Multiple sequence alignment - TraesCS2D01G426500

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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 TraesCS2D01G426500 chr2D 100.000 5299 0 0 1 5299 538725927 538731225 0.000000e+00 9786
1 TraesCS2D01G426500 chr2B 94.686 4573 144 25 206 4732 641863842 641868361 0.000000e+00 7007
2 TraesCS2D01G426500 chr2B 86.989 538 30 17 4775 5282 641868359 641868886 2.140000e-158 569
3 TraesCS2D01G426500 chr2B 90.323 124 9 2 52 174 641863219 641863340 5.490000e-35 159
4 TraesCS2D01G426500 chr2A 95.730 3185 96 11 1514 4671 681192753 681195924 0.000000e+00 5092
5 TraesCS2D01G426500 chr2A 89.956 1354 55 29 189 1515 681191209 681192508 0.000000e+00 1672
6 TraesCS2D01G426500 chr2A 83.842 557 61 16 4734 5267 681196082 681196632 2.200000e-138 503
7 TraesCS2D01G426500 chr2A 93.836 146 9 0 5 150 681191064 681191209 2.480000e-53 220


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 TraesCS2D01G426500 chr2D 538725927 538731225 5298 False 9786.000000 9786 100.000 1 5299 1 chr2D.!!$F1 5298
1 TraesCS2D01G426500 chr2B 641863219 641868886 5667 False 2578.333333 7007 90.666 52 5282 3 chr2B.!!$F1 5230
2 TraesCS2D01G426500 chr2A 681191064 681196632 5568 False 1871.750000 5092 90.841 5 5267 4 chr2A.!!$F1 5262

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
934 1452 0.108329 GAGAAAATCGGTCAGGCGGA 60.108 55.0 0.0 0.0 0.00 5.54 F
1297 1815 0.179018 GTGGGTCTGTTCTTGCTGGT 60.179 55.0 0.0 0.0 0.00 4.00 F
2228 3013 0.324943 CCATCCTGGTTTCCACTCGT 59.675 55.0 0.0 0.0 31.35 4.18 F
3255 4062 1.100510 CAATGGAGGCTGTGGATGTG 58.899 55.0 0.0 0.0 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 2865 0.764890 CTGAGACCACACCCCAAGAA 59.235 55.000 0.0 0.0 0.00 2.52 R
3255 4062 1.260544 ACCTTGCCATTTTCTCCAGC 58.739 50.000 0.0 0.0 0.00 4.85 R
3944 4751 1.684734 GGGACTAACCTCGGGAGCA 60.685 63.158 0.0 0.0 38.98 4.26 R
5127 6068 1.006922 GCCAGCAACACTTTCCAGC 60.007 57.895 0.0 0.0 0.00 4.85 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
24 25 3.274288 CACTATCCTCTTGCAAGGTTCC 58.726 50.000 25.73 0.00 37.69 3.62
33 34 3.075283 TCTTGCAAGGTTCCCCATTCTAA 59.925 43.478 25.73 0.00 0.00 2.10
45 46 7.014326 GGTTCCCCATTCTAAAACCTCATATTC 59.986 40.741 0.00 0.00 37.10 1.75
62 63 7.065923 CCTCATATTCTCATGATGCAAGTATGG 59.934 40.741 0.00 0.00 34.50 2.74
109 110 5.065218 ACAAACACAGTCAGACTTGTTGATC 59.935 40.000 21.75 0.00 33.26 2.92
119 121 3.686726 AGACTTGTTGATCGCTGGATTTC 59.313 43.478 0.00 0.00 31.51 2.17
174 176 6.519679 ACATATACGGACACTCAACTAACA 57.480 37.500 0.00 0.00 0.00 2.41
176 178 6.810182 ACATATACGGACACTCAACTAACAAC 59.190 38.462 0.00 0.00 0.00 3.32
177 179 3.814005 ACGGACACTCAACTAACAACT 57.186 42.857 0.00 0.00 0.00 3.16
178 180 4.924305 ACGGACACTCAACTAACAACTA 57.076 40.909 0.00 0.00 0.00 2.24
189 671 9.476928 ACTCAACTAACAACTACTGTATATCCT 57.523 33.333 0.00 0.00 37.23 3.24
219 701 2.806237 CGAACGAGTAGGAGGGGC 59.194 66.667 0.00 0.00 0.00 5.80
311 800 3.076104 CGGTAGCTCTCACGGAGTA 57.924 57.895 0.00 0.00 41.61 2.59
312 801 0.656785 CGGTAGCTCTCACGGAGTAC 59.343 60.000 0.00 0.00 41.61 2.73
313 802 1.023502 GGTAGCTCTCACGGAGTACC 58.976 60.000 0.00 0.00 41.61 3.34
314 803 1.408544 GGTAGCTCTCACGGAGTACCT 60.409 57.143 0.00 5.01 41.61 3.08
317 806 1.722677 CTCTCACGGAGTACCTCGC 59.277 63.158 5.52 0.00 41.61 5.03
318 807 2.037913 CTCTCACGGAGTACCTCGCG 62.038 65.000 0.00 0.00 41.61 5.87
319 808 2.359107 TCACGGAGTACCTCGCGT 60.359 61.111 5.77 0.00 41.61 6.01
356 847 2.732094 GCAGCACGCAAAGCCAAG 60.732 61.111 0.00 0.00 41.79 3.61
358 849 3.982241 AGCACGCAAAGCCAAGGC 61.982 61.111 2.02 2.02 42.33 4.35
422 913 2.626780 GGGCACGTTTCCAAGCTCC 61.627 63.158 6.01 0.00 0.00 4.70
423 914 2.626780 GGCACGTTTCCAAGCTCCC 61.627 63.158 0.00 0.00 0.00 4.30
424 915 2.626780 GCACGTTTCCAAGCTCCCC 61.627 63.158 0.00 0.00 0.00 4.81
425 916 2.032071 ACGTTTCCAAGCTCCCCG 59.968 61.111 0.00 0.00 0.00 5.73
426 917 2.746277 CGTTTCCAAGCTCCCCGG 60.746 66.667 0.00 0.00 0.00 5.73
492 1007 2.649190 GCATCTCCTTCCCTTTCCTTC 58.351 52.381 0.00 0.00 0.00 3.46
495 1010 1.132201 TCTCCTTCCCTTTCCTTCCCA 60.132 52.381 0.00 0.00 0.00 4.37
501 1016 0.926220 CCCTTTCCTTCCCATCCCCT 60.926 60.000 0.00 0.00 0.00 4.79
502 1017 0.553333 CCTTTCCTTCCCATCCCCTC 59.447 60.000 0.00 0.00 0.00 4.30
786 1303 2.294078 CCTCCGGTTTGCTCCCTCT 61.294 63.158 0.00 0.00 0.00 3.69
791 1308 0.610687 CGGTTTGCTCCCTCTTCTCT 59.389 55.000 0.00 0.00 0.00 3.10
900 1418 1.821061 CTCTCAGGACAAGGCCGTGT 61.821 60.000 25.07 25.07 0.00 4.49
934 1452 0.108329 GAGAAAATCGGTCAGGCGGA 60.108 55.000 0.00 0.00 0.00 5.54
1049 1567 0.647925 GGCAAGCTCTCGATCGAAAC 59.352 55.000 19.92 11.10 0.00 2.78
1120 1638 2.210116 GAGTTGACCGTTTGCTTCAGA 58.790 47.619 0.00 0.00 0.00 3.27
1123 1641 3.632145 AGTTGACCGTTTGCTTCAGAAAT 59.368 39.130 0.00 0.00 0.00 2.17
1246 1764 5.359009 AGGTGCTTGTTCTGAATTATCATGG 59.641 40.000 0.00 0.00 34.37 3.66
1291 1809 0.923358 TGGTTGGTGGGTCTGTTCTT 59.077 50.000 0.00 0.00 0.00 2.52
1292 1810 1.318576 GGTTGGTGGGTCTGTTCTTG 58.681 55.000 0.00 0.00 0.00 3.02
1293 1811 0.668535 GTTGGTGGGTCTGTTCTTGC 59.331 55.000 0.00 0.00 0.00 4.01
1294 1812 0.550914 TTGGTGGGTCTGTTCTTGCT 59.449 50.000 0.00 0.00 0.00 3.91
1295 1813 0.179020 TGGTGGGTCTGTTCTTGCTG 60.179 55.000 0.00 0.00 0.00 4.41
1296 1814 0.890996 GGTGGGTCTGTTCTTGCTGG 60.891 60.000 0.00 0.00 0.00 4.85
1297 1815 0.179018 GTGGGTCTGTTCTTGCTGGT 60.179 55.000 0.00 0.00 0.00 4.00
1298 1816 1.071699 GTGGGTCTGTTCTTGCTGGTA 59.928 52.381 0.00 0.00 0.00 3.25
1299 1817 1.985159 TGGGTCTGTTCTTGCTGGTAT 59.015 47.619 0.00 0.00 0.00 2.73
1300 1818 2.027192 TGGGTCTGTTCTTGCTGGTATC 60.027 50.000 0.00 0.00 0.00 2.24
1301 1819 2.633488 GGTCTGTTCTTGCTGGTATCC 58.367 52.381 0.00 0.00 0.00 2.59
1302 1820 2.237392 GGTCTGTTCTTGCTGGTATCCT 59.763 50.000 0.00 0.00 0.00 3.24
1303 1821 3.526534 GTCTGTTCTTGCTGGTATCCTC 58.473 50.000 0.00 0.00 0.00 3.71
1304 1822 2.501723 TCTGTTCTTGCTGGTATCCTCC 59.498 50.000 0.00 0.00 0.00 4.30
1305 1823 2.503356 CTGTTCTTGCTGGTATCCTCCT 59.497 50.000 0.00 0.00 0.00 3.69
1306 1824 2.912956 TGTTCTTGCTGGTATCCTCCTT 59.087 45.455 0.00 0.00 0.00 3.36
1307 1825 3.274288 GTTCTTGCTGGTATCCTCCTTG 58.726 50.000 0.00 0.00 0.00 3.61
1336 1871 3.302365 TTCATGCTTAAGTTGCTTGGC 57.698 42.857 4.02 0.00 36.59 4.52
1346 1881 2.944129 AGTTGCTTGGCCAGTAGAAAA 58.056 42.857 5.11 0.00 0.00 2.29
1395 1930 3.620929 TCTATCTAATGTCCGACGCAC 57.379 47.619 0.00 0.00 0.00 5.34
1422 1957 2.032290 CCTAACACTCATGATGCATGCG 60.032 50.000 14.09 0.00 41.18 4.73
1484 2021 5.701290 GCTTGGACATTAGTAGAAAGTGTGT 59.299 40.000 0.00 0.00 0.00 3.72
1515 2052 9.099071 ACTGCTTTTGGATCTAGTATGATCTAT 57.901 33.333 0.00 0.00 41.72 1.98
1516 2053 9.585099 CTGCTTTTGGATCTAGTATGATCTATC 57.415 37.037 0.00 0.00 41.72 2.08
1517 2054 8.246871 TGCTTTTGGATCTAGTATGATCTATCG 58.753 37.037 0.00 0.00 41.72 2.92
1548 2331 1.941975 TGCCTAACACATGATGCATCG 59.058 47.619 21.34 10.83 0.00 3.84
1826 2611 9.836864 TGACTGATGCTATATGAATAACAAGTT 57.163 29.630 0.00 0.00 0.00 2.66
1990 2775 2.945447 TGCTGCTATCATTTGTTGGC 57.055 45.000 0.00 0.00 0.00 4.52
2080 2865 6.841601 TGTTGGAATGCTAATAGGAGCTTAT 58.158 36.000 0.00 0.00 43.27 1.73
2153 2938 4.936891 ACTTCTTTCATGCAACTTTGTCC 58.063 39.130 0.00 0.00 0.00 4.02
2228 3013 0.324943 CCATCCTGGTTTCCACTCGT 59.675 55.000 0.00 0.00 31.35 4.18
2294 3079 4.884164 GCAAAGCTCTGATGTTAATACCCT 59.116 41.667 0.00 0.00 0.00 4.34
2295 3080 5.358160 GCAAAGCTCTGATGTTAATACCCTT 59.642 40.000 0.00 0.00 0.00 3.95
2296 3081 6.127619 GCAAAGCTCTGATGTTAATACCCTTT 60.128 38.462 0.00 0.00 0.00 3.11
2299 3084 9.528489 AAAGCTCTGATGTTAATACCCTTTTTA 57.472 29.630 0.00 0.00 0.00 1.52
2300 3085 9.528489 AAGCTCTGATGTTAATACCCTTTTTAA 57.472 29.630 0.00 0.00 0.00 1.52
2301 3086 9.528489 AGCTCTGATGTTAATACCCTTTTTAAA 57.472 29.630 0.00 0.00 0.00 1.52
2429 3214 7.826690 TGCATAAACCTTACCTGATTCTTTTC 58.173 34.615 0.00 0.00 0.00 2.29
2834 3619 8.379457 ACATCACTTTGGAAAGTAACTTCTAC 57.621 34.615 4.47 0.00 46.89 2.59
2945 3751 1.134670 GGTCCCTCTGTATCTGCACAC 60.135 57.143 0.00 0.00 0.00 3.82
3255 4062 1.100510 CAATGGAGGCTGTGGATGTG 58.899 55.000 0.00 0.00 0.00 3.21
3348 4155 3.109619 GCTAGATGAAGTTTCCGAGTCG 58.890 50.000 5.29 5.29 0.00 4.18
3423 4230 3.325135 ACATCAAGGAAGACGAAGGTTCT 59.675 43.478 0.00 0.00 0.00 3.01
3457 4264 5.208503 GTTTCAAGTCTGTTTCTAAGCTGC 58.791 41.667 0.00 0.00 0.00 5.25
3507 4314 2.163211 GCTTCTGTGGATGGCTTTCTTC 59.837 50.000 0.00 0.00 0.00 2.87
3522 4329 5.064441 CTTTCTTCGGGAATGCATTTTCT 57.936 39.130 14.33 0.00 33.53 2.52
3724 4531 6.149474 GTGCATACAATCTTACTTTGGTGACT 59.851 38.462 0.00 0.00 0.00 3.41
3857 4664 5.310451 TGTGTCTTTTTATTCCCGCTAGTT 58.690 37.500 0.00 0.00 0.00 2.24
3944 4751 8.873830 GCAAGCTTCACAATCGTATACATATAT 58.126 33.333 0.00 0.00 0.00 0.86
3960 4767 4.463186 ACATATATGCTCCCGAGGTTAGTC 59.537 45.833 12.79 0.00 0.00 2.59
3962 4769 1.049289 ATGCTCCCGAGGTTAGTCCC 61.049 60.000 0.00 0.00 36.75 4.46
3981 4791 3.318839 TCCCGTTCTACTCTTTTCGACAA 59.681 43.478 0.00 0.00 0.00 3.18
3982 4792 4.021719 TCCCGTTCTACTCTTTTCGACAAT 60.022 41.667 0.00 0.00 0.00 2.71
3991 4801 5.360591 ACTCTTTTCGACAATCAGTCTTGT 58.639 37.500 0.00 0.00 45.32 3.16
4028 4838 6.607019 ACCCTCTTGTCAGGTGTTAAAATTA 58.393 36.000 0.00 0.00 30.97 1.40
4100 4910 1.421268 TCTGTGAGGACAACAGGCATT 59.579 47.619 3.91 0.00 32.76 3.56
4214 5024 1.153939 CCTCTTCGAGCTCGTGGTG 60.154 63.158 33.33 24.37 40.80 4.17
4223 5033 0.827925 AGCTCGTGGTGTTCCTCTCA 60.828 55.000 0.00 0.00 34.23 3.27
4324 5135 3.558321 GGCGGGTTATATCATAGCACCAA 60.558 47.826 0.00 0.00 0.00 3.67
4365 5176 2.139917 GTGGCGGCATATTATCGAACA 58.860 47.619 17.19 0.00 0.00 3.18
4561 5373 8.960591 ACCTATACTTTGGACTTTTGAATGATG 58.039 33.333 0.00 0.00 0.00 3.07
4642 5454 0.464452 AAGAAATCGCGGGACCTAGG 59.536 55.000 7.41 7.41 0.00 3.02
4645 5457 0.906775 AAATCGCGGGACCTAGGAAA 59.093 50.000 17.98 0.00 0.00 3.13
4650 5462 1.202651 CGCGGGACCTAGGAAATCATT 60.203 52.381 17.98 0.00 0.00 2.57
4653 5465 3.131396 CGGGACCTAGGAAATCATTTCG 58.869 50.000 17.98 2.31 40.57 3.46
4678 5490 6.497785 TTCGTACAACTGAACCTTTTCAAA 57.502 33.333 0.00 0.00 41.34 2.69
4680 5492 5.032220 CGTACAACTGAACCTTTTCAAACC 58.968 41.667 0.00 0.00 41.34 3.27
4692 5504 5.184287 ACCTTTTCAAACCGTTTCTTTCTGA 59.816 36.000 0.00 0.00 0.00 3.27
4695 5507 6.503589 TTTCAAACCGTTTCTTTCTGAGAA 57.496 33.333 0.00 0.00 42.56 2.87
4728 5541 4.800993 CGTGTGCCAAAATAACAAACAGAA 59.199 37.500 0.00 0.00 0.00 3.02
4729 5542 5.461737 CGTGTGCCAAAATAACAAACAGAAT 59.538 36.000 0.00 0.00 0.00 2.40
4730 5543 6.019156 CGTGTGCCAAAATAACAAACAGAATT 60.019 34.615 0.00 0.00 0.00 2.17
4731 5544 7.125113 GTGTGCCAAAATAACAAACAGAATTG 58.875 34.615 0.00 0.00 36.37 2.32
4732 5545 6.820656 TGTGCCAAAATAACAAACAGAATTGT 59.179 30.769 0.00 0.00 45.12 2.71
4763 5670 1.458445 CAACGCTGACACTGACTGATG 59.542 52.381 0.00 0.00 0.00 3.07
4764 5671 0.676184 ACGCTGACACTGACTGATGT 59.324 50.000 0.00 0.00 0.00 3.06
4765 5672 1.066136 CGCTGACACTGACTGATGTG 58.934 55.000 0.00 0.00 39.80 3.21
4767 5674 2.487934 GCTGACACTGACTGATGTGTT 58.512 47.619 0.00 0.00 45.94 3.32
4773 5687 2.804527 CACTGACTGATGTGTTGTCCTG 59.195 50.000 0.00 0.00 0.00 3.86
4839 5756 3.453091 TGATCAATCAACGCTGCAAGCT 61.453 45.455 0.00 0.00 46.38 3.74
4867 5787 1.144708 TCAGAACCACCATGCTTCCAA 59.855 47.619 0.00 0.00 0.00 3.53
4892 5812 2.618241 TGTAGCAGCAAAGAACCAAGTG 59.382 45.455 0.00 0.00 0.00 3.16
4909 5829 1.156736 GTGCAGTACAGCGAACCAAT 58.843 50.000 5.73 0.00 37.31 3.16
4910 5830 1.535462 GTGCAGTACAGCGAACCAATT 59.465 47.619 5.73 0.00 37.31 2.32
4911 5831 2.031157 GTGCAGTACAGCGAACCAATTT 60.031 45.455 5.73 0.00 37.31 1.82
4912 5832 2.621055 TGCAGTACAGCGAACCAATTTT 59.379 40.909 5.73 0.00 37.31 1.82
4913 5833 3.067461 TGCAGTACAGCGAACCAATTTTT 59.933 39.130 5.73 0.00 37.31 1.94
4960 5895 3.067742 GGCAGCACATTTTCTGATGCTAT 59.932 43.478 8.39 0.00 46.49 2.97
4961 5896 4.042398 GCAGCACATTTTCTGATGCTATG 58.958 43.478 2.67 0.00 46.49 2.23
5013 5954 1.133761 AGTAGGACGATAGCTCTGCCA 60.134 52.381 0.00 0.00 42.67 4.92
5078 6019 6.543465 ACTGAAGTTTGATGTTGAAGTGATCA 59.457 34.615 0.00 0.00 35.85 2.92
5127 6068 0.250989 TGCTTTTACCCGGGTGGAAG 60.251 55.000 36.97 33.47 37.49 3.46
5138 6079 0.178990 GGGTGGAAGCTGGAAAGTGT 60.179 55.000 0.00 0.00 0.00 3.55
5139 6080 1.692411 GGTGGAAGCTGGAAAGTGTT 58.308 50.000 0.00 0.00 0.00 3.32
5250 6203 7.805083 ATTATGTTGATAGCTCTCCTATGGT 57.195 36.000 0.00 0.00 36.88 3.55
5252 6205 5.957771 TGTTGATAGCTCTCCTATGGTTT 57.042 39.130 0.00 0.00 36.88 3.27
5253 6206 6.313519 TGTTGATAGCTCTCCTATGGTTTT 57.686 37.500 0.00 0.00 36.88 2.43
5269 6222 8.032451 CCTATGGTTTTGTTTTGGGTAATACTG 58.968 37.037 0.00 0.00 0.00 2.74
5275 6228 4.073549 TGTTTTGGGTAATACTGGTTCGG 58.926 43.478 0.00 0.00 0.00 4.30
5282 6235 4.323409 GGGTAATACTGGTTCGGGTTTGTA 60.323 45.833 0.00 0.00 0.00 2.41
5283 6236 4.631377 GGTAATACTGGTTCGGGTTTGTAC 59.369 45.833 0.00 0.00 0.00 2.90
5284 6237 2.437200 TACTGGTTCGGGTTTGTACG 57.563 50.000 0.00 0.00 0.00 3.67
5285 6238 0.465287 ACTGGTTCGGGTTTGTACGT 59.535 50.000 0.00 0.00 0.00 3.57
5286 6239 0.863144 CTGGTTCGGGTTTGTACGTG 59.137 55.000 0.00 0.00 0.00 4.49
5287 6240 0.463204 TGGTTCGGGTTTGTACGTGA 59.537 50.000 0.00 0.00 0.00 4.35
5288 6241 1.134580 TGGTTCGGGTTTGTACGTGAA 60.135 47.619 0.00 0.00 0.00 3.18
5289 6242 1.939255 GGTTCGGGTTTGTACGTGAAA 59.061 47.619 0.00 0.00 0.00 2.69
5290 6243 2.032636 GGTTCGGGTTTGTACGTGAAAG 60.033 50.000 0.00 0.00 0.00 2.62
5291 6244 2.865551 GTTCGGGTTTGTACGTGAAAGA 59.134 45.455 0.00 0.00 0.00 2.52
5292 6245 3.389925 TCGGGTTTGTACGTGAAAGAT 57.610 42.857 0.00 0.00 0.00 2.40
5293 6246 3.731089 TCGGGTTTGTACGTGAAAGATT 58.269 40.909 0.00 0.00 0.00 2.40
5294 6247 3.742369 TCGGGTTTGTACGTGAAAGATTC 59.258 43.478 0.00 0.00 0.00 2.52
5295 6248 3.120442 CGGGTTTGTACGTGAAAGATTCC 60.120 47.826 0.00 0.00 0.00 3.01
5296 6249 3.816523 GGGTTTGTACGTGAAAGATTCCA 59.183 43.478 0.00 0.00 0.00 3.53
5297 6250 4.083484 GGGTTTGTACGTGAAAGATTCCAG 60.083 45.833 0.00 0.00 0.00 3.86
5298 6251 4.464112 GTTTGTACGTGAAAGATTCCAGC 58.536 43.478 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.107601 ACCTTGCAAGAGGATAGTGCTA 58.892 45.455 28.05 0.00 39.25 3.49
1 2 1.912043 ACCTTGCAAGAGGATAGTGCT 59.088 47.619 28.05 0.00 39.25 4.40
2 3 2.409948 ACCTTGCAAGAGGATAGTGC 57.590 50.000 28.05 0.00 39.25 4.40
3 4 3.274288 GGAACCTTGCAAGAGGATAGTG 58.726 50.000 28.05 10.55 39.25 2.74
24 25 8.790718 CATGAGAATATGAGGTTTTAGAATGGG 58.209 37.037 0.00 0.00 0.00 4.00
33 34 6.832384 ACTTGCATCATGAGAATATGAGGTTT 59.168 34.615 0.09 0.00 40.10 3.27
45 46 5.121105 TCTTCACCATACTTGCATCATGAG 58.879 41.667 0.09 0.00 0.00 2.90
109 110 3.273434 TCTGAAATCAGGAAATCCAGCG 58.727 45.455 10.37 0.00 43.91 5.18
140 142 3.880490 GTCCGTATATGTTGCCATGGAAA 59.120 43.478 18.40 9.10 32.29 3.13
156 158 4.924305 AGTTGTTAGTTGAGTGTCCGTA 57.076 40.909 0.00 0.00 0.00 4.02
158 160 4.680110 CAGTAGTTGTTAGTTGAGTGTCCG 59.320 45.833 0.00 0.00 0.00 4.79
159 161 5.598769 ACAGTAGTTGTTAGTTGAGTGTCC 58.401 41.667 0.00 0.00 36.31 4.02
174 176 3.641906 AGCGGCAAGGATATACAGTAGTT 59.358 43.478 1.45 0.00 0.00 2.24
176 178 3.944055 AGCGGCAAGGATATACAGTAG 57.056 47.619 1.45 0.00 0.00 2.57
177 179 5.995565 ATAAGCGGCAAGGATATACAGTA 57.004 39.130 1.45 0.00 0.00 2.74
178 180 4.891992 ATAAGCGGCAAGGATATACAGT 57.108 40.909 1.45 0.00 0.00 3.55
219 701 2.717190 GCGTTGCGTTCGTGTGTG 60.717 61.111 0.00 0.00 0.00 3.82
463 978 0.857935 GAAGGAGATGCGAAGATGCG 59.142 55.000 0.00 0.00 37.81 4.73
464 979 1.224965 GGAAGGAGATGCGAAGATGC 58.775 55.000 0.00 0.00 0.00 3.91
465 980 1.415659 AGGGAAGGAGATGCGAAGATG 59.584 52.381 0.00 0.00 0.00 2.90
466 981 1.799933 AGGGAAGGAGATGCGAAGAT 58.200 50.000 0.00 0.00 0.00 2.40
467 982 1.573108 AAGGGAAGGAGATGCGAAGA 58.427 50.000 0.00 0.00 0.00 2.87
468 983 2.284190 GAAAGGGAAGGAGATGCGAAG 58.716 52.381 0.00 0.00 0.00 3.79
492 1007 2.860971 GGATGGGGAGGGGATGGG 60.861 72.222 0.00 0.00 0.00 4.00
495 1010 3.394792 TGGGGATGGGGAGGGGAT 61.395 66.667 0.00 0.00 0.00 3.85
786 1303 2.494073 GGCGAGAGGAAGAAGAAGAGAA 59.506 50.000 0.00 0.00 0.00 2.87
791 1308 1.338200 GCTTGGCGAGAGGAAGAAGAA 60.338 52.381 5.76 0.00 0.00 2.52
918 1436 0.673644 CTGTCCGCCTGACCGATTTT 60.674 55.000 0.00 0.00 43.78 1.82
1049 1567 2.494918 GGTCGTGGATCCTCACCG 59.505 66.667 14.23 10.01 34.36 4.94
1137 1655 3.811722 TCGCATTGTCACAATCTGTTC 57.188 42.857 0.00 0.00 0.00 3.18
1167 1685 3.013276 TGGTAATAGCGATGAGAAGCG 57.987 47.619 0.00 0.00 38.61 4.68
1246 1764 1.202405 CCAACTGTGACCAAACAAGCC 60.202 52.381 0.00 0.00 0.00 4.35
1291 1809 1.278985 CACACAAGGAGGATACCAGCA 59.721 52.381 0.00 0.00 37.17 4.41
1292 1810 1.279271 ACACACAAGGAGGATACCAGC 59.721 52.381 0.00 0.00 37.17 4.85
1293 1811 2.303022 ACACACACAAGGAGGATACCAG 59.697 50.000 0.00 0.00 37.17 4.00
1294 1812 2.334977 ACACACACAAGGAGGATACCA 58.665 47.619 0.00 0.00 37.17 3.25
1295 1813 4.755266 ATACACACACAAGGAGGATACC 57.245 45.455 0.00 0.00 37.17 2.73
1296 1814 5.730550 TGAATACACACACAAGGAGGATAC 58.269 41.667 0.00 0.00 0.00 2.24
1297 1815 6.348498 CATGAATACACACACAAGGAGGATA 58.652 40.000 0.00 0.00 0.00 2.59
1298 1816 4.908601 TGAATACACACACAAGGAGGAT 57.091 40.909 0.00 0.00 0.00 3.24
1299 1817 4.578871 CATGAATACACACACAAGGAGGA 58.421 43.478 0.00 0.00 0.00 3.71
1300 1818 3.127548 GCATGAATACACACACAAGGAGG 59.872 47.826 0.00 0.00 0.00 4.30
1301 1819 4.005650 AGCATGAATACACACACAAGGAG 58.994 43.478 0.00 0.00 0.00 3.69
1302 1820 4.019792 AGCATGAATACACACACAAGGA 57.980 40.909 0.00 0.00 0.00 3.36
1303 1821 4.771590 AAGCATGAATACACACACAAGG 57.228 40.909 0.00 0.00 0.00 3.61
1304 1822 6.902341 ACTTAAGCATGAATACACACACAAG 58.098 36.000 1.29 0.00 0.00 3.16
1305 1823 6.875948 ACTTAAGCATGAATACACACACAA 57.124 33.333 1.29 0.00 0.00 3.33
1306 1824 6.667370 CAACTTAAGCATGAATACACACACA 58.333 36.000 1.29 0.00 0.00 3.72
1307 1825 5.569059 GCAACTTAAGCATGAATACACACAC 59.431 40.000 11.86 0.00 0.00 3.82
1336 1871 1.199789 TGCAAGCGCATTTTCTACTGG 59.800 47.619 11.47 0.00 45.36 4.00
1346 1881 0.942410 CAAAAGCACTGCAAGCGCAT 60.942 50.000 11.47 0.00 46.46 4.73
1357 1892 9.935241 TTAGATAGATCATAGATCCAAAAGCAC 57.065 33.333 3.52 0.00 0.00 4.40
1395 1930 2.602257 TCATGAGTGTTAGGCATCGG 57.398 50.000 0.00 0.00 0.00 4.18
1484 2021 2.574006 AGATCCAAAAGCAGTGCAGA 57.426 45.000 19.20 6.10 0.00 4.26
1548 2331 5.355071 TCCATTAACTGATGAACTCATGCAC 59.645 40.000 0.00 0.00 36.57 4.57
1611 2394 9.184523 TCTGAAAAATTGTAAGAAAAGGACAGA 57.815 29.630 0.00 0.00 0.00 3.41
1651 2436 5.478407 TGCAAAATCTAACATGAGACGAGA 58.522 37.500 0.00 0.00 0.00 4.04
1699 2484 6.523270 TTACGCGCGTTTAATAAACATTTC 57.477 33.333 42.10 1.77 41.44 2.17
1715 2500 1.585297 TTAGGGGCTTTATTACGCGC 58.415 50.000 5.73 0.00 38.24 6.86
1826 2611 8.378565 GTCCTCCATCTGGAAAATAGATATCAA 58.621 37.037 5.32 0.00 44.91 2.57
1990 2775 3.118408 TCCATTCTAACTGAACGGATGGG 60.118 47.826 0.00 0.00 41.49 4.00
2080 2865 0.764890 CTGAGACCACACCCCAAGAA 59.235 55.000 0.00 0.00 0.00 2.52
2153 2938 5.868801 GGAAATGGTCATGTGTAATTTGTGG 59.131 40.000 0.00 0.00 0.00 4.17
2228 3013 7.125204 ACTGTTGGTAACCATAAGCAGTATCTA 59.875 37.037 0.00 0.00 34.02 1.98
2263 3048 2.291209 TCAGAGCTTTGCCATTTCCA 57.709 45.000 0.00 0.00 0.00 3.53
2429 3214 7.658179 TTGTATGAGCTAAACAAGAAGAGTG 57.342 36.000 4.38 0.00 0.00 3.51
2834 3619 3.617288 GCTGACCTTTTATGCCCTTTTGG 60.617 47.826 0.00 0.00 39.97 3.28
2945 3751 5.122512 AGATGTTCTAATCCACGTATCCG 57.877 43.478 0.00 0.00 40.83 4.18
3255 4062 1.260544 ACCTTGCCATTTTCTCCAGC 58.739 50.000 0.00 0.00 0.00 4.85
3423 4230 5.200483 ACAGACTTGAAACCTCCAAAATCA 58.800 37.500 0.00 0.00 0.00 2.57
3457 4264 3.611057 GCTCTGAGCAATTTTGGTGACAG 60.611 47.826 24.02 2.82 41.17 3.51
3507 4314 6.748132 ACCATAATAAGAAAATGCATTCCCG 58.252 36.000 13.38 0.00 0.00 5.14
3857 4664 4.023536 GTCAGTATTTCTGTGCGGGAAAAA 60.024 41.667 3.40 0.00 43.97 1.94
3920 4727 8.873830 GCATATATGTATACGATTGTGAAGCTT 58.126 33.333 14.14 0.00 0.00 3.74
3944 4751 1.684734 GGGACTAACCTCGGGAGCA 60.685 63.158 0.00 0.00 38.98 4.26
3960 4767 3.293311 TGTCGAAAAGAGTAGAACGGG 57.707 47.619 0.00 0.00 0.00 5.28
3962 4769 5.629849 ACTGATTGTCGAAAAGAGTAGAACG 59.370 40.000 1.72 0.00 0.00 3.95
3991 4801 1.742308 AGAGGGTTCAGCCTTGGTTA 58.258 50.000 0.00 0.00 37.43 2.85
4028 4838 7.880195 AGCAAAGATGTGAATACTCTACTGTTT 59.120 33.333 0.00 0.00 0.00 2.83
4051 4861 5.371526 GGTAGATCTGGAAATGATGAAGCA 58.628 41.667 5.18 0.00 0.00 3.91
4214 5024 2.671682 GCCACCCCTGAGAGGAAC 59.328 66.667 0.00 0.00 37.67 3.62
4223 5033 3.256960 AACATGACGGCCACCCCT 61.257 61.111 2.24 0.00 0.00 4.79
4383 5194 9.617523 TCACTATAATCAATATCGGTATCGGTA 57.382 33.333 0.00 0.00 36.33 4.02
4384 5195 8.515695 TCACTATAATCAATATCGGTATCGGT 57.484 34.615 0.00 0.00 36.95 4.69
4385 5196 9.613957 GATCACTATAATCAATATCGGTATCGG 57.386 37.037 0.00 0.00 36.95 4.18
4442 5253 1.743772 CGACAAGTGGATGGGGATCAC 60.744 57.143 0.00 0.00 0.00 3.06
4468 5280 4.115199 AATCCCCTCTGCACCGCC 62.115 66.667 0.00 0.00 0.00 6.13
4469 5281 2.825836 CAATCCCCTCTGCACCGC 60.826 66.667 0.00 0.00 0.00 5.68
4470 5282 2.825836 GCAATCCCCTCTGCACCG 60.826 66.667 0.00 0.00 38.48 4.94
4553 5365 6.591001 TCCTTATTCCAACGATCATCATTCA 58.409 36.000 0.00 0.00 0.00 2.57
4561 5373 6.206634 TGGCATATTTCCTTATTCCAACGATC 59.793 38.462 0.00 0.00 0.00 3.69
4642 5454 7.067116 TCAGTTGTACGAAACGAAATGATTTC 58.933 34.615 7.83 7.83 35.13 2.17
4645 5457 6.360329 GTTCAGTTGTACGAAACGAAATGAT 58.640 36.000 0.00 0.00 35.13 2.45
4650 5462 3.784338 AGGTTCAGTTGTACGAAACGAA 58.216 40.909 0.00 0.00 33.94 3.85
4653 5465 5.871539 TGAAAAGGTTCAGTTGTACGAAAC 58.128 37.500 0.00 0.00 38.88 2.78
4706 5519 6.843069 ATTCTGTTTGTTATTTTGGCACAC 57.157 33.333 0.00 0.00 39.29 3.82
4707 5520 6.820656 ACAATTCTGTTTGTTATTTTGGCACA 59.179 30.769 0.00 0.00 36.43 4.57
4728 5541 2.231964 AGCGTTGATTGATTGCCACAAT 59.768 40.909 0.00 0.00 40.08 2.71
4729 5542 1.612950 AGCGTTGATTGATTGCCACAA 59.387 42.857 0.00 0.00 0.00 3.33
4730 5543 1.068402 CAGCGTTGATTGATTGCCACA 60.068 47.619 0.00 0.00 0.00 4.17
4731 5544 1.199789 TCAGCGTTGATTGATTGCCAC 59.800 47.619 0.00 0.00 0.00 5.01
4732 5545 1.199789 GTCAGCGTTGATTGATTGCCA 59.800 47.619 4.92 0.00 35.39 4.92
4773 5687 6.743575 ACTGCATATTAAGGAACTGTCAAC 57.256 37.500 0.00 0.00 40.86 3.18
4839 5756 3.005684 GCATGGTGGTTCTGAAACATTCA 59.994 43.478 11.84 13.07 37.10 2.57
4892 5812 2.989422 AAATTGGTTCGCTGTACTGC 57.011 45.000 14.26 14.26 0.00 4.40
4912 5832 5.304101 ACTGATGTGCCTGGTCATTTAAAAA 59.696 36.000 0.00 0.00 0.00 1.94
4913 5833 4.832266 ACTGATGTGCCTGGTCATTTAAAA 59.168 37.500 0.00 0.00 0.00 1.52
4915 5835 4.032960 ACTGATGTGCCTGGTCATTTAA 57.967 40.909 0.00 0.00 0.00 1.52
4924 5854 1.094073 GCTGCCTACTGATGTGCCTG 61.094 60.000 0.00 0.00 0.00 4.85
4925 5855 1.222936 GCTGCCTACTGATGTGCCT 59.777 57.895 0.00 0.00 0.00 4.75
5013 5954 3.307379 GGAAACGTCTTGTCCTGCT 57.693 52.632 0.00 0.00 0.00 4.24
5078 6019 2.817844 GGAAATAAGCACCACGGAAAGT 59.182 45.455 0.00 0.00 0.00 2.66
5127 6068 1.006922 GCCAGCAACACTTTCCAGC 60.007 57.895 0.00 0.00 0.00 4.85
5202 6155 1.413445 TCATGTTGCTTGCTTTTGCCT 59.587 42.857 0.00 0.00 46.87 4.75
5203 6156 1.868469 TCATGTTGCTTGCTTTTGCC 58.132 45.000 0.00 0.00 46.87 4.52
5248 6201 6.164417 ACCAGTATTACCCAAAACAAAACC 57.836 37.500 0.00 0.00 0.00 3.27
5249 6202 6.418523 CGAACCAGTATTACCCAAAACAAAAC 59.581 38.462 0.00 0.00 0.00 2.43
5250 6203 6.461231 CCGAACCAGTATTACCCAAAACAAAA 60.461 38.462 0.00 0.00 0.00 2.44
5252 6205 4.519730 CCGAACCAGTATTACCCAAAACAA 59.480 41.667 0.00 0.00 0.00 2.83
5253 6206 4.073549 CCGAACCAGTATTACCCAAAACA 58.926 43.478 0.00 0.00 0.00 2.83
5269 6222 1.580815 TTCACGTACAAACCCGAACC 58.419 50.000 0.00 0.00 0.00 3.62
5275 6228 4.612939 GCTGGAATCTTTCACGTACAAACC 60.613 45.833 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.