Multiple sequence alignment - TraesCS4D01G107200

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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 TraesCS4D01G107200 chr4D 100.000 5404 0 0 1 5404 85578208 85583611 0.000000e+00 9980.0
1 TraesCS4D01G107200 chr4A 96.820 4969 106 23 167 5096 499340693 499345648 0.000000e+00 8253.0
2 TraesCS4D01G107200 chr4A 89.583 144 9 2 5160 5297 499345656 499345799 1.550000e-40 178.0
3 TraesCS4D01G107200 chr4B 92.324 3218 145 43 2140 5289 122521623 122524806 0.000000e+00 4481.0
4 TraesCS4D01G107200 chr4B 92.904 2128 95 35 3 2107 122519534 122521628 0.000000e+00 3042.0
5 TraesCS4D01G107200 chr5D 90.545 550 46 4 1060 1609 177684261 177683718 0.000000e+00 723.0
6 TraesCS4D01G107200 chr5D 91.489 47 4 0 2919 2965 184874264 184874310 1.260000e-06 65.8
7 TraesCS4D01G107200 chr5A 90.416 553 47 4 1057 1609 191036295 191036841 0.000000e+00 723.0
8 TraesCS4D01G107200 chr5B 90.364 550 47 4 1060 1609 192383290 192382747 0.000000e+00 717.0
9 TraesCS4D01G107200 chr2D 80.040 496 85 11 1121 1609 564095494 564095006 6.660000e-94 355.0
10 TraesCS4D01G107200 chr2B 80.000 495 87 9 1121 1609 675356180 675355692 6.660000e-94 355.0
11 TraesCS4D01G107200 chr2A 79.435 496 88 11 1121 1609 704776749 704776261 6.700000e-89 339.0
12 TraesCS4D01G107200 chr6B 79.087 416 73 12 1131 1539 717076834 717076426 1.920000e-69 274.0
13 TraesCS4D01G107200 chr6B 75.000 480 108 11 1136 1609 519720425 519720898 1.520000e-50 211.0
14 TraesCS4D01G107200 chr6D 76.627 415 85 11 1136 1544 344207897 344208305 9.110000e-53 219.0
15 TraesCS4D01G107200 chr3A 96.053 76 1 2 1189 1264 638493541 638493614 7.350000e-24 122.0


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 TraesCS4D01G107200 chr4D 85578208 85583611 5403 False 9980.0 9980 100.0000 1 5404 1 chr4D.!!$F1 5403
1 TraesCS4D01G107200 chr4A 499340693 499345799 5106 False 4215.5 8253 93.2015 167 5297 2 chr4A.!!$F1 5130
2 TraesCS4D01G107200 chr4B 122519534 122524806 5272 False 3761.5 4481 92.6140 3 5289 2 chr4B.!!$F1 5286
3 TraesCS4D01G107200 chr5D 177683718 177684261 543 True 723.0 723 90.5450 1060 1609 1 chr5D.!!$R1 549
4 TraesCS4D01G107200 chr5A 191036295 191036841 546 False 723.0 723 90.4160 1057 1609 1 chr5A.!!$F1 552
5 TraesCS4D01G107200 chr5B 192382747 192383290 543 True 717.0 717 90.3640 1060 1609 1 chr5B.!!$R1 549

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
602 631 0.486879 TGTGCCAATCTTTTCCCCCT 59.513 50.000 0.00 0.00 0.00 4.79 F
985 1017 2.046023 CTTGATCCAGGGTGCGCA 60.046 61.111 5.66 5.66 0.00 6.09 F
1698 1735 4.876107 CCAGTTCGAGCTTTGTTGGTATAT 59.124 41.667 0.00 0.00 0.00 0.86 F
2772 2812 3.389329 TCCTCCTTATCACTCATGGAAGC 59.611 47.826 0.00 0.00 0.00 3.86 F
3031 3072 3.445008 TGAGCAGAAACTGTAGGGAGAT 58.555 45.455 0.00 0.00 33.43 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1464 1496 0.822164 CCTCTACGACCCCAACGATT 59.178 55.000 0.00 0.00 34.70 3.34 R
2308 2347 3.744660 AGTCTGGCTCGAACAGAAATTT 58.255 40.909 17.94 0.00 45.66 1.82 R
3332 3401 2.230660 AGTTGGCCAAGACTAGCAAAC 58.769 47.619 21.21 3.17 42.23 2.93 R
4193 4269 0.689412 TATGCATGGGACGGGACAGA 60.689 55.000 10.16 0.00 0.00 3.41 R
5022 5132 0.523546 CGGACAGGTTGATCGACTCG 60.524 60.000 12.89 6.86 0.00 4.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.079446 AGCCATTCCCAACGTGTG 57.921 55.556 0.00 0.00 0.00 3.82
21 22 1.285641 CATTCCCAACGTGTGTGGC 59.714 57.895 0.00 0.00 0.00 5.01
30 32 2.417097 GTGTGTGGCTGGGTTTGC 59.583 61.111 0.00 0.00 0.00 3.68
32 34 1.381056 TGTGTGGCTGGGTTTGCTT 60.381 52.632 0.00 0.00 0.00 3.91
48 50 5.627780 GGTTTGCTTTAAGGTTCGTGTTATG 59.372 40.000 0.00 0.00 0.00 1.90
49 51 6.203647 GTTTGCTTTAAGGTTCGTGTTATGT 58.796 36.000 0.00 0.00 0.00 2.29
79 82 4.002982 CAGTGAATGCAGGCTACTAAACA 58.997 43.478 0.00 0.00 0.00 2.83
80 83 4.637534 CAGTGAATGCAGGCTACTAAACAT 59.362 41.667 0.00 0.00 0.00 2.71
82 85 4.635765 GTGAATGCAGGCTACTAAACATGA 59.364 41.667 0.00 0.00 0.00 3.07
95 98 8.293867 GCTACTAAACATGACATTTTTACACCA 58.706 33.333 0.00 0.00 0.00 4.17
125 128 0.618458 TTTGGGCTGTACCTAGGCAG 59.382 55.000 9.30 10.39 44.38 4.85
129 132 2.107141 CTGTACCTAGGCAGCCGC 59.893 66.667 9.30 0.00 37.44 6.53
141 144 2.951457 GCAGCCGCCCTTAAATAAAA 57.049 45.000 0.00 0.00 0.00 1.52
142 145 3.452755 GCAGCCGCCCTTAAATAAAAT 57.547 42.857 0.00 0.00 0.00 1.82
143 146 3.123050 GCAGCCGCCCTTAAATAAAATG 58.877 45.455 0.00 0.00 0.00 2.32
144 147 3.430236 GCAGCCGCCCTTAAATAAAATGT 60.430 43.478 0.00 0.00 0.00 2.71
146 149 5.519722 CAGCCGCCCTTAAATAAAATGTAG 58.480 41.667 0.00 0.00 0.00 2.74
147 150 4.583073 AGCCGCCCTTAAATAAAATGTAGG 59.417 41.667 0.00 0.00 0.00 3.18
148 151 4.581409 GCCGCCCTTAAATAAAATGTAGGA 59.419 41.667 0.00 0.00 0.00 2.94
149 152 5.506815 GCCGCCCTTAAATAAAATGTAGGAC 60.507 44.000 0.00 0.00 0.00 3.85
150 153 5.591067 CCGCCCTTAAATAAAATGTAGGACA 59.409 40.000 0.00 0.00 0.00 4.02
151 154 6.459161 CCGCCCTTAAATAAAATGTAGGACAC 60.459 42.308 0.00 0.00 0.00 3.67
152 155 6.094325 CGCCCTTAAATAAAATGTAGGACACA 59.906 38.462 0.00 0.00 42.69 3.72
153 156 7.255569 GCCCTTAAATAAAATGTAGGACACAC 58.744 38.462 0.00 0.00 40.86 3.82
154 157 7.629866 GCCCTTAAATAAAATGTAGGACACACC 60.630 40.741 0.00 0.00 40.86 4.16
308 314 1.303317 CCTGAAAACCCCGTGGAGG 60.303 63.158 0.00 0.00 40.63 4.30
353 367 1.526887 CTGCCCGGCATTCTCCTTA 59.473 57.895 13.86 0.00 38.13 2.69
365 379 0.619255 TCTCCTTACCCCAATCGGCA 60.619 55.000 0.00 0.00 0.00 5.69
435 449 3.639094 CCAGAAGAGATTACCATCGTCCT 59.361 47.826 0.00 0.00 34.17 3.85
440 469 2.879646 GAGATTACCATCGTCCTCGTCT 59.120 50.000 0.00 0.00 38.33 4.18
471 500 1.703589 ATCATCCCATCCCCTCCCCT 61.704 60.000 0.00 0.00 0.00 4.79
472 501 1.849823 CATCCCATCCCCTCCCCTC 60.850 68.421 0.00 0.00 0.00 4.30
473 502 3.134322 ATCCCATCCCCTCCCCTCC 62.134 68.421 0.00 0.00 0.00 4.30
474 503 4.928520 CCCATCCCCTCCCCTCCC 62.929 77.778 0.00 0.00 0.00 4.30
491 520 0.983378 CCCCCTACCCCAGAGAACTG 60.983 65.000 0.00 0.00 43.12 3.16
602 631 0.486879 TGTGCCAATCTTTTCCCCCT 59.513 50.000 0.00 0.00 0.00 4.79
756 786 4.383118 CCTTTTTCTCGCCTCCTAATCTCA 60.383 45.833 0.00 0.00 0.00 3.27
797 827 3.023735 AATCCCCAGAGCCCCACC 61.024 66.667 0.00 0.00 0.00 4.61
954 986 2.489971 TCTTGATTCAAGGTTTCGCGT 58.510 42.857 22.86 0.00 41.33 6.01
985 1017 2.046023 CTTGATCCAGGGTGCGCA 60.046 61.111 5.66 5.66 0.00 6.09
1698 1735 4.876107 CCAGTTCGAGCTTTGTTGGTATAT 59.124 41.667 0.00 0.00 0.00 0.86
1984 2021 5.185828 AGACTTGCCAAAACTTGTCTTCTTT 59.814 36.000 0.00 0.00 31.71 2.52
2180 2218 8.803235 TGTAGTACCCATTACTAGCAATATCAG 58.197 37.037 0.00 0.00 42.85 2.90
2196 2234 7.555554 AGCAATATCAGCAATCTAGTTGTTTCT 59.444 33.333 3.33 0.00 40.07 2.52
2772 2812 3.389329 TCCTCCTTATCACTCATGGAAGC 59.611 47.826 0.00 0.00 0.00 3.86
3031 3072 3.445008 TGAGCAGAAACTGTAGGGAGAT 58.555 45.455 0.00 0.00 33.43 2.75
3139 3180 5.833406 TGTATCCATGTGGTTAATTGCTG 57.167 39.130 0.00 0.00 36.34 4.41
3332 3401 3.557595 CGTGCCTGCCTAATTTTCTCTAG 59.442 47.826 0.00 0.00 0.00 2.43
3615 3687 4.552355 CAACTTGCAATGCTCATCTTGAA 58.448 39.130 6.82 0.00 0.00 2.69
4186 4262 6.808008 ATGTCAGTGTTTCTTCATACTTGG 57.192 37.500 0.00 0.00 0.00 3.61
4193 4269 7.657761 CAGTGTTTCTTCATACTTGGTTCTACT 59.342 37.037 0.00 0.00 0.00 2.57
4201 4277 1.893801 ACTTGGTTCTACTCTGTCCCG 59.106 52.381 0.00 0.00 0.00 5.14
4227 4303 6.319911 TCCCATGCATATATGTTTTGTTCGAA 59.680 34.615 14.14 0.00 0.00 3.71
4319 4395 1.556911 ACAGCGATGATGAGAAAGGGT 59.443 47.619 8.12 0.00 0.00 4.34
4325 4401 3.499918 CGATGATGAGAAAGGGTAATGCC 59.500 47.826 0.00 0.00 0.00 4.40
4326 4402 4.464008 GATGATGAGAAAGGGTAATGCCA 58.536 43.478 0.00 0.00 39.65 4.92
4328 4404 2.128771 TGAGAAAGGGTAATGCCAGC 57.871 50.000 0.00 0.00 39.65 4.85
4405 4481 1.403323 GAATCCCAGCAACAGCTAAGC 59.597 52.381 0.00 0.00 36.70 3.09
4423 4499 2.507944 CGGCATGGGGAGGAGAAG 59.492 66.667 0.00 0.00 0.00 2.85
4500 4579 7.015779 GCTGGACTACTAATCTAAGAGGGAAAT 59.984 40.741 0.00 0.00 0.00 2.17
4668 4754 4.409718 TGGTAGCCGCATCAACTATTTA 57.590 40.909 0.00 0.00 0.00 1.40
4669 4755 4.124238 TGGTAGCCGCATCAACTATTTAC 58.876 43.478 0.00 0.00 0.00 2.01
4670 4756 4.141801 TGGTAGCCGCATCAACTATTTACT 60.142 41.667 0.00 0.00 0.00 2.24
4671 4757 4.211374 GGTAGCCGCATCAACTATTTACTG 59.789 45.833 0.00 0.00 0.00 2.74
4672 4758 3.873910 AGCCGCATCAACTATTTACTGT 58.126 40.909 0.00 0.00 0.00 3.55
4808 4898 9.745880 ATACAGTGACGAGGTAGTATAAAATTG 57.254 33.333 0.00 0.00 0.00 2.32
4900 4993 5.223382 CCCGTTAACTGCACTATCTATCTG 58.777 45.833 3.71 0.00 0.00 2.90
4910 5003 7.068103 ACTGCACTATCTATCTGTAGGCATATC 59.932 40.741 0.00 0.00 0.00 1.63
4914 5007 6.768861 ACTATCTATCTGTAGGCATATCCGTC 59.231 42.308 0.00 0.00 40.77 4.79
4939 5034 3.256631 CCTTGGAGTTTGGACCTTTGATG 59.743 47.826 0.00 0.00 0.00 3.07
4993 5095 4.635765 CGTATCACAGAAAACATGGGTCAT 59.364 41.667 0.00 0.00 0.00 3.06
5022 5132 3.708631 TCTCCATTGACTGAGAATCCCTC 59.291 47.826 0.00 0.00 42.30 4.30
5038 5148 0.811915 CCTCGAGTCGATCAACCTGT 59.188 55.000 16.94 0.00 34.61 4.00
5041 5151 0.523546 CGAGTCGATCAACCTGTCCG 60.524 60.000 6.73 0.00 0.00 4.79
5042 5152 0.802607 GAGTCGATCAACCTGTCCGC 60.803 60.000 0.00 0.00 0.00 5.54
5070 5180 0.179207 TCAGTGACGCGACGTGTATC 60.179 55.000 15.93 10.32 41.37 2.24
5071 5181 0.179197 CAGTGACGCGACGTGTATCT 60.179 55.000 15.93 12.40 41.37 1.98
5072 5182 0.096628 AGTGACGCGACGTGTATCTC 59.903 55.000 15.93 2.40 41.37 2.75
5077 5187 0.866061 CGCGACGTGTATCTCAAGGG 60.866 60.000 0.00 0.00 0.00 3.95
5102 5212 1.001268 TCAGGCGATTTAGAGCTAGCG 60.001 52.381 9.55 0.00 0.00 4.26
5108 5218 3.612955 GCGATTTAGAGCTAGCGATTCCT 60.613 47.826 9.55 5.58 0.00 3.36
5112 5222 6.641314 CGATTTAGAGCTAGCGATTCCTTTTA 59.359 38.462 9.55 0.00 0.00 1.52
5120 5230 7.104290 AGCTAGCGATTCCTTTTACTTAAACT 58.896 34.615 9.55 0.00 0.00 2.66
5171 5281 6.207221 TGTGCATTTGAAGATGTGTACTGAAT 59.793 34.615 0.00 0.00 0.00 2.57
5221 5344 7.719871 TTGAAAGAGTAGTCTACCTTATGCT 57.280 36.000 6.38 0.00 30.45 3.79
5293 5420 2.550180 GTGAAAACAGAGAGCTTCCACC 59.450 50.000 0.00 0.00 0.00 4.61
5297 5424 0.472734 ACAGAGAGCTTCCACCCACT 60.473 55.000 0.00 0.00 0.00 4.00
5298 5425 0.036577 CAGAGAGCTTCCACCCACTG 60.037 60.000 0.00 0.00 0.00 3.66
5299 5426 0.472734 AGAGAGCTTCCACCCACTGT 60.473 55.000 0.00 0.00 0.00 3.55
5300 5427 0.398318 GAGAGCTTCCACCCACTGTT 59.602 55.000 0.00 0.00 0.00 3.16
5301 5428 0.846693 AGAGCTTCCACCCACTGTTT 59.153 50.000 0.00 0.00 0.00 2.83
5302 5429 0.954452 GAGCTTCCACCCACTGTTTG 59.046 55.000 0.00 0.00 0.00 2.93
5303 5430 0.468029 AGCTTCCACCCACTGTTTGG 60.468 55.000 0.00 0.00 46.47 3.28
5304 5431 0.755327 GCTTCCACCCACTGTTTGGT 60.755 55.000 0.00 0.00 45.25 3.67
5305 5432 1.775385 CTTCCACCCACTGTTTGGTT 58.225 50.000 0.00 0.00 45.25 3.67
5306 5433 1.681264 CTTCCACCCACTGTTTGGTTC 59.319 52.381 0.00 0.00 45.25 3.62
5307 5434 0.464735 TCCACCCACTGTTTGGTTCG 60.465 55.000 0.00 0.00 45.25 3.95
5308 5435 1.452145 CCACCCACTGTTTGGTTCGG 61.452 60.000 0.00 0.00 45.25 4.30
5309 5436 1.152839 ACCCACTGTTTGGTTCGGG 60.153 57.895 0.00 0.00 45.25 5.14
5310 5437 1.152839 CCCACTGTTTGGTTCGGGT 60.153 57.895 0.00 0.00 45.25 5.28
5311 5438 1.452145 CCCACTGTTTGGTTCGGGTG 61.452 60.000 0.00 0.00 45.25 4.61
5312 5439 1.358759 CACTGTTTGGTTCGGGTGC 59.641 57.895 0.00 0.00 0.00 5.01
5313 5440 2.184167 ACTGTTTGGTTCGGGTGCG 61.184 57.895 0.00 0.00 0.00 5.34
5314 5441 2.902846 TGTTTGGTTCGGGTGCGG 60.903 61.111 0.00 0.00 0.00 5.69
5315 5442 2.903350 GTTTGGTTCGGGTGCGGT 60.903 61.111 0.00 0.00 0.00 5.68
5316 5443 2.902846 TTTGGTTCGGGTGCGGTG 60.903 61.111 0.00 0.00 0.00 4.94
5317 5444 3.402095 TTTGGTTCGGGTGCGGTGA 62.402 57.895 0.00 0.00 0.00 4.02
5318 5445 4.612412 TGGTTCGGGTGCGGTGAC 62.612 66.667 0.00 0.00 0.00 3.67
5320 5447 4.612412 GTTCGGGTGCGGTGACCA 62.612 66.667 1.11 0.00 37.80 4.02
5321 5448 4.612412 TTCGGGTGCGGTGACCAC 62.612 66.667 1.11 0.00 37.80 4.16
5339 5466 3.941188 CCCCGGTGCTGTGTGTCT 61.941 66.667 0.00 0.00 0.00 3.41
5340 5467 2.357517 CCCGGTGCTGTGTGTCTC 60.358 66.667 0.00 0.00 0.00 3.36
5341 5468 2.737180 CCGGTGCTGTGTGTCTCT 59.263 61.111 0.00 0.00 0.00 3.10
5342 5469 1.069765 CCGGTGCTGTGTGTCTCTT 59.930 57.895 0.00 0.00 0.00 2.85
5343 5470 1.224069 CCGGTGCTGTGTGTCTCTTG 61.224 60.000 0.00 0.00 0.00 3.02
5344 5471 0.530650 CGGTGCTGTGTGTCTCTTGT 60.531 55.000 0.00 0.00 0.00 3.16
5345 5472 0.940126 GGTGCTGTGTGTCTCTTGTG 59.060 55.000 0.00 0.00 0.00 3.33
5346 5473 0.940126 GTGCTGTGTGTCTCTTGTGG 59.060 55.000 0.00 0.00 0.00 4.17
5347 5474 0.179048 TGCTGTGTGTCTCTTGTGGG 60.179 55.000 0.00 0.00 0.00 4.61
5348 5475 0.106708 GCTGTGTGTCTCTTGTGGGA 59.893 55.000 0.00 0.00 0.00 4.37
5349 5476 1.271054 GCTGTGTGTCTCTTGTGGGAT 60.271 52.381 0.00 0.00 0.00 3.85
5350 5477 2.693069 CTGTGTGTCTCTTGTGGGATC 58.307 52.381 0.00 0.00 0.00 3.36
5351 5478 1.000843 TGTGTGTCTCTTGTGGGATCG 59.999 52.381 0.00 0.00 0.00 3.69
5352 5479 1.000955 GTGTGTCTCTTGTGGGATCGT 59.999 52.381 0.00 0.00 0.00 3.73
5353 5480 1.000843 TGTGTCTCTTGTGGGATCGTG 59.999 52.381 0.00 0.00 0.00 4.35
5354 5481 0.608130 TGTCTCTTGTGGGATCGTGG 59.392 55.000 0.00 0.00 0.00 4.94
5355 5482 0.108138 GTCTCTTGTGGGATCGTGGG 60.108 60.000 0.00 0.00 0.00 4.61
5356 5483 0.252057 TCTCTTGTGGGATCGTGGGA 60.252 55.000 0.00 0.00 0.00 4.37
5357 5484 0.613260 CTCTTGTGGGATCGTGGGAA 59.387 55.000 0.00 0.00 0.00 3.97
5358 5485 1.003118 CTCTTGTGGGATCGTGGGAAA 59.997 52.381 0.00 0.00 0.00 3.13
5359 5486 1.422024 TCTTGTGGGATCGTGGGAAAA 59.578 47.619 0.00 0.00 0.00 2.29
5360 5487 2.041081 TCTTGTGGGATCGTGGGAAAAT 59.959 45.455 0.00 0.00 0.00 1.82
5361 5488 1.832883 TGTGGGATCGTGGGAAAATG 58.167 50.000 0.00 0.00 0.00 2.32
5362 5489 1.102978 GTGGGATCGTGGGAAAATGG 58.897 55.000 0.00 0.00 0.00 3.16
5363 5490 0.033601 TGGGATCGTGGGAAAATGGG 60.034 55.000 0.00 0.00 0.00 4.00
5364 5491 0.755327 GGGATCGTGGGAAAATGGGG 60.755 60.000 0.00 0.00 0.00 4.96
5365 5492 0.755327 GGATCGTGGGAAAATGGGGG 60.755 60.000 0.00 0.00 0.00 5.40
5366 5493 0.033503 GATCGTGGGAAAATGGGGGT 60.034 55.000 0.00 0.00 0.00 4.95
5367 5494 0.324275 ATCGTGGGAAAATGGGGGTG 60.324 55.000 0.00 0.00 0.00 4.61
5368 5495 2.645192 CGTGGGAAAATGGGGGTGC 61.645 63.158 0.00 0.00 0.00 5.01
5369 5496 1.229177 GTGGGAAAATGGGGGTGCT 60.229 57.895 0.00 0.00 0.00 4.40
5370 5497 1.229145 TGGGAAAATGGGGGTGCTG 60.229 57.895 0.00 0.00 0.00 4.41
5371 5498 2.659063 GGGAAAATGGGGGTGCTGC 61.659 63.158 0.00 0.00 0.00 5.25
5372 5499 2.573340 GAAAATGGGGGTGCTGCG 59.427 61.111 0.00 0.00 0.00 5.18
5373 5500 3.647649 GAAAATGGGGGTGCTGCGC 62.648 63.158 0.00 0.00 0.00 6.09
5391 5518 4.452733 CGCCACCCTCCCTCGTTC 62.453 72.222 0.00 0.00 0.00 3.95
5392 5519 3.003763 GCCACCCTCCCTCGTTCT 61.004 66.667 0.00 0.00 0.00 3.01
5393 5520 3.020237 GCCACCCTCCCTCGTTCTC 62.020 68.421 0.00 0.00 0.00 2.87
5394 5521 1.305381 CCACCCTCCCTCGTTCTCT 60.305 63.158 0.00 0.00 0.00 3.10
5395 5522 1.324005 CCACCCTCCCTCGTTCTCTC 61.324 65.000 0.00 0.00 0.00 3.20
5396 5523 1.378778 ACCCTCCCTCGTTCTCTCG 60.379 63.158 0.00 0.00 0.00 4.04
5397 5524 2.776913 CCCTCCCTCGTTCTCTCGC 61.777 68.421 0.00 0.00 0.00 5.03
5398 5525 1.751162 CCTCCCTCGTTCTCTCGCT 60.751 63.158 0.00 0.00 0.00 4.93
5399 5526 1.316706 CCTCCCTCGTTCTCTCGCTT 61.317 60.000 0.00 0.00 0.00 4.68
5400 5527 0.179150 CTCCCTCGTTCTCTCGCTTG 60.179 60.000 0.00 0.00 0.00 4.01
5401 5528 0.894184 TCCCTCGTTCTCTCGCTTGT 60.894 55.000 0.00 0.00 0.00 3.16
5402 5529 0.809385 CCCTCGTTCTCTCGCTTGTA 59.191 55.000 0.00 0.00 0.00 2.41
5403 5530 1.201647 CCCTCGTTCTCTCGCTTGTAA 59.798 52.381 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.150536 ACACACGTTGGGAATGGCT 59.849 52.632 0.00 0.00 0.00 4.75
1 2 1.285641 CACACACGTTGGGAATGGC 59.714 57.895 0.00 0.00 0.00 4.40
4 5 1.150536 AGCCACACACGTTGGGAAT 59.849 52.632 6.88 0.00 0.00 3.01
7 8 3.286751 CCAGCCACACACGTTGGG 61.287 66.667 6.88 0.40 0.00 4.12
14 15 0.975040 AAAGCAAACCCAGCCACACA 60.975 50.000 0.00 0.00 0.00 3.72
17 18 1.000843 CCTTAAAGCAAACCCAGCCAC 59.999 52.381 0.00 0.00 0.00 5.01
21 22 2.621526 ACGAACCTTAAAGCAAACCCAG 59.378 45.455 0.00 0.00 0.00 4.45
30 32 5.640357 TGCCTACATAACACGAACCTTAAAG 59.360 40.000 0.00 0.00 0.00 1.85
32 34 5.149973 TGCCTACATAACACGAACCTTAA 57.850 39.130 0.00 0.00 0.00 1.85
72 75 7.136119 CGTGGTGTAAAAATGTCATGTTTAGT 58.864 34.615 8.24 0.00 0.00 2.24
73 76 6.087555 GCGTGGTGTAAAAATGTCATGTTTAG 59.912 38.462 8.24 0.00 0.00 1.85
74 77 5.915758 GCGTGGTGTAAAAATGTCATGTTTA 59.084 36.000 4.33 4.33 0.00 2.01
79 82 2.095466 CCGCGTGGTGTAAAAATGTCAT 60.095 45.455 6.91 0.00 0.00 3.06
80 83 1.264557 CCGCGTGGTGTAAAAATGTCA 59.735 47.619 6.91 0.00 0.00 3.58
82 85 0.594110 CCCGCGTGGTGTAAAAATGT 59.406 50.000 15.14 0.00 0.00 2.71
106 109 0.618458 CTGCCTAGGTACAGCCCAAA 59.382 55.000 11.31 0.00 38.26 3.28
108 111 4.050313 CTGCCTAGGTACAGCCCA 57.950 61.111 11.31 0.00 38.26 5.36
125 128 4.581409 TCCTACATTTTATTTAAGGGCGGC 59.419 41.667 0.00 0.00 0.00 6.53
128 131 7.255569 GTGTGTCCTACATTTTATTTAAGGGC 58.744 38.462 0.00 0.00 42.24 5.19
129 132 7.614192 AGGTGTGTCCTACATTTTATTTAAGGG 59.386 37.037 0.00 0.00 46.10 3.95
130 133 8.575649 AGGTGTGTCCTACATTTTATTTAAGG 57.424 34.615 0.00 0.00 46.10 2.69
164 167 8.977412 CCAACTAATGGGTCCTACATTTTATTT 58.023 33.333 0.00 0.00 46.27 1.40
165 168 8.533569 CCAACTAATGGGTCCTACATTTTATT 57.466 34.615 0.00 0.00 46.27 1.40
353 367 1.767692 GGGATATGCCGATTGGGGT 59.232 57.895 0.00 0.00 37.63 4.95
365 379 2.136026 GGTTGGTGAAGAGGGGGATAT 58.864 52.381 0.00 0.00 0.00 1.63
435 449 0.725686 GATGACGACGAGGAAGACGA 59.274 55.000 0.00 0.00 33.85 4.20
440 469 0.744874 GGGATGATGACGACGAGGAA 59.255 55.000 0.00 0.00 0.00 3.36
471 500 1.160289 AGTTCTCTGGGGTAGGGGGA 61.160 60.000 0.00 0.00 0.00 4.81
472 501 0.983378 CAGTTCTCTGGGGTAGGGGG 60.983 65.000 0.00 0.00 37.97 5.40
473 502 2.609046 CAGTTCTCTGGGGTAGGGG 58.391 63.158 0.00 0.00 37.97 4.79
602 631 4.072131 CCCAAGAATGAGAACGGAAGAAA 58.928 43.478 0.00 0.00 0.00 2.52
756 786 0.322546 GGCTTTCCAACCCTGTCGAT 60.323 55.000 0.00 0.00 0.00 3.59
797 827 1.068250 GAAAGCTCGGGATCTCGGG 59.932 63.158 16.43 14.12 0.00 5.14
908 939 3.961414 GGGGTCAGGAAACCGGCA 61.961 66.667 0.00 0.00 40.46 5.69
954 986 1.541310 ATCAAGAACCGCACGGAGGA 61.541 55.000 17.40 5.81 38.96 3.71
1152 1184 2.362120 CCCTGCCCCAGCTTCTTG 60.362 66.667 0.00 0.00 40.80 3.02
1464 1496 0.822164 CCTCTACGACCCCAACGATT 59.178 55.000 0.00 0.00 34.70 3.34
1727 1764 9.243105 TCTAGCAAAAGGAATAAAAGCACTATT 57.757 29.630 0.00 0.00 0.00 1.73
1984 2021 6.873605 CGGTATCTTGCAACCATCATATCTAA 59.126 38.462 6.13 0.00 35.35 2.10
2308 2347 3.744660 AGTCTGGCTCGAACAGAAATTT 58.255 40.909 17.94 0.00 45.66 1.82
2772 2812 4.250464 TGTCTAAAGCACCAAATCTACCG 58.750 43.478 0.00 0.00 0.00 4.02
2811 2851 4.201891 GGCAATGACAGTATGAGAAGCAAG 60.202 45.833 0.00 0.00 39.69 4.01
3332 3401 2.230660 AGTTGGCCAAGACTAGCAAAC 58.769 47.619 21.21 3.17 42.23 2.93
3516 3587 3.561313 GCCATAAACCCTCAAGACTCCAA 60.561 47.826 0.00 0.00 0.00 3.53
3681 3756 3.966665 GACCTCCAATCTCTTCCTCAGAT 59.033 47.826 0.00 0.00 31.51 2.90
3934 4009 2.070783 GTTGTCGATGTCCGCCTTAAA 58.929 47.619 0.00 0.00 38.37 1.52
4186 4262 0.816373 GGGACGGGACAGAGTAGAAC 59.184 60.000 0.00 0.00 0.00 3.01
4193 4269 0.689412 TATGCATGGGACGGGACAGA 60.689 55.000 10.16 0.00 0.00 3.41
4201 4277 5.914635 CGAACAAAACATATATGCATGGGAC 59.085 40.000 10.16 5.04 0.00 4.46
4227 4303 2.158623 TGGCAAACAGACAAGTCAGGAT 60.159 45.455 2.72 0.00 26.55 3.24
4405 4481 3.089874 TTCTCCTCCCCATGCCGG 61.090 66.667 0.00 0.00 0.00 6.13
4668 4754 5.730550 TGACAGTAAACAGAAGTGAACAGT 58.269 37.500 0.00 0.00 0.00 3.55
4669 4755 6.313905 AGTTGACAGTAAACAGAAGTGAACAG 59.686 38.462 3.44 0.00 0.00 3.16
4670 4756 6.092122 CAGTTGACAGTAAACAGAAGTGAACA 59.908 38.462 3.44 0.00 0.00 3.18
4671 4757 6.092259 ACAGTTGACAGTAAACAGAAGTGAAC 59.908 38.462 3.44 0.00 0.00 3.18
4672 4758 6.170506 ACAGTTGACAGTAAACAGAAGTGAA 58.829 36.000 3.44 0.00 0.00 3.18
4808 4898 9.986833 ATTGTTTGAAAATAGTTTTTGTTCAGC 57.013 25.926 0.00 0.00 35.20 4.26
4837 4930 5.678132 TGATAATGGATTCAATCTGTGCG 57.322 39.130 0.00 0.00 0.00 5.34
4866 4959 3.119280 GCAGTTAACGGGCCATGTTTATT 60.119 43.478 16.63 3.53 0.00 1.40
4876 4969 2.311124 AGATAGTGCAGTTAACGGGC 57.689 50.000 15.62 15.62 0.00 6.13
4900 4993 1.245732 AGGACGACGGATATGCCTAC 58.754 55.000 0.00 0.00 0.00 3.18
4910 5003 0.949105 CCAAACTCCAAGGACGACGG 60.949 60.000 0.00 0.00 0.00 4.79
4939 5034 8.728088 AACATACACGATGAATTTTTCAGAAC 57.272 30.769 0.00 0.00 43.98 3.01
5022 5132 0.523546 CGGACAGGTTGATCGACTCG 60.524 60.000 12.89 6.86 0.00 4.18
5038 5148 1.374125 CACTGATTCACGTGGCGGA 60.374 57.895 17.00 0.00 0.00 5.54
5041 5151 1.781555 CGTCACTGATTCACGTGGC 59.218 57.895 17.00 6.38 32.67 5.01
5042 5152 1.781555 GCGTCACTGATTCACGTGG 59.218 57.895 17.00 0.90 35.91 4.94
5070 5180 0.253044 TCGCCTGATTTCCCCTTGAG 59.747 55.000 0.00 0.00 0.00 3.02
5071 5181 0.918983 ATCGCCTGATTTCCCCTTGA 59.081 50.000 0.00 0.00 0.00 3.02
5072 5182 1.767759 AATCGCCTGATTTCCCCTTG 58.232 50.000 0.00 0.00 42.14 3.61
5096 5206 7.304919 AGTTTAAGTAAAAGGAATCGCTAGC 57.695 36.000 4.06 4.06 0.00 3.42
5120 5230 6.253942 CGCAATCAAGCATGTTGAATGAATTA 59.746 34.615 20.68 0.16 32.57 1.40
5126 5236 3.247442 CACGCAATCAAGCATGTTGAAT 58.753 40.909 12.60 4.48 31.55 2.57
5132 5242 2.355797 GCACACGCAATCAAGCATG 58.644 52.632 0.00 0.00 38.36 4.06
5158 5268 6.970484 ACCAAACAGAAATTCAGTACACATC 58.030 36.000 0.00 0.00 0.00 3.06
5205 5315 7.330208 TCGTTTTGAAAGCATAAGGTAGACTAC 59.670 37.037 3.86 3.86 0.00 2.73
5221 5344 0.869730 GGCTACGGCTCGTTTTGAAA 59.130 50.000 5.57 0.00 41.54 2.69
5297 5424 2.902846 CCGCACCCGAACCAAACA 60.903 61.111 0.00 0.00 36.29 2.83
5298 5425 2.903350 ACCGCACCCGAACCAAAC 60.903 61.111 0.00 0.00 36.29 2.93
5299 5426 2.902846 CACCGCACCCGAACCAAA 60.903 61.111 0.00 0.00 36.29 3.28
5300 5427 3.862991 TCACCGCACCCGAACCAA 61.863 61.111 0.00 0.00 36.29 3.67
5301 5428 4.612412 GTCACCGCACCCGAACCA 62.612 66.667 0.00 0.00 36.29 3.67
5303 5430 4.612412 TGGTCACCGCACCCGAAC 62.612 66.667 0.00 0.00 35.26 3.95
5304 5431 4.612412 GTGGTCACCGCACCCGAA 62.612 66.667 1.22 0.00 35.26 4.30
5322 5449 3.883744 GAGACACACAGCACCGGGG 62.884 68.421 6.32 0.84 0.00 5.73
5323 5450 2.357517 GAGACACACAGCACCGGG 60.358 66.667 6.32 0.00 0.00 5.73
5324 5451 1.069765 AAGAGACACACAGCACCGG 59.930 57.895 0.00 0.00 0.00 5.28
5325 5452 0.530650 ACAAGAGACACACAGCACCG 60.531 55.000 0.00 0.00 0.00 4.94
5326 5453 0.940126 CACAAGAGACACACAGCACC 59.060 55.000 0.00 0.00 0.00 5.01
5327 5454 0.940126 CCACAAGAGACACACAGCAC 59.060 55.000 0.00 0.00 0.00 4.40
5328 5455 0.179048 CCCACAAGAGACACACAGCA 60.179 55.000 0.00 0.00 0.00 4.41
5329 5456 0.106708 TCCCACAAGAGACACACAGC 59.893 55.000 0.00 0.00 0.00 4.40
5330 5457 2.693069 GATCCCACAAGAGACACACAG 58.307 52.381 0.00 0.00 0.00 3.66
5331 5458 1.000843 CGATCCCACAAGAGACACACA 59.999 52.381 0.00 0.00 0.00 3.72
5332 5459 1.000955 ACGATCCCACAAGAGACACAC 59.999 52.381 0.00 0.00 0.00 3.82
5333 5460 1.000843 CACGATCCCACAAGAGACACA 59.999 52.381 0.00 0.00 0.00 3.72
5334 5461 1.673033 CCACGATCCCACAAGAGACAC 60.673 57.143 0.00 0.00 0.00 3.67
5335 5462 0.608130 CCACGATCCCACAAGAGACA 59.392 55.000 0.00 0.00 0.00 3.41
5336 5463 0.108138 CCCACGATCCCACAAGAGAC 60.108 60.000 0.00 0.00 0.00 3.36
5337 5464 0.252057 TCCCACGATCCCACAAGAGA 60.252 55.000 0.00 0.00 0.00 3.10
5338 5465 0.613260 TTCCCACGATCCCACAAGAG 59.387 55.000 0.00 0.00 0.00 2.85
5339 5466 1.060729 TTTCCCACGATCCCACAAGA 58.939 50.000 0.00 0.00 0.00 3.02
5340 5467 1.904287 TTTTCCCACGATCCCACAAG 58.096 50.000 0.00 0.00 0.00 3.16
5341 5468 2.166829 CATTTTCCCACGATCCCACAA 58.833 47.619 0.00 0.00 0.00 3.33
5342 5469 1.615651 CCATTTTCCCACGATCCCACA 60.616 52.381 0.00 0.00 0.00 4.17
5343 5470 1.102978 CCATTTTCCCACGATCCCAC 58.897 55.000 0.00 0.00 0.00 4.61
5344 5471 0.033601 CCCATTTTCCCACGATCCCA 60.034 55.000 0.00 0.00 0.00 4.37
5345 5472 0.755327 CCCCATTTTCCCACGATCCC 60.755 60.000 0.00 0.00 0.00 3.85
5346 5473 0.755327 CCCCCATTTTCCCACGATCC 60.755 60.000 0.00 0.00 0.00 3.36
5347 5474 0.033503 ACCCCCATTTTCCCACGATC 60.034 55.000 0.00 0.00 0.00 3.69
5348 5475 0.324275 CACCCCCATTTTCCCACGAT 60.324 55.000 0.00 0.00 0.00 3.73
5349 5476 1.075836 CACCCCCATTTTCCCACGA 59.924 57.895 0.00 0.00 0.00 4.35
5350 5477 2.645192 GCACCCCCATTTTCCCACG 61.645 63.158 0.00 0.00 0.00 4.94
5351 5478 1.229177 AGCACCCCCATTTTCCCAC 60.229 57.895 0.00 0.00 0.00 4.61
5352 5479 1.229145 CAGCACCCCCATTTTCCCA 60.229 57.895 0.00 0.00 0.00 4.37
5353 5480 2.659063 GCAGCACCCCCATTTTCCC 61.659 63.158 0.00 0.00 0.00 3.97
5354 5481 2.981302 GCAGCACCCCCATTTTCC 59.019 61.111 0.00 0.00 0.00 3.13
5355 5482 2.573340 CGCAGCACCCCCATTTTC 59.427 61.111 0.00 0.00 0.00 2.29
5374 5501 4.452733 GAACGAGGGAGGGTGGCG 62.453 72.222 0.00 0.00 0.00 5.69
5375 5502 3.003763 AGAACGAGGGAGGGTGGC 61.004 66.667 0.00 0.00 0.00 5.01
5376 5503 1.305381 AGAGAACGAGGGAGGGTGG 60.305 63.158 0.00 0.00 0.00 4.61
5377 5504 1.658686 CGAGAGAACGAGGGAGGGTG 61.659 65.000 0.00 0.00 35.09 4.61
5378 5505 1.378778 CGAGAGAACGAGGGAGGGT 60.379 63.158 0.00 0.00 35.09 4.34
5379 5506 2.776913 GCGAGAGAACGAGGGAGGG 61.777 68.421 0.00 0.00 35.09 4.30
5380 5507 1.316706 AAGCGAGAGAACGAGGGAGG 61.317 60.000 0.00 0.00 35.09 4.30
5381 5508 0.179150 CAAGCGAGAGAACGAGGGAG 60.179 60.000 0.00 0.00 35.09 4.30
5382 5509 0.894184 ACAAGCGAGAGAACGAGGGA 60.894 55.000 0.00 0.00 35.09 4.20
5383 5510 0.809385 TACAAGCGAGAGAACGAGGG 59.191 55.000 0.00 0.00 35.09 4.30
5384 5511 2.631418 TTACAAGCGAGAGAACGAGG 57.369 50.000 0.00 0.00 35.09 4.63


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

AutoCloner maintained by Alex Coulton.