Multiple sequence alignment - TraesCS6D01G074000

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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 TraesCS6D01G074000 chr6D 100.000 2765 0 0 1 2765 37840089 37837325 0.000000e+00 5107
1 TraesCS6D01G074000 chr6D 94.737 1045 41 5 857 1895 37881333 37880297 0.000000e+00 1613
2 TraesCS6D01G074000 chr6D 90.874 1041 59 10 854 1874 37735990 37734966 0.000000e+00 1363
3 TraesCS6D01G074000 chr6D 91.393 883 63 5 1895 2764 374103604 374104486 0.000000e+00 1197
4 TraesCS6D01G074000 chr6D 90.572 891 67 5 1892 2765 7447855 7446965 0.000000e+00 1164
5 TraesCS6D01G074000 chr6D 94.194 310 10 4 529 837 37877936 37877634 1.500000e-127 466
6 TraesCS6D01G074000 chr6B 92.514 1042 67 3 857 1895 88572972 88571939 0.000000e+00 1482
7 TraesCS6D01G074000 chr6B 91.033 1026 69 8 854 1875 88498643 88497637 0.000000e+00 1363
8 TraesCS6D01G074000 chr6B 83.636 165 13 3 1892 2043 182592289 182592452 2.870000e-30 143
9 TraesCS6D01G074000 chr6A 91.732 1028 60 6 857 1875 49132100 49131089 0.000000e+00 1404
10 TraesCS6D01G074000 chr5D 93.832 843 46 5 1 842 542355275 542356112 0.000000e+00 1264
11 TraesCS6D01G074000 chr5D 90.930 882 64 5 1897 2765 382081773 382082651 0.000000e+00 1171
12 TraesCS6D01G074000 chr5D 91.234 308 24 3 531 837 542316931 542317236 1.530000e-112 416
13 TraesCS6D01G074000 chr4D 91.206 887 63 6 1893 2765 19347375 19346490 0.000000e+00 1192
14 TraesCS6D01G074000 chr7D 91.260 881 66 4 1896 2765 635996867 635995987 0.000000e+00 1190
15 TraesCS6D01G074000 chr7D 89.435 407 29 6 1893 2286 332883237 332883642 4.110000e-138 501
16 TraesCS6D01G074000 chr2D 91.094 887 65 7 1892 2765 399427339 399428224 0.000000e+00 1188
17 TraesCS6D01G074000 chr2D 91.146 881 60 9 1901 2765 458301706 458302584 0.000000e+00 1179
18 TraesCS6D01G074000 chr7A 90.868 887 66 10 1893 2765 92365650 92364765 0.000000e+00 1175
19 TraesCS6D01G074000 chr4A 90.858 886 68 1 1893 2765 71081753 71082638 0.000000e+00 1175
20 TraesCS6D01G074000 chr5A 90.600 883 70 5 1896 2765 521835060 521835942 0.000000e+00 1158
21 TraesCS6D01G074000 chr1B 90.271 884 66 6 1895 2764 637935480 637934603 0.000000e+00 1138
22 TraesCS6D01G074000 chr1D 91.709 784 51 2 1892 2661 461759411 461760194 0.000000e+00 1075
23 TraesCS6D01G074000 chr3A 88.984 817 76 2 1893 2696 596241349 596240534 0.000000e+00 998
24 TraesCS6D01G074000 chr3B 87.373 491 46 4 1893 2370 636120932 636121419 1.450000e-152 549
25 TraesCS6D01G074000 chr4B 80.686 554 78 15 1893 2431 156976094 156976633 1.190000e-108 403


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 TraesCS6D01G074000 chr6D 37837325 37840089 2764 True 5107.0 5107 100.0000 1 2765 1 chr6D.!!$R3 2764
1 TraesCS6D01G074000 chr6D 37734966 37735990 1024 True 1363.0 1363 90.8740 854 1874 1 chr6D.!!$R2 1020
2 TraesCS6D01G074000 chr6D 374103604 374104486 882 False 1197.0 1197 91.3930 1895 2764 1 chr6D.!!$F1 869
3 TraesCS6D01G074000 chr6D 7446965 7447855 890 True 1164.0 1164 90.5720 1892 2765 1 chr6D.!!$R1 873
4 TraesCS6D01G074000 chr6D 37877634 37881333 3699 True 1039.5 1613 94.4655 529 1895 2 chr6D.!!$R4 1366
5 TraesCS6D01G074000 chr6B 88571939 88572972 1033 True 1482.0 1482 92.5140 857 1895 1 chr6B.!!$R2 1038
6 TraesCS6D01G074000 chr6B 88497637 88498643 1006 True 1363.0 1363 91.0330 854 1875 1 chr6B.!!$R1 1021
7 TraesCS6D01G074000 chr6A 49131089 49132100 1011 True 1404.0 1404 91.7320 857 1875 1 chr6A.!!$R1 1018
8 TraesCS6D01G074000 chr5D 542355275 542356112 837 False 1264.0 1264 93.8320 1 842 1 chr5D.!!$F3 841
9 TraesCS6D01G074000 chr5D 382081773 382082651 878 False 1171.0 1171 90.9300 1897 2765 1 chr5D.!!$F1 868
10 TraesCS6D01G074000 chr4D 19346490 19347375 885 True 1192.0 1192 91.2060 1893 2765 1 chr4D.!!$R1 872
11 TraesCS6D01G074000 chr7D 635995987 635996867 880 True 1190.0 1190 91.2600 1896 2765 1 chr7D.!!$R1 869
12 TraesCS6D01G074000 chr2D 399427339 399428224 885 False 1188.0 1188 91.0940 1892 2765 1 chr2D.!!$F1 873
13 TraesCS6D01G074000 chr2D 458301706 458302584 878 False 1179.0 1179 91.1460 1901 2765 1 chr2D.!!$F2 864
14 TraesCS6D01G074000 chr7A 92364765 92365650 885 True 1175.0 1175 90.8680 1893 2765 1 chr7A.!!$R1 872
15 TraesCS6D01G074000 chr4A 71081753 71082638 885 False 1175.0 1175 90.8580 1893 2765 1 chr4A.!!$F1 872
16 TraesCS6D01G074000 chr5A 521835060 521835942 882 False 1158.0 1158 90.6000 1896 2765 1 chr5A.!!$F1 869
17 TraesCS6D01G074000 chr1B 637934603 637935480 877 True 1138.0 1138 90.2710 1895 2764 1 chr1B.!!$R1 869
18 TraesCS6D01G074000 chr1D 461759411 461760194 783 False 1075.0 1075 91.7090 1892 2661 1 chr1D.!!$F1 769
19 TraesCS6D01G074000 chr3A 596240534 596241349 815 True 998.0 998 88.9840 1893 2696 1 chr3A.!!$R1 803
20 TraesCS6D01G074000 chr4B 156976094 156976633 539 False 403.0 403 80.6860 1893 2431 1 chr4B.!!$F1 538

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
989 1001 0.032815 TCACGACTTGCGATCCAACA 59.967 50.0 0.0 0.0 44.57 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1958 1986 1.679944 CCCATACACAACCTCCTGCTG 60.68 57.143 0.0 0.0 0.0 4.41 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
35 36 1.699656 CTCAACCGAGCTCGCCAATG 61.700 60.000 30.49 22.56 38.18 2.82
66 67 1.953559 AAGCTGACAAGAAGCGTTCA 58.046 45.000 0.00 0.00 45.59 3.18
81 82 2.916111 CGTTCAGATCGGGTTTTTGTG 58.084 47.619 0.00 0.00 0.00 3.33
91 92 2.890945 CGGGTTTTTGTGGAAGGAGATT 59.109 45.455 0.00 0.00 0.00 2.40
94 95 3.006859 GGTTTTTGTGGAAGGAGATTGGG 59.993 47.826 0.00 0.00 0.00 4.12
108 109 4.502950 GGAGATTGGGTCTATCTGAAGCTG 60.503 50.000 0.00 0.00 37.29 4.24
137 138 0.953960 GTACAAACCTCGGTGGCAGG 60.954 60.000 0.00 0.00 40.22 4.85
161 162 2.949644 GGGCTAATCATAAGTTGGCGTT 59.050 45.455 0.00 0.00 34.33 4.84
164 165 3.625764 GCTAATCATAAGTTGGCGTTCCA 59.374 43.478 0.00 0.00 41.55 3.53
190 191 0.690762 TGGTCCCTTTCAGGTGCTAC 59.309 55.000 0.00 0.00 31.93 3.58
192 193 1.073284 GGTCCCTTTCAGGTGCTACAA 59.927 52.381 0.00 0.00 31.93 2.41
216 217 2.295602 GGGGGAGGTCGCCTACAAA 61.296 63.158 12.43 0.00 46.94 2.83
275 276 4.566545 TTCATGTTTCTCAATTGCGTGT 57.433 36.364 0.00 0.00 0.00 4.49
293 294 2.341101 TGGCTCTTCCTCCGTCGAC 61.341 63.158 5.18 5.18 35.26 4.20
294 295 2.047443 GGCTCTTCCTCCGTCGACT 61.047 63.158 14.70 0.00 0.00 4.18
333 334 1.688311 CCCGTCTTGGATGAGGACCTA 60.688 57.143 0.00 0.00 42.00 3.08
335 336 2.379972 CGTCTTGGATGAGGACCTACT 58.620 52.381 0.00 0.00 0.00 2.57
355 356 4.962155 ACTTCCACTTCAAGTTCCTACAG 58.038 43.478 0.00 0.00 29.29 2.74
383 384 1.785041 GAGAAACGGCTGCTGCAACA 61.785 55.000 17.89 0.00 41.91 3.33
400 401 2.099141 ACATGGACATCGTCAAGTGG 57.901 50.000 0.00 0.00 33.68 4.00
419 420 0.747283 GAGCAGGGCAAGATCCAGTG 60.747 60.000 0.00 0.00 0.00 3.66
450 451 2.268920 GCGTCCTTGGCCATCTGA 59.731 61.111 6.09 0.00 0.00 3.27
472 473 0.702902 AGACCTGGTACCTCTTCGGA 59.297 55.000 14.36 0.00 36.31 4.55
473 474 1.288335 AGACCTGGTACCTCTTCGGAT 59.712 52.381 14.36 0.00 36.31 4.18
481 482 1.892209 ACCTCTTCGGATGCGTTTTT 58.108 45.000 6.49 0.00 36.31 1.94
534 535 0.887387 AACGGTGGGGAAATGTCACG 60.887 55.000 0.00 0.00 32.65 4.35
547 548 1.890876 TGTCACGGGAATGGACAAAG 58.109 50.000 0.00 0.00 38.50 2.77
600 601 2.364317 CGGCCTGGGAGGAAGAGA 60.364 66.667 0.00 0.00 37.67 3.10
603 604 0.985490 GGCCTGGGAGGAAGAGACAT 60.985 60.000 0.00 0.00 37.67 3.06
617 618 0.608130 AGACATGCCAACTCACGCTA 59.392 50.000 0.00 0.00 0.00 4.26
623 624 1.298859 GCCAACTCACGCTACCAAGG 61.299 60.000 0.00 0.00 0.00 3.61
650 651 5.221244 CGATGTGGACCAACTGAGTATATGA 60.221 44.000 0.00 0.00 0.00 2.15
669 670 1.404479 AAGGTGTGCGTGGGTAGTGA 61.404 55.000 0.00 0.00 0.00 3.41
676 677 1.215647 CGTGGGTAGTGAGTGAGGC 59.784 63.158 0.00 0.00 0.00 4.70
685 686 3.444703 AGTGAGTGAGGCATCGATTAC 57.555 47.619 0.00 0.00 0.00 1.89
709 710 3.001406 ACTAGAACCGGCCGCCTT 61.001 61.111 22.85 13.36 0.00 4.35
737 738 2.234296 CCTCTCCCACCCTTGGCTT 61.234 63.158 0.00 0.00 42.35 4.35
739 740 0.322906 CTCTCCCACCCTTGGCTTTC 60.323 60.000 0.00 0.00 42.35 2.62
740 741 0.772124 TCTCCCACCCTTGGCTTTCT 60.772 55.000 0.00 0.00 42.35 2.52
741 742 0.322906 CTCCCACCCTTGGCTTTCTC 60.323 60.000 0.00 0.00 42.35 2.87
742 743 1.065410 TCCCACCCTTGGCTTTCTCA 61.065 55.000 0.00 0.00 42.35 3.27
785 786 4.537945 ACCCTAGCTACCTGTATCTTGA 57.462 45.455 0.00 0.00 0.00 3.02
786 787 5.081315 ACCCTAGCTACCTGTATCTTGAT 57.919 43.478 0.00 0.00 0.00 2.57
787 788 5.081032 ACCCTAGCTACCTGTATCTTGATC 58.919 45.833 0.00 0.00 0.00 2.92
788 789 4.464597 CCCTAGCTACCTGTATCTTGATCC 59.535 50.000 0.00 0.00 0.00 3.36
789 790 5.080337 CCTAGCTACCTGTATCTTGATCCA 58.920 45.833 0.00 0.00 0.00 3.41
790 791 5.184864 CCTAGCTACCTGTATCTTGATCCAG 59.815 48.000 0.00 0.00 0.00 3.86
791 792 3.323403 AGCTACCTGTATCTTGATCCAGC 59.677 47.826 0.00 0.00 0.00 4.85
792 793 3.556004 GCTACCTGTATCTTGATCCAGCC 60.556 52.174 0.00 0.00 0.00 4.85
793 794 2.481441 ACCTGTATCTTGATCCAGCCA 58.519 47.619 0.00 0.00 0.00 4.75
794 795 2.846206 ACCTGTATCTTGATCCAGCCAA 59.154 45.455 0.00 0.00 0.00 4.52
795 796 3.461085 ACCTGTATCTTGATCCAGCCAAT 59.539 43.478 0.00 0.00 0.00 3.16
796 797 4.079558 ACCTGTATCTTGATCCAGCCAATT 60.080 41.667 0.00 0.00 0.00 2.32
797 798 4.277672 CCTGTATCTTGATCCAGCCAATTG 59.722 45.833 0.00 0.00 0.00 2.32
798 799 5.114764 TGTATCTTGATCCAGCCAATTGA 57.885 39.130 7.12 0.00 0.00 2.57
799 800 5.128205 TGTATCTTGATCCAGCCAATTGAG 58.872 41.667 7.12 0.00 0.00 3.02
800 801 4.515028 ATCTTGATCCAGCCAATTGAGA 57.485 40.909 7.12 0.00 0.00 3.27
801 802 3.614092 TCTTGATCCAGCCAATTGAGAC 58.386 45.455 7.12 0.00 0.00 3.36
802 803 3.009363 TCTTGATCCAGCCAATTGAGACA 59.991 43.478 7.12 0.00 0.00 3.41
803 804 2.995283 TGATCCAGCCAATTGAGACAG 58.005 47.619 7.12 0.00 0.00 3.51
804 805 2.306805 TGATCCAGCCAATTGAGACAGT 59.693 45.455 7.12 0.00 0.00 3.55
805 806 2.189594 TCCAGCCAATTGAGACAGTG 57.810 50.000 7.12 0.00 0.00 3.66
806 807 1.699083 TCCAGCCAATTGAGACAGTGA 59.301 47.619 7.12 0.00 0.00 3.41
807 808 2.306805 TCCAGCCAATTGAGACAGTGAT 59.693 45.455 7.12 0.00 0.00 3.06
808 809 3.087031 CCAGCCAATTGAGACAGTGATT 58.913 45.455 7.12 0.00 0.00 2.57
809 810 3.128242 CCAGCCAATTGAGACAGTGATTC 59.872 47.826 7.12 0.00 0.00 2.52
810 811 3.128242 CAGCCAATTGAGACAGTGATTCC 59.872 47.826 7.12 0.00 0.00 3.01
811 812 3.009916 AGCCAATTGAGACAGTGATTCCT 59.990 43.478 7.12 0.00 0.00 3.36
812 813 4.225942 AGCCAATTGAGACAGTGATTCCTA 59.774 41.667 7.12 0.00 0.00 2.94
813 814 5.104193 AGCCAATTGAGACAGTGATTCCTAT 60.104 40.000 7.12 0.00 0.00 2.57
814 815 5.238214 GCCAATTGAGACAGTGATTCCTATC 59.762 44.000 7.12 0.00 0.00 2.08
815 816 6.351711 CCAATTGAGACAGTGATTCCTATCA 58.648 40.000 7.12 0.00 38.45 2.15
816 817 6.996879 CCAATTGAGACAGTGATTCCTATCAT 59.003 38.462 7.12 0.00 42.49 2.45
817 818 8.152898 CCAATTGAGACAGTGATTCCTATCATA 58.847 37.037 7.12 0.00 42.49 2.15
818 819 9.551734 CAATTGAGACAGTGATTCCTATCATAA 57.448 33.333 0.00 0.00 42.49 1.90
819 820 9.553064 AATTGAGACAGTGATTCCTATCATAAC 57.447 33.333 0.00 0.00 42.49 1.89
820 821 7.904558 TGAGACAGTGATTCCTATCATAACT 57.095 36.000 0.00 0.00 42.49 2.24
821 822 8.996651 TGAGACAGTGATTCCTATCATAACTA 57.003 34.615 0.00 0.00 42.49 2.24
822 823 9.072375 TGAGACAGTGATTCCTATCATAACTAG 57.928 37.037 0.00 0.00 42.49 2.57
823 824 9.073475 GAGACAGTGATTCCTATCATAACTAGT 57.927 37.037 0.00 0.00 42.49 2.57
824 825 9.427821 AGACAGTGATTCCTATCATAACTAGTT 57.572 33.333 13.68 13.68 42.49 2.24
825 826 9.469807 GACAGTGATTCCTATCATAACTAGTTG 57.530 37.037 18.56 3.11 42.49 3.16
826 827 8.982723 ACAGTGATTCCTATCATAACTAGTTGT 58.017 33.333 18.56 8.87 42.49 3.32
829 830 9.694137 GTGATTCCTATCATAACTAGTTGTACC 57.306 37.037 18.56 0.00 42.49 3.34
830 831 8.573885 TGATTCCTATCATAACTAGTTGTACCG 58.426 37.037 18.56 0.25 35.87 4.02
831 832 7.886629 TTCCTATCATAACTAGTTGTACCGT 57.113 36.000 18.56 2.39 0.00 4.83
832 833 7.268199 TCCTATCATAACTAGTTGTACCGTG 57.732 40.000 18.56 7.33 0.00 4.94
833 834 6.830324 TCCTATCATAACTAGTTGTACCGTGT 59.170 38.462 18.56 0.00 0.00 4.49
834 835 7.012704 TCCTATCATAACTAGTTGTACCGTGTC 59.987 40.741 18.56 0.00 0.00 3.67
835 836 5.963176 TCATAACTAGTTGTACCGTGTCA 57.037 39.130 18.56 0.00 0.00 3.58
836 837 6.519679 TCATAACTAGTTGTACCGTGTCAT 57.480 37.500 18.56 0.00 0.00 3.06
837 838 6.327154 TCATAACTAGTTGTACCGTGTCATG 58.673 40.000 18.56 9.43 0.00 3.07
838 839 4.595762 AACTAGTTGTACCGTGTCATGT 57.404 40.909 7.48 0.00 0.00 3.21
839 840 5.710513 AACTAGTTGTACCGTGTCATGTA 57.289 39.130 7.48 0.00 0.00 2.29
840 841 5.051891 ACTAGTTGTACCGTGTCATGTAC 57.948 43.478 8.10 8.10 38.22 2.90
841 842 4.763793 ACTAGTTGTACCGTGTCATGTACT 59.236 41.667 13.57 0.00 38.48 2.73
842 843 4.170292 AGTTGTACCGTGTCATGTACTC 57.830 45.455 13.57 8.80 38.48 2.59
843 844 3.057033 AGTTGTACCGTGTCATGTACTCC 60.057 47.826 13.57 6.91 38.48 3.85
844 845 1.820519 TGTACCGTGTCATGTACTCCC 59.179 52.381 13.57 0.00 38.48 4.30
845 846 2.097825 GTACCGTGTCATGTACTCCCT 58.902 52.381 0.00 0.00 35.55 4.20
846 847 1.183549 ACCGTGTCATGTACTCCCTC 58.816 55.000 0.00 0.00 0.00 4.30
847 848 0.460311 CCGTGTCATGTACTCCCTCC 59.540 60.000 0.00 0.00 0.00 4.30
848 849 0.100682 CGTGTCATGTACTCCCTCCG 59.899 60.000 0.00 0.00 0.00 4.63
849 850 1.183549 GTGTCATGTACTCCCTCCGT 58.816 55.000 0.00 0.00 0.00 4.69
850 851 2.372264 GTGTCATGTACTCCCTCCGTA 58.628 52.381 0.00 0.00 0.00 4.02
851 852 2.098770 GTGTCATGTACTCCCTCCGTAC 59.901 54.545 0.00 0.00 38.13 3.67
862 863 0.866061 CCTCCGTACACGCGATCAAG 60.866 60.000 15.93 0.21 38.18 3.02
885 886 1.668253 CGCCGACCGACGTAAACTTC 61.668 60.000 0.00 0.00 40.02 3.01
985 997 3.389206 GCTCACGACTTGCGATCC 58.611 61.111 0.00 0.00 44.57 3.36
986 998 1.446099 GCTCACGACTTGCGATCCA 60.446 57.895 0.00 0.00 44.57 3.41
987 999 1.014044 GCTCACGACTTGCGATCCAA 61.014 55.000 0.00 0.00 44.57 3.53
988 1000 0.716108 CTCACGACTTGCGATCCAAC 59.284 55.000 0.00 0.00 44.57 3.77
989 1001 0.032815 TCACGACTTGCGATCCAACA 59.967 50.000 0.00 0.00 44.57 3.33
990 1002 0.439985 CACGACTTGCGATCCAACAG 59.560 55.000 0.00 0.00 44.57 3.16
991 1003 0.317160 ACGACTTGCGATCCAACAGA 59.683 50.000 0.00 0.00 44.57 3.41
1550 1562 2.032681 GGAGAACAAGGCGCTGGT 59.967 61.111 7.64 0.00 0.00 4.00
1695 1707 2.813179 GATGGCCAACTACGCGCTG 61.813 63.158 10.96 0.62 0.00 5.18
1811 1823 6.252228 GCTGTTTTGATTCCAAGATCGATTTC 59.748 38.462 0.00 0.00 33.23 2.17
1829 1851 5.052040 CGATTTCGATACAACTCTCTCTTGC 60.052 44.000 0.00 0.00 43.02 4.01
1914 1938 2.180276 AGGATGCCGATATCTACCACC 58.820 52.381 0.34 0.00 0.00 4.61
1958 1986 2.546778 CCACATACGGTGTATGGTGTC 58.453 52.381 18.24 0.00 46.44 3.67
1974 2015 1.070134 GTGTCAGCAGGAGGTTGTGTA 59.930 52.381 0.00 0.00 0.00 2.90
2044 2085 3.815401 GCCACATGCCCAATAAGTACTAG 59.185 47.826 0.00 0.00 0.00 2.57
2087 2128 1.940752 GCACGAAGCAAAAATGCCCAT 60.941 47.619 0.00 0.00 44.79 4.00
2297 2338 3.994392 CGTGTGTGATTAACTACTTGCCT 59.006 43.478 0.00 0.00 0.00 4.75
2299 2340 4.091509 GTGTGTGATTAACTACTTGCCTCG 59.908 45.833 0.00 0.00 0.00 4.63
2342 2383 2.485903 TGTGTGTTTACCTAGTTGCCG 58.514 47.619 0.00 0.00 0.00 5.69
2344 2385 1.202663 TGTGTTTACCTAGTTGCCGCA 60.203 47.619 0.00 0.00 0.00 5.69
2416 2458 3.068560 GTTTATCTGGTTGCCACGTACA 58.931 45.455 0.00 0.00 0.00 2.90
2475 2519 2.610976 GCCATGTGTGTGTACCGAGTTA 60.611 50.000 0.00 0.00 0.00 2.24
2477 2521 3.305813 CCATGTGTGTGTACCGAGTTACT 60.306 47.826 0.00 0.00 0.00 2.24
2549 2596 0.751643 AAAAGCAGTTCGCCCACACT 60.752 50.000 0.00 0.00 44.04 3.55
2676 2810 3.066190 CAGCCCCGTCCTACGTGA 61.066 66.667 0.00 0.00 40.58 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.557443 GCTCGGTTGAGGTGTTGACG 61.557 60.000 0.00 0.00 42.79 4.35
35 36 7.426929 TTCTTGTCAGCTTTCTCTTTCATAC 57.573 36.000 0.00 0.00 0.00 2.39
66 67 2.107552 TCCTTCCACAAAAACCCGATCT 59.892 45.455 0.00 0.00 0.00 2.75
81 82 4.227197 TCAGATAGACCCAATCTCCTTCC 58.773 47.826 0.00 0.00 39.04 3.46
91 92 1.571955 TGCAGCTTCAGATAGACCCA 58.428 50.000 0.00 0.00 0.00 4.51
94 95 2.977914 TGGTTGCAGCTTCAGATAGAC 58.022 47.619 0.00 0.00 0.00 2.59
108 109 2.093152 CGAGGTTTGTACGTATGGTTGC 59.907 50.000 0.00 0.00 0.00 4.17
137 138 1.880027 CCAACTTATGATTAGCCCGGC 59.120 52.381 0.00 0.00 0.00 6.13
161 162 4.151883 CTGAAAGGGACCAAAGAAATGGA 58.848 43.478 0.00 0.00 43.54 3.41
190 191 1.303317 CGACCTCCCCCACCTTTTG 60.303 63.158 0.00 0.00 0.00 2.44
192 193 3.647771 GCGACCTCCCCCACCTTT 61.648 66.667 0.00 0.00 0.00 3.11
275 276 2.035155 TCGACGGAGGAAGAGCCA 59.965 61.111 0.00 0.00 40.02 4.75
293 294 3.754188 GCAACTCTGGCATAACTTCAG 57.246 47.619 0.00 0.00 0.00 3.02
333 334 4.743955 GCTGTAGGAACTTGAAGTGGAAGT 60.744 45.833 0.00 0.00 41.75 3.01
335 336 3.740115 GCTGTAGGAACTTGAAGTGGAA 58.260 45.455 0.00 0.00 41.75 3.53
383 384 1.406069 GCTCCACTTGACGATGTCCAT 60.406 52.381 0.00 0.00 0.00 3.41
400 401 0.747283 CACTGGATCTTGCCCTGCTC 60.747 60.000 0.00 0.00 0.00 4.26
446 447 2.650322 AGAGGTACCAGGTCTTCTCAGA 59.350 50.000 15.94 0.00 0.00 3.27
450 451 2.448453 CGAAGAGGTACCAGGTCTTCT 58.552 52.381 27.16 14.44 42.70 2.85
472 473 1.540435 AATGCCCGGGAAAAACGCAT 61.540 50.000 29.31 15.93 41.77 4.73
473 474 2.203771 AATGCCCGGGAAAAACGCA 61.204 52.632 29.31 14.00 0.00 5.24
481 482 4.757355 CCAAGCCAATGCCCGGGA 62.757 66.667 29.31 10.35 38.69 5.14
520 521 0.701731 ATTCCCGTGACATTTCCCCA 59.298 50.000 0.00 0.00 0.00 4.96
534 535 1.304134 ACGGCCTTTGTCCATTCCC 60.304 57.895 0.00 0.00 0.00 3.97
547 548 1.095807 GCCTTGGAGTAATCACGGCC 61.096 60.000 0.00 0.00 41.79 6.13
594 595 1.728971 CGTGAGTTGGCATGTCTCTTC 59.271 52.381 0.00 0.00 0.00 2.87
598 599 0.608130 TAGCGTGAGTTGGCATGTCT 59.392 50.000 0.00 0.00 0.00 3.41
600 601 0.673644 GGTAGCGTGAGTTGGCATGT 60.674 55.000 0.00 0.00 0.00 3.21
603 604 0.602638 CTTGGTAGCGTGAGTTGGCA 60.603 55.000 0.00 0.00 0.00 4.92
617 618 2.933287 TCCACATCGGCCCTTGGT 60.933 61.111 0.00 0.00 33.14 3.67
623 624 2.040544 CAGTTGGTCCACATCGGCC 61.041 63.158 0.00 0.00 33.14 6.13
650 651 1.070786 CACTACCCACGCACACCTT 59.929 57.895 0.00 0.00 0.00 3.50
685 686 0.030908 GGCCGGTTCTAGTCTGATCG 59.969 60.000 1.90 0.00 0.00 3.69
689 690 2.202756 GCGGCCGGTTCTAGTCTG 60.203 66.667 29.38 0.00 0.00 3.51
709 710 1.535444 TGGGAGAGGAGAACGCCAA 60.535 57.895 0.00 0.00 0.00 4.52
737 738 5.393068 AGCAAGAATGGGGATAATGAGAA 57.607 39.130 0.00 0.00 0.00 2.87
739 740 6.479006 TCATAGCAAGAATGGGGATAATGAG 58.521 40.000 0.00 0.00 0.00 2.90
740 741 6.452757 TCATAGCAAGAATGGGGATAATGA 57.547 37.500 0.00 0.00 0.00 2.57
741 742 6.071728 GGTTCATAGCAAGAATGGGGATAATG 60.072 42.308 0.00 0.00 0.00 1.90
742 743 6.012745 GGTTCATAGCAAGAATGGGGATAAT 58.987 40.000 0.00 0.00 0.00 1.28
785 786 2.306805 TCACTGTCTCAATTGGCTGGAT 59.693 45.455 5.42 0.00 0.00 3.41
786 787 1.699083 TCACTGTCTCAATTGGCTGGA 59.301 47.619 5.42 0.00 0.00 3.86
787 788 2.189594 TCACTGTCTCAATTGGCTGG 57.810 50.000 5.42 0.00 0.00 4.85
788 789 3.128242 GGAATCACTGTCTCAATTGGCTG 59.872 47.826 5.42 3.72 0.00 4.85
789 790 3.009916 AGGAATCACTGTCTCAATTGGCT 59.990 43.478 5.42 0.00 0.00 4.75
790 791 3.350833 AGGAATCACTGTCTCAATTGGC 58.649 45.455 5.42 0.00 0.00 4.52
791 792 6.351711 TGATAGGAATCACTGTCTCAATTGG 58.648 40.000 5.42 0.00 37.20 3.16
792 793 9.551734 TTATGATAGGAATCACTGTCTCAATTG 57.448 33.333 0.00 0.00 44.79 2.32
793 794 9.553064 GTTATGATAGGAATCACTGTCTCAATT 57.447 33.333 0.00 0.00 44.79 2.32
794 795 8.932610 AGTTATGATAGGAATCACTGTCTCAAT 58.067 33.333 0.00 0.00 44.79 2.57
795 796 8.311395 AGTTATGATAGGAATCACTGTCTCAA 57.689 34.615 0.00 0.00 44.79 3.02
796 797 7.904558 AGTTATGATAGGAATCACTGTCTCA 57.095 36.000 0.00 0.00 44.79 3.27
797 798 9.073475 ACTAGTTATGATAGGAATCACTGTCTC 57.927 37.037 0.00 0.00 44.79 3.36
798 799 9.427821 AACTAGTTATGATAGGAATCACTGTCT 57.572 33.333 6.26 0.00 44.79 3.41
799 800 9.469807 CAACTAGTTATGATAGGAATCACTGTC 57.530 37.037 8.04 0.00 44.79 3.51
800 801 8.982723 ACAACTAGTTATGATAGGAATCACTGT 58.017 33.333 8.04 0.00 44.79 3.55
803 804 9.694137 GGTACAACTAGTTATGATAGGAATCAC 57.306 37.037 8.04 0.00 44.79 3.06
804 805 8.573885 CGGTACAACTAGTTATGATAGGAATCA 58.426 37.037 8.04 0.00 46.01 2.57
805 806 8.574737 ACGGTACAACTAGTTATGATAGGAATC 58.425 37.037 8.04 0.00 0.00 2.52
806 807 8.358148 CACGGTACAACTAGTTATGATAGGAAT 58.642 37.037 8.04 0.00 0.00 3.01
807 808 7.340232 ACACGGTACAACTAGTTATGATAGGAA 59.660 37.037 8.04 0.00 0.00 3.36
808 809 6.830324 ACACGGTACAACTAGTTATGATAGGA 59.170 38.462 8.04 0.00 0.00 2.94
809 810 7.035840 ACACGGTACAACTAGTTATGATAGG 57.964 40.000 8.04 0.00 0.00 2.57
810 811 7.700505 TGACACGGTACAACTAGTTATGATAG 58.299 38.462 8.04 0.00 0.00 2.08
811 812 7.628769 TGACACGGTACAACTAGTTATGATA 57.371 36.000 8.04 0.00 0.00 2.15
812 813 6.519679 TGACACGGTACAACTAGTTATGAT 57.480 37.500 8.04 0.00 0.00 2.45
813 814 5.963176 TGACACGGTACAACTAGTTATGA 57.037 39.130 8.04 0.00 0.00 2.15
814 815 6.097356 ACATGACACGGTACAACTAGTTATG 58.903 40.000 8.04 6.93 0.00 1.90
815 816 6.276832 ACATGACACGGTACAACTAGTTAT 57.723 37.500 8.04 0.00 0.00 1.89
816 817 5.710513 ACATGACACGGTACAACTAGTTA 57.289 39.130 8.04 0.00 0.00 2.24
817 818 4.595762 ACATGACACGGTACAACTAGTT 57.404 40.909 1.12 1.12 0.00 2.24
818 819 4.763793 AGTACATGACACGGTACAACTAGT 59.236 41.667 17.04 0.00 41.74 2.57
819 820 5.306532 AGTACATGACACGGTACAACTAG 57.693 43.478 17.04 0.00 41.74 2.57
820 821 4.156556 GGAGTACATGACACGGTACAACTA 59.843 45.833 17.04 0.00 41.74 2.24
821 822 3.057033 GGAGTACATGACACGGTACAACT 60.057 47.826 17.04 3.41 41.74 3.16
822 823 3.248266 GGAGTACATGACACGGTACAAC 58.752 50.000 17.04 11.82 41.74 3.32
823 824 2.231964 GGGAGTACATGACACGGTACAA 59.768 50.000 17.04 0.00 41.74 2.41
824 825 1.820519 GGGAGTACATGACACGGTACA 59.179 52.381 17.04 0.00 41.74 2.90
825 826 2.097825 AGGGAGTACATGACACGGTAC 58.902 52.381 0.00 10.00 40.06 3.34
826 827 2.372264 GAGGGAGTACATGACACGGTA 58.628 52.381 0.00 0.00 0.00 4.02
827 828 1.183549 GAGGGAGTACATGACACGGT 58.816 55.000 0.00 0.00 0.00 4.83
828 829 0.460311 GGAGGGAGTACATGACACGG 59.540 60.000 0.00 0.00 0.00 4.94
829 830 0.100682 CGGAGGGAGTACATGACACG 59.899 60.000 0.00 0.00 0.00 4.49
830 831 1.183549 ACGGAGGGAGTACATGACAC 58.816 55.000 0.00 0.00 0.00 3.67
831 832 2.291089 TGTACGGAGGGAGTACATGACA 60.291 50.000 0.00 0.00 46.38 3.58
832 833 2.372264 TGTACGGAGGGAGTACATGAC 58.628 52.381 0.00 0.00 46.38 3.06
833 834 2.812836 TGTACGGAGGGAGTACATGA 57.187 50.000 0.00 0.00 46.38 3.07
837 838 1.431036 GCGTGTACGGAGGGAGTAC 59.569 63.158 6.55 0.08 43.34 2.73
838 839 2.108514 CGCGTGTACGGAGGGAGTA 61.109 63.158 6.55 0.00 40.23 2.59
839 840 3.437795 CGCGTGTACGGAGGGAGT 61.438 66.667 6.55 0.00 40.23 3.85
840 841 2.389866 GATCGCGTGTACGGAGGGAG 62.390 65.000 5.77 0.00 40.23 4.30
841 842 2.438975 ATCGCGTGTACGGAGGGA 60.439 61.111 5.77 4.75 40.23 4.20
842 843 2.025727 GATCGCGTGTACGGAGGG 59.974 66.667 5.77 0.00 40.23 4.30
843 844 0.866061 CTTGATCGCGTGTACGGAGG 60.866 60.000 5.77 0.00 40.23 4.30
844 845 0.098200 TCTTGATCGCGTGTACGGAG 59.902 55.000 5.77 0.00 40.23 4.63
845 846 0.179181 GTCTTGATCGCGTGTACGGA 60.179 55.000 5.77 2.69 40.23 4.69
846 847 1.461317 CGTCTTGATCGCGTGTACGG 61.461 60.000 5.77 0.00 40.23 4.02
847 848 1.901173 CGTCTTGATCGCGTGTACG 59.099 57.895 5.77 5.44 43.27 3.67
848 849 1.624323 GCGTCTTGATCGCGTGTAC 59.376 57.895 5.77 0.00 43.94 2.90
849 850 4.066769 GCGTCTTGATCGCGTGTA 57.933 55.556 5.77 0.00 43.94 2.90
963 975 4.077188 GCAAGTCGTGAGCGTGCC 62.077 66.667 0.00 0.00 36.94 5.01
984 996 0.961019 CCATGGTGTTGGTCTGTTGG 59.039 55.000 2.57 0.00 31.74 3.77
985 997 0.314935 GCCATGGTGTTGGTCTGTTG 59.685 55.000 14.67 0.00 39.11 3.33
986 998 0.827507 GGCCATGGTGTTGGTCTGTT 60.828 55.000 14.67 0.00 38.40 3.16
987 999 1.228552 GGCCATGGTGTTGGTCTGT 60.229 57.895 14.67 0.00 38.40 3.41
988 1000 2.334946 CGGCCATGGTGTTGGTCTG 61.335 63.158 14.67 0.00 39.32 3.51
989 1001 2.034066 CGGCCATGGTGTTGGTCT 59.966 61.111 14.67 0.00 39.32 3.85
990 1002 3.747976 GCGGCCATGGTGTTGGTC 61.748 66.667 14.67 0.00 39.11 4.02
1811 1823 5.612865 GTTTTGCAAGAGAGAGTTGTATCG 58.387 41.667 0.00 0.00 0.00 2.92
1914 1938 2.475111 GCATGTCGAATATACCACACGG 59.525 50.000 0.00 0.00 38.77 4.94
1958 1986 1.679944 CCCATACACAACCTCCTGCTG 60.680 57.143 0.00 0.00 0.00 4.41
1974 2015 1.956477 GCAATTCTAATGTCCGCCCAT 59.044 47.619 0.00 0.00 0.00 4.00
2044 2085 2.125106 GTGCGGGGTGGAGATGAC 60.125 66.667 0.00 0.00 0.00 3.06
2087 2128 2.125326 ATAGCTGCGCCAGGACGTA 61.125 57.895 4.18 0.00 34.88 3.57
2111 2152 3.612681 CGTCATCCCGCGGGGTAT 61.613 66.667 42.36 27.71 44.74 2.73
2227 2268 6.481976 CGGCAACTACCATAAATTAGACATGA 59.518 38.462 0.00 0.00 0.00 3.07
2297 2338 3.991773 GCAACTACTGTTTGACCATACGA 59.008 43.478 0.00 0.00 33.52 3.43
2299 2340 4.069304 TGGCAACTACTGTTTGACCATAC 58.931 43.478 0.00 0.00 33.52 2.39
2625 2759 2.594592 GAGTTTGCCCACACGCCT 60.595 61.111 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.