Multiple sequence alignment - TraesCS2D01G074000

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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 TraesCS2D01G074000 chr2D 100.000 2738 0 0 591 3328 31561864 31559127 0.000000e+00 5057.0
1 TraesCS2D01G074000 chr2D 90.122 1144 108 5 1214 2355 31729628 31728488 0.000000e+00 1482.0
2 TraesCS2D01G074000 chr2D 89.158 1116 121 0 1223 2338 31608109 31606994 0.000000e+00 1391.0
3 TraesCS2D01G074000 chr2D 100.000 394 0 0 1 394 31562454 31562061 0.000000e+00 728.0
4 TraesCS2D01G074000 chr2D 90.578 467 42 2 2795 3260 562486441 562486906 4.720000e-173 617.0
5 TraesCS2D01G074000 chr2D 82.353 102 17 1 676 776 209497405 209497506 1.640000e-13 87.9
6 TraesCS2D01G074000 chrUn 88.798 1946 131 30 867 2794 17252547 17254423 0.000000e+00 2305.0
7 TraesCS2D01G074000 chrUn 89.340 394 30 5 1 393 17249773 17250155 4.990000e-133 484.0
8 TraesCS2D01G074000 chrUn 87.302 252 27 3 623 873 17250199 17250446 1.950000e-72 283.0
9 TraesCS2D01G074000 chr2A 92.333 1513 82 11 858 2346 33344367 33342865 0.000000e+00 2121.0
10 TraesCS2D01G074000 chr2A 89.805 1177 108 11 1214 2386 33563964 33562796 0.000000e+00 1498.0
11 TraesCS2D01G074000 chr2A 89.103 1092 119 0 1223 2314 33382263 33381172 0.000000e+00 1358.0
12 TraesCS2D01G074000 chr2A 91.765 85 7 0 1 85 33347093 33347009 5.830000e-23 119.0
13 TraesCS2D01G074000 chr2B 88.889 1116 124 0 1223 2338 51706581 51705466 0.000000e+00 1375.0
14 TraesCS2D01G074000 chr2B 89.593 615 57 5 2183 2794 51077835 51078445 0.000000e+00 774.0
15 TraesCS2D01G074000 chr2B 91.641 323 26 1 1 323 51069144 51069465 2.360000e-121 446.0
16 TraesCS2D01G074000 chr2B 86.245 269 22 8 625 893 51069503 51069756 9.090000e-71 278.0
17 TraesCS2D01G074000 chr2B 89.671 213 14 2 896 1108 51069729 51069933 7.080000e-67 265.0
18 TraesCS2D01G074000 chr7D 81.366 1025 173 13 1290 2311 154376804 154377813 0.000000e+00 819.0
19 TraesCS2D01G074000 chr7D 91.023 479 34 3 2791 3260 626041710 626041232 3.620000e-179 638.0
20 TraesCS2D01G074000 chr7D 98.485 66 1 0 3261 3326 1754457 1754522 2.100000e-22 117.0
21 TraesCS2D01G074000 chr7D 95.588 68 3 0 3259 3326 105396994 105397061 3.510000e-20 110.0
22 TraesCS2D01G074000 chr7A 80.661 1029 173 17 1290 2311 156267808 156268817 0.000000e+00 774.0
23 TraesCS2D01G074000 chr7A 87.945 506 58 3 2784 3288 114354226 114353723 7.950000e-166 593.0
24 TraesCS2D01G074000 chr7A 96.970 66 2 0 3261 3326 79352363 79352298 9.760000e-21 111.0
25 TraesCS2D01G074000 chr7A 95.455 66 3 0 3261 3326 730184078 730184013 4.540000e-19 106.0
26 TraesCS2D01G074000 chr1D 92.719 467 31 3 2795 3260 115640459 115640923 0.000000e+00 671.0
27 TraesCS2D01G074000 chr1D 90.446 471 41 4 2791 3260 16141450 16141917 4.720000e-173 617.0
28 TraesCS2D01G074000 chr6D 92.077 467 33 3 2795 3260 15630816 15631279 0.000000e+00 654.0
29 TraesCS2D01G074000 chr6D 97.059 68 2 0 3261 3328 13832990 13832923 7.540000e-22 115.0
30 TraesCS2D01G074000 chr6D 95.714 70 2 1 3257 3326 392601761 392601829 9.760000e-21 111.0
31 TraesCS2D01G074000 chr4D 91.898 469 37 1 2793 3260 131960293 131960761 0.000000e+00 654.0
32 TraesCS2D01G074000 chr6A 91.006 467 40 2 2795 3260 3595009 3594544 2.180000e-176 628.0
33 TraesCS2D01G074000 chr1A 90.446 471 39 5 2794 3260 313597655 313598123 1.700000e-172 616.0
34 TraesCS2D01G074000 chr5D 75.196 766 156 30 1495 2243 353432502 353433250 6.880000e-87 331.0
35 TraesCS2D01G074000 chr5D 98.485 66 1 0 3261 3326 489734619 489734684 2.100000e-22 117.0
36 TraesCS2D01G074000 chr3A 94.203 69 4 0 3258 3326 49174395 49174463 4.540000e-19 106.0
37 TraesCS2D01G074000 chr3A 93.056 72 4 1 3257 3328 735303680 735303610 1.630000e-18 104.0
38 TraesCS2D01G074000 chr3D 81.203 133 13 3 262 393 128924915 128925036 2.730000e-16 97.1
39 TraesCS2D01G074000 chr7B 90.909 55 4 1 120 173 328803619 328803673 4.610000e-09 73.1
40 TraesCS2D01G074000 chr5B 84.746 59 9 0 116 174 697333643 697333585 3.590000e-05 60.2


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 TraesCS2D01G074000 chr2D 31559127 31562454 3327 True 2892.500000 5057 100.000000 1 3328 2 chr2D.!!$R3 3327
1 TraesCS2D01G074000 chr2D 31728488 31729628 1140 True 1482.000000 1482 90.122000 1214 2355 1 chr2D.!!$R2 1141
2 TraesCS2D01G074000 chr2D 31606994 31608109 1115 True 1391.000000 1391 89.158000 1223 2338 1 chr2D.!!$R1 1115
3 TraesCS2D01G074000 chrUn 17249773 17254423 4650 False 1024.000000 2305 88.480000 1 2794 3 chrUn.!!$F1 2793
4 TraesCS2D01G074000 chr2A 33562796 33563964 1168 True 1498.000000 1498 89.805000 1214 2386 1 chr2A.!!$R2 1172
5 TraesCS2D01G074000 chr2A 33381172 33382263 1091 True 1358.000000 1358 89.103000 1223 2314 1 chr2A.!!$R1 1091
6 TraesCS2D01G074000 chr2A 33342865 33347093 4228 True 1120.000000 2121 92.049000 1 2346 2 chr2A.!!$R3 2345
7 TraesCS2D01G074000 chr2B 51705466 51706581 1115 True 1375.000000 1375 88.889000 1223 2338 1 chr2B.!!$R1 1115
8 TraesCS2D01G074000 chr2B 51077835 51078445 610 False 774.000000 774 89.593000 2183 2794 1 chr2B.!!$F1 611
9 TraesCS2D01G074000 chr2B 51069144 51069933 789 False 329.666667 446 89.185667 1 1108 3 chr2B.!!$F2 1107
10 TraesCS2D01G074000 chr7D 154376804 154377813 1009 False 819.000000 819 81.366000 1290 2311 1 chr7D.!!$F3 1021
11 TraesCS2D01G074000 chr7A 156267808 156268817 1009 False 774.000000 774 80.661000 1290 2311 1 chr7A.!!$F1 1021
12 TraesCS2D01G074000 chr7A 114353723 114354226 503 True 593.000000 593 87.945000 2784 3288 1 chr7A.!!$R2 504
13 TraesCS2D01G074000 chr5D 353432502 353433250 748 False 331.000000 331 75.196000 1495 2243 1 chr5D.!!$F1 748

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
880 4974 0.616395 TCCCGGCACTTACTCATGGA 60.616 55.0 0.00 0.00 0.0 3.41 F
1056 5155 0.529378 CAGAAAGGCCATGGACAAGC 59.471 55.0 22.78 8.01 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 6091 0.249073 GACGACGCATCATGTAGGCT 60.249 55.0 0.00 0.0 30.97 4.58 R
2905 7044 0.029433 TGAGACGCGCTACTGCTATG 59.971 55.0 5.73 0.0 36.97 2.23 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
65 66 6.698329 CACAATCACACACAAAATTCAGACAT 59.302 34.615 0.00 0.00 0.00 3.06
103 1878 6.942976 AGTCTCCGATCCAAATTAACTAACA 58.057 36.000 0.00 0.00 0.00 2.41
215 1990 5.411977 TCAATTTAAACGGTTATTCTCGGCA 59.588 36.000 0.00 0.00 0.00 5.69
226 2001 2.839486 TTCTCGGCACTTGACTCATT 57.161 45.000 0.00 0.00 0.00 2.57
301 2077 6.705825 ACAGTTAACTGAATTTCAAATTGGGC 59.294 34.615 36.14 0.00 46.59 5.36
307 2083 4.885413 TGAATTTCAAATTGGGCTCAGTG 58.115 39.130 0.00 0.00 0.00 3.66
310 2086 1.909700 TCAAATTGGGCTCAGTGGAC 58.090 50.000 0.00 0.00 0.00 4.02
323 2099 4.697514 CTCAGTGGACTTTTGAGAGTTCA 58.302 43.478 0.00 0.00 40.54 3.18
327 2103 3.808728 TGGACTTTTGAGAGTTCACTGG 58.191 45.455 0.00 0.00 30.18 4.00
328 2104 3.454447 TGGACTTTTGAGAGTTCACTGGA 59.546 43.478 0.00 0.00 30.18 3.86
329 2105 4.061596 GGACTTTTGAGAGTTCACTGGAG 58.938 47.826 0.00 0.00 31.71 3.86
330 2106 4.443598 GGACTTTTGAGAGTTCACTGGAGT 60.444 45.833 0.00 0.00 31.71 3.85
331 2107 5.104259 ACTTTTGAGAGTTCACTGGAGTT 57.896 39.130 0.00 0.00 31.71 3.01
332 2108 5.501156 ACTTTTGAGAGTTCACTGGAGTTT 58.499 37.500 0.00 0.00 31.71 2.66
367 2143 0.988063 GAAGAAGGAAGGGGCTCACT 59.012 55.000 0.00 0.00 0.00 3.41
607 2383 2.908796 GTTCTAGGGAAGGCGGGG 59.091 66.667 0.00 0.00 31.46 5.73
608 2384 3.087906 TTCTAGGGAAGGCGGGGC 61.088 66.667 0.00 0.00 0.00 5.80
685 2671 2.564947 GGTCAGCTGAGGAAGAAGAAGA 59.435 50.000 18.89 0.00 0.00 2.87
686 2672 3.007398 GGTCAGCTGAGGAAGAAGAAGAA 59.993 47.826 18.89 0.00 0.00 2.52
687 2673 4.244862 GTCAGCTGAGGAAGAAGAAGAAG 58.755 47.826 18.89 0.00 0.00 2.85
695 2681 3.847184 AGGAAGAAGAAGAAGGGTTAGGG 59.153 47.826 0.00 0.00 0.00 3.53
697 2683 4.288887 GGAAGAAGAAGAAGGGTTAGGGAA 59.711 45.833 0.00 0.00 0.00 3.97
698 2684 5.044772 GGAAGAAGAAGAAGGGTTAGGGAAT 60.045 44.000 0.00 0.00 0.00 3.01
726 2712 4.079980 TCTTCATCCAACGGTCTGAAAA 57.920 40.909 0.00 0.00 30.15 2.29
728 2714 3.762407 TCATCCAACGGTCTGAAAAGA 57.238 42.857 0.00 0.00 0.00 2.52
738 2724 4.202264 ACGGTCTGAAAAGATTGACTGACT 60.202 41.667 7.65 0.00 38.68 3.41
776 2763 2.283298 CGACTTGCATGTAGCCATTCT 58.717 47.619 5.05 0.00 44.83 2.40
789 2776 8.653338 CATGTAGCCATTCTCTTTTTGAATTTG 58.347 33.333 0.00 0.00 32.47 2.32
880 4974 0.616395 TCCCGGCACTTACTCATGGA 60.616 55.000 0.00 0.00 0.00 3.41
907 5001 6.807789 AGTGAAGCTATAGGCACTTACTAAC 58.192 40.000 1.04 0.00 44.79 2.34
965 5059 4.293415 CAACCACACAAAAGAGAAGATGC 58.707 43.478 0.00 0.00 0.00 3.91
1040 5139 2.441375 TCAAACATCCTTGTCCACCAGA 59.559 45.455 0.00 0.00 34.06 3.86
1056 5155 0.529378 CAGAAAGGCCATGGACAAGC 59.471 55.000 22.78 8.01 0.00 4.01
1132 5250 6.016860 ACGTACATATGTACTTCAGGCGAATA 60.017 38.462 32.67 3.20 46.43 1.75
1169 5287 7.636150 AGTGTACGTAGGACTGTATAAATGT 57.364 36.000 0.00 0.00 0.00 2.71
1462 5580 4.451150 GTGCTGCGACATCCGGGA 62.451 66.667 0.00 0.00 39.04 5.14
1772 5890 2.445845 CGGAGCCCCTACCATGGA 60.446 66.667 21.47 0.67 0.00 3.41
2054 6172 0.747255 ATGACCTCTTCGCGCACTAT 59.253 50.000 8.75 0.00 0.00 2.12
2249 6367 2.920912 AAGGCCCACGAACGGAGA 60.921 61.111 0.00 0.00 0.00 3.71
2296 6414 3.588842 CCCATCCCATTTAGCTGGATCTA 59.411 47.826 0.00 0.00 36.76 1.98
2300 6418 5.489792 TCCCATTTAGCTGGATCTATGAC 57.510 43.478 0.00 0.00 38.69 3.06
2321 6439 2.388232 GCCCGTCAACATCACCGTC 61.388 63.158 0.00 0.00 0.00 4.79
2489 6626 8.461249 AGTCGTGAGTTATGGTATTGTACTAT 57.539 34.615 0.00 0.00 34.14 2.12
2585 6722 6.829298 TGTATGTCTTTTTGTCCCTGTAACAA 59.171 34.615 0.00 0.00 34.93 2.83
2727 6865 2.291540 CCATTTCCCACCATGTACCACT 60.292 50.000 0.00 0.00 0.00 4.00
2728 6866 2.577606 TTTCCCACCATGTACCACTG 57.422 50.000 0.00 0.00 0.00 3.66
2731 6869 1.073125 TCCCACCATGTACCACTGTTG 59.927 52.381 0.00 0.00 0.00 3.33
2771 6909 2.158385 TCCCTCCTCTATCTGCCTCTTC 60.158 54.545 0.00 0.00 0.00 2.87
2778 6916 0.175760 TATCTGCCTCTTCGGTGTGC 59.824 55.000 0.00 0.00 34.25 4.57
2837 6975 3.762288 ACACAGAATCTTACCAGTAGCGA 59.238 43.478 0.00 0.00 0.00 4.93
2847 6986 2.490991 ACCAGTAGCGAGGACAAAAAC 58.509 47.619 0.00 0.00 0.00 2.43
2859 6998 3.746492 AGGACAAAAACAAGCGCTACTAG 59.254 43.478 12.05 3.65 0.00 2.57
2866 7005 7.601508 ACAAAAACAAGCGCTACTAGTACTTAT 59.398 33.333 12.05 0.00 0.00 1.73
2867 7006 7.752557 AAAACAAGCGCTACTAGTACTTATC 57.247 36.000 12.05 0.00 0.00 1.75
2869 7008 6.062434 ACAAGCGCTACTAGTACTTATCAG 57.938 41.667 12.05 0.00 0.00 2.90
2891 7030 4.560856 GCGTGGCAACCAAACGCA 62.561 61.111 13.87 0.00 44.64 5.24
2903 7042 0.867746 CAAACGCACTGCAGCTAAGA 59.132 50.000 15.27 0.00 0.00 2.10
2905 7044 1.363744 AACGCACTGCAGCTAAGATC 58.636 50.000 15.27 0.00 0.00 2.75
2906 7045 0.247460 ACGCACTGCAGCTAAGATCA 59.753 50.000 15.27 0.00 0.00 2.92
2926 7065 2.179517 GCAGTAGCGCGTCTCAGT 59.820 61.111 8.43 0.00 0.00 3.41
2934 7073 1.347817 GCGCGTCTCAGTGAAGAAGG 61.348 60.000 8.43 0.00 0.00 3.46
2951 7090 5.763876 AGAAGGGCTACAACTACAATTCT 57.236 39.130 0.00 0.00 0.00 2.40
2955 7094 5.278061 AGGGCTACAACTACAATTCTCCTA 58.722 41.667 0.00 0.00 0.00 2.94
2963 7102 7.736893 ACAACTACAATTCTCCTACTGTTCTT 58.263 34.615 0.00 0.00 0.00 2.52
2973 7112 2.171448 CCTACTGTTCTTGCCAGGCTAT 59.829 50.000 14.15 0.00 34.16 2.97
2988 7127 4.142359 CCAGGCTATCAATAGTAGTAGCGG 60.142 50.000 0.00 0.00 40.24 5.52
2996 7135 4.280174 TCAATAGTAGTAGCGGGCTTAAGG 59.720 45.833 4.29 0.00 0.00 2.69
2999 7138 2.694109 AGTAGTAGCGGGCTTAAGGAAG 59.306 50.000 4.29 0.00 35.60 3.46
3016 7155 4.527157 GGCGCGCTGCTGCTAAAG 62.527 66.667 32.29 3.44 45.43 1.85
3026 7165 3.251004 GCTGCTGCTAAAGTTGTTGTAGT 59.749 43.478 8.53 0.00 36.03 2.73
3029 7168 4.959149 GCTGCTAAAGTTGTTGTAGTAGC 58.041 43.478 6.64 6.64 43.25 3.58
3036 7175 5.399604 AAGTTGTTGTAGTAGCGTGTTTC 57.600 39.130 0.00 0.00 0.00 2.78
3055 7194 0.388649 CACGGAGAAAGCGCTACTGT 60.389 55.000 12.05 11.24 0.00 3.55
3124 7263 9.777297 TGAAAATGAAAGAAATAGAAAAAGGGG 57.223 29.630 0.00 0.00 0.00 4.79
3184 7323 7.946655 AAAAGAAAAATAAAGGAGAAAGGCG 57.053 32.000 0.00 0.00 0.00 5.52
3223 7362 2.232452 CAGGACAGGCGCTATAGCTAAT 59.768 50.000 21.98 4.99 39.32 1.73
3245 7384 3.361443 GCAGTAGCGTGTTTTTCCG 57.639 52.632 0.00 0.00 0.00 4.30
3262 7401 2.666526 GGCCAGCGCTATAGCCAC 60.667 66.667 30.10 11.37 45.07 5.01
3264 7403 1.666011 GCCAGCGCTATAGCCACTA 59.334 57.895 19.00 0.00 37.91 2.74
3265 7404 0.389166 GCCAGCGCTATAGCCACTAG 60.389 60.000 19.00 10.68 37.91 2.57
3266 7405 0.962489 CCAGCGCTATAGCCACTAGT 59.038 55.000 19.00 0.00 37.91 2.57
3267 7406 2.160205 CCAGCGCTATAGCCACTAGTA 58.840 52.381 19.00 0.00 37.91 1.82
3268 7407 2.162608 CCAGCGCTATAGCCACTAGTAG 59.837 54.545 19.00 3.53 37.91 2.57
3271 7410 4.023107 CAGCGCTATAGCCACTAGTAGAAA 60.023 45.833 19.00 0.00 37.91 2.52
3273 7412 5.068723 AGCGCTATAGCCACTAGTAGAAAAA 59.931 40.000 19.00 0.00 37.91 1.94
3274 7413 5.402867 GCGCTATAGCCACTAGTAGAAAAAG 59.597 44.000 19.00 0.32 37.91 2.27
3276 7415 6.224584 GCTATAGCCACTAGTAGAAAAAGGG 58.775 44.000 14.13 0.00 34.31 3.95
3277 7416 5.632034 ATAGCCACTAGTAGAAAAAGGGG 57.368 43.478 3.59 0.00 36.84 4.79
3282 7421 4.700692 CCACTAGTAGAAAAAGGGGCTTTC 59.299 45.833 3.59 0.00 31.99 2.62
3283 7422 4.392138 CACTAGTAGAAAAAGGGGCTTTCG 59.608 45.833 3.59 0.00 37.76 3.46
3284 7423 3.503800 AGTAGAAAAAGGGGCTTTCGT 57.496 42.857 0.00 0.00 37.76 3.85
3285 7424 3.828921 AGTAGAAAAAGGGGCTTTCGTT 58.171 40.909 0.00 0.00 37.76 3.85
3286 7425 3.568430 AGTAGAAAAAGGGGCTTTCGTTG 59.432 43.478 0.00 0.00 37.76 4.10
3287 7426 1.686587 AGAAAAAGGGGCTTTCGTTGG 59.313 47.619 0.00 0.00 37.76 3.77
3288 7427 0.756294 AAAAAGGGGCTTTCGTTGGG 59.244 50.000 0.00 0.00 31.99 4.12
3289 7428 1.118965 AAAAGGGGCTTTCGTTGGGG 61.119 55.000 0.00 0.00 31.99 4.96
3290 7429 4.678743 AGGGGCTTTCGTTGGGGC 62.679 66.667 0.00 0.00 0.00 5.80
3292 7431 4.678743 GGGCTTTCGTTGGGGCCT 62.679 66.667 0.84 0.00 43.62 5.19
3293 7432 3.373565 GGCTTTCGTTGGGGCCTG 61.374 66.667 0.84 0.00 41.20 4.85
3294 7433 3.373565 GCTTTCGTTGGGGCCTGG 61.374 66.667 0.84 0.00 0.00 4.45
3295 7434 3.373565 CTTTCGTTGGGGCCTGGC 61.374 66.667 11.05 11.05 0.00 4.85
3306 7445 3.939564 GCCTGGCCAACCCATTAG 58.060 61.111 7.01 0.00 44.33 1.73
3307 7446 1.000359 GCCTGGCCAACCCATTAGT 60.000 57.895 7.01 0.00 44.33 2.24
3308 7447 1.037579 GCCTGGCCAACCCATTAGTC 61.038 60.000 7.01 0.00 44.33 2.59
3309 7448 0.395724 CCTGGCCAACCCATTAGTCC 60.396 60.000 7.01 0.00 44.33 3.85
3310 7449 0.395724 CTGGCCAACCCATTAGTCCC 60.396 60.000 7.01 0.00 44.33 4.46
3311 7450 1.453197 GGCCAACCCATTAGTCCCG 60.453 63.158 0.00 0.00 0.00 5.14
3312 7451 1.453197 GCCAACCCATTAGTCCCGG 60.453 63.158 0.00 0.00 0.00 5.73
3313 7452 1.996086 CCAACCCATTAGTCCCGGT 59.004 57.895 0.00 0.00 0.00 5.28
3314 7453 0.330267 CCAACCCATTAGTCCCGGTT 59.670 55.000 0.00 0.00 39.18 4.44
3315 7454 1.680860 CCAACCCATTAGTCCCGGTTC 60.681 57.143 0.00 0.00 36.45 3.62
3316 7455 1.280998 CAACCCATTAGTCCCGGTTCT 59.719 52.381 0.00 0.15 36.45 3.01
3317 7456 1.665137 ACCCATTAGTCCCGGTTCTT 58.335 50.000 0.00 0.00 0.00 2.52
3318 7457 2.836667 ACCCATTAGTCCCGGTTCTTA 58.163 47.619 0.00 0.00 0.00 2.10
3319 7458 3.390819 ACCCATTAGTCCCGGTTCTTAT 58.609 45.455 0.00 0.00 0.00 1.73
3320 7459 4.559726 ACCCATTAGTCCCGGTTCTTATA 58.440 43.478 0.00 0.00 0.00 0.98
3321 7460 4.346127 ACCCATTAGTCCCGGTTCTTATAC 59.654 45.833 0.00 0.00 0.00 1.47
3322 7461 4.553323 CCATTAGTCCCGGTTCTTATACG 58.447 47.826 0.00 0.00 0.00 3.06
3323 7462 4.279169 CCATTAGTCCCGGTTCTTATACGA 59.721 45.833 0.00 0.00 0.00 3.43
3324 7463 5.221303 CCATTAGTCCCGGTTCTTATACGAA 60.221 44.000 0.00 0.00 0.00 3.85
3325 7464 3.790152 AGTCCCGGTTCTTATACGAAC 57.210 47.619 12.48 12.48 41.91 3.95
3326 7465 3.359950 AGTCCCGGTTCTTATACGAACT 58.640 45.455 18.40 0.00 42.20 3.01
3327 7466 3.129988 AGTCCCGGTTCTTATACGAACTG 59.870 47.826 19.26 19.26 45.50 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.590850 AGAAAGGGCAAAATGAGTGAAC 57.409 40.909 0.00 0.00 0.00 3.18
65 66 7.068962 TGGATCGGAGACTACATTTTGTATACA 59.931 37.037 0.08 0.08 42.51 2.29
103 1878 3.780626 ACTAAAGCTGACCTGAGGTAGT 58.219 45.455 2.97 0.00 35.25 2.73
159 1934 5.879223 ACTTTTCTTCGTACTCTCTCCGATA 59.121 40.000 0.00 0.00 0.00 2.92
201 1976 1.659098 GTCAAGTGCCGAGAATAACCG 59.341 52.381 0.00 0.00 0.00 4.44
215 1990 3.562973 CAGCTTCACACAATGAGTCAAGT 59.437 43.478 0.00 0.00 38.99 3.16
226 2001 6.048732 TGATTTATAGACCAGCTTCACACA 57.951 37.500 0.00 0.00 0.00 3.72
301 2077 4.509600 GTGAACTCTCAAAAGTCCACTGAG 59.490 45.833 0.00 0.00 38.34 3.35
307 2083 4.061596 CTCCAGTGAACTCTCAAAAGTCC 58.938 47.826 0.00 0.00 31.88 3.85
310 2086 5.731686 GCAAACTCCAGTGAACTCTCAAAAG 60.732 44.000 0.00 0.00 31.88 2.27
323 2099 2.750350 CCTCCGGCAAACTCCAGT 59.250 61.111 0.00 0.00 0.00 4.00
324 2100 2.045926 CCCTCCGGCAAACTCCAG 60.046 66.667 0.00 0.00 0.00 3.86
325 2101 2.124507 CTTCCCTCCGGCAAACTCCA 62.125 60.000 0.00 0.00 0.00 3.86
326 2102 1.377333 CTTCCCTCCGGCAAACTCC 60.377 63.158 0.00 0.00 0.00 3.85
327 2103 0.036306 TTCTTCCCTCCGGCAAACTC 59.964 55.000 0.00 0.00 0.00 3.01
328 2104 0.476771 TTTCTTCCCTCCGGCAAACT 59.523 50.000 0.00 0.00 0.00 2.66
329 2105 0.881796 CTTTCTTCCCTCCGGCAAAC 59.118 55.000 0.00 0.00 0.00 2.93
330 2106 0.768622 TCTTTCTTCCCTCCGGCAAA 59.231 50.000 0.00 0.00 0.00 3.68
331 2107 0.768622 TTCTTTCTTCCCTCCGGCAA 59.231 50.000 0.00 0.00 0.00 4.52
332 2108 0.324943 CTTCTTTCTTCCCTCCGGCA 59.675 55.000 0.00 0.00 0.00 5.69
349 2125 0.695347 CAGTGAGCCCCTTCCTTCTT 59.305 55.000 0.00 0.00 0.00 2.52
367 2143 1.225694 AGATAATGGGGTAGCCCTCCA 59.774 52.381 29.64 14.97 44.66 3.86
590 2366 2.908796 CCCCGCCTTCCCTAGAAC 59.091 66.667 0.00 0.00 0.00 3.01
591 2367 3.087906 GCCCCGCCTTCCCTAGAA 61.088 66.667 0.00 0.00 0.00 2.10
612 2388 4.699522 GCCACCCACGACCACCTC 62.700 72.222 0.00 0.00 0.00 3.85
668 2651 2.571202 CCCTTCTTCTTCTTCCTCAGCT 59.429 50.000 0.00 0.00 0.00 4.24
685 2671 4.909284 AGATCCTACATTCCCTAACCCTT 58.091 43.478 0.00 0.00 0.00 3.95
686 2672 4.578149 AGATCCTACATTCCCTAACCCT 57.422 45.455 0.00 0.00 0.00 4.34
687 2673 4.658901 TGAAGATCCTACATTCCCTAACCC 59.341 45.833 0.00 0.00 0.00 4.11
789 2776 6.979817 TGCTCACATTATGACATTAATTTGCC 59.020 34.615 0.00 0.00 32.37 4.52
801 2788 1.860326 CGCGTCATGCTCACATTATGA 59.140 47.619 0.00 0.00 43.27 2.15
802 2789 1.070376 CCGCGTCATGCTCACATTATG 60.070 52.381 4.92 0.00 43.27 1.90
880 4974 3.039252 AGTGCCTATAGCTTCACTCCT 57.961 47.619 12.09 0.00 44.23 3.69
907 5001 0.102120 CAGCTAGCTTCACTCCTCCG 59.898 60.000 16.46 0.00 0.00 4.63
950 5044 3.070018 CGGAGTGCATCTTCTCTTTTGT 58.930 45.455 0.00 0.00 0.00 2.83
952 5046 2.079925 GCGGAGTGCATCTTCTCTTTT 58.920 47.619 0.00 0.00 45.45 2.27
953 5047 1.731720 GCGGAGTGCATCTTCTCTTT 58.268 50.000 0.00 0.00 45.45 2.52
965 5059 1.813513 ACCAAGATGAAAGCGGAGTG 58.186 50.000 0.00 0.00 0.00 3.51
1040 5139 0.469705 TGTGCTTGTCCATGGCCTTT 60.470 50.000 6.96 0.00 0.00 3.11
1056 5155 1.066143 AGACCCGTAGCATTCCTTGTG 60.066 52.381 0.00 0.00 0.00 3.33
1132 5250 9.909644 GTCCTACGTACACTTAATTCATCATAT 57.090 33.333 0.00 0.00 0.00 1.78
1186 5304 5.398169 TGCGTAAAATTCAGCGATCAAAAT 58.602 33.333 0.00 0.00 0.00 1.82
1187 5305 4.788690 TGCGTAAAATTCAGCGATCAAAA 58.211 34.783 0.00 0.00 0.00 2.44
1188 5306 4.402583 CTGCGTAAAATTCAGCGATCAAA 58.597 39.130 0.00 0.00 0.00 2.69
1189 5307 3.181511 CCTGCGTAAAATTCAGCGATCAA 60.182 43.478 0.00 0.00 0.00 2.57
1190 5308 2.351418 CCTGCGTAAAATTCAGCGATCA 59.649 45.455 0.00 0.00 0.00 2.92
1191 5309 2.851008 GCCTGCGTAAAATTCAGCGATC 60.851 50.000 0.00 0.00 0.00 3.69
1192 5310 1.064060 GCCTGCGTAAAATTCAGCGAT 59.936 47.619 0.00 0.00 0.00 4.58
1193 5311 0.446222 GCCTGCGTAAAATTCAGCGA 59.554 50.000 0.00 0.00 0.00 4.93
1199 5317 1.068816 GTGGTTCGCCTGCGTAAAATT 60.069 47.619 11.68 0.00 40.74 1.82
1257 5375 3.775654 GTCGGTGCCCTCCTCCTG 61.776 72.222 0.00 0.00 0.00 3.86
1769 5887 1.399714 AGGCGACGTAGATGAATCCA 58.600 50.000 0.00 0.00 0.00 3.41
1772 5890 1.754803 TGGAAGGCGACGTAGATGAAT 59.245 47.619 0.00 0.00 0.00 2.57
1973 6091 0.249073 GACGACGCATCATGTAGGCT 60.249 55.000 0.00 0.00 30.97 4.58
2300 6418 2.040544 GGTGATGTTGACGGGCCTG 61.041 63.158 11.02 11.02 0.00 4.85
2434 6568 2.429610 AGTATGATGTACTTTCGGCGGT 59.570 45.455 7.21 0.00 0.00 5.68
2435 6569 3.093717 AGTATGATGTACTTTCGGCGG 57.906 47.619 7.21 0.00 0.00 6.13
2534 6671 5.964958 ATACAACTTTCAACCTCCATGTG 57.035 39.130 0.00 0.00 0.00 3.21
2585 6722 9.739276 TTGACAACTCTCAGATATAATTTTGGT 57.261 29.630 0.00 0.00 0.00 3.67
2727 6865 5.867903 ATCCCAAAAATTCACTGTCAACA 57.132 34.783 0.00 0.00 0.00 3.33
2728 6866 5.696270 GGAATCCCAAAAATTCACTGTCAAC 59.304 40.000 0.00 0.00 35.30 3.18
2731 6869 4.820897 GGGAATCCCAAAAATTCACTGTC 58.179 43.478 14.67 0.00 44.65 3.51
2778 6916 1.966451 GTGGGTTCTTGGCACCTCG 60.966 63.158 0.00 0.00 34.36 4.63
2810 6948 7.919091 CGCTACTGGTAAGATTCTGTGTATAAA 59.081 37.037 0.00 0.00 0.00 1.40
2829 6967 3.607078 GCTTGTTTTTGTCCTCGCTACTG 60.607 47.826 0.00 0.00 0.00 2.74
2837 6975 2.572290 AGTAGCGCTTGTTTTTGTCCT 58.428 42.857 18.68 0.00 0.00 3.85
2847 6986 6.062434 ACTGATAAGTACTAGTAGCGCTTG 57.938 41.667 18.68 6.54 0.00 4.01
2859 6998 2.382519 CCACGCGCTACTGATAAGTAC 58.617 52.381 5.73 0.00 0.00 2.73
2866 7005 2.736995 GTTGCCACGCGCTACTGA 60.737 61.111 5.73 0.00 39.75 3.41
2867 7006 3.788766 GGTTGCCACGCGCTACTG 61.789 66.667 5.73 0.00 42.16 2.74
2869 7008 2.899044 TTTGGTTGCCACGCGCTAC 61.899 57.895 5.73 0.00 41.82 3.58
2883 7022 0.110056 CTTAGCTGCAGTGCGTTTGG 60.110 55.000 16.64 0.00 38.13 3.28
2884 7023 0.867746 TCTTAGCTGCAGTGCGTTTG 59.132 50.000 16.64 1.81 38.13 2.93
2890 7029 3.725490 TGCTATGATCTTAGCTGCAGTG 58.275 45.455 30.05 3.80 44.03 3.66
2891 7030 3.992643 CTGCTATGATCTTAGCTGCAGT 58.007 45.455 30.05 4.79 44.03 4.40
2903 7042 0.955178 AGACGCGCTACTGCTATGAT 59.045 50.000 5.73 0.00 36.97 2.45
2905 7044 0.029433 TGAGACGCGCTACTGCTATG 59.971 55.000 5.73 0.00 36.97 2.23
2906 7045 0.309302 CTGAGACGCGCTACTGCTAT 59.691 55.000 5.73 0.00 36.97 2.97
2914 7053 0.387878 CTTCTTCACTGAGACGCGCT 60.388 55.000 5.73 3.91 0.00 5.92
2923 7062 3.409026 AGTTGTAGCCCTTCTTCACTG 57.591 47.619 0.00 0.00 0.00 3.66
2926 7065 4.967084 TTGTAGTTGTAGCCCTTCTTCA 57.033 40.909 0.00 0.00 0.00 3.02
2934 7073 6.043411 CAGTAGGAGAATTGTAGTTGTAGCC 58.957 44.000 0.00 0.00 0.00 3.93
2951 7090 0.324943 GCCTGGCAAGAACAGTAGGA 59.675 55.000 15.17 0.00 34.16 2.94
2955 7094 1.630369 TGATAGCCTGGCAAGAACAGT 59.370 47.619 22.65 0.00 34.16 3.55
2963 7102 4.220821 GCTACTACTATTGATAGCCTGGCA 59.779 45.833 22.65 7.39 35.10 4.92
2973 7112 4.280174 CCTTAAGCCCGCTACTACTATTGA 59.720 45.833 0.00 0.00 0.00 2.57
2988 7127 3.877357 GCGCGCCTTCCTTAAGCC 61.877 66.667 23.24 0.00 0.00 4.35
3015 7154 4.269363 GTGAAACACGCTACTACAACAACT 59.731 41.667 0.00 0.00 36.32 3.16
3016 7155 4.511734 GTGAAACACGCTACTACAACAAC 58.488 43.478 0.00 0.00 36.32 3.32
3036 7175 0.388649 ACAGTAGCGCTTTCTCCGTG 60.389 55.000 18.68 6.48 0.00 4.94
3040 7179 5.779806 TTCATTAACAGTAGCGCTTTCTC 57.220 39.130 18.68 4.22 0.00 2.87
3045 7184 4.202245 TCCTTTCATTAACAGTAGCGCT 57.798 40.909 17.26 17.26 0.00 5.92
3105 7244 7.776618 TCCTTCCCCTTTTTCTATTTCTTTC 57.223 36.000 0.00 0.00 0.00 2.62
3164 7303 6.028368 GCTACGCCTTTCTCCTTTATTTTTC 58.972 40.000 0.00 0.00 0.00 2.29
3177 7316 2.787915 GCTGCTGCTACGCCTTTC 59.212 61.111 8.53 0.00 36.03 2.62
3191 7330 1.572085 CCTGTCCTGAAAGCACGCTG 61.572 60.000 0.00 0.00 0.00 5.18
3223 7362 3.059461 CGGAAAAACACGCTACTGCTAAA 60.059 43.478 0.00 0.00 36.97 1.85
3236 7375 3.972276 GCGCTGGCCGGAAAAACA 61.972 61.111 18.31 0.00 37.44 2.83
3237 7376 1.654023 ATAGCGCTGGCCGGAAAAAC 61.654 55.000 22.90 0.00 41.24 2.43
3245 7384 1.816863 TAGTGGCTATAGCGCTGGCC 61.817 60.000 30.49 30.49 43.26 5.36
3260 7399 4.392138 CGAAAGCCCCTTTTTCTACTAGTG 59.608 45.833 5.39 0.00 33.49 2.74
3262 7401 4.576879 ACGAAAGCCCCTTTTTCTACTAG 58.423 43.478 0.00 0.00 33.49 2.57
3264 7403 3.503800 ACGAAAGCCCCTTTTTCTACT 57.496 42.857 0.00 0.00 33.49 2.57
3265 7404 3.305131 CCAACGAAAGCCCCTTTTTCTAC 60.305 47.826 0.00 0.00 33.49 2.59
3266 7405 2.888414 CCAACGAAAGCCCCTTTTTCTA 59.112 45.455 0.00 0.00 33.49 2.10
3267 7406 1.686587 CCAACGAAAGCCCCTTTTTCT 59.313 47.619 0.00 0.00 33.49 2.52
3268 7407 1.270094 CCCAACGAAAGCCCCTTTTTC 60.270 52.381 0.00 0.00 33.49 2.29
3271 7410 1.533033 CCCCAACGAAAGCCCCTTT 60.533 57.895 0.00 0.00 36.29 3.11
3273 7412 4.678743 GCCCCAACGAAAGCCCCT 62.679 66.667 0.00 0.00 0.00 4.79
3276 7415 3.373565 CAGGCCCCAACGAAAGCC 61.374 66.667 0.00 0.00 46.13 4.35
3277 7416 3.373565 CCAGGCCCCAACGAAAGC 61.374 66.667 0.00 0.00 0.00 3.51
3278 7417 3.373565 GCCAGGCCCCAACGAAAG 61.374 66.667 0.00 0.00 0.00 2.62
3289 7428 1.000359 ACTAATGGGTTGGCCAGGC 60.000 57.895 5.11 1.26 36.17 4.85
3290 7429 0.395724 GGACTAATGGGTTGGCCAGG 60.396 60.000 5.11 0.00 36.17 4.45
3291 7430 0.395724 GGGACTAATGGGTTGGCCAG 60.396 60.000 5.11 0.00 36.17 4.85
3292 7431 1.694856 GGGACTAATGGGTTGGCCA 59.305 57.895 0.00 0.00 36.17 5.36
3293 7432 1.453197 CGGGACTAATGGGTTGGCC 60.453 63.158 0.00 0.00 0.00 5.36
3294 7433 1.453197 CCGGGACTAATGGGTTGGC 60.453 63.158 0.00 0.00 0.00 4.52
3295 7434 0.330267 AACCGGGACTAATGGGTTGG 59.670 55.000 6.32 0.00 41.04 3.77
3296 7435 1.280998 AGAACCGGGACTAATGGGTTG 59.719 52.381 6.32 0.00 42.54 3.77
3297 7436 1.665137 AGAACCGGGACTAATGGGTT 58.335 50.000 6.32 0.00 45.02 4.11
3298 7437 1.665137 AAGAACCGGGACTAATGGGT 58.335 50.000 6.32 0.00 0.00 4.51
3299 7438 4.560108 CGTATAAGAACCGGGACTAATGGG 60.560 50.000 6.32 0.00 0.00 4.00
3300 7439 4.279169 TCGTATAAGAACCGGGACTAATGG 59.721 45.833 6.32 0.00 0.00 3.16
3301 7440 5.443185 TCGTATAAGAACCGGGACTAATG 57.557 43.478 6.32 0.44 0.00 1.90
3302 7441 5.836347 GTTCGTATAAGAACCGGGACTAAT 58.164 41.667 17.67 0.00 43.33 1.73
3303 7442 5.248870 GTTCGTATAAGAACCGGGACTAA 57.751 43.478 17.67 0.00 43.33 2.24
3304 7443 4.900635 GTTCGTATAAGAACCGGGACTA 57.099 45.455 17.67 0.00 43.33 2.59
3305 7444 3.790152 GTTCGTATAAGAACCGGGACT 57.210 47.619 17.67 0.73 43.33 3.85


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

AutoCloner maintained by Alex Coulton.