Multiple sequence alignment - TraesCS2A01G456100

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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 TraesCS2A01G456100 chr2A 100.000 6014 0 0 1 6014 704778010 704771997 0.000000e+00 11106
1 TraesCS2A01G456100 chr2A 88.724 878 57 19 642 1506 704734920 704735768 0.000000e+00 1035
2 TraesCS2A01G456100 chr2B 95.025 3960 100 30 2115 6014 675355276 675351354 0.000000e+00 6131
3 TraesCS2A01G456100 chr2B 91.048 1698 50 31 477 2112 675356965 675355308 0.000000e+00 2200
4 TraesCS2A01G456100 chr2B 89.257 875 49 29 642 1504 675324210 675325051 0.000000e+00 1053
5 TraesCS2A01G456100 chr2B 77.389 429 30 27 1 383 675357621 675357214 6.150000e-45 193
6 TraesCS2A01G456100 chr2D 87.394 2245 90 72 1 2112 564096806 564094622 0.000000e+00 2399
7 TraesCS2A01G456100 chr2D 94.219 1453 52 9 4576 6014 564092109 564090675 0.000000e+00 2189
8 TraesCS2A01G456100 chr2D 94.953 951 40 6 2177 3121 564094510 564093562 0.000000e+00 1483
9 TraesCS2A01G456100 chr2D 86.554 766 62 8 3284 4015 564093379 564092621 0.000000e+00 806
10 TraesCS2A01G456100 chr2D 91.514 436 18 6 4071 4491 564092620 564092189 3.120000e-162 582
11 TraesCS2A01G456100 chr2D 96.053 76 1 1 3118 3193 376701261 376701188 8.190000e-24 122
12 TraesCS2A01G456100 chr6A 89.152 507 55 0 1247 1753 484608439 484608945 3.060000e-177 632
13 TraesCS2A01G456100 chr6A 96.203 79 2 1 3118 3196 509279058 509279135 1.760000e-25 128
14 TraesCS2A01G456100 chr6D 86.177 586 74 6 1172 1753 344207791 344208373 1.420000e-175 627
15 TraesCS2A01G456100 chr6D 86.940 268 31 4 4097 4361 344210870 344211136 1.270000e-76 298
16 TraesCS2A01G456100 chr6D 96.203 79 2 1 3118 3196 368365285 368365362 1.760000e-25 128
17 TraesCS2A01G456100 chr6B 87.938 514 62 0 1247 1760 519720395 519720908 1.850000e-169 606
18 TraesCS2A01G456100 chr6B 96.203 79 2 1 3118 3196 553057202 553057125 1.760000e-25 128
19 TraesCS2A01G456100 chr5D 82.809 477 70 11 1283 1753 489905883 489906353 3.350000e-112 416
20 TraesCS2A01G456100 chr5D 93.827 81 4 1 3118 3198 330709258 330709179 2.940000e-23 121
21 TraesCS2A01G456100 chr5A 82.526 475 75 8 1283 1753 611564618 611565088 1.560000e-110 411
22 TraesCS2A01G456100 chr5A 89.247 93 4 2 3100 3191 561531482 561531569 1.770000e-20 111
23 TraesCS2A01G456100 chr3D 94.048 84 2 2 3118 3198 169888215 169888132 2.280000e-24 124
24 TraesCS2A01G456100 chr3B 92.771 83 5 1 3112 3194 133204122 133204203 1.060000e-22 119


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 TraesCS2A01G456100 chr2A 704771997 704778010 6013 True 11106.000000 11106 100.000000 1 6014 1 chr2A.!!$R1 6013
1 TraesCS2A01G456100 chr2A 704734920 704735768 848 False 1035.000000 1035 88.724000 642 1506 1 chr2A.!!$F1 864
2 TraesCS2A01G456100 chr2B 675351354 675357621 6267 True 2841.333333 6131 87.820667 1 6014 3 chr2B.!!$R1 6013
3 TraesCS2A01G456100 chr2B 675324210 675325051 841 False 1053.000000 1053 89.257000 642 1504 1 chr2B.!!$F1 862
4 TraesCS2A01G456100 chr2D 564090675 564096806 6131 True 1491.800000 2399 90.926800 1 6014 5 chr2D.!!$R2 6013
5 TraesCS2A01G456100 chr6A 484608439 484608945 506 False 632.000000 632 89.152000 1247 1753 1 chr6A.!!$F1 506
6 TraesCS2A01G456100 chr6D 344207791 344211136 3345 False 462.500000 627 86.558500 1172 4361 2 chr6D.!!$F2 3189
7 TraesCS2A01G456100 chr6B 519720395 519720908 513 False 606.000000 606 87.938000 1247 1760 1 chr6B.!!$F1 513

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
347 410 0.602562 CCAGCCGCAAAAATCCAAGA 59.397 50.000 0.00 0.00 0.00 3.02 F
349 412 0.603065 AGCCGCAAAAATCCAAGACC 59.397 50.000 0.00 0.00 0.00 3.85 F
651 908 0.668401 GCAGGCAATCCAAACAGTGC 60.668 55.000 0.00 0.00 36.24 4.40 F
827 1111 1.150536 CCCCTCTCCTCTCCTCTCG 59.849 68.421 0.00 0.00 0.00 4.04 F
1868 2210 1.269051 GCCCGCATAATTAACTGTGGC 60.269 52.381 11.62 8.72 40.87 5.01 F
2912 3725 0.036105 GCAAGGAGGCAATTTTGGGG 60.036 55.000 0.00 0.00 0.00 4.96 F
3390 4307 1.101331 CAGAGGAGGAAATTGCAGGC 58.899 55.000 0.00 0.00 0.00 4.85 F
3399 4316 2.094338 GGAAATTGCAGGCTTGAAGGAG 60.094 50.000 0.00 0.00 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 1971 0.606673 GCAGGAAGTTCTCGGGCTTT 60.607 55.000 2.25 0.0 0.00 3.51 R
1768 2105 0.803117 CGTTGACCGACTAGAGCAGA 59.197 55.000 0.00 0.0 39.56 4.26 R
1906 2248 0.995024 AGGTTCTGCCCTGTAAGCAT 59.005 50.000 0.00 0.0 40.04 3.79 R
1912 2254 1.561542 CCAGATAAGGTTCTGCCCTGT 59.438 52.381 0.00 0.0 41.50 4.00 R
3609 4537 0.538287 GGAGGCAGCACAAGTTTCCT 60.538 55.000 0.00 0.0 0.00 3.36 R
3717 4666 1.546029 GCCCTAAAGAAAGCCACCAAG 59.454 52.381 0.00 0.0 0.00 3.61 R
4535 5599 2.493675 TGAGAGACCATGTTCCTCTTCG 59.506 50.000 9.26 0.0 37.40 3.79 R
5063 6145 3.008375 TGCAGGAAGTCTTTGTAGAGCAT 59.992 43.478 0.00 0.0 0.00 3.79 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
21 22 2.499685 GGCCCTCACGTAAGCGAT 59.500 61.111 0.00 0.00 45.62 4.58
43 44 2.292267 CGCAGAATGATTAGGCCAGTT 58.708 47.619 5.01 0.00 39.69 3.16
50 51 1.338674 TGATTAGGCCAGTTGACGTGG 60.339 52.381 5.01 0.00 38.21 4.94
209 229 4.041762 GGCGGGTCACCATCCCAA 62.042 66.667 0.00 0.00 44.81 4.12
236 276 2.268920 CCATCACCTGACCACCCG 59.731 66.667 0.00 0.00 0.00 5.28
260 310 2.005451 CTGCCATGAGTGTAGTTCAGC 58.995 52.381 0.00 0.00 0.00 4.26
262 312 1.002366 CCATGAGTGTAGTTCAGCGC 58.998 55.000 0.00 0.00 0.00 5.92
311 374 2.434359 CCTTCGCGTCACCTTCCC 60.434 66.667 5.77 0.00 0.00 3.97
312 375 2.434359 CTTCGCGTCACCTTCCCC 60.434 66.667 5.77 0.00 0.00 4.81
313 376 3.234630 CTTCGCGTCACCTTCCCCA 62.235 63.158 5.77 0.00 0.00 4.96
314 377 2.725203 CTTCGCGTCACCTTCCCCAA 62.725 60.000 5.77 0.00 0.00 4.12
315 378 2.046314 CGCGTCACCTTCCCCAAT 60.046 61.111 0.00 0.00 0.00 3.16
316 379 2.106683 CGCGTCACCTTCCCCAATC 61.107 63.158 0.00 0.00 0.00 2.67
317 380 1.749258 GCGTCACCTTCCCCAATCC 60.749 63.158 0.00 0.00 0.00 3.01
318 381 1.077716 CGTCACCTTCCCCAATCCC 60.078 63.158 0.00 0.00 0.00 3.85
319 382 1.562672 CGTCACCTTCCCCAATCCCT 61.563 60.000 0.00 0.00 0.00 4.20
322 385 1.622752 ACCTTCCCCAATCCCTCCC 60.623 63.158 0.00 0.00 0.00 4.30
324 387 1.622442 CTTCCCCAATCCCTCCCCA 60.622 63.158 0.00 0.00 0.00 4.96
331 394 1.930656 AATCCCTCCCCACCACCAG 60.931 63.158 0.00 0.00 0.00 4.00
347 410 0.602562 CCAGCCGCAAAAATCCAAGA 59.397 50.000 0.00 0.00 0.00 3.02
349 412 0.603065 AGCCGCAAAAATCCAAGACC 59.397 50.000 0.00 0.00 0.00 3.85
358 421 4.980805 TCCAAGACCACGCACGCC 62.981 66.667 0.00 0.00 0.00 5.68
375 438 1.298563 CCAACGCAAGCACACTGTG 60.299 57.895 6.19 6.19 45.62 3.66
402 616 2.144482 AATAAACCGGCGTATCCTCG 57.856 50.000 6.01 0.00 0.00 4.63
407 621 1.590792 CCGGCGTATCCTCGAAACC 60.591 63.158 6.01 0.00 0.00 3.27
428 662 3.550842 CCAACGGCTCTCCTTTTTCAAAG 60.551 47.826 0.00 0.00 0.00 2.77
435 669 4.037327 GCTCTCCTTTTTCAAAGAACAGCT 59.963 41.667 0.00 0.00 0.00 4.24
436 670 5.239525 GCTCTCCTTTTTCAAAGAACAGCTA 59.760 40.000 0.00 0.00 0.00 3.32
437 671 6.567511 GCTCTCCTTTTTCAAAGAACAGCTAG 60.568 42.308 0.00 0.00 0.00 3.42
438 672 6.357367 TCTCCTTTTTCAAAGAACAGCTAGT 58.643 36.000 0.00 0.00 0.00 2.57
439 673 7.506114 TCTCCTTTTTCAAAGAACAGCTAGTA 58.494 34.615 0.00 0.00 0.00 1.82
440 674 7.657761 TCTCCTTTTTCAAAGAACAGCTAGTAG 59.342 37.037 0.00 0.00 0.00 2.57
453 687 8.654215 AGAACAGCTAGTAGTAAAAATAAACGC 58.346 33.333 0.00 0.00 0.00 4.84
517 753 4.106029 CCGAGACGGTGATCTTCTTTTA 57.894 45.455 1.80 0.00 42.73 1.52
518 754 3.858238 CCGAGACGGTGATCTTCTTTTAC 59.142 47.826 1.80 0.00 42.73 2.01
519 755 3.542704 CGAGACGGTGATCTTCTTTTACG 59.457 47.826 0.00 0.00 0.00 3.18
520 756 4.670992 CGAGACGGTGATCTTCTTTTACGA 60.671 45.833 0.00 0.00 0.00 3.43
651 908 0.668401 GCAGGCAATCCAAACAGTGC 60.668 55.000 0.00 0.00 36.24 4.40
827 1111 1.150536 CCCCTCTCCTCTCCTCTCG 59.849 68.421 0.00 0.00 0.00 4.04
887 1180 2.844451 TTTCGCCGCTGCTTTGCTT 61.844 52.632 0.00 0.00 34.43 3.91
1126 1423 2.815647 CCGACTCGCCCAAGAAGC 60.816 66.667 0.00 0.00 0.00 3.86
1131 1434 3.907260 CTCGCCCAAGAAGCAGCCA 62.907 63.158 0.00 0.00 0.00 4.75
1659 1971 2.363975 GGTCATGCACCGGGACCTA 61.364 63.158 16.94 0.00 45.99 3.08
1761 2073 3.263170 TCAAGCCTGGTGAGCTACATTAA 59.737 43.478 0.00 0.00 40.49 1.40
1762 2074 4.080356 TCAAGCCTGGTGAGCTACATTAAT 60.080 41.667 0.00 0.00 40.49 1.40
1768 2105 5.440610 CTGGTGAGCTACATTAATCCCTTT 58.559 41.667 0.00 0.00 0.00 3.11
1802 2139 2.729882 GTCAACGACTACGATGTGCTTT 59.270 45.455 0.00 0.00 41.70 3.51
1811 2148 8.114290 ACGACTACGATGTGCTTTAATTAATTG 58.886 33.333 11.05 0.00 42.66 2.32
1868 2210 1.269051 GCCCGCATAATTAACTGTGGC 60.269 52.381 11.62 8.72 40.87 5.01
1875 2217 4.381932 GCATAATTAACTGTGGCTTGGCTT 60.382 41.667 0.00 0.00 0.00 4.35
1902 2244 7.091443 CGATTGGATTTGGATAGTACTCCTAC 58.909 42.308 0.00 0.00 36.20 3.18
1903 2245 7.039644 CGATTGGATTTGGATAGTACTCCTACT 60.040 40.741 0.00 0.00 37.04 2.57
1904 2246 9.310449 GATTGGATTTGGATAGTACTCCTACTA 57.690 37.037 0.00 0.00 39.36 1.82
1906 2248 8.053776 TGGATTTGGATAGTACTCCTACTAGA 57.946 38.462 0.00 0.00 38.59 2.43
1909 2251 7.762588 TTTGGATAGTACTCCTACTAGATGC 57.237 40.000 0.00 0.00 38.59 3.91
1912 2254 8.215954 TGGATAGTACTCCTACTAGATGCTTA 57.784 38.462 0.00 0.00 38.59 3.09
1916 2258 6.300703 AGTACTCCTACTAGATGCTTACAGG 58.699 44.000 0.00 0.00 30.81 4.00
1917 2259 4.475345 ACTCCTACTAGATGCTTACAGGG 58.525 47.826 0.00 0.00 0.00 4.45
1918 2260 3.231818 TCCTACTAGATGCTTACAGGGC 58.768 50.000 0.00 0.00 0.00 5.19
1919 2261 2.965831 CCTACTAGATGCTTACAGGGCA 59.034 50.000 0.00 0.00 44.05 5.36
1920 2262 3.006323 CCTACTAGATGCTTACAGGGCAG 59.994 52.174 0.00 0.00 43.15 4.85
1922 2264 3.107601 ACTAGATGCTTACAGGGCAGAA 58.892 45.455 0.00 0.00 43.15 3.02
1923 2265 2.409948 AGATGCTTACAGGGCAGAAC 57.590 50.000 0.00 0.00 43.15 3.01
1924 2266 1.065126 AGATGCTTACAGGGCAGAACC 60.065 52.381 0.00 0.00 43.15 3.62
1925 2267 0.995024 ATGCTTACAGGGCAGAACCT 59.005 50.000 0.00 0.00 43.15 3.50
1945 2287 5.678583 ACCTTATCTGGAATCATGTCACTG 58.321 41.667 0.00 0.00 0.00 3.66
1948 2290 6.825213 CCTTATCTGGAATCATGTCACTGAAA 59.175 38.462 0.00 0.00 0.00 2.69
1991 2333 9.988815 AGTATTAATGGTGATTAGTCATGAGAC 57.011 33.333 0.00 0.00 45.31 3.36
1993 2335 4.696479 ATGGTGATTAGTCATGAGACCC 57.304 45.455 0.00 0.00 46.15 4.46
2029 2371 3.181429 ACTGGACAACATTCCCTTGATGT 60.181 43.478 0.00 0.00 35.59 3.06
2030 2372 3.156293 TGGACAACATTCCCTTGATGTG 58.844 45.455 0.00 0.00 33.37 3.21
2073 2418 8.150945 TCTATAAAATACAAGCTCACTGGGATC 58.849 37.037 0.00 0.00 0.00 3.36
2074 2419 4.574674 AAATACAAGCTCACTGGGATCA 57.425 40.909 0.00 0.00 0.00 2.92
2077 2433 1.911357 ACAAGCTCACTGGGATCATCA 59.089 47.619 0.00 0.00 0.00 3.07
2112 2470 3.077359 GTGGAAGTCTGAAACTGATGGG 58.923 50.000 0.00 0.00 38.58 4.00
2114 2472 3.394274 TGGAAGTCTGAAACTGATGGGAA 59.606 43.478 0.00 0.00 38.58 3.97
2115 2473 4.141274 TGGAAGTCTGAAACTGATGGGAAA 60.141 41.667 0.00 0.00 38.58 3.13
2117 2475 5.105997 GGAAGTCTGAAACTGATGGGAAATG 60.106 44.000 0.00 0.00 38.58 2.32
2130 2516 5.136909 TGATGGGAAATGGTATATTTGGGGA 59.863 40.000 0.00 0.00 0.00 4.81
2142 2528 9.586732 TGGTATATTTGGGGAAAGAATATTCTG 57.413 33.333 18.61 0.00 37.65 3.02
2149 2535 5.428457 TGGGGAAAGAATATTCTGTAGCAGA 59.572 40.000 18.61 0.00 38.87 4.26
2170 2556 8.093927 AGCAGACTATTCTAGAATCTAAATGGC 58.906 37.037 21.17 15.91 32.50 4.40
2171 2557 7.875041 GCAGACTATTCTAGAATCTAAATGGCA 59.125 37.037 21.17 0.18 32.50 4.92
2172 2558 9.941325 CAGACTATTCTAGAATCTAAATGGCAT 57.059 33.333 21.17 0.00 32.50 4.40
2196 2601 5.826601 TTGTAAACTTTGTGATGCACTCA 57.173 34.783 0.00 0.00 35.11 3.41
2358 2767 6.108687 TGGTGTAATTCTCTACATTCTGCTG 58.891 40.000 0.00 0.00 34.41 4.41
2393 2802 1.102154 TTTTGGGCAGGTGCGATATG 58.898 50.000 0.00 0.00 43.26 1.78
2660 3082 6.500336 TCACTACCTTATACTCCTGGTTTCT 58.500 40.000 0.00 0.00 34.33 2.52
2864 3676 9.521503 AGTTCAATTCTTTTTAAGCTCAAGTTC 57.478 29.630 0.00 0.00 0.00 3.01
2884 3697 4.487714 TCTTAATTGCCTGTTCGGATCT 57.512 40.909 0.00 0.00 33.16 2.75
2912 3725 0.036105 GCAAGGAGGCAATTTTGGGG 60.036 55.000 0.00 0.00 0.00 4.96
2949 3762 3.995199 AGATTCTTGTTCGCTCTGTCAA 58.005 40.909 0.00 0.00 0.00 3.18
3110 3923 4.937620 TGCTTACTTGACTGGATTCACATC 59.062 41.667 0.00 0.00 0.00 3.06
3282 4199 9.921637 AAAACAAACTGTATTGAGTTCTGAAAA 57.078 25.926 8.86 0.00 35.01 2.29
3333 4250 6.615088 AGTGAATTGTGCATTAACTGACATC 58.385 36.000 0.00 0.00 35.42 3.06
3390 4307 1.101331 CAGAGGAGGAAATTGCAGGC 58.899 55.000 0.00 0.00 0.00 4.85
3399 4316 2.094338 GGAAATTGCAGGCTTGAAGGAG 60.094 50.000 0.00 0.00 0.00 3.69
3609 4537 5.714806 CCCCTAAGCTTAAATCCTTGTGAAA 59.285 40.000 7.74 0.00 0.00 2.69
3717 4666 7.915397 TGTTCTTCTTACAGTTGCATCTTTTTC 59.085 33.333 0.00 0.00 0.00 2.29
3811 4760 6.695713 GTCCTTTTGTCTGTTATGTTCCAAAC 59.304 38.462 0.00 0.00 0.00 2.93
3966 4917 2.231215 AGATGCGTATCTGTGGAAGC 57.769 50.000 15.69 0.00 42.04 3.86
4491 5555 5.047021 TGCAATAGAGCTTGTTCAGTAGTCT 60.047 40.000 0.00 0.00 34.99 3.24
4535 5599 2.545537 ACCGAGGTTTCCAGTCTTTC 57.454 50.000 0.00 0.00 0.00 2.62
4673 5738 5.102953 TCCACTTGAAGCTATGCACTATT 57.897 39.130 0.00 0.00 0.00 1.73
4674 5739 5.118990 TCCACTTGAAGCTATGCACTATTC 58.881 41.667 0.00 0.00 0.00 1.75
4675 5740 4.877823 CCACTTGAAGCTATGCACTATTCA 59.122 41.667 0.00 0.00 0.00 2.57
4676 5741 5.355071 CCACTTGAAGCTATGCACTATTCAA 59.645 40.000 14.06 14.06 37.49 2.69
4678 5743 6.674694 CTTGAAGCTATGCACTATTCAAGT 57.325 37.500 23.91 0.00 45.95 3.16
4693 5758 6.072452 ACTATTCAAGTTCAAGCAAGGCTTAC 60.072 38.462 0.00 0.00 40.55 2.34
4707 5772 6.589907 AGCAAGGCTTACGGATTAAATTTTTG 59.410 34.615 0.00 0.00 33.89 2.44
4751 5816 1.546029 TGCCCTATATAGTGCTGCTCG 59.454 52.381 16.70 0.00 0.00 5.03
4818 5883 8.636213 ACATAGCTCATTTGCTGCTTTATTAAT 58.364 29.630 0.00 0.00 43.87 1.40
4819 5884 9.472361 CATAGCTCATTTGCTGCTTTATTAATT 57.528 29.630 0.00 0.00 43.87 1.40
4941 6017 0.819582 CCATGATGACCAAGGGCAAC 59.180 55.000 0.00 0.00 30.22 4.17
5063 6145 4.319177 GCTTTAGCTTCTTCCTGTCTTCA 58.681 43.478 0.00 0.00 38.21 3.02
5072 6154 4.089361 TCTTCCTGTCTTCATGCTCTACA 58.911 43.478 0.00 0.00 0.00 2.74
5085 6167 2.368548 TGCTCTACAAAGACTTCCTGCA 59.631 45.455 0.00 0.00 0.00 4.41
5207 6289 0.950555 TGATCTCACACGTTGCTGCC 60.951 55.000 0.00 0.00 0.00 4.85
5334 6416 5.045651 TGAACAGTCCTGGATGTGATGTTAT 60.046 40.000 14.10 0.00 34.19 1.89
5383 6465 3.179830 CATGCTACCGTGTGAACTAGAC 58.820 50.000 0.00 0.00 0.00 2.59
5402 6484 9.836864 AACTAGACATGCTTATTGTCAATATGA 57.163 29.630 18.15 7.46 44.73 2.15
5553 6636 5.186198 CCTAAACCTCAGACAAATAGTGGG 58.814 45.833 0.00 0.00 0.00 4.61
5603 6686 7.784470 AGAGTAGACATTTTACTCCTCTGTT 57.216 36.000 8.38 0.00 45.18 3.16
5740 6823 1.076332 GAATCACAAACTCCCGACCG 58.924 55.000 0.00 0.00 0.00 4.79
5829 6912 1.076559 TGGGCATCCAATCAGGCAG 60.077 57.895 0.00 0.00 40.73 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.434336 ACTGGCCTAATCATTCTGCGTA 59.566 45.455 3.32 0.00 0.00 4.42
29 30 2.632377 CACGTCAACTGGCCTAATCAT 58.368 47.619 3.32 0.00 0.00 2.45
30 31 1.338674 CCACGTCAACTGGCCTAATCA 60.339 52.381 3.32 0.00 0.00 2.57
58 59 2.110006 GCCGATGCTTCTCTCCCC 59.890 66.667 0.00 0.00 33.53 4.81
208 228 4.360405 GTGATGGTGGGGGCGGTT 62.360 66.667 0.00 0.00 0.00 4.44
222 262 3.625897 CTGCGGGTGGTCAGGTGA 61.626 66.667 0.00 0.00 0.00 4.02
236 276 0.392193 ACTACACTCATGGCAGCTGC 60.392 55.000 30.88 30.88 41.14 5.25
260 310 2.811317 GCGAAGAGGACAGGTGCG 60.811 66.667 0.00 0.00 0.00 5.34
262 312 0.318441 TCTTGCGAAGAGGACAGGTG 59.682 55.000 0.00 0.00 32.71 4.00
311 374 2.683475 GTGGTGGGGAGGGATTGG 59.317 66.667 0.00 0.00 0.00 3.16
312 375 2.215451 CTGGTGGTGGGGAGGGATTG 62.215 65.000 0.00 0.00 0.00 2.67
313 376 1.930656 CTGGTGGTGGGGAGGGATT 60.931 63.158 0.00 0.00 0.00 3.01
314 377 2.286425 CTGGTGGTGGGGAGGGAT 60.286 66.667 0.00 0.00 0.00 3.85
322 385 2.098426 ATTTTTGCGGCTGGTGGTGG 62.098 55.000 0.00 0.00 0.00 4.61
324 387 1.665442 GATTTTTGCGGCTGGTGGT 59.335 52.632 0.00 0.00 0.00 4.16
331 394 0.316841 TGGTCTTGGATTTTTGCGGC 59.683 50.000 0.00 0.00 0.00 6.53
358 421 4.290326 CACAGTGTGCTTGCGTTG 57.710 55.556 10.97 0.00 0.00 4.10
375 438 1.469703 ACGCCGGTTTATTTAGTTGGC 59.530 47.619 1.90 0.00 37.66 4.52
402 616 1.605753 AAAGGAGAGCCGTTGGTTTC 58.394 50.000 0.00 0.00 39.96 2.78
407 621 3.315191 TCTTTGAAAAAGGAGAGCCGTTG 59.685 43.478 0.20 0.00 35.96 4.10
428 662 7.901889 GGCGTTTATTTTTACTACTAGCTGTTC 59.098 37.037 0.00 0.00 0.00 3.18
436 670 8.456471 GGAAGAATGGCGTTTATTTTTACTACT 58.544 33.333 0.00 0.00 0.00 2.57
437 671 8.238631 TGGAAGAATGGCGTTTATTTTTACTAC 58.761 33.333 0.00 0.00 0.00 2.73
438 672 8.338072 TGGAAGAATGGCGTTTATTTTTACTA 57.662 30.769 0.00 0.00 0.00 1.82
439 673 7.222000 TGGAAGAATGGCGTTTATTTTTACT 57.778 32.000 0.00 0.00 0.00 2.24
440 674 7.382759 TGTTGGAAGAATGGCGTTTATTTTTAC 59.617 33.333 0.00 0.00 0.00 2.01
513 749 0.797542 CGCGGGGAATGTTCGTAAAA 59.202 50.000 0.00 0.00 0.00 1.52
517 753 1.520787 GATCGCGGGGAATGTTCGT 60.521 57.895 6.13 0.00 0.00 3.85
518 754 2.585869 CGATCGCGGGGAATGTTCG 61.586 63.158 6.13 0.01 0.00 3.95
519 755 2.882366 GCGATCGCGGGGAATGTTC 61.882 63.158 26.12 0.00 38.16 3.18
520 756 2.895372 GCGATCGCGGGGAATGTT 60.895 61.111 26.12 0.00 38.16 2.71
586 834 2.570393 GTATTGGACGGACGTACGC 58.430 57.895 22.56 13.21 37.37 4.42
606 854 0.452987 CGTGTGGATTGATTGGCCTG 59.547 55.000 3.32 0.00 0.00 4.85
676 933 3.467226 TCCGGGGAAAGCTAGCGG 61.467 66.667 9.55 2.40 0.00 5.52
677 934 2.202892 GTCCGGGGAAAGCTAGCG 60.203 66.667 9.55 0.00 0.00 4.26
678 935 2.189784 GGTCCGGGGAAAGCTAGC 59.810 66.667 6.62 6.62 0.00 3.42
679 936 0.326927 TTTGGTCCGGGGAAAGCTAG 59.673 55.000 0.00 0.00 0.00 3.42
827 1111 2.610859 TGGGTGGAGGAGGAAGGC 60.611 66.667 0.00 0.00 0.00 4.35
1120 1417 2.354343 GGAGCCTGGCTGCTTCTT 59.646 61.111 30.12 3.20 43.58 2.52
1121 1418 3.726144 GGGAGCCTGGCTGCTTCT 61.726 66.667 34.27 7.92 46.13 2.85
1122 1419 3.991725 CTGGGAGCCTGGCTGCTTC 62.992 68.421 34.27 21.75 46.13 3.86
1659 1971 0.606673 GCAGGAAGTTCTCGGGCTTT 60.607 55.000 2.25 0.00 0.00 3.51
1761 2073 2.035632 CCGACTAGAGCAGAAAGGGAT 58.964 52.381 0.00 0.00 0.00 3.85
1762 2074 1.272536 ACCGACTAGAGCAGAAAGGGA 60.273 52.381 0.00 0.00 0.00 4.20
1768 2105 0.803117 CGTTGACCGACTAGAGCAGA 59.197 55.000 0.00 0.00 39.56 4.26
1811 2148 6.660949 TCTTACTGTAGTAGGAGTACCAAACC 59.339 42.308 0.30 0.00 38.94 3.27
1868 2210 2.264813 CAAATCCAATCGCAAGCCAAG 58.735 47.619 0.00 0.00 37.18 3.61
1875 2217 5.290493 AGTACTATCCAAATCCAATCGCA 57.710 39.130 0.00 0.00 0.00 5.10
1902 2244 3.462021 GTTCTGCCCTGTAAGCATCTAG 58.538 50.000 0.00 0.00 40.04 2.43
1903 2245 2.170607 GGTTCTGCCCTGTAAGCATCTA 59.829 50.000 0.00 0.00 40.04 1.98
1904 2246 1.065126 GGTTCTGCCCTGTAAGCATCT 60.065 52.381 0.00 0.00 40.04 2.90
1906 2248 0.995024 AGGTTCTGCCCTGTAAGCAT 59.005 50.000 0.00 0.00 40.04 3.79
1909 2251 4.446371 CAGATAAGGTTCTGCCCTGTAAG 58.554 47.826 0.00 0.00 36.96 2.34
1912 2254 1.561542 CCAGATAAGGTTCTGCCCTGT 59.438 52.381 0.00 0.00 41.50 4.00
1916 2258 4.156455 TGATTCCAGATAAGGTTCTGCC 57.844 45.455 0.00 0.00 41.50 4.85
1917 2259 5.128919 ACATGATTCCAGATAAGGTTCTGC 58.871 41.667 0.00 0.00 41.50 4.26
1918 2260 6.259608 GTGACATGATTCCAGATAAGGTTCTG 59.740 42.308 0.00 0.00 42.31 3.02
1919 2261 6.157645 AGTGACATGATTCCAGATAAGGTTCT 59.842 38.462 0.00 0.00 0.00 3.01
1920 2262 6.259608 CAGTGACATGATTCCAGATAAGGTTC 59.740 42.308 0.00 0.00 0.00 3.62
1922 2264 5.426509 TCAGTGACATGATTCCAGATAAGGT 59.573 40.000 0.00 0.00 0.00 3.50
1923 2265 5.922053 TCAGTGACATGATTCCAGATAAGG 58.078 41.667 0.00 0.00 0.00 2.69
1924 2266 7.854557 TTTCAGTGACATGATTCCAGATAAG 57.145 36.000 0.00 0.00 0.00 1.73
1977 2319 5.749109 CACGTAAAGGGTCTCATGACTAATC 59.251 44.000 0.00 0.00 42.54 1.75
1980 2322 4.338012 TCACGTAAAGGGTCTCATGACTA 58.662 43.478 0.00 0.00 42.54 2.59
2050 2392 6.662755 TGATCCCAGTGAGCTTGTATTTTAT 58.337 36.000 0.00 0.00 0.00 1.40
2054 2399 4.164796 TGATGATCCCAGTGAGCTTGTATT 59.835 41.667 0.00 0.00 0.00 1.89
2058 2403 2.704464 TGATGATCCCAGTGAGCTTG 57.296 50.000 0.00 0.00 0.00 4.01
2059 2404 3.972638 ACTATGATGATCCCAGTGAGCTT 59.027 43.478 0.00 0.00 0.00 3.74
2062 2407 5.541953 TCAACTATGATGATCCCAGTGAG 57.458 43.478 0.00 0.00 0.00 3.51
2073 2418 4.201657 TCCACTGCCATTCAACTATGATG 58.798 43.478 0.00 0.00 34.96 3.07
2074 2419 4.508551 TCCACTGCCATTCAACTATGAT 57.491 40.909 0.00 0.00 34.96 2.45
2077 2433 4.018960 AGACTTCCACTGCCATTCAACTAT 60.019 41.667 0.00 0.00 0.00 2.12
2117 2475 9.588096 ACAGAATATTCTTTCCCCAAATATACC 57.412 33.333 15.49 0.00 34.74 2.73
2165 2551 7.278424 GCATCACAAAGTTTACAATATGCCATT 59.722 33.333 0.00 0.00 32.95 3.16
2170 2556 8.022550 TGAGTGCATCACAAAGTTTACAATATG 58.977 33.333 0.00 0.00 36.74 1.78
2171 2557 8.109705 TGAGTGCATCACAAAGTTTACAATAT 57.890 30.769 0.00 0.00 36.74 1.28
2172 2558 7.503521 TGAGTGCATCACAAAGTTTACAATA 57.496 32.000 0.00 0.00 36.74 1.90
2173 2559 6.389830 TGAGTGCATCACAAAGTTTACAAT 57.610 33.333 0.00 0.00 36.74 2.71
2196 2601 1.707427 AGAAAGGGAGGCATGAGTGTT 59.293 47.619 0.00 0.00 0.00 3.32
2358 2767 2.167662 CAAAATGGGGGTACACCACTC 58.832 52.381 17.96 0.00 45.72 3.51
2393 2802 7.384115 GCTTCCAAGTTAATTGAAGGGTTAAAC 59.616 37.037 0.00 0.00 41.83 2.01
2660 3082 6.839454 ACGTATTGAGGAGTATAGAAGGAGA 58.161 40.000 0.00 0.00 0.00 3.71
2864 3676 5.991606 TCATAGATCCGAACAGGCAATTAAG 59.008 40.000 0.00 0.00 40.77 1.85
2884 3697 0.620030 TGCCTCCTTGCAAGCTCATA 59.380 50.000 21.43 4.00 38.56 2.15
2909 3722 2.152016 CTTTTGAAGAGACGAACCCCC 58.848 52.381 0.00 0.00 0.00 5.40
2912 3725 6.017852 ACAAGAATCTTTTGAAGAGACGAACC 60.018 38.462 0.00 0.00 41.61 3.62
2949 3762 8.284693 GCAAAGAATGAATGTGTAAAGCAATTT 58.715 29.630 0.00 0.00 0.00 1.82
3110 3923 6.531503 TCTTTACAGAGGGAGTACAAGATG 57.468 41.667 0.00 0.00 0.00 2.90
3159 3975 9.057089 CCTCCATAAAGAAATATAAGAGCGTTT 57.943 33.333 0.00 0.00 0.00 3.60
3161 3977 7.016268 TCCCTCCATAAAGAAATATAAGAGCGT 59.984 37.037 0.00 0.00 0.00 5.07
3162 3978 7.386851 TCCCTCCATAAAGAAATATAAGAGCG 58.613 38.462 0.00 0.00 0.00 5.03
3173 3989 9.892444 TCATATTAGTACTCCCTCCATAAAGAA 57.108 33.333 0.00 0.00 0.00 2.52
3177 3993 7.246027 TGCTCATATTAGTACTCCCTCCATAA 58.754 38.462 0.00 0.00 0.00 1.90
3179 3995 5.655394 TGCTCATATTAGTACTCCCTCCAT 58.345 41.667 0.00 0.00 0.00 3.41
3180 3996 5.074746 TGCTCATATTAGTACTCCCTCCA 57.925 43.478 0.00 0.00 0.00 3.86
3182 3998 7.708752 GCATATTGCTCATATTAGTACTCCCTC 59.291 40.741 0.00 0.00 40.96 4.30
3183 3999 7.560368 GCATATTGCTCATATTAGTACTCCCT 58.440 38.462 0.00 0.00 40.96 4.20
3184 4000 7.778470 GCATATTGCTCATATTAGTACTCCC 57.222 40.000 0.00 0.00 40.96 4.30
3282 4199 3.187227 GTGCTTCATCACACGAAGACATT 59.813 43.478 4.16 0.00 42.05 2.71
3317 4234 3.926527 TCACGAGATGTCAGTTAATGCAC 59.073 43.478 0.00 0.00 0.00 4.57
3333 4250 5.515797 TTACCTGGTAGAATGATCACGAG 57.484 43.478 6.66 0.00 0.00 4.18
3390 4307 4.550076 AGTCTGGAACATCTCCTTCAAG 57.450 45.455 0.00 0.00 45.64 3.02
3609 4537 0.538287 GGAGGCAGCACAAGTTTCCT 60.538 55.000 0.00 0.00 0.00 3.36
3664 4613 2.643551 GCATTAAGCAGCCTAGTTCCA 58.356 47.619 0.00 0.00 44.79 3.53
3717 4666 1.546029 GCCCTAAAGAAAGCCACCAAG 59.454 52.381 0.00 0.00 0.00 3.61
3811 4760 3.055094 AGAAGTACAGTTATGTGCCCCTG 60.055 47.826 0.00 0.00 42.48 4.45
4503 5567 9.730420 CTGGAAACCTCGGTATAAATTATTTTG 57.270 33.333 0.00 0.00 0.00 2.44
4535 5599 2.493675 TGAGAGACCATGTTCCTCTTCG 59.506 50.000 9.26 0.00 37.40 3.79
4693 5758 8.442384 CCACTGGAATTTCAAAAATTTAATCCG 58.558 33.333 0.00 0.00 0.00 4.18
4699 5764 9.492973 CTATGTCCACTGGAATTTCAAAAATTT 57.507 29.630 0.00 0.00 31.38 1.82
4707 5772 7.253422 CACAAATCTATGTCCACTGGAATTTC 58.747 38.462 0.00 0.00 31.38 2.17
4751 5816 6.128145 GCCTCTCTGAACCAAACTATCTTTTC 60.128 42.308 0.00 0.00 0.00 2.29
4822 5887 9.727859 TGTTACTAACAGAACCATAAGCATTAA 57.272 29.630 0.00 0.00 36.25 1.40
4941 6017 4.820744 CTTCGCCCCACCCCCATG 62.821 72.222 0.00 0.00 0.00 3.66
5063 6145 3.008375 TGCAGGAAGTCTTTGTAGAGCAT 59.992 43.478 0.00 0.00 0.00 3.79
5072 6154 5.514274 TTCGAAAATTGCAGGAAGTCTTT 57.486 34.783 0.00 0.00 0.00 2.52
5085 6167 7.872483 ACAGGCATTTTACAAGATTCGAAAATT 59.128 29.630 0.00 0.00 30.91 1.82
5207 6289 3.508744 ACATTTTGCAGGGATTAAGCG 57.491 42.857 0.00 0.00 0.00 4.68
5334 6416 8.191446 CGAGTGATATGTAGAGAGAAAAGGAAA 58.809 37.037 0.00 0.00 0.00 3.13
5402 6484 2.664402 AAACAGAGGCTTGGTCATGT 57.336 45.000 0.00 0.00 0.00 3.21
5469 6551 7.387673 CGATGAAAAACCCATGTGATAGCTATA 59.612 37.037 6.13 0.00 0.00 1.31
5603 6686 2.677902 GCCCGTCAGATTCATTGAGACA 60.678 50.000 5.08 0.00 0.00 3.41
5740 6823 2.858344 CAAGTTGATATCGACGGTGACC 59.142 50.000 18.28 0.00 35.42 4.02
5791 6874 4.141413 CCCATCCACATCATGAAGAACCTA 60.141 45.833 4.68 0.00 0.00 3.08
5822 6905 0.548031 GGGATCATGAACCTGCCTGA 59.452 55.000 20.25 0.00 0.00 3.86
5829 6912 2.094026 GTGGCTTTTGGGATCATGAACC 60.094 50.000 13.47 13.47 0.00 3.62
5872 6955 0.616111 AGTCCCTGCGGTCTGAGATT 60.616 55.000 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.