Multiple sequence alignment - TraesCS6A01G040400

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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 TraesCS6A01G040400 chr6A 100.000 2420 0 0 1 2420 21079672 21077253 0.000000e+00 4470
1 TraesCS6A01G040400 chr6A 90.855 667 60 1 1 667 88100737 88100072 0.000000e+00 893
2 TraesCS6A01G040400 chr6A 83.193 833 93 38 748 1544 16655969 16655148 0.000000e+00 719
3 TraesCS6A01G040400 chr6A 82.028 868 95 47 745 1564 16705109 16705963 0.000000e+00 682
4 TraesCS6A01G040400 chr6A 88.451 381 37 5 1810 2186 75097658 75097281 1.020000e-123 453
5 TraesCS6A01G040400 chr6D 93.417 957 43 9 721 1665 20813968 20813020 0.000000e+00 1400
6 TraesCS6A01G040400 chr6D 81.808 863 103 36 745 1564 16386778 16385927 0.000000e+00 675
7 TraesCS6A01G040400 chr6D 80.947 866 99 42 748 1564 16514375 16515223 2.040000e-175 625
8 TraesCS6A01G040400 chr6D 86.245 269 29 5 1877 2140 20812814 20812549 3.940000e-73 285
9 TraesCS6A01G040400 chr6D 92.903 155 10 1 723 876 20834232 20834078 8.710000e-55 224
10 TraesCS6A01G040400 chr6B 89.099 954 57 24 721 1665 35819130 35818215 0.000000e+00 1142
11 TraesCS6A01G040400 chr6B 81.329 873 107 39 726 1565 29044500 29045349 0.000000e+00 658
12 TraesCS6A01G040400 chr6B 90.071 423 30 5 1899 2321 35818001 35817591 2.740000e-149 538
13 TraesCS6A01G040400 chr6B 88.024 167 18 2 2156 2321 35630236 35630401 1.900000e-46 196
14 TraesCS6A01G040400 chr5A 91.416 664 56 1 1 664 570491953 570492615 0.000000e+00 909
15 TraesCS6A01G040400 chr7A 91.114 664 59 0 1 664 717560742 717561405 0.000000e+00 900
16 TraesCS6A01G040400 chr7A 89.251 307 31 2 1881 2186 7024263 7024568 1.360000e-102 383
17 TraesCS6A01G040400 chr7A 98.990 99 1 0 2322 2420 338291600 338291698 6.880000e-41 178
18 TraesCS6A01G040400 chr1A 91.114 664 58 1 1 663 452049117 452048454 0.000000e+00 898
19 TraesCS6A01G040400 chr1A 90.719 668 54 6 1 664 41373624 41374287 0.000000e+00 883
20 TraesCS6A01G040400 chr4A 90.705 667 62 0 1 667 171212930 171212264 0.000000e+00 889
21 TraesCS6A01G040400 chr4A 100.000 99 0 0 2322 2420 595871204 595871106 1.480000e-42 183
22 TraesCS6A01G040400 chr3A 90.827 665 57 4 1 664 531904464 531905125 0.000000e+00 887
23 TraesCS6A01G040400 chr3A 90.569 668 62 1 1 668 100434 101100 0.000000e+00 883
24 TraesCS6A01G040400 chr3A 91.706 422 26 6 1013 1427 57013489 57013070 5.800000e-161 577
25 TraesCS6A01G040400 chr2A 90.950 663 54 5 1 661 778822181 778822839 0.000000e+00 887
26 TraesCS6A01G040400 chr2A 98.990 99 1 0 2322 2420 65684952 65684854 6.880000e-41 178
27 TraesCS6A01G040400 chr1B 88.075 587 47 17 995 1564 587501304 587500724 0.000000e+00 675
28 TraesCS6A01G040400 chr1B 94.026 385 20 3 1030 1413 434429674 434429292 4.480000e-162 580
29 TraesCS6A01G040400 chr1B 96.364 110 4 0 2311 2420 572704045 572703936 5.310000e-42 182
30 TraesCS6A01G040400 chr5B 99.020 102 1 0 2319 2420 611825794 611825895 1.480000e-42 183
31 TraesCS6A01G040400 chr3D 100.000 99 0 0 2322 2420 577564801 577564703 1.480000e-42 183
32 TraesCS6A01G040400 chr4D 97.170 106 2 1 2315 2420 363670578 363670474 6.880000e-41 178
33 TraesCS6A01G040400 chr3B 98.990 99 1 0 2322 2420 821288943 821288845 6.880000e-41 178
34 TraesCS6A01G040400 chr4B 95.413 109 2 3 2313 2420 628034407 628034513 1.150000e-38 171


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 TraesCS6A01G040400 chr6A 21077253 21079672 2419 True 4470.0 4470 100.000 1 2420 1 chr6A.!!$R2 2419
1 TraesCS6A01G040400 chr6A 88100072 88100737 665 True 893.0 893 90.855 1 667 1 chr6A.!!$R4 666
2 TraesCS6A01G040400 chr6A 16655148 16655969 821 True 719.0 719 83.193 748 1544 1 chr6A.!!$R1 796
3 TraesCS6A01G040400 chr6A 16705109 16705963 854 False 682.0 682 82.028 745 1564 1 chr6A.!!$F1 819
4 TraesCS6A01G040400 chr6D 20812549 20813968 1419 True 842.5 1400 89.831 721 2140 2 chr6D.!!$R3 1419
5 TraesCS6A01G040400 chr6D 16385927 16386778 851 True 675.0 675 81.808 745 1564 1 chr6D.!!$R1 819
6 TraesCS6A01G040400 chr6D 16514375 16515223 848 False 625.0 625 80.947 748 1564 1 chr6D.!!$F1 816
7 TraesCS6A01G040400 chr6B 35817591 35819130 1539 True 840.0 1142 89.585 721 2321 2 chr6B.!!$R1 1600
8 TraesCS6A01G040400 chr6B 29044500 29045349 849 False 658.0 658 81.329 726 1565 1 chr6B.!!$F1 839
9 TraesCS6A01G040400 chr5A 570491953 570492615 662 False 909.0 909 91.416 1 664 1 chr5A.!!$F1 663
10 TraesCS6A01G040400 chr7A 717560742 717561405 663 False 900.0 900 91.114 1 664 1 chr7A.!!$F3 663
11 TraesCS6A01G040400 chr1A 452048454 452049117 663 True 898.0 898 91.114 1 663 1 chr1A.!!$R1 662
12 TraesCS6A01G040400 chr1A 41373624 41374287 663 False 883.0 883 90.719 1 664 1 chr1A.!!$F1 663
13 TraesCS6A01G040400 chr4A 171212264 171212930 666 True 889.0 889 90.705 1 667 1 chr4A.!!$R1 666
14 TraesCS6A01G040400 chr3A 531904464 531905125 661 False 887.0 887 90.827 1 664 1 chr3A.!!$F2 663
15 TraesCS6A01G040400 chr3A 100434 101100 666 False 883.0 883 90.569 1 668 1 chr3A.!!$F1 667
16 TraesCS6A01G040400 chr2A 778822181 778822839 658 False 887.0 887 90.950 1 661 1 chr2A.!!$F1 660
17 TraesCS6A01G040400 chr1B 587500724 587501304 580 True 675.0 675 88.075 995 1564 1 chr1B.!!$R3 569

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
884 887 0.036294 CCCACCTTCTTCCTCCGTTC 60.036 60.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2274 2439 0.463833 GAACCGCTCCCATACCCAAG 60.464 60.0 0.0 0.0 0.0 3.61 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
194 195 1.452470 TCGTCGGTGGATGATCGGA 60.452 57.895 0.00 0.00 33.29 4.55
234 235 3.270877 CTTGCAGTCGGCTTTTATAGGT 58.729 45.455 0.00 0.00 45.15 3.08
495 496 0.940519 AAAACGATTCGTCCGACGCA 60.941 50.000 16.24 5.82 42.21 5.24
551 552 2.171079 CCGCCAGCGCTAATTTCGA 61.171 57.895 10.99 0.00 38.24 3.71
595 596 5.774690 AGCTTTTGGAAATACAACTGGATCA 59.225 36.000 0.00 0.00 0.00 2.92
668 670 1.823041 GCTGAAGATGCCCTCAGCC 60.823 63.158 12.03 0.00 46.88 4.85
669 671 1.523258 CTGAAGATGCCCTCAGCCG 60.523 63.158 0.00 0.00 42.71 5.52
670 672 2.203126 GAAGATGCCCTCAGCCGG 60.203 66.667 0.00 0.00 42.71 6.13
682 684 4.774503 AGCCGGCAAGCTGCTCTC 62.775 66.667 31.54 0.00 44.28 3.20
683 685 4.774503 GCCGGCAAGCTGCTCTCT 62.775 66.667 24.80 0.00 44.28 3.10
684 686 2.818714 CCGGCAAGCTGCTCTCTG 60.819 66.667 1.00 0.00 44.28 3.35
685 687 2.047465 CGGCAAGCTGCTCTCTGT 60.047 61.111 1.00 0.00 44.28 3.41
686 688 2.389020 CGGCAAGCTGCTCTCTGTG 61.389 63.158 1.00 0.00 44.28 3.66
687 689 2.688794 GGCAAGCTGCTCTCTGTGC 61.689 63.158 13.41 13.41 44.28 4.57
688 690 1.964891 GCAAGCTGCTCTCTGTGCA 60.965 57.895 16.12 0.00 40.96 4.57
689 691 1.512996 GCAAGCTGCTCTCTGTGCAA 61.513 55.000 16.12 0.00 40.96 4.08
690 692 0.237761 CAAGCTGCTCTCTGTGCAAC 59.762 55.000 1.00 0.00 40.13 4.17
691 693 0.108207 AAGCTGCTCTCTGTGCAACT 59.892 50.000 1.00 0.00 40.13 3.16
692 694 0.603172 AGCTGCTCTCTGTGCAACTG 60.603 55.000 0.00 0.00 40.13 3.16
693 695 1.867615 CTGCTCTCTGTGCAACTGC 59.132 57.895 0.00 0.00 40.13 4.40
704 706 4.292208 CAACTGCAACGCGTCGCA 62.292 61.111 25.06 25.06 36.52 5.10
794 796 2.432300 ATCCGGTCCGTCCATCCAC 61.432 63.158 11.06 0.00 35.57 4.02
800 802 0.250124 GTCCGTCCATCCACACACAA 60.250 55.000 0.00 0.00 0.00 3.33
883 886 2.067197 CCCACCTTCTTCCTCCGTT 58.933 57.895 0.00 0.00 0.00 4.44
884 887 0.036294 CCCACCTTCTTCCTCCGTTC 60.036 60.000 0.00 0.00 0.00 3.95
886 889 0.685097 CACCTTCTTCCTCCGTTCCA 59.315 55.000 0.00 0.00 0.00 3.53
898 903 5.698104 TCCTCCGTTCCACTCTATATAACA 58.302 41.667 0.00 0.00 0.00 2.41
944 950 2.667536 ATCGCAGCATCCGCATCC 60.668 61.111 0.00 0.00 42.27 3.51
947 953 4.881440 GCAGCATCCGCATCCCCA 62.881 66.667 0.00 0.00 42.27 4.96
948 954 2.114625 CAGCATCCGCATCCCCAT 59.885 61.111 0.00 0.00 42.27 4.00
953 962 3.818105 ATCCGCATCCCCATCCCCT 62.818 63.158 0.00 0.00 0.00 4.79
960 993 2.275715 ATCCCCATCCCCTCTCAGCA 62.276 60.000 0.00 0.00 0.00 4.41
977 1019 0.820871 GCACACACCTTCCAACCAAA 59.179 50.000 0.00 0.00 0.00 3.28
1314 1401 0.251341 ACAAGAAGCCCACCATCACC 60.251 55.000 0.00 0.00 0.00 4.02
1414 1501 1.502231 CGTCACCAAGTTCACCTCAG 58.498 55.000 0.00 0.00 0.00 3.35
1441 1535 1.656095 CGTCTTCCTCGTTTCATGAGC 59.344 52.381 0.00 0.00 29.93 4.26
1577 1683 6.096695 ACGTGTGCTTGTTTTATTCAGTTTT 58.903 32.000 0.00 0.00 0.00 2.43
1602 1708 1.675116 GGAAGGTTCTTCTGTACGCCC 60.675 57.143 7.47 0.00 0.00 6.13
1614 1720 0.815734 GTACGCCCTGCTACTTCTCA 59.184 55.000 0.00 0.00 0.00 3.27
1651 1757 5.950883 TGAATCTGGTTCTGTAGTTCGTAG 58.049 41.667 1.90 0.00 37.72 3.51
1668 1822 2.165641 CGTAGGTCTGCAGGTACATTCA 59.834 50.000 15.13 0.00 0.00 2.57
1683 1837 6.015180 AGGTACATTCATGATTTTGCAGTTGT 60.015 34.615 0.00 0.00 0.00 3.32
1687 1841 8.075593 ACATTCATGATTTTGCAGTTGTTTAC 57.924 30.769 0.00 0.00 0.00 2.01
1688 1842 7.710044 ACATTCATGATTTTGCAGTTGTTTACA 59.290 29.630 0.00 0.00 0.00 2.41
1689 1843 7.697352 TTCATGATTTTGCAGTTGTTTACAG 57.303 32.000 0.00 0.00 0.00 2.74
1698 1852 8.439993 TTTGCAGTTGTTTACAGTAGATGTTA 57.560 30.769 0.00 0.00 39.96 2.41
1719 1873 7.051623 TGTTATCAGGTTTATCATTTAGGCGT 58.948 34.615 0.00 0.00 0.00 5.68
1729 1883 8.774586 GTTTATCATTTAGGCGTCATACTGAAT 58.225 33.333 0.00 0.00 0.00 2.57
1757 1911 1.453155 CTCTACGGTTGCTGGCATTT 58.547 50.000 0.00 0.00 0.00 2.32
1765 1919 3.367292 CGGTTGCTGGCATTTGAGTAAAT 60.367 43.478 0.00 0.00 36.97 1.40
1776 1930 5.574443 GCATTTGAGTAAATCTGAAGTTGGC 59.426 40.000 0.00 0.00 34.34 4.52
1796 1950 4.237724 GGCCAGCTTTGTTAATTTCTGAC 58.762 43.478 0.00 0.00 0.00 3.51
1798 1952 4.556699 GCCAGCTTTGTTAATTTCTGACGT 60.557 41.667 0.00 0.00 0.00 4.34
1800 1954 4.911610 CAGCTTTGTTAATTTCTGACGTGG 59.088 41.667 0.00 0.00 0.00 4.94
1801 1955 4.578928 AGCTTTGTTAATTTCTGACGTGGT 59.421 37.500 0.00 0.00 0.00 4.16
1802 1956 4.909880 GCTTTGTTAATTTCTGACGTGGTC 59.090 41.667 0.00 0.00 0.00 4.02
1803 1957 5.504994 GCTTTGTTAATTTCTGACGTGGTCA 60.505 40.000 0.00 0.00 40.50 4.02
1852 2012 6.957920 TCCATCAAGAACATGTCTGAAAAA 57.042 33.333 0.00 0.00 36.40 1.94
1860 2020 9.695526 CAAGAACATGTCTGAAAAATTGGAATA 57.304 29.630 0.00 0.00 36.40 1.75
1862 2022 9.865321 AGAACATGTCTGAAAAATTGGAATATG 57.135 29.630 0.00 0.00 34.29 1.78
1863 2023 9.643693 GAACATGTCTGAAAAATTGGAATATGT 57.356 29.630 0.00 0.00 0.00 2.29
1885 2045 8.632906 ATGTTTGATTCAGAGAAATCAGAAGT 57.367 30.769 0.24 0.00 44.23 3.01
1924 2084 8.709386 TCAGAGAAATTAGATGCTTTCTACAC 57.291 34.615 0.00 0.00 40.77 2.90
1965 2125 3.317603 AGCATTGTGCCCATGTTTTAC 57.682 42.857 0.00 0.00 46.52 2.01
2137 2302 9.260002 AGTGAAAATAAAGCTACCAATTTTGTG 57.740 29.630 10.95 0.00 33.03 3.33
2142 2307 5.869649 AAAGCTACCAATTTTGTGAAGGT 57.130 34.783 0.00 0.00 36.40 3.50
2241 2406 0.249031 GCAATAGCCATTTGCCGTCC 60.249 55.000 4.90 0.00 42.84 4.79
2244 2409 2.071778 ATAGCCATTTGCCGTCCATT 57.928 45.000 0.00 0.00 42.71 3.16
2245 2410 1.846007 TAGCCATTTGCCGTCCATTT 58.154 45.000 0.00 0.00 42.71 2.32
2256 2421 2.296792 CCGTCCATTTGATATGCACCA 58.703 47.619 0.00 0.00 0.00 4.17
2272 2437 2.029649 GCACCAACTGCACATTCTTCAT 60.030 45.455 0.00 0.00 46.29 2.57
2274 2439 2.821969 ACCAACTGCACATTCTTCATCC 59.178 45.455 0.00 0.00 0.00 3.51
2296 2461 0.535102 GGGTATGGGAGCGGTTCATG 60.535 60.000 12.56 0.00 0.00 3.07
2312 2477 5.460646 GGTTCATGTTCGTGTTTTGATGAT 58.539 37.500 0.00 0.00 0.00 2.45
2316 2481 7.195839 TCATGTTCGTGTTTTGATGATGTTA 57.804 32.000 0.00 0.00 0.00 2.41
2324 2489 9.767684 TCGTGTTTTGATGATGTTATTATTCAC 57.232 29.630 0.00 0.00 0.00 3.18
2325 2490 9.773328 CGTGTTTTGATGATGTTATTATTCACT 57.227 29.630 0.00 0.00 0.00 3.41
2331 2496 8.146479 TGATGATGTTATTATTCACTCTGTGC 57.854 34.615 0.00 0.00 32.98 4.57
2332 2497 7.769970 TGATGATGTTATTATTCACTCTGTGCA 59.230 33.333 0.00 0.00 32.98 4.57
2333 2498 8.687292 ATGATGTTATTATTCACTCTGTGCAT 57.313 30.769 0.00 0.00 32.98 3.96
2334 2499 8.510243 TGATGTTATTATTCACTCTGTGCATT 57.490 30.769 0.00 0.00 32.98 3.56
2335 2500 8.959548 TGATGTTATTATTCACTCTGTGCATTT 58.040 29.630 0.00 0.00 32.98 2.32
2336 2501 9.229784 GATGTTATTATTCACTCTGTGCATTTG 57.770 33.333 0.00 0.00 32.98 2.32
2337 2502 8.334263 TGTTATTATTCACTCTGTGCATTTGA 57.666 30.769 0.00 0.00 32.98 2.69
2338 2503 8.791675 TGTTATTATTCACTCTGTGCATTTGAA 58.208 29.630 0.00 0.00 32.98 2.69
2339 2504 9.624697 GTTATTATTCACTCTGTGCATTTGAAA 57.375 29.630 0.00 0.00 32.98 2.69
2341 2506 7.928908 TTATTCACTCTGTGCATTTGAAAAC 57.071 32.000 0.00 0.00 32.98 2.43
2342 2507 4.305989 TCACTCTGTGCATTTGAAAACC 57.694 40.909 0.00 0.00 32.98 3.27
2343 2508 3.044986 CACTCTGTGCATTTGAAAACCG 58.955 45.455 0.00 0.00 0.00 4.44
2344 2509 2.948979 ACTCTGTGCATTTGAAAACCGA 59.051 40.909 0.00 0.00 0.00 4.69
2345 2510 3.380004 ACTCTGTGCATTTGAAAACCGAA 59.620 39.130 0.00 0.00 0.00 4.30
2346 2511 3.701241 TCTGTGCATTTGAAAACCGAAC 58.299 40.909 0.00 0.00 0.00 3.95
2347 2512 2.794350 CTGTGCATTTGAAAACCGAACC 59.206 45.455 0.00 0.00 0.00 3.62
2348 2513 2.166459 TGTGCATTTGAAAACCGAACCA 59.834 40.909 0.00 0.00 0.00 3.67
2349 2514 3.190874 GTGCATTTGAAAACCGAACCAA 58.809 40.909 0.00 0.00 0.00 3.67
2350 2515 3.619038 GTGCATTTGAAAACCGAACCAAA 59.381 39.130 0.00 0.00 33.72 3.28
2351 2516 4.093556 GTGCATTTGAAAACCGAACCAAAA 59.906 37.500 0.00 0.00 33.05 2.44
2352 2517 4.695455 TGCATTTGAAAACCGAACCAAAAA 59.305 33.333 0.00 0.00 33.05 1.94
2373 2538 6.572167 AAAACCATACCGAAAATAAACCGA 57.428 33.333 0.00 0.00 0.00 4.69
2374 2539 6.572167 AAACCATACCGAAAATAAACCGAA 57.428 33.333 0.00 0.00 0.00 4.30
2375 2540 5.550232 ACCATACCGAAAATAAACCGAAC 57.450 39.130 0.00 0.00 0.00 3.95
2376 2541 4.395854 ACCATACCGAAAATAAACCGAACC 59.604 41.667 0.00 0.00 0.00 3.62
2377 2542 4.494526 CCATACCGAAAATAAACCGAACCG 60.495 45.833 0.00 0.00 0.00 4.44
2378 2543 2.765122 ACCGAAAATAAACCGAACCGA 58.235 42.857 0.00 0.00 0.00 4.69
2379 2544 3.137533 ACCGAAAATAAACCGAACCGAA 58.862 40.909 0.00 0.00 0.00 4.30
2380 2545 3.058983 ACCGAAAATAAACCGAACCGAAC 60.059 43.478 0.00 0.00 0.00 3.95
2381 2546 3.481839 CGAAAATAAACCGAACCGAACC 58.518 45.455 0.00 0.00 0.00 3.62
2382 2547 3.481839 GAAAATAAACCGAACCGAACCG 58.518 45.455 0.00 0.00 0.00 4.44
2383 2548 2.453983 AATAAACCGAACCGAACCGA 57.546 45.000 0.00 0.00 0.00 4.69
2384 2549 2.678471 ATAAACCGAACCGAACCGAT 57.322 45.000 0.00 0.00 0.00 4.18
2385 2550 2.453983 TAAACCGAACCGAACCGATT 57.546 45.000 0.00 0.00 0.00 3.34
2386 2551 1.596603 AAACCGAACCGAACCGATTT 58.403 45.000 0.00 0.00 0.00 2.17
2387 2552 1.596603 AACCGAACCGAACCGATTTT 58.403 45.000 0.00 0.00 0.00 1.82
2388 2553 2.453983 ACCGAACCGAACCGATTTTA 57.546 45.000 0.00 0.00 0.00 1.52
2389 2554 2.976589 ACCGAACCGAACCGATTTTAT 58.023 42.857 0.00 0.00 0.00 1.40
2390 2555 2.674357 ACCGAACCGAACCGATTTTATG 59.326 45.455 0.00 0.00 0.00 1.90
2391 2556 2.031191 CCGAACCGAACCGATTTTATGG 59.969 50.000 0.00 0.00 0.00 2.74
2392 2557 2.674357 CGAACCGAACCGATTTTATGGT 59.326 45.455 0.00 0.00 41.20 3.55
2404 2569 8.766000 ACCGATTTTATGGTTTTTATGGTTTC 57.234 30.769 0.00 0.00 33.81 2.78
2405 2570 8.590204 ACCGATTTTATGGTTTTTATGGTTTCT 58.410 29.630 0.00 0.00 33.81 2.52
2406 2571 8.868916 CCGATTTTATGGTTTTTATGGTTTCTG 58.131 33.333 0.00 0.00 0.00 3.02
2407 2572 8.868916 CGATTTTATGGTTTTTATGGTTTCTGG 58.131 33.333 0.00 0.00 0.00 3.86
2408 2573 9.719355 GATTTTATGGTTTTTATGGTTTCTGGT 57.281 29.630 0.00 0.00 0.00 4.00
2410 2575 9.907229 TTTTATGGTTTTTATGGTTTCTGGTTT 57.093 25.926 0.00 0.00 0.00 3.27
2411 2576 9.549078 TTTATGGTTTTTATGGTTTCTGGTTTC 57.451 29.630 0.00 0.00 0.00 2.78
2412 2577 5.593010 TGGTTTTTATGGTTTCTGGTTTCG 58.407 37.500 0.00 0.00 0.00 3.46
2413 2578 4.986034 GGTTTTTATGGTTTCTGGTTTCGG 59.014 41.667 0.00 0.00 0.00 4.30
2414 2579 5.452216 GGTTTTTATGGTTTCTGGTTTCGGT 60.452 40.000 0.00 0.00 0.00 4.69
2415 2580 6.238981 GGTTTTTATGGTTTCTGGTTTCGGTA 60.239 38.462 0.00 0.00 0.00 4.02
2416 2581 7.372714 GTTTTTATGGTTTCTGGTTTCGGTAT 58.627 34.615 0.00 0.00 0.00 2.73
2417 2582 6.503589 TTTATGGTTTCTGGTTTCGGTATG 57.496 37.500 0.00 0.00 0.00 2.39
2418 2583 2.785562 TGGTTTCTGGTTTCGGTATGG 58.214 47.619 0.00 0.00 0.00 2.74
2419 2584 2.106857 TGGTTTCTGGTTTCGGTATGGT 59.893 45.455 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 2.125106 GAGCGTTTCCCAGGCGAT 60.125 61.111 0.00 0.00 41.47 4.58
194 195 3.444805 GCGCCGGAGAGACTCACT 61.445 66.667 10.31 0.00 31.08 3.41
234 235 3.071837 TACCATGCGGCGTCTCCA 61.072 61.111 9.37 0.00 34.57 3.86
278 279 3.195002 CGGCCGTCACGCAATCAT 61.195 61.111 19.50 0.00 0.00 2.45
473 474 1.452773 CGTCGGACGAATCGTTTTTGA 59.547 47.619 25.29 3.01 46.05 2.69
538 539 0.527817 CTCGGGTCGAAATTAGCGCT 60.528 55.000 17.26 17.26 34.74 5.92
543 544 1.142314 CCGGCTCGGGTCGAAATTA 59.858 57.895 12.88 0.00 44.06 1.40
610 611 6.268566 GTCCTATAAGTATGTTTTCGTCCGT 58.731 40.000 0.00 0.00 0.00 4.69
623 624 4.900054 GCCTCCAAGAAGGTCCTATAAGTA 59.100 45.833 0.00 0.00 38.79 2.24
624 625 3.712218 GCCTCCAAGAAGGTCCTATAAGT 59.288 47.826 0.00 0.00 38.79 2.24
625 626 3.243907 CGCCTCCAAGAAGGTCCTATAAG 60.244 52.174 0.00 0.00 38.79 1.73
628 629 1.123928 CGCCTCCAAGAAGGTCCTAT 58.876 55.000 0.00 0.00 38.79 2.57
629 630 1.614241 GCGCCTCCAAGAAGGTCCTA 61.614 60.000 0.00 0.00 38.79 2.94
668 670 2.047465 ACAGAGAGCAGCTTGCCG 60.047 61.111 0.00 0.00 46.52 5.69
669 671 2.688794 GCACAGAGAGCAGCTTGCC 61.689 63.158 4.87 0.00 46.52 4.52
670 672 1.512996 TTGCACAGAGAGCAGCTTGC 61.513 55.000 8.81 8.81 43.75 4.01
671 673 0.237761 GTTGCACAGAGAGCAGCTTG 59.762 55.000 0.00 0.00 43.75 4.01
672 674 2.626582 GTTGCACAGAGAGCAGCTT 58.373 52.632 0.00 0.00 43.75 3.74
673 675 1.753470 AGTTGCACAGAGAGCAGCT 59.247 52.632 0.00 0.00 46.57 4.24
674 676 1.867615 CAGTTGCACAGAGAGCAGC 59.132 57.895 0.00 0.00 43.75 5.25
675 677 1.867615 GCAGTTGCACAGAGAGCAG 59.132 57.895 0.00 0.00 43.75 4.24
676 678 4.054085 GCAGTTGCACAGAGAGCA 57.946 55.556 0.00 0.00 41.59 4.26
687 689 4.292208 TGCGACGCGTTGCAGTTG 62.292 61.111 42.33 12.41 44.49 3.16
703 705 3.320879 ATCGACAGTGGCCTGGCTG 62.321 63.158 19.68 11.76 45.26 4.85
704 706 3.005539 ATCGACAGTGGCCTGGCT 61.006 61.111 19.68 0.00 45.26 4.75
705 707 2.512515 GATCGACAGTGGCCTGGC 60.513 66.667 11.05 11.05 43.87 4.85
706 708 2.202797 CGATCGACAGTGGCCTGG 60.203 66.667 10.26 0.00 43.36 4.45
707 709 1.517257 GTCGATCGACAGTGGCCTG 60.517 63.158 36.61 0.00 44.02 4.85
708 710 2.711922 GGTCGATCGACAGTGGCCT 61.712 63.158 39.98 0.00 46.20 5.19
709 711 2.202756 GGTCGATCGACAGTGGCC 60.203 66.667 39.98 23.85 46.20 5.36
710 712 2.579787 CGGTCGATCGACAGTGGC 60.580 66.667 39.98 25.36 46.20 5.01
711 713 3.184206 TCGGTCGATCGACAGTGG 58.816 61.111 39.98 27.66 46.20 4.00
794 796 2.235016 AGCCGTTCGTCGTTGTGTG 61.235 57.895 0.00 0.00 37.94 3.82
800 802 0.311790 TAGTTTCAGCCGTTCGTCGT 59.688 50.000 0.00 0.00 37.94 4.34
883 886 5.279809 GGCGGGATTTGTTATATAGAGTGGA 60.280 44.000 0.00 0.00 0.00 4.02
884 887 4.935808 GGCGGGATTTGTTATATAGAGTGG 59.064 45.833 0.00 0.00 0.00 4.00
886 889 4.817517 CGGCGGGATTTGTTATATAGAGT 58.182 43.478 0.00 0.00 0.00 3.24
898 903 4.929707 GATCGGGCGGCGGGATTT 62.930 66.667 16.49 0.00 0.00 2.17
912 917 1.592669 CGATGTGTGGAGGCGGATC 60.593 63.158 0.00 0.00 0.00 3.36
944 950 1.997311 TGTGCTGAGAGGGGATGGG 60.997 63.158 0.00 0.00 0.00 4.00
946 952 0.392193 GTGTGTGCTGAGAGGGGATG 60.392 60.000 0.00 0.00 0.00 3.51
947 953 1.557269 GGTGTGTGCTGAGAGGGGAT 61.557 60.000 0.00 0.00 0.00 3.85
948 954 2.217038 GGTGTGTGCTGAGAGGGGA 61.217 63.158 0.00 0.00 0.00 4.81
953 962 0.836606 TTGGAAGGTGTGTGCTGAGA 59.163 50.000 0.00 0.00 0.00 3.27
960 993 2.375146 GAGTTTGGTTGGAAGGTGTGT 58.625 47.619 0.00 0.00 0.00 3.72
977 1019 4.052229 CTTCGACGGCGGTGGAGT 62.052 66.667 12.58 0.00 38.28 3.85
1314 1401 1.834822 GGTCTGGATCTCCCGGGAG 60.835 68.421 40.33 40.33 41.84 4.30
1414 1501 1.946475 AACGAGGAAGACGCCTAGGC 61.946 60.000 24.75 24.75 38.73 3.93
1441 1535 2.434884 ACAGAACGCCGCCATCAG 60.435 61.111 0.00 0.00 0.00 2.90
1577 1683 3.493699 CGTACAGAAGAACCTTCCAACCA 60.494 47.826 3.33 0.00 0.00 3.67
1602 1708 5.112220 TGCACAAAAATGAGAAGTAGCAG 57.888 39.130 0.00 0.00 0.00 4.24
1614 1720 4.586001 ACCAGATTCAGACTGCACAAAAAT 59.414 37.500 0.00 0.00 34.47 1.82
1651 1757 3.266510 TCATGAATGTACCTGCAGACC 57.733 47.619 17.39 2.57 0.00 3.85
1668 1822 8.165239 TCTACTGTAAACAACTGCAAAATCAT 57.835 30.769 0.00 0.00 0.00 2.45
1698 1852 5.680619 TGACGCCTAAATGATAAACCTGAT 58.319 37.500 0.00 0.00 0.00 2.90
1719 1873 7.333423 CCGTAGAGGTTGAAAAATTCAGTATGA 59.667 37.037 0.00 0.00 41.38 2.15
1749 1903 6.506500 ACTTCAGATTTACTCAAATGCCAG 57.493 37.500 0.00 0.00 34.44 4.85
1752 1906 5.574443 GCCAACTTCAGATTTACTCAAATGC 59.426 40.000 0.00 0.00 34.44 3.56
1757 1911 4.326826 CTGGCCAACTTCAGATTTACTCA 58.673 43.478 7.01 0.00 33.11 3.41
1765 1919 1.321474 CAAAGCTGGCCAACTTCAGA 58.679 50.000 21.37 0.00 33.11 3.27
1776 1930 4.911610 CACGTCAGAAATTAACAAAGCTGG 59.088 41.667 0.00 0.00 0.00 4.85
1826 1986 4.520179 TCAGACATGTTCTTGATGGATGG 58.480 43.478 0.00 0.00 28.96 3.51
1860 2020 8.632906 ACTTCTGATTTCTCTGAATCAAACAT 57.367 30.769 2.42 0.00 43.35 2.71
1861 2021 8.455903 AACTTCTGATTTCTCTGAATCAAACA 57.544 30.769 2.42 0.00 43.35 2.83
1862 2022 9.741647 AAAACTTCTGATTTCTCTGAATCAAAC 57.258 29.630 2.42 0.00 43.35 2.93
1863 2023 9.956720 GAAAACTTCTGATTTCTCTGAATCAAA 57.043 29.630 2.42 0.76 43.35 2.69
1864 2024 9.347240 AGAAAACTTCTGATTTCTCTGAATCAA 57.653 29.630 2.42 0.00 43.35 2.57
1865 2025 8.915057 AGAAAACTTCTGATTTCTCTGAATCA 57.085 30.769 0.13 0.97 39.92 2.57
1883 2043 8.953368 ATTTCTCTGAAAATTTGCAGAAAACT 57.047 26.923 25.71 13.41 40.33 2.66
1921 2081 7.333174 GCTTCTAGCTTATCTCTTCTTTTGTGT 59.667 37.037 0.00 0.00 38.45 3.72
1924 2084 7.840342 TGCTTCTAGCTTATCTCTTCTTTTG 57.160 36.000 0.00 0.00 42.97 2.44
2019 2179 9.624697 GTGTCTCAATAGCAACAATTATCAAAA 57.375 29.630 0.00 0.00 0.00 2.44
2024 2184 7.112122 TCAGGTGTCTCAATAGCAACAATTAT 58.888 34.615 0.00 0.00 0.00 1.28
2033 2193 5.948992 AAAAACTCAGGTGTCTCAATAGC 57.051 39.130 0.00 0.00 0.00 2.97
2137 2302 7.856145 ATCATTAGATTCACTTCACACCTTC 57.144 36.000 0.00 0.00 0.00 3.46
2256 2421 3.508793 CCAAGGATGAAGAATGTGCAGTT 59.491 43.478 0.00 0.00 0.00 3.16
2272 2437 2.070039 CCGCTCCCATACCCAAGGA 61.070 63.158 0.00 0.00 0.00 3.36
2274 2439 0.463833 GAACCGCTCCCATACCCAAG 60.464 60.000 0.00 0.00 0.00 3.61
2312 2477 8.334263 TCAAATGCACAGAGTGAATAATAACA 57.666 30.769 0.58 0.00 29.16 2.41
2316 2481 7.599998 GGTTTTCAAATGCACAGAGTGAATAAT 59.400 33.333 0.58 0.00 29.16 1.28
2321 2486 3.243035 CGGTTTTCAAATGCACAGAGTGA 60.243 43.478 0.58 0.00 35.23 3.41
2322 2487 3.044986 CGGTTTTCAAATGCACAGAGTG 58.955 45.455 0.00 0.00 36.51 3.51
2323 2488 2.948979 TCGGTTTTCAAATGCACAGAGT 59.051 40.909 0.00 0.00 0.00 3.24
2324 2489 3.624326 TCGGTTTTCAAATGCACAGAG 57.376 42.857 0.00 0.00 0.00 3.35
2325 2490 3.490078 GGTTCGGTTTTCAAATGCACAGA 60.490 43.478 0.00 0.00 0.00 3.41
2326 2491 2.794350 GGTTCGGTTTTCAAATGCACAG 59.206 45.455 0.00 0.00 0.00 3.66
2327 2492 2.166459 TGGTTCGGTTTTCAAATGCACA 59.834 40.909 0.00 0.00 0.00 4.57
2328 2493 2.815478 TGGTTCGGTTTTCAAATGCAC 58.185 42.857 0.00 0.00 0.00 4.57
2329 2494 3.526931 TTGGTTCGGTTTTCAAATGCA 57.473 38.095 0.00 0.00 0.00 3.96
2330 2495 4.866682 TTTTGGTTCGGTTTTCAAATGC 57.133 36.364 0.00 0.00 0.00 3.56
2349 2514 6.979465 TCGGTTTATTTTCGGTATGGTTTTT 58.021 32.000 0.00 0.00 0.00 1.94
2350 2515 6.572167 TCGGTTTATTTTCGGTATGGTTTT 57.428 33.333 0.00 0.00 0.00 2.43
2351 2516 6.380995 GTTCGGTTTATTTTCGGTATGGTTT 58.619 36.000 0.00 0.00 0.00 3.27
2352 2517 5.106197 GGTTCGGTTTATTTTCGGTATGGTT 60.106 40.000 0.00 0.00 0.00 3.67
2353 2518 4.395854 GGTTCGGTTTATTTTCGGTATGGT 59.604 41.667 0.00 0.00 0.00 3.55
2354 2519 4.494526 CGGTTCGGTTTATTTTCGGTATGG 60.495 45.833 0.00 0.00 0.00 2.74
2355 2520 4.329528 TCGGTTCGGTTTATTTTCGGTATG 59.670 41.667 0.00 0.00 0.00 2.39
2356 2521 4.502962 TCGGTTCGGTTTATTTTCGGTAT 58.497 39.130 0.00 0.00 0.00 2.73
2357 2522 3.919216 TCGGTTCGGTTTATTTTCGGTA 58.081 40.909 0.00 0.00 0.00 4.02
2358 2523 2.765122 TCGGTTCGGTTTATTTTCGGT 58.235 42.857 0.00 0.00 0.00 4.69
2359 2524 3.481839 GTTCGGTTCGGTTTATTTTCGG 58.518 45.455 0.00 0.00 0.00 4.30
2360 2525 3.481839 GGTTCGGTTCGGTTTATTTTCG 58.518 45.455 0.00 0.00 0.00 3.46
2361 2526 3.186205 TCGGTTCGGTTCGGTTTATTTTC 59.814 43.478 0.00 0.00 0.00 2.29
2362 2527 3.137533 TCGGTTCGGTTCGGTTTATTTT 58.862 40.909 0.00 0.00 0.00 1.82
2363 2528 2.765122 TCGGTTCGGTTCGGTTTATTT 58.235 42.857 0.00 0.00 0.00 1.40
2364 2529 2.453983 TCGGTTCGGTTCGGTTTATT 57.546 45.000 0.00 0.00 0.00 1.40
2365 2530 2.678471 ATCGGTTCGGTTCGGTTTAT 57.322 45.000 0.00 0.00 0.00 1.40
2366 2531 2.453983 AATCGGTTCGGTTCGGTTTA 57.546 45.000 0.00 0.00 0.00 2.01
2367 2532 1.596603 AAATCGGTTCGGTTCGGTTT 58.403 45.000 0.00 0.00 35.25 3.27
2368 2533 1.596603 AAAATCGGTTCGGTTCGGTT 58.403 45.000 0.00 0.00 26.80 4.44
2369 2534 2.453983 TAAAATCGGTTCGGTTCGGT 57.546 45.000 0.00 0.00 26.80 4.69
2370 2535 2.031191 CCATAAAATCGGTTCGGTTCGG 59.969 50.000 0.00 0.00 26.80 4.30
2371 2536 2.674357 ACCATAAAATCGGTTCGGTTCG 59.326 45.455 0.00 0.00 28.43 3.95
2372 2537 4.690184 AACCATAAAATCGGTTCGGTTC 57.310 40.909 0.00 0.00 41.79 3.62
2373 2538 5.456548 AAAACCATAAAATCGGTTCGGTT 57.543 34.783 0.00 0.00 44.80 4.44
2374 2539 5.456548 AAAAACCATAAAATCGGTTCGGT 57.543 34.783 0.00 0.00 44.80 4.69
2375 2540 6.474102 CCATAAAAACCATAAAATCGGTTCGG 59.526 38.462 0.00 0.00 44.80 4.30
2376 2541 7.030768 ACCATAAAAACCATAAAATCGGTTCG 58.969 34.615 0.00 0.00 44.80 3.95
2377 2542 8.766000 AACCATAAAAACCATAAAATCGGTTC 57.234 30.769 0.00 0.00 44.80 3.62
2379 2544 8.590204 AGAAACCATAAAAACCATAAAATCGGT 58.410 29.630 0.00 0.00 36.98 4.69
2380 2545 8.868916 CAGAAACCATAAAAACCATAAAATCGG 58.131 33.333 0.00 0.00 0.00 4.18
2381 2546 8.868916 CCAGAAACCATAAAAACCATAAAATCG 58.131 33.333 0.00 0.00 0.00 3.34
2382 2547 9.719355 ACCAGAAACCATAAAAACCATAAAATC 57.281 29.630 0.00 0.00 0.00 2.17
2384 2549 9.907229 AAACCAGAAACCATAAAAACCATAAAA 57.093 25.926 0.00 0.00 0.00 1.52
2385 2550 9.549078 GAAACCAGAAACCATAAAAACCATAAA 57.451 29.630 0.00 0.00 0.00 1.40
2386 2551 7.868415 CGAAACCAGAAACCATAAAAACCATAA 59.132 33.333 0.00 0.00 0.00 1.90
2387 2552 7.371936 CGAAACCAGAAACCATAAAAACCATA 58.628 34.615 0.00 0.00 0.00 2.74
2388 2553 6.220201 CGAAACCAGAAACCATAAAAACCAT 58.780 36.000 0.00 0.00 0.00 3.55
2389 2554 5.452077 CCGAAACCAGAAACCATAAAAACCA 60.452 40.000 0.00 0.00 0.00 3.67
2390 2555 4.986034 CCGAAACCAGAAACCATAAAAACC 59.014 41.667 0.00 0.00 0.00 3.27
2391 2556 5.593968 ACCGAAACCAGAAACCATAAAAAC 58.406 37.500 0.00 0.00 0.00 2.43
2392 2557 5.855740 ACCGAAACCAGAAACCATAAAAA 57.144 34.783 0.00 0.00 0.00 1.94
2393 2558 6.071840 CCATACCGAAACCAGAAACCATAAAA 60.072 38.462 0.00 0.00 0.00 1.52
2394 2559 5.416326 CCATACCGAAACCAGAAACCATAAA 59.584 40.000 0.00 0.00 0.00 1.40
2395 2560 4.944930 CCATACCGAAACCAGAAACCATAA 59.055 41.667 0.00 0.00 0.00 1.90
2396 2561 4.019141 ACCATACCGAAACCAGAAACCATA 60.019 41.667 0.00 0.00 0.00 2.74
2397 2562 3.245122 ACCATACCGAAACCAGAAACCAT 60.245 43.478 0.00 0.00 0.00 3.55
2398 2563 2.106857 ACCATACCGAAACCAGAAACCA 59.893 45.455 0.00 0.00 0.00 3.67
2399 2564 2.786777 ACCATACCGAAACCAGAAACC 58.213 47.619 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.