Multiple sequence alignment - TraesCS5D01G291500

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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 TraesCS5D01G291500 chr5D 100.000 6084 0 0 1 6084 389114812 389108729 0.000000e+00 11236.0
1 TraesCS5D01G291500 chr5D 87.204 633 74 5 2146 2777 387114015 387114641 0.000000e+00 713.0
2 TraesCS5D01G291500 chr5D 85.616 584 70 9 3433 4006 387114922 387115501 8.730000e-168 601.0
3 TraesCS5D01G291500 chr5D 85.714 112 11 5 4139 4249 387115698 387115805 4.980000e-21 113.0
4 TraesCS5D01G291500 chr5B 93.942 5695 250 41 357 6003 467516068 467510421 0.000000e+00 8517.0
5 TraesCS5D01G291500 chr5B 90.429 303 27 2 1 303 467516367 467516067 1.230000e-106 398.0
6 TraesCS5D01G291500 chr5B 92.627 217 16 0 3739 3955 465871195 465870979 4.580000e-81 313.0
7 TraesCS5D01G291500 chr5A 94.884 5395 211 34 638 5994 492035460 492030093 0.000000e+00 8373.0
8 TraesCS5D01G291500 chr5A 81.941 742 78 17 2056 2786 489879943 489880639 1.470000e-160 577.0
9 TraesCS5D01G291500 chr5A 83.706 626 74 10 2 610 492036167 492035553 3.180000e-157 566.0
10 TraesCS5D01G291500 chr5A 81.863 408 43 9 4690 5066 489870714 489871121 1.270000e-81 315.0
11 TraesCS5D01G291500 chr4B 83.333 348 54 2 19 363 22804432 22804778 9.840000e-83 318.0
12 TraesCS5D01G291500 chr4B 91.045 67 6 0 375 441 619442429 619442495 2.340000e-14 91.6
13 TraesCS5D01G291500 chr7A 81.818 352 52 8 19 363 373859758 373859412 9.980000e-73 285.0
14 TraesCS5D01G291500 chr7A 80.114 352 58 9 19 363 6661859 6661513 1.010000e-62 252.0
15 TraesCS5D01G291500 chr7A 80.170 353 56 11 19 363 628898291 628897945 1.010000e-62 252.0
16 TraesCS5D01G291500 chr3A 80.516 349 61 6 19 363 220604559 220604904 1.680000e-65 261.0
17 TraesCS5D01G291500 chr7D 80.952 315 59 1 49 363 39771034 39770721 1.310000e-61 248.0


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 TraesCS5D01G291500 chr5D 389108729 389114812 6083 True 11236.000000 11236 100.0000 1 6084 1 chr5D.!!$R1 6083
1 TraesCS5D01G291500 chr5D 387114015 387115805 1790 False 475.666667 713 86.1780 2146 4249 3 chr5D.!!$F1 2103
2 TraesCS5D01G291500 chr5B 467510421 467516367 5946 True 4457.500000 8517 92.1855 1 6003 2 chr5B.!!$R2 6002
3 TraesCS5D01G291500 chr5A 492030093 492036167 6074 True 4469.500000 8373 89.2950 2 5994 2 chr5A.!!$R1 5992
4 TraesCS5D01G291500 chr5A 489879943 489880639 696 False 577.000000 577 81.9410 2056 2786 1 chr5A.!!$F2 730

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
307 314 0.409092 AGGATTGGTGTCCATGGCAA 59.591 50.000 6.96 5.88 40.90 4.52 F
352 359 0.693049 AGGATTGGTTTCCTCTGCGT 59.307 50.000 0.00 0.00 42.71 5.24 F
353 360 1.087501 GGATTGGTTTCCTCTGCGTC 58.912 55.000 0.00 0.00 32.68 5.19 F
1955 2074 0.251077 CACTGAGCCCAAAGAGCCTT 60.251 55.000 0.00 0.00 0.00 4.35 F
2012 2131 0.813210 GCTACCAGATGCAGGACAGC 60.813 60.000 0.00 2.39 33.22 4.40 F
2594 2721 1.062587 CTTGATTCCGCATGTTCGACC 59.937 52.381 0.00 0.00 0.00 4.79 F
3269 3451 1.080974 CCCGAGCTGCAGCAAAAAG 60.081 57.895 38.24 22.91 45.16 2.27 F
3360 3542 1.609208 AGGTGTGTGTGCAAATCCTC 58.391 50.000 0.00 0.00 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1481 1600 1.001641 GCAGTCCAAGCAGACCCAT 60.002 57.895 0.00 0.0 37.49 4.00 R
1691 1810 1.512926 CACCAAGAACCACCTTCTCG 58.487 55.000 0.00 0.0 38.37 4.04 R
2322 2444 1.810532 CAGGAGACACTCGGGTAGC 59.189 63.158 0.00 0.0 0.00 3.58 R
3191 3373 0.318441 TCTCCGCACTGTCCTTTCTG 59.682 55.000 0.00 0.0 0.00 3.02 R
3736 3928 2.111384 TCATTCTCTTCCTCCTTCCGG 58.889 52.381 0.00 0.0 0.00 5.14 R
4044 4236 1.741525 TGCAGGCAAGCAGAAAACC 59.258 52.632 0.22 0.0 40.11 3.27 R
4538 4812 2.231716 ACCCATTTTGAGCCCCTTAC 57.768 50.000 0.00 0.0 0.00 2.34 R
5092 5372 2.768527 CCATGAGTAGGTCACCAGACAT 59.231 50.000 0.00 0.0 46.80 3.06 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
85 86 3.121030 GAAGCGATGCCACTGCGT 61.121 61.111 0.00 0.00 41.78 5.24
165 166 3.110178 GCACGGACGAGGGAAACG 61.110 66.667 0.00 0.00 0.00 3.60
171 172 4.612412 ACGAGGGAAACGCGCCAA 62.612 61.111 5.73 0.00 46.87 4.52
282 289 0.985490 ATCAGAGGAGTGGGGGAAGC 60.985 60.000 0.00 0.00 0.00 3.86
307 314 0.409092 AGGATTGGTGTCCATGGCAA 59.591 50.000 6.96 5.88 40.90 4.52
314 321 1.303236 TGTCCATGGCAACGGAAGG 60.303 57.895 6.96 0.00 42.51 3.46
340 347 4.794648 TGGGCGCGGAAGGATTGG 62.795 66.667 8.83 0.00 0.00 3.16
350 357 2.095461 GGAAGGATTGGTTTCCTCTGC 58.905 52.381 0.00 0.00 45.63 4.26
351 358 1.740025 GAAGGATTGGTTTCCTCTGCG 59.260 52.381 0.00 0.00 45.63 5.18
352 359 0.693049 AGGATTGGTTTCCTCTGCGT 59.307 50.000 0.00 0.00 42.71 5.24
353 360 1.087501 GGATTGGTTTCCTCTGCGTC 58.912 55.000 0.00 0.00 32.68 5.19
354 361 1.339151 GGATTGGTTTCCTCTGCGTCT 60.339 52.381 0.00 0.00 32.68 4.18
355 362 1.734465 GATTGGTTTCCTCTGCGTCTG 59.266 52.381 0.00 0.00 0.00 3.51
373 380 6.713450 TGCGTCTGATACCATATAGAAGTGTA 59.287 38.462 0.00 0.00 0.00 2.90
381 388 9.675464 GATACCATATAGAAGTGTACTCTAGCT 57.325 37.037 0.00 0.00 0.00 3.32
420 427 7.604657 ACCGATCTAATGAAAGAGATTAGGT 57.395 36.000 0.00 0.00 38.03 3.08
570 608 4.403113 TCCGCATTGGTGTATTGTCTAGTA 59.597 41.667 0.00 0.00 39.52 1.82
662 765 5.221783 ACGGAGGGATTAAATGTATGGGTAC 60.222 44.000 0.00 0.00 0.00 3.34
704 812 6.089551 CGAAAAGACTACGACAGATTGTTCAT 59.910 38.462 0.00 0.00 0.00 2.57
705 813 7.272731 CGAAAAGACTACGACAGATTGTTCATA 59.727 37.037 0.00 0.00 0.00 2.15
706 814 7.813852 AAAGACTACGACAGATTGTTCATAC 57.186 36.000 0.00 0.00 0.00 2.39
753 861 1.447140 GCGTATCGGCACACCTTCA 60.447 57.895 0.00 0.00 0.00 3.02
1167 1286 1.270826 GAAAGAAGGTGAAGGCCAAGC 59.729 52.381 5.01 0.00 0.00 4.01
1293 1412 2.809601 GCCACTACAGCCGTGACG 60.810 66.667 0.00 0.00 34.35 4.35
1472 1591 2.041115 GGCCAAGGCGGAGAAGAAC 61.041 63.158 4.80 0.00 43.06 3.01
1481 1600 3.132289 AGGCGGAGAAGAACGATGATTTA 59.868 43.478 0.00 0.00 0.00 1.40
1535 1654 1.872234 CGGTGCCGTGTCAGATACG 60.872 63.158 12.50 12.50 40.98 3.06
1635 1754 2.430956 CGTATTGCTTGTCATGCGAAC 58.569 47.619 4.84 3.14 0.00 3.95
1712 1831 0.550914 AGAAGGTGGTTCTTGGTGCA 59.449 50.000 0.00 0.00 43.54 4.57
1867 1986 2.027192 TGCTAGGACCAGATGTTCCAAC 60.027 50.000 0.00 0.00 0.00 3.77
1896 2015 4.201891 CCATTGCTATGTCACTGAAGAAGC 60.202 45.833 7.37 0.00 0.00 3.86
1898 2017 3.854666 TGCTATGTCACTGAAGAAGCTC 58.145 45.455 0.00 0.00 0.00 4.09
1919 2038 2.842208 TTGTGGAAACAAGTGCTTCG 57.158 45.000 0.00 0.00 46.06 3.79
1955 2074 0.251077 CACTGAGCCCAAAGAGCCTT 60.251 55.000 0.00 0.00 0.00 4.35
1964 2083 2.029560 CCCAAAGAGCCTTTTCTCAAGC 60.030 50.000 0.00 0.00 35.59 4.01
2012 2131 0.813210 GCTACCAGATGCAGGACAGC 60.813 60.000 0.00 2.39 33.22 4.40
2210 2332 5.434408 CATGACCAATTCCTTGATCTCTCA 58.566 41.667 0.00 0.00 34.04 3.27
2322 2444 5.505173 AAATCGCAGATATGGAAAGGTTG 57.495 39.130 0.00 0.00 45.12 3.77
2518 2645 1.508088 CCGCTTCAAATGTGGAGGC 59.492 57.895 0.00 0.00 37.26 4.70
2582 2709 7.446001 AACAAAGTCTGAGATTCTTGATTCC 57.554 36.000 7.75 0.00 0.00 3.01
2594 2721 1.062587 CTTGATTCCGCATGTTCGACC 59.937 52.381 0.00 0.00 0.00 4.79
2891 3021 2.743636 CGTTATATGGCGGAGATGGT 57.256 50.000 0.00 0.00 0.00 3.55
2894 3024 3.589988 GTTATATGGCGGAGATGGTGAG 58.410 50.000 0.00 0.00 0.00 3.51
2940 3122 4.095483 GTGATATGTTTGGTGAGCCTGAAG 59.905 45.833 0.00 0.00 35.27 3.02
2969 3151 6.114187 TCTGATGCTAAGAAAGAAACTGGA 57.886 37.500 0.00 0.00 0.00 3.86
3114 3296 2.027285 TCGGAATCTTGGCATTGTGAGA 60.027 45.455 0.00 0.00 0.00 3.27
3122 3304 3.940209 TGGCATTGTGAGAATTGTTCC 57.060 42.857 0.00 0.00 0.00 3.62
3126 3308 4.427312 GCATTGTGAGAATTGTTCCATCC 58.573 43.478 0.00 0.00 0.00 3.51
3238 3420 4.441356 GGCAAGTGGTGATGAAAAACAAGA 60.441 41.667 0.00 0.00 0.00 3.02
3269 3451 1.080974 CCCGAGCTGCAGCAAAAAG 60.081 57.895 38.24 22.91 45.16 2.27
3344 3526 2.224185 TGACATGTGCTGTAACGAAGGT 60.224 45.455 1.15 0.00 38.54 3.50
3360 3542 1.609208 AGGTGTGTGTGCAAATCCTC 58.391 50.000 0.00 0.00 0.00 3.71
3419 3601 4.832823 TCTCCAGACATTGACACTACTGAA 59.167 41.667 0.00 0.00 0.00 3.02
3456 3638 2.043939 ACATACCACCAGGAGTGTAGGA 59.956 50.000 0.00 0.00 45.74 2.94
3500 3682 6.599244 TGGAATTTACATCTTCCAGTAAGCAG 59.401 38.462 0.00 0.00 44.56 4.24
3591 3773 4.393062 CAGTGAGTTGTGGTGATAATGACC 59.607 45.833 0.00 0.00 0.00 4.02
3772 3964 4.990526 AGAATGAAGATGGTTGTCAAGGT 58.009 39.130 0.00 0.00 0.00 3.50
3959 4151 2.143925 GTGCGCTTTAAGGAGACACTT 58.856 47.619 9.73 0.00 34.52 3.16
4020 4212 5.129634 TCTAACTCAGTTGAATTTGCCACA 58.870 37.500 0.00 0.00 0.00 4.17
4021 4213 4.734398 AACTCAGTTGAATTTGCCACAA 57.266 36.364 0.00 0.00 0.00 3.33
4022 4214 4.734398 ACTCAGTTGAATTTGCCACAAA 57.266 36.364 0.00 0.00 0.00 2.83
4023 4215 5.083533 ACTCAGTTGAATTTGCCACAAAA 57.916 34.783 0.00 0.00 0.00 2.44
4024 4216 5.486526 ACTCAGTTGAATTTGCCACAAAAA 58.513 33.333 0.00 0.00 0.00 1.94
4197 4470 7.118390 CACTATTCCTGTTCTCCACTTGTTTAG 59.882 40.741 0.00 0.00 0.00 1.85
4284 4558 6.705302 TCTTGTCAGCATAGAGAACTGAAAT 58.295 36.000 0.00 0.00 41.80 2.17
4286 4560 5.181009 TGTCAGCATAGAGAACTGAAATGG 58.819 41.667 0.00 0.00 41.80 3.16
4359 4633 7.020914 AGAACATTCTCCGCAGATATTTTTC 57.979 36.000 0.00 0.00 29.94 2.29
4365 4639 5.984725 TCTCCGCAGATATTTTTCCTACAA 58.015 37.500 0.00 0.00 0.00 2.41
4425 4699 4.191544 TGTCCATATCCTGAAAGAAAGCG 58.808 43.478 0.00 0.00 34.07 4.68
4472 4746 3.314541 ACGTGAATCTGGAGGTTACAC 57.685 47.619 0.00 0.00 0.00 2.90
4473 4747 2.259618 CGTGAATCTGGAGGTTACACG 58.740 52.381 0.00 0.00 42.04 4.49
4538 4812 3.871006 TGCTCAACAGTTTGTGTCTACAG 59.129 43.478 0.00 0.00 39.03 2.74
4545 4819 4.202326 ACAGTTTGTGTCTACAGTAAGGGG 60.202 45.833 0.00 0.00 38.23 4.79
4552 4826 3.649023 TGTCTACAGTAAGGGGCTCAAAA 59.351 43.478 0.00 0.00 0.00 2.44
4685 4960 8.528643 TGTAGCTCTCAAGTTTAGTATGCTTAA 58.471 33.333 0.00 0.00 0.00 1.85
4757 5032 2.620367 GGGACCTATTGTGCACCATTCA 60.620 50.000 15.69 0.00 36.96 2.57
4790 5067 5.692115 TTATGGGCAGAGAGTCATTTACA 57.308 39.130 0.00 0.00 0.00 2.41
4800 5077 8.940952 GCAGAGAGTCATTTACAGACTTTAAAT 58.059 33.333 1.49 1.49 45.79 1.40
4846 5126 5.291128 ACTGTTTTCCTTAATACGCAGATCG 59.709 40.000 0.00 0.00 45.38 3.69
4912 5192 0.994247 ACATGGGAAGCATGACAGGA 59.006 50.000 0.00 0.00 34.39 3.86
5074 5354 4.607239 ACATCCTTTTCTACGAGAGGGTA 58.393 43.478 0.00 0.00 0.00 3.69
5092 5372 5.638133 AGGGTAGCCGAGTAAGACAATATA 58.362 41.667 5.06 0.00 0.00 0.86
5200 5483 4.185467 ACTGCTATGACTGTCTCAGTTG 57.815 45.455 9.51 5.93 45.44 3.16
5201 5484 3.056250 ACTGCTATGACTGTCTCAGTTGG 60.056 47.826 9.51 3.94 45.44 3.77
5303 5586 1.188219 TCTGGAGAGCACAGGTGGAC 61.188 60.000 1.10 0.00 36.62 4.02
5392 5675 4.630069 CCTCGGTTGTATTGGTTTAGAGTG 59.370 45.833 0.00 0.00 0.00 3.51
5394 5677 5.856156 TCGGTTGTATTGGTTTAGAGTGAA 58.144 37.500 0.00 0.00 0.00 3.18
5480 5764 3.382227 CGTGATGGGGGCGTATATATACA 59.618 47.826 20.24 2.90 32.87 2.29
5590 5874 6.396829 AATCAAACCTGGAAGTTTCAAGAG 57.603 37.500 0.00 0.00 37.87 2.85
5594 5878 7.287061 TCAAACCTGGAAGTTTCAAGAGATTA 58.713 34.615 0.00 0.00 37.87 1.75
5595 5879 7.777910 TCAAACCTGGAAGTTTCAAGAGATTAA 59.222 33.333 0.00 0.00 37.87 1.40
5596 5880 8.579863 CAAACCTGGAAGTTTCAAGAGATTAAT 58.420 33.333 0.00 0.00 37.87 1.40
5597 5881 8.712228 AACCTGGAAGTTTCAAGAGATTAATT 57.288 30.769 0.00 0.00 29.28 1.40
5598 5882 8.712228 ACCTGGAAGTTTCAAGAGATTAATTT 57.288 30.769 0.00 0.00 29.28 1.82
5599 5883 8.579863 ACCTGGAAGTTTCAAGAGATTAATTTG 58.420 33.333 0.00 0.00 29.28 2.32
5600 5884 8.031277 CCTGGAAGTTTCAAGAGATTAATTTGG 58.969 37.037 0.00 0.00 29.28 3.28
5602 5886 8.359642 TGGAAGTTTCAAGAGATTAATTTGGTG 58.640 33.333 0.00 0.00 0.00 4.17
5603 5887 8.576442 GGAAGTTTCAAGAGATTAATTTGGTGA 58.424 33.333 0.00 0.00 0.00 4.02
5626 5910 8.620116 TGATTCTTCACAAATCACAAGACATA 57.380 30.769 0.00 0.00 38.02 2.29
5728 6012 6.413892 TGGATTTGGAAATTTTAGGGATTGC 58.586 36.000 0.00 0.00 0.00 3.56
5731 6015 6.678568 TTTGGAAATTTTAGGGATTGCAGA 57.321 33.333 0.00 0.00 0.00 4.26
5732 6016 5.920193 TGGAAATTTTAGGGATTGCAGAG 57.080 39.130 0.00 0.00 0.00 3.35
5736 6020 6.097412 GGAAATTTTAGGGATTGCAGAGACAT 59.903 38.462 0.00 0.00 0.00 3.06
5745 6029 2.916702 TGCAGAGACATGTCTTGTGT 57.083 45.000 28.46 11.76 40.61 3.72
5749 6033 3.677121 GCAGAGACATGTCTTGTGTACAG 59.323 47.826 28.46 12.86 40.61 2.74
5952 6259 1.742140 CTGGAGCTGTGCAGAGCAG 60.742 63.158 34.26 20.78 44.77 4.24
5966 6273 2.165437 CAGAGCAGTCTAGAGGTGAACC 59.835 54.545 6.26 0.00 0.00 3.62
6007 6314 1.891616 GTCTCTGACGACCCCTTCC 59.108 63.158 0.00 0.00 0.00 3.46
6008 6315 0.612453 GTCTCTGACGACCCCTTCCT 60.612 60.000 0.00 0.00 0.00 3.36
6009 6316 0.612174 TCTCTGACGACCCCTTCCTG 60.612 60.000 0.00 0.00 0.00 3.86
6010 6317 0.612174 CTCTGACGACCCCTTCCTGA 60.612 60.000 0.00 0.00 0.00 3.86
6011 6318 0.178944 TCTGACGACCCCTTCCTGAA 60.179 55.000 0.00 0.00 0.00 3.02
6012 6319 0.247736 CTGACGACCCCTTCCTGAAG 59.752 60.000 0.00 0.00 38.14 3.02
6013 6320 0.178944 TGACGACCCCTTCCTGAAGA 60.179 55.000 8.46 0.00 40.79 2.87
6014 6321 0.974383 GACGACCCCTTCCTGAAGAA 59.026 55.000 8.46 0.00 40.79 2.52
6023 6330 3.922366 CCTGAAGAAGGGGGTGGT 58.078 61.111 0.00 0.00 43.15 4.16
6024 6331 2.164393 CCTGAAGAAGGGGGTGGTT 58.836 57.895 0.00 0.00 43.15 3.67
6025 6332 0.251341 CCTGAAGAAGGGGGTGGTTG 60.251 60.000 0.00 0.00 43.15 3.77
6026 6333 0.251341 CTGAAGAAGGGGGTGGTTGG 60.251 60.000 0.00 0.00 0.00 3.77
6027 6334 1.606601 GAAGAAGGGGGTGGTTGGC 60.607 63.158 0.00 0.00 0.00 4.52
6028 6335 3.507377 AAGAAGGGGGTGGTTGGCG 62.507 63.158 0.00 0.00 0.00 5.69
6029 6336 3.961414 GAAGGGGGTGGTTGGCGA 61.961 66.667 0.00 0.00 0.00 5.54
6030 6337 4.280019 AAGGGGGTGGTTGGCGAC 62.280 66.667 0.00 0.00 0.00 5.19
6044 6351 2.512286 CGACTGGCGCATCCACAT 60.512 61.111 10.83 0.00 40.72 3.21
6045 6352 2.816360 CGACTGGCGCATCCACATG 61.816 63.158 10.83 0.00 40.72 3.21
6046 6353 1.450134 GACTGGCGCATCCACATGA 60.450 57.895 10.83 0.00 40.72 3.07
6047 6354 1.709147 GACTGGCGCATCCACATGAC 61.709 60.000 10.83 0.00 40.72 3.06
6048 6355 2.816360 CTGGCGCATCCACATGACG 61.816 63.158 10.83 0.00 40.72 4.35
6049 6356 4.241999 GGCGCATCCACATGACGC 62.242 66.667 10.83 12.37 46.20 5.19
6050 6357 3.197790 GCGCATCCACATGACGCT 61.198 61.111 0.30 0.00 44.84 5.07
6051 6358 3.009140 CGCATCCACATGACGCTC 58.991 61.111 0.00 0.00 30.57 5.03
6052 6359 2.863853 CGCATCCACATGACGCTCG 61.864 63.158 0.00 0.00 30.57 5.03
6053 6360 3.009140 CATCCACATGACGCTCGC 58.991 61.111 0.00 0.00 30.57 5.03
6054 6361 2.202932 ATCCACATGACGCTCGCC 60.203 61.111 0.00 0.00 0.00 5.54
6055 6362 4.794439 TCCACATGACGCTCGCCG 62.794 66.667 0.00 0.00 44.21 6.46
6075 6382 4.767255 CCTGCTCCAGCCACCGTC 62.767 72.222 0.00 0.00 41.18 4.79
6076 6383 3.699894 CTGCTCCAGCCACCGTCT 61.700 66.667 0.00 0.00 41.18 4.18
6077 6384 3.655810 CTGCTCCAGCCACCGTCTC 62.656 68.421 0.00 0.00 41.18 3.36
6078 6385 4.803426 GCTCCAGCCACCGTCTCG 62.803 72.222 0.00 0.00 34.31 4.04
6079 6386 4.803426 CTCCAGCCACCGTCTCGC 62.803 72.222 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 2.040213 CTTCACCATCGTCGGCATGC 62.040 60.000 9.90 9.90 0.00 4.06
53 54 1.656095 CGCTTCTTCTTCACCATCGTC 59.344 52.381 0.00 0.00 0.00 4.20
85 86 4.610714 TGCACGCCGGCAACTACA 62.611 61.111 28.98 13.86 41.65 2.74
137 138 1.086067 CGTCCGTGCTGCAGATGATT 61.086 55.000 20.43 0.00 0.00 2.57
282 289 0.824109 TGGACACCAATCCTCTAGCG 59.176 55.000 0.00 0.00 39.75 4.26
307 314 2.928396 CACCCACCCTCCTTCCGT 60.928 66.667 0.00 0.00 0.00 4.69
335 342 1.734465 CAGACGCAGAGGAAACCAATC 59.266 52.381 0.00 0.00 0.00 2.67
340 347 2.094182 TGGTATCAGACGCAGAGGAAAC 60.094 50.000 0.00 0.00 0.00 2.78
350 357 8.325421 AGTACACTTCTATATGGTATCAGACG 57.675 38.462 0.00 0.00 0.00 4.18
351 358 9.509956 AGAGTACACTTCTATATGGTATCAGAC 57.490 37.037 0.00 0.00 0.00 3.51
354 361 9.451002 GCTAGAGTACACTTCTATATGGTATCA 57.549 37.037 0.00 0.00 0.00 2.15
355 362 9.675464 AGCTAGAGTACACTTCTATATGGTATC 57.325 37.037 0.00 0.00 0.00 2.24
524 556 9.239002 CGGAATCGGTTGCAATATATTTTAAAA 57.761 29.630 0.59 2.51 0.00 1.52
525 557 7.380065 GCGGAATCGGTTGCAATATATTTTAAA 59.620 33.333 0.59 0.00 36.79 1.52
526 558 6.858993 GCGGAATCGGTTGCAATATATTTTAA 59.141 34.615 0.59 0.00 36.79 1.52
527 559 6.017026 TGCGGAATCGGTTGCAATATATTTTA 60.017 34.615 0.59 0.00 33.80 1.52
528 560 5.219633 GCGGAATCGGTTGCAATATATTTT 58.780 37.500 0.59 0.00 36.79 1.82
529 561 4.277174 TGCGGAATCGGTTGCAATATATTT 59.723 37.500 0.59 0.00 33.80 1.40
530 562 3.818210 TGCGGAATCGGTTGCAATATATT 59.182 39.130 0.59 2.53 33.80 1.28
531 563 3.407698 TGCGGAATCGGTTGCAATATAT 58.592 40.909 0.59 0.00 33.80 0.86
633 736 7.450323 CCCATACATTTAATCCCTCCGTTTTAT 59.550 37.037 0.00 0.00 0.00 1.40
635 738 5.596772 CCCATACATTTAATCCCTCCGTTTT 59.403 40.000 0.00 0.00 0.00 2.43
636 739 5.137551 CCCATACATTTAATCCCTCCGTTT 58.862 41.667 0.00 0.00 0.00 3.60
704 812 3.134623 TCTGAATACGAGTCGGGGTAGTA 59.865 47.826 18.30 0.00 0.00 1.82
705 813 2.092753 TCTGAATACGAGTCGGGGTAGT 60.093 50.000 18.30 0.00 0.00 2.73
706 814 2.548904 CTCTGAATACGAGTCGGGGTAG 59.451 54.545 18.30 8.41 0.00 3.18
753 861 1.303282 GGGGCACGGAGAGGAAAAT 59.697 57.895 0.00 0.00 0.00 1.82
970 1084 1.010797 CAATGCTCGAAATCGCGGG 60.011 57.895 6.13 0.00 39.60 6.13
973 1087 1.531883 GGAACCAATGCTCGAAATCGC 60.532 52.381 0.00 0.00 39.60 4.58
1088 1207 4.803426 CGAGACCAGCCGACAGCC 62.803 72.222 0.00 0.00 45.47 4.85
1167 1286 3.494336 CTGCTGCGCCTTCTTCGG 61.494 66.667 4.18 0.00 0.00 4.30
1293 1412 1.966451 CCTTGTCCAAGTGGCGACC 60.966 63.158 6.31 0.00 36.72 4.79
1472 1591 3.251729 CCAAGCAGACCCATAAATCATCG 59.748 47.826 0.00 0.00 0.00 3.84
1481 1600 1.001641 GCAGTCCAAGCAGACCCAT 60.002 57.895 0.00 0.00 37.49 4.00
1595 1714 3.615496 ACGCGACAGTTGGTTTATCATAC 59.385 43.478 15.93 0.00 0.00 2.39
1635 1754 2.274437 CAACTCGATGGACACCTCATG 58.726 52.381 0.00 0.00 0.00 3.07
1691 1810 1.512926 CACCAAGAACCACCTTCTCG 58.487 55.000 0.00 0.00 38.37 4.04
1712 1831 3.022557 ACCAATGCATTGCTATCCACT 57.977 42.857 30.15 4.96 36.48 4.00
1896 2015 4.354587 GAAGCACTTGTTTCCACAAAGAG 58.645 43.478 0.00 0.00 42.53 2.85
1898 2017 3.108144 CGAAGCACTTGTTTCCACAAAG 58.892 45.455 0.79 0.00 42.53 2.77
1964 2083 5.649782 ACTGAGGGTATTTTGAGCAAATG 57.350 39.130 0.00 0.00 35.71 2.32
2322 2444 1.810532 CAGGAGACACTCGGGTAGC 59.189 63.158 0.00 0.00 0.00 3.58
2518 2645 8.834465 CAAGATAATCTAACCAGGAAATGTCAG 58.166 37.037 0.00 0.00 0.00 3.51
2582 2709 3.554692 GCTCCGGTCGAACATGCG 61.555 66.667 0.00 0.00 0.00 4.73
2594 2721 1.039785 TCCAGATCTGTCCTGCTCCG 61.040 60.000 21.11 2.94 0.00 4.63
2891 3021 3.554934 ACCAAAACAGTCATCTTGCTCA 58.445 40.909 0.00 0.00 0.00 4.26
2894 3024 4.437390 CCGATACCAAAACAGTCATCTTGC 60.437 45.833 0.00 0.00 0.00 4.01
2940 3122 8.994170 AGTTTCTTTCTTAGCATCAGAAGTTAC 58.006 33.333 0.00 0.00 31.84 2.50
2969 3151 6.544931 CCATCACATCAATATCTCCAGTTGTT 59.455 38.462 0.00 0.00 0.00 2.83
3114 3296 2.299867 GTGCAACAGGGATGGAACAATT 59.700 45.455 0.00 0.00 38.74 2.32
3191 3373 0.318441 TCTCCGCACTGTCCTTTCTG 59.682 55.000 0.00 0.00 0.00 3.02
3238 3420 2.301296 CAGCTCGGGACCTTATCATCAT 59.699 50.000 0.00 0.00 0.00 2.45
3269 3451 4.699257 GCCATAATCTGATCAATGTCCTCC 59.301 45.833 0.00 0.00 0.00 4.30
3344 3526 2.361757 CAAAGGAGGATTTGCACACACA 59.638 45.455 0.00 0.00 33.71 3.72
3360 3542 3.803778 GTGTTTTCAGCATCAACCAAAGG 59.196 43.478 0.00 0.00 0.00 3.11
3419 3601 4.202419 TGGTATGTTTTACTGTCTGGCTGT 60.202 41.667 0.00 0.00 0.00 4.40
3456 3638 2.295349 CCACTGCTGAGCTGTTCAAATT 59.705 45.455 14.50 0.00 38.59 1.82
3517 3699 4.083324 CCACATTATGACCATCGTTATGCC 60.083 45.833 0.00 0.00 28.47 4.40
3736 3928 2.111384 TCATTCTCTTCCTCCTTCCGG 58.889 52.381 0.00 0.00 0.00 5.14
3772 3964 7.883391 TTTTGGTTATCTTGTCCTTTGTGTA 57.117 32.000 0.00 0.00 0.00 2.90
3959 4151 3.503363 GGTCCATGTACGGTCGTATATCA 59.497 47.826 9.26 3.04 31.56 2.15
4044 4236 1.741525 TGCAGGCAAGCAGAAAACC 59.258 52.632 0.22 0.00 40.11 3.27
4129 4402 4.782019 TCATTGTGGCAAAATCCTACAC 57.218 40.909 0.00 0.00 0.00 2.90
4181 4454 5.449999 CCACCAAACTAAACAAGTGGAGAAC 60.450 44.000 0.64 0.00 46.15 3.01
4183 4456 4.080243 TCCACCAAACTAAACAAGTGGAGA 60.080 41.667 5.61 0.00 46.60 3.71
4250 4523 7.761704 TCTCTATGCTGACAAGAAACATTCTAC 59.238 37.037 0.00 0.00 39.61 2.59
4320 4594 3.428413 TGTTCTAGGGTTTTACAGCCC 57.572 47.619 0.00 0.00 45.31 5.19
4425 4699 9.537192 TGATTATGAAAAGATTTCATGCATTCC 57.463 29.630 22.24 10.05 39.30 3.01
4522 4796 4.202326 CCCCTTACTGTAGACACAAACTGT 60.202 45.833 0.00 0.00 33.22 3.55
4538 4812 2.231716 ACCCATTTTGAGCCCCTTAC 57.768 50.000 0.00 0.00 0.00 2.34
4545 4819 6.919721 TGACATACTAAAACCCATTTTGAGC 58.080 36.000 0.00 0.00 38.50 4.26
4552 4826 8.034804 GCTGAAAAATGACATACTAAAACCCAT 58.965 33.333 0.00 0.00 0.00 4.00
4644 4919 3.637229 GAGCTACACATCTAGGCACCTAA 59.363 47.826 0.00 0.00 0.00 2.69
4685 4960 7.393515 GGGTTCTAAACTTGAGGATAACACATT 59.606 37.037 0.00 0.00 0.00 2.71
4757 5032 6.271857 ACTCTCTGCCCATAAATCACAGATAT 59.728 38.462 0.00 0.00 36.82 1.63
4790 5067 9.569122 TCCAAAGTACAAGCTAATTTAAAGTCT 57.431 29.630 0.00 0.00 0.00 3.24
4800 5077 9.127277 ACAGTTAATTTCCAAAGTACAAGCTAA 57.873 29.630 0.00 0.00 0.00 3.09
4802 5079 7.582667 ACAGTTAATTTCCAAAGTACAAGCT 57.417 32.000 0.00 0.00 0.00 3.74
4846 5126 7.116948 CGATAAGTGGTGATGTCATTATCCTTC 59.883 40.741 7.80 0.00 0.00 3.46
4912 5192 3.423539 ACATATGCGACATAATGCCCT 57.576 42.857 1.58 0.00 0.00 5.19
5092 5372 2.768527 CCATGAGTAGGTCACCAGACAT 59.231 50.000 0.00 0.00 46.80 3.06
5303 5586 3.426159 CGATTTCAGACAATTTCCACCCG 60.426 47.826 0.00 0.00 0.00 5.28
5392 5675 4.099266 AGGCTGTCTATGACTGACTGATTC 59.901 45.833 11.28 0.00 45.73 2.52
5394 5677 3.641046 AGGCTGTCTATGACTGACTGAT 58.359 45.455 11.28 0.00 45.73 2.90
5714 5998 5.954150 ACATGTCTCTGCAATCCCTAAAATT 59.046 36.000 0.00 0.00 0.00 1.82
5715 5999 5.513233 ACATGTCTCTGCAATCCCTAAAAT 58.487 37.500 0.00 0.00 0.00 1.82
5728 6012 4.876125 ACTGTACACAAGACATGTCTCTG 58.124 43.478 28.01 25.75 41.46 3.35
5731 6015 4.099419 TGTGACTGTACACAAGACATGTCT 59.901 41.667 22.89 22.89 45.81 3.41
5732 6016 4.368315 TGTGACTGTACACAAGACATGTC 58.632 43.478 18.47 18.47 45.81 3.06
5952 6259 1.135460 CGTTCCGGTTCACCTCTAGAC 60.135 57.143 0.00 0.00 0.00 2.59
5994 6301 0.178944 TCTTCAGGAAGGGGTCGTCA 60.179 55.000 9.03 0.00 38.88 4.35
5995 6302 0.974383 TTCTTCAGGAAGGGGTCGTC 59.026 55.000 9.03 0.00 38.88 4.20
6006 6313 0.251341 CAACCACCCCCTTCTTCAGG 60.251 60.000 0.00 0.00 43.49 3.86
6007 6314 0.251341 CCAACCACCCCCTTCTTCAG 60.251 60.000 0.00 0.00 0.00 3.02
6008 6315 1.850549 CCAACCACCCCCTTCTTCA 59.149 57.895 0.00 0.00 0.00 3.02
6009 6316 1.606601 GCCAACCACCCCCTTCTTC 60.607 63.158 0.00 0.00 0.00 2.87
6010 6317 2.526110 GCCAACCACCCCCTTCTT 59.474 61.111 0.00 0.00 0.00 2.52
6011 6318 3.966543 CGCCAACCACCCCCTTCT 61.967 66.667 0.00 0.00 0.00 2.85
6012 6319 3.961414 TCGCCAACCACCCCCTTC 61.961 66.667 0.00 0.00 0.00 3.46
6013 6320 4.280019 GTCGCCAACCACCCCCTT 62.280 66.667 0.00 0.00 0.00 3.95
6031 6338 2.819154 CGTCATGTGGATGCGCCA 60.819 61.111 4.18 0.00 46.96 5.69
6036 6343 2.528743 GGCGAGCGTCATGTGGATG 61.529 63.158 0.00 0.00 35.52 3.51
6037 6344 2.202932 GGCGAGCGTCATGTGGAT 60.203 61.111 0.00 0.00 0.00 3.41
6038 6345 4.794439 CGGCGAGCGTCATGTGGA 62.794 66.667 0.00 0.00 0.00 4.02
6040 6347 3.842126 CACGGCGAGCGTCATGTG 61.842 66.667 16.62 0.00 0.00 3.21
6058 6365 4.767255 GACGGTGGCTGGAGCAGG 62.767 72.222 0.20 0.00 44.36 4.85
6059 6366 3.655810 GAGACGGTGGCTGGAGCAG 62.656 68.421 0.20 0.00 44.36 4.24
6060 6367 3.695606 GAGACGGTGGCTGGAGCA 61.696 66.667 0.20 0.00 44.36 4.26
6061 6368 4.803426 CGAGACGGTGGCTGGAGC 62.803 72.222 0.00 0.00 41.14 4.70
6062 6369 4.803426 GCGAGACGGTGGCTGGAG 62.803 72.222 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.