Multiple sequence alignment - TraesCS3D01G038600

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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 TraesCS3D01G038600 chr3D 100.000 3058 0 0 1 3058 14231147 14228090 0.000000e+00 5648.0
1 TraesCS3D01G038600 chr3D 89.763 674 51 4 1172 1845 14278343 14278998 0.000000e+00 846.0
2 TraesCS3D01G038600 chr3D 92.578 256 17 2 2804 3058 14281072 14281326 1.730000e-97 366.0
3 TraesCS3D01G038600 chr3B 87.393 2110 120 58 415 2452 21004473 21002438 0.000000e+00 2289.0
4 TraesCS3D01G038600 chr3B 88.965 734 55 13 1172 1904 21161541 21162249 0.000000e+00 883.0
5 TraesCS3D01G038600 chr3B 81.939 526 47 20 1890 2383 21162858 21163367 4.750000e-108 401.0
6 TraesCS3D01G038600 chr3B 88.525 244 16 3 2820 3058 21002058 21001822 4.990000e-73 285.0
7 TraesCS3D01G038600 chr3B 91.275 149 7 2 1 143 21004821 21004673 6.690000e-47 198.0
8 TraesCS3D01G038600 chr3B 78.210 257 26 11 2479 2716 21002344 21002099 1.480000e-28 137.0
9 TraesCS3D01G038600 chr3B 83.951 81 10 3 2600 2678 21163600 21163679 1.180000e-09 75.0
10 TraesCS3D01G038600 chr3A 85.091 2361 175 88 161 2457 22474095 22476342 0.000000e+00 2246.0
11 TraesCS3D01G038600 chr3A 85.874 1076 104 26 1172 2240 22422661 22421627 0.000000e+00 1101.0
12 TraesCS3D01G038600 chr3A 84.036 1234 104 41 1172 2377 22429857 22428689 0.000000e+00 1101.0
13 TraesCS3D01G038600 chr3A 85.200 250 27 6 2810 3058 22421036 22420796 6.550000e-62 248.0
14 TraesCS3D01G038600 chr3A 89.103 156 13 4 2810 2963 22476859 22477012 1.120000e-44 191.0
15 TraesCS3D01G038600 chr3A 86.207 145 14 5 1406 1549 674539586 674539447 5.280000e-33 152.0
16 TraesCS3D01G038600 chr3A 86.598 97 10 3 2601 2695 22421199 22421104 1.500000e-18 104.0
17 TraesCS3D01G038600 chr3A 92.308 52 0 1 86 133 22474003 22474054 1.520000e-08 71.3
18 TraesCS3D01G038600 chr4A 90.909 121 7 3 1408 1528 153776721 153776837 3.160000e-35 159.0
19 TraesCS3D01G038600 chr2D 90.909 121 7 3 1408 1528 499309578 499309462 3.160000e-35 159.0


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 TraesCS3D01G038600 chr3D 14228090 14231147 3057 True 5648.000000 5648 100.000000 1 3058 1 chr3D.!!$R1 3057
1 TraesCS3D01G038600 chr3D 14278343 14281326 2983 False 606.000000 846 91.170500 1172 3058 2 chr3D.!!$F1 1886
2 TraesCS3D01G038600 chr3B 21001822 21004821 2999 True 727.250000 2289 86.350750 1 3058 4 chr3B.!!$R1 3057
3 TraesCS3D01G038600 chr3B 21161541 21163679 2138 False 453.000000 883 84.951667 1172 2678 3 chr3B.!!$F1 1506
4 TraesCS3D01G038600 chr3A 22428689 22429857 1168 True 1101.000000 1101 84.036000 1172 2377 1 chr3A.!!$R1 1205
5 TraesCS3D01G038600 chr3A 22474003 22477012 3009 False 836.100000 2246 88.834000 86 2963 3 chr3A.!!$F1 2877
6 TraesCS3D01G038600 chr3A 22420796 22422661 1865 True 484.333333 1101 85.890667 1172 3058 3 chr3A.!!$R3 1886

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
884 993 0.302288 CGTGAAAGAACGAAACCGCA 59.698 50.0 0.0 0.0 46.49 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2844 5300 0.179081 AGGCTTCGGCGAGAAATACC 60.179 55.0 10.46 6.75 42.91 2.73 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
50 51 3.749284 AAAGGGCGCCCAAGTTGGT 62.749 57.895 45.13 22.35 35.17 3.67
54 55 1.145156 GGCGCCCAAGTTGGTTTTT 59.855 52.632 18.11 0.00 35.17 1.94
81 82 4.204799 AGTTTATTCGGGATAAAGTGCCC 58.795 43.478 8.07 0.00 40.62 5.36
82 83 2.943036 TATTCGGGATAAAGTGCCCC 57.057 50.000 0.00 0.00 41.50 5.80
133 144 5.466393 GTCGCCTTACACTTGTTTAACCTTA 59.534 40.000 0.00 0.00 0.00 2.69
185 209 3.319689 TGATCGTGCCCTCGTGAAATATA 59.680 43.478 0.00 0.00 0.00 0.86
186 210 3.088194 TCGTGCCCTCGTGAAATATAC 57.912 47.619 0.00 0.00 0.00 1.47
190 214 4.304939 GTGCCCTCGTGAAATATACTACC 58.695 47.826 0.00 0.00 0.00 3.18
192 216 3.577415 GCCCTCGTGAAATATACTACCCT 59.423 47.826 0.00 0.00 0.00 4.34
193 217 4.321824 GCCCTCGTGAAATATACTACCCTC 60.322 50.000 0.00 0.00 0.00 4.30
195 219 5.047943 CCCTCGTGAAATATACTACCCTCAG 60.048 48.000 0.00 0.00 0.00 3.35
201 225 7.042658 CGTGAAATATACTACCCTCAGAAAAGC 60.043 40.741 0.00 0.00 0.00 3.51
203 227 8.494433 TGAAATATACTACCCTCAGAAAAGCAT 58.506 33.333 0.00 0.00 0.00 3.79
204 228 9.998106 GAAATATACTACCCTCAGAAAAGCATA 57.002 33.333 0.00 0.00 0.00 3.14
205 229 9.780186 AAATATACTACCCTCAGAAAAGCATAC 57.220 33.333 0.00 0.00 0.00 2.39
209 233 6.821388 ACTACCCTCAGAAAAGCATACTATG 58.179 40.000 0.00 0.00 0.00 2.23
211 235 3.817647 CCCTCAGAAAAGCATACTATGGC 59.182 47.826 0.00 0.00 0.00 4.40
212 236 3.496130 CCTCAGAAAAGCATACTATGGCG 59.504 47.826 0.00 0.00 34.54 5.69
214 238 5.270893 TCAGAAAAGCATACTATGGCGTA 57.729 39.130 0.00 0.00 34.54 4.42
215 239 5.666462 TCAGAAAAGCATACTATGGCGTAA 58.334 37.500 0.00 0.00 34.54 3.18
222 246 5.111989 AGCATACTATGGCGTAATAGCATG 58.888 41.667 12.07 12.07 37.13 4.06
223 247 5.105351 AGCATACTATGGCGTAATAGCATGA 60.105 40.000 17.20 1.34 36.56 3.07
224 248 5.580691 GCATACTATGGCGTAATAGCATGAA 59.419 40.000 17.20 0.00 36.56 2.57
227 252 5.793817 ACTATGGCGTAATAGCATGAATGA 58.206 37.500 0.00 0.00 39.27 2.57
266 291 2.006772 CACCGGCTAATTCTCGCAC 58.993 57.895 0.00 0.00 0.00 5.34
270 295 0.532862 CGGCTAATTCTCGCACCCAT 60.533 55.000 0.00 0.00 0.00 4.00
279 304 7.094805 GCTAATTCTCGCACCCATGATAAAATA 60.095 37.037 0.00 0.00 0.00 1.40
288 313 6.243900 CACCCATGATAAAATAGAGCCAGAT 58.756 40.000 0.00 0.00 0.00 2.90
290 315 5.583854 CCCATGATAAAATAGAGCCAGATCG 59.416 44.000 0.00 0.00 0.00 3.69
291 316 5.583854 CCATGATAAAATAGAGCCAGATCGG 59.416 44.000 0.00 0.00 38.11 4.18
308 333 2.773487 TCGGCAAAACTAGCTGCTAAA 58.227 42.857 11.02 0.00 38.65 1.85
309 334 2.742053 TCGGCAAAACTAGCTGCTAAAG 59.258 45.455 11.02 4.32 38.65 1.85
310 335 2.159517 CGGCAAAACTAGCTGCTAAAGG 60.160 50.000 11.02 1.92 38.65 3.11
325 350 6.128254 GCTGCTAAAGGAACGAAAACTAATCT 60.128 38.462 0.00 0.00 0.00 2.40
326 351 7.064253 GCTGCTAAAGGAACGAAAACTAATCTA 59.936 37.037 0.00 0.00 0.00 1.98
336 361 5.119743 ACGAAAACTAATCTAAGCCACGTTC 59.880 40.000 0.00 0.00 0.00 3.95
353 383 0.467290 TTCAAAGGCCACCACTCACC 60.467 55.000 5.01 0.00 0.00 4.02
354 384 1.903404 CAAAGGCCACCACTCACCC 60.903 63.158 5.01 0.00 0.00 4.61
355 385 3.491598 AAAGGCCACCACTCACCCG 62.492 63.158 5.01 0.00 0.00 5.28
392 432 2.186903 CCCCGTTCGACCCAGATG 59.813 66.667 0.00 0.00 0.00 2.90
394 434 2.511600 CCGTTCGACCCAGATGGC 60.512 66.667 0.00 0.00 37.83 4.40
404 444 3.034635 GACCCAGATGGCCGATAGATAT 58.965 50.000 0.00 0.00 37.83 1.63
405 445 4.215908 GACCCAGATGGCCGATAGATATA 58.784 47.826 0.00 0.00 37.83 0.86
406 446 3.961408 ACCCAGATGGCCGATAGATATAC 59.039 47.826 0.00 0.00 37.83 1.47
407 447 3.960755 CCCAGATGGCCGATAGATATACA 59.039 47.826 0.00 0.00 39.76 2.29
408 448 4.590647 CCCAGATGGCCGATAGATATACAT 59.409 45.833 0.00 0.00 39.76 2.29
409 449 5.775195 CCCAGATGGCCGATAGATATACATA 59.225 44.000 0.00 0.00 39.76 2.29
410 450 6.071672 CCCAGATGGCCGATAGATATACATAG 60.072 46.154 0.00 0.00 39.76 2.23
411 451 6.717084 CCAGATGGCCGATAGATATACATAGA 59.283 42.308 0.00 0.00 39.76 1.98
412 452 7.308891 CCAGATGGCCGATAGATATACATAGAC 60.309 44.444 0.00 0.00 39.76 2.59
413 453 6.428465 AGATGGCCGATAGATATACATAGACG 59.572 42.308 0.00 0.00 39.76 4.18
442 488 6.602179 GCCTTTTTAGTTTGCATGGAAAATC 58.398 36.000 16.01 4.13 0.00 2.17
456 502 9.631257 TGCATGGAAAATCTAAATCTAATCTGA 57.369 29.630 0.00 0.00 0.00 3.27
473 519 6.896021 AATCTGATGGCAGGAAAATATCAG 57.104 37.500 0.00 0.00 43.68 2.90
513 559 2.725641 GTTCAAACGGCACCACCC 59.274 61.111 0.00 0.00 33.26 4.61
653 711 2.084101 CGACGCGACGAAATCACCA 61.084 57.895 25.89 0.00 35.09 4.17
655 713 1.006571 ACGCGACGAAATCACCACT 60.007 52.632 15.93 0.00 0.00 4.00
737 808 1.271934 CACACAGTCACAGGAGAGAGG 59.728 57.143 0.00 0.00 0.00 3.69
740 811 1.148027 ACAGTCACAGGAGAGAGGGAA 59.852 52.381 0.00 0.00 0.00 3.97
741 812 1.548269 CAGTCACAGGAGAGAGGGAAC 59.452 57.143 0.00 0.00 0.00 3.62
746 832 0.814457 CAGGAGAGAGGGAACGTGAG 59.186 60.000 0.00 0.00 0.00 3.51
875 984 2.556287 CGCCAGCCGTGAAAGAAC 59.444 61.111 0.00 0.00 0.00 3.01
876 985 2.556287 GCCAGCCGTGAAAGAACG 59.444 61.111 0.00 0.00 43.20 3.95
878 987 1.503818 GCCAGCCGTGAAAGAACGAA 61.504 55.000 0.00 0.00 46.49 3.85
880 989 1.333791 CCAGCCGTGAAAGAACGAAAC 60.334 52.381 0.00 0.00 46.49 2.78
881 990 0.942252 AGCCGTGAAAGAACGAAACC 59.058 50.000 0.00 0.00 46.49 3.27
882 991 0.383860 GCCGTGAAAGAACGAAACCG 60.384 55.000 0.00 0.00 46.49 4.44
883 992 0.383860 CCGTGAAAGAACGAAACCGC 60.384 55.000 0.00 0.00 46.49 5.68
884 993 0.302288 CGTGAAAGAACGAAACCGCA 59.698 50.000 0.00 0.00 46.49 5.69
906 1019 1.859998 GCACGAGTGGTCTTTTTGCAC 60.860 52.381 5.32 0.00 0.00 4.57
1019 1132 1.527736 CACGCACCGCTTTTTGTACTA 59.472 47.619 0.00 0.00 0.00 1.82
1022 1135 2.159881 CGCACCGCTTTTTGTACTACTC 60.160 50.000 0.00 0.00 0.00 2.59
1024 1137 3.497262 GCACCGCTTTTTGTACTACTCTT 59.503 43.478 0.00 0.00 0.00 2.85
1037 1150 5.657302 TGTACTACTCTTTTCTCTCCCATCC 59.343 44.000 0.00 0.00 0.00 3.51
1076 1189 1.302033 CGCCCAGAGTGCTCTTTGT 60.302 57.895 5.69 0.00 37.98 2.83
1078 1191 0.877743 GCCCAGAGTGCTCTTTGTTC 59.122 55.000 5.69 0.00 37.98 3.18
1079 1192 1.815408 GCCCAGAGTGCTCTTTGTTCA 60.815 52.381 5.69 0.00 37.98 3.18
1080 1193 1.876156 CCCAGAGTGCTCTTTGTTCAC 59.124 52.381 5.69 0.00 37.98 3.18
1081 1194 1.528586 CCAGAGTGCTCTTTGTTCACG 59.471 52.381 5.69 0.00 37.98 4.35
1082 1195 2.205074 CAGAGTGCTCTTTGTTCACGT 58.795 47.619 0.00 0.00 37.98 4.49
1083 1196 2.609459 CAGAGTGCTCTTTGTTCACGTT 59.391 45.455 0.00 0.00 37.98 3.99
1084 1197 2.866762 AGAGTGCTCTTTGTTCACGTTC 59.133 45.455 0.00 0.00 36.31 3.95
1151 1264 3.885901 ACAGGAAACAAGAAAGAGAAGGC 59.114 43.478 0.00 0.00 0.00 4.35
1174 1288 1.070786 AAAAAGCTCGTCTGCCGGA 59.929 52.632 5.05 0.00 37.11 5.14
1262 1382 2.741092 GACCTTGACGTGGCCTCA 59.259 61.111 3.32 0.00 0.00 3.86
1292 1412 2.140792 GGAGGCCGCCAAGAGGATA 61.141 63.158 22.24 0.00 36.89 2.59
1325 1445 3.069980 GCTGGACCTGCTCGACGAT 62.070 63.158 15.65 0.00 0.00 3.73
1871 3105 7.283354 CCTTTGGGGATGTAAAGTTTCTAGATC 59.717 40.741 0.00 0.00 37.23 2.75
1942 3799 5.107530 GCTTCGAATGAATGATGTAGAGAGC 60.108 44.000 0.00 0.00 32.61 4.09
1994 3854 9.517868 AATCTCTCATGGATTCCATAAGAAATC 57.482 33.333 17.57 0.00 43.15 2.17
2003 3868 7.884877 TGGATTCCATAAGAAATCGCTTCATAT 59.115 33.333 0.00 0.00 38.21 1.78
2004 3869 9.383519 GGATTCCATAAGAAATCGCTTCATATA 57.616 33.333 0.00 0.00 38.21 0.86
2019 3884 9.981114 TCGCTTCATATATTTCATGTTCTTCTA 57.019 29.630 0.00 0.00 0.00 2.10
2177 4065 2.029470 TGGCCGTTGATGGAAATGTTTC 60.029 45.455 0.00 0.00 36.46 2.78
2183 4071 5.389725 CCGTTGATGGAAATGTTTCAAATGC 60.390 40.000 7.69 0.00 38.92 3.56
2291 4205 1.150081 CTGCCCACCCAGATGGATC 59.850 63.158 0.00 0.00 43.02 3.36
2323 4242 5.121454 GCTTCTAGTGTTCCTCATGTTTCTG 59.879 44.000 0.00 0.00 0.00 3.02
2327 4246 7.152645 TCTAGTGTTCCTCATGTTTCTGTTAC 58.847 38.462 0.00 0.00 0.00 2.50
2332 4251 7.432252 GTGTTCCTCATGTTTCTGTTACTTTTG 59.568 37.037 0.00 0.00 0.00 2.44
2333 4252 7.338196 TGTTCCTCATGTTTCTGTTACTTTTGA 59.662 33.333 0.00 0.00 0.00 2.69
2335 4254 8.287439 TCCTCATGTTTCTGTTACTTTTGAAA 57.713 30.769 0.00 0.00 0.00 2.69
2336 4255 8.744652 TCCTCATGTTTCTGTTACTTTTGAAAA 58.255 29.630 0.00 0.00 31.47 2.29
2337 4256 9.364989 CCTCATGTTTCTGTTACTTTTGAAAAA 57.635 29.630 0.00 0.00 31.47 1.94
2367 4286 4.036518 AGATAGGCTGACAATTCTCCAGT 58.963 43.478 0.00 0.00 0.00 4.00
2437 4560 3.756933 AAAACAAGTGCATCTGCCAAT 57.243 38.095 0.00 0.00 41.18 3.16
2518 4953 1.276421 AGCTGTCTTCGTGTAGCCATT 59.724 47.619 0.00 0.00 36.86 3.16
2524 4959 3.994392 GTCTTCGTGTAGCCATTCAAAGA 59.006 43.478 0.00 0.00 0.00 2.52
2635 5087 6.200475 GGATGTGCCGTCTTAGTAAAGTAATC 59.800 42.308 0.00 0.00 34.13 1.75
2636 5088 5.413499 TGTGCCGTCTTAGTAAAGTAATCC 58.587 41.667 0.00 0.00 34.13 3.01
2637 5089 4.501921 GTGCCGTCTTAGTAAAGTAATCCG 59.498 45.833 0.00 0.00 34.13 4.18
2695 5147 1.300620 TCGCGTCAAAGTGTCTGGG 60.301 57.895 5.77 0.00 0.00 4.45
2716 5168 2.234143 CTCTGGACACACACTCTCTCA 58.766 52.381 0.00 0.00 0.00 3.27
2717 5169 2.625314 CTCTGGACACACACTCTCTCAA 59.375 50.000 0.00 0.00 0.00 3.02
2718 5170 3.031013 TCTGGACACACACTCTCTCAAA 58.969 45.455 0.00 0.00 0.00 2.69
2719 5171 3.643320 TCTGGACACACACTCTCTCAAAT 59.357 43.478 0.00 0.00 0.00 2.32
2720 5172 4.832823 TCTGGACACACACTCTCTCAAATA 59.167 41.667 0.00 0.00 0.00 1.40
2721 5173 5.304357 TCTGGACACACACTCTCTCAAATAA 59.696 40.000 0.00 0.00 0.00 1.40
2722 5174 5.297547 TGGACACACACTCTCTCAAATAAC 58.702 41.667 0.00 0.00 0.00 1.89
2723 5175 5.070446 TGGACACACACTCTCTCAAATAACT 59.930 40.000 0.00 0.00 0.00 2.24
2726 5178 7.291411 ACACACACTCTCTCAAATAACTACT 57.709 36.000 0.00 0.00 0.00 2.57
2727 5179 7.371936 ACACACACTCTCTCAAATAACTACTC 58.628 38.462 0.00 0.00 0.00 2.59
2731 5183 8.908903 CACACTCTCTCAAATAACTACTCCTAT 58.091 37.037 0.00 0.00 0.00 2.57
2747 5203 8.662255 ACTACTCCTATAGTATAGACACAGCTT 58.338 37.037 17.31 0.00 39.96 3.74
2749 5205 7.519057 ACTCCTATAGTATAGACACAGCTTGA 58.481 38.462 17.31 3.54 36.36 3.02
2751 5207 8.941995 TCCTATAGTATAGACACAGCTTGATT 57.058 34.615 17.31 0.00 0.00 2.57
2752 5208 8.797438 TCCTATAGTATAGACACAGCTTGATTG 58.203 37.037 17.31 0.00 0.00 2.67
2765 5221 3.761311 CTTGATTGAAGCTGCTTCCTC 57.239 47.619 32.70 27.87 39.51 3.71
2766 5222 3.345414 CTTGATTGAAGCTGCTTCCTCT 58.655 45.455 32.70 20.16 39.51 3.69
2767 5223 2.708051 TGATTGAAGCTGCTTCCTCTG 58.292 47.619 32.70 0.00 39.51 3.35
2768 5224 2.039480 TGATTGAAGCTGCTTCCTCTGT 59.961 45.455 32.70 17.44 39.51 3.41
2769 5225 3.261643 TGATTGAAGCTGCTTCCTCTGTA 59.738 43.478 32.70 15.29 39.51 2.74
2770 5226 3.769739 TTGAAGCTGCTTCCTCTGTAA 57.230 42.857 32.70 19.62 39.51 2.41
2771 5227 3.769739 TGAAGCTGCTTCCTCTGTAAA 57.230 42.857 32.70 13.95 39.51 2.01
2772 5228 4.292186 TGAAGCTGCTTCCTCTGTAAAT 57.708 40.909 32.70 0.71 39.51 1.40
2773 5229 5.420725 TGAAGCTGCTTCCTCTGTAAATA 57.579 39.130 32.70 12.64 39.51 1.40
2774 5230 5.804639 TGAAGCTGCTTCCTCTGTAAATAA 58.195 37.500 32.70 12.17 39.51 1.40
2775 5231 6.237901 TGAAGCTGCTTCCTCTGTAAATAAA 58.762 36.000 32.70 11.99 39.51 1.40
2776 5232 6.886459 TGAAGCTGCTTCCTCTGTAAATAAAT 59.114 34.615 32.70 0.00 39.51 1.40
2777 5233 8.046708 TGAAGCTGCTTCCTCTGTAAATAAATA 58.953 33.333 32.70 11.01 39.51 1.40
2778 5234 8.986929 AAGCTGCTTCCTCTGTAAATAAATAT 57.013 30.769 9.53 0.00 0.00 1.28
2796 5252 9.862371 AATAAATATATAAGACGTCTGCAGAGG 57.138 33.333 29.78 29.78 36.14 3.69
2797 5253 5.906113 ATATATAAGACGTCTGCAGAGGG 57.094 43.478 33.05 23.02 34.50 4.30
2808 5264 2.012673 CTGCAGAGGGAGTAATTGTGC 58.987 52.381 8.42 0.00 0.00 4.57
2833 5289 0.038744 ATTGGGACAGCCAGACAAGG 59.961 55.000 0.00 0.00 42.39 3.61
2834 5290 2.067932 TTGGGACAGCCAGACAAGGG 62.068 60.000 0.00 0.00 42.39 3.95
2844 5300 3.152341 GCCAGACAAGGGATTATGGATG 58.848 50.000 0.00 0.00 0.00 3.51
2997 5458 0.543410 ACTGGGTATGACGTGGTGGA 60.543 55.000 0.00 0.00 0.00 4.02
3040 5501 1.842381 CTTTCGGGCCTGTCCTTCCT 61.842 60.000 12.43 0.00 34.39 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 1.135333 TCGTCAAAAACCAACTTGGGC 59.865 47.619 12.62 0.00 43.37 5.36
50 51 7.670009 TTATCCCGAATAAACTCGTCAAAAA 57.330 32.000 0.00 0.00 37.11 1.94
54 55 5.808540 CACTTTATCCCGAATAAACTCGTCA 59.191 40.000 0.00 0.00 35.38 4.35
82 83 2.438975 ACGTGATGCCATGCCCTG 60.439 61.111 0.00 0.00 32.58 4.45
144 155 5.925969 CGATCACTTGCAAAAATAAACCCTT 59.074 36.000 0.00 0.00 0.00 3.95
145 156 5.010617 ACGATCACTTGCAAAAATAAACCCT 59.989 36.000 0.00 0.00 0.00 4.34
146 157 5.118510 CACGATCACTTGCAAAAATAAACCC 59.881 40.000 0.00 0.00 0.00 4.11
147 158 5.388371 GCACGATCACTTGCAAAAATAAACC 60.388 40.000 0.00 0.00 40.31 3.27
152 163 2.610232 GGGCACGATCACTTGCAAAAAT 60.610 45.455 0.00 0.00 41.96 1.82
153 164 1.269517 GGGCACGATCACTTGCAAAAA 60.270 47.619 0.00 0.00 41.96 1.94
154 165 0.313672 GGGCACGATCACTTGCAAAA 59.686 50.000 0.00 0.00 41.96 2.44
155 166 0.537143 AGGGCACGATCACTTGCAAA 60.537 50.000 0.00 0.00 41.96 3.68
156 167 0.955428 GAGGGCACGATCACTTGCAA 60.955 55.000 11.79 0.00 41.96 4.08
157 168 1.375908 GAGGGCACGATCACTTGCA 60.376 57.895 11.79 0.00 41.96 4.08
159 170 1.079819 ACGAGGGCACGATCACTTG 60.080 57.895 9.99 0.00 37.03 3.16
185 209 6.183361 CCATAGTATGCTTTTCTGAGGGTAGT 60.183 42.308 4.47 0.00 0.00 2.73
186 210 6.226787 CCATAGTATGCTTTTCTGAGGGTAG 58.773 44.000 4.47 0.00 0.00 3.18
190 214 3.496130 CGCCATAGTATGCTTTTCTGAGG 59.504 47.826 4.47 0.00 0.00 3.86
192 216 4.137116 ACGCCATAGTATGCTTTTCTGA 57.863 40.909 4.47 0.00 0.00 3.27
193 217 5.984233 TTACGCCATAGTATGCTTTTCTG 57.016 39.130 4.47 0.00 0.00 3.02
195 219 6.147164 TGCTATTACGCCATAGTATGCTTTTC 59.853 38.462 4.47 0.00 0.00 2.29
201 225 7.492344 TCATTCATGCTATTACGCCATAGTATG 59.508 37.037 18.77 18.77 44.84 2.39
203 227 6.930731 TCATTCATGCTATTACGCCATAGTA 58.069 36.000 3.97 0.27 0.00 1.82
204 228 5.793817 TCATTCATGCTATTACGCCATAGT 58.206 37.500 3.97 0.00 0.00 2.12
205 229 6.726258 TTCATTCATGCTATTACGCCATAG 57.274 37.500 0.00 0.00 0.00 2.23
209 233 5.611796 TCATTCATTCATGCTATTACGCC 57.388 39.130 0.00 0.00 0.00 5.68
224 248 9.846248 GTGCTTGACTTTTATTAGTTCATTCAT 57.154 29.630 0.00 0.00 0.00 2.57
227 252 7.305474 CGGTGCTTGACTTTTATTAGTTCATT 58.695 34.615 0.00 0.00 0.00 2.57
260 285 4.153117 GCTCTATTTTATCATGGGTGCGAG 59.847 45.833 0.00 0.00 0.00 5.03
266 291 5.583854 CGATCTGGCTCTATTTTATCATGGG 59.416 44.000 0.00 0.00 0.00 4.00
288 313 2.465860 TTAGCAGCTAGTTTTGCCGA 57.534 45.000 1.49 0.36 41.17 5.54
290 315 3.081804 TCCTTTAGCAGCTAGTTTTGCC 58.918 45.455 1.49 0.00 41.17 4.52
291 316 4.476862 GTTCCTTTAGCAGCTAGTTTTGC 58.523 43.478 1.49 7.62 40.57 3.68
298 323 4.638304 AGTTTTCGTTCCTTTAGCAGCTA 58.362 39.130 0.00 0.00 0.00 3.32
308 333 5.642491 GTGGCTTAGATTAGTTTTCGTTCCT 59.358 40.000 0.00 0.00 0.00 3.36
309 334 5.445540 CGTGGCTTAGATTAGTTTTCGTTCC 60.446 44.000 0.00 0.00 0.00 3.62
310 335 5.119743 ACGTGGCTTAGATTAGTTTTCGTTC 59.880 40.000 0.00 0.00 0.00 3.95
325 350 0.179015 TGGCCTTTGAACGTGGCTTA 60.179 50.000 12.96 1.41 45.45 3.09
326 351 1.454847 TGGCCTTTGAACGTGGCTT 60.455 52.632 12.96 0.00 45.45 4.35
336 361 1.903404 GGGTGAGTGGTGGCCTTTG 60.903 63.158 3.32 0.00 0.00 2.77
355 385 2.125106 GATGGGTCGTGGCCTCAC 60.125 66.667 3.32 1.48 40.36 3.51
356 386 3.399181 GGATGGGTCGTGGCCTCA 61.399 66.667 3.32 0.00 0.00 3.86
357 387 4.530857 CGGATGGGTCGTGGCCTC 62.531 72.222 3.32 0.00 0.00 4.70
383 423 1.270907 ATCTATCGGCCATCTGGGTC 58.729 55.000 2.24 0.00 39.65 4.46
392 432 5.049543 GTCCGTCTATGTATATCTATCGGCC 60.050 48.000 0.00 0.00 36.16 6.13
394 434 5.177142 CGGTCCGTCTATGTATATCTATCGG 59.823 48.000 2.08 0.00 37.29 4.18
404 444 1.477553 AAAGGCGGTCCGTCTATGTA 58.522 50.000 20.78 0.00 42.48 2.29
405 445 0.611714 AAAAGGCGGTCCGTCTATGT 59.388 50.000 20.78 4.71 42.48 2.29
406 446 1.734163 AAAAAGGCGGTCCGTCTATG 58.266 50.000 20.78 0.00 42.48 2.23
407 447 2.498885 ACTAAAAAGGCGGTCCGTCTAT 59.501 45.455 20.78 8.67 42.48 1.98
408 448 1.895131 ACTAAAAAGGCGGTCCGTCTA 59.105 47.619 20.78 1.78 42.48 2.59
409 449 0.683412 ACTAAAAAGGCGGTCCGTCT 59.317 50.000 13.98 13.98 46.41 4.18
410 450 1.516161 AACTAAAAAGGCGGTCCGTC 58.484 50.000 8.12 8.12 37.47 4.79
411 451 1.605232 CAAACTAAAAAGGCGGTCCGT 59.395 47.619 13.94 0.00 37.47 4.69
412 452 1.664874 GCAAACTAAAAAGGCGGTCCG 60.665 52.381 6.99 6.99 37.47 4.79
413 453 1.338655 TGCAAACTAAAAAGGCGGTCC 59.661 47.619 0.00 0.00 0.00 4.46
442 488 8.455903 TTTTCCTGCCATCAGATTAGATTTAG 57.544 34.615 0.00 0.00 42.95 1.85
456 502 4.524802 TGACCTGATATTTTCCTGCCAT 57.475 40.909 0.00 0.00 0.00 4.40
473 519 2.257034 CGACGGCTACTAAACTTGACC 58.743 52.381 0.00 0.00 0.00 4.02
562 616 2.591311 TTCGTTCGTTCGCTGGCAC 61.591 57.895 0.00 0.00 0.00 5.01
563 617 2.279584 TTCGTTCGTTCGCTGGCA 60.280 55.556 0.00 0.00 0.00 4.92
565 619 2.012414 TCGTTCGTTCGTTCGCTGG 61.012 57.895 2.67 0.00 0.00 4.85
566 620 1.125266 GTCGTTCGTTCGTTCGCTG 59.875 57.895 2.67 0.00 0.00 5.18
567 621 2.352333 CGTCGTTCGTTCGTTCGCT 61.352 57.895 2.67 0.00 34.52 4.93
569 623 1.254986 TGTCGTCGTTCGTTCGTTCG 61.255 55.000 0.00 8.18 40.80 3.95
571 625 1.267365 TTTGTCGTCGTTCGTTCGTT 58.733 45.000 0.00 0.00 40.80 3.85
572 626 1.449418 GATTTGTCGTCGTTCGTTCGT 59.551 47.619 0.00 0.00 40.80 3.85
573 627 1.712350 AGATTTGTCGTCGTTCGTTCG 59.288 47.619 0.00 0.08 40.80 3.95
574 628 2.222007 CGAGATTTGTCGTCGTTCGTTC 60.222 50.000 0.00 0.00 40.80 3.95
653 711 2.039137 GGAAGGAGGACCCGGAGT 59.961 66.667 0.73 0.00 40.87 3.85
655 713 1.886730 ATCTGGAAGGAGGACCCGGA 61.887 60.000 0.73 0.00 40.87 5.14
825 920 2.184579 GTGGGCGGAGTGCTACTC 59.815 66.667 7.52 7.52 44.32 2.59
875 984 4.409588 CTCGTGCGTGCGGTTTCG 62.410 66.667 1.42 0.00 39.81 3.46
876 985 3.335534 ACTCGTGCGTGCGGTTTC 61.336 61.111 1.42 0.00 0.00 2.78
882 991 1.772063 AAAAGACCACTCGTGCGTGC 61.772 55.000 0.00 0.00 33.60 5.34
883 992 0.655733 AAAAAGACCACTCGTGCGTG 59.344 50.000 0.00 0.00 34.71 5.34
884 993 0.655733 CAAAAAGACCACTCGTGCGT 59.344 50.000 0.00 0.00 0.00 5.24
897 1010 1.000717 CAGGGGGTTACGTGCAAAAAG 60.001 52.381 0.00 0.00 0.00 2.27
898 1011 1.033574 CAGGGGGTTACGTGCAAAAA 58.966 50.000 0.00 0.00 0.00 1.94
906 1019 1.408453 GGATCTCCCAGGGGGTTACG 61.408 65.000 4.81 0.00 44.74 3.18
1019 1132 3.525862 ACAGGATGGGAGAGAAAAGAGT 58.474 45.455 0.00 0.00 43.62 3.24
1131 1244 4.140536 CTGCCTTCTCTTTCTTGTTTCCT 58.859 43.478 0.00 0.00 0.00 3.36
1942 3799 6.810888 TTTTTCTTCAGATGACTTTTTGCG 57.189 33.333 0.00 0.00 0.00 4.85
2033 3898 9.469807 TGTTTATTTTCTTGCGTCACATAAAAT 57.530 25.926 0.00 0.00 37.66 1.82
2070 3951 5.620011 GCCGAAATAAAAGATACTTTAGCGC 59.380 40.000 0.00 0.00 0.00 5.92
2091 3972 4.108699 TCAAGCATATTTTTCTTGGCCG 57.891 40.909 0.00 0.00 38.13 6.13
2177 4065 1.137404 GCAGGCACCGTAGCATTTG 59.863 57.895 0.00 0.00 35.83 2.32
2183 4071 2.357034 AACGTGCAGGCACCGTAG 60.357 61.111 17.92 7.10 43.49 3.51
2210 4099 4.485163 GTTTGTCATGTCATTAGGTTGGC 58.515 43.478 0.00 0.00 0.00 4.52
2212 4104 5.964958 AGGTTTGTCATGTCATTAGGTTG 57.035 39.130 0.00 0.00 0.00 3.77
2291 4205 5.083533 AGGAACACTAGAAGCTTCTGATG 57.916 43.478 34.26 30.39 38.19 3.07
2336 4255 8.864087 AGAATTGTCAGCCTATCTTTTCTTTTT 58.136 29.630 0.00 0.00 0.00 1.94
2337 4256 8.414629 AGAATTGTCAGCCTATCTTTTCTTTT 57.585 30.769 0.00 0.00 0.00 2.27
2338 4257 7.121907 GGAGAATTGTCAGCCTATCTTTTCTTT 59.878 37.037 4.83 0.00 0.00 2.52
2367 4286 3.335183 TCCACCCCATCCAAGAATAAACA 59.665 43.478 0.00 0.00 0.00 2.83
2465 4622 9.973450 GAAGATTCTCTGTACATATAGCAGAAA 57.027 33.333 0.00 0.00 38.58 2.52
2467 4624 8.697507 TGAAGATTCTCTGTACATATAGCAGA 57.302 34.615 0.00 0.00 37.63 4.26
2468 4625 9.409312 CTTGAAGATTCTCTGTACATATAGCAG 57.591 37.037 0.00 0.00 0.00 4.24
2469 4626 8.363390 CCTTGAAGATTCTCTGTACATATAGCA 58.637 37.037 0.00 0.00 0.00 3.49
2470 4627 8.580720 TCCTTGAAGATTCTCTGTACATATAGC 58.419 37.037 0.00 0.00 0.00 2.97
2475 4672 7.289782 AGCTATCCTTGAAGATTCTCTGTACAT 59.710 37.037 0.00 0.00 0.00 2.29
2614 5066 4.501921 CGGATTACTTTACTAAGACGGCAC 59.498 45.833 0.00 0.00 35.30 5.01
2637 5089 4.383774 TCGTGACAAAATCGATGTGTTC 57.616 40.909 14.33 10.55 0.00 3.18
2695 5147 0.965439 AGAGAGTGTGTGTCCAGAGC 59.035 55.000 0.00 0.00 0.00 4.09
2719 5171 9.941325 GCTGTGTCTATACTATAGGAGTAGTTA 57.059 37.037 4.43 0.00 43.99 2.24
2720 5172 8.662255 AGCTGTGTCTATACTATAGGAGTAGTT 58.338 37.037 4.43 0.00 43.99 2.24
2721 5173 8.209802 AGCTGTGTCTATACTATAGGAGTAGT 57.790 38.462 4.43 0.00 43.99 2.73
2722 5174 8.941977 CAAGCTGTGTCTATACTATAGGAGTAG 58.058 40.741 4.43 3.73 43.99 2.57
2723 5175 8.657712 TCAAGCTGTGTCTATACTATAGGAGTA 58.342 37.037 4.43 0.00 44.87 2.59
2726 5178 8.797438 CAATCAAGCTGTGTCTATACTATAGGA 58.203 37.037 4.43 0.00 0.00 2.94
2727 5179 8.797438 TCAATCAAGCTGTGTCTATACTATAGG 58.203 37.037 4.43 0.00 0.00 2.57
2747 5203 2.039480 ACAGAGGAAGCAGCTTCAATCA 59.961 45.455 31.68 0.00 41.77 2.57
2749 5205 2.875094 ACAGAGGAAGCAGCTTCAAT 57.125 45.000 31.68 21.53 41.77 2.57
2751 5207 3.769739 TTTACAGAGGAAGCAGCTTCA 57.230 42.857 31.68 11.47 41.77 3.02
2752 5208 6.743575 TTTATTTACAGAGGAAGCAGCTTC 57.256 37.500 24.93 24.93 39.52 3.86
2770 5226 9.862371 CCTCTGCAGACGTCTTATATATTTATT 57.138 33.333 17.26 0.00 0.00 1.40
2771 5227 8.470805 CCCTCTGCAGACGTCTTATATATTTAT 58.529 37.037 17.26 0.00 0.00 1.40
2772 5228 7.668469 TCCCTCTGCAGACGTCTTATATATTTA 59.332 37.037 17.26 0.00 0.00 1.40
2773 5229 6.493802 TCCCTCTGCAGACGTCTTATATATTT 59.506 38.462 17.26 0.00 0.00 1.40
2774 5230 6.010850 TCCCTCTGCAGACGTCTTATATATT 58.989 40.000 17.26 0.00 0.00 1.28
2775 5231 5.571285 TCCCTCTGCAGACGTCTTATATAT 58.429 41.667 17.26 0.00 0.00 0.86
2776 5232 4.981812 TCCCTCTGCAGACGTCTTATATA 58.018 43.478 17.26 0.00 0.00 0.86
2777 5233 3.823873 CTCCCTCTGCAGACGTCTTATAT 59.176 47.826 17.26 0.00 0.00 0.86
2778 5234 3.215151 CTCCCTCTGCAGACGTCTTATA 58.785 50.000 17.26 4.12 0.00 0.98
2779 5235 2.028130 CTCCCTCTGCAGACGTCTTAT 58.972 52.381 17.26 0.00 0.00 1.73
2780 5236 1.271982 ACTCCCTCTGCAGACGTCTTA 60.272 52.381 17.26 7.24 0.00 2.10
2781 5237 0.540830 ACTCCCTCTGCAGACGTCTT 60.541 55.000 17.26 0.00 0.00 3.01
2782 5238 0.328592 TACTCCCTCTGCAGACGTCT 59.671 55.000 13.74 13.58 0.00 4.18
2783 5239 1.174783 TTACTCCCTCTGCAGACGTC 58.825 55.000 13.74 7.70 0.00 4.34
2784 5240 1.853963 ATTACTCCCTCTGCAGACGT 58.146 50.000 13.74 10.04 0.00 4.34
2785 5241 2.093973 ACAATTACTCCCTCTGCAGACG 60.094 50.000 13.74 9.20 0.00 4.18
2786 5242 3.265791 CACAATTACTCCCTCTGCAGAC 58.734 50.000 13.74 0.00 0.00 3.51
2787 5243 2.355108 GCACAATTACTCCCTCTGCAGA 60.355 50.000 17.19 17.19 0.00 4.26
2788 5244 2.012673 GCACAATTACTCCCTCTGCAG 58.987 52.381 7.63 7.63 0.00 4.41
2789 5245 1.350684 TGCACAATTACTCCCTCTGCA 59.649 47.619 0.00 0.00 0.00 4.41
2790 5246 2.113860 TGCACAATTACTCCCTCTGC 57.886 50.000 0.00 0.00 0.00 4.26
2791 5247 5.649782 ATTTTGCACAATTACTCCCTCTG 57.350 39.130 0.00 0.00 0.00 3.35
2792 5248 7.147846 CCAATATTTTGCACAATTACTCCCTCT 60.148 37.037 2.94 0.00 0.00 3.69
2793 5249 6.980397 CCAATATTTTGCACAATTACTCCCTC 59.020 38.462 2.94 0.00 0.00 4.30
2794 5250 6.127083 CCCAATATTTTGCACAATTACTCCCT 60.127 38.462 2.94 0.00 0.00 4.20
2795 5251 6.048509 CCCAATATTTTGCACAATTACTCCC 58.951 40.000 2.94 0.00 0.00 4.30
2796 5252 6.756542 GTCCCAATATTTTGCACAATTACTCC 59.243 38.462 2.94 0.00 0.00 3.85
2797 5253 7.319646 TGTCCCAATATTTTGCACAATTACTC 58.680 34.615 2.94 0.00 0.00 2.59
2808 5264 3.763360 TGTCTGGCTGTCCCAATATTTTG 59.237 43.478 0.00 0.00 44.81 2.44
2833 5289 4.636206 GGCGAGAAATACCATCCATAATCC 59.364 45.833 0.00 0.00 0.00 3.01
2834 5290 4.330074 CGGCGAGAAATACCATCCATAATC 59.670 45.833 0.00 0.00 0.00 1.75
2844 5300 0.179081 AGGCTTCGGCGAGAAATACC 60.179 55.000 10.46 6.75 42.91 2.73
2997 5458 1.826054 CGAGCGAGGGAGAGGACAT 60.826 63.158 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.