Multiple sequence alignment - TraesCS1A01G035900

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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 TraesCS1A01G035900 chr1A 100.000 5747 0 0 1 5747 19934704 19928958 0.000000e+00 10613.0
1 TraesCS1A01G035900 chr1A 95.268 634 26 2 1 632 19985055 19984424 0.000000e+00 1002.0
2 TraesCS1A01G035900 chr1B 90.397 2874 241 23 1633 4481 26485873 26488736 0.000000e+00 3746.0
3 TraesCS1A01G035900 chr1B 90.397 2874 241 23 1633 4481 26495117 26497980 0.000000e+00 3746.0
4 TraesCS1A01G035900 chr1B 88.741 3073 286 35 1446 4476 25945882 25942828 0.000000e+00 3703.0
5 TraesCS1A01G035900 chr1B 88.338 2358 231 26 2458 4794 26427985 26430319 0.000000e+00 2791.0
6 TraesCS1A01G035900 chr1B 90.270 1963 167 11 2408 4352 25820758 25818802 0.000000e+00 2545.0
7 TraesCS1A01G035900 chr1B 86.721 2327 246 38 2421 4710 25895130 25892830 0.000000e+00 2527.0
8 TraesCS1A01G035900 chr1B 90.000 1580 136 8 732 2304 25822321 25820757 0.000000e+00 2023.0
9 TraesCS1A01G035900 chr1B 86.682 871 104 3 1367 2225 26426478 26427348 0.000000e+00 955.0
10 TraesCS1A01G035900 chr1B 85.012 834 120 3 1396 2225 25896855 25896023 0.000000e+00 843.0
11 TraesCS1A01G035900 chr1B 96.739 460 15 0 5288 5747 25815422 25814963 0.000000e+00 767.0
12 TraesCS1A01G035900 chr1B 96.739 460 15 0 5288 5747 25826375 25825916 0.000000e+00 767.0
13 TraesCS1A01G035900 chr1B 94.581 406 13 5 970 1375 26425980 26426376 2.270000e-173 619.0
14 TraesCS1A01G035900 chr1B 88.155 515 22 15 4801 5287 2326335 2325832 1.390000e-160 577.0
15 TraesCS1A01G035900 chr1B 87.905 463 29 13 4349 4788 25815885 25815427 2.370000e-143 520.0
16 TraesCS1A01G035900 chr1B 87.905 463 29 13 4349 4788 25826838 25826380 2.370000e-143 520.0
17 TraesCS1A01G035900 chr1B 85.135 518 54 11 3918 4431 26433240 26433738 5.140000e-140 508.0
18 TraesCS1A01G035900 chr1B 83.249 394 55 8 175 568 581103150 581102768 9.160000e-93 351.0
19 TraesCS1A01G035900 chr1B 81.843 369 37 18 728 1088 25946528 25946182 3.390000e-72 283.0
20 TraesCS1A01G035900 chr1B 94.048 168 9 1 2 169 112758236 112758402 2.660000e-63 254.0
21 TraesCS1A01G035900 chr1B 90.419 167 16 0 5581 5747 683326549 683326715 2.700000e-53 220.0
22 TraesCS1A01G035900 chr1B 86.932 176 6 4 5288 5463 26430314 26430472 1.270000e-41 182.0
23 TraesCS1A01G035900 chr1B 85.143 175 8 3 572 736 25824895 25824729 4.610000e-36 163.0
24 TraesCS1A01G035900 chr1B 86.992 123 10 4 5463 5581 26430517 26430637 3.610000e-27 134.0
25 TraesCS1A01G035900 chr1B 98.276 58 1 0 5463 5520 25814925 25814868 1.020000e-17 102.0
26 TraesCS1A01G035900 chr1B 93.443 61 4 0 4421 4481 26439393 26439453 2.210000e-14 91.6
27 TraesCS1A01G035900 chr1D 89.326 2061 176 15 2458 4476 17651039 17648981 0.000000e+00 2547.0
28 TraesCS1A01G035900 chr1D 77.868 1979 370 41 2456 4385 17659216 17657257 0.000000e+00 1166.0
29 TraesCS1A01G035900 chr1D 83.253 830 137 2 1397 2225 17652383 17651555 0.000000e+00 761.0
30 TraesCS1A01G035900 chr1D 87.778 450 44 4 647 1088 17653027 17652581 3.070000e-142 516.0
31 TraesCS1A01G035900 chr1D 87.937 315 28 7 4978 5287 1078335 1078026 4.230000e-96 363.0
32 TraesCS1A01G035900 chr1D 87.937 315 29 6 4978 5287 1079238 1078928 4.230000e-96 363.0
33 TraesCS1A01G035900 chr1D 85.942 313 35 4 175 482 17653560 17653252 5.550000e-85 326.0
34 TraesCS1A01G035900 chr1D 100.000 36 0 0 1263 1298 17652468 17652433 3.720000e-07 67.6
35 TraesCS1A01G035900 chr7A 75.888 1605 326 46 2458 4019 15539280 15537694 0.000000e+00 763.0
36 TraesCS1A01G035900 chr3A 89.101 523 17 15 4794 5288 35466144 35465634 1.060000e-171 614.0
37 TraesCS1A01G035900 chr3A 90.230 348 10 17 4794 5123 35468258 35467917 3.180000e-117 433.0
38 TraesCS1A01G035900 chr3A 80.658 486 56 26 4794 5256 743247155 743246685 5.510000e-90 342.0
39 TraesCS1A01G035900 chr3A 93.642 173 6 1 5115 5287 35466739 35466572 2.660000e-63 254.0
40 TraesCS1A01G035900 chr3A 88.393 112 11 2 5178 5287 37233916 37234027 3.610000e-27 134.0
41 TraesCS1A01G035900 chr3A 91.209 91 6 1 5199 5287 37232619 37232709 7.820000e-24 122.0
42 TraesCS1A01G035900 chr7B 88.931 524 19 12 4794 5289 726302264 726301752 1.370000e-170 610.0
43 TraesCS1A01G035900 chr4A 77.322 829 174 13 1407 2228 604772923 604773744 1.450000e-130 477.0
44 TraesCS1A01G035900 chr4A 93.567 171 11 0 2 172 519796404 519796234 7.390000e-64 255.0
45 TraesCS1A01G035900 chr4A 91.617 167 14 0 5581 5747 699589260 699589426 1.250000e-56 231.0
46 TraesCS1A01G035900 chr4A 90.643 171 15 1 2 171 614000548 614000718 5.790000e-55 226.0
47 TraesCS1A01G035900 chr4A 87.387 111 14 0 4792 4902 508145796 508145686 1.680000e-25 128.0
48 TraesCS1A01G035900 chr4A 85.135 74 7 3 3565 3636 732098717 732098788 7.990000e-09 73.1
49 TraesCS1A01G035900 chr5D 77.081 829 170 18 1410 2228 559915719 559916537 1.460000e-125 460.0
50 TraesCS1A01G035900 chr2A 94.152 171 10 0 2 172 181791232 181791402 1.590000e-65 261.0
51 TraesCS1A01G035900 chr2B 93.642 173 11 0 2 174 527660751 527660579 5.710000e-65 259.0
52 TraesCS1A01G035900 chr5B 93.827 162 10 0 5581 5742 353983188 353983027 1.600000e-60 244.0
53 TraesCS1A01G035900 chr2D 92.216 167 13 0 5581 5747 112005116 112005282 2.680000e-58 237.0
54 TraesCS1A01G035900 chr7D 92.216 167 11 1 5581 5747 458137266 458137430 9.630000e-58 235.0
55 TraesCS1A01G035900 chr7D 88.690 168 6 7 3 170 476703756 476703602 5.880000e-45 193.0
56 TraesCS1A01G035900 chr3D 91.124 169 14 1 5580 5747 175426983 175427151 1.610000e-55 228.0
57 TraesCS1A01G035900 chr6B 90.476 168 16 0 5580 5747 611990445 611990612 7.490000e-54 222.0


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 TraesCS1A01G035900 chr1A 19928958 19934704 5746 True 10613.000000 10613 100.000000 1 5747 1 chr1A.!!$R1 5746
1 TraesCS1A01G035900 chr1A 19984424 19985055 631 True 1002.000000 1002 95.268000 1 632 1 chr1A.!!$R2 631
2 TraesCS1A01G035900 chr1B 26485873 26488736 2863 False 3746.000000 3746 90.397000 1633 4481 1 chr1B.!!$F2 2848
3 TraesCS1A01G035900 chr1B 26495117 26497980 2863 False 3746.000000 3746 90.397000 1633 4481 1 chr1B.!!$F3 2848
4 TraesCS1A01G035900 chr1B 25942828 25946528 3700 True 1993.000000 3703 85.292000 728 4476 2 chr1B.!!$R5 3748
5 TraesCS1A01G035900 chr1B 25892830 25896855 4025 True 1685.000000 2527 85.866500 1396 4710 2 chr1B.!!$R4 3314
6 TraesCS1A01G035900 chr1B 25814868 25826838 11970 True 925.875000 2545 91.622125 572 5747 8 chr1B.!!$R3 5175
7 TraesCS1A01G035900 chr1B 26425980 26433738 7758 False 864.833333 2791 88.110000 970 5581 6 chr1B.!!$F6 4611
8 TraesCS1A01G035900 chr1B 2325832 2326335 503 True 577.000000 577 88.155000 4801 5287 1 chr1B.!!$R1 486
9 TraesCS1A01G035900 chr1D 17648981 17659216 10235 True 897.266667 2547 87.361167 175 4476 6 chr1D.!!$R2 4301
10 TraesCS1A01G035900 chr1D 1078026 1079238 1212 True 363.000000 363 87.937000 4978 5287 2 chr1D.!!$R1 309
11 TraesCS1A01G035900 chr7A 15537694 15539280 1586 True 763.000000 763 75.888000 2458 4019 1 chr7A.!!$R1 1561
12 TraesCS1A01G035900 chr3A 35465634 35468258 2624 True 433.666667 614 90.991000 4794 5288 3 chr3A.!!$R2 494
13 TraesCS1A01G035900 chr7B 726301752 726302264 512 True 610.000000 610 88.931000 4794 5289 1 chr7B.!!$R1 495
14 TraesCS1A01G035900 chr4A 604772923 604773744 821 False 477.000000 477 77.322000 1407 2228 1 chr4A.!!$F1 821
15 TraesCS1A01G035900 chr5D 559915719 559916537 818 False 460.000000 460 77.081000 1410 2228 1 chr5D.!!$F1 818

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
847 9863 0.249911 AGCGACGGCCTAATCATTCC 60.250 55.0 0.0 0.0 41.24 3.01 F
1345 10405 0.391130 TCCGGAAAGATTGAGCGTGG 60.391 55.0 0.0 0.0 0.00 4.94 F
2086 11291 0.244994 CTCTTGTGTCGGTCTCCCAG 59.755 60.0 0.0 0.0 0.00 4.45 F
3026 12995 0.539051 CTGAAGAGCGTGGGAGGAAT 59.461 55.0 0.0 0.0 0.00 3.01 F
4157 14168 0.593128 CTCCTTTTGGTGAAGGTGCG 59.407 55.0 3.8 0.0 45.24 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1712 10911 1.016653 GTCTTCAGAAGGTCAGCCGC 61.017 60.000 10.42 0.0 40.50 6.53 R
3252 13221 1.251251 GCAAGCTCCTGGTCAATGTT 58.749 50.000 0.00 0.0 0.00 2.71 R
3387 13359 1.073199 CCAGGCCTCGACAACCTTT 59.927 57.895 0.00 0.0 0.00 3.11 R
4229 14240 0.398381 AGAACCCTTTGGCCTTTGCA 60.398 50.000 3.32 0.0 40.13 4.08 R
5539 21601 0.597898 TTCATTGTCGAACGCACCGA 60.598 50.000 0.00 0.0 0.00 4.69 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
57 58 3.742882 CGACATATGCTGACGGAATTGAT 59.257 43.478 1.58 0.00 38.98 2.57
234 5717 5.437289 TCTGTAGTTTTTCGACGGTTCTA 57.563 39.130 0.00 0.00 31.49 2.10
261 5749 3.519510 TCAAGATCTTCAAGACCGGGATT 59.480 43.478 6.32 0.00 0.00 3.01
268 5756 5.076873 TCTTCAAGACCGGGATTCAAAATT 58.923 37.500 6.32 0.00 0.00 1.82
269 5757 6.242396 TCTTCAAGACCGGGATTCAAAATTA 58.758 36.000 6.32 0.00 0.00 1.40
272 5760 6.713276 TCAAGACCGGGATTCAAAATTAGTA 58.287 36.000 6.32 0.00 0.00 1.82
482 5970 7.106439 TGGTGATGTAAATTTCTTTGTGTGT 57.894 32.000 0.00 0.00 0.00 3.72
492 5980 2.285083 TCTTTGTGTGTGGTTTCTCCG 58.715 47.619 0.00 0.00 39.52 4.63
500 5988 1.210967 TGTGGTTTCTCCGGACTGTTT 59.789 47.619 0.00 0.00 39.52 2.83
501 5989 1.602377 GTGGTTTCTCCGGACTGTTTG 59.398 52.381 0.00 0.00 39.52 2.93
520 6008 7.601886 ACTGTTTGAGAGAGAAGTTCATGTATG 59.398 37.037 5.50 0.00 0.00 2.39
625 7217 1.002468 GCAGATTTGTTGTCTGTGCGT 60.002 47.619 5.19 0.00 43.86 5.24
626 7218 2.223144 GCAGATTTGTTGTCTGTGCGTA 59.777 45.455 5.19 0.00 43.86 4.42
627 7219 3.120199 GCAGATTTGTTGTCTGTGCGTAT 60.120 43.478 5.19 0.00 43.86 3.06
628 7220 4.092821 GCAGATTTGTTGTCTGTGCGTATA 59.907 41.667 5.19 0.00 43.86 1.47
629 7221 5.220662 GCAGATTTGTTGTCTGTGCGTATAT 60.221 40.000 5.19 0.00 43.86 0.86
630 7222 6.019075 GCAGATTTGTTGTCTGTGCGTATATA 60.019 38.462 5.19 0.00 43.86 0.86
631 7223 7.465379 GCAGATTTGTTGTCTGTGCGTATATAA 60.465 37.037 5.19 0.00 43.86 0.98
632 7224 7.846107 CAGATTTGTTGTCTGTGCGTATATAAC 59.154 37.037 0.00 0.00 38.58 1.89
650 7242 6.265196 TATATAACTATATAACACCGGGGCGG 59.735 42.308 1.73 0.00 39.09 6.13
651 7243 8.611035 TATATAACTATATAACACCGGGGCGGG 61.611 44.444 1.73 0.00 38.36 6.13
669 7261 2.251642 GCCCGCGAACACAAAGAGT 61.252 57.895 8.23 0.00 0.00 3.24
724 7323 4.394078 CCTTCGTCGTCGTCGCCA 62.394 66.667 7.01 0.00 38.33 5.69
786 9801 4.035102 GCCTTTCCTCCACGGCCT 62.035 66.667 0.00 0.00 36.56 5.19
805 9820 2.112297 TTTCGCCGCCCACTTTCT 59.888 55.556 0.00 0.00 0.00 2.52
806 9821 2.258013 TTTCGCCGCCCACTTTCTG 61.258 57.895 0.00 0.00 0.00 3.02
807 9822 2.668185 TTTCGCCGCCCACTTTCTGA 62.668 55.000 0.00 0.00 0.00 3.27
808 9823 2.436646 CGCCGCCCACTTTCTGAT 60.437 61.111 0.00 0.00 0.00 2.90
847 9863 0.249911 AGCGACGGCCTAATCATTCC 60.250 55.000 0.00 0.00 41.24 3.01
887 9908 1.704070 AGAGAGCCCCCATCAATCATC 59.296 52.381 0.00 0.00 0.00 2.92
914 9935 1.398390 CTACAGTTCCGCAATTGCTCC 59.602 52.381 26.86 12.15 39.32 4.70
971 9992 4.577152 CCCATGGCAGCCGATAAA 57.423 55.556 6.09 0.00 0.00 1.40
986 10007 4.816385 GCCGATAAACATCCATCAAGAGAA 59.184 41.667 0.00 0.00 0.00 2.87
1023 10045 1.903183 AGCTAGGTTTCCACTCTCCAC 59.097 52.381 0.00 0.00 0.00 4.02
1080 10102 2.655685 GGCTCGCGGATCTCGTTC 60.656 66.667 6.13 2.45 41.72 3.95
1345 10405 0.391130 TCCGGAAAGATTGAGCGTGG 60.391 55.000 0.00 0.00 0.00 4.94
1365 10535 2.032634 GCTCGGCCATGACGTGAAA 61.033 57.895 2.24 0.00 34.61 2.69
1393 10567 2.690510 AGGAGCAGAGGAAGGGGC 60.691 66.667 0.00 0.00 0.00 5.80
1444 10622 2.435059 GCGTTGGGTCCTCTGCTC 60.435 66.667 0.00 0.00 0.00 4.26
1517 10708 2.725008 GTGAGATCCGCTCCCTCG 59.275 66.667 0.00 0.00 43.26 4.63
1521 10712 0.820074 GAGATCCGCTCCCTCGAGAA 60.820 60.000 15.71 0.04 38.52 2.87
1604 10795 2.430694 CAGGTGAAGATATGGGTGTCGA 59.569 50.000 0.00 0.00 0.00 4.20
1668 10867 4.457496 CATCCACCAGCTCGGCGT 62.457 66.667 6.85 0.00 39.03 5.68
1697 10896 1.447838 GATGACGGCGGCTTCAAGA 60.448 57.895 21.77 0.00 0.00 3.02
1712 10911 3.058639 CTTCAAGAAGTTCTTCCGCAAGG 60.059 47.826 15.35 3.09 43.59 3.61
1736 10935 2.333014 CTGACCTTCTGAAGACGCTTC 58.667 52.381 18.68 11.24 0.00 3.86
1737 10936 1.686587 TGACCTTCTGAAGACGCTTCA 59.313 47.619 18.68 17.39 0.00 3.02
1802 11001 5.134202 TCGTATCAAGCAAGTCAAAGAGA 57.866 39.130 0.00 0.00 0.00 3.10
1818 11017 6.750039 GTCAAAGAGATGAAGACTAGCTACAC 59.250 42.308 0.00 0.00 0.00 2.90
1912 11114 3.543884 GGCACACCTTGTCGGAATA 57.456 52.632 0.00 0.00 36.31 1.75
1961 11163 3.868077 GTGGATGATGGAAGAAGAGAACG 59.132 47.826 0.00 0.00 0.00 3.95
2086 11291 0.244994 CTCTTGTGTCGGTCTCCCAG 59.755 60.000 0.00 0.00 0.00 4.45
2092 11297 3.068691 TCGGTCTCCCAGAAGCCG 61.069 66.667 0.00 0.00 43.32 5.52
2113 11318 6.152661 AGCCGGATACAAAGAAAATCATCAAA 59.847 34.615 5.05 0.00 0.00 2.69
2134 11339 1.315257 ATGTGATTTCGCAGGTGCCC 61.315 55.000 0.00 0.00 39.97 5.36
2146 11351 0.632835 AGGTGCCCCACAATGATGAT 59.367 50.000 0.00 0.00 35.86 2.45
2176 11381 4.077552 AGATATGGAGAGCTGGGATGAT 57.922 45.455 0.00 0.00 0.00 2.45
2398 11646 9.680315 ACGATTGGAATTTTACGATTGTTTTTA 57.320 25.926 0.00 0.00 26.70 1.52
2469 12438 3.068307 CCCCTGTCTTAGGTATCTTGTCG 59.932 52.174 0.00 0.00 45.80 4.35
2505 12474 7.986085 ATATGGTCTACATTAGCATGGAAAC 57.014 36.000 0.00 0.00 41.03 2.78
2506 12475 5.754782 ATGGTCTACATTAGCATGGAAACA 58.245 37.500 0.00 0.00 40.66 2.83
2507 12476 5.590259 ATGGTCTACATTAGCATGGAAACAC 59.410 40.000 0.00 0.00 39.41 3.32
2544 12513 6.668541 TTCCAGAGAATAATTCTTCAAGCG 57.331 37.500 6.37 0.00 40.87 4.68
2640 12609 1.149288 TGACACCTCTAAGTGACCCCT 59.851 52.381 0.00 0.00 40.34 4.79
2645 12614 2.024177 ACCTCTAAGTGACCCCTACTCC 60.024 54.545 0.00 0.00 0.00 3.85
3025 12994 0.541998 TCTGAAGAGCGTGGGAGGAA 60.542 55.000 0.00 0.00 0.00 3.36
3026 12995 0.539051 CTGAAGAGCGTGGGAGGAAT 59.461 55.000 0.00 0.00 0.00 3.01
3522 13494 5.049060 GTGATGCTACATGATCTAGAGACGT 60.049 44.000 0.00 0.00 0.00 4.34
3596 13568 8.459635 CAGCTCACTAAACTACAACATCTACTA 58.540 37.037 0.00 0.00 0.00 1.82
3609 13581 8.991783 ACAACATCTACTAGGTAACAGCTATA 57.008 34.615 0.00 0.00 41.41 1.31
3763 13771 9.208022 TGTACAGTGTAAAGAATCTCAAGAATG 57.792 33.333 4.11 0.00 0.00 2.67
3826 13834 1.142870 TGGCAGCTACAAACTCCAGTT 59.857 47.619 0.00 0.00 40.50 3.16
3837 13845 3.314541 AACTCCAGTTCGTGTGGATAC 57.685 47.619 4.06 0.00 43.33 2.24
3857 13865 3.614092 ACATGGTGGTAATTCAGCTCTG 58.386 45.455 0.00 0.00 36.25 3.35
3899 13907 2.238395 GTCTCCTCTTCCATCTTGCCTT 59.762 50.000 0.00 0.00 0.00 4.35
3907 13915 6.065976 TCTTCCATCTTGCCTTCAAAGATA 57.934 37.500 0.00 0.00 0.00 1.98
3910 13918 5.759059 TCCATCTTGCCTTCAAAGATATGT 58.241 37.500 0.00 0.00 0.00 2.29
3919 13927 4.277672 CCTTCAAAGATATGTGATGGGCAG 59.722 45.833 4.80 0.00 36.11 4.85
3921 13929 1.888215 AAGATATGTGATGGGCAGCG 58.112 50.000 0.00 0.00 0.00 5.18
3980 13991 2.238144 AGCACTCACCAGTCTTGCATAT 59.762 45.455 0.00 0.00 0.00 1.78
4049 14060 1.580815 GAGAGCTGCCTGCATTACTC 58.419 55.000 0.00 8.21 45.94 2.59
4056 14067 1.483827 TGCCTGCATTACTCTCTCTGG 59.516 52.381 0.00 0.00 0.00 3.86
4057 14068 1.484240 GCCTGCATTACTCTCTCTGGT 59.516 52.381 0.00 0.00 0.00 4.00
4058 14069 2.741228 GCCTGCATTACTCTCTCTGGTG 60.741 54.545 0.00 0.00 0.00 4.17
4065 14076 5.819901 GCATTACTCTCTCTGGTGCTTTATT 59.180 40.000 0.00 0.00 0.00 1.40
4115 14126 1.078143 GCAAGGCAGAGGATTCCGT 60.078 57.895 0.00 0.00 0.00 4.69
4124 14135 3.004315 GCAGAGGATTCCGTTGTTTGAAA 59.996 43.478 10.05 0.00 0.00 2.69
4138 14149 6.343924 CGTTGTTTGAAAGAGTTCGTTTATGC 60.344 38.462 0.00 0.00 36.46 3.14
4157 14168 0.593128 CTCCTTTTGGTGAAGGTGCG 59.407 55.000 3.80 0.00 45.24 5.34
4229 14240 9.199982 CTTCTGCTGTCAATTTTTGTATCAATT 57.800 29.630 0.00 0.00 0.00 2.32
4239 14250 4.613925 TTTGTATCAATTGCAAAGGCCA 57.386 36.364 5.01 0.00 40.13 5.36
4241 14252 4.613925 TGTATCAATTGCAAAGGCCAAA 57.386 36.364 5.01 0.00 40.13 3.28
4251 14262 2.593026 CAAAGGCCAAAGGGTTCTACA 58.407 47.619 5.01 0.00 36.17 2.74
4272 14283 1.003233 GGTCTTGAGCACCTCCCAC 60.003 63.158 0.00 0.00 0.00 4.61
4293 14304 5.374080 CACATCTGAAACATGTACACGTTC 58.626 41.667 7.90 7.76 32.48 3.95
4373 17304 2.338577 AGGAAGCAAATCTCCATCCG 57.661 50.000 0.00 0.00 32.22 4.18
4376 17307 3.016736 GGAAGCAAATCTCCATCCGAAA 58.983 45.455 0.00 0.00 0.00 3.46
4385 17316 1.486310 CTCCATCCGAAACATCCCAGA 59.514 52.381 0.00 0.00 0.00 3.86
4392 17323 5.174037 TCCGAAACATCCCAGATTAACTT 57.826 39.130 0.00 0.00 0.00 2.66
4398 17329 7.454260 AAACATCCCAGATTAACTTTCAGAC 57.546 36.000 0.00 0.00 0.00 3.51
4404 17338 8.617290 TCCCAGATTAACTTTCAGACTAAAAC 57.383 34.615 0.00 0.00 0.00 2.43
4407 17341 8.507249 CCAGATTAACTTTCAGACTAAAACTGG 58.493 37.037 0.00 0.00 36.22 4.00
4433 17367 8.723942 AAGAATGACATGAGGTATTGTTACTC 57.276 34.615 0.00 0.00 0.00 2.59
4435 17369 8.200792 AGAATGACATGAGGTATTGTTACTCTC 58.799 37.037 0.00 0.00 0.00 3.20
4637 17594 6.770746 AGCTACTATTCTCGTTACCTGAAA 57.229 37.500 0.00 0.00 0.00 2.69
4716 17674 6.226787 TGTGTGTGAACTTGGAATTTGTTTT 58.773 32.000 0.00 0.00 0.00 2.43
4717 17675 6.146837 TGTGTGTGAACTTGGAATTTGTTTTG 59.853 34.615 0.00 0.00 0.00 2.44
4742 17709 9.268282 TGAGGAGTATTACATTAAGAAGAAGGT 57.732 33.333 0.00 0.00 0.00 3.50
4747 17714 9.268282 AGTATTACATTAAGAAGAAGGTCTCCA 57.732 33.333 0.00 0.00 0.00 3.86
4785 17752 9.194271 CTTTGTCTTTCAGGAGTTAACTACTAC 57.806 37.037 20.16 14.31 34.13 2.73
4788 17755 8.358148 TGTCTTTCAGGAGTTAACTACTACTTG 58.642 37.037 20.16 9.09 46.41 3.16
4789 17756 8.574737 GTCTTTCAGGAGTTAACTACTACTTGA 58.425 37.037 20.16 11.31 46.41 3.02
4792 17759 9.706691 TTTCAGGAGTTAACTACTACTTGATTG 57.293 33.333 20.16 6.58 46.41 2.67
4878 17845 1.299541 CCTCTCTCTGTCTCTCTCGC 58.700 60.000 0.00 0.00 0.00 5.03
4892 17859 0.725686 TCTCGCTCGAACGAAGGTAG 59.274 55.000 12.50 0.31 42.39 3.18
4893 17860 0.725686 CTCGCTCGAACGAAGGTAGA 59.274 55.000 12.50 0.00 42.39 2.59
4894 17861 1.129998 CTCGCTCGAACGAAGGTAGAA 59.870 52.381 12.50 0.00 42.39 2.10
4895 17862 1.129998 TCGCTCGAACGAAGGTAGAAG 59.870 52.381 8.73 0.00 39.54 2.85
4896 17863 1.129998 CGCTCGAACGAAGGTAGAAGA 59.870 52.381 1.02 0.00 34.06 2.87
4897 17864 2.413765 CGCTCGAACGAAGGTAGAAGAA 60.414 50.000 1.02 0.00 34.06 2.52
4908 17875 3.870559 AGGTAGAAGAAGGAGGGAACAA 58.129 45.455 0.00 0.00 0.00 2.83
5005 18891 3.230976 TCTTCAGCTCTAACTGTGTGGA 58.769 45.455 0.00 0.00 38.84 4.02
5143 21152 1.067142 TCTGCACTACGGGCTAACAAG 60.067 52.381 0.00 0.00 0.00 3.16
5157 21166 1.533625 AACAAGCCATACGTGCATGT 58.466 45.000 17.19 17.19 41.89 3.21
5168 21185 5.359860 CCATACGTGCATGTATATCCTCCTA 59.640 44.000 27.01 2.43 33.37 2.94
5169 21186 6.127451 CCATACGTGCATGTATATCCTCCTAA 60.127 42.308 27.01 1.91 33.37 2.69
5170 21187 5.135508 ACGTGCATGTATATCCTCCTAAC 57.864 43.478 10.57 0.00 0.00 2.34
5171 21188 4.166523 CGTGCATGTATATCCTCCTAACG 58.833 47.826 0.00 0.00 0.00 3.18
5172 21189 4.321008 CGTGCATGTATATCCTCCTAACGT 60.321 45.833 0.00 0.00 0.00 3.99
5374 21391 0.376852 TGATATGCAAACGCTTCCGC 59.623 50.000 0.00 0.00 38.22 5.54
5532 21594 4.402474 GCCTTTTGTTTATGTGATAGGCCT 59.598 41.667 11.78 11.78 40.73 5.19
5539 21601 7.568128 TGTTTATGTGATAGGCCTGGTATAT 57.432 36.000 17.99 0.00 0.00 0.86
5626 21692 7.219535 GTCATGTACACGTACTTTGTAGGTATG 59.780 40.741 0.00 9.21 37.00 2.39
5629 21695 7.526608 TGTACACGTACTTTGTAGGTATGTAC 58.473 38.462 8.69 15.97 37.31 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 117 5.163077 TGTTGGTTCCCTATTTAACACTCCA 60.163 40.000 0.00 0.00 0.00 3.86
162 163 8.997621 AATCTTCATGTGGAATGAGAAAATTG 57.002 30.769 0.00 0.00 34.32 2.32
234 5717 3.306364 CGGTCTTGAAGATCTTGACTGGT 60.306 47.826 14.00 0.00 32.26 4.00
268 5756 5.106948 CGTCGGCCGAAGAAATACTATACTA 60.107 44.000 33.68 0.49 39.56 1.82
269 5757 4.320057 CGTCGGCCGAAGAAATACTATACT 60.320 45.833 33.68 0.00 39.56 2.12
272 5760 2.620115 TCGTCGGCCGAAGAAATACTAT 59.380 45.455 36.29 0.00 44.03 2.12
482 5970 1.487142 TCAAACAGTCCGGAGAAACCA 59.513 47.619 3.06 0.00 38.90 3.67
492 5980 4.950050 TGAACTTCTCTCTCAAACAGTCC 58.050 43.478 0.00 0.00 0.00 3.85
500 5988 6.997655 ACAACATACATGAACTTCTCTCTCA 58.002 36.000 0.00 0.00 0.00 3.27
501 5989 8.247562 AGTACAACATACATGAACTTCTCTCTC 58.752 37.037 0.00 0.00 0.00 3.20
520 6008 9.460906 GTAATAGTAGCAACATAGGAGTACAAC 57.539 37.037 0.00 0.00 0.00 3.32
625 7217 6.265196 CCGCCCCGGTGTTATATAGTTATATA 59.735 42.308 0.00 0.00 42.73 0.86
626 7218 5.069516 CCGCCCCGGTGTTATATAGTTATAT 59.930 44.000 0.00 0.00 42.73 0.86
627 7219 4.402155 CCGCCCCGGTGTTATATAGTTATA 59.598 45.833 0.00 0.00 42.73 0.98
628 7220 3.196254 CCGCCCCGGTGTTATATAGTTAT 59.804 47.826 0.00 0.00 42.73 1.89
629 7221 2.562298 CCGCCCCGGTGTTATATAGTTA 59.438 50.000 0.00 0.00 42.73 2.24
630 7222 1.345415 CCGCCCCGGTGTTATATAGTT 59.655 52.381 0.00 0.00 42.73 2.24
631 7223 0.971386 CCGCCCCGGTGTTATATAGT 59.029 55.000 0.00 0.00 42.73 2.12
632 7224 0.248289 CCCGCCCCGGTGTTATATAG 59.752 60.000 0.00 0.00 46.80 1.31
650 7242 2.966309 CTCTTTGTGTTCGCGGGCC 61.966 63.158 6.13 0.00 0.00 5.80
651 7243 2.171489 GACTCTTTGTGTTCGCGGGC 62.171 60.000 6.13 0.00 0.00 6.13
655 7247 1.527311 GACCAGACTCTTTGTGTTCGC 59.473 52.381 0.00 0.00 0.00 4.70
664 7256 4.521559 TGGCGAGACCAGACTCTT 57.478 55.556 0.00 0.00 46.36 2.85
722 7321 2.202932 CTTCATCTCCGGCGGTGG 60.203 66.667 27.32 19.40 0.00 4.61
724 7323 2.185310 AAAGCTTCATCTCCGGCGGT 62.185 55.000 27.32 3.11 0.00 5.68
786 9801 2.517402 AAAGTGGGCGGCGAAACA 60.517 55.556 12.98 2.13 0.00 2.83
847 9863 5.121298 TCTCTTTCTGAACTTGCGAATGATG 59.879 40.000 0.00 0.00 0.00 3.07
887 9908 0.179137 TGCGGAACTGTAGATGCTCG 60.179 55.000 0.00 0.00 0.00 5.03
914 9935 0.862283 GTAGAGCCGAGCGAGTTTCG 60.862 60.000 0.00 0.00 43.89 3.46
971 9992 2.025887 GGTGGGTTCTCTTGATGGATGT 60.026 50.000 0.00 0.00 0.00 3.06
986 10007 1.933812 CTAATGGGGTGGGGTGGGT 60.934 63.158 0.00 0.00 0.00 4.51
1142 10164 2.752030 TGTCCAGCTAGCCTAATCACT 58.248 47.619 12.13 0.00 0.00 3.41
1365 10535 1.220206 CTGCTCCTGGCGAGATTGT 59.780 57.895 0.00 0.00 45.43 2.71
1444 10622 2.511600 AAATCGGCGAGCTTCCCG 60.512 61.111 17.22 17.08 45.64 5.14
1517 10708 1.099879 ATGCCGGCAAGCTCATTCTC 61.100 55.000 36.33 0.00 0.00 2.87
1521 10712 3.524606 GCATGCCGGCAAGCTCAT 61.525 61.111 40.94 20.41 37.62 2.90
1668 10867 2.753701 CGTCATCACCCCCACCAA 59.246 61.111 0.00 0.00 0.00 3.67
1712 10911 1.016653 GTCTTCAGAAGGTCAGCCGC 61.017 60.000 10.42 0.00 40.50 6.53
1718 10917 2.440539 TGAAGCGTCTTCAGAAGGTC 57.559 50.000 15.33 3.67 33.43 3.85
1719 10918 2.760374 CTTGAAGCGTCTTCAGAAGGT 58.240 47.619 17.54 0.00 35.90 3.50
1736 10935 2.249535 CGATCCCATGCCGAGCTTG 61.250 63.158 0.00 0.00 34.20 4.01
1737 10936 2.109799 CGATCCCATGCCGAGCTT 59.890 61.111 0.00 0.00 0.00 3.74
1759 10958 1.272490 AGCTTCAGGTCGTCGATTTGA 59.728 47.619 0.00 2.83 0.00 2.69
1961 11163 3.414700 CACCCTGCGACGTTGCTC 61.415 66.667 27.33 1.24 35.36 4.26
2086 11291 5.560966 TGATTTTCTTTGTATCCGGCTTC 57.439 39.130 0.00 0.00 0.00 3.86
2113 11318 1.089920 GCACCTGCGAAATCACATCT 58.910 50.000 0.00 0.00 0.00 2.90
2134 11339 9.811995 ATATCTTTTGTGAAATCATCATTGTGG 57.188 29.630 0.00 0.00 40.97 4.17
2146 11351 5.649395 CCAGCTCTCCATATCTTTTGTGAAA 59.351 40.000 0.00 0.00 0.00 2.69
2176 11381 8.328758 TCTCTTAGCTTTCCAATGGATTTCTTA 58.671 33.333 1.39 0.00 0.00 2.10
2314 11561 2.587956 CAATGGTGTTCATTCTGTGCG 58.412 47.619 0.00 0.00 43.70 5.34
2369 11616 4.789095 ATCGTAAAATTCCAATCGTCCG 57.211 40.909 0.00 0.00 0.00 4.79
2505 12474 9.336850 ATTCTCTGGAAAAGCACAGTTGATGTG 62.337 40.741 3.66 3.66 46.72 3.21
2506 12475 3.554934 TCTGGAAAAGCACAGTTGATGT 58.445 40.909 0.00 0.00 45.43 3.06
2507 12476 3.817084 TCTCTGGAAAAGCACAGTTGATG 59.183 43.478 0.00 0.00 36.17 3.07
2718 12687 5.003804 GCCTCCACACTTTTTCAAGATAGA 58.996 41.667 0.00 0.00 33.72 1.98
3025 12994 4.210331 ACTTTCTGCAACCTCTTGACAAT 58.790 39.130 0.00 0.00 0.00 2.71
3026 12995 3.620488 ACTTTCTGCAACCTCTTGACAA 58.380 40.909 0.00 0.00 0.00 3.18
3248 13217 1.980765 AGCTCCTGGTCAATGTTCTGA 59.019 47.619 0.00 0.00 0.00 3.27
3252 13221 1.251251 GCAAGCTCCTGGTCAATGTT 58.749 50.000 0.00 0.00 0.00 2.71
3381 13353 4.022329 CAGGCCTCGACAACCTTTAAAATT 60.022 41.667 0.00 0.00 0.00 1.82
3387 13359 1.073199 CCAGGCCTCGACAACCTTT 59.927 57.895 0.00 0.00 0.00 3.11
3522 13494 5.251932 TGACTGATGTACCCCTTAAATCCAA 59.748 40.000 0.00 0.00 0.00 3.53
3596 13568 8.862085 GGTATCTTCTTCTTATAGCTGTTACCT 58.138 37.037 0.00 0.00 0.00 3.08
3609 13581 5.896073 ATCCCGATTGGTATCTTCTTCTT 57.104 39.130 0.00 0.00 34.77 2.52
3747 13755 6.713903 TGACTCTTGCATTCTTGAGATTCTTT 59.286 34.615 0.00 0.00 0.00 2.52
3763 13771 2.630158 ACATCTCTGCATGACTCTTGC 58.370 47.619 9.48 9.48 40.55 4.01
3826 13834 1.271856 ACCACCATGTATCCACACGA 58.728 50.000 0.00 0.00 37.54 4.35
3837 13845 2.357009 GCAGAGCTGAATTACCACCATG 59.643 50.000 0.85 0.00 0.00 3.66
3857 13865 5.010213 AGACCAGGAATCTAATAACTCGAGC 59.990 44.000 13.61 0.00 0.00 5.03
3899 13907 3.216800 GCTGCCCATCACATATCTTTGA 58.783 45.455 0.00 0.00 0.00 2.69
3907 13915 3.384275 TACGCGCTGCCCATCACAT 62.384 57.895 5.73 0.00 0.00 3.21
3910 13918 3.770040 AGTACGCGCTGCCCATCA 61.770 61.111 5.73 0.00 0.00 3.07
3919 13927 3.838550 CAGTTTTGATAAACAGTACGCGC 59.161 43.478 5.73 0.00 44.88 6.86
3921 13929 4.156182 GGCAGTTTTGATAAACAGTACGC 58.844 43.478 0.00 0.00 44.88 4.42
4049 14060 4.154918 GTGTTGGAATAAAGCACCAGAGAG 59.845 45.833 0.00 0.00 35.08 3.20
4056 14067 2.095415 GGACCGTGTTGGAATAAAGCAC 60.095 50.000 0.00 0.00 42.00 4.40
4057 14068 2.156098 GGACCGTGTTGGAATAAAGCA 58.844 47.619 0.00 0.00 42.00 3.91
4058 14069 2.156098 TGGACCGTGTTGGAATAAAGC 58.844 47.619 0.00 0.00 42.00 3.51
4065 14076 2.369203 TGTCTTTATGGACCGTGTTGGA 59.631 45.455 0.00 0.00 42.00 3.53
4115 14126 6.791303 AGCATAAACGAACTCTTTCAAACAA 58.209 32.000 0.00 0.00 0.00 2.83
4124 14135 4.455877 CCAAAAGGAGCATAAACGAACTCT 59.544 41.667 0.00 0.00 0.00 3.24
4157 14168 0.922243 TCCCAAATACAGGGGTCCCC 60.922 60.000 20.85 20.85 46.77 4.81
4165 14176 2.230130 TGCCCCTTTCCCAAATACAG 57.770 50.000 0.00 0.00 0.00 2.74
4167 14178 2.419990 GCAATGCCCCTTTCCCAAATAC 60.420 50.000 0.00 0.00 0.00 1.89
4169 14180 0.620030 GCAATGCCCCTTTCCCAAAT 59.380 50.000 0.00 0.00 0.00 2.32
4213 14224 6.802834 GGCCTTTGCAATTGATACAAAAATTG 59.197 34.615 10.34 4.21 43.52 2.32
4214 14225 6.489361 TGGCCTTTGCAATTGATACAAAAATT 59.511 30.769 10.34 0.00 40.13 1.82
4215 14226 6.002704 TGGCCTTTGCAATTGATACAAAAAT 58.997 32.000 10.34 0.00 40.13 1.82
4229 14240 0.398381 AGAACCCTTTGGCCTTTGCA 60.398 50.000 3.32 0.00 40.13 4.08
4239 14250 5.338463 GCTCAAGACCTATGTAGAACCCTTT 60.338 44.000 0.00 0.00 0.00 3.11
4241 14252 3.707102 GCTCAAGACCTATGTAGAACCCT 59.293 47.826 0.00 0.00 0.00 4.34
4251 14262 1.273838 TGGGAGGTGCTCAAGACCTAT 60.274 52.381 0.00 0.00 44.28 2.57
4272 14283 5.845985 AGAACGTGTACATGTTTCAGATG 57.154 39.130 29.20 0.00 40.35 2.90
4293 14304 1.373570 GCATCCCGGTTCTGAAGAAG 58.626 55.000 0.00 0.00 34.27 2.85
4373 17304 7.391833 AGTCTGAAAGTTAATCTGGGATGTTTC 59.608 37.037 0.00 0.00 33.76 2.78
4376 17307 6.380079 AGTCTGAAAGTTAATCTGGGATGT 57.620 37.500 0.00 0.00 33.76 3.06
4385 17316 9.847224 TCTTCCAGTTTTAGTCTGAAAGTTAAT 57.153 29.630 0.00 0.00 31.05 1.40
4392 17323 7.279615 TGTCATTCTTCCAGTTTTAGTCTGAA 58.720 34.615 0.00 0.00 35.20 3.02
4398 17329 6.656693 ACCTCATGTCATTCTTCCAGTTTTAG 59.343 38.462 0.00 0.00 0.00 1.85
4404 17338 6.118170 ACAATACCTCATGTCATTCTTCCAG 58.882 40.000 0.00 0.00 0.00 3.86
4407 17341 8.723942 AGTAACAATACCTCATGTCATTCTTC 57.276 34.615 0.00 0.00 32.08 2.87
4637 17594 7.013942 GGTAACCAAGACCACTTTTATTTGAGT 59.986 37.037 0.00 0.00 36.91 3.41
4716 17674 9.268282 ACCTTCTTCTTAATGTAATACTCCTCA 57.732 33.333 0.00 0.00 0.00 3.86
4717 17675 9.752961 GACCTTCTTCTTAATGTAATACTCCTC 57.247 37.037 0.00 0.00 0.00 3.71
4738 17705 2.030027 TCCACACAGATGGAGACCTT 57.970 50.000 0.00 0.00 44.14 3.50
4747 17714 3.498774 AAGACAAAGCTCCACACAGAT 57.501 42.857 0.00 0.00 0.00 2.90
4785 17752 4.701956 GGTATGTCCCAACACAATCAAG 57.298 45.455 0.00 0.00 38.48 3.02
4820 17787 2.898840 CGGAGGCTACTCGGCGTA 60.899 66.667 6.85 0.00 44.93 4.42
4878 17845 3.439476 TCCTTCTTCTACCTTCGTTCGAG 59.561 47.826 0.00 0.00 0.00 4.04
4892 17859 3.149981 CACCTTTGTTCCCTCCTTCTTC 58.850 50.000 0.00 0.00 0.00 2.87
4893 17860 2.158460 CCACCTTTGTTCCCTCCTTCTT 60.158 50.000 0.00 0.00 0.00 2.52
4894 17861 1.425448 CCACCTTTGTTCCCTCCTTCT 59.575 52.381 0.00 0.00 0.00 2.85
4895 17862 1.145119 ACCACCTTTGTTCCCTCCTTC 59.855 52.381 0.00 0.00 0.00 3.46
4896 17863 1.231963 ACCACCTTTGTTCCCTCCTT 58.768 50.000 0.00 0.00 0.00 3.36
4897 17864 1.231963 AACCACCTTTGTTCCCTCCT 58.768 50.000 0.00 0.00 0.00 3.69
4908 17875 1.152922 TCGCCGGAAAAACCACCTT 60.153 52.632 5.05 0.00 38.90 3.50
5005 18891 1.275291 CCTCCTTGTACGTGGTGTGAT 59.725 52.381 0.00 0.00 0.00 3.06
5143 21152 3.861840 AGGATATACATGCACGTATGGC 58.138 45.455 15.39 6.95 34.03 4.40
5157 21166 5.105877 GCATGTAGCACGTTAGGAGGATATA 60.106 44.000 0.00 0.00 44.79 0.86
5347 21364 2.536130 GCGTTTGCATATCACCACGTAC 60.536 50.000 0.00 0.00 42.15 3.67
5374 21391 1.651240 CTGGCTGCTGGTTGAATCGG 61.651 60.000 0.00 0.00 0.00 4.18
5532 21594 1.023502 TCGAACGCACCGATATACCA 58.976 50.000 0.00 0.00 0.00 3.25
5539 21601 0.597898 TTCATTGTCGAACGCACCGA 60.598 50.000 0.00 0.00 0.00 4.69
5655 21721 2.222027 CAAAGCCTCTCCACGTCTTTT 58.778 47.619 0.00 0.00 0.00 2.27
5659 21725 0.670854 GGACAAAGCCTCTCCACGTC 60.671 60.000 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.