACACAGTGC
1 GCACACACAGTGC
43140654 CTCTAATCAT
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
27 2 0.04
28 19 0.35
29 31 0.57
30 2 0.04
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (29 bp):
GCACACACAGTGCTCAGTTAAAGGAATTT
Found at i:43140874 original size:43 final size:43
Alignment explanation
Indices: 43140822--43141075 Score: 191
Period size: 43 Copynumber: 5.9 Consensus size: 43
43140812 CACCAGCATT
* *
43140822 AAGCTTGCTAGGCACGAAGACCCAAATACACATCACCGACACG
1 AAGCCTGCTAGGCACGAAGGCCCAAATACACATCACCGACACG
43140865 AAGCCTGCTAGGCACGAAGGCCCAAATACACATCACC-AGCACG
1 AAGCCTGCTAGGCACGAAGGCCCAAATACACATCACCGA-CACG
*** ** * * * * *
43140908 AAGGCCCAAATACACATC-ACCGGCACGAA-GC-C-TGCTA--GGCACG
1 AA-G-CCTGCTAGGCA-CGA-AGGCCCAAATACACAT-C-ACCGACACG
* **
43140951 AAGCCTGCTAGGCATGAAGGCCTGAATACACATCACC-AGCACG
1 AAGCCTGCTAGGCACGAAGGCCCAAATACACATCACCGA-CACG
* * * *
43140994 AAGCCTACTAGGCACGAAGGCTCGAATACACATCACCGGCACG
1 AAGCCTGCTAGGCACGAAGGCCCAAATACACATCACCGACACG
* *
43141037 TAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGA
1 AAGCCTGCTAGGCACGAAGGCCCAAATACACATCACCGA
43141076 GTTTCATGCA
Statistics
Matches: 163, Mismatches: 32, Indels: 32
0.72 0.14 0.14
Matches are distributed among these distances:
40 6 0.04
41 9 0.06
42 4 0.02
43 125 0.77
44 3 0.02
45 9 0.06
46 7 0.04
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (43 bp):
AAGCCTGCTAGGCACGAAGGCCCAAATACACATCACCGACACG
Found at i:43140914 original size:27 final size:27
Alignment explanation
Indices: 43140876--43140937 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
43140866 AGCCTGCTAG
43140876 GCACGAAGGCCCAAATACACATCACCA
1 GCACGAAGGCCCAAATACACATCACCA
*
43140903 GCACGAAGGCCCAAATACACATCACCG
1 GCACGAAGGCCCAAATACACATCACCA
43140930 GCACGAAG
1 GCACGAAG
43140938 CCTGCTAGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.39, C:0.35, G:0.19, T:0.06
Consensus pattern (27 bp):
GCACGAAGGCCCAAATACACATCACCA
Found at i:43140950 original size:16 final size:16
Alignment explanation
Indices: 43140929--43140974 Score: 74
Period size: 16 Copynumber: 2.8 Consensus size: 16
43140919 ACACATCACC
43140929 GGCACGAAGCCTGCTA
1 GGCACGAAGCCTGCTA
43140945 GGCACGAAGCCTGCTA
1 GGCACGAAGCCTGCTA
*
43140961 GGCATGAAGGCCTG
1 GGCACGAA-GCCTG
43140975 AATACACATC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 23 0.82
17 5 0.18
ACGTcount: A:0.24, C:0.28, G:0.35, T:0.13
Consensus pattern (16 bp):
GGCACGAAGCCTGCTA
Found at i:43141035 original size:86 final size:86
Alignment explanation
Indices: 43140810--43141073 Score: 261
Period size: 86 Copynumber: 3.1 Consensus size: 86
43140800 CCTTGCTCGA
** * * * * * *
43140810 ATCACCAGCATTAAGCTTGCTAGGCACGAAGACCCAAATACACATCACCGACACGAAGCCTGCTA
1 ATCACCAGCACGAAGCCTACTAGGCACGAAGGCACGAATACACATCACCGGCACGAAGCCTGCTA
*
43140875 GGCACGAAGGCCCAAATACAC
66 GGCACGAAGGCCCGAATACAC
* * ** * *
43140896 ATCACCAGCACGAAGGCCCAAATACACATC-ACCGGCACGAA-GC-C-TGCTA--GGCACGAAGC
1 ATCACCAGCACGAA-G-CCTACTAGGCA-CGA-AGGCACGAATACACAT-C-ACCGGCACGAAGC
* *
43140955 CTGCTAGGCATGAAGGCCTGAATACAC
60 CTGCTAGGCACGAAGGCCCGAATACAC
* *
43140982 ATCACCAGCACGAAGCCTACTAGGCACGAAGGCTCGAATACACATCACCGGCACGTAGCCTGCTA
1 ATCACCAGCACGAAGCCTACTAGGCACGAAGGCACGAATACACATCACCGGCACGAAGCCTGCTA
43141047 GGCACGAAGGCCCGAATACAC
66 GGCACGAAGGCCCGAATACAC
43141068 ATCACC
1 ATCACC
43141074 GAGTTTCATG
Statistics
Matches: 139, Mismatches: 27, Indels: 24
0.73 0.14 0.13
Matches are distributed among these distances:
83 8 0.06
84 10 0.07
85 3 0.02
86 101 0.73
87 3 0.02
88 8 0.06
89 6 0.04
ACGTcount: A:0.33, C:0.33, G:0.21, T:0.12
Consensus pattern (86 bp):
ATCACCAGCACGAAGCCTACTAGGCACGAAGGCACGAATACACATCACCGGCACGAAGCCTGCTA
GGCACGAAGGCCCGAATACAC
Found at i:43146023 original size:17 final size:17
Alignment explanation
Indices: 43146001--43146039 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
43145991 CTGCAATAGA
43146001 GCCCAATAGGCTTTCGG
1 GCCCAATAGGCTTTCGG
43146018 GCCCAATAGGCTTTCGG
1 GCCCAATAGGCTTTCGG
43146035 GCCCA
1 GCCCA
43146040 TTTGGGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.33, G:0.28, T:0.21
Consensus pattern (17 bp):
GCCCAATAGGCTTTCGG
Found at i:43146329 original size:25 final size:25
Alignment explanation
Indices: 43146300--43146347 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
43146290 TTATAACATG
* *
43146300 AAAATGACCATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
43146325 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
43146348 GTTTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:43146413 original size:20 final size:20
Alignment explanation
Indices: 43146390--43146430 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
43146380 ATAAACATTG
43146390 TATGGATGATATGCACATGA
1 TATGGATGATATGCACATGA
*
43146410 TATGTATGATATGCACATGA
1 TATGGATGATATGCACATGA
43146430 T
1 T
43146431 GTATTCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (20 bp):
TATGGATGATATGCACATGA
Found at i:43146536 original size:24 final size:24
Alignment explanation
Indices: 43146480--43146668 Score: 310
Period size: 24 Copynumber: 8.0 Consensus size: 24
43146470 GAGGAAGTGA
*
43146480 AAAAGGGCTTATGCCCCAATTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
43146503 TAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
43146527 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
43146551 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
43146575 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
*
43146599 AAAAGGGCTTACGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
* *
43146622 TAAAGGGCTTATGCCCCAGTTATA
1 AAAAGGGCTTATGCCCCAGTTATC
*
43146646 AAAAGGGCTTTTGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
43146669 TAGAAGAGGC
Statistics
Matches: 156, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
23 42 0.27
24 114 0.73
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:43146925 original size:31 final size:31
Alignment explanation
Indices: 43146887--43146950 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
43146877 CGTTTACAGT
*
43146887 AAAGGCTTCGACCCAGTAATATGAAATTTGA
1 AAAGGCTTCGACCCAGTAATATGAAATATGA
* **
43146918 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGACCCAGTAATATGAAATATGA
43146949 AA
1 AA
43146951 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGACCCAGTAATATGAAATATGA
Found at i:43148887 original size:40 final size:39
Alignment explanation
Indices: 43148805--43148995 Score: 134
Period size: 40 Copynumber: 4.8 Consensus size: 39
43148795 TCGAATGATG
* * * * * *
43148805 TCCGGGCTAAGTCCCAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCGAAGGCATTCGTGC-GAGTTAATAAA
* * *
43148844 TCCGGACTAGGATCTGAAGGCATTCGTGCGAGTTAATAAA
1 TCCGGGCTAAG-TCCGAAGGCATTCGTGCGAGTTAATAAA
* * * *
43148884 TCCGGGCTAAGCCCGAAGGCATTTGTGCAAGTTATTAAA
1 TCCGGGCTAAGTCCGAAGGCATTCGTGCGAGTTAATAAA
* * * *
43148923 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTCGTGCGAGTTAATA-AA
** * *
43148964 -CCGGGCTTCGTCCCGAAGGCATTTGAGCGAGT
1 TCCGGGCTAAGT-CCGAAGGCATTCGTGCGAGT
43148996 CGTTATATCC
Statistics
Matches: 120, Mismatches: 28, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
39 41 0.34
40 71 0.59
41 8 0.07
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTCGTGCGAGTTAATAAA
Found at i:43148904 original size:39 final size:39
Alignment explanation
Indices: 43148859--43148995 Score: 150
Period size: 40 Copynumber: 3.5 Consensus size: 39
43148849 ACTAGGATCT
43148859 GAAGGCATTCGTGCGAGTTAATAAATCCGGGCTAAG-CCC
1 GAAGGCATTCGTGCGAGTTAATAAA-CCGGGCTAAGTCCC
* * * *
43148898 GAAGGCATTTGTGCAAGTTATTAAACCCGGGTTAAGTCCC
1 GAAGGCATTCGTGCGAGTTAATAAA-CCGGGCTAAGTCCC
* * **
43148938 GAAGGCATTCGTGCGAGTCACTATAACCGGGCTTCGTCCC
1 GAAGGCATTCGTGCGAGTTAATA-AACCGGGCTAAGTCCC
* *
43148978 GAAGGCATTTGAGCGAGT
1 GAAGGCATTCGTGCGAGT
43148996 CGTTATATCC
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
39 31 0.38
40 49 0.60
41 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (39 bp):
GAAGGCATTCGTGCGAGTTAATAAACCGGGCTAAGTCCC
Found at i:43149010 original size:79 final size:79
Alignment explanation
Indices: 43148859--43149021 Score: 195
Period size: 79 Copynumber: 2.1 Consensus size: 79
43148849 ACTAGGATCT
* * *
43148859 GAAGGCATTCGTGCGAGTTAATAAATCCGGGCTAAGCCCGAAGGCATTTGTGCAAGTTATTAAAC
1 GAAGGCATTCGTGCGAGTCAATAAATCCGGGCTAAGCCCGAAGGCATTTGAGCAAGTCATTAAAC
43148924 CCGGGTTAAGTCCC
66 CCGGGTTAAGTCCC
* ** * * *
43148938 GAAGGCATTCGTGCGAGTCACTATAA-CCGGGCTTCGTCCCGAAGGCATTTGAGCGAGTCGTTAT
1 GAAGGCATTCGTGCGAGTCAATA-AATCCGGGCTAAG-CCCGAAGGCATTTGAGCAAGTCATTAA
* *
43149002 ATCC-GGTTAAGTTCC
64 ACCCGGGTTAAGTCCC
43149017 GAAGG
1 GAAGG
43149022 TACGTGATTC
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
79 44 0.62
80 27 0.38
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
GAAGGCATTCGTGCGAGTCAATAAATCCGGGCTAAGCCCGAAGGCATTTGAGCAAGTCATTAAAC
CCGGGTTAAGTCCC
Found at i:43160429 original size:42 final size:42
Alignment explanation
Indices: 43160382--43160518 Score: 166
Period size: 42 Copynumber: 3.3 Consensus size: 42
43160372 TGAGTTATCA
* *
43160382 TGTAAGACCATATTTGGGATATGGTGTTGATATGAGATTTCG
1 TGTAAGACCATATCTGGGATATGGCGTTGATATGAGATTTCG
* * * *
43160424 TGTAAGACCACATCTGGGACATGGCGTTGAAATGAGAATTCG
1 TGTAAGACCATATCTGGGATATGGCGTTGATATGAGATTTCG
* * * * * *
43160466 TATAAGACCATATCTGGGATATAGCATTGATGTGAGATTCCA
1 TGTAAGACCATATCTGGGATATGGCGTTGATATGAGATTTCG
43160508 TGTAAGACCAT
1 TGTAAGACCAT
43160519 GCGATACGTG
Statistics
Matches: 78, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 78 1.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCGTTGATATGAGATTTCG
Found at i:43166278 original size:38 final size:38
Alignment explanation
Indices: 43166222--43166301 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 38
43166212 GATGTGTATT
* * *
43166222 CGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATC
1 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
*
43166260 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATT
1 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
43166298 CGGG
1 CGGG
43166302 CCTTCGTGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.29
Consensus pattern (38 bp):
CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
Found at i:43166348 original size:43 final size:43
Alignment explanation
Indices: 43166294--43166461 Score: 237
Period size: 43 Copynumber: 3.9 Consensus size: 43
43166284 GCTGGTATTA
43166294 TATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCAGTGATGTG
* * **
43166337 TATTCGGGCCTTCGTACCTAGCAGGCTTCGTGCTGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCAGTGATGTG
* * * *
43166380 TATTCAGGCCTTCGTGCCTAGCAGGTTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCAGTGATGTG
* * *
43166423 TATTCGGGCCTTCGTTCCTAGCAGGCGTAATGCCAGTGA
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCAGTGA
43166462 AATGATATGT
Statistics
Matches: 110, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 110 1.00
ACGTcount: A:0.14, C:0.24, G:0.32, T:0.31
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCAGTGATGTG
Found at i:43166395 original size:86 final size:84
Alignment explanation
Indices: 43166273--43166448 Score: 262
Period size: 86 Copynumber: 2.1 Consensus size: 84
43166263 GATAAATCCC
*
43166273 GCAGGCCTAGTGCTGGTATTATATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCAGTGATGTGT
1 GCAGGCCTAGTGCTGGTATTATATTCAGGCCTTCGTGCCTAGCAGGCTTAGTGCCAGTGATGTGT
43166338 ATTCGGGCCTTCGTACCTA
66 ATTCGGGCCTTCGTACCTA
* * * * * *
43166357 GCAGGCTTCGTGCTGGTGATGTGTATTCAGGCCTTCGTGCCTAGCAGGTTTCGTGCCGGTGATGT
1 GCAGGCCTAGTGCTGGT-AT-TATATTCAGGCCTTCGTGCCTAGCAGGCTTAGTGCCAGTGATGT
*
43166422 GTATTCGGGCCTTCGTTCCTA
64 GTATTCGGGCCTTCGTACCTA
43166443 GCAGGC
1 GCAGGC
43166449 GTAATGCCAG
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
84 15 0.18
85 2 0.02
86 65 0.79
ACGTcount: A:0.13, C:0.24, G:0.32, T:0.31
Consensus pattern (84 bp):
GCAGGCCTAGTGCTGGTATTATATTCAGGCCTTCGTGCCTAGCAGGCTTAGTGCCAGTGATGTGT
ATTCGGGCCTTCGTACCTA
Found at i:43166852 original size:45 final size:42
Alignment explanation
Indices: 43166778--43166885 Score: 112
Period size: 45 Copynumber: 2.5 Consensus size: 42
43166768 TTGACTTGAT
* * *
43166778 TATTCGGGCCTTTGAGCTTAGCAAACTATAATGCTGGTGAGGTAC
1 TATTCGGGCCTTCGAGCCTAGCAAACTATAATGCCGGTGA---AC
*
43166823 TATTCGGGCCTTCGAGCCTAG-AAGGCTATAATGCCGGTGAAC
1 TATTCGGGCCTTCGAGCCTAGCAA-ACTATAATGCCGGTGAAC
43166865 TGATATCGGGCC-TCGAGCCTA
1 T-AT-TCGGGCCTTCGAGCCTA
43166886 ACAGGCGAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
42 3 0.05
43 11 0.20
44 9 0.16
45 33 0.59
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (42 bp):
TATTCGGGCCTTCGAGCCTAGCAAACTATAATGCCGGTGAAC
Found at i:43174032 original size:21 final size:21
Alignment explanation
Indices: 43174004--43174051 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
43173994 TTCATCTATG
43174004 TATG-TATGTGCCAAT-TTTAT
1 TATGATATG-GCCAATGTTTAT
*
43174024 TATGATATGGCCTATGTTTAT
1 TATGATATGGCCAATGTTTAT
43174045 TGATGAT
1 T-ATGAT
43174052 GGAATGTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 9 0.38
21 10 0.42
22 5 0.21
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.48
Consensus pattern (21 bp):
TATGATATGGCCAATGTTTAT
Found at i:43180823 original size:6 final size:5
Alignment explanation
Indices: 43180794--43180873 Score: 69
Period size: 5 Copynumber: 15.8 Consensus size: 5
43180784 TATGTCTTTC
* *
43180794 AAAAT AAAAT --AAT AAAATT GAAAT GAAAAT AAAAT AAAA- ATAA- AAAAT
1 AAAAT AAAAT AAAAT AAAA-T AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT
43180842 AAAAAT AAAAT AAAAT AATAAT AATAAT AAAA
1 -AAAAT AAAAT AAAAT AA-AAT AA-AAT AAAA
43180874 ATAGGAGGAG
Statistics
Matches: 64, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
3 3 0.05
4 6 0.09
5 31 0.48
6 24 0.38
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:43180842 original size:13 final size:14
Alignment explanation
Indices: 43180826--43180876 Score: 70
Period size: 13 Copynumber: 3.7 Consensus size: 14
43180816 ATGAAAATAA
43180826 AATAAAAATAAAA-
1 AATAAAAATAAAAT
43180839 AATAAAAATAAAAT
1 AATAAAAATAAAAT
*
43180853 AA-AATAATAATAAT
1 AATAAAAATAA-AAT
43180867 AATAAAAATA
1 AATAAAAATA
43180877 GGAGGAGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 20 0.61
14 7 0.21
15 6 0.18
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAAAAATAAAAT
Found at i:43180865 original size:35 final size:35
Alignment explanation
Indices: 43180794--43180874 Score: 110
Period size: 35 Copynumber: 2.3 Consensus size: 35
43180784 TATGTCTTTC
* *
43180794 AAAATAAAATAATAAAATTGAAATGAAAATAAAATA
1 AAAATAAAA-AATAAAAATAAAATGAAAATAAAATA
43180830 AAAATAAAAAATAAAAATAAAAT-AAAATAATAATA
1 AAAATAAAAAATAAAAATAAAATGAAAATAA-AATA
*
43180865 ATAATAAAAA
1 AAAATAAAAA
43180875 TAGGAGGAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
34 7 0.17
35 25 0.61
36 9 0.22
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (35 bp):
AAAATAAAAAATAAAAATAAAATGAAAATAAAATA
Found at i:43180876 original size:6 final size:6
Alignment explanation
Indices: 43180814--43180876 Score: 69
Period size: 6 Copynumber: 10.8 Consensus size: 6
43180804 AATAAAATTG
*
43180814 AAATGA AAAT-A AAATAA AAATAAA AAATAA AAAT-A AAAT-A AAATAA
1 AAATAA AAATAA AAATAA AAAT-AA AAATAA AAATAA AAATAA AAATAA
* *
43180860 TAATAA TAATAA AAATA
1 AAATAA AAATAA AAATA
43180877 GGAGGAGTCA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
5 15 0.29
6 31 0.60
7 6 0.12
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.21
Consensus pattern (6 bp):
AAATAA
Found at i:43180876 original size:18 final size:16
Alignment explanation
Indices: 43180804--43180873 Score: 74
Period size: 17 Copynumber: 4.4 Consensus size: 16
43180794 AAAATAAAAT
**
43180804 AATAAAATTGAAATGAA
1 AATAAAATAAAAAT-AA
43180821 AATAAAATAAAAAT--
1 AATAAAATAAAAATAA
43180835 AA-AAAATAAAAATAA
1 AATAAAATAAAAATAA
*
43180850 AATAAAATAATAATAA
1 AATAAAATAAAAATAA
43180866 TAATAAAA
1 -AATAAAA
43180874 ATAGGAGGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
13 11 0.24
14 2 0.04
15 2 0.04
16 12 0.26
17 19 0.41
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (16 bp):
AATAAAATAAAAATAA
Found at i:43197301 original size:28 final size:28
Alignment explanation
Indices: 43197269--43197367 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
43197259 GCAATAAGCC
*
43197269 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
43197297 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
43197325 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
43197354 CGCACACTTAGTGC
1 CGCACACTTAGTGC
43197368 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:43203443 original size:24 final size:24
Alignment explanation
Indices: 43203415--43203461 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
43203405 CTATAACATG
* * *
43203415 AAAATGACCGTTTTGCCCCTAGGT
1 AAAATGACCATTATACCCCTAGGT
43203439 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
43203462 GTTTATATAT
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:0.32, C:0.26, G:0.17, T:0.26
Consensus pattern (24 bp):
AAAATGACCATTATACCCCTAGGT
Found at i:43203526 original size:20 final size:20
Alignment explanation
Indices: 43203501--43203564 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
43203491 GATAAACATG
43203501 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
43203521 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
*
43203541 ATGTATGATATGCACATGAG
1 ATGTATGATATGCACATGAC
43203561 ATGT
1 ATGT
43203565 TCATAAATGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:43203541 original size:11 final size:11
Alignment explanation
Indices: 43203505--43203559 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
43203495 AACATGATGT
43203505 ATGATATGCAC
1 ATGATATGCAC
* *
43203516 ATGACATG--T
1 ATGATATGCAC
43203525 ATGATATGCAC
1 ATGATATGCAC
*
43203536 ATGATATG--T
1 ATGATATGCAC
43203545 ATGATATGCAC
1 ATGATATGCAC
43203556 ATGA
1 ATGA
43203560 GATGTTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:43203641 original size:23 final size:23
Alignment explanation
Indices: 43203611--43203749 Score: 210
Period size: 23 Copynumber: 6.0 Consensus size: 23
43203601 AGGAAGTGCA
43203611 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
43203634 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
43203658 AAAGGGCTTATG-CCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
43203681 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
43203704 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
43203727 AAAAAGGGCTT-TGCCCCAGTTAT
1 --AAAGGGCTTATGCCCCAGTTAT
43203750 AGAGGCTAGG
Statistics
Matches: 110, Mismatches: 2, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
23 68 0.62
24 33 0.30
25 9 0.08
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:43203685 original size:47 final size:47
Alignment explanation
Indices: 43203609--43203749 Score: 216
Period size: 47 Copynumber: 3.0 Consensus size: 47
43203599 GGAGGAAGTG
*
43203609 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTAT
43203656 CAAAAGGGCTTATG-CCCAGTTATCAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTAT
*
43203703 -TAAAGGGCTTATGCCCCAGTTATTAAAAAGGGCTT-TGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTA-T-AAAAGGGCTTATGCCCCAGTTAT
43203750 AGAGGCTAGG
Statistics
Matches: 88, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
46 21 0.24
47 56 0.64
48 11 0.12
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (47 bp):
CAAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTAT
Found at i:43203722 original size:70 final size:71
Alignment explanation
Indices: 43203609--43203749 Score: 250
Period size: 70 Copynumber: 2.0 Consensus size: 71
43203599 GGAGGAAGTG
*
43203609 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTA-TCAAAAGGGCTTATG-CC
1 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAAAGGGCTT-TGCCC
43203672 CAGTTAT
65 CAGTTAT
43203679 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAAAGGGCTTTGCCCC
1 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAAAGGGCTTTGCCCC
43203744 AGTTAT
66 AGTTAT
43203750 AGAGGCTAGG
Statistics
Matches: 68, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
70 48 0.71
71 20 0.29
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (71 bp):
CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAAAGGGCTTTGCCCC
AGTTAT
Found at i:43204022 original size:30 final size:31
Alignment explanation
Indices: 43203962--43204024 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
43203952 CGTTTACAGT
43203962 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
43203993 AAAGGCTTCGGCCCAGTGTTATG-AATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
43204023 AA
1 AA
43204025 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:43204906 original size:40 final size:40
Alignment explanation
Indices: 43204851--43205092 Score: 364
Period size: 40 Copynumber: 6.0 Consensus size: 40
43204841 GACGATAACT
* * *
43204851 GGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-TCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATCC
*
43204891 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
43204931 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGT-TCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATCC
43204971 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
*
43205011 GGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
* * *
43205051 GGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCC
43205091 GG
1 GG
43205093 TTAAATCCGA
Statistics
Matches: 189, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
39 4 0.02
40 184 0.97
41 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
Found at i:43207292 original size:19 final size:18
Alignment explanation
Indices: 43207268--43207303 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
43207258 TTGGGTTGTG
43207268 AATGGGCCGGAATGGGCTA
1 AATGGGCCGGAA-GGGCTA
*
43207287 AATGGGCCTGAAGGGCT
1 AATGGGCCGGAAGGGCT
43207304 GTTGGGCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.25, C:0.17, G:0.42, T:0.17
Consensus pattern (18 bp):
AATGGGCCGGAAGGGCTA
Found at i:43207403 original size:28 final size:29
Alignment explanation
Indices: 43207396--43207522 Score: 145
Period size: 28 Copynumber: 4.5 Consensus size: 29
43207386 GGGCTGGATA
* * *
43207396 GGCCATATAAATGAG-ATTGGGCCTAATG
1 GGCCATATGAATGTGAATTGGGCCTGATG
43207424 GGCCATATGAA-GTGAATTGGGCCTGATG
1 GGCCATATGAATGTGAATTGGGCCTGATG
* *
43207452 GGCCATATGAATGTGAATTGGGTCGGATG
1 GGCCATATGAATGTGAATTGGGCCTGATG
* *
43207481 GGCCATATAAATGAG-ATTGGGCCT-AGTG
1 GGCCATATGAATGTGAATTGGGCCTGA-TG
*
43207509 GGCCATATGCATGT
1 GGCCATATGAATGT
43207523 ATGTAGGGGT
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
27 3 0.04
28 53 0.63
29 28 0.33
ACGTcount: A:0.27, C:0.14, G:0.33, T:0.26
Consensus pattern (29 bp):
GGCCATATGAATGTGAATTGGGCCTGATG
Found at i:43212018 original size:29 final size:28
Alignment explanation
Indices: 43211949--43212083 Score: 150
Period size: 29 Copynumber: 4.8 Consensus size: 28
43211939 ATAATGTGAT
* *
43211949 TTGGGCCGGATGGTCCATAT-AAATGAGA
1 TTGGGCCTGATGGGCCATATGAAATGA-A
** *
43211977 TCAGGCCTAATGGGCCATATGAAAGTGAA
1 TTGGGCCTGATGGGCCATATGAAA-TGAA
43212006 TTGGGCCTGATGGGCCATATGAATATGAA
1 TTGGGCCTGATGGGCCATATGAA-ATGAA
*
43212035 TTGGGCCTGATAGGCCATAT-AAATGAGA
1 TTGGGCCTGATGGGCCATATGAAATGA-A
43212063 TTGGGCCT-AGTGGGCCATATG
1 TTGGGCCTGA-TGGGCCATATG
43212084 CATGTATGTA
Statistics
Matches: 91, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
27 5 0.05
28 35 0.38
29 47 0.52
30 4 0.04
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25
Consensus pattern (28 bp):
TTGGGCCTGATGGGCCATATGAAATGAA
Found at i:43212066 original size:57 final size:58
Alignment explanation
Indices: 43211944--43212083 Score: 155
Period size: 57 Copynumber: 2.4 Consensus size: 58
43211934 TGAATATAAT
* * * *
43211944 GTGATTTGGGCCGGATGGTCCATAT-AAATGAGATCAGGCCTAATGGGCCATATGAAA
1 GTGAATTGGGCCTGATGGGCCATATGAAATGAGATCAGGCCTAATAGGCCATATGAAA
** *
43212001 GTGAATTGGGCCTGATGGGCCATATGAATATGA-ATTGGGCCTGATAGGCCATAT-AAA
1 GTGAATTGGGCCTGATGGGCCATATGAA-ATGAGATCAGGCCTAATAGGCCATATGAAA
43212058 -TGAGATTGGGCCT-AGTGGGCCATATG
1 GTGA-ATTGGGCCTGA-TGGGCCATATG
43212084 CATGTATGTA
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
56 4 0.06
57 45 0.62
58 19 0.26
59 4 0.06
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (58 bp):
GTGAATTGGGCCTGATGGGCCATATGAAATGAGATCAGGCCTAATAGGCCATATGAAA
Found at i:43214642 original size:30 final size:30
Alignment explanation
Indices: 43214608--43214667 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
43214598 TTTTACGAGC
* *
43214608 TTAGGGGGCAAAGTGAAAATATGTGAAAGT
1 TTAGGGGGCAAAATGAAAATATGTAAAAGT
* * *
43214638 TTAGGGGTCAAAATGCAAATTTGTAAAAGT
1 TTAGGGGGCAAAATGAAAATATGTAAAAGT
43214668 ATGATTTTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.40, C:0.05, G:0.28, T:0.27
Consensus pattern (30 bp):
TTAGGGGGCAAAATGAAAATATGTAAAAGT
Found at i:43214923 original size:18 final size:20
Alignment explanation
Indices: 43214887--43214933 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
43214877 AATTGTAAGT
43214887 ATATATATGTGAATAATTTG
1 ATATATATGTGAATAATTTG
* *
43214907 ATAT-TATGTGATTATTTTG
1 ATATATATGTGAATAATTTG
43214926 ATGATATA
1 AT-ATATA
43214934 ACTTGTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.65
20 6 0.26
21 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (20 bp):
ATATATATGTGAATAATTTG
Found at i:43215361 original size:50 final size:50
Alignment explanation
Indices: 43215288--43215665 Score: 359
Period size: 50 Copynumber: 7.5 Consensus size: 50
43215278 GTGAGTCATG
**
43215288 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAAATCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCA
* * * * * * *
43215338 TGTGTAGTATTAAGTGCAGGCTACTATGCGTACTC-G-TTAACTTCGATCGCG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-CAGATTGA--TAGGTCGCA
* * * * * * * * ***
43215389 TGTGTAGTACTAAGTGTAGGCCACAACATGTATCAGATGGTTAAGTCATG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCA
*
43215439 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGATAGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCA
* * * * * *
43215489 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCCG-TTAACTTCGATCACA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGA--TAGGTCGCA
* * ** *
43215540 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGA-TGATTAAGTTACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGA-TAGGTCGCA
* * *
43215590 TGTGTAGTACTAAGTGTAGGCTACTACATGTACCAAATTGATAGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCA
43215640 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
43215666 TGCGTACTAG
Statistics
Matches: 259, Mismatches: 60, Indels: 18
0.77 0.18 0.05
Matches are distributed among these distances:
49 6 0.02
50 175 0.68
51 77 0.30
52 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCA
Found at i:43215555 original size:151 final size:151
Alignment explanation
Indices: 43215281--43215672 Score: 631
Period size: 151 Copynumber: 2.6 Consensus size: 151
43215271 ATTCGTCGTG
* **
43215281 AGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAAATCGCATGTGTAGT
1 AGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGATAGGTCGCATGTGTAGT
* * * * *
43215346 ATTAAGTGCAGGCTACTATGCGTACTCGTTAACTTCGATCGCGTGTGTAGTACTAAGTGTAGGCC
66 ACTAAGTGCAGGCTACTATGCGTACCCGTTAACTTCGATCACATGTGTAGTACTAAGTGCAGGCC
*
43215411 ACAACATGTATCAGATGGTTA
131 ACAACATGTATCAGATGATTA
43215432 AGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGATAGGTCGCATGTGTAGT
1 AGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGATAGGTCGCATGTGTAGT
* *
43215497 ACTAAGTGCAGGCTACTATGTGTACCCGTTAACTTCGATCACATGTGTAGTACTAAGTGCAGGCT
66 ACTAAGTGCAGGCTACTATGCGTACCCGTTAACTTCGATCACATGTGTAGTACTAAGTGCAGGCC
* *
43215562 ACTACGTGTATCAGATGATTA
131 ACAACATGTATCAGATGATTA
* * * *
43215583 AGTTACGTGTGTAGTACTAAGTGTAGGCTACTACATGTACCAAATTGATAGGTCGCATGTGTAGT
1 AGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGATAGGTCGCATGTGTAGT
43215648 ACTAAGTGCAGGCTACTATGCGTAC
66 ACTAAGTGCAGGCTACTATGCGTAC
43215673 TAGAGAGCTT
Statistics
Matches: 223, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
151 223 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (151 bp):
AGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGATAGGTCGCATGTGTAGT
ACTAAGTGCAGGCTACTATGCGTACCCGTTAACTTCGATCACATGTGTAGTACTAAGTGCAGGCC
ACAACATGTATCAGATGATTA
Found at i:43215689 original size:101 final size:100
Alignment explanation
Indices: 43215282--43215679 Score: 336
Period size: 101 Copynumber: 4.0 Consensus size: 100
43215272 TTCGTCGTGA
* * *
43215282 GTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAAATCGCATGTGTAGTA
1 GTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATTGATAAATCACATGTGTAGTA
* * * * *
43215347 TTAAGTGCAGGCTACTATGCGTACTCGTTA-ACTTCG
66 CTAAGTGCAGGCTACTACGCGTACTAG--AGAGTTAG
* * * * * * * * * **
43215383 ATCGCGTGTGTAGTACTAAGTGTAGGCCACAACATGTATCAGATGGTTAAGTCATGTGTGTAGTA
1 GTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATTGATAAATCACATGTGTAGTA
* * * ** *
43215448 CTAAGTGCAGGCTACTACGTGTACCAAATTGATAG
66 CTAAGTGCAGGCTACTACGCGTACTAGAGAGTTAG
* * ** * * **
43215483 GTCGCATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCCG-TTAACTTCGATCACATGTGTAG
1 GTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATTGA--TAAATCACATGTGTAG
* *
43215547 TACTAAGTGCAGGCTACTACGTGTA-TCAGATGA-TTAA
64 TACTAAGTGCAGGCTACTACGCGTACT-AGA-GAGTTAG
* * * ** *
43215584 GTTACGTGTGTAGTACTAAGTGTAGGCTACTACATGTACCAAATTGATAGGTCGCATGTGTAGTA
1 GTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATTGATAAATCACATGTGTAGTA
*
43215649 CTAAGTGCAGGCTACTATGCGTACTAGAGAG
66 CTAAGTGCAGGCTACTACGCGTACTAGAGAG
43215680 CTTCGGTTAC
Statistics
Matches: 228, Mismatches: 61, Indels: 17
0.75 0.20 0.06
Matches are distributed among these distances:
99 4 0.02
100 74 0.32
101 147 0.64
102 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (100 bp):
GTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATTGATAAATCACATGTGTAGTA
CTAAGTGCAGGCTACTACGCGTACTAGAGAGTTAG
Found at i:43217131 original size:13 final size:13
Alignment explanation
Indices: 43217113--43217137 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43217103 AAATTGATGT
43217113 TATAATGTGTATC
1 TATAATGTGTATC
43217126 TATAATGTGTAT
1 TATAATGTGTAT
43217138 AAGTATGGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (13 bp):
TATAATGTGTATC
Found at i:43220567 original size:43 final size:42
Alignment explanation
Indices: 43220509--43220673 Score: 145
Period size: 43 Copynumber: 3.9 Consensus size: 42
43220499 CAATGCCAAC
** *
43220509 GTCCCAGACGTGGTCTTACACGTAATCAAATATCGATGCCATT
1 GTCCCAGACAAGGTCTTACACGAAATCAAATATCGATGCCA-T
* *
43220552 GTCCCAGACAAGGTCTTACATGAAATCAAATA-CGATGCTGAT
1 GTCCCAGACAAGGTCTTACACGAAATCAAATATCGATGC-CAT
* * * * *
43220594 GTCCCAAACAAGGTCTTACATGTTAATCTCAA-ATCGATGCCAAC
1 GTCCCAGACAAGGTCTTACACG-AAATC-AAATATCGATGCC-AT
*** *
43220638 GTCCCAGATGTGGTCTTACACGAAATCACATATCGA
1 GTCCCAGACAAGGTCTTACACGAAATCAAATATCGA
43220674 AATCCTATGC
Statistics
Matches: 98, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
42 29 0.30
43 43 0.44
44 26 0.27
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (42 bp):
GTCCCAGACAAGGTCTTACACGAAATCAAATATCGATGCCAT
Found at i:43220831 original size:40 final size:40
Alignment explanation
Indices: 43220787--43220877 Score: 146
Period size: 40 Copynumber: 2.2 Consensus size: 40
43220777 TTCTATAACC
43220787 ATTCATCACAATTCAATATCATATAAACATGAATAAATCA
1 ATTCATCACAATTCAATATCATATAAACATGAATAAATCA
** *
43220827 ATTCAAAACAATTCAATATCATCTAAACATGAATAAATCA
1 ATTCATCACAATTCAATATCATATAAACATGAATAAATCA
43220867 ATTCAATCACA
1 ATTC-ATCACA
43220878 TTTATTTGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 41 0.91
41 4 0.09
ACGTcount: A:0.51, C:0.19, G:0.02, T:0.29
Consensus pattern (40 bp):
ATTCATCACAATTCAATATCATATAAACATGAATAAATCA
Found at i:43229695 original size:53 final size:54
Alignment explanation
Indices: 43229638--43230040 Score: 386
Period size: 53 Copynumber: 7.6 Consensus size: 54
43229628 AACTTACCAC
* * *
43229638 TGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCACCAA
1 TGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
* * * **
43229691 TGCCATGCCTTGGCATGATCTTACATGGGA-CCTTTGCCTTATAGTAACTCATCAA
1 TGCCATGTCTTGACATGGTCTTACATGATATCC-TTGCCTTATAG-AACTCATCAA
* * *
43229746 TGCCATGTCTTAACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAA
1 TGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
* * **
43229800 TGCCATGCCTTGGCATGGTCTTACATGATATCCTTATC-T-T---AC-CA--AA
1 TGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
* *** * * * *
43229846 TGTCATGTTCCAAACATGGTCTTACATGGTATCCTTGTCTTAT-GAAGTCACCAA
1 TGCCATG-TCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
** *
43229900 TGCCATGTCTTGACATGGTCTTACATGGGA-CCTTTTCCTTATAGTAACTCATCAA
1 TGCCATGTCTTGACATGGTCTTACATGATATCC-TTGCCTTATAG-AACTCATCAA
* *
43229955 TGCCATGTC-T-ACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAA
1 TGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
* *
43230007 TGCCATGCCTTGGCATGGTCTTAC-TGATATCCTT
1 TGCCATGTCTTGACATGGTCTTACATGATATCCTT
43230041 ATCTTACCAA
Statistics
Matches: 285, Mismatches: 47, Indels: 36
0.77 0.13 0.10
Matches are distributed among these distances:
46 8 0.03
47 24 0.08
48 2 0.01
49 3 0.01
51 1 0.00
52 24 0.08
53 96 0.34
54 65 0.23
55 60 0.21
56 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.36
Consensus pattern (54 bp):
TGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
Found at i:43230017 original size:207 final size:208
Alignment explanation
Indices: 43229650--43230093 Score: 793
Period size: 209 Copynumber: 2.1 Consensus size: 208
43229640 CCATGTCTTG
* * *
43229650 ACATGGTCTTACGTGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTGGCATGATCTTAC
1 ACATGGTCTTACATGGTATCCTTGTCTTATGAACTCACCAATGCCATGCCTTGACATGATCTTAC
43229715 ATGGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTAACATGGTCTTACATGATTTCCT
66 ATGGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTAACATGGTCTTACATGATTTCCT
43229780 TGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTACCAA
131 TGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTAC-TGATATCCTTATCTTACCAA
*
43229845 ATGTCATGTTCCAA
195 ATGCCATGTTCCAA
* * *
43229859 ACATGGTCTTACATGGTATCCTTGTCTTATGAAGTCACCAATGCCATGTCTTGACATGGTCTTAC
1 ACATGGTCTTACATGGTATCCTTGTCTTATGAACTCACCAATGCCATGCCTTGACATGATCTTAC
*
43229924 ATGGGACCTTTTCCTTATAGTAACTCATCAATGCCATGTC-T-ACATGGTCTTACATGATTTCCT
66 ATGGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTAACATGGTCTTACATGATTTCCT
43229987 TGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACTGATATCCTTATCTTACCAAA
131 TGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACTGATATCCTTATCTTACCAAA
43230052 TGCCATGTTCCAA
196 TGCCATGTTCCAA
43230065 ACATGGTCTTACATGGTATCCTTGTCTTA
1 ACATGGTCTTACATGGTATCCTTGTCTTA
43230094 GTGCCAATGC
Statistics
Matches: 227, Mismatches: 8, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
206 62 0.27
207 66 0.29
208 1 0.00
209 98 0.43
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (208 bp):
ACATGGTCTTACATGGTATCCTTGTCTTATGAACTCACCAATGCCATGCCTTGACATGATCTTAC
ATGGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTAACATGGTCTTACATGATTTCCT
TGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACTGATATCCTTATCTTACCAAA
TGCCATGTTCCAA
Found at i:43230897 original size:30 final size:30
Alignment explanation
Indices: 43230857--43230913 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
43230847 CTAACTCACA
*
43230857 CTTTGGAAAATTACAATTTTGCCCCTAAAC
1 CTTTGCAAAATTACAATTTTGCCCCTAAAC
*
43230887 CTTTGCAAAATTACGATTTTGCCCCTA
1 CTTTGCAAAATTACAATTTTGCCCCTA
43230914 GGCTCGGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.35
Consensus pattern (30 bp):
CTTTGCAAAATTACAATTTTGCCCCTAAAC
Found at i:43233551 original size:27 final size:28
Alignment explanation
Indices: 43233495--43233564 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
43233485 AAATTTGTAC
43233495 AGCACTAAGTGTGCGAGTTTGATCATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
43233523 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
43233550 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
43233565 GACTCACTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:43233575 original size:27 final size:27
Alignment explanation
Indices: 43233495--43233576 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
43233485 AAATTTGTAC
* *
43233495 AGCACTAAGTGTGCGAGTTTGA-TCATAT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
43233523 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
*
43233550 AGCACTGAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
43233577 GCTTTTGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.02
27 29 0.60
28 18 0.38
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:43237925 original size:11 final size:11
Alignment explanation
Indices: 43237909--43237968 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
43237899 CTTAATCATT
43237909 TTAATATTAAA
1 TTAATATTAAA
43237920 TTAATA-TAATA
1 TTAATATTAA-A
*
43237931 TTTAA-ATTTAAT
1 -TTAATA-TTAAA
43237943 TTAATATTAAA
1 TTAATATTAAA
43237954 -T-ATATTAAA
1 TTAATATTAAA
43237963 TTAATA
1 TTAATA
43237969 GAATACTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
9 8 0.20
10 5 0.12
11 19 0.47
12 5 0.12
13 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:43238039 original size:20 final size:18
Alignment explanation
Indices: 43237989--43238040 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
43237979 CTACAAGATA
43237989 AATATTAAATTAA-ATCT
1 AATATTAAATTAATATCT
*
43238006 AATATTAAGA-TAATCATTTT
1 AATATTAA-ATTAAT-A-TCT
43238026 AATATTAAATTAATA
1 AATATTAAATTAATA
43238041 AAATACTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 11 0.38
18 1 0.03
19 3 0.10
20 14 0.48
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATCT
Found at i:43240096 original size:93 final size:93
Alignment explanation
Indices: 43239984--43240154 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
43239974 GCCCATAAGT
* *
43239984 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
43240049 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
43240077 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
43240142 CGAGTTCGGATGC
66 CGAGTTCGGATGC
43240155 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:43240170 original size:46 final size:46
Alignment explanation
Indices: 43239976--43240156 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
43239966 TGTAACCCGC
* * *
43239976 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
43240022 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
43240072 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
*
43240115 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTC
43240157 AACCATCCTA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 72 0.62
47 32 0.28
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:43242556 original size:29 final size:29
Alignment explanation
Indices: 43242517--43242604 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
43242507 CAAAGATAAC
*
43242517 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
*
43242546 GAGAAACCCGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGAATAAAGAAATCCAAG-ATA
* * * *
43242575 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGA-AACCCGAATAAAGAAATCCAAGATA
43242605 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 2 0.04
29 27 0.55
30 18 0.37
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Found at i:43242575 original size:15 final size:15
Alignment explanation
Indices: 43242517--43242595 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
43242507 CAAAGATAAC
*
43242517 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
43242531 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
43242546 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
43242560 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
43242575 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
43242590 AAGAAA
1 AAGAAA
43242596 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.36
15 34 0.64
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:43242604 original size:15 final size:15
Alignment explanation
Indices: 43242528--43242604 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
43242518 AGAAAACCGA
43242528 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
43242543 ATAGAGAAACCCGA-
1 ATAAAGAAATCCAAG
43242557 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
43242571 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
43242587 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
43242602 ATA
1 ATA
43242605 CGATACTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 37 0.76
16 1 0.02
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:43245662 original size:93 final size:93
Alignment explanation
Indices: 43245550--43245720 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
43245540 GCCCATAAGT
* *
43245550 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
43245615 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
43245643 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
43245708 CGAGTTCGGATGC
66 CGAGTTCGGATGC
43245721 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:43245736 original size:46 final size:46
Alignment explanation
Indices: 43245542--43245722 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
43245532 TGTAACCCGC
* * *
43245542 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
43245588 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
43245638 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
*
43245681 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTC
43245723 AACCATCCTA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 72 0.62
47 32 0.28
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:43250495 original size:23 final size:23
Alignment explanation
Indices: 43250469--43250568 Score: 112
Period size: 23 Copynumber: 4.3 Consensus size: 23
43250459 AACTCGTAAA
* *
43250469 AGCTTACTGTTTCAGCTCATTGG
1 AGCTTACTGTTTCAGCTCAATAG
* * *
43250492 AGCTTACCGATTCAGCTCAAAAG
1 AGCTTACTGTTTCAGCTCAATAG
43250515 AGCTTACTG-TTCAGCTCAATAG
1 AGCTTACTGTTTCAGCTCAATAG
* * *
43250537 AGCTTATTGTTTTCAGCTTAGTAG
1 AGCTTACTG-TTTCAGCTCAATAG
43250561 AGCTTACT
1 AGCTTACT
43250569 ATTTATCAGC
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
22 20 0.31
23 26 0.41
24 18 0.28
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (23 bp):
AGCTTACTGTTTCAGCTCAATAG
Found at i:43251029 original size:40 final size:40
Alignment explanation
Indices: 43250969--43251058 Score: 126
Period size: 40 Copynumber: 2.2 Consensus size: 40
43250959 CGTTTGGATA
* * *
43250969 AAAAACACCACTATAAGTCGACCATTGGTGGTGATTTTTG
1 AAAAACGCCACTATAAGTCGACCATTAGCGGTGATTTTTG
* * *
43251009 AAAAACGCCGCTATAGGTCGACCATTAGCGGTGCTTTTTG
1 AAAAACGCCACTATAAGTCGACCATTAGCGGTGATTTTTG
43251049 AAAAACGCCA
1 AAAAACGCCA
43251059 TAAAAAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (40 bp):
AAAAACGCCACTATAAGTCGACCATTAGCGGTGATTTTTG
Found at i:43251162 original size:40 final size:40
Alignment explanation
Indices: 43251118--43251210 Score: 141
Period size: 40 Copynumber: 2.3 Consensus size: 40
43251108 TTAGAGGCGT
* *
43251118 TTTTTGAAAAACGCAGCAATAGATTGAGCATTAGCGGCAC
1 TTTTTGAAAAACACAGCAATAGATTGAGCATTAGCGCCAC
* *
43251158 TTTTTGAAAAACACAGCTATAGATTGAGCATTAGCGCCGC
1 TTTTTGAAAAACACAGCAATAGATTGAGCATTAGCGCCAC
*
43251198 TTTTCGAAAAACA
1 TTTTTGAAAAACA
43251211 ACACAAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (40 bp):
TTTTTGAAAAACACAGCAATAGATTGAGCATTAGCGCCAC
Found at i:43251271 original size:154 final size:153
Alignment explanation
Indices: 43251003--43251435 Score: 573
Period size: 154 Copynumber: 2.8 Consensus size: 153
43250993 TTGGTGGTGA
* * * * *
43251003 TTTTTGAAAAACGCCGCTATAGGTCGACCATTAGCGGTGCTTTTTGAAAAACGCCATAAAAAAAT
1 TTTTTGAAAAACGCAGCTATAGGTCGAGCATTAGCGGCGCTTTTTGAAAAAC-ACA-CAAAAAAT
43251068 TAAGCACAACGCCGTCGTTTTATGTTGAGCTTTAGTGGCATTAGAGGCGTTTTTTGAAAAACGCA
64 TAAGCACAACGCCGTCGTTTTATGTTGAGCTTTAGTGGCATTAGAGGCGTTTTTTGAAAAACGCA
43251133 GCAATAGATTGAGCATTAGCGGCAC
129 GCAATAGATTGAGCATTAGCGGCAC
* * * * *
43251158 TTTTTGAAAAACACAGCTATAGATTGAGCATTAGCGCCGCTTTTCGAAAAACAACACAAAAAATT
1 TTTTTGAAAAACGCAGCTATAGGTCGAGCATTAGCGGCGCTTTTTGAAAAAC-ACACAAAAAATT
* * * *
43251223 AAGCACAACGCCGTCATTTTATGTTGAGCTTTAGTGGCATTAGTGGCGTTTTTTAAAAAACGCCG
65 AAGCACAACGCCGTCGTTTTATGTTGAGCTTTAGTGGCATTAGAGGCGTTTTTTGAAAAACGCAG
* * **
43251288 CTATAGATTGAGCATTAGCTGTGC
130 CAATAGATTGAGCATTAGCGGCAC
* * *
43251312 TTTTTGAAAAACGCAGCTATAGGTCGAGCATTAGTGGCGCTTTTTGAAAAACGCTGCAAAAAATT
1 TTTTTGAAAAACGCAGCTATAGGTCGAGCATTAGCGGCGCTTTTTGAAAAACAC-ACAAAAAATT
* * * * *
43251377 TAGTA-AGACGCCATCGTTTTATGTTGAGCTTT-GTGGCATTAGAGACGCTTTTTGAAAAA
65 AAGCACA-ACGCCGTCGTTTTATGTTGAGCTTTAGTGGCATTAGAGGCGTTTTTTGAAAAA
43251436 TGCTGCAAAA
Statistics
Matches: 241, Mismatches: 35, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
153 25 0.10
154 170 0.71
155 46 0.19
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (153 bp):
TTTTTGAAAAACGCAGCTATAGGTCGAGCATTAGCGGCGCTTTTTGAAAAACACACAAAAAATTA
AGCACAACGCCGTCGTTTTATGTTGAGCTTTAGTGGCATTAGAGGCGTTTTTTGAAAAACGCAGC
AATAGATTGAGCATTAGCGGCAC
Found at i:43251316 original size:40 final size:40
Alignment explanation
Indices: 43251259--43251365 Score: 144
Period size: 40 Copynumber: 2.7 Consensus size: 40
43251249 AGCTTTAGTG
* * * *
43251259 GCATTAGTGGCGTTTTTTAAAAAACGCCGCTATAGATTGA
1 GCATTAGTGGCGCTTTTTGAAAAACGCAGCTATAGATCGA
* *
43251299 GCATTAGCT-GTGCTTTTTGAAAAACGCAGCTATAGGTCGA
1 GCATTAG-TGGCGCTTTTTGAAAAACGCAGCTATAGATCGA
43251339 GCATTAGTGGCGCTTTTTGAAAAACGC
1 GCATTAGTGGCGCTTTTTGAAAAACGC
43251366 TGCAAAAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 1 0.02
40 56 0.97
41 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (40 bp):
GCATTAGTGGCGCTTTTTGAAAAACGCAGCTATAGATCGA
Found at i:43251763 original size:14 final size:14
Alignment explanation
Indices: 43251744--43251770 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43251734 TTAATTACGA
43251744 TTATAGTTTAGGGC
1 TTATAGTTTAGGGC
43251758 TTATAGTTTAGGG
1 TTATAGTTTAGGG
43251771 TATATGGCTT
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:0.22, C:0.04, G:0.30, T:0.44
Consensus pattern (14 bp):
TTATAGTTTAGGGC
Found at i:43251832 original size:15 final size:15
Alignment explanation
Indices: 43251812--43251855 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
43251802 ACTATTTTAA
43251812 GGTTTATGGATTATG
1 GGTTTATGGATTATG
*
43251827 GGTTTAGGGATTATG
1 GGTTTATGGATTATG
*
43251842 GG-TTATGGTTTATG
1 GGTTTATGGATTATG
43251856 ATTTAAAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.45
Consensus pattern (15 bp):
GGTTTATGGATTATG
Found at i:43251832 original size:22 final size:21
Alignment explanation
Indices: 43251807--43251853 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
43251797 GAGTTACTAT
*
43251807 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGATTATGGATTAT-GG
* *
43251829 TTTAGGGATTATGGGTTATGG
1 TTTAAGGATTATGGATTATGG
43251850 TTTA
1 TTTA
43251854 TGATTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (21 bp):
TTTAAGGATTATGGATTATGG
Found at i:43251882 original size:14 final size:14
Alignment explanation
Indices: 43251865--43251901 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
43251855 GATTTAAAAG
*
43251865 TTAGGGTTTAAGGT
1 TTAGGGTTAAAGGT
43251879 TTAGGGGTTAAAGGT
1 TTA-GGGTTAAAGGT
43251894 TTAGGGTT
1 TTAGGGTT
43251902 GATGTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.22, C:0.00, G:0.38, T:0.41
Consensus pattern (14 bp):
TTAGGGTTAAAGGT
Found at i:43251912 original size:64 final size:65
Alignment explanation
Indices: 43251807--43251939 Score: 146
Period size: 64 Copynumber: 2.1 Consensus size: 65
43251797 GAGTTACTAT
* ** *
43251807 TTTAAGGTTTATGGATTATGGGTTTAGGGATTATGGGTTATGGTTTATGA-TTTAAAAGTTA-GG
1 TTTAAGGTTTAGGGATTAAAGGTTTAGGGATTATGGGTTATGATTTA-GAGTTTAAAAGTTAGGG
43251870 G
65 G
* ** **
43251871 TTTAAGGTTTAGGGGTTAAAGGTTTAGGG-TTGATGTTTTATGATTTAGAGTTTAAGGGTTAGGG
1 TTTAAGGTTTAGGGATTAAAGGTTTAGGGATT-ATGGGTTATGATTTAGAGTTTAAAAGTTAGGG
43251935 G
65 G
43251936 TTTA
1 TTTA
43251940 GAGTTTAAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
63 4 0.07
64 46 0.81
65 7 0.12
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (65 bp):
TTTAAGGTTTAGGGATTAAAGGTTTAGGGATTATGGGTTATGATTTAGAGTTTAAAAGTTAGGGG
Found at i:43254111 original size:18 final size:18
Alignment explanation
Indices: 43254088--43254123 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
43254078 GGTATTTATT
43254088 GATGGTGTAGTAAATCCA
1 GATGGTGTAGTAAATCCA
43254106 GATGGTGTAGTAAATCCA
1 GATGGTGTAGTAAATCCA
43254124 ATGAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (18 bp):
GATGGTGTAGTAAATCCA
Found at i:43254842 original size:19 final size:18
Alignment explanation
Indices: 43254815--43254850 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
43254805 GCACAATGAT
43254815 TGTTCAAGTGTCAGATTTG
1 TGTTCAAGTGTCA-ATTTG
*
43254834 TGTTTAAGTGTCAATTT
1 TGTTCAAGTGTCAATTT
43254851 TTTTAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.47
Consensus pattern (18 bp):
TGTTCAAGTGTCAATTTG
Found at i:43256586 original size:43 final size:43
Alignment explanation
Indices: 43256496--43256653 Score: 158
Period size: 43 Copynumber: 3.7 Consensus size: 43
43256486 AACTTTTAGA
* * *
43256496 GCTAAAGGTCATGTTCTTTTAGTGGCATTTGTAGGAAAAACACC
1 GCTAAAGGTCATGTTC-TTTAGCGGCGTTTGTGGGAAAAACACC
* **
43256540 GCTAAAGGTCATGTTCTTTAACGGCGTTTGTGGGAAAAACGTC
1 GCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAAACACC
* * * *
43256583 GCTAAATGTCATATT-TTTAGCGGCGTTTGT-GAAAAAAGTACC
1 GCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAAA-CACC
** * *
43256625 ATTAAAGGCCATGTTCTTTAGCGACGTTT
1 GCTAAAGGTCATGTTCTTTAGCGGCGTTT
43256654 CTTCACATAA
Statistics
Matches: 93, Mismatches: 19, Indels: 5
0.79 0.16 0.04
Matches are distributed among these distances:
41 6 0.06
42 25 0.27
43 46 0.49
44 16 0.17
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (43 bp):
GCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAAACACC
Found at i:43259711 original size:15 final size:16
Alignment explanation
Indices: 43259681--43259714 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
43259671 GTTAAAAGGG
*
43259681 TTAAAAATAATTTTTT
1 TTAAAAATAATGTTTT
43259697 TTAAAAAT-ATGTTTT
1 TTAAAAATAATGTTTT
43259712 TTA
1 TTA
43259715 CTTTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TTAAAAATAATGTTTT
Found at i:43259789 original size:61 final size:61
Alignment explanation
Indices: 43259724--43259851 Score: 168
Period size: 61 Copynumber: 2.1 Consensus size: 61
43259714 ACTTTTTTAA
* * **
43259724 TTTTTAGAATTAGAATT-AATTTGATAAATTTTATAAATGTTGAGGGCTAAATTTATAGAAT
1 TTTTTAGAATTAGAATTAAAATT-ACAAATTTTATAAACATTGAGGGCTAAATTTATAGAAT
* * * *
43259785 TTTTTAGAATTCGAATTAAAATTACAAATTTTGTAAACATTGAGGGCTAAGTTTATTGAAT
1 TTTTTAGAATTAGAATTAAAATTACAAATTTTATAAACATTGAGGGCTAAATTTATAGAAT
43259846 TTTTTA
1 TTTTTA
43259852 TATTTAGGAT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
61 54 0.93
62 4 0.07
ACGTcount: A:0.38, C:0.04, G:0.14, T:0.45
Consensus pattern (61 bp):
TTTTTAGAATTAGAATTAAAATTACAAATTTTATAAACATTGAGGGCTAAATTTATAGAAT
Found at i:43262266 original size:2 final size:2
Alignment explanation
Indices: 43262259--43262288 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
43262249 ATAGTCACTA
43262259 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43262289 ACTTCTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43263126 original size:18 final size:17
Alignment explanation
Indices: 43263103--43263163 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 17
43263093 GGGTGAGCAG
43263103 TAAAAGTTTAGGAGGAAA
1 TAAAAGTTTAGG-GGAAA
* *
43263121 TAAAAGGTTTTGGGGGGAA
1 TAAAA-G-TTTAGGGGAAA
43263140 TAAAA-TTTGAGGGGAAA
1 TAAAAGTTT-AGGGGAAA
43263157 GTAAAAG
1 -TAAAAG
43263164 GGAGTAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
16 3 0.09
17 6 0.18
18 10 0.29
19 10 0.29
20 5 0.15
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.23
Consensus pattern (17 bp):
TAAAAGTTTAGGGGAAA
Found at i:43263866 original size:27 final size:27
Alignment explanation
Indices: 43263828--43263883 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
43263818 TAAAACTTTT
*
43263828 AACGGCGCTTTTTAAAACGCCGTAAAA
1 AACGCCGCTTTTTAAAACGCCGTAAAA
43263855 AACGCCGCTTTTTAAAACGCCGTAAAA
1 AACGCCGCTTTTTAAAACGCCGTAAAA
43263882 AA
1 AA
43263884 TGCCACTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.21
Consensus pattern (27 bp):
AACGCCGCTTTTTAAAACGCCGTAAAA
Found at i:43263873 original size:15 final size:15
Alignment explanation
Indices: 43263828--43263876 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
43263818 TAAAACTTTT
*
43263828 AACGGCGCTTTTTAA
1 AACGCCGCTTTTTAA
**
43263843 AACGCCG---TAAAA
1 AACGCCGCTTTTTAA
43263855 AACGCCGCTTTTTAA
1 AACGCCGCTTTTTAA
43263870 AACGCCG
1 AACGCCG
43263877 TAAAAAATGC
Statistics
Matches: 26, Mismatches: 5, Indels: 6
0.70 0.14 0.16
Matches are distributed among these distances:
12 10 0.38
15 16 0.62
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (15 bp):
AACGCCGCTTTTTAA
Found at i:43264016 original size:17 final size:17
Alignment explanation
Indices: 43263990--43264022 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43263980 TTTGTGGGAC
*
43263990 AAGCGTCGCTAAAAGCT
1 AAGCGCCGCTAAAAGCT
43264007 AAGCGCCGCTAAAAGC
1 AAGCGCCGCTAAAAGC
43264023 CTCCCACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.27, G:0.24, T:0.12
Consensus pattern (17 bp):
AAGCGCCGCTAAAAGCT
Found at i:43264129 original size:31 final size:31
Alignment explanation
Indices: 43264094--43264176 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
43264084 CTTCTTACAT
* *
43264094 TAAAATCCAACCAAATACAACAAATATAGTA
1 TAAAATCCAACCAAAAACAACAAATATAGCA
* * *
43264125 TAAAATGCAGCCAAAAACAACAAATTTAGCA
1 TAAAATCCAACCAAAAACAACAAATATAGCA
*
43264156 TAAAAAATACAACCAAAAACA
1 T--AAAATCCAACCAAAAACA
43264177 TTAATTCTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 27 0.63
33 16 0.37
ACGTcount: A:0.60, C:0.19, G:0.05, T:0.16
Consensus pattern (31 bp):
TAAAATCCAACCAAAAACAACAAATATAGCA
Found at i:43264432 original size:21 final size:21
Alignment explanation
Indices: 43264408--43264483 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
43264398 TCTGCTGCCA
*
43264408 TCGCTACTGCCTCTACCTCCC
1 TCGCTACTGCCTCTGCCTCCC
43264429 TCGCT-CGTGCCTCTGCCTCCC
1 TCGCTAC-TGCCTCTGCCTCCC
* * *
43264450 TTGCTGCTGCCGCTGCCTCCC
1 TCGCTACTGCCTCTGCCTCCC
*
43264471 TCTCTACTGCCTC
1 TCGCTACTGCCTC
43264484 CGCTCTAAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 1 0.02
21 44 0.96
22 1 0.02
ACGTcount: A:0.04, C:0.50, G:0.16, T:0.30
Consensus pattern (21 bp):
TCGCTACTGCCTCTGCCTCCC
Found at i:43270078 original size:9 final size:9
Alignment explanation
Indices: 43270064--43270361 Score: 318
Period size: 9 Copynumber: 33.4 Consensus size: 9
43270054 TATTTAAGTA
*
43270064 TTATGTAAG
1 TTATATAAG
*
43270073 TTATGTAAG
1 TTATATAAG
*
43270082 TTATGATATG
1 TTAT-ATAAG
* *
43270092 ATATAT-AT
1 TTATATAAG
*
43270100 TTATGTAAAG
1 TTATAT-AAG
*
43270110 TTATAT-AT
1 TTATATAAG
*
43270118 TTATCTAAG
1 TTATATAAG
43270127 TTATATAAG
1 TTATATAAG
*
43270136 TTATGTAAG
1 TTATATAAG
* *
43270145 TTATGTCAG
1 TTATATAAG
*
43270154 TTATAT-AT
1 TTATATAAG
*
43270162 TTATCTAAG
1 TTATATAAG
43270171 TTATATAAG
1 TTATATAAG
43270180 TTATATAAG
1 TTATATAAG
*
43270189 TTATGTAAG
1 TTATATAAG
43270198 TTATATAAG
1 TTATATAAG
43270207 TTATATAAG
1 TTATATAAG
*
43270216 TTATAT-AT
1 TTATATAAG
*
43270224 TTATCTAAG
1 TTATATAAG
43270233 TTATATAAG
1 TTATATAAG
*
43270242 TTATGTAAG
1 TTATATAAG
*
43270251 TTATGTAAG
1 TTATATAAG
43270260 TTATATAAG
1 TTATATAAG
43270269 TTATATAAG
1 TTATATAAG
*
43270278 TTATGTAAG
1 TTATATAAG
43270287 TTATATAAG
1 TTATATAAG
43270296 TTATATAAG
1 TTATATAAG
*
43270305 TTATGTAAG
1 TTATATAAG
*
43270314 TTATAT-AT
1 TTATATAAG
*
43270322 TTATCTAAG
1 TTATATAAG
43270331 TTATATAAG
1 TTATATAAG
*
43270340 TTATGTAAG
1 TTATATAAG
* *
43270349 TTTTGTAAG
1 TTATATAAG
43270358 TTAT
1 TTAT
43270362 GTTAAATATT
Statistics
Matches: 243, Mismatches: 39, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
8 28 0.12
9 203 0.84
10 12 0.05
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (9 bp):
TTATATAAG
Found at i:43270191 original size:62 final size:62
Alignment explanation
Indices: 43270064--43270343 Score: 366
Period size: 62 Copynumber: 4.5 Consensus size: 62
43270054 TATTTAAGTA
* * * * * *
43270064 TTATGTAAGTTATGTAAGTTATGATATGATATATATTTATGTAAAGTTATAT-ATTTATCTAAG
1 TTATGTAAGTTATATAAGTTAT-ATAAGTTATATATTTATCT-AAGTTATATAAGTTATGTAAG
* * * * *
43270127 TTATATAAGTTATGTAAGTTATGTCAGTTATATATTTATCTAAGTTATATAAGTTATATAAG
1 TTATGTAAGTTATATAAGTTATATAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAG
43270189 TTATGTAAGTTATATAAGTTATATAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATATAAGTTATATAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAG
* * *
43270251 TTATGTAAGTTATATAAGTTATATAAGTTATGTAAGTTATATAAGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATATAAGTTATATAAGTTATAT-ATTTATCTAAGTTATATAAGTTATGTAAG
* * *
43270314 TTATAT-ATTTATCTAAGTTATATAAGTTAT
1 TTATGTAAGTTATATAAGTTATATAAGTTAT
43270344 GTAAGTTTTG
Statistics
Matches: 196, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
61 9 0.05
62 134 0.68
63 53 0.27
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (62 bp):
TTATGTAAGTTATATAAGTTATATAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAG
Found at i:43270382 original size:62 final size:62
Alignment explanation
Indices: 43270198--43270387 Score: 177
Period size: 62 Copynumber: 3.1 Consensus size: 62
43270188 GTTATGTAAG
* * * * *** * *
43270198 TTATATAAGTTATATAAGTTATAT-ATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAG
1 TTATATAAGTTATATAAGTTATGTAAGTTATATAAGTTATATAAGATATGTAACAAATAT-AT
* ***
43270260 TTATATAAGTTATATAAGTTATGTAAGTTATATAAGTTATATAAGTTATGTAAGTTATATAT
1 TTATATAAGTTATATAAGTTATGTAAGTTATATAAGTTATATAAGATATGTAACAAATATAT
* * * * * *
43270322 TTATCTAAGTTATATAAGTTATGTAAGTTTTGTAAGTTATGTTAA-ATATTTATCAAATATAT
1 TTATATAAGTTATATAAGTTATGTAAGTTATATAAGTTAT-ATAAGATATGTAACAAATATAT
43270384 TTAT
1 TTAT
43270388 GTATTATGTA
Statistics
Matches: 111, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
62 76 0.68
63 35 0.32
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (62 bp):
TTATATAAGTTATATAAGTTATGTAAGTTATATAAGTTATATAAGATATGTAACAAATATAT
Found at i:43270493 original size:15 final size:15
Alignment explanation
Indices: 43270473--43270530 Score: 77
Period size: 15 Copynumber: 3.9 Consensus size: 15
43270463 GTGAGTTGCG
43270473 AATTAAATAATATTT
1 AATTAAATAATATTT
43270488 AATTAAATAATATTT
1 AATTAAATAATATTT
43270503 -A-TAAA-AATTATTTT
1 AATTAAATAA-TA-TTT
43270517 AATTAAATAATATT
1 AATTAAATAATATT
43270531 GAAAAAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.05
13 6 0.16
14 4 0.11
15 18 0.47
16 6 0.16
17 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTAAATAATATTT
Found at i:43270522 original size:29 final size:29
Alignment explanation
Indices: 43270485--43270549 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
43270475 TTAAATAATA
* *
43270485 TTTAATTAAATAATATTTATAAAAATTAT
1 TTTAATTAAATAATATTGAAAAAAATTAT
43270514 TTTAATTAAATAATATTGAAAAAAATTAT
1 TTTAATTAAATAATATTGAAAAAAATTAT
43270543 TTTAATT
1 TTTAATT
43270550 CGTTCGTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
TTTAATTAAATAATATTGAAAAAAATTAT
Found at i:43270749 original size:24 final size:24
Alignment explanation
Indices: 43270717--43270787 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
43270707 TTAACTTAAA
43270717 TGATAAAACGGACGATAATATTTG
1 TGATAAAACGGACGATAATATTTG
* *
43270741 TGATAAAACTGACAATAATATTTG
1 TGATAAAACGGACGATAATATTTG
*
43270765 TGATAAAACGGACGAGAATATTT
1 TGATAAAACGGACGATAATATTT
43270788 CAATAATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (24 bp):
TGATAAAACGGACGATAATATTTG
Found at i:43270952 original size:64 final size:64
Alignment explanation
Indices: 43270835--43271017 Score: 314
Period size: 64 Copynumber: 2.9 Consensus size: 64
43270825 ATATTTTATT
*
43270835 AAATATTTGTATATTAGATGGGACAT-TTATATTAATAAATAAATTTATTAAAAATTGTGATAG
1 AAATATTTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAAATCGTGATAG
*
43270898 AAATATTTGTATATTAGATGGGACATATTATATTAATATATAAATTTATTAAAAATCGTGATAG
1 AAATATTTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAAATCGTGATAG
* * *
43270962 AAATATTTATATATTAGATGAGACATATTATATCAATAAATAAATTTATTAAAAAT
1 AAATATTTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAAAT
43271018 ATAGAAATAT
Statistics
Matches: 113, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
63 26 0.23
64 87 0.77
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.40
Consensus pattern (64 bp):
AAATATTTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAAATCGTGATAG
Found at i:43273312 original size:14 final size:14
Alignment explanation
Indices: 43273293--43273330 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
43273283 AAATTTAGGG
43273293 TTAGGGAGAAAATT
1 TTAGGGAGAAAATT
43273307 TTAGGGA-AAAATT
1 TTAGGGAGAAAATT
43273320 TTAGGG-GAAAA
1 TTAGGGAGAAAA
43273331 CACTTAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.26
Consensus pattern (14 bp):
TTAGGGAGAAAATT
Found at i:43273319 original size:13 final size:13
Alignment explanation
Indices: 43273293--43273330 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
43273283 AAATTTAGGG
43273293 TTAGGGAGAAAATT
1 TTAGGGA-AAAATT
43273307 TTAGGGAAAAATT
1 TTAGGGAAAAATT
43273320 TTAGGGGAAAA
1 TTA-GGGAAAA
43273331 CACTTAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.26
Consensus pattern (13 bp):
TTAGGGAAAAATT
Found at i:43274723 original size:39 final size:39
Alignment explanation
Indices: 43274662--43274839 Score: 275
Period size: 39 Copynumber: 4.6 Consensus size: 39
43274652 GAATTTAAGC
* *
43274662 CCGGATATAATTCCAGCTCATAGCCTACGGACCTGAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTGAAGT
* *
43274701 CTGGATAAAATTCCAGCACATAGCCTGCGGACCTGAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTGAAGT
*
43274740 CCAGATATAATTCCAGCACATAGCCTGCGGACCTGAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTGAAGT
*
43274779 CCGGATATAATTCCAGCACATAACCTGCGGACCTGAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTGAAGT
* * *
43274818 CTGGATAAAATTTCAGCACATA
1 CCGGATATAATTCCAGCACATA
43274840 CAATTATGAT
Statistics
Matches: 127, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 127 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCTGAAGT
Found at i:43282496 original size:39 final size:39
Alignment explanation
Indices: 43282453--43282591 Score: 242
Period size: 39 Copynumber: 3.6 Consensus size: 39
43282443 GAATTTAAGC
* *
43282453 CCGGATATAATTCCAGCTCATAGCCTGCGGACCTGAAGT
1 CCGGATAAAATTCCAGCACATAGCCTGCGGACCTGAAGT
43282492 CCGGATAAAATTCCAGCACATAGCCTGCGGACCTGAAGT
1 CCGGATAAAATTCCAGCACATAGCCTGCGGACCTGAAGT
*
43282531 CCGGATATAATTCCAGCACATAGCCTGCGGACCTGAAGT
1 CCGGATAAAATTCCAGCACATAGCCTGCGGACCTGAAGT
*
43282570 CCGGATAAAATTTCAGCACATA
1 CCGGATAAAATTCCAGCACATA
43282592 CAATTATGAT
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 95 1.00
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.21
Consensus pattern (39 bp):
CCGGATAAAATTCCAGCACATAGCCTGCGGACCTGAAGT
Found at i:43284861 original size:16 final size:16
Alignment explanation
Indices: 43284840--43284910 Score: 88
Period size: 16 Copynumber: 4.4 Consensus size: 16
43284830 GTTTGGTTCA
*
43284840 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
*
43284856 CTGTAATAGAATAGAG
1 CTGTAATGGAATAGAG
* * *
43284872 TTTTAATTGAATAGAG
1 CTGTAATGGAATAGAG
43284888 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
*
43284904 TTGTAAT
1 CTGTAAT
43284911 AAGTAATTCA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.32
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:43284891 original size:32 final size:32
Alignment explanation
Indices: 43284841--43284910 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
43284831 TTTGGTTCAC
*
43284841 TGTAATGGAATAGGGCTGTAATAGAATAGAGT
1 TGTAATGGAATAGAGCTGTAATAGAATAGAGT
* * *
43284873 TTTAATTGAATAGAGCTGTAATGGAATAGAGT
1 TGTAATGGAATAGAGCTGTAATAGAATAGAGT
43284905 TGTAAT
1 TGTAAT
43284911 AAGTAATTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (32 bp):
TGTAATGGAATAGAGCTGTAATAGAATAGAGT
Found at i:43284955 original size:46 final size:44
Alignment explanation
Indices: 43284892--43284985 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
43284882 ATAGAGCTGT
** *
43284892 AATGGAATAGAGTTGTAATAAGTAATTC-AACTTTTTGGTTGAATGG
1 AATGGAATAGAACTGTAAT-AGT-ATTCTAA-TGTTTGGTTGAATGG
*
43284938 AATGGAATAGAACTGTAATAGTATTCTTATGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTCTAATGTTTGGTTGAATGG
43284982 AATG
1 AATG
43284986 ATGATGTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
44 22 0.51
45 4 0.09
46 17 0.40
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCTAATGTTTGGTTGAATGG
Found at i:43285361 original size:19 final size:20
Alignment explanation
Indices: 43285337--43285379 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
43285327 CGGAAAATAA
*
43285337 TTTTTGGA-AAATGATTTAC
1 TTTTTGGAGAAATAATTTAC
*
43285356 TTTTTGTAGAAATAATTTAC
1 TTTTTGGAGAAATAATTTAC
43285376 TTTT
1 TTTT
43285380 CTGGTGTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (20 bp):
TTTTTGGAGAAATAATTTAC
Found at i:43285731 original size:18 final size:18
Alignment explanation
Indices: 43285708--43285742 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
43285698 ACGTGACAGT
*
43285708 CCAACTAGATTTTAAGTG
1 CCAACTAGATCTTAAGTG
43285726 CCAACTAGATCTTAAGT
1 CCAACTAGATCTTAAGT
43285743 ATATCTGTTA
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:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (18 bp):
CCAACTAGATCTTAAGTG
Found at i:43285767 original size:24 final size:24
Alignment explanation
Indices: 43285735--43285782 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
43285725 GCCAACTAGA
43285735 TCTTAAGTATATCTGTTAATACAT
1 TCTTAAGTATATCTGTTAATACAT
43285759 TCTTAAGTATATCTGTTAATACAT
1 TCTTAAGTATATCTGTTAATACAT
43285783 ACTTCATCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.46
Consensus pattern (24 bp):
TCTTAAGTATATCTGTTAATACAT
Found at i:43285931 original size:40 final size:40
Alignment explanation
Indices: 43285770--43285923 Score: 290
Period size: 40 Copynumber: 3.9 Consensus size: 40
43285760 CTTAAGTATA
*
43285770 TCTGTTAATACATACTTCATCCGAATAAATTATATAGGTT
1 TCTGTTAATACATACTTCATCCGGATAAATTATATAGGTT
43285810 TCTGTTAATACATACTTCATCCGGATAAATTATATAGGTT
1 TCTGTTAATACATACTTCATCCGGATAAATTATATAGGTT
*
43285850 TCTGTTAATACATACTTCATCCGGATAAATTATATAGTTT
1 TCTGTTAATACATACTTCATCCGGATAAATTATATAGGTT
43285890 TCTGTTAATACATACTTCATCCGGATAAATTATA
1 TCTGTTAATACATACTTCATCCGGATAAATTATA
43285924 CAGTTTTCAC
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 112 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (40 bp):
TCTGTTAATACATACTTCATCCGGATAAATTATATAGGTT
Found at i:43287021 original size:22 final size:22
Alignment explanation
Indices: 43286996--43287038 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
43286986 TGCTTGCGAT
**
43286996 TAATGATTTTAAATATTAATAG
1 TAATGATGATAAATATTAATAG
*
43287018 TAATGATGATAAATGTTAATA
1 TAATGATGATAAATATTAATA
43287039 TGATGATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.42
Consensus pattern (22 bp):
TAATGATGATAAATATTAATAG
Found at i:43287713 original size:14 final size:14
Alignment explanation
Indices: 43287696--43287746 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
43287686 AACTTTTAAC
43287696 CCTTAACCCCTAAT
1 CCTTAACCCCTAAT
* *
43287710 CCTTATCCCCTAAC
1 CCTTAACCCCTAAT
* *
43287724 CCCTAACCCATAAT
1 CCTTAACCCCTAAT
*
43287738 TCTTAACCC
1 CCTTAACCC
43287747 ATAACCCTAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.27, C:0.45, G:0.00, T:0.27
Consensus pattern (14 bp):
CCTTAACCCCTAAT
Found at i:43287744 original size:21 final size:20
Alignment explanation
Indices: 43287720--43287763 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
43287710 CCTTATCCCC
* *
43287720 TAACCCCTAACCCATAATTCT
1 TAACCCATAACCC-TAAATCT
43287741 TAACCCATAACCCTAAATCT
1 TAACCCATAACCCTAAATCT
43287761 TAA
1 TAA
43287764 ACTCCAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.39, C:0.34, G:0.00, T:0.27
Consensus pattern (20 bp):
TAACCCATAACCCTAAATCT
Found at i:43288500 original size:41 final size:41
Alignment explanation
Indices: 43288431--43288532 Score: 138
Period size: 41 Copynumber: 2.5 Consensus size: 41
43288421 TTTTGCGGTG
43288431 TTTTCTATAAAGCGCCGCTAA-TGACAACCGATAGCGGCGTT
1 TTTTCTA-AAAGCGCCGCTAATTGACAACCGATAGCGGCGTT
* *
43288472 TTTTCTAAAAGC-CTCGCTAATTGTCAACCTATAGCGGCGTT
1 TTTTCTAAAAGCGC-CGCTAATTGACAACCGATAGCGGCGTT
*
43288513 TTCT-TAAAAGCGCCGCTAAT
1 TTTTCTAAAAGCGCCGCTAAT
43288533 GCTCTTTTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
39 1 0.02
40 25 0.45
41 29 0.53
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (41 bp):
TTTTCTAAAAGCGCCGCTAATTGACAACCGATAGCGGCGTT
Found at i:43289284 original size:21 final size:21
Alignment explanation
Indices: 43289241--43289302 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
43289231 TGAATACGCC
*
43289241 AACAGAAGCTCG-AA-AGCTG
1 AACAGAAGCTCGTAAGAGCTT
*
43289260 AACAAAAGCTCGTAAGAGCTT
1 AACAGAAGCTCGTAAGAGCTT
*
43289281 AACAGAAGCTTGTAAGAGCTT
1 AACAGAAGCTCGTAAGAGCTT
43289302 A
1 A
43289303 TCCACCCGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.30
20 2 0.05
21 24 0.65
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.18
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCTT
Found at i:43291617 original size:27 final size:28
Alignment explanation
Indices: 43291587--43291656 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 28
43291577 ATAGTGAATC
* *
43291587 CGCACACTTAGTGCTATAAAAT-TAGCT
1 CGCACACTTAGTGCTATAAAATCAAACT
* * *
43291614 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATAAAATCAAACT
43291642 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43291657 GTACAATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 20 0.56
28 16 0.44
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATAAAATCAAACT
Found at i:43291728 original size:42 final size:42
Alignment explanation
Indices: 43291664--43291770 Score: 196
Period size: 42 Copynumber: 2.5 Consensus size: 42
43291654 GCTGTACAAT
* *
43291664 TTTAAACCCGCACACGTAGTGCCAATCTTGTCACCGTGTCCA
1 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
43291706 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
1 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
43291748 TTTATACCCGCACACTTAGTGCC
1 TTTATACCCGCACACTTAGTGCC
43291771 GAGACCAATA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.22, C:0.34, G:0.15, T:0.29
Consensus pattern (42 bp):
TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
Found at i:43294264 original size:30 final size:29
Alignment explanation
Indices: 43294141--43294330 Score: 233
Period size: 30 Copynumber: 6.5 Consensus size: 29
43294131 GACAAGATTG
* * *
43294141 GCACTAAGTGTGCGGGTCT-AAAATTGTACA
1 GCACTAAGTGTGCGAG-CTGAAAA-TATATA
* * *
43294171 GCACTGAGTGTGCGAGTTTG--ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATATATA
43294199 GCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATA
* *
43294228 GCACTAAGTGTGCGAGCTGAAAATTACATG
1 GCACTAAGTGTGCGAGCTGAAAA-TATATA
43294258 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAA-TATATA
*
43294288 GCACTAAGTGCGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATA
43294317 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
43294331 GATTCACTAC
Statistics
Matches: 141, Mismatches: 15, Indels: 9
0.85 0.09 0.05
Matches are distributed among these distances:
27 2 0.01
28 19 0.13
29 50 0.35
30 70 0.50
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGCTGAAAATATATA
Found at i:43294273 original size:59 final size:60
Alignment explanation
Indices: 43294141--43294330 Score: 248
Period size: 59 Copynumber: 3.2 Consensus size: 60
43294131 GACAAGATTG
* * * * *
43294141 GCACTAAGTGTGCGGGTCT-AAAATTGTACAGCACTGAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATAGCACTAAGTGTGCGAG-CTGAAAATTATATA
* *
43294199 GCACTAAGTGTGCGAGCTGAAAA-TATATAGCACTAAGTGTGCGAGCTGAAAATTACATG
1 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATTATATA
*
43294258 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGCGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATTATATA
43294317 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
43294331 GATTCACTAC
Statistics
Matches: 117, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
56 2 0.02
57 21 0.18
58 19 0.16
59 47 0.40
60 28 0.24
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (60 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:43302146 original size:30 final size:29
Alignment explanation
Indices: 43302110--43302299 Score: 240
Period size: 30 Copynumber: 6.5 Consensus size: 29
43302100 GACAAGATTG
* * * * *
43302110 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAA-TATATA
* *
43302140 GCACTAAGTGTGCGAGTTTG--ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATATATA
43302168 GCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATA
* *
43302197 GCACTAAGTGTGCGAGCTGAAAATTACATG
1 GCACTAAGTGTGCGAGCTGAAAA-TATATA
43302227 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAA-TATATA
*
43302257 GCACTAAGTGCGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATA
43302286 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
43302300 GATTCACTAC
Statistics
Matches: 143, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
27 2 0.01
28 20 0.14
29 50 0.35
30 69 0.48
31 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGCTGAAAATATATA
Found at i:43302295 original size:89 final size:87
Alignment explanation
Indices: 43302110--43302299 Score: 269
Period size: 89 Copynumber: 2.2 Consensus size: 87
43302100 GACAAGATTG
* * * *
43302110 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATATAGCACTAA
1 GCACTAAGTGTGCGAGCTGAAAATTGTACAGCACTAAGTGTGCGAGTCTGATTATATAGCACTAA
*
43302175 GTGTGCGAGCTGAAAATATATA
66 GTGCGCGAGCTGAAAATATATA
43302197 GCACTAAGTGTGCGAGCTGAAAA-T-TACATGGCACTAAGTGTGCGAG-CTGAAAATTATATAGC
1 GCACTAAGTGTGCGAGCTGAAAATTGTACA--GCACTAAGTGTGCGAGTCTG---ATTATATAGC
43302259 ACTAAGTGCGCGAGCTGAAAATATATA
61 ACTAAGTGCGCGAGCTGAAAATATATA
43302286 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
43302300 GATTCACTAC
Statistics
Matches: 93, Mismatches: 5, Indels: 8
0.88 0.05 0.08
Matches are distributed among these distances:
85 4 0.04
86 3 0.03
87 36 0.39
89 50 0.54
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (87 bp):
GCACTAAGTGTGCGAGCTGAAAATTGTACAGCACTAAGTGTGCGAGTCTGATTATATAGCACTAA
GTGCGCGAGCTGAAAATATATA
Found at i:43309992 original size:27 final size:28
Alignment explanation
Indices: 43309962--43310031 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
43309952 ATAGTGAATC
*
43309962 CGCACACTTAGTGCTATAAAATC-AGCT
1 CGCACACTTAGTGCTATAAAATCAAACT
* * *
43309989 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATAAAATCAAACT
43310017 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43310032 GTACAATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATAAAATCAAACT
Found at i:43310103 original size:42 final size:42
Alignment explanation
Indices: 43310039--43310145 Score: 196
Period size: 42 Copynumber: 2.5 Consensus size: 42
43310029 GCTGTACAAT
* *
43310039 TTTAAACCCGCACACGTAGTGCCAATCTTGTCACCGTGTCCA
1 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
43310081 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
1 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
43310123 TTTATACCCGCACACTTAGTGCC
1 TTTATACCCGCACACTTAGTGCC
43310146 GAGACCAATA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.22, C:0.34, G:0.15, T:0.29
Consensus pattern (42 bp):
TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
Found at i:43319519 original size:21 final size:21
Alignment explanation
Indices: 43319478--43319519 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
43319468 GACGTTTTGA
*
43319478 CATGTTTTAAGCTTGTTTAAT
1 CATGTTTTAAGCTTGTATAAT
*
43319499 CATGTTTTGAG-TTGGTATAAT
1 CATGTTTTAAGCTT-GTATAAT
43319520 TAATGGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.24, C:0.07, G:0.19, T:0.50
Consensus pattern (21 bp):
CATGTTTTAAGCTTGTATAAT
Found at i:43331380 original size:40 final size:39
Alignment explanation
Indices: 43331325--43331580 Score: 313
Period size: 40 Copynumber: 6.5 Consensus size: 39
43331315 TGGATGATAA
* * *
43331325 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TT
* *
43331365 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TT
* *
43331405 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TT
43331445 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-T
*
43331484 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-T
* *
43331524 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTAT-T
* *
43331563 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
43331581 TACTTGGCTT
Statistics
Matches: 198, Mismatches: 15, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
38 15 0.08
39 50 0.25
40 133 0.67
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATT
Found at i:43331515 original size:79 final size:79
Alignment explanation
Indices: 43331325--43331580 Score: 354
Period size: 79 Copynumber: 3.2 Consensus size: 79
43331315 TGGATGATAA
* * * **
43331325 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACATCCGGGCTAAGTCCCGAAGGCATTTG
* *
43331390 TGCGAGTTATTACAT
66 TGCGAG-TACTATAT
*
43331405 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACATCCGGGCTAAGTCCCGAAGGCATTTG
43331470 TGCGAGTACTATAT
66 TGCGAGTACTATAT
* * *
43331484 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATCCGGGCTATGTCCCGAAGGCA-TTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACATCCGGGCTAAGTCCCGAAGGCATTTG
*
43331548 AGCGAGTAGCTATAT
66 TGCGAGTA-CTATAT
* *
43331563 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
43331581 TACTTGGCTT
Statistics
Matches: 160, Mismatches: 15, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
78 24 0.15
79 71 0.44
80 65 0.41
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGTACTATAT
Found at i:43336549 original size:79 final size:81
Alignment explanation
Indices: 43336439--43336619 Score: 216
Period size: 79 Copynumber: 2.3 Consensus size: 81
43336429 CTACTCGTTG
* *
43336439 AAATGCCTTCGGGACATT-GCCCGGTTATAGTAACTCGCAGAAATGCCTTCGGGA-CTTAACT-C
1 AAATGCCTTCGGGAC-TTAGCCCGGATATAGTAACTCGCACAAATGCCTTC-GGATCTT-ACTCC
* *
43336501 GGATTTAGTAAC-TCGCAC
63 GGATATAGTAACTTAGCAC
*
43336519 AAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 AAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGATCTTACTCCGG
*
43336582 ATATAGTCACTTAGCAC
65 ATATAGTAACTTAGCAC
43336599 AAA-GCCTT-GGGACTTAGCCCG
1 AAATGCCTTCGGGACTTAGCCCG
43336620 ACATCATTCG
Statistics
Matches: 89, Mismatches: 6, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
78 11 0.12
79 57 0.64
80 21 0.24
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (81 bp):
AAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGATCTTACTCCGGA
TATAGTAACTTAGCAC
Found at i:43336557 original size:39 final size:40
Alignment explanation
Indices: 43336439--43336619 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 40
43336429 CTACTCGTTG
* *
43336439 AAATGCCTTCGGGACATT-GCCCGGTTATAGTAACTCGCAG
1 AAATGCCTTCGGGAC-TTAGCCCGGATATAGTAACTCGCAC
* * *
43336479 AAATGCCTTCGGGACTTAACTCGGATTTAGTAACTCGCAC
1 AAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCAC
43336519 AAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCAC
1 AAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCAC
* * *
43336558 AAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCAC
1 AAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCAC
43336599 AAA-GCCTT-GGGACTTAGCCCG
1 AAATGCCTTCGGGACTTAGCCCG
43336620 ACATCATTCG
Statistics
Matches: 122, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
38 2 0.02
39 42 0.34
40 69 0.57
41 9 0.07
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
AAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCAC
Found at i:43338011 original size:17 final size:17
Alignment explanation
Indices: 43337989--43338022 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
43337979 AATGAAAAAG
43337989 ATAGACACTTTTTTTTT
1 ATAGACACTTTTTTTTT
43338006 ATAGACACTTTTTTTTT
1 ATAGACACTTTTTTTTT
43338023 GTTTCTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.59
Consensus pattern (17 bp):
ATAGACACTTTTTTTTT
Found at i:43338485 original size:16 final size:16
Alignment explanation
Indices: 43338464--43338495 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
43338454 GGGCTGTCAC
*
43338464 ACACATAGTCACATAT
1 ACACATAATCACATAT
43338480 ACACATAATCACATAT
1 ACACATAATCACATAT
43338496 TTCCTAGTGA
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:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (16 bp):
ACACATAATCACATAT
Found at i:43343148 original size:2 final size:2
Alignment explanation
Indices: 43343141--43343165 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43343131 TTGATGGATC
43343141 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 T
43343166 GATAAATGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.