Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 167 of 352
Found at i:54707395 original size:8 final size:8
Alignment explanation
Indices: 54707372--54707406 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
54707362 GCACAGTATG
54707372 ATAATTTT
1 ATAATTTT
54707380 AT-ATTTT
1 ATAATTTT
54707387 ATAATTTT
1 ATAATTTT
54707395 ATAATTTT
1 ATAATTTT
54707403 ATAA
1 ATAA
54707407 CCGTTTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATAATTTT
Found at i:54712132 original size:18 final size:19
Alignment explanation
Indices: 54712098--54712133 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54712088 TATAACCACC
54712098 AAAATAAAAATAAAAAGAG
1 AAAATAAAAATAAAAAGAG
*
54712117 AAAATAAAGA-AAAAAGA
1 AAAATAAAAATAAAAAGA
54712134 TGATGGTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (19 bp):
AAAATAAAAATAAAAAGAG
Found at i:54713137 original size:21 final size:21
Alignment explanation
Indices: 54713096--54713138 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
54713086 TCGATTTGTA
*
54713096 AAAATTATAAAATTCATGTTT
1 AAAATTATAAAATTAATGTTT
*
54713117 AAAATTATGAAA-TAATGGTTT
1 AAAATTATAAAATTAAT-GTTT
54713138 A
1 A
54713139 TTTAGGTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (21 bp):
AAAATTATAAAATTAATGTTT
Found at i:54713570 original size:38 final size:38
Alignment explanation
Indices: 54713519--54713673 Score: 222
Period size: 38 Copynumber: 4.1 Consensus size: 38
54713509 CGAATTATAT
** *
54713519 TGTTATTCAGGCTTCATGCCTAGCAGACTTAGTG-TCGG
1 TGTTATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCT-GG
*
54713557 TGTTATTCGGGCTTTGTGCCTAGCAGGCTTAGTGCTGG
1 TGTTATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCTGG
* * *
54713595 TGTTATTCGGGCTTTGTGCCTAGAAGGCTTAGTGCTGA
1 TGTTATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCTGG
*
54713633 TGTTATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCCGG
1 TGTTATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCTGG
54713671 TGT
1 TGT
54713674 ATTAAAAGTT
Statistics
Matches: 106, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
38 105 0.99
39 1 0.01
ACGTcount: A:0.14, C:0.19, G:0.31, T:0.36
Consensus pattern (38 bp):
TGTTATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCTGG
Found at i:54715983 original size:48 final size:48
Alignment explanation
Indices: 54715912--54716202 Score: 345
Period size: 48 Copynumber: 6.1 Consensus size: 48
54715902 CACACCCTAG
* *
54715912 GTGCCAATATCATGGCCTGAAGCCAAATCAATG-AAGCTCGAACCCAAA
1 GTGCTAATATCATGGCCTGAAGCCAAATCAATGTAA-CTCGAACCCGAA
*
54715960 GTGCCAATATCATGGCCTGAAGCCAAATCAATGTAACTC-ACACCCGAA
1 GTGCTAATATCATGGCCTGAAGCCAAATCAATGTAACTCGA-ACCCGAA
* * *
54716008 GTGCTAATAGCATGG-CTCGAAGCCAAATCAATGTAACTCGCACCCAAA
1 GTGCTAATATCATGGCCT-GAAGCCAAATCAATGTAACTCGAACCCGAA
* * * * * *
54716056 GTGCTAATATCATGGCCTAAACCCAAATCGATGCAACTTGTACCCGAA
1 GTGCTAATATCATGGCCTGAAGCCAAATCAATGTAACTCGAACCCGAA
** * * *
54716104 GTGCTAATATCAAAGCCCGAAGCCAAATCAAAGTAACTCGCACCCGAA
1 GTGCTAATATCATGGCCTGAAGCCAAATCAATGTAACTCGAACCCGAA
** * *
54716152 GTGCTAATATCATGGCCCAAAGCCAAATCAATGTAACTCGCATCCGAA
1 GTGCTAATATCATGGCCTGAAGCCAAATCAATGTAACTCGAACCCGAA
54716200 GTG
1 GTG
54716203 AAGCCAAATC
Statistics
Matches: 210, Mismatches: 28, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
47 3 0.01
48 203 0.97
49 4 0.02
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (48 bp):
GTGCTAATATCATGGCCTGAAGCCAAATCAATGTAACTCGAACCCGAA
Found at i:54716065 original size:96 final size:95
Alignment explanation
Indices: 54715900--54716202 Score: 383
Period size: 96 Copynumber: 3.2 Consensus size: 95
54715890 ACTCAGAAGT
* * * *
54715900 CTCACACCCTAGGTGCCAATATCATGGCCTGAAGCCAAATCAATG-AAGCTCGAACCCAAAGTGC
1 CTCACACCCGAAGTGCTAATATCATGGCC-GAAGCCAAATCAATGTAA-CTCGCACCCAAAGTGC
* *
54715964 CAATATCATGGCCTGAAGCCAAATCAATGTAA
64 TAATATCATGGCCTAAAGCCAAATCAATGTAA
*
54715996 CTCACACCCGAAGTGCTAATAGCATGGCTCGAAGCCAAATCAATGTAACTCGCACCCAAAGTGCT
1 CTCACACCCGAAGTGCTAATATCATGGC-CGAAGCCAAATCAATGTAACTCGCACCCAAAGTGCT
* * *
54716061 AATATCATGGCCTAAACCCAAATCGATGCAA
65 AATATCATGGCCTAAAGCCAAATCAATGTAA
*** * * * *
54716092 CTTGTACCCGAAGTGCTAATATCAAAGCCCGAAGCCAAATCAAAGTAACTCGCACCCGAAGTGCT
1 CTCACACCCGAAGTGCTAATATC-ATGGCCGAAGCCAAATCAATGTAACTCGCACCCAAAGTGCT
*
54716157 AATATCATGGCCCAAAGCCAAATCAATGTAA
65 AATATCATGGCCTAAAGCCAAATCAATGTAA
* *
54716188 CTCGCATCCGAAGTG
1 CTCACACCCGAAGTG
54716203 AAGCCAAATC
Statistics
Matches: 179, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
96 173 0.97
97 6 0.03
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.19
Consensus pattern (95 bp):
CTCACACCCGAAGTGCTAATATCATGGCCGAAGCCAAATCAATGTAACTCGCACCCAAAGTGCTA
ATATCATGGCCTAAAGCCAAATCAATGTAA
Found at i:54716166 original size:144 final size:144
Alignment explanation
Indices: 54715912--54716202 Score: 404
Period size: 144 Copynumber: 2.0 Consensus size: 144
54715902 CACACCCTAG
* * **
54715912 GTGCCAATATCATGGCCTGAAGCCAAATCAATGAAGCTCGAACCCAAAGTGCCAATATCATGGCC
1 GTGCCAATATCATGGCCTAAACCCAAATCAATGAAGCTCGAACCCAAAGTGCCAATATCAAAGCC
* * * *
54715977 TGAAGCCAAATCAATGTAACTCACACCCGAAGTGCTAATAGCATGGCTCGAAGCCAAATCAATGT
66 CGAAGCCAAATCAAAGTAACTCACACCCGAAGTGCTAATAGCATGGCCCAAAGCCAAATCAATGT
54716042 AACTCGCACCCAAA
131 AACTCGCACCCAAA
* * * * * *
54716056 GTGCTAATATCATGGCCTAAACCCAAATCGATGCAA-CTTGTACCCGAAGTGCTAATATCAAAGC
1 GTGCCAATATCATGGCCTAAACCCAAATCAATG-AAGCTCGAACCCAAAGTGCCAATATCAAAGC
* *
54716120 CCGAAGCCAAATCAAAGTAACTCGCACCCGAAGTGCTAATATCATGGCCCAAAGCCAAATCAATG
65 CCGAAGCCAAATCAAAGTAACTCACACCCGAAGTGCTAATAGCATGGCCCAAAGCCAAATCAATG
* *
54716185 TAACTCGCATCCGAA
130 TAACTCGCACCCAAA
54716200 GTG
1 GTG
54716203 AAGCCAAATC
Statistics
Matches: 128, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
144 126 0.98
145 2 0.02
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (144 bp):
GTGCCAATATCATGGCCTAAACCCAAATCAATGAAGCTCGAACCCAAAGTGCCAATATCAAAGCC
CGAAGCCAAATCAAAGTAACTCACACCCGAAGTGCTAATAGCATGGCCCAAAGCCAAATCAATGT
AACTCGCACCCAAA
Found at i:54719076 original size:96 final size:96
Alignment explanation
Indices: 54718905--54719174 Score: 363
Period size: 96 Copynumber: 2.9 Consensus size: 96
54718895 TATCGGTGTC
* * *
54718905 GATGCCATGTTCCAAACATGGTCTTACA----C-CATATGTCAAGGCCGATGCCATGTCCCAGAC
1 GATGCCATGTTCCAAACATGGTCTTACATTGGCTCACATATCGAGGCCGATGCCATGTCCCAGAC
54718965 ATGGTCTTACACTAGCTCTCACATAAACTG-T
66 ATGGTCTTACACTAGCTCTCACATAAA-TGCT
* * * *
54718996 GATGCCATGTTCCAAACATGGTCTTATATTGGCTCACATATCGAGGTCGATGCCATGTCCTATAC
1 GATGCCATGTTCCAAACATGGTCTTACATTGGCTCACATATCGAGGCCGATGCCATGTCCCAGAC
** **
54719061 ATGGTCTTATGCTAGCTCTCGTATAAATGCT
66 ATGGTCTTACACTAGCTCTCACATAAATGCT
* *
54719092 GATGCCATGTTCCAAACATGGTCTTACATTGGCTCACATATCGAGACCAATGCCATGTCCCAGAC
1 GATGCCATGTTCCAAACATGGTCTTACATTGGCTCACATATCGAGGCCGATGCCATGTCCCAGAC
*
54719157 ATGGTCTTACACTGGCTC
66 ATGGTCTTACACTAGCTC
54719175 ACATATCCTT
Statistics
Matches: 153, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
91 27 0.18
95 3 0.02
96 123 0.80
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (96 bp):
GATGCCATGTTCCAAACATGGTCTTACATTGGCTCACATATCGAGGCCGATGCCATGTCCCAGAC
ATGGTCTTACACTAGCTCTCACATAAATGCT
Found at i:54719145 original size:48 final size:47
Alignment explanation
Indices: 54718857--54719181 Score: 211
Period size: 48 Copynumber: 6.9 Consensus size: 47
54718847 AAAATGCAGT
* * *
54718857 TGCCATG-TCTCAAACA-GGATCTTACACTGGTTCTCATATATCGGTGTCGA
1 TGCCATGTTC-CAAACATGG-TCTTACACTGG--CTCACATATC-GAGCCGA
* * *
54718907 TGCCATGTTCCAAACATGGTCTTACA----C-CATATGTCAAGGCCGA
1 TGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCGA-GCCGA
* * * * * *
54718950 TGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATAAAC-TG-TGA
1 TGCCATGTTCCAAACATGGTCTTACACT-G-GCTCACAT-ATCGAGCCGA
* * *
54718998 TGCCATGTTCCAAACATGGTCTTATATTGGCTCACATATCGAGGTCGA
1 TGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCGA-GCCGA
* ** * * * ** *
54719046 TGCCATG-TCCTATACATGGTCTTATGCTAGCTCTCGTATAAATGCTGA
1 TGCCATGTTCC-AAACATGGTCTTACACTGGCTCACATATCGA-GCCGA
* *
54719094 TGCCATGTTCCAAACATGGTCTTACATTGGCTCACATATCGAGACCAA
1 TGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCGAG-CCGA
* *
54719142 TGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATC
1 TGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATC
54719182 CTTAGTATCA
Statistics
Matches: 214, Mismatches: 44, Indels: 36
0.73 0.15 0.12
Matches are distributed among these distances:
43 35 0.16
44 1 0.00
45 2 0.01
46 7 0.03
47 6 0.03
48 129 0.60
49 5 0.02
50 24 0.11
51 5 0.02
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (47 bp):
TGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGCCGA
Found at i:54722665 original size:47 final size:46
Alignment explanation
Indices: 54722563--54722728 Score: 169
Period size: 47 Copynumber: 3.6 Consensus size: 46
54722553 GTGCCGTTTC
* * *
54722563 CATGTCCCAAACATGGTCTTACACT-G-ACACATCTCATAGCTGATG
1 CATGTCCCAGACATGGTCTTACACTAGCACTCATCTCAT-GCCGATG
* *
54722608 CATGTTCCAGACAT-GTCTTACACTAGCACTCGTCTCCATGCCGATG
1 CATGTCCCAGACATGGTCTTACACTAGCACTCATCT-CATGCCGATG
* * ** *
54722654 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATAACATTGTCGATG
1 -CATGTCCCAGACATGGTCTTACACTAGCACTCATCTCA-TGCCGATG
*
54722702 CTTGTCCCAGACAT-GTCTTACACTAGC
1 CATGTCCCAGACATGGTCTTACACTAGC
54722729 TCACACAAGT
Statistics
Matches: 101, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
44 10 0.10
45 13 0.13
46 24 0.24
47 31 0.31
48 23 0.23
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGGTCTTACACTAGCACTCATCTCATGCCGATG
Found at i:54728856 original size:18 final size:17
Alignment explanation
Indices: 54728818--54728856 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
54728808 TTTTGAAAAG
54728818 AAAAACAAATGAATCTT
1 AAAAACAAATGAATCTT
*
54728835 AAAAACGAATGAATCTT
1 AAAAACAAATGAATCTT
54728852 AAAAA
1 AAAAA
54728857 TGTAATAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.62, C:0.10, G:0.08, T:0.21
Consensus pattern (17 bp):
AAAAACAAATGAATCTT
Found at i:54739749 original size:59 final size:59
Alignment explanation
Indices: 54739657--54739773 Score: 225
Period size: 59 Copynumber: 2.0 Consensus size: 59
54739647 CTCAATAGTC
*
54739657 GCTTTCCTCCTCTCTTTTACTAGCTCTTCTGCCTTGCATGCTCTCTCAACGAGCACTAT
1 GCTTTCCTCCTCTCTTTTACCAGCTCTTCTGCCTTGCATGCTCTCTCAACGAGCACTAT
54739716 GCTTTCCTCCTCTCTTTTACCAGCTCTTCTGCCTTGCATGCTCTCTCAACGAGCACTA
1 GCTTTCCTCCTCTCTTTTACCAGCTCTTCTGCCTTGCATGCTCTCTCAACGAGCACTA
54739774 CAAATTCTCT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.14, C:0.37, G:0.12, T:0.38
Consensus pattern (59 bp):
GCTTTCCTCCTCTCTTTTACCAGCTCTTCTGCCTTGCATGCTCTCTCAACGAGCACTAT
Found at i:54743332 original size:16 final size:17
Alignment explanation
Indices: 54743311--54743344 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
54743301 GACCCTCAAT
54743311 TTTTAT-TCTCTAGCTA
1 TTTTATATCTCTAGCTA
*
54743327 TTTTATATCTTTAGCTA
1 TTTTATATCTCTAGCTA
54743344 T
1 T
54743345 CAATTTAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.21, C:0.15, G:0.06, T:0.59
Consensus pattern (17 bp):
TTTTATATCTCTAGCTA
Found at i:54744832 original size:40 final size:40
Alignment explanation
Indices: 54744754--54744832 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
54744744 ACACACCATG
* * *
54744754 TGGGGATAAAATCGACCCACCTAGCCCTGCACACCAAGTA
1 TGGGGATAAAATCAACCCACCTAACCCTACACACCAAGTA
* *
54744794 TGGGGATAGAATCAACCCATCC-AACCCTACACATCAAGT
1 TGGGGATAAAATCAACCCA-CCTAACCCTACACACCAAGT
54744833 GGTACCATAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 31 0.94
41 2 0.06
ACGTcount: A:0.34, C:0.32, G:0.18, T:0.16
Consensus pattern (40 bp):
TGGGGATAAAATCAACCCACCTAACCCTACACACCAAGTA
Found at i:54757099 original size:72 final size:72
Alignment explanation
Indices: 54756983--54757184 Score: 216
Period size: 72 Copynumber: 2.8 Consensus size: 72
54756973 CCACATATTT
* * *
54756983 TGTAATGCCCG--CATTTGAGCTACTCATGGGTCTGTACACAAAGTTA-TCAC-CTGGACCCCAA
1 TGTAATGCCCGCTCA-TTGAGCTACTCACGGGTTTATACACAAAGTTAGT-ACTC-GGACCCCAA
*
54757044 AGCATTATCA
63 AGCATTAACA
* * *
54757054 TGTAATGCCCGCTCATTGAGCTACTCACGGGTTTATATACCAAGTTAGTACTCGGACCCCATAGC
1 TGTAATGCCCGCTCATTGAGCTACTCACGGGTTTATACACAAAGTTAGTACTCGGACCCCAAAGC
54757119 ATTAACA
66 ATTAACA
* ** * * *
54757126 TG-ATATGCTCGCTCAGCGAGTTACTCACGGGTTTATACACAAAGTCAGTACCCGGACCC
1 TGTA-ATGCCCGCTCATTGAGCTACTCACGGGTTTATACACAAAGTTAGTACTCGGACCC
54757185 ATATTACATT
Statistics
Matches: 111, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
71 12 0.11
72 95 0.86
73 4 0.04
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.26
Consensus pattern (72 bp):
TGTAATGCCCGCTCATTGAGCTACTCACGGGTTTATACACAAAGTTAGTACTCGGACCCCAAAGC
ATTAACA
Found at i:54759302 original size:13 final size:13
Alignment explanation
Indices: 54759284--54759308 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54759274 CCTAGCACAC
54759284 GCCCGTGTCCCTG
1 GCCCGTGTCCCTG
54759297 GCCCGTGTCCCT
1 GCCCGTGTCCCT
54759309 CACACGGCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.48, G:0.28, T:0.24
Consensus pattern (13 bp):
GCCCGTGTCCCTG
Found at i:54766107 original size:96 final size:96
Alignment explanation
Indices: 54765906--54766224 Score: 442
Period size: 96 Copynumber: 3.3 Consensus size: 96
54765896 TAAAATGCCG
* **
54765906 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATCAGCGTCGATGCCATGTTCCAAA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATA--AATGTCGATGCCATGTTCCAAA
* * *
54765971 CATGGTCTTACACTAGC-CTATATGTCGAGGCCG
64 CATGGTCTTACACTGGCTC-ATATATCGAGGCCA
* * * * *
54766004 ATACCATGTACCAGACATGGTCTTACACTATCTCTCACATAAATGTCGATGCCATGTTTCAAACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGTCGATGCCATGTTCCAAACA
*
54766069 TGGTCTTACACTGGCTCATATATCGAGGCTA
66 TGGTCTTACACTGGCTCATATATCGAGGCCA
* * **
54766100 ATGCCATGTCCCAGACATGGTCTTACACTAGATATCATATAAATACCGATGCCATGTTCCAAACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGTCGATGCCATGTTCCAAACA
**
54766165 TGGTCTTACACTGGCTCACGTATCGAGGCCA
66 TGGTCTTACACTGGCTCATATATCGAGGCCA
54766196 ATGCCATGTCCCAGACATGGTCTTACACT
1 ATGCCATGTCCCAGACATGGTCTTACACT
54766225 GGCTTACATA
Statistics
Matches: 196, Mismatches: 24, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
96 159 0.81
97 1 0.01
98 36 0.18
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (96 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAAATGTCGATGCCATGTTCCAAACA
TGGTCTTACACTGGCTCATATATCGAGGCCA
Found at i:54766166 original size:144 final size:145
Alignment explanation
Indices: 54765898--54766227 Score: 362
Period size: 144 Copynumber: 2.3 Consensus size: 145
54765888 CAAAAGAGTA
* *
54765898 AAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATCAGCGTCGATGCCAT
1 AAATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGC-CTCATATATCAGCGTCAATGCCAT
* * * ** * *
54765963 GTTCCAAACATGGTCTTACACTAGCCTATATGTCGAGGCCGATACCATGTACCAGACATGGTCTT
65 GTCCCAAACATGGTCTTACACTAGCATATATATAAAGACCGATACCATGTACCAAACATGGTCTT
54766028 ACACTATCTCTCACAT
130 ACACTATCTCTCACAT
* **
54766044 AAATGTCGATGCCATGTTTCAAACATGGTCTTACACTGG-CTCATATATCGAG-G-CTAATGCCA
1 AAATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCCTCATATATC-AGCGTC-AATGCCA
* * * *
54766106 TGTCCCAGACATGGTCTTACACTAG-ATATCATATAAATACCGATGCCATGTTCCAAACATGGTC
64 TGTCCCAAACATGGTCTTACACTAGCATAT-ATATAAAGACCGATACCATGTACCAAACATGGTC
** * **
54766170 TTACACTGGCTCACGTAT
128 TTACACTATCTCTCACAT
** * * *
54766188 CGAGGCCAATGCCATGTCCCAGACATGGTCTTACACTGGC
1 AAATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGC
54766228 TTACATATCC
Statistics
Matches: 151, Mismatches: 29, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
143 4 0.03
144 110 0.73
145 2 0.01
146 35 0.23
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (145 bp):
AAATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCCTCATATATCAGCGTCAATGCCATG
TCCCAAACATGGTCTTACACTAGCATATATATAAAGACCGATACCATGTACCAAACATGGTCTTA
CACTATCTCTCACAT
Found at i:54766225 original size:48 final size:48
Alignment explanation
Indices: 54765902--54766236 Score: 298
Period size: 48 Copynumber: 6.9 Consensus size: 48
54765892 AGAGTAAAAT
*
54765902 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATC-AG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGG--CTCACATATCGAG
* * * * * *
54765951 CGTCGATGCCATGTTCCAAACATGGTCTTACACTAGC-CTATATGTCGAG
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-ACATATCGAG
* * ** * * ** *
54766000 GCCGATACCATGTACCAGACATGGTCTTACACTATCTCTCACATAAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCGAG
* ** * *
54766048 GTCGATGCCATGTTTCAAACATGGTCTTACACTGGCTCATATATCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCGAG
** * * ** *
54766096 GCTAATGCCATGTCCCAGACATGGTCTTACACTAGAT-ATCATATAAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCA-CATATCGAG
* * * *
54766144 ACCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACGTATCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCGAG
* *
54766192 GCCAATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATATC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATC
54766237 CCTAATATCA
Statistics
Matches: 221, Mismatches: 59, Indels: 12
0.76 0.20 0.04
Matches are distributed among these distances:
47 2 0.01
48 184 0.83
49 4 0.02
50 31 0.14
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCGAG
Found at i:54774194 original size:27 final size:27
Alignment explanation
Indices: 54774098--54774195 Score: 88
Period size: 27 Copynumber: 3.6 Consensus size: 27
54774088 TTAGTTTACG
** * *
54774098 AAATTACTGGAATACCCTCGACTTGTA
1 AAATTACTAAAATACCCTCGATTTATA
* * *
54774125 AAATTACCAAAGTACCCCCGATTTATA
1 AAATTACTAAAATACCCTCGATTTATA
* *** *
54774152 GAATTACTATTTTACCCTTGATTTATA
1 AAATTACTAAAATACCCTCGATTTATA
54774179 AAATTACTAAAATACCC
1 AAATTACTAAAATACCC
54774196 CTGTAGGGTA
Statistics
Matches: 53, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (27 bp):
AAATTACTAAAATACCCTCGATTTATA
Found at i:54774210 original size:27 final size:27
Alignment explanation
Indices: 54774188--54774321 Score: 187
Period size: 27 Copynumber: 5.0 Consensus size: 27
54774178 AAAATTACTA
* *
54774188 AAATACCCCTGTAGGGTAGAATTACTG
1 AAATACCCTTGTAGGGTAGAATTACCG
*
54774215 AAATACCCTTGTAGGGTAGAATTACCA
1 AAATACCCTTGTAGGGTAGAATTACCG
* **
54774242 AAATACCCTTGTAGGGTAGAAATAAGG
1 AAATACCCTTGTAGGGTAGAATTACCG
54774269 AAATACCCTTGTAGGGTAGAATTACCG
1 AAATACCCTTGTAGGGTAGAATTACCG
* * *
54774296 AGATACCCTTGTGGGGTAAAATTACC
1 AAATACCCTTGTAGGGTAGAATTACC
54774322 ATTTTGCCCT
Statistics
Matches: 94, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 94 1.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.25
Consensus pattern (27 bp):
AAATACCCTTGTAGGGTAGAATTACCG
Found at i:54774331 original size:27 final size:27
Alignment explanation
Indices: 54774301--54774364 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
54774291 TACCGAGATA
*
54774301 CCCTTGTGGGGTAAAATTACCATTTTG
1 CCCTTGTGGGGTAAAATGACCATTTTG
* * **
54774328 CCCTTAG-GGTGTTAAATGACTGTTTTG
1 CCCTT-GTGGGGTAAAATGACCATTTTG
54774355 CCCTTGTGGG
1 CCCTTGTGGG
54774365 CAAGTGACTG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
26 1 0.03
27 27 0.93
28 1 0.03
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.38
Consensus pattern (27 bp):
CCCTTGTGGGGTAAAATGACCATTTTG
Found at i:54774835 original size:96 final size:98
Alignment explanation
Indices: 54774626--54774845 Score: 293
Period size: 96 Copynumber: 2.3 Consensus size: 98
54774616 TCATCCGAGA
* *
54774626 TGATTATAGACCCGTTATCGATGGCTGAGTGCCGATCATGTTACTGAACGCTGTGTGCCTTTATT
1 TGATTATAGACCCGTTATCGATGGCTGAGTGCCGATCATGTTACCGAACGCTGTGTGCCATTATT
* * * *
54774691 ATGGGCTTTGTATTAATATTGTGGGCTTTGTAC
66 ATAGGCTTCGTATCAATATTGTGGGCTTCGTAC
* * * *
54774724 CGATTATAGATCCGTTATAGATGGCTGAGT-CTCGATCATGTTACCGAA-GGT-TGTGCCATTAT
1 TGATTATAGACCCGTTATCGATGGCTGAGTGC-CGATCATGTTACCGAACGCTGTGTGCCATTAT
* * *
54774786 TGTAGGCTTCGTATCGATATTGTGGGCTTCGTGC
65 TATAGGCTTCGTATCAATATTGTGGGCTTCGTAC
54774820 TGATTATAGACCCGTTATCGATGGCT
1 TGATTATAGACCCGTTATCGATGGCT
54774846 TTGTGCCACG
Statistics
Matches: 105, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
96 60 0.57
97 3 0.03
98 42 0.40
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (98 bp):
TGATTATAGACCCGTTATCGATGGCTGAGTGCCGATCATGTTACCGAACGCTGTGTGCCATTATT
ATAGGCTTCGTATCAATATTGTGGGCTTCGTAC
Found at i:54775051 original size:6 final size:6
Alignment explanation
Indices: 54775042--54775135 Score: 77
Period size: 6 Copynumber: 15.3 Consensus size: 6
54775032 TTGCATTTAC
* *
54775042 ATTCTG ATTCTG ATTCTG -TCACCTG ATTCTG ATTCTG ATTCTA ATTCTG
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
54775091 -TTACCTG ATTCTG ATTCTG GTTCTC ATTTTG ATTCT- AGTTCTG AT
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
54775136 AATGTTTCTT
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
5 4 0.06
6 56 0.80
7 7 0.10
8 3 0.04
ACGTcount: A:0.17, C:0.19, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:54775077 original size:31 final size:31
Alignment explanation
Indices: 54775042--54775114 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 31
54775032 TTGCATTTAC
*
54775042 ATTCTGATTCTGATTCTGTCACCTGATTCTG
1 ATTCTGATTCTAATTCTGTCACCTGATTCTG
*
54775073 ATTCTGATTCTAATTCTGTTACCTGATTCTG
1 ATTCTGATTCTAATTCTGTCACCTGATTCTG
*
54775104 ATTCTGGTTCT
1 ATTCTGATTCT
54775115 CATTTTGATT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.16, C:0.21, G:0.15, T:0.48
Consensus pattern (31 bp):
ATTCTGATTCTAATTCTGTCACCTGATTCTG
Found at i:54777220 original size:27 final size:27
Alignment explanation
Indices: 54777190--54777328 Score: 192
Period size: 27 Copynumber: 5.2 Consensus size: 27
54777180 CGATTTACAA
*
54777190 AATTATTGAAATACCCTTGTAGGGTAG
1 AATTATCGAAATACCCTTGTAGGGTAG
*
54777217 AATTA-CTGAAATACCC-TGTAAGGTAG
1 AATTATC-GAAATACCCTTGTAGGGTAG
*
54777243 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTATCGAAATACCCTTGTAGGGTAG
* *
54777270 AAATATCGAAATACCCCTGTAGGGTAG
1 AATTATCGAAATACCCTTGTAGGGTAG
* *
54777297 AATTATCGAGATACCCTTGTAGGGTAA
1 AATTATCGAAATACCCTTGTAGGGTAG
54777324 AATTA
1 AATTA
54777329 CCATTTTGCC
Statistics
Matches: 99, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
26 23 0.23
27 76 0.77
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (27 bp):
AATTATCGAAATACCCTTGTAGGGTAG
Found at i:54777312 original size:54 final size:53
Alignment explanation
Indices: 54777190--54777326 Score: 197
Period size: 53 Copynumber: 2.6 Consensus size: 53
54777180 CGATTTACAA
* *
54777190 AATTATTGAAATACCCTTGTAGGGTAGAATTACTGAAATACCCTGTAAGGTAG
1 AATTATCGAAATACCCTTGTAGGGTAGAAATACTGAAATACCCTGTAAGGTAG
* *
54777243 AATTACCGAAATACCCTTGTAGGGTAGAAATA-TCGAAATACCCCTGTAGGGTAG
1 AATTATCGAAATACCCTTGTAGGGTAGAAATACT-GAAATA-CCCTGTAAGGTAG
*
54777297 AATTATCGAGATACCCTTGTAGGGTA-AAAT
1 AATTATCGAAATACCCTTGTAGGGTAGAAAT
54777327 TACCATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
52 1 0.01
53 39 0.51
54 36 0.47
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (53 bp):
AATTATCGAAATACCCTTGTAGGGTAGAAATACTGAAATACCCTGTAAGGTAG
Found at i:54777807 original size:98 final size:98
Alignment explanation
Indices: 54777635--54777852 Score: 328
Period size: 98 Copynumber: 2.2 Consensus size: 98
54777625 TCGCTCGAGA
** * * * *
54777635 CGATTATAGACCCATTATCGATGGCTGAGTGCCGATCATGTTACCGAAGGCTGTGTGCCGTTATT
1 CGATTATAGACCTGTTATCGATAGCTGAGTACCGATCATGTTACCGAAGGCTATGTGCCATTATT
*
54777700 GTGGGCTTCGTATTGATATTGTGGGCTTCGTGC
66 GTGGGCTTCGTATCGATATTGTGGGCTTCGTGC
**
54777733 CGATTATAGACCTGTTATCGATATTTGAGTACCGATCATGTTACCGAAGGCTATGTGCCATTATT
1 CGATTATAGACCTGTTATCGATAGCTGAGTACCGATCATGTTACCGAAGGCTATGTGCCATTATT
*
54777798 GTGGTCTTCGTATCGATATTGTGGGCTTCGTGC
66 GTGGGCTTCGTATCGATATTGTGGGCTTCGTGC
* *
54777831 CAATTATAGACTTGTTATCGAT
1 CGATTATAGACCTGTTATCGAT
54777853 GGCTTTGTGC
Statistics
Matches: 108, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 108 1.00
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (98 bp):
CGATTATAGACCTGTTATCGATAGCTGAGTACCGATCATGTTACCGAAGGCTATGTGCCATTATT
GTGGGCTTCGTATCGATATTGTGGGCTTCGTGC
Found at i:54778062 original size:6 final size:6
Alignment explanation
Indices: 54778053--54778146 Score: 59
Period size: 6 Copynumber: 15.3 Consensus size: 6
54778043 TTGCATTCAC
* *
54778053 ATTCTG ATTCTG ATTCTG -TCACCTG ATTCTG ATTCTG ATTCTA ATTCTG
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * * *
54778102 CCA-CCTG ATTCTA ATTCTG GTTCTC ATTTTG ATTCT- AGTTCTG AT
1 --ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
54778147 AATGTTTCTT
Statistics
Matches: 66, Mismatches: 14, Indels: 16
0.69 0.15 0.17
Matches are distributed among these distances:
5 3 0.05
6 54 0.82
7 7 0.11
8 2 0.03
ACGTcount: A:0.18, C:0.21, G:0.14, T:0.47
Consensus pattern (6 bp):
ATTCTG
Found at i:54778088 original size:31 final size:31
Alignment explanation
Indices: 54778053--54778125 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
54778043 TTGCATTCAC
* * *
54778053 ATTCTGATTCTGATTCTGTCACCTGATTCTG
1 ATTCTGATTCTAATTCTGCCACCTGATTCTA
54778084 ATTCTGATTCTAATTCTGCCACCTGATTCTA
1 ATTCTGATTCTAATTCTGCCACCTGATTCTA
*
54778115 ATTCTGGTTCT
1 ATTCTGATTCT
54778126 CATTTTGATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.18, C:0.23, G:0.14, T:0.45
Consensus pattern (31 bp):
ATTCTGATTCTAATTCTGCCACCTGATTCTA
Found at i:54779190 original size:48 final size:48
Alignment explanation
Indices: 54779107--54779484 Score: 452
Period size: 48 Copynumber: 7.9 Consensus size: 48
54779097 ACTCAAAAGT
* * * *
54779107 CTCGCACCCTAGGTGCCAATATCATGGCCCGAAGCCAAATCAAT-AAA
1 CTCGCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGTAA
* * * * *
54779154 GCTCGTACCCAAAGTGCCAATATCATGGCCCGAAGCCAAATTAATATAA
1 -CTCGCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGTAA
* * * *
54779203 CTCGCACTCGAGGTGCTAATATCATGGCCTGAAGCCAAATCAATGTCA
1 CTCGCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGTAA
* * * *
54779251 GTCACACCTGAAGTGCTAATATCATGGCCCGAAGCCAAATTAATGTAA
1 CTCGCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGTAA
* * * *
54779299 CTTGCACCAGAAGTGCTAATATCGTGGCCTGAAGCCAAATCAATGTAA
1 CTCGCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGTAA
*** * *
54779347 CTCATTCCCGAAGTGCTAATATCATGGCCTGAAGCCAAATCAACGTAA
1 CTCGCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGTAA
* * *
54779395 CTCGCGCCTGAAGTACTAATATCATGGCCCGAAGCCAAATCAATGTAA
1 CTCGCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGTAA
** *
54779443 CTTACACTCGAAGTGCTAATATCATGGCCCGAAGCCAAATCA
1 CTCGCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCA
54779485 GTAAAACTTC
Statistics
Matches: 280, Mismatches: 49, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
48 278 0.99
49 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (48 bp):
CTCGCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGTAA
Found at i:54781634 original size:21 final size:21
Alignment explanation
Indices: 54781610--54781657 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
54781600 GTGATTGACA
* *
54781610 CACACGCCTGTGTGGTTATTC
1 CACACGCCTATGTGGATATTC
* * *
54781631 CACATGCTTATTTGGATATTC
1 CACACGCCTATGTGGATATTC
54781652 CACACG
1 CACACG
54781658 TCTGCGCTCT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (21 bp):
CACACGCCTATGTGGATATTC
Found at i:54785932 original size:31 final size:31
Alignment explanation
Indices: 54785896--54785965 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
54785886 ACATCCATAG
*
54785896 AGATAGTTT-GCTAGAACAATAGACACAAAAT
1 AGATAGTTTAG-TAGAACAATAAACACAAAAT
* * *
54785927 AGATAGTTTAGTGGGACAATAAACACAGAAT
1 AGATAGTTTAGTAGAACAATAAACACAAAAT
54785958 AGATAGTT
1 AGATAGTT
54785966 CGCAAGGACA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (31 bp):
AGATAGTTTAGTAGAACAATAAACACAAAAT
Found at i:54785975 original size:31 final size:31
Alignment explanation
Indices: 54785896--54785975 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 31
54785886 ACATCCATAG
* * *
54785896 AGATAGTTTGCTAGAACAATAGACACAAAAT
1 AGATAGTTAGCTAGGACAATAAACACAAAAT
* *
54785927 AGATAGTTTAG-TGGGACAATAAACACAGAAT
1 AGATAG-TTAGCTAGGACAATAAACACAAAAT
* *
54785958 AGATAGTTCGCAAGGACA
1 AGATAGTTAGCTAGGACA
54785976 GTGAACACGG
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
30 3 0.08
31 33 0.85
32 3 0.08
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.21
Consensus pattern (31 bp):
AGATAGTTAGCTAGGACAATAAACACAAAAT
Found at i:54788495 original size:93 final size:93
Alignment explanation
Indices: 54788380--54788550 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
54788370 GCCCCTAAGT
*
54788380 GAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
54788444 ACGAGTTCGGATGCCTAGTTACATTTCAA
65 ACGAGTTCGGATGCCTAGTTACATTTCAA
*
54788473 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54788538 CGAGTTCGGATGC
66 CGAGTTCGGATGC
54788551 TCAACCATCC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAA
Found at i:54788545 original size:46 final size:46
Alignment explanation
Indices: 54788375--54788547 Score: 205
Period size: 46 Copynumber: 3.7 Consensus size: 46
54788365 AACCGGCCCC
* *
54788375 TAAGTGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCA
* *
54788421 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
54788469 TCAA--GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 T-AAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
54788514 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54788548 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 6, Indels: 24
0.78 0.04 0.17
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 3 0.03
45 3 0.03
46 59 0.54
47 29 0.27
48 1 0.01
49 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:54789002 original size:30 final size:30
Alignment explanation
Indices: 54788968--54789027 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
54788958 ATTTAATACG
54788968 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
54788998 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
54789028 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:54796518 original size:30 final size:30
Alignment explanation
Indices: 54796484--54796543 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
54796474 ATTTAATACG
54796484 AACTTTGGA-AAAATTACACTTTTGCCCCTA
1 AACTTT-GACAAAATTACACTTTTGCCCCTA
* *
54796514 AACTTTTACATAATTACACTTTTGCCCCTA
1 AACTTTGACAAAATTACACTTTTGCCCCTA
54796544 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.37
Consensus pattern (30 bp):
AACTTTGACAAAATTACACTTTTGCCCCTA
Found at i:54801552 original size:47 final size:49
Alignment explanation
Indices: 54801478--54801608 Score: 142
Period size: 47 Copynumber: 2.7 Consensus size: 49
54801468 GGTATAAAGC
* *
54801478 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATC-C-ATC-AAGT
1 CGATACCATGTCCCAGACATGGTCTTACACTGGCTC-TCACAATCTAAGT
* * ** **
54801525 CGATACCATGTTCCAGACATTGTCTTACACTAACTCTCACATATCTGTGT
1 CGATACCATGTCCCAGACATGGTCTTACACTGGCTCTCACA-ATCTAAGT
*
54801575 CGATACCATGTCCCAGACATGGTCTTACATTGGC
1 CGATACCATGTCCCAGACATGGTCTTACACTGGC
54801609 ACATTTTGCA
Statistics
Matches: 67, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
46 2 0.03
47 31 0.46
49 3 0.04
50 31 0.46
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (49 bp):
CGATACCATGTCCCAGACATGGTCTTACACTGGCTCTCACAATCTAAGT
Found at i:54801675 original size:46 final size:46
Alignment explanation
Indices: 54801581--54801789 Score: 167
Period size: 46 Copynumber: 4.5 Consensus size: 46
54801571 GTGTCGATAC
* * * *
54801581 CATGTCCCAGACATGGTCTTACATTGGC--ACATTTTGCA-GCCGATG
1 CATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCG-AGGCCGAGG
*
54801626 CATGTCCCAGTCATGTCTTACACTGGCTTACATCTCGAGGCCGAGG
1 CATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCGAGG
* **** * * * *
54801672 CATGTCCCAGACATGTCTTACACTAGCTCGTGTCTCAATGCTGATGT
1 CATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCGA-GG
* * * *
54801719 CATGTCCCAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGCTGATG
1 CATGTCCCAGACAT-GTCTTACACTGGCT-TACAT-CTCGAGGCCGAGG
54801766 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
54801790 AGCACACAAA
Statistics
Matches: 132, Mismatches: 25, Indels: 13
0.78 0.15 0.08
Matches are distributed among these distances:
44 12 0.09
45 14 0.11
46 57 0.43
47 29 0.22
48 19 0.14
49 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCGAGG
Found at i:54801738 original size:94 final size:92
Alignment explanation
Indices: 54801622--54801792 Score: 247
Period size: 94 Copynumber: 1.8 Consensus size: 92
54801612 TTTTGCAGCC
* *
54801622 GATGCATGTCCCAGTCATGTCTTACACTGGCT-TACAT-CTCGAGGCCGAGGCATGTCCCAGACA
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCT-CATAAT-GAGGCCGAGGCATGTCCCAGACA
54801685 TGTCTTACACTAGCTCGTGTCTCAATGCT
64 TGTCTTACACTAGCTCGTGTCTCAATGCT
* * *
54801714 GATGTCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCTGATGCATGTCCCAGACA
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATAATGAGGCCGAGGCATGTCCCAGACA
54801779 TGTCTTACACTAGC
64 TGTCTTACACTAGC
54801793 ACACAAATGA
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
92 4 0.06
93 13 0.19
94 51 0.73
95 2 0.03
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.29
Consensus pattern (92 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAATGAGGCCGAGGCATGTCCCAGACATG
TCTTACACTAGCTCGTGTCTCAATGCT
Found at i:54805419 original size:20 final size:20
Alignment explanation
Indices: 54805394--54805439 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
54805384 CAGAAAATGA
54805394 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
54805414 TTTCT-GAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
54805433 TTTCTGG
1 TTTCTGG
54805440 TGTTTGGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:54805889 original size:46 final size:46
Alignment explanation
Indices: 54805819--54805940 Score: 190
Period size: 46 Copynumber: 2.7 Consensus size: 46
54805809 AATAATATTA
* * * *
54805819 TCCAAATGCATAATTAGTAGTACACCACATGATAACAACAACACTG
1 TCCAAGTGCATAACTAATATTACACCACATGATAACAACAACACTG
* *
54805865 TCCAAGTGCATAACTAATATTACACCACATGATTACAACAACATTG
1 TCCAAGTGCATAACTAATATTACACCACATGATAACAACAACACTG
54805911 TCCAAGTGCATAACTAATATTACACCACAT
1 TCCAAGTGCATAACTAATATTACACCACAT
54805941 TAAAAGTATC
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 70 1.00
ACGTcount: A:0.42, C:0.25, G:0.09, T:0.25
Consensus pattern (46 bp):
TCCAAGTGCATAACTAATATTACACCACATGATAACAACAACACTG
Found at i:54806937 original size:32 final size:32
Alignment explanation
Indices: 54806891--54806951 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
54806881 TGTCAATCAT
54806891 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
* *
54806923 TTCAATATCTAACAAGCTTGAAACATAAT
1 TTCAATATCCAACAAGCTTAAAACATAAT
54806952 CGATATCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.49, C:0.18, G:0.05, T:0.28
Consensus pattern (32 bp):
TTCAATATCCAACAAGCTTAAAACATAATAAA
Found at i:54806975 original size:27 final size:27
Alignment explanation
Indices: 54806927--54806978 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
54806917 AATAAATTCA
* *
54806927 ATATCTAACAAGCTTGAAACATAATCG
1 ATATCTAACAAGATTCAAACATAATCG
54806954 ATATCTAACAA-ATTCAAGACATAAT
1 ATATCTAACAAGATTCAA-ACATAAT
54806979 AATTTCAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.48, C:0.17, G:0.08, T:0.27
Consensus pattern (27 bp):
ATATCTAACAAGATTCAAACATAATCG
Found at i:54808507 original size:15 final size:15
Alignment explanation
Indices: 54808487--54808526 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
54808477 TTCTCAAGCA
*
54808487 ATGACTAAAGTTACT
1 ATGACTAAAGTTACC
54808502 ATGACTAAAGTTACC
1 ATGACTAAAGTTACC
*
54808517 ATGATTAAAG
1 ATGACTAAAG
54808527 GGAATGGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (15 bp):
ATGACTAAAGTTACC
Found at i:54812140 original size:3 final size:3
Alignment explanation
Indices: 54812132--54812170 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
54812122 TTTGAAGAAC
54812132 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
54812171 CTTACCTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:54812233 original size:31 final size:31
Alignment explanation
Indices: 54812198--54812260 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
54812188 GGAGGTGGAA
**
54812198 AAAGTTGAAGAATTGAAGAAAAAAAAGGCTT
1 AAAGTTGAAGAACGGAAGAAAAAAAAGGCTT
54812229 AAAGTTGAAGAACGGAAGAAAAAAAAGGCTT
1 AAAGTTGAAGAACGGAAGAAAAAAAAGGCTT
54812260 A
1 A
54812261 CCTGGATGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.56, C:0.05, G:0.24, T:0.16
Consensus pattern (31 bp):
AAAGTTGAAGAACGGAAGAAAAAAAAGGCTT
Found at i:54818163 original size:3 final size:3
Alignment explanation
Indices: 54818155--54818180 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
54818145 ATTACATCCA
54818155 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
54818181 AACATGTGAT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:54822490 original size:55 final size:55
Alignment explanation
Indices: 54822406--54822512 Score: 214
Period size: 55 Copynumber: 1.9 Consensus size: 55
54822396 AGTTGGAATA
54822406 CAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTACCATTC
1 CAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTACCATTC
54822461 CAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTACCA
1 CAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTACCA
54822513 CTAACAAACT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.39, C:0.31, G:0.02, T:0.28
Consensus pattern (55 bp):
CAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTACCATTC
Found at i:54822580 original size:73 final size:73
Alignment explanation
Indices: 54822461--54822631 Score: 333
Period size: 73 Copynumber: 2.3 Consensus size: 73
54822451 ACTACCATTC
54822461 CAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTACCACTAACAAACTTAG
1 CAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTACCACTAACAAACTTAG
54822526 TTGGAATA
66 TTGGAATA
54822534 CAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTACCACTAACAAACTTAG
1 CAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTACCACTAACAAACTTAG
54822599 TTGGAATA
66 TTGGAATA
*
54822607 CAACTAAGTTACATCATTACATCCA
1 CAACTAAGTTTCATCATTACATCCA
54822632 AATAATAATA
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 97 1.00
ACGTcount: A:0.41, C:0.26, G:0.05, T:0.27
Consensus pattern (73 bp):
CAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTACCACTAACAAACTTAG
TTGGAATA
Found at i:54829557 original size:72 final size:72
Alignment explanation
Indices: 54829471--54829654 Score: 228
Period size: 72 Copynumber: 2.6 Consensus size: 72
54829461 AATGTGGGTT
**
54829471 CGGGTACTGACTTTGTGTATAAACCCGTGAGTAACTCGCTGAGCGAGCA-TATCAT-ATTAATGC
1 CGGGTACTGACTTTGTGTATAAACCCGTGAGTAACTCAATGAGCGAGCATTA-CATGA-TAATGC
54829534 TTTGAGGTC
64 TTTGAGGTC
* * * *
54829543 CGGGTACTGACTTTGTGCATAAACCCTTGAGTAGCTCAATGAGCGGGCATTACATGATAATGCTT
1 CGGGTACTGACTTTGTGTATAAACCCGTGAGTAACTCAATGAGCGAGCATTACATGATAATGCTT
*
54829608 TGGGGTC
66 TGAGGTC
* * * * *
54829615 CGAGTGCTGACTTTGTGTACAGACCCGTGAGTAGCTCAAT
1 CGGGTACTGACTTTGTGTATAAACCCGTGAGTAACTCAAT
54829655 TGTGGGCATT
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
72 94 0.97
73 3 0.03
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (72 bp):
CGGGTACTGACTTTGTGTATAAACCCGTGAGTAACTCAATGAGCGAGCATTACATGATAATGCTT
TGAGGTC
Found at i:54838163 original size:30 final size:30
Alignment explanation
Indices: 54838129--54838189 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
54838119 TTCTCGAGCC
*
54838129 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGAAAAAGTATAAATATGCAAAAGTT
* * * *
54838159 TAGGGGCAAAATTATAATTTTGCAAAAGTT
1 TAGGGGAAAAAGTATAAATATGCAAAAGTT
54838189 T
1 T
54838190 GAGTTAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.43, C:0.05, G:0.23, T:0.30
Consensus pattern (30 bp):
TAGGGGAAAAAGTATAAATATGCAAAAGTT
Found at i:54839005 original size:64 final size:64
Alignment explanation
Indices: 54838924--54839107 Score: 219
Period size: 67 Copynumber: 2.8 Consensus size: 64
54838914 AGACATTATG
* * *
54838924 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * *
54838988 ATGTAGCTAGGTCGCATGCGTGGTTCTAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
54839053 AA
63 AA
* * * *
54839055 AT-TGGCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG-ACAAGAGAGC
54839108 CAAACTATAT
Statistics
Matches: 101, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 26 0.26
66 23 0.23
67 32 0.32
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:54844434 original size:15 final size:15
Alignment explanation
Indices: 54844414--54844442 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
54844404 ATTCCACGTT
54844414 TAAATGAAATGCATG
1 TAAATGAAATGCATG
54844429 TAAATGAAATGCAT
1 TAAATGAAATGCAT
54844443 CTATTGCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (15 bp):
TAAATGAAATGCATG
Found at i:54852967 original size:26 final size:26
Alignment explanation
Indices: 54852931--54853012 Score: 128
Period size: 26 Copynumber: 3.2 Consensus size: 26
54852921 TGAAATGCCC
* * *
54852931 ATCATGGAACATTTACTTAAACTATT
1 ATCATGGAACATTTACCTAACCCATT
54852957 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
54852983 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
54853009 ATCA
1 ATCA
54853013 ATTTGTACCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:54854466 original size:21 final size:20
Alignment explanation
Indices: 54854437--54854475 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
54854427 CTTGAGAGTA
*
54854437 TTGTCACACCGCAAGTTTTTC
1 TTGTAACACC-CAAGTTTTTC
*
54854458 TTGTAACACCCCAGTTTT
1 TTGTAACACCCAAGTTTT
54854476 GGCGAGTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.21, C:0.28, G:0.13, T:0.38
Consensus pattern (20 bp):
TTGTAACACCCAAGTTTTTC
Found at i:54856006 original size:43 final size:43
Alignment explanation
Indices: 54855945--54856184 Score: 408
Period size: 43 Copynumber: 5.6 Consensus size: 43
54855935 TTGGCATTAA
*
54855945 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTACGAAG
1 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAG
* * *
54855988 CCTGCTAGGCACGAAGGCCCGAATACATATCACCAGTACGAAG
1 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAG
* * *
54856031 CCTGCTAGGCACGAAGGCCCAAATACACATTACTGGCACGAAG
1 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAG
*
54856074 CCTGCTAGGCACGAAGGCTCGAATACACATCACCGGCACGAAG
1 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAG
54856117 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAG
1 CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAG
54856160 CCTGCTAGGCACGAAGGCCCGAATA
1 CCTGCTAGGCACGAAGGCCCGAATA
54856185 TAATACCAGC
Statistics
Matches: 184, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 184 1.00
ACGTcount: A:0.31, C:0.32, G:0.25, T:0.12
Consensus pattern (43 bp):
CCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAG
Found at i:54856225 original size:38 final size:38
Alignment explanation
Indices: 54856182--54856284 Score: 143
Period size: 38 Copynumber: 2.7 Consensus size: 38
54856172 GAAGGCCCGA
* * *
54856182 ATATAATACCAGCACTAGGCCTGCGGGATTTATCCAAG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCAAG
**
54856220 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCAAG
**
54856258 ATATTTTACCAGCACGAAGCCTGCGGG
1 ATATAATACCAGCACGAAGCCTGCGGG
54856285 TCTTTAAGCC
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 58 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.21
Consensus pattern (38 bp):
ATATAATACCAGCACGAAGCCTGCGGGATTTAACCAAG
Found at i:54859547 original size:48 final size:48
Alignment explanation
Indices: 54859487--54859589 Score: 120
Period size: 48 Copynumber: 2.1 Consensus size: 48
54859477 GTCCAACTAT
* * * *
54859487 GGTCTTATACTAGCTCTGCTCT-GACCGTGCTGATGCCTATTCCC-GATA
1 GGTCTTACACTAGCACT-CACTGGACCGTGCCGATGCCTA-TCCCAGATA
* *
54859535 GGTCTTACACTAGCACTCACTGGGCTGTGCCGATGCCTATCCCAGATA
1 GGTCTTACACTAGCACTCACTGGACCGTGCCGATGCCTATCCCAGATA
54859583 GGTCTTA
1 GGTCTTA
54859590 TGCTTAGCAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 7 0.15
48 40 0.85
ACGTcount: A:0.18, C:0.29, G:0.22, T:0.30
Consensus pattern (48 bp):
GGTCTTACACTAGCACTCACTGGACCGTGCCGATGCCTATCCCAGATA
Found at i:54861182 original size:43 final size:43
Alignment explanation
Indices: 54861122--54861362 Score: 365
Period size: 43 Copynumber: 5.6 Consensus size: 43
54861112 CCGGCATTAC
* * *
54861122 GCCTGTTAGGTACGAAGGCCCGAATACACATCACCGGCATGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* * * *
54861165 GCCTGCTAGGCATGAAGGCCCGAATATACATCACTGGTACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
54861208 GCCAGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
54861251 GCCTACTAGGCACGAAGGCCCGAATACACATCACCGGCACGGA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* * *
54861294 GCCTGGTAGGTACGAAGGCCTGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
54861337 GCCTGCTAGGCACGAAGGCCCGAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
54861363 TAATACCAGC
Statistics
Matches: 175, Mismatches: 23, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 175 1.00
ACGTcount: A:0.30, C:0.30, G:0.27, T:0.13
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:54861403 original size:38 final size:38
Alignment explanation
Indices: 54861355--54861439 Score: 125
Period size: 38 Copynumber: 2.2 Consensus size: 38
54861345 GGCACGAAGG
* * * * *
54861355 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGGATATAATACCAACACGAAGCCTGCGGGATTTAA
54861393 CCCGGATATAATACCAACACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAACACGAAGCCTGCGGGATTTAA
54861431 CCCGGATAT
1 CCCGGATAT
54861440 TTTACTAGCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (38 bp):
CCCGGATATAATACCAACACGAAGCCTGCGGGATTTAA
Found at i:54862286 original size:20 final size:20
Alignment explanation
Indices: 54862248--54862286 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
54862238 ATGATGGGGA
*
54862248 TCAAGAATATCAAGTTGGAT
1 TCAAGAATATCAAGCTGGAT
54862268 TCAAGAA-ATCGAAGCTGGA
1 TCAAGAATATC-AAGCTGGA
54862287 GGAGAGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.23
Consensus pattern (20 bp):
TCAAGAATATCAAGCTGGAT
Found at i:54864239 original size:46 final size:46
Alignment explanation
Indices: 54864187--54864506 Score: 507
Period size: 46 Copynumber: 7.0 Consensus size: 46
54864177 AGTGTGCTCT
*
54864187 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
54864233 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
54864279 CTAATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
54864325 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
54864371 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ***
54864417 GTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
54864463 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGATACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
54864507 TCATGTCAAA
Statistics
Matches: 260, Mismatches: 13, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
45 1 0.00
46 259 1.00
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:54868114 original size:54 final size:53
Alignment explanation
Indices: 54868038--54868223 Score: 207
Period size: 54 Copynumber: 3.5 Consensus size: 53
54868028 CTTTGTAGAT
* * * *
54868038 AAACATGAAAAAAAAGCCTTTGTGGAAAATCATGAAAGAAAAGCTTTTGTTGCG
1 AAACATGAAAGAAAAGCTTTTGTGG-AAATCATGAAAGAAAAGCCTTTGTTGTG
* * *
54868092 AAACATGAAAGAAAAGTTTTTGTGGCAAATCTTGAAAGAAAAGCCTTTGTGGTG
1 AAACATGAAAGAAAAGCTTTTGTGG-AAATCATGAAAGAAAAGCCTTTGTTGTG
* * *
54868146 AAATATGAAAGGAAAGCTTTATG-GTGAAAT-ATGAAAGAAAAACCTTTG-TGATG
1 AAACATGAAAGAAAAGCTTT-TGTG-GAAATCATGAAAGAAAAGCCTTTGTTG-TG
*
54868199 AAACATGAAAGAAAAACTTTTGTGG
1 AAACATGAAAGAAAAGCTTTTGTGG
54868224 CGAAATATGT
Statistics
Matches: 111, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
52 4 0.04
53 36 0.32
54 68 0.61
55 3 0.03
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.26
Consensus pattern (53 bp):
AAACATGAAAGAAAAGCTTTTGTGGAAATCATGAAAGAAAAGCCTTTGTTGTG
Found at i:54868221 original size:80 final size:79
Alignment explanation
Indices: 54868022--54868232 Score: 216
Period size: 80 Copynumber: 2.6 Consensus size: 79
54868012 CTAGGAAATA
*
54868022 AAAAACCTTTGTAGAT-AAACATGAAA-AAAAAGCCTTTGTGGAAAATCATGAAAGAAAAGCTTT
1 AAAAACCTTTGT-GATGAAACATGAAAGAAAAA-CCTTTGTGGGAAAT-ATGAAAGAAAAGCTTT
54868085 TGTTGCGAAACATGAAAG
63 TG-TGCGAAACATGAAAG
*** * * *
54868103 AAAAGTTTTTGTG--GCAAATCTTGAAAGAAAAGCCTTTGTGGTGAAATATGAAAGGAAAGCTTT
1 AAAAACCTTTGTGATG-AAA-CATGAAAGAAAAACCTTTGTGG-GAAATATGAAAGAAAAGCTTT
* *
54868166 ATG-GTGAAATATGAAAG
63 -TGTGCGAAACATGAAAG
*
54868183 AAAAACCTTTGTGATGAAACATGAAAGAAAAACTTTTGTGGCGAAATATG
1 AAAAACCTTTGTGATGAAACATGAAAGAAAAACCTTTGTGG-GAAATATG
54868233 TGTAACACCC
Statistics
Matches: 106, Mismatches: 16, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
80 53 0.50
81 42 0.40
82 11 0.10
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (79 bp):
AAAAACCTTTGTGATGAAACATGAAAGAAAAACCTTTGTGGGAAATATGAAAGAAAAGCTTTTGT
GCGAAACATGAAAG
Found at i:54868228 original size:27 final size:27
Alignment explanation
Indices: 54868038--54868228 Score: 181
Period size: 27 Copynumber: 7.1 Consensus size: 27
54868028 CTTTGTAGAT
* *
54868038 AAACATGAAAAAAAAGCCTTTGTGG-A
1 AAACATGAAAGAAAAGCCTTTGTGGCG
* *
54868064 AAATCATGAAAGAAAAGCTTTTGTTGCG
1 AAA-CATGAAAGAAAAGCCTTTGTGGCG
**
54868092 AAACATGAAAGAAAAGTTTTTGTGGC-
1 AAACATGAAAGAAAAGCCTTTGTGGCG
* *
54868118 AAATCTTGAAAGAAAAGCCTTTGTGGTG
1 AAA-CATGAAAGAAAAGCCTTTGTGGCG
* * * *
54868146 AAATATGAAAGGAAAG-CTTTATGGTG
1 AAACATGAAAGAAAAGCCTTTGTGGCG
* * **
54868172 AAATATGAAAGAAAAACCTTTGTGATG
1 AAACATGAAAGAAAAGCCTTTGTGGCG
* *
54868199 AAACATGAAAGAAAAACTTTTGTGGCG
1 AAACATGAAAGAAAAGCCTTTGTGGCG
54868226 AAA
1 AAA
54868229 TATGTGTAAC
Statistics
Matches: 138, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
26 29 0.21
27 103 0.75
28 6 0.04
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (27 bp):
AAACATGAAAGAAAAGCCTTTGTGGCG
Found at i:54869747 original size:42 final size:42
Alignment explanation
Indices: 54869632--54869786 Score: 170
Period size: 42 Copynumber: 3.7 Consensus size: 42
54869622 TATCATACCA
* * *
54869632 ATGCCATATCCCAGATATGGTCTTACATG-GGATCTCGT-TTCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAG-TCTCATATT-G
* * * * *
54869674 ATGCCAATAGCCTAGCTATGGCCTTATACGAAGTCTCATATTG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAGTCTCATATTG
* * *
54869717 ATGCCATATCCTAGATATGGTCTTACACGAAATCTCATATAG
1 ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATTG
54869759 ATGCCATATCCCAGATATGGTCTTACAC
1 ATGCCATATCCCAGATATGGTCTTACAC
54869787 ATAGTCTTAG
Statistics
Matches: 95, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
42 63 0.66
43 29 0.31
44 3 0.03
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATTG
Found at i:54880361 original size:42 final size:41
Alignment explanation
Indices: 54880267--54880379 Score: 127
Period size: 42 Copynumber: 2.7 Consensus size: 41
54880257 ATCTCATTTC
* * * * *
54880267 GATGCCAATAACCCAGCTATGGTCTTACACGAAGTCTCATATC
1 GATGCC-ATATCCCAGATAT-GTCTTACACGAAATCTAATATA
* *
54880310 GATGCCATATCCCATATATAGTCTTACATGAAATCTAATATA
1 GATGCCATATCCCAGATAT-GTCTTACACGAAATCTAATATA
*
54880352 GATGTCATATCCCAGATATGTCTTACAC
1 GATGCCATATCCCAGATATGTCTTACAC
54880380 ATGGTCTTAG
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 8 0.14
42 45 0.76
43 6 0.10
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (41 bp):
GATGCCATATCCCAGATATGTCTTACACGAAATCTAATATA
Found at i:54881038 original size:27 final size:27
Alignment explanation
Indices: 54881004--54881074 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
54880994 TACAATATGA
54881004 AAAG-AAAGCCTTTGTGGAAAAACATG
1 AAAGAAAAGCCTTTGTGGAAAAACATG
**** *
54881030 AAAGAAAAGCCTTTGTATCGAATCATG
1 AAAGAAAAGCCTTTGTGGAAAAACATG
*
54881057 AAAGAAAAGCCCTTGTGG
1 AAAGAAAAGCCTTTGTGG
54881075 TGAAATAGAA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
26 4 0.11
27 32 0.89
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (27 bp):
AAAGAAAAGCCTTTGTGGAAAAACATG
Found at i:54884434 original size:27 final size:27
Alignment explanation
Indices: 54884404--54884490 Score: 102
Period size: 27 Copynumber: 3.2 Consensus size: 27
54884394 ATTACCAAAG
* *
54884404 TACCCTTGATTTATAGAATCATTGTTT
1 TACCCTTGATTTACAGAATCACTGTTT
*
54884431 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTTGATTTACAGAATCACTGTTT
* * * * *
54884458 TACCCTCGACTTACAAAATTACCGTTT
1 TACCCTTGATTTACAGAATCACTGTTT
54884485 TACCCT
1 TACCCT
54884491 CAATTGTGAA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.41
Consensus pattern (27 bp):
TACCCTTGATTTACAGAATCACTGTTT
Found at i:54884620 original size:27 final size:28
Alignment explanation
Indices: 54884547--54884624 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
54884537 ATACCCCTAA
* *
54884547 TTTACAAAATTACAGAAATACCCTTGAC
1 TTTACAAAATTACTGAAATACCATTGAC
*
54884575 TTT-CTAAAAATTA-TAGAAATACCATTG-G
1 TTTAC--AAAATTACT-GAAATACCATTGAC
54884603 TTTACAAAATTACTGAAATACC
1 TTTACAAAATTACTGAAATACC
54884625 CTTAGTTTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
27 16 0.38
28 7 0.17
29 19 0.45
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.32
Consensus pattern (28 bp):
TTTACAAAATTACTGAAATACCATTGAC
Found at i:54884632 original size:27 final size:27
Alignment explanation
Indices: 54884535--54884632 Score: 92
Period size: 27 Copynumber: 3.6 Consensus size: 27
54884525 AGAATTACCA
* * *
54884535 AAATACCCCTAATTTACAAAATTACAG
1 AAATACCCTTAGTTTACAAAATTACTG
*
54884562 AAATACCCTTGACTTT-CTAAAAATTA-TAG
1 AAATACCCTT-AGTTTAC--AAAATTACT-G
* *
54884591 AAATACCATTGGTTTACAAAATTACTG
1 AAATACCCTTAGTTTACAAAATTACTG
54884618 AAATACCCTTAGTTT
1 AAATACCCTTAGTTT
54884633 GTAGATTTAC
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
27 31 0.54
28 8 0.14
29 18 0.32
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (27 bp):
AAATACCCTTAGTTTACAAAATTACTG
Found at i:54884716 original size:27 final size:27
Alignment explanation
Indices: 54884673--54884746 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
54884663 AAATGACTAA
* *
54884673 AATACCCCTAATA-GGTAAAAAGATCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
54884700 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
*
54884727 AATACCCCTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
54884747 TAATGAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:54885600 original size:25 final size:25
Alignment explanation
Indices: 54885560--54885629 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
54885550 AGGAAGTGCT
* **
54885560 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACAA
* *
54885585 AAAAGGGCTTTTCCCCAGTTTATAA
1 AAAAGGGCTTTGCCCCAGTTTACAA
54885610 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
54885630 ATTAAAAGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACAA
Found at i:54885642 original size:24 final size:23
Alignment explanation
Indices: 54885559--54885656 Score: 79
Period size: 25 Copynumber: 4.0 Consensus size: 23
54885549 GAGGAAGTGC
*
54885559 TAAAAGGGCTATGCCCCAGTTTACC
1 TAAAAGGGCTATGCCCCAG-TTA-T
* * *
54885584 GAAAAGGGCTTTTCCCCAGTTTAT
1 TAAAAGGGCTATGCCCCAG-TTAT
* *
54885608 AAAAAAGGGCTTTGCCCCAGTTAT
1 -TAAAAGGGCTATGCCCCAGTTAT
*
54885632 TAAAAGAGGCTAGGCCTCCAGTTAT
1 TAAAAG-GGCTATGCC-CCAGTTAT
54885657 ATGATAAAGC
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
23 5 0.08
24 11 0.18
25 45 0.74
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (23 bp):
TAAAAGGGCTATGCCCCAGTTAT
Found at i:54885918 original size:29 final size:28
Alignment explanation
Indices: 54885884--54885938 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
54885874 AGACTGAATT
* *
54885884 AGGGCTTAGGCCCATACTGCTACTGTTTA
1 AGGGCTAAGGCCCAGACTG-TACTGTTTA
54885913 AGGGCTAAGGCCCAGACTGTACTGTT
1 AGGGCTAAGGCCCAGACTGTACTGTT
54885939 ACTGAATAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (28 bp):
AGGGCTAAGGCCCAGACTGTACTGTTTA
Found at i:54892808 original size:28 final size:28
Alignment explanation
Indices: 54892768--54892921 Score: 274
Period size: 28 Copynumber: 5.5 Consensus size: 28
54892758 TAAATTGTAC
54892768 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
54892796 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
54892824 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
54892852 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
54892880 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
54892907 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
54892922 GACTTAATAT
Statistics
Matches: 124, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
27 24 0.19
28 100 0.81
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.34
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:54892834 original size:56 final size:56
Alignment explanation
Indices: 54892743--54892921 Score: 279
Period size: 56 Copynumber: 3.2 Consensus size: 56
54892733 GAGATTGGCG
* * * *
54892743 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
54892800 CTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
54892856 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
54892911 CTGAGTGTGCG
1 CTAAGTGTGCG
54892922 GACTTAATAT
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
55 23 0.20
56 76 0.67
57 15 0.13
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
Found at i:54896680 original size:27 final size:27
Alignment explanation
Indices: 54896650--54896741 Score: 130
Period size: 27 Copynumber: 3.4 Consensus size: 27
54896640 ATTACCAAAG
* *
54896650 TACCCTCGATTTATAGAATCACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
54896677 TACCCTTGATTTACAGAATTATTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
54896704 TACCCTCGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
54896731 TACCCTCGATT
1 TACCCTCGATT
54896742 GTGAAATTAC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:54896835 original size:29 final size:27
Alignment explanation
Indices: 54896773--54896878 Score: 106
Period size: 27 Copynumber: 3.9 Consensus size: 27
54896763 TATAGGGTAG
* * *
54896773 AATTACCAAAATACCCCTGATTTACAA
1 AATTACAAAAATACCCTTGGTTTACAA
54896800 AATTACAAAAATACCCTTGAGTTT-CTAAA
1 AATTACAAAAATACCCTTG-GTTTAC--AA
* * *
54896829 AATTACAGAAATACCATTGGTTTAGAA
1 AATTACAAAAATACCCTTGGTTTACAA
**
54896856 AATTACTGAAATACCCTTGGTTT
1 AATTACAAAAATACCCTTGGTTT
54896879 GTAGATTTAC
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
27 41 0.61
28 7 0.10
29 19 0.28
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (27 bp):
AATTACAAAAATACCCTTGGTTTACAA
Found at i:54897837 original size:25 final size:25
Alignment explanation
Indices: 54897799--54897868 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
54897789 AGGAAGTGCT
* *
54897799 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
* *
54897824 AAAAGGGCTTTGCCCCAATTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
54897849 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
54897869 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:54897881 original size:24 final size:23
Alignment explanation
Indices: 54897798--54897881 Score: 78
Period size: 25 Copynumber: 3.4 Consensus size: 23
54897788 GAGGAAGTGC
* *
54897798 TAAAAGGGCTATGCCCCAGTTTACC
1 TAAAAGGGCTTTGCCCCAG-TTA-T
* *
54897823 GAAAAGGGCTTTGCCCCAATTTAT
1 TAAAAGGGCTTTGCCCC-AGTTAT
*
54897847 CAAAAAGGGCTTTGCCCCAGTTAT
1 -TAAAAGGGCTTTGCCCCAGTTAT
54897871 TAAAAGAGGCT
1 TAAAAG-GGCT
54897882 AGGCCTCTAG
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
23 5 0.10
24 9 0.18
25 34 0.69
26 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (23 bp):
TAAAAGGGCTTTGCCCCAGTTAT
Found at i:54898157 original size:29 final size:28
Alignment explanation
Indices: 54898123--54898177 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
54898113 AGACTGAATT
* *
54898123 AGGGCTTAGGCCCATACTGCTACTGTTTA
1 AGGGCTAAGGCCCAGACTG-TACTGTTTA
54898152 AGGGCTAAGGCCCAGACTGTACTGTT
1 AGGGCTAAGGCCCAGACTGTACTGTT
54898178 ACTGAATAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (28 bp):
AGGGCTAAGGCCCAGACTGTACTGTTTA
Found at i:54898197 original size:33 final size:33
Alignment explanation
Indices: 54898115--54898208 Score: 90
Period size: 33 Copynumber: 2.9 Consensus size: 33
54898105 ATATGTCGAG
*
54898115 ACTGAATTAGGGCTTAGGCCCATACTGCTACTGTT
1 ACTGAA-TAGGGCTTAGGCCCAAACTG-TACTGTT
* *
54898150 --T--A-AGGGCTAAGGCCCAGACTGTACTGTT
1 ACTGAATAGGGCTTAGGCCCAAACTGTACTGTT
* *
54898178 ACTGAATAGGGCTTTGGCCCAAATTGTACTG
1 ACTGAATAGGGCTTAGGCCCAAACTGTACTG
54898209 ACACTATGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
28 7 0.15
29 17 0.35
30 1 0.02
31 1 0.02
32 1 0.02
33 21 0.44
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (33 bp):
ACTGAATAGGGCTTAGGCCCAAACTGTACTGTT
Found at i:54900126 original size:13 final size:13
Alignment explanation
Indices: 54900108--54900133 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54900098 AGGGTGAATT
54900108 TTTGAAAATTTTG
1 TTTGAAAATTTTG
54900121 TTTGAAAATTTTG
1 TTTGAAAATTTTG
54900134 ACGTTTGGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTTGAAAATTTTG
Found at i:54917841 original size:9 final size:9
Alignment explanation
Indices: 54917827--54917857 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
54917817 AAATAAATTT
54917827 AAAATATTA
1 AAAATATTA
54917836 AAAATATTA
1 AAAATATTA
54917845 AAAATATATA
1 AAAATAT-TA
54917855 AAA
1 AAA
54917858 TGCTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.76
10 5 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
AAAATATTA
Found at i:54919349 original size:6 final size:6
Alignment explanation
Indices: 54919340--54919368 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
54919330 ATATTTATAT
54919340 AAATTA AAATTA AAATTA AAATTA AAATT
1 AAATTA AAATTA AAATTA AAATTA AAATT
54919369 TATATTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AAATTA
Found at i:54921126 original size:23 final size:24
Alignment explanation
Indices: 54921074--54921128 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
54921064 TATAGAGATT
*
54921074 AATTTTTAATAATAAAAATAGTTA
1 AATTTTTAATAATAAAAATAATTA
* *
54921098 AATTTTTAATAA-AAAATTAATTT
1 AATTTTTAATAATAAAAATAATTA
*
54921121 ATTTTTTA
1 AATTTTTA
54921129 TTTATTTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
AATTTTTAATAATAAAAATAATTA
Found at i:54925383 original size:16 final size:17
Alignment explanation
Indices: 54925362--54925393 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
54925352 CGGCAAGGTT
54925362 AGGAAT-GATGAAATGG
1 AGGAATGGATGAAATGG
54925378 AGGAATGGATGAAATG
1 AGGAATGGATGAAATG
54925394 TGATTGGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.44, C:0.00, G:0.38, T:0.19
Consensus pattern (17 bp):
AGGAATGGATGAAATGG
Found at i:54927289 original size:20 final size:21
Alignment explanation
Indices: 54927266--54927320 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
54927256 TTTTGCAATT
*
54927266 AGAGGA-ATCGAAGTGCAAAC
1 AGAGGATACCGAAGTGCAAAC
54927286 AGA-GATACCGAAGTGCAAAC
1 AGAGGATACCGAAGTGCAAAC
*
54927306 AGA-GACACCGAAGTG
1 AGAGGATACCGAAGTG
54927321 AAATCTTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.44, C:0.18, G:0.29, T:0.09
Consensus pattern (21 bp):
AGAGGATACCGAAGTGCAAAC
Found at i:54937052 original size:17 final size:18
Alignment explanation
Indices: 54937030--54937075 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
54937020 TCAGGAACAC
*
54937030 CTTGATGACTAAA-GGAG
1 CTTGATGACTAAATGAAG
54937047 CTTGATGACTAAATGAAG
1 CTTGATGACTAAATGAAG
54937065 CTTGATGACTA
1 CTTGATGACTA
54937076 GCTTCTGGCG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (18 bp):
CTTGATGACTAAATGAAG
Found at i:54941910 original size:28 final size:28
Alignment explanation
Indices: 54941876--54941974 Score: 144
Period size: 28 Copynumber: 3.5 Consensus size: 28
54941866 TAGCCCTTTT
** *
54941876 AGGCCCAATTTCATTCATATGACCCATC
1 AGGCCCAATCACATTCATATGGCCCATC
*
54941904 GGGCCCAATCACATTCATATGGCCCATC
1 AGGCCCAATCACATTCATATGGCCCATC
* *
54941932 AGGCCCAATCACTTTCATATGGCCCGTC
1 AGGCCCAATCACATTCATATGGCCCATC
54941960 AGGCCCAATCACATT
1 AGGCCCAATCACATT
54941975 TATAGTCATG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 63 1.00
ACGTcount: A:0.26, C:0.34, G:0.15, T:0.24
Consensus pattern (28 bp):
AGGCCCAATCACATTCATATGGCCCATC
Found at i:54942234 original size:16 final size:16
Alignment explanation
Indices: 54942197--54942227 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
54942187 CAAACTTCTG
54942197 GCTTTTCGGCATTTCA
1 GCTTTTCGGCATTTCA
54942213 GCTTTTCGGCATTTC
1 GCTTTTCGGCATTTC
54942228 GGGTTTTGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.10, C:0.26, G:0.19, T:0.45
Consensus pattern (16 bp):
GCTTTTCGGCATTTCA
Found at i:54942515 original size:21 final size:21
Alignment explanation
Indices: 54942486--54942525 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
54942476 ACTAAAAAAC
*
54942486 AAGTGACTCACAAATCATCTT
1 AAGTCACTCACAAATCATCTT
**
54942507 AAGTCACTCTTAAATCATC
1 AAGTCACTCACAAATCATC
54942526 CATGAAGATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.30
Consensus pattern (21 bp):
AAGTCACTCACAAATCATCTT
Found at i:54960780 original size:14 final size:15
Alignment explanation
Indices: 54960761--54960790 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
54960751 AAAATGAAAG
54960761 AAGGAGGA-GAAGAA
1 AAGGAGGAGGAAGAA
54960775 AAGGAGGAGGAAGAA
1 AAGGAGGAGGAAGAA
54960790 A
1 A
54960791 CTTTTTGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (15 bp):
AAGGAGGAGGAAGAA
Found at i:54969072 original size:48 final size:48
Alignment explanation
Indices: 54968974--54969072 Score: 128
Period size: 48 Copynumber: 2.1 Consensus size: 48
54968964 CACCATGATT
* * * * *
54968974 TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAGA
1 TATGAGAGCCAGTGTAAGACCATGTCTGAGACATCGCATCGACATAGA
*
54969022 TATGAGAGCCAGTGTAAGACCATGT-TCGAGACATCGCATCGACATTGA
1 TATGAGAGCCAGTGTAAGACCATGTCT-GAGACATCGCATCGACATAGA
54969070 TAT
1 TAT
54969073 ATGTGCCATT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
47 1 0.02
48 43 0.98
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.24
Consensus pattern (48 bp):
TATGAGAGCCAGTGTAAGACCATGTCTGAGACATCGCATCGACATAGA
Found at i:54969234 original size:42 final size:42
Alignment explanation
Indices: 54969132--54969285 Score: 245
Period size: 42 Copynumber: 3.6 Consensus size: 42
54969122 TAATTTCATG
* * * *
54969132 TAAGACCATATCTGGGATATGGCATTGATATGAGATTTTCATG
1 TAAGACCATGTCTGGGACATGGCATCGATATGAGATTTT-ATA
*
54969175 TAAGACCATGTCTGGGACATGGCATCGATATGAGATTTTGTA
1 TAAGACCATGTCTGGGACATGGCATCGATATGAGATTTTATA
*
54969217 TAAGACCATGTCTGGGACATGGCATCGATATGAGGTTTTATA
1 TAAGACCATGTCTGGGACATGGCATCGATATGAGATTTTATA
54969259 TAAGACCATGTCTGGGACATGGCATCG
1 TAAGACCATGTCTGGGACATGGCATCG
54969286 GCACCGACAT
Statistics
Matches: 104, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
42 68 0.65
43 36 0.35
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.31
Consensus pattern (42 bp):
TAAGACCATGTCTGGGACATGGCATCGATATGAGATTTTATA
Found at i:54969329 original size:90 final size:85
Alignment explanation
Indices: 54969132--54969371 Score: 279
Period size: 90 Copynumber: 2.8 Consensus size: 85
54969122 TAATTTCATG
* *
54969132 TAAGACCATATCTGGGATATGGCATTGATATGAGATTTTCATGTAAGACCATGTCTGGGACATGG
1 TAAGACCATATCTGGGATATGGCATCGATATGAGATTTTCATATAAGACCATGTCTGGGACATGG
* * *
54969197 CATCGATATGAGATTTTGTA
66 CATCGACATGAGACTTCGTA
* * *
54969217 TAAGACCATGTCTGGGACATGGCATCGATATGAGGTTTT-ATATAAGACCATGTCTGGGACATGG
1 TAAGACCATATCTGGGATATGGCATCGATATGAGATTTTCATATAAGACCATGTCTGGGACATGG
54969281 CATCGGCACCGACATGAGACTTCGTA
66 CAT------CGACATGAGACTTCGTA
* ** * *
54969307 TAAGACCATATTTGGGATATGGCATCGATATGTAGA--CCCATGTAAGACCATGTCGGGGACATG
1 TAAGACCATATCTGGGATATGGCATCGATATG-AGATTTTCATATAAGACCATGTCTGGGACATG
54969370 GC
65 GC
54969372 TTTGACATTT
Statistics
Matches: 131, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
84 27 0.21
85 35 0.27
90 67 0.51
91 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (85 bp):
TAAGACCATATCTGGGATATGGCATCGATATGAGATTTTCATATAAGACCATGTCTGGGACATGG
CATCGACATGAGACTTCGTA
Found at i:54969371 original size:42 final size:41
Alignment explanation
Indices: 54969127--54969371 Score: 204
Period size: 42 Copynumber: 5.7 Consensus size: 41
54969117 GTATGTAATT
* * * *
54969127 TCATGTAAGACCATATCTGGGATATGGCATTGATATGAGATTT
1 TCATGTAAGACCATGTCTGGGACATGGCATCGATATGAGA--C
54969170 TCATGTAAGACCATGTCTGGGACATGGCATCGATATGAGA-
1 TCATGTAAGACCATGTCTGGGACATGGCATCGATATGAGAC
** **
54969210 TTTTGTATAAGACCATGTCTGGGACATGGCATCGATATGAGGTT
1 TCATG--TAAGACCATGTCTGGGACATGGCATCGATATGA-GAC
* * *
54969254 TTATATAAGACCATGTCTGGGACATGGCATCGGCACCGACATGAGAC
1 TCATGTAAGACCATGTCTGGGACATGGCAT------CGATATGAGAC
* * * * *
54969301 TTCGTATAAGACCATATTTGGGATATGGCATCGATATGTAGAC
1 -TCATGTAAGACCATGTCTGGGACATGGCATCGATATG-AGAC
* *
54969344 CCATGTAAGACCATGTCGGGGACATGGC
1 TCATGTAAGACCATGTCTGGGACATGGC
54969372 TTTGACATTT
Statistics
Matches: 166, Mismatches: 24, Indels: 25
0.77 0.11 0.12
Matches are distributed among these distances:
40 3 0.02
42 85 0.51
43 42 0.25
44 3 0.02
47 1 0.01
48 32 0.19
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (41 bp):
TCATGTAAGACCATGTCTGGGACATGGCATCGATATGAGAC
Found at i:54974186 original size:40 final size:40
Alignment explanation
Indices: 54974131--54974313 Score: 264
Period size: 40 Copynumber: 4.6 Consensus size: 40
54974121 CGGATGATAA
54974131 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
*
54974171 CCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
* * * *
54974211 TC-GGCTAAG-CCCGAAGGCATTTGTGCGAATTACCAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
* *
54974249 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACT-ATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-T
*
54974289 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
54974314 AGTGAGTAGC
Statistics
Matches: 126, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
38 27 0.21
39 14 0.11
40 85 0.67
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
Found at i:54974271 original size:78 final size:79
Alignment explanation
Indices: 54974134--54974313 Score: 256
Period size: 78 Copynumber: 2.3 Consensus size: 79
54974124 ATGATAACCG
* * * *
54974134 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAATCCCGAAGGCATTTGTGC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAATTACCAAATCCGGGCTAAATCCCGAAGGCATTGGTGC
54974199 GAGTTACTAATTTC
66 GAGTTACTAATTTC
*
54974213 GGCTAAG-CCCGAAGGCATTTGTGCGAATTACCAAATCCGGGCTAAGTCCCGAAGGCATTGGTGC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAATTACCAAATCCGGGCTAAATCCCGAAGGCATTGGTGC
**
54974277 GAGTTACT-ATAACC
66 GAGTTACTAAT-TTC
*
54974291 GGGCTATGTCCCGAAGGCATTTG
1 -GGCTAAGTCCCGAAGGCATTTG
54974314 AGTGAGTAGC
Statistics
Matches: 90, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
77 2 0.02
78 61 0.68
79 13 0.14
80 14 0.16
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (79 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAATTACCAAATCCGGGCTAAATCCCGAAGGCATTGGTGC
GAGTTACTAATTTC
Found at i:54976023 original size:37 final size:37
Alignment explanation
Indices: 54975962--54976040 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
54975952 TTATTACGAA
* * *
54975962 GTCTTACCCAGACATAATCTCCACACGGAGTTATCGG
1 GTCTTACCCAGACAAAATCCCCACACGGAGTCATCGG
* *
54975999 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCAGACAAAATCCCCACACGGAGTCATCGG
54976036 GTCTT
1 GTCTT
54976041 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCAGACAAAATCCCCACACGGAGTCATCGG
Found at i:54976309 original size:47 final size:47
Alignment explanation
Indices: 54976159--54976467 Score: 512
Period size: 47 Copynumber: 6.6 Consensus size: 47
54976149 CCCTTCGGGA
* * * * * * *
54976159 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54976206 CCTGTCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54976252 CTTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54976299 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54976346 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54976393 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54976440 CTTATCACATATATACACTTTCACATTC
1 CTTATCACATATATACACTTTCACATTC
54976468 CCAACCCTTT
Statistics
Matches: 246, Mismatches: 15, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
46 40 0.16
47 206 0.84
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54976762 original size:39 final size:40
Alignment explanation
Indices: 54976672--54976782 Score: 138
Period size: 39 Copynumber: 2.8 Consensus size: 40
54976662 CGGAATTTAA
**
54976672 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACATAGC
* *
54976712 CCGGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACATAGC
*
54976751 CCGGA-ATTAGTATCTCGCACAAATGCCTTCGG
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGG
54976783 ATCTTAGTCT
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
38 1 0.02
39 34 0.54
40 28 0.44
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACATAGC
Found at i:54986997 original size:40 final size:40
Alignment explanation
Indices: 54986942--54987131 Score: 260
Period size: 40 Copynumber: 4.8 Consensus size: 40
54986932 CGGATGATAA
54986942 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
*
54986982 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
* * *
54987022 CC-GGCTAAG-CCCGAAGGCATTTGTGCGAATTACCAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
* *
54987060 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACT-ATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-T
* * * *
54987100 CTGGGCTATGACCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
54987132 AGCCATATCT
Statistics
Matches: 132, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
38 27 0.20
39 15 0.11
40 90 0.68
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
Found at i:54987082 original size:78 final size:79
Alignment explanation
Indices: 54986945--54987096 Score: 261
Period size: 78 Copynumber: 1.9 Consensus size: 79
54986935 ATGATAACCG
* * * *
54986945 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAATTACCAAATCCGGGCTAAGTCCCGAAGGCATTGGTGC
54987010 GAGTTACTACTTCC
66 GAGTTACTACTTCC
54987024 GGCTAAG-CCCGAAGGCATTTGTGCGAATTACCAAATCCGGGCTAAGTCCCGAAGGCATTGGTGC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAATTACCAAATCCGGGCTAAGTCCCGAAGGCATTGGTGC
54987088 GAGTTACTA
66 GAGTTACTA
54987097 TAACTGGGCT
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
78 62 0.90
79 7 0.10
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (79 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAATTACCAAATCCGGGCTAAGTCCCGAAGGCATTGGTGC
GAGTTACTACTTCC
Found at i:54994267 original size:21 final size:21
Alignment explanation
Indices: 54994241--54994285 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
54994231 CCTAATTGTA
54994241 AAAGTTGTTAAAACTATGTGT
1 AAAGTTGTTAAAACTATGTGT
54994262 AAAGTTGTTAAAACTATGTGT
1 AAAGTTGTTAAAACTATGTGT
54994283 AAA
1 AAA
54994286 TATGTGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.36
Consensus pattern (21 bp):
AAAGTTGTTAAAACTATGTGT
Found at i:55003796 original size:48 final size:48
Alignment explanation
Indices: 55003741--55003839 Score: 171
Period size: 48 Copynumber: 2.1 Consensus size: 48
55003731 TTTTCCTAGG
*
55003741 TAATTTAACCTAAAGGTATTTTCGTCATTTTACCACCTATGGTAAAAC
1 TAATTTAACCTAAAGGTATTTTCATCATTTTACCACCTATGGTAAAAC
* *
55003789 TAATTTAACCTAAGGGTATTTTCATTATTTTACCACCTATGGTAAAAC
1 TAATTTAACCTAAAGGTATTTTCATCATTTTACCACCTATGGTAAAAC
55003837 TAA
1 TAA
55003840 CCCGATTTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.38
Consensus pattern (48 bp):
TAATTTAACCTAAAGGTATTTTCATCATTTTACCACCTATGGTAAAAC
Found at i:55020972 original size:20 final size:18
Alignment explanation
Indices: 55020922--55021031 Score: 66
Period size: 19 Copynumber: 5.9 Consensus size: 18
55020912 CTACAAGATA
55020922 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
*
55020939 AATATTAAGA-TAATCTCTT
1 AATATTAA-ATTAATAT-TT
**
55020958 CAATATTAAATTAATAAAAT
1 -AATATTAAATTAAT-ATTT
*
55020978 ACTATTAAGA-TAAGTATTT
1 AATATTAA-ATTAA-TATTT
* *
55020997 AAT-TTAATTTAATATTA
1 AATATTAAATTAATATTT
*
55021014 AATTATTAAAATAATATT
1 AA-TATTAAATTAATATT
55021032 ATTTTTGGAA
Statistics
Matches: 70, Mismatches: 12, Indels: 20
0.69 0.12 0.20
Matches are distributed among these distances:
17 17 0.24
18 10 0.14
19 28 0.40
20 15 0.21
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.44
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:55025824 original size:9 final size:9
Alignment explanation
Indices: 55025810--55025835 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
55025800 AATAAACTTG
55025810 AATGTGGAT
1 AATGTGGAT
55025819 AATGTGGAT
1 AATGTGGAT
55025828 AATGTGGA
1 AATGTGGA
55025836 AAACAACATT
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:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (9 bp):
AATGTGGAT
Found at i:55034790 original size:17 final size:17
Alignment explanation
Indices: 55034745--55034793 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
55034735 TATAAAGGAT
55034745 AAATAGATTGAAT-T-TG
1 AAAT-GATTGAATGTATG
*
55034761 -AATGA-TGATTGTATG
1 AAATGATTGAATGTATG
55034776 AAATGATTGAATGTATG
1 AAATGATTGAATGTATG
55034793 A
1 A
55034794 GAAAAGCATG
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
13 4 0.15
14 3 0.11
15 5 0.19
16 5 0.19
17 10 0.37
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (17 bp):
AAATGATTGAATGTATG
Found at i:55038049 original size:48 final size:48
Alignment explanation
Indices: 55037993--55038084 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
55037983 GCGTTAATAA
* * *
55037993 CATAGCTGGATTTTCATTTCCTTTGTTTTTTCTCACTCATTTGGCTGC
1 CATAGCTGGATTATCATTTCCTTTGTTTCTTCCCACTCATTTGGCTGC
**
55038041 CATAGCTGGATTATCATTTTTTTTGTTTCTTCCCACTCATTTGG
1 CATAGCTGGATTATCATTTCCTTTGTTTCTTCCCACTCATTTGG
55038085 TTAGGACTCC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.14, C:0.22, G:0.14, T:0.50
Consensus pattern (48 bp):
CATAGCTGGATTATCATTTCCTTTGTTTCTTCCCACTCATTTGGCTGC
Found at i:55048925 original size:25 final size:25
Alignment explanation
Indices: 55048874--55048946 Score: 80
Period size: 24 Copynumber: 3.0 Consensus size: 25
55048864 AAAATATTAC
**
55048874 ATTAATATTTTTA-TTTT-TTTAAT
1 ATTAATATAATTATTTTTATTTAAT
*
55048897 ATTAATATGATTATTTTTATTTAAT
1 ATTAATATAATTATTTTTATTTAAT
* *
55048922 ATTAATATAAAT-TTTTTAATTAAT
1 ATTAATATAATTATTTTTATTTAAT
55048946 A
1 A
55048947 AGATTTTAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.26
24 16 0.37
25 16 0.37
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (25 bp):
ATTAATATAATTATTTTTATTTAAT
Found at i:55057563 original size:74 final size:74
Alignment explanation
Indices: 55057442--55057589 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
55057432 AGTTACGCAG
55057442 AAATCAAAGGAAAAGAACCCCTTTTCAACCTCGTTTGTCGAGCCCCATTACGATCCCCCCTTCAC
1 AAATCAAAGGAAAAGAACCCCTTTTCAACCTCGTTTGTCGAGCCCCATTACGATCCCCCCTTCAC
55057507 CCTTCACCC
66 CCTTCACCC
55057516 AAATCAAAGGAAAAGAACCCCTTTTCAACCTCGTTTGTCGAGCCCCATTACGATCCCCCCTTCAC
1 AAATCAAAGGAAAAGAACCCCTTTTCAACCTCGTTTGTCGAGCCCCATTACGATCCCCCCTTCAC
55057581 CCTTCACCC
66 CCTTCACCC
55057590 TTCACCCTTC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.27, C:0.39, G:0.11, T:0.23
Consensus pattern (74 bp):
AAATCAAAGGAAAAGAACCCCTTTTCAACCTCGTTTGTCGAGCCCCATTACGATCCCCCCTTCAC
CCTTCACCC
Found at i:55057585 original size:7 final size:7
Alignment explanation
Indices: 55057573--55057609 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
55057563 TTACGATCCC
55057573 CCCTTCA
1 CCCTTCA
55057580 CCCTTCA
1 CCCTTCA
55057587 CCCTTCA
1 CCCTTCA
55057594 CCCTTCA
1 CCCTTCA
55057601 CCCTTCA
1 CCCTTCA
55057608 CC
1 CC
55057610 TTACAACAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.14, C:0.59, G:0.00, T:0.27
Consensus pattern (7 bp):
CCCTTCA
Found at i:55058664 original size:15 final size:15
Alignment explanation
Indices: 55058644--55058673 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55058634 TATTTCAAAT
*
55058644 GTTTAATTACTTTTA
1 GTTTAATTAATTTTA
55058659 GTTTAATTAATTTTA
1 GTTTAATTAATTTTA
55058674 ATTTTTTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.03, G:0.07, T:0.60
Consensus pattern (15 bp):
GTTTAATTAATTTTA
Found at i:55062850 original size:19 final size:21
Alignment explanation
Indices: 55062812--55062854 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
55062802 AATATTAATT
55062812 TAAAAAATGTCTAAATAATAA
1 TAAAAAATGTCTAAATAATAA
*
55062833 TAAAATATG-CTAAA-AATAA
1 TAAAAAATGTCTAAATAATAA
55062852 TAA
1 TAA
55062855 TACAAGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 5 0.24
21 8 0.38
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.28
Consensus pattern (21 bp):
TAAAAAATGTCTAAATAATAA
Found at i:55064888 original size:44 final size:45
Alignment explanation
Indices: 55064773--55064889 Score: 105
Period size: 45 Copynumber: 2.6 Consensus size: 45
55064763 GGCCCATCCT
* *
55064773 CTTTGATCTGTTTCCTTACTACTTAGGGGGTTAAGATTCGTCAAT
1 CTTTGATCTGTTTCCCTACTACTTAGGGGGTTAAGATTCGTCAAC
* * * ** * * *
55064818 CTTT-AGCCTGTTACCCTATTGTTTAGGGGTTTAAGGCTT-GT-TAC
1 CTTTGA-TCTGTTTCCCTACTACTTAGGGGGTTAA-GATTCGTCAAC
55064862 CTTTGATCTGTTTCCCTACTACTTAGGG
1 CTTTGATCTGTTTCCCTACTACTTAGGG
55064890 CGATAGGATC
Statistics
Matches: 54, Mismatches: 15, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
44 23 0.43
45 28 0.52
46 3 0.06
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.43
Consensus pattern (45 bp):
CTTTGATCTGTTTCCCTACTACTTAGGGGGTTAAGATTCGTCAAC
Found at i:55064960 original size:88 final size:86
Alignment explanation
Indices: 55064731--55065021 Score: 289
Period size: 88 Copynumber: 3.3 Consensus size: 86
55064721 ATTTGTAATT
* * ** * *
55064731 TTCAACCTGTTACCCTACTGCTTAAGGGTTAAGGC-CCATCCTCTTTGATCTGTTTCCTTACTAC
1 TTCAGCCTGTTACCCTACTGCTTAGGGGTTAAGGCTCGTTAC-CTTTGATCTGTTTCCCTACTAC
* * * *
55064795 TTAGGGGGTTAAGATTCGTCAATC
65 TTAGGGCGATAAGA-TC-TTAAAC
* * * *
55064819 TTTAGCCTGTTACCCTATTGTTTAGGGGTTTAAGGCTTGTTACCTTTGATCTGTTTCCCTACTAC
1 TTCAGCCTGTTACCCTACTGCTTAGGGG-TTAAGGCTCGTTACCTTTGATCTGTTTCCCTACTAC
*
55064884 TTAGGGCGATAGGATCTATAAAC
65 TTAGGGCGATAAGATCT-TAAAC
* * * * *
55064907 TTCAGCTTGTTACCCTACTGCTTAGGCGGTTAAAGCTCGTTGCCTTTGATCTGTTTTCCTACTGC
1 TTCAGCCTGTTACCCTACTGCTTAGG-GGTTAAGGCTCGTTACCTTTGATCTGTTTCCCTACTAC
* *
55064972 TTAGGGTGATAAGATCTGTGAA-
65 TTAGGGCGATAAGATCT-TAAAC
* *
55064994 TTCAACCTGTTACCCTACTTCTTAGGGG
1 TTCAGCCTGTTACCCTACTGCTTAGGGG
55065022 GTTTAAGGTC
Statistics
Matches: 168, Mismatches: 31, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
86 2 0.01
87 24 0.14
88 99 0.59
89 41 0.24
90 2 0.01
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (86 bp):
TTCAGCCTGTTACCCTACTGCTTAGGGGTTAAGGCTCGTTACCTTTGATCTGTTTCCCTACTACT
TAGGGCGATAAGATCTTAAAC
Done.