Multiple sequence alignment - TraesCS4A01G289400

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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 TraesCS4A01G289400 chr4A 100.000 5347 0 0 1 5347 593914422 593919768 0.000000e+00 9875.0
1 TraesCS4A01G289400 chr4A 94.643 56 3 0 4874 4929 593920895 593920840 2.650000e-13 87.9
2 TraesCS4A01G289400 chr4B 95.526 2414 78 14 2252 4638 18164471 18162061 0.000000e+00 3832.0
3 TraesCS4A01G289400 chr4B 94.374 2275 96 15 1 2260 18166747 18164490 0.000000e+00 3463.0
4 TraesCS4A01G289400 chr4B 95.652 46 2 0 4874 4919 18160201 18160246 2.070000e-09 75.0
5 TraesCS4A01G289400 chr4D 94.513 2442 100 18 1976 4399 9498385 9495960 0.000000e+00 3736.0
6 TraesCS4A01G289400 chr4D 96.280 1559 47 9 373 1925 9499938 9498385 0.000000e+00 2547.0
7 TraesCS4A01G289400 chr4D 88.370 963 63 19 4397 5345 9495879 9494952 0.000000e+00 1112.0
8 TraesCS4A01G289400 chr4D 92.523 321 10 2 1 310 9500263 9499946 1.060000e-121 448.0
9 TraesCS4A01G289400 chr5B 87.097 155 18 2 5193 5347 686639160 686639312 1.980000e-39 174.0
10 TraesCS4A01G289400 chr5B 85.806 155 20 2 5193 5347 686674676 686674828 4.280000e-36 163.0
11 TraesCS4A01G289400 chr5B 83.871 155 21 3 5193 5347 686711229 686711379 1.550000e-30 145.0
12 TraesCS4A01G289400 chr5B 83.226 155 22 2 5193 5347 686831575 686831725 7.220000e-29 139.0
13 TraesCS4A01G289400 chr5B 83.226 155 22 2 5193 5347 686899589 686899739 7.220000e-29 139.0
14 TraesCS4A01G289400 chrUn 86.452 155 19 2 5193 5347 372479643 372479491 9.210000e-38 169.0
15 TraesCS4A01G289400 chr2D 86.842 76 7 3 5243 5317 432867148 432867075 1.230000e-11 82.4
16 TraesCS4A01G289400 chr1A 87.500 72 7 1 5248 5319 48799401 48799332 1.230000e-11 82.4
17 TraesCS4A01G289400 chr6A 89.231 65 6 1 4809 4873 87923268 87923205 4.440000e-11 80.5
18 TraesCS4A01G289400 chr3B 90.741 54 5 0 4874 4927 13154775 13154722 7.430000e-09 73.1
19 TraesCS4A01G289400 chr1B 88.889 54 6 0 4874 4927 12731221 12731168 3.460000e-07 67.6
20 TraesCS4A01G289400 chr1D 91.111 45 4 0 4884 4928 339737000 339737044 1.610000e-05 62.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G289400 chr4A 593914422 593919768 5346 False 9875.00 9875 100.0000 1 5347 1 chr4A.!!$F1 5346
1 TraesCS4A01G289400 chr4B 18162061 18166747 4686 True 3647.50 3832 94.9500 1 4638 2 chr4B.!!$R1 4637
2 TraesCS4A01G289400 chr4D 9494952 9500263 5311 True 1960.75 3736 92.9215 1 5345 4 chr4D.!!$R1 5344

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
469 482 0.036164 TTCCCACCACATTCTCACCG 59.964 55.000 0.00 0.0 0.00 4.94 F
1446 1462 0.038744 CACCAGGCCAAGGATTGTCT 59.961 55.000 20.01 0.0 46.99 3.41 F
1671 1687 1.131420 GCAGAACGCGCAGAAAGAG 59.869 57.895 5.73 0.0 0.00 2.85 F
1676 1692 1.569479 AACGCGCAGAAAGAGAAGGC 61.569 55.000 5.73 0.0 0.00 4.35 F
2330 2376 1.886886 TGGTTCAACGGTTTCTAGGC 58.113 50.000 0.00 0.0 0.00 3.93 F
3740 3798 0.887933 GGTTCATCAATGCCCGTGTT 59.112 50.000 0.00 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1771 1787 0.742281 TCAGCCGCAGAAATCTCAGC 60.742 55.000 0.00 0.0 0.00 4.26 R
3438 3490 0.741927 ACGTACCCCTATTTGTGCGC 60.742 55.000 0.00 0.0 43.06 6.09 R
3621 3677 3.970610 CAGAAGTCATTTGCACACTTTCG 59.029 43.478 0.00 0.0 30.32 3.46 R
3673 3731 6.206829 AGGATGTAAAGTAAGTTCAGCAAACC 59.793 38.462 0.00 0.0 38.76 3.27 R
4094 4152 0.780637 TCTGATATCCCCCGAGCTCT 59.219 55.000 12.85 0.0 0.00 4.09 R
4988 5146 0.535335 TAGAAGTCGACCCATGCCAC 59.465 55.000 13.01 0.0 0.00 5.01 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
73 75 2.712057 AAATCCGAGCTGCAAACAAG 57.288 45.000 1.02 0.00 0.00 3.16
183 185 1.087771 CCGTATCTTCGGTGGTTGCC 61.088 60.000 0.00 0.00 44.77 4.52
227 240 2.514592 ACGCCTCGGCCATCAATG 60.515 61.111 2.24 0.00 37.98 2.82
358 371 7.199766 CAGTTTTGTGTTTGTATGTGTGGTAT 58.800 34.615 0.00 0.00 0.00 2.73
362 375 7.899178 TTGTGTTTGTATGTGTGGTATAGAG 57.101 36.000 0.00 0.00 0.00 2.43
363 376 6.403049 TGTGTTTGTATGTGTGGTATAGAGG 58.597 40.000 0.00 0.00 0.00 3.69
364 377 5.293569 GTGTTTGTATGTGTGGTATAGAGGC 59.706 44.000 0.00 0.00 0.00 4.70
365 378 4.682778 TTGTATGTGTGGTATAGAGGCC 57.317 45.455 0.00 0.00 0.00 5.19
395 408 2.358322 TCTGGTTTGGTGGTTCCTTC 57.642 50.000 0.00 0.00 37.07 3.46
458 471 5.245075 GTGAAACATAAGGAATTTCCCACCA 59.755 40.000 11.92 0.00 34.71 4.17
469 482 0.036164 TTCCCACCACATTCTCACCG 59.964 55.000 0.00 0.00 0.00 4.94
579 592 1.068748 CATCTTGCACTGTCACCTTGC 60.069 52.381 0.00 0.00 36.76 4.01
580 593 0.107263 TCTTGCACTGTCACCTTGCA 60.107 50.000 0.00 0.00 44.40 4.08
668 681 0.179468 ACAACGGTGGTAACTGCTGT 59.821 50.000 4.97 0.00 37.20 4.40
849 865 6.868622 TCTCTTACTGTTTGAGGATAGAAGC 58.131 40.000 8.96 0.00 0.00 3.86
861 877 5.707298 TGAGGATAGAAGCACTTCCTTTTTG 59.293 40.000 6.77 0.00 40.33 2.44
998 1014 2.292267 AGTGAGCAGTCAAAGTTGTGG 58.708 47.619 0.00 0.00 33.27 4.17
1173 1189 1.683943 GCATTATCCAGCCTCAGCAA 58.316 50.000 0.00 0.00 43.56 3.91
1248 1264 1.471676 CCTAACATGGTCACCTCGCTC 60.472 57.143 0.00 0.00 0.00 5.03
1446 1462 0.038744 CACCAGGCCAAGGATTGTCT 59.961 55.000 20.01 0.00 46.99 3.41
1542 1558 5.658190 CCAATCTTACCAGGGTGATGAAAAT 59.342 40.000 0.06 0.00 0.00 1.82
1671 1687 1.131420 GCAGAACGCGCAGAAAGAG 59.869 57.895 5.73 0.00 0.00 2.85
1676 1692 1.569479 AACGCGCAGAAAGAGAAGGC 61.569 55.000 5.73 0.00 0.00 4.35
1824 1840 5.601662 CTCCAGAATAAGATGGCGAAACTA 58.398 41.667 0.00 0.00 36.47 2.24
1849 1865 2.173519 CCATGCTGGATGAGGTTTGTT 58.826 47.619 10.99 0.00 40.96 2.83
1852 1868 3.788227 TGCTGGATGAGGTTTGTTAGT 57.212 42.857 0.00 0.00 0.00 2.24
1854 1870 3.072330 TGCTGGATGAGGTTTGTTAGTCA 59.928 43.478 0.00 0.00 0.00 3.41
1855 1871 3.437049 GCTGGATGAGGTTTGTTAGTCAC 59.563 47.826 0.00 0.00 0.00 3.67
1857 1873 3.392947 TGGATGAGGTTTGTTAGTCACCA 59.607 43.478 0.00 0.00 0.00 4.17
1858 1874 3.751698 GGATGAGGTTTGTTAGTCACCAC 59.248 47.826 0.00 0.00 0.00 4.16
1860 1876 2.506231 TGAGGTTTGTTAGTCACCACCA 59.494 45.455 0.00 0.00 33.97 4.17
1861 1877 2.876550 GAGGTTTGTTAGTCACCACCAC 59.123 50.000 0.00 0.00 33.97 4.16
1862 1878 1.951602 GGTTTGTTAGTCACCACCACC 59.048 52.381 0.00 0.00 32.58 4.61
1864 1880 3.219281 GTTTGTTAGTCACCACCACCAT 58.781 45.455 0.00 0.00 0.00 3.55
1872 1888 7.180587 TGTTAGTCACCACCACCATATTTACTA 59.819 37.037 0.00 0.00 0.00 1.82
1895 1911 4.545610 TCGAAATCAAACTGAAATGCCAC 58.454 39.130 0.00 0.00 0.00 5.01
1925 1941 6.801539 TTACCTTTGCTTGACTAATCACTG 57.198 37.500 0.00 0.00 33.38 3.66
1958 1974 4.347607 TCTCATGAAGATCCACAGACTCA 58.652 43.478 0.00 0.00 0.00 3.41
1960 1976 5.424573 TCTCATGAAGATCCACAGACTCATT 59.575 40.000 0.00 0.00 0.00 2.57
1962 1978 5.878669 TCATGAAGATCCACAGACTCATTTG 59.121 40.000 0.00 0.00 0.00 2.32
1963 1979 5.233083 TGAAGATCCACAGACTCATTTGT 57.767 39.130 0.00 0.00 0.00 2.83
1964 1980 4.999311 TGAAGATCCACAGACTCATTTGTG 59.001 41.667 0.00 0.00 43.27 3.33
1966 1982 5.233083 AGATCCACAGACTCATTTGTGAA 57.767 39.130 6.21 0.00 45.79 3.18
1967 1983 4.999950 AGATCCACAGACTCATTTGTGAAC 59.000 41.667 6.21 0.00 45.79 3.18
2077 2094 4.096382 TGGTTGCAGTTCAGAGTTTCTTTC 59.904 41.667 0.00 0.00 0.00 2.62
2160 2178 9.939802 GTCCTATCTTTGTTCTTAGAAAAGGTA 57.060 33.333 0.00 0.00 33.04 3.08
2214 2232 4.520492 GGGGCATGGACTTAATATTGACTG 59.480 45.833 0.00 0.00 0.00 3.51
2319 2365 3.971245 AGTCAGGAGAGATGGTTCAAC 57.029 47.619 0.00 0.00 0.00 3.18
2330 2376 1.886886 TGGTTCAACGGTTTCTAGGC 58.113 50.000 0.00 0.00 0.00 3.93
2336 2382 2.202703 CGGTTTCTAGGCGGGTCG 60.203 66.667 0.00 0.00 0.00 4.79
2419 2465 6.420604 GTGCATGCAAGTTTTTAGCTAAAGAA 59.579 34.615 24.58 12.64 0.00 2.52
2630 2676 9.850628 GTTGGTAAAGTTTTGGTATCTAAATCC 57.149 33.333 0.00 0.00 0.00 3.01
2730 2776 1.910671 ACACGGGCTAAACAGGGATAA 59.089 47.619 0.00 0.00 0.00 1.75
2747 2793 3.954258 GGATAATGGCTTAACTGGCAACT 59.046 43.478 0.00 0.00 45.43 3.16
2830 2880 7.168219 TGAACTATTCTGAACACCAAGCTATT 58.832 34.615 0.00 0.00 0.00 1.73
3080 3131 2.856557 GTTAACTCGCCTCCGTTACATC 59.143 50.000 0.00 0.00 35.54 3.06
3283 3334 3.466836 TCGCTTTTGTTCTGATGACAGT 58.533 40.909 0.00 0.00 43.81 3.55
3284 3335 3.876914 TCGCTTTTGTTCTGATGACAGTT 59.123 39.130 0.00 0.00 43.81 3.16
3285 3336 5.053811 TCGCTTTTGTTCTGATGACAGTTA 58.946 37.500 0.00 0.00 43.81 2.24
3287 3338 6.204688 TCGCTTTTGTTCTGATGACAGTTATT 59.795 34.615 0.00 0.00 43.81 1.40
3289 3340 7.379529 CGCTTTTGTTCTGATGACAGTTATTTT 59.620 33.333 0.00 0.00 43.81 1.82
3389 3441 7.865706 ATGATCTTACCAAGAATTACCACAC 57.134 36.000 0.00 0.00 41.63 3.82
3454 3506 2.020720 CAATGCGCACAAATAGGGGTA 58.979 47.619 14.90 0.00 0.00 3.69
3551 3607 6.811954 TGTATGTCGATAACCTGCAAATAGA 58.188 36.000 0.00 0.00 0.00 1.98
3552 3608 7.269316 TGTATGTCGATAACCTGCAAATAGAA 58.731 34.615 0.00 0.00 0.00 2.10
3621 3677 7.227156 TCTAGGAGAATTGGATATTTGGCTTC 58.773 38.462 0.00 0.00 0.00 3.86
3673 3731 6.364165 ACTTTGCATTCTGTGAAATGAAATCG 59.636 34.615 0.98 0.00 38.64 3.34
3740 3798 0.887933 GGTTCATCAATGCCCGTGTT 59.112 50.000 0.00 0.00 0.00 3.32
3746 3804 3.055719 AATGCCCGTGTTCGCCTG 61.056 61.111 0.00 0.00 35.54 4.85
4037 4095 4.394712 CAAAGACCGGGCGAGGCT 62.395 66.667 6.32 0.00 33.69 4.58
4055 4113 2.574399 GACGGCAGTCTCCTCCAC 59.426 66.667 9.95 0.00 43.80 4.02
4149 4207 0.740868 GACGCTAGGATTGCAGCACA 60.741 55.000 0.00 0.00 37.66 4.57
4196 4254 2.438434 CACCGGCCAGGATTCACC 60.438 66.667 18.74 0.00 45.00 4.02
4236 4297 2.495366 CTACAACACCACCGCGGCTA 62.495 60.000 28.58 0.73 39.03 3.93
4292 4353 0.952497 ACGAGTCGACGAACCAGCTA 60.952 55.000 21.50 0.00 37.03 3.32
4604 4760 4.941873 GGAGACGAACCATCCTGTAAAAAT 59.058 41.667 0.00 0.00 0.00 1.82
4615 4771 7.612633 ACCATCCTGTAAAAATGTTACGGTAAT 59.387 33.333 3.59 0.00 31.13 1.89
4638 4794 6.471233 TGGATACTTCTGGTCAGTTATCTG 57.529 41.667 0.00 0.00 39.37 2.90
4640 4796 6.440647 TGGATACTTCTGGTCAGTTATCTGTT 59.559 38.462 0.83 0.00 39.18 3.16
4642 4798 5.552870 ACTTCTGGTCAGTTATCTGTTGT 57.447 39.130 0.83 0.00 41.91 3.32
4648 4804 2.807967 GTCAGTTATCTGTTGTGCAGCA 59.192 45.455 0.00 0.00 44.66 4.41
4660 4816 1.827789 TGCAGCAGGTGGTTGAACC 60.828 57.895 7.57 7.57 40.85 3.62
4696 4852 5.236263 GGAAAAACCTGTAAAAATGCACTGG 59.764 40.000 0.00 0.00 39.10 4.00
4718 4874 1.464997 GGGAACGCTTCAGATTGTGTC 59.535 52.381 0.00 0.00 0.00 3.67
4720 4876 2.413453 GGAACGCTTCAGATTGTGTCTC 59.587 50.000 0.00 0.00 34.00 3.36
4723 4879 2.036475 ACGCTTCAGATTGTGTCTCTGT 59.964 45.455 0.71 0.00 40.79 3.41
4724 4880 2.665537 CGCTTCAGATTGTGTCTCTGTC 59.334 50.000 0.71 0.00 40.79 3.51
4758 4916 4.514577 CGGAGCAGCCCCGTACAG 62.515 72.222 7.30 0.00 41.91 2.74
4759 4917 4.162690 GGAGCAGCCCCGTACAGG 62.163 72.222 0.00 0.00 40.63 4.00
4767 4925 3.542676 CCCGTACAGGCCGGCATA 61.543 66.667 30.85 14.66 44.13 3.14
4768 4926 2.741092 CCGTACAGGCCGGCATAT 59.259 61.111 30.85 14.69 38.85 1.78
4769 4927 1.667830 CCGTACAGGCCGGCATATG 60.668 63.158 30.85 24.66 38.85 1.78
4770 4928 2.317609 CGTACAGGCCGGCATATGC 61.318 63.158 30.85 19.79 41.14 3.14
4783 4941 3.591196 GCATATGCCAGTTTGGAAACA 57.409 42.857 17.26 0.00 40.96 2.83
4784 4942 3.514645 GCATATGCCAGTTTGGAAACAG 58.485 45.455 17.26 0.00 40.96 3.16
4785 4943 3.056607 GCATATGCCAGTTTGGAAACAGT 60.057 43.478 17.26 0.00 40.96 3.55
4786 4944 4.561326 GCATATGCCAGTTTGGAAACAGTT 60.561 41.667 17.26 0.00 40.96 3.16
4787 4945 5.540911 CATATGCCAGTTTGGAAACAGTTT 58.459 37.500 0.00 0.00 40.96 2.66
4788 4946 3.244033 TGCCAGTTTGGAAACAGTTTG 57.756 42.857 2.34 0.00 40.96 2.93
4789 4947 2.093764 TGCCAGTTTGGAAACAGTTTGG 60.094 45.455 2.34 0.00 40.96 3.28
4790 4948 2.167487 GCCAGTTTGGAAACAGTTTGGA 59.833 45.455 2.34 0.00 40.96 3.53
4795 4953 6.374053 CCAGTTTGGAAACAGTTTGGAAAAAT 59.626 34.615 2.34 0.00 40.96 1.82
4796 4954 7.242783 CAGTTTGGAAACAGTTTGGAAAAATG 58.757 34.615 2.34 6.93 44.54 2.32
4815 4973 6.639632 AAATGGTAATATCATCTGTGGTGC 57.360 37.500 0.00 0.00 0.00 5.01
4823 4981 3.213206 TCATCTGTGGTGCTTGAACTT 57.787 42.857 0.00 0.00 0.00 2.66
4846 5004 5.456548 TGACACGGATGTTCACTTTAGTA 57.543 39.130 0.00 0.00 39.95 1.82
4847 5005 6.032956 TGACACGGATGTTCACTTTAGTAT 57.967 37.500 0.00 0.00 39.95 2.12
4850 5008 7.121611 TGACACGGATGTTCACTTTAGTATCTA 59.878 37.037 0.00 0.00 39.95 1.98
4882 5040 8.845942 AAAAATACGTCAAACTTTTAGTGTCC 57.154 30.769 0.00 0.00 0.00 4.02
4883 5041 5.834239 ATACGTCAAACTTTTAGTGTCCG 57.166 39.130 0.00 0.00 0.00 4.79
4889 5047 6.019640 CGTCAAACTTTTAGTGTCCGAACTTA 60.020 38.462 0.00 0.00 0.00 2.24
4949 5107 4.585162 ACACGGTGTTAATCCCATTTGAAA 59.415 37.500 8.21 0.00 0.00 2.69
4952 5110 5.069251 ACGGTGTTAATCCCATTTGAAAACA 59.931 36.000 0.00 0.00 0.00 2.83
4980 5138 2.143122 CGCTGATATGGCACCGTATTT 58.857 47.619 2.96 0.00 0.00 1.40
4987 5145 0.034574 TGGCACCGTATTTGGCTGAT 60.035 50.000 0.00 0.00 40.16 2.90
4988 5146 0.381801 GGCACCGTATTTGGCTGATG 59.618 55.000 0.00 0.00 36.62 3.07
5000 5158 2.475466 GCTGATGTGGCATGGGTCG 61.475 63.158 0.00 0.00 0.00 4.79
5014 5172 0.524862 GGGTCGACTTCTAGCAACGA 59.475 55.000 16.46 0.00 0.00 3.85
5020 5178 2.854777 CGACTTCTAGCAACGAATCAGG 59.145 50.000 0.00 0.00 0.00 3.86
5032 5190 7.752695 AGCAACGAATCAGGATTTTAGTTAAG 58.247 34.615 0.00 0.00 0.00 1.85
5050 5208 7.516450 AGTTAAGTACTACTAGTGGGTCCTA 57.484 40.000 11.30 0.00 34.56 2.94
5061 5219 2.100989 GTGGGTCCTACCTGTCAGTAG 58.899 57.143 0.00 1.47 38.64 2.57
5071 5229 5.126384 CCTACCTGTCAGTAGAGAAGGAAAG 59.874 48.000 0.00 0.00 41.98 2.62
5091 5249 7.651704 AGGAAAGTTGAAATGAAAAATGGTACG 59.348 33.333 0.00 0.00 0.00 3.67
5092 5250 7.436970 GGAAAGTTGAAATGAAAAATGGTACGT 59.563 33.333 0.00 0.00 0.00 3.57
5093 5251 9.453325 GAAAGTTGAAATGAAAAATGGTACGTA 57.547 29.630 0.00 0.00 0.00 3.57
5094 5252 8.791355 AAGTTGAAATGAAAAATGGTACGTAC 57.209 30.769 17.56 17.56 0.00 3.67
5101 5259 5.613329 TGAAAAATGGTACGTACCTGAAGT 58.387 37.500 37.37 23.31 46.58 3.01
5105 5263 2.309613 TGGTACGTACCTGAAGTGTGT 58.690 47.619 37.37 0.00 46.58 3.72
5113 5271 2.672098 ACCTGAAGTGTGTGAGAGACT 58.328 47.619 0.00 0.00 0.00 3.24
5134 5292 1.967779 TGTGCTAGCCACTCTAACACA 59.032 47.619 13.29 3.30 46.40 3.72
5135 5293 2.029020 TGTGCTAGCCACTCTAACACAG 60.029 50.000 13.29 0.00 44.77 3.66
5168 5326 5.286221 AGATAACAAAGGCCCCTTAGTCTA 58.714 41.667 0.00 0.00 34.84 2.59
5169 5327 5.367060 AGATAACAAAGGCCCCTTAGTCTAG 59.633 44.000 0.00 0.00 34.84 2.43
5240 5409 6.205853 CGGCCCATTTAGTGTATGCTAATTTA 59.794 38.462 0.00 0.00 31.83 1.40
5316 5485 8.500753 AAGTTCAACTATTCATGCGGTATTAA 57.499 30.769 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.833834 ACAGAGGTGGGAGTGGTGAG 60.834 60.000 0.00 0.00 0.00 3.51
183 185 1.447489 CTCCTTCACCAGCTCAGCG 60.447 63.158 0.00 0.00 0.00 5.18
227 240 4.024556 CGGCAATACCTTGTCTGATCAATC 60.025 45.833 0.00 0.00 34.73 2.67
358 371 1.741327 GATAACACGGCCGGCCTCTA 61.741 60.000 41.01 25.72 0.00 2.43
362 375 2.895372 CAGATAACACGGCCGGCC 60.895 66.667 36.69 36.69 0.00 6.13
363 376 2.895372 CCAGATAACACGGCCGGC 60.895 66.667 31.76 21.18 0.00 6.13
364 377 0.675522 AAACCAGATAACACGGCCGG 60.676 55.000 31.76 20.69 0.00 6.13
365 378 0.446222 CAAACCAGATAACACGGCCG 59.554 55.000 26.86 26.86 0.00 6.13
452 465 0.673644 GACGGTGAGAATGTGGTGGG 60.674 60.000 0.00 0.00 0.00 4.61
469 482 0.108585 TGCACCTTCCTCACCAAGAC 59.891 55.000 0.00 0.00 0.00 3.01
579 592 4.778534 ATGCTCAGGAAACAAGACAATG 57.221 40.909 0.00 0.00 0.00 2.82
580 593 4.021719 CCAATGCTCAGGAAACAAGACAAT 60.022 41.667 0.00 0.00 0.00 2.71
668 681 4.973168 AGCCTCACATTTGTACTCTTTGA 58.027 39.130 0.00 0.00 0.00 2.69
794 810 9.343539 GCAACCAATAGTAATTCCTTATCTCTT 57.656 33.333 0.00 0.00 0.00 2.85
849 865 7.716612 AGAATAACCAACTCAAAAAGGAAGTG 58.283 34.615 0.00 0.00 0.00 3.16
861 877 7.497925 AACACTGAAGAAGAATAACCAACTC 57.502 36.000 0.00 0.00 0.00 3.01
907 923 2.284112 ACCTGCCTGCAAATGGGG 60.284 61.111 0.00 0.00 0.00 4.96
911 927 3.700538 TCTAATTGACCTGCCTGCAAAT 58.299 40.909 0.00 0.00 0.00 2.32
998 1014 6.347725 CGGGCTTGAGTAATAATTAGACATGC 60.348 42.308 0.00 0.00 0.00 4.06
1173 1189 2.419574 GCCATGCAGCTCCATGAAATTT 60.420 45.455 19.55 0.00 44.12 1.82
1446 1462 3.118629 GGATATGTGTGTTGAGGCTCAGA 60.119 47.826 17.91 5.74 0.00 3.27
1542 1558 4.129380 CCGACTGCATATTCTTCATTCCA 58.871 43.478 0.00 0.00 0.00 3.53
1671 1687 3.582780 CATTTTTCCTGCTTCAGCCTTC 58.417 45.455 0.00 0.00 41.18 3.46
1676 1692 3.677976 GCCATCCATTTTTCCTGCTTCAG 60.678 47.826 0.00 0.00 0.00 3.02
1771 1787 0.742281 TCAGCCGCAGAAATCTCAGC 60.742 55.000 0.00 0.00 0.00 4.26
1849 1865 7.255695 CGATAGTAAATATGGTGGTGGTGACTA 60.256 40.741 0.00 0.00 0.00 2.59
1852 1868 5.599242 TCGATAGTAAATATGGTGGTGGTGA 59.401 40.000 0.00 0.00 37.40 4.02
1854 1870 6.488769 TTCGATAGTAAATATGGTGGTGGT 57.511 37.500 0.00 0.00 37.40 4.16
1855 1871 7.659799 TGATTTCGATAGTAAATATGGTGGTGG 59.340 37.037 0.00 0.00 37.40 4.61
1857 1873 9.621629 TTTGATTTCGATAGTAAATATGGTGGT 57.378 29.630 0.00 0.00 37.40 4.16
1858 1874 9.878599 GTTTGATTTCGATAGTAAATATGGTGG 57.121 33.333 0.00 0.00 37.40 4.61
1872 1888 5.163513 GTGGCATTTCAGTTTGATTTCGAT 58.836 37.500 0.00 0.00 0.00 3.59
1895 1911 5.613358 AGTCAAGCAAAGGTAAATCTTCG 57.387 39.130 0.00 0.00 0.00 3.79
1925 1941 7.170658 GTGGATCTTCATGAGAATTACAGCTAC 59.829 40.741 0.00 0.00 38.06 3.58
2039 2056 5.481473 ACTGCAACCATCACCAAATAAAGAT 59.519 36.000 0.00 0.00 0.00 2.40
2040 2057 4.832266 ACTGCAACCATCACCAAATAAAGA 59.168 37.500 0.00 0.00 0.00 2.52
2054 2071 3.281727 AGAAACTCTGAACTGCAACCA 57.718 42.857 0.00 0.00 0.00 3.67
2055 2072 4.336713 AGAAAGAAACTCTGAACTGCAACC 59.663 41.667 0.00 0.00 0.00 3.77
2092 2109 1.621992 TGAGAAACTCTGAGCTCCGT 58.378 50.000 12.15 2.77 0.00 4.69
2095 2112 6.262944 TCTGAGATATGAGAAACTCTGAGCTC 59.737 42.308 6.82 6.82 34.32 4.09
2188 2206 6.102615 AGTCAATATTAAGTCCATGCCCCTTA 59.897 38.462 0.00 0.00 0.00 2.69
2214 2232 6.431234 GGATCATGACCCATTTATGTTACTCC 59.569 42.308 0.00 0.00 0.00 3.85
2227 2245 3.805066 TGAACTTTGGATCATGACCCA 57.195 42.857 4.01 4.01 0.00 4.51
2319 2365 2.202703 CGACCCGCCTAGAAACCG 60.203 66.667 0.00 0.00 0.00 4.44
2330 2376 0.815734 TCTTAAGAAGCCTCGACCCG 59.184 55.000 1.68 0.00 0.00 5.28
2336 2382 5.064579 CAGCTAAGCTTTCTTAAGAAGCCTC 59.935 44.000 24.04 13.87 36.40 4.70
2419 2465 1.003696 GCTTAGTGCTTCCTTGGAGGT 59.996 52.381 0.85 0.00 36.22 3.85
2636 2682 9.120538 TCTCAGCAAAGTTTCTGTATTTAGTTT 57.879 29.630 12.04 0.00 0.00 2.66
2714 2760 2.158460 AGCCATTATCCCTGTTTAGCCC 60.158 50.000 0.00 0.00 0.00 5.19
2730 2776 2.875296 TCAAGTTGCCAGTTAAGCCAT 58.125 42.857 0.00 0.00 0.00 4.40
2747 2793 7.708752 ACTGAAAAATAAGAAAACCGCATTCAA 59.291 29.630 0.00 0.00 0.00 2.69
2802 2852 6.491403 AGCTTGGTGTTCAGAATAGTTCATTT 59.509 34.615 0.00 0.00 0.00 2.32
3080 3131 2.076100 TGTTGCCTTAACTGCTGATCG 58.924 47.619 0.00 0.00 40.05 3.69
3247 3298 2.200337 GCGAAAAGGGGCAAGTGGT 61.200 57.895 0.00 0.00 0.00 4.16
3289 3340 7.728083 TCTGAATCTTTTGGATACCTGGAAAAA 59.272 33.333 0.00 0.00 33.71 1.94
3294 3345 7.466746 TTTTCTGAATCTTTTGGATACCTGG 57.533 36.000 0.00 0.00 33.71 4.45
3401 3453 6.186957 ACTAACAAGGCATACCAATCATTGA 58.813 36.000 0.00 0.00 39.06 2.57
3402 3454 6.455360 ACTAACAAGGCATACCAATCATTG 57.545 37.500 0.00 0.00 39.06 2.82
3438 3490 0.741927 ACGTACCCCTATTTGTGCGC 60.742 55.000 0.00 0.00 43.06 6.09
3454 3506 7.356089 TGGATATTACCAAGATGAGTTACGT 57.644 36.000 0.00 0.00 36.96 3.57
3621 3677 3.970610 CAGAAGTCATTTGCACACTTTCG 59.029 43.478 0.00 0.00 30.32 3.46
3673 3731 6.206829 AGGATGTAAAGTAAGTTCAGCAAACC 59.793 38.462 0.00 0.00 38.76 3.27
3740 3798 1.375396 CATCGGTTTCCACAGGCGA 60.375 57.895 0.00 0.00 0.00 5.54
3746 3804 2.603560 GTCTTCGATCATCGGTTTCCAC 59.396 50.000 7.33 0.00 40.88 4.02
4094 4152 0.780637 TCTGATATCCCCCGAGCTCT 59.219 55.000 12.85 0.00 0.00 4.09
4149 4207 2.271940 CTGAGAGGCTGTTCTCGGT 58.728 57.895 0.00 0.00 45.26 4.69
4201 4259 1.041437 GTAGATGTCCTCTTCCCCGG 58.959 60.000 0.00 0.00 35.28 5.73
4214 4275 1.358725 CCGCGGTGGTGTTGTAGATG 61.359 60.000 19.50 0.00 0.00 2.90
4292 4353 0.877071 CAAACTGCTGCCGTTGATCT 59.123 50.000 10.20 0.00 0.00 2.75
4331 4392 2.487762 GTTCATTCAGGCCACGAAATCA 59.512 45.455 5.01 0.00 0.00 2.57
4604 4760 5.422970 ACCAGAAGTATCCATTACCGTAACA 59.577 40.000 0.00 0.00 0.00 2.41
4615 4771 5.958380 ACAGATAACTGACCAGAAGTATCCA 59.042 40.000 7.05 0.00 46.03 3.41
4638 4794 1.066257 CAACCACCTGCTGCACAAC 59.934 57.895 0.00 0.00 0.00 3.32
4640 4796 1.077140 TTCAACCACCTGCTGCACA 60.077 52.632 0.00 0.00 0.00 4.57
4642 4798 1.827789 GGTTCAACCACCTGCTGCA 60.828 57.895 0.01 0.88 38.42 4.41
4665 4821 7.279981 GCATTTTTACAGGTTTTTCCTTCTGTT 59.720 33.333 0.00 0.00 45.67 3.16
4666 4822 6.761242 GCATTTTTACAGGTTTTTCCTTCTGT 59.239 34.615 0.00 0.00 45.67 3.41
4667 4823 6.760770 TGCATTTTTACAGGTTTTTCCTTCTG 59.239 34.615 0.00 0.00 45.67 3.02
4668 4824 6.761242 GTGCATTTTTACAGGTTTTTCCTTCT 59.239 34.615 0.00 0.00 45.67 2.85
4669 4825 6.761242 AGTGCATTTTTACAGGTTTTTCCTTC 59.239 34.615 0.00 0.00 45.67 3.46
4673 4829 6.045955 TCCAGTGCATTTTTACAGGTTTTTC 58.954 36.000 0.00 0.00 0.00 2.29
4674 4830 5.983540 TCCAGTGCATTTTTACAGGTTTTT 58.016 33.333 0.00 0.00 0.00 1.94
4675 4831 5.453198 CCTCCAGTGCATTTTTACAGGTTTT 60.453 40.000 0.00 0.00 0.00 2.43
4693 4849 0.539051 ATCTGAAGCGTTCCCTCCAG 59.461 55.000 0.00 0.00 0.00 3.86
4696 4852 1.734465 CACAATCTGAAGCGTTCCCTC 59.266 52.381 0.00 0.00 0.00 4.30
4720 4876 2.746362 GGTTGGAAATGCTCTGAGACAG 59.254 50.000 9.28 0.00 0.00 3.51
4723 4879 1.339055 CCGGTTGGAAATGCTCTGAGA 60.339 52.381 9.28 0.00 37.49 3.27
4724 4880 1.089920 CCGGTTGGAAATGCTCTGAG 58.910 55.000 0.00 0.00 37.49 3.35
4734 4892 4.344865 GGGCTGCTCCGGTTGGAA 62.345 66.667 0.00 0.00 45.87 3.53
4752 4910 2.317609 GCATATGCCGGCCTGTACG 61.318 63.158 26.77 8.17 34.31 3.67
4753 4911 3.655481 GCATATGCCGGCCTGTAC 58.345 61.111 26.77 7.09 34.31 2.90
4763 4921 3.056607 ACTGTTTCCAAACTGGCATATGC 60.057 43.478 19.79 19.79 40.72 3.14
4764 4922 4.789012 ACTGTTTCCAAACTGGCATATG 57.211 40.909 12.15 0.00 40.72 1.78
4765 4923 5.511202 CCAAACTGTTTCCAAACTGGCATAT 60.511 40.000 2.13 0.00 40.72 1.78
4766 4924 4.202202 CCAAACTGTTTCCAAACTGGCATA 60.202 41.667 2.13 0.00 40.72 3.14
4767 4925 3.432046 CCAAACTGTTTCCAAACTGGCAT 60.432 43.478 2.13 0.00 40.72 4.40
4768 4926 2.093764 CCAAACTGTTTCCAAACTGGCA 60.094 45.455 2.13 0.00 40.72 4.92
4769 4927 2.167487 TCCAAACTGTTTCCAAACTGGC 59.833 45.455 2.13 0.00 40.72 4.85
4770 4928 4.464069 TTCCAAACTGTTTCCAAACTGG 57.536 40.909 2.13 0.84 40.72 4.00
4772 4930 6.374053 CCATTTTTCCAAACTGTTTCCAAACT 59.626 34.615 2.13 0.00 39.59 2.66
4773 4931 6.150307 ACCATTTTTCCAAACTGTTTCCAAAC 59.850 34.615 2.13 0.00 39.33 2.93
4774 4932 6.241645 ACCATTTTTCCAAACTGTTTCCAAA 58.758 32.000 2.13 2.81 0.00 3.28
4775 4933 5.810095 ACCATTTTTCCAAACTGTTTCCAA 58.190 33.333 2.13 0.00 0.00 3.53
4776 4934 5.428184 ACCATTTTTCCAAACTGTTTCCA 57.572 34.783 2.13 0.00 0.00 3.53
4777 4935 9.719355 ATATTACCATTTTTCCAAACTGTTTCC 57.281 29.630 2.13 0.00 0.00 3.13
4786 4944 8.694540 CCACAGATGATATTACCATTTTTCCAA 58.305 33.333 0.00 0.00 0.00 3.53
4787 4945 7.838696 ACCACAGATGATATTACCATTTTTCCA 59.161 33.333 0.00 0.00 0.00 3.53
4788 4946 8.137437 CACCACAGATGATATTACCATTTTTCC 58.863 37.037 0.00 0.00 0.00 3.13
4789 4947 7.649306 GCACCACAGATGATATTACCATTTTTC 59.351 37.037 0.00 0.00 0.00 2.29
4790 4948 7.342799 AGCACCACAGATGATATTACCATTTTT 59.657 33.333 0.00 0.00 0.00 1.94
4795 4953 5.104569 TCAAGCACCACAGATGATATTACCA 60.105 40.000 0.00 0.00 0.00 3.25
4796 4954 5.368145 TCAAGCACCACAGATGATATTACC 58.632 41.667 0.00 0.00 0.00 2.85
4807 4965 2.423185 TGTCAAAGTTCAAGCACCACAG 59.577 45.455 0.00 0.00 0.00 3.66
4808 4966 2.163412 GTGTCAAAGTTCAAGCACCACA 59.837 45.455 0.00 0.00 0.00 4.17
4815 4973 4.035091 TGAACATCCGTGTCAAAGTTCAAG 59.965 41.667 0.00 0.00 41.39 3.02
4823 4981 4.699637 ACTAAAGTGAACATCCGTGTCAA 58.300 39.130 0.00 0.00 37.67 3.18
4858 5016 7.011295 TCGGACACTAAAAGTTTGACGTATTTT 59.989 33.333 0.00 0.00 0.00 1.82
4864 5022 4.269363 AGTTCGGACACTAAAAGTTTGACG 59.731 41.667 0.00 0.00 0.00 4.35
4866 5024 7.846644 TTAAGTTCGGACACTAAAAGTTTGA 57.153 32.000 0.00 0.00 0.00 2.69
4906 5064 5.907391 CGTGTTCATGTCAAGTTTTAGAACC 59.093 40.000 0.00 0.00 36.39 3.62
4915 5073 2.325583 ACACCGTGTTCATGTCAAGT 57.674 45.000 0.00 0.00 0.00 3.16
4949 5107 6.293955 GGTGCCATATCAGCGTAATTTATGTT 60.294 38.462 0.00 0.00 0.00 2.71
4952 5110 5.880054 GGTGCCATATCAGCGTAATTTAT 57.120 39.130 0.00 0.00 0.00 1.40
4980 5138 2.043752 CCCATGCCACATCAGCCA 60.044 61.111 0.00 0.00 0.00 4.75
4987 5145 1.003839 GAAGTCGACCCATGCCACA 60.004 57.895 13.01 0.00 0.00 4.17
4988 5146 0.535335 TAGAAGTCGACCCATGCCAC 59.465 55.000 13.01 0.00 0.00 5.01
5000 5158 4.111375 TCCTGATTCGTTGCTAGAAGTC 57.889 45.455 0.00 0.00 0.00 3.01
5032 5190 4.080072 ACAGGTAGGACCCACTAGTAGTAC 60.080 50.000 1.57 0.00 39.75 2.73
5041 5199 2.100989 CTACTGACAGGTAGGACCCAC 58.899 57.143 7.51 0.00 39.75 4.61
5050 5208 4.484912 ACTTTCCTTCTCTACTGACAGGT 58.515 43.478 7.51 0.00 0.00 4.00
5061 5219 8.768019 CCATTTTTCATTTCAACTTTCCTTCTC 58.232 33.333 0.00 0.00 0.00 2.87
5071 5229 7.557036 GGTACGTACCATTTTTCATTTCAAC 57.443 36.000 34.65 5.50 45.73 3.18
5091 5249 3.570550 AGTCTCTCACACACTTCAGGTAC 59.429 47.826 0.00 0.00 0.00 3.34
5092 5250 3.833732 AGTCTCTCACACACTTCAGGTA 58.166 45.455 0.00 0.00 0.00 3.08
5093 5251 2.672098 AGTCTCTCACACACTTCAGGT 58.328 47.619 0.00 0.00 0.00 4.00
5094 5252 3.181471 ACAAGTCTCTCACACACTTCAGG 60.181 47.826 0.00 0.00 0.00 3.86
5101 5259 2.288457 GCTAGCACAAGTCTCTCACACA 60.288 50.000 10.63 0.00 0.00 3.72
5105 5263 1.273606 GTGGCTAGCACAAGTCTCTCA 59.726 52.381 18.24 0.00 0.00 3.27
5134 5292 5.825151 GGCCTTTGTTATCTCATAAAGCTCT 59.175 40.000 0.00 0.00 0.00 4.09
5135 5293 5.009110 GGGCCTTTGTTATCTCATAAAGCTC 59.991 44.000 0.84 0.00 0.00 4.09
5168 5326 3.853307 GCACAAGCTTTGTATTTCGCACT 60.853 43.478 0.00 0.00 43.23 4.40
5169 5327 2.405025 GCACAAGCTTTGTATTTCGCAC 59.595 45.455 0.00 0.00 43.23 5.34
5283 5452 9.767684 CGCATGAATAGTTGAACTTTATTTGTA 57.232 29.630 1.97 0.00 0.00 2.41
5290 5459 7.391148 AATACCGCATGAATAGTTGAACTTT 57.609 32.000 1.97 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.