Multiple sequence alignment - TraesCS6D01G150300

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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 TraesCS6D01G150300 chr6D 100.000 3657 0 0 1 3657 123971520 123967864 0.000000e+00 6754
1 TraesCS6D01G150300 chr6A 92.045 2753 137 30 959 3657 157132715 157135439 0.000000e+00 3795
2 TraesCS6D01G150300 chr6A 83.148 629 94 7 11 627 384387862 384387234 6.860000e-157 564
3 TraesCS6D01G150300 chr6A 90.498 221 11 5 677 896 157132106 157132317 2.150000e-72 283
4 TraesCS6D01G150300 chr6B 94.505 1110 47 9 2559 3657 219097914 219096808 0.000000e+00 1700
5 TraesCS6D01G150300 chr6B 90.236 891 46 15 1165 2026 219099406 219098528 0.000000e+00 1125
6 TraesCS6D01G150300 chr6B 87.729 546 26 11 2056 2569 219098530 219097994 1.880000e-167 599
7 TraesCS6D01G150300 chr6B 83.199 619 92 7 15 622 41466271 41466888 1.150000e-154 556
8 TraesCS6D01G150300 chr6B 89.320 206 15 2 966 1164 219101433 219101228 6.060000e-63 252
9 TraesCS6D01G150300 chr7A 90.267 637 52 3 1 627 407867448 407866812 0.000000e+00 824
10 TraesCS6D01G150300 chr7A 89.953 637 54 4 1 627 586314863 586314227 0.000000e+00 813
11 TraesCS6D01G150300 chr7A 90.389 437 32 3 201 627 719956695 719956259 1.910000e-157 566
12 TraesCS6D01G150300 chr5B 87.599 629 68 3 8 626 9586816 9586188 0.000000e+00 721
13 TraesCS6D01G150300 chr1D 86.006 636 77 7 3 627 90579312 90578678 0.000000e+00 671
14 TraesCS6D01G150300 chr2D 85.556 630 81 6 8 627 106138080 106137451 0.000000e+00 651
15 TraesCS6D01G150300 chr2D 84.019 632 91 3 1 622 447324461 447325092 1.880000e-167 599
16 TraesCS6D01G150300 chr3B 85.261 631 80 9 8 627 422202036 422202664 3.980000e-179 638
17 TraesCS6D01G150300 chr3B 82.249 507 80 3 1 497 160032339 160031833 2.610000e-116 429
18 TraesCS6D01G150300 chr7B 81.395 602 100 6 15 605 686912413 686913013 7.100000e-132 481
19 TraesCS6D01G150300 chrUn 80.635 630 111 5 4 622 303543869 303544498 9.190000e-131 477
20 TraesCS6D01G150300 chr3D 81.536 547 89 7 86 622 133282757 133283301 1.210000e-119 440


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 TraesCS6D01G150300 chr6D 123967864 123971520 3656 True 6754 6754 100.0000 1 3657 1 chr6D.!!$R1 3656
1 TraesCS6D01G150300 chr6A 157132106 157135439 3333 False 2039 3795 91.2715 677 3657 2 chr6A.!!$F1 2980
2 TraesCS6D01G150300 chr6A 384387234 384387862 628 True 564 564 83.1480 11 627 1 chr6A.!!$R1 616
3 TraesCS6D01G150300 chr6B 219096808 219101433 4625 True 919 1700 90.4475 966 3657 4 chr6B.!!$R1 2691
4 TraesCS6D01G150300 chr6B 41466271 41466888 617 False 556 556 83.1990 15 622 1 chr6B.!!$F1 607
5 TraesCS6D01G150300 chr7A 407866812 407867448 636 True 824 824 90.2670 1 627 1 chr7A.!!$R1 626
6 TraesCS6D01G150300 chr7A 586314227 586314863 636 True 813 813 89.9530 1 627 1 chr7A.!!$R2 626
7 TraesCS6D01G150300 chr5B 9586188 9586816 628 True 721 721 87.5990 8 626 1 chr5B.!!$R1 618
8 TraesCS6D01G150300 chr1D 90578678 90579312 634 True 671 671 86.0060 3 627 1 chr1D.!!$R1 624
9 TraesCS6D01G150300 chr2D 106137451 106138080 629 True 651 651 85.5560 8 627 1 chr2D.!!$R1 619
10 TraesCS6D01G150300 chr2D 447324461 447325092 631 False 599 599 84.0190 1 622 1 chr2D.!!$F1 621
11 TraesCS6D01G150300 chr3B 422202036 422202664 628 False 638 638 85.2610 8 627 1 chr3B.!!$F1 619
12 TraesCS6D01G150300 chr3B 160031833 160032339 506 True 429 429 82.2490 1 497 1 chr3B.!!$R1 496
13 TraesCS6D01G150300 chr7B 686912413 686913013 600 False 481 481 81.3950 15 605 1 chr7B.!!$F1 590
14 TraesCS6D01G150300 chrUn 303543869 303544498 629 False 477 477 80.6350 4 622 1 chrUn.!!$F1 618
15 TraesCS6D01G150300 chr3D 133282757 133283301 544 False 440 440 81.5360 86 622 1 chr3D.!!$F1 536

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
895 908 0.036858 GCTTCTTCTTCCAGGTCGCT 60.037 55.0 0.00 0.0 0.00 4.93 F
910 923 0.039256 TCGCTGTCTTTGCCATTTGC 60.039 50.0 0.00 0.0 41.77 3.68 F
1942 4175 0.103208 AATGTCAACCCGCGCAAAAA 59.897 45.0 8.75 0.0 0.00 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 4158 1.064946 CTTTTTGCGCGGGTTGACA 59.935 52.632 8.83 0.0 0.00 3.58 R
2475 4730 1.100510 TAGTACACGCAGTAGCCAGG 58.899 55.000 0.00 0.0 41.61 4.45 R
3311 5677 0.039074 CTCGACGTGCAAGAGGTTCT 60.039 55.000 6.65 0.0 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
82 83 0.326927 ACCATGTTTACCTGGTCCCG 59.673 55.000 0.63 0.00 40.16 5.14
129 130 1.135915 GGAGAAGCTCTGATCTTCGCA 59.864 52.381 20.90 0.00 43.40 5.10
239 241 1.046472 ACACGACACCTTCCCTGTGA 61.046 55.000 0.00 0.00 37.18 3.58
252 254 2.040278 TCCCTGTGAGGAGATTGGTTTG 59.960 50.000 0.00 0.00 37.67 2.93
385 388 0.864377 CCATGACGACGACGCGTTAT 60.864 55.000 15.53 14.65 45.72 1.89
450 463 1.265365 GCTTTCAAGACTTGAGCGCTT 59.735 47.619 23.04 0.00 41.38 4.68
594 607 2.158579 ACTTTCCTTTTACCTTCCGCCA 60.159 45.455 0.00 0.00 0.00 5.69
622 635 7.343357 CCCCAATAGAAGTTTCTTACCATACA 58.657 38.462 0.00 0.00 38.70 2.29
633 646 9.745880 AGTTTCTTACCATACAAGTATATGACG 57.254 33.333 0.00 0.00 34.94 4.35
634 647 9.525409 GTTTCTTACCATACAAGTATATGACGT 57.475 33.333 0.00 0.00 34.94 4.34
637 650 9.006839 TCTTACCATACAAGTATATGACGTAGG 57.993 37.037 0.00 0.00 34.94 3.18
638 651 8.922931 TTACCATACAAGTATATGACGTAGGA 57.077 34.615 0.00 0.00 34.94 2.94
639 652 7.211966 ACCATACAAGTATATGACGTAGGAC 57.788 40.000 0.00 0.00 34.94 3.85
640 653 7.002879 ACCATACAAGTATATGACGTAGGACT 58.997 38.462 0.00 0.00 34.94 3.85
641 654 7.504911 ACCATACAAGTATATGACGTAGGACTT 59.495 37.037 0.00 0.00 34.94 3.01
642 655 9.006839 CCATACAAGTATATGACGTAGGACTTA 57.993 37.037 0.00 0.00 34.94 2.24
649 662 8.675504 AGTATATGACGTAGGACTTATATGTGC 58.324 37.037 2.46 2.46 0.00 4.57
650 663 5.784578 ATGACGTAGGACTTATATGTGCA 57.215 39.130 11.91 0.00 0.00 4.57
651 664 5.784578 TGACGTAGGACTTATATGTGCAT 57.215 39.130 11.91 1.73 0.00 3.96
652 665 5.528870 TGACGTAGGACTTATATGTGCATG 58.471 41.667 11.91 6.68 0.00 4.06
653 666 5.300792 TGACGTAGGACTTATATGTGCATGA 59.699 40.000 11.91 0.00 0.00 3.07
654 667 5.529791 ACGTAGGACTTATATGTGCATGAC 58.470 41.667 11.91 6.51 0.00 3.06
655 668 4.617223 CGTAGGACTTATATGTGCATGACG 59.383 45.833 11.91 12.79 0.00 4.35
656 669 3.393800 AGGACTTATATGTGCATGACGC 58.606 45.455 11.91 0.00 42.89 5.19
657 670 2.155732 GGACTTATATGTGCATGACGCG 59.844 50.000 3.53 3.53 46.97 6.01
658 671 2.794910 GACTTATATGTGCATGACGCGT 59.205 45.455 13.85 13.85 46.97 6.01
659 672 2.794910 ACTTATATGTGCATGACGCGTC 59.205 45.455 31.66 31.66 46.97 5.19
660 673 2.793278 TATATGTGCATGACGCGTCT 57.207 45.000 36.27 20.97 46.97 4.18
661 674 2.793278 ATATGTGCATGACGCGTCTA 57.207 45.000 36.27 24.06 46.97 2.59
662 675 2.793278 TATGTGCATGACGCGTCTAT 57.207 45.000 36.27 25.07 46.97 1.98
663 676 1.939974 ATGTGCATGACGCGTCTATT 58.060 45.000 36.27 20.26 46.97 1.73
664 677 1.720805 TGTGCATGACGCGTCTATTT 58.279 45.000 36.27 17.86 46.97 1.40
665 678 2.882324 TGTGCATGACGCGTCTATTTA 58.118 42.857 36.27 19.09 46.97 1.40
666 679 2.857748 TGTGCATGACGCGTCTATTTAG 59.142 45.455 36.27 20.69 46.97 1.85
667 680 1.858458 TGCATGACGCGTCTATTTAGC 59.142 47.619 36.27 27.65 46.97 3.09
668 681 1.858458 GCATGACGCGTCTATTTAGCA 59.142 47.619 36.27 17.45 0.00 3.49
669 682 2.284150 GCATGACGCGTCTATTTAGCAA 59.716 45.455 36.27 16.10 0.00 3.91
670 683 3.242284 GCATGACGCGTCTATTTAGCAAA 60.242 43.478 36.27 15.35 0.00 3.68
671 684 4.726591 GCATGACGCGTCTATTTAGCAAAA 60.727 41.667 36.27 14.82 0.00 2.44
672 685 4.316375 TGACGCGTCTATTTAGCAAAAC 57.684 40.909 36.27 9.26 0.00 2.43
673 686 3.991773 TGACGCGTCTATTTAGCAAAACT 59.008 39.130 36.27 0.00 0.00 2.66
674 687 4.143200 TGACGCGTCTATTTAGCAAAACTG 60.143 41.667 36.27 0.00 0.00 3.16
675 688 3.744426 ACGCGTCTATTTAGCAAAACTGT 59.256 39.130 5.58 0.00 0.00 3.55
676 689 4.212636 ACGCGTCTATTTAGCAAAACTGTT 59.787 37.500 5.58 0.00 0.00 3.16
677 690 5.144359 CGCGTCTATTTAGCAAAACTGTTT 58.856 37.500 0.00 0.00 0.00 2.83
678 691 5.623673 CGCGTCTATTTAGCAAAACTGTTTT 59.376 36.000 12.50 12.50 0.00 2.43
721 734 0.249280 CGTGCCGCACTCATATGGTA 60.249 55.000 20.87 0.00 31.34 3.25
766 779 8.609176 GCACCTAAAATAACTTATCATTGACGA 58.391 33.333 0.00 0.00 0.00 4.20
790 803 3.341857 TTGTACGACAACCAAACATGC 57.658 42.857 0.00 0.00 32.34 4.06
791 804 1.604755 TGTACGACAACCAAACATGCC 59.395 47.619 0.00 0.00 0.00 4.40
799 812 0.779997 ACCAAACATGCCCTTCCTCT 59.220 50.000 0.00 0.00 0.00 3.69
807 820 3.915073 ACATGCCCTTCCTCTATCATCAT 59.085 43.478 0.00 0.00 0.00 2.45
808 821 4.019501 ACATGCCCTTCCTCTATCATCATC 60.020 45.833 0.00 0.00 0.00 2.92
809 822 3.590714 TGCCCTTCCTCTATCATCATCA 58.409 45.455 0.00 0.00 0.00 3.07
810 823 3.581770 TGCCCTTCCTCTATCATCATCAG 59.418 47.826 0.00 0.00 0.00 2.90
851 864 1.123756 GCTACGTGCGTACAACTTCAC 59.876 52.381 4.09 0.00 0.00 3.18
862 875 1.071471 AACTTCACCGGAGCCACAG 59.929 57.895 9.46 0.00 0.00 3.66
865 878 0.537188 CTTCACCGGAGCCACAGTAT 59.463 55.000 9.46 0.00 0.00 2.12
866 879 0.535335 TTCACCGGAGCCACAGTATC 59.465 55.000 9.46 0.00 0.00 2.24
895 908 0.036858 GCTTCTTCTTCCAGGTCGCT 60.037 55.000 0.00 0.00 0.00 4.93
896 909 1.719600 CTTCTTCTTCCAGGTCGCTG 58.280 55.000 0.00 0.00 0.00 5.18
897 910 1.001406 CTTCTTCTTCCAGGTCGCTGT 59.999 52.381 0.00 0.00 0.00 4.40
898 911 0.603569 TCTTCTTCCAGGTCGCTGTC 59.396 55.000 0.00 0.00 0.00 3.51
899 912 0.605589 CTTCTTCCAGGTCGCTGTCT 59.394 55.000 0.00 0.00 0.00 3.41
900 913 1.001406 CTTCTTCCAGGTCGCTGTCTT 59.999 52.381 0.00 0.00 0.00 3.01
901 914 1.048601 TCTTCCAGGTCGCTGTCTTT 58.951 50.000 0.00 0.00 0.00 2.52
902 915 1.151668 CTTCCAGGTCGCTGTCTTTG 58.848 55.000 0.00 0.00 0.00 2.77
903 916 0.884704 TTCCAGGTCGCTGTCTTTGC 60.885 55.000 0.00 0.00 0.00 3.68
904 917 2.328099 CCAGGTCGCTGTCTTTGCC 61.328 63.158 0.00 0.00 0.00 4.52
905 918 1.597854 CAGGTCGCTGTCTTTGCCA 60.598 57.895 0.00 0.00 0.00 4.92
906 919 0.957395 CAGGTCGCTGTCTTTGCCAT 60.957 55.000 0.00 0.00 0.00 4.40
907 920 0.250901 AGGTCGCTGTCTTTGCCATT 60.251 50.000 0.00 0.00 0.00 3.16
908 921 0.598065 GGTCGCTGTCTTTGCCATTT 59.402 50.000 0.00 0.00 0.00 2.32
909 922 1.666888 GGTCGCTGTCTTTGCCATTTG 60.667 52.381 0.00 0.00 0.00 2.32
910 923 0.039256 TCGCTGTCTTTGCCATTTGC 60.039 50.000 0.00 0.00 41.77 3.68
920 933 3.980583 GCCATTTGCATCCTCCATG 57.019 52.632 0.00 0.00 40.77 3.66
930 943 3.444742 TGCATCCTCCATGTTCAAATGTC 59.555 43.478 0.00 0.00 34.56 3.06
954 967 2.519013 GGCACACAAGGAGAAGGAATT 58.481 47.619 0.00 0.00 0.00 2.17
957 970 3.440522 GCACACAAGGAGAAGGAATTACC 59.559 47.826 0.00 0.00 39.35 2.85
1078 1459 4.077184 GCGTCGTGGGGGACATGA 62.077 66.667 0.00 0.00 42.69 3.07
1178 3380 4.742201 GAGGCGCCTGCTCGTCAA 62.742 66.667 38.41 0.00 42.25 3.18
1197 3399 3.587933 GTCGAGAGAGCCGCGGAT 61.588 66.667 33.48 27.37 43.49 4.18
1495 3728 2.504244 GCGGTCTCACGGAGTTCG 60.504 66.667 0.00 0.00 41.61 3.95
1617 3850 2.463876 GTTTTGGAGTTCTTGCTGCAC 58.536 47.619 0.00 0.00 36.57 4.57
1700 3933 3.379445 GGGGAAGACCACGCTCGA 61.379 66.667 0.00 0.00 42.91 4.04
1753 3986 0.249197 CCGCTTCTCGCTGATCATGA 60.249 55.000 0.00 0.00 36.73 3.07
1754 3987 1.564207 CGCTTCTCGCTGATCATGAA 58.436 50.000 0.00 0.00 36.13 2.57
1755 3988 2.133553 CGCTTCTCGCTGATCATGAAT 58.866 47.619 0.00 0.00 36.13 2.57
1837 4070 1.571460 GCACTCTGTTCACGCCAAG 59.429 57.895 0.00 0.00 0.00 3.61
1919 4152 0.765510 AGAGGTTTCTGGCCGTCTTT 59.234 50.000 0.00 0.00 30.72 2.52
1925 4158 2.270352 TTCTGGCCGTCTTTGACAAT 57.730 45.000 0.00 0.00 32.09 2.71
1942 4175 0.103208 AATGTCAACCCGCGCAAAAA 59.897 45.000 8.75 0.00 0.00 1.94
1944 4177 1.357334 GTCAACCCGCGCAAAAAGA 59.643 52.632 8.75 0.00 0.00 2.52
2380 4623 2.903357 GGCTTGCCGATGAGAGGA 59.097 61.111 0.00 0.00 0.00 3.71
2473 4728 0.749091 TGCTGCTGTGCAAGTCTGTT 60.749 50.000 0.00 0.00 40.29 3.16
2474 4729 0.040603 GCTGCTGTGCAAGTCTGTTC 60.041 55.000 0.00 0.00 38.41 3.18
2475 4730 0.590195 CTGCTGTGCAAGTCTGTTCC 59.410 55.000 0.00 0.00 38.41 3.62
2487 4751 1.448540 CTGTTCCCTGGCTACTGCG 60.449 63.158 0.00 0.00 40.82 5.18
2540 4804 6.809196 ACAGAGAGATCAATCAGTAAAACGTC 59.191 38.462 0.00 0.00 0.00 4.34
2556 4821 3.859221 TCCGTCGGACAGTTCCAA 58.141 55.556 10.71 0.00 43.00 3.53
2557 4822 1.364901 TCCGTCGGACAGTTCCAAC 59.635 57.895 10.71 0.00 43.00 3.77
2583 4938 4.859304 AATGCTGCTGTGAAGAAAATCA 57.141 36.364 0.00 0.00 0.00 2.57
2628 4983 2.885135 TCATCCAACTGGCTGAATGT 57.115 45.000 0.00 0.00 37.39 2.71
2639 4997 6.165700 ACTGGCTGAATGTTTTTGAAGAAT 57.834 33.333 0.00 0.00 0.00 2.40
2643 5001 7.218614 TGGCTGAATGTTTTTGAAGAATGAAT 58.781 30.769 0.00 0.00 0.00 2.57
2662 5020 8.674263 AATGAATAAGCACATGGTTTGAAAAA 57.326 26.923 1.05 0.00 37.00 1.94
2836 5202 1.073025 TTCCTTGGCATGCGACAGT 59.927 52.632 12.44 0.00 0.00 3.55
2865 5231 1.525077 GTGGTCCAAACTGCGGTCA 60.525 57.895 0.00 0.00 0.00 4.02
2874 5240 0.454196 AACTGCGGTCACAACCAAAC 59.546 50.000 0.00 0.00 46.86 2.93
2884 5250 3.743396 GTCACAACCAAACAAAGCACAAA 59.257 39.130 0.00 0.00 0.00 2.83
3041 5407 3.305676 GCAAGCTCTCTTCGATATAGCCA 60.306 47.826 0.00 0.00 33.63 4.75
3084 5450 1.255667 CCTCTTGCCTGCAAAGCCAT 61.256 55.000 6.00 0.00 35.33 4.40
3100 5466 6.128472 GCAAAGCCATGGAGAAATAAAAGTTG 60.128 38.462 18.40 3.29 0.00 3.16
3115 5481 4.848562 AAAGTTGCTAGTGGCTAAAACC 57.151 40.909 0.00 0.00 42.39 3.27
3150 5516 5.009010 CAGAAAATGCCTGAAACTGTACAGT 59.991 40.000 22.95 22.95 37.23 3.55
3206 5572 2.366916 AGGCCTCGAATCATCTACAAGG 59.633 50.000 0.00 0.00 0.00 3.61
3215 5581 8.146479 TCGAATCATCTACAAGGAAAATGATG 57.854 34.615 0.00 0.00 37.20 3.07
3224 5590 4.142534 ACAAGGAAAATGATGCATCTGTCG 60.143 41.667 26.32 8.54 0.00 4.35
3225 5591 2.947652 AGGAAAATGATGCATCTGTCGG 59.052 45.455 26.32 0.00 0.00 4.79
3226 5592 2.542411 GGAAAATGATGCATCTGTCGGC 60.542 50.000 26.32 11.75 0.00 5.54
3229 5595 0.534427 ATGATGCATCTGTCGGCAGG 60.534 55.000 26.32 2.63 44.24 4.85
3257 5623 6.458615 CCATGAACGATGTGAAATTGCTATGA 60.459 38.462 0.00 0.00 0.00 2.15
3258 5624 6.493449 TGAACGATGTGAAATTGCTATGAA 57.507 33.333 0.00 0.00 0.00 2.57
3311 5677 3.181329 TGCCAAGAGAAATCCTGTCCTA 58.819 45.455 0.00 0.00 0.00 2.94
3343 5709 0.235144 CGTCGAGTCGAAGTGTCACT 59.765 55.000 18.42 0.00 37.72 3.41
3373 5739 1.016130 CGCCGCTGAACTGATTCACT 61.016 55.000 0.00 0.00 40.01 3.41
3390 5756 1.732809 CACTGTGCTGCATCAGAGAAG 59.267 52.381 27.15 9.09 35.84 2.85
3400 5766 2.418471 GCATCAGAGAAGACAGACAGGG 60.418 54.545 0.00 0.00 0.00 4.45
3409 5775 2.787994 AGACAGACAGGGAAAAGCATG 58.212 47.619 0.00 0.00 0.00 4.06
3431 5797 3.037431 TGAGAGTCAAAGAAGAGCAGC 57.963 47.619 0.00 0.00 0.00 5.25
3438 5804 2.555325 TCAAAGAAGAGCAGCATTGGTG 59.445 45.455 11.46 11.46 34.61 4.17
3440 5806 0.964358 AGAAGAGCAGCATTGGTGGC 60.964 55.000 16.94 9.50 34.61 5.01
3459 5825 3.320256 TGGCACTGAAAATGCAACACATA 59.680 39.130 0.00 0.00 45.27 2.29
3516 5882 6.462552 TGAACAACACATTCAAGGATTCAA 57.537 33.333 0.00 0.00 33.16 2.69
3609 5975 1.618876 TAAATCGCCTTCCCGAGCCA 61.619 55.000 0.00 0.00 40.97 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 2.362397 TGGAGGAAGATGTGATAGCGTC 59.638 50.000 0.00 0.00 0.00 5.19
129 130 5.048013 TGTCGATGCGGATATACAAGAGATT 60.048 40.000 1.92 0.00 0.00 2.40
239 241 7.699878 ACCTTATTCTTACAAACCAATCTCCT 58.300 34.615 0.00 0.00 0.00 3.69
252 254 6.783482 ACTGGATCCCTAGACCTTATTCTTAC 59.217 42.308 9.90 0.00 0.00 2.34
385 388 4.545208 TGGATGATACAGTTTTCACGGA 57.455 40.909 0.00 0.00 0.00 4.69
450 463 4.553323 GCGTGGAGACTTCTAACTAAACA 58.447 43.478 0.00 0.00 0.00 2.83
594 607 5.222254 TGGTAAGAAACTTCTATTGGGGCTT 60.222 40.000 0.00 0.00 36.28 4.35
627 640 6.887626 TGCACATATAAGTCCTACGTCATA 57.112 37.500 0.00 0.00 0.00 2.15
628 641 5.784578 TGCACATATAAGTCCTACGTCAT 57.215 39.130 0.00 0.00 0.00 3.06
629 642 5.300792 TCATGCACATATAAGTCCTACGTCA 59.699 40.000 0.00 0.00 0.00 4.35
630 643 5.629849 GTCATGCACATATAAGTCCTACGTC 59.370 44.000 0.00 0.00 0.00 4.34
631 644 5.529791 GTCATGCACATATAAGTCCTACGT 58.470 41.667 0.00 0.00 0.00 3.57
632 645 4.617223 CGTCATGCACATATAAGTCCTACG 59.383 45.833 0.00 0.00 0.00 3.51
633 646 4.386049 GCGTCATGCACATATAAGTCCTAC 59.614 45.833 0.00 0.00 45.45 3.18
634 647 4.556233 GCGTCATGCACATATAAGTCCTA 58.444 43.478 0.00 0.00 45.45 2.94
635 648 3.393800 GCGTCATGCACATATAAGTCCT 58.606 45.455 0.00 0.00 45.45 3.85
636 649 2.155732 CGCGTCATGCACATATAAGTCC 59.844 50.000 0.00 0.00 46.97 3.85
637 650 2.794910 ACGCGTCATGCACATATAAGTC 59.205 45.455 5.58 0.00 46.97 3.01
638 651 2.794910 GACGCGTCATGCACATATAAGT 59.205 45.455 33.09 0.00 46.97 2.24
639 652 3.052745 AGACGCGTCATGCACATATAAG 58.947 45.455 37.85 0.00 46.97 1.73
640 653 3.092334 AGACGCGTCATGCACATATAA 57.908 42.857 37.85 0.00 46.97 0.98
641 654 2.793278 AGACGCGTCATGCACATATA 57.207 45.000 37.85 0.00 46.97 0.86
642 655 2.793278 TAGACGCGTCATGCACATAT 57.207 45.000 37.85 18.31 46.97 1.78
643 656 2.793278 ATAGACGCGTCATGCACATA 57.207 45.000 37.85 21.24 46.97 2.29
644 657 1.939974 AATAGACGCGTCATGCACAT 58.060 45.000 37.85 19.76 46.97 3.21
645 658 1.720805 AAATAGACGCGTCATGCACA 58.279 45.000 37.85 17.17 46.97 4.57
646 659 2.347661 GCTAAATAGACGCGTCATGCAC 60.348 50.000 37.85 18.39 46.97 4.57
647 660 1.858458 GCTAAATAGACGCGTCATGCA 59.142 47.619 37.85 21.27 46.97 3.96
648 661 1.858458 TGCTAAATAGACGCGTCATGC 59.142 47.619 37.85 28.23 41.47 4.06
649 662 4.514545 TTTGCTAAATAGACGCGTCATG 57.485 40.909 37.85 21.27 0.00 3.07
650 663 4.630069 AGTTTTGCTAAATAGACGCGTCAT 59.370 37.500 37.85 25.71 0.00 3.06
651 664 3.991773 AGTTTTGCTAAATAGACGCGTCA 59.008 39.130 37.85 24.72 0.00 4.35
652 665 4.143179 ACAGTTTTGCTAAATAGACGCGTC 60.143 41.667 31.30 31.30 0.00 5.19
653 666 3.744426 ACAGTTTTGCTAAATAGACGCGT 59.256 39.130 13.85 13.85 0.00 6.01
654 667 4.322101 ACAGTTTTGCTAAATAGACGCG 57.678 40.909 3.53 3.53 0.00 6.01
655 668 6.986424 AAAACAGTTTTGCTAAATAGACGC 57.014 33.333 10.62 0.00 0.00 5.19
656 669 8.782533 AGAAAAACAGTTTTGCTAAATAGACG 57.217 30.769 16.71 0.00 36.75 4.18
661 674 9.599866 AGCTTAAGAAAAACAGTTTTGCTAAAT 57.400 25.926 18.26 7.10 37.54 1.40
662 675 8.868916 CAGCTTAAGAAAAACAGTTTTGCTAAA 58.131 29.630 18.26 8.32 37.54 1.85
663 676 7.491048 CCAGCTTAAGAAAAACAGTTTTGCTAA 59.509 33.333 18.26 11.97 37.54 3.09
664 677 6.978080 CCAGCTTAAGAAAAACAGTTTTGCTA 59.022 34.615 18.26 4.64 37.54 3.49
665 678 5.812127 CCAGCTTAAGAAAAACAGTTTTGCT 59.188 36.000 13.00 13.00 40.27 3.91
666 679 5.502382 GCCAGCTTAAGAAAAACAGTTTTGC 60.502 40.000 12.13 10.32 37.07 3.68
667 680 5.812127 AGCCAGCTTAAGAAAAACAGTTTTG 59.188 36.000 12.13 0.05 37.07 2.44
668 681 5.977635 AGCCAGCTTAAGAAAAACAGTTTT 58.022 33.333 6.67 5.37 39.70 2.43
669 682 5.127031 TGAGCCAGCTTAAGAAAAACAGTTT 59.873 36.000 6.67 0.00 0.00 2.66
670 683 4.644685 TGAGCCAGCTTAAGAAAAACAGTT 59.355 37.500 6.67 0.00 0.00 3.16
671 684 4.036852 GTGAGCCAGCTTAAGAAAAACAGT 59.963 41.667 6.67 0.00 0.00 3.55
672 685 4.540824 GTGAGCCAGCTTAAGAAAAACAG 58.459 43.478 6.67 0.00 0.00 3.16
673 686 3.003275 CGTGAGCCAGCTTAAGAAAAACA 59.997 43.478 6.67 0.00 0.00 2.83
674 687 3.003378 ACGTGAGCCAGCTTAAGAAAAAC 59.997 43.478 6.67 0.00 0.00 2.43
675 688 3.211045 ACGTGAGCCAGCTTAAGAAAAA 58.789 40.909 6.67 0.00 0.00 1.94
676 689 2.846193 ACGTGAGCCAGCTTAAGAAAA 58.154 42.857 6.67 0.00 0.00 2.29
677 690 2.543777 ACGTGAGCCAGCTTAAGAAA 57.456 45.000 6.67 0.00 0.00 2.52
678 691 2.561419 ACTACGTGAGCCAGCTTAAGAA 59.439 45.455 6.67 0.00 0.00 2.52
684 697 1.587054 GTGACTACGTGAGCCAGCT 59.413 57.895 0.00 0.00 0.00 4.24
704 717 0.249280 CGTACCATATGAGTGCGGCA 60.249 55.000 19.46 0.00 39.29 5.69
721 734 0.586319 CACTTCGCCATGTTTGTCGT 59.414 50.000 0.00 0.00 0.00 4.34
787 800 4.173594 TGATGATGATAGAGGAAGGGCAT 58.826 43.478 0.00 0.00 0.00 4.40
788 801 3.581770 CTGATGATGATAGAGGAAGGGCA 59.418 47.826 0.00 0.00 0.00 5.36
789 802 3.582208 ACTGATGATGATAGAGGAAGGGC 59.418 47.826 0.00 0.00 0.00 5.19
790 803 5.822132 AACTGATGATGATAGAGGAAGGG 57.178 43.478 0.00 0.00 0.00 3.95
791 804 9.217278 CATTAAACTGATGATGATAGAGGAAGG 57.783 37.037 0.00 0.00 0.00 3.46
807 820 4.093703 CGCCGGTAAACATCATTAAACTGA 59.906 41.667 1.90 0.00 0.00 3.41
808 821 4.339429 CGCCGGTAAACATCATTAAACTG 58.661 43.478 1.90 0.00 0.00 3.16
809 822 3.375922 CCGCCGGTAAACATCATTAAACT 59.624 43.478 1.90 0.00 0.00 2.66
810 823 3.687200 CCGCCGGTAAACATCATTAAAC 58.313 45.455 1.90 0.00 0.00 2.01
821 834 2.125991 CACGTAGCCGCCGGTAAA 60.126 61.111 4.45 0.00 37.70 2.01
851 864 1.101635 TCTCGATACTGTGGCTCCGG 61.102 60.000 0.00 0.00 0.00 5.14
889 902 0.598065 AAATGGCAAAGACAGCGACC 59.402 50.000 0.00 0.00 0.00 4.79
902 915 1.117150 ACATGGAGGATGCAAATGGC 58.883 50.000 0.00 0.00 42.43 4.40
903 916 2.761767 TGAACATGGAGGATGCAAATGG 59.238 45.455 0.00 0.00 42.43 3.16
904 917 4.459390 TTGAACATGGAGGATGCAAATG 57.541 40.909 0.00 0.00 42.43 2.32
905 918 5.046159 ACATTTGAACATGGAGGATGCAAAT 60.046 36.000 0.00 0.00 42.43 2.32
906 919 4.283978 ACATTTGAACATGGAGGATGCAAA 59.716 37.500 0.00 0.00 42.43 3.68
907 920 3.833650 ACATTTGAACATGGAGGATGCAA 59.166 39.130 0.00 0.00 42.43 4.08
908 921 3.433343 ACATTTGAACATGGAGGATGCA 58.567 40.909 0.00 0.00 44.23 3.96
909 922 3.444742 TGACATTTGAACATGGAGGATGC 59.555 43.478 0.00 0.00 35.15 3.91
910 923 4.437794 CGTGACATTTGAACATGGAGGATG 60.438 45.833 0.00 0.00 38.15 3.51
911 924 3.691118 CGTGACATTTGAACATGGAGGAT 59.309 43.478 0.00 0.00 0.00 3.24
912 925 3.073678 CGTGACATTTGAACATGGAGGA 58.926 45.455 0.00 0.00 0.00 3.71
913 926 2.162208 CCGTGACATTTGAACATGGAGG 59.838 50.000 0.00 0.00 41.55 4.30
914 927 2.162208 CCCGTGACATTTGAACATGGAG 59.838 50.000 16.13 7.76 41.55 3.86
915 928 2.158559 CCCGTGACATTTGAACATGGA 58.841 47.619 16.13 0.00 41.55 3.41
916 929 1.402720 GCCCGTGACATTTGAACATGG 60.403 52.381 0.00 0.00 39.54 3.66
917 930 1.269174 TGCCCGTGACATTTGAACATG 59.731 47.619 0.00 0.00 0.00 3.21
918 931 1.269448 GTGCCCGTGACATTTGAACAT 59.731 47.619 0.00 0.00 0.00 2.71
919 932 0.665835 GTGCCCGTGACATTTGAACA 59.334 50.000 0.00 0.00 0.00 3.18
920 933 0.665835 TGTGCCCGTGACATTTGAAC 59.334 50.000 0.00 0.00 0.00 3.18
930 943 1.227823 TTCTCCTTGTGTGCCCGTG 60.228 57.895 0.00 0.00 0.00 4.94
954 967 3.006756 GCAGCTCAGTGCCTCGGTA 62.007 63.158 0.00 0.00 44.23 4.02
957 970 2.508887 GAGCAGCTCAGTGCCTCG 60.509 66.667 18.17 0.00 45.20 4.63
1488 3721 1.975363 GCAGCAGCATGACGAACTCC 61.975 60.000 0.00 0.00 39.69 3.85
1617 3850 4.933064 GGCTCGCCCTCGTCATCG 62.933 72.222 0.00 0.00 36.96 3.84
1753 3986 6.238953 GCAATGGAAGTCTAGCATCATGAATT 60.239 38.462 0.00 0.00 0.00 2.17
1754 3987 5.241064 GCAATGGAAGTCTAGCATCATGAAT 59.759 40.000 0.00 0.00 0.00 2.57
1755 3988 4.577693 GCAATGGAAGTCTAGCATCATGAA 59.422 41.667 0.00 0.00 0.00 2.57
1821 4054 4.049393 GCTTGGCGTGAACAGAGT 57.951 55.556 0.00 0.00 0.00 3.24
1837 4070 4.577246 CGGAGAGGCTAGTGGCGC 62.577 72.222 0.00 0.00 44.18 6.53
1877 4110 1.513158 GTGCAGCTTCCGCTCTAGA 59.487 57.895 0.00 0.00 45.15 2.43
1894 4127 2.593956 GCCAGAAACCTCTCCCCGT 61.594 63.158 0.00 0.00 0.00 5.28
1898 4131 1.079057 GACGGCCAGAAACCTCTCC 60.079 63.158 2.24 0.00 0.00 3.71
1919 4152 2.612567 GCGCGGGTTGACATTGTCA 61.613 57.895 15.41 15.41 41.09 3.58
1925 4158 1.064946 CTTTTTGCGCGGGTTGACA 59.935 52.632 8.83 0.00 0.00 3.58
1942 4175 2.267681 GATCGCGTCGACCACCTTCT 62.268 60.000 10.58 0.00 39.18 2.85
1944 4177 1.945354 ATGATCGCGTCGACCACCTT 61.945 55.000 10.58 0.00 39.18 3.50
2367 4610 1.377366 GACGAGTCCTCTCATCGGCA 61.377 60.000 0.00 0.00 43.93 5.69
2380 4623 1.404315 GCTTCTTGGATTCCGACGAGT 60.404 52.381 0.00 0.00 0.00 4.18
2473 4728 1.304630 TACACGCAGTAGCCAGGGA 60.305 57.895 0.00 0.00 41.61 4.20
2474 4729 1.153628 GTACACGCAGTAGCCAGGG 60.154 63.158 0.00 0.00 41.61 4.45
2475 4730 1.100510 TAGTACACGCAGTAGCCAGG 58.899 55.000 0.00 0.00 41.61 4.45
2540 4804 3.946907 GTTGGAACTGTCCGACGG 58.053 61.111 7.84 7.84 46.35 4.79
2556 4821 4.212143 TCTTCACAGCAGCATTATCAGT 57.788 40.909 0.00 0.00 0.00 3.41
2557 4822 5.556355 TTTCTTCACAGCAGCATTATCAG 57.444 39.130 0.00 0.00 0.00 2.90
2563 4918 5.168569 CAATGATTTTCTTCACAGCAGCAT 58.831 37.500 0.00 0.00 0.00 3.79
2569 4924 6.921857 AGAAAGCACAATGATTTTCTTCACAG 59.078 34.615 0.00 0.00 35.96 3.66
2583 4938 7.856415 AGGTATAGAAGAGAAGAAAGCACAAT 58.144 34.615 0.00 0.00 0.00 2.71
2628 4983 8.149647 ACCATGTGCTTATTCATTCTTCAAAAA 58.850 29.630 0.00 0.00 0.00 1.94
2865 5231 5.471456 TCATTTTTGTGCTTTGTTTGGTTGT 59.529 32.000 0.00 0.00 0.00 3.32
2874 5240 7.631822 TGATTTGTGATCATTTTTGTGCTTTG 58.368 30.769 0.00 0.00 0.00 2.77
2884 5250 9.767228 TTGTTTTCTGATGATTTGTGATCATTT 57.233 25.926 0.00 0.00 38.73 2.32
3029 5395 3.071023 CCCCTGAAGTTGGCTATATCGAA 59.929 47.826 0.00 0.00 0.00 3.71
3041 5407 1.840635 GCTCTGATACCCCCTGAAGTT 59.159 52.381 0.00 0.00 0.00 2.66
3084 5450 5.183140 GCCACTAGCAACTTTTATTTCTCCA 59.817 40.000 0.00 0.00 42.97 3.86
3100 5466 4.519350 AGTTTTCTGGTTTTAGCCACTAGC 59.481 41.667 0.00 0.00 44.25 3.42
3206 5572 2.097954 TGCCGACAGATGCATCATTTTC 59.902 45.455 27.81 15.92 31.31 2.29
3225 5591 0.745845 ACATCGTTCATGGCTCCTGC 60.746 55.000 0.00 0.00 36.72 4.85
3226 5592 1.012086 CACATCGTTCATGGCTCCTG 58.988 55.000 0.00 0.00 36.72 3.86
3229 5595 4.100529 CAATTTCACATCGTTCATGGCTC 58.899 43.478 0.00 0.00 36.72 4.70
3236 5602 7.795431 TTTTCATAGCAATTTCACATCGTTC 57.205 32.000 0.00 0.00 0.00 3.95
3239 5605 6.808212 AGGTTTTTCATAGCAATTTCACATCG 59.192 34.615 0.00 0.00 0.00 3.84
3311 5677 0.039074 CTCGACGTGCAAGAGGTTCT 60.039 55.000 6.65 0.00 0.00 3.01
3373 5739 1.345415 TGTCTTCTCTGATGCAGCACA 59.655 47.619 0.00 0.00 0.00 4.57
3390 5756 2.783135 TCATGCTTTTCCCTGTCTGTC 58.217 47.619 0.00 0.00 0.00 3.51
3400 5766 6.492007 TCTTTGACTCTCATCATGCTTTTC 57.508 37.500 0.00 0.00 0.00 2.29
3409 5775 3.618150 GCTGCTCTTCTTTGACTCTCATC 59.382 47.826 0.00 0.00 0.00 2.92
3431 5797 2.070783 GCATTTTCAGTGCCACCAATG 58.929 47.619 0.00 0.00 38.34 2.82
3438 5804 2.222007 TGTGTTGCATTTTCAGTGCC 57.778 45.000 0.00 0.00 41.83 5.01
3440 5806 7.275999 TGCATATTATGTGTTGCATTTTCAGTG 59.724 33.333 5.60 0.00 39.98 3.66
3504 5870 4.151121 TGCCATTGACTTGAATCCTTGAA 58.849 39.130 0.00 0.00 0.00 2.69
3516 5882 4.217118 GTCAAGAGAACATTGCCATTGACT 59.783 41.667 7.67 0.00 40.98 3.41


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

AutoCloner maintained by Alex Coulton.