Multiple sequence alignment - TraesCS4A01G145400

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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 TraesCS4A01G145400 chr4A 100.000 2703 0 0 2162 4864 248831560 248834262 0.000000e+00 4992
1 TraesCS4A01G145400 chr4A 100.000 1826 0 0 1 1826 248829399 248831224 0.000000e+00 3373
2 TraesCS4A01G145400 chr4D 96.950 2000 54 4 2162 4161 195017523 195019515 0.000000e+00 3349
3 TraesCS4A01G145400 chr4D 93.504 1247 34 13 624 1826 195016135 195017378 0.000000e+00 1810
4 TraesCS4A01G145400 chr4D 93.949 628 34 3 1 624 420149096 420148469 0.000000e+00 946
5 TraesCS4A01G145400 chr4D 94.089 626 32 4 1 622 454777496 454778120 0.000000e+00 946
6 TraesCS4A01G145400 chr4D 97.500 320 8 0 4540 4859 195020301 195020620 9.200000e-152 547
7 TraesCS4A01G145400 chr4D 97.744 266 4 1 4265 4528 195019512 195019777 1.600000e-124 457
8 TraesCS4A01G145400 chr4B 96.600 2000 57 3 2162 4161 150739562 150737574 0.000000e+00 3306
9 TraesCS4A01G145400 chr4B 90.375 1226 51 36 624 1826 150740888 150739707 0.000000e+00 1548
10 TraesCS4A01G145400 chr4B 97.674 602 12 1 4265 4864 150737577 150736976 0.000000e+00 1033
11 TraesCS4A01G145400 chr6D 94.737 627 28 4 1 623 350289970 350289345 0.000000e+00 970
12 TraesCS4A01G145400 chr6D 94.268 628 31 4 1 624 111607550 111608176 0.000000e+00 955
13 TraesCS4A01G145400 chr2D 94.146 632 31 5 1 627 456507137 456507767 0.000000e+00 957
14 TraesCS4A01G145400 chr7D 93.949 628 34 3 1 624 610231132 610231759 0.000000e+00 946
15 TraesCS4A01G145400 chrUn 93.949 628 33 4 1 624 26510683 26510057 0.000000e+00 944
16 TraesCS4A01G145400 chr3D 94.089 626 30 6 1 622 24450405 24451027 0.000000e+00 944
17 TraesCS4A01G145400 chr5D 93.790 628 35 3 1 624 255568279 255567652 0.000000e+00 941


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 TraesCS4A01G145400 chr4A 248829399 248834262 4863 False 4182.500000 4992 100.0000 1 4864 2 chr4A.!!$F1 4863
1 TraesCS4A01G145400 chr4D 195016135 195020620 4485 False 1540.750000 3349 96.4245 624 4859 4 chr4D.!!$F2 4235
2 TraesCS4A01G145400 chr4D 420148469 420149096 627 True 946.000000 946 93.9490 1 624 1 chr4D.!!$R1 623
3 TraesCS4A01G145400 chr4D 454777496 454778120 624 False 946.000000 946 94.0890 1 622 1 chr4D.!!$F1 621
4 TraesCS4A01G145400 chr4B 150736976 150740888 3912 True 1962.333333 3306 94.8830 624 4864 3 chr4B.!!$R1 4240
5 TraesCS4A01G145400 chr6D 350289345 350289970 625 True 970.000000 970 94.7370 1 623 1 chr6D.!!$R1 622
6 TraesCS4A01G145400 chr6D 111607550 111608176 626 False 955.000000 955 94.2680 1 624 1 chr6D.!!$F1 623
7 TraesCS4A01G145400 chr2D 456507137 456507767 630 False 957.000000 957 94.1460 1 627 1 chr2D.!!$F1 626
8 TraesCS4A01G145400 chr7D 610231132 610231759 627 False 946.000000 946 93.9490 1 624 1 chr7D.!!$F1 623
9 TraesCS4A01G145400 chrUn 26510057 26510683 626 True 944.000000 944 93.9490 1 624 1 chrUn.!!$R1 623
10 TraesCS4A01G145400 chr3D 24450405 24451027 622 False 944.000000 944 94.0890 1 622 1 chr3D.!!$F1 621
11 TraesCS4A01G145400 chr5D 255567652 255568279 627 True 941.000000 941 93.7900 1 624 1 chr5D.!!$R1 623

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
777 785 0.183492 TCCTTGGCTGCAGTGAAAGT 59.817 50.0 16.64 0.0 0.00 2.66 F
1723 1780 0.254178 ACTGCACCCTTGATAGCTGG 59.746 55.0 0.00 0.0 0.00 4.85 F
2536 2610 0.314935 CAAACAATCCTTGTGGCGCT 59.685 50.0 7.64 0.0 44.59 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2577 2651 0.319383 CTGTGCTCGTGAACTCTGCT 60.319 55.000 0.0 0.0 0.0 4.24 R
3588 3662 1.202463 CCACATCCTAGCGGTTCAGAG 60.202 57.143 0.0 0.0 0.0 3.35 R
4241 4315 0.037326 TCCTTAGACCGCAAGCACAG 60.037 55.000 0.0 0.0 0.0 3.66 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
45 46 3.452264 TGATGTGGAAGACTCGGATCATT 59.548 43.478 0.00 0.00 0.00 2.57
114 116 1.376037 GGCTTCGTGTCTCTTGGGG 60.376 63.158 0.00 0.00 0.00 4.96
140 142 4.741781 CCTTTGCCGAGTTGCGCG 62.742 66.667 0.00 0.00 39.11 6.86
157 159 1.903404 CGGCTTGGCTTCCAACCTT 60.903 57.895 12.16 0.00 38.75 3.50
205 208 0.700963 TGGGCTTGGGGGCTATATGT 60.701 55.000 0.00 0.00 40.65 2.29
254 257 6.476243 AATTTACTATCGAGCACGTGTTTT 57.524 33.333 18.38 3.05 40.69 2.43
388 392 1.472276 GACGGCGACTCAGTTATGCG 61.472 60.000 16.62 0.00 0.00 4.73
389 393 2.860628 CGGCGACTCAGTTATGCGC 61.861 63.158 0.00 0.00 46.20 6.09
426 430 2.045524 TGATTGCTTCTTTTGGGCCAA 58.954 42.857 16.66 16.66 0.00 4.52
519 523 3.754850 TGACTTTATCCTTCGTCGTCTCA 59.245 43.478 0.00 0.00 0.00 3.27
524 528 0.611062 TCCTTCGTCGTCTCACCCAT 60.611 55.000 0.00 0.00 0.00 4.00
538 542 1.299648 CCCATCGTTGGAGCTTGGA 59.700 57.895 14.27 0.00 46.92 3.53
583 587 3.081804 GTTGTTGCTACCTGCCTTATGT 58.918 45.455 0.00 0.00 42.00 2.29
617 623 0.323725 TTGGGCATGCCTTTCCTCTC 60.324 55.000 34.70 16.78 36.10 3.20
640 646 0.250901 AAATCCTGCGGTGTGAGCTT 60.251 50.000 0.00 0.00 35.28 3.74
777 785 0.183492 TCCTTGGCTGCAGTGAAAGT 59.817 50.000 16.64 0.00 0.00 2.66
884 892 3.738429 AAATACGCCCCGTACGCCC 62.738 63.158 10.49 0.00 45.07 6.13
902 910 1.226046 CCGTGACTAGCGACGACAG 60.226 63.158 14.11 0.00 37.81 3.51
973 985 4.624913 TCCTCTCTCTCTCTCTCTCTCTT 58.375 47.826 0.00 0.00 0.00 2.85
1050 1081 2.672996 CCAACCCCCGCTGTGAAG 60.673 66.667 0.00 0.00 0.00 3.02
1351 1385 3.647771 GCCAGGTCCGGGGACTTT 61.648 66.667 16.86 4.01 44.04 2.66
1512 1566 7.709613 GGTGACATCGAAATACTAGTACCATTT 59.290 37.037 4.31 3.20 0.00 2.32
1636 1693 2.656069 TACGACCTGCTTGGCTCCC 61.656 63.158 0.00 0.00 40.22 4.30
1691 1748 7.362802 AGTTCTAACTTCCAACTCAGTTAGT 57.637 36.000 15.36 0.00 46.88 2.24
1693 1750 6.971726 TCTAACTTCCAACTCAGTTAGTCA 57.028 37.500 15.36 0.00 46.88 3.41
1694 1751 6.982852 TCTAACTTCCAACTCAGTTAGTCAG 58.017 40.000 15.36 0.00 46.88 3.51
1695 1752 5.615925 AACTTCCAACTCAGTTAGTCAGT 57.384 39.130 0.00 0.00 37.50 3.41
1696 1753 5.615925 ACTTCCAACTCAGTTAGTCAGTT 57.384 39.130 0.00 0.00 37.50 3.16
1723 1780 0.254178 ACTGCACCCTTGATAGCTGG 59.746 55.000 0.00 0.00 0.00 4.85
1739 1796 2.239654 AGCTGGCAACCACACATATACT 59.760 45.455 0.00 0.00 0.00 2.12
1740 1797 3.454447 AGCTGGCAACCACACATATACTA 59.546 43.478 0.00 0.00 0.00 1.82
1741 1798 3.809832 GCTGGCAACCACACATATACTAG 59.190 47.826 0.00 0.00 0.00 2.57
1744 1801 6.156748 TGGCAACCACACATATACTAGTAG 57.843 41.667 8.85 0.00 0.00 2.57
1746 1803 6.834969 TGGCAACCACACATATACTAGTAGTA 59.165 38.462 12.38 12.38 34.82 1.82
1788 1856 4.501400 GCAGACCAACAAAGCTAACCATTT 60.501 41.667 0.00 0.00 0.00 2.32
2221 2289 1.301423 TTCTTTGTAACAGCGCGGTT 58.699 45.000 28.05 28.05 34.81 4.44
2236 2304 2.426023 GTTGCCGACCACCTGTCT 59.574 61.111 0.00 0.00 42.13 3.41
2275 2349 2.105128 CGCATCCGGGAGTCTGAC 59.895 66.667 0.00 0.00 0.00 3.51
2322 2396 0.816825 GCGATCACTGCCATCACCAT 60.817 55.000 0.00 0.00 0.00 3.55
2336 2410 4.033776 CCATGGTGCTCGGTGGGT 62.034 66.667 2.57 0.00 0.00 4.51
2341 2415 4.083862 GTGCTCGGTGGGTCTCCC 62.084 72.222 0.00 0.00 45.71 4.30
2536 2610 0.314935 CAAACAATCCTTGTGGCGCT 59.685 50.000 7.64 0.00 44.59 5.92
2577 2651 1.229051 TCCAGGTGACCATCGGACA 60.229 57.895 3.63 0.00 0.00 4.02
2616 2690 1.670967 GCTTGCTGCATCCTGAAAACC 60.671 52.381 1.84 0.00 42.31 3.27
2771 2845 7.327064 ACTGCATCCCTTGATCTATAGATTT 57.673 36.000 16.37 0.00 34.37 2.17
2795 2869 1.413118 AACTGCAAAAGAGTTGGGGG 58.587 50.000 0.00 0.00 32.30 5.40
2969 3043 3.567164 GGCATTCTGTGATCCTAATGGTG 59.433 47.826 0.00 0.00 31.46 4.17
3027 3101 4.980339 TTCTCCATTGCTGGCTATATGA 57.020 40.909 0.00 0.00 42.80 2.15
3249 3323 2.673368 GGATGAACATGACGAGTTCCAC 59.327 50.000 0.00 0.00 43.57 4.02
3295 3369 1.136500 CTGCTGCTGATGCTCTCTACA 59.864 52.381 0.00 0.00 40.48 2.74
3471 3545 0.508641 CACTTCACTTCTGTTCGGCG 59.491 55.000 0.00 0.00 0.00 6.46
3492 3566 3.058016 CGTTGCAGATGACATGGACTTTT 60.058 43.478 0.00 0.00 0.00 2.27
3496 3570 4.005650 GCAGATGACATGGACTTTTCTCA 58.994 43.478 0.00 0.00 0.00 3.27
3596 3670 5.416271 TGACCTTATAACCACTCTGAACC 57.584 43.478 0.00 0.00 0.00 3.62
3620 3694 5.278808 CGCTAGGATGTGGTAAGCAATACTA 60.279 44.000 0.00 0.00 34.74 1.82
3630 3704 7.104290 GTGGTAAGCAATACTAGAAGTTCCTT 58.896 38.462 0.00 0.00 34.74 3.36
3668 3742 1.135944 GTGGCTTCTGCGTTCTTAAGC 60.136 52.381 0.00 0.00 42.81 3.09
4038 4112 9.606631 TGCAACAAATTTACAGAATAAAGGTTT 57.393 25.926 0.00 0.00 0.00 3.27
4095 4169 7.442656 AGCAGCAATACTATTACCGTCTATTT 58.557 34.615 0.00 0.00 0.00 1.40
4134 4208 4.870426 TGAGCCACAAGATCGACTTTATTC 59.130 41.667 0.00 0.00 36.61 1.75
4161 4235 4.744570 TCGAGCTACAACCATTGTAAGAG 58.255 43.478 3.23 0.00 44.80 2.85
4162 4236 4.461431 TCGAGCTACAACCATTGTAAGAGA 59.539 41.667 3.23 0.00 44.80 3.10
4163 4237 5.047590 TCGAGCTACAACCATTGTAAGAGAA 60.048 40.000 3.23 0.00 44.80 2.87
4164 4238 5.637810 CGAGCTACAACCATTGTAAGAGAAA 59.362 40.000 3.23 0.00 44.80 2.52
4165 4239 6.147164 CGAGCTACAACCATTGTAAGAGAAAA 59.853 38.462 3.23 0.00 44.80 2.29
4166 4240 7.307751 CGAGCTACAACCATTGTAAGAGAAAAA 60.308 37.037 3.23 0.00 44.80 1.94
4189 4263 3.813529 ACAGCTGAATGTTCTAAACGC 57.186 42.857 23.35 0.00 0.00 4.84
4190 4264 2.484264 ACAGCTGAATGTTCTAAACGCC 59.516 45.455 23.35 0.00 0.00 5.68
4191 4265 2.483877 CAGCTGAATGTTCTAAACGCCA 59.516 45.455 8.42 0.00 0.00 5.69
4192 4266 3.058293 CAGCTGAATGTTCTAAACGCCAA 60.058 43.478 8.42 0.00 0.00 4.52
4193 4267 3.189287 AGCTGAATGTTCTAAACGCCAAG 59.811 43.478 0.00 0.00 0.00 3.61
4194 4268 3.058224 GCTGAATGTTCTAAACGCCAAGT 60.058 43.478 0.00 0.00 0.00 3.16
4195 4269 4.153475 GCTGAATGTTCTAAACGCCAAGTA 59.847 41.667 0.00 0.00 0.00 2.24
4196 4270 5.600908 TGAATGTTCTAAACGCCAAGTAC 57.399 39.130 0.00 0.00 0.00 2.73
4197 4271 5.057819 TGAATGTTCTAAACGCCAAGTACA 58.942 37.500 0.00 0.00 0.00 2.90
4198 4272 5.527951 TGAATGTTCTAAACGCCAAGTACAA 59.472 36.000 0.00 0.00 0.00 2.41
4199 4273 6.205853 TGAATGTTCTAAACGCCAAGTACAAT 59.794 34.615 0.00 0.00 0.00 2.71
4200 4274 7.388224 TGAATGTTCTAAACGCCAAGTACAATA 59.612 33.333 0.00 0.00 0.00 1.90
4201 4275 7.859325 ATGTTCTAAACGCCAAGTACAATAT 57.141 32.000 0.00 0.00 0.00 1.28
4202 4276 7.675962 TGTTCTAAACGCCAAGTACAATATT 57.324 32.000 0.00 0.00 0.00 1.28
4203 4277 7.523219 TGTTCTAAACGCCAAGTACAATATTG 58.477 34.615 14.01 14.01 0.00 1.90
4204 4278 7.388224 TGTTCTAAACGCCAAGTACAATATTGA 59.612 33.333 22.16 3.15 0.00 2.57
4205 4279 8.395633 GTTCTAAACGCCAAGTACAATATTGAT 58.604 33.333 22.16 8.81 0.00 2.57
4206 4280 9.602568 TTCTAAACGCCAAGTACAATATTGATA 57.397 29.630 22.16 7.87 0.00 2.15
4207 4281 9.602568 TCTAAACGCCAAGTACAATATTGATAA 57.397 29.630 22.16 4.32 0.00 1.75
4210 4284 9.515020 AAACGCCAAGTACAATATTGATAATTG 57.485 29.630 22.16 20.61 0.00 2.32
4211 4285 8.220755 ACGCCAAGTACAATATTGATAATTGT 57.779 30.769 22.16 2.66 40.97 2.71
4212 4286 8.682710 ACGCCAAGTACAATATTGATAATTGTT 58.317 29.630 22.16 9.22 39.08 2.83
4213 4287 8.957028 CGCCAAGTACAATATTGATAATTGTTG 58.043 33.333 22.16 13.80 39.08 3.33
4214 4288 9.248291 GCCAAGTACAATATTGATAATTGTTGG 57.752 33.333 22.16 20.06 39.08 3.77
4225 4299 6.494666 TGATAATTGTTGGTAGTAGGAGGG 57.505 41.667 0.00 0.00 0.00 4.30
4226 4300 5.968167 TGATAATTGTTGGTAGTAGGAGGGT 59.032 40.000 0.00 0.00 0.00 4.34
4227 4301 7.134162 TGATAATTGTTGGTAGTAGGAGGGTA 58.866 38.462 0.00 0.00 0.00 3.69
4228 4302 7.792736 TGATAATTGTTGGTAGTAGGAGGGTAT 59.207 37.037 0.00 0.00 0.00 2.73
4229 4303 9.317827 GATAATTGTTGGTAGTAGGAGGGTATA 57.682 37.037 0.00 0.00 0.00 1.47
4230 4304 9.678981 ATAATTGTTGGTAGTAGGAGGGTATAA 57.321 33.333 0.00 0.00 0.00 0.98
4231 4305 8.396619 AATTGTTGGTAGTAGGAGGGTATAAA 57.603 34.615 0.00 0.00 0.00 1.40
4232 4306 7.427989 TTGTTGGTAGTAGGAGGGTATAAAG 57.572 40.000 0.00 0.00 0.00 1.85
4233 4307 6.505754 TGTTGGTAGTAGGAGGGTATAAAGT 58.494 40.000 0.00 0.00 0.00 2.66
4234 4308 6.961721 TGTTGGTAGTAGGAGGGTATAAAGTT 59.038 38.462 0.00 0.00 0.00 2.66
4235 4309 8.121833 TGTTGGTAGTAGGAGGGTATAAAGTTA 58.878 37.037 0.00 0.00 0.00 2.24
4236 4310 8.637099 GTTGGTAGTAGGAGGGTATAAAGTTAG 58.363 40.741 0.00 0.00 0.00 2.34
4237 4311 8.117870 TGGTAGTAGGAGGGTATAAAGTTAGA 57.882 38.462 0.00 0.00 0.00 2.10
4238 4312 8.001292 TGGTAGTAGGAGGGTATAAAGTTAGAC 58.999 40.741 0.00 0.00 0.00 2.59
4239 4313 8.001292 GGTAGTAGGAGGGTATAAAGTTAGACA 58.999 40.741 0.00 0.00 0.00 3.41
4240 4314 9.413734 GTAGTAGGAGGGTATAAAGTTAGACAA 57.586 37.037 0.00 0.00 0.00 3.18
4241 4315 8.303780 AGTAGGAGGGTATAAAGTTAGACAAC 57.696 38.462 0.00 0.00 34.67 3.32
4243 4317 7.184067 AGGAGGGTATAAAGTTAGACAACTG 57.816 40.000 0.00 0.00 44.41 3.16
4244 4318 6.729569 AGGAGGGTATAAAGTTAGACAACTGT 59.270 38.462 0.00 0.00 44.41 3.55
4245 4319 6.817140 GGAGGGTATAAAGTTAGACAACTGTG 59.183 42.308 0.00 0.00 44.41 3.66
4246 4320 6.171213 AGGGTATAAAGTTAGACAACTGTGC 58.829 40.000 0.00 0.00 44.41 4.57
4247 4321 6.013639 AGGGTATAAAGTTAGACAACTGTGCT 60.014 38.462 0.00 0.00 44.41 4.40
4248 4322 6.653740 GGGTATAAAGTTAGACAACTGTGCTT 59.346 38.462 0.00 0.00 44.41 3.91
4249 4323 7.360946 GGGTATAAAGTTAGACAACTGTGCTTG 60.361 40.741 0.00 0.00 44.41 4.01
4250 4324 3.971032 AAGTTAGACAACTGTGCTTGC 57.029 42.857 0.00 0.00 44.41 4.01
4251 4325 1.867233 AGTTAGACAACTGTGCTTGCG 59.133 47.619 0.00 0.00 43.50 4.85
4252 4326 1.069906 GTTAGACAACTGTGCTTGCGG 60.070 52.381 0.00 0.00 0.00 5.69
4253 4327 0.105964 TAGACAACTGTGCTTGCGGT 59.894 50.000 0.00 0.00 0.00 5.68
4254 4328 1.160329 AGACAACTGTGCTTGCGGTC 61.160 55.000 0.00 0.00 0.00 4.79
4255 4329 1.153168 ACAACTGTGCTTGCGGTCT 60.153 52.632 0.00 0.00 0.00 3.85
4256 4330 0.105964 ACAACTGTGCTTGCGGTCTA 59.894 50.000 0.00 0.00 0.00 2.59
4257 4331 1.225855 CAACTGTGCTTGCGGTCTAA 58.774 50.000 0.00 0.00 0.00 2.10
4258 4332 1.195448 CAACTGTGCTTGCGGTCTAAG 59.805 52.381 0.00 0.00 0.00 2.18
4259 4333 0.320771 ACTGTGCTTGCGGTCTAAGG 60.321 55.000 0.00 0.00 0.00 2.69
4260 4334 0.037326 CTGTGCTTGCGGTCTAAGGA 60.037 55.000 0.00 0.00 0.00 3.36
4261 4335 0.037326 TGTGCTTGCGGTCTAAGGAG 60.037 55.000 0.00 0.00 0.00 3.69
4262 4336 0.741221 GTGCTTGCGGTCTAAGGAGG 60.741 60.000 0.00 0.00 0.00 4.30
4263 4337 0.902984 TGCTTGCGGTCTAAGGAGGA 60.903 55.000 0.00 0.00 0.00 3.71
4264 4338 0.249398 GCTTGCGGTCTAAGGAGGAA 59.751 55.000 0.00 0.00 0.00 3.36
4265 4339 1.338769 GCTTGCGGTCTAAGGAGGAAA 60.339 52.381 0.00 0.00 0.00 3.13
4266 4340 2.622436 CTTGCGGTCTAAGGAGGAAAG 58.378 52.381 0.00 0.00 0.00 2.62
4267 4341 1.933021 TGCGGTCTAAGGAGGAAAGA 58.067 50.000 0.00 0.00 0.00 2.52
4538 4614 3.567164 AGACATTGAACAAAGACCAGCTG 59.433 43.478 6.78 6.78 0.00 4.24
4631 5219 9.169592 TCATATGGCAAAAGTAGGTAGTAAAAC 57.830 33.333 2.13 0.00 0.00 2.43
4684 5272 2.192624 GCTCAAGCAAGCGAACAAAAA 58.807 42.857 0.00 0.00 41.59 1.94
4861 5449 2.145397 TTCAGGCTACCGATCTGTCT 57.855 50.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
157 159 1.375013 GCGCCTAGAAACACCGGAA 60.375 57.895 9.46 0.00 0.00 4.30
166 168 1.004277 ACCCAAAAGATGCGCCTAGAA 59.996 47.619 4.18 0.00 0.00 2.10
376 380 2.341257 CTCTTGTGCGCATAACTGAGT 58.659 47.619 15.91 0.00 0.00 3.41
426 430 7.709149 AAGATCCAACTAAAGCTAAAGCATT 57.291 32.000 4.54 0.96 45.16 3.56
524 528 0.396435 ACACATCCAAGCTCCAACGA 59.604 50.000 0.00 0.00 0.00 3.85
538 542 8.169977 ACATCACAGAAAAGTATCAAACACAT 57.830 30.769 0.00 0.00 0.00 3.21
583 587 7.344352 AGGCATGCCCAACTTTATAAATAAAGA 59.656 33.333 33.14 5.86 42.84 2.52
599 603 1.304282 GAGAGGAAAGGCATGCCCA 59.696 57.895 33.14 0.00 36.58 5.36
697 703 4.499019 CGAGAGAGGGAGAGATTTACAAGC 60.499 50.000 0.00 0.00 0.00 4.01
884 892 1.226046 CTGTCGTCGCTAGTCACGG 60.226 63.158 13.52 0.00 36.64 4.94
902 910 0.100146 CTAGGCGTACGTGAGGGTTC 59.900 60.000 17.90 0.00 0.00 3.62
973 985 2.938451 CAGACTCTGCACACAAACAGAA 59.062 45.455 0.00 0.00 42.12 3.02
1228 1262 4.351054 CCCTTGTCCTTGCCGGCT 62.351 66.667 29.70 0.00 0.00 5.52
1401 1435 1.026182 ACATGGCATGCGACGAACAT 61.026 50.000 26.70 5.29 0.00 2.71
1489 1543 8.867112 TCAAATGGTACTAGTATTTCGATGTC 57.133 34.615 5.75 0.00 0.00 3.06
1512 1566 1.811965 AGTGCTTTGCAATGCGTATCA 59.188 42.857 26.41 10.66 41.47 2.15
1636 1693 0.469917 ATTGATAGTCCAGGTGGCGG 59.530 55.000 0.00 0.00 34.44 6.13
1689 1746 3.243771 GGTGCAGTGTAGTACAACTGACT 60.244 47.826 24.76 9.74 32.68 3.41
1690 1747 3.057734 GGTGCAGTGTAGTACAACTGAC 58.942 50.000 24.76 19.98 32.68 3.51
1691 1748 2.036733 GGGTGCAGTGTAGTACAACTGA 59.963 50.000 24.76 13.79 32.68 3.41
1693 1750 2.326428 AGGGTGCAGTGTAGTACAACT 58.674 47.619 4.11 2.26 0.00 3.16
1694 1751 2.806244 CAAGGGTGCAGTGTAGTACAAC 59.194 50.000 4.11 0.00 0.00 3.32
1695 1752 2.701423 TCAAGGGTGCAGTGTAGTACAA 59.299 45.455 4.11 0.00 0.00 2.41
1696 1753 2.321719 TCAAGGGTGCAGTGTAGTACA 58.678 47.619 0.00 0.00 0.00 2.90
1723 1780 8.162878 TCTACTACTAGTATATGTGTGGTTGC 57.837 38.462 2.33 0.00 29.08 4.17
1740 1797 8.361139 GCATATCCTGTTTGTACATCTACTACT 58.639 37.037 0.00 0.00 32.86 2.57
1741 1798 8.141909 TGCATATCCTGTTTGTACATCTACTAC 58.858 37.037 0.00 0.00 32.86 2.73
1744 1801 7.169982 GTCTGCATATCCTGTTTGTACATCTAC 59.830 40.741 0.00 0.00 32.86 2.59
1746 1803 6.051717 GTCTGCATATCCTGTTTGTACATCT 58.948 40.000 0.00 0.00 32.86 2.90
1788 1856 1.511850 CAGTGACATGAACGGCTTGA 58.488 50.000 0.00 0.00 0.00 3.02
2231 2299 2.125753 GCCGGCAGACAGAGACAG 60.126 66.667 24.80 0.00 0.00 3.51
2232 2300 2.917227 TGCCGGCAGACAGAGACA 60.917 61.111 29.03 0.00 0.00 3.41
2233 2301 2.433318 GTGCCGGCAGACAGAGAC 60.433 66.667 33.73 12.14 0.00 3.36
2234 2302 2.917227 TGTGCCGGCAGACAGAGA 60.917 61.111 33.73 0.91 0.00 3.10
2235 2303 2.740055 GTGTGCCGGCAGACAGAG 60.740 66.667 42.20 0.00 39.61 3.35
2236 2304 3.545574 TGTGTGCCGGCAGACAGA 61.546 61.111 44.94 29.74 43.71 3.41
2275 2349 1.071019 CTCCGACCGTCATGAACACG 61.071 60.000 0.00 0.00 36.99 4.49
2322 2396 3.311110 GAGACCCACCGAGCACCA 61.311 66.667 0.00 0.00 0.00 4.17
2336 2410 1.764854 GGATGTTAGCCCCGGGAGA 60.765 63.158 26.32 2.78 0.00 3.71
2341 2415 1.524621 CAGCAGGATGTTAGCCCCG 60.525 63.158 0.00 0.00 39.31 5.73
2375 2449 2.774351 GGCTGCCTCATAGGGGGT 60.774 66.667 12.43 0.00 35.37 4.95
2536 2610 2.644676 AGATGCTGCGTAGAGTAGACA 58.355 47.619 4.08 0.00 34.21 3.41
2577 2651 0.319383 CTGTGCTCGTGAACTCTGCT 60.319 55.000 0.00 0.00 0.00 4.24
2605 2679 5.476599 TCATTGTGATTTCGGTTTTCAGGAT 59.523 36.000 0.00 0.00 0.00 3.24
2717 2791 6.173427 TCAGTGCTATGCCAGTAAATCATA 57.827 37.500 0.00 0.00 0.00 2.15
2771 2845 3.381272 CCCAACTCTTTTGCAGTTTCAGA 59.619 43.478 0.00 0.00 31.40 3.27
2795 2869 3.069729 ACCTCATCCGCTATTACTGGAAC 59.930 47.826 0.00 0.00 34.97 3.62
2969 3043 4.691860 AGTGTCTTACATGCTTGATTGC 57.308 40.909 6.60 0.00 0.00 3.56
3027 3101 3.827008 ATGGATCTGCGTACATGAGTT 57.173 42.857 0.00 0.00 0.00 3.01
3249 3323 3.996150 AGCAAGTTCACAACATTCTGG 57.004 42.857 0.00 0.00 0.00 3.86
3295 3369 4.041444 AGCTTCAATCTGGTTCACTCTTCT 59.959 41.667 0.00 0.00 0.00 2.85
3471 3545 4.217118 AGAAAAGTCCATGTCATCTGCAAC 59.783 41.667 0.00 0.00 0.00 4.17
3492 3566 7.603784 TGATTCTTCTTTGATCAATTCGTGAGA 59.396 33.333 9.40 5.08 40.43 3.27
3496 3570 7.678947 ACTGATTCTTCTTTGATCAATTCGT 57.321 32.000 9.40 0.00 0.00 3.85
3587 3661 1.478510 CACATCCTAGCGGTTCAGAGT 59.521 52.381 0.00 0.00 0.00 3.24
3588 3662 1.202463 CCACATCCTAGCGGTTCAGAG 60.202 57.143 0.00 0.00 0.00 3.35
3596 3670 2.309528 TTGCTTACCACATCCTAGCG 57.690 50.000 0.00 0.00 34.65 4.26
3630 3704 5.815581 AGCCACTACAAGATCAACCATTTA 58.184 37.500 0.00 0.00 0.00 1.40
3856 3930 4.127171 CCCTATATGGTGGTTTCAGAACG 58.873 47.826 0.00 0.00 36.61 3.95
3979 4053 4.401519 TCTGCTACACACTATCTGGTAACC 59.598 45.833 0.00 0.00 0.00 2.85
4081 4155 9.991388 GTTATTTGCAACAAATAGACGGTAATA 57.009 29.630 0.00 0.00 0.00 0.98
4095 4169 3.382865 TGGCTCACTTGTTATTTGCAACA 59.617 39.130 0.00 0.00 36.65 3.33
4134 4208 2.332063 ATGGTTGTAGCTCGATTGGG 57.668 50.000 0.00 0.00 0.00 4.12
4165 4239 5.458779 GCGTTTAGAACATTCAGCTGTTTTT 59.541 36.000 14.67 2.99 39.40 1.94
4166 4240 4.976116 GCGTTTAGAACATTCAGCTGTTTT 59.024 37.500 14.67 2.63 39.40 2.43
4167 4241 4.537015 GCGTTTAGAACATTCAGCTGTTT 58.463 39.130 14.67 3.00 39.40 2.83
4168 4242 3.058224 GGCGTTTAGAACATTCAGCTGTT 60.058 43.478 14.67 0.34 41.92 3.16
4169 4243 2.484264 GGCGTTTAGAACATTCAGCTGT 59.516 45.455 14.67 0.00 0.00 4.40
4170 4244 2.483877 TGGCGTTTAGAACATTCAGCTG 59.516 45.455 7.63 7.63 0.00 4.24
4171 4245 2.778299 TGGCGTTTAGAACATTCAGCT 58.222 42.857 0.00 0.00 0.00 4.24
4172 4246 3.058224 ACTTGGCGTTTAGAACATTCAGC 60.058 43.478 0.00 0.00 0.00 4.26
4173 4247 4.749245 ACTTGGCGTTTAGAACATTCAG 57.251 40.909 0.00 0.00 0.00 3.02
4174 4248 5.057819 TGTACTTGGCGTTTAGAACATTCA 58.942 37.500 0.00 0.00 0.00 2.57
4175 4249 5.600908 TGTACTTGGCGTTTAGAACATTC 57.399 39.130 0.00 0.00 0.00 2.67
4176 4250 6.569179 ATTGTACTTGGCGTTTAGAACATT 57.431 33.333 0.00 0.00 0.00 2.71
4177 4251 7.859325 ATATTGTACTTGGCGTTTAGAACAT 57.141 32.000 0.00 0.00 0.00 2.71
4178 4252 7.388224 TCAATATTGTACTTGGCGTTTAGAACA 59.612 33.333 14.97 0.00 0.00 3.18
4179 4253 7.745015 TCAATATTGTACTTGGCGTTTAGAAC 58.255 34.615 14.97 0.00 0.00 3.01
4180 4254 7.908827 TCAATATTGTACTTGGCGTTTAGAA 57.091 32.000 14.97 0.00 0.00 2.10
4181 4255 9.602568 TTATCAATATTGTACTTGGCGTTTAGA 57.397 29.630 14.97 0.00 0.00 2.10
4184 4258 9.515020 CAATTATCAATATTGTACTTGGCGTTT 57.485 29.630 14.97 0.00 0.00 3.60
4185 4259 8.682710 ACAATTATCAATATTGTACTTGGCGTT 58.317 29.630 14.97 1.35 36.83 4.84
4186 4260 8.220755 ACAATTATCAATATTGTACTTGGCGT 57.779 30.769 14.97 2.67 36.83 5.68
4187 4261 8.957028 CAACAATTATCAATATTGTACTTGGCG 58.043 33.333 14.97 8.82 37.52 5.69
4188 4262 9.248291 CCAACAATTATCAATATTGTACTTGGC 57.752 33.333 14.97 0.00 37.52 4.52
4199 4273 8.656806 CCCTCCTACTACCAACAATTATCAATA 58.343 37.037 0.00 0.00 0.00 1.90
4200 4274 7.128883 ACCCTCCTACTACCAACAATTATCAAT 59.871 37.037 0.00 0.00 0.00 2.57
4201 4275 6.445786 ACCCTCCTACTACCAACAATTATCAA 59.554 38.462 0.00 0.00 0.00 2.57
4202 4276 5.968167 ACCCTCCTACTACCAACAATTATCA 59.032 40.000 0.00 0.00 0.00 2.15
4203 4277 6.496144 ACCCTCCTACTACCAACAATTATC 57.504 41.667 0.00 0.00 0.00 1.75
4204 4278 9.678981 TTATACCCTCCTACTACCAACAATTAT 57.321 33.333 0.00 0.00 0.00 1.28
4205 4279 9.504705 TTTATACCCTCCTACTACCAACAATTA 57.495 33.333 0.00 0.00 0.00 1.40
4206 4280 8.396619 TTTATACCCTCCTACTACCAACAATT 57.603 34.615 0.00 0.00 0.00 2.32
4207 4281 7.626487 ACTTTATACCCTCCTACTACCAACAAT 59.374 37.037 0.00 0.00 0.00 2.71
4208 4282 6.961721 ACTTTATACCCTCCTACTACCAACAA 59.038 38.462 0.00 0.00 0.00 2.83
4209 4283 6.505754 ACTTTATACCCTCCTACTACCAACA 58.494 40.000 0.00 0.00 0.00 3.33
4210 4284 7.429374 AACTTTATACCCTCCTACTACCAAC 57.571 40.000 0.00 0.00 0.00 3.77
4211 4285 8.568723 TCTAACTTTATACCCTCCTACTACCAA 58.431 37.037 0.00 0.00 0.00 3.67
4212 4286 8.001292 GTCTAACTTTATACCCTCCTACTACCA 58.999 40.741 0.00 0.00 0.00 3.25
4213 4287 8.001292 TGTCTAACTTTATACCCTCCTACTACC 58.999 40.741 0.00 0.00 0.00 3.18
4214 4288 8.986929 TGTCTAACTTTATACCCTCCTACTAC 57.013 38.462 0.00 0.00 0.00 2.73
4215 4289 9.413734 GTTGTCTAACTTTATACCCTCCTACTA 57.586 37.037 0.00 0.00 33.94 1.82
4216 4290 8.121185 AGTTGTCTAACTTTATACCCTCCTACT 58.879 37.037 0.00 0.00 44.57 2.57
4217 4291 8.196103 CAGTTGTCTAACTTTATACCCTCCTAC 58.804 40.741 0.00 0.00 44.57 3.18
4218 4292 7.897565 ACAGTTGTCTAACTTTATACCCTCCTA 59.102 37.037 0.00 0.00 44.57 2.94
4219 4293 6.729569 ACAGTTGTCTAACTTTATACCCTCCT 59.270 38.462 0.00 0.00 44.57 3.69
4220 4294 6.817140 CACAGTTGTCTAACTTTATACCCTCC 59.183 42.308 0.00 0.00 44.57 4.30
4221 4295 6.313164 GCACAGTTGTCTAACTTTATACCCTC 59.687 42.308 0.00 0.00 44.57 4.30
4222 4296 6.013639 AGCACAGTTGTCTAACTTTATACCCT 60.014 38.462 0.00 0.00 44.57 4.34
4223 4297 6.171213 AGCACAGTTGTCTAACTTTATACCC 58.829 40.000 0.00 0.00 44.57 3.69
4224 4298 7.519002 CAAGCACAGTTGTCTAACTTTATACC 58.481 38.462 0.00 0.00 44.57 2.73
4225 4299 7.015877 GCAAGCACAGTTGTCTAACTTTATAC 58.984 38.462 0.00 0.00 44.57 1.47
4226 4300 6.128661 CGCAAGCACAGTTGTCTAACTTTATA 60.129 38.462 0.00 0.00 44.57 0.98
4227 4301 5.334105 CGCAAGCACAGTTGTCTAACTTTAT 60.334 40.000 0.00 0.00 44.57 1.40
4228 4302 4.025229 CGCAAGCACAGTTGTCTAACTTTA 60.025 41.667 0.00 0.00 44.57 1.85
4229 4303 3.242739 CGCAAGCACAGTTGTCTAACTTT 60.243 43.478 0.00 0.00 44.57 2.66
4230 4304 2.287915 CGCAAGCACAGTTGTCTAACTT 59.712 45.455 0.00 0.00 44.57 2.66
4232 4306 1.069906 CCGCAAGCACAGTTGTCTAAC 60.070 52.381 0.00 0.00 37.06 2.34
4233 4307 1.225855 CCGCAAGCACAGTTGTCTAA 58.774 50.000 0.00 0.00 0.00 2.10
4234 4308 0.105964 ACCGCAAGCACAGTTGTCTA 59.894 50.000 0.00 0.00 0.00 2.59
4235 4309 1.153168 ACCGCAAGCACAGTTGTCT 60.153 52.632 0.00 0.00 0.00 3.41
4236 4310 1.160329 AGACCGCAAGCACAGTTGTC 61.160 55.000 0.00 0.00 0.00 3.18
4237 4311 0.105964 TAGACCGCAAGCACAGTTGT 59.894 50.000 0.00 0.00 0.00 3.32
4238 4312 1.195448 CTTAGACCGCAAGCACAGTTG 59.805 52.381 0.00 0.00 0.00 3.16
4239 4313 1.512926 CTTAGACCGCAAGCACAGTT 58.487 50.000 0.00 0.00 0.00 3.16
4240 4314 0.320771 CCTTAGACCGCAAGCACAGT 60.321 55.000 0.00 0.00 0.00 3.55
4241 4315 0.037326 TCCTTAGACCGCAAGCACAG 60.037 55.000 0.00 0.00 0.00 3.66
4242 4316 0.037326 CTCCTTAGACCGCAAGCACA 60.037 55.000 0.00 0.00 0.00 4.57
4243 4317 0.741221 CCTCCTTAGACCGCAAGCAC 60.741 60.000 0.00 0.00 0.00 4.40
4244 4318 0.902984 TCCTCCTTAGACCGCAAGCA 60.903 55.000 0.00 0.00 0.00 3.91
4245 4319 0.249398 TTCCTCCTTAGACCGCAAGC 59.751 55.000 0.00 0.00 0.00 4.01
4246 4320 2.233922 TCTTTCCTCCTTAGACCGCAAG 59.766 50.000 0.00 0.00 0.00 4.01
4247 4321 2.253610 TCTTTCCTCCTTAGACCGCAA 58.746 47.619 0.00 0.00 0.00 4.85
4248 4322 1.933021 TCTTTCCTCCTTAGACCGCA 58.067 50.000 0.00 0.00 0.00 5.69
4249 4323 2.234168 ACTTCTTTCCTCCTTAGACCGC 59.766 50.000 0.00 0.00 0.00 5.68
4250 4324 3.851098 CACTTCTTTCCTCCTTAGACCG 58.149 50.000 0.00 0.00 0.00 4.79
4251 4325 3.008049 TGCACTTCTTTCCTCCTTAGACC 59.992 47.826 0.00 0.00 0.00 3.85
4252 4326 4.273148 TGCACTTCTTTCCTCCTTAGAC 57.727 45.455 0.00 0.00 0.00 2.59
4253 4327 6.620877 TTATGCACTTCTTTCCTCCTTAGA 57.379 37.500 0.00 0.00 0.00 2.10
4254 4328 6.484977 GGATTATGCACTTCTTTCCTCCTTAG 59.515 42.308 0.00 0.00 0.00 2.18
4255 4329 6.069673 TGGATTATGCACTTCTTTCCTCCTTA 60.070 38.462 0.00 0.00 0.00 2.69
4256 4330 5.196695 GGATTATGCACTTCTTTCCTCCTT 58.803 41.667 0.00 0.00 0.00 3.36
4257 4331 4.228210 TGGATTATGCACTTCTTTCCTCCT 59.772 41.667 0.00 0.00 0.00 3.69
4258 4332 4.526970 TGGATTATGCACTTCTTTCCTCC 58.473 43.478 0.00 0.00 0.00 4.30
4259 4333 6.515272 TTTGGATTATGCACTTCTTTCCTC 57.485 37.500 0.00 0.00 0.00 3.71
4260 4334 6.097412 GGATTTGGATTATGCACTTCTTTCCT 59.903 38.462 0.00 0.00 0.00 3.36
4261 4335 6.097412 AGGATTTGGATTATGCACTTCTTTCC 59.903 38.462 0.00 0.00 0.00 3.13
4262 4336 7.105241 AGGATTTGGATTATGCACTTCTTTC 57.895 36.000 0.00 0.00 0.00 2.62
4263 4337 7.486407 AAGGATTTGGATTATGCACTTCTTT 57.514 32.000 0.00 0.00 0.00 2.52
4264 4338 7.486407 AAAGGATTTGGATTATGCACTTCTT 57.514 32.000 0.00 0.00 36.60 2.52
4349 4423 7.954788 AAACAGATGAAGAGAGAACACTTAC 57.045 36.000 0.00 0.00 0.00 2.34
4538 4614 5.050159 GTGTTTGCATGTTTTCCTGGAATTC 60.050 40.000 10.45 7.14 0.00 2.17
4631 5219 3.690460 AGAATAACCAGGCTTCCACTTG 58.310 45.455 0.00 0.00 0.00 3.16
4684 5272 4.857509 ACAGAGAACTCTTTTACTCGCT 57.142 40.909 1.24 0.00 37.98 4.93
4747 5335 0.669625 GTGCCCTACCACGACTGTTC 60.670 60.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.