Multiple sequence alignment - TraesCS1D01G177500

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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 TraesCS1D01G177500 chr1D 100.000 2303 0 0 1 2303 252566153 252568455 0.000000e+00 4253.0
1 TraesCS1D01G177500 chr1D 91.395 337 25 4 1934 2267 255497423 255497088 2.090000e-125 459.0
2 TraesCS1D01G177500 chr1D 86.930 329 27 6 1331 1644 476186908 476186581 2.810000e-94 355.0
3 TraesCS1D01G177500 chr1D 81.215 362 57 7 964 1321 252596072 252596426 4.840000e-72 281.0
4 TraesCS1D01G177500 chr1B 92.251 1355 57 28 1 1321 360513250 360511910 0.000000e+00 1877.0
5 TraesCS1D01G177500 chr1B 86.523 512 46 16 1375 1867 113983083 113983590 2.010000e-150 542.0
6 TraesCS1D01G177500 chr1A 88.681 910 62 26 43 946 323894277 323895151 0.000000e+00 1072.0
7 TraesCS1D01G177500 chr1A 90.000 340 16 2 1000 1321 323895148 323895487 7.610000e-115 424.0
8 TraesCS1D01G177500 chr1A 81.768 362 55 7 964 1321 323961200 323961554 2.240000e-75 292.0
9 TraesCS1D01G177500 chr1A 82.583 333 36 6 174 485 323960174 323960505 8.110000e-70 274.0
10 TraesCS1D01G177500 chr1A 97.674 43 0 1 1 43 323891656 323891697 3.170000e-09 73.1
11 TraesCS1D01G177500 chr3D 87.868 577 50 9 1331 1889 275624414 275623840 0.000000e+00 660.0
12 TraesCS1D01G177500 chr3D 87.522 577 52 9 1331 1889 32159176 32158602 0.000000e+00 649.0
13 TraesCS1D01G177500 chr3D 88.679 530 40 10 1339 1850 604878243 604877716 1.500000e-176 628.0
14 TraesCS1D01G177500 chr3D 88.128 438 42 7 1868 2298 11943210 11943644 1.580000e-141 512.0
15 TraesCS1D01G177500 chr3D 87.679 349 36 7 1955 2298 120525460 120525114 1.280000e-107 399.0
16 TraesCS1D01G177500 chr2D 88.321 548 44 13 1338 1867 645181545 645181000 6.940000e-180 640.0
17 TraesCS1D01G177500 chr2D 81.881 436 65 13 1870 2298 481701924 481702352 2.810000e-94 355.0
18 TraesCS1D01G177500 chr6D 87.993 558 42 14 1331 1867 87245512 87244959 8.970000e-179 636.0
19 TraesCS1D01G177500 chr6D 85.152 559 50 18 1331 1872 203051772 203052314 2.010000e-150 542.0
20 TraesCS1D01G177500 chr2A 87.500 560 45 10 1331 1865 755399099 755398540 6.990000e-175 623.0
21 TraesCS1D01G177500 chrUn 87.319 552 55 10 1331 1870 114967200 114966652 3.250000e-173 617.0
22 TraesCS1D01G177500 chr7D 86.294 591 50 12 1320 1889 116817948 116818528 4.210000e-172 614.0
23 TraesCS1D01G177500 chr5B 87.902 529 47 13 1354 1867 108821142 108820616 7.040000e-170 606.0
24 TraesCS1D01G177500 chr5B 87.608 347 31 9 1532 1867 193485933 193486278 2.140000e-105 392.0
25 TraesCS1D01G177500 chr5B 82.989 435 63 10 1870 2298 652526632 652526203 1.290000e-102 383.0
26 TraesCS1D01G177500 chr5B 83.375 403 56 11 1902 2298 265749359 265748962 1.680000e-96 363.0
27 TraesCS1D01G177500 chr4D 87.474 479 41 9 1339 1800 450361208 450361684 3.370000e-148 534.0
28 TraesCS1D01G177500 chr3B 84.124 548 57 14 1331 1850 698383530 698384075 9.500000e-139 503.0
29 TraesCS1D01G177500 chr6B 93.031 287 15 4 1586 1867 474271153 474271439 4.580000e-112 414.0
30 TraesCS1D01G177500 chr5D 83.938 386 56 5 1918 2298 529815570 529815186 4.680000e-97 364.0
31 TraesCS1D01G177500 chr5D 81.910 398 55 9 1905 2294 238784332 238784720 1.030000e-83 320.0
32 TraesCS1D01G177500 chr3A 85.632 348 40 10 1956 2298 475722969 475723311 7.820000e-95 357.0


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 TraesCS1D01G177500 chr1D 252566153 252568455 2302 False 4253.000000 4253 100.000000 1 2303 1 chr1D.!!$F1 2302
1 TraesCS1D01G177500 chr1B 360511910 360513250 1340 True 1877.000000 1877 92.251000 1 1321 1 chr1B.!!$R1 1320
2 TraesCS1D01G177500 chr1B 113983083 113983590 507 False 542.000000 542 86.523000 1375 1867 1 chr1B.!!$F1 492
3 TraesCS1D01G177500 chr1A 323891656 323895487 3831 False 523.033333 1072 92.118333 1 1321 3 chr1A.!!$F1 1320
4 TraesCS1D01G177500 chr1A 323960174 323961554 1380 False 283.000000 292 82.175500 174 1321 2 chr1A.!!$F2 1147
5 TraesCS1D01G177500 chr3D 275623840 275624414 574 True 660.000000 660 87.868000 1331 1889 1 chr3D.!!$R3 558
6 TraesCS1D01G177500 chr3D 32158602 32159176 574 True 649.000000 649 87.522000 1331 1889 1 chr3D.!!$R1 558
7 TraesCS1D01G177500 chr3D 604877716 604878243 527 True 628.000000 628 88.679000 1339 1850 1 chr3D.!!$R4 511
8 TraesCS1D01G177500 chr2D 645181000 645181545 545 True 640.000000 640 88.321000 1338 1867 1 chr2D.!!$R1 529
9 TraesCS1D01G177500 chr6D 87244959 87245512 553 True 636.000000 636 87.993000 1331 1867 1 chr6D.!!$R1 536
10 TraesCS1D01G177500 chr6D 203051772 203052314 542 False 542.000000 542 85.152000 1331 1872 1 chr6D.!!$F1 541
11 TraesCS1D01G177500 chr2A 755398540 755399099 559 True 623.000000 623 87.500000 1331 1865 1 chr2A.!!$R1 534
12 TraesCS1D01G177500 chrUn 114966652 114967200 548 True 617.000000 617 87.319000 1331 1870 1 chrUn.!!$R1 539
13 TraesCS1D01G177500 chr7D 116817948 116818528 580 False 614.000000 614 86.294000 1320 1889 1 chr7D.!!$F1 569
14 TraesCS1D01G177500 chr5B 108820616 108821142 526 True 606.000000 606 87.902000 1354 1867 1 chr5B.!!$R1 513
15 TraesCS1D01G177500 chr3B 698383530 698384075 545 False 503.000000 503 84.124000 1331 1850 1 chr3B.!!$F1 519

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
954 3907 0.321564 TTGGGTTGATGAGCAGGTCG 60.322 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1895 4930 0.911053 TGGAGCATGGTAGCATGTGA 59.089 50.0 29.91 13.04 36.85 3.58 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
120 2710 1.308069 GGCACAGCATTCATCACGGT 61.308 55.000 0.00 0.00 0.00 4.83
136 2726 2.226437 CACGGTCATTTAGTTTGCTGCT 59.774 45.455 0.00 0.00 0.00 4.24
214 2804 4.219070 CCAACAATGGCAAGATTCTTCTCA 59.781 41.667 0.00 0.00 40.58 3.27
308 2898 2.187946 GCTCCTGCTACACGCCAT 59.812 61.111 0.00 0.00 38.05 4.40
332 2922 1.888018 CCAACTCCGGCGTCTTCTA 59.112 57.895 6.01 0.00 0.00 2.10
346 2945 1.899814 TCTTCTAGCCAACGTGACCAT 59.100 47.619 0.00 0.00 0.00 3.55
478 3098 3.314331 CCACCACCACTCTCGCCT 61.314 66.667 0.00 0.00 0.00 5.52
548 3207 2.203139 CAGCCCACGACCACAACA 60.203 61.111 0.00 0.00 0.00 3.33
642 3301 6.179756 TCACCACATTGTATCTGCAGTTTAT 58.820 36.000 14.67 2.30 0.00 1.40
643 3302 6.658816 TCACCACATTGTATCTGCAGTTTATT 59.341 34.615 14.67 0.00 0.00 1.40
644 3303 7.826744 TCACCACATTGTATCTGCAGTTTATTA 59.173 33.333 14.67 0.00 0.00 0.98
657 3316 8.792633 TCTGCAGTTTATTACATGTTTTAAGCT 58.207 29.630 14.67 7.28 0.00 3.74
709 3374 5.046663 TGGATTTTTATCTTCCTTTGCCCAC 60.047 40.000 0.00 0.00 0.00 4.61
752 3417 5.241949 AGTGCGGATATCGAAGTATTCTCTT 59.758 40.000 0.00 0.00 44.75 2.85
828 3498 1.917872 TGGGTTTCTACATGGCCAAC 58.082 50.000 10.96 0.00 0.00 3.77
905 3675 0.953471 TCCGGGACAAATGCAAGTCG 60.953 55.000 0.00 2.62 35.63 4.18
954 3907 0.321564 TTGGGTTGATGAGCAGGTCG 60.322 55.000 0.00 0.00 0.00 4.79
984 3937 1.942657 GAGCAGCAGTGTTCAGTTTCA 59.057 47.619 0.00 0.00 34.19 2.69
1089 4045 1.688811 GCCAGTTGGTGTATGGGGA 59.311 57.895 0.00 0.00 37.57 4.81
1092 4048 1.633432 CCAGTTGGTGTATGGGGAAGA 59.367 52.381 0.00 0.00 0.00 2.87
1093 4049 2.242196 CCAGTTGGTGTATGGGGAAGAT 59.758 50.000 0.00 0.00 0.00 2.40
1309 4283 2.730934 ACCGTGCCACTAGATCTAGA 57.269 50.000 31.91 10.42 36.97 2.43
1321 4295 7.592164 GCCACTAGATCTAGATTTCGACTTAAC 59.408 40.741 31.91 6.38 36.97 2.01
1322 4296 8.842280 CCACTAGATCTAGATTTCGACTTAACT 58.158 37.037 31.91 5.47 36.97 2.24
1326 4300 8.453238 AGATCTAGATTTCGACTTAACTAGCA 57.547 34.615 6.70 0.00 0.00 3.49
1327 4301 8.904834 AGATCTAGATTTCGACTTAACTAGCAA 58.095 33.333 6.70 0.00 0.00 3.91
1357 4332 1.095228 CCGTGTGTTGCAACAGGAGT 61.095 55.000 31.81 0.00 40.05 3.85
1364 4339 4.095782 TGTGTTGCAACAGGAGTAAAGAAC 59.904 41.667 31.81 15.71 40.05 3.01
1369 4344 3.821033 GCAACAGGAGTAAAGAACACCAT 59.179 43.478 0.00 0.00 41.03 3.55
1543 4543 6.801539 ACGAGCAAGTGATCTTCAATTTTA 57.198 33.333 0.00 0.00 31.77 1.52
1548 4548 8.571461 AGCAAGTGATCTTCAATTTTATCTCA 57.429 30.769 0.00 0.00 31.77 3.27
1555 4555 8.960591 TGATCTTCAATTTTATCTCAAACCCTC 58.039 33.333 0.00 0.00 0.00 4.30
1582 4582 4.338012 TGCTGAGATGTTCATCCACAATT 58.662 39.130 8.89 0.00 34.68 2.32
1619 4635 6.791887 AGACGGATAATGCACTATTGATTG 57.208 37.500 0.00 0.00 0.00 2.67
1788 4819 3.374220 TGATATGTACCGCGGGTTTAG 57.626 47.619 31.76 2.56 37.09 1.85
1889 4924 8.552296 AGATCTGGGAAAATATCATATGGTACC 58.448 37.037 4.43 4.43 0.00 3.34
1890 4925 7.640577 TCTGGGAAAATATCATATGGTACCA 57.359 36.000 18.99 18.99 0.00 3.25
1891 4926 7.458397 TCTGGGAAAATATCATATGGTACCAC 58.542 38.462 19.09 0.00 0.00 4.16
1892 4927 6.548321 TGGGAAAATATCATATGGTACCACC 58.452 40.000 19.09 9.55 39.22 4.61
1902 4937 1.832883 TGGTACCACCATTCACATGC 58.167 50.000 11.60 0.00 44.79 4.06
1903 4938 1.354031 TGGTACCACCATTCACATGCT 59.646 47.619 11.60 0.00 44.79 3.79
1904 4939 2.573915 TGGTACCACCATTCACATGCTA 59.426 45.455 11.60 0.00 44.79 3.49
1905 4940 2.943033 GGTACCACCATTCACATGCTAC 59.057 50.000 7.15 0.00 38.42 3.58
1906 4941 2.128771 ACCACCATTCACATGCTACC 57.871 50.000 0.00 0.00 0.00 3.18
1907 4942 1.354031 ACCACCATTCACATGCTACCA 59.646 47.619 0.00 0.00 0.00 3.25
1908 4943 2.025037 ACCACCATTCACATGCTACCAT 60.025 45.455 0.00 0.00 0.00 3.55
1917 4952 2.048444 CATGCTACCATGCTCCAAGT 57.952 50.000 0.00 0.00 42.08 3.16
1918 4953 2.372264 CATGCTACCATGCTCCAAGTT 58.628 47.619 0.00 0.00 42.08 2.66
1919 4954 2.584835 TGCTACCATGCTCCAAGTTT 57.415 45.000 0.00 0.00 0.00 2.66
1920 4955 2.875296 TGCTACCATGCTCCAAGTTTT 58.125 42.857 0.00 0.00 0.00 2.43
1921 4956 2.557924 TGCTACCATGCTCCAAGTTTTG 59.442 45.455 0.00 0.00 0.00 2.44
1922 4957 2.819608 GCTACCATGCTCCAAGTTTTGA 59.180 45.455 0.00 0.00 0.00 2.69
1923 4958 3.255642 GCTACCATGCTCCAAGTTTTGAA 59.744 43.478 0.00 0.00 0.00 2.69
1924 4959 4.261994 GCTACCATGCTCCAAGTTTTGAAA 60.262 41.667 0.00 0.00 0.00 2.69
1925 4960 4.751767 ACCATGCTCCAAGTTTTGAAAA 57.248 36.364 0.00 0.00 0.00 2.29
1926 4961 5.096443 ACCATGCTCCAAGTTTTGAAAAA 57.904 34.783 0.00 0.00 0.00 1.94
1927 4962 5.683681 ACCATGCTCCAAGTTTTGAAAAAT 58.316 33.333 0.00 0.00 0.00 1.82
1928 4963 5.528320 ACCATGCTCCAAGTTTTGAAAAATG 59.472 36.000 0.00 0.00 0.00 2.32
1929 4964 5.049267 CCATGCTCCAAGTTTTGAAAAATGG 60.049 40.000 14.32 14.32 32.08 3.16
1930 4965 3.876320 TGCTCCAAGTTTTGAAAAATGGC 59.124 39.130 15.23 8.11 31.30 4.40
1931 4966 3.876320 GCTCCAAGTTTTGAAAAATGGCA 59.124 39.130 15.23 0.00 31.30 4.92
1932 4967 4.516321 GCTCCAAGTTTTGAAAAATGGCAT 59.484 37.500 15.23 0.00 31.30 4.40
1933 4968 5.008911 GCTCCAAGTTTTGAAAAATGGCATT 59.991 36.000 6.96 6.96 31.30 3.56
1934 4969 6.459985 GCTCCAAGTTTTGAAAAATGGCATTT 60.460 34.615 19.39 19.39 31.30 2.32
1935 4970 7.255070 GCTCCAAGTTTTGAAAAATGGCATTTA 60.255 33.333 24.58 7.81 31.30 1.40
1936 4971 8.511604 TCCAAGTTTTGAAAAATGGCATTTAA 57.488 26.923 24.58 13.34 31.30 1.52
1937 4972 8.960591 TCCAAGTTTTGAAAAATGGCATTTAAA 58.039 25.926 24.58 18.00 31.30 1.52
1938 4973 9.747293 CCAAGTTTTGAAAAATGGCATTTAAAT 57.253 25.926 24.58 14.37 0.00 1.40
1986 5021 5.559770 TGTGGATGTTCACAAGACATATGT 58.440 37.500 8.43 8.43 43.70 2.29
1987 5022 6.003326 TGTGGATGTTCACAAGACATATGTT 58.997 36.000 10.30 0.00 43.70 2.71
1988 5023 7.164803 TGTGGATGTTCACAAGACATATGTTA 58.835 34.615 10.30 0.00 43.70 2.41
1989 5024 7.828717 TGTGGATGTTCACAAGACATATGTTAT 59.171 33.333 10.30 0.00 43.70 1.89
1990 5025 9.325198 GTGGATGTTCACAAGACATATGTTATA 57.675 33.333 10.30 0.00 37.57 0.98
1991 5026 9.898152 TGGATGTTCACAAGACATATGTTATAA 57.102 29.630 10.30 0.00 0.00 0.98
1994 5029 8.500753 TGTTCACAAGACATATGTTATAACCC 57.499 34.615 10.30 0.00 0.00 4.11
1995 5030 8.325787 TGTTCACAAGACATATGTTATAACCCT 58.674 33.333 10.30 0.00 0.00 4.34
1996 5031 9.174166 GTTCACAAGACATATGTTATAACCCTT 57.826 33.333 10.30 3.95 0.00 3.95
2029 5064 9.859427 TCCAGATCAAAATTCAAAATGTACATC 57.141 29.630 9.23 0.00 0.00 3.06
2030 5065 8.800972 CCAGATCAAAATTCAAAATGTACATCG 58.199 33.333 9.23 1.20 0.00 3.84
2031 5066 9.558648 CAGATCAAAATTCAAAATGTACATCGA 57.441 29.630 9.23 3.72 0.00 3.59
2032 5067 9.778993 AGATCAAAATTCAAAATGTACATCGAG 57.221 29.630 9.23 2.05 0.00 4.04
2033 5068 9.773328 GATCAAAATTCAAAATGTACATCGAGA 57.227 29.630 9.23 4.50 0.00 4.04
2035 5070 9.958234 TCAAAATTCAAAATGTACATCGAGAAA 57.042 25.926 9.23 1.36 0.00 2.52
2036 5071 9.993881 CAAAATTCAAAATGTACATCGAGAAAC 57.006 29.630 9.23 0.00 0.00 2.78
2037 5072 9.743057 AAAATTCAAAATGTACATCGAGAAACA 57.257 25.926 9.23 0.00 0.00 2.83
2038 5073 9.743057 AAATTCAAAATGTACATCGAGAAACAA 57.257 25.926 9.23 0.00 0.00 2.83
2039 5074 9.743057 AATTCAAAATGTACATCGAGAAACAAA 57.257 25.926 9.23 0.00 0.00 2.83
2040 5075 9.743057 ATTCAAAATGTACATCGAGAAACAAAA 57.257 25.926 9.23 0.00 0.00 2.44
2041 5076 9.574458 TTCAAAATGTACATCGAGAAACAAAAA 57.426 25.926 9.23 0.00 0.00 1.94
2067 5102 8.853077 AGACAAATCTAGAATGAATTGTGTCA 57.147 30.769 14.00 0.00 39.35 3.58
2068 5103 9.288576 AGACAAATCTAGAATGAATTGTGTCAA 57.711 29.630 14.00 0.00 39.35 3.18
2069 5104 9.897744 GACAAATCTAGAATGAATTGTGTCAAA 57.102 29.630 14.00 0.00 39.35 2.69
2075 5110 9.559732 TCTAGAATGAATTGTGTCAAAAGAAGA 57.440 29.630 0.00 0.00 0.00 2.87
2076 5111 9.604626 CTAGAATGAATTGTGTCAAAAGAAGAC 57.395 33.333 0.00 0.00 36.55 3.01
2077 5112 7.999679 AGAATGAATTGTGTCAAAAGAAGACA 58.000 30.769 0.00 0.00 43.23 3.41
2078 5113 8.469200 AGAATGAATTGTGTCAAAAGAAGACAA 58.531 29.630 0.00 0.00 46.50 3.18
2079 5114 9.086336 GAATGAATTGTGTCAAAAGAAGACAAA 57.914 29.630 0.00 0.00 46.50 2.83
2080 5115 9.434420 AATGAATTGTGTCAAAAGAAGACAAAA 57.566 25.926 1.84 1.84 46.50 2.44
2203 5238 6.932356 GACATATGTCTTGTGAACATCCAT 57.068 37.500 25.52 0.00 41.65 3.41
2205 5240 8.437360 GACATATGTCTTGTGAACATCCATAA 57.563 34.615 25.52 0.00 41.65 1.90
2206 5241 8.806429 ACATATGTCTTGTGAACATCCATAAA 57.194 30.769 1.41 0.00 0.00 1.40
2207 5242 9.241919 ACATATGTCTTGTGAACATCCATAAAA 57.758 29.630 1.41 0.00 0.00 1.52
2263 5298 8.830201 TGACTTTTCAAAATTTGTATCATGGG 57.170 30.769 5.56 0.00 0.00 4.00
2264 5299 8.646004 TGACTTTTCAAAATTTGTATCATGGGA 58.354 29.630 5.56 0.00 0.00 4.37
2265 5300 9.143631 GACTTTTCAAAATTTGTATCATGGGAG 57.856 33.333 5.56 0.00 0.00 4.30
2266 5301 7.603784 ACTTTTCAAAATTTGTATCATGGGAGC 59.396 33.333 5.56 0.00 0.00 4.70
2267 5302 6.602410 TTCAAAATTTGTATCATGGGAGCA 57.398 33.333 5.56 0.00 0.00 4.26
2268 5303 6.795144 TCAAAATTTGTATCATGGGAGCAT 57.205 33.333 5.56 0.00 0.00 3.79
2269 5304 6.808829 TCAAAATTTGTATCATGGGAGCATC 58.191 36.000 5.56 0.00 0.00 3.91
2270 5305 6.608405 TCAAAATTTGTATCATGGGAGCATCT 59.392 34.615 5.56 0.00 33.73 2.90
2271 5306 7.779326 TCAAAATTTGTATCATGGGAGCATCTA 59.221 33.333 5.56 0.00 33.73 1.98
2272 5307 8.415553 CAAAATTTGTATCATGGGAGCATCTAA 58.584 33.333 0.00 0.00 33.73 2.10
2273 5308 8.537728 AAATTTGTATCATGGGAGCATCTAAA 57.462 30.769 0.00 0.00 33.73 1.85
2274 5309 7.756395 ATTTGTATCATGGGAGCATCTAAAG 57.244 36.000 0.00 0.00 33.73 1.85
2275 5310 5.894298 TGTATCATGGGAGCATCTAAAGT 57.106 39.130 0.00 0.00 33.73 2.66
2276 5311 5.614308 TGTATCATGGGAGCATCTAAAGTG 58.386 41.667 0.00 0.00 33.73 3.16
2277 5312 4.785346 ATCATGGGAGCATCTAAAGTGT 57.215 40.909 0.00 0.00 33.73 3.55
2278 5313 3.877559 TCATGGGAGCATCTAAAGTGTG 58.122 45.455 0.00 0.00 33.73 3.82
2279 5314 2.787473 TGGGAGCATCTAAAGTGTGG 57.213 50.000 0.00 0.00 33.73 4.17
2280 5315 1.985159 TGGGAGCATCTAAAGTGTGGT 59.015 47.619 0.00 0.00 33.73 4.16
2281 5316 3.178046 TGGGAGCATCTAAAGTGTGGTA 58.822 45.455 0.00 0.00 33.73 3.25
2282 5317 3.780294 TGGGAGCATCTAAAGTGTGGTAT 59.220 43.478 0.00 0.00 33.73 2.73
2283 5318 4.141711 TGGGAGCATCTAAAGTGTGGTATC 60.142 45.833 0.00 0.00 33.73 2.24
2284 5319 4.141711 GGGAGCATCTAAAGTGTGGTATCA 60.142 45.833 0.00 0.00 33.73 2.15
2285 5320 4.811557 GGAGCATCTAAAGTGTGGTATCAC 59.188 45.833 0.00 0.00 38.79 3.06
2286 5321 4.770795 AGCATCTAAAGTGTGGTATCACC 58.229 43.478 3.07 0.00 42.98 4.02
2287 5322 4.471386 AGCATCTAAAGTGTGGTATCACCT 59.529 41.667 3.07 0.00 42.98 4.00
2288 5323 4.572389 GCATCTAAAGTGTGGTATCACCTG 59.428 45.833 3.07 0.00 42.98 4.00
2289 5324 5.626809 GCATCTAAAGTGTGGTATCACCTGA 60.627 44.000 3.07 0.00 42.98 3.86
2290 5325 6.586344 CATCTAAAGTGTGGTATCACCTGAT 58.414 40.000 3.07 0.00 42.98 2.90
2291 5326 7.686859 GCATCTAAAGTGTGGTATCACCTGATA 60.687 40.741 3.07 0.00 42.98 2.15
2292 5327 7.914427 TCTAAAGTGTGGTATCACCTGATAT 57.086 36.000 3.07 0.00 42.98 1.63
2293 5328 7.952671 TCTAAAGTGTGGTATCACCTGATATC 58.047 38.462 3.07 0.00 42.98 1.63
2294 5329 6.814954 AAAGTGTGGTATCACCTGATATCT 57.185 37.500 3.07 0.00 42.98 1.98
2295 5330 7.914427 AAAGTGTGGTATCACCTGATATCTA 57.086 36.000 3.07 0.00 42.98 1.98
2296 5331 6.902771 AGTGTGGTATCACCTGATATCTAC 57.097 41.667 3.07 6.37 42.98 2.59
2297 5332 5.775701 AGTGTGGTATCACCTGATATCTACC 59.224 44.000 3.07 6.92 42.98 3.18
2298 5333 4.765339 TGTGGTATCACCTGATATCTACCG 59.235 45.833 3.07 0.00 42.98 4.02
2299 5334 4.158025 GTGGTATCACCTGATATCTACCGG 59.842 50.000 0.00 0.00 38.60 5.28
2300 5335 4.202641 TGGTATCACCTGATATCTACCGGT 60.203 45.833 13.98 13.98 38.60 5.28
2301 5336 5.014438 TGGTATCACCTGATATCTACCGGTA 59.986 44.000 14.95 14.95 38.60 4.02
2302 5337 6.127793 GGTATCACCTGATATCTACCGGTAT 58.872 44.000 16.25 4.71 39.03 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 2710 8.746922 CTGAATTTAAGCAGCAAACTAAATGA 57.253 30.769 0.00 0.00 0.00 2.57
136 2726 5.338219 CCATTCCATTGTGGGCTGAATTTAA 60.338 40.000 0.00 0.00 38.32 1.52
214 2804 2.754658 GCCTGAGCCAGCAAGCAT 60.755 61.111 0.55 0.00 34.23 3.79
332 2922 1.298667 GGGTATGGTCACGTTGGCT 59.701 57.895 0.00 0.00 0.00 4.75
346 2945 1.603842 CACTGATGCTGCTGGGGTA 59.396 57.895 0.00 0.00 0.00 3.69
460 3080 3.626924 GGCGAGAGTGGTGGTGGT 61.627 66.667 0.00 0.00 0.00 4.16
478 3098 1.813859 CGAGAATGGTAGTGGCGGA 59.186 57.895 0.00 0.00 0.00 5.54
486 3139 2.812499 GCGGAGGCGAGAATGGTA 59.188 61.111 0.00 0.00 0.00 3.25
529 3188 4.947147 TTGTGGTCGTGGGCTGGC 62.947 66.667 0.00 0.00 0.00 4.85
530 3189 2.978010 GTTGTGGTCGTGGGCTGG 60.978 66.667 0.00 0.00 0.00 4.85
531 3190 1.172180 ATTGTTGTGGTCGTGGGCTG 61.172 55.000 0.00 0.00 0.00 4.85
539 3198 7.145932 ACTGCTAATTAAGATTGTTGTGGTC 57.854 36.000 0.00 0.00 0.00 4.02
548 3207 9.464714 CACGTGATAGTACTGCTAATTAAGATT 57.535 33.333 10.90 0.00 32.72 2.40
709 3374 3.077359 ACTGGCTCGGAAAATTTCTCAG 58.923 45.455 5.65 8.28 0.00 3.35
752 3417 0.250081 GGGCGGGCAAACAAAAATCA 60.250 50.000 3.27 0.00 0.00 2.57
918 3871 8.161699 TCAACCCAACTTATACTGAAAACTTC 57.838 34.615 0.00 0.00 0.00 3.01
954 3907 1.153862 CTGCTGCTCTCGGTGAGAC 60.154 63.158 11.04 3.51 45.39 3.36
984 3937 2.036992 TCGCATCTTGGCCAAACAAAAT 59.963 40.909 20.91 5.46 0.00 1.82
1089 4045 3.541713 GCTCTCCCCGGCGATCTT 61.542 66.667 9.30 0.00 0.00 2.40
1236 4192 3.560278 CGTTGGCGATACGGTGGC 61.560 66.667 0.00 0.00 41.33 5.01
1336 4310 2.118404 CCTGTTGCAACACACGGGT 61.118 57.895 27.96 0.00 34.70 5.28
1448 4433 2.031769 TGTGAATCTTGAACTTGCGCTG 60.032 45.455 9.73 3.92 0.00 5.18
1543 4543 4.410099 TCAGCAAAATGAGGGTTTGAGAT 58.590 39.130 1.23 0.00 38.05 2.75
1548 4548 4.154942 ACATCTCAGCAAAATGAGGGTTT 58.845 39.130 4.05 0.00 45.60 3.27
1551 4551 3.760151 TGAACATCTCAGCAAAATGAGGG 59.240 43.478 4.05 0.55 45.60 4.30
1555 4555 5.100259 GTGGATGAACATCTCAGCAAAATG 58.900 41.667 13.34 0.00 42.55 2.32
1582 4582 8.559536 GCATTATCCGTCTTTCTTTCATATTGA 58.440 33.333 0.00 0.00 0.00 2.57
1758 4783 5.229052 CCGCGGTACATATCAAATGTTTTTG 59.771 40.000 19.50 0.00 42.98 2.44
1788 4819 5.372547 GAAACCCCTAATGTTTCTGACAC 57.627 43.478 8.25 0.00 45.10 3.67
1867 4902 6.659242 GGTGGTACCATATGATATTTTCCCAG 59.341 42.308 19.72 0.00 38.42 4.45
1884 4919 2.128771 AGCATGTGAATGGTGGTACC 57.871 50.000 4.43 4.43 39.22 3.34
1889 4924 2.223641 GCATGGTAGCATGTGAATGGTG 60.224 50.000 29.91 9.02 35.16 4.17
1890 4925 2.026641 GCATGGTAGCATGTGAATGGT 58.973 47.619 29.91 0.00 35.16 3.55
1891 4926 2.292569 GAGCATGGTAGCATGTGAATGG 59.707 50.000 29.91 8.90 36.85 3.16
1892 4927 2.292569 GGAGCATGGTAGCATGTGAATG 59.707 50.000 29.91 11.05 36.85 2.67
1893 4928 2.092267 TGGAGCATGGTAGCATGTGAAT 60.092 45.455 29.91 16.96 36.85 2.57
1894 4929 1.281577 TGGAGCATGGTAGCATGTGAA 59.718 47.619 29.91 14.67 36.85 3.18
1895 4930 0.911053 TGGAGCATGGTAGCATGTGA 59.089 50.000 29.91 13.04 36.85 3.58
1896 4931 1.674441 CTTGGAGCATGGTAGCATGTG 59.326 52.381 29.91 13.09 36.85 3.21
1897 4932 1.283029 ACTTGGAGCATGGTAGCATGT 59.717 47.619 29.91 19.30 36.85 3.21
1898 4933 2.048444 ACTTGGAGCATGGTAGCATG 57.952 50.000 26.83 26.83 36.85 4.06
1899 4934 2.814805 AACTTGGAGCATGGTAGCAT 57.185 45.000 0.40 0.40 36.85 3.79
1900 4935 2.557924 CAAAACTTGGAGCATGGTAGCA 59.442 45.455 0.00 0.00 36.85 3.49
1901 4936 2.819608 TCAAAACTTGGAGCATGGTAGC 59.180 45.455 0.00 0.00 0.00 3.58
1902 4937 5.452078 TTTCAAAACTTGGAGCATGGTAG 57.548 39.130 0.00 0.00 0.00 3.18
1903 4938 5.860941 TTTTCAAAACTTGGAGCATGGTA 57.139 34.783 0.00 0.00 0.00 3.25
1904 4939 4.751767 TTTTCAAAACTTGGAGCATGGT 57.248 36.364 0.00 0.00 0.00 3.55
1905 4940 5.049267 CCATTTTTCAAAACTTGGAGCATGG 60.049 40.000 5.42 0.00 32.37 3.66
1906 4941 5.561339 GCCATTTTTCAAAACTTGGAGCATG 60.561 40.000 13.14 0.00 32.37 4.06
1907 4942 4.516321 GCCATTTTTCAAAACTTGGAGCAT 59.484 37.500 13.14 0.00 32.37 3.79
1908 4943 3.876320 GCCATTTTTCAAAACTTGGAGCA 59.124 39.130 13.14 0.00 32.37 4.26
1909 4944 3.876320 TGCCATTTTTCAAAACTTGGAGC 59.124 39.130 13.14 2.31 32.37 4.70
1910 4945 6.622833 AATGCCATTTTTCAAAACTTGGAG 57.377 33.333 13.14 0.00 32.37 3.86
1911 4946 8.511604 TTAAATGCCATTTTTCAAAACTTGGA 57.488 26.923 8.15 0.00 32.37 3.53
1912 4947 9.747293 ATTTAAATGCCATTTTTCAAAACTTGG 57.253 25.926 8.15 6.65 33.32 3.61
1963 4998 5.559770 ACATATGTCTTGTGAACATCCACA 58.440 37.500 1.41 0.00 44.45 4.17
1964 4999 6.500684 AACATATGTCTTGTGAACATCCAC 57.499 37.500 9.23 0.00 37.55 4.02
1965 5000 9.898152 TTATAACATATGTCTTGTGAACATCCA 57.102 29.630 9.23 0.00 0.00 3.41
1968 5003 9.120538 GGGTTATAACATATGTCTTGTGAACAT 57.879 33.333 17.16 0.00 0.00 2.71
1969 5004 8.325787 AGGGTTATAACATATGTCTTGTGAACA 58.674 33.333 17.16 0.00 0.00 3.18
1970 5005 8.732746 AGGGTTATAACATATGTCTTGTGAAC 57.267 34.615 17.16 7.87 0.00 3.18
2003 5038 9.859427 GATGTACATTTTGAATTTTGATCTGGA 57.141 29.630 10.30 0.00 0.00 3.86
2004 5039 8.800972 CGATGTACATTTTGAATTTTGATCTGG 58.199 33.333 10.30 0.00 0.00 3.86
2005 5040 9.558648 TCGATGTACATTTTGAATTTTGATCTG 57.441 29.630 10.30 0.00 0.00 2.90
2006 5041 9.778993 CTCGATGTACATTTTGAATTTTGATCT 57.221 29.630 10.30 0.00 0.00 2.75
2007 5042 9.773328 TCTCGATGTACATTTTGAATTTTGATC 57.227 29.630 10.30 0.00 0.00 2.92
2009 5044 9.958234 TTTCTCGATGTACATTTTGAATTTTGA 57.042 25.926 10.30 0.27 0.00 2.69
2010 5045 9.993881 GTTTCTCGATGTACATTTTGAATTTTG 57.006 29.630 10.30 0.00 0.00 2.44
2011 5046 9.743057 TGTTTCTCGATGTACATTTTGAATTTT 57.257 25.926 10.30 0.00 0.00 1.82
2012 5047 9.743057 TTGTTTCTCGATGTACATTTTGAATTT 57.257 25.926 10.30 0.00 0.00 1.82
2013 5048 9.743057 TTTGTTTCTCGATGTACATTTTGAATT 57.257 25.926 10.30 0.00 0.00 2.17
2014 5049 9.743057 TTTTGTTTCTCGATGTACATTTTGAAT 57.257 25.926 10.30 0.00 0.00 2.57
2015 5050 9.574458 TTTTTGTTTCTCGATGTACATTTTGAA 57.426 25.926 10.30 11.15 0.00 2.69
2041 5076 9.288576 TGACACAATTCATTCTAGATTTGTCTT 57.711 29.630 12.56 3.59 39.01 3.01
2042 5077 8.853077 TGACACAATTCATTCTAGATTTGTCT 57.147 30.769 12.56 0.00 39.01 3.41
2043 5078 9.897744 TTTGACACAATTCATTCTAGATTTGTC 57.102 29.630 0.00 1.07 39.01 3.18
2049 5084 9.559732 TCTTCTTTTGACACAATTCATTCTAGA 57.440 29.630 0.00 0.00 0.00 2.43
2050 5085 9.604626 GTCTTCTTTTGACACAATTCATTCTAG 57.395 33.333 0.00 0.00 34.80 2.43
2051 5086 9.119418 TGTCTTCTTTTGACACAATTCATTCTA 57.881 29.630 0.00 0.00 39.23 2.10
2052 5087 7.999679 TGTCTTCTTTTGACACAATTCATTCT 58.000 30.769 0.00 0.00 39.23 2.40
2053 5088 8.633075 TTGTCTTCTTTTGACACAATTCATTC 57.367 30.769 0.00 0.00 43.13 2.67
2054 5089 9.434420 TTTTGTCTTCTTTTGACACAATTCATT 57.566 25.926 0.00 0.00 43.13 2.57
2055 5090 9.603921 ATTTTGTCTTCTTTTGACACAATTCAT 57.396 25.926 0.00 0.00 40.01 2.57
2180 5215 6.932356 ATGGATGTTCACAAGACATATGTC 57.068 37.500 25.47 25.47 45.08 3.06
2181 5216 8.806429 TTTATGGATGTTCACAAGACATATGT 57.194 30.769 8.43 8.43 0.00 2.29
2237 5272 9.439500 CCCATGATACAAATTTTGAAAAGTCAT 57.561 29.630 15.81 12.46 32.48 3.06
2238 5273 8.646004 TCCCATGATACAAATTTTGAAAAGTCA 58.354 29.630 15.81 11.05 0.00 3.41
2239 5274 9.143631 CTCCCATGATACAAATTTTGAAAAGTC 57.856 33.333 15.81 6.59 0.00 3.01
2240 5275 7.603784 GCTCCCATGATACAAATTTTGAAAAGT 59.396 33.333 15.81 0.00 0.00 2.66
2241 5276 7.603404 TGCTCCCATGATACAAATTTTGAAAAG 59.397 33.333 15.81 1.27 0.00 2.27
2242 5277 7.448420 TGCTCCCATGATACAAATTTTGAAAA 58.552 30.769 15.81 0.00 0.00 2.29
2243 5278 7.002250 TGCTCCCATGATACAAATTTTGAAA 57.998 32.000 15.81 4.08 0.00 2.69
2244 5279 6.602410 TGCTCCCATGATACAAATTTTGAA 57.398 33.333 15.81 0.00 0.00 2.69
2245 5280 6.608405 AGATGCTCCCATGATACAAATTTTGA 59.392 34.615 15.81 0.55 0.00 2.69
2246 5281 6.812998 AGATGCTCCCATGATACAAATTTTG 58.187 36.000 7.59 7.59 0.00 2.44
2247 5282 8.537728 TTAGATGCTCCCATGATACAAATTTT 57.462 30.769 0.00 0.00 0.00 1.82
2248 5283 8.537728 TTTAGATGCTCCCATGATACAAATTT 57.462 30.769 0.00 0.00 0.00 1.82
2249 5284 7.781693 ACTTTAGATGCTCCCATGATACAAATT 59.218 33.333 0.00 0.00 0.00 1.82
2250 5285 7.230108 CACTTTAGATGCTCCCATGATACAAAT 59.770 37.037 0.00 0.00 0.00 2.32
2251 5286 6.543465 CACTTTAGATGCTCCCATGATACAAA 59.457 38.462 0.00 0.00 0.00 2.83
2252 5287 6.057533 CACTTTAGATGCTCCCATGATACAA 58.942 40.000 0.00 0.00 0.00 2.41
2253 5288 5.130975 ACACTTTAGATGCTCCCATGATACA 59.869 40.000 0.00 0.00 0.00 2.29
2254 5289 5.468072 CACACTTTAGATGCTCCCATGATAC 59.532 44.000 0.00 0.00 0.00 2.24
2255 5290 5.455183 CCACACTTTAGATGCTCCCATGATA 60.455 44.000 0.00 0.00 0.00 2.15
2256 5291 4.458397 CACACTTTAGATGCTCCCATGAT 58.542 43.478 0.00 0.00 0.00 2.45
2257 5292 3.370846 CCACACTTTAGATGCTCCCATGA 60.371 47.826 0.00 0.00 0.00 3.07
2258 5293 2.947652 CCACACTTTAGATGCTCCCATG 59.052 50.000 0.00 0.00 0.00 3.66
2259 5294 2.578021 ACCACACTTTAGATGCTCCCAT 59.422 45.455 0.00 0.00 0.00 4.00
2260 5295 1.985159 ACCACACTTTAGATGCTCCCA 59.015 47.619 0.00 0.00 0.00 4.37
2261 5296 2.789409 ACCACACTTTAGATGCTCCC 57.211 50.000 0.00 0.00 0.00 4.30
2262 5297 4.811557 GTGATACCACACTTTAGATGCTCC 59.188 45.833 0.00 0.00 42.72 4.70
2263 5298 4.811557 GGTGATACCACACTTTAGATGCTC 59.188 45.833 0.00 0.00 44.93 4.26
2264 5299 4.471386 AGGTGATACCACACTTTAGATGCT 59.529 41.667 0.28 0.00 44.93 3.79
2265 5300 4.572389 CAGGTGATACCACACTTTAGATGC 59.428 45.833 0.28 0.00 44.93 3.91
2266 5301 5.977635 TCAGGTGATACCACACTTTAGATG 58.022 41.667 0.28 0.00 44.93 2.90
2267 5302 6.814954 ATCAGGTGATACCACACTTTAGAT 57.185 37.500 0.28 0.00 44.93 1.98
2268 5303 7.785028 AGATATCAGGTGATACCACACTTTAGA 59.215 37.037 5.32 0.00 44.93 2.10
2269 5304 7.957002 AGATATCAGGTGATACCACACTTTAG 58.043 38.462 5.32 0.00 44.93 1.85
2270 5305 7.914427 AGATATCAGGTGATACCACACTTTA 57.086 36.000 5.32 0.00 44.93 1.85
2271 5306 6.814954 AGATATCAGGTGATACCACACTTT 57.185 37.500 5.32 0.00 44.93 2.66
2272 5307 6.267928 GGTAGATATCAGGTGATACCACACTT 59.732 42.308 5.32 0.00 44.93 3.16
2273 5308 5.775701 GGTAGATATCAGGTGATACCACACT 59.224 44.000 5.32 1.46 44.93 3.55
2274 5309 5.335740 CGGTAGATATCAGGTGATACCACAC 60.336 48.000 13.89 0.00 44.93 3.82
2275 5310 4.765339 CGGTAGATATCAGGTGATACCACA 59.235 45.833 13.89 0.00 44.93 4.17
2276 5311 4.158025 CCGGTAGATATCAGGTGATACCAC 59.842 50.000 13.89 1.56 41.95 4.16
2277 5312 4.202641 ACCGGTAGATATCAGGTGATACCA 60.203 45.833 4.49 0.00 41.95 3.25
2278 5313 4.342359 ACCGGTAGATATCAGGTGATACC 58.658 47.826 4.49 6.06 39.57 2.73


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

AutoCloner maintained by Alex Coulton.