Multiple sequence alignment - TraesCS4A01G478900

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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 TraesCS4A01G478900 chr4A 100.000 5912 0 0 1 5912 735775411 735781322 0.000000e+00 10918.0
1 TraesCS4A01G478900 chr4A 90.016 4427 386 33 575 4993 735368349 735363971 0.000000e+00 5675.0
2 TraesCS4A01G478900 chr4A 91.369 3337 221 27 502 3805 734996228 734999530 0.000000e+00 4505.0
3 TraesCS4A01G478900 chr4A 82.479 4840 705 78 380 5162 734384550 734389303 0.000000e+00 4108.0
4 TraesCS4A01G478900 chr4A 82.997 4064 618 43 959 5009 736413338 736409335 0.000000e+00 3609.0
5 TraesCS4A01G478900 chr4A 83.940 2447 358 26 2557 4993 735317843 735320264 0.000000e+00 2309.0
6 TraesCS4A01G478900 chr4A 81.919 2804 436 52 2550 5327 736469166 736466408 0.000000e+00 2303.0
7 TraesCS4A01G478900 chr4A 83.641 2439 370 23 2563 4995 735561158 735558743 0.000000e+00 2266.0
8 TraesCS4A01G478900 chr4A 82.495 2445 391 23 2560 4991 735748665 735751085 0.000000e+00 2109.0
9 TraesCS4A01G478900 chr4A 83.078 2287 345 26 2550 4819 736898286 736900547 0.000000e+00 2041.0
10 TraesCS4A01G478900 chr4A 84.895 2006 272 20 526 2507 735315828 735317826 0.000000e+00 1997.0
11 TraesCS4A01G478900 chr4A 86.832 1534 196 5 978 2507 735487968 735486437 0.000000e+00 1709.0
12 TraesCS4A01G478900 chr4A 86.654 1536 195 6 978 2507 735003408 735004939 0.000000e+00 1692.0
13 TraesCS4A01G478900 chr4A 82.743 1750 281 15 3250 4993 734482988 734484722 0.000000e+00 1539.0
14 TraesCS4A01G478900 chr4A 90.812 751 51 4 378 1111 736471524 736470775 0.000000e+00 989.0
15 TraesCS4A01G478900 chr4A 89.043 721 47 14 4992 5681 735000842 735001561 0.000000e+00 865.0
16 TraesCS4A01G478900 chr4A 96.047 506 14 3 1 502 735368893 735368390 0.000000e+00 819.0
17 TraesCS4A01G478900 chr4A 87.801 705 73 11 2553 3257 734481674 734482365 0.000000e+00 813.0
18 TraesCS4A01G478900 chr4A 90.414 459 19 2 378 822 736895696 736896143 1.100000e-161 580.0
19 TraesCS4A01G478900 chr4A 92.580 283 20 1 98 380 736895360 736895641 7.130000e-109 405.0
20 TraesCS4A01G478900 chr4A 79.714 419 51 14 379 768 734478713 734479126 7.550000e-69 272.0
21 TraesCS4A01G478900 chr4A 89.764 127 12 1 252 377 734384356 734384482 1.710000e-35 161.0
22 TraesCS4A01G478900 chr4A 91.919 99 5 1 1 96 734995861 734995959 1.030000e-27 135.0
23 TraesCS4A01G478900 chr4A 94.595 74 3 1 304 377 734996079 734996151 4.840000e-21 113.0
24 TraesCS4A01G478900 chr4A 93.651 63 4 0 315 377 736471654 736471592 1.750000e-15 95.3
25 TraesCS4A01G478900 chr4A 77.444 133 21 6 5549 5678 736003578 736003452 2.960000e-08 71.3
26 TraesCS4A01G478900 chr4A 90.909 44 4 0 5635 5678 735482251 735482208 6.400000e-05 60.2
27 TraesCS4A01G478900 chr7D 90.360 5498 428 52 430 5888 5638669 5633235 0.000000e+00 7123.0
28 TraesCS4A01G478900 chr7D 88.382 2169 206 19 378 2507 5449755 5447594 0.000000e+00 2567.0
29 TraesCS4A01G478900 chr7D 82.536 2468 373 43 2550 4996 5447586 5445156 0.000000e+00 2117.0
30 TraesCS4A01G478900 chr7D 86.662 1537 197 5 978 2507 5649401 5647866 0.000000e+00 1696.0
31 TraesCS4A01G478900 chr7D 86.275 102 11 3 379 479 5639433 5639334 2.250000e-19 108.0
32 TraesCS4A01G478900 chr7D 96.774 62 2 0 5620 5681 5804926 5804865 2.910000e-18 104.0
33 TraesCS4A01G478900 chr7D 93.651 63 4 0 315 377 5449885 5449823 1.750000e-15 95.3
34 TraesCS4A01G478900 chr7D 90.141 71 4 2 5711 5781 5804796 5804729 8.160000e-14 89.8
35 TraesCS4A01G478900 chr7A 87.679 2167 218 20 379 2507 6929287 6927132 0.000000e+00 2477.0
36 TraesCS4A01G478900 chr7A 82.834 2802 413 50 2550 5327 6927124 6924367 0.000000e+00 2447.0
37 TraesCS4A01G478900 chr7A 89.286 308 32 1 5582 5888 6968529 6968222 9.290000e-103 385.0
38 TraesCS4A01G478900 chr7A 90.000 220 20 1 98 317 6929588 6929371 3.490000e-72 283.0
39 TraesCS4A01G478900 chr7A 96.396 111 4 0 5329 5439 6968720 6968610 3.640000e-42 183.0
40 TraesCS4A01G478900 chr7A 87.500 80 7 2 5602 5680 6923795 6923718 8.160000e-14 89.8
41 TraesCS4A01G478900 chr7A 100.000 42 0 0 339 380 6929374 6929333 1.770000e-10 78.7


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 TraesCS4A01G478900 chr4A 735775411 735781322 5911 False 10918.000000 10918 100.000000 1 5912 1 chr4A.!!$F2 5911
1 TraesCS4A01G478900 chr4A 736409335 736413338 4003 True 3609.000000 3609 82.997000 959 5009 1 chr4A.!!$R5 4050
2 TraesCS4A01G478900 chr4A 735363971 735368893 4922 True 3247.000000 5675 93.031500 1 4993 2 chr4A.!!$R6 4992
3 TraesCS4A01G478900 chr4A 735558743 735561158 2415 True 2266.000000 2266 83.641000 2563 4995 1 chr4A.!!$R3 2432
4 TraesCS4A01G478900 chr4A 735315828 735320264 4436 False 2153.000000 2309 84.417500 526 4993 2 chr4A.!!$F6 4467
5 TraesCS4A01G478900 chr4A 734384356 734389303 4947 False 2134.500000 4108 86.121500 252 5162 2 chr4A.!!$F3 4910
6 TraesCS4A01G478900 chr4A 735748665 735751085 2420 False 2109.000000 2109 82.495000 2560 4991 1 chr4A.!!$F1 2431
7 TraesCS4A01G478900 chr4A 735486437 735487968 1531 True 1709.000000 1709 86.832000 978 2507 1 chr4A.!!$R2 1529
8 TraesCS4A01G478900 chr4A 734995861 735004939 9078 False 1462.000000 4505 90.716000 1 5681 5 chr4A.!!$F5 5680
9 TraesCS4A01G478900 chr4A 736466408 736471654 5246 True 1129.100000 2303 88.794000 315 5327 3 chr4A.!!$R7 5012
10 TraesCS4A01G478900 chr4A 736895360 736900547 5187 False 1008.666667 2041 88.690667 98 4819 3 chr4A.!!$F7 4721
11 TraesCS4A01G478900 chr4A 734478713 734484722 6009 False 874.666667 1539 83.419333 379 4993 3 chr4A.!!$F4 4614
12 TraesCS4A01G478900 chr7D 5633235 5639433 6198 True 3615.500000 7123 88.317500 379 5888 2 chr7D.!!$R3 5509
13 TraesCS4A01G478900 chr7D 5647866 5649401 1535 True 1696.000000 1696 86.662000 978 2507 1 chr7D.!!$R1 1529
14 TraesCS4A01G478900 chr7D 5445156 5449885 4729 True 1593.100000 2567 88.189667 315 4996 3 chr7D.!!$R2 4681
15 TraesCS4A01G478900 chr7A 6923718 6929588 5870 True 1075.100000 2477 89.602600 98 5680 5 chr7A.!!$R1 5582

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
802 1750 3.130633 CGATATTCAGGTCATTCCGCAA 58.869 45.455 0.00 0.00 41.99 4.85 F
1931 4357 0.178992 TTTGAACCTGGCAGTGAGGG 60.179 55.000 14.43 0.27 34.56 4.30 F
3558 6637 0.669619 TTGTCCTGTGCAATGTGCTG 59.330 50.000 1.43 0.00 45.31 4.41 F
3943 7031 0.767375 ATATGGAAGGAGCATGGCGT 59.233 50.000 0.00 0.00 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2136 4576 1.269936 CCTGCAAAACCTTCCAGCTTG 60.270 52.381 0.00 0.0 0.00 4.01 R
3687 6775 0.598065 GTTGTGATGCCAAGTGGTCC 59.402 55.000 0.00 0.0 37.57 4.46 R
4589 7677 0.169009 GCAGAGAAATGCCGGAACAC 59.831 55.000 5.05 0.0 40.43 3.32 R
5084 8361 0.250081 GGACGAAGATCATGGGCCTC 60.250 60.000 4.53 0.0 0.00 4.70 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
120 125 9.650714 TGGTATGTATTTAGTGGTATGTACTCT 57.349 33.333 0.00 0.00 0.00 3.24
462 594 4.388577 AGAAAGGGCAAGTAGTTGGATT 57.611 40.909 12.19 0.00 33.87 3.01
483 1329 6.264067 GGATTAGATCTGCTATTGCCTTGTTT 59.736 38.462 5.18 0.00 38.71 2.83
771 1676 3.499918 CGATCCAGAAGCACTTTCAGTTT 59.500 43.478 0.00 0.00 38.31 2.66
802 1750 3.130633 CGATATTCAGGTCATTCCGCAA 58.869 45.455 0.00 0.00 41.99 4.85
806 1754 3.904800 TTCAGGTCATTCCGCAATCTA 57.095 42.857 0.00 0.00 41.99 1.98
924 2334 7.985634 TTTACTGCTTCAACAGATTTTTCAC 57.014 32.000 0.00 0.00 40.25 3.18
1196 3605 2.364970 CAAACAAGGGAAATCACAGGCA 59.635 45.455 0.00 0.00 0.00 4.75
1263 3672 1.949525 GCTGAAGACTTGCTGGACAAA 59.050 47.619 0.00 0.00 37.96 2.83
1275 3684 5.981088 TGCTGGACAAACATGAATACAAT 57.019 34.783 0.00 0.00 0.00 2.71
1288 3697 3.118629 TGAATACAATCTCCTCAAGCGCT 60.119 43.478 2.64 2.64 0.00 5.92
1289 3698 3.550437 ATACAATCTCCTCAAGCGCTT 57.450 42.857 18.98 18.98 0.00 4.68
1380 3792 1.702886 CTGTGTCAAGTAGGCTGTCG 58.297 55.000 0.00 0.00 0.00 4.35
1713 4137 5.183140 ACAACTTGTTTACAACAGCAAGAGT 59.817 36.000 9.68 5.51 43.27 3.24
1767 4191 3.747099 AGCATATCACGCAAACTTGAC 57.253 42.857 0.00 0.00 0.00 3.18
1890 4316 3.013219 GCAAGACTCAGGGAAATTCCTC 58.987 50.000 12.28 1.02 36.57 3.71
1931 4357 0.178992 TTTGAACCTGGCAGTGAGGG 60.179 55.000 14.43 0.27 34.56 4.30
2042 4469 1.413812 TCTCTGCTGTGAAGAAGTGCA 59.586 47.619 0.00 0.00 0.00 4.57
2115 4542 4.842531 TGCATTCTCTGGACCAGAAATA 57.157 40.909 24.34 12.95 40.18 1.40
2238 4678 6.968263 TTGAAAGGGAAAACATGTATCACA 57.032 33.333 14.30 4.54 0.00 3.58
2271 4711 9.995003 AAGGATGCTCTTACTATAAAGATTGAG 57.005 33.333 0.00 0.00 35.04 3.02
2287 4727 2.099141 TGAGAAATTCAGTGAGCCCG 57.901 50.000 0.00 0.00 0.00 6.13
2509 4949 6.489127 TCTCTGTTTCGTTCTTTCAACAAA 57.511 33.333 0.00 0.00 0.00 2.83
2513 4953 9.450807 CTCTGTTTCGTTCTTTCAACAAATTAT 57.549 29.630 0.00 0.00 0.00 1.28
2525 4965 9.471084 CTTTCAACAAATTATTACGGAAAAGGT 57.529 29.630 0.00 0.00 0.00 3.50
2526 4966 8.804688 TTCAACAAATTATTACGGAAAAGGTG 57.195 30.769 0.00 0.00 0.00 4.00
2527 4967 8.167605 TCAACAAATTATTACGGAAAAGGTGA 57.832 30.769 0.00 0.00 0.00 4.02
2528 4968 8.077386 TCAACAAATTATTACGGAAAAGGTGAC 58.923 33.333 0.00 0.00 0.00 3.67
2530 4970 8.851541 ACAAATTATTACGGAAAAGGTGACTA 57.148 30.769 0.00 0.00 42.68 2.59
2531 4971 8.724229 ACAAATTATTACGGAAAAGGTGACTAC 58.276 33.333 0.00 0.00 42.68 2.73
2532 4972 8.943002 CAAATTATTACGGAAAAGGTGACTACT 58.057 33.333 0.00 0.00 42.68 2.57
2533 4973 9.511272 AAATTATTACGGAAAAGGTGACTACTT 57.489 29.630 0.00 0.00 42.68 2.24
2535 4975 5.534207 TTACGGAAAAGGTGACTACTTCA 57.466 39.130 0.00 0.00 42.68 3.02
2536 4976 4.618920 ACGGAAAAGGTGACTACTTCAT 57.381 40.909 0.00 0.00 42.68 2.57
2537 4977 5.733620 ACGGAAAAGGTGACTACTTCATA 57.266 39.130 0.00 0.00 42.68 2.15
2538 4978 6.295719 ACGGAAAAGGTGACTACTTCATAT 57.704 37.500 0.00 0.00 42.68 1.78
2539 4979 6.708285 ACGGAAAAGGTGACTACTTCATATT 58.292 36.000 0.00 0.00 42.68 1.28
2541 4981 6.037172 CGGAAAAGGTGACTACTTCATATTGG 59.963 42.308 0.00 0.00 42.68 3.16
2542 4982 7.110155 GGAAAAGGTGACTACTTCATATTGGA 58.890 38.462 0.00 0.00 42.68 3.53
2543 4983 7.610305 GGAAAAGGTGACTACTTCATATTGGAA 59.390 37.037 0.00 0.00 42.68 3.53
2544 4984 8.934023 AAAAGGTGACTACTTCATATTGGAAA 57.066 30.769 0.00 0.00 42.68 3.13
2545 4985 9.533831 AAAAGGTGACTACTTCATATTGGAAAT 57.466 29.630 0.00 0.00 42.68 2.17
2546 4986 9.533831 AAAGGTGACTACTTCATATTGGAAATT 57.466 29.630 0.00 0.00 42.68 1.82
2547 4987 9.533831 AAGGTGACTACTTCATATTGGAAATTT 57.466 29.630 0.00 0.00 42.68 1.82
2548 4988 8.960591 AGGTGACTACTTCATATTGGAAATTTG 58.039 33.333 0.00 0.00 40.61 2.32
2549 4989 8.956426 GGTGACTACTTCATATTGGAAATTTGA 58.044 33.333 0.00 0.00 36.32 2.69
2550 4990 9.994432 GTGACTACTTCATATTGGAAATTTGAG 57.006 33.333 0.00 0.00 36.32 3.02
2671 5111 1.362717 CCGTCCACTGTTCGACACT 59.637 57.895 5.82 0.00 0.00 3.55
2820 5260 2.036556 ATTTGAAGAAGTTGCGCGTG 57.963 45.000 8.43 0.00 0.00 5.34
3032 5480 8.554835 TTATGGAAATTACGTCATCTTGAACA 57.445 30.769 0.00 0.00 0.00 3.18
3037 5485 2.078849 ACGTCATCTTGAACATCGCA 57.921 45.000 0.00 0.00 0.00 5.10
3084 5532 2.805671 CACGTCATACAAAGAAGCACCA 59.194 45.455 0.00 0.00 0.00 4.17
3089 5537 3.684305 TCATACAAAGAAGCACCACATCG 59.316 43.478 0.00 0.00 0.00 3.84
3201 5649 2.159226 GGACATGAACGAGATTCGAGGT 60.159 50.000 0.00 0.00 43.74 3.85
3246 5694 3.053842 AGAATGTCACTGGCAAGGATCAT 60.054 43.478 0.00 0.00 0.00 2.45
3346 6425 7.011389 CGAATGCAGAGGATAGTTTACATTTGA 59.989 37.037 0.00 0.00 32.00 2.69
3407 6486 6.106673 AGGATCTTGTAATTGACGGTTACAG 58.893 40.000 0.00 0.00 41.50 2.74
3546 6625 3.190118 GGAATTGCTCTTCACTTGTCCTG 59.810 47.826 0.00 0.00 0.00 3.86
3558 6637 0.669619 TTGTCCTGTGCAATGTGCTG 59.330 50.000 1.43 0.00 45.31 4.41
3564 6643 1.338973 CTGTGCAATGTGCTGAACCTT 59.661 47.619 1.43 0.00 45.31 3.50
3672 6760 3.580022 TGGAACATCAAGAGCAGAGAGAA 59.420 43.478 0.00 0.00 0.00 2.87
3687 6775 7.144661 AGCAGAGAGAAAATATCACGAGTATG 58.855 38.462 0.00 0.00 0.00 2.39
3709 6797 3.146066 GACCACTTGGCATCACAACTTA 58.854 45.455 0.00 0.00 39.32 2.24
3710 6798 3.758554 GACCACTTGGCATCACAACTTAT 59.241 43.478 0.00 0.00 39.32 1.73
3733 6821 5.528600 TTTAATCTGGGAGGTGGATTCAA 57.471 39.130 0.00 0.00 32.78 2.69
3760 6848 8.862325 ATCAGATATTAGGAGTGTACTCTCAG 57.138 38.462 22.68 4.94 42.48 3.35
3768 6856 3.321111 GGAGTGTACTCTCAGTGGAACAA 59.679 47.826 22.68 0.00 41.22 2.83
3785 6873 4.321452 GGAACAATCATTTCTGAAGCAGCA 60.321 41.667 0.00 0.00 34.37 4.41
3845 6933 9.071276 TCAAAATCTTGAAATTGCTCTAGAAGT 57.929 29.630 0.00 0.00 38.65 3.01
3885 6973 9.125026 GTATTGGTAAAAGAGGATGTCATCAAT 57.875 33.333 14.72 2.45 0.00 2.57
3921 7009 3.089284 TCACGAGCAAAGGATGAGACTA 58.911 45.455 0.00 0.00 0.00 2.59
3943 7031 0.767375 ATATGGAAGGAGCATGGCGT 59.233 50.000 0.00 0.00 0.00 5.68
3979 7067 4.436584 CGCCATCAAGACTTCATGAACTTC 60.437 45.833 3.38 4.18 0.00 3.01
4048 7136 1.868713 TGGCCTGGCATCATTGAAAT 58.131 45.000 22.05 0.00 0.00 2.17
4155 7243 2.084610 TCGAAGATTGCTGGTGTCTG 57.915 50.000 0.00 0.00 0.00 3.51
4178 7266 1.761198 GTCATTAGGGGGCTTACGAGT 59.239 52.381 0.00 0.00 0.00 4.18
4179 7267 1.760613 TCATTAGGGGGCTTACGAGTG 59.239 52.381 0.00 0.00 0.00 3.51
4198 7286 5.563867 CGAGTGGCTACCTCTCTTTCATATC 60.564 48.000 12.44 0.00 40.68 1.63
4202 7290 6.041523 GTGGCTACCTCTCTTTCATATCTTCT 59.958 42.308 0.00 0.00 0.00 2.85
4241 7329 2.762887 CTCTAGAGTTGGCACATGGAGA 59.237 50.000 11.89 0.00 39.30 3.71
4310 7398 3.308401 TGCTTGCATATGACTCCCTCTA 58.692 45.455 6.97 0.00 0.00 2.43
4313 7401 5.723405 TGCTTGCATATGACTCCCTCTATAT 59.277 40.000 6.97 0.00 0.00 0.86
4323 7411 2.232452 CTCCCTCTATATTGACTGGCCG 59.768 54.545 0.00 0.00 0.00 6.13
4381 7469 1.001048 CCACATGCTTGTCTGTTGGTG 60.001 52.381 1.56 0.00 32.34 4.17
4386 7474 1.109323 GCTTGTCTGTTGGTGGCCTT 61.109 55.000 3.32 0.00 0.00 4.35
4412 7500 7.391554 TGCCTCTATTAAATCATTCATACTGGC 59.608 37.037 0.00 0.00 0.00 4.85
4413 7501 7.391554 GCCTCTATTAAATCATTCATACTGGCA 59.608 37.037 0.00 0.00 32.80 4.92
4419 7507 8.800370 TTAAATCATTCATACTGGCACACTTA 57.200 30.769 0.00 0.00 0.00 2.24
4431 7519 2.228822 GGCACACTTACCAGATTTGTGG 59.771 50.000 0.00 0.00 44.01 4.17
4453 7541 4.262635 GGATGCTCGAAGGATTATCTTCCA 60.263 45.833 0.00 0.00 39.82 3.53
4457 7545 3.653344 TCGAAGGATTATCTTCCATGCG 58.347 45.455 0.00 0.00 39.82 4.73
4485 7573 6.039829 TGCACAACTTACATTTGGTTGATGTA 59.960 34.615 11.21 0.00 41.71 2.29
4608 7696 0.169009 GTGTTCCGGCATTTCTCTGC 59.831 55.000 0.00 0.00 41.53 4.26
4623 7711 2.165167 CTCTGCCTTCAAGGATGCAAA 58.835 47.619 7.98 0.00 37.67 3.68
4624 7712 2.559668 CTCTGCCTTCAAGGATGCAAAA 59.440 45.455 7.98 0.00 37.67 2.44
4671 7759 8.600449 AATTCGCAAATTTTAAATCTGTCCAA 57.400 26.923 0.00 0.00 30.79 3.53
4737 7825 3.181329 TCTGAAGTGCTTCCCCAATCTA 58.819 45.455 9.18 0.00 38.77 1.98
4740 7828 4.934356 TGAAGTGCTTCCCCAATCTAAAT 58.066 39.130 9.18 0.00 38.77 1.40
4823 7911 2.673258 TCAGATAAGCGTATGGGGTCA 58.327 47.619 0.00 0.00 0.00 4.02
4852 7946 1.677217 GCTTGAAGGAGAGTTGCCGAT 60.677 52.381 0.00 0.00 0.00 4.18
4884 7978 2.967887 AGAAAGTTGGCCAAAGATTGCT 59.032 40.909 22.47 16.14 0.00 3.91
5001 8269 7.164803 GCACTCTCAAAGATATATAGCCCTTT 58.835 38.462 0.00 0.00 0.00 3.11
5041 8317 7.009357 TCGTTATTTTGTTTTTCCAAAACTCCG 59.991 33.333 12.15 4.80 44.51 4.63
5050 8326 4.799419 TTCCAAAACTCCGTTTACTTCG 57.201 40.909 0.00 0.00 34.43 3.79
5056 8333 6.293244 CCAAAACTCCGTTTACTTCGAATTCT 60.293 38.462 0.00 0.00 34.43 2.40
5098 8375 2.995746 TGATAGGAGGCCCATGATCTT 58.004 47.619 0.00 0.00 33.88 2.40
5101 8378 0.692419 AGGAGGCCCATGATCTTCGT 60.692 55.000 0.00 0.00 33.88 3.85
5193 8475 1.153823 CGAGTACTTCACTGGCCGG 60.154 63.158 11.02 11.02 37.72 6.13
5210 8492 0.802494 CGGTTTTGATCCCTTCGGTG 59.198 55.000 0.00 0.00 0.00 4.94
5367 8947 3.482436 TGAACAATTGCCGGAAGTAGTT 58.518 40.909 5.05 3.28 0.00 2.24
5407 8988 0.595567 GTCGTGCTGTCGTGTTACCA 60.596 55.000 0.00 0.00 0.00 3.25
5430 9011 4.197750 TCTCCTGGAGTATGTCGTACTTC 58.802 47.826 22.50 4.94 43.66 3.01
5439 9020 5.850614 AGTATGTCGTACTTCTGGTTTGTT 58.149 37.500 0.00 0.00 40.80 2.83
5441 9022 4.126208 TGTCGTACTTCTGGTTTGTTCA 57.874 40.909 0.00 0.00 0.00 3.18
5443 9024 3.059800 GTCGTACTTCTGGTTTGTTCAGC 60.060 47.826 0.00 0.00 32.63 4.26
5444 9025 2.096909 CGTACTTCTGGTTTGTTCAGCG 60.097 50.000 0.00 0.00 32.63 5.18
5474 9072 4.100035 TGCTCTTAGATACCATGTGACTGG 59.900 45.833 0.00 0.48 42.35 4.00
5477 9075 4.895889 TCTTAGATACCATGTGACTGGAGG 59.104 45.833 7.84 0.00 39.73 4.30
5502 9100 6.312918 GTCGCTTTTATCATTCACTCCTGTAA 59.687 38.462 0.00 0.00 0.00 2.41
5513 9120 3.572682 TCACTCCTGTAACGATGTCTTGT 59.427 43.478 0.00 0.00 0.00 3.16
5531 9139 7.383687 TGTCTTGTAGTACTTGGGTTTCATAG 58.616 38.462 0.00 0.00 0.00 2.23
5534 9142 8.092687 TCTTGTAGTACTTGGGTTTCATAGTTC 58.907 37.037 0.00 0.00 0.00 3.01
5566 9174 2.355756 CCTTGTGCCATGACTATTTCCG 59.644 50.000 0.00 0.00 0.00 4.30
5574 9182 3.243168 CCATGACTATTTCCGTTGCATGG 60.243 47.826 0.00 0.00 43.42 3.66
5581 9189 0.179004 TTCCGTTGCATGGTGGAACT 60.179 50.000 11.56 0.00 44.94 3.01
5695 9432 5.069518 TGTACTACATATACAGGCCCTGA 57.930 43.478 19.90 1.01 35.18 3.86
5701 9438 3.071602 ACATATACAGGCCCTGACATCAC 59.928 47.826 19.90 0.00 35.18 3.06
5713 9450 4.804139 CCCTGACATCACGTATACAGTTTC 59.196 45.833 3.32 0.00 0.00 2.78
5731 9468 6.373779 CAGTTTCCTGTGTTGAACATGATAC 58.626 40.000 0.00 4.91 38.39 2.24
5770 9507 2.165167 TCGGTTGAGGTACGTCTGAAT 58.835 47.619 16.00 0.00 0.00 2.57
5835 9572 1.444895 GCCATTTGGTTCAGCAGCG 60.445 57.895 0.00 0.00 37.57 5.18
5838 9575 0.453282 CATTTGGTTCAGCAGCGACG 60.453 55.000 0.00 0.00 0.00 5.12
5868 9605 6.154021 GGTTAGAGGATATATAGAAACGGCCA 59.846 42.308 2.24 0.00 0.00 5.36
5870 9607 6.227298 AGAGGATATATAGAAACGGCCATG 57.773 41.667 2.24 0.00 0.00 3.66
5888 9625 3.384467 CCATGCCCTACCCTGTTTATTTG 59.616 47.826 0.00 0.00 0.00 2.32
5889 9626 3.094484 TGCCCTACCCTGTTTATTTGG 57.906 47.619 0.00 0.00 0.00 3.28
5890 9627 2.650322 TGCCCTACCCTGTTTATTTGGA 59.350 45.455 0.00 0.00 0.00 3.53
5893 9630 4.134563 CCCTACCCTGTTTATTTGGATCG 58.865 47.826 0.00 0.00 0.00 3.69
5894 9631 4.134563 CCTACCCTGTTTATTTGGATCGG 58.865 47.826 0.00 0.00 0.00 4.18
5895 9632 2.375146 ACCCTGTTTATTTGGATCGGC 58.625 47.619 0.00 0.00 0.00 5.54
5897 9634 2.358898 CCCTGTTTATTTGGATCGGCTG 59.641 50.000 0.00 0.00 0.00 4.85
5898 9635 3.278574 CCTGTTTATTTGGATCGGCTGA 58.721 45.455 0.00 0.00 0.00 4.26
5899 9636 3.065371 CCTGTTTATTTGGATCGGCTGAC 59.935 47.826 0.00 0.00 0.00 3.51
5900 9637 3.013921 TGTTTATTTGGATCGGCTGACC 58.986 45.455 0.00 1.99 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 125 6.166984 AGCAGATTTCTAGCTAATGCACTA 57.833 37.500 0.00 0.00 42.74 2.74
462 594 6.055588 GGTAAACAAGGCAATAGCAGATCTA 58.944 40.000 0.00 0.00 44.61 1.98
483 1329 1.992557 AGAATCCCCAAACAGCAGGTA 59.007 47.619 0.00 0.00 0.00 3.08
822 2222 3.510388 TCAGTAGACGATGGCAAAGAG 57.490 47.619 0.00 0.00 0.00 2.85
924 2334 3.743521 TGTTTCTTGACTCAGTGATGGG 58.256 45.455 0.00 0.00 0.00 4.00
1131 3540 2.433604 CTGTGGCATGATAGTGGTCTCT 59.566 50.000 0.00 0.00 0.00 3.10
1196 3605 2.024414 GAAGCCACTTGTCCAACTTGT 58.976 47.619 0.00 0.00 0.00 3.16
1263 3672 4.813161 CGCTTGAGGAGATTGTATTCATGT 59.187 41.667 0.00 0.00 0.00 3.21
1275 3684 0.608130 TTGCTAAGCGCTTGAGGAGA 59.392 50.000 32.23 10.49 40.11 3.71
1315 3724 0.841961 CTGATGGAGGAGGCATTGGA 59.158 55.000 0.00 0.00 0.00 3.53
1630 4054 3.802948 AGCCAAACTCGAGTACATAGG 57.197 47.619 20.39 16.33 0.00 2.57
1890 4316 3.321682 ACCAAACATCATCCAACACAAGG 59.678 43.478 0.00 0.00 0.00 3.61
1931 4357 2.723273 CTAACAGTTGGTCCCATTCCC 58.277 52.381 0.00 0.00 0.00 3.97
2042 4469 6.014840 AGCATCTCCAATGTTTTTCAGTGAAT 60.015 34.615 6.36 0.00 43.71 2.57
2058 4485 1.339438 GCCAAGAACTGAGCATCTCCA 60.339 52.381 0.00 0.00 34.92 3.86
2136 4576 1.269936 CCTGCAAAACCTTCCAGCTTG 60.270 52.381 0.00 0.00 0.00 4.01
2271 4711 1.734465 CTCACGGGCTCACTGAATTTC 59.266 52.381 0.00 0.00 0.00 2.17
2277 4717 2.125753 GCTCTCACGGGCTCACTG 60.126 66.667 0.00 0.00 0.00 3.66
2287 4727 1.342819 ACTCCACAACAGAGCTCTCAC 59.657 52.381 14.96 0.00 34.56 3.51
2509 4949 8.316214 TGAAGTAGTCACCTTTTCCGTAATAAT 58.684 33.333 0.00 0.00 0.00 1.28
2513 4953 5.534207 TGAAGTAGTCACCTTTTCCGTAA 57.466 39.130 0.00 0.00 0.00 3.18
2516 4956 6.037172 CCAATATGAAGTAGTCACCTTTTCCG 59.963 42.308 0.00 0.00 39.72 4.30
2525 4965 9.958180 TCTCAAATTTCCAATATGAAGTAGTCA 57.042 29.630 0.00 0.00 41.67 3.41
2527 4967 9.965902 AGTCTCAAATTTCCAATATGAAGTAGT 57.034 29.630 0.00 0.00 0.00 2.73
2530 4970 7.340487 GGGAGTCTCAAATTTCCAATATGAAGT 59.660 37.037 1.47 0.00 0.00 3.01
2531 4971 7.340232 TGGGAGTCTCAAATTTCCAATATGAAG 59.660 37.037 1.47 0.00 0.00 3.02
2532 4972 7.122650 GTGGGAGTCTCAAATTTCCAATATGAA 59.877 37.037 0.00 0.00 0.00 2.57
2533 4973 6.603201 GTGGGAGTCTCAAATTTCCAATATGA 59.397 38.462 0.00 0.00 0.00 2.15
2535 4975 6.493166 TGTGGGAGTCTCAAATTTCCAATAT 58.507 36.000 0.00 0.00 0.00 1.28
2536 4976 5.886609 TGTGGGAGTCTCAAATTTCCAATA 58.113 37.500 0.00 0.00 0.00 1.90
2537 4977 4.739793 TGTGGGAGTCTCAAATTTCCAAT 58.260 39.130 0.00 0.00 0.00 3.16
2538 4978 4.177537 TGTGGGAGTCTCAAATTTCCAA 57.822 40.909 0.00 0.00 0.00 3.53
2539 4979 3.874383 TGTGGGAGTCTCAAATTTCCA 57.126 42.857 0.00 0.00 0.00 3.53
2541 4981 7.770897 ACATAGTATGTGGGAGTCTCAAATTTC 59.229 37.037 15.07 0.00 43.01 2.17
2542 4982 7.633789 ACATAGTATGTGGGAGTCTCAAATTT 58.366 34.615 15.07 0.00 43.01 1.82
2543 4983 7.200434 ACATAGTATGTGGGAGTCTCAAATT 57.800 36.000 15.07 0.00 43.01 1.82
2544 4984 6.814954 ACATAGTATGTGGGAGTCTCAAAT 57.185 37.500 15.07 0.20 43.01 2.32
2545 4985 6.620877 AACATAGTATGTGGGAGTCTCAAA 57.379 37.500 16.46 0.00 44.07 2.69
2546 4986 7.686859 GCATAACATAGTATGTGGGAGTCTCAA 60.687 40.741 16.46 0.00 44.07 3.02
2547 4987 6.239317 GCATAACATAGTATGTGGGAGTCTCA 60.239 42.308 16.46 0.00 44.07 3.27
2548 4988 6.159988 GCATAACATAGTATGTGGGAGTCTC 58.840 44.000 16.46 0.00 44.07 3.36
2549 4989 5.602561 TGCATAACATAGTATGTGGGAGTCT 59.397 40.000 16.46 1.89 44.07 3.24
2550 4990 5.853936 TGCATAACATAGTATGTGGGAGTC 58.146 41.667 16.46 5.35 44.07 3.36
2671 5111 9.093970 CTTCATACTATCAACACAAACCGATAA 57.906 33.333 0.00 0.00 0.00 1.75
2820 5260 7.721286 ACTGCTGTAAGATGACAAATATAGC 57.279 36.000 0.00 0.00 34.07 2.97
3032 5480 3.489355 TCATTATGCCAATCCTTGCGAT 58.511 40.909 0.00 0.00 0.00 4.58
3201 5649 8.275015 TCTCAAGATTTGTGACACTTAAACAA 57.725 30.769 7.20 0.00 32.19 2.83
3246 5694 1.066215 TGCAGCTTCGATTCTAAGGCA 60.066 47.619 0.00 0.30 0.00 4.75
3346 6425 4.718774 TGGCATCAGTCCTTCTAGAATCTT 59.281 41.667 5.44 0.00 0.00 2.40
3407 6486 3.503748 CCAGCCGGGATATTTTGAAGATC 59.496 47.826 2.18 0.00 40.01 2.75
3649 6728 3.056250 TCTCTCTGCTCTTGATGTTCCAC 60.056 47.826 0.00 0.00 0.00 4.02
3672 6760 5.871396 AGTGGTCCATACTCGTGATATTT 57.129 39.130 0.00 0.00 0.00 1.40
3687 6775 0.598065 GTTGTGATGCCAAGTGGTCC 59.402 55.000 0.00 0.00 37.57 4.46
3709 6797 6.091076 TGAATCCACCTCCCAGATTAAAAT 57.909 37.500 0.00 0.00 0.00 1.82
3710 6798 5.528600 TGAATCCACCTCCCAGATTAAAA 57.471 39.130 0.00 0.00 0.00 1.52
3733 6821 8.664992 TGAGAGTACACTCCTAATATCTGATCT 58.335 37.037 16.41 0.00 43.88 2.75
3760 6848 5.125100 TGCTTCAGAAATGATTGTTCCAC 57.875 39.130 0.00 0.00 0.00 4.02
3768 6856 4.524053 TCATCTGCTGCTTCAGAAATGAT 58.476 39.130 11.43 0.00 45.17 2.45
3785 6873 5.946377 ACATCAGCATGCATCAATATCATCT 59.054 36.000 21.98 0.00 34.76 2.90
3833 6921 7.946381 TCATCTTTCTCTACTTCTAGAGCAA 57.054 36.000 0.00 0.00 44.19 3.91
3921 7009 2.590821 GCCATGCTCCTTCCATATGTT 58.409 47.619 1.24 0.00 0.00 2.71
3943 7031 4.577677 TGGCGGAACCAGCAGCAA 62.578 61.111 0.00 0.00 46.36 3.91
4122 7210 2.688507 TCTTCGATGCACAAGAAGTCC 58.311 47.619 20.18 0.00 41.36 3.85
4155 7243 1.070289 CGTAAGCCCCCTAATGACCTC 59.930 57.143 0.00 0.00 0.00 3.85
4178 7266 6.139671 AGAAGATATGAAAGAGAGGTAGCCA 58.860 40.000 0.00 0.00 0.00 4.75
4179 7267 6.664428 AGAAGATATGAAAGAGAGGTAGCC 57.336 41.667 0.00 0.00 0.00 3.93
4198 7286 3.922171 AGGGCAGGAACTCAATAGAAG 57.078 47.619 0.00 0.00 34.60 2.85
4202 7290 3.454858 AGAGAAGGGCAGGAACTCAATA 58.545 45.455 0.00 0.00 34.60 1.90
4241 7329 5.721000 TCAAGGGATAATGGCAAACATTCTT 59.279 36.000 0.00 0.00 46.67 2.52
4298 7386 4.530161 GCCAGTCAATATAGAGGGAGTCAT 59.470 45.833 0.00 0.00 0.00 3.06
4304 7392 1.338200 GCGGCCAGTCAATATAGAGGG 60.338 57.143 2.24 0.00 0.00 4.30
4310 7398 2.653726 TCATTTGCGGCCAGTCAATAT 58.346 42.857 2.24 0.00 0.00 1.28
4313 7401 1.067706 CATTCATTTGCGGCCAGTCAA 60.068 47.619 2.24 0.02 0.00 3.18
4386 7474 7.391554 GCCAGTATGAATGATTTAATAGAGGCA 59.608 37.037 13.58 0.00 39.69 4.75
4393 7481 7.886629 AGTGTGCCAGTATGAATGATTTAAT 57.113 32.000 0.00 0.00 39.69 1.40
4412 7500 4.379813 GCATCCACAAATCTGGTAAGTGTG 60.380 45.833 0.00 0.00 39.41 3.82
4413 7501 3.758554 GCATCCACAAATCTGGTAAGTGT 59.241 43.478 0.00 0.00 32.50 3.55
4419 7507 1.278985 TCGAGCATCCACAAATCTGGT 59.721 47.619 0.00 0.00 32.50 4.00
4428 7516 4.264460 AGATAATCCTTCGAGCATCCAC 57.736 45.455 0.00 0.00 0.00 4.02
4431 7519 4.887748 TGGAAGATAATCCTTCGAGCATC 58.112 43.478 0.00 0.00 42.53 3.91
4457 7545 5.982516 TCAACCAAATGTAAGTTGTGCAATC 59.017 36.000 0.00 0.00 40.94 2.67
4468 7556 6.487331 AGTTTCGGTACATCAACCAAATGTAA 59.513 34.615 0.00 0.00 40.33 2.41
4485 7573 0.903454 ACTCGGGGATGAGTTTCGGT 60.903 55.000 0.00 0.00 46.85 4.69
4516 7604 1.748493 GAGTGAGCTCTGGACTCGAAT 59.252 52.381 16.19 0.00 38.66 3.34
4589 7677 0.169009 GCAGAGAAATGCCGGAACAC 59.831 55.000 5.05 0.00 40.43 3.32
4590 7678 2.555123 GCAGAGAAATGCCGGAACA 58.445 52.632 5.05 0.00 40.43 3.18
4661 7749 6.119240 TGAATCTCAGTCTTTGGACAGATT 57.881 37.500 9.77 9.77 42.59 2.40
4687 7775 3.129988 GGCAGGGAAATCATTTCACAGAG 59.870 47.826 14.95 5.29 45.51 3.35
4737 7825 5.504665 GCAGCTAACAATGTCGAGCATATTT 60.505 40.000 18.49 0.00 36.67 1.40
4740 7828 2.866156 GCAGCTAACAATGTCGAGCATA 59.134 45.455 18.49 0.00 36.67 3.14
4823 7911 0.320247 CTCCTTCAAGCGCTCACAGT 60.320 55.000 12.06 0.00 0.00 3.55
4852 7946 2.553028 GCCAACTTTCTCCATCAGGTGA 60.553 50.000 0.00 0.00 35.70 4.02
4884 7978 8.958119 ATAAAAAGTACTTCCTGCGAATATGA 57.042 30.769 8.95 0.00 0.00 2.15
4922 8024 9.451002 TTTCCGTTTATTTGTATGTAGGAATCA 57.549 29.630 0.00 0.00 35.51 2.57
4972 8078 7.095017 GGGCTATATATCTTTGAGAGTGCAAAC 60.095 40.741 0.00 0.00 34.35 2.93
5084 8361 0.250081 GGACGAAGATCATGGGCCTC 60.250 60.000 4.53 0.00 0.00 4.70
5098 8375 1.052124 ACCAGGTTGTTGGAGGACGA 61.052 55.000 0.00 0.00 40.87 4.20
5101 8378 0.682852 CGTACCAGGTTGTTGGAGGA 59.317 55.000 0.00 0.00 40.87 3.71
5407 8988 4.440826 AGTACGACATACTCCAGGAGAT 57.559 45.455 24.45 9.34 40.31 2.75
5430 9011 0.381801 ACAAGCGCTGAACAAACCAG 59.618 50.000 12.58 0.00 34.88 4.00
5439 9020 2.427095 TCTAAGAGCATACAAGCGCTGA 59.573 45.455 12.58 0.00 44.01 4.26
5441 9022 3.742433 ATCTAAGAGCATACAAGCGCT 57.258 42.857 2.64 2.64 46.81 5.92
5443 9024 4.871513 TGGTATCTAAGAGCATACAAGCG 58.128 43.478 0.00 0.00 40.15 4.68
5444 9025 6.146837 CACATGGTATCTAAGAGCATACAAGC 59.853 42.308 0.00 0.00 33.38 4.01
5474 9072 4.271291 GGAGTGAATGATAAAAGCGACCTC 59.729 45.833 0.00 0.00 0.00 3.85
5477 9075 4.631813 ACAGGAGTGAATGATAAAAGCGAC 59.368 41.667 0.00 0.00 0.00 5.19
5480 9078 6.312918 TCGTTACAGGAGTGAATGATAAAAGC 59.687 38.462 0.00 0.00 0.00 3.51
5502 9100 3.830755 ACCCAAGTACTACAAGACATCGT 59.169 43.478 0.00 0.00 0.00 3.73
5513 9120 9.038072 TGTATGAACTATGAAACCCAAGTACTA 57.962 33.333 0.00 0.00 0.00 1.82
5531 9139 2.350772 GCACAAGGCACACTGTATGAAC 60.351 50.000 0.00 0.00 43.97 3.18
5534 9142 2.152674 TGGCACAAGGCACACTGTATG 61.153 52.381 0.00 0.00 46.46 2.39
5566 9174 3.530535 ACAAAAAGTTCCACCATGCAAC 58.469 40.909 0.00 0.00 0.00 4.17
5574 9182 5.699001 ACAAGACCAAAACAAAAAGTTCCAC 59.301 36.000 0.00 0.00 40.26 4.02
5581 9189 5.300752 TGAAGCACAAGACCAAAACAAAAA 58.699 33.333 0.00 0.00 0.00 1.94
5686 9423 0.465705 ATACGTGATGTCAGGGCCTG 59.534 55.000 28.01 28.01 36.17 4.85
5731 9468 6.422776 ACCGAAAAGATAGCTAAATGTGTG 57.577 37.500 0.00 0.00 0.00 3.82
5770 9507 1.606668 CTTTTTGCCGGTCAGCACTAA 59.393 47.619 1.90 0.00 43.97 2.24
5835 9572 1.972872 TATCCTCTAACCGTCCCGTC 58.027 55.000 0.00 0.00 0.00 4.79
5838 9575 7.414984 CGTTTCTATATATCCTCTAACCGTCCC 60.415 44.444 0.00 0.00 0.00 4.46
5843 9580 6.154021 TGGCCGTTTCTATATATCCTCTAACC 59.846 42.308 0.00 0.00 0.00 2.85
5868 9605 3.270960 TCCAAATAAACAGGGTAGGGCAT 59.729 43.478 0.00 0.00 0.00 4.40
5870 9607 3.375647 TCCAAATAAACAGGGTAGGGC 57.624 47.619 0.00 0.00 0.00 5.19
5875 9612 2.025321 AGCCGATCCAAATAAACAGGGT 60.025 45.455 0.00 0.00 0.00 4.34
5877 9614 3.065371 GTCAGCCGATCCAAATAAACAGG 59.935 47.826 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.