Multiple sequence alignment - TraesCS2D01G048600

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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 TraesCS2D01G048600 chr2D 100.000 4412 0 0 1 4412 17794198 17789787 0.000000e+00 8148.0
1 TraesCS2D01G048600 chr2D 83.300 1000 139 13 1939 2912 17761725 17760728 0.000000e+00 896.0
2 TraesCS2D01G048600 chr2D 77.717 736 142 12 1214 1944 17768085 17767367 8.770000e-117 431.0
3 TraesCS2D01G048600 chr2D 84.127 315 29 8 849 1160 17768383 17768087 7.220000e-73 285.0
4 TraesCS2D01G048600 chr2D 82.468 308 29 14 526 831 17768811 17768527 3.410000e-61 246.0
5 TraesCS2D01G048600 chr2A 94.740 3422 137 16 996 4412 19073293 19069910 0.000000e+00 5282.0
6 TraesCS2D01G048600 chr2A 81.126 2167 356 28 1370 3498 19050139 19047988 0.000000e+00 1687.0
7 TraesCS2D01G048600 chr2A 86.369 917 102 10 3508 4412 19045398 19044493 0.000000e+00 979.0
8 TraesCS2D01G048600 chr2A 82.682 358 48 9 11 364 19074634 19074287 5.540000e-79 305.0
9 TraesCS2D01G048600 chr2A 85.609 271 19 11 526 794 19074288 19074036 2.620000e-67 267.0
10 TraesCS2D01G048600 chr2A 93.333 45 3 0 889 933 19073449 19073405 2.850000e-07 67.6
11 TraesCS2D01G048600 chr2B 92.396 2696 179 14 836 3515 29184332 29187017 0.000000e+00 3819.0
12 TraesCS2D01G048600 chr2B 86.331 2619 305 25 841 3430 29251045 29253639 0.000000e+00 2804.0
13 TraesCS2D01G048600 chr2B 93.062 908 49 7 3508 4412 29187804 29188700 0.000000e+00 1315.0
14 TraesCS2D01G048600 chr2B 93.046 906 45 8 3508 4412 29254050 29254938 0.000000e+00 1308.0
15 TraesCS2D01G048600 chr2B 80.521 1766 287 29 841 2576 29533330 29535068 0.000000e+00 1303.0
16 TraesCS2D01G048600 chr2B 87.802 910 79 11 2629 3514 29535065 29535966 0.000000e+00 1037.0
17 TraesCS2D01G048600 chr2B 89.835 364 22 7 2 364 29183535 29183884 1.870000e-123 453.0
18 TraesCS2D01G048600 chr2B 88.274 307 14 4 524 828 29183881 29184167 9.080000e-92 348.0
19 TraesCS2D01G048600 chr2B 83.713 307 30 12 524 828 29532913 29533201 5.620000e-69 272.0
20 TraesCS2D01G048600 chr2B 85.321 218 18 9 579 794 29250649 29250854 3.460000e-51 213.0
21 TraesCS2D01G048600 chr6B 94.350 177 10 0 356 532 211161472 211161648 5.620000e-69 272.0
22 TraesCS2D01G048600 chr5D 95.322 171 8 0 363 533 25040144 25039974 5.620000e-69 272.0
23 TraesCS2D01G048600 chr3B 94.350 177 8 2 363 538 571752689 571752514 2.020000e-68 270.0
24 TraesCS2D01G048600 chr7D 94.318 176 8 2 363 537 205230482 205230656 7.270000e-68 268.0
25 TraesCS2D01G048600 chr6D 95.266 169 8 0 360 528 452949797 452949629 7.270000e-68 268.0
26 TraesCS2D01G048600 chr5A 94.767 172 9 0 356 527 429513458 429513629 7.270000e-68 268.0
27 TraesCS2D01G048600 chr4D 94.286 175 9 1 357 531 75782048 75782221 2.620000e-67 267.0
28 TraesCS2D01G048600 chr5B 92.473 186 10 4 359 543 481654836 481654654 3.380000e-66 263.0
29 TraesCS2D01G048600 chr1D 93.296 179 9 3 363 540 270329456 270329632 1.220000e-65 261.0
30 TraesCS2D01G048600 chr7A 91.765 85 7 0 819 903 37193124 37193208 7.750000e-23 119.0


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 TraesCS2D01G048600 chr2D 17789787 17794198 4411 True 8148.000000 8148 100.000000 1 4412 1 chr2D.!!$R2 4411
1 TraesCS2D01G048600 chr2D 17760728 17761725 997 True 896.000000 896 83.300000 1939 2912 1 chr2D.!!$R1 973
2 TraesCS2D01G048600 chr2D 17767367 17768811 1444 True 320.666667 431 81.437333 526 1944 3 chr2D.!!$R3 1418
3 TraesCS2D01G048600 chr2A 19069910 19074634 4724 True 1480.400000 5282 89.091000 11 4412 4 chr2A.!!$R2 4401
4 TraesCS2D01G048600 chr2A 19044493 19050139 5646 True 1333.000000 1687 83.747500 1370 4412 2 chr2A.!!$R1 3042
5 TraesCS2D01G048600 chr2B 29183535 29188700 5165 False 1483.750000 3819 90.891750 2 4412 4 chr2B.!!$F1 4410
6 TraesCS2D01G048600 chr2B 29250649 29254938 4289 False 1441.666667 2804 88.232667 579 4412 3 chr2B.!!$F2 3833
7 TraesCS2D01G048600 chr2B 29532913 29535966 3053 False 870.666667 1303 84.012000 524 3514 3 chr2B.!!$F3 2990

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
839 1312 0.471617 ACATGGGAGCATAGGAGCAC 59.528 55.000 0.00 0.0 36.85 4.40 F
842 1315 1.147153 GGGAGCATAGGAGCACACC 59.853 63.158 0.00 0.0 36.85 4.16 F
2266 2900 0.038310 ACCCCTGAAGTTTGCTAGCC 59.962 55.000 13.29 0.0 0.00 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2168 2802 1.269958 AGCCTTTTTCCCATTCAGCC 58.730 50.000 0.00 0.0 0.00 4.85 R
2506 3140 3.831715 ATGTTCTTCTTTTAGCACCGC 57.168 42.857 0.00 0.0 0.00 5.68 R
4196 7479 2.244651 ACACGAACTTCGCTGGTGC 61.245 57.895 11.15 0.0 45.12 5.01 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
26 27 4.582701 CACATAACTGCCAAAGTGGAAA 57.417 40.909 0.00 0.00 40.96 3.13
49 50 1.366111 AAATTCATCGACCGGCCACG 61.366 55.000 0.00 5.54 40.55 4.94
117 119 7.254852 TGTGGTTATTTTGTCACTTTTCTGAC 58.745 34.615 0.00 0.00 40.98 3.51
130 132 8.181573 GTCACTTTTCTGACAGTTCATTACAAA 58.818 33.333 1.59 0.00 40.40 2.83
206 211 9.348476 TGATGTATTATAGCCTTTTGTAATGCA 57.652 29.630 0.00 0.00 34.98 3.96
304 309 7.129622 CGACAGCTAGAACAACAATAAACAAA 58.870 34.615 0.00 0.00 0.00 2.83
367 376 9.819267 ATAACAATCTAAGCAGTAAAGTACTCC 57.181 33.333 0.00 0.00 36.76 3.85
368 377 6.641474 ACAATCTAAGCAGTAAAGTACTCCC 58.359 40.000 0.00 0.00 36.76 4.30
369 378 6.440965 ACAATCTAAGCAGTAAAGTACTCCCT 59.559 38.462 0.00 0.00 36.76 4.20
370 379 6.718522 ATCTAAGCAGTAAAGTACTCCCTC 57.281 41.667 0.00 0.00 36.76 4.30
371 380 4.954826 TCTAAGCAGTAAAGTACTCCCTCC 59.045 45.833 0.00 0.00 36.76 4.30
372 381 3.185880 AGCAGTAAAGTACTCCCTCCA 57.814 47.619 0.00 0.00 36.76 3.86
373 382 3.725634 AGCAGTAAAGTACTCCCTCCAT 58.274 45.455 0.00 0.00 36.76 3.41
374 383 4.104831 AGCAGTAAAGTACTCCCTCCATT 58.895 43.478 0.00 0.00 36.76 3.16
375 384 4.162509 AGCAGTAAAGTACTCCCTCCATTC 59.837 45.833 0.00 0.00 36.76 2.67
376 385 4.683671 GCAGTAAAGTACTCCCTCCATTCC 60.684 50.000 0.00 0.00 36.76 3.01
377 386 4.717280 CAGTAAAGTACTCCCTCCATTCCT 59.283 45.833 0.00 0.00 36.76 3.36
378 387 5.897824 CAGTAAAGTACTCCCTCCATTCCTA 59.102 44.000 0.00 0.00 36.76 2.94
379 388 6.383147 CAGTAAAGTACTCCCTCCATTCCTAA 59.617 42.308 0.00 0.00 36.76 2.69
380 389 6.964086 AGTAAAGTACTCCCTCCATTCCTAAA 59.036 38.462 0.00 0.00 32.47 1.85
381 390 6.910259 AAAGTACTCCCTCCATTCCTAAAT 57.090 37.500 0.00 0.00 0.00 1.40
382 391 8.931568 GTAAAGTACTCCCTCCATTCCTAAATA 58.068 37.037 0.00 0.00 0.00 1.40
383 392 8.582891 AAAGTACTCCCTCCATTCCTAAATAT 57.417 34.615 0.00 0.00 0.00 1.28
384 393 8.582891 AAGTACTCCCTCCATTCCTAAATATT 57.417 34.615 0.00 0.00 0.00 1.28
385 394 8.582891 AGTACTCCCTCCATTCCTAAATATTT 57.417 34.615 5.89 5.89 0.00 1.40
386 395 8.440771 AGTACTCCCTCCATTCCTAAATATTTG 58.559 37.037 11.05 1.40 0.00 2.32
387 396 7.226059 ACTCCCTCCATTCCTAAATATTTGT 57.774 36.000 11.05 0.00 0.00 2.83
388 397 7.290813 ACTCCCTCCATTCCTAAATATTTGTC 58.709 38.462 11.05 0.00 0.00 3.18
389 398 7.129504 ACTCCCTCCATTCCTAAATATTTGTCT 59.870 37.037 11.05 0.00 0.00 3.41
390 399 7.882755 TCCCTCCATTCCTAAATATTTGTCTT 58.117 34.615 11.05 0.00 0.00 3.01
391 400 8.343787 TCCCTCCATTCCTAAATATTTGTCTTT 58.656 33.333 11.05 0.00 0.00 2.52
392 401 8.981659 CCCTCCATTCCTAAATATTTGTCTTTT 58.018 33.333 11.05 0.00 0.00 2.27
410 419 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
411 420 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
417 426 9.958180 TTTAGAGATTTCAAATGGACTATCACA 57.042 29.630 0.00 0.00 0.00 3.58
457 466 9.440761 AGACATATTTTAGAGGGTAGATTCACT 57.559 33.333 0.00 0.00 0.00 3.41
458 467 9.699703 GACATATTTTAGAGGGTAGATTCACTC 57.300 37.037 0.00 0.00 38.06 3.51
459 468 9.213777 ACATATTTTAGAGGGTAGATTCACTCA 57.786 33.333 0.00 0.00 40.03 3.41
463 472 9.981460 ATTTTAGAGGGTAGATTCACTCATTTT 57.019 29.630 0.00 0.00 40.03 1.82
464 473 8.792830 TTTAGAGGGTAGATTCACTCATTTTG 57.207 34.615 0.00 0.00 40.03 2.44
465 474 5.189180 AGAGGGTAGATTCACTCATTTTGC 58.811 41.667 0.00 0.00 40.03 3.68
466 475 5.045286 AGAGGGTAGATTCACTCATTTTGCT 60.045 40.000 0.00 0.00 40.03 3.91
467 476 5.574188 AGGGTAGATTCACTCATTTTGCTT 58.426 37.500 0.00 0.00 0.00 3.91
468 477 5.649831 AGGGTAGATTCACTCATTTTGCTTC 59.350 40.000 0.00 0.00 0.00 3.86
469 478 5.447818 GGGTAGATTCACTCATTTTGCTTCG 60.448 44.000 0.00 0.00 0.00 3.79
470 479 5.122396 GGTAGATTCACTCATTTTGCTTCGT 59.878 40.000 0.00 0.00 0.00 3.85
471 480 6.312918 GGTAGATTCACTCATTTTGCTTCGTA 59.687 38.462 0.00 0.00 0.00 3.43
472 481 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
473 482 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
474 483 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
475 484 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
476 485 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
477 486 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
478 487 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
479 488 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
480 489 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
481 490 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
482 491 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
483 492 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
484 493 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
485 494 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
486 495 4.684242 TGCTTCGTATGTAGTCACTTGTTG 59.316 41.667 0.00 0.00 0.00 3.33
487 496 4.921515 GCTTCGTATGTAGTCACTTGTTGA 59.078 41.667 0.00 0.00 0.00 3.18
488 497 5.404366 GCTTCGTATGTAGTCACTTGTTGAA 59.596 40.000 0.00 0.00 35.39 2.69
489 498 6.073980 GCTTCGTATGTAGTCACTTGTTGAAA 60.074 38.462 0.00 0.00 35.39 2.69
490 499 7.360101 GCTTCGTATGTAGTCACTTGTTGAAAT 60.360 37.037 0.00 0.00 35.39 2.17
491 500 9.135843 CTTCGTATGTAGTCACTTGTTGAAATA 57.864 33.333 0.00 0.00 35.39 1.40
492 501 9.647797 TTCGTATGTAGTCACTTGTTGAAATAT 57.352 29.630 0.00 0.00 35.39 1.28
493 502 9.297586 TCGTATGTAGTCACTTGTTGAAATATC 57.702 33.333 0.00 0.00 35.39 1.63
494 503 9.302345 CGTATGTAGTCACTTGTTGAAATATCT 57.698 33.333 0.00 0.00 35.39 1.98
503 512 9.996554 TCACTTGTTGAAATATCTAGAAAGACA 57.003 29.630 0.00 0.00 33.57 3.41
563 572 1.079503 CTAGCCTTGGACGTTCTTGC 58.920 55.000 0.00 0.00 0.00 4.01
576 585 3.005554 CGTTCTTGCTCCTGATCATTGT 58.994 45.455 0.00 0.00 0.00 2.71
697 706 3.071312 TGGAGCATGCTGTCCAAATTTTT 59.929 39.130 28.27 0.00 40.01 1.94
814 830 3.734902 GCTGCATAAGTTAACACATGGCC 60.735 47.826 8.61 0.00 0.00 5.36
828 844 1.976132 ATGGCCGAGTCACATGGGAG 61.976 60.000 0.00 0.00 0.00 4.30
829 845 2.512515 GCCGAGTCACATGGGAGC 60.513 66.667 0.00 0.00 0.00 4.70
830 846 2.981302 CCGAGTCACATGGGAGCA 59.019 61.111 0.00 0.00 0.00 4.26
832 848 0.752658 CCGAGTCACATGGGAGCATA 59.247 55.000 0.00 0.00 0.00 3.14
836 852 2.036992 GAGTCACATGGGAGCATAGGAG 59.963 54.545 0.00 0.00 0.00 3.69
839 1312 0.471617 ACATGGGAGCATAGGAGCAC 59.528 55.000 0.00 0.00 36.85 4.40
842 1315 1.147153 GGGAGCATAGGAGCACACC 59.853 63.158 0.00 0.00 36.85 4.16
847 1320 1.443407 CATAGGAGCACACCGAGGG 59.557 63.158 0.00 0.00 34.73 4.30
854 1327 3.097614 GGAGCACACCGAGGGTATATAT 58.902 50.000 0.00 0.00 32.11 0.86
885 1435 2.880268 CAACAAGGTGCTGAATGAGACA 59.120 45.455 0.00 0.00 0.00 3.41
919 1469 3.636764 CTGAAGGTAAGTGCCAAAGGTTT 59.363 43.478 0.00 0.00 0.00 3.27
944 1494 5.235186 CAGTTTCAGTCTTAGTGTTGTCCAG 59.765 44.000 0.00 0.00 0.00 3.86
962 1512 5.783111 GTCCAGCAAACAAAAGGACATTAT 58.217 37.500 0.00 0.00 46.15 1.28
1020 1625 5.949354 CCTTCAGGTAAATTATGGTCCACAA 59.051 40.000 0.00 0.00 0.00 3.33
1031 1636 3.358111 TGGTCCACAAACTGACAAAGA 57.642 42.857 0.00 0.00 33.09 2.52
1034 1641 4.709397 TGGTCCACAAACTGACAAAGAAAT 59.291 37.500 0.00 0.00 33.09 2.17
1035 1642 5.043248 GGTCCACAAACTGACAAAGAAATG 58.957 41.667 0.00 0.00 33.09 2.32
1057 1664 5.995055 TGTGGCAAAAACAAAGTTGAAAAG 58.005 33.333 0.00 0.00 0.00 2.27
1058 1665 4.851014 GTGGCAAAAACAAAGTTGAAAAGC 59.149 37.500 0.00 0.00 0.00 3.51
1059 1666 4.087956 GGCAAAAACAAAGTTGAAAAGCG 58.912 39.130 0.00 0.00 0.00 4.68
1060 1667 4.143009 GGCAAAAACAAAGTTGAAAAGCGA 60.143 37.500 0.00 0.00 0.00 4.93
1061 1668 5.447144 GGCAAAAACAAAGTTGAAAAGCGAT 60.447 36.000 0.00 0.00 0.00 4.58
1084 1691 8.808529 CGATGTTTACTAACCTTCACTAGAATG 58.191 37.037 0.00 0.00 33.15 2.67
1093 1701 3.181465 CCTTCACTAGAATGTGGGCGTAT 60.181 47.826 0.00 0.00 38.40 3.06
1094 1702 3.452755 TCACTAGAATGTGGGCGTATG 57.547 47.619 0.00 0.00 38.40 2.39
1113 1721 2.730069 TGCAAAACAAGACGATGCAAG 58.270 42.857 0.00 0.00 43.39 4.01
1204 1814 6.082338 CCAACTCTCTTCAAATCAACATTCG 58.918 40.000 0.00 0.00 0.00 3.34
1342 1952 1.694150 AGCTAGTTGAGAAGGTGTGCA 59.306 47.619 0.00 0.00 0.00 4.57
1398 2008 7.603024 CGGAAAGATACAAAGGAGAAACTAAGT 59.397 37.037 0.00 0.00 0.00 2.24
1469 2079 2.157738 GAGAGTGCAGGCAAAGAACAT 58.842 47.619 0.00 0.00 0.00 2.71
1636 2246 2.005451 CTTCTTCATCCTCAAGCACCG 58.995 52.381 0.00 0.00 0.00 4.94
1827 2437 2.932614 CAAGATAGAGGACAGCAAACCG 59.067 50.000 0.00 0.00 0.00 4.44
1874 2484 1.493861 AGCTCTATGCCAAGCTCAGA 58.506 50.000 0.00 0.00 45.57 3.27
2091 2701 6.855836 TGTCTCAGATAAATTTGATGTTGGC 58.144 36.000 0.00 0.00 0.00 4.52
2266 2900 0.038310 ACCCCTGAAGTTTGCTAGCC 59.962 55.000 13.29 0.00 0.00 3.93
2321 2955 8.243289 AGTAAAAATGTTGCAAGTATGAATGC 57.757 30.769 0.00 0.00 42.86 3.56
2432 3066 6.698766 CCTTCTGATTTTCCACAACTGAAAAG 59.301 38.462 0.00 0.00 42.91 2.27
2506 3140 4.580167 TGACAGTTGGGAGTTCATTGAAAG 59.420 41.667 0.00 0.00 0.00 2.62
2521 3155 3.896648 TGAAAGCGGTGCTAAAAGAAG 57.103 42.857 0.00 0.00 38.25 2.85
2546 3180 6.126863 ACATTGGAGTTCTATCTGTGGAAA 57.873 37.500 0.00 0.00 0.00 3.13
3061 3728 7.039882 GGTCTCCTCGTCAAACTTTAATCATA 58.960 38.462 0.00 0.00 0.00 2.15
3648 6910 3.552684 GCAGCAAAACATTTGGACAGCTA 60.553 43.478 5.12 0.00 0.00 3.32
4012 7295 2.547211 CTGAACAAGTGCTTGACTGAGG 59.453 50.000 17.62 1.04 42.93 3.86
4043 7326 2.500910 CAGCTCTCTTCTCCCTTGTGAT 59.499 50.000 0.00 0.00 0.00 3.06
4044 7327 3.055240 CAGCTCTCTTCTCCCTTGTGATT 60.055 47.826 0.00 0.00 0.00 2.57
4045 7328 3.055240 AGCTCTCTTCTCCCTTGTGATTG 60.055 47.826 0.00 0.00 0.00 2.67
4046 7329 3.307339 GCTCTCTTCTCCCTTGTGATTGT 60.307 47.826 0.00 0.00 0.00 2.71
4047 7330 4.252073 CTCTCTTCTCCCTTGTGATTGTG 58.748 47.826 0.00 0.00 0.00 3.33
4048 7331 3.903714 TCTCTTCTCCCTTGTGATTGTGA 59.096 43.478 0.00 0.00 0.00 3.58
4068 7351 6.220201 TGTGACGACAAGAATCAAGAATACA 58.780 36.000 0.00 0.00 0.00 2.29
4078 7361 9.467258 CAAGAATCAAGAATACACACATTGTTT 57.533 29.630 0.00 0.00 39.91 2.83
4196 7479 1.538512 CCAGCACACTTGATTCACTGG 59.461 52.381 4.82 4.82 37.47 4.00
4369 7652 3.387962 TGACTAGCAGATTCAGGGGATT 58.612 45.455 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.096382 CCACTTTGGCAGTTATGTGGTATC 59.904 45.833 12.31 0.00 39.80 2.24
20 21 4.669197 CGGTCGATGAATTTCAGTTTCCAC 60.669 45.833 5.21 0.00 0.00 4.02
26 27 1.369625 GCCGGTCGATGAATTTCAGT 58.630 50.000 1.90 0.00 0.00 3.41
49 50 9.255304 CCTTTATCTAGAGAGCAACAGAAATAC 57.745 37.037 0.00 0.00 0.00 1.89
200 205 0.326595 TCCCGGTCAGCTTTGCATTA 59.673 50.000 0.00 0.00 0.00 1.90
205 210 1.750399 CCCATCCCGGTCAGCTTTG 60.750 63.158 0.00 0.00 0.00 2.77
206 211 2.677228 CCCATCCCGGTCAGCTTT 59.323 61.111 0.00 0.00 0.00 3.51
304 309 4.162131 AGCCAAATGGTGTCTTGTTTCTTT 59.838 37.500 0.71 0.00 37.57 2.52
330 339 6.260936 TGCTTAGATTGTTATTAGCAGAAGCC 59.739 38.462 0.00 0.00 43.56 4.35
364 373 7.521669 AGACAAATATTTAGGAATGGAGGGAG 58.478 38.462 0.00 0.00 0.00 4.30
365 374 7.465900 AGACAAATATTTAGGAATGGAGGGA 57.534 36.000 0.00 0.00 0.00 4.20
366 375 8.539117 AAAGACAAATATTTAGGAATGGAGGG 57.461 34.615 0.00 0.00 0.00 4.30
384 393 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
385 394 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
391 400 9.958180 TGTGATAGTCCATTTGAAATCTCTAAA 57.042 29.630 0.00 0.00 0.00 1.85
400 409 9.631257 ACATTCATATGTGATAGTCCATTTGAA 57.369 29.630 1.90 7.58 43.29 2.69
431 440 9.440761 AGTGAATCTACCCTCTAAAATATGTCT 57.559 33.333 0.00 0.00 0.00 3.41
432 441 9.699703 GAGTGAATCTACCCTCTAAAATATGTC 57.300 37.037 0.00 0.00 0.00 3.06
433 442 9.213777 TGAGTGAATCTACCCTCTAAAATATGT 57.786 33.333 0.00 0.00 0.00 2.29
437 446 9.981460 AAAATGAGTGAATCTACCCTCTAAAAT 57.019 29.630 0.00 0.00 0.00 1.82
438 447 9.231297 CAAAATGAGTGAATCTACCCTCTAAAA 57.769 33.333 0.00 0.00 0.00 1.52
439 448 7.336931 GCAAAATGAGTGAATCTACCCTCTAAA 59.663 37.037 0.00 0.00 0.00 1.85
440 449 6.823689 GCAAAATGAGTGAATCTACCCTCTAA 59.176 38.462 0.00 0.00 0.00 2.10
441 450 6.156949 AGCAAAATGAGTGAATCTACCCTCTA 59.843 38.462 0.00 0.00 0.00 2.43
442 451 5.045286 AGCAAAATGAGTGAATCTACCCTCT 60.045 40.000 0.00 0.00 0.00 3.69
443 452 5.189180 AGCAAAATGAGTGAATCTACCCTC 58.811 41.667 0.00 0.00 0.00 4.30
444 453 5.184892 AGCAAAATGAGTGAATCTACCCT 57.815 39.130 0.00 0.00 0.00 4.34
445 454 5.447818 CGAAGCAAAATGAGTGAATCTACCC 60.448 44.000 0.00 0.00 0.00 3.69
446 455 5.122396 ACGAAGCAAAATGAGTGAATCTACC 59.878 40.000 0.00 0.00 0.00 3.18
447 456 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
448 457 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
449 458 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
450 459 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
451 460 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
452 461 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
453 462 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
454 463 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
455 464 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
456 465 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
457 466 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
458 467 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
459 468 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
460 469 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
461 470 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
462 471 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
463 472 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
464 473 4.921515 TCAACAAGTGACTACATACGAAGC 59.078 41.667 0.00 0.00 0.00 3.86
465 474 7.402811 TTTCAACAAGTGACTACATACGAAG 57.597 36.000 0.00 0.00 35.39 3.79
466 475 7.956420 ATTTCAACAAGTGACTACATACGAA 57.044 32.000 0.00 0.00 35.39 3.85
467 476 9.297586 GATATTTCAACAAGTGACTACATACGA 57.702 33.333 0.00 0.00 35.39 3.43
468 477 9.302345 AGATATTTCAACAAGTGACTACATACG 57.698 33.333 0.00 0.00 35.39 3.06
477 486 9.996554 TGTCTTTCTAGATATTTCAACAAGTGA 57.003 29.630 0.00 0.00 31.86 3.41
497 506 9.807921 TCCTTCTGTTCCTAAATATTTGTCTTT 57.192 29.630 11.05 0.00 0.00 2.52
498 507 9.454859 CTCCTTCTGTTCCTAAATATTTGTCTT 57.545 33.333 11.05 0.00 0.00 3.01
499 508 8.606830 ACTCCTTCTGTTCCTAAATATTTGTCT 58.393 33.333 11.05 0.00 0.00 3.41
500 509 8.794335 ACTCCTTCTGTTCCTAAATATTTGTC 57.206 34.615 11.05 0.00 0.00 3.18
515 524 9.570468 TCGTTTACTATCATATACTCCTTCTGT 57.430 33.333 0.00 0.00 0.00 3.41
639 648 2.492088 CTCGAGTTGTGGTCCAGATACA 59.508 50.000 3.62 0.00 0.00 2.29
728 737 5.014228 AGGGCTTAAACTTCTACACCTTCAT 59.986 40.000 0.00 0.00 0.00 2.57
729 738 4.349930 AGGGCTTAAACTTCTACACCTTCA 59.650 41.667 0.00 0.00 0.00 3.02
730 739 4.907809 AGGGCTTAAACTTCTACACCTTC 58.092 43.478 0.00 0.00 0.00 3.46
732 741 3.263681 GGAGGGCTTAAACTTCTACACCT 59.736 47.826 0.00 0.00 0.00 4.00
777 787 1.753078 CAGCATCTGGCCTGTGCAT 60.753 57.895 26.57 15.58 46.50 3.96
814 830 1.269988 CCTATGCTCCCATGTGACTCG 60.270 57.143 0.00 0.00 32.85 4.18
828 844 1.227380 CCTCGGTGTGCTCCTATGC 60.227 63.158 0.00 0.00 0.00 3.14
829 845 1.330655 ACCCTCGGTGTGCTCCTATG 61.331 60.000 0.00 0.00 32.98 2.23
830 846 0.260816 TACCCTCGGTGTGCTCCTAT 59.739 55.000 0.00 0.00 36.19 2.57
832 848 0.260816 TATACCCTCGGTGTGCTCCT 59.739 55.000 0.00 0.00 36.19 3.69
836 852 4.267349 ACAATATATACCCTCGGTGTGC 57.733 45.455 0.00 0.00 36.19 4.57
839 1312 6.395629 CAGGTAACAATATATACCCTCGGTG 58.604 44.000 8.08 0.00 42.11 4.94
842 1315 6.032956 TGCAGGTAACAATATATACCCTCG 57.967 41.667 8.08 0.00 42.11 4.63
847 1320 8.342634 CACCTTGTTGCAGGTAACAATATATAC 58.657 37.037 14.48 0.00 46.27 1.47
854 1327 1.407258 GCACCTTGTTGCAGGTAACAA 59.593 47.619 13.63 13.63 46.27 2.83
885 1435 5.696724 CACTTACCTTCAGAAAGAATCGTGT 59.303 40.000 0.00 0.00 35.25 4.49
919 1469 5.105106 TGGACAACACTAAGACTGAAACTGA 60.105 40.000 0.00 0.00 0.00 3.41
944 1494 7.247728 TCATCGTATAATGTCCTTTTGTTTGC 58.752 34.615 0.00 0.00 0.00 3.68
1015 1620 4.805192 CCACATTTCTTTGTCAGTTTGTGG 59.195 41.667 4.55 4.55 37.37 4.17
1020 1625 4.734398 TTGCCACATTTCTTTGTCAGTT 57.266 36.364 0.00 0.00 0.00 3.16
1031 1636 6.566197 TTCAACTTTGTTTTTGCCACATTT 57.434 29.167 0.00 0.00 0.00 2.32
1034 1641 5.561725 GCTTTTCAACTTTGTTTTTGCCACA 60.562 36.000 0.00 0.00 0.00 4.17
1035 1642 4.851014 GCTTTTCAACTTTGTTTTTGCCAC 59.149 37.500 0.00 0.00 0.00 5.01
1057 1664 6.327934 TCTAGTGAAGGTTAGTAAACATCGC 58.672 40.000 8.35 8.35 37.34 4.58
1058 1665 8.808529 CATTCTAGTGAAGGTTAGTAAACATCG 58.191 37.037 0.00 0.00 34.15 3.84
1059 1666 9.654663 ACATTCTAGTGAAGGTTAGTAAACATC 57.345 33.333 0.00 0.00 43.53 3.06
1060 1667 9.436957 CACATTCTAGTGAAGGTTAGTAAACAT 57.563 33.333 0.00 0.00 43.53 2.71
1061 1668 7.876068 CCACATTCTAGTGAAGGTTAGTAAACA 59.124 37.037 0.00 0.00 43.53 2.83
1084 1691 1.268352 TCTTGTTTTGCATACGCCCAC 59.732 47.619 0.00 0.00 37.32 4.61
1093 1701 2.098934 ACTTGCATCGTCTTGTTTTGCA 59.901 40.909 0.00 0.00 41.22 4.08
1094 1702 2.721090 GACTTGCATCGTCTTGTTTTGC 59.279 45.455 8.86 0.00 0.00 3.68
1113 1721 2.301009 TGTCCTTAGAAACTTCCCCGAC 59.699 50.000 0.00 0.00 0.00 4.79
1152 1762 3.870419 GGATGCAGTCAAGAGAGAATCAC 59.130 47.826 0.00 0.00 37.82 3.06
1204 1814 1.544246 AGTGGCCGCATAAAGGAAAAC 59.456 47.619 20.59 0.00 0.00 2.43
1288 1898 1.133136 TGAGGCTACCCATCCTCCTAC 60.133 57.143 5.90 0.00 46.39 3.18
1311 1921 5.227569 TCTCAACTAGCTTGGTGATGAAA 57.772 39.130 16.32 0.62 0.00 2.69
1398 2008 6.014755 TCGACGATAGATTCTTCTCTAGGGTA 60.015 42.308 0.00 0.00 41.38 3.69
1400 2010 5.239351 TCGACGATAGATTCTTCTCTAGGG 58.761 45.833 0.00 0.00 41.38 3.53
1636 2246 0.037232 GTGGTAGAGGCAGTGGTGAC 60.037 60.000 0.00 0.00 0.00 3.67
1677 2287 3.572584 ACGAACCGACTGATTTACTGTC 58.427 45.455 0.00 0.00 41.77 3.51
1874 2484 5.987347 TCATTAACTCGACCGAAAAACTTCT 59.013 36.000 0.00 0.00 0.00 2.85
2091 2701 5.470368 TCTGTCATCTCTTTTGTTAGACGG 58.530 41.667 0.00 0.00 33.41 4.79
2168 2802 1.269958 AGCCTTTTTCCCATTCAGCC 58.730 50.000 0.00 0.00 0.00 4.85
2266 2900 4.941263 TGTAACTATTACTTTGCTGCCCTG 59.059 41.667 0.00 0.00 37.06 4.45
2321 2955 6.343703 TGTAACTCCATGATCTCTGTTGATG 58.656 40.000 0.00 0.00 0.00 3.07
2506 3140 3.831715 ATGTTCTTCTTTTAGCACCGC 57.168 42.857 0.00 0.00 0.00 5.68
2521 3155 5.734720 TCCACAGATAGAACTCCAATGTTC 58.265 41.667 0.00 0.00 44.67 3.18
2546 3180 7.869429 CCTTTTGCTCTATTTGACACAATTTCT 59.131 33.333 0.00 0.00 0.00 2.52
3648 6910 3.008330 GCTTGTGTTGATCTCAGAGCAT 58.992 45.455 0.00 0.00 0.00 3.79
3863 7138 6.974622 CAGCAATCCATGTGGTAAAGTATTTC 59.025 38.462 0.00 0.00 40.09 2.17
4043 7326 6.704050 TGTATTCTTGATTCTTGTCGTCACAA 59.296 34.615 0.00 0.00 40.40 3.33
4044 7327 6.145534 GTGTATTCTTGATTCTTGTCGTCACA 59.854 38.462 0.00 0.00 0.00 3.58
4045 7328 6.145534 TGTGTATTCTTGATTCTTGTCGTCAC 59.854 38.462 0.00 0.00 0.00 3.67
4046 7329 6.145534 GTGTGTATTCTTGATTCTTGTCGTCA 59.854 38.462 0.00 0.00 0.00 4.35
4047 7330 6.145534 TGTGTGTATTCTTGATTCTTGTCGTC 59.854 38.462 0.00 0.00 0.00 4.20
4048 7331 5.989168 TGTGTGTATTCTTGATTCTTGTCGT 59.011 36.000 0.00 0.00 0.00 4.34
4068 7351 3.327757 TCAGAGCCTCCTAAACAATGTGT 59.672 43.478 0.00 0.00 0.00 3.72
4078 7361 5.846164 TCCATTCATTATTCAGAGCCTCCTA 59.154 40.000 0.00 0.00 0.00 2.94
4196 7479 2.244651 ACACGAACTTCGCTGGTGC 61.245 57.895 11.15 0.00 45.12 5.01
4369 7652 3.559171 GGGTGAGTAGAACCAGAATTGCA 60.559 47.826 0.00 0.00 39.65 4.08


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

AutoCloner maintained by Alex Coulton.