Multiple sequence alignment - TraesCS1D01G254400

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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 TraesCS1D01G254400 chr1D 100.000 8366 0 0 1 8366 346401441 346393076 0.000000e+00 15450.0
1 TraesCS1D01G254400 chr1D 89.908 218 15 4 1 218 393121118 393121328 2.980000e-69 274.0
2 TraesCS1D01G254400 chr1D 97.917 48 1 0 243 290 393121325 393121372 5.380000e-12 84.2
3 TraesCS1D01G254400 chr1D 97.917 48 1 0 243 290 475305017 475304970 5.380000e-12 84.2
4 TraesCS1D01G254400 chr1A 97.738 4112 49 14 2633 6725 446547236 446543150 0.000000e+00 7038.0
5 TraesCS1D01G254400 chr1A 96.720 1677 50 5 165 1839 446548891 446547218 0.000000e+00 2787.0
6 TraesCS1D01G254400 chr1A 93.894 1261 59 11 7118 8366 446542731 446541477 0.000000e+00 1886.0
7 TraesCS1D01G254400 chr1A 91.294 425 22 2 6668 7077 446543152 446542728 4.380000e-157 566.0
8 TraesCS1D01G254400 chr1A 86.957 92 12 0 6910 7001 409855356 409855447 4.130000e-18 104.0
9 TraesCS1D01G254400 chr1B 94.830 3849 119 35 2634 6453 463526940 463530737 0.000000e+00 5932.0
10 TraesCS1D01G254400 chr1B 91.575 1733 82 21 6659 8366 463530954 463532647 0.000000e+00 2333.0
11 TraesCS1D01G254400 chr1B 94.945 1009 37 9 835 1839 463525959 463526957 0.000000e+00 1568.0
12 TraesCS1D01G254400 chr1B 88.075 805 66 10 1859 2636 654516884 654516083 0.000000e+00 928.0
13 TraesCS1D01G254400 chr1B 92.759 290 20 1 241 530 463525504 463525792 1.300000e-112 418.0
14 TraesCS1D01G254400 chr1B 94.091 220 11 1 6498 6717 463530738 463530955 4.840000e-87 333.0
15 TraesCS1D01G254400 chr1B 92.130 216 11 4 1 212 463525185 463525398 4.910000e-77 300.0
16 TraesCS1D01G254400 chr7D 90.821 828 51 2 1838 2641 629651451 629650625 0.000000e+00 1085.0
17 TraesCS1D01G254400 chr7D 87.229 830 69 13 1833 2636 16173085 16173903 0.000000e+00 911.0
18 TraesCS1D01G254400 chr7D 89.863 730 44 11 1932 2636 195272543 195271819 0.000000e+00 911.0
19 TraesCS1D01G254400 chr7D 85.855 509 48 4 1843 2327 16243965 16244473 3.460000e-143 520.0
20 TraesCS1D01G254400 chr3B 88.285 828 67 15 1836 2636 804851278 804850454 0.000000e+00 965.0
21 TraesCS1D01G254400 chr3B 77.553 842 136 37 1836 2636 559097212 559096383 7.650000e-125 459.0
22 TraesCS1D01G254400 chr3B 87.640 89 11 0 6913 7001 804117566 804117478 4.130000e-18 104.0
23 TraesCS1D01G254400 chr3B 85.882 85 7 4 6910 6994 431583451 431583530 1.500000e-12 86.1
24 TraesCS1D01G254400 chr7B 87.923 828 69 15 1836 2636 423144188 423143365 0.000000e+00 946.0
25 TraesCS1D01G254400 chr7B 87.798 672 54 9 1990 2636 234376573 234377241 0.000000e+00 761.0
26 TraesCS1D01G254400 chr7B 77.976 840 134 40 1836 2636 11873341 11872514 5.870000e-131 479.0
27 TraesCS1D01G254400 chr7B 77.896 846 134 41 1833 2636 321348626 321349460 2.110000e-130 477.0
28 TraesCS1D01G254400 chr7B 89.908 218 15 4 1 218 655564522 655564732 2.980000e-69 274.0
29 TraesCS1D01G254400 chr6A 87.636 825 75 10 1836 2636 609736879 609736058 0.000000e+00 933.0
30 TraesCS1D01G254400 chr6A 91.026 234 15 4 529 757 230642128 230641896 2.270000e-80 311.0
31 TraesCS1D01G254400 chr6A 91.026 234 15 4 529 757 230646036 230645804 2.270000e-80 311.0
32 TraesCS1D01G254400 chr6A 91.026 234 15 4 529 757 230651626 230651394 2.270000e-80 311.0
33 TraesCS1D01G254400 chr6A 97.917 48 1 0 243 290 102695604 102695651 5.380000e-12 84.2
34 TraesCS1D01G254400 chr3A 89.256 726 50 10 1936 2636 41374531 41373809 0.000000e+00 883.0
35 TraesCS1D01G254400 chr5D 87.195 492 33 6 1853 2320 51918761 51919246 4.450000e-147 532.0
36 TraesCS1D01G254400 chr5D 88.789 223 15 6 1 218 22210047 22210264 1.790000e-66 265.0
37 TraesCS1D01G254400 chr6B 77.885 832 132 36 1846 2637 672880176 672879357 3.540000e-128 470.0
38 TraesCS1D01G254400 chr6B 88.210 229 19 4 530 757 295973260 295973039 4.980000e-67 267.0
39 TraesCS1D01G254400 chr7A 77.541 846 136 38 1833 2637 18058743 18059575 2.130000e-125 460.0
40 TraesCS1D01G254400 chr4B 77.632 836 132 39 1844 2636 194002499 194003322 2.750000e-124 457.0
41 TraesCS1D01G254400 chr4B 90.826 218 15 3 1 218 506591408 506591196 3.820000e-73 287.0
42 TraesCS1D01G254400 chr4B 84.884 86 13 0 6909 6994 63847129 63847044 4.160000e-13 87.9
43 TraesCS1D01G254400 chr4B 97.917 48 1 0 243 290 57249915 57249868 5.380000e-12 84.2
44 TraesCS1D01G254400 chr4B 97.917 48 1 0 243 290 506591199 506591152 5.380000e-12 84.2
45 TraesCS1D01G254400 chr5A 77.396 845 138 37 1833 2636 554241074 554241906 3.560000e-123 453.0
46 TraesCS1D01G254400 chr5B 77.343 843 139 36 1836 2635 629414445 629413612 1.280000e-122 451.0
47 TraesCS1D01G254400 chr5B 77.404 832 135 37 1846 2636 106805919 106805100 5.960000e-121 446.0
48 TraesCS1D01G254400 chr5B 88.991 218 17 4 1 218 617731253 617731043 6.440000e-66 263.0
49 TraesCS1D01G254400 chr6D 90.213 235 17 4 528 757 423454564 423454797 1.360000e-77 302.0
50 TraesCS1D01G254400 chr6D 100.000 43 0 0 7646 7688 363180567 363180525 6.960000e-11 80.5
51 TraesCS1D01G254400 chr2B 91.866 209 12 2 1 209 735909709 735909912 3.820000e-73 287.0
52 TraesCS1D01G254400 chr2B 88.991 218 19 3 1 218 12408391 12408179 1.790000e-66 265.0
53 TraesCS1D01G254400 chr4A 88.991 218 16 4 1 218 724177185 724177394 6.440000e-66 263.0
54 TraesCS1D01G254400 chr4A 92.708 96 7 0 243 338 175693424 175693329 1.130000e-28 139.0
55 TraesCS1D01G254400 chr4A 85.366 82 12 0 6913 6994 200089246 200089165 1.500000e-12 86.1
56 TraesCS1D01G254400 chr2D 88.679 212 20 3 547 757 19508335 19508543 1.080000e-63 255.0
57 TraesCS1D01G254400 chr3D 86.813 91 10 2 6913 7002 611499113 611499024 5.340000e-17 100.0
58 TraesCS1D01G254400 chr3D 85.393 89 13 0 6913 7001 571465175 571465087 8.940000e-15 93.5
59 TraesCS1D01G254400 chr4D 97.917 48 1 0 243 290 466649676 466649723 5.380000e-12 84.2
60 TraesCS1D01G254400 chr2A 97.059 34 0 1 5590 5622 43144087 43144120 1.000000e-03 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G254400 chr1D 346393076 346401441 8365 True 15450.00 15450 100.000000 1 8366 1 chr1D.!!$R1 8365
1 TraesCS1D01G254400 chr1A 446541477 446548891 7414 True 3069.25 7038 94.911500 165 8366 4 chr1A.!!$R1 8201
2 TraesCS1D01G254400 chr1B 463525185 463532647 7462 False 1814.00 5932 93.388333 1 8366 6 chr1B.!!$F1 8365
3 TraesCS1D01G254400 chr1B 654516083 654516884 801 True 928.00 928 88.075000 1859 2636 1 chr1B.!!$R1 777
4 TraesCS1D01G254400 chr7D 629650625 629651451 826 True 1085.00 1085 90.821000 1838 2641 1 chr7D.!!$R2 803
5 TraesCS1D01G254400 chr7D 16173085 16173903 818 False 911.00 911 87.229000 1833 2636 1 chr7D.!!$F1 803
6 TraesCS1D01G254400 chr7D 195271819 195272543 724 True 911.00 911 89.863000 1932 2636 1 chr7D.!!$R1 704
7 TraesCS1D01G254400 chr7D 16243965 16244473 508 False 520.00 520 85.855000 1843 2327 1 chr7D.!!$F2 484
8 TraesCS1D01G254400 chr3B 804850454 804851278 824 True 965.00 965 88.285000 1836 2636 1 chr3B.!!$R3 800
9 TraesCS1D01G254400 chr3B 559096383 559097212 829 True 459.00 459 77.553000 1836 2636 1 chr3B.!!$R1 800
10 TraesCS1D01G254400 chr7B 423143365 423144188 823 True 946.00 946 87.923000 1836 2636 1 chr7B.!!$R2 800
11 TraesCS1D01G254400 chr7B 234376573 234377241 668 False 761.00 761 87.798000 1990 2636 1 chr7B.!!$F1 646
12 TraesCS1D01G254400 chr7B 11872514 11873341 827 True 479.00 479 77.976000 1836 2636 1 chr7B.!!$R1 800
13 TraesCS1D01G254400 chr7B 321348626 321349460 834 False 477.00 477 77.896000 1833 2636 1 chr7B.!!$F2 803
14 TraesCS1D01G254400 chr6A 609736058 609736879 821 True 933.00 933 87.636000 1836 2636 1 chr6A.!!$R2 800
15 TraesCS1D01G254400 chr6A 230641896 230646036 4140 True 311.00 311 91.026000 529 757 2 chr6A.!!$R3 228
16 TraesCS1D01G254400 chr3A 41373809 41374531 722 True 883.00 883 89.256000 1936 2636 1 chr3A.!!$R1 700
17 TraesCS1D01G254400 chr6B 672879357 672880176 819 True 470.00 470 77.885000 1846 2637 1 chr6B.!!$R2 791
18 TraesCS1D01G254400 chr7A 18058743 18059575 832 False 460.00 460 77.541000 1833 2637 1 chr7A.!!$F1 804
19 TraesCS1D01G254400 chr4B 194002499 194003322 823 False 457.00 457 77.632000 1844 2636 1 chr4B.!!$F1 792
20 TraesCS1D01G254400 chr5A 554241074 554241906 832 False 453.00 453 77.396000 1833 2636 1 chr5A.!!$F1 803
21 TraesCS1D01G254400 chr5B 629413612 629414445 833 True 451.00 451 77.343000 1836 2635 1 chr5B.!!$R3 799
22 TraesCS1D01G254400 chr5B 106805100 106805919 819 True 446.00 446 77.404000 1846 2636 1 chr5B.!!$R1 790

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
245 249 0.538287 AGCTGCCTGAAACAAGGGAC 60.538 55.000 0.00 0.00 37.84 4.46 F
625 706 1.673665 GAGGCTCCTGCAACCACAG 60.674 63.158 2.15 0.00 41.91 3.66 F
2328 4227 1.337823 CCTGGAGGGTGTAGTTGTTCG 60.338 57.143 0.00 0.00 0.00 3.95 F
2585 4502 0.530870 GCCCCAGCGATCTGTACTTC 60.531 60.000 0.00 0.00 38.66 3.01 F
3946 5873 1.227556 AGGCATCGGCGGACATTAC 60.228 57.895 7.21 0.00 42.47 1.89 F
4275 6206 9.383519 TCATGTATAAAAAGCTAGGAAGTTCTG 57.616 33.333 2.25 0.00 0.00 3.02 F
5222 8144 0.163788 CGACAGAACATGTTGGACGC 59.836 55.000 17.58 0.39 44.17 5.19 F
5235 8157 0.948623 TGGACGCAAGATGTTGGACG 60.949 55.000 4.57 3.08 43.62 4.79 F
6017 8946 2.928334 CAGGCAGTCTGCTTAATCCAT 58.072 47.619 23.68 0.00 44.28 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 3698 1.152881 GCCCGAGCCCAAATCAGAT 60.153 57.895 0.0 0.0 0.00 2.90 R
2585 4502 0.893270 TCCAAGGCAATCAACACCGG 60.893 55.000 0.0 0.0 0.00 5.28 R
3930 5857 1.014352 AAAGTAATGTCCGCCGATGC 58.986 50.000 0.0 0.0 0.00 3.91 R
4275 6206 2.396590 TAAATTCCCGACTGGAGCAC 57.603 50.000 0.0 0.0 46.24 4.40 R
4981 6917 2.091720 TCAGCAATATGGAGGGTGCAAT 60.092 45.455 0.0 0.0 39.50 3.56 R
5623 8552 2.171659 TGCTTGTCCTGTTGTCCACTAA 59.828 45.455 0.0 0.0 0.00 2.24 R
6247 9176 4.344978 AGTTCCTGAGCAGTCACAGTATA 58.655 43.478 0.0 0.0 32.93 1.47 R
6464 9397 5.220931 GGCAAGTAAAAGGATGCAGATAGTG 60.221 44.000 0.0 0.0 40.51 2.74 R
7432 10451 0.108329 CAAACCGTGCCGAGTATCCT 60.108 55.000 0.0 0.0 0.00 3.24 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 1.456296 CAATAGCTGCTGCCTGTTGA 58.544 50.000 13.43 0.00 40.80 3.18
41 42 1.211969 GCTGCTGCCTGTTGATGTG 59.788 57.895 3.85 0.00 0.00 3.21
145 149 0.736053 TGACGGCTTCAACGCTTTTT 59.264 45.000 0.00 0.00 34.00 1.94
225 229 5.755409 TGAAATTGGTAGGAGTAGCTCAA 57.245 39.130 0.00 0.00 31.08 3.02
245 249 0.538287 AGCTGCCTGAAACAAGGGAC 60.538 55.000 0.00 0.00 37.84 4.46
290 370 7.443879 TCATTGTTTGTTCTTGCTCACTATGTA 59.556 33.333 0.00 0.00 0.00 2.29
411 491 4.020662 GCTCTGAATACCTCCTTCATAGGG 60.021 50.000 0.00 0.00 42.26 3.53
598 679 2.677836 TCGCTTGCCATCAACTAATCAC 59.322 45.455 0.00 0.00 0.00 3.06
625 706 1.673665 GAGGCTCCTGCAACCACAG 60.674 63.158 2.15 0.00 41.91 3.66
659 740 3.898517 TCCACTCTCGACATATAAGCG 57.101 47.619 0.00 0.00 0.00 4.68
689 770 4.219944 TCTGCAGTCCTATTCTGTAAACGT 59.780 41.667 14.67 0.00 35.60 3.99
695 776 6.036083 CAGTCCTATTCTGTAAACGTCCAATG 59.964 42.308 0.00 0.00 0.00 2.82
698 779 3.889196 TTCTGTAAACGTCCAATGTGC 57.111 42.857 0.00 0.00 0.00 4.57
716 801 7.415989 CCAATGTGCATACATAAAAGCTCTCTT 60.416 37.037 0.00 0.00 46.54 2.85
794 879 8.724229 GGGTTGTTATTTTCAATTACTCGTAGT 58.276 33.333 0.00 0.00 0.00 2.73
836 921 7.094377 GGGTAAACATATCTTGCTCTTGTCAAA 60.094 37.037 0.00 0.00 0.00 2.69
858 1014 9.777297 TCAAACATATATAACTCTTATGCAGCA 57.223 29.630 0.00 0.00 0.00 4.41
881 1037 6.016777 GCATATGCTTTTACCTACTTGCTCAT 60.017 38.462 20.64 0.00 38.21 2.90
892 1137 5.645497 ACCTACTTGCTCATTCACATCTTTC 59.355 40.000 0.00 0.00 0.00 2.62
896 1148 7.047460 ACTTGCTCATTCACATCTTTCTTTT 57.953 32.000 0.00 0.00 0.00 2.27
897 1149 7.495055 ACTTGCTCATTCACATCTTTCTTTTT 58.505 30.769 0.00 0.00 0.00 1.94
1074 2922 8.420222 CAGAATAGTGATGGATCTAGTTCAGTT 58.580 37.037 3.30 0.00 0.00 3.16
1664 3535 4.855298 TCGGTTCATCTTAATTTCCCCT 57.145 40.909 0.00 0.00 0.00 4.79
1665 3536 4.523083 TCGGTTCATCTTAATTTCCCCTG 58.477 43.478 0.00 0.00 0.00 4.45
1746 3617 4.807834 TCGATTCATGCAGTCAATCTCTTC 59.192 41.667 11.32 0.00 0.00 2.87
1827 3698 9.268282 AGAGGATGAACTGAACTTTATAAGGTA 57.732 33.333 0.02 0.00 0.00 3.08
2218 4114 3.056328 GGCTGGTCGGCTTTGGTC 61.056 66.667 1.58 0.00 34.85 4.02
2320 4219 5.715496 ACCATTCCTTCCTGGAGGGTGTA 62.715 52.174 22.72 11.17 46.18 2.90
2328 4227 1.337823 CCTGGAGGGTGTAGTTGTTCG 60.338 57.143 0.00 0.00 0.00 3.95
2585 4502 0.530870 GCCCCAGCGATCTGTACTTC 60.531 60.000 0.00 0.00 38.66 3.01
2599 4517 1.467342 GTACTTCCGGTGTTGATTGCC 59.533 52.381 0.00 0.00 0.00 4.52
2637 4557 3.928727 GGAAACCCTTTTTCGGTAAGG 57.071 47.619 0.00 0.00 41.51 2.69
2638 4558 3.225104 GGAAACCCTTTTTCGGTAAGGT 58.775 45.455 0.00 0.00 40.47 3.50
2688 4608 5.046376 GGGGGTGTGCTTTTAGTACTTACTA 60.046 44.000 0.00 0.00 37.73 1.82
2841 4761 9.134734 GCTAAATTCGAACATATTGGAAAAACA 57.865 29.630 0.00 0.00 36.31 2.83
2907 4827 1.271656 CTTCGTCGGTTACCTGTTCCT 59.728 52.381 0.00 0.00 0.00 3.36
3622 5547 3.942115 GGGTTTCTTATCTCACTGGAAGC 59.058 47.826 0.00 0.00 37.60 3.86
3946 5873 1.227556 AGGCATCGGCGGACATTAC 60.228 57.895 7.21 0.00 42.47 1.89
4275 6206 9.383519 TCATGTATAAAAAGCTAGGAAGTTCTG 57.616 33.333 2.25 0.00 0.00 3.02
5222 8144 0.163788 CGACAGAACATGTTGGACGC 59.836 55.000 17.58 0.39 44.17 5.19
5223 8145 1.225855 GACAGAACATGTTGGACGCA 58.774 50.000 17.58 0.00 44.17 5.24
5224 8146 1.601903 GACAGAACATGTTGGACGCAA 59.398 47.619 17.58 0.00 44.17 4.85
5225 8147 1.603802 ACAGAACATGTTGGACGCAAG 59.396 47.619 17.58 0.93 39.96 4.01
5226 8148 1.872952 CAGAACATGTTGGACGCAAGA 59.127 47.619 17.58 0.00 43.62 3.02
5227 8149 2.485426 CAGAACATGTTGGACGCAAGAT 59.515 45.455 17.58 0.00 43.62 2.40
5228 8150 2.485426 AGAACATGTTGGACGCAAGATG 59.515 45.455 17.58 10.13 40.38 2.90
5229 8151 1.896220 ACATGTTGGACGCAAGATGT 58.104 45.000 11.17 11.17 42.01 3.06
5230 8152 2.229792 ACATGTTGGACGCAAGATGTT 58.770 42.857 11.17 0.04 43.56 2.71
5231 8153 2.030893 ACATGTTGGACGCAAGATGTTG 60.031 45.455 11.17 0.00 43.56 3.33
5232 8154 0.950836 TGTTGGACGCAAGATGTTGG 59.049 50.000 4.57 0.00 43.62 3.77
5233 8155 1.234821 GTTGGACGCAAGATGTTGGA 58.765 50.000 4.57 0.00 43.62 3.53
5234 8156 1.069227 GTTGGACGCAAGATGTTGGAC 60.069 52.381 4.57 0.00 43.62 4.02
5235 8157 0.948623 TGGACGCAAGATGTTGGACG 60.949 55.000 4.57 3.08 43.62 4.79
5336 8258 6.456181 CGCTGTCCTGATTCTTAATTCTCAAC 60.456 42.308 0.00 0.00 0.00 3.18
6017 8946 2.928334 CAGGCAGTCTGCTTAATCCAT 58.072 47.619 23.68 0.00 44.28 3.41
6247 9176 8.376270 GCTATTTTTCTCCCACATATAGGTACT 58.624 37.037 0.00 0.00 46.37 2.73
6280 9209 3.282021 GCTCAGGAACTTGGCATCATTA 58.718 45.455 0.00 0.00 34.60 1.90
6283 9212 5.532406 GCTCAGGAACTTGGCATCATTATTA 59.468 40.000 0.00 0.00 34.60 0.98
6287 9216 8.980596 TCAGGAACTTGGCATCATTATTATTTT 58.019 29.630 0.00 0.00 34.60 1.82
6288 9217 9.603921 CAGGAACTTGGCATCATTATTATTTTT 57.396 29.630 0.00 0.00 34.60 1.94
6289 9218 9.822185 AGGAACTTGGCATCATTATTATTTTTC 57.178 29.630 0.00 0.00 27.25 2.29
6464 9397 8.652810 TCTTTTGTTCTTGTTGTACTACTACC 57.347 34.615 8.88 0.00 0.00 3.18
6724 9726 9.220767 AGATACTTGAAGTACAATTTCTTGGAC 57.779 33.333 7.28 0.00 45.21 4.02
6834 9850 5.779922 ATGACAACATTACTACGTGAGTGT 58.220 37.500 0.00 0.00 39.39 3.55
7109 10128 4.038402 ACAATCCACTTTTGCTCCTTTCAG 59.962 41.667 0.00 0.00 0.00 3.02
7123 10142 6.716628 TGCTCCTTTCAGTTATGAGAAATTGT 59.283 34.615 0.00 0.00 36.61 2.71
7127 10146 9.219603 TCCTTTCAGTTATGAGAAATTGTACTG 57.780 33.333 0.00 0.00 36.61 2.74
7131 10150 9.719355 TTCAGTTATGAGAAATTGTACTGCTAA 57.281 29.630 0.00 0.00 36.61 3.09
7215 10234 0.320374 TTCAGGTAAGTGGGTCGCAG 59.680 55.000 0.00 0.00 0.00 5.18
7312 10331 1.271127 TTCATCATGGGACGGCCAGA 61.271 55.000 11.00 3.68 35.15 3.86
7344 10363 1.447489 CAGGACTCGCTCCAAGCAG 60.447 63.158 0.00 0.00 42.58 4.24
7387 10406 1.671328 TCGAGTCTGCAGATACTTCGG 59.329 52.381 27.21 14.60 0.00 4.30
7390 10409 2.950309 GAGTCTGCAGATACTTCGGGTA 59.050 50.000 21.47 0.00 34.62 3.69
7432 10451 2.382882 TGTGCAATCTTGGGTCACAAA 58.617 42.857 0.00 0.00 38.91 2.83
7487 10506 8.554835 AGAAAATGAAAAGGAACTCTAGCTAC 57.445 34.615 0.00 0.00 38.49 3.58
7563 10582 3.735181 CCTTCGGAGAAGGTAACGG 57.265 57.895 18.05 0.00 45.90 4.44
7585 10604 4.103311 GGAACAGCCTATCCTTAGATGGTT 59.897 45.833 0.00 0.00 33.67 3.67
7626 10645 8.164733 TCCTTTGTTTATGTGATTACTGGGTTA 58.835 33.333 0.00 0.00 0.00 2.85
7768 10791 0.798389 GCAAGAAATTTCTCGCGGCC 60.798 55.000 20.71 0.00 36.28 6.13
7827 10850 8.840833 TTCAGTATGTTAAGTTGTCTATTGCA 57.159 30.769 0.00 0.00 37.40 4.08
7828 10851 8.479313 TCAGTATGTTAAGTTGTCTATTGCAG 57.521 34.615 0.00 0.00 37.40 4.41
7829 10852 8.311109 TCAGTATGTTAAGTTGTCTATTGCAGA 58.689 33.333 0.00 0.00 37.40 4.26
7831 10854 5.862924 TGTTAAGTTGTCTATTGCAGAGC 57.137 39.130 0.00 0.00 32.51 4.09
7832 10855 5.304778 TGTTAAGTTGTCTATTGCAGAGCA 58.695 37.500 0.00 0.00 36.47 4.26
7833 10856 5.179368 TGTTAAGTTGTCTATTGCAGAGCAC 59.821 40.000 0.00 0.00 38.71 4.40
7835 10858 4.808414 AGTTGTCTATTGCAGAGCACTA 57.192 40.909 0.00 0.00 38.71 2.74
7879 10902 4.719040 CGGAAGGAAAAACTTTATCGGTG 58.281 43.478 0.00 0.00 0.00 4.94
7880 10903 4.453136 CGGAAGGAAAAACTTTATCGGTGA 59.547 41.667 0.00 0.00 0.00 4.02
7881 10904 5.049267 CGGAAGGAAAAACTTTATCGGTGAA 60.049 40.000 0.00 0.00 0.00 3.18
7882 10905 6.513720 CGGAAGGAAAAACTTTATCGGTGAAA 60.514 38.462 0.00 0.00 0.00 2.69
7883 10906 7.375834 GGAAGGAAAAACTTTATCGGTGAAAT 58.624 34.615 0.00 0.00 0.00 2.17
7884 10907 7.870954 GGAAGGAAAAACTTTATCGGTGAAATT 59.129 33.333 0.00 0.00 0.00 1.82
7885 10908 8.587952 AAGGAAAAACTTTATCGGTGAAATTG 57.412 30.769 0.00 0.00 0.00 2.32
7886 10909 7.722363 AGGAAAAACTTTATCGGTGAAATTGT 58.278 30.769 0.00 0.00 0.00 2.71
7887 10910 8.852135 AGGAAAAACTTTATCGGTGAAATTGTA 58.148 29.630 0.00 0.00 0.00 2.41
7888 10911 9.634163 GGAAAAACTTTATCGGTGAAATTGTAT 57.366 29.630 0.00 0.00 0.00 2.29
7906 10945 1.438651 ATACGCGCAACATGTTCTGT 58.561 45.000 8.48 7.36 40.84 3.41
7963 11002 3.316029 TGACACTTGTGCTTCATCCTTTG 59.684 43.478 0.10 0.00 0.00 2.77
7985 11029 4.338964 TGAACAGCAGATTGAAGCAGAAAA 59.661 37.500 0.00 0.00 0.00 2.29
7986 11030 5.010314 TGAACAGCAGATTGAAGCAGAAAAT 59.990 36.000 0.00 0.00 0.00 1.82
8091 11135 1.372582 TTCAGGCGTTCATGATGAGC 58.627 50.000 0.00 2.48 0.00 4.26
8182 11226 6.161855 AGTTGAATGCGTAAGAGGATATCA 57.838 37.500 4.83 0.00 43.02 2.15
8248 11292 0.396811 AACTAACGGGCTCTGTTGCT 59.603 50.000 9.01 0.00 0.00 3.91
8339 11385 8.771521 TGGGATCATAGTTTCATCATCAAAAT 57.228 30.769 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.743126 GCAGCTATTGGAGATGATGCTC 59.257 50.000 0.00 0.00 44.86 4.26
7 8 2.372504 AGCAGCTATTGGAGATGATGCT 59.627 45.455 0.00 0.00 44.86 3.79
8 9 2.780714 AGCAGCTATTGGAGATGATGC 58.219 47.619 0.00 0.00 44.86 3.91
11 12 1.202734 GGCAGCAGCTATTGGAGATGA 60.203 52.381 0.00 0.00 44.86 2.92
37 38 1.100463 TGACGCCACAACAAGCACAT 61.100 50.000 0.00 0.00 0.00 3.21
41 42 0.661187 CACATGACGCCACAACAAGC 60.661 55.000 0.00 0.00 0.00 4.01
109 110 5.180680 AGCCGTCAGACCAAAATACTAAAAC 59.819 40.000 0.00 0.00 0.00 2.43
112 113 4.546829 AGCCGTCAGACCAAAATACTAA 57.453 40.909 0.00 0.00 0.00 2.24
145 149 8.902540 TCATCAGTTAAGAACTTGAGCTAAAA 57.097 30.769 0.00 0.00 40.46 1.52
152 156 8.097038 ACATAAGCTCATCAGTTAAGAACTTGA 58.903 33.333 0.00 0.00 40.46 3.02
158 162 8.097038 ACTTCAACATAAGCTCATCAGTTAAGA 58.903 33.333 0.00 0.00 0.00 2.10
162 166 6.000219 ACACTTCAACATAAGCTCATCAGTT 59.000 36.000 0.00 0.00 0.00 3.16
201 205 5.488341 TGAGCTACTCCTACCAATTTCAAC 58.512 41.667 0.00 0.00 0.00 3.18
203 207 5.755409 TTGAGCTACTCCTACCAATTTCA 57.245 39.130 0.00 0.00 0.00 2.69
225 229 0.185901 TCCCTTGTTTCAGGCAGCTT 59.814 50.000 0.00 0.00 31.69 3.74
245 249 8.107399 ACAATGAATCTTGCATCCATAGTATG 57.893 34.615 2.90 2.90 0.00 2.39
352 432 0.458543 AGCAACTGAGCGTGATACCG 60.459 55.000 0.00 0.00 40.15 4.02
411 491 3.696051 TGGAAGGATCAGTTTAGCAATGC 59.304 43.478 0.00 0.00 0.00 3.56
573 653 1.825090 AGTTGATGGCAAGCGATTGA 58.175 45.000 19.19 0.00 34.01 2.57
598 679 1.065199 TGCAGGAGCCTCCAAATACTG 60.065 52.381 14.46 2.06 39.61 2.74
625 706 3.212450 GTGGAACTCTGAACCGACC 57.788 57.895 0.00 0.00 0.00 4.79
659 740 4.505922 CAGAATAGGACTGCAGATCGTTTC 59.494 45.833 23.35 16.27 0.00 2.78
689 770 5.887598 AGAGCTTTTATGTATGCACATTGGA 59.112 36.000 0.00 0.00 42.98 3.53
695 776 6.317391 AGGAAAGAGAGCTTTTATGTATGCAC 59.683 38.462 0.00 0.00 44.10 4.57
698 779 8.498054 TGAAGGAAAGAGAGCTTTTATGTATG 57.502 34.615 0.00 0.00 44.10 2.39
716 801 5.726308 TGAGATAAAGGAGGTGATGAAGGAA 59.274 40.000 0.00 0.00 0.00 3.36
858 1014 7.775093 TGAATGAGCAAGTAGGTAAAAGCATAT 59.225 33.333 0.00 0.00 0.00 1.78
896 1148 5.650703 ACCGAAGAAGTTCCAAAAAGAGAAA 59.349 36.000 0.00 0.00 0.00 2.52
897 1149 5.190677 ACCGAAGAAGTTCCAAAAAGAGAA 58.809 37.500 0.00 0.00 0.00 2.87
898 1150 4.777463 ACCGAAGAAGTTCCAAAAAGAGA 58.223 39.130 0.00 0.00 0.00 3.10
899 1151 4.816925 AGACCGAAGAAGTTCCAAAAAGAG 59.183 41.667 0.00 0.00 0.00 2.85
900 1152 4.777463 AGACCGAAGAAGTTCCAAAAAGA 58.223 39.130 0.00 0.00 0.00 2.52
901 1153 4.023963 GGAGACCGAAGAAGTTCCAAAAAG 60.024 45.833 0.00 0.00 0.00 2.27
1664 3535 1.561076 AGCCCATGCATACAGAGTTCA 59.439 47.619 0.00 0.00 41.13 3.18
1665 3536 2.216898 GAGCCCATGCATACAGAGTTC 58.783 52.381 0.00 0.00 41.13 3.01
1746 3617 8.853126 TGCATTTCCTCTCAATAAGAATAATGG 58.147 33.333 0.00 0.00 32.31 3.16
1827 3698 1.152881 GCCCGAGCCCAAATCAGAT 60.153 57.895 0.00 0.00 0.00 2.90
1828 3699 2.272146 GCCCGAGCCCAAATCAGA 59.728 61.111 0.00 0.00 0.00 3.27
1829 3700 3.204827 CGCCCGAGCCCAAATCAG 61.205 66.667 0.00 0.00 34.57 2.90
1830 3701 4.794648 CCGCCCGAGCCCAAATCA 62.795 66.667 0.00 0.00 34.57 2.57
2320 4219 2.075355 TTGGGGGATGGCGAACAACT 62.075 55.000 0.00 0.00 0.00 3.16
2328 4227 3.023735 AGGGAGTTGGGGGATGGC 61.024 66.667 0.00 0.00 0.00 4.40
2585 4502 0.893270 TCCAAGGCAATCAACACCGG 60.893 55.000 0.00 0.00 0.00 5.28
2599 4517 1.102978 CCCCCGCTTTGTATTCCAAG 58.897 55.000 0.00 0.00 33.75 3.61
2637 4557 3.381590 GCCTTGTTCCCCAAATCAGATAC 59.618 47.826 0.00 0.00 31.20 2.24
2638 4558 3.269381 AGCCTTGTTCCCCAAATCAGATA 59.731 43.478 0.00 0.00 31.20 1.98
2688 4608 7.364762 CCCTCACAATGTTTCCACTACTAGTAT 60.365 40.741 2.33 0.00 0.00 2.12
2907 4827 5.862845 TGCATGCAAAAAGGGAAGATAAAA 58.137 33.333 20.30 0.00 0.00 1.52
3100 5020 2.497675 GGTGGCACTATCTCAACAGAGA 59.502 50.000 18.45 0.00 42.25 3.10
3208 5128 4.819630 GTGGACCTGTTGAATCACAAAGTA 59.180 41.667 0.00 0.00 40.36 2.24
3209 5129 3.632145 GTGGACCTGTTGAATCACAAAGT 59.368 43.478 0.00 0.00 40.36 2.66
3355 5280 1.565288 TCCATCATGGATGTCCTGCAA 59.435 47.619 0.66 0.00 42.67 4.08
3492 5417 1.676006 ACTTTGTTTGCCTGAAGGTCG 59.324 47.619 0.00 0.00 37.57 4.79
3559 5484 7.860872 GGCAAATATTTAAGAAGATACAACCCG 59.139 37.037 0.00 0.00 0.00 5.28
3597 5522 5.165961 TCCAGTGAGATAAGAAACCCAAG 57.834 43.478 0.00 0.00 0.00 3.61
3930 5857 1.014352 AAAGTAATGTCCGCCGATGC 58.986 50.000 0.00 0.00 0.00 3.91
4275 6206 2.396590 TAAATTCCCGACTGGAGCAC 57.603 50.000 0.00 0.00 46.24 4.40
4578 6511 4.545823 TCTAAACTGCCAAAACGTCTTG 57.454 40.909 0.00 0.00 0.00 3.02
4981 6917 2.091720 TCAGCAATATGGAGGGTGCAAT 60.092 45.455 0.00 0.00 39.50 3.56
5222 8144 5.118990 AGGATAATGACGTCCAACATCTTG 58.881 41.667 14.12 0.00 36.96 3.02
5223 8145 5.359194 AGGATAATGACGTCCAACATCTT 57.641 39.130 14.12 4.42 36.96 2.40
5224 8146 6.098409 AGTTAGGATAATGACGTCCAACATCT 59.902 38.462 14.12 6.90 36.96 2.90
5225 8147 6.281405 AGTTAGGATAATGACGTCCAACATC 58.719 40.000 14.12 10.08 36.96 3.06
5226 8148 6.235231 AGTTAGGATAATGACGTCCAACAT 57.765 37.500 14.12 0.75 36.96 2.71
5227 8149 5.670792 AGTTAGGATAATGACGTCCAACA 57.329 39.130 14.12 0.00 36.96 3.33
5228 8150 9.924650 ATATAAGTTAGGATAATGACGTCCAAC 57.075 33.333 14.12 4.82 36.96 3.77
5623 8552 2.171659 TGCTTGTCCTGTTGTCCACTAA 59.828 45.455 0.00 0.00 0.00 2.24
5763 8692 8.918202 TCACATACCACAAAGTTTCTAAGATT 57.082 30.769 0.00 0.00 0.00 2.40
5766 8695 7.607991 AGGATCACATACCACAAAGTTTCTAAG 59.392 37.037 0.00 0.00 0.00 2.18
6247 9176 4.344978 AGTTCCTGAGCAGTCACAGTATA 58.655 43.478 0.00 0.00 32.93 1.47
6287 9216 8.432013 AGCACATATCCACTACATTAATCTGAA 58.568 33.333 0.00 0.00 0.00 3.02
6288 9217 7.874528 CAGCACATATCCACTACATTAATCTGA 59.125 37.037 0.00 0.00 0.00 3.27
6289 9218 7.874528 TCAGCACATATCCACTACATTAATCTG 59.125 37.037 0.00 0.00 0.00 2.90
6291 9220 8.783833 ATCAGCACATATCCACTACATTAATC 57.216 34.615 0.00 0.00 0.00 1.75
6292 9221 9.881649 CTATCAGCACATATCCACTACATTAAT 57.118 33.333 0.00 0.00 0.00 1.40
6293 9222 8.314021 CCTATCAGCACATATCCACTACATTAA 58.686 37.037 0.00 0.00 0.00 1.40
6295 9224 6.705302 CCTATCAGCACATATCCACTACATT 58.295 40.000 0.00 0.00 0.00 2.71
6464 9397 5.220931 GGCAAGTAAAAGGATGCAGATAGTG 60.221 44.000 0.00 0.00 40.51 2.74
6724 9726 6.002062 AGAGAACAAGTAAAAGGAAATGCG 57.998 37.500 0.00 0.00 0.00 4.73
6834 9850 5.243954 GTGCCTATGTAGAGATCCATACACA 59.756 44.000 9.20 0.00 34.88 3.72
6911 9928 7.439381 TGTCTTATATTTTGATACGGAGGGAC 58.561 38.462 0.00 0.00 0.00 4.46
6973 9991 6.567602 AGCTACTCCCTCTGTATCAAAATT 57.432 37.500 0.00 0.00 0.00 1.82
7010 10028 8.200120 CACCTCACTGAAAGATCTATGTTATCA 58.800 37.037 0.00 0.00 37.43 2.15
7109 10128 9.638300 CGAATTAGCAGTACAATTTCTCATAAC 57.362 33.333 0.00 0.00 0.00 1.89
7123 10142 9.820229 CATGAAAAGTAAAACGAATTAGCAGTA 57.180 29.630 0.00 0.00 0.00 2.74
7131 10150 8.586570 TGCAAATCATGAAAAGTAAAACGAAT 57.413 26.923 0.00 0.00 0.00 3.34
7312 10331 1.383109 TCCTGGACCATCTGGCGAT 60.383 57.895 0.00 0.00 39.32 4.58
7432 10451 0.108329 CAAACCGTGCCGAGTATCCT 60.108 55.000 0.00 0.00 0.00 3.24
7459 10478 9.389755 AGCTAGAGTTCCTTTTCATTTTCTATC 57.610 33.333 0.00 0.00 0.00 2.08
7487 10506 7.433708 TGGCTTCCATTTTATATGTACATCG 57.566 36.000 12.68 0.00 0.00 3.84
7563 10582 4.965200 ACCATCTAAGGATAGGCTGTTC 57.035 45.455 0.00 0.00 0.00 3.18
7739 10762 7.121974 CGAGAAATTTCTTGCAAAGTAGAGA 57.878 36.000 21.33 0.00 46.34 3.10
7768 10791 3.594603 ATGAAACCACGACTACCTCTG 57.405 47.619 0.00 0.00 0.00 3.35
7822 10845 0.460987 GCGTCCTAGTGCTCTGCAAT 60.461 55.000 0.00 0.00 41.47 3.56
7824 10847 1.536073 AAGCGTCCTAGTGCTCTGCA 61.536 55.000 0.00 0.00 41.46 4.41
7825 10848 1.080995 CAAGCGTCCTAGTGCTCTGC 61.081 60.000 0.00 0.00 41.46 4.26
7827 10850 1.067495 GTTCAAGCGTCCTAGTGCTCT 60.067 52.381 2.32 0.00 41.46 4.09
7828 10851 1.336887 TGTTCAAGCGTCCTAGTGCTC 60.337 52.381 2.32 0.00 41.46 4.26
7829 10852 0.679505 TGTTCAAGCGTCCTAGTGCT 59.320 50.000 0.00 0.00 44.97 4.40
7831 10854 3.795561 CTTTGTTCAAGCGTCCTAGTG 57.204 47.619 0.00 0.00 0.00 2.74
7873 10896 2.220133 GCGCGTATACAATTTCACCGAT 59.780 45.455 8.43 0.00 0.00 4.18
7874 10897 1.589320 GCGCGTATACAATTTCACCGA 59.411 47.619 8.43 0.00 0.00 4.69
7875 10898 1.325037 TGCGCGTATACAATTTCACCG 59.675 47.619 8.43 0.00 0.00 4.94
7876 10899 3.095738 GTTGCGCGTATACAATTTCACC 58.904 45.455 8.43 0.00 0.00 4.02
7877 10900 3.738399 TGTTGCGCGTATACAATTTCAC 58.262 40.909 8.43 0.00 0.00 3.18
7878 10901 4.142795 ACATGTTGCGCGTATACAATTTCA 60.143 37.500 8.43 0.00 0.00 2.69
7879 10902 4.339429 ACATGTTGCGCGTATACAATTTC 58.661 39.130 8.43 0.00 0.00 2.17
7880 10903 4.349663 ACATGTTGCGCGTATACAATTT 57.650 36.364 8.43 0.00 0.00 1.82
7881 10904 4.094294 AGAACATGTTGCGCGTATACAATT 59.906 37.500 17.58 9.42 0.00 2.32
7882 10905 3.621268 AGAACATGTTGCGCGTATACAAT 59.379 39.130 17.58 1.49 0.00 2.71
7883 10906 2.997303 AGAACATGTTGCGCGTATACAA 59.003 40.909 17.58 0.00 0.00 2.41
7884 10907 2.347150 CAGAACATGTTGCGCGTATACA 59.653 45.455 17.58 11.11 0.00 2.29
7885 10908 2.347452 ACAGAACATGTTGCGCGTATAC 59.653 45.455 17.58 5.28 39.96 1.47
7886 10909 2.347150 CACAGAACATGTTGCGCGTATA 59.653 45.455 17.58 0.00 41.41 1.47
7887 10910 1.128507 CACAGAACATGTTGCGCGTAT 59.871 47.619 17.58 0.00 41.41 3.06
7888 10911 0.510790 CACAGAACATGTTGCGCGTA 59.489 50.000 17.58 0.00 41.41 4.42
7889 10912 1.279539 CACAGAACATGTTGCGCGT 59.720 52.632 17.58 4.43 41.41 6.01
7906 10945 6.203915 ACAGAAACAACATAGTCGCAAATACA 59.796 34.615 0.00 0.00 0.00 2.29
7963 11002 4.494350 TTTCTGCTTCAATCTGCTGTTC 57.506 40.909 0.00 0.00 0.00 3.18
7985 11029 5.644636 CCTGCCAAACTTTTTATGCATCAAT 59.355 36.000 0.19 0.00 0.00 2.57
7986 11030 4.996122 CCTGCCAAACTTTTTATGCATCAA 59.004 37.500 0.19 0.00 0.00 2.57
8113 11157 9.228949 AGATAAATTCACGTCGACTATATACCT 57.771 33.333 14.70 0.00 0.00 3.08
8114 11158 9.837525 AAGATAAATTCACGTCGACTATATACC 57.162 33.333 14.70 0.00 0.00 2.73
8182 11226 4.892934 TCTTCTAAAATGTGCAACCCAGTT 59.107 37.500 0.00 0.00 34.36 3.16
8248 11292 4.622260 TCATATCATCGGAAATCCTGCA 57.378 40.909 0.00 0.00 0.00 4.41
8339 11385 5.690865 AGAAAACATCACCTGGTTAACTGA 58.309 37.500 5.42 1.57 32.04 3.41


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

AutoCloner maintained by Alex Coulton.