Multiple sequence alignment - TraesCS3D01G451900

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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 TraesCS3D01G451900 chr3D 100.000 3020 0 0 1 3020 559229248 559226229 0.000000e+00 5578.0
1 TraesCS3D01G451900 chr3D 89.304 1365 105 20 967 2298 559219747 559218391 0.000000e+00 1674.0
2 TraesCS3D01G451900 chr3D 88.301 1171 113 15 984 2137 559162579 559163742 0.000000e+00 1382.0
3 TraesCS3D01G451900 chr3D 82.767 1207 162 25 984 2172 559165372 559166550 0.000000e+00 1035.0
4 TraesCS3D01G451900 chr3A 94.545 2145 82 11 477 2590 695755845 695753705 0.000000e+00 3280.0
5 TraesCS3D01G451900 chr3A 91.474 1079 81 6 951 2028 695745693 695744625 0.000000e+00 1472.0
6 TraesCS3D01G451900 chr3A 85.563 1226 142 18 984 2182 695668482 695669699 0.000000e+00 1251.0
7 TraesCS3D01G451900 chr3A 92.077 467 24 4 29 483 695756340 695755875 0.000000e+00 645.0
8 TraesCS3D01G451900 chr3A 95.402 174 8 0 2590 2763 695753589 695753416 8.250000e-71 278.0
9 TraesCS3D01G451900 chr3A 80.000 170 20 7 672 840 695745929 695745773 2.460000e-21 113.0
10 TraesCS3D01G451900 chr3B 87.203 1602 118 33 670 2226 742256770 742255211 0.000000e+00 1742.0
11 TraesCS3D01G451900 chr3B 90.736 1209 90 8 976 2183 742476763 742477950 0.000000e+00 1592.0
12 TraesCS3D01G451900 chr3B 81.300 1246 180 34 950 2182 742163685 742164890 0.000000e+00 961.0
13 TraesCS3D01G451900 chr3B 81.299 385 59 6 103 474 24550871 24551255 1.760000e-77 300.0
14 TraesCS3D01G451900 chr3B 85.385 260 19 8 2766 3007 779624843 779625101 5.000000e-63 252.0
15 TraesCS3D01G451900 chr3B 89.286 84 8 1 24 107 24550767 24550849 1.480000e-18 104.0
16 TraesCS3D01G451900 chr2D 81.818 385 57 6 103 474 599298889 599298505 8.130000e-81 311.0
17 TraesCS3D01G451900 chr2D 89.516 248 17 2 2769 3015 648089060 648089299 3.780000e-79 305.0
18 TraesCS3D01G451900 chr2D 85.375 253 30 3 2768 3014 36426441 36426190 3.860000e-64 255.0
19 TraesCS3D01G451900 chr2D 77.143 490 69 19 24 474 99341329 99341814 8.360000e-61 244.0
20 TraesCS3D01G451900 chr2D 86.275 51 4 3 1096 1144 43671130 43671179 5.000000e-03 52.8
21 TraesCS3D01G451900 chr7A 81.462 383 58 6 105 474 634955040 634955422 4.890000e-78 302.0
22 TraesCS3D01G451900 chr7A 82.879 257 34 6 2769 3017 709765567 709765821 3.920000e-54 222.0
23 TraesCS3D01G451900 chr7A 82.558 258 33 7 2769 3015 19165411 19165667 1.820000e-52 217.0
24 TraesCS3D01G451900 chr7A 78.261 184 28 8 2265 2448 577198391 577198562 1.140000e-19 108.0
25 TraesCS3D01G451900 chr5D 81.299 385 59 8 103 474 236420253 236420637 1.760000e-77 300.0
26 TraesCS3D01G451900 chr5D 82.443 262 26 7 2771 3012 481641598 481641859 8.480000e-51 211.0
27 TraesCS3D01G451900 chr7B 80.779 385 61 6 103 474 66406326 66406710 3.810000e-74 289.0
28 TraesCS3D01G451900 chr7D 78.571 490 65 19 27 477 42668359 42667871 1.370000e-73 287.0
29 TraesCS3D01G451900 chr6A 80.519 385 62 2 103 474 616972543 616972927 1.770000e-72 283.0
30 TraesCS3D01G451900 chr6A 76.797 487 73 18 27 474 64590921 64590436 1.400000e-58 237.0
31 TraesCS3D01G451900 chr6A 100.000 33 0 0 1 33 557974037 557974069 9.040000e-06 62.1
32 TraesCS3D01G451900 chr2A 80.519 385 62 6 103 474 762102830 762103214 1.770000e-72 283.0
33 TraesCS3D01G451900 chr1D 78.395 486 65 18 27 473 111542837 111542353 2.290000e-71 279.0
34 TraesCS3D01G451900 chr1D 92.500 40 1 2 3 42 59099803 59099840 4.210000e-04 56.5
35 TraesCS3D01G451900 chr2B 80.260 385 63 6 103 474 25159880 25160264 8.250000e-71 278.0
36 TraesCS3D01G451900 chr2B 89.744 78 7 1 24 101 25159776 25159852 6.890000e-17 99.0
37 TraesCS3D01G451900 chr4A 81.159 345 52 6 143 474 618998499 618998843 6.420000e-67 265.0
38 TraesCS3D01G451900 chr1B 85.484 248 33 3 2769 3014 47204938 47204692 3.860000e-64 255.0
39 TraesCS3D01G451900 chr1B 86.275 51 4 3 1096 1144 3144179 3144228 5.000000e-03 52.8
40 TraesCS3D01G451900 chrUn 84.109 258 25 7 2763 3008 97140891 97140638 5.030000e-58 235.0
41 TraesCS3D01G451900 chrUn 82.397 267 22 13 2763 3008 316023465 316023727 3.050000e-50 209.0
42 TraesCS3D01G451900 chrUn 100.000 33 0 0 1 33 143914113 143914145 9.040000e-06 62.1
43 TraesCS3D01G451900 chrUn 100.000 33 0 0 1 33 208665119 208665151 9.040000e-06 62.1
44 TraesCS3D01G451900 chr1A 85.333 225 31 2 2770 2992 511634524 511634300 6.510000e-57 231.0
45 TraesCS3D01G451900 chr6D 77.719 377 71 6 111 474 276136808 276136432 5.070000e-53 219.0
46 TraesCS3D01G451900 chr6D 80.081 246 30 9 2769 2995 467161056 467161301 6.700000e-37 165.0
47 TraesCS3D01G451900 chr6D 100.000 33 0 0 1 33 4396379 4396347 9.040000e-06 62.1
48 TraesCS3D01G451900 chr6D 100.000 33 0 0 1 33 35673013 35673045 9.040000e-06 62.1
49 TraesCS3D01G451900 chr6D 100.000 33 0 0 1 33 391931227 391931259 9.040000e-06 62.1
50 TraesCS3D01G451900 chr4D 100.000 33 0 0 1 33 154928172 154928204 9.040000e-06 62.1
51 TraesCS3D01G451900 chr4B 100.000 33 0 0 1 33 322683545 322683577 9.040000e-06 62.1
52 TraesCS3D01G451900 chr5A 96.774 31 1 0 581 611 549880530 549880500 5.000000e-03 52.8


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 TraesCS3D01G451900 chr3D 559226229 559229248 3019 True 5578.0 5578 100.000 1 3020 1 chr3D.!!$R2 3019
1 TraesCS3D01G451900 chr3D 559218391 559219747 1356 True 1674.0 1674 89.304 967 2298 1 chr3D.!!$R1 1331
2 TraesCS3D01G451900 chr3D 559162579 559166550 3971 False 1208.5 1382 85.534 984 2172 2 chr3D.!!$F1 1188
3 TraesCS3D01G451900 chr3A 695753416 695756340 2924 True 1401.0 3280 94.008 29 2763 3 chr3A.!!$R2 2734
4 TraesCS3D01G451900 chr3A 695668482 695669699 1217 False 1251.0 1251 85.563 984 2182 1 chr3A.!!$F1 1198
5 TraesCS3D01G451900 chr3A 695744625 695745929 1304 True 792.5 1472 85.737 672 2028 2 chr3A.!!$R1 1356
6 TraesCS3D01G451900 chr3B 742255211 742256770 1559 True 1742.0 1742 87.203 670 2226 1 chr3B.!!$R1 1556
7 TraesCS3D01G451900 chr3B 742476763 742477950 1187 False 1592.0 1592 90.736 976 2183 1 chr3B.!!$F2 1207
8 TraesCS3D01G451900 chr3B 742163685 742164890 1205 False 961.0 961 81.300 950 2182 1 chr3B.!!$F1 1232

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
21 22 0.037697 GTGTGCGGACAGTGGTCATA 60.038 55.0 11.09 0.00 46.17 2.15 F
450 463 0.108186 TCAAGTATCACCTGGCAGCG 60.108 55.0 9.56 5.16 0.00 5.18 F
549 597 0.319900 CGATCGATGGGGTGTGGATC 60.320 60.0 10.26 0.00 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1341 1447 2.122989 GGTATGGGGCCCGAGAGA 60.123 66.667 19.83 0.00 0.00 3.10 R
1815 1928 2.539953 GCTCACATCGACGAAGTAGAGG 60.540 54.545 22.16 7.85 46.84 3.69 R
2301 5266 4.209288 CCTCGCATAAAACTGACTTATCCG 59.791 45.833 0.00 0.00 0.00 4.18 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
17 18 2.908015 AAGTGTGCGGACAGTGGT 59.092 55.556 18.71 0.16 35.80 4.16
18 19 1.227556 AAGTGTGCGGACAGTGGTC 60.228 57.895 18.71 2.05 43.55 4.02
19 20 1.966901 AAGTGTGCGGACAGTGGTCA 61.967 55.000 18.71 0.00 46.17 4.02
20 21 1.301716 GTGTGCGGACAGTGGTCAT 60.302 57.895 11.09 0.00 46.17 3.06
21 22 0.037697 GTGTGCGGACAGTGGTCATA 60.038 55.000 11.09 0.00 46.17 2.15
22 23 0.901827 TGTGCGGACAGTGGTCATAT 59.098 50.000 5.33 0.00 46.17 1.78
23 24 1.290203 GTGCGGACAGTGGTCATATG 58.710 55.000 0.63 0.00 46.17 1.78
24 25 0.177836 TGCGGACAGTGGTCATATGG 59.822 55.000 2.13 0.00 46.17 2.74
25 26 0.532862 GCGGACAGTGGTCATATGGG 60.533 60.000 2.13 0.00 46.17 4.00
26 27 0.532862 CGGACAGTGGTCATATGGGC 60.533 60.000 2.13 0.00 46.17 5.36
27 28 0.179018 GGACAGTGGTCATATGGGCC 60.179 60.000 2.13 0.00 46.17 5.80
32 33 1.922057 TGGTCATATGGGCCACAGG 59.078 57.895 9.28 0.00 0.00 4.00
91 92 1.134670 CGAAGAAGAGTCCACATCCCC 60.135 57.143 0.00 0.00 0.00 4.81
101 102 2.304761 GTCCACATCCCCAAGACAGTAA 59.695 50.000 0.00 0.00 0.00 2.24
137 138 0.532862 AAGTGAGGACAGCCACAACG 60.533 55.000 0.00 0.00 36.49 4.10
140 141 3.858868 GAGGACAGCCACAACGCGA 62.859 63.158 15.93 0.00 36.29 5.87
158 159 2.207590 CGACCATCATCATCACACCAG 58.792 52.381 0.00 0.00 0.00 4.00
173 174 2.838736 CACCAGTGAGTGTAAGCAGTT 58.161 47.619 0.00 0.00 32.89 3.16
179 180 4.795795 CAGTGAGTGTAAGCAGTTAGATCG 59.204 45.833 0.00 0.00 0.00 3.69
183 184 5.125578 TGAGTGTAAGCAGTTAGATCGTCAT 59.874 40.000 0.00 0.00 0.00 3.06
190 191 9.197694 GTAAGCAGTTAGATCGTCATGATAAAT 57.802 33.333 0.00 0.00 37.47 1.40
314 315 4.680537 AGAGTCGGTGGCCTCGGT 62.681 66.667 16.62 6.83 32.88 4.69
390 391 1.497991 TGAAGACCGCAAAGACGAAG 58.502 50.000 0.00 0.00 34.06 3.79
391 392 1.067974 TGAAGACCGCAAAGACGAAGA 59.932 47.619 0.00 0.00 34.06 2.87
392 393 2.132762 GAAGACCGCAAAGACGAAGAA 58.867 47.619 0.00 0.00 34.06 2.52
393 394 2.457366 AGACCGCAAAGACGAAGAAT 57.543 45.000 0.00 0.00 34.06 2.40
394 395 2.069273 AGACCGCAAAGACGAAGAATG 58.931 47.619 0.00 0.00 34.06 2.67
395 396 0.517316 ACCGCAAAGACGAAGAATGC 59.483 50.000 0.00 0.00 34.06 3.56
396 397 0.516877 CCGCAAAGACGAAGAATGCA 59.483 50.000 0.00 0.00 36.84 3.96
409 422 4.615682 CGAAGAATGCACATAAAGGCAACA 60.616 41.667 0.00 0.00 44.20 3.33
416 429 4.142071 TGCACATAAAGGCAACAAACTCAA 60.142 37.500 0.00 0.00 37.03 3.02
435 448 9.799106 AAACTCAATATAGTTATCCCCATCAAG 57.201 33.333 0.00 0.00 38.76 3.02
450 463 0.108186 TCAAGTATCACCTGGCAGCG 60.108 55.000 9.56 5.16 0.00 5.18
490 538 4.154347 GGCGAGAGGTGGAGGCAG 62.154 72.222 0.00 0.00 0.00 4.85
498 546 2.985847 GTGGAGGCAGGCGCTTTT 60.986 61.111 7.64 0.00 38.60 2.27
534 582 1.403814 TGGTGGGATGTCTCTCGATC 58.596 55.000 0.00 0.00 0.00 3.69
549 597 0.319900 CGATCGATGGGGTGTGGATC 60.320 60.000 10.26 0.00 0.00 3.36
571 619 0.975135 TCGATGGGGGTAACGAAACA 59.025 50.000 0.00 0.00 37.60 2.83
597 645 5.130292 TGACGTACCAACTTCTCCTTTAG 57.870 43.478 0.00 0.00 0.00 1.85
649 697 1.069227 GTTAGAAAGGCAGCGTGTTGG 60.069 52.381 0.00 0.00 0.00 3.77
817 894 3.499918 GCACCTTATTCTTGATGGATCCG 59.500 47.826 7.39 0.00 0.00 4.18
830 907 1.076332 GGATCCGTGTTTGGTCTTCG 58.924 55.000 0.00 0.00 0.00 3.79
975 1072 0.734889 ACACGCATAGCATCAAAGCC 59.265 50.000 0.00 0.00 34.23 4.35
1203 1309 2.735772 CCCCTGCTGCGACTGGTAT 61.736 63.158 0.00 0.00 0.00 2.73
1293 1399 3.341629 ACCATCCCCACTGCCCTG 61.342 66.667 0.00 0.00 0.00 4.45
1413 1519 3.842923 CGCATCTCCTGGACGGCT 61.843 66.667 0.00 0.00 0.00 5.52
1415 1521 2.202987 CATCTCCTGGACGGCTGC 60.203 66.667 0.00 0.00 0.00 5.25
1416 1522 3.474570 ATCTCCTGGACGGCTGCC 61.475 66.667 9.11 9.11 0.00 4.85
1443 1549 4.410400 GTGCCGTCCTTCCTGGGG 62.410 72.222 0.00 0.00 36.20 4.96
1764 1874 2.426024 GGAGTTGCAGTACATCGACCTA 59.574 50.000 0.00 0.00 0.00 3.08
1798 1908 0.457851 CGATTTCGACCTCTCAGGCT 59.542 55.000 0.00 0.00 39.63 4.58
1849 1962 1.307355 TGTGAGCCACAATGCCATCG 61.307 55.000 5.65 0.00 41.69 3.84
1863 1976 1.970114 CATCGATGGCAGCATCCCC 60.970 63.158 17.96 0.00 0.00 4.81
2017 4908 2.381941 GCTCCCCTCCCTTCATGCT 61.382 63.158 0.00 0.00 0.00 3.79
2022 4913 1.419387 CCCCTCCCTTCATGCTAGAAG 59.581 57.143 10.56 10.56 43.60 2.85
2196 5150 4.062293 TCTGTTTTAACTGTCCCACATCG 58.938 43.478 0.00 0.00 0.00 3.84
2206 5161 4.202161 ACTGTCCCACATCGTATTCATCTC 60.202 45.833 0.00 0.00 0.00 2.75
2410 5382 0.185175 AGGCCCAGAAAACCGACTTT 59.815 50.000 0.00 0.00 0.00 2.66
2438 5410 8.837059 CCAAAATTAATTTTCAGACGACTTACG 58.163 33.333 20.71 7.30 41.63 3.18
2624 5712 2.346803 AGTGCCATCGTCAATACACAC 58.653 47.619 0.00 0.00 0.00 3.82
2706 5794 0.878523 GATATGTACAAGCGCCCGCA 60.879 55.000 15.50 0.00 44.88 5.69
2735 5823 1.000385 TCTTTTCCCAAATGCACGCAG 60.000 47.619 0.00 0.00 0.00 5.18
2745 5833 0.961857 ATGCACGCAGCCTTGATCAA 60.962 50.000 8.12 8.12 44.83 2.57
2763 5851 7.395190 TGATCAATCCTTTCTATGGTTGTTG 57.605 36.000 0.00 0.00 0.00 3.33
2764 5852 7.174413 TGATCAATCCTTTCTATGGTTGTTGA 58.826 34.615 0.00 0.00 0.00 3.18
2765 5853 7.835682 TGATCAATCCTTTCTATGGTTGTTGAT 59.164 33.333 0.00 0.00 36.29 2.57
2766 5854 7.395190 TCAATCCTTTCTATGGTTGTTGATG 57.605 36.000 0.00 0.00 0.00 3.07
2767 5855 7.174413 TCAATCCTTTCTATGGTTGTTGATGA 58.826 34.615 0.00 0.00 0.00 2.92
2768 5856 7.121168 TCAATCCTTTCTATGGTTGTTGATGAC 59.879 37.037 0.00 0.00 0.00 3.06
2769 5857 5.875224 TCCTTTCTATGGTTGTTGATGACA 58.125 37.500 0.00 0.00 36.19 3.58
2770 5858 6.303054 TCCTTTCTATGGTTGTTGATGACAA 58.697 36.000 0.00 0.00 45.70 3.18
2804 5892 8.742554 ATTTCAGAAACACAATAATTTCGGAC 57.257 30.769 0.00 0.00 38.29 4.79
2805 5893 6.249035 TCAGAAACACAATAATTTCGGACC 57.751 37.500 0.00 0.00 39.36 4.46
2806 5894 6.001460 TCAGAAACACAATAATTTCGGACCT 58.999 36.000 0.00 0.00 39.36 3.85
2807 5895 6.148811 TCAGAAACACAATAATTTCGGACCTC 59.851 38.462 0.00 0.00 39.36 3.85
2808 5896 6.001460 AGAAACACAATAATTTCGGACCTCA 58.999 36.000 0.00 0.00 39.36 3.86
2809 5897 5.622770 AACACAATAATTTCGGACCTCAC 57.377 39.130 0.00 0.00 0.00 3.51
2810 5898 4.906618 ACACAATAATTTCGGACCTCACT 58.093 39.130 0.00 0.00 0.00 3.41
2811 5899 4.695455 ACACAATAATTTCGGACCTCACTG 59.305 41.667 0.00 0.00 0.00 3.66
2812 5900 4.935205 CACAATAATTTCGGACCTCACTGA 59.065 41.667 0.00 0.00 0.00 3.41
2813 5901 5.411361 CACAATAATTTCGGACCTCACTGAA 59.589 40.000 0.00 0.00 33.98 3.02
2814 5902 6.001460 ACAATAATTTCGGACCTCACTGAAA 58.999 36.000 0.00 0.00 45.21 2.69
2819 5907 3.179443 TCGGACCTCACTGAAATATGC 57.821 47.619 0.00 0.00 0.00 3.14
2820 5908 1.860950 CGGACCTCACTGAAATATGCG 59.139 52.381 0.00 0.00 0.00 4.73
2821 5909 2.481276 CGGACCTCACTGAAATATGCGA 60.481 50.000 0.00 0.00 0.00 5.10
2822 5910 3.531538 GGACCTCACTGAAATATGCGAA 58.468 45.455 0.00 0.00 0.00 4.70
2823 5911 3.938963 GGACCTCACTGAAATATGCGAAA 59.061 43.478 0.00 0.00 0.00 3.46
2824 5912 4.576463 GGACCTCACTGAAATATGCGAAAT 59.424 41.667 0.00 0.00 0.00 2.17
2825 5913 5.066505 GGACCTCACTGAAATATGCGAAATT 59.933 40.000 0.00 0.00 0.00 1.82
2826 5914 6.404734 GGACCTCACTGAAATATGCGAAATTT 60.405 38.462 0.00 0.00 0.00 1.82
2827 5915 6.555315 ACCTCACTGAAATATGCGAAATTTC 58.445 36.000 8.20 8.20 41.60 2.17
2933 6021 8.391075 AGTTTGGATCTAACTCAAAATTTCGA 57.609 30.769 7.63 0.00 33.05 3.71
2934 6022 8.507249 AGTTTGGATCTAACTCAAAATTTCGAG 58.493 33.333 4.55 4.55 33.05 4.04
2935 6023 6.985188 TGGATCTAACTCAAAATTTCGAGG 57.015 37.500 10.78 0.00 33.36 4.63
2936 6024 6.472887 TGGATCTAACTCAAAATTTCGAGGT 58.527 36.000 10.78 6.51 33.36 3.85
2937 6025 6.940298 TGGATCTAACTCAAAATTTCGAGGTT 59.060 34.615 10.78 5.44 33.36 3.50
2938 6026 8.098286 TGGATCTAACTCAAAATTTCGAGGTTA 58.902 33.333 10.78 6.18 33.36 2.85
2939 6027 8.943002 GGATCTAACTCAAAATTTCGAGGTTAA 58.057 33.333 10.78 0.00 33.36 2.01
2952 6040 9.563898 AATTTCGAGGTTAAAAATATTTCGGAC 57.436 29.630 0.10 0.86 0.00 4.79
2953 6041 6.667007 TCGAGGTTAAAAATATTTCGGACC 57.333 37.500 14.37 14.37 0.00 4.46
2954 6042 6.171921 TCGAGGTTAAAAATATTTCGGACCA 58.828 36.000 20.13 5.85 32.65 4.02
2955 6043 6.092533 TCGAGGTTAAAAATATTTCGGACCAC 59.907 38.462 20.13 15.60 32.65 4.16
2956 6044 6.128227 CGAGGTTAAAAATATTTCGGACCACA 60.128 38.462 20.13 0.00 32.65 4.17
2957 6045 6.916440 AGGTTAAAAATATTTCGGACCACAC 58.084 36.000 20.13 4.99 32.65 3.82
2958 6046 6.717997 AGGTTAAAAATATTTCGGACCACACT 59.282 34.615 20.13 5.61 32.65 3.55
2959 6047 6.804783 GGTTAAAAATATTTCGGACCACACTG 59.195 38.462 16.11 0.00 31.53 3.66
2960 6048 7.308710 GGTTAAAAATATTTCGGACCACACTGA 60.309 37.037 16.11 0.00 31.53 3.41
2961 6049 6.642707 AAAAATATTTCGGACCACACTGAA 57.357 33.333 0.10 0.00 33.98 3.02
2962 6050 6.642707 AAAATATTTCGGACCACACTGAAA 57.357 33.333 0.10 0.00 45.21 2.69
2966 6054 5.818136 ATTTCGGACCACACTGAAATATG 57.182 39.130 11.97 0.00 46.98 1.78
2967 6055 3.973206 TCGGACCACACTGAAATATGT 57.027 42.857 0.00 0.00 0.00 2.29
2968 6056 3.595173 TCGGACCACACTGAAATATGTG 58.405 45.455 0.00 0.00 44.79 3.21
2969 6057 7.022568 ATTTCGGACCACACTGAAATATGTGA 61.023 38.462 11.97 0.00 46.98 3.58
2970 6058 8.441089 ATTTCGGACCACACTGAAATATGTGAA 61.441 37.037 11.97 0.00 46.98 3.18
2980 6068 9.743057 ACACTGAAATATGTGAAATTTCGAAAA 57.257 25.926 15.66 0.00 43.30 2.29
3014 6102 6.843069 ATTTCGTTGAAATTTTTGACCCTG 57.157 33.333 0.00 0.00 38.89 4.45
3015 6103 3.712187 TCGTTGAAATTTTTGACCCTGC 58.288 40.909 0.00 0.00 0.00 4.85
3016 6104 3.383185 TCGTTGAAATTTTTGACCCTGCT 59.617 39.130 0.00 0.00 0.00 4.24
3017 6105 4.119136 CGTTGAAATTTTTGACCCTGCTT 58.881 39.130 0.00 0.00 0.00 3.91
3018 6106 4.025813 CGTTGAAATTTTTGACCCTGCTTG 60.026 41.667 0.00 0.00 0.00 4.01
3019 6107 5.115480 GTTGAAATTTTTGACCCTGCTTGA 58.885 37.500 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.227556 GACCACTGTCCGCACACTT 60.228 57.895 0.00 0.00 35.34 3.16
2 3 0.037697 TATGACCACTGTCCGCACAC 60.038 55.000 0.00 0.00 41.01 3.82
3 4 0.901827 ATATGACCACTGTCCGCACA 59.098 50.000 0.00 0.00 41.01 4.57
4 5 1.290203 CATATGACCACTGTCCGCAC 58.710 55.000 0.00 0.00 41.01 5.34
5 6 0.177836 CCATATGACCACTGTCCGCA 59.822 55.000 3.65 0.00 41.01 5.69
6 7 0.532862 CCCATATGACCACTGTCCGC 60.533 60.000 3.65 0.00 41.01 5.54
7 8 0.532862 GCCCATATGACCACTGTCCG 60.533 60.000 3.65 0.00 41.01 4.79
8 9 0.179018 GGCCCATATGACCACTGTCC 60.179 60.000 3.65 0.00 41.01 4.02
9 10 0.546122 TGGCCCATATGACCACTGTC 59.454 55.000 12.04 0.00 42.12 3.51
10 11 2.708671 TGGCCCATATGACCACTGT 58.291 52.632 12.04 0.00 0.00 3.55
14 15 1.922057 CCTGTGGCCCATATGACCA 59.078 57.895 12.04 12.04 0.00 4.02
15 16 1.529244 GCCTGTGGCCCATATGACC 60.529 63.158 3.65 6.04 44.06 4.02
16 17 4.164258 GCCTGTGGCCCATATGAC 57.836 61.111 3.65 0.00 44.06 3.06
57 58 0.248661 TCTTCGTCAGCGCTATCAGC 60.249 55.000 10.99 0.00 38.02 4.26
91 92 7.065085 CCAATGTTCTACCTCATTACTGTCTTG 59.935 40.741 0.00 0.00 33.69 3.02
101 102 5.338708 CCTCACTTCCAATGTTCTACCTCAT 60.339 44.000 0.00 0.00 0.00 2.90
137 138 0.940126 GGTGTGATGATGATGGTCGC 59.060 55.000 0.00 0.00 0.00 5.19
140 141 2.995283 CACTGGTGTGATGATGATGGT 58.005 47.619 0.00 0.00 46.55 3.55
158 159 4.734917 ACGATCTAACTGCTTACACTCAC 58.265 43.478 0.00 0.00 0.00 3.51
211 212 3.054875 TGCTTATGATCAGCAGGTCTTGT 60.055 43.478 0.09 0.00 42.49 3.16
314 315 0.325860 ATGCGGTTCCTACCCCACTA 60.326 55.000 0.00 0.00 41.75 2.74
390 391 4.990426 AGTTTGTTGCCTTTATGTGCATTC 59.010 37.500 0.00 0.00 37.33 2.67
391 392 4.959723 AGTTTGTTGCCTTTATGTGCATT 58.040 34.783 0.00 0.00 37.33 3.56
392 393 4.039004 TGAGTTTGTTGCCTTTATGTGCAT 59.961 37.500 0.00 0.00 37.33 3.96
393 394 3.382865 TGAGTTTGTTGCCTTTATGTGCA 59.617 39.130 0.00 0.00 35.27 4.57
394 395 3.976169 TGAGTTTGTTGCCTTTATGTGC 58.024 40.909 0.00 0.00 0.00 4.57
395 396 9.507280 CTATATTGAGTTTGTTGCCTTTATGTG 57.493 33.333 0.00 0.00 0.00 3.21
396 397 9.243105 ACTATATTGAGTTTGTTGCCTTTATGT 57.757 29.630 0.00 0.00 0.00 2.29
409 422 9.799106 CTTGATGGGGATAACTATATTGAGTTT 57.201 33.333 0.00 0.00 40.22 2.66
416 429 8.993424 GGTGATACTTGATGGGGATAACTATAT 58.007 37.037 0.00 0.00 0.00 0.86
435 448 3.264897 CGCGCTGCCAGGTGATAC 61.265 66.667 5.56 0.00 0.00 2.24
450 463 0.601311 GGGCTATGTCACCATCTCGC 60.601 60.000 0.00 0.00 32.29 5.03
469 482 2.415010 CTCCACCTCTCGCCATCG 59.585 66.667 0.00 0.00 0.00 3.84
530 578 0.319900 GATCCACACCCCATCGATCG 60.320 60.000 9.36 9.36 0.00 3.69
534 582 2.108976 CCGATCCACACCCCATCG 59.891 66.667 0.00 0.00 39.31 3.84
549 597 1.947597 TTCGTTACCCCCATCGACCG 61.948 60.000 0.00 0.00 32.14 4.79
571 619 4.969484 AGGAGAAGTTGGTACGTCATTTT 58.031 39.130 0.00 0.00 35.53 1.82
614 662 9.402320 TGCCTTTCTAACAAGTATAATTGCATA 57.598 29.630 12.62 5.97 33.28 3.14
664 730 6.209192 TCTGACCAGTACAATTGCATGAATTT 59.791 34.615 5.05 0.00 31.41 1.82
668 734 4.020307 TCTCTGACCAGTACAATTGCATGA 60.020 41.667 5.05 0.00 0.00 3.07
817 894 2.795470 GTCAGAGACGAAGACCAAACAC 59.205 50.000 0.00 0.00 0.00 3.32
830 907 6.484308 GGAGTGGTATCTAACTAGTCAGAGAC 59.516 46.154 11.74 11.74 40.01 3.36
975 1072 1.765161 CGGCTGTGTCTGTGTGTGTG 61.765 60.000 0.00 0.00 0.00 3.82
1179 1285 2.281484 TCGCAGCAGGGGTTGTTC 60.281 61.111 0.00 0.00 0.00 3.18
1203 1309 4.337060 CGGTCGCAGGTGACGTCA 62.337 66.667 15.76 15.76 39.83 4.35
1341 1447 2.122989 GGTATGGGGCCCGAGAGA 60.123 66.667 19.83 0.00 0.00 3.10
1764 1874 2.869503 AATCGAAGGCGTTGCGGGAT 62.870 55.000 0.00 0.00 38.98 3.85
1815 1928 2.539953 GCTCACATCGACGAAGTAGAGG 60.540 54.545 22.16 7.85 46.84 3.69
1954 4845 4.817517 TGAAAGTTGTAGAGATCGAACCC 58.182 43.478 0.00 0.00 0.00 4.11
2017 4908 8.010697 TCCACCAGATAATTCCATCTACTTCTA 58.989 37.037 0.00 0.00 33.41 2.10
2022 4913 7.939039 TCAAATCCACCAGATAATTCCATCTAC 59.061 37.037 0.00 0.00 33.41 2.59
2196 5150 6.828502 TCTTTGCATACACGAGATGAATAC 57.171 37.500 0.00 0.00 0.00 1.89
2206 5161 4.260907 CCATCAAGGATCTTTGCATACACG 60.261 45.833 12.50 0.00 41.22 4.49
2301 5266 4.209288 CCTCGCATAAAACTGACTTATCCG 59.791 45.833 0.00 0.00 0.00 4.18
2410 5382 7.519032 AGTCGTCTGAAAATTAATTTTGGGA 57.481 32.000 26.69 20.19 39.86 4.37
2526 5498 4.590222 AGTTGAAGGTCTAAAGTACCGGAA 59.410 41.667 9.46 0.00 42.15 4.30
2531 5503 4.385146 GTGCGAGTTGAAGGTCTAAAGTAC 59.615 45.833 0.00 0.00 0.00 2.73
2699 5787 4.918201 GAGGGAAGGATGCGGGCG 62.918 72.222 0.00 0.00 0.00 6.13
2706 5794 4.356436 CATTTGGGAAAAGAGGGAAGGAT 58.644 43.478 0.00 0.00 0.00 3.24
2735 5823 5.136105 ACCATAGAAAGGATTGATCAAGGC 58.864 41.667 14.54 8.29 0.00 4.35
2745 5833 6.484288 TGTCATCAACAACCATAGAAAGGAT 58.516 36.000 0.00 0.00 34.03 3.24
2778 5866 9.834628 GTCCGAAATTATTGTGTTTCTGAAATA 57.165 29.630 6.06 0.30 32.14 1.40
2779 5867 7.812669 GGTCCGAAATTATTGTGTTTCTGAAAT 59.187 33.333 6.06 0.00 32.14 2.17
2780 5868 7.013846 AGGTCCGAAATTATTGTGTTTCTGAAA 59.986 33.333 0.00 0.00 32.14 2.69
2781 5869 6.488683 AGGTCCGAAATTATTGTGTTTCTGAA 59.511 34.615 0.00 0.00 32.14 3.02
2782 5870 6.001460 AGGTCCGAAATTATTGTGTTTCTGA 58.999 36.000 0.00 0.00 33.32 3.27
2783 5871 6.072728 TGAGGTCCGAAATTATTGTGTTTCTG 60.073 38.462 0.00 0.00 33.32 3.02
2784 5872 6.001460 TGAGGTCCGAAATTATTGTGTTTCT 58.999 36.000 0.00 0.00 33.32 2.52
2785 5873 6.072673 AGTGAGGTCCGAAATTATTGTGTTTC 60.073 38.462 0.00 0.00 0.00 2.78
2786 5874 5.768164 AGTGAGGTCCGAAATTATTGTGTTT 59.232 36.000 0.00 0.00 0.00 2.83
2787 5875 5.181245 CAGTGAGGTCCGAAATTATTGTGTT 59.819 40.000 0.00 0.00 0.00 3.32
2788 5876 4.695455 CAGTGAGGTCCGAAATTATTGTGT 59.305 41.667 0.00 0.00 0.00 3.72
2789 5877 4.935205 TCAGTGAGGTCCGAAATTATTGTG 59.065 41.667 0.00 0.00 0.00 3.33
2790 5878 5.160607 TCAGTGAGGTCCGAAATTATTGT 57.839 39.130 0.00 0.00 0.00 2.71
2791 5879 6.494893 TTTCAGTGAGGTCCGAAATTATTG 57.505 37.500 0.00 0.00 0.00 1.90
2792 5880 8.840321 CATATTTCAGTGAGGTCCGAAATTATT 58.160 33.333 6.91 0.00 38.61 1.40
2793 5881 7.041098 GCATATTTCAGTGAGGTCCGAAATTAT 60.041 37.037 6.91 0.00 38.61 1.28
2794 5882 6.260050 GCATATTTCAGTGAGGTCCGAAATTA 59.740 38.462 6.91 0.00 38.61 1.40
2795 5883 5.066505 GCATATTTCAGTGAGGTCCGAAATT 59.933 40.000 6.91 0.00 38.61 1.82
2796 5884 4.576463 GCATATTTCAGTGAGGTCCGAAAT 59.424 41.667 6.83 6.83 40.30 2.17
2797 5885 3.938963 GCATATTTCAGTGAGGTCCGAAA 59.061 43.478 0.00 0.00 0.00 3.46
2798 5886 3.531538 GCATATTTCAGTGAGGTCCGAA 58.468 45.455 0.00 0.00 0.00 4.30
2799 5887 2.481276 CGCATATTTCAGTGAGGTCCGA 60.481 50.000 0.00 0.00 0.00 4.55
2800 5888 1.860950 CGCATATTTCAGTGAGGTCCG 59.139 52.381 0.00 0.00 0.00 4.79
2801 5889 3.179443 TCGCATATTTCAGTGAGGTCC 57.821 47.619 0.00 0.00 0.00 4.46
2802 5890 5.741388 ATTTCGCATATTTCAGTGAGGTC 57.259 39.130 0.00 0.00 0.00 3.85
2803 5891 6.515272 AAATTTCGCATATTTCAGTGAGGT 57.485 33.333 0.00 0.00 0.00 3.85
2804 5892 5.678483 CGAAATTTCGCATATTTCAGTGAGG 59.322 40.000 26.01 0.00 44.26 3.86
2805 5893 6.707752 CGAAATTTCGCATATTTCAGTGAG 57.292 37.500 26.01 0.00 44.26 3.51
2907 5995 9.496873 TCGAAATTTTGAGTTAGATCCAAACTA 57.503 29.630 10.24 0.00 37.31 2.24
2908 5996 8.391075 TCGAAATTTTGAGTTAGATCCAAACT 57.609 30.769 10.09 10.09 39.84 2.66
2909 5997 7.750903 CCTCGAAATTTTGAGTTAGATCCAAAC 59.249 37.037 26.68 1.19 37.05 2.93
2910 5998 7.447238 ACCTCGAAATTTTGAGTTAGATCCAAA 59.553 33.333 26.68 0.00 37.05 3.28
2911 5999 6.940298 ACCTCGAAATTTTGAGTTAGATCCAA 59.060 34.615 26.68 0.00 37.05 3.53
2912 6000 6.472887 ACCTCGAAATTTTGAGTTAGATCCA 58.527 36.000 26.68 0.00 37.05 3.41
2913 6001 6.986904 ACCTCGAAATTTTGAGTTAGATCC 57.013 37.500 26.68 0.00 37.05 3.36
2926 6014 9.563898 GTCCGAAATATTTTTAACCTCGAAATT 57.436 29.630 1.43 0.00 0.00 1.82
2927 6015 8.186163 GGTCCGAAATATTTTTAACCTCGAAAT 58.814 33.333 14.70 0.00 0.00 2.17
2928 6016 7.174599 TGGTCCGAAATATTTTTAACCTCGAAA 59.825 33.333 19.27 4.98 0.00 3.46
2929 6017 6.654161 TGGTCCGAAATATTTTTAACCTCGAA 59.346 34.615 19.27 5.23 0.00 3.71
2930 6018 6.092533 GTGGTCCGAAATATTTTTAACCTCGA 59.907 38.462 19.27 0.00 0.00 4.04
2931 6019 6.128227 TGTGGTCCGAAATATTTTTAACCTCG 60.128 38.462 19.27 10.64 0.00 4.63
2932 6020 7.025365 GTGTGGTCCGAAATATTTTTAACCTC 58.975 38.462 19.27 17.14 0.00 3.85
2933 6021 6.717997 AGTGTGGTCCGAAATATTTTTAACCT 59.282 34.615 19.27 5.23 0.00 3.50
2934 6022 6.804783 CAGTGTGGTCCGAAATATTTTTAACC 59.195 38.462 14.94 14.94 0.00 2.85
2935 6023 7.586747 TCAGTGTGGTCCGAAATATTTTTAAC 58.413 34.615 1.43 1.36 0.00 2.01
2936 6024 7.747155 TCAGTGTGGTCCGAAATATTTTTAA 57.253 32.000 1.43 0.00 0.00 1.52
2937 6025 7.747155 TTCAGTGTGGTCCGAAATATTTTTA 57.253 32.000 1.43 0.00 0.00 1.52
2938 6026 6.642707 TTCAGTGTGGTCCGAAATATTTTT 57.357 33.333 1.43 0.00 0.00 1.94
2939 6027 6.642707 TTTCAGTGTGGTCCGAAATATTTT 57.357 33.333 1.43 0.00 0.00 1.82
2940 6028 6.834168 ATTTCAGTGTGGTCCGAAATATTT 57.166 33.333 0.00 0.00 36.56 1.40
2941 6029 7.556275 ACATATTTCAGTGTGGTCCGAAATATT 59.444 33.333 14.34 7.70 43.47 1.28
2942 6030 7.012327 CACATATTTCAGTGTGGTCCGAAATAT 59.988 37.037 12.44 12.44 45.32 1.28
2943 6031 6.315144 CACATATTTCAGTGTGGTCCGAAATA 59.685 38.462 9.83 9.83 41.82 1.40
2944 6032 5.123820 CACATATTTCAGTGTGGTCCGAAAT 59.876 40.000 6.83 6.83 41.46 2.17
2945 6033 4.454161 CACATATTTCAGTGTGGTCCGAAA 59.546 41.667 0.00 0.00 41.46 3.46
2946 6034 4.000325 CACATATTTCAGTGTGGTCCGAA 59.000 43.478 0.00 0.00 41.46 4.30
2947 6035 3.259625 TCACATATTTCAGTGTGGTCCGA 59.740 43.478 5.76 0.00 44.41 4.55
2948 6036 3.595173 TCACATATTTCAGTGTGGTCCG 58.405 45.455 5.76 0.00 44.41 4.79
2949 6037 5.957842 TTTCACATATTTCAGTGTGGTCC 57.042 39.130 5.76 0.00 44.41 4.46
2950 6038 7.271223 CGAAATTTCACATATTTCAGTGTGGTC 59.729 37.037 17.99 0.00 44.41 4.02
2951 6039 7.040755 TCGAAATTTCACATATTTCAGTGTGGT 60.041 33.333 17.99 0.00 44.41 4.16
2952 6040 7.304735 TCGAAATTTCACATATTTCAGTGTGG 58.695 34.615 17.99 0.00 44.41 4.17
2953 6041 8.726650 TTCGAAATTTCACATATTTCAGTGTG 57.273 30.769 17.99 0.00 45.37 3.82
2954 6042 9.743057 TTTTCGAAATTTCACATATTTCAGTGT 57.257 25.926 17.99 0.00 40.40 3.55
2991 6079 5.236263 GCAGGGTCAAAAATTTCAACGAAAT 59.764 36.000 0.00 0.00 43.07 2.17
2992 6080 4.568760 GCAGGGTCAAAAATTTCAACGAAA 59.431 37.500 0.00 0.00 35.94 3.46
2993 6081 4.116238 GCAGGGTCAAAAATTTCAACGAA 58.884 39.130 0.00 0.00 0.00 3.85
2994 6082 3.383185 AGCAGGGTCAAAAATTTCAACGA 59.617 39.130 0.00 0.00 0.00 3.85
2995 6083 3.716601 AGCAGGGTCAAAAATTTCAACG 58.283 40.909 0.00 0.00 0.00 4.10
2996 6084 5.115480 TCAAGCAGGGTCAAAAATTTCAAC 58.885 37.500 0.00 0.00 0.00 3.18
2997 6085 5.350504 TCAAGCAGGGTCAAAAATTTCAA 57.649 34.783 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.