Multiple sequence alignment - TraesCS2D01G551800

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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 TraesCS2D01G551800 chr2D 100.000 4286 0 0 1 4286 627235843 627231558 0.000000e+00 7915.0
1 TraesCS2D01G551800 chr2D 81.790 3218 477 62 1105 4286 627198886 627195742 0.000000e+00 2595.0
2 TraesCS2D01G551800 chr2D 81.656 3031 481 51 913 3921 627168854 627165877 0.000000e+00 2447.0
3 TraesCS2D01G551800 chr2D 82.342 2656 399 47 979 3605 627174117 627171503 0.000000e+00 2242.0
4 TraesCS2D01G551800 chr2D 74.583 240 41 15 1 221 627171195 627170957 2.120000e-13 87.9
5 TraesCS2D01G551800 chr2D 94.340 53 3 0 4201 4253 630125247 630125299 9.880000e-12 82.4
6 TraesCS2D01G551800 chr2B 94.617 4310 186 27 1 4284 769049181 769044892 0.000000e+00 6632.0
7 TraesCS2D01G551800 chr2B 92.212 1682 109 15 2240 3906 768663391 768661717 0.000000e+00 2361.0
8 TraesCS2D01G551800 chr2B 82.173 2687 440 29 913 3568 768615440 768612762 0.000000e+00 2272.0
9 TraesCS2D01G551800 chr2B 82.243 2675 421 40 917 3570 769039894 769037253 0.000000e+00 2259.0
10 TraesCS2D01G551800 chr2B 93.956 1274 74 3 972 2242 768775462 768774189 0.000000e+00 1923.0
11 TraesCS2D01G551800 chr2B 87.371 388 45 3 3900 4284 768661690 768661304 3.930000e-120 442.0
12 TraesCS2D01G551800 chr2B 88.252 349 33 6 11 357 768778333 768777991 1.110000e-110 411.0
13 TraesCS2D01G551800 chr2B 86.826 167 21 1 3998 4164 768612456 768612291 7.320000e-43 185.0
14 TraesCS2D01G551800 chr2B 88.489 139 16 0 526 664 768775591 768775453 7.370000e-38 169.0
15 TraesCS2D01G551800 chr2B 81.553 103 15 3 120 221 768617842 768617743 9.880000e-12 82.4
16 TraesCS2D01G551800 chr2A 82.047 3381 506 58 910 4249 757929565 757926245 0.000000e+00 2787.0
17 TraesCS2D01G551800 chr2A 81.098 3042 493 55 913 3923 757920472 757917482 0.000000e+00 2357.0
18 TraesCS2D01G551800 chr2A 82.109 2655 416 42 979 3605 757925210 757922587 0.000000e+00 2217.0


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 TraesCS2D01G551800 chr2D 627231558 627235843 4285 True 7915.000000 7915 100.000000 1 4286 1 chr2D.!!$R2 4285
1 TraesCS2D01G551800 chr2D 627195742 627198886 3144 True 2595.000000 2595 81.790000 1105 4286 1 chr2D.!!$R1 3181
2 TraesCS2D01G551800 chr2D 627165877 627174117 8240 True 1592.300000 2447 79.527000 1 3921 3 chr2D.!!$R3 3920
3 TraesCS2D01G551800 chr2B 769044892 769049181 4289 True 6632.000000 6632 94.617000 1 4284 1 chr2B.!!$R2 4283
4 TraesCS2D01G551800 chr2B 769037253 769039894 2641 True 2259.000000 2259 82.243000 917 3570 1 chr2B.!!$R1 2653
5 TraesCS2D01G551800 chr2B 768661304 768663391 2087 True 1401.500000 2361 89.791500 2240 4284 2 chr2B.!!$R4 2044
6 TraesCS2D01G551800 chr2B 768612291 768617842 5551 True 846.466667 2272 83.517333 120 4164 3 chr2B.!!$R3 4044
7 TraesCS2D01G551800 chr2B 768774189 768778333 4144 True 834.333333 1923 90.232333 11 2242 3 chr2B.!!$R5 2231
8 TraesCS2D01G551800 chr2A 757917482 757929565 12083 True 2453.666667 2787 81.751333 910 4249 3 chr2A.!!$R1 3339

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
893 4038 0.105039 GGTATCTCCGAGGCAACAGG 59.895 60.0 0.00 0.00 41.41 4.00 F
903 4048 0.182775 AGGCAACAGGTTCGGTCTTT 59.817 50.0 0.00 0.00 41.41 2.52 F
904 4049 0.591659 GGCAACAGGTTCGGTCTTTC 59.408 55.0 0.00 0.00 0.00 2.62 F
1451 10688 0.620556 ATGAACATGTTCTCCGGGCT 59.379 50.0 32.57 10.98 40.14 5.19 F
2271 20597 0.835971 TGAGGGTCTTGCAGCACCTA 60.836 55.0 14.15 1.66 32.69 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1890 15406 0.466555 TCCTCAAACCCCCAAACACG 60.467 55.000 0.00 0.0 0.00 4.49 R
2341 20667 0.662619 TGCAAGCTCTTGAAACCACG 59.337 50.000 13.33 0.0 42.93 4.94 R
2498 20824 3.690139 TGACAGGTCGACATAGAAGAGAC 59.310 47.826 18.91 0.0 0.00 3.36 R
3007 21345 0.323360 CAGGGGCCATTCCGAAGAAA 60.323 55.000 4.39 0.0 35.09 2.52 R
3994 22414 1.068083 CCGCGACAGCCATCTATGT 59.932 57.895 8.23 0.0 41.18 2.29 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
174 175 5.627499 TTAATCATTTGTCAGGTGTGCTC 57.373 39.130 0.00 0.00 0.00 4.26
278 279 9.434559 GTTCTAACAGAAGACAAAAATGTACAC 57.565 33.333 0.00 0.00 34.42 2.90
343 344 2.043526 AGTCAAGCCCTTCCCAATCATT 59.956 45.455 0.00 0.00 0.00 2.57
363 364 7.435068 TCATTTAAGCTTCCTGAGTTTACAC 57.565 36.000 0.00 0.00 31.75 2.90
390 2383 2.303600 TGTTACCGGGCATTTAGACTGT 59.696 45.455 6.32 0.00 0.00 3.55
509 2634 4.092383 CGACTTCTTATGGTTGGGTAAACG 59.908 45.833 0.00 0.00 39.91 3.60
514 2639 6.297080 TCTTATGGTTGGGTAAACGTATCA 57.703 37.500 0.00 0.00 39.91 2.15
628 3331 7.340487 GGACATTGACTCTTCCAAGGAATAAAT 59.660 37.037 1.35 0.00 33.28 1.40
780 3483 3.278574 TCATGGGAAATGGAATGACGTC 58.721 45.455 9.11 9.11 0.00 4.34
782 3927 1.002659 TGGGAAATGGAATGACGTCGT 59.997 47.619 11.62 7.97 0.00 4.34
796 3941 3.119955 TGACGTCGTCATAGACTTTGAGG 60.120 47.826 23.70 8.73 37.67 3.86
798 3943 3.695060 ACGTCGTCATAGACTTTGAGGAT 59.305 43.478 17.47 4.44 39.40 3.24
803 3948 4.979197 CGTCATAGACTTTGAGGATAGCAC 59.021 45.833 9.24 0.00 32.17 4.40
806 3951 1.482593 AGACTTTGAGGATAGCACCCG 59.517 52.381 0.00 0.00 0.00 5.28
807 3952 1.207329 GACTTTGAGGATAGCACCCGT 59.793 52.381 0.00 0.00 0.00 5.28
811 3956 3.985019 TTGAGGATAGCACCCGTAAAA 57.015 42.857 0.00 0.00 0.00 1.52
815 3960 4.259356 GAGGATAGCACCCGTAAAAGTTT 58.741 43.478 0.00 0.00 0.00 2.66
816 3961 4.659115 AGGATAGCACCCGTAAAAGTTTT 58.341 39.130 6.06 6.06 0.00 2.43
817 3962 5.807909 AGGATAGCACCCGTAAAAGTTTTA 58.192 37.500 3.88 3.88 0.00 1.52
818 3963 6.420638 AGGATAGCACCCGTAAAAGTTTTAT 58.579 36.000 11.12 0.00 0.00 1.40
819 3964 6.317893 AGGATAGCACCCGTAAAAGTTTTATG 59.682 38.462 17.29 17.29 0.00 1.90
820 3965 6.094464 GGATAGCACCCGTAAAAGTTTTATGT 59.906 38.462 20.84 12.20 0.00 2.29
821 3966 5.777850 AGCACCCGTAAAAGTTTTATGTT 57.222 34.783 20.84 8.05 0.00 2.71
822 3967 6.151663 AGCACCCGTAAAAGTTTTATGTTT 57.848 33.333 20.84 8.78 0.00 2.83
823 3968 6.210796 AGCACCCGTAAAAGTTTTATGTTTC 58.789 36.000 20.84 10.53 0.00 2.78
825 3970 5.921976 CACCCGTAAAAGTTTTATGTTTCCC 59.078 40.000 20.84 4.08 0.00 3.97
826 3971 5.010922 ACCCGTAAAAGTTTTATGTTTCCCC 59.989 40.000 20.84 3.49 0.00 4.81
828 3973 5.921976 CCGTAAAAGTTTTATGTTTCCCCAC 59.078 40.000 20.84 4.31 0.00 4.61
830 3975 6.418523 CGTAAAAGTTTTATGTTTCCCCACAC 59.581 38.462 16.36 0.59 0.00 3.82
831 3976 4.948341 AAGTTTTATGTTTCCCCACACC 57.052 40.909 0.00 0.00 0.00 4.16
832 3977 3.917300 AGTTTTATGTTTCCCCACACCA 58.083 40.909 0.00 0.00 0.00 4.17
835 3980 5.368230 AGTTTTATGTTTCCCCACACCAATT 59.632 36.000 0.00 0.00 0.00 2.32
836 3981 5.476091 TTTATGTTTCCCCACACCAATTC 57.524 39.130 0.00 0.00 0.00 2.17
837 3982 1.710816 TGTTTCCCCACACCAATTCC 58.289 50.000 0.00 0.00 0.00 3.01
839 3984 1.893137 GTTTCCCCACACCAATTCCTC 59.107 52.381 0.00 0.00 0.00 3.71
840 3985 1.153539 TTCCCCACACCAATTCCTCA 58.846 50.000 0.00 0.00 0.00 3.86
841 3986 0.698238 TCCCCACACCAATTCCTCAG 59.302 55.000 0.00 0.00 0.00 3.35
842 3987 0.405585 CCCCACACCAATTCCTCAGT 59.594 55.000 0.00 0.00 0.00 3.41
843 3988 1.203050 CCCCACACCAATTCCTCAGTT 60.203 52.381 0.00 0.00 0.00 3.16
845 3990 2.558359 CCCACACCAATTCCTCAGTTTC 59.442 50.000 0.00 0.00 0.00 2.78
847 3992 3.254166 CCACACCAATTCCTCAGTTTCTG 59.746 47.826 0.00 0.00 0.00 3.02
848 3993 3.254166 CACACCAATTCCTCAGTTTCTGG 59.746 47.826 0.00 0.00 31.51 3.86
850 3995 3.503748 CACCAATTCCTCAGTTTCTGGTC 59.496 47.826 0.00 0.00 33.46 4.02
851 3996 3.138283 ACCAATTCCTCAGTTTCTGGTCA 59.862 43.478 0.00 0.00 29.76 4.02
852 3997 4.202609 ACCAATTCCTCAGTTTCTGGTCAT 60.203 41.667 0.00 0.00 29.76 3.06
853 3998 4.768968 CCAATTCCTCAGTTTCTGGTCATT 59.231 41.667 0.00 0.00 31.51 2.57
854 3999 5.244626 CCAATTCCTCAGTTTCTGGTCATTT 59.755 40.000 0.00 0.00 31.51 2.32
855 4000 6.434028 CCAATTCCTCAGTTTCTGGTCATTTA 59.566 38.462 0.00 0.00 31.51 1.40
857 4002 7.872113 ATTCCTCAGTTTCTGGTCATTTATC 57.128 36.000 0.00 0.00 31.51 1.75
858 4003 6.373005 TCCTCAGTTTCTGGTCATTTATCA 57.627 37.500 0.00 0.00 31.51 2.15
859 4004 6.409704 TCCTCAGTTTCTGGTCATTTATCAG 58.590 40.000 0.00 0.00 37.71 2.90
860 4005 5.587844 CCTCAGTTTCTGGTCATTTATCAGG 59.412 44.000 0.00 0.00 36.91 3.86
861 4006 4.943705 TCAGTTTCTGGTCATTTATCAGGC 59.056 41.667 0.00 0.00 36.91 4.85
863 4008 5.416952 CAGTTTCTGGTCATTTATCAGGCTT 59.583 40.000 0.00 0.00 36.91 4.35
864 4009 6.012745 AGTTTCTGGTCATTTATCAGGCTTT 58.987 36.000 0.00 0.00 36.91 3.51
865 4010 6.151817 AGTTTCTGGTCATTTATCAGGCTTTC 59.848 38.462 0.00 0.00 36.91 2.62
866 4011 5.441718 TCTGGTCATTTATCAGGCTTTCT 57.558 39.130 0.00 0.00 36.91 2.52
867 4012 5.188434 TCTGGTCATTTATCAGGCTTTCTG 58.812 41.667 0.00 0.00 44.68 3.02
869 4014 6.061022 TGGTCATTTATCAGGCTTTCTGTA 57.939 37.500 0.00 0.00 43.76 2.74
871 4016 5.880332 GGTCATTTATCAGGCTTTCTGTACA 59.120 40.000 0.00 0.00 43.76 2.90
873 4018 7.244192 GTCATTTATCAGGCTTTCTGTACAAC 58.756 38.462 0.00 0.00 43.76 3.32
874 4019 5.856126 TTTATCAGGCTTTCTGTACAACG 57.144 39.130 0.00 0.00 43.76 4.10
875 4020 2.163818 TCAGGCTTTCTGTACAACGG 57.836 50.000 0.00 0.00 43.76 4.44
876 4021 1.414919 TCAGGCTTTCTGTACAACGGT 59.585 47.619 0.00 0.00 43.76 4.83
877 4022 2.629137 TCAGGCTTTCTGTACAACGGTA 59.371 45.455 0.00 0.00 43.76 4.02
878 4023 3.259876 TCAGGCTTTCTGTACAACGGTAT 59.740 43.478 0.00 0.00 43.76 2.73
879 4024 3.617263 CAGGCTTTCTGTACAACGGTATC 59.383 47.826 0.00 0.00 38.64 2.24
882 4027 3.864003 GCTTTCTGTACAACGGTATCTCC 59.136 47.826 0.00 0.00 0.00 3.71
892 4037 3.669354 GGTATCTCCGAGGCAACAG 57.331 57.895 0.00 0.00 41.41 3.16
893 4038 0.105039 GGTATCTCCGAGGCAACAGG 59.895 60.000 0.00 0.00 41.41 4.00
894 4039 0.824759 GTATCTCCGAGGCAACAGGT 59.175 55.000 0.00 0.00 37.80 4.00
895 4040 1.207329 GTATCTCCGAGGCAACAGGTT 59.793 52.381 0.00 0.00 37.80 3.50
896 4041 0.250513 ATCTCCGAGGCAACAGGTTC 59.749 55.000 0.00 0.00 37.80 3.62
897 4042 1.738099 CTCCGAGGCAACAGGTTCG 60.738 63.158 0.00 0.00 37.80 3.95
898 4043 2.742372 CCGAGGCAACAGGTTCGG 60.742 66.667 0.00 0.00 45.45 4.30
899 4044 2.030562 CGAGGCAACAGGTTCGGT 59.969 61.111 0.00 0.00 41.41 4.69
900 4045 2.027625 CGAGGCAACAGGTTCGGTC 61.028 63.158 0.00 0.00 41.41 4.79
901 4046 1.371558 GAGGCAACAGGTTCGGTCT 59.628 57.895 0.00 0.00 41.41 3.85
902 4047 0.250338 GAGGCAACAGGTTCGGTCTT 60.250 55.000 0.00 0.00 41.41 3.01
903 4048 0.182775 AGGCAACAGGTTCGGTCTTT 59.817 50.000 0.00 0.00 41.41 2.52
904 4049 0.591659 GGCAACAGGTTCGGTCTTTC 59.408 55.000 0.00 0.00 0.00 2.62
905 4050 0.591659 GCAACAGGTTCGGTCTTTCC 59.408 55.000 0.00 0.00 0.00 3.13
906 4051 1.814248 GCAACAGGTTCGGTCTTTCCT 60.814 52.381 0.00 0.00 0.00 3.36
907 4052 2.572290 CAACAGGTTCGGTCTTTCCTT 58.428 47.619 0.00 0.00 0.00 3.36
908 4053 2.256117 ACAGGTTCGGTCTTTCCTTG 57.744 50.000 0.00 0.00 0.00 3.61
910 4055 2.092592 ACAGGTTCGGTCTTTCCTTGTT 60.093 45.455 0.00 0.00 0.00 2.83
913 4058 2.686405 GGTTCGGTCTTTCCTTGTTTGT 59.314 45.455 0.00 0.00 0.00 2.83
925 4070 5.913137 TCCTTGTTTGTGTGTTCTTGATT 57.087 34.783 0.00 0.00 0.00 2.57
933 4078 7.701924 TGTTTGTGTGTTCTTGATTCTTGAATC 59.298 33.333 14.45 14.45 0.00 2.52
940 4085 5.571784 TCTTGATTCTTGAATCCATGCAC 57.428 39.130 17.50 0.00 0.00 4.57
942 4087 3.025978 TGATTCTTGAATCCATGCACCC 58.974 45.455 17.50 0.00 0.00 4.61
946 4091 2.173519 CTTGAATCCATGCACCCTTGT 58.826 47.619 0.00 0.00 0.00 3.16
949 4094 3.979911 TGAATCCATGCACCCTTGTAAT 58.020 40.909 0.00 0.00 0.00 1.89
971 10205 1.145738 AGGTGTGAGTTTGGCCAAGAT 59.854 47.619 19.48 11.39 0.00 2.40
1137 10373 1.303561 TCTGAACCAGGCATGCCAC 60.304 57.895 37.18 21.59 38.92 5.01
1451 10688 0.620556 ATGAACATGTTCTCCGGGCT 59.379 50.000 32.57 10.98 40.14 5.19
2271 20597 0.835971 TGAGGGTCTTGCAGCACCTA 60.836 55.000 14.15 1.66 32.69 3.08
2498 20824 6.150641 CCATCATGGTTAGGCAATCTGAATAG 59.849 42.308 0.00 0.00 31.35 1.73
2700 21029 3.854669 CCTCCGGCGCTGATCCTT 61.855 66.667 20.25 0.00 0.00 3.36
3085 21426 2.874701 GGCACCAATACTGTATCTGCAG 59.125 50.000 7.63 7.63 41.92 4.41
3142 21483 5.184479 GGATTTACTTTCGGGCTTTTAACCT 59.816 40.000 0.00 0.00 0.00 3.50
3297 21645 7.205515 AGATCATCCTTGAAATAAGTCACCT 57.794 36.000 0.00 0.00 34.96 4.00
3298 21646 7.052873 AGATCATCCTTGAAATAAGTCACCTG 58.947 38.462 0.00 0.00 34.96 4.00
3316 21664 2.533266 TGTGGCTCTTCACAGTTCTC 57.467 50.000 0.00 0.00 42.05 2.87
3322 21679 2.869636 GCTCTTCACAGTTCTCACCTGG 60.870 54.545 0.00 0.00 34.16 4.45
3323 21680 2.630098 CTCTTCACAGTTCTCACCTGGA 59.370 50.000 0.00 0.00 34.16 3.86
3324 21681 3.038280 TCTTCACAGTTCTCACCTGGAA 58.962 45.455 0.00 0.00 34.16 3.53
3339 21698 5.009610 TCACCTGGAAGCAAATGTTCTTTAC 59.990 40.000 0.00 0.00 0.00 2.01
3352 21716 6.552445 ATGTTCTTTACTATGCTGTCTCCT 57.448 37.500 0.00 0.00 0.00 3.69
3390 21758 2.206576 ATCTTCTTTGCTTCCGCCTT 57.793 45.000 0.00 0.00 34.43 4.35
3391 21759 1.238439 TCTTCTTTGCTTCCGCCTTG 58.762 50.000 0.00 0.00 34.43 3.61
3408 21776 2.041081 CCTTGGGTGTCATTACCTGGAA 59.959 50.000 0.00 0.00 40.66 3.53
3437 21805 0.777446 AGCAGGGGTTGTGTGGTTAT 59.223 50.000 0.00 0.00 0.00 1.89
3524 21895 8.908786 ATTTATGAACTGTATGGTGGATACTG 57.091 34.615 0.00 0.00 40.58 2.74
3617 21993 7.545265 GCTAATCAAAGATGGTGCATGTAAAAA 59.455 33.333 0.00 0.00 0.00 1.94
3618 21994 9.590451 CTAATCAAAGATGGTGCATGTAAAAAT 57.410 29.630 0.00 0.00 0.00 1.82
3731 22114 3.889538 GGTTGTTCTAGCTTTTGGAAGGT 59.110 43.478 0.00 0.00 45.08 3.50
3738 22121 4.758165 TCTAGCTTTTGGAAGGTTTAACCG 59.242 41.667 8.63 0.00 44.90 4.44
3762 22145 6.806249 CGATTACATTTTAGCAAGGCTTTTGA 59.194 34.615 0.00 0.00 40.44 2.69
3795 22180 7.851228 AGGAGGTGAAAGAAAAGAAAATGTTT 58.149 30.769 0.00 0.00 0.00 2.83
3848 22234 7.380065 TCAACATAAACATTGCGTTAAAACCTC 59.620 33.333 0.00 0.00 36.59 3.85
3897 22283 5.880054 TGCAGCTGAAACTAGGAAAATAC 57.120 39.130 20.43 0.00 0.00 1.89
3935 22355 3.230134 TGAAAATGAACCTGGGTTGAGG 58.770 45.455 9.95 0.00 38.60 3.86
3944 22364 1.075374 CCTGGGTTGAGGTGGATTGAA 59.925 52.381 0.00 0.00 0.00 2.69
3948 22368 4.230455 TGGGTTGAGGTGGATTGAAATTT 58.770 39.130 0.00 0.00 0.00 1.82
3983 22403 5.123344 TCATTTGTTGTCTGCAGATGATGAG 59.877 40.000 21.47 6.67 34.11 2.90
3991 22411 1.003928 TGCAGATGATGAGTGCCACTT 59.996 47.619 0.00 0.00 36.31 3.16
3994 22414 3.340928 CAGATGATGAGTGCCACTTTCA 58.659 45.455 12.13 12.13 0.00 2.69
4010 22430 1.939974 TTCACATAGATGGCTGTCGC 58.060 50.000 0.00 0.00 0.00 5.19
4013 22433 2.029666 ATAGATGGCTGTCGCGGC 59.970 61.111 2.29 2.29 36.88 6.53
4057 22477 8.137437 GGGAAACATGGAATTGTCATATAGTTG 58.863 37.037 0.00 0.00 0.00 3.16
4099 22519 6.377996 TCAAGTTGCTAAGTTGCCATGAATAT 59.622 34.615 0.00 0.00 40.75 1.28
4139 22559 1.553706 AAGCTGCTTTCCATTGAGGG 58.446 50.000 9.53 0.00 38.24 4.30
4266 22688 3.812053 AGTTGTGAAAGACTTGCTGCTAG 59.188 43.478 9.53 9.53 0.00 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 5.505173 TTATAGCTCAAAATTCTGCTGGC 57.495 39.130 0.00 0.00 37.02 4.85
174 175 1.996191 GTGTCTTTCCTAGAAGCAGCG 59.004 52.381 0.00 0.00 33.81 5.18
228 229 7.456725 ACAATTCCAGTATAATCTCTGGGATG 58.543 38.462 10.64 9.57 46.03 3.51
343 344 8.911918 TTAATGTGTAAACTCAGGAAGCTTAA 57.088 30.769 0.00 0.00 0.00 1.85
363 364 6.262273 AGTCTAAATGCCCGGTAACATTAATG 59.738 38.462 14.01 14.01 35.49 1.90
439 2437 8.980481 ATTTAGTTGTCTTGATAAGGGTATGG 57.020 34.615 0.00 0.00 0.00 2.74
509 2634 6.373774 CCTCCTAAGCAATGATGGATTGATAC 59.626 42.308 0.00 0.00 43.87 2.24
514 2639 4.202545 CCTCCTCCTAAGCAATGATGGATT 60.203 45.833 0.00 0.00 0.00 3.01
628 3331 5.362105 ACGGTGCCAAATCCTAACTTATA 57.638 39.130 0.00 0.00 0.00 0.98
780 3483 4.979197 GTGCTATCCTCAAAGTCTATGACG 59.021 45.833 0.00 0.00 37.67 4.35
782 3927 4.345257 GGGTGCTATCCTCAAAGTCTATGA 59.655 45.833 0.00 0.00 0.00 2.15
786 3931 1.482593 CGGGTGCTATCCTCAAAGTCT 59.517 52.381 0.00 0.00 0.00 3.24
792 3937 2.835764 ACTTTTACGGGTGCTATCCTCA 59.164 45.455 0.00 0.00 0.00 3.86
796 3941 7.080353 ACATAAAACTTTTACGGGTGCTATC 57.920 36.000 0.00 0.00 0.00 2.08
798 3943 6.880942 AACATAAAACTTTTACGGGTGCTA 57.119 33.333 0.00 0.00 0.00 3.49
803 3948 5.010820 TGGGGAAACATAAAACTTTTACGGG 59.989 40.000 0.00 0.00 0.00 5.28
806 3951 6.702723 GGTGTGGGGAAACATAAAACTTTTAC 59.297 38.462 0.00 0.00 31.49 2.01
807 3952 6.383147 TGGTGTGGGGAAACATAAAACTTTTA 59.617 34.615 0.00 0.00 31.49 1.52
811 3956 3.917300 TGGTGTGGGGAAACATAAAACT 58.083 40.909 0.00 0.00 31.49 2.66
815 3960 3.835395 GGAATTGGTGTGGGGAAACATAA 59.165 43.478 0.00 0.00 31.49 1.90
816 3961 3.076785 AGGAATTGGTGTGGGGAAACATA 59.923 43.478 0.00 0.00 31.49 2.29
817 3962 2.158173 AGGAATTGGTGTGGGGAAACAT 60.158 45.455 0.00 0.00 31.49 2.71
818 3963 1.219213 AGGAATTGGTGTGGGGAAACA 59.781 47.619 0.00 0.00 0.00 2.83
819 3964 1.893137 GAGGAATTGGTGTGGGGAAAC 59.107 52.381 0.00 0.00 0.00 2.78
820 3965 1.501170 TGAGGAATTGGTGTGGGGAAA 59.499 47.619 0.00 0.00 0.00 3.13
821 3966 1.075374 CTGAGGAATTGGTGTGGGGAA 59.925 52.381 0.00 0.00 0.00 3.97
822 3967 0.698238 CTGAGGAATTGGTGTGGGGA 59.302 55.000 0.00 0.00 0.00 4.81
823 3968 0.405585 ACTGAGGAATTGGTGTGGGG 59.594 55.000 0.00 0.00 0.00 4.96
825 3970 3.254166 CAGAAACTGAGGAATTGGTGTGG 59.746 47.826 0.00 0.00 32.44 4.17
826 3971 3.254166 CCAGAAACTGAGGAATTGGTGTG 59.746 47.826 0.00 0.00 32.44 3.82
828 3973 3.490348 ACCAGAAACTGAGGAATTGGTG 58.510 45.455 0.00 0.00 36.20 4.17
830 3975 3.754965 TGACCAGAAACTGAGGAATTGG 58.245 45.455 0.00 0.00 32.44 3.16
831 3976 5.972107 AATGACCAGAAACTGAGGAATTG 57.028 39.130 0.00 0.00 32.44 2.32
832 3977 7.890127 TGATAAATGACCAGAAACTGAGGAATT 59.110 33.333 0.00 0.00 32.44 2.17
835 3980 6.373005 TGATAAATGACCAGAAACTGAGGA 57.627 37.500 0.00 0.00 32.44 3.71
836 3981 5.587844 CCTGATAAATGACCAGAAACTGAGG 59.412 44.000 0.00 0.00 32.44 3.86
837 3982 5.065731 GCCTGATAAATGACCAGAAACTGAG 59.934 44.000 0.00 0.00 32.44 3.35
839 3984 4.946157 AGCCTGATAAATGACCAGAAACTG 59.054 41.667 0.00 0.00 0.00 3.16
840 3985 5.184892 AGCCTGATAAATGACCAGAAACT 57.815 39.130 0.00 0.00 0.00 2.66
841 3986 5.904362 AAGCCTGATAAATGACCAGAAAC 57.096 39.130 0.00 0.00 0.00 2.78
842 3987 6.151648 CAGAAAGCCTGATAAATGACCAGAAA 59.848 38.462 0.00 0.00 45.78 2.52
843 3988 5.649395 CAGAAAGCCTGATAAATGACCAGAA 59.351 40.000 0.00 0.00 45.78 3.02
845 3990 4.946157 ACAGAAAGCCTGATAAATGACCAG 59.054 41.667 0.00 0.00 45.78 4.00
847 3992 5.880332 TGTACAGAAAGCCTGATAAATGACC 59.120 40.000 0.00 0.00 45.78 4.02
848 3993 6.985188 TGTACAGAAAGCCTGATAAATGAC 57.015 37.500 0.00 0.00 45.78 3.06
850 3995 6.250819 CGTTGTACAGAAAGCCTGATAAATG 58.749 40.000 0.00 0.00 45.78 2.32
851 3996 5.354234 CCGTTGTACAGAAAGCCTGATAAAT 59.646 40.000 0.00 0.00 45.78 1.40
852 3997 4.693566 CCGTTGTACAGAAAGCCTGATAAA 59.306 41.667 0.00 0.00 45.78 1.40
853 3998 4.250464 CCGTTGTACAGAAAGCCTGATAA 58.750 43.478 0.00 0.00 45.78 1.75
854 3999 3.259876 ACCGTTGTACAGAAAGCCTGATA 59.740 43.478 0.00 0.00 45.78 2.15
855 4000 2.038557 ACCGTTGTACAGAAAGCCTGAT 59.961 45.455 0.00 0.00 45.78 2.90
858 4003 3.514309 AGATACCGTTGTACAGAAAGCCT 59.486 43.478 0.00 0.00 0.00 4.58
859 4004 3.858247 AGATACCGTTGTACAGAAAGCC 58.142 45.455 0.00 0.00 0.00 4.35
860 4005 3.864003 GGAGATACCGTTGTACAGAAAGC 59.136 47.826 0.00 0.00 0.00 3.51
874 4019 0.105039 CCTGTTGCCTCGGAGATACC 59.895 60.000 6.58 0.00 33.89 2.73
875 4020 0.824759 ACCTGTTGCCTCGGAGATAC 59.175 55.000 6.58 2.19 33.89 2.24
876 4021 1.480954 GAACCTGTTGCCTCGGAGATA 59.519 52.381 6.58 0.00 33.89 1.98
877 4022 0.250513 GAACCTGTTGCCTCGGAGAT 59.749 55.000 6.58 0.00 33.89 2.75
878 4023 1.671742 GAACCTGTTGCCTCGGAGA 59.328 57.895 6.58 0.00 0.00 3.71
879 4024 1.738099 CGAACCTGTTGCCTCGGAG 60.738 63.158 0.00 0.00 0.00 4.63
882 4027 2.027625 GACCGAACCTGTTGCCTCG 61.028 63.158 0.00 0.00 0.00 4.63
883 4028 0.250338 AAGACCGAACCTGTTGCCTC 60.250 55.000 0.00 0.00 0.00 4.70
884 4029 0.182775 AAAGACCGAACCTGTTGCCT 59.817 50.000 0.00 0.00 0.00 4.75
885 4030 0.591659 GAAAGACCGAACCTGTTGCC 59.408 55.000 0.00 0.00 0.00 4.52
886 4031 0.591659 GGAAAGACCGAACCTGTTGC 59.408 55.000 0.00 0.00 0.00 4.17
887 4032 2.256117 AGGAAAGACCGAACCTGTTG 57.744 50.000 0.00 0.00 44.74 3.33
888 4033 2.092592 ACAAGGAAAGACCGAACCTGTT 60.093 45.455 0.00 0.00 44.74 3.16
889 4034 1.489230 ACAAGGAAAGACCGAACCTGT 59.511 47.619 0.00 0.00 44.74 4.00
890 4035 2.256117 ACAAGGAAAGACCGAACCTG 57.744 50.000 0.00 0.00 44.74 4.00
891 4036 2.949644 CAAACAAGGAAAGACCGAACCT 59.050 45.455 0.00 0.00 44.74 3.50
892 4037 2.686405 ACAAACAAGGAAAGACCGAACC 59.314 45.455 0.00 0.00 44.74 3.62
893 4038 3.128068 ACACAAACAAGGAAAGACCGAAC 59.872 43.478 0.00 0.00 44.74 3.95
894 4039 3.127895 CACACAAACAAGGAAAGACCGAA 59.872 43.478 0.00 0.00 44.74 4.30
895 4040 2.680841 CACACAAACAAGGAAAGACCGA 59.319 45.455 0.00 0.00 44.74 4.69
896 4041 2.422127 ACACACAAACAAGGAAAGACCG 59.578 45.455 0.00 0.00 44.74 4.79
897 4042 4.157840 AGAACACACAAACAAGGAAAGACC 59.842 41.667 0.00 0.00 39.35 3.85
898 4043 5.310720 AGAACACACAAACAAGGAAAGAC 57.689 39.130 0.00 0.00 0.00 3.01
899 4044 5.475220 TCAAGAACACACAAACAAGGAAAGA 59.525 36.000 0.00 0.00 0.00 2.52
900 4045 5.708948 TCAAGAACACACAAACAAGGAAAG 58.291 37.500 0.00 0.00 0.00 2.62
901 4046 5.713792 TCAAGAACACACAAACAAGGAAA 57.286 34.783 0.00 0.00 0.00 3.13
902 4047 5.913137 ATCAAGAACACACAAACAAGGAA 57.087 34.783 0.00 0.00 0.00 3.36
903 4048 5.652014 AGAATCAAGAACACACAAACAAGGA 59.348 36.000 0.00 0.00 0.00 3.36
904 4049 5.894807 AGAATCAAGAACACACAAACAAGG 58.105 37.500 0.00 0.00 0.00 3.61
905 4050 7.028962 TCAAGAATCAAGAACACACAAACAAG 58.971 34.615 0.00 0.00 0.00 3.16
906 4051 6.918626 TCAAGAATCAAGAACACACAAACAA 58.081 32.000 0.00 0.00 0.00 2.83
907 4052 6.507958 TCAAGAATCAAGAACACACAAACA 57.492 33.333 0.00 0.00 0.00 2.83
908 4053 7.168135 GGATTCAAGAATCAAGAACACACAAAC 59.832 37.037 20.73 0.00 46.77 2.93
910 4055 6.320926 TGGATTCAAGAATCAAGAACACACAA 59.679 34.615 20.73 0.00 46.77 3.33
913 4058 6.570957 GCATGGATTCAAGAATCAAGAACACA 60.571 38.462 20.73 10.32 46.77 3.72
925 4070 2.225091 ACAAGGGTGCATGGATTCAAGA 60.225 45.455 0.00 0.00 0.00 3.02
933 4078 3.381272 CACCTTATTACAAGGGTGCATGG 59.619 47.826 7.88 0.00 41.87 3.66
940 4085 5.183140 CCAAACTCACACCTTATTACAAGGG 59.817 44.000 7.88 0.16 41.71 3.95
942 4087 5.335661 GGCCAAACTCACACCTTATTACAAG 60.336 44.000 0.00 0.00 0.00 3.16
946 4091 4.374689 TGGCCAAACTCACACCTTATTA 57.625 40.909 0.61 0.00 0.00 0.98
949 4094 2.173782 TCTTGGCCAAACTCACACCTTA 59.826 45.455 20.91 0.00 0.00 2.69
971 10205 2.140224 TGGAAGGACTTGGGAAGGAAA 58.860 47.619 0.00 0.00 0.00 3.13
1137 10373 3.721706 GCCTCCAGGTCAGTGGGG 61.722 72.222 0.00 0.00 37.90 4.96
1713 15229 3.104766 GTGATGCCACTGCCATCG 58.895 61.111 0.00 0.00 40.10 3.84
1890 15406 0.466555 TCCTCAAACCCCCAAACACG 60.467 55.000 0.00 0.00 0.00 4.49
2106 20432 1.016130 CGGTGCACCACATGAGACTC 61.016 60.000 34.16 3.97 35.86 3.36
2341 20667 0.662619 TGCAAGCTCTTGAAACCACG 59.337 50.000 13.33 0.00 42.93 4.94
2498 20824 3.690139 TGACAGGTCGACATAGAAGAGAC 59.310 47.826 18.91 0.00 0.00 3.36
2700 21029 5.190677 GGCCCAATAAGCAAGTTACTAGAA 58.809 41.667 0.00 0.00 0.00 2.10
2962 21300 6.127366 ACAAAACTCTCATTTGTGAATGTGGT 60.127 34.615 4.03 0.00 46.26 4.16
3007 21345 0.323360 CAGGGGCCATTCCGAAGAAA 60.323 55.000 4.39 0.00 35.09 2.52
3297 21645 1.762370 TGAGAACTGTGAAGAGCCACA 59.238 47.619 0.00 0.00 43.98 4.17
3298 21646 2.139118 GTGAGAACTGTGAAGAGCCAC 58.861 52.381 0.00 0.00 37.55 5.01
3312 21660 3.228188 ACATTTGCTTCCAGGTGAGAA 57.772 42.857 0.00 0.00 0.00 2.87
3314 21662 3.152341 AGAACATTTGCTTCCAGGTGAG 58.848 45.455 0.00 0.00 0.00 3.51
3315 21663 3.228188 AGAACATTTGCTTCCAGGTGA 57.772 42.857 0.00 0.00 0.00 4.02
3316 21664 4.326504 AAAGAACATTTGCTTCCAGGTG 57.673 40.909 0.00 0.00 0.00 4.00
3322 21679 7.308435 ACAGCATAGTAAAGAACATTTGCTTC 58.692 34.615 0.00 0.00 37.58 3.86
3323 21680 7.175641 AGACAGCATAGTAAAGAACATTTGCTT 59.824 33.333 0.00 0.00 37.58 3.91
3324 21681 6.656693 AGACAGCATAGTAAAGAACATTTGCT 59.343 34.615 0.00 0.00 39.16 3.91
3390 21758 2.983192 TCTTTCCAGGTAATGACACCCA 59.017 45.455 0.00 0.00 39.62 4.51
3391 21759 3.009143 ACTCTTTCCAGGTAATGACACCC 59.991 47.826 0.00 0.00 39.62 4.61
3408 21776 1.068121 AACCCCTGCTGCTAACTCTT 58.932 50.000 0.00 0.00 0.00 2.85
3524 21895 5.344665 CAGAGAACAACGAAGTCTTCAGATC 59.655 44.000 12.99 6.22 45.00 2.75
3571 21946 5.248380 AGCAAAACAGATAGAGAAAGGGT 57.752 39.130 0.00 0.00 0.00 4.34
3617 21993 8.679344 AAAATGTAAGGGGAAGAAACCAATAT 57.321 30.769 0.00 0.00 0.00 1.28
3618 21994 8.499288 AAAAATGTAAGGGGAAGAAACCAATA 57.501 30.769 0.00 0.00 0.00 1.90
3619 21995 7.387265 AAAAATGTAAGGGGAAGAAACCAAT 57.613 32.000 0.00 0.00 0.00 3.16
3655 22038 7.287696 ACAAACCAAAATTCCAGAAGTAGTCAT 59.712 33.333 0.00 0.00 0.00 3.06
3686 22069 1.732941 AACAACAGTCGCACACAGAA 58.267 45.000 0.00 0.00 0.00 3.02
3731 22114 7.030768 GCCTTGCTAAAATGTAATCGGTTAAA 58.969 34.615 0.00 0.00 0.00 1.52
3738 22121 8.707938 ATCAAAAGCCTTGCTAAAATGTAATC 57.292 30.769 0.00 0.00 38.25 1.75
3762 22145 2.907892 TCTTTCACCTCCTCACAGGAT 58.092 47.619 0.00 0.00 44.81 3.24
3828 22214 7.024768 GCATAGAGGTTTTAACGCAATGTTTA 58.975 34.615 0.00 0.00 42.09 2.01
3906 22292 4.040217 CCCAGGTTCATTTTCAACCATCAA 59.960 41.667 4.48 0.00 45.20 2.57
3907 22293 3.577848 CCCAGGTTCATTTTCAACCATCA 59.422 43.478 4.48 0.00 45.20 3.07
3991 22411 1.802508 CGCGACAGCCATCTATGTGAA 60.803 52.381 0.00 0.00 41.18 3.18
3994 22414 1.068083 CCGCGACAGCCATCTATGT 59.932 57.895 8.23 0.00 41.18 2.29
4010 22430 3.797256 CCTTAAGTCTAATCAACTCGCCG 59.203 47.826 0.97 0.00 0.00 6.46
4013 22433 6.872020 TGTTTCCCTTAAGTCTAATCAACTCG 59.128 38.462 0.97 0.00 0.00 4.18
4020 22440 8.971073 CAATTCCATGTTTCCCTTAAGTCTAAT 58.029 33.333 0.97 0.00 0.00 1.73
4057 22477 8.470002 AGCAACTTGATAGGGATTTATTTTCAC 58.530 33.333 0.00 0.00 0.00 3.18
4065 22485 6.127619 GCAACTTAGCAACTTGATAGGGATTT 60.128 38.462 1.77 0.00 0.00 2.17
4069 22489 3.378427 GGCAACTTAGCAACTTGATAGGG 59.622 47.826 1.77 0.00 35.83 3.53
4070 22490 4.009675 TGGCAACTTAGCAACTTGATAGG 58.990 43.478 0.00 0.00 35.83 2.57
4073 22493 4.081406 TCATGGCAACTTAGCAACTTGAT 58.919 39.130 0.00 0.00 35.83 2.57
4080 22500 8.462589 TGAAATATATTCATGGCAACTTAGCA 57.537 30.769 0.00 0.00 35.83 3.49
4115 22535 5.360714 CCCTCAATGGAAAGCAGCTTAATTA 59.639 40.000 8.45 0.00 38.35 1.40
4117 22537 3.703052 CCCTCAATGGAAAGCAGCTTAAT 59.297 43.478 8.45 0.00 38.35 1.40
4120 22540 1.553706 CCCTCAATGGAAAGCAGCTT 58.446 50.000 0.21 0.21 38.35 3.74
4161 22581 1.204146 TCTGAATACAGCTCACCCCC 58.796 55.000 0.00 0.00 43.17 5.40
4202 22622 2.233271 CTTTCCAACCATCAGCACTGT 58.767 47.619 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.