Multiple sequence alignment - TraesCS5A01G539400

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 TraesCS5A01G539400 chr5A 100.000 3104 0 0 1 3104 697687591 697690694 0.000000e+00 5733.0
1 TraesCS5A01G539400 chr5A 86.809 561 53 12 237 785 709488624 709489175 9.520000e-170 606.0
2 TraesCS5A01G539400 chr5A 92.145 331 14 3 1545 1875 709491449 709491767 1.010000e-124 457.0
3 TraesCS5A01G539400 chr5A 86.598 388 32 11 1898 2274 315843527 315843149 8.010000e-111 411.0
4 TraesCS5A01G539400 chr5A 81.238 517 48 26 1778 2276 272867374 272866889 3.780000e-99 372.0
5 TraesCS5A01G539400 chr5A 93.590 234 9 3 5 237 709486654 709486882 8.240000e-91 344.0
6 TraesCS5A01G539400 chr5A 86.404 228 4 9 799 1010 709491076 709491292 1.120000e-54 224.0
7 TraesCS5A01G539400 chr5A 93.548 124 6 2 2257 2379 299502460 299502582 1.900000e-42 183.0
8 TraesCS5A01G539400 chr5A 77.260 365 42 17 1923 2267 709491781 709492124 3.180000e-40 176.0
9 TraesCS5A01G539400 chr5A 87.218 133 3 6 2405 2523 315843107 315842975 4.170000e-29 139.0
10 TraesCS5A01G539400 chr5A 93.548 62 4 0 2399 2460 709492153 709492214 3.300000e-15 93.5
11 TraesCS5A01G539400 chrUn 87.181 1334 71 34 1001 2268 100211054 100209755 0.000000e+00 1424.0
12 TraesCS5A01G539400 chrUn 91.980 798 38 17 3 782 100212098 100211309 0.000000e+00 1096.0
13 TraesCS5A01G539400 chrUn 94.872 507 24 2 2523 3028 368715113 368714608 0.000000e+00 791.0
14 TraesCS5A01G539400 chrUn 97.126 174 3 2 799 971 100211224 100211052 3.030000e-75 292.0
15 TraesCS5A01G539400 chrUn 87.500 216 11 7 315 514 410093429 410093214 5.170000e-58 235.0
16 TraesCS5A01G539400 chrUn 87.500 216 11 7 315 514 439509706 439509921 5.170000e-58 235.0
17 TraesCS5A01G539400 chrUn 86.275 102 3 4 2430 2524 100209013 100208916 1.970000e-17 100.0
18 TraesCS5A01G539400 chr4B 85.702 1133 63 49 799 1891 671844281 671845354 0.000000e+00 1103.0
19 TraesCS5A01G539400 chr4B 86.364 198 9 5 1949 2128 671845363 671845560 1.890000e-47 200.0
20 TraesCS5A01G539400 chr4B 93.333 120 6 2 2150 2267 671845721 671845840 3.180000e-40 176.0
21 TraesCS5A01G539400 chr4B 98.413 63 0 1 736 798 671844140 671844201 3.270000e-20 110.0
22 TraesCS5A01G539400 chr4B 91.250 80 4 3 2446 2524 671845907 671845984 4.230000e-19 106.0
23 TraesCS5A01G539400 chr7B 95.276 508 22 2 2523 3029 479234656 479235162 0.000000e+00 804.0
24 TraesCS5A01G539400 chr7B 96.429 112 4 0 2271 2382 191777195 191777306 5.290000e-43 185.0
25 TraesCS5A01G539400 chr7B 95.652 115 5 0 2266 2380 523681968 523682082 5.290000e-43 185.0
26 TraesCS5A01G539400 chr7B 94.667 75 4 0 3030 3104 72618442 72618368 1.960000e-22 117.0
27 TraesCS5A01G539400 chr6A 91.537 579 39 5 2523 3099 602949881 602950451 0.000000e+00 789.0
28 TraesCS5A01G539400 chr6A 93.886 507 28 3 2523 3029 24204578 24204075 0.000000e+00 761.0
29 TraesCS5A01G539400 chr6A 93.230 517 31 4 2516 3031 616963299 616962786 0.000000e+00 758.0
30 TraesCS5A01G539400 chr4A 94.314 510 27 2 2523 3031 512536884 512536376 0.000000e+00 780.0
31 TraesCS5A01G539400 chr4A 87.500 216 11 6 315 514 67543746 67543961 5.170000e-58 235.0
32 TraesCS5A01G539400 chr5B 94.280 507 27 2 2523 3028 430172651 430172146 0.000000e+00 774.0
33 TraesCS5A01G539400 chr5B 94.083 507 28 2 2523 3028 430270700 430270195 0.000000e+00 769.0
34 TraesCS5A01G539400 chr5B 94.667 75 4 0 3030 3104 644892483 644892557 1.960000e-22 117.0
35 TraesCS5A01G539400 chr7A 93.898 508 29 2 2523 3029 724902618 724903124 0.000000e+00 765.0
36 TraesCS5A01G539400 chr4D 80.000 980 67 50 1328 2276 358455388 358454507 3.420000e-169 604.0
37 TraesCS5A01G539400 chr4D 87.963 216 10 7 315 514 123589759 123589544 1.110000e-59 241.0
38 TraesCS5A01G539400 chr4D 87.500 216 11 4 315 514 123378974 123378759 5.170000e-58 235.0
39 TraesCS5A01G539400 chr2A 81.346 520 50 25 1778 2276 645903798 645904291 2.260000e-101 379.0
40 TraesCS5A01G539400 chr2A 92.742 124 6 3 2268 2388 762743755 762743632 3.180000e-40 176.0
41 TraesCS5A01G539400 chr2A 98.667 75 1 0 3030 3104 691655197 691655271 1.940000e-27 134.0
42 TraesCS5A01G539400 chr2A 97.143 70 2 0 3030 3099 2458037 2457968 5.440000e-23 119.0
43 TraesCS5A01G539400 chr7D 88.426 216 9 4 315 514 307053742 307053957 2.390000e-61 246.0
44 TraesCS5A01G539400 chr2D 87.963 216 10 4 315 514 635048405 635048190 1.110000e-59 241.0
45 TraesCS5A01G539400 chr2D 95.614 114 5 0 2266 2379 68867474 68867361 1.900000e-42 183.0
46 TraesCS5A01G539400 chr1A 87.500 216 11 4 315 514 238145077 238145292 5.170000e-58 235.0
47 TraesCS5A01G539400 chr1A 87.037 216 12 7 315 514 238142454 238142669 2.410000e-56 230.0
48 TraesCS5A01G539400 chr1A 97.143 70 2 0 3030 3099 562471248 562471179 5.440000e-23 119.0
49 TraesCS5A01G539400 chr3B 87.037 216 12 4 315 514 575758783 575758998 2.410000e-56 230.0
50 TraesCS5A01G539400 chr3B 95.833 72 3 0 3030 3101 68226352 68226423 1.960000e-22 117.0
51 TraesCS5A01G539400 chr3A 87.192 203 19 2 1200 1395 120239476 120239274 1.120000e-54 224.0
52 TraesCS5A01G539400 chr3D 81.091 275 25 13 1200 1473 592966112 592965864 8.780000e-46 195.0
53 TraesCS5A01G539400 chr3D 92.857 126 8 1 2254 2379 582122914 582123038 6.840000e-42 182.0
54 TraesCS5A01G539400 chr6D 84.305 223 3 11 799 1010 934355 934154 4.090000e-44 189.0
55 TraesCS5A01G539400 chr6D 96.429 112 4 0 2271 2382 457694099 457693988 5.290000e-43 185.0
56 TraesCS5A01G539400 chr2B 93.701 127 6 2 2255 2380 123063292 123063417 4.090000e-44 189.0
57 TraesCS5A01G539400 chr2B 96.000 75 3 0 3030 3104 774085452 774085526 4.200000e-24 122.0
58 TraesCS5A01G539400 chr6B 93.496 123 7 1 2258 2379 679090912 679091034 6.840000e-42 182.0
59 TraesCS5A01G539400 chr6B 94.667 75 4 0 3030 3104 289819155 289819229 1.960000e-22 117.0


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 TraesCS5A01G539400 chr5A 697687591 697690694 3103 False 5733.00 5733 100.000000 1 3104 1 chr5A.!!$F2 3103
1 TraesCS5A01G539400 chr5A 709486654 709492214 5560 False 316.75 606 88.292667 5 2460 6 chr5A.!!$F3 2455
2 TraesCS5A01G539400 chr5A 315842975 315843527 552 True 275.00 411 86.908000 1898 2523 2 chr5A.!!$R2 625
3 TraesCS5A01G539400 chrUn 368714608 368715113 505 True 791.00 791 94.872000 2523 3028 1 chrUn.!!$R1 505
4 TraesCS5A01G539400 chrUn 100208916 100212098 3182 True 728.00 1424 90.640500 3 2524 4 chrUn.!!$R3 2521
5 TraesCS5A01G539400 chr4B 671844140 671845984 1844 False 339.00 1103 91.012400 736 2524 5 chr4B.!!$F1 1788
6 TraesCS5A01G539400 chr7B 479234656 479235162 506 False 804.00 804 95.276000 2523 3029 1 chr7B.!!$F2 506
7 TraesCS5A01G539400 chr6A 602949881 602950451 570 False 789.00 789 91.537000 2523 3099 1 chr6A.!!$F1 576
8 TraesCS5A01G539400 chr6A 24204075 24204578 503 True 761.00 761 93.886000 2523 3029 1 chr6A.!!$R1 506
9 TraesCS5A01G539400 chr6A 616962786 616963299 513 True 758.00 758 93.230000 2516 3031 1 chr6A.!!$R2 515
10 TraesCS5A01G539400 chr4A 512536376 512536884 508 True 780.00 780 94.314000 2523 3031 1 chr4A.!!$R1 508
11 TraesCS5A01G539400 chr5B 430172146 430172651 505 True 774.00 774 94.280000 2523 3028 1 chr5B.!!$R1 505
12 TraesCS5A01G539400 chr5B 430270195 430270700 505 True 769.00 769 94.083000 2523 3028 1 chr5B.!!$R2 505
13 TraesCS5A01G539400 chr7A 724902618 724903124 506 False 765.00 765 93.898000 2523 3029 1 chr7A.!!$F1 506
14 TraesCS5A01G539400 chr4D 358454507 358455388 881 True 604.00 604 80.000000 1328 2276 1 chr4D.!!$R3 948
15 TraesCS5A01G539400 chr1A 238142454 238145292 2838 False 232.50 235 87.268500 315 514 2 chr1A.!!$F1 199

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
267 2012 1.599071 GGCACAAGCAAAAGAAAAGGC 59.401 47.619 0.0 0.0 44.61 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2189 6754 0.17668 TCGATCCTCTGAGCTTTGGC 59.823 55.0 0.0 0.0 39.06 4.52 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
214 216 6.183324 GCGAATTGAGTAATAGGTCGAAAAC 58.817 40.000 0.00 0.00 29.76 2.43
267 2012 1.599071 GGCACAAGCAAAAGAAAAGGC 59.401 47.619 0.00 0.00 44.61 4.35
270 2015 3.492482 GCACAAGCAAAAGAAAAGGCCTA 60.492 43.478 5.16 0.00 41.58 3.93
344 2654 6.158695 AGGGCTAGTTCAATTCCAGAGAAATA 59.841 38.462 0.00 0.00 35.09 1.40
392 2712 6.440965 AGGCTCACTATACCAAGTTAAGTTCT 59.559 38.462 0.00 0.00 0.00 3.01
413 2733 9.300681 AGTTCTTCCAAAGTATTTTCATCATCA 57.699 29.630 0.00 0.00 35.03 3.07
414 2734 9.346725 GTTCTTCCAAAGTATTTTCATCATCAC 57.653 33.333 0.00 0.00 35.03 3.06
420 2746 6.690194 AAGTATTTTCATCATCACCAGAGC 57.310 37.500 0.00 0.00 0.00 4.09
432 2758 2.906389 TCACCAGAGCCACAAGATAAGT 59.094 45.455 0.00 0.00 0.00 2.24
502 2828 7.016153 ACTTATCAGGGTCTAACAATGTTGA 57.984 36.000 9.15 1.74 0.00 3.18
541 2867 5.518848 TTTACTTTCACTCGTGGAGTACA 57.481 39.130 11.18 5.56 41.37 2.90
610 2941 4.195416 TGGGCCAGAATTTTTGTTGTTTC 58.805 39.130 0.00 0.00 0.00 2.78
658 2992 8.977267 TTTTCAAAACAAAATTCCATGGATCT 57.023 26.923 17.06 3.06 0.00 2.75
663 2997 7.781324 AAACAAAATTCCATGGATCTGTAGT 57.219 32.000 17.06 7.79 0.00 2.73
664 2998 6.764308 ACAAAATTCCATGGATCTGTAGTG 57.236 37.500 17.06 10.04 0.00 2.74
665 2999 6.484288 ACAAAATTCCATGGATCTGTAGTGA 58.516 36.000 17.06 0.00 0.00 3.41
674 3008 6.037940 CCATGGATCTGTAGTGATGAACAAAG 59.962 42.308 5.56 0.00 0.00 2.77
689 3023 1.760029 ACAAAGCAAATTTCCACGGGT 59.240 42.857 0.00 0.00 0.00 5.28
848 5082 9.649167 TTTTTACTCCTACTGATTAAGTGTAGC 57.351 33.333 0.00 0.00 40.26 3.58
1070 5340 4.812626 GGCAATTAAAACTAGCTAGCGGTA 59.187 41.667 20.91 7.17 0.00 4.02
1159 5433 1.115467 CACGGGGAGATAGCTCTTGT 58.885 55.000 8.10 1.42 41.06 3.16
1169 5443 1.813513 TAGCTCTTGTTTGCTGAGGC 58.186 50.000 0.00 0.00 40.08 4.70
1172 5446 1.580845 CTCTTGTTTGCTGAGGCGGG 61.581 60.000 0.00 0.00 42.25 6.13
1182 5474 4.329545 GAGGCGGGCTTGGTGTGA 62.330 66.667 5.24 0.00 0.00 3.58
1186 5478 4.988598 CGGGCTTGGTGTGAGCGT 62.989 66.667 0.00 0.00 41.03 5.07
1187 5479 3.357079 GGGCTTGGTGTGAGCGTG 61.357 66.667 0.00 0.00 41.03 5.34
1188 5480 2.591715 GGCTTGGTGTGAGCGTGT 60.592 61.111 0.00 0.00 41.03 4.49
1435 5760 4.969196 CACGCCGTGCCACAGAGT 62.969 66.667 3.47 0.00 0.00 3.24
1841 6193 5.486526 ACCTCTGAATCTCATCTCAACAAC 58.513 41.667 0.00 0.00 0.00 3.32
1844 6196 6.128336 CCTCTGAATCTCATCTCAACAACAAC 60.128 42.308 0.00 0.00 0.00 3.32
1864 6216 5.010922 ACAACAAGAAGAAAATGCCTGCATA 59.989 36.000 4.84 0.00 35.31 3.14
1954 6347 2.988549 GCGCGCGTCCTAATCGATG 61.989 63.158 32.35 0.00 0.00 3.84
2053 6468 3.222603 ACAAAACCCTCTGTTCATGTCC 58.777 45.455 0.00 0.00 35.67 4.02
2130 6560 2.090760 TGTTTGCTGCTGTTGACTGAA 58.909 42.857 0.00 0.00 0.00 3.02
2137 6576 6.088016 TGCTGCTGTTGACTGAAAATTATT 57.912 33.333 0.00 0.00 0.00 1.40
2277 6847 8.004087 TCCACACATACAGTAAATAGTACTCC 57.996 38.462 0.00 0.00 0.00 3.85
2278 6848 7.069085 TCCACACATACAGTAAATAGTACTCCC 59.931 40.741 0.00 0.00 0.00 4.30
2279 6849 7.069578 CCACACATACAGTAAATAGTACTCCCT 59.930 40.741 0.00 0.00 0.00 4.20
2280 6850 8.136165 CACACATACAGTAAATAGTACTCCCTC 58.864 40.741 0.00 0.00 0.00 4.30
2281 6851 7.287235 ACACATACAGTAAATAGTACTCCCTCC 59.713 40.741 0.00 0.00 0.00 4.30
2282 6852 6.489361 ACATACAGTAAATAGTACTCCCTCCG 59.511 42.308 0.00 0.00 0.00 4.63
2283 6853 4.864726 ACAGTAAATAGTACTCCCTCCGT 58.135 43.478 0.00 0.00 0.00 4.69
2284 6854 5.267587 ACAGTAAATAGTACTCCCTCCGTT 58.732 41.667 0.00 0.00 0.00 4.44
2285 6855 5.359292 ACAGTAAATAGTACTCCCTCCGTTC 59.641 44.000 0.00 0.00 0.00 3.95
2286 6856 4.578105 AGTAAATAGTACTCCCTCCGTTCG 59.422 45.833 0.00 0.00 0.00 3.95
2287 6857 1.978454 ATAGTACTCCCTCCGTTCGG 58.022 55.000 0.00 4.74 0.00 4.30
2288 6858 0.911769 TAGTACTCCCTCCGTTCGGA 59.088 55.000 13.34 13.34 0.00 4.55
2289 6859 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
2290 6860 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
2291 6861 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
2292 6862 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2293 6863 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2294 6864 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2295 6865 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2296 6866 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2297 6867 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2298 6868 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2299 6869 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
2300 6870 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
2301 6871 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
2302 6872 2.222508 CGTTCGGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
2303 6873 2.991190 GTTCGGAATTACTTGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
2304 6874 3.306917 TCGGAATTACTTGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
2305 6875 3.655486 TCGGAATTACTTGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
2306 6876 4.250464 TCGGAATTACTTGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
2307 6877 4.092821 TCGGAATTACTTGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
2308 6878 4.662145 GGAATTACTTGTCGCAGAAATGG 58.338 43.478 0.00 0.00 39.69 3.16
2309 6879 4.394920 GGAATTACTTGTCGCAGAAATGGA 59.605 41.667 0.00 0.00 39.69 3.41
2310 6880 5.066505 GGAATTACTTGTCGCAGAAATGGAT 59.933 40.000 0.00 0.00 39.69 3.41
2311 6881 4.944962 TTACTTGTCGCAGAAATGGATG 57.055 40.909 0.00 0.00 39.69 3.51
2312 6882 2.783135 ACTTGTCGCAGAAATGGATGT 58.217 42.857 0.00 0.00 39.69 3.06
2313 6883 3.937814 ACTTGTCGCAGAAATGGATGTA 58.062 40.909 0.00 0.00 39.69 2.29
2314 6884 4.517285 ACTTGTCGCAGAAATGGATGTAT 58.483 39.130 0.00 0.00 39.69 2.29
2315 6885 4.572389 ACTTGTCGCAGAAATGGATGTATC 59.428 41.667 0.00 0.00 39.69 2.24
2316 6886 4.406648 TGTCGCAGAAATGGATGTATCT 57.593 40.909 0.00 0.00 39.69 1.98
2317 6887 5.529581 TGTCGCAGAAATGGATGTATCTA 57.470 39.130 0.00 0.00 39.69 1.98
2318 6888 5.912892 TGTCGCAGAAATGGATGTATCTAA 58.087 37.500 0.00 0.00 39.69 2.10
2319 6889 6.345298 TGTCGCAGAAATGGATGTATCTAAA 58.655 36.000 0.00 0.00 39.69 1.85
2320 6890 6.257849 TGTCGCAGAAATGGATGTATCTAAAC 59.742 38.462 0.00 0.00 39.69 2.01
2321 6891 6.257849 GTCGCAGAAATGGATGTATCTAAACA 59.742 38.462 0.00 0.00 39.69 2.83
2322 6892 6.992123 TCGCAGAAATGGATGTATCTAAACAT 59.008 34.615 0.00 0.00 42.75 2.71
2323 6893 8.147704 TCGCAGAAATGGATGTATCTAAACATA 58.852 33.333 0.00 0.00 40.17 2.29
2324 6894 8.939929 CGCAGAAATGGATGTATCTAAACATAT 58.060 33.333 0.00 0.00 40.17 1.78
2350 6920 9.542462 TTTTAGTTCTAGATACATCCATTTCCG 57.458 33.333 0.00 0.00 0.00 4.30
2351 6921 6.978674 AGTTCTAGATACATCCATTTCCGA 57.021 37.500 0.00 0.00 0.00 4.55
2352 6922 6.987386 AGTTCTAGATACATCCATTTCCGAG 58.013 40.000 0.00 0.00 0.00 4.63
2353 6923 6.778069 AGTTCTAGATACATCCATTTCCGAGA 59.222 38.462 0.00 0.00 0.00 4.04
2354 6924 6.576662 TCTAGATACATCCATTTCCGAGAC 57.423 41.667 0.00 0.00 0.00 3.36
2355 6925 6.068670 TCTAGATACATCCATTTCCGAGACA 58.931 40.000 0.00 0.00 0.00 3.41
2356 6926 5.614324 AGATACATCCATTTCCGAGACAA 57.386 39.130 0.00 0.00 0.00 3.18
2357 6927 5.605534 AGATACATCCATTTCCGAGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
2358 6928 3.703001 ACATCCATTTCCGAGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
2359 6929 4.819105 ACATCCATTTCCGAGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
2360 6930 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
2361 6931 5.745227 ACATCCATTTCCGAGACAAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
2362 6932 6.180472 ACATCCATTTCCGAGACAAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
2363 6933 7.335627 ACATCCATTTCCGAGACAAGTAATTA 58.664 34.615 0.00 0.00 0.00 1.40
2364 6934 7.280205 ACATCCATTTCCGAGACAAGTAATTAC 59.720 37.037 7.57 7.57 0.00 1.89
2365 6935 6.703319 TCCATTTCCGAGACAAGTAATTACA 58.297 36.000 17.65 0.00 0.00 2.41
2366 6936 7.162761 TCCATTTCCGAGACAAGTAATTACAA 58.837 34.615 17.65 0.00 0.00 2.41
2367 6937 7.662258 TCCATTTCCGAGACAAGTAATTACAAA 59.338 33.333 17.65 6.43 0.00 2.83
2368 6938 7.749126 CCATTTCCGAGACAAGTAATTACAAAC 59.251 37.037 17.65 6.26 0.00 2.93
2369 6939 6.456447 TTCCGAGACAAGTAATTACAAACG 57.544 37.500 17.65 12.48 0.00 3.60
2370 6940 4.925054 TCCGAGACAAGTAATTACAAACGG 59.075 41.667 17.65 19.04 37.37 4.44
2371 6941 4.925054 CCGAGACAAGTAATTACAAACGGA 59.075 41.667 17.65 0.00 38.09 4.69
2372 6942 5.061808 CCGAGACAAGTAATTACAAACGGAG 59.938 44.000 17.65 4.41 38.09 4.63
2373 6943 5.061808 CGAGACAAGTAATTACAAACGGAGG 59.938 44.000 17.65 1.00 0.00 4.30
2374 6944 5.243207 AGACAAGTAATTACAAACGGAGGG 58.757 41.667 17.65 0.00 0.00 4.30
2375 6945 5.012354 AGACAAGTAATTACAAACGGAGGGA 59.988 40.000 17.65 0.00 0.00 4.20
2390 6964 4.966805 ACGGAGGGAGTATTTTATCCTCAA 59.033 41.667 9.49 0.00 44.17 3.02
2398 6972 6.016777 GGAGTATTTTATCCTCAATGTGGCAG 60.017 42.308 0.00 0.00 32.51 4.85
2427 7010 4.395231 GTCCCAAACAATACTTACCTCTGC 59.605 45.833 0.00 0.00 0.00 4.26
2442 7711 2.286872 CTCTGCTAAGCCCATTGTGAG 58.713 52.381 0.00 0.00 0.00 3.51
2533 7813 0.178767 TTGACATGAGGGCATCTCCG 59.821 55.000 0.00 0.00 41.76 4.63
2611 7892 2.579201 CAGTCACGCTCCCGGAAT 59.421 61.111 0.73 0.00 39.22 3.01
2633 7914 2.671619 TTTTTCGCCGGCTCAGGG 60.672 61.111 26.68 8.63 0.00 4.45
2829 8110 1.834263 CATTCTCTCCCTTTCTCCCGT 59.166 52.381 0.00 0.00 0.00 5.28
2890 8171 0.460284 CGAAGAAGTACGCCATGCCT 60.460 55.000 0.00 0.00 0.00 4.75
3012 8293 3.479269 GGAAGTTCAGCGACGCGG 61.479 66.667 15.18 14.61 0.00 6.46
3032 8313 4.778415 CAGTCACCGCCGACCGAG 62.778 72.222 0.00 0.00 40.02 4.63
3035 8316 4.720902 TCACCGCCGACCGAGGTA 62.721 66.667 8.63 0.00 40.02 3.08
3046 8327 1.950909 GACCGAGGTAGTGGATCTCAG 59.049 57.143 0.00 0.00 34.60 3.35
3050 8331 0.033011 AGGTAGTGGATCTCAGCGGT 60.033 55.000 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
214 216 6.830873 ATTTTCATGAGAAGTTCTCCCTTG 57.169 37.500 26.37 20.52 42.73 3.61
306 2052 4.881157 ACTAGCCCTTGGGATTTTACAT 57.119 40.909 10.36 0.00 0.00 2.29
344 2654 2.420022 GCAGTCCAATACGATTGCTTGT 59.580 45.455 0.00 0.00 41.04 3.16
392 2712 7.669304 TCTGGTGATGATGAAAATACTTTGGAA 59.331 33.333 0.00 0.00 0.00 3.53
413 2733 2.906389 TCACTTATCTTGTGGCTCTGGT 59.094 45.455 0.00 0.00 36.21 4.00
414 2734 3.616956 TCACTTATCTTGTGGCTCTGG 57.383 47.619 0.00 0.00 36.21 3.86
475 2801 8.576442 CAACATTGTTAGACCCTGATAAGTTTT 58.424 33.333 0.86 0.00 0.00 2.43
602 2933 5.798015 TTTGTAAGCTGTACGAAACAACA 57.202 34.783 0.00 0.00 37.74 3.33
658 2992 6.922957 GGAAATTTGCTTTGTTCATCACTACA 59.077 34.615 1.93 0.00 0.00 2.74
663 2997 4.744137 CGTGGAAATTTGCTTTGTTCATCA 59.256 37.500 11.22 0.00 0.00 3.07
664 2998 4.150451 CCGTGGAAATTTGCTTTGTTCATC 59.850 41.667 11.22 0.00 0.00 2.92
665 2999 4.057432 CCGTGGAAATTTGCTTTGTTCAT 58.943 39.130 11.22 0.00 0.00 2.57
724 3059 3.917985 GCGAATTATTTGGTGCTCGTTTT 59.082 39.130 0.00 0.00 0.00 2.43
729 3064 3.487544 GGAGTGCGAATTATTTGGTGCTC 60.488 47.826 0.00 0.00 0.00 4.26
739 3076 3.093814 TCTAGTGGTGGAGTGCGAATTA 58.906 45.455 0.00 0.00 0.00 1.40
740 3077 1.899814 TCTAGTGGTGGAGTGCGAATT 59.100 47.619 0.00 0.00 0.00 2.17
826 5051 7.569639 CTGCTACACTTAATCAGTAGGAGTA 57.430 40.000 15.94 0.00 44.35 2.59
1051 5321 4.296690 CGCTACCGCTAGCTAGTTTTAAT 58.703 43.478 21.62 5.21 43.07 1.40
1053 5323 2.033801 CCGCTACCGCTAGCTAGTTTTA 59.966 50.000 21.62 9.33 43.07 1.52
1070 5340 1.562672 AAGTATTGGGTCTGGCCGCT 61.563 55.000 0.00 0.00 38.44 5.52
1159 5433 2.985282 CAAGCCCGCCTCAGCAAA 60.985 61.111 0.00 0.00 39.83 3.68
1169 5443 4.988598 ACGCTCACACCAAGCCCG 62.989 66.667 0.00 0.00 36.36 6.13
1172 5446 1.887242 TCACACGCTCACACCAAGC 60.887 57.895 0.00 0.00 36.38 4.01
1194 5486 4.807631 TCTCCATCGACCGGCCGA 62.808 66.667 30.73 17.19 43.16 5.54
1198 5490 2.029666 GGCATCTCCATCGACCGG 59.970 66.667 0.00 0.00 34.01 5.28
1204 5496 1.006805 CGACCTCGGCATCTCCATC 60.007 63.158 0.00 0.00 35.37 3.51
1288 5580 1.080501 CTCGTCCAGCTCGAAGCAA 60.081 57.895 9.09 0.00 45.56 3.91
1429 5754 1.006102 CGACAGCCCGAAACTCTGT 60.006 57.895 0.00 0.00 43.06 3.41
1435 5760 3.909258 GAGCGACGACAGCCCGAAA 62.909 63.158 0.00 0.00 34.64 3.46
1841 6193 3.719924 TGCAGGCATTTTCTTCTTGTTG 58.280 40.909 0.00 0.00 0.00 3.33
1844 6196 4.427312 GGTATGCAGGCATTTTCTTCTTG 58.573 43.478 12.54 0.00 37.82 3.02
1891 6243 0.392998 GTTGACCATCATCGGTGGCT 60.393 55.000 0.00 0.00 40.22 4.75
1892 6244 0.676466 TGTTGACCATCATCGGTGGC 60.676 55.000 0.00 0.00 40.22 5.01
1954 6347 1.823041 GCTGGAATGGCAGGAGCTC 60.823 63.158 4.71 4.71 41.70 4.09
2053 6468 1.802880 CGGGCAGTATCCAGAGTTTCG 60.803 57.143 0.00 0.00 0.00 3.46
2177 6742 4.507710 TGAGCTTTGGCAGATACTGTAAG 58.492 43.478 0.00 0.00 41.70 2.34
2189 6754 0.176680 TCGATCCTCTGAGCTTTGGC 59.823 55.000 0.00 0.00 39.06 4.52
2268 6838 1.492176 TCCGAACGGAGGGAGTACTAT 59.508 52.381 12.04 0.00 39.76 2.12
2276 6846 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2277 6847 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2278 6848 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
2279 6849 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
2280 6850 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
2281 6851 1.722464 TGCGACAAGTAATTCCGAACG 59.278 47.619 0.00 0.00 0.00 3.95
2282 6852 2.991190 TCTGCGACAAGTAATTCCGAAC 59.009 45.455 0.00 0.00 0.00 3.95
2283 6853 3.306917 TCTGCGACAAGTAATTCCGAA 57.693 42.857 0.00 0.00 0.00 4.30
2284 6854 3.306917 TTCTGCGACAAGTAATTCCGA 57.693 42.857 0.00 0.00 0.00 4.55
2285 6855 4.334443 CATTTCTGCGACAAGTAATTCCG 58.666 43.478 0.00 0.00 0.00 4.30
2286 6856 4.394920 TCCATTTCTGCGACAAGTAATTCC 59.605 41.667 0.00 0.00 0.00 3.01
2287 6857 5.545658 TCCATTTCTGCGACAAGTAATTC 57.454 39.130 0.00 0.00 0.00 2.17
2288 6858 5.415701 ACATCCATTTCTGCGACAAGTAATT 59.584 36.000 0.00 0.00 0.00 1.40
2289 6859 4.943705 ACATCCATTTCTGCGACAAGTAAT 59.056 37.500 0.00 0.00 0.00 1.89
2290 6860 4.323417 ACATCCATTTCTGCGACAAGTAA 58.677 39.130 0.00 0.00 0.00 2.24
2291 6861 3.937814 ACATCCATTTCTGCGACAAGTA 58.062 40.909 0.00 0.00 0.00 2.24
2292 6862 2.783135 ACATCCATTTCTGCGACAAGT 58.217 42.857 0.00 0.00 0.00 3.16
2293 6863 4.813161 AGATACATCCATTTCTGCGACAAG 59.187 41.667 0.00 0.00 0.00 3.16
2294 6864 4.769688 AGATACATCCATTTCTGCGACAA 58.230 39.130 0.00 0.00 0.00 3.18
2295 6865 4.406648 AGATACATCCATTTCTGCGACA 57.593 40.909 0.00 0.00 0.00 4.35
2296 6866 6.257849 TGTTTAGATACATCCATTTCTGCGAC 59.742 38.462 0.00 0.00 0.00 5.19
2297 6867 6.345298 TGTTTAGATACATCCATTTCTGCGA 58.655 36.000 0.00 0.00 0.00 5.10
2298 6868 6.603237 TGTTTAGATACATCCATTTCTGCG 57.397 37.500 0.00 0.00 0.00 5.18
2324 6894 9.542462 CGGAAATGGATGTATCTAGAACTAAAA 57.458 33.333 0.00 0.00 0.00 1.52
2325 6895 8.920174 TCGGAAATGGATGTATCTAGAACTAAA 58.080 33.333 0.00 0.00 0.00 1.85
2326 6896 8.473358 TCGGAAATGGATGTATCTAGAACTAA 57.527 34.615 0.00 0.00 0.00 2.24
2327 6897 7.942894 TCTCGGAAATGGATGTATCTAGAACTA 59.057 37.037 0.00 0.00 0.00 2.24
2328 6898 6.778069 TCTCGGAAATGGATGTATCTAGAACT 59.222 38.462 0.00 0.00 0.00 3.01
2329 6899 6.864165 GTCTCGGAAATGGATGTATCTAGAAC 59.136 42.308 0.00 0.00 0.00 3.01
2330 6900 6.549736 TGTCTCGGAAATGGATGTATCTAGAA 59.450 38.462 0.00 0.00 0.00 2.10
2331 6901 6.068670 TGTCTCGGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
2332 6902 6.332735 TGTCTCGGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
2333 6903 6.323996 ACTTGTCTCGGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
2334 6904 5.129485 ACTTGTCTCGGAAATGGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
2335 6905 5.360591 ACTTGTCTCGGAAATGGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
2336 6906 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
2337 6907 4.819105 ACTTGTCTCGGAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
2338 6908 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
2339 6909 6.683974 AATTACTTGTCTCGGAAATGGATG 57.316 37.500 0.00 0.00 0.00 3.51
2340 6910 7.335627 TGTAATTACTTGTCTCGGAAATGGAT 58.664 34.615 16.33 0.00 0.00 3.41
2341 6911 6.703319 TGTAATTACTTGTCTCGGAAATGGA 58.297 36.000 16.33 0.00 0.00 3.41
2342 6912 6.978343 TGTAATTACTTGTCTCGGAAATGG 57.022 37.500 16.33 0.00 0.00 3.16
2343 6913 7.477422 CGTTTGTAATTACTTGTCTCGGAAATG 59.523 37.037 16.33 7.01 0.00 2.32
2344 6914 7.360607 CCGTTTGTAATTACTTGTCTCGGAAAT 60.361 37.037 16.33 0.00 35.94 2.17
2345 6915 6.073657 CCGTTTGTAATTACTTGTCTCGGAAA 60.074 38.462 16.33 3.07 35.94 3.13
2346 6916 5.406175 CCGTTTGTAATTACTTGTCTCGGAA 59.594 40.000 16.33 0.00 35.94 4.30
2347 6917 4.925054 CCGTTTGTAATTACTTGTCTCGGA 59.075 41.667 16.33 0.00 35.94 4.55
2348 6918 4.925054 TCCGTTTGTAATTACTTGTCTCGG 59.075 41.667 16.33 17.87 35.35 4.63
2349 6919 5.061808 CCTCCGTTTGTAATTACTTGTCTCG 59.938 44.000 16.33 11.38 0.00 4.04
2350 6920 5.350640 CCCTCCGTTTGTAATTACTTGTCTC 59.649 44.000 16.33 1.71 0.00 3.36
2351 6921 5.012354 TCCCTCCGTTTGTAATTACTTGTCT 59.988 40.000 16.33 0.00 0.00 3.41
2352 6922 5.240121 TCCCTCCGTTTGTAATTACTTGTC 58.760 41.667 16.33 4.42 0.00 3.18
2353 6923 5.221783 ACTCCCTCCGTTTGTAATTACTTGT 60.222 40.000 16.33 0.00 0.00 3.16
2354 6924 5.243207 ACTCCCTCCGTTTGTAATTACTTG 58.757 41.667 16.33 4.08 0.00 3.16
2355 6925 5.494390 ACTCCCTCCGTTTGTAATTACTT 57.506 39.130 16.33 0.00 0.00 2.24
2356 6926 6.803366 ATACTCCCTCCGTTTGTAATTACT 57.197 37.500 16.33 0.00 0.00 2.24
2357 6927 7.854557 AAATACTCCCTCCGTTTGTAATTAC 57.145 36.000 8.75 8.75 0.00 1.89
2359 6929 9.117183 GATAAAATACTCCCTCCGTTTGTAATT 57.883 33.333 0.00 0.00 0.00 1.40
2360 6930 7.718314 GGATAAAATACTCCCTCCGTTTGTAAT 59.282 37.037 0.00 0.00 0.00 1.89
2361 6931 7.049754 GGATAAAATACTCCCTCCGTTTGTAA 58.950 38.462 0.00 0.00 0.00 2.41
2362 6932 6.384886 AGGATAAAATACTCCCTCCGTTTGTA 59.615 38.462 0.00 0.00 31.49 2.41
2363 6933 5.191124 AGGATAAAATACTCCCTCCGTTTGT 59.809 40.000 0.00 0.00 31.49 2.83
2364 6934 5.681639 AGGATAAAATACTCCCTCCGTTTG 58.318 41.667 0.00 0.00 31.49 2.93
2365 6935 5.427481 TGAGGATAAAATACTCCCTCCGTTT 59.573 40.000 0.00 0.00 39.62 3.60
2366 6936 4.966805 TGAGGATAAAATACTCCCTCCGTT 59.033 41.667 0.00 0.00 39.62 4.44
2367 6937 4.553678 TGAGGATAAAATACTCCCTCCGT 58.446 43.478 0.00 0.00 39.62 4.69
2368 6938 5.546621 TTGAGGATAAAATACTCCCTCCG 57.453 43.478 0.00 0.00 39.62 4.63
2369 6939 6.712547 CACATTGAGGATAAAATACTCCCTCC 59.287 42.308 0.00 0.00 39.62 4.30
2370 6940 6.712547 CCACATTGAGGATAAAATACTCCCTC 59.287 42.308 0.00 0.00 39.62 4.30
2371 6941 6.605119 CCACATTGAGGATAAAATACTCCCT 58.395 40.000 0.00 0.00 39.62 4.20
2372 6942 5.241728 GCCACATTGAGGATAAAATACTCCC 59.758 44.000 4.11 0.00 39.62 4.30
2373 6943 5.827797 TGCCACATTGAGGATAAAATACTCC 59.172 40.000 4.11 0.00 39.62 3.85
2374 6944 6.514048 GCTGCCACATTGAGGATAAAATACTC 60.514 42.308 4.11 0.00 40.81 2.59
2375 6945 5.300286 GCTGCCACATTGAGGATAAAATACT 59.700 40.000 4.11 0.00 0.00 2.12
2390 6964 2.036256 GGACCTTGGCTGCCACAT 59.964 61.111 23.30 9.74 30.78 3.21
2398 6972 2.525368 AGTATTGTTTGGGACCTTGGC 58.475 47.619 0.00 0.00 0.00 4.52
2427 7010 3.005554 CACACTCTCACAATGGGCTTAG 58.994 50.000 0.00 0.00 0.00 2.18
2442 7711 1.129251 CGCCATGTTGACATCACACTC 59.871 52.381 0.00 0.00 33.61 3.51
2540 7820 2.204090 GGGAGGACCTGTTGGGGA 60.204 66.667 0.00 0.00 40.03 4.81
2551 7831 1.378514 GCAAAATCGCCTGGGAGGA 60.379 57.895 0.00 0.00 37.67 3.71
2607 7888 1.135939 CGGCGAAAAACGGGATTCC 59.864 57.895 0.00 0.00 42.83 3.01
2633 7914 4.999939 CGCCGGCACCAGTTTTGC 63.000 66.667 28.98 0.00 39.41 3.68
2829 8110 3.327404 GAGCGGGAGGGGGTTTGA 61.327 66.667 0.00 0.00 0.00 2.69
3031 8312 0.033011 ACCGCTGAGATCCACTACCT 60.033 55.000 0.00 0.00 0.00 3.08
3032 8313 0.103208 CACCGCTGAGATCCACTACC 59.897 60.000 0.00 0.00 0.00 3.18
3033 8314 1.103803 TCACCGCTGAGATCCACTAC 58.896 55.000 0.00 0.00 0.00 2.73
3034 8315 1.103803 GTCACCGCTGAGATCCACTA 58.896 55.000 0.00 0.00 0.00 2.74
3035 8316 0.900182 TGTCACCGCTGAGATCCACT 60.900 55.000 0.00 0.00 0.00 4.00
3050 8331 2.685017 AGCTCGGCCTCCATGTCA 60.685 61.111 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.