Multiple sequence alignment - TraesCS2B01G228900

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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 TraesCS2B01G228900 chr2B 100.000 3507 0 0 1 3507 223153118 223156624 0.000000e+00 6477.0
1 TraesCS2B01G228900 chr2B 93.983 349 19 2 122 469 152166944 152166597 8.620000e-146 527.0
2 TraesCS2B01G228900 chr2B 81.208 149 28 0 1090 1238 85177910 85177762 1.710000e-23 121.0
3 TraesCS2B01G228900 chr2B 92.157 51 2 2 456 504 453334307 453334357 1.750000e-08 71.3
4 TraesCS2B01G228900 chr2B 95.000 40 2 0 3468 3507 148145804 148145843 2.920000e-06 63.9
5 TraesCS2B01G228900 chr2D 95.243 2859 72 21 506 3331 175330692 175333519 0.000000e+00 4468.0
6 TraesCS2B01G228900 chr2D 92.550 349 24 2 122 469 624917817 624918164 1.880000e-137 499.0
7 TraesCS2B01G228900 chr2D 89.412 85 6 2 3165 3249 378756867 378756786 1.720000e-18 104.0
8 TraesCS2B01G228900 chr2D 90.741 54 3 2 456 507 28430693 28430746 1.750000e-08 71.3
9 TraesCS2B01G228900 chr2D 92.157 51 2 2 456 504 624918230 624918280 1.750000e-08 71.3
10 TraesCS2B01G228900 chr2D 100.000 28 0 0 2932 2959 175333240 175333267 6.000000e-03 52.8
11 TraesCS2B01G228900 chr2A 95.676 2590 71 18 500 3059 175467109 175469687 0.000000e+00 4124.0
12 TraesCS2B01G228900 chr2A 87.226 274 13 6 3058 3331 175469903 175470154 3.420000e-75 292.0
13 TraesCS2B01G228900 chr6D 86.244 2130 112 74 719 2736 60488234 60486174 0.000000e+00 2143.0
14 TraesCS2B01G228900 chr6D 89.809 157 9 5 518 668 60488390 60488235 9.930000e-46 195.0
15 TraesCS2B01G228900 chr6D 95.122 41 2 0 3467 3507 317859705 317859745 8.130000e-07 65.8
16 TraesCS2B01G228900 chr6D 94.737 38 2 0 3470 3507 20266918 20266955 3.780000e-05 60.2
17 TraesCS2B01G228900 chr6D 87.755 49 4 2 2833 2881 60486217 60486171 4.890000e-04 56.5
18 TraesCS2B01G228900 chr6A 85.028 2124 143 79 719 2736 77100380 77098326 0.000000e+00 1999.0
19 TraesCS2B01G228900 chr6A 88.608 158 10 5 518 668 77100537 77100381 5.980000e-43 185.0
20 TraesCS2B01G228900 chr6A 86.957 115 7 2 2878 2991 77098282 77098175 4.750000e-24 122.0
21 TraesCS2B01G228900 chr6A 97.500 40 0 1 3468 3507 574635758 574635796 2.260000e-07 67.6
22 TraesCS2B01G228900 chr6A 90.909 44 2 2 2837 2880 77098365 77098324 1.360000e-04 58.4
23 TraesCS2B01G228900 chr6B 84.071 2147 126 77 718 2736 134665082 134663024 0.000000e+00 1871.0
24 TraesCS2B01G228900 chr6B 89.172 157 10 5 518 668 134665234 134665079 4.620000e-44 189.0
25 TraesCS2B01G228900 chr6B 86.957 115 5 3 2878 2991 134662978 134662873 1.710000e-23 121.0
26 TraesCS2B01G228900 chr6B 95.238 42 1 1 3347 3387 169477549 169477508 8.130000e-07 65.8
27 TraesCS2B01G228900 chr4B 98.081 469 9 0 1 469 135820012 135820480 0.000000e+00 817.0
28 TraesCS2B01G228900 chr4B 95.226 398 18 1 1 397 628953470 628953867 2.300000e-176 628.0
29 TraesCS2B01G228900 chr4B 80.488 246 39 8 1425 1667 380653779 380654018 2.780000e-41 180.0
30 TraesCS2B01G228900 chr4B 82.394 142 23 2 1090 1230 380653478 380653618 4.750000e-24 122.0
31 TraesCS2B01G228900 chr7B 97.655 469 11 0 1 469 295085832 295085364 0.000000e+00 806.0
32 TraesCS2B01G228900 chr7B 100.000 38 0 0 467 504 295085343 295085306 1.750000e-08 71.3
33 TraesCS2B01G228900 chr7B 97.561 41 1 0 3347 3387 705609428 705609388 1.750000e-08 71.3
34 TraesCS2B01G228900 chr7B 97.561 41 1 0 3347 3387 705655512 705655472 1.750000e-08 71.3
35 TraesCS2B01G228900 chr7B 88.889 54 5 1 467 520 622493709 622493657 8.130000e-07 65.8
36 TraesCS2B01G228900 chr3B 94.269 349 18 2 122 469 140997115 140996768 1.850000e-147 532.0
37 TraesCS2B01G228900 chr3B 100.000 40 0 0 467 506 140996747 140996708 1.350000e-09 75.0
38 TraesCS2B01G228900 chr3B 97.674 43 1 0 467 509 754637112 754637070 1.350000e-09 75.0
39 TraesCS2B01G228900 chr3B 97.436 39 0 1 3462 3499 55006814 55006852 8.130000e-07 65.8
40 TraesCS2B01G228900 chr7A 90.000 350 31 4 122 469 534141015 534141362 1.920000e-122 449.0
41 TraesCS2B01G228900 chr7A 89.143 350 34 4 122 469 648099116 648098769 1.930000e-117 433.0
42 TraesCS2B01G228900 chr7A 97.561 41 1 0 3467 3507 272926835 272926875 1.750000e-08 71.3
43 TraesCS2B01G228900 chr3A 89.655 348 35 1 122 469 54474040 54474386 3.210000e-120 442.0
44 TraesCS2B01G228900 chr3A 84.979 233 32 2 1446 1675 50727785 50727553 2.100000e-57 233.0
45 TraesCS2B01G228900 chr3A 87.952 83 8 2 3165 3245 434000892 434000974 2.880000e-16 97.1
46 TraesCS2B01G228900 chr7D 88.315 368 38 4 122 488 572169596 572169233 1.490000e-118 436.0
47 TraesCS2B01G228900 chr7D 87.640 89 8 3 3167 3252 204247274 204247186 2.230000e-17 100.0
48 TraesCS2B01G228900 chr7D 87.059 85 8 3 3164 3246 119165940 119166023 3.730000e-15 93.5
49 TraesCS2B01G228900 chr3D 84.979 233 32 2 1446 1675 39325676 39325444 2.100000e-57 233.0
50 TraesCS2B01G228900 chr3D 80.000 250 43 5 1420 1667 148224359 148224603 1.000000e-40 178.0
51 TraesCS2B01G228900 chr3D 86.047 86 10 2 3167 3250 565374416 565374331 1.340000e-14 91.6
52 TraesCS2B01G228900 chr3D 97.561 41 1 0 3347 3387 99810623 99810583 1.750000e-08 71.3
53 TraesCS2B01G228900 chr3D 97.561 41 0 1 3467 3507 315464959 315464920 6.280000e-08 69.4
54 TraesCS2B01G228900 chr5A 83.951 243 34 4 1434 1675 317247919 317247681 9.790000e-56 228.0
55 TraesCS2B01G228900 chr5A 95.238 42 1 1 3347 3387 513224464 513224505 8.130000e-07 65.8
56 TraesCS2B01G228900 chr4D 79.511 327 31 12 122 447 100346126 100345835 2.130000e-47 200.0
57 TraesCS2B01G228900 chr4D 82.394 142 23 2 1090 1230 304690191 304690331 4.750000e-24 122.0
58 TraesCS2B01G228900 chr4D 97.500 40 1 0 3347 3386 416054690 416054729 6.280000e-08 69.4
59 TraesCS2B01G228900 chr4D 94.737 38 2 0 3470 3507 346147965 346147928 3.780000e-05 60.2
60 TraesCS2B01G228900 chr4A 82.394 142 23 2 1090 1230 174157472 174157332 4.750000e-24 122.0
61 TraesCS2B01G228900 chr4A 89.535 86 7 2 3167 3252 733665191 733665108 1.330000e-19 108.0
62 TraesCS2B01G228900 chr4A 97.778 45 1 0 3347 3391 534236601 534236645 1.040000e-10 78.7
63 TraesCS2B01G228900 chr4A 97.500 40 1 0 3347 3386 47757139 47757100 6.280000e-08 69.4
64 TraesCS2B01G228900 chr5B 85.556 90 10 3 3164 3250 279098261 279098350 1.340000e-14 91.6
65 TraesCS2B01G228900 chr1B 100.000 36 0 0 3353 3388 171407785 171407820 2.260000e-07 67.6
66 TraesCS2B01G228900 chrUn 94.872 39 2 0 3469 3507 73656611 73656573 1.050000e-05 62.1


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 TraesCS2B01G228900 chr2B 223153118 223156624 3506 False 6477.000000 6477 100.000000 1 3507 1 chr2B.!!$F2 3506
1 TraesCS2B01G228900 chr2D 175330692 175333519 2827 False 2260.400000 4468 97.621500 506 3331 2 chr2D.!!$F2 2825
2 TraesCS2B01G228900 chr2A 175467109 175470154 3045 False 2208.000000 4124 91.451000 500 3331 2 chr2A.!!$F1 2831
3 TraesCS2B01G228900 chr6D 60486171 60488390 2219 True 798.166667 2143 87.936000 518 2881 3 chr6D.!!$R1 2363
4 TraesCS2B01G228900 chr6A 77098175 77100537 2362 True 591.100000 1999 87.875500 518 2991 4 chr6A.!!$R1 2473
5 TraesCS2B01G228900 chr6B 134662873 134665234 2361 True 727.000000 1871 86.733333 518 2991 3 chr6B.!!$R2 2473
6 TraesCS2B01G228900 chr7B 295085306 295085832 526 True 438.650000 806 98.827500 1 504 2 chr7B.!!$R4 503

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
386 387 0.178068 ATGTGGGGAGATCGAAACCG 59.822 55.0 0.0 0.0 0.0 4.44 F
1032 1068 0.174389 GCAGCTCGGACTCATCTTCA 59.826 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 1848 0.394488 CGTACCCTGAGAGAGGCAGA 60.394 60.0 0.00 0.0 41.19 4.26 R
2651 2862 0.321671 AAGTACGTGCTCATGGTGCT 59.678 50.0 6.63 0.0 0.00 4.40 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
321 322 4.794278 TTGCCTCTGTTACTAATCACGA 57.206 40.909 0.00 0.00 0.00 4.35
325 326 5.047590 TGCCTCTGTTACTAATCACGAAAGA 60.048 40.000 0.00 0.00 0.00 2.52
337 338 3.635331 TCACGAAAGACAAGTAGTTCGG 58.365 45.455 16.92 9.49 45.39 4.30
355 356 2.436109 GTGGATGGTGGCACCTGT 59.564 61.111 34.69 24.04 39.58 4.00
386 387 0.178068 ATGTGGGGAGATCGAAACCG 59.822 55.000 0.00 0.00 0.00 4.44
495 496 3.038417 GCCTGCAGCGCCGTATAG 61.038 66.667 8.66 0.00 0.00 1.31
496 497 2.356313 CCTGCAGCGCCGTATAGG 60.356 66.667 8.66 1.07 44.97 2.57
497 498 2.728180 CTGCAGCGCCGTATAGGA 59.272 61.111 2.29 0.00 45.00 2.94
498 499 1.372251 CTGCAGCGCCGTATAGGAG 60.372 63.158 2.29 0.00 45.00 3.69
503 504 2.963371 CGCCGTATAGGAGCTCCC 59.037 66.667 29.54 12.87 45.00 4.30
504 505 2.637383 CGCCGTATAGGAGCTCCCC 61.637 68.421 29.54 13.59 45.00 4.81
505 506 1.228925 GCCGTATAGGAGCTCCCCT 60.229 63.158 29.54 18.70 45.00 4.79
506 507 0.832559 GCCGTATAGGAGCTCCCCTT 60.833 60.000 29.54 16.27 45.00 3.95
507 508 1.718280 CCGTATAGGAGCTCCCCTTT 58.282 55.000 29.54 13.43 45.00 3.11
508 509 2.047830 CCGTATAGGAGCTCCCCTTTT 58.952 52.381 29.54 13.02 45.00 2.27
509 510 2.438392 CCGTATAGGAGCTCCCCTTTTT 59.562 50.000 29.54 12.24 45.00 1.94
510 511 3.494573 CCGTATAGGAGCTCCCCTTTTTC 60.495 52.174 29.54 12.09 45.00 2.29
511 512 3.388350 CGTATAGGAGCTCCCCTTTTTCT 59.612 47.826 29.54 10.66 37.74 2.52
512 513 4.141688 CGTATAGGAGCTCCCCTTTTTCTT 60.142 45.833 29.54 9.89 37.74 2.52
513 514 2.889170 AGGAGCTCCCCTTTTTCTTC 57.111 50.000 29.54 0.00 36.42 2.87
514 515 2.065799 AGGAGCTCCCCTTTTTCTTCA 58.934 47.619 29.54 0.00 36.42 3.02
750 761 3.273834 CGCCACGGTTTCACGGTT 61.274 61.111 0.00 0.00 38.39 4.44
804 815 1.220206 CAGATCACTCGCCTGCCTT 59.780 57.895 0.00 0.00 0.00 4.35
869 889 0.393077 CCAGTCCGTTCCTTCACACT 59.607 55.000 0.00 0.00 0.00 3.55
989 1012 4.039973 TGTGTTTGTTGGTAGCTAGCTAGT 59.960 41.667 24.78 11.13 0.00 2.57
1032 1068 0.174389 GCAGCTCGGACTCATCTTCA 59.826 55.000 0.00 0.00 0.00 3.02
1189 1246 1.971505 GCTCCCCGTCACCATCATCA 61.972 60.000 0.00 0.00 0.00 3.07
1279 1349 1.524848 TCAAGCGCCGTAATTTTCCA 58.475 45.000 2.29 0.00 0.00 3.53
1299 1372 8.682128 TTTCCAGTGCAATTAAATAATCGAAC 57.318 30.769 0.00 0.00 0.00 3.95
1319 1397 4.307032 ACCCATCCATCATGCTTATACC 57.693 45.455 0.00 0.00 0.00 2.73
1768 1894 2.554775 GATCGATCGCGCGGTCTA 59.445 61.111 36.86 29.09 38.33 2.59
1769 1895 1.510204 GATCGATCGCGCGGTCTAG 60.510 63.158 36.86 24.29 38.33 2.43
1770 1896 3.596667 ATCGATCGCGCGGTCTAGC 62.597 63.158 36.86 17.59 37.46 3.42
1771 1897 4.607606 CGATCGCGCGGTCTAGCA 62.608 66.667 36.86 14.73 36.85 3.49
1772 1898 2.049985 GATCGCGCGGTCTAGCAT 60.050 61.111 34.35 16.82 36.85 3.79
1829 1972 5.594317 GCTTAGGGTATTGTGGTTGATGAAT 59.406 40.000 0.00 0.00 0.00 2.57
1978 2121 2.125269 GTCACCGCATACCCGCTT 60.125 61.111 0.00 0.00 0.00 4.68
2348 2503 1.380403 CGGGGGCAATGCGATAAACA 61.380 55.000 0.00 0.00 0.00 2.83
2362 2517 3.003689 CGATAAACACCATGCCTCCATTC 59.996 47.826 0.00 0.00 0.00 2.67
2378 2533 5.382616 CTCCATTCATGAATCATCTTCCCA 58.617 41.667 18.16 0.00 0.00 4.37
2651 2862 4.201657 GCATGGATATATGTGGCTGCATA 58.798 43.478 0.50 5.18 36.01 3.14
3048 3333 7.869016 TTGCGAAGTAAGTATATATGCAGTC 57.131 36.000 3.52 0.00 0.00 3.51
3092 3594 4.826733 CCTGTATGTAAATAGGGCATGCAA 59.173 41.667 21.36 4.38 35.48 4.08
3269 3771 8.571336 GGAATAGTATCTTACCGTGCTTAGTTA 58.429 37.037 0.00 0.00 0.00 2.24
3272 3774 7.578310 AGTATCTTACCGTGCTTAGTTATCA 57.422 36.000 0.00 0.00 0.00 2.15
3274 3776 8.082852 AGTATCTTACCGTGCTTAGTTATCATG 58.917 37.037 0.00 0.00 0.00 3.07
3277 3779 4.465632 ACCGTGCTTAGTTATCATGTGA 57.534 40.909 0.00 0.00 0.00 3.58
3278 3780 4.827692 ACCGTGCTTAGTTATCATGTGAA 58.172 39.130 0.00 0.00 0.00 3.18
3279 3781 5.428253 ACCGTGCTTAGTTATCATGTGAAT 58.572 37.500 0.00 0.00 0.00 2.57
3280 3782 5.294306 ACCGTGCTTAGTTATCATGTGAATG 59.706 40.000 0.00 0.00 0.00 2.67
3281 3783 5.277490 CCGTGCTTAGTTATCATGTGAATGG 60.277 44.000 0.00 0.00 0.00 3.16
3282 3784 5.514279 GTGCTTAGTTATCATGTGAATGGC 58.486 41.667 0.00 0.00 0.00 4.40
3283 3785 4.580167 TGCTTAGTTATCATGTGAATGGCC 59.420 41.667 0.00 0.00 0.00 5.36
3284 3786 4.319766 GCTTAGTTATCATGTGAATGGCCG 60.320 45.833 0.00 0.00 0.00 6.13
3285 3787 3.281727 AGTTATCATGTGAATGGCCGT 57.718 42.857 0.00 0.00 0.00 5.68
3286 3788 3.620488 AGTTATCATGTGAATGGCCGTT 58.380 40.909 10.83 10.83 0.00 4.44
3287 3789 4.776349 AGTTATCATGTGAATGGCCGTTA 58.224 39.130 11.03 0.00 0.00 3.18
3288 3790 5.376625 AGTTATCATGTGAATGGCCGTTAT 58.623 37.500 11.03 1.68 0.00 1.89
3289 3791 5.239306 AGTTATCATGTGAATGGCCGTTATG 59.761 40.000 11.03 11.21 0.00 1.90
3290 3792 2.997980 TCATGTGAATGGCCGTTATGT 58.002 42.857 11.03 0.00 0.00 2.29
3363 3865 9.907576 TTTTAACACGCAAAATTTTGTTGATAG 57.092 25.926 27.56 18.92 40.24 2.08
3364 3866 5.574815 ACACGCAAAATTTTGTTGATAGC 57.425 34.783 27.56 15.46 40.24 2.97
3365 3867 5.288804 ACACGCAAAATTTTGTTGATAGCT 58.711 33.333 27.56 12.12 40.24 3.32
3366 3868 5.752955 ACACGCAAAATTTTGTTGATAGCTT 59.247 32.000 27.56 9.77 40.24 3.74
3367 3869 6.920758 ACACGCAAAATTTTGTTGATAGCTTA 59.079 30.769 27.56 0.00 40.24 3.09
3368 3870 7.096230 ACACGCAAAATTTTGTTGATAGCTTAC 60.096 33.333 27.56 11.75 40.24 2.34
3369 3871 6.364976 ACGCAAAATTTTGTTGATAGCTTACC 59.635 34.615 27.13 8.89 40.24 2.85
3370 3872 6.364706 CGCAAAATTTTGTTGATAGCTTACCA 59.635 34.615 27.13 0.00 40.24 3.25
3371 3873 7.095857 CGCAAAATTTTGTTGATAGCTTACCAA 60.096 33.333 27.13 0.00 40.24 3.67
3372 3874 8.223100 GCAAAATTTTGTTGATAGCTTACCAAG 58.777 33.333 27.13 1.19 40.24 3.61
3373 3875 8.223100 CAAAATTTTGTTGATAGCTTACCAAGC 58.777 33.333 20.57 2.65 42.64 4.01
3403 3905 8.514594 CCACTTGGTATATACAAATATGCTTGG 58.485 37.037 14.70 6.05 32.82 3.61
3404 3906 9.283768 CACTTGGTATATACAAATATGCTTGGA 57.716 33.333 14.70 0.00 32.82 3.53
3405 3907 9.860650 ACTTGGTATATACAAATATGCTTGGAA 57.139 29.630 14.70 0.00 32.82 3.53
3423 3925 9.866655 TGCTTGGAAAATATGTTATTATCTCCT 57.133 29.630 0.00 0.00 0.00 3.69
3442 3944 7.928307 TCTCCTTGATGTTCTATTTTGAAGG 57.072 36.000 0.00 0.00 0.00 3.46
3443 3945 7.689299 TCTCCTTGATGTTCTATTTTGAAGGA 58.311 34.615 0.00 0.00 36.28 3.36
3444 3946 8.163408 TCTCCTTGATGTTCTATTTTGAAGGAA 58.837 33.333 0.00 0.00 37.78 3.36
3445 3947 8.704849 TCCTTGATGTTCTATTTTGAAGGAAA 57.295 30.769 0.00 0.00 35.83 3.13
3446 3948 9.142014 TCCTTGATGTTCTATTTTGAAGGAAAA 57.858 29.630 0.00 0.00 35.83 2.29
3447 3949 9.196552 CCTTGATGTTCTATTTTGAAGGAAAAC 57.803 33.333 0.00 0.00 36.35 2.43
3448 3950 9.748708 CTTGATGTTCTATTTTGAAGGAAAACA 57.251 29.630 0.00 0.00 36.35 2.83
3450 3952 9.912634 TGATGTTCTATTTTGAAGGAAAACATC 57.087 29.630 14.68 14.68 36.35 3.06
3451 3953 9.912634 GATGTTCTATTTTGAAGGAAAACATCA 57.087 29.630 16.00 0.00 36.35 3.07
3452 3954 9.918630 ATGTTCTATTTTGAAGGAAAACATCAG 57.081 29.630 0.00 0.00 36.35 2.90
3453 3955 7.867403 TGTTCTATTTTGAAGGAAAACATCAGC 59.133 33.333 0.00 0.00 36.35 4.26
3454 3956 7.765695 TCTATTTTGAAGGAAAACATCAGCT 57.234 32.000 0.00 0.00 36.35 4.24
3455 3957 8.181904 TCTATTTTGAAGGAAAACATCAGCTT 57.818 30.769 0.00 0.00 36.35 3.74
3456 3958 8.084073 TCTATTTTGAAGGAAAACATCAGCTTG 58.916 33.333 0.00 0.00 36.35 4.01
3457 3959 4.589216 TTGAAGGAAAACATCAGCTTGG 57.411 40.909 0.00 0.00 0.00 3.61
3458 3960 3.831323 TGAAGGAAAACATCAGCTTGGA 58.169 40.909 0.00 0.00 0.00 3.53
3459 3961 3.822735 TGAAGGAAAACATCAGCTTGGAG 59.177 43.478 0.00 0.00 0.00 3.86
3460 3962 2.165998 AGGAAAACATCAGCTTGGAGC 58.834 47.619 0.00 0.00 42.84 4.70
3461 3963 1.888512 GGAAAACATCAGCTTGGAGCA 59.111 47.619 2.47 0.00 45.56 4.26
3462 3964 2.494870 GGAAAACATCAGCTTGGAGCAT 59.505 45.455 2.47 0.00 45.56 3.79
3463 3965 3.428589 GGAAAACATCAGCTTGGAGCATC 60.429 47.826 2.47 0.00 45.56 3.91
3464 3966 2.502142 AACATCAGCTTGGAGCATCA 57.498 45.000 2.47 0.00 45.56 3.07
3465 3967 2.502142 ACATCAGCTTGGAGCATCAA 57.498 45.000 2.47 0.00 45.56 2.57
3466 3968 2.089980 ACATCAGCTTGGAGCATCAAC 58.910 47.619 2.47 0.00 45.56 3.18
3467 3969 2.290768 ACATCAGCTTGGAGCATCAACT 60.291 45.455 2.47 0.00 45.56 3.16
3468 3970 3.054875 ACATCAGCTTGGAGCATCAACTA 60.055 43.478 2.47 0.00 45.56 2.24
3469 3971 3.701205 TCAGCTTGGAGCATCAACTAA 57.299 42.857 2.47 0.00 45.56 2.24
3470 3972 3.603532 TCAGCTTGGAGCATCAACTAAG 58.396 45.455 2.47 0.00 45.56 2.18
3471 3973 2.681848 CAGCTTGGAGCATCAACTAAGG 59.318 50.000 2.47 0.00 45.56 2.69
3472 3974 2.019984 GCTTGGAGCATCAACTAAGGG 58.980 52.381 0.00 0.00 41.89 3.95
3473 3975 2.019984 CTTGGAGCATCAACTAAGGGC 58.980 52.381 0.00 0.00 36.25 5.19
3474 3976 0.991146 TGGAGCATCAACTAAGGGCA 59.009 50.000 0.00 0.00 36.25 5.36
3475 3977 1.565759 TGGAGCATCAACTAAGGGCAT 59.434 47.619 0.00 0.00 36.25 4.40
3476 3978 2.225467 GGAGCATCAACTAAGGGCATC 58.775 52.381 0.00 0.00 36.25 3.91
3477 3979 2.158696 GGAGCATCAACTAAGGGCATCT 60.159 50.000 0.00 0.00 36.25 2.90
3478 3980 3.137533 GAGCATCAACTAAGGGCATCTC 58.862 50.000 0.00 0.00 33.17 2.75
3479 3981 2.158696 AGCATCAACTAAGGGCATCTCC 60.159 50.000 0.00 0.00 0.00 3.71
3480 3982 2.421952 GCATCAACTAAGGGCATCTCCA 60.422 50.000 0.00 0.00 36.21 3.86
3481 3983 3.889815 CATCAACTAAGGGCATCTCCAA 58.110 45.455 0.00 0.00 36.21 3.53
3482 3984 3.350219 TCAACTAAGGGCATCTCCAAC 57.650 47.619 0.00 0.00 36.21 3.77
3483 3985 2.009774 CAACTAAGGGCATCTCCAACG 58.990 52.381 0.00 0.00 36.21 4.10
3484 3986 0.541863 ACTAAGGGCATCTCCAACGG 59.458 55.000 0.00 0.00 36.21 4.44
3485 3987 0.541863 CTAAGGGCATCTCCAACGGT 59.458 55.000 0.00 0.00 36.21 4.83
3486 3988 0.251916 TAAGGGCATCTCCAACGGTG 59.748 55.000 0.00 0.00 36.21 4.94
3487 3989 1.488705 AAGGGCATCTCCAACGGTGA 61.489 55.000 0.00 0.00 36.21 4.02
3488 3990 1.745489 GGGCATCTCCAACGGTGAC 60.745 63.158 0.00 0.00 36.21 3.67
3489 3991 1.745489 GGCATCTCCAACGGTGACC 60.745 63.158 0.00 0.00 34.01 4.02
3490 3992 1.745489 GCATCTCCAACGGTGACCC 60.745 63.158 0.00 0.00 0.00 4.46
3502 4004 2.347697 GGTGACCCGCAAATTTTCTC 57.652 50.000 0.00 0.00 0.00 2.87
3503 4005 1.067846 GGTGACCCGCAAATTTTCTCC 60.068 52.381 0.00 0.00 0.00 3.71
3504 4006 1.067846 GTGACCCGCAAATTTTCTCCC 60.068 52.381 0.00 0.00 0.00 4.30
3505 4007 0.170339 GACCCGCAAATTTTCTCCCG 59.830 55.000 0.00 0.00 0.00 5.14
3506 4008 1.153842 CCCGCAAATTTTCTCCCGC 60.154 57.895 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 145 9.906660 TTAAAGTAAGTTCATCGATTTTGCAAT 57.093 25.926 0.00 0.00 0.00 3.56
321 322 2.701951 TCCACCCGAACTACTTGTCTTT 59.298 45.455 0.00 0.00 0.00 2.52
325 326 1.278127 CCATCCACCCGAACTACTTGT 59.722 52.381 0.00 0.00 0.00 3.16
371 372 1.153429 CACCGGTTTCGATCTCCCC 60.153 63.158 2.97 0.00 39.00 4.81
386 387 0.874175 GGAAAAGGTTGCGTTGCACC 60.874 55.000 0.00 0.00 38.71 5.01
478 479 3.038417 CTATACGGCGCTGCAGGC 61.038 66.667 18.15 16.58 37.64 4.85
479 480 2.356313 CCTATACGGCGCTGCAGG 60.356 66.667 18.15 16.47 0.00 4.85
480 481 1.372251 CTCCTATACGGCGCTGCAG 60.372 63.158 18.15 10.11 0.00 4.41
481 482 2.728180 CTCCTATACGGCGCTGCA 59.272 61.111 18.15 2.92 0.00 4.41
482 483 2.735100 GCTCCTATACGGCGCTGC 60.735 66.667 18.15 0.00 40.41 5.25
485 486 2.258897 GGAGCTCCTATACGGCGC 59.741 66.667 26.25 0.00 43.98 6.53
486 487 2.637383 GGGGAGCTCCTATACGGCG 61.637 68.421 31.36 4.80 35.95 6.46
487 488 0.832559 AAGGGGAGCTCCTATACGGC 60.833 60.000 31.36 13.25 35.80 5.68
488 489 1.718280 AAAGGGGAGCTCCTATACGG 58.282 55.000 31.36 0.00 35.80 4.02
489 490 3.388350 AGAAAAAGGGGAGCTCCTATACG 59.612 47.826 31.36 0.00 35.80 3.06
490 491 5.104485 TGAAGAAAAAGGGGAGCTCCTATAC 60.104 44.000 31.36 18.72 35.80 1.47
491 492 5.036916 TGAAGAAAAAGGGGAGCTCCTATA 58.963 41.667 31.36 0.99 35.80 1.31
492 493 3.852578 TGAAGAAAAAGGGGAGCTCCTAT 59.147 43.478 31.36 17.77 35.80 2.57
493 494 3.256704 TGAAGAAAAAGGGGAGCTCCTA 58.743 45.455 31.36 2.16 35.80 2.94
494 495 2.065799 TGAAGAAAAAGGGGAGCTCCT 58.934 47.619 31.36 11.45 39.17 3.69
495 496 2.558795 GTTGAAGAAAAAGGGGAGCTCC 59.441 50.000 25.59 25.59 0.00 4.70
496 497 3.222603 TGTTGAAGAAAAAGGGGAGCTC 58.777 45.455 4.71 4.71 0.00 4.09
497 498 3.312736 TGTTGAAGAAAAAGGGGAGCT 57.687 42.857 0.00 0.00 0.00 4.09
498 499 4.400529 TTTGTTGAAGAAAAAGGGGAGC 57.599 40.909 0.00 0.00 0.00 4.70
804 815 0.843309 AGAGATGAGGAGAGGCGAGA 59.157 55.000 0.00 0.00 0.00 4.04
989 1012 1.341976 TGGATCTCATCAGACCGTCCA 60.342 52.381 0.00 0.00 32.26 4.02
1189 1246 2.291670 ACTTGTAGAGATCCACCTCGGT 60.292 50.000 0.00 0.00 38.19 4.69
1273 1343 9.134734 GTTCGATTATTTAATTGCACTGGAAAA 57.865 29.630 0.00 0.00 0.00 2.29
1279 1349 6.767524 TGGGTTCGATTATTTAATTGCACT 57.232 33.333 0.00 0.00 0.00 4.40
1299 1372 3.273434 CGGTATAAGCATGATGGATGGG 58.727 50.000 0.00 0.00 31.99 4.00
1438 1535 2.310779 AGAAGTACCACTCCTGCTCA 57.689 50.000 0.00 0.00 0.00 4.26
1510 1607 0.680921 CCTTCCAGTACCCCGACGTA 60.681 60.000 0.00 0.00 0.00 3.57
1727 1848 0.394488 CGTACCCTGAGAGAGGCAGA 60.394 60.000 0.00 0.00 41.19 4.26
1768 1894 3.198068 CACGATTGGTTACTGCTATGCT 58.802 45.455 0.00 0.00 0.00 3.79
1769 1895 2.936498 ACACGATTGGTTACTGCTATGC 59.064 45.455 0.00 0.00 0.00 3.14
1770 1896 5.545658 AAACACGATTGGTTACTGCTATG 57.454 39.130 0.00 0.00 27.55 2.23
1771 1897 7.859325 ATTAAACACGATTGGTTACTGCTAT 57.141 32.000 0.00 0.00 34.47 2.97
1772 1898 7.675962 AATTAAACACGATTGGTTACTGCTA 57.324 32.000 0.00 0.00 34.47 3.49
2114 2263 4.767255 GTGGCTCAGCGAGGTGGG 62.767 72.222 2.30 0.00 0.00 4.61
2348 2503 2.832643 TTCATGAATGGAGGCATGGT 57.167 45.000 3.38 0.00 41.60 3.55
2362 2517 4.583073 TCTTGCATGGGAAGATGATTCATG 59.417 41.667 3.32 0.00 38.46 3.07
2378 2533 0.907704 TGGTAGGTCCCGTCTTGCAT 60.908 55.000 0.00 0.00 34.77 3.96
2651 2862 0.321671 AAGTACGTGCTCATGGTGCT 59.678 50.000 6.63 0.00 0.00 4.40
2796 3077 1.333177 ACTATCTGACTGGGGATCGC 58.667 55.000 0.06 0.06 0.00 4.58
3022 3307 8.833231 ACTGCATATATACTTACTTCGCAAAT 57.167 30.769 0.00 0.00 0.00 2.32
3070 3572 5.764686 TCTTGCATGCCCTATTTACATACAG 59.235 40.000 16.68 0.00 0.00 2.74
3092 3594 4.815846 TCATACACGTGCATGCAATTATCT 59.184 37.500 24.58 3.43 0.00 1.98
3239 3741 4.523558 GCACGGTAAGATACTATTCCCTCT 59.476 45.833 0.00 0.00 0.00 3.69
3240 3742 4.523558 AGCACGGTAAGATACTATTCCCTC 59.476 45.833 0.00 0.00 0.00 4.30
3241 3743 4.481072 AGCACGGTAAGATACTATTCCCT 58.519 43.478 0.00 0.00 0.00 4.20
3242 3744 4.868314 AGCACGGTAAGATACTATTCCC 57.132 45.455 0.00 0.00 0.00 3.97
3243 3745 6.979465 ACTAAGCACGGTAAGATACTATTCC 58.021 40.000 0.00 0.00 0.00 3.01
3246 3748 9.293404 TGATAACTAAGCACGGTAAGATACTAT 57.707 33.333 0.00 0.00 0.00 2.12
3269 3771 3.316029 CACATAACGGCCATTCACATGAT 59.684 43.478 2.24 0.00 31.07 2.45
3271 3773 2.795681 GCACATAACGGCCATTCACATG 60.796 50.000 2.24 0.00 0.00 3.21
3272 3774 1.405105 GCACATAACGGCCATTCACAT 59.595 47.619 2.24 0.00 0.00 3.21
3274 3776 3.622459 GCACATAACGGCCATTCAC 57.378 52.632 2.24 0.00 0.00 3.18
3281 3783 2.939460 AAAGATTGGCACATAACGGC 57.061 45.000 0.00 0.00 39.30 5.68
3337 3839 9.907576 CTATCAACAAAATTTTGCGTGTTAAAA 57.092 25.926 26.94 11.69 41.79 1.52
3338 3840 8.058915 GCTATCAACAAAATTTTGCGTGTTAAA 58.941 29.630 26.94 11.99 41.79 1.52
3339 3841 7.436673 AGCTATCAACAAAATTTTGCGTGTTAA 59.563 29.630 26.94 12.28 41.79 2.01
3340 3842 6.920758 AGCTATCAACAAAATTTTGCGTGTTA 59.079 30.769 26.94 20.89 41.79 2.41
3341 3843 5.752955 AGCTATCAACAAAATTTTGCGTGTT 59.247 32.000 26.94 20.89 41.79 3.32
3342 3844 5.288804 AGCTATCAACAAAATTTTGCGTGT 58.711 33.333 26.94 17.47 41.79 4.49
3343 3845 5.827568 AGCTATCAACAAAATTTTGCGTG 57.172 34.783 26.94 23.65 41.79 5.34
3344 3846 6.364976 GGTAAGCTATCAACAAAATTTTGCGT 59.635 34.615 26.94 14.81 41.79 5.24
3345 3847 6.364706 TGGTAAGCTATCAACAAAATTTTGCG 59.635 34.615 26.94 19.28 41.79 4.85
3346 3848 7.650834 TGGTAAGCTATCAACAAAATTTTGC 57.349 32.000 26.94 13.59 41.79 3.68
3377 3879 8.514594 CCAAGCATATTTGTATATACCAAGTGG 58.485 37.037 10.38 0.00 42.17 4.00
3378 3880 9.283768 TCCAAGCATATTTGTATATACCAAGTG 57.716 33.333 10.38 9.55 0.00 3.16
3379 3881 9.860650 TTCCAAGCATATTTGTATATACCAAGT 57.139 29.630 10.38 4.83 0.00 3.16
3397 3899 9.866655 AGGAGATAATAACATATTTTCCAAGCA 57.133 29.630 0.00 0.00 0.00 3.91
3416 3918 9.618890 CCTTCAAAATAGAACATCAAGGAGATA 57.381 33.333 0.00 0.00 34.43 1.98
3417 3919 8.331740 TCCTTCAAAATAGAACATCAAGGAGAT 58.668 33.333 0.00 0.00 34.53 2.75
3418 3920 7.689299 TCCTTCAAAATAGAACATCAAGGAGA 58.311 34.615 0.00 0.00 34.53 3.71
3419 3921 7.928307 TCCTTCAAAATAGAACATCAAGGAG 57.072 36.000 0.00 0.00 34.53 3.69
3420 3922 8.704849 TTTCCTTCAAAATAGAACATCAAGGA 57.295 30.769 0.00 0.00 37.08 3.36
3421 3923 9.196552 GTTTTCCTTCAAAATAGAACATCAAGG 57.803 33.333 0.00 0.00 36.35 3.61
3422 3924 9.748708 TGTTTTCCTTCAAAATAGAACATCAAG 57.251 29.630 0.00 0.00 36.35 3.02
3424 3926 9.912634 GATGTTTTCCTTCAAAATAGAACATCA 57.087 29.630 16.53 0.00 45.50 3.07
3425 3927 9.912634 TGATGTTTTCCTTCAAAATAGAACATC 57.087 29.630 15.24 15.24 45.98 3.06
3426 3928 9.918630 CTGATGTTTTCCTTCAAAATAGAACAT 57.081 29.630 0.00 0.00 38.68 2.71
3427 3929 7.867403 GCTGATGTTTTCCTTCAAAATAGAACA 59.133 33.333 0.00 0.00 36.35 3.18
3428 3930 8.084684 AGCTGATGTTTTCCTTCAAAATAGAAC 58.915 33.333 0.00 0.00 36.35 3.01
3429 3931 8.181904 AGCTGATGTTTTCCTTCAAAATAGAA 57.818 30.769 0.00 0.00 36.35 2.10
3430 3932 7.765695 AGCTGATGTTTTCCTTCAAAATAGA 57.234 32.000 0.00 0.00 36.35 1.98
3431 3933 7.330208 CCAAGCTGATGTTTTCCTTCAAAATAG 59.670 37.037 0.00 0.00 36.35 1.73
3432 3934 7.015098 TCCAAGCTGATGTTTTCCTTCAAAATA 59.985 33.333 0.00 0.00 36.35 1.40
3433 3935 5.993441 CCAAGCTGATGTTTTCCTTCAAAAT 59.007 36.000 0.00 0.00 36.35 1.82
3434 3936 5.128499 TCCAAGCTGATGTTTTCCTTCAAAA 59.872 36.000 0.00 0.00 0.00 2.44
3435 3937 4.648762 TCCAAGCTGATGTTTTCCTTCAAA 59.351 37.500 0.00 0.00 0.00 2.69
3436 3938 4.214310 TCCAAGCTGATGTTTTCCTTCAA 58.786 39.130 0.00 0.00 0.00 2.69
3437 3939 3.822735 CTCCAAGCTGATGTTTTCCTTCA 59.177 43.478 0.00 0.00 0.00 3.02
3438 3940 3.366781 GCTCCAAGCTGATGTTTTCCTTC 60.367 47.826 0.00 0.00 38.45 3.46
3439 3941 2.560105 GCTCCAAGCTGATGTTTTCCTT 59.440 45.455 0.00 0.00 38.45 3.36
3440 3942 2.165998 GCTCCAAGCTGATGTTTTCCT 58.834 47.619 0.00 0.00 38.45 3.36
3441 3943 1.888512 TGCTCCAAGCTGATGTTTTCC 59.111 47.619 0.11 0.00 42.97 3.13
3442 3944 3.192001 TGATGCTCCAAGCTGATGTTTTC 59.808 43.478 0.11 0.00 42.97 2.29
3443 3945 3.159472 TGATGCTCCAAGCTGATGTTTT 58.841 40.909 0.11 0.00 42.97 2.43
3444 3946 2.799017 TGATGCTCCAAGCTGATGTTT 58.201 42.857 0.11 0.00 42.97 2.83
3445 3947 2.490903 GTTGATGCTCCAAGCTGATGTT 59.509 45.455 0.11 0.00 42.97 2.71
3446 3948 2.089980 GTTGATGCTCCAAGCTGATGT 58.910 47.619 0.11 0.00 42.97 3.06
3447 3949 2.366533 AGTTGATGCTCCAAGCTGATG 58.633 47.619 0.11 0.00 42.97 3.07
3448 3950 2.803030 AGTTGATGCTCCAAGCTGAT 57.197 45.000 0.11 0.00 42.97 2.90
3449 3951 3.603532 CTTAGTTGATGCTCCAAGCTGA 58.396 45.455 0.11 0.00 42.97 4.26
3450 3952 2.681848 CCTTAGTTGATGCTCCAAGCTG 59.318 50.000 0.11 0.00 42.97 4.24
3451 3953 2.356535 CCCTTAGTTGATGCTCCAAGCT 60.357 50.000 0.11 0.00 42.97 3.74
3452 3954 2.019984 CCCTTAGTTGATGCTCCAAGC 58.980 52.381 0.00 0.00 42.82 4.01
3453 3955 2.019984 GCCCTTAGTTGATGCTCCAAG 58.980 52.381 0.00 0.00 0.00 3.61
3454 3956 1.354031 TGCCCTTAGTTGATGCTCCAA 59.646 47.619 0.00 0.00 0.00 3.53
3455 3957 0.991146 TGCCCTTAGTTGATGCTCCA 59.009 50.000 0.00 0.00 0.00 3.86
3456 3958 2.158696 AGATGCCCTTAGTTGATGCTCC 60.159 50.000 0.00 0.00 0.00 4.70
3457 3959 3.137533 GAGATGCCCTTAGTTGATGCTC 58.862 50.000 0.00 0.00 0.00 4.26
3458 3960 2.158696 GGAGATGCCCTTAGTTGATGCT 60.159 50.000 0.00 0.00 0.00 3.79
3459 3961 2.225467 GGAGATGCCCTTAGTTGATGC 58.775 52.381 0.00 0.00 0.00 3.91
3460 3962 3.565764 TGGAGATGCCCTTAGTTGATG 57.434 47.619 0.00 0.00 34.97 3.07
3461 3963 3.682718 CGTTGGAGATGCCCTTAGTTGAT 60.683 47.826 0.00 0.00 34.97 2.57
3462 3964 2.354704 CGTTGGAGATGCCCTTAGTTGA 60.355 50.000 0.00 0.00 34.97 3.18
3463 3965 2.009774 CGTTGGAGATGCCCTTAGTTG 58.990 52.381 0.00 0.00 34.97 3.16
3464 3966 1.065418 CCGTTGGAGATGCCCTTAGTT 60.065 52.381 0.00 0.00 34.97 2.24
3465 3967 0.541863 CCGTTGGAGATGCCCTTAGT 59.458 55.000 0.00 0.00 34.97 2.24
3466 3968 0.541863 ACCGTTGGAGATGCCCTTAG 59.458 55.000 0.00 0.00 34.97 2.18
3467 3969 0.251916 CACCGTTGGAGATGCCCTTA 59.748 55.000 0.00 0.00 34.97 2.69
3468 3970 1.002134 CACCGTTGGAGATGCCCTT 60.002 57.895 0.00 0.00 34.97 3.95
3469 3971 1.918293 TCACCGTTGGAGATGCCCT 60.918 57.895 0.00 0.00 34.97 5.19
3470 3972 1.745489 GTCACCGTTGGAGATGCCC 60.745 63.158 0.00 0.00 34.97 5.36
3471 3973 1.745489 GGTCACCGTTGGAGATGCC 60.745 63.158 0.00 0.00 37.10 4.40
3472 3974 1.745489 GGGTCACCGTTGGAGATGC 60.745 63.158 0.00 0.00 0.00 3.91
3473 3975 4.617875 GGGTCACCGTTGGAGATG 57.382 61.111 0.00 0.00 0.00 2.90
3483 3985 1.067846 GGAGAAAATTTGCGGGTCACC 60.068 52.381 0.00 0.00 0.00 4.02
3484 3986 1.067846 GGGAGAAAATTTGCGGGTCAC 60.068 52.381 0.00 0.00 0.00 3.67
3485 3987 1.253100 GGGAGAAAATTTGCGGGTCA 58.747 50.000 0.00 0.00 0.00 4.02
3486 3988 0.170339 CGGGAGAAAATTTGCGGGTC 59.830 55.000 0.00 0.00 0.00 4.46
3487 3989 1.873270 GCGGGAGAAAATTTGCGGGT 61.873 55.000 0.00 0.00 0.00 5.28
3488 3990 1.153842 GCGGGAGAAAATTTGCGGG 60.154 57.895 0.00 0.00 0.00 6.13
3489 3991 4.476361 GCGGGAGAAAATTTGCGG 57.524 55.556 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.