Multiple sequence alignment - TraesCS1D01G146500

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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 TraesCS1D01G146500 chr1D 100.000 5110 0 0 1 5110 202560741 202565850 0.000000e+00 9437.0
1 TraesCS1D01G146500 chr1D 86.207 87 11 1 3604 3689 122770085 122770171 5.450000e-15 93.5
2 TraesCS1D01G146500 chr1B 91.999 4037 176 65 882 4834 296493810 296497783 0.000000e+00 5529.0
3 TraesCS1D01G146500 chr1B 91.284 654 45 6 11 661 296492176 296492820 0.000000e+00 881.0
4 TraesCS1D01G146500 chr1B 95.288 191 9 0 679 869 296493424 296493614 2.310000e-78 303.0
5 TraesCS1D01G146500 chr1B 85.000 280 13 16 4831 5110 296498055 296498305 1.830000e-64 257.0
6 TraesCS1D01G146500 chr1A 88.955 2010 134 40 1469 3420 256819781 256821760 0.000000e+00 2401.0
7 TraesCS1D01G146500 chr1A 93.214 1061 51 14 3414 4460 256821792 256822845 0.000000e+00 1541.0
8 TraesCS1D01G146500 chr1A 92.708 672 36 10 756 1424 256819116 256819777 0.000000e+00 957.0
9 TraesCS1D01G146500 chr1A 79.417 549 83 22 158 687 256818432 256818969 1.350000e-95 361.0
10 TraesCS1D01G146500 chr1A 95.302 149 7 0 11 159 393948470 393948618 2.380000e-58 237.0
11 TraesCS1D01G146500 chr1A 82.833 233 10 13 4906 5110 256823105 256823335 1.130000e-41 182.0
12 TraesCS1D01G146500 chr6B 95.333 150 7 0 11 160 545182730 545182581 6.610000e-59 239.0
13 TraesCS1D01G146500 chr6B 94.667 150 8 0 11 160 211161627 211161478 3.080000e-57 233.0
14 TraesCS1D01G146500 chr7B 95.302 149 7 0 11 159 714315958 714316106 2.380000e-58 237.0
15 TraesCS1D01G146500 chr7A 95.302 149 7 0 11 159 347249367 347249515 2.380000e-58 237.0
16 TraesCS1D01G146500 chr7A 87.059 85 10 1 3604 3687 369476279 369476363 1.510000e-15 95.3
17 TraesCS1D01G146500 chr7A 86.585 82 10 1 3607 3687 50054345 50054264 7.050000e-14 89.8
18 TraesCS1D01G146500 chr3D 95.302 149 7 0 11 159 2113403 2113255 2.380000e-58 237.0
19 TraesCS1D01G146500 chr3D 85.057 87 12 1 3603 3688 486153998 486153912 2.530000e-13 87.9
20 TraesCS1D01G146500 chr5A 94.667 150 8 0 11 160 690414031 690414180 3.080000e-57 233.0
21 TraesCS1D01G146500 chr5A 86.905 84 6 2 3603 3685 397253524 397253445 7.050000e-14 89.8
22 TraesCS1D01G146500 chr2D 93.548 155 10 0 11 165 426427949 426427795 1.110000e-56 231.0
23 TraesCS1D01G146500 chr4D 89.157 83 8 1 3607 3688 165260867 165260785 9.050000e-18 102.0
24 TraesCS1D01G146500 chr2A 86.420 81 10 1 3609 3688 660287364 660287444 2.530000e-13 87.9


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 TraesCS1D01G146500 chr1D 202560741 202565850 5109 False 9437.0 9437 100.00000 1 5110 1 chr1D.!!$F2 5109
1 TraesCS1D01G146500 chr1B 296492176 296498305 6129 False 1742.5 5529 90.89275 11 5110 4 chr1B.!!$F1 5099
2 TraesCS1D01G146500 chr1A 256818432 256823335 4903 False 1088.4 2401 87.42540 158 5110 5 chr1A.!!$F2 4952

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
459 476 0.097674 GCCTACGCACAAATGAGCAG 59.902 55.000 3.83 0.00 34.03 4.24 F
869 1553 0.537188 AAGACCCACACGGCTCATAG 59.463 55.000 0.00 0.00 33.26 2.23 F
890 1757 0.692419 CTCATACCCACCTCTGCCCT 60.692 60.000 0.00 0.00 0.00 5.19 F
2546 3468 0.035152 ATCCAGAGTGCGCAAATGGA 60.035 50.000 30.35 30.35 43.82 3.41 F
3347 4286 1.072173 TGGTGCTGCACTGATGTTACT 59.928 47.619 29.54 0.00 34.40 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 2993 0.251916 CCATAAAGGGAGCACCGACA 59.748 55.000 0.0 0.0 46.96 4.35 R
2418 3337 1.271379 GCTGTAGAAACCAGGAAGGCA 60.271 52.381 0.0 0.0 43.14 4.75 R
2577 3499 3.053395 AGCCACATGGTATCAAGATTGGT 60.053 43.478 0.0 0.0 37.57 3.67 R
3885 4869 0.322456 TGCCAATGTCCACCTGTAGC 60.322 55.000 0.0 0.0 0.00 3.58 R
4420 5414 0.673437 TTTTCCTGCCAGCTTTTCGG 59.327 50.000 0.0 0.0 0.00 4.30 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
53 54 9.731819 GAGATTTCAATAAGTGACTACATACGA 57.268 33.333 0.00 0.00 35.39 3.43
57 58 6.859017 TCAATAAGTGACTACATACGAAGCA 58.141 36.000 0.00 0.00 0.00 3.91
58 59 7.317390 TCAATAAGTGACTACATACGAAGCAA 58.683 34.615 0.00 0.00 0.00 3.91
118 119 5.571784 ATCTGCATGTGGTAGTTCATTTG 57.428 39.130 0.00 0.00 0.00 2.32
169 170 3.246167 ACAGAGGGAGTAGGAGTTTCCAT 60.246 47.826 0.00 0.00 39.61 3.41
170 171 3.777522 CAGAGGGAGTAGGAGTTTCCATT 59.222 47.826 0.00 0.00 39.61 3.16
194 196 5.309543 TCCCAAGAGTAACAAGATCAAAGGA 59.690 40.000 0.00 0.00 0.00 3.36
195 197 6.003950 CCCAAGAGTAACAAGATCAAAGGAA 58.996 40.000 0.00 0.00 0.00 3.36
214 216 6.625873 AGGAAAAAGCTTGTAACTTCTCAG 57.374 37.500 0.00 0.00 0.00 3.35
233 235 3.071023 TCAGATCGAGAAAGTGGTTGGTT 59.929 43.478 0.00 0.00 0.00 3.67
339 341 2.490115 GGTCAAGAGAGAGCGAGAAGAA 59.510 50.000 0.00 0.00 0.00 2.52
404 406 4.726583 GGGAAAAACTACTCCCTTTGTCT 58.273 43.478 0.00 0.00 46.91 3.41
405 407 4.519350 GGGAAAAACTACTCCCTTTGTCTG 59.481 45.833 0.00 0.00 46.91 3.51
407 409 6.004574 GGAAAAACTACTCCCTTTGTCTGAT 58.995 40.000 0.00 0.00 0.00 2.90
409 411 7.334671 GGAAAAACTACTCCCTTTGTCTGATAG 59.665 40.741 0.00 0.00 0.00 2.08
425 440 3.330110 CTGATAGGCCCATCTGAAAGGAT 59.670 47.826 12.62 0.00 0.00 3.24
429 444 2.173569 AGGCCCATCTGAAAGGATACAC 59.826 50.000 0.00 0.00 41.41 2.90
431 446 3.209410 GCCCATCTGAAAGGATACACAG 58.791 50.000 0.83 0.00 41.41 3.66
432 447 3.370953 GCCCATCTGAAAGGATACACAGT 60.371 47.826 0.83 0.00 41.41 3.55
433 448 4.848357 CCCATCTGAAAGGATACACAGTT 58.152 43.478 0.00 0.00 41.41 3.16
434 449 4.878397 CCCATCTGAAAGGATACACAGTTC 59.122 45.833 0.00 0.00 41.41 3.01
435 450 4.568359 CCATCTGAAAGGATACACAGTTCG 59.432 45.833 0.00 0.00 41.41 3.95
436 451 5.410924 CATCTGAAAGGATACACAGTTCGA 58.589 41.667 0.00 0.00 41.41 3.71
437 452 4.806330 TCTGAAAGGATACACAGTTCGAC 58.194 43.478 0.00 0.00 41.41 4.20
438 453 4.523173 TCTGAAAGGATACACAGTTCGACT 59.477 41.667 0.00 0.00 41.41 4.18
444 461 3.119245 GGATACACAGTTCGACTTGCCTA 60.119 47.826 0.00 0.00 0.00 3.93
459 476 0.097674 GCCTACGCACAAATGAGCAG 59.902 55.000 3.83 0.00 34.03 4.24
554 572 5.207768 CACAACAAGAGAAGCACATACAAC 58.792 41.667 0.00 0.00 0.00 3.32
555 573 4.881273 ACAACAAGAGAAGCACATACAACA 59.119 37.500 0.00 0.00 0.00 3.33
556 574 5.356751 ACAACAAGAGAAGCACATACAACAA 59.643 36.000 0.00 0.00 0.00 2.83
557 575 5.424121 ACAAGAGAAGCACATACAACAAC 57.576 39.130 0.00 0.00 0.00 3.32
558 576 4.881273 ACAAGAGAAGCACATACAACAACA 59.119 37.500 0.00 0.00 0.00 3.33
611 630 5.813513 ATATGAGATTGGGCATTTTTCCC 57.186 39.130 0.00 0.00 44.17 3.97
619 638 3.044235 GGGCATTTTTCCCAGTTTCTG 57.956 47.619 0.00 0.00 43.37 3.02
620 639 2.368548 GGGCATTTTTCCCAGTTTCTGT 59.631 45.455 0.00 0.00 43.37 3.41
723 1329 9.965824 TGAAATTTTTCTAGATCACAGGAAAAC 57.034 29.630 13.08 5.09 34.19 2.43
820 1504 2.287849 GCTTCTTCAGCCCACAAAAGAC 60.288 50.000 0.00 0.00 43.65 3.01
869 1553 0.537188 AAGACCCACACGGCTCATAG 59.463 55.000 0.00 0.00 33.26 2.23
890 1757 0.692419 CTCATACCCACCTCTGCCCT 60.692 60.000 0.00 0.00 0.00 5.19
931 1801 3.135530 GCTCCTCTCTCTCTCTCTCTCTT 59.864 52.174 0.00 0.00 0.00 2.85
1418 2296 9.706691 GGTTATTCCGAAGATATCTGTTGATTA 57.293 33.333 5.86 1.99 34.32 1.75
1453 2332 8.796475 AGTGCTACAAATTTCAGATGTTGTTAT 58.204 29.630 0.00 0.00 35.82 1.89
1455 2334 9.624697 TGCTACAAATTTCAGATGTTGTTATTC 57.375 29.630 0.00 0.00 35.82 1.75
1456 2335 8.788813 GCTACAAATTTCAGATGTTGTTATTCG 58.211 33.333 0.00 0.00 35.82 3.34
1457 2336 7.566858 ACAAATTTCAGATGTTGTTATTCGC 57.433 32.000 0.00 0.00 30.11 4.70
1458 2337 7.144661 ACAAATTTCAGATGTTGTTATTCGCA 58.855 30.769 0.00 0.00 30.11 5.10
1459 2338 7.651304 ACAAATTTCAGATGTTGTTATTCGCAA 59.349 29.630 0.00 0.00 30.11 4.85
1460 2339 8.486383 CAAATTTCAGATGTTGTTATTCGCAAA 58.514 29.630 0.00 0.00 0.00 3.68
1461 2340 8.586570 AATTTCAGATGTTGTTATTCGCAAAA 57.413 26.923 0.00 0.00 0.00 2.44
1462 2341 7.993821 TTTCAGATGTTGTTATTCGCAAAAA 57.006 28.000 0.00 0.00 0.00 1.94
1490 2369 3.372206 CAGATGTTGTTACTGCTGTAGGC 59.628 47.826 3.54 2.71 42.22 3.93
1516 2395 3.306019 GGTCGGATTGCTTTTGGACAATT 60.306 43.478 0.00 0.00 36.65 2.32
1523 2402 6.912051 GGATTGCTTTTGGACAATTTTGTTTC 59.088 34.615 0.00 0.00 42.43 2.78
1532 2411 6.796426 TGGACAATTTTGTTTCGTTGTATGA 58.204 32.000 0.00 0.00 42.43 2.15
1533 2412 7.429633 TGGACAATTTTGTTTCGTTGTATGAT 58.570 30.769 0.00 0.00 42.43 2.45
1556 2435 2.107366 GCTCTCATATCTAGGGAGGGC 58.893 57.143 9.59 9.59 46.69 5.19
1568 2460 1.607467 GGAGGGCCTTGTGCATTGT 60.607 57.895 7.89 0.00 43.89 2.71
1598 2490 7.288810 ACTTTGTTGTATGTTGGAATGATGT 57.711 32.000 0.00 0.00 0.00 3.06
1600 2492 8.296713 ACTTTGTTGTATGTTGGAATGATGTAC 58.703 33.333 0.00 0.00 0.00 2.90
1604 2496 9.108284 TGTTGTATGTTGGAATGATGTACTATG 57.892 33.333 0.00 0.00 0.00 2.23
1611 2503 9.710900 TGTTGGAATGATGTACTATGTGATATC 57.289 33.333 0.00 0.00 0.00 1.63
1632 2524 5.690997 TCATTCGGTACTGTAGCTGATAG 57.309 43.478 14.34 8.98 0.00 2.08
1648 2540 6.821388 AGCTGATAGAGGATTATTTCGTTGT 58.179 36.000 0.00 0.00 0.00 3.32
1667 2559 2.306219 TGTTATCAACGGTCCCATGGAA 59.694 45.455 15.22 0.00 31.38 3.53
1674 2566 4.833380 TCAACGGTCCCATGGAATTTTAAA 59.167 37.500 15.22 0.00 31.38 1.52
1773 2665 4.046462 CCACTTGAGCATGACAAGTTTTG 58.954 43.478 25.28 17.99 0.00 2.44
1776 2670 5.682862 CACTTGAGCATGACAAGTTTTGTAC 59.317 40.000 25.28 0.00 45.52 2.90
1800 2694 4.413851 AGTTTCTTCTCCAACTTCCTCCTT 59.586 41.667 0.00 0.00 28.27 3.36
1803 2697 4.097418 TCTTCTCCAACTTCCTCCTTAGG 58.903 47.826 0.00 0.00 45.21 2.69
1822 2716 6.936335 CCTTAGGATTTTGTGCAAGGAAAATT 59.064 34.615 11.57 3.16 35.58 1.82
1862 2756 8.409358 AGAATAATATGGTGTTATTTGGGAGC 57.591 34.615 0.00 0.00 33.23 4.70
1863 2757 7.451566 AGAATAATATGGTGTTATTTGGGAGCC 59.548 37.037 0.00 0.00 33.23 4.70
1879 2789 4.202567 TGGGAGCCAAACAAGTAATCTTCT 60.203 41.667 0.00 0.00 0.00 2.85
1931 2843 8.626576 GTGTCATTATTTGTGTTGTGATAAACG 58.373 33.333 0.00 0.00 32.47 3.60
1932 2844 8.346300 TGTCATTATTTGTGTTGTGATAAACGT 58.654 29.630 0.00 0.00 32.47 3.99
1940 2852 5.816258 TGTGTTGTGATAAACGTACCTTTGA 59.184 36.000 0.00 0.00 32.47 2.69
1955 2868 9.620660 ACGTACCTTTGATGTTTTAATTGAATC 57.379 29.630 0.00 0.00 0.00 2.52
2006 2920 0.895100 TGGACACCATTGCTTGAGCC 60.895 55.000 0.00 0.00 41.18 4.70
2023 2937 2.043450 CCAGTCTCCGGCTCTCCT 60.043 66.667 0.00 0.00 0.00 3.69
2053 2968 8.835467 TTCATTGTTTCTTTCTGTTTCTTACG 57.165 30.769 0.00 0.00 0.00 3.18
2055 2970 8.455682 TCATTGTTTCTTTCTGTTTCTTACGTT 58.544 29.630 0.00 0.00 0.00 3.99
2060 2975 7.605410 TTCTTTCTGTTTCTTACGTTGTTCT 57.395 32.000 0.00 0.00 0.00 3.01
2073 2988 2.225727 CGTTGTTCTTTTAGGCACCCTC 59.774 50.000 0.00 0.00 34.61 4.30
2077 2992 3.259902 GTTCTTTTAGGCACCCTCTACG 58.740 50.000 0.00 0.00 34.61 3.51
2078 2993 2.532843 TCTTTTAGGCACCCTCTACGT 58.467 47.619 0.00 0.00 34.61 3.57
2081 2996 1.180029 TTAGGCACCCTCTACGTGTC 58.820 55.000 0.00 0.00 36.06 3.67
2088 3003 1.136984 CCTCTACGTGTCGGTGCTC 59.863 63.158 0.00 0.00 0.00 4.26
2119 3034 8.781928 ATGGGAATAAGGGAAAACCCTATATA 57.218 34.615 8.30 0.00 39.63 0.86
2120 3035 8.781928 TGGGAATAAGGGAAAACCCTATATAT 57.218 34.615 8.30 0.82 39.63 0.86
2275 3190 6.818644 AGTAGTAGATTCAAATGCACGTGATT 59.181 34.615 22.23 13.10 0.00 2.57
2434 3353 5.514500 AACTTATGCCTTCCTGGTTTCTA 57.486 39.130 0.00 0.00 38.35 2.10
2546 3468 0.035152 ATCCAGAGTGCGCAAATGGA 60.035 50.000 30.35 30.35 43.82 3.41
2577 3499 4.830046 GGACTGTGATATCTAGCAGGAAGA 59.170 45.833 19.15 0.00 33.62 2.87
2669 3607 2.722094 TCGCATGCTTTATCTGGGTTT 58.278 42.857 17.13 0.00 0.00 3.27
2685 3623 2.641321 GGGTTTGTAAGTCCCTACCAGT 59.359 50.000 0.00 0.00 38.29 4.00
2697 3635 4.226620 GTCCCTACCAGTGGAATCCTTTTA 59.773 45.833 18.40 0.00 31.03 1.52
2885 3823 4.546829 ACATTTTGCAAATCAGCCTCAT 57.453 36.364 13.65 0.00 0.00 2.90
3067 4005 2.688446 CCACAGCTCTGATGCATGAAAT 59.312 45.455 2.46 0.00 34.99 2.17
3076 4014 6.688637 TCTGATGCATGAAATAGACCAAAG 57.311 37.500 2.46 0.00 0.00 2.77
3077 4015 6.182627 TCTGATGCATGAAATAGACCAAAGT 58.817 36.000 2.46 0.00 0.00 2.66
3158 4097 2.699954 ACTTTACTGGTCCATGAAGCG 58.300 47.619 0.00 0.00 0.00 4.68
3284 4223 2.938354 CTGTTTAGCTGCAGCCTGT 58.062 52.632 34.39 19.34 43.38 4.00
3302 4241 2.695666 CTGTAGGGATGGTACCAGTCAG 59.304 54.545 21.41 15.90 0.00 3.51
3306 4245 1.679032 GGGATGGTACCAGTCAGTTGC 60.679 57.143 21.41 7.32 0.00 4.17
3347 4286 1.072173 TGGTGCTGCACTGATGTTACT 59.928 47.619 29.54 0.00 34.40 2.24
3354 4295 4.060900 CTGCACTGATGTTACTTGTGTCT 58.939 43.478 0.00 0.00 0.00 3.41
3355 4296 3.809279 TGCACTGATGTTACTTGTGTCTG 59.191 43.478 0.00 0.00 0.00 3.51
3443 4422 7.046652 TGAGAATTGGAAGAAGATGCTCTTAG 58.953 38.462 0.00 0.00 36.73 2.18
3580 4562 4.634004 CACTTATTGAAGGACGTTGCCATA 59.366 41.667 0.00 0.00 36.95 2.74
3581 4563 4.634443 ACTTATTGAAGGACGTTGCCATAC 59.366 41.667 0.00 0.00 36.95 2.39
3698 4681 8.694581 AGACAGAGGGAGTACAATATAACTAC 57.305 38.462 0.00 0.00 0.00 2.73
3885 4869 4.081406 TGTTCACCCCTTCTTTCATCATG 58.919 43.478 0.00 0.00 0.00 3.07
4017 5007 3.335579 AGGCACTCGTAGAAAACATTCC 58.664 45.455 0.00 0.00 34.09 3.01
4260 5253 2.611292 GCTTGTGGTATGCAGAGATGTC 59.389 50.000 0.00 0.00 0.00 3.06
4373 5366 8.292444 TCACTGTTTTAAGCATATATTTGCCT 57.708 30.769 13.70 4.67 43.83 4.75
4474 5469 1.649171 CGGTTCGAAGTTGATGAGACG 59.351 52.381 0.00 0.00 0.00 4.18
4475 5470 1.390463 GGTTCGAAGTTGATGAGACGC 59.610 52.381 0.00 0.00 0.00 5.19
4494 5489 2.095853 CGCTGTTCCATACATGTCCAAC 59.904 50.000 0.00 1.94 35.85 3.77
4495 5490 2.423538 GCTGTTCCATACATGTCCAACC 59.576 50.000 0.00 0.00 35.85 3.77
4496 5491 3.684908 CTGTTCCATACATGTCCAACCA 58.315 45.455 0.00 0.00 35.85 3.67
4497 5492 4.078537 CTGTTCCATACATGTCCAACCAA 58.921 43.478 0.00 0.00 35.85 3.67
4498 5493 4.474394 TGTTCCATACATGTCCAACCAAA 58.526 39.130 0.00 0.00 0.00 3.28
4499 5494 5.083122 TGTTCCATACATGTCCAACCAAAT 58.917 37.500 0.00 0.00 0.00 2.32
4500 5495 5.541868 TGTTCCATACATGTCCAACCAAATT 59.458 36.000 0.00 0.00 0.00 1.82
4501 5496 6.042552 TGTTCCATACATGTCCAACCAAATTT 59.957 34.615 0.00 0.00 0.00 1.82
4502 5497 7.233553 TGTTCCATACATGTCCAACCAAATTTA 59.766 33.333 0.00 0.00 0.00 1.40
4503 5498 7.403312 TCCATACATGTCCAACCAAATTTAG 57.597 36.000 0.00 0.00 0.00 1.85
4504 5499 6.951198 TCCATACATGTCCAACCAAATTTAGT 59.049 34.615 0.00 0.00 0.00 2.24
4505 5500 7.122055 TCCATACATGTCCAACCAAATTTAGTC 59.878 37.037 0.00 0.00 0.00 2.59
4506 5501 5.371115 ACATGTCCAACCAAATTTAGTCG 57.629 39.130 0.00 0.00 0.00 4.18
4523 5518 4.156455 AGTCGGCATAATCTGTTTCCAT 57.844 40.909 0.00 0.00 0.00 3.41
4628 5710 6.373216 CCCAATGATACCTTTTACGTTTGAGA 59.627 38.462 0.00 0.00 0.00 3.27
4644 5726 6.424207 ACGTTTGAGAAAGTGGAAGTAAGATC 59.576 38.462 0.00 0.00 0.00 2.75
4700 5782 3.624861 GGTATCATCTGGCTTGTGAGTTG 59.375 47.826 0.00 0.00 0.00 3.16
4708 5790 2.568956 TGGCTTGTGAGTTGAGCTCTAT 59.431 45.455 16.19 0.00 44.41 1.98
4709 5791 3.769300 TGGCTTGTGAGTTGAGCTCTATA 59.231 43.478 16.19 0.00 44.41 1.31
4720 5802 8.535335 TGAGTTGAGCTCTATAGTCTTTGAATT 58.465 33.333 16.19 0.00 44.41 2.17
4741 5823 3.815856 TTGTTGAATGTGGTTGCACAT 57.184 38.095 0.00 0.00 46.63 3.21
4809 5891 3.198853 GGTAATGCTCCTTCTGACCTTCT 59.801 47.826 0.00 0.00 0.00 2.85
4810 5892 4.323868 GGTAATGCTCCTTCTGACCTTCTT 60.324 45.833 0.00 0.00 0.00 2.52
4811 5893 3.625649 ATGCTCCTTCTGACCTTCTTC 57.374 47.619 0.00 0.00 0.00 2.87
4860 6217 5.131642 TGCTCACCAATGAATAGAGAGGAAT 59.868 40.000 0.00 0.00 33.30 3.01
4861 6218 6.060788 GCTCACCAATGAATAGAGAGGAATT 58.939 40.000 0.00 0.00 33.30 2.17
4864 6221 9.618890 CTCACCAATGAATAGAGAGGAATTAAA 57.381 33.333 0.00 0.00 33.30 1.52
4865 6222 9.618890 TCACCAATGAATAGAGAGGAATTAAAG 57.381 33.333 0.00 0.00 0.00 1.85
4866 6223 8.348507 CACCAATGAATAGAGAGGAATTAAAGC 58.651 37.037 0.00 0.00 0.00 3.51
4867 6224 8.277918 ACCAATGAATAGAGAGGAATTAAAGCT 58.722 33.333 0.00 0.00 0.00 3.74
4868 6225 8.566260 CCAATGAATAGAGAGGAATTAAAGCTG 58.434 37.037 0.00 0.00 0.00 4.24
4869 6226 9.118300 CAATGAATAGAGAGGAATTAAAGCTGT 57.882 33.333 0.00 0.00 0.00 4.40
4870 6227 8.900983 ATGAATAGAGAGGAATTAAAGCTGTC 57.099 34.615 0.00 0.00 0.00 3.51
4966 6323 3.365472 AGAAGTTTGTTCTTGGTTGCCT 58.635 40.909 0.00 0.00 0.00 4.75
4968 6325 1.676006 AGTTTGTTCTTGGTTGCCTCG 59.324 47.619 0.00 0.00 0.00 4.63
5025 6404 3.661944 CACTGACTTGAAGCTCACTCAT 58.338 45.455 0.00 0.00 0.00 2.90
5026 6405 3.679025 CACTGACTTGAAGCTCACTCATC 59.321 47.826 0.00 0.00 0.00 2.92
5053 6436 2.113139 ACCCTGGCACAAGGAACG 59.887 61.111 0.00 0.00 44.19 3.95
5087 6470 4.807039 CGCGAACCACCCCTACGG 62.807 72.222 0.00 0.00 37.81 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 7.815549 TCATTTTGCTTCGTATGTAGTCACTTA 59.184 33.333 0.00 0.00 0.00 2.24
93 94 8.210265 TCAAATGAACTACCACATGCAGATATA 58.790 33.333 0.00 0.00 0.00 0.86
94 95 7.056006 TCAAATGAACTACCACATGCAGATAT 58.944 34.615 0.00 0.00 0.00 1.63
95 96 6.413892 TCAAATGAACTACCACATGCAGATA 58.586 36.000 0.00 0.00 0.00 1.98
99 100 5.781210 TTTCAAATGAACTACCACATGCA 57.219 34.783 0.00 0.00 33.13 3.96
101 102 8.048534 AGAGATTTCAAATGAACTACCACATG 57.951 34.615 0.00 0.00 33.13 3.21
145 146 3.583526 GGAAACTCCTACTCCCTCTGTTT 59.416 47.826 0.00 0.00 32.53 2.83
149 150 3.786213 ATGGAAACTCCTACTCCCTCT 57.214 47.619 0.00 0.00 37.46 3.69
169 170 6.003950 CCTTTGATCTTGTTACTCTTGGGAA 58.996 40.000 0.00 0.00 0.00 3.97
170 171 5.309543 TCCTTTGATCTTGTTACTCTTGGGA 59.690 40.000 0.00 0.00 0.00 4.37
194 196 6.706270 TCGATCTGAGAAGTTACAAGCTTTTT 59.294 34.615 0.00 0.00 0.00 1.94
195 197 6.223852 TCGATCTGAGAAGTTACAAGCTTTT 58.776 36.000 0.00 0.00 0.00 2.27
214 216 5.934935 TTTAACCAACCACTTTCTCGATC 57.065 39.130 0.00 0.00 0.00 3.69
299 301 3.637229 GACCCTACTTCATCGATTCCTCA 59.363 47.826 0.00 0.00 0.00 3.86
339 341 4.613437 ACATTTAGGACATGGGCAAGAAT 58.387 39.130 0.00 0.00 0.00 2.40
399 401 2.763039 TCAGATGGGCCTATCAGACAA 58.237 47.619 28.72 4.68 0.00 3.18
400 402 2.477104 TCAGATGGGCCTATCAGACA 57.523 50.000 28.72 8.32 0.00 3.41
404 406 2.775418 TCCTTTCAGATGGGCCTATCA 58.225 47.619 28.72 8.42 0.00 2.15
405 407 4.287067 TGTATCCTTTCAGATGGGCCTATC 59.713 45.833 20.95 20.95 0.00 2.08
407 409 3.391296 GTGTATCCTTTCAGATGGGCCTA 59.609 47.826 4.53 0.00 0.00 3.93
409 411 2.092429 TGTGTATCCTTTCAGATGGGCC 60.092 50.000 0.00 0.00 0.00 5.80
425 440 2.351060 CGTAGGCAAGTCGAACTGTGTA 60.351 50.000 0.00 0.00 0.00 2.90
429 444 2.070861 GCGTAGGCAAGTCGAACTG 58.929 57.895 1.75 0.00 39.62 3.16
444 461 2.069273 GACTACTGCTCATTTGTGCGT 58.931 47.619 0.77 4.45 37.35 5.24
451 468 3.354948 TGCATTGGACTACTGCTCATT 57.645 42.857 2.93 0.00 36.84 2.57
702 1308 6.292923 TCGGTTTTCCTGTGATCTAGAAAAA 58.707 36.000 0.00 0.00 39.26 1.94
723 1329 5.758296 TCTCGATTTATTTTGATTCCCTCGG 59.242 40.000 0.00 0.00 0.00 4.63
869 1553 1.147153 GCAGAGGTGGGTATGAGGC 59.853 63.158 0.00 0.00 0.00 4.70
872 1556 0.691078 GAGGGCAGAGGTGGGTATGA 60.691 60.000 0.00 0.00 0.00 2.15
874 1558 1.384643 GGAGGGCAGAGGTGGGTAT 60.385 63.158 0.00 0.00 0.00 2.73
877 1561 4.748798 AGGGAGGGCAGAGGTGGG 62.749 72.222 0.00 0.00 0.00 4.61
878 1562 2.203549 GAAAGGGAGGGCAGAGGTGG 62.204 65.000 0.00 0.00 0.00 4.61
880 1564 1.925972 GGAAAGGGAGGGCAGAGGT 60.926 63.158 0.00 0.00 0.00 3.85
1418 2296 9.890629 TCTGAAATTTGTAGCACTTAGTCATAT 57.109 29.630 0.00 0.00 0.00 1.78
1463 2342 6.207691 ACAGCAGTAACAACATCTGTTTTT 57.792 33.333 0.00 0.00 46.49 1.94
1464 2343 5.835113 ACAGCAGTAACAACATCTGTTTT 57.165 34.783 0.00 0.00 46.49 2.43
1465 2344 5.470098 CCTACAGCAGTAACAACATCTGTTT 59.530 40.000 0.00 0.00 46.49 2.83
1466 2345 6.540982 GCCTACAGCAGTAACAACATCTGTT 61.541 44.000 0.00 0.00 45.71 3.16
1467 2346 4.569943 CCTACAGCAGTAACAACATCTGT 58.430 43.478 0.00 0.00 41.27 3.41
1516 2395 7.386573 TGAGAGCTAATCATACAACGAAACAAA 59.613 33.333 0.00 0.00 0.00 2.83
1523 2402 9.715123 CTAGATATGAGAGCTAATCATACAACG 57.285 37.037 18.61 8.33 41.24 4.10
1532 2411 5.776358 CCCTCCCTAGATATGAGAGCTAAT 58.224 45.833 0.00 0.00 0.00 1.73
1533 2412 4.570933 GCCCTCCCTAGATATGAGAGCTAA 60.571 50.000 0.00 0.00 28.46 3.09
1556 2435 6.042143 ACAAAGTTCTAAACAATGCACAAGG 58.958 36.000 0.00 0.00 0.00 3.61
1568 2460 9.743057 CATTCCAACATACAACAAAGTTCTAAA 57.257 29.630 0.00 0.00 0.00 1.85
1598 2490 8.631480 ACAGTACCGAATGATATCACATAGTA 57.369 34.615 7.78 5.58 0.00 1.82
1600 2492 7.698550 GCTACAGTACCGAATGATATCACATAG 59.301 40.741 7.78 0.73 0.00 2.23
1604 2496 5.859114 CAGCTACAGTACCGAATGATATCAC 59.141 44.000 7.78 0.00 0.00 3.06
1610 2502 5.374071 TCTATCAGCTACAGTACCGAATGA 58.626 41.667 0.00 0.00 0.00 2.57
1611 2503 5.335269 CCTCTATCAGCTACAGTACCGAATG 60.335 48.000 0.00 0.00 0.00 2.67
1615 2507 3.741249 TCCTCTATCAGCTACAGTACCG 58.259 50.000 0.00 0.00 0.00 4.02
1648 2540 3.943671 ATTCCATGGGACCGTTGATAA 57.056 42.857 13.02 0.00 0.00 1.75
1740 2632 3.334691 TGCTCAAGTGGGAAAATACGAG 58.665 45.455 0.00 0.00 0.00 4.18
1747 2639 2.655090 TGTCATGCTCAAGTGGGAAA 57.345 45.000 0.00 0.00 0.00 3.13
1773 2665 5.612351 AGGAAGTTGGAGAAGAAACTGTAC 58.388 41.667 0.00 0.00 36.75 2.90
1776 2670 4.068599 GGAGGAAGTTGGAGAAGAAACTG 58.931 47.826 0.00 0.00 36.75 3.16
1800 2694 8.376889 GAAAATTTTCCTTGCACAAAATCCTA 57.623 30.769 18.43 0.00 32.22 2.94
1853 2747 6.295292 GAAGATTACTTGTTTGGCTCCCAAAT 60.295 38.462 12.09 0.17 44.15 2.32
1859 2753 5.239525 ACACAGAAGATTACTTGTTTGGCTC 59.760 40.000 0.00 0.00 33.36 4.70
1861 2755 5.438761 ACACAGAAGATTACTTGTTTGGC 57.561 39.130 0.00 0.00 33.36 4.52
1862 2756 6.795399 ACAACACAGAAGATTACTTGTTTGG 58.205 36.000 0.00 0.00 33.36 3.28
1863 2757 8.687824 AAACAACACAGAAGATTACTTGTTTG 57.312 30.769 0.00 0.00 36.39 2.93
1896 2806 8.815189 CAACACAAATAATGACACATTCAAACA 58.185 29.630 0.00 0.00 37.92 2.83
1976 2889 4.142600 GCAATGGTGTCCAACTATCTGAAC 60.143 45.833 0.00 0.00 36.95 3.18
1980 2894 4.012374 CAAGCAATGGTGTCCAACTATCT 58.988 43.478 0.00 0.00 36.95 1.98
2006 2920 2.043450 AGGAGAGCCGGAGACTGG 60.043 66.667 5.05 0.00 39.96 4.00
2023 2937 8.477256 AGAAACAGAAAGAAACAATGAAATGGA 58.523 29.630 0.00 0.00 0.00 3.41
2053 2968 3.487372 AGAGGGTGCCTAAAAGAACAAC 58.513 45.455 0.00 0.00 31.76 3.32
2055 2970 3.306502 CGTAGAGGGTGCCTAAAAGAACA 60.307 47.826 0.00 0.00 31.76 3.18
2060 2975 1.972795 ACACGTAGAGGGTGCCTAAAA 59.027 47.619 0.00 0.00 38.98 1.52
2073 2988 1.874345 AAGGGAGCACCGACACGTAG 61.874 60.000 0.00 0.00 46.96 3.51
2077 2992 1.369625 CATAAAGGGAGCACCGACAC 58.630 55.000 0.00 0.00 46.96 3.67
2078 2993 0.251916 CCATAAAGGGAGCACCGACA 59.748 55.000 0.00 0.00 46.96 4.35
2175 3090 6.463995 AATATATGTTGCGATGGTTTGGTT 57.536 33.333 0.00 0.00 0.00 3.67
2255 3170 7.552458 ACATAATCACGTGCATTTGAATCTA 57.448 32.000 11.67 0.00 0.00 1.98
2258 3173 6.308524 CACAACATAATCACGTGCATTTGAAT 59.691 34.615 11.67 0.00 0.00 2.57
2259 3174 5.628606 CACAACATAATCACGTGCATTTGAA 59.371 36.000 11.67 0.00 0.00 2.69
2275 3190 5.069318 TGATTTCACTTCCTGCACAACATA 58.931 37.500 0.00 0.00 0.00 2.29
2405 3324 6.311735 ACCAGGAAGGCATAAGTTAAAGAAA 58.688 36.000 0.00 0.00 43.14 2.52
2418 3337 1.271379 GCTGTAGAAACCAGGAAGGCA 60.271 52.381 0.00 0.00 43.14 4.75
2434 3353 5.295292 CGGAAAATCTGATCATACAAGCTGT 59.705 40.000 0.00 0.00 0.00 4.40
2546 3468 4.785346 AGATATCACAGTCCATTTGCCT 57.215 40.909 5.32 0.00 0.00 4.75
2577 3499 3.053395 AGCCACATGGTATCAAGATTGGT 60.053 43.478 0.00 0.00 37.57 3.67
2669 3607 3.263369 TTCCACTGGTAGGGACTTACA 57.737 47.619 0.00 0.00 41.75 2.41
2697 3635 7.095695 ACACTGCATGTTTACAAAGTTAGTT 57.904 32.000 0.00 0.00 38.98 2.24
3158 4097 7.378181 TGTCAATTGAATAGAAGGCTTTTTCC 58.622 34.615 10.35 0.00 0.00 3.13
3284 4223 3.104512 CAACTGACTGGTACCATCCCTA 58.895 50.000 16.75 0.00 0.00 3.53
3306 4245 1.197721 CAAAGACTAGCCTTGCCAACG 59.802 52.381 0.00 0.00 0.00 4.10
3347 4286 2.950975 ACATTGCATGACACAGACACAA 59.049 40.909 0.00 0.00 0.00 3.33
3354 4295 4.907879 TGTAAACACATTGCATGACACA 57.092 36.364 0.00 0.00 0.00 3.72
3355 4296 5.280945 ACTTGTAAACACATTGCATGACAC 58.719 37.500 0.00 0.00 33.42 3.67
3452 4433 4.324267 TCCTTTAGTGCTTTTCCTAGTGC 58.676 43.478 0.00 0.00 0.00 4.40
3549 4531 4.688879 CGTCCTTCAATAAGTGCACAAGTA 59.311 41.667 21.04 8.48 0.00 2.24
3558 4540 3.134574 TGGCAACGTCCTTCAATAAGT 57.865 42.857 0.00 0.00 42.51 2.24
3559 4541 4.260212 CGTATGGCAACGTCCTTCAATAAG 60.260 45.833 12.09 0.00 38.07 1.73
3580 4562 4.057432 CAAAACAGATGAAAAATGCCCGT 58.943 39.130 0.00 0.00 0.00 5.28
3581 4563 4.057432 ACAAAACAGATGAAAAATGCCCG 58.943 39.130 0.00 0.00 0.00 6.13
3661 4643 2.224305 CCCTCTGTCTCAAAACGAAGGT 60.224 50.000 0.00 0.00 0.00 3.50
3666 4648 2.821991 ACTCCCTCTGTCTCAAAACG 57.178 50.000 0.00 0.00 0.00 3.60
3667 4649 4.602340 TGTACTCCCTCTGTCTCAAAAC 57.398 45.455 0.00 0.00 0.00 2.43
3885 4869 0.322456 TGCCAATGTCCACCTGTAGC 60.322 55.000 0.00 0.00 0.00 3.58
4017 5007 1.337917 ACAGAGTCAGCTGCAGACATG 60.338 52.381 24.15 22.21 39.51 3.21
4106 5096 2.635714 TCATCATGTGTGCAGCCTTAG 58.364 47.619 0.00 0.00 0.00 2.18
4260 5253 3.785505 GCGAGGAAAATTGAGTGCATACG 60.786 47.826 0.00 0.00 0.00 3.06
4325 5318 1.074775 GCATCCCACTTCCCACACA 59.925 57.895 0.00 0.00 0.00 3.72
4373 5366 4.217550 GCCAATACCTAAGTCTTGCACAAA 59.782 41.667 0.00 0.00 30.69 2.83
4420 5414 0.673437 TTTTCCTGCCAGCTTTTCGG 59.327 50.000 0.00 0.00 0.00 4.30
4460 5455 2.413453 GGAACAGCGTCTCATCAACTTC 59.587 50.000 0.00 0.00 0.00 3.01
4494 5489 6.377327 ACAGATTATGCCGACTAAATTTGG 57.623 37.500 0.00 0.00 0.00 3.28
4495 5490 7.432252 GGAAACAGATTATGCCGACTAAATTTG 59.568 37.037 0.00 0.00 0.00 2.32
4496 5491 7.122055 TGGAAACAGATTATGCCGACTAAATTT 59.878 33.333 0.00 0.00 35.01 1.82
4497 5492 6.601613 TGGAAACAGATTATGCCGACTAAATT 59.398 34.615 0.00 0.00 35.01 1.82
4498 5493 6.119536 TGGAAACAGATTATGCCGACTAAAT 58.880 36.000 0.00 0.00 35.01 1.40
4499 5494 5.492895 TGGAAACAGATTATGCCGACTAAA 58.507 37.500 0.00 0.00 35.01 1.85
4500 5495 5.092554 TGGAAACAGATTATGCCGACTAA 57.907 39.130 0.00 0.00 35.01 2.24
4501 5496 4.746535 TGGAAACAGATTATGCCGACTA 57.253 40.909 0.00 0.00 35.01 2.59
4502 5497 3.627395 TGGAAACAGATTATGCCGACT 57.373 42.857 0.00 0.00 35.01 4.18
4523 5518 1.339055 CGAGGAAGGGAAGATTGCACA 60.339 52.381 0.00 0.00 0.00 4.57
4628 5710 4.042187 ACAGCCAGATCTTACTTCCACTTT 59.958 41.667 0.00 0.00 0.00 2.66
4700 5782 9.766277 CAACAAAATTCAAAGACTATAGAGCTC 57.234 33.333 5.27 5.27 0.00 4.09
4708 5790 8.474025 ACCACATTCAACAAAATTCAAAGACTA 58.526 29.630 0.00 0.00 0.00 2.59
4709 5791 7.330262 ACCACATTCAACAAAATTCAAAGACT 58.670 30.769 0.00 0.00 0.00 3.24
4720 5802 3.599730 TGTGCAACCACATTCAACAAA 57.400 38.095 0.00 0.00 46.51 2.83
4741 5823 9.632638 AAAATTCTAGCAATCCTAGCTAATTCA 57.367 29.630 0.00 0.00 43.39 2.57
4777 5859 3.450904 AGGAGCATTACCTAACCACTCA 58.549 45.455 0.00 0.00 35.84 3.41
4809 5891 3.716431 ACATCTTTACGTAGGAGGGGAA 58.284 45.455 13.75 0.00 0.00 3.97
4810 5892 3.393426 ACATCTTTACGTAGGAGGGGA 57.607 47.619 13.75 2.16 0.00 4.81
4811 5893 4.501058 GCTTACATCTTTACGTAGGAGGGG 60.501 50.000 13.75 7.37 0.00 4.79
4877 6234 6.380079 AGATCATACTTTCACCACCTTCTT 57.620 37.500 0.00 0.00 0.00 2.52
4879 6236 5.163713 GCAAGATCATACTTTCACCACCTTC 60.164 44.000 0.00 0.00 0.00 3.46
4880 6237 4.702131 GCAAGATCATACTTTCACCACCTT 59.298 41.667 0.00 0.00 0.00 3.50
4881 6238 4.265073 GCAAGATCATACTTTCACCACCT 58.735 43.478 0.00 0.00 0.00 4.00
4882 6239 3.378427 GGCAAGATCATACTTTCACCACC 59.622 47.826 0.00 0.00 0.00 4.61
4883 6240 3.378427 GGGCAAGATCATACTTTCACCAC 59.622 47.826 0.00 0.00 0.00 4.16
4884 6241 3.266772 AGGGCAAGATCATACTTTCACCA 59.733 43.478 0.00 0.00 0.00 4.17
4885 6242 3.629398 CAGGGCAAGATCATACTTTCACC 59.371 47.826 0.00 0.00 0.00 4.02
4934 6291 3.593442 ACAAACTTCTTGTCCCATGGA 57.407 42.857 15.22 0.00 0.00 3.41
4966 6323 1.737735 CATGCGACCTTGTGAGCGA 60.738 57.895 0.00 0.00 0.00 4.93
4968 6325 1.237285 AACCATGCGACCTTGTGAGC 61.237 55.000 0.00 0.00 0.00 4.26
5053 6436 3.272334 GGTGACGCATCCATCGGC 61.272 66.667 0.00 0.00 35.09 5.54
5087 6470 1.702299 CGGTGAATTGAGACGTCGC 59.298 57.895 12.80 12.80 0.00 5.19


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

AutoCloner maintained by Alex Coulton.