Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 83 of 290
Found at i:27720127 original size:15 final size:15
Alignment explanation
Indices: 27720109--27720140 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
27720099 AAAAAATTGA
27720109 TAATAAAATGGCTAG
1 TAATAAAATGGCTAG
27720124 TAATAAAATGGCTAG
1 TAATAAAATGGCTAG
27720139 TA
1 TA
27720141 TAGTTTACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
TAATAAAATGGCTAG
Found at i:27720659 original size:10 final size:11
Alignment explanation
Indices: 27720618--27720656 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
27720608 ATAAATTATT
*
27720618 AAAAATCATAA
1 AAAAATTATAA
27720629 AGAAAATTTATAA
1 A-AAAA-TTATAA
27720642 AAAAATTATAA
1 AAAAATTATAA
27720653 AAAA
1 AAAA
27720657 TTAAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 11 0.44
12 8 0.32
13 6 0.24
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:27720664 original size:16 final size:17
Alignment explanation
Indices: 27720643--27720674 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27720633 AATTTATAAA
27720643 AAAATTA-TAAAAAATT
1 AAAATTATTAAAAAATT
27720659 AAAATTATTAAAAAAT
1 AAAATTATTAAAAAAT
27720675 AACAATATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATTATTAAAAAATT
Found at i:27720773 original size:38 final size:38
Alignment explanation
Indices: 27720678--27720795 Score: 130
Period size: 38 Copynumber: 3.0 Consensus size: 38
27720668 AAAAAATAAC
*
27720678 AATATCCAACCT-TTAAATTTTAATGGTCATAACATTATTTTT
1 AATATCCAA-CTATTAAATTTTAATGGTCAT-A-A-GA-TTTT
* ** *
27720720 AATTTTTAACAATTAAATTTTAATGGTCATAAGATTTT
1 AATATCCAACTATTAAATTTTAATGGTCATAAGATTTT
*
27720758 AATATCCAACTATTAAATTTTAATGTTCATAAGATTTT
1 AATATCCAACTATTAAATTTTAATGGTCATAAGATTTT
27720796 CAACACCCAG
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
38 37 0.57
39 1 0.02
40 1 0.02
41 2 0.03
42 24 0.37
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (38 bp):
AATATCCAACTATTAAATTTTAATGGTCATAAGATTTT
Found at i:27720850 original size:11 final size:11
Alignment explanation
Indices: 27720836--27720869 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
27720826 AAATTTATAA
27720836 TTATAATTTTT
1 TTATAATTTTT
27720847 TTATAATTTTT
1 TTATAATTTTT
27720858 TTAATAATTTTT
1 TT-ATAATTTTT
27720870 AAAATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 13 0.59
12 9 0.41
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATAATTTTT
Found at i:27720859 original size:12 final size:12
Alignment explanation
Indices: 27720836--27720869 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
27720826 AAATTTATAA
27720836 TTATAA-TTTTT
1 TTATAATTTTTT
27720847 TTATAATTTTTT
1 TTATAATTTTTT
*
27720859 TAATAATTTTT
1 TTATAATTTTT
27720870 AAAATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATAATTTTTT
Found at i:27723530 original size:6 final size:6
Alignment explanation
Indices: 27723489--27723529 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
27723479 TATGAACCAT
*
27723489 GAATAG GAATAG GAATAG GAATAG GAATAG GAATAA GAATA
1 GAATAG GAATAG GAATAG GAATAG GAATAG GAATAG GAATA
27723530 AAAAGATGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.17
Consensus pattern (6 bp):
GAATAG
Found at i:27726029 original size:26 final size:26
Alignment explanation
Indices: 27726005--27726091 Score: 93
Period size: 26 Copynumber: 3.3 Consensus size: 26
27725995 ATTCGATTCG
* *
27726005 ATTCGATTCAAATTTCATCTTATTCA
1 ATTCGATTCTAATTTCATCTTACTCA
** * * *
27726031 ATTTTATTCTAATTCCAGCTTTACTCG
1 ATTCGATTCTAATTTCATC-TTACTCA
*
27726058 ATTCAATTCTAATTTCATCTTACTCA
1 ATTCGATTCTAATTTCATCTTACTCA
27726084 ATTCGATT
1 ATTCGATT
27726092 TGATAAATTT
Statistics
Matches: 47, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
26 27 0.57
27 20 0.43
ACGTcount: A:0.28, C:0.21, G:0.05, T:0.47
Consensus pattern (26 bp):
ATTCGATTCTAATTTCATCTTACTCA
Found at i:27728520 original size:61 final size:61
Alignment explanation
Indices: 27728425--27728545 Score: 233
Period size: 61 Copynumber: 2.0 Consensus size: 61
27728415 CTCCATTCCA
27728425 AGTATCTTCTTTACTGGTCCTAAATCTTTCATCTCAAATTCTTTACTTAGTTGGGTTTTGC
1 AGTATCTTCTTTACTGGTCCTAAATCTTTCATCTCAAATTCTTTACTTAGTTGGGTTTTGC
*
27728486 AGTATCTTTTTTACTGGTCCTAAATCTTTCATCTCAAATTCTTTACTTAGTTGGGTTTTG
1 AGTATCTTCTTTACTGGTCCTAAATCTTTCATCTCAAATTCTTTACTTAGTTGGGTTTTG
27728546 ACATTTCTTA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.20, C:0.18, G:0.13, T:0.49
Consensus pattern (61 bp):
AGTATCTTCTTTACTGGTCCTAAATCTTTCATCTCAAATTCTTTACTTAGTTGGGTTTTGC
Found at i:27731288 original size:10 final size:11
Alignment explanation
Indices: 27731272--27731301 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
27731262 CAATTTGAGA
27731272 AAAAATAAAAT
1 AAAAATAAAAT
27731283 -AAAATAAAAT
1 AAAAATAAAAT
27731293 AAAAATAAA
1 AAAAATAAA
27731302 GAACACACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:27732741 original size:12 final size:12
Alignment explanation
Indices: 27732724--27732748 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27732714 GTTACTCAAG
27732724 TATATTTAAAAA
1 TATATTTAAAAA
27732736 TATATTTAAAAA
1 TATATTTAAAAA
27732748 T
1 T
27732749 TTAAACCCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATATTTAAAAA
Found at i:27732988 original size:20 final size:21
Alignment explanation
Indices: 27732948--27733015 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
27732938 TTTAGAGGTT
27732948 TAAATTTTTAAATATATTTTA
1 TAAATTTTTAAATATATTTTA
27732969 TAAATTTTATAAATA-A-TTTA
1 TAAATTTT-TAAATATATTTTA
*
27732989 TTAGATTTTT--ATAT-TTTTA
1 -TAAATTTTTAAATATATTTTA
27733008 TAATATTT
1 TAA-ATTT
27733016 ATAAGTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
18 5 0.12
19 8 0.20
20 5 0.12
21 16 0.40
22 6 0.15
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (21 bp):
TAAATTTTTAAATATATTTTA
Found at i:27733258 original size:9 final size:9
Alignment explanation
Indices: 27733175--27733283 Score: 51
Period size: 10 Copynumber: 11.4 Consensus size: 9
27733165 CTTTATTAAA
27733175 TTTATAATT
1 TTTATAATT
27733184 TTTATAAGTT
1 TTTATAA-TT
* * *
27733194 ATTAGATTT
1 TTTATAATT
27733203 TTTA-AATACT
1 TTTATAAT--T
**
27733213 TTTACTAAAA
1 TTTA-TAATT
27733223 TTTATAAGTT
1 TTTATAA-TT
* *
27733233 TCTATTATT
1 TTTATAATT
27733242 TTTAATAATT
1 TTT-ATAATT
27733252 TTTATAAGTT
1 TTTATAA-TT
* *
27733262 TATATAAAT
1 TTTATAATT
27733271 TTTA-ATATT
1 TTTATA-ATT
27733280 TTTA
1 TTTA
27733284 ATATTTAATA
Statistics
Matches: 74, Mismatches: 17, Indels: 18
0.68 0.16 0.17
Matches are distributed among these distances:
8 3 0.04
9 33 0.45
10 36 0.49
12 2 0.03
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.58
Consensus pattern (9 bp):
TTTATAATT
Found at i:27733273 original size:29 final size:28
Alignment explanation
Indices: 27733223--27733283 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
27733213 TTTACTAAAA
* * *
27733223 TTTATAAGTTTCTATTATTTTTAATAATT
1 TTTATAAGTTTATATAAATTTTAAT-ATT
27733252 TTTATAAGTTTATATAAATTTTAATATT
1 TTTATAAGTTTATATAAATTTTAATATT
27733280 TTTA
1 TTTA
27733284 ATATTTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 7 0.24
29 22 0.76
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (28 bp):
TTTATAAGTTTATATAAATTTTAATATT
Found at i:27733284 original size:9 final size:9
Alignment explanation
Indices: 27733238--27733349 Score: 60
Period size: 10 Copynumber: 12.7 Consensus size: 9
27733228 AAGTTTCTAT
27733238 TATTTTTAA
1 TATTTTTAA
27733247 TAATTTTT-A
1 T-ATTTTTAA
**
27733256 TAAGTTTATA
1 TATTTTTA-A
*
27733266 TAAATTTTAA
1 T-ATTTTTAA
27733276 TATTTTTAA
1 TATTTTTAA
27733285 TA--TTTAA
1 TATTTTTAA
27733292 TA--TTTAA
1 TATTTTTAA
27733299 TACTTTTTATA
1 TA-TTTTTA-A
*
27733310 CATTTTT--
1 TATTTTTAA
*
27733317 TATTTTT-T
1 TATTTTTAA
27733325 TATTTTTAA
1 TATTTTTAA
*
27733334 TTTTTTTTAA
1 -TATTTTTAA
27733344 TATTTT
1 TATTTT
27733350 ATGAAAAAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
7 20 0.24
8 11 0.13
9 17 0.20
10 27 0.33
11 8 0.10
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (9 bp):
TATTTTTAA
Found at i:27733332 original size:14 final size:15
Alignment explanation
Indices: 27733311--27733340 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27733301 CTTTTTATAC
*
27733311 ATTTTTTATTTTTTT
1 ATTTTTAATTTTTTT
27733326 ATTTTTAATTTTTTT
1 ATTTTTAATTTTTTT
27733341 TAATATTTTA
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:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
ATTTTTAATTTTTTT
Found at i:27738149 original size:16 final size:16
Alignment explanation
Indices: 27738128--27738159 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
27738118 CATTGCATTG
27738128 TCATCAATTGTGAGTT
1 TCATCAATTGTGAGTT
27738144 TCATCAATTGTGAGTT
1 TCATCAATTGTGAGTT
27738160 AATTTCAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (16 bp):
TCATCAATTGTGAGTT
Found at i:27742384 original size:40 final size:40
Alignment explanation
Indices: 27742296--27742384 Score: 142
Period size: 40 Copynumber: 2.2 Consensus size: 40
27742286 ATCAAGCAAC
* *
27742296 TAGATTACACGTGATTCCACGATAAACAAATGCATAAAAT
1 TAGATTACTCGTGATTCCACGATAAACAAATACATAAAAT
* *
27742336 TAGATTACTCGTGATTCTATGATAAACAAATACATAAAAT
1 TAGATTACTCGTGATTCCACGATAAACAAATACATAAAAT
27742376 TAGATTACT
1 TAGATTACT
27742385 TTGTTGATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (40 bp):
TAGATTACTCGTGATTCCACGATAAACAAATACATAAAAT
Found at i:27742858 original size:140 final size:141
Alignment explanation
Indices: 27742584--27742931 Score: 378
Period size: 140 Copynumber: 2.5 Consensus size: 141
27742574 CTCTTCTACG
*
27742584 CACATTTGTATTTTTTATTTCA---TA-TT-AAGCTTTTTAAATTTTTAATT-A-ATTTTTTAAC
1 CACATTTGTATTTTTTATTTCATGTTACTTCAAGCTTTTTAATTTTTTAATTAATATTTTTTAAC
* * * * * * *
27742642 ATATTAGTTCTTTTGTTAGATTGTTTAGTTAGTTGCAATTACATCCTTTAGTCTCGAATTTAATT
66 ATATTAATTCTTTTGTTAGATAGTTAAGATAGTTGCAATTACAACATTGAGTCTCGAATTTAATT
27742707 CTTCTCTTACT
131 CTTCTCTTACT
* * *
27742718 CATATTTTTATTTTTTATTTCATGTTACTTCAAGCTTTTTAATTTTTTAATTAATATTTTTTAAG
1 CACATTTGTATTTTTTATTTCATGTTACTTCAAGCTTTTTAATTTTTTAATTAATATTTTTTAAC
* * *
27742783 ATATTAATT-TTTTCGTTAGATAG-TAAGATAGTTGTAATTACAACATTGAGTCTCGAGTTTTAT
66 ATATTAATTCTTTT-GTTAGATAGTTAAGATAGTTGCAATTACAACATTGAGTCTCGAATTTAAT
27742846 TCATT-TAC-TACT
130 TC-TTCT-CTTACT
* * * * *
27742858 CACATTTGTAATTTTTATTTTATGTTGCTTCAAGTTTTTTATTTTTATTTTTAATTAATA-TTTT
1 CACATTTGTATTTTTTATTTCATGTTACTTCAAGCTTTTTA---AT-TTTTTAATTAATATTTTT
27742922 TAACATATTA
62 TAACATATTA
27742932 CCTCATTTCG
Statistics
Matches: 178, Mismatches: 22, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
134 20 0.11
137 2 0.01
138 2 0.01
139 20 0.11
140 79 0.44
141 28 0.16
143 14 0.08
144 13 0.07
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.55
Consensus pattern (141 bp):
CACATTTGTATTTTTTATTTCATGTTACTTCAAGCTTTTTAATTTTTTAATTAATATTTTTTAAC
ATATTAATTCTTTTGTTAGATAGTTAAGATAGTTGCAATTACAACATTGAGTCTCGAATTTAATT
CTTCTCTTACT
Found at i:27743057 original size:23 final size:23
Alignment explanation
Indices: 27743019--27743075 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
27743009 ATGTAATTTT
*
27743019 TATTTTA-TATTGTTTTAATGATG
1 TATTTTATTATTCTTTTAAT-ATG
*
27743042 T-TTTTATTATTCTTTTTATATG
1 TATTTTATTATTCTTTTAATATG
*
27743064 TATATTATTATT
1 TATTTTATTATT
27743076 TTTCTTTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 9 0.31
23 20 0.69
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.67
Consensus pattern (23 bp):
TATTTTATTATTCTTTTAATATG
Found at i:27758091 original size:43 final size:43
Alignment explanation
Indices: 27758043--27758127 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
27758033 TGATATATGT
*
27758043 AGCATCCGAGCTCATTGAGTGGTCCGAGTTCATTATGGATGCG
1 AGCATCCGAGCTCATTGAGTGGTCCGAGTTCATAATGGATGCG
* *
27758086 AGCATCCGAGCTCGTTGAGTGGTCTGAGTTCATAATGGATGC
1 AGCATCCGAGCTCATTGAGTGGTCCGAGTTCATAATGGATGC
27758128 AGTACATGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (43 bp):
AGCATCCGAGCTCATTGAGTGGTCCGAGTTCATAATGGATGCG
Found at i:27764790 original size:25 final size:25
Alignment explanation
Indices: 27764735--27764814 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
27764725 AAGCTATAAA
* *
27764735 CGGTAAGCTCCT-CTGAGCTGAATAA
1 CGGTAAGCTCATAC-GAGCTGAATAT
*
27764760 CAGTAAGCTCATACGAGCTGAATAT
1 CGGTAAGCTCATACGAGCTGAATAT
* * * *
27764785 CGGTAAGATCATAAGAGTTGGA-AT
1 CGGTAAGCTCATACGAGCTGAATAT
27764809 CGGTAA
1 CGGTAA
27764815 CCCTAATGAC
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
24 8 0.17
25 37 0.80
26 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (25 bp):
CGGTAAGCTCATACGAGCTGAATAT
Found at i:27771803 original size:31 final size:31
Alignment explanation
Indices: 27771767--27771825 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
27771757 TACTTCCCCC
*
27771767 AAACCCCCAAAACTTTTTTCCTTTTACTCCT
1 AAACCCCCAAAACTTTTTCCCTTTTACTCCT
27771798 AAACCCCCAAAACTTTTTCCCTTTTACT
1 AAACCCCCAAAACTTTTTCCCTTTTACT
27771826 TTCTCTCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.36, G:0.00, T:0.37
Consensus pattern (31 bp):
AAACCCCCAAAACTTTTTCCCTTTTACTCCT
Found at i:27771899 original size:19 final size:19
Alignment explanation
Indices: 27771871--27771926 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
27771861 AAAAAAATTC
27771871 CTTTTACTTTCCCCCAAAA
1 CTTTTACTTTCCCCCAAAA
*
27771890 CTTTTGCTTTCCCCCAAAA
1 CTTTTACTTTCCCCCAAAA
*
27771909 GTTTTACTTTCCCCCAAA
1 CTTTTACTTTCCCCCAAA
27771927 CCTCAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.23, C:0.36, G:0.04, T:0.38
Consensus pattern (19 bp):
CTTTTACTTTCCCCCAAAA
Found at i:27775774 original size:40 final size:40
Alignment explanation
Indices: 27775714--27775852 Score: 119
Period size: 40 Copynumber: 3.5 Consensus size: 40
27775704 AACACACCAG
* * *
27775714 TTTGGCACCCAGTGCCTCATCGGATAATTCGAAGTGATAA
1 TTTGACACCCAGTGTCTCATCGGATAATACGAAGTGATAA
*
27775754 TTTGACACCCAGTGTCTCATCGGCTAA-ACTGAA--G-TAA
1 TTTGACACCCAGTGTCTCATCGGATAATAC-GAAGTGATAA
* * * *
27775791 TTTGGCATCCAGTG-CATCATCGAATTAATCCGAAGT-AGTAA
1 TTTGACACCCAGTGTC-TCATCGGA-TAATACGAAGTGA-TAA
*
27775832 ATTGACACCCAGTGTCTCATC
1 TTTGACACCCAGTGTCTCATC
27775853 AACTTGAAGT
Statistics
Matches: 78, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
36 1 0.01
37 21 0.27
38 7 0.09
39 2 0.03
40 27 0.35
41 19 0.24
42 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (40 bp):
TTTGACACCCAGTGTCTCATCGGATAATACGAAGTGATAA
Found at i:27777654 original size:47 final size:47
Alignment explanation
Indices: 27777548--27777715 Score: 137
Period size: 47 Copynumber: 3.6 Consensus size: 47
27777538 AGCTTAGCCA
* **
27777548 ATGCATGTCCCAGACACATCTTACATTGGCTACCATCAATGAGGCCG
1 ATGCATGTCCCAGACACATCTTACACTGGCTACCATCAATGACACCG
* **
27777595 ATGCATGGCCCAGACACATCTTACACTGGC-ACTCATCTCT-ACACCG
1 ATGCATGTCCCAGACACATCTTACACTGGCTAC-CATCAATGACACCG
** * * ** *
27777641 ATGCCATGTCCCAGACATGGTCTTACA-TAGGCTATCGT-AATGTGACTG
1 ATG-CATGTCCCAGACA-CATCTTACACT-GGCTACCATCAATGACACCG
* *
27777689 ATGCATATCCCAGACACGTCTTACACT
1 ATGCATGTCCCAGACACATCTTACACT
27777716 AGCCCTCGTC
Statistics
Matches: 96, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
46 17 0.18
47 60 0.62
48 18 0.19
49 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (47 bp):
ATGCATGTCCCAGACACATCTTACACTGGCTACCATCAATGACACCG
Found at i:27777692 original size:94 final size:92
Alignment explanation
Indices: 27777450--27777761 Score: 281
Period size: 94 Copynumber: 3.3 Consensus size: 92
27777440 CTTCATCGAG
* * * *
27777450 GCCGGTGCCATGTCCCAGACATGGTCTTACACTA-GCTCTCGTGTATAAGTGTTGATGCATGTCC
1 GCCGATGCCATGTCCCAGACATGGTCTTACA-TAGGCTATC--GTA-ATGTGCTGATGCATGTCC
* * ** *
27777514 CAAACATGTCTTACACTAGCACGAAGCT-TA
62 CAGACACGTCTTACACTAGCACTCATCTCTA
* ** * * * * * *
27777544 GCCAATG-CATGTCCCAGACA-CATCTTACATTGGCTACCATCAATGAGGCCGATGCATGGCCCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACATAGGCTATCGT-AATG-TGCTGATGCATGTCCCA
* *
27777607 GACACATCTTACACTGGCACTCATCTCTA
64 GACACGTCTTACACTAGCACTCATCTCTA
* *
27777636 CACCGATGCCATGTCCCAGACATGGTCTTACATAGGCTATCGTAATGTGACTGATGCATATCCCA
1 -GCCGATGCCATGTCCCAGACATGGTCTTACATAGGCTATCGTAATGTG-CTGATGCATGTCCCA
* * *
27777701 GACACGTCTTACACTAGCCCTCGTCTCAA
64 GACACGTCTTACACTAGCACTCATCTCTA
*
27777730 TGCCGATGCCATGTCCTAGACATGGTCTTACA
1 -GCCGATGCCATGTCCCAGACATGGTCTTACA
27777762 CTGGCTCTCA
Statistics
Matches: 171, Mismatches: 39, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
90 3 0.02
91 34 0.20
92 13 0.08
93 19 0.11
94 87 0.51
95 15 0.09
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (92 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACATAGGCTATCGTAATGTGCTGATGCATGTCCCAGA
CACGTCTTACACTAGCACTCATCTCTA
Found at i:27779392 original size:4 final size:4
Alignment explanation
Indices: 27779383--27779454 Score: 69
Period size: 4 Copynumber: 17.5 Consensus size: 4
27779373 GGCTTTCTCC
27779383 TTCT TTCT TTCCT TT-T TTCT ATTCT TTCT TTCT TTC- TT-T TTCT TTCTGT
1 TTCT TTCT TT-CT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT TTCT TTC--T
*
27779432 TTCAT TTCT ATCT TTCT TTCT TT
1 TTC-T TTCT TTCT TTCT TTCT TT
27779455 TTATTTATTC
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
3 7 0.12
4 35 0.60
5 12 0.21
6 4 0.07
ACGTcount: A:0.04, C:0.22, G:0.01, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:27779417 original size:29 final size:28
Alignment explanation
Indices: 27779383--27779467 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 28
27779373 GGCTTTCTCC
27779383 TTCTTTCTTTCCTTTTTTCTATTCTTTCT
1 TTCTTTCTTT-CTTTTTTCTATTCTTTCT
* *
27779412 TTCTTTCTTT-TTCTTTCTGTTTCATTTCT
1 TTCTTTCTTTCTTTTTTCT-ATTC-TTTCT
* *
27779441 ATCTTTCTTTCTTTTTATTTATTCTTT
1 TTCTTTCTTTCTTTTT-TCTATTCTTT
27779468 ATTTATTTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
27 7 0.15
28 3 0.07
29 27 0.59
30 7 0.15
31 2 0.04
ACGTcount: A:0.06, C:0.20, G:0.01, T:0.73
Consensus pattern (28 bp):
TTCTTTCTTTCTTTTTTCTATTCTTTCT
Found at i:27779440 original size:25 final size:23
Alignment explanation
Indices: 27779383--27779429 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 23
27779373 GGCTTTCTCC
27779383 TTCTTTCTTTCCTTTTTTCTATTCT
1 TTCTTTCTTT-C-TTTTTCTATTCT
27779408 TTCTTTCTTTCTTTTTCT-TTCT
1 TTCTTTCTTTCTTTTTCTATTCT
27779430 GTTTCATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.18
23 7 0.32
24 1 0.05
25 10 0.45
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (23 bp):
TTCTTTCTTTCTTTTTCTATTCT
Found at i:27779492 original size:5 final size:5
Alignment explanation
Indices: 27779484--27779516 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
27779474 TTTGTTTTAT
27779484 TATAA TATAA TATAA TATAA TATAA TAT-A TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATA
27779517 CTTAATAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:27785756 original size:29 final size:29
Alignment explanation
Indices: 27785700--27785755 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
27785690 ATGCCAACAA
27785700 ATAAATCAAAATTTATAAAAATAAAAAAT
1 ATAAATCAAAATTTATAAAAATAAAAAAT
27785729 ATAAATCAAAA-TTA-AAGAAATAAAAAA
1 ATAAATCAAAATTTATAA-AAATAAAAAA
27785756 AAGTTTACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 2 0.08
28 13 0.50
29 11 0.42
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (29 bp):
ATAAATCAAAATTTATAAAAATAAAAAAT
Found at i:27785929 original size:31 final size:32
Alignment explanation
Indices: 27785866--27785931 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
27785856 AAGCCATAAT
* * * * *
27785866 TTTGACTCTTTTTTAAAAGGTTGATGATCAAA
1 TTTGACTCTATTTTAAAAGATTAAGGAACAAA
27785898 TTTGACTC-ATTTTAAAAGATTAAGGAACAAA
1 TTTGACTCTATTTTAAAAGATTAAGGAACAAA
27785929 TTT
1 TTT
27785932 AGCTAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 21 0.72
32 8 0.28
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (32 bp):
TTTGACTCTATTTTAAAAGATTAAGGAACAAA
Found at i:27786099 original size:19 final size:19
Alignment explanation
Indices: 27786072--27786108 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
27786062 AAAAATTAAA
*
27786072 TAAATTTATATTAAAATAG
1 TAAAATTATATTAAAATAG
*
27786091 TAAAATTATTTTAAAATA
1 TAAAATTATATTAAAATA
27786109 TGAAATATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (19 bp):
TAAAATTATATTAAAATAG
Found at i:27786149 original size:19 final size:17
Alignment explanation
Indices: 27786116--27786163 Score: 51
Period size: 19 Copynumber: 2.7 Consensus size: 17
27786106 ATATGAAATA
* * *
27786116 TAAATTTTAAATATTTT
1 TAAAATTTAATTATTTG
27786133 TAATAATATTAATTATTTG
1 TAA-AAT-TTAATTATTTG
27786152 TAAAATTTAATT
1 TAAAATTTAATT
27786164 TGAATATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 9 0.35
18 5 0.19
19 12 0.46
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
TAAAATTTAATTATTTG
Found at i:27786182 original size:25 final size:23
Alignment explanation
Indices: 27786152--27786234 Score: 75
Period size: 22 Copynumber: 3.7 Consensus size: 23
27786142 TAATTATTTG
*
27786152 TAAAATTTAATTTGAATATATAATT
1 TAAAATATAATTT-AATATA-AATT
*
27786177 TAAAATATAA-TTATTATAAATT
1 TAAAATATAATTTAATATAAATT
*
27786199 TAAATATATAATTT--TATATATT
1 TAAA-ATATAATTTAATATAAATT
*
27786221 TGAAATA-AATTTAA
1 TAAAATATAATTTAA
27786235 GTAGAAGCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
20 5 0.10
21 3 0.06
22 18 0.36
23 11 0.22
24 4 0.08
25 9 0.18
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TAAAATATAATTTAATATAAATT
Found at i:27786207 original size:23 final size:22
Alignment explanation
Indices: 27786168--27786227 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 22
27786158 TTAATTTGAA
27786168 TATATAATTTAAA-ATATAATTAT
1 TATA-AATTTAAATATATAATT-T
27786191 TATAAATTTAAATATATAATTT
1 TATAAATTTAAATATATAATTT
*
27786213 TATATATTTGAAATA
1 TATAAATTT-AAATA
27786228 AATTTAAGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
22 17 0.50
23 17 0.50
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TATAAATTTAAATATATAATTT
Found at i:27786214 original size:14 final size:13
Alignment explanation
Indices: 27786159--27786212 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 13
27786149 TTGTAAAATT
*
27786159 TAATTTGAATATA
1 TAATTTAAATATA
27786172 TAATTTAAA-ATA
1 TAATTTAAATATA
*
27786184 TAA-TT-ATTATA
1 TAATTTAAATATA
27786195 -AATTTAAATATA
1 TAATTTAAATATA
27786207 TAATTT
1 TAATTT
27786213 TATATATTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
10 3 0.09
11 7 0.21
12 11 0.32
13 13 0.38
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (13 bp):
TAATTTAAATATA
Found at i:27786217 original size:12 final size:12
Alignment explanation
Indices: 27786159--27786219 Score: 63
Period size: 12 Copynumber: 5.1 Consensus size: 12
27786149 TTGTAAAATT
27786159 TAATTTGAATATA
1 TAATTT-AATATA
*
27786172 TAATTTAAAATA
1 TAATTTAATATA
*
27786184 TAA-TTATTATA
1 TAATTTAATATA
27786195 -AATTTAAATATA
1 TAATTT-AATATA
*
27786207 TAATTTTATATA
1 TAATTTAATATA
27786219 T
1 T
27786220 TTGAAATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
10 2 0.05
11 8 0.20
12 19 0.47
13 11 0.28
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (12 bp):
TAATTTAATATA
Found at i:27788002 original size:2 final size:2
Alignment explanation
Indices: 27787995--27788019 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27787985 CCATGGATTG
27787995 CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA C
27788020 CTGCAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:27793532 original size:23 final size:20
Alignment explanation
Indices: 27793487--27793526 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
27793477 ACAATATAAG
27793487 TTAAAATAATAAAATATTTC
1 TTAAAATAATAAAATATTTC
27793507 TTAAAATAATAAAATATTTC
1 TTAAAATAATAAAATATTTC
27793527 ATCTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAAAATAATAAAATATTTC
Found at i:27798374 original size:22 final size:22
Alignment explanation
Indices: 27798347--27798424 Score: 68
Period size: 22 Copynumber: 3.3 Consensus size: 22
27798337 TTAGTACTAC
27798347 ACACGTGACCTAACTATCTGAT
1 ACACGTGACCTAACTATCTGAT
* *
27798369 ACACGTAGTAGCCTGCACTTAGTACT-AC
1 ACACGT-G-A-CCT-AAC-TA-T-CTGAT
27798397 ACACGTGACCTAACTATCTGAT
1 ACACGTGACCTAACTATCTGAT
27798419 ACACGT
1 ACACGT
27798425 AGTAGCCTGC
Statistics
Matches: 44, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
21 2 0.05
22 14 0.32
23 3 0.07
24 3 0.07
25 6 0.14
26 3 0.07
27 3 0.07
28 8 0.18
29 2 0.05
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (22 bp):
ACACGTGACCTAACTATCTGAT
Found at i:27798391 original size:50 final size:50
Alignment explanation
Indices: 27798260--27798509 Score: 315
Period size: 50 Copynumber: 5.0 Consensus size: 50
27798250 TATGTAGCCA
* * * *
27798260 AACTATCTGGTACGCATAGTAG-CTGCACTTAGTACTACACATGCGACC-
1 AACTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCT
* * *
27798308 AATTATCCGGTACATGTAGTAGCCTGCACTTAGTACTACACACGTGACCT
1 AACTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCT
*
27798358 AACTATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCT
1 AACTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCT
* * *
27798408 AACTATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCG
1 AACTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCT
* * ** * * *
27798458 AAGTTATCAGGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCT
1 AA-CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCT
27798509 A
1 A
27798510 GCTACATATA
Statistics
Matches: 176, Mismatches: 23, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
48 17 0.10
49 24 0.14
50 96 0.55
51 39 0.22
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (50 bp):
AACTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCT
Found at i:27798422 original size:24 final size:24
Alignment explanation
Indices: 27798344--27798422 Score: 58
Period size: 24 Copynumber: 3.2 Consensus size: 24
27798334 CACTTAGTAC
27798344 TACACACGTGACCTAACTATCTGA
1 TACACACGTGACCTAACTATCTGA
* *
27798368 T--ACACGTAGTAGCCTGCACT-T-AGTA
1 TACACACGT-G-A-CCT-AACTATCTG-A
27798393 CTACACACGTGACCTAACTATCTGA
1 -TACACACGTGACCTAACTATCTGA
27798418 TACAC
1 TACAC
27798423 GTAGTAGCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 20
0.63 0.06 0.31
Matches are distributed among these distances:
22 6 0.15
23 1 0.02
24 11 0.27
25 10 0.24
26 6 0.15
27 1 0.02
28 6 0.15
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (24 bp):
TACACACGTGACCTAACTATCTGA
Found at i:27798441 original size:100 final size:100
Alignment explanation
Indices: 27798260--27798509 Score: 351
Period size: 100 Copynumber: 2.5 Consensus size: 100
27798250 TATGTAGCCA
* * *
27798260 AACTATCTGGTACGCATAGTAG-CTGCACTTAGTACTACACATGCGACC-AATTATCCGGTACAT
1 AACTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACTATCCGATACAC
*
27798323 GTAGTAGCCTGCACTTAGTACTACACACGTGACCT
66 GTAGTAGCCTGCACTTAGTACTACACACGTGACCG
* * * * * *
27798358 AACTATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACTATCTGATACAC
1 AACTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACTATCCGATACAC
*
27798423 GTAGTAGCCTGCACTTAGTACTACACACGTGATCG
66 GTAGTAGCCTGCACTTAGTACTACACACGTGACCG
* * *
27798458 AAGTTATCAGGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTA
1 AA-CTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTA
27798510 GCTACATATA
Statistics
Matches: 130, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
98 19 0.15
99 24 0.18
100 46 0.35
101 41 0.32
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (100 bp):
AACTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACTATCCGATACAC
GTAGTAGCCTGCACTTAGTACTACACACGTGACCG
Found at i:27799351 original size:30 final size:30
Alignment explanation
Indices: 27799315--27799375 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
27799305 TCCTTCACTC
*
27799315 AAACTTTGGAAAATTTACAATTTTTCCCCT
1 AAACTTTGGAAAATTTACAATTTTGCCCCT
* * * *
27799345 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAATTTACAATTTTGCCCCT
27799375 A
1 A
27799376 GGCTCGGGAA
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:0.30, C:0.23, G:0.07, T:0.41
Consensus pattern (30 bp):
AAACTTTGGAAAATTTACAATTTTGCCCCT
Found at i:27803531 original size:44 final size:44
Alignment explanation
Indices: 27803473--27803558 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
27803463 TATGTATGAG
27803473 GCATCCGAGCTTGTTGAGTTAGTCCGAGTTCATTATGGATGCCA
1 GCATCCGAGCTTGTTGAGTTAGTCCGAGTTCATTATGGATGCCA
* * *
27803517 GCATCCGAGTTTGTTGAGTTGGTCTGAGTTCATTATGGATGC
1 GCATCCGAGCTTGTTGAGTTAGTCCGAGTTCATTATGGATGC
27803559 GATACATGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.19, C:0.17, G:0.29, T:0.35
Consensus pattern (44 bp):
GCATCCGAGCTTGTTGAGTTAGTCCGAGTTCATTATGGATGCCA
Found at i:27806127 original size:20 final size:20
Alignment explanation
Indices: 27806102--27806149 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
27806092 CTGAGGACAC
27806102 GGGCGTGTCCCATGCCACAT
1 GGGCGTGTCCCATGCCACAT
27806122 GGGCGTGTCCCATGCCACAT
1 GGGCGTGTCCCATGCCACAT
27806142 GGGCGTGT
1 GGGCGTGT
27806150 GTGACCACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.12, C:0.31, G:0.35, T:0.21
Consensus pattern (20 bp):
GGGCGTGTCCCATGCCACAT
Found at i:27807307 original size:25 final size:25
Alignment explanation
Indices: 27807279--27807330 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
27807269 GCCACATAGA
* *
27807279 CTTTTCAAATAAATCACCATAAGGG
1 CTTTACAAATAAATCACCATAAAGG
* *
27807304 CTTTACATATAACTCACCATAAAGG
1 CTTTACAAATAAATCACCATAAAGG
27807329 CT
1 CT
27807331 CTATTTGGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (25 bp):
CTTTACAAATAAATCACCATAAAGG
Found at i:27826703 original size:21 final size:22
Alignment explanation
Indices: 27826658--27826711 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
27826648 TATAGAGCTC
* *
27826658 ACACACCCGTGTGGTCCAAGGG
1 ACACGCCCGTGTGGACCAAGGG
* *
27826680 ACATGCCCGTGT-GACCATGGG
1 ACACGCCCGTGTGGACCAAGGG
27826701 ACACGCCCGTG
1 ACACGCCCGTG
27826712 CTACAGGCTG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.20, C:0.33, G:0.31, T:0.15
Consensus pattern (22 bp):
ACACGCCCGTGTGGACCAAGGG
Found at i:27828557 original size:27 final size:27
Alignment explanation
Indices: 27828527--27828704 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
27828517 ATATTGAGTC
* * * *
27828527 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
27828554 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
27828581 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
27828609 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
27828636 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
27828663 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
27828690 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
27828705 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:27828666 original size:82 final size:81
Alignment explanation
Indices: 27828548--27828703 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
27828538 TGCTATATAA
* *
27828548 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
27828613 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
27828630 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
27828694 CACTTAGTGC
65 CACTTAGTGC
27828704 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:27836744 original size:27 final size:27
Alignment explanation
Indices: 27836714--27836891 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
27836704 ATATTGAGTC
* * * *
27836714 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
27836741 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
27836768 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
27836796 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
27836823 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
27836850 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
27836877 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
27836892 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:27836853 original size:82 final size:81
Alignment explanation
Indices: 27836735--27836890 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
27836725 TGCTATATAA
* *
27836735 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
27836800 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
27836817 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
27836881 CACTTAGTGC
65 CACTTAGTGC
27836891 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:27837392 original size:12 final size:12
Alignment explanation
Indices: 27837375--27837401 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
27837365 ATGGCATACT
27837375 TATGTATATATA
1 TATGTATATATA
27837387 TATGTATATATA
1 TATGTATATATA
27837399 TAT
1 TAT
27837402 ACTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:27843928 original size:25 final size:25
Alignment explanation
Indices: 27843900--27843960 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
27843890 AAATAATACA
* * *
27843900 CCACAAAGTCTTTTA-AGATAATTTG
1 CCACAAAGGC-TTTACAAATAACTTG
*
27843925 CCACAAGGGCTTTACAAATAACTTG
1 CCACAAAGGCTTTACAAATAACTTG
27843950 CCACAAAGGCT
1 CCACAAAGGCT
27843961 ATGTTTGGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (25 bp):
CCACAAAGGCTTTACAAATAACTTG
Found at i:27849585 original size:21 final size:21
Alignment explanation
Indices: 27849560--27849609 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
27849550 AGGAATTGTA
* *
27849560 ATGTGAACACGTAGAAGTTAT
1 ATGTGAACACATAGAAATTAT
*
27849581 ATGTGAACCCATAGAAATTAT
1 ATGTGAACACATAGAAATTAT
*
27849602 ATGCGAAC
1 ATGTGAAC
27849610 CTTAGCTGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (21 bp):
ATGTGAACACATAGAAATTAT
Found at i:27855751 original size:34 final size:35
Alignment explanation
Indices: 27855712--27855785 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 35
27855702 TGAATAAGTA
27855712 AAAGAAAAAG-AAAGATAAAAACGAAACAAAA-AGG
1 AAAGAAAAAGAAAAGA-AAAAACGAAACAAAAGAGG
** *
27855746 AAAG-AAAAGAAAAGAAAAAGGGAAAGAAAAGAGG
1 AAAGAAAAAGAAAAGAAAAAACGAAACAAAAGAGG
27855780 AAAGAA
1 AAAGAA
27855786 GGAGACAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 17 0.50
34 16 0.47
35 1 0.03
ACGTcount: A:0.73, C:0.03, G:0.23, T:0.01
Consensus pattern (35 bp):
AAAGAAAAAGAAAAGAAAAAACGAAACAAAAGAGG
Found at i:27855773 original size:12 final size:11
Alignment explanation
Indices: 27855712--27855785 Score: 71
Period size: 12 Copynumber: 6.5 Consensus size: 11
27855702 TGAATAAGTA
27855712 AAAGAAAAA-G
1 AAAGAAAAAGG
*
27855722 AAAGATAAAAACG
1 AAAG--AAAAAGG
*
27855735 AAACAAAAAGG
1 AAAGAAAAAGG
*
27855746 AAAG-AAAAGA
1 AAAGAAAAAGG
27855756 AAAGAAAAAGGG
1 AAAGAAAAA-GG
27855768 AAAGAAAAGAGG
1 AAAGAAAA-AGG
27855780 AAAGAA
1 AAAGAA
27855786 GGAGACAAAC
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
10 13 0.25
11 13 0.25
12 22 0.42
13 5 0.09
ACGTcount: A:0.73, C:0.03, G:0.23, T:0.01
Consensus pattern (11 bp):
AAAGAAAAAGG
Found at i:27858562 original size:215 final size:215
Alignment explanation
Indices: 27858191--27858612 Score: 799
Period size: 215 Copynumber: 2.0 Consensus size: 215
27858181 TATTCAGATT
*
27858191 TTGGAAGACATGTTTCGTACTTGTGTTATTGATTTTGAATCAGGTTGGGAGCGTTACTTAGCTTT
1 TTGGAAGACATGTTTCGTACTTGTGTTATTGATTTTGAATCAGGTTGGGAGCGTTACTTACCTTT
*
27858256 GGTTGAATTTGTTTATAATAATAGTTTTCAATTGAGTATTCAAATGGCTCCATATTAAGCCTTAT
66 GGCTGAATTTGTTTATAATAATAGTTTTCAATTGAGTATTCAAATGGCTCCATATTAAGCCTTAT
*
27858321 ACGGTTGTAGGTGCTGGTCACCTGTTTGTTGGATAGAATTGAGTGAAAGAAGAATGATCGAGCAG
131 ACGGTTGTAGGTGCTGGTCACCTGTTTGTTGGATAGAATTGAGTAAAAGAAGAATGATCGAGCAG
27858386 GAATTAATTCAATAAACGGC
196 GAATTAATTCAATAAACGGC
27858406 TTGGAAGACATGTTTCGTACTTGTGTTATTGATTTTGAATCAGGTTGGGAGCGTTACTTACCTTT
1 TTGGAAGACATGTTTCGTACTTGTGTTATTGATTTTGAATCAGGTTGGGAGCGTTACTTACCTTT
*
27858471 GGCTGAATTTGTTTATAATAATAGTTTTCAATTGAGTATTCAAATGGCTCCGTATTAAGCCTTAT
66 GGCTGAATTTGTTTATAATAATAGTTTTCAATTGAGTATTCAAATGGCTCCATATTAAGCCTTAT
*
27858536 ACGGTTGTAGGTGTTGGTCACCTGTTTGTTGGATAGAATTGAGTAAAAGAAGAATGATCGAGCAG
131 ACGGTTGTAGGTGCTGGTCACCTGTTTGTTGGATAGAATTGAGTAAAAGAAGAATGATCGAGCAG
27858601 GAATTAATTCAA
196 GAATTAATTCAA
27858613 CAAATGGAAG
Statistics
Matches: 202, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
215 202 1.00
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (215 bp):
TTGGAAGACATGTTTCGTACTTGTGTTATTGATTTTGAATCAGGTTGGGAGCGTTACTTACCTTT
GGCTGAATTTGTTTATAATAATAGTTTTCAATTGAGTATTCAAATGGCTCCATATTAAGCCTTAT
ACGGTTGTAGGTGCTGGTCACCTGTTTGTTGGATAGAATTGAGTAAAAGAAGAATGATCGAGCAG
GAATTAATTCAATAAACGGC
Found at i:27868996 original size:27 final size:27
Alignment explanation
Indices: 27868966--27869143 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
27868956 ATATTGAGTC
* * * *
27868966 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
27868993 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
27869020 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
27869048 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
27869075 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
27869102 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
27869129 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
27869144 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:27869105 original size:82 final size:81
Alignment explanation
Indices: 27868987--27869142 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
27868977 TGCTATATAA
* *
27868987 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
27869052 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
27869069 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
27869133 CACTTAGTGC
65 CACTTAGTGC
27869143 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:27881286 original size:15 final size:15
Alignment explanation
Indices: 27881263--27881292 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27881253 TCTAAGTGAT
*
27881263 AACATGGTGATTGAA
1 AACACGGTGATTGAA
27881278 AACACGGTGATTGAA
1 AACACGGTGATTGAA
27881293 GCATGAAATT
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:0.40, C:0.10, G:0.27, T:0.23
Consensus pattern (15 bp):
AACACGGTGATTGAA
Found at i:27891589 original size:27 final size:27
Alignment explanation
Indices: 27891559--27891620 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
27891549 CTAAATTGAC
27891559 AAAATGACTGTTTTACCCTTAT-GTGGT
1 AAAATGACTGTTTTACCCTTATAG-GGT
* *
27891586 AAAATGATTGTTTTGCCCTTATAGGGT
1 AAAATGACTGTTTTACCCTTATAGGGT
27891613 AAAATGAC
1 AAAATGAC
27891621 CCCCTATATG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (27 bp):
AAAATGACTGTTTTACCCTTATAGGGT
Found at i:27899049 original size:47 final size:47
Alignment explanation
Indices: 27898938--27899068 Score: 181
Period size: 47 Copynumber: 2.8 Consensus size: 47
27898928 GTGCGAGTGA
* * * * *
27898938 TACCTTGATTTGGCTATGGGCCATGGTATAGGTATTTTAGTGAGGAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTA-CTCAGGGAGAAGT
* * *
27898986 TACCTTGTTTTGGCTACGGGCCATGGTATAGGTACTCCGGGATAAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCAGGGAGAAGT
27899033 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACT
27899069 TATCGATTGA
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
47 42 0.57
48 32 0.43
ACGTcount: A:0.20, C:0.16, G:0.30, T:0.34
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCAGGGAGAAGT
Found at i:27901476 original size:26 final size:27
Alignment explanation
Indices: 27901422--27901487 Score: 132
Period size: 27 Copynumber: 2.4 Consensus size: 27
27901412 TTCAAAGTTC
27901422 AAACCCTAAAATTTATTTTTTCTCAAA
1 AAACCCTAAAATTTATTTTTTCTCAAA
27901449 AAACCCTAAAATTTATTTTTTCTCAAA
1 AAACCCTAAAATTTATTTTTTCTCAAA
27901476 AAACCCTAAAAT
1 AAACCCTAAAAT
27901488 AAATCCTTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (27 bp):
AAACCCTAAAATTTATTTTTTCTCAAA
Found at i:27901497 original size:26 final size:27
Alignment explanation
Indices: 27901422--27901497 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 27
27901412 TTCAAAGTTC
* * **
27901422 AAACCCTAAAATTTATTTTTTCTCAAA
1 AAACCCTAAAATTAAATCCTTCTCAAA
* * **
27901449 AAACCCTAAAATTTATTTTTTCTCAAA
1 AAACCCTAAAATTAAATCCTTCTCAAA
27901476 AAACCCTAAAA-TAAATCCTTCT
1 AAACCCTAAAATTAAATCCTTCT
27901498 TCCTTCTTCT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
26 7 0.16
27 38 0.84
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (27 bp):
AAACCCTAAAATTAAATCCTTCTCAAA
Found at i:27902576 original size:97 final size:97
Alignment explanation
Indices: 27902429--27902710 Score: 537
Period size: 97 Copynumber: 2.9 Consensus size: 97
27902419 ATTTATGCTG
27902429 TTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAACTGTGGTCTAACAT
1 TTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAACTGTGGTCTAACAT
27902494 ACTTTTTTTTTGTTTAATTTATGTTGTTGTAC
66 ACTTTTTTTTTGTTTAATTTATGTTGTTGTAC
27902526 TTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAACTGTGGTCTAACAT
1 TTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAACTGTGGTCTAACAT
27902591 ACTTTTTTTTTGTTTAATTTATGTTGTTGTAC
66 ACTTTTTTTTTGTTTAATTTATGTTGTTGTAC
* * *
27902623 TTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAAATGTAGTTTAACAT
1 TTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAACTGTGGTCTAACAT
27902688 ACTTTTTTTTTGTTTAATTTATG
66 ACTTTTTTTTTGTTTAATTTATG
27902711 CTTCCATACT
Statistics
Matches: 182, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 182 1.00
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.51
Consensus pattern (97 bp):
TTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAACTGTGGTCTAACAT
ACTTTTTTTTTGTTTAATTTATGTTGTTGTAC
Found at i:27905551 original size:13 final size:13
Alignment explanation
Indices: 27905533--27905562 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
27905523 ATAAAGTTAG
27905533 GATTCAAAAACTC
1 GATTCAAAAACTC
27905546 GATTCAAAAACTC
1 GATTCAAAAACTC
27905559 GATT
1 GATT
27905563 AACTCGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (13 bp):
GATTCAAAAACTC
Found at i:27905846 original size:23 final size:26
Alignment explanation
Indices: 27905814--27905861 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
27905804 TGCTTTAAAT
27905814 ATATCATTTAAAA-TTAAA-ATTTTA
1 ATATCATTTAAAATTTAAATATTTTA
27905838 ATATC-TTTAAAATTTAAATATTTT
1 ATATCATTTAAAATTTAAATATTTT
27905862 TAGATAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.32
24 10 0.45
25 5 0.23
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (26 bp):
ATATCATTTAAAATTTAAATATTTTA
Found at i:27905849 original size:17 final size:17
Alignment explanation
Indices: 27905827--27905863 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
27905817 TCATTTAAAA
*
27905827 TTAAAATTTTAATATCT
1 TTAAAATTTAAATATCT
*
27905844 TTAAAATTTAAATATTT
1 TTAAAATTTAAATATCT
27905861 TTA
1 TTA
27905864 GATAATTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
TTAAAATTTAAATATCT
Found at i:27907745 original size:34 final size:35
Alignment explanation
Indices: 27907691--27907764 Score: 98
Period size: 34 Copynumber: 2.1 Consensus size: 35
27907681 TAATTAATAA
27907691 AATAAAGATAATTAAAATTA-TTTTATATTACTATT
1 AATAAAGATAATTAAAATTATTTTTATATTA-TATT
* * *
27907726 AATAAA-ATAGTTATAATTATTTTTATTTTATATT
1 AATAAAGATAATTAAAATTATTTTTATATTATATT
27907760 AATAA
1 AATAA
27907765 TATTTTATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
34 20 0.57
35 15 0.43
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (35 bp):
AATAAAGATAATTAAAATTATTTTTATATTATATT
Found at i:27911319 original size:47 final size:46
Alignment explanation
Indices: 27911263--27911386 Score: 135
Period size: 47 Copynumber: 2.7 Consensus size: 46
27911253 CGTGAAGCTG
* * * *
27911263 ATGCATGTCCTAGACATGTCTTACACTAGCTCT-CGTCTCA-ATGCCA
1 ATGCATGTCCCAGACATGTCTTACACTAGCT-TACATC-AAGAGGCCA
* * *
27911309 ATGCCATGTCCCAGACATGGTATTACATTAGCTTACATCAAGAGGCCG
1 ATG-CATGTCCCAGACAT-GTCTTACACTAGCTTACATCAAGAGGCCA
27911357 ATGCATGTCCCAGACATGTCTTACACTAGC
1 ATGCATGTCCCAGACATGTCTTACACTAGC
27911387 ACACAAACAT
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
46 14 0.22
47 29 0.45
48 22 0.34
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (46 bp):
ATGCATGTCCCAGACATGTCTTACACTAGCTTACATCAAGAGGCCA
Found at i:27917519 original size:21 final size:22
Alignment explanation
Indices: 27917493--27917533 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
27917483 CACTAGACAT
27917493 AGGGGC-ACACGCCTGTGTGGG
1 AGGGGCAACACGCCTGTGTGGG
27917514 AGGGGCAACACGCCTGTGTG
1 AGGGGCAACACGCCTGTGTG
27917534 ACTAATTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.17, C:0.24, G:0.44, T:0.15
Consensus pattern (22 bp):
AGGGGCAACACGCCTGTGTGGG
Found at i:27917721 original size:28 final size:28
Alignment explanation
Indices: 27917684--27917749 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
27917674 TGTGTCCATG
*
27917684 GCCCGTGTCCCTCACACGGCCATGACAT
1 GCCCGTGTCCCTAACACGGCCATGACAT
* *
27917712 GCCCGTGTCCCTAACATGGCCATTACAT
1 GCCCGTGTCCCTAACACGGCCATGACAT
27917740 GCCCGTGTCC
1 GCCCGTGTCC
27917750 TGGTCCGTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.17, C:0.41, G:0.21, T:0.21
Consensus pattern (28 bp):
GCCCGTGTCCCTAACACGGCCATGACAT
Found at i:27918840 original size:46 final size:46
Alignment explanation
Indices: 27918738--27918951 Score: 211
Period size: 46 Copynumber: 4.6 Consensus size: 46
27918728 CACGTTACGT
* * *
27918738 CGATGCCATGTCCCAGACATGGTCTTATACT-GAC--ACATCATGAAGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAG-CTTACATCAAGAGGC
* * * * *
27918784 TGATGCATGTCCTAGACATGTCTTACATTGGCTTACATGAAGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTTACATCAAGAGGC
* * * * *
27918830 CGATGCATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCA-ATGT
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTTACATC-AAGAGGC
*
27918876 CAATGCCATGTCCCAGACATGGTCTTACACTAGCTTACATCAAGAGGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTTACATCAAGAGGC
*
27918924 TGATGCATGTCCCAGACATGTCTTACAC
1 CGATGCATGTCCCAGACATGTCTTACAC
27918952 GAGCACACAA
Statistics
Matches: 136, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
44 9 0.07
45 14 0.10
46 60 0.44
47 30 0.22
48 23 0.17
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.28
Consensus pattern (46 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCTTACATCAAGAGGC
Found at i:27926366 original size:79 final size:81
Alignment explanation
Indices: 27926230--27926414 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
27926220 TTGAATGATG
* *
27926230 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
27926294 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
27926309 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
27926371 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
27926389 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
27926415 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:27926428 original size:40 final size:40
Alignment explanation
Indices: 27926231--27926414 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
27926221 TGAATGATGT
* * * *
27926231 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
27926271 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
27926311 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
27926349 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
27926390 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
27926415 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:27926436 original size:79 final size:79
Alignment explanation
Indices: 27926283--27926447 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
27926273 GGACTAAGAT
* * **
27926283 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
27926348 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
27926362 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
27926425 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
27926441 CCGAAGG
1 CCGAAGG
27926448 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:27937168 original size:25 final size:23
Alignment explanation
Indices: 27937126--27937173 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
27937116 TATATTTGAG
**
27937126 ATTTAATCTTTTTTATTTTTAAAA
1 ATTTAATCTTTTACA-TTTTAAAA
27937150 ATTTAATTCTTTTACATTTTAAAA
1 ATTTAA-TCTTTTACATTTTAAAA
27937174 TTATAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTTAATCTTTTACATTTTAAAA
Found at i:27950644 original size:46 final size:46
Alignment explanation
Indices: 27950591--27950715 Score: 223
Period size: 46 Copynumber: 2.7 Consensus size: 46
27950581 TGGGCATCTA
* * *
27950591 AACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCG
27950637 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCG
27950683 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
27950716 GCGGGTTACA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.31
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCG
Found at i:27953357 original size:15 final size:15
Alignment explanation
Indices: 27953335--27953414 Score: 69
Period size: 15 Copynumber: 5.4 Consensus size: 15
27953325 GTATCTTGGG
*
27953335 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
27953350 TCTT-TTTATTCTGGA
1 T-TTCTTTATTCTGGA
*
27953365 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
*
27953380 TTT-TTCTA-TCTTGAA
1 TTTCTT-TATTC-TGGA
*
27953395 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
27953409 TTTCTT
1 TTTCTT
27953415 GTTATCTTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
14 13 0.25
15 34 0.64
16 6 0.11
ACGTcount: A:0.11, C:0.15, G:0.12, T:0.61
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:27953371 original size:30 final size:30
Alignment explanation
Indices: 27953326--27953403 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
27953316 CATAGTATCG
**
27953326 TATCTTGGGTTTCTTTATCCTGGATCTTTT-
1 TATCTTGAATTTCTTTATCCTGGAT-TTTTC
* * *
27953356 TAT-TCTGGATTTCTTTATTCTGGGTTTTTC
1 TATCT-TGAATTTCTTTATCCTGGATTTTTC
27953386 TATCTTGAATTTCTTTAT
1 TATCTTGAATTTCTTTAT
27953404 TCGGTTTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 5 0.12
30 35 0.85
31 1 0.02
ACGTcount: A:0.13, C:0.14, G:0.14, T:0.59
Consensus pattern (30 bp):
TATCTTGAATTTCTTTATCCTGGATTTTTC
Found at i:27955853 original size:46 final size:46
Alignment explanation
Indices: 27955792--27955955 Score: 183
Period size: 46 Copynumber: 3.5 Consensus size: 46
27955782 TAAACATCTA
27955792 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
* * * *
27955838 AACTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATG-TAACTAGGAATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCCG
* **
27955885 AACTTGTTGAGTTGAGTTTGAGTTCACTTATGGATGCGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
*
27955931 AGCTCGTTGAGTTGAGTCCGAGTTC
1 AACTCGTTGAGTTGAGTCCGAGTTC
27955956 GTGAGATGTA
Statistics
Matches: 96, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 49 0.51
47 27 0.28
48 3 0.03
50 5 0.05
51 2 0.02
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.32
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
Found at i:27955901 original size:47 final size:47
Alignment explanation
Indices: 27955743--27955983 Score: 162
Period size: 47 Copynumber: 5.2 Consensus size: 47
27955733 ATTTGAGTTT
* * * *
27955743 CGAACTCGTTGAGTTGAGGCCGAATTCGTGAGATGTAACTA-AACATC
1 CGAACTCGTTGAGTTGAGTCTGAGTTCGTGAGATGTAACTAGGA-ATC
** * * * *
27955790 TAAACTCGTTGAGTTGAGTCCGAGTTCACT--TATG-GA-T-GCGAATGTC
1 CGAACTCGTTGAGTTGAGTCTGAGTTC-GTGAGATGTAACTAG-GAA--TC
27955836 CGAACTCGTTGAGTTGAGTCTGAGTTCGTGAGATGTAACTAGGAATC
1 CGAACTCGTTGAGTTGAGTCTGAGTTCGTGAGATGTAACTAGGAATC
* * * * *
27955883 CGAACTTGTTGAGTTGAGTTTGAGTTCACT--TATG-GA-T-GCGAATGTC
1 CGAACTCGTTGAGTTGAGTCTGAGTTC-GTGAGATGTAACTAG-GAA--TC
* * *
27955929 CGAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCTGAGTTCGTGAGATGTAACTAGGAATC
27955976 CGAACTCG
1 CGAACTCG
27955984 NNNNNNNNNN
Statistics
Matches: 147, Mismatches: 28, Indels: 38
0.69 0.13 0.18
Matches are distributed among these distances:
43 1 0.01
44 6 0.04
45 5 0.03
46 57 0.39
47 65 0.44
48 4 0.03
49 7 0.05
50 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (47 bp):
CGAACTCGTTGAGTTGAGTCTGAGTTCGTGAGATGTAACTAGGAATC
Found at i:27955908 original size:93 final size:93
Alignment explanation
Indices: 27955743--27955983 Score: 367
Period size: 93 Copynumber: 2.6 Consensus size: 93
27955733 ATTTGAGTTT
* * * **
27955743 CGAACTCGTTGAGTTGAGGCCGAATTCGTGAGATGTAACTA-AACATCTAAACTCGTTGAGTTGA
1 CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGA-ATCCGAACTCGTTGAGTTGA
27955807 GTCCGAGTTCACTTATGGATGCGAATGTC
65 GTCCGAGTTCACTTATGGATGCGAATGTC
* *
27955836 CGAACTCGTTGAGTTGAGTCTGAGTTCGTGAGATGTAACTAGGAATCCGAACTTGTTGAGTTGAG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGAATCCGAACTCGTTGAGTTGAG
**
27955901 TTTGAGTTCACTTATGGATGCGAATGTC
66 TCCGAGTTCACTTATGGATGCGAATGTC
* *
27955929 CGAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCGAACTCG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGAATCCGAACTCG
27955984 NNNNNNNNNN
Statistics
Matches: 134, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
93 133 0.99
94 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (93 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGAATCCGAACTCGTTGAGTTGAG
TCCGAGTTCACTTATGGATGCGAATGTC
Found at i:27957780 original size:39 final size:39
Alignment explanation
Indices: 27957726--27957803 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
27957716 CAGAATTTTT
27957726 GGTTTGGCCAATCAATACCAGATATTTCTTAAAGTTTCC
1 GGTTTGGCCAATCAATACCAGATATTTCTTAAAGTTTCC
* *
27957765 GGTTTGGCCAATCAATACCATATTTTTCTTAAAGTTTCC
1 GGTTTGGCCAATCAATACCAGATATTTCTTAAAGTTTCC
27957804 CCTGTTTCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (39 bp):
GGTTTGGCCAATCAATACCAGATATTTCTTAAAGTTTCC
Found at i:27962399 original size:21 final size:22
Alignment explanation
Indices: 27962373--27962414 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
27962363 CACTTGACAT
27962373 AGGGGC-ACACGCCCGTGTGAG
1 AGGGGCAACACGCCCGTGTGAG
*
27962394 AGGGGCAACACGCTCGTGTGA
1 AGGGGCAACACGCCCGTGTGA
27962415 CCATTTAGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.21, C:0.26, G:0.40, T:0.12
Consensus pattern (22 bp):
AGGGGCAACACGCCCGTGTGAG
Found at i:27967244 original size:14 final size:14
Alignment explanation
Indices: 27967218--27967255 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
27967208 GTTTGCCAGT
*
27967218 AAAATATTTTCT-G
1 AAAATAATTTCTGG
27967231 AAAGATAATTTCTGG
1 AAA-ATAATTTCTGG
27967246 AAAATAATTT
1 AAAATAATTT
27967256 ACTTTTCTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 3 0.14
14 15 0.68
15 4 0.18
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (14 bp):
AAAATAATTTCTGG
Found at i:27967281 original size:20 final size:20
Alignment explanation
Indices: 27967239--27967280 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
27967229 TGAAAGATAA
27967239 TTTCTGGAAAATAATTTACT
1 TTTCTGGAAAATAATTTACT
*
27967259 TTTCTGG-AAATGATTTACT
1 TTTCTGGAAAATAATTTACT
27967278 TTT
1 TTT
27967281 TTGGTGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATAATTTACT
Found at i:27969177 original size:40 final size:39
Alignment explanation
Indices: 27969133--27969227 Score: 127
Period size: 40 Copynumber: 2.4 Consensus size: 39
27969123 GCTAAATGTG
* *
27969133 GCACTTAGTGTGCGGTTCGAGATAGCGTCAGCTATGTAC
1 GCACTTAGTGTGCGATTCGAGATAACGTCAGCTATGTAC
* * *
27969172 AGCACTTAGTGTGCGATTTGAGATAACTTCGGCTATGTAC
1 -GCACTTAGTGTGCGATTCGAGATAACGTCAGCTATGTAC
27969212 GACACTTAGTGTGCGA
1 G-CACTTAGTGTGCGA
27969228 GATATTGAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
39 1 0.02
40 48 0.98
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.29
Consensus pattern (39 bp):
GCACTTAGTGTGCGATTCGAGATAACGTCAGCTATGTAC
Found at i:27969262 original size:28 final size:28
Alignment explanation
Indices: 27969214--27969313 Score: 155
Period size: 28 Copynumber: 3.6 Consensus size: 28
27969204 CTATGTACGA
27969214 CACTTAGTGTGCGAGATATTGAGTATGG
1 CACTTAGTGTGCGAGATATTGAGTATGG
* * * *
27969242 CACTTAGTGTACGAAACATTGAGAATGG
1 CACTTAGTGTGCGAGATATTGAGTATGG
*
27969270 CACTTAGTGTGCGAGATGTTGAGTATGG
1 CACTTAGTGTGCGAGATATTGAGTATGG
27969298 CACTTAGTGTGCGAGA
1 CACTTAGTGTGCGAGA
27969314 CGTCGAATAT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 63 1.00
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.29
Consensus pattern (28 bp):
CACTTAGTGTGCGAGATATTGAGTATGG
Found at i:27978109 original size:41 final size:41
Alignment explanation
Indices: 27978031--27978109 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
27978021 ATGTTTGTGA
* *
27978031 TGTTCGGGCTTTGAGCCTAGCAAGCCTTGTGCTGGTGACTT
1 TGTTCGGGCTTCGAGCCTAGCAAGCCTTGTGCCGGTGACTT
* *
27978072 TGTTCGGGCTTCGTGCCTAGC-AGGCTTAGTGCCGGTGA
1 TGTTCGGGCTTCGAGCCTAGCAAGCCTT-GTGCCGGTGA
27978110 ATGAATTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 5 0.15
41 28 0.85
ACGTcount: A:0.11, C:0.23, G:0.34, T:0.32
Consensus pattern (41 bp):
TGTTCGGGCTTCGAGCCTAGCAAGCCTTGTGCCGGTGACTT
Found at i:27978342 original size:35 final size:35
Alignment explanation
Indices: 27978303--27978378 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 35
27978293 ACAAGTAAGC
*
27978303 TTATATCAAACTTGAGTATTCGGTTACATGTGAAT
1 TTATATCAAACATGAGTATTCGGTTACATGTGAAT
** * * *
27978338 TTATATTGAACATGTGTATTTGGTTACATGTGAGT
1 TTATATCAAACATGAGTATTCGGTTACATGTGAAT
27978373 TTATAT
1 TTATAT
27978379 TGAGGTTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (35 bp):
TTATATCAAACATGAGTATTCGGTTACATGTGAAT
Found at i:27984431 original size:29 final size:29
Alignment explanation
Indices: 27984398--27984490 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 29
27984388 TTAAGGGTTG
* *
27984398 GGGTTTAAGGTTTAGGTGTTAGGGGTTAA
1 GGGTTTAAGGTTTAGGTATTAGGGGTTTA
* * *
27984427 GGG-TTAAGGGTTTATGTTTTA-GGATTTA
1 GGGTTTAA-GGTTTAGGTATTAGGGGTTTA
*
27984455 GGGTTTAAGGTTTAAGG-ATTAGGAGTTTA
1 GGGTTTAAGGTTT-AGGTATTAGGGGTTTA
27984484 GGGTTTA
1 GGGTTTA
27984491 GATTAATTAG
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
28 20 0.38
29 32 0.62
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.41
Consensus pattern (29 bp):
GGGTTTAAGGTTTAGGTATTAGGGGTTTA
Found at i:27984448 original size:36 final size:36
Alignment explanation
Indices: 27984388--27984471 Score: 100
Period size: 36 Copynumber: 2.4 Consensus size: 36
27984378 TAAGAGTGGT
*
27984388 TTAAGGGTT-GGGGTTTAAGGTTTAGG-TGTTAGGGG
1 TTAAGGGTTAAGGGTTTAAGGTTTAGGAT-TTAGGGG
* * *
27984423 TTAAGGGTTAAGGGTTTATGTTTTAGGATTTAGGGT
1 TTAAGGGTTAAGGGTTTAAGGTTTAGGATTTAGGGG
*
27984459 TTAAGGTTTAAGG
1 TTAAGGGTTAAGG
27984472 ATTAGGAGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
35 9 0.21
36 32 0.76
37 1 0.02
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.40
Consensus pattern (36 bp):
TTAAGGGTTAAGGGTTTAAGGTTTAGGATTTAGGGG
Found at i:27984491 original size:7 final size:7
Alignment explanation
Indices: 27984385--27984491 Score: 74
Period size: 7 Copynumber: 15.0 Consensus size: 7
27984375 GTTTAAGAGT
27984385 GGTTTAAG
1 GGTTT-AG
*
27984393 GG-TTGG
1 GGTTTAG
*
27984399 GGTTTAA
1 GGTTTAG
27984406 GGTTTA-
1 GGTTTAG
27984412 GGTGTTAGG
1 GGT-TTA-G
*
27984421 GGTTAAG
1 GGTTTAG
*
27984428 GGTTAAG
1 GGTTTAG
*
27984435 GGTTTAT
1 GGTTTAG
*
27984442 GTTTTAG
1 GGTTTAG
*
27984449 GATTTAG
1 GGTTTAG
*
27984456 GGTTTAA
1 GGTTTAG
*
27984463 GGTTTAA
1 GGTTTAG
*
27984470 GGATTAG
1 GGTTTAG
27984477 GAGTTTAG
1 G-GTTTAG
27984485 GGTTTAG
1 GGTTTAG
27984492 ATTAATTAGT
Statistics
Matches: 80, Mismatches: 14, Indels: 11
0.76 0.13 0.10
Matches are distributed among these distances:
6 6 0.08
7 61 0.76
8 10 0.12
9 3 0.04
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.40
Consensus pattern (7 bp):
GGTTTAG
Found at i:27984659 original size:22 final size:21
Alignment explanation
Indices: 27984634--27984683 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
27984624 GAGTTACTAT
* *
27984634 TTTAAGGTTTGTGGATTATAGG
1 TTTAAGGATTATGGATTAT-GG
* *
27984656 TTTAGGGATTATGGTTTATGG
1 TTTAAGGATTATGGATTATGG
27984677 TTTAAGG
1 TTTAAGG
27984684 GTTAGGGTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (21 bp):
TTTAAGGATTATGGATTATGG
Found at i:27984680 original size:21 final size:20
Alignment explanation
Indices: 27984649--27984711 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
27984639 GGTTTGTGGA
*
27984649 TTATAGGTTTAGGGATTATGGT
1 TTAT-GGTTTAGGG-TTAGGGT
27984671 TTATGGTTTAAGGGTTAGGGT
1 TTATGGTTT-AGGGTTAGGGT
* *
27984692 TTAGGGCTTAGGGGTTAGGG
1 TTATGGTTTA-GGGTTAGGG
27984712 GTTAAGTGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.03
21 27 0.75
22 8 0.22
ACGTcount: A:0.19, C:0.02, G:0.40, T:0.40
Consensus pattern (20 bp):
TTATGGTTTAGGGTTAGGGT
Found at i:27984695 original size:7 final size:7
Alignment explanation
Indices: 27984654--27984711 Score: 55
Period size: 7 Copynumber: 8.3 Consensus size: 7
27984644 GTGGATTATA
27984654 GGTTTAG
1 GGTTTAG
* *
27984661 GGATTAT
1 GGTTTAG
*
27984668 GGTTTAT
1 GGTTTAG
27984675 GGTTTAAG
1 GGTTT-AG
27984683 GG-TTAG
1 GGTTTAG
27984689 GGTTTAG
1 GGTTTAG
*
27984696 GGCTTAG
1 GGTTTAG
*
27984703 GGGTTAG
1 GGTTTAG
27984710 GG
1 GG
27984712 GTTAAGTGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.09
7 36 0.84
8 3 0.07
ACGTcount: A:0.17, C:0.02, G:0.43, T:0.38
Consensus pattern (7 bp):
GGTTTAG
Found at i:27984712 original size:7 final size:7
Alignment explanation
Indices: 27984682--27984715 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
27984672 TATGGTTTAA
27984682 GGGTTAG
1 GGGTTAG
*
27984689 GGTTTAG
1 GGGTTAG
*
27984696 GGCTTAG
1 GGGTTAG
27984703 GGGTTAG
1 GGGTTAG
27984710 GGGTTA
1 GGGTTA
27984716 AGTGTTAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.15, C:0.03, G:0.50, T:0.32
Consensus pattern (7 bp):
GGGTTAG
Found at i:27985281 original size:7 final size:7
Alignment explanation
Indices: 27985269--27985376 Score: 126
Period size: 7 Copynumber: 14.7 Consensus size: 7
27985259 AATCTTCAAA
27985269 AAAAATT
1 AAAAATT
27985276 AAAAATT
1 AAAAATT
27985283 AAAAATT
1 AAAAATT
27985290 AAAAATT
1 AAAAATT
27985297 AAAAATTT
1 AAAAA-TT
*
27985305 AAAATTT
1 AAAAATT
27985312 AAAAAATT
1 -AAAAATT
27985320 AAAAATT
1 AAAAATT
*
27985327 AAATATT
1 AAAAATT
*
27985334 CAAAATTT
1 -AAAAATT
27985342 AAAAAATT
1 -AAAAATT
27985350 AAAAATT
1 AAAAATT
*
27985357 AAATATT
1 AAAAATT
*
27985364 CAAAATTT
1 -AAAAATT
27985372 AAAAA
1 AAAAA
27985377 AAATTCCCAA
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
7 58 0.67
8 28 0.33
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (7 bp):
AAAAATT
Found at i:27985317 original size:30 final size:30
Alignment explanation
Indices: 27985269--27985377 Score: 168
Period size: 30 Copynumber: 3.7 Consensus size: 30
27985259 AATCTTCAAA
*
27985269 AAAAATT-AAAAATT-AAAAATTAAAAATT
1 AAAAATTCAAAATTTAAAAAATTAAAAATT
*
27985297 AAAAATTTAAAATTTAAAAAATTAAAAATT
1 AAAAATTCAAAATTTAAAAAATTAAAAATT
*
27985327 AAATATTCAAAATTTAAAAAATTAAAAATT
1 AAAAATTCAAAATTTAAAAAATTAAAAATT
*
27985357 AAATATTCAAAATTTAAAAAA
1 AAAAATTCAAAATTTAAAAAA
27985378 AATTCCCAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
28 7 0.09
29 6 0.08
30 63 0.83
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (30 bp):
AAAAATTCAAAATTTAAAAAATTAAAAATT
Found at i:27985326 original size:37 final size:37
Alignment explanation
Indices: 27985268--27985376 Score: 148
Period size: 37 Copynumber: 2.9 Consensus size: 37
27985258 AAATCTTCAA
27985268 AAAAAATTAAAAATTAAAAATTAAAAATTAAAAATTT
1 AAAAAATTAAAAATTAAAAATTAAAAATTAAAAATTT
* * *
27985305 -AAAATTTAAAAAATTAAAAATTAAATATTCAAAATTT
1 AAAAAATT-AAAAATTAAAAATTAAAAATTAAAAATTT
* *
27985342 AAAAAATTAAAAATTAAATATTCAAAATTTAAAAA
1 AAAAAATTAAAAATTAAAAATT-AAAAATTAAAAA
27985377 AAATTCCCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
36 6 0.10
37 40 0.66
38 15 0.25
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (37 bp):
AAAAAATTAAAAATTAAAAATTAAAAATTAAAAATTT
Found at i:27996291 original size:199 final size:196
Alignment explanation
Indices: 27995951--27996328 Score: 533
Period size: 199 Copynumber: 1.9 Consensus size: 196
27995941 TCAATATAAT
* * * **
27995951 GACTTATTATGAAACATGTGTGTTCAAGAAAGTGTCTAACAATGCATTTATATTACATAAAGTAG
1 GACTTATTATGAAACATGCGTGTTCAAGAAAATGTCTAACAATGCATTTATATTAAATAAAACAG
* * ** *
27996016 GTCATATCATGTAAATATTGTAAAATATGTCTAGCAATATGTTCCCACTAAGTAAAATTATTCAC
66 GTCATATCATGTAAATATTGAAAAAAACATCTAGCAATATATTCCCACTAAGTAAAATTATTCAC
* * * *
27996081 ATTATGTAAATGTGTTACCCATGATTGTTGTTGAGTTGTCAAAAGAGCACTCTGCCACGATATAT
131 ATTAAGTAAATGTGTTACCCATGATTGTTGCTAAGCTGTCAAAAGAGCACTCTGCCACGATATAT
27996146 A
196 A
*
27996147 GACTTATTATGAAACATGCGTGTTCAAGAAAATGTCTAA-AGTGCATTTATATTAAATAAAACAG
1 GACTTATTATGAAACATGCGTGTTCAAGAAAATGTCTAACAATGCATTTATATTAAATAAAACAG
* *
27996211 GTCATATCATGTAAATATTTGAAAAAAAAAACATCTAGCAATATATTCTCGCTAAGTAAAATTAT
66 GTCATATCATGTAAATA-TTG---AAAAAAACATCTAGCAATATATTCCCACTAAGTAAAATTAT
***
27996276 TCACATTAAGTAAATGTGTTACTTGTGATTGTTGCTAAGCTGTCAAAAGAGCA
127 TCACATTAAGTAAATGTGTTACCCATGATTGTTGCTAAGCTGTCAAAAGAGCA
27996329 TTCCGCCATG
Statistics
Matches: 158, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
195 38 0.24
196 40 0.25
199 80 0.51
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (196 bp):
GACTTATTATGAAACATGCGTGTTCAAGAAAATGTCTAACAATGCATTTATATTAAATAAAACAG
GTCATATCATGTAAATATTGAAAAAAACATCTAGCAATATATTCCCACTAAGTAAAATTATTCAC
ATTAAGTAAATGTGTTACCCATGATTGTTGCTAAGCTGTCAAAAGAGCACTCTGCCACGATATAT
A
Found at i:28000086 original size:24 final size:24
Alignment explanation
Indices: 28000057--28000198 Score: 96
Period size: 24 Copynumber: 5.9 Consensus size: 24
28000047 CCTTGTAACT
28000057 GGAAGCTCACAAAGAGCCATATTG
1 GGAAGCTCACAAAGAGCCATATTG
* **
28000081 GGAAGC-CTACAAAGAG-CTTATCA
1 GGAAGCTC-ACAAAGAGCCATATTG
* * * * *
28000104 GGAACCTTATC--CGGGCTACATAATG
1 GGAAGCTCA-CAAAGAGC--CATATTG
* *
28000129 GGAAGCTCA-TAAGAGCCATAATCG
1 GGAAGCTCACAAAGAGCCAT-ATTG
* *
28000153 GGAAGTTCACAAAGAACCATATTG
1 GGAAGCTCACAAAGAGCCATATTG
28000177 GGAAGCTCACAAAGAGCCATAT
1 GGAAGCTCACAAAGAGCCATAT
28000199 AACGAGAGCT
Statistics
Matches: 85, Mismatches: 23, Indels: 20
0.66 0.18 0.16
Matches are distributed among these distances:
22 2 0.02
23 14 0.16
24 48 0.56
25 21 0.25
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.18
Consensus pattern (24 bp):
GGAAGCTCACAAAGAGCCATATTG
Found at i:28001691 original size:23 final size:23
Alignment explanation
Indices: 28001661--28001710 Score: 91
Period size: 23 Copynumber: 2.1 Consensus size: 23
28001651 TCCCGACACT
28001661 TAGAAAAATAATTTCAAGGAATCA
1 TAGAAAAA-AATTTCAAGGAATCA
28001685 TAGAAAAAAATTTCAAGGAATCA
1 TAGAAAAAAATTTCAAGGAATCA
28001708 TAG
1 TAG
28001711 GTCACACGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.54, C:0.08, G:0.14, T:0.24
Consensus pattern (23 bp):
TAGAAAAAAATTTCAAGGAATCA
Found at i:28003000 original size:43 final size:43
Alignment explanation
Indices: 28002938--28003101 Score: 176
Period size: 43 Copynumber: 3.8 Consensus size: 43
28002928 CAATGCCAAC
*
28002938 GTCCCAGACGTGGTCTTACATGTAATCAAATATCGATTCCAGT
1 GTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCAGT
* * *
28002981 ATCCCAGACAG-GGTCTTACACGAAATCAAATA-CGATGCC-GAT
1 GTCCCAGAC-GTGGTCTTACATGTAATCAAATATCGATGCCAG-T
* * **
28003023 GTCCCAGACATGGTCTTACATGTAAATCTCAA-ATCGATGCCAAC
1 GTCCCAGACGTGGTCTTACATGT-AATC-AAATATCGATGCCAGT
28003067 GTCCCAGACGTGGTCTTACATG-AACTCAAATATCG
1 GTCCCAGACGTGGTCTTACATGTAA-TCAAATATCG
28003102 GAAATCCTAT
Statistics
Matches: 99, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
41 1 0.01
42 29 0.29
43 38 0.38
44 31 0.31
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (43 bp):
GTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCAGT
Found at i:28003074 original size:44 final size:44
Alignment explanation
Indices: 28002930--28003088 Score: 166
Period size: 44 Copynumber: 3.7 Consensus size: 44
28002920 AGCTCGTACA
* *
28002930 ATGCCAACGTCCCAGACGTGGTCTTACATGT-AATC-AAATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACATGTAAATCTCAA-ATCG
* *** * *
28002973 ATTCCAGTATCCCAGACAGGGTCTTACACG-AAA--TCAAATACG
1 ATGCCAACGTCCCAGACATGGTCTTACATGTAAATCTCAAAT-CG
* *
28003015 ATGCCGATGTCCCAGACATGGTCTTACATGTAAATCTCAAATCG
1 ATGCCAACGTCCCAGACATGGTCTTACATGTAAATCTCAAATCG
*
28003059 ATGCCAACGTCCCAGACGTGGTCTTACATG
1 ATGCCAACGTCCCAGACATGGTCTTACATG
28003089 AACTCAAATA
Statistics
Matches: 93, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
41 2 0.02
42 28 0.30
43 28 0.30
44 29 0.31
45 6 0.06
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (44 bp):
ATGCCAACGTCCCAGACATGGTCTTACATGTAAATCTCAAATCG
Found at i:28003097 original size:86 final size:85
Alignment explanation
Indices: 28002938--28003098 Score: 209
Period size: 86 Copynumber: 1.9 Consensus size: 85
28002928 CAATGCCAAC
* * **
28002938 GTCCCAGACGTGGTCTTACATGTAATCAAATATCGATTCCAGTATCCCAGACAGGGTCTTACACG
1 GTCCCAGACATGGTCTTACATGTAATCAAATATCGATGCCAACATCCCAGACAGGGTCTTACACG
28003003 AAATCAAATACGATGCCGAT
66 AAATCAAATACGATGCCGAT
* *
28003023 GTCCCAGACATGGTCTTACATGTAAATCTCAA-ATCGATGCCAACGTCCCAGAC-GTGGTCTTAC
1 GTCCCAGACATGGTCTTACATGT-AATC-AAATATCGATGCCAACATCCCAGACAG-GGTCTTAC
* *
28003086 ATGAACTCAAATA
63 ACGAAATCAAATA
28003099 TCGGAAATCC
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
85 23 0.35
86 40 0.62
87 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (85 bp):
GTCCCAGACATGGTCTTACATGTAATCAAATATCGATGCCAACATCCCAGACAGGGTCTTACACG
AAATCAAATACGATGCCGAT
Found at i:28006906 original size:43 final size:42
Alignment explanation
Indices: 28006858--28007014 Score: 131
Period size: 43 Copynumber: 3.7 Consensus size: 42
28006848 AGCATATACA
28006858 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAACATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAA-ATCG
** * * *
28006901 ATGCCATTGTCCCAGACAG-GGTCTTACACGGAATCAGATAT-G
1 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCA-AAATCG
* * * * *
28006943 ATGCCGATGTCCAAGACATGGTCTTACATGTAAAAT-AGAAGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGT--AATCA-AAATCG
* *
28006987 TTGCCAACGTCCGAGACGTGGTCTTACA
1 ATGCCAACGTCCCAGACGTGGTCTTACA
28007015 CGATAACACA
Statistics
Matches: 90, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
42 25 0.28
43 36 0.40
44 29 0.32
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAAATCG
Found at i:28006960 original size:42 final size:43
Alignment explanation
Indices: 28006877--28006970 Score: 111
Period size: 42 Copynumber: 2.2 Consensus size: 43
28006867 TCCCAGACGT
* * *
28006877 GGTCTTACATGTAATCAAACATCGATGCCATTGTCCCAGACAG
1 GGTCTTACACGGAATCAAACATCGATGCCATTGTCCAAGACAG
* * *
28006920 GGTCTTACACGGAATCAGATAT-GATGCCGA-TGTCCAAGACAT
1 GGTCTTACACGGAATCAAACATCGATGCC-ATTGTCCAAGACAG
28006962 GGTCTTACA
1 GGTCTTACA
28006971 TGTAAAATAG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
42 25 0.57
43 19 0.43
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (43 bp):
GGTCTTACACGGAATCAAACATCGATGCCATTGTCCAAGACAG
Found at i:28015013 original size:49 final size:50
Alignment explanation
Indices: 28014941--28015070 Score: 172
Period size: 49 Copynumber: 2.6 Consensus size: 50
28014931 CGAAGCTATC
* * * *
28014941 TGATACGCATAGTAGCCTACACTTAGTACTACACATGCG-GTCAACAATC
1 TGATACACGTAGTAGCCTACACTTAGTACTACACATGCGACTCAACAATA
* * * *
28014990 TGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACTTAACAGTA
1 TGATACACGTAGTAGCCTACACTTAGTACTACACATGCGACTCAACAATA
*
28015040 TGATACACGTAGTAGCCTCCACTTAGTACTA
1 TGATACACGTAGTAGCCTACACTTAGTACTA
28015071 AACACGTGTA
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
49 35 0.50
50 35 0.50
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (50 bp):
TGATACACGTAGTAGCCTACACTTAGTACTACACATGCGACTCAACAATA
Found at i:28017846 original size:45 final size:45
Alignment explanation
Indices: 28017782--28017873 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
28017772 ATAAATCACA
*
28017782 AATTCTTTCCCCGACTCGGGTTGCACTAACACTGGTGCTTTGGTC
1 AATTCTTTCCCCGACTCGGGTTGCACTAACACTGGTGCTTCGGTC
28017827 AATTCTTTCCCCGACTCGGGTTGCACTAACACTGGTGCTTCGGTC
1 AATTCTTTCCCCGACTCGGGTTGCACTAACACTGGTGCTTCGGTC
28017872 AA
1 AA
28017874 CCGCTCTTTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.17, C:0.29, G:0.22, T:0.32
Consensus pattern (45 bp):
AATTCTTTCCCCGACTCGGGTTGCACTAACACTGGTGCTTCGGTC
Found at i:28018275 original size:49 final size:49
Alignment explanation
Indices: 28018212--28018311 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 49
28018202 CTTAAATGTT
*
28018212 CAGCATGCTCGGACTCGTTTCGAGAATAAATCAGGATATCATCTATGAA
1 CAGCAGGCTCGGACTCGTTTCGAGAATAAATCAGGATATCATCTATGAA
*
28018261 CAGCAGGCTTGGACTCGTTTCGAGAATAAATCAGGATATCATCTATGAA
1 CAGCAGGCTCGGACTCGTTTCGAGAATAAATCAGGATATCATCTATGAA
28018310 CA
1 CA
28018312 CAACCACAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (49 bp):
CAGCAGGCTCGGACTCGTTTCGAGAATAAATCAGGATATCATCTATGAA
Found at i:28022146 original size:50 final size:49
Alignment explanation
Indices: 28022023--28022259 Score: 264
Period size: 50 Copynumber: 4.8 Consensus size: 49
28022013 CCGAAGCTAC
* * *
28022023 CTGATACGCATAGTAGCCTACACTTAGTACTACACATGTGA-TCAACAAT
1 CTGATACACGTAGTAGCCTACACTTAGTACTACACACGTGACTCAAC-AT
* *
28022072 CTGGTACACGTAGTAGCCTACACTTAGTACTACACACGTGACCTCATCAT
1 CTGATACACGTAGTAGCCTACACTTAGTACTACACACGTGA-CTCAACAT
*
28022122 CTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-TCGAAGTCAT
1 CTGATACACGTAGTAGCCTACACTTAGTACTACACACGTGACTC-AA--CAT
* * * * * * *
28022173 -TAAGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACTTAACAGT
1 CTGA-TACACGTAGTAGCCTACACTTAGTACTACACACGTGACTCAACA-T
*
28022223 ATGATACACGTAGTAGCCTACACTTAGTACTACACAC
1 CTGATACACGTAGTAGCCTACACTTAGTACTACACAC
28022260 ATGTATTCAC
Statistics
Matches: 160, Mismatches: 19, Indels: 17
0.82 0.10 0.09
Matches are distributed among these distances:
48 2 0.01
49 40 0.25
50 73 0.46
51 44 0.28
52 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (49 bp):
CTGATACACGTAGTAGCCTACACTTAGTACTACACACGTGACTCAACAT
Found at i:28022229 original size:101 final size:99
Alignment explanation
Indices: 28022024--28022259 Score: 289
Period size: 101 Copynumber: 2.4 Consensus size: 99
28022014 CGAAGCTACC
* * * * *
28022024 TGATACGCATAGTAGCCTACACTTAGTACTACACATGTGATCAACAATCTGGTACACGTAGTAGC
1 TGATACACGTAGTAGCCTACACTTAGTACTACACACGTGATCAACAATCTAGTACACATAGTAGC
* * *
28022089 CTACACTTAGTACTACACACGTGACCTCATCATC
66 CTACACTTAGTACTACACACGCGACCTCAACATA
* *
28022123 TGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTC-AT-TAAGTACGCATAG
1 TGATACACGTAGTAGCCTACACTTAGTACTACACACGTGATC-AA--CAATCT-AGTACACATAG
* * *
28022186 TAGCCTGCACTTAGTACTACACATGCGA-CTTAACAGTA
62 TAGCCTACACTTAGTACTACACACGCGACCTCAACA-TA
28022224 TGATACACGTAGTAGCCTACACTTAGTACTACACAC
1 TGATACACGTAGTAGCCTACACTTAGTACTACACAC
28022260 ATGTATTCAC
Statistics
Matches: 118, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
99 38 0.32
100 8 0.07
101 71 0.60
102 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.26
Consensus pattern (99 bp):
TGATACACGTAGTAGCCTACACTTAGTACTACACACGTGATCAACAATCTAGTACACATAGTAGC
CTACACTTAGTACTACACACGCGACCTCAACATA
Found at i:28022882 original size:60 final size:60
Alignment explanation
Indices: 28022795--28022909 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
28022785 AAGCAATTTC
* ** *
28022795 ATACTAAAAACTTCTAGAATGCAAGTTTTGCAAATTATTCGATTTAGTCCCTAATTTCAA
1 ATACTAAAAACTTCTAAAACACAAGTTTTACAAATTATTCGATTTAGTCCCTAATTTCAA
* * *
28022855 ATACTAAAAGCTTCTAAAACACGAGTTTTACAATTTATTCGATTTAGTCCCTAAT
1 ATACTAAAAACTTCTAAAACACAAGTTTTACAAATTATTCGATTTAGTCCCTAAT
28022910 CCCAACTTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (60 bp):
ATACTAAAAACTTCTAAAACACAAGTTTTACAAATTATTCGATTTAGTCCCTAATTTCAA
Found at i:28023936 original size:277 final size:278
Alignment explanation
Indices: 28023434--28023987 Score: 921
Period size: 277 Copynumber: 2.0 Consensus size: 278
28023424 ATACTTCAAT
* * **
28023434 ATATATATTTTCAAAAGTACCAAAATAAGGTTCGATAATGTGGTGACAATCCTCGATGATCCCCG
1 ATATACATTTTCAAAAGTACCAAAATAAGGTTCAATAATGTGGTGACAATCCTCGACAATCCCCG
* * * *
28023499 AGCTCCCAATAGCTTCGATATCTATAAAACAATGAAAACTTACACAGAGTAAGCTTTCAAAAGCT
66 AGCTCACAATAGCTTCGATATCTATAAAACAATGAAAACATACACAGAATAAGCTTTCAAAAGAT
* * *
28023564 TAGTAAGCCATATACAAACAAACTTATCAACATAAGTATATAAACATTAAGAATACATGTACTTT
131 TAGTAAGCCATATACAAACAAACTTATCAACATAAGCATATAAACATCAAGAATAAATGTACTTT
*
28023629 AGGACCAAGATGCTAACATATATCACATGGTTCACCTATAATTCATATGTTCTCAAAGATATATG
196 AGGACCAAGATGCTAACATATATCACATGGTTCACCTATAATTCATATGTTCTCAAAGATACATG
28023694 TACTTACCTTTCATTCTG
261 TACTTACCTTTCATTCTG
* *
28023712 ATATACATTTTCAAAAGTACCAAAATAATGTTCAATAATGTGGTGACAATCCTCGACAATCGCCG
1 ATATACATTTTCAAAAGTACCAAAATAAGGTTCAATAATGTGGTGACAATCCTCGACAATCCCCG
* * *
28023777 AGCTCACAGTAGCTTCGATATCTATAAAATAATGTAAACATACACAGAATAAGCTTTC-AAAGAT
66 AGCTCACAATAGCTTCGATATCTATAAAACAATGAAAACATACACAGAATAAGCTTTCAAAAGAT
*
28023841 TAGTAAGCCATATACAAATAAACTTATCAACATAAGCATATAAACATCAAGAATAAATGTACTTT
131 TAGTAAGCCATATACAAACAAACTTATCAACATAAGCATATAAACATCAAGAATAAATGTACTTT
* *
28023906 ATGACCAAGATGCTAACATATATCACATGGTTCACCTATAATTCATATTTTCTCAAAGATACATG
196 AGGACCAAGATGCTAACATATATCACATGGTTCACCTATAATTCATATGTTCTCAAAGATACATG
28023971 TACTTACCTTTCATTCT
261 TACTTACCTTTCATTCT
28023988 CAACATAATG
Statistics
Matches: 256, Mismatches: 20, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
277 145 0.57
278 111 0.43
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (278 bp):
ATATACATTTTCAAAAGTACCAAAATAAGGTTCAATAATGTGGTGACAATCCTCGACAATCCCCG
AGCTCACAATAGCTTCGATATCTATAAAACAATGAAAACATACACAGAATAAGCTTTCAAAAGAT
TAGTAAGCCATATACAAACAAACTTATCAACATAAGCATATAAACATCAAGAATAAATGTACTTT
AGGACCAAGATGCTAACATATATCACATGGTTCACCTATAATTCATATGTTCTCAAAGATACATG
TACTTACCTTTCATTCTG
Found at i:28024163 original size:43 final size:42
Alignment explanation
Indices: 28024116--28024272 Score: 131
Period size: 43 Copynumber: 3.7 Consensus size: 42
28024106 AGCATATACA
*
28024116 ATGCCAACATCCCAGACGTGGTCTTACATGTAATCAAACATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAA-ATCG
** * * *
28024159 ATGCCATTGTCCCAGACAG-GGTCTTACACGGAATCAGATAT-G
1 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCA-AAATCG
* * * * *
28024201 ATGCCGATGTCCAAGACATGGTCTTACATGTAAAAT-AGAAGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGT--AATCA-AAATCG
*
28024245 ATGCCAACGTCCGAGACGTGGTCTTACA
1 ATGCCAACGTCCCAGACGTGGTCTTACA
28024273 CGATAACACA
Statistics
Matches: 90, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
42 25 0.28
43 35 0.39
44 30 0.33
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAAATCG
Done.