Multiple sequence alignment - TraesCS5D01G118300

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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 TraesCS5D01G118300 chr5D 100.000 5341 0 0 1 5341 158171080 158165740 0.000000e+00 9864.0
1 TraesCS5D01G118300 chr5D 100.000 212 0 0 5565 5776 158165516 158165305 5.430000e-105 392.0
2 TraesCS5D01G118300 chr5D 95.349 43 2 0 5734 5776 550400437 550400395 1.040000e-07 69.4
3 TraesCS5D01G118300 chr5A 98.098 4784 77 8 1 4776 207660366 207655589 0.000000e+00 8318.0
4 TraesCS5D01G118300 chr5A 90.947 486 39 3 4860 5341 207655590 207655106 0.000000e+00 649.0
5 TraesCS5D01G118300 chr5B 98.650 2223 27 2 1161 3380 159711444 159713666 0.000000e+00 3936.0
6 TraesCS5D01G118300 chr5B 97.794 1405 24 2 3373 4776 159715160 159716558 0.000000e+00 2416.0
7 TraesCS5D01G118300 chr5B 90.186 377 20 5 4860 5234 159716557 159716918 5.240000e-130 475.0
8 TraesCS5D01G118300 chr5B 85.849 212 21 2 5565 5776 159717098 159717300 3.500000e-52 217.0
9 TraesCS5D01G118300 chr5B 88.660 97 9 2 4765 4861 227830952 227831046 3.660000e-22 117.0
10 TraesCS5D01G118300 chr6B 79.859 283 56 1 5059 5341 206021509 206021790 7.590000e-49 206.0
11 TraesCS5D01G118300 chr6B 76.190 252 47 8 5097 5336 485289798 485289548 2.830000e-23 121.0
12 TraesCS5D01G118300 chr2B 80.000 300 42 11 5059 5341 415387381 415387679 7.590000e-49 206.0
13 TraesCS5D01G118300 chr3A 83.482 224 22 4 5568 5776 594344204 594343981 1.640000e-45 195.0
14 TraesCS5D01G118300 chr3A 79.505 283 44 6 5059 5341 25538550 25538282 7.640000e-44 189.0
15 TraesCS5D01G118300 chr3A 79.798 99 19 1 5241 5339 692617132 692617035 2.890000e-08 71.3
16 TraesCS5D01G118300 chr3D 83.938 193 29 2 5585 5776 488276807 488276616 3.550000e-42 183.0
17 TraesCS5D01G118300 chr7D 78.689 244 36 8 5098 5340 511666423 511666195 1.300000e-31 148.0
18 TraesCS5D01G118300 chr2D 81.818 187 25 5 5590 5776 517893356 517893179 1.300000e-31 148.0
19 TraesCS5D01G118300 chr2D 90.217 92 7 2 4771 4862 259811877 259811788 1.020000e-22 119.0
20 TraesCS5D01G118300 chr2D 86.957 92 8 3 5052 5142 600982769 600982857 3.680000e-17 100.0
21 TraesCS5D01G118300 chr4D 80.435 184 32 3 5587 5770 84259146 84259325 2.810000e-28 137.0
22 TraesCS5D01G118300 chr4D 84.348 115 15 3 4775 4888 116821999 116821887 6.120000e-20 110.0
23 TraesCS5D01G118300 chr1B 88.679 106 12 0 5236 5341 654914643 654914538 4.700000e-26 130.0
24 TraesCS5D01G118300 chr1B 100.000 31 0 0 3255 3285 606845918 606845888 2.250000e-04 58.4
25 TraesCS5D01G118300 chr3B 91.954 87 6 1 4775 4861 545181616 545181701 2.830000e-23 121.0
26 TraesCS5D01G118300 chr3B 89.474 95 9 1 4768 4862 395693663 395693756 1.020000e-22 119.0
27 TraesCS5D01G118300 chr3B 91.011 89 7 1 4775 4863 594831050 594831137 1.020000e-22 119.0
28 TraesCS5D01G118300 chr7B 87.037 108 8 5 4762 4866 696592240 696592344 3.660000e-22 117.0
29 TraesCS5D01G118300 chr1A 90.110 91 7 2 4772 4861 436426949 436427038 3.660000e-22 117.0
30 TraesCS5D01G118300 chr1A 73.764 263 44 16 5094 5339 373260421 373260675 4.800000e-11 80.5
31 TraesCS5D01G118300 chr1A 81.720 93 15 2 5059 5150 565467399 565467308 6.210000e-10 76.8
32 TraesCS5D01G118300 chr1A 100.000 31 0 0 3255 3285 541387887 541387857 2.250000e-04 58.4
33 TraesCS5D01G118300 chr2A 85.714 105 12 3 4758 4862 24958847 24958948 2.200000e-19 108.0
34 TraesCS5D01G118300 chr1D 74.517 259 46 11 5090 5339 478402254 478402501 1.710000e-15 95.3
35 TraesCS5D01G118300 chr4B 76.744 172 30 7 5603 5766 479393586 479393755 2.870000e-13 87.9


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 TraesCS5D01G118300 chr5D 158165305 158171080 5775 True 5128.0 9864 100.00000 1 5776 2 chr5D.!!$R2 5775
1 TraesCS5D01G118300 chr5A 207655106 207660366 5260 True 4483.5 8318 94.52250 1 5341 2 chr5A.!!$R1 5340
2 TraesCS5D01G118300 chr5B 159711444 159717300 5856 False 1761.0 3936 93.11975 1161 5776 4 chr5B.!!$F2 4615

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
975 979 0.671251 TTGCGGCGTTTCCTTTTGAT 59.329 45.000 9.37 0.0 0.00 2.57 F
1139 1143 1.761784 CTCCTCTCCATCCAAGGACTG 59.238 57.143 0.00 0.0 35.38 3.51 F
2014 2019 0.830648 TGGCGCCTAAAGCAGTAGAT 59.169 50.000 29.70 0.0 44.04 1.98 F
2984 2993 2.140138 TGGGTCGCCGATGGATGAT 61.140 57.895 0.00 0.0 0.00 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1991 1996 0.251916 ACTGCTTTAGGCGCCACATA 59.748 50.000 31.54 9.92 45.43 2.29 R
2742 2749 1.134699 CCACATATCCACAGCGACACT 60.135 52.381 0.00 0.00 0.00 3.55 R
3418 4928 2.916702 AGATGCACAGTCACACAAGA 57.083 45.000 0.00 0.00 0.00 3.02 R
4898 6412 0.035152 ATTCAGTCATGCCCTGCGAA 60.035 50.000 7.20 0.03 0.00 4.70 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
112 113 5.220815 GCATGATGAAGCTCTCGAGATTTTT 60.221 40.000 17.03 10.50 37.15 1.94
414 415 4.770795 ACTAACCAGTAATGCCATCAGTC 58.229 43.478 0.00 0.00 31.45 3.51
492 493 3.153919 TGCCTTTATTCCCTCACAACAC 58.846 45.455 0.00 0.00 0.00 3.32
493 494 2.161609 GCCTTTATTCCCTCACAACACG 59.838 50.000 0.00 0.00 0.00 4.49
536 537 3.778075 GGGGTTTGGGTTTATGGCTTATT 59.222 43.478 0.00 0.00 0.00 1.40
554 555 6.016111 GCTTATTTGTTCGCTTCAGTTAGAC 58.984 40.000 0.00 0.00 0.00 2.59
646 647 8.157476 ACTGAGCCATAATAAATAGGGTTAGTG 58.843 37.037 6.20 0.00 43.79 2.74
716 717 9.809395 ATGTATAGCTAGTAGTCTAATTGTCCA 57.191 33.333 0.00 0.00 0.00 4.02
963 967 0.949105 ACTTCTAGTGGTTTGCGGCG 60.949 55.000 0.51 0.51 0.00 6.46
975 979 0.671251 TTGCGGCGTTTCCTTTTGAT 59.329 45.000 9.37 0.00 0.00 2.57
1139 1143 1.761784 CTCCTCTCCATCCAAGGACTG 59.238 57.143 0.00 0.00 35.38 3.51
1822 1827 6.347725 CCGAAAACAGAGAACCATCAAGTAAG 60.348 42.308 0.00 0.00 0.00 2.34
1968 1973 3.141398 TCTCAGGTGAGCATGTTGTTTC 58.859 45.455 1.81 0.00 41.80 2.78
2014 2019 0.830648 TGGCGCCTAAAGCAGTAGAT 59.169 50.000 29.70 0.00 44.04 1.98
2076 2081 4.339247 AGACAAGGTGAACAACTGATTTGG 59.661 41.667 0.00 0.00 39.84 3.28
2380 2385 6.761242 TGTATCTGGTTTTCGAATACATGGAG 59.239 38.462 18.46 9.48 0.00 3.86
2615 2622 2.426024 CCTCTTGATTGACAGCAATGGG 59.574 50.000 0.00 0.00 44.47 4.00
2670 2677 2.370519 TCTTTCGACCCTGACAATCCAA 59.629 45.455 0.00 0.00 0.00 3.53
2742 2749 6.877322 GCTTTTACTTGGTTCCACAGAGTATA 59.123 38.462 3.65 0.00 0.00 1.47
2905 2912 7.994425 TTTTATGCTGGTTGAAGTCTTATGA 57.006 32.000 0.00 0.00 0.00 2.15
2906 2913 8.579850 TTTTATGCTGGTTGAAGTCTTATGAT 57.420 30.769 0.00 0.00 0.00 2.45
2984 2993 2.140138 TGGGTCGCCGATGGATGAT 61.140 57.895 0.00 0.00 0.00 2.45
3113 3122 4.377839 TCTCATAGACTCCTTGCTTTCG 57.622 45.455 0.00 0.00 0.00 3.46
3201 3210 9.050601 CCTCTCATAAGAATCTTTTGTATGGTC 57.949 37.037 12.00 0.00 0.00 4.02
3418 4928 1.677217 GCTGCCGGTTTTCTGATCTCT 60.677 52.381 1.90 0.00 0.00 3.10
3468 4978 6.040878 AGTACTTTGCTTACGCGAATATCTT 58.959 36.000 15.93 0.00 38.79 2.40
3558 5068 3.581332 TGACCCTTCAAGTCTACCGAAAT 59.419 43.478 0.00 0.00 35.21 2.17
3759 5269 2.026822 ACGAGGAGCTGAATGTTCCAAT 60.027 45.455 0.00 0.00 46.89 3.16
3842 5352 4.883585 AGCGATTCCAGATTATTGCTTGAA 59.116 37.500 0.00 0.00 38.10 2.69
4068 5581 1.402456 GCATGCCAGTTCAAAGAGCAG 60.402 52.381 6.36 0.00 36.80 4.24
4244 5757 3.189080 TGTTCATGTCGCAAATTCCTCTG 59.811 43.478 0.00 0.00 0.00 3.35
4459 5972 1.329906 CTTTCATCTCACATGGCTCGC 59.670 52.381 0.00 0.00 0.00 5.03
4756 6270 3.546815 CCGTGCATAGAGTTTTAGCATGC 60.547 47.826 10.51 10.51 40.04 4.06
4776 6290 3.930229 TGCAACCGTGTGTTCTCATATAC 59.070 43.478 0.00 0.00 34.00 1.47
4777 6291 4.181578 GCAACCGTGTGTTCTCATATACT 58.818 43.478 0.00 0.00 34.00 2.12
4778 6292 4.267928 GCAACCGTGTGTTCTCATATACTC 59.732 45.833 0.00 0.00 34.00 2.59
4779 6293 4.650754 ACCGTGTGTTCTCATATACTCC 57.349 45.455 0.00 0.00 0.00 3.85
4780 6294 3.383825 ACCGTGTGTTCTCATATACTCCC 59.616 47.826 0.00 0.00 0.00 4.30
4782 6296 4.261656 CCGTGTGTTCTCATATACTCCCTC 60.262 50.000 0.00 0.00 0.00 4.30
4783 6297 4.261656 CGTGTGTTCTCATATACTCCCTCC 60.262 50.000 0.00 0.00 0.00 4.30
4784 6298 3.889538 TGTGTTCTCATATACTCCCTCCG 59.110 47.826 0.00 0.00 0.00 4.63
4785 6299 3.890147 GTGTTCTCATATACTCCCTCCGT 59.110 47.826 0.00 0.00 0.00 4.69
4786 6300 4.341520 GTGTTCTCATATACTCCCTCCGTT 59.658 45.833 0.00 0.00 0.00 4.44
4787 6301 4.583489 TGTTCTCATATACTCCCTCCGTTC 59.417 45.833 0.00 0.00 0.00 3.95
4788 6302 3.764218 TCTCATATACTCCCTCCGTTCC 58.236 50.000 0.00 0.00 0.00 3.62
4789 6303 3.139584 TCTCATATACTCCCTCCGTTCCA 59.860 47.826 0.00 0.00 0.00 3.53
4790 6304 3.895656 CTCATATACTCCCTCCGTTCCAA 59.104 47.826 0.00 0.00 0.00 3.53
4791 6305 4.291792 TCATATACTCCCTCCGTTCCAAA 58.708 43.478 0.00 0.00 0.00 3.28
4792 6306 4.717778 TCATATACTCCCTCCGTTCCAAAA 59.282 41.667 0.00 0.00 0.00 2.44
4793 6307 5.368523 TCATATACTCCCTCCGTTCCAAAAT 59.631 40.000 0.00 0.00 0.00 1.82
4794 6308 6.555738 TCATATACTCCCTCCGTTCCAAAATA 59.444 38.462 0.00 0.00 0.00 1.40
4795 6309 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
4796 6310 2.238898 ACTCCCTCCGTTCCAAAATAGG 59.761 50.000 0.00 0.00 0.00 2.57
4797 6311 2.238898 CTCCCTCCGTTCCAAAATAGGT 59.761 50.000 0.00 0.00 0.00 3.08
4798 6312 2.026636 TCCCTCCGTTCCAAAATAGGTG 60.027 50.000 0.00 0.00 0.00 4.00
4799 6313 2.026636 CCCTCCGTTCCAAAATAGGTGA 60.027 50.000 0.00 0.00 0.00 4.02
4800 6314 3.007635 CCTCCGTTCCAAAATAGGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
4802 6316 3.933332 CTCCGTTCCAAAATAGGTGACTC 59.067 47.826 0.00 0.00 43.67 3.36
4803 6317 3.325425 TCCGTTCCAAAATAGGTGACTCA 59.675 43.478 0.00 0.00 43.67 3.41
4804 6318 4.069304 CCGTTCCAAAATAGGTGACTCAA 58.931 43.478 0.00 0.00 43.67 3.02
4805 6319 4.083484 CCGTTCCAAAATAGGTGACTCAAC 60.083 45.833 0.00 0.00 43.67 3.18
4806 6320 4.755123 CGTTCCAAAATAGGTGACTCAACT 59.245 41.667 1.31 1.31 43.67 3.16
4807 6321 5.238650 CGTTCCAAAATAGGTGACTCAACTT 59.761 40.000 0.84 0.00 43.67 2.66
4808 6322 6.238648 CGTTCCAAAATAGGTGACTCAACTTT 60.239 38.462 0.84 0.00 43.67 2.66
4809 6323 6.633500 TCCAAAATAGGTGACTCAACTTTG 57.367 37.500 0.84 1.17 43.67 2.77
4810 6324 6.126409 TCCAAAATAGGTGACTCAACTTTGT 58.874 36.000 0.84 0.00 43.67 2.83
4811 6325 7.284074 TCCAAAATAGGTGACTCAACTTTGTA 58.716 34.615 0.84 0.00 43.67 2.41
4812 6326 7.776030 TCCAAAATAGGTGACTCAACTTTGTAA 59.224 33.333 0.84 0.00 43.67 2.41
4813 6327 8.410141 CCAAAATAGGTGACTCAACTTTGTAAA 58.590 33.333 0.84 0.00 43.67 2.01
4814 6328 9.965824 CAAAATAGGTGACTCAACTTTGTAAAT 57.034 29.630 0.84 0.00 43.67 1.40
4815 6329 9.965824 AAAATAGGTGACTCAACTTTGTAAATG 57.034 29.630 0.84 0.00 43.67 2.32
4816 6330 7.687941 ATAGGTGACTCAACTTTGTAAATGG 57.312 36.000 0.84 0.00 43.67 3.16
4817 6331 5.690865 AGGTGACTCAACTTTGTAAATGGA 58.309 37.500 0.00 0.00 32.90 3.41
4818 6332 5.765182 AGGTGACTCAACTTTGTAAATGGAG 59.235 40.000 0.00 0.00 32.90 3.86
4819 6333 5.048713 GGTGACTCAACTTTGTAAATGGAGG 60.049 44.000 0.00 0.00 0.00 4.30
4820 6334 5.531287 GTGACTCAACTTTGTAAATGGAGGT 59.469 40.000 0.00 0.00 0.00 3.85
4821 6335 6.708949 GTGACTCAACTTTGTAAATGGAGGTA 59.291 38.462 0.00 0.00 0.00 3.08
4822 6336 6.934645 TGACTCAACTTTGTAAATGGAGGTAG 59.065 38.462 0.00 0.00 0.00 3.18
4823 6337 6.838382 ACTCAACTTTGTAAATGGAGGTAGT 58.162 36.000 0.00 0.00 0.00 2.73
4824 6338 7.970102 ACTCAACTTTGTAAATGGAGGTAGTA 58.030 34.615 0.00 0.00 0.00 1.82
4825 6339 7.876582 ACTCAACTTTGTAAATGGAGGTAGTAC 59.123 37.037 0.00 0.00 0.00 2.73
4826 6340 7.737869 TCAACTTTGTAAATGGAGGTAGTACA 58.262 34.615 2.06 0.00 0.00 2.90
4827 6341 8.212312 TCAACTTTGTAAATGGAGGTAGTACAA 58.788 33.333 2.06 0.00 33.91 2.41
4828 6342 8.842280 CAACTTTGTAAATGGAGGTAGTACAAA 58.158 33.333 2.06 7.00 40.51 2.83
4831 6345 8.983702 TTTGTAAATGGAGGTAGTACAAAGTT 57.016 30.769 2.06 0.00 38.86 2.66
4832 6346 7.972832 TGTAAATGGAGGTAGTACAAAGTTG 57.027 36.000 2.06 0.00 0.00 3.16
4833 6347 6.938030 TGTAAATGGAGGTAGTACAAAGTTGG 59.062 38.462 2.06 0.00 0.00 3.77
4834 6348 4.569719 ATGGAGGTAGTACAAAGTTGGG 57.430 45.455 2.06 0.00 0.00 4.12
4835 6349 3.320129 TGGAGGTAGTACAAAGTTGGGT 58.680 45.455 2.06 0.00 0.00 4.51
4836 6350 3.325716 TGGAGGTAGTACAAAGTTGGGTC 59.674 47.826 2.06 0.00 0.00 4.46
4837 6351 3.325716 GGAGGTAGTACAAAGTTGGGTCA 59.674 47.826 2.06 0.00 0.00 4.02
4838 6352 4.019591 GGAGGTAGTACAAAGTTGGGTCAT 60.020 45.833 2.06 0.00 0.00 3.06
4839 6353 5.161943 AGGTAGTACAAAGTTGGGTCATC 57.838 43.478 2.06 0.00 0.00 2.92
4840 6354 4.844655 AGGTAGTACAAAGTTGGGTCATCT 59.155 41.667 2.06 0.00 0.00 2.90
4841 6355 6.021030 AGGTAGTACAAAGTTGGGTCATCTA 58.979 40.000 2.06 0.00 0.00 1.98
4842 6356 6.672657 AGGTAGTACAAAGTTGGGTCATCTAT 59.327 38.462 2.06 0.00 0.00 1.98
4843 6357 7.182206 AGGTAGTACAAAGTTGGGTCATCTATT 59.818 37.037 2.06 0.00 0.00 1.73
4844 6358 7.827729 GGTAGTACAAAGTTGGGTCATCTATTT 59.172 37.037 2.06 0.00 0.00 1.40
4845 6359 9.227777 GTAGTACAAAGTTGGGTCATCTATTTT 57.772 33.333 0.00 0.00 0.00 1.82
4846 6360 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
4847 6361 7.942341 AGTACAAAGTTGGGTCATCTATTTTGA 59.058 33.333 0.00 0.00 0.00 2.69
4848 6362 7.595819 ACAAAGTTGGGTCATCTATTTTGAA 57.404 32.000 0.00 0.00 0.00 2.69
4849 6363 8.017418 ACAAAGTTGGGTCATCTATTTTGAAA 57.983 30.769 0.00 0.00 0.00 2.69
4850 6364 7.926018 ACAAAGTTGGGTCATCTATTTTGAAAC 59.074 33.333 0.00 0.00 0.00 2.78
4851 6365 7.595819 AAGTTGGGTCATCTATTTTGAAACA 57.404 32.000 0.00 0.00 0.00 2.83
4852 6366 7.219484 AGTTGGGTCATCTATTTTGAAACAG 57.781 36.000 0.00 0.00 0.00 3.16
4853 6367 7.004086 AGTTGGGTCATCTATTTTGAAACAGA 58.996 34.615 0.00 0.00 0.00 3.41
4854 6368 7.175641 AGTTGGGTCATCTATTTTGAAACAGAG 59.824 37.037 0.00 0.00 0.00 3.35
4855 6369 5.945784 TGGGTCATCTATTTTGAAACAGAGG 59.054 40.000 0.00 0.00 0.00 3.69
4856 6370 5.358160 GGGTCATCTATTTTGAAACAGAGGG 59.642 44.000 0.00 0.00 0.00 4.30
4857 6371 6.180472 GGTCATCTATTTTGAAACAGAGGGA 58.820 40.000 0.00 0.00 0.00 4.20
4858 6372 6.317391 GGTCATCTATTTTGAAACAGAGGGAG 59.683 42.308 0.00 0.00 0.00 4.30
5010 6525 5.413309 ACCTGAACCTAGAGTTTCATCAG 57.587 43.478 0.00 0.00 39.40 2.90
5066 6584 4.323104 GCTTAGACAGACCTGAACTCCAAT 60.323 45.833 3.76 0.00 0.00 3.16
5081 6599 3.099141 CTCCAATGCAGGTACCCATTTT 58.901 45.455 8.74 0.00 30.19 1.82
5085 6603 2.969821 TGCAGGTACCCATTTTGTCT 57.030 45.000 8.74 0.00 0.00 3.41
5087 6605 2.158534 TGCAGGTACCCATTTTGTCTGT 60.159 45.455 8.74 0.00 0.00 3.41
5092 6610 0.179004 ACCCATTTTGTCTGTCGCCA 60.179 50.000 0.00 0.00 0.00 5.69
5152 6670 1.828979 GCCGACCCATTCCTAAAACA 58.171 50.000 0.00 0.00 0.00 2.83
5155 6673 1.129811 CGACCCATTCCTAAAACACGC 59.870 52.381 0.00 0.00 0.00 5.34
5160 6678 0.606944 ATTCCTAAAACACGCCCGCA 60.607 50.000 0.00 0.00 0.00 5.69
5165 6684 1.579084 TAAAACACGCCCGCATGGAC 61.579 55.000 0.00 0.00 37.49 4.02
5180 6699 2.409870 GGACCCATTTGCGGCTCAG 61.410 63.158 0.00 0.00 0.00 3.35
5216 6735 4.728102 TCGGTGCGGACGCGAAAT 62.728 61.111 15.93 0.00 45.51 2.17
5243 6762 2.733593 GCGTGTCCACTCGGTGTC 60.734 66.667 3.60 0.00 33.93 3.67
5588 7107 1.470098 CAGCGACAAAGCCTAGCAAAT 59.530 47.619 0.00 0.00 38.01 2.32
5594 7113 4.518249 GACAAAGCCTAGCAAATCCTAGT 58.482 43.478 0.00 0.00 34.34 2.57
5599 7118 2.803492 GCCTAGCAAATCCTAGTCACCG 60.803 54.545 0.00 0.00 34.34 4.94
5615 7134 1.379044 CCGCAATGGGCCTCTTCTT 60.379 57.895 4.53 0.00 40.31 2.52
5671 7190 3.056328 GCGTGCTTCCCCCACTTC 61.056 66.667 0.00 0.00 0.00 3.01
5672 7191 2.359975 CGTGCTTCCCCCACTTCC 60.360 66.667 0.00 0.00 0.00 3.46
5673 7192 2.359975 GTGCTTCCCCCACTTCCG 60.360 66.667 0.00 0.00 0.00 4.30
5721 7240 4.457496 ATCGCCGTCCCAGTGCAG 62.457 66.667 0.00 0.00 0.00 4.41
5745 7264 2.029844 GAAGTGGCACTCGGAGCAC 61.030 63.158 22.31 5.58 0.00 4.40
5770 7289 4.084147 CCCTCCCCTACCCCGACA 62.084 72.222 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 113 2.038863 ACCCTTGTACCATGGAGTCA 57.961 50.000 21.47 11.26 31.33 3.41
212 213 3.556775 GCAGCTTTCAAATCAGCAAAACA 59.443 39.130 0.00 0.00 38.61 2.83
398 399 1.945387 AGCGACTGATGGCATTACTG 58.055 50.000 0.00 0.00 30.59 2.74
414 415 7.797123 GGTTAATATTGAATTTTCGACCTAGCG 59.203 37.037 0.00 0.00 0.00 4.26
492 493 6.807230 CCCCTAACTTTCTGATACGATAATCG 59.193 42.308 0.00 0.00 46.93 3.34
493 494 7.668492 ACCCCTAACTTTCTGATACGATAATC 58.332 38.462 0.00 0.00 0.00 1.75
536 537 6.431198 AAAAAGTCTAACTGAAGCGAACAA 57.569 33.333 0.00 0.00 0.00 2.83
554 555 2.749076 TCATGCATGAGTCCGGAAAAAG 59.251 45.455 25.42 0.00 32.11 2.27
646 647 9.744468 TTGCTGGAAAAAGAACTTAAGTAAATC 57.256 29.630 8.92 2.99 0.00 2.17
653 654 7.286775 ACACCTATTGCTGGAAAAAGAACTTAA 59.713 33.333 0.00 0.00 0.00 1.85
725 729 6.723298 AAAGGTCAATGTTCCACATAACAA 57.277 33.333 0.00 0.00 42.33 2.83
839 843 7.335422 AGTTATCAGCTATGTTCTGTTCCAAAG 59.665 37.037 0.00 0.00 33.48 2.77
944 948 0.949105 CGCCGCAAACCACTAGAAGT 60.949 55.000 0.00 0.00 0.00 3.01
983 987 1.605165 GCACGGACCAAAATGGGGA 60.605 57.895 0.87 0.00 43.37 4.81
1035 1039 4.909696 TTTCGCAGAAATGAAGTTCCAA 57.090 36.364 0.00 0.00 45.90 3.53
1036 1040 4.761739 AGATTTCGCAGAAATGAAGTTCCA 59.238 37.500 17.26 0.00 45.90 3.53
1052 1056 6.568869 ACCAGAACAGAAGATAGAGATTTCG 58.431 40.000 0.00 0.00 0.00 3.46
1139 1143 1.209621 TGGTGCCTACTCCCCATTAC 58.790 55.000 0.00 0.00 0.00 1.89
1375 1379 8.592529 TCCTTTCATTGAATTATGTGATTCCA 57.407 30.769 0.00 0.00 35.61 3.53
1822 1827 2.435805 TGATGCAGTCTTAGGGTCATCC 59.564 50.000 0.00 0.00 31.85 3.51
1991 1996 0.251916 ACTGCTTTAGGCGCCACATA 59.748 50.000 31.54 9.92 45.43 2.29
2076 2081 9.458374 AAATTTAATATACATAAGCCACGCAAC 57.542 29.630 0.00 0.00 0.00 4.17
2615 2622 4.154918 CCAAAGTCTGCAATCTTCAGTACC 59.845 45.833 3.97 0.00 33.48 3.34
2670 2677 3.135994 CAACACGGCTAGTTAGTGGTTT 58.864 45.455 15.21 3.31 39.95 3.27
2742 2749 1.134699 CCACATATCCACAGCGACACT 60.135 52.381 0.00 0.00 0.00 3.55
2984 2993 5.221601 TGGCACCTTTGATTTCTTGCAATAA 60.222 36.000 0.00 0.00 0.00 1.40
3418 4928 2.916702 AGATGCACAGTCACACAAGA 57.083 45.000 0.00 0.00 0.00 3.02
3558 5068 2.949177 TACTCCTTGCTTGCTGGAAA 57.051 45.000 8.58 0.34 0.00 3.13
3759 5269 6.723515 TGGTTACATGATTTTCATTTCCTGGA 59.276 34.615 0.00 0.00 34.28 3.86
4068 5581 1.019805 GGGGTAGAACTTCACGCTGC 61.020 60.000 0.00 0.00 0.00 5.25
4459 5972 1.270550 GACCACAGAAAGGCAATGGTG 59.729 52.381 0.00 0.00 43.73 4.17
4570 6083 1.452833 GCCTCTTGGATGTGCCTCC 60.453 63.158 0.00 0.00 37.63 4.30
4736 6250 4.621068 TGCATGCTAAAACTCTATGCAC 57.379 40.909 20.33 0.00 46.31 4.57
4739 6253 4.094887 ACGGTTGCATGCTAAAACTCTATG 59.905 41.667 20.33 6.84 0.00 2.23
4756 6270 4.804139 GGAGTATATGAGAACACACGGTTG 59.196 45.833 0.00 0.00 40.63 3.77
4776 6290 2.238898 ACCTATTTTGGAACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
4777 6291 2.026636 CACCTATTTTGGAACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
4778 6292 2.026636 TCACCTATTTTGGAACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
4779 6293 3.007635 GTCACCTATTTTGGAACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
4780 6294 3.933332 GAGTCACCTATTTTGGAACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
4782 6296 3.670625 TGAGTCACCTATTTTGGAACGG 58.329 45.455 0.00 0.00 0.00 4.44
4783 6297 4.755123 AGTTGAGTCACCTATTTTGGAACG 59.245 41.667 0.00 0.00 0.00 3.95
4784 6298 6.635030 AAGTTGAGTCACCTATTTTGGAAC 57.365 37.500 0.00 0.00 0.00 3.62
4785 6299 6.605594 ACAAAGTTGAGTCACCTATTTTGGAA 59.394 34.615 12.94 0.00 0.00 3.53
4786 6300 6.126409 ACAAAGTTGAGTCACCTATTTTGGA 58.874 36.000 12.94 0.00 0.00 3.53
4787 6301 6.391227 ACAAAGTTGAGTCACCTATTTTGG 57.609 37.500 12.94 0.00 0.00 3.28
4788 6302 9.965824 ATTTACAAAGTTGAGTCACCTATTTTG 57.034 29.630 8.80 8.80 0.00 2.44
4789 6303 9.965824 CATTTACAAAGTTGAGTCACCTATTTT 57.034 29.630 0.00 0.00 0.00 1.82
4790 6304 8.576442 CCATTTACAAAGTTGAGTCACCTATTT 58.424 33.333 0.00 0.00 0.00 1.40
4791 6305 7.942341 TCCATTTACAAAGTTGAGTCACCTATT 59.058 33.333 0.00 0.00 0.00 1.73
4792 6306 7.458397 TCCATTTACAAAGTTGAGTCACCTAT 58.542 34.615 0.00 0.00 0.00 2.57
4793 6307 6.833041 TCCATTTACAAAGTTGAGTCACCTA 58.167 36.000 0.00 0.00 0.00 3.08
4794 6308 5.690865 TCCATTTACAAAGTTGAGTCACCT 58.309 37.500 0.00 0.00 0.00 4.00
4795 6309 5.048713 CCTCCATTTACAAAGTTGAGTCACC 60.049 44.000 0.00 0.00 0.00 4.02
4796 6310 5.531287 ACCTCCATTTACAAAGTTGAGTCAC 59.469 40.000 0.00 0.00 0.00 3.67
4797 6311 5.690865 ACCTCCATTTACAAAGTTGAGTCA 58.309 37.500 0.00 0.00 0.00 3.41
4798 6312 6.935208 ACTACCTCCATTTACAAAGTTGAGTC 59.065 38.462 0.00 0.00 0.00 3.36
4799 6313 6.838382 ACTACCTCCATTTACAAAGTTGAGT 58.162 36.000 0.00 0.00 0.00 3.41
4800 6314 7.876068 TGTACTACCTCCATTTACAAAGTTGAG 59.124 37.037 0.00 0.00 0.00 3.02
4801 6315 7.737869 TGTACTACCTCCATTTACAAAGTTGA 58.262 34.615 0.00 0.00 0.00 3.18
4802 6316 7.972832 TGTACTACCTCCATTTACAAAGTTG 57.027 36.000 0.00 0.00 0.00 3.16
4803 6317 8.983702 TTTGTACTACCTCCATTTACAAAGTT 57.016 30.769 0.00 0.00 37.59 2.66
4804 6318 8.617290 CTTTGTACTACCTCCATTTACAAAGT 57.383 34.615 18.15 0.00 46.35 2.66
4806 6320 8.842280 CAACTTTGTACTACCTCCATTTACAAA 58.158 33.333 0.00 0.00 39.27 2.83
4807 6321 7.446013 CCAACTTTGTACTACCTCCATTTACAA 59.554 37.037 0.00 0.00 32.23 2.41
4808 6322 6.938030 CCAACTTTGTACTACCTCCATTTACA 59.062 38.462 0.00 0.00 0.00 2.41
4809 6323 6.373495 CCCAACTTTGTACTACCTCCATTTAC 59.627 42.308 0.00 0.00 0.00 2.01
4810 6324 6.044637 ACCCAACTTTGTACTACCTCCATTTA 59.955 38.462 0.00 0.00 0.00 1.40
4811 6325 5.163023 ACCCAACTTTGTACTACCTCCATTT 60.163 40.000 0.00 0.00 0.00 2.32
4812 6326 4.352893 ACCCAACTTTGTACTACCTCCATT 59.647 41.667 0.00 0.00 0.00 3.16
4813 6327 3.914435 ACCCAACTTTGTACTACCTCCAT 59.086 43.478 0.00 0.00 0.00 3.41
4814 6328 3.320129 ACCCAACTTTGTACTACCTCCA 58.680 45.455 0.00 0.00 0.00 3.86
4815 6329 3.325716 TGACCCAACTTTGTACTACCTCC 59.674 47.826 0.00 0.00 0.00 4.30
4816 6330 4.612264 TGACCCAACTTTGTACTACCTC 57.388 45.455 0.00 0.00 0.00 3.85
4817 6331 4.844655 AGATGACCCAACTTTGTACTACCT 59.155 41.667 0.00 0.00 0.00 3.08
4818 6332 5.161943 AGATGACCCAACTTTGTACTACC 57.838 43.478 0.00 0.00 0.00 3.18
4819 6333 8.788325 AAATAGATGACCCAACTTTGTACTAC 57.212 34.615 0.00 0.00 0.00 2.73
4820 6334 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
4821 6335 7.942341 TCAAAATAGATGACCCAACTTTGTACT 59.058 33.333 0.00 0.00 0.00 2.73
4822 6336 8.106247 TCAAAATAGATGACCCAACTTTGTAC 57.894 34.615 0.00 0.00 0.00 2.90
4823 6337 8.698973 TTCAAAATAGATGACCCAACTTTGTA 57.301 30.769 0.00 0.00 0.00 2.41
4824 6338 7.595819 TTCAAAATAGATGACCCAACTTTGT 57.404 32.000 0.00 0.00 0.00 2.83
4825 6339 7.925483 TGTTTCAAAATAGATGACCCAACTTTG 59.075 33.333 0.00 0.00 0.00 2.77
4826 6340 8.017418 TGTTTCAAAATAGATGACCCAACTTT 57.983 30.769 0.00 0.00 0.00 2.66
4827 6341 7.505585 TCTGTTTCAAAATAGATGACCCAACTT 59.494 33.333 0.00 0.00 32.24 2.66
4828 6342 7.004086 TCTGTTTCAAAATAGATGACCCAACT 58.996 34.615 0.00 0.00 32.24 3.16
4829 6343 7.214467 TCTGTTTCAAAATAGATGACCCAAC 57.786 36.000 0.00 0.00 32.24 3.77
4830 6344 6.434028 CCTCTGTTTCAAAATAGATGACCCAA 59.566 38.462 2.91 0.00 35.92 4.12
4831 6345 5.945784 CCTCTGTTTCAAAATAGATGACCCA 59.054 40.000 2.91 0.00 35.92 4.51
4832 6346 5.358160 CCCTCTGTTTCAAAATAGATGACCC 59.642 44.000 2.91 0.00 35.92 4.46
4833 6347 6.180472 TCCCTCTGTTTCAAAATAGATGACC 58.820 40.000 2.91 0.00 35.92 4.02
4834 6348 6.881602 ACTCCCTCTGTTTCAAAATAGATGAC 59.118 38.462 2.91 0.00 35.92 3.06
4835 6349 7.020827 ACTCCCTCTGTTTCAAAATAGATGA 57.979 36.000 2.91 3.20 35.92 2.92
4836 6350 7.497249 CCTACTCCCTCTGTTTCAAAATAGATG 59.503 40.741 2.91 1.27 35.92 2.90
4837 6351 7.403231 TCCTACTCCCTCTGTTTCAAAATAGAT 59.597 37.037 2.91 0.00 35.92 1.98
4838 6352 6.729100 TCCTACTCCCTCTGTTTCAAAATAGA 59.271 38.462 2.56 2.56 35.32 1.98
4839 6353 6.947464 TCCTACTCCCTCTGTTTCAAAATAG 58.053 40.000 0.00 0.00 0.00 1.73
4840 6354 6.945636 TCCTACTCCCTCTGTTTCAAAATA 57.054 37.500 0.00 0.00 0.00 1.40
4841 6355 5.843019 TCCTACTCCCTCTGTTTCAAAAT 57.157 39.130 0.00 0.00 0.00 1.82
4842 6356 5.843019 ATCCTACTCCCTCTGTTTCAAAA 57.157 39.130 0.00 0.00 0.00 2.44
4843 6357 7.338710 CAATATCCTACTCCCTCTGTTTCAAA 58.661 38.462 0.00 0.00 0.00 2.69
4844 6358 6.126768 CCAATATCCTACTCCCTCTGTTTCAA 60.127 42.308 0.00 0.00 0.00 2.69
4845 6359 5.366768 CCAATATCCTACTCCCTCTGTTTCA 59.633 44.000 0.00 0.00 0.00 2.69
4846 6360 5.221742 CCCAATATCCTACTCCCTCTGTTTC 60.222 48.000 0.00 0.00 0.00 2.78
4847 6361 4.660771 CCCAATATCCTACTCCCTCTGTTT 59.339 45.833 0.00 0.00 0.00 2.83
4848 6362 4.235372 CCCAATATCCTACTCCCTCTGTT 58.765 47.826 0.00 0.00 0.00 3.16
4849 6363 3.440154 CCCCAATATCCTACTCCCTCTGT 60.440 52.174 0.00 0.00 0.00 3.41
4850 6364 3.177228 CCCCAATATCCTACTCCCTCTG 58.823 54.545 0.00 0.00 0.00 3.35
4851 6365 2.804440 ACCCCAATATCCTACTCCCTCT 59.196 50.000 0.00 0.00 0.00 3.69
4852 6366 2.907042 CACCCCAATATCCTACTCCCTC 59.093 54.545 0.00 0.00 0.00 4.30
4853 6367 2.252945 ACACCCCAATATCCTACTCCCT 59.747 50.000 0.00 0.00 0.00 4.20
4854 6368 2.702748 ACACCCCAATATCCTACTCCC 58.297 52.381 0.00 0.00 0.00 4.30
4855 6369 4.790718 AAACACCCCAATATCCTACTCC 57.209 45.455 0.00 0.00 0.00 3.85
4857 6371 9.854303 AGTATATAAACACCCCAATATCCTACT 57.146 33.333 0.00 0.00 0.00 2.57
4898 6412 0.035152 ATTCAGTCATGCCCTGCGAA 60.035 50.000 7.20 0.03 0.00 4.70
4899 6413 0.035152 AATTCAGTCATGCCCTGCGA 60.035 50.000 7.20 0.89 0.00 5.10
5010 6525 6.625081 GCTCATAATTCAAGTGTACCAAACCC 60.625 42.308 0.00 0.00 0.00 4.11
5087 6605 1.375396 CGACCCAAACAGATGGCGA 60.375 57.895 0.00 0.00 39.26 5.54
5092 6610 1.736645 CGCGACGACCCAAACAGAT 60.737 57.895 0.00 0.00 0.00 2.90
5155 6673 3.080045 GCAAATGGGTCCATGCGGG 62.080 63.158 2.91 0.00 36.68 6.13
5160 6678 2.360191 AGCCGCAAATGGGTCCAT 59.640 55.556 0.00 0.00 33.58 3.41
5165 6684 0.819582 AAATCTGAGCCGCAAATGGG 59.180 50.000 0.00 0.00 0.00 4.00
5180 6699 2.705154 GACGCATTTCAGCCGTAAATC 58.295 47.619 0.00 0.00 0.00 2.17
5215 6734 4.796231 GACACGCGGCGAGTCCAT 62.796 66.667 32.90 10.61 40.45 3.41
5258 6777 3.627952 TAGTTGGGCGGCCGTCAA 61.628 61.111 33.48 28.26 0.00 3.18
5567 7086 0.955428 TTGCTAGGCTTTGTCGCTGG 60.955 55.000 0.00 0.00 0.00 4.85
5569 7088 1.740025 GATTTGCTAGGCTTTGTCGCT 59.260 47.619 0.00 0.00 0.00 4.93
5573 7092 4.019321 TGACTAGGATTTGCTAGGCTTTGT 60.019 41.667 12.48 0.00 32.62 2.83
5588 7107 1.904771 CCCATTGCGGTGACTAGGA 59.095 57.895 0.00 0.00 0.00 2.94
5594 7113 2.819984 GAAGAGGCCCATTGCGGTGA 62.820 60.000 0.00 0.00 42.61 4.02
5599 7118 1.379642 CCGAAGAAGAGGCCCATTGC 61.380 60.000 0.00 0.00 40.16 3.56
5615 7134 3.140073 TTGCCCTTTCCCTTGCCGA 62.140 57.895 0.00 0.00 0.00 5.54
5654 7173 3.056328 GAAGTGGGGGAAGCACGC 61.056 66.667 0.00 0.00 0.00 5.34
5656 7175 2.359975 CGGAAGTGGGGGAAGCAC 60.360 66.667 0.00 0.00 0.00 4.40
5666 7185 3.966026 GAGGACGACGGCGGAAGTG 62.966 68.421 18.49 0.00 43.17 3.16
5667 7186 3.745803 GAGGACGACGGCGGAAGT 61.746 66.667 18.49 7.97 43.17 3.01
5668 7187 4.493747 GGAGGACGACGGCGGAAG 62.494 72.222 18.49 4.21 43.17 3.46
5721 7240 3.426568 GAGTGCCACTTCGCCTGC 61.427 66.667 0.00 0.00 0.00 4.85
5724 7243 4.373116 TCCGAGTGCCACTTCGCC 62.373 66.667 0.00 0.00 0.00 5.54
5726 7245 2.811317 GCTCCGAGTGCCACTTCG 60.811 66.667 0.00 4.30 0.00 3.79
5753 7272 3.406113 ATGTCGGGGTAGGGGAGGG 62.406 68.421 0.00 0.00 0.00 4.30
5754 7273 2.140792 CATGTCGGGGTAGGGGAGG 61.141 68.421 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.