Multiple sequence alignment - TraesCS5D01G053100

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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 TraesCS5D01G053100 chr5D 100.000 2860 0 0 1 2860 50820344 50817485 0.000000e+00 5282.0
1 TraesCS5D01G053100 chr5D 97.527 1092 22 1 1769 2860 515106353 515105267 0.000000e+00 1862.0
2 TraesCS5D01G053100 chr5D 96.839 601 16 3 1 599 307477013 307477612 0.000000e+00 1002.0
3 TraesCS5D01G053100 chr5D 96.333 600 20 2 1 599 447698445 447697847 0.000000e+00 985.0
4 TraesCS5D01G053100 chr5D 94.391 624 32 3 1 623 313781943 313782564 0.000000e+00 955.0
5 TraesCS5D01G053100 chr5D 91.696 289 23 1 1314 1601 50733744 50734032 1.600000e-107 399.0
6 TraesCS5D01G053100 chr5D 93.333 210 13 1 2054 2262 327614612 327614403 2.770000e-80 309.0
7 TraesCS5D01G053100 chr5D 95.775 142 4 2 2256 2396 327613837 327613697 7.970000e-56 228.0
8 TraesCS5D01G053100 chr5D 94.928 138 6 1 2259 2395 407765525 407765388 6.210000e-52 215.0
9 TraesCS5D01G053100 chr5D 88.119 101 11 1 1596 1696 50771427 50771526 5.010000e-23 119.0
10 TraesCS5D01G053100 chr5B 96.097 1076 28 7 628 1696 53737539 53736471 0.000000e+00 1742.0
11 TraesCS5D01G053100 chr5B 100.000 29 0 0 840 868 53737291 53737263 1.000000e-03 54.7
12 TraesCS5D01G053100 chr2D 97.331 974 26 0 1887 2860 85760690 85759717 0.000000e+00 1655.0
13 TraesCS5D01G053100 chr2D 96.167 600 21 2 1 599 334028981 334029579 0.000000e+00 979.0
14 TraesCS5D01G053100 chr2D 94.703 623 28 5 1 621 165180509 165179890 0.000000e+00 963.0
15 TraesCS5D01G053100 chr2D 94.286 210 11 1 2054 2262 436557055 436556846 1.280000e-83 320.0
16 TraesCS5D01G053100 chr2D 98.400 125 2 0 1767 1891 85765955 85765831 1.330000e-53 220.0
17 TraesCS5D01G053100 chr2D 94.891 137 7 0 2259 2395 436556649 436556513 6.210000e-52 215.0
18 TraesCS5D01G053100 chr4D 96.302 622 22 1 1 621 25367610 25366989 0.000000e+00 1020.0
19 TraesCS5D01G053100 chr4D 91.803 61 3 2 2556 2615 5588558 5588499 1.830000e-12 84.2
20 TraesCS5D01G053100 chr3D 95.024 623 27 4 1 621 42898878 42898258 0.000000e+00 976.0
21 TraesCS5D01G053100 chr3D 96.007 601 22 2 1 599 539349554 539350154 0.000000e+00 976.0
22 TraesCS5D01G053100 chr3D 94.155 633 29 6 1 631 597236390 597235764 0.000000e+00 957.0
23 TraesCS5D01G053100 chr5A 95.685 533 23 0 1164 1696 40153763 40153231 0.000000e+00 857.0
24 TraesCS5D01G053100 chr5A 88.945 398 40 3 1299 1696 40086826 40087219 3.310000e-134 488.0
25 TraesCS5D01G053100 chr5A 89.189 222 18 2 956 1174 40154694 40154476 3.630000e-69 272.0
26 TraesCS5D01G053100 chr5A 83.420 193 7 8 622 809 40154943 40154771 3.820000e-34 156.0
27 TraesCS5D01G053100 chr5A 88.000 125 9 5 863 983 40154822 40154700 2.970000e-30 143.0
28 TraesCS5D01G053100 chr5A 100.000 30 0 0 839 868 40154810 40154781 3.980000e-04 56.5
29 TraesCS5D01G053100 chr1B 92.453 318 18 3 2547 2860 399001135 399001450 1.560000e-122 449.0
30 TraesCS5D01G053100 chr1B 88.889 63 5 2 2550 2612 633778729 633778669 3.060000e-10 76.8
31 TraesCS5D01G053100 chr6B 89.490 314 14 10 2550 2860 642384195 642383898 2.080000e-101 379.0
32 TraesCS5D01G053100 chr1D 94.286 210 11 1 2054 2262 48904306 48904515 1.280000e-83 320.0
33 TraesCS5D01G053100 chr2B 78.472 288 58 4 2550 2834 414613929 414614215 4.870000e-43 185.0
34 TraesCS5D01G053100 chr3A 85.714 140 17 3 2125 2261 211186111 211186250 8.260000e-31 145.0
35 TraesCS5D01G053100 chr7D 96.000 75 3 0 2321 2395 422573487 422573413 3.870000e-24 122.0
36 TraesCS5D01G053100 chr6A 80.263 152 28 2 2093 2242 572870805 572870956 2.330000e-21 113.0
37 TraesCS5D01G053100 chrUn 82.796 93 13 3 2547 2638 89796555 89796465 2.360000e-11 80.5
38 TraesCS5D01G053100 chr6D 79.339 121 19 5 2126 2242 428229164 428229282 2.360000e-11 80.5
39 TraesCS5D01G053100 chr3B 88.889 63 6 1 2547 2609 580808670 580808731 3.060000e-10 76.8


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 TraesCS5D01G053100 chr5D 50817485 50820344 2859 True 5282.00 5282 100.0000 1 2860 1 chr5D.!!$R1 2859
1 TraesCS5D01G053100 chr5D 515105267 515106353 1086 True 1862.00 1862 97.5270 1769 2860 1 chr5D.!!$R4 1091
2 TraesCS5D01G053100 chr5D 307477013 307477612 599 False 1002.00 1002 96.8390 1 599 1 chr5D.!!$F3 598
3 TraesCS5D01G053100 chr5D 447697847 447698445 598 True 985.00 985 96.3330 1 599 1 chr5D.!!$R3 598
4 TraesCS5D01G053100 chr5D 313781943 313782564 621 False 955.00 955 94.3910 1 623 1 chr5D.!!$F4 622
5 TraesCS5D01G053100 chr5D 327613697 327614612 915 True 268.50 309 94.5540 2054 2396 2 chr5D.!!$R5 342
6 TraesCS5D01G053100 chr5B 53736471 53737539 1068 True 898.35 1742 98.0485 628 1696 2 chr5B.!!$R1 1068
7 TraesCS5D01G053100 chr2D 85759717 85760690 973 True 1655.00 1655 97.3310 1887 2860 1 chr2D.!!$R1 973
8 TraesCS5D01G053100 chr2D 334028981 334029579 598 False 979.00 979 96.1670 1 599 1 chr2D.!!$F1 598
9 TraesCS5D01G053100 chr2D 165179890 165180509 619 True 963.00 963 94.7030 1 621 1 chr2D.!!$R3 620
10 TraesCS5D01G053100 chr2D 436556513 436557055 542 True 267.50 320 94.5885 2054 2395 2 chr2D.!!$R4 341
11 TraesCS5D01G053100 chr4D 25366989 25367610 621 True 1020.00 1020 96.3020 1 621 1 chr4D.!!$R2 620
12 TraesCS5D01G053100 chr3D 42898258 42898878 620 True 976.00 976 95.0240 1 621 1 chr3D.!!$R1 620
13 TraesCS5D01G053100 chr3D 539349554 539350154 600 False 976.00 976 96.0070 1 599 1 chr3D.!!$F1 598
14 TraesCS5D01G053100 chr3D 597235764 597236390 626 True 957.00 957 94.1550 1 631 1 chr3D.!!$R2 630
15 TraesCS5D01G053100 chr5A 40153231 40154943 1712 True 296.90 857 91.2588 622 1696 5 chr5A.!!$R1 1074

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
891 1011 0.038526 TGCGAACCGACTTCCTTCTC 60.039 55.0 0.0 0.0 0.0 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2066 2956 0.673644 ACCGACGCTGCAATTAAGCT 60.674 50.0 0.0 0.0 38.57 3.74 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
121 122 9.411801 CGTATGTTGTAGCTGTATGATTCTAAT 57.588 33.333 0.00 0.00 0.00 1.73
133 134 8.696043 TGTATGATTCTAATGGCAATTAAGCT 57.304 30.769 0.00 0.00 34.17 3.74
225 227 5.843019 AGTAAAAGTTGAGATCAAGGGGA 57.157 39.130 0.00 0.00 36.39 4.81
389 392 1.288127 GCAGTACGAGGTTCACCGT 59.712 57.895 0.00 0.00 42.08 4.83
396 399 2.203294 AGGTTCACCGTGTTGCCC 60.203 61.111 0.00 0.00 42.08 5.36
407 410 3.637273 GTTGCCCGTCTCCCCACT 61.637 66.667 0.00 0.00 0.00 4.00
480 484 1.377202 CCGCCACTGCCTACACATT 60.377 57.895 0.00 0.00 0.00 2.71
599 605 4.768968 GGTGTACCGGAATATCTAGCCTAA 59.231 45.833 9.46 0.00 0.00 2.69
668 675 0.622665 AGGCCAAGGACCTTCATCAG 59.377 55.000 5.01 0.00 31.87 2.90
724 732 3.484547 CGGTTGGACTAACGGCGC 61.485 66.667 6.90 0.00 40.28 6.53
725 733 2.357760 GGTTGGACTAACGGCGCA 60.358 61.111 10.83 0.00 40.28 6.09
729 740 1.260561 GTTGGACTAACGGCGCATATG 59.739 52.381 10.83 0.00 0.00 1.78
787 907 1.613925 TGTGAACCGACTTCCTCTCAG 59.386 52.381 0.00 0.00 0.00 3.35
796 916 3.096092 GACTTCCTCTCAGACTCCATGT 58.904 50.000 0.00 0.00 0.00 3.21
797 917 4.274147 GACTTCCTCTCAGACTCCATGTA 58.726 47.826 0.00 0.00 0.00 2.29
798 918 4.678256 ACTTCCTCTCAGACTCCATGTAA 58.322 43.478 0.00 0.00 0.00 2.41
799 919 5.087323 ACTTCCTCTCAGACTCCATGTAAA 58.913 41.667 0.00 0.00 0.00 2.01
800 920 5.544176 ACTTCCTCTCAGACTCCATGTAAAA 59.456 40.000 0.00 0.00 0.00 1.52
801 921 6.043243 ACTTCCTCTCAGACTCCATGTAAAAA 59.957 38.462 0.00 0.00 0.00 1.94
802 922 5.794894 TCCTCTCAGACTCCATGTAAAAAC 58.205 41.667 0.00 0.00 0.00 2.43
803 923 4.938226 CCTCTCAGACTCCATGTAAAAACC 59.062 45.833 0.00 0.00 0.00 3.27
804 924 4.566004 TCTCAGACTCCATGTAAAAACCG 58.434 43.478 0.00 0.00 0.00 4.44
805 925 4.282449 TCTCAGACTCCATGTAAAAACCGA 59.718 41.667 0.00 0.00 0.00 4.69
806 926 4.312443 TCAGACTCCATGTAAAAACCGAC 58.688 43.478 0.00 0.00 0.00 4.79
807 927 4.039973 TCAGACTCCATGTAAAAACCGACT 59.960 41.667 0.00 0.00 0.00 4.18
808 928 4.755123 CAGACTCCATGTAAAAACCGACTT 59.245 41.667 0.00 0.00 0.00 3.01
809 929 5.929992 CAGACTCCATGTAAAAACCGACTTA 59.070 40.000 0.00 0.00 0.00 2.24
810 930 6.594159 CAGACTCCATGTAAAAACCGACTTAT 59.406 38.462 0.00 0.00 0.00 1.73
811 931 7.762615 CAGACTCCATGTAAAAACCGACTTATA 59.237 37.037 0.00 0.00 0.00 0.98
812 932 8.483758 AGACTCCATGTAAAAACCGACTTATAT 58.516 33.333 0.00 0.00 0.00 0.86
813 933 9.106070 GACTCCATGTAAAAACCGACTTATATT 57.894 33.333 0.00 0.00 0.00 1.28
814 934 9.457436 ACTCCATGTAAAAACCGACTTATATTT 57.543 29.630 0.00 0.00 0.00 1.40
815 935 9.716507 CTCCATGTAAAAACCGACTTATATTTG 57.283 33.333 0.00 0.00 0.00 2.32
816 936 8.679100 TCCATGTAAAAACCGACTTATATTTGG 58.321 33.333 0.00 0.00 0.00 3.28
817 937 8.679100 CCATGTAAAAACCGACTTATATTTGGA 58.321 33.333 0.00 0.00 0.00 3.53
837 957 6.903883 TGGATTCTTATTACGTTTCTGAGC 57.096 37.500 0.00 0.00 0.00 4.26
838 958 6.640518 TGGATTCTTATTACGTTTCTGAGCT 58.359 36.000 0.00 0.00 0.00 4.09
839 959 6.535150 TGGATTCTTATTACGTTTCTGAGCTG 59.465 38.462 0.00 0.00 0.00 4.24
840 960 6.757010 GGATTCTTATTACGTTTCTGAGCTGA 59.243 38.462 0.00 0.00 0.00 4.26
841 961 7.277981 GGATTCTTATTACGTTTCTGAGCTGAA 59.722 37.037 0.00 0.00 0.00 3.02
842 962 6.946229 TCTTATTACGTTTCTGAGCTGAAC 57.054 37.500 0.00 0.00 0.00 3.18
843 963 5.867716 TCTTATTACGTTTCTGAGCTGAACC 59.132 40.000 0.00 0.00 0.00 3.62
844 964 2.060326 TACGTTTCTGAGCTGAACCG 57.940 50.000 0.00 0.00 37.75 4.44
845 965 0.387929 ACGTTTCTGAGCTGAACCGA 59.612 50.000 10.10 0.00 35.82 4.69
846 966 0.784778 CGTTTCTGAGCTGAACCGAC 59.215 55.000 0.00 0.00 34.53 4.79
847 967 1.603172 CGTTTCTGAGCTGAACCGACT 60.603 52.381 0.00 0.00 34.53 4.18
848 968 2.484889 GTTTCTGAGCTGAACCGACTT 58.515 47.619 0.00 0.00 0.00 3.01
849 969 2.440539 TTCTGAGCTGAACCGACTTC 57.559 50.000 0.00 0.00 0.00 3.01
850 970 0.603569 TCTGAGCTGAACCGACTTCC 59.396 55.000 0.00 0.00 0.00 3.46
851 971 0.605589 CTGAGCTGAACCGACTTCCT 59.394 55.000 0.00 0.00 0.00 3.36
852 972 0.603569 TGAGCTGAACCGACTTCCTC 59.396 55.000 0.00 0.00 0.00 3.71
853 973 0.892063 GAGCTGAACCGACTTCCTCT 59.108 55.000 0.00 0.00 0.00 3.69
854 974 0.892063 AGCTGAACCGACTTCCTCTC 59.108 55.000 0.00 0.00 0.00 3.20
855 975 0.603569 GCTGAACCGACTTCCTCTCA 59.396 55.000 0.00 0.00 0.00 3.27
856 976 1.000955 GCTGAACCGACTTCCTCTCAA 59.999 52.381 0.00 0.00 0.00 3.02
857 977 2.548067 GCTGAACCGACTTCCTCTCAAA 60.548 50.000 0.00 0.00 0.00 2.69
858 978 3.060602 CTGAACCGACTTCCTCTCAAAC 58.939 50.000 0.00 0.00 0.00 2.93
859 979 2.698797 TGAACCGACTTCCTCTCAAACT 59.301 45.455 0.00 0.00 0.00 2.66
860 980 3.243771 TGAACCGACTTCCTCTCAAACTC 60.244 47.826 0.00 0.00 0.00 3.01
861 981 1.619332 ACCGACTTCCTCTCAAACTCC 59.381 52.381 0.00 0.00 0.00 3.85
862 982 1.618837 CCGACTTCCTCTCAAACTCCA 59.381 52.381 0.00 0.00 0.00 3.86
863 983 2.234908 CCGACTTCCTCTCAAACTCCAT 59.765 50.000 0.00 0.00 0.00 3.41
864 984 3.257393 CGACTTCCTCTCAAACTCCATG 58.743 50.000 0.00 0.00 0.00 3.66
865 985 3.306364 CGACTTCCTCTCAAACTCCATGT 60.306 47.826 0.00 0.00 0.00 3.21
866 986 4.082190 CGACTTCCTCTCAAACTCCATGTA 60.082 45.833 0.00 0.00 0.00 2.29
867 987 5.566826 CGACTTCCTCTCAAACTCCATGTAA 60.567 44.000 0.00 0.00 0.00 2.41
868 988 5.552178 ACTTCCTCTCAAACTCCATGTAAC 58.448 41.667 0.00 0.00 0.00 2.50
869 989 4.188247 TCCTCTCAAACTCCATGTAACG 57.812 45.455 0.00 0.00 0.00 3.18
870 990 3.576982 TCCTCTCAAACTCCATGTAACGT 59.423 43.478 0.00 0.00 0.00 3.99
871 991 3.679980 CCTCTCAAACTCCATGTAACGTG 59.320 47.826 0.00 0.00 0.00 4.49
872 992 4.307432 CTCTCAAACTCCATGTAACGTGT 58.693 43.478 0.00 0.00 0.00 4.49
873 993 4.055360 TCTCAAACTCCATGTAACGTGTG 58.945 43.478 0.00 0.00 0.00 3.82
874 994 2.546368 TCAAACTCCATGTAACGTGTGC 59.454 45.455 0.00 0.00 0.00 4.57
875 995 1.144969 AACTCCATGTAACGTGTGCG 58.855 50.000 0.00 0.00 44.93 5.34
876 996 0.315886 ACTCCATGTAACGTGTGCGA 59.684 50.000 0.00 0.00 42.00 5.10
877 997 1.269883 ACTCCATGTAACGTGTGCGAA 60.270 47.619 0.00 0.00 42.00 4.70
878 998 1.126113 CTCCATGTAACGTGTGCGAAC 59.874 52.381 0.00 0.00 42.00 3.95
879 999 0.165079 CCATGTAACGTGTGCGAACC 59.835 55.000 0.00 0.00 42.00 3.62
880 1000 0.179260 CATGTAACGTGTGCGAACCG 60.179 55.000 3.23 3.23 42.00 4.44
881 1001 0.318869 ATGTAACGTGTGCGAACCGA 60.319 50.000 10.83 0.00 42.00 4.69
882 1002 1.208009 TGTAACGTGTGCGAACCGAC 61.208 55.000 10.83 1.49 42.00 4.79
883 1003 0.936297 GTAACGTGTGCGAACCGACT 60.936 55.000 10.83 1.57 42.00 4.18
884 1004 0.248990 TAACGTGTGCGAACCGACTT 60.249 50.000 10.83 0.00 42.00 3.01
885 1005 1.485032 AACGTGTGCGAACCGACTTC 61.485 55.000 10.83 0.00 42.00 3.01
886 1006 2.654912 CGTGTGCGAACCGACTTCC 61.655 63.158 0.00 0.00 41.33 3.46
887 1007 1.300697 GTGTGCGAACCGACTTCCT 60.301 57.895 0.00 0.00 0.00 3.36
888 1008 0.878961 GTGTGCGAACCGACTTCCTT 60.879 55.000 0.00 0.00 0.00 3.36
889 1009 0.599204 TGTGCGAACCGACTTCCTTC 60.599 55.000 0.00 0.00 0.00 3.46
890 1010 0.319641 GTGCGAACCGACTTCCTTCT 60.320 55.000 0.00 0.00 0.00 2.85
891 1011 0.038526 TGCGAACCGACTTCCTTCTC 60.039 55.000 0.00 0.00 0.00 2.87
892 1012 0.038526 GCGAACCGACTTCCTTCTCA 60.039 55.000 0.00 0.00 0.00 3.27
893 1013 1.604693 GCGAACCGACTTCCTTCTCAA 60.605 52.381 0.00 0.00 0.00 3.02
894 1014 2.750948 CGAACCGACTTCCTTCTCAAA 58.249 47.619 0.00 0.00 0.00 2.69
895 1015 2.475487 CGAACCGACTTCCTTCTCAAAC 59.525 50.000 0.00 0.00 0.00 2.93
896 1016 3.729966 GAACCGACTTCCTTCTCAAACT 58.270 45.455 0.00 0.00 0.00 2.66
897 1017 3.388345 ACCGACTTCCTTCTCAAACTC 57.612 47.619 0.00 0.00 0.00 3.01
898 1018 2.037381 ACCGACTTCCTTCTCAAACTCC 59.963 50.000 0.00 0.00 0.00 3.85
899 1019 2.037251 CCGACTTCCTTCTCAAACTCCA 59.963 50.000 0.00 0.00 0.00 3.86
900 1020 3.307059 CCGACTTCCTTCTCAAACTCCAT 60.307 47.826 0.00 0.00 0.00 3.41
901 1021 3.681897 CGACTTCCTTCTCAAACTCCATG 59.318 47.826 0.00 0.00 0.00 3.66
946 1067 1.996292 TCTGAGCCGAATTCTTGTCG 58.004 50.000 3.52 0.00 38.24 4.35
1024 1180 5.011738 ACAACTGTTTGCCTAGCTAGACTAA 59.988 40.000 22.70 11.04 36.00 2.24
1603 2488 1.544691 GTCGAGGCAGTCTTTCCTACA 59.455 52.381 0.00 0.00 31.71 2.74
1696 2581 3.642901 CATGGCTTGCTTGCATCTC 57.357 52.632 0.00 0.00 34.04 2.75
1697 2582 0.102481 CATGGCTTGCTTGCATCTCC 59.898 55.000 0.00 0.00 34.04 3.71
1698 2583 0.323999 ATGGCTTGCTTGCATCTCCA 60.324 50.000 11.32 11.32 34.04 3.86
1699 2584 0.323999 TGGCTTGCTTGCATCTCCAT 60.324 50.000 0.00 0.00 34.04 3.41
1700 2585 1.064537 TGGCTTGCTTGCATCTCCATA 60.065 47.619 0.00 0.00 34.04 2.74
1701 2586 2.026641 GGCTTGCTTGCATCTCCATAA 58.973 47.619 0.00 0.00 34.04 1.90
1702 2587 2.626743 GGCTTGCTTGCATCTCCATAAT 59.373 45.455 0.00 0.00 34.04 1.28
1703 2588 3.822735 GGCTTGCTTGCATCTCCATAATA 59.177 43.478 0.00 0.00 34.04 0.98
1704 2589 4.461781 GGCTTGCTTGCATCTCCATAATAT 59.538 41.667 0.00 0.00 34.04 1.28
1705 2590 5.649395 GGCTTGCTTGCATCTCCATAATATA 59.351 40.000 0.00 0.00 34.04 0.86
1706 2591 6.151648 GGCTTGCTTGCATCTCCATAATATAA 59.848 38.462 0.00 0.00 34.04 0.98
1707 2592 7.249147 GCTTGCTTGCATCTCCATAATATAAG 58.751 38.462 0.00 0.00 0.00 1.73
1708 2593 7.120285 GCTTGCTTGCATCTCCATAATATAAGA 59.880 37.037 0.00 0.00 0.00 2.10
1709 2594 7.912056 TGCTTGCATCTCCATAATATAAGAC 57.088 36.000 0.00 0.00 0.00 3.01
1710 2595 6.881065 TGCTTGCATCTCCATAATATAAGACC 59.119 38.462 0.00 0.00 0.00 3.85
1711 2596 6.881065 GCTTGCATCTCCATAATATAAGACCA 59.119 38.462 0.00 0.00 0.00 4.02
1712 2597 7.555554 GCTTGCATCTCCATAATATAAGACCAT 59.444 37.037 0.00 0.00 0.00 3.55
1713 2598 9.458727 CTTGCATCTCCATAATATAAGACCATT 57.541 33.333 0.00 0.00 0.00 3.16
1714 2599 9.812347 TTGCATCTCCATAATATAAGACCATTT 57.188 29.630 0.00 0.00 0.00 2.32
1715 2600 9.812347 TGCATCTCCATAATATAAGACCATTTT 57.188 29.630 0.00 0.00 0.00 1.82
1755 2640 9.976776 ACGATCTTATATTATAAGACAGAGGGA 57.023 33.333 22.47 4.82 36.51 4.20
1825 2710 3.421728 ATAAGCCGCCTTCCCAGCC 62.422 63.158 0.00 0.00 32.47 4.85
1848 2733 5.107220 CCGCTCGTTTAATATAACCATGACC 60.107 44.000 0.00 0.00 0.00 4.02
1919 2804 3.062099 TCGCGTTTGCATTCTCATAGTTC 59.938 43.478 5.77 0.00 42.97 3.01
2008 2898 3.910627 ACCTTGGAACTAGGAAGTGACAT 59.089 43.478 3.82 0.00 35.62 3.06
2009 2899 4.256920 CCTTGGAACTAGGAAGTGACATG 58.743 47.826 0.00 0.00 35.62 3.21
2010 2900 4.020218 CCTTGGAACTAGGAAGTGACATGA 60.020 45.833 0.00 0.00 35.62 3.07
2011 2901 5.338708 CCTTGGAACTAGGAAGTGACATGAT 60.339 44.000 0.00 0.00 35.62 2.45
2012 2902 6.127054 CCTTGGAACTAGGAAGTGACATGATA 60.127 42.308 0.00 0.00 35.62 2.15
2081 2971 1.927174 CGACTAGCTTAATTGCAGCGT 59.073 47.619 0.00 0.38 42.55 5.07
2284 3748 1.815421 GCTCCATTGCATCGACGGT 60.815 57.895 0.00 0.00 0.00 4.83
2350 3814 2.283298 CTCGGCAGTGCTTCAATACAT 58.717 47.619 16.11 0.00 0.00 2.29
2355 3819 3.379372 GGCAGTGCTTCAATACATCACAT 59.621 43.478 16.11 0.00 0.00 3.21
2413 3877 6.400568 CAACCCTTCATAACAAAGCATGAAT 58.599 36.000 0.00 0.00 39.69 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 2.177394 TCGTCACAGCTTAATTGCCA 57.823 45.000 0.00 0.00 0.00 4.92
133 134 3.044235 AGAGCATGTTTCATCGTCACA 57.956 42.857 0.00 0.00 0.00 3.58
225 227 7.661847 ACGAAAAGAGATCAACCTAACATTCTT 59.338 33.333 0.00 0.00 0.00 2.52
341 344 1.844497 GCCCCCACCTCTTTATGTAGT 59.156 52.381 0.00 0.00 0.00 2.73
389 392 3.948719 GTGGGGAGACGGGCAACA 61.949 66.667 0.00 0.00 39.74 3.33
396 399 0.605589 GGGTTTTCAGTGGGGAGACG 60.606 60.000 0.00 0.00 0.00 4.18
407 410 1.196104 AGATCGGGTCGGGGTTTTCA 61.196 55.000 0.00 0.00 0.00 2.69
599 605 4.020573 TGTGATAGACCCACTTGAATCGTT 60.021 41.667 0.00 0.00 35.66 3.85
668 675 0.187606 ACAAACCAGGGGTTCCTTCC 59.812 55.000 0.40 0.00 46.20 3.46
669 676 2.082140 AACAAACCAGGGGTTCCTTC 57.918 50.000 0.40 0.00 46.20 3.46
670 677 2.503765 CAAAACAAACCAGGGGTTCCTT 59.496 45.455 0.40 0.00 46.20 3.36
724 732 6.745116 TCGTGAGGTCCTACAAATACATATG 58.255 40.000 0.00 0.00 0.00 1.78
725 733 6.776116 TCTCGTGAGGTCCTACAAATACATAT 59.224 38.462 0.00 0.00 0.00 1.78
729 740 4.978083 TCTCGTGAGGTCCTACAAATAC 57.022 45.455 0.00 0.00 0.00 1.89
787 907 6.980051 ATAAGTCGGTTTTTACATGGAGTC 57.020 37.500 0.00 0.00 0.00 3.36
811 931 8.398665 GCTCAGAAACGTAATAAGAATCCAAAT 58.601 33.333 0.00 0.00 0.00 2.32
812 932 7.606456 AGCTCAGAAACGTAATAAGAATCCAAA 59.394 33.333 0.00 0.00 0.00 3.28
813 933 7.064609 CAGCTCAGAAACGTAATAAGAATCCAA 59.935 37.037 0.00 0.00 0.00 3.53
814 934 6.535150 CAGCTCAGAAACGTAATAAGAATCCA 59.465 38.462 0.00 0.00 0.00 3.41
815 935 6.757010 TCAGCTCAGAAACGTAATAAGAATCC 59.243 38.462 0.00 0.00 0.00 3.01
816 936 7.757097 TCAGCTCAGAAACGTAATAAGAATC 57.243 36.000 0.00 0.00 0.00 2.52
817 937 7.064728 GGTTCAGCTCAGAAACGTAATAAGAAT 59.935 37.037 0.00 0.00 0.00 2.40
818 938 6.367969 GGTTCAGCTCAGAAACGTAATAAGAA 59.632 38.462 0.00 0.00 0.00 2.52
819 939 5.867716 GGTTCAGCTCAGAAACGTAATAAGA 59.132 40.000 0.00 0.00 0.00 2.10
820 940 6.095947 GGTTCAGCTCAGAAACGTAATAAG 57.904 41.667 0.00 0.00 0.00 1.73
828 948 2.156343 AGTCGGTTCAGCTCAGAAAC 57.844 50.000 0.00 0.00 31.87 2.78
829 949 2.548067 GGAAGTCGGTTCAGCTCAGAAA 60.548 50.000 0.00 0.00 36.82 2.52
830 950 1.000955 GGAAGTCGGTTCAGCTCAGAA 59.999 52.381 0.00 0.00 36.82 3.02
831 951 0.603569 GGAAGTCGGTTCAGCTCAGA 59.396 55.000 0.00 0.00 36.82 3.27
832 952 0.605589 AGGAAGTCGGTTCAGCTCAG 59.394 55.000 0.00 0.00 36.82 3.35
833 953 0.603569 GAGGAAGTCGGTTCAGCTCA 59.396 55.000 0.00 0.00 36.82 4.26
834 954 0.892063 AGAGGAAGTCGGTTCAGCTC 59.108 55.000 0.00 0.00 36.82 4.09
835 955 0.892063 GAGAGGAAGTCGGTTCAGCT 59.108 55.000 1.61 0.00 36.82 4.24
836 956 0.603569 TGAGAGGAAGTCGGTTCAGC 59.396 55.000 1.61 0.00 36.82 4.26
837 957 3.060602 GTTTGAGAGGAAGTCGGTTCAG 58.939 50.000 1.61 0.00 36.82 3.02
838 958 2.698797 AGTTTGAGAGGAAGTCGGTTCA 59.301 45.455 1.61 0.00 36.82 3.18
839 959 3.318886 GAGTTTGAGAGGAAGTCGGTTC 58.681 50.000 0.00 0.00 0.00 3.62
840 960 2.037381 GGAGTTTGAGAGGAAGTCGGTT 59.963 50.000 0.00 0.00 0.00 4.44
841 961 1.619332 GGAGTTTGAGAGGAAGTCGGT 59.381 52.381 0.00 0.00 0.00 4.69
842 962 1.618837 TGGAGTTTGAGAGGAAGTCGG 59.381 52.381 0.00 0.00 0.00 4.79
843 963 3.257393 CATGGAGTTTGAGAGGAAGTCG 58.743 50.000 0.00 0.00 0.00 4.18
844 964 4.278975 ACATGGAGTTTGAGAGGAAGTC 57.721 45.455 0.00 0.00 0.00 3.01
845 965 5.552178 GTTACATGGAGTTTGAGAGGAAGT 58.448 41.667 0.00 0.00 0.00 3.01
846 966 4.627467 CGTTACATGGAGTTTGAGAGGAAG 59.373 45.833 0.00 0.00 0.00 3.46
847 967 4.039973 ACGTTACATGGAGTTTGAGAGGAA 59.960 41.667 0.00 0.00 0.00 3.36
848 968 3.576982 ACGTTACATGGAGTTTGAGAGGA 59.423 43.478 0.00 0.00 0.00 3.71
849 969 3.679980 CACGTTACATGGAGTTTGAGAGG 59.320 47.826 0.00 0.00 0.00 3.69
850 970 4.150627 CACACGTTACATGGAGTTTGAGAG 59.849 45.833 0.00 0.00 0.00 3.20
851 971 4.055360 CACACGTTACATGGAGTTTGAGA 58.945 43.478 0.00 0.00 0.00 3.27
852 972 3.363970 GCACACGTTACATGGAGTTTGAG 60.364 47.826 0.00 0.00 0.00 3.02
853 973 2.546368 GCACACGTTACATGGAGTTTGA 59.454 45.455 0.00 0.00 0.00 2.69
854 974 2.661709 CGCACACGTTACATGGAGTTTG 60.662 50.000 0.00 0.00 33.53 2.93
855 975 1.529438 CGCACACGTTACATGGAGTTT 59.471 47.619 0.00 0.00 33.53 2.66
856 976 1.144969 CGCACACGTTACATGGAGTT 58.855 50.000 0.00 0.00 33.53 3.01
857 977 0.315886 TCGCACACGTTACATGGAGT 59.684 50.000 0.00 0.00 41.18 3.85
858 978 1.126113 GTTCGCACACGTTACATGGAG 59.874 52.381 0.00 0.00 41.18 3.86
859 979 1.141645 GTTCGCACACGTTACATGGA 58.858 50.000 0.00 0.00 41.18 3.41
860 980 0.165079 GGTTCGCACACGTTACATGG 59.835 55.000 0.00 0.00 41.18 3.66
861 981 0.179260 CGGTTCGCACACGTTACATG 60.179 55.000 0.00 0.00 41.18 3.21
862 982 0.318869 TCGGTTCGCACACGTTACAT 60.319 50.000 0.00 0.00 41.18 2.29
863 983 1.065436 TCGGTTCGCACACGTTACA 59.935 52.632 0.00 0.00 41.18 2.41
864 984 0.936297 AGTCGGTTCGCACACGTTAC 60.936 55.000 0.00 0.00 41.18 2.50
865 985 0.248990 AAGTCGGTTCGCACACGTTA 60.249 50.000 0.00 0.00 41.18 3.18
866 986 1.485032 GAAGTCGGTTCGCACACGTT 61.485 55.000 0.00 0.00 41.18 3.99
867 987 1.947642 GAAGTCGGTTCGCACACGT 60.948 57.895 0.00 0.00 41.18 4.49
868 988 2.654912 GGAAGTCGGTTCGCACACG 61.655 63.158 0.00 0.00 42.01 4.49
869 989 0.878961 AAGGAAGTCGGTTCGCACAC 60.879 55.000 0.00 0.00 35.80 3.82
870 990 0.599204 GAAGGAAGTCGGTTCGCACA 60.599 55.000 0.00 0.00 35.80 4.57
871 991 0.319641 AGAAGGAAGTCGGTTCGCAC 60.320 55.000 0.00 0.00 35.80 5.34
872 992 0.038526 GAGAAGGAAGTCGGTTCGCA 60.039 55.000 0.00 0.00 35.80 5.10
873 993 0.038526 TGAGAAGGAAGTCGGTTCGC 60.039 55.000 0.00 0.00 35.80 4.70
874 994 2.433868 TTGAGAAGGAAGTCGGTTCG 57.566 50.000 0.00 0.00 35.80 3.95
875 995 3.729966 AGTTTGAGAAGGAAGTCGGTTC 58.270 45.455 0.00 0.00 0.00 3.62
876 996 3.494573 GGAGTTTGAGAAGGAAGTCGGTT 60.495 47.826 0.00 0.00 0.00 4.44
877 997 2.037381 GGAGTTTGAGAAGGAAGTCGGT 59.963 50.000 0.00 0.00 0.00 4.69
878 998 2.037251 TGGAGTTTGAGAAGGAAGTCGG 59.963 50.000 0.00 0.00 0.00 4.79
879 999 3.386768 TGGAGTTTGAGAAGGAAGTCG 57.613 47.619 0.00 0.00 0.00 4.18
880 1000 4.646572 ACATGGAGTTTGAGAAGGAAGTC 58.353 43.478 0.00 0.00 0.00 3.01
881 1001 4.713792 ACATGGAGTTTGAGAAGGAAGT 57.286 40.909 0.00 0.00 0.00 3.01
882 1002 7.510549 TTTTACATGGAGTTTGAGAAGGAAG 57.489 36.000 0.00 0.00 0.00 3.46
883 1003 7.201875 GGTTTTTACATGGAGTTTGAGAAGGAA 60.202 37.037 0.00 0.00 0.00 3.36
884 1004 6.264518 GGTTTTTACATGGAGTTTGAGAAGGA 59.735 38.462 0.00 0.00 0.00 3.36
885 1005 6.447162 GGTTTTTACATGGAGTTTGAGAAGG 58.553 40.000 0.00 0.00 0.00 3.46
886 1006 6.017440 TCGGTTTTTACATGGAGTTTGAGAAG 60.017 38.462 0.00 0.00 0.00 2.85
887 1007 5.823570 TCGGTTTTTACATGGAGTTTGAGAA 59.176 36.000 0.00 0.00 0.00 2.87
888 1008 5.237779 GTCGGTTTTTACATGGAGTTTGAGA 59.762 40.000 0.00 0.00 0.00 3.27
889 1009 5.238650 AGTCGGTTTTTACATGGAGTTTGAG 59.761 40.000 0.00 0.00 0.00 3.02
890 1010 5.127491 AGTCGGTTTTTACATGGAGTTTGA 58.873 37.500 0.00 0.00 0.00 2.69
891 1011 5.432885 AGTCGGTTTTTACATGGAGTTTG 57.567 39.130 0.00 0.00 0.00 2.93
892 1012 5.221165 CCAAGTCGGTTTTTACATGGAGTTT 60.221 40.000 0.00 0.00 36.75 2.66
893 1013 4.277423 CCAAGTCGGTTTTTACATGGAGTT 59.723 41.667 0.00 0.00 36.75 3.01
894 1014 3.818773 CCAAGTCGGTTTTTACATGGAGT 59.181 43.478 0.00 0.00 36.75 3.85
895 1015 4.069304 TCCAAGTCGGTTTTTACATGGAG 58.931 43.478 0.00 0.00 38.27 3.86
896 1016 4.088056 TCCAAGTCGGTTTTTACATGGA 57.912 40.909 0.00 0.00 40.23 3.41
897 1017 5.183140 AGAATCCAAGTCGGTTTTTACATGG 59.817 40.000 0.00 0.00 36.13 3.66
898 1018 6.254281 AGAATCCAAGTCGGTTTTTACATG 57.746 37.500 0.00 0.00 35.57 3.21
899 1019 6.894339 AAGAATCCAAGTCGGTTTTTACAT 57.106 33.333 0.00 0.00 35.57 2.29
900 1020 6.073657 CGTAAGAATCCAAGTCGGTTTTTACA 60.074 38.462 0.00 0.00 43.02 2.41
901 1021 6.073602 ACGTAAGAATCCAAGTCGGTTTTTAC 60.074 38.462 0.00 0.00 43.62 2.01
946 1067 4.254492 AGCCGTAAGAATCCTTTGAGTTC 58.746 43.478 0.00 0.00 43.02 3.01
993 1149 2.374184 AGGCAAACAGTTGTGTAGCAA 58.626 42.857 0.00 0.00 38.79 3.91
1024 1180 5.938125 ACTTACAAGATGTGCCGTAAGAATT 59.062 36.000 13.46 0.00 42.11 2.17
1411 2296 0.809385 ATTCACGTCCGTCGATGACT 59.191 50.000 6.11 0.00 42.86 3.41
1603 2488 3.289834 CAGGCTTTGCACGGCAGT 61.290 61.111 11.44 0.00 40.61 4.40
1729 2614 9.976776 TCCCTCTGTCTTATAATATAAGATCGT 57.023 33.333 21.43 0.00 36.16 3.73
1743 2628 9.992442 CCCTAATATATTACTCCCTCTGTCTTA 57.008 37.037 0.81 0.00 0.00 2.10
1744 2629 7.901861 CCCCTAATATATTACTCCCTCTGTCTT 59.098 40.741 0.81 0.00 0.00 3.01
1745 2630 7.423341 CCCCTAATATATTACTCCCTCTGTCT 58.577 42.308 0.81 0.00 0.00 3.41
1746 2631 6.098552 GCCCCTAATATATTACTCCCTCTGTC 59.901 46.154 0.81 0.00 0.00 3.51
1747 2632 5.965091 GCCCCTAATATATTACTCCCTCTGT 59.035 44.000 0.81 0.00 0.00 3.41
1748 2633 5.964477 TGCCCCTAATATATTACTCCCTCTG 59.036 44.000 0.81 0.00 0.00 3.35
1749 2634 6.180328 TGCCCCTAATATATTACTCCCTCT 57.820 41.667 0.81 0.00 0.00 3.69
1750 2635 5.965091 ACTGCCCCTAATATATTACTCCCTC 59.035 44.000 0.81 0.00 0.00 4.30
1751 2636 5.726793 CACTGCCCCTAATATATTACTCCCT 59.273 44.000 0.81 0.00 0.00 4.20
1752 2637 5.629366 GCACTGCCCCTAATATATTACTCCC 60.629 48.000 0.81 0.00 0.00 4.30
1753 2638 5.189934 AGCACTGCCCCTAATATATTACTCC 59.810 44.000 0.81 0.00 0.00 3.85
1754 2639 6.301169 AGCACTGCCCCTAATATATTACTC 57.699 41.667 0.81 0.00 0.00 2.59
1755 2640 6.729100 TGTAGCACTGCCCCTAATATATTACT 59.271 38.462 0.81 0.00 0.00 2.24
1756 2641 6.942976 TGTAGCACTGCCCCTAATATATTAC 58.057 40.000 0.81 0.00 0.00 1.89
1757 2642 7.562259 TTGTAGCACTGCCCCTAATATATTA 57.438 36.000 5.10 5.10 0.00 0.98
1758 2643 6.448369 TTGTAGCACTGCCCCTAATATATT 57.552 37.500 2.97 2.97 0.00 1.28
1759 2644 6.448369 TTTGTAGCACTGCCCCTAATATAT 57.552 37.500 0.00 0.00 0.00 0.86
1760 2645 5.897851 TTTGTAGCACTGCCCCTAATATA 57.102 39.130 0.00 0.00 0.00 0.86
1761 2646 4.788925 TTTGTAGCACTGCCCCTAATAT 57.211 40.909 0.00 0.00 0.00 1.28
1762 2647 4.165180 TGATTTGTAGCACTGCCCCTAATA 59.835 41.667 0.00 0.00 0.00 0.98
1763 2648 3.053693 TGATTTGTAGCACTGCCCCTAAT 60.054 43.478 0.00 0.00 0.00 1.73
1764 2649 2.307392 TGATTTGTAGCACTGCCCCTAA 59.693 45.455 0.00 0.00 0.00 2.69
1765 2650 1.912731 TGATTTGTAGCACTGCCCCTA 59.087 47.619 0.00 0.00 0.00 3.53
1766 2651 0.698238 TGATTTGTAGCACTGCCCCT 59.302 50.000 0.00 0.00 0.00 4.79
1767 2652 1.678101 GATGATTTGTAGCACTGCCCC 59.322 52.381 0.00 0.00 0.00 5.80
1825 2710 5.388061 CGGTCATGGTTATATTAAACGAGCG 60.388 44.000 0.00 0.00 34.47 5.03
1919 2804 3.181462 TGAGCACTATTAGGTGAGCATGG 60.181 47.826 0.00 0.00 39.34 3.66
2066 2956 0.673644 ACCGACGCTGCAATTAAGCT 60.674 50.000 0.00 0.00 38.57 3.74
2284 3748 1.881591 CCGGGGTCGTTTAAACTTCA 58.118 50.000 16.01 0.00 33.95 3.02
2336 3800 3.064408 CGCATGTGATGTATTGAAGCACT 59.936 43.478 0.00 0.00 0.00 4.40
2413 3877 1.155424 GCCGACCACAACTTTCGTCA 61.155 55.000 0.00 0.00 0.00 4.35
2606 4070 1.753078 CCCTCGGTCAGATCGGACA 60.753 63.158 24.43 7.03 39.59 4.02
2768 4232 1.530323 GGGTTACAATGAAGCACCGT 58.470 50.000 0.00 0.00 0.00 4.83


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

AutoCloner maintained by Alex Coulton.