Multiple sequence alignment - TraesCS7A01G145000

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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 TraesCS7A01G145000 chr7A 100.000 2589 0 0 1 2589 96202848 96205436 0.000000e+00 4782.0
1 TraesCS7A01G145000 chr7A 93.927 247 15 0 322 568 576347620 576347374 8.750000e-100 374.0
2 TraesCS7A01G145000 chr2A 95.867 1839 64 7 1 1833 108514180 108512348 0.000000e+00 2964.0
3 TraesCS7A01G145000 chr2A 97.172 778 22 0 803 1580 622753207 622753984 0.000000e+00 1315.0
4 TraesCS7A01G145000 chr2A 92.599 581 31 1 1868 2436 108512375 108511795 0.000000e+00 824.0
5 TraesCS7A01G145000 chr2A 73.011 704 109 48 1784 2436 748151306 748150633 3.430000e-39 172.0
6 TraesCS7A01G145000 chr2D 91.834 894 29 16 1556 2436 427948192 427949054 0.000000e+00 1206.0
7 TraesCS7A01G145000 chr2D 91.377 893 34 13 1556 2436 142706311 142705450 0.000000e+00 1182.0
8 TraesCS7A01G145000 chr2D 90.716 894 39 14 1556 2437 288992618 288993479 0.000000e+00 1151.0
9 TraesCS7A01G145000 chr2D 96.538 260 7 2 544 801 427947875 427948134 1.840000e-116 429.0
10 TraesCS7A01G145000 chr2D 81.772 395 49 13 2062 2436 563470866 563470475 2.500000e-80 309.0
11 TraesCS7A01G145000 chr2D 95.455 132 4 2 48 179 427947579 427947708 2.610000e-50 209.0
12 TraesCS7A01G145000 chr2D 75.163 459 70 21 2013 2438 580790673 580791120 2.650000e-40 176.0
13 TraesCS7A01G145000 chr2D 100.000 36 0 0 1 36 142707017 142706982 1.660000e-07 67.6
14 TraesCS7A01G145000 chr3D 91.163 894 35 3 1556 2436 54769552 54768690 0.000000e+00 1173.0
15 TraesCS7A01G145000 chr3D 90.380 894 42 17 1556 2436 382823036 382823898 0.000000e+00 1134.0
16 TraesCS7A01G145000 chr3D 73.978 538 87 34 1932 2436 382034403 382033886 4.430000e-38 169.0
17 TraesCS7A01G145000 chr1D 90.970 897 37 14 1556 2439 408523007 408523872 0.000000e+00 1168.0
18 TraesCS7A01G145000 chr1D 88.143 894 42 19 1556 2436 207145898 207145056 0.000000e+00 1005.0
19 TraesCS7A01G145000 chr1D 100.000 36 0 0 1 36 408522301 408522336 1.660000e-07 67.6
20 TraesCS7A01G145000 chr6D 90.716 894 40 14 1556 2437 76077600 76076738 0.000000e+00 1151.0
21 TraesCS7A01G145000 chr6D 84.365 307 30 12 57 354 52723348 52723051 4.220000e-73 285.0
22 TraesCS7A01G145000 chr4D 90.625 896 38 15 1556 2437 486435147 486434284 0.000000e+00 1147.0
23 TraesCS7A01G145000 chr4D 100.000 36 0 0 1 36 486435853 486435818 1.660000e-07 67.6
24 TraesCS7A01G145000 chr5A 92.649 789 26 16 48 806 664983943 664984729 0.000000e+00 1107.0
25 TraesCS7A01G145000 chr5A 95.142 247 12 0 322 568 216665399 216665153 8.690000e-105 390.0
26 TraesCS7A01G145000 chr5A 91.954 261 20 1 931 1190 565757926 565757666 5.270000e-97 364.0
27 TraesCS7A01G145000 chr5A 92.520 254 17 1 1311 1562 565757540 565757287 1.890000e-96 363.0
28 TraesCS7A01G145000 chr5A 96.104 77 3 0 799 875 565758018 565757942 2.700000e-25 126.0
29 TraesCS7A01G145000 chr3A 87.234 893 46 21 1556 2436 530203753 530204589 0.000000e+00 955.0
30 TraesCS7A01G145000 chr3A 95.220 523 19 4 48 570 530202883 530203399 0.000000e+00 822.0
31 TraesCS7A01G145000 chr3A 96.538 260 7 2 544 801 530203421 530203680 1.840000e-116 429.0
32 TraesCS7A01G145000 chr5D 92.006 638 39 8 931 1561 447885550 447884918 0.000000e+00 885.0
33 TraesCS7A01G145000 chr5D 96.104 77 3 0 799 875 447885642 447885566 2.700000e-25 126.0
34 TraesCS7A01G145000 chr2B 92.520 615 34 1 1834 2436 800714959 800715573 0.000000e+00 870.0
35 TraesCS7A01G145000 chr2B 97.318 261 4 3 544 801 796606740 796607000 8.500000e-120 440.0
36 TraesCS7A01G145000 chr2B 96.935 261 5 3 544 801 800714411 800714671 3.960000e-118 435.0
37 TraesCS7A01G145000 chr2B 85.357 280 24 10 48 319 361867159 361866889 9.130000e-70 274.0
38 TraesCS7A01G145000 chr6B 80.091 879 75 38 1586 2436 144885926 144886732 1.740000e-156 562.0
39 TraesCS7A01G145000 chr6B 96.538 260 7 2 544 801 660223168 660223427 1.840000e-116 429.0
40 TraesCS7A01G145000 chr6B 94.977 219 8 1 48 266 371604761 371604546 8.870000e-90 340.0
41 TraesCS7A01G145000 chr6B 85.358 321 25 10 48 354 119848256 119847944 1.930000e-81 313.0
42 TraesCS7A01G145000 chr5B 91.709 398 19 4 807 1190 546831581 546831184 8.150000e-150 540.0
43 TraesCS7A01G145000 chr5B 95.385 260 9 3 544 801 251418942 251418684 6.670000e-111 411.0
44 TraesCS7A01G145000 chr5B 94.841 252 10 3 1312 1562 546831055 546830806 8.690000e-105 390.0
45 TraesCS7A01G145000 chrUn 94.253 261 12 3 544 801 84524810 84524550 1.870000e-106 396.0
46 TraesCS7A01G145000 chrUn 93.927 247 15 0 322 568 339003574 339003820 8.750000e-100 374.0
47 TraesCS7A01G145000 chrUn 100.000 36 0 0 1 36 423876789 423876824 1.660000e-07 67.6
48 TraesCS7A01G145000 chr1A 95.547 247 11 0 322 568 588672463 588672709 1.870000e-106 396.0
49 TraesCS7A01G145000 chr1A 95.455 242 11 0 322 563 65238231 65237990 1.120000e-103 387.0
50 TraesCS7A01G145000 chr1A 95.816 239 10 0 322 560 65258685 65258923 1.120000e-103 387.0
51 TraesCS7A01G145000 chr1A 98.592 71 1 0 48 118 65238299 65238229 2.700000e-25 126.0
52 TraesCS7A01G145000 chr1A 100.000 36 0 0 1 36 65238982 65238947 1.660000e-07 67.6
53 TraesCS7A01G145000 chr1A 100.000 36 0 0 1 36 65257964 65257999 1.660000e-07 67.6
54 TraesCS7A01G145000 chr1A 100.000 36 0 0 1 36 100276034 100275999 1.660000e-07 67.6
55 TraesCS7A01G145000 chr1A 100.000 36 0 0 1 36 588671713 588671748 1.660000e-07 67.6
56 TraesCS7A01G145000 chr7B 85.106 282 23 11 48 319 387895873 387896145 1.180000e-68 270.0


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 TraesCS7A01G145000 chr7A 96202848 96205436 2588 False 4782.000000 4782 100.000000 1 2589 1 chr7A.!!$F1 2588
1 TraesCS7A01G145000 chr2A 108511795 108514180 2385 True 1894.000000 2964 94.233000 1 2436 2 chr2A.!!$R2 2435
2 TraesCS7A01G145000 chr2A 622753207 622753984 777 False 1315.000000 1315 97.172000 803 1580 1 chr2A.!!$F1 777
3 TraesCS7A01G145000 chr2D 288992618 288993479 861 False 1151.000000 1151 90.716000 1556 2437 1 chr2D.!!$F1 881
4 TraesCS7A01G145000 chr2D 142705450 142707017 1567 True 624.800000 1182 95.688500 1 2436 2 chr2D.!!$R2 2435
5 TraesCS7A01G145000 chr2D 427947579 427949054 1475 False 614.666667 1206 94.609000 48 2436 3 chr2D.!!$F3 2388
6 TraesCS7A01G145000 chr3D 54768690 54769552 862 True 1173.000000 1173 91.163000 1556 2436 1 chr3D.!!$R1 880
7 TraesCS7A01G145000 chr3D 382823036 382823898 862 False 1134.000000 1134 90.380000 1556 2436 1 chr3D.!!$F1 880
8 TraesCS7A01G145000 chr1D 207145056 207145898 842 True 1005.000000 1005 88.143000 1556 2436 1 chr1D.!!$R1 880
9 TraesCS7A01G145000 chr1D 408522301 408523872 1571 False 617.800000 1168 95.485000 1 2439 2 chr1D.!!$F1 2438
10 TraesCS7A01G145000 chr6D 76076738 76077600 862 True 1151.000000 1151 90.716000 1556 2437 1 chr6D.!!$R2 881
11 TraesCS7A01G145000 chr4D 486434284 486435853 1569 True 607.300000 1147 95.312500 1 2437 2 chr4D.!!$R1 2436
12 TraesCS7A01G145000 chr5A 664983943 664984729 786 False 1107.000000 1107 92.649000 48 806 1 chr5A.!!$F1 758
13 TraesCS7A01G145000 chr5A 565757287 565758018 731 True 284.333333 364 93.526000 799 1562 3 chr5A.!!$R2 763
14 TraesCS7A01G145000 chr3A 530202883 530204589 1706 False 735.333333 955 92.997333 48 2436 3 chr3A.!!$F1 2388
15 TraesCS7A01G145000 chr5D 447884918 447885642 724 True 505.500000 885 94.055000 799 1561 2 chr5D.!!$R1 762
16 TraesCS7A01G145000 chr2B 800714411 800715573 1162 False 652.500000 870 94.727500 544 2436 2 chr2B.!!$F2 1892
17 TraesCS7A01G145000 chr6B 144885926 144886732 806 False 562.000000 562 80.091000 1586 2436 1 chr6B.!!$F1 850
18 TraesCS7A01G145000 chr5B 546830806 546831581 775 True 465.000000 540 93.275000 807 1562 2 chr5B.!!$R2 755
19 TraesCS7A01G145000 chr1A 588671713 588672709 996 False 231.800000 396 97.773500 1 568 2 chr1A.!!$F2 567
20 TraesCS7A01G145000 chr1A 65257964 65258923 959 False 227.300000 387 97.908000 1 560 2 chr1A.!!$F1 559

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
540 1181 1.326245 TGCTTTGACACTGTCGAAACG 59.674 47.619 12.15 4.26 35.78 3.6 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 2874 0.178921 TCCTCCTCAAGCTCCAGTGT 60.179 55.0 0.0 0.0 0.0 3.55 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
102 739 7.093814 TGCTAATGCCACTAAATCATCTTGTTT 60.094 33.333 0.00 0.00 38.71 2.83
172 813 6.109156 TCACAATTTCACAGCTACTCCTAA 57.891 37.500 0.00 0.00 0.00 2.69
442 1083 6.872547 TCATAATTGCTCTGCATCTACTGATC 59.127 38.462 0.00 0.00 38.76 2.92
540 1181 1.326245 TGCTTTGACACTGTCGAAACG 59.674 47.619 12.15 4.26 35.78 3.60
560 1201 7.412563 CGAAACGGATTTAGTGTGAATATGTGT 60.413 37.037 0.00 0.00 0.00 3.72
563 1204 7.778083 ACGGATTTAGTGTGAATATGTGTCTA 58.222 34.615 0.00 0.00 0.00 2.59
593 1282 4.648762 TGATTTTCTCCCAACAAGCTTCAA 59.351 37.500 0.00 0.00 0.00 2.69
774 1466 3.146104 ACTCAACTGAACCAGATTGGG 57.854 47.619 0.45 4.74 43.37 4.12
1074 1781 1.399791 GAAAAGAGCCTTGATCAGCCG 59.600 52.381 3.46 0.00 0.00 5.52
1081 1788 0.178767 CCTTGATCAGCCGATGGACA 59.821 55.000 0.00 0.00 29.66 4.02
1126 1833 9.178758 GGAATATGTACAGAGAAAAGGTGATTT 57.821 33.333 0.33 0.00 0.00 2.17
1225 1989 5.927281 AAGAACATGGCTTTAGCATTGAT 57.073 34.783 3.88 0.00 44.36 2.57
1226 1990 5.927281 AGAACATGGCTTTAGCATTGATT 57.073 34.783 3.88 0.00 44.36 2.57
1272 2036 6.430925 AGCACATTCTTTTCAGCAGTACATTA 59.569 34.615 0.00 0.00 0.00 1.90
1466 2232 5.500234 TGATGCTACAACTAGCTTTCCAAT 58.500 37.500 0.00 0.00 45.20 3.16
1736 2522 1.547372 GGAGCAACTCCTTACGGTACA 59.453 52.381 6.38 0.00 46.41 2.90
1769 2555 2.038007 AGAAGGAGCTCTGGCGGA 59.962 61.111 14.64 0.00 44.37 5.54
1848 2674 4.479993 CGGGCAGGGGAGAAGCAG 62.480 72.222 0.00 0.00 0.00 4.24
1849 2675 4.811364 GGGCAGGGGAGAAGCAGC 62.811 72.222 0.00 0.00 0.00 5.25
1850 2676 4.811364 GGCAGGGGAGAAGCAGCC 62.811 72.222 0.00 0.00 34.71 4.85
1915 2741 0.392998 GAAAGATTGAGGAGGGCGCA 60.393 55.000 10.83 0.00 0.00 6.09
1984 2810 2.043980 GGAGGCAATTTCCGGCGAA 61.044 57.895 9.30 0.00 0.00 4.70
2048 2874 1.073373 CGGGAGCTCGAGGAGGATA 59.927 63.158 15.58 0.00 0.00 2.59
2138 2964 4.671590 TCGAGGAGGACGTGGCCA 62.672 66.667 0.00 0.00 0.00 5.36
2283 3109 0.824109 CGGTGGAGCACTTCCTGATA 59.176 55.000 0.00 0.00 46.92 2.15
2339 3174 1.392710 ATCGACGGCGGAGGAAGAAT 61.393 55.000 12.58 0.00 38.28 2.40
2345 3180 1.120530 GGCGGAGGAAGAATACAGGA 58.879 55.000 0.00 0.00 0.00 3.86
2437 3284 0.178926 TTTGGGACGGAGGGAGTACA 60.179 55.000 0.00 0.00 0.00 2.90
2438 3285 0.901580 TTGGGACGGAGGGAGTACAC 60.902 60.000 0.00 0.00 0.00 2.90
2439 3286 1.304713 GGGACGGAGGGAGTACACA 60.305 63.158 0.00 0.00 0.00 3.72
2440 3287 0.901580 GGGACGGAGGGAGTACACAA 60.902 60.000 0.00 0.00 0.00 3.33
2441 3288 1.192428 GGACGGAGGGAGTACACAAT 58.808 55.000 0.00 0.00 0.00 2.71
2442 3289 1.553704 GGACGGAGGGAGTACACAATT 59.446 52.381 0.00 0.00 0.00 2.32
2443 3290 2.027469 GGACGGAGGGAGTACACAATTT 60.027 50.000 0.00 0.00 0.00 1.82
2444 3291 3.259902 GACGGAGGGAGTACACAATTTC 58.740 50.000 0.00 0.00 0.00 2.17
2445 3292 2.027469 ACGGAGGGAGTACACAATTTCC 60.027 50.000 0.00 0.00 0.00 3.13
2446 3293 2.027561 CGGAGGGAGTACACAATTTCCA 60.028 50.000 0.00 0.00 0.00 3.53
2447 3294 3.558321 CGGAGGGAGTACACAATTTCCAA 60.558 47.826 0.00 0.00 0.00 3.53
2448 3295 4.403734 GGAGGGAGTACACAATTTCCAAA 58.596 43.478 0.00 0.00 0.00 3.28
2449 3296 5.016831 GGAGGGAGTACACAATTTCCAAAT 58.983 41.667 0.00 0.00 0.00 2.32
2450 3297 6.184789 GGAGGGAGTACACAATTTCCAAATA 58.815 40.000 0.00 0.00 0.00 1.40
2451 3298 6.661805 GGAGGGAGTACACAATTTCCAAATAA 59.338 38.462 0.00 0.00 0.00 1.40
2452 3299 7.342026 GGAGGGAGTACACAATTTCCAAATAAT 59.658 37.037 0.00 0.00 0.00 1.28
2453 3300 8.066612 AGGGAGTACACAATTTCCAAATAATG 57.933 34.615 0.00 0.00 0.00 1.90
2454 3301 7.673926 AGGGAGTACACAATTTCCAAATAATGT 59.326 33.333 0.00 6.42 33.63 2.71
2455 3302 8.311109 GGGAGTACACAATTTCCAAATAATGTT 58.689 33.333 0.00 0.00 32.28 2.71
2456 3303 9.353999 GGAGTACACAATTTCCAAATAATGTTC 57.646 33.333 0.00 3.35 32.28 3.18
2476 3323 9.889128 AATGTTCTCTTTTCAGAATTTCCAAAA 57.111 25.926 0.00 0.00 34.86 2.44
2477 3324 9.889128 ATGTTCTCTTTTCAGAATTTCCAAAAA 57.111 25.926 0.00 0.52 34.86 1.94
2478 3325 9.369904 TGTTCTCTTTTCAGAATTTCCAAAAAG 57.630 29.630 18.69 18.69 37.96 2.27
2479 3326 9.586435 GTTCTCTTTTCAGAATTTCCAAAAAGA 57.414 29.630 22.41 22.41 41.27 2.52
2484 3331 9.442033 CTTTTCAGAATTTCCAAAAAGATTTGC 57.558 29.630 19.41 0.00 43.73 3.68
2485 3332 8.503458 TTTCAGAATTTCCAAAAAGATTTGCA 57.497 26.923 0.00 0.00 43.73 4.08
2486 3333 8.503458 TTCAGAATTTCCAAAAAGATTTGCAA 57.497 26.923 0.00 0.00 43.73 4.08
2487 3334 8.503458 TCAGAATTTCCAAAAAGATTTGCAAA 57.497 26.923 15.44 15.44 43.73 3.68
2488 3335 8.954350 TCAGAATTTCCAAAAAGATTTGCAAAA 58.046 25.926 17.19 0.00 39.08 2.44
2489 3336 9.012448 CAGAATTTCCAAAAAGATTTGCAAAAC 57.988 29.630 17.19 13.97 39.08 2.43
2490 3337 8.190122 AGAATTTCCAAAAAGATTTGCAAAACC 58.810 29.630 17.19 11.12 39.08 3.27
2491 3338 5.826601 TTCCAAAAAGATTTGCAAAACCC 57.173 34.783 17.19 8.58 43.73 4.11
2492 3339 4.203226 TCCAAAAAGATTTGCAAAACCCC 58.797 39.130 17.19 6.09 43.73 4.95
2493 3340 3.950395 CCAAAAAGATTTGCAAAACCCCA 59.050 39.130 17.19 0.00 43.73 4.96
2494 3341 4.583907 CCAAAAAGATTTGCAAAACCCCAT 59.416 37.500 17.19 0.00 43.73 4.00
2495 3342 5.068855 CCAAAAAGATTTGCAAAACCCCATT 59.931 36.000 17.19 4.95 43.73 3.16
2496 3343 6.406737 CCAAAAAGATTTGCAAAACCCCATTT 60.407 34.615 17.19 7.21 43.73 2.32
2497 3344 7.201857 CCAAAAAGATTTGCAAAACCCCATTTA 60.202 33.333 17.19 0.00 43.73 1.40
2498 3345 6.875948 AAAGATTTGCAAAACCCCATTTAC 57.124 33.333 17.19 0.00 0.00 2.01
2499 3346 4.905429 AGATTTGCAAAACCCCATTTACC 58.095 39.130 17.19 0.00 0.00 2.85
2500 3347 4.349342 AGATTTGCAAAACCCCATTTACCA 59.651 37.500 17.19 0.00 0.00 3.25
2501 3348 4.503714 TTTGCAAAACCCCATTTACCAA 57.496 36.364 10.02 0.00 0.00 3.67
2502 3349 4.503714 TTGCAAAACCCCATTTACCAAA 57.496 36.364 0.00 0.00 0.00 3.28
2503 3350 4.503714 TGCAAAACCCCATTTACCAAAA 57.496 36.364 0.00 0.00 0.00 2.44
2504 3351 4.855340 TGCAAAACCCCATTTACCAAAAA 58.145 34.783 0.00 0.00 0.00 1.94
2526 3373 6.757897 AAAAACTCACACTTCTGAATGTCA 57.242 33.333 0.00 0.00 0.00 3.58
2527 3374 6.949352 AAAACTCACACTTCTGAATGTCAT 57.051 33.333 0.00 0.00 0.00 3.06
2528 3375 6.949352 AAACTCACACTTCTGAATGTCATT 57.051 33.333 0.00 0.00 0.00 2.57
2529 3376 6.949352 AACTCACACTTCTGAATGTCATTT 57.051 33.333 0.00 0.00 0.00 2.32
2530 3377 6.309712 ACTCACACTTCTGAATGTCATTTG 57.690 37.500 0.00 0.00 0.00 2.32
2531 3378 5.824624 ACTCACACTTCTGAATGTCATTTGT 59.175 36.000 0.00 0.00 0.00 2.83
2532 3379 6.063640 TCACACTTCTGAATGTCATTTGTG 57.936 37.500 15.24 15.24 34.46 3.33
2533 3380 5.589855 TCACACTTCTGAATGTCATTTGTGT 59.410 36.000 18.53 15.27 35.09 3.72
2534 3381 6.095300 TCACACTTCTGAATGTCATTTGTGTT 59.905 34.615 18.53 6.13 33.70 3.32
2535 3382 7.281999 TCACACTTCTGAATGTCATTTGTGTTA 59.718 33.333 18.53 10.21 33.70 2.41
2536 3383 8.077991 CACACTTCTGAATGTCATTTGTGTTAT 58.922 33.333 13.92 0.00 33.70 1.89
2537 3384 8.077991 ACACTTCTGAATGTCATTTGTGTTATG 58.922 33.333 0.00 0.00 32.84 1.90
2538 3385 7.061441 CACTTCTGAATGTCATTTGTGTTATGC 59.939 37.037 0.00 0.00 0.00 3.14
2539 3386 6.572167 TCTGAATGTCATTTGTGTTATGCA 57.428 33.333 0.00 0.00 0.00 3.96
2540 3387 6.979465 TCTGAATGTCATTTGTGTTATGCAA 58.021 32.000 0.00 0.00 0.00 4.08
2541 3388 7.432059 TCTGAATGTCATTTGTGTTATGCAAA 58.568 30.769 0.00 0.00 39.69 3.68
2542 3389 7.924947 TCTGAATGTCATTTGTGTTATGCAAAA 59.075 29.630 0.00 0.00 38.98 2.44
2543 3390 8.429493 TGAATGTCATTTGTGTTATGCAAAAA 57.571 26.923 0.00 0.00 38.54 1.94
2544 3391 9.053840 TGAATGTCATTTGTGTTATGCAAAAAT 57.946 25.926 0.00 0.00 43.77 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 739 2.224992 TGGATCTTGTTAAGCCAGGCAA 60.225 45.455 15.80 0.00 0.00 4.52
172 813 7.658261 CATTGATTGGCATCAGAAGAATGTAT 58.342 34.615 0.00 0.00 40.66 2.29
386 1027 9.561069 AACAAACACTGTCTCTAGAATTGTTAT 57.439 29.630 0.00 0.00 37.23 1.89
392 1033 7.055667 TCTGAACAAACACTGTCTCTAGAAT 57.944 36.000 0.00 0.00 37.23 2.40
560 1201 9.527157 TTGTTGGGAGAAAATCATTACATTAGA 57.473 29.630 0.00 0.00 0.00 2.10
563 1204 7.038799 AGCTTGTTGGGAGAAAATCATTACATT 60.039 33.333 0.00 0.00 0.00 2.71
593 1282 2.713877 AGGTGTGTACAAAACGTGGTT 58.286 42.857 0.00 0.00 0.00 3.67
774 1466 4.112634 GCAGAAACCTTGGAACTTGAAAC 58.887 43.478 0.00 0.00 0.00 2.78
1045 1752 1.746991 GGCTCTTTTCCAGCTCCCG 60.747 63.158 0.00 0.00 37.05 5.14
1074 1781 2.187946 CCGGCCTCTGTGTCCATC 59.812 66.667 0.00 0.00 0.00 3.51
1081 1788 2.681778 CAGTCTCCCGGCCTCTGT 60.682 66.667 0.00 0.00 0.00 3.41
1126 1833 8.708378 ACTGACAAATACTTGGATGATGATAGA 58.292 33.333 0.00 0.00 36.82 1.98
1272 2036 4.227300 TGCATAAAGACAACTACCAGGGAT 59.773 41.667 0.00 0.00 0.00 3.85
1466 2232 1.326213 CCAAACACCACACCAAGGCA 61.326 55.000 0.00 0.00 0.00 4.75
1736 2522 4.090090 TCCTTCTCGTCAAGAGGAAGAAT 58.910 43.478 0.00 0.00 46.82 2.40
1769 2555 2.437359 GCTCGTCTGCCCATGCTT 60.437 61.111 0.00 0.00 38.71 3.91
1862 2688 4.479993 CTGCTTCTCCCCTGCCCG 62.480 72.222 0.00 0.00 0.00 6.13
1863 2689 4.811364 GCTGCTTCTCCCCTGCCC 62.811 72.222 0.00 0.00 0.00 5.36
1864 2690 4.811364 GGCTGCTTCTCCCCTGCC 62.811 72.222 0.00 0.00 38.58 4.85
2029 2855 1.706995 TATCCTCCTCGAGCTCCCGT 61.707 60.000 6.99 0.00 0.00 5.28
2048 2874 0.178921 TCCTCCTCAAGCTCCAGTGT 60.179 55.000 0.00 0.00 0.00 3.55
2138 2964 3.148279 GGCATCGTCGGGACCTCT 61.148 66.667 0.00 0.00 0.00 3.69
2160 2986 2.131709 CCCTCCCGCCTCGATTACA 61.132 63.158 0.00 0.00 0.00 2.41
2339 3174 2.280404 ATCGTCCTCCGCCTCCTGTA 62.280 60.000 0.00 0.00 36.19 2.74
2345 3180 2.745821 GTTTTAAAATCGTCCTCCGCCT 59.254 45.455 3.52 0.00 36.19 5.52
2450 3297 9.889128 TTTTGGAAATTCTGAAAAGAGAACATT 57.111 25.926 0.00 0.00 34.79 2.71
2451 3298 9.889128 TTTTTGGAAATTCTGAAAAGAGAACAT 57.111 25.926 0.00 0.00 34.79 2.71
2452 3299 9.369904 CTTTTTGGAAATTCTGAAAAGAGAACA 57.630 29.630 19.52 0.00 38.79 3.18
2453 3300 9.586435 TCTTTTTGGAAATTCTGAAAAGAGAAC 57.414 29.630 21.26 0.00 39.83 3.01
2458 3305 9.442033 GCAAATCTTTTTGGAAATTCTGAAAAG 57.558 29.630 18.81 18.81 42.09 2.27
2459 3306 8.954350 TGCAAATCTTTTTGGAAATTCTGAAAA 58.046 25.926 0.00 0.79 39.81 2.29
2460 3307 8.503458 TGCAAATCTTTTTGGAAATTCTGAAA 57.497 26.923 0.00 0.00 39.81 2.69
2461 3308 8.503458 TTGCAAATCTTTTTGGAAATTCTGAA 57.497 26.923 0.00 0.00 46.18 3.02
2470 3317 4.203226 GGGGTTTTGCAAATCTTTTTGGA 58.797 39.130 13.65 0.00 42.09 3.53
2471 3318 3.950395 TGGGGTTTTGCAAATCTTTTTGG 59.050 39.130 13.65 0.00 42.09 3.28
2472 3319 5.771153 ATGGGGTTTTGCAAATCTTTTTG 57.229 34.783 13.65 0.00 44.18 2.44
2473 3320 6.788598 AAATGGGGTTTTGCAAATCTTTTT 57.211 29.167 13.65 6.18 0.00 1.94
2474 3321 6.264292 GGTAAATGGGGTTTTGCAAATCTTTT 59.736 34.615 13.65 14.10 0.00 2.27
2475 3322 5.767665 GGTAAATGGGGTTTTGCAAATCTTT 59.232 36.000 13.65 10.68 0.00 2.52
2476 3323 5.163152 TGGTAAATGGGGTTTTGCAAATCTT 60.163 36.000 13.65 5.01 0.00 2.40
2477 3324 4.349342 TGGTAAATGGGGTTTTGCAAATCT 59.651 37.500 13.65 0.00 0.00 2.40
2478 3325 4.646572 TGGTAAATGGGGTTTTGCAAATC 58.353 39.130 13.65 12.22 0.00 2.17
2479 3326 4.713792 TGGTAAATGGGGTTTTGCAAAT 57.286 36.364 13.65 0.00 0.00 2.32
2480 3327 4.503714 TTGGTAAATGGGGTTTTGCAAA 57.496 36.364 8.05 8.05 0.00 3.68
2481 3328 4.503714 TTTGGTAAATGGGGTTTTGCAA 57.496 36.364 0.00 0.00 0.00 4.08
2482 3329 4.503714 TTTTGGTAAATGGGGTTTTGCA 57.496 36.364 0.00 0.00 0.00 4.08
2503 3350 6.757897 TGACATTCAGAAGTGTGAGTTTTT 57.242 33.333 3.73 0.00 0.00 1.94
2504 3351 6.949352 ATGACATTCAGAAGTGTGAGTTTT 57.051 33.333 3.73 0.00 0.00 2.43
2505 3352 6.949352 AATGACATTCAGAAGTGTGAGTTT 57.051 33.333 0.00 0.00 0.00 2.66
2506 3353 6.319658 ACAAATGACATTCAGAAGTGTGAGTT 59.680 34.615 0.05 0.00 0.00 3.01
2507 3354 5.824624 ACAAATGACATTCAGAAGTGTGAGT 59.175 36.000 0.05 0.00 0.00 3.41
2508 3355 6.140786 CACAAATGACATTCAGAAGTGTGAG 58.859 40.000 17.68 0.68 33.35 3.51
2509 3356 5.589855 ACACAAATGACATTCAGAAGTGTGA 59.410 36.000 24.76 2.16 37.13 3.58
2510 3357 5.824429 ACACAAATGACATTCAGAAGTGTG 58.176 37.500 19.65 19.65 37.13 3.82
2511 3358 6.455360 AACACAAATGACATTCAGAAGTGT 57.545 33.333 0.05 8.77 38.80 3.55
2512 3359 7.061441 GCATAACACAAATGACATTCAGAAGTG 59.939 37.037 0.05 8.21 33.91 3.16
2513 3360 7.086376 GCATAACACAAATGACATTCAGAAGT 58.914 34.615 0.05 0.68 0.00 3.01
2514 3361 7.085746 TGCATAACACAAATGACATTCAGAAG 58.914 34.615 0.05 0.14 0.00 2.85
2515 3362 6.979465 TGCATAACACAAATGACATTCAGAA 58.021 32.000 0.05 0.00 0.00 3.02
2516 3363 6.572167 TGCATAACACAAATGACATTCAGA 57.428 33.333 0.05 0.00 0.00 3.27
2517 3364 7.640616 TTTGCATAACACAAATGACATTCAG 57.359 32.000 0.05 0.29 32.27 3.02
2518 3365 8.429493 TTTTTGCATAACACAAATGACATTCA 57.571 26.923 0.05 0.00 36.91 2.57
2526 3373 8.218338 TCCAAACATTTTTGCATAACACAAAT 57.782 26.923 0.00 0.00 40.84 2.32
2527 3374 7.615582 TCCAAACATTTTTGCATAACACAAA 57.384 28.000 0.00 0.00 40.84 2.83
2528 3375 7.798596 ATCCAAACATTTTTGCATAACACAA 57.201 28.000 0.00 0.00 40.84 3.33
2529 3376 7.798596 AATCCAAACATTTTTGCATAACACA 57.201 28.000 0.00 0.00 40.84 3.72
2530 3377 8.341173 TGAAATCCAAACATTTTTGCATAACAC 58.659 29.630 0.00 0.00 40.84 3.32
2531 3378 8.442632 TGAAATCCAAACATTTTTGCATAACA 57.557 26.923 0.00 0.00 40.84 2.41
2532 3379 9.727627 TTTGAAATCCAAACATTTTTGCATAAC 57.272 25.926 0.00 0.00 40.84 1.89
2535 3382 9.819267 AATTTTGAAATCCAAACATTTTTGCAT 57.181 22.222 0.00 0.00 43.82 3.96


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

AutoCloner maintained by Alex Coulton.