Multiple sequence alignment - TraesCS7B01G193100

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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 TraesCS7B01G193100 chr7B 100.000 3775 0 0 1 3775 332127886 332131660 0.000000e+00 6972.0
1 TraesCS7B01G193100 chr7B 93.023 43 3 0 781 823 614293576 614293534 3.150000e-06 63.9
2 TraesCS7B01G193100 chr7A 92.936 1897 94 24 2 1872 195832734 195830852 0.000000e+00 2724.0
3 TraesCS7B01G193100 chr7A 93.708 747 35 7 2017 2756 195830762 195830021 0.000000e+00 1109.0
4 TraesCS7B01G193100 chr7D 93.503 1570 82 6 311 1872 188288389 188289946 0.000000e+00 2316.0
5 TraesCS7B01G193100 chr7D 95.289 1019 47 1 2757 3775 428051055 428050038 0.000000e+00 1615.0
6 TraesCS7B01G193100 chr7D 93.657 741 36 6 2023 2756 188290039 188290775 0.000000e+00 1098.0
7 TraesCS7B01G193100 chr7D 92.395 263 18 2 1 262 188190075 188190336 1.280000e-99 374.0
8 TraesCS7B01G193100 chr7D 100.000 54 0 0 258 311 188263977 188264030 2.400000e-17 100.0
9 TraesCS7B01G193100 chr6D 95.584 1019 43 2 2757 3775 420346606 420345590 0.000000e+00 1631.0
10 TraesCS7B01G193100 chr6D 95.294 1020 46 2 2757 3775 414012960 414013978 0.000000e+00 1616.0
11 TraesCS7B01G193100 chr6D 95.196 1020 47 2 2757 3775 30529296 30528278 0.000000e+00 1611.0
12 TraesCS7B01G193100 chr6D 76.391 809 161 26 1000 1790 7292496 7291700 3.510000e-110 409.0
13 TraesCS7B01G193100 chr6D 80.357 336 66 0 2295 2630 7290477 7290142 4.840000e-64 255.0
14 TraesCS7B01G193100 chr2D 95.379 1017 46 1 2757 3773 476394248 476395263 0.000000e+00 1616.0
15 TraesCS7B01G193100 chr2D 95.103 1021 46 3 2757 3775 496374139 496373121 0.000000e+00 1605.0
16 TraesCS7B01G193100 chr2D 77.091 777 148 23 1000 1758 639691232 639690468 4.510000e-114 422.0
17 TraesCS7B01G193100 chr5D 95.093 1019 49 1 2757 3775 23016076 23017093 0.000000e+00 1604.0
18 TraesCS7B01G193100 chr4D 95.093 1019 49 1 2757 3775 28493159 28494176 0.000000e+00 1604.0
19 TraesCS7B01G193100 chr3D 95.093 1019 49 1 2757 3775 593104421 593103404 0.000000e+00 1604.0
20 TraesCS7B01G193100 chr2B 77.477 777 144 23 1000 1758 798826379 798825616 1.610000e-118 436.0
21 TraesCS7B01G193100 chr2A 76.056 852 176 21 1000 1834 765175581 765174741 5.830000e-113 418.0
22 TraesCS7B01G193100 chr2A 90.476 42 4 0 781 822 83783191 83783232 5.270000e-04 56.5
23 TraesCS7B01G193100 chr6A 76.299 789 161 20 1017 1790 7009392 7008615 7.600000e-107 398.0
24 TraesCS7B01G193100 chr6A 76.243 724 138 24 1017 1729 6976845 6976145 1.670000e-93 353.0
25 TraesCS7B01G193100 chr6A 77.629 599 104 17 2182 2756 7006315 7005723 1.680000e-88 337.0
26 TraesCS7B01G193100 chr6A 77.273 462 97 6 2301 2760 611337270 611336815 8.040000e-67 265.0
27 TraesCS7B01G193100 chr6B 77.155 464 96 8 2300 2760 708729727 708729271 1.040000e-65 261.0
28 TraesCS7B01G193100 chr6B 76.458 463 99 8 2301 2760 708722882 708722427 3.770000e-60 243.0
29 TraesCS7B01G193100 chr6B 73.184 716 173 18 1010 1717 708730902 708730198 1.350000e-59 241.0
30 TraesCS7B01G193100 chr6B 73.464 716 154 26 1014 1717 708723886 708723195 1.750000e-58 237.0
31 TraesCS7B01G193100 chr4A 84.091 132 20 1 2535 2666 647381192 647381062 3.960000e-25 126.0
32 TraesCS7B01G193100 chr5B 95.238 42 2 0 778 819 648855339 648855298 2.430000e-07 67.6
33 TraesCS7B01G193100 chr1A 92.857 42 3 0 781 822 522556802 522556843 1.130000e-05 62.1
34 TraesCS7B01G193100 chrUn 94.737 38 2 0 785 822 21191230 21191193 4.070000e-05 60.2
35 TraesCS7B01G193100 chr5A 87.037 54 6 1 774 827 646183833 646183781 4.070000e-05 60.2
36 TraesCS7B01G193100 chr1D 100.000 32 0 0 2303 2334 7729873 7729904 4.070000e-05 60.2
37 TraesCS7B01G193100 chr1D 100.000 31 0 0 2304 2334 7759436 7759466 1.460000e-04 58.4
38 TraesCS7B01G193100 chr1B 86.000 50 7 0 774 823 444064215 444064166 2.000000e-03 54.7


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 TraesCS7B01G193100 chr7B 332127886 332131660 3774 False 6972.0 6972 100.0000 1 3775 1 chr7B.!!$F1 3774
1 TraesCS7B01G193100 chr7A 195830021 195832734 2713 True 1916.5 2724 93.3220 2 2756 2 chr7A.!!$R1 2754
2 TraesCS7B01G193100 chr7D 188288389 188290775 2386 False 1707.0 2316 93.5800 311 2756 2 chr7D.!!$F3 2445
3 TraesCS7B01G193100 chr7D 428050038 428051055 1017 True 1615.0 1615 95.2890 2757 3775 1 chr7D.!!$R1 1018
4 TraesCS7B01G193100 chr6D 420345590 420346606 1016 True 1631.0 1631 95.5840 2757 3775 1 chr6D.!!$R2 1018
5 TraesCS7B01G193100 chr6D 414012960 414013978 1018 False 1616.0 1616 95.2940 2757 3775 1 chr6D.!!$F1 1018
6 TraesCS7B01G193100 chr6D 30528278 30529296 1018 True 1611.0 1611 95.1960 2757 3775 1 chr6D.!!$R1 1018
7 TraesCS7B01G193100 chr6D 7290142 7292496 2354 True 332.0 409 78.3740 1000 2630 2 chr6D.!!$R3 1630
8 TraesCS7B01G193100 chr2D 476394248 476395263 1015 False 1616.0 1616 95.3790 2757 3773 1 chr2D.!!$F1 1016
9 TraesCS7B01G193100 chr2D 496373121 496374139 1018 True 1605.0 1605 95.1030 2757 3775 1 chr2D.!!$R1 1018
10 TraesCS7B01G193100 chr2D 639690468 639691232 764 True 422.0 422 77.0910 1000 1758 1 chr2D.!!$R2 758
11 TraesCS7B01G193100 chr5D 23016076 23017093 1017 False 1604.0 1604 95.0930 2757 3775 1 chr5D.!!$F1 1018
12 TraesCS7B01G193100 chr4D 28493159 28494176 1017 False 1604.0 1604 95.0930 2757 3775 1 chr4D.!!$F1 1018
13 TraesCS7B01G193100 chr3D 593103404 593104421 1017 True 1604.0 1604 95.0930 2757 3775 1 chr3D.!!$R1 1018
14 TraesCS7B01G193100 chr2B 798825616 798826379 763 True 436.0 436 77.4770 1000 1758 1 chr2B.!!$R1 758
15 TraesCS7B01G193100 chr2A 765174741 765175581 840 True 418.0 418 76.0560 1000 1834 1 chr2A.!!$R1 834
16 TraesCS7B01G193100 chr6A 7005723 7009392 3669 True 367.5 398 76.9640 1017 2756 2 chr6A.!!$R3 1739
17 TraesCS7B01G193100 chr6A 6976145 6976845 700 True 353.0 353 76.2430 1017 1729 1 chr6A.!!$R1 712
18 TraesCS7B01G193100 chr6B 708729271 708730902 1631 True 251.0 261 75.1695 1010 2760 2 chr6B.!!$R2 1750
19 TraesCS7B01G193100 chr6B 708722427 708723886 1459 True 240.0 243 74.9610 1014 2760 2 chr6B.!!$R1 1746

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
176 177 0.319083 TGCAGCTCAAAATTGGCAGG 59.681 50.000 0.00 3.29 0.0 4.85 F
498 504 0.322816 CCAACCACTCCCACCAGATG 60.323 60.000 0.00 0.00 0.0 2.90 F
1920 3213 1.135575 GCTGCACAGTGAAGTATTGGC 60.136 52.381 10.51 0.00 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1900 3193 1.135575 GCCAATACTTCACTGTGCAGC 60.136 52.381 7.37 0.0 0.0 5.25 R
1998 3298 1.234821 AGGCGCACAAAATTCGAAGA 58.765 45.000 10.83 0.0 0.0 2.87 R
3360 5465 0.534203 GAGAAACTGACACCCGCCAA 60.534 55.000 0.00 0.0 0.0 4.52 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
24 25 4.630069 TGAGTTCGCTACTAAAATTCAGGC 59.370 41.667 0.00 0.00 37.17 4.85
130 131 2.098614 ACGCTGTGAGTCTGAGATGAT 58.901 47.619 0.00 0.00 0.00 2.45
135 136 4.538917 CTGTGAGTCTGAGATGATGATCG 58.461 47.826 0.00 0.00 33.34 3.69
148 149 1.071385 GATGATCGAGGTCAGCCCATT 59.929 52.381 0.00 0.00 34.66 3.16
149 150 1.788229 TGATCGAGGTCAGCCCATTA 58.212 50.000 0.00 0.00 34.66 1.90
150 151 2.115427 TGATCGAGGTCAGCCCATTAA 58.885 47.619 0.00 0.00 34.66 1.40
151 152 2.103094 TGATCGAGGTCAGCCCATTAAG 59.897 50.000 0.00 0.00 34.66 1.85
152 153 1.860641 TCGAGGTCAGCCCATTAAGA 58.139 50.000 0.00 0.00 34.66 2.10
153 154 2.398588 TCGAGGTCAGCCCATTAAGAT 58.601 47.619 0.00 0.00 34.66 2.40
155 156 2.548920 CGAGGTCAGCCCATTAAGATCC 60.549 54.545 0.00 0.00 34.66 3.36
156 157 2.439507 GAGGTCAGCCCATTAAGATCCA 59.560 50.000 0.00 0.00 34.66 3.41
157 158 3.059097 AGGTCAGCCCATTAAGATCCAT 58.941 45.455 0.00 0.00 34.66 3.41
158 159 3.152341 GGTCAGCCCATTAAGATCCATG 58.848 50.000 0.00 0.00 0.00 3.66
159 160 2.555757 GTCAGCCCATTAAGATCCATGC 59.444 50.000 0.00 0.00 0.00 4.06
176 177 0.319083 TGCAGCTCAAAATTGGCAGG 59.681 50.000 0.00 3.29 0.00 4.85
195 196 5.237344 GGCAGGCAATACTAATACTGAACTG 59.763 44.000 0.00 0.00 0.00 3.16
198 199 7.254590 GCAGGCAATACTAATACTGAACTGAAG 60.255 40.741 0.00 0.00 0.00 3.02
201 202 7.439655 GGCAATACTAATACTGAACTGAAGAGG 59.560 40.741 0.00 0.00 0.00 3.69
208 209 9.632807 CTAATACTGAACTGAAGAGGCATATAC 57.367 37.037 0.00 0.00 0.00 1.47
225 226 5.163703 GCATATACGATGGGAAAACACAACA 60.164 40.000 0.00 0.00 0.00 3.33
228 229 2.878406 ACGATGGGAAAACACAACAGAG 59.122 45.455 0.00 0.00 0.00 3.35
233 234 5.930837 TGGGAAAACACAACAGAGAAAAT 57.069 34.783 0.00 0.00 0.00 1.82
275 276 0.537188 ACAGTTACATCCAGAGGGCG 59.463 55.000 0.00 0.00 0.00 6.13
286 287 1.688735 CCAGAGGGCGACTAATCATCA 59.311 52.381 0.00 0.00 0.00 3.07
294 295 4.213482 GGGCGACTAATCATCATGGTTTAC 59.787 45.833 0.00 0.00 0.00 2.01
336 342 7.471890 TCCTGTAATGTTTATACCCCTTGTTT 58.528 34.615 0.00 0.00 0.00 2.83
427 433 2.475818 TGCGAAGTACGAACACACAAT 58.524 42.857 0.00 0.00 45.77 2.71
428 434 2.219903 TGCGAAGTACGAACACACAATG 59.780 45.455 0.00 0.00 45.77 2.82
429 435 2.473609 GCGAAGTACGAACACACAATGA 59.526 45.455 0.00 0.00 45.77 2.57
430 436 3.660904 GCGAAGTACGAACACACAATGAC 60.661 47.826 0.00 0.00 45.77 3.06
431 437 3.487942 CGAAGTACGAACACACAATGACA 59.512 43.478 0.00 0.00 45.77 3.58
432 438 4.605354 CGAAGTACGAACACACAATGACAC 60.605 45.833 0.00 0.00 45.77 3.67
433 439 2.792674 AGTACGAACACACAATGACACG 59.207 45.455 0.00 0.00 0.00 4.49
434 440 1.929230 ACGAACACACAATGACACGA 58.071 45.000 0.00 0.00 0.00 4.35
453 459 7.108841 ACACGACCTCAATTGTATATGTACT 57.891 36.000 5.13 0.00 0.00 2.73
454 460 8.229253 ACACGACCTCAATTGTATATGTACTA 57.771 34.615 5.13 0.00 0.00 1.82
455 461 8.133627 ACACGACCTCAATTGTATATGTACTAC 58.866 37.037 5.13 0.00 0.00 2.73
462 468 7.998580 TCAATTGTATATGTACTACGTGGACA 58.001 34.615 5.70 5.68 0.00 4.02
469 475 4.859304 TGTACTACGTGGACATGACTTT 57.141 40.909 5.70 0.00 0.00 2.66
498 504 0.322816 CCAACCACTCCCACCAGATG 60.323 60.000 0.00 0.00 0.00 2.90
521 527 4.378563 GCATATCATCGCGTACTACTCTGT 60.379 45.833 5.77 0.00 0.00 3.41
545 551 3.596214 GTTCCTCTCCTTATTTCGCACA 58.404 45.455 0.00 0.00 0.00 4.57
626 633 3.998672 CGTACGGCCACCACCAGT 61.999 66.667 7.57 0.00 0.00 4.00
696 704 5.360429 AGGTTATTAACTCTCTCCGAACTCC 59.640 44.000 6.52 0.00 0.00 3.85
708 716 1.269051 CCGAACTCCGCTTTGCTTTTT 60.269 47.619 0.00 0.00 36.84 1.94
783 795 3.316868 TGGGTAAACAGCTACAAAGTTGC 59.683 43.478 0.00 0.00 37.45 4.17
811 823 9.950680 CTAAAGTTGCGACAATTAATATGGATT 57.049 29.630 6.90 0.00 0.00 3.01
820 832 7.445402 CGACAATTAATATGGATTGAAGGGAGT 59.555 37.037 14.77 0.00 36.87 3.85
833 845 8.968969 GGATTGAAGGGAGTACGATATAGTATT 58.031 37.037 0.00 0.00 0.00 1.89
1331 1363 1.595794 TCGACGCCTCAAAACTTTGAC 59.404 47.619 0.69 0.00 41.88 3.18
1338 1370 1.864711 CTCAAAACTTTGACGGCTCGA 59.135 47.619 0.69 0.00 41.88 4.04
1536 1577 8.792830 ATGAGCTTATTAACTTGCTAAGTGAA 57.207 30.769 0.00 2.69 41.91 3.18
1575 1616 7.054124 TGAAAGTGGTATCTATTGTGGGATTC 58.946 38.462 0.00 0.00 0.00 2.52
1780 1824 4.946157 ACATGCTCAGGGAACATCTAAAAG 59.054 41.667 0.00 0.00 0.00 2.27
1887 3180 7.918076 AGTATATTTTCCCAACTCAGTTCAGA 58.082 34.615 0.00 0.00 0.00 3.27
1888 3181 8.383175 AGTATATTTTCCCAACTCAGTTCAGAA 58.617 33.333 0.00 0.00 0.00 3.02
1889 3182 9.010029 GTATATTTTCCCAACTCAGTTCAGAAA 57.990 33.333 7.22 7.22 0.00 2.52
1890 3183 6.790232 ATTTTCCCAACTCAGTTCAGAAAA 57.210 33.333 19.48 19.48 37.65 2.29
1892 3185 5.835113 TTCCCAACTCAGTTCAGAAAAAG 57.165 39.130 0.00 0.00 0.00 2.27
1893 3186 5.110814 TCCCAACTCAGTTCAGAAAAAGA 57.889 39.130 0.00 0.00 0.00 2.52
1895 3188 5.949354 TCCCAACTCAGTTCAGAAAAAGAAA 59.051 36.000 0.00 0.00 0.00 2.52
1896 3189 6.435904 TCCCAACTCAGTTCAGAAAAAGAAAA 59.564 34.615 0.00 0.00 0.00 2.29
1897 3190 7.124147 TCCCAACTCAGTTCAGAAAAAGAAAAT 59.876 33.333 0.00 0.00 0.00 1.82
1898 3191 8.413229 CCCAACTCAGTTCAGAAAAAGAAAATA 58.587 33.333 0.00 0.00 0.00 1.40
1901 3194 9.468532 AACTCAGTTCAGAAAAAGAAAATATGC 57.531 29.630 0.00 0.00 0.00 3.14
1902 3195 8.854117 ACTCAGTTCAGAAAAAGAAAATATGCT 58.146 29.630 0.00 0.00 0.00 3.79
1903 3196 9.125906 CTCAGTTCAGAAAAAGAAAATATGCTG 57.874 33.333 0.00 0.00 0.00 4.41
1905 3198 7.383029 CAGTTCAGAAAAAGAAAATATGCTGCA 59.617 33.333 4.13 4.13 0.00 4.41
1907 3200 6.747125 TCAGAAAAAGAAAATATGCTGCACA 58.253 32.000 3.57 0.00 0.00 4.57
1908 3201 6.864685 TCAGAAAAAGAAAATATGCTGCACAG 59.135 34.615 3.57 0.00 0.00 3.66
1910 3203 6.643770 AGAAAAAGAAAATATGCTGCACAGTG 59.356 34.615 3.57 0.00 0.00 3.66
1915 3208 5.939883 AGAAAATATGCTGCACAGTGAAGTA 59.060 36.000 10.51 6.06 0.00 2.24
1920 3213 1.135575 GCTGCACAGTGAAGTATTGGC 60.136 52.381 10.51 0.00 0.00 4.52
1946 3246 9.880064 CAGAAAATCATTAGATGAGCATAACAG 57.120 33.333 0.00 0.00 43.53 3.16
1950 3250 7.959689 ATCATTAGATGAGCATAACAGACAC 57.040 36.000 0.00 0.00 43.53 3.67
1956 3256 4.071961 TGAGCATAACAGACACACAACT 57.928 40.909 0.00 0.00 0.00 3.16
2003 3303 9.307121 ACATCTACATTCTACTGAATTTCTTCG 57.693 33.333 0.00 0.00 40.61 3.79
2014 3553 5.399301 ACTGAATTTCTTCGAATTTTGTGCG 59.601 36.000 0.00 0.00 33.86 5.34
2015 3554 4.148000 TGAATTTCTTCGAATTTTGTGCGC 59.852 37.500 0.00 0.00 33.86 6.09
2016 3557 2.044888 TTCTTCGAATTTTGTGCGCC 57.955 45.000 4.18 0.00 0.00 6.53
2021 3562 1.463056 TCGAATTTTGTGCGCCTACTG 59.537 47.619 4.18 0.00 0.00 2.74
2022 3563 1.463056 CGAATTTTGTGCGCCTACTGA 59.537 47.619 4.18 0.00 0.00 3.41
2075 3618 8.589335 ACCGTATTAGTCTAATTTGTATGCTG 57.411 34.615 10.36 0.00 0.00 4.41
2111 3667 6.359617 CGGTGACAACATTGATCTTAAACAAC 59.640 38.462 0.00 0.00 0.00 3.32
2447 4543 2.307496 AGGCATGTTGTTTCCATGGA 57.693 45.000 11.44 11.44 40.03 3.41
2494 4590 2.352814 CCCTCAACGACAAAGACTCGAT 60.353 50.000 0.00 0.00 35.08 3.59
2648 4744 4.501071 CCAGCAAAGATTCCATCCAAAAG 58.499 43.478 0.00 0.00 0.00 2.27
2774 4876 6.720309 TCATCTACAACAATTGATCCCTTGA 58.280 36.000 13.59 4.26 0.00 3.02
2829 4931 7.068716 CCATCATAGTCCACCTCGATAATATCA 59.931 40.741 0.87 0.00 0.00 2.15
2833 4935 9.126151 CATAGTCCACCTCGATAATATCATAGT 57.874 37.037 0.87 0.00 0.00 2.12
2865 4968 1.614241 AAGCCCTGCGTCGGTAGAAT 61.614 55.000 0.00 0.00 0.00 2.40
2879 4982 6.556212 GTCGGTAGAATATCATCATCGTCAT 58.444 40.000 0.00 0.00 0.00 3.06
3056 5159 1.145803 GCTAACGCTTCCACTTTCGT 58.854 50.000 0.00 0.00 36.67 3.85
3114 5217 3.495434 TGCTATGCATCACCATGATCA 57.505 42.857 0.19 0.00 34.28 2.92
3124 5227 1.813786 CACCATGATCATGTGTGTGCA 59.186 47.619 29.95 0.00 36.32 4.57
3185 5290 0.393808 TCCGAGCCAGGTTTTATGCC 60.394 55.000 0.00 0.00 0.00 4.40
3283 5388 0.035036 TGGTTCGGCGGTATTGTTGA 59.965 50.000 7.21 0.00 0.00 3.18
3360 5465 3.743714 TGCTTTGCACATAGGTGGT 57.256 47.368 9.91 0.00 45.38 4.16
3473 5578 7.072177 ACTATCATTGTGGTTTTGATACGTG 57.928 36.000 0.00 0.00 32.58 4.49
3528 5633 4.109050 CCACGTAAAACTTGCAACAACAT 58.891 39.130 0.00 0.00 0.00 2.71
3582 5687 4.577693 GCATGTTGTGATGTGATATGGTCT 59.422 41.667 0.00 0.00 0.00 3.85
3586 5691 5.425217 TGTTGTGATGTGATATGGTCTAGGT 59.575 40.000 0.00 0.00 0.00 3.08
3587 5692 5.535753 TGTGATGTGATATGGTCTAGGTG 57.464 43.478 0.00 0.00 0.00 4.00
3726 5833 6.755607 GCTTTACTTTATCACTAAGCGGTAGT 59.244 38.462 0.00 0.00 44.33 2.73
3747 5854 6.909550 AGTGATAGTCCTAGAAGCAATAGG 57.090 41.667 0.00 3.19 41.11 2.57
3752 5859 2.170607 GTCCTAGAAGCAATAGGTGGCA 59.829 50.000 8.29 0.00 40.67 4.92
3754 5861 3.265737 TCCTAGAAGCAATAGGTGGCAAA 59.734 43.478 8.29 0.00 40.67 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.121768 GCCTGAATTTTAGTAGCGAACTCAA 59.878 40.000 0.00 0.00 39.80 3.02
24 25 6.203530 TCTGCAGACAAGAAACATTCAGTTAG 59.796 38.462 13.74 0.00 40.26 2.34
79 80 7.660112 TGAACTTGCATTGAAATTGACAGTAT 58.340 30.769 0.00 0.00 0.00 2.12
130 131 1.788229 TAATGGGCTGACCTCGATCA 58.212 50.000 0.00 0.00 41.11 2.92
135 136 2.439507 TGGATCTTAATGGGCTGACCTC 59.560 50.000 0.00 0.00 41.11 3.85
148 149 5.163488 CCAATTTTGAGCTGCATGGATCTTA 60.163 40.000 1.02 0.00 0.00 2.10
149 150 4.382685 CCAATTTTGAGCTGCATGGATCTT 60.383 41.667 1.02 0.00 0.00 2.40
150 151 3.132289 CCAATTTTGAGCTGCATGGATCT 59.868 43.478 1.02 0.00 0.00 2.75
151 152 3.454375 CCAATTTTGAGCTGCATGGATC 58.546 45.455 1.02 0.00 0.00 3.36
152 153 2.419574 GCCAATTTTGAGCTGCATGGAT 60.420 45.455 1.02 0.00 0.00 3.41
153 154 1.066716 GCCAATTTTGAGCTGCATGGA 60.067 47.619 1.02 0.00 0.00 3.41
155 156 1.999735 CTGCCAATTTTGAGCTGCATG 59.000 47.619 1.02 0.00 0.00 4.06
156 157 1.066430 CCTGCCAATTTTGAGCTGCAT 60.066 47.619 1.02 0.00 0.00 3.96
157 158 0.319083 CCTGCCAATTTTGAGCTGCA 59.681 50.000 1.02 0.00 0.00 4.41
158 159 1.017701 GCCTGCCAATTTTGAGCTGC 61.018 55.000 0.00 0.00 0.00 5.25
159 160 0.319083 TGCCTGCCAATTTTGAGCTG 59.681 50.000 0.00 0.00 0.00 4.24
176 177 7.042389 GCCTCTTCAGTTCAGTATTAGTATTGC 60.042 40.741 0.00 0.00 0.00 3.56
195 196 4.537135 TTCCCATCGTATATGCCTCTTC 57.463 45.455 0.00 0.00 0.00 2.87
198 199 4.213482 GTGTTTTCCCATCGTATATGCCTC 59.787 45.833 0.00 0.00 0.00 4.70
201 202 5.163703 TGTTGTGTTTTCCCATCGTATATGC 60.164 40.000 0.00 0.00 0.00 3.14
208 209 3.138304 TCTCTGTTGTGTTTTCCCATCG 58.862 45.455 0.00 0.00 0.00 3.84
233 234 8.684386 TGTCAGTCTGAATGTTATTACCAAAA 57.316 30.769 3.51 0.00 0.00 2.44
275 276 5.822519 TGCAGGTAAACCATGATGATTAGTC 59.177 40.000 1.26 0.00 38.89 2.59
286 287 2.487762 CGACAATGTGCAGGTAAACCAT 59.512 45.455 1.26 0.00 38.89 3.55
294 295 1.021390 GGAGGTCGACAATGTGCAGG 61.021 60.000 18.91 0.00 0.00 4.85
336 342 1.134007 GCATGACATGGGAGGTGATCA 60.134 52.381 17.03 0.00 0.00 2.92
399 405 0.387494 TCGTACTTCGCACGCATTCA 60.387 50.000 0.00 0.00 39.23 2.57
427 433 5.972935 ACATATACAATTGAGGTCGTGTCA 58.027 37.500 13.59 0.00 0.00 3.58
428 434 7.201145 AGTACATATACAATTGAGGTCGTGTC 58.799 38.462 13.59 4.39 33.30 3.67
429 435 7.108841 AGTACATATACAATTGAGGTCGTGT 57.891 36.000 13.59 10.91 33.30 4.49
430 436 7.322938 CGTAGTACATATACAATTGAGGTCGTG 59.677 40.741 13.59 5.72 33.30 4.35
431 437 7.012704 ACGTAGTACATATACAATTGAGGTCGT 59.987 37.037 13.59 6.17 41.94 4.34
432 438 7.322938 CACGTAGTACATATACAATTGAGGTCG 59.677 40.741 13.59 0.62 41.61 4.79
433 439 7.594015 CCACGTAGTACATATACAATTGAGGTC 59.406 40.741 13.59 0.00 41.61 3.85
434 440 7.286087 TCCACGTAGTACATATACAATTGAGGT 59.714 37.037 13.59 0.00 41.61 3.85
453 459 4.345859 AGGAAAAAGTCATGTCCACGTA 57.654 40.909 0.00 0.00 32.19 3.57
454 460 3.208747 AGGAAAAAGTCATGTCCACGT 57.791 42.857 1.10 0.00 32.19 4.49
455 461 4.537015 GAAAGGAAAAAGTCATGTCCACG 58.463 43.478 1.10 0.00 32.19 4.94
462 468 3.646162 GGTTGGGGAAAGGAAAAAGTCAT 59.354 43.478 0.00 0.00 0.00 3.06
469 475 1.133294 GGAGTGGTTGGGGAAAGGAAA 60.133 52.381 0.00 0.00 0.00 3.13
498 504 4.092120 CAGAGTAGTACGCGATGATATGC 58.908 47.826 15.93 0.00 0.00 3.14
510 516 4.094739 GGAGAGGAACGAACAGAGTAGTAC 59.905 50.000 0.00 0.00 0.00 2.73
521 527 3.056393 TGCGAAATAAGGAGAGGAACGAA 60.056 43.478 0.00 0.00 0.00 3.85
560 566 1.174783 TTTTCGGAGTCGGAGGAGAG 58.825 55.000 0.31 0.00 36.95 3.20
696 704 1.004715 CAGGCAACAAAAAGCAAAGCG 60.005 47.619 0.00 0.00 41.41 4.68
783 795 8.394877 TCCATATTAATTGTCGCAACTTTAGTG 58.605 33.333 0.00 0.00 0.00 2.74
811 823 8.701908 ACAAATACTATATCGTACTCCCTTCA 57.298 34.615 0.00 0.00 0.00 3.02
860 872 9.368921 GCATGTTAATTGAAACAAAAACTAAGC 57.631 29.630 0.00 0.00 42.33 3.09
1536 1577 3.181439 CCACTTTCAACTTCTTCTCCCCT 60.181 47.826 0.00 0.00 0.00 4.79
1575 1616 1.804748 GTTGTTTTGCCTAGACCTCCG 59.195 52.381 0.00 0.00 0.00 4.63
1780 1824 7.212976 TGAAGTAAGAATATGCACCTCTCATC 58.787 38.462 0.00 0.00 0.00 2.92
1872 3165 5.835113 TTCTTTTTCTGAACTGAGTTGGG 57.165 39.130 0.90 0.00 0.00 4.12
1873 3166 9.971922 ATATTTTCTTTTTCTGAACTGAGTTGG 57.028 29.630 0.90 0.00 0.00 3.77
1875 3168 9.468532 GCATATTTTCTTTTTCTGAACTGAGTT 57.531 29.630 0.00 0.00 0.00 3.01
1877 3170 9.125906 CAGCATATTTTCTTTTTCTGAACTGAG 57.874 33.333 0.00 0.00 0.00 3.35
1879 3172 7.383029 TGCAGCATATTTTCTTTTTCTGAACTG 59.617 33.333 0.00 0.00 0.00 3.16
1880 3173 7.383300 GTGCAGCATATTTTCTTTTTCTGAACT 59.617 33.333 0.00 0.00 0.00 3.01
1881 3174 7.169645 TGTGCAGCATATTTTCTTTTTCTGAAC 59.830 33.333 0.00 0.00 31.30 3.18
1882 3175 7.208777 TGTGCAGCATATTTTCTTTTTCTGAA 58.791 30.769 0.00 0.00 0.00 3.02
1884 3177 6.643770 ACTGTGCAGCATATTTTCTTTTTCTG 59.356 34.615 0.00 0.00 0.00 3.02
1885 3178 6.643770 CACTGTGCAGCATATTTTCTTTTTCT 59.356 34.615 0.00 0.00 0.00 2.52
1887 3180 6.514947 TCACTGTGCAGCATATTTTCTTTTT 58.485 32.000 0.00 0.00 0.00 1.94
1888 3181 6.088016 TCACTGTGCAGCATATTTTCTTTT 57.912 33.333 0.00 0.00 0.00 2.27
1889 3182 5.710513 TCACTGTGCAGCATATTTTCTTT 57.289 34.783 0.00 0.00 0.00 2.52
1890 3183 5.242393 ACTTCACTGTGCAGCATATTTTCTT 59.758 36.000 7.37 0.00 0.00 2.52
1892 3185 5.051891 ACTTCACTGTGCAGCATATTTTC 57.948 39.130 7.37 0.00 0.00 2.29
1893 3186 6.764308 ATACTTCACTGTGCAGCATATTTT 57.236 33.333 7.37 0.00 0.00 1.82
1895 3188 5.066893 CCAATACTTCACTGTGCAGCATATT 59.933 40.000 7.37 3.07 0.00 1.28
1896 3189 4.577693 CCAATACTTCACTGTGCAGCATAT 59.422 41.667 7.37 0.00 0.00 1.78
1897 3190 3.940852 CCAATACTTCACTGTGCAGCATA 59.059 43.478 7.37 0.00 0.00 3.14
1898 3191 2.751259 CCAATACTTCACTGTGCAGCAT 59.249 45.455 7.37 0.00 0.00 3.79
1900 3193 1.135575 GCCAATACTTCACTGTGCAGC 60.136 52.381 7.37 0.00 0.00 5.25
1901 3194 2.153645 TGCCAATACTTCACTGTGCAG 58.846 47.619 5.90 5.90 0.00 4.41
1902 3195 2.153645 CTGCCAATACTTCACTGTGCA 58.846 47.619 2.12 0.00 0.00 4.57
1903 3196 2.426522 TCTGCCAATACTTCACTGTGC 58.573 47.619 2.12 0.00 0.00 4.57
1905 3198 5.769662 TGATTTTCTGCCAATACTTCACTGT 59.230 36.000 0.00 0.00 0.00 3.55
1907 3200 7.472334 AATGATTTTCTGCCAATACTTCACT 57.528 32.000 0.00 0.00 0.00 3.41
1908 3201 8.677300 TCTAATGATTTTCTGCCAATACTTCAC 58.323 33.333 0.00 0.00 0.00 3.18
1910 3203 9.674824 CATCTAATGATTTTCTGCCAATACTTC 57.325 33.333 0.00 0.00 0.00 3.01
1915 3208 6.322969 TGCTCATCTAATGATTTTCTGCCAAT 59.677 34.615 0.00 0.00 38.85 3.16
1920 3213 9.880064 CTGTTATGCTCATCTAATGATTTTCTG 57.120 33.333 0.00 0.00 38.85 3.02
1977 3277 9.307121 CGAAGAAATTCAGTAGAATGTAGATGT 57.693 33.333 0.00 0.00 43.52 3.06
1988 3288 7.201182 CGCACAAAATTCGAAGAAATTCAGTAG 60.201 37.037 3.35 0.00 45.90 2.57
1990 3290 5.399301 CGCACAAAATTCGAAGAAATTCAGT 59.601 36.000 3.35 0.00 45.90 3.41
1991 3291 5.663773 GCGCACAAAATTCGAAGAAATTCAG 60.664 40.000 0.30 0.00 45.90 3.02
1993 3293 4.432892 GGCGCACAAAATTCGAAGAAATTC 60.433 41.667 10.83 0.00 45.90 2.17
1994 3294 3.428534 GGCGCACAAAATTCGAAGAAATT 59.571 39.130 10.83 0.00 45.90 1.82
1995 3295 2.986479 GGCGCACAAAATTCGAAGAAAT 59.014 40.909 10.83 0.00 45.90 2.17
1998 3298 1.234821 AGGCGCACAAAATTCGAAGA 58.765 45.000 10.83 0.00 0.00 2.87
2001 3301 1.463056 CAGTAGGCGCACAAAATTCGA 59.537 47.619 10.83 0.00 0.00 3.71
2002 3302 1.463056 TCAGTAGGCGCACAAAATTCG 59.537 47.619 10.83 0.00 0.00 3.34
2003 3303 3.764885 ATCAGTAGGCGCACAAAATTC 57.235 42.857 10.83 0.00 0.00 2.17
2006 3306 2.881513 TGAAATCAGTAGGCGCACAAAA 59.118 40.909 10.83 0.00 0.00 2.44
2064 3607 9.897744 CACCGATAATAAAATCAGCATACAAAT 57.102 29.630 0.00 0.00 0.00 2.32
2075 3618 9.950680 ATCAATGTTGTCACCGATAATAAAATC 57.049 29.630 0.00 0.00 0.00 2.17
2379 4475 6.567602 AGTTATTACTCTGCTCCCAAGATT 57.432 37.500 0.00 0.00 0.00 2.40
2420 4516 1.256812 AACAACATGCCTTAGCCACC 58.743 50.000 0.00 0.00 38.69 4.61
2447 4543 7.977853 GGCTTCATTTCTAAAATGTGATCATGT 59.022 33.333 0.00 0.00 34.19 3.21
2522 4618 0.326264 GAGGGCAAGCTTCCTCAGAA 59.674 55.000 23.09 0.00 46.54 3.02
2648 4744 3.089284 CCTTACATGTTCCCACCTTTCC 58.911 50.000 2.30 0.00 0.00 3.13
2774 4876 3.050703 CGCACACGGCTAAGAGATT 57.949 52.632 0.00 0.00 41.67 2.40
2806 4908 9.343539 CTATGATATTATCGAGGTGGACTATGA 57.656 37.037 0.00 0.00 0.00 2.15
2829 4931 2.604046 CTTCGCCTAAGCACCACTAT 57.396 50.000 0.00 0.00 39.83 2.12
3056 5159 1.271325 TGTCCACGTACCCTCGTAGAA 60.271 52.381 0.00 0.00 42.27 2.10
3146 5251 0.827089 TGCCACTGTTGGGGAACATG 60.827 55.000 0.00 0.00 44.15 3.21
3185 5290 8.290325 TGTTCTACTCGTGCATATAACATCTAG 58.710 37.037 0.00 0.00 0.00 2.43
3283 5388 4.796495 GGTCCGGGCCGCTTCATT 62.796 66.667 23.20 0.00 0.00 2.57
3360 5465 0.534203 GAGAAACTGACACCCGCCAA 60.534 55.000 0.00 0.00 0.00 4.52
3528 5633 7.516198 AAAACAAGTTAGACGTCCTCTACTA 57.484 36.000 13.01 0.00 30.56 1.82
3646 5752 0.921896 ACAACCATATGGCTCCTGCT 59.078 50.000 22.18 0.00 39.32 4.24
3726 5833 5.540337 CCACCTATTGCTTCTAGGACTATCA 59.460 44.000 12.05 0.00 38.44 2.15
3734 5841 5.357878 TCATTTTGCCACCTATTGCTTCTAG 59.642 40.000 0.00 0.00 0.00 2.43
3747 5854 1.720852 GCATCGTTGTCATTTTGCCAC 59.279 47.619 0.00 0.00 0.00 5.01
3752 5859 4.897224 CATCGTAGCATCGTTGTCATTTT 58.103 39.130 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.