Multiple sequence alignment - TraesCS6D01G307100

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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 TraesCS6D01G307100 chr6D 100.000 3506 0 0 2420 5925 417897637 417894132 0.000000e+00 6475.0
1 TraesCS6D01G307100 chr6D 100.000 2167 0 0 1 2167 417900056 417897890 0.000000e+00 4002.0
2 TraesCS6D01G307100 chr6D 96.004 1126 37 5 4178 5302 417691143 417692261 0.000000e+00 1823.0
3 TraesCS6D01G307100 chr6D 85.413 521 48 11 5294 5810 417692293 417692789 3.170000e-142 516.0
4 TraesCS6D01G307100 chr6D 82.624 282 38 6 2493 2770 414460890 414461164 7.670000e-59 239.0
5 TraesCS6D01G307100 chr6D 88.514 148 12 2 4686 4833 417777857 417777715 2.190000e-39 174.0
6 TraesCS6D01G307100 chr6D 91.892 74 6 0 2093 2166 97717498 97717571 2.920000e-18 104.0
7 TraesCS6D01G307100 chr6D 93.333 60 4 0 5480 5539 417894518 417894577 8.180000e-14 89.8
8 TraesCS6D01G307100 chr6A 96.811 2822 74 9 2493 5302 560573564 560570747 0.000000e+00 4698.0
9 TraesCS6D01G307100 chr6A 92.206 1899 88 32 305 2167 560575784 560573910 0.000000e+00 2632.0
10 TraesCS6D01G307100 chr6A 94.612 798 36 1 4149 4946 560101616 560102406 0.000000e+00 1229.0
11 TraesCS6D01G307100 chr6A 88.872 647 37 13 5294 5925 560570615 560569989 0.000000e+00 763.0
12 TraesCS6D01G307100 chr6A 89.388 245 24 2 3 247 215633741 215633499 2.070000e-79 307.0
13 TraesCS6D01G307100 chr6A 96.471 85 3 0 5841 5925 560102414 560102498 2.230000e-29 141.0
14 TraesCS6D01G307100 chr6B 88.849 1677 97 46 282 1904 626893180 626891540 0.000000e+00 1978.0
15 TraesCS6D01G307100 chr6B 96.319 652 22 2 4653 5302 626887385 626886734 0.000000e+00 1070.0
16 TraesCS6D01G307100 chr6B 93.265 683 39 2 3169 3847 626608465 626609144 0.000000e+00 1000.0
17 TraesCS6D01G307100 chr6B 90.282 710 47 13 3169 3873 626891133 626890441 0.000000e+00 909.0
18 TraesCS6D01G307100 chr6B 88.752 729 48 16 5219 5925 626455072 626455788 0.000000e+00 861.0
19 TraesCS6D01G307100 chr6B 91.376 603 43 4 3985 4585 626888069 626887474 0.000000e+00 817.0
20 TraesCS6D01G307100 chr6B 87.665 681 48 12 2420 3087 626607809 626608466 0.000000e+00 760.0
21 TraesCS6D01G307100 chr6B 87.358 617 40 15 5294 5902 626886637 626886051 0.000000e+00 673.0
22 TraesCS6D01G307100 chr6B 90.054 372 16 10 5561 5925 626587718 626588075 4.180000e-126 462.0
23 TraesCS6D01G307100 chr6B 89.264 326 24 5 2552 2872 626891535 626891216 1.200000e-106 398.0
24 TraesCS6D01G307100 chr6B 91.026 234 21 0 3 236 194036753 194036520 3.450000e-82 316.0
25 TraesCS6D01G307100 chr6B 90.863 197 18 0 5027 5223 626643122 626643318 1.270000e-66 265.0
26 TraesCS6D01G307100 chr6B 80.412 194 22 6 2580 2770 624777234 624777414 3.730000e-27 134.0
27 TraesCS6D01G307100 chr6B 92.000 50 4 0 4583 4632 626887419 626887370 2.960000e-08 71.3
28 TraesCS6D01G307100 chr4B 95.110 409 19 1 2680 3087 608066393 608066801 1.390000e-180 643.0
29 TraesCS6D01G307100 chr4B 94.377 409 22 1 2680 3087 9935675 9935267 1.400000e-175 627.0
30 TraesCS6D01G307100 chr4B 98.220 337 6 0 3169 3505 9935268 9934932 1.840000e-164 590.0
31 TraesCS6D01G307100 chr4B 97.033 337 10 0 3169 3505 608066800 608067136 8.620000e-158 568.0
32 TraesCS6D01G307100 chr4B 91.064 235 21 0 3 237 494016369 494016603 9.580000e-83 318.0
33 TraesCS6D01G307100 chr4B 90.217 92 7 2 3080 3171 21938051 21937962 1.040000e-22 119.0
34 TraesCS6D01G307100 chr4B 93.333 75 4 1 2093 2167 32267281 32267208 6.280000e-20 110.0
35 TraesCS6D01G307100 chr2D 91.064 235 21 0 1 235 315859222 315858988 9.580000e-83 318.0
36 TraesCS6D01G307100 chr2D 85.938 64 7 1 5463 5526 107899866 107899805 3.830000e-07 67.6
37 TraesCS6D01G307100 chr3B 90.987 233 21 0 3 235 401219978 401220210 1.240000e-81 315.0
38 TraesCS6D01G307100 chr3B 95.946 74 2 1 2093 2166 425722682 425722610 1.040000e-22 119.0
39 TraesCS6D01G307100 chr3B 90.000 80 6 1 3092 3171 76488483 76488406 1.050000e-17 102.0
40 TraesCS6D01G307100 chr3B 85.714 70 7 2 5457 5526 798639380 798639446 2.960000e-08 71.3
41 TraesCS6D01G307100 chr3B 82.432 74 10 2 5452 5524 605277771 605277842 1.780000e-05 62.1
42 TraesCS6D01G307100 chr2A 90.638 235 22 0 3 237 562065405 562065171 4.460000e-81 313.0
43 TraesCS6D01G307100 chr2A 90.336 238 20 3 3 239 439199094 439198859 5.770000e-80 309.0
44 TraesCS6D01G307100 chr2A 89.388 245 24 2 3 247 498200851 498200609 2.070000e-79 307.0
45 TraesCS6D01G307100 chr2A 94.595 74 4 0 2093 2166 675456325 675456398 1.350000e-21 115.0
46 TraesCS6D01G307100 chr2A 87.368 95 9 3 3079 3170 613480727 613480633 8.120000e-19 106.0
47 TraesCS6D01G307100 chr2A 100.000 32 0 0 5495 5526 672626861 672626892 6.410000e-05 60.2
48 TraesCS6D01G307100 chr7A 90.598 234 22 0 3 236 163628548 163628315 1.600000e-80 311.0
49 TraesCS6D01G307100 chr7A 93.243 74 5 0 2093 2166 478042635 478042562 6.280000e-20 110.0
50 TraesCS6D01G307100 chr7A 85.507 69 8 2 5490 5557 513221066 513221133 2.960000e-08 71.3
51 TraesCS6D01G307100 chr4A 90.217 92 7 2 3080 3171 590662246 590662157 1.040000e-22 119.0
52 TraesCS6D01G307100 chr1D 88.421 95 10 1 3081 3175 77013457 77013364 4.850000e-21 113.0
53 TraesCS6D01G307100 chr1D 93.056 72 5 0 2093 2164 453421599 453421528 8.120000e-19 106.0
54 TraesCS6D01G307100 chr1D 85.938 64 7 1 5463 5526 3824268 3824207 3.830000e-07 67.6
55 TraesCS6D01G307100 chr7D 93.243 74 5 0 2093 2166 415950899 415950826 6.280000e-20 110.0
56 TraesCS6D01G307100 chr3D 93.333 75 4 1 2093 2166 328545732 328545658 6.280000e-20 110.0
57 TraesCS6D01G307100 chr5B 89.286 84 7 1 3084 3165 116684085 116684168 2.920000e-18 104.0
58 TraesCS6D01G307100 chr5B 86.765 68 3 5 5465 5530 215889768 215889705 2.960000e-08 71.3
59 TraesCS6D01G307100 chr4D 87.640 89 9 2 3080 3168 11860943 11861029 1.050000e-17 102.0
60 TraesCS6D01G307100 chr4D 83.333 72 10 1 5455 5526 254829816 254829885 1.380000e-06 65.8
61 TraesCS6D01G307100 chr2B 87.500 88 11 0 3085 3172 665188441 665188354 1.050000e-17 102.0
62 TraesCS6D01G307100 chr2B 84.286 70 7 3 5457 5526 162544204 162544269 1.380000e-06 65.8
63 TraesCS6D01G307100 chr1A 97.222 36 1 0 2420 2455 439991099 439991064 1.780000e-05 62.1


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 TraesCS6D01G307100 chr6D 417894132 417900056 5924 True 5238.500000 6475 100.000000 1 5925 2 chr6D.!!$R2 5924
1 TraesCS6D01G307100 chr6D 417691143 417692789 1646 False 1169.500000 1823 90.708500 4178 5810 2 chr6D.!!$F4 1632
2 TraesCS6D01G307100 chr6A 560569989 560575784 5795 True 2697.666667 4698 92.629667 305 5925 3 chr6A.!!$R2 5620
3 TraesCS6D01G307100 chr6A 560101616 560102498 882 False 685.000000 1229 95.541500 4149 5925 2 chr6A.!!$F1 1776
4 TraesCS6D01G307100 chr6B 626607809 626609144 1335 False 880.000000 1000 90.465000 2420 3847 2 chr6B.!!$F5 1427
5 TraesCS6D01G307100 chr6B 626455072 626455788 716 False 861.000000 861 88.752000 5219 5925 1 chr6B.!!$F2 706
6 TraesCS6D01G307100 chr6B 626886051 626893180 7129 True 845.185714 1978 90.778286 282 5902 7 chr6B.!!$R2 5620
7 TraesCS6D01G307100 chr4B 9934932 9935675 743 True 608.500000 627 96.298500 2680 3505 2 chr4B.!!$R3 825
8 TraesCS6D01G307100 chr4B 608066393 608067136 743 False 605.500000 643 96.071500 2680 3505 2 chr4B.!!$F2 825

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
297 298 0.030908 GAGGATGCGACCGGTAAGAG 59.969 60.000 7.34 0.0 34.73 2.85 F
820 879 0.108585 AGCGGCAAACAGAGGAGAAA 59.891 50.000 1.45 0.0 0.00 2.52 F
1601 1678 0.250234 CCGGAGAATGCAGGTGAAGA 59.750 55.000 0.00 0.0 0.00 2.87 F
1725 1802 0.531974 TCGTTGTTGCAGAGTCCACC 60.532 55.000 0.00 0.0 0.00 4.61 F
2016 2094 0.937699 TGCGCTACACTTGTCGTGAC 60.938 55.000 9.73 0.0 46.81 3.67 F
2453 2533 1.364626 CCATGAAGCTCCGTCACTGC 61.365 60.000 0.00 0.0 0.00 4.40 F
3924 4053 0.984230 AACACGAGTCCATGGTCCAT 59.016 50.000 12.58 0.0 0.00 3.41 F
4644 7130 1.616374 GACCCATTTTCCCGCAAAAGA 59.384 47.619 0.00 0.0 37.40 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1392 1469 0.666913 GCAACCTAGAGGCGACGATA 59.333 55.000 0.00 0.0 39.32 2.92 R
2438 2516 1.372997 TTCGCAGTGACGGAGCTTC 60.373 57.895 0.00 0.0 0.00 3.86 R
2447 2527 2.094700 GTCATGTAGAGGTTCGCAGTGA 60.095 50.000 0.00 0.0 0.00 3.41 R
3111 3223 4.516698 ACACTGCCACAGACTCTAAAAATG 59.483 41.667 0.78 0.0 35.18 2.32 R
3907 4036 0.250234 ACATGGACCATGGACTCGTG 59.750 55.000 32.82 18.5 45.16 4.35 R
4684 7170 8.237267 CACAACTCTGATATTAAGAAAACCACC 58.763 37.037 0.00 0.0 0.00 4.61 R
4848 7334 0.313987 CCGGTCCTTTTGGTTTGCTC 59.686 55.000 0.00 0.0 41.38 4.26 R
5486 8127 1.268352 TGAACTAAAACCACGGCATGC 59.732 47.619 9.90 9.9 0.00 4.06 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
30 31 5.712152 CTTTGGTCAAAGTCAAGCCTTAT 57.288 39.130 13.58 0.00 42.02 1.73
31 32 6.817765 CTTTGGTCAAAGTCAAGCCTTATA 57.182 37.500 13.58 0.00 42.02 0.98
32 33 7.214467 CTTTGGTCAAAGTCAAGCCTTATAA 57.786 36.000 13.58 0.00 42.02 0.98
33 34 7.589958 TTTGGTCAAAGTCAAGCCTTATAAA 57.410 32.000 0.00 0.00 0.00 1.40
34 35 6.569179 TGGTCAAAGTCAAGCCTTATAAAC 57.431 37.500 0.00 0.00 0.00 2.01
35 36 5.180492 TGGTCAAAGTCAAGCCTTATAAACG 59.820 40.000 0.00 0.00 0.00 3.60
36 37 5.180680 GGTCAAAGTCAAGCCTTATAAACGT 59.819 40.000 0.00 0.00 0.00 3.99
37 38 6.293790 GGTCAAAGTCAAGCCTTATAAACGTT 60.294 38.462 0.00 0.00 0.00 3.99
38 39 6.577427 GTCAAAGTCAAGCCTTATAAACGTTG 59.423 38.462 0.00 5.53 0.00 4.10
39 40 6.483974 TCAAAGTCAAGCCTTATAAACGTTGA 59.516 34.615 0.00 0.00 34.40 3.18
40 41 5.857822 AGTCAAGCCTTATAAACGTTGAC 57.142 39.130 17.72 17.72 42.59 3.18
41 42 4.387862 AGTCAAGCCTTATAAACGTTGACG 59.612 41.667 18.55 1.41 45.40 4.35
42 43 4.386652 GTCAAGCCTTATAAACGTTGACGA 59.613 41.667 10.87 0.00 43.02 4.20
43 44 4.989797 TCAAGCCTTATAAACGTTGACGAA 59.010 37.500 10.87 0.00 43.02 3.85
44 45 5.119588 TCAAGCCTTATAAACGTTGACGAAG 59.880 40.000 10.87 1.75 43.02 3.79
229 230 7.894376 TGTGTAGAGTAAATAAAAACGGAGG 57.106 36.000 0.00 0.00 0.00 4.30
230 231 7.669427 TGTGTAGAGTAAATAAAAACGGAGGA 58.331 34.615 0.00 0.00 0.00 3.71
231 232 8.149647 TGTGTAGAGTAAATAAAAACGGAGGAA 58.850 33.333 0.00 0.00 0.00 3.36
232 233 8.654215 GTGTAGAGTAAATAAAAACGGAGGAAG 58.346 37.037 0.00 0.00 0.00 3.46
233 234 8.370182 TGTAGAGTAAATAAAAACGGAGGAAGT 58.630 33.333 0.00 0.00 0.00 3.01
234 235 9.860898 GTAGAGTAAATAAAAACGGAGGAAGTA 57.139 33.333 0.00 0.00 0.00 2.24
236 237 9.955102 AGAGTAAATAAAAACGGAGGAAGTATT 57.045 29.630 0.00 0.00 0.00 1.89
241 242 9.524496 AAATAAAAACGGAGGAAGTATTTAGGT 57.476 29.630 0.00 0.00 0.00 3.08
243 244 7.912056 AAAAACGGAGGAAGTATTTAGGTAC 57.088 36.000 0.00 0.00 0.00 3.34
244 245 4.907879 ACGGAGGAAGTATTTAGGTACG 57.092 45.455 0.00 0.00 0.00 3.67
245 246 4.273318 ACGGAGGAAGTATTTAGGTACGT 58.727 43.478 0.00 0.00 0.00 3.57
246 247 4.096984 ACGGAGGAAGTATTTAGGTACGTG 59.903 45.833 0.00 0.00 0.00 4.49
247 248 4.336433 CGGAGGAAGTATTTAGGTACGTGA 59.664 45.833 0.00 0.00 0.00 4.35
248 249 5.586339 GGAGGAAGTATTTAGGTACGTGAC 58.414 45.833 0.00 0.00 0.00 3.67
249 250 5.126061 GGAGGAAGTATTTAGGTACGTGACA 59.874 44.000 0.00 0.00 0.00 3.58
250 251 6.350445 GGAGGAAGTATTTAGGTACGTGACAA 60.350 42.308 0.00 0.00 0.00 3.18
251 252 6.393171 AGGAAGTATTTAGGTACGTGACAAC 58.607 40.000 0.00 0.00 0.00 3.32
252 253 6.015180 AGGAAGTATTTAGGTACGTGACAACA 60.015 38.462 0.00 0.00 0.00 3.33
253 254 6.309737 GGAAGTATTTAGGTACGTGACAACAG 59.690 42.308 0.00 0.00 0.00 3.16
254 255 6.336842 AGTATTTAGGTACGTGACAACAGT 57.663 37.500 0.00 0.00 0.00 3.55
255 256 6.154445 AGTATTTAGGTACGTGACAACAGTG 58.846 40.000 0.00 0.00 0.00 3.66
256 257 2.427232 TAGGTACGTGACAACAGTGC 57.573 50.000 0.00 0.00 0.00 4.40
257 258 0.462375 AGGTACGTGACAACAGTGCA 59.538 50.000 0.00 0.00 0.00 4.57
258 259 0.859232 GGTACGTGACAACAGTGCAG 59.141 55.000 0.00 0.00 0.00 4.41
259 260 1.537348 GGTACGTGACAACAGTGCAGA 60.537 52.381 0.00 0.00 0.00 4.26
260 261 2.198406 GTACGTGACAACAGTGCAGAA 58.802 47.619 0.00 0.00 0.00 3.02
261 262 1.732941 ACGTGACAACAGTGCAGAAA 58.267 45.000 0.00 0.00 0.00 2.52
262 263 1.665679 ACGTGACAACAGTGCAGAAAG 59.334 47.619 0.00 0.00 0.00 2.62
263 264 1.595489 CGTGACAACAGTGCAGAAAGC 60.595 52.381 0.00 0.00 45.96 3.51
295 296 1.299165 CGAGGATGCGACCGGTAAG 60.299 63.158 7.34 6.05 34.73 2.34
296 297 1.721664 CGAGGATGCGACCGGTAAGA 61.722 60.000 7.34 0.00 34.73 2.10
297 298 0.030908 GAGGATGCGACCGGTAAGAG 59.969 60.000 7.34 0.00 34.73 2.85
298 299 0.683504 AGGATGCGACCGGTAAGAGT 60.684 55.000 7.34 0.00 34.73 3.24
299 300 0.527817 GGATGCGACCGGTAAGAGTG 60.528 60.000 7.34 0.00 0.00 3.51
300 301 0.454600 GATGCGACCGGTAAGAGTGA 59.545 55.000 7.34 0.00 0.00 3.41
301 302 0.172803 ATGCGACCGGTAAGAGTGAC 59.827 55.000 7.34 0.00 0.00 3.67
302 303 0.892358 TGCGACCGGTAAGAGTGACT 60.892 55.000 7.34 0.00 0.00 3.41
507 534 3.393800 CATCCATCGTCCTTGACATACC 58.606 50.000 0.00 0.00 32.09 2.73
508 535 2.462723 TCCATCGTCCTTGACATACCA 58.537 47.619 0.00 0.00 32.09 3.25
649 692 4.617520 TCTTGCGTCGCAGGGCAA 62.618 61.111 26.50 8.85 42.81 4.52
660 703 1.077265 CAGGGCAACAGATTGGGGT 59.923 57.895 0.00 0.00 36.23 4.95
677 724 2.439701 TACGACCTGCTCCTCCCG 60.440 66.667 0.00 0.00 0.00 5.14
820 879 0.108585 AGCGGCAAACAGAGGAGAAA 59.891 50.000 1.45 0.00 0.00 2.52
836 895 1.202818 AGAAACCCACCAAGTCAGAGC 60.203 52.381 0.00 0.00 0.00 4.09
960 1024 4.862092 GCTCGCGCTGCTCTGCTA 62.862 66.667 5.56 0.00 0.00 3.49
1069 1146 0.824109 CATGCGGAACTCCTCCTACA 59.176 55.000 0.00 0.00 42.85 2.74
1469 1546 2.205074 CGAATTGGTCCAATCGGAGAG 58.795 52.381 17.60 2.73 43.99 3.20
1601 1678 0.250234 CCGGAGAATGCAGGTGAAGA 59.750 55.000 0.00 0.00 0.00 2.87
1609 1686 1.301293 GCAGGTGAAGAGAAGGGGG 59.699 63.158 0.00 0.00 0.00 5.40
1684 1761 3.089838 TGGAGGCCACAAGGGATG 58.910 61.111 5.01 0.00 40.01 3.51
1685 1762 2.440980 GGAGGCCACAAGGGATGC 60.441 66.667 5.01 0.00 40.01 3.91
1686 1763 2.679716 GAGGCCACAAGGGATGCT 59.320 61.111 5.01 0.00 40.01 3.79
1687 1764 1.635817 GGAGGCCACAAGGGATGCTA 61.636 60.000 5.01 0.00 40.01 3.49
1690 1767 0.749454 GGCCACAAGGGATGCTACTG 60.749 60.000 0.00 0.00 40.01 2.74
1691 1768 0.749454 GCCACAAGGGATGCTACTGG 60.749 60.000 0.00 0.00 40.01 4.00
1724 1801 0.861837 CTCGTTGTTGCAGAGTCCAC 59.138 55.000 0.00 0.00 0.00 4.02
1725 1802 0.531974 TCGTTGTTGCAGAGTCCACC 60.532 55.000 0.00 0.00 0.00 4.61
1845 1922 2.044555 CGGGTCAGTCTACGAGGCA 61.045 63.158 0.00 0.00 0.00 4.75
1930 2007 6.151144 AGTTAGTGTCTATGGGTTTGCAATTC 59.849 38.462 0.00 0.00 0.00 2.17
1935 2012 2.056985 TGGGTTTGCAATTCCCAGC 58.943 52.632 28.09 12.42 45.19 4.85
1950 2028 6.855763 ATTCCCAGCTTGTCAAATTTGATA 57.144 33.333 23.05 18.02 39.73 2.15
1992 2070 5.899299 AGCAGAAGATGTTTCATAATTGGC 58.101 37.500 0.00 0.00 0.00 4.52
2016 2094 0.937699 TGCGCTACACTTGTCGTGAC 60.938 55.000 9.73 0.00 46.81 3.67
2020 2098 2.240040 GCTACACTTGTCGTGACGTAG 58.760 52.381 4.40 4.02 46.81 3.51
2030 2108 1.738099 GTGACGTAGGCAGCCACTG 60.738 63.158 15.80 4.61 34.12 3.66
2129 2207 1.874129 TGAGGGGGCGAAGAAGATAA 58.126 50.000 0.00 0.00 0.00 1.75
2447 2527 4.115199 GCCCCCATGAAGCTCCGT 62.115 66.667 0.00 0.00 0.00 4.69
2453 2533 1.364626 CCATGAAGCTCCGTCACTGC 61.365 60.000 0.00 0.00 0.00 4.40
2466 2546 2.263077 GTCACTGCGAACCTCTACATG 58.737 52.381 0.00 0.00 0.00 3.21
2485 2565 8.445588 TCTACATGACTCTATTATACCACCTGA 58.554 37.037 0.00 0.00 0.00 3.86
2486 2566 9.249053 CTACATGACTCTATTATACCACCTGAT 57.751 37.037 0.00 0.00 0.00 2.90
2488 2568 9.026121 ACATGACTCTATTATACCACCTGATAC 57.974 37.037 0.00 0.00 0.00 2.24
2489 2569 8.470805 CATGACTCTATTATACCACCTGATACC 58.529 40.741 0.00 0.00 0.00 2.73
2491 2571 8.897692 TGACTCTATTATACCACCTGATACCTA 58.102 37.037 0.00 0.00 0.00 3.08
2622 2726 4.543590 TGGGTTTTTCTTTGCTGTCAAA 57.456 36.364 0.00 0.00 39.67 2.69
3000 3111 7.116736 TCTCATTACCTTCTGTTATTTTCCCC 58.883 38.462 0.00 0.00 0.00 4.81
3036 3148 6.801862 GCATAATTTGGATTTAGCCGATGTAC 59.198 38.462 0.00 0.00 0.00 2.90
3083 3195 8.918202 TTTTTCCTGCTTTCTCTGAGTAAATA 57.082 30.769 4.32 0.00 0.00 1.40
3135 3247 2.820059 TTAGAGTCTGTGGCAGTGTG 57.180 50.000 1.86 0.00 32.61 3.82
3721 3838 3.738434 TGGCCCCTGAGGTTAGTTTATA 58.262 45.455 0.00 0.00 38.26 0.98
3759 3876 4.832266 TGCCTTTTCTACATCATGTTGGTT 59.168 37.500 0.00 0.00 0.00 3.67
3801 3920 3.935203 AGGCATCATGTTGTTCTTACTCG 59.065 43.478 5.69 0.00 0.00 4.18
3852 3971 3.545703 AGCATATTTGTGCCTGGTCTAC 58.454 45.455 0.00 0.00 46.19 2.59
3865 3986 4.315803 CCTGGTCTACTGTGATCGTTTTT 58.684 43.478 0.00 0.00 0.00 1.94
3907 4036 3.942829 TGTGACCTGAATGATCCAGAAC 58.057 45.455 0.00 0.00 33.65 3.01
3924 4053 0.984230 AACACGAGTCCATGGTCCAT 59.016 50.000 12.58 0.00 0.00 3.41
4644 7130 1.616374 GACCCATTTTCCCGCAAAAGA 59.384 47.619 0.00 0.00 37.40 2.52
4684 7170 4.147321 CCCATTCCCTGTATTTGGATCTG 58.853 47.826 0.00 0.00 0.00 2.90
4801 7287 3.841255 GGGGAATACCACCAAAAATTCCA 59.159 43.478 13.34 0.00 46.09 3.53
4848 7334 5.088739 GGATTTCATAGCAAAGTGTGTTCG 58.911 41.667 0.00 0.00 0.00 3.95
4989 7475 2.994578 GCTGGTAAGTCTTTCGTCCTTC 59.005 50.000 0.00 0.00 0.00 3.46
5092 7578 6.127925 GCAAACATAGTGATTTGTCTCCATCA 60.128 38.462 0.00 0.00 37.96 3.07
5242 7728 4.392921 TGAGATAGCTAGCTTCCAACAC 57.607 45.455 24.88 8.95 0.00 3.32
5326 7954 1.457009 GGAGCCCGTAGCCTAGTCTG 61.457 65.000 0.00 0.00 45.47 3.51
5341 7969 1.625818 AGTCTGGGAGTGTGGAATGAC 59.374 52.381 0.00 0.00 0.00 3.06
5408 8039 1.632422 CGACCGCGTTTACATACCTT 58.368 50.000 4.92 0.00 0.00 3.50
5486 8127 0.748450 TCCCTCCGTAATAAGTGCCG 59.252 55.000 0.00 0.00 0.00 5.69
5488 8129 0.179094 CCTCCGTAATAAGTGCCGCA 60.179 55.000 0.00 0.00 0.00 5.69
5552 8197 1.064952 GTCACTTGTGTTTGGAACGGG 59.935 52.381 0.46 0.00 0.00 5.28
5594 8239 4.565652 CCTTGCTCCATACCTGTACAGTTT 60.566 45.833 21.18 10.41 0.00 2.66
5626 8272 9.784531 CTATGGAATACAATCTGTTTCTACCAT 57.215 33.333 0.00 0.00 0.00 3.55
5649 8295 5.825593 AGAAGGTCCAGAATTTCAGTGTA 57.174 39.130 0.00 0.00 0.00 2.90
5747 8399 4.139786 GGCCTGCTCATCAAAGATTCATA 58.860 43.478 0.00 0.00 0.00 2.15
5859 8511 6.696411 AGAGACCAAAGAACTGAAGATACAG 58.304 40.000 0.00 0.00 42.78 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 7.430441 GTTTATAAGGCTTGACTTTGACCAAA 58.570 34.615 10.69 0.00 32.02 3.28
10 11 6.293735 CGTTTATAAGGCTTGACTTTGACCAA 60.294 38.462 10.69 0.00 32.02 3.67
11 12 5.180492 CGTTTATAAGGCTTGACTTTGACCA 59.820 40.000 10.69 0.00 32.02 4.02
12 13 5.180680 ACGTTTATAAGGCTTGACTTTGACC 59.819 40.000 10.69 0.00 32.02 4.02
13 14 6.237313 ACGTTTATAAGGCTTGACTTTGAC 57.763 37.500 10.69 0.00 32.02 3.18
14 15 6.483974 TCAACGTTTATAAGGCTTGACTTTGA 59.516 34.615 10.69 14.07 32.02 2.69
15 16 6.577427 GTCAACGTTTATAAGGCTTGACTTTG 59.423 38.462 10.69 12.27 36.10 2.77
16 17 6.565247 CGTCAACGTTTATAAGGCTTGACTTT 60.565 38.462 10.69 1.02 36.42 2.66
17 18 5.107220 CGTCAACGTTTATAAGGCTTGACTT 60.107 40.000 10.69 0.00 36.42 3.01
18 19 4.387862 CGTCAACGTTTATAAGGCTTGACT 59.612 41.667 10.69 0.00 36.42 3.41
19 20 4.386652 TCGTCAACGTTTATAAGGCTTGAC 59.613 41.667 10.69 15.01 40.80 3.18
20 21 4.558178 TCGTCAACGTTTATAAGGCTTGA 58.442 39.130 10.69 0.00 40.80 3.02
21 22 4.914312 TCGTCAACGTTTATAAGGCTTG 57.086 40.909 10.69 0.00 40.80 4.01
22 23 4.992951 ACTTCGTCAACGTTTATAAGGCTT 59.007 37.500 4.58 4.58 40.80 4.35
23 24 4.563061 ACTTCGTCAACGTTTATAAGGCT 58.437 39.130 0.00 0.00 40.80 4.58
24 25 4.916099 ACTTCGTCAACGTTTATAAGGC 57.084 40.909 0.00 0.00 40.80 4.35
30 31 9.979270 TTTGTTTATAAACTTCGTCAACGTTTA 57.021 25.926 24.81 1.51 39.59 2.01
31 32 8.892887 TTTGTTTATAAACTTCGTCAACGTTT 57.107 26.923 24.81 0.00 39.59 3.60
32 33 8.892887 TTTTGTTTATAAACTTCGTCAACGTT 57.107 26.923 24.81 0.00 39.59 3.99
33 34 8.892887 TTTTTGTTTATAAACTTCGTCAACGT 57.107 26.923 24.81 0.00 39.59 3.99
203 204 8.943002 CCTCCGTTTTTATTTACTCTACACATT 58.057 33.333 0.00 0.00 0.00 2.71
204 205 8.316214 TCCTCCGTTTTTATTTACTCTACACAT 58.684 33.333 0.00 0.00 0.00 3.21
205 206 7.669427 TCCTCCGTTTTTATTTACTCTACACA 58.331 34.615 0.00 0.00 0.00 3.72
206 207 8.538409 TTCCTCCGTTTTTATTTACTCTACAC 57.462 34.615 0.00 0.00 0.00 2.90
207 208 8.370182 ACTTCCTCCGTTTTTATTTACTCTACA 58.630 33.333 0.00 0.00 0.00 2.74
208 209 8.768957 ACTTCCTCCGTTTTTATTTACTCTAC 57.231 34.615 0.00 0.00 0.00 2.59
210 211 9.955102 AATACTTCCTCCGTTTTTATTTACTCT 57.045 29.630 0.00 0.00 0.00 3.24
215 216 9.524496 ACCTAAATACTTCCTCCGTTTTTATTT 57.476 29.630 0.00 0.00 0.00 1.40
217 218 9.605275 GTACCTAAATACTTCCTCCGTTTTTAT 57.395 33.333 0.00 0.00 0.00 1.40
218 219 7.759433 CGTACCTAAATACTTCCTCCGTTTTTA 59.241 37.037 0.00 0.00 0.00 1.52
219 220 6.591448 CGTACCTAAATACTTCCTCCGTTTTT 59.409 38.462 0.00 0.00 0.00 1.94
220 221 6.101997 CGTACCTAAATACTTCCTCCGTTTT 58.898 40.000 0.00 0.00 0.00 2.43
221 222 5.185828 ACGTACCTAAATACTTCCTCCGTTT 59.814 40.000 0.00 0.00 0.00 3.60
222 223 4.706962 ACGTACCTAAATACTTCCTCCGTT 59.293 41.667 0.00 0.00 0.00 4.44
223 224 4.096984 CACGTACCTAAATACTTCCTCCGT 59.903 45.833 0.00 0.00 0.00 4.69
224 225 4.336433 TCACGTACCTAAATACTTCCTCCG 59.664 45.833 0.00 0.00 0.00 4.63
225 226 5.126061 TGTCACGTACCTAAATACTTCCTCC 59.874 44.000 0.00 0.00 0.00 4.30
226 227 6.199937 TGTCACGTACCTAAATACTTCCTC 57.800 41.667 0.00 0.00 0.00 3.71
227 228 6.015180 TGTTGTCACGTACCTAAATACTTCCT 60.015 38.462 0.00 0.00 0.00 3.36
228 229 6.158598 TGTTGTCACGTACCTAAATACTTCC 58.841 40.000 0.00 0.00 0.00 3.46
229 230 6.865205 ACTGTTGTCACGTACCTAAATACTTC 59.135 38.462 0.00 0.00 0.00 3.01
230 231 6.643770 CACTGTTGTCACGTACCTAAATACTT 59.356 38.462 0.00 0.00 0.00 2.24
231 232 6.154445 CACTGTTGTCACGTACCTAAATACT 58.846 40.000 0.00 0.00 0.00 2.12
232 233 5.164022 GCACTGTTGTCACGTACCTAAATAC 60.164 44.000 0.00 0.00 0.00 1.89
233 234 4.925054 GCACTGTTGTCACGTACCTAAATA 59.075 41.667 0.00 0.00 0.00 1.40
234 235 3.744426 GCACTGTTGTCACGTACCTAAAT 59.256 43.478 0.00 0.00 0.00 1.40
235 236 3.125316 GCACTGTTGTCACGTACCTAAA 58.875 45.455 0.00 0.00 0.00 1.85
236 237 2.101082 TGCACTGTTGTCACGTACCTAA 59.899 45.455 0.00 0.00 0.00 2.69
237 238 1.682323 TGCACTGTTGTCACGTACCTA 59.318 47.619 0.00 0.00 0.00 3.08
238 239 0.462375 TGCACTGTTGTCACGTACCT 59.538 50.000 0.00 0.00 0.00 3.08
239 240 0.859232 CTGCACTGTTGTCACGTACC 59.141 55.000 0.00 0.00 0.00 3.34
240 241 1.847818 TCTGCACTGTTGTCACGTAC 58.152 50.000 0.00 0.00 0.00 3.67
241 242 2.588027 TTCTGCACTGTTGTCACGTA 57.412 45.000 0.00 0.00 0.00 3.57
242 243 1.665679 CTTTCTGCACTGTTGTCACGT 59.334 47.619 0.00 0.00 0.00 4.49
243 244 1.595489 GCTTTCTGCACTGTTGTCACG 60.595 52.381 0.00 0.00 42.31 4.35
244 245 2.111041 GCTTTCTGCACTGTTGTCAC 57.889 50.000 0.00 0.00 42.31 3.67
263 264 3.120580 GCATCCTCGGCAAAAATTGTTTG 60.121 43.478 0.00 0.00 0.00 2.93
264 265 3.066380 GCATCCTCGGCAAAAATTGTTT 58.934 40.909 0.00 0.00 0.00 2.83
265 266 2.687370 GCATCCTCGGCAAAAATTGTT 58.313 42.857 0.00 0.00 0.00 2.83
266 267 1.402720 CGCATCCTCGGCAAAAATTGT 60.403 47.619 0.00 0.00 0.00 2.71
267 268 1.135431 TCGCATCCTCGGCAAAAATTG 60.135 47.619 0.00 0.00 0.00 2.32
268 269 1.135402 GTCGCATCCTCGGCAAAAATT 60.135 47.619 0.00 0.00 33.72 1.82
269 270 0.451783 GTCGCATCCTCGGCAAAAAT 59.548 50.000 0.00 0.00 33.72 1.82
270 271 1.582610 GGTCGCATCCTCGGCAAAAA 61.583 55.000 0.00 0.00 35.49 1.94
271 272 2.038269 GGTCGCATCCTCGGCAAAA 61.038 57.895 0.00 0.00 35.49 2.44
272 273 2.435938 GGTCGCATCCTCGGCAAA 60.436 61.111 0.00 0.00 35.49 3.68
273 274 4.812476 CGGTCGCATCCTCGGCAA 62.812 66.667 0.00 0.00 35.49 4.52
276 277 2.679132 CTTACCGGTCGCATCCTCGG 62.679 65.000 12.40 0.00 46.95 4.63
277 278 1.299165 CTTACCGGTCGCATCCTCG 60.299 63.158 12.40 0.00 0.00 4.63
278 279 0.030908 CTCTTACCGGTCGCATCCTC 59.969 60.000 12.40 0.00 0.00 3.71
279 280 0.683504 ACTCTTACCGGTCGCATCCT 60.684 55.000 12.40 0.00 0.00 3.24
280 281 0.527817 CACTCTTACCGGTCGCATCC 60.528 60.000 12.40 0.00 0.00 3.51
295 296 5.522460 TGTTTGCTTTGTGTACTAGTCACTC 59.478 40.000 19.44 10.34 36.83 3.51
296 297 5.424757 TGTTTGCTTTGTGTACTAGTCACT 58.575 37.500 19.44 0.00 36.83 3.41
297 298 5.728351 TGTTTGCTTTGTGTACTAGTCAC 57.272 39.130 0.00 8.49 36.48 3.67
298 299 6.292649 CGAATGTTTGCTTTGTGTACTAGTCA 60.293 38.462 0.00 0.00 0.00 3.41
299 300 6.071463 CGAATGTTTGCTTTGTGTACTAGTC 58.929 40.000 0.00 0.00 0.00 2.59
300 301 5.049680 CCGAATGTTTGCTTTGTGTACTAGT 60.050 40.000 0.00 0.00 0.00 2.57
301 302 5.382303 CCGAATGTTTGCTTTGTGTACTAG 58.618 41.667 0.00 0.00 0.00 2.57
302 303 4.319911 GCCGAATGTTTGCTTTGTGTACTA 60.320 41.667 0.00 0.00 0.00 1.82
396 423 3.312709 GTGGCCTACGTACGTGTAC 57.687 57.895 30.25 17.80 0.00 2.90
442 469 2.486042 GCGACCACGTCTCTCTCC 59.514 66.667 0.00 0.00 41.98 3.71
507 534 1.282817 TCGTGAACGACAAAGGTGTG 58.717 50.000 0.50 0.00 44.22 3.82
508 535 3.744941 TCGTGAACGACAAAGGTGT 57.255 47.368 0.50 0.00 44.22 4.16
649 692 0.902531 CAGGTCGTACCCCAATCTGT 59.097 55.000 1.06 0.00 39.75 3.41
660 703 2.439701 CGGGAGGAGCAGGTCGTA 60.440 66.667 0.00 0.00 0.00 3.43
807 866 1.850345 TGGTGGGTTTCTCCTCTGTTT 59.150 47.619 0.00 0.00 36.25 2.83
820 879 1.770110 TGGCTCTGACTTGGTGGGT 60.770 57.895 0.00 0.00 0.00 4.51
1117 1194 2.894387 GACGCTGAGCTGGATGCC 60.894 66.667 1.78 0.00 44.23 4.40
1387 1464 3.884496 ACCTAGAGGCGACGATAACGTG 61.884 54.545 1.57 0.00 45.82 4.49
1392 1469 0.666913 GCAACCTAGAGGCGACGATA 59.333 55.000 0.00 0.00 39.32 2.92
1524 1601 3.506810 CACTCTCTCTGATTCGACCAAC 58.493 50.000 0.00 0.00 0.00 3.77
1567 1644 3.117171 CGGCTCAGACACAGCAGC 61.117 66.667 0.00 0.00 38.77 5.25
1609 1686 2.482864 CACTTTGGCCAATTTGTCACC 58.517 47.619 21.26 0.00 0.00 4.02
1610 1687 2.102252 TCCACTTTGGCCAATTTGTCAC 59.898 45.455 21.26 0.00 37.47 3.67
1636 1713 3.118555 TCTCTTGTCCTCTCCTCTCGTAG 60.119 52.174 0.00 0.00 0.00 3.51
1637 1714 2.838813 TCTCTTGTCCTCTCCTCTCGTA 59.161 50.000 0.00 0.00 0.00 3.43
1724 1801 4.421058 CAAATGCTCAATGTCACATGAGG 58.579 43.478 15.65 0.00 42.62 3.86
1725 1802 4.082408 ACCAAATGCTCAATGTCACATGAG 60.082 41.667 0.00 11.45 44.66 2.90
1845 1922 5.049405 CAGGTGAAAAACTTACTCGCTGATT 60.049 40.000 0.00 0.00 0.00 2.57
1910 1987 3.119137 GGGAATTGCAAACCCATAGACAC 60.119 47.826 28.68 8.68 42.81 3.67
1930 2007 5.389859 TGTATCAAATTTGACAAGCTGGG 57.610 39.130 22.71 0.00 40.49 4.45
1934 2011 9.372541 CAAAATGTTGTATCAAATTTGACAAGC 57.627 29.630 22.71 16.31 40.49 4.01
1966 2044 7.646314 CCAATTATGAAACATCTTCTGCTAGG 58.354 38.462 0.00 0.00 0.00 3.02
1992 2070 1.583856 CGACAAGTGTAGCGCATACAG 59.416 52.381 11.47 6.68 45.06 2.74
2030 2108 1.526464 CAAACCAATTTGCGAAGTGCC 59.474 47.619 8.66 0.00 45.60 5.01
2091 2169 5.183969 CCTCAAGAATCTTCATCAAGCTCA 58.816 41.667 0.00 0.00 0.00 4.26
2129 2207 7.337167 AGATTTCTCAGAGTTCATGCATAACT 58.663 34.615 16.49 16.49 39.84 2.24
2438 2516 1.372997 TTCGCAGTGACGGAGCTTC 60.373 57.895 0.00 0.00 0.00 3.86
2447 2527 2.094700 GTCATGTAGAGGTTCGCAGTGA 60.095 50.000 0.00 0.00 0.00 3.41
2453 2533 8.452534 GGTATAATAGAGTCATGTAGAGGTTCG 58.547 40.741 0.00 0.00 0.00 3.95
2466 2546 9.398538 CTAGGTATCAGGTGGTATAATAGAGTC 57.601 40.741 0.00 0.00 0.00 3.36
2485 2565 5.130145 AGCTGAAGTTGCATTCTCTAGGTAT 59.870 40.000 1.98 0.00 0.00 2.73
2486 2566 4.467795 AGCTGAAGTTGCATTCTCTAGGTA 59.532 41.667 1.98 0.00 0.00 3.08
2487 2567 3.262915 AGCTGAAGTTGCATTCTCTAGGT 59.737 43.478 1.98 2.93 0.00 3.08
2488 2568 3.622163 CAGCTGAAGTTGCATTCTCTAGG 59.378 47.826 8.42 0.00 0.00 3.02
2489 2569 4.252073 ACAGCTGAAGTTGCATTCTCTAG 58.748 43.478 23.35 0.00 0.00 2.43
2491 2571 3.137446 ACAGCTGAAGTTGCATTCTCT 57.863 42.857 23.35 0.00 0.00 3.10
2976 3087 7.119387 AGGGGAAAATAACAGAAGGTAATGAG 58.881 38.462 0.00 0.00 0.00 2.90
3000 3111 6.896021 ATCCAAATTATGCCATTCTCAGAG 57.104 37.500 0.00 0.00 0.00 3.35
3111 3223 4.516698 ACACTGCCACAGACTCTAAAAATG 59.483 41.667 0.78 0.00 35.18 2.32
3142 3254 7.781693 ACTCCCTCCGTAACTTAATATAAGACA 59.218 37.037 4.24 0.00 0.00 3.41
3149 3261 8.199449 CACAAATACTCCCTCCGTAACTTAATA 58.801 37.037 0.00 0.00 0.00 0.98
3721 3838 5.302823 AGAAAAGGCACAATAGCTCAACTTT 59.697 36.000 0.00 0.00 34.17 2.66
3801 3920 5.362556 AATTGTACACACACTCTGAATGC 57.637 39.130 0.00 0.00 33.30 3.56
3894 4023 3.190874 GGACTCGTGTTCTGGATCATTC 58.809 50.000 0.00 0.00 0.00 2.67
3907 4036 0.250234 ACATGGACCATGGACTCGTG 59.750 55.000 32.82 18.50 45.16 4.35
4684 7170 8.237267 CACAACTCTGATATTAAGAAAACCACC 58.763 37.037 0.00 0.00 0.00 4.61
4801 7287 4.750098 CGGGCATCTTCTGATAACGTATTT 59.250 41.667 0.00 0.00 0.00 1.40
4848 7334 0.313987 CCGGTCCTTTTGGTTTGCTC 59.686 55.000 0.00 0.00 41.38 4.26
4989 7475 3.693085 CACCCACATTTCTTGATGAGGAG 59.307 47.826 3.39 0.00 39.31 3.69
5326 7954 2.026822 ACATCTGTCATTCCACACTCCC 60.027 50.000 0.00 0.00 0.00 4.30
5341 7969 1.154197 CACTCCACACTGCACATCTG 58.846 55.000 0.00 0.00 0.00 2.90
5362 7990 2.677836 TGAACTGTTGTGTGAGCACTTC 59.322 45.455 0.00 0.00 45.44 3.01
5486 8127 1.268352 TGAACTAAAACCACGGCATGC 59.732 47.619 9.90 9.90 0.00 4.06
5488 8129 4.864704 ATTTGAACTAAAACCACGGCAT 57.135 36.364 0.00 0.00 0.00 4.40
5533 8178 1.384525 CCCGTTCCAAACACAAGTGA 58.615 50.000 7.28 0.00 0.00 3.41
5552 8197 4.779993 AGGTCAGAGTCAAATATTCCCC 57.220 45.455 0.00 0.00 0.00 4.81
5557 8202 4.225942 TGGAGCAAGGTCAGAGTCAAATAT 59.774 41.667 1.42 0.00 0.00 1.28
5567 8212 1.556911 ACAGGTATGGAGCAAGGTCAG 59.443 52.381 1.42 0.00 0.00 3.51
5594 8239 9.832445 GAAACAGATTGTATTCCATAGGAACTA 57.168 33.333 0.00 0.00 45.07 2.24
5626 8272 5.825593 ACACTGAAATTCTGGACCTTCTA 57.174 39.130 4.93 0.00 0.00 2.10
5649 8295 5.664457 CGCATCTGGTGGTATATGACATAT 58.336 41.667 12.51 12.51 0.00 1.78
5764 8416 9.120538 GGATCCAACATGTACAGTAATACAAAT 57.879 33.333 6.95 0.00 38.53 2.32
5765 8417 8.325787 AGGATCCAACATGTACAGTAATACAAA 58.674 33.333 15.82 0.00 38.53 2.83
5859 8511 8.515414 AGAACCAACAGTAGATTAGAAATTTGC 58.485 33.333 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.