Multiple sequence alignment - TraesCS4B01G162700

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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 TraesCS4B01G162700 chr4B 100.000 3816 0 0 1 3816 328326913 328330728 0.000000e+00 7047.0
1 TraesCS4B01G162700 chr4B 91.667 60 4 1 2352 2411 489088108 489088050 8.790000e-12 82.4
2 TraesCS4B01G162700 chr4D 96.620 1982 59 2 873 2850 283883597 283881620 0.000000e+00 3282.0
3 TraesCS4B01G162700 chr3A 93.717 939 50 8 2881 3816 742912498 742911566 0.000000e+00 1399.0
4 TraesCS4B01G162700 chr3A 98.203 779 9 5 1 776 663677452 663676676 0.000000e+00 1356.0
5 TraesCS4B01G162700 chr2B 93.045 949 60 5 2869 3816 83934955 83935898 0.000000e+00 1382.0
6 TraesCS4B01G162700 chr2B 94.872 39 2 0 1919 1957 78047785 78047747 1.140000e-05 62.1
7 TraesCS4B01G162700 chr2B 88.235 51 6 0 1907 1957 78071963 78072013 1.140000e-05 62.1
8 TraesCS4B01G162700 chr1B 92.857 952 57 10 2868 3816 554145253 554144310 0.000000e+00 1371.0
9 TraesCS4B01G162700 chr1B 98.581 775 10 1 1 774 673416656 673415882 0.000000e+00 1369.0
10 TraesCS4B01G162700 chr7A 93.170 937 56 6 2881 3816 23121247 23120318 0.000000e+00 1369.0
11 TraesCS4B01G162700 chr7A 98.446 772 10 2 1 771 542101261 542102031 0.000000e+00 1358.0
12 TraesCS4B01G162700 chr6A 93.170 937 57 5 2881 3816 378254681 378255611 0.000000e+00 1369.0
13 TraesCS4B01G162700 chr6A 92.495 946 63 8 2872 3815 305474043 305474982 0.000000e+00 1347.0
14 TraesCS4B01G162700 chr6A 84.231 1040 129 19 1805 2834 12119158 12118144 0.000000e+00 979.0
15 TraesCS4B01G162700 chr1D 92.842 950 57 9 2869 3816 292547912 292548852 0.000000e+00 1367.0
16 TraesCS4B01G162700 chr2A 98.573 771 9 2 1 770 238721792 238721023 0.000000e+00 1362.0
17 TraesCS4B01G162700 chr2A 98.448 773 10 2 1 771 98162469 98161697 0.000000e+00 1360.0
18 TraesCS4B01G162700 chr2A 88.235 51 6 0 1907 1957 51945126 51945176 1.140000e-05 62.1
19 TraesCS4B01G162700 chr5B 98.446 772 10 2 1 771 430675491 430674721 0.000000e+00 1358.0
20 TraesCS4B01G162700 chr5B 92.743 937 62 4 2881 3816 457501276 457500345 0.000000e+00 1349.0
21 TraesCS4B01G162700 chr1A 98.323 775 11 2 1 774 145994763 145993990 0.000000e+00 1358.0
22 TraesCS4B01G162700 chr1A 98.446 772 11 1 1 771 532926092 532925321 0.000000e+00 1358.0
23 TraesCS4B01G162700 chr6B 98.198 777 11 3 1 776 184908265 184909039 0.000000e+00 1354.0
24 TraesCS4B01G162700 chr6B 84.348 1035 127 18 1809 2834 19776834 19775826 0.000000e+00 981.0
25 TraesCS4B01G162700 chr6B 82.343 589 66 18 1163 1726 19777873 19777298 9.590000e-131 477.0
26 TraesCS4B01G162700 chr2D 92.624 949 58 8 2869 3814 620564930 620563991 0.000000e+00 1354.0
27 TraesCS4B01G162700 chr6D 84.860 1037 119 20 1809 2834 10514022 10513013 0.000000e+00 1011.0
28 TraesCS4B01G162700 chrUn 85.714 343 47 2 2218 2560 328226113 328225773 1.010000e-95 361.0
29 TraesCS4B01G162700 chrUn 85.714 343 47 2 2218 2560 382573949 382573609 1.010000e-95 361.0
30 TraesCS4B01G162700 chrUn 85.714 343 47 2 2218 2560 465144234 465143894 1.010000e-95 361.0
31 TraesCS4B01G162700 chr7D 94.737 57 3 0 2340 2396 617641507 617641451 5.250000e-14 89.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G162700 chr4B 328326913 328330728 3815 False 7047 7047 100.0000 1 3816 1 chr4B.!!$F1 3815
1 TraesCS4B01G162700 chr4D 283881620 283883597 1977 True 3282 3282 96.6200 873 2850 1 chr4D.!!$R1 1977
2 TraesCS4B01G162700 chr3A 742911566 742912498 932 True 1399 1399 93.7170 2881 3816 1 chr3A.!!$R2 935
3 TraesCS4B01G162700 chr3A 663676676 663677452 776 True 1356 1356 98.2030 1 776 1 chr3A.!!$R1 775
4 TraesCS4B01G162700 chr2B 83934955 83935898 943 False 1382 1382 93.0450 2869 3816 1 chr2B.!!$F2 947
5 TraesCS4B01G162700 chr1B 554144310 554145253 943 True 1371 1371 92.8570 2868 3816 1 chr1B.!!$R1 948
6 TraesCS4B01G162700 chr1B 673415882 673416656 774 True 1369 1369 98.5810 1 774 1 chr1B.!!$R2 773
7 TraesCS4B01G162700 chr7A 23120318 23121247 929 True 1369 1369 93.1700 2881 3816 1 chr7A.!!$R1 935
8 TraesCS4B01G162700 chr7A 542101261 542102031 770 False 1358 1358 98.4460 1 771 1 chr7A.!!$F1 770
9 TraesCS4B01G162700 chr6A 378254681 378255611 930 False 1369 1369 93.1700 2881 3816 1 chr6A.!!$F2 935
10 TraesCS4B01G162700 chr6A 305474043 305474982 939 False 1347 1347 92.4950 2872 3815 1 chr6A.!!$F1 943
11 TraesCS4B01G162700 chr6A 12118144 12119158 1014 True 979 979 84.2310 1805 2834 1 chr6A.!!$R1 1029
12 TraesCS4B01G162700 chr1D 292547912 292548852 940 False 1367 1367 92.8420 2869 3816 1 chr1D.!!$F1 947
13 TraesCS4B01G162700 chr2A 238721023 238721792 769 True 1362 1362 98.5730 1 770 1 chr2A.!!$R2 769
14 TraesCS4B01G162700 chr2A 98161697 98162469 772 True 1360 1360 98.4480 1 771 1 chr2A.!!$R1 770
15 TraesCS4B01G162700 chr5B 430674721 430675491 770 True 1358 1358 98.4460 1 771 1 chr5B.!!$R1 770
16 TraesCS4B01G162700 chr5B 457500345 457501276 931 True 1349 1349 92.7430 2881 3816 1 chr5B.!!$R2 935
17 TraesCS4B01G162700 chr1A 145993990 145994763 773 True 1358 1358 98.3230 1 774 1 chr1A.!!$R1 773
18 TraesCS4B01G162700 chr1A 532925321 532926092 771 True 1358 1358 98.4460 1 771 1 chr1A.!!$R2 770
19 TraesCS4B01G162700 chr6B 184908265 184909039 774 False 1354 1354 98.1980 1 776 1 chr6B.!!$F1 775
20 TraesCS4B01G162700 chr6B 19775826 19777873 2047 True 729 981 83.3455 1163 2834 2 chr6B.!!$R1 1671
21 TraesCS4B01G162700 chr2D 620563991 620564930 939 True 1354 1354 92.6240 2869 3814 1 chr2D.!!$R1 945
22 TraesCS4B01G162700 chr6D 10513013 10514022 1009 True 1011 1011 84.8600 1809 2834 1 chr6D.!!$R1 1025

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
823 827 0.46840 GCTCCGACACCTAGGATCCT 60.468 60.0 20.48 20.48 35.75 3.24 F
2155 2594 0.60864 ATTGGATCGATCTACCGGCC 59.391 55.0 23.96 7.69 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2234 2673 0.033504 GCCAGTCCGAAGTCTGACAA 59.966 55.000 10.88 0.00 33.32 3.18 R
3139 3584 2.038837 GCGTTGTACAAGGGGGAGC 61.039 63.158 25.12 13.17 0.00 4.70 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
67 68 3.853355 AGCAGGATCCGATGATTCTTT 57.147 42.857 5.98 0.00 34.36 2.52
230 231 0.541764 GCTTGGTTGGGTTCCCATGA 60.542 55.000 11.65 0.00 35.84 3.07
287 288 4.163078 CCATCCTAGAGAACATTGTGTCCT 59.837 45.833 0.00 0.00 0.00 3.85
652 655 9.849166 TTGTTCGGTGAAATTTCCTAATATTTC 57.151 29.630 15.48 0.00 39.86 2.17
775 779 7.842525 GCACGAGCGTTATACTAGTAAATAA 57.157 36.000 6.70 0.24 0.00 1.40
776 780 7.926345 GCACGAGCGTTATACTAGTAAATAAG 58.074 38.462 6.70 0.00 0.00 1.73
777 781 7.060403 GCACGAGCGTTATACTAGTAAATAAGG 59.940 40.741 6.70 9.66 0.00 2.69
778 782 7.536622 CACGAGCGTTATACTAGTAAATAAGGG 59.463 40.741 6.70 0.42 0.00 3.95
779 783 7.025963 CGAGCGTTATACTAGTAAATAAGGGG 58.974 42.308 6.70 0.00 0.00 4.79
780 784 7.237209 AGCGTTATACTAGTAAATAAGGGGG 57.763 40.000 6.70 0.00 0.00 5.40
781 785 7.012607 AGCGTTATACTAGTAAATAAGGGGGA 58.987 38.462 6.70 0.00 0.00 4.81
782 786 7.178097 AGCGTTATACTAGTAAATAAGGGGGAG 59.822 40.741 6.70 0.00 0.00 4.30
783 787 7.039434 GCGTTATACTAGTAAATAAGGGGGAGT 60.039 40.741 6.70 0.00 0.00 3.85
784 788 9.520515 CGTTATACTAGTAAATAAGGGGGAGTA 57.479 37.037 6.70 0.00 0.00 2.59
788 792 9.964408 ATACTAGTAAATAAGGGGGAGTAACTT 57.036 33.333 6.70 0.00 0.00 2.66
790 794 9.788815 ACTAGTAAATAAGGGGGAGTAACTTAA 57.211 33.333 0.00 0.00 31.25 1.85
793 797 9.745018 AGTAAATAAGGGGGAGTAACTTAAAAC 57.255 33.333 0.00 0.00 31.25 2.43
794 798 7.692460 AAATAAGGGGGAGTAACTTAAAACG 57.308 36.000 0.00 0.00 31.25 3.60
795 799 4.712051 AAGGGGGAGTAACTTAAAACGT 57.288 40.909 0.00 0.00 0.00 3.99
796 800 4.011966 AGGGGGAGTAACTTAAAACGTG 57.988 45.455 0.00 0.00 0.00 4.49
797 801 3.392285 AGGGGGAGTAACTTAAAACGTGT 59.608 43.478 0.00 0.00 0.00 4.49
798 802 4.592778 AGGGGGAGTAACTTAAAACGTGTA 59.407 41.667 0.00 0.00 0.00 2.90
799 803 5.071653 AGGGGGAGTAACTTAAAACGTGTAA 59.928 40.000 0.00 0.00 0.00 2.41
800 804 5.762711 GGGGGAGTAACTTAAAACGTGTAAA 59.237 40.000 0.00 0.00 0.00 2.01
801 805 6.073058 GGGGGAGTAACTTAAAACGTGTAAAG 60.073 42.308 0.00 0.00 0.00 1.85
802 806 6.365839 GGGAGTAACTTAAAACGTGTAAAGC 58.634 40.000 0.00 0.00 0.00 3.51
803 807 6.067039 GGAGTAACTTAAAACGTGTAAAGCG 58.933 40.000 0.00 0.00 0.00 4.68
804 808 5.977731 AGTAACTTAAAACGTGTAAAGCGG 58.022 37.500 0.00 0.00 0.00 5.52
805 809 3.257745 ACTTAAAACGTGTAAAGCGGC 57.742 42.857 0.00 0.00 0.00 6.53
806 810 2.874086 ACTTAAAACGTGTAAAGCGGCT 59.126 40.909 0.00 0.00 0.00 5.52
807 811 3.059393 ACTTAAAACGTGTAAAGCGGCTC 60.059 43.478 1.45 0.00 0.00 4.70
808 812 0.589708 AAAACGTGTAAAGCGGCTCC 59.410 50.000 1.45 0.00 0.00 4.70
809 813 1.562575 AAACGTGTAAAGCGGCTCCG 61.563 55.000 1.45 3.56 43.09 4.63
810 814 2.126228 CGTGTAAAGCGGCTCCGA 60.126 61.111 13.11 0.00 42.83 4.55
811 815 2.442188 CGTGTAAAGCGGCTCCGAC 61.442 63.158 13.11 2.33 42.83 4.79
812 816 1.373748 GTGTAAAGCGGCTCCGACA 60.374 57.895 13.11 5.20 42.83 4.35
813 817 1.373748 TGTAAAGCGGCTCCGACAC 60.374 57.895 13.11 4.11 42.83 3.67
814 818 2.098831 GTAAAGCGGCTCCGACACC 61.099 63.158 13.11 0.00 42.83 4.16
815 819 2.280552 TAAAGCGGCTCCGACACCT 61.281 57.895 13.11 0.00 42.83 4.00
816 820 0.966875 TAAAGCGGCTCCGACACCTA 60.967 55.000 13.11 0.00 42.83 3.08
817 821 2.227089 AAAGCGGCTCCGACACCTAG 62.227 60.000 13.11 0.00 42.83 3.02
818 822 4.208686 GCGGCTCCGACACCTAGG 62.209 72.222 13.11 7.41 42.83 3.02
819 823 2.439701 CGGCTCCGACACCTAGGA 60.440 66.667 17.98 0.00 42.83 2.94
820 824 1.828660 CGGCTCCGACACCTAGGAT 60.829 63.158 17.98 2.27 42.83 3.24
821 825 1.797211 CGGCTCCGACACCTAGGATC 61.797 65.000 17.98 11.62 42.83 3.36
822 826 1.465200 GGCTCCGACACCTAGGATCC 61.465 65.000 17.98 2.48 35.91 3.36
823 827 0.468400 GCTCCGACACCTAGGATCCT 60.468 60.000 20.48 20.48 35.75 3.24
824 828 1.202903 GCTCCGACACCTAGGATCCTA 60.203 57.143 20.53 20.53 35.75 2.94
825 829 2.506444 CTCCGACACCTAGGATCCTAC 58.494 57.143 18.00 6.82 35.75 3.18
826 830 1.848388 TCCGACACCTAGGATCCTACA 59.152 52.381 18.00 0.01 0.00 2.74
827 831 2.445905 TCCGACACCTAGGATCCTACAT 59.554 50.000 18.00 5.81 0.00 2.29
828 832 2.820787 CCGACACCTAGGATCCTACATC 59.179 54.545 18.00 11.12 0.00 3.06
829 833 2.820787 CGACACCTAGGATCCTACATCC 59.179 54.545 18.00 5.54 38.47 3.51
835 839 8.072422 ACACCTAGGATCCTACATCCTGTGTA 62.072 46.154 18.00 0.00 45.59 2.90
836 840 9.978629 ACACCTAGGATCCTACATCCTGTGTAC 62.979 48.148 18.00 0.00 45.59 2.90
837 841 4.544564 AGGATCCTACATCCTGTGTACT 57.455 45.455 14.27 0.00 46.18 2.73
838 842 4.219115 AGGATCCTACATCCTGTGTACTG 58.781 47.826 14.27 0.00 46.18 2.74
839 843 3.322254 GGATCCTACATCCTGTGTACTGG 59.678 52.174 3.84 1.86 42.29 4.00
840 844 3.750501 TCCTACATCCTGTGTACTGGA 57.249 47.619 12.20 12.20 45.92 3.86
841 845 3.632333 TCCTACATCCTGTGTACTGGAG 58.368 50.000 14.61 9.90 45.24 3.86
842 846 3.011369 TCCTACATCCTGTGTACTGGAGT 59.989 47.826 14.61 13.82 45.24 3.85
843 847 3.769844 CCTACATCCTGTGTACTGGAGTT 59.230 47.826 14.61 7.67 45.24 3.01
844 848 3.685139 ACATCCTGTGTACTGGAGTTG 57.315 47.619 14.61 11.56 45.24 3.16
845 849 2.303022 ACATCCTGTGTACTGGAGTTGG 59.697 50.000 14.61 7.91 45.24 3.77
846 850 2.097110 TCCTGTGTACTGGAGTTGGT 57.903 50.000 6.55 0.00 38.77 3.67
847 851 3.247948 TCCTGTGTACTGGAGTTGGTA 57.752 47.619 6.55 0.00 38.77 3.25
848 852 2.895404 TCCTGTGTACTGGAGTTGGTAC 59.105 50.000 6.55 0.00 38.77 3.34
849 853 2.028385 CCTGTGTACTGGAGTTGGTACC 60.028 54.545 4.43 4.43 37.92 3.34
850 854 2.631062 CTGTGTACTGGAGTTGGTACCA 59.369 50.000 11.60 11.60 37.92 3.25
851 855 2.366266 TGTGTACTGGAGTTGGTACCAC 59.634 50.000 16.04 10.20 37.92 4.16
852 856 1.614903 TGTACTGGAGTTGGTACCACG 59.385 52.381 16.04 2.63 37.92 4.94
853 857 1.067354 GTACTGGAGTTGGTACCACGG 60.067 57.143 16.04 10.84 34.10 4.94
854 858 1.295423 CTGGAGTTGGTACCACGGG 59.705 63.158 16.04 0.00 32.44 5.28
855 859 1.459921 TGGAGTTGGTACCACGGGT 60.460 57.895 16.04 0.00 40.16 5.28
856 860 1.004200 GGAGTTGGTACCACGGGTG 60.004 63.158 16.04 0.00 36.19 4.61
870 874 4.874970 CCACGGGTGGTGTATTATACTAC 58.125 47.826 9.72 0.00 45.52 2.73
871 875 4.341806 CCACGGGTGGTGTATTATACTACA 59.658 45.833 9.72 0.00 45.52 2.74
872 876 5.163426 CCACGGGTGGTGTATTATACTACAA 60.163 44.000 9.72 0.00 45.52 2.41
873 877 6.463331 CCACGGGTGGTGTATTATACTACAAT 60.463 42.308 9.72 0.00 45.52 2.71
874 878 6.987992 CACGGGTGGTGTATTATACTACAATT 59.012 38.462 4.64 0.00 41.89 2.32
875 879 7.496591 CACGGGTGGTGTATTATACTACAATTT 59.503 37.037 4.64 0.00 41.89 1.82
876 880 7.712205 ACGGGTGGTGTATTATACTACAATTTC 59.288 37.037 4.64 0.00 33.59 2.17
1488 1504 2.438434 CCATGGACGGCAAGGACC 60.438 66.667 5.56 0.00 0.00 4.46
1550 1581 1.048601 ACTCCTTCAGCCTCAACGAA 58.951 50.000 0.00 0.00 0.00 3.85
1631 1662 1.597027 CGTCCACAAGGGCTTCGTT 60.597 57.895 0.00 0.00 37.38 3.85
1741 1778 4.806286 GCTGGTAATATAATCCTTGCCCGT 60.806 45.833 0.00 0.00 0.00 5.28
1747 1784 6.628919 AATATAATCCTTGCCCGTTGTTAC 57.371 37.500 0.00 0.00 0.00 2.50
1779 2206 5.311121 TGTCAGATTCCTTACCAACCCTAAA 59.689 40.000 0.00 0.00 0.00 1.85
1953 2380 1.605058 GCAGCCTCGAGAACCACCTA 61.605 60.000 15.71 0.00 0.00 3.08
2076 2503 1.281419 TCTACCGGGATTTCAAGGCA 58.719 50.000 6.32 0.00 0.00 4.75
2154 2593 2.338500 GAATTGGATCGATCTACCGGC 58.662 52.381 23.96 7.67 0.00 6.13
2155 2594 0.608640 ATTGGATCGATCTACCGGCC 59.391 55.000 23.96 7.69 0.00 6.13
2157 2596 2.567049 GATCGATCTACCGGCCGG 59.433 66.667 42.17 42.17 42.03 6.13
2234 2673 0.034896 ACAGGAATTCACGGCGAAGT 59.965 50.000 16.62 0.00 36.95 3.01
2263 2702 2.971598 CGGACTGGCCAAGATGGGT 61.972 63.158 7.01 0.00 38.19 4.51
2272 2711 1.689233 CAAGATGGGTCCCGAGGGA 60.689 63.158 6.80 6.80 42.90 4.20
2341 2780 1.292223 GCCCGAGTACTTGCAGACA 59.708 57.895 4.39 0.00 0.00 3.41
2740 3182 1.358725 CGCTCTCCGCCAAATTTCGA 61.359 55.000 1.16 0.00 34.21 3.71
2763 3205 2.825836 GATGAAGGGTGCCGGCAG 60.826 66.667 33.73 0.00 0.00 4.85
2844 3286 3.849951 CGTCCGCCTACCTGCCAT 61.850 66.667 0.00 0.00 0.00 4.40
2847 3289 2.203070 CCGCCTACCTGCCATGAC 60.203 66.667 0.00 0.00 0.00 3.06
2850 3292 1.521681 GCCTACCTGCCATGACGTC 60.522 63.158 9.11 9.11 0.00 4.34
2851 3293 1.961180 GCCTACCTGCCATGACGTCT 61.961 60.000 17.92 0.00 0.00 4.18
2852 3294 0.537188 CCTACCTGCCATGACGTCTT 59.463 55.000 17.92 7.74 0.00 3.01
2853 3295 1.066143 CCTACCTGCCATGACGTCTTT 60.066 52.381 17.92 1.03 0.00 2.52
2854 3296 2.615493 CCTACCTGCCATGACGTCTTTT 60.615 50.000 17.92 0.00 0.00 2.27
2855 3297 1.523758 ACCTGCCATGACGTCTTTTC 58.476 50.000 17.92 5.08 0.00 2.29
2856 3298 0.443869 CCTGCCATGACGTCTTTTCG 59.556 55.000 17.92 1.68 0.00 3.46
2857 3299 0.179215 CTGCCATGACGTCTTTTCGC 60.179 55.000 17.92 11.66 0.00 4.70
2858 3300 1.225745 GCCATGACGTCTTTTCGCG 60.226 57.895 17.92 0.00 0.00 5.87
2859 3301 1.225745 CCATGACGTCTTTTCGCGC 60.226 57.895 17.92 0.00 0.00 6.86
2860 3302 1.491127 CATGACGTCTTTTCGCGCA 59.509 52.632 17.92 0.00 0.00 6.09
2861 3303 0.095245 CATGACGTCTTTTCGCGCAT 59.905 50.000 17.92 0.00 32.43 4.73
2862 3304 0.796312 ATGACGTCTTTTCGCGCATT 59.204 45.000 17.92 0.00 0.00 3.56
2863 3305 0.110867 TGACGTCTTTTCGCGCATTG 60.111 50.000 17.92 0.00 0.00 2.82
2864 3306 0.110823 GACGTCTTTTCGCGCATTGT 60.111 50.000 8.75 0.00 0.00 2.71
2865 3307 1.125384 GACGTCTTTTCGCGCATTGTA 59.875 47.619 8.75 0.00 0.00 2.41
2866 3308 1.730064 ACGTCTTTTCGCGCATTGTAT 59.270 42.857 8.75 0.00 0.00 2.29
3032 3476 7.432148 TGAGAGCCAAGGAATTACATAGTTA 57.568 36.000 0.00 0.00 0.00 2.24
3066 3510 4.307032 AGGAACTACATGGTTGCTTGAT 57.693 40.909 0.00 0.00 43.46 2.57
3170 3615 1.308998 ACAACGCCTCTTCTTTGGTG 58.691 50.000 0.00 0.00 39.53 4.17
3193 3638 7.420800 GTGTATCCATCATCTTGACAAATTCC 58.579 38.462 0.00 0.00 0.00 3.01
3377 3826 7.989826 TGAGAAAAACCTTTGAAGAAGAAGAG 58.010 34.615 0.00 0.00 0.00 2.85
3576 4026 6.644347 TGCCATTGAAAACTCCTTTAAAACA 58.356 32.000 0.00 0.00 0.00 2.83
3633 4085 6.704493 ACATATACGGGCACTTGTGTTTATAG 59.296 38.462 2.61 0.00 0.00 1.31
3636 4088 2.418628 CGGGCACTTGTGTTTATAGTGG 59.581 50.000 0.00 0.00 39.66 4.00
3686 4138 4.627284 TTACGGAAAACTCATGAAGGGA 57.373 40.909 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 0.539986 GACTTTGGCTATCCCCACGA 59.460 55.000 0.00 0.00 33.82 4.35
230 231 0.693049 ACGAGGAGGCCACATTCTTT 59.307 50.000 5.01 0.00 0.00 2.52
652 655 7.538678 GGTGCTCTAATTAGAAACACAACAATG 59.461 37.037 30.48 14.14 39.42 2.82
775 779 3.392285 ACACGTTTTAAGTTACTCCCCCT 59.608 43.478 0.00 0.00 0.00 4.79
776 780 3.743521 ACACGTTTTAAGTTACTCCCCC 58.256 45.455 0.00 0.00 0.00 5.40
777 781 6.566564 GCTTTACACGTTTTAAGTTACTCCCC 60.567 42.308 2.81 0.00 0.00 4.81
778 782 6.365839 GCTTTACACGTTTTAAGTTACTCCC 58.634 40.000 2.81 0.00 0.00 4.30
779 783 6.067039 CGCTTTACACGTTTTAAGTTACTCC 58.933 40.000 2.81 0.00 0.00 3.85
780 784 6.067039 CCGCTTTACACGTTTTAAGTTACTC 58.933 40.000 2.81 0.00 0.00 2.59
781 785 5.558844 GCCGCTTTACACGTTTTAAGTTACT 60.559 40.000 2.81 0.00 0.00 2.24
782 786 4.608470 GCCGCTTTACACGTTTTAAGTTAC 59.392 41.667 2.81 0.00 0.00 2.50
783 787 4.511082 AGCCGCTTTACACGTTTTAAGTTA 59.489 37.500 2.81 0.00 0.00 2.24
784 788 3.313249 AGCCGCTTTACACGTTTTAAGTT 59.687 39.130 2.81 0.00 0.00 2.66
785 789 2.874086 AGCCGCTTTACACGTTTTAAGT 59.126 40.909 2.81 0.00 0.00 2.24
786 790 3.476181 GAGCCGCTTTACACGTTTTAAG 58.524 45.455 0.00 0.00 0.00 1.85
787 791 2.223845 GGAGCCGCTTTACACGTTTTAA 59.776 45.455 0.00 0.00 0.00 1.52
788 792 1.799994 GGAGCCGCTTTACACGTTTTA 59.200 47.619 0.00 0.00 0.00 1.52
789 793 0.589708 GGAGCCGCTTTACACGTTTT 59.410 50.000 0.00 0.00 0.00 2.43
790 794 1.562575 CGGAGCCGCTTTACACGTTT 61.563 55.000 0.00 0.00 0.00 3.60
791 795 2.025418 CGGAGCCGCTTTACACGTT 61.025 57.895 0.00 0.00 0.00 3.99
792 796 2.431942 CGGAGCCGCTTTACACGT 60.432 61.111 0.00 0.00 0.00 4.49
793 797 2.126228 TCGGAGCCGCTTTACACG 60.126 61.111 3.59 0.00 39.59 4.49
794 798 1.373748 TGTCGGAGCCGCTTTACAC 60.374 57.895 3.59 0.00 39.59 2.90
795 799 1.373748 GTGTCGGAGCCGCTTTACA 60.374 57.895 3.59 0.41 39.59 2.41
796 800 2.098831 GGTGTCGGAGCCGCTTTAC 61.099 63.158 3.59 0.00 39.59 2.01
797 801 0.966875 TAGGTGTCGGAGCCGCTTTA 60.967 55.000 3.59 0.00 39.59 1.85
798 802 2.227089 CTAGGTGTCGGAGCCGCTTT 62.227 60.000 3.59 0.00 39.59 3.51
799 803 2.678934 TAGGTGTCGGAGCCGCTT 60.679 61.111 3.59 0.00 39.59 4.68
800 804 3.141488 CTAGGTGTCGGAGCCGCT 61.141 66.667 3.59 0.00 39.59 5.52
801 805 4.208686 CCTAGGTGTCGGAGCCGC 62.209 72.222 3.59 0.29 39.59 6.53
802 806 1.797211 GATCCTAGGTGTCGGAGCCG 61.797 65.000 9.08 1.74 41.35 5.52
803 807 2.042800 GATCCTAGGTGTCGGAGCC 58.957 63.158 9.08 0.00 31.82 4.70
804 808 0.468400 AGGATCCTAGGTGTCGGAGC 60.468 60.000 14.27 0.00 35.04 4.70
805 809 2.158652 TGTAGGATCCTAGGTGTCGGAG 60.159 54.545 22.30 0.00 31.82 4.63
806 810 1.848388 TGTAGGATCCTAGGTGTCGGA 59.152 52.381 22.30 0.00 0.00 4.55
807 811 2.359981 TGTAGGATCCTAGGTGTCGG 57.640 55.000 22.30 0.00 0.00 4.79
808 812 2.820787 GGATGTAGGATCCTAGGTGTCG 59.179 54.545 22.30 0.00 35.36 4.35
809 813 3.829601 CAGGATGTAGGATCCTAGGTGTC 59.170 52.174 22.30 15.67 46.22 3.67
810 814 3.850752 CAGGATGTAGGATCCTAGGTGT 58.149 50.000 22.30 8.16 46.22 4.16
825 829 2.303022 ACCAACTCCAGTACACAGGATG 59.697 50.000 0.00 0.00 46.00 3.51
826 830 2.621070 ACCAACTCCAGTACACAGGAT 58.379 47.619 0.00 0.00 30.85 3.24
827 831 2.097110 ACCAACTCCAGTACACAGGA 57.903 50.000 0.00 0.00 0.00 3.86
828 832 2.028385 GGTACCAACTCCAGTACACAGG 60.028 54.545 7.15 0.00 40.51 4.00
829 833 2.631062 TGGTACCAACTCCAGTACACAG 59.369 50.000 13.60 0.00 40.51 3.66
830 834 2.366266 GTGGTACCAACTCCAGTACACA 59.634 50.000 18.31 0.00 40.51 3.72
831 835 2.608752 CGTGGTACCAACTCCAGTACAC 60.609 54.545 18.31 0.00 40.51 2.90
832 836 1.614903 CGTGGTACCAACTCCAGTACA 59.385 52.381 18.31 0.00 40.51 2.90
833 837 1.067354 CCGTGGTACCAACTCCAGTAC 60.067 57.143 18.31 0.00 38.49 2.73
834 838 1.259609 CCGTGGTACCAACTCCAGTA 58.740 55.000 18.31 0.00 34.16 2.74
835 839 1.477685 CCCGTGGTACCAACTCCAGT 61.478 60.000 18.31 0.00 34.16 4.00
836 840 1.295423 CCCGTGGTACCAACTCCAG 59.705 63.158 18.31 4.10 34.16 3.86
837 841 1.459921 ACCCGTGGTACCAACTCCA 60.460 57.895 18.31 0.00 32.11 3.86
838 842 1.004200 CACCCGTGGTACCAACTCC 60.004 63.158 18.31 2.76 32.11 3.85
839 843 1.004200 CCACCCGTGGTACCAACTC 60.004 63.158 18.31 3.18 45.53 3.01
840 844 3.153825 CCACCCGTGGTACCAACT 58.846 61.111 18.31 0.00 45.53 3.16
850 854 6.736110 ATTGTAGTATAATACACCACCCGT 57.264 37.500 12.35 0.00 35.44 5.28
851 855 7.711772 TGAAATTGTAGTATAATACACCACCCG 59.288 37.037 12.35 0.00 35.44 5.28
852 856 8.967664 TGAAATTGTAGTATAATACACCACCC 57.032 34.615 12.35 3.14 35.44 4.61
862 866 8.394877 CGCACCTGAAATGAAATTGTAGTATAA 58.605 33.333 0.00 0.00 36.10 0.98
863 867 7.766738 TCGCACCTGAAATGAAATTGTAGTATA 59.233 33.333 0.00 0.00 36.10 1.47
864 868 6.597672 TCGCACCTGAAATGAAATTGTAGTAT 59.402 34.615 0.00 0.00 36.10 2.12
865 869 5.935206 TCGCACCTGAAATGAAATTGTAGTA 59.065 36.000 0.00 0.00 36.10 1.82
866 870 4.759693 TCGCACCTGAAATGAAATTGTAGT 59.240 37.500 0.00 0.00 36.10 2.73
867 871 5.295431 TCGCACCTGAAATGAAATTGTAG 57.705 39.130 0.00 0.00 36.10 2.74
868 872 5.447144 CGATCGCACCTGAAATGAAATTGTA 60.447 40.000 0.26 0.00 36.10 2.41
869 873 4.672542 CGATCGCACCTGAAATGAAATTGT 60.673 41.667 0.26 0.00 36.10 2.71
870 874 3.787634 CGATCGCACCTGAAATGAAATTG 59.212 43.478 0.26 0.00 36.10 2.32
871 875 3.689161 TCGATCGCACCTGAAATGAAATT 59.311 39.130 11.09 0.00 38.98 1.82
872 876 3.270027 TCGATCGCACCTGAAATGAAAT 58.730 40.909 11.09 0.00 0.00 2.17
873 877 2.694213 TCGATCGCACCTGAAATGAAA 58.306 42.857 11.09 0.00 0.00 2.69
874 878 2.378445 TCGATCGCACCTGAAATGAA 57.622 45.000 11.09 0.00 0.00 2.57
875 879 2.473816 GATCGATCGCACCTGAAATGA 58.526 47.619 11.09 0.00 0.00 2.57
876 880 1.190984 CGATCGATCGCACCTGAAATG 59.809 52.381 32.34 4.59 43.84 2.32
896 900 6.436843 ACCATCCATTTTAAACTGATCGTC 57.563 37.500 7.10 0.00 0.00 4.20
902 906 8.561738 AGTGTAGTACCATCCATTTTAAACTG 57.438 34.615 0.00 0.00 0.00 3.16
910 914 5.539193 GCCTAGTAGTGTAGTACCATCCATT 59.461 44.000 0.00 0.00 0.00 3.16
1362 1378 4.323477 CTCGTTCCCGGCCACCAA 62.323 66.667 2.24 0.00 33.95 3.67
1474 1490 4.308458 CGTGGTCCTTGCCGTCCA 62.308 66.667 0.00 0.00 0.00 4.02
1568 1599 1.605058 GGTAGCCGCTGGAGAAGTCA 61.605 60.000 2.16 0.00 0.00 3.41
1665 1696 3.782244 CTGCTTGACGGCGACTGC 61.782 66.667 16.62 16.60 41.71 4.40
1741 1778 3.706802 TCTGACAACCGTACGTAACAA 57.293 42.857 15.21 0.00 0.00 2.83
1747 1784 2.649331 AGGAATCTGACAACCGTACG 57.351 50.000 8.69 8.69 0.00 3.67
1953 2380 2.800544 CGTCGCGGATATCCTTTTGAAT 59.199 45.455 19.61 0.00 0.00 2.57
2022 2449 2.735772 GCCATGGAGGAAGGCGAGA 61.736 63.158 18.40 0.00 41.22 4.04
2076 2503 2.035632 GAGTCGAGGAGGATGTTGGAT 58.964 52.381 0.00 0.00 0.00 3.41
2157 2596 0.103572 TAATTACGAGGCTGCCGGAC 59.896 55.000 13.96 8.17 0.00 4.79
2234 2673 0.033504 GCCAGTCCGAAGTCTGACAA 59.966 55.000 10.88 0.00 33.32 3.18
2263 2702 2.359404 GTGTCCTCTCCCTCGGGA 59.641 66.667 4.32 4.32 42.90 5.14
2272 2711 2.335369 GTGACGTGCGTGTCCTCT 59.665 61.111 0.67 0.00 38.11 3.69
2333 2772 2.431683 GAGGTGGCCTGTCTGCAA 59.568 61.111 3.32 0.00 31.76 4.08
2341 2780 0.904865 TCTTCATCGTGAGGTGGCCT 60.905 55.000 3.32 0.00 44.13 5.19
2627 3066 3.681835 GAGTGCCTCGACCACGGT 61.682 66.667 5.98 0.00 38.22 4.83
2740 3182 2.586792 GCACCCTTCATCTCGGCT 59.413 61.111 0.00 0.00 0.00 5.52
2811 3253 0.950555 GACGTGGCAAGCAGATCACA 60.951 55.000 0.00 0.00 0.00 3.58
2844 3286 0.110867 CAATGCGCGAAAAGACGTCA 60.111 50.000 19.50 0.00 35.59 4.35
2847 3289 2.435685 ATACAATGCGCGAAAAGACG 57.564 45.000 12.10 0.00 0.00 4.18
2850 3292 7.657846 TTAAACATATACAATGCGCGAAAAG 57.342 32.000 12.10 0.00 0.00 2.27
2851 3293 7.751348 ACTTTAAACATATACAATGCGCGAAAA 59.249 29.630 12.10 0.00 0.00 2.29
2852 3294 7.244898 ACTTTAAACATATACAATGCGCGAAA 58.755 30.769 12.10 0.00 0.00 3.46
2853 3295 6.777101 ACTTTAAACATATACAATGCGCGAA 58.223 32.000 12.10 0.00 0.00 4.70
2854 3296 6.352682 ACTTTAAACATATACAATGCGCGA 57.647 33.333 12.10 0.00 0.00 5.87
2855 3297 7.560700 TCTACTTTAAACATATACAATGCGCG 58.439 34.615 0.00 0.00 0.00 6.86
2856 3298 9.710979 TTTCTACTTTAAACATATACAATGCGC 57.289 29.630 0.00 0.00 0.00 6.09
2883 3327 9.650539 TTCATTCAACTCTCTCTCATTCTTTAG 57.349 33.333 0.00 0.00 0.00 1.85
2900 3344 9.118300 AGACTAATGGATCATCTTTCATTCAAC 57.882 33.333 0.00 0.00 32.81 3.18
2945 3389 4.595781 ACTTCCGCCTGGATATAAATACCA 59.404 41.667 0.00 0.00 45.91 3.25
2983 3427 6.752168 AGTAACTATGTGTTTACTTGACCGT 58.248 36.000 0.00 0.00 39.89 4.83
3139 3584 2.038837 GCGTTGTACAAGGGGGAGC 61.039 63.158 25.12 13.17 0.00 4.70
3170 3615 7.814264 AGGAATTTGTCAAGATGATGGATAC 57.186 36.000 0.00 0.00 0.00 2.24
3193 3638 7.772292 TGGAGGAGACATTCAAGATTATTCAAG 59.228 37.037 0.00 0.00 0.00 3.02
3224 3670 4.540099 TCCTCATATTTTTCCCACAGGTCT 59.460 41.667 0.00 0.00 0.00 3.85
3225 3671 4.855340 TCCTCATATTTTTCCCACAGGTC 58.145 43.478 0.00 0.00 0.00 3.85
3226 3672 4.540099 TCTCCTCATATTTTTCCCACAGGT 59.460 41.667 0.00 0.00 0.00 4.00
3396 3845 8.204836 AGTACTCAAGACACATTAGTTGTTCTT 58.795 33.333 0.00 0.00 36.00 2.52
3409 3858 9.499585 GGTTTTTAAAGAAAGTACTCAAGACAC 57.500 33.333 0.00 0.00 0.00 3.67
3597 4048 6.204688 AGTGCCCGTATATGTCATACATTTTG 59.795 38.462 0.00 0.00 39.88 2.44
3633 4085 3.720949 AAAGGTTTTTAACGAGGCCAC 57.279 42.857 5.01 0.00 0.00 5.01
3636 4088 6.490566 TCTCATAAAGGTTTTTAACGAGGC 57.509 37.500 0.00 0.00 35.34 4.70
3637 4089 7.806487 GGTTTCTCATAAAGGTTTTTAACGAGG 59.194 37.037 0.00 0.00 35.34 4.63
3668 4120 4.846779 TTTTCCCTTCATGAGTTTTCCG 57.153 40.909 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.