Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 159 of 214
Found at i:47171081 original size:251 final size:251
Alignment explanation
Indices: 47170582--47171229 Score: 897
Period size: 251 Copynumber: 2.6 Consensus size: 251
47170572 TTTTGTTTTT
* * * *
47170582 TTTTTCTTTAGTAGTT-TCAGAAAAATTAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCGAA
1 TTTTTCTATAGTAGTTCT-TGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAA
* *
47170646 AACGCTTCAAGTAAGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTCTTT
65 AACGCTTCAAGTAAGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGGACGCTCTTT
*
47170711 TTCTACAGTTGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAAAGC
130 TTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAAAGC
* * ** *
47170776 TTCAAGCAAGATGCATTGTCAGCAAAATTACTGAAAAATGCTCCCATGTAGACGCTC
195 TTCAAACAAGATGCACTGTCAGCAAAATTACTGAAAAATGCTCCCACATAGACGCCC
* * ** * *
47170833 TTTTTCTATAGTAGTTCTTGAAAAAATGATTTTGAAAAGACAATTCTAAAAAAATAGTATCAAAA
1 TTTTTCTATAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
* * * * * *
47170898 ACGCTTCAAGCAAGATGCACTGTCAGCAAAGTTACTGAAAAATGCTCCCACATGGACGGTTTTTT
66 ACGCTTCAAGTAAGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGGACGCTCTTTT
* *
47170963 TCTACAGTAGTTCTTGAAAAAATTATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAAACGC
131 TCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAAA-GC
* * * *
47171028 TTCAAACAGGATGCACTGTTAGCAAAATTATTGAAAAA-GCTCCTACATAGACGCCC
195 TTCAAACAAGATGCACTGTCAGCAAAATTACTGAAAAATGCTCCCACATAGACGCCC
* * * * *
47171084 TTTTTGTACAATAGTTCCTGAAAAAATAATATTT-AGAAGACGGTTCTGAAAAAATAGTGTAAAA
1 TTTTTCTATAGTAGTTCTTGAAAAAATAAT-TTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAA
** * *
47171148 AATACTTCAAGTAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGGACACTCTTT
65 AACGCTTCAAGTAAGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGGACGCTCTTT
47171213 TTCTACAGTAGTTCCTG
130 TTCTACAGTAGTTCCTG
47171230 CTTGGCCTTA
Statistics
Matches: 342, Mismatches: 52, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
251 303 0.89
252 39 0.11
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (251 bp):
TTTTTCTATAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
ACGCTTCAAGTAAGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGGACGCTCTTTT
TCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAAAGCT
TCAAACAAGATGCACTGTCAGCAAAATTACTGAAAAATGCTCCCACATAGACGCCC
Found at i:47177031 original size:16 final size:16
Alignment explanation
Indices: 47177006--47177036 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47176996 ATTTGATGTG
*
47177006 TATCTCTTTTTTTAAA
1 TATCTATTTTTTTAAA
47177022 TATCTATTTTTTTAA
1 TATCTATTTTTTTAA
47177037 TATTTTAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (16 bp):
TATCTATTTTTTTAAA
Found at i:47178981 original size:25 final size:24
Alignment explanation
Indices: 47178953--47178999 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
47178943 CAAATATTTA
47178953 ATAGTTATAT-TTAAATATTTAAAAT
1 ATAGTTATATATT--ATATTTAAAAT
*
47178978 ATAGTTTTATATTATATTTAAA
1 ATAGTTATATATTATATTTAAA
47179000 TTTTATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 9 0.45
26 2 0.10
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
ATAGTTATATATTATATTTAAAAT
Found at i:47179295 original size:13 final size:13
Alignment explanation
Indices: 47179279--47179357 Score: 56
Period size: 13 Copynumber: 6.2 Consensus size: 13
47179269 TTATTTTTCC
47179279 AAAGCACTTTTTA
1 AAAGCACTTTTTA
*
47179292 AAAG--CTTTTCA
1 AAAGCACTTTTTA
** **
47179303 AAAATACTTTTCC
1 AAAGCACTTTTTA
*
47179316 AAATCACTTTTCT-
1 AAAGCACTTTT-TA
47179329 AAAGCACTTTTTA
1 AAAGCACTTTTTA
* *
47179342 AAAACACTTCTTA
1 AAAGCACTTTTTA
47179355 AAA
1 AAA
47179358 ACAATGCTAA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
11 9 0.17
12 1 0.02
13 43 0.81
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.37
Consensus pattern (13 bp):
AAAGCACTTTTTA
Found at i:47179305 original size:50 final size:50
Alignment explanation
Indices: 47179248--47179344 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 50
47179238 AAACCAAATA
* * *
47179248 TTTCAAAAGTACTTATCAAAATTATTTTTCCAAAGCACTTTTTAAAAGCT
1 TTTCAAAAATACTTATCAAAATCACTTTTCCAAAGCACTTTTTAAAAGCT
* * *
47179298 TTTCAAAAATACTTTTCCAAATCACTTTTCTAAAGCACTTTTTAAAA
1 TTTCAAAAATACTTATCAAAATCACTTTTCCAAAGCACTTTTTAAAA
47179345 ACACTTCTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (50 bp):
TTTCAAAAATACTTATCAAAATCACTTTTCCAAAGCACTTTTTAAAAGCT
Found at i:47184958 original size:16 final size:16
Alignment explanation
Indices: 47184909--47184961 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
47184899 AAAGAAATTT
*
47184909 AAAAATAAAATATTCA
1 AAAAATAATATATTCA
* *
47184925 AAAAATAATA-AGT-G
1 AAAAATAATATATTCA
*
47184939 AAAAATGATATATTCA
1 AAAAATAATATATTCA
47184955 AAAAATA
1 AAAAATA
47184962 CTATGTCAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
14 9 0.32
15 4 0.14
16 15 0.54
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.25
Consensus pattern (16 bp):
AAAAATAATATATTCA
Found at i:47188061 original size:38 final size:39
Alignment explanation
Indices: 47188006--47188143 Score: 154
Period size: 38 Copynumber: 3.4 Consensus size: 39
47187996 GGCTACCACT
* *
47188006 TATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGC
1 TATCACTTTATCACTTGATCAGATAAGTGTAGTTAAAGC
*
47188045 TATCAC-TTATCACTTGATGAGATAAGTGTAGTTAAAGCTACCAC
1 TATCACTTTATCACTTGATCAGATAAGTGTAGTTAAAG------C
*
47188089 TTATCACTTTGTCACTTGATCAGATAAGTGTAGTTAAAGC
1 -TATCACTTTATCACTTGATCAGATAAGTGTAGTTAAAGC
*
47188129 TACCAC-TTATCACTT
1 TATCACTTTATCACTT
47188144 TGTCACTTGA
Statistics
Matches: 84, Mismatches: 7, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
38 36 0.43
39 11 0.13
40 1 0.01
44 1 0.01
45 6 0.07
46 29 0.35
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (39 bp):
TATCACTTTATCACTTGATCAGATAAGTGTAGTTAAAGC
Found at i:47188096 original size:84 final size:83
Alignment explanation
Indices: 47187963--47188143 Score: 283
Period size: 84 Copynumber: 2.2 Consensus size: 83
47187953 TACGATCTCT
* * *
47187963 TATCACTTGTC-CCTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTTGATCA
1 TATCACTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTTGATCA
47188027 GATAAGTGTAGCTAAAGC
66 GATAAGTGTAGCTAAAGC
* *
47188045 TATCACTTATCACTTGATGAGATAAGTGTAGTTAAAGCTACCACTTATCACTTTGTCACTTGATC
1 TATCACTTATCACTTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTGTCACTTGATC
*
47188110 AGATAAGTGTAGTTAAAGC
65 AGATAAGTGTAGCTAAAGC
*
47188129 TACCACTTATCACTT
1 TATCACTTATCACTT
47188144 TGTCACTTGA
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
82 10 0.11
83 18 0.20
84 62 0.69
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (83 bp):
TATCACTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTTGATCA
GATAAGTGTAGCTAAAGC
Found at i:47188104 original size:46 final size:46
Alignment explanation
Indices: 47187961--47188158 Score: 274
Period size: 46 Copynumber: 4.5 Consensus size: 46
47187951 CATACGATCT
* *
47187961 CTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
*
47188004 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
*
47188050 CTTATCAC-TTG--A--TG---AGATAAGTGTAGTTAAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
*
47188088 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGTTAAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
47188134 CTTATCACTTTGTCACTTGATCAGA
1 CTTATCACTTTGTCACTTGATCAGA
47188159 AGTACTCAAA
Statistics
Matches: 139, Mismatches: 5, Indels: 19
0.85 0.03 0.12
Matches are distributed among these distances:
38 30 0.22
39 3 0.02
41 3 0.02
43 11 0.08
44 5 0.04
45 23 0.17
46 64 0.46
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
Found at i:47190313 original size:13 final size:13
Alignment explanation
Indices: 47190295--47190324 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
47190285 AAAAAATTCT
47190295 AAAATTATGATAA
1 AAAATTATGATAA
*
47190308 AAAATTATTATAA
1 AAAATTATGATAA
47190321 AAAA
1 AAAA
47190325 CTAATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
AAAATTATGATAA
Found at i:47190783 original size:16 final size:16
Alignment explanation
Indices: 47190762--47190792 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47190752 TAGTGGTTTA
47190762 ATATAAATAAATATAG
1 ATATAAATAAATATAG
*
47190778 ATATAAATATATATA
1 ATATAAATAAATATA
47190793 ATCATTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
ATATAAATAAATATAG
Found at i:47203215 original size:2 final size:2
Alignment explanation
Indices: 47203208--47203243 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
47203198 CTAAGAATTT
47203208 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
47203244 ATGAGTAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:47203751 original size:13 final size:13
Alignment explanation
Indices: 47203733--47203761 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
47203723 CTTATCTTCC
47203733 AAATTAGAATGAT
1 AAATTAGAATGAT
47203746 AAATTAGAATGAT
1 AAATTAGAATGAT
47203759 AAA
1 AAA
47203762 AAGAGAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.28
Consensus pattern (13 bp):
AAATTAGAATGAT
Found at i:47209063 original size:45 final size:45
Alignment explanation
Indices: 47208999--47209102 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 45
47208989 TCTAATTTAT
* *
47208999 ATTACAAAGTTTGTTCCAAGTTTGTTCCAATACGTGCCAATTAAA
1 ATTACAAAGTTTGTTCCAAGTTTGTTCCAACACCTGCCAATTAAA
* * *
47209044 ATTACAAAGTTTGTTCCAAGTTTGTTTCAACACCTGTCATTTAAA
1 ATTACAAAGTTTGTTCCAAGTTTGTTCCAACACCTGCCAATTAAA
47209089 ATTACAAAGTTTGT
1 ATTACAAAGTTTGT
47209103 ATTTTTGCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (45 bp):
ATTACAAAGTTTGTTCCAAGTTTGTTCCAACACCTGCCAATTAAA
Found at i:47231125 original size:88 final size:88
Alignment explanation
Indices: 47230955--47231125 Score: 236
Period size: 88 Copynumber: 1.9 Consensus size: 88
47230945 TGAAATTCCA
* * *
47230955 GCCTTGTCTCCCTGAGCAGCAATGGAGTAGGTTAAAAATAGCAGATCTTGTTTGCCTGTATTGAC
1 GCCTTGTCTCCCTGAGCAGCAATGGAGTAGGTTAAAAATAACAGATCTTGCTTGCCTGTACTGAC
* *
47231020 AGCAAAGTAGATCGAAGATACCT
66 AGCAAAGCAGATAGAAGATACCT
* * *
47231043 GCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAACAGATCTTGCCTT-CCTGTACTGG
1 GCCTTGTCTCCCTGAGCAGCAATGGAGTAGGTTAAAAATAACAGATCTTG-CTTGCCTGTACTGA
**
47231107 CAGTGAAGCAGATAGAAGA
65 CAGCAAAGCAGATAGAAGA
47231126 CTTTAGTCTT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
88 70 0.97
89 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (88 bp):
GCCTTGTCTCCCTGAGCAGCAATGGAGTAGGTTAAAAATAACAGATCTTGCTTGCCTGTACTGAC
AGCAAAGCAGATAGAAGATACCT
Found at i:47231536 original size:44 final size:44
Alignment explanation
Indices: 47231442--47231691 Score: 151
Period size: 44 Copynumber: 5.8 Consensus size: 44
47231432 GAAGATGGCG
* * *
47231442 AATCTTATCTCCCTGAAGTTGCAGTGGAGCATATTAAAGCTAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAAC
* * *
47231486 AATCTTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAA-ATCAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAAC
* * * *
47231529 AATTCTTATTTCTCTGAAGTTGCAG-AGAGCAGA-T--CGCAT--C
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-ATAAC
* * * * * *
47231569 TAGTCTTATCTCCTTGAAGTTGCAGAGGAGTAGACT-GAG-TAAGC
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAA-C
* * * * ***
47231613 AGGTCTGATCTCCCTGAAGTTGCAATGGAGTAGACCCAAGA-AAGC
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAA-C
*
47231658 GAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
47231692 CTCAAGAAAG
Statistics
Matches: 164, Mismatches: 28, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
40 20 0.12
41 8 0.05
42 4 0.02
43 12 0.07
44 84 0.51
45 35 0.21
46 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAAC
Found at i:47231680 original size:45 final size:44
Alignment explanation
Indices: 47231570--47231712 Score: 164
Period size: 45 Copynumber: 3.2 Consensus size: 44
47231560 GATCGCATCT
* ** *
47231570 AGTCTTATCTCCTTGAAGTTGCAGA-GGAGTAGA-CTGAGTAAGC
1 AGTCTTATCTCCCTGAAGTTGCA-ATGGAGTAGACCCAAGAAAGC
*
47231613 AGGTCTGATCTCCCTGAAGTTGCAATGGAGTAGACCCAAGAAAGC
1 A-GTCTTATCTCCCTGAAGTTGCAATGGAGTAGACCCAAGAAAGC
* * *
47231658 GAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGC
1 -AGTCTTATCTCCCTGAAGTTGCAATGGAGTAGACCCAAGAAAGC
47231703 AAGTCTTATC
1 -AGTCTTATC
47231713 CCCCAGAAAT
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
43 2 0.02
44 28 0.33
45 55 0.64
46 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.24
Consensus pattern (44 bp):
AGTCTTATCTCCCTGAAGTTGCAATGGAGTAGACCCAAGAAAGC
Found at i:47231729 original size:45 final size:45
Alignment explanation
Indices: 47231638--47231730 Score: 123
Period size: 45 Copynumber: 2.1 Consensus size: 45
47231628 GAAGTTGCAA
* * * * * *
47231638 TGGAGTAGACCCAAGAAAGCGAGTCTTATCTCCCTGAAGTTGCAG
1 TGGAGCAGACCCAAGAAAGCAAGTCTTATCCCCCAGAAATTACAG
*
47231683 TGGAGCAGACTCAAGAAAGCAAGTCTTATCCCCCAGAAATTACAG
1 TGGAGCAGACCCAAGAAAGCAAGTCTTATCCCCCAGAAATTACAG
47231728 TGG
1 TGG
47231731 GGCAAACTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (45 bp):
TGGAGCAGACCCAAGAAAGCAAGTCTTATCCCCCAGAAATTACAG
Found at i:47235094 original size:58 final size:57
Alignment explanation
Indices: 47235021--47235155 Score: 146
Period size: 58 Copynumber: 2.3 Consensus size: 57
47235011 ATGTTATTTT
* * * *
47235021 GATTTTGGCTGAGGGTTTTGAAGTTTGGGAATTTTGCTTT-AGGATTTTTTACTTTTGA
1 GATTTTGGTTTAGGGTTTTGAAGTTTGAGAATTTTG-TTTAAGG-TTTTTGACTTTTGA
** * * *
47235079 GATTTTGGTTTAGGGTTTTTGATTTTTGATATTTTTGTTTAAGGTTTTTGATTTTTGA
1 GATTTTGGTTTAGGG-TTTTGAAGTTTGAGAATTTTGTTTAAGGTTTTTGACTTTTGA
*
47235137 GATATTGGTTTAGGGTTTT
1 GATTTTGGTTTAGGGTTTT
47235156 CTATTTGACT
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
57 4 0.06
58 42 0.65
59 19 0.29
ACGTcount: A:0.16, C:0.02, G:0.26, T:0.56
Consensus pattern (57 bp):
GATTTTGGTTTAGGGTTTTGAAGTTTGAGAATTTTGTTTAAGGTTTTTGACTTTTGA
Found at i:47235161 original size:29 final size:29
Alignment explanation
Indices: 47235051--47235155 Score: 138
Period size: 29 Copynumber: 3.6 Consensus size: 29
47235041 AAGTTTGGGA
* * * *
47235051 ATTTTGCTTTAGGATTTTTTACTTTTGAG
1 ATTTTGGTTTAGGGTTTTTGATTTTTGAG
*
47235080 ATTTTGGTTTAGGGTTTTTGATTTTTGAT
1 ATTTTGGTTTAGGGTTTTTGATTTTTGAG
* *
47235109 ATTTTTGTTTAAGGTTTTTGATTTTTGAG
1 ATTTTGGTTTAGGGTTTTTGATTTTTGAG
*
47235138 ATATTGGTTTAGGGTTTT
1 ATTTTGGTTTAGGGTTTT
47235156 CTATTTGACT
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.16, C:0.02, G:0.22, T:0.60
Consensus pattern (29 bp):
ATTTTGGTTTAGGGTTTTTGATTTTTGAG
Found at i:47237419 original size:29 final size:30
Alignment explanation
Indices: 47237373--47237466 Score: 87
Period size: 29 Copynumber: 3.3 Consensus size: 30
47237363 TTAAATGATT
47237373 TTTTTAT-AG-TTTTA--AATTTTTAATAA
1 TTTTTATAAGTTTTTAGGAATTTTTAATAA
47237399 TTTTTATAA-TTTATT-GGAATTTTTAAT-A
1 TTTTTATAAGTTT-TTAGGAATTTTTAATAA
* *
47237427 TTATTTATAAGTTTTTATGAATTTTT-ATATG
1 TT-TTTATAAGTTTTTAGGAATTTTTAATA-A
47237458 TTTTTATAA
1 TTTTTATAA
47237467 ACTTTTAAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 16
0.76 0.03 0.22
Matches are distributed among these distances:
26 7 0.12
27 3 0.05
28 5 0.09
29 21 0.38
30 18 0.32
31 2 0.04
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (30 bp):
TTTTTATAAGTTTTTAGGAATTTTTAATAA
Found at i:47237550 original size:54 final size:57
Alignment explanation
Indices: 47237419--47237559 Score: 146
Period size: 54 Copynumber: 2.5 Consensus size: 57
47237409 TTATTGGAAT
* * * *
47237419 TTTTAATATTATTTATAAGTTTTTATGAATTTTTATATGTTTTTATAAACTTTTAAATATA
1 TTTTAATA--ATTAATAA-TTTTTAT-AATATTTATAAGTTTATATAAACTTTTAAATATA
* *
47237480 TTTTATTAATTTATAATTTTT-TAATATTTATAAGTTTATAT-AA-TTTT-AATATA
1 TTTTAATAATTAATAATTTTTATAATATTTATAAGTTTATATAAACTTTTAAATATA
*
47237533 TTTTAAATACTTAATAATTTTTATAAT
1 TTTT-AATAATTAATAATTTTTATAAT
47237560 TTTTTTTATT
Statistics
Matches: 71, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
53 10 0.14
54 18 0.25
55 6 0.08
56 16 0.23
57 1 0.01
58 5 0.07
59 8 0.11
61 7 0.10
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (57 bp):
TTTTAATAATTAATAATTTTTATAATATTTATAAGTTTATATAAACTTTTAAATATA
Found at i:47237560 original size:9 final size:9
Alignment explanation
Indices: 47237373--47237596 Score: 115
Period size: 10 Copynumber: 24.0 Consensus size: 9
47237363 TTAAATGATT
47237373 TTTTTAT-A
1 TTTTTATAA
*
47237381 GTTTTA-AA
1 TTTTTATAA
47237389 TTTTTAATAA
1 TTTTT-ATAA
47237399 TTTTTATAA
1 TTTTTATAA
**
47237408 TTTATTGGAA
1 TTT-TTATAA
47237418 TTTTTA-ATA
1 TTTTTATA-A
47237427 TTATTTATAA
1 TT-TTTATAA
47237437 GTTTTTATGAA
1 -TTTTTAT-AA
*
47237448 TTTTTATATG
1 TTTTTATA-A
47237458 TTTTTATAAA
1 TTTTTAT-AA
* *
47237468 CTTTTAAATA
1 TTTTTATA-A
47237478 TATTTTATTAA
1 T-TTTTA-TAA
47237489 --TTTATAA
1 TTTTTATAA
47237496 TTTTT-TAA
1 TTTTTATAA
*
47237504 TATTTATAA
1 TTTTTATAA
*
47237513 GTTTATATAA
1 -TTTTTATAA
*
47237523 TTTTAAT-A
1 TTTTTATAA
47237531 TATTTTA-AA
1 T-TTTTATAA
* *
47237540 TACTTAATAA
1 T-TTTTATAA
47237550 TTTTTATAA
1 TTTTTATAA
* *
47237559 TTTTTTTTA
1 TTTTTATAA
47237568 TTTTTA-ACGA
1 TTTTTATA--A
47237578 TTTTTATAA
1 TTTTTATAA
47237587 CTTTTTATAA
1 -TTTTTATAA
47237597 CCATAAGCTA
Statistics
Matches: 166, Mismatches: 25, Indels: 48
0.69 0.10 0.20
Matches are distributed among these distances:
7 3 0.02
8 24 0.14
9 55 0.33
10 70 0.42
11 13 0.08
12 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:47246467 original size:20 final size:21
Alignment explanation
Indices: 47246442--47246486 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
47246432 AAAAATGAAA
47246442 TTTGAAATTTTT-ATAAA-TAT
1 TTTGAAATTTTTGA-AAATTAT
47246462 TTTG-AATTTTTGAAAATTAT
1 TTTGAAATTTTTGAAAATTAT
47246482 TTTGA
1 TTTGA
47246487 TTTTTTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTGAAATTTTTGAAAATTAT
Found at i:47246469 original size:19 final size:20
Alignment explanation
Indices: 47246442--47246491 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
47246432 AAAAATGAAA
47246442 TTTGAAATTTTT-ATAAA-TAT
1 TTTG-AATTTTTGA-AAATTAT
47246462 TTTGAATTTTTGAAAATTAT
1 TTTGAATTTTTGAAAATTAT
47246482 TTTG-ATTTTT
1 TTTGAATTTTT
47246492 TTTGTAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (20 bp):
TTTGAATTTTTGAAAATTAT
Found at i:47251709 original size:17 final size:17
Alignment explanation
Indices: 47251666--47251710 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
47251656 CTACAGTTTA
* * *
47251666 TTGGAAGCTCGATTGGG
1 TTGGAAACTTGATTAGG
47251683 TTGGAAACTTGATTAGG
1 TTGGAAACTTGATTAGG
47251700 TTGGAAACTTG
1 TTGGAAACTTG
47251711 TCGGAGATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.24, C:0.09, G:0.33, T:0.33
Consensus pattern (17 bp):
TTGGAAACTTGATTAGG
Found at i:47266869 original size:73 final size:73
Alignment explanation
Indices: 47266749--47266895 Score: 195
Period size: 73 Copynumber: 2.0 Consensus size: 73
47266739 TTTTATCATC
* * * * *
47266749 TTAATTCGATTTAAAATTTTTTTGAGTTGAGTTAAACGAGATAAAATTCAAATTGAAGTGAATTG
1 TTAATTCGATTTAAAATTTTTTTGAATTCAGTCAAACGAGATAAAATTCAAATCGAAGCGAATTG
47266814 AATATATT
66 AATATATT
* * ** * *
47266822 TTAATTCGATTTAAATTTTTTTTGAATTCAGTCGAGTGAGATCAAATTTAAATCGAAGCGAATTG
1 TTAATTCGATTTAAAATTTTTTTGAATTCAGTCAAACGAGATAAAATTCAAATCGAAGCGAATTG
47266887 AATATATT
66 AATATATT
47266895 T
1 T
47266896 GTTTGAACTA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
73 63 1.00
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.41
Consensus pattern (73 bp):
TTAATTCGATTTAAAATTTTTTTGAATTCAGTCAAACGAGATAAAATTCAAATCGAAGCGAATTG
AATATATT
Found at i:47269906 original size:25 final size:25
Alignment explanation
Indices: 47269829--47269920 Score: 62
Period size: 25 Copynumber: 3.7 Consensus size: 25
47269819 TACACCACAA
* * *
47269829 CTCTCTTGAGCTTTCCAATACTTGG
1 CTCTCTTGAGCTTCCCGATATTTGG
* ***
47269854 CTCT-TATGAGCTTCTCGAT-TAACAG
1 CTCTCT-TGAGCTTCCCGATAT-TTGG
47269879 CTCTCTTGAGCTTCCCGATATTTGG
1 CTCTCTTGAGCTTCCCGATATTTGG
* **
47269904 CTCGCAAGAGCTTCCCG
1 CTCTCTTGAGCTTCCCG
47269921 TTTACATGCT
Statistics
Matches: 49, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
24 1 0.02
25 46 0.94
26 2 0.04
ACGTcount: A:0.17, C:0.29, G:0.18, T:0.35
Consensus pattern (25 bp):
CTCTCTTGAGCTTCCCGATATTTGG
Found at i:47272096 original size:42 final size:42
Alignment explanation
Indices: 47272040--47272184 Score: 184
Period size: 42 Copynumber: 3.4 Consensus size: 42
47272030 TTACTAAGAT
47272040 GACCATATTTGGGATATGGCATCGATATGAGAATTCGTGTAA
1 GACCATATTTGGGATATGGCATCGATATGAGAATTCGTGTAA
*
47272082 GACCATATTTGGGATATGACATCGATATGAGAATTCGTGTAA
1 GACCATATTTGGGATATGGCATCGATATGAGAATTCGTGTAA
*** * * * *
47272124 GACCATGGATGGGTTATTGGCATCAATACGAG-ATTACATGTAA
1 GACCATATTTGGGATA-TGGCATCGATATGAGAATT-CGTGTAA
*
47272167 GACCATATCTGGGATATG
1 GACCATATTTGGGATATG
47272185 AAATTGTTAC
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
42 58 0.66
43 30 0.34
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (42 bp):
GACCATATTTGGGATATGGCATCGATATGAGAATTCGTGTAA
Found at i:47285994 original size:40 final size:40
Alignment explanation
Indices: 47285950--47286041 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
47285940 ATCTAATGTT
* *
47285950 CCATTTCATATATCTATTTCCATATAACTGATTCATATCA
1 CCATTTCATATATCTATTTCCATATAACCGATTCATATAA
* * * *
47285990 CCATTTCGTACATTTATTTCTATATAACCGATTCATATAA
1 CCATTTCATATATCTATTTCCATATAACCGATTCATATAA
*
47286030 CTATTTCATATA
1 CCATTTCATATA
47286042 AACACTTCAT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (40 bp):
CCATTTCATATATCTATTTCCATATAACCGATTCATATAA
Found at i:47286027 original size:13 final size:13
Alignment explanation
Indices: 47286011--47286058 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
47286001 ATTTATTTCT
47286011 ATATAACCGA-TTC
1 ATATAACC-ACTTC
* *
47286024 ATATAACTATTTC
1 ATATAACCACTTC
*
47286037 ATATAAACACTTC
1 ATATAACCACTTC
47286050 ATATAACCA
1 ATATAACCA
47286059 TTTCTATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
12 1 0.03
13 28 0.97
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (13 bp):
ATATAACCACTTC
Found at i:47286042 original size:26 final size:27
Alignment explanation
Indices: 47286004--47286065 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
47285994 TTCGTACATT
*
47286004 TATTTCTATATAACCGA-TTCATATAAC
1 TATTTCTATATAAAC-ACTTCATATAAC
47286031 TATTTC-ATATAAACACTTCATATAAC
1 TATTTCTATATAAACACTTCATATAAC
*
47286057 CATTTCTAT
1 TATTTCTAT
47286066 TTACTCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 1 0.03
26 22 0.71
27 8 0.26
ACGTcount: A:0.37, C:0.19, G:0.02, T:0.42
Consensus pattern (27 bp):
TATTTCTATATAAACACTTCATATAAC
Found at i:47287436 original size:18 final size:18
Alignment explanation
Indices: 47287403--47287455 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
47287393 ATTCACCTAA
*
47287403 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
** *
47287422 ATTCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
47287440 ACCCAACCCAACCCAA
1 ACCCAACCCAACCCAA
47287456 TCATAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.42, C:0.45, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:47287582 original size:18 final size:18
Alignment explanation
Indices: 47287559--47287625 Score: 107
Period size: 18 Copynumber: 3.7 Consensus size: 18
47287549 GTAGTGATTC
47287559 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
47287577 AATTCGGTTAATTTGGGT
1 AATTCGGTTAATTCGGGT
*
47287595 AATCCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
47287613 AATTTGGTTAATT
1 AATTCGGTTAATT
47287626 TTTAACCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.42
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:47287626 original size:9 final size:9
Alignment explanation
Indices: 47287559--47287625 Score: 80
Period size: 9 Copynumber: 7.4 Consensus size: 9
47287549 GTAGTGATTC
47287559 AATTCGGTT
1 AATTCGGTT
*
47287568 AATTCGGGT
1 AATTCGGTT
47287577 AATTCGGTT
1 AATTCGGTT
* *
47287586 AATTTGGGT
1 AATTCGGTT
*
47287595 AATCCGGTT
1 AATTCGGTT
*
47287604 AATTCGGGT
1 AATTCGGTT
*
47287613 AATTTGGTT
1 AATTCGGTT
47287622 AATT
1 AATT
47287626 TTTAACCAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 47 1.00
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:47301032 original size:44 final size:45
Alignment explanation
Indices: 47300979--47301081 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 45
47300969 TGTCTTTAAC
* * * *
47300979 ATGGACTTACATGAATTATTCTTGTCTCCAATGCCATA-TATAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
** *
47301023 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATA-TTATAAT
47301069 ATGGACTTACATG
1 ATGGACTTACATG
47301082 GCTCATTTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 32 0.64
46 18 0.36
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (45 bp):
ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
Found at i:47301080 original size:46 final size:44
Alignment explanation
Indices: 47301001--47301086 Score: 136
Period size: 46 Copynumber: 1.9 Consensus size: 44
47300991 GAATTATTCT
*
47301001 TGTCTCCAATGCCATATATAATATGGACTTACATGGCTCAATCC
1 TGTCTCCAAAGCCATATATAATATGGACTTACATGGCTCAATCC
*
47301045 TGTCTCCAAAGCCATATTTCTAATATGGACTTACATGGCTCA
1 TGTCTCCAAAGCCATA--TATAATATGGACTTACATGGCTCA
47301087 TTTCTGTTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 15 0.39
46 23 0.61
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (44 bp):
TGTCTCCAAAGCCATATATAATATGGACTTACATGGCTCAATCC
Found at i:47303495 original size:32 final size:32
Alignment explanation
Indices: 47303448--47303526 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 32
47303438 GTTTGCCATT
*
47303448 TGAACTTGTTC-AAAAGTACCTAGTTGGTGCC
1 TGAACTTGTCCAAAAAGTACCTAGTTGGTGCC
*
47303479 T-ACACTTGTCCAAAAAGTACCTAGTTGGTGCT
1 TGA-ACTTGTCCAAAAAGTACCTAGTTGGTGCC
*
47303511 TGAACTTATCCAAAAA
1 TGAACTTGTCCAAAAA
47303527 ATTATATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 1 0.02
31 8 0.19
32 32 0.76
33 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (32 bp):
TGAACTTGTCCAAAAAGTACCTAGTTGGTGCC
Found at i:47312684 original size:21 final size:21
Alignment explanation
Indices: 47312658--47312698 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
47312648 AGACGAGCAA
* *
47312658 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
47312679 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
47312699 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:47316580 original size:38 final size:38
Alignment explanation
Indices: 47316536--47316613 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
47316526 AAAAACGAAT
47316536 AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
1 AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
47316574 AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
1 AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
47316612 AA
1 AA
47316614 TAAATAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (38 bp):
AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
Found at i:47318789 original size:43 final size:43
Alignment explanation
Indices: 47318742--47318873 Score: 119
Period size: 44 Copynumber: 3.0 Consensus size: 43
47318732 TAACCAGCTC
47318742 CACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTT
1 CACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTT
* * * * *
47318785 CACTATCAA-TGCAG-GAAGGCAAGATCTTTTGTCTTCAACCAGC-T
1 CACTA-CAACCG-AGAG-AGGCAAGGT-TTGTGTCTTCGACCTGCTT
* *
47318829 CTA-TCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTT
1 C-ACT-ACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTT
47318873 C
1 C
47318874 GCTGTCAATG
Statistics
Matches: 68, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
43 20 0.29
44 30 0.44
45 18 0.26
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (43 bp):
CACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTT
Found at i:47318807 original size:44 final size:43
Alignment explanation
Indices: 47318757--47318891 Score: 105
Period size: 44 Copynumber: 3.1 Consensus size: 43
47318747 CAACCGAGAG
47318757 AGGCAAGGTTTGTGTCTTCGACCTGCTTCACTATCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTC-CTATCAATGCAGGA
* * * * * * *
47318801 AGGCAAGATCTTTTGTCTTCAACCAGC-T-CTATCACA-ACCGAAA
1 AGGCAAGGT-TTGTGTCTTCGACCTGCTTCCTATCA-ATGCAG-GA
* * *
47318844 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGA
1 -AGGCAAGGTTTGTGTCTTCGACCTGCTTC-CTATCAATGCAGGA
47318889 AGG
1 AGG
47318892 TAAGATCTTT
Statistics
Matches: 66, Mismatches: 17, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
42 8 0.12
43 15 0.23
44 21 0.32
45 16 0.24
46 6 0.09
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (43 bp):
AGGCAAGGTTTGTGTCTTCGACCTGCTTCCTATCAATGCAGGA
Found at i:47318978 original size:42 final size:42
Alignment explanation
Indices: 47318931--47319065 Score: 139
Period size: 42 Copynumber: 3.2 Consensus size: 42
47318921 TGTAACCAAT
47318931 GAAGGCAAAGCTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
1 GAAGGCAAAGCTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
* ** ** * * * * *
47318973 GAAGGCAAGATCTACTTCTTTAACCAGCTCCACTG-TAAC-CAAT
1 GAAGGCAA-AGCTTGTT-TTCGATCTGCTTCGCTGTTAACGC-AG
47319016 GAAGGCAAAGCTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
1 GAAGGCAAAGCTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
47319058 GAAGGCAA
1 GAAGGCAA
47319066 GATCTGCTGT
Statistics
Matches: 68, Mismatches: 20, Indels: 10
0.69 0.20 0.10
Matches are distributed among these distances:
41 11 0.16
42 27 0.40
43 19 0.28
44 11 0.16
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (42 bp):
GAAGGCAAAGCTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
Found at i:47319004 original size:85 final size:86
Alignment explanation
Indices: 47318681--47319070 Score: 439
Period size: 88 Copynumber: 4.5 Consensus size: 86
47318671 ATGCAAGGCT
* *
47318681 TTGTTTTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCAC
1 TTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTTCTATCTTTAACCAGCTCCAC
* * *
47318745 TACAACCGA-GAGAGGCAAGGT
66 TACAACCAATGA-AGGCAAAGC
* * * * * * * *
47318766 TTGTGTCTTCGACCTGCTTCACTATCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCT
1 TTGT-T-TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTTCTATCTTTAACCAGCTCC
* * *
47318831 A-TCACAACCGAAAG-AGGCAAGGT
64 ACT-ACAACC-AATGAAGGCAAAGC
* * * *
47318854 TTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGTAAGATCTTTTATCTTTAACCAGCTCC
1 TTGT-T-TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTTCTATCTTTAACCAGCTCC
**
47318919 ACTGTAACCAATGAAGGCAAAGC
64 ACTACAACCAATGAAGGCAAAGC
* *
47318942 TTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTACT-TCTTTAACCAGCTCCAC
1 TTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTTCTATCTTTAACCAGCTCCAC
**
47319006 TGTAACCAATGAAGGCAAAGC
66 TACAACCAATGAAGGCAAAGC
*
47319027 TTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCT
1 TTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCT
47319071 GCTGTCTTCA
Statistics
Matches: 268, Mismatches: 29, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
85 86 0.32
86 37 0.14
87 40 0.15
88 102 0.38
89 2 0.01
90 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.30
Consensus pattern (86 bp):
TTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTTCTATCTTTAACCAGCTCCAC
TACAACCAATGAAGGCAAAGC
Found at i:47321190 original size:20 final size:18
Alignment explanation
Indices: 47321172--47321235 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 18
47321162 TTTGATCTTG
*
47321172 ATTTTGATTTTTTCTTCT
1 ATTTTGATTTTTTCTTTT
* *
47321190 -TTTTGTTTTTTTATTTTT
1 ATTTTGATTTTTT-CTTTT
47321208 ATTTTTGATTTTTTCATTTT
1 A-TTTTGATTTTTTC-TTTT
47321228 CATTTTGA
1 -ATTTTGA
47321236 CTTTGATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
17 11 0.31
18 3 0.08
20 21 0.58
21 1 0.03
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.75
Consensus pattern (18 bp):
ATTTTGATTTTTTCTTTT
Found at i:47321219 original size:21 final size:20
Alignment explanation
Indices: 47321189--47321233 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
47321179 TTTTTTCTTC
* *
47321189 TTTTTGTTTTTTTATTTTTA
1 TTTTTGTTTTTTCATTTTCA
47321209 TTTTTGATTTTTTCATTTTCA
1 TTTTTG-TTTTTTCATTTTCA
47321230 TTTT
1 TTTT
47321234 GACTTTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.11, C:0.04, G:0.04, T:0.80
Consensus pattern (20 bp):
TTTTTGTTTTTTCATTTTCA
Found at i:47325664 original size:21 final size:21
Alignment explanation
Indices: 47325640--47325702 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
47325630 CGAATAAAAT
47325640 TAATATATTCAATTAGAATAA
1 TAATATATTCAATTAGAATAA
*
47325661 TAATA-A---AA-T-GAAAAA
1 TAATATATTCAATTAGAATAA
47325676 TTAATATATTCAATTAGAATAA
1 -TAATATATTCAATTAGAATAA
47325698 TAATA
1 TAATA
47325703 AAAATGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
15 5 0.15
16 6 0.18
17 3 0.09
20 3 0.09
21 11 0.33
22 5 0.15
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (21 bp):
TAATATATTCAATTAGAATAA
Found at i:47325677 original size:37 final size:38
Alignment explanation
Indices: 47325635--47325711 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 38
47325625 AAAAACGAAT
47325635 AAAATTAATATATTCAATTAGAATAATAAT-AAAATGA
1 AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
47325672 AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
1 AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
47325710 AA
1 AA
47325712 TAAATAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
37 30 0.77
38 9 0.23
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (38 bp):
AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
Found at i:47331694 original size:17 final size:18
Alignment explanation
Indices: 47331660--47331695 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
47331650 CAAGTTGTCG
*
47331660 GCCCGTGTGGGCCTACAC
1 GCCCGTGTGGGCCCACAC
47331678 GCCCGTGT-GGCCCACAC
1 GCCCGTGTGGGCCCACAC
47331695 G
1 G
47331696 GCTTAGAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.11, C:0.42, G:0.33, T:0.14
Consensus pattern (18 bp):
GCCCGTGTGGGCCCACAC
Found at i:47331973 original size:24 final size:24
Alignment explanation
Indices: 47331918--47331966 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
47331908 TCGACAGCCC
47331918 CACTTTTTAACTTTTCGCCTCTTT
1 CACTTTTTAACTTTTCGCCTCTTT
47331942 CACTTTTTAACTTTTCGCCTCTTT
1 CACTTTTTAACTTTTCGCCTCTTT
47331966 C
1 C
47331967 CATTTTTCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.31, G:0.04, T:0.53
Consensus pattern (24 bp):
CACTTTTTAACTTTTCGCCTCTTT
Found at i:47363890 original size:18 final size:18
Alignment explanation
Indices: 47363867--47363909 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
47363857 TGATAATGTA
47363867 ACACTTTAAAATTGTATC
1 ACACTTTAAAATTGTATC
47363885 ACACTTTAAAATTGTATC
1 ACACTTTAAAATTGTATC
47363903 ACACTTT
1 ACACTTT
47363910 CACATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.40
Consensus pattern (18 bp):
ACACTTTAAAATTGTATC
Found at i:47372566 original size:34 final size:34
Alignment explanation
Indices: 47372530--47372596 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
47372520 TCTATTTCAA
* *
47372530 ATAAAAACATAAAAAGTATCATTTTTATTTAAAAAT
1 ATAAAAAAATAAAAA-T-TCAATTTTATTTAAAAAT
*
47372566 ATAAAAAAATTAAAATTCAATTTTATTTAAA
1 ATAAAAAAATAAAAATTCAATTTTATTTAAA
47372597 TCGAATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 14 0.50
35 1 0.04
36 13 0.46
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (34 bp):
ATAAAAAAATAAAAATTCAATTTTATTTAAAAAT
Found at i:47375898 original size:2 final size:2
Alignment explanation
Indices: 47375891--47375925 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
47375881 TTTAGACATC
47375891 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
47375926 CACCTGCTGT
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:47378971 original size:3 final size:3
Alignment explanation
Indices: 47378965--47378990 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
47378955 ATTGAAAAAT
47378965 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
47378991 GGCAAGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:47382462 original size:41 final size:40
Alignment explanation
Indices: 47382417--47382554 Score: 195
Period size: 41 Copynumber: 3.4 Consensus size: 40
47382407 GATTCACCGG
* * *
47382417 CACTTAGCCTGCTAGGCTTATAGCCTGATTTAGATCATCGA
1 CACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCA-CGA
*
47382458 CACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCA
1 CACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACGA
* *
47382498 GCACTTAGTCTGCTAGGTTTATAACCTGATTCAGATCACCGG
1 -CACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCA-CGA
47382540 CACTTAGCCTGCTAG
1 CACTTAGCCTGCTAG
47382555 ACGTATAGTC
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
40 2 0.02
41 84 0.97
42 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (40 bp):
CACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACGA
Found at i:47386118 original size:57 final size:58
Alignment explanation
Indices: 47386026--47386134 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 58
47386016 AATATAGATT
* * * *
47386026 CGCGAGCTGTTTTGTACTTGGGAAAATTTTGTAAAGTAATAAGCTT-GGAATGCGACTC
1 CGCGAACTGTTTTATACTTGGGAAAATTTTCTAAAGTAACAAG-TTGGGAATGCGACTC
*
47386084 CGCGAACTTTTTTATACTT-GGAAAATTTTCTAAAGTAACAAGTTGGGAATG
1 CGCGAACTGTTTTATACTTGGGAAAATTTTCTAAAGTAACAAGTTGGGAATG
47386135 TGAAGTTGCG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
56 2 0.04
57 27 0.60
58 16 0.36
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (58 bp):
CGCGAACTGTTTTATACTTGGGAAAATTTTCTAAAGTAACAAGTTGGGAATGCGACTC
Found at i:47386146 original size:57 final size:57
Alignment explanation
Indices: 47386026--47386157 Score: 144
Period size: 57 Copynumber: 2.3 Consensus size: 57
47386016 AATATAGATT
* * * *
47386026 CGCGAGCTGTTTTGTACTTGGGAAAATTTTGTAAAGTAATAAGCTTGGAATGCGACTC
1 CGCGAACT-TTTTATACTTGGGAAAATTTTCTAAAGTAACAAGCTTGGAATGCGACTC
* *
47386084 CGCGAACTTTTTTATACTT-GGAAAATTTTCTAAAGTAACAAG-TTGGGAATGTGAAGT-
1 CGCGAAC-TTTTTATACTTGGGAAAATTTTCTAAAGTAACAAGCTT-GGAATGCG-ACTC
*
47386141 TGCGAACTTTTTATACT
1 CGCGAACTTTTTATACT
47386158 AGTAGAATTT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
56 12 0.19
57 34 0.53
58 17 0.27
59 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.36
Consensus pattern (57 bp):
CGCGAACTTTTTATACTTGGGAAAATTTTCTAAAGTAACAAGCTTGGAATGCGACTC
Found at i:47386453 original size:69 final size:69
Alignment explanation
Indices: 47386364--47386864 Score: 439
Period size: 69 Copynumber: 7.3 Consensus size: 69
47386354 TCTTTGCATA
* * * * * * *
47386364 CGAGCCTTAATATGACAGTTGGGAGCTTTTCTCTCGCTAACTATTTTGGAGGCTGC-GACTTTTC
1 CGAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAG-CTCTTC
*
47386428 GCTTG
65 GCCTG
* * * * ** ** *
47386433 TGAGCCTTAGTGTGATAGTTGGAAGCTTTGCTCTCGTTAACTGTACTGGAGACTGCGGCTCTTCG
1 CGAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAGCTCTTCG
47386498 CCTG
66 CCTG
* * * *
47386502 CGAGCCATAGTGTGACAGCTGAGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTTGCAGCTCTTCG
1 CGAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAGCTCTTCG
47386567 CCTG
66 CCTG
* * * * *
47386571 CAAGCCATAGTGTGATAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTAGAGGTTAC-GACTCTTC
1 CGAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAG-CTCTTC
47386635 GCCTG
65 GCCTG
* * * * * * * * * * *
47386640 CAAGCCTTAGTGTGACAGCTGAGAACTTTGCTCTCGTTAACTATTTTGAAAGTTGCAGTTTTTCG
1 CGAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAGCTCTTCG
47386705 CCTG
66 CCTG
* * * * ** * *
47386709 CGAGCCTTAGTGTGACAGTTGAGAGCTTTGCTCTAGTTAATTGTGTTGGAGACTGTAGCTCTTCA
1 CGAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAGCTCTTCG
47386774 CCTG
66 CCTG
* * * * * * * * * *
47386778 TGAGCCTTAGTTTAATAGTTGGGAGCTTTACTTTCGCTAATTGTTTTGAAGGTTGCAGCTTTTCG
1 CGAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAGCTCTTCG
* *
47386843 CTTA
66 CCTG
* *
47386847 CGAGCTTTAGTATGACAG
1 CGAGCCTTAGTGTGACAG
47386865 AAATGCTAGT
Statistics
Matches: 346, Mismatches: 83, Indels: 6
0.80 0.19 0.01
Matches are distributed among these distances:
68 1 0.00
69 343 0.99
70 2 0.01
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.35
Consensus pattern (69 bp):
CGAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAGCTCTTCG
CCTG
Found at i:47386582 original size:138 final size:138
Alignment explanation
Indices: 47386364--47386857 Score: 506
Period size: 138 Copynumber: 3.6 Consensus size: 138
47386354 TCTTTGCATA
* * * * * * *
47386364 CGAGCCTTAATATGACAGTTGGGAGCTTTTCTCTCGCTAACTATTTTGGAGGCTGC-GACTTTTC
1 CGAGCCTTAGTGTGACAGCTGAGAGCTTTGCTCTCGCTAACTATTTTGAAGGTTGCAG-CTTTTC
* * **
47386428 GCTTGTGAGCCTTAGTGTGATAGTTGGAAGCTTTGCTCTCGTTAACTGTACTGGAGACTGCGGCT
65 GCCTGCGAGCCTTAGTGTGATAGTTGGAAGCTTTGCTCTCGTTAACTGTGTTGGAGACTGCGGCT
47386493 CTTCGCCTG
130 CTTCGCCTG
* * ** * *
47386502 CGAGCCATAGTGTGACAGCTGAGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTTGCAGCTCTTCG
1 CGAGCCTTAGTGTGACAGCTGAGAGCTTTGCTCTCGCTAACTATTTTGAAGGTTGCAGCTTTTCG
* * * * * ** * *
47386567 CCTGCAAGCCATAGTGTGATAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTAGAGGTTACGACTC
66 CCTGCGAGCCTTAGTGTGATAGTTGGAAGCTTTGCTCTCGTTAACTGTGTTGGAGACTGCGGCTC
47386632 TTCGCCTG
131 TTCGCCTG
* * * * *
47386640 CAAGCCTTAGTGTGACAGCTGAGAACTTTGCTCTCGTTAACTATTTTGAAAGTTGCAGTTTTTCG
1 CGAGCCTTAGTGTGACAGCTGAGAGCTTTGCTCTCGCTAACTATTTTGAAGGTTGCAGCTTTTCG
* * * **
47386705 CCTGCGAGCCTTAGTGTGACAGTT-GAGAGCTTTGCTCTAGTTAATTGTGTTGGAGACTGTAGCT
66 CCTGCGAGCCTTAGTGTGATAGTTGGA-AGCTTTGCTCTCGTTAACTGTGTTGGAGACTGCGGCT
*
47386769 CTTCACCTG
130 CTTCGCCTG
* * * * * * * * * *
47386778 TGAGCCTTAGTTTAATAGTTGGGAGCTTTACTTTCGCTAATTGTTTTGAAGGTTGCAGCTTTTCG
1 CGAGCCTTAGTGTGACAGCTGAGAGCTTTGCTCTCGCTAACTATTTTGAAGGTTGCAGCTTTTCG
* * *
47386843 CTTACGAGCTTTAGT
66 CCTGCGAGCCTTAGT
47386858 ATGACAGAAA
Statistics
Matches: 286, Mismatches: 68, Indels: 4
0.80 0.19 0.01
Matches are distributed among these distances:
137 1 0.00
138 284 0.99
139 1 0.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (138 bp):
CGAGCCTTAGTGTGACAGCTGAGAGCTTTGCTCTCGCTAACTATTTTGAAGGTTGCAGCTTTTCG
CCTGCGAGCCTTAGTGTGATAGTTGGAAGCTTTGCTCTCGTTAACTGTGTTGGAGACTGCGGCTC
TTCGCCTG
Found at i:47386611 original size:207 final size:207
Alignment explanation
Indices: 47386380--47386864 Score: 535
Period size: 207 Copynumber: 2.3 Consensus size: 207
47386370 TTAATATGAC
* * * **
47386380 AGTTGGGAGCTTTTCTCTCGCTAACTATTTTGGAGGCTGCGACTTTTCGCTTGTGAGCCTTAGTG
1 AGTTGGGAGCTTTACTCTCGCTAACTGTTTTGGAGGTTGCGACTTTTCGCTTGCAAGCCTTAGTG
* * * * *
47386445 TGATAGTTG-GAAGCTTTGCTCTCGTTAACTGTACTGGAGA-CTGCGGCTCTTCGCCTGCGAGCC
66 TGACAGCTGAGAA-CTTTGCTCTCGTTAACTAT-CTGGAAAGCTGCAGCTCTTCGCCTGCGAGCC
* ** *
47386508 ATAGTGTGACAGCTGAGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTTGCAGCTCTTCGCCTGCA
129 ATAGTGTGACAGCTGAGAGCTTTGCTCTAGCTAACTGTGCTGGAGACTGCAGCTCTTCACCTGCA
*
47386573 AGCCATAGTGTGAT
194 AGCCATAGTGTAAT
* * * * * *
47386587 AGTTGGGAGCTTTGCTCTCGCTAACTGTGTTAGAGGTTACGACTCTTCGCCTGCAAGCCTTAGTG
1 AGTTGGGAGCTTTACTCTCGCTAACTGTTTTGGAGGTTGCGACTTTTCGCTTGCAAGCCTTAGTG
* * * * * *
47386652 TGACAGCTGAGAACTTTGCTCTCGTTAACTATTTTGAAAGTTGCAGTTTTTCGCCTGCGAGCCTT
66 TGACAGCTGAGAACTTTGCTCTCGTTAACTATCTGGAAAGCTGCAGCTCTTCGCCTGCGAGCCAT
* * * * * **
47386717 AGTGTGACAGTTGAGAGCTTTGCTCTAGTTAATTGTGTTGGAGACTGTAGCTCTTCACCTGTGAG
131 AGTGTGACAGCTGAGAGCTTTGCTCTAGCTAACTGTGCTGGAGACTGCAGCTCTTCACCTGCAAG
* *
47386782 CCTTAGTTTAAT
196 CCATAGTGTAAT
* * * * * *
47386794 AGTTGGGAGCTTTACTTTCGCTAATTGTTTTGAAGGTTGC-AGCTTTTCGCTTACGAGCTTTAGT
1 AGTTGGGAGCTTTACTCTCGCTAACTGTTTTGGAGGTTGCGA-CTTTTCGCTTGCAAGCCTTAGT
*
47386858 ATGACAG
65 GTGACAG
47386865 AAATGCTAGT
Statistics
Matches: 227, Mismatches: 48, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
206 5 0.02
207 219 0.96
208 3 0.01
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (207 bp):
AGTTGGGAGCTTTACTCTCGCTAACTGTTTTGGAGGTTGCGACTTTTCGCTTGCAAGCCTTAGTG
TGACAGCTGAGAACTTTGCTCTCGTTAACTATCTGGAAAGCTGCAGCTCTTCGCCTGCGAGCCAT
AGTGTGACAGCTGAGAGCTTTGCTCTAGCTAACTGTGCTGGAGACTGCAGCTCTTCACCTGCAAG
CCATAGTGTAAT
Found at i:47387831 original size:22 final size:20
Alignment explanation
Indices: 47387776--47387832 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 20
47387766 TTTTTTTAAA
* *
47387776 AAAAATTCAATAAAAATATT
1 AAAATTTCAAAAAAAATATT
*
47387796 AAAATTTTATAAAAAAATACTT
1 AAAATTTCA-AAAAAAATA-TT
*
47387818 AGAGATTTCAAAAAA
1 A-AAATTTCAAAAAA
47387833 TTATAAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 7 0.24
21 8 0.28
22 8 0.28
23 6 0.21
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.30
Consensus pattern (20 bp):
AAAATTTCAAAAAAAATATT
Found at i:47388743 original size:5 final size:5
Alignment explanation
Indices: 47388737--47388766 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
47388727 ATATATGGTA
*
47388737 TGATA TGATT TGATT TGATT TGATT TGATT
1 TGATT TGATT TGATT TGATT TGATT TGATT
47388767 AAATATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (5 bp):
TGATT
Found at i:47404564 original size:42 final size:42
Alignment explanation
Indices: 47404510--47404635 Score: 164
Period size: 42 Copynumber: 3.0 Consensus size: 42
47404500 AAATATATAC
*
47404510 TCTCAATGTGGATTGAAA-TTTAGTTTAGTTAGCACGGTTGTT
1 TCTCAACGTGGATT-AAATTTTAGTTTAGTTAGCACGGTTGTT
* * * *
47404552 TCTTAACGTGGATTAAATTTTACTTTAGTTGGCACGGTTGAT
1 TCTCAACGTGGATTAAATTTTAGTTTAGTTAGCACGGTTGTT
* * *
47404594 TCTCAATGTGGATTAAATTTTAGTTTAGTTAACACGTTTGTT
1 TCTCAACGTGGATTAAATTTTAGTTTAGTTAGCACGGTTGTT
47404636 ATTATACTAA
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 3 0.04
42 68 0.96
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (42 bp):
TCTCAACGTGGATTAAATTTTAGTTTAGTTAGCACGGTTGTT
Found at i:47407148 original size:22 final size:24
Alignment explanation
Indices: 47407123--47407166 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
47407113 CATAAAACTG
47407123 TTAAAG-ATTTTA-TGATTTTTCA
1 TTAAAGAATTTTAGTGATTTTTCA
* *
47407145 TTAATGAATTTTAGTTATTTTT
1 TTAAAGAATTTTAGTGATTTTT
47407167 TATGTTAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 6 0.33
24 7 0.39
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (24 bp):
TTAAAGAATTTTAGTGATTTTTCA
Found at i:47407684 original size:25 final size:26
Alignment explanation
Indices: 47407651--47407699 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
47407641 TATGTTGTTT
47407651 TGAATTATTTTGA-ATTGAAATGTTGC
1 TGAATTA-TTTGACATTGAAATGTTGC
*
47407677 TGAA-TATTTGACATTGGAATGTT
1 TGAATTATTTGACATTGAAATGTT
47407700 AATTATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 12 0.57
26 4 0.19
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.45
Consensus pattern (26 bp):
TGAATTATTTGACATTGAAATGTTGC
Found at i:47410488 original size:21 final size:22
Alignment explanation
Indices: 47410464--47410509 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
47410454 TACAATCGTT
47410464 CTGT-GGCAAAGGATGAATTGA
1 CTGTAGGCAAAGGATGAATTGA
*
47410485 CTGTAAATGCAAAGGATGAATTGA
1 CTGT--AGGCAAAGGATGAATTGA
47410509 C
1 C
47410510 AACAAATTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
24 17 0.81
ACGTcount: A:0.37, C:0.11, G:0.28, T:0.24
Consensus pattern (22 bp):
CTGTAGGCAAAGGATGAATTGA
Found at i:47410516 original size:24 final size:24
Alignment explanation
Indices: 47410469--47410516 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
47410459 TCGTTCTGTG
***
47410469 GCAAAGGATGAATTGACTGTAAAT
1 GCAAAGGATGAATTGACAACAAAT
47410493 GCAAAGGATGAATTGACAACAAAT
1 GCAAAGGATGAATTGACAACAAAT
47410517 TACCCAACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.21
Consensus pattern (24 bp):
GCAAAGGATGAATTGACAACAAAT
Found at i:47410671 original size:42 final size:43
Alignment explanation
Indices: 47410612--47410735 Score: 162
Period size: 42 Copynumber: 2.9 Consensus size: 43
47410602 ATGAGTTCCT
* *
47410612 GTTTAACCCTAATGGGTTTTCGTTCAGCTCTTTTGAGC-TTCA
1 GTTTAACCCTTATGGGTTTTCGTTCAGCTCTTATGAGCTTTCA
*
47410654 GTTTAACCCTTATGGGTTTCCGTTCAGCTCTTATGAGCTTTCA
1 GTTTAACCCTTATGGGTTTTCGTTCAGCTCTTATGAGCTTTCA
* * * * *
47410697 -TTCAACCCTTATGGGTTTTTGTTTAGCACTTATGTGCTT
1 GTTTAACCCTTATGGGTTTTCGTTCAGCTCTTATGAGCTT
47410736 CTATTCAGCC
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 68 0.94
43 4 0.06
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (43 bp):
GTTTAACCCTTATGGGTTTTCGTTCAGCTCTTATGAGCTTTCA
Found at i:47410688 original size:21 final size:21
Alignment explanation
Indices: 47410607--47410714 Score: 65
Period size: 21 Copynumber: 5.1 Consensus size: 21
47410597 CTCATATGAG
* *
47410607 TTCCTGTTTAACCCTAATGGGT
1 TTCC-GTTCAACCCTTATGGGT
* * * * * *
47410629 TTTCGTTCAGCTCTTTTGAGC
1 TTCCGTTCAACCCTTATGGGT
* *
47410650 TTCAGTTTAACCCTTATGGGT
1 TTCCGTTCAACCCTTATGGGT
* * *
47410671 TTCCGTTCAGCTCTTATGAGCT
1 TTCCGTTCAACCCTTATG-GGT
*
47410693 TT-CATTCAACCCTTATGGGT
1 TTCCGTTCAACCCTTATGGGT
47410713 TT
1 TT
47410715 TTGTTTAGCA
Statistics
Matches: 60, Mismatches: 25, Indels: 4
0.67 0.28 0.04
Matches are distributed among these distances:
20 4 0.07
21 49 0.82
22 7 0.12
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.44
Consensus pattern (21 bp):
TTCCGTTCAACCCTTATGGGT
Found at i:47417240 original size:66 final size:66
Alignment explanation
Indices: 47417134--47417259 Score: 252
Period size: 66 Copynumber: 1.9 Consensus size: 66
47417124 CATTTCAGAG
47417134 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA
1 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA
47417199 T
66 T
47417200 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
47417260 TAATATAAAC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.26, C:0.37, G:0.18, T:0.18
Consensus pattern (66 bp):
AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA
T
Found at i:47417478 original size:57 final size:60
Alignment explanation
Indices: 47417381--47417528 Score: 196
Period size: 57 Copynumber: 2.5 Consensus size: 60
47417371 ACCCTAATTC
* * * *
47417381 GGATTACCCGTCCGGACTAAATCCATTTTCCACATATTCTTCGGGAGGGCTATATC-A-A
1 GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGGGAGGGCTATATCGATA
*
47417439 -GATCACCTGTCCGGGCTAGAT-CTTTTTCACACATATTCTTCGGGAGGGCTATATCAGGATA
1 GGATCACCCGTCCGGGCTAGATCCTTTTTC-CACATATTCTTCGGGAGGGCTATATC--GATA
47417500 GGATCACCCGTCCGGGCTAGATCCTTTTT
1 GGATCACCCGTCCGGGCTAGATCCTTTTT
47417529 ACCGTCAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
56 6 0.08
57 43 0.56
60 1 0.01
61 1 0.01
62 20 0.26
63 6 0.08
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (60 bp):
GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGGGAGGGCTATATCGATA
Found at i:47425658 original size:101 final size:101
Alignment explanation
Indices: 47425533--47425738 Score: 376
Period size: 101 Copynumber: 2.0 Consensus size: 101
47425523 ATCTTCTAAC
*
47425533 TTTTCACCACTAAGGTTTTGTTTAGCATTGCTCATAGGGGTGGAAAAGCACTTTTTGACAGCACA
1 TTTTCACCACTAAGGTTTTGTTTAGCATTGCTCATAGAGGTGGAAAAGCACTTTTTGACAGCACA
*
47425598 AGCAATGCCAAACAATCAGCTTTAACATCAAATTAA
66 AACAATGCCAAACAATCAGCTTTAACATCAAATTAA
*
47425634 TTTTCACCACTAAGGTTTTGTTTAGCATTGCTCATAGAGGTGGAAAAGCACTTTTTGACAGCATA
1 TTTTCACCACTAAGGTTTTGTTTAGCATTGCTCATAGAGGTGGAAAAGCACTTTTTGACAGCACA
*
47425699 AACAATGCCAAACAATCAGCTTTAACATCAAATTAG
66 AACAATGCCAAACAATCAGCTTTAACATCAAATTAA
47425735 TTTT
1 TTTT
47425739 TCAACCCAAA
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (101 bp):
TTTTCACCACTAAGGTTTTGTTTAGCATTGCTCATAGAGGTGGAAAAGCACTTTTTGACAGCACA
AACAATGCCAAACAATCAGCTTTAACATCAAATTAA
Found at i:47432609 original size:3 final size:3
Alignment explanation
Indices: 47432601--47432633 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
47432591 CAAATTTGAC
47432601 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
47432634 GTTAACAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:47432805 original size:21 final size:21
Alignment explanation
Indices: 47432766--47432806 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
47432756 AATTTATTAT
**
47432766 TATATTTATAATTGTAATATA
1 TATATTTATAATTAAAATATA
*
47432787 TATATTTATTATTAAAATAT
1 TATATTTATAATTAAAATAT
47432807 TAATATAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TATATTTATAATTAAAATATA
Found at i:47432812 original size:21 final size:21
Alignment explanation
Indices: 47432763--47432812 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
47432753 AAAAATTTAT
**
47432763 TATT-ATATTTATAATTGTAA
1 TATTAATATTTATAATTAAAA
*
47432783 TA-TATATATTTATTATTAAAA
1 TATTA-ATATTTATAATTAAAA
47432804 TATTAATAT
1 TATTAATAT
47432813 AAATAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 1 0.04
20 2 0.08
21 19 0.79
22 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TATTAATATTTATAATTAAAA
Found at i:47432874 original size:17 final size:19
Alignment explanation
Indices: 47432838--47432877 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
47432828 ATATATCAAG
47432838 AATATTATTTAAAATTTAAA
1 AATATTATTTAAAA-TTAAA
47432858 AATATTA-TTAAAA-TAAA
1 AATATTATTTAAAATTAAA
47432875 AAT
1 AAT
47432878 GTAATATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
19 6 0.30
20 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATATTATTTAAAATTAAA
Found at i:47432928 original size:26 final size:27
Alignment explanation
Indices: 47432899--47432950 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
47432889 TAATTTATTA
* *
47432899 AAATAATTCATTATAT-TATTAAATAT
1 AAATAATTAAATATATATATTAAATAT
*
47432925 AAATAATTAAATATGTATATTAAATA
1 AAATAATTAAATATATATATTAAATA
47432951 ATATTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
AAATAATTAAATATATATATTAAATAT
Found at i:47432933 original size:22 final size:21
Alignment explanation
Indices: 47432893--47432933 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
47432883 ATTAAATAAT
* *
47432893 TTATTAAAATAATTCATTATA
1 TTATTAAAATAAATAATTATA
47432914 TTATTAAATATAAATAATTA
1 TTATTAAA-ATAAATAATTA
47432934 AATATGTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TTATTAAAATAAATAATTATA
Found at i:47432976 original size:22 final size:22
Alignment explanation
Indices: 47432951--47432993 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
47432941 ATATTAAATA
47432951 ATATTAAAA-TTTATAATATTTG
1 ATATTAAAATTTTA-AATATTTG
*
47432973 ATATTAATATTTTAAATATTT
1 ATATTAAAATTTTAAATATTT
47432994 TCAAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATATTAAAATTTTAAATATTTG
Found at i:47440061 original size:14 final size:14
Alignment explanation
Indices: 47440042--47440069 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
47440032 AAAAAAAGAA
47440042 AGGAAATAAAGTTT
1 AGGAAATAAAGTTT
47440056 AGGAAATAAAGTTT
1 AGGAAATAAAGTTT
47440070 CAAGATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (14 bp):
AGGAAATAAAGTTT
Found at i:47442761 original size:20 final size:21
Alignment explanation
Indices: 47442733--47442780 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
47442723 AATGGTTATA
* *
47442733 GAAAATAATTTTTA-AAAAAT
1 GAAATTAATTTTAATAAAAAT
47442753 GAAATTAATTTTAATAAAAAT
1 GAAATTAATTTTAATAAAAAT
47442774 GATAATT
1 GA-AATT
47442781 CCGGGGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.50
21 8 0.33
22 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (21 bp):
GAAATTAATTTTAATAAAAAT
Found at i:47444800 original size:20 final size:20
Alignment explanation
Indices: 47444775--47444813 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
47444765 CGCCTATGTG
* *
47444775 AAGGAGGCATACGCCCGTGA
1 AAGGAGGCACACGACCGTGA
47444795 AAGGAGGCACACGACCGTG
1 AAGGAGGCACACGACCGTG
47444814 TGTCGATAAC
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:0.31, C:0.26, G:0.36, T:0.08
Consensus pattern (20 bp):
AAGGAGGCACACGACCGTGA
Found at i:47453038 original size:14 final size:14
Alignment explanation
Indices: 47453015--47453048 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
47453005 TGGTATGGTT
47453015 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
47453028 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
47453042 TTATAGG
1 TTATAGG
47453049 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:47453203 original size:22 final size:23
Alignment explanation
Indices: 47453178--47453224 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
47453168 GAGGAAAGTT
47453178 TAAAGAACATAAAA-GAAAAAAA
1 TAAAGAACATAAAACGAAAAAAA
** *
47453200 TAAATTACTTAAAACGAAAAAAA
1 TAAAGAACATAAAACGAAAAAAA
47453223 TA
1 TA
47453225 TGGGGATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.17
Consensus pattern (23 bp):
TAAAGAACATAAAACGAAAAAAA
Found at i:47455220 original size:27 final size:27
Alignment explanation
Indices: 47455156--47455220 Score: 62
Period size: 27 Copynumber: 2.4 Consensus size: 27
47455146 TATTTTATTA
47455156 TTATTATTTATTTCTTTTTGGTCACTTT
1 TTATTATTT-TTTCTTTTTGGTCACTTT
* * *
47455184 CTATCT-TTTTTTCTTCTTT-TTCATTTT
1 TTAT-TATTTTTTCTT-TTTGGTCACTTT
47455211 TTATTATTTT
1 TTATTATTTT
47455221 GTTAATCGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
26 1 0.03
27 19 0.63
28 9 0.30
29 1 0.03
ACGTcount: A:0.12, C:0.12, G:0.03, T:0.72
Consensus pattern (27 bp):
TTATTATTTTTTCTTTTTGGTCACTTT
Found at i:47459968 original size:16 final size:16
Alignment explanation
Indices: 47459937--47459966 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
47459927 TGATATCTCT
47459937 TTTTTTTAAATATTTA
1 TTTTTTTAAATATTTA
47459953 TTTTTTT-AATATTT
1 TTTTTTTAAATATTT
47459967 TACTATACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTTAAATATTTA
Found at i:47473961 original size:26 final size:26
Alignment explanation
Indices: 47473894--47473955 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
47473884 CTTGTAAGTG
* *
47473894 TTCTGAAACTGATACATGCTATGATA
1 TTCTGAAACTGATATATGCTACGATA
* *
47473920 TTCTGAAAGTGATATATGTTACGATA
1 TTCTGAAACTGATATATGCTACGATA
47473946 TTCTGAAACT
1 TTCTGAAACT
47473956 ACTATAGGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (26 bp):
TTCTGAAACTGATATATGCTACGATA
Found at i:47474080 original size:31 final size:33
Alignment explanation
Indices: 47474018--47474081 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 33
47474008 GTCTGCCCAA
*
47474018 AAAATAGGAGGTTTCGGGTAAAAATATAGGCCC
1 AAAATAGGAGGTTTCGGGCAAAAATATAGGCCC
*
47474051 AAAATATG-GGTTT-GGGCAAAAA-ATGAGGCCC
1 AAAATAGGAGGTTTCGGGCAAAAATAT-AGGCCC
47474082 GTTTTCCTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 2 0.07
31 14 0.50
32 5 0.18
33 7 0.25
ACGTcount: A:0.39, C:0.12, G:0.28, T:0.20
Consensus pattern (33 bp):
AAAATAGGAGGTTTCGGGCAAAAATATAGGCCC
Found at i:47474184 original size:17 final size:17
Alignment explanation
Indices: 47474164--47474196 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
47474154 TATATTTTTA
*
47474164 TTTTTAATTAAATATAC
1 TTTTTAATCAAATATAC
47474181 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
47474197 TATATTAAAT
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:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTTAATCAAATATAC
Found at i:47482721 original size:13 final size:13
Alignment explanation
Indices: 47482699--47482728 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
47482689 TCTTTAGGTA
*
47482699 TTTAATTGACTTG
1 TTTAACTGACTTG
47482712 TTTAACTGACTTG
1 TTTAACTGACTTG
47482725 TTTA
1 TTTA
47482729 GTTTGATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.53
Consensus pattern (13 bp):
TTTAACTGACTTG
Found at i:47486421 original size:9 final size:9
Alignment explanation
Indices: 47486403--47486444 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
47486393 TTTGGTTAAA
47486403 AATTAACCG
1 AATTAACCG
*
47486412 AATTACCCG
1 AATTAACCG
*
47486421 AATTAACTG
1 AATTAACCG
47486430 AATTAACCG
1 AATTAACCG
47486439 AATTAA
1 AATTAA
47486445 ATCACTACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:47486544 original size:18 final size:18
Alignment explanation
Indices: 47486521--47486574 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
47486511 AATTTTTATG
47486521 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGGTA
* *
47486539 ATTGGGTTGAGTTGGATA
1 ATTGGGTTGGGTTGGGTA
* *
47486557 CTTGGGTTTGGATTGGGT
1 ATTGGG-TTGGGTTGGGT
47486575 TTAGGTGAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
18 21 0.72
19 8 0.28
ACGTcount: A:0.13, C:0.02, G:0.44, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGGTA
Found at i:47487296 original size:30 final size:30
Alignment explanation
Indices: 47487260--47487323 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
47487250 ATTACATTCC
47487260 AATAATTCTAATAAGAATACAACATCCTTA
1 AATAATTCTAATAAGAATACAACATCCTTA
47487290 AATAATTCTAATAAGAATACAACATCCTTA
1 AATAATTCTAATAAGAATACAACATCCTTA
47487320 AATA
1 AATA
47487324 TTTGATAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.52, C:0.16, G:0.03, T:0.30
Consensus pattern (30 bp):
AATAATTCTAATAAGAATACAACATCCTTA
Found at i:47489163 original size:42 final size:42
Alignment explanation
Indices: 47489073--47489165 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
47489063 TTTAACCCTA
* * *
47489073 ATGGGTTTCAGTTAAGCTCTTTTGAGCTTCAGTTTAACCCCT
1 ATGGGTTTCAGTTAAGCTCTTATGAGCTTCAGTTCAACACCT
* * * * *
47489115 ACGGGTTTCCGTTCAGCTCTTATGAGCTTCCGTTCAACACTT
1 ATGGGTTTCAGTTAAGCTCTTATGAGCTTCAGTTCAACACCT
*
47489157 TTGGGTTTC
1 ATGGGTTTC
47489166 TGTTTAGCAC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (42 bp):
ATGGGTTTCAGTTAAGCTCTTATGAGCTTCAGTTCAACACCT
Found at i:47497131 original size:20 final size:21
Alignment explanation
Indices: 47497099--47497142 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
47497089 CAATCACTTT
47497099 ATAATATAATTAAAAAATAAA
1 ATAATATAATTAAAAAATAAA
**
47497120 ATAATA-AATTAAGTAATAAA
1 ATAATATAATTAAAAAATAAA
47497140 ATA
1 ATA
47497143 TATTCATATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
ATAATATAATTAAAAAATAAA
Found at i:47499162 original size:21 final size:21
Alignment explanation
Indices: 47499138--47499177 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
47499128 TTTTAAATTT
47499138 TAAAAATTATTAAA-AAAATCA
1 TAAAAATTA-TAAACAAAATCA
47499159 TAAAAATTATAAACAAAAT
1 TAAAAATTATAAACAAAAT
47499178 TTATAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAAATTATAAACAAAATCA
Found at i:47499333 original size:13 final size:12
Alignment explanation
Indices: 47499307--47499339 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
47499297 AATATAATTT
47499307 TAAATTTTTTTA
1 TAAATTTTTTTA
47499319 TAAATTTTGTTTA
1 TAAATTTT-TTTA
47499332 T-AATTTTT
1 TAAATTTTT
47499340 ATGGATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.05
12 14 0.70
13 5 0.25
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (12 bp):
TAAATTTTTTTA
Found at i:47501772 original size:2 final size:2
Alignment explanation
Indices: 47501767--47501791 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47501757 TGTCAAATTC
47501767 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
47501792 AAGCACATAA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47513879 original size:40 final size:41
Alignment explanation
Indices: 47513749--47513880 Score: 137
Period size: 41 Copynumber: 3.2 Consensus size: 41
47513739 TCGCATAGCG
* * * * * *
47513749 GAAGCTATTAT-AATCCCGCACTCTAAGTGCCTTACATAGCC
1 GAAGCTATTCTCAAT-CTGCACACTAAGTGCCATAAATAGTC
47513790 GAAGCTA-TCTCAATCT-CACAGACTAAGTGCCATATATATAGTC
1 GAAGCTATTCTCAATCTGCAC--ACTAAGTGCCATA-A-ATAGTC
47513833 GAAGCTATTCTCAAT-TGCACACTAAGTGCCATAAATAGTC
1 GAAGCTATTCTCAATCTGCACACTAAGTGCCATAAATAGTC
47513873 GAAGCTAT
1 GAAGCTAT
47513881 CTCGAGTCGA
Statistics
Matches: 78, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
39 3 0.04
40 17 0.22
41 22 0.28
42 13 0.17
43 13 0.17
44 10 0.13
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.27
Consensus pattern (41 bp):
GAAGCTATTCTCAATCTGCACACTAAGTGCCATAAATAGTC
Found at i:47515835 original size:25 final size:27
Alignment explanation
Indices: 47515807--47515856 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
47515797 ATTTGTAAAT
47515807 TAGAAAAATATC-TCA-AGAATTTTTC
1 TAGAAAAATATCTTCAGAGAATTTTTC
* *
47515832 TAGAATAATCTCTTCAGAGAATTTT
1 TAGAAAAATATCTTCAGAGAATTTT
47515857 CTCTCTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
26 3 0.14
27 8 0.38
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (27 bp):
TAGAAAAATATCTTCAGAGAATTTTTC
Found at i:47517934 original size:43 final size:43
Alignment explanation
Indices: 47517820--47517935 Score: 155
Period size: 43 Copynumber: 2.7 Consensus size: 43
47517810 TATTTTTTTG
* * * *
47517820 TGTAAGACCACGTCTGGGACGTCGGCATCGACTTGTGTTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATTGACTTGTGATTACA
*
47517863 TGTAAGACCATGTCTGGGACAG-TGGCATTGA-TATGTGATTACA
1 TGTAAGACCACGTCTGGGAC-GTTGGCATTGACT-TGTGATTACA
47517906 TGTAAGACCACGTCTGGGACGTTGGCATTG
1 TGTAAGACCACGTCTGGGACGTTGGCATTG
47517936 TACGAGTTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
42 2 0.03
43 61 0.95
44 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.28
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATTGACTTGTGATTACA
Found at i:47519266 original size:15 final size:14
Alignment explanation
Indices: 47519245--47519280 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
47519235 ATAATCCTTA
*
47519245 ATAATTATCTTAAT
1 ATAATTATCCTAAT
47519259 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
47519274 ATAATTA
1 ATAATTA
47519281 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:47528793 original size:18 final size:18
Alignment explanation
Indices: 47528757--47528793 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
47528747 TAAACTTTCG
* *
47528757 AATTCAAATAATCTCAAT
1 AATTCAAATAAACTAAAT
47528775 AATTCAAATAAACTAAAT
1 AATTCAAATAAACTAAAT
47528793 A
1 A
47528794 TCAAATTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (18 bp):
AATTCAAATAAACTAAAT
Found at i:47528998 original size:27 final size:28
Alignment explanation
Indices: 47528951--47529019 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 28
47528941 CTTTTTCTTT
* **
47528951 TCCCCTAAAACTTTTGTTTCCACC-AAA
1 TCCCCTAAAATTTTTACTTCCACCTAAA
*
47528978 TCCCCTAAAATTTTTACTTCCTCCTAAA
1 TCCCCTAAAATTTTTACTTCCACCTAAA
47529006 --CCCTAAAATCTTTT
1 TCCCCTAAAAT-TTTT
47529020 TTTTTTGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 9 0.25
27 24 0.67
28 3 0.08
ACGTcount: A:0.29, C:0.32, G:0.01, T:0.38
Consensus pattern (28 bp):
TCCCCTAAAATTTTTACTTCCACCTAAA
Found at i:47529361 original size:19 final size:19
Alignment explanation
Indices: 47529337--47529373 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
47529327 AAGTTAAAAT
47529337 CAAATTTGATTACGGTGGA
1 CAAATTTGATTACGGTGGA
*
47529356 CAAATTTGATTATGGTGG
1 CAAATTTGATTACGGTGG
47529374 GTGGCGATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.35
Consensus pattern (19 bp):
CAAATTTGATTACGGTGGA
Found at i:47535022 original size:21 final size:23
Alignment explanation
Indices: 47534996--47535040 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
47534986 GAAAGGTATC
*
47534996 TACAAATTA-AATC-TCTAATAT
1 TACAAAATAGAATCTTCTAATAT
*
47535017 TACAAAATAGTATCTTCTAATAT
1 TACAAAATAGAATCTTCTAATAT
47535040 T
1 T
47535041 GCATATCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 3 0.15
23 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.40
Consensus pattern (23 bp):
TACAAAATAGAATCTTCTAATAT
Found at i:47536276 original size:17 final size:17
Alignment explanation
Indices: 47536254--47536291 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
47536244 TTGGAAAACA
*
47536254 AGAAGGAAAATAATGAT
1 AGAAGGAAAAAAATGAT
*
47536271 AGAAGGAAAAAAATGGT
1 AGAAGGAAAAAAATGAT
47536288 AGAA
1 AGAA
47536292 AACTTTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.26, T:0.13
Consensus pattern (17 bp):
AGAAGGAAAAAAATGAT
Found at i:47550678 original size:19 final size:19
Alignment explanation
Indices: 47550654--47550691 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
47550644 AAAGTTAAAA
47550654 ACAAATTTGATTACGGTGG
1 ACAAATTTGATTACGGTGG
*
47550673 ACAAATTTGATTATGGTGG
1 ACAAATTTGATTACGGTGG
47550692 GTGGCGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (19 bp):
ACAAATTTGATTACGGTGG
Found at i:47552822 original size:9 final size:9
Alignment explanation
Indices: 47552808--47552833 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
47552798 CAAACCTAAA
47552808 ACCCAACAG
1 ACCCAACAG
47552817 ACCCAACAG
1 ACCCAACAG
47552826 ACCCAACA
1 ACCCAACA
47552834 CCCAAATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.46, G:0.08, T:0.00
Consensus pattern (9 bp):
ACCCAACAG
Found at i:47561218 original size:21 final size:23
Alignment explanation
Indices: 47561192--47561236 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
47561182 GAAAGGTATC
*
47561192 TACAAATTA-AATC-TCTAATAT
1 TACAAAATAGAATCTTCTAATAT
*
47561213 TACAAAATAGTATCTTCTAATAT
1 TACAAAATAGAATCTTCTAATAT
47561236 T
1 T
47561237 GCATATCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 3 0.15
23 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.40
Consensus pattern (23 bp):
TACAAAATAGAATCTTCTAATAT
Found at i:47571786 original size:16 final size:16
Alignment explanation
Indices: 47571756--47571789 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
47571746 TAAACTTTCG
47571756 ATTCAATAACTTAAAT
1 ATTCAATAACTTAAAT
47571772 ATTCGAATAAC-TAAAT
1 ATTC-AATAACTTAAAT
47571788 AT
1 AT
47571790 CAAATTTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (16 bp):
ATTCAATAACTTAAAT
Found at i:47572700 original size:17 final size:16
Alignment explanation
Indices: 47572662--47572705 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
47572652 AAAAAAAGGT
*
47572662 AAAAAAAAAATAAAACT
1 AAAAAAAAAATAAAA-A
* *
47572679 GAAAAAATAATAAAAA
1 AAAAAAAAAATAAAAA
47572695 AAAAAAAAAAT
1 AAAAAAAAAAT
47572706 TTTCAACTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.11
Consensus pattern (16 bp):
AAAAAAAAAATAAAAA
Found at i:47573922 original size:9 final size:9
Alignment explanation
Indices: 47573908--47573933 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
47573898 CAAACCTAAA
47573908 ACCCAACAG
1 ACCCAACAG
47573917 ACCCAACAG
1 ACCCAACAG
47573926 ACCCAACA
1 ACCCAACA
47573934 CCCAAATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.46, G:0.08, T:0.00
Consensus pattern (9 bp):
ACCCAACAG
Found at i:47582330 original size:21 final size:23
Alignment explanation
Indices: 47582304--47582348 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
47582294 GAAAGGTATC
*
47582304 TACAAATTA-AATC-TCTAATAT
1 TACAAAATAGAATCTTCTAATAT
*
47582325 TACAAAATAGTATCTTCTAATAT
1 TACAAAATAGAATCTTCTAATAT
47582348 T
1 T
47582349 GCATATCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 3 0.15
23 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.40
Consensus pattern (23 bp):
TACAAAATAGAATCTTCTAATAT
Found at i:47583583 original size:17 final size:17
Alignment explanation
Indices: 47583561--47583598 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
47583551 TTGGAAAACA
*
47583561 AGAAGGAAAATAATGAT
1 AGAAGGAAAAAAATGAT
*
47583578 AGAAGGAAAAAAATGGT
1 AGAAGGAAAAAAATGAT
47583595 AGAA
1 AGAA
47583599 AACTTTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.26, T:0.13
Consensus pattern (17 bp):
AGAAGGAAAAAAATGAT
Found at i:47592922 original size:24 final size:23
Alignment explanation
Indices: 47592895--47592940 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
47592885 TTTTTTTGAA
*
47592895 TTTCGAGTTCAAATCAAGTTAAAC
1 TTTCGAGTTCAAAT-AACTTAAAC
*
47592919 TTTCGATTTCAAATAACTTAAA
1 TTTCGAGTTCAAATAACTTAAA
47592941 TAATTCGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (23 bp):
TTTCGAGTTCAAATAACTTAAAC
Found at i:47593510 original size:19 final size:19
Alignment explanation
Indices: 47593486--47593523 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
47593476 AAAGTTAAAA
47593486 ACAAATTTGATTACGGTGG
1 ACAAATTTGATTACGGTGG
*
47593505 ACAAATTTGATTATGGTGG
1 ACAAATTTGATTACGGTGG
47593524 GTGGCGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (19 bp):
ACAAATTTGATTACGGTGG
Found at i:47597023 original size:23 final size:23
Alignment explanation
Indices: 47596971--47597023 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
47596961 TAGGGTAGAT
* *
47596971 AATTAAATTATTAGAAATTAGTA
1 AATTAAAATATTAGAAATAAGTA
* *
47596994 AAATAAAATATTA-AAATAATTA
1 AATTAAAATATTAGAAATAAGTA
47597016 GAATTAAA
1 -AATTAAA
47597024 TTTTTAGGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (23 bp):
AATTAAAATATTAGAAATAAGTA
Found at i:47599493 original size:17 final size:18
Alignment explanation
Indices: 47599471--47599507 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
47599461 TTTTGGGTTG
47599471 TGTGGG-CCACACGGGCA
1 TGTGGGCCCACACGGGCA
*
47599488 TGTGGGCCCACATGGGCA
1 TGTGGGCCCACACGGGCA
47599506 TG
1 TG
47599508 CAGCATGAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.16, C:0.27, G:0.41, T:0.16
Consensus pattern (18 bp):
TGTGGGCCCACACGGGCA
Found at i:47601536 original size:22 final size:21
Alignment explanation
Indices: 47601510--47601555 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
47601500 ATAGAGACCA
47601510 CCATTCAGTGGTATCGCGATAT
1 CCATTCAG-GGTATCGCGATAT
**
47601532 CCATTTTGGGTATCGCGATAT
1 CCATTCAGGGTATCGCGATAT
47601553 CCA
1 CCA
47601556 CCTGCCAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (21 bp):
CCATTCAGGGTATCGCGATAT
Done.