Multiple sequence alignment - TraesCS5B01G237700

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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 TraesCS5B01G237700 chr5B 100.000 2466 0 0 1 2466 418548820 418551285 0.000000e+00 4554
1 TraesCS5B01G237700 chr5D 91.032 1405 63 26 532 1916 354268653 354270014 0.000000e+00 1838
2 TraesCS5B01G237700 chr5D 88.055 293 28 6 223 512 354268381 354268669 8.450000e-90 340
3 TraesCS5B01G237700 chr5D 90.683 161 12 2 69 226 352933443 352933603 6.910000e-51 211
4 TraesCS5B01G237700 chr5A 90.126 1195 62 30 532 1688 455205888 455207064 0.000000e+00 1502
5 TraesCS5B01G237700 chr5A 85.666 293 30 10 223 512 455205621 455205904 5.160000e-77 298
6 TraesCS5B01G237700 chr2B 97.500 520 13 0 1947 2466 788225202 788225721 0.000000e+00 889
7 TraesCS5B01G237700 chr2B 85.333 150 18 3 70 219 514861806 514861661 4.250000e-33 152
8 TraesCS5B01G237700 chr4D 93.282 521 33 2 1947 2466 446898149 446898668 0.000000e+00 767
9 TraesCS5B01G237700 chr3A 90.826 545 34 6 1928 2466 713222186 713221652 0.000000e+00 715
10 TraesCS5B01G237700 chr3A 91.585 511 37 3 1957 2466 705228678 705229183 0.000000e+00 701
11 TraesCS5B01G237700 chr2D 89.358 545 42 11 1927 2466 413949940 413950473 0.000000e+00 671
12 TraesCS5B01G237700 chr2D 85.965 171 13 7 73 232 351985774 351985604 3.260000e-39 172
13 TraesCS5B01G237700 chr3B 90.522 517 29 11 1952 2466 479988243 479987745 0.000000e+00 665
14 TraesCS5B01G237700 chr7D 87.425 167 13 1 67 225 274817208 274817042 4.190000e-43 185
15 TraesCS5B01G237700 chr1B 87.425 167 11 4 69 225 120967654 120967820 1.510000e-42 183
16 TraesCS5B01G237700 chr1D 87.059 170 11 5 70 228 409539765 409539934 5.420000e-42 182
17 TraesCS5B01G237700 chr4A 87.500 160 15 2 70 224 621296719 621296560 1.950000e-41 180
18 TraesCS5B01G237700 chr4A 87.821 156 14 4 70 220 643088859 643088704 7.010000e-41 178
19 TraesCS5B01G237700 chr6B 86.792 159 15 4 69 225 136827218 136827064 3.260000e-39 172
20 TraesCS5B01G237700 chr6A 86.250 160 20 1 70 227 550743670 550743511 3.260000e-39 172
21 TraesCS5B01G237700 chr3D 84.756 164 14 7 70 225 395641460 395641620 1.180000e-33 154


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 TraesCS5B01G237700 chr5B 418548820 418551285 2465 False 4554 4554 100.0000 1 2466 1 chr5B.!!$F1 2465
1 TraesCS5B01G237700 chr5D 354268381 354270014 1633 False 1089 1838 89.5435 223 1916 2 chr5D.!!$F2 1693
2 TraesCS5B01G237700 chr5A 455205621 455207064 1443 False 900 1502 87.8960 223 1688 2 chr5A.!!$F1 1465
3 TraesCS5B01G237700 chr2B 788225202 788225721 519 False 889 889 97.5000 1947 2466 1 chr2B.!!$F1 519
4 TraesCS5B01G237700 chr4D 446898149 446898668 519 False 767 767 93.2820 1947 2466 1 chr4D.!!$F1 519
5 TraesCS5B01G237700 chr3A 713221652 713222186 534 True 715 715 90.8260 1928 2466 1 chr3A.!!$R1 538
6 TraesCS5B01G237700 chr3A 705228678 705229183 505 False 701 701 91.5850 1957 2466 1 chr3A.!!$F1 509
7 TraesCS5B01G237700 chr2D 413949940 413950473 533 False 671 671 89.3580 1927 2466 1 chr2D.!!$F1 539

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
309 312 0.673437 ACCACAATGCTGGAAAACGG 59.327 50.0 8.46 0.0 35.04 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 1945 0.889994 ATGCGGCTGCTCAAATTTGA 59.11 45.0 20.27 19.45 43.34 2.69 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
28 29 5.520376 AACTCATGGAACTTTTGACTTGG 57.480 39.130 0.00 0.00 0.00 3.61
29 30 3.891366 ACTCATGGAACTTTTGACTTGGG 59.109 43.478 0.00 0.00 0.00 4.12
30 31 3.230134 TCATGGAACTTTTGACTTGGGG 58.770 45.455 0.00 0.00 0.00 4.96
31 32 1.408969 TGGAACTTTTGACTTGGGGC 58.591 50.000 0.00 0.00 0.00 5.80
32 33 1.342474 TGGAACTTTTGACTTGGGGCA 60.342 47.619 0.00 0.00 0.00 5.36
33 34 1.760029 GGAACTTTTGACTTGGGGCAA 59.240 47.619 0.00 0.00 0.00 4.52
34 35 2.368548 GGAACTTTTGACTTGGGGCAAT 59.631 45.455 0.00 0.00 0.00 3.56
35 36 3.576550 GGAACTTTTGACTTGGGGCAATA 59.423 43.478 0.00 0.00 0.00 1.90
36 37 4.039852 GGAACTTTTGACTTGGGGCAATAA 59.960 41.667 0.00 0.00 0.00 1.40
37 38 4.600692 ACTTTTGACTTGGGGCAATAAC 57.399 40.909 0.00 0.00 0.00 1.89
38 39 4.223144 ACTTTTGACTTGGGGCAATAACT 58.777 39.130 0.00 0.00 0.00 2.24
39 40 5.390387 ACTTTTGACTTGGGGCAATAACTA 58.610 37.500 0.00 0.00 0.00 2.24
40 41 5.476945 ACTTTTGACTTGGGGCAATAACTAG 59.523 40.000 0.00 0.00 0.00 2.57
41 42 4.919774 TTGACTTGGGGCAATAACTAGA 57.080 40.909 0.00 0.00 0.00 2.43
42 43 4.919774 TGACTTGGGGCAATAACTAGAA 57.080 40.909 0.00 0.00 0.00 2.10
43 44 4.585879 TGACTTGGGGCAATAACTAGAAC 58.414 43.478 0.00 0.00 0.00 3.01
44 45 3.945921 GACTTGGGGCAATAACTAGAACC 59.054 47.826 0.00 0.00 0.00 3.62
45 46 3.332485 ACTTGGGGCAATAACTAGAACCA 59.668 43.478 0.00 0.00 0.00 3.67
46 47 4.017499 ACTTGGGGCAATAACTAGAACCAT 60.017 41.667 0.00 0.00 0.00 3.55
47 48 4.601406 TGGGGCAATAACTAGAACCATT 57.399 40.909 0.00 0.00 0.00 3.16
48 49 4.941713 TGGGGCAATAACTAGAACCATTT 58.058 39.130 0.00 0.00 0.00 2.32
49 50 6.080969 TGGGGCAATAACTAGAACCATTTA 57.919 37.500 0.00 0.00 0.00 1.40
50 51 5.889289 TGGGGCAATAACTAGAACCATTTAC 59.111 40.000 0.00 0.00 0.00 2.01
51 52 6.127101 GGGGCAATAACTAGAACCATTTACT 58.873 40.000 0.00 0.00 0.00 2.24
52 53 6.605995 GGGGCAATAACTAGAACCATTTACTT 59.394 38.462 0.00 0.00 0.00 2.24
53 54 7.123697 GGGGCAATAACTAGAACCATTTACTTT 59.876 37.037 0.00 0.00 0.00 2.66
54 55 8.528643 GGGCAATAACTAGAACCATTTACTTTT 58.471 33.333 0.00 0.00 0.00 2.27
55 56 9.923143 GGCAATAACTAGAACCATTTACTTTTT 57.077 29.630 0.00 0.00 0.00 1.94
75 76 3.795623 TTGAGCAGACGTAATACTCCC 57.204 47.619 0.00 0.00 0.00 4.30
76 77 3.014304 TGAGCAGACGTAATACTCCCT 57.986 47.619 0.00 0.00 0.00 4.20
77 78 2.950309 TGAGCAGACGTAATACTCCCTC 59.050 50.000 0.00 0.00 0.00 4.30
78 79 2.293955 GAGCAGACGTAATACTCCCTCC 59.706 54.545 0.00 0.00 0.00 4.30
79 80 1.001597 GCAGACGTAATACTCCCTCCG 60.002 57.143 0.00 0.00 0.00 4.63
80 81 2.295885 CAGACGTAATACTCCCTCCGT 58.704 52.381 0.00 0.00 0.00 4.69
81 82 2.686915 CAGACGTAATACTCCCTCCGTT 59.313 50.000 0.00 0.00 0.00 4.44
82 83 3.129988 CAGACGTAATACTCCCTCCGTTT 59.870 47.826 0.00 0.00 0.00 3.60
83 84 3.766051 AGACGTAATACTCCCTCCGTTTT 59.234 43.478 0.00 0.00 0.00 2.43
84 85 4.221482 AGACGTAATACTCCCTCCGTTTTT 59.779 41.667 0.00 0.00 0.00 1.94
85 86 5.418840 AGACGTAATACTCCCTCCGTTTTTA 59.581 40.000 0.00 0.00 0.00 1.52
86 87 6.036577 ACGTAATACTCCCTCCGTTTTTAA 57.963 37.500 0.00 0.00 0.00 1.52
87 88 6.463360 ACGTAATACTCCCTCCGTTTTTAAA 58.537 36.000 0.00 0.00 0.00 1.52
88 89 7.105588 ACGTAATACTCCCTCCGTTTTTAAAT 58.894 34.615 0.00 0.00 0.00 1.40
89 90 8.257306 ACGTAATACTCCCTCCGTTTTTAAATA 58.743 33.333 0.00 0.00 0.00 1.40
90 91 9.264719 CGTAATACTCCCTCCGTTTTTAAATAT 57.735 33.333 0.00 0.00 0.00 1.28
94 95 7.770366 ACTCCCTCCGTTTTTAAATATTTGT 57.230 32.000 11.05 0.00 0.00 2.83
95 96 8.866970 ACTCCCTCCGTTTTTAAATATTTGTA 57.133 30.769 11.05 0.00 0.00 2.41
96 97 9.470399 ACTCCCTCCGTTTTTAAATATTTGTAT 57.530 29.630 11.05 0.00 0.00 2.29
118 119 9.996554 TGTATTTCTAGAGATTTCAACAAGTGA 57.003 29.630 0.42 0.00 0.00 3.41
123 124 9.996554 TTCTAGAGATTTCAACAAGTGATTACA 57.003 29.630 0.00 0.00 35.70 2.41
127 128 8.873830 AGAGATTTCAACAAGTGATTACATACG 58.126 33.333 0.00 0.00 35.70 3.06
128 129 8.771920 AGATTTCAACAAGTGATTACATACGA 57.228 30.769 0.00 0.00 35.70 3.43
129 130 9.214957 AGATTTCAACAAGTGATTACATACGAA 57.785 29.630 0.00 0.00 35.70 3.85
130 131 9.478019 GATTTCAACAAGTGATTACATACGAAG 57.522 33.333 0.00 0.00 35.70 3.79
131 132 6.403333 TCAACAAGTGATTACATACGAAGC 57.597 37.500 0.00 0.00 0.00 3.86
132 133 6.163476 TCAACAAGTGATTACATACGAAGCT 58.837 36.000 0.00 0.00 0.00 3.74
133 134 6.090763 TCAACAAGTGATTACATACGAAGCTG 59.909 38.462 0.00 0.00 0.00 4.24
134 135 5.720202 ACAAGTGATTACATACGAAGCTGA 58.280 37.500 0.00 0.00 0.00 4.26
135 136 6.163476 ACAAGTGATTACATACGAAGCTGAA 58.837 36.000 0.00 0.00 0.00 3.02
136 137 6.818644 ACAAGTGATTACATACGAAGCTGAAT 59.181 34.615 0.00 0.00 0.00 2.57
137 138 7.010552 ACAAGTGATTACATACGAAGCTGAATC 59.989 37.037 0.00 0.00 0.00 2.52
138 139 6.810911 AGTGATTACATACGAAGCTGAATCT 58.189 36.000 0.00 0.00 0.00 2.40
139 140 7.941919 AGTGATTACATACGAAGCTGAATCTA 58.058 34.615 0.00 0.00 0.00 1.98
140 141 7.863375 AGTGATTACATACGAAGCTGAATCTAC 59.137 37.037 0.00 0.00 0.00 2.59
141 142 7.648112 GTGATTACATACGAAGCTGAATCTACA 59.352 37.037 0.00 0.00 0.00 2.74
142 143 7.648112 TGATTACATACGAAGCTGAATCTACAC 59.352 37.037 0.00 0.00 0.00 2.90
143 144 5.584253 ACATACGAAGCTGAATCTACACT 57.416 39.130 0.00 0.00 0.00 3.55
144 145 6.694877 ACATACGAAGCTGAATCTACACTA 57.305 37.500 0.00 0.00 0.00 2.74
145 146 7.096884 ACATACGAAGCTGAATCTACACTAA 57.903 36.000 0.00 0.00 0.00 2.24
146 147 7.544622 ACATACGAAGCTGAATCTACACTAAA 58.455 34.615 0.00 0.00 0.00 1.85
147 148 8.033038 ACATACGAAGCTGAATCTACACTAAAA 58.967 33.333 0.00 0.00 0.00 1.52
148 149 9.035607 CATACGAAGCTGAATCTACACTAAAAT 57.964 33.333 0.00 0.00 0.00 1.82
151 152 9.035607 ACGAAGCTGAATCTACACTAAAATATG 57.964 33.333 0.00 0.00 0.00 1.78
152 153 9.035607 CGAAGCTGAATCTACACTAAAATATGT 57.964 33.333 0.00 0.00 0.00 2.29
176 177 9.081204 TGTTTATATACATCCGTATGTGGTAGT 57.919 33.333 3.56 0.00 45.99 2.73
177 178 9.565213 GTTTATATACATCCGTATGTGGTAGTC 57.435 37.037 3.56 0.00 45.99 2.59
178 179 8.866970 TTATATACATCCGTATGTGGTAGTCA 57.133 34.615 3.56 0.00 45.99 3.41
179 180 7.770366 ATATACATCCGTATGTGGTAGTCAA 57.230 36.000 3.56 0.00 45.99 3.18
180 181 6.665992 ATACATCCGTATGTGGTAGTCAAT 57.334 37.500 3.56 0.00 45.99 2.57
181 182 5.353394 ACATCCGTATGTGGTAGTCAATT 57.647 39.130 0.00 0.00 44.79 2.32
182 183 5.741011 ACATCCGTATGTGGTAGTCAATTT 58.259 37.500 0.00 0.00 44.79 1.82
183 184 6.880484 ACATCCGTATGTGGTAGTCAATTTA 58.120 36.000 0.00 0.00 44.79 1.40
184 185 7.332557 ACATCCGTATGTGGTAGTCAATTTAA 58.667 34.615 0.00 0.00 44.79 1.52
185 186 7.825270 ACATCCGTATGTGGTAGTCAATTTAAA 59.175 33.333 0.00 0.00 44.79 1.52
186 187 8.670135 CATCCGTATGTGGTAGTCAATTTAAAA 58.330 33.333 0.00 0.00 0.00 1.52
187 188 8.795842 TCCGTATGTGGTAGTCAATTTAAAAT 57.204 30.769 0.00 0.00 0.00 1.82
188 189 8.885722 TCCGTATGTGGTAGTCAATTTAAAATC 58.114 33.333 0.00 0.00 0.00 2.17
189 190 8.889717 CCGTATGTGGTAGTCAATTTAAAATCT 58.110 33.333 0.00 0.00 0.00 2.40
190 191 9.916397 CGTATGTGGTAGTCAATTTAAAATCTC 57.084 33.333 0.00 0.00 0.00 2.75
218 219 9.923143 AAAAAGAAAATTATTTAGGAACGGAGG 57.077 29.630 0.00 0.00 0.00 4.30
219 220 7.640597 AAGAAAATTATTTAGGAACGGAGGG 57.359 36.000 0.00 0.00 0.00 4.30
220 221 6.127101 AGAAAATTATTTAGGAACGGAGGGG 58.873 40.000 0.00 0.00 0.00 4.79
221 222 4.448720 AATTATTTAGGAACGGAGGGGG 57.551 45.455 0.00 0.00 0.00 5.40
227 228 2.574074 AGGAACGGAGGGGGTATTAA 57.426 50.000 0.00 0.00 0.00 1.40
237 238 5.020795 GGAGGGGGTATTAATTTGTGTGTT 58.979 41.667 0.00 0.00 0.00 3.32
240 241 5.245075 AGGGGGTATTAATTTGTGTGTTGTG 59.755 40.000 0.00 0.00 0.00 3.33
249 250 6.900568 AATTTGTGTGTTGTGTTACAATGG 57.099 33.333 0.00 0.00 40.59 3.16
252 253 5.392767 TGTGTGTTGTGTTACAATGGTTT 57.607 34.783 0.00 0.00 40.59 3.27
253 254 6.510879 TGTGTGTTGTGTTACAATGGTTTA 57.489 33.333 0.00 0.00 40.59 2.01
254 255 6.556212 TGTGTGTTGTGTTACAATGGTTTAG 58.444 36.000 0.00 0.00 40.59 1.85
255 256 6.151312 TGTGTGTTGTGTTACAATGGTTTAGT 59.849 34.615 0.00 0.00 40.59 2.24
256 257 6.470877 GTGTGTTGTGTTACAATGGTTTAGTG 59.529 38.462 0.00 0.00 40.59 2.74
257 258 5.457473 GTGTTGTGTTACAATGGTTTAGTGC 59.543 40.000 0.00 0.00 40.59 4.40
258 259 5.358442 TGTTGTGTTACAATGGTTTAGTGCT 59.642 36.000 0.00 0.00 40.59 4.40
269 272 5.794726 TGGTTTAGTGCTAGAGTTACACA 57.205 39.130 0.00 0.00 36.76 3.72
277 280 2.345641 GCTAGAGTTACACACACATGCG 59.654 50.000 0.00 0.00 0.00 4.73
286 289 1.069364 CACACACATGCGCACACAATA 60.069 47.619 14.90 0.00 0.00 1.90
308 311 3.634568 TTACCACAATGCTGGAAAACG 57.365 42.857 8.46 0.00 35.04 3.60
309 312 0.673437 ACCACAATGCTGGAAAACGG 59.327 50.000 8.46 0.00 35.04 4.44
311 314 1.068434 CCACAATGCTGGAAAACGGTT 59.932 47.619 0.00 0.00 32.30 4.44
315 318 2.279935 ATGCTGGAAAACGGTTGGTA 57.720 45.000 0.00 0.00 0.00 3.25
331 334 6.073602 ACGGTTGGTAGTTTTATTTTCGACTC 60.074 38.462 0.00 0.00 0.00 3.36
334 337 4.389687 TGGTAGTTTTATTTTCGACTCCGC 59.610 41.667 0.00 0.00 35.37 5.54
335 338 4.628766 GGTAGTTTTATTTTCGACTCCGCT 59.371 41.667 0.00 0.00 35.37 5.52
339 342 1.640428 TATTTTCGACTCCGCTGCAG 58.360 50.000 10.11 10.11 35.37 4.41
345 348 4.711949 ACTCCGCTGCAGCAAGGG 62.712 66.667 36.03 28.24 42.21 3.95
407 410 3.119743 ACATGAGGAAAATGATGCACACG 60.120 43.478 0.00 0.00 0.00 4.49
438 441 1.201343 GGAGAATTCTAGACGCGTGC 58.799 55.000 20.70 8.74 0.00 5.34
457 460 4.036734 CGTGCACAATAATTTCAGGCCTAT 59.963 41.667 18.64 0.00 0.00 2.57
458 461 5.238432 CGTGCACAATAATTTCAGGCCTATA 59.762 40.000 18.64 0.00 0.00 1.31
459 462 6.566564 CGTGCACAATAATTTCAGGCCTATAG 60.567 42.308 18.64 0.00 0.00 1.31
464 467 7.226720 CACAATAATTTCAGGCCTATAGTCGTT 59.773 37.037 3.98 0.00 0.00 3.85
495 498 8.523658 CCTGTTCCGTCTCTAAATATCATATCA 58.476 37.037 0.00 0.00 0.00 2.15
497 500 9.860898 TGTTCCGTCTCTAAATATCATATCATG 57.139 33.333 0.00 0.00 0.00 3.07
498 501 9.862371 GTTCCGTCTCTAAATATCATATCATGT 57.138 33.333 0.00 0.00 0.00 3.21
500 503 8.687242 TCCGTCTCTAAATATCATATCATGTCC 58.313 37.037 0.00 0.00 0.00 4.02
501 504 8.470002 CCGTCTCTAAATATCATATCATGTCCA 58.530 37.037 0.00 0.00 0.00 4.02
502 505 9.860898 CGTCTCTAAATATCATATCATGTCCAA 57.139 33.333 0.00 0.00 0.00 3.53
509 512 9.645128 AAATATCATATCATGTCCAACCTTTCA 57.355 29.630 0.00 0.00 0.00 2.69
510 513 9.818270 AATATCATATCATGTCCAACCTTTCAT 57.182 29.630 0.00 0.00 0.00 2.57
511 514 9.818270 ATATCATATCATGTCCAACCTTTCATT 57.182 29.630 0.00 0.00 0.00 2.57
513 516 9.818270 ATCATATCATGTCCAACCTTTCATTAT 57.182 29.630 0.00 0.00 0.00 1.28
514 517 9.645128 TCATATCATGTCCAACCTTTCATTATT 57.355 29.630 0.00 0.00 0.00 1.40
515 518 9.903682 CATATCATGTCCAACCTTTCATTATTC 57.096 33.333 0.00 0.00 0.00 1.75
516 519 6.435430 TCATGTCCAACCTTTCATTATTCG 57.565 37.500 0.00 0.00 0.00 3.34
517 520 4.695217 TGTCCAACCTTTCATTATTCGC 57.305 40.909 0.00 0.00 0.00 4.70
518 521 3.442273 TGTCCAACCTTTCATTATTCGCC 59.558 43.478 0.00 0.00 0.00 5.54
519 522 3.442273 GTCCAACCTTTCATTATTCGCCA 59.558 43.478 0.00 0.00 0.00 5.69
520 523 4.082463 GTCCAACCTTTCATTATTCGCCAA 60.082 41.667 0.00 0.00 0.00 4.52
521 524 4.524714 TCCAACCTTTCATTATTCGCCAAA 59.475 37.500 0.00 0.00 0.00 3.28
522 525 5.011125 TCCAACCTTTCATTATTCGCCAAAA 59.989 36.000 0.00 0.00 0.00 2.44
523 526 5.698545 CCAACCTTTCATTATTCGCCAAAAA 59.301 36.000 0.00 0.00 0.00 1.94
574 577 2.436646 CGATGCGGAAGTTGCCCT 60.437 61.111 0.00 0.00 0.00 5.19
666 669 0.749454 ACCGAAATGCATCTCCAGCC 60.749 55.000 0.00 0.00 0.00 4.85
691 694 5.441718 TGCTCCATACATTTCCTTTCTCT 57.558 39.130 0.00 0.00 0.00 3.10
697 700 5.751028 CCATACATTTCCTTTCTCTCTCGAC 59.249 44.000 0.00 0.00 0.00 4.20
738 741 0.678048 GCCTTTCAACGAGCATCCCT 60.678 55.000 0.00 0.00 0.00 4.20
741 744 2.874701 CCTTTCAACGAGCATCCCTATG 59.125 50.000 0.00 0.00 36.09 2.23
807 815 6.427974 TCGACAACGAGTATCTATCATCAAC 58.572 40.000 0.00 0.00 43.81 3.18
809 817 6.465439 ACAACGAGTATCTATCATCAACCA 57.535 37.500 0.00 0.00 0.00 3.67
902 936 1.207791 AAGCTATGCTGCAGGTAGGT 58.792 50.000 17.12 8.75 39.62 3.08
1004 1039 2.974148 CGAACAGGCAGCTGCACA 60.974 61.111 37.63 0.00 44.36 4.57
1005 1040 2.330372 CGAACAGGCAGCTGCACAT 61.330 57.895 37.63 21.42 44.36 3.21
1006 1041 1.859427 CGAACAGGCAGCTGCACATT 61.859 55.000 37.63 26.85 44.36 2.71
1007 1042 1.167851 GAACAGGCAGCTGCACATTA 58.832 50.000 37.63 0.00 44.36 1.90
1047 1084 0.529773 TCATACATCGACGGCCAAGC 60.530 55.000 2.24 0.00 0.00 4.01
1069 1107 2.492090 CCTCGTCGGAGCAAGGAG 59.508 66.667 0.00 0.00 39.06 3.69
1404 1442 3.646637 AGAGAGGAGTCTAGCTAGGTCTC 59.353 52.174 25.03 25.03 30.97 3.36
1405 1443 3.646637 GAGAGGAGTCTAGCTAGGTCTCT 59.353 52.174 28.36 25.81 30.97 3.10
1437 1475 4.029520 AGCTAGCTCCATATCTACCCATG 58.970 47.826 12.68 0.00 0.00 3.66
1513 1566 8.678199 GCTTTCTTGTCTACTTATTGGCTAATT 58.322 33.333 0.00 0.00 0.00 1.40
1565 1619 6.223120 ACTATCATGATGTATTTGCAGCGTA 58.777 36.000 18.72 0.00 0.00 4.42
1566 1620 6.875726 ACTATCATGATGTATTTGCAGCGTAT 59.124 34.615 18.72 0.00 0.00 3.06
1567 1621 6.564709 ATCATGATGTATTTGCAGCGTATT 57.435 33.333 7.59 0.00 0.00 1.89
1713 1777 4.536765 AGTGTTTCTTCTGGTGATTTGGT 58.463 39.130 0.00 0.00 0.00 3.67
1769 1833 2.708861 TCAACCTGAGGGCAACTCTAAA 59.291 45.455 2.38 0.00 46.72 1.85
1881 1945 1.070758 TCAAAAGTTGCCTCTCTCGCT 59.929 47.619 0.00 0.00 0.00 4.93
1907 1971 2.034687 AGCAGCCGCATCCACTTT 59.965 55.556 0.00 0.00 42.27 2.66
1916 1980 4.947388 AGCCGCATCCACTTTTCTAATTAA 59.053 37.500 0.00 0.00 0.00 1.40
1917 1981 5.417580 AGCCGCATCCACTTTTCTAATTAAA 59.582 36.000 0.00 0.00 0.00 1.52
1918 1982 6.071616 AGCCGCATCCACTTTTCTAATTAAAA 60.072 34.615 0.00 0.00 0.00 1.52
1919 1983 6.253512 GCCGCATCCACTTTTCTAATTAAAAG 59.746 38.462 10.56 10.56 46.98 2.27
2002 2070 1.631405 CTCAACCAATTTGCCTCCCA 58.369 50.000 0.00 0.00 34.88 4.37
2119 2187 3.559024 GCGATCTCATGATGGCGG 58.441 61.111 0.00 0.00 42.71 6.13
2211 2279 2.438975 CACCGGTGCATGATGGCT 60.439 61.111 24.02 0.00 34.04 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.143835 CCAAGTCAAAAGTTCCATGAGTTTAAT 58.856 33.333 0.00 0.00 35.19 1.40
4 5 6.040391 CCCAAGTCAAAAGTTCCATGAGTTTA 59.960 38.462 0.00 0.00 35.19 2.01
6 7 4.342092 CCCAAGTCAAAAGTTCCATGAGTT 59.658 41.667 0.00 0.00 37.24 3.01
7 8 3.891366 CCCAAGTCAAAAGTTCCATGAGT 59.109 43.478 0.00 0.00 0.00 3.41
8 9 3.256631 CCCCAAGTCAAAAGTTCCATGAG 59.743 47.826 0.00 0.00 0.00 2.90
9 10 3.230134 CCCCAAGTCAAAAGTTCCATGA 58.770 45.455 0.00 0.00 0.00 3.07
10 11 2.289010 GCCCCAAGTCAAAAGTTCCATG 60.289 50.000 0.00 0.00 0.00 3.66
11 12 1.970640 GCCCCAAGTCAAAAGTTCCAT 59.029 47.619 0.00 0.00 0.00 3.41
12 13 1.342474 TGCCCCAAGTCAAAAGTTCCA 60.342 47.619 0.00 0.00 0.00 3.53
13 14 1.408969 TGCCCCAAGTCAAAAGTTCC 58.591 50.000 0.00 0.00 0.00 3.62
14 15 3.751479 ATTGCCCCAAGTCAAAAGTTC 57.249 42.857 0.00 0.00 0.00 3.01
15 16 4.653801 AGTTATTGCCCCAAGTCAAAAGTT 59.346 37.500 0.00 0.00 0.00 2.66
16 17 4.223144 AGTTATTGCCCCAAGTCAAAAGT 58.777 39.130 0.00 0.00 0.00 2.66
17 18 4.871933 AGTTATTGCCCCAAGTCAAAAG 57.128 40.909 0.00 0.00 0.00 2.27
18 19 5.636123 TCTAGTTATTGCCCCAAGTCAAAA 58.364 37.500 0.00 0.00 0.00 2.44
19 20 5.249780 TCTAGTTATTGCCCCAAGTCAAA 57.750 39.130 0.00 0.00 0.00 2.69
20 21 4.919774 TCTAGTTATTGCCCCAAGTCAA 57.080 40.909 0.00 0.00 0.00 3.18
21 22 4.566907 GGTTCTAGTTATTGCCCCAAGTCA 60.567 45.833 0.00 0.00 0.00 3.41
22 23 3.945921 GGTTCTAGTTATTGCCCCAAGTC 59.054 47.826 0.00 0.00 0.00 3.01
23 24 3.332485 TGGTTCTAGTTATTGCCCCAAGT 59.668 43.478 0.00 0.00 0.00 3.16
24 25 3.963129 TGGTTCTAGTTATTGCCCCAAG 58.037 45.455 0.00 0.00 0.00 3.61
25 26 4.601406 ATGGTTCTAGTTATTGCCCCAA 57.399 40.909 0.00 0.00 0.00 4.12
26 27 4.601406 AATGGTTCTAGTTATTGCCCCA 57.399 40.909 0.00 0.00 0.00 4.96
27 28 6.127101 AGTAAATGGTTCTAGTTATTGCCCC 58.873 40.000 0.00 0.00 0.00 5.80
28 29 7.640597 AAGTAAATGGTTCTAGTTATTGCCC 57.359 36.000 0.00 0.00 0.00 5.36
29 30 9.923143 AAAAAGTAAATGGTTCTAGTTATTGCC 57.077 29.630 0.00 0.00 0.00 4.52
52 53 4.933400 GGGAGTATTACGTCTGCTCAAAAA 59.067 41.667 14.90 0.00 0.00 1.94
53 54 4.222145 AGGGAGTATTACGTCTGCTCAAAA 59.778 41.667 14.90 0.00 0.00 2.44
54 55 3.767673 AGGGAGTATTACGTCTGCTCAAA 59.232 43.478 14.90 0.00 0.00 2.69
55 56 3.362706 AGGGAGTATTACGTCTGCTCAA 58.637 45.455 14.90 0.00 0.00 3.02
56 57 2.950309 GAGGGAGTATTACGTCTGCTCA 59.050 50.000 14.90 0.00 0.00 4.26
57 58 2.293955 GGAGGGAGTATTACGTCTGCTC 59.706 54.545 0.00 0.00 0.00 4.26
58 59 2.308690 GGAGGGAGTATTACGTCTGCT 58.691 52.381 0.00 0.00 0.00 4.24
59 60 1.001597 CGGAGGGAGTATTACGTCTGC 60.002 57.143 0.00 0.00 0.00 4.26
60 61 2.295885 ACGGAGGGAGTATTACGTCTG 58.704 52.381 0.00 0.00 34.85 3.51
61 62 2.725221 ACGGAGGGAGTATTACGTCT 57.275 50.000 0.00 0.00 0.00 4.18
62 63 3.790152 AAACGGAGGGAGTATTACGTC 57.210 47.619 0.00 0.00 32.98 4.34
63 64 4.541973 AAAAACGGAGGGAGTATTACGT 57.458 40.909 0.00 0.00 35.95 3.57
64 65 6.966435 TTTAAAAACGGAGGGAGTATTACG 57.034 37.500 0.00 0.00 0.00 3.18
68 69 9.470399 ACAAATATTTAAAAACGGAGGGAGTAT 57.530 29.630 0.00 0.00 0.00 2.12
69 70 8.866970 ACAAATATTTAAAAACGGAGGGAGTA 57.133 30.769 0.00 0.00 0.00 2.59
70 71 7.770366 ACAAATATTTAAAAACGGAGGGAGT 57.230 32.000 0.00 0.00 0.00 3.85
92 93 9.996554 TCACTTGTTGAAATCTCTAGAAATACA 57.003 29.630 0.00 0.00 0.00 2.29
97 98 9.996554 TGTAATCACTTGTTGAAATCTCTAGAA 57.003 29.630 0.00 0.00 37.92 2.10
101 102 8.873830 CGTATGTAATCACTTGTTGAAATCTCT 58.126 33.333 0.00 0.00 37.92 3.10
102 103 8.869897 TCGTATGTAATCACTTGTTGAAATCTC 58.130 33.333 0.00 0.00 37.92 2.75
103 104 8.771920 TCGTATGTAATCACTTGTTGAAATCT 57.228 30.769 0.00 0.00 37.92 2.40
104 105 9.478019 CTTCGTATGTAATCACTTGTTGAAATC 57.522 33.333 0.00 0.00 37.92 2.17
105 106 7.962918 GCTTCGTATGTAATCACTTGTTGAAAT 59.037 33.333 0.00 0.00 37.92 2.17
106 107 7.172532 AGCTTCGTATGTAATCACTTGTTGAAA 59.827 33.333 0.00 0.00 37.92 2.69
107 108 6.649141 AGCTTCGTATGTAATCACTTGTTGAA 59.351 34.615 0.00 0.00 37.92 2.69
108 109 6.090763 CAGCTTCGTATGTAATCACTTGTTGA 59.909 38.462 0.00 0.00 39.11 3.18
109 110 6.090763 TCAGCTTCGTATGTAATCACTTGTTG 59.909 38.462 0.00 0.00 0.00 3.33
110 111 6.163476 TCAGCTTCGTATGTAATCACTTGTT 58.837 36.000 0.00 0.00 0.00 2.83
111 112 5.720202 TCAGCTTCGTATGTAATCACTTGT 58.280 37.500 0.00 0.00 0.00 3.16
112 113 6.647212 TTCAGCTTCGTATGTAATCACTTG 57.353 37.500 0.00 0.00 0.00 3.16
113 114 7.268586 AGATTCAGCTTCGTATGTAATCACTT 58.731 34.615 0.00 0.00 0.00 3.16
114 115 6.810911 AGATTCAGCTTCGTATGTAATCACT 58.189 36.000 0.00 0.00 0.00 3.41
115 116 7.648112 TGTAGATTCAGCTTCGTATGTAATCAC 59.352 37.037 0.00 0.00 0.00 3.06
116 117 7.648112 GTGTAGATTCAGCTTCGTATGTAATCA 59.352 37.037 0.00 0.00 0.00 2.57
117 118 7.863375 AGTGTAGATTCAGCTTCGTATGTAATC 59.137 37.037 0.00 0.00 0.00 1.75
118 119 7.717568 AGTGTAGATTCAGCTTCGTATGTAAT 58.282 34.615 0.00 0.00 0.00 1.89
119 120 7.096884 AGTGTAGATTCAGCTTCGTATGTAA 57.903 36.000 0.00 0.00 0.00 2.41
120 121 6.694877 AGTGTAGATTCAGCTTCGTATGTA 57.305 37.500 0.00 0.00 0.00 2.29
121 122 5.584253 AGTGTAGATTCAGCTTCGTATGT 57.416 39.130 0.00 0.00 0.00 2.29
122 123 7.987268 TTTAGTGTAGATTCAGCTTCGTATG 57.013 36.000 0.00 0.00 0.00 2.39
125 126 9.035607 CATATTTTAGTGTAGATTCAGCTTCGT 57.964 33.333 0.00 0.00 0.00 3.85
126 127 9.035607 ACATATTTTAGTGTAGATTCAGCTTCG 57.964 33.333 0.00 0.00 0.00 3.79
150 151 9.081204 ACTACCACATACGGATGTATATAAACA 57.919 33.333 14.23 0.00 44.82 2.83
151 152 9.565213 GACTACCACATACGGATGTATATAAAC 57.435 37.037 14.23 0.00 44.82 2.01
152 153 9.299465 TGACTACCACATACGGATGTATATAAA 57.701 33.333 14.23 0.00 44.82 1.40
153 154 8.866970 TGACTACCACATACGGATGTATATAA 57.133 34.615 14.23 0.00 44.82 0.98
154 155 8.866970 TTGACTACCACATACGGATGTATATA 57.133 34.615 14.23 5.36 44.82 0.86
155 156 7.770366 TTGACTACCACATACGGATGTATAT 57.230 36.000 14.23 4.37 44.82 0.86
156 157 7.770366 ATTGACTACCACATACGGATGTATA 57.230 36.000 14.23 8.27 44.82 1.47
157 158 6.665992 ATTGACTACCACATACGGATGTAT 57.334 37.500 14.23 7.46 44.82 2.29
158 159 6.474140 AATTGACTACCACATACGGATGTA 57.526 37.500 14.23 0.00 44.82 2.29
160 161 7.780008 TTAAATTGACTACCACATACGGATG 57.220 36.000 5.94 5.94 39.16 3.51
161 162 8.795842 TTTTAAATTGACTACCACATACGGAT 57.204 30.769 0.00 0.00 0.00 4.18
162 163 8.795842 ATTTTAAATTGACTACCACATACGGA 57.204 30.769 0.00 0.00 0.00 4.69
163 164 8.889717 AGATTTTAAATTGACTACCACATACGG 58.110 33.333 0.00 0.00 0.00 4.02
164 165 9.916397 GAGATTTTAAATTGACTACCACATACG 57.084 33.333 0.00 0.00 0.00 3.06
192 193 9.923143 CCTCCGTTCCTAAATAATTTTCTTTTT 57.077 29.630 0.00 0.00 0.00 1.94
193 194 8.528643 CCCTCCGTTCCTAAATAATTTTCTTTT 58.471 33.333 0.00 0.00 0.00 2.27
194 195 7.123697 CCCCTCCGTTCCTAAATAATTTTCTTT 59.876 37.037 0.00 0.00 0.00 2.52
195 196 6.605995 CCCCTCCGTTCCTAAATAATTTTCTT 59.394 38.462 0.00 0.00 0.00 2.52
196 197 6.127101 CCCCTCCGTTCCTAAATAATTTTCT 58.873 40.000 0.00 0.00 0.00 2.52
197 198 5.301045 CCCCCTCCGTTCCTAAATAATTTTC 59.699 44.000 0.00 0.00 0.00 2.29
198 199 5.205821 CCCCCTCCGTTCCTAAATAATTTT 58.794 41.667 0.00 0.00 0.00 1.82
199 200 4.231195 ACCCCCTCCGTTCCTAAATAATTT 59.769 41.667 0.00 0.00 0.00 1.82
200 201 3.789840 ACCCCCTCCGTTCCTAAATAATT 59.210 43.478 0.00 0.00 0.00 1.40
201 202 3.400419 ACCCCCTCCGTTCCTAAATAAT 58.600 45.455 0.00 0.00 0.00 1.28
202 203 2.849537 ACCCCCTCCGTTCCTAAATAA 58.150 47.619 0.00 0.00 0.00 1.40
203 204 2.574074 ACCCCCTCCGTTCCTAAATA 57.426 50.000 0.00 0.00 0.00 1.40
204 205 2.574074 TACCCCCTCCGTTCCTAAAT 57.426 50.000 0.00 0.00 0.00 1.40
205 206 2.574074 ATACCCCCTCCGTTCCTAAA 57.426 50.000 0.00 0.00 0.00 1.85
206 207 2.574074 AATACCCCCTCCGTTCCTAA 57.426 50.000 0.00 0.00 0.00 2.69
207 208 3.704545 TTAATACCCCCTCCGTTCCTA 57.295 47.619 0.00 0.00 0.00 2.94
208 209 2.574074 TTAATACCCCCTCCGTTCCT 57.426 50.000 0.00 0.00 0.00 3.36
209 210 3.870538 AATTAATACCCCCTCCGTTCC 57.129 47.619 0.00 0.00 0.00 3.62
210 211 4.337274 CACAAATTAATACCCCCTCCGTTC 59.663 45.833 0.00 0.00 0.00 3.95
211 212 4.264038 ACACAAATTAATACCCCCTCCGTT 60.264 41.667 0.00 0.00 0.00 4.44
212 213 3.267551 ACACAAATTAATACCCCCTCCGT 59.732 43.478 0.00 0.00 0.00 4.69
213 214 3.630312 CACACAAATTAATACCCCCTCCG 59.370 47.826 0.00 0.00 0.00 4.63
214 215 4.606210 ACACACAAATTAATACCCCCTCC 58.394 43.478 0.00 0.00 0.00 4.30
215 216 5.479027 ACAACACACAAATTAATACCCCCTC 59.521 40.000 0.00 0.00 0.00 4.30
216 217 5.245075 CACAACACACAAATTAATACCCCCT 59.755 40.000 0.00 0.00 0.00 4.79
217 218 5.011227 ACACAACACACAAATTAATACCCCC 59.989 40.000 0.00 0.00 0.00 5.40
218 219 6.091718 ACACAACACACAAATTAATACCCC 57.908 37.500 0.00 0.00 0.00 4.95
219 220 8.136165 TGTAACACAACACACAAATTAATACCC 58.864 33.333 0.00 0.00 0.00 3.69
220 221 9.517609 TTGTAACACAACACACAAATTAATACC 57.482 29.630 0.00 0.00 32.34 2.73
227 228 5.971763 ACCATTGTAACACAACACACAAAT 58.028 33.333 0.00 0.00 41.40 2.32
237 238 6.526526 TCTAGCACTAAACCATTGTAACACA 58.473 36.000 0.00 0.00 0.00 3.72
240 241 7.668525 AACTCTAGCACTAAACCATTGTAAC 57.331 36.000 0.00 0.00 0.00 2.50
249 250 5.981315 TGTGTGTGTAACTCTAGCACTAAAC 59.019 40.000 0.00 0.00 38.04 2.01
252 253 5.709966 CATGTGTGTGTAACTCTAGCACTA 58.290 41.667 0.00 0.00 38.04 2.74
253 254 4.560128 CATGTGTGTGTAACTCTAGCACT 58.440 43.478 0.00 0.00 38.04 4.40
254 255 3.123621 GCATGTGTGTGTAACTCTAGCAC 59.876 47.826 0.00 0.00 38.04 4.40
255 256 3.325870 GCATGTGTGTGTAACTCTAGCA 58.674 45.455 0.00 0.00 38.04 3.49
256 257 2.345641 CGCATGTGTGTGTAACTCTAGC 59.654 50.000 0.00 0.00 38.04 3.42
257 258 2.345641 GCGCATGTGTGTGTAACTCTAG 59.654 50.000 0.30 0.00 38.13 2.43
258 259 2.288518 TGCGCATGTGTGTGTAACTCTA 60.289 45.455 5.66 0.00 38.13 2.43
269 272 3.574284 AATTATTGTGTGCGCATGTGT 57.426 38.095 15.91 1.56 0.00 3.72
277 280 5.289193 CAGCATTGTGGTAATTATTGTGTGC 59.711 40.000 0.00 0.00 0.00 4.57
286 289 4.555262 CGTTTTCCAGCATTGTGGTAATT 58.445 39.130 5.54 0.00 38.88 1.40
308 311 6.605849 GGAGTCGAAAATAAAACTACCAACC 58.394 40.000 0.00 0.00 0.00 3.77
309 312 6.301861 CGGAGTCGAAAATAAAACTACCAAC 58.698 40.000 0.00 0.00 39.00 3.77
311 314 4.389687 GCGGAGTCGAAAATAAAACTACCA 59.610 41.667 0.00 0.00 39.00 3.25
315 318 3.120304 GCAGCGGAGTCGAAAATAAAACT 60.120 43.478 0.00 0.00 39.00 2.66
331 334 2.086251 TTTTTCCCTTGCTGCAGCGG 62.086 55.000 32.11 26.66 45.83 5.52
351 354 4.657436 TGGCAAGTTAAAATCCGTTGTT 57.343 36.364 0.00 0.00 0.00 2.83
407 410 7.646130 CGTCTAGAATTCTCCAATCTTGTAGTC 59.354 40.741 12.24 0.00 0.00 2.59
438 441 6.706270 ACGACTATAGGCCTGAAATTATTGTG 59.294 38.462 17.99 4.82 0.00 3.33
457 460 1.403647 CGGAACAGGATGCAACGACTA 60.404 52.381 0.00 0.00 42.53 2.59
458 461 0.670546 CGGAACAGGATGCAACGACT 60.671 55.000 0.00 0.00 42.53 4.18
459 462 0.949105 ACGGAACAGGATGCAACGAC 60.949 55.000 0.00 0.00 42.53 4.34
464 467 1.847328 TAGAGACGGAACAGGATGCA 58.153 50.000 0.00 0.00 42.53 3.96
495 498 4.097892 GGCGAATAATGAAAGGTTGGACAT 59.902 41.667 0.00 0.00 0.00 3.06
496 499 3.442273 GGCGAATAATGAAAGGTTGGACA 59.558 43.478 0.00 0.00 0.00 4.02
497 500 3.442273 TGGCGAATAATGAAAGGTTGGAC 59.558 43.478 0.00 0.00 0.00 4.02
498 501 3.691575 TGGCGAATAATGAAAGGTTGGA 58.308 40.909 0.00 0.00 0.00 3.53
499 502 4.448537 TTGGCGAATAATGAAAGGTTGG 57.551 40.909 0.00 0.00 0.00 3.77
500 503 6.777526 TTTTTGGCGAATAATGAAAGGTTG 57.222 33.333 0.00 0.00 0.00 3.77
524 527 7.337938 ACAATGAAAGGTTGGACATTCTTTTT 58.662 30.769 0.00 0.00 31.85 1.94
525 528 6.888105 ACAATGAAAGGTTGGACATTCTTTT 58.112 32.000 0.00 0.00 31.85 2.27
526 529 6.484364 ACAATGAAAGGTTGGACATTCTTT 57.516 33.333 0.00 0.00 31.85 2.52
527 530 7.004086 TCTACAATGAAAGGTTGGACATTCTT 58.996 34.615 0.00 0.00 31.85 2.52
528 531 6.542821 TCTACAATGAAAGGTTGGACATTCT 58.457 36.000 0.00 0.00 31.85 2.40
529 532 6.817765 TCTACAATGAAAGGTTGGACATTC 57.182 37.500 0.00 0.00 31.85 2.67
530 533 7.595819 TTTCTACAATGAAAGGTTGGACATT 57.404 32.000 0.00 0.00 32.82 2.71
610 613 8.421673 AATTAAGAATCGTGTAAAGCTCTACC 57.578 34.615 0.00 0.00 0.00 3.18
666 669 6.376581 AGAGAAAGGAAATGTATGGAGCAAAG 59.623 38.462 0.00 0.00 0.00 2.77
697 700 1.915141 AAGAATCTGCACCAAGTGGG 58.085 50.000 1.69 0.00 44.81 4.61
738 741 7.039784 GCTGTTTTAATTGGGCCATCTATCATA 60.040 37.037 7.26 0.00 0.00 2.15
741 744 5.068987 TGCTGTTTTAATTGGGCCATCTATC 59.931 40.000 7.26 0.00 0.00 2.08
856 890 1.920574 CACGCGGTGTAGATTCTCAAG 59.079 52.381 12.47 0.00 0.00 3.02
858 892 0.885879 ACACGCGGTGTAGATTCTCA 59.114 50.000 12.47 0.00 45.56 3.27
877 911 3.889815 ACCTGCAGCATAGCTTATTCAA 58.110 40.909 8.66 0.00 36.40 2.69
1047 1084 2.343163 CTTGCTCCGACGAGGGCTAG 62.343 65.000 9.17 7.31 41.52 3.42
1052 1089 2.492090 CTCCTTGCTCCGACGAGG 59.508 66.667 0.00 0.00 41.98 4.63
1069 1107 1.617947 AACTGATCAGTCTCCGGCCC 61.618 60.000 28.01 0.00 41.58 5.80
1137 1175 1.176619 ACTCGTCCACCGTCATGTCA 61.177 55.000 0.00 0.00 37.94 3.58
1332 1370 2.277949 TGCGCGTACTCGATGAGC 60.278 61.111 9.88 0.00 39.71 4.26
1404 1442 4.244425 TGGAGCTAGCTTCGCTTAATAG 57.756 45.455 20.42 0.00 40.44 1.73
1405 1443 4.873746 ATGGAGCTAGCTTCGCTTAATA 57.126 40.909 20.42 0.00 40.44 0.98
1437 1475 2.138320 TCAGCGCTTATTCTAGCATGC 58.862 47.619 7.50 10.51 41.28 4.06
1539 1593 6.875726 ACGCTGCAAATACATCATGATAGTAT 59.124 34.615 8.15 14.55 0.00 2.12
1540 1594 6.223120 ACGCTGCAAATACATCATGATAGTA 58.777 36.000 8.15 13.02 0.00 1.82
1541 1595 5.059161 ACGCTGCAAATACATCATGATAGT 58.941 37.500 8.15 11.30 0.00 2.12
1591 1645 3.435186 GTGCAGGAAAGGCGAGCC 61.435 66.667 5.89 5.89 0.00 4.70
1592 1646 3.793144 CGTGCAGGAAAGGCGAGC 61.793 66.667 0.00 0.00 0.00 5.03
1593 1647 3.121030 CCGTGCAGGAAAGGCGAG 61.121 66.667 8.24 0.00 45.00 5.03
1611 1665 1.976045 GCAAATTAACAACGACGGCAG 59.024 47.619 0.00 0.00 0.00 4.85
1693 1757 4.580167 CAGACCAAATCACCAGAAGAAACA 59.420 41.667 0.00 0.00 0.00 2.83
1698 1762 5.392380 GCATTACAGACCAAATCACCAGAAG 60.392 44.000 0.00 0.00 0.00 2.85
1713 1777 1.749063 AGACCATCGACGCATTACAGA 59.251 47.619 0.00 0.00 0.00 3.41
1769 1833 9.117183 AGGAGTAAAAGACTTTTTATTGTTCGT 57.883 29.630 17.92 6.76 40.01 3.85
1800 1864 7.775093 AGTGCTTAACTGCTTAATATGGAATCA 59.225 33.333 0.00 0.00 37.88 2.57
1833 1897 2.472695 TCAACCGTTTGAGGGATCAG 57.527 50.000 0.00 0.00 36.79 2.90
1881 1945 0.889994 ATGCGGCTGCTCAAATTTGA 59.110 45.000 20.27 19.45 43.34 2.69
1907 1971 9.457436 GGTCAGTTGGGATACTTTTAATTAGAA 57.543 33.333 0.00 0.00 0.00 2.10
1916 1980 1.639108 GGGGGTCAGTTGGGATACTTT 59.361 52.381 0.00 0.00 0.00 2.66
1917 1981 1.296002 GGGGGTCAGTTGGGATACTT 58.704 55.000 0.00 0.00 0.00 2.24
1918 1982 0.981277 CGGGGGTCAGTTGGGATACT 60.981 60.000 0.00 0.00 0.00 2.12
1919 1983 1.525442 CGGGGGTCAGTTGGGATAC 59.475 63.158 0.00 0.00 0.00 2.24
1920 1984 2.372074 GCGGGGGTCAGTTGGGATA 61.372 63.158 0.00 0.00 0.00 2.59
1921 1985 3.728373 GCGGGGGTCAGTTGGGAT 61.728 66.667 0.00 0.00 0.00 3.85
2002 2070 3.842923 CTCAGGTGGCGGCGAGAT 61.843 66.667 12.98 0.00 0.00 2.75
2138 2206 4.309950 GGGAACCGCACCAGACGT 62.310 66.667 0.00 0.00 40.86 4.34
2211 2279 2.974148 CCTGCGCTTGCTGTCACA 60.974 61.111 9.73 0.00 40.12 3.58
2440 2508 2.363680 ACATAGCCTGTCATCGAAGAGG 59.636 50.000 0.00 0.00 41.08 3.69


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

AutoCloner maintained by Alex Coulton.