Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 89 of 311
Found at i:28473731 original size:28 final size:28
Alignment explanation
Indices: 28473646--28473734 Score: 99
Period size: 28 Copynumber: 3.2 Consensus size: 28
28473636 CCTTCATAGA
* * * *
28473646 GAACTCTTAAAGAAATTATGTTCATGGA
1 GAACTCTAAAAGAAATGATGTTCTTGGT
* * *
28473674 GAACTCTGAAGGAAATGATGTT-TATAGT
1 GAACTCTAAAAGAAATGATGTTCT-TGGT
28473702 GAACTCTAAAAGAAATGATGTTCTTGGT
1 GAACTCTAAAAGAAATGATGTTCTTGGT
28473730 GAACT
1 GAACT
28473735 TTGAAGAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
28 49 0.98
29 1 0.02
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.31
Consensus pattern (28 bp):
GAACTCTAAAAGAAATGATGTTCTTGGT
Found at i:28473752 original size:27 final size:27
Alignment explanation
Indices: 28473730--28473817 Score: 115
Period size: 27 Copynumber: 3.3 Consensus size: 27
28473720 TGTTCTTGGT
*
28473730 GAACTTTGAAGAAATGGAATTCTTGAA
1 GAACTCTGAAGAAATGGAATTCTTGAA
* *
28473757 GAACCCTGAAGAAATGAAATTCTT-AA
1 GAACTCTGAAGAAATGGAATTCTTGAA
* *
28473783 CGAACTCTGAAGAAATTGAATTCTTGAC
1 -GAACTCTGAAGAAATGGAATTCTTGAA
28473811 GAACTCT
1 GAACTCT
28473818 AAGTGAAAGC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
26 2 0.04
27 49 0.94
28 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (27 bp):
GAACTCTGAAGAAATGGAATTCTTGAA
Found at i:28476758 original size:68 final size:68
Alignment explanation
Indices: 28476611--28476766 Score: 149
Period size: 68 Copynumber: 2.2 Consensus size: 68
28476601 AGCCGATTTG
* * * * *
28476611 TCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATT
1 TCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAATCACACATGCGACCTAGCTACATA
*
28476676 TATC
65 TATA
* *
28476680 TCTCACGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGTATCACACATGTGACCTAGCTACT
1 TCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGAATCACACATGCGACCTAGCTAC-
28476742 ATATAGTA
62 ATATA-TA
28476750 TCTCGTAGC-CTTCTTGT
1 TCTCGTAGCTC-TCTTGT
28476767 ACACATGATG
Statistics
Matches: 73, Mismatches: 8, Indels: 13
0.78 0.09 0.14
Matches are distributed among these distances:
67 1 0.01
68 33 0.45
69 7 0.10
70 6 0.08
71 26 0.36
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.35
Consensus pattern (68 bp):
TCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATCACACATGCGACCTAGCTACATAT
ATA
Found at i:28574965 original size:27 final size:27
Alignment explanation
Indices: 28574927--28574989 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
28574917 TTGAATTGTA
*
28574927 TTAGATCAAGAACAAAGAAAATCAGAC
1 TTAGATCGAGAACAAAGAAAATCAGAC
28574954 TTAGATCGAGAACAAAGAAAATCAGAC
1 TTAGATCGAGAACAAAGAAAATCAGAC
28574981 TTAGATCGA
1 TTAGATCGA
28574990 AGGAAGTCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.51, C:0.14, G:0.17, T:0.17
Consensus pattern (27 bp):
TTAGATCGAGAACAAAGAAAATCAGAC
Found at i:28586824 original size:5 final size:5
Alignment explanation
Indices: 28586814--28586841 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
28586804 ACAATTTGTG
28586814 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
28586842 GAACATACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:28588237 original size:7 final size:7
Alignment explanation
Indices: 28588218--28588308 Score: 66
Period size: 7 Copynumber: 13.4 Consensus size: 7
28588208 TTTGAATCCC
28588218 AAACCCTT
1 AAACCC-T
28588226 AAACCCT
1 AAACCCT
28588233 AAA-CCT
1 AAACCCT
28588239 AAA-CCT
1 AAACCCT
28588245 AAA-CCT
1 AAACCCT
*
28588251 AAACCTT
1 AAACCCT
28588258 AAACCCT
1 AAACCCT
**
28588265 AAACTTT
1 AAACCCT
*
28588272 AAACCTT
1 AAACCCT
**
28588279 AAACATT
1 AAACCCT
*
28588286 AAA-TCT
1 AAACCCT
28588292 GAAACCC-
1 -AAACCCT
28588299 AAACCCT
1 AAACCCT
28588306 AAA
1 AAA
28588309 TTTTAGGGTT
Statistics
Matches: 70, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
6 25 0.36
7 38 0.54
8 7 0.10
ACGTcount: A:0.47, C:0.31, G:0.01, T:0.21
Consensus pattern (7 bp):
AAACCCT
Found at i:28588267 original size:14 final size:14
Alignment explanation
Indices: 28588218--28588288 Score: 76
Period size: 14 Copynumber: 5.2 Consensus size: 14
28588208 TTTGAATCCC
*
28588218 AAACCCTTAAACCCT
1 AAACCC-TAAACCTT
28588233 AAA-CCTAAACC-T
1 AAACCCTAAACCTT
28588245 AAA-CCTAAACCTT
1 AAACCCTAAACCTT
*
28588258 AAACCCTAAACTTT
1 AAACCCTAAACCTT
* *
28588272 AAACCTTAAACATT
1 AAACCCTAAACCTT
28588286 AAA
1 AAA
28588289 TCTGAAACCC
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
12 12 0.24
13 10 0.20
14 26 0.51
15 3 0.06
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.23
Consensus pattern (14 bp):
AAACCCTAAACCTT
Found at i:28588341 original size:21 final size:21
Alignment explanation
Indices: 28588315--28588378 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
28588305 TAAATTTTAG
* *
28588315 GGTTCGAGGTTCGAGGTTCGA
1 GGTTCGAGGTTCAAGGTTCAA
28588336 GGTTCGAGGTTCAAGGTTCAA
1 GGTTCGAGGTTCAAGGTTCAA
** *
28588357 GGTTTAAGGTTTAAGGTTCAA
1 GGTTCGAGGTTCAAGGTTCAA
28588378 G
1 G
28588379 ATAAAATAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.22, C:0.11, G:0.36, T:0.31
Consensus pattern (21 bp):
GGTTCGAGGTTCAAGGTTCAA
Found at i:28588365 original size:7 final size:7
Alignment explanation
Indices: 28588315--28588378 Score: 74
Period size: 7 Copynumber: 9.1 Consensus size: 7
28588305 TAAATTTTAG
*
28588315 GGTTCGA
1 GGTTCAA
*
28588322 GGTTCGA
1 GGTTCAA
*
28588329 GGTTCGA
1 GGTTCAA
*
28588336 GGTTCGA
1 GGTTCAA
28588343 GGTTCAA
1 GGTTCAA
28588350 GGTTCAA
1 GGTTCAA
*
28588357 GGTTTAA
1 GGTTCAA
*
28588364 GGTTTAA
1 GGTTCAA
28588371 GGTTCAA
1 GGTTCAA
28588378 G
1 G
28588379 ATAAAATAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 54 1.00
ACGTcount: A:0.22, C:0.11, G:0.36, T:0.31
Consensus pattern (7 bp):
GGTTCAA
Found at i:28591654 original size:44 final size:46
Alignment explanation
Indices: 28591562--28591655 Score: 140
Period size: 44 Copynumber: 2.1 Consensus size: 46
28591552 TGTTCGCTGT
*
28591562 AATGGAATAGAGCTATAATCAGTAATTCAATTGTTTGGTTGAATGG
1 AATGGAATAGAACTATAATCAGTAATTCAATTGTTTGGTTGAATGG
*
28591608 AATGGAATAGAACTATAAT-AGT-ATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTATAATCAGTAATTCAAT-TGTTTGGTTGAATGG
28591652 AATG
1 AATG
28591656 ACGTTGTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 3 0.07
46 18 0.40
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (46 bp):
AATGGAATAGAACTATAATCAGTAATTCAATTGTTTGGTTGAATGG
Found at i:28591840 original size:61 final size:63
Alignment explanation
Indices: 28591768--28591894 Score: 179
Period size: 61 Copynumber: 2.0 Consensus size: 63
28591758 TATTAAATTT
* * * *
28591768 AATAATAATAAATAATTTAATCATATT-TTAATATAATTATTA-CCAAATAT-AATTTAATAAA
1 AATAAAAATAAATAATTTAATAACATTCTTAATATAATTATTATCAAAATATGAA-TTAATAAA
*
28591829 AATAAAAATAAATAATTTAATAACATTCTTAATATAATTATTATTAAAATATGAATTAATAAA
1 AATAAAAATAAATAATTTAATAACATTCTTAATATAATTATTATCAAAATATGAATTAATAAA
28591892 AAT
1 AAT
28591895 CTTAACATAA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
61 24 0.41
62 15 0.26
63 17 0.29
64 2 0.03
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (63 bp):
AATAAAAATAAATAATTTAATAACATTCTTAATATAATTATTATCAAAATATGAATTAATAAA
Found at i:28592813 original size:63 final size:63
Alignment explanation
Indices: 28592714--28592843 Score: 183
Period size: 63 Copynumber: 2.1 Consensus size: 63
28592704 ATCACATGGA
* * * *
28592714 TATATTCTTATCACATAGGGAATGAGGGGCATCTTAA-TAGAGTTTGAAATACCAAATTTAAGT
1 TATATCCTTATCACATAGAGAATGAGGCGCATCTTAATTA-AGCTTGAAATACCAAATTTAAGT
*
28592777 TATATCCTTATCACATCA-AGAATGAGGCGCATCTTAATTAAGCTTGAATTACCAAATTTAAGT
1 TATATCCTTATCACAT-AGAGAATGAGGCGCATCTTAATTAAGCTTGAAATACCAAATTTAAGT
28592840 TATA
1 TATA
28592844 AATTAGGTTG
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
63 57 0.95
64 3 0.05
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (63 bp):
TATATCCTTATCACATAGAGAATGAGGCGCATCTTAATTAAGCTTGAAATACCAAATTTAAGT
Found at i:28596095 original size:42 final size:42
Alignment explanation
Indices: 28596036--28596197 Score: 175
Period size: 42 Copynumber: 3.8 Consensus size: 42
28596026 AAGGTTACTA
*
28596036 AGACTACGTGTAAGACCATATCTAGGATATGGCATCAGTATG
1 AGACTTCGTGTAAGACCATATCTAGGATATGGCATCAGTATG
*
28596078 AGACTTCGTGTAAGACCATATCTAGGATATGGCAT-TGATATG
1 AGACTTCGTGTAAGACCATATCTAGGATATGGCATCAG-TATG
* * * * * * *
28596120 AGACTTCGTATAAGGCCATAGCTGGGCTATTGGCATCGGTACG
1 AGACTTCGTGTAAGACCATATCTAGGATA-TGGCATCAGTATG
* * *
28596163 AGA-TCCCATGTAAGACCATATCTCGGATATGGCAT
1 AGACT-TCGTGTAAGACCATATCTAGGATATGGCAT
28596198 TGGTATGGTA
Statistics
Matches: 100, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
41 1 0.01
42 69 0.69
43 29 0.29
44 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.27
Consensus pattern (42 bp):
AGACTTCGTGTAAGACCATATCTAGGATATGGCATCAGTATG
Found at i:28617637 original size:42 final size:42
Alignment explanation
Indices: 28617585--28617688 Score: 156
Period size: 42 Copynumber: 2.5 Consensus size: 42
28617575 GAGGTTATTA
*
28617585 AGACTACGTGTAAGACCATATCTAGGATATGGCATC-AGTATG
1 AGACTTCGTGTAAGACCATATCTAGGATATGGCATCGA-TATG
* *
28617627 AGACTTCGTGTAAGACCATATTTGGGATATGGCATCGATATG
1 AGACTTCGTGTAAGACCATATCTAGGATATGGCATCGATATG
*
28617669 AGACTTCGTATAAGACCATA
1 AGACTTCGTGTAAGACCATA
28617689 ACTGGGCTAT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
42 56 0.98
43 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (42 bp):
AGACTTCGTGTAAGACCATATCTAGGATATGGCATCGATATG
Found at i:28619201 original size:45 final size:45
Alignment explanation
Indices: 28619152--28619322 Score: 206
Period size: 45 Copynumber: 3.8 Consensus size: 45
28619142 TGGTTGAGCA
28619152 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATG
* * *
28619197 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA-T--G
*
28619242 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AATG
* *
28619289 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
28619323 GGGCGGGTTA
Statistics
Matches: 108, Mismatches: 8, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
42 6 0.06
43 1 0.01
44 2 0.02
45 58 0.54
46 3 0.03
47 32 0.30
49 4 0.04
50 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATG
Found at i:28619306 original size:92 final size:92
Alignment explanation
Indices: 28619149--28619317 Score: 295
Period size: 92 Copynumber: 1.8 Consensus size: 92
28619139 GGATGGTTGA
* *
28619149 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATGTCCGAACTCGTTGAGTT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGCCCGAACTCGTTGAGTT
28619214 GAGTCCGAGTTCGTGAGATGTAACTAG
66 GAGTCCGAGTTCGTGAGATGTAACTAG
*
28619241 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AACGCCCGAACTCGTTGAGT
28619305 TGAGTCCGAGTTC
65 TGAGTCCGAGTTC
28619318 ACTTAGGGCG
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
91 10 0.14
92 63 0.86
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGCCCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:28622286 original size:15 final size:15
Alignment explanation
Indices: 28622247--28622325 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
28622237 GTATCTTGGG
*
28622247 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
28622262 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
28622277 TTTCTTTATTC-GGG
1 TTTCTTTATTCTGGA
*
28622291 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
28622306 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
28622320 TTTCTT
1 TTTCTT
28622326 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
13 2 0.04
14 17 0.32
15 32 0.60
16 2 0.04
ACGTcount: A:0.10, C:0.18, G:0.14, T:0.58
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:28622310 original size:29 final size:29
Alignment explanation
Indices: 28622238--28622324 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
28622228 CATAGTATCG
* * * *
28622238 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTC-GGATTTCTC
*
28622268 TAT-TCTGGATTTCTTTATTCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCGGATTTCTC
*
28622297 TATCTTGGATTTCTTTATTCGGTTTTCT
1 TATCTTGGATTTCTTTATTCGGATTTCT
28622325 TGTTATCTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 32 0.65
30 17 0.35
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.56
Consensus pattern (29 bp):
TATCTTGGATTTCTTTATTCGGATTTCTC
Found at i:28624856 original size:45 final size:46
Alignment explanation
Indices: 28624693--28624867 Score: 223
Period size: 45 Copynumber: 3.8 Consensus size: 46
28624683 TGGTTGAGCA
*
28624693 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
28624739 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
*
28624786 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*
28624832 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28624868 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
43 6 0.05
45 38 0.34
46 30 0.27
47 29 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:28638777 original size:6 final size:6
Alignment explanation
Indices: 28638759--28638909 Score: 114
Period size: 6 Copynumber: 24.3 Consensus size: 6
28638749 AAGAAACATT
*
28638759 ATCAGA A-CTAGA ATCAGA ATCAGA ATTAGA ATCAAGTA A-CAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATC-AG-A ATCAGA ATCAGA
* * *
28638808 ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA ATCAGT ATCAGGTA
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A
* * *
28638859 A-CAGA ATCAAA ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAAA ATCAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATC-AGA ATCAGA
28638908 AT
1 AT
28638910 GTGAATGCAA
Statistics
Matches: 116, Mismatches: 14, Indels: 30
0.73 0.09 0.19
Matches are distributed among these distances:
5 9 0.08
6 84 0.72
7 18 0.16
8 5 0.04
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:28638804 original size:31 final size:31
Alignment explanation
Indices: 28638768--28638909 Score: 230
Period size: 31 Copynumber: 4.5 Consensus size: 31
28638758 TATCAGAACT
* * * *
28638768 AGAATCAGAATCAGAATTAGAATCAAGTAAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
*
28638799 AGAATCAGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
28638830 AGAATCAAAATCAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
28638861 AGAATCAAAATCAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
28638892 AGAATCAAAAATCAGAAT
1 AGAATC-AAAATCAGAAT
28638910 GTGAATGCAA
Statistics
Matches: 106, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
31 95 0.90
32 11 0.10
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.19
Consensus pattern (31 bp):
AGAATCAAAATCAGAATCAGTATCAGGTAAC
Found at i:28638842 original size:62 final size:62
Alignment explanation
Indices: 28638743--28638909 Score: 230
Period size: 62 Copynumber: 2.7 Consensus size: 62
28638733 TAACCCATTA
* * * * *
28638743 CAGAATAAGAAACATTATCA-G-AACTAGAATCAGAATCAGAATTAGAATCAAGTAACAGAAT
1 CAGAATCAGAATCAGTATCAGGTAAC-AGAATCAAAATCAGAATCAGAATCAAGTAACAGAAT
* *
28638804 CAGAATCAGAATCAGTATCAGGTAACAGAATCAAAATCAGAATCAGTATCAGGTAACAGAAT
1 CAGAATCAGAATCAGTATCAGGTAACAGAATCAAAATCAGAATCAGAATCAAGTAACAGAAT
*
28638866 CAAAATCAGAATCAGTATCAGGTAACAGAATCAAAAATCAGAAT
1 CAGAATCAGAATCAGTATCAGGTAACAGAATC-AAAATCAGAAT
28638910 GTGAATGCAA
Statistics
Matches: 95, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
61 17 0.18
62 64 0.67
63 14 0.15
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.19
Consensus pattern (62 bp):
CAGAATCAGAATCAGTATCAGGTAACAGAATCAAAATCAGAATCAGAATCAAGTAACAGAAT
Found at i:28639109 original size:26 final size:27
Alignment explanation
Indices: 28639046--28639119 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
28639036 ACTCAGTTAT
* *
28639046 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGATA
28639073 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
* *
28639099 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
28639120 TTAACAGAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
26 20 0.47
27 23 0.53
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:28639312 original size:22 final size:22
Alignment explanation
Indices: 28639278--28639342 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
28639268 GCAATTACGT
*
28639278 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* * *
28639300 TTGGCATAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
28639322 TTGACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
28639343 AAGGCTTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
21 2 0.06
22 30 0.88
23 2 0.06
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.22
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:28640199 original size:27 final size:27
Alignment explanation
Indices: 28639787--28640206 Score: 572
Period size: 27 Copynumber: 15.6 Consensus size: 27
28639777 TACTCCACAA
* * * *
28639787 GGTATCTCGATAATTCCACCCTATAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
**
28639814 GGTATTTTAGTAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
28639841 GGTATTTCGATAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* * * *
28639868 AGTATTGCGATAATTCTACCCTACAAG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
28639895 GGTATTTCGGTAATTCTACCCTACAAG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
28639922 GGTATTTCGATAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* * *
28639949 GGTATTACGATAATTCTACTCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* *
28639976 GGTATTTCGATAATTCTACTCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* *
28640003 GGTATTTCGGTAATTCTACCATACAAG
1 GGTATTTCGGTAATTCTACCCTACAGG
28640030 GGTATTTCGGTAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
28640057 GGTATTTCAGTAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* *
28640084 GGTATTTTGGTAATTCTACCCTAAAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* * *
28640111 GGTATTGT-GATAATTCTACCCTATAAG
1 GGTATT-TCGGTAATTCTACCCTACAGG
28640138 GGTATTTCGGTAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
28640165 GGTATTTTGGTAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
28640192 GGTATTTTGGTAATT
1 GGTATTTCGGTAATT
28640207 TTGTAAATCG
Statistics
Matches: 354, Mismatches: 37, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
26 1 0.00
27 352 0.99
28 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (27 bp):
GGTATTTCGGTAATTCTACCCTACAGG
Found at i:28640592 original size:27 final size:27
Alignment explanation
Indices: 28640164--28640585 Score: 380
Period size: 27 Copynumber: 15.6 Consensus size: 27
28640154 TACCCTACAG
* ** *
28640164 GGGTATTTTGGTAATTCTACCCTA-CAG
1 GGGTATTTTGGTAATTTTA-CAAACCAA
** * *
28640191 GGGTATTTTGGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
**** * * *
28640218 GGGTAAAACGGTAATTCTATAAATCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
* * ** *
28640245 TGGTACTTTGGTAATTTTACAAGTCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
*** *** *
28640272 GGGTATTTCCATAATTTTACAGGTCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
** * ** *
28640299 GGGTATTTCAGTAATTTCACAAATTAG
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
28640326 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
28640353 GGGTATTTTGATAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
*
28640380 GGGTATTTTGGTAATTTTACAAA-CTA
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
28640406 GTGGTATTTTGGTAATTTTATAAACAAA
1 G-GGTATTTTGGTAATTTTACAAACCAA
*
28640434 GGGTATTTTAGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
** *
28640461 GGGTATTTTGGTAATTTTGTAAACAAA
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
28640488 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACCAA
*
28640515 GGGTATTTTGGTAATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
*
28640542 GGGTATTTTAGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
28640569 GGGTATTTTGGTAATTT
1 GGGTATTTTGGTAATTT
28640586 GGTAAACTAA
Statistics
Matches: 326, Mismatches: 66, Indels: 6
0.82 0.17 0.02
Matches are distributed among these distances:
26 3 0.01
27 321 0.98
28 2 0.01
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAA
Found at i:28642534 original size:6 final size:6
Alignment explanation
Indices: 28642516--28642643 Score: 102
Period size: 6 Copynumber: 20.8 Consensus size: 6
28642506 AAGAAACATT
* *
28642516 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATCAG- GTGACAAA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * *
28642565 ATCAGA ATCAGT ATCAAGTA A-CAGA ATCAAA ATCAGA ATCAGT ATCAGGTA
1 ATCAGA ATCAGA ATC-AG-A ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A
* *
28642616 A-CAGA ATCAAA ATCAGA ATCAGT ATCAG
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAG
28642644 GTAATAGAAT
Statistics
Matches: 98, Mismatches: 13, Indels: 22
0.74 0.10 0.17
Matches are distributed among these distances:
5 6 0.06
6 80 0.82
7 9 0.09
8 3 0.03
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:28642537 original size:18 final size:18
Alignment explanation
Indices: 28642516--28642643 Score: 102
Period size: 19 Copynumber: 6.9 Consensus size: 18
28642506 AAGAAACATT
28642516 ATCAGAA-CTAGAATCAGA
1 ATCAGAATC-AGAATCAGA
28642534 ATCAGAATCAGAATCAG-
1 ATCAGAATCAGAATCAGA
* *
28642551 GTGACAAAATCAGAATCAGA
1 AT--CAGAATCAGAATCAGA
*
28642571 ATCAGTATCAAGTAA-CAGA
1 ATCAGAATC-AG-AATCAGA
* *
28642590 ATCAAAATCAGAATCAGT
1 ATCAGAATCAGAATCAGA
*
28642608 ATCAGGTAA-CAGAATCAAA
1 ATCA-G-AATCAGAATCAGA
*
28642627 ATCAGAATCAGTATCAG
1 ATCAGAATCAGAATCAG
28642644 GTAATAGAAT
Statistics
Matches: 87, Mismatches: 13, Indels: 20
0.73 0.11 0.17
Matches are distributed among these distances:
17 5 0.06
18 37 0.43
19 40 0.46
20 5 0.06
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.19
Consensus pattern (18 bp):
ATCAGAATCAGAATCAGA
Found at i:28642565 original size:31 final size:31
Alignment explanation
Indices: 28642525--28642666 Score: 203
Period size: 31 Copynumber: 4.5 Consensus size: 31
28642515 TATCAGAACT
* * *
28642525 AGAATCAGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
* * *
28642556 AAAATCAGAATCAGAATCAGTATCAAGTAAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
28642587 AGAATCAAAATCAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
*
28642618 AGAATCAAAATCAGAATCAGTATCAGGTAAT
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
*
28642649 AGAATAAAAAATCAGAAT
1 AGAAT-CAAAATCAGAAT
28642667 GTGAATGCAA
Statistics
Matches: 101, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
31 90 0.89
32 11 0.11
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.19
Consensus pattern (31 bp):
AGAATCAAAATCAGAATCAGTATCAGGTAAC
Found at i:28642589 original size:25 final size:24
Alignment explanation
Indices: 28642528--28642605 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 24
28642518 CAGAACTAGA
*
28642528 ATCAGAATCAGAATCAGAATCAGGT
1 ATCAAAATCAGAATCAGAATCA-GT
28642553 GA-CAAAATCAGAATCAGAATCAGT
1 -ATCAAAATCAGAATCAGAATCAGT
* *
28642577 ATCAAGTAA-CAGAATCAAAATCAGA
1 ATCAA--AATCAGAATCAGAATCAGT
28642602 ATCA
1 ATCA
28642606 GTATCAGGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
23 1 0.02
24 5 0.11
25 37 0.80
26 3 0.07
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.18
Consensus pattern (24 bp):
ATCAAAATCAGAATCAGAATCAGT
Found at i:28642599 original size:62 final size:62
Alignment explanation
Indices: 28642500--28642666 Score: 203
Period size: 62 Copynumber: 2.7 Consensus size: 62
28642490 TAACCCATTA
* * * * *
28642500 CAGAATAAGAAACATTATC-AG-AACTAGAATCAGAATCAGAATCAGAATCAGGTGACAAAAT
1 CAGAATCAGAATCAGTATCAAGTAAC-AGAATCAAAATCAGAATCAGAATCAGGTAACAAAAT
* *
28642561 CAGAATCAGAATCAGTATCAAGTAACAGAATCAAAATCAGAATCAGTATCAGGTAACAGAAT
1 CAGAATCAGAATCAGTATCAAGTAACAGAATCAAAATCAGAATCAGAATCAGGTAACAAAAT
* * * *
28642623 CAAAATCAGAATCAGTATCAGGTAATAGAATAAAAAATCAGAAT
1 CAGAATCAGAATCAGTATCAAGTAACAGAAT-CAAAATCAGAAT
28642667 GTGAATGCAA
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
61 16 0.17
62 62 0.67
63 14 0.15
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.19
Consensus pattern (62 bp):
CAGAATCAGAATCAGTATCAAGTAACAGAATCAAAATCAGAATCAGAATCAGGTAACAAAAT
Found at i:28642833 original size:27 final size:26
Alignment explanation
Indices: 28642803--28642876 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
28642793 GGTCAGTTAT
* * *
28642803 CAGATATTGTGACAGAGTCACCTGATA
1 CAGATATTGTGACAAAGCCACCAGA-A
*
28642830 CAGATATTGTGGCAAAGCCACCAGAA
1 CAGATATTGTGACAAAGCCACCAGAA
* *
28642856 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGACAAAGCCAC
28642877 TTAACAGAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 21 0.50
27 21 0.50
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGACAAAGCCACCAGAA
Found at i:28643060 original size:22 final size:22
Alignment explanation
Indices: 28643035--28643099 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
28643025 GCAAATAAGT
*
28643035 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
28643057 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
* *
28643079 TTGACACAAATCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
28643100 AAGGCTTGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.22
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:28643583 original size:27 final size:28
Alignment explanation
Indices: 28643554--28644098 Score: 682
Period size: 27 Copynumber: 20.2 Consensus size: 28
28643544 GGTATCTCGG
* *
28643554 TAATTCCACCCTACAGGGGTATTTTAG-
1 TAATTCTACCCTACAGGGGTATTTTCGA
*
28643581 TAATTCTACCTTACAGGGGTA-TTTCGA
1 TAATTCTACCCTACAGGGGTATTTTCGA
* *
28643608 TAATTCCACCCTACAGGGGTA-TTGCGA
1 TAATTCTACCCTACAGGGGTATTTTCGA
* *
28643635 TAATTCTACCCTAGAGGGGTA-TTTCGG
1 TAATTCTACCCTACAGGGGTATTTTCGA
*
28643662 TAATTCTACCCTACAGGGGTATTTTAG-
1 TAATTCTACCCTACAGGGGTATTTTCGA
*
28643689 TAATTCTACACTACAGGGGTATTTT-GA
1 TAATTCTACCCTACAGGGGTATTTTCGA
*
28643716 TAATTCTACCCTACAGGGGTA-TTGCGA
1 TAATTCTACCCTACAGGGGTATTTTCGA
28643743 TAATTCTACCCTACAGGGGTA-TTTC-A
1 TAATTCTACCCTACAGGGGTATTTTCGA
* *
28643769 GTAATTCTACCCTATAGGGGTATTTT-GG
1 -TAATTCTACCCTACAGGGGTATTTTCGA
* *
28643797 TAATTCTACCCTACAGGGGCA-TTGCGA
1 TAATTCTACCCTACAGGGGTATTTTCGA
* *
28643824 TAATTCTACCCTATAGGGGTA-TTTCGG
1 TAATTCTACCCTACAGGGGTATTTTCGA
28643851 TAATTCTACCCTACAGGGGTA-TTTCGA
1 TAATTCTACCCTACAGGGGTATTTTCGA
* *
28643878 TAATTCTGCCCTACAGGGGTA-TTTCGG
1 TAATTCTACCCTACAGGGGTATTTTCGA
*
28643905 TAATTCTACCCTACAGGGGTA-TTGCGA
1 TAATTCTACCCTACAGGGGTATTTTCGA
*
28643932 TAATTCTACCCTATAGGGGTA-TTTCGA
1 TAATTCTACCCTACAGGGGTATTTTCGA
* *
28643959 TAATTCTACCCTACAAGGGTA-TTTCGG
1 TAATTCTACCCTACAGGGGTATTTTCGA
*
28643986 TAATTCTACCCTACAGGGGTA-TTACGA
1 TAATTCTACCCTACAGGGGTATTTTCGA
*
28644013 TAATTCTACCCTACAGGGGTA-TTTCGT
1 TAATTCTACCCTACAGGGGTATTTTCGA
* *
28644040 TAATTCTACTCTACAGGGGTA-TTTCGG
1 TAATTCTACCCTACAGGGGTATTTTCGA
* *
28644067 TTATTCTACCCTACAGGGGTA-TTTCGG
1 TAATTCTACCCTACAGGGGTATTTTCGA
28644094 TAATT
1 TAATT
28644099 TTGTAAATTG
Statistics
Matches: 462, Mismatches: 48, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
26 10 0.02
27 445 0.96
28 7 0.02
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (28 bp):
TAATTCTACCCTACAGGGGTATTTTCGA
Found at i:28643612 original size:54 final size:54
Alignment explanation
Indices: 28643525--28644098 Score: 756
Period size: 54 Copynumber: 10.6 Consensus size: 54
28643515 AAGGGCAAAA
* * * * * *
28643525 TGGTAATTTTACCCCACA-AGGTATCTCGGTAATTCCACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTT
* * * *
28643578 TAGTAATTCTACCTTACAGGGGTATTTCGATAATTCCACCCTACAGGGGTATTG
1 TGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTT
* * * *
28643632 CGATAATTCTACCCTAGAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTT
* * * *
28643686 TAGTAATTCTACACTACAGGGGTATTTTGATAATTCTACCCTACAGGGGTATTG
1 TGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTT
* * *
28643740 CGATAATTCTACCCTACAGGGGTATTTC-AGTAATTCTACCCTATAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTTCGA-TAATTCTACCCTACAGGGGTATTT
* * *
28643794 TGGTAATTCTACCCTACAGGGGCATTGCGATAATTCTACCCTATAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTT
* *
28643848 CGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTGCCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTT
* * *
28643902 CGGTAATTCTACCCTACAGGGGTATTGCGATAATTCTACCCTATAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTT
* * * * *
28643956 CGATAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTA
1 TGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTT
* * * *
28644010 CGATAATTCTACCCTACAGGGGTATTTCGTTAATTCTACTCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTT
* * *
28644064 CGGTTATTCTACCCTACAGGGGTATTTCGGTAATT
1 TGGTAATTCTACCCTACAGGGGTATTTCGATAATT
28644099 TTGTAAATTG
Statistics
Matches: 462, Mismatches: 56, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
53 15 0.03
54 446 0.97
55 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (54 bp):
TGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTT
Found at i:28643646 original size:81 final size:81
Alignment explanation
Indices: 28643544--28644098 Score: 799
Period size: 81 Copynumber: 6.9 Consensus size: 81
28643534 TACCCCACAA
* * * ** *
28643544 GGTATCTCGGTAATTCCACCCTACAGGGGTATTTTAGTAATTCTACCTTACAGGGGTATTTCGAT
1 GGTATTTCGATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGAT
*
28643609 AATTCCACCCTACAGG
66 AATTCTACCCTACAGG
* * *
28643625 GGTATTGCGATAATTCTACCCTAGAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTT-TAG
1 GGTATTTCGATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGA-
*
28643689 TAATTCTACACTACAGG
65 TAATTCTACCCTACAGG
* * *
28643706 GGTATTTTGATAATTCTACCCTACAGGGGTATTGCGATAATTCTACCCTACAGGGGTATTTC-AG
1 GGTATTTCGATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGA-
*
28643770 TAATTCTACCCTATAGG
65 TAATTCTACCCTACAGG
* * * * * * *
28643787 GGTATTTTGGTAATTCTACCCTACAGGGGCATTGCGATAATTCTACCCTATAGGGGTATTTCGGT
1 GGTATTTCGATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGAT
28643852 AATTCTACCCTACAGG
66 AATTCTACCCTACAGG
* *
28643868 GGTATTTCGATAATTCTGCCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTGCGAT
1 GGTATTTCGATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGAT
*
28643933 AATTCTACCCTATAGG
66 AATTCTACCCTACAGG
* *
28643949 GGTATTTCGATAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTACGAT
1 GGTATTTCGATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGAT
28644014 AATTCTACCCTACAGG
66 AATTCTACCCTACAGG
* * * *
28644030 GGTATTTCGTTAATTCTACTCTACAGGGGTATTTCGGTTATTCTACCCTACAGGGGTATTTCGGT
1 GGTATTTCGATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGAT
28644095 AATT
66 AATT
28644099 TTGTAAATTG
Statistics
Matches: 428, Mismatches: 43, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
80 1 0.00
81 427 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (81 bp):
GGTATTTCGATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGAT
AATTCTACCCTACAGG
Found at i:28644204 original size:26 final size:25
Alignment explanation
Indices: 28644136--28644229 Score: 77
Period size: 26 Copynumber: 3.7 Consensus size: 25
28644126 CTATAAATAA
* *
28644136 AGGGTACTTTGGTAATTTTACAAGTCG
1 AGGGTATTTTAGTAA-TTTAC-AGTCG
*
28644163 AGGGTATTTCCA-TAATTTACAGGTCG
1 AGGGTATTT-TAGTAATTTACA-GTCG
* *
28644189 AGGGTATTTTAGTAATTCACAATC-
1 AGGGTATTTTAGTAATTTACAGTCG
*
28644213 AGGGTA-TTTGGTAATTT
1 AGGGTATTTTAGTAATTT
28644230 TACAAACTAG
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
23 9 0.16
24 6 0.11
25 4 0.07
26 26 0.46
27 11 0.20
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.38
Consensus pattern (25 bp):
AGGGTATTTTAGTAATTTACAGTCG
Found at i:28644254 original size:27 final size:27
Alignment explanation
Indices: 28644135--28644471 Score: 294
Period size: 27 Copynumber: 12.7 Consensus size: 27
28644125 TCTATAAATA
* **
28644135 AAGGGTACTTTGGTAATTTTACAAGTC
1 AAGGGTATTTTGGTAATTTTACAAACC
* *** ***
28644162 GAGGGTATTTCCATAA-TTTACAGGTC
1 AAGGGTATTTTGGTAATTTTACAAACC
* * * *
28644188 GAGGGTATTTTAGTAA-TTCAC-AATC
1 AAGGGTATTTTGGTAATTTTACAAACC
*
28644213 -AGGGTA-TTTGGTAATTTTACAAACT
1 AAGGGTATTTTGGTAATTTTACAAACC
* * * *
28644238 AGGGGTATTTTGATAATTTTATAAACT
1 AAGGGTATTTTGGTAATTTTACAAACC
* * *
28644265 AGGGGTATTTTAGTAATTTTGCAAACC
1 AAGGGTATTTTGGTAATTTTACAAACC
* * *
28644292 AATGGTATTTTGGTAATTTTATAAACA
1 AAGGGTATTTTGGTAATTTTACAAACC
*
28644319 AAGGGTATTTTAGTAATTTTACAAA-C
1 AAGGGTATTTTGGTAATTTTACAAACC
* * * **
28644345 TAGGTGTATTTTGGAAATTCTGTAAACC
1 AAGG-GTATTTTGGTAATTTTACAAACC
28644373 AAGGGTATTTTGGTAATTTTACAAACC
1 AAGGGTATTTTGGTAATTTTACAAACC
* *
28644400 -AGGGTTATTTTGGTGATTTTATAAACC
1 AAGGG-TATTTTGGTAATTTTACAAACC
28644427 AAGGGTATTTTGGTAATTTTACAAACC
1 AAGGGTATTTTGGTAATTTTACAAACC
*
28644454 -AGTGTATTTTGGTAATTT
1 AAGGGTATTTTGGTAATTT
28644472 GGTAAACTAA
Statistics
Matches: 252, Mismatches: 50, Indels: 17
0.79 0.16 0.05
Matches are distributed among these distances:
23 7 0.03
24 10 0.04
25 4 0.02
26 55 0.22
27 168 0.67
28 8 0.03
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (27 bp):
AAGGGTATTTTGGTAATTTTACAAACC
Found at i:28644299 original size:54 final size:54
Alignment explanation
Indices: 28644213--28644471 Score: 328
Period size: 54 Copynumber: 4.8 Consensus size: 54
28644203 ATTCACAATC
* * * *
28644213 AGGGTA-TTTGGTAATTTTACAAACTAGGGGTATTTTGATAATTTTATAAACTA
1 AGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTATAAACCA
* * * * *
28644266 GGGGTATTTTAGTAATTTTGCAAACCAATGGTATTTTGGTAATTTTATAAACAA
1 AGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTATAAACCA
* * * * *
28644320 AGGGTATTTTAGTAATTTTACAAA-CTAGGTGTATTTTGGAAATTCTGTAAACCA
1 AGGGTATTTTGGTAATTTTACAAACCAAGG-GTATTTTGGTAATTTTATAAACCA
*
28644374 AGGGTATTTTGGTAATTTTACAAACC-AGGGTTATTTTGGTGATTTTATAAACCA
1 AGGGTATTTTGGTAATTTTACAAACCAAGGG-TATTTTGGTAATTTTATAAACCA
*
28644428 AGGGTATTTTGGTAATTTTACAAACC-AGTGTATTTTGGTAATTT
1 AGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTT
28644472 GGTAAACTAA
Statistics
Matches: 179, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
53 22 0.12
54 156 0.87
55 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (54 bp):
AGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTATAAACCA
Found at i:28644695 original size:20 final size:20
Alignment explanation
Indices: 28644670--28644708 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28644660 TTAGGCCCAC
*
28644670 ATGGCCCCTTTCTGCCCATT
1 ATGGCCCCTTTCAGCCCATT
28644690 ATGGCCCCTTTCAGCCCAT
1 ATGGCCCCTTTCAGCCCAT
28644709 CGCGGCCCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.41, G:0.15, T:0.31
Consensus pattern (20 bp):
ATGGCCCCTTTCAGCCCATT
Found at i:28644715 original size:20 final size:20
Alignment explanation
Indices: 28644672--28644716 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
28644662 AGGCCCACAT
* * *
28644672 GGCCCCTTTCTGCCCATTAT
1 GGCCCCTTTCAGCCCATCAC
*
28644692 GGCCCCTTTCAGCCCATCGC
1 GGCCCCTTTCAGCCCATCAC
28644712 GGCCC
1 GGCCC
28644717 GAAGTAGCCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.09, C:0.47, G:0.20, T:0.24
Consensus pattern (20 bp):
GGCCCCTTTCAGCCCATCAC
Found at i:28646458 original size:6 final size:6
Alignment explanation
Indices: 28646440--28646536 Score: 65
Period size: 6 Copynumber: 15.8 Consensus size: 6
28646430 AAGAAACATT
* *
28646440 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATCAG- GTGAGAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * * * *
28646489 ATTAGA ATCAGT ATCAGGTA A-CAGG ATCAAA ATCAGA ATCAGT ATCAG
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCAG
28646537 GTAACAAAAT
Statistics
Matches: 70, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
5 3 0.04
6 59 0.84
7 6 0.09
8 2 0.03
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:28646484 original size:31 final size:31
Alignment explanation
Indices: 28646449--28646548 Score: 137
Period size: 31 Copynumber: 3.2 Consensus size: 31
28646439 TATCAGAACT
* * *
28646449 AGAATCAGAATCAGAATCAGAATCAGGTGAG
1 AGAATCAGAATCAGAATCAGTATCAGGTAAC
*
28646480 AGAATCAGAATTAGAATCAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGTATCAGGTAAC
* *
28646511 AGGATCAAAATCAGAATCAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGTATCAGGTAAC
*
28646542 AAAATCA
1 AGAATCA
28646549 AAAATTAGAA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.47, C:0.14, G:0.20, T:0.19
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGTATCAGGTAAC
Found at i:28646522 original size:25 final size:25
Alignment explanation
Indices: 28646494--28646548 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
28646484 TCAGAATTAG
* *
28646494 AATCAGTATCAGGTAACAGG-ATCAA
1 AATCAGAATCA-GTAACAGGTAACAA
*
28646519 AATCAGAATCAGTATCAGGTAACAA
1 AATCAGAATCAGTAACAGGTAACAA
28646544 AATCA
1 AATCA
28646549 AAAATTAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.20
Consensus pattern (25 bp):
AATCAGAATCAGTAACAGGTAACAA
Found at i:28646549 original size:31 final size:31
Alignment explanation
Indices: 28646424--28646551 Score: 134
Period size: 31 Copynumber: 4.2 Consensus size: 31
28646414 TAACCCATTA
* * *
28646424 CAAAATAAGAAACATTATCA-G-AACTAGAAT
1 CAAAATCAGAATCAGTATCAGGTAAC-AGAAT
* * * *
28646454 CAGAATCAGAATCAGAATCAGGTGAGAGAAT
1 CAAAATCAGAATCAGTATCAGGTAACAGAAT
* * *
28646485 CAGAATTAGAATCAGTATCAGGTAACAGGAT
1 CAAAATCAGAATCAGTATCAGGTAACAGAAT
*
28646516 CAAAATCAGAATCAGTATCAGGTAACAAAAT
1 CAAAATCAGAATCAGTATCAGGTAACAGAAT
28646547 CAAAA
1 CAAAA
28646552 ATTAGAATGT
Statistics
Matches: 80, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
30 15 0.19
31 64 0.80
32 1 0.01
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.19
Consensus pattern (31 bp):
CAAAATCAGAATCAGTATCAGGTAACAGAAT
Found at i:28646738 original size:27 final size:26
Alignment explanation
Indices: 28646696--28646769 Score: 94
Period size: 27 Copynumber: 2.8 Consensus size: 26
28646686 GCTCAGTTAT
* *
28646696 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGA-A
28646723 CAGATATTGTGGCAGAGCCACCAGAA
1 CAGATATTGTGGCAGAGCCACCAGAA
* * *
28646749 CAGGTAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
28646770 TTAACAGAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 19 0.45
27 23 0.55
ACGTcount: A:0.35, C:0.22, G:0.26, T:0.18
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAA
Found at i:28646956 original size:22 final size:22
Alignment explanation
Indices: 28646928--28646992 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
28646918 GAAAATACGT
*
28646928 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
28646950 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
28646972 TTGACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
28646993 AAGGCTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:28647796 original size:27 final size:27
Alignment explanation
Indices: 28647419--28647802 Score: 455
Period size: 27 Copynumber: 14.3 Consensus size: 27
28647409 GGGGTGAAAT
* * * *
28647419 GGTAATTTTACCCCACA-AGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
28647445 GGTAATTCCACCCCACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
28647472 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* ** *
28647499 GATAATTCTACCCTACAGGAATATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
28647526 GATAATTCTACCCTACAGGGGTATGTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
28647553 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
28647580 GATAATTCTACACTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
28647607 GGTAATTCTATCCTATAGGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
28647634 GATAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
28647661 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
28647688 GATAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
28647715 GATAATTCAACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
28647742 GGTAATTCTACCTTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
28647769 GGTAATTCTACCTTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
28647796 GATAATT
1 GGTAATT
28647803 TTGTAAATCG
Statistics
Matches: 306, Mismatches: 51, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
26 15 0.05
27 291 0.95
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:28647816 original size:27 final size:27
Alignment explanation
Indices: 28647786--28648025 Score: 80
Period size: 27 Copynumber: 8.9 Consensus size: 27
28647776 CTACCTTACA
*
28647786 AGGGTATTTCGATAATTTTGTAAATCG
1 AGGGTATTTCGATAATTTTATAAATCG
*** * * **
28647813 AGGGTAAAACGGTAATTCTATAAATTA
1 AGGGTATTTCGATAATTTTATAAATCG
* * *
28647840 AGGGTACTTT-GGTAATTTTACAAGTCG
1 AGGGTA-TTTCGATAATTTTATAAATCG
* * ** *
28647867 AGGGTATTTCTATAATTTTACAGGTTG
1 AGGGTATTTCGATAATTTTATAAATCG
* * * *
28647894 AGGGTATTTC-AGTAATTTCACAGAT-T
1 AGGGTATTTCGA-TAATTTTATAAATCG
* * *
28647920 AGGGGTATTT-TAGTAATTTTACAAA-CT
1 A-GGGTATTTCGA-TAATTTTATAAATCG
* * *
28647947 AGGGGTATTTTGATAATTTTACAAA-CT
1 A-GGGTATTTCGATAATTTTATAAATCG
* * * *
28647974 AGGGGTATTTTGGTAATTTTACAAA-CC
1 A-GGGTATTTCGATAATTTTATAAATCG
* *
28648001 AGTGGTATTTTGGTAATTTTATAAA
1 AG-GGTATTTCGATAATTTTATAAA
28648026 CAAAGGGTAT
Statistics
Matches: 176, Mismatches: 29, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
26 6 0.03
27 169 0.96
28 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.40
Consensus pattern (27 bp):
AGGGTATTTCGATAATTTTATAAATCG
Found at i:28647898 original size:54 final size:54
Alignment explanation
Indices: 28647851--28647996 Score: 129
Period size: 54 Copynumber: 2.7 Consensus size: 54
28647841 GGGTACTTTG
* *
28647851 GTAATTTTACA-AGTCGAGGGTATTTCTA-TAATTTTACAGGTTGAGGGTATTTCA
1 GTAATTTCACAGAGTAG-GGGTATTT-TAGTAATTTTACAGGTTGAGGGTATTTCA
* *** *
28647905 GTAATTTCACAGATTAGGGGTATTTTAGTAATTTTACAAACT-AGGGGTATTT-T
1 GTAATTTCACAGAGTAGGGGTATTTTAGTAATTTTACAGGTTGA-GGGTATTTCA
* * * *
28647958 GATAATTTTACAAACTAGGGGTATTTTGGTAATTTTACA
1 G-TAATTTCACAGAGTAGGGGTATTTTAGTAATTTTACA
28647997 AACCAGTGGT
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
53 4 0.05
54 70 0.91
55 3 0.04
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (54 bp):
GTAATTTCACAGAGTAGGGGTATTTTAGTAATTTTACAGGTTGAGGGTATTTCA
Found at i:28648161 original size:27 final size:27
Alignment explanation
Indices: 28647920--28648154 Score: 335
Period size: 27 Copynumber: 8.7 Consensus size: 27
28647910 TTCACAGATT
* *
28647920 AGGGGTATTTTAGTAATTTTACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACC
* *
28647947 AGGGGTATTTTGATAATTTTACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACC
28647974 AGGGGTATTTTGGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
* * *
28648001 AGTGGTATTTTGGTAATTTTATAAACA
1 AGGGGTATTTTGGTAATTTTACAAACC
* *
28648028 AAGGGTATTTTAGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
*
28648055 AGGGGTATTTTGGTAATTTTGCAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
* *
28648082 AGGGGTATTTTGGTGATTTTATAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
* *
28648109 AAGGGTATTTTAGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
*
28648136 AGAGGTATTTTGGTAATTT
1 AGGGGTATTTTGGTAATTT
28648155 GGTAAACTAA
Statistics
Matches: 183, Mismatches: 25, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 183 1.00
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.40
Consensus pattern (27 bp):
AGGGGTATTTTGGTAATTTTACAAACC
Found at i:28649471 original size:39 final size:39
Alignment explanation
Indices: 28649397--28649471 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 39
28649387 ACCTATTATT
* * *
28649397 GAGTATTGTGATATATGCTTGAATGTTATGCAATTAAAC
1 GAGTATTGCGATATATGCTTGAATATTAAGCAATTAAAC
* * *
28649436 GAGTATTGCGATTTGTGCTTGAATATTAAGTAATTA
1 GAGTATTGCGATATATGCTTGAATATTAAGCAATTA
28649472 TACGTGTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 30 1.00
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.40
Consensus pattern (39 bp):
GAGTATTGCGATATATGCTTGAATATTAAGCAATTAAAC
Found at i:28651601 original size:37 final size:37
Alignment explanation
Indices: 28651541--28651649 Score: 175
Period size: 37 Copynumber: 2.9 Consensus size: 37
28651531 AGCTCAGATG
*
28651541 AAATCTCCACACGAAGT-TATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCT-TCGGGTCTTACCCGGACA
28651578 AAATCTCCACACGTAGTCTTCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCTTCGGGTCTTACCCGGACA
* *
28651615 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCTTCGGGTCTTACCCGGA
28651650 ATATATTTCC
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
37 67 0.99
38 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCTTCGGGTCTTACCCGGACA
Found at i:28651851 original size:48 final size:48
Alignment explanation
Indices: 28651796--28652440 Score: 941
Period size: 48 Copynumber: 13.1 Consensus size: 48
28651786 ACACATCACC
*
28651796 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* *
28651844 TACATATTTCACACTAGCCATTCAGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* *
28651892 TATATATACTTCACATT-GACCATTCGGCTTTACCACATATGCATATCTCA
1 TACATAT--TTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
*
28651942 TACATATTTCATATTAGCCATTCGGCTTTACCACATATACATATCTCATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC----A
* * *
28651994 TATATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
* * *
28652044 TATATATTTCGCATTAGCCATTCGGCTTTACCACATGTACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
28652092 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
28652140 TACATATTTCACATTAGCCATTCGGCTTTTCCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
28652188 TACATATTTCACATTAGCCATTCGGCTTTACCAGATATACATATCTTATACA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATC---T-CA
* * *
28652240 TATATATTTCGCATTAGCCATTCGGCTTTACCAGATATACATATCTTATACA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATC---T-CA
* *
28652292 TATATATTTCGCATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
28652340 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* *
28652388 TACATATTTCACATTATCCATTCGGCTTTACCACATATACATATCTTA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
28652436 TACAT
1 TACAT
28652441 CAATTTCAGC
Statistics
Matches: 556, Mismatches: 29, Indels: 24
0.91 0.05 0.04
Matches are distributed among these distances:
48 324 0.58
49 3 0.01
50 88 0.16
51 1 0.00
52 140 0.25
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.37
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:28652245 original size:248 final size:245
Alignment explanation
Indices: 28651799--28652440 Score: 1036
Period size: 248 Copynumber: 2.6 Consensus size: 245
28651789 CATCACCTAC
* * *
28651799 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACACTAGCCA
1 ATATTTCGCATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
* *
28651864 TTCAGCTTTACCACATATACATATCTCATATATATACTTCACATT-GACCATTCGGCTTTACCAC
66 TTCGGCTTTACCACATATACATATCTCATACATAT--TTCACATTAG-CCATTCGGCTTTACCAC
* *
28651928 ATATGCATATCTCATACATATTTCATATTAGCCATTCGGCTTTACCACATATACATATCTCATAT
128 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--AT
28651993 ATATATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCAT-ATAT
191 ATATATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCATAATAT
*
28652047 ATATTTCGCATTAGCCATTCGGCTTTACCACATGTACATATCTCATACATATTTCACATTAGCCA
1 ATATTTCGCATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
*
28652112 TTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTTCCACATA
66 TTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
* *
28652177 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAGATATACATATCTTATACATA
131 TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCAT--ATA
* * * * *
28652242 TATATTTCGCATTAGCCATTCGGCTTTACCAGATATACATATCTTATACATAT
194 TATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCATA-ATAT
28652295 ATATTTCGCATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
1 ATATTTCGCATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
*
28652360 TTCGGCTTTACCACATATACATATCTCATACATATTTCACATTATCCATTCGGCTTTACCACATA
66 TTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
*
28652425 TACATATCTTATACAT
131 TACATATCTCATACAT
28652441 CAATTTCAGC
Statistics
Matches: 369, Mismatches: 20, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
244 2 0.01
246 126 0.34
247 1 0.00
248 240 0.65
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.37
Consensus pattern (245 bp):
ATATTTCGCATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCA
TTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATA
TACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATA
TATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCATAATAT
Found at i:28652440 original size:200 final size:197
Alignment explanation
Indices: 28651796--28652436 Score: 974
Period size: 200 Copynumber: 3.2 Consensus size: 197
28651786 ACACATCACC
* * * *
28651796 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATC---TCATACATATTTCACAC
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTTATCATATATATTTCGCAT
* *
28651858 TAGCCATTCAGCTTTACCACATATACATATCTCAT-ATATATACTTCACATT-GACCATTCGGCT
66 TAGCCATTCGGCTTTACCACATATACATATCT-ATCATATATATTTCACATTAG-CCATTCGGCT
* *
28651921 TTACCACATATGCATATCTCATACATATTTCATATTAGCCATTCGGCTTTACCACATATACATAT
129 TTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATAT
28651986 CTCATATA
194 CTC----A
* * * *
28651994 TATATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCAT-ATATATATTTCGCAT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTTATCATATATATTTCGCAT
* *
28652058 TAGCCATTCGGCTTTACCACATGTACATATC--TCATACATATTTCACATTAGCCATTCGGCTTT
66 TAGCCATTCGGCTTTACCACATATACATATCTATCATATATATTTCACATTAGCCATTCGGCTTT
*
28652121 ACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTTCCACATATACATATCT
131 ACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCT
28652186 CA
196 CA
*
28652188 TACATATTTCACATTAGCCATTCGGCTTTACCAGATATACATATCTTATACATATATATTTCGCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTTAT-CATATATATTTCGCA
* *
28652253 TTAGCCATTCGGCTTTACCAGATATACATATCTTATACATATATATTTCGCATTAGCCATTCGGC
65 TTAGCCATTCGGCTTTACCACATATACATATC-TAT-CATATATATTTCACATTAGCCATTCGGC
28652318 TTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
128 TTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
28652383 TCTCA
193 TCTCA
*
28652388 TACATATTTCACATTATCCATTCGGCTTTACCACATATACATATCTTAT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTTAT
28652437 ACATCAATTT
Statistics
Matches: 406, Mismatches: 26, Indels: 20
0.90 0.06 0.04
Matches are distributed among these distances:
194 45 0.11
196 44 0.11
197 1 0.00
198 130 0.32
199 2 0.00
200 183 0.45
201 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.37
Consensus pattern (197 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTTATCATATATATTTCGCAT
TAGCCATTCGGCTTTACCACATATACATATCTATCATATATATTTCACATTAGCCATTCGGCTTT
ACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCT
CA
Found at i:28667112 original size:23 final size:23
Alignment explanation
Indices: 28667086--28667134 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
28667076 ATTTTTGATC
28667086 AAGTTTCATAAGCTTATTTAGAA
1 AAGTTTCATAAGCTTATTTAGAA
*
28667109 AAGTTTCATAAGCTTATTTAGCA
1 AAGTTTCATAAGCTTATTTAGAA
28667132 AAG
1 AAG
28667135 GCAATGTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (23 bp):
AAGTTTCATAAGCTTATTTAGAA
Found at i:28672106 original size:28 final size:29
Alignment explanation
Indices: 28672033--28672119 Score: 92
Period size: 28 Copynumber: 3.1 Consensus size: 29
28672023 AGCATGGCTG
* * * *
28672033 CCAGATACAGA-AA-ATGTGACAGAGTCA
1 CCAGATACAGATAATTTGTGGCATAGCCA
*
28672060 CCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAATTTGTGGCA-TAGCCA
28672089 CCAGA-ACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAATTTGTGGCATAGCCA
28672117 CCA
1 CCA
28672120 AGACGCTTCC
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
27 12 0.24
28 24 0.48
29 14 0.28
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.21
Consensus pattern (29 bp):
CCAGATACAGATAATTTGTGGCATAGCCA
Found at i:28672273 original size:28 final size:28
Alignment explanation
Indices: 28672226--28672290 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
28672216 AAATTAACCC
*
28672226 TAGGGGTATAAAGGTCATTTAGCATACA
1 TAGGGGTATAAAGGTAATTTAGCATACA
* *
28672254 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTAGCATACA
28672282 TAGGGGTAT
1 TAGGGGTAT
28672291 GCTAGTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTAGCATACA
Found at i:28679315 original size:19 final size:19
Alignment explanation
Indices: 28679279--28679317 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
28679269 TTTTCATCAT
* *
28679279 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
28679298 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
28679317 A
1 A
28679318 TAATTAAAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:28679828 original size:28 final size:29
Alignment explanation
Indices: 28679755--28679842 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 29
28679745 AGCATGGCTG
* * * *
28679755 CCAGATACAGA-AA-ATGTGACAGAGTCA
1 CCAGATACAGATAATTTGTGGCATAGCCA
*
28679782 CCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAATTTGTGGCA-TAGCCA
28679811 CCAGA-ACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAATTTGTGGCATAGCCA
28679839 CCAG
1 CCAG
28679843 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
27 12 0.24
28 25 0.49
29 14 0.27
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (29 bp):
CCAGATACAGATAATTTGTGGCATAGCCA
Found at i:28679995 original size:28 final size:28
Alignment explanation
Indices: 28679948--28680012 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
28679938 AAATTAACCC
*
28679948 TAGGGGTATAAAGGTCATTTAGCATACA
1 TAGGGGTATAAAGGTAATTTAGCATACA
* *
28679976 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTAGCATACA
28680004 TAGGGGTAT
1 TAGGGGTAT
28680013 TCTAGTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTAGCATACA
Found at i:28684595 original size:38 final size:37
Alignment explanation
Indices: 28684544--28684615 Score: 126
Period size: 38 Copynumber: 1.9 Consensus size: 37
28684534 CTTTTCAGCC
*
28684544 CTCAATGCCGATATCACATTAGACAAATAGTCCCTTCG
1 CTCAATGCCGATATCACATTAAACAAATAG-CCCTTCG
28684582 CTCAATGCCGATATCACATTAAACAAATAGCCCT
1 CTCAATGCCGATATCACATTAAACAAATAGCCCT
28684616 CAATCTGTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 4 0.12
38 29 0.88
ACGTcount: A:0.35, C:0.29, G:0.11, T:0.25
Consensus pattern (37 bp):
CTCAATGCCGATATCACATTAAACAAATAGCCCTTCG
Found at i:28685191 original size:24 final size:24
Alignment explanation
Indices: 28685159--28685247 Score: 133
Period size: 24 Copynumber: 3.7 Consensus size: 24
28685149 CTGTCAAGAG
*
28685159 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGCTGATAAGGGAT
28685183 AGGATTTAGGAGCTGATAAGGGAT
1 AGGATTTAGGAGCTGATAAGGGAT
* *
28685207 AGGATTTAGGAGCTGATGAGGGAG
1 AGGATTTAGGAGCTGATAAGGGAT
* *
28685231 AAGATTTAGGAACTGAT
1 AGGATTTAGGAGCTGAT
28685248 TAGAGAGAAC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.34, C:0.03, G:0.37, T:0.26
Consensus pattern (24 bp):
AGGATTTAGGAGCTGATAAGGGAT
Found at i:28685255 original size:24 final size:24
Alignment explanation
Indices: 28685156--28685256 Score: 112
Period size: 24 Copynumber: 4.2 Consensus size: 24
28685146 AGTCTGTCAA
* *
28685156 GAGAGGATTTAGGAGTTGATAAGG
1 GAGAAGATTTAGGAGCTGATAAGG
* *
28685180 GATAGGATTTAGGAGCTGATAAGG
1 GAGAAGATTTAGGAGCTGATAAGG
* * *
28685204 GATAGGATTTAGGAGCTGATGAGG
1 GAGAAGATTTAGGAGCTGATAAGG
* * *
28685228 GAGAAGATTTAGGAACTGATTAGA
1 GAGAAGATTTAGGAGCTGATAAGG
28685252 GAGAA
1 GAGAA
28685257 CAGTGTTGGC
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.36, C:0.03, G:0.38, T:0.24
Consensus pattern (24 bp):
GAGAAGATTTAGGAGCTGATAAGG
Found at i:28686703 original size:27 final size:26
Alignment explanation
Indices: 28686663--28686767 Score: 129
Period size: 27 Copynumber: 3.9 Consensus size: 26
28686653 AGGAAGCGTC
*
28686663 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
28686690 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
28686717 TTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* *
28686745 CTGGTGACTCTGTCACATTATCT
1 CTGGTGGCTCTGCCACATTATCT
28686768 ATTTTGGCAG
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.03
27 50 0.74
28 16 0.24
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:28686767 original size:54 final size:54
Alignment explanation
Indices: 28686664--28686774 Score: 161
Period size: 54 Copynumber: 2.1 Consensus size: 54
28686654 GGAAGCGTCC
* *
28686664 TGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTT
1 TGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTATTT
* * *
28686718 TGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTATTT
1 TGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTATTT
28686772 TGG
1 TGG
28686775 CAGCCATGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
54 33 0.65
55 18 0.35
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.39
Consensus pattern (54 bp):
TGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTATTT
Found at i:28690020 original size:24 final size:24
Alignment explanation
Indices: 28689976--28690023 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
28689966 TAATTCAATC
*
28689976 TAACCATATTAAGCATACATATAT
1 TAACCATATTAAACATACATATAT
*
28690000 TAACCATATTATAACCT-CATATAT
1 TAACCATATTA-AACATACATATAT
28690024 ATATATATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (24 bp):
TAACCATATTAAACATACATATAT
Found at i:28700085 original size:44 final size:44
Alignment explanation
Indices: 28700021--28700105 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
28700011 TTAGGTATCA
* * *
28700021 CATCCATTATGAACTCGGACCAACTCAACGAGTTCGGATGCTCG
1 CATCCATAATGAACTCGGACCAACTCAACGAGCTCAGATGCTCG
*
28700065 CATCCATAATGAACTTGGACCAACTCAACGAGCTCAGATGC
1 CATCCATAATGAACTCGGACCAACTCAACGAGCTCAGATGC
28700106 CTCAAATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (44 bp):
CATCCATAATGAACTCGGACCAACTCAACGAGCTCAGATGCTCG
Found at i:28700587 original size:28 final size:28
Alignment explanation
Indices: 28700549--28700605 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
28700539 ATAGAATTAA
28700549 AAAAAAAAGAAGGATGATATCATCCCTT
1 AAAAAAAAGAAGGATGATATCATCCCTT
28700577 AAAAAAAAGAAGGATGATATCATCCCTT
1 AAAAAAAAGAAGGATGATATCATCCCTT
28700605 A
1 A
28700606 CTCATCTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.14, T:0.21
Consensus pattern (28 bp):
AAAAAAAAGAAGGATGATATCATCCCTT
Found at i:28706411 original size:37 final size:37
Alignment explanation
Indices: 28706358--28706497 Score: 235
Period size: 37 Copynumber: 3.8 Consensus size: 37
28706348 CGAATAGTCC
* * *
28706358 CCACACATAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
*
28706395 CCACACGTAGTCATCGGGTCTTACCAGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
28706432 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
*
28706469 CCACACGTAGTCATCGGGTTTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
28706498 ATATATTTCC
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 97 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
Found at i:28706724 original size:48 final size:48
Alignment explanation
Indices: 28706667--28706930 Score: 483
Period size: 48 Copynumber: 5.5 Consensus size: 48
28706657 CTAGCCGAAT
*
28706667 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCG
1 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
*
28706715 CATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
* *
28706763 CACTAGCCATTCGGCTTTACCACGTATACATATCTCATACATAGTTCA
1 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
28706811 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
28706859 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
*
28706907 CATTAGCCATTCGGCTTTACCACA
1 CACTAGCCATTCGGCTTTACCACA
28706931 CACATATATA
Statistics
Matches: 208, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 208 1.00
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (48 bp):
CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
Found at i:28719205 original size:56 final size:56
Alignment explanation
Indices: 28719098--28719205 Score: 146
Period size: 56 Copynumber: 1.9 Consensus size: 56
28719088 GATTTGTGAG
* *
28719098 ACCCTAAACTATTATTACATGTAAAACCTATATATTGCATGCGAACTCCATAATAA
1 ACCCTAAACTATTATTACATGTAAAACCTATATATTGCAGGCGAACCCCATAATAA
* * * *
28719154 ACCCTAAATTGTTATTACATGCT-AACCCTATATATTGCAGGTGAACCCCATA
1 ACCCTAAACTATTATTACATG-TAAAACCTATATATTGCAGGCGAACCCCATA
28719206 TGTTAGATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
56 44 0.98
57 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.31
Consensus pattern (56 bp):
ACCCTAAACTATTATTACATGTAAAACCTATATATTGCAGGCGAACCCCATAATAA
Found at i:28723296 original size:20 final size:20
Alignment explanation
Indices: 28723267--28723308 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
28723257 TTCTTTTTTT
28723267 TTTTAGAAAAGTACA-TAAAA
1 TTTTAGAAAA-TACATTAAAA
*
28723287 TTTTATAAAATACATTAAAA
1 TTTTAGAAAATACATTAAAA
28723307 TT
1 TT
28723309 ATAAATGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (20 bp):
TTTTAGAAAATACATTAAAA
Found at i:28726379 original size:25 final size:26
Alignment explanation
Indices: 28726351--28726401 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
28726341 CATTTCTACT
28726351 CTTTCAAGC-TAT-GATCAGTAAGCTC
1 CTTTCAAGCTTATGGA-CAGTAAGCTC
**
28726376 CTTTTGAGCTTATGGACAGTAAGCTC
1 CTTTCAAGCTTATGGACAGTAAGCTC
28726402 TATTGAGCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 7 0.32
26 13 0.59
27 2 0.09
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (26 bp):
CTTTCAAGCTTATGGACAGTAAGCTC
Found at i:28730768 original size:43 final size:43
Alignment explanation
Indices: 28730688--28730770 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
28730678 CGTGGTCGCG
* ** **
28730688 AAACCACTGTTTCGACTAGGCCTTAATTTGGGATGTTACACCA
1 AAACCACTGTTTCGACTAGACCCAAAAATGGGATGTTACACCA
* *
28730731 AAACCACTGTTTCGATTAGACCCAAAAATGGGTTGTTACA
1 AAACCACTGTTTCGACTAGACCCAAAAATGGGATGTTACA
28730771 ATGACTTTCA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (43 bp):
AAACCACTGTTTCGACTAGACCCAAAAATGGGATGTTACACCA
Found at i:28737386 original size:58 final size:58
Alignment explanation
Indices: 28737309--28737476 Score: 223
Period size: 58 Copynumber: 2.9 Consensus size: 58
28737299 GATTATTGTT
*
28737309 ATTAAATTTTAATAGAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
1 ATTAAATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
* * * * *
28737367 ATTATATTTTAACATAATTATTATTAAATACAATTT-TTAAAAAATAATATATAATTTA
1 ATTAAATTTTAATATAATTATTATTAAATATAATTTAAT-AAAAATAATAAATAATTTA
*
28737425 A-TAACATTCTTAATATAATTATTATTAAAATATAATTTAATAAAAATCATAA
1 ATTAA-ATT-TTAATATAATTATTATT-AAATATAATTTAATAAAAATAATAA
28737477 TATATAATAT
Statistics
Matches: 93, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
57 3 0.03
58 54 0.58
59 16 0.17
60 19 0.20
61 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (58 bp):
ATTAAATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
Found at i:28746180 original size:68 final size:67
Alignment explanation
Indices: 28746108--28746257 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
28746098 CATCATGTGT
* * * *
28746108 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAGGGACACC
28746170 ATGTAG
62 ATGTAG
** * *
28746176 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAGGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAGGGACACCATGT
28746241 AG
66 AG
28746243 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
28746258 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAGGGACACCATGT
AG
Found at i:28746213 original size:64 final size:64
Alignment explanation
Indices: 28746132--28746303 Score: 186
Period size: 67 Copynumber: 2.7 Consensus size: 64
28746122 AGACATTATG
* *
28746132 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
28746196 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAGGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
28746261 AA
63 AA
* * * *
28746263 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGT
28746304 GTATAAGAGA
Statistics
Matches: 87, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
63 9 0.10
64 21 0.24
65 8 0.09
66 16 0.18
67 31 0.36
68 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:28749330 original size:46 final size:46
Alignment explanation
Indices: 28749280--28749455 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
28749270 TGGTTGAGCA
28749280 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28749326 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
28749371 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28749419 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28749456 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:28749436 original size:93 final size:93
Alignment explanation
Indices: 28749277--28749448 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
28749267 GGATGGTTGA
* *
28749277 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28749342 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
28749370 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28749435 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
28749449 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:28756899 original size:46 final size:46
Alignment explanation
Indices: 28756849--28757024 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
28756839 TGGTTGAGCA
28756849 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28756895 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
28756940 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28756988 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28757025 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:28757005 original size:93 final size:93
Alignment explanation
Indices: 28756846--28757017 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
28756836 GGATGGTTGA
* *
28756846 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28756911 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
28756939 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28757004 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
28757018 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:28760955 original size:41 final size:41
Alignment explanation
Indices: 28760899--28760981 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
28760889 ATTTGCATTA
*
28760899 AAAATTTGGTGACACTATTTGTTTGGTGAAAAATGTTACAT
1 AAAATTTGGCGACACTATTTGTTTGGTGAAAAATGTTACAT
28760940 AAAATTTGGCGACACTATTTGTTTGGTGAAAAATGTTACAT
1 AAAATTTGGCGACACTATTTGTTTGGTGAAAAATGTTACAT
28760981 A
1 A
28760982 TACACTGATC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.37
Consensus pattern (41 bp):
AAAATTTGGCGACACTATTTGTTTGGTGAAAAATGTTACAT
Found at i:28778930 original size:27 final size:27
Alignment explanation
Indices: 28778572--28778955 Score: 285
Period size: 27 Copynumber: 14.2 Consensus size: 27
28778562 TTAGTTTACC
* * * *
28778572 AAATTACTAAAATGCCCTCAATTGGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
28778599 AAATTACTAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTGTA
* *
28778626 AAATTACCAAAATACCC-CTAATTTGTG
1 AAATTACCAAAATACCCTC-GATTTGTA
* *
28778653 AAATTACTAAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
28778680 AAATTACCAAAATACCC-CTAATTTGTG
1 AAATTACCAAAATACCCTC-GATTTGTA
** * * *
28778707 AAATTACTGAAATACCCTTGACTTATA
1 AAATTACCAAAATACCCTCGATTTGTA
* * * **
28778734 AAATTATCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
28778761 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
*
28778788 AAATTACCAAAATACCC-CTGATTTGTG
1 AAATTACCAAAATACCCTC-GATTTGTA
* * *
28778815 AAATTATCGAAATACCCTC-AGTTTGCA
1 AAATTACCAAAATACCCTCGA-TTTGTA
**
28778842 AAATTACTGAAATACCCTCGATTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
*** * *
28778869 AAATTATTGAAATACCC-CGACTTATAA
1 AAATTACCAAAATACCCTCGATTTGT-A
* *
28778896 AAATTACCAAAGTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTGTA
* *** **
28778923 GAATTACCATTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTGTA
28778950 AAATTA
1 AAATTA
28778956 TTGAATACCC
Statistics
Matches: 292, Mismatches: 54, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
26 10 0.03
27 271 0.93
28 11 0.04
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.32
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTGTA
Found at i:28778989 original size:27 final size:27
Alignment explanation
Indices: 28778959--28779117 Score: 212
Period size: 27 Copynumber: 5.9 Consensus size: 27
28778949 AAAATTATTG
* *
28778959 AATACCCCTATAGGGTAGAATTACCAA
1 AATACCCCTGTAGGGTAGAATTACCGA
**
28778986 AATACCCCTGTAGGGTAGAATTATTGA
1 AATACCCCTGTAGGGTAGAATTACCGA
*
28779013 AATACCCCTGTAGGGTAGAATTACTGA
1 AATACCCCTGTAGGGTAGAATTACCGA
* *
28779040 AATACCCTTGTAGGGTAGAATTACTGA
1 AATACCCCTGTAGGGTAGAATTACCGA
*
28779067 AACA-CCCTGTAGGGTAGAATTACCGA
1 AATACCCCTGTAGGGTAGAATTACCGA
* * *
28779093 AATACCCTTGTGGGGTAAAATTACC
1 AATACCCCTGTAGGGTAGAATTACC
28779118 ATTTTGCCCC
Statistics
Matches: 118, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
26 23 0.19
27 95 0.81
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAGAATTACCGA
Found at i:28779008 original size:53 final size:53
Alignment explanation
Indices: 28778951--28779115 Score: 242
Period size: 53 Copynumber: 3.1 Consensus size: 53
28778941 CGATTTACAA
* * *
28778951 AATTATTGAATACCCCTATAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
1 AATTATTGAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAG
*
28779004 AATTATTGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCTTGTAGGGTAG
1 AATTATTG-AATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAG
* * *
28779058 AATTACTGAA-ACACCCTGTAGGGTAGAATTACCGAAATACCCTTGTGGGGTAA
1 AATTATTGAATAC-CCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAG
28779111 AATTA
1 AATTA
28779116 CCATTTTGCC
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 2 0.02
53 52 0.51
54 48 0.47
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (53 bp):
AATTATTGAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAG
Found at i:28779043 original size:54 final size:54
Alignment explanation
Indices: 28778951--28779115 Score: 244
Period size: 54 Copynumber: 3.1 Consensus size: 54
28778941 CGATTTACAA
* * *
28778951 AATTATTG-AATACCCCTATAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
1 AATTATTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAG
*
28779004 AATTATTGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCTTGTAGGGTAG
1 AATTATTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAG
* * * *
28779058 AATTACTGAAACA-CCCTGTAGGGTAGAATTACCGAAATACCCTTGTGGGGTAA
1 AATTATTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAG
28779111 AATTA
1 AATTA
28779116 CCATTTTGCC
Statistics
Matches: 102, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
53 50 0.49
54 52 0.51
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (54 bp):
AATTATTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAG
Found at i:28779396 original size:24 final size:25
Alignment explanation
Indices: 28779320--28779389 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
28779310 AGGAACTGCT
* * * * *
28779320 AAAAGGACTATGCCCCAATTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
28779345 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
28779370 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
28779390 ATTAAAAGAA
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:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:28782301 original size:23 final size:23
Alignment explanation
Indices: 28782271--28782319 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
28782261 CAAGACTCCA
*
28782271 CACGCCCGTGTGGACATAGAATG
1 CACGCCCGTGTGGACATAAAATG
28782294 CACGCCCGTGTGGACATAAAATG
1 CACGCCCGTGTGGACATAAAATG
28782317 CAC
1 CAC
28782320 AACTGTGTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.16
Consensus pattern (23 bp):
CACGCCCGTGTGGACATAAAATG
Found at i:28782327 original size:23 final size:23
Alignment explanation
Indices: 28782276--28782327 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
28782266 CTCCACACGC
* **
28782276 CCGTGTGGACATAGAATGCACGC
1 CCGTGTGGACATAAAATGCACAA
28782299 CCGTGTGGACATAAAATGCACAA
1 CCGTGTGGACATAAAATGCACAA
*
28782322 CTGTGT
1 CCGTGT
28782328 CCTAGGGACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (23 bp):
CCGTGTGGACATAAAATGCACAA
Found at i:28785403 original size:20 final size:20
Alignment explanation
Indices: 28785378--28785422 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
28785368 AGAGACTAAA
* *
28785378 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
28785398 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
28785418 ATGAA
1 ATGAA
28785423 TACATGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:28797742 original size:17 final size:18
Alignment explanation
Indices: 28797706--28797742 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28797696 TATCTGGACT
28797706 TTTATCCAACACATATAA
1 TTTATCCAACACATATAA
*
28797724 TTTATCCAACCCA-ATAA
1 TTTATCCAACACATATAA
28797741 TT
1 TT
28797743 ATTTTCTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTATCCAACACATATAA
Found at i:28800249 original size:45 final size:46
Alignment explanation
Indices: 28800028--28800344 Score: 288
Period size: 48 Copynumber: 6.8 Consensus size: 46
28800018 GTGAGTTGCT
* * * * * * *
28800028 GATGCCATGTCCCAGACATAGTCTTACTCTAGCTCTCATGTCGAGGCC
1 GATGCCATGT-CCA-ACATGGTCTTACACTGGCTCACATATCAATGCC
* * *
28800076 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAATGCC
1 GATGCCATGT-CCA-ACATGGTCTTACACTGGCTCACATATCAATGCC
* * ** *
28800124 GAGGCCATGTCCAACATGGTCTTACACTGGCTCTCATAT-GGTGGTC
1 GATGCCATGTCCAACATGGTCTTACACTGGCTCACATATCAAT-GCC
*
28800170 GACGCCATGTCCCAGACATGGTCTTACACTGGCTCACA-ATCAATGCC
1 GATGCCATGT-CCA-ACATGGTCTTACACTGGCTCACATATCAATGCC
* *
28800217 GATGCCATGTCCAACATGGTCTTACACTGGCTCACA-GTCAATGCT
1 GATGCCATGTCCAACATGGTCTTACACTGGCTCACATATCAATGCC
* *
28800262 GATGCCATGTCTAACATGGTCTTACACTGGCAT-ACA-A--AATGTGGCT
1 GATGCCATGTCCAACATGGTCTTACACTGGC-TCACATATCAA--T-GCC
* *
28800308 GATGCCATGTCCAACATGGTCTTACACTAGTTCACAT
1 GATGCCATGTCCAACATGGTCTTACACTGGCTCACAT
28800345 GTCACCCCGA
Statistics
Matches: 235, Mismatches: 24, Indels: 21
0.84 0.09 0.08
Matches are distributed among these distances:
43 2 0.01
45 66 0.28
46 73 0.31
47 19 0.08
48 75 0.32
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (46 bp):
GATGCCATGTCCAACATGGTCTTACACTGGCTCACATATCAATGCC
Found at i:28800324 original size:46 final size:43
Alignment explanation
Indices: 28800076--28800335 Score: 234
Period size: 45 Copynumber: 5.7 Consensus size: 43
28800066 TGTCGAGGCC
* ** *
28800076 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAATGCC
1 GATGCCATGT-CCA-ACATGGTCTTACACT-G-GCTCA-CAAAATGCT
* * ** *
28800124 GAGGCCATGTCCAACATGGTCTTACACTGGCTCTCATATGGTGGT
1 GATGCCATGTCCAACATGGTCTTACACTGGCTCACA-A-AATGCT
* *
28800169 CGACGCCATGTCCCAGACATGGTCTTACACTGGCTCACAATCAATGCC
1 -GATGCCATGT-CCA-ACATGGTCTTACACTGGCTCACAA--AATGCT
*
28800217 GATGCCATGTCCAACATGGTCTTACACTGGCTCACAGTCAATGCT
1 GATGCCATGTCCAACATGGTCTTACACTGGCTCACA--AAATGCT
*
28800262 GATGCCATGTCTAACATGGTCTTACACTGGCAT-ACAAAATGTGGCT
1 GATGCCATGTCCAACATGGTCTTACACTGGC-TCACAAAA--T-GCT
28800308 GATGCCATGTCCAACATGGTCTTACACT
1 GATGCCATGTCCAACATGGTCTTACACT
28800336 AGTTCACATG
Statistics
Matches: 178, Mismatches: 22, Indels: 26
0.79 0.10 0.12
Matches are distributed among these distances:
43 3 0.02
44 3 0.02
45 65 0.37
46 58 0.33
47 16 0.09
48 33 0.19
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (43 bp):
GATGCCATGTCCAACATGGTCTTACACTGGCTCACAAAATGCT
Found at i:28802287 original size:94 final size:94
Alignment explanation
Indices: 28802136--28802311 Score: 316
Period size: 94 Copynumber: 1.9 Consensus size: 94
28802126 ATTCAAATCT
* *
28802136 GCACACATAGTGCCAATGTTAACTCATTATAATAAGGCAATTTACTTACTTCGAATAGCATATAA
1 GCACACATAGTGCCAATGTTAACTCATTATAATAAGGCAATTAACTTACTTCAAATAGCATATAA
*
28802201 AATCTGCACACAAAGTGACATTTAATTCC
66 AATCCGCACACAAAGTGACATTTAATTCC
28802230 GCACACATAGTGCCAATGTTAACTCATTATAATAAGGCAATTAACTTACTTCAAATAGCATATAA
1 GCACACATAGTGCCAATGTTAACTCATTATAATAAGGCAATTAACTTACTTCAAATAGCATATAA
*
28802295 AATCCGCACACATAGTG
66 AATCCGCACACAAAGTG
28802312 CCAATGTTGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 78 1.00
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.28
Consensus pattern (94 bp):
GCACACATAGTGCCAATGTTAACTCATTATAATAAGGCAATTAACTTACTTCAAATAGCATATAA
AATCCGCACACAAAGTGACATTTAATTCC
Found at i:28802362 original size:69 final size:70
Alignment explanation
Indices: 28802227--28802362 Score: 220
Period size: 69 Copynumber: 2.0 Consensus size: 70
28802217 GACATTTAAT
*
28802227 TCCGCACACATAGTGCCAATGTTAACTCATTATAATAAGGCAATTAACTTACTTCAAATAGCATA
1 TCCGCACACATAGTGCCAATGTTAACTCATTATAATAAGGCAATTAACTTAATTCAAATAGCATA
28802292 TAAAA
66 TAAAA
* * * *
28802297 TCCGCACACATAGTGCCAATGTTGACTCA-TATAATAAGGCAATTTACTTAATTCGATTAGCATA
1 TCCGCACACATAGTGCCAATGTTAACTCATTATAATAAGGCAATTAACTTAATTCAAATAGCATA
28802361 TA
66 TA
28802363 TGGTTATAGT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
69 33 0.54
70 28 0.46
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (70 bp):
TCCGCACACATAGTGCCAATGTTAACTCATTATAATAAGGCAATTAACTTAATTCAAATAGCATA
TAAAA
Found at i:28812002 original size:58 final size:58
Alignment explanation
Indices: 28811896--28812006 Score: 172
Period size: 58 Copynumber: 1.9 Consensus size: 58
28811886 TATTTCAAGT
* *
28811896 ATAATTTATGCTCGAGAGGACTTATATCAGGATTACTCGTCCGAGCTAAATCCAATCC
1 ATAATATATGCTCGAGAGGACTTATATCAGGATTACTCGTCAGAGCTAAATCCAATCC
28811954 ATAATATATGCTCGAGAGGACTTATATCAGGATTAC-CTGTCTAG-GCTAAATCC
1 ATAATATATGCTCGAGAGGACTTATATCAGGATTACTC-GTC-AGAGCTAAATCC
28812007 TACCAGAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
57 1 0.02
58 47 0.96
59 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (58 bp):
ATAATATATGCTCGAGAGGACTTATATCAGGATTACTCGTCAGAGCTAAATCCAATCC
Found at i:28818624 original size:45 final size:45
Alignment explanation
Indices: 28818546--28818631 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
28818536 CATATAACCC
* * * * *
28818546 TTATGTTGATATGGGTATTGGGTTATAAGACCCTTACGTGGGCCA
1 TTATGTTGATATGGGTATTAGGTCACAAAACCCTCACGTGGGCCA
28818591 TTATGTTGATATGGGTATTAGGTCACAAAACCCTCACGTGG
1 TTATGTTGATATGGGTATTAGGTCACAAAACCCTCACGTGG
28818632 TCCTTACTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (45 bp):
TTATGTTGATATGGGTATTAGGTCACAAAACCCTCACGTGGGCCA
Found at i:28818671 original size:27 final size:27
Alignment explanation
Indices: 28818641--28818699 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
28818631 GTCCTTACTA
* *
28818641 GGCCAAATGATGCAGGCCTAAGTTTTG
1 GGCCAAATGATGCAGGCCAAAGGTTTG
* **
28818668 GGCCAAATGGTGTTGGCCAAAGGTTTG
1 GGCCAAATGATGCAGGCCAAAGGTTTG
28818695 GGCCA
1 GGCCA
28818700 TATACGCCTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.24
Consensus pattern (27 bp):
GGCCAAATGATGCAGGCCAAAGGTTTG
Found at i:28819587 original size:30 final size:30
Alignment explanation
Indices: 28819552--28819618 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
28819542 GTACGCATGG
28819552 CCGTGTGTTACACACGGCTGAGACACACGC
1 CCGTGTGTTACACACGGCTGAGACACACGC
28819582 CCGTGTGTTACACACGGCTGAGACACACGC
1 CCGTGTGTTACACACGGCTGAGACACACGC
28819612 CCGTGTG
1 CCGTGTG
28819619 GACAAAATAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.21, C:0.33, G:0.28, T:0.18
Consensus pattern (30 bp):
CCGTGTGTTACACACGGCTGAGACACACGC
Found at i:28825004 original size:19 final size:19
Alignment explanation
Indices: 28824980--28825019 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
28824970 ATAAGTATGA
28824980 AATTATTACGAGATGGTAC
1 AATTATTACGAGATGGTAC
28824999 AATTATTACGAGATGGTAC
1 AATTATTACGAGATGGTAC
28825018 AA
1 AA
28825020 GTATGTACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (19 bp):
AATTATTACGAGATGGTAC
Found at i:28837457 original size:38 final size:38
Alignment explanation
Indices: 28837400--28837474 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
28837390 TCAAATTAAC
28837400 ATGTATAACCATGGCATATCCACTTAGCACCACATTAT
1 ATGTATAACCATGGCATATCCACTTAGCACCACATTAT
* **
28837438 ATGTTTAACCATGTTATATCCACTTAGCACCACATTA
1 ATGTATAACCATGGCATATCCACTTAGCACCACATTA
28837475 ATTAATCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.32
Consensus pattern (38 bp):
ATGTATAACCATGGCATATCCACTTAGCACCACATTAT
Found at i:28837501 original size:85 final size:85
Alignment explanation
Indices: 28837405--28837621 Score: 254
Period size: 95 Copynumber: 2.4 Consensus size: 85
28837395 TTAACATGTA
* * *
28837405 TAACCATGGCATATCCACTTAGCACCACATTATATGTTTAACCATGTTATATCCACTTAGCACCA
1 TAACCGTGGCATATCCACTTAGCACCACATTATATGTGTAACCATGGTATATCCACTTAGCACCA
*
28837470 CATTAATTAATCAATATATG
66 CATTAATGAATCAATATATG
***
28837490 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTGTAATTGTGGTATATCCA
1 TAACCGTGGCATATCCACTTAGCA-C-C---ACA--T-T--ATATGTGTAACCATGGTATATCCA
*
28837555 CTTAGCACCACGTTAATGAATCAATATATG
56 CTTAGCACCACATTAATGAATCAATATATG
* *
28837585 TAACCGTGGCATATCCACTTAGCACCACGTTACATGT
1 TAACCGTGGCATATCCACTTAGCACCACATTATATGT
28837622 ATCAATAGTG
Statistics
Matches: 112, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
85 28 0.25
86 1 0.01
87 2 0.02
88 1 0.01
90 5 0.04
92 1 0.01
93 2 0.02
94 1 0.01
95 71 0.63
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (85 bp):
TAACCGTGGCATATCCACTTAGCACCACATTATATGTGTAACCATGGTATATCCACTTAGCACCA
CATTAATGAATCAATATATG
Found at i:28837506 original size:47 final size:48
Alignment explanation
Indices: 28837453--28837670 Score: 300
Period size: 47 Copynumber: 4.6 Consensus size: 48
28837443 TAACCATGTT
*
28837453 ATATCCACTTAGCACCACATTA-AT-TAATCAATATATGTAACCGTGGC
1 ATATCCACTTAGCACCACGTTACATGT-ATCAATATATGTAACCGTGGC
* ** *
28837500 ATATCCACTTAGCACCACGTTACATGTATCAATATGTGTAATTGTGGT
1 ATATCCACTTAGCACCACGTTACATGTATCAATATATGTAACCGTGGC
*
28837548 ATATCCACTTAGCACCACGTTA-ATGAATCAATATATGTAACCGTGGC
1 ATATCCACTTAGCACCACGTTACATGTATCAATATATGTAACCGTGGC
* * *
28837595 ATATCCACTTAGCACCACGTTACATGTATCAATA-GTGTAATCGTGGT
1 ATATCCACTTAGCACCACGTTACATGTATCAATATATGTAACCGTGGC
* *
28837642 ATATCCACTTAACACCACGTTACACGTAT
1 ATATCCACTTAGCACCACGTTACATGTAT
28837671 AACCGTGGTA
Statistics
Matches: 152, Mismatches: 16, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
47 100 0.66
48 51 0.34
49 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.31
Consensus pattern (48 bp):
ATATCCACTTAGCACCACGTTACATGTATCAATATATGTAACCGTGGC
Found at i:28837599 original size:95 final size:94
Alignment explanation
Indices: 28837452--28837663 Score: 379
Period size: 95 Copynumber: 2.2 Consensus size: 94
28837442 TTAACCATGT
* *
28837452 TATATCCACTTAGCACCACATTAATTAATCAATATATGTAACCGTGGCATATCCACTTAGCACCA
1 TATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCA
*
28837517 CGTTACATGTATCAATATGTGTAATTGTGG
66 CGTTACATGTATCAATA-GTGTAATCGTGG
28837547 TATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCA
1 TATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCA
28837612 CGTTACATGTATCAATAGTGTAATCGTGG
66 CGTTACATGTATCAATAGTGTAATCGTGG
*
28837641 TATATCCACTTAACACCACGTTA
1 TATATCCACTTAGCACCACGTTA
28837664 CACGTATAAC
Statistics
Matches: 113, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
94 33 0.29
95 80 0.71
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.31
Consensus pattern (94 bp):
TATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCA
CGTTACATGTATCAATAGTGTAATCGTGG
Found at i:28843279 original size:38 final size:38
Alignment explanation
Indices: 28843220--28843433 Score: 176
Period size: 38 Copynumber: 5.2 Consensus size: 38
28843210 TTACAAATTA
* * *
28843220 ACATGTATAACCATGGCATATCCACTTAGCACCACGTT
1 ACATGTTTAACCGTGGTATATCCACTTAGCACCACGTT
* *
28843258 ACATGTTTAACCGTGTTATATCCACTTAGCACCACATTAATT
1 ACATGTTTAACCGTGGTATATCCACTTAGCACCAC----GTT
* * *
28843300 AATCAATATATGTAACCGTGGCATATCCACTTAGCACTACGTT
1 -A-C-ATGT-T-TAACCGTGGTATATCCACTTAGCACCACGTT
28843343 ACATGTTTAACCGTGGTATATCCACTTAGCACCACGTTAAT
1 ACATGTTTAACCGTGGTATATCCACTTAGCACCACG-T--T
* *
28843384 GAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
1 --A-C-ATGT-T-TAACCGTGGTATATCCACTTAGCACCACGTT
28843428 ACATGT
1 ACATGT
28843434 ATCAATATGT
Statistics
Matches: 142, Mismatches: 16, Indels: 34
0.74 0.08 0.18
Matches are distributed among these distances:
38 58 0.41
39 2 0.01
40 6 0.04
41 3 0.02
42 4 0.03
43 4 0.03
44 3 0.02
45 6 0.04
46 3 0.02
47 53 0.37
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (38 bp):
ACATGTTTAACCGTGGTATATCCACTTAGCACCACGTT
Found at i:28843325 original size:85 final size:85
Alignment explanation
Indices: 28843196--28843528 Score: 454
Period size: 85 Copynumber: 3.8 Consensus size: 85
28843186 ATGGCATACG
* * * * *
28843196 CACTTAGCACCACGTTACA--AATTAACATGTATAACCATGGCATATCCACTTAGCACCACGTTA
1 CACTTAGCACCACGTTA-ATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTTA
*
28843259 CATGTTTAACCGTGTTATATC
65 CATGTTTAACCGTGGTATATC
* * *
28843280 CACTTAGCACCACATTAATTAATCAATATATGTAACCGTGGCATATCCACTTAGCACTACGTTAC
1 CACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTTAC
28843345 ATGTTTAACCGTGGTATATC
66 ATGTTTAACCGTGGTATATC
28843365 CACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTTAC
1 CACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTTAC
**
28843430 ATGTATCAATATGTGTAATTGTGGTATATC
66 ATG--------T-T-TAACCGTGGTATATC
28843460 CACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTTAC
1 CACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTTAC
28843525 ATGT
66 ATGT
28843529 ATCAATATGT
Statistics
Matches: 224, Mismatches: 13, Indels: 21
0.87 0.05 0.08
Matches are distributed among these distances:
83 1 0.00
84 16 0.07
85 123 0.55
87 1 0.00
93 1 0.00
94 1 0.00
95 81 0.36
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (85 bp):
CACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTTAC
ATGTTTAACCGTGGTATATC
Found at i:28843334 original size:47 final size:46
Alignment explanation
Indices: 28843265--28843567 Score: 361
Period size: 47 Copynumber: 6.6 Consensus size: 46
28843255 GTTACATGTT
* *
28843265 TAACCGTGTTATATCCACTTAGCACCACATTAATTAATCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTAATT-ATCAATATATG
* * *
28843312 TAACCGTGGCATATCCACTTAGCACTACG----TTA-C-ATGT-T-
1 TAACCGTGGTATATCCACTTAGCACCACGTTAATTATCAATATATG
*
28843350 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTAAT-TATCAATATATG
* *
28843397 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTG
1 TAACCGTGGTATATCCACTTAGCACCACGTTA-AT-TATCAATATATG
** *
28843445 TAATTGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTAAT-TATCAATATATG
* *
28843492 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTG
1 TAACCGTGGTATATCCACTTAGCACCACGTTA-AT-TATCAATATATG
*
28843540 TAATCGTGGTATATCCACTTAGCACCAC
1 TAACCGTGGTATATCCACTTAGCACCAC
28843568 ATTTTTCCAT
Statistics
Matches: 221, Mismatches: 24, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
38 27 0.12
39 1 0.00
40 3 0.01
41 1 0.00
42 2 0.01
43 3 0.01
44 1 0.00
45 3 0.01
46 1 0.00
47 98 0.44
48 81 0.37
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (46 bp):
TAACCGTGGTATATCCACTTAGCACCACGTTAATTATCAATATATG
Found at i:28843459 original size:48 final size:47
Alignment explanation
Indices: 28843350--28843567 Score: 337
Period size: 48 Copynumber: 4.6 Consensus size: 47
28843340 GTTACATGTT
28843350 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
* * *
28843397 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTG
1 TAACCGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAATATATG
**
28843445 TAATTGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
* * *
28843492 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTG
1 TAACCGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAATATATG
*
28843540 TAATCGTGGTATATCCACTTAGCACCAC
1 TAACCGTGGTATATCCACTTAGCACCAC
28843568 ATTTTTCCAT
Statistics
Matches: 154, Mismatches: 15, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
47 73 0.47
48 81 0.53
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (47 bp):
TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
Found at i:28843518 original size:95 final size:95
Alignment explanation
Indices: 28843345--28843567 Score: 419
Period size: 95 Copynumber: 2.3 Consensus size: 95
28843335 ACTACGTTAC
* *
28843345 ATGTTTAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATA
1 ATGTGTAATCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATA
28843410 TCCACTTAGCACCACGTTACATGTATCAAT
66 TCCACTTAGCACCACGTTACATGTATCAAT
*
28843440 ATGTGTAATTGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATA
1 ATGTGTAATCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATA
28843505 TCCACTTAGCACCACGTTACATGTATCAAT
66 TCCACTTAGCACCACGTTACATGTATCAAT
28843535 ATGTGTAATCGTGGTATATCCACTTAGCACCAC
1 ATGTGTAATCGTGGTATATCCACTTAGCACCAC
28843568 ATTTTTCCAT
Statistics
Matches: 124, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 124 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (95 bp):
ATGTGTAATCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATA
TCCACTTAGCACCACGTTACATGTATCAAT
Found at i:28844139 original size:14 final size:14
Alignment explanation
Indices: 28844122--28844168 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
28844112 ACATTTGGGG
28844122 TTTAAAATTTGTCT
1 TTTAAAATTTGTCT
* ***
28844136 TTTAATATTTGGGG
1 TTTAAAATTTGTCT
28844150 TTTAAAATTTGTCT
1 TTTAAAATTTGTCT
28844164 TTTAA
1 TTTAA
28844169 TTTATTTTAC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.13, T:0.55
Consensus pattern (14 bp):
TTTAAAATTTGTCT
Found at i:28844145 original size:28 final size:28
Alignment explanation
Indices: 28844114--28844169 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
28844104 AAAGGGACAC
28844114 ATTTGGGGTTTAAAATTTGTCTTTTAAT
1 ATTTGGGGTTTAAAATTTGTCTTTTAAT
28844142 ATTTGGGGTTTAAAATTTGTCTTTTAAT
1 ATTTGGGGTTTAAAATTTGTCTTTTAAT
28844170 TTATTTTACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.04, G:0.18, T:0.54
Consensus pattern (28 bp):
ATTTGGGGTTTAAAATTTGTCTTTTAAT
Found at i:28845003 original size:19 final size:19
Alignment explanation
Indices: 28844979--28845018 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
28844969 TAAGCAATAA
*
28844979 TCAATCATTTCAATTCATT
1 TCAATCATTCCAATTCATT
28844998 TCAATCATTCCAATTCATT
1 TCAATCATTCCAATTCATT
28845017 TC
1 TC
28845019 TACTAGTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.00, T:0.45
Consensus pattern (19 bp):
TCAATCATTCCAATTCATT
Found at i:28845005 original size:9 final size:10
Alignment explanation
Indices: 28844979--28845018 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
28844969 TAAGCAATAA
28844979 TCAA-TCATT
1 TCAATTCATT
28844988 TCAATTCATT
1 TCAATTCATT
28844998 TCAA-TCATT
1 TCAATTCATT
*
28845007 CCAATTCATT
1 TCAATTCATT
28845017 TC
1 TC
28845019 TACTAGTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
9 12 0.44
10 15 0.56
ACGTcount: A:0.30, C:0.25, G:0.00, T:0.45
Consensus pattern (10 bp):
TCAATTCATT
Found at i:28847259 original size:28 final size:28
Alignment explanation
Indices: 28847192--28847279 Score: 97
Period size: 28 Copynumber: 3.1 Consensus size: 28
28847182 TTCTTACGAC
* *
28847192 TTTATAAAAATTAATATATTTTTTATATT
1 TTTATAAAATTTTATA-ATTTTTTATATT
* * * *
28847221 TCTGT-ATATTTTATAATTTTTTATGTT
1 TTTATAAAATTTTATAATTTTTTATATT
*
28847248 TTTATAAAATTTTACAATTTTTTATATT
1 TTTATAAAATTTTATAATTTTTTATATT
28847276 TTTA
1 TTTA
28847280 CGATTTTTCT
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
27 14 0.30
28 30 0.64
29 3 0.06
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTATAAAATTTTATAATTTTTTATATT
Found at i:28847277 original size:27 final size:26
Alignment explanation
Indices: 28847209--28847303 Score: 75
Period size: 27 Copynumber: 3.5 Consensus size: 26
28847199 AAATTAATAT
* *
28847209 ATTTTTTATATTTCTGT-ATATTTTATA
1 ATTTTTTATATTT-T-TAAAATTTTACA
*
28847236 ATTTTTTATGTTTTTATAAAATTTTACA
1 ATTTTTTAT-ATTTT-TAAAATTTTACA
** *
28847264 ATTTTTTATATTTTTACGATTTTTCTA
1 ATTTTTTATATTTTTAAAATTTTAC-A
*
28847291 ATTTTTAATATTT
1 ATTTTTTATATTT
28847304 GAATTTTTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
26 8 0.14
27 28 0.50
28 20 0.36
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.65
Consensus pattern (26 bp):
ATTTTTTATATTTTTAAAATTTTACA
Found at i:28847278 original size:18 final size:18
Alignment explanation
Indices: 28847257--28847297 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
28847247 TTTTATAAAA
28847257 TTTTACAATTTTT-TATAT
1 TTTTACAATTTTTCTA-AT
*
28847275 TTTTACGATTTTTCTAAT
1 TTTTACAATTTTTCTAAT
28847293 TTTTA
1 TTTTA
28847298 ATATTTGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTTACAATTTTTCTAAT
Found at i:28847573 original size:87 final size:87
Alignment explanation
Indices: 28847402--28847577 Score: 205
Period size: 87 Copynumber: 2.0 Consensus size: 87
28847392 ACTTAATTGC
* * * * *
28847402 TTTTTTTGAAAAAGTTTGAGGGTCTTTTCTATGCATTTTGAAAATTTAAGTACCCAATTGAGTGC
1 TTTTTTTGAAAAAGTTTGAAGGCCTTTTCTATGCATTATGAAAATTTAAGTACCCAAATGAAT-C
*
28847467 AAAAAAAATAAAGGCTTTTTTTT
65 AAAAAAAATAAAGACTTTTTTTT
* * * *
28847490 TTTTTTTG-AAATGTTTGAAGGCCTTTTTTATGTATTATGAAAGTTTAAGTACCCAAATGAAT-A
1 TTTTTTTGAAAAAGTTTGAAGGCCTTTTCTATGCATTATGAAAATTTAAGTACCCAAATGAATCA
*
28847553 AAAAAAAGTAGGAGA-TTTTTTTT
66 AAAAAAA-TA-AAGACTTTTTTTT
28847576 TT
1 TT
28847578 GAAAAAATTG
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
85 8 0.11
86 12 0.16
87 47 0.63
88 8 0.11
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (87 bp):
TTTTTTTGAAAAAGTTTGAAGGCCTTTTCTATGCATTATGAAAATTTAAGTACCCAAATGAATCA
AAAAAAATAAAGACTTTTTTTT
Found at i:28848766 original size:55 final size:55
Alignment explanation
Indices: 28848687--28848818 Score: 169
Period size: 55 Copynumber: 2.4 Consensus size: 55
28848677 TAATAAGATT
* * * *
28848687 ATTATTAAATATATTTAATAAAAAATAATAAATAATTTAGTCATATT-TTAACATA
1 ATTATTAAATAAATTTAAT-AAAAATAATAAATAATTTAATAACATTATTAACATA
* *
28848742 ATTATTAAATACAATTTAATAAAAATAATATATAATTTAATAACATTATTAATATA
1 ATTATTAAATA-AATTTAATAAAAATAATAAATAATTTAATAACATTATTAACATA
28848798 ATTATT-AATAATATTTAATAA
1 ATTATTAAATAA-ATTTAATAA
28848819 TAATTTTAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
54 1 0.01
55 47 0.69
56 20 0.29
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (55 bp):
ATTATTAAATAAATTTAATAAAAATAATAAATAATTTAATAACATTATTAACATA
Done.