Multiple sequence alignment - TraesCS5A01G404200

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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 TraesCS5A01G404200 chr5A 100.000 2703 0 0 1 2703 596085661 596088363 0.000000e+00 4992
1 TraesCS5A01G404200 chr5A 87.006 962 88 15 878 1817 596054645 596055591 0.000000e+00 1050
2 TraesCS5A01G404200 chr5A 91.424 653 49 5 103 749 325834502 325833851 0.000000e+00 889
3 TraesCS5A01G404200 chr5A 83.837 959 98 28 846 1786 596044220 596045139 0.000000e+00 859
4 TraesCS5A01G404200 chr5A 83.316 989 94 29 865 1795 596032321 596033296 0.000000e+00 846
5 TraesCS5A01G404200 chr5A 82.260 761 71 31 1 749 417250859 417251567 1.380000e-167 599
6 TraesCS5A01G404200 chr5A 81.925 769 84 26 1 748 621226575 621227309 1.380000e-167 599
7 TraesCS5A01G404200 chr5A 81.662 758 81 20 1 749 294024394 294025102 6.490000e-161 577
8 TraesCS5A01G404200 chr5A 80.826 751 83 22 1 743 459688308 459687611 1.420000e-147 532
9 TraesCS5A01G404200 chr5A 79.774 707 70 38 1 698 348709336 348709978 1.910000e-121 446
10 TraesCS5A01G404200 chr5A 96.319 163 6 0 1819 1981 36286980 36286818 4.440000e-68 268
11 TraesCS5A01G404200 chr2D 96.903 904 10 1 1818 2703 36408892 36409795 0.000000e+00 1498
12 TraesCS5A01G404200 chr2D 94.356 567 10 3 1818 2366 87299608 87299046 0.000000e+00 850
13 TraesCS5A01G404200 chr6D 96.681 904 11 2 1818 2703 453657774 453656872 0.000000e+00 1485
14 TraesCS5A01G404200 chr6D 96.456 903 12 2 1818 2700 58203104 58204006 0.000000e+00 1472
15 TraesCS5A01G404200 chr3D 96.243 905 15 2 1818 2703 537326355 537327259 0.000000e+00 1465
16 TraesCS5A01G404200 chr6B 96.239 904 15 2 1818 2703 643440533 643441435 0.000000e+00 1463
17 TraesCS5A01G404200 chr5D 91.374 939 55 14 863 1795 476784808 476785726 0.000000e+00 1262
18 TraesCS5A01G404200 chr5D 87.436 971 73 17 865 1815 476749563 476750504 0.000000e+00 1072
19 TraesCS5A01G404200 chr5D 85.166 964 95 22 865 1795 476708270 476709218 0.000000e+00 944
20 TraesCS5A01G404200 chr5D 85.484 930 83 20 883 1786 476724986 476725889 0.000000e+00 922
21 TraesCS5A01G404200 chr6A 92.430 753 51 5 1 750 49748283 49749032 0.000000e+00 1070
22 TraesCS5A01G404200 chr5B 87.797 926 73 14 863 1784 584291781 584292670 0.000000e+00 1048
23 TraesCS5A01G404200 chr5B 87.721 847 69 10 865 1704 584245503 584246321 0.000000e+00 955
24 TraesCS5A01G404200 chr5B 84.624 943 97 22 888 1795 584126562 584127491 0.000000e+00 894
25 TraesCS5A01G404200 chr5B 85.578 839 78 11 883 1709 584142353 584143160 0.000000e+00 839
26 TraesCS5A01G404200 chr3A 91.667 756 54 7 1 749 688900918 688901671 0.000000e+00 1038
27 TraesCS5A01G404200 chr3A 90.981 754 61 5 1 749 547328491 547329242 0.000000e+00 1009
28 TraesCS5A01G404200 chr7A 93.145 671 17 6 1818 2469 679858893 679858233 0.000000e+00 957
29 TraesCS5A01G404200 chr7A 92.422 673 46 3 76 746 191749106 191749775 0.000000e+00 955
30 TraesCS5A01G404200 chr7A 88.046 778 52 24 1 748 695039720 695040486 0.000000e+00 883
31 TraesCS5A01G404200 chr7A 97.207 179 5 0 1818 1996 106687280 106687102 1.220000e-78 303
32 TraesCS5A01G404200 chr4A 91.335 704 53 6 52 750 602051664 602052364 0.000000e+00 955
33 TraesCS5A01G404200 chr4A 89.536 755 66 6 1 749 66747946 66748693 0.000000e+00 944
34 TraesCS5A01G404200 chr4A 91.992 487 28 6 2228 2703 91226118 91226604 0.000000e+00 673
35 TraesCS5A01G404200 chr4A 89.712 486 40 5 2228 2703 492041624 492042109 1.780000e-171 612
36 TraesCS5A01G404200 chr2A 91.045 670 55 3 81 746 72606639 72605971 0.000000e+00 900
37 TraesCS5A01G404200 chr2A 91.345 647 50 6 103 746 713175668 713176311 0.000000e+00 880
38 TraesCS5A01G404200 chr2A 91.340 485 28 7 2228 2703 615516493 615516972 0.000000e+00 651
39 TraesCS5A01G404200 chr2A 82.790 767 69 36 1 750 699444104 699444824 6.350000e-176 627
40 TraesCS5A01G404200 chr2A 81.747 767 82 21 1 749 770408323 770407597 3.000000e-164 588
41 TraesCS5A01G404200 chr2B 87.201 586 41 8 2150 2703 529292110 529291527 1.060000e-178 636
42 TraesCS5A01G404200 chr2B 77.474 768 96 47 1 749 43220442 43221151 3.260000e-104 388
43 TraesCS5A01G404200 chr3B 79.434 778 95 44 1 756 667689986 667690720 8.700000e-135 490
44 TraesCS5A01G404200 chr3B 79.156 758 95 39 5 744 11011236 11010524 1.470000e-127 466
45 TraesCS5A01G404200 chr3B 78.831 770 89 43 1 750 666796868 666797583 4.100000e-123 451


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 TraesCS5A01G404200 chr5A 596085661 596088363 2702 False 4992 4992 100.000 1 2703 1 chr5A.!!$F7 2702
1 TraesCS5A01G404200 chr5A 596054645 596055591 946 False 1050 1050 87.006 878 1817 1 chr5A.!!$F6 939
2 TraesCS5A01G404200 chr5A 325833851 325834502 651 True 889 889 91.424 103 749 1 chr5A.!!$R2 646
3 TraesCS5A01G404200 chr5A 596044220 596045139 919 False 859 859 83.837 846 1786 1 chr5A.!!$F5 940
4 TraesCS5A01G404200 chr5A 596032321 596033296 975 False 846 846 83.316 865 1795 1 chr5A.!!$F4 930
5 TraesCS5A01G404200 chr5A 417250859 417251567 708 False 599 599 82.260 1 749 1 chr5A.!!$F3 748
6 TraesCS5A01G404200 chr5A 621226575 621227309 734 False 599 599 81.925 1 748 1 chr5A.!!$F8 747
7 TraesCS5A01G404200 chr5A 294024394 294025102 708 False 577 577 81.662 1 749 1 chr5A.!!$F1 748
8 TraesCS5A01G404200 chr5A 459687611 459688308 697 True 532 532 80.826 1 743 1 chr5A.!!$R3 742
9 TraesCS5A01G404200 chr5A 348709336 348709978 642 False 446 446 79.774 1 698 1 chr5A.!!$F2 697
10 TraesCS5A01G404200 chr2D 36408892 36409795 903 False 1498 1498 96.903 1818 2703 1 chr2D.!!$F1 885
11 TraesCS5A01G404200 chr2D 87299046 87299608 562 True 850 850 94.356 1818 2366 1 chr2D.!!$R1 548
12 TraesCS5A01G404200 chr6D 453656872 453657774 902 True 1485 1485 96.681 1818 2703 1 chr6D.!!$R1 885
13 TraesCS5A01G404200 chr6D 58203104 58204006 902 False 1472 1472 96.456 1818 2700 1 chr6D.!!$F1 882
14 TraesCS5A01G404200 chr3D 537326355 537327259 904 False 1465 1465 96.243 1818 2703 1 chr3D.!!$F1 885
15 TraesCS5A01G404200 chr6B 643440533 643441435 902 False 1463 1463 96.239 1818 2703 1 chr6B.!!$F1 885
16 TraesCS5A01G404200 chr5D 476784808 476785726 918 False 1262 1262 91.374 863 1795 1 chr5D.!!$F4 932
17 TraesCS5A01G404200 chr5D 476749563 476750504 941 False 1072 1072 87.436 865 1815 1 chr5D.!!$F3 950
18 TraesCS5A01G404200 chr5D 476708270 476709218 948 False 944 944 85.166 865 1795 1 chr5D.!!$F1 930
19 TraesCS5A01G404200 chr5D 476724986 476725889 903 False 922 922 85.484 883 1786 1 chr5D.!!$F2 903
20 TraesCS5A01G404200 chr6A 49748283 49749032 749 False 1070 1070 92.430 1 750 1 chr6A.!!$F1 749
21 TraesCS5A01G404200 chr5B 584291781 584292670 889 False 1048 1048 87.797 863 1784 1 chr5B.!!$F4 921
22 TraesCS5A01G404200 chr5B 584245503 584246321 818 False 955 955 87.721 865 1704 1 chr5B.!!$F3 839
23 TraesCS5A01G404200 chr5B 584126562 584127491 929 False 894 894 84.624 888 1795 1 chr5B.!!$F1 907
24 TraesCS5A01G404200 chr5B 584142353 584143160 807 False 839 839 85.578 883 1709 1 chr5B.!!$F2 826
25 TraesCS5A01G404200 chr3A 688900918 688901671 753 False 1038 1038 91.667 1 749 1 chr3A.!!$F2 748
26 TraesCS5A01G404200 chr3A 547328491 547329242 751 False 1009 1009 90.981 1 749 1 chr3A.!!$F1 748
27 TraesCS5A01G404200 chr7A 679858233 679858893 660 True 957 957 93.145 1818 2469 1 chr7A.!!$R2 651
28 TraesCS5A01G404200 chr7A 191749106 191749775 669 False 955 955 92.422 76 746 1 chr7A.!!$F1 670
29 TraesCS5A01G404200 chr7A 695039720 695040486 766 False 883 883 88.046 1 748 1 chr7A.!!$F2 747
30 TraesCS5A01G404200 chr4A 602051664 602052364 700 False 955 955 91.335 52 750 1 chr4A.!!$F4 698
31 TraesCS5A01G404200 chr4A 66747946 66748693 747 False 944 944 89.536 1 749 1 chr4A.!!$F1 748
32 TraesCS5A01G404200 chr2A 72605971 72606639 668 True 900 900 91.045 81 746 1 chr2A.!!$R1 665
33 TraesCS5A01G404200 chr2A 713175668 713176311 643 False 880 880 91.345 103 746 1 chr2A.!!$F3 643
34 TraesCS5A01G404200 chr2A 699444104 699444824 720 False 627 627 82.790 1 750 1 chr2A.!!$F2 749
35 TraesCS5A01G404200 chr2A 770407597 770408323 726 True 588 588 81.747 1 749 1 chr2A.!!$R2 748
36 TraesCS5A01G404200 chr2B 529291527 529292110 583 True 636 636 87.201 2150 2703 1 chr2B.!!$R1 553
37 TraesCS5A01G404200 chr2B 43220442 43221151 709 False 388 388 77.474 1 749 1 chr2B.!!$F1 748
38 TraesCS5A01G404200 chr3B 667689986 667690720 734 False 490 490 79.434 1 756 1 chr3B.!!$F2 755
39 TraesCS5A01G404200 chr3B 11010524 11011236 712 True 466 466 79.156 5 744 1 chr3B.!!$R1 739
40 TraesCS5A01G404200 chr3B 666796868 666797583 715 False 451 451 78.831 1 750 1 chr3B.!!$F1 749

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
812 954 0.036388 ACCGTCCGTGAGCATGATTT 60.036 50.0 0.0 0.0 0.0 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 2033 1.366111 CCGCCGTTCGATCCAACATT 61.366 55.0 4.06 0.0 41.67 2.71 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
227 298 0.752009 TAGCGATGGAGAAGGAGCGT 60.752 55.000 0.00 0.00 0.00 5.07
604 737 4.094887 ACTGTGCCGAAATTTGCTATACAG 59.905 41.667 13.48 13.48 35.99 2.74
693 832 0.606944 ATTTTTACGCCGGCTCACCA 60.607 50.000 26.68 4.01 34.57 4.17
724 866 3.243569 CGATTTTAGACGCCTCCTGAGAT 60.244 47.826 0.00 0.00 0.00 2.75
726 868 1.403814 TTAGACGCCTCCTGAGATGG 58.596 55.000 0.00 0.00 0.00 3.51
750 892 0.250252 GGCTGGAGATGCTCTTAGCC 60.250 60.000 19.43 19.43 45.34 3.93
751 893 0.599728 GCTGGAGATGCTCTTAGCCG 60.600 60.000 10.80 0.00 41.51 5.52
752 894 0.599728 CTGGAGATGCTCTTAGCCGC 60.600 60.000 0.00 0.00 41.51 6.53
753 895 1.663074 GGAGATGCTCTTAGCCGCG 60.663 63.158 0.00 0.00 41.51 6.46
754 896 1.066587 GAGATGCTCTTAGCCGCGT 59.933 57.895 4.92 0.00 41.51 6.01
755 897 1.211818 GAGATGCTCTTAGCCGCGTG 61.212 60.000 4.92 0.00 41.51 5.34
756 898 2.202932 ATGCTCTTAGCCGCGTGG 60.203 61.111 11.67 11.67 41.51 4.94
757 899 2.907897 GATGCTCTTAGCCGCGTGGT 62.908 60.000 17.91 6.10 41.51 4.16
758 900 2.886124 GCTCTTAGCCGCGTGGTC 60.886 66.667 17.91 9.11 34.48 4.02
759 901 2.571757 CTCTTAGCCGCGTGGTCA 59.428 61.111 17.91 1.24 37.67 4.02
760 902 1.517257 CTCTTAGCCGCGTGGTCAG 60.517 63.158 17.91 10.15 37.67 3.51
761 903 2.509336 CTTAGCCGCGTGGTCAGG 60.509 66.667 17.91 1.14 37.67 3.86
762 904 4.077184 TTAGCCGCGTGGTCAGGG 62.077 66.667 17.91 0.00 37.67 4.45
766 908 2.593436 CCGCGTGGTCAGGGTTTT 60.593 61.111 6.91 0.00 0.00 2.43
767 909 2.637025 CGCGTGGTCAGGGTTTTG 59.363 61.111 0.00 0.00 0.00 2.44
768 910 2.335011 GCGTGGTCAGGGTTTTGC 59.665 61.111 0.00 0.00 0.00 3.68
769 911 2.193536 GCGTGGTCAGGGTTTTGCT 61.194 57.895 0.00 0.00 0.00 3.91
770 912 0.887387 GCGTGGTCAGGGTTTTGCTA 60.887 55.000 0.00 0.00 0.00 3.49
771 913 1.156736 CGTGGTCAGGGTTTTGCTAG 58.843 55.000 0.00 0.00 0.00 3.42
772 914 1.542547 CGTGGTCAGGGTTTTGCTAGT 60.543 52.381 0.00 0.00 0.00 2.57
773 915 2.583143 GTGGTCAGGGTTTTGCTAGTT 58.417 47.619 0.00 0.00 0.00 2.24
774 916 2.293399 GTGGTCAGGGTTTTGCTAGTTG 59.707 50.000 0.00 0.00 0.00 3.16
775 917 1.886542 GGTCAGGGTTTTGCTAGTTGG 59.113 52.381 0.00 0.00 0.00 3.77
776 918 1.269723 GTCAGGGTTTTGCTAGTTGGC 59.730 52.381 0.00 0.00 0.00 4.52
777 919 0.603065 CAGGGTTTTGCTAGTTGGCC 59.397 55.000 0.00 0.00 0.00 5.36
778 920 0.541998 AGGGTTTTGCTAGTTGGCCC 60.542 55.000 0.00 0.00 35.04 5.80
779 921 1.584495 GGTTTTGCTAGTTGGCCCG 59.416 57.895 0.00 0.00 0.00 6.13
780 922 1.176619 GGTTTTGCTAGTTGGCCCGT 61.177 55.000 0.00 0.00 0.00 5.28
781 923 0.671796 GTTTTGCTAGTTGGCCCGTT 59.328 50.000 0.00 0.00 0.00 4.44
782 924 0.671251 TTTTGCTAGTTGGCCCGTTG 59.329 50.000 0.00 0.00 0.00 4.10
783 925 1.175983 TTTGCTAGTTGGCCCGTTGG 61.176 55.000 0.00 0.00 0.00 3.77
808 950 2.261361 TCACCGTCCGTGAGCATG 59.739 61.111 0.00 0.00 46.80 4.06
809 951 2.261361 CACCGTCCGTGAGCATGA 59.739 61.111 0.00 0.00 46.20 3.07
810 952 1.153568 CACCGTCCGTGAGCATGAT 60.154 57.895 0.00 0.00 46.20 2.45
811 953 0.740868 CACCGTCCGTGAGCATGATT 60.741 55.000 0.00 0.00 46.20 2.57
812 954 0.036388 ACCGTCCGTGAGCATGATTT 60.036 50.000 0.00 0.00 0.00 2.17
813 955 0.652592 CCGTCCGTGAGCATGATTTC 59.347 55.000 0.00 0.00 0.00 2.17
814 956 0.298707 CGTCCGTGAGCATGATTTCG 59.701 55.000 0.00 0.00 0.00 3.46
815 957 1.640428 GTCCGTGAGCATGATTTCGA 58.360 50.000 0.00 0.00 0.00 3.71
816 958 1.999735 GTCCGTGAGCATGATTTCGAA 59.000 47.619 0.00 0.00 0.00 3.71
817 959 2.609459 GTCCGTGAGCATGATTTCGAAT 59.391 45.455 0.00 0.00 0.00 3.34
818 960 3.802139 GTCCGTGAGCATGATTTCGAATA 59.198 43.478 0.00 0.00 0.00 1.75
819 961 4.270084 GTCCGTGAGCATGATTTCGAATAA 59.730 41.667 0.00 0.00 0.00 1.40
820 962 5.050091 GTCCGTGAGCATGATTTCGAATAAT 60.050 40.000 0.00 0.00 0.00 1.28
821 963 5.177511 TCCGTGAGCATGATTTCGAATAATC 59.822 40.000 0.00 0.21 35.54 1.75
822 964 5.178252 CCGTGAGCATGATTTCGAATAATCT 59.822 40.000 10.38 0.00 35.89 2.40
823 965 6.293081 CCGTGAGCATGATTTCGAATAATCTT 60.293 38.462 10.38 2.78 35.89 2.40
824 966 6.789403 CGTGAGCATGATTTCGAATAATCTTC 59.211 38.462 10.38 5.07 35.89 2.87
825 967 7.517259 CGTGAGCATGATTTCGAATAATCTTCA 60.517 37.037 10.38 6.94 35.89 3.02
826 968 7.585573 GTGAGCATGATTTCGAATAATCTTCAC 59.414 37.037 10.38 12.72 35.89 3.18
827 969 6.653183 AGCATGATTTCGAATAATCTTCACG 58.347 36.000 10.38 0.00 35.89 4.35
828 970 6.479990 AGCATGATTTCGAATAATCTTCACGA 59.520 34.615 10.38 0.00 35.89 4.35
829 971 6.789403 GCATGATTTCGAATAATCTTCACGAG 59.211 38.462 10.38 0.00 35.89 4.18
830 972 7.517417 GCATGATTTCGAATAATCTTCACGAGT 60.517 37.037 10.38 0.00 35.89 4.18
831 973 8.968242 CATGATTTCGAATAATCTTCACGAGTA 58.032 33.333 10.38 0.00 35.89 2.59
832 974 8.561932 TGATTTCGAATAATCTTCACGAGTAG 57.438 34.615 10.38 0.00 35.89 2.57
833 975 6.807708 TTTCGAATAATCTTCACGAGTAGC 57.192 37.500 0.00 0.00 34.64 3.58
834 976 4.856664 TCGAATAATCTTCACGAGTAGCC 58.143 43.478 0.00 0.00 0.00 3.93
835 977 3.982058 CGAATAATCTTCACGAGTAGCCC 59.018 47.826 0.00 0.00 0.00 5.19
836 978 4.499188 CGAATAATCTTCACGAGTAGCCCA 60.499 45.833 0.00 0.00 0.00 5.36
837 979 2.674796 AATCTTCACGAGTAGCCCAC 57.325 50.000 0.00 0.00 0.00 4.61
838 980 1.853963 ATCTTCACGAGTAGCCCACT 58.146 50.000 0.00 0.00 41.47 4.00
839 981 0.888619 TCTTCACGAGTAGCCCACTG 59.111 55.000 0.00 0.00 37.72 3.66
840 982 0.888619 CTTCACGAGTAGCCCACTGA 59.111 55.000 0.00 0.00 37.72 3.41
841 983 0.601558 TTCACGAGTAGCCCACTGAC 59.398 55.000 0.00 0.00 37.72 3.51
842 984 0.251209 TCACGAGTAGCCCACTGACT 60.251 55.000 0.00 0.00 37.72 3.41
843 985 0.109086 CACGAGTAGCCCACTGACTG 60.109 60.000 0.00 0.00 37.72 3.51
844 986 1.251527 ACGAGTAGCCCACTGACTGG 61.252 60.000 0.00 0.00 37.72 4.00
858 1000 4.081030 CTGGTGACTGCGCTTGCG 62.081 66.667 9.73 10.90 43.34 4.85
874 1018 0.250124 TGCGAAGAAGAAAAGCCCGA 60.250 50.000 0.00 0.00 0.00 5.14
1020 1175 4.828387 CCGCTATATATACCTCTTCCTCCC 59.172 50.000 0.00 0.00 0.00 4.30
1100 1287 4.241681 CAAGAGAAGAACCAGACAGTAGC 58.758 47.826 0.00 0.00 0.00 3.58
1101 1288 3.501349 AGAGAAGAACCAGACAGTAGCA 58.499 45.455 0.00 0.00 0.00 3.49
1103 1290 4.021544 AGAGAAGAACCAGACAGTAGCAAG 60.022 45.833 0.00 0.00 0.00 4.01
1104 1291 2.464157 AGAACCAGACAGTAGCAAGC 57.536 50.000 0.00 0.00 0.00 4.01
1127 1341 1.956170 GCAGCAGTAGCACACACGT 60.956 57.895 0.00 0.00 45.49 4.49
1148 1384 1.295423 CGACCAAGACGGAATGGGT 59.705 57.895 7.42 0.00 41.17 4.51
1609 1854 4.035102 GAAGCGGAGGGTGGCCTT 62.035 66.667 3.32 0.00 0.00 4.35
1773 2039 2.437716 ACCCGGCCGCTAATGTTG 60.438 61.111 22.85 2.64 0.00 3.33
1779 2045 0.531974 GGCCGCTAATGTTGGATCGA 60.532 55.000 0.00 0.00 0.00 3.59
1787 2053 3.861263 GTTGGATCGAACGGCGGC 61.861 66.667 13.24 0.00 41.33 6.53
1807 2077 2.409752 GCGACGCGGTAAATGATATGTG 60.410 50.000 12.47 0.00 0.00 3.21
1810 2080 3.390135 ACGCGGTAAATGATATGTGGAG 58.610 45.455 12.47 0.00 0.00 3.86
1812 2082 3.807622 CGCGGTAAATGATATGTGGAGTT 59.192 43.478 0.00 0.00 0.00 3.01
1813 2083 4.986034 CGCGGTAAATGATATGTGGAGTTA 59.014 41.667 0.00 0.00 0.00 2.24
1815 2085 5.408604 GCGGTAAATGATATGTGGAGTTAGG 59.591 44.000 0.00 0.00 0.00 2.69
1816 2086 5.932303 CGGTAAATGATATGTGGAGTTAGGG 59.068 44.000 0.00 0.00 0.00 3.53
1977 2247 2.037687 CCATTGGGCTGGCTGGAA 59.962 61.111 0.00 0.00 0.00 3.53
2200 2474 5.019470 ACAGGAACATGTACAGAGAGATCA 58.981 41.667 0.00 0.00 0.00 2.92
2203 2478 4.160439 GGAACATGTACAGAGAGATCACCA 59.840 45.833 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 50 3.453679 GAAGCGCGGAGGAGGAGT 61.454 66.667 8.83 0.00 0.00 3.85
195 266 0.760567 ATCGCTATGGAGTCCCTGCA 60.761 55.000 6.74 0.00 36.05 4.41
227 298 1.608717 GCTCCTTCGCCTTCTCCAGA 61.609 60.000 0.00 0.00 0.00 3.86
302 373 1.506718 GCAGATGACGACGACTCCA 59.493 57.895 0.00 0.00 0.00 3.86
440 541 2.402787 GAGTAGTCGCCGTCGTCC 59.597 66.667 0.00 0.00 36.96 4.79
604 737 6.037720 CCCCCGGCATGTTTAAAAATAAAATC 59.962 38.462 0.00 0.00 0.00 2.17
693 832 0.743345 GTCTAAAATCGCCGCCTGGT 60.743 55.000 0.00 0.00 37.67 4.00
724 866 1.755395 GCATCTCCAGCCATTGCCA 60.755 57.895 0.00 0.00 38.69 4.92
726 868 2.031360 GAGCATCTCCAGCCATTGC 58.969 57.895 0.00 0.00 37.95 3.56
750 892 2.637025 CAAAACCCTGACCACGCG 59.363 61.111 3.53 3.53 0.00 6.01
751 893 0.887387 TAGCAAAACCCTGACCACGC 60.887 55.000 0.00 0.00 0.00 5.34
752 894 1.156736 CTAGCAAAACCCTGACCACG 58.843 55.000 0.00 0.00 0.00 4.94
753 895 2.271944 ACTAGCAAAACCCTGACCAC 57.728 50.000 0.00 0.00 0.00 4.16
754 896 2.582052 CAACTAGCAAAACCCTGACCA 58.418 47.619 0.00 0.00 0.00 4.02
755 897 1.886542 CCAACTAGCAAAACCCTGACC 59.113 52.381 0.00 0.00 0.00 4.02
756 898 1.269723 GCCAACTAGCAAAACCCTGAC 59.730 52.381 0.00 0.00 0.00 3.51
757 899 1.616159 GCCAACTAGCAAAACCCTGA 58.384 50.000 0.00 0.00 0.00 3.86
758 900 0.603065 GGCCAACTAGCAAAACCCTG 59.397 55.000 0.00 0.00 0.00 4.45
759 901 0.541998 GGGCCAACTAGCAAAACCCT 60.542 55.000 4.39 0.00 32.88 4.34
760 902 1.873270 CGGGCCAACTAGCAAAACCC 61.873 60.000 4.39 0.00 0.00 4.11
761 903 1.176619 ACGGGCCAACTAGCAAAACC 61.177 55.000 4.39 0.00 0.00 3.27
762 904 0.671796 AACGGGCCAACTAGCAAAAC 59.328 50.000 4.39 0.00 0.00 2.43
763 905 0.671251 CAACGGGCCAACTAGCAAAA 59.329 50.000 4.39 0.00 0.00 2.44
764 906 1.175983 CCAACGGGCCAACTAGCAAA 61.176 55.000 4.39 0.00 0.00 3.68
765 907 1.602323 CCAACGGGCCAACTAGCAA 60.602 57.895 4.39 0.00 0.00 3.91
766 908 2.033448 CCAACGGGCCAACTAGCA 59.967 61.111 4.39 0.00 0.00 3.49
793 935 0.036388 AAATCATGCTCACGGACGGT 60.036 50.000 0.00 0.00 0.00 4.83
794 936 0.652592 GAAATCATGCTCACGGACGG 59.347 55.000 0.00 0.00 0.00 4.79
795 937 0.298707 CGAAATCATGCTCACGGACG 59.701 55.000 0.00 0.00 0.00 4.79
796 938 1.640428 TCGAAATCATGCTCACGGAC 58.360 50.000 0.00 0.00 0.00 4.79
797 939 2.378445 TTCGAAATCATGCTCACGGA 57.622 45.000 0.00 0.00 0.00 4.69
798 940 4.794248 TTATTCGAAATCATGCTCACGG 57.206 40.909 0.00 0.00 0.00 4.94
799 941 6.220579 AGATTATTCGAAATCATGCTCACG 57.779 37.500 0.00 0.00 38.16 4.35
800 942 7.585573 GTGAAGATTATTCGAAATCATGCTCAC 59.414 37.037 0.00 9.47 38.16 3.51
801 943 7.517259 CGTGAAGATTATTCGAAATCATGCTCA 60.517 37.037 0.00 1.68 38.16 4.26
802 944 6.789403 CGTGAAGATTATTCGAAATCATGCTC 59.211 38.462 0.00 0.00 38.16 4.26
803 945 6.479990 TCGTGAAGATTATTCGAAATCATGCT 59.520 34.615 0.00 0.00 38.16 3.79
804 946 6.649436 TCGTGAAGATTATTCGAAATCATGC 58.351 36.000 0.00 0.00 38.16 4.06
805 947 7.845483 ACTCGTGAAGATTATTCGAAATCATG 58.155 34.615 0.00 6.19 38.16 3.07
806 948 9.186323 CTACTCGTGAAGATTATTCGAAATCAT 57.814 33.333 0.00 0.00 38.16 2.45
807 949 7.167635 GCTACTCGTGAAGATTATTCGAAATCA 59.832 37.037 0.00 0.00 38.16 2.57
808 950 7.358517 GGCTACTCGTGAAGATTATTCGAAATC 60.359 40.741 0.00 1.32 36.33 2.17
809 951 6.421202 GGCTACTCGTGAAGATTATTCGAAAT 59.579 38.462 0.00 0.00 0.00 2.17
810 952 5.747197 GGCTACTCGTGAAGATTATTCGAAA 59.253 40.000 0.00 0.00 0.00 3.46
811 953 5.279384 GGCTACTCGTGAAGATTATTCGAA 58.721 41.667 0.00 0.00 0.00 3.71
812 954 4.261489 GGGCTACTCGTGAAGATTATTCGA 60.261 45.833 0.00 0.00 0.00 3.71
813 955 3.982058 GGGCTACTCGTGAAGATTATTCG 59.018 47.826 0.00 0.00 0.00 3.34
814 956 4.745620 GTGGGCTACTCGTGAAGATTATTC 59.254 45.833 0.00 0.00 0.00 1.75
815 957 4.406003 AGTGGGCTACTCGTGAAGATTATT 59.594 41.667 0.00 0.00 33.17 1.40
816 958 3.961408 AGTGGGCTACTCGTGAAGATTAT 59.039 43.478 0.00 0.00 33.17 1.28
817 959 3.130516 CAGTGGGCTACTCGTGAAGATTA 59.869 47.826 0.00 0.00 37.60 1.75
818 960 2.093973 CAGTGGGCTACTCGTGAAGATT 60.094 50.000 0.00 0.00 37.60 2.40
819 961 1.478510 CAGTGGGCTACTCGTGAAGAT 59.521 52.381 0.00 0.00 37.60 2.40
820 962 0.888619 CAGTGGGCTACTCGTGAAGA 59.111 55.000 0.00 0.00 37.60 2.87
821 963 0.888619 TCAGTGGGCTACTCGTGAAG 59.111 55.000 0.00 0.00 37.60 3.02
822 964 0.601558 GTCAGTGGGCTACTCGTGAA 59.398 55.000 0.00 0.00 37.60 3.18
823 965 0.251209 AGTCAGTGGGCTACTCGTGA 60.251 55.000 0.00 0.00 37.60 4.35
824 966 0.109086 CAGTCAGTGGGCTACTCGTG 60.109 60.000 0.00 0.00 37.60 4.35
825 967 1.251527 CCAGTCAGTGGGCTACTCGT 61.252 60.000 0.00 0.00 43.63 4.18
826 968 1.513158 CCAGTCAGTGGGCTACTCG 59.487 63.158 0.00 0.00 43.63 4.18
835 977 2.313172 GCGCAGTCACCAGTCAGTG 61.313 63.158 0.30 0.00 39.20 3.66
836 978 2.029666 GCGCAGTCACCAGTCAGT 59.970 61.111 0.30 0.00 0.00 3.41
837 979 1.301244 AAGCGCAGTCACCAGTCAG 60.301 57.895 11.47 0.00 0.00 3.51
838 980 1.595109 CAAGCGCAGTCACCAGTCA 60.595 57.895 11.47 0.00 0.00 3.41
839 981 2.959357 GCAAGCGCAGTCACCAGTC 61.959 63.158 11.47 0.00 38.36 3.51
840 982 2.974698 GCAAGCGCAGTCACCAGT 60.975 61.111 11.47 0.00 38.36 4.00
841 983 4.081030 CGCAAGCGCAGTCACCAG 62.081 66.667 11.47 0.00 38.40 4.00
842 984 4.600576 TCGCAAGCGCAGTCACCA 62.601 61.111 11.47 0.00 38.40 4.17
843 985 3.300667 CTTCGCAAGCGCAGTCACC 62.301 63.158 11.47 0.00 38.40 4.02
844 986 1.831389 TTCTTCGCAAGCGCAGTCAC 61.831 55.000 11.47 0.00 38.40 3.67
858 1000 1.727335 CTCGTCGGGCTTTTCTTCTTC 59.273 52.381 0.00 0.00 0.00 2.87
874 1018 3.681835 GTGGAGCCGTGGACTCGT 61.682 66.667 0.00 0.00 34.87 4.18
1049 1214 2.202427 GCGGTGGTAATGTTGCGC 60.202 61.111 0.00 0.00 0.00 6.09
1100 1287 1.794864 CTACTGCTGCTGCTGCTTG 59.205 57.895 27.67 22.10 41.07 4.01
1101 1288 2.039405 GCTACTGCTGCTGCTGCTT 61.039 57.895 27.67 18.47 41.07 3.91
1103 1290 2.745100 TGCTACTGCTGCTGCTGC 60.745 61.111 22.51 22.51 41.07 5.25
1104 1291 1.670083 TGTGCTACTGCTGCTGCTG 60.670 57.895 18.66 18.66 42.70 4.41
1127 1341 0.037697 CCATTCCGTCTTGGTCGTCA 60.038 55.000 0.00 0.00 39.52 4.35
1148 1384 1.745566 CGTCGTACGACACACAAAGA 58.254 50.000 38.60 5.57 46.05 2.52
1151 1387 2.005012 CGCGTCGTACGACACACAA 61.005 57.895 38.60 7.83 46.05 3.33
1756 2022 2.437716 CAACATTAGCGGCCGGGT 60.438 61.111 29.38 15.71 0.00 5.28
1767 2033 1.366111 CCGCCGTTCGATCCAACATT 61.366 55.000 4.06 0.00 41.67 2.71
1787 2053 2.154963 CCACATATCATTTACCGCGTCG 59.845 50.000 4.92 0.00 0.00 5.12
1795 2065 6.558775 AGAGCCCTAACTCCACATATCATTTA 59.441 38.462 0.00 0.00 37.39 1.40
1977 2247 2.045242 CTGCACATCTGGGCTGCT 60.045 61.111 5.93 0.00 46.62 4.24
2203 2478 5.743636 ATTTGTTGCTCCATGTACCAAAT 57.256 34.783 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.