Multiple sequence alignment - TraesCS7B01G501700

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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 TraesCS7B01G501700 chr7B 100.000 3425 0 0 1 3425 750412030 750415454 0.000000e+00 6325.0
1 TraesCS7B01G501700 chr7B 98.711 1940 19 3 1 1939 750609351 750607417 0.000000e+00 3439.0
2 TraesCS7B01G501700 chr7B 98.273 521 9 0 1937 2457 750607272 750606752 0.000000e+00 913.0
3 TraesCS7B01G501700 chr7B 76.756 598 86 27 2817 3383 750606748 750606173 5.590000e-73 285.0
4 TraesCS7B01G501700 chr7B 97.561 41 1 0 3379 3419 750429707 750429747 1.710000e-08 71.3
5 TraesCS7B01G501700 chr7B 97.500 40 1 0 3386 3425 750606119 750606080 6.130000e-08 69.4
6 TraesCS7B01G501700 chr7A 87.949 863 86 9 1965 2822 732808253 732807404 0.000000e+00 1002.0
7 TraesCS7B01G501700 chr7A 78.556 900 179 14 661 1553 62728737 62727845 6.370000e-162 580.0
8 TraesCS7B01G501700 chr7A 97.872 47 1 0 3379 3425 732801617 732801571 7.880000e-12 82.4
9 TraesCS7B01G501700 chr4A 77.369 897 195 8 661 1553 674616436 674615544 3.030000e-145 525.0
10 TraesCS7B01G501700 chr3B 77.186 938 188 14 628 1548 814807834 814806906 1.090000e-144 523.0
11 TraesCS7B01G501700 chr5D 78.814 118 23 2 1822 1938 72544708 72544592 1.020000e-10 78.7
12 TraesCS7B01G501700 chr5B 78.151 119 24 2 1822 1939 81474592 81474709 1.320000e-09 75.0


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 TraesCS7B01G501700 chr7B 750412030 750415454 3424 False 6325.0 6325 100.000 1 3425 1 chr7B.!!$F1 3424
1 TraesCS7B01G501700 chr7B 750606080 750609351 3271 True 1176.6 3439 92.810 1 3425 4 chr7B.!!$R1 3424
2 TraesCS7B01G501700 chr7A 732807404 732808253 849 True 1002.0 1002 87.949 1965 2822 1 chr7A.!!$R3 857
3 TraesCS7B01G501700 chr7A 62727845 62728737 892 True 580.0 580 78.556 661 1553 1 chr7A.!!$R1 892
4 TraesCS7B01G501700 chr4A 674615544 674616436 892 True 525.0 525 77.369 661 1553 1 chr4A.!!$R1 892
5 TraesCS7B01G501700 chr3B 814806906 814807834 928 True 523.0 523 77.186 628 1548 1 chr3B.!!$R1 920

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
985 996 0.911769 TTCAAGGGAGATGCGTGGAT 59.088 50.000 0.0 0.0 0.00 3.41 F
1861 1872 1.154150 GCAGTGAACATCGCAAGGC 60.154 57.895 0.0 0.0 38.47 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2190 2348 0.394488 GCTTAGGGGTTGCTCCTTCC 60.394 60.0 0.00 0.00 35.92 3.46 R
3058 3282 0.389025 TGCTGTTCTGCTCGAGTGAA 59.611 50.0 15.13 15.36 0.00 3.18 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
89 90 5.555017 AGAACTAAGTGACTGCATGTTGAT 58.445 37.500 0.00 0.00 0.00 2.57
313 314 5.504853 AGAATTCCTGGCCTCTTTTCTAAG 58.495 41.667 3.32 0.00 0.00 2.18
899 910 4.974645 AGTCATGTTTTCTGTACCTGGA 57.025 40.909 0.00 0.00 0.00 3.86
985 996 0.911769 TTCAAGGGAGATGCGTGGAT 59.088 50.000 0.00 0.00 0.00 3.41
993 1004 2.548707 GGAGATGCGTGGATAATCTGCA 60.549 50.000 0.00 0.00 38.31 4.41
1366 1377 5.923733 AGACTTAGAAGGTGTATCAGGTG 57.076 43.478 0.00 0.00 0.00 4.00
1861 1872 1.154150 GCAGTGAACATCGCAAGGC 60.154 57.895 0.00 0.00 38.47 4.35
2546 2704 6.764308 ATCCAATTTGATTTGTCGAGACAT 57.236 33.333 6.77 0.00 41.52 3.06
2558 2716 5.097742 TGTCGAGACATTGGATTTGGTAT 57.902 39.130 1.24 0.00 36.21 2.73
2559 2717 5.116180 TGTCGAGACATTGGATTTGGTATC 58.884 41.667 1.24 0.00 36.21 2.24
2560 2718 5.104941 TGTCGAGACATTGGATTTGGTATCT 60.105 40.000 1.24 0.00 36.21 1.98
2561 2719 5.463724 GTCGAGACATTGGATTTGGTATCTC 59.536 44.000 0.00 0.00 0.00 2.75
2562 2720 5.128663 TCGAGACATTGGATTTGGTATCTCA 59.871 40.000 0.00 0.00 32.61 3.27
2563 2721 5.994054 CGAGACATTGGATTTGGTATCTCAT 59.006 40.000 0.00 0.00 32.61 2.90
2564 2722 6.146837 CGAGACATTGGATTTGGTATCTCATC 59.853 42.308 0.00 0.00 32.61 2.92
2591 2749 7.670559 ACTTTCACTCCTATATATAGAAGGCGT 59.329 37.037 19.51 5.69 32.05 5.68
2600 2758 7.711339 CCTATATATAGAAGGCGTTGGAAATCC 59.289 40.741 19.51 0.00 32.05 3.01
2613 2771 6.866248 GCGTTGGAAATCCTCAAAAGAAATTA 59.134 34.615 0.44 0.00 36.82 1.40
2620 2778 5.659440 TCCTCAAAAGAAATTATGGCCAC 57.341 39.130 8.16 0.00 0.00 5.01
2629 2787 7.961326 AAGAAATTATGGCCACTGATTTACT 57.039 32.000 8.16 10.90 0.00 2.24
2634 2792 7.986085 ATTATGGCCACTGATTTACTACATC 57.014 36.000 8.16 0.00 0.00 3.06
2635 2793 3.792401 TGGCCACTGATTTACTACATCG 58.208 45.455 0.00 0.00 0.00 3.84
2642 2800 5.294306 CACTGATTTACTACATCGGCATGTT 59.706 40.000 7.65 0.00 40.66 2.71
2658 2816 5.215160 GGCATGTTACAATCGATGGATTTC 58.785 41.667 6.84 0.00 40.90 2.17
2659 2817 5.215160 GCATGTTACAATCGATGGATTTCC 58.785 41.667 6.84 0.00 40.90 3.13
2661 2819 4.509616 TGTTACAATCGATGGATTTCCGT 58.490 39.130 6.84 0.00 40.90 4.69
2666 2824 4.331717 ACAATCGATGGATTTCCGTAACAC 59.668 41.667 6.84 0.00 40.90 3.32
2685 2843 2.049372 ACTGCAAATGCCTCCCTTTTT 58.951 42.857 2.46 0.00 41.18 1.94
2707 2865 7.766219 TTTTCTCTACCGTATAGCAAATGAC 57.234 36.000 0.00 0.00 0.00 3.06
2709 2867 6.459670 TCTCTACCGTATAGCAAATGACAA 57.540 37.500 0.00 0.00 0.00 3.18
2712 2870 8.635328 TCTCTACCGTATAGCAAATGACAAATA 58.365 33.333 0.00 0.00 0.00 1.40
2714 2872 9.602568 TCTACCGTATAGCAAATGACAAATAAA 57.397 29.630 0.00 0.00 0.00 1.40
2725 2883 9.739786 GCAAATGACAAATAAATTTACGAAAGG 57.260 29.630 0.00 0.00 0.00 3.11
2751 2911 4.399004 AAAATGTACCACTTTGCTTGCA 57.601 36.364 0.00 0.00 0.00 4.08
2755 2915 0.179043 TACCACTTTGCTTGCACGGA 60.179 50.000 0.00 0.00 0.00 4.69
2780 2940 4.074526 GCAGACCAGAGAGCGCCA 62.075 66.667 2.29 0.00 0.00 5.69
2782 2942 2.283532 AGACCAGAGAGCGCCAGT 60.284 61.111 2.29 0.00 0.00 4.00
2786 2946 4.383861 CAGAGAGCGCCAGTGCCA 62.384 66.667 2.29 0.00 34.65 4.92
2789 2949 2.203337 AGAGCGCCAGTGCCAAAA 60.203 55.556 2.29 0.00 34.65 2.44
2796 2956 2.411290 CAGTGCCAAAAACGCCGT 59.589 55.556 0.00 0.00 0.00 5.68
2834 2996 2.432456 GGCAGCGACACGACATCA 60.432 61.111 0.00 0.00 0.00 3.07
2842 3004 1.468054 CGACACGACATCATCAGCAGA 60.468 52.381 0.00 0.00 0.00 4.26
2843 3005 1.923204 GACACGACATCATCAGCAGAC 59.077 52.381 0.00 0.00 0.00 3.51
2847 3009 1.134877 CGACATCATCAGCAGACCTGT 60.135 52.381 0.00 0.00 42.38 4.00
2848 3010 2.277969 GACATCATCAGCAGACCTGTG 58.722 52.381 0.00 0.00 42.38 3.66
2849 3011 1.065636 ACATCATCAGCAGACCTGTGG 60.066 52.381 0.00 0.00 42.38 4.17
2850 3012 1.065636 CATCATCAGCAGACCTGTGGT 60.066 52.381 0.00 0.00 42.38 4.16
2851 3013 0.322648 TCATCAGCAGACCTGTGGTG 59.677 55.000 0.00 0.00 45.47 4.17
2852 3014 0.675837 CATCAGCAGACCTGTGGTGG 60.676 60.000 3.44 0.00 44.46 4.61
2853 3015 1.130054 ATCAGCAGACCTGTGGTGGT 61.130 55.000 3.44 0.00 44.46 4.16
2855 3017 0.320771 CAGCAGACCTGTGGTGGTAC 60.321 60.000 0.00 0.00 41.35 3.34
2896 3060 1.192428 GAGGATACCACGGTGAAGGT 58.808 55.000 10.28 1.43 41.89 3.50
2921 3085 2.971598 CGCCATGGTGGAGAGGGTT 61.972 63.158 18.06 0.00 39.92 4.11
2923 3087 1.852157 GCCATGGTGGAGAGGGTTCA 61.852 60.000 14.67 0.00 40.96 3.18
2934 3109 0.613777 GAGGGTTCAACCGAGGATGT 59.386 55.000 0.00 0.00 39.83 3.06
2953 3128 3.806667 ATCCTGCCTGCTGCCTCC 61.807 66.667 0.00 0.00 40.16 4.30
3027 3251 3.567164 GCAAATACTCTGCTGTATGGCAT 59.433 43.478 4.88 4.88 41.63 4.40
3028 3252 4.756642 GCAAATACTCTGCTGTATGGCATA 59.243 41.667 2.32 2.32 41.63 3.14
3032 3256 2.082231 CTCTGCTGTATGGCATATGGC 58.918 52.381 21.76 21.76 41.63 4.40
3041 3265 0.753867 TGGCATATGGCAGCATTTGG 59.246 50.000 26.67 0.00 46.12 3.28
3042 3266 1.965806 TGGCATATGGCAGCATTTGGT 60.966 47.619 26.67 0.00 46.12 3.67
3043 3267 2.689118 TGGCATATGGCAGCATTTGGTA 60.689 45.455 26.67 1.15 46.12 3.25
3044 3268 3.017265 GCATATGGCAGCATTTGGTAC 57.983 47.619 4.56 0.00 43.97 3.34
3045 3269 2.361757 GCATATGGCAGCATTTGGTACA 59.638 45.455 4.56 0.00 43.97 2.90
3046 3270 3.551454 GCATATGGCAGCATTTGGTACAG 60.551 47.826 4.56 0.00 41.26 2.74
3047 3271 0.819582 ATGGCAGCATTTGGTACAGC 59.180 50.000 0.00 0.00 42.39 4.40
3048 3272 0.539207 TGGCAGCATTTGGTACAGCA 60.539 50.000 0.00 0.00 42.39 4.41
3049 3273 0.602562 GGCAGCATTTGGTACAGCAA 59.397 50.000 0.00 0.00 42.39 3.91
3050 3274 1.205417 GGCAGCATTTGGTACAGCAAT 59.795 47.619 0.00 0.00 42.39 3.56
3051 3275 2.533266 GCAGCATTTGGTACAGCAATC 58.467 47.619 0.00 0.00 42.39 2.67
3052 3276 2.094597 GCAGCATTTGGTACAGCAATCA 60.095 45.455 0.00 0.00 42.39 2.57
3053 3277 3.614630 GCAGCATTTGGTACAGCAATCAA 60.615 43.478 0.00 0.00 42.39 2.57
3054 3278 4.558178 CAGCATTTGGTACAGCAATCAAA 58.442 39.130 0.00 0.00 42.39 2.69
3055 3279 4.989797 CAGCATTTGGTACAGCAATCAAAA 59.010 37.500 0.00 0.00 42.39 2.44
3056 3280 4.990426 AGCATTTGGTACAGCAATCAAAAC 59.010 37.500 0.00 0.00 42.39 2.43
3057 3281 4.152223 GCATTTGGTACAGCAATCAAAACC 59.848 41.667 0.00 0.00 42.39 3.27
3058 3282 5.540911 CATTTGGTACAGCAATCAAAACCT 58.459 37.500 0.00 0.00 42.39 3.50
3059 3283 5.606348 TTTGGTACAGCAATCAAAACCTT 57.394 34.783 0.00 0.00 42.39 3.50
3060 3284 4.846779 TGGTACAGCAATCAAAACCTTC 57.153 40.909 0.00 0.00 0.00 3.46
3061 3285 4.211125 TGGTACAGCAATCAAAACCTTCA 58.789 39.130 0.00 0.00 0.00 3.02
3062 3286 4.037446 TGGTACAGCAATCAAAACCTTCAC 59.963 41.667 0.00 0.00 0.00 3.18
3063 3287 4.278419 GGTACAGCAATCAAAACCTTCACT 59.722 41.667 0.00 0.00 0.00 3.41
3064 3288 4.574599 ACAGCAATCAAAACCTTCACTC 57.425 40.909 0.00 0.00 0.00 3.51
3065 3289 3.003689 ACAGCAATCAAAACCTTCACTCG 59.996 43.478 0.00 0.00 0.00 4.18
3066 3290 3.250762 CAGCAATCAAAACCTTCACTCGA 59.749 43.478 0.00 0.00 0.00 4.04
3067 3291 3.499918 AGCAATCAAAACCTTCACTCGAG 59.500 43.478 11.84 11.84 0.00 4.04
3068 3292 3.814945 CAATCAAAACCTTCACTCGAGC 58.185 45.455 13.61 0.00 0.00 5.03
3069 3293 2.613026 TCAAAACCTTCACTCGAGCA 57.387 45.000 13.61 0.00 0.00 4.26
3070 3294 2.483876 TCAAAACCTTCACTCGAGCAG 58.516 47.619 13.61 5.66 0.00 4.24
3071 3295 2.102420 TCAAAACCTTCACTCGAGCAGA 59.898 45.455 13.61 8.31 0.00 4.26
3072 3296 2.872245 CAAAACCTTCACTCGAGCAGAA 59.128 45.455 13.61 15.71 0.00 3.02
3073 3297 2.156343 AACCTTCACTCGAGCAGAAC 57.844 50.000 13.61 0.00 0.00 3.01
3074 3298 1.040646 ACCTTCACTCGAGCAGAACA 58.959 50.000 13.61 0.00 0.00 3.18
3075 3299 1.000283 ACCTTCACTCGAGCAGAACAG 60.000 52.381 13.61 11.16 0.00 3.16
3076 3300 1.066914 CTTCACTCGAGCAGAACAGC 58.933 55.000 13.61 0.00 0.00 4.40
3077 3301 0.389025 TTCACTCGAGCAGAACAGCA 59.611 50.000 13.61 0.00 36.85 4.41
3078 3302 0.605083 TCACTCGAGCAGAACAGCAT 59.395 50.000 13.61 0.00 36.85 3.79
3079 3303 0.720027 CACTCGAGCAGAACAGCATG 59.280 55.000 13.61 0.00 46.00 4.06
3080 3304 0.390866 ACTCGAGCAGAACAGCATGG 60.391 55.000 13.61 0.00 43.62 3.66
3081 3305 1.078918 TCGAGCAGAACAGCATGGG 60.079 57.895 0.00 0.00 43.62 4.00
3082 3306 1.078918 CGAGCAGAACAGCATGGGA 60.079 57.895 0.00 0.00 43.62 4.37
3083 3307 0.674581 CGAGCAGAACAGCATGGGAA 60.675 55.000 0.00 0.00 43.62 3.97
3084 3308 1.538047 GAGCAGAACAGCATGGGAAA 58.462 50.000 0.00 0.00 43.62 3.13
3085 3309 1.888512 GAGCAGAACAGCATGGGAAAA 59.111 47.619 0.00 0.00 43.62 2.29
3086 3310 1.891150 AGCAGAACAGCATGGGAAAAG 59.109 47.619 0.00 0.00 43.62 2.27
3087 3311 1.067354 GCAGAACAGCATGGGAAAAGG 60.067 52.381 0.00 0.00 43.62 3.11
3088 3312 2.517959 CAGAACAGCATGGGAAAAGGA 58.482 47.619 0.00 0.00 43.62 3.36
3089 3313 2.490903 CAGAACAGCATGGGAAAAGGAG 59.509 50.000 0.00 0.00 43.62 3.69
3090 3314 2.376518 AGAACAGCATGGGAAAAGGAGA 59.623 45.455 0.00 0.00 43.62 3.71
3091 3315 3.011032 AGAACAGCATGGGAAAAGGAGAT 59.989 43.478 0.00 0.00 43.62 2.75
3092 3316 3.010200 ACAGCATGGGAAAAGGAGATC 57.990 47.619 0.00 0.00 43.62 2.75
3093 3317 2.305009 CAGCATGGGAAAAGGAGATCC 58.695 52.381 0.00 0.00 34.85 3.36
3094 3318 4.663460 ACAGCATGGGAAAAGGAGATCCT 61.663 47.826 0.00 0.00 46.27 3.24
3123 3347 3.464907 AGCATCGATCTCCAATCAACAG 58.535 45.455 0.00 0.00 0.00 3.16
3166 3390 4.708726 AAAGATTGTATGCAGCAACTCC 57.291 40.909 0.00 2.83 0.00 3.85
3169 3393 1.725641 TTGTATGCAGCAACTCCGAG 58.274 50.000 0.00 0.00 0.00 4.63
3170 3394 0.740868 TGTATGCAGCAACTCCGAGC 60.741 55.000 0.00 0.00 0.00 5.03
3175 3399 1.376424 CAGCAACTCCGAGCCATGT 60.376 57.895 0.00 0.00 0.00 3.21
3176 3400 1.376424 AGCAACTCCGAGCCATGTG 60.376 57.895 0.00 0.00 0.00 3.21
3177 3401 1.672356 GCAACTCCGAGCCATGTGT 60.672 57.895 0.00 0.00 0.00 3.72
3178 3402 1.237285 GCAACTCCGAGCCATGTGTT 61.237 55.000 0.00 0.00 0.00 3.32
3179 3403 0.518636 CAACTCCGAGCCATGTGTTG 59.481 55.000 0.00 0.00 31.99 3.33
3181 3405 0.603707 ACTCCGAGCCATGTGTTGTG 60.604 55.000 0.00 0.00 0.00 3.33
3182 3406 0.320683 CTCCGAGCCATGTGTTGTGA 60.321 55.000 0.00 0.00 0.00 3.58
3183 3407 0.324614 TCCGAGCCATGTGTTGTGAT 59.675 50.000 0.00 0.00 0.00 3.06
3186 3410 1.662629 CGAGCCATGTGTTGTGATCTC 59.337 52.381 0.00 0.00 0.00 2.75
3196 3427 4.811024 TGTGTTGTGATCTCAGTTCAGAAC 59.189 41.667 15.67 15.67 43.75 3.01
3198 3429 5.176590 GTGTTGTGATCTCAGTTCAGAACTC 59.823 44.000 20.66 15.59 43.80 3.01
3204 3435 4.608948 TCTCAGTTCAGAACTCCCTTTC 57.391 45.455 13.27 0.00 40.46 2.62
3205 3436 3.325135 TCTCAGTTCAGAACTCCCTTTCC 59.675 47.826 13.27 0.00 40.46 3.13
3206 3437 3.318313 TCAGTTCAGAACTCCCTTTCCT 58.682 45.455 13.27 0.00 40.46 3.36
3249 3482 2.229062 TGAGAGTACCAGAAACAGCTCG 59.771 50.000 0.00 0.00 0.00 5.03
3256 3489 1.066573 CCAGAAACAGCTCGATGTCCT 60.067 52.381 0.00 0.00 31.50 3.85
3266 3499 3.195610 AGCTCGATGTCCTGTGAACATAA 59.804 43.478 0.00 0.00 37.47 1.90
3267 3500 4.122776 GCTCGATGTCCTGTGAACATAAT 58.877 43.478 0.00 0.00 37.47 1.28
3268 3501 4.572389 GCTCGATGTCCTGTGAACATAATT 59.428 41.667 0.00 0.00 37.47 1.40
3270 3503 6.257849 GCTCGATGTCCTGTGAACATAATTTA 59.742 38.462 0.00 0.00 37.47 1.40
3271 3504 7.201609 GCTCGATGTCCTGTGAACATAATTTAA 60.202 37.037 0.00 0.00 37.47 1.52
3272 3505 8.731275 TCGATGTCCTGTGAACATAATTTAAT 57.269 30.769 0.00 0.00 37.47 1.40
3301 3534 7.751768 AAAATAGAAGCTTTGTTCAGTAGCT 57.248 32.000 0.00 0.00 46.63 3.32
3309 3542 5.767168 AGCTTTGTTCAGTAGCTTCAAGAAT 59.233 36.000 0.00 0.00 42.30 2.40
3319 3552 4.996788 AGCTTCAAGAATATTTGCAGGG 57.003 40.909 0.00 0.00 0.00 4.45
3326 3559 3.019564 AGAATATTTGCAGGGTCACAGC 58.980 45.455 0.00 0.00 0.00 4.40
3329 3562 0.896940 ATTTGCAGGGTCACAGCCAG 60.897 55.000 0.00 0.00 38.48 4.85
3332 3565 1.228245 GCAGGGTCACAGCCAGAAA 60.228 57.895 0.00 0.00 38.48 2.52
3335 3568 0.109342 AGGGTCACAGCCAGAAACAG 59.891 55.000 0.00 0.00 38.48 3.16
3337 3570 1.517242 GGTCACAGCCAGAAACAGAG 58.483 55.000 0.00 0.00 0.00 3.35
3339 3572 2.289945 GGTCACAGCCAGAAACAGAGAT 60.290 50.000 0.00 0.00 0.00 2.75
3353 3586 8.181573 CAGAAACAGAGATAGAGAGACAGTAAC 58.818 40.741 0.00 0.00 0.00 2.50
3357 3590 5.008613 CAGAGATAGAGAGACAGTAACCAGC 59.991 48.000 0.00 0.00 0.00 4.85
3363 3596 2.234908 AGAGACAGTAACCAGCCATCAC 59.765 50.000 0.00 0.00 0.00 3.06
3383 3616 4.642437 TCACAGTATGCACAAAGAAACCAA 59.358 37.500 0.00 0.00 42.53 3.67
3384 3617 4.739716 CACAGTATGCACAAAGAAACCAAC 59.260 41.667 0.00 0.00 42.53 3.77
3415 3699 5.799435 CCAACCACAATTTTGTTTTGCTTTC 59.201 36.000 8.22 0.00 39.91 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
899 910 4.324099 CCTCATGGTCTTCAGGAAAGATGT 60.324 45.833 0.00 0.00 45.57 3.06
985 996 3.939740 AGCCATTTCCTCTGCAGATTA 57.060 42.857 18.63 5.38 0.00 1.75
993 1004 6.755542 AAATAGCTACTAGCCATTTCCTCT 57.244 37.500 8.23 0.00 37.90 3.69
1366 1377 5.106197 TGTGCACAAGGTGATGATCAAATAC 60.106 40.000 19.28 0.00 35.23 1.89
1628 1639 6.712547 ACAAAGCATAGAGAATAAGGGCATAC 59.287 38.462 0.00 0.00 0.00 2.39
1765 1776 5.006153 TGTACACTTAGACGCATTAGCAT 57.994 39.130 0.00 0.00 42.27 3.79
1861 1872 0.468214 TCATCTAGAGTGGCCTCCCG 60.468 60.000 3.32 0.00 38.58 5.14
1875 1886 5.724328 TGAGCGAGTCTTTTTATGTCATCT 58.276 37.500 0.00 0.00 0.00 2.90
2190 2348 0.394488 GCTTAGGGGTTGCTCCTTCC 60.394 60.000 0.00 0.00 35.92 3.46
2460 2618 9.039870 CCAAACACAACAATGTTACAATAACAT 57.960 29.630 8.14 8.14 42.01 2.71
2461 2619 8.035394 ACCAAACACAACAATGTTACAATAACA 58.965 29.630 0.00 4.01 42.01 2.41
2462 2620 8.324567 CACCAAACACAACAATGTTACAATAAC 58.675 33.333 0.00 0.00 42.01 1.89
2546 2704 7.121168 GTGAAAGTGATGAGATACCAAATCCAA 59.879 37.037 0.00 0.00 0.00 3.53
2563 2721 9.026121 GCCTTCTATATATAGGAGTGAAAGTGA 57.974 37.037 21.78 0.00 34.73 3.41
2564 2722 7.971168 CGCCTTCTATATATAGGAGTGAAAGTG 59.029 40.741 21.78 11.76 34.73 3.16
2582 2740 2.569853 TGAGGATTTCCAACGCCTTCTA 59.430 45.455 0.00 0.00 38.89 2.10
2591 2749 7.823799 GCCATAATTTCTTTTGAGGATTTCCAA 59.176 33.333 0.00 0.00 38.89 3.53
2600 2758 6.271488 TCAGTGGCCATAATTTCTTTTGAG 57.729 37.500 9.72 0.00 0.00 3.02
2613 2771 4.380531 CGATGTAGTAAATCAGTGGCCAT 58.619 43.478 9.72 0.00 0.00 4.40
2620 2778 5.991328 AACATGCCGATGTAGTAAATCAG 57.009 39.130 1.25 0.00 42.30 2.90
2629 2787 4.048241 TCGATTGTAACATGCCGATGTA 57.952 40.909 0.00 0.00 42.30 2.29
2634 2792 2.209273 TCCATCGATTGTAACATGCCG 58.791 47.619 0.00 0.00 0.00 5.69
2635 2793 4.836125 AATCCATCGATTGTAACATGCC 57.164 40.909 0.00 0.00 37.33 4.40
2642 2800 5.521010 GTGTTACGGAAATCCATCGATTGTA 59.479 40.000 0.00 0.00 38.75 2.41
2658 2816 0.881118 AGGCATTTGCAGTGTTACGG 59.119 50.000 4.74 0.00 44.36 4.02
2659 2817 1.135689 GGAGGCATTTGCAGTGTTACG 60.136 52.381 4.74 0.00 44.36 3.18
2661 2819 1.075374 AGGGAGGCATTTGCAGTGTTA 59.925 47.619 4.74 0.00 44.36 2.41
2666 2824 2.845363 AAAAAGGGAGGCATTTGCAG 57.155 45.000 4.74 0.00 44.36 4.41
2685 2843 6.459670 TGTCATTTGCTATACGGTAGAGAA 57.540 37.500 13.66 0.00 0.00 2.87
2686 2844 6.459670 TTGTCATTTGCTATACGGTAGAGA 57.540 37.500 13.66 0.00 0.00 3.10
2687 2845 7.715265 ATTTGTCATTTGCTATACGGTAGAG 57.285 36.000 5.45 5.45 0.00 2.43
2688 2846 9.602568 TTTATTTGTCATTTGCTATACGGTAGA 57.397 29.630 1.75 0.00 0.00 2.59
2731 2891 3.716601 GTGCAAGCAAAGTGGTACATTT 58.283 40.909 0.00 0.00 44.52 2.32
2734 2894 0.660488 CGTGCAAGCAAAGTGGTACA 59.340 50.000 0.00 0.00 0.00 2.90
2740 2900 0.465460 TCCTTCCGTGCAAGCAAAGT 60.465 50.000 0.00 0.00 0.00 2.66
2743 2903 0.465460 ACTTCCTTCCGTGCAAGCAA 60.465 50.000 0.00 0.00 0.00 3.91
2750 2910 0.951040 GGTCTGCACTTCCTTCCGTG 60.951 60.000 0.00 0.00 0.00 4.94
2751 2911 1.371558 GGTCTGCACTTCCTTCCGT 59.628 57.895 0.00 0.00 0.00 4.69
2755 2915 1.622811 CTCTCTGGTCTGCACTTCCTT 59.377 52.381 0.00 0.00 0.00 3.36
2780 2940 2.058829 CTGACGGCGTTTTTGGCACT 62.059 55.000 16.19 0.00 0.00 4.40
2782 2942 2.718731 CTGACGGCGTTTTTGGCA 59.281 55.556 16.19 5.20 0.00 4.92
2786 2946 2.258726 GGAGGCTGACGGCGTTTTT 61.259 57.895 16.19 0.00 42.94 1.94
2789 2949 4.379243 CTGGAGGCTGACGGCGTT 62.379 66.667 16.19 0.00 42.94 4.84
2834 2996 1.130054 ACCACCACAGGTCTGCTGAT 61.130 55.000 0.00 0.00 37.28 2.90
2842 3004 1.461461 AGGCTGTACCACCACAGGT 60.461 57.895 5.49 0.00 45.03 4.00
2843 3005 1.003355 CAGGCTGTACCACCACAGG 60.003 63.158 6.28 0.00 45.03 4.00
2847 3009 1.480212 CCTGACAGGCTGTACCACCA 61.480 60.000 22.11 12.81 43.14 4.17
2848 3010 1.296715 CCTGACAGGCTGTACCACC 59.703 63.158 22.11 8.30 43.14 4.61
2900 3064 2.187946 CTCTCCACCATGGCGACC 59.812 66.667 13.04 0.00 37.47 4.79
2901 3065 2.187946 CCTCTCCACCATGGCGAC 59.812 66.667 13.04 0.00 37.47 5.19
2911 3075 1.192146 CCTCGGTTGAACCCTCTCCA 61.192 60.000 9.08 0.00 33.75 3.86
2912 3076 0.903454 TCCTCGGTTGAACCCTCTCC 60.903 60.000 9.08 0.00 33.75 3.71
2913 3077 1.134670 CATCCTCGGTTGAACCCTCTC 60.135 57.143 9.08 0.00 33.75 3.20
2953 3128 2.089980 CAGAGCCTGATTCCTTGTTGG 58.910 52.381 0.00 0.00 32.44 3.77
2981 3156 2.427095 GTGGTTTGCTATTTGCCCCTAG 59.573 50.000 0.00 0.00 42.00 3.02
2986 3161 2.068519 GCTTGTGGTTTGCTATTTGCC 58.931 47.619 0.00 0.00 42.00 4.52
2989 3164 6.758254 AGTATTTGCTTGTGGTTTGCTATTT 58.242 32.000 0.00 0.00 0.00 1.40
2990 3165 6.209391 AGAGTATTTGCTTGTGGTTTGCTATT 59.791 34.615 0.00 0.00 0.00 1.73
2991 3166 5.711976 AGAGTATTTGCTTGTGGTTTGCTAT 59.288 36.000 0.00 0.00 0.00 2.97
2993 3168 3.891366 AGAGTATTTGCTTGTGGTTTGCT 59.109 39.130 0.00 0.00 0.00 3.91
3005 3229 2.945008 TGCCATACAGCAGAGTATTTGC 59.055 45.455 0.00 0.00 38.00 3.68
3020 3244 2.563620 CCAAATGCTGCCATATGCCATA 59.436 45.455 0.00 0.00 40.16 2.74
3027 3251 2.023673 GCTGTACCAAATGCTGCCATA 58.976 47.619 0.00 0.00 32.70 2.74
3028 3252 0.819582 GCTGTACCAAATGCTGCCAT 59.180 50.000 0.00 0.00 32.70 4.40
3032 3256 3.853831 TGATTGCTGTACCAAATGCTG 57.146 42.857 0.00 0.00 0.00 4.41
3034 3258 4.152223 GGTTTTGATTGCTGTACCAAATGC 59.848 41.667 0.00 0.00 0.00 3.56
3035 3259 5.540911 AGGTTTTGATTGCTGTACCAAATG 58.459 37.500 0.00 0.00 0.00 2.32
3036 3260 5.806654 AGGTTTTGATTGCTGTACCAAAT 57.193 34.783 0.00 0.00 0.00 2.32
3037 3261 5.127845 TGAAGGTTTTGATTGCTGTACCAAA 59.872 36.000 0.00 0.00 0.00 3.28
3038 3262 4.646945 TGAAGGTTTTGATTGCTGTACCAA 59.353 37.500 0.00 0.00 0.00 3.67
3039 3263 4.037446 GTGAAGGTTTTGATTGCTGTACCA 59.963 41.667 0.00 0.00 0.00 3.25
3040 3264 4.278419 AGTGAAGGTTTTGATTGCTGTACC 59.722 41.667 0.00 0.00 0.00 3.34
3041 3265 5.438761 AGTGAAGGTTTTGATTGCTGTAC 57.561 39.130 0.00 0.00 0.00 2.90
3042 3266 4.213270 CGAGTGAAGGTTTTGATTGCTGTA 59.787 41.667 0.00 0.00 0.00 2.74
3043 3267 3.003689 CGAGTGAAGGTTTTGATTGCTGT 59.996 43.478 0.00 0.00 0.00 4.40
3044 3268 3.250762 TCGAGTGAAGGTTTTGATTGCTG 59.749 43.478 0.00 0.00 0.00 4.41
3045 3269 3.476552 TCGAGTGAAGGTTTTGATTGCT 58.523 40.909 0.00 0.00 0.00 3.91
3046 3270 3.814945 CTCGAGTGAAGGTTTTGATTGC 58.185 45.455 3.62 0.00 0.00 3.56
3047 3271 3.250762 TGCTCGAGTGAAGGTTTTGATTG 59.749 43.478 15.13 0.00 0.00 2.67
3048 3272 3.476552 TGCTCGAGTGAAGGTTTTGATT 58.523 40.909 15.13 0.00 0.00 2.57
3049 3273 3.070018 CTGCTCGAGTGAAGGTTTTGAT 58.930 45.455 15.13 0.00 0.00 2.57
3050 3274 2.102420 TCTGCTCGAGTGAAGGTTTTGA 59.898 45.455 15.13 0.00 0.00 2.69
3051 3275 2.483876 TCTGCTCGAGTGAAGGTTTTG 58.516 47.619 15.13 0.00 0.00 2.44
3052 3276 2.872858 GTTCTGCTCGAGTGAAGGTTTT 59.127 45.455 15.13 0.00 0.00 2.43
3053 3277 2.158957 TGTTCTGCTCGAGTGAAGGTTT 60.159 45.455 15.13 0.00 0.00 3.27
3054 3278 1.412710 TGTTCTGCTCGAGTGAAGGTT 59.587 47.619 15.13 0.00 0.00 3.50
3055 3279 1.000283 CTGTTCTGCTCGAGTGAAGGT 60.000 52.381 15.13 0.00 0.00 3.50
3056 3280 1.707632 CTGTTCTGCTCGAGTGAAGG 58.292 55.000 15.13 10.39 0.00 3.46
3057 3281 1.066914 GCTGTTCTGCTCGAGTGAAG 58.933 55.000 15.13 9.70 0.00 3.02
3058 3282 0.389025 TGCTGTTCTGCTCGAGTGAA 59.611 50.000 15.13 15.36 0.00 3.18
3059 3283 0.605083 ATGCTGTTCTGCTCGAGTGA 59.395 50.000 15.13 10.08 0.00 3.41
3060 3284 0.720027 CATGCTGTTCTGCTCGAGTG 59.280 55.000 15.13 7.74 0.00 3.51
3061 3285 0.390866 CCATGCTGTTCTGCTCGAGT 60.391 55.000 15.13 0.00 0.00 4.18
3062 3286 1.088340 CCCATGCTGTTCTGCTCGAG 61.088 60.000 8.45 8.45 0.00 4.04
3063 3287 1.078918 CCCATGCTGTTCTGCTCGA 60.079 57.895 3.65 0.00 0.00 4.04
3064 3288 0.674581 TTCCCATGCTGTTCTGCTCG 60.675 55.000 3.65 0.00 0.00 5.03
3065 3289 1.538047 TTTCCCATGCTGTTCTGCTC 58.462 50.000 3.65 0.00 0.00 4.26
3066 3290 1.891150 CTTTTCCCATGCTGTTCTGCT 59.109 47.619 3.65 0.00 0.00 4.24
3067 3291 1.067354 CCTTTTCCCATGCTGTTCTGC 60.067 52.381 0.00 0.00 0.00 4.26
3068 3292 2.490903 CTCCTTTTCCCATGCTGTTCTG 59.509 50.000 0.00 0.00 0.00 3.02
3069 3293 2.376518 TCTCCTTTTCCCATGCTGTTCT 59.623 45.455 0.00 0.00 0.00 3.01
3070 3294 2.795329 TCTCCTTTTCCCATGCTGTTC 58.205 47.619 0.00 0.00 0.00 3.18
3071 3295 2.978156 TCTCCTTTTCCCATGCTGTT 57.022 45.000 0.00 0.00 0.00 3.16
3072 3296 2.357569 GGATCTCCTTTTCCCATGCTGT 60.358 50.000 0.00 0.00 0.00 4.40
3073 3297 2.091994 AGGATCTCCTTTTCCCATGCTG 60.092 50.000 0.00 0.00 46.09 4.41
3074 3298 2.212420 AGGATCTCCTTTTCCCATGCT 58.788 47.619 0.00 0.00 46.09 3.79
3075 3299 2.744352 AGGATCTCCTTTTCCCATGC 57.256 50.000 0.00 0.00 46.09 4.06
3086 3310 3.553922 CGATGCTAGTTGGAAGGATCTCC 60.554 52.174 0.00 0.00 39.06 3.71
3087 3311 3.319405 TCGATGCTAGTTGGAAGGATCTC 59.681 47.826 0.00 0.00 39.06 2.75
3088 3312 3.300388 TCGATGCTAGTTGGAAGGATCT 58.700 45.455 0.00 0.00 39.06 2.75
3089 3313 3.735237 TCGATGCTAGTTGGAAGGATC 57.265 47.619 0.00 0.00 38.16 3.36
3090 3314 3.900601 AGATCGATGCTAGTTGGAAGGAT 59.099 43.478 0.54 0.00 0.00 3.24
3091 3315 3.300388 AGATCGATGCTAGTTGGAAGGA 58.700 45.455 0.54 0.00 0.00 3.36
3092 3316 3.553922 GGAGATCGATGCTAGTTGGAAGG 60.554 52.174 0.54 0.00 0.00 3.46
3093 3317 3.068732 TGGAGATCGATGCTAGTTGGAAG 59.931 47.826 0.54 0.00 0.00 3.46
3094 3318 3.031013 TGGAGATCGATGCTAGTTGGAA 58.969 45.455 0.54 0.00 0.00 3.53
3095 3319 2.666317 TGGAGATCGATGCTAGTTGGA 58.334 47.619 0.54 0.00 0.00 3.53
3099 3323 4.100035 TGTTGATTGGAGATCGATGCTAGT 59.900 41.667 0.54 0.00 0.00 2.57
3141 3365 6.336842 AGTTGCTGCATACAATCTTTTCTT 57.663 33.333 1.84 0.00 0.00 2.52
3144 3368 4.379813 CGGAGTTGCTGCATACAATCTTTT 60.380 41.667 1.84 0.00 0.00 2.27
3145 3369 3.127548 CGGAGTTGCTGCATACAATCTTT 59.872 43.478 1.84 0.00 0.00 2.52
3146 3370 2.679837 CGGAGTTGCTGCATACAATCTT 59.320 45.455 1.84 0.00 0.00 2.40
3147 3371 2.093500 TCGGAGTTGCTGCATACAATCT 60.093 45.455 1.84 5.39 0.00 2.40
3148 3372 2.279741 TCGGAGTTGCTGCATACAATC 58.720 47.619 1.84 0.00 0.00 2.67
3153 3377 1.153369 GGCTCGGAGTTGCTGCATA 60.153 57.895 1.84 0.00 0.00 3.14
3156 3380 2.437359 ATGGCTCGGAGTTGCTGC 60.437 61.111 6.90 0.00 0.00 5.25
3166 3390 1.662629 GAGATCACAACACATGGCTCG 59.337 52.381 0.00 0.00 0.00 5.03
3169 3393 2.430465 ACTGAGATCACAACACATGGC 58.570 47.619 0.00 0.00 0.00 4.40
3170 3394 4.067192 TGAACTGAGATCACAACACATGG 58.933 43.478 0.00 0.00 0.00 3.66
3175 3399 5.282055 AGTTCTGAACTGAGATCACAACA 57.718 39.130 21.47 0.00 41.01 3.33
3176 3400 4.688413 GGAGTTCTGAACTGAGATCACAAC 59.312 45.833 26.47 8.59 43.03 3.32
3177 3401 4.262635 GGGAGTTCTGAACTGAGATCACAA 60.263 45.833 26.47 0.00 43.03 3.33
3178 3402 3.259374 GGGAGTTCTGAACTGAGATCACA 59.741 47.826 26.47 0.00 43.03 3.58
3179 3403 3.513515 AGGGAGTTCTGAACTGAGATCAC 59.486 47.826 26.47 13.39 43.03 3.06
3181 3405 4.817318 AAGGGAGTTCTGAACTGAGATC 57.183 45.455 26.47 12.18 43.03 2.75
3182 3406 4.019771 GGAAAGGGAGTTCTGAACTGAGAT 60.020 45.833 26.47 9.48 43.03 2.75
3183 3407 3.325135 GGAAAGGGAGTTCTGAACTGAGA 59.675 47.826 26.47 0.00 43.03 3.27
3186 3410 3.071602 TGAGGAAAGGGAGTTCTGAACTG 59.928 47.826 26.47 0.00 43.03 3.16
3196 3427 8.465201 CAGAAATCTTTTAATGAGGAAAGGGAG 58.535 37.037 0.00 0.00 34.45 4.30
3198 3429 8.353423 TCAGAAATCTTTTAATGAGGAAAGGG 57.647 34.615 0.00 0.00 34.45 3.95
3233 3466 2.924290 GACATCGAGCTGTTTCTGGTAC 59.076 50.000 0.00 0.00 0.00 3.34
3290 3523 7.174772 TGCAAATATTCTTGAAGCTACTGAACA 59.825 33.333 0.00 0.00 0.00 3.18
3291 3524 7.530010 TGCAAATATTCTTGAAGCTACTGAAC 58.470 34.615 0.00 0.00 0.00 3.18
3292 3525 7.148188 CCTGCAAATATTCTTGAAGCTACTGAA 60.148 37.037 0.00 0.00 31.36 3.02
3301 3534 5.076182 TGTGACCCTGCAAATATTCTTGAA 58.924 37.500 0.00 0.00 0.00 2.69
3302 3535 4.661222 TGTGACCCTGCAAATATTCTTGA 58.339 39.130 0.00 0.00 0.00 3.02
3304 3537 3.445096 GCTGTGACCCTGCAAATATTCTT 59.555 43.478 0.00 0.00 37.89 2.52
3305 3538 3.019564 GCTGTGACCCTGCAAATATTCT 58.980 45.455 0.00 0.00 37.89 2.40
3309 3542 0.403655 TGGCTGTGACCCTGCAAATA 59.596 50.000 0.00 0.00 39.60 1.40
3319 3552 2.533266 TCTCTGTTTCTGGCTGTGAC 57.467 50.000 0.00 0.00 0.00 3.67
3326 3559 5.652014 ACTGTCTCTCTATCTCTGTTTCTGG 59.348 44.000 0.00 0.00 0.00 3.86
3329 3562 7.121463 TGGTTACTGTCTCTCTATCTCTGTTTC 59.879 40.741 0.00 0.00 0.00 2.78
3332 3565 6.068461 TGGTTACTGTCTCTCTATCTCTGT 57.932 41.667 0.00 0.00 0.00 3.41
3335 3568 4.277423 GGCTGGTTACTGTCTCTCTATCTC 59.723 50.000 0.00 0.00 0.00 2.75
3337 3570 3.954904 TGGCTGGTTACTGTCTCTCTATC 59.045 47.826 0.00 0.00 0.00 2.08
3339 3572 3.451402 TGGCTGGTTACTGTCTCTCTA 57.549 47.619 0.00 0.00 0.00 2.43
3353 3586 1.019673 GTGCATACTGTGATGGCTGG 58.980 55.000 0.00 0.00 0.00 4.85
3357 3590 5.156355 GTTTCTTTGTGCATACTGTGATGG 58.844 41.667 0.00 0.00 0.00 3.51
3363 3596 4.930963 TGTTGGTTTCTTTGTGCATACTG 58.069 39.130 0.00 0.00 0.00 2.74
3383 3616 1.122227 AATTGTGGTTGGCTTGCTGT 58.878 45.000 0.00 0.00 0.00 4.40
3384 3617 2.243602 AAATTGTGGTTGGCTTGCTG 57.756 45.000 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.