Multiple sequence alignment - TraesCS3D01G043000

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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 TraesCS3D01G043000 chr3D 100.000 2646 0 0 1 2646 16448328 16450973 0.000000e+00 4887.0
1 TraesCS3D01G043000 chr3D 89.390 820 49 17 1 812 32172495 32173284 0.000000e+00 998.0
2 TraesCS3D01G043000 chr7D 97.947 1705 32 2 944 2646 446550966 446549263 0.000000e+00 2952.0
3 TraesCS3D01G043000 chr7D 95.197 812 10 4 1 812 446552534 446551752 0.000000e+00 1256.0
4 TraesCS3D01G043000 chr7D 98.551 138 1 1 811 948 446550985 446551121 2.630000e-60 243.0
5 TraesCS3D01G043000 chr2A 96.073 1706 43 5 944 2646 46336903 46338587 0.000000e+00 2758.0
6 TraesCS3D01G043000 chr2A 97.119 729 13 5 1 729 46335192 46335912 0.000000e+00 1223.0
7 TraesCS3D01G043000 chr2A 84.659 880 95 26 948 1809 631856765 631857622 0.000000e+00 841.0
8 TraesCS3D01G043000 chr2A 90.456 461 35 5 1 456 363365416 363365872 1.360000e-167 599.0
9 TraesCS3D01G043000 chr2A 81.938 609 73 22 1934 2525 375041088 375041676 5.120000e-132 481.0
10 TraesCS3D01G043000 chr2A 87.500 384 37 6 433 812 6455453 6455829 1.450000e-117 433.0
11 TraesCS3D01G043000 chr2A 94.928 138 6 1 811 948 46336884 46336748 5.740000e-52 215.0
12 TraesCS3D01G043000 chr3B 91.342 1744 65 38 944 2646 555550448 555548750 0.000000e+00 2305.0
13 TraesCS3D01G043000 chr3B 93.162 819 28 14 2 812 555552033 555551235 0.000000e+00 1177.0
14 TraesCS3D01G043000 chr3B 88.321 822 54 18 1 812 685078262 685077473 0.000000e+00 948.0
15 TraesCS3D01G043000 chr3B 96.377 138 4 1 811 948 555550467 555550603 2.650000e-55 226.0
16 TraesCS3D01G043000 chr4B 91.227 1744 67 38 944 2646 16787351 16789049 0.000000e+00 2294.0
17 TraesCS3D01G043000 chr4B 93.154 818 30 13 2 812 16785766 16786564 0.000000e+00 1177.0
18 TraesCS3D01G043000 chr4B 96.377 138 4 1 811 948 16787332 16787196 2.650000e-55 226.0
19 TraesCS3D01G043000 chr7A 87.794 1106 53 23 1576 2646 321635879 321634821 0.000000e+00 1219.0
20 TraesCS3D01G043000 chr7A 97.109 588 16 1 944 1531 321636451 321635865 0.000000e+00 990.0
21 TraesCS3D01G043000 chr7A 79.572 607 85 27 1934 2525 282333433 282334015 5.310000e-107 398.0
22 TraesCS3D01G043000 chr7A 84.962 266 30 8 2144 2405 425836668 425836409 7.260000e-66 261.0
23 TraesCS3D01G043000 chr7A 93.478 138 4 2 811 948 321636470 321636602 1.610000e-47 200.0
24 TraesCS3D01G043000 chrUn 90.373 831 48 9 1013 1814 195337988 195338815 0.000000e+00 1062.0
25 TraesCS3D01G043000 chrUn 87.175 538 37 12 1444 1953 40170468 40169935 1.370000e-162 582.0
26 TraesCS3D01G043000 chrUn 87.175 538 37 12 1444 1953 422925608 422926141 1.370000e-162 582.0
27 TraesCS3D01G043000 chrUn 91.732 254 13 6 1705 1953 431172399 431172649 1.950000e-91 346.0
28 TraesCS3D01G043000 chr6B 92.789 735 26 14 84 812 247036663 247035950 0.000000e+00 1038.0
29 TraesCS3D01G043000 chr6B 92.408 461 24 5 1 456 247042023 247041569 0.000000e+00 647.0
30 TraesCS3D01G043000 chr6B 96.377 138 4 1 811 948 247035182 247035318 2.650000e-55 226.0
31 TraesCS3D01G043000 chr4A 92.653 735 27 10 84 812 729645949 729645236 0.000000e+00 1033.0
32 TraesCS3D01G043000 chr4A 90.313 702 37 10 1830 2525 729644473 729643797 0.000000e+00 891.0
33 TraesCS3D01G043000 chr4A 80.460 609 82 26 1934 2525 575685871 575686459 5.230000e-117 431.0
34 TraesCS3D01G043000 chr4A 93.793 145 7 2 804 948 729644462 729644604 1.590000e-52 217.0
35 TraesCS3D01G043000 chr4A 95.122 123 4 1 2526 2646 729643768 729643646 2.690000e-45 193.0
36 TraesCS3D01G043000 chr5A 94.755 572 18 6 1 566 606395565 606395000 0.000000e+00 880.0
37 TraesCS3D01G043000 chr2D 85.080 878 94 18 944 1809 486391910 486392762 0.000000e+00 861.0
38 TraesCS3D01G043000 chr2D 81.818 242 28 7 952 1190 487592986 487592758 3.480000e-44 189.0
39 TraesCS3D01G043000 chr2D 93.976 83 5 0 812 894 488057070 488057152 2.760000e-25 126.0
40 TraesCS3D01G043000 chr2B 84.493 877 92 19 944 1809 571347150 571347993 0.000000e+00 826.0
41 TraesCS3D01G043000 chr6A 78.046 829 118 30 1850 2646 617579912 617580708 5.160000e-127 464.0
42 TraesCS3D01G043000 chr6A 84.278 388 37 9 2142 2525 25067631 25067998 9.010000e-95 357.0
43 TraesCS3D01G043000 chr1D 81.414 608 68 25 1934 2525 339095559 339094981 3.100000e-124 455.0
44 TraesCS3D01G043000 chr1A 97.059 34 0 1 2156 2188 532371508 532371541 3.680000e-04 56.5


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 TraesCS3D01G043000 chr3D 16448328 16450973 2645 False 4887.000000 4887 100.0000 1 2646 1 chr3D.!!$F1 2645
1 TraesCS3D01G043000 chr3D 32172495 32173284 789 False 998.000000 998 89.3900 1 812 1 chr3D.!!$F2 811
2 TraesCS3D01G043000 chr7D 446549263 446552534 3271 True 2104.000000 2952 96.5720 1 2646 2 chr7D.!!$R1 2645
3 TraesCS3D01G043000 chr2A 46335192 46338587 3395 False 1990.500000 2758 96.5960 1 2646 2 chr2A.!!$F5 2645
4 TraesCS3D01G043000 chr2A 631856765 631857622 857 False 841.000000 841 84.6590 948 1809 1 chr2A.!!$F4 861
5 TraesCS3D01G043000 chr2A 375041088 375041676 588 False 481.000000 481 81.9380 1934 2525 1 chr2A.!!$F3 591
6 TraesCS3D01G043000 chr3B 555548750 555552033 3283 True 1741.000000 2305 92.2520 2 2646 2 chr3B.!!$R2 2644
7 TraesCS3D01G043000 chr3B 685077473 685078262 789 True 948.000000 948 88.3210 1 812 1 chr3B.!!$R1 811
8 TraesCS3D01G043000 chr4B 16785766 16789049 3283 False 1735.500000 2294 92.1905 2 2646 2 chr4B.!!$F1 2644
9 TraesCS3D01G043000 chr7A 321634821 321636451 1630 True 1104.500000 1219 92.4515 944 2646 2 chr7A.!!$R2 1702
10 TraesCS3D01G043000 chr7A 282333433 282334015 582 False 398.000000 398 79.5720 1934 2525 1 chr7A.!!$F1 591
11 TraesCS3D01G043000 chrUn 195337988 195338815 827 False 1062.000000 1062 90.3730 1013 1814 1 chrUn.!!$F1 801
12 TraesCS3D01G043000 chrUn 40169935 40170468 533 True 582.000000 582 87.1750 1444 1953 1 chrUn.!!$R1 509
13 TraesCS3D01G043000 chrUn 422925608 422926141 533 False 582.000000 582 87.1750 1444 1953 1 chrUn.!!$F2 509
14 TraesCS3D01G043000 chr6B 247035950 247036663 713 True 1038.000000 1038 92.7890 84 812 1 chr6B.!!$R1 728
15 TraesCS3D01G043000 chr4A 729643646 729645949 2303 True 705.666667 1033 92.6960 84 2646 3 chr4A.!!$R1 2562
16 TraesCS3D01G043000 chr4A 575685871 575686459 588 False 431.000000 431 80.4600 1934 2525 1 chr4A.!!$F1 591
17 TraesCS3D01G043000 chr5A 606395000 606395565 565 True 880.000000 880 94.7550 1 566 1 chr5A.!!$R1 565
18 TraesCS3D01G043000 chr2D 486391910 486392762 852 False 861.000000 861 85.0800 944 1809 1 chr2D.!!$F1 865
19 TraesCS3D01G043000 chr2B 571347150 571347993 843 False 826.000000 826 84.4930 944 1809 1 chr2B.!!$F1 865
20 TraesCS3D01G043000 chr6A 617579912 617580708 796 False 464.000000 464 78.0460 1850 2646 1 chr6A.!!$F2 796
21 TraesCS3D01G043000 chr1D 339094981 339095559 578 True 455.000000 455 81.4140 1934 2525 1 chr1D.!!$R1 591

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
819 962 0.107643 TGGAACCATGTGACTTCGCA 59.892 50.0 0.0 0.0 40.98 5.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2288 3313 0.388649 GAGTCCAGAATCGCACACGT 60.389 55.0 0.0 0.0 41.18 4.49 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
361 369 8.829612 CATTGCTTCTTGGTCTTTATTTTGTTT 58.170 29.630 0.00 0.00 0.00 2.83
509 521 1.269883 TGCTTGCCAATGTGCTCTTTG 60.270 47.619 7.27 7.27 0.00 2.77
595 607 7.775561 GGTTGTAGATTTTATTGACCCTCTCAT 59.224 37.037 0.00 0.00 0.00 2.90
604 616 7.496346 TTATTGACCCTCTCATGTAAACTCT 57.504 36.000 0.00 0.00 0.00 3.24
712 725 7.403312 TTCAGAGGATAAGTTGAAGAGAGAG 57.597 40.000 0.00 0.00 0.00 3.20
812 955 2.359850 GCCGCTGGAACCATGTGA 60.360 61.111 0.00 0.00 0.00 3.58
813 956 2.690778 GCCGCTGGAACCATGTGAC 61.691 63.158 0.00 0.00 0.00 3.67
814 957 1.003355 CCGCTGGAACCATGTGACT 60.003 57.895 0.00 0.00 0.00 3.41
815 958 0.606401 CCGCTGGAACCATGTGACTT 60.606 55.000 0.00 0.00 0.00 3.01
816 959 0.798776 CGCTGGAACCATGTGACTTC 59.201 55.000 0.00 0.00 0.00 3.01
817 960 0.798776 GCTGGAACCATGTGACTTCG 59.201 55.000 0.00 0.00 0.00 3.79
818 961 0.798776 CTGGAACCATGTGACTTCGC 59.201 55.000 0.00 0.00 0.00 4.70
819 962 0.107643 TGGAACCATGTGACTTCGCA 59.892 50.000 0.00 0.00 40.98 5.10
820 963 0.798776 GGAACCATGTGACTTCGCAG 59.201 55.000 0.00 0.00 39.97 5.18
821 964 0.798776 GAACCATGTGACTTCGCAGG 59.201 55.000 0.00 0.00 39.97 4.85
822 965 0.396435 AACCATGTGACTTCGCAGGA 59.604 50.000 6.03 0.00 40.17 3.86
823 966 0.615331 ACCATGTGACTTCGCAGGAT 59.385 50.000 6.03 0.00 40.17 3.24
824 967 1.831106 ACCATGTGACTTCGCAGGATA 59.169 47.619 6.03 0.00 40.17 2.59
825 968 2.159043 ACCATGTGACTTCGCAGGATAG 60.159 50.000 6.03 0.00 40.17 2.08
826 969 2.101415 CCATGTGACTTCGCAGGATAGA 59.899 50.000 6.03 0.00 40.17 1.98
827 970 3.430790 CCATGTGACTTCGCAGGATAGAA 60.431 47.826 6.03 0.00 40.17 2.10
828 971 3.953712 TGTGACTTCGCAGGATAGAAA 57.046 42.857 0.00 0.00 31.95 2.52
829 972 3.585862 TGTGACTTCGCAGGATAGAAAC 58.414 45.455 0.00 0.00 31.95 2.78
830 973 2.930682 GTGACTTCGCAGGATAGAAACC 59.069 50.000 0.00 0.00 0.00 3.27
831 974 2.832129 TGACTTCGCAGGATAGAAACCT 59.168 45.455 0.00 0.00 38.40 3.50
832 975 3.260884 TGACTTCGCAGGATAGAAACCTT 59.739 43.478 0.00 0.00 35.35 3.50
833 976 3.600388 ACTTCGCAGGATAGAAACCTTG 58.400 45.455 0.00 0.00 35.35 3.61
834 977 3.260884 ACTTCGCAGGATAGAAACCTTGA 59.739 43.478 0.00 0.00 35.35 3.02
835 978 4.080863 ACTTCGCAGGATAGAAACCTTGAT 60.081 41.667 0.00 0.00 35.35 2.57
836 979 5.128827 ACTTCGCAGGATAGAAACCTTGATA 59.871 40.000 0.00 0.00 35.35 2.15
837 980 5.607939 TCGCAGGATAGAAACCTTGATAA 57.392 39.130 0.00 0.00 35.35 1.75
838 981 5.984725 TCGCAGGATAGAAACCTTGATAAA 58.015 37.500 0.00 0.00 35.35 1.40
839 982 6.049149 TCGCAGGATAGAAACCTTGATAAAG 58.951 40.000 0.00 0.00 35.35 1.85
840 983 5.237344 CGCAGGATAGAAACCTTGATAAAGG 59.763 44.000 7.38 7.38 45.46 3.11
841 984 6.357367 GCAGGATAGAAACCTTGATAAAGGA 58.643 40.000 16.52 0.00 42.62 3.36
842 985 6.828785 GCAGGATAGAAACCTTGATAAAGGAA 59.171 38.462 16.52 0.00 42.62 3.36
843 986 7.339466 GCAGGATAGAAACCTTGATAAAGGAAA 59.661 37.037 16.52 0.00 42.62 3.13
844 987 9.243105 CAGGATAGAAACCTTGATAAAGGAAAA 57.757 33.333 16.52 0.00 42.62 2.29
845 988 9.467796 AGGATAGAAACCTTGATAAAGGAAAAG 57.532 33.333 16.52 0.00 42.62 2.27
846 989 8.191446 GGATAGAAACCTTGATAAAGGAAAAGC 58.809 37.037 16.52 0.49 42.62 3.51
847 990 8.885693 ATAGAAACCTTGATAAAGGAAAAGCT 57.114 30.769 16.52 7.57 42.62 3.74
848 991 7.603180 AGAAACCTTGATAAAGGAAAAGCTT 57.397 32.000 16.52 0.00 42.62 3.74
849 992 7.436933 AGAAACCTTGATAAAGGAAAAGCTTG 58.563 34.615 16.52 0.00 42.62 4.01
850 993 6.731292 AACCTTGATAAAGGAAAAGCTTGT 57.269 33.333 16.52 0.00 42.62 3.16
851 994 6.332735 ACCTTGATAAAGGAAAAGCTTGTC 57.667 37.500 16.52 8.23 42.62 3.18
852 995 5.833131 ACCTTGATAAAGGAAAAGCTTGTCA 59.167 36.000 16.52 0.00 42.62 3.58
853 996 6.494835 ACCTTGATAAAGGAAAAGCTTGTCAT 59.505 34.615 16.52 8.62 42.62 3.06
854 997 7.031975 CCTTGATAAAGGAAAAGCTTGTCATC 58.968 38.462 18.39 12.25 42.62 2.92
855 998 6.515272 TGATAAAGGAAAAGCTTGTCATCC 57.485 37.500 18.39 14.26 0.00 3.51
856 999 6.248433 TGATAAAGGAAAAGCTTGTCATCCT 58.752 36.000 18.39 16.08 42.22 3.24
858 1001 4.861102 AAGGAAAAGCTTGTCATCCTTG 57.139 40.909 24.18 0.00 46.10 3.61
859 1002 4.104383 AGGAAAAGCTTGTCATCCTTGA 57.896 40.909 18.39 0.00 37.20 3.02
860 1003 4.473444 AGGAAAAGCTTGTCATCCTTGAA 58.527 39.130 18.39 0.00 37.20 2.69
861 1004 5.082425 AGGAAAAGCTTGTCATCCTTGAAT 58.918 37.500 18.39 0.00 37.20 2.57
862 1005 5.047519 AGGAAAAGCTTGTCATCCTTGAATG 60.048 40.000 18.39 0.00 37.20 2.67
863 1006 5.279156 GGAAAAGCTTGTCATCCTTGAATGT 60.279 40.000 18.39 0.00 32.48 2.71
864 1007 5.382618 AAAGCTTGTCATCCTTGAATGTC 57.617 39.130 0.00 0.00 32.48 3.06
865 1008 4.298103 AGCTTGTCATCCTTGAATGTCT 57.702 40.909 0.00 0.00 32.48 3.41
866 1009 4.660168 AGCTTGTCATCCTTGAATGTCTT 58.340 39.130 0.00 0.00 32.48 3.01
867 1010 4.458295 AGCTTGTCATCCTTGAATGTCTTG 59.542 41.667 0.00 0.00 32.48 3.02
868 1011 4.217118 GCTTGTCATCCTTGAATGTCTTGT 59.783 41.667 0.00 0.00 32.48 3.16
869 1012 5.618640 GCTTGTCATCCTTGAATGTCTTGTC 60.619 44.000 0.00 0.00 32.48 3.18
870 1013 4.971939 TGTCATCCTTGAATGTCTTGTCA 58.028 39.130 0.00 0.00 32.48 3.58
871 1014 4.756642 TGTCATCCTTGAATGTCTTGTCAC 59.243 41.667 0.00 0.00 32.48 3.67
872 1015 4.154918 GTCATCCTTGAATGTCTTGTCACC 59.845 45.833 0.00 0.00 32.48 4.02
873 1016 3.855255 TCCTTGAATGTCTTGTCACCA 57.145 42.857 0.00 0.00 0.00 4.17
874 1017 4.371624 TCCTTGAATGTCTTGTCACCAT 57.628 40.909 0.00 0.00 0.00 3.55
875 1018 5.497464 TCCTTGAATGTCTTGTCACCATA 57.503 39.130 0.00 0.00 0.00 2.74
876 1019 5.245531 TCCTTGAATGTCTTGTCACCATAC 58.754 41.667 0.00 0.00 0.00 2.39
877 1020 5.013079 TCCTTGAATGTCTTGTCACCATACT 59.987 40.000 0.00 0.00 0.00 2.12
878 1021 5.352569 CCTTGAATGTCTTGTCACCATACTC 59.647 44.000 0.00 0.00 0.00 2.59
879 1022 4.832248 TGAATGTCTTGTCACCATACTCC 58.168 43.478 0.00 0.00 0.00 3.85
880 1023 3.914426 ATGTCTTGTCACCATACTCCC 57.086 47.619 0.00 0.00 0.00 4.30
881 1024 2.902608 TGTCTTGTCACCATACTCCCT 58.097 47.619 0.00 0.00 0.00 4.20
882 1025 2.567169 TGTCTTGTCACCATACTCCCTG 59.433 50.000 0.00 0.00 0.00 4.45
883 1026 2.832129 GTCTTGTCACCATACTCCCTGA 59.168 50.000 0.00 0.00 0.00 3.86
884 1027 2.832129 TCTTGTCACCATACTCCCTGAC 59.168 50.000 0.00 0.00 34.74 3.51
885 1028 2.319025 TGTCACCATACTCCCTGACA 57.681 50.000 0.00 0.00 40.51 3.58
886 1029 2.832838 TGTCACCATACTCCCTGACAT 58.167 47.619 0.00 0.00 38.45 3.06
887 1030 2.501316 TGTCACCATACTCCCTGACATG 59.499 50.000 0.00 0.00 38.45 3.21
888 1031 2.766263 GTCACCATACTCCCTGACATGA 59.234 50.000 0.00 0.00 34.38 3.07
889 1032 3.033909 TCACCATACTCCCTGACATGAG 58.966 50.000 0.00 1.61 34.73 2.90
890 1033 3.033909 CACCATACTCCCTGACATGAGA 58.966 50.000 0.00 0.00 32.84 3.27
893 1036 3.181461 CCATACTCCCTGACATGAGAACC 60.181 52.174 0.00 0.00 32.84 3.62
894 1037 0.898320 ACTCCCTGACATGAGAACCG 59.102 55.000 0.00 0.00 32.84 4.44
895 1038 1.186200 CTCCCTGACATGAGAACCGA 58.814 55.000 0.00 0.00 0.00 4.69
898 1041 3.576118 CTCCCTGACATGAGAACCGATAT 59.424 47.826 0.00 0.00 0.00 1.63
900 1043 4.060900 CCCTGACATGAGAACCGATATTG 58.939 47.826 0.00 0.00 0.00 1.90
901 1044 4.060900 CCTGACATGAGAACCGATATTGG 58.939 47.826 7.52 7.52 0.00 3.16
904 1047 4.405680 TGACATGAGAACCGATATTGGAGT 59.594 41.667 16.48 2.84 0.00 3.85
909 1052 5.989477 TGAGAACCGATATTGGAGTCATTT 58.011 37.500 16.48 0.00 0.00 2.32
913 1056 3.149196 CCGATATTGGAGTCATTTGGGG 58.851 50.000 2.32 0.00 0.00 4.96
914 1057 3.149196 CGATATTGGAGTCATTTGGGGG 58.851 50.000 0.00 0.00 0.00 5.40
915 1058 3.435026 CGATATTGGAGTCATTTGGGGGT 60.435 47.826 0.00 0.00 0.00 4.95
918 1061 1.682344 GGAGTCATTTGGGGGTGCC 60.682 63.158 0.00 0.00 0.00 5.01
920 1063 2.282887 GTCATTTGGGGGTGCCGT 60.283 61.111 0.00 0.00 0.00 5.68
926 1069 4.966787 TGGGGGTGCCGTTCTTGC 62.967 66.667 0.00 0.00 0.00 4.01
928 1071 2.597510 GGGGTGCCGTTCTTGCTT 60.598 61.111 0.00 0.00 0.00 3.91
929 1072 2.200337 GGGGTGCCGTTCTTGCTTT 61.200 57.895 0.00 0.00 0.00 3.51
930 1073 0.891904 GGGGTGCCGTTCTTGCTTTA 60.892 55.000 0.00 0.00 0.00 1.85
933 1076 1.335597 GGTGCCGTTCTTGCTTTAACC 60.336 52.381 0.00 0.00 0.00 2.85
934 1077 1.335496 GTGCCGTTCTTGCTTTAACCA 59.665 47.619 0.00 0.00 0.00 3.67
935 1078 1.335496 TGCCGTTCTTGCTTTAACCAC 59.665 47.619 0.00 0.00 0.00 4.16
936 1079 1.335597 GCCGTTCTTGCTTTAACCACC 60.336 52.381 0.00 0.00 0.00 4.61
937 1080 2.227194 CCGTTCTTGCTTTAACCACCT 58.773 47.619 0.00 0.00 0.00 4.00
938 1081 2.225727 CCGTTCTTGCTTTAACCACCTC 59.774 50.000 0.00 0.00 0.00 3.85
939 1082 2.096417 CGTTCTTGCTTTAACCACCTCG 60.096 50.000 0.00 0.00 0.00 4.63
941 1084 3.202829 TCTTGCTTTAACCACCTCGTT 57.797 42.857 0.00 0.00 0.00 3.85
942 1085 3.135994 TCTTGCTTTAACCACCTCGTTC 58.864 45.455 0.00 0.00 0.00 3.95
1125 2031 4.331168 ACAATGTATCTTCTCGCTTTCAGC 59.669 41.667 0.00 0.00 38.02 4.26
1527 2446 3.038017 CGTTCACAAACATCTGCAACAG 58.962 45.455 0.00 0.00 34.93 3.16
2094 3118 3.634448 TGCCTCTACTTTGAGCTAGCTAG 59.366 47.826 19.38 16.84 33.02 3.42
2134 3159 7.336396 TCAGCTACTAATTTTAAAGACCCCTC 58.664 38.462 0.00 0.00 0.00 4.30
2288 3313 6.813293 TGTGATCTGGAATGGAAAGAGATA 57.187 37.500 0.00 0.00 0.00 1.98
2406 3452 8.770438 AGAAGTGCAAAACAAAAGAAACATAA 57.230 26.923 0.00 0.00 0.00 1.90
2407 3453 9.382275 AGAAGTGCAAAACAAAAGAAACATAAT 57.618 25.926 0.00 0.00 0.00 1.28
2408 3454 9.986833 GAAGTGCAAAACAAAAGAAACATAATT 57.013 25.926 0.00 0.00 0.00 1.40
2471 3517 8.981647 AGAAAATCAACATAGCAAAAACATGTC 58.018 29.630 0.00 0.00 31.82 3.06
2638 3715 2.287644 GCAAACATGAAAAGTGGCAACC 59.712 45.455 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
361 369 4.759183 TCACTGCACTACAATTTATGCACA 59.241 37.500 0.00 0.00 42.92 4.57
509 521 3.565516 GAAGGCCAAAAGATTGTTCGAC 58.434 45.455 5.01 0.00 34.60 4.20
595 607 7.055667 AGAGTCACTCAATTCAGAGTTTACA 57.944 36.000 7.77 0.00 46.26 2.41
604 616 8.405531 CCAAAGTAAAAAGAGTCACTCAATTCA 58.594 33.333 7.77 0.00 32.06 2.57
712 725 9.482627 TCCAAAACATGTACAATTAATGAAACC 57.517 29.630 0.00 0.00 0.00 3.27
812 955 3.260884 TCAAGGTTTCTATCCTGCGAAGT 59.739 43.478 0.00 0.00 35.27 3.01
813 956 3.861840 TCAAGGTTTCTATCCTGCGAAG 58.138 45.455 0.00 0.00 35.27 3.79
814 957 3.973206 TCAAGGTTTCTATCCTGCGAA 57.027 42.857 0.00 0.00 35.27 4.70
815 958 5.607939 TTATCAAGGTTTCTATCCTGCGA 57.392 39.130 0.00 0.00 35.27 5.10
816 959 5.237344 CCTTTATCAAGGTTTCTATCCTGCG 59.763 44.000 0.00 0.00 44.46 5.18
817 960 6.625873 CCTTTATCAAGGTTTCTATCCTGC 57.374 41.667 0.00 0.00 44.46 4.85
830 973 7.031975 GGATGACAAGCTTTTCCTTTATCAAG 58.968 38.462 10.04 0.00 0.00 3.02
831 974 6.721208 AGGATGACAAGCTTTTCCTTTATCAA 59.279 34.615 10.04 0.00 32.94 2.57
832 975 6.248433 AGGATGACAAGCTTTTCCTTTATCA 58.752 36.000 10.04 0.00 32.94 2.15
833 976 6.765915 AGGATGACAAGCTTTTCCTTTATC 57.234 37.500 10.04 6.21 32.94 1.75
834 977 6.721208 TCAAGGATGACAAGCTTTTCCTTTAT 59.279 34.615 19.67 5.32 42.69 1.40
835 978 6.068010 TCAAGGATGACAAGCTTTTCCTTTA 58.932 36.000 19.67 13.31 42.69 1.85
836 979 4.895297 TCAAGGATGACAAGCTTTTCCTTT 59.105 37.500 19.67 4.46 42.69 3.11
837 980 4.473444 TCAAGGATGACAAGCTTTTCCTT 58.527 39.130 17.76 17.76 45.40 3.36
838 981 4.104383 TCAAGGATGACAAGCTTTTCCT 57.896 40.909 10.04 10.01 38.45 3.36
839 982 4.853924 TTCAAGGATGACAAGCTTTTCC 57.146 40.909 10.04 8.02 34.61 3.13
840 983 5.776744 ACATTCAAGGATGACAAGCTTTTC 58.223 37.500 5.63 5.63 34.61 2.29
841 984 5.537674 AGACATTCAAGGATGACAAGCTTTT 59.462 36.000 0.00 0.00 34.61 2.27
842 985 5.075493 AGACATTCAAGGATGACAAGCTTT 58.925 37.500 0.00 0.00 34.61 3.51
843 986 4.660168 AGACATTCAAGGATGACAAGCTT 58.340 39.130 0.00 0.00 34.61 3.74
844 987 4.298103 AGACATTCAAGGATGACAAGCT 57.702 40.909 0.00 0.00 34.61 3.74
845 988 4.217118 ACAAGACATTCAAGGATGACAAGC 59.783 41.667 0.00 0.00 34.61 4.01
846 989 5.471116 TGACAAGACATTCAAGGATGACAAG 59.529 40.000 0.00 0.00 34.61 3.16
847 990 5.239306 GTGACAAGACATTCAAGGATGACAA 59.761 40.000 0.00 0.00 34.61 3.18
848 991 4.756642 GTGACAAGACATTCAAGGATGACA 59.243 41.667 0.00 0.00 34.61 3.58
849 992 4.154918 GGTGACAAGACATTCAAGGATGAC 59.845 45.833 0.00 0.00 34.61 3.06
850 993 4.202451 TGGTGACAAGACATTCAAGGATGA 60.202 41.667 0.00 0.00 37.44 2.92
851 994 4.074259 TGGTGACAAGACATTCAAGGATG 58.926 43.478 0.00 0.00 37.44 3.51
852 995 4.371624 TGGTGACAAGACATTCAAGGAT 57.628 40.909 0.00 0.00 37.44 3.24
853 996 3.855255 TGGTGACAAGACATTCAAGGA 57.145 42.857 0.00 0.00 37.44 3.36
862 1005 5.835495 TGTCAGGGAGTATGGTGACAAGAC 61.835 50.000 1.62 0.00 44.79 3.01
863 1006 3.757130 TGTCAGGGAGTATGGTGACAAGA 60.757 47.826 1.62 0.00 44.79 3.02
864 1007 2.567169 TGTCAGGGAGTATGGTGACAAG 59.433 50.000 1.62 0.00 44.79 3.16
865 1008 2.615391 TGTCAGGGAGTATGGTGACAA 58.385 47.619 1.62 0.00 44.79 3.18
866 1009 2.319025 TGTCAGGGAGTATGGTGACA 57.681 50.000 0.00 0.00 45.39 3.58
867 1010 2.766263 TCATGTCAGGGAGTATGGTGAC 59.234 50.000 0.00 0.00 39.85 3.67
868 1011 3.033909 CTCATGTCAGGGAGTATGGTGA 58.966 50.000 0.00 0.00 0.00 4.02
869 1012 3.033909 TCTCATGTCAGGGAGTATGGTG 58.966 50.000 0.00 0.00 32.93 4.17
870 1013 3.404869 TCTCATGTCAGGGAGTATGGT 57.595 47.619 0.00 0.00 32.93 3.55
871 1014 3.181461 GGTTCTCATGTCAGGGAGTATGG 60.181 52.174 0.00 0.00 32.93 2.74
872 1015 3.491619 CGGTTCTCATGTCAGGGAGTATG 60.492 52.174 0.00 0.00 32.93 2.39
873 1016 2.695666 CGGTTCTCATGTCAGGGAGTAT 59.304 50.000 0.00 0.00 32.93 2.12
874 1017 2.100197 CGGTTCTCATGTCAGGGAGTA 58.900 52.381 0.00 0.00 32.93 2.59
875 1018 0.898320 CGGTTCTCATGTCAGGGAGT 59.102 55.000 0.00 0.00 32.93 3.85
876 1019 1.186200 TCGGTTCTCATGTCAGGGAG 58.814 55.000 0.00 0.00 0.00 4.30
877 1020 1.866015 ATCGGTTCTCATGTCAGGGA 58.134 50.000 0.00 0.00 0.00 4.20
878 1021 4.060900 CAATATCGGTTCTCATGTCAGGG 58.939 47.826 0.00 0.00 0.00 4.45
879 1022 4.060900 CCAATATCGGTTCTCATGTCAGG 58.939 47.826 0.00 0.00 0.00 3.86
880 1023 4.948847 TCCAATATCGGTTCTCATGTCAG 58.051 43.478 0.00 0.00 0.00 3.51
881 1024 4.405680 ACTCCAATATCGGTTCTCATGTCA 59.594 41.667 0.00 0.00 0.00 3.58
882 1025 4.950050 ACTCCAATATCGGTTCTCATGTC 58.050 43.478 0.00 0.00 0.00 3.06
883 1026 4.405680 TGACTCCAATATCGGTTCTCATGT 59.594 41.667 0.00 0.00 0.00 3.21
884 1027 4.948847 TGACTCCAATATCGGTTCTCATG 58.051 43.478 0.00 0.00 0.00 3.07
885 1028 5.815233 ATGACTCCAATATCGGTTCTCAT 57.185 39.130 0.00 0.00 0.00 2.90
886 1029 5.614324 AATGACTCCAATATCGGTTCTCA 57.386 39.130 0.00 0.00 0.00 3.27
887 1030 5.237344 CCAAATGACTCCAATATCGGTTCTC 59.763 44.000 0.00 0.00 0.00 2.87
888 1031 5.126067 CCAAATGACTCCAATATCGGTTCT 58.874 41.667 0.00 0.00 0.00 3.01
889 1032 4.275936 CCCAAATGACTCCAATATCGGTTC 59.724 45.833 0.00 0.00 0.00 3.62
890 1033 4.207165 CCCAAATGACTCCAATATCGGTT 58.793 43.478 0.00 0.00 0.00 4.44
893 1036 3.149196 CCCCCAAATGACTCCAATATCG 58.851 50.000 0.00 0.00 0.00 2.92
894 1037 3.891366 CACCCCCAAATGACTCCAATATC 59.109 47.826 0.00 0.00 0.00 1.63
895 1038 3.914771 CACCCCCAAATGACTCCAATAT 58.085 45.455 0.00 0.00 0.00 1.28
898 1041 0.541764 GCACCCCCAAATGACTCCAA 60.542 55.000 0.00 0.00 0.00 3.53
900 1043 1.682344 GGCACCCCCAAATGACTCC 60.682 63.158 0.00 0.00 0.00 3.85
901 1044 2.046285 CGGCACCCCCAAATGACTC 61.046 63.158 0.00 0.00 0.00 3.36
904 1047 1.605165 GAACGGCACCCCCAAATGA 60.605 57.895 0.00 0.00 0.00 2.57
909 1052 4.966787 GCAAGAACGGCACCCCCA 62.967 66.667 0.00 0.00 0.00 4.96
913 1056 1.335597 GGTTAAAGCAAGAACGGCACC 60.336 52.381 0.00 0.00 0.00 5.01
914 1057 1.335496 TGGTTAAAGCAAGAACGGCAC 59.665 47.619 0.00 0.00 0.00 5.01
915 1058 1.335496 GTGGTTAAAGCAAGAACGGCA 59.665 47.619 0.00 0.00 0.00 5.69
918 1061 2.096417 CGAGGTGGTTAAAGCAAGAACG 60.096 50.000 0.00 0.00 0.00 3.95
920 1063 3.202829 ACGAGGTGGTTAAAGCAAGAA 57.797 42.857 0.00 0.00 0.00 2.52
926 1069 1.804748 GCAGGAACGAGGTGGTTAAAG 59.195 52.381 0.00 0.00 0.00 1.85
928 1071 1.053424 AGCAGGAACGAGGTGGTTAA 58.947 50.000 0.00 0.00 0.00 2.01
929 1072 1.053424 AAGCAGGAACGAGGTGGTTA 58.947 50.000 0.00 0.00 30.37 2.85
930 1073 0.182775 AAAGCAGGAACGAGGTGGTT 59.817 50.000 0.00 0.00 33.45 3.67
933 1076 2.153913 CGAAAGCAGGAACGAGGTG 58.846 57.895 0.00 0.00 0.00 4.00
934 1077 4.675404 CGAAAGCAGGAACGAGGT 57.325 55.556 0.00 0.00 0.00 3.85
1125 2031 6.094464 TCTGATCCAACATTTAACTGCTCATG 59.906 38.462 0.00 0.00 0.00 3.07
1527 2446 2.179517 CGGTCTCAGAGACGCCAC 59.820 66.667 21.98 9.07 45.96 5.01
2155 3180 4.021016 AGTCAACTGAGATTTAGCGAACCT 60.021 41.667 0.00 0.00 0.00 3.50
2277 3302 1.542472 TCGCACACGTATCTCTTTCCA 59.458 47.619 0.00 0.00 41.18 3.53
2288 3313 0.388649 GAGTCCAGAATCGCACACGT 60.389 55.000 0.00 0.00 41.18 4.49
2406 3452 8.682936 TGGTTGTTTGGTTTGCAATATTAAAT 57.317 26.923 0.00 0.00 0.00 1.40
2407 3453 8.398665 GTTGGTTGTTTGGTTTGCAATATTAAA 58.601 29.630 0.00 0.00 0.00 1.52
2408 3454 7.552687 TGTTGGTTGTTTGGTTTGCAATATTAA 59.447 29.630 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.