Multiple sequence alignment - TraesCS6A01G248900

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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 TraesCS6A01G248900 chr6A 100.000 5074 0 0 1 5074 461835399 461840472 0.000000e+00 9371.0
1 TraesCS6A01G248900 chr6A 76.687 163 26 9 4917 5074 585361936 585361781 4.210000e-11 80.5
2 TraesCS6A01G248900 chr3A 99.181 3786 24 3 527 4310 108918382 108922162 0.000000e+00 6813.0
3 TraesCS6A01G248900 chr3A 92.371 603 40 5 872 1472 46616346 46615748 0.000000e+00 854.0
4 TraesCS6A01G248900 chr3A 83.750 880 96 18 3424 4275 271639715 271640575 0.000000e+00 789.0
5 TraesCS6A01G248900 chr3A 84.472 805 86 14 1551 2351 46615749 46614980 0.000000e+00 758.0
6 TraesCS6A01G248900 chr3A 89.078 412 31 5 3775 4178 209650947 209651352 2.730000e-137 499.0
7 TraesCS6A01G248900 chr3A 85.243 515 40 14 2345 2840 46614946 46614449 9.810000e-137 497.0
8 TraesCS6A01G248900 chr3A 86.667 450 39 11 2815 3245 46612013 46611566 3.550000e-131 479.0
9 TraesCS6A01G248900 chr3A 85.411 377 39 10 3405 3771 209642654 209643024 1.330000e-100 377.0
10 TraesCS6A01G248900 chr3A 96.465 198 7 0 4329 4526 108922147 108922344 1.360000e-85 327.0
11 TraesCS6A01G248900 chr3A 88.636 264 20 7 3405 3668 46611502 46611249 3.810000e-81 313.0
12 TraesCS6A01G248900 chr3A 85.572 201 18 7 3048 3242 209642392 209642587 3.100000e-47 200.0
13 TraesCS6A01G248900 chr3A 96.000 75 3 0 1470 1544 507291577 507291503 6.900000e-24 122.0
14 TraesCS6A01G248900 chr3A 98.039 51 1 0 4331 4381 108922358 108922408 7.000000e-14 89.8
15 TraesCS6A01G248900 chr6B 95.345 3802 120 25 527 4302 499018218 499014448 0.000000e+00 5987.0
16 TraesCS6A01G248900 chr6B 99.811 529 0 1 1 528 51213566 51213038 0.000000e+00 970.0
17 TraesCS6A01G248900 chr6B 83.918 883 91 23 3424 4275 605767146 605766284 0.000000e+00 797.0
18 TraesCS6A01G248900 chr6B 86.942 291 26 9 2721 3005 605767438 605767154 2.950000e-82 316.0
19 TraesCS6A01G248900 chr6D 90.968 919 58 11 3405 4306 324521803 324522713 0.000000e+00 1214.0
20 TraesCS6A01G248900 chr6D 89.901 911 55 9 590 1472 324519136 324520037 0.000000e+00 1138.0
21 TraesCS6A01G248900 chr6D 90.505 653 46 8 1551 2194 324520036 324520681 0.000000e+00 848.0
22 TraesCS6A01G248900 chr6D 88.367 447 19 14 2812 3242 324521311 324521740 1.630000e-139 507.0
23 TraesCS6A01G248900 chr6D 86.562 320 18 6 2441 2760 324521008 324521302 3.790000e-86 329.0
24 TraesCS6A01G248900 chr6D 94.203 138 7 1 3249 3385 124511793 124511930 5.150000e-50 209.0
25 TraesCS6A01G248900 chr3D 86.140 1075 91 29 2199 3245 35670489 35669445 0.000000e+00 1107.0
26 TraesCS6A01G248900 chr3D 86.739 739 75 18 1101 1830 35694926 35694202 0.000000e+00 800.0
27 TraesCS6A01G248900 chr3D 90.189 265 21 4 3405 3668 35669381 35669121 1.750000e-89 340.0
28 TraesCS6A01G248900 chr3D 85.057 348 36 12 1825 2166 35689494 35689157 1.750000e-89 340.0
29 TraesCS6A01G248900 chrUn 83.865 1097 108 44 2197 3242 39274640 39275718 0.000000e+00 981.0
30 TraesCS6A01G248900 chrUn 93.023 602 37 4 872 1472 39273139 39273736 0.000000e+00 874.0
31 TraesCS6A01G248900 chrUn 85.687 517 51 7 1551 2066 39273735 39274229 1.620000e-144 523.0
32 TraesCS6A01G248900 chrUn 91.698 265 13 7 3405 3662 39275785 39276047 4.830000e-95 359.0
33 TraesCS6A01G248900 chrUn 94.203 138 7 1 3249 3385 402628903 402628766 5.150000e-50 209.0
34 TraesCS6A01G248900 chrUn 88.889 81 9 0 2087 2167 39274556 39274636 3.230000e-17 100.0
35 TraesCS6A01G248900 chrUn 76.074 163 27 9 4917 5074 36540249 36540404 1.960000e-09 75.0
36 TraesCS6A01G248900 chr1A 99.810 527 1 0 1 527 96468769 96469295 0.000000e+00 968.0
37 TraesCS6A01G248900 chr1A 96.875 64 2 0 441 504 96468704 96468641 1.930000e-19 108.0
38 TraesCS6A01G248900 chr1A 87.879 66 7 1 1588 1652 68373695 68373760 5.450000e-10 76.8
39 TraesCS6A01G248900 chr7A 85.455 880 81 16 3424 4275 165528857 165529717 0.000000e+00 872.0
40 TraesCS6A01G248900 chr7A 88.802 384 28 11 2637 3009 165528474 165528853 1.670000e-124 457.0
41 TraesCS6A01G248900 chr1D 84.960 871 101 16 3424 4275 28959755 28958896 0.000000e+00 856.0
42 TraesCS6A01G248900 chr1D 84.777 381 27 8 2637 3009 28960116 28959759 2.250000e-93 353.0
43 TraesCS6A01G248900 chr1D 94.203 138 7 1 3249 3385 12982860 12982997 5.150000e-50 209.0
44 TraesCS6A01G248900 chr5A 84.205 880 92 20 3424 4275 237942087 237941227 0.000000e+00 811.0
45 TraesCS6A01G248900 chr5A 89.556 383 29 8 2637 3009 237942472 237942091 4.600000e-130 475.0
46 TraesCS6A01G248900 chr5A 87.037 108 13 1 246 353 9511584 9511478 2.480000e-23 121.0
47 TraesCS6A01G248900 chr7D 87.349 664 56 11 804 1466 72448015 72447379 0.000000e+00 736.0
48 TraesCS6A01G248900 chr7D 80.531 339 27 13 1551 1854 72447376 72447042 1.840000e-54 224.0
49 TraesCS6A01G248900 chr7D 94.203 138 7 1 3249 3385 203494267 203494404 5.150000e-50 209.0
50 TraesCS6A01G248900 chr7D 94.203 138 7 1 3249 3385 381914245 381914382 5.150000e-50 209.0
51 TraesCS6A01G248900 chr7D 94.203 138 7 1 3249 3385 381979494 381979357 5.150000e-50 209.0
52 TraesCS6A01G248900 chr2B 82.887 859 90 34 3410 4225 62995174 62994330 0.000000e+00 719.0
53 TraesCS6A01G248900 chr2B 86.964 583 61 6 877 1453 62996415 62995842 4.280000e-180 641.0
54 TraesCS6A01G248900 chr2B 83.916 429 44 14 2841 3245 62995670 62995243 2.220000e-103 387.0
55 TraesCS6A01G248900 chr2B 80.889 225 34 9 4853 5074 38650552 38650770 8.740000e-38 169.0
56 TraesCS6A01G248900 chr2B 92.500 80 3 2 1470 1548 394910784 394910861 1.490000e-20 111.0
57 TraesCS6A01G248900 chr2B 77.301 163 25 9 4917 5074 359879314 359879159 9.050000e-13 86.1
58 TraesCS6A01G248900 chr2D 91.288 528 26 12 1 528 63023823 63023316 0.000000e+00 702.0
59 TraesCS6A01G248900 chr2D 86.801 447 47 6 1001 1445 36584578 36584142 5.900000e-134 488.0
60 TraesCS6A01G248900 chr2D 82.234 394 46 14 1543 1925 36584006 36583626 8.200000e-83 318.0
61 TraesCS6A01G248900 chr2D 94.203 138 6 2 3249 3385 39525326 39525462 5.150000e-50 209.0
62 TraesCS6A01G248900 chr2D 93.902 82 3 2 1471 1550 512165838 512165919 6.900000e-24 122.0
63 TraesCS6A01G248900 chr2D 89.583 96 7 3 416 509 63023858 63023952 8.920000e-23 119.0
64 TraesCS6A01G248900 chr2D 91.667 84 6 1 1468 1550 564093468 564093385 1.150000e-21 115.0
65 TraesCS6A01G248900 chr2A 82.479 702 81 19 760 1453 40561175 40560508 1.220000e-160 577.0
66 TraesCS6A01G248900 chr2A 81.867 557 46 22 3408 3930 40559562 40559027 7.860000e-113 418.0
67 TraesCS6A01G248900 chr2A 77.997 709 112 32 4375 5072 427300704 427300029 6.120000e-109 405.0
68 TraesCS6A01G248900 chr2A 85.075 402 38 9 2822 3205 40560072 40559675 1.710000e-104 390.0
69 TraesCS6A01G248900 chr2A 80.711 394 49 14 1551 1925 40560499 40560114 1.080000e-71 281.0
70 TraesCS6A01G248900 chr2A 76.687 163 26 9 4917 5074 453520456 453520611 4.210000e-11 80.5
71 TraesCS6A01G248900 chr3B 77.388 712 96 43 4381 5074 775636302 775635638 3.730000e-96 363.0
72 TraesCS6A01G248900 chr3B 93.590 78 3 2 1473 1548 474402086 474402009 1.150000e-21 115.0
73 TraesCS6A01G248900 chr5D 84.028 144 15 3 217 353 12169543 12169401 1.150000e-26 132.0
74 TraesCS6A01G248900 chr5D 93.671 79 4 1 1466 1544 188826529 188826606 3.210000e-22 117.0
75 TraesCS6A01G248900 chr5D 86.111 108 14 1 246 353 12169054 12168948 1.150000e-21 115.0
76 TraesCS6A01G248900 chr5D 87.500 96 8 4 246 340 12168594 12168502 1.930000e-19 108.0
77 TraesCS6A01G248900 chr7B 81.646 158 22 6 4820 4975 161232061 161232213 1.920000e-24 124.0
78 TraesCS6A01G248900 chr7B 76.687 163 26 9 4917 5074 624723830 624723675 4.210000e-11 80.5
79 TraesCS6A01G248900 chr5B 92.405 79 5 1 1466 1544 217907677 217907754 1.490000e-20 111.0


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 TraesCS6A01G248900 chr6A 461835399 461840472 5073 False 9371.000000 9371 100.0000 1 5074 1 chr6A.!!$F1 5073
1 TraesCS6A01G248900 chr3A 108918382 108922408 4026 False 2409.933333 6813 97.8950 527 4526 3 chr3A.!!$F3 3999
2 TraesCS6A01G248900 chr3A 271639715 271640575 860 False 789.000000 789 83.7500 3424 4275 1 chr3A.!!$F2 851
3 TraesCS6A01G248900 chr3A 46611249 46616346 5097 True 580.200000 854 87.4778 872 3668 5 chr3A.!!$R2 2796
4 TraesCS6A01G248900 chr3A 209642392 209643024 632 False 288.500000 377 85.4915 3048 3771 2 chr3A.!!$F4 723
5 TraesCS6A01G248900 chr6B 499014448 499018218 3770 True 5987.000000 5987 95.3450 527 4302 1 chr6B.!!$R2 3775
6 TraesCS6A01G248900 chr6B 51213038 51213566 528 True 970.000000 970 99.8110 1 528 1 chr6B.!!$R1 527
7 TraesCS6A01G248900 chr6B 605766284 605767438 1154 True 556.500000 797 85.4300 2721 4275 2 chr6B.!!$R3 1554
8 TraesCS6A01G248900 chr6D 324519136 324522713 3577 False 807.200000 1214 89.2606 590 4306 5 chr6D.!!$F2 3716
9 TraesCS6A01G248900 chr3D 35694202 35694926 724 True 800.000000 800 86.7390 1101 1830 1 chr3D.!!$R2 729
10 TraesCS6A01G248900 chr3D 35669121 35670489 1368 True 723.500000 1107 88.1645 2199 3668 2 chr3D.!!$R3 1469
11 TraesCS6A01G248900 chrUn 39273139 39276047 2908 False 567.400000 981 88.6324 872 3662 5 chrUn.!!$F2 2790
12 TraesCS6A01G248900 chr1A 96468769 96469295 526 False 968.000000 968 99.8100 1 527 1 chr1A.!!$F2 526
13 TraesCS6A01G248900 chr7A 165528474 165529717 1243 False 664.500000 872 87.1285 2637 4275 2 chr7A.!!$F1 1638
14 TraesCS6A01G248900 chr1D 28958896 28960116 1220 True 604.500000 856 84.8685 2637 4275 2 chr1D.!!$R1 1638
15 TraesCS6A01G248900 chr5A 237941227 237942472 1245 True 643.000000 811 86.8805 2637 4275 2 chr5A.!!$R2 1638
16 TraesCS6A01G248900 chr7D 72447042 72448015 973 True 480.000000 736 83.9400 804 1854 2 chr7D.!!$R2 1050
17 TraesCS6A01G248900 chr2B 62994330 62996415 2085 True 582.333333 719 84.5890 877 4225 3 chr2B.!!$R2 3348
18 TraesCS6A01G248900 chr2D 63023316 63023823 507 True 702.000000 702 91.2880 1 528 1 chr2D.!!$R1 527
19 TraesCS6A01G248900 chr2D 36583626 36584578 952 True 403.000000 488 84.5175 1001 1925 2 chr2D.!!$R3 924
20 TraesCS6A01G248900 chr2A 40559027 40561175 2148 True 416.500000 577 82.5330 760 3930 4 chr2A.!!$R2 3170
21 TraesCS6A01G248900 chr2A 427300029 427300704 675 True 405.000000 405 77.9970 4375 5072 1 chr2A.!!$R1 697
22 TraesCS6A01G248900 chr3B 775635638 775636302 664 True 363.000000 363 77.3880 4381 5074 1 chr3B.!!$R2 693

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
707 713 0.250513 GCCACTAGGTACTGCAGCTT 59.749 55.000 15.27 0.00 41.52 3.74 F
3032 6186 4.988029 AGTATTACTGAGAGCCTCCGTAT 58.012 43.478 0.00 2.92 32.11 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3032 6186 0.396435 AACCATCAACTGCCGAGACA 59.604 50.0 0.00 0.0 0.0 3.41 R
4795 8075 0.033781 TGCAGCAAAAAGGCCACATC 59.966 50.0 5.01 0.0 0.0 3.06 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
542 544 0.446222 CCCGTTAGATGCGTGTTTGG 59.554 55.000 0.00 0.00 0.00 3.28
707 713 0.250513 GCCACTAGGTACTGCAGCTT 59.749 55.000 15.27 0.00 41.52 3.74
3032 6186 4.988029 AGTATTACTGAGAGCCTCCGTAT 58.012 43.478 0.00 2.92 32.11 3.06
4302 7570 8.796475 AGTTATAATGCATTCTCTCTCTCTCTC 58.204 37.037 16.86 0.00 0.00 3.20
4303 7571 8.796475 GTTATAATGCATTCTCTCTCTCTCTCT 58.204 37.037 16.86 0.00 0.00 3.10
4304 7572 5.779529 AATGCATTCTCTCTCTCTCTCTC 57.220 43.478 5.99 0.00 0.00 3.20
4305 7573 4.508551 TGCATTCTCTCTCTCTCTCTCT 57.491 45.455 0.00 0.00 0.00 3.10
4306 7574 4.454678 TGCATTCTCTCTCTCTCTCTCTC 58.545 47.826 0.00 0.00 0.00 3.20
4307 7575 4.164796 TGCATTCTCTCTCTCTCTCTCTCT 59.835 45.833 0.00 0.00 0.00 3.10
4308 7576 4.754114 GCATTCTCTCTCTCTCTCTCTCTC 59.246 50.000 0.00 0.00 0.00 3.20
4309 7577 5.454471 GCATTCTCTCTCTCTCTCTCTCTCT 60.454 48.000 0.00 0.00 0.00 3.10
4310 7578 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
4311 7579 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
4312 7580 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4313 7581 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4314 7582 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4315 7583 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4316 7584 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
4317 7585 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
4318 7586 6.101881 TCTCTCTCTCTCTCTCTCTCTCTCTA 59.898 46.154 0.00 0.00 0.00 2.43
4319 7587 6.673583 TCTCTCTCTCTCTCTCTCTCTCTAA 58.326 44.000 0.00 0.00 0.00 2.10
4320 7588 6.547880 TCTCTCTCTCTCTCTCTCTCTCTAAC 59.452 46.154 0.00 0.00 0.00 2.34
4321 7589 5.598830 TCTCTCTCTCTCTCTCTCTCTAACC 59.401 48.000 0.00 0.00 0.00 2.85
4322 7590 4.654262 TCTCTCTCTCTCTCTCTCTAACCC 59.346 50.000 0.00 0.00 0.00 4.11
4323 7591 4.631234 TCTCTCTCTCTCTCTCTAACCCT 58.369 47.826 0.00 0.00 0.00 4.34
4324 7592 5.784023 TCTCTCTCTCTCTCTCTAACCCTA 58.216 45.833 0.00 0.00 0.00 3.53
4325 7593 6.206787 TCTCTCTCTCTCTCTCTAACCCTAA 58.793 44.000 0.00 0.00 0.00 2.69
4326 7594 6.674861 TCTCTCTCTCTCTCTCTAACCCTAAA 59.325 42.308 0.00 0.00 0.00 1.85
4327 7595 6.655930 TCTCTCTCTCTCTCTAACCCTAAAC 58.344 44.000 0.00 0.00 0.00 2.01
4328 7596 5.757988 TCTCTCTCTCTCTAACCCTAAACC 58.242 45.833 0.00 0.00 0.00 3.27
4329 7597 5.493250 TCTCTCTCTCTCTAACCCTAAACCT 59.507 44.000 0.00 0.00 0.00 3.50
4336 7604 5.757988 TCTCTAACCCTAAACCTCTCTCTC 58.242 45.833 0.00 0.00 0.00 3.20
4340 7608 4.245251 ACCCTAAACCTCTCTCTCTCTC 57.755 50.000 0.00 0.00 0.00 3.20
4537 7805 2.644299 TCCTCACCACACATTCCATCTT 59.356 45.455 0.00 0.00 0.00 2.40
4538 7806 3.074390 TCCTCACCACACATTCCATCTTT 59.926 43.478 0.00 0.00 0.00 2.52
4543 7811 2.096496 CCACACATTCCATCTTTCTCGC 59.904 50.000 0.00 0.00 0.00 5.03
4615 7892 1.620819 TCTCTGCTTCTTCCTCCACAC 59.379 52.381 0.00 0.00 0.00 3.82
4620 7897 2.154798 CTTCTTCCTCCACACGGCGA 62.155 60.000 16.62 0.00 0.00 5.54
4635 7912 2.434884 CGAGGCAGCGGTTGACAT 60.435 61.111 0.00 0.00 37.23 3.06
4647 7924 1.406887 GGTTGACATATGGTCCTGCGT 60.407 52.381 7.80 0.00 46.38 5.24
4696 7973 1.562672 GGGAGCACCACCATACACCT 61.563 60.000 1.58 0.00 39.85 4.00
4698 7975 1.271926 GGAGCACCACCATACACCTTT 60.272 52.381 0.00 0.00 35.97 3.11
4699 7976 1.812571 GAGCACCACCATACACCTTTG 59.187 52.381 0.00 0.00 0.00 2.77
4701 7978 1.614996 CACCACCATACACCTTTGCA 58.385 50.000 0.00 0.00 0.00 4.08
4702 7979 1.269448 CACCACCATACACCTTTGCAC 59.731 52.381 0.00 0.00 0.00 4.57
4703 7980 1.133637 ACCACCATACACCTTTGCACA 60.134 47.619 0.00 0.00 0.00 4.57
4706 7986 1.133637 ACCATACACCTTTGCACACCA 60.134 47.619 0.00 0.00 0.00 4.17
4730 8010 1.299926 GTCGACGGTGACAAGTGCT 60.300 57.895 0.00 0.00 38.75 4.40
4736 8016 2.143122 ACGGTGACAAGTGCTACAATG 58.857 47.619 0.00 0.00 0.00 2.82
4739 8019 2.160417 GGTGACAAGTGCTACAATGAGC 59.840 50.000 0.00 0.00 43.16 4.26
4782 8062 0.674895 GCGACAATTGCTGGAGACCT 60.675 55.000 5.05 0.00 0.00 3.85
4784 8064 0.807496 GACAATTGCTGGAGACCTGC 59.193 55.000 5.05 11.66 46.46 4.85
4789 8069 2.343758 GCTGGAGACCTGCGACAA 59.656 61.111 4.13 0.00 38.59 3.18
4795 8075 1.891060 GAGACCTGCGACAACAAGCG 61.891 60.000 0.00 0.00 35.87 4.68
4796 8076 1.954146 GACCTGCGACAACAAGCGA 60.954 57.895 0.00 0.00 35.87 4.93
4797 8077 1.291877 GACCTGCGACAACAAGCGAT 61.292 55.000 0.00 0.00 35.87 4.58
4819 8099 1.227234 GCCTTTTTGCTGCAACCGT 60.227 52.632 15.72 0.00 0.00 4.83
4831 8111 1.296392 CAACCGTGCATCCCAGAGA 59.704 57.895 0.00 0.00 0.00 3.10
4859 8140 1.980232 TGCCCCTGCTGCTTCAATG 60.980 57.895 0.00 0.00 38.71 2.82
4863 8144 1.318158 CCCTGCTGCTTCAATGGACC 61.318 60.000 0.00 0.00 0.00 4.46
4882 8163 0.878523 CAAAGGTCTTCACGCCGTGA 60.879 55.000 17.22 17.22 41.09 4.35
4955 8236 3.512516 GCTGGAACCGGCATGAGC 61.513 66.667 18.38 0.00 46.81 4.26
4972 8253 1.290009 GCTTTTGCTGCCATTCGGT 59.710 52.632 0.00 0.00 43.35 4.69
4978 8259 2.409055 GCTGCCATTCGGTCATGCA 61.409 57.895 0.00 0.00 33.28 3.96
4994 8275 1.179152 TGCAATGTGCTGGAATCAGG 58.821 50.000 1.43 0.00 45.31 3.86
4996 8277 0.458669 CAATGTGCTGGAATCAGGCC 59.541 55.000 0.00 0.00 41.19 5.19
4998 8279 2.440980 GTGCTGGAATCAGGCCCC 60.441 66.667 0.00 0.00 41.19 5.80
4999 8280 2.614969 TGCTGGAATCAGGCCCCT 60.615 61.111 0.00 0.00 41.19 4.79
5001 8282 2.683465 GCTGGAATCAGGCCCCTCA 61.683 63.158 0.00 0.00 41.19 3.86
5002 8283 1.225704 CTGGAATCAGGCCCCTCAC 59.774 63.158 0.00 0.00 37.36 3.51
5005 8286 3.406595 GAATCAGGCCCCTCACCGG 62.407 68.421 0.00 0.00 0.00 5.28
5014 8295 4.003788 CCTCACCGGCTTCCACGT 62.004 66.667 0.00 0.00 0.00 4.49
5017 8298 2.590575 CACCGGCTTCCACGTGTT 60.591 61.111 15.65 0.00 0.00 3.32
5051 8351 8.190784 GCTGAAACCACTGTATATTTTTGCTAT 58.809 33.333 0.00 0.00 0.00 2.97
5069 8369 7.559590 TTGCTATAATCCTTCTTCTCTTTGC 57.440 36.000 0.00 0.00 0.00 3.68
5070 8370 6.893583 TGCTATAATCCTTCTTCTCTTTGCT 58.106 36.000 0.00 0.00 0.00 3.91
5071 8371 8.023021 TGCTATAATCCTTCTTCTCTTTGCTA 57.977 34.615 0.00 0.00 0.00 3.49
5072 8372 7.928706 TGCTATAATCCTTCTTCTCTTTGCTAC 59.071 37.037 0.00 0.00 0.00 3.58
5073 8373 7.928706 GCTATAATCCTTCTTCTCTTTGCTACA 59.071 37.037 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
542 544 2.529744 AAGGTGGTGGGGTGAGAGC 61.530 63.158 0.00 0.00 0.00 4.09
624 626 1.213296 AGGTGGTCCAACTCAACAGT 58.787 50.000 2.59 0.00 35.89 3.55
1445 1483 8.985315 ATCAAATTAATGGAGCATACTCTGAA 57.015 30.769 0.00 0.00 42.98 3.02
3032 6186 0.396435 AACCATCAACTGCCGAGACA 59.604 50.000 0.00 0.00 0.00 3.41
4302 7570 6.494666 TTAGGGTTAGAGAGAGAGAGAGAG 57.505 45.833 0.00 0.00 0.00 3.20
4303 7571 6.353255 GGTTTAGGGTTAGAGAGAGAGAGAGA 60.353 46.154 0.00 0.00 0.00 3.10
4304 7572 5.826208 GGTTTAGGGTTAGAGAGAGAGAGAG 59.174 48.000 0.00 0.00 0.00 3.20
4305 7573 5.493250 AGGTTTAGGGTTAGAGAGAGAGAGA 59.507 44.000 0.00 0.00 0.00 3.10
4306 7574 5.762279 AGGTTTAGGGTTAGAGAGAGAGAG 58.238 45.833 0.00 0.00 0.00 3.20
4307 7575 5.493250 AGAGGTTTAGGGTTAGAGAGAGAGA 59.507 44.000 0.00 0.00 0.00 3.10
4308 7576 5.762279 AGAGGTTTAGGGTTAGAGAGAGAG 58.238 45.833 0.00 0.00 0.00 3.20
4309 7577 5.493250 AGAGAGGTTTAGGGTTAGAGAGAGA 59.507 44.000 0.00 0.00 0.00 3.10
4310 7578 5.762279 AGAGAGGTTTAGGGTTAGAGAGAG 58.238 45.833 0.00 0.00 0.00 3.20
4311 7579 5.493250 AGAGAGAGGTTTAGGGTTAGAGAGA 59.507 44.000 0.00 0.00 0.00 3.10
4312 7580 5.762279 AGAGAGAGGTTTAGGGTTAGAGAG 58.238 45.833 0.00 0.00 0.00 3.20
4313 7581 5.493250 AGAGAGAGAGGTTTAGGGTTAGAGA 59.507 44.000 0.00 0.00 0.00 3.10
4314 7582 5.762279 AGAGAGAGAGGTTTAGGGTTAGAG 58.238 45.833 0.00 0.00 0.00 2.43
4315 7583 5.493250 AGAGAGAGAGAGGTTTAGGGTTAGA 59.507 44.000 0.00 0.00 0.00 2.10
4316 7584 5.762279 AGAGAGAGAGAGGTTTAGGGTTAG 58.238 45.833 0.00 0.00 0.00 2.34
4317 7585 5.493250 AGAGAGAGAGAGAGGTTTAGGGTTA 59.507 44.000 0.00 0.00 0.00 2.85
4318 7586 4.293901 AGAGAGAGAGAGAGGTTTAGGGTT 59.706 45.833 0.00 0.00 0.00 4.11
4319 7587 3.856206 AGAGAGAGAGAGAGGTTTAGGGT 59.144 47.826 0.00 0.00 0.00 4.34
4320 7588 4.166144 AGAGAGAGAGAGAGAGGTTTAGGG 59.834 50.000 0.00 0.00 0.00 3.53
4321 7589 5.373812 AGAGAGAGAGAGAGAGGTTTAGG 57.626 47.826 0.00 0.00 0.00 2.69
4322 7590 6.884832 TGTAGAGAGAGAGAGAGAGGTTTAG 58.115 44.000 0.00 0.00 0.00 1.85
4323 7591 6.877668 TGTAGAGAGAGAGAGAGAGGTTTA 57.122 41.667 0.00 0.00 0.00 2.01
4324 7592 5.772393 TGTAGAGAGAGAGAGAGAGGTTT 57.228 43.478 0.00 0.00 0.00 3.27
4325 7593 5.975988 ATGTAGAGAGAGAGAGAGAGGTT 57.024 43.478 0.00 0.00 0.00 3.50
4326 7594 5.975988 AATGTAGAGAGAGAGAGAGAGGT 57.024 43.478 0.00 0.00 0.00 3.85
4327 7595 6.043243 AGGTAATGTAGAGAGAGAGAGAGAGG 59.957 46.154 0.00 0.00 0.00 3.69
4328 7596 7.067496 AGGTAATGTAGAGAGAGAGAGAGAG 57.933 44.000 0.00 0.00 0.00 3.20
4329 7597 7.279615 CAAGGTAATGTAGAGAGAGAGAGAGA 58.720 42.308 0.00 0.00 0.00 3.10
4336 7604 5.205056 ACTCCCAAGGTAATGTAGAGAGAG 58.795 45.833 0.00 0.00 0.00 3.20
4340 7608 8.480133 ACTAATACTCCCAAGGTAATGTAGAG 57.520 38.462 0.00 0.00 0.00 2.43
4459 7727 1.669760 GGTGAAACGGTGCATCGGA 60.670 57.895 25.34 1.02 38.12 4.55
4537 7805 2.452064 GGGATGGATGGGGCGAGAA 61.452 63.158 0.00 0.00 0.00 2.87
4538 7806 2.849162 GGGATGGATGGGGCGAGA 60.849 66.667 0.00 0.00 0.00 4.04
4543 7811 1.076095 AGGATTGGGGATGGATGGGG 61.076 60.000 0.00 0.00 0.00 4.96
4585 7861 1.350706 GAAGCAGAGACGAGCACAGC 61.351 60.000 0.00 0.00 0.00 4.40
4588 7864 1.345410 GAAGAAGCAGAGACGAGCAC 58.655 55.000 0.00 0.00 0.00 4.40
4620 7897 0.464373 CCATATGTCAACCGCTGCCT 60.464 55.000 1.24 0.00 0.00 4.75
4626 7903 1.299541 GCAGGACCATATGTCAACCG 58.700 55.000 1.24 0.00 46.38 4.44
4630 7907 0.177836 CCACGCAGGACCATATGTCA 59.822 55.000 1.24 0.00 46.38 3.58
4683 7960 1.133637 TGTGCAAAGGTGTATGGTGGT 60.134 47.619 0.00 0.00 0.00 4.16
4691 7968 2.101249 CAGAAATGGTGTGCAAAGGTGT 59.899 45.455 0.00 0.00 0.00 4.16
4696 7973 2.032799 GTCGACAGAAATGGTGTGCAAA 59.967 45.455 11.55 0.00 0.00 3.68
4698 7975 1.225855 GTCGACAGAAATGGTGTGCA 58.774 50.000 11.55 0.00 0.00 4.57
4699 7976 0.163788 CGTCGACAGAAATGGTGTGC 59.836 55.000 17.16 0.00 0.00 4.57
4701 7978 0.391597 ACCGTCGACAGAAATGGTGT 59.608 50.000 17.16 0.00 30.48 4.16
4702 7979 0.790207 CACCGTCGACAGAAATGGTG 59.210 55.000 19.20 19.20 38.88 4.17
4703 7980 0.677288 TCACCGTCGACAGAAATGGT 59.323 50.000 17.16 10.51 0.00 3.55
4706 7986 2.223971 ACTTGTCACCGTCGACAGAAAT 60.224 45.455 17.16 0.00 46.14 2.17
4730 8010 1.739929 CCGGCGTGTGCTCATTGTA 60.740 57.895 6.01 0.00 42.25 2.41
4754 8034 3.118454 AATTGTCGCCGCCGTCTG 61.118 61.111 0.00 0.00 35.54 3.51
4770 8050 2.038814 TTGTCGCAGGTCTCCAGCAA 62.039 55.000 4.27 0.00 35.71 3.91
4782 8062 1.569003 CACATCGCTTGTTGTCGCA 59.431 52.632 0.00 0.00 36.00 5.10
4784 8064 1.154413 GCCACATCGCTTGTTGTCG 60.154 57.895 0.00 0.00 36.00 4.35
4789 8069 1.039856 AAAAAGGCCACATCGCTTGT 58.960 45.000 5.01 0.00 39.91 3.16
4795 8075 0.033781 TGCAGCAAAAAGGCCACATC 59.966 50.000 5.01 0.00 0.00 3.06
4796 8076 0.469070 TTGCAGCAAAAAGGCCACAT 59.531 45.000 4.99 0.00 0.00 3.21
4797 8077 0.461693 GTTGCAGCAAAAAGGCCACA 60.462 50.000 10.11 0.00 0.00 4.17
4863 8144 0.878523 TCACGGCGTGAAGACCTTTG 60.879 55.000 37.53 10.38 39.78 2.77
4952 8233 0.457337 CCGAATGGCAGCAAAAGCTC 60.457 55.000 0.00 0.00 0.00 4.09
4955 8236 0.597568 TGACCGAATGGCAGCAAAAG 59.402 50.000 0.00 0.00 39.70 2.27
4978 8259 0.685458 GGGCCTGATTCCAGCACATT 60.685 55.000 0.84 0.00 39.07 2.71
4981 8262 2.440980 GGGGCCTGATTCCAGCAC 60.441 66.667 0.84 0.00 39.07 4.40
4996 8277 4.760047 CGTGGAAGCCGGTGAGGG 62.760 72.222 1.90 0.00 41.48 4.30
4998 8279 2.738521 CACGTGGAAGCCGGTGAG 60.739 66.667 7.95 0.00 34.08 3.51
4999 8280 2.596553 AAACACGTGGAAGCCGGTGA 62.597 55.000 21.57 0.00 35.23 4.02
5001 8282 1.033202 AAAAACACGTGGAAGCCGGT 61.033 50.000 21.57 0.00 0.00 5.28
5002 8283 1.731093 AAAAACACGTGGAAGCCGG 59.269 52.632 21.57 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.