Multiple sequence alignment - TraesCS7A01G072100

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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 TraesCS7A01G072100 chr7A 100.000 3662 0 0 1 3662 37727594 37723933 0.000000e+00 6763.0
1 TraesCS7A01G072100 chr7A 88.479 3255 270 48 6 3199 25688153 25691363 0.000000e+00 3836.0
2 TraesCS7A01G072100 chr7A 92.337 2336 150 12 936 3265 25746283 25748595 0.000000e+00 3295.0
3 TraesCS7A01G072100 chr7A 89.975 399 30 6 3266 3661 25691445 25691836 1.170000e-139 507.0
4 TraesCS7A01G072100 chr7A 91.740 339 24 2 3267 3601 25748632 25748970 5.540000e-128 468.0
5 TraesCS7A01G072100 chr7A 97.778 45 1 0 3221 3265 25691365 25691409 1.090000e-10 78.7
6 TraesCS7A01G072100 chr7D 93.611 1894 107 6 1380 3271 24942102 24943983 0.000000e+00 2815.0
7 TraesCS7A01G072100 chr7D 84.130 1046 93 34 355 1347 24940982 24942007 0.000000e+00 944.0
8 TraesCS7A01G072100 chr7D 90.025 401 33 5 3267 3661 24944014 24944413 2.520000e-141 512.0
9 TraesCS7A01G072100 chr4A 92.666 1909 125 6 1364 3271 708618147 708616253 0.000000e+00 2736.0
10 TraesCS7A01G072100 chr4A 91.457 398 30 2 3267 3661 708616222 708615826 8.940000e-151 544.0


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 TraesCS7A01G072100 chr7A 37723933 37727594 3661 True 6763.000000 6763 100.000000 1 3662 1 chr7A.!!$R1 3661
1 TraesCS7A01G072100 chr7A 25746283 25748970 2687 False 1881.500000 3295 92.038500 936 3601 2 chr7A.!!$F2 2665
2 TraesCS7A01G072100 chr7A 25688153 25691836 3683 False 1473.900000 3836 92.077333 6 3661 3 chr7A.!!$F1 3655
3 TraesCS7A01G072100 chr7D 24940982 24944413 3431 False 1423.666667 2815 89.255333 355 3661 3 chr7D.!!$F1 3306
4 TraesCS7A01G072100 chr4A 708615826 708618147 2321 True 1640.000000 2736 92.061500 1364 3661 2 chr4A.!!$R1 2297

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
420 422 0.106918 TTCACCCGAGTTGCAACCTT 60.107 50.0 25.62 8.63 0.00 3.50 F
456 458 0.615850 AGCCCTTAGAGCCACAACTC 59.384 55.0 0.00 0.00 36.91 3.01 F
1644 1765 0.687354 ACCTCGTCTCCTGCAACATT 59.313 50.0 0.00 0.00 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2359 2480 1.480954 GAAGGCCTCGTAAGTCATGGA 59.519 52.381 5.23 0.00 39.48 3.41 R
2379 2500 5.106078 CCCAATTTTGCAAAATCCCTTGATG 60.106 40.000 31.78 23.95 37.62 3.07 R
3303 3476 0.112412 TGTTGCCTTTCCCTTCCCTC 59.888 55.000 0.00 0.00 0.00 4.30 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
33 34 2.421073 ACCTTGATGTGTCGAATGCATG 59.579 45.455 0.00 0.00 0.00 4.06
56 57 7.462109 TGTAATTCAGCAACATTTCAAACAC 57.538 32.000 0.00 0.00 0.00 3.32
58 59 3.077229 TCAGCAACATTTCAAACACGG 57.923 42.857 0.00 0.00 0.00 4.94
69 70 0.863957 CAAACACGGGTGCACGAAAC 60.864 55.000 11.45 0.00 37.61 2.78
96 97 5.787953 TCCAAATCACACATGTTCACAAT 57.212 34.783 0.00 0.00 0.00 2.71
109 110 8.020819 CACATGTTCACAATTTATACCGAAAGT 58.979 33.333 0.00 0.00 0.00 2.66
153 155 1.152694 ATGCCACAACCACACTGCT 60.153 52.632 0.00 0.00 0.00 4.24
179 181 1.219124 CCATAGCAGCACGACCACT 59.781 57.895 0.00 0.00 0.00 4.00
180 182 1.086067 CCATAGCAGCACGACCACTG 61.086 60.000 0.00 0.00 36.96 3.66
213 215 2.951745 GTCGTCGCTCCAGCATCG 60.952 66.667 0.00 3.02 42.21 3.84
214 216 4.854784 TCGTCGCTCCAGCATCGC 62.855 66.667 0.00 0.00 42.21 4.58
239 241 1.361993 GCCAAAACACGCACCATCA 59.638 52.632 0.00 0.00 0.00 3.07
243 245 1.336440 CAAAACACGCACCATCAAGGA 59.664 47.619 0.00 0.00 41.22 3.36
258 260 3.106827 TCAAGGACCATCACTATGCTCA 58.893 45.455 0.00 0.00 0.00 4.26
261 263 2.158842 AGGACCATCACTATGCTCAAGC 60.159 50.000 0.00 0.00 42.50 4.01
289 291 0.681733 ATATGCAACGCCGAGGAGAT 59.318 50.000 0.00 0.00 0.00 2.75
292 294 2.167861 GCAACGCCGAGGAGATGAC 61.168 63.158 7.26 0.00 0.00 3.06
309 311 3.443045 CCCCACCAGCATTGTCGC 61.443 66.667 0.00 0.00 0.00 5.19
310 312 3.443045 CCCACCAGCATTGTCGCC 61.443 66.667 0.00 0.00 0.00 5.54
328 330 1.986882 CCCAAAGAGGCTTTGTCTGT 58.013 50.000 16.11 0.00 35.39 3.41
334 336 1.001860 AGAGGCTTTGTCTGTCAGCTC 59.998 52.381 0.00 0.00 0.00 4.09
346 348 0.526524 GTCAGCTCCCTTCGATGACG 60.527 60.000 0.00 0.00 37.93 4.35
362 364 1.458777 ACGGTGAGGTGGGTGAGAA 60.459 57.895 0.00 0.00 0.00 2.87
381 383 4.561105 AGAAAAGATGAGACGAGGACAAC 58.439 43.478 0.00 0.00 0.00 3.32
382 384 4.039245 AGAAAAGATGAGACGAGGACAACA 59.961 41.667 0.00 0.00 0.00 3.33
388 390 2.093921 TGAGACGAGGACAACAACAACA 60.094 45.455 0.00 0.00 0.00 3.33
390 392 2.676342 AGACGAGGACAACAACAACAAC 59.324 45.455 0.00 0.00 0.00 3.32
391 393 2.417239 GACGAGGACAACAACAACAACA 59.583 45.455 0.00 0.00 0.00 3.33
392 394 2.814919 ACGAGGACAACAACAACAACAA 59.185 40.909 0.00 0.00 0.00 2.83
393 395 3.168193 CGAGGACAACAACAACAACAAC 58.832 45.455 0.00 0.00 0.00 3.32
394 396 3.119990 CGAGGACAACAACAACAACAACT 60.120 43.478 0.00 0.00 0.00 3.16
395 397 4.093703 CGAGGACAACAACAACAACAACTA 59.906 41.667 0.00 0.00 0.00 2.24
397 399 5.890334 AGGACAACAACAACAACAACTATG 58.110 37.500 0.00 0.00 0.00 2.23
399 401 5.393678 GGACAACAACAACAACAACTATGGT 60.394 40.000 0.00 0.00 0.00 3.55
407 409 4.929819 ACAACAACTATGGTTTTCACCC 57.070 40.909 0.00 0.00 43.49 4.61
416 418 0.741915 GGTTTTCACCCGAGTTGCAA 59.258 50.000 0.00 0.00 37.03 4.08
420 422 0.106918 TTCACCCGAGTTGCAACCTT 60.107 50.000 25.62 8.63 0.00 3.50
427 429 2.817258 CCGAGTTGCAACCTTAATCCAA 59.183 45.455 25.62 0.00 0.00 3.53
429 431 3.502211 CGAGTTGCAACCTTAATCCAAGT 59.498 43.478 25.62 2.43 31.77 3.16
456 458 0.615850 AGCCCTTAGAGCCACAACTC 59.384 55.000 0.00 0.00 36.91 3.01
463 484 1.448013 GAGCCACAACTCCTACGGC 60.448 63.158 0.00 0.00 43.31 5.68
466 487 2.125673 CACAACTCCTACGGCCCG 60.126 66.667 0.00 0.00 0.00 6.13
492 513 1.077787 TGGGCCAAGCTATTGACCG 60.078 57.895 2.13 0.00 39.71 4.79
518 539 2.132762 ACGGTCAGTGTTCATCGTTTC 58.867 47.619 0.00 0.00 0.00 2.78
531 552 3.745975 TCATCGTTTCTGTTGTAGCAAGG 59.254 43.478 0.00 0.00 0.00 3.61
550 571 3.863041 AGGGATGCGAAGAAAAGTACTC 58.137 45.455 0.00 0.00 0.00 2.59
564 585 1.220750 AGTACTCCCTCCACCCCATAG 59.779 57.143 0.00 0.00 0.00 2.23
572 593 2.421952 CCTCCACCCCATAGTCATTGTG 60.422 54.545 0.00 0.00 0.00 3.33
574 595 1.284785 CCACCCCATAGTCATTGTGGT 59.715 52.381 0.00 0.00 38.70 4.16
582 604 5.394443 CCCATAGTCATTGTGGTTGAAATGG 60.394 44.000 8.36 8.36 37.98 3.16
585 607 7.285172 CCATAGTCATTGTGGTTGAAATGGATA 59.715 37.037 9.22 0.00 39.25 2.59
632 654 8.930846 AGTGAGAATTAATATGAAATGGAGGG 57.069 34.615 0.00 0.00 0.00 4.30
656 681 7.776500 GGGAATAGCCATGTTAACCTACTTTTA 59.224 37.037 2.48 0.00 38.95 1.52
660 685 9.914834 ATAGCCATGTTAACCTACTTTTAATGA 57.085 29.630 2.48 0.00 0.00 2.57
689 714 9.233232 CAAATTTATTTAGGACCTTGATAACGC 57.767 33.333 0.00 0.00 0.00 4.84
695 720 1.287425 GACCTTGATAACGCCCGAAG 58.713 55.000 0.00 0.00 0.00 3.79
717 755 8.265998 CGAAGGTTTGTTTATTGACATGTTTTC 58.734 33.333 0.00 0.00 0.00 2.29
718 756 7.692908 AGGTTTGTTTATTGACATGTTTTCG 57.307 32.000 0.00 0.00 0.00 3.46
733 771 8.506140 ACATGTTTTCGATGACATTTTTAGTG 57.494 30.769 10.46 3.98 34.42 2.74
736 774 7.698628 TGTTTTCGATGACATTTTTAGTGACA 58.301 30.769 0.00 0.00 0.00 3.58
737 775 7.642194 TGTTTTCGATGACATTTTTAGTGACAC 59.358 33.333 0.00 0.00 0.00 3.67
744 782 5.995282 TGACATTTTTAGTGACACGAGGATT 59.005 36.000 0.00 0.00 0.00 3.01
745 783 6.485313 TGACATTTTTAGTGACACGAGGATTT 59.515 34.615 0.00 0.00 0.00 2.17
749 787 6.928979 TTTTAGTGACACGAGGATTTCAAA 57.071 33.333 0.00 0.00 0.00 2.69
784 822 3.303593 GCATGATAAATCCGTGCTCAGTG 60.304 47.826 0.00 0.00 35.70 3.66
820 873 4.342772 CCGAACTAAATTTGCAATCCTCG 58.657 43.478 0.00 2.58 0.00 4.63
821 874 4.142687 CCGAACTAAATTTGCAATCCTCGT 60.143 41.667 0.00 0.00 0.00 4.18
822 875 4.788100 CGAACTAAATTTGCAATCCTCGTG 59.212 41.667 0.00 0.00 0.00 4.35
823 876 5.616866 CGAACTAAATTTGCAATCCTCGTGT 60.617 40.000 0.00 0.00 0.00 4.49
824 877 5.296813 ACTAAATTTGCAATCCTCGTGTC 57.703 39.130 0.00 0.00 0.00 3.67
825 878 4.759693 ACTAAATTTGCAATCCTCGTGTCA 59.240 37.500 0.00 0.00 0.00 3.58
826 879 3.559238 AATTTGCAATCCTCGTGTCAC 57.441 42.857 0.00 0.00 0.00 3.67
827 880 2.254546 TTTGCAATCCTCGTGTCACT 57.745 45.000 0.00 0.00 0.00 3.41
828 881 3.394674 TTTGCAATCCTCGTGTCACTA 57.605 42.857 0.00 0.00 0.00 2.74
837 890 3.074412 CCTCGTGTCACTAAAATTGCCT 58.926 45.455 0.65 0.00 0.00 4.75
838 891 4.020928 TCCTCGTGTCACTAAAATTGCCTA 60.021 41.667 0.65 0.00 0.00 3.93
843 896 7.136119 TCGTGTCACTAAAATTGCCTAAAAAG 58.864 34.615 0.65 0.00 0.00 2.27
845 898 7.112984 CGTGTCACTAAAATTGCCTAAAAAGAC 59.887 37.037 0.65 0.00 0.00 3.01
846 899 8.135529 GTGTCACTAAAATTGCCTAAAAAGACT 58.864 33.333 0.00 0.00 0.00 3.24
868 921 8.533657 AGACTTTTCATTTGCCATGATCAAATA 58.466 29.630 18.82 7.97 40.86 1.40
874 927 9.839817 TTCATTTGCCATGATCAAATAATGAAT 57.160 25.926 18.82 7.18 42.54 2.57
879 932 8.426881 TGCCATGATCAAATAATGAATGTTTG 57.573 30.769 0.00 0.00 42.54 2.93
880 933 7.496263 TGCCATGATCAAATAATGAATGTTTGG 59.504 33.333 0.00 0.00 42.54 3.28
957 1012 3.432252 CAGTTCTTATTCGCACGTCCTTT 59.568 43.478 0.00 0.00 0.00 3.11
977 1032 7.115805 GTCCTTTTGATTTCCCGTTTGTAATTC 59.884 37.037 0.00 0.00 0.00 2.17
985 1040 4.094476 TCCCGTTTGTAATTCCTCTCTCT 58.906 43.478 0.00 0.00 0.00 3.10
1514 1635 1.481056 CCGTCCTTCAACTCCCACCT 61.481 60.000 0.00 0.00 0.00 4.00
1644 1765 0.687354 ACCTCGTCTCCTGCAACATT 59.313 50.000 0.00 0.00 0.00 2.71
1812 1933 5.347093 CGCACAGAAGCTATTCGATGATATT 59.653 40.000 0.00 0.00 40.58 1.28
2110 2231 1.498865 AAAGGCAGACGAAGCACACG 61.499 55.000 0.00 0.00 0.00 4.49
2178 2299 5.578336 CACAATCACGAACACACTGATCTAT 59.422 40.000 0.00 0.00 0.00 1.98
2193 2314 5.762218 ACTGATCTATTGGTTATGCAAGAGC 59.238 40.000 0.00 0.00 42.57 4.09
2299 2420 4.511786 TCCGGATTATGTGAAAATGGGA 57.488 40.909 0.00 0.00 0.00 4.37
2310 2431 7.595819 ATGTGAAAATGGGAAGTTACAAGAA 57.404 32.000 0.00 0.00 0.00 2.52
2349 2470 4.753516 TGACATGGTTGAACGGAGATAT 57.246 40.909 0.00 0.00 0.00 1.63
2359 2480 4.780815 TGAACGGAGATATGAGCCAAATT 58.219 39.130 0.00 0.00 0.00 1.82
2379 2500 1.480954 TCCATGACTTACGAGGCCTTC 59.519 52.381 6.77 0.00 0.00 3.46
2521 2642 5.239963 TCTGAGCCAATACACGACGATATTA 59.760 40.000 0.00 0.00 0.00 0.98
2574 2695 1.689258 GGTGGGGATTTCTTGGATGGG 60.689 57.143 0.00 0.00 0.00 4.00
2587 2708 0.178978 GGATGGGGATTCTTGGGAGC 60.179 60.000 0.00 0.00 0.00 4.70
2623 2744 8.564574 GGAGAGTGTTAGATACTAAGAGTGATG 58.435 40.741 0.00 0.00 0.00 3.07
2666 2787 8.360390 CAACTCAGTGCTAGATACATAACCATA 58.640 37.037 0.00 0.00 0.00 2.74
2684 2805 1.128200 TAAGGTGTGGTGTGCAGACT 58.872 50.000 14.32 0.00 0.00 3.24
2685 2806 1.128200 AAGGTGTGGTGTGCAGACTA 58.872 50.000 14.32 4.67 0.00 2.59
2712 2835 3.258872 TGAAAGCCCCAAACTGATCATTG 59.741 43.478 0.00 0.00 0.00 2.82
2753 2876 2.097825 AGGAAGTTGATGCCTTGATGC 58.902 47.619 0.00 0.00 0.00 3.91
2772 2895 3.236047 TGCCACTAGTCTTCCACTGTAA 58.764 45.455 0.00 0.00 36.43 2.41
2773 2896 3.006537 TGCCACTAGTCTTCCACTGTAAC 59.993 47.826 0.00 0.00 36.43 2.50
2774 2897 3.006537 GCCACTAGTCTTCCACTGTAACA 59.993 47.826 0.00 0.00 36.43 2.41
2775 2898 4.502604 GCCACTAGTCTTCCACTGTAACAA 60.503 45.833 0.00 0.00 36.43 2.83
2776 2899 4.989168 CCACTAGTCTTCCACTGTAACAAC 59.011 45.833 0.00 0.00 36.43 3.32
2777 2900 5.221461 CCACTAGTCTTCCACTGTAACAACT 60.221 44.000 0.00 0.00 36.43 3.16
2778 2901 6.015688 CCACTAGTCTTCCACTGTAACAACTA 60.016 42.308 0.00 0.00 36.43 2.24
2779 2902 7.431249 CACTAGTCTTCCACTGTAACAACTAA 58.569 38.462 0.00 0.00 36.43 2.24
2780 2903 7.381678 CACTAGTCTTCCACTGTAACAACTAAC 59.618 40.741 0.00 0.00 36.43 2.34
2781 2904 6.229936 AGTCTTCCACTGTAACAACTAACA 57.770 37.500 0.00 0.00 32.26 2.41
2791 2914 6.761714 ACTGTAACAACTAACAACTTCTCTGG 59.238 38.462 0.00 0.00 0.00 3.86
2795 2918 6.679327 ACAACTAACAACTTCTCTGGAAAC 57.321 37.500 0.00 0.00 0.00 2.78
2796 2919 5.293569 ACAACTAACAACTTCTCTGGAAACG 59.706 40.000 0.00 0.00 0.00 3.60
2806 2929 3.493334 TCTCTGGAAACGTCTTCCACTA 58.507 45.455 20.99 14.13 43.17 2.74
2807 2930 4.087182 TCTCTGGAAACGTCTTCCACTAT 58.913 43.478 20.99 0.00 43.17 2.12
2816 2943 7.763071 GGAAACGTCTTCCACTATAACTAACAT 59.237 37.037 18.66 0.00 38.45 2.71
2817 2944 8.475331 AAACGTCTTCCACTATAACTAACATG 57.525 34.615 0.00 0.00 0.00 3.21
2822 2949 7.707035 GTCTTCCACTATAACTAACATGGTCAG 59.293 40.741 0.00 0.00 0.00 3.51
2830 2957 3.926616 ACTAACATGGTCAGTAGCACAC 58.073 45.455 0.00 0.00 35.57 3.82
2854 2981 8.833493 CACTGATCTATTGATTGTGCAAGAATA 58.167 33.333 9.71 0.00 33.93 1.75
2860 2987 9.399797 TCTATTGATTGTGCAAGAATAGAATGT 57.600 29.630 17.67 0.00 35.26 2.71
2864 2991 7.092079 TGATTGTGCAAGAATAGAATGTTTGG 58.908 34.615 0.00 0.00 25.38 3.28
2866 2993 5.076182 TGTGCAAGAATAGAATGTTTGGGA 58.924 37.500 0.00 0.00 0.00 4.37
2873 3000 6.183347 AGAATAGAATGTTTGGGAAGGTGAG 58.817 40.000 0.00 0.00 0.00 3.51
2888 3015 1.457346 GTGAGGAGGCTGTTTGATGG 58.543 55.000 0.00 0.00 0.00 3.51
2914 3041 1.345422 TGGAGGGGTCCATATCAAGCT 60.345 52.381 0.00 0.00 34.33 3.74
2917 3044 3.373110 GGAGGGGTCCATATCAAGCTTTT 60.373 47.826 0.00 0.00 0.00 2.27
2921 3048 4.651045 GGGGTCCATATCAAGCTTTTTGAT 59.349 41.667 0.00 0.00 41.54 2.57
2924 3051 6.536224 GGGTCCATATCAAGCTTTTTGATTTG 59.464 38.462 4.76 7.35 39.59 2.32
2925 3052 7.099120 GGTCCATATCAAGCTTTTTGATTTGT 58.901 34.615 13.09 0.00 39.59 2.83
2927 3054 9.294030 GTCCATATCAAGCTTTTTGATTTGTAG 57.706 33.333 13.09 3.51 39.59 2.74
2938 3065 8.504005 GCTTTTTGATTTGTAGCTCACTTAGTA 58.496 33.333 0.00 0.00 0.00 1.82
2942 3069 9.719355 TTTGATTTGTAGCTCACTTAGTATCAA 57.281 29.630 0.00 0.00 0.00 2.57
3110 3237 3.733443 AAATGGTGTTCTTGGTTGCTC 57.267 42.857 0.00 0.00 0.00 4.26
3112 3239 1.679139 TGGTGTTCTTGGTTGCTCAG 58.321 50.000 0.00 0.00 0.00 3.35
3126 3261 3.730215 TGCTCAGCTAAAACCCCATTA 57.270 42.857 0.00 0.00 0.00 1.90
3186 3322 1.339438 TGCAACTCAGATCTTCCTGGC 60.339 52.381 0.00 0.00 34.99 4.85
3259 3396 9.522804 CCTATATTGAAGTACTTTGTGAGAGAC 57.477 37.037 10.02 0.00 0.00 3.36
3269 3441 4.349342 ACTTTGTGAGAGACCTTCAATCCT 59.651 41.667 0.00 0.00 0.00 3.24
3286 3458 0.692476 CCTCATGGTCACTGGTGGAA 59.308 55.000 0.70 0.00 0.00 3.53
3303 3476 1.799258 GAAACTGCTGGGCTGTGGTG 61.799 60.000 3.06 0.00 40.40 4.17
3317 3490 0.038310 GTGGTGAGGGAAGGGAAAGG 59.962 60.000 0.00 0.00 0.00 3.11
3338 3511 0.539051 AACAGAGAGGAAGATGGCGG 59.461 55.000 0.00 0.00 0.00 6.13
3419 3595 8.837389 AGTGTATTCCTCTTAGTTTTGTGAAAC 58.163 33.333 0.00 0.00 44.35 2.78
3521 3700 6.149973 TCAACCTGATGAATTGCTCTTGTAAG 59.850 38.462 0.00 0.00 0.00 2.34
3531 3710 2.995939 TGCTCTTGTAAGCTCAATGTCG 59.004 45.455 0.00 0.00 42.94 4.35
3603 3782 9.990868 AAATATCTTTGTTCCCTATTTGTACCT 57.009 29.630 0.00 0.00 0.00 3.08
3661 3840 3.070159 TGTCAACAGCTAGAGTTCTGCTT 59.930 43.478 0.00 0.00 34.51 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.029649 ACACATCAAGGTTTGCATCTGC 60.030 45.455 0.00 0.00 42.50 4.26
3 4 3.668757 CGACACATCAAGGTTTGCATCTG 60.669 47.826 0.00 0.00 0.00 2.90
4 5 2.485426 CGACACATCAAGGTTTGCATCT 59.515 45.455 0.00 0.00 0.00 2.90
11 12 2.503331 TGCATTCGACACATCAAGGTT 58.497 42.857 0.00 0.00 0.00 3.50
21 22 3.688673 TGCTGAATTACATGCATTCGACA 59.311 39.130 0.00 9.75 33.91 4.35
33 34 6.345723 CCGTGTTTGAAATGTTGCTGAATTAC 60.346 38.462 0.00 0.00 0.00 1.89
56 57 0.452122 GATTTCGTTTCGTGCACCCG 60.452 55.000 12.15 8.79 0.00 5.28
58 59 0.589223 TGGATTTCGTTTCGTGCACC 59.411 50.000 12.15 0.00 0.00 5.01
69 70 5.343058 GTGAACATGTGTGATTTGGATTTCG 59.657 40.000 0.00 0.00 0.00 3.46
136 138 1.823470 GAGCAGTGTGGTTGTGGCA 60.823 57.895 0.00 0.00 0.00 4.92
138 140 0.664761 CAAGAGCAGTGTGGTTGTGG 59.335 55.000 0.00 0.00 0.00 4.17
139 141 0.029834 GCAAGAGCAGTGTGGTTGTG 59.970 55.000 0.00 0.00 41.58 3.33
140 142 0.107017 AGCAAGAGCAGTGTGGTTGT 60.107 50.000 0.00 0.00 45.49 3.32
141 143 0.309922 CAGCAAGAGCAGTGTGGTTG 59.690 55.000 0.00 0.00 45.49 3.77
142 144 1.450531 GCAGCAAGAGCAGTGTGGTT 61.451 55.000 0.00 0.00 45.49 3.67
143 145 1.895707 GCAGCAAGAGCAGTGTGGT 60.896 57.895 0.00 0.00 45.49 4.16
167 169 2.591429 TTGGCAGTGGTCGTGCTG 60.591 61.111 0.00 0.00 40.97 4.41
168 170 2.281070 CTTGGCAGTGGTCGTGCT 60.281 61.111 0.00 0.00 40.97 4.40
220 222 1.729131 GATGGTGCGTGTTTTGGCG 60.729 57.895 0.00 0.00 0.00 5.69
230 232 0.392863 TGATGGTCCTTGATGGTGCG 60.393 55.000 0.00 0.00 37.07 5.34
243 245 2.502947 TCAGCTTGAGCATAGTGATGGT 59.497 45.455 5.70 0.00 46.46 3.55
258 260 2.607635 CGTTGCATATACCGTTCAGCTT 59.392 45.455 0.00 0.00 0.00 3.74
261 263 1.260561 GGCGTTGCATATACCGTTCAG 59.739 52.381 0.00 0.00 0.00 3.02
289 291 1.074775 GACAATGCTGGTGGGGTCA 59.925 57.895 0.00 0.00 0.00 4.02
292 294 3.443045 GCGACAATGCTGGTGGGG 61.443 66.667 0.00 0.00 0.00 4.96
309 311 1.882623 GACAGACAAAGCCTCTTTGGG 59.117 52.381 19.55 12.54 36.00 4.12
310 312 2.551459 CTGACAGACAAAGCCTCTTTGG 59.449 50.000 19.55 7.91 39.35 3.28
328 330 1.667154 CCGTCATCGAAGGGAGCTGA 61.667 60.000 0.00 0.00 39.71 4.26
334 336 1.141881 CCTCACCGTCATCGAAGGG 59.858 63.158 0.00 0.00 35.56 3.95
346 348 1.420138 TCTTTTCTCACCCACCTCACC 59.580 52.381 0.00 0.00 0.00 4.02
362 364 4.058817 GTTGTTGTCCTCGTCTCATCTTT 58.941 43.478 0.00 0.00 0.00 2.52
381 383 6.035542 GGTGAAAACCATAGTTGTTGTTGTTG 59.964 38.462 0.00 0.00 35.97 3.33
382 384 6.103330 GGTGAAAACCATAGTTGTTGTTGTT 58.897 36.000 0.00 0.00 35.97 2.83
388 390 3.818773 CTCGGGTGAAAACCATAGTTGTT 59.181 43.478 0.00 0.00 35.97 2.83
390 392 3.408634 ACTCGGGTGAAAACCATAGTTG 58.591 45.455 0.00 0.00 35.97 3.16
391 393 3.782656 ACTCGGGTGAAAACCATAGTT 57.217 42.857 0.00 0.00 38.03 2.24
392 394 3.408634 CAACTCGGGTGAAAACCATAGT 58.591 45.455 0.00 0.00 0.00 2.12
393 395 2.161609 GCAACTCGGGTGAAAACCATAG 59.838 50.000 0.00 0.00 0.00 2.23
394 396 2.156098 GCAACTCGGGTGAAAACCATA 58.844 47.619 0.00 0.00 0.00 2.74
395 397 0.958822 GCAACTCGGGTGAAAACCAT 59.041 50.000 0.00 0.00 0.00 3.55
397 399 0.741915 TTGCAACTCGGGTGAAAACC 59.258 50.000 0.00 0.00 0.00 3.27
399 401 0.741915 GGTTGCAACTCGGGTGAAAA 59.258 50.000 27.64 0.00 0.00 2.29
407 409 3.502211 ACTTGGATTAAGGTTGCAACTCG 59.498 43.478 27.64 8.23 40.84 4.18
416 418 2.304761 TCGCTTGGACTTGGATTAAGGT 59.695 45.455 0.00 0.00 40.84 3.50
420 422 1.406887 GGCTCGCTTGGACTTGGATTA 60.407 52.381 0.00 0.00 0.00 1.75
427 429 0.614979 TCTAAGGGCTCGCTTGGACT 60.615 55.000 8.29 0.00 0.00 3.85
429 431 1.961180 GCTCTAAGGGCTCGCTTGGA 61.961 60.000 11.12 11.12 0.00 3.53
481 502 1.202533 CCGTCAATCCGGTCAATAGCT 60.203 52.381 0.00 0.00 43.07 3.32
482 503 1.217882 CCGTCAATCCGGTCAATAGC 58.782 55.000 0.00 0.00 43.07 2.97
492 513 2.163818 TGAACACTGACCGTCAATCC 57.836 50.000 2.19 0.00 0.00 3.01
507 528 4.725556 TGCTACAACAGAAACGATGAAC 57.274 40.909 0.00 0.00 0.00 3.18
531 552 2.937149 GGGAGTACTTTTCTTCGCATCC 59.063 50.000 0.00 0.00 0.00 3.51
536 557 3.586892 GTGGAGGGAGTACTTTTCTTCG 58.413 50.000 0.00 0.00 0.00 3.79
550 571 1.143684 CAATGACTATGGGGTGGAGGG 59.856 57.143 0.00 0.00 0.00 4.30
564 585 9.071276 AGATATATCCATTTCAACCACAATGAC 57.929 33.333 9.18 0.00 32.91 3.06
623 645 3.979501 ACATGGCTATTCCCTCCATTT 57.020 42.857 0.00 0.00 38.46 2.32
626 648 3.117663 GGTTAACATGGCTATTCCCTCCA 60.118 47.826 8.10 0.00 0.00 3.86
631 653 7.640597 AAAAGTAGGTTAACATGGCTATTCC 57.359 36.000 8.10 0.00 0.00 3.01
680 705 1.807742 CAAACCTTCGGGCGTTATCAA 59.192 47.619 0.00 0.00 39.10 2.57
689 714 4.839668 TGTCAATAAACAAACCTTCGGG 57.160 40.909 0.00 0.00 41.87 5.14
695 720 7.687005 TCGAAAACATGTCAATAAACAAACC 57.313 32.000 0.00 0.00 31.81 3.27
704 729 8.592105 AAAAATGTCATCGAAAACATGTCAAT 57.408 26.923 14.56 0.00 36.28 2.57
717 755 5.444613 CCTCGTGTCACTAAAAATGTCATCG 60.445 44.000 0.65 0.00 0.00 3.84
718 756 5.637810 TCCTCGTGTCACTAAAAATGTCATC 59.362 40.000 0.65 0.00 0.00 2.92
733 771 7.534239 GTCAACTAAATTTGAAATCCTCGTGTC 59.466 37.037 0.00 0.00 37.24 3.67
736 774 7.360361 GTGTCAACTAAATTTGAAATCCTCGT 58.640 34.615 0.00 0.00 37.24 4.18
737 775 6.519761 CGTGTCAACTAAATTTGAAATCCTCG 59.480 38.462 0.00 0.00 37.24 4.63
744 782 6.066054 TCATGCGTGTCAACTAAATTTGAA 57.934 33.333 5.68 0.00 37.24 2.69
745 783 5.681337 TCATGCGTGTCAACTAAATTTGA 57.319 34.783 5.68 0.00 32.94 2.69
749 787 7.417612 GGATTTATCATGCGTGTCAACTAAAT 58.582 34.615 5.68 8.71 0.00 1.40
795 833 3.859386 GGATTGCAAATTTAGTTCGGCAG 59.141 43.478 1.71 0.00 33.39 4.85
796 834 3.509575 AGGATTGCAAATTTAGTTCGGCA 59.490 39.130 1.71 0.00 0.00 5.69
798 836 4.142687 ACGAGGATTGCAAATTTAGTTCGG 60.143 41.667 1.71 0.00 0.00 4.30
799 837 4.788100 CACGAGGATTGCAAATTTAGTTCG 59.212 41.667 1.71 8.97 0.00 3.95
800 838 5.699839 ACACGAGGATTGCAAATTTAGTTC 58.300 37.500 1.71 0.00 0.00 3.01
820 873 8.135529 AGTCTTTTTAGGCAATTTTAGTGACAC 58.864 33.333 0.00 0.00 0.00 3.67
821 874 8.232913 AGTCTTTTTAGGCAATTTTAGTGACA 57.767 30.769 0.00 0.00 0.00 3.58
822 875 9.529325 AAAGTCTTTTTAGGCAATTTTAGTGAC 57.471 29.630 0.00 0.00 0.00 3.67
837 890 9.206870 GATCATGGCAAATGAAAAGTCTTTTTA 57.793 29.630 11.80 8.39 36.66 1.52
838 891 7.716123 TGATCATGGCAAATGAAAAGTCTTTTT 59.284 29.630 11.80 0.00 39.16 1.94
843 896 7.605410 ATTTGATCATGGCAAATGAAAAGTC 57.395 32.000 19.71 0.62 42.54 3.01
845 898 9.929722 CATTATTTGATCATGGCAAATGAAAAG 57.070 29.630 24.90 13.22 43.57 2.27
846 899 9.668497 TCATTATTTGATCATGGCAAATGAAAA 57.332 25.926 24.90 16.98 43.57 2.29
850 903 9.051679 ACATTCATTATTTGATCATGGCAAATG 57.948 29.630 24.90 16.24 43.57 2.32
927 982 2.352960 GCGAATAAGAACTGCCTTCTGG 59.647 50.000 0.00 0.00 39.36 3.86
928 983 3.002791 TGCGAATAAGAACTGCCTTCTG 58.997 45.455 0.00 0.00 39.36 3.02
957 1012 6.007703 AGAGGAATTACAAACGGGAAATCAA 58.992 36.000 0.00 0.00 0.00 2.57
977 1032 3.841255 GGTATTTGGGGGATAGAGAGAGG 59.159 52.174 0.00 0.00 0.00 3.69
985 1040 1.074727 CGGCATGGTATTTGGGGGATA 59.925 52.381 0.00 0.00 0.00 2.59
1015 1074 2.105128 GCGGGTGAGGTCGAGATG 59.895 66.667 0.00 0.00 0.00 2.90
1016 1075 3.518998 CGCGGGTGAGGTCGAGAT 61.519 66.667 0.00 0.00 0.00 2.75
1514 1635 2.570284 TTGAAGGAGCGCACGGAGA 61.570 57.895 11.47 0.00 0.00 3.71
1536 1657 2.363147 ACGAGGGAGTGGAGGAGC 60.363 66.667 0.00 0.00 0.00 4.70
1644 1765 2.604686 ACGAGCCCCTTGAGCAGA 60.605 61.111 0.00 0.00 0.00 4.26
2034 2155 1.834896 AGTGGTGTGTCTGGTGTGTAA 59.165 47.619 0.00 0.00 0.00 2.41
2110 2231 2.173356 TCACCATCCATCTCCACATTCC 59.827 50.000 0.00 0.00 0.00 3.01
2120 2241 3.600388 ACGTTCTTCTTCACCATCCATC 58.400 45.455 0.00 0.00 0.00 3.51
2178 2299 2.192664 TTCCGCTCTTGCATAACCAA 57.807 45.000 0.00 0.00 39.64 3.67
2193 2314 2.513897 GCCTCCCGAACCATTCCG 60.514 66.667 0.00 0.00 0.00 4.30
2299 2420 2.508526 CTGCCCAGCTTCTTGTAACTT 58.491 47.619 0.00 0.00 0.00 2.66
2325 2446 1.660607 CTCCGTTCAACCATGTCATCG 59.339 52.381 0.00 0.00 0.00 3.84
2349 2470 3.689161 CGTAAGTCATGGAATTTGGCTCA 59.311 43.478 0.00 0.00 0.00 4.26
2359 2480 1.480954 GAAGGCCTCGTAAGTCATGGA 59.519 52.381 5.23 0.00 39.48 3.41
2379 2500 5.106078 CCCAATTTTGCAAAATCCCTTGATG 60.106 40.000 31.78 23.95 37.62 3.07
2521 2642 4.883006 AGCAGTTTGAACAATTTTGCCAAT 59.117 33.333 11.67 0.00 0.00 3.16
2574 2695 5.041191 TGATAAAGAGCTCCCAAGAATCC 57.959 43.478 10.93 0.00 0.00 3.01
2587 2708 9.349713 AGTATCTAACACTCTCCTGATAAAGAG 57.650 37.037 0.00 0.00 43.78 2.85
2623 2744 2.555757 AGTTGAGATGCTTGTTCCAAGC 59.444 45.455 19.33 19.33 43.29 4.01
2643 2764 8.031864 CCTTATGGTTATGTATCTAGCACTGAG 58.968 40.741 0.00 0.00 0.00 3.35
2666 2787 1.128200 TAGTCTGCACACCACACCTT 58.872 50.000 0.00 0.00 0.00 3.50
2753 2876 4.866508 TGTTACAGTGGAAGACTAGTGG 57.133 45.455 0.00 0.00 33.21 4.00
2772 2895 5.293569 CGTTTCCAGAGAAGTTGTTAGTTGT 59.706 40.000 0.00 0.00 32.35 3.32
2773 2896 5.293569 ACGTTTCCAGAGAAGTTGTTAGTTG 59.706 40.000 0.00 0.00 32.35 3.16
2774 2897 5.425630 ACGTTTCCAGAGAAGTTGTTAGTT 58.574 37.500 0.00 0.00 32.35 2.24
2775 2898 5.019785 ACGTTTCCAGAGAAGTTGTTAGT 57.980 39.130 0.00 0.00 32.35 2.24
2776 2899 5.290386 AGACGTTTCCAGAGAAGTTGTTAG 58.710 41.667 0.00 0.00 32.35 2.34
2777 2900 5.272283 AGACGTTTCCAGAGAAGTTGTTA 57.728 39.130 0.00 0.00 32.35 2.41
2778 2901 4.138487 AGACGTTTCCAGAGAAGTTGTT 57.862 40.909 0.00 0.00 32.35 2.83
2779 2902 3.821421 AGACGTTTCCAGAGAAGTTGT 57.179 42.857 0.00 0.00 32.35 3.32
2780 2903 3.495001 GGAAGACGTTTCCAGAGAAGTTG 59.505 47.826 18.66 0.00 38.45 3.16
2781 2904 3.134081 TGGAAGACGTTTCCAGAGAAGTT 59.866 43.478 20.99 0.00 43.17 2.66
2791 2914 8.592998 CATGTTAGTTATAGTGGAAGACGTTTC 58.407 37.037 0.00 0.00 0.00 2.78
2795 2918 6.570692 ACCATGTTAGTTATAGTGGAAGACG 58.429 40.000 0.00 0.00 0.00 4.18
2796 2919 7.553334 TGACCATGTTAGTTATAGTGGAAGAC 58.447 38.462 0.00 0.00 0.00 3.01
2806 2929 6.070767 AGTGTGCTACTGACCATGTTAGTTAT 60.071 38.462 0.00 0.00 38.49 1.89
2807 2930 5.245301 AGTGTGCTACTGACCATGTTAGTTA 59.755 40.000 0.00 0.00 38.49 2.24
2822 2949 6.941802 CACAATCAATAGATCAGTGTGCTAC 58.058 40.000 0.00 0.00 35.15 3.58
2830 2957 9.269453 TCTATTCTTGCACAATCAATAGATCAG 57.731 33.333 14.86 0.00 32.65 2.90
2854 2981 2.716424 TCCTCACCTTCCCAAACATTCT 59.284 45.455 0.00 0.00 0.00 2.40
2860 2987 0.772124 AGCCTCCTCACCTTCCCAAA 60.772 55.000 0.00 0.00 0.00 3.28
2864 2991 0.402121 AAACAGCCTCCTCACCTTCC 59.598 55.000 0.00 0.00 0.00 3.46
2866 2993 1.140312 TCAAACAGCCTCCTCACCTT 58.860 50.000 0.00 0.00 0.00 3.50
2873 3000 1.000396 AGCCCATCAAACAGCCTCC 60.000 57.895 0.00 0.00 0.00 4.30
2888 3015 2.692368 TGGACCCCTCCATGAGCC 60.692 66.667 0.00 0.00 42.15 4.70
2906 3033 8.023128 GTGAGCTACAAATCAAAAAGCTTGATA 58.977 33.333 0.00 0.00 43.31 2.15
2917 3044 9.719355 TTTGATACTAAGTGAGCTACAAATCAA 57.281 29.630 0.00 0.00 0.00 2.57
2921 3048 9.502091 ACAATTTGATACTAAGTGAGCTACAAA 57.498 29.630 2.79 0.00 0.00 2.83
2924 3051 8.383619 CACACAATTTGATACTAAGTGAGCTAC 58.616 37.037 2.79 0.00 0.00 3.58
2925 3052 8.311109 TCACACAATTTGATACTAAGTGAGCTA 58.689 33.333 2.79 0.00 0.00 3.32
2927 3054 7.364522 TCACACAATTTGATACTAAGTGAGC 57.635 36.000 2.79 0.00 0.00 4.26
2938 3065 7.781324 ACTCCCTATTTTCACACAATTTGAT 57.219 32.000 2.79 0.00 0.00 2.57
2942 3069 7.176690 CCTGTAACTCCCTATTTTCACACAATT 59.823 37.037 0.00 0.00 0.00 2.32
2946 3073 5.801380 TCCTGTAACTCCCTATTTTCACAC 58.199 41.667 0.00 0.00 0.00 3.82
2955 3082 2.467880 CAAGCCTCCTGTAACTCCCTA 58.532 52.381 0.00 0.00 0.00 3.53
3017 3144 4.891756 CCAGTGCCTCAAATATTCTCCAAT 59.108 41.667 0.00 0.00 0.00 3.16
3110 3237 6.828785 ACAGAGTAATAATGGGGTTTTAGCTG 59.171 38.462 0.00 0.00 0.00 4.24
3112 3239 8.919777 ATACAGAGTAATAATGGGGTTTTAGC 57.080 34.615 0.00 0.00 0.00 3.09
3126 3261 9.606631 GGAAATGAGAACTGAATACAGAGTAAT 57.393 33.333 0.00 0.00 46.03 1.89
3186 3322 6.726258 TCTACACTGCAGAAATACAATGTG 57.274 37.500 23.35 7.31 0.00 3.21
3259 3396 3.276857 CAGTGACCATGAGGATTGAAGG 58.723 50.000 0.00 0.00 38.69 3.46
3269 3441 1.774254 AGTTTCCACCAGTGACCATGA 59.226 47.619 0.00 0.00 0.00 3.07
3286 3458 2.203394 CACCACAGCCCAGCAGTT 60.203 61.111 0.00 0.00 0.00 3.16
3303 3476 0.112412 TGTTGCCTTTCCCTTCCCTC 59.888 55.000 0.00 0.00 0.00 4.30
3317 3490 1.377536 GCCATCTTCCTCTCTGTTGC 58.622 55.000 0.00 0.00 0.00 4.17
3338 3511 5.411781 ACTCTAAATGGTCGTCAGAATCAC 58.588 41.667 0.00 0.00 0.00 3.06
3370 3543 4.614555 TCATCATCAACAACAATACCGC 57.385 40.909 0.00 0.00 0.00 5.68
3426 3605 8.618240 TTCTGATCACTAGGGACCTTTTTATA 57.382 34.615 0.00 0.00 0.00 0.98
3436 3615 1.751351 CGTGCTTCTGATCACTAGGGA 59.249 52.381 0.00 0.00 0.00 4.20
3441 3620 5.774498 TCATATACGTGCTTCTGATCACT 57.226 39.130 0.00 1.08 0.00 3.41
3496 3675 4.401022 ACAAGAGCAATTCATCAGGTTGA 58.599 39.130 0.00 0.00 0.00 3.18
3521 3700 2.605366 GGAAGCTTCTACGACATTGAGC 59.395 50.000 25.05 0.75 0.00 4.26
3531 3710 2.693267 AATCCGTGGGAAGCTTCTAC 57.307 50.000 25.05 21.19 34.34 2.59


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

AutoCloner maintained by Alex Coulton.