Multiple sequence alignment - TraesCS3D01G189200

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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 TraesCS3D01G189200 chr3D 100.000 7622 0 0 1 7622 177022920 177030541 0.000000e+00 14076.0
1 TraesCS3D01G189200 chr3D 93.258 89 6 0 2292 2380 177025165 177025253 1.730000e-26 132.0
2 TraesCS3D01G189200 chr3D 93.258 89 6 0 2246 2334 177025211 177025299 1.730000e-26 132.0
3 TraesCS3D01G189200 chr3D 96.667 60 1 1 7249 7308 177030057 177030115 1.750000e-16 99.0
4 TraesCS3D01G189200 chr3D 96.667 60 1 1 7138 7196 177030168 177030227 1.750000e-16 99.0
5 TraesCS3D01G189200 chr3D 89.655 58 5 1 7272 7328 38212349 38212406 1.060000e-08 73.1
6 TraesCS3D01G189200 chr3D 92.308 39 1 1 4262 4298 409967807 409967769 4.000000e-03 54.7
7 TraesCS3D01G189200 chr3B 96.119 3710 96 15 2292 5964 255985447 255989145 0.000000e+00 6010.0
8 TraesCS3D01G189200 chr3B 96.188 1679 61 2 658 2334 255983858 255985535 0.000000e+00 2743.0
9 TraesCS3D01G189200 chr3B 93.980 1113 41 8 5940 7036 255990854 255991956 0.000000e+00 1661.0
10 TraesCS3D01G189200 chr3B 82.529 435 22 20 7138 7529 255991985 255992408 4.410000e-87 333.0
11 TraesCS3D01G189200 chr3B 86.264 182 9 7 7151 7316 255991943 255992124 4.700000e-42 183.0
12 TraesCS3D01G189200 chr3B 94.175 103 5 1 7207 7308 255991942 255992044 1.020000e-33 156.0
13 TraesCS3D01G189200 chr3B 94.643 56 3 0 7141 7196 255992061 255992116 3.790000e-13 87.9
14 TraesCS3D01G189200 chr3A 96.994 2927 47 6 4421 7316 217720640 217723556 0.000000e+00 4879.0
15 TraesCS3D01G189200 chr3A 98.183 2146 31 5 2292 4436 217715192 217717330 0.000000e+00 3740.0
16 TraesCS3D01G189200 chr3A 96.373 1682 45 6 658 2334 217713610 217715280 0.000000e+00 2754.0
17 TraesCS3D01G189200 chr3A 92.698 315 19 3 7310 7622 217723660 217723972 1.170000e-122 451.0
18 TraesCS3D01G189200 chr3A 96.552 116 3 1 7193 7308 217723378 217723492 2.810000e-44 191.0
19 TraesCS3D01G189200 chr3A 93.966 116 6 1 7138 7252 217723433 217723548 2.830000e-39 174.0
20 TraesCS3D01G189200 chr3A 96.667 60 1 1 7249 7308 217723378 217723436 1.750000e-16 99.0
21 TraesCS3D01G189200 chr3A 95.000 60 2 1 7138 7196 217723489 217723548 8.140000e-15 93.5
22 TraesCS3D01G189200 chr3A 100.000 46 0 0 7271 7316 217723602 217723647 1.360000e-12 86.1
23 TraesCS3D01G189200 chr3A 94.118 51 2 1 7570 7620 595920533 595920484 8.200000e-10 76.8
24 TraesCS3D01G189200 chr3A 95.455 44 2 0 7577 7620 388952585 388952542 3.820000e-08 71.3
25 TraesCS3D01G189200 chr3A 87.500 48 4 1 7573 7620 381300768 381300813 4.000000e-03 54.7
26 TraesCS3D01G189200 chr3A 87.500 48 5 1 7574 7620 449105434 449105481 4.000000e-03 54.7
27 TraesCS3D01G189200 chr2D 96.505 658 19 4 1 655 430180558 430181214 0.000000e+00 1085.0
28 TraesCS3D01G189200 chr2D 93.192 661 44 1 1 660 483624837 483625497 0.000000e+00 970.0
29 TraesCS3D01G189200 chr2D 92.006 663 44 9 1 660 573487839 573488495 0.000000e+00 922.0
30 TraesCS3D01G189200 chr2D 90.090 111 10 1 7032 7142 14772134 14772025 7.970000e-30 143.0
31 TraesCS3D01G189200 chr2D 89.474 114 11 1 7029 7142 241661915 241662027 7.970000e-30 143.0
32 TraesCS3D01G189200 chr5D 96.061 660 23 3 1 659 322522928 322523585 0.000000e+00 1072.0
33 TraesCS3D01G189200 chr5D 92.436 661 47 3 1 660 35118851 35118193 0.000000e+00 941.0
34 TraesCS3D01G189200 chr5D 100.000 30 0 0 7222 7251 128587291 128587320 1.000000e-03 56.5
35 TraesCS3D01G189200 chr5D 96.970 33 0 1 4272 4304 446499548 446499579 4.000000e-03 54.7
36 TraesCS3D01G189200 chr1D 95.067 669 31 2 1 668 64206029 64205362 0.000000e+00 1051.0
37 TraesCS3D01G189200 chr7D 93.646 661 40 2 1 660 185783132 185782473 0.000000e+00 987.0
38 TraesCS3D01G189200 chr7D 87.755 49 5 1 7572 7620 520288676 520288723 1.000000e-03 56.5
39 TraesCS3D01G189200 chr6D 92.632 665 42 6 1 661 464503881 464504542 0.000000e+00 950.0
40 TraesCS3D01G189200 chr6D 91.390 662 52 5 1 661 354267223 354267880 0.000000e+00 902.0
41 TraesCS3D01G189200 chr7A 90.435 115 9 2 7029 7142 674819439 674819326 4.760000e-32 150.0
42 TraesCS3D01G189200 chr7A 84.874 119 14 4 7031 7148 718431009 718430894 4.830000e-22 117.0
43 TraesCS3D01G189200 chr7A 100.000 28 0 0 7300 7327 91538131 91538158 1.400000e-02 52.8
44 TraesCS3D01G189200 chr7B 90.351 114 6 5 7029 7142 477814948 477814840 2.220000e-30 145.0
45 TraesCS3D01G189200 chr7B 80.808 99 13 5 7051 7148 720935678 720935585 1.060000e-08 73.1
46 TraesCS3D01G189200 chr5B 89.565 115 10 2 7029 7142 230883516 230883403 2.220000e-30 145.0
47 TraesCS3D01G189200 chr5B 87.500 56 4 3 7567 7620 278243730 278243676 2.300000e-05 62.1
48 TraesCS3D01G189200 chr5B 100.000 30 0 0 7222 7251 140975424 140975453 1.000000e-03 56.5
49 TraesCS3D01G189200 chr1B 89.565 115 10 2 7029 7142 646931126 646931239 2.220000e-30 145.0
50 TraesCS3D01G189200 chr1B 85.075 134 12 7 7029 7158 211626931 211627060 6.210000e-26 130.0
51 TraesCS3D01G189200 chr1B 94.444 36 0 2 4268 4301 602517924 602517959 4.000000e-03 54.7
52 TraesCS3D01G189200 chr1B 94.444 36 0 2 4268 4301 602530602 602530637 4.000000e-03 54.7
53 TraesCS3D01G189200 chr1B 94.444 36 0 2 4268 4301 602543587 602543622 4.000000e-03 54.7
54 TraesCS3D01G189200 chr6A 88.696 115 11 2 7029 7142 532026633 532026746 1.030000e-28 139.0
55 TraesCS3D01G189200 chr4A 89.796 49 4 1 7573 7620 290378615 290378663 2.300000e-05 62.1
56 TraesCS3D01G189200 chr2A 91.304 46 2 2 4257 4301 184498515 184498559 2.300000e-05 62.1
57 TraesCS3D01G189200 chr6B 100.000 32 0 0 4269 4300 693329366 693329397 8.260000e-05 60.2
58 TraesCS3D01G189200 chr4B 89.362 47 5 0 7574 7620 522307863 522307909 8.260000e-05 60.2
59 TraesCS3D01G189200 chr1A 94.286 35 2 0 7301 7335 9091448 9091414 4.000000e-03 54.7


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 TraesCS3D01G189200 chr3D 177022920 177030541 7621 False 14076.000000 14076 100.000000 1 7622 1 chr3D.!!$F2 7621
1 TraesCS3D01G189200 chr3B 255983858 255992408 8550 False 1596.271429 6010 91.985429 658 7529 7 chr3B.!!$F1 6871
2 TraesCS3D01G189200 chr3A 217713610 217723972 10362 False 1385.288889 4879 96.270333 658 7622 9 chr3A.!!$F3 6964
3 TraesCS3D01G189200 chr2D 430180558 430181214 656 False 1085.000000 1085 96.505000 1 655 1 chr2D.!!$F2 654
4 TraesCS3D01G189200 chr2D 483624837 483625497 660 False 970.000000 970 93.192000 1 660 1 chr2D.!!$F3 659
5 TraesCS3D01G189200 chr2D 573487839 573488495 656 False 922.000000 922 92.006000 1 660 1 chr2D.!!$F4 659
6 TraesCS3D01G189200 chr5D 322522928 322523585 657 False 1072.000000 1072 96.061000 1 659 1 chr5D.!!$F2 658
7 TraesCS3D01G189200 chr5D 35118193 35118851 658 True 941.000000 941 92.436000 1 660 1 chr5D.!!$R1 659
8 TraesCS3D01G189200 chr1D 64205362 64206029 667 True 1051.000000 1051 95.067000 1 668 1 chr1D.!!$R1 667
9 TraesCS3D01G189200 chr7D 185782473 185783132 659 True 987.000000 987 93.646000 1 660 1 chr7D.!!$R1 659
10 TraesCS3D01G189200 chr6D 464503881 464504542 661 False 950.000000 950 92.632000 1 661 1 chr6D.!!$F2 660
11 TraesCS3D01G189200 chr6D 354267223 354267880 657 False 902.000000 902 91.390000 1 661 1 chr6D.!!$F1 660

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
887 892 2.756283 CCGAGAAGAGGAGGCGGT 60.756 66.667 0.00 0.00 37.35 5.68 F
2302 2312 0.035056 GCTGGAGGCCTATGTTGTGT 60.035 55.000 4.42 0.00 34.27 3.72 F
2304 2314 0.322456 TGGAGGCCTATGTTGTGTGC 60.322 55.000 4.42 0.00 0.00 4.57 F
2309 2319 0.523072 GCCTATGTTGTGTGCCACAG 59.477 55.000 0.00 0.00 45.39 3.66 F
2507 2517 0.605860 AGCTATACCGACGAGGCGAT 60.606 55.000 0.00 0.00 46.52 4.58 F
3189 3210 1.095228 ATATGACCTTTGGCGCACGG 61.095 55.000 10.83 5.80 0.00 4.94 F
4184 4207 3.186613 GGCTCTGCTACTTTGTAACACAC 59.813 47.826 0.00 0.00 0.00 3.82 F
4729 8079 0.942252 CCCGTGTGATCATGAGCATG 59.058 55.000 17.94 12.41 40.09 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2329 2339 0.035056 ACACAACATAGGCCTCCAGC 60.035 55.000 9.68 0.00 42.60 4.85 R
4214 4237 5.065731 CCAGCCATCTCAAGAACATCTTAAC 59.934 44.000 0.00 0.00 33.78 2.01 R
4494 7842 3.145286 GCAGAGAGAAGCCAAAGAAAGT 58.855 45.455 0.00 0.00 0.00 2.66 R
4507 7855 2.627515 ACAACAGCAAAGCAGAGAGA 57.372 45.000 0.00 0.00 0.00 3.10 R
4691 8041 2.053627 GGTGAAACAAAGCAATGCTCG 58.946 47.619 8.71 5.58 36.60 5.03 R
4729 8079 5.062683 CGAGTACATATGCTCACAATATGCC 59.937 44.000 1.58 0.00 37.41 4.40 R
5579 8951 0.950836 TGCAAGGAACACCGACAATG 59.049 50.000 0.00 0.00 0.00 2.82 R
6649 11764 1.819632 CCAGTTCAGCCCGCCATAC 60.820 63.158 0.00 0.00 0.00 2.39 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
82 84 3.686016 ACCACGTCTTTTTAGATGCCAT 58.314 40.909 0.00 0.00 0.00 4.40
228 230 4.469883 CGTAGGGGCGCTACTCTA 57.530 61.111 30.99 0.00 0.00 2.43
259 261 3.483901 GGACGACGCGCAATAAAATTACA 60.484 43.478 5.73 0.00 0.00 2.41
480 485 5.932619 TTATGTTAGCTAGGTCTTCAGCA 57.067 39.130 0.00 0.00 40.36 4.41
654 659 3.181552 CGTCTAGCGTCTTCGTTCAAAAG 60.182 47.826 0.00 0.00 39.49 2.27
887 892 2.756283 CCGAGAAGAGGAGGCGGT 60.756 66.667 0.00 0.00 37.35 5.68
1195 1200 2.294791 CCTCTCTGTCGTCTTCAGTGTT 59.705 50.000 0.00 0.00 34.86 3.32
1276 1281 3.512680 CGCCGAATCTTGACTAGTTCTT 58.487 45.455 0.00 0.00 0.00 2.52
1326 1331 1.365699 CGTGAATCCGTTGGTTAGGG 58.634 55.000 0.00 0.00 0.00 3.53
1372 1377 9.793259 ATATATACCCCTGTGAACATTTTACAG 57.207 33.333 4.31 4.31 41.04 2.74
1409 1414 5.043737 TCTACTAGCCACCAACAAAACTT 57.956 39.130 0.00 0.00 0.00 2.66
1575 1580 2.158959 CGTCGTCCATGAACTCGCC 61.159 63.158 0.00 0.00 0.00 5.54
1640 1645 1.664649 CACTCTCGTCGCAGCCAAA 60.665 57.895 0.00 0.00 0.00 3.28
1661 1666 0.671781 GTCATGAGTTCACTGCCGCT 60.672 55.000 0.00 0.00 0.00 5.52
1687 1692 1.055040 ATAGAGCTCACTCCCATGGC 58.945 55.000 17.77 0.00 44.65 4.40
1771 1776 6.001460 ACTTTCATCGGAAAATAAGTGTGGA 58.999 36.000 0.00 0.00 42.18 4.02
1823 1828 2.057922 AGTGGCCCAGGAATGGTATAG 58.942 52.381 0.00 0.00 0.00 1.31
1870 1875 3.653344 GGACATCCAAGCAAGTTTTTCC 58.347 45.455 0.00 0.00 35.64 3.13
2006 2013 3.924686 GTGTCTAATCGTCGAATTGGTGT 59.075 43.478 0.00 0.00 0.00 4.16
2008 2015 4.624024 TGTCTAATCGTCGAATTGGTGTTC 59.376 41.667 0.00 0.00 0.00 3.18
2301 2311 2.785868 GCTGGAGGCCTATGTTGTG 58.214 57.895 4.42 0.00 34.27 3.33
2302 2312 0.035056 GCTGGAGGCCTATGTTGTGT 60.035 55.000 4.42 0.00 34.27 3.72
2303 2313 1.742761 CTGGAGGCCTATGTTGTGTG 58.257 55.000 4.42 0.00 0.00 3.82
2304 2314 0.322456 TGGAGGCCTATGTTGTGTGC 60.322 55.000 4.42 0.00 0.00 4.57
2305 2315 1.032114 GGAGGCCTATGTTGTGTGCC 61.032 60.000 4.42 0.00 42.48 5.01
2306 2316 0.322456 GAGGCCTATGTTGTGTGCCA 60.322 55.000 4.42 0.00 44.60 4.92
2307 2317 0.609131 AGGCCTATGTTGTGTGCCAC 60.609 55.000 1.29 0.00 44.60 5.01
2308 2318 0.893270 GGCCTATGTTGTGTGCCACA 60.893 55.000 0.00 0.00 43.02 4.17
2309 2319 0.523072 GCCTATGTTGTGTGCCACAG 59.477 55.000 0.00 0.00 45.39 3.66
2310 2320 0.523072 CCTATGTTGTGTGCCACAGC 59.477 55.000 0.00 12.86 45.39 4.40
2325 2335 5.113502 GCCACAGCAATATGAATCCTTAC 57.886 43.478 0.00 0.00 39.53 2.34
2326 2336 4.823989 GCCACAGCAATATGAATCCTTACT 59.176 41.667 0.00 0.00 39.53 2.24
2327 2337 5.278169 GCCACAGCAATATGAATCCTTACTG 60.278 44.000 0.00 0.00 39.53 2.74
2328 2338 5.240183 CCACAGCAATATGAATCCTTACTGG 59.760 44.000 0.00 0.00 37.10 4.00
2329 2339 5.240183 CACAGCAATATGAATCCTTACTGGG 59.760 44.000 0.00 0.00 36.20 4.45
2330 2340 4.217118 CAGCAATATGAATCCTTACTGGGC 59.783 45.833 0.00 0.00 36.20 5.36
2331 2341 4.105377 AGCAATATGAATCCTTACTGGGCT 59.895 41.667 0.00 0.00 36.20 5.19
2332 2342 4.217118 GCAATATGAATCCTTACTGGGCTG 59.783 45.833 0.00 0.00 36.20 4.85
2333 2343 4.647564 ATATGAATCCTTACTGGGCTGG 57.352 45.455 0.00 0.00 36.20 4.85
2334 2344 1.965414 TGAATCCTTACTGGGCTGGA 58.035 50.000 0.00 0.00 36.20 3.86
2335 2345 1.839994 TGAATCCTTACTGGGCTGGAG 59.160 52.381 0.00 0.00 36.20 3.86
2336 2346 1.141858 GAATCCTTACTGGGCTGGAGG 59.858 57.143 0.00 0.00 36.20 4.30
2337 2347 1.348775 ATCCTTACTGGGCTGGAGGC 61.349 60.000 0.00 0.00 40.90 4.70
2486 2496 4.100084 CCCGATGCCTGCACTGGA 62.100 66.667 11.83 0.00 0.00 3.86
2507 2517 0.605860 AGCTATACCGACGAGGCGAT 60.606 55.000 0.00 0.00 46.52 4.58
2592 2603 1.982660 TAGTGAGTAGAGGCATCCCG 58.017 55.000 0.00 0.00 35.76 5.14
2957 2977 9.967451 TTCATTGAAGTACACCTATTGGAATTA 57.033 29.630 0.00 0.00 37.04 1.40
2992 3012 5.306394 ACAGAAGGTTGTTAGCTTAGGTTC 58.694 41.667 0.00 0.00 41.92 3.62
3119 3140 8.760980 ACAGGGCATATAGCTTAAATGTTAAA 57.239 30.769 0.00 0.00 44.79 1.52
3121 3142 8.850156 CAGGGCATATAGCTTAAATGTTAAACT 58.150 33.333 0.00 0.00 44.79 2.66
3189 3210 1.095228 ATATGACCTTTGGCGCACGG 61.095 55.000 10.83 5.80 0.00 4.94
3416 3437 3.187227 GGTCGGCTGCATATGTTCTATTG 59.813 47.826 4.29 0.00 0.00 1.90
3424 3445 5.439721 TGCATATGTTCTATTGCTTGGAGT 58.560 37.500 4.29 0.00 36.10 3.85
4183 4206 3.399330 GGCTCTGCTACTTTGTAACACA 58.601 45.455 0.00 0.00 0.00 3.72
4184 4207 3.186613 GGCTCTGCTACTTTGTAACACAC 59.813 47.826 0.00 0.00 0.00 3.82
4214 4237 5.534654 CCATTCTCCTCTAGAACCTCTGTAG 59.465 48.000 0.00 0.00 46.90 2.74
4507 7855 9.746457 ATCTAAGATTTAGACTTTCTTTGGCTT 57.254 29.630 0.94 0.00 32.28 4.35
4509 7857 9.225436 CTAAGATTTAGACTTTCTTTGGCTTCT 57.775 33.333 0.00 0.00 32.28 2.85
4691 8041 5.734855 ATGGCAATTAGTCGTGTAATCAC 57.265 39.130 0.00 0.00 40.79 3.06
4729 8079 0.942252 CCCGTGTGATCATGAGCATG 59.058 55.000 17.94 12.41 40.09 4.06
4876 8226 3.380004 TGGCCTTATATTTGCCTCGTTTG 59.620 43.478 3.32 0.00 45.56 2.93
5002 8352 8.352942 GTTTGTATCAGAACTGAACCATTTCTT 58.647 33.333 8.59 0.00 43.58 2.52
6164 11279 5.473504 ACTGAAGTGAACATGGACCAATTAC 59.526 40.000 0.00 0.00 0.00 1.89
6230 11345 5.957842 TGGTTGATATTGTTGACAAGACC 57.042 39.130 2.77 6.12 39.47 3.85
6233 11348 7.171653 TGGTTGATATTGTTGACAAGACCATA 58.828 34.615 2.77 0.00 39.47 2.74
6389 11504 9.715121 ATTGAATTTCTATGCACTTCACAAAAT 57.285 25.926 0.00 0.00 0.00 1.82
6416 11531 6.699575 ATCAACAACCTGATGCTATTTACC 57.300 37.500 0.00 0.00 34.69 2.85
6475 11590 3.625745 CAGCCGTCTACTGGGTTTT 57.374 52.632 0.00 0.00 34.30 2.43
6588 11703 6.540995 AGCCAGAAATGATATCAATGTAGCT 58.459 36.000 9.99 10.94 0.00 3.32
6687 11802 5.163055 ACTGGTTATATCTGGCCATGAATGT 60.163 40.000 5.51 1.44 0.00 2.71
6926 12041 9.979578 AATCATAGTGTAAAATTGTTTTGCAGA 57.020 25.926 6.26 2.20 44.01 4.26
6977 12092 5.521906 TGAATCAGATCTAAGTTCCTCCG 57.478 43.478 0.00 0.00 0.00 4.63
7089 12207 7.650504 CAGATTGAAATGAGTGAACAAACACAT 59.349 33.333 0.00 0.00 42.45 3.21
7168 12341 7.054124 TCCCTTCATTCCTAAATATGTGACAC 58.946 38.462 0.00 0.00 0.00 3.67
7207 12380 9.139734 ACGTCATATATTTAGTACTCCCTTCAA 57.860 33.333 0.00 0.00 0.00 2.69
7222 12411 8.050316 ACTCCCTTCAATCCTAAATATGTGAT 57.950 34.615 0.00 0.00 0.00 3.06
7317 12547 7.281040 ACGTCATATATTTAGAAACGGAGGA 57.719 36.000 0.00 0.00 33.26 3.71
7369 12618 4.747108 CGGGCTGTCATAATAGTGAAGAAG 59.253 45.833 0.00 0.00 0.00 2.85
7377 12626 9.436957 TGTCATAATAGTGAAGAAGGAAAAGAC 57.563 33.333 0.00 0.00 0.00 3.01
7394 12643 8.598041 AGGAAAAGACTACTAATTGTGATCACT 58.402 33.333 25.55 9.24 0.00 3.41
7429 12678 6.264292 TGGCGCATGGTTATATATGAAACTTT 59.736 34.615 10.83 0.00 0.00 2.66
7530 12779 3.782046 ACATCTTCGAAACTGATACCGG 58.218 45.455 0.00 0.00 0.00 5.28
7535 12784 2.165167 TCGAAACTGATACCGGACTGT 58.835 47.619 9.46 6.61 0.00 3.55
7539 12788 4.504858 GAAACTGATACCGGACTGTCATT 58.495 43.478 9.46 2.05 0.00 2.57
7542 12791 4.504858 ACTGATACCGGACTGTCATTTTC 58.495 43.478 9.46 0.77 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 84 4.680237 CACGCGAACCTGGCCAGA 62.680 66.667 34.91 0.00 0.00 3.86
146 148 5.848369 TGAGGATGGATATCAAGTCATTCCT 59.152 40.000 4.83 1.90 34.90 3.36
228 230 1.518572 CGCGTCGTCCAAATAGCCT 60.519 57.895 0.00 0.00 0.00 4.58
285 288 2.378445 TTTGAAGATCACATCCGCGA 57.622 45.000 8.23 0.00 0.00 5.87
419 423 2.069273 CCAAAAGCTTCATCGACTCGT 58.931 47.619 0.00 0.00 0.00 4.18
480 485 3.711863 ACAACCAGCCATAACATCCAAT 58.288 40.909 0.00 0.00 0.00 3.16
654 659 2.849081 TCCGGCGTGGAGATTTTTC 58.151 52.632 6.01 0.00 43.74 2.29
847 852 1.001633 GGCTCTCGTTTACTGGTTCCA 59.998 52.381 0.00 0.00 0.00 3.53
1276 1281 0.166597 CACGTCGCGTCTAAGGTACA 59.833 55.000 5.77 0.00 38.32 2.90
1409 1414 7.976734 ACTTTCACAACCGAAAATGTATTCAAA 59.023 29.630 0.00 0.00 34.59 2.69
1640 1645 0.667487 CGGCAGTGAACTCATGACGT 60.667 55.000 0.00 0.00 40.56 4.34
1661 1666 2.021068 GAGTGAGCTCTATGGCGGCA 62.021 60.000 16.34 16.34 38.66 5.69
1687 1692 1.137086 AGCTAGTAACAGTGGCGATGG 59.863 52.381 0.00 0.00 29.61 3.51
1695 1700 3.936372 TGCGAAAGAGCTAGTAACAGT 57.064 42.857 0.00 0.00 38.13 3.55
1823 1828 8.898792 CGTTTTAGTTTTCTTAAATACCAGTGC 58.101 33.333 0.00 0.00 32.39 4.40
1870 1875 1.490621 CAGTTTTTCCAAGCAAGGCG 58.509 50.000 0.00 0.00 0.00 5.52
2006 2013 8.877195 ACCTATAGTTCTTACCACAAAGAAGAA 58.123 33.333 0.00 0.00 44.09 2.52
2008 2015 8.095169 ACACCTATAGTTCTTACCACAAAGAAG 58.905 37.037 0.00 0.00 44.09 2.85
2303 2313 4.823989 AGTAAGGATTCATATTGCTGTGGC 59.176 41.667 0.00 0.00 39.26 5.01
2304 2314 5.240183 CCAGTAAGGATTCATATTGCTGTGG 59.760 44.000 10.43 0.00 41.22 4.17
2305 2315 5.240183 CCCAGTAAGGATTCATATTGCTGTG 59.760 44.000 10.43 0.34 41.22 3.66
2306 2316 5.380043 CCCAGTAAGGATTCATATTGCTGT 58.620 41.667 10.43 0.00 41.22 4.40
2307 2317 4.217118 GCCCAGTAAGGATTCATATTGCTG 59.783 45.833 6.62 6.62 41.22 4.41
2308 2318 4.105377 AGCCCAGTAAGGATTCATATTGCT 59.895 41.667 0.00 0.00 41.22 3.91
2309 2319 4.217118 CAGCCCAGTAAGGATTCATATTGC 59.783 45.833 0.00 0.00 41.22 3.56
2310 2320 4.763793 CCAGCCCAGTAAGGATTCATATTG 59.236 45.833 0.00 0.00 41.22 1.90
2311 2321 4.665009 TCCAGCCCAGTAAGGATTCATATT 59.335 41.667 0.00 0.00 41.22 1.28
2312 2322 4.242811 TCCAGCCCAGTAAGGATTCATAT 58.757 43.478 0.00 0.00 41.22 1.78
2313 2323 3.648067 CTCCAGCCCAGTAAGGATTCATA 59.352 47.826 0.00 0.00 41.22 2.15
2314 2324 2.441001 CTCCAGCCCAGTAAGGATTCAT 59.559 50.000 0.00 0.00 41.22 2.57
2315 2325 1.839994 CTCCAGCCCAGTAAGGATTCA 59.160 52.381 0.00 0.00 41.22 2.57
2316 2326 1.141858 CCTCCAGCCCAGTAAGGATTC 59.858 57.143 0.00 0.00 41.22 2.52
2317 2327 1.216990 CCTCCAGCCCAGTAAGGATT 58.783 55.000 0.00 0.00 41.22 3.01
2318 2328 1.348775 GCCTCCAGCCCAGTAAGGAT 61.349 60.000 0.00 0.00 41.22 3.24
2319 2329 1.995626 GCCTCCAGCCCAGTAAGGA 60.996 63.158 0.00 0.00 41.22 3.36
2320 2330 2.592308 GCCTCCAGCCCAGTAAGG 59.408 66.667 0.00 0.00 34.35 2.69
2329 2339 0.035056 ACACAACATAGGCCTCCAGC 60.035 55.000 9.68 0.00 42.60 4.85
2330 2340 1.742761 CACACAACATAGGCCTCCAG 58.257 55.000 9.68 2.31 0.00 3.86
2331 2341 0.322456 GCACACAACATAGGCCTCCA 60.322 55.000 9.68 0.00 0.00 3.86
2332 2342 1.032114 GGCACACAACATAGGCCTCC 61.032 60.000 9.68 0.00 41.39 4.30
2333 2343 0.322456 TGGCACACAACATAGGCCTC 60.322 55.000 9.68 0.00 44.85 4.70
2334 2344 1.767036 TGGCACACAACATAGGCCT 59.233 52.632 11.78 11.78 44.85 5.19
2335 2345 4.413928 TGGCACACAACATAGGCC 57.586 55.556 0.00 0.00 44.82 5.19
2346 2356 2.358957 GATTCATGCTACTGTGGCACA 58.641 47.619 21.26 20.76 42.69 4.57
2485 2495 0.518195 GCCTCGTCGGTATAGCTCTC 59.482 60.000 0.00 0.00 34.25 3.20
2486 2496 1.229315 CGCCTCGTCGGTATAGCTCT 61.229 60.000 0.00 0.00 34.25 4.09
2592 2603 7.152645 TGAGTCTTAACAGGTGTTATTGAGAC 58.847 38.462 17.80 17.80 41.52 3.36
2957 2977 4.532521 ACAACCTTCTGTAGCTCCTTATGT 59.467 41.667 0.00 0.00 0.00 2.29
2992 3012 4.692625 CCATCAGTCAGTTAACAGTTGAGG 59.307 45.833 8.61 9.83 0.00 3.86
4214 4237 5.065731 CCAGCCATCTCAAGAACATCTTAAC 59.934 44.000 0.00 0.00 33.78 2.01
4494 7842 3.145286 GCAGAGAGAAGCCAAAGAAAGT 58.855 45.455 0.00 0.00 0.00 2.66
4507 7855 2.627515 ACAACAGCAAAGCAGAGAGA 57.372 45.000 0.00 0.00 0.00 3.10
4509 7857 2.485426 GCATACAACAGCAAAGCAGAGA 59.515 45.455 0.00 0.00 0.00 3.10
4691 8041 2.053627 GGTGAAACAAAGCAATGCTCG 58.946 47.619 8.71 5.58 36.60 5.03
4729 8079 5.062683 CGAGTACATATGCTCACAATATGCC 59.937 44.000 1.58 0.00 37.41 4.40
5278 8630 9.956720 AGAGAACTACACAGAAAAATGAAAATG 57.043 29.630 0.00 0.00 0.00 2.32
5503 8875 1.210478 GTCAGCATGGACCATACTGGT 59.790 52.381 27.49 12.68 45.79 4.00
5579 8951 0.950836 TGCAAGGAACACCGACAATG 59.049 50.000 0.00 0.00 0.00 2.82
5770 9142 4.819783 TGCGAAGGCACATTTCCT 57.180 50.000 0.00 0.00 46.21 3.36
6233 11348 8.554490 AGTAACCCATTAGATGTGAACTATCT 57.446 34.615 0.00 0.00 38.40 1.98
6389 11504 9.056005 GTAAATAGCATCAGGTTGTTGATATCA 57.944 33.333 0.00 0.00 36.08 2.15
6416 11531 7.123247 AGGAACATGATCAAAAGATTAACCAGG 59.877 37.037 0.00 0.00 0.00 4.45
6649 11764 1.819632 CCAGTTCAGCCCGCCATAC 60.820 63.158 0.00 0.00 0.00 2.39
6687 11802 2.958576 GAATGCGCGGGGAACAAA 59.041 55.556 8.83 0.00 0.00 2.83
7067 12185 9.645059 TTAAATGTGTTTGTTCACTCATTTCAA 57.355 25.926 14.04 7.54 42.84 2.69
7096 12214 5.687780 TCTGAATTGGATGTGCATAGACAT 58.312 37.500 0.00 0.00 39.34 3.06
7132 12250 8.798975 TTAGGAATGAAGGGAGTATAAGATGT 57.201 34.615 0.00 0.00 0.00 3.06
7139 12257 9.170890 TCACATATTTAGGAATGAAGGGAGTAT 57.829 33.333 0.00 0.00 0.00 2.12
7252 12441 8.429641 GTCACATATTTAGGAATGAAGGGAGTA 58.570 37.037 0.00 0.00 0.00 2.59
7254 12443 7.282585 TGTCACATATTTAGGAATGAAGGGAG 58.717 38.462 0.00 0.00 0.00 4.30
7255 12444 7.206789 TGTCACATATTTAGGAATGAAGGGA 57.793 36.000 0.00 0.00 0.00 4.20
7256 12445 8.355169 CAATGTCACATATTTAGGAATGAAGGG 58.645 37.037 0.00 0.00 0.00 3.95
7257 12446 9.123902 TCAATGTCACATATTTAGGAATGAAGG 57.876 33.333 0.00 0.00 0.00 3.46
7260 12449 9.685276 AGTTCAATGTCACATATTTAGGAATGA 57.315 29.630 0.00 0.00 0.00 2.57
7317 12547 9.959721 CCCCAAATGTTATGCTATATACTACTT 57.040 33.333 0.00 0.00 0.00 2.24
7369 12618 8.779354 AGTGATCACAATTAGTAGTCTTTTCC 57.221 34.615 27.02 0.00 0.00 3.13
7377 12626 5.515797 TCCGGAGTGATCACAATTAGTAG 57.484 43.478 27.02 9.26 0.00 2.57
7394 12643 4.028490 ATGCGCCAACCTTCCGGA 62.028 61.111 4.18 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.