Multiple sequence alignment - TraesCS2A01G395200

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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 TraesCS2A01G395200 chr2A 100.000 3023 0 0 1 3023 646850854 646853876 0.000000e+00 5583.0
1 TraesCS2A01G395200 chr2B 91.474 2205 102 26 6 2178 589035682 589037832 0.000000e+00 2952.0
2 TraesCS2A01G395200 chr2D 91.898 1728 73 17 509 2206 501554833 501553143 0.000000e+00 2353.0
3 TraesCS2A01G395200 chr2D 90.291 721 43 11 2319 3023 2665067 2664358 0.000000e+00 918.0
4 TraesCS2A01G395200 chr3D 89.903 723 37 13 2321 3023 75159175 75158469 0.000000e+00 898.0
5 TraesCS2A01G395200 chr7D 89.804 716 41 13 2319 3023 198051249 198051943 0.000000e+00 889.0
6 TraesCS2A01G395200 chr1D 88.219 730 57 15 2319 3023 299760905 299760180 0.000000e+00 845.0
7 TraesCS2A01G395200 chr1D 84.499 729 58 24 2336 3023 150953506 150954220 0.000000e+00 669.0
8 TraesCS2A01G395200 chr6D 87.900 719 60 13 2319 3023 422033831 422033126 0.000000e+00 821.0
9 TraesCS2A01G395200 chr6D 91.250 320 16 5 2704 3023 353360136 353360443 2.790000e-115 425.0
10 TraesCS2A01G395200 chr4B 87.448 725 52 16 2317 3023 31513484 31514187 0.000000e+00 798.0
11 TraesCS2A01G395200 chr3A 87.604 718 52 10 2316 3006 28887990 28888697 0.000000e+00 798.0
12 TraesCS2A01G395200 chr5D 87.273 715 62 12 2321 3023 538183481 538182784 0.000000e+00 789.0
13 TraesCS2A01G395200 chr1A 87.045 687 54 16 2319 2987 10427315 10426646 0.000000e+00 743.0
14 TraesCS2A01G395200 chr4A 100.000 31 0 0 2102 2132 666190530 666190560 1.170000e-04 58.4


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 TraesCS2A01G395200 chr2A 646850854 646853876 3022 False 5583 5583 100.000 1 3023 1 chr2A.!!$F1 3022
1 TraesCS2A01G395200 chr2B 589035682 589037832 2150 False 2952 2952 91.474 6 2178 1 chr2B.!!$F1 2172
2 TraesCS2A01G395200 chr2D 501553143 501554833 1690 True 2353 2353 91.898 509 2206 1 chr2D.!!$R2 1697
3 TraesCS2A01G395200 chr2D 2664358 2665067 709 True 918 918 90.291 2319 3023 1 chr2D.!!$R1 704
4 TraesCS2A01G395200 chr3D 75158469 75159175 706 True 898 898 89.903 2321 3023 1 chr3D.!!$R1 702
5 TraesCS2A01G395200 chr7D 198051249 198051943 694 False 889 889 89.804 2319 3023 1 chr7D.!!$F1 704
6 TraesCS2A01G395200 chr1D 299760180 299760905 725 True 845 845 88.219 2319 3023 1 chr1D.!!$R1 704
7 TraesCS2A01G395200 chr1D 150953506 150954220 714 False 669 669 84.499 2336 3023 1 chr1D.!!$F1 687
8 TraesCS2A01G395200 chr6D 422033126 422033831 705 True 821 821 87.900 2319 3023 1 chr6D.!!$R1 704
9 TraesCS2A01G395200 chr4B 31513484 31514187 703 False 798 798 87.448 2317 3023 1 chr4B.!!$F1 706
10 TraesCS2A01G395200 chr3A 28887990 28888697 707 False 798 798 87.604 2316 3006 1 chr3A.!!$F1 690
11 TraesCS2A01G395200 chr5D 538182784 538183481 697 True 789 789 87.273 2321 3023 1 chr5D.!!$R1 702
12 TraesCS2A01G395200 chr1A 10426646 10427315 669 True 743 743 87.045 2319 2987 1 chr1A.!!$R1 668

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
779 796 0.037697 TCGACTGTCCCACCGAATTG 60.038 55.0 1.55 0.0 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2297 2332 0.828022 AGTCACCGTCTCACCAACAA 59.172 50.0 0.0 0.0 0.0 2.83 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
30 31 3.548214 GCTCGGAAACACAAAAGAACTCC 60.548 47.826 0.00 0.00 0.00 3.85
31 32 3.877508 CTCGGAAACACAAAAGAACTCCT 59.122 43.478 0.00 0.00 0.00 3.69
36 37 4.639135 AACACAAAAGAACTCCTTGCTC 57.361 40.909 0.00 0.00 34.79 4.26
54 55 3.322466 CAGAGGCCCCGTGTCCTT 61.322 66.667 0.00 0.00 31.71 3.36
63 64 1.609501 CCGTGTCCTTCCTCCTCCA 60.610 63.158 0.00 0.00 0.00 3.86
64 65 1.192146 CCGTGTCCTTCCTCCTCCAA 61.192 60.000 0.00 0.00 0.00 3.53
65 66 0.247736 CGTGTCCTTCCTCCTCCAAG 59.752 60.000 0.00 0.00 0.00 3.61
66 67 1.353091 GTGTCCTTCCTCCTCCAAGT 58.647 55.000 0.00 0.00 0.00 3.16
71 72 1.352083 CTTCCTCCTCCAAGTGGACA 58.648 55.000 0.00 0.00 39.78 4.02
87 88 2.170397 TGGACAAAGTCACTGAAGCTGA 59.830 45.455 0.00 0.00 33.68 4.26
103 104 2.129607 GCTGACAACAAAACCTGCATG 58.870 47.619 0.00 0.00 0.00 4.06
143 144 7.065563 CAGTAGATTTTCCAGATCAGAACCAAG 59.934 40.741 0.00 0.00 0.00 3.61
167 168 3.118371 GGGTTCCGAATATCACAAGAGGT 60.118 47.826 0.00 0.00 0.00 3.85
192 193 3.814283 GTGCTGAATCTCTTGGGATCATC 59.186 47.826 0.00 0.00 0.00 2.92
193 194 3.065655 GCTGAATCTCTTGGGATCATCG 58.934 50.000 0.00 0.00 0.00 3.84
194 195 3.065655 CTGAATCTCTTGGGATCATCGC 58.934 50.000 0.00 0.00 0.00 4.58
195 196 2.435437 TGAATCTCTTGGGATCATCGCA 59.565 45.455 0.00 0.00 37.56 5.10
196 197 3.072038 TGAATCTCTTGGGATCATCGCAT 59.928 43.478 5.04 0.00 39.13 4.73
210 211 0.175531 TCGCATCGGCTCTGATGAAA 59.824 50.000 19.75 6.21 46.98 2.69
214 215 3.488047 CGCATCGGCTCTGATGAAATTTT 60.488 43.478 19.75 0.00 46.98 1.82
246 247 4.320456 CCTCAGGTGTGCCGCAGT 62.320 66.667 0.00 0.00 40.50 4.40
255 256 1.738099 GTGCCGCAGTGGACAGTAG 60.738 63.158 3.39 0.00 42.00 2.57
256 257 2.815647 GCCGCAGTGGACAGTAGC 60.816 66.667 3.39 0.00 42.00 3.58
257 258 2.656646 CCGCAGTGGACAGTAGCA 59.343 61.111 0.00 0.00 42.00 3.49
262 263 1.737363 GCAGTGGACAGTAGCAGTAGC 60.737 57.143 0.00 0.00 42.56 3.58
272 273 2.941720 AGTAGCAGTAGCACTACGTACC 59.058 50.000 2.29 0.00 45.49 3.34
275 276 1.530646 GCAGTAGCACTACGTACCGTC 60.531 57.143 2.29 0.00 40.06 4.79
297 298 3.885484 GGATAACTGCATCCGACAATG 57.115 47.619 0.00 0.00 35.42 2.82
309 310 5.230726 GCATCCGACAATGAATTCAATCAAC 59.769 40.000 13.09 2.99 32.06 3.18
344 345 8.438513 CGTGGTATATCTAGAGCAAAAATCATG 58.561 37.037 0.00 0.00 0.00 3.07
368 369 4.713321 AGCAATGCCTTAGAAATGACCAAT 59.287 37.500 0.00 0.00 0.00 3.16
370 371 5.594926 CAATGCCTTAGAAATGACCAATCC 58.405 41.667 0.00 0.00 0.00 3.01
371 372 3.278574 TGCCTTAGAAATGACCAATCCG 58.721 45.455 0.00 0.00 0.00 4.18
372 373 2.033424 GCCTTAGAAATGACCAATCCGC 59.967 50.000 0.00 0.00 0.00 5.54
373 374 2.287915 CCTTAGAAATGACCAATCCGCG 59.712 50.000 0.00 0.00 0.00 6.46
375 376 1.086696 AGAAATGACCAATCCGCGTG 58.913 50.000 4.92 0.00 0.00 5.34
376 377 1.083489 GAAATGACCAATCCGCGTGA 58.917 50.000 4.92 1.95 0.00 4.35
377 378 1.062587 GAAATGACCAATCCGCGTGAG 59.937 52.381 4.92 0.00 0.00 3.51
378 379 0.249120 AATGACCAATCCGCGTGAGA 59.751 50.000 4.92 0.00 0.00 3.27
379 380 0.465705 ATGACCAATCCGCGTGAGAT 59.534 50.000 4.92 0.00 0.00 2.75
380 381 0.179111 TGACCAATCCGCGTGAGATC 60.179 55.000 4.92 0.00 0.00 2.75
381 382 0.876342 GACCAATCCGCGTGAGATCC 60.876 60.000 4.92 0.00 0.00 3.36
382 383 1.595382 CCAATCCGCGTGAGATCCC 60.595 63.158 4.92 0.00 0.00 3.85
383 384 1.443407 CAATCCGCGTGAGATCCCT 59.557 57.895 4.92 0.00 0.00 4.20
384 385 0.673985 CAATCCGCGTGAGATCCCTA 59.326 55.000 4.92 0.00 0.00 3.53
385 386 0.674534 AATCCGCGTGAGATCCCTAC 59.325 55.000 4.92 0.00 0.00 3.18
386 387 0.178987 ATCCGCGTGAGATCCCTACT 60.179 55.000 4.92 0.00 0.00 2.57
387 388 0.818445 TCCGCGTGAGATCCCTACTC 60.818 60.000 4.92 0.00 35.26 2.59
388 389 1.280142 CGCGTGAGATCCCTACTCG 59.720 63.158 0.00 0.00 37.22 4.18
389 390 1.655329 GCGTGAGATCCCTACTCGG 59.345 63.158 0.00 0.00 37.22 4.63
390 391 1.655329 CGTGAGATCCCTACTCGGC 59.345 63.158 0.00 0.00 37.22 5.54
391 392 0.820074 CGTGAGATCCCTACTCGGCT 60.820 60.000 0.00 0.00 37.22 5.52
392 393 1.542767 CGTGAGATCCCTACTCGGCTA 60.543 57.143 0.00 0.00 37.22 3.93
393 394 2.584236 GTGAGATCCCTACTCGGCTAA 58.416 52.381 0.00 0.00 37.22 3.09
394 395 3.158676 GTGAGATCCCTACTCGGCTAAT 58.841 50.000 0.00 0.00 37.22 1.73
395 396 3.191791 GTGAGATCCCTACTCGGCTAATC 59.808 52.174 0.00 0.00 37.22 1.75
396 397 2.756207 GAGATCCCTACTCGGCTAATCC 59.244 54.545 0.00 0.00 0.00 3.01
406 407 1.076777 GGCTAATCCCTGCTTGGCA 60.077 57.895 0.00 0.00 36.92 4.92
408 409 1.387295 GCTAATCCCTGCTTGGCACC 61.387 60.000 0.00 0.00 33.79 5.01
426 427 3.857854 GCACTCTGCCGCACGATG 61.858 66.667 0.00 0.00 37.42 3.84
458 461 0.104304 AACGTGCTCTGTTCTTCCGT 59.896 50.000 0.00 0.00 0.00 4.69
477 481 1.274728 GTCTGTCACTCTGTCAGGCAT 59.725 52.381 0.00 0.00 37.90 4.40
500 504 3.725754 CCTGTGGCAGGTTACTTGT 57.274 52.632 6.99 0.00 45.82 3.16
515 519 7.486551 CAGGTTACTTGTTATCTTTCTCTCTCG 59.513 40.741 0.00 0.00 0.00 4.04
580 597 1.878522 GATCACGCTGTGCCGGTAG 60.879 63.158 1.90 0.14 32.98 3.18
633 650 1.446272 AAACGGCAGAGCTCGCTAC 60.446 57.895 23.23 11.54 0.00 3.58
676 693 0.401738 TGGAGAGGCCAAGAACCTTG 59.598 55.000 5.01 0.00 45.87 3.61
706 723 3.731136 TGTCTCGCAAGTGGCAAC 58.269 55.556 0.00 0.00 43.11 4.17
779 796 0.037697 TCGACTGTCCCACCGAATTG 60.038 55.000 1.55 0.00 0.00 2.32
793 810 1.002134 AATTGACACCGCTCCCCTG 60.002 57.895 0.00 0.00 0.00 4.45
803 820 2.868253 GCTCCCCTGCGTACATTTT 58.132 52.632 0.00 0.00 0.00 1.82
870 901 1.218316 GACTTTGATCGGGCGTCCT 59.782 57.895 3.66 0.00 0.00 3.85
871 902 0.391263 GACTTTGATCGGGCGTCCTT 60.391 55.000 3.66 0.00 0.00 3.36
872 903 0.391263 ACTTTGATCGGGCGTCCTTC 60.391 55.000 3.66 1.06 0.00 3.46
873 904 1.078708 TTTGATCGGGCGTCCTTCC 60.079 57.895 3.66 0.00 0.00 3.46
914 945 1.136147 CCATGCTTCACTCGCAAGC 59.864 57.895 0.00 0.00 45.59 4.01
1011 1042 1.010350 CGCCATCATGCTCGCTTTC 60.010 57.895 0.00 0.00 0.00 2.62
1014 1045 1.010350 CATCATGCTCGCTTTCGCC 60.010 57.895 0.00 0.00 35.26 5.54
1041 1072 1.002315 ACAAAAATGTCCCCATGCTGC 59.998 47.619 0.00 0.00 0.00 5.25
1055 1086 2.812619 GCTGCCCGCTCCTCCTATT 61.813 63.158 0.00 0.00 35.14 1.73
1056 1087 1.472662 GCTGCCCGCTCCTCCTATTA 61.473 60.000 0.00 0.00 35.14 0.98
1057 1088 1.270907 CTGCCCGCTCCTCCTATTAT 58.729 55.000 0.00 0.00 0.00 1.28
1069 1100 5.072741 TCCTCCTATTATTTCCAGCAATGC 58.927 41.667 0.00 0.00 0.00 3.56
1367 1398 4.796231 CGAGTTCTCCGTGCCCCG 62.796 72.222 0.00 0.00 0.00 5.73
1449 1480 1.139095 CAACCTCTCGGCCGTCTAC 59.861 63.158 27.15 0.00 0.00 2.59
1524 1555 0.535335 TCATGTTCTACGGCCTGGAC 59.465 55.000 0.00 0.00 0.00 4.02
1590 1621 1.084370 CCATCCGCGTCAACTTCTCC 61.084 60.000 4.92 0.00 0.00 3.71
1713 1744 2.352805 CACCTGAGGGACCAAGGC 59.647 66.667 2.38 0.00 36.25 4.35
1794 1825 2.670934 AGCAAGTGGAAGCTGGCG 60.671 61.111 0.00 0.00 40.26 5.69
1851 1882 3.827898 CTGGGGCTCGTCCTCGTC 61.828 72.222 0.00 0.00 38.56 4.20
1858 1889 4.531912 TCGTCCTCGTCGCGATGC 62.532 66.667 23.40 8.45 34.61 3.91
2007 2038 0.803740 ACGAGCTGGAGAACGAGTAC 59.196 55.000 1.44 0.00 0.00 2.73
2025 2056 2.542907 CCGTGCCACCTTGTGACAC 61.543 63.158 0.00 0.00 42.06 3.67
2151 2184 6.648725 AATCGATGTAAACTGTGAAGTAGC 57.351 37.500 0.00 0.00 0.00 3.58
2178 2211 5.050126 ACTTGATCCAGAGATGCATGATT 57.950 39.130 2.46 0.00 30.90 2.57
2179 2212 6.183810 ACTTGATCCAGAGATGCATGATTA 57.816 37.500 2.46 0.00 30.90 1.75
2180 2213 5.996513 ACTTGATCCAGAGATGCATGATTAC 59.003 40.000 2.46 0.00 30.90 1.89
2181 2214 4.903054 TGATCCAGAGATGCATGATTACC 58.097 43.478 2.46 0.00 30.90 2.85
2182 2215 4.348754 TGATCCAGAGATGCATGATTACCA 59.651 41.667 2.46 0.00 30.90 3.25
2183 2216 4.077300 TCCAGAGATGCATGATTACCAC 57.923 45.455 2.46 0.00 0.00 4.16
2184 2217 2.804527 CCAGAGATGCATGATTACCACG 59.195 50.000 2.46 0.00 0.00 4.94
2206 2241 8.597227 CCACGATCGTTCATTTTAGTTACATTA 58.403 33.333 20.14 0.00 0.00 1.90
2207 2242 9.405083 CACGATCGTTCATTTTAGTTACATTAC 57.595 33.333 20.14 0.00 0.00 1.89
2208 2243 9.142515 ACGATCGTTCATTTTAGTTACATTACA 57.857 29.630 16.60 0.00 0.00 2.41
2221 2256 7.724305 AGTTACATTACATTGTTATAGGCGG 57.276 36.000 0.00 0.00 0.00 6.13
2222 2257 6.708949 AGTTACATTACATTGTTATAGGCGGG 59.291 38.462 0.00 0.00 0.00 6.13
2223 2258 4.394729 ACATTACATTGTTATAGGCGGGG 58.605 43.478 0.00 0.00 0.00 5.73
2224 2259 3.495434 TTACATTGTTATAGGCGGGGG 57.505 47.619 0.00 0.00 0.00 5.40
2255 2290 7.506328 AACTTTAGCCTCTAAATTTCGTTGT 57.494 32.000 0.00 0.00 0.00 3.32
2256 2291 8.611654 AACTTTAGCCTCTAAATTTCGTTGTA 57.388 30.769 0.00 0.00 0.00 2.41
2257 2292 8.611654 ACTTTAGCCTCTAAATTTCGTTGTAA 57.388 30.769 0.00 0.00 0.00 2.41
2258 2293 8.501580 ACTTTAGCCTCTAAATTTCGTTGTAAC 58.498 33.333 0.00 0.00 0.00 2.50
2259 2294 8.611654 TTTAGCCTCTAAATTTCGTTGTAACT 57.388 30.769 0.00 0.00 0.00 2.24
2260 2295 9.709495 TTTAGCCTCTAAATTTCGTTGTAACTA 57.291 29.630 0.00 0.00 0.00 2.24
2261 2296 7.829378 AGCCTCTAAATTTCGTTGTAACTAG 57.171 36.000 0.00 0.00 0.00 2.57
2262 2297 6.313164 AGCCTCTAAATTTCGTTGTAACTAGC 59.687 38.462 0.00 0.00 0.00 3.42
2263 2298 6.313164 GCCTCTAAATTTCGTTGTAACTAGCT 59.687 38.462 0.00 0.00 0.00 3.32
2264 2299 7.490402 GCCTCTAAATTTCGTTGTAACTAGCTA 59.510 37.037 0.00 0.00 0.00 3.32
2265 2300 9.362539 CCTCTAAATTTCGTTGTAACTAGCTAA 57.637 33.333 0.00 0.00 0.00 3.09
2267 2302 9.695526 TCTAAATTTCGTTGTAACTAGCTAACA 57.304 29.630 0.00 0.00 0.00 2.41
2271 2306 9.607285 AATTTCGTTGTAACTAGCTAACAAATG 57.393 29.630 10.34 7.27 35.08 2.32
2272 2307 7.718272 TTCGTTGTAACTAGCTAACAAATGT 57.282 32.000 10.34 0.00 35.08 2.71
2273 2308 7.718272 TCGTTGTAACTAGCTAACAAATGTT 57.282 32.000 10.34 4.01 41.73 2.71
2274 2309 7.790000 TCGTTGTAACTAGCTAACAAATGTTC 58.210 34.615 10.34 0.00 39.31 3.18
2275 2310 7.438757 TCGTTGTAACTAGCTAACAAATGTTCA 59.561 33.333 10.34 1.89 39.31 3.18
2276 2311 8.065407 CGTTGTAACTAGCTAACAAATGTTCAA 58.935 33.333 10.34 6.58 39.31 2.69
2277 2312 9.724839 GTTGTAACTAGCTAACAAATGTTCAAA 57.275 29.630 10.34 0.00 39.31 2.69
2284 2319 7.873739 AGCTAACAAATGTTCAAAATAGTGC 57.126 32.000 1.37 0.00 39.31 4.40
2285 2320 7.432869 AGCTAACAAATGTTCAAAATAGTGCA 58.567 30.769 1.37 0.00 39.31 4.57
2286 2321 8.090214 AGCTAACAAATGTTCAAAATAGTGCAT 58.910 29.630 1.37 0.00 39.31 3.96
2287 2322 9.352784 GCTAACAAATGTTCAAAATAGTGCATA 57.647 29.630 1.37 0.00 39.31 3.14
2290 2325 9.926158 AACAAATGTTCAAAATAGTGCATATCA 57.074 25.926 0.00 0.00 31.64 2.15
2291 2326 9.357652 ACAAATGTTCAAAATAGTGCATATCAC 57.642 29.630 0.00 0.00 45.98 3.06
2303 2338 4.726416 GTGCATATCACTCACTTTGTTGG 58.274 43.478 0.00 0.00 42.38 3.77
2304 2339 4.216257 GTGCATATCACTCACTTTGTTGGT 59.784 41.667 0.00 0.00 42.38 3.67
2305 2340 4.216042 TGCATATCACTCACTTTGTTGGTG 59.784 41.667 0.00 0.00 36.17 4.17
2306 2341 4.455533 GCATATCACTCACTTTGTTGGTGA 59.544 41.667 0.00 0.00 40.78 4.02
2311 2346 1.948104 TCACTTTGTTGGTGAGACGG 58.052 50.000 0.00 0.00 38.57 4.79
2312 2347 1.208535 TCACTTTGTTGGTGAGACGGT 59.791 47.619 0.00 0.00 38.57 4.83
2313 2348 1.330521 CACTTTGTTGGTGAGACGGTG 59.669 52.381 0.00 0.00 36.89 4.94
2314 2349 1.208535 ACTTTGTTGGTGAGACGGTGA 59.791 47.619 0.00 0.00 0.00 4.02
2432 2472 4.796495 ATTGAACCGCGGCCTCCC 62.796 66.667 28.58 10.50 0.00 4.30
2455 2495 4.545610 CGTGATGTAAAATGCAACACCTT 58.454 39.130 0.00 0.00 36.64 3.50
2996 3124 1.026718 GCCATCTTCTTCCACCACGG 61.027 60.000 0.00 0.00 0.00 4.94
3006 3134 2.428187 CACCACGGGCACAAGGTA 59.572 61.111 0.00 0.00 32.01 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.414549 TTTGTGTTTCCGAGCAAACTC 57.585 42.857 6.27 4.00 37.20 3.01
3 4 3.442273 TCTTTTGTGTTTCCGAGCAAACT 59.558 39.130 6.27 0.00 37.20 2.66
4 5 3.765026 TCTTTTGTGTTTCCGAGCAAAC 58.235 40.909 0.00 0.00 36.87 2.93
16 17 2.952310 GGAGCAAGGAGTTCTTTTGTGT 59.048 45.455 0.00 0.00 32.41 3.72
30 31 4.479993 CGGGGCCTCTGGAGCAAG 62.480 72.222 0.00 0.00 0.00 4.01
54 55 1.699634 CTTTGTCCACTTGGAGGAGGA 59.300 52.381 0.00 0.00 46.49 3.71
63 64 2.945668 GCTTCAGTGACTTTGTCCACTT 59.054 45.455 0.00 0.00 0.00 3.16
64 65 2.171448 AGCTTCAGTGACTTTGTCCACT 59.829 45.455 0.00 0.00 0.00 4.00
65 66 2.289002 CAGCTTCAGTGACTTTGTCCAC 59.711 50.000 0.00 0.00 0.00 4.02
66 67 2.170397 TCAGCTTCAGTGACTTTGTCCA 59.830 45.455 0.00 0.00 0.00 4.02
71 72 3.609853 TGTTGTCAGCTTCAGTGACTTT 58.390 40.909 0.00 0.00 44.02 2.66
87 88 4.305989 CAGTACATGCAGGTTTTGTTGT 57.694 40.909 10.25 0.00 32.48 3.32
109 110 2.419673 TGGAAAATCTACTGCGCACATG 59.580 45.455 5.66 0.00 0.00 3.21
115 116 4.686972 TCTGATCTGGAAAATCTACTGCG 58.313 43.478 0.00 0.00 0.00 5.18
143 144 4.372656 CTCTTGTGATATTCGGAACCCTC 58.627 47.826 0.00 0.00 0.00 4.30
167 168 2.259917 TCCCAAGAGATTCAGCACTCA 58.740 47.619 0.00 0.00 35.83 3.41
192 193 1.224075 ATTTCATCAGAGCCGATGCG 58.776 50.000 3.99 0.00 42.15 4.73
193 194 3.705043 AAATTTCATCAGAGCCGATGC 57.295 42.857 3.99 0.00 42.15 3.91
194 195 5.239359 TGAAAATTTCATCAGAGCCGATG 57.761 39.130 4.03 2.69 43.50 3.84
195 196 4.201990 GCTGAAAATTTCATCAGAGCCGAT 60.202 41.667 19.55 0.00 44.64 4.18
196 197 3.127548 GCTGAAAATTTCATCAGAGCCGA 59.872 43.478 19.55 0.00 44.64 5.54
210 211 3.751518 AGGTACAAAGGTCGCTGAAAAT 58.248 40.909 0.00 0.00 0.00 1.82
214 215 1.272490 CTGAGGTACAAAGGTCGCTGA 59.728 52.381 0.00 0.00 0.00 4.26
246 247 1.924731 AGTGCTACTGCTACTGTCCA 58.075 50.000 0.00 0.00 40.48 4.02
272 273 1.067060 TCGGATGCAGTTATCCTGACG 59.933 52.381 2.71 0.00 44.49 4.35
275 276 2.602257 TGTCGGATGCAGTTATCCTG 57.398 50.000 2.71 0.00 43.64 3.86
297 298 4.161333 CGTCCTTGCAGTTGATTGAATTC 58.839 43.478 0.00 0.00 0.00 2.17
309 310 3.735237 AGATATACCACGTCCTTGCAG 57.265 47.619 0.00 0.00 0.00 4.41
344 345 3.696051 TGGTCATTTCTAAGGCATTGCTC 59.304 43.478 8.82 0.00 0.00 4.26
368 369 0.818445 GAGTAGGGATCTCACGCGGA 60.818 60.000 12.47 3.82 32.79 5.54
370 371 1.280142 CGAGTAGGGATCTCACGCG 59.720 63.158 3.53 3.53 32.79 6.01
371 372 1.655329 CCGAGTAGGGATCTCACGC 59.345 63.158 0.00 0.00 35.97 5.34
372 373 0.820074 AGCCGAGTAGGGATCTCACG 60.820 60.000 0.00 0.00 41.48 4.35
373 374 2.273538 TAGCCGAGTAGGGATCTCAC 57.726 55.000 0.00 0.00 41.48 3.51
375 376 2.756207 GGATTAGCCGAGTAGGGATCTC 59.244 54.545 0.00 0.00 41.48 2.75
376 377 2.557901 GGGATTAGCCGAGTAGGGATCT 60.558 54.545 0.00 0.00 41.48 2.75
377 378 1.826096 GGGATTAGCCGAGTAGGGATC 59.174 57.143 0.00 0.00 41.48 3.36
378 379 1.433592 AGGGATTAGCCGAGTAGGGAT 59.566 52.381 0.00 0.00 41.48 3.85
379 380 0.858369 AGGGATTAGCCGAGTAGGGA 59.142 55.000 0.00 0.00 41.48 4.20
380 381 0.969894 CAGGGATTAGCCGAGTAGGG 59.030 60.000 0.00 0.00 41.48 3.53
381 382 0.318762 GCAGGGATTAGCCGAGTAGG 59.681 60.000 0.00 0.00 44.97 3.18
382 383 1.333177 AGCAGGGATTAGCCGAGTAG 58.667 55.000 0.00 0.00 37.63 2.57
383 384 1.412710 CAAGCAGGGATTAGCCGAGTA 59.587 52.381 0.00 0.00 37.63 2.59
384 385 0.179000 CAAGCAGGGATTAGCCGAGT 59.821 55.000 0.00 0.00 37.63 4.18
385 386 0.533755 CCAAGCAGGGATTAGCCGAG 60.534 60.000 0.00 0.00 37.63 4.63
386 387 1.526887 CCAAGCAGGGATTAGCCGA 59.473 57.895 0.00 0.00 37.63 5.54
387 388 2.189499 GCCAAGCAGGGATTAGCCG 61.189 63.158 0.00 0.00 38.09 5.52
388 389 1.076777 TGCCAAGCAGGGATTAGCC 60.077 57.895 0.00 0.00 38.09 3.93
389 390 1.387295 GGTGCCAAGCAGGGATTAGC 61.387 60.000 0.00 0.00 41.14 3.09
390 391 1.097547 CGGTGCCAAGCAGGGATTAG 61.098 60.000 0.00 0.00 41.14 1.73
391 392 1.077787 CGGTGCCAAGCAGGGATTA 60.078 57.895 0.00 0.00 41.14 1.75
392 393 2.361610 CGGTGCCAAGCAGGGATT 60.362 61.111 0.00 0.00 41.14 3.01
419 420 4.668576 TTCTTCATTCAGAACATCGTGC 57.331 40.909 0.00 0.00 31.61 5.34
426 427 3.743396 AGAGCACGTTCTTCATTCAGAAC 59.257 43.478 3.86 3.86 46.40 3.01
442 443 1.269831 ACAGACGGAAGAACAGAGCAC 60.270 52.381 0.00 0.00 0.00 4.40
444 445 1.000163 TGACAGACGGAAGAACAGAGC 60.000 52.381 0.00 0.00 0.00 4.09
455 458 0.242286 CCTGACAGAGTGACAGACGG 59.758 60.000 3.32 0.00 41.47 4.79
458 461 1.637338 ATGCCTGACAGAGTGACAGA 58.363 50.000 3.32 0.00 41.47 3.41
499 503 7.484975 TCTGATTTCCGAGAGAGAAAGATAAC 58.515 38.462 0.00 0.00 36.71 1.89
500 504 7.646548 TCTGATTTCCGAGAGAGAAAGATAA 57.353 36.000 0.00 0.00 36.71 1.75
515 519 3.057596 TGCAATGGAACGTTCTGATTTCC 60.058 43.478 26.32 10.62 39.51 3.13
580 597 5.770663 AAAAGAGGCCTTTTCTAGGAAACTC 59.229 40.000 6.77 4.98 46.49 3.01
633 650 0.464373 AGTAGCCATTCATGCCGGTG 60.464 55.000 1.90 0.00 0.00 4.94
706 723 3.350031 ATGAGGGGGCAGGAAAGCG 62.350 63.158 0.00 0.00 34.64 4.68
757 774 2.049433 CGGTGGGACAGTCGACAC 60.049 66.667 19.50 15.27 41.80 3.67
870 901 3.369052 CGAGGTAACAACATGGCTAGGAA 60.369 47.826 0.00 0.00 41.41 3.36
871 902 2.167693 CGAGGTAACAACATGGCTAGGA 59.832 50.000 0.00 0.00 41.41 2.94
872 903 2.093658 ACGAGGTAACAACATGGCTAGG 60.094 50.000 0.00 0.00 41.41 3.02
873 904 2.930040 CACGAGGTAACAACATGGCTAG 59.070 50.000 0.00 0.00 41.41 3.42
914 945 0.397941 TTCTCTTGTGGGAGCTGTGG 59.602 55.000 0.00 0.00 33.70 4.17
947 978 2.584418 CATGGCGTCGAGAGCAGG 60.584 66.667 13.82 0.47 36.08 4.85
954 985 1.860484 TTTGCAATGCATGGCGTCGA 61.860 50.000 21.00 0.17 38.76 4.20
1011 1042 0.678950 ACATTTTTGTTGGAGGGGCG 59.321 50.000 0.00 0.00 0.00 6.13
1014 1045 1.623311 GGGGACATTTTTGTTGGAGGG 59.377 52.381 0.00 0.00 0.00 4.30
1041 1072 2.637872 TGGAAATAATAGGAGGAGCGGG 59.362 50.000 0.00 0.00 0.00 6.13
1050 1081 3.820467 TCGGCATTGCTGGAAATAATAGG 59.180 43.478 17.19 0.00 35.34 2.57
1055 1086 1.388547 GGTCGGCATTGCTGGAAATA 58.611 50.000 17.19 0.00 35.34 1.40
1056 1087 1.656818 CGGTCGGCATTGCTGGAAAT 61.657 55.000 17.19 0.00 35.34 2.17
1057 1088 2.331893 CGGTCGGCATTGCTGGAAA 61.332 57.895 17.19 0.00 35.34 3.13
1099 1130 3.506096 CATCAGCAGCAGCACGGG 61.506 66.667 3.17 0.00 45.49 5.28
1100 1131 4.175489 GCATCAGCAGCAGCACGG 62.175 66.667 3.17 0.00 45.49 4.94
1101 1132 3.097137 GAGCATCAGCAGCAGCACG 62.097 63.158 3.17 0.00 45.49 5.34
1102 1133 2.792599 GAGCATCAGCAGCAGCAC 59.207 61.111 3.17 0.00 45.49 4.40
1103 1134 2.818274 CGAGCATCAGCAGCAGCA 60.818 61.111 3.17 0.00 45.49 4.41
1104 1135 4.239203 GCGAGCATCAGCAGCAGC 62.239 66.667 0.00 0.00 45.49 5.25
1105 1136 3.574445 GGCGAGCATCAGCAGCAG 61.574 66.667 0.00 0.00 44.74 4.24
1685 1716 1.601759 CTCAGGTGGCAGGTGTTGG 60.602 63.158 0.00 0.00 0.00 3.77
1760 1791 4.753662 TCACCTCCCCGTCCTCCG 62.754 72.222 0.00 0.00 0.00 4.63
1773 1804 1.239968 CCAGCTTCCACTTGCTCACC 61.240 60.000 0.00 0.00 37.44 4.02
1842 1873 4.538283 AGCATCGCGACGAGGACG 62.538 66.667 12.93 0.00 40.15 4.79
2007 2038 2.203139 TGTCACAAGGTGGCACGG 60.203 61.111 12.17 6.29 43.49 4.94
2025 2056 3.931468 TGTTCCAAATGTGCACTTGTTTG 59.069 39.130 23.74 23.74 0.00 2.93
2151 2184 4.763073 TGCATCTCTGGATCAAGTTACAG 58.237 43.478 0.00 0.00 0.00 2.74
2178 2211 7.089538 TGTAACTAAAATGAACGATCGTGGTA 58.910 34.615 23.51 11.56 0.00 3.25
2179 2212 5.927689 TGTAACTAAAATGAACGATCGTGGT 59.072 36.000 23.51 6.88 0.00 4.16
2180 2213 6.397831 TGTAACTAAAATGAACGATCGTGG 57.602 37.500 23.51 1.10 0.00 4.94
2181 2214 9.405083 GTAATGTAACTAAAATGAACGATCGTG 57.595 33.333 23.51 9.00 0.00 4.35
2182 2215 9.142515 TGTAATGTAACTAAAATGAACGATCGT 57.857 29.630 16.60 16.60 0.00 3.73
2229 2264 8.718734 ACAACGAAATTTAGAGGCTAAAGTTAG 58.281 33.333 11.18 12.85 0.00 2.34
2230 2265 8.611654 ACAACGAAATTTAGAGGCTAAAGTTA 57.388 30.769 11.18 0.00 0.00 2.24
2231 2266 7.506328 ACAACGAAATTTAGAGGCTAAAGTT 57.494 32.000 11.06 11.06 0.00 2.66
2232 2267 8.501580 GTTACAACGAAATTTAGAGGCTAAAGT 58.498 33.333 5.22 0.76 0.00 2.66
2233 2268 8.718734 AGTTACAACGAAATTTAGAGGCTAAAG 58.281 33.333 5.22 0.00 0.00 1.85
2234 2269 8.611654 AGTTACAACGAAATTTAGAGGCTAAA 57.388 30.769 5.22 2.49 0.00 1.85
2235 2270 9.362539 CTAGTTACAACGAAATTTAGAGGCTAA 57.637 33.333 5.22 0.00 0.00 3.09
2236 2271 7.490402 GCTAGTTACAACGAAATTTAGAGGCTA 59.510 37.037 5.22 2.64 0.00 3.93
2237 2272 6.313164 GCTAGTTACAACGAAATTTAGAGGCT 59.687 38.462 5.22 0.00 0.00 4.58
2238 2273 6.313164 AGCTAGTTACAACGAAATTTAGAGGC 59.687 38.462 5.22 0.00 0.00 4.70
2239 2274 7.829378 AGCTAGTTACAACGAAATTTAGAGG 57.171 36.000 5.22 0.00 0.00 3.69
2241 2276 9.695526 TGTTAGCTAGTTACAACGAAATTTAGA 57.304 29.630 5.22 0.00 0.00 2.10
2245 2280 9.607285 CATTTGTTAGCTAGTTACAACGAAATT 57.393 29.630 8.64 0.00 32.00 1.82
2246 2281 8.780249 ACATTTGTTAGCTAGTTACAACGAAAT 58.220 29.630 8.64 4.89 32.00 2.17
2247 2282 8.145316 ACATTTGTTAGCTAGTTACAACGAAA 57.855 30.769 8.64 3.15 32.00 3.46
2248 2283 7.718272 ACATTTGTTAGCTAGTTACAACGAA 57.282 32.000 8.64 4.78 32.00 3.85
2249 2284 7.438757 TGAACATTTGTTAGCTAGTTACAACGA 59.561 33.333 8.64 0.00 38.56 3.85
2250 2285 7.569297 TGAACATTTGTTAGCTAGTTACAACG 58.431 34.615 8.64 6.46 38.56 4.10
2251 2286 9.724839 TTTGAACATTTGTTAGCTAGTTACAAC 57.275 29.630 8.64 0.00 38.56 3.32
2258 2293 9.065871 GCACTATTTTGAACATTTGTTAGCTAG 57.934 33.333 0.00 0.00 38.56 3.42
2259 2294 8.572185 TGCACTATTTTGAACATTTGTTAGCTA 58.428 29.630 0.00 0.00 38.56 3.32
2260 2295 7.432869 TGCACTATTTTGAACATTTGTTAGCT 58.567 30.769 0.00 0.00 38.56 3.32
2261 2296 7.636259 TGCACTATTTTGAACATTTGTTAGC 57.364 32.000 0.00 0.00 38.56 3.09
2264 2299 9.926158 TGATATGCACTATTTTGAACATTTGTT 57.074 25.926 0.00 0.00 41.64 2.83
2265 2300 9.357652 GTGATATGCACTATTTTGAACATTTGT 57.642 29.630 0.00 0.00 44.27 2.83
2281 2316 7.949365 TCACCAACAAAGTGAGTGATATGCAC 61.949 42.308 0.00 0.00 39.29 4.57
2282 2317 4.216042 CACCAACAAAGTGAGTGATATGCA 59.784 41.667 0.00 0.00 37.42 3.96
2283 2318 4.455533 TCACCAACAAAGTGAGTGATATGC 59.544 41.667 0.00 0.00 39.29 3.14
2292 2327 1.208535 ACCGTCTCACCAACAAAGTGA 59.791 47.619 0.00 0.00 41.84 3.41
2293 2328 1.330521 CACCGTCTCACCAACAAAGTG 59.669 52.381 0.00 0.00 36.54 3.16
2294 2329 1.208535 TCACCGTCTCACCAACAAAGT 59.791 47.619 0.00 0.00 0.00 2.66
2295 2330 1.597663 GTCACCGTCTCACCAACAAAG 59.402 52.381 0.00 0.00 0.00 2.77
2296 2331 1.208535 AGTCACCGTCTCACCAACAAA 59.791 47.619 0.00 0.00 0.00 2.83
2297 2332 0.828022 AGTCACCGTCTCACCAACAA 59.172 50.000 0.00 0.00 0.00 2.83
2298 2333 0.828022 AAGTCACCGTCTCACCAACA 59.172 50.000 0.00 0.00 0.00 3.33
2299 2334 2.295349 TCTAAGTCACCGTCTCACCAAC 59.705 50.000 0.00 0.00 0.00 3.77
2300 2335 2.557056 CTCTAAGTCACCGTCTCACCAA 59.443 50.000 0.00 0.00 0.00 3.67
2301 2336 2.160205 CTCTAAGTCACCGTCTCACCA 58.840 52.381 0.00 0.00 0.00 4.17
2302 2337 1.135344 GCTCTAAGTCACCGTCTCACC 60.135 57.143 0.00 0.00 0.00 4.02
2303 2338 1.540267 TGCTCTAAGTCACCGTCTCAC 59.460 52.381 0.00 0.00 0.00 3.51
2304 2339 1.905637 TGCTCTAAGTCACCGTCTCA 58.094 50.000 0.00 0.00 0.00 3.27
2305 2340 2.685897 AGATGCTCTAAGTCACCGTCTC 59.314 50.000 0.00 0.00 0.00 3.36
2306 2341 2.685897 GAGATGCTCTAAGTCACCGTCT 59.314 50.000 0.00 0.00 0.00 4.18
2307 2342 2.223618 GGAGATGCTCTAAGTCACCGTC 60.224 54.545 0.00 0.00 0.00 4.79
2308 2343 1.751924 GGAGATGCTCTAAGTCACCGT 59.248 52.381 0.00 0.00 0.00 4.83
2309 2344 1.751351 TGGAGATGCTCTAAGTCACCG 59.249 52.381 0.00 0.00 0.00 4.94
2310 2345 3.895232 TTGGAGATGCTCTAAGTCACC 57.105 47.619 0.00 0.00 0.00 4.02
2311 2346 6.398234 TCTATTGGAGATGCTCTAAGTCAC 57.602 41.667 0.00 0.00 34.66 3.67
2312 2347 6.210385 GGATCTATTGGAGATGCTCTAAGTCA 59.790 42.308 0.00 0.00 46.70 3.41
2313 2348 6.630071 GGATCTATTGGAGATGCTCTAAGTC 58.370 44.000 0.00 0.00 46.70 3.01
2314 2349 6.603940 GGATCTATTGGAGATGCTCTAAGT 57.396 41.667 0.00 0.00 46.70 2.24
2360 2398 3.835790 TTTTGCCCCAGACGGTCCG 62.836 63.158 10.48 10.48 0.00 4.79
2432 2472 3.057596 AGGTGTTGCATTTTACATCACGG 60.058 43.478 2.54 0.00 38.20 4.94
2678 2803 2.017559 GCCGGCTACCACTCGATTCT 62.018 60.000 22.15 0.00 0.00 2.40
2742 2867 2.266689 GCCTAAAAGACCCGGCGA 59.733 61.111 9.30 0.00 32.22 5.54
2949 3077 1.237285 GGATTGGCTGCTGTTGACGT 61.237 55.000 0.00 0.00 0.00 4.34
2955 3083 1.973281 CGGTTGGATTGGCTGCTGT 60.973 57.895 0.00 0.00 0.00 4.40
2996 3124 0.108520 TCCGTCGAATACCTTGTGCC 60.109 55.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.