Multiple sequence alignment - TraesCS2B01G419900

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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 TraesCS2B01G419900 chr2B 100.000 2606 0 0 1 2606 601391952 601389347 0.000000e+00 4813.0
1 TraesCS2B01G419900 chr2B 95.420 917 36 3 1692 2606 692103642 692102730 0.000000e+00 1456.0
2 TraesCS2B01G419900 chr2B 96.667 60 2 0 758 817 154838682 154838741 1.650000e-17 100.0
3 TraesCS2B01G419900 chr2A 95.972 869 19 6 845 1700 655288215 655287350 0.000000e+00 1397.0
4 TraesCS2B01G419900 chr2D 95.745 846 17 3 863 1700 512099372 512098538 0.000000e+00 1345.0
5 TraesCS2B01G419900 chr2D 85.482 923 119 7 1693 2606 446656812 446657728 0.000000e+00 948.0
6 TraesCS2B01G419900 chr2D 87.994 708 77 8 1 703 110021998 110022702 0.000000e+00 830.0
7 TraesCS2B01G419900 chr2D 86.629 703 81 11 7 698 577614662 577613962 0.000000e+00 765.0
8 TraesCS2B01G419900 chr2D 94.366 71 3 1 747 817 636546176 636546245 9.860000e-20 108.0
9 TraesCS2B01G419900 chr3B 91.304 782 59 6 1827 2606 782474944 782474170 0.000000e+00 1059.0
10 TraesCS2B01G419900 chr3B 84.404 109 13 4 1684 1790 460326591 460326485 1.280000e-18 104.0
11 TraesCS2B01G419900 chr3B 84.404 109 13 4 1684 1790 460332391 460332285 1.280000e-18 104.0
12 TraesCS2B01G419900 chr5A 87.216 923 105 8 1693 2606 651550281 651549363 0.000000e+00 1038.0
13 TraesCS2B01G419900 chr5A 87.166 787 90 5 1692 2469 578085374 578084590 0.000000e+00 883.0
14 TraesCS2B01G419900 chr5A 91.892 74 4 1 747 820 355188249 355188178 4.590000e-18 102.0
15 TraesCS2B01G419900 chr5A 90.789 76 6 1 745 820 422040536 422040462 1.650000e-17 100.0
16 TraesCS2B01G419900 chr7A 85.049 923 121 9 1692 2606 14418428 14417515 0.000000e+00 924.0
17 TraesCS2B01G419900 chr7D 84.845 937 110 12 1693 2606 63410104 63411031 0.000000e+00 915.0
18 TraesCS2B01G419900 chr7D 87.429 700 77 9 10 703 135440521 135439827 0.000000e+00 795.0
19 TraesCS2B01G419900 chrUn 87.310 788 88 6 1692 2469 259780093 259780878 0.000000e+00 891.0
20 TraesCS2B01G419900 chr6D 88.873 710 70 9 1 703 6830614 6831321 0.000000e+00 865.0
21 TraesCS2B01G419900 chr6D 88.575 709 70 8 1 703 431451245 431450542 0.000000e+00 850.0
22 TraesCS2B01G419900 chr6D 87.447 701 79 6 7 703 311897878 311898573 0.000000e+00 798.0
23 TraesCS2B01G419900 chr6D 97.778 45 1 0 845 889 459268041 459268085 7.730000e-11 78.7
24 TraesCS2B01G419900 chr3D 88.235 697 77 5 10 703 400750477 400749783 0.000000e+00 828.0
25 TraesCS2B01G419900 chr3D 87.037 702 79 10 10 703 5389537 5388840 0.000000e+00 782.0
26 TraesCS2B01G419900 chr3D 95.775 71 2 1 747 817 426160539 426160608 2.120000e-21 113.0
27 TraesCS2B01G419900 chr3A 87.536 698 81 6 10 703 520447309 520446614 0.000000e+00 802.0
28 TraesCS2B01G419900 chr4D 80.682 440 69 12 1695 2129 248920363 248920791 6.950000e-86 327.0
29 TraesCS2B01G419900 chr4B 79.684 443 71 12 1695 2129 252001433 252001864 4.210000e-78 302.0
30 TraesCS2B01G419900 chr7B 84.512 297 43 3 2023 2318 525884475 525884181 9.120000e-75 291.0
31 TraesCS2B01G419900 chr5B 90.789 76 6 1 745 820 375943502 375943428 1.650000e-17 100.0
32 TraesCS2B01G419900 chr5B 94.030 67 2 2 745 811 681660188 681660252 1.650000e-17 100.0
33 TraesCS2B01G419900 chr1B 93.939 66 2 2 751 816 60129899 60129836 5.940000e-17 99.0
34 TraesCS2B01G419900 chr5D 88.158 76 8 1 745 820 324411741 324411667 3.570000e-14 89.8
35 TraesCS2B01G419900 chr6B 97.778 45 1 0 845 889 667784366 667784410 7.730000e-11 78.7


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 TraesCS2B01G419900 chr2B 601389347 601391952 2605 True 4813 4813 100.000 1 2606 1 chr2B.!!$R1 2605
1 TraesCS2B01G419900 chr2B 692102730 692103642 912 True 1456 1456 95.420 1692 2606 1 chr2B.!!$R2 914
2 TraesCS2B01G419900 chr2A 655287350 655288215 865 True 1397 1397 95.972 845 1700 1 chr2A.!!$R1 855
3 TraesCS2B01G419900 chr2D 512098538 512099372 834 True 1345 1345 95.745 863 1700 1 chr2D.!!$R1 837
4 TraesCS2B01G419900 chr2D 446656812 446657728 916 False 948 948 85.482 1693 2606 1 chr2D.!!$F2 913
5 TraesCS2B01G419900 chr2D 110021998 110022702 704 False 830 830 87.994 1 703 1 chr2D.!!$F1 702
6 TraesCS2B01G419900 chr2D 577613962 577614662 700 True 765 765 86.629 7 698 1 chr2D.!!$R2 691
7 TraesCS2B01G419900 chr3B 782474170 782474944 774 True 1059 1059 91.304 1827 2606 1 chr3B.!!$R3 779
8 TraesCS2B01G419900 chr5A 651549363 651550281 918 True 1038 1038 87.216 1693 2606 1 chr5A.!!$R4 913
9 TraesCS2B01G419900 chr5A 578084590 578085374 784 True 883 883 87.166 1692 2469 1 chr5A.!!$R3 777
10 TraesCS2B01G419900 chr7A 14417515 14418428 913 True 924 924 85.049 1692 2606 1 chr7A.!!$R1 914
11 TraesCS2B01G419900 chr7D 63410104 63411031 927 False 915 915 84.845 1693 2606 1 chr7D.!!$F1 913
12 TraesCS2B01G419900 chr7D 135439827 135440521 694 True 795 795 87.429 10 703 1 chr7D.!!$R1 693
13 TraesCS2B01G419900 chrUn 259780093 259780878 785 False 891 891 87.310 1692 2469 1 chrUn.!!$F1 777
14 TraesCS2B01G419900 chr6D 6830614 6831321 707 False 865 865 88.873 1 703 1 chr6D.!!$F1 702
15 TraesCS2B01G419900 chr6D 431450542 431451245 703 True 850 850 88.575 1 703 1 chr6D.!!$R1 702
16 TraesCS2B01G419900 chr6D 311897878 311898573 695 False 798 798 87.447 7 703 1 chr6D.!!$F2 696
17 TraesCS2B01G419900 chr3D 400749783 400750477 694 True 828 828 88.235 10 703 1 chr3D.!!$R2 693
18 TraesCS2B01G419900 chr3D 5388840 5389537 697 True 782 782 87.037 10 703 1 chr3D.!!$R1 693
19 TraesCS2B01G419900 chr3A 520446614 520447309 695 True 802 802 87.536 10 703 1 chr3A.!!$R1 693

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
733 754 0.038159 GCTAGCTAGGTATGCGGGTG 60.038 60.0 22.1 0.0 35.28 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 2002 0.318762 CCCGACCTGCTATAAGAGGC 59.681 60.0 0.0 0.0 31.9 4.7 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
39 40 3.204827 GCACCACCATAGCAGCCG 61.205 66.667 0.00 0.00 0.00 5.52
90 94 4.872485 GAGCTCGACGCGACTCCG 62.872 72.222 15.93 10.89 45.59 4.63
112 119 0.930310 GCTGATATGCGACTTTGCGA 59.070 50.000 0.00 0.00 37.81 5.10
163 171 3.063452 CCATTACCGTTGAACGAATCAGG 59.937 47.826 20.47 11.20 46.05 3.86
186 194 2.028484 GCAACACTCCGGACACGA 59.972 61.111 0.00 0.00 44.60 4.35
210 218 1.268794 CGAACTCCAGATCTAGCACCG 60.269 57.143 0.00 0.00 0.00 4.94
282 290 1.227853 GAGCCCAACACACGTTCCT 60.228 57.895 0.00 0.00 31.13 3.36
337 345 0.106619 ATCCGCTCCTCGACTACCTT 60.107 55.000 0.00 0.00 41.67 3.50
345 353 1.550976 CCTCGACTACCTTCCAAGCTT 59.449 52.381 0.00 0.00 0.00 3.74
366 374 2.125512 GCCGACGTTGGAGCAGAT 60.126 61.111 26.69 0.00 0.00 2.90
396 405 1.157276 AGTGGAGCCTGAGGACACT 59.843 57.895 15.20 15.20 37.55 3.55
406 417 0.468226 TGAGGACACTTCCACCACAC 59.532 55.000 0.00 0.00 45.72 3.82
438 452 2.344500 CCACAACGTCCCCGCTTA 59.656 61.111 0.00 0.00 37.70 3.09
579 593 3.895656 GGTCCAAAACCCTAAGCTTCTTT 59.104 43.478 0.00 0.00 42.85 2.52
590 605 5.773176 CCCTAAGCTTCTTTGACCCTAAAAA 59.227 40.000 0.00 0.00 0.00 1.94
613 629 5.548406 ACTAAAGCTAAAACGATCCACACT 58.452 37.500 0.00 0.00 0.00 3.55
621 637 2.202756 GATCCACACTCGCGGGAC 60.203 66.667 15.95 0.00 32.60 4.46
642 660 4.567597 ACGACCCCCTCACCACCA 62.568 66.667 0.00 0.00 0.00 4.17
648 666 2.516888 CCCCTCACCACCAACGACT 61.517 63.158 0.00 0.00 0.00 4.18
705 726 3.452786 CGAGAAGGAGCGGCTGGA 61.453 66.667 7.50 0.00 0.00 3.86
706 727 2.498726 GAGAAGGAGCGGCTGGAG 59.501 66.667 7.50 0.00 0.00 3.86
707 728 2.284258 AGAAGGAGCGGCTGGAGT 60.284 61.111 7.50 0.00 0.00 3.85
708 729 1.893919 GAGAAGGAGCGGCTGGAGTT 61.894 60.000 7.50 0.00 0.00 3.01
709 730 1.003233 GAAGGAGCGGCTGGAGTTT 60.003 57.895 7.50 0.00 0.00 2.66
710 731 1.301677 GAAGGAGCGGCTGGAGTTTG 61.302 60.000 7.50 0.00 0.00 2.93
711 732 2.032681 GGAGCGGCTGGAGTTTGT 59.967 61.111 7.50 0.00 0.00 2.83
712 733 1.600916 GGAGCGGCTGGAGTTTGTT 60.601 57.895 7.50 0.00 0.00 2.83
713 734 1.576421 GAGCGGCTGGAGTTTGTTG 59.424 57.895 7.50 0.00 0.00 3.33
714 735 1.856265 GAGCGGCTGGAGTTTGTTGG 61.856 60.000 7.50 0.00 0.00 3.77
715 736 2.644992 CGGCTGGAGTTTGTTGGC 59.355 61.111 0.00 0.00 0.00 4.52
716 737 1.898574 CGGCTGGAGTTTGTTGGCT 60.899 57.895 0.00 0.00 0.00 4.75
717 738 0.605319 CGGCTGGAGTTTGTTGGCTA 60.605 55.000 0.00 0.00 0.00 3.93
718 739 1.168714 GGCTGGAGTTTGTTGGCTAG 58.831 55.000 0.00 0.00 0.00 3.42
719 740 0.523519 GCTGGAGTTTGTTGGCTAGC 59.476 55.000 6.04 6.04 0.00 3.42
720 741 1.884067 GCTGGAGTTTGTTGGCTAGCT 60.884 52.381 15.72 0.00 0.00 3.32
721 742 2.615493 GCTGGAGTTTGTTGGCTAGCTA 60.615 50.000 15.72 5.44 0.00 3.32
722 743 3.265791 CTGGAGTTTGTTGGCTAGCTAG 58.734 50.000 16.84 16.84 0.00 3.42
723 744 2.027192 TGGAGTTTGTTGGCTAGCTAGG 60.027 50.000 22.10 4.48 0.00 3.02
724 745 2.027100 GGAGTTTGTTGGCTAGCTAGGT 60.027 50.000 22.10 0.00 0.00 3.08
725 746 3.197116 GGAGTTTGTTGGCTAGCTAGGTA 59.803 47.826 22.10 0.99 0.00 3.08
726 747 4.141688 GGAGTTTGTTGGCTAGCTAGGTAT 60.142 45.833 22.10 0.00 0.00 2.73
727 748 4.770795 AGTTTGTTGGCTAGCTAGGTATG 58.229 43.478 22.10 0.00 0.00 2.39
728 749 2.910688 TGTTGGCTAGCTAGGTATGC 57.089 50.000 22.10 8.09 0.00 3.14
729 750 1.068588 TGTTGGCTAGCTAGGTATGCG 59.931 52.381 22.10 0.00 35.28 4.73
730 751 0.679505 TTGGCTAGCTAGGTATGCGG 59.320 55.000 22.10 0.00 35.28 5.69
731 752 1.185618 TGGCTAGCTAGGTATGCGGG 61.186 60.000 22.10 0.00 35.28 6.13
732 753 1.186267 GGCTAGCTAGGTATGCGGGT 61.186 60.000 22.10 0.00 35.28 5.28
733 754 0.038159 GCTAGCTAGGTATGCGGGTG 60.038 60.000 22.10 0.00 35.28 4.61
734 755 1.329256 CTAGCTAGGTATGCGGGTGT 58.671 55.000 13.32 0.00 35.28 4.16
735 756 1.687123 CTAGCTAGGTATGCGGGTGTT 59.313 52.381 13.32 0.00 35.28 3.32
736 757 0.464452 AGCTAGGTATGCGGGTGTTC 59.536 55.000 0.00 0.00 35.28 3.18
737 758 0.532196 GCTAGGTATGCGGGTGTTCC 60.532 60.000 0.00 0.00 0.00 3.62
755 776 3.267974 GGTAAGTCCGTCGGTCGT 58.732 61.111 11.88 6.68 37.94 4.34
756 777 1.581447 GGTAAGTCCGTCGGTCGTT 59.419 57.895 11.88 6.01 37.94 3.85
757 778 0.039165 GGTAAGTCCGTCGGTCGTTT 60.039 55.000 11.88 4.59 37.94 3.60
758 779 1.602920 GGTAAGTCCGTCGGTCGTTTT 60.603 52.381 11.88 0.00 37.94 2.43
759 780 2.127251 GTAAGTCCGTCGGTCGTTTTT 58.873 47.619 11.88 0.00 37.94 1.94
782 803 9.520204 TTTTTCTTTCTAGCTCAAAATCAAGTG 57.480 29.630 0.00 0.00 0.00 3.16
783 804 7.807977 TTCTTTCTAGCTCAAAATCAAGTGT 57.192 32.000 0.00 0.00 0.00 3.55
784 805 7.194607 TCTTTCTAGCTCAAAATCAAGTGTG 57.805 36.000 0.00 0.00 0.00 3.82
785 806 5.947228 TTCTAGCTCAAAATCAAGTGTGG 57.053 39.130 0.00 0.00 0.00 4.17
786 807 3.753272 TCTAGCTCAAAATCAAGTGTGGC 59.247 43.478 0.00 0.00 0.00 5.01
787 808 1.615392 AGCTCAAAATCAAGTGTGGCC 59.385 47.619 0.00 0.00 0.00 5.36
788 809 1.666888 GCTCAAAATCAAGTGTGGCCG 60.667 52.381 0.00 0.00 0.00 6.13
789 810 0.958091 TCAAAATCAAGTGTGGCCGG 59.042 50.000 0.00 0.00 0.00 6.13
790 811 0.673437 CAAAATCAAGTGTGGCCGGT 59.327 50.000 1.90 0.00 0.00 5.28
791 812 1.883275 CAAAATCAAGTGTGGCCGGTA 59.117 47.619 1.90 0.00 0.00 4.02
792 813 2.491693 CAAAATCAAGTGTGGCCGGTAT 59.508 45.455 1.90 0.00 0.00 2.73
793 814 2.507407 AATCAAGTGTGGCCGGTATT 57.493 45.000 1.90 0.00 0.00 1.89
794 815 3.637911 AATCAAGTGTGGCCGGTATTA 57.362 42.857 1.90 0.00 0.00 0.98
795 816 3.857157 ATCAAGTGTGGCCGGTATTAT 57.143 42.857 1.90 0.00 0.00 1.28
796 817 4.967084 ATCAAGTGTGGCCGGTATTATA 57.033 40.909 1.90 0.00 0.00 0.98
797 818 4.062677 TCAAGTGTGGCCGGTATTATAC 57.937 45.455 1.90 0.00 0.00 1.47
798 819 3.451540 TCAAGTGTGGCCGGTATTATACA 59.548 43.478 1.90 0.00 0.00 2.29
799 820 3.464111 AGTGTGGCCGGTATTATACAC 57.536 47.619 1.90 9.99 38.84 2.90
800 821 2.103601 AGTGTGGCCGGTATTATACACC 59.896 50.000 13.41 3.49 39.24 4.16
801 822 2.103601 GTGTGGCCGGTATTATACACCT 59.896 50.000 1.90 0.00 34.05 4.00
802 823 2.103432 TGTGGCCGGTATTATACACCTG 59.897 50.000 1.90 0.00 33.62 4.00
803 824 2.103601 GTGGCCGGTATTATACACCTGT 59.896 50.000 1.90 0.00 33.62 4.00
804 825 3.321682 GTGGCCGGTATTATACACCTGTA 59.678 47.826 1.90 0.00 33.62 2.74
805 826 3.966006 TGGCCGGTATTATACACCTGTAA 59.034 43.478 1.90 0.00 33.76 2.41
806 827 4.408270 TGGCCGGTATTATACACCTGTAAA 59.592 41.667 1.90 0.00 33.76 2.01
807 828 5.104610 TGGCCGGTATTATACACCTGTAAAA 60.105 40.000 1.90 0.00 33.76 1.52
808 829 5.999600 GGCCGGTATTATACACCTGTAAAAT 59.000 40.000 1.90 0.00 33.76 1.82
809 830 7.160726 GGCCGGTATTATACACCTGTAAAATA 58.839 38.462 1.90 0.00 33.76 1.40
810 831 7.661027 GGCCGGTATTATACACCTGTAAAATAA 59.339 37.037 1.90 0.00 33.76 1.40
811 832 9.054922 GCCGGTATTATACACCTGTAAAATAAA 57.945 33.333 1.90 0.00 33.76 1.40
821 842 8.574251 ACACCTGTAAAATAAATACAGATGCA 57.426 30.769 13.69 0.00 45.14 3.96
822 843 8.458843 ACACCTGTAAAATAAATACAGATGCAC 58.541 33.333 13.69 0.00 45.14 4.57
827 848 9.767684 TGTAAAATAAATACAGATGCACTTTCG 57.232 29.630 0.00 0.00 0.00 3.46
828 849 9.982291 GTAAAATAAATACAGATGCACTTTCGA 57.018 29.630 0.00 0.00 0.00 3.71
830 851 7.849804 AATAAATACAGATGCACTTTCGAGT 57.150 32.000 0.00 0.00 0.00 4.18
831 852 8.942338 AATAAATACAGATGCACTTTCGAGTA 57.058 30.769 0.00 0.00 0.00 2.59
832 853 9.547753 AATAAATACAGATGCACTTTCGAGTAT 57.452 29.630 0.00 0.00 0.00 2.12
833 854 6.834959 AATACAGATGCACTTTCGAGTATG 57.165 37.500 0.00 0.00 0.00 2.39
834 855 4.193826 ACAGATGCACTTTCGAGTATGT 57.806 40.909 0.00 0.00 0.00 2.29
835 856 5.324784 ACAGATGCACTTTCGAGTATGTA 57.675 39.130 0.00 0.00 0.00 2.29
836 857 5.907207 ACAGATGCACTTTCGAGTATGTAT 58.093 37.500 0.00 0.00 0.00 2.29
837 858 6.341316 ACAGATGCACTTTCGAGTATGTATT 58.659 36.000 0.00 0.00 0.00 1.89
838 859 6.818644 ACAGATGCACTTTCGAGTATGTATTT 59.181 34.615 0.00 0.00 0.00 1.40
839 860 7.121911 CAGATGCACTTTCGAGTATGTATTTG 58.878 38.462 0.00 0.00 0.00 2.32
840 861 7.010460 CAGATGCACTTTCGAGTATGTATTTGA 59.990 37.037 0.00 0.00 0.00 2.69
841 862 6.647212 TGCACTTTCGAGTATGTATTTGAG 57.353 37.500 0.00 0.00 0.00 3.02
842 863 6.394809 TGCACTTTCGAGTATGTATTTGAGA 58.605 36.000 0.00 0.00 0.00 3.27
843 864 6.871492 TGCACTTTCGAGTATGTATTTGAGAA 59.129 34.615 0.00 0.00 0.00 2.87
900 926 2.251371 GCGGCCGAAGTTTGTGAC 59.749 61.111 33.48 2.06 0.00 3.67
1407 1441 2.362375 GATTTCCCTGGGCGCCAA 60.362 61.111 30.85 18.34 30.80 4.52
1624 1658 2.622436 AGTCCGATGCTACAGCTTTTC 58.378 47.619 2.44 0.00 42.66 2.29
1791 1836 2.941064 CTGCAGATGTGATGAATCCGTT 59.059 45.455 8.42 0.00 0.00 4.44
1818 1864 3.558099 CTCGAGTCACGCACTGGCA 62.558 63.158 3.62 0.00 41.24 4.92
1925 1971 3.130164 CGACATCATCTCCTCTTGTCACT 59.870 47.826 0.00 0.00 37.20 3.41
1956 2002 0.596600 CCATCCACCCGTTATCGTCG 60.597 60.000 0.00 0.00 35.01 5.12
1990 2036 4.410400 GGGGTTGTGGAGCCTCCG 62.410 72.222 6.21 0.00 45.51 4.63
2089 2149 7.397761 GGGTAGGGCTAGATACATATATCCATC 59.602 44.444 0.00 0.00 38.43 3.51
2160 2220 1.406539 CTTTGCACTTCAAGCCACACT 59.593 47.619 0.00 0.00 35.84 3.55
2164 2224 1.265365 GCACTTCAAGCCACACTCTTC 59.735 52.381 0.00 0.00 0.00 2.87
2170 2230 4.090761 TCAAGCCACACTCTTCATTTCT 57.909 40.909 0.00 0.00 0.00 2.52
2238 2299 0.987294 CCTCACACTCCCCACATTCT 59.013 55.000 0.00 0.00 0.00 2.40
2568 2634 9.570468 AACATCATGATCTTCTTTGCTATGTAT 57.430 29.630 4.86 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.583441 CGGAGGCAGGTGAAGGACA 61.583 63.158 0.00 0.00 0.00 4.02
39 40 1.268625 ACCCGTCATTTTTCTTTCGGC 59.731 47.619 0.00 0.00 37.17 5.54
103 107 2.544726 CCTGGAGGTTCGCAAAGTC 58.455 57.895 0.00 0.00 0.00 3.01
104 108 4.800554 CCTGGAGGTTCGCAAAGT 57.199 55.556 0.00 0.00 0.00 2.66
132 140 4.517952 TCAACGGTAATGGTTTCGTCTA 57.482 40.909 0.00 0.00 34.60 2.59
186 194 3.067461 GTGCTAGATCTGGAGTTCGATGT 59.933 47.826 10.75 0.00 0.00 3.06
210 218 1.269166 CGACGTCTTAGTCATGTGGC 58.731 55.000 14.70 0.00 40.98 5.01
282 290 3.181480 TGCATCGACGACATCTGGAATAA 60.181 43.478 0.00 0.00 0.00 1.40
366 374 1.299850 CTCCACTGTTGCGACGACA 60.300 57.895 0.00 0.00 0.00 4.35
396 405 1.963855 CGGCATTCGTGTGGTGGAA 60.964 57.895 0.00 0.00 0.00 3.53
428 442 0.879090 CAACCTGTTTAAGCGGGGAC 59.121 55.000 20.07 0.00 39.19 4.46
536 550 2.049433 CGACGTCTTGGCTTCGGT 60.049 61.111 14.70 0.00 0.00 4.69
558 572 4.583073 TCAAAGAAGCTTAGGGTTTTGGAC 59.417 41.667 0.00 0.00 32.93 4.02
579 593 7.498570 TCGTTTTAGCTTTAGTTTTTAGGGTCA 59.501 33.333 0.00 0.00 0.00 4.02
590 605 5.548406 AGTGTGGATCGTTTTAGCTTTAGT 58.452 37.500 0.00 0.00 0.00 2.24
625 641 4.567597 TGGTGGTGAGGGGGTCGT 62.568 66.667 0.00 0.00 0.00 4.34
676 697 3.626680 CTTCTCGCGCCGTCTTCCA 62.627 63.158 0.00 0.00 0.00 3.53
703 724 2.027100 ACCTAGCTAGCCAACAAACTCC 60.027 50.000 15.74 0.00 0.00 3.85
704 725 3.336138 ACCTAGCTAGCCAACAAACTC 57.664 47.619 15.74 0.00 0.00 3.01
705 726 4.770795 CATACCTAGCTAGCCAACAAACT 58.229 43.478 15.74 0.00 0.00 2.66
706 727 3.312697 GCATACCTAGCTAGCCAACAAAC 59.687 47.826 15.74 0.00 0.00 2.93
707 728 3.541632 GCATACCTAGCTAGCCAACAAA 58.458 45.455 15.74 0.00 0.00 2.83
708 729 2.483013 CGCATACCTAGCTAGCCAACAA 60.483 50.000 15.74 0.00 0.00 2.83
709 730 1.068588 CGCATACCTAGCTAGCCAACA 59.931 52.381 15.74 0.00 0.00 3.33
710 731 1.605712 CCGCATACCTAGCTAGCCAAC 60.606 57.143 15.74 2.46 0.00 3.77
711 732 0.679505 CCGCATACCTAGCTAGCCAA 59.320 55.000 15.74 2.90 0.00 4.52
712 733 1.185618 CCCGCATACCTAGCTAGCCA 61.186 60.000 15.74 5.13 0.00 4.75
713 734 1.186267 ACCCGCATACCTAGCTAGCC 61.186 60.000 15.74 0.09 0.00 3.93
714 735 0.038159 CACCCGCATACCTAGCTAGC 60.038 60.000 15.74 6.62 0.00 3.42
715 736 1.329256 ACACCCGCATACCTAGCTAG 58.671 55.000 14.20 14.20 0.00 3.42
716 737 1.684983 GAACACCCGCATACCTAGCTA 59.315 52.381 0.00 0.00 0.00 3.32
717 738 0.464452 GAACACCCGCATACCTAGCT 59.536 55.000 0.00 0.00 0.00 3.32
718 739 0.532196 GGAACACCCGCATACCTAGC 60.532 60.000 0.00 0.00 0.00 3.42
719 740 3.680842 GGAACACCCGCATACCTAG 57.319 57.895 0.00 0.00 0.00 3.02
756 777 9.520204 CACTTGATTTTGAGCTAGAAAGAAAAA 57.480 29.630 0.00 0.00 0.00 1.94
757 778 8.686334 ACACTTGATTTTGAGCTAGAAAGAAAA 58.314 29.630 0.00 0.00 0.00 2.29
758 779 8.131100 CACACTTGATTTTGAGCTAGAAAGAAA 58.869 33.333 0.00 0.00 0.00 2.52
759 780 7.255242 CCACACTTGATTTTGAGCTAGAAAGAA 60.255 37.037 0.00 0.00 0.00 2.52
760 781 6.205464 CCACACTTGATTTTGAGCTAGAAAGA 59.795 38.462 0.00 0.00 0.00 2.52
761 782 6.376978 CCACACTTGATTTTGAGCTAGAAAG 58.623 40.000 0.00 0.00 0.00 2.62
762 783 5.278463 GCCACACTTGATTTTGAGCTAGAAA 60.278 40.000 0.00 0.00 0.00 2.52
763 784 4.216257 GCCACACTTGATTTTGAGCTAGAA 59.784 41.667 0.00 0.00 0.00 2.10
764 785 3.753272 GCCACACTTGATTTTGAGCTAGA 59.247 43.478 0.00 0.00 0.00 2.43
765 786 3.119708 GGCCACACTTGATTTTGAGCTAG 60.120 47.826 0.00 0.00 0.00 3.42
766 787 2.819608 GGCCACACTTGATTTTGAGCTA 59.180 45.455 0.00 0.00 0.00 3.32
767 788 1.615392 GGCCACACTTGATTTTGAGCT 59.385 47.619 0.00 0.00 0.00 4.09
768 789 1.666888 CGGCCACACTTGATTTTGAGC 60.667 52.381 2.24 0.00 0.00 4.26
769 790 1.068333 CCGGCCACACTTGATTTTGAG 60.068 52.381 2.24 0.00 0.00 3.02
770 791 0.958091 CCGGCCACACTTGATTTTGA 59.042 50.000 2.24 0.00 0.00 2.69
771 792 0.673437 ACCGGCCACACTTGATTTTG 59.327 50.000 0.00 0.00 0.00 2.44
772 793 2.279935 TACCGGCCACACTTGATTTT 57.720 45.000 0.00 0.00 0.00 1.82
773 794 2.507407 ATACCGGCCACACTTGATTT 57.493 45.000 0.00 0.00 0.00 2.17
774 795 2.507407 AATACCGGCCACACTTGATT 57.493 45.000 0.00 0.00 0.00 2.57
775 796 3.857157 ATAATACCGGCCACACTTGAT 57.143 42.857 0.00 0.00 0.00 2.57
776 797 3.451540 TGTATAATACCGGCCACACTTGA 59.548 43.478 0.00 0.00 0.00 3.02
777 798 3.558418 GTGTATAATACCGGCCACACTTG 59.442 47.826 0.00 0.00 34.78 3.16
778 799 3.432608 GGTGTATAATACCGGCCACACTT 60.433 47.826 15.75 1.57 37.15 3.16
779 800 2.103601 GGTGTATAATACCGGCCACACT 59.896 50.000 15.75 0.00 37.15 3.55
780 801 2.103601 AGGTGTATAATACCGGCCACAC 59.896 50.000 0.00 6.88 43.06 3.82
781 802 2.103432 CAGGTGTATAATACCGGCCACA 59.897 50.000 0.00 0.00 43.06 4.17
782 803 2.103601 ACAGGTGTATAATACCGGCCAC 59.896 50.000 0.00 0.00 43.06 5.01
783 804 2.400573 ACAGGTGTATAATACCGGCCA 58.599 47.619 0.00 0.00 43.06 5.36
784 805 4.605640 TTACAGGTGTATAATACCGGCC 57.394 45.455 0.00 0.00 43.06 6.13
785 806 8.606040 TTATTTTACAGGTGTATAATACCGGC 57.394 34.615 0.00 0.00 43.06 6.13
798 819 8.807948 AGTGCATCTGTATTTATTTTACAGGT 57.192 30.769 10.10 1.56 44.30 4.00
801 822 9.767684 CGAAAGTGCATCTGTATTTATTTTACA 57.232 29.630 0.00 0.00 0.00 2.41
802 823 9.982291 TCGAAAGTGCATCTGTATTTATTTTAC 57.018 29.630 0.00 0.00 0.00 2.01
804 825 8.730680 ACTCGAAAGTGCATCTGTATTTATTTT 58.269 29.630 0.00 0.00 33.32 1.82
805 826 8.268850 ACTCGAAAGTGCATCTGTATTTATTT 57.731 30.769 0.00 0.00 33.32 1.40
806 827 7.849804 ACTCGAAAGTGCATCTGTATTTATT 57.150 32.000 0.00 0.00 33.32 1.40
807 828 8.982685 CATACTCGAAAGTGCATCTGTATTTAT 58.017 33.333 0.00 0.00 36.92 1.40
808 829 7.979537 ACATACTCGAAAGTGCATCTGTATTTA 59.020 33.333 0.00 0.00 36.92 1.40
809 830 6.818644 ACATACTCGAAAGTGCATCTGTATTT 59.181 34.615 0.00 0.00 36.92 1.40
810 831 6.341316 ACATACTCGAAAGTGCATCTGTATT 58.659 36.000 0.00 0.00 36.92 1.89
811 832 5.907207 ACATACTCGAAAGTGCATCTGTAT 58.093 37.500 0.00 0.00 36.92 2.29
812 833 5.324784 ACATACTCGAAAGTGCATCTGTA 57.675 39.130 0.00 0.00 36.92 2.74
813 834 4.193826 ACATACTCGAAAGTGCATCTGT 57.806 40.909 0.00 0.00 36.92 3.41
814 835 6.834959 AATACATACTCGAAAGTGCATCTG 57.165 37.500 0.00 0.00 36.92 2.90
815 836 7.041721 TCAAATACATACTCGAAAGTGCATCT 58.958 34.615 0.00 0.00 36.92 2.90
816 837 7.222805 TCTCAAATACATACTCGAAAGTGCATC 59.777 37.037 0.00 0.00 36.92 3.91
817 838 7.041721 TCTCAAATACATACTCGAAAGTGCAT 58.958 34.615 0.00 0.00 36.92 3.96
818 839 6.394809 TCTCAAATACATACTCGAAAGTGCA 58.605 36.000 0.00 0.00 36.92 4.57
819 840 6.887376 TCTCAAATACATACTCGAAAGTGC 57.113 37.500 0.00 0.00 36.92 4.40
857 878 6.239572 GCTTGGCATGGGGTATTTTTATACAT 60.240 38.462 2.33 0.00 0.00 2.29
900 926 0.250295 ATGCGGTTGATGGGGTATCG 60.250 55.000 0.00 0.00 38.71 2.92
963 997 2.724977 TTATCTTATCCGCGGCTCTG 57.275 50.000 23.51 11.01 0.00 3.35
969 1003 6.207213 AGACTACAAGTTTATCTTATCCGCG 58.793 40.000 0.00 0.00 34.66 6.46
1575 1609 4.740822 GTGTGGCGGGCCCTCATT 62.741 66.667 22.43 0.00 39.16 2.57
1639 1673 2.616376 CGGTTGGTCACAATCTTTCACA 59.384 45.455 0.00 0.00 39.13 3.58
1640 1674 2.875933 TCGGTTGGTCACAATCTTTCAC 59.124 45.455 0.00 0.00 39.13 3.18
1641 1675 3.201353 TCGGTTGGTCACAATCTTTCA 57.799 42.857 0.00 0.00 39.13 2.69
1642 1676 3.670627 GCATCGGTTGGTCACAATCTTTC 60.671 47.826 0.00 0.00 39.13 2.62
1643 1677 2.228822 GCATCGGTTGGTCACAATCTTT 59.771 45.455 0.00 0.00 39.13 2.52
1645 1679 1.003580 AGCATCGGTTGGTCACAATCT 59.996 47.619 0.00 0.00 39.13 2.40
1646 1680 1.453155 AGCATCGGTTGGTCACAATC 58.547 50.000 0.00 0.00 39.13 2.67
1648 1682 1.686355 AAAGCATCGGTTGGTCACAA 58.314 45.000 0.00 0.00 34.16 3.33
1791 1836 1.838568 CGTGACTCGAGGACGTGACA 61.839 60.000 23.66 8.32 42.86 3.58
1818 1864 8.686739 AGCATATATAGGATGTAAAGGGAAGT 57.313 34.615 0.00 0.00 0.00 3.01
1925 1971 1.546773 GGTGGATGGTGGTAAGCAACA 60.547 52.381 0.00 0.00 37.35 3.33
1956 2002 0.318762 CCCGACCTGCTATAAGAGGC 59.681 60.000 0.00 0.00 31.90 4.70
2160 2220 5.702670 GTGGAGTGTCATGAAGAAATGAAGA 59.297 40.000 0.00 0.00 38.28 2.87
2164 2224 4.999311 TCAGTGGAGTGTCATGAAGAAATG 59.001 41.667 0.00 0.00 0.00 2.32
2170 2230 5.355071 GCAAATATCAGTGGAGTGTCATGAA 59.645 40.000 0.00 0.00 0.00 2.57
2570 2636 9.193806 CCTTAAGTTTACACTAGAGGGTACATA 57.806 37.037 0.00 0.00 34.03 2.29
2571 2637 7.677319 ACCTTAAGTTTACACTAGAGGGTACAT 59.323 37.037 12.63 0.00 38.61 2.29


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

AutoCloner maintained by Alex Coulton.