Multiple sequence alignment - TraesCS1A01G399200

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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 TraesCS1A01G399200 chr1A 100.000 2603 0 0 1 2603 563783236 563785838 0.000000e+00 4807
1 TraesCS1A01G399200 chr1A 85.467 2250 214 49 28 2247 563773790 563775956 0.000000e+00 2239
2 TraesCS1A01G399200 chr1A 80.600 1433 238 29 373 1786 563765434 563766845 0.000000e+00 1070
3 TraesCS1A01G399200 chr1A 82.002 1039 120 40 1248 2272 563799386 563800371 0.000000e+00 821
4 TraesCS1A01G399200 chr1A 85.333 225 22 4 2379 2603 563776218 563776431 3.370000e-54 222
5 TraesCS1A01G399200 chr1D 96.104 1463 39 10 99 1556 470189835 470191284 0.000000e+00 2370
6 TraesCS1A01G399200 chr1D 85.315 2145 197 49 127 2247 470183744 470185794 0.000000e+00 2108
7 TraesCS1A01G399200 chr1D 81.619 1458 233 26 345 1786 470077534 470078972 0.000000e+00 1175
8 TraesCS1A01G399200 chr1D 80.327 1469 233 37 255 1691 470198294 470199738 0.000000e+00 1061
9 TraesCS1A01G399200 chr1D 83.502 1085 130 29 926 1995 470191312 470192362 0.000000e+00 966
10 TraesCS1A01G399200 chr1D 83.465 635 66 15 1977 2594 470195383 470195995 2.930000e-154 555
11 TraesCS1A01G399200 chr1D 84.889 225 23 4 2379 2603 470186056 470186269 1.570000e-52 217
12 TraesCS1A01G399200 chr1D 93.939 66 3 1 3 67 470188509 470188574 5.930000e-17 99
13 TraesCS1A01G399200 chr1B 86.080 2069 209 39 119 2166 652564403 652566413 0.000000e+00 2152
14 TraesCS1A01G399200 chr1B 82.235 1942 240 58 83 1995 652569677 652571542 0.000000e+00 1578
15 TraesCS1A01G399200 chr1B 81.382 1606 210 57 115 1691 652574544 652576089 0.000000e+00 1227
16 TraesCS1A01G399200 chr1B 80.848 1603 235 47 122 1691 652632898 652634461 0.000000e+00 1194
17 TraesCS1A01G399200 chr1B 94.286 770 22 9 3 758 652567807 652568568 0.000000e+00 1158
18 TraesCS1A01G399200 chr1B 80.874 1464 237 32 345 1786 652459706 652461148 0.000000e+00 1112
19 TraesCS1A01G399200 chr1B 86.017 472 52 5 2059 2518 652571800 652572269 6.470000e-136 494
20 TraesCS1A01G399200 chr2B 96.166 313 11 1 2292 2603 184421485 184421797 6.430000e-141 510


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 TraesCS1A01G399200 chr1A 563783236 563785838 2602 False 4807.000000 4807 100.000000 1 2603 1 chr1A.!!$F2 2602
1 TraesCS1A01G399200 chr1A 563773790 563776431 2641 False 1230.500000 2239 85.400000 28 2603 2 chr1A.!!$F4 2575
2 TraesCS1A01G399200 chr1A 563765434 563766845 1411 False 1070.000000 1070 80.600000 373 1786 1 chr1A.!!$F1 1413
3 TraesCS1A01G399200 chr1A 563799386 563800371 985 False 821.000000 821 82.002000 1248 2272 1 chr1A.!!$F3 1024
4 TraesCS1A01G399200 chr1D 470077534 470078972 1438 False 1175.000000 1175 81.619000 345 1786 1 chr1D.!!$F1 1441
5 TraesCS1A01G399200 chr1D 470183744 470199738 15994 False 1053.714286 2370 86.791571 3 2603 7 chr1D.!!$F2 2600
6 TraesCS1A01G399200 chr1B 652564403 652576089 11686 False 1321.800000 2152 86.000000 3 2518 5 chr1B.!!$F3 2515
7 TraesCS1A01G399200 chr1B 652632898 652634461 1563 False 1194.000000 1194 80.848000 122 1691 1 chr1B.!!$F2 1569
8 TraesCS1A01G399200 chr1B 652459706 652461148 1442 False 1112.000000 1112 80.874000 345 1786 1 chr1B.!!$F1 1441

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
332 337 0.165944 GGTGGTTGCGATGTTCGAAG 59.834 55.0 0.0 0.0 43.74 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2319 27014 0.664166 CGCAGTGCAAATCAACACCC 60.664 55.0 16.83 0.0 37.51 4.61 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
25 26 4.341783 GCCTGGGCTGCACTCACT 62.342 66.667 2.50 0.00 38.26 3.41
26 27 2.433446 CCTGGGCTGCACTCACTT 59.567 61.111 2.50 0.00 0.00 3.16
36 37 1.301716 CACTCACTTGGTCACCCGG 60.302 63.158 0.00 0.00 0.00 5.73
37 38 2.358737 CTCACTTGGTCACCCGGC 60.359 66.667 0.00 0.00 0.00 6.13
65 67 4.007644 CTCCACGCTGCACTCCCA 62.008 66.667 0.00 0.00 0.00 4.37
66 68 4.314440 TCCACGCTGCACTCCCAC 62.314 66.667 0.00 0.00 0.00 4.61
148 150 4.444838 CGGACGGCCAATCGACCA 62.445 66.667 8.76 0.00 43.14 4.02
149 151 2.189521 GGACGGCCAATCGACCAT 59.810 61.111 0.00 0.00 42.68 3.55
150 152 1.451387 GGACGGCCAATCGACCATT 60.451 57.895 0.00 0.00 42.68 3.16
161 163 2.125512 GACCATTCGACCGCTGCT 60.126 61.111 0.00 0.00 0.00 4.24
162 164 2.434884 ACCATTCGACCGCTGCTG 60.435 61.111 0.00 0.00 0.00 4.41
207 210 2.592512 ACCTCTTCCTTCTCCCCTCATA 59.407 50.000 0.00 0.00 0.00 2.15
209 212 3.837731 CCTCTTCCTTCTCCCCTCATATC 59.162 52.174 0.00 0.00 0.00 1.63
215 218 2.203938 TCCCCTCATATCCCGGCC 60.204 66.667 0.00 0.00 0.00 6.13
223 226 2.494073 CTCATATCCCGGCCTACTCTTC 59.506 54.545 0.00 0.00 0.00 2.87
235 238 1.742831 CTACTCTTCTGCTCGCTCACT 59.257 52.381 0.00 0.00 0.00 3.41
254 257 0.250467 TGGAGCTTTCTTCGCTGCTT 60.250 50.000 5.22 0.00 44.82 3.91
303 306 0.725784 GTGTTCGACGCATTGCTTGG 60.726 55.000 7.12 0.00 0.00 3.61
312 315 2.049248 ATTGCTTGGCGCGTTTGG 60.049 55.556 8.43 0.00 43.27 3.28
331 336 1.231958 GGGTGGTTGCGATGTTCGAA 61.232 55.000 0.00 0.00 43.74 3.71
332 337 0.165944 GGTGGTTGCGATGTTCGAAG 59.834 55.000 0.00 0.00 43.74 3.79
333 338 0.865769 GTGGTTGCGATGTTCGAAGT 59.134 50.000 0.00 0.00 43.74 3.01
353 358 6.743172 CGAAGTACGATATCATTCGATGATGT 59.257 38.462 17.60 11.53 46.06 3.06
359 364 6.564686 ACGATATCATTCGATGATGTTGTTGC 60.565 38.462 16.01 0.00 46.83 4.17
368 373 3.797451 TGATGTTGTTGCTTCTTTGCA 57.203 38.095 0.00 0.00 41.65 4.08
369 374 3.708890 TGATGTTGTTGCTTCTTTGCAG 58.291 40.909 0.00 0.00 44.27 4.41
372 377 1.113788 TTGTTGCTTCTTTGCAGCCT 58.886 45.000 0.00 0.00 44.27 4.58
387 6553 0.333993 AGCCTTGCAGGAATGATGGT 59.666 50.000 0.00 0.00 37.67 3.55
392 6558 3.220110 CTTGCAGGAATGATGGTAGCAT 58.780 45.455 7.23 7.23 0.00 3.79
423 6589 4.988598 CCCGCAGCCACAGTCGTT 62.989 66.667 0.00 0.00 0.00 3.85
501 6667 4.072088 CGACCGTGCCGTCTTTGC 62.072 66.667 0.00 0.00 0.00 3.68
637 6803 1.903404 CTTCCCTGGTTGCGGCTTT 60.903 57.895 0.00 0.00 0.00 3.51
721 6887 0.552848 TCAATCCATTCTCCAGGGCC 59.447 55.000 0.00 0.00 0.00 5.80
764 6930 4.176851 GCGTCCGACTCCGTCCTC 62.177 72.222 0.00 0.00 0.00 3.71
1102 7269 0.673644 CGGCGATCCACAGGTTTCTT 60.674 55.000 0.00 0.00 0.00 2.52
1408 15895 0.109226 GTCTGTGTCTCAGTACGGGC 60.109 60.000 2.02 0.00 43.97 6.13
1457 15944 6.528321 TGGATGATGATGAGGAGAATTGTAC 58.472 40.000 0.00 0.00 0.00 2.90
1492 15979 4.119862 CGACAAGGAGAACACTTCTTTCA 58.880 43.478 0.00 0.00 40.87 2.69
1525 16012 1.552337 TGAGATCCAGCAGTGTCCTTC 59.448 52.381 0.00 0.00 0.00 3.46
1527 16014 0.460987 GATCCAGCAGTGTCCTTCCG 60.461 60.000 0.00 0.00 0.00 4.30
1530 16017 3.241530 AGCAGTGTCCTTCCGGCA 61.242 61.111 0.00 0.00 0.00 5.69
1531 16018 2.045926 GCAGTGTCCTTCCGGCAT 60.046 61.111 0.00 0.00 0.00 4.40
1532 16019 2.401766 GCAGTGTCCTTCCGGCATG 61.402 63.158 0.00 0.00 0.00 4.06
1538 16025 2.124570 CCTTCCGGCATGTCCCAG 60.125 66.667 0.00 0.00 0.00 4.45
1620 16107 6.258727 ACCGATGAGAATGTGTCATAATGTTC 59.741 38.462 0.00 0.00 34.69 3.18
1640 16127 4.115401 TCTATATATGCAAGCTGCTCCG 57.885 45.455 1.00 0.00 45.31 4.63
1650 16137 2.362397 CAAGCTGCTCCGAGGTTATCTA 59.638 50.000 1.00 0.00 32.42 1.98
1662 16149 5.221145 CCGAGGTTATCTAGCCATGCTATAG 60.221 48.000 0.00 0.00 40.54 1.31
1685 16172 2.885894 TGTTGTTGTTCCGGGGTTATTC 59.114 45.455 0.00 0.00 0.00 1.75
1687 16174 3.062122 TGTTGTTCCGGGGTTATTCTC 57.938 47.619 0.00 0.00 0.00 2.87
1692 16179 1.961133 TCCGGGGTTATTCTCCAACT 58.039 50.000 0.00 0.00 36.19 3.16
1694 16181 2.645797 TCCGGGGTTATTCTCCAACTTT 59.354 45.455 0.00 0.00 36.19 2.66
1701 16188 7.116736 GGGGTTATTCTCCAACTTTCTCATAA 58.883 38.462 0.00 0.00 36.51 1.90
1718 16205 9.973450 TTTCTCATAAGTTATCTATCTGACTGC 57.027 33.333 0.00 0.00 0.00 4.40
1719 16206 7.811653 TCTCATAAGTTATCTATCTGACTGCG 58.188 38.462 0.00 0.00 0.00 5.18
1721 16208 6.490381 TCATAAGTTATCTATCTGACTGCGGT 59.510 38.462 0.00 0.00 0.00 5.68
1722 16209 7.664318 TCATAAGTTATCTATCTGACTGCGGTA 59.336 37.037 0.00 0.00 0.00 4.02
1724 16211 5.378332 AGTTATCTATCTGACTGCGGTAGT 58.622 41.667 0.00 0.00 44.02 2.73
1725 16212 6.531923 AGTTATCTATCTGACTGCGGTAGTA 58.468 40.000 0.00 0.00 40.53 1.82
1738 21537 2.549349 GCGGTAGTATATGGTGGTTGGG 60.549 54.545 0.00 0.00 0.00 4.12
1749 21548 2.224670 TGGTGGTTGGGATAGTGTTCAC 60.225 50.000 0.00 0.00 0.00 3.18
1755 21554 3.695830 TGGGATAGTGTTCACTGGTTC 57.304 47.619 14.69 8.99 0.00 3.62
1764 21563 2.714250 TGTTCACTGGTTCCCCTACAAT 59.286 45.455 0.00 0.00 0.00 2.71
1767 21566 0.909623 ACTGGTTCCCCTACAATCCG 59.090 55.000 0.00 0.00 0.00 4.18
1786 21585 7.224753 ACAATCCGTGAAATGCATTAGTAGTAG 59.775 37.037 13.39 1.42 0.00 2.57
1787 21586 6.459670 TCCGTGAAATGCATTAGTAGTAGA 57.540 37.500 13.39 1.65 0.00 2.59
1789 21588 7.324935 TCCGTGAAATGCATTAGTAGTAGAAA 58.675 34.615 13.39 0.00 0.00 2.52
1790 21589 7.820386 TCCGTGAAATGCATTAGTAGTAGAAAA 59.180 33.333 13.39 0.00 0.00 2.29
1808 21607 9.838339 AGTAGAAAATAGTAATATTGCTGCTGT 57.162 29.630 15.50 0.00 0.00 4.40
1810 21609 8.970859 AGAAAATAGTAATATTGCTGCTGTCT 57.029 30.769 15.50 9.23 0.00 3.41
1817 21616 7.377398 AGTAATATTGCTGCTGTCTATCTGAG 58.623 38.462 5.15 0.00 0.00 3.35
1831 21630 5.518487 GTCTATCTGAGCTTTGTTACTCTGC 59.482 44.000 0.00 0.00 33.92 4.26
1840 21639 4.377841 GCTTTGTTACTCTGCTAAGTGCTG 60.378 45.833 2.29 0.00 43.37 4.41
1841 21640 4.336889 TTGTTACTCTGCTAAGTGCTGT 57.663 40.909 2.29 0.00 43.37 4.40
1842 21641 4.336889 TGTTACTCTGCTAAGTGCTGTT 57.663 40.909 2.29 0.00 43.37 3.16
1843 21642 4.703897 TGTTACTCTGCTAAGTGCTGTTT 58.296 39.130 2.29 0.00 43.37 2.83
1844 21643 4.511454 TGTTACTCTGCTAAGTGCTGTTTG 59.489 41.667 2.29 0.00 43.37 2.93
1847 21646 3.561725 ACTCTGCTAAGTGCTGTTTGTTC 59.438 43.478 0.00 0.00 43.37 3.18
1856 21655 2.033801 GTGCTGTTTGTTCATCAGTGCT 59.966 45.455 0.00 0.00 0.00 4.40
1859 21658 3.489738 GCTGTTTGTTCATCAGTGCTTGT 60.490 43.478 0.00 0.00 0.00 3.16
1865 21664 3.811497 TGTTCATCAGTGCTTGTCTGAAG 59.189 43.478 0.00 0.00 43.65 3.02
1868 21667 3.811497 TCATCAGTGCTTGTCTGAAGTTG 59.189 43.478 0.00 0.00 43.65 3.16
1871 21670 3.374988 TCAGTGCTTGTCTGAAGTTGTTG 59.625 43.478 0.00 0.00 38.71 3.33
1874 21673 2.423185 TGCTTGTCTGAAGTTGTTGTGG 59.577 45.455 0.00 0.00 0.00 4.17
1878 21677 2.290641 TGTCTGAAGTTGTTGTGGTGGT 60.291 45.455 0.00 0.00 0.00 4.16
1882 21681 3.945285 CTGAAGTTGTTGTGGTGGTTACT 59.055 43.478 0.00 0.00 0.00 2.24
1891 21693 4.811969 TGTGGTGGTTACTACTATGGTG 57.188 45.455 0.00 0.00 38.90 4.17
1897 21699 6.005823 GGTGGTTACTACTATGGTGGTTTTT 58.994 40.000 3.02 0.00 38.17 1.94
1898 21700 6.072342 GGTGGTTACTACTATGGTGGTTTTTG 60.072 42.308 3.02 0.00 38.17 2.44
1912 21714 8.024145 TGGTGGTTTTTGATTACTAAAATGGT 57.976 30.769 0.00 0.00 34.56 3.55
1914 21716 8.769891 GGTGGTTTTTGATTACTAAAATGGTTG 58.230 33.333 0.00 0.00 34.56 3.77
1925 21727 1.122227 AAATGGTTGTTGCTGTGCCT 58.878 45.000 0.00 0.00 0.00 4.75
1927 21729 1.247567 ATGGTTGTTGCTGTGCCTAC 58.752 50.000 0.00 0.00 0.00 3.18
1947 21749 6.853362 GCCTACGAAAGATCTTAAAATGCATC 59.147 38.462 8.75 0.00 0.00 3.91
1966 21768 5.330295 GCATCACTGCTTAATCTTTGACTG 58.670 41.667 0.00 0.00 45.32 3.51
1967 21769 5.122869 GCATCACTGCTTAATCTTTGACTGA 59.877 40.000 0.00 0.00 45.32 3.41
1968 21770 6.675002 GCATCACTGCTTAATCTTTGACTGAG 60.675 42.308 0.00 0.00 45.32 3.35
1969 21771 5.858381 TCACTGCTTAATCTTTGACTGAGT 58.142 37.500 0.00 0.00 0.00 3.41
1970 21772 5.698089 TCACTGCTTAATCTTTGACTGAGTG 59.302 40.000 0.00 0.00 0.00 3.51
1971 21773 4.999950 ACTGCTTAATCTTTGACTGAGTGG 59.000 41.667 0.00 0.00 0.00 4.00
1995 21811 9.025041 TGGTCTCTCTTTTTCTTTCTTTCTTTT 57.975 29.630 0.00 0.00 0.00 2.27
2001 21817 8.173321 TCTTTTTCTTTCTTTCTTTTTCTGCG 57.827 30.769 0.00 0.00 0.00 5.18
2006 21822 6.662616 TCTTTCTTTCTTTTTCTGCGATGAG 58.337 36.000 0.00 0.00 0.00 2.90
2010 21826 4.488126 TTCTTTTTCTGCGATGAGTTGG 57.512 40.909 0.00 0.00 0.00 3.77
2015 21831 0.745486 TCTGCGATGAGTTGGCATGG 60.745 55.000 0.00 0.00 35.91 3.66
2016 21832 2.332362 CTGCGATGAGTTGGCATGGC 62.332 60.000 13.29 13.29 46.21 4.40
2017 21833 2.409055 GCGATGAGTTGGCATGGCA 61.409 57.895 19.43 19.43 45.60 4.92
2018 21834 1.731433 GCGATGAGTTGGCATGGCAT 61.731 55.000 23.96 9.20 45.60 4.40
2019 21835 0.742505 CGATGAGTTGGCATGGCATT 59.257 50.000 23.96 14.43 0.00 3.56
2020 21836 1.268896 CGATGAGTTGGCATGGCATTC 60.269 52.381 23.96 21.93 0.00 2.67
2021 21837 2.029623 GATGAGTTGGCATGGCATTCT 58.970 47.619 23.96 22.30 0.00 2.40
2022 21838 1.927487 TGAGTTGGCATGGCATTCTT 58.073 45.000 23.96 8.81 0.00 2.52
2053 26708 1.933853 GGCTGACTACCTTGTAATGCG 59.066 52.381 0.00 0.00 0.00 4.73
2054 26709 1.327764 GCTGACTACCTTGTAATGCGC 59.672 52.381 0.00 0.00 0.00 6.09
2076 26731 1.287730 CTTGTGCTGCTCGTGAGGTC 61.288 60.000 0.00 0.00 0.00 3.85
2250 26935 8.467402 TTCAAAAGCACGAAGTTAATTTGAAA 57.533 26.923 7.96 0.00 43.20 2.69
2284 26969 5.652014 TGAACCCAGTAATGCTAAAATGGAG 59.348 40.000 1.62 0.00 0.00 3.86
2314 27009 2.357009 GGTGCAGTGCCATTAGAATGAG 59.643 50.000 13.72 0.00 38.70 2.90
2317 27012 2.686915 GCAGTGCCATTAGAATGAGCTT 59.313 45.455 2.85 0.00 38.70 3.74
2319 27014 4.669318 CAGTGCCATTAGAATGAGCTTTG 58.331 43.478 3.76 5.28 38.70 2.77
2327 27022 3.228188 AGAATGAGCTTTGGGTGTTGA 57.772 42.857 0.00 0.00 0.00 3.18
2343 27038 2.144833 TTGATTTGCACTGCGCCAGG 62.145 55.000 4.18 0.00 41.33 4.45
2346 27041 3.866379 TTTGCACTGCGCCAGGGAT 62.866 57.895 4.18 0.00 36.97 3.85
2366 27061 1.483827 TCATCTGGTGCATGTCTCCTC 59.516 52.381 0.00 0.00 0.00 3.71
2373 27068 2.355108 GGTGCATGTCTCCTCTGCTTAA 60.355 50.000 0.00 0.00 36.84 1.85
2454 27241 1.014044 CGTTACTCCAGTGCACGCAT 61.014 55.000 12.01 0.00 32.16 4.73
2455 27242 0.443869 GTTACTCCAGTGCACGCATG 59.556 55.000 12.01 4.23 0.00 4.06
2490 27277 7.271511 TGCAGAACAAATTAAACTTGGAACAT 58.728 30.769 5.84 0.00 39.30 2.71
2512 27299 6.706716 ACATGATCAGATCAGCTAAGTGATTG 59.293 38.462 18.13 9.82 43.53 2.67
2520 27307 0.453390 GCTAAGTGATTGCCAGTGCC 59.547 55.000 0.00 0.00 36.33 5.01
2525 27312 0.940126 GTGATTGCCAGTGCCTATCG 59.060 55.000 0.00 0.00 36.33 2.92
2526 27313 0.179048 TGATTGCCAGTGCCTATCGG 60.179 55.000 0.00 0.00 36.33 4.18
2528 27315 1.635817 ATTGCCAGTGCCTATCGGGT 61.636 55.000 0.00 0.00 37.43 5.28
2536 27323 2.026262 AGTGCCTATCGGGTCATGTTTT 60.026 45.455 0.00 0.00 37.43 2.43
2540 27327 3.681594 GCCTATCGGGTCATGTTTTCAGA 60.682 47.826 0.00 0.00 37.43 3.27
2541 27328 4.122776 CCTATCGGGTCATGTTTTCAGAG 58.877 47.826 0.00 0.00 0.00 3.35
2543 27330 3.762407 TCGGGTCATGTTTTCAGAGAA 57.238 42.857 0.00 0.00 0.00 2.87
2544 27331 3.664107 TCGGGTCATGTTTTCAGAGAAG 58.336 45.455 0.00 0.00 0.00 2.85
2545 27332 3.071023 TCGGGTCATGTTTTCAGAGAAGT 59.929 43.478 0.00 0.00 0.00 3.01
2546 27333 4.282449 TCGGGTCATGTTTTCAGAGAAGTA 59.718 41.667 0.00 0.00 0.00 2.24
2547 27334 5.046591 TCGGGTCATGTTTTCAGAGAAGTAT 60.047 40.000 0.00 0.00 0.00 2.12
2548 27335 5.063944 CGGGTCATGTTTTCAGAGAAGTATG 59.936 44.000 0.00 0.00 0.00 2.39
2549 27336 5.940470 GGGTCATGTTTTCAGAGAAGTATGT 59.060 40.000 0.00 0.00 0.00 2.29
2550 27337 6.128172 GGGTCATGTTTTCAGAGAAGTATGTG 60.128 42.308 0.00 0.00 0.00 3.21
2551 27338 6.128172 GGTCATGTTTTCAGAGAAGTATGTGG 60.128 42.308 0.00 0.00 0.00 4.17
2552 27339 6.650807 GTCATGTTTTCAGAGAAGTATGTGGA 59.349 38.462 0.00 0.00 0.00 4.02
2553 27340 6.650807 TCATGTTTTCAGAGAAGTATGTGGAC 59.349 38.462 0.00 0.00 0.00 4.02
2599 27386 7.993183 ACACCTGGACCTAGATTTATTAACATG 59.007 37.037 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.857309 AAGTGAGTGCAGCCCAGGC 62.857 63.158 0.00 0.00 42.33 4.85
9 10 1.970114 CAAGTGAGTGCAGCCCAGG 60.970 63.158 0.00 0.00 0.00 4.45
10 11 1.970114 CCAAGTGAGTGCAGCCCAG 60.970 63.158 0.00 0.00 0.00 4.45
11 12 2.113774 CCAAGTGAGTGCAGCCCA 59.886 61.111 0.00 0.00 0.00 5.36
12 13 1.968540 GACCAAGTGAGTGCAGCCC 60.969 63.158 0.00 0.00 0.00 5.19
13 14 1.227943 TGACCAAGTGAGTGCAGCC 60.228 57.895 0.00 0.00 0.00 4.85
14 15 1.510480 GGTGACCAAGTGAGTGCAGC 61.510 60.000 0.00 0.00 0.00 5.25
15 16 2.621763 GGTGACCAAGTGAGTGCAG 58.378 57.895 0.00 0.00 0.00 4.41
16 17 4.876701 GGTGACCAAGTGAGTGCA 57.123 55.556 0.00 0.00 0.00 4.57
75 77 2.675056 GCTGCTGTGCGACTTGAGG 61.675 63.158 0.00 0.00 0.00 3.86
79 81 2.667536 CTGGCTGCTGTGCGACTT 60.668 61.111 0.00 0.00 0.00 3.01
81 83 3.117171 CTCTGGCTGCTGTGCGAC 61.117 66.667 0.00 0.00 0.00 5.19
207 210 1.403687 GCAGAAGAGTAGGCCGGGAT 61.404 60.000 2.18 0.00 0.00 3.85
209 212 2.022240 GAGCAGAAGAGTAGGCCGGG 62.022 65.000 2.18 0.00 0.00 5.73
215 218 1.742831 AGTGAGCGAGCAGAAGAGTAG 59.257 52.381 0.00 0.00 0.00 2.57
235 238 0.250467 AAGCAGCGAAGAAAGCTCCA 60.250 50.000 0.00 0.00 44.06 3.86
303 306 4.639171 CAACCACCCCAAACGCGC 62.639 66.667 5.73 0.00 0.00 6.86
312 315 1.231958 TTCGAACATCGCAACCACCC 61.232 55.000 0.00 0.00 40.21 4.61
353 358 1.113788 AGGCTGCAAAGAAGCAACAA 58.886 45.000 0.50 0.00 45.13 2.83
372 377 2.804986 TGCTACCATCATTCCTGCAA 57.195 45.000 0.00 0.00 0.00 4.08
376 381 5.894298 TCTTGTATGCTACCATCATTCCT 57.106 39.130 0.00 0.00 32.85 3.36
377 382 6.238759 GGTTTCTTGTATGCTACCATCATTCC 60.239 42.308 0.00 0.00 32.85 3.01
387 6553 3.681593 GGGTGTGGTTTCTTGTATGCTA 58.318 45.455 0.00 0.00 0.00 3.49
392 6558 0.180642 TGCGGGTGTGGTTTCTTGTA 59.819 50.000 0.00 0.00 0.00 2.41
423 6589 3.311110 GCGGGAGGTCTGACCACA 61.311 66.667 27.48 0.00 41.95 4.17
637 6803 0.251209 AGACACTCTCGTACCCTGCA 60.251 55.000 0.00 0.00 0.00 4.41
764 6930 1.131126 CCACTTAGCGACTGCATTTGG 59.869 52.381 0.00 0.00 46.23 3.28
1102 7269 4.025360 CCCTTGATGATTTGTCCAATCCA 58.975 43.478 0.00 0.00 40.80 3.41
1339 15826 1.217057 AGCACTTGGTCATCCCCCAT 61.217 55.000 0.00 0.00 0.00 4.00
1408 15895 6.987386 AGAAGAAGATATAATCACCCGACAG 58.013 40.000 0.00 0.00 0.00 3.51
1457 15944 1.202154 CCTTGTCGTAGCAGTAGTCCG 60.202 57.143 0.00 0.00 0.00 4.79
1492 15979 1.274728 GGATCTCATGTCATAGGCGCT 59.725 52.381 7.64 0.00 0.00 5.92
1525 16012 1.676006 GAAAATACTGGGACATGCCGG 59.324 52.381 0.00 0.00 38.20 6.13
1538 16025 8.999431 TCTCATTACAACACTTCCAGAAAATAC 58.001 33.333 0.00 0.00 0.00 1.89
1552 16039 3.261580 CCAGACGCATCTCATTACAACA 58.738 45.455 0.00 0.00 30.42 3.33
1558 16045 1.094073 GCAGCCAGACGCATCTCATT 61.094 55.000 0.00 0.00 41.38 2.57
1640 16127 7.069331 ACATCTATAGCATGGCTAGATAACCTC 59.931 40.741 13.37 0.00 44.66 3.85
1650 16137 4.785301 ACAACAACATCTATAGCATGGCT 58.215 39.130 13.37 0.00 43.41 4.75
1662 16149 1.324383 AACCCCGGAACAACAACATC 58.676 50.000 0.73 0.00 0.00 3.06
1692 16179 9.973450 GCAGTCAGATAGATAACTTATGAGAAA 57.027 33.333 0.00 0.00 0.00 2.52
1694 16181 7.094592 CCGCAGTCAGATAGATAACTTATGAGA 60.095 40.741 0.00 0.00 0.00 3.27
1701 16188 5.378332 ACTACCGCAGTCAGATAGATAACT 58.622 41.667 0.00 0.00 28.33 2.24
1713 16200 2.626743 ACCACCATATACTACCGCAGTC 59.373 50.000 0.00 0.00 38.80 3.51
1714 16201 2.674420 ACCACCATATACTACCGCAGT 58.326 47.619 0.00 0.00 41.62 4.40
1718 16205 2.967201 TCCCAACCACCATATACTACCG 59.033 50.000 0.00 0.00 0.00 4.02
1719 16206 5.783875 ACTATCCCAACCACCATATACTACC 59.216 44.000 0.00 0.00 0.00 3.18
1721 16208 6.387127 ACACTATCCCAACCACCATATACTA 58.613 40.000 0.00 0.00 0.00 1.82
1722 16209 5.224441 ACACTATCCCAACCACCATATACT 58.776 41.667 0.00 0.00 0.00 2.12
1724 16211 5.668080 TGAACACTATCCCAACCACCATATA 59.332 40.000 0.00 0.00 0.00 0.86
1725 16212 4.476846 TGAACACTATCCCAACCACCATAT 59.523 41.667 0.00 0.00 0.00 1.78
1755 21554 1.676006 GCATTTCACGGATTGTAGGGG 59.324 52.381 0.00 0.00 0.00 4.79
1764 21563 6.459670 TCTACTACTAATGCATTTCACGGA 57.540 37.500 18.75 5.35 0.00 4.69
1789 21588 9.650539 CAGATAGACAGCAGCAATATTACTATT 57.349 33.333 0.00 0.00 0.00 1.73
1790 21589 9.029368 TCAGATAGACAGCAGCAATATTACTAT 57.971 33.333 0.00 0.00 0.00 2.12
1792 21591 7.295322 TCAGATAGACAGCAGCAATATTACT 57.705 36.000 0.00 0.00 0.00 2.24
1793 21592 6.090628 GCTCAGATAGACAGCAGCAATATTAC 59.909 42.308 0.00 0.00 33.06 1.89
1795 21594 4.996122 GCTCAGATAGACAGCAGCAATATT 59.004 41.667 0.00 0.00 33.06 1.28
1796 21595 4.283978 AGCTCAGATAGACAGCAGCAATAT 59.716 41.667 0.00 0.00 35.46 1.28
1798 21597 2.435069 AGCTCAGATAGACAGCAGCAAT 59.565 45.455 0.00 0.00 35.46 3.56
1799 21598 1.829849 AGCTCAGATAGACAGCAGCAA 59.170 47.619 0.00 0.00 35.46 3.91
1800 21599 1.482954 AGCTCAGATAGACAGCAGCA 58.517 50.000 0.00 0.00 35.46 4.41
1801 21600 2.600470 AAGCTCAGATAGACAGCAGC 57.400 50.000 0.00 0.00 35.46 5.25
1802 21601 3.859443 ACAAAGCTCAGATAGACAGCAG 58.141 45.455 0.00 0.00 35.46 4.24
1803 21602 3.969287 ACAAAGCTCAGATAGACAGCA 57.031 42.857 0.00 0.00 35.46 4.41
1804 21603 5.415221 AGTAACAAAGCTCAGATAGACAGC 58.585 41.667 0.00 0.00 0.00 4.40
1805 21604 6.751425 CAGAGTAACAAAGCTCAGATAGACAG 59.249 42.308 0.00 0.00 34.39 3.51
1806 21605 6.625362 CAGAGTAACAAAGCTCAGATAGACA 58.375 40.000 0.00 0.00 34.39 3.41
1807 21606 5.518487 GCAGAGTAACAAAGCTCAGATAGAC 59.482 44.000 0.00 0.00 34.39 2.59
1808 21607 5.420421 AGCAGAGTAACAAAGCTCAGATAGA 59.580 40.000 0.00 0.00 34.39 1.98
1809 21608 5.659463 AGCAGAGTAACAAAGCTCAGATAG 58.341 41.667 0.00 0.00 34.39 2.08
1810 21609 5.667539 AGCAGAGTAACAAAGCTCAGATA 57.332 39.130 0.00 0.00 34.39 1.98
1811 21610 4.550076 AGCAGAGTAACAAAGCTCAGAT 57.450 40.909 0.00 0.00 34.39 2.90
1817 21616 4.071875 GCACTTAGCAGAGTAACAAAGC 57.928 45.455 0.00 0.00 44.79 3.51
1831 21630 5.446709 CACTGATGAACAAACAGCACTTAG 58.553 41.667 0.00 0.00 35.38 2.18
1840 21639 4.035558 TCAGACAAGCACTGATGAACAAAC 59.964 41.667 0.00 0.00 39.10 2.93
1841 21640 4.198530 TCAGACAAGCACTGATGAACAAA 58.801 39.130 0.00 0.00 39.10 2.83
1842 21641 3.807553 TCAGACAAGCACTGATGAACAA 58.192 40.909 0.00 0.00 39.10 2.83
1843 21642 3.473923 TCAGACAAGCACTGATGAACA 57.526 42.857 0.00 0.00 39.10 3.18
1844 21643 3.812053 ACTTCAGACAAGCACTGATGAAC 59.188 43.478 14.46 0.00 42.68 3.18
1847 21646 3.562973 ACAACTTCAGACAAGCACTGATG 59.437 43.478 0.00 0.00 42.68 3.07
1856 21655 2.752354 CCACCACAACAACTTCAGACAA 59.248 45.455 0.00 0.00 0.00 3.18
1859 21658 2.799126 ACCACCACAACAACTTCAGA 57.201 45.000 0.00 0.00 0.00 3.27
1865 21664 5.410439 CCATAGTAGTAACCACCACAACAAC 59.590 44.000 0.00 0.00 0.00 3.32
1868 21667 4.933400 CACCATAGTAGTAACCACCACAAC 59.067 45.833 0.00 0.00 0.00 3.32
1871 21670 3.516700 ACCACCATAGTAGTAACCACCAC 59.483 47.826 0.00 0.00 0.00 4.16
1874 21673 6.711645 TCAAAAACCACCATAGTAGTAACCAC 59.288 38.462 0.00 0.00 0.00 4.16
1897 21699 7.144661 CACAGCAACAACCATTTTAGTAATCA 58.855 34.615 0.00 0.00 0.00 2.57
1898 21700 6.089417 GCACAGCAACAACCATTTTAGTAATC 59.911 38.462 0.00 0.00 0.00 1.75
1903 21705 3.059166 GGCACAGCAACAACCATTTTAG 58.941 45.455 0.00 0.00 0.00 1.85
1907 21709 1.613437 GTAGGCACAGCAACAACCATT 59.387 47.619 0.00 0.00 0.00 3.16
1908 21710 1.247567 GTAGGCACAGCAACAACCAT 58.752 50.000 0.00 0.00 0.00 3.55
1912 21714 1.601903 CTTTCGTAGGCACAGCAACAA 59.398 47.619 0.00 0.00 0.00 2.83
1914 21716 1.508632 TCTTTCGTAGGCACAGCAAC 58.491 50.000 0.00 0.00 0.00 4.17
1925 21727 8.390354 CAGTGATGCATTTTAAGATCTTTCGTA 58.610 33.333 14.36 0.00 0.00 3.43
1927 21729 6.195983 GCAGTGATGCATTTTAAGATCTTTCG 59.804 38.462 14.36 0.00 34.41 3.46
1947 21749 5.106791 CCACTCAGTCAAAGATTAAGCAGTG 60.107 44.000 0.00 0.00 0.00 3.66
1955 21757 4.837860 AGAGAGACCACTCAGTCAAAGATT 59.162 41.667 0.00 0.00 44.79 2.40
1956 21758 4.415596 AGAGAGACCACTCAGTCAAAGAT 58.584 43.478 0.00 0.00 44.79 2.40
1958 21760 4.599047 AAGAGAGACCACTCAGTCAAAG 57.401 45.455 0.00 0.00 44.79 2.77
1959 21761 5.359194 AAAAGAGAGACCACTCAGTCAAA 57.641 39.130 0.00 0.00 44.79 2.69
1960 21762 5.129485 AGAAAAAGAGAGACCACTCAGTCAA 59.871 40.000 0.00 0.00 44.79 3.18
1961 21763 4.651503 AGAAAAAGAGAGACCACTCAGTCA 59.348 41.667 0.00 0.00 44.79 3.41
1962 21764 5.208463 AGAAAAAGAGAGACCACTCAGTC 57.792 43.478 0.00 0.00 44.79 3.51
1963 21765 5.622346 AAGAAAAAGAGAGACCACTCAGT 57.378 39.130 0.00 0.00 44.79 3.41
1964 21766 6.287525 AGAAAGAAAAAGAGAGACCACTCAG 58.712 40.000 0.00 0.00 44.79 3.35
1966 21768 7.497579 AGAAAGAAAGAAAAAGAGAGACCACTC 59.502 37.037 0.00 0.00 42.90 3.51
1967 21769 7.342581 AGAAAGAAAGAAAAAGAGAGACCACT 58.657 34.615 0.00 0.00 0.00 4.00
1968 21770 7.561021 AGAAAGAAAGAAAAAGAGAGACCAC 57.439 36.000 0.00 0.00 0.00 4.16
1969 21771 8.581253 AAAGAAAGAAAGAAAAAGAGAGACCA 57.419 30.769 0.00 0.00 0.00 4.02
1970 21772 9.862371 AAAAAGAAAGAAAGAAAAAGAGAGACC 57.138 29.630 0.00 0.00 0.00 3.85
1995 21811 1.089112 CATGCCAACTCATCGCAGAA 58.911 50.000 0.00 0.00 43.58 3.02
1997 21813 1.725665 CCATGCCAACTCATCGCAG 59.274 57.895 0.00 0.00 35.66 5.18
2001 21817 2.029623 AGAATGCCATGCCAACTCATC 58.970 47.619 0.00 0.00 0.00 2.92
2039 26684 3.623060 ACAAGATGCGCATTACAAGGTAG 59.377 43.478 26.12 9.47 0.00 3.18
2054 26709 0.720027 CTCACGAGCAGCACAAGATG 59.280 55.000 0.00 0.00 0.00 2.90
2068 26723 2.139917 TCAAATCAAACGGACCTCACG 58.860 47.619 0.00 0.00 37.36 4.35
2076 26731 6.034256 GCTGAATCTCAAATCAAATCAAACGG 59.966 38.462 0.00 0.00 0.00 4.44
2250 26935 5.687706 GCATTACTGGGTTCATAAGTAGCCT 60.688 44.000 0.00 0.00 34.22 4.58
2284 26969 2.670934 CACTGCACCCCTGTCTGC 60.671 66.667 0.00 0.00 0.00 4.26
2289 26984 1.001020 TAATGGCACTGCACCCCTG 60.001 57.895 2.82 0.00 0.00 4.45
2314 27009 1.866601 GTGCAAATCAACACCCAAAGC 59.133 47.619 0.00 0.00 0.00 3.51
2317 27012 1.202510 GCAGTGCAAATCAACACCCAA 60.203 47.619 11.09 0.00 37.51 4.12
2319 27014 0.664166 CGCAGTGCAAATCAACACCC 60.664 55.000 16.83 0.00 37.51 4.61
2343 27038 2.492012 GAGACATGCACCAGATGATCC 58.508 52.381 0.00 0.00 0.00 3.36
2346 27041 1.483827 GAGGAGACATGCACCAGATGA 59.516 52.381 0.00 0.00 0.00 2.92
2435 27222 1.014044 ATGCGTGCACTGGAGTAACG 61.014 55.000 16.19 8.94 39.09 3.18
2454 27241 0.403655 TGTTCTGCAGGGTTATGGCA 59.596 50.000 15.13 0.00 35.96 4.92
2455 27242 1.544724 TTGTTCTGCAGGGTTATGGC 58.455 50.000 15.13 0.00 0.00 4.40
2490 27277 5.055144 GCAATCACTTAGCTGATCTGATCA 58.945 41.667 18.61 18.61 37.76 2.92
2520 27307 5.011090 TCTCTGAAAACATGACCCGATAG 57.989 43.478 0.00 0.00 0.00 2.08
2525 27312 5.940470 ACATACTTCTCTGAAAACATGACCC 59.060 40.000 0.00 0.00 0.00 4.46
2526 27313 6.128172 CCACATACTTCTCTGAAAACATGACC 60.128 42.308 0.00 0.00 0.00 4.02
2528 27315 6.650807 GTCCACATACTTCTCTGAAAACATGA 59.349 38.462 0.00 0.00 0.00 3.07
2536 27323 5.019470 ACATGAGTCCACATACTTCTCTGA 58.981 41.667 0.00 0.00 0.00 3.27
2547 27334 9.183368 TGCATTAATATTTAACATGAGTCCACA 57.817 29.630 0.00 0.00 0.00 4.17
2548 27335 9.450807 GTGCATTAATATTTAACATGAGTCCAC 57.549 33.333 0.00 0.00 0.00 4.02
2549 27336 9.183368 TGTGCATTAATATTTAACATGAGTCCA 57.817 29.630 0.00 0.00 0.00 4.02
2550 27337 9.450807 GTGTGCATTAATATTTAACATGAGTCC 57.549 33.333 0.00 0.00 0.00 3.85
2551 27338 9.450807 GGTGTGCATTAATATTTAACATGAGTC 57.549 33.333 0.00 0.00 0.00 3.36
2552 27339 9.189156 AGGTGTGCATTAATATTTAACATGAGT 57.811 29.630 0.00 0.00 0.00 3.41
2553 27340 9.454585 CAGGTGTGCATTAATATTTAACATGAG 57.545 33.333 0.00 0.00 0.00 2.90
2567 27354 2.827755 TCTAGGTCCAGGTGTGCATTA 58.172 47.619 0.00 0.00 0.00 1.90
2568 27355 1.656587 TCTAGGTCCAGGTGTGCATT 58.343 50.000 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.