Multiple sequence alignment - TraesCS6D01G229900

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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 TraesCS6D01G229900 chr6D 100.000 2624 0 0 1 2624 322462121 322459498 0.000000e+00 4846.0
1 TraesCS6D01G229900 chr6D 76.348 575 111 12 65 617 398237297 398237868 4.270000e-73 285.0
2 TraesCS6D01G229900 chr6D 90.909 176 14 2 632 805 389700707 389700532 4.370000e-58 235.0
3 TraesCS6D01G229900 chr6A 94.574 1843 79 9 797 2624 459849868 459848032 0.000000e+00 2830.0
4 TraesCS6D01G229900 chr6A 87.526 489 44 10 149 635 459850340 459849867 1.370000e-152 549.0
5 TraesCS6D01G229900 chr6A 93.506 77 5 0 1 77 459850415 459850339 5.930000e-22 115.0
6 TraesCS6D01G229900 chr6B 92.347 1777 83 21 797 2559 501104164 501105901 0.000000e+00 2479.0
7 TraesCS6D01G229900 chr6B 92.405 632 42 4 4 635 501103540 501104165 0.000000e+00 896.0
8 TraesCS6D01G229900 chr6B 100.000 52 0 0 2573 2624 501105896 501105947 2.150000e-16 97.1
9 TraesCS6D01G229900 chr2D 76.438 539 105 14 108 635 325825118 325825645 3.330000e-69 272.0
10 TraesCS6D01G229900 chr2D 90.503 179 17 0 631 809 5663392 5663214 1.210000e-58 237.0
11 TraesCS6D01G229900 chr2D 75.532 188 28 7 364 536 596159129 596158945 2.800000e-10 76.8
12 TraesCS6D01G229900 chr1B 76.415 530 100 11 103 617 618388279 618387760 2.000000e-66 263.0
13 TraesCS6D01G229900 chr2B 75.746 536 108 14 112 635 528160040 528159515 1.560000e-62 250.0
14 TraesCS6D01G229900 chr2B 92.727 165 11 1 634 798 514028022 514027859 1.210000e-58 237.0
15 TraesCS6D01G229900 chr3B 92.262 168 13 0 634 801 778707118 778706951 3.380000e-59 239.0
16 TraesCS6D01G229900 chr7B 92.216 167 12 1 631 797 382277269 382277434 4.370000e-58 235.0
17 TraesCS6D01G229900 chr1D 92.169 166 13 0 633 798 206955536 206955701 4.370000e-58 235.0
18 TraesCS6D01G229900 chr1D 74.876 402 75 16 255 635 465526414 465526018 2.700000e-35 159.0
19 TraesCS6D01G229900 chr1A 91.716 169 14 0 630 798 67697240 67697408 4.370000e-58 235.0
20 TraesCS6D01G229900 chrUn 90.805 174 16 0 634 807 74119451 74119624 1.570000e-57 233.0
21 TraesCS6D01G229900 chr4B 91.617 167 14 0 632 798 71600790 71600624 5.650000e-57 231.0
22 TraesCS6D01G229900 chr4B 78.090 178 32 4 476 652 41746822 41746651 3.570000e-19 106.0
23 TraesCS6D01G229900 chr3D 77.250 400 69 12 253 635 594238515 594238121 5.690000e-52 215.0
24 TraesCS6D01G229900 chr3D 74.474 333 68 8 288 605 107655245 107654915 7.620000e-26 128.0
25 TraesCS6D01G229900 chr4D 76.056 284 46 12 371 635 13604444 13604724 7.620000e-26 128.0
26 TraesCS6D01G229900 chr5D 73.885 314 51 18 308 617 339961234 339960948 2.150000e-16 97.1
27 TraesCS6D01G229900 chr5B 91.071 56 5 0 1094 1149 677806399 677806344 2.800000e-10 76.8


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 TraesCS6D01G229900 chr6D 322459498 322462121 2623 True 4846.000000 4846 100.000000 1 2624 1 chr6D.!!$R1 2623
1 TraesCS6D01G229900 chr6D 398237297 398237868 571 False 285.000000 285 76.348000 65 617 1 chr6D.!!$F1 552
2 TraesCS6D01G229900 chr6A 459848032 459850415 2383 True 1164.666667 2830 91.868667 1 2624 3 chr6A.!!$R1 2623
3 TraesCS6D01G229900 chr6B 501103540 501105947 2407 False 1157.366667 2479 94.917333 4 2624 3 chr6B.!!$F1 2620
4 TraesCS6D01G229900 chr2D 325825118 325825645 527 False 272.000000 272 76.438000 108 635 1 chr2D.!!$F1 527
5 TraesCS6D01G229900 chr1B 618387760 618388279 519 True 263.000000 263 76.415000 103 617 1 chr1B.!!$R1 514
6 TraesCS6D01G229900 chr2B 528159515 528160040 525 True 250.000000 250 75.746000 112 635 1 chr2B.!!$R2 523

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
919 974 0.685131 TTCCAATCCTCCGGCTCGTA 60.685 55.0 0.0 0.0 0.0 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2185 2252 0.038166 TGGATGACAGGTGCCCTTTC 59.962 55.0 1.61 1.61 31.52 2.62 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
61 62 6.822667 TCACACTATAGTAACGTTTCCTCA 57.177 37.500 5.91 0.00 0.00 3.86
91 92 5.417894 CCCTAGGTGGTTAGGACAAATTTTC 59.582 44.000 8.29 0.00 42.39 2.29
132 133 1.991230 CCCGTGGATTTGTCTCCCT 59.009 57.895 0.00 0.00 34.12 4.20
332 337 0.741326 TAGTCGATGAGCTCCAGTGC 59.259 55.000 12.15 0.00 0.00 4.40
522 560 3.695606 GTGGGGAGCAGCGACAGA 61.696 66.667 0.00 0.00 0.00 3.41
524 562 2.293318 TGGGGAGCAGCGACAGAAT 61.293 57.895 0.00 0.00 0.00 2.40
575 622 3.367743 TCGTTCGGTGGTCTCGGG 61.368 66.667 0.00 0.00 0.00 5.14
635 682 7.992180 TTTACTCCCGACGAATCTTTTATAC 57.008 36.000 0.00 0.00 0.00 1.47
636 683 5.848833 ACTCCCGACGAATCTTTTATACT 57.151 39.130 0.00 0.00 0.00 2.12
637 684 5.829829 ACTCCCGACGAATCTTTTATACTC 58.170 41.667 0.00 0.00 0.00 2.59
638 685 5.192327 TCCCGACGAATCTTTTATACTCC 57.808 43.478 0.00 0.00 0.00 3.85
639 686 4.646040 TCCCGACGAATCTTTTATACTCCA 59.354 41.667 0.00 0.00 0.00 3.86
640 687 5.303589 TCCCGACGAATCTTTTATACTCCAT 59.696 40.000 0.00 0.00 0.00 3.41
641 688 5.634020 CCCGACGAATCTTTTATACTCCATC 59.366 44.000 0.00 0.00 0.00 3.51
642 689 5.634020 CCGACGAATCTTTTATACTCCATCC 59.366 44.000 0.00 0.00 0.00 3.51
643 690 5.342525 CGACGAATCTTTTATACTCCATCCG 59.657 44.000 0.00 0.00 0.00 4.18
644 691 6.158023 ACGAATCTTTTATACTCCATCCGT 57.842 37.500 0.00 0.00 0.00 4.69
645 692 6.579865 ACGAATCTTTTATACTCCATCCGTT 58.420 36.000 0.00 0.00 0.00 4.44
646 693 6.700520 ACGAATCTTTTATACTCCATCCGTTC 59.299 38.462 0.00 0.00 0.00 3.95
647 694 6.145696 CGAATCTTTTATACTCCATCCGTTCC 59.854 42.308 0.00 0.00 0.00 3.62
648 695 6.749036 ATCTTTTATACTCCATCCGTTCCT 57.251 37.500 0.00 0.00 0.00 3.36
649 696 7.850935 ATCTTTTATACTCCATCCGTTCCTA 57.149 36.000 0.00 0.00 0.00 2.94
650 697 7.664552 TCTTTTATACTCCATCCGTTCCTAA 57.335 36.000 0.00 0.00 0.00 2.69
651 698 8.081517 TCTTTTATACTCCATCCGTTCCTAAA 57.918 34.615 0.00 0.00 0.00 1.85
652 699 8.711170 TCTTTTATACTCCATCCGTTCCTAAAT 58.289 33.333 0.00 0.00 0.00 1.40
653 700 9.991906 CTTTTATACTCCATCCGTTCCTAAATA 57.008 33.333 0.00 0.00 0.00 1.40
657 704 8.848474 ATACTCCATCCGTTCCTAAATATTTG 57.152 34.615 11.05 1.40 0.00 2.32
658 705 6.659824 ACTCCATCCGTTCCTAAATATTTGT 58.340 36.000 11.05 0.00 0.00 2.83
659 706 6.766467 ACTCCATCCGTTCCTAAATATTTGTC 59.234 38.462 11.05 0.00 0.00 3.18
660 707 6.895782 TCCATCCGTTCCTAAATATTTGTCT 58.104 36.000 11.05 0.00 0.00 3.41
661 708 7.343357 TCCATCCGTTCCTAAATATTTGTCTT 58.657 34.615 11.05 0.00 0.00 3.01
662 709 7.832187 TCCATCCGTTCCTAAATATTTGTCTTT 59.168 33.333 11.05 0.00 0.00 2.52
663 710 8.129211 CCATCCGTTCCTAAATATTTGTCTTTC 58.871 37.037 11.05 0.00 0.00 2.62
664 711 8.893727 CATCCGTTCCTAAATATTTGTCTTTCT 58.106 33.333 11.05 0.00 0.00 2.52
666 713 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
667 714 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
687 734 9.832445 TTCTAGATATTTCAAATAGACCACCAC 57.168 33.333 0.00 0.00 0.00 4.16
688 735 8.141909 TCTAGATATTTCAAATAGACCACCACG 58.858 37.037 0.00 0.00 0.00 4.94
689 736 6.650120 AGATATTTCAAATAGACCACCACGT 58.350 36.000 0.00 0.00 0.00 4.49
690 737 7.788026 AGATATTTCAAATAGACCACCACGTA 58.212 34.615 0.00 0.00 0.00 3.57
691 738 8.262227 AGATATTTCAAATAGACCACCACGTAA 58.738 33.333 0.00 0.00 0.00 3.18
693 740 4.196626 TCAAATAGACCACCACGTAAGG 57.803 45.455 0.00 0.00 46.39 2.69
694 741 3.833650 TCAAATAGACCACCACGTAAGGA 59.166 43.478 7.06 0.00 46.39 3.36
695 742 4.468510 TCAAATAGACCACCACGTAAGGAT 59.531 41.667 7.06 0.00 46.39 3.24
696 743 4.402056 AATAGACCACCACGTAAGGATG 57.598 45.455 7.06 0.00 46.39 3.51
697 744 1.640917 AGACCACCACGTAAGGATGT 58.359 50.000 7.06 0.00 46.39 3.06
698 745 2.811410 AGACCACCACGTAAGGATGTA 58.189 47.619 7.06 0.00 46.39 2.29
699 746 3.371965 AGACCACCACGTAAGGATGTAT 58.628 45.455 7.06 0.00 46.39 2.29
700 747 4.539726 AGACCACCACGTAAGGATGTATA 58.460 43.478 7.06 0.00 46.39 1.47
701 748 5.145564 AGACCACCACGTAAGGATGTATAT 58.854 41.667 7.06 0.00 46.39 0.86
702 749 6.309357 AGACCACCACGTAAGGATGTATATA 58.691 40.000 7.06 0.00 46.39 0.86
703 750 6.433404 AGACCACCACGTAAGGATGTATATAG 59.567 42.308 7.06 0.00 46.39 1.31
704 751 6.309357 ACCACCACGTAAGGATGTATATAGA 58.691 40.000 7.06 0.00 46.39 1.98
705 752 6.208204 ACCACCACGTAAGGATGTATATAGAC 59.792 42.308 7.06 0.00 46.39 2.59
706 753 6.208007 CCACCACGTAAGGATGTATATAGACA 59.792 42.308 2.07 2.07 46.39 3.41
707 754 7.093902 CCACCACGTAAGGATGTATATAGACAT 60.094 40.741 12.70 12.70 41.40 3.06
708 755 8.953313 CACCACGTAAGGATGTATATAGACATA 58.047 37.037 12.82 0.00 39.72 2.29
709 756 9.696572 ACCACGTAAGGATGTATATAGACATAT 57.303 33.333 12.82 5.74 39.72 1.78
727 774 8.804688 AGACATATTTTAGAGCGTAGATTCAC 57.195 34.615 0.00 0.00 0.00 3.18
728 775 8.634444 AGACATATTTTAGAGCGTAGATTCACT 58.366 33.333 0.00 0.00 0.00 3.41
729 776 8.804688 ACATATTTTAGAGCGTAGATTCACTC 57.195 34.615 0.00 0.00 0.00 3.51
730 777 8.414003 ACATATTTTAGAGCGTAGATTCACTCA 58.586 33.333 0.00 0.00 0.00 3.41
731 778 9.416794 CATATTTTAGAGCGTAGATTCACTCAT 57.583 33.333 0.00 0.00 0.00 2.90
732 779 9.988815 ATATTTTAGAGCGTAGATTCACTCATT 57.011 29.630 0.00 0.00 0.00 2.57
733 780 8.723942 ATTTTAGAGCGTAGATTCACTCATTT 57.276 30.769 0.00 0.00 0.00 2.32
734 781 8.547967 TTTTAGAGCGTAGATTCACTCATTTT 57.452 30.769 0.00 0.00 0.00 1.82
735 782 8.547967 TTTAGAGCGTAGATTCACTCATTTTT 57.452 30.769 0.00 0.00 0.00 1.94
736 783 6.654793 AGAGCGTAGATTCACTCATTTTTC 57.345 37.500 0.00 0.00 0.00 2.29
737 784 6.402222 AGAGCGTAGATTCACTCATTTTTCT 58.598 36.000 0.00 0.00 0.00 2.52
738 785 6.533367 AGAGCGTAGATTCACTCATTTTTCTC 59.467 38.462 0.00 0.00 0.00 2.87
739 786 5.582665 AGCGTAGATTCACTCATTTTTCTCC 59.417 40.000 0.00 0.00 0.00 3.71
740 787 5.500931 GCGTAGATTCACTCATTTTTCTCCG 60.501 44.000 0.00 0.00 0.00 4.63
741 788 5.577164 CGTAGATTCACTCATTTTTCTCCGT 59.423 40.000 0.00 0.00 0.00 4.69
742 789 6.750501 CGTAGATTCACTCATTTTTCTCCGTA 59.249 38.462 0.00 0.00 0.00 4.02
743 790 7.435488 CGTAGATTCACTCATTTTTCTCCGTAT 59.565 37.037 0.00 0.00 0.00 3.06
744 791 7.545362 AGATTCACTCATTTTTCTCCGTATG 57.455 36.000 0.00 0.00 0.00 2.39
745 792 7.106239 AGATTCACTCATTTTTCTCCGTATGT 58.894 34.615 0.00 0.00 0.00 2.29
746 793 8.258007 AGATTCACTCATTTTTCTCCGTATGTA 58.742 33.333 0.00 0.00 0.00 2.29
747 794 7.827819 TTCACTCATTTTTCTCCGTATGTAG 57.172 36.000 0.00 0.00 0.00 2.74
748 795 6.931838 TCACTCATTTTTCTCCGTATGTAGT 58.068 36.000 0.00 0.00 0.00 2.73
749 796 7.033791 TCACTCATTTTTCTCCGTATGTAGTC 58.966 38.462 0.00 0.00 0.00 2.59
750 797 6.811665 CACTCATTTTTCTCCGTATGTAGTCA 59.188 38.462 0.00 0.00 0.00 3.41
751 798 7.492669 CACTCATTTTTCTCCGTATGTAGTCAT 59.507 37.037 0.00 0.00 38.00 3.06
752 799 8.041323 ACTCATTTTTCTCCGTATGTAGTCATT 58.959 33.333 0.00 0.00 35.70 2.57
753 800 8.786826 TCATTTTTCTCCGTATGTAGTCATTT 57.213 30.769 0.00 0.00 35.70 2.32
754 801 8.664798 TCATTTTTCTCCGTATGTAGTCATTTG 58.335 33.333 0.00 0.00 35.70 2.32
755 802 7.972832 TTTTTCTCCGTATGTAGTCATTTGT 57.027 32.000 0.00 0.00 35.70 2.83
756 803 7.972832 TTTTCTCCGTATGTAGTCATTTGTT 57.027 32.000 0.00 0.00 35.70 2.83
757 804 6.961359 TTCTCCGTATGTAGTCATTTGTTG 57.039 37.500 0.00 0.00 35.70 3.33
758 805 6.275494 TCTCCGTATGTAGTCATTTGTTGA 57.725 37.500 0.00 0.00 35.70 3.18
759 806 6.693466 TCTCCGTATGTAGTCATTTGTTGAA 58.307 36.000 0.00 0.00 35.70 2.69
760 807 7.156000 TCTCCGTATGTAGTCATTTGTTGAAA 58.844 34.615 0.00 0.00 35.70 2.69
761 808 7.822334 TCTCCGTATGTAGTCATTTGTTGAAAT 59.178 33.333 0.00 0.00 35.70 2.17
762 809 7.970384 TCCGTATGTAGTCATTTGTTGAAATC 58.030 34.615 0.00 0.00 35.70 2.17
763 810 7.822334 TCCGTATGTAGTCATTTGTTGAAATCT 59.178 33.333 0.00 0.00 35.70 2.40
764 811 8.116753 CCGTATGTAGTCATTTGTTGAAATCTC 58.883 37.037 0.00 0.00 35.70 2.75
765 812 8.873830 CGTATGTAGTCATTTGTTGAAATCTCT 58.126 33.333 0.00 0.00 35.70 3.10
769 816 9.996554 TGTAGTCATTTGTTGAAATCTCTAGAA 57.003 29.630 0.00 0.00 35.70 2.10
772 819 9.784531 AGTCATTTGTTGAAATCTCTAGAAAGA 57.215 29.630 0.00 0.00 35.70 2.52
796 843 9.165057 AGATAAATATTTAGGAGCAGAAGGAGT 57.835 33.333 13.15 0.00 0.00 3.85
914 969 1.453928 CCCTTTCCAATCCTCCGGC 60.454 63.158 0.00 0.00 0.00 6.13
917 972 0.811616 CTTTCCAATCCTCCGGCTCG 60.812 60.000 0.00 0.00 0.00 5.03
918 973 1.550130 TTTCCAATCCTCCGGCTCGT 61.550 55.000 0.00 0.00 0.00 4.18
919 974 0.685131 TTCCAATCCTCCGGCTCGTA 60.685 55.000 0.00 0.00 0.00 3.43
920 975 1.107538 TCCAATCCTCCGGCTCGTAG 61.108 60.000 0.00 0.00 0.00 3.51
972 1029 2.258591 CGACCGACAGACACCTGG 59.741 66.667 0.00 0.00 44.60 4.45
1253 1310 2.835895 GGTCTCCCCTCTCCTCGC 60.836 72.222 0.00 0.00 0.00 5.03
1359 1416 2.202570 GCGGACATGTACGTCGCT 60.203 61.111 30.03 0.00 39.57 4.93
1597 1654 5.311265 ACTTGATCTTGAGATTCTTGTGCA 58.689 37.500 0.00 0.00 34.37 4.57
1629 1686 4.884164 AGCTTTCTTGTGTGCTAGTTCTTT 59.116 37.500 0.00 0.00 33.64 2.52
1634 1691 5.610398 TCTTGTGTGCTAGTTCTTTCATGA 58.390 37.500 0.00 0.00 0.00 3.07
1644 1701 7.025963 GCTAGTTCTTTCATGATTTTGGTCAG 58.974 38.462 0.00 0.00 0.00 3.51
1651 1708 3.758023 TCATGATTTTGGTCAGTCGCATT 59.242 39.130 0.00 0.00 0.00 3.56
1670 1727 4.469552 CATTACTGTCACACAAGTGCATG 58.530 43.478 0.00 0.00 45.49 4.06
1869 1928 7.599998 ACCTTTCAGTTATTGCAAATGACAATC 59.400 33.333 1.71 0.00 38.62 2.67
1879 1938 4.754618 TGCAAATGACAATCGACAACTAGT 59.245 37.500 0.00 0.00 0.00 2.57
1894 1953 6.591750 ACAACTAGTAGCAGTACTGATGTT 57.408 37.500 27.08 16.67 39.96 2.71
1930 1989 2.133281 TTCTTCATCATGCCAGGTGG 57.867 50.000 0.00 0.00 38.53 4.61
2093 2157 4.434725 CGTAAAATGGATATGCTGCTAGCG 60.435 45.833 10.77 6.22 46.26 4.26
2127 2193 9.635520 CTAGATATTCCATGCCAATTTGATTTC 57.364 33.333 0.00 0.00 0.00 2.17
2166 2233 4.518249 AGGTTTAAGAAGTGCTATCAGCC 58.482 43.478 0.00 0.00 41.51 4.85
2185 2252 1.904032 GCAGGAGGTTCCTCTCAGG 59.096 63.158 16.95 6.93 45.66 3.86
2214 2281 6.476378 GGCACCTGTCATCCAGTTATATTAT 58.524 40.000 0.00 0.00 39.74 1.28
2253 2320 5.848406 TCAAGAAAGAGTCTTCTCAGAACC 58.152 41.667 5.70 0.00 45.25 3.62
2262 2329 4.020662 AGTCTTCTCAGAACCAGGATGTTC 60.021 45.833 0.00 0.00 43.95 3.18
2277 2345 3.505293 GGATGTTCTTCAGCTTGCTTCTT 59.495 43.478 0.00 0.00 32.48 2.52
2282 2350 1.811359 CTTCAGCTTGCTTCTTGGAGG 59.189 52.381 0.00 0.00 0.00 4.30
2283 2351 1.059098 TCAGCTTGCTTCTTGGAGGA 58.941 50.000 0.00 0.00 0.00 3.71
2421 2492 2.416893 GGATGAGAAAACAAGGAGCGAC 59.583 50.000 0.00 0.00 0.00 5.19
2422 2493 2.613026 TGAGAAAACAAGGAGCGACA 57.387 45.000 0.00 0.00 0.00 4.35
2424 2495 2.102420 TGAGAAAACAAGGAGCGACAGA 59.898 45.455 0.00 0.00 0.00 3.41
2446 2517 3.801594 AGGCATTTTTGTACTGTTTTGCG 59.198 39.130 0.00 0.00 0.00 4.85
2475 2546 7.168219 AGACCTTTGATATTTCAGCAACACTA 58.832 34.615 0.00 0.00 30.73 2.74
2486 2557 4.191544 TCAGCAACACTACATAATCAGCC 58.808 43.478 0.00 0.00 0.00 4.85
2527 2598 0.605319 TTTGACCGTGGCATGTCCTC 60.605 55.000 14.92 0.00 35.26 3.71
2547 2618 0.033090 GGAGAAAGTGGACGACGGTT 59.967 55.000 0.00 0.00 0.00 4.44
2554 2625 1.300620 TGGACGACGGTTGCTGAAG 60.301 57.895 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 6.884836 GTGATTCCATAGAAACCCAACTAACT 59.115 38.462 0.00 0.00 35.09 2.24
20 21 5.010282 GTGTGATTCCATAGAAACCCAACT 58.990 41.667 0.00 0.00 35.09 3.16
91 92 1.202580 CGCCAGTGAATTCTAGAGGGG 60.203 57.143 7.05 7.98 0.00 4.79
332 337 2.203126 GGAGGCGGCAGGAATCTG 60.203 66.667 13.08 0.00 43.64 2.90
635 682 6.992715 AGACAAATATTTAGGAACGGATGGAG 59.007 38.462 0.00 0.00 0.00 3.86
636 683 6.895782 AGACAAATATTTAGGAACGGATGGA 58.104 36.000 0.00 0.00 0.00 3.41
637 684 7.568199 AAGACAAATATTTAGGAACGGATGG 57.432 36.000 0.00 0.00 0.00 3.51
638 685 8.893727 AGAAAGACAAATATTTAGGAACGGATG 58.106 33.333 0.00 0.00 0.00 3.51
640 687 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
641 688 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
661 708 9.832445 GTGGTGGTCTATTTGAAATATCTAGAA 57.168 33.333 0.00 0.00 0.00 2.10
662 709 8.141909 CGTGGTGGTCTATTTGAAATATCTAGA 58.858 37.037 0.00 0.00 0.00 2.43
663 710 7.926555 ACGTGGTGGTCTATTTGAAATATCTAG 59.073 37.037 0.00 0.00 0.00 2.43
664 711 7.788026 ACGTGGTGGTCTATTTGAAATATCTA 58.212 34.615 0.00 0.00 0.00 1.98
665 712 6.650120 ACGTGGTGGTCTATTTGAAATATCT 58.350 36.000 0.00 0.00 0.00 1.98
666 713 6.920569 ACGTGGTGGTCTATTTGAAATATC 57.079 37.500 0.00 0.00 0.00 1.63
667 714 7.497909 CCTTACGTGGTGGTCTATTTGAAATAT 59.502 37.037 0.00 0.00 0.00 1.28
668 715 6.819649 CCTTACGTGGTGGTCTATTTGAAATA 59.180 38.462 0.00 0.00 0.00 1.40
669 716 5.646360 CCTTACGTGGTGGTCTATTTGAAAT 59.354 40.000 0.00 0.00 0.00 2.17
670 717 4.998672 CCTTACGTGGTGGTCTATTTGAAA 59.001 41.667 0.00 0.00 0.00 2.69
671 718 4.283978 TCCTTACGTGGTGGTCTATTTGAA 59.716 41.667 0.00 0.00 0.00 2.69
672 719 3.833650 TCCTTACGTGGTGGTCTATTTGA 59.166 43.478 0.00 0.00 0.00 2.69
673 720 4.196626 TCCTTACGTGGTGGTCTATTTG 57.803 45.455 0.00 0.00 0.00 2.32
674 721 4.224370 ACATCCTTACGTGGTGGTCTATTT 59.776 41.667 0.00 0.00 0.00 1.40
675 722 3.773119 ACATCCTTACGTGGTGGTCTATT 59.227 43.478 0.00 0.00 0.00 1.73
676 723 3.371965 ACATCCTTACGTGGTGGTCTAT 58.628 45.455 0.00 0.00 0.00 1.98
677 724 2.811410 ACATCCTTACGTGGTGGTCTA 58.189 47.619 0.00 0.00 0.00 2.59
678 725 1.640917 ACATCCTTACGTGGTGGTCT 58.359 50.000 0.00 0.00 0.00 3.85
679 726 3.814005 ATACATCCTTACGTGGTGGTC 57.186 47.619 0.00 0.00 0.00 4.02
680 727 6.208204 GTCTATATACATCCTTACGTGGTGGT 59.792 42.308 0.00 0.00 0.00 4.16
681 728 6.208007 TGTCTATATACATCCTTACGTGGTGG 59.792 42.308 0.00 0.00 0.00 4.61
682 729 7.210718 TGTCTATATACATCCTTACGTGGTG 57.789 40.000 0.00 0.00 0.00 4.17
683 730 9.696572 ATATGTCTATATACATCCTTACGTGGT 57.303 33.333 7.00 0.00 40.52 4.16
701 748 9.894783 GTGAATCTACGCTCTAAAATATGTCTA 57.105 33.333 0.00 0.00 0.00 2.59
702 749 8.634444 AGTGAATCTACGCTCTAAAATATGTCT 58.366 33.333 0.00 0.00 0.00 3.41
703 750 8.804688 AGTGAATCTACGCTCTAAAATATGTC 57.195 34.615 0.00 0.00 0.00 3.06
704 751 8.414003 TGAGTGAATCTACGCTCTAAAATATGT 58.586 33.333 0.00 0.00 44.58 2.29
705 752 8.803201 TGAGTGAATCTACGCTCTAAAATATG 57.197 34.615 0.00 0.00 44.58 1.78
706 753 9.988815 AATGAGTGAATCTACGCTCTAAAATAT 57.011 29.630 0.00 0.00 44.58 1.28
707 754 9.817809 AAATGAGTGAATCTACGCTCTAAAATA 57.182 29.630 0.00 0.00 44.58 1.40
708 755 8.723942 AAATGAGTGAATCTACGCTCTAAAAT 57.276 30.769 0.00 0.00 44.58 1.82
709 756 8.547967 AAAATGAGTGAATCTACGCTCTAAAA 57.452 30.769 0.00 0.00 44.58 1.52
710 757 8.547967 AAAAATGAGTGAATCTACGCTCTAAA 57.452 30.769 0.00 0.00 44.58 1.85
711 758 8.035394 AGAAAAATGAGTGAATCTACGCTCTAA 58.965 33.333 0.00 0.00 44.58 2.10
712 759 7.548097 AGAAAAATGAGTGAATCTACGCTCTA 58.452 34.615 0.00 0.00 44.58 2.43
713 760 6.402222 AGAAAAATGAGTGAATCTACGCTCT 58.598 36.000 0.00 0.00 44.58 4.09
714 761 6.237969 GGAGAAAAATGAGTGAATCTACGCTC 60.238 42.308 0.00 0.00 44.55 5.03
715 762 5.582665 GGAGAAAAATGAGTGAATCTACGCT 59.417 40.000 0.00 0.00 0.00 5.07
716 763 5.500931 CGGAGAAAAATGAGTGAATCTACGC 60.501 44.000 0.00 0.00 34.85 4.42
717 764 5.577164 ACGGAGAAAAATGAGTGAATCTACG 59.423 40.000 3.84 3.84 44.61 3.51
718 765 6.969828 ACGGAGAAAAATGAGTGAATCTAC 57.030 37.500 0.00 0.00 0.00 2.59
719 766 8.258007 ACATACGGAGAAAAATGAGTGAATCTA 58.742 33.333 0.00 0.00 0.00 1.98
720 767 7.106239 ACATACGGAGAAAAATGAGTGAATCT 58.894 34.615 0.00 0.00 0.00 2.40
721 768 7.308782 ACATACGGAGAAAAATGAGTGAATC 57.691 36.000 0.00 0.00 0.00 2.52
722 769 8.041323 ACTACATACGGAGAAAAATGAGTGAAT 58.959 33.333 0.00 0.00 0.00 2.57
723 770 7.383687 ACTACATACGGAGAAAAATGAGTGAA 58.616 34.615 0.00 0.00 0.00 3.18
724 771 6.931838 ACTACATACGGAGAAAAATGAGTGA 58.068 36.000 0.00 0.00 0.00 3.41
725 772 6.811665 TGACTACATACGGAGAAAAATGAGTG 59.188 38.462 0.00 0.00 0.00 3.51
726 773 6.931838 TGACTACATACGGAGAAAAATGAGT 58.068 36.000 0.00 0.00 0.00 3.41
727 774 8.425577 AATGACTACATACGGAGAAAAATGAG 57.574 34.615 0.00 0.00 35.50 2.90
728 775 8.664798 CAAATGACTACATACGGAGAAAAATGA 58.335 33.333 0.00 0.00 35.50 2.57
729 776 8.450964 ACAAATGACTACATACGGAGAAAAATG 58.549 33.333 0.00 0.00 35.50 2.32
730 777 8.561738 ACAAATGACTACATACGGAGAAAAAT 57.438 30.769 0.00 0.00 35.50 1.82
731 778 7.972832 ACAAATGACTACATACGGAGAAAAA 57.027 32.000 0.00 0.00 35.50 1.94
732 779 7.658167 TCAACAAATGACTACATACGGAGAAAA 59.342 33.333 0.00 0.00 35.50 2.29
733 780 7.156000 TCAACAAATGACTACATACGGAGAAA 58.844 34.615 0.00 0.00 35.50 2.52
734 781 6.693466 TCAACAAATGACTACATACGGAGAA 58.307 36.000 0.00 0.00 35.50 2.87
735 782 6.275494 TCAACAAATGACTACATACGGAGA 57.725 37.500 0.00 0.00 35.50 3.71
736 783 6.961359 TTCAACAAATGACTACATACGGAG 57.039 37.500 0.00 0.00 37.92 4.63
737 784 7.822334 AGATTTCAACAAATGACTACATACGGA 59.178 33.333 0.00 0.00 37.92 4.69
738 785 7.974675 AGATTTCAACAAATGACTACATACGG 58.025 34.615 0.00 0.00 37.92 4.02
739 786 8.873830 AGAGATTTCAACAAATGACTACATACG 58.126 33.333 0.00 0.00 37.92 3.06
743 790 9.996554 TTCTAGAGATTTCAACAAATGACTACA 57.003 29.630 0.00 0.00 37.92 2.74
746 793 9.784531 TCTTTCTAGAGATTTCAACAAATGACT 57.215 29.630 0.00 0.00 37.92 3.41
770 817 9.165057 ACTCCTTCTGCTCCTAAATATTTATCT 57.835 33.333 8.34 0.00 0.00 1.98
776 823 9.830186 TCTATTACTCCTTCTGCTCCTAAATAT 57.170 33.333 0.00 0.00 0.00 1.28
777 824 9.830186 ATCTATTACTCCTTCTGCTCCTAAATA 57.170 33.333 0.00 0.00 0.00 1.40
778 825 8.734593 ATCTATTACTCCTTCTGCTCCTAAAT 57.265 34.615 0.00 0.00 0.00 1.40
779 826 9.830186 ATATCTATTACTCCTTCTGCTCCTAAA 57.170 33.333 0.00 0.00 0.00 1.85
780 827 9.249053 CATATCTATTACTCCTTCTGCTCCTAA 57.751 37.037 0.00 0.00 0.00 2.69
781 828 8.615705 TCATATCTATTACTCCTTCTGCTCCTA 58.384 37.037 0.00 0.00 0.00 2.94
782 829 7.474445 TCATATCTATTACTCCTTCTGCTCCT 58.526 38.462 0.00 0.00 0.00 3.69
783 830 7.710676 TCATATCTATTACTCCTTCTGCTCC 57.289 40.000 0.00 0.00 0.00 4.70
784 831 8.413229 GGATCATATCTATTACTCCTTCTGCTC 58.587 40.741 0.00 0.00 0.00 4.26
785 832 8.121833 AGGATCATATCTATTACTCCTTCTGCT 58.878 37.037 0.00 0.00 0.00 4.24
786 833 8.305046 AGGATCATATCTATTACTCCTTCTGC 57.695 38.462 0.00 0.00 0.00 4.26
914 969 1.741706 TCTTTGGCCTACGACTACGAG 59.258 52.381 3.32 0.00 42.66 4.18
917 972 1.203994 TGCTCTTTGGCCTACGACTAC 59.796 52.381 3.32 0.00 0.00 2.73
918 973 1.552578 TGCTCTTTGGCCTACGACTA 58.447 50.000 3.32 0.00 0.00 2.59
919 974 0.685097 TTGCTCTTTGGCCTACGACT 59.315 50.000 3.32 0.00 0.00 4.18
920 975 1.519408 TTTGCTCTTTGGCCTACGAC 58.481 50.000 3.32 0.00 0.00 4.34
1359 1416 2.279851 CAGTGGTCAACGGCGACA 60.280 61.111 16.62 1.02 37.66 4.35
1629 1686 2.777094 TGCGACTGACCAAAATCATGA 58.223 42.857 0.00 0.00 0.00 3.07
1644 1701 2.800544 ACTTGTGTGACAGTAATGCGAC 59.199 45.455 0.00 0.00 0.00 5.19
1651 1708 3.192541 ACATGCACTTGTGTGACAGTA 57.807 42.857 0.00 0.00 46.55 2.74
1670 1727 8.113675 ACAAACGTAAATCAATTGCAAGAAAAC 58.886 29.630 4.94 0.00 0.00 2.43
1787 1844 7.307694 TCATAAAAGTGCTAATGAAAGTGCTG 58.692 34.615 0.00 0.00 0.00 4.41
1799 1856 8.511321 CCAACAATTGTACTCATAAAAGTGCTA 58.489 33.333 12.39 0.00 33.54 3.49
1801 1858 7.114811 CACCAACAATTGTACTCATAAAAGTGC 59.885 37.037 12.39 0.00 28.36 4.40
1869 1928 4.941325 TCAGTACTGCTACTAGTTGTCG 57.059 45.455 18.45 0.00 31.46 4.35
1879 1938 7.404671 TCATGTTAGAACATCAGTACTGCTA 57.595 36.000 18.45 10.15 46.10 3.49
1912 1971 0.994247 ACCACCTGGCATGATGAAGA 59.006 50.000 0.00 0.00 39.32 2.87
1930 1989 5.175308 GCCTAAGCAACGTAAATCTAGCTAC 59.825 44.000 0.00 0.00 39.53 3.58
1982 2041 2.484602 GGGGTAAGAACACCTGGGATA 58.515 52.381 0.00 0.00 46.68 2.59
2070 2134 4.434725 CGCTAGCAGCATATCCATTTTACG 60.435 45.833 16.45 0.00 42.58 3.18
2093 2157 6.830912 TGGCATGGAATATCTAGCATATACC 58.169 40.000 0.00 0.00 0.00 2.73
2127 2193 4.457834 AACCTCTCGAATGTAACCTGAG 57.542 45.455 0.00 0.00 0.00 3.35
2185 2252 0.038166 TGGATGACAGGTGCCCTTTC 59.962 55.000 1.61 1.61 31.52 2.62
2214 2281 5.453567 TTCTTGATCGAGAGTGAACAGAA 57.546 39.130 12.50 0.00 0.00 3.02
2253 2320 2.434428 AGCAAGCTGAAGAACATCCTG 58.566 47.619 0.00 0.00 0.00 3.86
2262 2329 1.811359 CCTCCAAGAAGCAAGCTGAAG 59.189 52.381 0.00 0.00 0.00 3.02
2277 2345 4.560716 CGATTACTTTCTGTGTGTCCTCCA 60.561 45.833 0.00 0.00 0.00 3.86
2282 2350 4.201724 GCCATCGATTACTTTCTGTGTGTC 60.202 45.833 0.00 0.00 0.00 3.67
2283 2351 3.684788 GCCATCGATTACTTTCTGTGTGT 59.315 43.478 0.00 0.00 0.00 3.72
2421 2492 5.050837 GCAAAACAGTACAAAAATGCCTCTG 60.051 40.000 0.00 0.00 0.00 3.35
2422 2493 5.049828 GCAAAACAGTACAAAAATGCCTCT 58.950 37.500 0.00 0.00 0.00 3.69
2424 2495 3.801594 CGCAAAACAGTACAAAAATGCCT 59.198 39.130 0.00 0.00 0.00 4.75
2446 2517 4.158394 TGCTGAAATATCAAAGGTCTTGCC 59.842 41.667 0.00 0.00 34.49 4.52
2475 2546 6.886459 AGAATTGTTACTGTGGCTGATTATGT 59.114 34.615 0.00 0.00 0.00 2.29
2527 2598 1.443872 CCGTCGTCCACTTTCTCCG 60.444 63.158 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.