Multiple sequence alignment - TraesCS3D01G329800

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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 TraesCS3D01G329800 chr3D 100.000 2924 0 0 1 2924 442510403 442513326 0.000000e+00 5400.0
1 TraesCS3D01G329800 chr3B 90.438 2897 133 54 75 2924 580061753 580064552 0.000000e+00 3683.0
2 TraesCS3D01G329800 chr3A 92.701 1370 64 11 960 2312 583748098 583749448 0.000000e+00 1943.0
3 TraesCS3D01G329800 chr3A 88.067 1257 75 23 978 2207 434799142 434800350 0.000000e+00 1421.0
4 TraesCS3D01G329800 chr3A 91.696 578 34 5 2347 2924 583749449 583750012 0.000000e+00 789.0
5 TraesCS3D01G329800 chr3A 88.473 347 23 7 422 758 583747612 583747951 1.260000e-108 403.0
6 TraesCS3D01G329800 chr3A 84.375 256 16 14 51 300 583747343 583747580 2.270000e-56 230.0
7 TraesCS3D01G329800 chr3A 87.791 172 15 4 2243 2409 434800349 434800519 2.300000e-46 196.0
8 TraesCS3D01G329800 chr3A 86.957 92 10 2 2638 2728 448326160 448326070 5.160000e-18 102.0
9 TraesCS3D01G329800 chr2D 89.641 1255 70 18 978 2205 568757266 568758487 0.000000e+00 1543.0
10 TraesCS3D01G329800 chr5B 89.181 1257 70 20 984 2207 524221799 524220576 0.000000e+00 1507.0
11 TraesCS3D01G329800 chr1B 89.075 1254 74 19 984 2207 443488940 443487720 0.000000e+00 1498.0
12 TraesCS3D01G329800 chr1B 86.316 95 13 0 2812 2906 310311839 310311933 1.430000e-18 104.0
13 TraesCS3D01G329800 chr7A 88.649 1251 67 22 984 2207 48766857 48765655 0.000000e+00 1454.0
14 TraesCS3D01G329800 chr4D 88.146 1257 67 26 978 2207 30394026 30395227 0.000000e+00 1421.0
15 TraesCS3D01G329800 chr7D 89.818 1100 53 21 1134 2207 207789238 207788172 0.000000e+00 1356.0
16 TraesCS3D01G329800 chr6A 88.090 487 32 10 1739 2207 535421589 535421111 3.290000e-154 555.0
17 TraesCS3D01G329800 chr6A 84.085 377 20 10 984 1345 535421938 535421587 7.810000e-86 327.0
18 TraesCS3D01G329800 chr4A 100.000 31 0 0 2678 2708 491685886 491685916 1.130000e-04 58.4


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 TraesCS3D01G329800 chr3D 442510403 442513326 2923 False 5400.00 5400 100.00000 1 2924 1 chr3D.!!$F1 2923
1 TraesCS3D01G329800 chr3B 580061753 580064552 2799 False 3683.00 3683 90.43800 75 2924 1 chr3B.!!$F1 2849
2 TraesCS3D01G329800 chr3A 583747343 583750012 2669 False 841.25 1943 89.31125 51 2924 4 chr3A.!!$F2 2873
3 TraesCS3D01G329800 chr3A 434799142 434800519 1377 False 808.50 1421 87.92900 978 2409 2 chr3A.!!$F1 1431
4 TraesCS3D01G329800 chr2D 568757266 568758487 1221 False 1543.00 1543 89.64100 978 2205 1 chr2D.!!$F1 1227
5 TraesCS3D01G329800 chr5B 524220576 524221799 1223 True 1507.00 1507 89.18100 984 2207 1 chr5B.!!$R1 1223
6 TraesCS3D01G329800 chr1B 443487720 443488940 1220 True 1498.00 1498 89.07500 984 2207 1 chr1B.!!$R1 1223
7 TraesCS3D01G329800 chr7A 48765655 48766857 1202 True 1454.00 1454 88.64900 984 2207 1 chr7A.!!$R1 1223
8 TraesCS3D01G329800 chr4D 30394026 30395227 1201 False 1421.00 1421 88.14600 978 2207 1 chr4D.!!$F1 1229
9 TraesCS3D01G329800 chr7D 207788172 207789238 1066 True 1356.00 1356 89.81800 1134 2207 1 chr7D.!!$R1 1073
10 TraesCS3D01G329800 chr6A 535421111 535421938 827 True 441.00 555 86.08750 984 2207 2 chr6A.!!$R1 1223

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
877 949 0.024619 GTGCGTCGCCGTCTTAATTC 59.975 55.0 15.88 0.0 36.15 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1984 2088 0.171903 GCAGCACGAATCCTTTGCAT 59.828 50.0 0.0 0.0 38.81 3.96 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
37 38 3.727146 GCGGGTGGCGTAAATAGG 58.273 61.111 0.00 0.00 0.00 2.57
38 39 1.144496 GCGGGTGGCGTAAATAGGA 59.856 57.895 0.00 0.00 0.00 2.94
39 40 0.250166 GCGGGTGGCGTAAATAGGAT 60.250 55.000 0.00 0.00 0.00 3.24
40 41 1.812708 GCGGGTGGCGTAAATAGGATT 60.813 52.381 0.00 0.00 0.00 3.01
41 42 2.548493 GCGGGTGGCGTAAATAGGATTA 60.548 50.000 0.00 0.00 0.00 1.75
42 43 3.867216 GCGGGTGGCGTAAATAGGATTAT 60.867 47.826 0.00 0.00 0.00 1.28
43 44 4.621274 GCGGGTGGCGTAAATAGGATTATA 60.621 45.833 0.00 0.00 0.00 0.98
44 45 4.866486 CGGGTGGCGTAAATAGGATTATAC 59.134 45.833 0.00 0.00 0.00 1.47
45 46 5.567224 CGGGTGGCGTAAATAGGATTATACA 60.567 44.000 0.00 0.00 0.00 2.29
46 47 5.640783 GGGTGGCGTAAATAGGATTATACAC 59.359 44.000 0.00 0.00 0.00 2.90
47 48 6.461640 GGTGGCGTAAATAGGATTATACACT 58.538 40.000 0.00 0.00 0.00 3.55
48 49 7.309990 GGGTGGCGTAAATAGGATTATACACTA 60.310 40.741 0.00 0.00 0.00 2.74
49 50 7.758528 GGTGGCGTAAATAGGATTATACACTAG 59.241 40.741 0.00 0.00 0.00 2.57
50 51 8.302438 GTGGCGTAAATAGGATTATACACTAGT 58.698 37.037 0.00 0.00 0.00 2.57
51 52 9.519191 TGGCGTAAATAGGATTATACACTAGTA 57.481 33.333 0.00 0.00 34.10 1.82
53 54 9.500864 GCGTAAATAGGATTATACACTAGTAGC 57.499 37.037 0.00 0.00 32.86 3.58
160 170 2.357034 CGCGTTGCCTACCTGTGT 60.357 61.111 0.00 0.00 0.00 3.72
161 171 2.667318 CGCGTTGCCTACCTGTGTG 61.667 63.158 0.00 0.00 0.00 3.82
162 172 2.966309 GCGTTGCCTACCTGTGTGC 61.966 63.158 0.00 0.00 0.00 4.57
163 173 2.325082 CGTTGCCTACCTGTGTGCC 61.325 63.158 0.00 0.00 0.00 5.01
164 174 1.971695 GTTGCCTACCTGTGTGCCC 60.972 63.158 0.00 0.00 0.00 5.36
192 202 2.811317 CGTCTCTGCCGGCAGTTC 60.811 66.667 45.86 34.52 43.96 3.01
193 203 2.659610 GTCTCTGCCGGCAGTTCT 59.340 61.111 45.86 0.00 43.96 3.01
194 204 1.446966 GTCTCTGCCGGCAGTTCTC 60.447 63.158 45.86 31.72 43.96 2.87
197 207 2.507992 CTGCCGGCAGTTCTCTCG 60.508 66.667 42.09 20.23 39.10 4.04
199 209 4.443266 GCCGGCAGTTCTCTCGCT 62.443 66.667 24.80 0.00 0.00 4.93
202 212 2.202676 GGCAGTTCTCTCGCTCCG 60.203 66.667 0.00 0.00 0.00 4.63
337 348 4.314440 TGCTCTGGTGGCCGTGAC 62.314 66.667 0.00 0.00 0.00 3.67
346 357 0.378257 GTGGCCGTGACATTGCATAG 59.622 55.000 0.00 0.00 0.00 2.23
361 372 0.923403 CATAGACCACATGACACGCG 59.077 55.000 3.53 3.53 0.00 6.01
380 391 1.397693 CGTGCAGAGTGAAGCGAAAAG 60.398 52.381 0.00 0.00 0.00 2.27
381 392 1.599542 GTGCAGAGTGAAGCGAAAAGT 59.400 47.619 0.00 0.00 0.00 2.66
382 393 1.599071 TGCAGAGTGAAGCGAAAAGTG 59.401 47.619 0.00 0.00 0.00 3.16
383 394 1.599542 GCAGAGTGAAGCGAAAAGTGT 59.400 47.619 0.00 0.00 0.00 3.55
384 395 2.600792 GCAGAGTGAAGCGAAAAGTGTG 60.601 50.000 0.00 0.00 0.00 3.82
385 396 2.609459 CAGAGTGAAGCGAAAAGTGTGT 59.391 45.455 0.00 0.00 0.00 3.72
386 397 2.609459 AGAGTGAAGCGAAAAGTGTGTG 59.391 45.455 0.00 0.00 0.00 3.82
387 398 1.064060 AGTGAAGCGAAAAGTGTGTGC 59.936 47.619 0.00 0.00 0.00 4.57
388 399 0.027455 TGAAGCGAAAAGTGTGTGCG 59.973 50.000 0.00 0.00 0.00 5.34
389 400 0.027586 GAAGCGAAAAGTGTGTGCGT 59.972 50.000 0.00 0.00 0.00 5.24
390 401 0.248054 AAGCGAAAAGTGTGTGCGTG 60.248 50.000 0.00 0.00 0.00 5.34
391 402 2.285857 GCGAAAAGTGTGTGCGTGC 61.286 57.895 0.00 0.00 0.00 5.34
415 426 5.442649 CGTGTGTGTGTGACAATTTTTGTTC 60.443 40.000 0.00 0.00 45.52 3.18
419 430 5.184864 TGTGTGTGACAATTTTTGTTCCTCT 59.815 36.000 0.00 0.00 45.52 3.69
420 431 5.743872 GTGTGTGACAATTTTTGTTCCTCTC 59.256 40.000 0.00 0.00 45.52 3.20
421 432 5.163561 TGTGTGACAATTTTTGTTCCTCTCC 60.164 40.000 0.00 0.00 45.52 3.71
423 434 3.568007 TGACAATTTTTGTTCCTCTCCGG 59.432 43.478 0.00 0.00 45.52 5.14
425 436 1.545841 ATTTTTGTTCCTCTCCGGGC 58.454 50.000 0.00 0.00 0.00 6.13
426 437 0.538746 TTTTTGTTCCTCTCCGGGCC 60.539 55.000 0.00 0.00 0.00 5.80
473 487 2.608546 CTCGAACTACTCTACTCACCGG 59.391 54.545 0.00 0.00 0.00 5.28
474 488 2.234661 TCGAACTACTCTACTCACCGGA 59.765 50.000 9.46 0.00 0.00 5.14
475 489 2.608546 CGAACTACTCTACTCACCGGAG 59.391 54.545 9.46 0.00 46.96 4.63
476 490 3.678252 CGAACTACTCTACTCACCGGAGA 60.678 52.174 9.46 4.36 44.26 3.71
631 650 4.962995 TCAAAACCTTCCATAAACCCACAA 59.037 37.500 0.00 0.00 0.00 3.33
668 687 3.423154 CGCGGTTTCCAGTCCAGC 61.423 66.667 0.00 0.00 0.00 4.85
703 727 3.884774 AAGCAGCCCGACCCAACA 61.885 61.111 0.00 0.00 0.00 3.33
710 734 3.931247 CCGACCCAACACGACCCA 61.931 66.667 0.00 0.00 0.00 4.51
789 824 3.681835 ACCTCCTCGCACGTCACC 61.682 66.667 0.00 0.00 0.00 4.02
793 828 4.778415 CCTCGCACGTCACCTCCG 62.778 72.222 0.00 0.00 0.00 4.63
797 832 2.338984 GCACGTCACCTCCGTCTT 59.661 61.111 0.00 0.00 36.17 3.01
805 840 0.612174 CACCTCCGTCTTCTCCTCCA 60.612 60.000 0.00 0.00 0.00 3.86
806 841 0.336737 ACCTCCGTCTTCTCCTCCAT 59.663 55.000 0.00 0.00 0.00 3.41
809 844 0.631753 TCCGTCTTCTCCTCCATCCT 59.368 55.000 0.00 0.00 0.00 3.24
814 886 1.007600 TCTTCTCCTCCATCCTCTGCA 59.992 52.381 0.00 0.00 0.00 4.41
816 888 1.198713 TCTCCTCCATCCTCTGCAAC 58.801 55.000 0.00 0.00 0.00 4.17
820 892 1.280133 CCTCCATCCTCTGCAACAAGA 59.720 52.381 0.00 0.00 0.00 3.02
873 945 2.922950 AAGGTGCGTCGCCGTCTTA 61.923 57.895 15.88 0.00 39.30 2.10
874 946 2.424705 AAGGTGCGTCGCCGTCTTAA 62.425 55.000 15.88 0.00 39.30 1.85
875 947 1.808390 GGTGCGTCGCCGTCTTAAT 60.808 57.895 15.88 0.00 36.15 1.40
877 949 0.024619 GTGCGTCGCCGTCTTAATTC 59.975 55.000 15.88 0.00 36.15 2.17
878 950 1.079875 TGCGTCGCCGTCTTAATTCC 61.080 55.000 15.88 0.00 36.15 3.01
879 951 1.915093 CGTCGCCGTCTTAATTCCG 59.085 57.895 0.00 0.00 0.00 4.30
880 952 0.523968 CGTCGCCGTCTTAATTCCGA 60.524 55.000 0.00 0.00 0.00 4.55
881 953 1.849097 GTCGCCGTCTTAATTCCGAT 58.151 50.000 0.00 0.00 0.00 4.18
883 955 1.679680 TCGCCGTCTTAATTCCGATCT 59.320 47.619 0.00 0.00 0.00 2.75
884 956 2.100252 TCGCCGTCTTAATTCCGATCTT 59.900 45.455 0.00 0.00 0.00 2.40
885 957 2.218759 CGCCGTCTTAATTCCGATCTTG 59.781 50.000 0.00 0.00 0.00 3.02
887 959 3.458189 CCGTCTTAATTCCGATCTTGCT 58.542 45.455 0.00 0.00 0.00 3.91
888 960 3.491267 CCGTCTTAATTCCGATCTTGCTC 59.509 47.826 0.00 0.00 0.00 4.26
889 961 3.180584 CGTCTTAATTCCGATCTTGCTCG 59.819 47.826 0.00 0.00 38.37 5.03
890 962 3.060205 GTCTTAATTCCGATCTTGCTCGC 60.060 47.826 0.00 0.00 37.33 5.03
891 963 2.595124 TAATTCCGATCTTGCTCGCA 57.405 45.000 0.00 0.00 37.33 5.10
892 964 1.009829 AATTCCGATCTTGCTCGCAC 58.990 50.000 0.00 0.00 37.33 5.34
893 965 0.176680 ATTCCGATCTTGCTCGCACT 59.823 50.000 0.00 0.00 37.33 4.40
894 966 0.037326 TTCCGATCTTGCTCGCACTT 60.037 50.000 0.00 0.00 37.33 3.16
895 967 0.037326 TCCGATCTTGCTCGCACTTT 60.037 50.000 0.00 0.00 37.33 2.66
896 968 0.371645 CCGATCTTGCTCGCACTTTC 59.628 55.000 0.00 0.00 37.33 2.62
914 986 6.639212 CACTTTCGATTTGTTTGTCAATTGG 58.361 36.000 5.42 0.00 35.84 3.16
919 991 5.925397 TCGATTTGTTTGTCAATTGGGAATG 59.075 36.000 5.42 0.00 35.84 2.67
920 992 5.389725 CGATTTGTTTGTCAATTGGGAATGC 60.390 40.000 5.42 0.00 35.84 3.56
940 1012 3.825812 GTGACGCTTCACCTGTTTG 57.174 52.632 12.13 0.00 45.77 2.93
941 1013 0.307760 GTGACGCTTCACCTGTTTGG 59.692 55.000 12.13 0.00 45.77 3.28
942 1014 0.179234 TGACGCTTCACCTGTTTGGA 59.821 50.000 0.00 0.00 39.71 3.53
943 1015 0.868406 GACGCTTCACCTGTTTGGAG 59.132 55.000 0.00 0.00 39.71 3.86
944 1016 1.166531 ACGCTTCACCTGTTTGGAGC 61.167 55.000 0.00 0.00 39.71 4.70
945 1017 1.576421 GCTTCACCTGTTTGGAGCG 59.424 57.895 0.00 0.00 39.71 5.03
946 1018 1.576421 CTTCACCTGTTTGGAGCGC 59.424 57.895 0.00 0.00 39.71 5.92
947 1019 1.153066 TTCACCTGTTTGGAGCGCA 60.153 52.632 11.47 0.00 39.71 6.09
948 1020 1.444119 TTCACCTGTTTGGAGCGCAC 61.444 55.000 11.47 1.97 39.71 5.34
949 1021 2.594592 ACCTGTTTGGAGCGCACC 60.595 61.111 17.78 17.78 39.71 5.01
950 1022 2.594303 CCTGTTTGGAGCGCACCA 60.594 61.111 23.37 23.37 38.35 4.17
951 1023 2.192861 CCTGTTTGGAGCGCACCAA 61.193 57.895 31.70 31.70 46.44 3.67
956 1028 2.853159 TTGGAGCGCACCAATGTAG 58.147 52.632 31.70 0.00 43.79 2.74
957 1029 0.676466 TTGGAGCGCACCAATGTAGG 60.676 55.000 31.70 0.00 43.79 3.18
958 1030 1.220749 GGAGCGCACCAATGTAGGA 59.779 57.895 19.70 0.00 0.00 2.94
961 1033 1.136305 GAGCGCACCAATGTAGGAGTA 59.864 52.381 11.47 0.00 0.00 2.59
1004 1079 0.949105 GCACGGACGGTTCTGATGTT 60.949 55.000 0.00 0.00 31.76 2.71
1648 1742 3.458163 CCTTCTACCAGGCGCCGA 61.458 66.667 23.20 9.13 0.00 5.54
1932 2031 2.048127 AGGAACTGACGCCGAAGC 60.048 61.111 0.00 0.00 37.18 3.86
1933 2032 2.357034 GGAACTGACGCCGAAGCA 60.357 61.111 0.00 0.00 39.83 3.91
1935 2034 1.493311 GAACTGACGCCGAAGCAAG 59.507 57.895 0.00 0.00 39.83 4.01
2006 2110 1.336240 GCAAAGGATTCGTGCTGCTTT 60.336 47.619 0.00 0.00 35.02 3.51
2059 2164 3.058293 TGTTGGTTTGATCGAGCAATGTC 60.058 43.478 17.94 10.54 36.94 3.06
2086 2204 2.278026 TTGTCCGTCGAGATCATGTG 57.722 50.000 0.00 0.00 0.00 3.21
2099 2217 1.584483 CATGTGCTGCCGCGAAATC 60.584 57.895 8.23 0.00 39.65 2.17
2127 2245 3.123621 GCAGTTAAGATGTTCACGAGGTG 59.876 47.826 0.00 0.00 34.45 4.00
2128 2246 3.123621 CAGTTAAGATGTTCACGAGGTGC 59.876 47.826 0.00 0.00 32.98 5.01
2129 2247 3.064207 GTTAAGATGTTCACGAGGTGCA 58.936 45.455 0.00 0.00 32.98 4.57
2294 2412 8.932791 AACTATACGTTTTAATCTGGAACAGTG 58.067 33.333 0.00 0.00 45.48 3.66
2489 2612 2.106511 GGCATGCTTATTAGTCCAGGGA 59.893 50.000 18.92 0.00 0.00 4.20
2567 2690 3.717707 TGTTCAGACTAACACTGACTGC 58.282 45.455 0.00 0.00 42.84 4.40
2586 2709 2.416202 TGCACAAATCAGCTCGTACATG 59.584 45.455 0.00 0.00 0.00 3.21
2588 2711 3.616821 GCACAAATCAGCTCGTACATGTA 59.383 43.478 0.08 0.08 0.00 2.29
2589 2712 4.259970 GCACAAATCAGCTCGTACATGTAG 60.260 45.833 5.62 0.00 0.00 2.74
2590 2713 4.268644 CACAAATCAGCTCGTACATGTAGG 59.731 45.833 17.54 17.54 0.00 3.18
2591 2714 4.159693 ACAAATCAGCTCGTACATGTAGGA 59.840 41.667 23.04 23.04 0.00 2.94
2592 2715 5.163405 ACAAATCAGCTCGTACATGTAGGAT 60.163 40.000 24.29 11.31 30.73 3.24
2593 2716 3.990318 TCAGCTCGTACATGTAGGATG 57.010 47.619 24.29 20.48 30.73 3.51
2594 2717 3.551846 TCAGCTCGTACATGTAGGATGA 58.448 45.455 24.29 22.02 30.73 2.92
2595 2718 3.315470 TCAGCTCGTACATGTAGGATGAC 59.685 47.826 24.29 17.51 30.73 3.06
2596 2719 3.066760 CAGCTCGTACATGTAGGATGACA 59.933 47.826 24.29 6.29 30.73 3.58
2597 2720 3.699538 AGCTCGTACATGTAGGATGACAA 59.300 43.478 24.29 5.66 31.83 3.18
2618 2741 2.233431 AGATCAGACTTGCAGGTCAGAC 59.767 50.000 28.25 19.07 38.57 3.51
2665 2788 4.806247 AGAATCGTTCAGATCCATTTCGAC 59.194 41.667 0.00 0.00 38.98 4.20
2666 2789 3.868757 TCGTTCAGATCCATTTCGACT 57.131 42.857 0.00 0.00 0.00 4.18
2675 2798 2.500229 TCCATTTCGACTGTGGTTTCC 58.500 47.619 9.10 0.00 34.61 3.13
2676 2799 1.539827 CCATTTCGACTGTGGTTTCCC 59.460 52.381 0.00 0.00 0.00 3.97
2679 2802 1.670791 TTCGACTGTGGTTTCCCAAC 58.329 50.000 0.00 0.00 44.15 3.77
2681 2804 1.142060 TCGACTGTGGTTTCCCAACAT 59.858 47.619 0.00 0.00 44.15 2.71
2711 2834 7.466746 AGTGTGTATGCCAAATTAAATCAGT 57.533 32.000 0.00 0.00 0.00 3.41
2712 2835 7.315142 AGTGTGTATGCCAAATTAAATCAGTG 58.685 34.615 0.00 0.00 0.00 3.66
2741 2864 7.013750 TCAGCACAACAACCTTTGACAATATAA 59.986 33.333 0.00 0.00 0.00 0.98
2809 2932 3.006430 TCTTTGTCGTCTGGTCAATGCTA 59.994 43.478 0.00 0.00 0.00 3.49
2871 2994 4.379243 ACGTCTTGGCCGGCTGAG 62.379 66.667 28.56 23.14 0.00 3.35
2912 3035 7.549842 CAGAGAAATTGTCAGAATCTGATCTGT 59.450 37.037 20.89 13.87 45.65 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.469308 CTATTTACGCCACCCGCAAAA 59.531 47.619 0.00 0.00 41.76 2.44
17 18 1.088306 CTATTTACGCCACCCGCAAA 58.912 50.000 0.00 0.00 41.76 3.68
19 20 1.153329 CCTATTTACGCCACCCGCA 60.153 57.895 0.00 0.00 41.76 5.69
20 21 0.250166 ATCCTATTTACGCCACCCGC 60.250 55.000 0.00 0.00 41.76 6.13
21 22 2.249844 AATCCTATTTACGCCACCCG 57.750 50.000 0.00 0.00 44.21 5.28
22 23 5.640783 GTGTATAATCCTATTTACGCCACCC 59.359 44.000 0.00 0.00 0.00 4.61
23 24 6.461640 AGTGTATAATCCTATTTACGCCACC 58.538 40.000 0.00 0.00 0.00 4.61
24 25 8.302438 ACTAGTGTATAATCCTATTTACGCCAC 58.698 37.037 0.00 0.00 0.00 5.01
25 26 8.413309 ACTAGTGTATAATCCTATTTACGCCA 57.587 34.615 0.00 0.00 0.00 5.69
27 28 9.500864 GCTACTAGTGTATAATCCTATTTACGC 57.499 37.037 5.39 0.00 0.00 4.42
199 209 4.063967 CTGCACACGGGTAGCGGA 62.064 66.667 13.70 0.00 36.79 5.54
202 212 3.423154 GCACTGCACACGGGTAGC 61.423 66.667 0.00 0.00 0.00 3.58
231 242 1.008538 GTGAAAACAGCAGGCCGTG 60.009 57.895 0.00 0.00 0.00 4.94
277 288 2.652530 CGGCAGCTGTTTGGCAAT 59.347 55.556 16.64 0.00 43.26 3.56
318 329 4.007644 CACGGCCACCAGAGCAGA 62.008 66.667 2.24 0.00 0.00 4.26
337 348 3.242511 CGTGTCATGTGGTCTATGCAATG 60.243 47.826 0.00 0.00 0.00 2.82
346 357 2.853210 CACGCGTGTCATGTGGTC 59.147 61.111 30.50 0.00 0.00 4.02
361 372 1.599542 ACTTTTCGCTTCACTCTGCAC 59.400 47.619 0.00 0.00 0.00 4.57
380 391 3.860125 ACACACGCACGCACACAC 61.860 61.111 0.00 0.00 0.00 3.82
381 392 3.858989 CACACACGCACGCACACA 61.859 61.111 0.00 0.00 0.00 3.72
382 393 3.860125 ACACACACGCACGCACAC 61.860 61.111 0.00 0.00 0.00 3.82
383 394 3.858989 CACACACACGCACGCACA 61.859 61.111 0.00 0.00 0.00 4.57
384 395 3.860125 ACACACACACGCACGCAC 61.860 61.111 0.00 0.00 0.00 5.34
385 396 3.858989 CACACACACACGCACGCA 61.859 61.111 0.00 0.00 0.00 5.24
386 397 3.559344 TCACACACACACGCACGC 61.559 61.111 0.00 0.00 0.00 5.34
387 398 1.960994 TTGTCACACACACACGCACG 61.961 55.000 0.00 0.00 33.41 5.34
388 399 0.376852 ATTGTCACACACACACGCAC 59.623 50.000 0.00 0.00 33.41 5.34
389 400 1.090728 AATTGTCACACACACACGCA 58.909 45.000 0.00 0.00 33.41 5.24
390 401 2.187351 AAATTGTCACACACACACGC 57.813 45.000 0.00 0.00 33.41 5.34
391 402 3.917380 ACAAAAATTGTCACACACACACG 59.083 39.130 0.00 0.00 40.56 4.49
425 436 2.124736 ATCGCATGGTGAACCGGG 60.125 61.111 6.32 0.00 39.43 5.73
426 437 3.101209 CATCGCATGGTGAACCGG 58.899 61.111 0.00 0.00 39.43 5.28
473 487 1.287503 GGATCCATCGGCGTCTCTC 59.712 63.158 6.95 0.00 0.00 3.20
474 488 1.455773 TGGATCCATCGGCGTCTCT 60.456 57.895 11.44 0.00 0.00 3.10
475 489 1.006805 CTGGATCCATCGGCGTCTC 60.007 63.158 16.63 0.00 0.00 3.36
476 490 3.133014 CTGGATCCATCGGCGTCT 58.867 61.111 16.63 0.00 0.00 4.18
576 595 5.278266 GGAAACAAAGGTGTGAAATCGATCA 60.278 40.000 0.00 0.00 38.27 2.92
649 668 2.027625 CTGGACTGGAAACCGCGTC 61.028 63.158 4.92 0.00 0.00 5.19
710 734 0.109412 GTTATATAGAGCGCGGCGGT 60.109 55.000 28.23 28.23 41.33 5.68
759 792 1.074951 GGAGGTGAACAAGGGGTGG 59.925 63.158 0.00 0.00 0.00 4.61
761 794 1.481056 CGAGGAGGTGAACAAGGGGT 61.481 60.000 0.00 0.00 0.00 4.95
789 824 1.036707 GGATGGAGGAGAAGACGGAG 58.963 60.000 0.00 0.00 0.00 4.63
793 828 1.412343 GCAGAGGATGGAGGAGAAGAC 59.588 57.143 0.00 0.00 0.00 3.01
797 832 1.198713 GTTGCAGAGGATGGAGGAGA 58.801 55.000 0.00 0.00 0.00 3.71
805 840 4.202398 TGTTTCTCTCTTGTTGCAGAGGAT 60.202 41.667 1.28 0.00 40.82 3.24
806 841 3.134623 TGTTTCTCTCTTGTTGCAGAGGA 59.865 43.478 1.28 0.00 40.82 3.71
809 844 3.309682 CGTTGTTTCTCTCTTGTTGCAGA 59.690 43.478 0.00 0.00 0.00 4.26
814 886 1.597663 CGGCGTTGTTTCTCTCTTGTT 59.402 47.619 0.00 0.00 0.00 2.83
816 888 0.512952 CCGGCGTTGTTTCTCTCTTG 59.487 55.000 6.01 0.00 0.00 3.02
820 892 3.041940 CGCCGGCGTTGTTTCTCT 61.042 61.111 39.71 0.00 34.35 3.10
873 945 1.009829 GTGCGAGCAAGATCGGAATT 58.990 50.000 9.87 0.00 44.80 2.17
874 946 0.176680 AGTGCGAGCAAGATCGGAAT 59.823 50.000 9.87 2.88 44.80 3.01
875 947 0.037326 AAGTGCGAGCAAGATCGGAA 60.037 50.000 9.87 0.00 44.80 4.30
877 949 0.371645 GAAAGTGCGAGCAAGATCGG 59.628 55.000 9.87 0.00 42.94 4.18
878 950 0.024238 CGAAAGTGCGAGCAAGATCG 59.976 55.000 3.01 3.01 45.48 3.69
879 951 1.350193 TCGAAAGTGCGAGCAAGATC 58.650 50.000 0.00 0.00 35.01 2.75
880 952 2.015736 ATCGAAAGTGCGAGCAAGAT 57.984 45.000 0.00 0.00 44.26 2.40
881 953 1.795768 AATCGAAAGTGCGAGCAAGA 58.204 45.000 0.00 0.00 44.26 3.02
883 955 1.601903 ACAAATCGAAAGTGCGAGCAA 59.398 42.857 0.00 0.00 44.26 3.91
884 956 1.225855 ACAAATCGAAAGTGCGAGCA 58.774 45.000 0.00 0.00 44.26 4.26
885 957 2.316119 AACAAATCGAAAGTGCGAGC 57.684 45.000 0.00 0.00 44.26 5.03
887 959 3.064134 TGACAAACAAATCGAAAGTGCGA 59.936 39.130 0.00 0.00 45.22 5.10
888 960 3.358775 TGACAAACAAATCGAAAGTGCG 58.641 40.909 0.00 0.00 0.00 5.34
889 961 5.888412 ATTGACAAACAAATCGAAAGTGC 57.112 34.783 0.00 0.00 42.03 4.40
890 962 6.292274 CCCAATTGACAAACAAATCGAAAGTG 60.292 38.462 7.12 0.00 42.03 3.16
891 963 5.752955 CCCAATTGACAAACAAATCGAAAGT 59.247 36.000 7.12 0.00 42.03 2.66
892 964 5.982516 TCCCAATTGACAAACAAATCGAAAG 59.017 36.000 7.12 0.00 42.03 2.62
893 965 5.907207 TCCCAATTGACAAACAAATCGAAA 58.093 33.333 7.12 0.00 42.03 3.46
894 966 5.521906 TCCCAATTGACAAACAAATCGAA 57.478 34.783 7.12 0.00 42.03 3.71
895 967 5.521906 TTCCCAATTGACAAACAAATCGA 57.478 34.783 7.12 0.00 42.03 3.59
896 968 5.389725 GCATTCCCAATTGACAAACAAATCG 60.390 40.000 7.12 0.00 42.03 3.34
927 999 1.576421 CGCTCCAAACAGGTGAAGC 59.424 57.895 0.00 0.00 39.02 3.86
928 1000 1.165907 TGCGCTCCAAACAGGTGAAG 61.166 55.000 9.73 0.00 39.02 3.02
929 1001 1.153066 TGCGCTCCAAACAGGTGAA 60.153 52.632 9.73 0.00 39.02 3.18
931 1003 2.639286 GTGCGCTCCAAACAGGTG 59.361 61.111 9.73 0.00 39.02 4.00
932 1004 2.594592 GGTGCGCTCCAAACAGGT 60.595 61.111 23.09 0.00 39.02 4.00
933 1005 2.192861 TTGGTGCGCTCCAAACAGG 61.193 57.895 34.82 0.00 43.40 4.00
934 1006 3.431055 TTGGTGCGCTCCAAACAG 58.569 55.556 34.82 0.00 43.40 3.16
939 1011 1.078497 CCTACATTGGTGCGCTCCA 60.078 57.895 26.46 26.46 35.49 3.86
940 1012 0.811616 CTCCTACATTGGTGCGCTCC 60.812 60.000 21.41 21.41 0.00 4.70
941 1013 0.108138 ACTCCTACATTGGTGCGCTC 60.108 55.000 9.73 4.47 0.00 5.03
942 1014 1.134788 GTACTCCTACATTGGTGCGCT 60.135 52.381 9.73 0.00 0.00 5.92
943 1015 1.287425 GTACTCCTACATTGGTGCGC 58.713 55.000 0.00 0.00 0.00 6.09
944 1016 2.665649 TGTACTCCTACATTGGTGCG 57.334 50.000 0.00 0.00 0.00 5.34
945 1017 4.137116 TGATGTACTCCTACATTGGTGC 57.863 45.455 0.00 0.00 42.66 5.01
946 1018 8.204160 TCTAATTGATGTACTCCTACATTGGTG 58.796 37.037 0.00 0.00 42.66 4.17
947 1019 8.319057 TCTAATTGATGTACTCCTACATTGGT 57.681 34.615 0.00 0.00 42.66 3.67
948 1020 9.046296 GTTCTAATTGATGTACTCCTACATTGG 57.954 37.037 0.00 0.00 42.66 3.16
949 1021 9.823647 AGTTCTAATTGATGTACTCCTACATTG 57.176 33.333 0.00 0.00 42.66 2.82
950 1022 9.823647 CAGTTCTAATTGATGTACTCCTACATT 57.176 33.333 0.00 0.00 42.66 2.71
951 1023 9.201989 TCAGTTCTAATTGATGTACTCCTACAT 57.798 33.333 0.00 0.00 44.87 2.29
952 1024 8.467598 GTCAGTTCTAATTGATGTACTCCTACA 58.532 37.037 0.00 0.00 37.28 2.74
953 1025 8.467598 TGTCAGTTCTAATTGATGTACTCCTAC 58.532 37.037 0.00 0.00 0.00 3.18
954 1026 8.589701 TGTCAGTTCTAATTGATGTACTCCTA 57.410 34.615 0.00 0.00 0.00 2.94
955 1027 7.179338 ACTGTCAGTTCTAATTGATGTACTCCT 59.821 37.037 0.00 0.00 0.00 3.69
956 1028 7.276658 CACTGTCAGTTCTAATTGATGTACTCC 59.723 40.741 1.67 0.00 0.00 3.85
957 1029 7.815068 ACACTGTCAGTTCTAATTGATGTACTC 59.185 37.037 1.67 0.00 0.00 2.59
958 1030 7.600375 CACACTGTCAGTTCTAATTGATGTACT 59.400 37.037 1.67 0.00 0.00 2.73
961 1033 5.702670 CCACACTGTCAGTTCTAATTGATGT 59.297 40.000 1.67 0.00 0.00 3.06
971 1043 1.498865 CCGTGCCACACTGTCAGTTC 61.499 60.000 1.67 0.00 31.34 3.01
1004 1079 1.425031 GCGTGCGAATCAATCTGCA 59.575 52.632 0.00 0.00 35.98 4.41
1336 1426 3.593794 GGCGACGGCGAGGTAGAT 61.594 66.667 18.90 0.00 41.24 1.98
1354 1448 2.519780 GACGGCGAGGGAGAGGAT 60.520 66.667 16.62 0.00 0.00 3.24
1648 1742 2.234613 CGAACACCGTGATGTTGCT 58.765 52.632 5.28 0.00 42.89 3.91
1932 2031 3.254657 TCGGCCAGTAACCATTTTTCTTG 59.745 43.478 2.24 0.00 0.00 3.02
1933 2032 3.492337 TCGGCCAGTAACCATTTTTCTT 58.508 40.909 2.24 0.00 0.00 2.52
1935 2034 4.450082 AATCGGCCAGTAACCATTTTTC 57.550 40.909 2.24 0.00 0.00 2.29
1984 2088 0.171903 GCAGCACGAATCCTTTGCAT 59.828 50.000 0.00 0.00 38.81 3.96
1985 2089 0.890542 AGCAGCACGAATCCTTTGCA 60.891 50.000 0.00 0.00 38.81 4.08
1986 2090 0.242017 AAGCAGCACGAATCCTTTGC 59.758 50.000 0.00 0.00 36.45 3.68
1987 2091 2.589014 GAAAGCAGCACGAATCCTTTG 58.411 47.619 0.00 0.00 0.00 2.77
2029 2134 5.739161 GCTCGATCAAACCAACATACAAATC 59.261 40.000 0.00 0.00 0.00 2.17
2059 2164 4.388773 TGATCTCGACGGACAAAAGAATTG 59.611 41.667 0.00 0.00 0.00 2.32
2099 2217 2.480037 TGAACATCTTAACTGCAGCACG 59.520 45.455 15.27 0.00 0.00 5.34
2127 2245 0.612744 AGGAGAAGAGAGGTTGCTGC 59.387 55.000 0.00 0.00 0.00 5.25
2128 2246 1.898472 TCAGGAGAAGAGAGGTTGCTG 59.102 52.381 0.00 0.00 0.00 4.41
2129 2247 2.317371 TCAGGAGAAGAGAGGTTGCT 57.683 50.000 0.00 0.00 0.00 3.91
2276 2394 4.846779 TGCCACTGTTCCAGATTAAAAC 57.153 40.909 0.00 0.00 35.18 2.43
2294 2412 7.598869 TCATATTCAGAACGATATGTAGTTGCC 59.401 37.037 0.00 0.00 0.00 4.52
2489 2612 9.391006 TGTCTACACAGAATTTTGAGTTACTTT 57.609 29.630 2.48 0.00 30.85 2.66
2561 2684 1.150827 CGAGCTGATTTGTGCAGTCA 58.849 50.000 0.00 0.00 35.81 3.41
2567 2690 4.268644 CCTACATGTACGAGCTGATTTGTG 59.731 45.833 0.08 0.00 0.00 3.33
2586 2709 4.808364 GCAAGTCTGATCTTGTCATCCTAC 59.192 45.833 16.03 0.00 44.41 3.18
2588 2711 3.262660 TGCAAGTCTGATCTTGTCATCCT 59.737 43.478 16.03 0.00 44.41 3.24
2589 2712 3.603532 TGCAAGTCTGATCTTGTCATCC 58.396 45.455 16.03 5.44 44.41 3.51
2590 2713 3.622163 CCTGCAAGTCTGATCTTGTCATC 59.378 47.826 16.03 5.68 44.41 2.92
2591 2714 3.008813 ACCTGCAAGTCTGATCTTGTCAT 59.991 43.478 16.03 4.67 44.41 3.06
2592 2715 2.369860 ACCTGCAAGTCTGATCTTGTCA 59.630 45.455 16.03 13.76 44.41 3.58
2593 2716 2.999355 GACCTGCAAGTCTGATCTTGTC 59.001 50.000 8.25 11.28 44.41 3.18
2594 2717 2.369860 TGACCTGCAAGTCTGATCTTGT 59.630 45.455 16.18 2.99 44.41 3.16
2595 2718 3.001414 CTGACCTGCAAGTCTGATCTTG 58.999 50.000 16.18 12.59 45.09 3.02
2596 2719 2.902486 TCTGACCTGCAAGTCTGATCTT 59.098 45.455 18.06 0.00 39.09 2.40
2597 2720 2.233431 GTCTGACCTGCAAGTCTGATCT 59.767 50.000 22.92 0.00 43.71 2.75
2618 2741 2.812591 AGAAGTGCTTGAACTGCAGATG 59.187 45.455 23.35 6.29 41.41 2.90
2712 2835 2.159254 TCAAAGGTTGTTGTGCTGAAGC 60.159 45.455 0.00 0.00 42.50 3.86
2809 2932 3.960102 TGGGAGCTCACAACATTCTTTTT 59.040 39.130 18.48 0.00 0.00 1.94
2871 2994 7.977853 ACAATTTCTCTGATATGGTTTTCATGC 59.022 33.333 0.00 0.00 37.30 4.06


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

AutoCloner maintained by Alex Coulton.