Multiple sequence alignment - TraesCS1A01G096100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G096100 chr1A 100.000 3303 0 0 829 4131 91505373 91502071 0.000000e+00 6100.0
1 TraesCS1A01G096100 chr1A 100.000 421 0 0 1 421 91506201 91505781 0.000000e+00 778.0
2 TraesCS1A01G096100 chr1D 92.823 2299 98 18 1381 3652 96921534 96923792 0.000000e+00 3269.0
3 TraesCS1A01G096100 chr1D 93.504 508 11 5 889 1380 96920881 96921382 0.000000e+00 736.0
4 TraesCS1A01G096100 chr1D 90.782 499 17 3 3662 4131 96920877 96920379 1.250000e-179 640.0
5 TraesCS1A01G096100 chr1D 89.474 380 37 3 1 377 96929710 96929331 1.040000e-130 477.0
6 TraesCS1A01G096100 chr1D 100.000 40 0 0 855 894 96923931 96923892 1.590000e-09 75.0
7 TraesCS1A01G096100 chr1D 95.349 43 2 0 2119 2161 17195763 17195805 7.410000e-08 69.4
8 TraesCS1A01G096100 chr1D 97.368 38 0 1 2128 2165 78977680 78977644 3.450000e-06 63.9
9 TraesCS1A01G096100 chr1B 91.466 2039 120 28 840 2833 156591737 156593766 0.000000e+00 2752.0
10 TraesCS1A01G096100 chr1B 89.548 775 46 10 2892 3642 156593855 156594618 0.000000e+00 950.0
11 TraesCS1A01G096100 chr1B 90.782 499 17 3 3662 4131 156595014 156595512 1.250000e-179 640.0
12 TraesCS1A01G096100 chr1B 85.000 120 16 2 196 315 156588774 156588891 2.020000e-23 121.0
13 TraesCS1A01G096100 chr1B 100.000 39 0 0 2854 2892 156593761 156593799 5.730000e-09 73.1
14 TraesCS1A01G096100 chr7D 95.238 42 2 0 2119 2160 237415121 237415080 2.670000e-07 67.6
15 TraesCS1A01G096100 chr6A 97.500 40 0 1 2117 2156 461133220 461133258 2.670000e-07 67.6
16 TraesCS1A01G096100 chr3B 97.436 39 1 0 2122 2160 405231319 405231281 2.670000e-07 67.6
17 TraesCS1A01G096100 chr7A 92.857 42 3 0 2119 2160 252719913 252719954 1.240000e-05 62.1
18 TraesCS1A01G096100 chr5A 94.872 39 2 0 2122 2160 597290375 597290337 1.240000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G096100 chr1A 91502071 91506201 4130 True 3439.00 6100 100.0000 1 4131 2 chr1A.!!$R1 4130
1 TraesCS1A01G096100 chr1D 96920881 96923792 2911 False 2002.50 3269 93.1635 889 3652 2 chr1D.!!$F2 2763
2 TraesCS1A01G096100 chr1D 96920379 96923931 3552 True 357.50 640 95.3910 855 4131 2 chr1D.!!$R3 3276
3 TraesCS1A01G096100 chr1B 156588774 156595512 6738 False 907.22 2752 91.3592 196 4131 5 chr1B.!!$F1 3935

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
152 153 0.038526 AAGACGTAGCAGAACCGTGG 60.039 55.0 0.0 0.0 34.51 4.94 F
356 1678 0.040157 CACACCACGATGCTGGTTTG 60.040 55.0 0.0 0.0 42.29 2.93 F
1504 4009 0.259647 CCAGGGATTTCATGGAGGCA 59.740 55.0 0.0 0.0 36.09 4.75 F
1676 4194 0.415429 AGGGGAGAGACAGTGGTGAT 59.585 55.0 0.0 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1299 3653 0.110373 CTAAAACGAACACCTGGCGC 60.110 55.000 0.00 0.00 0.00 6.53 R
1872 4391 1.068474 GGGTTGATCAACTCGTGTCG 58.932 55.000 31.81 0.00 40.94 4.35 R
3030 7783 1.093159 CTTGGCAATGAGCTCAGACC 58.907 55.000 22.96 21.38 44.79 3.85 R
3533 8365 1.613437 CAAAACTTTCCGTGCCATCCT 59.387 47.619 0.00 0.00 0.00 3.24 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.099267 CTCCCTCGTGAATGGATGTAC 57.901 52.381 0.00 0.00 0.00 2.90
21 22 1.760613 TCCCTCGTGAATGGATGTACC 59.239 52.381 0.00 0.00 39.54 3.34
44 45 1.949465 AAAATCCCACCGATCGTAGC 58.051 50.000 15.09 0.00 0.00 3.58
45 46 0.828022 AAATCCCACCGATCGTAGCA 59.172 50.000 15.09 0.00 0.00 3.49
46 47 0.828022 AATCCCACCGATCGTAGCAA 59.172 50.000 15.09 0.00 0.00 3.91
47 48 0.828022 ATCCCACCGATCGTAGCAAA 59.172 50.000 15.09 0.00 0.00 3.68
48 49 0.609151 TCCCACCGATCGTAGCAAAA 59.391 50.000 15.09 0.00 0.00 2.44
49 50 1.002201 TCCCACCGATCGTAGCAAAAA 59.998 47.619 15.09 0.00 0.00 1.94
67 68 3.505464 AAAAGAGATGATGCTTGCAGC 57.495 42.857 3.72 3.72 42.82 5.25
79 80 2.117137 GCTTGCAGCAAATCATCATCG 58.883 47.619 9.65 0.00 41.89 3.84
80 81 2.117137 CTTGCAGCAAATCATCATCGC 58.883 47.619 9.65 0.00 0.00 4.58
81 82 0.382873 TGCAGCAAATCATCATCGCC 59.617 50.000 0.00 0.00 0.00 5.54
82 83 0.318445 GCAGCAAATCATCATCGCCC 60.318 55.000 0.00 0.00 0.00 6.13
83 84 0.040692 CAGCAAATCATCATCGCCCG 60.041 55.000 0.00 0.00 0.00 6.13
84 85 1.370900 GCAAATCATCATCGCCCGC 60.371 57.895 0.00 0.00 0.00 6.13
85 86 1.789078 GCAAATCATCATCGCCCGCT 61.789 55.000 0.00 0.00 0.00 5.52
86 87 0.040692 CAAATCATCATCGCCCGCTG 60.041 55.000 0.00 0.00 0.00 5.18
87 88 0.464373 AAATCATCATCGCCCGCTGT 60.464 50.000 0.00 0.00 0.00 4.40
88 89 0.464373 AATCATCATCGCCCGCTGTT 60.464 50.000 0.00 0.00 0.00 3.16
89 90 0.392706 ATCATCATCGCCCGCTGTTA 59.607 50.000 0.00 0.00 0.00 2.41
90 91 0.529773 TCATCATCGCCCGCTGTTAC 60.530 55.000 0.00 0.00 0.00 2.50
91 92 0.809636 CATCATCGCCCGCTGTTACA 60.810 55.000 0.00 0.00 0.00 2.41
92 93 0.530650 ATCATCGCCCGCTGTTACAG 60.531 55.000 8.18 8.18 34.12 2.74
93 94 2.173669 CATCGCCCGCTGTTACAGG 61.174 63.158 14.63 4.35 31.21 4.00
94 95 2.656069 ATCGCCCGCTGTTACAGGT 61.656 57.895 14.63 0.00 31.21 4.00
95 96 2.573609 ATCGCCCGCTGTTACAGGTC 62.574 60.000 14.63 0.00 31.21 3.85
96 97 2.813908 GCCCGCTGTTACAGGTCG 60.814 66.667 14.63 9.67 31.21 4.79
97 98 2.813908 CCCGCTGTTACAGGTCGC 60.814 66.667 14.63 0.00 31.21 5.19
98 99 2.048597 CCGCTGTTACAGGTCGCA 60.049 61.111 14.63 0.00 31.21 5.10
99 100 1.666553 CCGCTGTTACAGGTCGCAA 60.667 57.895 14.63 0.00 31.21 4.85
100 101 1.491563 CGCTGTTACAGGTCGCAAC 59.508 57.895 14.63 0.00 31.21 4.17
101 102 0.944311 CGCTGTTACAGGTCGCAACT 60.944 55.000 14.63 0.00 31.21 3.16
102 103 0.790814 GCTGTTACAGGTCGCAACTC 59.209 55.000 14.63 0.00 31.21 3.01
103 104 1.605712 GCTGTTACAGGTCGCAACTCT 60.606 52.381 14.63 0.00 31.21 3.24
104 105 2.061773 CTGTTACAGGTCGCAACTCTG 58.938 52.381 4.14 0.00 32.87 3.35
105 106 1.411246 TGTTACAGGTCGCAACTCTGT 59.589 47.619 4.65 4.65 39.08 3.41
106 107 2.159014 TGTTACAGGTCGCAACTCTGTT 60.159 45.455 4.57 0.00 37.75 3.16
107 108 2.148916 TACAGGTCGCAACTCTGTTG 57.851 50.000 4.57 6.12 37.75 3.33
108 109 0.178068 ACAGGTCGCAACTCTGTTGT 59.822 50.000 11.35 0.00 34.98 3.32
109 110 0.583438 CAGGTCGCAACTCTGTTGTG 59.417 55.000 15.29 15.29 0.00 3.33
110 111 0.464036 AGGTCGCAACTCTGTTGTGA 59.536 50.000 18.76 18.76 36.68 3.58
111 112 1.134521 AGGTCGCAACTCTGTTGTGAA 60.135 47.619 22.62 9.16 40.15 3.18
112 113 1.873591 GGTCGCAACTCTGTTGTGAAT 59.126 47.619 22.62 0.00 40.15 2.57
113 114 2.349817 GGTCGCAACTCTGTTGTGAATG 60.350 50.000 22.62 5.70 40.15 2.67
114 115 1.872952 TCGCAACTCTGTTGTGAATGG 59.127 47.619 19.91 2.44 36.17 3.16
115 116 1.872952 CGCAACTCTGTTGTGAATGGA 59.127 47.619 16.12 0.00 32.02 3.41
116 117 2.349817 CGCAACTCTGTTGTGAATGGAC 60.350 50.000 16.12 0.00 32.02 4.02
117 118 2.618241 GCAACTCTGTTGTGAATGGACA 59.382 45.455 11.35 0.00 0.00 4.02
118 119 3.254166 GCAACTCTGTTGTGAATGGACAT 59.746 43.478 11.35 0.00 0.00 3.06
119 120 4.455533 GCAACTCTGTTGTGAATGGACATA 59.544 41.667 11.35 0.00 0.00 2.29
120 121 5.617751 GCAACTCTGTTGTGAATGGACATAC 60.618 44.000 11.35 0.00 0.00 2.39
121 122 4.579869 ACTCTGTTGTGAATGGACATACC 58.420 43.478 0.00 0.00 39.54 2.73
135 136 6.573664 TGGACATACCAAGAAAATCACAAG 57.426 37.500 0.00 0.00 46.75 3.16
136 137 6.303054 TGGACATACCAAGAAAATCACAAGA 58.697 36.000 0.00 0.00 46.75 3.02
137 138 6.206634 TGGACATACCAAGAAAATCACAAGAC 59.793 38.462 0.00 0.00 46.75 3.01
138 139 6.241207 ACATACCAAGAAAATCACAAGACG 57.759 37.500 0.00 0.00 0.00 4.18
139 140 5.763204 ACATACCAAGAAAATCACAAGACGT 59.237 36.000 0.00 0.00 0.00 4.34
140 141 6.932400 ACATACCAAGAAAATCACAAGACGTA 59.068 34.615 0.00 0.00 0.00 3.57
141 142 5.924475 ACCAAGAAAATCACAAGACGTAG 57.076 39.130 0.00 0.00 0.00 3.51
142 143 4.213482 ACCAAGAAAATCACAAGACGTAGC 59.787 41.667 0.00 0.00 0.00 3.58
143 144 4.213270 CCAAGAAAATCACAAGACGTAGCA 59.787 41.667 0.00 0.00 0.00 3.49
144 145 5.377358 CAAGAAAATCACAAGACGTAGCAG 58.623 41.667 0.00 0.00 0.00 4.24
145 146 4.883083 AGAAAATCACAAGACGTAGCAGA 58.117 39.130 0.00 0.00 0.00 4.26
146 147 5.297547 AGAAAATCACAAGACGTAGCAGAA 58.702 37.500 0.00 0.00 0.00 3.02
147 148 4.992381 AAATCACAAGACGTAGCAGAAC 57.008 40.909 0.00 0.00 0.00 3.01
148 149 2.433868 TCACAAGACGTAGCAGAACC 57.566 50.000 0.00 0.00 0.00 3.62
149 150 1.060713 CACAAGACGTAGCAGAACCG 58.939 55.000 0.00 0.00 0.00 4.44
150 151 0.672342 ACAAGACGTAGCAGAACCGT 59.328 50.000 0.00 0.00 37.56 4.83
151 152 1.060713 CAAGACGTAGCAGAACCGTG 58.939 55.000 0.00 0.00 34.51 4.94
152 153 0.038526 AAGACGTAGCAGAACCGTGG 60.039 55.000 0.00 0.00 34.51 4.94
153 154 0.892358 AGACGTAGCAGAACCGTGGA 60.892 55.000 0.00 0.00 34.51 4.02
154 155 0.731855 GACGTAGCAGAACCGTGGAC 60.732 60.000 0.00 0.00 34.51 4.02
155 156 1.800315 CGTAGCAGAACCGTGGACG 60.800 63.158 0.00 0.00 39.44 4.79
166 167 3.587933 GTGGACGGTTGCGGCAAA 61.588 61.111 18.23 0.00 0.00 3.68
167 168 2.829003 TGGACGGTTGCGGCAAAA 60.829 55.556 18.23 0.00 0.00 2.44
168 169 2.413765 GGACGGTTGCGGCAAAAA 59.586 55.556 18.23 0.00 0.00 1.94
182 183 4.289312 AAAAATCGTAGCCGCCGT 57.711 50.000 0.00 0.00 0.00 5.68
183 184 2.084013 AAAAATCGTAGCCGCCGTC 58.916 52.632 0.00 0.00 0.00 4.79
184 185 1.689352 AAAAATCGTAGCCGCCGTCG 61.689 55.000 0.00 0.00 0.00 5.12
226 227 6.455360 TGGATGAATGTAGCAAAATTCCTC 57.545 37.500 0.00 0.00 32.81 3.71
230 231 4.142622 TGAATGTAGCAAAATTCCTCGCTG 60.143 41.667 0.00 0.00 35.93 5.18
233 234 0.610232 AGCAAAATTCCTCGCTGGCT 60.610 50.000 0.00 0.00 32.33 4.75
234 235 1.094785 GCAAAATTCCTCGCTGGCTA 58.905 50.000 0.00 0.00 35.26 3.93
237 238 3.058639 GCAAAATTCCTCGCTGGCTATAG 60.059 47.826 0.00 0.00 35.26 1.31
243 244 1.599542 CCTCGCTGGCTATAGCAAAAC 59.400 52.381 25.53 9.16 43.87 2.43
245 246 0.663153 CGCTGGCTATAGCAAAACCC 59.337 55.000 25.53 8.15 43.87 4.11
248 249 1.940613 CTGGCTATAGCAAAACCCGAC 59.059 52.381 25.53 6.02 44.36 4.79
249 250 1.279558 TGGCTATAGCAAAACCCGACA 59.720 47.619 25.53 8.56 44.36 4.35
250 251 2.290387 TGGCTATAGCAAAACCCGACAA 60.290 45.455 25.53 0.00 44.36 3.18
252 253 2.222953 GCTATAGCAAAACCCGACAACG 60.223 50.000 20.01 0.00 41.59 4.10
260 261 0.534203 AACCCGACAACGATTGCAGT 60.534 50.000 0.00 0.00 42.66 4.40
271 272 3.386486 ACGATTGCAGTAAAAGACGTCA 58.614 40.909 19.50 0.00 0.00 4.35
287 288 0.091344 GTCATCGTTGTCGCAAGTCG 59.909 55.000 0.00 0.00 40.15 4.18
303 304 2.280524 CGCACCTCCACCGTGAAA 60.281 61.111 0.00 0.00 32.77 2.69
305 306 1.440938 CGCACCTCCACCGTGAAAAA 61.441 55.000 0.00 0.00 32.77 1.94
306 307 0.958822 GCACCTCCACCGTGAAAAAT 59.041 50.000 0.00 0.00 32.77 1.82
307 308 1.335872 GCACCTCCACCGTGAAAAATG 60.336 52.381 0.00 0.00 32.77 2.32
308 309 1.269448 CACCTCCACCGTGAAAAATGG 59.731 52.381 0.00 0.00 41.27 3.16
309 310 1.144093 ACCTCCACCGTGAAAAATGGA 59.856 47.619 0.00 0.00 38.94 3.41
310 311 2.235016 CCTCCACCGTGAAAAATGGAA 58.765 47.619 0.00 0.00 40.69 3.53
311 312 2.228822 CCTCCACCGTGAAAAATGGAAG 59.771 50.000 0.00 0.00 40.69 3.46
313 314 4.069304 CTCCACCGTGAAAAATGGAAGTA 58.931 43.478 0.00 0.00 40.69 2.24
317 318 5.878116 CCACCGTGAAAAATGGAAGTAGATA 59.122 40.000 0.00 0.00 38.47 1.98
318 319 6.373216 CCACCGTGAAAAATGGAAGTAGATAA 59.627 38.462 0.00 0.00 38.47 1.75
320 321 7.749126 CACCGTGAAAAATGGAAGTAGATAAAC 59.251 37.037 0.00 0.00 38.47 2.01
336 337 8.164070 AGTAGATAAACTTCTTGTTGGTTCCAT 58.836 33.333 0.00 0.00 39.13 3.41
340 341 3.897239 ACTTCTTGTTGGTTCCATCACA 58.103 40.909 2.52 0.00 0.00 3.58
341 342 3.632145 ACTTCTTGTTGGTTCCATCACAC 59.368 43.478 2.52 0.00 0.00 3.82
342 343 2.582052 TCTTGTTGGTTCCATCACACC 58.418 47.619 2.52 0.00 0.00 4.16
343 344 2.092158 TCTTGTTGGTTCCATCACACCA 60.092 45.455 2.52 0.00 41.55 4.17
344 345 1.686355 TGTTGGTTCCATCACACCAC 58.314 50.000 0.00 0.00 43.02 4.16
345 346 0.591170 GTTGGTTCCATCACACCACG 59.409 55.000 0.00 0.00 43.02 4.94
346 347 0.470341 TTGGTTCCATCACACCACGA 59.530 50.000 0.00 0.00 43.02 4.35
347 348 0.690192 TGGTTCCATCACACCACGAT 59.310 50.000 0.00 0.00 38.20 3.73
350 1672 0.324614 TTCCATCACACCACGATGCT 59.675 50.000 0.00 0.00 39.17 3.79
351 1673 0.391528 TCCATCACACCACGATGCTG 60.392 55.000 0.00 0.00 39.17 4.41
355 1677 0.179032 TCACACCACGATGCTGGTTT 60.179 50.000 0.00 0.00 42.29 3.27
356 1678 0.040157 CACACCACGATGCTGGTTTG 60.040 55.000 0.00 0.00 42.29 2.93
368 1690 3.723348 GGTTTGAGCACGCGGTCC 61.723 66.667 12.47 0.00 38.96 4.46
390 1712 3.543537 CTCCATGTCGGGGAGGAG 58.456 66.667 0.00 0.00 46.65 3.69
393 1715 2.503061 CATGTCGGGGAGGAGCAG 59.497 66.667 0.00 0.00 0.00 4.24
394 1716 2.039624 ATGTCGGGGAGGAGCAGT 59.960 61.111 0.00 0.00 0.00 4.40
395 1717 1.613630 ATGTCGGGGAGGAGCAGTT 60.614 57.895 0.00 0.00 0.00 3.16
396 1718 1.201429 ATGTCGGGGAGGAGCAGTTT 61.201 55.000 0.00 0.00 0.00 2.66
399 1721 1.078848 CGGGGAGGAGCAGTTTGAG 60.079 63.158 0.00 0.00 0.00 3.02
401 1723 1.492993 GGGGAGGAGCAGTTTGAGGT 61.493 60.000 0.00 0.00 0.00 3.85
403 1725 1.066071 GGGAGGAGCAGTTTGAGGTAC 60.066 57.143 0.00 0.00 0.00 3.34
405 1727 2.354203 GGAGGAGCAGTTTGAGGTACTG 60.354 54.545 0.00 0.00 41.55 2.74
407 1729 2.037772 AGGAGCAGTTTGAGGTACTGTG 59.962 50.000 0.00 0.00 43.81 3.66
408 1730 2.037251 GGAGCAGTTTGAGGTACTGTGA 59.963 50.000 0.00 0.00 43.81 3.58
410 1732 2.965831 AGCAGTTTGAGGTACTGTGAGA 59.034 45.455 0.00 0.00 43.81 3.27
411 1733 3.006323 AGCAGTTTGAGGTACTGTGAGAG 59.994 47.826 0.00 0.00 43.81 3.20
412 1734 3.862642 GCAGTTTGAGGTACTGTGAGAGG 60.863 52.174 0.00 0.00 43.81 3.69
414 1736 1.938585 TTGAGGTACTGTGAGAGGGG 58.061 55.000 0.00 0.00 41.55 4.79
415 1737 1.081481 TGAGGTACTGTGAGAGGGGA 58.919 55.000 0.00 0.00 41.55 4.81
418 1740 1.362932 AGGTACTGTGAGAGGGGATGT 59.637 52.381 0.00 0.00 37.18 3.06
419 1741 2.188817 GGTACTGTGAGAGGGGATGTT 58.811 52.381 0.00 0.00 0.00 2.71
420 1742 2.572104 GGTACTGTGAGAGGGGATGTTT 59.428 50.000 0.00 0.00 0.00 2.83
990 3318 4.008933 CGCGATCCCCATCTCCCC 62.009 72.222 0.00 0.00 0.00 4.81
991 3319 4.008933 GCGATCCCCATCTCCCCG 62.009 72.222 0.00 0.00 0.00 5.73
1217 3571 1.758906 CGTCCTCCCTTCTCCTCCC 60.759 68.421 0.00 0.00 0.00 4.30
1261 3615 0.446616 GTTTCGGGCCAAGATTCGTC 59.553 55.000 4.39 0.00 0.00 4.20
1340 3694 4.665009 AGGGATTATCTTGTGATTGGCCTA 59.335 41.667 3.32 0.00 34.32 3.93
1407 3912 6.672357 GCAATTTGTGTATCTGTAGTTCCGAC 60.672 42.308 0.00 0.00 0.00 4.79
1449 3954 3.698040 GCCAAATTGGAGATGATGACTGT 59.302 43.478 17.47 0.00 40.96 3.55
1504 4009 0.259647 CCAGGGATTTCATGGAGGCA 59.740 55.000 0.00 0.00 36.09 4.75
1524 4029 2.225963 CAGCCAAGAAGCTTCAGTCTTG 59.774 50.000 27.57 21.17 46.80 3.02
1533 4038 2.028658 AGCTTCAGTCTTGCTTCATCGA 60.029 45.455 0.00 0.00 32.61 3.59
1676 4194 0.415429 AGGGGAGAGACAGTGGTGAT 59.585 55.000 0.00 0.00 0.00 3.06
1713 4231 9.548631 CTGGGATCTCTAGGAATAAACCTATAA 57.451 37.037 0.00 0.00 41.03 0.98
1741 4259 3.450817 TCTTACATTGCTGCTACTAGGCA 59.549 43.478 0.00 0.00 40.15 4.75
1835 4354 3.621558 GGAGAGGGTGGTAAAAGGAATG 58.378 50.000 0.00 0.00 0.00 2.67
1838 4357 3.161866 GAGGGTGGTAAAAGGAATGCAA 58.838 45.455 0.00 0.00 0.00 4.08
1841 4360 3.428862 GGGTGGTAAAAGGAATGCAATCG 60.429 47.826 0.00 0.00 0.00 3.34
2075 4596 3.181527 GCAAGGCAGCGAATTGAATTTTC 60.182 43.478 7.59 0.00 0.00 2.29
2188 4725 6.915544 TTCTTGCATGAGTTTATCAGCTAG 57.084 37.500 0.00 0.00 42.53 3.42
2296 4833 4.101585 TCAGATCGGATGGTTCTAAGCATT 59.898 41.667 8.65 0.00 46.18 3.56
2481 5295 4.223923 AGCATAGGTATGTGAATAGGGAGC 59.776 45.833 0.00 0.00 36.11 4.70
2544 5358 3.675698 GCTACTATTAGCCTCGATTGTGC 59.324 47.826 0.66 0.00 44.55 4.57
2618 5432 4.082245 AGGGAGCGTAATTTTTGTGATTGG 60.082 41.667 0.00 0.00 0.00 3.16
2744 5916 9.582648 TTAAGAAACCAGTAGCCTTCTTAAAAT 57.417 29.630 11.49 0.00 42.80 1.82
2805 5977 7.597369 CCCACATGAATATGCAATTATGTTGAG 59.403 37.037 0.00 0.00 37.85 3.02
2947 6175 4.526438 ATGGCCTTGAAGCTTAATAGGT 57.474 40.909 17.53 1.60 0.00 3.08
2948 6176 5.646692 ATGGCCTTGAAGCTTAATAGGTA 57.353 39.130 17.53 10.56 0.00 3.08
2951 6179 6.431722 TGGCCTTGAAGCTTAATAGGTAAAT 58.568 36.000 17.53 0.00 0.00 1.40
2953 6181 7.501225 TGGCCTTGAAGCTTAATAGGTAAATAC 59.499 37.037 17.53 4.94 0.00 1.89
3028 7781 4.349342 ACAATGGAGGAAGAACTGAAGACT 59.651 41.667 0.00 0.00 0.00 3.24
3030 7783 5.930837 ATGGAGGAAGAACTGAAGACTAG 57.069 43.478 0.00 0.00 0.00 2.57
3112 7865 3.846180 CTGGGCAAGCACAACACT 58.154 55.556 0.00 0.00 0.00 3.55
3231 8046 3.558931 TTCTGTCAGCCAAGAGACAAA 57.441 42.857 0.00 0.00 43.48 2.83
3278 8093 4.503741 AACCAGTCAAATTGTTCATCGG 57.496 40.909 0.00 0.00 0.00 4.18
3373 8205 6.606234 TGCAAAACATGTACTCGAAAGTTA 57.394 33.333 0.00 0.00 36.92 2.24
3377 8209 8.469125 GCAAAACATGTACTCGAAAGTTAAAAG 58.531 33.333 0.00 0.00 36.92 2.27
3431 8263 2.737252 GCAGCGAGGCATATAACTTACC 59.263 50.000 0.00 0.00 0.00 2.85
3542 8374 3.384789 TGAGTATGTGTAGAGGATGGCAC 59.615 47.826 0.00 0.00 0.00 5.01
3615 8448 9.487790 AATTTAATGTAGGACATGGTTTTGTTG 57.512 29.630 0.00 0.00 37.97 3.33
3646 8484 6.934645 TGAGTTAACAGTATGACAAGGAAAGG 59.065 38.462 8.61 0.00 39.69 3.11
3650 8488 8.626526 GTTAACAGTATGACAAGGAAAGGAAAA 58.373 33.333 0.00 0.00 39.69 2.29
3651 8489 7.839680 AACAGTATGACAAGGAAAGGAAAAT 57.160 32.000 0.00 0.00 39.69 1.82
3652 8490 7.839680 ACAGTATGACAAGGAAAGGAAAATT 57.160 32.000 0.00 0.00 39.69 1.82
3653 8491 8.934023 ACAGTATGACAAGGAAAGGAAAATTA 57.066 30.769 0.00 0.00 39.69 1.40
3654 8492 9.533831 ACAGTATGACAAGGAAAGGAAAATTAT 57.466 29.630 0.00 0.00 39.69 1.28
3655 8493 9.793252 CAGTATGACAAGGAAAGGAAAATTATG 57.207 33.333 0.00 0.00 39.69 1.90
3656 8494 8.971073 AGTATGACAAGGAAAGGAAAATTATGG 58.029 33.333 0.00 0.00 0.00 2.74
3657 8495 7.797121 ATGACAAGGAAAGGAAAATTATGGT 57.203 32.000 0.00 0.00 0.00 3.55
3658 8496 7.610580 TGACAAGGAAAGGAAAATTATGGTT 57.389 32.000 0.00 0.00 0.00 3.67
3659 8497 7.441017 TGACAAGGAAAGGAAAATTATGGTTG 58.559 34.615 0.00 0.00 0.00 3.77
3660 8498 7.070571 TGACAAGGAAAGGAAAATTATGGTTGT 59.929 33.333 0.00 0.00 0.00 3.32
3670 8884 8.739972 AGGAAAATTATGGTTGTCATGTTCTAC 58.260 33.333 0.00 0.00 37.30 2.59
3779 8994 8.395633 CAAAAGTAGGAAATGGTTATTAGACGG 58.604 37.037 0.00 0.00 0.00 4.79
3882 9118 5.749596 TGGACGCATTAATTTACTGGATG 57.250 39.130 0.00 0.00 0.00 3.51
3918 9161 7.607991 ACCTTACATGTGAAGAAAATCTACCAG 59.392 37.037 9.11 0.00 0.00 4.00
3935 9178 1.606224 CCAGATGGTGCAAAAACAGGC 60.606 52.381 0.00 0.00 0.00 4.85
4047 9290 1.228552 AAGGTTCATGGCTGCGGTT 60.229 52.632 0.00 0.00 0.00 4.44
4122 9365 2.325082 CCGCACTTCCTTGAACCCG 61.325 63.158 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.224066 GGTACATCCATTCACGAGGGAG 60.224 54.545 0.00 0.00 33.47 4.30
1 2 1.760613 GGTACATCCATTCACGAGGGA 59.239 52.381 0.00 0.00 35.97 4.20
2 3 1.484653 TGGTACATCCATTCACGAGGG 59.515 52.381 0.00 0.00 41.93 4.30
3 4 2.979814 TGGTACATCCATTCACGAGG 57.020 50.000 0.00 0.00 41.93 4.63
4 5 5.621197 TTTTTGGTACATCCATTCACGAG 57.379 39.130 0.00 0.00 46.60 4.18
24 25 2.285977 GCTACGATCGGTGGGATTTTT 58.714 47.619 20.98 0.00 34.82 1.94
25 26 1.208535 TGCTACGATCGGTGGGATTTT 59.791 47.619 20.98 0.00 34.82 1.82
26 27 0.828022 TGCTACGATCGGTGGGATTT 59.172 50.000 20.98 0.00 34.82 2.17
27 28 0.828022 TTGCTACGATCGGTGGGATT 59.172 50.000 20.98 0.00 34.82 3.01
28 29 0.828022 TTTGCTACGATCGGTGGGAT 59.172 50.000 20.98 0.00 38.35 3.85
29 30 0.609151 TTTTGCTACGATCGGTGGGA 59.391 50.000 20.98 7.19 0.00 4.37
30 31 1.444836 TTTTTGCTACGATCGGTGGG 58.555 50.000 20.98 7.25 0.00 4.61
60 61 2.117137 GCGATGATGATTTGCTGCAAG 58.883 47.619 15.39 1.81 0.00 4.01
61 62 1.202325 GGCGATGATGATTTGCTGCAA 60.202 47.619 11.69 11.69 0.00 4.08
62 63 0.382873 GGCGATGATGATTTGCTGCA 59.617 50.000 0.00 0.00 0.00 4.41
63 64 0.318445 GGGCGATGATGATTTGCTGC 60.318 55.000 0.00 0.00 0.00 5.25
64 65 0.040692 CGGGCGATGATGATTTGCTG 60.041 55.000 0.00 0.00 0.00 4.41
65 66 1.789078 GCGGGCGATGATGATTTGCT 61.789 55.000 0.00 0.00 0.00 3.91
66 67 1.370900 GCGGGCGATGATGATTTGC 60.371 57.895 0.00 0.00 0.00 3.68
67 68 0.040692 CAGCGGGCGATGATGATTTG 60.041 55.000 0.00 0.00 32.62 2.32
68 69 0.464373 ACAGCGGGCGATGATGATTT 60.464 50.000 0.00 0.00 35.26 2.17
69 70 0.464373 AACAGCGGGCGATGATGATT 60.464 50.000 0.00 0.00 35.26 2.57
70 71 0.392706 TAACAGCGGGCGATGATGAT 59.607 50.000 0.00 0.00 35.26 2.45
71 72 0.529773 GTAACAGCGGGCGATGATGA 60.530 55.000 0.00 0.00 35.26 2.92
72 73 0.809636 TGTAACAGCGGGCGATGATG 60.810 55.000 0.00 0.00 35.26 3.07
73 74 0.530650 CTGTAACAGCGGGCGATGAT 60.531 55.000 0.00 0.00 35.26 2.45
74 75 1.153647 CTGTAACAGCGGGCGATGA 60.154 57.895 0.00 0.00 35.26 2.92
75 76 2.173669 CCTGTAACAGCGGGCGATG 61.174 63.158 0.00 0.00 37.56 3.84
76 77 2.186903 CCTGTAACAGCGGGCGAT 59.813 61.111 0.00 0.00 0.00 4.58
77 78 3.291101 GACCTGTAACAGCGGGCGA 62.291 63.158 0.00 0.00 38.45 5.54
78 79 2.813908 GACCTGTAACAGCGGGCG 60.814 66.667 0.00 0.00 38.45 6.13
79 80 2.813908 CGACCTGTAACAGCGGGC 60.814 66.667 0.00 0.00 38.45 6.13
80 81 2.813908 GCGACCTGTAACAGCGGG 60.814 66.667 0.00 0.00 40.67 6.13
81 82 1.666553 TTGCGACCTGTAACAGCGG 60.667 57.895 0.00 0.00 0.00 5.52
82 83 0.944311 AGTTGCGACCTGTAACAGCG 60.944 55.000 0.00 0.00 44.65 5.18
83 84 0.790814 GAGTTGCGACCTGTAACAGC 59.209 55.000 0.00 0.00 44.65 4.40
84 85 2.061773 CAGAGTTGCGACCTGTAACAG 58.938 52.381 12.16 0.00 44.65 3.16
85 86 1.411246 ACAGAGTTGCGACCTGTAACA 59.589 47.619 20.40 0.00 44.65 2.41
86 87 2.150397 ACAGAGTTGCGACCTGTAAC 57.850 50.000 20.40 0.34 42.80 2.50
87 88 2.159014 ACAACAGAGTTGCGACCTGTAA 60.159 45.455 21.46 0.00 36.74 2.41
88 89 1.411246 ACAACAGAGTTGCGACCTGTA 59.589 47.619 21.46 0.00 36.74 2.74
89 90 0.178068 ACAACAGAGTTGCGACCTGT 59.822 50.000 17.64 17.64 38.26 4.00
90 91 0.583438 CACAACAGAGTTGCGACCTG 59.417 55.000 16.63 16.63 33.18 4.00
91 92 0.464036 TCACAACAGAGTTGCGACCT 59.536 50.000 9.60 0.00 0.00 3.85
92 93 1.295792 TTCACAACAGAGTTGCGACC 58.704 50.000 9.60 0.00 0.00 4.79
93 94 2.349817 CCATTCACAACAGAGTTGCGAC 60.350 50.000 9.60 0.00 0.00 5.19
94 95 1.872952 CCATTCACAACAGAGTTGCGA 59.127 47.619 9.60 3.35 0.00 5.10
95 96 1.872952 TCCATTCACAACAGAGTTGCG 59.127 47.619 9.60 0.91 0.00 4.85
96 97 2.618241 TGTCCATTCACAACAGAGTTGC 59.382 45.455 9.60 0.00 0.00 4.17
97 98 5.106555 GGTATGTCCATTCACAACAGAGTTG 60.107 44.000 8.24 8.24 35.97 3.16
98 99 5.003804 GGTATGTCCATTCACAACAGAGTT 58.996 41.667 0.00 0.00 35.97 3.01
99 100 4.041567 TGGTATGTCCATTCACAACAGAGT 59.958 41.667 0.00 0.00 41.93 3.24
100 101 4.578871 TGGTATGTCCATTCACAACAGAG 58.421 43.478 0.00 0.00 41.93 3.35
101 102 4.632327 TGGTATGTCCATTCACAACAGA 57.368 40.909 0.00 0.00 41.93 3.41
102 103 5.003160 TCTTGGTATGTCCATTCACAACAG 58.997 41.667 0.00 0.00 46.60 3.16
103 104 4.979335 TCTTGGTATGTCCATTCACAACA 58.021 39.130 0.00 0.00 46.60 3.33
104 105 5.957842 TTCTTGGTATGTCCATTCACAAC 57.042 39.130 0.00 0.00 46.60 3.32
105 106 6.968263 TTTTCTTGGTATGTCCATTCACAA 57.032 33.333 0.00 0.00 46.60 3.33
106 107 6.718912 TGATTTTCTTGGTATGTCCATTCACA 59.281 34.615 0.00 0.00 46.60 3.58
107 108 7.029563 GTGATTTTCTTGGTATGTCCATTCAC 58.970 38.462 0.00 0.00 46.60 3.18
108 109 6.718912 TGTGATTTTCTTGGTATGTCCATTCA 59.281 34.615 0.00 0.00 46.60 2.57
109 110 7.156876 TGTGATTTTCTTGGTATGTCCATTC 57.843 36.000 0.00 0.00 46.60 2.67
110 111 7.451255 TCTTGTGATTTTCTTGGTATGTCCATT 59.549 33.333 0.00 0.00 46.60 3.16
111 112 6.947733 TCTTGTGATTTTCTTGGTATGTCCAT 59.052 34.615 0.00 0.00 46.60 3.41
112 113 6.206634 GTCTTGTGATTTTCTTGGTATGTCCA 59.793 38.462 0.00 0.00 45.60 4.02
113 114 6.612306 GTCTTGTGATTTTCTTGGTATGTCC 58.388 40.000 0.00 0.00 0.00 4.02
114 115 6.073222 ACGTCTTGTGATTTTCTTGGTATGTC 60.073 38.462 0.00 0.00 0.00 3.06
115 116 5.763204 ACGTCTTGTGATTTTCTTGGTATGT 59.237 36.000 0.00 0.00 0.00 2.29
116 117 6.241207 ACGTCTTGTGATTTTCTTGGTATG 57.759 37.500 0.00 0.00 0.00 2.39
117 118 6.092259 GCTACGTCTTGTGATTTTCTTGGTAT 59.908 38.462 0.00 0.00 0.00 2.73
118 119 5.407387 GCTACGTCTTGTGATTTTCTTGGTA 59.593 40.000 0.00 0.00 0.00 3.25
119 120 4.213482 GCTACGTCTTGTGATTTTCTTGGT 59.787 41.667 0.00 0.00 0.00 3.67
120 121 4.213270 TGCTACGTCTTGTGATTTTCTTGG 59.787 41.667 0.00 0.00 0.00 3.61
121 122 5.177511 TCTGCTACGTCTTGTGATTTTCTTG 59.822 40.000 0.00 0.00 0.00 3.02
122 123 5.297547 TCTGCTACGTCTTGTGATTTTCTT 58.702 37.500 0.00 0.00 0.00 2.52
123 124 4.883083 TCTGCTACGTCTTGTGATTTTCT 58.117 39.130 0.00 0.00 0.00 2.52
124 125 5.374898 GTTCTGCTACGTCTTGTGATTTTC 58.625 41.667 0.00 0.00 0.00 2.29
125 126 4.213482 GGTTCTGCTACGTCTTGTGATTTT 59.787 41.667 0.00 0.00 0.00 1.82
126 127 3.746492 GGTTCTGCTACGTCTTGTGATTT 59.254 43.478 0.00 0.00 0.00 2.17
127 128 3.326747 GGTTCTGCTACGTCTTGTGATT 58.673 45.455 0.00 0.00 0.00 2.57
128 129 2.671351 CGGTTCTGCTACGTCTTGTGAT 60.671 50.000 0.00 0.00 0.00 3.06
129 130 1.335597 CGGTTCTGCTACGTCTTGTGA 60.336 52.381 0.00 0.00 0.00 3.58
130 131 1.060713 CGGTTCTGCTACGTCTTGTG 58.939 55.000 0.00 0.00 0.00 3.33
131 132 0.672342 ACGGTTCTGCTACGTCTTGT 59.328 50.000 0.00 0.00 35.77 3.16
132 133 1.060713 CACGGTTCTGCTACGTCTTG 58.939 55.000 0.00 0.00 39.02 3.02
133 134 0.038526 CCACGGTTCTGCTACGTCTT 60.039 55.000 0.00 0.00 39.02 3.01
134 135 0.892358 TCCACGGTTCTGCTACGTCT 60.892 55.000 0.00 0.00 39.02 4.18
135 136 0.731855 GTCCACGGTTCTGCTACGTC 60.732 60.000 0.00 0.00 39.02 4.34
136 137 1.288127 GTCCACGGTTCTGCTACGT 59.712 57.895 0.00 0.00 42.17 3.57
137 138 1.800315 CGTCCACGGTTCTGCTACG 60.800 63.158 0.00 0.00 35.37 3.51
138 139 4.164252 CGTCCACGGTTCTGCTAC 57.836 61.111 0.00 0.00 35.37 3.58
149 150 2.615262 TTTTTGCCGCAACCGTCCAC 62.615 55.000 4.98 0.00 0.00 4.02
150 151 2.415608 TTTTTGCCGCAACCGTCCA 61.416 52.632 4.98 0.00 0.00 4.02
151 152 2.413765 TTTTTGCCGCAACCGTCC 59.586 55.556 4.98 0.00 0.00 4.79
165 166 1.689352 CGACGGCGGCTACGATTTTT 61.689 55.000 12.58 0.00 44.60 1.94
166 167 2.162754 CGACGGCGGCTACGATTTT 61.163 57.895 12.58 0.00 44.60 1.82
167 168 2.581409 CGACGGCGGCTACGATTT 60.581 61.111 12.58 0.00 44.60 2.17
180 181 1.342082 CTAAGTTGTGACCCGCGACG 61.342 60.000 8.23 0.00 33.87 5.12
181 182 1.623973 GCTAAGTTGTGACCCGCGAC 61.624 60.000 8.23 0.00 0.00 5.19
182 183 1.373748 GCTAAGTTGTGACCCGCGA 60.374 57.895 8.23 0.00 0.00 5.87
183 184 1.225376 TTGCTAAGTTGTGACCCGCG 61.225 55.000 0.00 0.00 0.00 6.46
184 185 1.135689 CATTGCTAAGTTGTGACCCGC 60.136 52.381 0.00 0.00 0.00 6.13
185 186 1.468520 CCATTGCTAAGTTGTGACCCG 59.531 52.381 0.00 0.00 0.00 5.28
186 187 2.790433 TCCATTGCTAAGTTGTGACCC 58.210 47.619 0.00 0.00 0.00 4.46
187 188 4.009675 TCATCCATTGCTAAGTTGTGACC 58.990 43.478 0.00 0.00 0.00 4.02
188 189 5.627499 TTCATCCATTGCTAAGTTGTGAC 57.373 39.130 0.00 0.00 0.00 3.67
189 190 5.711506 ACATTCATCCATTGCTAAGTTGTGA 59.288 36.000 0.00 0.00 0.00 3.58
190 191 5.957798 ACATTCATCCATTGCTAAGTTGTG 58.042 37.500 0.00 0.00 0.00 3.33
191 192 6.183360 GCTACATTCATCCATTGCTAAGTTGT 60.183 38.462 0.00 0.00 0.00 3.32
192 193 6.183360 TGCTACATTCATCCATTGCTAAGTTG 60.183 38.462 0.00 0.00 0.00 3.16
193 194 5.887598 TGCTACATTCATCCATTGCTAAGTT 59.112 36.000 0.00 0.00 0.00 2.66
194 195 5.439721 TGCTACATTCATCCATTGCTAAGT 58.560 37.500 0.00 0.00 0.00 2.24
226 227 0.663153 GGGTTTTGCTATAGCCAGCG 59.337 55.000 21.84 0.00 44.88 5.18
230 231 2.032680 TGTCGGGTTTTGCTATAGCC 57.967 50.000 21.84 6.23 41.18 3.93
233 234 3.316071 TCGTTGTCGGGTTTTGCTATA 57.684 42.857 0.00 0.00 37.69 1.31
234 235 2.172851 TCGTTGTCGGGTTTTGCTAT 57.827 45.000 0.00 0.00 37.69 2.97
237 238 1.404477 CAATCGTTGTCGGGTTTTGC 58.596 50.000 0.00 0.00 37.69 3.68
243 244 1.434555 TTACTGCAATCGTTGTCGGG 58.565 50.000 0.00 0.00 37.69 5.14
245 246 4.141680 GTCTTTTACTGCAATCGTTGTCG 58.858 43.478 0.00 0.00 38.55 4.35
248 249 4.128554 ACGTCTTTTACTGCAATCGTTG 57.871 40.909 0.00 0.00 0.00 4.10
249 250 3.805422 TGACGTCTTTTACTGCAATCGTT 59.195 39.130 17.92 0.00 0.00 3.85
250 251 3.386486 TGACGTCTTTTACTGCAATCGT 58.614 40.909 17.92 0.00 0.00 3.73
252 253 4.569029 CGATGACGTCTTTTACTGCAATC 58.431 43.478 17.92 6.15 34.56 2.67
271 272 3.156334 GCGACTTGCGACAACGAT 58.844 55.556 0.00 0.00 44.57 3.73
287 288 0.958822 ATTTTTCACGGTGGAGGTGC 59.041 50.000 8.50 0.00 35.39 5.01
309 310 7.996644 TGGAACCAACAAGAAGTTTATCTACTT 59.003 33.333 0.00 0.00 38.74 2.24
310 311 7.514721 TGGAACCAACAAGAAGTTTATCTACT 58.485 34.615 0.00 0.00 38.74 2.57
311 312 7.739498 TGGAACCAACAAGAAGTTTATCTAC 57.261 36.000 0.00 0.00 38.74 2.59
313 314 7.004086 TGATGGAACCAACAAGAAGTTTATCT 58.996 34.615 1.41 0.00 38.74 1.98
317 318 4.709397 TGTGATGGAACCAACAAGAAGTTT 59.291 37.500 5.43 0.00 38.74 2.66
318 319 4.097892 GTGTGATGGAACCAACAAGAAGTT 59.902 41.667 5.43 0.00 42.42 2.66
320 321 3.004734 GGTGTGATGGAACCAACAAGAAG 59.995 47.826 5.43 0.00 36.41 2.85
328 329 0.690192 ATCGTGGTGTGATGGAACCA 59.310 50.000 0.00 0.00 44.20 3.67
341 342 1.236616 TGCTCAAACCAGCATCGTGG 61.237 55.000 0.00 0.00 44.73 4.94
342 343 2.246841 TGCTCAAACCAGCATCGTG 58.753 52.632 0.00 0.00 44.73 4.35
343 344 4.798433 TGCTCAAACCAGCATCGT 57.202 50.000 0.00 0.00 44.73 3.73
350 1672 2.970324 GACCGCGTGCTCAAACCA 60.970 61.111 4.92 0.00 0.00 3.67
351 1673 3.723348 GGACCGCGTGCTCAAACC 61.723 66.667 4.92 0.00 0.00 3.27
374 1696 2.764128 GCTCCTCCCCGACATGGA 60.764 66.667 0.00 0.00 42.00 3.41
377 1699 1.201429 AAACTGCTCCTCCCCGACAT 61.201 55.000 0.00 0.00 0.00 3.06
378 1700 1.841556 AAACTGCTCCTCCCCGACA 60.842 57.895 0.00 0.00 0.00 4.35
379 1701 1.376037 CAAACTGCTCCTCCCCGAC 60.376 63.158 0.00 0.00 0.00 4.79
380 1702 1.535444 TCAAACTGCTCCTCCCCGA 60.535 57.895 0.00 0.00 0.00 5.14
382 1704 1.301293 CCTCAAACTGCTCCTCCCC 59.699 63.158 0.00 0.00 0.00 4.81
383 1705 1.066071 GTACCTCAAACTGCTCCTCCC 60.066 57.143 0.00 0.00 0.00 4.30
384 1706 1.903183 AGTACCTCAAACTGCTCCTCC 59.097 52.381 0.00 0.00 0.00 4.30
385 1707 2.300437 ACAGTACCTCAAACTGCTCCTC 59.700 50.000 3.24 0.00 46.73 3.71
387 1709 2.037251 TCACAGTACCTCAAACTGCTCC 59.963 50.000 3.24 0.00 46.73 4.70
388 1710 3.005897 TCTCACAGTACCTCAAACTGCTC 59.994 47.826 3.24 0.00 46.73 4.26
389 1711 2.965831 TCTCACAGTACCTCAAACTGCT 59.034 45.455 3.24 0.00 46.73 4.24
390 1712 3.321497 CTCTCACAGTACCTCAAACTGC 58.679 50.000 3.24 0.00 46.73 4.40
393 1715 2.028020 CCCCTCTCACAGTACCTCAAAC 60.028 54.545 0.00 0.00 0.00 2.93
394 1716 2.158219 TCCCCTCTCACAGTACCTCAAA 60.158 50.000 0.00 0.00 0.00 2.69
395 1717 1.431633 TCCCCTCTCACAGTACCTCAA 59.568 52.381 0.00 0.00 0.00 3.02
396 1718 1.081481 TCCCCTCTCACAGTACCTCA 58.919 55.000 0.00 0.00 0.00 3.86
399 1721 1.867363 ACATCCCCTCTCACAGTACC 58.133 55.000 0.00 0.00 0.00 3.34
959 3287 2.223272 GGATCGCGAAATCCTTTGGAAC 60.223 50.000 19.27 0.00 41.78 3.62
990 3318 3.621225 TCTGCCATGGGAGAGACG 58.379 61.111 30.28 7.51 37.67 4.18
1217 3571 2.815308 CTCGGATCGACAAGGGGG 59.185 66.667 0.00 0.00 0.00 5.40
1220 3574 2.278857 CCGCTCGGATCGACAAGG 60.279 66.667 1.35 0.00 37.50 3.61
1261 3615 0.954452 GCCAGTGACCAACCAAGAAG 59.046 55.000 0.00 0.00 0.00 2.85
1299 3653 0.110373 CTAAAACGAACACCTGGCGC 60.110 55.000 0.00 0.00 0.00 6.53
1340 3694 9.046846 TGATATCTAATCTACCGGGAATCAAAT 57.953 33.333 6.32 0.00 0.00 2.32
1407 3912 3.927142 GGCACTAGTAAGTAACACAGCAG 59.073 47.826 0.00 0.00 33.48 4.24
1504 4009 2.502295 CAAGACTGAAGCTTCTTGGCT 58.498 47.619 26.09 21.85 43.38 4.75
1676 4194 1.909302 GAGATCCCAGGACAACTCCAA 59.091 52.381 0.00 0.00 39.39 3.53
1713 4231 3.045601 AGCAGCAATGTAAGAGAACGT 57.954 42.857 0.00 0.00 0.00 3.99
1741 4259 2.529389 AAACCTCGCCCACCCTCT 60.529 61.111 0.00 0.00 0.00 3.69
1835 4354 6.532365 TGAAATTAAACCAAAACCGATTGC 57.468 33.333 0.00 0.00 0.00 3.56
1838 4357 7.220740 ACCAATGAAATTAAACCAAAACCGAT 58.779 30.769 0.00 0.00 32.46 4.18
1841 4360 8.896320 ACTACCAATGAAATTAAACCAAAACC 57.104 30.769 0.00 0.00 32.46 3.27
1872 4391 1.068474 GGGTTGATCAACTCGTGTCG 58.932 55.000 31.81 0.00 40.94 4.35
1988 4509 3.515502 TGTGCTTGAGACTACTGCCTTAT 59.484 43.478 0.00 0.00 0.00 1.73
2060 4581 4.397417 CCCTCTCTGAAAATTCAATTCGCT 59.603 41.667 0.00 0.00 36.64 4.93
2075 4596 5.302823 ACAAAAACTCAAAATCCCCTCTCTG 59.697 40.000 0.00 0.00 0.00 3.35
2188 4725 3.319031 AATCACTCCCCCATCAATTCC 57.681 47.619 0.00 0.00 0.00 3.01
2296 4833 8.721478 GCAACTGAGAAATAACTCATTAAGTCA 58.279 33.333 0.00 0.00 44.32 3.41
2418 5232 9.436957 GAAAGTGAGGTCAGATTACAATTAGAA 57.563 33.333 0.00 0.00 0.00 2.10
2481 5295 4.070581 CTCCTCAAGCACAAACATTACG 57.929 45.455 0.00 0.00 0.00 3.18
2576 5390 4.126437 CCCTGCAAACATACATCGTGATA 58.874 43.478 0.00 0.00 0.00 2.15
2578 5392 2.027653 TCCCTGCAAACATACATCGTGA 60.028 45.455 0.00 0.00 0.00 4.35
2579 5393 2.352651 CTCCCTGCAAACATACATCGTG 59.647 50.000 0.00 0.00 0.00 4.35
2580 5394 2.632377 CTCCCTGCAAACATACATCGT 58.368 47.619 0.00 0.00 0.00 3.73
2581 5395 1.331756 GCTCCCTGCAAACATACATCG 59.668 52.381 0.00 0.00 42.31 3.84
2582 5396 1.331756 CGCTCCCTGCAAACATACATC 59.668 52.381 0.00 0.00 43.06 3.06
2592 5406 2.030363 CACAAAAATTACGCTCCCTGCA 60.030 45.455 0.00 0.00 43.06 4.41
2618 5432 3.308438 AAAGCATTGCATCAAGTCACC 57.692 42.857 11.91 0.00 0.00 4.02
2683 5787 8.421784 ACTTCTGAATCTGTCTAACTGTGTTAA 58.578 33.333 0.00 0.00 0.00 2.01
2684 5788 7.867909 CACTTCTGAATCTGTCTAACTGTGTTA 59.132 37.037 0.00 0.00 0.00 2.41
2805 5977 5.236911 TGTGAAGTGTTTAATTGTACCCGTC 59.763 40.000 0.00 0.00 0.00 4.79
2947 6175 8.447833 CGTTCAGAGTTGGCAATTTAGTATTTA 58.552 33.333 1.92 0.00 0.00 1.40
2948 6176 7.040686 ACGTTCAGAGTTGGCAATTTAGTATTT 60.041 33.333 1.92 0.00 0.00 1.40
2951 6179 5.302360 ACGTTCAGAGTTGGCAATTTAGTA 58.698 37.500 1.92 0.00 0.00 1.82
2953 6181 4.749245 ACGTTCAGAGTTGGCAATTTAG 57.251 40.909 1.92 0.00 0.00 1.85
3028 7781 1.571955 TGGCAATGAGCTCAGACCTA 58.428 50.000 22.96 7.35 44.79 3.08
3030 7783 1.093159 CTTGGCAATGAGCTCAGACC 58.907 55.000 22.96 21.38 44.79 3.85
3112 7865 3.997021 GGAATCAAACTCTTTCGAGCTCA 59.003 43.478 15.40 0.00 41.09 4.26
3231 8046 7.806180 AGATCCTAAACATTAGTTATGCTGGT 58.194 34.615 0.00 0.00 36.84 4.00
3278 8093 3.120130 TGTTCCACAACGAAACAAGACAC 60.120 43.478 0.00 0.00 34.95 3.67
3387 8219 5.755375 GCAATGCAGAGACAATTAGCTAGTA 59.245 40.000 0.00 0.00 0.00 1.82
3533 8365 1.613437 CAAAACTTTCCGTGCCATCCT 59.387 47.619 0.00 0.00 0.00 3.24
3590 8423 8.865090 TCAACAAAACCATGTCCTACATTAAAT 58.135 29.630 0.00 0.00 36.53 1.40
3615 8448 8.660373 CCTTGTCATACTGTTAACTCAAATCTC 58.340 37.037 7.22 0.00 0.00 2.75
3646 8484 9.559958 CTGTAGAACATGACAACCATAATTTTC 57.440 33.333 0.00 0.00 33.31 2.29
3650 8488 8.730680 GTTTCTGTAGAACATGACAACCATAAT 58.269 33.333 0.00 0.00 33.31 1.28
3651 8489 7.717436 TGTTTCTGTAGAACATGACAACCATAA 59.283 33.333 0.00 0.00 33.31 1.90
3652 8490 7.220740 TGTTTCTGTAGAACATGACAACCATA 58.779 34.615 0.00 0.00 33.31 2.74
3653 8491 6.061441 TGTTTCTGTAGAACATGACAACCAT 58.939 36.000 0.00 0.00 33.13 3.55
3654 8492 5.432645 TGTTTCTGTAGAACATGACAACCA 58.567 37.500 0.00 0.00 33.13 3.67
3655 8493 6.371809 TTGTTTCTGTAGAACATGACAACC 57.628 37.500 0.00 0.00 33.13 3.77
3656 8494 7.915397 ACAATTGTTTCTGTAGAACATGACAAC 59.085 33.333 4.92 0.00 31.66 3.32
3657 8495 7.995289 ACAATTGTTTCTGTAGAACATGACAA 58.005 30.769 4.92 10.35 32.62 3.18
3658 8496 7.281999 TGACAATTGTTTCTGTAGAACATGACA 59.718 33.333 13.36 0.00 33.13 3.58
3659 8497 7.639039 TGACAATTGTTTCTGTAGAACATGAC 58.361 34.615 13.36 0.00 33.13 3.06
3660 8498 7.800155 TGACAATTGTTTCTGTAGAACATGA 57.200 32.000 13.36 0.00 33.13 3.07
3670 8884 7.435784 TGATGTTTGTGATGACAATTGTTTCTG 59.564 33.333 13.36 0.00 41.77 3.02
3779 8994 7.830940 TTGTCAAATCATATGTTGCCAATTC 57.169 32.000 1.90 0.00 0.00 2.17
3882 9118 7.997482 TCTTCACATGTAAGGTAGACTACATC 58.003 38.462 14.48 0.00 31.51 3.06
3918 9161 0.681175 AGGCCTGTTTTTGCACCATC 59.319 50.000 3.11 0.00 0.00 3.51
3930 9173 6.010219 ACTTGAATTAATGTTGTAGGCCTGT 58.990 36.000 17.99 0.00 0.00 4.00
4092 9335 1.148157 AAGTGCGGATGATCGAAGCG 61.148 55.000 0.00 0.00 0.00 4.68


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.