Multiple sequence alignment - TraesCS5A01G429700

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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 TraesCS5A01G429700 chr5A 100.000 3221 0 0 1 3221 613702797 613699577 0.000000e+00 5949.0
1 TraesCS5A01G429700 chr5A 79.526 1055 192 19 1098 2134 36331901 36330853 0.000000e+00 730.0
2 TraesCS5A01G429700 chr5B 90.449 3026 141 63 261 3221 606303475 606300533 0.000000e+00 3851.0
3 TraesCS5A01G429700 chr5B 79.186 1057 195 19 1098 2134 45394599 45393548 0.000000e+00 710.0
4 TraesCS5A01G429700 chr5B 93.496 123 4 3 1 120 606303606 606303485 2.550000e-41 180.0
5 TraesCS5A01G429700 chr5D 92.540 2520 117 38 738 3221 491529154 491526670 0.000000e+00 3546.0
6 TraesCS5A01G429700 chr5D 93.696 349 11 4 354 696 491529501 491529158 2.220000e-141 512.0
7 TraesCS5A01G429700 chr5D 95.522 201 7 2 1 200 491529744 491529545 1.440000e-83 320.0
8 TraesCS5A01G429700 chr5D 100.000 36 0 0 238 273 491529534 491529499 2.070000e-07 67.6
9 TraesCS5A01G429700 chr2B 93.860 798 36 3 1141 1938 298514427 298515211 0.000000e+00 1190.0
10 TraesCS5A01G429700 chr2B 93.217 457 31 0 1145 1601 105743366 105742910 0.000000e+00 673.0
11 TraesCS5A01G429700 chr4A 79.541 1046 185 21 1105 2134 597015730 597014698 0.000000e+00 719.0
12 TraesCS5A01G429700 chr4D 79.559 1042 182 23 1110 2134 6425451 6424424 0.000000e+00 715.0
13 TraesCS5A01G429700 chr4B 79.271 1042 195 16 1105 2134 11656198 11657230 0.000000e+00 708.0
14 TraesCS5A01G429700 chr3B 93.886 458 28 0 1144 1601 130115694 130115237 0.000000e+00 691.0
15 TraesCS5A01G429700 chr3B 76.714 992 192 30 1158 2125 795840863 795839887 1.710000e-142 516.0
16 TraesCS5A01G429700 chr3B 85.567 97 6 3 301 389 147718596 147718500 9.510000e-16 95.3
17 TraesCS5A01G429700 chr3A 77.149 989 186 32 1160 2125 724516582 724515611 3.660000e-149 538.0
18 TraesCS5A01G429700 chr6A 74.774 995 196 36 1160 2128 609158789 609157824 2.330000e-106 396.0
19 TraesCS5A01G429700 chr6B 74.472 995 193 42 1160 2125 704851666 704852628 1.090000e-99 374.0


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 TraesCS5A01G429700 chr5A 613699577 613702797 3220 True 5949.0 5949 100.0000 1 3221 1 chr5A.!!$R2 3220
1 TraesCS5A01G429700 chr5A 36330853 36331901 1048 True 730.0 730 79.5260 1098 2134 1 chr5A.!!$R1 1036
2 TraesCS5A01G429700 chr5B 606300533 606303606 3073 True 2015.5 3851 91.9725 1 3221 2 chr5B.!!$R2 3220
3 TraesCS5A01G429700 chr5B 45393548 45394599 1051 True 710.0 710 79.1860 1098 2134 1 chr5B.!!$R1 1036
4 TraesCS5A01G429700 chr5D 491526670 491529744 3074 True 1111.4 3546 95.4395 1 3221 4 chr5D.!!$R1 3220
5 TraesCS5A01G429700 chr2B 298514427 298515211 784 False 1190.0 1190 93.8600 1141 1938 1 chr2B.!!$F1 797
6 TraesCS5A01G429700 chr4A 597014698 597015730 1032 True 719.0 719 79.5410 1105 2134 1 chr4A.!!$R1 1029
7 TraesCS5A01G429700 chr4D 6424424 6425451 1027 True 715.0 715 79.5590 1110 2134 1 chr4D.!!$R1 1024
8 TraesCS5A01G429700 chr4B 11656198 11657230 1032 False 708.0 708 79.2710 1105 2134 1 chr4B.!!$F1 1029
9 TraesCS5A01G429700 chr3B 795839887 795840863 976 True 516.0 516 76.7140 1158 2125 1 chr3B.!!$R3 967
10 TraesCS5A01G429700 chr3A 724515611 724516582 971 True 538.0 538 77.1490 1160 2125 1 chr3A.!!$R1 965
11 TraesCS5A01G429700 chr6A 609157824 609158789 965 True 396.0 396 74.7740 1160 2128 1 chr6A.!!$R1 968
12 TraesCS5A01G429700 chr6B 704851666 704852628 962 False 374.0 374 74.4720 1160 2125 1 chr6B.!!$F1 965

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
218 224 0.036010 ACACTAGCAGGTGACCATGC 60.036 55.0 15.28 15.28 42.87 4.06 F
228 234 0.036732 GTGACCATGCCTCCACTTCA 59.963 55.0 0.00 0.00 0.00 3.02 F
2116 2175 0.040204 CCAGGAAGGGTTCATTGCCT 59.960 55.0 0.00 0.00 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2116 2175 0.325272 TTTGCAGGTATGTGGCCGTA 59.675 50.0 0.0 0.0 0.00 4.02 R
2187 2256 0.673022 CTTCCTCTTGCTCGCTGCTT 60.673 55.0 0.0 0.0 43.37 3.91 R
2994 3105 0.038159 ACTCGACTCAAAAGCCTCCG 60.038 55.0 0.0 0.0 0.00 4.63 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
32 35 5.771469 TGTGTTCAAATCAGCAATACTTGG 58.229 37.500 0.00 0.00 0.00 3.61
64 67 8.880991 TTATACTATGAGTTGGAGAGGGATAC 57.119 38.462 0.00 0.00 0.00 2.24
164 170 1.699083 TGAGGGTGATGCAGAGACAAA 59.301 47.619 0.00 0.00 0.00 2.83
195 201 0.535780 TGCCTCCACTTCAGTGCTTG 60.536 55.000 1.01 0.00 44.34 4.01
200 206 3.251004 CCTCCACTTCAGTGCTTGTTTAC 59.749 47.826 1.01 0.00 44.34 2.01
202 208 3.625764 TCCACTTCAGTGCTTGTTTACAC 59.374 43.478 1.01 0.00 44.34 2.90
204 210 4.814234 CCACTTCAGTGCTTGTTTACACTA 59.186 41.667 1.01 0.00 45.15 2.74
213 219 4.992381 CTTGTTTACACTAGCAGGTGAC 57.008 45.455 14.45 4.79 40.13 3.67
214 220 3.396260 TGTTTACACTAGCAGGTGACC 57.604 47.619 14.45 0.00 40.13 4.02
215 221 2.701423 TGTTTACACTAGCAGGTGACCA 59.299 45.455 3.63 4.27 40.13 4.02
216 222 3.326588 TGTTTACACTAGCAGGTGACCAT 59.673 43.478 3.63 0.00 40.13 3.55
217 223 3.610040 TTACACTAGCAGGTGACCATG 57.390 47.619 3.63 0.14 40.13 3.66
218 224 0.036010 ACACTAGCAGGTGACCATGC 60.036 55.000 15.28 15.28 42.87 4.06
219 225 0.745845 CACTAGCAGGTGACCATGCC 60.746 60.000 18.16 5.39 43.60 4.40
220 226 0.911525 ACTAGCAGGTGACCATGCCT 60.912 55.000 18.16 10.77 43.60 4.75
221 227 0.179062 CTAGCAGGTGACCATGCCTC 60.179 60.000 18.16 0.00 43.60 4.70
222 228 1.626356 TAGCAGGTGACCATGCCTCC 61.626 60.000 18.16 0.00 43.60 4.30
223 229 3.080641 CAGGTGACCATGCCTCCA 58.919 61.111 3.63 0.00 31.73 3.86
224 230 1.377725 CAGGTGACCATGCCTCCAC 60.378 63.158 3.63 0.00 31.73 4.02
225 231 1.539869 AGGTGACCATGCCTCCACT 60.540 57.895 3.63 0.00 0.00 4.00
226 232 1.136329 AGGTGACCATGCCTCCACTT 61.136 55.000 3.63 0.00 0.00 3.16
227 233 0.678048 GGTGACCATGCCTCCACTTC 60.678 60.000 0.00 0.00 0.00 3.01
228 234 0.036732 GTGACCATGCCTCCACTTCA 59.963 55.000 0.00 0.00 0.00 3.02
229 235 0.325933 TGACCATGCCTCCACTTCAG 59.674 55.000 0.00 0.00 0.00 3.02
230 236 0.326264 GACCATGCCTCCACTTCAGT 59.674 55.000 0.00 0.00 0.00 3.41
231 237 1.555075 GACCATGCCTCCACTTCAGTA 59.445 52.381 0.00 0.00 0.00 2.74
232 238 1.279271 ACCATGCCTCCACTTCAGTAC 59.721 52.381 0.00 0.00 0.00 2.73
233 239 1.407437 CCATGCCTCCACTTCAGTACC 60.407 57.143 0.00 0.00 0.00 3.34
234 240 1.278985 CATGCCTCCACTTCAGTACCA 59.721 52.381 0.00 0.00 0.00 3.25
235 241 0.976641 TGCCTCCACTTCAGTACCAG 59.023 55.000 0.00 0.00 0.00 4.00
236 242 0.391793 GCCTCCACTTCAGTACCAGC 60.392 60.000 0.00 0.00 0.00 4.85
277 283 6.596888 TGCCTGATTGATTTTGTTTTGTTTCA 59.403 30.769 0.00 0.00 0.00 2.69
278 284 6.906678 GCCTGATTGATTTTGTTTTGTTTCAC 59.093 34.615 0.00 0.00 0.00 3.18
284 290 7.769272 TGATTTTGTTTTGTTTCACCAGATC 57.231 32.000 0.00 0.00 0.00 2.75
292 298 7.717436 TGTTTTGTTTCACCAGATCACATAGTA 59.283 33.333 0.00 0.00 0.00 1.82
295 301 6.398095 TGTTTCACCAGATCACATAGTAGTG 58.602 40.000 0.00 0.00 40.85 2.74
297 303 3.384789 TCACCAGATCACATAGTAGTGCC 59.615 47.826 0.00 0.00 39.35 5.01
305 311 5.011090 TCACATAGTAGTGCCTGTTGATC 57.989 43.478 0.00 0.00 39.35 2.92
307 313 5.046663 TCACATAGTAGTGCCTGTTGATCAA 60.047 40.000 3.38 3.38 39.35 2.57
332 338 9.927081 AATACAATGATATAATCTCCATTCCCC 57.073 33.333 0.00 0.00 0.00 4.81
334 340 7.408543 ACAATGATATAATCTCCATTCCCCTG 58.591 38.462 0.00 0.00 0.00 4.45
336 342 5.675077 TGATATAATCTCCATTCCCCTGGA 58.325 41.667 0.00 0.00 43.09 3.86
342 348 2.587060 TCCATTCCCCTGGAGTACAT 57.413 50.000 0.00 0.00 40.43 2.29
343 349 2.408565 TCCATTCCCCTGGAGTACATC 58.591 52.381 0.00 0.00 40.43 3.06
344 350 2.126882 CCATTCCCCTGGAGTACATCA 58.873 52.381 0.00 0.00 38.69 3.07
345 351 2.158755 CCATTCCCCTGGAGTACATCAC 60.159 54.545 0.00 0.00 38.69 3.06
346 352 2.335681 TTCCCCTGGAGTACATCACA 57.664 50.000 0.00 0.00 31.21 3.58
347 353 1.866015 TCCCCTGGAGTACATCACAG 58.134 55.000 0.00 0.00 0.00 3.66
348 354 1.078823 TCCCCTGGAGTACATCACAGT 59.921 52.381 0.00 0.00 0.00 3.55
390 410 5.577100 AGGCGTATAATCATCTGGTAGGTA 58.423 41.667 0.00 0.00 0.00 3.08
394 414 6.807230 GCGTATAATCATCTGGTAGGTAGTTG 59.193 42.308 0.00 0.00 0.00 3.16
527 551 3.883997 TTTTTGCCGACCTGCATTC 57.116 47.368 0.00 0.00 41.70 2.67
532 556 1.243342 TGCCGACCTGCATTCAAAGG 61.243 55.000 0.00 0.00 36.04 3.11
550 574 6.240894 TCAAAGGAAAGTTGTGCATCTAGAT 58.759 36.000 0.00 0.00 0.00 1.98
552 576 4.775236 AGGAAAGTTGTGCATCTAGATCC 58.225 43.478 1.03 0.00 0.00 3.36
553 577 3.879892 GGAAAGTTGTGCATCTAGATCCC 59.120 47.826 1.03 0.00 0.00 3.85
554 578 4.384647 GGAAAGTTGTGCATCTAGATCCCT 60.385 45.833 1.03 0.00 0.00 4.20
555 579 5.163301 GGAAAGTTGTGCATCTAGATCCCTA 60.163 44.000 1.03 0.00 0.00 3.53
556 580 5.957771 AAGTTGTGCATCTAGATCCCTAA 57.042 39.130 1.03 0.00 0.00 2.69
561 585 5.614308 TGTGCATCTAGATCCCTAAATGTG 58.386 41.667 1.03 0.00 28.44 3.21
564 588 6.370994 GTGCATCTAGATCCCTAAATGTGATG 59.629 42.308 1.03 0.00 28.44 3.07
589 613 0.745486 TCCAGGATTCATGTGCTGCG 60.745 55.000 0.00 0.00 36.37 5.18
646 672 0.848735 ATACTCCATGGCCATGCTGT 59.151 50.000 36.08 32.91 37.49 4.40
677 703 4.382147 GGGACTCTGAATCAACTGTACTCC 60.382 50.000 0.00 0.00 0.00 3.85
696 722 5.426504 ACTCCATTTCAGTCATCACTCATC 58.573 41.667 0.00 0.00 0.00 2.92
697 723 5.046087 ACTCCATTTCAGTCATCACTCATCA 60.046 40.000 0.00 0.00 0.00 3.07
698 724 5.425630 TCCATTTCAGTCATCACTCATCAG 58.574 41.667 0.00 0.00 0.00 2.90
700 726 6.155049 TCCATTTCAGTCATCACTCATCAGTA 59.845 38.462 0.00 0.00 0.00 2.74
701 727 6.479331 CCATTTCAGTCATCACTCATCAGTAG 59.521 42.308 0.00 0.00 0.00 2.57
736 762 5.409520 TCAGCAAGTACAACACATCAAGATC 59.590 40.000 0.00 0.00 0.00 2.75
745 771 9.103048 GTACAACACATCAAGATCTTTTTAACG 57.897 33.333 4.86 0.00 0.00 3.18
746 772 7.703328 ACAACACATCAAGATCTTTTTAACGT 58.297 30.769 4.86 0.00 0.00 3.99
747 773 8.188139 ACAACACATCAAGATCTTTTTAACGTT 58.812 29.630 4.86 5.88 0.00 3.99
748 774 9.019764 CAACACATCAAGATCTTTTTAACGTTT 57.980 29.630 5.91 0.00 0.00 3.60
749 775 8.560576 ACACATCAAGATCTTTTTAACGTTTG 57.439 30.769 5.91 0.00 0.00 2.93
788 814 4.849813 ATCACTGGAACATTGGATCTGA 57.150 40.909 0.00 0.00 39.59 3.27
791 817 3.937706 CACTGGAACATTGGATCTGAGAC 59.062 47.826 0.00 0.00 38.20 3.36
830 856 4.272748 CACCATAGTCATCAAGCACATCAG 59.727 45.833 0.00 0.00 0.00 2.90
900 926 7.512746 AGGTATATATGCCTCCAGTACAAAGAA 59.487 37.037 16.02 0.00 38.64 2.52
915 941 6.753744 AGTACAAAGAATCGTACCGAATTACC 59.246 38.462 0.00 0.00 39.99 2.85
916 942 5.481105 ACAAAGAATCGTACCGAATTACCA 58.519 37.500 0.00 0.00 39.99 3.25
975 1004 3.615496 GGCAACAAATGATCAACTGATGC 59.385 43.478 23.40 23.40 36.99 3.91
980 1009 7.572353 GCAACAAATGATCAACTGATGCAAAAT 60.572 33.333 25.10 0.00 37.48 1.82
990 1019 7.140705 TCAACTGATGCAAAATAAGTCTGTTG 58.859 34.615 19.61 19.61 43.76 3.33
1033 1062 2.861730 TGGACCAGAGCCAGGAGA 59.138 61.111 0.00 0.00 0.00 3.71
2107 2166 1.988406 GTAGGACGCCAGGAAGGGT 60.988 63.158 0.00 0.00 38.09 4.34
2116 2175 0.040204 CCAGGAAGGGTTCATTGCCT 59.960 55.000 0.00 0.00 0.00 4.75
2138 2197 0.965439 GGCCACATACCTGCAAACAA 59.035 50.000 0.00 0.00 0.00 2.83
2139 2198 1.336795 GGCCACATACCTGCAAACAAC 60.337 52.381 0.00 0.00 0.00 3.32
2144 2213 4.217334 CCACATACCTGCAAACAACACATA 59.783 41.667 0.00 0.00 0.00 2.29
2145 2214 5.153513 CACATACCTGCAAACAACACATAC 58.846 41.667 0.00 0.00 0.00 2.39
2146 2215 4.083537 ACATACCTGCAAACAACACATACG 60.084 41.667 0.00 0.00 0.00 3.06
2147 2216 1.606668 ACCTGCAAACAACACATACGG 59.393 47.619 0.00 0.00 0.00 4.02
2148 2217 1.068610 CCTGCAAACAACACATACGGG 60.069 52.381 0.00 0.00 0.00 5.28
2149 2218 1.606668 CTGCAAACAACACATACGGGT 59.393 47.619 0.00 0.00 0.00 5.28
2150 2219 1.604755 TGCAAACAACACATACGGGTC 59.395 47.619 0.00 0.00 0.00 4.46
2152 2221 2.227865 GCAAACAACACATACGGGTCAT 59.772 45.455 0.00 0.00 0.00 3.06
2154 2223 4.670735 GCAAACAACACATACGGGTCATAC 60.671 45.833 0.00 0.00 0.00 2.39
2156 2225 4.274602 ACAACACATACGGGTCATACAA 57.725 40.909 0.00 0.00 0.00 2.41
2157 2226 3.998341 ACAACACATACGGGTCATACAAC 59.002 43.478 0.00 0.00 0.00 3.32
2158 2227 3.255969 ACACATACGGGTCATACAACC 57.744 47.619 0.00 0.00 38.69 3.77
2162 2231 2.888534 CGGGTCATACAACCGCGG 60.889 66.667 26.86 26.86 41.23 6.46
2163 2232 3.199891 GGGTCATACAACCGCGGC 61.200 66.667 28.58 5.70 40.46 6.53
2164 2233 3.560278 GGTCATACAACCGCGGCG 61.560 66.667 28.58 20.08 0.00 6.46
2182 2251 3.059386 GGCGCCATGAACGGGAAA 61.059 61.111 24.80 0.00 0.00 3.13
2184 2253 2.038269 GCGCCATGAACGGGAAAGA 61.038 57.895 0.00 0.00 0.00 2.52
2185 2254 1.982073 GCGCCATGAACGGGAAAGAG 61.982 60.000 0.00 0.00 0.00 2.85
2186 2255 1.803289 GCCATGAACGGGAAAGAGC 59.197 57.895 0.00 0.00 0.00 4.09
2187 2256 0.960364 GCCATGAACGGGAAAGAGCA 60.960 55.000 0.00 0.00 0.00 4.26
2188 2257 1.533625 CCATGAACGGGAAAGAGCAA 58.466 50.000 0.00 0.00 0.00 3.91
2190 2259 1.135575 CATGAACGGGAAAGAGCAAGC 60.136 52.381 0.00 0.00 0.00 4.01
2207 2297 2.105466 GCAGCGAGCAAGAGGAAGG 61.105 63.158 0.00 0.00 44.79 3.46
2211 2301 1.990060 CGAGCAAGAGGAAGGGGGA 60.990 63.158 0.00 0.00 0.00 4.81
2390 2489 3.926497 TCGGCGTCGAACAGTTTC 58.074 55.556 10.97 0.00 43.03 2.78
2412 2511 0.804989 CTTCTTGATGCCGTTGTCCC 59.195 55.000 0.00 0.00 0.00 4.46
2419 2518 2.281484 GCCGTTGTCCCTGAGCAA 60.281 61.111 0.00 0.00 0.00 3.91
2573 2672 1.210478 GCCATTGTTCAGGCCTCTCTA 59.790 52.381 0.00 0.00 45.18 2.43
2575 2674 2.420687 CCATTGTTCAGGCCTCTCTACC 60.421 54.545 0.00 0.00 0.00 3.18
2581 2680 2.007568 AGGCCTCTCTACCCTCCGA 61.008 63.158 0.00 0.00 0.00 4.55
2595 2694 1.402456 CCTCCGACGAACTGACGAAAT 60.402 52.381 0.00 0.00 37.99 2.17
2620 2722 3.471244 GATCTCTGGACGCGACGGG 62.471 68.421 15.93 10.72 0.00 5.28
2637 2739 0.324368 GGGTTGGGAATCCAGGAACC 60.324 60.000 15.06 15.06 45.04 3.62
2678 2780 2.282391 TCCGAACGGAGTCGGGAA 60.282 61.111 20.04 3.83 45.00 3.97
2679 2781 1.679977 TCCGAACGGAGTCGGGAAT 60.680 57.895 20.04 0.00 45.00 3.01
2714 2816 2.433436 TCGAGATTCAGTCGAACAGGA 58.567 47.619 0.00 0.00 43.26 3.86
2717 2819 3.119814 CGAGATTCAGTCGAACAGGAGAA 60.120 47.826 0.00 0.00 39.92 2.87
2719 2821 5.215252 AGATTCAGTCGAACAGGAGAAAA 57.785 39.130 0.00 0.00 32.81 2.29
2721 2823 2.739292 TCAGTCGAACAGGAGAAAACG 58.261 47.619 0.00 0.00 0.00 3.60
2725 2827 1.413445 TCGAACAGGAGAAAACGGGAA 59.587 47.619 0.00 0.00 0.00 3.97
2726 2828 2.158928 TCGAACAGGAGAAAACGGGAAA 60.159 45.455 0.00 0.00 0.00 3.13
2727 2829 2.032290 CGAACAGGAGAAAACGGGAAAC 60.032 50.000 0.00 0.00 0.00 2.78
2729 2831 3.007473 ACAGGAGAAAACGGGAAACAA 57.993 42.857 0.00 0.00 0.00 2.83
2730 2832 3.562182 ACAGGAGAAAACGGGAAACAAT 58.438 40.909 0.00 0.00 0.00 2.71
2731 2833 3.317993 ACAGGAGAAAACGGGAAACAATG 59.682 43.478 0.00 0.00 0.00 2.82
2740 2846 3.370231 GAAACAATGCCGGGCGGT 61.370 61.111 15.40 9.73 37.65 5.68
2777 2883 1.553704 GCGGAGTATAAATCGGGGGAT 59.446 52.381 0.00 0.00 0.00 3.85
2907 3013 2.243221 ACAGATGGGGAAGAAAGGGATG 59.757 50.000 0.00 0.00 0.00 3.51
2979 3090 2.158813 AGGCAAGAAACGAAACAGAGGA 60.159 45.455 0.00 0.00 0.00 3.71
2992 3103 4.576330 AACAGAGGAAGGTATGGAAAGG 57.424 45.455 0.00 0.00 0.00 3.11
2994 3105 1.847088 AGAGGAAGGTATGGAAAGGGC 59.153 52.381 0.00 0.00 0.00 5.19
2995 3106 0.546598 AGGAAGGTATGGAAAGGGCG 59.453 55.000 0.00 0.00 0.00 6.13
3032 3143 2.073816 GTTGAATCCGGCGAAAGAGAA 58.926 47.619 9.30 0.00 0.00 2.87
3033 3144 2.010145 TGAATCCGGCGAAAGAGAAG 57.990 50.000 9.30 0.00 0.00 2.85
3035 3146 0.902531 AATCCGGCGAAAGAGAAGGA 59.097 50.000 9.30 0.00 0.00 3.36
3036 3147 0.461961 ATCCGGCGAAAGAGAAGGAG 59.538 55.000 9.30 0.00 0.00 3.69
3037 3148 0.611062 TCCGGCGAAAGAGAAGGAGA 60.611 55.000 9.30 0.00 0.00 3.71
3050 3161 5.501156 AGAGAAGGAGAGAAAGAGAGAGTC 58.499 45.833 0.00 0.00 0.00 3.36
3052 3163 3.992943 AGGAGAGAAAGAGAGAGTCGA 57.007 47.619 0.00 0.00 0.00 4.20
3053 3164 3.873910 AGGAGAGAAAGAGAGAGTCGAG 58.126 50.000 0.00 0.00 0.00 4.04
3054 3165 2.943033 GGAGAGAAAGAGAGAGTCGAGG 59.057 54.545 0.00 0.00 0.00 4.63
3055 3166 2.354821 GAGAGAAAGAGAGAGTCGAGGC 59.645 54.545 0.00 0.00 0.00 4.70
3056 3167 2.088423 GAGAAAGAGAGAGTCGAGGCA 58.912 52.381 0.00 0.00 0.00 4.75
3057 3168 2.091541 AGAAAGAGAGAGTCGAGGCAG 58.908 52.381 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 35 8.662781 TCTCCAACTCATAGTATAAAATGCAC 57.337 34.615 0.00 0.00 0.00 4.57
122 128 5.067936 TCAACAAACGAACACCCAACATATT 59.932 36.000 0.00 0.00 0.00 1.28
164 170 0.837691 TGGAGGCATGGACACTCTGT 60.838 55.000 0.00 0.00 0.00 3.41
195 201 3.396260 TGGTCACCTGCTAGTGTAAAC 57.604 47.619 0.00 0.00 38.91 2.01
200 206 0.745845 GGCATGGTCACCTGCTAGTG 60.746 60.000 15.32 0.74 38.45 2.74
202 208 0.179062 GAGGCATGGTCACCTGCTAG 60.179 60.000 15.32 0.00 36.05 3.42
203 209 1.626356 GGAGGCATGGTCACCTGCTA 61.626 60.000 15.32 0.00 40.94 3.49
204 210 2.673523 GAGGCATGGTCACCTGCT 59.326 61.111 15.32 4.73 36.05 4.24
206 212 1.377725 GTGGAGGCATGGTCACCTG 60.378 63.158 0.00 0.00 36.05 4.00
209 215 0.036732 TGAAGTGGAGGCATGGTCAC 59.963 55.000 0.00 0.00 0.00 3.67
210 216 0.325933 CTGAAGTGGAGGCATGGTCA 59.674 55.000 0.00 0.00 0.00 4.02
211 217 0.326264 ACTGAAGTGGAGGCATGGTC 59.674 55.000 0.00 0.00 0.00 4.02
212 218 1.279271 GTACTGAAGTGGAGGCATGGT 59.721 52.381 0.00 0.00 0.00 3.55
213 219 1.407437 GGTACTGAAGTGGAGGCATGG 60.407 57.143 0.00 0.00 0.00 3.66
214 220 1.278985 TGGTACTGAAGTGGAGGCATG 59.721 52.381 0.00 0.00 0.00 4.06
215 221 1.556911 CTGGTACTGAAGTGGAGGCAT 59.443 52.381 0.00 0.00 0.00 4.40
216 222 0.976641 CTGGTACTGAAGTGGAGGCA 59.023 55.000 0.00 0.00 0.00 4.75
217 223 0.391793 GCTGGTACTGAAGTGGAGGC 60.392 60.000 0.00 0.00 0.00 4.70
218 224 0.976641 TGCTGGTACTGAAGTGGAGG 59.023 55.000 0.00 0.00 0.00 4.30
219 225 1.895798 TCTGCTGGTACTGAAGTGGAG 59.104 52.381 0.00 0.00 34.25 3.86
220 226 2.009681 TCTGCTGGTACTGAAGTGGA 57.990 50.000 0.00 0.00 34.25 4.02
221 227 2.037772 AGTTCTGCTGGTACTGAAGTGG 59.962 50.000 0.00 0.00 34.25 4.00
222 228 3.393089 AGTTCTGCTGGTACTGAAGTG 57.607 47.619 0.00 0.00 34.25 3.16
223 229 3.134804 ACAAGTTCTGCTGGTACTGAAGT 59.865 43.478 0.00 0.00 34.25 3.01
224 230 3.733337 ACAAGTTCTGCTGGTACTGAAG 58.267 45.455 0.00 0.00 33.83 3.02
225 231 3.494398 GGACAAGTTCTGCTGGTACTGAA 60.494 47.826 0.00 0.00 29.75 3.02
226 232 2.037251 GGACAAGTTCTGCTGGTACTGA 59.963 50.000 0.00 0.00 29.75 3.41
227 233 2.224281 TGGACAAGTTCTGCTGGTACTG 60.224 50.000 0.00 0.00 32.91 2.74
228 234 2.047061 TGGACAAGTTCTGCTGGTACT 58.953 47.619 0.00 0.00 32.91 2.73
229 235 2.543777 TGGACAAGTTCTGCTGGTAC 57.456 50.000 0.00 0.00 32.29 3.34
230 236 2.224523 CCTTGGACAAGTTCTGCTGGTA 60.225 50.000 10.81 0.00 36.72 3.25
231 237 1.477558 CCTTGGACAAGTTCTGCTGGT 60.478 52.381 10.81 0.00 36.72 4.00
232 238 1.242076 CCTTGGACAAGTTCTGCTGG 58.758 55.000 10.81 0.00 36.72 4.85
233 239 1.605710 CACCTTGGACAAGTTCTGCTG 59.394 52.381 10.81 0.00 36.72 4.41
234 240 1.972872 CACCTTGGACAAGTTCTGCT 58.027 50.000 10.81 0.00 36.72 4.24
235 241 0.312102 GCACCTTGGACAAGTTCTGC 59.688 55.000 10.81 10.02 36.72 4.26
236 242 0.954452 GGCACCTTGGACAAGTTCTG 59.046 55.000 10.81 4.77 36.72 3.02
277 283 3.386078 CAGGCACTACTATGTGATCTGGT 59.614 47.826 0.00 0.00 40.12 4.00
278 284 3.386078 ACAGGCACTACTATGTGATCTGG 59.614 47.826 16.25 5.61 40.96 3.86
284 290 4.758688 TGATCAACAGGCACTACTATGTG 58.241 43.478 0.00 0.00 36.02 3.21
292 298 5.255687 TCATTGTATTGATCAACAGGCACT 58.744 37.500 11.07 0.00 43.88 4.40
307 313 9.301430 AGGGGAATGGAGATTATATCATTGTAT 57.699 33.333 0.00 0.00 30.97 2.29
329 335 1.573108 ACTGTGATGTACTCCAGGGG 58.427 55.000 0.00 0.00 30.65 4.79
330 336 3.366396 ACTACTGTGATGTACTCCAGGG 58.634 50.000 0.00 0.00 30.65 4.45
332 338 7.334844 TCAATACTACTGTGATGTACTCCAG 57.665 40.000 0.00 0.00 0.00 3.86
334 340 7.941919 TGATCAATACTACTGTGATGTACTCC 58.058 38.462 0.00 0.00 32.18 3.85
336 342 8.749354 TGTTGATCAATACTACTGTGATGTACT 58.251 33.333 12.12 0.00 32.18 2.73
337 343 8.926715 TGTTGATCAATACTACTGTGATGTAC 57.073 34.615 12.12 0.00 32.18 2.90
338 344 7.706607 GCTGTTGATCAATACTACTGTGATGTA 59.293 37.037 12.12 0.00 32.18 2.29
339 345 6.536582 GCTGTTGATCAATACTACTGTGATGT 59.463 38.462 12.12 0.00 32.18 3.06
340 346 6.536224 TGCTGTTGATCAATACTACTGTGATG 59.464 38.462 12.12 0.00 32.18 3.07
342 348 6.036577 TGCTGTTGATCAATACTACTGTGA 57.963 37.500 12.12 0.00 0.00 3.58
343 349 6.101997 TCTGCTGTTGATCAATACTACTGTG 58.898 40.000 12.12 0.00 0.00 3.66
344 350 6.286240 TCTGCTGTTGATCAATACTACTGT 57.714 37.500 12.12 0.00 0.00 3.55
345 351 5.752472 CCTCTGCTGTTGATCAATACTACTG 59.248 44.000 12.12 4.32 0.00 2.74
346 352 5.683509 GCCTCTGCTGTTGATCAATACTACT 60.684 44.000 12.12 0.00 33.53 2.57
347 353 4.509600 GCCTCTGCTGTTGATCAATACTAC 59.490 45.833 12.12 0.00 33.53 2.73
348 354 4.697514 GCCTCTGCTGTTGATCAATACTA 58.302 43.478 12.12 0.00 33.53 1.82
390 410 6.039717 TCTGCTGCTATTTTCAGTTTTCAACT 59.960 34.615 0.00 0.00 44.06 3.16
394 414 9.017669 CATTATCTGCTGCTATTTTCAGTTTTC 57.982 33.333 0.00 0.00 34.21 2.29
527 551 5.947228 TCTAGATGCACAACTTTCCTTTG 57.053 39.130 0.00 0.00 0.00 2.77
532 556 4.775236 AGGGATCTAGATGCACAACTTTC 58.225 43.478 23.71 5.79 0.00 2.62
550 574 3.181440 GGATCCAGCATCACATTTAGGGA 60.181 47.826 6.95 0.00 32.33 4.20
552 576 3.819337 CTGGATCCAGCATCACATTTAGG 59.181 47.826 28.45 0.93 37.24 2.69
553 577 3.819337 CCTGGATCCAGCATCACATTTAG 59.181 47.826 32.97 13.16 42.35 1.85
554 578 3.459227 TCCTGGATCCAGCATCACATTTA 59.541 43.478 32.97 7.23 42.35 1.40
555 579 2.242965 TCCTGGATCCAGCATCACATTT 59.757 45.455 32.97 0.00 42.35 2.32
556 580 1.848388 TCCTGGATCCAGCATCACATT 59.152 47.619 32.97 0.00 42.35 2.71
561 585 2.945080 TGAATCCTGGATCCAGCATC 57.055 50.000 32.97 27.03 42.35 3.91
564 588 2.228059 CACATGAATCCTGGATCCAGC 58.772 52.381 32.97 20.73 42.35 4.85
589 613 6.016276 CAGGATTTGGTTGGCAATATAGTACC 60.016 42.308 1.92 0.00 0.00 3.34
646 672 3.986435 TGATTCAGAGTCCCAGATCTCA 58.014 45.455 0.00 0.00 33.63 3.27
677 703 7.040494 ACTACTGATGAGTGATGACTGAAATG 58.960 38.462 0.00 0.00 33.21 2.32
788 814 4.588951 TGGTGTACAGTTCATTCAGAGTCT 59.411 41.667 0.00 0.00 0.00 3.24
791 817 6.634805 ACTATGGTGTACAGTTCATTCAGAG 58.365 40.000 0.00 0.00 0.00 3.35
830 856 6.256321 GGCATTTCACATGATATTCAAACACC 59.744 38.462 0.00 0.00 0.00 4.16
840 866 5.887035 TGTTCAGATGGCATTTCACATGATA 59.113 36.000 0.00 0.00 0.00 2.15
915 941 5.836821 TGGATCAGCAGTAGTTACTAGTG 57.163 43.478 19.70 19.70 39.58 2.74
916 942 6.852420 TTTGGATCAGCAGTAGTTACTAGT 57.148 37.500 0.00 0.00 34.13 2.57
1030 1059 2.883253 GCCGCTCTGCTCGTTCTC 60.883 66.667 0.00 0.00 0.00 2.87
2116 2175 0.325272 TTTGCAGGTATGTGGCCGTA 59.675 50.000 0.00 0.00 0.00 4.02
2138 2197 2.417651 CGGTTGTATGACCCGTATGTGT 60.418 50.000 0.00 0.00 36.28 3.72
2139 2198 2.198406 CGGTTGTATGACCCGTATGTG 58.802 52.381 0.00 0.00 36.28 3.21
2144 2213 2.125832 CGCGGTTGTATGACCCGT 60.126 61.111 0.00 0.00 43.56 5.28
2145 2214 2.888534 CCGCGGTTGTATGACCCG 60.889 66.667 19.50 0.00 44.46 5.28
2146 2215 3.199891 GCCGCGGTTGTATGACCC 61.200 66.667 28.70 0.93 36.28 4.46
2147 2216 3.560278 CGCCGCGGTTGTATGACC 61.560 66.667 28.70 5.16 36.31 4.02
2148 2217 3.560278 CCGCCGCGGTTGTATGAC 61.560 66.667 28.70 5.98 42.73 3.06
2149 2218 4.823419 CCCGCCGCGGTTGTATGA 62.823 66.667 29.21 0.00 46.80 2.15
2165 2234 3.051392 CTTTCCCGTTCATGGCGCC 62.051 63.158 22.73 22.73 0.00 6.53
2166 2235 1.982073 CTCTTTCCCGTTCATGGCGC 61.982 60.000 0.00 0.00 0.00 6.53
2167 2236 1.982073 GCTCTTTCCCGTTCATGGCG 61.982 60.000 0.00 0.00 0.00 5.69
2168 2237 0.960364 TGCTCTTTCCCGTTCATGGC 60.960 55.000 0.00 0.00 0.00 4.40
2177 2246 1.642952 CTCGCTGCTTGCTCTTTCCC 61.643 60.000 0.00 0.00 40.11 3.97
2181 2250 1.575576 CTTGCTCGCTGCTTGCTCTT 61.576 55.000 13.19 0.00 43.37 2.85
2182 2251 2.031616 TTGCTCGCTGCTTGCTCT 59.968 55.556 13.19 0.00 43.37 4.09
2184 2253 2.031616 TCTTGCTCGCTGCTTGCT 59.968 55.556 13.19 0.00 43.37 3.91
2185 2254 2.479650 CTCTTGCTCGCTGCTTGC 59.520 61.111 0.00 2.32 43.37 4.01
2186 2255 0.952497 TTCCTCTTGCTCGCTGCTTG 60.952 55.000 0.00 0.00 43.37 4.01
2187 2256 0.673022 CTTCCTCTTGCTCGCTGCTT 60.673 55.000 0.00 0.00 43.37 3.91
2188 2257 1.079266 CTTCCTCTTGCTCGCTGCT 60.079 57.895 0.00 0.00 43.37 4.24
2190 2259 1.449246 CCCTTCCTCTTGCTCGCTG 60.449 63.158 0.00 0.00 0.00 5.18
2194 2284 0.912006 AGTCCCCCTTCCTCTTGCTC 60.912 60.000 0.00 0.00 0.00 4.26
2195 2285 0.912006 GAGTCCCCCTTCCTCTTGCT 60.912 60.000 0.00 0.00 0.00 3.91
2207 2297 2.427506 GTCAACATCAAGTGAGTCCCC 58.572 52.381 0.00 0.00 0.00 4.81
2211 2301 1.512926 GGCGTCAACATCAAGTGAGT 58.487 50.000 0.00 0.00 0.00 3.41
2384 2483 2.095567 CGGCATCAAGAAGGTGAAACTG 60.096 50.000 0.00 0.00 36.74 3.16
2387 2486 2.270352 ACGGCATCAAGAAGGTGAAA 57.730 45.000 0.00 0.00 0.00 2.69
2390 2489 1.197721 GACAACGGCATCAAGAAGGTG 59.802 52.381 0.00 0.00 0.00 4.00
2412 2511 1.010935 ATCGTCGTGCAGTTGCTCAG 61.011 55.000 5.62 0.00 42.66 3.35
2419 2518 2.573869 CCAGGATCGTCGTGCAGT 59.426 61.111 0.00 0.00 31.43 4.40
2505 2604 2.750350 GCTGGTAGTGGTGGCACT 59.250 61.111 18.45 0.00 39.08 4.40
2506 2605 2.742372 CGCTGGTAGTGGTGGCAC 60.742 66.667 9.70 9.70 0.00 5.01
2507 2606 4.697756 GCGCTGGTAGTGGTGGCA 62.698 66.667 0.00 0.00 0.00 4.92
2511 2610 4.742201 CTGCGCGCTGGTAGTGGT 62.742 66.667 33.29 0.00 0.00 4.16
2514 2613 4.803426 GCTCTGCGCGCTGGTAGT 62.803 66.667 33.04 0.00 0.00 2.73
2547 2646 4.481112 CTGAACAATGGCGGCGGC 62.481 66.667 27.76 27.76 38.90 6.53
2573 2672 2.623915 CGTCAGTTCGTCGGAGGGT 61.624 63.158 0.00 0.00 0.00 4.34
2575 2674 0.039798 TTTCGTCAGTTCGTCGGAGG 60.040 55.000 0.00 0.00 0.00 4.30
2581 2680 3.508793 TCTCCCTTATTTCGTCAGTTCGT 59.491 43.478 0.00 0.00 0.00 3.85
2595 2694 1.693627 GCGTCCAGAGATCTCCCTTA 58.306 55.000 19.30 0.00 0.00 2.69
2620 2722 0.679960 CCGGTTCCTGGATTCCCAAC 60.680 60.000 0.00 0.89 42.98 3.77
2637 2739 1.098050 CAAATCTTGAGCCTTCCCCG 58.902 55.000 0.00 0.00 0.00 5.73
2672 2774 1.605232 TCGATTCGATTCGATTCCCGA 59.395 47.619 24.07 16.76 42.81 5.14
2714 2816 1.000717 CGGCATTGTTTCCCGTTTTCT 60.001 47.619 0.00 0.00 37.36 2.52
2717 2819 1.663173 CCGGCATTGTTTCCCGTTT 59.337 52.632 0.00 0.00 40.38 3.60
2719 2821 2.675075 CCCGGCATTGTTTCCCGT 60.675 61.111 0.00 0.00 40.38 5.28
2721 2823 4.128388 CGCCCGGCATTGTTTCCC 62.128 66.667 10.77 0.00 0.00 3.97
2740 2846 4.308458 CACGGGGCACTTCGTCCA 62.308 66.667 0.00 0.00 43.46 4.02
2752 2858 1.415374 CGATTTATACTCCGCACGGG 58.585 55.000 9.58 2.66 35.59 5.28
2754 2860 1.415374 CCCGATTTATACTCCGCACG 58.585 55.000 0.00 0.00 0.00 5.34
2755 2861 1.607251 CCCCCGATTTATACTCCGCAC 60.607 57.143 0.00 0.00 0.00 5.34
2756 2862 0.682852 CCCCCGATTTATACTCCGCA 59.317 55.000 0.00 0.00 0.00 5.69
2757 2863 0.971386 TCCCCCGATTTATACTCCGC 59.029 55.000 0.00 0.00 0.00 5.54
2758 2864 2.093658 CCATCCCCCGATTTATACTCCG 60.094 54.545 0.00 0.00 0.00 4.63
2777 2883 2.776670 CTTGCAGCTCTCGCAGTCCA 62.777 60.000 0.00 0.00 41.18 4.02
2916 3027 1.167851 CCGGCATTCACATGTGAGTT 58.832 50.000 26.48 16.46 41.13 3.01
2979 3090 0.546598 CTCCGCCCTTTCCATACCTT 59.453 55.000 0.00 0.00 0.00 3.50
2992 3103 2.391389 CGACTCAAAAGCCTCCGCC 61.391 63.158 0.00 0.00 34.57 6.13
2994 3105 0.038159 ACTCGACTCAAAAGCCTCCG 60.038 55.000 0.00 0.00 0.00 4.63
2995 3106 1.801178 CAACTCGACTCAAAAGCCTCC 59.199 52.381 0.00 0.00 0.00 4.30
3032 3143 3.370527 CCTCGACTCTCTCTTTCTCTCCT 60.371 52.174 0.00 0.00 0.00 3.69
3033 3144 2.943033 CCTCGACTCTCTCTTTCTCTCC 59.057 54.545 0.00 0.00 0.00 3.71
3035 3146 2.290641 TGCCTCGACTCTCTCTTTCTCT 60.291 50.000 0.00 0.00 0.00 3.10
3036 3147 2.088423 TGCCTCGACTCTCTCTTTCTC 58.912 52.381 0.00 0.00 0.00 2.87
3037 3148 2.091541 CTGCCTCGACTCTCTCTTTCT 58.908 52.381 0.00 0.00 0.00 2.52
3050 3161 3.207669 GCCATTGCCTCTGCCTCG 61.208 66.667 0.00 0.00 36.33 4.63
3052 3163 3.720601 TCGCCATTGCCTCTGCCT 61.721 61.111 0.00 0.00 36.33 4.75
3053 3164 3.512516 GTCGCCATTGCCTCTGCC 61.513 66.667 0.00 0.00 36.33 4.85
3054 3165 3.869272 CGTCGCCATTGCCTCTGC 61.869 66.667 0.00 0.00 38.26 4.26
3055 3166 3.869272 GCGTCGCCATTGCCTCTG 61.869 66.667 5.75 0.00 0.00 3.35
3146 3257 2.127758 CCAACGAAGCAACGCGTC 60.128 61.111 14.44 0.00 40.23 5.19


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

AutoCloner maintained by Alex Coulton.