Multiple sequence alignment - TraesCS1A01G315000

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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 TraesCS1A01G315000 chr1A 100.000 2878 0 0 1 2878 506521274 506524151 0.000000e+00 5315
1 TraesCS1A01G315000 chr1A 88.889 99 11 0 2780 2878 343679173 343679271 3.890000e-24 122
2 TraesCS1A01G315000 chr5B 92.181 2788 201 11 1 2776 678643871 678641089 0.000000e+00 3925
3 TraesCS1A01G315000 chr5B 90.977 2815 198 17 1 2781 345850435 345853227 0.000000e+00 3740
4 TraesCS1A01G315000 chr2B 91.535 2788 183 21 1 2781 72759226 72761967 0.000000e+00 3792
5 TraesCS1A01G315000 chr2B 91.101 2798 197 19 1 2780 72270071 72272834 0.000000e+00 3740
6 TraesCS1A01G315000 chr2B 87.687 869 77 7 1942 2781 153229682 153228815 0.000000e+00 985
7 TraesCS1A01G315000 chr2B 90.935 353 29 2 1 352 71594006 71594356 3.360000e-129 472
8 TraesCS1A01G315000 chr2B 88.889 99 11 0 2780 2878 67211507 67211409 3.890000e-24 122
9 TraesCS1A01G315000 chr2A 91.290 2813 189 20 1 2782 15468938 15471725 0.000000e+00 3786
10 TraesCS1A01G315000 chr2A 90.722 97 9 0 2780 2876 692242307 692242211 2.330000e-26 130
11 TraesCS1A01G315000 chr2A 87.629 97 12 0 2781 2877 771885524 771885620 2.340000e-21 113
12 TraesCS1A01G315000 chr4A 91.934 2715 199 13 1 2697 632190849 632188137 0.000000e+00 3783
13 TraesCS1A01G315000 chr4A 91.195 2794 228 9 1 2786 104136074 104138857 0.000000e+00 3781
14 TraesCS1A01G315000 chr3B 90.935 2769 205 16 1 2737 643838884 643836130 0.000000e+00 3681
15 TraesCS1A01G315000 chr3B 91.022 2506 179 13 315 2780 503769579 503772078 0.000000e+00 3339
16 TraesCS1A01G315000 chr3B 89.967 917 67 12 1871 2782 476390911 476391807 0.000000e+00 1160
17 TraesCS1A01G315000 chr3B 88.338 343 36 4 1 341 726745755 726746095 2.670000e-110 409
18 TraesCS1A01G315000 chr3B 87.815 238 29 0 1 238 503769104 503769341 2.180000e-71 279
19 TraesCS1A01G315000 chr7A 90.628 2785 211 21 1 2747 441284387 441287159 0.000000e+00 3651
20 TraesCS1A01G315000 chr4B 90.096 2827 231 26 1 2786 40833827 40831009 0.000000e+00 3624
21 TraesCS1A01G315000 chr4B 89.535 2819 225 27 1 2781 370937122 370934336 0.000000e+00 3507
22 TraesCS1A01G315000 chr4B 87.755 98 10 2 2780 2876 70060935 70060839 2.340000e-21 113
23 TraesCS1A01G315000 chr5D 93.197 2440 144 8 357 2780 58529595 58532028 0.000000e+00 3567
24 TraesCS1A01G315000 chr6A 91.304 92 8 0 2785 2876 21226539 21226630 3.010000e-25 126
25 TraesCS1A01G315000 chr4D 87.629 97 12 0 2780 2876 421546413 421546317 2.340000e-21 113
26 TraesCS1A01G315000 chr3A 90.588 85 8 0 2780 2864 96947264 96947348 2.340000e-21 113
27 TraesCS1A01G315000 chr1D 87.629 97 12 0 2780 2876 430320390 430320486 2.340000e-21 113


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 TraesCS1A01G315000 chr1A 506521274 506524151 2877 False 5315 5315 100.0000 1 2878 1 chr1A.!!$F2 2877
1 TraesCS1A01G315000 chr5B 678641089 678643871 2782 True 3925 3925 92.1810 1 2776 1 chr5B.!!$R1 2775
2 TraesCS1A01G315000 chr5B 345850435 345853227 2792 False 3740 3740 90.9770 1 2781 1 chr5B.!!$F1 2780
3 TraesCS1A01G315000 chr2B 72759226 72761967 2741 False 3792 3792 91.5350 1 2781 1 chr2B.!!$F3 2780
4 TraesCS1A01G315000 chr2B 72270071 72272834 2763 False 3740 3740 91.1010 1 2780 1 chr2B.!!$F2 2779
5 TraesCS1A01G315000 chr2B 153228815 153229682 867 True 985 985 87.6870 1942 2781 1 chr2B.!!$R2 839
6 TraesCS1A01G315000 chr2A 15468938 15471725 2787 False 3786 3786 91.2900 1 2782 1 chr2A.!!$F1 2781
7 TraesCS1A01G315000 chr4A 632188137 632190849 2712 True 3783 3783 91.9340 1 2697 1 chr4A.!!$R1 2696
8 TraesCS1A01G315000 chr4A 104136074 104138857 2783 False 3781 3781 91.1950 1 2786 1 chr4A.!!$F1 2785
9 TraesCS1A01G315000 chr3B 643836130 643838884 2754 True 3681 3681 90.9350 1 2737 1 chr3B.!!$R1 2736
10 TraesCS1A01G315000 chr3B 503769104 503772078 2974 False 1809 3339 89.4185 1 2780 2 chr3B.!!$F3 2779
11 TraesCS1A01G315000 chr3B 476390911 476391807 896 False 1160 1160 89.9670 1871 2782 1 chr3B.!!$F1 911
12 TraesCS1A01G315000 chr7A 441284387 441287159 2772 False 3651 3651 90.6280 1 2747 1 chr7A.!!$F1 2746
13 TraesCS1A01G315000 chr4B 40831009 40833827 2818 True 3624 3624 90.0960 1 2786 1 chr4B.!!$R1 2785
14 TraesCS1A01G315000 chr4B 370934336 370937122 2786 True 3507 3507 89.5350 1 2781 1 chr4B.!!$R3 2780
15 TraesCS1A01G315000 chr5D 58529595 58532028 2433 False 3567 3567 93.1970 357 2780 1 chr5D.!!$F1 2423

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
294 311 0.181114 CAAGCTGTAGCCATGGCCTA 59.819 55.0 33.14 20.57 43.38 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2170 2399 1.140852 TGGAGCACACAAGTAGCAAGT 59.859 47.619 0.0 0.0 0.0 3.16 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
69 70 2.124695 GCGGGAGGATTTCGGCTT 60.125 61.111 0.00 0.00 0.00 4.35
133 136 1.303236 CAACTCCCGCCACCATTCA 60.303 57.895 0.00 0.00 0.00 2.57
153 156 1.592223 CCTCCGTTCGAGCTTTCCT 59.408 57.895 0.00 0.00 37.27 3.36
239 251 4.699522 GGCGCTCCTTCACCGGTT 62.700 66.667 2.97 0.00 0.00 4.44
294 311 0.181114 CAAGCTGTAGCCATGGCCTA 59.819 55.000 33.14 20.57 43.38 3.93
390 563 4.123497 TGGTTGATTAGTGGTCTGATCG 57.877 45.455 0.00 0.00 38.85 3.69
486 659 9.341078 GTAGGCTAGATTAGTAGTAGAGTTTGT 57.659 37.037 0.00 0.00 0.00 2.83
523 696 5.091431 GCTTGTGTTGAATCATGCTTAGAC 58.909 41.667 0.00 0.00 33.79 2.59
526 699 6.048732 TGTGTTGAATCATGCTTAGACCTA 57.951 37.500 0.00 0.00 0.00 3.08
551 724 8.701908 ATGATTTGTAGCTATTGATTGTCCAT 57.298 30.769 0.00 0.00 0.00 3.41
575 749 6.443934 TTGTAGCATGTTGTTTGTTGTAGT 57.556 33.333 0.00 0.00 0.00 2.73
605 779 2.546795 CCTGCTCATAGATTGTCCGGTC 60.547 54.545 0.00 0.00 0.00 4.79
615 789 0.320374 TTGTCCGGTCTGCTTGGTAG 59.680 55.000 0.00 0.00 0.00 3.18
617 791 1.987855 TCCGGTCTGCTTGGTAGGG 60.988 63.158 0.00 0.00 0.00 3.53
659 835 9.088987 TGCTTACTATGATAGTGATGAACCATA 57.911 33.333 15.08 0.00 39.81 2.74
756 932 1.005037 GGACATGACCACGCAGACA 60.005 57.895 9.48 0.00 0.00 3.41
781 957 2.327325 TCTTAGTCAGGCCCTTGTCT 57.673 50.000 0.00 0.00 0.00 3.41
835 1011 1.068250 GACTCGCAGCCTATGTCCC 59.932 63.158 0.00 0.00 0.00 4.46
857 1033 1.135721 GATGGCACCTGATTCAAAGGC 59.864 52.381 0.00 0.00 38.48 4.35
913 1089 2.076100 TCGTTGAGCCAACTATTGCTG 58.924 47.619 13.76 0.69 41.62 4.41
920 1102 1.270550 GCCAACTATTGCTGCTGTTGT 59.729 47.619 18.58 6.79 38.35 3.32
974 1164 2.649816 AGGCAAAGAAGGATGGTAGGTT 59.350 45.455 0.00 0.00 0.00 3.50
1032 1223 2.481568 CGTGCTGAACAAGATGTGTGAT 59.518 45.455 0.00 0.00 40.60 3.06
1094 1285 0.450184 GTGCACTTGAACACCGTTGT 59.550 50.000 10.32 0.00 37.67 3.32
1190 1381 1.482182 TCGATGGATCCAAGTGTCCAG 59.518 52.381 20.67 4.34 46.87 3.86
1307 1498 5.770162 CACAACCCTCTTCCTTTTCATACTT 59.230 40.000 0.00 0.00 0.00 2.24
1406 1597 3.587061 TCCTCAACACACCCATACAGAAT 59.413 43.478 0.00 0.00 0.00 2.40
1579 1771 2.154462 CTTCGACAAGCCATTTGACCT 58.846 47.619 0.00 0.00 39.21 3.85
1637 1829 3.708631 TGGAGGAGGAGATCAATGTCTTC 59.291 47.826 0.00 0.00 0.00 2.87
1650 1842 3.900966 ATGTCTTCTGCAGCATGACTA 57.099 42.857 23.60 15.39 39.69 2.59
1713 1905 1.745890 CTCAACGTCCACCCTGACA 59.254 57.895 0.00 0.00 34.88 3.58
2047 2269 0.981183 TGAACTTGCGGTGGTAGGAT 59.019 50.000 0.00 0.00 0.00 3.24
2113 2336 5.064071 GTGCTAGGAAGAACTTGCTATGTTC 59.936 44.000 14.20 8.32 41.52 3.18
2170 2399 6.095580 TCCATTGTTGTTTGTGTGCTACTTTA 59.904 34.615 0.00 0.00 0.00 1.85
2193 2435 2.862541 TGCTACTTGTGTGCTCCATTT 58.137 42.857 0.00 0.00 0.00 2.32
2216 2458 1.683943 TGCTGCTTCAACTCTTGCTT 58.316 45.000 0.00 0.00 0.00 3.91
2290 2532 5.132816 AGGGGTTTATAGTTCATGGGAAGAG 59.867 44.000 0.00 0.00 32.62 2.85
2294 2536 5.531122 TTATAGTTCATGGGAAGAGGTCG 57.469 43.478 0.00 0.00 32.62 4.79
2311 2553 1.968017 CGGTGCACAAGTGGCATCT 60.968 57.895 20.43 0.00 44.11 2.90
2364 2606 3.755434 GCAGGCAGCAGAACAAGT 58.245 55.556 0.00 0.00 44.79 3.16
2385 2627 2.922740 TACTCCAACTGGGTGTGAAC 57.077 50.000 0.00 0.00 43.08 3.18
2404 2652 1.007502 GCACGGCAGCAATGTTGAA 60.008 52.632 0.07 0.00 0.00 2.69
2408 2656 1.408702 ACGGCAGCAATGTTGAAAGTT 59.591 42.857 0.07 0.00 0.00 2.66
2409 2657 2.621055 ACGGCAGCAATGTTGAAAGTTA 59.379 40.909 0.07 0.00 0.00 2.24
2522 2812 1.164041 GCGTTGGTGTGCTAGGTGTT 61.164 55.000 0.00 0.00 0.00 3.32
2606 2896 1.743995 GTTTATGTGCCGCTCGGGT 60.744 57.895 10.57 0.00 38.44 5.28
2612 2902 4.015406 TGCCGCTCGGGTCAATGT 62.015 61.111 10.57 0.00 38.44 2.71
2683 2974 0.175302 TGCAGGCAACCAAACAACTG 59.825 50.000 0.00 0.00 37.17 3.16
2726 3017 2.623416 GTTTTTGCTCAACCAGGCTAGT 59.377 45.455 0.00 0.00 0.00 2.57
2730 3021 0.523519 GCTCAACCAGGCTAGTTTGC 59.476 55.000 0.00 0.44 0.00 3.68
2751 3042 1.097547 AAGTGTATGCGATGCAGGCC 61.098 55.000 9.74 0.00 43.65 5.19
2786 3077 0.467290 ACCAAACACGCCCTTGATGT 60.467 50.000 0.00 0.00 0.00 3.06
2787 3078 1.202830 ACCAAACACGCCCTTGATGTA 60.203 47.619 0.00 0.00 0.00 2.29
2788 3079 1.468520 CCAAACACGCCCTTGATGTAG 59.531 52.381 0.00 0.00 0.00 2.74
2789 3080 2.151202 CAAACACGCCCTTGATGTAGT 58.849 47.619 0.00 0.00 0.00 2.73
2790 3081 3.331150 CAAACACGCCCTTGATGTAGTA 58.669 45.455 0.00 0.00 0.00 1.82
2791 3082 2.961526 ACACGCCCTTGATGTAGTAG 57.038 50.000 0.00 0.00 0.00 2.57
2792 3083 2.453521 ACACGCCCTTGATGTAGTAGA 58.546 47.619 0.00 0.00 0.00 2.59
2793 3084 2.165845 ACACGCCCTTGATGTAGTAGAC 59.834 50.000 0.00 0.00 0.00 2.59
2794 3085 2.165641 CACGCCCTTGATGTAGTAGACA 59.834 50.000 0.00 0.00 43.97 3.41
2795 3086 2.427453 ACGCCCTTGATGTAGTAGACAG 59.573 50.000 0.00 0.00 42.79 3.51
2796 3087 2.427453 CGCCCTTGATGTAGTAGACAGT 59.573 50.000 0.00 0.00 42.79 3.55
2797 3088 3.489398 CGCCCTTGATGTAGTAGACAGTC 60.489 52.174 0.00 0.00 42.79 3.51
2798 3089 3.489398 GCCCTTGATGTAGTAGACAGTCG 60.489 52.174 0.00 0.00 42.79 4.18
2799 3090 3.945921 CCCTTGATGTAGTAGACAGTCGA 59.054 47.826 0.00 0.00 42.79 4.20
2800 3091 4.398358 CCCTTGATGTAGTAGACAGTCGAA 59.602 45.833 0.00 0.00 42.79 3.71
2801 3092 5.105877 CCCTTGATGTAGTAGACAGTCGAAA 60.106 44.000 0.00 0.00 42.79 3.46
2802 3093 6.387465 CCTTGATGTAGTAGACAGTCGAAAA 58.613 40.000 0.00 0.00 42.79 2.29
2803 3094 6.528423 CCTTGATGTAGTAGACAGTCGAAAAG 59.472 42.308 0.00 0.00 42.79 2.27
2804 3095 6.570672 TGATGTAGTAGACAGTCGAAAAGT 57.429 37.500 0.00 0.00 42.79 2.66
2805 3096 7.677454 TGATGTAGTAGACAGTCGAAAAGTA 57.323 36.000 0.00 0.00 42.79 2.24
2806 3097 7.749808 TGATGTAGTAGACAGTCGAAAAGTAG 58.250 38.462 0.00 0.00 42.79 2.57
2807 3098 7.389884 TGATGTAGTAGACAGTCGAAAAGTAGT 59.610 37.037 0.00 0.00 42.79 2.73
2808 3099 7.126726 TGTAGTAGACAGTCGAAAAGTAGTC 57.873 40.000 0.00 0.00 32.86 2.59
2809 3100 5.280328 AGTAGACAGTCGAAAAGTAGTCG 57.720 43.478 0.00 0.00 39.88 4.18
2810 3101 4.754114 AGTAGACAGTCGAAAAGTAGTCGT 59.246 41.667 0.00 0.00 39.52 4.34
2811 3102 3.886549 AGACAGTCGAAAAGTAGTCGTG 58.113 45.455 0.00 0.00 39.52 4.35
2812 3103 2.391879 ACAGTCGAAAAGTAGTCGTGC 58.608 47.619 0.00 0.00 39.52 5.34
2813 3104 2.034305 ACAGTCGAAAAGTAGTCGTGCT 59.966 45.455 0.00 0.00 39.52 4.40
2814 3105 3.251729 ACAGTCGAAAAGTAGTCGTGCTA 59.748 43.478 0.00 0.00 39.52 3.49
2815 3106 4.224433 CAGTCGAAAAGTAGTCGTGCTAA 58.776 43.478 0.00 0.00 39.52 3.09
2816 3107 4.321217 CAGTCGAAAAGTAGTCGTGCTAAG 59.679 45.833 0.00 0.00 39.52 2.18
2817 3108 3.607209 GTCGAAAAGTAGTCGTGCTAAGG 59.393 47.826 0.00 0.00 39.52 2.69
2818 3109 2.344741 CGAAAAGTAGTCGTGCTAAGGC 59.655 50.000 0.00 0.00 39.26 4.35
2819 3110 2.381725 AAAGTAGTCGTGCTAAGGCC 57.618 50.000 0.00 0.00 37.74 5.19
2820 3111 1.558233 AAGTAGTCGTGCTAAGGCCT 58.442 50.000 0.00 0.00 37.74 5.19
2821 3112 1.104630 AGTAGTCGTGCTAAGGCCTC 58.895 55.000 5.23 0.00 37.74 4.70
2822 3113 0.815734 GTAGTCGTGCTAAGGCCTCA 59.184 55.000 5.23 0.00 37.74 3.86
2823 3114 1.409427 GTAGTCGTGCTAAGGCCTCAT 59.591 52.381 5.23 0.00 37.74 2.90
2824 3115 1.776662 AGTCGTGCTAAGGCCTCATA 58.223 50.000 5.23 0.00 37.74 2.15
2825 3116 1.683917 AGTCGTGCTAAGGCCTCATAG 59.316 52.381 5.23 6.39 37.74 2.23
2826 3117 1.040646 TCGTGCTAAGGCCTCATAGG 58.959 55.000 5.23 0.00 38.80 2.57
2827 3118 1.040646 CGTGCTAAGGCCTCATAGGA 58.959 55.000 5.23 3.07 37.67 2.94
2828 3119 1.269831 CGTGCTAAGGCCTCATAGGAC 60.270 57.143 20.66 20.66 46.64 3.85
2833 3124 2.423446 GGCCTCATAGGACCAGCG 59.577 66.667 0.00 0.00 37.46 5.18
2834 3125 2.280457 GCCTCATAGGACCAGCGC 60.280 66.667 0.00 0.00 37.67 5.92
2835 3126 3.094062 GCCTCATAGGACCAGCGCA 62.094 63.158 11.47 0.00 37.67 6.09
2836 3127 1.227380 CCTCATAGGACCAGCGCAC 60.227 63.158 11.47 0.00 37.67 5.34
2837 3128 1.680522 CCTCATAGGACCAGCGCACT 61.681 60.000 11.47 1.70 37.67 4.40
2838 3129 1.032794 CTCATAGGACCAGCGCACTA 58.967 55.000 11.47 4.17 0.00 2.74
2839 3130 1.000827 CTCATAGGACCAGCGCACTAG 60.001 57.143 11.47 0.00 0.00 2.57
2840 3131 1.032794 CATAGGACCAGCGCACTAGA 58.967 55.000 11.47 0.00 0.00 2.43
2841 3132 1.409064 CATAGGACCAGCGCACTAGAA 59.591 52.381 11.47 0.00 0.00 2.10
2842 3133 0.815734 TAGGACCAGCGCACTAGAAC 59.184 55.000 11.47 0.00 0.00 3.01
2843 3134 1.185618 AGGACCAGCGCACTAGAACA 61.186 55.000 11.47 0.00 0.00 3.18
2844 3135 0.737715 GGACCAGCGCACTAGAACAG 60.738 60.000 11.47 0.00 0.00 3.16
2845 3136 1.355066 GACCAGCGCACTAGAACAGC 61.355 60.000 11.47 0.00 0.00 4.40
2846 3137 1.374631 CCAGCGCACTAGAACAGCA 60.375 57.895 11.47 0.00 0.00 4.41
2847 3138 0.950555 CCAGCGCACTAGAACAGCAA 60.951 55.000 11.47 0.00 0.00 3.91
2848 3139 0.164647 CAGCGCACTAGAACAGCAAC 59.835 55.000 11.47 0.00 0.00 4.17
2849 3140 0.034059 AGCGCACTAGAACAGCAACT 59.966 50.000 11.47 0.00 0.00 3.16
2850 3141 0.164647 GCGCACTAGAACAGCAACTG 59.835 55.000 0.30 0.00 37.52 3.16
2852 3143 1.457303 CGCACTAGAACAGCAACTGTC 59.543 52.381 0.00 0.00 44.62 3.51
2853 3144 1.457303 GCACTAGAACAGCAACTGTCG 59.543 52.381 0.00 0.00 44.62 4.35
2854 3145 1.457303 CACTAGAACAGCAACTGTCGC 59.543 52.381 0.00 0.00 44.62 5.19
2855 3146 1.341531 ACTAGAACAGCAACTGTCGCT 59.658 47.619 0.00 4.78 44.62 4.93
2861 3152 3.612517 AGCAACTGTCGCTGATGAA 57.387 47.368 0.00 0.00 38.60 2.57
2862 3153 1.436600 AGCAACTGTCGCTGATGAAG 58.563 50.000 0.00 0.00 38.60 3.02
2863 3154 1.001293 AGCAACTGTCGCTGATGAAGA 59.999 47.619 0.00 0.00 38.60 2.87
2864 3155 1.392853 GCAACTGTCGCTGATGAAGAG 59.607 52.381 0.00 0.00 0.00 2.85
2865 3156 2.681706 CAACTGTCGCTGATGAAGAGT 58.318 47.619 0.00 0.00 0.00 3.24
2866 3157 3.838120 CAACTGTCGCTGATGAAGAGTA 58.162 45.455 0.00 0.00 0.00 2.59
2867 3158 3.773860 ACTGTCGCTGATGAAGAGTAG 57.226 47.619 0.00 0.00 0.00 2.57
2868 3159 2.159310 ACTGTCGCTGATGAAGAGTAGC 60.159 50.000 0.00 0.00 0.00 3.58
2869 3160 1.818674 TGTCGCTGATGAAGAGTAGCA 59.181 47.619 0.00 0.00 35.98 3.49
2870 3161 2.428530 TGTCGCTGATGAAGAGTAGCAT 59.571 45.455 0.00 0.00 35.98 3.79
2871 3162 3.632145 TGTCGCTGATGAAGAGTAGCATA 59.368 43.478 0.00 0.00 35.98 3.14
2872 3163 4.097892 TGTCGCTGATGAAGAGTAGCATAA 59.902 41.667 0.00 0.00 35.98 1.90
2873 3164 5.043903 GTCGCTGATGAAGAGTAGCATAAA 58.956 41.667 0.00 0.00 35.98 1.40
2874 3165 5.694006 GTCGCTGATGAAGAGTAGCATAAAT 59.306 40.000 0.00 0.00 35.98 1.40
2875 3166 5.923114 TCGCTGATGAAGAGTAGCATAAATC 59.077 40.000 0.00 0.00 35.98 2.17
2876 3167 5.693555 CGCTGATGAAGAGTAGCATAAATCA 59.306 40.000 0.00 0.00 35.98 2.57
2877 3168 6.201615 CGCTGATGAAGAGTAGCATAAATCAA 59.798 38.462 0.00 0.00 35.98 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.473647 CGCCATCTCCCCTGCTCA 61.474 66.667 0.00 0.00 0.00 4.26
133 136 1.292541 GAAAGCTCGAACGGAGGGT 59.707 57.895 0.00 0.00 43.36 4.34
178 181 0.882042 AAGATGCGCCGCTTATCTGG 60.882 55.000 11.67 0.00 31.89 3.86
182 185 1.151668 GATGAAGATGCGCCGCTTAT 58.848 50.000 11.67 0.00 0.00 1.73
238 250 0.034198 TCGTGGAAGATCAACGCCAA 59.966 50.000 2.44 0.00 31.85 4.52
239 251 0.669318 GTCGTGGAAGATCAACGCCA 60.669 55.000 2.44 0.00 0.00 5.69
294 311 4.290722 AGAGAAAGGGGATTGAACTCACAT 59.709 41.667 0.00 0.00 0.00 3.21
347 520 5.012458 CCATGCATCTAGATCAAACCCTAGA 59.988 44.000 1.03 0.00 43.62 2.43
390 563 3.004106 GCAATCAACCATATCAGCTCACC 59.996 47.826 0.00 0.00 0.00 4.02
486 659 3.616219 ACACAAGCACAAGGTTCAACTA 58.384 40.909 0.00 0.00 32.07 2.24
523 696 8.725148 GGACAATCAATAGCTACAAATCATAGG 58.275 37.037 0.00 0.00 0.00 2.57
526 699 8.701908 ATGGACAATCAATAGCTACAAATCAT 57.298 30.769 0.00 0.00 0.00 2.45
545 718 5.163468 ACAAACAACATGCTACAAATGGACA 60.163 36.000 0.00 0.00 0.00 4.02
551 724 6.857956 ACTACAACAAACAACATGCTACAAA 58.142 32.000 0.00 0.00 0.00 2.83
575 749 6.653020 ACAATCTATGAGCAGGAACATACAA 58.347 36.000 0.00 0.00 0.00 2.41
605 779 0.753262 ATCGCTACCCTACCAAGCAG 59.247 55.000 0.00 0.00 35.98 4.24
615 789 0.940126 CACATGCTTCATCGCTACCC 59.060 55.000 0.00 0.00 0.00 3.69
617 791 3.814049 GCACATGCTTCATCGCTAC 57.186 52.632 0.00 0.00 38.21 3.58
659 835 6.016527 CCATGAAAGCAGAAGCATACATGTAT 60.017 38.462 12.75 12.75 45.49 2.29
756 932 2.839228 AGGGCCTGACTAAGATCTTGT 58.161 47.619 18.47 13.32 0.00 3.16
781 957 1.444119 GCAAACTGGCTGTCGGACAA 61.444 55.000 12.54 0.00 29.31 3.18
835 1011 2.426024 CCTTTGAATCAGGTGCCATCTG 59.574 50.000 0.00 0.00 0.00 2.90
857 1033 0.528684 GAGGGAATCAGAGGCGAACG 60.529 60.000 0.00 0.00 0.00 3.95
864 1040 2.702478 TGGCACATAGAGGGAATCAGAG 59.298 50.000 0.00 0.00 0.00 3.35
908 1084 1.227031 GCAGCAACAACAGCAGCAA 60.227 52.632 0.00 0.00 43.05 3.91
909 1085 2.414179 GCAGCAACAACAGCAGCA 59.586 55.556 0.00 0.00 43.05 4.41
910 1086 2.355481 GGCAGCAACAACAGCAGC 60.355 61.111 0.00 0.00 42.85 5.25
974 1164 3.146066 GGCTACCACTTCATGTTGTTCA 58.854 45.455 0.00 0.00 0.00 3.18
1032 1223 5.430417 AGTCCTAACTCCACTAGAGATGAGA 59.570 44.000 0.00 0.00 46.50 3.27
1094 1285 1.412710 AGAACTCGAACACCTGCTTCA 59.587 47.619 0.00 0.00 0.00 3.02
1157 1348 2.525368 TCCATCGACTTCTCCACTTCA 58.475 47.619 0.00 0.00 0.00 3.02
1190 1381 1.439644 CCGCTAAGGTCTCTCAGCC 59.560 63.158 0.00 0.00 34.51 4.85
1307 1498 1.668826 AGGAGTAGGCAATGGTGGAA 58.331 50.000 0.00 0.00 0.00 3.53
1406 1597 2.268762 TGTGCTGCATCTGGTTGTAA 57.731 45.000 5.27 0.00 0.00 2.41
1529 1721 2.825836 GGCTTGTCAGGGCCATCG 60.826 66.667 6.18 0.00 46.84 3.84
1579 1771 3.595190 TCCTCTTCCTATCATGGACGA 57.405 47.619 0.00 0.00 35.58 4.20
1637 1829 1.284657 CCGTCTTAGTCATGCTGCAG 58.715 55.000 10.11 10.11 0.00 4.41
1650 1842 2.058675 CCACCTCCTTCACCGTCTT 58.941 57.895 0.00 0.00 0.00 3.01
1713 1905 2.355108 GGGTCATGATAGCGCCATACAT 60.355 50.000 2.29 2.16 0.00 2.29
1975 2197 6.038603 CACCTCACCAAAATATACAGACCATG 59.961 42.308 0.00 0.00 0.00 3.66
2113 2336 7.388224 AGAGAAGTAAAGCATGCATGATCATAG 59.612 37.037 30.64 1.83 0.00 2.23
2170 2399 1.140852 TGGAGCACACAAGTAGCAAGT 59.859 47.619 0.00 0.00 0.00 3.16
2193 2435 3.822735 AGCAAGAGTTGAAGCAGCAAATA 59.177 39.130 0.00 0.00 0.00 1.40
2290 2532 3.660111 GCCACTTGTGCACCGACC 61.660 66.667 15.69 0.00 0.00 4.79
2294 2536 1.533625 TAAGATGCCACTTGTGCACC 58.466 50.000 15.69 0.00 42.38 5.01
2311 2553 4.202357 CCTCTATGGGTGCTGTTGCTATAA 60.202 45.833 0.00 0.00 40.48 0.98
2343 2585 0.110295 TTGTTCTGCTGCCTGCCTAA 59.890 50.000 0.00 0.00 42.00 2.69
2364 2606 3.547746 GTTCACACCCAGTTGGAGTAAA 58.452 45.455 0.00 0.00 35.52 2.01
2385 2627 2.730006 TTCAACATTGCTGCCGTGCG 62.730 55.000 0.00 0.00 35.36 5.34
2404 2652 3.201266 TGACACCTCCAACCTTGTAACTT 59.799 43.478 0.00 0.00 0.00 2.66
2408 2656 2.105821 CCTTGACACCTCCAACCTTGTA 59.894 50.000 0.00 0.00 0.00 2.41
2409 2657 1.133792 CCTTGACACCTCCAACCTTGT 60.134 52.381 0.00 0.00 0.00 3.16
2591 2881 1.966901 ATTGACCCGAGCGGCACATA 61.967 55.000 1.45 0.00 33.26 2.29
2606 2896 4.404073 ACTTTGTTTGGTTGCCTACATTGA 59.596 37.500 0.00 0.00 0.00 2.57
2612 2902 2.103373 TGCACTTTGTTTGGTTGCCTA 58.897 42.857 0.00 0.00 0.00 3.93
2683 2974 1.467920 GCCCTAATATGCCATCTGCC 58.532 55.000 0.00 0.00 40.16 4.85
2726 3017 1.202020 GCATCGCATACACTTCGCAAA 60.202 47.619 0.00 0.00 0.00 3.68
2730 3021 0.578683 CCTGCATCGCATACACTTCG 59.421 55.000 0.00 0.00 38.13 3.79
2751 3042 1.169661 TGGTTGCCGTTTGCTACAGG 61.170 55.000 1.62 0.00 45.92 4.00
2786 3077 5.928839 ACGACTACTTTTCGACTGTCTACTA 59.071 40.000 6.21 0.00 39.83 1.82
2787 3078 4.754114 ACGACTACTTTTCGACTGTCTACT 59.246 41.667 6.21 0.00 39.83 2.57
2788 3079 4.845060 CACGACTACTTTTCGACTGTCTAC 59.155 45.833 6.21 0.00 39.83 2.59
2789 3080 4.612259 GCACGACTACTTTTCGACTGTCTA 60.612 45.833 6.21 0.00 39.83 2.59
2790 3081 3.852572 GCACGACTACTTTTCGACTGTCT 60.853 47.826 6.21 0.00 39.83 3.41
2791 3082 2.404361 GCACGACTACTTTTCGACTGTC 59.596 50.000 0.00 0.00 39.83 3.51
2792 3083 2.034305 AGCACGACTACTTTTCGACTGT 59.966 45.455 0.00 0.00 39.83 3.55
2793 3084 2.662700 AGCACGACTACTTTTCGACTG 58.337 47.619 0.00 0.00 39.83 3.51
2794 3085 4.474113 CTTAGCACGACTACTTTTCGACT 58.526 43.478 0.00 0.00 39.83 4.18
2795 3086 3.607209 CCTTAGCACGACTACTTTTCGAC 59.393 47.826 0.00 0.00 39.83 4.20
2796 3087 3.829948 CCTTAGCACGACTACTTTTCGA 58.170 45.455 0.00 0.00 39.83 3.71
2797 3088 2.344741 GCCTTAGCACGACTACTTTTCG 59.655 50.000 0.00 0.00 42.36 3.46
2798 3089 2.671888 GGCCTTAGCACGACTACTTTTC 59.328 50.000 0.00 0.00 42.56 2.29
2799 3090 2.302157 AGGCCTTAGCACGACTACTTTT 59.698 45.455 0.00 0.00 42.56 2.27
2800 3091 1.900486 AGGCCTTAGCACGACTACTTT 59.100 47.619 0.00 0.00 42.56 2.66
2801 3092 1.477295 GAGGCCTTAGCACGACTACTT 59.523 52.381 6.77 0.00 42.56 2.24
2802 3093 1.104630 GAGGCCTTAGCACGACTACT 58.895 55.000 6.77 0.00 42.56 2.57
2803 3094 0.815734 TGAGGCCTTAGCACGACTAC 59.184 55.000 6.77 0.00 42.56 2.73
2804 3095 1.776662 ATGAGGCCTTAGCACGACTA 58.223 50.000 6.77 0.00 42.56 2.59
2805 3096 1.683917 CTATGAGGCCTTAGCACGACT 59.316 52.381 6.77 0.00 42.56 4.18
2806 3097 1.269831 CCTATGAGGCCTTAGCACGAC 60.270 57.143 6.77 0.00 42.56 4.34
2807 3098 1.040646 CCTATGAGGCCTTAGCACGA 58.959 55.000 6.77 0.00 42.56 4.35
2808 3099 1.040646 TCCTATGAGGCCTTAGCACG 58.959 55.000 6.77 0.00 42.56 5.34
2809 3100 1.070914 GGTCCTATGAGGCCTTAGCAC 59.929 57.143 6.77 1.09 42.56 4.40
2810 3101 1.343985 TGGTCCTATGAGGCCTTAGCA 60.344 52.381 6.77 0.00 42.56 3.49
2811 3102 1.346068 CTGGTCCTATGAGGCCTTAGC 59.654 57.143 6.77 0.00 34.61 3.09
2812 3103 1.346068 GCTGGTCCTATGAGGCCTTAG 59.654 57.143 6.77 5.46 34.61 2.18
2813 3104 1.424638 GCTGGTCCTATGAGGCCTTA 58.575 55.000 6.77 1.66 34.61 2.69
2814 3105 1.690219 CGCTGGTCCTATGAGGCCTT 61.690 60.000 6.77 0.00 34.61 4.35
2815 3106 2.136878 CGCTGGTCCTATGAGGCCT 61.137 63.158 3.86 3.86 34.61 5.19
2816 3107 2.423446 CGCTGGTCCTATGAGGCC 59.577 66.667 0.00 0.00 34.61 5.19
2817 3108 2.280457 GCGCTGGTCCTATGAGGC 60.280 66.667 0.00 0.00 34.61 4.70
2818 3109 1.227380 GTGCGCTGGTCCTATGAGG 60.227 63.158 9.73 0.00 36.46 3.86
2819 3110 1.000827 CTAGTGCGCTGGTCCTATGAG 60.001 57.143 10.80 0.00 0.00 2.90
2820 3111 1.032794 CTAGTGCGCTGGTCCTATGA 58.967 55.000 10.80 0.00 0.00 2.15
2821 3112 1.032794 TCTAGTGCGCTGGTCCTATG 58.967 55.000 10.80 0.00 0.00 2.23
2822 3113 1.409427 GTTCTAGTGCGCTGGTCCTAT 59.591 52.381 10.80 0.00 0.00 2.57
2823 3114 0.815734 GTTCTAGTGCGCTGGTCCTA 59.184 55.000 10.80 0.21 0.00 2.94
2824 3115 1.185618 TGTTCTAGTGCGCTGGTCCT 61.186 55.000 10.80 0.00 0.00 3.85
2825 3116 0.737715 CTGTTCTAGTGCGCTGGTCC 60.738 60.000 10.80 2.79 0.00 4.46
2826 3117 1.355066 GCTGTTCTAGTGCGCTGGTC 61.355 60.000 10.80 5.89 0.00 4.02
2827 3118 1.374758 GCTGTTCTAGTGCGCTGGT 60.375 57.895 10.80 0.00 0.00 4.00
2828 3119 0.950555 TTGCTGTTCTAGTGCGCTGG 60.951 55.000 10.80 7.28 0.00 4.85
2829 3120 0.164647 GTTGCTGTTCTAGTGCGCTG 59.835 55.000 10.80 0.00 0.00 5.18
2830 3121 0.034059 AGTTGCTGTTCTAGTGCGCT 59.966 50.000 9.73 4.58 0.00 5.92
2831 3122 0.164647 CAGTTGCTGTTCTAGTGCGC 59.835 55.000 0.00 0.00 0.00 6.09
2832 3123 1.457303 GACAGTTGCTGTTCTAGTGCG 59.543 52.381 3.16 0.00 45.44 5.34
2833 3124 1.457303 CGACAGTTGCTGTTCTAGTGC 59.543 52.381 3.16 0.00 45.44 4.40
2834 3125 1.457303 GCGACAGTTGCTGTTCTAGTG 59.543 52.381 5.41 0.00 45.44 2.74
2835 3126 1.341531 AGCGACAGTTGCTGTTCTAGT 59.658 47.619 15.10 0.00 45.44 2.57
2836 3127 2.071688 AGCGACAGTTGCTGTTCTAG 57.928 50.000 15.10 0.00 45.44 2.43
2843 3134 1.001293 TCTTCATCAGCGACAGTTGCT 59.999 47.619 9.80 9.80 45.31 3.91
2844 3135 1.392853 CTCTTCATCAGCGACAGTTGC 59.607 52.381 4.35 4.35 0.00 4.17
2845 3136 2.681706 ACTCTTCATCAGCGACAGTTG 58.318 47.619 0.00 0.00 0.00 3.16
2846 3137 3.674682 GCTACTCTTCATCAGCGACAGTT 60.675 47.826 0.00 0.00 0.00 3.16
2847 3138 2.159310 GCTACTCTTCATCAGCGACAGT 60.159 50.000 0.00 0.00 0.00 3.55
2848 3139 2.159324 TGCTACTCTTCATCAGCGACAG 60.159 50.000 0.00 0.00 36.81 3.51
2849 3140 1.818674 TGCTACTCTTCATCAGCGACA 59.181 47.619 0.00 0.00 36.81 4.35
2850 3141 2.568696 TGCTACTCTTCATCAGCGAC 57.431 50.000 0.00 0.00 36.81 5.19
2851 3142 4.918810 TTATGCTACTCTTCATCAGCGA 57.081 40.909 0.00 0.00 36.81 4.93
2852 3143 5.693555 TGATTTATGCTACTCTTCATCAGCG 59.306 40.000 0.00 0.00 36.81 5.18
2853 3144 7.488187 TTGATTTATGCTACTCTTCATCAGC 57.512 36.000 0.00 0.00 34.56 4.26


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

AutoCloner maintained by Alex Coulton.