Multiple sequence alignment - TraesCS5D01G099500

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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 TraesCS5D01G099500 chr5D 100.000 5286 0 0 1 5286 111949993 111955278 0.000000e+00 9762.0
1 TraesCS5D01G099500 chr5D 89.474 76 7 1 4960 5034 449052390 449052465 1.570000e-15 95.3
2 TraesCS5D01G099500 chr5A 93.750 4160 154 49 568 4695 114703118 114707203 0.000000e+00 6144.0
3 TraesCS5D01G099500 chr5A 91.470 551 35 2 4747 5286 114707202 114707751 0.000000e+00 747.0
4 TraesCS5D01G099500 chr5A 86.679 548 51 8 1 527 114702576 114703122 5.900000e-164 588.0
5 TraesCS5D01G099500 chr5A 89.286 84 8 1 4955 5037 472902137 472902220 2.600000e-18 104.0
6 TraesCS5D01G099500 chr5B 92.296 3336 129 37 2041 5286 121001887 121005184 0.000000e+00 4619.0
7 TraesCS5D01G099500 chr5B 94.874 1307 28 11 692 1988 121000614 121001891 0.000000e+00 2006.0
8 TraesCS5D01G099500 chr5B 87.226 548 49 7 1 527 120997881 120998428 5.860000e-169 604.0
9 TraesCS5D01G099500 chr5B 96.491 57 2 0 611 667 120999025 120999081 1.570000e-15 95.3
10 TraesCS5D01G099500 chr6D 87.608 581 58 9 1908 2484 447742462 447743032 0.000000e+00 662.0
11 TraesCS5D01G099500 chr7D 88.151 557 50 8 1911 2465 63618725 63619267 0.000000e+00 649.0
12 TraesCS5D01G099500 chr7D 88.401 319 30 4 1909 2226 63635202 63635514 1.390000e-100 377.0
13 TraesCS5D01G099500 chr6B 86.464 591 51 13 1911 2484 676813526 676812948 5.810000e-174 621.0
14 TraesCS5D01G099500 chr6B 88.075 478 41 6 1908 2382 678218613 678219077 2.150000e-153 553.0
15 TraesCS5D01G099500 chr6B 85.783 415 41 6 1907 2307 677064966 677064556 1.760000e-114 424.0
16 TraesCS5D01G099500 chr6B 88.814 295 24 7 1911 2196 677071613 677071319 2.340000e-93 353.0
17 TraesCS5D01G099500 chr6B 88.475 295 25 6 1911 2196 678069158 678068864 1.090000e-91 348.0
18 TraesCS5D01G099500 chr6B 100.000 28 0 0 1455 1482 32740445 32740472 1.000000e-02 52.8
19 TraesCS5D01G099500 chr6A 88.409 509 48 6 1908 2413 594341422 594341922 2.110000e-168 603.0
20 TraesCS5D01G099500 chr7B 91.954 174 12 2 2314 2485 4142479 4142652 5.290000e-60 243.0
21 TraesCS5D01G099500 chr4D 79.817 218 39 4 4869 5081 43624318 43624535 2.550000e-33 154.0
22 TraesCS5D01G099500 chr4D 83.000 100 12 5 4759 4857 65580518 65580613 9.430000e-13 86.1
23 TraesCS5D01G099500 chr4B 92.857 84 5 1 4955 5037 63120307 63120390 2.590000e-23 121.0
24 TraesCS5D01G099500 chr4B 81.046 153 26 3 4808 4959 593196444 593196594 9.300000e-23 119.0
25 TraesCS5D01G099500 chr4B 85.714 98 14 0 4865 4962 62974579 62974482 2.600000e-18 104.0
26 TraesCS5D01G099500 chr4B 85.714 70 9 1 4956 5024 446766923 446766854 7.340000e-09 73.1
27 TraesCS5D01G099500 chr3A 79.710 138 25 3 4955 5089 515827523 515827386 4.360000e-16 97.1
28 TraesCS5D01G099500 chr2A 80.147 136 18 2 4955 5081 727165595 727165730 5.640000e-15 93.5
29 TraesCS5D01G099500 chr2A 84.043 94 13 1 4869 4962 196518332 196518423 7.290000e-14 89.8
30 TraesCS5D01G099500 chr2A 81.522 92 14 3 4775 4866 532848677 532848765 7.340000e-09 73.1
31 TraesCS5D01G099500 chr4A 83.168 101 14 3 4759 4858 530119372 530119274 7.290000e-14 89.8
32 TraesCS5D01G099500 chr4A 86.567 67 9 0 4800 4866 716970142 716970076 2.040000e-09 75.0
33 TraesCS5D01G099500 chr2B 95.349 43 2 0 4920 4962 190145192 190145150 9.500000e-08 69.4
34 TraesCS5D01G099500 chr2D 80.435 92 15 3 4775 4866 394780804 394780892 3.420000e-07 67.6
35 TraesCS5D01G099500 chr2D 100.000 28 0 0 1455 1482 623118472 623118499 1.000000e-02 52.8


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 TraesCS5D01G099500 chr5D 111949993 111955278 5285 False 9762.000 9762 100.00000 1 5286 1 chr5D.!!$F1 5285
1 TraesCS5D01G099500 chr5A 114702576 114707751 5175 False 2493.000 6144 90.63300 1 5286 3 chr5A.!!$F2 5285
2 TraesCS5D01G099500 chr5B 120997881 121005184 7303 False 1831.075 4619 92.72175 1 5286 4 chr5B.!!$F1 5285
3 TraesCS5D01G099500 chr6D 447742462 447743032 570 False 662.000 662 87.60800 1908 2484 1 chr6D.!!$F1 576
4 TraesCS5D01G099500 chr7D 63618725 63619267 542 False 649.000 649 88.15100 1911 2465 1 chr7D.!!$F1 554
5 TraesCS5D01G099500 chr6B 676812948 676813526 578 True 621.000 621 86.46400 1911 2484 1 chr6B.!!$R1 573
6 TraesCS5D01G099500 chr6A 594341422 594341922 500 False 603.000 603 88.40900 1908 2413 1 chr6A.!!$F1 505

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
574 597 0.032017 ATGGAACGGAGGGAGTAGCT 60.032 55.0 0.00 0.0 0.00 3.32 F
1235 3338 0.322546 ATCCAACCCGAAGAACCTGC 60.323 55.0 0.00 0.0 0.00 4.85 F
1826 3934 0.389426 GCCACGCGAGAGAGGTTTAA 60.389 55.0 15.93 0.0 34.13 1.52 F
1948 4056 1.196012 CCCTCTGTTCCTCACCCTAC 58.804 60.0 0.00 0.0 0.00 3.18 F
3772 5919 0.593128 AACCATGCTGAACGCTTGTC 59.407 50.0 0.00 0.0 40.97 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1949 4057 0.179048 TGAGCGGCACCATGGATTAG 60.179 55.000 21.47 8.19 0.00 1.73 R
2940 5085 0.465705 TTGATCCTAGCTTGCCTCCG 59.534 55.000 0.00 0.00 0.00 4.63 R
3275 5421 2.161410 TGTCGCAACAATATCCAAGCAC 59.839 45.455 0.00 0.00 30.70 4.40 R
3866 6013 1.409412 CACGCGAATAGATTCCCTCG 58.591 55.000 15.93 1.84 33.28 4.63 R
4837 6989 0.169009 GCCATCCTCGCAACAACTTC 59.831 55.000 0.00 0.00 0.00 3.01 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
17 18 3.781307 TGGCGACCCGGATCAAGG 61.781 66.667 0.73 0.00 0.00 3.61
60 61 2.554032 CGAGCCTCCATGTTTGACTTTT 59.446 45.455 0.00 0.00 0.00 2.27
92 93 9.476202 ACAAAACAAAAGAACCAGCTAATAATC 57.524 29.630 0.00 0.00 0.00 1.75
129 131 7.299246 TGTATAACCTCCTTAATGGTAGAGC 57.701 40.000 0.00 0.00 35.17 4.09
175 178 4.094294 TGTTCTACATGATAGTTTTGCGGC 59.906 41.667 0.00 0.00 0.00 6.53
179 182 2.760092 ACATGATAGTTTTGCGGCCAAT 59.240 40.909 2.24 0.00 0.00 3.16
188 191 0.528017 TTGCGGCCAATTGCGATAAA 59.472 45.000 2.24 0.00 42.61 1.40
260 263 1.198759 AAGGCAAGAGAAGGCGGGTA 61.199 55.000 0.00 0.00 36.55 3.69
338 342 3.043999 ATACTGCACCCGCTTCCCC 62.044 63.158 0.00 0.00 39.64 4.81
345 349 0.611896 CACCCGCTTCCCCAGAATTT 60.612 55.000 0.00 0.00 0.00 1.82
352 356 2.833943 GCTTCCCCAGAATTTCCATTGT 59.166 45.455 0.00 0.00 0.00 2.71
361 365 2.028561 ATTTCCATTGTGGGGCACTT 57.971 45.000 0.00 0.00 38.32 3.16
368 372 0.105760 TTGTGGGGCACTTCACCATT 60.106 50.000 0.00 0.00 36.54 3.16
435 458 2.121786 GAGTAACGAGCACGACAACAA 58.878 47.619 11.40 0.00 42.66 2.83
484 507 3.028850 CAGAGATGTACCTACCCCGAAA 58.971 50.000 0.00 0.00 0.00 3.46
501 524 0.391597 AAAAGGTTCGCCGAGAGTGA 59.608 50.000 0.00 0.00 43.66 3.41
515 538 5.173854 GCCGAGAGTGAACTTTGAAAAATTG 59.826 40.000 0.00 0.00 0.00 2.32
528 551 9.768662 ACTTTGAAAAATTGCTTCATGAATACT 57.231 25.926 8.96 0.00 32.98 2.12
530 553 8.761575 TTGAAAAATTGCTTCATGAATACTCC 57.238 30.769 8.96 0.00 32.98 3.85
531 554 7.322664 TGAAAAATTGCTTCATGAATACTCCC 58.677 34.615 8.96 0.00 0.00 4.30
532 555 7.178983 TGAAAAATTGCTTCATGAATACTCCCT 59.821 33.333 8.96 0.00 0.00 4.20
533 556 7.486407 AAAATTGCTTCATGAATACTCCCTT 57.514 32.000 8.96 0.00 0.00 3.95
534 557 7.486407 AAATTGCTTCATGAATACTCCCTTT 57.514 32.000 8.96 0.97 0.00 3.11
535 558 5.902613 TTGCTTCATGAATACTCCCTTTG 57.097 39.130 8.96 0.00 0.00 2.77
536 559 4.922206 TGCTTCATGAATACTCCCTTTGT 58.078 39.130 8.96 0.00 0.00 2.83
537 560 4.701651 TGCTTCATGAATACTCCCTTTGTG 59.298 41.667 8.96 0.00 0.00 3.33
538 561 4.943705 GCTTCATGAATACTCCCTTTGTGA 59.056 41.667 8.96 0.00 0.00 3.58
539 562 5.591877 GCTTCATGAATACTCCCTTTGTGAT 59.408 40.000 8.96 0.00 0.00 3.06
540 563 6.096001 GCTTCATGAATACTCCCTTTGTGATT 59.904 38.462 8.96 0.00 0.00 2.57
541 564 7.283127 GCTTCATGAATACTCCCTTTGTGATTA 59.717 37.037 8.96 0.00 0.00 1.75
542 565 9.177608 CTTCATGAATACTCCCTTTGTGATTAA 57.822 33.333 8.96 0.00 0.00 1.40
543 566 9.527157 TTCATGAATACTCCCTTTGTGATTAAA 57.473 29.630 3.38 0.00 0.00 1.52
544 567 9.527157 TCATGAATACTCCCTTTGTGATTAAAA 57.473 29.630 0.00 0.00 0.00 1.52
548 571 9.503427 GAATACTCCCTTTGTGATTAAAAATCG 57.497 33.333 0.00 0.00 0.00 3.34
549 572 5.709966 ACTCCCTTTGTGATTAAAAATCGC 58.290 37.500 6.30 6.30 0.00 4.58
550 573 5.066968 TCCCTTTGTGATTAAAAATCGCC 57.933 39.130 9.91 0.00 0.00 5.54
551 574 3.857093 CCCTTTGTGATTAAAAATCGCCG 59.143 43.478 9.91 0.00 0.00 6.46
552 575 4.380023 CCCTTTGTGATTAAAAATCGCCGA 60.380 41.667 9.91 0.00 0.00 5.54
553 576 4.793216 CCTTTGTGATTAAAAATCGCCGAG 59.207 41.667 9.91 7.82 0.00 4.63
554 577 5.391523 CCTTTGTGATTAAAAATCGCCGAGA 60.392 40.000 9.91 0.00 0.00 4.04
555 578 5.614923 TTGTGATTAAAAATCGCCGAGAA 57.385 34.783 9.91 0.00 0.00 2.87
556 579 5.811399 TGTGATTAAAAATCGCCGAGAAT 57.189 34.783 9.91 0.00 0.00 2.40
557 580 5.568482 TGTGATTAAAAATCGCCGAGAATG 58.432 37.500 9.91 0.00 0.00 2.67
558 581 4.970003 GTGATTAAAAATCGCCGAGAATGG 59.030 41.667 0.00 0.00 0.00 3.16
559 582 4.878971 TGATTAAAAATCGCCGAGAATGGA 59.121 37.500 0.00 0.00 0.00 3.41
560 583 5.355630 TGATTAAAAATCGCCGAGAATGGAA 59.644 36.000 0.00 0.00 0.00 3.53
561 584 3.487563 AAAAATCGCCGAGAATGGAAC 57.512 42.857 0.00 0.00 0.00 3.62
562 585 1.006832 AAATCGCCGAGAATGGAACG 58.993 50.000 0.00 0.00 0.00 3.95
567 590 4.835927 CGAGAATGGAACGGAGGG 57.164 61.111 0.00 0.00 0.00 4.30
568 591 2.199117 CGAGAATGGAACGGAGGGA 58.801 57.895 0.00 0.00 0.00 4.20
569 592 0.103208 CGAGAATGGAACGGAGGGAG 59.897 60.000 0.00 0.00 0.00 4.30
570 593 1.196012 GAGAATGGAACGGAGGGAGT 58.804 55.000 0.00 0.00 0.00 3.85
571 594 2.385803 GAGAATGGAACGGAGGGAGTA 58.614 52.381 0.00 0.00 0.00 2.59
572 595 2.362717 GAGAATGGAACGGAGGGAGTAG 59.637 54.545 0.00 0.00 0.00 2.57
573 596 0.831307 AATGGAACGGAGGGAGTAGC 59.169 55.000 0.00 0.00 0.00 3.58
574 597 0.032017 ATGGAACGGAGGGAGTAGCT 60.032 55.000 0.00 0.00 0.00 3.32
605 635 2.300152 CGCCTTCAAGATAGCCCATAGA 59.700 50.000 0.00 0.00 0.00 1.98
616 646 7.380423 AGATAGCCCATAGATAACAACAAGT 57.620 36.000 0.00 0.00 0.00 3.16
660 1828 6.480320 GGTAGAATATCCATCATGCCGAATAC 59.520 42.308 0.00 0.00 0.00 1.89
924 3027 1.979155 GGCTTGGGCACTTTCTCCC 60.979 63.158 0.00 0.00 42.93 4.30
1167 3270 3.073946 CCTTCCTCCAAGAAAGGTAACCA 59.926 47.826 0.00 0.00 35.29 3.67
1235 3338 0.322546 ATCCAACCCGAAGAACCTGC 60.323 55.000 0.00 0.00 0.00 4.85
1361 3466 1.198094 TTGGTGGATTCGGGAGCTGA 61.198 55.000 0.00 0.00 0.00 4.26
1468 3576 1.838112 TACCGTGTACTCCATCCGTT 58.162 50.000 0.00 0.00 0.00 4.44
1516 3624 7.227156 ACATCCAATATGAGTACCTTTGATCC 58.773 38.462 0.00 0.00 0.00 3.36
1539 3647 2.232452 TCTCAGCAAAGCTCCTCTACAC 59.768 50.000 0.00 0.00 36.40 2.90
1608 3716 2.741228 GCCAGACTAGCTCACAGATTGG 60.741 54.545 0.00 0.00 0.00 3.16
1620 3728 1.270839 ACAGATTGGAGTGGTCGTTGG 60.271 52.381 0.00 0.00 0.00 3.77
1720 3828 2.158842 GCCTACTTGTGGATGAGCATCT 60.159 50.000 10.04 0.00 37.92 2.90
1806 3914 1.271543 ACTCTGCCATAAGCTGTGCAA 60.272 47.619 0.00 0.00 44.23 4.08
1822 3930 2.992114 AAGCCACGCGAGAGAGGT 60.992 61.111 15.93 0.00 34.13 3.85
1826 3934 0.389426 GCCACGCGAGAGAGGTTTAA 60.389 55.000 15.93 0.00 34.13 1.52
1948 4056 1.196012 CCCTCTGTTCCTCACCCTAC 58.804 60.000 0.00 0.00 0.00 3.18
1949 4057 1.196012 CCTCTGTTCCTCACCCTACC 58.804 60.000 0.00 0.00 0.00 3.18
1950 4058 1.273324 CCTCTGTTCCTCACCCTACCT 60.273 57.143 0.00 0.00 0.00 3.08
1951 4059 2.024273 CCTCTGTTCCTCACCCTACCTA 60.024 54.545 0.00 0.00 0.00 3.08
2161 4282 4.430007 TGTAATAAGGTCTCATCACGCAC 58.570 43.478 0.00 0.00 0.00 5.34
2196 4319 4.290155 CGCCGGATTTGAATAAATTCCAG 58.710 43.478 5.05 0.00 36.66 3.86
2211 4334 3.507162 TTCCAGTTCAAATCTGCAGGA 57.493 42.857 15.13 0.00 0.00 3.86
2307 4432 8.623310 AAACAAAGTTTAATTTCCAGTACACG 57.377 30.769 0.00 0.00 0.00 4.49
2331 4458 2.704572 ACTGTACTTCCAGCATGAAGC 58.295 47.619 13.38 1.90 44.50 3.86
2390 4517 6.389622 CATGTACACCGTACATGTATATGC 57.610 41.667 27.54 7.76 45.75 3.14
2460 4589 7.806014 AGTAAAATAAATGTTGTAAGCCACACG 59.194 33.333 0.00 0.00 36.69 4.49
2518 4649 5.129634 TGACAGTTCCTGCAAATAAAGTCA 58.870 37.500 5.01 5.01 34.37 3.41
2670 4814 1.938585 TCTAGTTGGTAGGCAGCTGT 58.061 50.000 16.64 0.00 0.00 4.40
2681 4825 5.183228 GGTAGGCAGCTGTAACTGATTTTA 58.817 41.667 16.64 0.00 40.25 1.52
2686 4830 4.795278 GCAGCTGTAACTGATTTTATGCAC 59.205 41.667 16.64 0.00 40.25 4.57
2740 4884 8.758715 GCAATTCAATATAATTTCTCCAGCAAC 58.241 33.333 0.00 0.00 0.00 4.17
2771 4915 7.375053 GCAAAAATCTTGTTTGTCCCTACATA 58.625 34.615 0.00 0.00 38.09 2.29
2953 5098 3.460857 AGATTTACGGAGGCAAGCTAG 57.539 47.619 0.00 0.00 0.00 3.42
2999 5144 9.023967 GTGGAAGTTTGCTTAATTGCTTATATG 57.976 33.333 0.00 0.00 34.61 1.78
3275 5421 7.158021 AGGCGAAAATTCCTGATATAGAGAAG 58.842 38.462 0.00 0.00 0.00 2.85
3341 5487 7.013834 TGGGTGAGGTTTGTATAATTTCCTTT 58.986 34.615 0.00 0.00 0.00 3.11
3359 5505 3.120304 CCTTTAACTCCGCTCCTTTTTCG 60.120 47.826 0.00 0.00 0.00 3.46
3403 5549 3.191162 GCATTGAATTTTCCCCTTTTGCC 59.809 43.478 0.00 0.00 0.00 4.52
3629 5775 7.040478 CCTGTTTCAGTTATCTCCAAAATGTGA 60.040 37.037 0.00 0.00 0.00 3.58
3641 5787 5.879237 TCCAAAATGTGAAATACAGATCGC 58.121 37.500 0.00 0.00 43.80 4.58
3772 5919 0.593128 AACCATGCTGAACGCTTGTC 59.407 50.000 0.00 0.00 40.97 3.18
3866 6013 7.806960 GCACTCATAGCTGATTTTGAATTATCC 59.193 37.037 0.00 0.00 0.00 2.59
3893 6040 5.277828 GGGAATCTATTCGCGTGCTAAAATT 60.278 40.000 5.77 0.00 39.42 1.82
3980 6127 6.537660 ACGAGGTATAGTTTTAAGCATTGTCC 59.462 38.462 0.00 0.00 0.00 4.02
4014 6161 5.947566 CCTTCGATTTTTAGTTTCCCCCTTA 59.052 40.000 0.00 0.00 0.00 2.69
4019 6166 8.872134 TCGATTTTTAGTTTCCCCCTTAATTTT 58.128 29.630 0.00 0.00 0.00 1.82
4081 6228 0.318120 AAAATGCGAGGGCCAGTTTG 59.682 50.000 6.18 0.00 38.85 2.93
4153 6300 3.355378 TCAGGTAAAATGGCCATGACTG 58.645 45.455 21.63 20.92 0.00 3.51
4282 6429 5.597813 AGCAGTCTGTTATGAAAGAAACG 57.402 39.130 0.93 0.00 0.00 3.60
4300 6447 7.067496 AGAAACGTGATCATCATAGGGTATT 57.933 36.000 0.00 0.00 0.00 1.89
4303 6450 4.523173 ACGTGATCATCATAGGGTATTCGT 59.477 41.667 0.00 0.00 0.00 3.85
4317 6464 4.819630 GGGTATTCGTAGCCAATGAAATCA 59.180 41.667 0.00 0.00 36.69 2.57
4348 6495 1.002544 GTACTTCTTGCTGCCTCTGGT 59.997 52.381 0.00 0.00 0.00 4.00
4538 6686 6.680874 TGATGAAACAAAATTTGCAAAGCT 57.319 29.167 18.19 4.36 0.00 3.74
4702 6854 4.341235 TGTTAATCGATAGGGTCTCAGGTG 59.659 45.833 0.00 0.00 0.00 4.00
4706 6858 1.685180 CGATAGGGTCTCAGGTGGTCA 60.685 57.143 0.00 0.00 0.00 4.02
4837 6989 7.216693 GCAAATCGAATGTTTTTATGGCAAATG 59.783 33.333 0.00 0.00 0.00 2.32
4867 7046 2.164219 GCGAGGATGGCAATTTTCTTGA 59.836 45.455 0.00 0.00 40.68 3.02
5010 7214 2.029110 CGTTGGAATTTGCCATCCTTGT 60.029 45.455 0.00 0.00 37.86 3.16
5023 7250 3.828451 CCATCCTTGTTGACTGGAATTGT 59.172 43.478 0.00 0.00 33.20 2.71
5034 7261 6.573664 TGACTGGAATTGTCATCGAAAAAT 57.426 33.333 0.00 0.00 39.23 1.82
5037 7264 6.381801 ACTGGAATTGTCATCGAAAAATGTC 58.618 36.000 0.00 0.00 0.00 3.06
5041 7268 3.046968 TGTCATCGAAAAATGTCGGGA 57.953 42.857 0.00 0.00 41.43 5.14
5118 7345 6.072286 AGCAAACATAGAAAATCCTGTCAGTG 60.072 38.462 0.00 0.00 0.00 3.66
5146 7373 5.893687 TGAACATGGCATGTATTTGTCATC 58.106 37.500 31.58 22.02 44.07 2.92
5154 7382 6.819146 TGGCATGTATTTGTCATCGTTACTAA 59.181 34.615 0.00 0.00 0.00 2.24
5169 7397 6.539324 TCGTTACTAAAGAAAATTGCCATCG 58.461 36.000 0.00 0.00 0.00 3.84
5171 7399 7.331440 TCGTTACTAAAGAAAATTGCCATCGTA 59.669 33.333 0.00 0.00 0.00 3.43
5174 7402 4.782019 AAAGAAAATTGCCATCGTAGCA 57.218 36.364 0.00 0.00 38.81 3.49
5184 7412 5.574891 TGCCATCGTAGCAACAATTTAAT 57.425 34.783 0.00 0.00 37.28 1.40
5218 7446 9.995003 AAGAAACATTCAATTTGCTATGGTAAA 57.005 25.926 12.77 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 7.093322 TCGTAACCTAGAGTTTACTCATTCC 57.907 40.000 12.10 0.00 45.21 3.01
25 26 3.950395 GGAGGCTCGTAACCTAGAGTTTA 59.050 47.826 8.69 0.00 40.05 2.01
60 61 3.578716 TGGTTCTTTTGTTTTGTGGGTCA 59.421 39.130 0.00 0.00 0.00 4.02
106 108 6.269307 TGGCTCTACCATTAAGGAGGTTATAC 59.731 42.308 2.79 0.00 46.36 1.47
123 125 4.664188 CTTCGTAGTCTCTTTGGCTCTAC 58.336 47.826 0.00 0.00 0.00 2.59
129 131 1.550976 AGGGCTTCGTAGTCTCTTTGG 59.449 52.381 0.00 0.00 0.00 3.28
175 178 4.815269 TCCAAGGTTTTTATCGCAATTGG 58.185 39.130 7.72 0.00 37.80 3.16
179 182 5.067936 TCACTTTCCAAGGTTTTTATCGCAA 59.932 36.000 0.00 0.00 0.00 4.85
188 191 6.836007 AGAAGATCTTTCACTTTCCAAGGTTT 59.164 34.615 9.87 0.00 0.00 3.27
260 263 5.365605 TCGATTGTATTCCCAGAGGTTACAT 59.634 40.000 0.00 0.00 34.78 2.29
338 342 1.901159 TGCCCCACAATGGAAATTCTG 59.099 47.619 0.00 0.00 40.96 3.02
345 349 0.539438 GTGAAGTGCCCCACAATGGA 60.539 55.000 0.00 0.00 40.96 3.41
352 356 0.539438 GTCAATGGTGAAGTGCCCCA 60.539 55.000 0.00 0.00 34.87 4.96
356 360 3.921119 TCAATGTCAATGGTGAAGTGC 57.079 42.857 0.00 0.00 34.87 4.40
361 365 4.392754 CGTGAAGATCAATGTCAATGGTGA 59.607 41.667 0.00 0.00 0.00 4.02
368 372 2.076100 GCCACGTGAAGATCAATGTCA 58.924 47.619 19.30 0.00 0.00 3.58
418 422 3.904571 ACTATTGTTGTCGTGCTCGTTA 58.095 40.909 8.17 0.00 38.33 3.18
435 458 4.512944 CGAATGCATCACAAAGGCTACTAT 59.487 41.667 0.00 0.00 0.00 2.12
484 507 0.319641 GTTCACTCTCGGCGAACCTT 60.320 55.000 12.13 0.00 34.31 3.50
515 538 4.943705 TCACAAAGGGAGTATTCATGAAGC 59.056 41.667 14.54 9.24 0.00 3.86
527 550 5.102313 GGCGATTTTTAATCACAAAGGGAG 58.898 41.667 0.00 0.00 0.00 4.30
528 551 4.380023 CGGCGATTTTTAATCACAAAGGGA 60.380 41.667 0.00 0.00 0.00 4.20
529 552 3.857093 CGGCGATTTTTAATCACAAAGGG 59.143 43.478 0.00 0.00 0.00 3.95
530 553 4.728534 TCGGCGATTTTTAATCACAAAGG 58.271 39.130 4.99 0.00 0.00 3.11
531 554 5.627172 TCTCGGCGATTTTTAATCACAAAG 58.373 37.500 11.27 0.00 0.00 2.77
532 555 5.614923 TCTCGGCGATTTTTAATCACAAA 57.385 34.783 11.27 0.00 0.00 2.83
533 556 5.614923 TTCTCGGCGATTTTTAATCACAA 57.385 34.783 11.27 0.00 0.00 3.33
534 557 5.448496 CCATTCTCGGCGATTTTTAATCACA 60.448 40.000 11.27 0.00 0.00 3.58
535 558 4.970003 CCATTCTCGGCGATTTTTAATCAC 59.030 41.667 11.27 0.00 0.00 3.06
536 559 4.878971 TCCATTCTCGGCGATTTTTAATCA 59.121 37.500 11.27 0.00 0.00 2.57
537 560 5.418310 TCCATTCTCGGCGATTTTTAATC 57.582 39.130 11.27 0.00 0.00 1.75
538 561 5.578776 GTTCCATTCTCGGCGATTTTTAAT 58.421 37.500 11.27 3.01 0.00 1.40
539 562 4.436317 CGTTCCATTCTCGGCGATTTTTAA 60.436 41.667 11.27 0.48 0.00 1.52
540 563 3.062909 CGTTCCATTCTCGGCGATTTTTA 59.937 43.478 11.27 0.00 0.00 1.52
541 564 2.159572 CGTTCCATTCTCGGCGATTTTT 60.160 45.455 11.27 0.00 0.00 1.94
542 565 1.396996 CGTTCCATTCTCGGCGATTTT 59.603 47.619 11.27 0.00 0.00 1.82
543 566 1.006832 CGTTCCATTCTCGGCGATTT 58.993 50.000 11.27 0.00 0.00 2.17
544 567 0.810031 CCGTTCCATTCTCGGCGATT 60.810 55.000 11.27 0.00 37.90 3.34
545 568 1.227263 CCGTTCCATTCTCGGCGAT 60.227 57.895 11.27 0.00 37.90 4.58
546 569 2.183300 CCGTTCCATTCTCGGCGA 59.817 61.111 10.14 10.14 37.90 5.54
547 570 1.878522 CTCCGTTCCATTCTCGGCG 60.879 63.158 0.00 0.00 43.35 6.46
548 571 1.521681 CCTCCGTTCCATTCTCGGC 60.522 63.158 0.00 0.00 43.35 5.54
549 572 1.144057 CCCTCCGTTCCATTCTCGG 59.856 63.158 0.00 0.00 44.76 4.63
550 573 0.103208 CTCCCTCCGTTCCATTCTCG 59.897 60.000 0.00 0.00 0.00 4.04
551 574 1.196012 ACTCCCTCCGTTCCATTCTC 58.804 55.000 0.00 0.00 0.00 2.87
552 575 2.389715 CTACTCCCTCCGTTCCATTCT 58.610 52.381 0.00 0.00 0.00 2.40
553 576 1.202545 GCTACTCCCTCCGTTCCATTC 60.203 57.143 0.00 0.00 0.00 2.67
554 577 0.831307 GCTACTCCCTCCGTTCCATT 59.169 55.000 0.00 0.00 0.00 3.16
555 578 0.032017 AGCTACTCCCTCCGTTCCAT 60.032 55.000 0.00 0.00 0.00 3.41
556 579 0.252103 AAGCTACTCCCTCCGTTCCA 60.252 55.000 0.00 0.00 0.00 3.53
557 580 0.903236 AAAGCTACTCCCTCCGTTCC 59.097 55.000 0.00 0.00 0.00 3.62
558 581 2.764439 AAAAGCTACTCCCTCCGTTC 57.236 50.000 0.00 0.00 0.00 3.95
591 614 7.806180 ACTTGTTGTTATCTATGGGCTATCTT 58.194 34.615 0.00 0.00 0.00 2.40
605 635 6.373779 CGAGCTTCATCAAACTTGTTGTTAT 58.626 36.000 0.00 0.00 38.03 1.89
616 646 2.011947 CCTCATGCGAGCTTCATCAAA 58.988 47.619 0.00 0.00 38.00 2.69
792 2895 2.469765 CCCCCGGCCCAATTAGGAT 61.470 63.158 0.00 0.00 41.22 3.24
917 3020 1.619977 CGAAGAGAGGAGGGGGAGAAA 60.620 57.143 0.00 0.00 0.00 2.52
924 3027 2.430610 CCAGCCGAAGAGAGGAGGG 61.431 68.421 0.00 0.00 0.00 4.30
1235 3338 3.431725 GCGAGAACCCAAAGCCGG 61.432 66.667 0.00 0.00 0.00 6.13
1488 3596 8.319057 TCAAAGGTACTCATATTGGATGTAGT 57.681 34.615 0.00 0.00 38.49 2.73
1489 3597 9.429359 GATCAAAGGTACTCATATTGGATGTAG 57.571 37.037 0.00 0.00 38.49 2.74
1516 3624 2.695127 AGAGGAGCTTTGCTGAGATG 57.305 50.000 0.00 0.00 39.88 2.90
1539 3647 2.034305 CGACCCCTACAAGGATCTAACG 59.966 54.545 0.00 0.00 37.67 3.18
1608 3716 0.531200 CCTACTCCCAACGACCACTC 59.469 60.000 0.00 0.00 0.00 3.51
1620 3728 1.439679 CAGTCGCAAAACCCTACTCC 58.560 55.000 0.00 0.00 0.00 3.85
1806 3914 1.248785 TAAACCTCTCTCGCGTGGCT 61.249 55.000 5.77 0.00 0.00 4.75
1822 3930 5.825532 TCCCATGATTGAGTGGACATTAAA 58.174 37.500 0.00 0.00 37.72 1.52
1826 3934 4.503817 CGTATCCCATGATTGAGTGGACAT 60.504 45.833 0.00 0.00 37.72 3.06
1948 4056 0.886490 GAGCGGCACCATGGATTAGG 60.886 60.000 21.47 4.47 0.00 2.69
1949 4057 0.179048 TGAGCGGCACCATGGATTAG 60.179 55.000 21.47 8.19 0.00 1.73
1950 4058 0.463654 GTGAGCGGCACCATGGATTA 60.464 55.000 21.47 0.00 41.78 1.75
1951 4059 1.750399 GTGAGCGGCACCATGGATT 60.750 57.895 21.47 0.00 41.78 3.01
2161 4282 3.842126 CGGCGCATGACTCACACG 61.842 66.667 10.83 0.00 0.00 4.49
2307 4432 4.188247 TCATGCTGGAAGTACAGTACAC 57.812 45.455 13.37 6.46 40.59 2.90
2331 4458 0.895530 TTAGTCTGAGGAAGCCGGTG 59.104 55.000 1.90 0.00 0.00 4.94
2390 4517 5.413833 AGTGTAGATGTGGAATTGAAAGCAG 59.586 40.000 0.00 0.00 0.00 4.24
2460 4589 9.831737 GAATGTTGGAATATTCAGTATATGTGC 57.168 33.333 17.07 0.00 36.76 4.57
2518 4649 8.116026 AGGTTCAAATATAATGGAAGGAACAGT 58.884 33.333 0.00 0.00 36.13 3.55
2670 4814 6.892658 AACTGTGGTGCATAAAATCAGTTA 57.107 33.333 15.40 0.00 40.98 2.24
2681 4825 6.238731 CGGATAAATATCAAACTGTGGTGCAT 60.239 38.462 0.00 0.00 34.40 3.96
2720 4864 9.090692 CCAAAAGTTGCTGGAGAAATTATATTG 57.909 33.333 0.00 0.00 34.35 1.90
2726 4870 3.134442 TGCCAAAAGTTGCTGGAGAAATT 59.866 39.130 8.18 0.00 34.35 1.82
2740 4884 6.257423 GGACAAACAAGATTTTTGCCAAAAG 58.743 36.000 2.46 0.00 37.45 2.27
2744 4888 3.454082 AGGGACAAACAAGATTTTTGCCA 59.546 39.130 0.00 0.00 37.45 4.92
2771 4915 8.573035 CAACCAGGTAAAAAGTGTAATGTACAT 58.427 33.333 1.41 1.41 41.34 2.29
2940 5085 0.465705 TTGATCCTAGCTTGCCTCCG 59.534 55.000 0.00 0.00 0.00 4.63
2953 5098 7.630242 TCCACTCAAAAGTCATATTTGATCC 57.370 36.000 2.54 0.00 43.61 3.36
2999 5144 6.846283 CACAAAGAACATCGTCAAAGAAGTAC 59.154 38.462 0.00 0.00 0.00 2.73
3275 5421 2.161410 TGTCGCAACAATATCCAAGCAC 59.839 45.455 0.00 0.00 30.70 4.40
3359 5505 6.977213 TGCACAGAAATAGAAAAGGTAAACC 58.023 36.000 0.00 0.00 0.00 3.27
3526 5672 6.035975 AGCAAACTGTTAAGAAACATGCAAAC 59.964 34.615 14.29 0.00 45.33 2.93
3673 5819 7.308782 ACAGATGTTAGTAACTAGCAAATGC 57.691 36.000 14.00 0.00 42.49 3.56
3824 5971 8.341173 GCTATGAGTGCCTGCATTAAATATATC 58.659 37.037 0.00 0.00 0.00 1.63
3866 6013 1.409412 CACGCGAATAGATTCCCTCG 58.591 55.000 15.93 1.84 33.28 4.63
3893 6040 2.234143 CACACTGAGTCAGAGTCCTCA 58.766 52.381 26.86 0.00 33.38 3.86
3980 6127 8.494016 AACTAAAAATCGAAGGACAGGAATAG 57.506 34.615 0.00 0.00 0.00 1.73
4014 6161 3.213506 GCCTGCAAAACTCCCAAAAATT 58.786 40.909 0.00 0.00 0.00 1.82
4019 6166 0.689080 TTGGCCTGCAAAACTCCCAA 60.689 50.000 3.32 0.00 0.00 4.12
4081 6228 1.087501 GATCGCCAACAAGGACTTCC 58.912 55.000 0.00 0.00 41.22 3.46
4153 6300 5.091261 AGATGATGGTGAGTAGTCAAACC 57.909 43.478 0.69 0.91 33.27 3.27
4282 6429 6.037098 GCTACGAATACCCTATGATGATCAC 58.963 44.000 0.00 0.00 0.00 3.06
4300 6447 3.627395 ACCTGATTTCATTGGCTACGA 57.373 42.857 0.00 0.00 0.00 3.43
4303 6450 8.592809 ACAAAAATAACCTGATTTCATTGGCTA 58.407 29.630 0.00 0.00 0.00 3.93
4317 6464 6.447162 GCAGCAAGAAGTACAAAAATAACCT 58.553 36.000 0.00 0.00 0.00 3.50
4348 6495 8.129211 CACACACTATGACGATAGACTAAATCA 58.871 37.037 0.00 0.00 35.90 2.57
4652 6804 1.398390 CGTAACCAGCCTGCAGAAATC 59.602 52.381 17.39 1.00 0.00 2.17
4702 6854 3.254060 CATACTGCGTATAGGCATGACC 58.746 50.000 19.61 0.00 42.99 4.02
4706 6858 3.194968 GGTACCATACTGCGTATAGGCAT 59.805 47.826 19.61 12.46 42.99 4.40
4821 6973 7.678218 GCAACAACTTCATTTGCCATAAAAACA 60.678 33.333 0.00 0.00 39.82 2.83
4837 6989 0.169009 GCCATCCTCGCAACAACTTC 59.831 55.000 0.00 0.00 0.00 3.01
4867 7046 4.041567 TGACATGTGACACTTATCAGGGTT 59.958 41.667 1.15 0.00 36.47 4.11
5023 7250 2.352388 GGTCCCGACATTTTTCGATGA 58.648 47.619 0.00 0.00 41.78 2.92
5118 7345 6.158598 ACAAATACATGCCATGTTCAGTTTC 58.841 36.000 16.67 0.00 41.63 2.78
5146 7373 6.311723 ACGATGGCAATTTTCTTTAGTAACG 58.688 36.000 0.00 0.00 0.00 3.18
5154 7382 4.782019 TTGCTACGATGGCAATTTTCTT 57.218 36.364 9.46 0.00 43.50 2.52
5184 7412 9.545105 AGCAAATTGAATGTTTCTTATGACAAA 57.455 25.926 0.00 0.00 0.00 2.83
5218 7446 4.561213 GCTACAAACAAACGTCAGCTTTTT 59.439 37.500 0.00 0.00 0.00 1.94
5223 7451 1.259507 TCGCTACAAACAAACGTCAGC 59.740 47.619 0.00 0.00 0.00 4.26
5229 7457 6.822073 AAAAGGATTTCGCTACAAACAAAC 57.178 33.333 0.00 0.00 37.28 2.93
5232 7460 6.385649 AGAAAAAGGATTTCGCTACAAACA 57.614 33.333 0.00 0.00 37.28 2.83


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

AutoCloner maintained by Alex Coulton.