Multiple sequence alignment - TraesCS6B01G238900

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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 TraesCS6B01G238900 chr6B 100.000 3861 0 0 1441 5301 415868649 415864789 0.000000e+00 7131.0
1 TraesCS6B01G238900 chr6B 100.000 1112 0 0 1 1112 415870089 415868978 0.000000e+00 2054.0
2 TraesCS6B01G238900 chr6B 81.481 108 13 6 3767 3870 511701434 511701538 1.220000e-11 82.4
3 TraesCS6B01G238900 chr6D 91.286 3810 172 77 1441 5178 267519695 267515974 0.000000e+00 5049.0
4 TraesCS6B01G238900 chr6D 92.409 606 21 2 515 1112 267520294 267519706 0.000000e+00 841.0
5 TraesCS6B01G238900 chr6D 91.414 396 31 2 136 531 267520707 267520315 1.680000e-149 540.0
6 TraesCS6B01G238900 chr6D 94.309 123 5 2 1 123 267524513 267524393 2.520000e-43 187.0
7 TraesCS6B01G238900 chr6D 91.379 116 8 2 5187 5301 267515924 267515810 1.980000e-34 158.0
8 TraesCS6B01G238900 chr6D 81.651 109 14 5 3765 3870 315597954 315597849 9.460000e-13 86.1
9 TraesCS6B01G238900 chr6A 95.059 3137 114 23 1444 4544 381034504 381031373 0.000000e+00 4896.0
10 TraesCS6B01G238900 chr6A 92.988 599 24 2 515 1112 381035096 381034515 0.000000e+00 857.0
11 TraesCS6B01G238900 chr6A 90.885 373 23 5 167 531 381035486 381035117 1.720000e-134 490.0
12 TraesCS6B01G238900 chr6A 85.934 391 35 10 4789 5178 381027318 381026947 2.970000e-107 399.0
13 TraesCS6B01G238900 chr6A 87.879 297 15 5 4264 4541 381030835 381030541 3.960000e-86 329.0
14 TraesCS6B01G238900 chr6A 93.966 116 6 1 1 116 381080157 381080043 1.960000e-39 174.0
15 TraesCS6B01G238900 chr6A 93.103 116 7 1 1 116 381035737 381035623 9.130000e-38 169.0
16 TraesCS6B01G238900 chr6A 88.983 118 9 3 5187 5301 381026894 381026778 5.530000e-30 143.0
17 TraesCS6B01G238900 chr6A 96.491 57 2 0 4264 4320 381031333 381031277 1.570000e-15 95.3
18 TraesCS6B01G238900 chr6A 81.651 109 14 5 3765 3870 452637917 452637812 9.460000e-13 86.1
19 TraesCS6B01G238900 chr1D 87.898 628 50 12 2252 2868 453793077 453793689 0.000000e+00 715.0
20 TraesCS6B01G238900 chr1B 91.045 402 17 9 2482 2868 624085088 624085485 4.700000e-145 525.0
21 TraesCS6B01G238900 chr1B 85.659 258 29 7 2245 2500 624084819 624085070 1.130000e-66 265.0
22 TraesCS6B01G238900 chr1A 90.421 261 10 6 2610 2868 548529297 548529544 3.960000e-86 329.0
23 TraesCS6B01G238900 chr5B 94.030 67 4 0 2742 2808 550228014 550227948 9.390000e-18 102.0
24 TraesCS6B01G238900 chr5D 92.537 67 5 0 2742 2808 450208435 450208369 4.370000e-16 97.1
25 TraesCS6B01G238900 chr5A 93.651 63 4 0 2742 2804 569548287 569548225 1.570000e-15 95.3
26 TraesCS6B01G238900 chr4A 93.617 47 2 1 5039 5084 640218868 640218914 9.530000e-08 69.4


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 TraesCS6B01G238900 chr6B 415864789 415870089 5300 True 4592.5000 7131 100.00000 1 5301 2 chr6B.!!$R1 5300
1 TraesCS6B01G238900 chr6D 267515810 267524513 8703 True 1355.0000 5049 92.15940 1 5301 5 chr6D.!!$R2 5300
2 TraesCS6B01G238900 chr6A 381026778 381035737 8959 True 922.2875 4896 91.41525 1 5301 8 chr6A.!!$R3 5300
3 TraesCS6B01G238900 chr1D 453793077 453793689 612 False 715.0000 715 87.89800 2252 2868 1 chr1D.!!$F1 616
4 TraesCS6B01G238900 chr1B 624084819 624085485 666 False 395.0000 525 88.35200 2245 2868 2 chr1B.!!$F1 623

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
341 4034 0.036010 CCAATTCCTCCGCAGAGTGT 60.036 55.0 0.00 0.00 38.58 3.55 F
990 4736 0.179205 CGTTCGGTAGAGTGTCGACC 60.179 60.0 14.12 4.42 38.57 4.79 F
1778 5545 0.966179 AAAAGCAAACGGGGATCCAC 59.034 50.0 15.23 9.60 0.00 4.02 F
2454 6252 0.949105 ATTGTTGACGTCGGCAGGAC 60.949 55.0 11.62 0.00 42.48 3.85 F
3581 7439 0.600057 CTTCCCTTCAGCCAGTTTGC 59.400 55.0 0.00 0.00 0.00 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1589 5348 0.971386 AAGAAAAGTGCATGGCCAGG 59.029 50.000 14.45 14.45 0.00 4.45 R
2142 5936 1.793820 AAAGCCCTTGGGTCTCCTGG 61.794 60.000 7.61 0.00 30.76 4.45 R
3292 7147 0.961753 AACTGCAAGGCCAAGTTAGC 59.038 50.000 5.01 0.00 39.30 3.09 R
3870 7728 1.138859 TGGTATGGATCAAGGACTGCG 59.861 52.381 0.00 0.00 0.00 5.18 R
4997 12698 0.163146 GACACGGCAGTTAAAGTCGC 59.837 55.000 3.40 0.00 37.67 5.19 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
56 57 5.278957 GGCCGCACAGGATAATTATGATTTT 60.279 40.000 1.78 0.00 45.00 1.82
103 104 6.348498 TGTGTTGAGAAAATCTTGAGTCTCA 58.652 36.000 0.00 0.00 43.58 3.27
123 124 7.120285 AGTCTCAAAAATATCACATGTGTGGAG 59.880 37.037 24.63 15.99 45.65 3.86
124 125 6.375174 TCTCAAAAATATCACATGTGTGGAGG 59.625 38.462 24.63 8.92 45.65 4.30
126 127 5.902613 AAAATATCACATGTGTGGAGGTG 57.097 39.130 24.63 0.00 45.65 4.00
127 128 4.842531 AATATCACATGTGTGGAGGTGA 57.157 40.909 24.63 3.87 45.65 4.02
132 133 5.178096 TCACATGTGTGGAGGTGATATTT 57.822 39.130 24.63 0.00 45.65 1.40
133 134 5.185454 TCACATGTGTGGAGGTGATATTTC 58.815 41.667 24.63 0.00 45.65 2.17
134 135 4.336433 CACATGTGTGGAGGTGATATTTCC 59.664 45.833 18.03 0.00 42.10 3.13
154 3830 3.741476 CTCTTGCTGGCGGTTGGC 61.741 66.667 0.00 0.00 42.51 4.52
186 3879 1.285280 TCCGATAATATGCCCTGGGG 58.715 55.000 16.03 4.75 38.57 4.96
197 3890 1.152963 CCCTGGGGATTTAGGTGCG 60.153 63.158 4.27 0.00 37.50 5.34
220 3913 6.734871 GCGGAATATTCCTTTTCATAACCCAC 60.735 42.308 27.86 0.92 45.33 4.61
300 3993 5.184671 CCGTAACTCAACTAGGGTTAGAAGT 59.815 44.000 0.00 0.00 33.88 3.01
312 4005 1.068055 GTTAGAAGTCCGAACCGCAGA 60.068 52.381 0.00 0.00 0.00 4.26
333 4026 5.877012 CAGATATATGTTCCCAATTCCTCCG 59.123 44.000 0.00 0.00 0.00 4.63
341 4034 0.036010 CCAATTCCTCCGCAGAGTGT 60.036 55.000 0.00 0.00 38.58 3.55
408 4109 2.196749 CCACATGTCATACTCACGAGC 58.803 52.381 0.00 0.00 0.00 5.03
430 4131 0.603569 GAACTGCTTCCTCTCGTGGA 59.396 55.000 0.00 0.00 0.00 4.02
469 4170 4.724602 TGCAGAGGACGAGCGTGC 62.725 66.667 6.41 6.41 36.69 5.34
484 4185 1.659794 GTGCGGCTCATGGTTTTGT 59.340 52.632 0.00 0.00 0.00 2.83
502 4203 5.930837 TTTGTCCTTCAATTGTTTGGTCT 57.069 34.783 5.13 0.00 35.84 3.85
503 4204 7.262048 GTTTTGTCCTTCAATTGTTTGGTCTA 58.738 34.615 5.13 0.00 35.84 2.59
504 4205 6.385649 TTGTCCTTCAATTGTTTGGTCTAC 57.614 37.500 5.13 2.43 33.44 2.59
505 4206 5.690865 TGTCCTTCAATTGTTTGGTCTACT 58.309 37.500 5.13 0.00 33.44 2.57
526 4227 2.945456 ACCAAACCAAGAAGGAAGGAC 58.055 47.619 0.00 0.00 41.22 3.85
540 4278 2.508526 GAAGGACACAGCACAAGGATT 58.491 47.619 0.00 0.00 0.00 3.01
560 4298 2.052468 TGATCCATCTGACATCTGGGG 58.948 52.381 4.16 0.00 0.00 4.96
710 4448 3.379445 CGTCTACCACGCCCACCT 61.379 66.667 0.00 0.00 42.87 4.00
712 4450 1.597797 CGTCTACCACGCCCACCTAA 61.598 60.000 0.00 0.00 42.87 2.69
713 4451 0.609662 GTCTACCACGCCCACCTAAA 59.390 55.000 0.00 0.00 0.00 1.85
717 4455 1.125711 ACCACGCCCACCTAAACTCT 61.126 55.000 0.00 0.00 0.00 3.24
725 4463 2.640826 CCCACCTAAACTCTTACCCACA 59.359 50.000 0.00 0.00 0.00 4.17
903 4641 1.685491 CGGGTGCTAGGGTTAGAGACT 60.685 57.143 0.00 0.00 0.00 3.24
980 4726 3.221834 CGAGAGCTTCGTTCGGTAG 57.778 57.895 9.30 0.00 44.27 3.18
981 4727 0.725686 CGAGAGCTTCGTTCGGTAGA 59.274 55.000 9.30 0.00 44.27 2.59
982 4728 1.267632 CGAGAGCTTCGTTCGGTAGAG 60.268 57.143 9.30 0.00 44.27 2.43
983 4729 1.738908 GAGAGCTTCGTTCGGTAGAGT 59.261 52.381 0.00 0.00 0.00 3.24
984 4730 1.469308 AGAGCTTCGTTCGGTAGAGTG 59.531 52.381 0.00 0.00 0.00 3.51
985 4731 1.199558 GAGCTTCGTTCGGTAGAGTGT 59.800 52.381 0.00 0.00 0.00 3.55
986 4732 1.199558 AGCTTCGTTCGGTAGAGTGTC 59.800 52.381 0.00 0.00 0.00 3.67
987 4733 1.879646 CTTCGTTCGGTAGAGTGTCG 58.120 55.000 0.00 0.00 0.00 4.35
988 4734 1.462283 CTTCGTTCGGTAGAGTGTCGA 59.538 52.381 0.00 0.00 0.00 4.20
989 4735 0.792640 TCGTTCGGTAGAGTGTCGAC 59.207 55.000 9.11 9.11 32.39 4.20
990 4736 0.179205 CGTTCGGTAGAGTGTCGACC 60.179 60.000 14.12 4.42 38.57 4.79
1669 5428 9.945904 ATCCTTTAATTTTTGCCCGTATAAAAA 57.054 25.926 0.00 0.00 39.30 1.94
1704 5465 9.563748 TTTAGGTATATATTCCCCAGTTTTTCG 57.436 33.333 4.84 0.00 0.00 3.46
1770 5537 2.697431 TCCGATCAAAAAGCAAACGG 57.303 45.000 0.00 0.00 40.16 4.44
1778 5545 0.966179 AAAAGCAAACGGGGATCCAC 59.034 50.000 15.23 9.60 0.00 4.02
1782 5549 2.404559 AGCAAACGGGGATCCACTATA 58.595 47.619 13.38 0.00 0.00 1.31
1790 5557 4.072131 CGGGGATCCACTATATTGTTTGG 58.928 47.826 13.38 0.00 0.00 3.28
1847 5635 4.286032 TGATCTGTGGTGCTTAAGTAGGTT 59.714 41.667 4.02 0.00 0.00 3.50
1855 5643 8.984855 TGTGGTGCTTAAGTAGGTTATAAGTAT 58.015 33.333 4.02 0.00 0.00 2.12
1857 5645 9.826574 TGGTGCTTAAGTAGGTTATAAGTATTG 57.173 33.333 4.02 0.00 0.00 1.90
2094 5888 1.200020 GGGGAAGAAGTCGCAAATGTG 59.800 52.381 0.00 0.00 40.96 3.21
2124 5918 3.515602 ATGACAATGGGGCTATCTTCC 57.484 47.619 0.00 0.00 0.00 3.46
2138 5932 4.638865 GCTATCTTCCGGTGGTATTGTTTT 59.361 41.667 0.00 0.00 0.00 2.43
2142 5936 3.062122 TCCGGTGGTATTGTTTTCTCC 57.938 47.619 0.00 0.00 0.00 3.71
2294 6089 8.342634 GTTTGTTTATTTCTGAACTGAGTAGCA 58.657 33.333 0.00 0.00 0.00 3.49
2424 6222 2.094417 CGGAATTCTCAAGGCGTTTCTC 59.906 50.000 5.23 0.00 0.00 2.87
2454 6252 0.949105 ATTGTTGACGTCGGCAGGAC 60.949 55.000 11.62 0.00 42.48 3.85
3034 6887 1.278127 GCACACTTCTGCTACCCCTTA 59.722 52.381 0.00 0.00 34.06 2.69
3356 7212 5.703978 TTGTGTATGCTGTTTGTGCTAAT 57.296 34.783 0.00 0.00 0.00 1.73
3473 7329 4.804868 TTTTGGCAGCACAACATATGAT 57.195 36.364 10.38 0.00 0.00 2.45
3581 7439 0.600057 CTTCCCTTCAGCCAGTTTGC 59.400 55.000 0.00 0.00 0.00 3.68
3589 7447 0.881118 CAGCCAGTTTGCGGTTGTAT 59.119 50.000 0.00 0.00 36.02 2.29
3711 7569 2.159382 ACGTCATTGGGGCTTTACTTG 58.841 47.619 0.00 0.00 0.00 3.16
3722 7580 4.202050 GGGGCTTTACTTGCATCTGTTATG 60.202 45.833 0.00 0.00 0.00 1.90
3870 7728 3.194062 GCTCAAGAAGGCTGAGTATGTC 58.806 50.000 3.78 0.00 32.67 3.06
3873 7731 1.186200 AGAAGGCTGAGTATGTCGCA 58.814 50.000 0.00 0.00 0.00 5.10
4325 8197 2.424956 GCCCAAGATCCTAGCAAACTTG 59.575 50.000 0.00 0.00 38.02 3.16
4330 8202 5.123979 CCAAGATCCTAGCAAACTTGTAACC 59.876 44.000 0.00 0.00 37.02 2.85
4527 9238 3.637229 TGTAACCGGGATGAGATTCTCTC 59.363 47.826 14.54 9.24 43.65 3.20
4573 10601 9.919348 CAACACTAATTTTGTTGGAAATTCTTG 57.081 29.630 18.44 1.13 46.74 3.02
4667 10695 1.338337 ACGACTCACTTCACCAGTCTG 59.662 52.381 0.00 0.00 35.37 3.51
4669 10697 1.069204 GACTCACTTCACCAGTCTGCA 59.931 52.381 0.00 0.00 34.79 4.41
4670 10698 1.069823 ACTCACTTCACCAGTCTGCAG 59.930 52.381 7.63 7.63 30.92 4.41
4671 10699 0.250038 TCACTTCACCAGTCTGCAGC 60.250 55.000 9.47 4.26 30.92 5.25
4672 10700 0.533531 CACTTCACCAGTCTGCAGCA 60.534 55.000 9.47 0.00 30.92 4.41
4673 10701 0.533755 ACTTCACCAGTCTGCAGCAC 60.534 55.000 9.47 8.49 0.00 4.40
4741 10819 5.355670 AGGGAGCCTAGATATGAAACCTA 57.644 43.478 0.00 0.00 28.47 3.08
4744 10822 6.795000 AGGGAGCCTAGATATGAAACCTAAAT 59.205 38.462 0.00 0.00 28.47 1.40
4756 10834 9.936329 ATATGAAACCTAAATAATTGTGACCCT 57.064 29.630 0.00 0.00 0.00 4.34
4757 10835 8.664669 ATGAAACCTAAATAATTGTGACCCTT 57.335 30.769 0.00 0.00 0.00 3.95
4758 10836 8.117813 TGAAACCTAAATAATTGTGACCCTTC 57.882 34.615 0.00 0.00 0.00 3.46
4759 10837 7.947890 TGAAACCTAAATAATTGTGACCCTTCT 59.052 33.333 0.00 0.00 0.00 2.85
4760 10838 7.703058 AACCTAAATAATTGTGACCCTTCTG 57.297 36.000 0.00 0.00 0.00 3.02
4772 12470 4.092968 GTGACCCTTCTGCGTTTTATACAG 59.907 45.833 0.00 0.00 0.00 2.74
4835 12536 2.178764 TCCTCCTATCACTCTCATGGCT 59.821 50.000 0.00 0.00 0.00 4.75
4843 12544 6.204301 CCTATCACTCTCATGGCTTGTAAATG 59.796 42.308 0.00 0.00 0.00 2.32
4848 12549 6.257411 CACTCTCATGGCTTGTAAATGAGTAG 59.743 42.308 10.70 9.44 44.95 2.57
4854 12555 3.623510 GGCTTGTAAATGAGTAGCTGTCC 59.376 47.826 0.00 0.00 32.58 4.02
4881 12582 4.452455 AGTCAAATGGCTTCTCTTACGTTG 59.548 41.667 0.00 0.00 0.00 4.10
4891 12592 6.019479 GGCTTCTCTTACGTTGTGATTGATAG 60.019 42.308 0.00 0.00 0.00 2.08
4893 12594 7.275779 GCTTCTCTTACGTTGTGATTGATAGAA 59.724 37.037 0.00 0.00 0.00 2.10
4894 12595 9.140286 CTTCTCTTACGTTGTGATTGATAGAAA 57.860 33.333 0.00 0.00 0.00 2.52
4895 12596 9.483916 TTCTCTTACGTTGTGATTGATAGAAAA 57.516 29.630 0.00 0.00 0.00 2.29
4897 12598 9.746711 CTCTTACGTTGTGATTGATAGAAAAAG 57.253 33.333 0.00 0.00 0.00 2.27
4898 12599 9.268268 TCTTACGTTGTGATTGATAGAAAAAGT 57.732 29.630 0.00 0.00 0.00 2.66
4899 12600 9.318041 CTTACGTTGTGATTGATAGAAAAAGTG 57.682 33.333 0.00 0.00 0.00 3.16
4900 12601 7.490962 ACGTTGTGATTGATAGAAAAAGTGA 57.509 32.000 0.00 0.00 0.00 3.41
4901 12602 7.925993 ACGTTGTGATTGATAGAAAAAGTGAA 58.074 30.769 0.00 0.00 0.00 3.18
4902 12603 8.070171 ACGTTGTGATTGATAGAAAAAGTGAAG 58.930 33.333 0.00 0.00 0.00 3.02
4943 12644 2.137810 TGTAGCCTTTGGTTATGGCC 57.862 50.000 0.00 0.00 45.84 5.36
4944 12645 1.638589 TGTAGCCTTTGGTTATGGCCT 59.361 47.619 3.32 0.00 45.84 5.19
4962 12663 2.033550 GCCTAGAGTCACGTGACCTATG 59.966 54.545 38.00 30.88 45.85 2.23
4963 12664 3.280295 CCTAGAGTCACGTGACCTATGT 58.720 50.000 38.00 23.57 45.85 2.29
4964 12665 4.449131 CCTAGAGTCACGTGACCTATGTA 58.551 47.826 38.00 23.72 45.85 2.29
4965 12666 5.064558 CCTAGAGTCACGTGACCTATGTAT 58.935 45.833 38.00 22.18 45.85 2.29
4966 12667 5.179742 CCTAGAGTCACGTGACCTATGTATC 59.820 48.000 38.00 27.75 45.85 2.24
4967 12668 4.783055 AGAGTCACGTGACCTATGTATCT 58.217 43.478 38.00 29.23 45.85 1.98
4992 12693 1.672145 GCCTCGGACCTCTTGTTGTAC 60.672 57.143 0.00 0.00 0.00 2.90
4997 12698 2.417719 GGACCTCTTGTTGTACTGCAG 58.582 52.381 13.48 13.48 0.00 4.41
4998 12699 1.801178 GACCTCTTGTTGTACTGCAGC 59.199 52.381 15.27 0.00 0.00 5.25
5000 12701 1.605457 CCTCTTGTTGTACTGCAGCGA 60.605 52.381 15.27 0.00 0.00 4.93
5028 12732 3.058115 CCGTGTCAATGTCGGCATA 57.942 52.632 1.27 0.00 37.90 3.14
5029 12733 0.650512 CCGTGTCAATGTCGGCATAC 59.349 55.000 1.27 0.00 37.90 2.39
5080 12784 6.180472 AGAAACATATGGAAATCCGTTGAGT 58.820 36.000 7.80 0.00 39.43 3.41
5084 12788 6.852664 ACATATGGAAATCCGTTGAGTTTTC 58.147 36.000 7.80 0.00 39.43 2.29
5089 12793 2.270352 ATCCGTTGAGTTTTCTGGCA 57.730 45.000 0.00 0.00 0.00 4.92
5098 12802 2.260869 TTTTCTGGCAGCAGTCCGC 61.261 57.895 10.34 0.00 42.91 5.54
5113 12817 4.236935 CAGTCCGCTGCACAATAAAATTT 58.763 39.130 0.00 0.00 35.77 1.82
5114 12818 4.090354 CAGTCCGCTGCACAATAAAATTTG 59.910 41.667 0.00 0.00 35.77 2.32
5121 12825 5.284428 TGCACAATAAAATTTGCAGCATG 57.716 34.783 0.00 0.00 40.01 4.06
5124 12831 5.566016 GCACAATAAAATTTGCAGCATGTTG 59.434 36.000 5.00 5.00 39.31 3.33
5129 12836 8.473016 CAATAAAATTTGCAGCATGTTGTTTTG 58.527 29.630 11.44 0.00 39.31 2.44
5138 12845 4.155644 CAGCATGTTGTTTTGTTTTTGGGT 59.844 37.500 0.65 0.00 0.00 4.51
5159 12866 6.435904 TGGGTATAAAATTTGCAACAGCTAGT 59.564 34.615 0.00 0.00 0.00 2.57
5171 12878 3.971032 ACAGCTAGTTGAACACTTTGC 57.029 42.857 14.09 0.00 36.88 3.68
5178 12885 4.292977 AGTTGAACACTTTGCAAGCTAC 57.707 40.909 0.00 0.00 27.32 3.58
5179 12886 3.035942 GTTGAACACTTTGCAAGCTACG 58.964 45.455 0.00 0.00 0.00 3.51
5181 12888 3.459145 TGAACACTTTGCAAGCTACGTA 58.541 40.909 0.00 0.00 0.00 3.57
5182 12889 3.872182 TGAACACTTTGCAAGCTACGTAA 59.128 39.130 0.00 0.00 0.00 3.18
5183 12890 4.513692 TGAACACTTTGCAAGCTACGTAAT 59.486 37.500 0.00 0.00 0.00 1.89
5184 12891 5.008217 TGAACACTTTGCAAGCTACGTAATT 59.992 36.000 0.00 0.00 0.00 1.40
5185 12892 4.783242 ACACTTTGCAAGCTACGTAATTG 58.217 39.130 13.32 13.32 0.00 2.32
5223 12975 2.277373 GACGCGACGCTAGTCTGG 60.277 66.667 15.93 2.48 44.93 3.86
5238 12992 0.394762 TCTGGCAATGTCTGGATGGC 60.395 55.000 0.00 0.00 39.81 4.40
5240 12994 0.918258 TGGCAATGTCTGGATGGCTA 59.082 50.000 0.00 0.00 40.04 3.93
5245 12999 2.889045 CAATGTCTGGATGGCTAATGGG 59.111 50.000 0.00 0.00 0.00 4.00
5246 13000 1.595311 TGTCTGGATGGCTAATGGGT 58.405 50.000 0.00 0.00 0.00 4.51
5272 13026 6.858478 AGAAATGTCGACGATGATACATGTAG 59.142 38.462 11.91 0.00 33.04 2.74
5295 13049 4.213694 GTCGATTGAGGACGAGCTAATAGA 59.786 45.833 0.00 0.00 39.16 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 6.549952 CCTGAACTTCTGTAATTCATTGAGC 58.450 40.000 0.00 0.00 32.16 4.26
69 70 9.657419 AAGATTTTCTCAACACAATTTTCAACT 57.343 25.926 0.00 0.00 0.00 3.16
80 81 6.851222 TGAGACTCAAGATTTTCTCAACAC 57.149 37.500 1.64 0.00 41.16 3.32
123 124 3.557595 CAGCAAGAGACGGAAATATCACC 59.442 47.826 0.00 0.00 0.00 4.02
124 125 3.557595 CCAGCAAGAGACGGAAATATCAC 59.442 47.826 0.00 0.00 0.00 3.06
126 127 2.545946 GCCAGCAAGAGACGGAAATATC 59.454 50.000 0.00 0.00 0.00 1.63
127 128 2.565841 GCCAGCAAGAGACGGAAATAT 58.434 47.619 0.00 0.00 0.00 1.28
129 130 1.021390 CGCCAGCAAGAGACGGAAAT 61.021 55.000 0.00 0.00 0.00 2.17
132 133 4.069232 CCGCCAGCAAGAGACGGA 62.069 66.667 0.00 0.00 46.71 4.69
134 135 2.357517 AACCGCCAGCAAGAGACG 60.358 61.111 0.00 0.00 0.00 4.18
154 3830 6.260936 GCATATTATCGGATTCCCCAATACAG 59.739 42.308 0.00 0.00 34.14 2.74
220 3913 3.072211 GTTTTCTAACCCGAGTTGGAGG 58.928 50.000 0.00 0.00 43.41 4.30
300 3993 3.305813 GGAACATATATCTGCGGTTCGGA 60.306 47.826 0.00 0.00 38.90 4.55
312 4005 4.042809 TGCGGAGGAATTGGGAACATATAT 59.957 41.667 0.00 0.00 42.32 0.86
333 4026 1.202698 ACCTTCCAGAACACACTCTGC 60.203 52.381 0.00 0.00 41.36 4.26
341 4034 3.572642 TCTGTGACTACCTTCCAGAACA 58.427 45.455 0.00 0.00 0.00 3.18
383 4076 1.632920 TGAGTATGACATGTGGGCCAA 59.367 47.619 8.40 0.00 0.00 4.52
408 4109 0.039074 ACGAGAGGAAGCAGTTCACG 60.039 55.000 0.00 0.00 33.93 4.35
412 4113 1.270907 ATCCACGAGAGGAAGCAGTT 58.729 50.000 0.00 0.00 41.92 3.16
430 4131 7.227156 TGCAATTGGTTGGGTGTTTATTAAAT 58.773 30.769 7.72 0.00 35.83 1.40
469 4170 1.200020 GAAGGACAAAACCATGAGCCG 59.800 52.381 0.00 0.00 0.00 5.52
502 4203 4.909088 TCCTTCCTTCTTGGTTTGGTAGTA 59.091 41.667 0.00 0.00 37.07 1.82
503 4204 3.720002 TCCTTCCTTCTTGGTTTGGTAGT 59.280 43.478 0.00 0.00 37.07 2.73
504 4205 4.072839 GTCCTTCCTTCTTGGTTTGGTAG 58.927 47.826 0.00 0.00 37.07 3.18
505 4206 3.460340 TGTCCTTCCTTCTTGGTTTGGTA 59.540 43.478 0.00 0.00 37.07 3.25
518 4219 0.109342 CCTTGTGCTGTGTCCTTCCT 59.891 55.000 0.00 0.00 0.00 3.36
540 4278 2.052468 CCCCAGATGTCAGATGGATCA 58.948 52.381 7.52 0.00 36.09 2.92
560 4298 1.000843 GTGGGACCAAATTCAGGTTGC 59.999 52.381 4.24 0.00 40.09 4.17
568 4306 1.228003 TGACGCGTGGGACCAAATT 60.228 52.632 20.70 0.00 0.00 1.82
703 4441 1.631898 TGGGTAAGAGTTTAGGTGGGC 59.368 52.381 0.00 0.00 0.00 5.36
710 4448 2.564062 CGGAGGTGTGGGTAAGAGTTTA 59.436 50.000 0.00 0.00 0.00 2.01
712 4450 0.974383 CGGAGGTGTGGGTAAGAGTT 59.026 55.000 0.00 0.00 0.00 3.01
713 4451 1.542187 GCGGAGGTGTGGGTAAGAGT 61.542 60.000 0.00 0.00 0.00 3.24
717 4455 3.697747 CGGCGGAGGTGTGGGTAA 61.698 66.667 0.00 0.00 0.00 2.85
725 4463 3.039988 CGATGTATCGGCGGAGGT 58.960 61.111 7.21 0.00 45.93 3.85
978 4724 2.481854 GCTAGATCGGTCGACACTCTA 58.518 52.381 18.91 16.91 0.00 2.43
979 4725 1.301423 GCTAGATCGGTCGACACTCT 58.699 55.000 18.91 16.69 0.00 3.24
980 4726 0.042013 CGCTAGATCGGTCGACACTC 60.042 60.000 18.91 10.27 0.00 3.51
981 4727 0.461516 TCGCTAGATCGGTCGACACT 60.462 55.000 18.91 12.55 0.00 3.55
982 4728 0.587285 ATCGCTAGATCGGTCGACAC 59.413 55.000 18.91 5.92 33.59 3.67
983 4729 0.586802 CATCGCTAGATCGGTCGACA 59.413 55.000 18.91 0.00 34.23 4.35
984 4730 0.110147 CCATCGCTAGATCGGTCGAC 60.110 60.000 7.13 7.13 34.23 4.20
985 4731 0.250166 TCCATCGCTAGATCGGTCGA 60.250 55.000 0.00 8.25 34.23 4.20
986 4732 0.167033 CTCCATCGCTAGATCGGTCG 59.833 60.000 0.00 0.00 34.23 4.79
987 4733 1.068885 CACTCCATCGCTAGATCGGTC 60.069 57.143 0.00 0.00 34.23 4.79
988 4734 0.955178 CACTCCATCGCTAGATCGGT 59.045 55.000 0.00 0.00 34.23 4.69
989 4735 0.387878 GCACTCCATCGCTAGATCGG 60.388 60.000 0.00 0.00 34.23 4.18
990 4736 0.387878 GGCACTCCATCGCTAGATCG 60.388 60.000 0.00 0.00 34.23 3.69
991 4737 0.965439 AGGCACTCCATCGCTAGATC 59.035 55.000 0.00 0.00 34.23 2.75
992 4738 1.069823 CAAGGCACTCCATCGCTAGAT 59.930 52.381 0.00 0.00 38.49 1.98
993 4739 0.461548 CAAGGCACTCCATCGCTAGA 59.538 55.000 0.00 0.00 38.49 2.43
994 4740 1.156645 GCAAGGCACTCCATCGCTAG 61.157 60.000 0.00 0.00 38.49 3.42
1589 5348 0.971386 AAGAAAAGTGCATGGCCAGG 59.029 50.000 14.45 14.45 0.00 4.45
1704 5465 1.202405 CCAAAGGGCGTGCCAATTATC 60.202 52.381 13.76 0.00 37.98 1.75
1770 5537 5.941788 AGTCCAAACAATATAGTGGATCCC 58.058 41.667 9.90 0.11 42.01 3.85
1782 5549 7.872483 GGTCAACATAAATCAAGTCCAAACAAT 59.128 33.333 0.00 0.00 0.00 2.71
1790 5557 9.559958 CAATAACAGGTCAACATAAATCAAGTC 57.440 33.333 0.00 0.00 0.00 3.01
1825 5613 4.473477 ACCTACTTAAGCACCACAGATC 57.527 45.455 1.29 0.00 0.00 2.75
1832 5620 9.269453 CCAATACTTATAACCTACTTAAGCACC 57.731 37.037 1.29 0.00 0.00 5.01
1900 5689 7.001073 AGCAAGAACAAAACTAGAGGAATCTT 58.999 34.615 0.00 0.00 0.00 2.40
2034 5828 8.096414 AGCTGCACCAGAAAACAATTATAAAAT 58.904 29.630 1.02 0.00 32.44 1.82
2094 5888 3.503748 GCCCCATTGTCATAGCACTAATC 59.496 47.826 0.00 0.00 0.00 1.75
2124 5918 2.747446 CTGGGAGAAAACAATACCACCG 59.253 50.000 0.00 0.00 0.00 4.94
2142 5936 1.793820 AAAGCCCTTGGGTCTCCTGG 61.794 60.000 7.61 0.00 30.76 4.45
2330 6127 7.828508 TTTTGCATTAATCCTATCTGCAGAT 57.171 32.000 30.85 30.85 43.07 2.90
3034 6887 6.672266 ACAATAGCATACTACTGCAGGTAT 57.328 37.500 19.93 13.68 44.77 2.73
3098 6951 9.059485 GCGATCATGATCAAATAATAAAGAAGC 57.941 33.333 30.13 17.94 37.69 3.86
3292 7147 0.961753 AACTGCAAGGCCAAGTTAGC 59.038 50.000 5.01 0.00 39.30 3.09
3333 7189 5.506686 TTAGCACAAACAGCATACACAAA 57.493 34.783 0.00 0.00 0.00 2.83
3356 7212 7.996098 AACCTAGCAGTTATTAGCAAAGAAA 57.004 32.000 0.00 0.00 0.00 2.52
3473 7329 1.273267 ACATAGGTCTGGTCCTGCTGA 60.273 52.381 0.00 0.00 38.41 4.26
3581 7439 9.906660 ATGGCAAATATAAATAACATACAACCG 57.093 29.630 0.00 0.00 0.00 4.44
3589 7447 7.904558 TCCACCATGGCAAATATAAATAACA 57.095 32.000 13.04 0.00 37.47 2.41
3704 7562 7.443879 TGTGACTTCATAACAGATGCAAGTAAA 59.556 33.333 0.00 0.00 0.00 2.01
3711 7569 4.937620 TCCTTGTGACTTCATAACAGATGC 59.062 41.667 0.00 0.00 0.00 3.91
3722 7580 5.299279 TCAAAAACTCCATCCTTGTGACTTC 59.701 40.000 0.00 0.00 0.00 3.01
3870 7728 1.138859 TGGTATGGATCAAGGACTGCG 59.861 52.381 0.00 0.00 0.00 5.18
3873 7731 3.452627 GACACTGGTATGGATCAAGGACT 59.547 47.826 0.00 0.00 0.00 3.85
4249 8107 2.004408 ATGGATGCTCAAGGGCCTCC 62.004 60.000 6.46 9.06 43.90 4.30
4325 8197 3.124636 CACGGCTCAAACATACAGGTTAC 59.875 47.826 0.00 0.00 0.00 2.50
4330 8202 2.688507 AGTCACGGCTCAAACATACAG 58.311 47.619 0.00 0.00 0.00 2.74
4469 9180 8.491152 GTCAACATATGTACAGATAATGAGCAC 58.509 37.037 9.21 4.45 0.00 4.40
4527 9238 9.537192 AGTGTTGCCATCAAAATATATTCATTG 57.463 29.630 0.00 1.26 33.37 2.82
4573 10601 6.531240 TCAAAACACAAAAGCTGAATGACTTC 59.469 34.615 0.00 0.00 0.00 3.01
4700 10764 2.486592 CCTTTGGACTTACGCGGATTTT 59.513 45.455 12.47 0.00 0.00 1.82
4709 10773 3.105283 TCTAGGCTCCCTTTGGACTTAC 58.895 50.000 0.00 0.00 35.03 2.34
4741 10819 4.079253 ACGCAGAAGGGTCACAATTATTT 58.921 39.130 0.00 0.00 35.88 1.40
4744 10822 2.851263 ACGCAGAAGGGTCACAATTA 57.149 45.000 0.00 0.00 35.88 1.40
4750 10828 4.250464 CTGTATAAAACGCAGAAGGGTCA 58.750 43.478 0.00 0.00 40.41 4.02
4752 10830 4.281898 ACTGTATAAAACGCAGAAGGGT 57.718 40.909 0.00 0.00 43.52 4.34
4754 10832 6.307155 CAAGAACTGTATAAAACGCAGAAGG 58.693 40.000 0.00 0.00 34.60 3.46
4755 10833 5.790495 GCAAGAACTGTATAAAACGCAGAAG 59.210 40.000 0.00 0.00 34.60 2.85
4756 10834 5.468746 AGCAAGAACTGTATAAAACGCAGAA 59.531 36.000 0.00 0.00 34.60 3.02
4757 10835 4.994852 AGCAAGAACTGTATAAAACGCAGA 59.005 37.500 0.00 0.00 34.60 4.26
4758 10836 5.082059 CAGCAAGAACTGTATAAAACGCAG 58.918 41.667 0.00 0.00 36.41 5.18
4759 10837 5.029650 CAGCAAGAACTGTATAAAACGCA 57.970 39.130 0.00 0.00 32.78 5.24
4772 12470 2.494059 TCAACCTAGCACAGCAAGAAC 58.506 47.619 0.00 0.00 0.00 3.01
4835 12536 5.222079 TGTGGACAGCTACTCATTTACAA 57.778 39.130 0.00 0.00 0.00 2.41
4843 12544 3.386768 TTGACTTGTGGACAGCTACTC 57.613 47.619 0.00 0.00 0.00 2.59
4848 12549 1.336240 GCCATTTGACTTGTGGACAGC 60.336 52.381 0.00 0.00 34.94 4.40
4854 12555 4.843220 AAGAGAAGCCATTTGACTTGTG 57.157 40.909 0.00 0.00 0.00 3.33
4881 12582 8.099364 TCACCTTCACTTTTTCTATCAATCAC 57.901 34.615 0.00 0.00 0.00 3.06
4891 12592 8.490355 CATTATTTGCTTCACCTTCACTTTTTC 58.510 33.333 0.00 0.00 0.00 2.29
4893 12594 7.951530 CATTATTTGCTTCACCTTCACTTTT 57.048 32.000 0.00 0.00 0.00 2.27
4943 12644 5.992829 AGATACATAGGTCACGTGACTCTAG 59.007 44.000 39.01 28.98 44.20 2.43
4944 12645 5.758784 CAGATACATAGGTCACGTGACTCTA 59.241 44.000 39.01 34.55 44.20 2.43
4962 12663 2.229302 GAGGTCCGAGGCATACAGATAC 59.771 54.545 0.00 0.00 0.00 2.24
4963 12664 2.108425 AGAGGTCCGAGGCATACAGATA 59.892 50.000 0.00 0.00 0.00 1.98
4964 12665 1.133325 AGAGGTCCGAGGCATACAGAT 60.133 52.381 0.00 0.00 0.00 2.90
4965 12666 0.259065 AGAGGTCCGAGGCATACAGA 59.741 55.000 0.00 0.00 0.00 3.41
4966 12667 1.115467 AAGAGGTCCGAGGCATACAG 58.885 55.000 0.00 0.00 0.00 2.74
4967 12668 0.824109 CAAGAGGTCCGAGGCATACA 59.176 55.000 0.00 0.00 0.00 2.29
4997 12698 0.163146 GACACGGCAGTTAAAGTCGC 59.837 55.000 3.40 0.00 37.67 5.19
4998 12699 1.493772 TGACACGGCAGTTAAAGTCG 58.506 50.000 2.06 2.06 40.47 4.18
5000 12701 3.211045 ACATTGACACGGCAGTTAAAGT 58.789 40.909 0.00 0.00 0.00 2.66
5028 12732 5.931146 TGTTGAATTTGTTGACAGCAAAAGT 59.069 32.000 19.44 11.61 38.98 2.66
5029 12733 6.406093 TGTTGAATTTGTTGACAGCAAAAG 57.594 33.333 19.44 0.00 38.98 2.27
5080 12784 2.260869 GCGGACTGCTGCCAGAAAA 61.261 57.895 0.00 0.00 41.77 2.29
5113 12817 4.379186 CCAAAAACAAAACAACATGCTGCA 60.379 37.500 4.13 4.13 0.00 4.41
5114 12818 4.097012 CCAAAAACAAAACAACATGCTGC 58.903 39.130 0.00 0.00 0.00 5.25
5117 12821 4.693538 ACCCAAAAACAAAACAACATGC 57.306 36.364 0.00 0.00 0.00 4.06
5124 12831 9.788960 TGCAAATTTTATACCCAAAAACAAAAC 57.211 25.926 0.00 0.00 31.54 2.43
5129 12836 7.589587 GCTGTTGCAAATTTTATACCCAAAAAC 59.410 33.333 0.00 0.00 39.41 2.43
5171 12878 4.085055 CCGACTATGCAATTACGTAGCTTG 60.085 45.833 12.96 12.96 33.24 4.01
5178 12885 1.070577 GCAGCCGACTATGCAATTACG 60.071 52.381 0.00 0.00 42.11 3.18
5179 12886 1.264288 GGCAGCCGACTATGCAATTAC 59.736 52.381 0.00 0.00 44.37 1.89
5181 12888 0.394216 TGGCAGCCGACTATGCAATT 60.394 50.000 7.03 0.00 44.37 2.32
5182 12889 1.097547 GTGGCAGCCGACTATGCAAT 61.098 55.000 7.03 0.00 44.37 3.56
5183 12890 1.745115 GTGGCAGCCGACTATGCAA 60.745 57.895 7.03 0.00 44.37 4.08
5184 12891 2.125147 GTGGCAGCCGACTATGCA 60.125 61.111 7.03 0.00 44.37 3.96
5185 12892 1.884926 GAGTGGCAGCCGACTATGC 60.885 63.158 14.41 2.27 41.80 3.14
5223 12975 2.295349 CCATTAGCCATCCAGACATTGC 59.705 50.000 0.00 0.00 0.00 3.56
5238 12992 4.928601 TCGTCGACATTTCTACCCATTAG 58.071 43.478 17.16 0.00 0.00 1.73
5240 12994 3.880047 TCGTCGACATTTCTACCCATT 57.120 42.857 17.16 0.00 0.00 3.16
5245 12999 6.637254 ACATGTATCATCGTCGACATTTCTAC 59.363 38.462 17.16 11.20 30.13 2.59
5246 13000 6.735130 ACATGTATCATCGTCGACATTTCTA 58.265 36.000 17.16 0.00 30.13 2.10
5272 13026 2.846039 TTAGCTCGTCCTCAATCGAC 57.154 50.000 0.00 0.00 32.65 4.20
5277 13031 6.078202 CAAGATCTATTAGCTCGTCCTCAA 57.922 41.667 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.