Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 190 of 211
Found at i:56311713 original size:39 final size:39
Alignment explanation
Indices: 56311659--56311735 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
56311649 GAAAAGTTGT
56311659 GGATTTGTATCCATCCCTTGGATTGAACTCCTAGTGAAC
1 GGATTTGTATCCATCCCTTGGATTGAACTCCTAGTGAAC
*
56311698 GGATTTGTATCCATCCCTTGGCTTGAACTCCTAGTGAA
1 GGATTTGTATCCATCCCTTGGATTGAACTCCTAGTGAA
56311736 GAACTGTGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (39 bp):
GGATTTGTATCCATCCCTTGGATTGAACTCCTAGTGAAC
Found at i:56314404 original size:20 final size:20
Alignment explanation
Indices: 56314367--56314405 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
56314357 AGATGTCGCC
**
56314367 GTCATGTGCTGGTGACTTTA
1 GTCATGTGCTGGCAACTTTA
56314387 GTCATGTGCTGGCAACTTT
1 GTCATGTGCTGGCAACTTT
56314406 GATACAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.18, G:0.28, T:0.38
Consensus pattern (20 bp):
GTCATGTGCTGGCAACTTTA
Found at i:56314803 original size:38 final size:39
Alignment explanation
Indices: 56314731--56314815 Score: 127
Period size: 38 Copynumber: 2.2 Consensus size: 39
56314721 GATTTTACAT
* *
56314731 GTTATATAACGAGATCTAGCATTTGTTATAGATTCTCGG
1 GTTATATAACGAGATCTAGCATTTGTTACAGATTCTCAG
* *
56314770 GTTATTTAACGAGATCTAGC-TTTGTTGCAGATTCTCAG
1 GTTATATAACGAGATCTAGCATTTGTTACAGATTCTCAG
56314808 GTTATATA
1 GTTATATA
56314816 TAACATAGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
38 22 0.54
39 19 0.46
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (39 bp):
GTTATATAACGAGATCTAGCATTTGTTACAGATTCTCAG
Found at i:56316284 original size:2 final size:2
Alignment explanation
Indices: 56316277--56316301 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56316267 GGGTGTTACG
56316277 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
56316302 GTGAGTGAGC
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:56319725 original size:48 final size:48
Alignment explanation
Indices: 56319641--56319878 Score: 289
Period size: 48 Copynumber: 5.0 Consensus size: 48
56319631 TGCCAGCAGC
* * * * * * * * *
56319641 TTTTCCCTGGGAGTTCAAACTAAGGAACGAACACAAATTCAAAACGGT
1 TTTTCACTGGGAGTTCAAGCCAAGGAATGGATACAAATCCACAACAGT
* * * *
56319689 TTTTCATTGGGAGTTCAAGTCAAGAAATGGATACAAATCGACAACAGTT
1 TTTTCACTGGGAGTTCAAGCCAAGGAATGGATACAAATCCACAACAG-T
* * *
56319738 TTTTC-CTGGGAGTTCAAGTCAAGGAATGGATACAAATCCATAATAGT
1 TTTTCACTGGGAGTTCAAGCCAAGGAATGGATACAAATCCACAACAGT
*
56319785 TTTTCACTGGAAGTTCAAGCCAAGGAATGGATACAAATCCACAACAGT
1 TTTTCACTGGGAGTTCAAGCCAAGGAATGGATACAAATCCACAACAGT
* *
56319833 TTTTCACTGGGAGTTCAAGCCAAGGGATGGATTCAAATCCACAACA
1 TTTTCACTGGGAGTTCAAGCCAAGGAATGGATACAAATCCACAACA
56319879 TCCACCACAA
Statistics
Matches: 163, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
47 6 0.04
48 151 0.93
49 6 0.04
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (48 bp):
TTTTCACTGGGAGTTCAAGCCAAGGAATGGATACAAATCCACAACAGT
Found at i:56319909 original size:57 final size:56
Alignment explanation
Indices: 56319817--56319928 Score: 170
Period size: 57 Copynumber: 2.0 Consensus size: 56
56319807 AGGAATGGAT
* * * *
56319817 ACAAATCCACAACAGTTTTTCACTGGGAGTTCAAGCCAAGGGATGGATTCAAATCC
1 ACAAATCCACAACAATTCTTCACTAGGAGTTCAAGCCAAGGGATGGATACAAATCC
*
56319873 ACAACATCCACCACAATTCTTCACTAGGAGTTCAAGCCAAGGGATGGATACAAATC
1 ACAA-ATCCACAACAATTCTTCACTAGGAGTTCAAGCCAAGGGATGGATACAAATC
56319929 TGTTCACTGG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
56 4 0.08
57 46 0.92
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (56 bp):
ACAAATCCACAACAATTCTTCACTAGGAGTTCAAGCCAAGGGATGGATACAAATCC
Found at i:56319935 original size:39 final size:39
Alignment explanation
Indices: 56319892--56319967 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
56319882 ACCACAATTC
56319892 TTCACTAGGAGTTCAAGCCAAGGGATGGATACAAATCTG
1 TTCACTAGGAGTTCAAGCCAAGGGATGGATACAAATCTG
* * *
56319931 TTCACTGGGAGTTCGATCCAAGGGATGGATACAAATC
1 TTCACTAGGAGTTCAAGCCAAGGGATGGATACAAATC
56319968 CACAACTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (39 bp):
TTCACTAGGAGTTCAAGCCAAGGGATGGATACAAATCTG
Found at i:56324238 original size:7 final size:7
Alignment explanation
Indices: 56324220--56324301 Score: 67
Period size: 7 Copynumber: 10.9 Consensus size: 7
56324210 CAACCCAATT
56324220 TTTATT-
1 TTTATTA
56324226 TTTATTA
1 TTTATTA
*
56324233 TATATTA
1 TTTATTA
56324240 TTTATTA
1 TTTATTA
*
56324247 TTTATTTC
1 TTTA-TTA
56324255 TTTACTTTA
1 TTTA--TTA
56324264 TTTATTA
1 TTTATTA
56324271 CTTTATTTTA
1 -TTTA--TTA
56324281 TTTTATTA
1 -TTTATTA
56324289 TTTATTA
1 TTTATTA
*
56324296 CTTATT
1 TTTATT
56324302 TCGATATTAA
Statistics
Matches: 64, Mismatches: 6, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
6 6 0.09
7 31 0.48
8 13 0.20
9 7 0.11
10 7 0.11
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTATTA
Found at i:56324251 original size:4 final size:4
Alignment explanation
Indices: 56324226--56324294 Score: 54
Period size: 4 Copynumber: 16.5 Consensus size: 4
56324216 AATTTTTATT
*
56324226 TTTA TTATA TATTA TTTA -TTA TTTA TTTC TTTA CTTTA TTTA -TTA CTTTA
1 TTTA TT-TA T-TTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA -TTTA
56324276 TTTTA TTT- TATTA TTTA TT
1 -TTTA TTTA T-TTA TTTA TT
56324295 ACTTATTTCG
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
3 7 0.13
4 28 0.52
5 18 0.33
6 1 0.02
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:56324293 original size:17 final size:16
Alignment explanation
Indices: 56324217--56324294 Score: 65
Period size: 17 Copynumber: 4.9 Consensus size: 16
56324207 AGGCAACCCA
56324217 ATTT-TTATTT-TTATT
1 ATTTATTATTTATT-TT
*
56324232 ATATATTATTTA--TT
1 ATTTATTATTTATTTT
* *
56324246 ATTTATTTCTTTACTTT
1 ATTTA-TTATTTATTTT
56324263 ATTTATTACTTTATTTT
1 ATTTATTA-TTTATTTT
56324280 ATTTTATTATTTATT
1 A-TTTATTATTTATT
56324295 ACTTATTTCG
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
14 6 0.12
15 9 0.18
16 8 0.16
17 21 0.41
18 7 0.14
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTATTATTTATTTT
Found at i:56327177 original size:48 final size:48
Alignment explanation
Indices: 56327112--56327355 Score: 247
Period size: 48 Copynumber: 4.9 Consensus size: 48
56327102 ACATCCACCG
* * *
56327112 CAGTTCTTCACTGGGAGTTCAATCCAAGGGATGGATACAAATCCATAA
1 CAGTTTTTCACTAGGAGTTCAATCCAAGGGATGGATACAAATCCACAA
* * * *
56327160 TAGTTTTTCACTAGGAGTTCAAGCCAAGGAATAGATACAAATCCACAACACTCACCA
1 CAGTTTTTCACTAGGAGTTCAATCCAAGGGATGGATACAAAT---C--CA--CA--A
* * *
56327217 CAGTTCTTCACTGGGAGTTCAATCCAAGGGATGGATACAAACCCACAA
1 CAGTTTTTCACTAGGAGTTCAATCCAAGGGATGGATACAAATCCACAA
*
56327265 CAGTTTTTCACTAGGAGTTCAATCCAAGGGATGGATACAAATCCACGA
1 CAGTTTTTCACTAGGAGTTCAATCCAAGGGATGGATACAAATCCACAA
* * * * *
56327313 CAGCTTTTCCCTGAGAAG-TCAAGCCAAGGAATGGATACAAATC
1 CAGTTTTTCACT-AGGAGTTCAATCCAAGGGATGGATACAAATC
56327356 ACTACTTTTC
Statistics
Matches: 163, Mismatches: 23, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
48 114 0.70
49 4 0.02
50 2 0.01
51 1 0.01
52 2 0.01
53 2 0.01
54 1 0.01
55 1 0.01
57 36 0.22
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (48 bp):
CAGTTTTTCACTAGGAGTTCAATCCAAGGGATGGATACAAATCCACAA
Found at i:56327233 original size:105 final size:103
Alignment explanation
Indices: 56326971--56327310 Score: 434
Period size: 105 Copynumber: 3.3 Consensus size: 103
56326961 CCGCATCAAG
* * *
56326971 TCAAGTCAAGGAATGGAGACAAATCCACAACATGCACCACAGTTCTTCACTGGGAGTTCAATTCA
1 TCAAGCCAAGGAATGGAGACAAATCCACAACATCCACCACAGTTCTTCACTGGGAGTTCAATCCA
** * * * *
56327036 AGGGATGGATGTAAATCCACAA-CTTTTCAATGAGAAG-
66 AGGGATGGATACAAATCCAAAAGTTTTTCACT-AGGAGT
* * * *
56327073 TCAAGCCAAGAAATGTAGACAAATCCATAACATCCACCGCAGTTCTTCACTGGGAGTTCAATCCA
1 TCAAGCCAAGGAATGGAGACAAATCCACAACATCCACCACAGTTCTTCACTGGGAGTTCAATCCA
56327138 AGGGATGGATACAAATCCATAATAGTTTTTCACTAGGAGT
66 AGGGATGGATACAAATCCA-AA-AGTTTTTCACTAGGAGT
* *
56327178 TCAAGCCAAGGAATAGATACAAATCCACAACA-CTCACCACAGTTCTTCACTGGGAGTTCAATCC
1 TCAAGCCAAGGAATGGAGACAAATCCACAACATC-CACCACAGTTCTTCACTGGGAGTTCAATCC
*
56327242 AAGGGATGGATACAAACCCACAACAGTTTTTCACTAGGAGT
65 AAGGGATGGATACAAATCCA-AA-AGTTTTTCACTAGGAGT
* * *
56327283 TCAATCCAAGGGATGGATACAAATCCAC
1 TCAAGCCAAGGAATGGAGACAAATCCAC
56327311 GACAGCTTTT
Statistics
Matches: 208, Mismatches: 25, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
102 75 0.36
103 1 0.00
104 6 0.03
105 126 0.61
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (103 bp):
TCAAGCCAAGGAATGGAGACAAATCCACAACATCCACCACAGTTCTTCACTGGGAGTTCAATCCA
AGGGATGGATACAAATCCAAAAGTTTTTCACTAGGAGT
Found at i:56327539 original size:26 final size:26
Alignment explanation
Indices: 56327510--56327592 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
56327500 TTTTATTTTT
56327510 AAAAATCTAAACTTTCTCATTTAAAA
1 AAAAATCTAAACTTTCTCATTTAAAA
* * * **
56327536 AAAAAACAAAACCTATTCTTATTT--TT
1 AAAAATCTAAA-CT-TTCTCATTTAAAA
* *
56327562 CAAAATCTAAACTTTATCATTTAAAA
1 AAAAATCTAAACTTTCTCATTTAAAA
56327588 AAAAA
1 AAAAA
56327593 CCAAAAACTT
Statistics
Matches: 40, Mismatches: 13, Indels: 8
0.66 0.21 0.13
Matches are distributed among these distances:
24 7 0.17
25 2 0.05
26 21 0.52
27 2 0.05
28 8 0.20
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (26 bp):
AAAAATCTAAACTTTCTCATTTAAAA
Found at i:56327547 original size:52 final size:52
Alignment explanation
Indices: 56327491--56327598 Score: 171
Period size: 52 Copynumber: 2.1 Consensus size: 52
56327481 AAATGGCTAA
* *
56327491 AAAACATATTTTTATTTTTAAAAATCTAAACTTTCTCATTTAAAAAAAAAAC
1 AAAACATATTCTTATTTTTAAAAATCTAAACTTTATCATTTAAAAAAAAAAC
* * *
56327543 AAAACCTATTCTTATTTTTCAAAATCTAAACTTTATCATTTAAAAAAAAACC
1 AAAACATATTCTTATTTTTAAAAATCTAAACTTTATCATTTAAAAAAAAAAC
56327595 AAAA
1 AAAA
56327599 ACTTTCCTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (52 bp):
AAAACATATTCTTATTTTTAAAAATCTAAACTTTATCATTTAAAAAAAAAAC
Found at i:56329687 original size:2 final size:2
Alignment explanation
Indices: 56329680--56329714 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
56329670 GCTCACTCAC
56329680 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
56329715 CGTAACACCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:56331260 original size:39 final size:38
Alignment explanation
Indices: 56331176--56331260 Score: 125
Period size: 38 Copynumber: 2.2 Consensus size: 38
56331166 ACCTATGTTA
* *
56331176 TATATAACCTGAGAATCTGCAACAAAGCTAGATCTCGT
1 TATATAACCCGAGAATCTACAACAAAGCTAGATCTCGT
* *
56331214 TAAATAACCCGAGAATCTATAACAAATGCTAGATCTCGT
1 TATATAACCCGAGAATCTACAACAAA-GCTAGATCTCGT
56331253 TATATAAC
1 TATATAAC
56331261 ATGTAAAATC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
38 22 0.54
39 19 0.46
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (38 bp):
TATATAACCCGAGAATCTACAACAAAGCTAGATCTCGT
Found at i:56348546 original size:2 final size:2
Alignment explanation
Indices: 56348539--56348563 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56348529 ATAAGCAACA
56348539 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
56348564 TTAGTATGCA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:56348811 original size:57 final size:56
Alignment explanation
Indices: 56348738--56348874 Score: 141
Period size: 57 Copynumber: 2.4 Consensus size: 56
56348728 TGGCAATAGC
* ** * *
56348738 TCCCACATTGGTGCCTAAACTTTTTTGTCATTGTTAGCCCCTAAAATTTAT-ATTTAT
1 TCCCATATTGGTGCCTAAACTTTTTTAACATAGTTAGCCCCT-AAATTGATAATTT-T
* * * * *
56348795 TCCCATATTGGGGCCTAATCATTTTTTAACCTAGTTAGTCCCTAACTTGATAATTTT
1 TCCCATATTGGTGCCTAAAC-TTTTTTAACATAGTTAGCCCCTAAATTGATAATTTT
*
56348852 TCCTATATTGGTGCCTAAACTTT
1 TCCCATATTGGTGCCTAAACTTT
56348875 AGGCTTTTTA
Statistics
Matches: 65, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
56 3 0.05
57 41 0.63
58 21 0.32
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (56 bp):
TCCCATATTGGTGCCTAAACTTTTTTAACATAGTTAGCCCCTAAATTGATAATTTT
Found at i:56365955 original size:68 final size:70
Alignment explanation
Indices: 56365849--56366084 Score: 257
Period size: 69 Copynumber: 3.4 Consensus size: 70
56365839 AACCCTATAT
* ** * *
56365849 GTTGTTATAGTCGAATTATGGT-TTCAAACATTATGAACTCATGTCTAACATCTTAGCAGACTCT
1 GTTGTCATAGTCGAGCTATGGTCTT-ACACATTATGAACTCATGTTTAACATCTTAGCAGACTCT
56365913 CTA-T-
65 CTATTG
* * * *
56365917 GTTGCCATAGTCGAGCTATGGTCTTACACATTATGAACTCATATTTAACATCCTAGCGGACTCTC
1 GTTGTCATAGTCGAGCTATGGTCTTACACATTATGAACTCATGTTTAACATCTTAGCAGACTCTC
56365982 TATTG
66 TATTG
* * * ** * *
56365987 GTTGTCATAGCCGAGTTATGGTCTTACACACTAT-TCCTCATGTTTAACAT-TCTGGCAAACTCT
1 GTTGTCATAGTCGAGCTATGGTCTTACACATTATGAACTCATGTTTAACATCT-TAGCAGACTCT
56366050 CTATTG
65 CTATTG
* *
56366056 GTTGTCATAGTCGAGGTATGGTTTTACAC
1 GTTGTCATAGTCGAGCTATGGTCTTACAC
56366085 TTTAAACCTC
Statistics
Matches: 141, Mismatches: 23, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
68 55 0.39
69 56 0.40
70 30 0.21
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.37
Consensus pattern (70 bp):
GTTGTCATAGTCGAGCTATGGTCTTACACATTATGAACTCATGTTTAACATCTTAGCAGACTCTC
TATTG
Found at i:56366623 original size:20 final size:21
Alignment explanation
Indices: 56366598--56366638 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
56366588 GAGCGAAACT
*
56366598 GCCCTT-GATGTCATGACATA
1 GCCCTTCGATGTCACGACATA
*
56366618 GCCCTTCTATGTCACGACATA
1 GCCCTTCGATGTCACGACATA
56366639 CCCCCTGCGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (21 bp):
GCCCTTCGATGTCACGACATA
Found at i:56372648 original size:43 final size:43
Alignment explanation
Indices: 56372595--56372714 Score: 129
Period size: 43 Copynumber: 2.8 Consensus size: 43
56372585 TTTTTTTATA
* * *
56372595 AGTGTTTTCATGTAAGACCACGTCTGGGACGTTGACATCGACTT
1 AGTGATTTCATGTAAGACCACGTCTGGGACGTTGACATC-AATC
* * *
56372639 A-TGATTTCATGTAAGACC-CTGTCCGGGACAG-CGGCATCAATC
1 AGTGATTTCATGTAAGACCAC-GTCTGGGAC-GTTGACATCAATC
*
56372681 AGTGATTACATGTAAGACCACGTCTGGGACGTTG
1 AGTGATTTCATGTAAGACCACGTCTGGGACGTTG
56372715 GCGTTGTATA
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
42 5 0.08
43 54 0.87
44 3 0.05
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.28
Consensus pattern (43 bp):
AGTGATTTCATGTAAGACCACGTCTGGGACGTTGACATCAATC
Found at i:56379964 original size:9 final size:9
Alignment explanation
Indices: 56379952--56379987 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
56379942 CAAAATATAT
56379952 AAAAAAACAA
1 AAAAAAAC-A
56379962 AAAAAAACA
1 AAAAAAACA
56379971 AAAAAAACA
1 AAAAAAACA
56379980 GAAAAAAA
1 -AAAAAAA
56379988 ACCTGGACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 10 0.40
10 15 0.60
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:56379989 original size:11 final size:10
Alignment explanation
Indices: 56379952--56379989 Score: 60
Period size: 9 Copynumber: 3.8 Consensus size: 10
56379942 CAAAATATAT
56379952 AAAAAAACAA
1 AAAAAAACAA
56379962 AAAAAAAC-A
1 AAAAAAACAA
56379971 AAAAAAACAGA
1 AAAAAAACA-A
56379982 AAAAAAAC
1 AAAAAAAC
56379990 CTGGACTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.35
10 8 0.31
11 9 0.35
ACGTcount: A:0.87, C:0.11, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:56380058 original size:27 final size:27
Alignment explanation
Indices: 56380018--56380095 Score: 111
Period size: 27 Copynumber: 2.9 Consensus size: 27
56380008 TCCCTGGGTG
** *
56380018 AAGGGAACATTGTTGGTGGCACCAAAC
1 AAGGGAACCCTGTTGGCGGCACCAAAC
56380045 AAGGGAACCCTGTTGGCGGCACCAAAC
1 AAGGGAACCCTGTTGGCGGCACCAAAC
**
56380072 AAGGGTTCCCTGTTGGCGGCACCA
1 AAGGGAACCCTGTTGGCGGCACCA
56380096 CTCGTGTTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.27, C:0.26, G:0.31, T:0.17
Consensus pattern (27 bp):
AAGGGAACCCTGTTGGCGGCACCAAAC
Found at i:56380532 original size:14 final size:14
Alignment explanation
Indices: 56380513--56380541 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
56380503 TAACTGAAAC
56380513 TAGAATAATTAAAT
1 TAGAATAATTAAAT
56380527 TAGAATAATTAAAT
1 TAGAATAATTAAAT
56380541 T
1 T
56380542 GATACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (14 bp):
TAGAATAATTAAAT
Found at i:56381387 original size:14 final size:14
Alignment explanation
Indices: 56381368--56381396 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
56381358 TTTTTGTATC
56381368 AATTTAATTATTCT
1 AATTTAATTATTCT
56381382 AATTTAATTATTCT
1 AATTTAATTATTCT
56381396 A
1 A
56381397 GTTTCAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:56381908 original size:12 final size:12
Alignment explanation
Indices: 56381891--56381935 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
56381881 AATCAATCCA
56381891 GTTTT-TTTTTCT
1 GTTTTGTTTTT-T
56381903 GTTTT-TTATTTT
1 GTTTTGTT-TTTT
56381915 -TTTTGTTTTTT
1 GTTTTGTTTTTT
56381926 GTTTTGTTTT
1 GTTTTGTTTT
56381936 GGATGTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 8 0.27
12 19 0.63
13 3 0.10
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.84
Consensus pattern (12 bp):
GTTTTGTTTTTT
Found at i:56381916 original size:16 final size:16
Alignment explanation
Indices: 56381895--56381930 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
56381885 AATCCAGTTT
56381895 TTTTTTCTGTTTTTTA
1 TTTTTTCTGTTTTTTA
* *
56381911 TTTTTTTTGTTTTTTG
1 TTTTTTCTGTTTTTTA
56381927 TTTT
1 TTTT
56381931 GTTTTGGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.03, C:0.03, G:0.08, T:0.86
Consensus pattern (16 bp):
TTTTTTCTGTTTTTTA
Found at i:56387026 original size:62 final size:62
Alignment explanation
Indices: 56386956--56387088 Score: 257
Period size: 62 Copynumber: 2.1 Consensus size: 62
56386946 TCATAATTCA
*
56386956 ATCTTCAAATCTTAAATTTCAACTCAATTGTTCTTCAATTTATGGGCTTTACTCGTTCAAAT
1 ATCTTCAAATCTTAAATTTCAACTCAATTGTTCTTCAATTTATGGGCTTAACTCGTTCAAAT
56387018 ATCTTCAAATCTTAAATTTCAACTCAATTGTTCTTCAATTTATGGGCTTAACTCGTTCAAAT
1 ATCTTCAAATCTTAAATTTCAACTCAATTGTTCTTCAATTTATGGGCTTAACTCGTTCAAAT
56387080 ATCTTCAAA
1 ATCTTCAAA
56387089 ATAATCAGTC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 70 1.00
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.42
Consensus pattern (62 bp):
ATCTTCAAATCTTAAATTTCAACTCAATTGTTCTTCAATTTATGGGCTTAACTCGTTCAAAT
Found at i:56388892 original size:22 final size:23
Alignment explanation
Indices: 56388867--56388909 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
56388857 GATTTAGGCA
* *
56388867 CTATGTTTTTCTTT-CATTAATG
1 CTATGCTTCTCTTTGCATTAATG
56388889 CTATGCTTCTCTTTGCATTAA
1 CTATGCTTCTCTTTGCATTAA
56388910 CTATTGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.19, C:0.19, G:0.09, T:0.53
Consensus pattern (23 bp):
CTATGCTTCTCTTTGCATTAATG
Found at i:56409313 original size:17 final size:16
Alignment explanation
Indices: 56409263--56409320 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 16
56409253 GGGTGAGAAG
56409263 TAAAAGTTTAGGGGAAAAA
1 TAAAAGTTTA-GGG--AAA
*
56409282 TAAAAAGTTTTGGGAAA
1 T-AAAAGTTTAGGGAAA
56409299 TAAAAGTTTGAGGGAAA
1 TAAAAGTTT-AGGGAAA
56409316 GTAAA
1 -TAAA
56409321 TAGGGGGGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 8 0.24
17 10 0.29
18 4 0.12
19 4 0.12
20 8 0.24
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (16 bp):
TAAAAGTTTAGGGAAA
Found at i:56409439 original size:30 final size:31
Alignment explanation
Indices: 56409400--56409459 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
56409390 AGAGGTGTGA
* *
56409400 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTGTAGGGGAAAAG
* *
56409431 TGGG-AGGGAGTAAAAATTGTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTGTAGGGGAAAA
56409460 TAAAAGATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.40, C:0.00, G:0.42, T:0.18
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTGTAGGGGAAAAG
Found at i:56417442 original size:28 final size:29
Alignment explanation
Indices: 56417375--56417443 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 29
56417365 TTTCAACCTC
*
56417375 TATAATTTTATAATTTTTAAAGAATTAAA
1 TATAATTTTATAATTTTTAAAGAATAAAA
*
56417404 T-TAATTTTTTATAA-TTTT-AGGAGATAAAA
1 TATAA--TTTTATAATTTTTAAAGA-ATAAAA
56417433 TATAATTTTAT
1 TATAATTTTAT
56417444 CTTTATTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
28 12 0.35
29 11 0.32
30 11 0.32
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (29 bp):
TATAATTTTATAATTTTTAAAGAATAAAA
Found at i:56423520 original size:86 final size:86
Alignment explanation
Indices: 56423375--56423547 Score: 346
Period size: 86 Copynumber: 2.0 Consensus size: 86
56423365 ATAACCTGAG
56423375 AAGGAAATAAAATAAAATGGTAATTTAGTTGAAATTAAAAAAATAAAACAAATGGCCAATTGACT
1 AAGGAAATAAAATAAAATGGTAATTTAGTTGAAATTAAAAAAATAAAACAAATGGCCAATTGACT
56423440 TCTAGACATTTGTTCTCCAAA
66 TCTAGACATTTGTTCTCCAAA
56423461 AAGGAAATAAAATAAAATGGTAATTTAGTTGAAATTAAAAAAATAAAACAAATGGCCAATTGACT
1 AAGGAAATAAAATAAAATGGTAATTTAGTTGAAATTAAAAAAATAAAACAAATGGCCAATTGACT
56423526 TCTAGACATTTGTTCTCCAAA
66 TCTAGACATTTGTTCTCCAAA
56423547 A
1 A
56423548 TTCAGCCAAA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (86 bp):
AAGGAAATAAAATAAAATGGTAATTTAGTTGAAATTAAAAAAATAAAACAAATGGCCAATTGACT
TCTAGACATTTGTTCTCCAAA
Found at i:56424583 original size:41 final size:43
Alignment explanation
Indices: 56424496--56424585 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 43
56424486 TTATGAGTAT
* * *
56424496 TGAGC-TTCTATTTAACCCTTATGGGTTCCCGTTTAGCTTTTA
1 TGAGCTTTCTATTCAACCCTTATGGGTTCCCGTTTAACTCTTA
*
56424538 TGAGCTTTC-ATTCAACCCTTATGGGTT-CTGTTTAACTCTTA
1 TGAGCTTTCTATTCAACCCTTATGGGTTCCCGTTTAACTCTTA
56424579 TGAGCTT
1 TGAGCTT
56424586 CTGTTCAGCC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
41 18 0.42
42 22 0.51
43 3 0.07
ACGTcount: A:0.18, C:0.21, G:0.17, T:0.44
Consensus pattern (43 bp):
TGAGCTTTCTATTCAACCCTTATGGGTTCCCGTTTAACTCTTA
Found at i:56424589 original size:21 final size:21
Alignment explanation
Indices: 56424496--56424590 Score: 61
Period size: 21 Copynumber: 4.6 Consensus size: 21
56424486 TTATGAGTAT
*
56424496 TGAGCTTCTATTTAACCCTTA
1 TGAGCTTCTGTTTAACCCTTA
* * * **
56424517 TG-GGTTCCCGTTTAGCTTTTA
1 TGAGCTT-CTGTTTAACCCTTA
* *
56424538 TGAGCTT-TCATTCAACCCTTA
1 TGAGCTTCT-GTTTAACCCTTA
* *
56424559 TG-GGTTCTGTTTAACTCTTA
1 TGAGCTTCTGTTTAACCCTTA
56424579 TGAGCTTCTGTT
1 TGAGCTTCTGTT
56424591 CAGCCTTCGT
Statistics
Matches: 51, Mismatches: 18, Indels: 10
0.65 0.23 0.13
Matches are distributed among these distances:
20 17 0.33
21 31 0.61
22 3 0.06
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (21 bp):
TGAGCTTCTGTTTAACCCTTA
Found at i:56426468 original size:45 final size:45
Alignment explanation
Indices: 56426418--56426506 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
56426408 AACAGATACT
* * *
56426418 CGGTGGATTTAGCACATAGCAACCACCTTATTAATCAATAATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATAATGTC
*
56426463 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATAATGT
56426507 TCGATTCACA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATAATGTC
Found at i:56426580 original size:51 final size:50
Alignment explanation
Indices: 56426508--56426703 Score: 232
Period size: 51 Copynumber: 3.9 Consensus size: 50
56426498 CAATGATGTT
* * *
56426508 CGATTCACATAGTAGCTTGCACATATTACTACACATGTGACCATTACCATC
1 CGATACACATAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCATC
* * * * *
56426559 CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATC
1 CGATACACATAGTAGCCTGCACATAGTACTACACATGTGA-CCATACCATC
* * * *
56426610 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTC
1 CGATACACATAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TC
* *
56426660 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAT
1 CGATACACATAGTAGCCTGCACATAGTACTACACATGTGACCAT
56426704 CACTTTCACT
Statistics
Matches: 122, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
49 2 0.02
50 42 0.34
51 76 0.62
52 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (50 bp):
CGATACACATAGTAGCCTGCACATAGTACTACACATGTGACCATACCATC
Found at i:56426691 original size:101 final size:101
Alignment explanation
Indices: 56426515--56426699 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 101
56426505 GTTCGATTCA
* * *
56426515 CATAGTAGCTTGCACATATTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTGCA
56426580 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
* *
56426617 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCTGCA
*
56426681 CATAGTACTACACATGTGA
65 CATAGTACTACACACGTGA
56426700 CCATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 4 0.05
101 40 0.53
102 32 0.42
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:56431875 original size:29 final size:27
Alignment explanation
Indices: 56431768--56431892 Score: 78
Period size: 29 Copynumber: 4.4 Consensus size: 27
56431758 ACATGTCGCG
* *
56431768 AAAAATGATAAAA-AAT-AAAAT-TAA
1 AAAAATTATAAAATTATAAAAATATAA
* *
56431792 ATAAAATTTATTAAATTATTAAAATTTAATAA
1 A-AAAA-TTATAAAATTA-TAAAA-AT-ATAA
* *
56431824 AAAATATTA-AAAATTTTAAAAATCGTAA
1 AAAA-ATTATAAAATTATAAAAAT-ATAA
*
56431852 AAAAATTATAAAATATATAGAAATATAGA
1 AAAAATTATAAAAT-TATAAAAATATA-A
56431881 AAAAATTATAAA
1 AAAAATTATAAA
56431893 GTTTTATAAA
Statistics
Matches: 77, Mismatches: 12, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
24 1 0.01
25 4 0.05
26 6 0.08
27 5 0.06
28 16 0.21
29 28 0.36
30 6 0.08
31 6 0.08
32 5 0.06
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (27 bp):
AAAAATTATAAAATTATAAAAATATAA
Found at i:56432164 original size:19 final size:19
Alignment explanation
Indices: 56432132--56432169 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
56432122 TTAAAGTGTC
*
56432132 TTTTTGATGCATTTTATAA
1 TTTTTGATGAATTTTATAA
*
56432151 TTTTTTATGAATTTTATAA
1 TTTTTGATGAATTTTATAA
56432170 AATTTTACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.61
Consensus pattern (19 bp):
TTTTTGATGAATTTTATAA
Found at i:56432249 original size:19 final size:19
Alignment explanation
Indices: 56432215--56432261 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
56432205 TATTTCTTTT
56432215 ATTTTTATTAAATTTTAATA
1 ATTTTTA-TAAATTTTAATA
* * *
56432235 ATTTTTATAACTTTTATTG
1 ATTTTTATAAATTTTAATA
56432254 ATTTTTAT
1 ATTTTTAT
56432262 TTTTATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTTTTATAAATTTTAATA
Found at i:56432261 original size:10 final size:10
Alignment explanation
Indices: 56432215--56432262 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
56432205 TATTTCTTTT
56432215 ATTTTTATTA
1 ATTTTTATTA
* *
56432225 AATTTTAATA
1 ATTTTTATTA
56432235 ATTTTTA-TA
1 ATTTTTATTA
* *
56432244 ACTTTTATTG
1 ATTTTTATTA
56432254 ATTTTTATT
1 ATTTTTATT
56432263 TTTATAATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
9 8 0.26
10 23 0.74
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (10 bp):
ATTTTTATTA
Found at i:56433305 original size:53 final size:50
Alignment explanation
Indices: 56433247--56433377 Score: 138
Period size: 49 Copynumber: 2.5 Consensus size: 50
56433237 ATAAGTTTTG
*
56433247 AAATAAAAAGATAAATTAGTTTAAATTCAAAAATAAATCTAATTACCTAAGAT
1 AAATAAAAAGATAAAATAGTTTAAATT--AAAA-AAATCTAATTACCTAAGAT
* * * **
56433300 AAATAAAAA-ATAAAAAATTTTAAATTAAAAAAATCTATTTATTTAAGAT
1 AAATAAAAAGATAAAATAGTTTAAATTAAAAAAATCTAATTACCTAAGAT
56433349 AAATTAAAAAAGAATAAAACTAGTTTAAA
1 AAA-T-AAAAAG-ATAAAA-TAGTTTAAA
56433378 AAAAATCTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
49 19 0.29
50 5 0.08
51 5 0.08
52 14 0.22
53 15 0.23
54 7 0.11
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.31
Consensus pattern (50 bp):
AAATAAAAAGATAAAATAGTTTAAATTAAAAAAATCTAATTACCTAAGAT
Found at i:56438053 original size:4 final size:4
Alignment explanation
Indices: 56438037--56438066 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
56438027 AGATTTCCAA
*
56438037 TATG TAAG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TA
56438067 ACTCGAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:56438954 original size:20 final size:22
Alignment explanation
Indices: 56438912--56438961 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
56438902 ATTTTAGATC
* *
56438912 TTTAAGTTTAATTATTAATATT
1 TTTAAGTTTAATTAATAACATT
56438934 TTTAA-TTT-ATTAATAACATT
1 TTTAAGTTTAATTAATAACATT
*
56438954 TTAAAGTT
1 TTTAAGTT
56438962 AAAAAATACA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 14 0.58
21 5 0.21
22 5 0.21
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTAAGTTTAATTAATAACATT
Found at i:56456304 original size:14 final size:13
Alignment explanation
Indices: 56456279--56456320 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
56456269 ACCACGTAAT
*
56456279 AAGAAAACAAAGA
1 AAGAAAAAAAAGA
56456292 AAGTAAAAAAAAGA
1 AAG-AAAAAAAAGA
*
56456306 AAGAAAGAAAAGA
1 AAGAAAAAAAAGA
56456319 AA
1 AA
56456321 TAAGCATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (13 bp):
AAGAAAAAAAAGA
Found at i:56456308 original size:18 final size:17
Alignment explanation
Indices: 56456282--56456316 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56456272 ACGTAATAAG
56456282 AAAACAAAGAAAGTAAAA
1 AAAACAAAGAAAG-AAAA
*
56456300 AAAAGAAAGAAAGAAAA
1 AAAACAAAGAAAGAAAA
56456317 GAAATAAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.80, C:0.03, G:0.14, T:0.03
Consensus pattern (17 bp):
AAAACAAAGAAAGAAAA
Found at i:56466440 original size:17 final size:17
Alignment explanation
Indices: 56466408--56466441 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
56466398 ATTTTTTGAC
56466408 ATTTTTAAATATATATA
1 ATTTTTAAATATATATA
56466425 ATTTATTAAATA-ATATA
1 ATTT-TTAAATATATATA
56466442 CTGGTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTTAAATATATATA
Found at i:56480105 original size:91 final size:91
Alignment explanation
Indices: 56479936--56480117 Score: 240
Period size: 91 Copynumber: 2.0 Consensus size: 91
56479926 GATTAAATTA
* ** **
56479936 TTGAATGATATAATGTTTAAATGTTTCTAATTGTACGGTAATGCTCTGTAACCCCAATCTGGCGA
1 TTGAATGATATAATGTTTAAATGTTTCTAATTGTACGATAACACTCTGTAACCCCAATCCAGCGA
*
56480001 CGGAGACAAGTTAGGGGTGTTACATG
66 CGAAGACAAGTTAGGGGTGTTACATG
* * *
56480027 TTGAATGATATAATGTTTAAATGTTT-TCGATTGTACGATAACACTCTGTAACCCTAATCCAGTG
1 TTGAATGATATAATGTTTAAATGTTTCT-AATTGTACGATAACACTCTGTAACCCCAATCCAGCG
***
56480091 ACGAAGATGGGTTAGGGGTGTTACATG
65 ACGAAGACAAGTTAGGGGTGTTACATG
56480118 GAAAATGAAG
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
90 1 0.01
91 77 0.99
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.34
Consensus pattern (91 bp):
TTGAATGATATAATGTTTAAATGTTTCTAATTGTACGATAACACTCTGTAACCCCAATCCAGCGA
CGAAGACAAGTTAGGGGTGTTACATG
Found at i:56480988 original size:28 final size:26
Alignment explanation
Indices: 56480935--56480993 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 26
56480925 TTTTTGACAA
*
56480935 AAATATCAAATAGAGATTAAATTGTG
1 AAATATCAAATAGAGATTAAAATGTG
* *
56480961 AAATATGCAAATTGAGTGTTAAAATGTG
1 AAATAT-CAAATAGAG-ATTAAAATGTG
56480989 AAATA
1 AAATA
56480994 AATGAAAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 6 0.21
27 8 0.29
28 14 0.50
ACGTcount: A:0.49, C:0.03, G:0.17, T:0.31
Consensus pattern (26 bp):
AAATATCAAATAGAGATTAAAATGTG
Found at i:56481369 original size:34 final size:33
Alignment explanation
Indices: 56481319--56481407 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 33
56481309 AATGTTTTTA
* * *
56481319 AATTTATTTGTGTATGTATACATATATATTGCCG
1 AATTAATTTGTATATGTATA-ATATATATTACCG
56481353 AATTAATTTGTATATG--T-ATATATATTACCG
1 AATTAATTTGTATATGTATAATATATATTACCG
*
56481383 AATTGATTTGTATATGTAT-ATATAT
1 AATTAATTTGTATATGTATAATATAT
56481408 TGTTGAATTG
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 27 0.55
32 8 0.16
34 14 0.29
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.48
Consensus pattern (33 bp):
AATTAATTTGTATATGTATAATATATATTACCG
Found at i:56481416 original size:30 final size:30
Alignment explanation
Indices: 56481340--56481422 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
56481330 GTATGTATAC
*
56481340 ATATATATTGCCGAATTAATTTGTATATGT
1 ATATATATTGCCGAATTGATTTGTATATGT
*
56481370 ATATATATTACCGAATTGATTTGTATATGT
1 ATATATATTGCCGAATTGATTTGTATATGT
**
56481400 ATATATATTGTTGAATTGATTTG
1 ATATATATTGCCGAATTGATTTG
56481423 AGCATTGGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (30 bp):
ATATATATTGCCGAATTGATTTGTATATGT
Found at i:56485518 original size:13 final size:13
Alignment explanation
Indices: 56485501--56485559 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
56485491 CATTGCTGTG
56485501 GAAAAGTGCTTTT
1 GAAAAGTGCTTTT
* * * *
56485514 TAAAAGTACTGTG
1 GAAAAGTGCTTTT
56485527 GAAAAGTGCTTTT
1 GAAAAGTGCTTTT
* *
56485540 GAGAAGTGTTTTT
1 GAAAAGTGCTTTT
56485553 GAAAAGT
1 GAAAAGT
56485560 TTGGTTTAAA
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (13 bp):
GAAAAGTGCTTTT
Found at i:56485546 original size:26 final size:26
Alignment explanation
Indices: 56485496--56485546 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
56485486 TTCTTCATTG
*
56485496 CTGTGGAAAAGTGCTTTTTAAAAGTA
1 CTGTGGAAAAGTGCTTTTGAAAAGTA
*
56485522 CTGTGGAAAAGTGCTTTTGAGAAGT
1 CTGTGGAAAAGTGCTTTTGAAAAGT
56485547 GTTTTTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.33
Consensus pattern (26 bp):
CTGTGGAAAAGTGCTTTTGAAAAGTA
Found at i:56485787 original size:24 final size:24
Alignment explanation
Indices: 56485753--56485798 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
56485743 TATATGAAAT
* *
56485753 ATAAATTTTAAATATTTTTAAACA
1 ATAAATATTAAATATTTATAAACA
*
56485777 ATAAATATTAATTATTTATAAA
1 ATAAATATTAAATATTTATAAA
56485799 ATTTAATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAATATTAAATATTTATAAACA
Found at i:56489047 original size:34 final size:31
Alignment explanation
Indices: 56489009--56489097 Score: 110
Period size: 30 Copynumber: 2.8 Consensus size: 31
56488999 AATGTTTTTA
*
56489009 AATTTATTTGTATATGTAAACATATATATTCCCG
1 AATTTATTTGTATATGT--A-ATATATATGCCCG
*
56489043 AATTTATTTGTATATGT-ATATATATGGCCG
1 AATTTATTTGTATATGTAATATATATGCCCG
*
56489073 AATTGATTTGTATATGT-ATATATAT
1 AATTTATTTGTATATGTAATATATAT
56489098 TGTCGAATTG
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
30 35 0.67
34 17 0.33
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (31 bp):
AATTTATTTGTATATGTAATATATATGCCCG
Found at i:56489066 original size:30 final size:30
Alignment explanation
Indices: 56489030--56489112 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
56489020 ATATGTAAAC
* *
56489030 ATATATATTCCCGAATTTATTTGTATATGT
1 ATATATATTGCCGAATTGATTTGTATATGT
*
56489060 ATATATATGGCCGAATTGATTTGTATATGT
1 ATATATATTGCCGAATTGATTTGTATATGT
*
56489090 ATATATATTGTCGAATTGATTTG
1 ATATATATTGCCGAATTGATTTG
56489113 AGCATTGGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (30 bp):
ATATATATTGCCGAATTGATTTGTATATGT
Found at i:56493010 original size:41 final size:41
Alignment explanation
Indices: 56492965--56493101 Score: 159
Period size: 41 Copynumber: 3.3 Consensus size: 41
56492955 GACTCAGTAC
* * **
56492965 CTAGCAGGCTT-GTTGCCAGTGAAACCATTCAGACTTTACGT
1 CTAGCAGGCTTAATT-CCAGTAAAAAAATTCAGACTTTACGT
56493006 CTAGCAGGCTTAATTCCAGTAAAAAAATTCAGACTTTACGT
1 CTAGCAGGCTTAATTCCAGTAAAAAAATTCAGACTTTACGT
* * * * *
56493047 CTAGCAGGCTTAATGCCGGTAAAATAAATTCGGACTATAAGT
1 CTAGCAGGCTTAATTCCAGTAAAA-AAATTCAGACTTTACGT
*
56493089 CTAGCGGGCTTAA
1 CTAGCAGGCTTAA
56493102 AGCTGGTGTA
Statistics
Matches: 84, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
41 56 0.67
42 28 0.33
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (41 bp):
CTAGCAGGCTTAATTCCAGTAAAAAAATTCAGACTTTACGT
Found at i:56501789 original size:23 final size:22
Alignment explanation
Indices: 56501746--56501789 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
56501736 AAAAAAAGGA
* * *
56501746 TAAAAATAGTTTAAATTGTAAG
1 TAAAAAGAATTTAAATGGTAAG
56501768 TAAAAAGAATTTAAATAGGTAA
1 TAAAAAGAATTTAAAT-GGTAA
56501790 ATACATCAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.32
Consensus pattern (22 bp):
TAAAAAGAATTTAAATGGTAAG
Found at i:56505853 original size:8 final size:8
Alignment explanation
Indices: 56505832--56505860 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
56505822 TATTTTATTT
56505832 TATTTTAA
1 TATTTTAA
56505840 TA-TTTAA
1 TATTTTAA
56505847 TATTTTAA
1 TATTTTAA
56505855 TATTTT
1 TATTTT
56505861 TTTATATAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TATTTTAA
Found at i:56508684 original size:43 final size:43
Alignment explanation
Indices: 56508637--56508755 Score: 141
Period size: 43 Copynumber: 2.8 Consensus size: 43
56508627 TCTTGTATCT
*
56508637 ATGCCAATAGCCCAGCTACGGTCTTATACGAAATCTCAAATCA
1 ATGCCAATAGCCCAGCTACGGTCTTACACGAAATCTCAAATCA
* ** **
56508680 ATGCCAATAGCCTAGCTATTGTCTTACACGAAATCTCAAATTG
1 ATGCCAATAGCCCAGCTACGGTCTTACACGAAATCTCAAATCA
* * *
56508723 ATGTCAATAGCCCAGAC-ATGGTCTTACATGAAA
1 ATGCCAATAGCCCAG-CTACGGTCTTACACGAAA
56508756 CCACACCTCG
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 64 0.98
44 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.26
Consensus pattern (43 bp):
ATGCCAATAGCCCAGCTACGGTCTTACACGAAATCTCAAATCA
Found at i:56508936 original size:31 final size:31
Alignment explanation
Indices: 56508875--56508969 Score: 129
Period size: 31 Copynumber: 3.1 Consensus size: 31
56508865 ATCCAATGCT
* *
56508875 CAAATC-AATTCGGCAATATATATCCATATA
1 CAAATCAAATTCGGCAATGTATAACCATATA
* *
56508905 CAAATCAAATTAGCCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATAACCATATA
*
56508936 CAAATCAAATTCGGCAATGTATAAAACATATA
1 CAAATCAAATTCGGCAATGTAT-AACCATATA
56508968 CA
1 CA
56508970 TTTAAATTCA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
30 6 0.11
31 40 0.71
32 10 0.18
ACGTcount: A:0.47, C:0.19, G:0.07, T:0.26
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATAACCATATA
Found at i:56511504 original size:6 final size:6
Alignment explanation
Indices: 56511487--56511516 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
56511477 CAATAATATG
56511487 AAAATAT AAAATT AAAATT AAAATT AAAAT
1 AAAAT-T AAAATT AAAATT AAAATT AAAAT
56511517 GAAGTTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAAATT
Found at i:56525477 original size:18 final size:18
Alignment explanation
Indices: 56525454--56525489 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
56525444 AAATTACATA
56525454 AAATTATGA-AAATATAAT
1 AAATTAT-ACAAATATAAT
56525472 AAATTATACAAATATAAT
1 AAATTATACAAATATAAT
56525490 GATCAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 16 0.94
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (18 bp):
AAATTATACAAATATAAT
Found at i:56526521 original size:27 final size:28
Alignment explanation
Indices: 56526424--56526523 Score: 75
Period size: 27 Copynumber: 3.6 Consensus size: 28
56526414 GTTTTTTTTC
* * *
56526424 TAATTTTATAA-TATGATATATTTTTCA
1 TAATTTTATAATTTTTATATATTTTTAA
*
56526451 TAATTTTATATATACTTTCTATA-ATTTTCTAT
1 TAATTTTATA-AT--TTT-TATATATTTT-TAA
*
56526483 TAATTTT-T-ATTTTTATATATTTTT-G
1 TAATTTTATAATTTTTATATATTTTTAA
56526508 TAATTTTATAATTTTT
1 TAATTTTATAATTTTT
56526524 TAAACATTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
25 7 0.12
26 6 0.10
27 24 0.41
28 1 0.02
29 2 0.03
31 8 0.14
32 11 0.19
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (28 bp):
TAATTTTATAATTTTTATATATTTTTAA
Found at i:56537500 original size:209 final size:209
Alignment explanation
Indices: 56537140--56537559 Score: 822
Period size: 209 Copynumber: 2.0 Consensus size: 209
56537130 TTCGGAATCG
56537140 TTGTTGGATGCTGAATCAGCGATCAAACTTAAGTACTTAATCTGCTCACGGAAAACAAAACCGTA
1 TTGTTGGATGCTGAATCAGCGATCAAACTTAAGTACTTAATCTGCTCACGGAAAACAAAACCGTA
* *
56537205 CACTGAGTAAAAACTCAGTGGTATTTCTATAATCTGAATTTTTAAAAAATAAAAAATAAAATATG
66 CACTGAGTAAAAACTCAGTGGTATTTCTATAATCCGAATTTTTAAAAAATAAAAAACAAAATATG
56537270 TATAATAAAATGTTAAGCACAATTAAACATTTAAAATCACACAATATTTAATTTTCATCACTTGC
131 TATAATAAAATGTTAAGCACAATTAAACATTTAAAATCACACAATATTTAATTTTCATCACTTGC
56537335 TATATATAATACAT
196 TATATATAATACAT
56537349 TTGTTGGATGCTGAATCAGCGATCAAACTTAAGTACTTAATCTGCTCACGGAAAACAAAACCGTA
1 TTGTTGGATGCTGAATCAGCGATCAAACTTAAGTACTTAATCTGCTCACGGAAAACAAAACCGTA
56537414 CACTGAGTAAAAACTCAGTGGTATTTCTATAATCCGAATTTTTAAAAAATAAAAAACAAAATATG
66 CACTGAGTAAAAACTCAGTGGTATTTCTATAATCCGAATTTTTAAAAAATAAAAAACAAAATATG
56537479 TATAATAAAATGTTAAGCACAATTAAACATTTAAAATCACACAATATTTAATTTTCATCACTTGC
131 TATAATAAAATGTTAAGCACAATTAAACATTTAAAATCACACAATATTTAATTTTCATCACTTGC
56537544 TATATATAATACAT
196 TATATATAATACAT
56537558 TT
1 TT
56537560 CCATAATTTA
Statistics
Matches: 209, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
209 209 1.00
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (209 bp):
TTGTTGGATGCTGAATCAGCGATCAAACTTAAGTACTTAATCTGCTCACGGAAAACAAAACCGTA
CACTGAGTAAAAACTCAGTGGTATTTCTATAATCCGAATTTTTAAAAAATAAAAAACAAAATATG
TATAATAAAATGTTAAGCACAATTAAACATTTAAAATCACACAATATTTAATTTTCATCACTTGC
TATATATAATACAT
Found at i:56537809 original size:22 final size:22
Alignment explanation
Indices: 56537768--56537833 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
56537758 TGCACTAATG
* * *
56537768 AACAGAGAGCACTAAAGTGCTA
1 AACAAAGAGCACTGATGTGCTA
*
56537790 TACAAAGAGCACAT-ATGTGCTA
1 AACAAAGAGCAC-TGATGTGCTA
**
56537812 AACGGAGAGCACTGATGTGCTA
1 AACAAAGAGCACTGATGTGCTA
56537834 GTAATCAGAG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.18
Consensus pattern (22 bp):
AACAAAGAGCACTGATGTGCTA
Found at i:56538842 original size:5 final size:5
Alignment explanation
Indices: 56538832--56538919 Score: 110
Period size: 5 Copynumber: 17.6 Consensus size: 5
56538822 TGTTTATATA
* *
56538832 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -TACT -TATTT ATTAAGT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT A-TAA-T
56538878 -TAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
56538920 TATTAATTAA
Statistics
Matches: 75, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
4 6 0.08
5 66 0.88
7 3 0.04
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (5 bp):
ATAAT
Found at i:56538926 original size:15 final size:14
Alignment explanation
Indices: 56538827--56538926 Score: 105
Period size: 15 Copynumber: 6.8 Consensus size: 14
56538817 TTATTTGTTT
56538827 ATATAA-TAATATA
1 ATATAATTAATATA
56538840 ATATAATATAATATA
1 ATATAAT-TAATATA
*
56538855 ATATAATTACT-TA
1 ATATAATTAATATA
*
56538868 TTTATTAAGTTAATATA
1 -ATA-TAA-TTAATATA
56538885 ATATAATATAATATA
1 ATATAAT-TAATATA
56538900 ATATAATATAATATA
1 ATATAAT-TAATATA
56538915 ATATATATTAAT
1 ATATA-ATTAAT
56538927 TAAAAATATC
Statistics
Matches: 75, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
13 8 0.11
14 6 0.08
15 51 0.68
16 8 0.11
17 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (14 bp):
ATATAATTAATATA
Found at i:56539145 original size:20 final size:20
Alignment explanation
Indices: 56539120--56539159 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
56539110 ACACAACTAG
56539120 CTTCGTAAATATTTATTAAA
1 CTTCGTAAATATTTATTAAA
56539140 CTTCGTAAATATTTATTAAA
1 CTTCGTAAATATTTATTAAA
56539160 AATATTTACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (20 bp):
CTTCGTAAATATTTATTAAA
Found at i:56539624 original size:5 final size:5
Alignment explanation
Indices: 56539599--56539640 Score: 57
Period size: 5 Copynumber: 8.0 Consensus size: 5
56539589 AAACTACTAA
*
56539599 TATAT TATAT ATGATAT TATAC TATAT TATAT TATAT TATAT
1 TATAT TATAT -T-ATAT TATAT TATAT TATAT TATAT TATAT
56539641 AGTAGGAGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 27 0.82
6 2 0.06
7 4 0.12
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (5 bp):
TATAT
Found at i:56539717 original size:18 final size:18
Alignment explanation
Indices: 56539694--56539729 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
56539684 ATAATATATA
*
56539694 ATAATTAATATATTATGT
1 ATAATTAATATAGTATGT
*
56539712 ATAATTATTATAGTATGT
1 ATAATTAATATAGTATGT
56539730 GCTATAGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (18 bp):
ATAATTAATATAGTATGT
Found at i:56541403 original size:19 final size:18
Alignment explanation
Indices: 56541365--56541399 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
56541355 GTTTAATTGA
56541365 TAGATAATTAATGTAAAT
1 TAGATAATTAATGTAAAT
56541383 TAGACTAATTAAT-TAAA
1 TAGA-TAATTAATGTAAA
56541400 ATTAAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (18 bp):
TAGATAATTAATGTAAAT
Found at i:56542300 original size:34 final size:34
Alignment explanation
Indices: 56542222--56542328 Score: 99
Period size: 34 Copynumber: 3.1 Consensus size: 34
56542212 TGACAAAGCG
* * * * *
56542222 TGACACAGTATGTGAACCCTCACGTTACATAGAA
1 TGACAGAGTATGCGAACCCTCATGTTATATAGTA
* * ** *
56542256 TGAAAAAGTATGCGAA-ATTCTATGTTGTATAGTA
1 TGACAGAGTATGCGAACCCTC-ATGTTATATAGTA
*
56542290 TGACAGAGTATGTGAACCCTCATGTTATATAGTA
1 TGACAGAGTATGCGAACCCTCATGTTATATAGTA
56542324 TGACA
1 TGACA
56542329 TAGTGAACTG
Statistics
Matches: 56, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
33 2 0.04
34 52 0.93
35 2 0.04
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.30
Consensus pattern (34 bp):
TGACAGAGTATGCGAACCCTCATGTTATATAGTA
Found at i:56542426 original size:14 final size:13
Alignment explanation
Indices: 56542390--56542422 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
56542380 TGAATATGTG
56542390 CGAACCCTATAGA
1 CGAACCCTATAGA
*
56542403 CTAACCCTATAGA
1 CGAACCCTATAGA
56542416 CGAACCC
1 CGAACCC
56542423 CTATGTGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.36, C:0.36, G:0.12, T:0.15
Consensus pattern (13 bp):
CGAACCCTATAGA
Found at i:56542500 original size:14 final size:15
Alignment explanation
Indices: 56542468--56542500 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
56542458 AAACCGTAGG
*
56542468 TGTGAGAACCCTGTA
1 TGTGAGAACCCTATA
56542483 TGTGAGAACCC-ATA
1 TGTGAGAACCCTATA
56542497 TGTG
1 TGTG
56542501 TGACCCTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (15 bp):
TGTGAGAACCCTATA
Found at i:56542634 original size:22 final size:22
Alignment explanation
Indices: 56542605--56542656 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
56542595 ATGTGATAAC
56542605 ATGCAAACTTTATTTGTTATAT
1 ATGCAAACTTTATTTGTTATAT
*
56542627 ATGTAAACTTTATTTGTTATAT
1 ATGCAAACTTTATTTGTTATAT
56542649 ATGCAAAC
1 ATGCAAAC
56542657 CCTTAAGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.46
Consensus pattern (22 bp):
ATGCAAACTTTATTTGTTATAT
Found at i:56545521 original size:25 final size:25
Alignment explanation
Indices: 56545463--56545521 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
56545453 TGTAAATAGA
* * * *
56545463 AAGCTCCTCCGAGCTGAATAACGGG
1 AAGCTCATGCGAGCTAAATAACAGG
*
56545488 AAGCTCATGCGAGCTAAATATCAGG
1 AAGCTCATGCGAGCTAAATAACAGG
56545513 AAGCTCATG
1 AAGCTCATG
56545522 AAAGTTGTGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (25 bp):
AAGCTCATGCGAGCTAAATAACAGG
Found at i:56548996 original size:10 final size:10
Alignment explanation
Indices: 56548983--56549049 Score: 64
Period size: 10 Copynumber: 6.4 Consensus size: 10
56548973 AAAAACAAAT
56548983 AAAGAAAGAA
1 AAAGAAAGAA
56548993 AAAGAAATAGAA
1 AAAG-AA-AGAA
*
56549005 ACAACAAACGAA
1 A-AAGAAA-GAA
56549017 AAAGAAAGAA
1 AAAGAAAGAA
* *
56549027 ACAGAAAG-G
1 AAAGAAAGAA
56549036 AAAGAAAGAA
1 AAAGAAAGAA
56549046 AAAG
1 AAAG
56549050 GGAAGGAAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
9 7 0.15
10 18 0.39
11 8 0.17
12 11 0.24
13 2 0.04
ACGTcount: A:0.73, C:0.06, G:0.19, T:0.01
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:56549057 original size:20 final size:19
Alignment explanation
Indices: 56549017--56549063 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
56549007 AACAAACGAA
*
56549017 AAAGAAAGAAACAGAAAGG
1 AAAGAAAGAAAAAGAAAGG
*
56549036 AAAGAAAGAAAAAGGGAAGG
1 AAAGAAAGAAAAA-GAAAGG
56549056 AAAGAAAG
1 AAAGAAAG
56549064 GAGAAAGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.68, C:0.02, G:0.30, T:0.00
Consensus pattern (19 bp):
AAAGAAAGAAAAAGAAAGG
Found at i:56551441 original size:9 final size:9
Alignment explanation
Indices: 56551424--56551460 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
56551414 TGAGTTTTCG
56551424 AATTCGAAT
1 AATTCGAAT
*
56551433 AACTCGAAT
1 AATTCGAAT
56551442 AATTCGAAT
1 AATTCGAAT
56551451 AATTCGAAT
1 AATTCGAAT
56551460 A
1 A
56551461 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:56554134 original size:40 final size:40
Alignment explanation
Indices: 56554089--56554223 Score: 107
Period size: 40 Copynumber: 3.4 Consensus size: 40
56554079 GTTTGGAACA
*
56554089 AAAGCGCCACAAAAAATCGAGCATTAGCGGCGATTTATCC
1 AAAGCGCCACAAAAAATAGAGCATTAGCGGCGATTTATCC
* * **
56554129 AAAGCGCCGCTAAAGGTAGAGC-TTCAGCGGCGA-TTATCC
1 AAAGCGCCACAAAAAATAGAGCATT-AGCGGCGATTTATCC
* * * * * *
56554168 GGAAGCGCCGCTAAAAATAG-GAATTAGCGGCGTTTTA-CAT
1 -AAAGCGCCACAAAAAATAGAGCATTAGCGGCGATTTATC-C
*
56554208 AAAACGCCACAAAAAA
1 AAAGCGCCACAAAAAA
56554224 CCTAAGACCA
Statistics
Matches: 75, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
39 29 0.39
40 46 0.61
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (40 bp):
AAAGCGCCACAAAAAATAGAGCATTAGCGGCGATTTATCC
Found at i:56554197 original size:39 final size:39
Alignment explanation
Indices: 56554089--56554204 Score: 110
Period size: 40 Copynumber: 2.9 Consensus size: 39
56554079 GTTTGGAACA
* * *
56554089 AAAGCGCCACAAAAAATCGAGCATTAGCGGCGATTTATCC
1 AAAGCGCCGCTAAAAATAGAG-ATTAGCGGCGATTTATCC
** *
56554129 AAAGCGCCGCTAAAGGTAGAGCTTCAGCGGCGA-TTATCC
1 AAAGCGCCGCTAAAAATAGAGATT-AGCGGCGATTTATCC
* *
56554168 GGAAGCGCCGCTAAAAATAG-GAATTAGCGGCGTTTTA
1 -AAAGCGCCGCTAAAAATAGAG-ATTAGCGGCGATTTA
56554205 CATAAAACGC
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
39 16 0.26
40 45 0.74
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (39 bp):
AAAGCGCCGCTAAAAATAGAGATTAGCGGCGATTTATCC
Found at i:56554319 original size:41 final size:41
Alignment explanation
Indices: 56554262--56554441 Score: 272
Period size: 41 Copynumber: 4.4 Consensus size: 41
56554252 TTTTTTAAAC
*
56554262 CTTTAGCGGCGTTTTTGTGTAAGCGCCGCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTGTGTAGGCGCCGCTAATGCTCGGAT
*
56554303 CTTTAGCGGCGTTTTTGTGTAGGCGTCGCTAATGCTC-GAGT
1 CTTTAGCGGCGTTTTTGTGTAGGCGCCGCTAATGCTCGGA-T
* *
56554344 CTTTAGCGGCGTTTTCGTGTAGGCGCCTCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTGTGTAGGCGCCGCTAATGCTCGGAT
* * *
56554385 CTTTAGCGGCGTTTTTGTCTATGCGCCGCTAATGCTTGGAT
1 CTTTAGCGGCGTTTTTGTGTAGGCGCCGCTAATGCTCGGAT
*
56554426 CTTTATCGGCGTTTTT
1 CTTTAGCGGCGTTTTT
56554442 AACTGAGCGC
Statistics
Matches: 126, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
40 2 0.02
41 122 0.97
42 2 0.02
ACGTcount: A:0.12, C:0.22, G:0.28, T:0.38
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGTGTAGGCGCCGCTAATGCTCGGAT
Found at i:56554452 original size:82 final size:81
Alignment explanation
Indices: 56554262--56554500 Score: 252
Period size: 82 Copynumber: 2.9 Consensus size: 81
56554252 TTTTTTAAAC
* * * *
56554262 CTTTAGCGGCGTTTTTGTGTAAGCGCCGCTAATGCTCGGATCTTTAGCGGCGTTTTTGTGTAGGC
1 CTTTAGCGGCGTTTTCGTGT-AGCGCCACTAATGCTCGGATCTTTAGCGGCGTTTTTGTCTAAGC
*
56554327 GTCGCTAATGCTCGAGT
65 GCCGCTAATGCTCGAGT
* *
56554344 CTTTAGCGGCGTTTTCGTGTAGGCGCCTCTAATGCTCGGATCTTTAGCGGCGTTTTTGTCTATGC
1 CTTTAGCGGCGTTTTCGTGTA-GCGCCACTAATGCTCGGATCTTTAGCGGCGTTTTTGTCTAAGC
*
56554409 GCCGCTAATGCTTG-GAT
65 GCCGCTAATGCTCGAG-T
* * * * * * *
56554426 CTTTATCGGCGTTTTTAAC-TG-AGCGCCACTAATTCTCTTG-TCTTCAGCGGTGTTTGTATCTA
1 CTTTAGCGGCG-TTTT--CGTGTAGCGCCACTAATGCTC-GGATCTTTAGCGGCGTTTTTGTCTA
56554488 AGCGCCGCTAATG
62 AGCGCCGCTAATG
56554501 TATTTACCTT
Statistics
Matches: 136, Mismatches: 15, Indels: 12
0.83 0.09 0.07
Matches are distributed among these distances:
81 2 0.01
82 125 0.92
83 6 0.04
84 2 0.01
85 1 0.01
ACGTcount: A:0.14, C:0.23, G:0.27, T:0.36
Consensus pattern (81 bp):
CTTTAGCGGCGTTTTCGTGTAGCGCCACTAATGCTCGGATCTTTAGCGGCGTTTTTGTCTAAGCG
CCGCTAATGCTCGAGT
Found at i:56554493 original size:123 final size:123
Alignment explanation
Indices: 56554262--56554540 Score: 287
Period size: 123 Copynumber: 2.3 Consensus size: 123
56554252 TTTTTTAAAC
* *
56554262 CTTTAGCGGCGTTTTTGTGTAAGCGCCGCTAATGCTCGGATCTTTAGCGGCGTTTTTGTGTAGGC
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGATCTTTAGCGGCGTTTTTCTGTAGGC
* * * * * * *
56554327 GTCGCTAATGCTCGAGTCTTTAGCGGCGTTTTCGTGTAGGCGCCTCTAATGCTCGGAT
66 GCCACTAATGCTCGAGTCTTCAGCGGCGTTTTCATCTAAGCGCCGCTAATGCTCGGAT
* * *
56554385 CTTTAGCGGCGTTTTTGTCTATGCGCCGCTAATGCTTGGATCTTTATCGGCGTTTTTAACTG-A-
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGATCTTTAGCGGCGTTTTT--CTGTAG
* ** * *** *
56554448 GCGCCACTAATTCTCTTGTCTTCAGCGGTGTTTGT-ATCTAAGCGCCGCTAATG-TATTTAC
64 GCGCCACTAATGCTCGAGTCTTCAGCGGCGTTT-TCATCTAAGCGCCGCTAATGCT-CGGAT
** *
56554508 CTTTAGCGGCGTTTTTACCGAAGCGCCGCTAAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAAT
56554541 AGTAACAAAA
Statistics
Matches: 128, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
122 1 0.01
123 123 0.96
124 2 0.02
125 2 0.02
ACGTcount: A:0.15, C:0.23, G:0.26, T:0.36
Consensus pattern (123 bp):
CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGATCTTTAGCGGCGTTTTTCTGTAGGC
GCCACTAATGCTCGAGTCTTCAGCGGCGTTTTCATCTAAGCGCCGCTAATGCTCGGAT
Found at i:56554974 original size:16 final size:17
Alignment explanation
Indices: 56554953--56554984 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
56554943 TACGGGGTAT
56554953 AGATTTAAGG-TAATTG
1 AGATTTAAGGTTAATTG
56554969 AGATTTAAGGTTAATT
1 AGATTTAAGGTTAATT
56554985 TAGGGGTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.41
Consensus pattern (17 bp):
AGATTTAAGGTTAATTG
Found at i:56559377 original size:23 final size:23
Alignment explanation
Indices: 56559344--56559390 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
56559334 AATATTATAC
56559344 ATAACTGACAACTTACATAACTT
1 ATAACTGACAACTTACATAACTT
*
56559367 ATAACTTACAACTTACATAACTT
1 ATAACTGACAACTTACATAACTT
56559390 A
1 A
56559391 CATTTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.32
Consensus pattern (23 bp):
ATAACTGACAACTTACATAACTT
Found at i:56559386 original size:16 final size:16
Alignment explanation
Indices: 56559341--56559393 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
56559331 ATTAATATTA
*
56559341 TACATAACTGACAACT
1 TACATAACTTACAACT
*
56559357 TACATAACTTATAACT
1 TACATAACTTACAACT
56559373 TAC--AACTTACATAACT
1 TACATAACTTAC--AACT
56559389 TACAT
1 TACAT
56559394 TTTTTTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 6 0.20
16 24 0.80
ACGTcount: A:0.43, C:0.23, G:0.02, T:0.32
Consensus pattern (16 bp):
TACATAACTTACAACT
Found at i:56559421 original size:34 final size:33
Alignment explanation
Indices: 56559379--56560012 Score: 203
Period size: 34 Copynumber: 19.4 Consensus size: 33
56559369 AACTTACAAC
*
56559379 TTACATAACTTACATTTTTTTAATTATTCATAAA
1 TTACATAACTTA-ATTTTTTTAATTATACATAAA
* **
56559413 TTACATAACATACA--TTAAT-ATTATACATAAA
1 TTACATAACTTA-ATTTTTTTAATTATACATAAA
* ** *
56559444 TTACATAACTTAGTTAATTAATATTATACATAAA
1 TTACATAACTTAATTTTTTTA-ATTATACATAAA
* *
56559478 TTACATAACTTAATTTTATGTT-CTTATACATAAC
1 TTACATAACTTAATTTT-T-TTAATTATACATAAA
56559512 TTAC---A-TTAA------T-ATTATACATAAA
1 TTACATAACTTAATTTTTTTAATTATACATAAA
*
56559534 TTACATAACTTAATTTTATGTT-ATTATACATAAC
1 TTACATAACTTAATTTT-T-TTAATTATACATAAA
56559568 TTAC---A-TTAA------T-ATTATACATAAA
1 TTACATAACTTAATTTTTTTAATTATACATAAA
** *
56559590 TTACATAACTTAA-TTAATTAA-TATACATAAG
1 TTACATAACTTAATTTTTTTAATTATACATAAA
** *
56559621 TTACATAACTTACA--TTAAT-ATGATACATAAA
1 TTACATAACTTA-ATTTTTTTAATTATACATAAA
* ** * **
56559652 TTACATAACTTAGTTAATTAATATTATACATATG
1 TTACATAACTTAATTTTTTTA-ATTATACATAAA
* ** *
56559686 TTACATAACTT--TATTAAT-ATGATACATAAA
1 TTACATAACTTAATTTTTTTAATTATACATAAA
* ** * *
56559716 TTACATAACTTAGTTAATTAATATTATACATAAC
1 TTACATAACTTAATTTTTTTA-ATTATACATAAA
** ** *
56559750 TTAC--AACTTACATAACTTACAACTTACAACTTACATAAC
1 TTACATAACTTA-AT-TTTTTTAA-TT---A--TACATAAA
*
56559789 TTACATAACTTACATTTTTTTAATTATTCATAAA
1 TTACATAACTTA-ATTTTTTTAATTATACATAAA
**
56559823 TTACATAACTTAA-TTAGTTAA-TATACATAAA
1 TTACATAACTTAATTTTTTTAATTATACATAAA
*
56559854 TTACATAACTTAATTAATTAATTAATATTATACATAAA
1 TTACATAACTTAATT--TT--TTTA-ATTATACATAAA
* ** *
56559892 TTACATAACTTAGTTAATTAATATTATACATAATTTACAA
1 TTACATAACTTAATTTTTTTA-ATTATAC---A--TA-AA
* * *
56559932 CTTACATAACTTACAATTTTTTAATTATTCGTAAA
1 -TTACATAACTTA-ATTTTTTTAATTATACATAAA
* * * * * *
56559967 TTACATAACTTACTTAATTTTCATAATAAATAAC
1 TTACATAACTTAATT-TTTTTAATTATACATAAA
56560001 TTACATAACTTA
1 TTACATAACTTA
56560013 CAACTTACAT
Statistics
Matches: 447, Mismatches: 89, Indels: 128
0.67 0.13 0.19
Matches are distributed among these distances:
22 31 0.07
25 2 0.00
26 8 0.02
30 29 0.06
31 91 0.20
32 20 0.04
33 4 0.01
34 173 0.39
35 3 0.01
36 6 0.01
37 3 0.01
38 24 0.05
39 16 0.04
40 6 0.01
41 27 0.06
42 4 0.01
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (33 bp):
TTACATAACTTAATTTTTTTAATTATACATAAA
Found at i:56559521 original size:30 final size:30
Alignment explanation
Indices: 56559487--56559582 Score: 85
Period size: 30 Copynumber: 3.3 Consensus size: 30
56559477 ATTACATAAC
*
56559487 TTAATTTTATGTTCTTATACATAACTTACA
1 TTAATATTATGTTCTTATACATAACTTACA
* * * *
56559517 TTAATATTA--TAC--ATAAATTACATA-A
1 TTAATATTATGTTCTTATACATAACTTACA
* *
56559542 CTTAATTTTATGTTATTATACATAACTTACA
1 -TTAATATTATGTTCTTATACATAACTTACA
56559573 TTAATATTAT
1 TTAATATTAT
56559583 ACATAAATTA
Statistics
Matches: 48, Mismatches: 12, Indels: 12
0.67 0.17 0.17
Matches are distributed among these distances:
25 1 0.02
26 17 0.35
28 3 0.06
30 26 0.54
31 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (30 bp):
TTAATATTATGTTCTTATACATAACTTACA
Found at i:56559582 original size:25 final size:25
Alignment explanation
Indices: 56559479--56559582 Score: 77
Period size: 25 Copynumber: 3.9 Consensus size: 25
56559469 ATACATAAAT
* * *
56559479 TACATAACTTAATTTTATGTTCTTA
1 TACATAACTTAATTTAATATTATTA
56559504 TACATAACTTACA-TTAATATTATACATAAA
1 TACATAACTTA-ATTTAATATTAT---T--A
* *
56559534 TTACATAACTTAATTTTATGTTATTA
1 -TACATAACTTAATTTAATATTATTA
56559560 TACATAACTTACA-TTAATATTAT
1 TACATAACTTA-ATTTAATATTAT
56559583 ACATAAATTA
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
25 37 0.59
26 3 0.05
28 2 0.03
30 2 0.03
31 19 0.30
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.46
Consensus pattern (25 bp):
TACATAACTTAATTTAATATTATTA
Found at i:56559583 original size:22 final size:22
Alignment explanation
Indices: 56559555--56559657 Score: 76
Period size: 22 Copynumber: 4.9 Consensus size: 22
56559545 AATTTTATGT
*
56559555 TATTATACATAACTTACATTAA
1 TATTATACATAAATTACATTAA
56559577 TATTATACATAAATTACA-T-A
1 TATTATACATAAATTACATTAA
* *
56559597 -ACT-TA-ATTAATTA-ATATACA
1 TATTATACATAAATTACAT-TA-A
* *
56559617 TAAGT-TACATAACTTACATTAA
1 T-ATTATACATAAATTACATTAA
*
56559639 TATGATACATAAATTACAT
1 TATTATACATAAATTACAT
56559658 AACTTAGTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
16 1 0.02
17 7 0.11
18 3 0.05
19 2 0.03
20 2 0.03
21 2 0.03
22 36 0.57
23 8 0.13
24 2 0.03
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.39
Consensus pattern (22 bp):
TATTATACATAAATTACATTAA
Found at i:56559690 original size:56 final size:56
Alignment explanation
Indices: 56559460--56559754 Score: 328
Period size: 56 Copynumber: 5.0 Consensus size: 56
56559450 AACTTAGTTA
* *
56559460 ATTAATATTATACATAAATTACATAACTTAATT--TTATGTTCTTATACATAACTTAC
1 ATTAATATTATACATAAATTACATAACTTAATTAATTA--ATATTATACATAACTTAC
*
56559516 ATTAATATTATACATAAATTACATAACTTAATT--TTATGTTATTATACATAACTTAC
1 ATTAATATTATACATAAATTACATAACTTAATTAATTA--ATATTATACATAACTTAC
56559572 ATTAATATTATACATAAATTACATAACTTAATTAATTAATATACATAAGTTACATAACTTAC
1 ATTAATATTATACATAAATTACATAACTTAATTAATTAATAT---T-A--TACATAACTTAC
* * *
56559634 ATTAATATGATACATAAATTACATAACTTAGTTAATTAATATTATACATATGTTACATAAC
1 ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATA----AC-TTAC
* *
56559695 TTTATTAATATGATACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTAC
1 ---ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
56559754 A
1 A
56559755 ACTTACATAA
Statistics
Matches: 217, Mismatches: 6, Indels: 32
0.85 0.02 0.13
Matches are distributed among these distances:
56 98 0.45
58 4 0.02
59 5 0.02
60 5 0.02
61 3 0.01
62 52 0.24
64 50 0.23
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.42
Consensus pattern (56 bp):
ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
Found at i:56559725 original size:64 final size:65
Alignment explanation
Indices: 56559560--56559762 Score: 319
Period size: 64 Copynumber: 3.2 Consensus size: 65
56559550 TATGTTATTA
* *
56559560 TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATT-A-A-TATACATAAGT
1 TACATAACTTACATTAATATGATACATAAATTACATAACTTAGTTAATTAATATTATACATAAGT
*
56559622 TACATAACTTACATTAATATGATACATAAATTACATAACTTAGTTAATTAATATTATACATATGT
1 TACATAACTTACATTAATATGATACATAAATTACATAACTTAGTTAATTAATATTATACATAAGT
* *
56559687 TACATAACTT-TATTAATATGATACATAAATTACATAACTTAGTTAATTAATATTATACATAACT
1 TACATAACTTACATTAATATGATACATAAATTACATAACTTAGTTAATTAATATTATACATAAGT
56559751 TAC--AACTTACAT
1 TACATAACTTACAT
56559763 AACTTACAAC
Statistics
Matches: 130, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
62 52 0.40
63 3 0.02
64 55 0.42
65 20 0.15
ACGTcount: A:0.46, C:0.12, G:0.03, T:0.39
Consensus pattern (65 bp):
TACATAACTTACATTAATATGATACATAAATTACATAACTTAGTTAATTAATATTATACATAAGT
Found at i:56559759 original size:7 final size:7
Alignment explanation
Indices: 56559747--56559784 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
56559737 TATTATACAT
56559747 AACTTAC
1 AACTTAC
56559754 AACTTAC
1 AACTTAC
56559761 ATAACTTAC
1 --AACTTAC
56559770 AACTTAC
1 AACTTAC
56559777 AACTTAC
1 AACTTAC
56559784 A
1 A
56559785 TAACTTACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 22 0.76
9 7 0.24
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (7 bp):
AACTTAC
Found at i:56559763 original size:16 final size:16
Alignment explanation
Indices: 56559742--56559802 Score: 90
Period size: 16 Copynumber: 3.8 Consensus size: 16
56559732 ATTAATATTA
56559742 TACATAACTTACAACT
1 TACATAACTTACAACT
56559758 TACATAACTTACAACT
1 TACATAACTTACAACT
56559774 TAC--AACTTACATAACT
1 TACATAACTTAC--AACT
56559790 TACATAACTTACA
1 TACATAACTTACA
56559803 TTTTTTTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 7 0.17
16 27 0.66
18 7 0.17
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (16 bp):
TACATAACTTACAACT
Found at i:56559766 original size:9 final size:9
Alignment explanation
Indices: 56559708--56560118 Score: 95
Period size: 9 Copynumber: 48.3 Consensus size: 9
56559698 ATTAATATGA
*
56559708 TACATAAAT
1 TACATAACT
56559717 TACATAACT
1 TACATAACT
**
56559726 TAGTTAA-T
1 TACATAACT
*
56559734 TA-AT-ATT
1 TACATAACT
56559741 ATACATAACT
1 -TACATAACT
56559751 TAC--AACT
1 TACATAACT
56559758 TACATAACT
1 TACATAACT
56559767 TAC--AACT
1 TACATAACT
56559774 TAC--AACT
1 TACATAACT
56559781 TACATAACT
1 TACATAACT
56559790 TACATAACT
1 TACATAACT
***
56559799 TACATTTTTT
1 TACA-TAACT
*
56559809 TA-ATTA-T
1 TACATAACT
*
56559816 T-CATAAAT
1 TACATAACT
56559824 TACATAACT
1 TACATAACT
* *
56559833 TA-ATTAGT
1 TACATAACT
56559841 TA-AT-A--
1 TACATAACT
*
56559846 TACATAAAT
1 TACATAACT
56559855 TACATAACT
1 TACATAACT
56559864 TA-ATTAA-T
1 TACA-TAACT
*
56559872 TA-ATTAATATT
1 TACA-T-A-ACT
*
56559883 ATACATAAAT
1 -TACATAACT
56559893 TACATAACT
1 TACATAACT
**
56559902 TAGTTAA-T
1 TACATAACT
*
56559910 TA-AT-ATT
1 TACATAACT
*
56559917 ATACATAATT
1 -TACATAACT
56559927 TAC--AACT
1 TACATAACT
56559934 TACATAACT
1 TACATAACT
***
56559943 TACAATTTTT
1 TAC-ATAACT
*
56559953 TA-ATTA-T
1 TACATAACT
* *
56559960 T-CGTAAAT
1 TACATAACT
56559968 TACATAACT
1 TACATAACT
* *
56559977 TACTTAATT
1 TACATAACT
*
56559986 TTCATAA--
1 TACATAACT
*
56559993 TAAATAACT
1 TACATAACT
56560002 TACATAACT
1 TACATAACT
56560011 TAC--AACT
1 TACATAACT
56560018 TACATAACT
1 TACATAACT
* ** *
56560027 TATACGACA
1 TACATAACT
56560036 TACATAACT
1 TACATAACT
* *
56560045 TACATAGCA
1 TACATAACT
*
56560054 TA-ATTTGACT
1 TACA--TAACT
*
56560064 AATACACAACT
1 --TACATAACT
*
56560075 TACATAATT
1 TACATAACT
*
56560084 TTCATAA--
1 TACATAACT
*
56560091 TAAATAACT
1 TACATAACT
56560100 TACATAA--
1 TACATAACT
56560107 TACATAACT
1 TACATAACT
56560116 TAC
1 TAC
56560119 GTAGCTTAGT
Statistics
Matches: 301, Mismatches: 56, Indels: 90
0.67 0.13 0.20
Matches are distributed among these distances:
5 2 0.01
6 4 0.01
7 66 0.22
8 35 0.12
9 163 0.54
10 19 0.06
11 5 0.02
12 5 0.02
13 2 0.01
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.39
Consensus pattern (9 bp):
TACATAACT
Found at i:56559777 original size:23 final size:24
Alignment explanation
Indices: 56559742--56559802 Score: 97
Period size: 23 Copynumber: 2.5 Consensus size: 24
56559732 ATTAATATTA
56559742 TACATAACTTACAACTTACATAACT
1 TACA-AACTTACAACTTACATAACT
56559767 TAC-AACTTACAACTTACATAACT
1 TACAAACTTACAACTTACATAACT
56559790 TACATAACTTACA
1 TACA-AACTTACA
56559803 TTTTTTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 23 0.68
25 11 0.32
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (24 bp):
TACAAACTTACAACTTACATAACT
Found at i:56560017 original size:16 final size:16
Alignment explanation
Indices: 56559998--56560048 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
56559988 CATAATAAAT
56559998 AACTTACATAACTTAC
1 AACTTACATAACTTAC
56560014 AACTTACATAACTTATAC
1 AACTTACATAAC-T-TAC
* *
56560032 GACATACATAACTTAC
1 AACTTACATAACTTAC
56560048 A
1 A
56560049 TAGCATAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 15 0.50
17 2 0.07
18 13 0.43
ACGTcount: A:0.45, C:0.24, G:0.02, T:0.29
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:56560097 original size:16 final size:16
Alignment explanation
Indices: 56560086--56560118 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
56560076 ACATAATTTT
56560086 CATAATAAATAACTTA
1 CATAATAAATAACTTA
*
56560102 CATAATACATAACTTA
1 CATAATAAATAACTTA
56560118 C
1 C
56560119 GTAGCTTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (16 bp):
CATAATAAATAACTTA
Found at i:56565622 original size:66 final size:65
Alignment explanation
Indices: 56565527--56565697 Score: 209
Period size: 66 Copynumber: 2.6 Consensus size: 65
56565517 TGACAAATTA
* * * *
56565527 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
56565591 G
65 G
* *
56565592 CTACAACTGAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
56565657 G
65 G
* * * * *
56565658 CAGCAGCTTAAAGTAGATGCGGCAGCAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
56565698 CGGCAGCGAG
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 2 0.02
66 85 0.93
67 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.28, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:56565719 original size:21 final size:21
Alignment explanation
Indices: 56565676--56565719 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
56565666 TAAAGTAGAT
*
56565676 GCGGCAGCAAGAGAAGCAGAG
1 GCGGCAGCAAGAGAAGCACAG
* *
56565697 GCGGCAGCGAGAGAAGTACAG
1 GCGGCAGCAAGAGAAGCACAG
56565718 GC
1 GC
56565720 TAAAGCGAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.43, T:0.02
Consensus pattern (21 bp):
GCGGCAGCAAGAGAAGCACAG
Found at i:56565740 original size:21 final size:21
Alignment explanation
Indices: 56565688--56565759 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
56565678 GGCAGCAAGA
* * *
56565688 GAAGCAGAGGCGGCAGCGAGA
1 GAAGCAGAGGCTGAAGCGAGG
* * *
56565709 GAAGTACAGGCTAAAGCGAGG
1 GAAGCAGAGGCTGAAGCGAGG
*
56565730 GAAGCAGAGGCTGTAGCGAGG
1 GAAGCAGAGGCTGAAGCGAGG
56565751 GAAGCAGAG
1 GAAGCAGAG
56565760 CAGCGTCAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.35, C:0.15, G:0.44, T:0.06
Consensus pattern (21 bp):
GAAGCAGAGGCTGAAGCGAGG
Found at i:56566164 original size:43 final size:42
Alignment explanation
Indices: 56566117--56566421 Score: 177
Period size: 43 Copynumber: 7.1 Consensus size: 42
56566107 GGCCTTTAGT
* * *
56566117 GGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGGCTTTGGC
1 GGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGTCTTT-GC
** * ** *
56566160 GGCGTTTGTGGAAAAAGCGCCACTAAAGATCATAGTCTTTAAC
1 GGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGTCTTT-GC
*
56566203 GGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGTCTATTGC
1 GGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGTCT-TTGC
* ** * ** * *
56566246 GGCGTTTGAGGGGAAAGCGCCGCTAAAGACCCTGATCTTTAGT
1 GGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGTCTTT-GC
* * * * *
56566289 GGCGTTTTTGG-GAGAAGTGCCGCTAAAGATAAGGATCTTTAGC
1 GGCGTTTGTGGTCA-AAGCGCCGCTAAAGATCAGGGTCTTT-GC
** * * **
56566332 GGCGTTTAAGAG--AGAAGCGTCGCTAAAGACCATTGTCTTTAGC
1 GGCGTTTGTG-GTCA-AAGCGCCGCTAAAGATCAGGGTCTTT-GC
* * ** *
56566375 GGCGCTTCT-CCCAAAAACGCCGCTAAAGATCAGGGTCTTTAGC
1 GGCGTTTGTGGTC-AAAGCGCCGCTAAAGATCAGGGTCTTT-GC
56566418 GGCG
1 GGCG
56566422 CTTCCACTAA
Statistics
Matches: 203, Mismatches: 52, Indels: 14
0.75 0.19 0.05
Matches are distributed among these distances:
42 4 0.02
43 195 0.96
44 4 0.02
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (42 bp):
GGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGTCTTTGC
Found at i:56566230 original size:86 final size:85
Alignment explanation
Indices: 56566117--56566421 Score: 278
Period size: 86 Copynumber: 3.5 Consensus size: 85
56566107 GGCCTTTAGT
* *
56566117 GGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGGCTTTGGCGGCGTTTGTGGAAAAAGCGCCA
1 GGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTT-GCGGCGTTTGAGGAAAAAGCGCCA
*
56566182 CTAAAGATCAT-AGTCTTTAAC
65 CTAAAGACCATGA-TCTTTAAC
* ** *
56566203 GGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGTCTATTGCGGCGTTTGAGGGGAAAGCGCCG
1 GGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCT-TTGCGGCGTTTGAGGAAAAAGCGCCA
* **
56566268 CTAAAGACCCTGATCTTTAGT
65 CTAAAGACCATGATCTTTAAC
* * * * * *
56566289 GGCGTTTTTGG-GAGAAGTGCCGCTAAAGATAAGGATCTTTAGCGGCGTTT-AAGAGAGAAGCGT
1 GGCGTTTTTGGTCA-AAGCGCCGCTAAAGATAAGGGTCTTT-GCGGCGTTTGAGGA-AAAAGCGC
* *
56566352 CGCTAAAGACCATTG-TCTTTAGC
63 CACTAAAGACCA-TGATCTTTAAC
* * ** * *
56566375 GGCGCTTCT-CCCAAAAACGCCGCTAAAGATCAGGGTCTTTAGCGGCG
1 GGCGTTTTTGGTC-AAAGCGCCGCTAAAGATAAGGGTCTTT-GCGGCG
56566422 CTTCCACTAA
Statistics
Matches: 182, Mismatches: 29, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
85 5 0.03
86 171 0.94
87 6 0.03
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (85 bp):
GGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTCTTTGCGGCGTTTGAGGAAAAAGCGCCAC
TAAAGACCATGATCTTTAAC
Found at i:56566422 original size:43 final size:42
Alignment explanation
Indices: 56566352--56566444 Score: 123
Period size: 43 Copynumber: 2.2 Consensus size: 42
56566342 AGAGAAGCGT
** *
56566352 CGCTAAAGACCATTGTCTTTAGCGGCGCTTCTCCCAAAAACGC
1 CGCTAAAGACCAGGGTCTTTAGCGGCGCTTC-CACAAAAACGC
* * *
56566395 CGCTAAAGATCAGGGTCTTTAGCGGCGCTTCCACTAAAGCGC
1 CGCTAAAGACCAGGGTCTTTAGCGGCGCTTCCACAAAAACGC
56566437 CGCTAAAG
1 CGCTAAAG
56566445 GTCTTAGTCT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 16 0.36
43 28 0.64
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.22
Consensus pattern (42 bp):
CGCTAAAGACCAGGGTCTTTAGCGGCGCTTCCACAAAAACGC
Found at i:56566455 original size:42 final size:43
Alignment explanation
Indices: 56566352--56566463 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 43
56566342 AGAGAAGCGT
* ** *
56566352 CGCTAAAGACCATTGTCTTTAGCGGCGCTTCTCCCAAAAACGC
1 CGCTAAAGATCAGAGTCTTTAGCGGCGCTTCTCACAAAAACGC
* * *
56566395 CGCTAAAGATCAGGGTCTTTAGCGGCGCTTC-CACTAAAGCGC
1 CGCTAAAGATCAGAGTCTTTAGCGGCGCTTCTCACAAAAACGC
* ** *
56566437 CGCTAAAGGTCTTAGTCTTCAGCGGCG
1 CGCTAAAGATCAGAGTCTTTAGCGGCG
56566464 TTTGTGCAAG
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
42 30 0.52
43 28 0.48
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.23
Consensus pattern (43 bp):
CGCTAAAGATCAGAGTCTTTAGCGGCGCTTCTCACAAAAACGC
Found at i:56566587 original size:22 final size:22
Alignment explanation
Indices: 56566559--56566601 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
56566549 CTGCGGCGCT
*
56566559 AAAAAGCACCGCTAAAGGCCTA
1 AAAAAGCACCGCTAAAAGCCTA
*
56566581 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCACCGCTAAAAGCCT
56566602 GTTTTAGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAAGCACCGCTAAAAGCCTA
Found at i:56578260 original size:19 final size:17
Alignment explanation
Indices: 56578230--56578283 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 17
56578220 GTTTTAGGGT
*
56578230 TTTTAATTTTTTAAATAG
1 TTTTAAATTTTTAAA-AG
56578248 TTTTAAATATTTTATAAAG
1 TTTTAAAT-TTTTA-AAAG
*
56578267 TATATAAATTTTTAAAA
1 T-TTTAAATTTTTAAAA
56578284 CATGTTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 10 0.32
19 13 0.42
20 8 0.26
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTTAAATTTTTAAAAG
Found at i:56580815 original size:108 final size:109
Alignment explanation
Indices: 56580619--56580841 Score: 349
Period size: 108 Copynumber: 2.1 Consensus size: 109
56580609 TGGGAACATG
* *
56580619 TTTTTTTATACACATGGAATCAAACTAATCTCTAAATATAAGTAAAGAATTATATTTAAATGCTT
1 TTTTTTTATACACATGGAATCAAACCAATCTCTAAATACAAGTAAAGAATTATATTTAAATGCTT
*
56580684 TTATATCAAAATTCGACA-CTTTTTCCTAATTTCGCATCTAAAT
66 TTATACCAAAATTCGACATCTTTTTCCTAATTTCGCATCTAAAT
*
56580727 TTTTTTTATACACATGGAATCAAACCAATCTTTAAATACAAGTAAAGAATTATATTTAAATGCTT
1 TTTTTTTATACACATGGAATCAAACCAATCTCTAAATACAAGTAAAGAATTATATTTAAATGCTT
** * * * *
56580792 TTATACCTGAATTCGATATTTTTTTCTTAATTTCGTATCTAAAT
66 TTATACCAAAATTCGACATCTTTTTCCTAATTTCGCATCTAAAT
56580836 TTTTTT
1 TTTTTT
56580842 GGGTCTAATT
Statistics
Matches: 104, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
108 76 0.73
109 28 0.27
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (109 bp):
TTTTTTTATACACATGGAATCAAACCAATCTCTAAATACAAGTAAAGAATTATATTTAAATGCTT
TTATACCAAAATTCGACATCTTTTTCCTAATTTCGCATCTAAAT
Found at i:56581440 original size:3 final size:3
Alignment explanation
Indices: 56581432--56581477 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
56581422 AAGGGCCTTA
56581432 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
56581478 TAGATAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:56582004 original size:27 final size:26
Alignment explanation
Indices: 56581974--56582033 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
56581964 TATGGTGTTT
56581974 TAAAAATTGAAT-TTGAATAGTATTTAA
1 TAAAAATT-AATATTG-ATAGTATTTAA
* *
56582001 TAAAAAATATTATTGATAGTATTTAA
1 TAAAAATTAATATTGATAGTATTTAA
56582027 TAAAAAT
1 TAAAAAT
56582034 AAATTAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (26 bp):
TAAAAATTAATATTGATAGTATTTAA
Found at i:56582045 original size:26 final size:26
Alignment explanation
Indices: 56581989--56582045 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
56581979 ATTGAATTTG
* *
56581989 AATAGTATTTAATAAAAAATATTATT
1 AATAGTATTTAATAAAAAAAATTATA
*
56582015 GATAGTATTTAATAAAAATAAATTA-A
1 AATAGTATTTAATAAAAA-AAATTATA
56582041 AATAG
1 AATAG
56582046 ATAGTTGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (26 bp):
AATAGTATTTAATAAAAAAAATTATA
Found at i:56582369 original size:17 final size:16
Alignment explanation
Indices: 56582312--56582352 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
56582302 TAAAAGTCCA
56582312 AAAAATATATATTTAAT
1 AAAAATATAT-TTTAAT
*
56582329 AAAAAGTATATTTTATT
1 AAAAA-TATATTTTAAT
56582346 AAAAATA
1 AAAAATA
56582353 AAAATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 15 0.68
18 5 0.23
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
AAAAATATATTTTAAT
Found at i:56583474 original size:108 final size:107
Alignment explanation
Indices: 56583248--56583576 Score: 466
Period size: 108 Copynumber: 3.1 Consensus size: 107
56583238 GGCATGGATT
* * *
56583248 AAAATTCAAGAGGATATTTGGCTATTTGGTTAAACGAG--AAATCGAAACCCAGCACATTAGGGC
1 AAAATTTAAAAGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGC
* * *
56583311 ACG-TTCCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGA
66 ACGTTTTCTCGAA-TTCCAAACGCAAAATATTGCCTTACTTT-A
** * *
56583354 AATTTTTGAAAGGATATTTGGCTATTTGGTTGAATGAGAAAAATCGAAACCCAGCACATTAGGGC
1 AAAATTTAAAAGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGC
* *
56583419 ACGTTTTCTCAAATCTCCAAACGCAAAATATTACCTTACTTTA
66 ACGTTTTCTCGAAT-TCCAAACGCAAAATATTGCCTTACTTTA
* * *
56583462 AAAATTTAAAAGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCAGATTAGAGC
1 AAAATTTAAAAGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGC
56583527 ACGTTTTCTCGAATTCCCAAACGCAAAATATTGCCTTACTTTA
66 ACGTTTTCTCGAATT-CCAAACGCAAAATATTGCCTTACTTTA
56583570 AAAATTT
1 AAAATTT
56583577 TTCCTTTTTG
Statistics
Matches: 197, Mismatches: 21, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
106 31 0.16
107 1 0.01
108 134 0.68
109 31 0.16
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (107 bp):
AAAATTTAAAAGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGC
ACGTTTTCTCGAATTCCAAACGCAAAATATTGCCTTACTTTA
Found at i:56583717 original size:4 final size:4
Alignment explanation
Indices: 56583708--56583784 Score: 59
Period size: 4 Copynumber: 18.8 Consensus size: 4
56583698 ATACAATAAC
* ** * *
56583708 AAAT AAAT AAAT AAAT AAACT AAA- ACAT AAA- AAAT GGAC ATAT AAAT
1 AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT AAAT
56583755 AAAT AAAT AAAT AAAT GAACAT AAAGT AAA
1 AAAT AAAT AAAT AAAT -AA-AT AAA-T AAA
56583785 ATAATAATAA
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
3 5 0.09
4 39 0.67
5 12 0.21
6 2 0.03
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:56583823 original size:23 final size:21
Alignment explanation
Indices: 56583772--56583824 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
56583762 TAAATAAATG
* *
56583772 AACATAAAGTAAAATAATAAT
1 AACATAAAGGAAAATAATAAA
56583793 AACAATAAAGGAAAATAGATAAA
1 AAC-ATAAAGGAAAATA-ATAAA
56583816 AATCATAAA
1 AA-CATAAA
56583825 ATATGAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 3 0.11
22 12 0.44
23 11 0.41
24 1 0.04
ACGTcount: A:0.68, C:0.06, G:0.08, T:0.19
Consensus pattern (21 bp):
AACATAAAGGAAAATAATAAA
Found at i:56583927 original size:16 final size:16
Alignment explanation
Indices: 56583890--56583928 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
56583880 AATTATAAAA
56583890 ATATATAAAAACATGT
1 ATATATAAAAACATGT
* **
56583906 ACATATAAAAGTATGT
1 ATATATAAAAACATGT
56583922 ATATATA
1 ATATATA
56583929 TGTATACTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (16 bp):
ATATATAAAAACATGT
Done.