Multiple sequence alignment - TraesCS6B01G427600

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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 TraesCS6B01G427600 chr6B 100.000 2684 0 0 1 2684 696078888 696081571 0.000000e+00 4957.0
1 TraesCS6B01G427600 chr6B 85.077 717 98 5 978 1686 696015879 696015164 0.000000e+00 723.0
2 TraesCS6B01G427600 chr6B 84.104 541 80 3 1134 1668 696020872 696020332 3.960000e-143 518.0
3 TraesCS6B01G427600 chr6B 85.417 144 21 0 2076 2219 500290671 500290814 1.660000e-32 150.0
4 TraesCS6B01G427600 chr6B 79.545 132 12 11 2330 2450 696013618 696013491 2.220000e-11 80.5
5 TraesCS6B01G427600 chr5D 95.308 959 38 4 1 953 234041385 234040428 0.000000e+00 1515.0
6 TraesCS6B01G427600 chr5D 94.643 952 42 5 1 945 560517780 560516831 0.000000e+00 1467.0
7 TraesCS6B01G427600 chr5D 86.928 153 19 1 2077 2229 450851369 450851520 1.280000e-38 171.0
8 TraesCS6B01G427600 chr5D 86.755 151 19 1 2077 2227 2311072 2310923 1.650000e-37 167.0
9 TraesCS6B01G427600 chr1D 95.089 957 39 5 1 949 3238347 3237391 0.000000e+00 1500.0
10 TraesCS6B01G427600 chr6D 95.843 890 37 0 31 920 460309947 460310836 0.000000e+00 1439.0
11 TraesCS6B01G427600 chr6D 92.316 885 63 4 943 1822 457629995 457630879 0.000000e+00 1253.0
12 TraesCS6B01G427600 chr6D 84.828 758 103 7 945 1691 457585520 457584764 0.000000e+00 752.0
13 TraesCS6B01G427600 chr6D 81.550 645 103 9 1079 1708 457590788 457590145 3.960000e-143 518.0
14 TraesCS6B01G427600 chr6D 82.828 396 41 12 2223 2608 457631074 457631452 1.990000e-86 329.0
15 TraesCS6B01G427600 chr6D 91.209 91 6 2 2595 2684 457631537 457631626 3.630000e-24 122.0
16 TraesCS6B01G427600 chr7D 91.675 949 66 8 1 944 8552909 8551969 0.000000e+00 1303.0
17 TraesCS6B01G427600 chr7D 95.663 807 35 0 1 807 36232062 36231256 0.000000e+00 1297.0
18 TraesCS6B01G427600 chr7D 83.022 536 87 4 1127 1660 590652395 590652928 1.440000e-132 483.0
19 TraesCS6B01G427600 chr4A 90.411 949 83 6 2 944 715985745 715984799 0.000000e+00 1242.0
20 TraesCS6B01G427600 chr6A 91.638 885 66 6 970 1846 604537480 604538364 0.000000e+00 1218.0
21 TraesCS6B01G427600 chr6A 85.904 752 96 5 945 1686 604446403 604445652 0.000000e+00 793.0
22 TraesCS6B01G427600 chr6A 81.551 374 29 18 2243 2608 604538894 604539235 3.400000e-69 272.0
23 TraesCS6B01G427600 chr6A 93.407 91 5 1 2595 2684 604562997 604563087 1.680000e-27 134.0
24 TraesCS6B01G427600 chr6A 97.727 44 0 1 2330 2372 604444187 604444144 1.030000e-09 75.0
25 TraesCS6B01G427600 chr2D 89.864 957 84 12 4 949 636125596 636124642 0.000000e+00 1218.0
26 TraesCS6B01G427600 chr3B 89.684 950 87 9 1 944 606222866 606221922 0.000000e+00 1201.0
27 TraesCS6B01G427600 chr3B 86.667 150 20 0 2077 2226 225174055 225174204 1.650000e-37 167.0
28 TraesCS6B01G427600 chr7B 83.613 537 84 4 1126 1660 23317749 23317215 3.990000e-138 501.0
29 TraesCS6B01G427600 chr3A 87.919 149 18 0 2077 2225 387295306 387295454 2.750000e-40 176.0
30 TraesCS6B01G427600 chr3A 85.430 151 21 1 2077 2226 176147392 176147242 3.580000e-34 156.0
31 TraesCS6B01G427600 chr3D 87.333 150 19 0 2077 2226 153507873 153508022 3.550000e-39 172.0
32 TraesCS6B01G427600 chr1B 84.564 149 23 0 2077 2225 649336973 649337121 5.990000e-32 148.0
33 TraesCS6B01G427600 chr1B 84.106 151 24 0 2077 2227 652464914 652464764 2.150000e-31 147.0


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 TraesCS6B01G427600 chr6B 696078888 696081571 2683 False 4957.00 4957 100.000000 1 2684 1 chr6B.!!$F2 2683
1 TraesCS6B01G427600 chr6B 696020332 696020872 540 True 518.00 518 84.104000 1134 1668 1 chr6B.!!$R1 534
2 TraesCS6B01G427600 chr6B 696013491 696015879 2388 True 401.75 723 82.311000 978 2450 2 chr6B.!!$R2 1472
3 TraesCS6B01G427600 chr5D 234040428 234041385 957 True 1515.00 1515 95.308000 1 953 1 chr5D.!!$R2 952
4 TraesCS6B01G427600 chr5D 560516831 560517780 949 True 1467.00 1467 94.643000 1 945 1 chr5D.!!$R3 944
5 TraesCS6B01G427600 chr1D 3237391 3238347 956 True 1500.00 1500 95.089000 1 949 1 chr1D.!!$R1 948
6 TraesCS6B01G427600 chr6D 460309947 460310836 889 False 1439.00 1439 95.843000 31 920 1 chr6D.!!$F1 889
7 TraesCS6B01G427600 chr6D 457584764 457585520 756 True 752.00 752 84.828000 945 1691 1 chr6D.!!$R1 746
8 TraesCS6B01G427600 chr6D 457629995 457631626 1631 False 568.00 1253 88.784333 943 2684 3 chr6D.!!$F2 1741
9 TraesCS6B01G427600 chr6D 457590145 457590788 643 True 518.00 518 81.550000 1079 1708 1 chr6D.!!$R2 629
10 TraesCS6B01G427600 chr7D 8551969 8552909 940 True 1303.00 1303 91.675000 1 944 1 chr7D.!!$R1 943
11 TraesCS6B01G427600 chr7D 36231256 36232062 806 True 1297.00 1297 95.663000 1 807 1 chr7D.!!$R2 806
12 TraesCS6B01G427600 chr7D 590652395 590652928 533 False 483.00 483 83.022000 1127 1660 1 chr7D.!!$F1 533
13 TraesCS6B01G427600 chr4A 715984799 715985745 946 True 1242.00 1242 90.411000 2 944 1 chr4A.!!$R1 942
14 TraesCS6B01G427600 chr6A 604537480 604539235 1755 False 745.00 1218 86.594500 970 2608 2 chr6A.!!$F2 1638
15 TraesCS6B01G427600 chr6A 604444144 604446403 2259 True 434.00 793 91.815500 945 2372 2 chr6A.!!$R1 1427
16 TraesCS6B01G427600 chr2D 636124642 636125596 954 True 1218.00 1218 89.864000 4 949 1 chr2D.!!$R1 945
17 TraesCS6B01G427600 chr3B 606221922 606222866 944 True 1201.00 1201 89.684000 1 944 1 chr3B.!!$R1 943
18 TraesCS6B01G427600 chr7B 23317215 23317749 534 True 501.00 501 83.613000 1126 1660 1 chr7B.!!$R1 534

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
630 633 0.105408 AACTTTGTCGGCGTGGTAGT 59.895 50.0 6.85 4.25 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2525 3811 0.031178 ACGCAAAAGAAAGCTGCAGG 59.969 50.0 17.12 0.0 35.78 4.85 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
66 67 4.660938 GCCTCCAGTTTGGGCGGT 62.661 66.667 0.00 0.00 38.32 5.68
230 231 4.069232 CTCCGCGTTCTCTGGCCA 62.069 66.667 4.71 4.71 0.00 5.36
278 279 2.837291 TGTGGCTGGTTTGGTGGC 60.837 61.111 0.00 0.00 0.00 5.01
370 371 2.298163 GTCACCGTTCTACTTCTTGGGA 59.702 50.000 0.00 0.00 0.00 4.37
379 380 0.911769 ACTTCTTGGGATCGGCATCA 59.088 50.000 0.00 0.00 0.00 3.07
423 425 0.179001 CCTTGTCCCGGGTGAAAACT 60.179 55.000 22.86 0.00 0.00 2.66
530 533 2.700773 GGCTTTGGCATGGTCGGTC 61.701 63.158 0.00 0.00 40.87 4.79
531 534 1.971167 GCTTTGGCATGGTCGGTCA 60.971 57.895 0.00 0.00 38.54 4.02
618 621 2.735134 GCGTTGATCGGAGTAACTTTGT 59.265 45.455 5.86 0.00 40.26 2.83
630 633 0.105408 AACTTTGTCGGCGTGGTAGT 59.895 50.000 6.85 4.25 0.00 2.73
656 659 2.334023 GCCATCCTCTCCTAGTCCATT 58.666 52.381 0.00 0.00 0.00 3.16
713 717 2.280797 GGAGTTGACGGCTGTGCA 60.281 61.111 0.80 0.00 0.00 4.57
722 726 2.431683 GGCTGTGCACTTCCTCCA 59.568 61.111 19.41 0.00 0.00 3.86
851 855 3.539604 GCATCTTGTATCCTCTGTTGCT 58.460 45.455 0.00 0.00 0.00 3.91
886 902 8.122472 TCTTCTTCTTCTTTCTTTTTGTGGTT 57.878 30.769 0.00 0.00 0.00 3.67
890 906 6.262193 TCTTCTTTCTTTTTGTGGTTTCGT 57.738 33.333 0.00 0.00 0.00 3.85
911 927 2.577700 TGGTTGTATGCTCGGTTGTTT 58.422 42.857 0.00 0.00 0.00 2.83
920 936 8.325421 TGTATGCTCGGTTGTTTCTTTATAAA 57.675 30.769 0.00 0.00 0.00 1.40
921 937 8.447833 TGTATGCTCGGTTGTTTCTTTATAAAG 58.552 33.333 17.60 17.60 37.36 1.85
922 938 5.695818 TGCTCGGTTGTTTCTTTATAAAGC 58.304 37.500 18.68 7.24 35.99 3.51
966 988 6.824958 ATATTCCTAGCTGGGACTTACAAA 57.175 37.500 19.93 2.14 34.78 2.83
1044 1073 2.356793 GCGATCCAGATGCCTCCG 60.357 66.667 0.00 0.00 0.00 4.63
1073 1102 1.443872 CCAAGGAAGTCGACGACGG 60.444 63.158 21.44 12.04 37.67 4.79
1074 1103 1.285023 CAAGGAAGTCGACGACGGT 59.715 57.895 21.44 14.00 37.67 4.83
1132 1170 2.613696 CCCCCACCATGGACAGGA 60.614 66.667 21.47 0.00 40.96 3.86
1158 1196 1.954146 GAGCGTCACGAACCTTGCA 60.954 57.895 0.00 0.00 0.00 4.08
1392 1433 2.687566 AACTTCCCCGGCGAGGAT 60.688 61.111 12.03 0.00 45.00 3.24
1494 1538 1.129917 TGGTTTTCCTCACGGTGGTA 58.870 50.000 8.50 0.00 41.38 3.25
1594 1638 2.480555 GCATGGCGTTTCTGTCCG 59.519 61.111 0.00 0.00 0.00 4.79
1680 1724 3.371285 GCAGGAAGGTCGATCACTTAAAC 59.629 47.826 0.00 0.00 0.00 2.01
1746 1804 1.001633 GGAAAACGTAGCTGGGACTGA 59.998 52.381 0.00 0.00 0.00 3.41
1755 1813 2.949447 AGCTGGGACTGAAAACAATGT 58.051 42.857 0.00 0.00 0.00 2.71
1809 1869 7.119262 TCGAAGGAGAAAATAATGGTGAGTTTC 59.881 37.037 0.00 0.00 0.00 2.78
1837 1901 2.348411 ATATCCCCTGCCAAAGTTCG 57.652 50.000 0.00 0.00 0.00 3.95
1859 1933 6.728200 TCGCATGAGAACAATGAAATATTCC 58.272 36.000 0.00 0.00 0.00 3.01
1861 1935 5.916883 GCATGAGAACAATGAAATATTCCCG 59.083 40.000 0.00 0.00 0.00 5.14
1863 1937 6.677781 TGAGAACAATGAAATATTCCCGTC 57.322 37.500 0.00 0.00 0.00 4.79
1865 1939 6.657117 TGAGAACAATGAAATATTCCCGTCAA 59.343 34.615 0.00 0.00 0.00 3.18
1868 1942 8.028938 AGAACAATGAAATATTCCCGTCAAAAG 58.971 33.333 0.00 0.00 0.00 2.27
1870 1944 7.891561 ACAATGAAATATTCCCGTCAAAAGAA 58.108 30.769 0.00 0.00 0.00 2.52
1873 2087 7.278461 TGAAATATTCCCGTCAAAAGAACAA 57.722 32.000 0.00 0.00 0.00 2.83
1876 2090 8.532977 AAATATTCCCGTCAAAAGAACAATTG 57.467 30.769 3.24 3.24 0.00 2.32
1878 2092 6.642707 ATTCCCGTCAAAAGAACAATTGTA 57.357 33.333 12.39 0.00 0.00 2.41
1880 2094 4.882427 TCCCGTCAAAAGAACAATTGTACA 59.118 37.500 12.39 0.00 0.00 2.90
1883 2097 5.173131 CCGTCAAAAGAACAATTGTACAAGC 59.827 40.000 12.39 0.00 0.00 4.01
1885 2099 6.417635 CGTCAAAAGAACAATTGTACAAGCAT 59.582 34.615 12.39 0.01 0.00 3.79
1887 2101 7.222611 GTCAAAAGAACAATTGTACAAGCATGT 59.777 33.333 12.39 14.88 43.74 3.21
1889 2103 8.693504 CAAAAGAACAATTGTACAAGCATGTAG 58.306 33.333 12.39 6.18 42.54 2.74
1890 2104 6.500684 AGAACAATTGTACAAGCATGTAGG 57.499 37.500 12.39 5.09 42.54 3.18
1891 2105 6.237901 AGAACAATTGTACAAGCATGTAGGA 58.762 36.000 12.39 0.00 42.54 2.94
1893 2107 5.560724 ACAATTGTACAAGCATGTAGGAGT 58.439 37.500 9.97 0.00 42.54 3.85
1919 2133 2.603021 CCTTCTCCTAGGCTAGCATCA 58.397 52.381 18.24 0.00 0.00 3.07
1920 2134 2.562298 CCTTCTCCTAGGCTAGCATCAG 59.438 54.545 18.24 9.60 0.00 2.90
1934 2295 8.660435 AGGCTAGCATCAGGTATTCTTTATTTA 58.340 33.333 18.24 0.00 0.00 1.40
1981 2358 2.747446 CCCGGTTTCATGAACGAAATCT 59.253 45.455 17.31 0.00 39.22 2.40
1987 2364 7.011109 CCGGTTTCATGAACGAAATCTTAGTAT 59.989 37.037 17.31 0.00 39.22 2.12
2031 2412 3.055385 ACAGAACGCATGTATAACCACCT 60.055 43.478 0.00 0.00 0.00 4.00
2059 2480 2.032178 GCAAAACGCATGAGAGGATACC 59.968 50.000 2.50 0.00 41.79 2.73
2077 2498 2.740055 CTGTCGCCGCAAGCTTCT 60.740 61.111 0.00 0.00 40.39 2.85
2081 2502 1.014564 GTCGCCGCAAGCTTCTAAGT 61.015 55.000 0.00 0.00 40.39 2.24
2082 2503 0.528924 TCGCCGCAAGCTTCTAAGTA 59.471 50.000 0.00 0.00 40.39 2.24
2083 2504 1.136305 TCGCCGCAAGCTTCTAAGTAT 59.864 47.619 0.00 0.00 40.39 2.12
2084 2505 2.359848 TCGCCGCAAGCTTCTAAGTATA 59.640 45.455 0.00 0.00 40.39 1.47
2088 2509 4.209495 GCCGCAAGCTTCTAAGTATAAGAC 59.791 45.833 0.00 0.00 38.99 3.01
2090 2511 5.452077 CCGCAAGCTTCTAAGTATAAGACCT 60.452 44.000 0.00 0.00 0.00 3.85
2091 2512 6.043411 CGCAAGCTTCTAAGTATAAGACCTT 58.957 40.000 0.00 0.00 0.00 3.50
2092 2513 6.535508 CGCAAGCTTCTAAGTATAAGACCTTT 59.464 38.462 0.00 0.00 0.00 3.11
2093 2514 7.064728 CGCAAGCTTCTAAGTATAAGACCTTTT 59.935 37.037 0.00 0.00 0.00 2.27
2171 2593 9.162793 GTAGATTCATTCATTTTGCTTCGTATG 57.837 33.333 0.00 0.00 0.00 2.39
2173 2595 8.892723 AGATTCATTCATTTTGCTTCGTATGTA 58.107 29.630 0.00 0.00 0.00 2.29
2174 2596 9.162793 GATTCATTCATTTTGCTTCGTATGTAG 57.837 33.333 0.00 0.00 0.00 2.74
2175 2597 7.609760 TCATTCATTTTGCTTCGTATGTAGT 57.390 32.000 0.00 0.00 0.00 2.73
2176 2598 8.039603 TCATTCATTTTGCTTCGTATGTAGTT 57.960 30.769 0.00 0.00 0.00 2.24
2177 2599 8.175069 TCATTCATTTTGCTTCGTATGTAGTTC 58.825 33.333 0.00 0.00 0.00 3.01
2179 2601 7.609760 TCATTTTGCTTCGTATGTAGTTCAT 57.390 32.000 0.00 0.00 40.25 2.57
2180 2602 7.463544 TCATTTTGCTTCGTATGTAGTTCATG 58.536 34.615 0.00 0.00 37.91 3.07
2181 2603 5.794687 TTTGCTTCGTATGTAGTTCATGG 57.205 39.130 0.00 0.00 37.91 3.66
2182 2604 4.465632 TGCTTCGTATGTAGTTCATGGT 57.534 40.909 0.00 0.00 37.91 3.55
2183 2605 4.180817 TGCTTCGTATGTAGTTCATGGTG 58.819 43.478 0.00 0.00 37.91 4.17
2184 2606 3.555956 GCTTCGTATGTAGTTCATGGTGG 59.444 47.826 0.00 0.00 37.91 4.61
2186 2608 5.408880 TTCGTATGTAGTTCATGGTGGAA 57.591 39.130 0.00 0.00 37.91 3.53
2187 2609 5.607939 TCGTATGTAGTTCATGGTGGAAT 57.392 39.130 0.00 0.00 37.91 3.01
2188 2610 5.597806 TCGTATGTAGTTCATGGTGGAATC 58.402 41.667 0.00 0.00 37.91 2.52
2189 2611 4.750098 CGTATGTAGTTCATGGTGGAATCC 59.250 45.833 0.00 0.00 37.91 3.01
2190 2612 3.644966 TGTAGTTCATGGTGGAATCCC 57.355 47.619 0.00 0.00 0.00 3.85
2191 2613 3.189606 TGTAGTTCATGGTGGAATCCCT 58.810 45.455 0.00 0.00 0.00 4.20
2194 2616 4.946160 AGTTCATGGTGGAATCCCTAAA 57.054 40.909 0.00 0.00 0.00 1.85
2195 2617 5.269554 AGTTCATGGTGGAATCCCTAAAA 57.730 39.130 0.00 0.00 0.00 1.52
2196 2618 5.264395 AGTTCATGGTGGAATCCCTAAAAG 58.736 41.667 0.00 0.00 0.00 2.27
2197 2619 4.249638 TCATGGTGGAATCCCTAAAAGG 57.750 45.455 0.00 0.00 34.30 3.11
2198 2620 3.596046 TCATGGTGGAATCCCTAAAAGGT 59.404 43.478 0.00 0.00 31.93 3.50
2199 2621 3.732048 TGGTGGAATCCCTAAAAGGTC 57.268 47.619 0.00 0.00 31.93 3.85
2202 2624 4.853276 TGGTGGAATCCCTAAAAGGTCTTA 59.147 41.667 0.00 0.00 31.93 2.10
2205 2627 7.352522 TGGTGGAATCCCTAAAAGGTCTTATAT 59.647 37.037 0.00 0.00 31.93 0.86
2206 2628 8.225416 GGTGGAATCCCTAAAAGGTCTTATATT 58.775 37.037 0.00 0.00 31.93 1.28
2221 2643 9.392259 AGGTCTTATATTTAAAAACGAAGGGAG 57.608 33.333 0.00 0.00 0.00 4.30
2279 3118 2.238646 ACAGACCATAAGGATCGCCAAA 59.761 45.455 0.00 0.00 38.69 3.28
2281 3120 3.885297 CAGACCATAAGGATCGCCAAATT 59.115 43.478 0.00 0.00 38.69 1.82
2282 3121 5.063204 CAGACCATAAGGATCGCCAAATTA 58.937 41.667 0.00 0.00 38.69 1.40
2283 3122 5.530915 CAGACCATAAGGATCGCCAAATTAA 59.469 40.000 0.00 0.00 38.69 1.40
2293 3559 7.386059 AGGATCGCCAAATTAAAGTTTCAAAT 58.614 30.769 0.00 0.00 36.29 2.32
2325 3591 8.549548 TGAAAGTAAAAACGTTTGATCGATGTA 58.450 29.630 15.46 0.00 34.70 2.29
2327 3593 7.410800 AGTAAAAACGTTTGATCGATGTACA 57.589 32.000 15.46 0.00 34.70 2.90
2328 3594 8.025243 AGTAAAAACGTTTGATCGATGTACAT 57.975 30.769 15.46 8.43 34.70 2.29
2403 3674 6.910536 AGATAGCCAGAGTAATCGTTTTTG 57.089 37.500 0.00 0.00 0.00 2.44
2460 3742 2.700897 CTCCGTCCAAGGTCCATATCTT 59.299 50.000 0.00 0.00 0.00 2.40
2461 3743 2.434336 TCCGTCCAAGGTCCATATCTTG 59.566 50.000 0.00 0.00 42.55 3.02
2513 3799 3.795101 GCACGTACGTACATAGATGCTTT 59.205 43.478 22.34 0.00 0.00 3.51
2514 3800 4.266976 GCACGTACGTACATAGATGCTTTT 59.733 41.667 22.34 0.00 0.00 2.27
2515 3801 5.220340 GCACGTACGTACATAGATGCTTTTT 60.220 40.000 22.34 0.00 0.00 1.94
2516 3802 6.020440 GCACGTACGTACATAGATGCTTTTTA 60.020 38.462 22.34 0.00 0.00 1.52
2517 3803 7.306399 GCACGTACGTACATAGATGCTTTTTAT 60.306 37.037 22.34 0.00 0.00 1.40
2518 3804 7.996551 CACGTACGTACATAGATGCTTTTTATG 59.003 37.037 22.34 5.31 0.00 1.90
2519 3805 7.001922 CGTACGTACATAGATGCTTTTTATGC 58.998 38.462 24.50 0.00 0.00 3.14
2520 3806 7.096189 CGTACGTACATAGATGCTTTTTATGCT 60.096 37.037 24.50 0.00 0.00 3.79
2521 3807 7.553881 ACGTACATAGATGCTTTTTATGCTT 57.446 32.000 0.00 0.00 0.00 3.91
2525 3811 6.719365 ACATAGATGCTTTTTATGCTTCGAC 58.281 36.000 0.00 0.00 38.89 4.20
2541 3827 1.603802 TCGACCTGCAGCTTTCTTTTG 59.396 47.619 8.66 0.00 0.00 2.44
2554 3840 4.374013 GCTTTCTTTTGCGTTTGATTCGTC 60.374 41.667 0.00 0.00 0.00 4.20
2578 3869 6.011879 CGGTCATACGTACGTACATATCTTC 58.988 44.000 28.99 13.33 33.01 2.87
2582 3873 6.707608 TCATACGTACGTACATATCTTCTGGT 59.292 38.462 28.99 12.45 33.01 4.00
2584 3875 4.274459 ACGTACGTACATATCTTCTGGTCC 59.726 45.833 21.41 0.00 0.00 4.46
2613 4003 5.277345 CGTTTCTTTCTTTCTCCGTGTCAAT 60.277 40.000 0.00 0.00 0.00 2.57
2632 4022 1.109609 TCGATGCAGCATGTCTCTCT 58.890 50.000 14.22 0.00 39.31 3.10
2636 4026 2.311124 TGCAGCATGTCTCTCTCATG 57.689 50.000 0.00 0.00 43.58 3.07
2650 4040 5.071384 TCTCTCTCATGACATTACCATGCAT 59.929 40.000 0.00 0.00 40.74 3.96
2653 4043 4.577283 TCTCATGACATTACCATGCATGTG 59.423 41.667 24.58 17.95 41.21 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 2.770868 ATCAGCACCACCTCCTCCCA 62.771 60.000 0.00 0.00 0.00 4.37
122 123 1.136329 AACCATCAGCACCACCTCCT 61.136 55.000 0.00 0.00 0.00 3.69
278 279 0.107017 CCATAGCCCACTCCAACCAG 60.107 60.000 0.00 0.00 0.00 4.00
352 353 2.165845 CGATCCCAAGAAGTAGAACGGT 59.834 50.000 0.00 0.00 0.00 4.83
370 371 0.394565 GGCTAGGACTTGATGCCGAT 59.605 55.000 0.00 0.00 33.96 4.18
396 397 1.000486 CCGGGACAAGGAGAGGAGA 60.000 63.158 0.00 0.00 0.00 3.71
530 533 0.602905 GACCCACTGAAGAACCGGTG 60.603 60.000 8.52 0.00 41.78 4.94
531 534 1.752833 GACCCACTGAAGAACCGGT 59.247 57.895 0.00 0.00 0.00 5.28
618 621 1.300311 CAACACACTACCACGCCGA 60.300 57.895 0.00 0.00 0.00 5.54
656 659 1.143183 GGAGCACGCTTAATCCCGA 59.857 57.895 0.00 0.00 0.00 5.14
663 666 2.499205 CATCCGGGAGCACGCTTA 59.501 61.111 0.00 0.00 0.00 3.09
713 717 3.710722 CCCGCTGCTGGAGGAAGT 61.711 66.667 3.77 0.00 37.02 3.01
739 743 2.146519 CACGACACGCTCACGCTAG 61.147 63.158 0.00 0.00 45.53 3.42
861 869 7.703058 ACCACAAAAAGAAAGAAGAAGAAGA 57.297 32.000 0.00 0.00 0.00 2.87
886 902 1.270412 ACCGAGCATACAACCAACGAA 60.270 47.619 0.00 0.00 0.00 3.85
890 906 2.264005 ACAACCGAGCATACAACCAA 57.736 45.000 0.00 0.00 0.00 3.67
966 988 1.815421 GATGTGGGTGCGCTCGAAT 60.815 57.895 9.73 0.00 0.00 3.34
1073 1102 1.713830 GCGGTTGTTATCTCGCCAC 59.286 57.895 0.00 0.00 42.02 5.01
1074 1103 4.195308 GCGGTTGTTATCTCGCCA 57.805 55.556 0.00 0.00 42.02 5.69
1111 1143 1.776293 TGTCCATGGTGGGGGTTGA 60.776 57.895 12.58 0.00 38.32 3.18
1132 1170 0.170339 TTCGTGACGCTCGACATGAT 59.830 50.000 14.88 0.00 36.20 2.45
1392 1433 2.363018 CCCCACTCTCGGCTCTCA 60.363 66.667 0.00 0.00 0.00 3.27
1415 1459 3.894947 GGAGACTCCGGAGCTCGC 61.895 72.222 31.64 26.62 37.59 5.03
1443 1487 1.374758 GGAGTGCACGAAGTCCAGG 60.375 63.158 15.94 0.00 41.61 4.45
1494 1538 1.449601 CAGCCCCACGTCGCTAAAT 60.450 57.895 1.27 0.00 32.92 1.40
1594 1638 2.029918 GGAAGATGGTGAACACAAAGCC 60.030 50.000 7.25 0.00 0.00 4.35
1697 1752 7.178983 AGCTCCTTGTTTTCCATCAAATTATGA 59.821 33.333 0.00 0.00 43.67 2.15
1702 1757 5.420104 CCTAGCTCCTTGTTTTCCATCAAAT 59.580 40.000 0.00 0.00 0.00 2.32
1708 1766 2.344592 TCCCTAGCTCCTTGTTTTCCA 58.655 47.619 0.00 0.00 0.00 3.53
1710 1768 4.320275 CGTTTTCCCTAGCTCCTTGTTTTC 60.320 45.833 0.00 0.00 0.00 2.29
1776 1834 9.408648 ACCATTATTTTCTCCTTCGATACAATT 57.591 29.630 0.00 0.00 0.00 2.32
1809 1869 3.104512 TGGCAGGGGATATATACTTCGG 58.895 50.000 0.00 0.00 0.00 4.30
1822 1882 1.978617 ATGCGAACTTTGGCAGGGG 60.979 57.895 4.92 0.00 44.90 4.79
1837 1901 5.916883 CGGGAATATTTCATTGTTCTCATGC 59.083 40.000 0.00 0.00 0.00 4.06
1846 1920 7.812191 TGTTCTTTTGACGGGAATATTTCATTG 59.188 33.333 0.00 0.00 0.00 2.82
1849 1923 6.885952 TGTTCTTTTGACGGGAATATTTCA 57.114 33.333 0.00 0.00 0.00 2.69
1850 1924 8.647226 CAATTGTTCTTTTGACGGGAATATTTC 58.353 33.333 0.00 0.00 0.00 2.17
1851 1925 8.147704 ACAATTGTTCTTTTGACGGGAATATTT 58.852 29.630 4.92 0.00 0.00 1.40
1854 1928 6.642707 ACAATTGTTCTTTTGACGGGAATA 57.357 33.333 4.92 0.00 0.00 1.75
1856 1930 4.993029 ACAATTGTTCTTTTGACGGGAA 57.007 36.364 4.92 0.00 0.00 3.97
1857 1931 4.882427 TGTACAATTGTTCTTTTGACGGGA 59.118 37.500 17.78 0.00 0.00 5.14
1859 1933 5.173131 GCTTGTACAATTGTTCTTTTGACGG 59.827 40.000 17.78 5.35 0.00 4.79
1861 1935 7.222611 ACATGCTTGTACAATTGTTCTTTTGAC 59.777 33.333 17.78 7.42 33.16 3.18
1863 1937 7.467557 ACATGCTTGTACAATTGTTCTTTTG 57.532 32.000 17.78 8.83 33.16 2.44
1865 1939 7.230510 TCCTACATGCTTGTACAATTGTTCTTT 59.769 33.333 17.78 0.00 37.28 2.52
1868 1942 6.149474 ACTCCTACATGCTTGTACAATTGTTC 59.851 38.462 17.78 12.52 37.28 3.18
1870 1944 5.560724 ACTCCTACATGCTTGTACAATTGT 58.439 37.500 16.68 16.68 37.28 2.71
1873 2087 4.471386 AGGACTCCTACATGCTTGTACAAT 59.529 41.667 9.13 0.00 37.28 2.71
1876 2090 4.500035 GCTAGGACTCCTACATGCTTGTAC 60.500 50.000 8.29 0.00 37.28 2.90
1878 2092 2.432510 GCTAGGACTCCTACATGCTTGT 59.567 50.000 10.40 10.40 39.98 3.16
1880 2094 2.043227 GGCTAGGACTCCTACATGCTT 58.957 52.381 12.37 0.00 34.61 3.91
1883 2097 3.571590 AGAAGGCTAGGACTCCTACATG 58.428 50.000 0.03 0.00 34.61 3.21
1885 2099 2.091775 GGAGAAGGCTAGGACTCCTACA 60.092 54.545 16.93 0.00 43.64 2.74
1889 2103 2.490168 CCTAGGAGAAGGCTAGGACTCC 60.490 59.091 1.05 16.66 46.28 3.85
1890 2104 2.871453 CCTAGGAGAAGGCTAGGACTC 58.129 57.143 1.05 0.00 41.96 3.36
1938 2299 9.262358 CCGGGAGAAAACTCTTCTATTAATAAG 57.738 37.037 0.00 0.00 0.00 1.73
1939 2300 8.765517 ACCGGGAGAAAACTCTTCTATTAATAA 58.234 33.333 6.32 0.00 0.00 1.40
1941 2302 7.196637 ACCGGGAGAAAACTCTTCTATTAAT 57.803 36.000 6.32 0.00 0.00 1.40
1942 2303 6.616237 ACCGGGAGAAAACTCTTCTATTAA 57.384 37.500 6.32 0.00 0.00 1.40
1987 2364 9.863845 TCTGTCTTGATATATTTGTGTACGAAA 57.136 29.630 0.00 0.00 0.00 3.46
1996 2373 7.633621 ACATGCGTTCTGTCTTGATATATTTG 58.366 34.615 0.00 0.00 0.00 2.32
2004 2381 4.868171 GGTTATACATGCGTTCTGTCTTGA 59.132 41.667 0.00 0.00 0.00 3.02
2140 2561 9.722056 GAAGCAAAATGAATGAATCTACGTTAT 57.278 29.630 0.00 0.00 0.00 1.89
2141 2562 7.902917 CGAAGCAAAATGAATGAATCTACGTTA 59.097 33.333 0.00 0.00 0.00 3.18
2142 2563 6.742718 CGAAGCAAAATGAATGAATCTACGTT 59.257 34.615 0.00 0.00 0.00 3.99
2143 2564 6.128282 ACGAAGCAAAATGAATGAATCTACGT 60.128 34.615 0.00 0.00 0.00 3.57
2144 2565 6.250819 ACGAAGCAAAATGAATGAATCTACG 58.749 36.000 0.00 0.00 0.00 3.51
2145 2566 9.162793 CATACGAAGCAAAATGAATGAATCTAC 57.837 33.333 0.00 0.00 0.00 2.59
2146 2567 8.892723 ACATACGAAGCAAAATGAATGAATCTA 58.107 29.630 0.00 0.00 0.00 1.98
2147 2568 7.765307 ACATACGAAGCAAAATGAATGAATCT 58.235 30.769 0.00 0.00 0.00 2.40
2148 2569 7.975866 ACATACGAAGCAAAATGAATGAATC 57.024 32.000 0.00 0.00 0.00 2.52
2152 2573 7.962373 TGAACTACATACGAAGCAAAATGAATG 59.038 33.333 0.00 0.00 0.00 2.67
2153 2574 8.039603 TGAACTACATACGAAGCAAAATGAAT 57.960 30.769 0.00 0.00 0.00 2.57
2154 2575 7.428282 TGAACTACATACGAAGCAAAATGAA 57.572 32.000 0.00 0.00 0.00 2.57
2157 2578 6.374333 ACCATGAACTACATACGAAGCAAAAT 59.626 34.615 0.00 0.00 37.46 1.82
2163 2584 5.006153 TCCACCATGAACTACATACGAAG 57.994 43.478 0.00 0.00 37.46 3.79
2171 2593 3.933861 AGGGATTCCACCATGAACTAC 57.066 47.619 4.80 0.00 34.83 2.73
2173 2595 4.946160 TTTAGGGATTCCACCATGAACT 57.054 40.909 4.80 0.00 34.83 3.01
2174 2596 4.402474 CCTTTTAGGGATTCCACCATGAAC 59.598 45.833 4.80 0.00 34.83 3.18
2175 2597 4.045334 ACCTTTTAGGGATTCCACCATGAA 59.955 41.667 4.80 0.00 40.58 2.57
2176 2598 3.596046 ACCTTTTAGGGATTCCACCATGA 59.404 43.478 4.80 0.00 40.58 3.07
2177 2599 3.954258 GACCTTTTAGGGATTCCACCATG 59.046 47.826 4.80 0.00 40.58 3.66
2179 2601 3.265489 AGACCTTTTAGGGATTCCACCA 58.735 45.455 4.80 0.00 40.58 4.17
2180 2602 4.317530 AAGACCTTTTAGGGATTCCACC 57.682 45.455 4.80 0.00 40.58 4.61
2181 2603 9.642343 AAATATAAGACCTTTTAGGGATTCCAC 57.358 33.333 4.80 0.00 40.58 4.02
2194 2616 9.743581 TCCCTTCGTTTTTAAATATAAGACCTT 57.256 29.630 0.00 0.00 0.00 3.50
2195 2617 9.392259 CTCCCTTCGTTTTTAAATATAAGACCT 57.608 33.333 0.00 0.00 0.00 3.85
2196 2618 9.170734 ACTCCCTTCGTTTTTAAATATAAGACC 57.829 33.333 0.00 0.00 0.00 3.85
2206 2628 9.860898 GTTAGATACTACTCCCTTCGTTTTTAA 57.139 33.333 0.00 0.00 0.00 1.52
2214 2636 7.600752 GCAATCATGTTAGATACTACTCCCTTC 59.399 40.741 0.00 0.00 0.00 3.46
2217 2639 6.870965 CAGCAATCATGTTAGATACTACTCCC 59.129 42.308 0.00 0.00 0.00 4.30
2218 2640 7.661968 TCAGCAATCATGTTAGATACTACTCC 58.338 38.462 0.00 0.00 0.00 3.85
2219 2641 9.190858 CTTCAGCAATCATGTTAGATACTACTC 57.809 37.037 0.00 0.00 0.00 2.59
2221 2643 7.358765 CGCTTCAGCAATCATGTTAGATACTAC 60.359 40.741 0.00 0.00 42.21 2.73
2229 2906 3.126858 GGAACGCTTCAGCAATCATGTTA 59.873 43.478 0.00 0.00 42.21 2.41
2300 3566 7.831750 ACATCGATCAAACGTTTTTACTTTC 57.168 32.000 11.66 1.75 34.70 2.62
2304 3570 8.166706 AGATGTACATCGATCAAACGTTTTTAC 58.833 33.333 26.13 4.55 42.48 2.01
2305 3571 8.166066 CAGATGTACATCGATCAAACGTTTTTA 58.834 33.333 26.13 2.82 42.48 1.52
2325 3591 2.636830 GGCTGCTACAATGACAGATGT 58.363 47.619 0.00 2.63 33.10 3.06
2327 3593 1.208052 ACGGCTGCTACAATGACAGAT 59.792 47.619 0.00 0.00 33.10 2.90
2328 3594 0.608130 ACGGCTGCTACAATGACAGA 59.392 50.000 0.00 0.00 33.10 3.41
2372 3643 7.818930 ACGATTACTCTGGCTATCTAGTACTAC 59.181 40.741 0.00 0.00 0.00 2.73
2373 3644 7.905265 ACGATTACTCTGGCTATCTAGTACTA 58.095 38.462 1.89 1.89 0.00 1.82
2374 3645 6.771573 ACGATTACTCTGGCTATCTAGTACT 58.228 40.000 0.00 0.00 0.00 2.73
2375 3646 7.437793 AACGATTACTCTGGCTATCTAGTAC 57.562 40.000 0.00 0.00 0.00 2.73
2380 3651 5.817816 CCAAAAACGATTACTCTGGCTATCT 59.182 40.000 0.00 0.00 0.00 1.98
2382 3653 5.497474 ACCAAAAACGATTACTCTGGCTAT 58.503 37.500 0.00 0.00 0.00 2.97
2383 3654 4.901868 ACCAAAAACGATTACTCTGGCTA 58.098 39.130 0.00 0.00 0.00 3.93
2403 3674 4.750098 CGACATAACATATGTCCTTGGACC 59.250 45.833 19.49 0.65 43.98 4.46
2460 3742 1.289066 GTACGTGGACAGCTCTGCA 59.711 57.895 0.00 0.00 0.00 4.41
2461 3743 1.801913 CGTACGTGGACAGCTCTGC 60.802 63.158 7.22 0.00 0.00 4.26
2513 3799 1.086696 GCTGCAGGTCGAAGCATAAA 58.913 50.000 17.12 0.00 40.42 1.40
2514 3800 0.250234 AGCTGCAGGTCGAAGCATAA 59.750 50.000 13.85 0.00 40.42 1.90
2515 3801 0.250234 AAGCTGCAGGTCGAAGCATA 59.750 50.000 20.46 0.00 40.42 3.14
2516 3802 0.607489 AAAGCTGCAGGTCGAAGCAT 60.607 50.000 20.46 0.00 40.42 3.79
2517 3803 1.227943 AAAGCTGCAGGTCGAAGCA 60.228 52.632 20.46 8.30 39.47 3.91
2518 3804 0.952984 AGAAAGCTGCAGGTCGAAGC 60.953 55.000 20.46 0.42 37.20 3.86
2519 3805 1.517242 AAGAAAGCTGCAGGTCGAAG 58.483 50.000 20.46 0.00 0.00 3.79
2520 3806 1.967319 AAAGAAAGCTGCAGGTCGAA 58.033 45.000 20.46 0.00 0.00 3.71
2521 3807 1.603802 CAAAAGAAAGCTGCAGGTCGA 59.396 47.619 20.46 0.00 0.00 4.20
2525 3811 0.031178 ACGCAAAAGAAAGCTGCAGG 59.969 50.000 17.12 0.00 35.78 4.85
2541 3827 0.719465 ATGACCGACGAATCAAACGC 59.281 50.000 0.00 0.00 0.00 4.84
2554 3840 5.521516 AGATATGTACGTACGTATGACCG 57.478 43.478 34.20 11.48 38.23 4.79
2578 3869 3.467803 AGAAAGAAACGTTCAGGACCAG 58.532 45.455 0.00 0.00 0.00 4.00
2582 3873 4.814771 GGAGAAAGAAAGAAACGTTCAGGA 59.185 41.667 0.00 0.00 0.00 3.86
2584 3875 4.270325 ACGGAGAAAGAAAGAAACGTTCAG 59.730 41.667 0.00 0.00 0.00 3.02
2613 4003 1.066757 GAGAGAGACATGCTGCATCGA 59.933 52.381 13.10 0.00 0.00 3.59
2632 4022 3.067040 GCACATGCATGGTAATGTCATGA 59.933 43.478 29.41 0.00 43.51 3.07
2636 4026 2.424601 ACAGCACATGCATGGTAATGTC 59.575 45.455 29.41 14.23 45.16 3.06
2642 4032 2.495155 TTAGACAGCACATGCATGGT 57.505 45.000 29.41 17.72 45.16 3.55
2653 4043 8.693542 AAAATTGTGCTAATCAATTAGACAGC 57.306 30.769 12.82 1.89 42.31 4.40


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

AutoCloner maintained by Alex Coulton.