Multiple sequence alignment - TraesCS1B01G395200

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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 TraesCS1B01G395200 chr1B 100.000 3169 0 0 1 3169 626856114 626852946 0.000000e+00 5853
1 TraesCS1B01G395200 chr1A 88.427 2981 162 84 279 3169 549933792 549930905 0.000000e+00 3424
2 TraesCS1B01G395200 chr1A 88.034 234 9 9 3 235 549934007 549933792 3.140000e-65 259
3 TraesCS1B01G395200 chr1D 87.066 2853 144 98 393 3166 457248178 457245472 0.000000e+00 3016
4 TraesCS1B01G395200 chr1D 90.934 364 22 7 3 360 457248536 457248178 2.210000e-131 479


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 TraesCS1B01G395200 chr1B 626852946 626856114 3168 True 5853.0 5853 100.0000 1 3169 1 chr1B.!!$R1 3168
1 TraesCS1B01G395200 chr1A 549930905 549934007 3102 True 1841.5 3424 88.2305 3 3169 2 chr1A.!!$R1 3166
2 TraesCS1B01G395200 chr1D 457245472 457248536 3064 True 1747.5 3016 89.0000 3 3166 2 chr1D.!!$R1 3163

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
764 835 0.163788 CGACCTTGCACGCTAACAAG 59.836 55.0 0.0 0.0 42.35 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2278 2402 0.250513 CCAAGACTGACCCAGTAGCC 59.749 60.0 0.0 0.0 45.44 3.93 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
37 41 4.182339 GAGATAGAACGAACCCAGGTTTC 58.818 47.826 3.05 0.00 38.60 2.78
46 50 2.337532 CCAGGTTTCGGACGACGT 59.662 61.111 0.00 0.00 44.69 4.34
79 83 3.838271 GCCGATGCTCTCCACCGA 61.838 66.667 0.00 0.00 33.53 4.69
238 261 5.705609 TTTCCGCTGCTCTTTCTTTAATT 57.294 34.783 0.00 0.00 0.00 1.40
241 264 6.811253 TCCGCTGCTCTTTCTTTAATTAAA 57.189 33.333 10.16 10.16 0.00 1.52
243 266 7.826690 TCCGCTGCTCTTTCTTTAATTAAATT 58.173 30.769 10.97 0.00 0.00 1.82
244 267 8.952278 TCCGCTGCTCTTTCTTTAATTAAATTA 58.048 29.630 10.97 0.70 0.00 1.40
277 300 0.875474 CCGTTTTGGGCAGCAGTTTG 60.875 55.000 0.00 0.00 0.00 2.93
291 314 0.958822 AGTTTGTCCGGTCAAATGCC 59.041 50.000 25.83 15.29 39.09 4.40
300 323 4.408821 TCAAATGCCCGGCGCTCT 62.409 61.111 7.64 1.64 38.78 4.09
369 393 1.000060 GCAGCCAGCACTTGATTTTCA 60.000 47.619 0.00 0.00 44.79 2.69
380 404 2.332063 TGATTTTCAGATCCTCCGGC 57.668 50.000 0.00 0.00 0.00 6.13
382 406 0.918983 ATTTTCAGATCCTCCGGCCA 59.081 50.000 2.24 0.00 0.00 5.36
386 410 2.123251 AGATCCTCCGGCCATCGT 60.123 61.111 2.24 0.00 37.11 3.73
391 415 4.570663 CTCCGGCCATCGTCGTCC 62.571 72.222 2.24 0.00 37.11 4.79
442 466 1.671742 GGCGGGAAGACTTCACTGA 59.328 57.895 15.36 0.00 0.00 3.41
712 751 5.732288 GCGACAGCATTTTCTAAGTGATAG 58.268 41.667 0.00 0.00 44.35 2.08
727 781 8.209584 TCTAAGTGATAGGACGACAAGTATACT 58.790 37.037 0.00 0.00 32.09 2.12
762 833 3.945436 CGACCTTGCACGCTAACA 58.055 55.556 0.00 0.00 0.00 2.41
763 834 2.230892 CGACCTTGCACGCTAACAA 58.769 52.632 0.00 0.00 0.00 2.83
764 835 0.163788 CGACCTTGCACGCTAACAAG 59.836 55.000 0.00 0.00 42.35 3.16
765 836 1.226746 GACCTTGCACGCTAACAAGT 58.773 50.000 8.17 0.00 41.36 3.16
766 837 2.409975 GACCTTGCACGCTAACAAGTA 58.590 47.619 8.17 0.00 41.36 2.24
767 838 2.412089 GACCTTGCACGCTAACAAGTAG 59.588 50.000 8.17 0.00 41.36 2.57
769 840 1.128692 CTTGCACGCTAACAAGTAGGC 59.871 52.381 0.00 0.00 38.75 3.93
770 841 0.672401 TGCACGCTAACAAGTAGGCC 60.672 55.000 0.00 0.00 0.00 5.19
771 842 1.366854 GCACGCTAACAAGTAGGCCC 61.367 60.000 0.00 0.00 0.00 5.80
779 850 2.606519 AAGTAGGCCCTGGCGTGA 60.607 61.111 13.35 0.00 43.06 4.35
929 1006 1.268335 ACAAAAACAAACGCGAGCGAT 60.268 42.857 24.72 9.75 42.83 4.58
930 1007 1.778591 CAAAAACAAACGCGAGCGATT 59.221 42.857 24.72 15.80 42.83 3.34
956 1033 1.613630 TGCCTCAAGACCTCCTCCC 60.614 63.158 0.00 0.00 0.00 4.30
957 1034 1.306568 GCCTCAAGACCTCCTCCCT 60.307 63.158 0.00 0.00 0.00 4.20
960 1037 0.338120 CTCAAGACCTCCTCCCTCCT 59.662 60.000 0.00 0.00 0.00 3.69
961 1038 0.336737 TCAAGACCTCCTCCCTCCTC 59.663 60.000 0.00 0.00 0.00 3.71
962 1039 1.040339 CAAGACCTCCTCCCTCCTCG 61.040 65.000 0.00 0.00 0.00 4.63
964 1041 4.467107 ACCTCCTCCCTCCTCGCC 62.467 72.222 0.00 0.00 0.00 5.54
966 1043 4.507916 CTCCTCCCTCCTCGCCGA 62.508 72.222 0.00 0.00 0.00 5.54
967 1044 4.507916 TCCTCCCTCCTCGCCGAG 62.508 72.222 7.25 7.25 0.00 4.63
980 1057 4.452733 CCGAGCCAACCCGACTCC 62.453 72.222 0.00 0.00 0.00 3.85
981 1058 4.796231 CGAGCCAACCCGACTCCG 62.796 72.222 0.00 0.00 0.00 4.63
1391 1468 2.203788 ACCTCCCACGGAAGAGCA 60.204 61.111 0.00 0.00 0.00 4.26
1401 1478 2.511145 GAAGAGCAGCAGCCTCCG 60.511 66.667 0.00 0.00 43.56 4.63
1713 1790 6.526566 ACTAATGCTCGAATTTACCGAATC 57.473 37.500 0.00 0.00 35.48 2.52
1723 1800 1.555477 TTACCGAATCGCCCCTTGGT 61.555 55.000 0.00 0.00 0.00 3.67
1959 2036 3.129502 CCCGACGACGAGTAGCCA 61.130 66.667 9.28 0.00 42.66 4.75
1965 2042 1.226717 CGACGAGTAGCCAAGCTCC 60.227 63.158 0.00 0.00 40.44 4.70
1966 2043 1.142097 GACGAGTAGCCAAGCTCCC 59.858 63.158 0.00 0.00 40.44 4.30
2115 2221 6.747125 TGTACTCGTGTTCACCAGTTATTAA 58.253 36.000 8.30 0.00 0.00 1.40
2116 2222 6.864685 TGTACTCGTGTTCACCAGTTATTAAG 59.135 38.462 8.30 0.00 0.00 1.85
2117 2223 5.850614 ACTCGTGTTCACCAGTTATTAAGT 58.149 37.500 0.00 0.00 0.00 2.24
2118 2224 6.285990 ACTCGTGTTCACCAGTTATTAAGTT 58.714 36.000 0.00 0.00 0.00 2.66
2119 2225 6.764560 ACTCGTGTTCACCAGTTATTAAGTTT 59.235 34.615 0.00 0.00 0.00 2.66
2120 2226 7.927629 ACTCGTGTTCACCAGTTATTAAGTTTA 59.072 33.333 0.00 0.00 0.00 2.01
2121 2227 8.075593 TCGTGTTCACCAGTTATTAAGTTTAC 57.924 34.615 0.00 0.00 0.00 2.01
2191 2310 2.426183 CGTCTGTACAGTCGCGTGC 61.426 63.158 25.25 0.00 33.80 5.34
2272 2396 2.093869 GCTTCCATCCTGGTTGTACGTA 60.094 50.000 4.19 0.00 39.03 3.57
2278 2402 4.439700 CCATCCTGGTTGTACGTACTACTG 60.440 50.000 29.98 23.62 33.47 2.74
2279 2403 3.084039 TCCTGGTTGTACGTACTACTGG 58.916 50.000 29.98 28.71 33.47 4.00
2280 2404 2.416431 CCTGGTTGTACGTACTACTGGC 60.416 54.545 29.98 18.86 33.47 4.85
2281 2405 2.490903 CTGGTTGTACGTACTACTGGCT 59.509 50.000 29.98 0.00 33.47 4.75
2282 2406 3.684908 TGGTTGTACGTACTACTGGCTA 58.315 45.455 29.98 14.82 33.47 3.93
2283 2407 3.440173 TGGTTGTACGTACTACTGGCTAC 59.560 47.826 29.98 17.75 33.47 3.58
2284 2408 3.691609 GGTTGTACGTACTACTGGCTACT 59.308 47.826 29.98 0.00 33.47 2.57
2285 2409 4.437930 GGTTGTACGTACTACTGGCTACTG 60.438 50.000 29.98 0.00 33.47 2.74
2299 2423 1.270907 CTACTGGGTCAGTCTTGGCT 58.729 55.000 3.65 0.00 41.21 4.75
2301 2425 0.109342 ACTGGGTCAGTCTTGGCTTG 59.891 55.000 0.00 0.00 41.21 4.01
2304 2428 1.456287 GGTCAGTCTTGGCTTGGGT 59.544 57.895 0.00 0.00 0.00 4.51
2305 2429 0.890996 GGTCAGTCTTGGCTTGGGTG 60.891 60.000 0.00 0.00 0.00 4.61
2306 2430 0.890996 GTCAGTCTTGGCTTGGGTGG 60.891 60.000 0.00 0.00 0.00 4.61
2307 2431 1.151450 CAGTCTTGGCTTGGGTGGT 59.849 57.895 0.00 0.00 0.00 4.16
2308 2432 1.151450 AGTCTTGGCTTGGGTGGTG 59.849 57.895 0.00 0.00 0.00 4.17
2309 2433 2.203480 TCTTGGCTTGGGTGGTGC 60.203 61.111 0.00 0.00 0.00 5.01
2310 2434 2.203538 CTTGGCTTGGGTGGTGCT 60.204 61.111 0.00 0.00 0.00 4.40
2360 2484 3.843240 CGCTTTCCGTGCTCGCTC 61.843 66.667 1.89 0.00 35.54 5.03
2361 2485 2.433318 GCTTTCCGTGCTCGCTCT 60.433 61.111 1.89 0.00 35.54 4.09
2367 2491 4.767841 CGTGCTCGCTCTCGCAGT 62.768 66.667 0.00 0.00 36.73 4.40
2411 2537 2.117156 TCCCGATCCGGTCTTCGTC 61.117 63.158 18.05 2.82 46.80 4.20
2418 2544 2.362632 CGGTCTTCGTCCCCTCCT 60.363 66.667 0.00 0.00 0.00 3.69
2445 2579 3.431725 GCGTTTTCTCGGGGGCTG 61.432 66.667 0.00 0.00 0.00 4.85
2446 2580 2.746277 CGTTTTCTCGGGGGCTGG 60.746 66.667 0.00 0.00 0.00 4.85
2447 2581 3.062466 GTTTTCTCGGGGGCTGGC 61.062 66.667 0.00 0.00 0.00 4.85
2448 2582 3.256960 TTTTCTCGGGGGCTGGCT 61.257 61.111 0.00 0.00 0.00 4.75
2485 2619 1.296056 CGTCGGGCGTTTTGGATTCT 61.296 55.000 0.00 0.00 35.54 2.40
2489 2623 1.821216 GGGCGTTTTGGATTCTCTCA 58.179 50.000 0.00 0.00 0.00 3.27
2491 2625 2.356069 GGGCGTTTTGGATTCTCTCATC 59.644 50.000 0.00 0.00 0.00 2.92
2493 2627 3.274288 GCGTTTTGGATTCTCTCATCCT 58.726 45.455 1.54 0.00 43.12 3.24
2494 2628 3.311048 GCGTTTTGGATTCTCTCATCCTC 59.689 47.826 1.54 0.00 43.12 3.71
2506 2654 1.765314 CTCATCCTCTGGGTAGGGTTG 59.235 57.143 0.00 0.00 37.24 3.77
2678 2830 2.161030 AGCGCTACTGGCTACTATACC 58.839 52.381 8.99 0.00 39.39 2.73
2681 2833 2.889045 CGCTACTGGCTACTATACCCAA 59.111 50.000 0.00 0.00 39.13 4.12
2682 2834 3.057456 CGCTACTGGCTACTATACCCAAG 60.057 52.174 0.00 0.00 39.13 3.61
2683 2835 4.150359 GCTACTGGCTACTATACCCAAGA 58.850 47.826 0.00 0.00 38.06 3.02
2684 2836 4.587684 GCTACTGGCTACTATACCCAAGAA 59.412 45.833 0.00 0.00 38.06 2.52
2685 2837 5.070047 GCTACTGGCTACTATACCCAAGAAA 59.930 44.000 0.00 0.00 38.06 2.52
2686 2838 5.615925 ACTGGCTACTATACCCAAGAAAG 57.384 43.478 0.00 0.00 0.00 2.62
2687 2839 5.278061 ACTGGCTACTATACCCAAGAAAGA 58.722 41.667 0.00 0.00 0.00 2.52
2688 2840 5.724854 ACTGGCTACTATACCCAAGAAAGAA 59.275 40.000 0.00 0.00 0.00 2.52
2689 2841 6.214819 ACTGGCTACTATACCCAAGAAAGAAA 59.785 38.462 0.00 0.00 0.00 2.52
2690 2842 7.023171 TGGCTACTATACCCAAGAAAGAAAA 57.977 36.000 0.00 0.00 0.00 2.29
2691 2843 6.882678 TGGCTACTATACCCAAGAAAGAAAAC 59.117 38.462 0.00 0.00 0.00 2.43
2692 2844 6.036844 GGCTACTATACCCAAGAAAGAAAACG 59.963 42.308 0.00 0.00 0.00 3.60
2693 2845 6.036844 GCTACTATACCCAAGAAAGAAAACGG 59.963 42.308 0.00 0.00 0.00 4.44
2708 2860 9.495754 GAAAGAAAACGGATGATTAATCAAGAG 57.504 33.333 21.50 16.36 40.69 2.85
2711 2863 8.260818 AGAAAACGGATGATTAATCAAGAGAGA 58.739 33.333 21.50 0.00 40.69 3.10
2712 2864 8.970859 AAAACGGATGATTAATCAAGAGAGAT 57.029 30.769 21.50 3.75 40.69 2.75
2713 2865 7.959689 AACGGATGATTAATCAAGAGAGATG 57.040 36.000 21.50 8.67 40.69 2.90
2714 2866 6.462500 ACGGATGATTAATCAAGAGAGATGG 58.538 40.000 21.50 6.84 40.69 3.51
2715 2867 6.042552 ACGGATGATTAATCAAGAGAGATGGT 59.957 38.462 21.50 1.52 40.69 3.55
2716 2868 7.233553 ACGGATGATTAATCAAGAGAGATGGTA 59.766 37.037 21.50 0.00 40.69 3.25
2717 2869 7.758980 CGGATGATTAATCAAGAGAGATGGTAG 59.241 40.741 21.50 0.00 40.69 3.18
2718 2870 8.592809 GGATGATTAATCAAGAGAGATGGTAGT 58.407 37.037 21.50 0.36 40.69 2.73
2719 2871 9.421806 GATGATTAATCAAGAGAGATGGTAGTG 57.578 37.037 21.50 0.00 40.69 2.74
2720 2872 7.730084 TGATTAATCAAGAGAGATGGTAGTGG 58.270 38.462 15.82 0.00 33.08 4.00
2721 2873 7.345653 TGATTAATCAAGAGAGATGGTAGTGGT 59.654 37.037 15.82 0.00 33.08 4.16
2722 2874 8.783660 ATTAATCAAGAGAGATGGTAGTGGTA 57.216 34.615 0.00 0.00 0.00 3.25
2726 2878 3.904717 AGAGAGATGGTAGTGGTACAGG 58.095 50.000 0.00 0.00 41.80 4.00
2738 2890 4.697756 TACAGGTGCAGCACGGGC 62.698 66.667 19.42 0.00 41.61 6.13
2750 2902 3.064324 ACGGGCTTGCATGGAAGC 61.064 61.111 35.91 35.91 46.49 3.86
2760 2912 0.953727 GCATGGAAGCAAGTGTCACA 59.046 50.000 5.62 0.00 0.00 3.58
2761 2913 1.542915 GCATGGAAGCAAGTGTCACAT 59.457 47.619 5.62 0.00 0.00 3.21
2762 2914 2.670229 GCATGGAAGCAAGTGTCACATG 60.670 50.000 5.62 4.65 37.77 3.21
2796 2948 3.124921 GGACGACCCATGCAACGG 61.125 66.667 0.00 0.00 34.14 4.44
2797 2949 2.358247 GACGACCCATGCAACGGT 60.358 61.111 7.75 7.75 34.13 4.83
2799 2951 3.124921 CGACCCATGCAACGGTCC 61.125 66.667 23.05 10.66 44.88 4.46
2800 2952 2.351276 GACCCATGCAACGGTCCT 59.649 61.111 20.00 0.00 42.39 3.85
2801 2953 2.034066 ACCCATGCAACGGTCCTG 59.966 61.111 2.27 0.00 0.00 3.86
2837 2993 3.668596 ACGTGTTCTTCGTTTTCCTTG 57.331 42.857 0.00 0.00 38.38 3.61
2851 3007 0.690192 TCCTTGGCCATGTCGAAGAA 59.310 50.000 6.09 0.00 39.69 2.52
2879 3050 5.415545 GCGTGTACGTACGTAAGTTAGCAA 61.416 45.833 28.34 3.51 46.29 3.91
2880 3051 6.832503 GCGTGTACGTACGTAAGTTAGCAAA 61.833 44.000 28.34 2.71 46.29 3.68
2881 3052 8.518816 GCGTGTACGTACGTAAGTTAGCAAAG 62.519 46.154 28.34 17.53 46.29 2.77
2886 3057 1.816074 CGTAAGTTAGCAAAGGGGCA 58.184 50.000 0.00 0.00 35.83 5.36
2889 3060 2.603075 AAGTTAGCAAAGGGGCATCA 57.397 45.000 0.00 0.00 35.83 3.07
2890 3061 2.834638 AGTTAGCAAAGGGGCATCAT 57.165 45.000 0.00 0.00 35.83 2.45
2891 3062 3.105959 AGTTAGCAAAGGGGCATCATT 57.894 42.857 0.00 0.00 35.83 2.57
2892 3063 3.026694 AGTTAGCAAAGGGGCATCATTC 58.973 45.455 0.00 0.00 35.83 2.67
2893 3064 3.026694 GTTAGCAAAGGGGCATCATTCT 58.973 45.455 0.00 0.00 35.83 2.40
2895 3066 0.462789 GCAAAGGGGCATCATTCTGG 59.537 55.000 0.00 0.00 0.00 3.86
2898 3069 0.554792 AAGGGGCATCATTCTGGGAG 59.445 55.000 0.00 0.00 0.00 4.30
2900 3071 0.110104 GGGGCATCATTCTGGGAGAG 59.890 60.000 0.00 0.00 0.00 3.20
2902 3073 0.536915 GGCATCATTCTGGGAGAGGC 60.537 60.000 0.00 0.00 38.25 4.70
2903 3074 0.536915 GCATCATTCTGGGAGAGGCC 60.537 60.000 0.00 0.00 33.39 5.19
2904 3075 0.250209 CATCATTCTGGGAGAGGCCG 60.250 60.000 0.00 0.00 37.63 6.13
2905 3076 0.692419 ATCATTCTGGGAGAGGCCGT 60.692 55.000 0.00 0.00 37.63 5.68
2906 3077 1.153289 CATTCTGGGAGAGGCCGTG 60.153 63.158 0.00 0.00 37.63 4.94
2907 3078 3.036429 ATTCTGGGAGAGGCCGTGC 62.036 63.158 0.00 0.00 37.63 5.34
2911 3082 4.509737 GGGAGAGGCCGTGCGTAC 62.510 72.222 0.00 0.00 37.63 3.67
2920 3091 4.659002 CGTGCGTACGTACCTCTC 57.341 61.111 27.11 11.26 44.99 3.20
2921 3092 1.296432 CGTGCGTACGTACCTCTCG 60.296 63.158 27.11 17.94 44.99 4.04
2922 3093 1.790387 GTGCGTACGTACCTCTCGT 59.210 57.895 23.78 0.00 43.86 4.18
2923 3094 0.519999 GTGCGTACGTACCTCTCGTG 60.520 60.000 23.78 5.24 41.62 4.35
2924 3095 0.950555 TGCGTACGTACCTCTCGTGT 60.951 55.000 19.67 0.00 41.62 4.49
2933 3104 0.680280 ACCTCTCGTGTCGCCATACT 60.680 55.000 0.00 0.00 0.00 2.12
2935 3106 0.733150 CTCTCGTGTCGCCATACTGA 59.267 55.000 0.00 0.00 0.00 3.41
2968 3140 1.063972 TACGTATACACACGGGCGC 59.936 57.895 0.00 0.00 46.12 6.53
2981 3153 4.367023 GGCGCACCACGTCCACTA 62.367 66.667 10.83 0.00 46.11 2.74
2998 3170 0.384309 CTACAAGAGCCCGTATGCGA 59.616 55.000 4.21 0.00 41.33 5.10
2999 3171 1.000163 CTACAAGAGCCCGTATGCGAT 60.000 52.381 4.21 0.00 41.33 4.58
3000 3172 0.530650 ACAAGAGCCCGTATGCGATG 60.531 55.000 4.21 0.00 41.33 3.84
3001 3173 1.595382 AAGAGCCCGTATGCGATGC 60.595 57.895 4.21 7.18 41.33 3.91
3002 3174 3.406361 GAGCCCGTATGCGATGCG 61.406 66.667 4.21 0.00 41.33 4.73
3003 3175 4.221422 AGCCCGTATGCGATGCGT 62.221 61.111 4.21 0.00 41.33 5.24
3005 3177 4.000557 CCCGTATGCGATGCGTGC 62.001 66.667 4.21 0.00 41.33 5.34
3007 3179 2.053984 CGTATGCGATGCGTGCAC 60.054 61.111 6.82 6.82 46.57 4.57
3008 3180 2.324477 GTATGCGATGCGTGCACC 59.676 61.111 12.15 4.74 46.57 5.01
3009 3181 3.261216 TATGCGATGCGTGCACCG 61.261 61.111 12.15 3.76 46.57 4.94
3042 3219 2.282110 TCGGGTTGGCCATGTGTG 60.282 61.111 6.09 0.00 36.17 3.82
3043 3220 4.054825 CGGGTTGGCCATGTGTGC 62.055 66.667 6.09 0.00 36.17 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 64 3.785859 GGTGGAGAGCATCGGCCA 61.786 66.667 2.24 0.00 42.67 5.36
90 94 3.716006 CTGCGTGAACCTGCCGTG 61.716 66.667 0.00 0.00 0.00 4.94
95 99 3.114616 CTCCGCTGCGTGAACCTG 61.115 66.667 21.59 3.49 0.00 4.00
96 100 3.288308 CTCTCCGCTGCGTGAACCT 62.288 63.158 21.59 0.00 0.00 3.50
97 101 2.811317 CTCTCCGCTGCGTGAACC 60.811 66.667 21.59 0.00 0.00 3.62
98 102 1.803519 CTCTCTCCGCTGCGTGAAC 60.804 63.158 21.59 0.00 0.00 3.18
99 103 1.524008 TTCTCTCTCCGCTGCGTGAA 61.524 55.000 21.59 11.43 0.00 3.18
100 104 1.315981 ATTCTCTCTCCGCTGCGTGA 61.316 55.000 21.59 16.57 0.00 4.35
218 241 6.811253 TTTAATTAAAGAAAGAGCAGCGGA 57.189 33.333 6.54 0.00 0.00 5.54
241 264 8.007405 CCAAAACGGAGGGAGATTAATTTAAT 57.993 34.615 1.25 1.25 36.56 1.40
244 267 5.914898 CCAAAACGGAGGGAGATTAATTT 57.085 39.130 0.00 0.00 36.56 1.82
255 278 2.597217 TGCTGCCCAAAACGGAGG 60.597 61.111 0.00 0.00 36.56 4.30
256 279 1.455383 AACTGCTGCCCAAAACGGAG 61.455 55.000 0.00 0.00 36.56 4.63
257 280 1.040339 AAACTGCTGCCCAAAACGGA 61.040 50.000 0.00 0.00 36.56 4.69
258 281 0.875474 CAAACTGCTGCCCAAAACGG 60.875 55.000 0.00 0.00 0.00 4.44
259 282 0.179113 ACAAACTGCTGCCCAAAACG 60.179 50.000 0.00 0.00 0.00 3.60
298 321 2.201436 GAGGAGCAACGACGAGCAGA 62.201 60.000 16.62 0.00 0.00 4.26
300 323 2.258591 GAGGAGCAACGACGAGCA 59.741 61.111 16.62 0.00 0.00 4.26
391 415 1.079543 GATCATCAGCCGATCGGGG 60.080 63.158 33.98 11.68 35.78 5.73
433 457 3.560226 ACCTCCTGGTCAGTGAAGT 57.440 52.632 0.00 0.00 44.78 3.01
712 751 1.836383 CCGCAGTATACTTGTCGTCC 58.164 55.000 1.56 0.00 0.00 4.79
748 819 1.732259 CCTACTTGTTAGCGTGCAAGG 59.268 52.381 17.02 0.00 44.45 3.61
756 827 0.748367 GCCAGGGCCTACTTGTTAGC 60.748 60.000 5.28 0.00 34.56 3.09
757 828 0.462047 CGCCAGGGCCTACTTGTTAG 60.462 60.000 5.28 0.00 37.98 2.34
758 829 1.196104 ACGCCAGGGCCTACTTGTTA 61.196 55.000 5.28 0.00 37.98 2.41
760 831 2.928396 ACGCCAGGGCCTACTTGT 60.928 61.111 5.28 0.00 37.98 3.16
762 833 2.606519 TCACGCCAGGGCCTACTT 60.607 61.111 5.28 0.00 37.98 2.24
763 834 3.391382 GTCACGCCAGGGCCTACT 61.391 66.667 5.28 0.00 37.98 2.57
764 835 4.814294 CGTCACGCCAGGGCCTAC 62.814 72.222 5.28 0.00 37.98 3.18
785 856 0.251877 TACATCACTGACCCGTGGGA 60.252 55.000 13.01 0.00 38.96 4.37
833 905 2.825836 GGCAGCCCGGTCATTCTG 60.826 66.667 0.00 0.61 0.00 3.02
929 1006 1.847506 TCTTGAGGCAGCAGGGGAA 60.848 57.895 0.00 0.00 0.00 3.97
930 1007 2.203983 TCTTGAGGCAGCAGGGGA 60.204 61.111 0.00 0.00 0.00 4.81
956 1033 4.821589 GGTTGGCTCGGCGAGGAG 62.822 72.222 35.03 14.51 37.11 3.69
964 1041 4.796231 CGGAGTCGGGTTGGCTCG 62.796 72.222 0.00 0.00 40.60 5.03
1296 1373 1.212250 GGGGCAGGGGAGGACTTTTA 61.212 60.000 0.00 0.00 0.00 1.52
1713 1790 1.453197 GGGATACAACCAAGGGGCG 60.453 63.158 0.00 0.00 36.09 6.13
1959 2036 4.806339 CGGGAGGGAGGGGAGCTT 62.806 72.222 0.00 0.00 0.00 3.74
1989 2066 3.998672 GGTCCGTCGGAACCTGCA 61.999 66.667 19.10 0.00 32.29 4.41
2014 2120 0.541863 AATTCGGGCTACCTGTCCTG 59.458 55.000 0.00 0.00 38.58 3.86
2116 2222 6.865205 TCGGTAGCTAGAGTTTTTCAGTAAAC 59.135 38.462 0.00 0.00 38.09 2.01
2117 2223 6.865205 GTCGGTAGCTAGAGTTTTTCAGTAAA 59.135 38.462 0.00 0.00 0.00 2.01
2118 2224 6.208204 AGTCGGTAGCTAGAGTTTTTCAGTAA 59.792 38.462 0.00 0.00 0.00 2.24
2119 2225 5.709164 AGTCGGTAGCTAGAGTTTTTCAGTA 59.291 40.000 0.00 0.00 0.00 2.74
2120 2226 4.523558 AGTCGGTAGCTAGAGTTTTTCAGT 59.476 41.667 0.00 0.00 0.00 3.41
2121 2227 5.061920 AGTCGGTAGCTAGAGTTTTTCAG 57.938 43.478 0.00 0.00 0.00 3.02
2132 2251 3.057033 GTGACAAGGAAAGTCGGTAGCTA 60.057 47.826 0.00 0.00 38.83 3.32
2191 2310 3.784701 ACCAGCAGTAGATTGTACGAG 57.215 47.619 0.00 0.00 0.00 4.18
2244 2364 3.483954 CAGGATGGAAGCGGTTCAT 57.516 52.632 26.94 18.09 33.93 2.57
2272 2396 1.077334 ACTGACCCAGTAGCCAGTAGT 59.923 52.381 0.00 0.00 43.46 2.73
2278 2402 0.250513 CCAAGACTGACCCAGTAGCC 59.749 60.000 0.00 0.00 45.44 3.93
2279 2403 0.391793 GCCAAGACTGACCCAGTAGC 60.392 60.000 0.00 0.00 45.44 3.58
2280 2404 1.270907 AGCCAAGACTGACCCAGTAG 58.729 55.000 0.00 0.00 45.44 2.57
2281 2405 1.347707 CAAGCCAAGACTGACCCAGTA 59.652 52.381 0.00 0.00 45.44 2.74
2283 2407 0.607489 CCAAGCCAAGACTGACCCAG 60.607 60.000 0.00 0.00 37.52 4.45
2284 2408 1.455849 CCAAGCCAAGACTGACCCA 59.544 57.895 0.00 0.00 0.00 4.51
2285 2409 1.303643 CCCAAGCCAAGACTGACCC 60.304 63.158 0.00 0.00 0.00 4.46
2299 2423 3.819652 AGCACCAGCACCACCCAA 61.820 61.111 0.00 0.00 45.49 4.12
2359 2483 1.332195 CATCCATCCCTACTGCGAGA 58.668 55.000 0.00 0.00 0.00 4.04
2360 2484 0.319728 CCATCCATCCCTACTGCGAG 59.680 60.000 0.00 0.00 0.00 5.03
2361 2485 1.758440 GCCATCCATCCCTACTGCGA 61.758 60.000 0.00 0.00 0.00 5.10
2367 2491 0.764890 CCGAAAGCCATCCATCCCTA 59.235 55.000 0.00 0.00 0.00 3.53
2411 2537 2.335712 GCAACGCAAAGAGGAGGGG 61.336 63.158 0.00 0.00 0.00 4.79
2418 2544 1.593551 CGAGAAAACGCAACGCAAAGA 60.594 47.619 0.00 0.00 0.00 2.52
2485 2619 1.319947 ACCCTACCCAGAGGATGAGA 58.680 55.000 0.00 0.00 39.15 3.27
2489 2623 0.327576 CCCAACCCTACCCAGAGGAT 60.328 60.000 0.00 0.00 39.15 3.24
2491 2625 2.001269 CCCCAACCCTACCCAGAGG 61.001 68.421 0.00 0.00 40.04 3.69
2493 2627 1.137594 CAACCCCAACCCTACCCAGA 61.138 60.000 0.00 0.00 0.00 3.86
2494 2628 1.382629 CAACCCCAACCCTACCCAG 59.617 63.158 0.00 0.00 0.00 4.45
2559 2707 3.413846 TCTCCTGCTGCAATCATATCC 57.586 47.619 3.02 0.00 0.00 2.59
2560 2708 4.948608 CATCTCCTGCTGCAATCATATC 57.051 45.455 3.02 0.00 0.00 1.63
2672 2824 6.821665 TCATCCGTTTTCTTTCTTGGGTATAG 59.178 38.462 0.00 0.00 0.00 1.31
2674 2826 5.566469 TCATCCGTTTTCTTTCTTGGGTAT 58.434 37.500 0.00 0.00 0.00 2.73
2675 2827 4.975631 TCATCCGTTTTCTTTCTTGGGTA 58.024 39.130 0.00 0.00 0.00 3.69
2676 2828 3.827722 TCATCCGTTTTCTTTCTTGGGT 58.172 40.909 0.00 0.00 0.00 4.51
2677 2829 5.391312 AATCATCCGTTTTCTTTCTTGGG 57.609 39.130 0.00 0.00 0.00 4.12
2678 2830 8.243426 TGATTAATCATCCGTTTTCTTTCTTGG 58.757 33.333 14.23 0.00 0.00 3.61
2681 2833 9.231297 TCTTGATTAATCATCCGTTTTCTTTCT 57.769 29.630 18.61 0.00 36.56 2.52
2682 2834 9.495754 CTCTTGATTAATCATCCGTTTTCTTTC 57.504 33.333 18.61 0.00 36.56 2.62
2683 2835 9.231297 TCTCTTGATTAATCATCCGTTTTCTTT 57.769 29.630 18.61 0.00 36.56 2.52
2684 2836 8.792830 TCTCTTGATTAATCATCCGTTTTCTT 57.207 30.769 18.61 0.00 36.56 2.52
2685 2837 8.260818 TCTCTCTTGATTAATCATCCGTTTTCT 58.739 33.333 18.61 0.00 36.56 2.52
2686 2838 8.425577 TCTCTCTTGATTAATCATCCGTTTTC 57.574 34.615 18.61 0.00 36.56 2.29
2687 2839 8.834465 CATCTCTCTTGATTAATCATCCGTTTT 58.166 33.333 18.61 0.80 36.56 2.43
2688 2840 7.443575 CCATCTCTCTTGATTAATCATCCGTTT 59.556 37.037 18.61 0.08 36.56 3.60
2689 2841 6.933521 CCATCTCTCTTGATTAATCATCCGTT 59.066 38.462 18.61 0.00 36.56 4.44
2690 2842 6.042552 ACCATCTCTCTTGATTAATCATCCGT 59.957 38.462 18.61 3.36 36.56 4.69
2691 2843 6.462500 ACCATCTCTCTTGATTAATCATCCG 58.538 40.000 18.61 10.46 36.56 4.18
2692 2844 8.592809 ACTACCATCTCTCTTGATTAATCATCC 58.407 37.037 18.61 0.00 36.56 3.51
2693 2845 9.421806 CACTACCATCTCTCTTGATTAATCATC 57.578 37.037 18.61 0.00 36.56 2.92
2708 2860 2.159085 GCACCTGTACCACTACCATCTC 60.159 54.545 0.00 0.00 0.00 2.75
2711 2863 1.555075 CTGCACCTGTACCACTACCAT 59.445 52.381 0.00 0.00 0.00 3.55
2712 2864 0.973632 CTGCACCTGTACCACTACCA 59.026 55.000 0.00 0.00 0.00 3.25
2713 2865 0.391263 GCTGCACCTGTACCACTACC 60.391 60.000 0.00 0.00 0.00 3.18
2714 2866 0.320374 TGCTGCACCTGTACCACTAC 59.680 55.000 0.00 0.00 0.00 2.73
2715 2867 0.320374 GTGCTGCACCTGTACCACTA 59.680 55.000 21.78 0.00 0.00 2.74
2716 2868 1.071471 GTGCTGCACCTGTACCACT 59.929 57.895 21.78 0.00 0.00 4.00
2717 2869 2.317609 CGTGCTGCACCTGTACCAC 61.318 63.158 25.61 0.00 0.00 4.16
2718 2870 2.030412 CGTGCTGCACCTGTACCA 59.970 61.111 25.61 0.00 0.00 3.25
2719 2871 2.742372 CCGTGCTGCACCTGTACC 60.742 66.667 25.61 0.51 0.00 3.34
2720 2872 2.742372 CCCGTGCTGCACCTGTAC 60.742 66.667 25.61 1.27 0.00 2.90
2721 2873 4.697756 GCCCGTGCTGCACCTGTA 62.698 66.667 25.61 0.00 33.53 2.74
2750 2902 7.025365 CCACAGAATTTATCATGTGACACTTG 58.975 38.462 13.85 13.85 44.56 3.16
2760 2912 2.174639 TCCCGGCCACAGAATTTATCAT 59.825 45.455 2.24 0.00 0.00 2.45
2761 2913 1.562008 TCCCGGCCACAGAATTTATCA 59.438 47.619 2.24 0.00 0.00 2.15
2762 2914 1.947456 GTCCCGGCCACAGAATTTATC 59.053 52.381 2.24 0.00 0.00 1.75
2800 2952 4.075854 TATGCACGGCTCGGCACA 62.076 61.111 10.88 0.95 43.75 4.57
2801 2953 3.564027 GTATGCACGGCTCGGCAC 61.564 66.667 10.88 0.79 43.75 5.01
2837 2993 1.963747 CGTTTTTCTTCGACATGGCC 58.036 50.000 0.00 0.00 0.00 5.36
2851 3007 2.025544 TACGTACGTACACGCGTTTT 57.974 45.000 23.60 1.15 45.77 2.43
2879 3050 0.554792 CTCCCAGAATGATGCCCCTT 59.445 55.000 0.00 0.00 39.69 3.95
2880 3051 0.327867 TCTCCCAGAATGATGCCCCT 60.328 55.000 0.00 0.00 39.69 4.79
2881 3052 0.110104 CTCTCCCAGAATGATGCCCC 59.890 60.000 0.00 0.00 39.69 5.80
2883 3054 0.536915 GCCTCTCCCAGAATGATGCC 60.537 60.000 0.00 0.00 39.69 4.40
2884 3055 0.536915 GGCCTCTCCCAGAATGATGC 60.537 60.000 0.00 0.00 39.69 3.91
2885 3056 0.250209 CGGCCTCTCCCAGAATGATG 60.250 60.000 0.00 0.00 39.69 3.07
2886 3057 0.692419 ACGGCCTCTCCCAGAATGAT 60.692 55.000 0.00 0.00 39.69 2.45
2889 3060 3.036429 GCACGGCCTCTCCCAGAAT 62.036 63.158 0.00 0.00 0.00 2.40
2890 3061 3.706373 GCACGGCCTCTCCCAGAA 61.706 66.667 0.00 0.00 0.00 3.02
2895 3066 4.849329 CGTACGCACGGCCTCTCC 62.849 72.222 0.52 0.00 44.59 3.71
2904 3075 0.519999 CACGAGAGGTACGTACGCAC 60.520 60.000 16.72 13.27 42.07 5.34
2905 3076 0.950555 ACACGAGAGGTACGTACGCA 60.951 55.000 16.72 0.00 42.07 5.24
2906 3077 0.247458 GACACGAGAGGTACGTACGC 60.247 60.000 16.72 13.40 42.07 4.42
2907 3078 0.024238 CGACACGAGAGGTACGTACG 59.976 60.000 18.98 15.01 42.07 3.67
2908 3079 0.247458 GCGACACGAGAGGTACGTAC 60.247 60.000 17.56 17.56 42.07 3.67
2909 3080 1.361668 GGCGACACGAGAGGTACGTA 61.362 60.000 0.00 0.00 42.07 3.57
2910 3081 2.684843 GGCGACACGAGAGGTACGT 61.685 63.158 0.00 0.00 44.83 3.57
2911 3082 2.099831 GGCGACACGAGAGGTACG 59.900 66.667 0.00 0.00 0.00 3.67
2912 3083 3.271014 TGGCGACACGAGAGGTAC 58.729 61.111 0.00 0.00 33.40 3.34
2948 3119 0.592247 CGCCCGTGTGTATACGTACC 60.592 60.000 0.00 0.00 42.24 3.34
2968 3140 1.935300 GCTCTTGTAGTGGACGTGGTG 60.935 57.143 0.00 0.00 0.00 4.17
2977 3149 1.571919 GCATACGGGCTCTTGTAGTG 58.428 55.000 0.00 0.00 0.00 2.74
2978 3150 0.102481 CGCATACGGGCTCTTGTAGT 59.898 55.000 0.00 0.00 34.97 2.73
2981 3153 0.530650 CATCGCATACGGGCTCTTGT 60.531 55.000 0.00 0.00 40.63 3.16
2998 3170 3.659092 CAACACCGGTGCACGCAT 61.659 61.111 34.26 11.24 42.52 4.73
3005 3177 3.645975 GACCGTGCAACACCGGTG 61.646 66.667 32.83 32.83 39.72 4.94
3009 3181 3.343421 GACCGACCGTGCAACACC 61.343 66.667 0.00 0.00 35.74 4.16
3010 3182 3.698463 CGACCGACCGTGCAACAC 61.698 66.667 0.00 0.00 35.74 3.32
3011 3183 4.953868 CCGACCGACCGTGCAACA 62.954 66.667 0.00 0.00 35.74 3.33
3145 3323 4.082523 CTCCTCTTCCCCGCGCAA 62.083 66.667 8.75 0.00 0.00 4.85
3151 3329 4.718143 CTCCCTCTCCTCTTCCCC 57.282 66.667 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.