Multiple sequence alignment - TraesCS1B01G281000

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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 TraesCS1B01G281000 chr1B 100.000 3408 0 0 1 3408 489246476 489243069 0.000000e+00 6294.0
1 TraesCS1B01G281000 chr1D 86.433 1629 116 48 503 2097 365718814 365717257 0.000000e+00 1687.0
2 TraesCS1B01G281000 chr1D 86.279 1392 106 28 1 1344 365724360 365723006 0.000000e+00 1434.0
3 TraesCS1B01G281000 chr1D 86.045 1254 103 35 2183 3408 365716915 365715706 0.000000e+00 1280.0
4 TraesCS1B01G281000 chr1D 87.247 494 46 5 1 478 365719529 365719037 6.430000e-152 547.0
5 TraesCS1B01G281000 chr1D 97.561 82 2 0 2100 2181 365717138 365717057 1.280000e-29 141.0
6 TraesCS1B01G281000 chr1D 95.556 45 2 0 475 519 365718877 365718833 4.720000e-09 73.1
7 TraesCS1B01G281000 chr1A 88.025 1119 66 26 477 1559 464811687 464810601 0.000000e+00 1262.0
8 TraesCS1B01G281000 chr1A 87.018 986 69 22 2105 3067 464810015 464809066 0.000000e+00 1057.0
9 TraesCS1B01G281000 chr1A 86.590 522 37 7 1602 2098 464810604 464810091 2.310000e-151 545.0
10 TraesCS1B01G281000 chr1A 88.791 339 31 2 147 478 464812187 464811849 3.170000e-110 409.0
11 TraesCS1B01G281000 chr1A 93.939 99 5 1 50 148 464812532 464812435 7.620000e-32 148.0
12 TraesCS1B01G281000 chr1A 87.368 95 6 3 3062 3150 464806672 464806578 1.670000e-18 104.0


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 TraesCS1B01G281000 chr1B 489243069 489246476 3407 True 6294.00 6294 100.000000 1 3408 1 chr1B.!!$R1 3407
1 TraesCS1B01G281000 chr1D 365715706 365724360 8654 True 860.35 1687 89.853500 1 3408 6 chr1D.!!$R1 3407
2 TraesCS1B01G281000 chr1A 464806578 464812532 5954 True 587.50 1262 88.621833 50 3150 6 chr1A.!!$R1 3100

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
447 713 0.104855 GCGGTGAGAGGTGATATGCA 59.895 55.0 0.0 0.0 0.0 3.96 F
815 6155 0.457851 CGGCAACCAGTCAAAAACCA 59.542 50.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1332 6704 0.040781 AATCAACGCCAAAACGACCG 60.041 50.0 0.0 0.0 36.7 4.79 R
2414 8090 1.187087 AGAAGAACAGAGCCTACCCG 58.813 55.0 0.0 0.0 0.0 5.28 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
35 36 7.764901 GGTTCTAACTAAGGACTTCAACATAGG 59.235 40.741 0.00 0.00 33.68 2.57
55 56 5.656213 AGGCTAGTTACGTGATGTTAAGT 57.344 39.130 0.00 0.00 0.00 2.24
91 92 6.831868 TGACTAGCTATAAGTGACACATACCA 59.168 38.462 8.59 0.00 0.00 3.25
115 116 7.808381 CCAAATTAACATTTTTGCATTGATGCA 59.192 29.630 14.25 14.25 45.01 3.96
192 442 4.132336 GACATTGATTATGGCAGCTCTCA 58.868 43.478 0.00 0.00 42.29 3.27
206 456 4.424626 CAGCTCTCACTAGCATTCGTAAA 58.575 43.478 0.00 0.00 45.30 2.01
254 505 3.021695 GGTTTGGCTCCTATTACCCAAC 58.978 50.000 0.00 0.00 37.10 3.77
342 608 2.484287 ATCCCACGGTTGGCTCCTTG 62.484 60.000 0.00 0.00 42.35 3.61
368 634 0.179070 CCGCTTTAGAGCCCTTCTCC 60.179 60.000 0.00 0.00 46.42 3.71
370 636 2.032620 CGCTTTAGAGCCCTTCTCCTA 58.967 52.381 0.00 0.00 46.42 2.94
403 669 3.692101 CCGTTTATGTGGTCCTTGCATAA 59.308 43.478 0.00 8.84 34.48 1.90
429 695 4.665212 CATTGTGGTCATAGTCACATTGC 58.335 43.478 0.00 0.00 42.51 3.56
443 709 1.831106 ACATTGCGGTGAGAGGTGATA 59.169 47.619 0.00 0.00 0.00 2.15
447 713 0.104855 GCGGTGAGAGGTGATATGCA 59.895 55.000 0.00 0.00 0.00 3.96
486 5755 4.823790 ACATTGTCCACTTTCGGTTTAC 57.176 40.909 0.00 0.00 0.00 2.01
547 5852 6.889198 AGTGAAATACATATCATATCGGGGG 58.111 40.000 0.00 0.00 0.00 5.40
556 5862 2.862541 TCATATCGGGGGAAAATGCAG 58.137 47.619 0.00 0.00 0.00 4.41
565 5871 4.499696 CGGGGGAAAATGCAGTATTGATTC 60.500 45.833 0.00 0.00 0.00 2.52
567 5873 4.405358 GGGGAAAATGCAGTATTGATTCCA 59.595 41.667 14.53 0.00 0.00 3.53
568 5874 5.351458 GGGAAAATGCAGTATTGATTCCAC 58.649 41.667 14.53 3.20 0.00 4.02
629 5935 8.735303 TGTCAAACAAATTATCCAACAATACG 57.265 30.769 0.00 0.00 0.00 3.06
630 5936 8.353684 TGTCAAACAAATTATCCAACAATACGT 58.646 29.630 0.00 0.00 0.00 3.57
650 5956 6.861065 ACGTATGTGCCTTATAAATCCAAG 57.139 37.500 0.00 0.00 0.00 3.61
651 5957 5.238650 ACGTATGTGCCTTATAAATCCAAGC 59.761 40.000 0.00 0.00 0.00 4.01
690 5997 8.408601 TGTAACCTAACTTGGTCGACTATTATC 58.591 37.037 16.46 0.00 39.83 1.75
765 6103 6.619801 AGTTCTGACTACAAAAATCCACAC 57.380 37.500 0.00 0.00 33.32 3.82
771 6109 2.774439 ACAAAAATCCACACGCTCAC 57.226 45.000 0.00 0.00 0.00 3.51
772 6110 2.297701 ACAAAAATCCACACGCTCACT 58.702 42.857 0.00 0.00 0.00 3.41
815 6155 0.457851 CGGCAACCAGTCAAAAACCA 59.542 50.000 0.00 0.00 0.00 3.67
823 6164 6.225318 CAACCAGTCAAAAACCATCATCAAT 58.775 36.000 0.00 0.00 0.00 2.57
830 6171 7.816031 AGTCAAAAACCATCATCAATAAGCAAG 59.184 33.333 0.00 0.00 0.00 4.01
832 6173 6.855763 AAAACCATCATCAATAAGCAAGGA 57.144 33.333 0.00 0.00 0.00 3.36
838 6179 6.489022 CCATCATCAATAAGCAAGGAGATGAA 59.511 38.462 12.86 1.41 43.27 2.57
839 6180 6.932356 TCATCAATAAGCAAGGAGATGAAC 57.068 37.500 8.19 0.00 38.95 3.18
840 6181 5.824624 TCATCAATAAGCAAGGAGATGAACC 59.175 40.000 8.19 0.00 38.95 3.62
841 6182 5.441718 TCAATAAGCAAGGAGATGAACCT 57.558 39.130 0.00 0.00 39.69 3.50
842 6183 5.819991 TCAATAAGCAAGGAGATGAACCTT 58.180 37.500 0.00 0.00 47.00 3.50
850 6206 5.555017 CAAGGAGATGAACCTTCTTCAGAA 58.445 41.667 0.00 0.00 44.65 3.02
851 6207 6.179040 CAAGGAGATGAACCTTCTTCAGAAT 58.821 40.000 0.00 0.00 44.65 2.40
859 6215 2.485814 ACCTTCTTCAGAATTTGCGAGC 59.514 45.455 0.00 0.00 33.01 5.03
949 6305 3.479269 GTCGCGCACACAGCCTAC 61.479 66.667 8.75 0.00 41.38 3.18
950 6306 3.984749 TCGCGCACACAGCCTACA 61.985 61.111 8.75 0.00 41.38 2.74
951 6307 3.777925 CGCGCACACAGCCTACAC 61.778 66.667 8.75 0.00 41.38 2.90
963 6319 2.357034 CTACACAGCCGCACGGTT 60.357 61.111 11.27 0.83 37.65 4.44
972 6328 2.095668 CAGCCGCACGGTTGTTATTAAA 60.096 45.455 16.65 0.00 40.86 1.52
973 6329 2.553172 AGCCGCACGGTTGTTATTAAAA 59.447 40.909 11.27 0.00 37.65 1.52
974 6330 2.912345 GCCGCACGGTTGTTATTAAAAG 59.088 45.455 11.27 0.00 37.65 2.27
975 6331 2.912345 CCGCACGGTTGTTATTAAAAGC 59.088 45.455 0.00 0.00 0.00 3.51
977 6333 3.609644 CGCACGGTTGTTATTAAAAGCCA 60.610 43.478 1.02 0.00 0.00 4.75
978 6334 3.671459 GCACGGTTGTTATTAAAAGCCAC 59.329 43.478 1.02 0.00 0.00 5.01
980 6336 3.890147 ACGGTTGTTATTAAAAGCCACCA 59.110 39.130 1.02 0.00 0.00 4.17
982 6338 4.562082 GGTTGTTATTAAAAGCCACCACC 58.438 43.478 0.00 0.00 0.00 4.61
983 6339 4.231439 GTTGTTATTAAAAGCCACCACCG 58.769 43.478 0.00 0.00 0.00 4.94
1247 6606 3.740397 CAGGTACCGTGCCGTCGA 61.740 66.667 6.18 0.00 0.00 4.20
1248 6607 3.437795 AGGTACCGTGCCGTCGAG 61.438 66.667 6.18 0.00 0.00 4.04
1311 6683 1.894282 GCGGGATCTAGGCCTTTGC 60.894 63.158 12.58 1.12 0.00 3.68
1332 6704 1.239347 GATCCGATTTAGCTTGGCCC 58.761 55.000 0.00 0.00 0.00 5.80
1375 6747 4.127907 GTTCTCTTGAGACTTTTTCCGGT 58.872 43.478 0.00 0.00 0.00 5.28
1400 6772 2.821969 GTGTCAATTTGCTGATCTGGGT 59.178 45.455 1.46 0.00 0.00 4.51
1526 6898 2.529744 AAGAGTGAGCGCCCCCTTT 61.530 57.895 2.29 0.00 0.00 3.11
1533 6905 1.005450 TGAGCGCCCCCTTTCTTTTAT 59.995 47.619 2.29 0.00 0.00 1.40
1535 6907 3.284617 GAGCGCCCCCTTTCTTTTATTA 58.715 45.455 2.29 0.00 0.00 0.98
1536 6908 3.288092 AGCGCCCCCTTTCTTTTATTAG 58.712 45.455 2.29 0.00 0.00 1.73
1537 6909 2.223735 GCGCCCCCTTTCTTTTATTAGC 60.224 50.000 0.00 0.00 0.00 3.09
1565 6940 4.844884 AGTTCCAGTTATACTTGCTTCCC 58.155 43.478 0.00 0.00 0.00 3.97
1571 6946 3.844211 AGTTATACTTGCTTCCCCTGTGA 59.156 43.478 0.00 0.00 0.00 3.58
1575 6950 1.707427 ACTTGCTTCCCCTGTGAAGAT 59.293 47.619 5.03 0.00 43.60 2.40
1580 6955 4.735369 TGCTTCCCCTGTGAAGATTTTTA 58.265 39.130 5.03 0.00 43.60 1.52
1582 6957 5.779771 TGCTTCCCCTGTGAAGATTTTTAAT 59.220 36.000 5.03 0.00 43.60 1.40
1585 6960 8.478066 GCTTCCCCTGTGAAGATTTTTAATTAT 58.522 33.333 5.03 0.00 43.60 1.28
1670 7045 5.698832 CGGAATTTAGTTGCATTGAGTCAA 58.301 37.500 8.27 8.27 0.00 3.18
1768 7144 4.142534 ACTTGCCAAATCATCTCATCAACG 60.143 41.667 0.00 0.00 0.00 4.10
1782 7158 7.956420 TCTCATCAACGTGTAGTGTAAAATT 57.044 32.000 0.00 0.00 0.00 1.82
1789 7165 6.695292 ACGTGTAGTGTAAAATTAAGTCCG 57.305 37.500 0.00 0.00 0.00 4.79
1866 7266 9.665719 TCAGAGTAAAATATTTCACTGCACATA 57.334 29.630 8.79 0.00 29.14 2.29
1899 7299 7.946207 TCACATGCTAAAAAGAATGTTTGGTA 58.054 30.769 0.00 0.00 35.96 3.25
1946 7346 3.809832 AGTCTTTCTGTTTCATGTGGACG 59.190 43.478 0.00 0.00 0.00 4.79
1987 7388 4.641396 TCATTAATCATCCCACTTAGCCG 58.359 43.478 0.00 0.00 0.00 5.52
2023 7430 5.237344 GCTTGGTGGATGATAGTTATGTGAC 59.763 44.000 0.00 0.00 0.00 3.67
2024 7431 5.290493 TGGTGGATGATAGTTATGTGACC 57.710 43.478 0.00 0.00 0.00 4.02
2098 7505 4.793071 TGCGAAACAGGATTTATGTTGTG 58.207 39.130 0.00 0.00 39.91 3.33
2117 7653 7.403421 TGTTGTGTGAATTTTAGTTGTACTCG 58.597 34.615 0.00 0.00 0.00 4.18
2181 7717 5.243730 GCCTATCTCATCTGACTAGAAGCTT 59.756 44.000 0.00 0.00 36.32 3.74
2202 7878 7.428826 AGCTTTTATGCTGGATATGCTAAAAC 58.571 34.615 8.99 0.00 42.33 2.43
2204 7880 5.940192 TTATGCTGGATATGCTAAAACCG 57.060 39.130 0.00 0.00 0.00 4.44
2215 7891 3.847542 TGCTAAAACCGCGTGTTAGATA 58.152 40.909 19.11 10.45 35.90 1.98
2216 7892 4.244066 TGCTAAAACCGCGTGTTAGATAA 58.756 39.130 19.11 6.18 35.90 1.75
2217 7893 4.091800 TGCTAAAACCGCGTGTTAGATAAC 59.908 41.667 19.11 8.47 35.90 1.89
2218 7894 4.328169 GCTAAAACCGCGTGTTAGATAACT 59.672 41.667 19.11 0.57 35.90 2.24
2219 7895 4.657075 AAAACCGCGTGTTAGATAACTG 57.343 40.909 4.92 0.00 35.67 3.16
2220 7896 3.581024 AACCGCGTGTTAGATAACTGA 57.419 42.857 4.92 0.00 34.69 3.41
2221 7897 3.795623 ACCGCGTGTTAGATAACTGAT 57.204 42.857 4.92 0.00 37.12 2.90
2386 8062 1.902918 TGGACATGCCAGCACAACC 60.903 57.895 4.93 0.00 43.33 3.77
2414 8090 1.043116 GGGCCTTATGTGAAAGCCCC 61.043 60.000 7.14 0.00 37.01 5.80
2416 8092 1.384222 GCCTTATGTGAAAGCCCCGG 61.384 60.000 0.00 0.00 0.00 5.73
2536 8212 8.862325 TCCTGAAGTGTGTAAATGTAATGAAT 57.138 30.769 0.00 0.00 0.00 2.57
2551 8245 6.151004 TGTAATGAATTAATGCATGATGGCG 58.849 36.000 9.81 0.00 36.28 5.69
2574 8268 6.417327 CGAACAAATGTGCTGATCTAATCTC 58.583 40.000 0.00 0.00 0.00 2.75
2576 8270 5.423015 ACAAATGTGCTGATCTAATCTCGT 58.577 37.500 0.00 0.00 0.00 4.18
2581 8275 3.001736 GTGCTGATCTAATCTCGTTTGGC 59.998 47.826 0.00 0.00 0.00 4.52
2624 8318 1.151668 GCAAACTGATGTGCTCGTCT 58.848 50.000 9.26 0.00 37.78 4.18
2625 8319 2.337583 GCAAACTGATGTGCTCGTCTA 58.662 47.619 9.26 0.00 37.78 2.59
2626 8320 2.736721 GCAAACTGATGTGCTCGTCTAA 59.263 45.455 9.26 0.00 37.78 2.10
2628 8322 4.493220 GCAAACTGATGTGCTCGTCTAATC 60.493 45.833 9.26 0.00 37.78 1.75
2629 8323 4.727507 AACTGATGTGCTCGTCTAATCT 57.272 40.909 9.26 0.00 0.00 2.40
2630 8324 4.039151 ACTGATGTGCTCGTCTAATCTG 57.961 45.455 9.26 0.31 0.00 2.90
2631 8325 3.181482 ACTGATGTGCTCGTCTAATCTGG 60.181 47.826 9.26 0.00 0.00 3.86
2632 8326 3.023832 TGATGTGCTCGTCTAATCTGGA 58.976 45.455 9.26 0.00 0.00 3.86
2633 8327 3.638627 TGATGTGCTCGTCTAATCTGGAT 59.361 43.478 9.26 0.00 0.00 3.41
2634 8328 3.443099 TGTGCTCGTCTAATCTGGATG 57.557 47.619 0.00 0.00 0.00 3.51
2637 8331 1.689273 GCTCGTCTAATCTGGATGGGT 59.311 52.381 0.00 0.00 0.00 4.51
2644 8338 2.905415 AATCTGGATGGGTTTGCTCA 57.095 45.000 0.00 0.00 0.00 4.26
2679 8373 5.486526 CTCATGAGCTGTTTATAGGGATCC 58.513 45.833 10.38 1.92 0.00 3.36
2717 8430 1.488390 ATGCACCCTGCTATTTTGGG 58.512 50.000 0.00 0.00 45.31 4.12
2734 8447 2.988570 TGGGCCATTGCATGAAAATTC 58.011 42.857 0.00 0.00 40.13 2.17
2777 8490 3.983344 GTCGCATTTGCAGAATTGTCTTT 59.017 39.130 3.13 0.00 42.21 2.52
2778 8491 4.445385 GTCGCATTTGCAGAATTGTCTTTT 59.555 37.500 3.13 0.00 42.21 2.27
2780 8493 5.050904 TCGCATTTGCAGAATTGTCTTTTTG 60.051 36.000 3.13 0.00 42.21 2.44
2829 8542 5.473162 TGGTCTAGACACAAAAATGGTCATG 59.527 40.000 23.91 0.00 34.04 3.07
2840 8553 8.281893 CACAAAAATGGTCATGTATTTCAAACC 58.718 33.333 0.00 0.00 36.84 3.27
2842 8555 6.582677 AAATGGTCATGTATTTCAAACCGA 57.417 33.333 0.00 0.00 38.19 4.69
2852 8566 6.107343 TGTATTTCAAACCGAATGTCCGATA 58.893 36.000 0.00 0.00 32.32 2.92
2904 8620 5.601662 TGACGAGATCTTTGAAACAAGACT 58.398 37.500 0.00 0.00 0.00 3.24
2905 8621 5.463392 TGACGAGATCTTTGAAACAAGACTG 59.537 40.000 0.00 0.00 0.00 3.51
2976 8693 5.011125 TGTTGTGGTCAAGTTTCAAAAAGGA 59.989 36.000 0.00 0.00 33.97 3.36
2981 8698 7.172361 TGTGGTCAAGTTTCAAAAAGGAAAAAG 59.828 33.333 0.00 0.00 38.41 2.27
2984 8701 8.779303 GGTCAAGTTTCAAAAAGGAAAAAGAAA 58.221 29.630 0.00 0.00 38.41 2.52
2985 8702 9.594038 GTCAAGTTTCAAAAAGGAAAAAGAAAC 57.406 29.630 0.00 0.00 42.93 2.78
3139 11265 4.230502 AGGCTTTAATGATGGGAGAGGAAA 59.769 41.667 0.00 0.00 0.00 3.13
3140 11266 4.339530 GGCTTTAATGATGGGAGAGGAAAC 59.660 45.833 0.00 0.00 0.00 2.78
3150 11276 0.670854 GAGAGGAAACGGTGGAGTGC 60.671 60.000 0.00 0.00 0.00 4.40
3153 11279 0.981183 AGGAAACGGTGGAGTGCATA 59.019 50.000 0.00 0.00 0.00 3.14
3154 11280 1.349688 AGGAAACGGTGGAGTGCATAA 59.650 47.619 0.00 0.00 0.00 1.90
3155 11281 1.467342 GGAAACGGTGGAGTGCATAAC 59.533 52.381 0.00 0.00 0.00 1.89
3156 11282 1.127951 GAAACGGTGGAGTGCATAACG 59.872 52.381 0.00 5.15 0.00 3.18
3157 11283 1.296056 AACGGTGGAGTGCATAACGC 61.296 55.000 0.00 0.00 42.89 4.84
3158 11284 2.798501 CGGTGGAGTGCATAACGCG 61.799 63.158 3.53 3.53 46.97 6.01
3159 11285 1.740296 GGTGGAGTGCATAACGCGT 60.740 57.895 5.58 5.58 46.97 6.01
3160 11286 1.419922 GTGGAGTGCATAACGCGTG 59.580 57.895 14.98 0.34 46.97 5.34
3161 11287 1.011968 GTGGAGTGCATAACGCGTGA 61.012 55.000 14.98 5.19 46.97 4.35
3162 11288 0.319986 TGGAGTGCATAACGCGTGAA 60.320 50.000 14.98 4.35 46.97 3.18
3163 11289 0.370273 GGAGTGCATAACGCGTGAAG 59.630 55.000 14.98 2.46 46.97 3.02
3194 11320 7.976135 AAAATTTGCTAATGTGCCAACAATA 57.024 28.000 0.00 0.00 40.46 1.90
3201 11327 6.071447 TGCTAATGTGCCAACAATACATTTCT 60.071 34.615 7.08 0.00 40.93 2.52
3206 11332 5.065859 TGTGCCAACAATACATTTCTATCCG 59.934 40.000 0.00 0.00 31.82 4.18
3266 11393 2.164422 TGCACTGGATACGTTCTCTCTG 59.836 50.000 0.00 0.00 42.51 3.35
3267 11394 2.164624 GCACTGGATACGTTCTCTCTGT 59.835 50.000 0.00 0.00 42.51 3.41
3286 11413 4.080919 TCTGTGTATATGCTCAGCTTGGTT 60.081 41.667 15.51 0.00 32.05 3.67
3304 11431 2.463876 GTTGTTGTTTGAAGAGCTGGC 58.536 47.619 0.00 0.00 0.00 4.85
3307 11434 2.694628 TGTTGTTTGAAGAGCTGGCATT 59.305 40.909 0.00 0.00 0.00 3.56
3309 11436 3.374220 TGTTTGAAGAGCTGGCATTTG 57.626 42.857 0.00 0.00 0.00 2.32
3317 11444 4.978438 AGAGCTGGCATTTGATAGAGAT 57.022 40.909 0.00 0.00 0.00 2.75
3336 11463 5.415701 AGAGATTGCGTTGATTGTACCAATT 59.584 36.000 0.00 0.00 0.00 2.32
3350 11477 4.832266 TGTACCAATTCCTGCAAAGTTGAT 59.168 37.500 5.79 0.00 0.00 2.57
3354 11481 5.481473 ACCAATTCCTGCAAAGTTGATGTAT 59.519 36.000 5.79 0.00 0.00 2.29
3366 11493 5.965033 AGTTGATGTATCCCACTCATCTT 57.035 39.130 0.00 0.00 38.78 2.40
3389 11516 2.372264 CATAGGCTGGCAGTTTGATGT 58.628 47.619 17.16 0.00 0.00 3.06
3400 11527 4.546570 GCAGTTTGATGTAAGGACCAAAC 58.453 43.478 0.00 0.00 45.00 2.93
3405 11532 4.216411 TGATGTAAGGACCAAACTAGGC 57.784 45.455 0.00 0.00 0.00 3.93
3406 11533 3.844211 TGATGTAAGGACCAAACTAGGCT 59.156 43.478 0.00 0.00 0.00 4.58
3407 11534 3.975168 TGTAAGGACCAAACTAGGCTC 57.025 47.619 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.367352 TGTTGAAGTCCTTAGTTAGAACCCA 59.633 40.000 0.00 0.00 0.00 4.51
35 36 7.982371 ATACACTTAACATCACGTAACTAGC 57.018 36.000 0.00 0.00 0.00 3.42
115 116 0.112412 GTTGTGGGAGGGGTTCACAT 59.888 55.000 0.00 0.00 42.31 3.21
163 413 4.707105 TGCCATAATCAATGTCTCGATGT 58.293 39.130 0.00 0.00 33.34 3.06
167 417 3.136763 AGCTGCCATAATCAATGTCTCG 58.863 45.455 0.00 0.00 33.34 4.04
170 420 4.024218 GTGAGAGCTGCCATAATCAATGTC 60.024 45.833 0.00 0.00 33.34 3.06
173 423 4.434545 AGTGAGAGCTGCCATAATCAAT 57.565 40.909 0.00 0.00 0.00 2.57
206 456 7.307989 GCGCCAATACTGACATATGTTAGAATT 60.308 37.037 28.70 15.15 35.49 2.17
342 608 2.586357 CTCTAAAGCGGCGCCTCC 60.586 66.667 30.40 15.55 0.00 4.30
368 634 6.083630 CCACATAAACGGACAAAACATGTAG 58.916 40.000 0.00 0.00 44.12 2.74
403 669 4.334552 TGTGACTATGACCACAATGCAAT 58.665 39.130 0.00 0.00 39.97 3.56
417 683 2.159043 CCTCTCACCGCAATGTGACTAT 60.159 50.000 0.00 0.00 40.22 2.12
422 688 0.320683 TCACCTCTCACCGCAATGTG 60.321 55.000 0.00 0.00 37.59 3.21
429 695 1.136891 TGTGCATATCACCTCTCACCG 59.863 52.381 0.00 0.00 45.03 4.94
466 732 4.320202 CCTGTAAACCGAAAGTGGACAATG 60.320 45.833 0.00 0.00 0.00 2.82
467 733 3.818773 CCTGTAAACCGAAAGTGGACAAT 59.181 43.478 0.00 0.00 0.00 2.71
486 5755 5.233083 TCTAGAAATACATGGATGCCCTG 57.767 43.478 0.00 0.00 0.00 4.45
546 5851 5.964758 TGTGGAATCAATACTGCATTTTCC 58.035 37.500 0.00 0.00 35.41 3.13
547 5852 7.760794 TGAATGTGGAATCAATACTGCATTTTC 59.239 33.333 0.00 0.00 0.00 2.29
556 5862 7.269084 CGCGATAATTGAATGTGGAATCAATAC 59.731 37.037 0.00 0.00 43.54 1.89
565 5871 1.333308 TGCCGCGATAATTGAATGTGG 59.667 47.619 8.23 0.00 0.00 4.17
567 5873 2.618241 ACATGCCGCGATAATTGAATGT 59.382 40.909 8.23 2.62 0.00 2.71
568 5874 3.272439 ACATGCCGCGATAATTGAATG 57.728 42.857 8.23 1.86 0.00 2.67
629 5935 5.468746 TCGCTTGGATTTATAAGGCACATAC 59.531 40.000 0.00 0.00 0.00 2.39
630 5936 5.616270 TCGCTTGGATTTATAAGGCACATA 58.384 37.500 0.00 0.00 0.00 2.29
667 5973 6.460676 CCGATAATAGTCGACCAAGTTAGGTT 60.461 42.308 13.01 0.00 43.38 3.50
712 6019 9.696917 GGGCGATCTTGAATTTTATAAATTGAT 57.303 29.630 0.00 0.52 0.00 2.57
795 6135 0.458260 GGTTTTTGACTGGTTGCCGT 59.542 50.000 0.00 0.00 0.00 5.68
815 6155 6.489361 GGTTCATCTCCTTGCTTATTGATGAT 59.511 38.462 0.00 0.00 39.60 2.45
823 6164 5.013079 TGAAGAAGGTTCATCTCCTTGCTTA 59.987 40.000 1.80 0.00 44.19 3.09
830 6171 6.624642 GCAAATTCTGAAGAAGGTTCATCTCC 60.625 42.308 0.00 0.00 37.48 3.71
832 6173 5.106396 CGCAAATTCTGAAGAAGGTTCATCT 60.106 40.000 0.00 0.00 37.48 2.90
838 6179 2.485814 GCTCGCAAATTCTGAAGAAGGT 59.514 45.455 0.00 0.00 37.48 3.50
839 6180 2.746362 AGCTCGCAAATTCTGAAGAAGG 59.254 45.455 0.00 0.00 37.48 3.46
840 6181 3.425892 CCAGCTCGCAAATTCTGAAGAAG 60.426 47.826 0.00 0.00 37.48 2.85
841 6182 2.485426 CCAGCTCGCAAATTCTGAAGAA 59.515 45.455 0.00 0.00 38.56 2.52
842 6183 2.079158 CCAGCTCGCAAATTCTGAAGA 58.921 47.619 0.00 0.00 0.00 2.87
850 6206 2.229792 TCTTTTGTCCAGCTCGCAAAT 58.770 42.857 7.43 0.00 33.00 2.32
851 6207 1.674359 TCTTTTGTCCAGCTCGCAAA 58.326 45.000 3.57 3.57 0.00 3.68
859 6215 2.348666 CCGCGAAGTATCTTTTGTCCAG 59.651 50.000 8.23 0.00 0.00 3.86
943 6299 4.742201 CGTGCGGCTGTGTAGGCT 62.742 66.667 0.00 0.00 46.62 4.58
945 6301 3.876589 AACCGTGCGGCTGTGTAGG 62.877 63.158 10.87 0.00 39.32 3.18
946 6302 2.357034 AACCGTGCGGCTGTGTAG 60.357 61.111 10.87 0.00 39.32 2.74
947 6303 2.663520 CAACCGTGCGGCTGTGTA 60.664 61.111 10.87 0.00 39.32 2.90
948 6304 2.926901 TAACAACCGTGCGGCTGTGT 62.927 55.000 18.53 13.28 43.02 3.72
949 6305 1.573829 ATAACAACCGTGCGGCTGTG 61.574 55.000 18.53 12.71 43.02 3.66
950 6306 0.887387 AATAACAACCGTGCGGCTGT 60.887 50.000 13.13 13.13 45.43 4.40
951 6307 1.080298 TAATAACAACCGTGCGGCTG 58.920 50.000 10.87 11.41 39.32 4.85
963 6319 3.752665 TCGGTGGTGGCTTTTAATAACA 58.247 40.909 0.00 0.00 0.00 2.41
964 6320 4.769859 TTCGGTGGTGGCTTTTAATAAC 57.230 40.909 0.00 0.00 0.00 1.89
972 6328 1.303317 GTGGATTCGGTGGTGGCTT 60.303 57.895 0.00 0.00 0.00 4.35
973 6329 2.185310 GAGTGGATTCGGTGGTGGCT 62.185 60.000 0.00 0.00 0.00 4.75
974 6330 1.745489 GAGTGGATTCGGTGGTGGC 60.745 63.158 0.00 0.00 0.00 5.01
975 6331 1.078426 GGAGTGGATTCGGTGGTGG 60.078 63.158 0.00 0.00 0.00 4.61
977 6333 1.677552 GTGGAGTGGATTCGGTGGT 59.322 57.895 0.00 0.00 0.00 4.16
978 6334 1.447838 CGTGGAGTGGATTCGGTGG 60.448 63.158 0.00 0.00 0.00 4.61
980 6336 2.978824 CCGTGGAGTGGATTCGGT 59.021 61.111 0.00 0.00 36.99 4.69
982 6338 2.629050 ATCGCCGTGGAGTGGATTCG 62.629 60.000 0.00 0.00 0.00 3.34
983 6339 1.144057 ATCGCCGTGGAGTGGATTC 59.856 57.895 0.00 0.00 0.00 2.52
1091 6447 2.280389 CCATGGCGATCTGGACGG 60.280 66.667 0.00 0.00 34.24 4.79
1243 6602 1.063811 GGATCCGGTTCGACTCGAC 59.936 63.158 0.00 0.00 34.89 4.20
1244 6603 1.377594 TGGATCCGGTTCGACTCGA 60.378 57.895 7.39 0.00 0.00 4.04
1247 6606 1.890894 CTGTGGATCCGGTTCGACT 59.109 57.895 23.05 0.00 0.00 4.18
1248 6607 1.810030 GCTGTGGATCCGGTTCGAC 60.810 63.158 17.91 17.91 0.00 4.20
1294 6666 1.595382 CGCAAAGGCCTAGATCCCG 60.595 63.158 5.16 0.00 36.38 5.14
1305 6677 1.264288 GCTAAATCGGATCCGCAAAGG 59.736 52.381 29.62 18.32 42.97 3.11
1311 6683 0.868406 GCCAAGCTAAATCGGATCCG 59.132 55.000 28.62 28.62 41.35 4.18
1332 6704 0.040781 AATCAACGCCAAAACGACCG 60.041 50.000 0.00 0.00 36.70 4.79
1375 6747 4.261698 CCAGATCAGCAAATTGACACACAA 60.262 41.667 0.00 0.00 42.95 3.33
1400 6772 0.251121 TCCTCGCTGCCAAAATTCCA 60.251 50.000 0.00 0.00 0.00 3.53
1517 6889 3.288092 AGCTAATAAAAGAAAGGGGGCG 58.712 45.455 0.00 0.00 0.00 6.13
1526 6898 8.090788 ACTGGAACTCCATAGCTAATAAAAGA 57.909 34.615 0.00 0.00 46.46 2.52
1533 6905 8.421784 CAAGTATAACTGGAACTCCATAGCTAA 58.578 37.037 0.00 0.00 46.46 3.09
1535 6907 6.686632 GCAAGTATAACTGGAACTCCATAGCT 60.687 42.308 0.00 0.00 46.46 3.32
1536 6908 5.467063 GCAAGTATAACTGGAACTCCATAGC 59.533 44.000 0.00 0.00 46.46 2.97
1537 6909 6.821388 AGCAAGTATAACTGGAACTCCATAG 58.179 40.000 0.00 0.00 46.46 2.23
1565 6940 7.973388 TGCGGAATAATTAAAAATCTTCACAGG 59.027 33.333 0.00 0.00 0.00 4.00
1580 6955 9.912634 CTAAATTCCACATTATGCGGAATAATT 57.087 29.630 22.86 17.59 45.58 1.40
1582 6957 7.367285 GCTAAATTCCACATTATGCGGAATAA 58.633 34.615 22.86 15.09 45.58 1.40
1585 6960 4.037446 GGCTAAATTCCACATTATGCGGAA 59.963 41.667 15.83 15.83 42.11 4.30
1751 7126 6.091305 ACACTACACGTTGATGAGATGATTTG 59.909 38.462 0.00 0.00 0.00 2.32
1768 7144 6.870439 AGGTCGGACTTAATTTTACACTACAC 59.130 38.462 8.23 0.00 0.00 2.90
1782 7158 2.803030 AGAGTAGCAGGTCGGACTTA 57.197 50.000 8.23 0.00 0.00 2.24
1810 7210 4.773674 TGCATCTTTGATCCCACATTTCTT 59.226 37.500 0.00 0.00 0.00 2.52
1872 7272 7.933033 ACCAAACATTCTTTTTAGCATGTGATT 59.067 29.630 0.00 0.00 30.15 2.57
1984 7385 1.576356 CAAGCCTCTTCACTATCGGC 58.424 55.000 0.00 0.00 40.99 5.54
1987 7388 2.501723 TCCACCAAGCCTCTTCACTATC 59.498 50.000 0.00 0.00 0.00 2.08
2023 7430 6.071952 CCATATTCCACCAGAAATTAATCCGG 60.072 42.308 0.00 0.00 38.21 5.14
2024 7431 6.714810 TCCATATTCCACCAGAAATTAATCCG 59.285 38.462 0.00 0.00 38.21 4.18
2054 7461 8.946085 TCGCAACATAAATCTTACTGAAGAAAT 58.054 29.630 0.00 0.00 44.85 2.17
2098 7505 9.953825 CTGAATACGAGTACAACTAAAATTCAC 57.046 33.333 0.00 0.00 31.72 3.18
2117 7653 9.846248 AAATCTTGTTAGTTCAATGCTGAATAC 57.154 29.630 0.00 0.00 43.39 1.89
2181 7717 5.278266 GCGGTTTTAGCATATCCAGCATAAA 60.278 40.000 0.00 0.00 34.19 1.40
2202 7878 4.148348 GCTTATCAGTTATCTAACACGCGG 59.852 45.833 12.47 1.27 38.62 6.46
2204 7880 6.583912 TTGCTTATCAGTTATCTAACACGC 57.416 37.500 3.15 0.00 38.62 5.34
2215 7891 8.036575 ACATGCACAAAATATTGCTTATCAGTT 58.963 29.630 0.00 0.00 40.34 3.16
2216 7892 7.549839 ACATGCACAAAATATTGCTTATCAGT 58.450 30.769 0.00 0.00 40.34 3.41
2217 7893 7.997107 ACATGCACAAAATATTGCTTATCAG 57.003 32.000 0.00 0.00 40.34 2.90
2218 7894 7.492020 GGAACATGCACAAAATATTGCTTATCA 59.508 33.333 0.00 0.00 40.34 2.15
2219 7895 7.707893 AGGAACATGCACAAAATATTGCTTATC 59.292 33.333 0.00 0.00 40.34 1.75
2220 7896 7.558604 AGGAACATGCACAAAATATTGCTTAT 58.441 30.769 0.00 0.00 40.34 1.73
2221 7897 6.934056 AGGAACATGCACAAAATATTGCTTA 58.066 32.000 0.00 0.00 40.34 3.09
2233 7909 2.369860 AGTGAGAAGAGGAACATGCACA 59.630 45.455 0.00 0.00 0.00 4.57
2386 8062 2.195567 CATAAGGCCCATGGTGCGG 61.196 63.158 11.73 0.00 0.00 5.69
2414 8090 1.187087 AGAAGAACAGAGCCTACCCG 58.813 55.000 0.00 0.00 0.00 5.28
2416 8092 5.112686 CACATTAGAAGAACAGAGCCTACC 58.887 45.833 0.00 0.00 0.00 3.18
2536 8212 4.446994 TTTGTTCGCCATCATGCATTAA 57.553 36.364 0.00 0.00 0.00 1.40
2551 8245 6.036517 ACGAGATTAGATCAGCACATTTGTTC 59.963 38.462 0.00 0.00 0.00 3.18
2574 8268 7.381139 ACATTAATTCAAACTTGTAGCCAAACG 59.619 33.333 0.00 0.00 0.00 3.60
2576 8270 8.417106 TCACATTAATTCAAACTTGTAGCCAAA 58.583 29.630 0.00 0.00 0.00 3.28
2581 8275 8.028354 TGCCATCACATTAATTCAAACTTGTAG 58.972 33.333 0.00 0.00 0.00 2.74
2624 8318 4.209538 CATGAGCAAACCCATCCAGATTA 58.790 43.478 0.00 0.00 0.00 1.75
2625 8319 2.905415 TGAGCAAACCCATCCAGATT 57.095 45.000 0.00 0.00 0.00 2.40
2626 8320 2.024655 ACATGAGCAAACCCATCCAGAT 60.025 45.455 0.00 0.00 0.00 2.90
2628 8322 1.843368 ACATGAGCAAACCCATCCAG 58.157 50.000 0.00 0.00 0.00 3.86
2629 8323 2.308570 ACTACATGAGCAAACCCATCCA 59.691 45.455 0.00 0.00 0.00 3.41
2630 8324 3.004752 ACTACATGAGCAAACCCATCC 57.995 47.619 0.00 0.00 0.00 3.51
2631 8325 5.163513 CAAAACTACATGAGCAAACCCATC 58.836 41.667 0.00 0.00 0.00 3.51
2632 8326 4.021192 CCAAAACTACATGAGCAAACCCAT 60.021 41.667 0.00 0.00 0.00 4.00
2633 8327 3.320541 CCAAAACTACATGAGCAAACCCA 59.679 43.478 0.00 0.00 0.00 4.51
2634 8328 3.860754 GCCAAAACTACATGAGCAAACCC 60.861 47.826 0.00 0.00 0.00 4.11
2637 8331 3.888323 TGAGCCAAAACTACATGAGCAAA 59.112 39.130 0.00 0.00 0.00 3.68
2664 8358 5.785423 TGGATACAGGGATCCCTATAAACAG 59.215 44.000 33.41 20.56 46.28 3.16
2717 8430 2.353579 GCCAGAATTTTCATGCAATGGC 59.646 45.455 4.96 4.96 46.73 4.40
2734 8447 5.220548 CGACAACAATTCATCTTCTAGCCAG 60.221 44.000 0.00 0.00 0.00 4.85
2796 8509 8.925161 TTTTTGTGTCTAGACCAAGAAATTTG 57.075 30.769 20.11 0.00 0.00 2.32
2803 8516 5.530915 TGACCATTTTTGTGTCTAGACCAAG 59.469 40.000 20.11 12.46 0.00 3.61
2829 8542 4.932268 TCGGACATTCGGTTTGAAATAC 57.068 40.909 0.00 0.00 40.71 1.89
2840 8553 3.057736 ACGGATTAGGTATCGGACATTCG 60.058 47.826 0.00 0.00 37.12 3.34
2842 8555 4.950205 AACGGATTAGGTATCGGACATT 57.050 40.909 0.00 0.00 37.12 2.71
2852 8566 5.997384 AGTCTAGTGAAAACGGATTAGGT 57.003 39.130 0.00 0.00 0.00 3.08
3021 8742 6.639671 TCTTTGTTTTGTTGAAATGTTCGG 57.360 33.333 0.00 0.00 0.00 4.30
3029 8750 6.871844 TGACCATCATCTTTGTTTTGTTGAA 58.128 32.000 0.00 0.00 0.00 2.69
3033 8754 6.048509 GGTTTGACCATCATCTTTGTTTTGT 58.951 36.000 0.00 0.00 38.42 2.83
3116 11242 3.397527 TCCTCTCCCATCATTAAAGCCT 58.602 45.455 0.00 0.00 0.00 4.58
3139 11265 1.740296 GCGTTATGCACTCCACCGT 60.740 57.895 0.00 0.00 45.45 4.83
3140 11266 2.798501 CGCGTTATGCACTCCACCG 61.799 63.158 0.00 0.00 46.97 4.94
3174 11300 5.459536 TGTATTGTTGGCACATTAGCAAA 57.540 34.783 0.00 0.00 39.30 3.68
3187 11313 8.992073 TGATCATCGGATAGAAATGTATTGTTG 58.008 33.333 0.00 0.00 32.67 3.33
3194 11320 8.725148 GCTATTTTGATCATCGGATAGAAATGT 58.275 33.333 14.38 0.00 33.60 2.71
3201 11327 5.013079 ACCCTGCTATTTTGATCATCGGATA 59.987 40.000 0.00 0.00 32.67 2.59
3206 11332 3.633525 TGCACCCTGCTATTTTGATCATC 59.366 43.478 0.00 0.00 45.31 2.92
3229 11356 4.007644 CACTGGAGCTGCACCGGA 62.008 66.667 28.16 4.06 37.25 5.14
3266 11393 3.941483 ACAACCAAGCTGAGCATATACAC 59.059 43.478 7.39 0.00 0.00 2.90
3267 11394 4.220693 ACAACCAAGCTGAGCATATACA 57.779 40.909 7.39 0.00 0.00 2.29
3286 11413 1.761449 TGCCAGCTCTTCAAACAACA 58.239 45.000 0.00 0.00 0.00 3.33
3304 11431 7.191551 ACAATCAACGCAATCTCTATCAAATG 58.808 34.615 0.00 0.00 0.00 2.32
3307 11434 6.257849 GGTACAATCAACGCAATCTCTATCAA 59.742 38.462 0.00 0.00 0.00 2.57
3309 11436 5.753438 TGGTACAATCAACGCAATCTCTATC 59.247 40.000 0.00 0.00 31.92 2.08
3336 11463 3.010027 TGGGATACATCAACTTTGCAGGA 59.990 43.478 0.00 0.00 39.74 3.86
3350 11477 5.481824 CCTATGCTAAGATGAGTGGGATACA 59.518 44.000 0.00 0.00 39.74 2.29
3354 11481 2.634940 GCCTATGCTAAGATGAGTGGGA 59.365 50.000 0.00 0.00 33.53 4.37
3381 11508 5.106277 GCCTAGTTTGGTCCTTACATCAAAC 60.106 44.000 9.04 9.04 45.24 2.93


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

AutoCloner maintained by Alex Coulton.