Multiple sequence alignment - TraesCS1D01G317100

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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 TraesCS1D01G317100 chr1D 100.000 5157 0 0 1495 6651 412074377 412079533 0.000000e+00 9524.0
1 TraesCS1D01G317100 chr1D 100.000 1195 0 0 1 1195 412072883 412074077 0.000000e+00 2207.0
2 TraesCS1D01G317100 chr1D 92.235 425 28 5 142 562 460919525 460919102 1.230000e-166 597.0
3 TraesCS1D01G317100 chr1D 88.836 421 41 6 149 567 203869893 203869477 4.600000e-141 512.0
4 TraesCS1D01G317100 chr1D 81.605 299 25 15 563 845 446813809 446813525 3.120000e-53 220.0
5 TraesCS1D01G317100 chr1D 93.478 92 5 1 2282 2372 412074479 412074570 1.160000e-27 135.0
6 TraesCS1D01G317100 chr1D 93.478 92 5 1 1597 1688 412075164 412075254 1.160000e-27 135.0
7 TraesCS1D01G317100 chr1D 94.118 51 3 0 4100 4150 7036935 7036985 1.990000e-10 78.7
8 TraesCS1D01G317100 chr1B 93.650 5213 195 44 1495 6651 555624731 555629863 0.000000e+00 7668.0
9 TraesCS1D01G317100 chr1B 90.315 1239 54 26 1 1193 555623302 555624520 0.000000e+00 1563.0
10 TraesCS1D01G317100 chr1B 81.847 314 25 14 563 846 436991882 436991571 1.120000e-57 235.0
11 TraesCS1D01G317100 chr1B 93.396 106 4 2 6172 6277 572529353 572529455 3.210000e-33 154.0
12 TraesCS1D01G317100 chr1B 92.453 106 7 1 6180 6285 301264579 301264475 4.150000e-32 150.0
13 TraesCS1D01G317100 chr1B 91.579 95 3 2 2283 2372 555624848 555624942 7.000000e-25 126.0
14 TraesCS1D01G317100 chr1B 91.228 57 5 0 2162 2218 574282521 574282577 1.990000e-10 78.7
15 TraesCS1D01G317100 chr1A 93.383 3521 142 35 3166 6651 508630029 508633493 0.000000e+00 5127.0
16 TraesCS1D01G317100 chr1A 95.115 1044 48 2 2166 3208 508628988 508630029 0.000000e+00 1642.0
17 TraesCS1D01G317100 chr1A 89.080 1218 45 31 3 1193 508626587 508627743 0.000000e+00 1432.0
18 TraesCS1D01G317100 chr1A 91.763 692 39 6 1495 2168 508628248 508628939 0.000000e+00 946.0
19 TraesCS1D01G317100 chr1A 94.624 93 3 2 1599 1690 508629107 508629198 6.950000e-30 143.0
20 TraesCS1D01G317100 chr1A 93.478 92 5 1 2282 2372 508628361 508628452 1.160000e-27 135.0
21 TraesCS1D01G317100 chr1A 90.476 63 6 0 4101 4163 477033501 477033563 4.270000e-12 84.2
22 TraesCS1D01G317100 chr2A 86.264 779 82 19 4321 5082 136341527 136340757 0.000000e+00 822.0
23 TraesCS1D01G317100 chr2A 84.380 685 95 9 2227 2904 136343858 136343179 0.000000e+00 662.0
24 TraesCS1D01G317100 chr2A 84.615 598 77 13 2899 3492 136343025 136342439 1.240000e-161 580.0
25 TraesCS1D01G317100 chr2A 85.325 477 63 5 5039 5512 136340754 136340282 2.790000e-133 486.0
26 TraesCS1D01G317100 chr2A 80.952 378 67 4 2452 2826 53076270 53076645 1.810000e-75 294.0
27 TraesCS1D01G317100 chr2A 79.452 365 66 8 2453 2812 53068310 53068670 3.980000e-62 250.0
28 TraesCS1D01G317100 chr2A 81.703 317 23 16 563 848 728596505 728596193 1.440000e-56 231.0
29 TraesCS1D01G317100 chr2A 77.836 379 70 8 2436 2812 53055362 53055728 8.680000e-54 222.0
30 TraesCS1D01G317100 chr2A 77.165 381 69 8 2436 2812 53052509 53052875 8.740000e-49 206.0
31 TraesCS1D01G317100 chr2D 85.954 776 89 15 4321 5082 130431155 130430386 0.000000e+00 811.0
32 TraesCS1D01G317100 chr2D 84.255 597 80 11 2899 3491 130432917 130432331 2.690000e-158 569.0
33 TraesCS1D01G317100 chr2D 85.748 428 51 6 5039 5463 130430383 130429963 1.700000e-120 444.0
34 TraesCS1D01G317100 chr2D 80.964 394 68 6 2437 2826 51938613 51939003 8.380000e-79 305.0
35 TraesCS1D01G317100 chr2D 82.132 319 25 13 563 851 308981728 308981412 1.850000e-60 244.0
36 TraesCS1D01G317100 chr2D 79.191 173 23 6 1697 1858 130433852 130433682 2.540000e-19 108.0
37 TraesCS1D01G317100 chr2D 96.000 50 2 0 4100 4149 638323118 638323167 1.540000e-11 82.4
38 TraesCS1D01G317100 chr2B 85.935 775 90 14 4321 5082 183659823 183659055 0.000000e+00 809.0
39 TraesCS1D01G317100 chr2B 84.899 596 77 10 2899 3491 183661323 183660738 2.070000e-164 590.0
40 TraesCS1D01G317100 chr2B 86.093 453 53 6 5039 5489 183659052 183658608 4.670000e-131 479.0
41 TraesCS1D01G317100 chr2B 83.391 289 22 10 565 836 671166065 671166344 1.850000e-60 244.0
42 TraesCS1D01G317100 chr2B 79.769 173 23 5 1697 1858 183662256 183662085 1.520000e-21 115.0
43 TraesCS1D01G317100 chr4D 90.780 423 34 4 143 562 505256182 505256602 1.620000e-155 560.0
44 TraesCS1D01G317100 chr4D 88.626 422 46 2 143 563 126895543 126895963 4.600000e-141 512.0
45 TraesCS1D01G317100 chr6D 90.307 423 37 4 143 562 39567679 39568100 9.750000e-153 551.0
46 TraesCS1D01G317100 chr6D 89.474 418 42 2 148 563 3319624 3319207 1.640000e-145 527.0
47 TraesCS1D01G317100 chr7D 89.549 421 41 3 143 560 422616996 422617416 1.270000e-146 531.0
48 TraesCS1D01G317100 chr7D 93.396 106 5 2 6180 6285 190163215 190163112 8.930000e-34 156.0
49 TraesCS1D01G317100 chr5B 86.992 246 13 10 563 791 503082289 503082046 6.620000e-65 259.0
50 TraesCS1D01G317100 chr5B 85.143 175 14 6 603 765 654948141 654948315 1.150000e-37 169.0
51 TraesCS1D01G317100 chr5B 85.714 70 7 3 4101 4168 218214388 218214456 3.330000e-08 71.3
52 TraesCS1D01G317100 chr6A 81.620 321 20 17 563 846 325139012 325139330 5.190000e-56 230.0
53 TraesCS1D01G317100 chr3A 80.328 305 31 14 563 846 59422900 59423196 3.140000e-48 204.0
54 TraesCS1D01G317100 chr5D 93.750 112 5 2 6177 6287 228446959 228447069 4.130000e-37 167.0
55 TraesCS1D01G317100 chr7B 93.578 109 5 2 6180 6287 171060386 171060279 1.920000e-35 161.0
56 TraesCS1D01G317100 chr3D 94.231 104 4 2 6180 6283 502889145 502889246 2.480000e-34 158.0
57 TraesCS1D01G317100 chr3D 91.228 57 5 0 4101 4157 603265244 603265188 1.990000e-10 78.7
58 TraesCS1D01G317100 chr4B 91.743 109 7 2 6180 6287 426876349 426876242 4.150000e-32 150.0
59 TraesCS1D01G317100 chr4B 81.481 135 13 5 728 850 633294306 633294440 4.240000e-17 100.0
60 TraesCS1D01G317100 chr7A 77.990 209 16 15 673 854 94702339 94702544 3.280000e-18 104.0
61 TraesCS1D01G317100 chr3B 87.671 73 9 0 726 798 704288914 704288986 1.190000e-12 86.1
62 TraesCS1D01G317100 chr5A 88.525 61 6 1 4100 4159 362781652 362781592 9.250000e-09 73.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G317100 chr1D 412072883 412079533 6650 False 5865.500000 9524 100.000000 1 6651 2 chr1D.!!$F2 6650
1 TraesCS1D01G317100 chr1B 555623302 555629863 6561 False 4615.500000 7668 91.982500 1 6651 2 chr1B.!!$F4 6650
2 TraesCS1D01G317100 chr1A 508626587 508633493 6906 False 1570.833333 5127 92.907167 3 6651 6 chr1A.!!$F2 6648
3 TraesCS1D01G317100 chr2A 136340282 136343858 3576 True 637.500000 822 85.146000 2227 5512 4 chr2A.!!$R2 3285
4 TraesCS1D01G317100 chr2A 53052509 53055728 3219 False 214.000000 222 77.500500 2436 2812 2 chr2A.!!$F3 376
5 TraesCS1D01G317100 chr2D 130429963 130433852 3889 True 483.000000 811 83.787000 1697 5463 4 chr2D.!!$R2 3766
6 TraesCS1D01G317100 chr2B 183658608 183662256 3648 True 498.250000 809 84.174000 1697 5489 4 chr2B.!!$R1 3792


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
867 914 2.275380 GGGCCGTGGCATTTGTCTT 61.275 57.895 13.76 0.0 44.11 3.01 F
1952 2232 0.400213 CCAGCCCTTCCTTGTGTACA 59.600 55.000 0.00 0.0 0.00 2.90 F
2570 4695 0.537143 TTGCGGCTGGTTCTGTCATT 60.537 50.000 0.00 0.0 0.00 2.57 F
4080 6767 0.179089 CCTCTCAGATCCAACGCTGG 60.179 60.000 0.00 0.0 45.08 4.85 F
5622 8708 0.963962 TCTTTGAGGAGTACGCCGTT 59.036 50.000 10.22 0.0 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2723 4852 0.313672 GAGGCCTGACTAGAGCGATG 59.686 60.000 12.00 0.00 0.00 3.84 R
3015 5432 2.821546 TGAACATCCCAATCGACGATC 58.178 47.619 11.42 0.00 0.00 3.69 R
4207 6904 3.535561 AGATTCATCAGCCAAGGTAACG 58.464 45.455 0.00 0.00 46.39 3.18 R
5625 8711 0.242825 TGACGGCGTACTCCTCAAAG 59.757 55.000 14.74 0.00 0.00 2.77 R
6496 9595 4.345859 TGGTTTCTACATGTTCGAACCT 57.654 40.909 24.78 13.13 0.00 3.50 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 83 7.221452 GCAGCTACATCATTAAAAACTTCCATG 59.779 37.037 0.00 0.00 0.00 3.66
275 283 8.902806 CAAGAATGTTATGTGTATGTGGGTAAT 58.097 33.333 0.00 0.00 0.00 1.89
315 323 4.612712 CGTTGAAATGCGACCTGTACAAAT 60.613 41.667 0.00 0.00 0.00 2.32
417 425 4.497473 TTTCAACGTATTTTGCCCTGAG 57.503 40.909 0.00 0.00 0.00 3.35
429 437 3.500448 TGCCCTGAGAATTTACACACA 57.500 42.857 0.00 0.00 0.00 3.72
430 438 4.032960 TGCCCTGAGAATTTACACACAT 57.967 40.909 0.00 0.00 0.00 3.21
526 538 6.938542 TGAAATTCGAAATTTTCAAAACCGG 58.061 32.000 19.54 0.00 38.52 5.28
531 543 2.432206 AATTTTCAAAACCGGGCTCG 57.568 45.000 6.32 0.00 0.00 5.03
571 583 7.017645 CCAAAGACAATATTCGACAAAGACTG 58.982 38.462 0.00 0.00 0.00 3.51
850 897 2.350498 CCGTTTGTTCGGCTATAGTTGG 59.650 50.000 0.84 0.00 43.96 3.77
866 913 2.676471 GGGCCGTGGCATTTGTCT 60.676 61.111 13.76 0.00 44.11 3.41
867 914 2.275380 GGGCCGTGGCATTTGTCTT 61.275 57.895 13.76 0.00 44.11 3.01
873 920 3.074412 CCGTGGCATTTGTCTTAGACTT 58.926 45.455 13.86 0.00 33.15 3.01
874 921 4.250464 CCGTGGCATTTGTCTTAGACTTA 58.750 43.478 13.86 1.93 33.15 2.24
875 922 4.693566 CCGTGGCATTTGTCTTAGACTTAA 59.306 41.667 13.86 8.21 33.15 1.85
876 923 5.180492 CCGTGGCATTTGTCTTAGACTTAAA 59.820 40.000 13.86 7.08 33.15 1.52
877 924 6.077838 CGTGGCATTTGTCTTAGACTTAAAC 58.922 40.000 13.86 5.21 33.15 2.01
878 925 6.077838 GTGGCATTTGTCTTAGACTTAAACG 58.922 40.000 13.86 0.86 33.15 3.60
879 926 5.761234 TGGCATTTGTCTTAGACTTAAACGT 59.239 36.000 13.86 0.00 33.15 3.99
880 927 6.930164 TGGCATTTGTCTTAGACTTAAACGTA 59.070 34.615 13.86 0.00 33.15 3.57
881 928 7.604927 TGGCATTTGTCTTAGACTTAAACGTAT 59.395 33.333 13.86 0.00 33.15 3.06
1067 1115 3.391382 GGGGCTGCTGTACGACCT 61.391 66.667 0.00 0.00 0.00 3.85
1193 1241 4.443266 GCCGCCAGCGACTCTCTT 62.443 66.667 14.67 0.00 42.83 2.85
1527 1778 5.879237 ACAATAGGTTCAAACATGTATGCG 58.121 37.500 0.00 0.00 0.00 4.73
1549 1800 1.343142 TGTAGCGCTGAAAGGAACAGA 59.657 47.619 22.90 0.00 37.54 3.41
1666 1936 1.032014 TTTGCAAGGTTCTGTGGCTC 58.968 50.000 0.00 0.00 0.00 4.70
1835 2115 4.822685 TGAACATTGGCATTATGGCTTT 57.177 36.364 19.22 7.58 44.10 3.51
1879 2159 7.592533 GCATTATAGGTTCAAACATGTATGCAG 59.407 37.037 13.99 0.00 34.89 4.41
1881 2161 8.574251 TTATAGGTTCAAACATGTATGCAGTT 57.426 30.769 0.00 0.00 0.00 3.16
1882 2162 5.789643 AGGTTCAAACATGTATGCAGTTT 57.210 34.783 0.00 0.00 36.00 2.66
1884 2164 7.283625 AGGTTCAAACATGTATGCAGTTTAA 57.716 32.000 0.00 0.00 34.03 1.52
1886 2166 6.920758 GGTTCAAACATGTATGCAGTTTAACA 59.079 34.615 0.00 0.00 34.03 2.41
1949 2229 1.062488 ACTCCAGCCCTTCCTTGTGT 61.062 55.000 0.00 0.00 0.00 3.72
1950 2230 0.984230 CTCCAGCCCTTCCTTGTGTA 59.016 55.000 0.00 0.00 0.00 2.90
1951 2231 0.690762 TCCAGCCCTTCCTTGTGTAC 59.309 55.000 0.00 0.00 0.00 2.90
1952 2232 0.400213 CCAGCCCTTCCTTGTGTACA 59.600 55.000 0.00 0.00 0.00 2.90
1953 2233 1.611673 CCAGCCCTTCCTTGTGTACAG 60.612 57.143 0.00 0.00 0.00 2.74
1954 2234 1.072331 CAGCCCTTCCTTGTGTACAGT 59.928 52.381 0.00 0.00 0.00 3.55
1955 2235 2.301870 CAGCCCTTCCTTGTGTACAGTA 59.698 50.000 0.00 0.00 0.00 2.74
1971 2252 2.291153 ACAGTAACTTGGATGCCTGCAT 60.291 45.455 3.90 3.90 39.69 3.96
2088 2375 7.386851 TGAACTTAGTTCTTCCTCCATTGTAG 58.613 38.462 23.27 0.00 42.39 2.74
2207 2545 3.403038 ACAAAAATACGCAGCAGAGTCT 58.597 40.909 0.00 0.00 0.00 3.24
2221 2559 2.551459 CAGAGTCTTGCTGTTTCCCTTG 59.449 50.000 0.00 0.00 0.00 3.61
2267 2606 1.197721 GTGGAGTTTGAACATCGGCAG 59.802 52.381 0.00 0.00 0.00 4.85
2310 2649 6.183360 CCATTGCTTGCATTACTTTGATTGAC 60.183 38.462 0.00 0.00 0.00 3.18
2398 2738 4.115199 GGGCATGAGGGCGAAGGT 62.115 66.667 0.00 0.00 44.56 3.50
2429 2769 7.454225 AGGAAAAATATATAGCCTCTGTCCAC 58.546 38.462 0.00 0.00 0.00 4.02
2570 4695 0.537143 TTGCGGCTGGTTCTGTCATT 60.537 50.000 0.00 0.00 0.00 2.57
2583 4709 5.946377 GGTTCTGTCATTGAGGTAATTTCCT 59.054 40.000 2.81 2.81 40.97 3.36
2645 4771 1.508088 CAGCAATTCTGGTTCCGCC 59.492 57.895 0.00 0.00 39.15 6.13
2723 4852 0.673022 CTGGTGAGCTGAGTTCTGCC 60.673 60.000 0.00 1.17 41.03 4.85
3015 5432 7.875041 CCTGACCTAGGTATCAACAAGATATTG 59.125 40.741 16.29 0.00 41.10 1.90
3107 5524 2.813754 TCTTTTCAGTGCACAGGTATGC 59.186 45.455 21.04 0.00 46.32 3.14
3333 5792 4.776435 TGAATGGATGTAGGATGCTGAA 57.224 40.909 0.00 0.00 0.00 3.02
3359 5818 5.230942 CGTTTTCTTACAGTGGATCTCTGT 58.769 41.667 20.92 20.92 46.10 3.41
3454 5913 5.300792 AGCTCACCTTACTATAGTGCTCTTC 59.699 44.000 15.90 0.00 0.00 2.87
3501 6046 6.149640 GGGATTAAGTCTCCTCAGTTTTGTTC 59.850 42.308 0.00 0.00 33.05 3.18
3508 6053 4.516698 TCTCCTCAGTTTTGTTCATTCAGC 59.483 41.667 0.00 0.00 0.00 4.26
4065 6752 7.203910 CGACATATGTAAAAGTTCTAGCCTCT 58.796 38.462 8.71 0.00 0.00 3.69
4080 6767 0.179089 CCTCTCAGATCCAACGCTGG 60.179 60.000 0.00 0.00 45.08 4.85
4097 6784 7.305474 CAACGCTGGAACTTATTCTAACATTT 58.695 34.615 0.00 0.00 34.98 2.32
4144 6831 1.887797 ACATTATGGGACGGAGGGAA 58.112 50.000 0.00 0.00 0.00 3.97
4207 6904 9.646336 CCGCTTATCATTTAAGTTTACATACAC 57.354 33.333 0.00 0.00 0.00 2.90
4249 7215 8.621532 AATCTACAGATTGTGTACATGTTTGT 57.378 30.769 2.30 3.75 42.66 2.83
4251 7217 8.445275 TCTACAGATTGTGTACATGTTTGTTT 57.555 30.769 2.30 0.00 40.94 2.83
4390 7402 7.845037 TGCTCTGTAGATATGATTATGGAAGG 58.155 38.462 0.00 0.00 0.00 3.46
4592 7604 0.981183 TGGGTTTGACGCAGGTAGAT 59.019 50.000 0.00 0.00 36.06 1.98
4730 7749 2.263077 CTAGATGTGCACTGGTTCGAC 58.737 52.381 19.41 0.82 0.00 4.20
4737 7759 1.007336 GCACTGGTTCGACTACACCG 61.007 60.000 0.00 0.00 35.60 4.94
4740 7762 1.808945 ACTGGTTCGACTACACCGTAG 59.191 52.381 0.00 0.00 35.60 3.51
4745 7767 3.873952 GGTTCGACTACACCGTAGATACT 59.126 47.826 8.11 0.00 0.00 2.12
4753 7775 6.493116 ACTACACCGTAGATACTTGATTTCG 58.507 40.000 8.11 0.00 0.00 3.46
4755 7777 6.441093 ACACCGTAGATACTTGATTTCGTA 57.559 37.500 0.00 0.00 0.00 3.43
4766 7788 6.500684 ACTTGATTTCGTATTTGCATGACT 57.499 33.333 0.00 0.00 0.00 3.41
4800 7822 7.719193 TCTTCACTGAAGATATTTTGACAACCA 59.281 33.333 16.22 0.00 42.78 3.67
4854 7876 4.270245 TGCCAATGGAATCAAAACTTCC 57.730 40.909 2.05 0.00 42.15 3.46
4858 7880 4.261994 CCAATGGAATCAAAACTTCCGTGT 60.262 41.667 0.00 0.00 44.29 4.49
4859 7881 4.766404 ATGGAATCAAAACTTCCGTGTC 57.234 40.909 0.00 0.00 44.29 3.67
4860 7882 3.815809 TGGAATCAAAACTTCCGTGTCT 58.184 40.909 0.00 0.00 44.29 3.41
4861 7883 3.813166 TGGAATCAAAACTTCCGTGTCTC 59.187 43.478 0.00 0.00 44.29 3.36
5001 8028 4.332819 GCACTGCTACTAACAAAGGTATGG 59.667 45.833 0.00 0.00 0.00 2.74
5031 8058 3.248363 GGTTTGCAGCAAAATGACCTTTC 59.752 43.478 22.26 6.47 35.03 2.62
5173 8248 3.957497 TCATGCTTTGGTGTTACCTGTTT 59.043 39.130 0.00 0.00 39.58 2.83
5459 8544 8.713971 ACATGGAGAGTCATACAAATGGTAATA 58.286 33.333 0.00 0.00 35.14 0.98
5463 8548 7.873505 GGAGAGTCATACAAATGGTAATAGTCC 59.126 40.741 0.00 0.00 35.14 3.85
5531 8617 7.036863 TCTGTAATTTAGTTCTCATTCCCCCTT 60.037 37.037 0.00 0.00 0.00 3.95
5532 8618 6.889722 TGTAATTTAGTTCTCATTCCCCCTTG 59.110 38.462 0.00 0.00 0.00 3.61
5561 8647 3.247648 CCAGGTACGCGATGAATTAAAGG 59.752 47.826 15.93 0.00 0.00 3.11
5620 8706 2.728922 GTATCTTTGAGGAGTACGCCG 58.271 52.381 10.22 0.00 0.00 6.46
5622 8708 0.963962 TCTTTGAGGAGTACGCCGTT 59.036 50.000 10.22 0.00 0.00 4.44
5625 8711 2.857592 TTGAGGAGTACGCCGTTATC 57.142 50.000 10.22 2.93 0.00 1.75
5626 8712 2.048444 TGAGGAGTACGCCGTTATCT 57.952 50.000 10.22 0.00 0.00 1.98
5627 8713 2.372264 TGAGGAGTACGCCGTTATCTT 58.628 47.619 10.22 0.00 0.00 2.40
5628 8714 2.756760 TGAGGAGTACGCCGTTATCTTT 59.243 45.455 10.22 0.00 0.00 2.52
5629 8715 3.114065 GAGGAGTACGCCGTTATCTTTG 58.886 50.000 10.22 0.00 0.00 2.77
5630 8716 2.756760 AGGAGTACGCCGTTATCTTTGA 59.243 45.455 10.22 0.00 0.00 2.69
5631 8717 3.114065 GGAGTACGCCGTTATCTTTGAG 58.886 50.000 0.00 0.00 0.00 3.02
5632 8718 3.114065 GAGTACGCCGTTATCTTTGAGG 58.886 50.000 0.00 0.00 0.00 3.86
5633 8719 2.756760 AGTACGCCGTTATCTTTGAGGA 59.243 45.455 0.00 0.00 0.00 3.71
5634 8720 2.295253 ACGCCGTTATCTTTGAGGAG 57.705 50.000 0.00 0.00 0.00 3.69
5635 8721 1.549170 ACGCCGTTATCTTTGAGGAGT 59.451 47.619 0.00 0.00 0.00 3.85
5636 8722 2.756760 ACGCCGTTATCTTTGAGGAGTA 59.243 45.455 0.00 0.00 33.39 2.59
5637 8723 3.114065 CGCCGTTATCTTTGAGGAGTAC 58.886 50.000 0.00 0.00 0.00 2.73
5638 8724 3.114065 GCCGTTATCTTTGAGGAGTACG 58.886 50.000 0.00 0.00 0.00 3.67
5639 8725 3.114065 CCGTTATCTTTGAGGAGTACGC 58.886 50.000 0.00 0.00 0.00 4.42
5640 8726 3.114065 CGTTATCTTTGAGGAGTACGCC 58.886 50.000 7.70 7.70 0.00 5.68
5641 8727 3.114065 GTTATCTTTGAGGAGTACGCCG 58.886 50.000 10.22 0.00 0.00 6.46
5642 8728 1.183549 ATCTTTGAGGAGTACGCCGT 58.816 50.000 10.22 0.00 0.00 5.68
5643 8729 0.524862 TCTTTGAGGAGTACGCCGTC 59.475 55.000 10.22 8.74 0.00 4.79
5648 8734 2.304092 TGAGGAGTACGCCGTCATATT 58.696 47.619 10.22 0.00 0.00 1.28
5649 8735 2.034179 TGAGGAGTACGCCGTCATATTG 59.966 50.000 10.22 0.00 0.00 1.90
5725 8814 2.359531 GGTCTGACCTCCGACTAATGAG 59.640 54.545 19.53 0.00 34.73 2.90
5733 8822 3.589988 CTCCGACTAATGAGTTGTGCTT 58.410 45.455 0.00 0.00 35.45 3.91
5768 8857 1.833630 TGGATCGCTCTGTTCCAGATT 59.166 47.619 0.00 0.00 40.72 2.40
5848 8937 1.136891 AGTTGCAGCTTTCAAACCACC 59.863 47.619 0.00 0.00 0.00 4.61
5906 8996 9.003658 GTTATAATGAAGCACCATAATGTAGCT 57.996 33.333 0.00 0.00 37.08 3.32
5912 9002 6.038603 TGAAGCACCATAATGTAGCTCAATTC 59.961 38.462 0.00 0.00 33.83 2.17
6014 9112 2.353803 GCAGTCCGTACTTGATGAACCT 60.354 50.000 0.00 0.00 31.97 3.50
6050 9148 6.126568 TGTGATCAATGCTTCATGTGTATG 57.873 37.500 0.00 0.00 35.57 2.39
6089 9187 8.789762 TGCCTATCAACTTTTAAACTCTTAACC 58.210 33.333 0.00 0.00 0.00 2.85
6090 9188 9.011095 GCCTATCAACTTTTAAACTCTTAACCT 57.989 33.333 0.00 0.00 0.00 3.50
6123 9221 7.711846 AGAACATACAGAGTTATACAGCTCAG 58.288 38.462 0.00 0.00 34.63 3.35
6128 9226 8.951243 CATACAGAGTTATACAGCTCAGCTATA 58.049 37.037 0.00 0.00 36.40 1.31
6215 9313 8.074370 GTCCCAAAATAAGTGTCTCAACTTTAC 58.926 37.037 0.00 0.00 40.77 2.01
6226 9324 6.905609 GTGTCTCAACTTTACTACAACTTTGC 59.094 38.462 0.00 0.00 0.00 3.68
6318 9416 4.220821 GCATGGAGGCTTACTGTATAGCTA 59.779 45.833 16.12 0.00 37.54 3.32
6344 9442 9.503399 AAGACGATCAATAGGAAATATTAACCC 57.497 33.333 7.66 1.86 32.61 4.11
6413 9512 2.089980 GATGAACAGCCATGCACTTCT 58.910 47.619 0.00 0.00 0.00 2.85
6417 9516 3.244526 TGAACAGCCATGCACTTCTTCTA 60.245 43.478 0.00 0.00 0.00 2.10
6496 9595 6.833416 AGTTCAATATTTGGTATGCCAGCTTA 59.167 34.615 1.75 0.00 46.91 3.09
6502 9601 1.134521 TGGTATGCCAGCTTAGGTTCG 60.135 52.381 0.00 0.00 40.46 3.95
6510 9609 3.857052 CCAGCTTAGGTTCGAACATGTA 58.143 45.455 28.24 14.13 0.00 2.29
6620 9719 8.383947 AGGTTCCTCTATTTAAAGTTTGTAGCT 58.616 33.333 0.00 0.00 0.00 3.32
6626 9725 8.597662 TCTATTTAAAGTTTGTAGCTTGTCGT 57.402 30.769 0.00 0.00 0.00 4.34
6638 9737 2.751259 AGCTTGTCGTTGCATTCATCAT 59.249 40.909 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 8.686739 AGCTCTAGATTTACCCCACATAATAT 57.313 34.615 0.00 0.00 0.00 1.28
59 60 8.243426 TGACATGGAAGTTTTTAATGATGTAGC 58.757 33.333 0.00 0.00 0.00 3.58
138 139 1.076332 CCAAACGTCCATTCTCCGTC 58.924 55.000 0.00 0.00 32.95 4.79
139 140 0.953960 GCCAAACGTCCATTCTCCGT 60.954 55.000 0.00 0.00 36.17 4.69
140 141 0.673644 AGCCAAACGTCCATTCTCCG 60.674 55.000 0.00 0.00 0.00 4.63
141 142 1.087501 GAGCCAAACGTCCATTCTCC 58.912 55.000 0.00 0.00 0.00 3.71
275 283 9.190858 CATTTCAACGTTTTTCATCCTGAAATA 57.809 29.630 15.03 0.00 44.75 1.40
315 323 2.305928 CCGGGCCATGAATTTGTCATA 58.694 47.619 4.39 0.00 45.69 2.15
510 522 2.729360 CGAGCCCGGTTTTGAAAATTTC 59.271 45.455 0.00 0.00 0.00 2.17
531 543 3.157252 TGGAGGCCGAGCTCCATC 61.157 66.667 8.47 1.88 44.02 3.51
767 804 3.692370 GACACGGCCCGGGCTAAAT 62.692 63.158 42.70 26.82 41.60 1.40
839 886 1.227853 CCACGGCCCAACTATAGCC 60.228 63.158 0.00 0.00 43.53 3.93
850 897 0.451783 CTAAGACAAATGCCACGGCC 59.548 55.000 5.42 0.00 41.09 6.13
866 913 6.071952 ACGACCTTGGATACGTTTAAGTCTAA 60.072 38.462 0.00 0.00 42.51 2.10
867 914 5.415701 ACGACCTTGGATACGTTTAAGTCTA 59.584 40.000 0.00 0.00 42.51 2.59
873 920 2.609350 GCACGACCTTGGATACGTTTA 58.391 47.619 0.00 0.00 42.51 2.01
874 921 1.435577 GCACGACCTTGGATACGTTT 58.564 50.000 0.00 0.00 42.51 3.60
875 922 0.734942 CGCACGACCTTGGATACGTT 60.735 55.000 0.00 0.00 42.51 3.99
876 923 1.153901 CGCACGACCTTGGATACGT 60.154 57.895 0.00 0.00 42.51 3.57
877 924 0.734942 AACGCACGACCTTGGATACG 60.735 55.000 0.00 0.00 42.51 3.06
878 925 0.719465 CAACGCACGACCTTGGATAC 59.281 55.000 0.00 0.00 0.00 2.24
879 926 0.319083 ACAACGCACGACCTTGGATA 59.681 50.000 0.00 0.00 0.00 2.59
880 927 1.070786 ACAACGCACGACCTTGGAT 59.929 52.632 0.00 0.00 0.00 3.41
881 928 1.885388 CACAACGCACGACCTTGGA 60.885 57.895 0.00 0.00 0.00 3.53
1497 1748 8.862325 ACATGTTTGAACCTATTGTATGAAGA 57.138 30.769 0.00 0.00 0.00 2.87
1527 1778 0.444260 GTTCCTTTCAGCGCTACAGC 59.556 55.000 10.99 0.00 37.78 4.40
1666 1936 8.994429 ATCTGAAGAAACTTATGTCACACTAG 57.006 34.615 0.00 0.00 0.00 2.57
1701 1971 3.575858 CGCTACTGTGCATACATGTTC 57.424 47.619 2.30 0.00 35.97 3.18
1757 2027 1.686115 GGCAATGGCTTGAGTACCCAT 60.686 52.381 0.00 0.00 40.94 4.00
1835 2115 1.815196 CAAACAGTGGGCAGCACAA 59.185 52.632 0.00 0.00 0.00 3.33
1879 2159 4.573607 ACTCCGTTCCTTTCAGTGTTAAAC 59.426 41.667 0.00 0.00 0.00 2.01
1881 2161 4.374399 GACTCCGTTCCTTTCAGTGTTAA 58.626 43.478 0.00 0.00 0.00 2.01
1882 2162 3.243975 GGACTCCGTTCCTTTCAGTGTTA 60.244 47.826 0.00 0.00 32.24 2.41
1884 2164 1.070289 GGACTCCGTTCCTTTCAGTGT 59.930 52.381 0.00 0.00 32.24 3.55
1886 2166 1.718280 AGGACTCCGTTCCTTTCAGT 58.282 50.000 0.00 0.00 44.22 3.41
1898 2178 3.055094 TGCAGAAATACCAGAAGGACTCC 60.055 47.826 0.00 0.00 38.69 3.85
1949 2229 2.304470 TGCAGGCATCCAAGTTACTGTA 59.696 45.455 0.00 0.00 0.00 2.74
1950 2230 1.073763 TGCAGGCATCCAAGTTACTGT 59.926 47.619 0.00 0.00 0.00 3.55
1951 2231 1.825090 TGCAGGCATCCAAGTTACTG 58.175 50.000 0.00 0.00 0.00 2.74
1952 2232 2.372264 CATGCAGGCATCCAAGTTACT 58.628 47.619 3.30 0.00 33.90 2.24
1953 2233 1.202336 GCATGCAGGCATCCAAGTTAC 60.202 52.381 20.11 0.00 33.90 2.50
1954 2234 1.105457 GCATGCAGGCATCCAAGTTA 58.895 50.000 20.11 0.00 33.90 2.24
1955 2235 1.895238 GCATGCAGGCATCCAAGTT 59.105 52.632 20.11 0.00 33.90 2.66
1971 2252 3.751175 CAGTTCCTCTTTAAATGGACGCA 59.249 43.478 8.93 0.00 0.00 5.24
2088 2375 7.770801 AACAAGGAACAGAAAATACAAAAGC 57.229 32.000 0.00 0.00 0.00 3.51
2207 2545 4.817318 ACTTTTTCAAGGGAAACAGCAA 57.183 36.364 3.89 0.00 42.08 3.91
2221 2559 5.453567 AGTGGCATCCAAGTTACTTTTTC 57.546 39.130 0.00 0.00 34.18 2.29
2250 2589 4.025647 GCTATACTGCCGATGTTCAAACTC 60.026 45.833 0.00 0.00 0.00 3.01
2267 2606 3.526931 TGGACAGCACAGAAGCTATAC 57.473 47.619 0.00 0.00 44.54 1.47
2320 2659 6.088824 CAGAACCTTGCAAAGTCATACAATC 58.911 40.000 0.14 0.00 44.25 2.67
2398 2738 8.103305 CAGAGGCTATATATTTTTCCTTGGCTA 58.897 37.037 0.00 0.00 0.00 3.93
2429 2769 3.426117 ATCTACGTGCTTCCGGGCG 62.426 63.158 0.00 1.52 34.52 6.13
2507 2850 4.215399 CCTTTGCTGAAGTAAACGGAATCA 59.785 41.667 0.00 0.00 33.29 2.57
2645 4771 2.084610 TTTGTCAGCACTCAGGATCG 57.915 50.000 0.00 0.00 0.00 3.69
2723 4852 0.313672 GAGGCCTGACTAGAGCGATG 59.686 60.000 12.00 0.00 0.00 3.84
3015 5432 2.821546 TGAACATCCCAATCGACGATC 58.178 47.619 11.42 0.00 0.00 3.69
3269 5728 3.215975 TGTAGGCAACAAAACTACCACC 58.784 45.455 0.00 0.00 37.00 4.61
3333 5792 4.642429 AGATCCACTGTAAGAAAACGCTT 58.358 39.130 0.00 0.00 37.43 4.68
3454 5913 4.091945 CCGATCATTGCAGGTACAATATCG 59.908 45.833 14.81 14.81 38.19 2.92
3637 6182 9.271828 GGTAAAACCATGATGAAACAGAAAAAT 57.728 29.630 0.00 0.00 38.42 1.82
3908 6585 6.764308 ACATAAGCACTGAAGTTGCATTAT 57.236 33.333 0.00 0.00 0.00 1.28
4050 6736 4.780021 TGGATCTGAGAGGCTAGAACTTTT 59.220 41.667 0.00 0.00 0.00 2.27
4097 6784 7.013083 AGACGTTTCTTGACACTAGACTAGAAA 59.987 37.037 16.55 8.82 38.24 2.52
4115 6802 4.269363 CCGTCCCATAATGTAAGACGTTTC 59.731 45.833 9.63 0.00 46.62 2.78
4207 6904 3.535561 AGATTCATCAGCCAAGGTAACG 58.464 45.455 0.00 0.00 46.39 3.18
4390 7402 3.814005 TCCGCTTCATAAGGGTAGAAC 57.186 47.619 3.47 0.00 39.60 3.01
4671 7690 4.516698 ACAATGCCAGTATATAGCAACAGC 59.483 41.667 0.00 0.00 40.46 4.40
4730 7749 6.493116 ACGAAATCAAGTATCTACGGTGTAG 58.507 40.000 0.00 0.00 0.00 2.74
4737 7759 9.586150 CATGCAAATACGAAATCAAGTATCTAC 57.414 33.333 0.00 0.00 32.91 2.59
4740 7762 8.338259 AGTCATGCAAATACGAAATCAAGTATC 58.662 33.333 0.00 0.00 32.91 2.24
4745 7767 8.672815 TCATTAGTCATGCAAATACGAAATCAA 58.327 29.630 0.00 0.00 32.13 2.57
4753 7775 9.049523 TGAAGATCTCATTAGTCATGCAAATAC 57.950 33.333 0.00 0.00 32.13 1.89
4755 7777 7.774157 AGTGAAGATCTCATTAGTCATGCAAAT 59.226 33.333 0.00 0.00 36.14 2.32
4800 7822 7.122650 AGCAATATAATACAACAAAGCCACAGT 59.877 33.333 0.00 0.00 0.00 3.55
4854 7876 4.858140 GCATGATCATATGAGAGAGACACG 59.142 45.833 8.15 0.00 0.00 4.49
4858 7880 6.607004 ACATGCATGATCATATGAGAGAGA 57.393 37.500 32.75 0.00 0.00 3.10
4859 7881 7.100409 AGAACATGCATGATCATATGAGAGAG 58.900 38.462 32.75 0.59 32.67 3.20
4860 7882 7.005709 AGAACATGCATGATCATATGAGAGA 57.994 36.000 32.75 0.00 32.67 3.10
4861 7883 7.173390 ACAAGAACATGCATGATCATATGAGAG 59.827 37.037 32.75 12.45 32.67 3.20
4934 7961 3.424703 CAATCACCCATATGATCACCCC 58.575 50.000 3.65 0.00 38.40 4.95
5031 8058 3.441222 TGCATGGTTCAGTGAGCTTAATG 59.559 43.478 6.95 0.00 0.00 1.90
5037 8064 0.801251 GAGTGCATGGTTCAGTGAGC 59.199 55.000 0.00 0.00 0.00 4.26
5224 8303 6.918569 GCATCGATTAGCTGAGTAGAAAGTAA 59.081 38.462 0.00 0.00 0.00 2.24
5246 8325 6.064060 TGTAGAAAGGCATAAGCATAAGCAT 58.936 36.000 0.00 0.00 45.49 3.79
5459 8544 5.086104 ACAGAAATAGTACATTGCGGACT 57.914 39.130 0.00 0.00 0.00 3.85
5463 8548 9.425893 CAAATTAGACAGAAATAGTACATTGCG 57.574 33.333 0.00 0.00 0.00 4.85
5531 8617 2.342279 GCGTACCTGGTCAGTGCA 59.658 61.111 0.63 0.00 0.00 4.57
5532 8618 2.558554 ATCGCGTACCTGGTCAGTGC 62.559 60.000 0.63 2.40 0.00 4.40
5561 8647 1.135286 GCTCAAAACAGGCCAGTATGC 60.135 52.381 5.01 0.25 31.97 3.14
5620 8706 3.114065 CGGCGTACTCCTCAAAGATAAC 58.886 50.000 0.00 0.00 0.00 1.89
5622 8708 2.357009 GACGGCGTACTCCTCAAAGATA 59.643 50.000 14.74 0.00 0.00 1.98
5625 8711 0.242825 TGACGGCGTACTCCTCAAAG 59.757 55.000 14.74 0.00 0.00 2.77
5626 8712 0.892755 ATGACGGCGTACTCCTCAAA 59.107 50.000 14.74 0.00 0.00 2.69
5627 8713 1.753930 TATGACGGCGTACTCCTCAA 58.246 50.000 14.74 0.00 0.00 3.02
5628 8714 1.977056 ATATGACGGCGTACTCCTCA 58.023 50.000 14.74 5.80 0.00 3.86
5629 8715 2.292569 TCAATATGACGGCGTACTCCTC 59.707 50.000 14.74 0.00 0.00 3.71
5630 8716 2.293677 CTCAATATGACGGCGTACTCCT 59.706 50.000 14.74 0.00 0.00 3.69
5631 8717 2.607282 CCTCAATATGACGGCGTACTCC 60.607 54.545 14.74 0.00 0.00 3.85
5632 8718 2.034305 ACCTCAATATGACGGCGTACTC 59.966 50.000 14.74 0.18 0.00 2.59
5633 8719 2.029623 ACCTCAATATGACGGCGTACT 58.970 47.619 14.74 5.69 0.00 2.73
5634 8720 2.124903 CACCTCAATATGACGGCGTAC 58.875 52.381 14.74 7.58 0.00 3.67
5635 8721 2.025898 TCACCTCAATATGACGGCGTA 58.974 47.619 14.74 0.00 0.00 4.42
5636 8722 0.821517 TCACCTCAATATGACGGCGT 59.178 50.000 14.65 14.65 0.00 5.68
5637 8723 1.934589 TTCACCTCAATATGACGGCG 58.065 50.000 4.80 4.80 0.00 6.46
5638 8724 4.261197 GGAAATTCACCTCAATATGACGGC 60.261 45.833 0.00 0.00 0.00 5.68
5639 8725 5.126067 AGGAAATTCACCTCAATATGACGG 58.874 41.667 0.00 0.00 31.43 4.79
5725 8814 6.968904 CCACATCTCATACATAAAAGCACAAC 59.031 38.462 0.00 0.00 0.00 3.32
5733 8822 6.015095 AGAGCGATCCACATCTCATACATAAA 60.015 38.462 0.00 0.00 0.00 1.40
5768 8857 1.673920 GTCAAGTTTCCCAGCAAACGA 59.326 47.619 0.00 0.00 40.60 3.85
5823 8912 1.761449 TTGAAAGCTGCAACTGTGGA 58.239 45.000 1.02 0.00 0.00 4.02
5906 8996 7.285858 TGAACATGCATTCATCTATGGAATTGA 59.714 33.333 0.00 0.00 33.62 2.57
5912 9002 4.512571 TCGTGAACATGCATTCATCTATGG 59.487 41.667 6.05 0.00 40.60 2.74
5996 9094 5.684550 AAAAAGGTTCATCAAGTACGGAC 57.315 39.130 0.00 0.00 0.00 4.79
6050 9148 4.342862 TGATAGGCACCTCAGAATAAGC 57.657 45.455 0.00 0.00 0.00 3.09
6215 9313 6.787085 ACTAGCTTTAGTGCAAAGTTGTAG 57.213 37.500 0.00 0.00 44.73 2.74
6226 9324 8.488764 GTCTCAAACTTTGTACTAGCTTTAGTG 58.511 37.037 0.00 0.00 0.00 2.74
6245 9343 4.517453 CCGTCCCAAAATAAGTGTCTCAAA 59.483 41.667 0.00 0.00 0.00 2.69
6318 9416 9.503399 GGGTTAATATTTCCTATTGATCGTCTT 57.497 33.333 0.00 0.00 32.26 3.01
6344 9442 0.107017 ATTCAAGGGCTCCACCATCG 60.107 55.000 0.00 0.00 42.05 3.84
6413 9512 7.726216 TCAAAACATCAGACTCAGAACTAGAA 58.274 34.615 0.00 0.00 0.00 2.10
6417 9516 5.923204 ACTCAAAACATCAGACTCAGAACT 58.077 37.500 0.00 0.00 0.00 3.01
6496 9595 4.345859 TGGTTTCTACATGTTCGAACCT 57.654 40.909 24.78 13.13 0.00 3.50
6502 9601 7.805071 CACAAGAATCTTGGTTTCTACATGTTC 59.195 37.037 24.77 0.00 33.17 3.18
6510 9609 5.376625 TGTAGCACAAGAATCTTGGTTTCT 58.623 37.500 24.77 16.96 34.95 2.52
6620 9719 6.622833 ATGATATGATGAATGCAACGACAA 57.377 33.333 0.00 0.00 0.00 3.18



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

AutoCloner maintained by Alex Coulton.