Multiple sequence alignment - TraesCS6B01G429700

Loading Multiple Alignment...

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 TraesCS6B01G429700 chr6B 100.000 4798 0 0 1 4798 697541884 697537087 0.000000e+00 8861.0
1 TraesCS6B01G429700 chr6B 99.421 1210 3 3 3592 4798 697465854 697464646 0.000000e+00 2193.0
2 TraesCS6B01G429700 chr6B 99.097 886 8 0 975 1860 697466735 697465850 0.000000e+00 1592.0
3 TraesCS6B01G429700 chr6B 89.374 847 48 14 2072 2887 505485396 505484561 0.000000e+00 1027.0
4 TraesCS6B01G429700 chr6B 91.457 714 38 10 2351 3047 680880048 680880755 0.000000e+00 959.0
5 TraesCS6B01G429700 chr6B 99.783 461 0 1 1861 2321 697538753 697538294 0.000000e+00 845.0
6 TraesCS6B01G429700 chr6B 99.783 461 0 1 3132 3591 697540024 697539564 0.000000e+00 845.0
7 TraesCS6B01G429700 chr6B 83.915 516 46 22 2956 3434 372305730 372306245 4.380000e-125 459.0
8 TraesCS6B01G429700 chr6B 89.925 268 26 1 535 802 225863512 225863778 1.280000e-90 344.0
9 TraesCS6B01G429700 chr6B 80.122 327 38 16 3289 3605 142677580 142677271 8.080000e-53 219.0
10 TraesCS6B01G429700 chr6B 85.000 60 4 4 239 294 40440117 40440175 6.710000e-04 56.5
11 TraesCS6B01G429700 chr7B 99.770 1738 2 2 1855 3591 696906808 696908544 0.000000e+00 3186.0
12 TraesCS6B01G429700 chr7B 90.310 774 56 7 2351 3108 641880325 641879555 0.000000e+00 996.0
13 TraesCS6B01G429700 chr7B 89.348 798 54 5 2350 3137 427836366 427835590 0.000000e+00 974.0
14 TraesCS6B01G429700 chr7B 100.000 460 0 0 3132 3591 696906815 696907274 0.000000e+00 850.0
15 TraesCS6B01G429700 chr7B 99.783 461 0 1 1861 2321 696908085 696908544 0.000000e+00 845.0
16 TraesCS6B01G429700 chr7B 89.865 444 31 3 2350 2780 193957827 193958269 4.190000e-155 558.0
17 TraesCS6B01G429700 chr7B 82.151 437 32 14 3174 3566 646032232 646032666 2.770000e-87 333.0
18 TraesCS6B01G429700 chr6A 95.498 933 39 1 928 1860 605043481 605044410 0.000000e+00 1487.0
19 TraesCS6B01G429700 chr6A 90.583 669 44 14 239 903 605041435 605042088 0.000000e+00 869.0
20 TraesCS6B01G429700 chr6A 95.469 309 14 0 3592 3900 605044406 605044714 1.200000e-135 494.0
21 TraesCS6B01G429700 chr6A 86.650 412 39 10 4390 4795 605049525 605049926 4.410000e-120 442.0
22 TraesCS6B01G429700 chr6A 90.033 301 16 5 3915 4215 605044701 605044987 1.260000e-100 377.0
23 TraesCS6B01G429700 chr6A 85.417 336 16 9 1861 2185 42174264 42174577 7.750000e-83 318.0
24 TraesCS6B01G429700 chr6A 91.406 128 11 0 4278 4405 605044988 605045115 4.940000e-40 176.0
25 TraesCS6B01G429700 chr6A 96.923 65 2 0 1 65 605041168 605041232 5.080000e-20 110.0
26 TraesCS6B01G429700 chr3B 90.943 795 56 13 2351 3142 362052323 362051542 0.000000e+00 1055.0
27 TraesCS6B01G429700 chr3B 88.212 772 41 17 2317 3050 36434340 36433581 0.000000e+00 876.0
28 TraesCS6B01G429700 chr3B 89.755 449 33 6 2360 2795 409327026 409327474 3.240000e-156 562.0
29 TraesCS6B01G429700 chr3B 83.673 98 13 3 4066 4162 497713420 497713515 6.610000e-14 89.8
30 TraesCS6B01G429700 chr5B 89.857 769 43 15 2360 3115 682132361 682131615 0.000000e+00 955.0
31 TraesCS6B01G429700 chr5B 90.199 755 40 14 2360 3101 682094502 682093769 0.000000e+00 953.0
32 TraesCS6B01G429700 chr5B 87.311 331 15 1 1861 2164 666299924 666300254 2.120000e-93 353.0
33 TraesCS6B01G429700 chr5A 91.193 704 43 7 2360 3046 110278963 110279664 0.000000e+00 939.0
34 TraesCS6B01G429700 chr1A 87.259 777 61 13 2350 3109 182075932 182076687 0.000000e+00 852.0
35 TraesCS6B01G429700 chr1A 89.246 623 60 7 2531 3148 567832527 567831907 0.000000e+00 773.0
36 TraesCS6B01G429700 chr4B 88.253 681 57 6 2473 3149 537796961 537797622 0.000000e+00 793.0
37 TraesCS6B01G429700 chr4B 89.630 270 26 2 533 802 494016606 494016339 4.600000e-90 342.0
38 TraesCS6B01G429700 chrUn 88.283 623 65 8 2531 3148 277736101 277735482 0.000000e+00 739.0
39 TraesCS6B01G429700 chrUn 98.515 404 5 1 1854 2256 67415966 67416369 0.000000e+00 712.0
40 TraesCS6B01G429700 chrUn 98.737 396 4 1 3132 3526 67415974 67416369 0.000000e+00 702.0
41 TraesCS6B01G429700 chr4A 93.333 450 26 4 2638 3085 652460946 652461393 0.000000e+00 662.0
42 TraesCS6B01G429700 chr1B 86.751 551 65 5 2892 3434 324409319 324408769 1.480000e-169 606.0
43 TraesCS6B01G429700 chr1B 90.615 309 25 1 1860 2164 324409077 324408769 1.610000e-109 407.0
44 TraesCS6B01G429700 chr1B 96.087 230 9 0 2360 2589 616025106 616025335 4.530000e-100 375.0
45 TraesCS6B01G429700 chr1B 90.476 273 22 1 1861 2129 324410335 324410063 1.640000e-94 357.0
46 TraesCS6B01G429700 chr1B 90.146 274 22 2 3131 3399 324410336 324410063 7.640000e-93 351.0
47 TraesCS6B01G429700 chr1B 90.226 266 25 1 536 801 16452786 16452522 3.550000e-91 346.0
48 TraesCS6B01G429700 chr1B 89.668 271 24 4 534 802 670279907 670280175 4.600000e-90 342.0
49 TraesCS6B01G429700 chr7A 80.116 860 76 42 2792 3591 38524356 38523532 1.950000e-153 553.0
50 TraesCS6B01G429700 chr7A 85.934 455 34 12 1907 2335 38523967 38523517 4.380000e-125 459.0
51 TraesCS6B01G429700 chr7A 90.152 264 25 1 537 800 101271799 101272061 4.600000e-90 342.0
52 TraesCS6B01G429700 chr7A 84.053 301 32 13 2111 2406 112796341 112796052 4.730000e-70 276.0
53 TraesCS6B01G429700 chr7A 90.566 53 3 2 221 273 84823770 84823820 8.620000e-08 69.4
54 TraesCS6B01G429700 chr7A 94.595 37 1 1 238 273 456255209 456255173 6.710000e-04 56.5
55 TraesCS6B01G429700 chr4D 82.848 653 63 16 2984 3591 445104125 445104773 1.520000e-149 540.0
56 TraesCS6B01G429700 chr4D 80.868 507 51 14 1860 2324 445104274 445104776 1.640000e-94 357.0
57 TraesCS6B01G429700 chr2D 84.238 571 51 11 2990 3525 167766145 167765579 1.980000e-143 520.0
58 TraesCS6B01G429700 chr2D 92.395 263 19 1 539 801 315858988 315859249 1.630000e-99 374.0
59 TraesCS6B01G429700 chr2D 90.217 276 20 6 2113 2383 573453835 573454108 2.120000e-93 353.0
60 TraesCS6B01G429700 chr2D 93.033 244 11 5 2140 2379 21508822 21508581 7.640000e-93 351.0
61 TraesCS6B01G429700 chr2D 94.348 230 6 6 2140 2364 22307997 22308224 3.550000e-91 346.0
62 TraesCS6B01G429700 chr3A 89.925 268 25 2 535 801 15505571 15505305 1.280000e-90 344.0
63 TraesCS6B01G429700 chr3A 90.152 264 25 1 538 801 522717636 522717898 4.600000e-90 342.0
64 TraesCS6B01G429700 chr3A 84.133 271 12 17 1880 2119 746843212 746843482 2.890000e-57 233.0
65 TraesCS6B01G429700 chr3A 94.595 37 1 1 238 273 677840598 677840562 6.710000e-04 56.5
66 TraesCS6B01G429700 chr7D 85.185 324 36 10 2019 2335 327375666 327375984 5.990000e-84 322.0
67 TraesCS6B01G429700 chr7D 84.790 309 36 9 3289 3591 327375666 327375969 2.810000e-77 300.0
68 TraesCS6B01G429700 chr7D 80.000 90 17 1 4074 4162 554319005 554318916 1.110000e-06 65.8
69 TraesCS6B01G429700 chr1D 82.789 337 45 12 3289 3616 442905481 442905813 6.080000e-74 289.0
70 TraesCS6B01G429700 chr1D 94.286 35 2 0 239 273 35782450 35782484 2.000000e-03 54.7
71 TraesCS6B01G429700 chr6D 87.027 185 18 2 3694 3876 458534114 458533934 2.260000e-48 204.0
72 TraesCS6B01G429700 chr5D 78.846 208 38 5 4046 4249 297985291 297985496 8.380000e-28 135.0
73 TraesCS6B01G429700 chr3D 100.000 28 0 0 246 273 319858738 319858765 9.000000e-03 52.8


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 TraesCS6B01G429700 chr6B 697537087 697541884 4797 True 3517.00 8861 99.855333 1 4798 3 chr6B.!!$R4 4797
1 TraesCS6B01G429700 chr6B 697464646 697466735 2089 True 1892.50 2193 99.259000 975 4798 2 chr6B.!!$R3 3823
2 TraesCS6B01G429700 chr6B 505484561 505485396 835 True 1027.00 1027 89.374000 2072 2887 1 chr6B.!!$R2 815
3 TraesCS6B01G429700 chr6B 680880048 680880755 707 False 959.00 959 91.457000 2351 3047 1 chr6B.!!$F4 696
4 TraesCS6B01G429700 chr6B 372305730 372306245 515 False 459.00 459 83.915000 2956 3434 1 chr6B.!!$F3 478
5 TraesCS6B01G429700 chr7B 696906808 696908544 1736 False 1627.00 3186 99.851000 1855 3591 3 chr7B.!!$F3 1736
6 TraesCS6B01G429700 chr7B 641879555 641880325 770 True 996.00 996 90.310000 2351 3108 1 chr7B.!!$R2 757
7 TraesCS6B01G429700 chr7B 427835590 427836366 776 True 974.00 974 89.348000 2350 3137 1 chr7B.!!$R1 787
8 TraesCS6B01G429700 chr6A 605041168 605045115 3947 False 585.50 1487 93.318667 1 4405 6 chr6A.!!$F3 4404
9 TraesCS6B01G429700 chr3B 362051542 362052323 781 True 1055.00 1055 90.943000 2351 3142 1 chr3B.!!$R2 791
10 TraesCS6B01G429700 chr3B 36433581 36434340 759 True 876.00 876 88.212000 2317 3050 1 chr3B.!!$R1 733
11 TraesCS6B01G429700 chr5B 682131615 682132361 746 True 955.00 955 89.857000 2360 3115 1 chr5B.!!$R2 755
12 TraesCS6B01G429700 chr5B 682093769 682094502 733 True 953.00 953 90.199000 2360 3101 1 chr5B.!!$R1 741
13 TraesCS6B01G429700 chr5A 110278963 110279664 701 False 939.00 939 91.193000 2360 3046 1 chr5A.!!$F1 686
14 TraesCS6B01G429700 chr1A 182075932 182076687 755 False 852.00 852 87.259000 2350 3109 1 chr1A.!!$F1 759
15 TraesCS6B01G429700 chr1A 567831907 567832527 620 True 773.00 773 89.246000 2531 3148 1 chr1A.!!$R1 617
16 TraesCS6B01G429700 chr4B 537796961 537797622 661 False 793.00 793 88.253000 2473 3149 1 chr4B.!!$F1 676
17 TraesCS6B01G429700 chrUn 277735482 277736101 619 True 739.00 739 88.283000 2531 3148 1 chrUn.!!$R1 617
18 TraesCS6B01G429700 chr1B 324408769 324410336 1567 True 430.25 606 89.497000 1860 3434 4 chr1B.!!$R2 1574
19 TraesCS6B01G429700 chr7A 38523517 38524356 839 True 506.00 553 83.025000 1907 3591 2 chr7A.!!$R3 1684
20 TraesCS6B01G429700 chr4D 445104125 445104776 651 False 448.50 540 81.858000 1860 3591 2 chr4D.!!$F1 1731
21 TraesCS6B01G429700 chr2D 167765579 167766145 566 True 520.00 520 84.238000 2990 3525 1 chr2D.!!$R2 535

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
909 976 0.034337 TGTGGGTGACTAAACGGAGC 59.966 55.000 0.0 0.0 0.0 4.70 F
910 977 0.034337 GTGGGTGACTAAACGGAGCA 59.966 55.000 0.0 0.0 0.0 4.26 F
913 980 1.338769 GGGTGACTAAACGGAGCACAT 60.339 52.381 0.0 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1728 3166 3.403038 CCACATCTGGTCGAAGTTCTTT 58.597 45.455 0.56 0.0 32.03 2.52 R
1859 3297 5.710099 CACCTAACATGGTTTACTCCAACAT 59.290 40.000 0.00 0.0 41.09 2.71 R
4651 6452 1.002773 GTTTACATCCACACGGGTCCT 59.997 52.381 0.00 0.0 38.11 3.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 1.686052 GTGCAAGGTGATTCAAACCCA 59.314 47.619 0.00 0.00 38.57 4.51
46 47 3.835978 TCAAACCCACGATCTCCTTCTTA 59.164 43.478 0.00 0.00 0.00 2.10
65 66 9.167311 CCTTCTTATTGATAAACTGCAGTAACT 57.833 33.333 22.01 10.46 0.00 2.24
71 72 7.443259 TTGATAAACTGCAGTAACTTTACCC 57.557 36.000 22.01 10.66 34.19 3.69
72 73 6.775708 TGATAAACTGCAGTAACTTTACCCT 58.224 36.000 22.01 0.06 34.19 4.34
73 74 7.909518 TGATAAACTGCAGTAACTTTACCCTA 58.090 34.615 22.01 0.00 34.19 3.53
74 75 8.377034 TGATAAACTGCAGTAACTTTACCCTAA 58.623 33.333 22.01 0.00 34.19 2.69
75 76 9.223099 GATAAACTGCAGTAACTTTACCCTAAA 57.777 33.333 22.01 0.00 34.19 1.85
76 77 7.885009 AAACTGCAGTAACTTTACCCTAAAA 57.115 32.000 22.01 0.00 34.19 1.52
77 78 7.885009 AACTGCAGTAACTTTACCCTAAAAA 57.115 32.000 22.01 0.00 34.19 1.94
134 135 5.348724 CACACATGTTGCGATTACTTACTCT 59.651 40.000 0.00 0.00 0.00 3.24
170 171 9.307121 CTTTCTTCTCTTTTCCTTTTCCTTTTC 57.693 33.333 0.00 0.00 0.00 2.29
171 172 7.348080 TCTTCTCTTTTCCTTTTCCTTTTCC 57.652 36.000 0.00 0.00 0.00 3.13
174 175 7.733773 TCTCTTTTCCTTTTCCTTTTCCTTT 57.266 32.000 0.00 0.00 0.00 3.11
176 177 8.258007 TCTCTTTTCCTTTTCCTTTTCCTTTTC 58.742 33.333 0.00 0.00 0.00 2.29
178 179 8.602424 TCTTTTCCTTTTCCTTTTCCTTTTCTT 58.398 29.630 0.00 0.00 0.00 2.52
181 182 9.581289 TTTCCTTTTCCTTTTCCTTTTCTTTTT 57.419 25.926 0.00 0.00 0.00 1.94
182 183 8.786826 TCCTTTTCCTTTTCCTTTTCTTTTTC 57.213 30.769 0.00 0.00 0.00 2.29
396 461 6.867519 TGGTTCTTATCTACCAGATCAACA 57.132 37.500 0.00 0.00 39.44 3.33
446 511 0.592754 CGTAGCGAACTCTGCTAGGC 60.593 60.000 2.31 0.00 45.00 3.93
451 516 3.064987 GAACTCTGCTAGGCCGCGA 62.065 63.158 8.23 0.00 0.00 5.87
497 562 0.179124 CTGAAGGCGTCTAGAGCACC 60.179 60.000 13.76 6.93 36.08 5.01
505 570 1.736126 CGTCTAGAGCACCACGAGTAA 59.264 52.381 0.00 0.00 34.06 2.24
527 592 5.796424 ATGTGCCTTGATTTGTTTTCTCT 57.204 34.783 0.00 0.00 0.00 3.10
534 599 6.294955 GCCTTGATTTGTTTTCTCTTCCTCAT 60.295 38.462 0.00 0.00 0.00 2.90
547 612 8.887264 TTCTCTTCCTCATATATACTCCCTTC 57.113 38.462 0.00 0.00 0.00 3.46
548 613 8.001300 TCTCTTCCTCATATATACTCCCTTCA 57.999 38.462 0.00 0.00 0.00 3.02
564 629 6.070767 ACTCCCTTCATTTTTATCGACTCTGA 60.071 38.462 0.00 0.00 0.00 3.27
568 633 9.277783 CCCTTCATTTTTATCGACTCTGAATAT 57.722 33.333 0.00 0.00 0.00 1.28
613 678 5.744666 TCGGAAAGTTTGACCAAGTTTAG 57.255 39.130 0.00 0.00 38.02 1.85
615 680 5.526111 TCGGAAAGTTTGACCAAGTTTAGAG 59.474 40.000 0.00 0.00 38.02 2.43
620 685 8.981724 AAAGTTTGACCAAGTTTAGAGAAAAC 57.018 30.769 0.00 0.00 46.61 2.43
757 822 9.233232 CGTCAAAGTTTATAAAGCTTGACTTTT 57.767 29.630 28.64 10.05 46.73 2.27
775 840 9.820229 TTGACTTTTGATTAAAGCTAATACACG 57.180 29.630 0.00 0.00 45.87 4.49
776 841 8.995220 TGACTTTTGATTAAAGCTAATACACGT 58.005 29.630 0.00 0.00 45.87 4.49
777 842 9.262472 GACTTTTGATTAAAGCTAATACACGTG 57.738 33.333 15.48 15.48 45.87 4.49
789 854 9.550811 AAGCTAATACACGTGCTAAATAAAAAC 57.449 29.630 17.22 0.00 35.09 2.43
794 859 4.083696 ACACGTGCTAAATAAAAACGGAGG 60.084 41.667 17.22 0.00 38.52 4.30
802 867 6.183360 GCTAAATAAAAACGGAGGGAGTACAC 60.183 42.308 0.00 0.00 0.00 2.90
803 868 2.159327 AAAAACGGAGGGAGTACACG 57.841 50.000 0.00 0.00 0.00 4.49
804 869 0.319405 AAAACGGAGGGAGTACACGG 59.681 55.000 0.00 0.00 0.00 4.94
805 870 0.829182 AAACGGAGGGAGTACACGGT 60.829 55.000 0.00 0.00 0.00 4.83
806 871 1.246737 AACGGAGGGAGTACACGGTC 61.247 60.000 0.00 0.00 0.00 4.79
807 872 1.676635 CGGAGGGAGTACACGGTCA 60.677 63.158 0.00 0.00 0.00 4.02
808 873 1.035932 CGGAGGGAGTACACGGTCAT 61.036 60.000 0.00 0.00 0.00 3.06
809 874 0.745468 GGAGGGAGTACACGGTCATC 59.255 60.000 0.00 0.00 0.00 2.92
810 875 1.471119 GAGGGAGTACACGGTCATCA 58.529 55.000 0.00 0.00 0.00 3.07
811 876 1.405821 GAGGGAGTACACGGTCATCAG 59.594 57.143 0.00 0.00 0.00 2.90
812 877 0.460311 GGGAGTACACGGTCATCAGG 59.540 60.000 0.00 0.00 0.00 3.86
854 921 1.166531 AAAGACAACGAGGCACCAGC 61.167 55.000 0.00 0.00 41.10 4.85
866 933 1.001764 CACCAGCCTGATGAGCCAA 60.002 57.895 0.00 0.00 0.00 4.52
868 935 2.119655 CCAGCCTGATGAGCCAAGC 61.120 63.158 0.00 0.00 0.00 4.01
872 939 0.893447 GCCTGATGAGCCAAGCTTTT 59.107 50.000 0.00 0.00 39.88 2.27
879 946 3.608316 TGAGCCAAGCTTTTTGTGTTT 57.392 38.095 0.00 0.00 39.88 2.83
903 970 4.396790 GTGTGTTTCTTGTGGGTGACTAAA 59.603 41.667 0.00 0.00 0.00 1.85
904 971 4.396790 TGTGTTTCTTGTGGGTGACTAAAC 59.603 41.667 0.00 0.00 0.00 2.01
905 972 3.623960 TGTTTCTTGTGGGTGACTAAACG 59.376 43.478 0.00 0.00 30.93 3.60
906 973 2.536761 TCTTGTGGGTGACTAAACGG 57.463 50.000 0.00 0.00 0.00 4.44
907 974 2.040939 TCTTGTGGGTGACTAAACGGA 58.959 47.619 0.00 0.00 0.00 4.69
909 976 0.034337 TGTGGGTGACTAAACGGAGC 59.966 55.000 0.00 0.00 0.00 4.70
910 977 0.034337 GTGGGTGACTAAACGGAGCA 59.966 55.000 0.00 0.00 0.00 4.26
911 978 0.034337 TGGGTGACTAAACGGAGCAC 59.966 55.000 0.00 0.00 0.00 4.40
912 979 0.034337 GGGTGACTAAACGGAGCACA 59.966 55.000 0.00 0.00 0.00 4.57
913 980 1.338769 GGGTGACTAAACGGAGCACAT 60.339 52.381 0.00 0.00 0.00 3.21
943 2378 2.433004 GGCCCGGCCGGTTATTAT 59.567 61.111 40.52 0.00 39.62 1.28
967 2402 5.258456 TGTAGCTTGTATAGGAAAGACCG 57.742 43.478 0.00 0.00 44.74 4.79
1664 3102 4.078516 GCCCTACTTCGGTGGCGT 62.079 66.667 0.00 0.00 0.00 5.68
1728 3166 1.975407 GTCCGAGTTCGACCCTGGA 60.975 63.158 2.59 0.00 43.02 3.86
1855 3293 3.190738 TTCCCTCCGGTGCTGGTTG 62.191 63.158 0.00 0.00 0.00 3.77
1858 3296 4.641645 CTCCGGTGCTGGTTGCCA 62.642 66.667 0.00 0.00 42.00 4.92
1859 3297 4.196778 TCCGGTGCTGGTTGCCAA 62.197 61.111 0.00 0.00 42.00 4.52
4651 6452 3.743911 TCTTATCGCAAACGCTTTCAGAA 59.256 39.130 0.00 0.00 39.84 3.02
4656 6457 1.335051 GCAAACGCTTTCAGAAGGACC 60.335 52.381 0.00 0.00 33.34 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 7.439655 GCAGTTTATCAATAAGAAGGAGATCGT 59.560 37.037 0.00 0.00 0.00 3.73
46 47 7.888546 AGGGTAAAGTTACTGCAGTTTATCAAT 59.111 33.333 27.06 7.44 34.16 2.57
77 78 8.007405 AGTTGGTTACTGCAGTTTATCTTTTT 57.993 30.769 27.06 0.00 35.19 1.94
78 79 7.582667 AGTTGGTTACTGCAGTTTATCTTTT 57.417 32.000 27.06 2.40 35.19 2.27
92 93 1.357272 TGGTGCCCCAGTTGGTTACT 61.357 55.000 0.00 0.00 35.17 2.24
93 94 1.151908 TGGTGCCCCAGTTGGTTAC 59.848 57.895 0.00 0.00 35.17 2.50
94 95 1.151908 GTGGTGCCCCAGTTGGTTA 59.848 57.895 0.00 0.00 42.94 2.85
95 96 2.123468 GTGGTGCCCCAGTTGGTT 60.123 61.111 0.00 0.00 42.94 3.67
96 97 3.425014 TGTGGTGCCCCAGTTGGT 61.425 61.111 0.00 0.00 42.94 3.67
97 98 2.912025 GTGTGGTGCCCCAGTTGG 60.912 66.667 0.00 0.00 42.94 3.77
103 104 3.050339 CAACATGTGTGGTGCCCC 58.950 61.111 0.00 0.00 36.02 5.80
134 135 9.467796 AGGAAAAGAGAAGAAAGAAGAAAAAGA 57.532 29.630 0.00 0.00 0.00 2.52
451 516 4.082523 CGCACACCCCGATCAGGT 62.083 66.667 0.00 0.00 38.74 4.00
497 562 4.083324 ACAAATCAAGGCACATTACTCGTG 60.083 41.667 0.00 0.00 37.43 4.35
505 570 5.796424 AGAGAAAACAAATCAAGGCACAT 57.204 34.783 0.00 0.00 0.00 3.21
559 624 9.515020 GACTTCAGTCAACTCTAATATTCAGAG 57.485 37.037 15.00 15.00 44.18 3.35
594 659 9.073368 GTTTTCTCTAAACTTGGTCAAACTTTC 57.927 33.333 0.00 0.00 42.32 2.62
747 812 9.840427 TGTATTAGCTTTAATCAAAAGTCAAGC 57.160 29.630 0.00 0.00 45.46 4.01
757 822 8.481974 TTTAGCACGTGTATTAGCTTTAATCA 57.518 30.769 18.38 0.00 38.47 2.57
775 840 4.698780 ACTCCCTCCGTTTTTATTTAGCAC 59.301 41.667 0.00 0.00 0.00 4.40
776 841 4.913784 ACTCCCTCCGTTTTTATTTAGCA 58.086 39.130 0.00 0.00 0.00 3.49
777 842 5.876460 TGTACTCCCTCCGTTTTTATTTAGC 59.124 40.000 0.00 0.00 0.00 3.09
789 854 1.035932 ATGACCGTGTACTCCCTCCG 61.036 60.000 0.00 0.00 0.00 4.63
794 859 0.179108 GCCTGATGACCGTGTACTCC 60.179 60.000 0.00 0.00 0.00 3.85
802 867 0.811616 GCCTAGTTGCCTGATGACCG 60.812 60.000 0.00 0.00 0.00 4.79
803 868 0.253044 TGCCTAGTTGCCTGATGACC 59.747 55.000 0.00 0.00 0.00 4.02
804 869 1.373570 GTGCCTAGTTGCCTGATGAC 58.626 55.000 0.00 0.00 0.00 3.06
805 870 0.253044 GGTGCCTAGTTGCCTGATGA 59.747 55.000 0.00 0.00 0.00 2.92
806 871 0.035152 TGGTGCCTAGTTGCCTGATG 60.035 55.000 0.00 0.00 0.00 3.07
807 872 0.921896 ATGGTGCCTAGTTGCCTGAT 59.078 50.000 0.00 0.00 0.00 2.90
808 873 0.698238 AATGGTGCCTAGTTGCCTGA 59.302 50.000 0.00 0.00 0.00 3.86
809 874 1.098050 GAATGGTGCCTAGTTGCCTG 58.902 55.000 0.00 0.00 0.00 4.85
810 875 0.034089 GGAATGGTGCCTAGTTGCCT 60.034 55.000 0.00 0.00 0.00 4.75
811 876 1.037579 GGGAATGGTGCCTAGTTGCC 61.038 60.000 0.00 0.00 31.01 4.52
812 877 0.034089 AGGGAATGGTGCCTAGTTGC 60.034 55.000 0.00 0.00 45.36 4.17
854 921 2.298163 ACAAAAAGCTTGGCTCATCAGG 59.702 45.455 0.00 0.00 38.25 3.86
857 924 3.375782 ACACAAAAAGCTTGGCTCATC 57.624 42.857 0.00 0.00 38.25 2.92
866 933 5.296748 AGAAACACACAAACACAAAAAGCT 58.703 33.333 0.00 0.00 0.00 3.74
868 935 6.845280 CACAAGAAACACACAAACACAAAAAG 59.155 34.615 0.00 0.00 0.00 2.27
872 939 4.302455 CCACAAGAAACACACAAACACAA 58.698 39.130 0.00 0.00 0.00 3.33
879 946 2.088423 GTCACCCACAAGAAACACACA 58.912 47.619 0.00 0.00 0.00 3.72
903 970 1.673033 GCAACTCTACATGTGCTCCGT 60.673 52.381 9.11 0.00 0.00 4.69
904 971 1.002366 GCAACTCTACATGTGCTCCG 58.998 55.000 9.11 0.00 0.00 4.63
905 972 2.393271 AGCAACTCTACATGTGCTCC 57.607 50.000 9.11 0.00 0.00 4.70
906 973 2.417933 CCAAGCAACTCTACATGTGCTC 59.582 50.000 9.11 0.00 0.00 4.26
907 974 2.430465 CCAAGCAACTCTACATGTGCT 58.570 47.619 9.11 4.34 0.00 4.40
909 976 1.470098 GGCCAAGCAACTCTACATGTG 59.530 52.381 9.11 0.00 0.00 3.21
910 977 1.614317 GGGCCAAGCAACTCTACATGT 60.614 52.381 4.39 2.69 0.00 3.21
911 978 1.098050 GGGCCAAGCAACTCTACATG 58.902 55.000 4.39 0.00 0.00 3.21
912 979 0.392998 CGGGCCAAGCAACTCTACAT 60.393 55.000 4.39 0.00 0.00 2.29
913 980 1.003839 CGGGCCAAGCAACTCTACA 60.004 57.895 4.39 0.00 0.00 2.74
943 2378 6.103997 CGGTCTTTCCTATACAAGCTACAAA 58.896 40.000 0.00 0.00 0.00 2.83
967 2402 1.993369 GATTGGCTTGGCTACACGGC 61.993 60.000 0.00 0.00 41.10 5.68
1063 2498 2.551721 CCATGCAGTCCTCCACCATATC 60.552 54.545 0.00 0.00 0.00 1.63
1066 2504 1.611419 CCATGCAGTCCTCCACCAT 59.389 57.895 0.00 0.00 0.00 3.55
1728 3166 3.403038 CCACATCTGGTCGAAGTTCTTT 58.597 45.455 0.56 0.00 32.03 2.52
1856 3294 8.663305 ACCTAACATGGTTTACTCCAACATTGG 61.663 40.741 4.11 4.11 42.91 3.16
1857 3295 6.208599 ACCTAACATGGTTTACTCCAACATTG 59.791 38.462 0.00 0.00 41.09 2.82
1858 3296 6.208599 CACCTAACATGGTTTACTCCAACATT 59.791 38.462 0.00 0.00 41.09 2.71
1859 3297 5.710099 CACCTAACATGGTTTACTCCAACAT 59.290 40.000 0.00 0.00 41.09 2.71
4651 6452 1.002773 GTTTACATCCACACGGGTCCT 59.997 52.381 0.00 0.00 38.11 3.85
4656 6457 2.432444 ACATGGTTTACATCCACACGG 58.568 47.619 0.00 0.00 37.84 4.94


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

AutoCloner maintained by Alex Coulton.