Multiple sequence alignment - TraesCS4A01G118500

Loading Multiple Alignment...

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 TraesCS4A01G118500 chr4A 100.000 3105 0 0 1 3105 146048578 146045474 0.000000e+00 5734.0
1 TraesCS4A01G118500 chr4A 92.835 1619 98 11 1 1614 53752075 53753680 0.000000e+00 2331.0
2 TraesCS4A01G118500 chr4A 92.857 1470 93 9 1 1466 12669235 12667774 0.000000e+00 2122.0
3 TraesCS4A01G118500 chr4A 92.857 154 7 3 2525 2677 53753677 53753827 1.450000e-53 220.0
4 TraesCS4A01G118500 chr3A 98.593 2915 39 2 1 2914 667660897 667663810 0.000000e+00 5155.0
5 TraesCS4A01G118500 chr4B 98.491 2915 41 3 1 2912 417375031 417372117 0.000000e+00 5136.0
6 TraesCS4A01G118500 chr4B 95.652 46 2 0 2869 2914 245455328 245455373 1.190000e-09 75.0
7 TraesCS4A01G118500 chr2D 91.406 2490 151 29 1 2453 299657539 299655076 0.000000e+00 3354.0
8 TraesCS4A01G118500 chr2D 91.100 2191 134 22 305 2453 327321670 327323841 0.000000e+00 2909.0
9 TraesCS4A01G118500 chr2D 86.777 121 12 1 2797 2913 299654897 299654777 6.990000e-27 132.0
10 TraesCS4A01G118500 chr2D 87.156 109 10 1 2794 2898 327324027 327324135 1.510000e-23 121.0
11 TraesCS4A01G118500 chr2D 100.000 35 0 0 2755 2789 299655069 299655035 7.190000e-07 65.8
12 TraesCS4A01G118500 chr2D 95.238 42 0 2 2748 2789 327323843 327323882 7.190000e-07 65.8
13 TraesCS4A01G118500 chr2D 100.000 30 0 0 2756 2785 299655037 299655008 4.330000e-04 56.5
14 TraesCS4A01G118500 chr2D 100.000 30 0 0 2756 2785 327323880 327323909 4.330000e-04 56.5
15 TraesCS4A01G118500 chr1D 91.171 2186 136 21 305 2453 319528362 319526197 0.000000e+00 2915.0
16 TraesCS4A01G118500 chr1D 91.639 2093 96 21 1 2054 242558217 242560269 0.000000e+00 2822.0
17 TraesCS4A01G118500 chr1D 95.503 845 29 3 2053 2888 242560431 242561275 0.000000e+00 1341.0
18 TraesCS4A01G118500 chr1D 94.595 148 8 0 2958 3105 452630267 452630120 2.410000e-56 230.0
19 TraesCS4A01G118500 chr1D 87.395 119 10 2 2797 2910 319526018 319525900 6.990000e-27 132.0
20 TraesCS4A01G118500 chr1D 100.000 35 0 0 2755 2789 319526190 319526156 7.190000e-07 65.8
21 TraesCS4A01G118500 chr1D 100.000 30 0 0 2756 2785 319526158 319526129 4.330000e-04 56.5
22 TraesCS4A01G118500 chr6A 85.617 2489 260 48 1 2415 241737621 241740085 0.000000e+00 2523.0
23 TraesCS4A01G118500 chr6A 84.652 2085 236 46 1 2027 261024182 261026240 0.000000e+00 2001.0
24 TraesCS4A01G118500 chr6A 87.167 413 24 11 2029 2413 261026800 261027211 2.840000e-120 442.0
25 TraesCS4A01G118500 chr6A 97.674 43 0 1 2869 2910 261036034 261036076 4.300000e-09 73.1
26 TraesCS4A01G118500 chr6A 90.741 54 4 1 2865 2917 97387225 97387278 1.540000e-08 71.3
27 TraesCS4A01G118500 chr7A 92.857 1470 93 9 1 1466 67563021 67564482 0.000000e+00 2122.0
28 TraesCS4A01G118500 chr7A 92.857 1470 92 10 1 1466 2540339 2541799 0.000000e+00 2121.0
29 TraesCS4A01G118500 chr1A 92.789 1470 94 9 1 1466 502837518 502836057 0.000000e+00 2117.0
30 TraesCS4A01G118500 chr5A 92.653 1470 94 10 1 1466 280764658 280766117 0.000000e+00 2104.0
31 TraesCS4A01G118500 chr5B 96.667 150 5 0 2956 3105 426595575 426595426 1.850000e-62 250.0
32 TraesCS4A01G118500 chr2B 96.667 150 5 0 2956 3105 608362416 608362267 1.850000e-62 250.0
33 TraesCS4A01G118500 chr2B 96.622 148 5 0 2958 3105 717008663 717008516 2.390000e-61 246.0
34 TraesCS4A01G118500 chr2B 90.385 52 3 2 2863 2914 792770407 792770358 2.000000e-07 67.6
35 TraesCS4A01G118500 chr3B 93.789 161 10 0 2945 3105 161140294 161140454 3.090000e-60 243.0
36 TraesCS4A01G118500 chr3B 95.946 148 6 0 2958 3105 641673337 641673190 1.110000e-59 241.0
37 TraesCS4A01G118500 chr3B 93.506 154 10 0 2952 3105 221750785 221750938 2.410000e-56 230.0
38 TraesCS4A01G118500 chr7B 94.118 153 8 1 2953 3105 641595149 641594998 6.700000e-57 231.0
39 TraesCS4A01G118500 chr7B 84.058 69 8 3 2858 2925 355849397 355849463 2.590000e-06 63.9
40 TraesCS4A01G118500 chr3D 94.040 151 9 0 2955 3105 155952286 155952136 2.410000e-56 230.0
41 TraesCS4A01G118500 chr3D 94.737 57 2 1 2905 2961 85297640 85297695 1.530000e-13 87.9


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 TraesCS4A01G118500 chr4A 146045474 146048578 3104 True 5734.000 5734 100.00000 1 3105 1 chr4A.!!$R2 3104
1 TraesCS4A01G118500 chr4A 12667774 12669235 1461 True 2122.000 2122 92.85700 1 1466 1 chr4A.!!$R1 1465
2 TraesCS4A01G118500 chr4A 53752075 53753827 1752 False 1275.500 2331 92.84600 1 2677 2 chr4A.!!$F1 2676
3 TraesCS4A01G118500 chr3A 667660897 667663810 2913 False 5155.000 5155 98.59300 1 2914 1 chr3A.!!$F1 2913
4 TraesCS4A01G118500 chr4B 417372117 417375031 2914 True 5136.000 5136 98.49100 1 2912 1 chr4B.!!$R1 2911
5 TraesCS4A01G118500 chr2D 299654777 299657539 2762 True 902.075 3354 94.54575 1 2913 4 chr2D.!!$R1 2912
6 TraesCS4A01G118500 chr2D 327321670 327324135 2465 False 788.075 2909 93.37350 305 2898 4 chr2D.!!$F1 2593
7 TraesCS4A01G118500 chr1D 242558217 242561275 3058 False 2081.500 2822 93.57100 1 2888 2 chr1D.!!$F1 2887
8 TraesCS4A01G118500 chr1D 319525900 319528362 2462 True 792.325 2915 94.64150 305 2910 4 chr1D.!!$R2 2605
9 TraesCS4A01G118500 chr6A 241737621 241740085 2464 False 2523.000 2523 85.61700 1 2415 1 chr6A.!!$F2 2414
10 TraesCS4A01G118500 chr6A 261024182 261027211 3029 False 1221.500 2001 85.90950 1 2413 2 chr6A.!!$F4 2412
11 TraesCS4A01G118500 chr7A 67563021 67564482 1461 False 2122.000 2122 92.85700 1 1466 1 chr7A.!!$F2 1465
12 TraesCS4A01G118500 chr7A 2540339 2541799 1460 False 2121.000 2121 92.85700 1 1466 1 chr7A.!!$F1 1465
13 TraesCS4A01G118500 chr1A 502836057 502837518 1461 True 2117.000 2117 92.78900 1 1466 1 chr1A.!!$R1 1465
14 TraesCS4A01G118500 chr5A 280764658 280766117 1459 False 2104.000 2104 92.65300 1 1466 1 chr5A.!!$F1 1465

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
324 326 0.877649 CGATGGAGTGCAATCCCGAG 60.878 60.0 29.08 16.21 38.72 4.63 F
1767 1824 0.321996 GTCTCTTCCAAGAAGGGCGT 59.678 55.0 4.60 0.00 38.24 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1823 1897 0.608640 GTCGTCTCCAATGGTCCTGT 59.391 55.0 0.0 0.0 0.0 4.0 R
2931 3909 0.400213 TGCGGAAACACAGGGAGATT 59.600 50.0 0.0 0.0 0.0 2.4 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
324 326 0.877649 CGATGGAGTGCAATCCCGAG 60.878 60.000 29.08 16.21 38.72 4.63
684 695 4.080863 GGATCATGGTGAGGTTACTGAGTT 60.081 45.833 0.00 0.00 0.00 3.01
1285 1311 7.667219 AGATTCTCATTGTCAAGTTGTTATGGT 59.333 33.333 2.11 0.00 0.00 3.55
1668 1722 1.656652 AAATTCTGGCATCGTCTCCG 58.343 50.000 0.00 0.00 0.00 4.63
1767 1824 0.321996 GTCTCTTCCAAGAAGGGCGT 59.678 55.000 4.60 0.00 38.24 5.68
1823 1897 1.896660 GCACGAGCCAACAAAGGGA 60.897 57.895 0.00 0.00 33.58 4.20
2703 3536 5.452356 GGAAATAGGAGGCATGAAAACATGG 60.452 44.000 11.29 0.00 33.41 3.66
2816 3789 6.640907 ACTTGAAAAATCGCATTTGGTACTTC 59.359 34.615 0.00 0.00 31.77 3.01
2909 3887 6.073440 CGCACGGGCATTTTTACTAGTAATAT 60.073 38.462 15.92 9.89 41.24 1.28
2935 3913 5.607168 AAAAGGAAGAAAGGAGGGAATCT 57.393 39.130 0.00 0.00 0.00 2.40
2936 3914 4.853468 AAGGAAGAAAGGAGGGAATCTC 57.147 45.455 0.00 0.00 41.71 2.75
2948 3926 1.739067 GGAATCTCCCTGTGTTTCCG 58.261 55.000 0.00 0.00 0.00 4.30
2949 3927 1.087501 GAATCTCCCTGTGTTTCCGC 58.912 55.000 0.00 0.00 0.00 5.54
2950 3928 0.400213 AATCTCCCTGTGTTTCCGCA 59.600 50.000 0.00 0.00 0.00 5.69
2951 3929 0.620556 ATCTCCCTGTGTTTCCGCAT 59.379 50.000 0.00 0.00 0.00 4.73
2952 3930 1.271856 TCTCCCTGTGTTTCCGCATA 58.728 50.000 0.00 0.00 0.00 3.14
2953 3931 1.207089 TCTCCCTGTGTTTCCGCATAG 59.793 52.381 0.00 0.00 0.00 2.23
2954 3932 1.207089 CTCCCTGTGTTTCCGCATAGA 59.793 52.381 0.00 0.00 30.51 1.98
2955 3933 1.837439 TCCCTGTGTTTCCGCATAGAT 59.163 47.619 0.00 0.00 30.51 1.98
2956 3934 1.942657 CCCTGTGTTTCCGCATAGATG 59.057 52.381 0.00 0.00 30.51 2.90
2957 3935 1.942657 CCTGTGTTTCCGCATAGATGG 59.057 52.381 0.00 0.00 30.51 3.51
2958 3936 2.419990 CCTGTGTTTCCGCATAGATGGA 60.420 50.000 0.00 0.00 30.51 3.41
2959 3937 2.868583 CTGTGTTTCCGCATAGATGGAG 59.131 50.000 0.00 0.00 35.26 3.86
2960 3938 2.236146 TGTGTTTCCGCATAGATGGAGT 59.764 45.455 0.00 0.00 35.26 3.85
2961 3939 3.449377 TGTGTTTCCGCATAGATGGAGTA 59.551 43.478 0.00 0.00 35.26 2.59
2962 3940 4.081365 TGTGTTTCCGCATAGATGGAGTAA 60.081 41.667 0.00 0.00 35.26 2.24
2963 3941 4.873827 GTGTTTCCGCATAGATGGAGTAAA 59.126 41.667 0.00 0.00 35.26 2.01
2964 3942 5.527582 GTGTTTCCGCATAGATGGAGTAAAT 59.472 40.000 0.00 0.00 35.26 1.40
2965 3943 6.038271 GTGTTTCCGCATAGATGGAGTAAATT 59.962 38.462 0.00 0.00 35.26 1.82
2966 3944 6.038161 TGTTTCCGCATAGATGGAGTAAATTG 59.962 38.462 0.00 0.00 35.26 2.32
2967 3945 4.065088 TCCGCATAGATGGAGTAAATTGC 58.935 43.478 0.00 0.00 0.00 3.56
2968 3946 3.814842 CCGCATAGATGGAGTAAATTGCA 59.185 43.478 0.00 0.00 0.00 4.08
2969 3947 4.319766 CCGCATAGATGGAGTAAATTGCAC 60.320 45.833 0.00 0.00 0.00 4.57
2970 3948 4.273235 CGCATAGATGGAGTAAATTGCACA 59.727 41.667 0.00 0.00 0.00 4.57
2971 3949 5.559608 CGCATAGATGGAGTAAATTGCACAG 60.560 44.000 0.00 0.00 0.00 3.66
2972 3950 5.528690 GCATAGATGGAGTAAATTGCACAGA 59.471 40.000 0.00 0.00 0.00 3.41
2973 3951 6.038603 GCATAGATGGAGTAAATTGCACAGAA 59.961 38.462 0.00 0.00 0.00 3.02
2974 3952 7.637229 CATAGATGGAGTAAATTGCACAGAAG 58.363 38.462 0.00 0.00 0.00 2.85
2975 3953 5.564550 AGATGGAGTAAATTGCACAGAAGT 58.435 37.500 0.00 0.00 0.00 3.01
2976 3954 6.711277 AGATGGAGTAAATTGCACAGAAGTA 58.289 36.000 0.00 0.00 0.00 2.24
2977 3955 6.595716 AGATGGAGTAAATTGCACAGAAGTAC 59.404 38.462 0.00 0.00 0.00 2.73
2978 3956 5.001232 TGGAGTAAATTGCACAGAAGTACC 58.999 41.667 0.00 0.00 0.00 3.34
2979 3957 5.001232 GGAGTAAATTGCACAGAAGTACCA 58.999 41.667 0.00 0.00 0.00 3.25
2980 3958 5.106673 GGAGTAAATTGCACAGAAGTACCAC 60.107 44.000 0.00 0.00 0.00 4.16
2981 3959 5.373222 AGTAAATTGCACAGAAGTACCACA 58.627 37.500 0.00 0.00 0.00 4.17
2982 3960 5.825679 AGTAAATTGCACAGAAGTACCACAA 59.174 36.000 0.00 0.00 0.00 3.33
2983 3961 5.789643 AAATTGCACAGAAGTACCACAAT 57.210 34.783 0.00 0.00 0.00 2.71
2984 3962 5.789643 AATTGCACAGAAGTACCACAATT 57.210 34.783 0.00 0.00 32.89 2.32
2985 3963 4.566545 TTGCACAGAAGTACCACAATTG 57.433 40.909 3.24 3.24 0.00 2.32
2996 3974 2.855209 CCACAATTGGGGCATTGAAA 57.145 45.000 15.25 0.00 39.57 2.69
2997 3975 2.702261 CCACAATTGGGGCATTGAAAG 58.298 47.619 15.25 0.00 39.57 2.62
2998 3976 2.078392 CACAATTGGGGCATTGAAAGC 58.922 47.619 10.83 0.00 0.00 3.51
2999 3977 1.698532 ACAATTGGGGCATTGAAAGCA 59.301 42.857 10.83 0.00 0.00 3.91
3000 3978 2.289819 ACAATTGGGGCATTGAAAGCAG 60.290 45.455 10.83 0.00 0.00 4.24
3001 3979 1.941377 ATTGGGGCATTGAAAGCAGA 58.059 45.000 0.00 0.00 0.00 4.26
3002 3980 1.941377 TTGGGGCATTGAAAGCAGAT 58.059 45.000 0.00 0.00 0.00 2.90
3003 3981 1.941377 TGGGGCATTGAAAGCAGATT 58.059 45.000 0.00 0.00 0.00 2.40
3004 3982 1.551430 TGGGGCATTGAAAGCAGATTG 59.449 47.619 0.00 0.00 0.00 2.67
3005 3983 1.134610 GGGGCATTGAAAGCAGATTGG 60.135 52.381 0.00 0.00 0.00 3.16
3006 3984 1.551883 GGGCATTGAAAGCAGATTGGT 59.448 47.619 0.00 0.00 0.00 3.67
3007 3985 2.760092 GGGCATTGAAAGCAGATTGGTA 59.240 45.455 0.00 0.00 0.00 3.25
3008 3986 3.385755 GGGCATTGAAAGCAGATTGGTAT 59.614 43.478 0.00 0.00 0.00 2.73
3009 3987 4.500375 GGGCATTGAAAGCAGATTGGTATC 60.500 45.833 0.00 0.00 0.00 2.24
3010 3988 4.098349 GGCATTGAAAGCAGATTGGTATCA 59.902 41.667 0.00 0.00 32.95 2.15
3011 3989 5.394443 GGCATTGAAAGCAGATTGGTATCAA 60.394 40.000 0.00 0.00 37.28 2.57
3012 3990 5.747197 GCATTGAAAGCAGATTGGTATCAAG 59.253 40.000 0.00 0.00 36.19 3.02
3013 3991 6.405065 GCATTGAAAGCAGATTGGTATCAAGA 60.405 38.462 0.00 0.00 36.19 3.02
3014 3992 7.683704 GCATTGAAAGCAGATTGGTATCAAGAT 60.684 37.037 0.00 0.00 36.19 2.40
3015 3993 7.707624 TTGAAAGCAGATTGGTATCAAGATT 57.292 32.000 0.00 0.00 36.19 2.40
3016 3994 7.092137 TGAAAGCAGATTGGTATCAAGATTG 57.908 36.000 0.00 0.00 36.19 2.67
3017 3995 6.095860 TGAAAGCAGATTGGTATCAAGATTGG 59.904 38.462 0.00 0.00 36.19 3.16
3018 3996 5.121380 AGCAGATTGGTATCAAGATTGGT 57.879 39.130 0.00 0.00 36.19 3.67
3019 3997 6.252599 AGCAGATTGGTATCAAGATTGGTA 57.747 37.500 0.00 0.00 36.19 3.25
3020 3998 6.662755 AGCAGATTGGTATCAAGATTGGTAA 58.337 36.000 0.00 0.00 36.19 2.85
3021 3999 7.293073 AGCAGATTGGTATCAAGATTGGTAAT 58.707 34.615 0.00 0.00 36.19 1.89
3022 4000 7.781693 AGCAGATTGGTATCAAGATTGGTAATT 59.218 33.333 0.00 0.00 36.19 1.40
3023 4001 8.416329 GCAGATTGGTATCAAGATTGGTAATTT 58.584 33.333 0.00 0.00 36.19 1.82
3029 4007 9.233649 TGGTATCAAGATTGGTAATTTTTACGT 57.766 29.630 0.00 0.00 0.00 3.57
3030 4008 9.498307 GGTATCAAGATTGGTAATTTTTACGTG 57.502 33.333 0.00 0.00 0.00 4.49
3033 4011 8.155821 TCAAGATTGGTAATTTTTACGTGTCA 57.844 30.769 0.00 0.00 0.00 3.58
3034 4012 8.286800 TCAAGATTGGTAATTTTTACGTGTCAG 58.713 33.333 0.00 0.00 0.00 3.51
3035 4013 7.739498 AGATTGGTAATTTTTACGTGTCAGT 57.261 32.000 0.00 0.00 0.00 3.41
3036 4014 8.836268 AGATTGGTAATTTTTACGTGTCAGTA 57.164 30.769 0.00 0.00 0.00 2.74
3037 4015 8.715088 AGATTGGTAATTTTTACGTGTCAGTAC 58.285 33.333 0.00 0.00 0.00 2.73
3038 4016 6.783892 TGGTAATTTTTACGTGTCAGTACC 57.216 37.500 0.00 3.56 0.00 3.34
3039 4017 6.286758 TGGTAATTTTTACGTGTCAGTACCA 58.713 36.000 11.71 11.71 36.89 3.25
3040 4018 6.765036 TGGTAATTTTTACGTGTCAGTACCAA 59.235 34.615 12.78 2.05 36.44 3.67
3041 4019 7.071414 GGTAATTTTTACGTGTCAGTACCAAC 58.929 38.462 0.00 0.00 0.00 3.77
3042 4020 6.930667 AATTTTTACGTGTCAGTACCAACT 57.069 33.333 0.00 0.00 35.91 3.16
3043 4021 6.930667 ATTTTTACGTGTCAGTACCAACTT 57.069 33.333 0.00 0.00 31.97 2.66
3044 4022 6.740411 TTTTTACGTGTCAGTACCAACTTT 57.260 33.333 0.00 0.00 31.97 2.66
3045 4023 5.721876 TTTACGTGTCAGTACCAACTTTG 57.278 39.130 0.00 0.00 31.97 2.77
3054 4032 3.373565 CCAACTTTGGGGCGAGGC 61.374 66.667 0.00 0.00 44.70 4.70
3055 4033 3.737172 CAACTTTGGGGCGAGGCG 61.737 66.667 0.00 0.00 0.00 5.52
3056 4034 4.265056 AACTTTGGGGCGAGGCGT 62.265 61.111 0.00 0.00 0.00 5.68
3057 4035 3.785122 AACTTTGGGGCGAGGCGTT 62.785 57.895 0.00 0.00 0.00 4.84
3058 4036 3.737172 CTTTGGGGCGAGGCGTTG 61.737 66.667 0.00 0.00 0.00 4.10
3063 4041 3.972276 GGGCGAGGCGTTGCAAAA 61.972 61.111 19.74 0.00 34.26 2.44
3064 4042 2.026879 GGCGAGGCGTTGCAAAAA 59.973 55.556 19.74 0.00 34.26 1.94
3087 4065 8.986477 AAAAGGCTAAAACTGCAGTTTATATG 57.014 30.769 37.70 27.46 46.47 1.78
3088 4066 7.703058 AAGGCTAAAACTGCAGTTTATATGT 57.297 32.000 37.70 26.27 46.47 2.29
3089 4067 8.801882 AAGGCTAAAACTGCAGTTTATATGTA 57.198 30.769 37.70 26.02 46.47 2.29
3090 4068 8.980481 AGGCTAAAACTGCAGTTTATATGTAT 57.020 30.769 37.70 25.02 46.47 2.29
3091 4069 9.408648 AGGCTAAAACTGCAGTTTATATGTATT 57.591 29.630 37.70 24.38 46.47 1.89
3092 4070 9.450807 GGCTAAAACTGCAGTTTATATGTATTG 57.549 33.333 37.70 23.71 46.47 1.90
3097 4075 7.792374 ACTGCAGTTTATATGTATTGACAGG 57.208 36.000 15.25 0.00 39.50 4.00
3098 4076 6.767902 ACTGCAGTTTATATGTATTGACAGGG 59.232 38.462 15.25 0.00 39.50 4.45
3099 4077 6.894682 TGCAGTTTATATGTATTGACAGGGA 58.105 36.000 0.00 0.00 39.50 4.20
3100 4078 7.342581 TGCAGTTTATATGTATTGACAGGGAA 58.657 34.615 0.00 0.00 39.50 3.97
3101 4079 7.998383 TGCAGTTTATATGTATTGACAGGGAAT 59.002 33.333 0.00 0.00 39.50 3.01
3102 4080 8.507249 GCAGTTTATATGTATTGACAGGGAATC 58.493 37.037 0.00 0.00 39.50 2.52
3103 4081 9.784531 CAGTTTATATGTATTGACAGGGAATCT 57.215 33.333 0.00 0.00 39.50 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
324 326 6.419116 GTCTTTCTTTGCAATGTTCTTCTTCC 59.581 38.462 11.67 0.00 0.00 3.46
1130 1153 6.479006 AGATCAACACCATCTCTGAATTTCA 58.521 36.000 0.00 0.00 0.00 2.69
1285 1311 8.579850 AAAGGAACATATTTTCACTCATGCTA 57.420 30.769 4.11 0.00 0.00 3.49
1593 1631 3.552604 GCAAGTACGCCTTCAAATTCA 57.447 42.857 0.00 0.00 0.00 2.57
1668 1722 1.495069 GTTGCTTGCGACAGAGCTC 59.505 57.895 5.27 5.27 39.60 4.09
1767 1824 1.207089 CGTTATGCTCCTCCAAGGTGA 59.793 52.381 0.00 0.00 36.53 4.02
1823 1897 0.608640 GTCGTCTCCAATGGTCCTGT 59.391 55.000 0.00 0.00 0.00 4.00
2560 3393 9.396022 AGAGTTTTTGTTTCATCTTCTGAACTA 57.604 29.630 0.00 0.00 43.54 2.24
2703 3536 1.396301 CAGTGATCTTTCCTCGCTTGC 59.604 52.381 0.00 0.00 31.28 4.01
2705 3538 1.277557 AGCAGTGATCTTTCCTCGCTT 59.722 47.619 0.00 0.00 31.28 4.68
2843 3816 7.695820 ACAAAAACATGTGGTGAATTTTGATG 58.304 30.769 26.32 10.68 43.08 3.07
2914 3892 5.186256 GAGATTCCCTCCTTTCTTCCTTT 57.814 43.478 0.00 0.00 35.87 3.11
2915 3893 4.853468 GAGATTCCCTCCTTTCTTCCTT 57.147 45.455 0.00 0.00 35.87 3.36
2929 3907 1.739067 CGGAAACACAGGGAGATTCC 58.261 55.000 0.00 0.00 36.92 3.01
2930 3908 1.087501 GCGGAAACACAGGGAGATTC 58.912 55.000 0.00 0.00 0.00 2.52
2931 3909 0.400213 TGCGGAAACACAGGGAGATT 59.600 50.000 0.00 0.00 0.00 2.40
2932 3910 0.620556 ATGCGGAAACACAGGGAGAT 59.379 50.000 0.00 0.00 0.00 2.75
2933 3911 1.207089 CTATGCGGAAACACAGGGAGA 59.793 52.381 0.00 0.00 0.00 3.71
2934 3912 1.207089 TCTATGCGGAAACACAGGGAG 59.793 52.381 0.00 0.00 0.00 4.30
2935 3913 1.271856 TCTATGCGGAAACACAGGGA 58.728 50.000 0.00 0.00 0.00 4.20
2936 3914 1.942657 CATCTATGCGGAAACACAGGG 59.057 52.381 0.00 0.00 0.00 4.45
2937 3915 1.942657 CCATCTATGCGGAAACACAGG 59.057 52.381 0.00 0.00 0.00 4.00
2938 3916 2.868583 CTCCATCTATGCGGAAACACAG 59.131 50.000 0.00 0.00 0.00 3.66
2939 3917 2.236146 ACTCCATCTATGCGGAAACACA 59.764 45.455 0.00 0.00 0.00 3.72
2940 3918 2.906354 ACTCCATCTATGCGGAAACAC 58.094 47.619 0.00 0.00 0.00 3.32
2941 3919 4.746535 TTACTCCATCTATGCGGAAACA 57.253 40.909 0.00 0.00 0.00 2.83
2942 3920 6.430451 CAATTTACTCCATCTATGCGGAAAC 58.570 40.000 0.00 0.00 0.00 2.78
2943 3921 5.008613 GCAATTTACTCCATCTATGCGGAAA 59.991 40.000 0.00 0.00 0.00 3.13
2944 3922 4.515191 GCAATTTACTCCATCTATGCGGAA 59.485 41.667 0.00 0.00 0.00 4.30
2945 3923 4.065088 GCAATTTACTCCATCTATGCGGA 58.935 43.478 0.00 0.00 0.00 5.54
2946 3924 3.814842 TGCAATTTACTCCATCTATGCGG 59.185 43.478 0.00 0.00 35.40 5.69
2947 3925 4.273235 TGTGCAATTTACTCCATCTATGCG 59.727 41.667 0.00 0.00 35.40 4.73
2948 3926 5.528690 TCTGTGCAATTTACTCCATCTATGC 59.471 40.000 0.00 0.00 0.00 3.14
2949 3927 7.281774 ACTTCTGTGCAATTTACTCCATCTATG 59.718 37.037 0.00 0.00 0.00 2.23
2950 3928 7.341805 ACTTCTGTGCAATTTACTCCATCTAT 58.658 34.615 0.00 0.00 0.00 1.98
2951 3929 6.711277 ACTTCTGTGCAATTTACTCCATCTA 58.289 36.000 0.00 0.00 0.00 1.98
2952 3930 5.564550 ACTTCTGTGCAATTTACTCCATCT 58.435 37.500 0.00 0.00 0.00 2.90
2953 3931 5.886960 ACTTCTGTGCAATTTACTCCATC 57.113 39.130 0.00 0.00 0.00 3.51
2954 3932 5.648092 GGTACTTCTGTGCAATTTACTCCAT 59.352 40.000 0.00 0.00 0.00 3.41
2955 3933 5.001232 GGTACTTCTGTGCAATTTACTCCA 58.999 41.667 0.00 0.00 0.00 3.86
2956 3934 5.001232 TGGTACTTCTGTGCAATTTACTCC 58.999 41.667 0.00 0.00 0.00 3.85
2957 3935 5.468746 TGTGGTACTTCTGTGCAATTTACTC 59.531 40.000 0.00 0.00 0.00 2.59
2958 3936 5.373222 TGTGGTACTTCTGTGCAATTTACT 58.627 37.500 0.00 0.00 0.00 2.24
2959 3937 5.682943 TGTGGTACTTCTGTGCAATTTAC 57.317 39.130 0.00 0.00 0.00 2.01
2960 3938 6.892658 ATTGTGGTACTTCTGTGCAATTTA 57.107 33.333 0.00 0.00 0.00 1.40
2961 3939 5.789643 ATTGTGGTACTTCTGTGCAATTT 57.210 34.783 0.00 0.00 0.00 1.82
2962 3940 5.509501 CCAATTGTGGTACTTCTGTGCAATT 60.510 40.000 4.43 0.00 40.42 2.32
2963 3941 4.022068 CCAATTGTGGTACTTCTGTGCAAT 60.022 41.667 4.43 0.00 40.42 3.56
2964 3942 3.317711 CCAATTGTGGTACTTCTGTGCAA 59.682 43.478 4.43 0.00 40.42 4.08
2965 3943 2.884012 CCAATTGTGGTACTTCTGTGCA 59.116 45.455 4.43 0.00 40.42 4.57
2966 3944 2.228822 CCCAATTGTGGTACTTCTGTGC 59.771 50.000 4.43 0.00 44.30 4.57
2967 3945 2.819608 CCCCAATTGTGGTACTTCTGTG 59.180 50.000 4.43 0.00 44.30 3.66
2968 3946 2.817839 GCCCCAATTGTGGTACTTCTGT 60.818 50.000 8.84 0.00 44.30 3.41
2969 3947 1.818674 GCCCCAATTGTGGTACTTCTG 59.181 52.381 8.84 0.00 44.30 3.02
2970 3948 1.427368 TGCCCCAATTGTGGTACTTCT 59.573 47.619 8.84 0.00 44.30 2.85
2971 3949 1.917872 TGCCCCAATTGTGGTACTTC 58.082 50.000 8.84 0.00 44.30 3.01
2972 3950 2.566724 CAATGCCCCAATTGTGGTACTT 59.433 45.455 8.84 0.00 44.30 2.24
2973 3951 2.178580 CAATGCCCCAATTGTGGTACT 58.821 47.619 8.84 0.00 44.30 2.73
2974 3952 2.175202 TCAATGCCCCAATTGTGGTAC 58.825 47.619 8.84 3.30 44.30 3.34
2975 3953 2.612285 TCAATGCCCCAATTGTGGTA 57.388 45.000 8.84 4.38 44.30 3.25
2976 3954 1.727062 TTCAATGCCCCAATTGTGGT 58.273 45.000 8.84 0.00 44.30 4.16
2977 3955 2.702261 CTTTCAATGCCCCAATTGTGG 58.298 47.619 2.04 2.04 45.53 4.17
2978 3956 2.078392 GCTTTCAATGCCCCAATTGTG 58.922 47.619 4.43 0.00 38.46 3.33
2979 3957 1.698532 TGCTTTCAATGCCCCAATTGT 59.301 42.857 4.43 0.00 38.46 2.71
2980 3958 2.027929 TCTGCTTTCAATGCCCCAATTG 60.028 45.455 0.00 0.00 38.63 2.32
2981 3959 2.259012 TCTGCTTTCAATGCCCCAATT 58.741 42.857 0.00 0.00 0.00 2.32
2982 3960 1.941377 TCTGCTTTCAATGCCCCAAT 58.059 45.000 0.00 0.00 0.00 3.16
2983 3961 1.941377 ATCTGCTTTCAATGCCCCAA 58.059 45.000 0.00 0.00 0.00 4.12
2984 3962 1.551430 CAATCTGCTTTCAATGCCCCA 59.449 47.619 0.00 0.00 0.00 4.96
2985 3963 1.134610 CCAATCTGCTTTCAATGCCCC 60.135 52.381 0.00 0.00 0.00 5.80
2986 3964 1.551883 ACCAATCTGCTTTCAATGCCC 59.448 47.619 0.00 0.00 0.00 5.36
2987 3965 4.098349 TGATACCAATCTGCTTTCAATGCC 59.902 41.667 0.00 0.00 32.93 4.40
2988 3966 5.252969 TGATACCAATCTGCTTTCAATGC 57.747 39.130 0.00 0.00 32.93 3.56
2989 3967 7.092137 TCTTGATACCAATCTGCTTTCAATG 57.908 36.000 0.00 0.00 32.93 2.82
2990 3968 7.893124 ATCTTGATACCAATCTGCTTTCAAT 57.107 32.000 0.00 0.00 32.93 2.57
2991 3969 7.363181 CCAATCTTGATACCAATCTGCTTTCAA 60.363 37.037 0.00 0.00 32.93 2.69
2992 3970 6.095860 CCAATCTTGATACCAATCTGCTTTCA 59.904 38.462 0.00 0.00 32.93 2.69
2993 3971 6.096001 ACCAATCTTGATACCAATCTGCTTTC 59.904 38.462 0.00 0.00 32.93 2.62
2994 3972 5.954150 ACCAATCTTGATACCAATCTGCTTT 59.046 36.000 0.00 0.00 32.93 3.51
2995 3973 5.513233 ACCAATCTTGATACCAATCTGCTT 58.487 37.500 0.00 0.00 32.93 3.91
2996 3974 5.121380 ACCAATCTTGATACCAATCTGCT 57.879 39.130 0.00 0.00 32.93 4.24
2997 3975 6.942532 TTACCAATCTTGATACCAATCTGC 57.057 37.500 0.00 0.00 32.93 4.26
3003 3981 9.233649 ACGTAAAAATTACCAATCTTGATACCA 57.766 29.630 0.00 0.00 0.00 3.25
3004 3982 9.498307 CACGTAAAAATTACCAATCTTGATACC 57.502 33.333 0.00 0.00 0.00 2.73
3007 3985 8.788806 TGACACGTAAAAATTACCAATCTTGAT 58.211 29.630 0.00 0.00 0.00 2.57
3008 3986 8.155821 TGACACGTAAAAATTACCAATCTTGA 57.844 30.769 0.00 0.00 0.00 3.02
3009 3987 8.073768 ACTGACACGTAAAAATTACCAATCTTG 58.926 33.333 0.00 0.00 0.00 3.02
3010 3988 8.161699 ACTGACACGTAAAAATTACCAATCTT 57.838 30.769 0.00 0.00 0.00 2.40
3011 3989 7.739498 ACTGACACGTAAAAATTACCAATCT 57.261 32.000 0.00 0.00 0.00 2.40
3012 3990 7.959109 GGTACTGACACGTAAAAATTACCAATC 59.041 37.037 0.00 0.00 0.00 2.67
3013 3991 7.444792 TGGTACTGACACGTAAAAATTACCAAT 59.555 33.333 10.19 0.00 34.82 3.16
3014 3992 6.765036 TGGTACTGACACGTAAAAATTACCAA 59.235 34.615 10.19 0.00 34.82 3.67
3015 3993 6.286758 TGGTACTGACACGTAAAAATTACCA 58.713 36.000 9.05 9.05 35.26 3.25
3016 3994 6.783892 TGGTACTGACACGTAAAAATTACC 57.216 37.500 0.00 0.00 0.00 2.85
3017 3995 7.854534 AGTTGGTACTGACACGTAAAAATTAC 58.145 34.615 0.00 0.00 31.99 1.89
3018 3996 8.436046 AAGTTGGTACTGACACGTAAAAATTA 57.564 30.769 0.00 0.00 34.01 1.40
3019 3997 6.930667 AGTTGGTACTGACACGTAAAAATT 57.069 33.333 0.00 0.00 31.99 1.82
3020 3998 6.930667 AAGTTGGTACTGACACGTAAAAAT 57.069 33.333 0.00 0.00 34.01 1.82
3021 3999 6.403418 CCAAAGTTGGTACTGACACGTAAAAA 60.403 38.462 1.63 0.00 43.43 1.94
3022 4000 5.064962 CCAAAGTTGGTACTGACACGTAAAA 59.935 40.000 1.63 0.00 43.43 1.52
3023 4001 4.571580 CCAAAGTTGGTACTGACACGTAAA 59.428 41.667 1.63 0.00 43.43 2.01
3024 4002 4.121317 CCAAAGTTGGTACTGACACGTAA 58.879 43.478 1.63 0.00 43.43 3.18
3025 4003 3.719924 CCAAAGTTGGTACTGACACGTA 58.280 45.455 1.63 0.00 43.43 3.57
3026 4004 2.557317 CCAAAGTTGGTACTGACACGT 58.443 47.619 1.63 0.00 43.43 4.49
3038 4016 3.737172 CGCCTCGCCCCAAAGTTG 61.737 66.667 0.00 0.00 0.00 3.16
3039 4017 3.785122 AACGCCTCGCCCCAAAGTT 62.785 57.895 0.00 0.00 0.00 2.66
3040 4018 4.265056 AACGCCTCGCCCCAAAGT 62.265 61.111 0.00 0.00 0.00 2.66
3041 4019 3.737172 CAACGCCTCGCCCCAAAG 61.737 66.667 0.00 0.00 0.00 2.77
3046 4024 3.492311 TTTTTGCAACGCCTCGCCC 62.492 57.895 0.00 0.00 0.00 6.13
3047 4025 2.026879 TTTTTGCAACGCCTCGCC 59.973 55.556 0.00 0.00 0.00 5.54
3061 4039 9.423061 CATATAAACTGCAGTTTTAGCCTTTTT 57.577 29.630 40.87 21.04 45.07 1.94
3062 4040 8.585018 ACATATAAACTGCAGTTTTAGCCTTTT 58.415 29.630 40.87 21.71 45.07 2.27
3063 4041 8.122472 ACATATAAACTGCAGTTTTAGCCTTT 57.878 30.769 40.87 22.37 45.07 3.11
3064 4042 7.703058 ACATATAAACTGCAGTTTTAGCCTT 57.297 32.000 40.87 23.04 45.07 4.35
3065 4043 8.980481 ATACATATAAACTGCAGTTTTAGCCT 57.020 30.769 40.87 25.45 45.07 4.58
3066 4044 9.450807 CAATACATATAAACTGCAGTTTTAGCC 57.549 33.333 40.87 0.00 45.07 3.93
3071 4049 8.677300 CCTGTCAATACATATAAACTGCAGTTT 58.323 33.333 38.59 38.59 41.87 2.66
3072 4050 7.283127 CCCTGTCAATACATATAAACTGCAGTT 59.717 37.037 26.36 26.36 35.81 3.16
3073 4051 6.767902 CCCTGTCAATACATATAAACTGCAGT 59.232 38.462 15.25 15.25 34.37 4.40
3074 4052 6.992123 TCCCTGTCAATACATATAAACTGCAG 59.008 38.462 13.48 13.48 34.37 4.41
3075 4053 6.894682 TCCCTGTCAATACATATAAACTGCA 58.105 36.000 0.00 0.00 34.37 4.41
3076 4054 7.801716 TTCCCTGTCAATACATATAAACTGC 57.198 36.000 0.00 0.00 34.37 4.40
3077 4055 9.784531 AGATTCCCTGTCAATACATATAAACTG 57.215 33.333 0.00 0.00 34.37 3.16
3078 4056 9.784531 CAGATTCCCTGTCAATACATATAAACT 57.215 33.333 0.00 0.00 38.10 2.66


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

AutoCloner maintained by Alex Coulton.