Multiple sequence alignment - TraesCS3B01G426600

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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 TraesCS3B01G426600 chr3B 100.000 5129 0 0 1 5129 665252213 665257341 0 9472
1 TraesCS3B01G426600 chr3D 93.310 4768 201 55 136 4842 503851581 503856291 0 6929
2 TraesCS3B01G426600 chr3A 91.071 5208 265 104 1 5061 642153303 642158457 0 6857


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 TraesCS3B01G426600 chr3B 665252213 665257341 5128 False 9472 9472 100.000 1 5129 1 chr3B.!!$F1 5128
1 TraesCS3B01G426600 chr3D 503851581 503856291 4710 False 6929 6929 93.310 136 4842 1 chr3D.!!$F1 4706
2 TraesCS3B01G426600 chr3A 642153303 642158457 5154 False 6857 6857 91.071 1 5061 1 chr3A.!!$F1 5060

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
379 403 0.106149 AGGTTCACGCGAGGAAAAGT 59.894 50.000 15.93 1.53 0.0 2.66 F
744 794 0.674895 ATGGAAAGGTCGTGCTCAGC 60.675 55.000 0.00 0.00 0.0 4.26 F
984 1035 1.005097 TGCAATCAGATGGTGGAGCTT 59.995 47.619 0.00 0.00 0.0 3.74 F
2542 2624 0.911053 TGCAGCTGATGTATGACCCA 59.089 50.000 20.43 0.00 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 2241 0.248843 AGCTTCTTGAGGGCTCTTCG 59.751 55.000 0.00 0.0 0.00 3.79 R
2542 2624 4.989168 GTCTGACCAGACGAAACAATAACT 59.011 41.667 13.59 0.0 46.93 2.24 R
2982 3064 0.524862 CTGCTCAACCAATCTGCACC 59.475 55.000 0.00 0.0 0.00 5.01 R
4446 4565 0.385751 CATGCAGAGGGTCGTCGTAT 59.614 55.000 0.00 0.0 0.00 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
134 138 1.073177 ACGGTGCGTCTTTATTTCGG 58.927 50.000 0.00 0.00 33.69 4.30
145 149 4.265792 GTCTTTATTTCGGCTCGTCTCTTC 59.734 45.833 0.00 0.00 0.00 2.87
170 174 3.099211 ATGGATCGCTGCTCGCCTT 62.099 57.895 0.00 0.00 38.27 4.35
171 175 2.512515 GGATCGCTGCTCGCCTTT 60.513 61.111 0.00 0.00 38.27 3.11
172 176 2.109126 GGATCGCTGCTCGCCTTTT 61.109 57.895 0.00 0.00 38.27 2.27
173 177 1.648467 GGATCGCTGCTCGCCTTTTT 61.648 55.000 0.00 0.00 38.27 1.94
189 193 1.068921 TTTTTCCTTTGCCCGCTGC 59.931 52.632 0.00 0.00 41.77 5.25
190 194 2.376228 TTTTTCCTTTGCCCGCTGCC 62.376 55.000 0.00 0.00 40.16 4.85
208 212 1.179814 CCCGGTCCGAGAGATTAGGG 61.180 65.000 14.39 0.00 0.00 3.53
209 213 1.660917 CGGTCCGAGAGATTAGGGC 59.339 63.158 4.91 0.00 0.00 5.19
217 221 3.254657 CCGAGAGATTAGGGCTTAGAGTG 59.745 52.174 0.00 0.00 0.00 3.51
223 227 4.343814 AGATTAGGGCTTAGAGTGAGCTTC 59.656 45.833 0.00 0.00 40.01 3.86
272 295 1.227764 CTGAGCTGCCTGTGTGTGT 60.228 57.895 0.00 0.00 0.00 3.72
276 299 1.103398 AGCTGCCTGTGTGTGTTTCC 61.103 55.000 0.00 0.00 0.00 3.13
290 313 2.554462 GTGTTTCCCTGCTCCTCTTTTC 59.446 50.000 0.00 0.00 0.00 2.29
294 317 0.987294 CCCTGCTCCTCTTTTCCTGA 59.013 55.000 0.00 0.00 0.00 3.86
359 383 4.120331 GTGCGGCTTCACCATGCC 62.120 66.667 0.00 0.00 45.25 4.40
365 389 1.885871 GCTTCACCATGCCAGGTTC 59.114 57.895 0.00 0.00 40.77 3.62
372 396 2.434884 ATGCCAGGTTCACGCGAG 60.435 61.111 15.93 4.59 0.00 5.03
377 401 0.882927 CCAGGTTCACGCGAGGAAAA 60.883 55.000 15.93 0.00 0.00 2.29
379 403 0.106149 AGGTTCACGCGAGGAAAAGT 59.894 50.000 15.93 1.53 0.00 2.66
385 409 0.680061 ACGCGAGGAAAAGTCTCCTT 59.320 50.000 15.93 0.00 46.33 3.36
414 438 5.481122 TGGATTTCTGGCATTTCATTTGAGA 59.519 36.000 0.00 0.00 0.00 3.27
418 442 4.797471 TCTGGCATTTCATTTGAGAAACG 58.203 39.130 0.00 0.00 40.03 3.60
547 571 1.048601 TGTCAGGCCGAGAGAAACTT 58.951 50.000 0.00 0.00 0.00 2.66
550 574 1.691976 TCAGGCCGAGAGAAACTTGAA 59.308 47.619 0.00 0.00 31.94 2.69
552 576 1.416401 AGGCCGAGAGAAACTTGAACA 59.584 47.619 0.00 0.00 31.94 3.18
553 577 1.801178 GGCCGAGAGAAACTTGAACAG 59.199 52.381 0.00 0.00 31.94 3.16
595 622 3.123392 TCTTTTGGGTTTTCTTGGGGT 57.877 42.857 0.00 0.00 0.00 4.95
663 712 1.387737 CCCCTTGGATTTGCTGGGA 59.612 57.895 0.00 0.00 40.23 4.37
742 792 0.955428 GCATGGAAAGGTCGTGCTCA 60.955 55.000 0.00 0.00 34.79 4.26
743 793 1.081892 CATGGAAAGGTCGTGCTCAG 58.918 55.000 0.00 0.00 0.00 3.35
744 794 0.674895 ATGGAAAGGTCGTGCTCAGC 60.675 55.000 0.00 0.00 0.00 4.26
856 906 4.699522 GGTTCCGGGAGCGTTGCT 62.700 66.667 0.00 0.00 43.88 3.91
866 916 1.398390 GGAGCGTTGCTTTGTCCTATG 59.602 52.381 0.00 0.00 39.88 2.23
984 1035 1.005097 TGCAATCAGATGGTGGAGCTT 59.995 47.619 0.00 0.00 0.00 3.74
986 1037 2.877168 GCAATCAGATGGTGGAGCTTAG 59.123 50.000 0.00 0.00 0.00 2.18
1086 1137 7.595819 ACTGTGGTTTTATCTTGATTTCCAA 57.404 32.000 0.00 0.00 0.00 3.53
1184 1245 6.515272 TGAGATCTATTTGGGTTTGCTTTC 57.485 37.500 0.00 0.00 0.00 2.62
1296 1373 8.504005 CAGTTACAAATTACTGGAACCTTGTAG 58.496 37.037 2.21 0.00 40.50 2.74
1408 1486 4.000988 TCATCCTGCGGTTTCTAAACTTC 58.999 43.478 5.62 0.00 38.89 3.01
1648 1729 9.474920 TTGCTTTTCAATATTTGTGTCTTTAGG 57.525 29.630 0.00 0.00 0.00 2.69
1867 1948 3.558033 TGTTTGGTTTCCTTGGACTACC 58.442 45.455 11.25 11.25 0.00 3.18
2159 2241 1.378250 AGGGCAGCATTGACTGAGC 60.378 57.895 10.89 0.00 40.25 4.26
2293 2375 1.759445 AGTGAAGCAGGCGATGATACT 59.241 47.619 0.00 0.00 0.00 2.12
2542 2624 0.911053 TGCAGCTGATGTATGACCCA 59.089 50.000 20.43 0.00 0.00 4.51
2587 2669 2.624316 ATGAGCGTGTTTGCATTGAG 57.376 45.000 0.00 0.00 37.31 3.02
2869 2951 5.510009 GGAGAACGAGAGAAAAGAAGAACCT 60.510 44.000 0.00 0.00 0.00 3.50
2982 3064 4.213270 TGAAAGAAACAACATACTGAGCCG 59.787 41.667 0.00 0.00 0.00 5.52
3272 3358 7.841915 ACTTACCAAAAACCATTCTTGTTTG 57.158 32.000 0.00 0.00 36.14 2.93
3342 3428 0.387202 AGCAGATGACCTCGAATCCG 59.613 55.000 0.00 0.00 37.07 4.18
3426 3512 2.037847 ATTGCTTCCACCCAGGCC 59.962 61.111 0.00 0.00 37.29 5.19
3430 3516 3.953775 CTTCCACCCAGGCCGTGT 61.954 66.667 8.25 0.00 37.29 4.49
3687 3773 2.203126 GCCGGCAGGAAGGAGATG 60.203 66.667 24.80 0.00 41.02 2.90
3813 3899 3.422303 GACAAGTGCATCGCGCCA 61.422 61.111 0.00 0.00 40.23 5.69
4132 4236 1.133450 CCCTCTACCAGTGCTAGCCTA 60.133 57.143 13.29 0.00 0.00 3.93
4133 4237 2.235016 CCTCTACCAGTGCTAGCCTAG 58.765 57.143 13.29 4.74 0.00 3.02
4166 4270 0.189574 TTTTGGGGCCTGGTTCATCA 59.810 50.000 0.84 0.00 0.00 3.07
4167 4271 0.413037 TTTGGGGCCTGGTTCATCAT 59.587 50.000 0.84 0.00 0.00 2.45
4168 4272 0.033208 TTGGGGCCTGGTTCATCATC 60.033 55.000 0.84 0.00 0.00 2.92
4209 4313 7.155328 TGTACATCTCCTCTTTCTTGTTTCTC 58.845 38.462 0.00 0.00 0.00 2.87
4224 4328 4.207165 TGTTTCTCTTTTCCTTGGGTCTG 58.793 43.478 0.00 0.00 0.00 3.51
4233 4337 1.743252 CTTGGGTCTGCTTCCGCTC 60.743 63.158 0.00 0.00 36.97 5.03
4276 4384 5.526434 TCCTTTGGGTTTGGGTTAAGTAAA 58.474 37.500 0.00 0.00 0.00 2.01
4277 4385 5.962641 TCCTTTGGGTTTGGGTTAAGTAAAA 59.037 36.000 0.00 0.00 0.00 1.52
4299 4407 4.551388 AGTTGAAAGAGACTAGTGCTTCG 58.449 43.478 0.00 0.00 0.00 3.79
4360 4468 0.677731 TCTTTGCCGCCTTCTCATGG 60.678 55.000 0.00 0.00 0.00 3.66
4401 4509 1.009829 CCTGCCTTGTTACGAGATGC 58.990 55.000 0.31 0.00 0.00 3.91
4403 4511 1.929836 CTGCCTTGTTACGAGATGCTC 59.070 52.381 0.31 0.00 0.00 4.26
4406 4514 2.815478 CCTTGTTACGAGATGCTCCTC 58.185 52.381 0.31 0.00 0.00 3.71
4407 4515 2.428890 CCTTGTTACGAGATGCTCCTCT 59.571 50.000 0.31 0.00 0.00 3.69
4408 4516 3.490078 CCTTGTTACGAGATGCTCCTCTC 60.490 52.174 0.31 3.68 38.64 3.20
4416 4535 3.734597 CGAGATGCTCCTCTCTTTCAGTG 60.735 52.174 9.00 0.00 39.65 3.66
4442 4561 3.668596 ACCGTTTGTTCTCTTTTGTCG 57.331 42.857 0.00 0.00 0.00 4.35
4446 4565 5.524646 ACCGTTTGTTCTCTTTTGTCGATAA 59.475 36.000 0.00 0.00 0.00 1.75
4447 4566 6.204108 ACCGTTTGTTCTCTTTTGTCGATAAT 59.796 34.615 0.00 0.00 0.00 1.28
4460 4579 3.117491 TCGATAATACGACGACCCTCT 57.883 47.619 0.00 0.00 37.37 3.69
4461 4580 2.804527 TCGATAATACGACGACCCTCTG 59.195 50.000 0.00 0.00 37.37 3.35
4462 4581 2.664971 CGATAATACGACGACCCTCTGC 60.665 54.545 0.00 0.00 35.09 4.26
4463 4582 1.753930 TAATACGACGACCCTCTGCA 58.246 50.000 0.00 0.00 0.00 4.41
4501 4623 0.325933 CTCCATGGTCCTGTGAAGCA 59.674 55.000 12.58 0.00 0.00 3.91
4573 4695 2.905075 TGTTCACGATAATCCTGCTGG 58.095 47.619 2.58 2.58 0.00 4.85
4591 4713 0.326264 GGTTGCTCATCCAGGTGAGT 59.674 55.000 9.57 0.00 45.80 3.41
4613 4736 2.176798 TGGGTTCCTTTTGTCCTGTCAT 59.823 45.455 0.00 0.00 0.00 3.06
4627 4753 3.134623 TCCTGTCATTGATTATCGGCTGT 59.865 43.478 0.00 0.00 0.00 4.40
4671 4802 1.067060 CCTCGCCGAGATAATGACACA 59.933 52.381 17.19 0.00 0.00 3.72
4672 4803 2.120232 CTCGCCGAGATAATGACACAC 58.880 52.381 8.82 0.00 0.00 3.82
4673 4804 1.749063 TCGCCGAGATAATGACACACT 59.251 47.619 0.00 0.00 0.00 3.55
4674 4805 1.854743 CGCCGAGATAATGACACACTG 59.145 52.381 0.00 0.00 0.00 3.66
4676 4807 2.860735 GCCGAGATAATGACACACTGAC 59.139 50.000 0.00 0.00 0.00 3.51
4677 4808 3.676049 GCCGAGATAATGACACACTGACA 60.676 47.826 0.00 0.00 0.00 3.58
4678 4809 4.686972 CCGAGATAATGACACACTGACAT 58.313 43.478 0.00 0.00 34.44 3.06
4679 4810 4.505556 CCGAGATAATGACACACTGACATG 59.494 45.833 0.00 0.00 33.39 3.21
4680 4811 4.505556 CGAGATAATGACACACTGACATGG 59.494 45.833 0.00 0.00 33.39 3.66
4681 4812 4.194640 AGATAATGACACACTGACATGGC 58.805 43.478 0.00 0.00 33.39 4.40
4682 4813 1.538047 AATGACACACTGACATGGCC 58.462 50.000 0.00 0.00 33.39 5.36
4683 4814 0.401356 ATGACACACTGACATGGCCA 59.599 50.000 8.56 8.56 31.98 5.36
4684 4815 0.250424 TGACACACTGACATGGCCAG 60.250 55.000 13.05 13.67 37.64 4.85
4685 4816 0.957395 GACACACTGACATGGCCAGG 60.957 60.000 17.55 17.55 36.03 4.45
4704 4835 2.361104 GCCAGGGCCGACATGAAA 60.361 61.111 0.00 0.00 31.04 2.69
4761 4898 1.661509 CTTGCGTCTGACAGCACGA 60.662 57.895 22.95 10.91 43.69 4.35
4763 4900 0.599991 TTGCGTCTGACAGCACGAAT 60.600 50.000 22.95 0.00 43.69 3.34
4765 4902 1.959899 GCGTCTGACAGCACGAATGG 61.960 60.000 22.95 3.47 38.32 3.16
4766 4903 0.667487 CGTCTGACAGCACGAATGGT 60.667 55.000 17.22 0.00 38.32 3.55
4767 4904 1.071605 GTCTGACAGCACGAATGGTC 58.928 55.000 2.24 0.00 33.06 4.02
4781 4922 4.766891 ACGAATGGTCAGGTTCATTTTCAT 59.233 37.500 0.00 0.00 34.18 2.57
4800 4941 3.403057 CACGTGCTGTCCCGTTCG 61.403 66.667 0.82 0.00 34.59 3.95
4844 4996 0.038526 TTTCGAGTTCGGCAGGAGTC 60.039 55.000 1.26 0.00 40.29 3.36
4848 5000 0.820871 GAGTTCGGCAGGAGTCTCAT 59.179 55.000 1.47 0.00 31.90 2.90
4849 5001 1.205893 GAGTTCGGCAGGAGTCTCATT 59.794 52.381 1.47 0.00 31.90 2.57
4854 5006 1.066573 CGGCAGGAGTCTCATTTCACT 60.067 52.381 1.47 0.00 0.00 3.41
4866 5018 0.034896 ATTTCACTTGGTCGAGCGGT 59.965 50.000 10.46 8.58 0.00 5.68
4871 5023 1.289066 CTTGGTCGAGCGGTTCTCA 59.711 57.895 10.46 0.00 41.98 3.27
4877 5029 1.153745 CGAGCGGTTCTCAAGGAGG 60.154 63.158 0.00 0.00 41.98 4.30
4881 5033 1.838073 GCGGTTCTCAAGGAGGGGAA 61.838 60.000 0.00 0.00 0.00 3.97
4884 5036 0.673956 GTTCTCAAGGAGGGGAACGC 60.674 60.000 0.00 0.00 43.76 4.84
4885 5037 1.838073 TTCTCAAGGAGGGGAACGCC 61.838 60.000 0.00 0.00 44.92 5.68
4886 5038 2.528127 TCAAGGAGGGGAACGCCA 60.528 61.111 10.35 0.00 44.92 5.69
4890 5047 0.105913 AAGGAGGGGAACGCCAAAAA 60.106 50.000 10.35 0.00 44.92 1.94
4909 5066 2.102357 CGCCGCTCGCTCTAAAGA 59.898 61.111 0.00 0.00 34.21 2.52
4914 5071 1.067821 CCGCTCGCTCTAAAGAGGATT 59.932 52.381 8.99 0.00 42.29 3.01
4916 5073 3.243434 CCGCTCGCTCTAAAGAGGATTTA 60.243 47.826 8.99 0.00 42.29 1.40
4920 5077 6.641314 CGCTCGCTCTAAAGAGGATTTAATTA 59.359 38.462 8.99 0.00 42.29 1.40
4921 5078 7.148885 CGCTCGCTCTAAAGAGGATTTAATTAG 60.149 40.741 8.99 0.00 42.29 1.73
4956 5113 0.882474 CGGTTATTTGTGGCGGGAAA 59.118 50.000 0.00 0.00 0.00 3.13
4957 5114 1.135517 CGGTTATTTGTGGCGGGAAAG 60.136 52.381 0.00 0.00 0.00 2.62
5077 5248 1.518302 GGGACGAGGAGGAGAAAGC 59.482 63.158 0.00 0.00 0.00 3.51
5078 5249 1.518302 GGACGAGGAGGAGAAAGCC 59.482 63.158 0.00 0.00 0.00 4.35
5079 5250 1.139947 GACGAGGAGGAGAAAGCCG 59.860 63.158 0.00 0.00 0.00 5.52
5080 5251 2.286127 GACGAGGAGGAGAAAGCCGG 62.286 65.000 0.00 0.00 0.00 6.13
5081 5252 2.188207 GAGGAGGAGAAAGCCGGC 59.812 66.667 21.89 21.89 0.00 6.13
5082 5253 3.393149 GAGGAGGAGAAAGCCGGCC 62.393 68.421 26.15 8.19 0.00 6.13
5083 5254 3.403558 GGAGGAGAAAGCCGGCCT 61.404 66.667 26.15 14.08 0.00 5.19
5084 5255 2.124942 GAGGAGAAAGCCGGCCTG 60.125 66.667 26.15 0.00 0.00 4.85
5085 5256 4.416738 AGGAGAAAGCCGGCCTGC 62.417 66.667 26.15 18.83 0.00 4.85
5086 5257 4.416738 GGAGAAAGCCGGCCTGCT 62.417 66.667 26.15 16.05 45.43 4.24
5087 5258 3.130160 GAGAAAGCCGGCCTGCTG 61.130 66.667 26.15 0.00 41.80 4.41
5088 5259 3.612247 GAGAAAGCCGGCCTGCTGA 62.612 63.158 26.15 0.00 41.80 4.26
5089 5260 2.672996 GAAAGCCGGCCTGCTGAA 60.673 61.111 26.15 0.00 41.80 3.02
5090 5261 2.203480 AAAGCCGGCCTGCTGAAA 60.203 55.556 26.15 0.00 41.80 2.69
5091 5262 1.805428 GAAAGCCGGCCTGCTGAAAA 61.805 55.000 26.15 0.00 41.80 2.29
5092 5263 1.809567 AAAGCCGGCCTGCTGAAAAG 61.810 55.000 26.15 0.00 41.80 2.27
5093 5264 2.983725 AAGCCGGCCTGCTGAAAAGT 62.984 55.000 26.15 2.30 41.80 2.66
5094 5265 2.956987 CCGGCCTGCTGAAAAGTG 59.043 61.111 0.00 0.00 0.00 3.16
5095 5266 1.600636 CCGGCCTGCTGAAAAGTGA 60.601 57.895 0.00 0.00 0.00 3.41
5096 5267 1.172180 CCGGCCTGCTGAAAAGTGAA 61.172 55.000 0.00 0.00 0.00 3.18
5097 5268 0.883833 CGGCCTGCTGAAAAGTGAAT 59.116 50.000 0.00 0.00 0.00 2.57
5098 5269 1.135575 CGGCCTGCTGAAAAGTGAATC 60.136 52.381 0.00 0.00 0.00 2.52
5099 5270 1.203287 GGCCTGCTGAAAAGTGAATCC 59.797 52.381 0.00 0.00 0.00 3.01
5100 5271 1.135575 GCCTGCTGAAAAGTGAATCCG 60.136 52.381 0.00 0.00 0.00 4.18
5101 5272 2.426522 CCTGCTGAAAAGTGAATCCGA 58.573 47.619 0.00 0.00 0.00 4.55
5102 5273 3.012518 CCTGCTGAAAAGTGAATCCGAT 58.987 45.455 0.00 0.00 0.00 4.18
5103 5274 3.441572 CCTGCTGAAAAGTGAATCCGATT 59.558 43.478 0.00 0.00 0.00 3.34
5104 5275 4.437930 CCTGCTGAAAAGTGAATCCGATTC 60.438 45.833 13.37 13.37 39.70 2.52
5105 5276 3.440173 TGCTGAAAAGTGAATCCGATTCC 59.560 43.478 16.82 9.33 38.50 3.01
5106 5277 3.440173 GCTGAAAAGTGAATCCGATTCCA 59.560 43.478 16.82 6.91 38.50 3.53
5107 5278 4.672801 GCTGAAAAGTGAATCCGATTCCAC 60.673 45.833 16.82 14.20 38.50 4.02
5108 5279 3.435327 TGAAAAGTGAATCCGATTCCACG 59.565 43.478 16.82 0.00 38.50 4.94
5109 5280 1.369625 AAGTGAATCCGATTCCACGC 58.630 50.000 16.82 6.39 38.50 5.34
5110 5281 0.462047 AGTGAATCCGATTCCACGCC 60.462 55.000 16.82 2.38 38.50 5.68
5111 5282 1.153249 TGAATCCGATTCCACGCCC 60.153 57.895 16.82 0.00 38.50 6.13
5112 5283 1.153249 GAATCCGATTCCACGCCCA 60.153 57.895 9.66 0.00 33.17 5.36
5113 5284 0.535102 GAATCCGATTCCACGCCCAT 60.535 55.000 9.66 0.00 33.17 4.00
5114 5285 0.535102 AATCCGATTCCACGCCCATC 60.535 55.000 0.00 0.00 0.00 3.51
5115 5286 2.397413 ATCCGATTCCACGCCCATCC 62.397 60.000 0.00 0.00 0.00 3.51
5116 5287 2.591715 CGATTCCACGCCCATCCC 60.592 66.667 0.00 0.00 0.00 3.85
5117 5288 2.203351 GATTCCACGCCCATCCCC 60.203 66.667 0.00 0.00 0.00 4.81
5118 5289 3.792185 GATTCCACGCCCATCCCCC 62.792 68.421 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 84 4.918201 CGGGAGGGAATGCCTCGC 62.918 72.222 24.32 24.32 41.71 5.03
101 105 2.400158 ACCGTCTCGAGCGAAGAGG 61.400 63.158 24.28 15.15 36.45 3.69
124 128 3.240861 CGAAGAGACGAGCCGAAATAAAG 59.759 47.826 1.50 0.00 35.09 1.85
127 131 1.533338 GCGAAGAGACGAGCCGAAATA 60.533 52.381 1.50 0.00 35.09 1.40
128 132 0.802607 GCGAAGAGACGAGCCGAAAT 60.803 55.000 1.50 0.00 35.09 2.17
129 133 1.443872 GCGAAGAGACGAGCCGAAA 60.444 57.895 1.50 0.00 35.09 3.46
130 134 2.178521 GCGAAGAGACGAGCCGAA 59.821 61.111 1.50 0.00 35.09 4.30
131 135 3.812019 GGCGAAGAGACGAGCCGA 61.812 66.667 1.50 0.00 40.17 5.54
171 175 1.068921 GCAGCGGGCAAAGGAAAAA 59.931 52.632 0.00 0.00 43.97 1.94
172 176 2.733945 GCAGCGGGCAAAGGAAAA 59.266 55.556 0.00 0.00 43.97 2.29
189 193 1.179814 CCCTAATCTCTCGGACCGGG 61.180 65.000 15.25 11.73 0.00 5.73
190 194 1.807495 GCCCTAATCTCTCGGACCGG 61.807 65.000 15.25 0.00 0.00 5.28
198 202 3.895041 GCTCACTCTAAGCCCTAATCTCT 59.105 47.826 0.00 0.00 33.53 3.10
272 295 2.065799 AGGAAAAGAGGAGCAGGGAAA 58.934 47.619 0.00 0.00 0.00 3.13
276 299 2.399916 CTCAGGAAAAGAGGAGCAGG 57.600 55.000 0.00 0.00 0.00 4.85
350 374 1.302431 CGTGAACCTGGCATGGTGA 60.302 57.895 9.00 0.00 40.73 4.02
359 383 0.512952 CTTTTCCTCGCGTGAACCTG 59.487 55.000 10.21 2.18 0.00 4.00
362 386 1.456165 GAGACTTTTCCTCGCGTGAAC 59.544 52.381 10.21 1.22 0.00 3.18
365 389 0.038159 AGGAGACTTTTCCTCGCGTG 60.038 55.000 5.77 2.75 44.33 5.34
379 403 2.435805 CCAGAAATCCATCGGAAGGAGA 59.564 50.000 8.09 0.00 38.83 3.71
385 409 2.734755 AATGCCAGAAATCCATCGGA 57.265 45.000 0.00 0.00 35.55 4.55
547 571 3.240134 GAGGTCGGCAGCCTGTTCA 62.240 63.158 10.54 0.00 36.29 3.18
550 574 3.005539 ATGAGGTCGGCAGCCTGT 61.006 61.111 10.54 0.00 36.29 4.00
552 576 0.687757 TAAGATGAGGTCGGCAGCCT 60.688 55.000 10.54 0.00 39.42 4.58
553 577 0.178068 TTAAGATGAGGTCGGCAGCC 59.822 55.000 0.00 0.00 0.00 4.85
663 712 0.108585 TGACCAAGCTCGCCTCTTTT 59.891 50.000 0.00 0.00 0.00 2.27
742 792 1.318576 CTTTCGGAAAACCACCAGCT 58.681 50.000 4.53 0.00 0.00 4.24
743 793 0.313987 CCTTTCGGAAAACCACCAGC 59.686 55.000 4.53 0.00 0.00 4.85
744 794 1.336755 CACCTTTCGGAAAACCACCAG 59.663 52.381 4.53 0.00 0.00 4.00
828 878 1.415659 TCCCGGAACCAGTACGAAAAA 59.584 47.619 0.73 0.00 0.00 1.94
856 906 2.026262 GGACTTGGGAGCATAGGACAAA 60.026 50.000 0.00 0.00 0.00 2.83
866 916 3.334054 AGGCCTGGACTTGGGAGC 61.334 66.667 3.11 0.00 0.00 4.70
984 1035 3.570125 CGTCCATGCTTGACTATCTCCTA 59.430 47.826 0.22 0.00 0.00 2.94
986 1037 2.748605 CGTCCATGCTTGACTATCTCC 58.251 52.381 0.22 0.00 0.00 3.71
1054 1105 9.739276 ATCAAGATAAAACCACAGTTAAGATGA 57.261 29.630 0.00 0.00 34.19 2.92
1083 1134 8.627403 AGCTTGAACAACAGATATTATCATTGG 58.373 33.333 17.90 5.36 34.06 3.16
1116 1167 8.947115 ACTCTTAACTACAAATAATTGCAGACC 58.053 33.333 0.00 0.00 40.34 3.85
1184 1245 9.967346 TGCTGCTATACTAAGATGTAAGTTTAG 57.033 33.333 0.00 0.00 33.18 1.85
1202 1270 7.651027 AAAATGGAATTAAGAGTGCTGCTAT 57.349 32.000 0.00 0.00 33.67 2.97
1276 1353 6.575162 AAGCTACAAGGTTCCAGTAATTTG 57.425 37.500 0.00 0.00 28.30 2.32
1327 1405 5.183904 ACCACAATTTCTTCAGATTAGGCAC 59.816 40.000 0.00 0.00 0.00 5.01
1408 1486 2.218759 CGATGAACGGGAAAATCGCTAG 59.781 50.000 0.00 0.00 35.95 3.42
1470 1548 3.069289 CAGAGCTACATGCAGTGAACAA 58.931 45.455 0.00 0.00 45.94 2.83
1537 1615 6.232692 GGGTACAACATCTTACCAAGTACAA 58.767 40.000 0.00 0.00 39.77 2.41
1653 1734 6.934056 TCAGTGCAATAGTTTGGCATTTTAT 58.066 32.000 0.00 0.00 33.22 1.40
1668 1749 8.627403 CCTGAAAGTGAATATTATCAGTGCAAT 58.373 33.333 0.00 0.00 33.33 3.56
1671 1752 6.433766 GCCTGAAAGTGAATATTATCAGTGC 58.566 40.000 0.00 0.00 33.33 4.40
1759 1840 1.076533 CTATGCTTTCGACACGCCGT 61.077 55.000 0.00 0.00 0.00 5.68
1867 1948 3.025978 ACTGGTGCATAATGTGGGATTG 58.974 45.455 0.00 0.00 0.00 2.67
2159 2241 0.248843 AGCTTCTTGAGGGCTCTTCG 59.751 55.000 0.00 0.00 0.00 3.79
2260 2342 6.215845 GCCTGCTTCACTTCTGAAAAATTTA 58.784 36.000 0.00 0.00 35.92 1.40
2542 2624 4.989168 GTCTGACCAGACGAAACAATAACT 59.011 41.667 13.59 0.00 46.93 2.24
2587 2669 5.807011 GCTGTGACCATCATTAAACCATTTC 59.193 40.000 0.00 0.00 0.00 2.17
2869 2951 2.253758 GCCTGACTCGCTGTTTGCA 61.254 57.895 0.00 0.00 43.06 4.08
2881 2963 2.551459 GCTATCATCCAATGTGCCTGAC 59.449 50.000 0.00 0.00 0.00 3.51
2982 3064 0.524862 CTGCTCAACCAATCTGCACC 59.475 55.000 0.00 0.00 0.00 5.01
3022 3104 1.139654 TGGATCCTTGCTTCCTCATCG 59.860 52.381 14.23 0.00 32.95 3.84
3248 3334 7.390823 ACAAACAAGAATGGTTTTTGGTAAGT 58.609 30.769 0.00 0.00 32.99 2.24
3258 3344 7.595311 GTTTCTGAAACAAACAAGAATGGTT 57.405 32.000 24.32 0.00 41.04 3.67
3272 3358 4.640647 ACAGAAGTCCCTTGTTTCTGAAAC 59.359 41.667 22.94 22.94 46.71 2.78
3363 3449 2.093606 GGAAAGGTTAAGGTAGAGCGCT 60.094 50.000 11.27 11.27 0.00 5.92
4132 4236 3.457329 AAAACCCTGCCTGCCTGCT 62.457 57.895 0.00 0.00 0.00 4.24
4133 4237 2.919328 AAAACCCTGCCTGCCTGC 60.919 61.111 0.00 0.00 0.00 4.85
4134 4238 2.576832 CCAAAACCCTGCCTGCCTG 61.577 63.158 0.00 0.00 0.00 4.85
4135 4239 2.203684 CCAAAACCCTGCCTGCCT 60.204 61.111 0.00 0.00 0.00 4.75
4136 4240 3.313524 CCCAAAACCCTGCCTGCC 61.314 66.667 0.00 0.00 0.00 4.85
4166 4270 7.894897 AGATGTACAGATCCTACTGATGATGAT 59.105 37.037 0.33 0.00 40.63 2.45
4167 4271 7.237255 AGATGTACAGATCCTACTGATGATGA 58.763 38.462 0.33 0.00 40.63 2.92
4168 4272 7.362834 GGAGATGTACAGATCCTACTGATGATG 60.363 44.444 17.82 0.00 40.63 3.07
4209 4313 1.889170 GGAAGCAGACCCAAGGAAAAG 59.111 52.381 0.00 0.00 0.00 2.27
4250 4354 1.128200 AACCCAAACCCAAAGGAAGC 58.872 50.000 0.00 0.00 36.73 3.86
4276 4384 4.985409 CGAAGCACTAGTCTCTTTCAACTT 59.015 41.667 7.98 0.00 0.00 2.66
4277 4385 4.038162 ACGAAGCACTAGTCTCTTTCAACT 59.962 41.667 7.98 0.00 0.00 3.16
4360 4468 7.010552 GCAGGCTATATATACATTGTACAGTGC 59.989 40.741 17.45 1.11 0.00 4.40
4401 4509 3.674528 TGCTTCACTGAAAGAGAGGAG 57.325 47.619 0.00 0.00 34.30 3.69
4403 4511 2.810852 GGTTGCTTCACTGAAAGAGAGG 59.189 50.000 0.00 0.00 34.30 3.69
4406 4514 2.213499 ACGGTTGCTTCACTGAAAGAG 58.787 47.619 0.00 0.00 37.43 2.85
4407 4515 2.325583 ACGGTTGCTTCACTGAAAGA 57.674 45.000 0.00 0.00 37.43 2.52
4408 4516 3.108144 CAAACGGTTGCTTCACTGAAAG 58.892 45.455 0.00 0.00 42.29 2.62
4416 4535 3.692791 AAGAGAACAAACGGTTGCTTC 57.307 42.857 14.43 15.46 40.63 3.86
4442 4561 2.292569 TGCAGAGGGTCGTCGTATTATC 59.707 50.000 0.00 0.00 0.00 1.75
4446 4565 0.385751 CATGCAGAGGGTCGTCGTAT 59.614 55.000 0.00 0.00 0.00 3.06
4447 4566 1.807226 CATGCAGAGGGTCGTCGTA 59.193 57.895 0.00 0.00 0.00 3.43
4452 4571 1.812922 GTGAGCATGCAGAGGGTCG 60.813 63.158 21.98 0.00 33.04 4.79
4453 4572 0.743701 CAGTGAGCATGCAGAGGGTC 60.744 60.000 21.98 7.99 0.00 4.46
4454 4573 1.196766 TCAGTGAGCATGCAGAGGGT 61.197 55.000 21.98 0.00 0.00 4.34
4455 4574 0.743701 GTCAGTGAGCATGCAGAGGG 60.744 60.000 21.98 6.40 0.00 4.30
4457 4576 1.666189 CATGTCAGTGAGCATGCAGAG 59.334 52.381 21.98 4.89 36.49 3.35
4458 4577 1.002773 ACATGTCAGTGAGCATGCAGA 59.997 47.619 21.98 6.59 44.43 4.26
4459 4578 1.130561 CACATGTCAGTGAGCATGCAG 59.869 52.381 21.98 17.22 44.43 4.41
4460 4579 1.161843 CACATGTCAGTGAGCATGCA 58.838 50.000 21.98 8.64 44.43 3.96
4461 4580 0.450583 CCACATGTCAGTGAGCATGC 59.549 55.000 23.90 10.51 44.43 4.06
4462 4581 1.092348 CCCACATGTCAGTGAGCATG 58.908 55.000 23.04 23.04 45.61 4.06
4463 4582 0.679002 GCCCACATGTCAGTGAGCAT 60.679 55.000 0.00 0.00 42.10 3.79
4501 4623 2.820197 GCCTCCCTGAAGAACGAAATTT 59.180 45.455 0.00 0.00 0.00 1.82
4555 4677 3.270027 CAACCAGCAGGATTATCGTGAA 58.730 45.455 17.65 0.00 34.44 3.18
4591 4713 2.024846 TGACAGGACAAAAGGAACCCAA 60.025 45.455 0.00 0.00 0.00 4.12
4613 4736 2.287644 CGCATCAACAGCCGATAATCAA 59.712 45.455 0.00 0.00 0.00 2.57
4627 4753 2.027285 TCTGGATCCTTTCACGCATCAA 60.027 45.455 14.23 0.00 0.00 2.57
4658 4787 4.272018 GCCATGTCAGTGTGTCATTATCTC 59.728 45.833 0.00 0.00 0.00 2.75
4665 4794 0.250424 CTGGCCATGTCAGTGTGTCA 60.250 55.000 5.51 0.00 29.72 3.58
4671 4802 4.052518 GCCCCTGGCCATGTCAGT 62.053 66.667 5.51 0.00 44.06 3.41
4689 4820 0.107017 ATCCTTTCATGTCGGCCCTG 60.107 55.000 0.00 0.00 0.00 4.45
4704 4835 3.744940 TTTTTCCCTCTCATGCATCCT 57.255 42.857 0.00 0.00 0.00 3.24
4761 4898 6.458210 GTGAATGAAAATGAACCTGACCATT 58.542 36.000 0.00 0.00 34.75 3.16
4763 4900 4.023279 CGTGAATGAAAATGAACCTGACCA 60.023 41.667 0.00 0.00 0.00 4.02
4765 4902 4.911610 CACGTGAATGAAAATGAACCTGAC 59.088 41.667 10.90 0.00 0.00 3.51
4766 4903 4.556501 GCACGTGAATGAAAATGAACCTGA 60.557 41.667 22.23 0.00 0.00 3.86
4767 4904 3.670055 GCACGTGAATGAAAATGAACCTG 59.330 43.478 22.23 0.00 0.00 4.00
4800 4941 0.025513 GCACAATCATCTCGTGCGAC 59.974 55.000 0.00 0.00 45.69 5.19
4808 4949 3.745975 TCGAAACGAAAGCACAATCATCT 59.254 39.130 0.00 0.00 31.06 2.90
4844 4996 1.391485 CGCTCGACCAAGTGAAATGAG 59.609 52.381 0.00 0.00 0.00 2.90
4848 5000 0.179067 AACCGCTCGACCAAGTGAAA 60.179 50.000 0.00 0.00 0.00 2.69
4849 5001 0.599204 GAACCGCTCGACCAAGTGAA 60.599 55.000 0.00 0.00 0.00 3.18
4866 5018 1.677552 GCGTTCCCCTCCTTGAGAA 59.322 57.895 0.00 0.00 0.00 2.87
4871 5023 0.105913 TTTTTGGCGTTCCCCTCCTT 60.106 50.000 0.00 0.00 0.00 3.36
4909 5066 8.782927 GGGCCTCCTATAATCTAATTAAATCCT 58.217 37.037 0.84 0.00 0.00 3.24
4914 5071 5.427481 CGGGGGCCTCCTATAATCTAATTAA 59.573 44.000 22.56 0.00 35.33 1.40
4916 5073 3.780850 CGGGGGCCTCCTATAATCTAATT 59.219 47.826 22.56 0.00 35.33 1.40
4920 5077 0.252742 CCGGGGGCCTCCTATAATCT 60.253 60.000 22.56 0.00 35.33 2.40
4921 5078 0.546988 ACCGGGGGCCTCCTATAATC 60.547 60.000 22.56 0.00 35.33 1.75
4926 5083 0.327770 AAATAACCGGGGGCCTCCTA 60.328 55.000 22.56 5.68 35.33 2.94
4927 5084 1.621514 AAATAACCGGGGGCCTCCT 60.622 57.895 22.56 2.87 35.33 3.69
4928 5085 1.455032 CAAATAACCGGGGGCCTCC 60.455 63.158 13.54 13.54 0.00 4.30
4929 5086 1.035385 CACAAATAACCGGGGGCCTC 61.035 60.000 6.32 0.00 0.00 4.70
4930 5087 1.000145 CACAAATAACCGGGGGCCT 60.000 57.895 6.32 0.00 0.00 5.19
4931 5088 2.055633 CCACAAATAACCGGGGGCC 61.056 63.158 6.32 0.00 0.00 5.80
5061 5232 1.139947 CGGCTTTCTCCTCCTCGTC 59.860 63.158 0.00 0.00 0.00 4.20
5062 5233 2.352032 CCGGCTTTCTCCTCCTCGT 61.352 63.158 0.00 0.00 0.00 4.18
5063 5234 2.496817 CCGGCTTTCTCCTCCTCG 59.503 66.667 0.00 0.00 0.00 4.63
5064 5235 2.188207 GCCGGCTTTCTCCTCCTC 59.812 66.667 22.15 0.00 0.00 3.71
5065 5236 3.403558 GGCCGGCTTTCTCCTCCT 61.404 66.667 28.56 0.00 0.00 3.69
5066 5237 3.403558 AGGCCGGCTTTCTCCTCC 61.404 66.667 28.56 5.83 0.00 4.30
5067 5238 2.124942 CAGGCCGGCTTTCTCCTC 60.125 66.667 28.56 6.68 0.00 3.71
5068 5239 4.416738 GCAGGCCGGCTTTCTCCT 62.417 66.667 28.56 11.02 0.00 3.69
5069 5240 4.416738 AGCAGGCCGGCTTTCTCC 62.417 66.667 25.87 8.41 42.71 3.71
5070 5241 3.130160 CAGCAGGCCGGCTTTCTC 61.130 66.667 28.94 9.28 42.71 2.87
5071 5242 2.697147 TTTCAGCAGGCCGGCTTTCT 62.697 55.000 28.94 17.06 42.71 2.52
5072 5243 1.805428 TTTTCAGCAGGCCGGCTTTC 61.805 55.000 28.94 14.47 42.71 2.62
5073 5244 1.809567 CTTTTCAGCAGGCCGGCTTT 61.810 55.000 28.94 12.72 42.71 3.51
5074 5245 2.203480 TTTTCAGCAGGCCGGCTT 60.203 55.556 28.94 18.19 42.71 4.35
5076 5247 2.985847 ACTTTTCAGCAGGCCGGC 60.986 61.111 21.36 21.36 0.00 6.13
5077 5248 1.172180 TTCACTTTTCAGCAGGCCGG 61.172 55.000 0.00 0.00 0.00 6.13
5078 5249 0.883833 ATTCACTTTTCAGCAGGCCG 59.116 50.000 0.00 0.00 0.00 6.13
5079 5250 1.203287 GGATTCACTTTTCAGCAGGCC 59.797 52.381 0.00 0.00 0.00 5.19
5080 5251 1.135575 CGGATTCACTTTTCAGCAGGC 60.136 52.381 0.00 0.00 0.00 4.85
5081 5252 2.426522 TCGGATTCACTTTTCAGCAGG 58.573 47.619 0.00 0.00 0.00 4.85
5082 5253 4.437930 GGAATCGGATTCACTTTTCAGCAG 60.438 45.833 26.93 0.00 41.03 4.24
5083 5254 3.440173 GGAATCGGATTCACTTTTCAGCA 59.560 43.478 26.93 0.00 41.03 4.41
5084 5255 3.440173 TGGAATCGGATTCACTTTTCAGC 59.560 43.478 26.93 10.73 41.03 4.26
5085 5256 4.436050 CGTGGAATCGGATTCACTTTTCAG 60.436 45.833 26.93 9.36 41.03 3.02
5086 5257 3.435327 CGTGGAATCGGATTCACTTTTCA 59.565 43.478 26.93 14.59 41.03 2.69
5087 5258 3.727970 GCGTGGAATCGGATTCACTTTTC 60.728 47.826 26.93 12.52 41.03 2.29
5088 5259 2.161609 GCGTGGAATCGGATTCACTTTT 59.838 45.455 26.93 0.00 41.03 2.27
5089 5260 1.737793 GCGTGGAATCGGATTCACTTT 59.262 47.619 26.93 0.00 41.03 2.66
5090 5261 1.369625 GCGTGGAATCGGATTCACTT 58.630 50.000 26.93 0.00 41.03 3.16
5091 5262 0.462047 GGCGTGGAATCGGATTCACT 60.462 55.000 26.93 0.00 41.03 3.41
5092 5263 1.436983 GGGCGTGGAATCGGATTCAC 61.437 60.000 26.93 21.09 41.03 3.18
5093 5264 1.153249 GGGCGTGGAATCGGATTCA 60.153 57.895 26.93 13.71 41.03 2.57
5094 5265 0.535102 ATGGGCGTGGAATCGGATTC 60.535 55.000 20.01 20.01 38.55 2.52
5095 5266 0.535102 GATGGGCGTGGAATCGGATT 60.535 55.000 2.19 2.19 0.00 3.01
5096 5267 1.071471 GATGGGCGTGGAATCGGAT 59.929 57.895 0.00 0.00 0.00 4.18
5097 5268 2.504032 GATGGGCGTGGAATCGGA 59.496 61.111 0.00 0.00 0.00 4.55
5098 5269 2.591715 GGATGGGCGTGGAATCGG 60.592 66.667 0.00 0.00 0.00 4.18
5099 5270 2.591715 GGGATGGGCGTGGAATCG 60.592 66.667 0.00 0.00 0.00 3.34
5100 5271 2.203351 GGGGATGGGCGTGGAATC 60.203 66.667 0.00 0.00 0.00 2.52
5101 5272 3.820843 GGGGGATGGGCGTGGAAT 61.821 66.667 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.