Multiple sequence alignment - TraesCS2D01G173400

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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 TraesCS2D01G173400 chr2D 100.000 4555 0 0 1 4555 117184485 117189039 0.000000e+00 8412.0
1 TraesCS2D01G173400 chr2D 82.223 2132 304 42 963 3033 83839605 83841722 0.000000e+00 1768.0
2 TraesCS2D01G173400 chr2D 81.593 1695 288 11 1314 2993 84934120 84932435 0.000000e+00 1380.0
3 TraesCS2D01G173400 chr2D 80.461 1735 313 14 1314 3034 84773939 84772217 0.000000e+00 1303.0
4 TraesCS2D01G173400 chr2D 95.385 715 27 4 3847 4555 102661238 102660524 0.000000e+00 1133.0
5 TraesCS2D01G173400 chr2D 82.113 1079 172 6 1965 3034 85403967 85402901 0.000000e+00 904.0
6 TraesCS2D01G173400 chr2D 78.189 784 142 17 3061 3832 83841780 83842546 1.480000e-129 473.0
7 TraesCS2D01G173400 chr2A 94.522 2574 118 13 1283 3847 118477262 118479821 0.000000e+00 3951.0
8 TraesCS2D01G173400 chr2A 80.610 1738 309 20 1314 3034 85608346 85606620 0.000000e+00 1317.0
9 TraesCS2D01G173400 chr2A 92.551 537 31 3 780 1308 118476644 118477179 0.000000e+00 761.0
10 TraesCS2D01G173400 chr2A 77.807 766 143 17 3061 3817 84608965 84609712 8.990000e-122 448.0
11 TraesCS2D01G173400 chr2A 77.078 794 150 16 3061 3838 86050830 86050053 3.260000e-116 429.0
12 TraesCS2D01G173400 chr2A 77.470 759 142 15 3061 3806 85803946 85803204 1.170000e-115 427.0
13 TraesCS2D01G173400 chr2A 87.124 233 22 4 430 657 118476160 118476389 1.630000e-64 257.0
14 TraesCS2D01G173400 chr2A 81.356 295 41 12 977 1261 85604183 85603893 1.270000e-55 228.0
15 TraesCS2D01G173400 chr2A 92.929 99 4 2 673 771 118476442 118476537 1.710000e-29 141.0
16 TraesCS2D01G173400 chr2A 76.836 177 39 2 254 429 176654780 176654955 1.040000e-16 99.0
17 TraesCS2D01G173400 chr2B 93.854 2587 135 7 1283 3847 167494430 167497014 0.000000e+00 3875.0
18 TraesCS2D01G173400 chr2B 83.832 1738 254 15 1314 3033 135707997 135709725 0.000000e+00 1628.0
19 TraesCS2D01G173400 chr2B 89.519 1288 75 25 50 1308 167493163 167494419 0.000000e+00 1576.0
20 TraesCS2D01G173400 chr2B 81.311 1739 295 14 1314 3034 137618304 137616578 0.000000e+00 1384.0
21 TraesCS2D01G173400 chr2B 81.106 1736 304 10 1314 3034 136633878 136632152 0.000000e+00 1367.0
22 TraesCS2D01G173400 chr2B 81.715 1318 235 4 1723 3034 136811177 136809860 0.000000e+00 1094.0
23 TraesCS2D01G173400 chr2B 78.062 743 144 10 3061 3796 135709783 135710513 6.950000e-123 451.0
24 TraesCS2D01G173400 chr2B 77.331 697 142 11 3061 3754 137800804 137800121 9.180000e-107 398.0
25 TraesCS2D01G173400 chr2B 78.818 203 30 8 1060 1256 136634181 136633986 1.720000e-24 124.0
26 TraesCS2D01G173400 chr5A 96.338 710 25 1 3846 4555 691990584 691991292 0.000000e+00 1166.0
27 TraesCS2D01G173400 chr5A 81.714 175 25 5 261 431 51793031 51793202 6.140000e-29 139.0
28 TraesCS2D01G173400 chr7B 96.056 710 28 0 3846 4555 381910571 381909862 0.000000e+00 1157.0
29 TraesCS2D01G173400 chr7B 94.854 719 34 3 3838 4555 745068974 745069690 0.000000e+00 1120.0
30 TraesCS2D01G173400 chr3A 95.628 709 31 0 3847 4555 442902136 442902844 0.000000e+00 1138.0
31 TraesCS2D01G173400 chr4D 96.377 690 25 0 3846 4535 95519610 95518921 0.000000e+00 1136.0
32 TraesCS2D01G173400 chr5D 95.372 713 29 3 3847 4555 423357223 423357935 0.000000e+00 1131.0
33 TraesCS2D01G173400 chr5D 83.422 187 23 3 253 431 462454613 462454799 2.820000e-37 167.0
34 TraesCS2D01G173400 chr7A 95.359 711 30 3 3847 4555 288229496 288230205 0.000000e+00 1127.0
35 TraesCS2D01G173400 chr7A 80.371 1294 237 11 1314 2601 571323197 571321915 0.000000e+00 966.0
36 TraesCS2D01G173400 chr7A 83.855 415 67 0 2619 3033 571320487 571320073 3.300000e-106 396.0
37 TraesCS2D01G173400 chr3D 95.084 712 33 2 3846 4555 568484804 568485515 0.000000e+00 1120.0
38 TraesCS2D01G173400 chr3B 92.355 484 29 4 179 662 166526456 166526931 0.000000e+00 682.0
39 TraesCS2D01G173400 chr3B 91.386 267 16 6 665 928 166526967 166527229 4.330000e-95 359.0
40 TraesCS2D01G173400 chr3B 79.781 183 28 3 258 431 107966104 107966286 1.720000e-24 124.0
41 TraesCS2D01G173400 chr4A 78.457 687 126 13 3126 3806 349799400 349798730 3.260000e-116 429.0
42 TraesCS2D01G173400 chr6D 80.392 204 30 6 249 443 388209938 388209736 3.670000e-31 147.0
43 TraesCS2D01G173400 chr1A 78.462 195 36 6 254 442 565188656 565188462 6.190000e-24 122.0
44 TraesCS2D01G173400 chr1A 92.157 51 1 3 399 449 574387552 574387599 8.180000e-08 69.4
45 TraesCS2D01G173400 chr5B 78.378 148 24 5 257 397 61147939 61148085 6.280000e-14 89.8
46 TraesCS2D01G173400 chr7D 79.487 117 20 3 257 369 220025361 220025245 3.780000e-11 80.5


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 TraesCS2D01G173400 chr2D 117184485 117189039 4554 False 8412.0 8412 100.0000 1 4555 1 chr2D.!!$F1 4554
1 TraesCS2D01G173400 chr2D 84932435 84934120 1685 True 1380.0 1380 81.5930 1314 2993 1 chr2D.!!$R2 1679
2 TraesCS2D01G173400 chr2D 84772217 84773939 1722 True 1303.0 1303 80.4610 1314 3034 1 chr2D.!!$R1 1720
3 TraesCS2D01G173400 chr2D 102660524 102661238 714 True 1133.0 1133 95.3850 3847 4555 1 chr2D.!!$R4 708
4 TraesCS2D01G173400 chr2D 83839605 83842546 2941 False 1120.5 1768 80.2060 963 3832 2 chr2D.!!$F2 2869
5 TraesCS2D01G173400 chr2D 85402901 85403967 1066 True 904.0 904 82.1130 1965 3034 1 chr2D.!!$R3 1069
6 TraesCS2D01G173400 chr2A 118476160 118479821 3661 False 1277.5 3951 91.7815 430 3847 4 chr2A.!!$F3 3417
7 TraesCS2D01G173400 chr2A 85603893 85608346 4453 True 772.5 1317 80.9830 977 3034 2 chr2A.!!$R3 2057
8 TraesCS2D01G173400 chr2A 84608965 84609712 747 False 448.0 448 77.8070 3061 3817 1 chr2A.!!$F1 756
9 TraesCS2D01G173400 chr2A 86050053 86050830 777 True 429.0 429 77.0780 3061 3838 1 chr2A.!!$R2 777
10 TraesCS2D01G173400 chr2A 85803204 85803946 742 True 427.0 427 77.4700 3061 3806 1 chr2A.!!$R1 745
11 TraesCS2D01G173400 chr2B 167493163 167497014 3851 False 2725.5 3875 91.6865 50 3847 2 chr2B.!!$F2 3797
12 TraesCS2D01G173400 chr2B 137616578 137618304 1726 True 1384.0 1384 81.3110 1314 3034 1 chr2B.!!$R2 1720
13 TraesCS2D01G173400 chr2B 136809860 136811177 1317 True 1094.0 1094 81.7150 1723 3034 1 chr2B.!!$R1 1311
14 TraesCS2D01G173400 chr2B 135707997 135710513 2516 False 1039.5 1628 80.9470 1314 3796 2 chr2B.!!$F1 2482
15 TraesCS2D01G173400 chr2B 136632152 136634181 2029 True 745.5 1367 79.9620 1060 3034 2 chr2B.!!$R4 1974
16 TraesCS2D01G173400 chr2B 137800121 137800804 683 True 398.0 398 77.3310 3061 3754 1 chr2B.!!$R3 693
17 TraesCS2D01G173400 chr5A 691990584 691991292 708 False 1166.0 1166 96.3380 3846 4555 1 chr5A.!!$F2 709
18 TraesCS2D01G173400 chr7B 381909862 381910571 709 True 1157.0 1157 96.0560 3846 4555 1 chr7B.!!$R1 709
19 TraesCS2D01G173400 chr7B 745068974 745069690 716 False 1120.0 1120 94.8540 3838 4555 1 chr7B.!!$F1 717
20 TraesCS2D01G173400 chr3A 442902136 442902844 708 False 1138.0 1138 95.6280 3847 4555 1 chr3A.!!$F1 708
21 TraesCS2D01G173400 chr4D 95518921 95519610 689 True 1136.0 1136 96.3770 3846 4535 1 chr4D.!!$R1 689
22 TraesCS2D01G173400 chr5D 423357223 423357935 712 False 1131.0 1131 95.3720 3847 4555 1 chr5D.!!$F1 708
23 TraesCS2D01G173400 chr7A 288229496 288230205 709 False 1127.0 1127 95.3590 3847 4555 1 chr7A.!!$F1 708
24 TraesCS2D01G173400 chr7A 571320073 571323197 3124 True 681.0 966 82.1130 1314 3033 2 chr7A.!!$R1 1719
25 TraesCS2D01G173400 chr3D 568484804 568485515 711 False 1120.0 1120 95.0840 3846 4555 1 chr3D.!!$F1 709
26 TraesCS2D01G173400 chr3B 166526456 166527229 773 False 520.5 682 91.8705 179 928 2 chr3B.!!$F2 749
27 TraesCS2D01G173400 chr4A 349798730 349799400 670 True 429.0 429 78.4570 3126 3806 1 chr4A.!!$R1 680

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
341 360 0.108041 TCCCGCATTAAGGTCGGTTC 60.108 55.0 17.32 0.0 41.46 3.62 F
1958 2307 0.034670 GGGCAAGACAGATGGCTCTT 60.035 55.0 0.00 0.0 42.51 2.85 F
2125 2474 0.671251 TGTTGGGCGTTTGGACAATC 59.329 50.0 0.00 0.0 0.00 2.67 F
2634 4398 2.093288 GGGTCAGTCAAGCATGATGAGA 60.093 50.0 0.00 0.0 38.01 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2107 2456 0.038618 GGATTGTCCAAACGCCCAAC 60.039 55.000 0.0 0.0 36.28 3.77 R
2926 4690 1.279840 GCTGCGTCACCTGTGTTTC 59.720 57.895 0.0 0.0 0.00 2.78 R
3246 5047 1.312815 GGGGACATGTATTCAGCAGC 58.687 55.000 0.0 0.0 0.00 5.25 R
4419 6898 1.000052 GTCCCTCGGCTACTTATGCTC 60.000 57.143 0.0 0.0 0.00 4.26 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 2.355363 TTCGTCGCCTTCACGGTG 60.355 61.111 0.56 0.56 44.95 4.94
18 19 3.141522 TTCGTCGCCTTCACGGTGT 62.142 57.895 8.17 0.00 43.94 4.16
19 20 2.632136 TTCGTCGCCTTCACGGTGTT 62.632 55.000 8.17 0.00 43.94 3.32
20 21 2.241880 CGTCGCCTTCACGGTGTTT 61.242 57.895 8.17 0.00 43.94 2.83
21 22 1.768112 CGTCGCCTTCACGGTGTTTT 61.768 55.000 8.17 0.00 43.94 2.43
22 23 1.219646 GTCGCCTTCACGGTGTTTTA 58.780 50.000 8.17 0.00 43.94 1.52
23 24 1.598601 GTCGCCTTCACGGTGTTTTAA 59.401 47.619 8.17 0.00 43.94 1.52
24 25 1.598601 TCGCCTTCACGGTGTTTTAAC 59.401 47.619 8.17 0.00 43.94 2.01
25 26 1.331138 CGCCTTCACGGTGTTTTAACA 59.669 47.619 8.17 0.00 38.52 2.41
26 27 2.601266 CGCCTTCACGGTGTTTTAACAG 60.601 50.000 8.17 0.00 40.05 3.16
27 28 2.356695 GCCTTCACGGTGTTTTAACAGT 59.643 45.455 8.17 0.00 40.05 3.55
28 29 3.790789 GCCTTCACGGTGTTTTAACAGTG 60.791 47.826 8.17 8.07 44.51 3.66
29 30 3.375922 CCTTCACGGTGTTTTAACAGTGT 59.624 43.478 8.17 0.00 43.85 3.55
30 31 4.495184 CCTTCACGGTGTTTTAACAGTGTC 60.495 45.833 8.17 0.00 43.85 3.67
31 32 2.937799 TCACGGTGTTTTAACAGTGTCC 59.062 45.455 8.17 0.00 43.85 4.02
32 33 2.678836 CACGGTGTTTTAACAGTGTCCA 59.321 45.455 0.00 0.00 40.17 4.02
33 34 3.314080 CACGGTGTTTTAACAGTGTCCAT 59.686 43.478 0.00 0.00 40.17 3.41
34 35 3.949113 ACGGTGTTTTAACAGTGTCCATT 59.051 39.130 0.00 0.00 40.05 3.16
35 36 4.399934 ACGGTGTTTTAACAGTGTCCATTT 59.600 37.500 0.00 0.00 40.05 2.32
36 37 4.973663 CGGTGTTTTAACAGTGTCCATTTC 59.026 41.667 0.00 0.00 40.05 2.17
37 38 5.449314 CGGTGTTTTAACAGTGTCCATTTCA 60.449 40.000 0.00 0.00 40.05 2.69
38 39 5.977129 GGTGTTTTAACAGTGTCCATTTCAG 59.023 40.000 0.00 0.00 40.05 3.02
39 40 6.405397 GGTGTTTTAACAGTGTCCATTTCAGT 60.405 38.462 0.00 0.00 40.05 3.41
40 41 7.033185 GTGTTTTAACAGTGTCCATTTCAGTT 58.967 34.615 0.00 0.00 40.05 3.16
41 42 7.220108 GTGTTTTAACAGTGTCCATTTCAGTTC 59.780 37.037 0.00 0.00 40.05 3.01
42 43 7.094162 TGTTTTAACAGTGTCCATTTCAGTTCA 60.094 33.333 0.00 0.00 34.30 3.18
43 44 6.618287 TTAACAGTGTCCATTTCAGTTCAG 57.382 37.500 0.00 0.00 0.00 3.02
44 45 2.880890 ACAGTGTCCATTTCAGTTCAGC 59.119 45.455 0.00 0.00 0.00 4.26
45 46 3.144506 CAGTGTCCATTTCAGTTCAGCT 58.855 45.455 0.00 0.00 0.00 4.24
46 47 3.058432 CAGTGTCCATTTCAGTTCAGCTG 60.058 47.826 7.63 7.63 46.34 4.24
47 48 2.227388 GTGTCCATTTCAGTTCAGCTGG 59.773 50.000 15.13 0.00 45.08 4.85
48 49 1.200948 GTCCATTTCAGTTCAGCTGGC 59.799 52.381 15.13 7.50 45.08 4.85
80 81 2.099921 AGGAATTCCGTCGATCTCAGTG 59.900 50.000 18.82 0.00 42.08 3.66
101 103 9.429109 TCAGTGTTGGTAAATCTATATCTGGTA 57.571 33.333 0.00 0.00 0.00 3.25
103 105 8.368668 AGTGTTGGTAAATCTATATCTGGTAGC 58.631 37.037 0.00 0.00 0.00 3.58
121 123 3.679824 AGCAGTACCTTTTTCGTAGCT 57.320 42.857 0.00 0.00 0.00 3.32
123 125 3.006537 AGCAGTACCTTTTTCGTAGCTGA 59.993 43.478 0.00 0.00 0.00 4.26
143 145 8.358582 AGCTGAATTTGTGATCTTTTATTCCT 57.641 30.769 0.00 0.00 0.00 3.36
176 178 4.003788 CGTCGGCAAGTGGACCCT 62.004 66.667 0.00 0.00 0.00 4.34
177 179 2.047179 GTCGGCAAGTGGACCCTC 60.047 66.667 0.00 0.00 0.00 4.30
251 253 2.751806 CTCTCTGCATGGGGAACTTTTC 59.248 50.000 0.00 0.00 0.00 2.29
266 268 6.080406 GGAACTTTTCTTATTCAGTCTTGCG 58.920 40.000 0.00 0.00 0.00 4.85
269 271 7.259290 ACTTTTCTTATTCAGTCTTGCGAAA 57.741 32.000 0.00 0.00 0.00 3.46
270 272 7.875971 ACTTTTCTTATTCAGTCTTGCGAAAT 58.124 30.769 0.00 0.00 0.00 2.17
280 282 2.342948 GTCTTGCGAAATCTCAGTCGAC 59.657 50.000 7.70 7.70 39.64 4.20
304 306 2.349297 ACTTCGTTAAGTCTCAGCCG 57.651 50.000 0.00 0.00 42.42 5.52
305 307 1.884579 ACTTCGTTAAGTCTCAGCCGA 59.115 47.619 0.00 0.00 42.42 5.54
306 308 2.492484 ACTTCGTTAAGTCTCAGCCGAT 59.508 45.455 0.00 0.00 42.42 4.18
307 309 2.561733 TCGTTAAGTCTCAGCCGATG 57.438 50.000 0.00 0.00 0.00 3.84
308 310 0.924090 CGTTAAGTCTCAGCCGATGC 59.076 55.000 0.00 0.00 37.95 3.91
334 353 2.103094 TCTGTGAGATCCCGCATTAAGG 59.897 50.000 0.00 0.00 0.00 2.69
340 359 0.544697 ATCCCGCATTAAGGTCGGTT 59.455 50.000 17.32 6.22 41.46 4.44
341 360 0.108041 TCCCGCATTAAGGTCGGTTC 60.108 55.000 17.32 0.00 41.46 3.62
382 401 7.482654 TTTTCCTCTCTTGCATGTTATATCG 57.517 36.000 0.00 0.00 0.00 2.92
383 402 5.139435 TCCTCTCTTGCATGTTATATCGG 57.861 43.478 0.00 0.00 0.00 4.18
389 408 4.814234 TCTTGCATGTTATATCGGTTGACC 59.186 41.667 0.00 0.00 0.00 4.02
409 428 5.246656 TGACCGAGACTTAGTTAAATCCCAA 59.753 40.000 0.00 0.00 0.00 4.12
411 430 6.346896 ACCGAGACTTAGTTAAATCCCAATC 58.653 40.000 0.00 0.00 0.00 2.67
432 451 1.474879 GACTGAGACCTAGCCACACTC 59.525 57.143 0.00 0.00 0.00 3.51
527 546 8.191446 GGGTTCAAAAGATAAAATAAGAGCTCC 58.809 37.037 10.93 0.00 0.00 4.70
564 588 7.707035 CGAAAGTAGCATCTTTGGAGTAATAGT 59.293 37.037 10.12 0.00 37.70 2.12
586 610 1.585297 TTTTTCCCACGACTTCGACC 58.415 50.000 5.47 0.00 43.02 4.79
606 630 5.936372 CGACCAATGTGATCCTATGATGAAT 59.064 40.000 0.00 0.00 0.00 2.57
734 795 1.988293 TGAGGCAATCCGTTTTTCCA 58.012 45.000 0.00 0.00 37.47 3.53
771 832 2.556189 TCTTGCGGCAATCTGCTTTTTA 59.444 40.909 16.80 0.00 44.28 1.52
772 833 3.005261 TCTTGCGGCAATCTGCTTTTTAA 59.995 39.130 16.80 0.00 44.28 1.52
792 953 3.744238 ATTTTTGGTTCCTTTGTCCCG 57.256 42.857 0.00 0.00 0.00 5.14
870 1034 1.299648 CGAACCATCCAGAGCCCAA 59.700 57.895 0.00 0.00 0.00 4.12
876 1040 2.240918 ATCCAGAGCCCAAAGCCCA 61.241 57.895 0.00 0.00 45.47 5.36
939 1103 1.807142 CAGAAGCGAGGGAAAAACTCC 59.193 52.381 0.00 0.00 44.54 3.85
951 1116 1.063654 AAAACTCCTTCCCGTCCCCA 61.064 55.000 0.00 0.00 0.00 4.96
955 1120 0.111639 CTCCTTCCCGTCCCCAAAAA 59.888 55.000 0.00 0.00 0.00 1.94
1273 1464 2.287194 CCATCAACCCCCTCCCCT 60.287 66.667 0.00 0.00 0.00 4.79
1308 1559 4.436242 TGGTAGTCTGATTCGTCTGAAC 57.564 45.455 0.00 0.00 36.81 3.18
1545 1880 4.582869 TCCAGAAACACAAGATCTCCATG 58.417 43.478 0.00 0.00 0.00 3.66
1670 2011 4.922206 ACAAATACTGGAGATCCTTTGCA 58.078 39.130 9.88 0.00 33.36 4.08
1703 2052 4.848757 AGAAAAAGAGAAATGTGACGCAC 58.151 39.130 0.00 3.44 34.56 5.34
1958 2307 0.034670 GGGCAAGACAGATGGCTCTT 60.035 55.000 0.00 0.00 42.51 2.85
2057 2406 5.070001 CCTGGTGGTTTTGTAGAGATCAAA 58.930 41.667 0.00 0.00 33.76 2.69
2061 2410 7.004086 TGGTGGTTTTGTAGAGATCAAAGATT 58.996 34.615 0.00 0.00 36.40 2.40
2064 2413 8.017946 GTGGTTTTGTAGAGATCAAAGATTCAC 58.982 37.037 0.00 0.00 36.40 3.18
2107 2456 3.898517 TCGAGTCCTTCAGCGTATATG 57.101 47.619 0.00 0.00 0.00 1.78
2125 2474 0.671251 TGTTGGGCGTTTGGACAATC 59.329 50.000 0.00 0.00 0.00 2.67
2249 2598 7.572523 TGCTAATAATTTCTCCATTCCAGTG 57.427 36.000 0.00 0.00 0.00 3.66
2558 2912 3.769844 TCGATAAACTCTGGAAGGAGCTT 59.230 43.478 0.00 0.00 36.87 3.74
2634 4398 2.093288 GGGTCAGTCAAGCATGATGAGA 60.093 50.000 0.00 0.00 38.01 3.27
2670 4434 2.203181 GCTCATCCAGCCAGCCTC 60.203 66.667 0.00 0.00 43.17 4.70
2702 4466 2.780010 GGATGGGAAGGAAGGAGATCAA 59.220 50.000 0.00 0.00 0.00 2.57
2938 4702 4.649674 AGAGTACTTCAGAAACACAGGTGA 59.350 41.667 6.40 0.00 0.00 4.02
3245 5046 5.497474 GTCTGTTGTCATATTGGGGTTAGT 58.503 41.667 0.00 0.00 0.00 2.24
3246 5047 5.354234 GTCTGTTGTCATATTGGGGTTAGTG 59.646 44.000 0.00 0.00 0.00 2.74
3363 5170 4.895224 TTACCACGCTACTACAGAGATG 57.105 45.455 0.00 0.00 0.00 2.90
3412 5219 4.593956 ACTTGGATCCCAGACAAAAGATC 58.406 43.478 19.41 0.00 33.81 2.75
3519 5329 3.512329 TGAATCAGTTGCAGGCAATGAAT 59.488 39.130 10.21 8.02 38.28 2.57
3527 5337 4.274602 TGCAGGCAATGAATCAACAAAT 57.725 36.364 0.00 0.00 0.00 2.32
3648 5460 8.039538 GGTAGTTACTGTGCTTTAAGTTATCCT 58.960 37.037 0.00 0.00 0.00 3.24
3706 5518 3.152341 ACTTTCCATGCTGTCCTGAAAG 58.848 45.455 13.50 13.50 44.57 2.62
3760 5633 5.068636 ACAGTCTGATGCTGAATTTCTTGT 58.931 37.500 6.91 0.00 37.40 3.16
3767 5640 7.811236 TCTGATGCTGAATTTCTTGTTTGATTC 59.189 33.333 0.00 0.00 0.00 2.52
3842 5718 1.021202 CTTGGCTGACGGTGTTTCAA 58.979 50.000 0.00 0.00 0.00 2.69
4034 6367 4.814234 TGCCACAAATTAGATCATCGGTAC 59.186 41.667 0.00 0.00 0.00 3.34
4093 6426 7.478667 CGAGTAGCTGTAAACTTGCATTAAAAG 59.521 37.037 0.00 0.00 0.00 2.27
4158 6635 4.870991 TGAACTCGTGAACATTGTGTACAA 59.129 37.500 0.00 0.00 40.51 2.41
4419 6898 4.134379 ACATACTCTCATTGTCTGGCAG 57.866 45.455 8.58 8.58 0.00 4.85
4528 7432 2.022718 TAAGTGGCAAAAGCCCCATT 57.977 45.000 3.77 0.00 32.95 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.355363 CACCGTGAAGGCGACGAA 60.355 61.111 0.00 0.00 46.52 3.85
5 6 1.331138 TGTTAAAACACCGTGAAGGCG 59.669 47.619 5.28 0.00 46.52 5.52
6 7 2.356695 ACTGTTAAAACACCGTGAAGGC 59.643 45.455 5.28 0.00 46.52 4.35
8 9 4.495184 GGACACTGTTAAAACACCGTGAAG 60.495 45.833 17.25 0.08 37.30 3.02
9 10 3.374678 GGACACTGTTAAAACACCGTGAA 59.625 43.478 17.25 0.00 37.30 3.18
10 11 2.937799 GGACACTGTTAAAACACCGTGA 59.062 45.455 17.25 0.00 37.30 4.35
11 12 2.678836 TGGACACTGTTAAAACACCGTG 59.321 45.455 11.54 11.54 39.55 4.94
12 13 2.988570 TGGACACTGTTAAAACACCGT 58.011 42.857 0.00 0.00 34.70 4.83
13 14 4.561735 AATGGACACTGTTAAAACACCG 57.438 40.909 0.00 0.00 34.70 4.94
14 15 5.897050 TGAAATGGACACTGTTAAAACACC 58.103 37.500 0.00 0.00 34.70 4.16
15 16 6.560711 ACTGAAATGGACACTGTTAAAACAC 58.439 36.000 0.00 0.00 34.70 3.32
16 17 6.767524 ACTGAAATGGACACTGTTAAAACA 57.232 33.333 0.00 0.00 37.37 2.83
17 18 7.254852 TGAACTGAAATGGACACTGTTAAAAC 58.745 34.615 0.00 0.00 0.00 2.43
18 19 7.397892 TGAACTGAAATGGACACTGTTAAAA 57.602 32.000 0.00 0.00 0.00 1.52
19 20 6.459573 GCTGAACTGAAATGGACACTGTTAAA 60.460 38.462 0.00 0.00 0.00 1.52
20 21 5.008613 GCTGAACTGAAATGGACACTGTTAA 59.991 40.000 0.00 0.00 0.00 2.01
21 22 4.515191 GCTGAACTGAAATGGACACTGTTA 59.485 41.667 0.00 0.00 0.00 2.41
22 23 3.316308 GCTGAACTGAAATGGACACTGTT 59.684 43.478 0.00 0.00 0.00 3.16
23 24 2.880890 GCTGAACTGAAATGGACACTGT 59.119 45.455 0.00 0.00 0.00 3.55
24 25 3.144506 AGCTGAACTGAAATGGACACTG 58.855 45.455 0.00 0.00 0.00 3.66
25 26 3.498774 AGCTGAACTGAAATGGACACT 57.501 42.857 0.00 0.00 0.00 3.55
55 56 4.575885 TGAGATCGACGGAATTCCTTTTT 58.424 39.130 22.05 3.82 0.00 1.94
56 57 4.184629 CTGAGATCGACGGAATTCCTTTT 58.815 43.478 22.05 6.38 0.00 2.27
65 66 0.526211 CCAACACTGAGATCGACGGA 59.474 55.000 8.37 0.00 0.00 4.69
67 68 2.913777 TACCAACACTGAGATCGACG 57.086 50.000 0.00 0.00 0.00 5.12
80 81 8.368668 ACTGCTACCAGATATAGATTTACCAAC 58.631 37.037 0.00 0.00 41.77 3.77
101 103 3.006537 TCAGCTACGAAAAAGGTACTGCT 59.993 43.478 0.00 0.00 40.86 4.24
103 105 6.481954 AATTCAGCTACGAAAAAGGTACTG 57.518 37.500 0.00 0.00 40.86 2.74
143 145 1.676678 GACGGCATGCTCCCTGTCTA 61.677 60.000 18.92 0.00 0.00 2.59
230 232 2.503895 AAAGTTCCCCATGCAGAGAG 57.496 50.000 0.00 0.00 0.00 3.20
231 233 2.376518 AGAAAAGTTCCCCATGCAGAGA 59.623 45.455 0.00 0.00 0.00 3.10
232 234 2.800250 AGAAAAGTTCCCCATGCAGAG 58.200 47.619 0.00 0.00 0.00 3.35
233 235 2.978156 AGAAAAGTTCCCCATGCAGA 57.022 45.000 0.00 0.00 0.00 4.26
234 236 5.185635 TGAATAAGAAAAGTTCCCCATGCAG 59.814 40.000 0.00 0.00 0.00 4.41
301 303 2.826428 TCTCACAGAAATAGCATCGGC 58.174 47.619 0.00 0.00 41.61 5.54
302 304 3.993081 GGATCTCACAGAAATAGCATCGG 59.007 47.826 0.00 0.00 0.00 4.18
303 305 3.993081 GGGATCTCACAGAAATAGCATCG 59.007 47.826 0.00 0.00 0.00 3.84
304 306 3.993081 CGGGATCTCACAGAAATAGCATC 59.007 47.826 0.00 0.00 0.00 3.91
305 307 3.805108 GCGGGATCTCACAGAAATAGCAT 60.805 47.826 0.00 0.00 0.00 3.79
306 308 2.483714 GCGGGATCTCACAGAAATAGCA 60.484 50.000 0.00 0.00 0.00 3.49
307 309 2.139118 GCGGGATCTCACAGAAATAGC 58.861 52.381 0.00 0.00 0.00 2.97
308 310 3.459232 TGCGGGATCTCACAGAAATAG 57.541 47.619 0.00 0.00 0.00 1.73
309 311 4.422073 AATGCGGGATCTCACAGAAATA 57.578 40.909 0.00 0.00 0.00 1.40
310 312 3.287867 AATGCGGGATCTCACAGAAAT 57.712 42.857 0.00 0.00 0.00 2.17
311 313 2.787473 AATGCGGGATCTCACAGAAA 57.213 45.000 0.00 0.00 0.00 2.52
312 314 3.432186 CCTTAATGCGGGATCTCACAGAA 60.432 47.826 0.00 0.00 0.00 3.02
362 381 4.887748 ACCGATATAACATGCAAGAGAGG 58.112 43.478 0.00 0.00 0.00 3.69
382 401 5.579904 GGATTTAACTAAGTCTCGGTCAACC 59.420 44.000 0.00 0.00 0.00 3.77
383 402 5.579904 GGGATTTAACTAAGTCTCGGTCAAC 59.420 44.000 0.00 0.00 0.00 3.18
389 408 6.198591 GTCGATTGGGATTTAACTAAGTCTCG 59.801 42.308 0.00 0.00 0.00 4.04
392 411 7.039882 TCAGTCGATTGGGATTTAACTAAGTC 58.960 38.462 8.17 0.00 0.00 3.01
397 416 5.420409 GTCTCAGTCGATTGGGATTTAACT 58.580 41.667 14.10 0.00 28.66 2.24
409 428 1.341089 TGTGGCTAGGTCTCAGTCGAT 60.341 52.381 0.00 0.00 0.00 3.59
411 430 0.171455 GTGTGGCTAGGTCTCAGTCG 59.829 60.000 0.00 0.00 0.00 4.18
432 451 9.646427 CTAGCTAGGCAGAAAGTAATAATAAGG 57.354 37.037 13.32 0.00 0.00 2.69
527 546 4.209452 TGCTACTTTCGAAAGCACTTTG 57.791 40.909 32.49 17.46 41.15 2.77
586 610 9.569167 GCAAATATTCATCATAGGATCACATTG 57.431 33.333 0.00 0.00 0.00 2.82
662 688 2.100252 CTCAAATGAGCCCGCATGAATT 59.900 45.455 0.00 0.00 35.13 2.17
663 689 1.679680 CTCAAATGAGCCCGCATGAAT 59.320 47.619 0.00 0.00 35.13 2.57
771 832 3.452990 ACGGGACAAAGGAACCAAAAATT 59.547 39.130 0.00 0.00 0.00 1.82
772 833 3.035363 ACGGGACAAAGGAACCAAAAAT 58.965 40.909 0.00 0.00 0.00 1.82
792 953 4.592426 GTGGGCCTCACGTCTAAC 57.408 61.111 4.53 0.00 36.56 2.34
840 1001 3.124560 GGATGGTTCGTCTTTAGCTAGC 58.875 50.000 6.62 6.62 0.00 3.42
841 1002 4.098044 TCTGGATGGTTCGTCTTTAGCTAG 59.902 45.833 0.00 0.00 0.00 3.42
842 1003 4.021229 TCTGGATGGTTCGTCTTTAGCTA 58.979 43.478 0.00 0.00 0.00 3.32
843 1004 2.832129 TCTGGATGGTTCGTCTTTAGCT 59.168 45.455 0.00 0.00 0.00 3.32
876 1040 2.590092 GATGGTGGGCCGTTAGCT 59.410 61.111 0.00 0.00 43.05 3.32
939 1103 1.862602 CGCTTTTTGGGGACGGGAAG 61.863 60.000 0.00 0.00 0.00 3.46
1545 1880 3.004002 CGTTGTTTGAGGAACCCCTTAAC 59.996 47.826 0.00 0.00 44.53 2.01
1643 1984 3.133003 AGGATCTCCAGTATTTGTCGGTG 59.867 47.826 0.00 0.00 38.89 4.94
1703 2052 4.804608 TTCCACGTACAACATGAACTTG 57.195 40.909 0.00 0.00 0.00 3.16
1763 2112 7.147585 ACCTGCTGAGAGTAATCATCATTTACT 60.148 37.037 0.00 0.00 41.41 2.24
1795 2144 2.669569 CCGTCCCAGGCAACACAG 60.670 66.667 0.00 0.00 41.41 3.66
1958 2307 4.903045 AAAGGTACCGAATTCCTTCTCA 57.097 40.909 6.18 0.00 40.18 3.27
2051 2400 5.105997 CCCTGAAACCAGTGAATCTTTGATC 60.106 44.000 0.00 0.00 0.00 2.92
2057 2406 2.443255 ACACCCTGAAACCAGTGAATCT 59.557 45.455 0.00 0.00 0.00 2.40
2061 2410 2.105821 CCTTACACCCTGAAACCAGTGA 59.894 50.000 0.00 0.00 0.00 3.41
2064 2413 3.721087 ATCCTTACACCCTGAAACCAG 57.279 47.619 0.00 0.00 0.00 4.00
2107 2456 0.038618 GGATTGTCCAAACGCCCAAC 60.039 55.000 0.00 0.00 36.28 3.77
2232 2581 3.173953 TGCCACTGGAATGGAGAAATT 57.826 42.857 0.00 0.00 43.02 1.82
2558 2912 7.175467 GCCATATATTTGGATGTCAACTCATCA 59.825 37.037 15.64 0.00 44.00 3.07
2670 4434 2.422519 CCTTCCCATCCTCCACTGAATG 60.423 54.545 0.00 0.00 0.00 2.67
2702 4466 0.036732 TTCCTTTGCTGTCATCGGCT 59.963 50.000 0.90 0.00 45.38 5.52
2926 4690 1.279840 GCTGCGTCACCTGTGTTTC 59.720 57.895 0.00 0.00 0.00 2.78
2938 4702 1.490621 GATTGCTTTGTTTGCTGCGT 58.509 45.000 0.00 0.00 0.00 5.24
3245 5046 1.408683 GGGGACATGTATTCAGCAGCA 60.409 52.381 0.00 0.00 0.00 4.41
3246 5047 1.312815 GGGGACATGTATTCAGCAGC 58.687 55.000 0.00 0.00 0.00 5.25
3363 5170 5.679792 GTGTTTCACGTTCAAATGGTCTAAC 59.320 40.000 0.00 0.00 0.00 2.34
3412 5219 1.675552 AACAGGAAAACCACACTCCG 58.324 50.000 0.00 0.00 34.22 4.63
3519 5329 1.592064 TCTGAGCGTGCATTTGTTGA 58.408 45.000 0.00 0.00 0.00 3.18
3527 5337 2.071540 CTTGATTCTTCTGAGCGTGCA 58.928 47.619 0.00 0.00 0.00 4.57
3649 5461 9.924010 ACTACTAGAGGTTCAGAGTTTACATAT 57.076 33.333 0.00 0.00 0.00 1.78
3674 5486 5.106157 ACAGCATGGAAAGTACTGCAAATAC 60.106 40.000 0.00 0.00 43.62 1.89
3727 5596 3.762288 AGCATCAGACTGTAACGGAGTAA 59.238 43.478 1.59 0.00 45.00 2.24
3742 5615 7.597369 TGAATCAAACAAGAAATTCAGCATCAG 59.403 33.333 0.00 0.00 34.20 2.90
3767 5640 9.683069 GGCATACAGGAGTTTCAAAAATATATG 57.317 33.333 0.00 0.00 0.00 1.78
3772 5645 6.418057 TTGGCATACAGGAGTTTCAAAAAT 57.582 33.333 0.00 0.00 0.00 1.82
3775 5648 5.860941 TTTTGGCATACAGGAGTTTCAAA 57.139 34.783 0.00 0.00 0.00 2.69
3842 5718 2.093973 CGCAACTGGTCATCTAGTTCCT 60.094 50.000 0.00 0.00 42.09 3.36
4034 6367 9.227490 CTAATTGTAGACTCAACTATCTTGACG 57.773 37.037 0.00 0.00 0.00 4.35
4061 6394 5.106673 GCAAGTTTACAGCTACTCGGAATTT 60.107 40.000 0.00 0.00 0.00 1.82
4093 6426 6.417191 TTGTGTCACTTGTGTTTACTCTTC 57.583 37.500 4.27 0.00 0.00 2.87
4419 6898 1.000052 GTCCCTCGGCTACTTATGCTC 60.000 57.143 0.00 0.00 0.00 4.26
4528 7432 5.448654 ACTGGATGGCAAATGCTAATTCTA 58.551 37.500 5.25 0.00 41.70 2.10


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

AutoCloner maintained by Alex Coulton.