Multiple sequence alignment - TraesCS4D01G036900

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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 TraesCS4D01G036900 chr4D 100.000 3106 0 0 1 3106 16263532 16266637 0.000000e+00 5736
1 TraesCS4D01G036900 chr4D 99.388 3107 18 1 1 3106 16304620 16307726 0.000000e+00 5631
2 TraesCS4D01G036900 chr4D 99.356 3106 20 0 1 3106 16344904 16348009 0.000000e+00 5626
3 TraesCS4D01G036900 chr4D 95.196 2477 92 17 1 2460 16325501 16327967 0.000000e+00 3890
4 TraesCS4D01G036900 chr4D 94.994 2477 97 17 1 2460 16300262 16302728 0.000000e+00 3862
5 TraesCS4D01G036900 chr4D 96.138 2175 77 7 1 2170 16330015 16332187 0.000000e+00 3544
6 TraesCS4D01G036900 chr4D 89.259 810 58 11 2301 3106 16332189 16332973 0.000000e+00 987
7 TraesCS4D01G036900 chr4B 91.345 2773 189 15 348 3106 28168479 28171214 0.000000e+00 3744
8 TraesCS4D01G036900 chr4B 89.604 1741 141 22 715 2441 28185468 28187182 0.000000e+00 2176
9 TraesCS4D01G036900 chr4B 89.546 1741 143 21 715 2441 28174360 28176075 0.000000e+00 2170
10 TraesCS4D01G036900 chr4B 86.892 679 73 5 2443 3106 28176171 28176848 0.000000e+00 747
11 TraesCS4D01G036900 chr4B 86.745 679 74 5 2443 3106 28183198 28183875 0.000000e+00 741
12 TraesCS4D01G036900 chr4B 86.451 679 76 5 2443 3106 28187279 28187956 0.000000e+00 730
13 TraesCS4D01G036900 chr4B 94.286 315 13 4 1 314 28168170 28168480 7.790000e-131 477
14 TraesCS4D01G036900 chr4A 91.366 2328 153 17 785 3106 584073158 584070873 0.000000e+00 3142
15 TraesCS4D01G036900 chr4A 93.046 417 27 2 134 550 584074658 584074244 2.650000e-170 608
16 TraesCS4D01G036900 chr4A 93.305 239 16 0 548 786 584073479 584073241 1.370000e-93 353
17 TraesCS4D01G036900 chrUn 100.000 371 0 0 1 371 444815612 444815982 0.000000e+00 686


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 TraesCS4D01G036900 chr4D 16263532 16266637 3105 False 5736.000000 5736 100.000000 1 3106 1 chr4D.!!$F1 3105
1 TraesCS4D01G036900 chr4D 16344904 16348009 3105 False 5626.000000 5626 99.356000 1 3106 1 chr4D.!!$F2 3105
2 TraesCS4D01G036900 chr4D 16300262 16307726 7464 False 4746.500000 5631 97.191000 1 3106 2 chr4D.!!$F3 3105
3 TraesCS4D01G036900 chr4D 16325501 16332973 7472 False 2807.000000 3890 93.531000 1 3106 3 chr4D.!!$F4 3105
4 TraesCS4D01G036900 chr4B 28168170 28176848 8678 False 1784.500000 3744 90.517250 1 3106 4 chr4B.!!$F1 3105
5 TraesCS4D01G036900 chr4B 28183198 28187956 4758 False 1215.666667 2176 87.600000 715 3106 3 chr4B.!!$F2 2391
6 TraesCS4D01G036900 chr4A 584070873 584074658 3785 True 1367.666667 3142 92.572333 134 3106 3 chr4A.!!$R1 2972

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
614 4974 0.028110 GCTGCTAATACTTGCACGGC 59.972 55.0 0.0 0.0 35.2 5.68 F
633 4993 0.108615 CCGGCTGTTCGTTCTCTCAT 60.109 55.0 0.0 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 13652 3.411446 TGATGATGAACTTGAAGGCGTT 58.589 40.909 0.0 0.0 0.0 4.84 R
2795 14897 5.011635 TGGTCATGTTACTCTTGCACTTCTA 59.988 40.000 0.0 0.0 0.0 2.10 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
371 4731 0.732571 CGCACGCTGGGTATCATTTT 59.267 50.000 0.00 0.00 0.00 1.82
443 4803 4.239495 ACATATGTGGGTAGGGATTGCTA 58.761 43.478 7.78 0.00 0.00 3.49
465 4825 3.030415 AAAAACTGCGGGTAGGGTG 57.970 52.632 0.00 0.00 0.00 4.61
466 4826 0.475044 AAAAACTGCGGGTAGGGTGA 59.525 50.000 0.00 0.00 0.00 4.02
467 4827 0.696501 AAAACTGCGGGTAGGGTGAT 59.303 50.000 0.00 0.00 0.00 3.06
469 4829 0.907704 AACTGCGGGTAGGGTGATCA 60.908 55.000 0.00 0.00 0.00 2.92
470 4830 0.691078 ACTGCGGGTAGGGTGATCAT 60.691 55.000 0.00 0.00 0.00 2.45
474 4834 1.826042 GCGGGTAGGGTGATCATCCTA 60.826 57.143 27.84 27.84 40.98 2.94
475 4835 2.171840 CGGGTAGGGTGATCATCCTAG 58.828 57.143 31.29 18.06 44.39 3.02
477 4837 2.111972 GGGTAGGGTGATCATCCTAGGA 59.888 54.545 31.29 15.46 44.39 2.94
479 4839 3.835395 GGTAGGGTGATCATCCTAGGAAG 59.165 52.174 31.29 12.24 44.39 3.46
482 4842 4.837218 AGGGTGATCATCCTAGGAAGAAT 58.163 43.478 26.69 11.56 40.98 2.40
483 4843 4.843516 AGGGTGATCATCCTAGGAAGAATC 59.156 45.833 26.69 18.85 40.98 2.52
484 4844 4.843516 GGGTGATCATCCTAGGAAGAATCT 59.156 45.833 20.02 4.58 0.00 2.40
485 4845 5.279910 GGGTGATCATCCTAGGAAGAATCTG 60.280 48.000 20.02 10.81 0.00 2.90
486 4846 5.541868 GGTGATCATCCTAGGAAGAATCTGA 59.458 44.000 20.02 15.69 0.00 3.27
488 4848 7.256619 GGTGATCATCCTAGGAAGAATCTGAAT 60.257 40.741 20.02 2.36 0.00 2.57
489 4849 7.603404 GTGATCATCCTAGGAAGAATCTGAATG 59.397 40.741 20.02 7.95 0.00 2.67
491 4851 5.907662 TCATCCTAGGAAGAATCTGAATGGT 59.092 40.000 17.30 0.00 0.00 3.55
495 4855 6.886459 TCCTAGGAAGAATCTGAATGGTTTTG 59.114 38.462 9.71 0.00 0.00 2.44
496 4856 6.886459 CCTAGGAAGAATCTGAATGGTTTTGA 59.114 38.462 1.05 0.00 0.00 2.69
497 4857 7.559170 CCTAGGAAGAATCTGAATGGTTTTGAT 59.441 37.037 1.05 0.00 0.00 2.57
498 4858 7.166691 AGGAAGAATCTGAATGGTTTTGATG 57.833 36.000 0.00 0.00 0.00 3.07
499 4859 5.809051 GGAAGAATCTGAATGGTTTTGATGC 59.191 40.000 0.00 0.00 0.00 3.91
500 4860 6.350780 GGAAGAATCTGAATGGTTTTGATGCT 60.351 38.462 0.00 0.00 0.00 3.79
503 4863 6.872020 AGAATCTGAATGGTTTTGATGCTTTG 59.128 34.615 0.00 0.00 0.00 2.77
504 4864 5.534207 TCTGAATGGTTTTGATGCTTTGT 57.466 34.783 0.00 0.00 0.00 2.83
506 4866 5.754406 TCTGAATGGTTTTGATGCTTTGTTG 59.246 36.000 0.00 0.00 0.00 3.33
507 4867 5.426504 TGAATGGTTTTGATGCTTTGTTGT 58.573 33.333 0.00 0.00 0.00 3.32
510 4870 5.793026 TGGTTTTGATGCTTTGTTGTTTC 57.207 34.783 0.00 0.00 0.00 2.78
511 4871 5.486526 TGGTTTTGATGCTTTGTTGTTTCT 58.513 33.333 0.00 0.00 0.00 2.52
514 4874 7.604164 TGGTTTTGATGCTTTGTTGTTTCTTTA 59.396 29.630 0.00 0.00 0.00 1.85
515 4875 8.611757 GGTTTTGATGCTTTGTTGTTTCTTTAT 58.388 29.630 0.00 0.00 0.00 1.40
517 4877 9.985318 TTTTGATGCTTTGTTGTTTCTTTATTG 57.015 25.926 0.00 0.00 0.00 1.90
518 4878 8.715191 TTGATGCTTTGTTGTTTCTTTATTGT 57.285 26.923 0.00 0.00 0.00 2.71
519 4879 8.351495 TGATGCTTTGTTGTTTCTTTATTGTC 57.649 30.769 0.00 0.00 0.00 3.18
520 4880 8.196771 TGATGCTTTGTTGTTTCTTTATTGTCT 58.803 29.630 0.00 0.00 0.00 3.41
521 4881 7.754069 TGCTTTGTTGTTTCTTTATTGTCTG 57.246 32.000 0.00 0.00 0.00 3.51
522 4882 7.319646 TGCTTTGTTGTTTCTTTATTGTCTGT 58.680 30.769 0.00 0.00 0.00 3.41
523 4883 7.487829 TGCTTTGTTGTTTCTTTATTGTCTGTC 59.512 33.333 0.00 0.00 0.00 3.51
524 4884 7.487829 GCTTTGTTGTTTCTTTATTGTCTGTCA 59.512 33.333 0.00 0.00 0.00 3.58
525 4885 9.520204 CTTTGTTGTTTCTTTATTGTCTGTCAT 57.480 29.630 0.00 0.00 0.00 3.06
526 4886 9.515020 TTTGTTGTTTCTTTATTGTCTGTCATC 57.485 29.630 0.00 0.00 0.00 2.92
527 4887 7.351981 TGTTGTTTCTTTATTGTCTGTCATCG 58.648 34.615 0.00 0.00 0.00 3.84
528 4888 7.011950 TGTTGTTTCTTTATTGTCTGTCATCGT 59.988 33.333 0.00 0.00 0.00 3.73
529 4889 7.117241 TGTTTCTTTATTGTCTGTCATCGTC 57.883 36.000 0.00 0.00 0.00 4.20
530 4890 6.128929 TGTTTCTTTATTGTCTGTCATCGTCG 60.129 38.462 0.00 0.00 0.00 5.12
531 4891 5.055642 TCTTTATTGTCTGTCATCGTCGT 57.944 39.130 0.00 0.00 0.00 4.34
533 4893 1.350193 ATTGTCTGTCATCGTCGTGC 58.650 50.000 0.00 0.00 0.00 5.34
534 4894 0.031449 TTGTCTGTCATCGTCGTGCA 59.969 50.000 0.00 0.00 0.00 4.57
535 4895 0.243636 TGTCTGTCATCGTCGTGCAT 59.756 50.000 0.00 0.00 0.00 3.96
536 4896 0.917259 GTCTGTCATCGTCGTGCATC 59.083 55.000 0.00 0.00 0.00 3.91
537 4897 0.811281 TCTGTCATCGTCGTGCATCT 59.189 50.000 0.00 0.00 0.00 2.90
540 4900 1.726248 TGTCATCGTCGTGCATCTTTG 59.274 47.619 0.00 0.00 0.00 2.77
541 4901 1.992667 GTCATCGTCGTGCATCTTTGA 59.007 47.619 0.00 0.00 0.00 2.69
543 4903 2.411748 TCATCGTCGTGCATCTTTGAAC 59.588 45.455 0.00 0.00 0.00 3.18
545 4905 2.058798 TCGTCGTGCATCTTTGAACTC 58.941 47.619 0.00 0.00 0.00 3.01
546 4906 1.201704 CGTCGTGCATCTTTGAACTCG 60.202 52.381 0.00 0.00 0.00 4.18
552 4912 4.319190 CGTGCATCTTTGAACTCGGTTTTA 60.319 41.667 0.00 0.00 0.00 1.52
553 4913 5.616866 CGTGCATCTTTGAACTCGGTTTTAT 60.617 40.000 0.00 0.00 0.00 1.40
554 4914 6.401688 CGTGCATCTTTGAACTCGGTTTTATA 60.402 38.462 0.00 0.00 0.00 0.98
555 4915 7.472543 GTGCATCTTTGAACTCGGTTTTATAT 58.527 34.615 0.00 0.00 0.00 0.86
557 4917 8.519526 TGCATCTTTGAACTCGGTTTTATATTT 58.480 29.630 0.00 0.00 0.00 1.40
558 4918 9.353999 GCATCTTTGAACTCGGTTTTATATTTT 57.646 29.630 0.00 0.00 0.00 1.82
570 4930 9.465985 TCGGTTTTATATTTTCTTTTGTTGGAC 57.534 29.630 0.00 0.00 0.00 4.02
571 4931 8.705134 CGGTTTTATATTTTCTTTTGTTGGACC 58.295 33.333 0.00 0.00 0.00 4.46
592 4952 9.550406 TGGACCATTTTAATATAAGTACTTCCG 57.450 33.333 12.39 0.00 0.00 4.30
593 4953 8.996271 GGACCATTTTAATATAAGTACTTCCGG 58.004 37.037 12.39 0.00 0.00 5.14
596 4956 8.718734 CCATTTTAATATAAGTACTTCCGGAGC 58.281 37.037 12.39 0.00 0.00 4.70
597 4957 9.490379 CATTTTAATATAAGTACTTCCGGAGCT 57.510 33.333 12.39 0.00 0.00 4.09
599 4959 2.892784 ATAAGTACTTCCGGAGCTGC 57.107 50.000 12.39 0.00 0.00 5.25
600 4960 1.848652 TAAGTACTTCCGGAGCTGCT 58.151 50.000 12.39 0.00 0.00 4.24
602 4962 1.848652 AGTACTTCCGGAGCTGCTAA 58.151 50.000 3.34 0.00 0.00 3.09
603 4963 2.389715 AGTACTTCCGGAGCTGCTAAT 58.610 47.619 3.34 0.00 0.00 1.73
604 4964 3.563223 AGTACTTCCGGAGCTGCTAATA 58.437 45.455 3.34 0.00 0.00 0.98
605 4965 2.892784 ACTTCCGGAGCTGCTAATAC 57.107 50.000 3.34 0.00 0.00 1.89
606 4966 2.389715 ACTTCCGGAGCTGCTAATACT 58.610 47.619 3.34 0.00 0.00 2.12
607 4967 2.766828 ACTTCCGGAGCTGCTAATACTT 59.233 45.455 3.34 0.00 0.00 2.24
608 4968 2.890808 TCCGGAGCTGCTAATACTTG 57.109 50.000 0.00 0.00 0.00 3.16
609 4969 1.202533 TCCGGAGCTGCTAATACTTGC 60.203 52.381 0.00 0.00 0.00 4.01
611 4971 1.594862 CGGAGCTGCTAATACTTGCAC 59.405 52.381 0.15 0.00 35.20 4.57
613 4973 1.594862 GAGCTGCTAATACTTGCACGG 59.405 52.381 0.15 0.00 35.20 4.94
614 4974 0.028110 GCTGCTAATACTTGCACGGC 59.972 55.000 0.00 0.00 35.20 5.68
615 4975 0.657840 CTGCTAATACTTGCACGGCC 59.342 55.000 0.00 0.00 35.20 6.13
616 4976 1.087202 TGCTAATACTTGCACGGCCG 61.087 55.000 26.86 26.86 33.94 6.13
618 4978 1.772063 CTAATACTTGCACGGCCGGC 61.772 60.000 31.76 28.27 0.00 6.13
619 4979 2.246761 TAATACTTGCACGGCCGGCT 62.247 55.000 31.76 15.86 0.00 5.52
630 4990 2.048127 GCCGGCTGTTCGTTCTCT 60.048 61.111 22.15 0.00 0.00 3.10
631 4991 2.095252 GCCGGCTGTTCGTTCTCTC 61.095 63.158 22.15 0.00 0.00 3.20
632 4992 1.289066 CCGGCTGTTCGTTCTCTCA 59.711 57.895 0.00 0.00 0.00 3.27
633 4993 0.108615 CCGGCTGTTCGTTCTCTCAT 60.109 55.000 0.00 0.00 0.00 2.90
634 4994 1.673033 CCGGCTGTTCGTTCTCTCATT 60.673 52.381 0.00 0.00 0.00 2.57
636 4996 2.417719 GGCTGTTCGTTCTCTCATTGT 58.582 47.619 0.00 0.00 0.00 2.71
637 4997 2.808543 GGCTGTTCGTTCTCTCATTGTT 59.191 45.455 0.00 0.00 0.00 2.83
639 4999 4.261197 GGCTGTTCGTTCTCTCATTGTTTT 60.261 41.667 0.00 0.00 0.00 2.43
640 5000 4.672413 GCTGTTCGTTCTCTCATTGTTTTG 59.328 41.667 0.00 0.00 0.00 2.44
641 5001 5.730568 GCTGTTCGTTCTCTCATTGTTTTGT 60.731 40.000 0.00 0.00 0.00 2.83
642 5002 5.568482 TGTTCGTTCTCTCATTGTTTTGTG 58.432 37.500 0.00 0.00 0.00 3.33
643 5003 5.123186 TGTTCGTTCTCTCATTGTTTTGTGT 59.877 36.000 0.00 0.00 0.00 3.72
644 5004 5.811399 TCGTTCTCTCATTGTTTTGTGTT 57.189 34.783 0.00 0.00 0.00 3.32
645 5005 5.806286 TCGTTCTCTCATTGTTTTGTGTTC 58.194 37.500 0.00 0.00 0.00 3.18
646 5006 5.352846 TCGTTCTCTCATTGTTTTGTGTTCA 59.647 36.000 0.00 0.00 0.00 3.18
648 5008 5.499139 TCTCTCATTGTTTTGTGTTCACC 57.501 39.130 0.37 0.00 0.00 4.02
649 5009 5.192927 TCTCTCATTGTTTTGTGTTCACCT 58.807 37.500 0.37 0.00 0.00 4.00
650 5010 5.066375 TCTCTCATTGTTTTGTGTTCACCTG 59.934 40.000 0.37 0.00 0.00 4.00
651 5011 3.779759 TCATTGTTTTGTGTTCACCTGC 58.220 40.909 0.37 0.00 0.00 4.85
652 5012 3.446873 TCATTGTTTTGTGTTCACCTGCT 59.553 39.130 0.37 0.00 0.00 4.24
653 5013 3.502191 TTGTTTTGTGTTCACCTGCTC 57.498 42.857 0.37 0.00 0.00 4.26
654 5014 2.441410 TGTTTTGTGTTCACCTGCTCA 58.559 42.857 0.37 0.00 0.00 4.26
655 5015 2.163412 TGTTTTGTGTTCACCTGCTCAC 59.837 45.455 0.37 0.00 0.00 3.51
656 5016 1.388547 TTTGTGTTCACCTGCTCACC 58.611 50.000 0.37 0.00 0.00 4.02
657 5017 0.546122 TTGTGTTCACCTGCTCACCT 59.454 50.000 0.37 0.00 0.00 4.00
660 5020 1.618837 GTGTTCACCTGCTCACCTAGA 59.381 52.381 0.00 0.00 0.00 2.43
661 5021 2.037251 GTGTTCACCTGCTCACCTAGAA 59.963 50.000 0.00 0.00 0.00 2.10
664 5024 0.888619 CACCTGCTCACCTAGAACGA 59.111 55.000 0.00 0.00 0.00 3.85
665 5025 1.272490 CACCTGCTCACCTAGAACGAA 59.728 52.381 0.00 0.00 0.00 3.85
666 5026 1.272769 ACCTGCTCACCTAGAACGAAC 59.727 52.381 0.00 0.00 0.00 3.95
667 5027 1.546476 CCTGCTCACCTAGAACGAACT 59.454 52.381 0.00 0.00 0.00 3.01
668 5028 2.753452 CCTGCTCACCTAGAACGAACTA 59.247 50.000 0.00 0.00 0.00 2.24
669 5029 3.181495 CCTGCTCACCTAGAACGAACTAG 60.181 52.174 11.51 11.51 39.40 2.57
671 5031 4.270834 TGCTCACCTAGAACGAACTAGAT 58.729 43.478 17.20 2.90 41.42 1.98
672 5032 4.335874 TGCTCACCTAGAACGAACTAGATC 59.664 45.833 17.20 0.00 41.42 2.75
674 5034 4.205587 TCACCTAGAACGAACTAGATCCC 58.794 47.826 17.20 0.00 41.42 3.85
675 5035 4.079901 TCACCTAGAACGAACTAGATCCCT 60.080 45.833 17.20 0.00 41.42 4.20
676 5036 5.131642 TCACCTAGAACGAACTAGATCCCTA 59.868 44.000 17.20 0.00 41.42 3.53
679 5039 4.173290 AGAACGAACTAGATCCCTAGCT 57.827 45.455 0.00 0.00 44.87 3.32
680 5040 3.886505 AGAACGAACTAGATCCCTAGCTG 59.113 47.826 0.00 0.00 44.87 4.24
681 5041 1.957877 ACGAACTAGATCCCTAGCTGC 59.042 52.381 0.00 0.00 44.87 5.25
682 5042 1.957177 CGAACTAGATCCCTAGCTGCA 59.043 52.381 1.02 0.00 44.87 4.41
683 5043 2.362397 CGAACTAGATCCCTAGCTGCAA 59.638 50.000 1.02 0.00 44.87 4.08
684 5044 3.723260 GAACTAGATCCCTAGCTGCAAC 58.277 50.000 1.02 0.00 44.87 4.17
685 5045 2.752030 ACTAGATCCCTAGCTGCAACA 58.248 47.619 1.02 0.00 44.87 3.33
686 5046 3.312890 ACTAGATCCCTAGCTGCAACAT 58.687 45.455 1.02 0.00 44.87 2.71
687 5047 4.483950 ACTAGATCCCTAGCTGCAACATA 58.516 43.478 1.02 0.00 44.87 2.29
691 5051 3.543680 TCCCTAGCTGCAACATACTTC 57.456 47.619 1.02 0.00 0.00 3.01
692 5052 3.107601 TCCCTAGCTGCAACATACTTCT 58.892 45.455 1.02 0.00 0.00 2.85
693 5053 3.519510 TCCCTAGCTGCAACATACTTCTT 59.480 43.478 1.02 0.00 0.00 2.52
694 5054 4.019321 TCCCTAGCTGCAACATACTTCTTT 60.019 41.667 1.02 0.00 0.00 2.52
695 5055 4.702131 CCCTAGCTGCAACATACTTCTTTT 59.298 41.667 1.02 0.00 0.00 2.27
696 5056 5.183904 CCCTAGCTGCAACATACTTCTTTTT 59.816 40.000 1.02 0.00 0.00 1.94
717 5077 5.554822 TTTAACAAGAGTTGAACGCACTT 57.445 34.783 1.24 1.24 38.69 3.16
718 5078 3.675467 AACAAGAGTTGAACGCACTTC 57.325 42.857 1.24 0.00 36.39 3.01
800 12782 7.548075 GCTAACATACTATGTACAACCACAAGT 59.452 37.037 0.00 0.03 44.07 3.16
1038 13031 2.507058 ACTGCTTCTTGCCATCATAGGA 59.493 45.455 0.00 0.00 42.00 2.94
1659 13652 2.284625 AGGGTGGCGAGATGGACA 60.285 61.111 0.00 0.00 0.00 4.02
2795 14897 2.665185 GTCGGCTTGCCGTTGAGT 60.665 61.111 29.41 0.00 34.52 3.41
2912 15017 2.102252 TGCCTCCACAAAAATTGTCACC 59.898 45.455 0.00 0.00 43.23 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
371 4731 8.200024 TGGTCCATCAAAATTTCAGGAAATAA 57.800 30.769 7.62 0.00 39.88 1.40
452 4812 0.034059 GATGATCACCCTACCCGCAG 59.966 60.000 0.00 0.00 0.00 5.18
453 4813 1.407656 GGATGATCACCCTACCCGCA 61.408 60.000 0.00 0.00 0.00 5.69
454 4814 1.122019 AGGATGATCACCCTACCCGC 61.122 60.000 6.92 0.00 0.00 6.13
455 4815 2.171840 CTAGGATGATCACCCTACCCG 58.828 57.143 12.28 0.00 34.11 5.28
456 4816 2.111972 TCCTAGGATGATCACCCTACCC 59.888 54.545 12.28 0.31 34.11 3.69
459 4819 5.418692 TTCTTCCTAGGATGATCACCCTA 57.581 43.478 23.97 15.53 34.11 3.53
460 4820 4.286813 TTCTTCCTAGGATGATCACCCT 57.713 45.455 23.97 14.76 36.60 4.34
461 4821 4.843516 AGATTCTTCCTAGGATGATCACCC 59.156 45.833 23.97 0.00 0.00 4.61
464 4824 7.256583 CCATTCAGATTCTTCCTAGGATGATCA 60.257 40.741 23.97 13.30 0.00 2.92
465 4825 7.104939 CCATTCAGATTCTTCCTAGGATGATC 58.895 42.308 23.97 21.00 0.00 2.92
466 4826 6.561838 ACCATTCAGATTCTTCCTAGGATGAT 59.438 38.462 23.97 15.50 0.00 2.45
467 4827 5.907662 ACCATTCAGATTCTTCCTAGGATGA 59.092 40.000 20.63 20.63 0.00 2.92
469 4829 6.838401 AACCATTCAGATTCTTCCTAGGAT 57.162 37.500 13.57 0.00 0.00 3.24
470 4830 6.642733 AAACCATTCAGATTCTTCCTAGGA 57.357 37.500 7.62 7.62 0.00 2.94
474 4834 6.350780 GCATCAAAACCATTCAGATTCTTCCT 60.351 38.462 0.00 0.00 0.00 3.36
475 4835 5.809051 GCATCAAAACCATTCAGATTCTTCC 59.191 40.000 0.00 0.00 0.00 3.46
477 4837 6.600882 AGCATCAAAACCATTCAGATTCTT 57.399 33.333 0.00 0.00 0.00 2.52
479 4839 6.647895 ACAAAGCATCAAAACCATTCAGATTC 59.352 34.615 0.00 0.00 0.00 2.52
482 4842 5.534207 ACAAAGCATCAAAACCATTCAGA 57.466 34.783 0.00 0.00 0.00 3.27
483 4843 5.524646 ACAACAAAGCATCAAAACCATTCAG 59.475 36.000 0.00 0.00 0.00 3.02
484 4844 5.426504 ACAACAAAGCATCAAAACCATTCA 58.573 33.333 0.00 0.00 0.00 2.57
485 4845 5.989551 ACAACAAAGCATCAAAACCATTC 57.010 34.783 0.00 0.00 0.00 2.67
486 4846 6.598850 AGAAACAACAAAGCATCAAAACCATT 59.401 30.769 0.00 0.00 0.00 3.16
488 4848 5.486526 AGAAACAACAAAGCATCAAAACCA 58.513 33.333 0.00 0.00 0.00 3.67
489 4849 6.421377 AAGAAACAACAAAGCATCAAAACC 57.579 33.333 0.00 0.00 0.00 3.27
491 4851 9.985318 CAATAAAGAAACAACAAAGCATCAAAA 57.015 25.926 0.00 0.00 0.00 2.44
495 4855 8.482429 CAGACAATAAAGAAACAACAAAGCATC 58.518 33.333 0.00 0.00 0.00 3.91
496 4856 7.981225 ACAGACAATAAAGAAACAACAAAGCAT 59.019 29.630 0.00 0.00 0.00 3.79
497 4857 7.319646 ACAGACAATAAAGAAACAACAAAGCA 58.680 30.769 0.00 0.00 0.00 3.91
498 4858 7.487829 TGACAGACAATAAAGAAACAACAAAGC 59.512 33.333 0.00 0.00 0.00 3.51
499 4859 8.909708 TGACAGACAATAAAGAAACAACAAAG 57.090 30.769 0.00 0.00 0.00 2.77
500 4860 9.515020 GATGACAGACAATAAAGAAACAACAAA 57.485 29.630 0.00 0.00 0.00 2.83
503 4863 7.352739 ACGATGACAGACAATAAAGAAACAAC 58.647 34.615 0.00 0.00 0.00 3.32
504 4864 7.490962 ACGATGACAGACAATAAAGAAACAA 57.509 32.000 0.00 0.00 0.00 2.83
506 4866 6.128902 ACGACGATGACAGACAATAAAGAAAC 60.129 38.462 0.00 0.00 0.00 2.78
507 4867 5.924254 ACGACGATGACAGACAATAAAGAAA 59.076 36.000 0.00 0.00 0.00 2.52
510 4870 4.490959 GCACGACGATGACAGACAATAAAG 60.491 45.833 0.00 0.00 0.00 1.85
511 4871 3.366724 GCACGACGATGACAGACAATAAA 59.633 43.478 0.00 0.00 0.00 1.40
514 4874 1.336795 TGCACGACGATGACAGACAAT 60.337 47.619 0.00 0.00 0.00 2.71
515 4875 0.031449 TGCACGACGATGACAGACAA 59.969 50.000 0.00 0.00 0.00 3.18
517 4877 0.917259 GATGCACGACGATGACAGAC 59.083 55.000 0.00 0.00 0.00 3.51
518 4878 0.811281 AGATGCACGACGATGACAGA 59.189 50.000 0.00 0.00 0.00 3.41
519 4879 1.633561 AAGATGCACGACGATGACAG 58.366 50.000 0.00 0.00 0.00 3.51
520 4880 1.726248 CAAAGATGCACGACGATGACA 59.274 47.619 0.00 0.10 0.00 3.58
521 4881 1.992667 TCAAAGATGCACGACGATGAC 59.007 47.619 0.00 0.00 0.00 3.06
522 4882 2.362169 TCAAAGATGCACGACGATGA 57.638 45.000 0.00 0.00 0.00 2.92
523 4883 2.413112 AGTTCAAAGATGCACGACGATG 59.587 45.455 0.00 0.00 0.00 3.84
524 4884 2.668457 GAGTTCAAAGATGCACGACGAT 59.332 45.455 0.00 0.00 0.00 3.73
525 4885 2.058798 GAGTTCAAAGATGCACGACGA 58.941 47.619 0.00 0.00 0.00 4.20
526 4886 1.201704 CGAGTTCAAAGATGCACGACG 60.202 52.381 0.00 0.00 0.00 5.12
527 4887 1.126846 CCGAGTTCAAAGATGCACGAC 59.873 52.381 0.00 0.00 0.00 4.34
528 4888 1.270094 ACCGAGTTCAAAGATGCACGA 60.270 47.619 0.00 0.00 0.00 4.35
529 4889 1.148310 ACCGAGTTCAAAGATGCACG 58.852 50.000 0.00 0.00 0.00 5.34
530 4890 3.626028 AAACCGAGTTCAAAGATGCAC 57.374 42.857 0.00 0.00 0.00 4.57
531 4891 5.957842 ATAAAACCGAGTTCAAAGATGCA 57.042 34.783 0.00 0.00 0.00 3.96
543 4903 9.685828 TCCAACAAAAGAAAATATAAAACCGAG 57.314 29.630 0.00 0.00 0.00 4.63
545 4905 8.705134 GGTCCAACAAAAGAAAATATAAAACCG 58.295 33.333 0.00 0.00 0.00 4.44
546 4906 9.549078 TGGTCCAACAAAAGAAAATATAAAACC 57.451 29.630 0.00 0.00 0.00 3.27
567 4927 8.996271 CCGGAAGTACTTATATTAAAATGGTCC 58.004 37.037 8.42 0.00 0.00 4.46
570 4930 8.718734 GCTCCGGAAGTACTTATATTAAAATGG 58.281 37.037 8.42 0.00 0.00 3.16
571 4931 9.490379 AGCTCCGGAAGTACTTATATTAAAATG 57.510 33.333 8.42 0.00 0.00 2.32
573 4933 7.440255 GCAGCTCCGGAAGTACTTATATTAAAA 59.560 37.037 8.42 0.00 0.00 1.52
574 4934 6.927381 GCAGCTCCGGAAGTACTTATATTAAA 59.073 38.462 8.42 0.00 0.00 1.52
575 4935 6.267014 AGCAGCTCCGGAAGTACTTATATTAA 59.733 38.462 8.42 0.00 0.00 1.40
576 4936 5.773680 AGCAGCTCCGGAAGTACTTATATTA 59.226 40.000 8.42 0.00 0.00 0.98
577 4937 4.589374 AGCAGCTCCGGAAGTACTTATATT 59.411 41.667 8.42 0.00 0.00 1.28
579 4939 3.563223 AGCAGCTCCGGAAGTACTTATA 58.437 45.455 8.42 0.00 0.00 0.98
580 4940 2.389715 AGCAGCTCCGGAAGTACTTAT 58.610 47.619 8.42 0.00 0.00 1.73
581 4941 1.848652 AGCAGCTCCGGAAGTACTTA 58.151 50.000 8.42 0.00 0.00 2.24
582 4942 1.848652 TAGCAGCTCCGGAAGTACTT 58.151 50.000 8.13 8.13 0.00 2.24
584 4944 2.892784 ATTAGCAGCTCCGGAAGTAC 57.107 50.000 5.23 0.00 0.00 2.73
585 4945 3.563223 AGTATTAGCAGCTCCGGAAGTA 58.437 45.455 5.23 0.00 0.00 2.24
586 4946 2.389715 AGTATTAGCAGCTCCGGAAGT 58.610 47.619 5.23 0.00 0.00 3.01
588 4948 2.741878 GCAAGTATTAGCAGCTCCGGAA 60.742 50.000 5.23 0.00 0.00 4.30
589 4949 1.202533 GCAAGTATTAGCAGCTCCGGA 60.203 52.381 2.93 2.93 0.00 5.14
591 4951 1.594862 GTGCAAGTATTAGCAGCTCCG 59.405 52.381 0.00 0.00 42.14 4.63
592 4952 1.594862 CGTGCAAGTATTAGCAGCTCC 59.405 52.381 0.00 0.00 42.14 4.70
593 4953 1.594862 CCGTGCAAGTATTAGCAGCTC 59.405 52.381 0.00 0.00 42.14 4.09
596 4956 0.657840 GGCCGTGCAAGTATTAGCAG 59.342 55.000 0.00 0.00 42.14 4.24
597 4957 1.087202 CGGCCGTGCAAGTATTAGCA 61.087 55.000 19.50 0.00 38.65 3.49
599 4959 1.772063 GCCGGCCGTGCAAGTATTAG 61.772 60.000 27.01 9.15 0.00 1.73
600 4960 1.816259 GCCGGCCGTGCAAGTATTA 60.816 57.895 27.01 0.00 0.00 0.98
602 4962 4.096003 AGCCGGCCGTGCAAGTAT 62.096 61.111 31.19 14.22 0.00 2.12
613 4973 2.048127 AGAGAACGAACAGCCGGC 60.048 61.111 21.89 21.89 0.00 6.13
614 4974 0.108615 ATGAGAGAACGAACAGCCGG 60.109 55.000 0.00 0.00 0.00 6.13
615 4975 1.391485 CAATGAGAGAACGAACAGCCG 59.609 52.381 0.00 0.00 0.00 5.52
616 4976 2.417719 ACAATGAGAGAACGAACAGCC 58.582 47.619 0.00 0.00 0.00 4.85
618 4978 5.678483 CACAAAACAATGAGAGAACGAACAG 59.322 40.000 0.00 0.00 0.00 3.16
619 4979 5.123186 ACACAAAACAATGAGAGAACGAACA 59.877 36.000 0.00 0.00 0.00 3.18
620 4980 5.569413 ACACAAAACAATGAGAGAACGAAC 58.431 37.500 0.00 0.00 0.00 3.95
622 4982 5.352846 TGAACACAAAACAATGAGAGAACGA 59.647 36.000 0.00 0.00 0.00 3.85
624 4984 5.743872 GGTGAACACAAAACAATGAGAGAAC 59.256 40.000 7.25 0.00 0.00 3.01
625 4985 5.652014 AGGTGAACACAAAACAATGAGAGAA 59.348 36.000 7.25 0.00 0.00 2.87
626 4986 5.066375 CAGGTGAACACAAAACAATGAGAGA 59.934 40.000 7.25 0.00 0.00 3.10
627 4987 5.276270 CAGGTGAACACAAAACAATGAGAG 58.724 41.667 7.25 0.00 0.00 3.20
628 4988 4.439974 GCAGGTGAACACAAAACAATGAGA 60.440 41.667 7.25 0.00 0.00 3.27
630 4990 3.446873 AGCAGGTGAACACAAAACAATGA 59.553 39.130 7.25 0.00 0.00 2.57
631 4991 3.784338 AGCAGGTGAACACAAAACAATG 58.216 40.909 7.25 0.00 0.00 2.82
632 4992 3.446873 TGAGCAGGTGAACACAAAACAAT 59.553 39.130 7.25 0.00 0.00 2.71
633 4993 2.822561 TGAGCAGGTGAACACAAAACAA 59.177 40.909 7.25 0.00 0.00 2.83
634 4994 2.163412 GTGAGCAGGTGAACACAAAACA 59.837 45.455 7.25 0.00 34.05 2.83
636 4996 1.748493 GGTGAGCAGGTGAACACAAAA 59.252 47.619 7.25 0.00 35.33 2.44
637 4997 1.064758 AGGTGAGCAGGTGAACACAAA 60.065 47.619 7.25 0.00 35.33 2.83
639 4999 1.344438 CTAGGTGAGCAGGTGAACACA 59.656 52.381 7.25 0.00 35.33 3.72
640 5000 1.618837 TCTAGGTGAGCAGGTGAACAC 59.381 52.381 0.00 0.00 0.00 3.32
641 5001 2.009681 TCTAGGTGAGCAGGTGAACA 57.990 50.000 0.00 0.00 0.00 3.18
642 5002 2.689646 GTTCTAGGTGAGCAGGTGAAC 58.310 52.381 0.00 0.00 0.00 3.18
643 5003 1.272490 CGTTCTAGGTGAGCAGGTGAA 59.728 52.381 0.00 0.00 0.00 3.18
644 5004 0.888619 CGTTCTAGGTGAGCAGGTGA 59.111 55.000 0.00 0.00 0.00 4.02
645 5005 0.888619 TCGTTCTAGGTGAGCAGGTG 59.111 55.000 0.00 0.00 0.00 4.00
646 5006 1.272769 GTTCGTTCTAGGTGAGCAGGT 59.727 52.381 0.00 0.00 0.00 4.00
648 5008 3.690139 TCTAGTTCGTTCTAGGTGAGCAG 59.310 47.826 13.41 0.00 38.25 4.24
649 5009 3.682696 TCTAGTTCGTTCTAGGTGAGCA 58.317 45.455 13.41 0.00 38.25 4.26
650 5010 4.261280 GGATCTAGTTCGTTCTAGGTGAGC 60.261 50.000 13.41 0.00 38.25 4.26
651 5011 4.276431 GGGATCTAGTTCGTTCTAGGTGAG 59.724 50.000 13.41 0.00 38.25 3.51
652 5012 4.079901 AGGGATCTAGTTCGTTCTAGGTGA 60.080 45.833 13.41 0.70 38.25 4.02
653 5013 4.208746 AGGGATCTAGTTCGTTCTAGGTG 58.791 47.826 13.41 0.00 38.25 4.00
654 5014 4.523168 AGGGATCTAGTTCGTTCTAGGT 57.477 45.455 13.41 8.68 38.25 3.08
655 5015 4.456566 GCTAGGGATCTAGTTCGTTCTAGG 59.543 50.000 17.03 7.37 43.68 3.02
656 5016 5.180492 CAGCTAGGGATCTAGTTCGTTCTAG 59.820 48.000 14.01 14.01 43.68 2.43
657 5017 5.064558 CAGCTAGGGATCTAGTTCGTTCTA 58.935 45.833 0.00 0.00 43.68 2.10
660 5020 2.362717 GCAGCTAGGGATCTAGTTCGTT 59.637 50.000 0.00 0.00 43.68 3.85
661 5021 1.957877 GCAGCTAGGGATCTAGTTCGT 59.042 52.381 0.00 0.00 43.68 3.85
664 5024 3.107601 TGTTGCAGCTAGGGATCTAGTT 58.892 45.455 1.17 0.00 43.68 2.24
665 5025 2.752030 TGTTGCAGCTAGGGATCTAGT 58.248 47.619 1.17 0.00 43.68 2.57
666 5026 4.526262 AGTATGTTGCAGCTAGGGATCTAG 59.474 45.833 1.17 0.00 44.40 2.43
667 5027 4.483950 AGTATGTTGCAGCTAGGGATCTA 58.516 43.478 1.17 0.00 0.00 1.98
668 5028 3.312890 AGTATGTTGCAGCTAGGGATCT 58.687 45.455 1.17 0.00 0.00 2.75
669 5029 3.760580 AGTATGTTGCAGCTAGGGATC 57.239 47.619 1.17 0.00 0.00 3.36
671 5031 3.107601 AGAAGTATGTTGCAGCTAGGGA 58.892 45.455 1.17 0.00 0.00 4.20
672 5032 3.550437 AGAAGTATGTTGCAGCTAGGG 57.450 47.619 1.17 0.00 0.00 3.53
693 5053 5.945155 AGTGCGTTCAACTCTTGTTAAAAA 58.055 33.333 0.00 0.00 34.60 1.94
694 5054 5.554822 AGTGCGTTCAACTCTTGTTAAAA 57.445 34.783 0.00 0.00 34.60 1.52
695 5055 5.448089 GGAAGTGCGTTCAACTCTTGTTAAA 60.448 40.000 1.46 0.00 36.82 1.52
696 5056 4.034742 GGAAGTGCGTTCAACTCTTGTTAA 59.965 41.667 1.46 0.00 36.82 2.01
697 5057 3.558418 GGAAGTGCGTTCAACTCTTGTTA 59.442 43.478 1.46 0.00 36.82 2.41
699 5059 1.940613 GGAAGTGCGTTCAACTCTTGT 59.059 47.619 1.46 0.00 36.82 3.16
700 5060 1.070577 CGGAAGTGCGTTCAACTCTTG 60.071 52.381 1.46 0.00 36.82 3.02
701 5061 1.217882 CGGAAGTGCGTTCAACTCTT 58.782 50.000 1.46 0.00 36.82 2.85
702 5062 1.222115 GCGGAAGTGCGTTCAACTCT 61.222 55.000 1.46 0.00 36.82 3.24
703 5063 1.204312 GCGGAAGTGCGTTCAACTC 59.796 57.895 1.46 0.00 36.82 3.01
705 5065 1.204312 GAGCGGAAGTGCGTTCAAC 59.796 57.895 4.30 0.00 40.67 3.18
706 5066 2.307309 CGAGCGGAAGTGCGTTCAA 61.307 57.895 9.45 0.00 40.67 2.69
707 5067 2.686956 TTCGAGCGGAAGTGCGTTCA 62.687 55.000 9.45 0.00 40.67 3.18
709 5069 0.949105 AATTCGAGCGGAAGTGCGTT 60.949 50.000 0.00 0.00 38.24 4.84
710 5070 0.949105 AAATTCGAGCGGAAGTGCGT 60.949 50.000 0.00 0.00 38.24 5.24
711 5071 0.165944 AAAATTCGAGCGGAAGTGCG 59.834 50.000 0.06 0.00 38.24 5.34
713 5073 4.151689 TCAGTAAAAATTCGAGCGGAAGTG 59.848 41.667 0.06 0.00 38.24 3.16
714 5074 4.312443 TCAGTAAAAATTCGAGCGGAAGT 58.688 39.130 0.06 0.00 38.24 3.01
715 5075 4.921470 TCAGTAAAAATTCGAGCGGAAG 57.079 40.909 0.06 0.00 38.24 3.46
717 5077 4.059511 TGTTCAGTAAAAATTCGAGCGGA 58.940 39.130 0.00 0.00 0.00 5.54
718 5078 4.148891 GTGTTCAGTAAAAATTCGAGCGG 58.851 43.478 0.00 0.00 0.00 5.52
1547 13540 3.831333 TGCTTAATTTCACAATGCCCTCA 59.169 39.130 0.00 0.00 0.00 3.86
1659 13652 3.411446 TGATGATGAACTTGAAGGCGTT 58.589 40.909 0.00 0.00 0.00 4.84
2795 14897 5.011635 TGGTCATGTTACTCTTGCACTTCTA 59.988 40.000 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.