Multiple sequence alignment - TraesCS3A01G239900

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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 TraesCS3A01G239900 chr3A 100.000 6036 0 0 1 6036 450008118 450014153 0.000000e+00 11147.0
1 TraesCS3A01G239900 chr3A 86.607 560 48 13 9 545 9829550 9828995 1.450000e-165 593.0
2 TraesCS3A01G239900 chr3B 94.128 2231 62 18 1538 3732 431579517 431581714 0.000000e+00 3330.0
3 TraesCS3A01G239900 chr3B 96.287 1670 40 8 3739 5402 431582090 431583743 0.000000e+00 2721.0
4 TraesCS3A01G239900 chr3B 94.737 760 20 10 789 1540 431578706 431579453 0.000000e+00 1164.0
5 TraesCS3A01G239900 chr3B 95.455 638 26 3 5400 6036 431583906 431584541 0.000000e+00 1014.0
6 TraesCS3A01G239900 chr3B 86.787 719 66 8 43 740 603796326 603797036 0.000000e+00 774.0
7 TraesCS3A01G239900 chr3D 95.269 1374 58 5 2354 3726 332628633 332630000 0.000000e+00 2170.0
8 TraesCS3A01G239900 chr3D 95.405 1001 39 4 4163 5160 332631109 332632105 0.000000e+00 1587.0
9 TraesCS3A01G239900 chr3D 94.534 805 32 6 743 1540 332626861 332627660 0.000000e+00 1232.0
10 TraesCS3A01G239900 chr3D 88.830 752 67 6 3 742 240516519 240515773 0.000000e+00 907.0
11 TraesCS3A01G239900 chr3D 90.229 655 42 10 5395 6036 332632768 332633413 0.000000e+00 835.0
12 TraesCS3A01G239900 chr3D 94.954 436 12 4 3739 4164 332630374 332630809 0.000000e+00 675.0
13 TraesCS3A01G239900 chr3D 95.980 398 16 0 1539 1936 332627725 332628122 0.000000e+00 647.0
14 TraesCS3A01G239900 chr3D 94.142 239 10 4 1958 2193 332628395 332628632 1.600000e-95 361.0
15 TraesCS3A01G239900 chr3D 86.522 230 29 2 5580 5808 314681783 314681555 1.000000e-62 252.0
16 TraesCS3A01G239900 chr3D 93.333 165 11 0 2192 2356 87926161 87925997 1.680000e-60 244.0
17 TraesCS3A01G239900 chr3D 84.270 89 6 4 5109 5190 254362235 254362322 5.010000e-11 80.5
18 TraesCS3A01G239900 chr3D 82.955 88 10 3 5111 5194 565081590 565081504 2.330000e-09 75.0
19 TraesCS3A01G239900 chr3D 97.436 39 1 0 1936 1974 332628353 332628391 3.900000e-07 67.6
20 TraesCS3A01G239900 chr7D 88.243 757 63 5 9 742 227560712 227559959 0.000000e+00 881.0
21 TraesCS3A01G239900 chr7D 91.429 210 18 0 533 742 564658260 564658051 7.650000e-74 289.0
22 TraesCS3A01G239900 chr7D 92.090 177 12 2 2176 2352 183790248 183790422 1.300000e-61 248.0
23 TraesCS3A01G239900 chr1D 87.648 761 67 5 3 742 373416331 373417085 0.000000e+00 859.0
24 TraesCS3A01G239900 chr2B 86.667 765 75 6 3 746 20030698 20031456 0.000000e+00 822.0
25 TraesCS3A01G239900 chr2B 87.739 261 30 2 5548 5808 520204306 520204564 2.730000e-78 303.0
26 TraesCS3A01G239900 chr2B 92.814 167 11 1 2187 2352 361574826 361574992 2.170000e-59 241.0
27 TraesCS3A01G239900 chr2B 82.292 96 9 6 5103 5190 33942173 33942268 6.490000e-10 76.8
28 TraesCS3A01G239900 chr6B 87.252 706 62 9 3 687 426817905 426818603 0.000000e+00 780.0
29 TraesCS3A01G239900 chr6B 86.498 711 64 11 46 742 236569684 236570376 0.000000e+00 752.0
30 TraesCS3A01G239900 chr6B 84.163 663 74 9 98 742 426456995 426457644 1.110000e-171 614.0
31 TraesCS3A01G239900 chr6B 83.910 665 72 11 98 742 426456047 426456696 2.410000e-168 603.0
32 TraesCS3A01G239900 chr7A 96.796 437 14 0 1 437 50629774 50630210 0.000000e+00 730.0
33 TraesCS3A01G239900 chr7A 84.077 672 77 7 95 744 237526994 237526331 6.640000e-174 621.0
34 TraesCS3A01G239900 chr7A 94.853 272 14 0 473 744 50630565 50630836 5.590000e-115 425.0
35 TraesCS3A01G239900 chr7A 90.270 185 14 3 2176 2360 187107863 187107683 7.820000e-59 239.0
36 TraesCS3A01G239900 chr2D 86.163 701 60 14 3 680 25746882 25747568 0.000000e+00 723.0
37 TraesCS3A01G239900 chr6A 83.208 667 75 12 110 753 386316461 386315809 1.460000e-160 577.0
38 TraesCS3A01G239900 chr6A 86.902 397 36 6 301 687 385750709 385750319 1.200000e-116 431.0
39 TraesCS3A01G239900 chr1B 85.558 547 55 10 94 623 452366545 452366006 8.840000e-153 551.0
40 TraesCS3A01G239900 chr1B 88.652 423 36 1 3 413 319250982 319251404 6.980000e-139 505.0
41 TraesCS3A01G239900 chr1B 88.511 235 18 1 517 742 319251725 319251959 5.960000e-70 276.0
42 TraesCS3A01G239900 chr1B 83.908 87 7 4 5105 5184 20174194 20174280 6.490000e-10 76.8
43 TraesCS3A01G239900 chr5D 89.323 384 27 3 3 373 360978959 360979341 2.550000e-128 470.0
44 TraesCS3A01G239900 chr5A 93.865 163 10 0 2190 2352 320214407 320214245 4.670000e-61 246.0
45 TraesCS3A01G239900 chr4A 94.937 158 6 1 2191 2348 47750182 47750337 4.670000e-61 246.0
46 TraesCS3A01G239900 chr4A 92.899 169 10 1 2191 2359 298243885 298243719 1.680000e-60 244.0
47 TraesCS3A01G239900 chr4D 93.789 161 10 0 2192 2352 34661527 34661687 6.040000e-60 243.0
48 TraesCS3A01G239900 chr4D 85.714 91 8 4 5105 5190 395380206 395380116 2.320000e-14 91.6
49 TraesCS3A01G239900 chr6D 85.714 84 10 1 5110 5193 211444023 211443942 3.000000e-13 87.9
50 TraesCS3A01G239900 chr1A 84.706 85 7 4 5112 5190 446542895 446542811 5.010000e-11 80.5


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 TraesCS3A01G239900 chr3A 450008118 450014153 6035 False 11147.000 11147 100.000000 1 6036 1 chr3A.!!$F1 6035
1 TraesCS3A01G239900 chr3A 9828995 9829550 555 True 593.000 593 86.607000 9 545 1 chr3A.!!$R1 536
2 TraesCS3A01G239900 chr3B 431578706 431584541 5835 False 2057.250 3330 95.151750 789 6036 4 chr3B.!!$F2 5247
3 TraesCS3A01G239900 chr3B 603796326 603797036 710 False 774.000 774 86.787000 43 740 1 chr3B.!!$F1 697
4 TraesCS3A01G239900 chr3D 332626861 332633413 6552 False 946.825 2170 94.743625 743 6036 8 chr3D.!!$F2 5293
5 TraesCS3A01G239900 chr3D 240515773 240516519 746 True 907.000 907 88.830000 3 742 1 chr3D.!!$R2 739
6 TraesCS3A01G239900 chr7D 227559959 227560712 753 True 881.000 881 88.243000 9 742 1 chr7D.!!$R1 733
7 TraesCS3A01G239900 chr1D 373416331 373417085 754 False 859.000 859 87.648000 3 742 1 chr1D.!!$F1 739
8 TraesCS3A01G239900 chr2B 20030698 20031456 758 False 822.000 822 86.667000 3 746 1 chr2B.!!$F1 743
9 TraesCS3A01G239900 chr6B 426817905 426818603 698 False 780.000 780 87.252000 3 687 1 chr6B.!!$F2 684
10 TraesCS3A01G239900 chr6B 236569684 236570376 692 False 752.000 752 86.498000 46 742 1 chr6B.!!$F1 696
11 TraesCS3A01G239900 chr6B 426456047 426457644 1597 False 608.500 614 84.036500 98 742 2 chr6B.!!$F3 644
12 TraesCS3A01G239900 chr7A 237526331 237526994 663 True 621.000 621 84.077000 95 744 1 chr7A.!!$R2 649
13 TraesCS3A01G239900 chr7A 50629774 50630836 1062 False 577.500 730 95.824500 1 744 2 chr7A.!!$F1 743
14 TraesCS3A01G239900 chr2D 25746882 25747568 686 False 723.000 723 86.163000 3 680 1 chr2D.!!$F1 677
15 TraesCS3A01G239900 chr6A 386315809 386316461 652 True 577.000 577 83.208000 110 753 1 chr6A.!!$R2 643
16 TraesCS3A01G239900 chr1B 452366006 452366545 539 True 551.000 551 85.558000 94 623 1 chr1B.!!$R1 529
17 TraesCS3A01G239900 chr1B 319250982 319251959 977 False 390.500 505 88.581500 3 742 2 chr1B.!!$F2 739

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
756 2075 0.179222 GCGCGTGAGGTAAGCTTTTC 60.179 55.000 3.20 1.11 0.00 2.29 F
1116 2441 0.179129 TCCGCGGATTTCGACTAACC 60.179 55.000 27.28 0.00 42.43 2.85 F
1120 2445 0.828677 CGGATTTCGACTAACCCCCT 59.171 55.000 0.00 0.00 42.43 4.79 F
2917 4568 1.306997 TCCCCATCTTCCTTCGCCT 60.307 57.895 0.00 0.00 0.00 5.52 F
3637 5302 0.889186 GCAGGTTCCGTTGTGGTCAT 60.889 55.000 0.00 0.00 39.52 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2667 4318 1.450531 AAGGCAGAACAGCACTGTGC 61.451 55.000 24.59 24.59 44.13 4.57 R
2902 4553 0.175760 TCGAAGGCGAAGGAAGATGG 59.824 55.000 0.00 0.00 44.78 3.51 R
2944 4595 0.179111 CTGCCTTAGCGACGGATTCA 60.179 55.000 0.00 0.00 44.31 2.57 R
4486 6834 3.663025 ACAAATATGCAACAGTTTGGCC 58.337 40.909 15.89 0.00 36.23 5.36 R
5565 8659 3.564235 TGAAACATGCAGTGCAATCTC 57.436 42.857 23.90 15.98 43.62 2.75 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
50 51 3.242804 CGTGTAGGAGCTACTCTAGTTGC 60.243 52.174 0.00 8.26 44.91 4.17
57 58 3.233684 GCTACTCTAGTTGCGAAACCT 57.766 47.619 1.56 0.00 37.09 3.50
58 59 3.180613 GCTACTCTAGTTGCGAAACCTC 58.819 50.000 1.56 0.00 37.09 3.85
59 60 3.367087 GCTACTCTAGTTGCGAAACCTCA 60.367 47.826 1.56 0.00 37.09 3.86
60 61 3.963428 ACTCTAGTTGCGAAACCTCAT 57.037 42.857 1.56 0.00 0.00 2.90
61 62 3.851098 ACTCTAGTTGCGAAACCTCATC 58.149 45.455 1.56 0.00 0.00 2.92
62 63 3.511934 ACTCTAGTTGCGAAACCTCATCT 59.488 43.478 1.56 0.00 0.00 2.90
63 64 4.021016 ACTCTAGTTGCGAAACCTCATCTT 60.021 41.667 1.56 0.00 0.00 2.40
64 65 4.495422 TCTAGTTGCGAAACCTCATCTTC 58.505 43.478 1.56 0.00 0.00 2.87
65 66 3.409026 AGTTGCGAAACCTCATCTTCT 57.591 42.857 1.56 0.00 0.00 2.85
66 67 3.330267 AGTTGCGAAACCTCATCTTCTC 58.670 45.455 1.56 0.00 0.00 2.87
67 68 3.007398 AGTTGCGAAACCTCATCTTCTCT 59.993 43.478 1.56 0.00 0.00 3.10
68 69 4.220821 AGTTGCGAAACCTCATCTTCTCTA 59.779 41.667 1.56 0.00 0.00 2.43
69 70 4.801330 TGCGAAACCTCATCTTCTCTAA 57.199 40.909 0.00 0.00 0.00 2.10
70 71 5.344743 TGCGAAACCTCATCTTCTCTAAT 57.655 39.130 0.00 0.00 0.00 1.73
71 72 5.734720 TGCGAAACCTCATCTTCTCTAATT 58.265 37.500 0.00 0.00 0.00 1.40
72 73 6.173339 TGCGAAACCTCATCTTCTCTAATTT 58.827 36.000 0.00 0.00 0.00 1.82
73 74 6.313905 TGCGAAACCTCATCTTCTCTAATTTC 59.686 38.462 0.00 0.00 0.00 2.17
74 75 6.536941 GCGAAACCTCATCTTCTCTAATTTCT 59.463 38.462 0.00 0.00 0.00 2.52
75 76 7.065204 GCGAAACCTCATCTTCTCTAATTTCTT 59.935 37.037 0.00 0.00 0.00 2.52
76 77 8.386606 CGAAACCTCATCTTCTCTAATTTCTTG 58.613 37.037 0.00 0.00 0.00 3.02
77 78 7.622893 AACCTCATCTTCTCTAATTTCTTGC 57.377 36.000 0.00 0.00 0.00 4.01
78 79 6.715280 ACCTCATCTTCTCTAATTTCTTGCA 58.285 36.000 0.00 0.00 0.00 4.08
79 80 7.170965 ACCTCATCTTCTCTAATTTCTTGCAA 58.829 34.615 0.00 0.00 0.00 4.08
80 81 7.120432 ACCTCATCTTCTCTAATTTCTTGCAAC 59.880 37.037 0.00 0.00 0.00 4.17
81 82 7.120285 CCTCATCTTCTCTAATTTCTTGCAACA 59.880 37.037 0.00 0.00 0.00 3.33
82 83 8.394971 TCATCTTCTCTAATTTCTTGCAACAA 57.605 30.769 0.00 0.00 0.00 2.83
83 84 8.849168 TCATCTTCTCTAATTTCTTGCAACAAA 58.151 29.630 2.22 2.22 0.00 2.83
84 85 9.467258 CATCTTCTCTAATTTCTTGCAACAAAA 57.533 29.630 3.92 4.56 0.00 2.44
85 86 9.688592 ATCTTCTCTAATTTCTTGCAACAAAAG 57.311 29.630 3.92 0.00 0.00 2.27
86 87 7.649306 TCTTCTCTAATTTCTTGCAACAAAAGC 59.351 33.333 3.92 0.00 0.00 3.51
87 88 7.042797 TCTCTAATTTCTTGCAACAAAAGCT 57.957 32.000 3.92 0.00 0.00 3.74
88 89 7.491682 TCTCTAATTTCTTGCAACAAAAGCTT 58.508 30.769 3.92 0.00 0.00 3.74
89 90 7.981225 TCTCTAATTTCTTGCAACAAAAGCTTT 59.019 29.630 5.69 5.69 0.00 3.51
90 91 7.908230 TCTAATTTCTTGCAACAAAAGCTTTG 58.092 30.769 13.54 9.55 0.00 2.77
91 92 6.499234 AATTTCTTGCAACAAAAGCTTTGT 57.501 29.167 13.54 10.20 0.00 2.83
92 93 5.529014 TTTCTTGCAACAAAAGCTTTGTC 57.471 34.783 13.54 3.53 0.00 3.18
102 103 2.844122 AAGCTTTGTCGCGAAACTTT 57.156 40.000 12.06 0.00 34.40 2.66
106 107 2.286184 GCTTTGTCGCGAAACTTTCTCA 60.286 45.455 12.06 0.00 0.00 3.27
445 1417 2.938798 AGAAATGCGGGGGTGGGA 60.939 61.111 0.00 0.00 0.00 4.37
447 1419 4.060667 AAATGCGGGGGTGGGAGG 62.061 66.667 0.00 0.00 0.00 4.30
749 2068 2.202690 CGGATGCGCGTGAGGTAA 60.203 61.111 6.97 0.00 0.00 2.85
750 2069 2.230940 CGGATGCGCGTGAGGTAAG 61.231 63.158 6.97 0.00 0.00 2.34
751 2070 2.526120 GGATGCGCGTGAGGTAAGC 61.526 63.158 6.97 0.00 0.00 3.09
752 2071 1.519455 GATGCGCGTGAGGTAAGCT 60.519 57.895 6.97 0.00 0.00 3.74
756 2075 0.179222 GCGCGTGAGGTAAGCTTTTC 60.179 55.000 3.20 1.11 0.00 2.29
758 2077 0.803117 GCGTGAGGTAAGCTTTTCCC 59.197 55.000 3.20 2.56 0.00 3.97
841 2160 0.679505 CTCACAGTTCGGTCCAAGGA 59.320 55.000 0.00 0.00 0.00 3.36
847 2166 0.602905 GTTCGGTCCAAGGACACCAG 60.603 60.000 20.03 8.77 46.20 4.00
849 2168 1.004918 CGGTCCAAGGACACCAGAC 60.005 63.158 20.03 1.71 46.20 3.51
865 2184 2.909965 ACCAAACACGGCGCCATT 60.910 55.556 28.98 14.74 0.00 3.16
902 2227 1.415659 CCCATCTACTCCTGAAGGCAG 59.584 57.143 0.00 0.00 41.93 4.85
1116 2441 0.179129 TCCGCGGATTTCGACTAACC 60.179 55.000 27.28 0.00 42.43 2.85
1120 2445 0.828677 CGGATTTCGACTAACCCCCT 59.171 55.000 0.00 0.00 42.43 4.79
1184 2509 3.148279 ATCCTGGACCTCGCCGAC 61.148 66.667 0.00 0.00 0.00 4.79
1462 2789 2.093500 TCTGGTTTGCGCTCATAGATGT 60.093 45.455 9.73 0.00 0.00 3.06
1675 3069 8.345565 CAATATCACTAAACTAATGTGGAAGCC 58.654 37.037 0.00 0.00 33.04 4.35
1815 3209 4.451096 GCAGTGTATATGTATTGTTCCGGG 59.549 45.833 0.00 0.00 0.00 5.73
2311 3961 9.424319 CATTTTGCTCCGTATGTAGTCTATATT 57.576 33.333 0.00 0.00 0.00 1.28
2312 3962 8.812147 TTTTGCTCCGTATGTAGTCTATATTG 57.188 34.615 0.00 0.00 0.00 1.90
2313 3963 6.510879 TGCTCCGTATGTAGTCTATATTGG 57.489 41.667 0.00 0.00 0.00 3.16
2314 3964 6.243148 TGCTCCGTATGTAGTCTATATTGGA 58.757 40.000 8.84 8.84 0.00 3.53
2315 3965 6.717997 TGCTCCGTATGTAGTCTATATTGGAA 59.282 38.462 9.87 0.00 0.00 3.53
2316 3966 7.396339 TGCTCCGTATGTAGTCTATATTGGAAT 59.604 37.037 9.87 0.00 0.00 3.01
2317 3967 7.916450 GCTCCGTATGTAGTCTATATTGGAATC 59.084 40.741 9.87 4.29 0.00 2.52
2318 3968 9.179909 CTCCGTATGTAGTCTATATTGGAATCT 57.820 37.037 9.87 0.00 0.00 2.40
2319 3969 9.175312 TCCGTATGTAGTCTATATTGGAATCTC 57.825 37.037 7.43 0.00 0.00 2.75
2320 3970 9.179909 CCGTATGTAGTCTATATTGGAATCTCT 57.820 37.037 0.00 0.00 0.00 3.10
2397 4047 2.215196 GCGAATTTTACCATAGGGCGA 58.785 47.619 0.00 0.00 37.90 5.54
2488 4138 3.308046 GGATTCTTTCCCTTCTGCTGAGT 60.308 47.826 0.00 0.00 38.75 3.41
2667 4318 9.009327 CAATTATAGGTTATTTTGTGTGAAGCG 57.991 33.333 0.00 0.00 0.00 4.68
2763 4414 3.637911 TTGCAACGGGGATACACTAAT 57.362 42.857 0.00 0.00 38.54 1.73
2917 4568 1.306997 TCCCCATCTTCCTTCGCCT 60.307 57.895 0.00 0.00 0.00 5.52
2927 4578 2.126463 CTTCGCCTTCGACGCTCA 60.126 61.111 2.47 0.00 45.43 4.26
2944 4595 4.903010 ACACAGTCGCCGGCGTTT 62.903 61.111 44.16 31.21 40.74 3.60
3185 4844 4.023536 GTCTAAACAGCGAAAACCCAATGA 60.024 41.667 0.00 0.00 0.00 2.57
3319 4981 5.104900 ACTTGGGCTCATTTTCGTAGTCTAT 60.105 40.000 0.00 0.00 0.00 1.98
3429 5091 2.353505 GGTTCCGAGTACACCTTCCTTC 60.354 54.545 0.00 0.00 0.00 3.46
3498 5160 2.669569 CACCTGGCCGTGGAACAG 60.670 66.667 19.87 0.00 41.80 3.16
3580 5242 1.372683 GCTCCCTGCAGACTGTTCA 59.627 57.895 17.39 0.00 42.31 3.18
3592 5254 1.302832 CTGTTCACCACCTGGGAGC 60.303 63.158 0.00 0.00 41.15 4.70
3593 5255 2.034221 GTTCACCACCTGGGAGCC 59.966 66.667 0.00 0.00 41.15 4.70
3594 5256 2.449518 TTCACCACCTGGGAGCCA 60.450 61.111 0.00 0.00 41.15 4.75
3634 5299 2.590575 CGCAGGTTCCGTTGTGGT 60.591 61.111 0.00 0.00 39.52 4.16
3637 5302 0.889186 GCAGGTTCCGTTGTGGTCAT 60.889 55.000 0.00 0.00 39.52 3.06
3683 5348 4.737177 TGGTCGCATGGCATGGCA 62.737 61.111 27.48 25.52 0.00 4.92
3735 5400 4.711949 CAGGGAAGGCGCTGCAGT 62.712 66.667 16.64 0.00 46.16 4.40
3737 5402 4.704833 GGGAAGGCGCTGCAGTCA 62.705 66.667 16.64 0.00 0.00 3.41
4078 6122 1.931172 CGCCCCGTTATGTAGTTTCAG 59.069 52.381 0.00 0.00 0.00 3.02
4255 6602 1.471684 CCTTCCTTGAGCTTGATGCAC 59.528 52.381 0.00 0.00 45.94 4.57
4257 6604 1.136147 CCTTGAGCTTGATGCACGC 59.864 57.895 0.00 0.00 45.94 5.34
4462 6809 4.505566 GGAATCTTGGCTCATATGGCTGTA 60.506 45.833 13.60 2.04 0.00 2.74
4486 6834 5.308825 AGATCTTGGAGTACAGTGTTTTGG 58.691 41.667 0.00 0.00 0.00 3.28
4819 7167 3.825014 GGTCGAGTATGGGTATGCTTCTA 59.175 47.826 0.00 0.00 28.70 2.10
4856 7204 9.411801 GTTTTTCTTTCTCTTTTGAAGACTTGT 57.588 29.630 0.00 0.00 33.12 3.16
4957 7306 7.485913 CCAAGTAATGTCATTGTTGTATCAAGC 59.514 37.037 8.39 0.00 0.00 4.01
4963 7312 5.123027 TGTCATTGTTGTATCAAGCGCAATA 59.877 36.000 11.47 1.12 0.00 1.90
5098 7447 2.092429 TGGCACCCCATTCTCATTAGTC 60.092 50.000 0.00 0.00 35.79 2.59
5105 7454 5.726793 ACCCCATTCTCATTAGTCTGTACTT 59.273 40.000 0.00 0.00 37.15 2.24
5169 7521 4.271776 ACAGTCAGTGTTAAAACGCCTTAC 59.728 41.667 2.89 0.33 40.18 2.34
5179 7531 8.632551 GTGTTAAAACGCCTTACATTTTGATAC 58.367 33.333 0.00 0.00 33.44 2.24
5180 7532 8.350722 TGTTAAAACGCCTTACATTTTGATACA 58.649 29.630 0.00 0.00 0.00 2.29
5184 7536 5.488341 ACGCCTTACATTTTGATACAGAGT 58.512 37.500 0.00 0.00 0.00 3.24
5294 7647 3.057315 GCATTTGTCAACAGTGCACCTAT 60.057 43.478 14.63 0.00 38.41 2.57
5295 7648 4.155826 GCATTTGTCAACAGTGCACCTATA 59.844 41.667 14.63 0.00 38.41 1.31
5300 7653 5.744171 TGTCAACAGTGCACCTATATCATT 58.256 37.500 14.63 0.00 0.00 2.57
5430 8517 3.038946 CAGCATGCGAACCATTTGG 57.961 52.632 13.01 0.00 42.17 3.28
5474 8561 6.757897 TGATCGCAAATGTTAATTCTTCCT 57.242 33.333 0.00 0.00 0.00 3.36
5565 8659 4.037927 TCTATTCCACTGGGTTAAGGAGG 58.962 47.826 0.00 0.00 34.93 4.30
5599 8693 3.969117 TGTTTCATGTCTGCTGTTGTC 57.031 42.857 0.00 0.00 0.00 3.18
5739 8833 3.243569 CCGGAAAGATGGCTAGTCACTAG 60.244 52.174 7.56 7.56 37.16 2.57
5819 8913 3.387374 TGGTTGGTGCTTTTTGATGATGT 59.613 39.130 0.00 0.00 0.00 3.06
5825 8919 3.763897 GTGCTTTTTGATGATGTAGGGGT 59.236 43.478 0.00 0.00 0.00 4.95
5860 8954 7.487829 CCGGTTGATTGGTAAACATTCTAAATG 59.512 37.037 0.00 0.00 32.15 2.32
5868 8962 7.160049 TGGTAAACATTCTAAATGACCGTGTA 58.840 34.615 6.67 0.00 0.00 2.90
5903 8997 4.100344 TGCGGATACATGGTTTCTTAGCTA 59.900 41.667 0.00 0.00 0.00 3.32
5917 9011 9.152595 GGTTTCTTAGCTATGTAATATGCTACC 57.847 37.037 6.53 0.00 36.21 3.18
5971 9065 6.881570 TGCTCTACTGAAAGATGATTGATGA 58.118 36.000 0.00 0.00 37.43 2.92
5983 9077 8.850007 AAGATGATTGATGAATATGACTCCTG 57.150 34.615 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.781158 GGCGGCGGGCATATTTTGT 61.781 57.895 9.78 0.00 46.16 2.83
50 51 8.386606 CAAGAAATTAGAGAAGATGAGGTTTCG 58.613 37.037 0.00 0.00 0.00 3.46
51 52 8.180920 GCAAGAAATTAGAGAAGATGAGGTTTC 58.819 37.037 0.00 0.00 0.00 2.78
52 53 7.667219 TGCAAGAAATTAGAGAAGATGAGGTTT 59.333 33.333 0.00 0.00 0.00 3.27
53 54 7.170965 TGCAAGAAATTAGAGAAGATGAGGTT 58.829 34.615 0.00 0.00 0.00 3.50
54 55 6.715280 TGCAAGAAATTAGAGAAGATGAGGT 58.285 36.000 0.00 0.00 0.00 3.85
55 56 7.120285 TGTTGCAAGAAATTAGAGAAGATGAGG 59.880 37.037 0.00 0.00 0.00 3.86
56 57 8.037382 TGTTGCAAGAAATTAGAGAAGATGAG 57.963 34.615 0.00 0.00 0.00 2.90
57 58 7.984422 TGTTGCAAGAAATTAGAGAAGATGA 57.016 32.000 0.00 0.00 0.00 2.92
58 59 9.467258 TTTTGTTGCAAGAAATTAGAGAAGATG 57.533 29.630 20.94 0.00 0.00 2.90
59 60 9.688592 CTTTTGTTGCAAGAAATTAGAGAAGAT 57.311 29.630 20.94 0.00 0.00 2.40
60 61 7.649306 GCTTTTGTTGCAAGAAATTAGAGAAGA 59.351 33.333 20.94 3.76 0.00 2.87
61 62 7.650903 AGCTTTTGTTGCAAGAAATTAGAGAAG 59.349 33.333 20.94 14.40 0.00 2.85
62 63 7.491682 AGCTTTTGTTGCAAGAAATTAGAGAA 58.508 30.769 20.94 5.09 0.00 2.87
63 64 7.042797 AGCTTTTGTTGCAAGAAATTAGAGA 57.957 32.000 20.94 5.76 0.00 3.10
64 65 7.704789 AAGCTTTTGTTGCAAGAAATTAGAG 57.295 32.000 20.94 15.96 0.00 2.43
65 66 7.548780 ACAAAGCTTTTGTTGCAAGAAATTAGA 59.451 29.630 20.94 6.77 0.00 2.10
66 67 7.687445 ACAAAGCTTTTGTTGCAAGAAATTAG 58.313 30.769 20.94 16.90 0.00 1.73
67 68 7.463913 CGACAAAGCTTTTGTTGCAAGAAATTA 60.464 33.333 20.94 7.78 31.96 1.40
68 69 6.499234 ACAAAGCTTTTGTTGCAAGAAATT 57.501 29.167 20.94 10.85 0.00 1.82
69 70 5.220453 CGACAAAGCTTTTGTTGCAAGAAAT 60.220 36.000 20.94 5.76 31.96 2.17
70 71 4.091220 CGACAAAGCTTTTGTTGCAAGAAA 59.909 37.500 17.04 17.04 31.96 2.52
71 72 3.611986 CGACAAAGCTTTTGTTGCAAGAA 59.388 39.130 9.53 4.66 31.96 2.52
72 73 3.178267 CGACAAAGCTTTTGTTGCAAGA 58.822 40.909 9.53 0.00 31.96 3.02
73 74 3.557908 CGACAAAGCTTTTGTTGCAAG 57.442 42.857 9.53 0.00 31.96 4.01
77 78 1.821336 TCGCGACAAAGCTTTTGTTG 58.179 45.000 9.53 14.99 36.98 3.33
78 79 2.553079 TTCGCGACAAAGCTTTTGTT 57.447 40.000 9.15 0.00 31.96 2.83
79 80 2.159435 AGTTTCGCGACAAAGCTTTTGT 60.159 40.909 9.15 11.20 34.97 2.83
80 81 2.450160 AGTTTCGCGACAAAGCTTTTG 58.550 42.857 9.15 7.95 34.40 2.44
81 82 2.844122 AGTTTCGCGACAAAGCTTTT 57.156 40.000 9.15 1.05 34.40 2.27
82 83 2.844122 AAGTTTCGCGACAAAGCTTT 57.156 40.000 9.15 5.69 34.40 3.51
83 84 2.354821 AGAAAGTTTCGCGACAAAGCTT 59.645 40.909 9.15 5.29 34.40 3.74
84 85 1.940613 AGAAAGTTTCGCGACAAAGCT 59.059 42.857 9.15 0.00 34.40 3.74
85 86 2.286184 TGAGAAAGTTTCGCGACAAAGC 60.286 45.455 9.15 0.00 31.63 3.51
86 87 3.585748 TGAGAAAGTTTCGCGACAAAG 57.414 42.857 9.15 0.00 31.63 2.77
87 88 5.637810 AGATATGAGAAAGTTTCGCGACAAA 59.362 36.000 9.15 0.00 31.63 2.83
88 89 5.168569 AGATATGAGAAAGTTTCGCGACAA 58.831 37.500 9.15 3.71 31.63 3.18
89 90 4.744570 AGATATGAGAAAGTTTCGCGACA 58.255 39.130 9.15 0.00 31.63 4.35
90 91 6.807708 TTAGATATGAGAAAGTTTCGCGAC 57.192 37.500 9.15 0.00 31.63 5.19
91 92 8.420374 AAATTAGATATGAGAAAGTTTCGCGA 57.580 30.769 3.71 3.71 31.63 5.87
92 93 7.794349 GGAAATTAGATATGAGAAAGTTTCGCG 59.206 37.037 13.64 0.00 31.63 5.87
102 103 5.924356 TGTTGCGGGAAATTAGATATGAGA 58.076 37.500 0.00 0.00 0.00 3.27
106 107 5.239525 GCTCTTGTTGCGGGAAATTAGATAT 59.760 40.000 0.00 0.00 0.00 1.63
456 1436 0.471211 GGTATGGATCGGAGACCCCA 60.471 60.000 0.00 0.00 44.53 4.96
747 2066 8.706322 AAAACTATCTCAAAGGGAAAAGCTTA 57.294 30.769 0.00 0.00 0.00 3.09
749 2068 7.603180 AAAAACTATCTCAAAGGGAAAAGCT 57.397 32.000 0.00 0.00 0.00 3.74
778 2097 8.952278 TGGTGGTATTAACTATGTCAAATTCAC 58.048 33.333 0.00 0.00 0.00 3.18
779 2098 8.952278 GTGGTGGTATTAACTATGTCAAATTCA 58.048 33.333 0.00 0.00 0.00 2.57
781 2100 9.528489 AAGTGGTGGTATTAACTATGTCAAATT 57.472 29.630 0.00 0.00 0.00 1.82
782 2101 8.956426 CAAGTGGTGGTATTAACTATGTCAAAT 58.044 33.333 0.00 0.00 0.00 2.32
788 2107 7.065803 CCTTGTCAAGTGGTGGTATTAACTATG 59.934 40.741 11.61 0.00 0.00 2.23
841 2160 1.822186 GCCGTGTTTGGTCTGGTGT 60.822 57.895 0.00 0.00 0.00 4.16
847 2166 2.914908 AATGGCGCCGTGTTTGGTC 61.915 57.895 24.67 0.00 0.00 4.02
849 2168 2.430582 CAATGGCGCCGTGTTTGG 60.431 61.111 24.67 6.02 0.00 3.28
865 2184 2.282180 GCCTGGGCCTCGAAAACA 60.282 61.111 4.53 0.00 34.56 2.83
902 2227 2.025359 CTTCTTCGTTCCGATGCGCC 62.025 60.000 4.18 0.00 35.23 6.53
908 2233 1.733041 CTGCGCTTCTTCGTTCCGA 60.733 57.895 9.73 0.00 0.00 4.55
1095 2420 0.101759 TTAGTCGAAATCCGCGGAGG 59.898 55.000 33.87 21.12 42.97 4.30
1184 2509 2.495155 TGATGGTCTGGTTGGTCATG 57.505 50.000 0.00 0.00 0.00 3.07
1485 2812 8.595362 TCACAGATACAATATCCTACATAGGG 57.405 38.462 5.10 0.00 43.79 3.53
1500 2827 8.886719 CAAGCAGAGATAAAATTCACAGATACA 58.113 33.333 0.00 0.00 0.00 2.29
1505 2832 8.509690 TCTTTCAAGCAGAGATAAAATTCACAG 58.490 33.333 0.00 0.00 0.00 3.66
1815 3209 6.313658 AGTTGAAACTTGATCCAAAACAAAGC 59.686 34.615 0.00 0.00 35.21 3.51
1974 3599 8.573885 CATTGTATGAATAGGCAGTCATTGAAT 58.426 33.333 5.48 0.00 39.95 2.57
2153 3803 2.971330 ACAGGGAGGATGTCATCAGATC 59.029 50.000 14.72 8.81 0.00 2.75
2321 3971 8.957466 CCTCCGTTCCTAAATAGAAATCTTTTT 58.043 33.333 4.64 4.64 33.07 1.94
2322 3972 7.556635 CCCTCCGTTCCTAAATAGAAATCTTTT 59.443 37.037 0.00 0.00 0.00 2.27
2323 3973 7.054751 CCCTCCGTTCCTAAATAGAAATCTTT 58.945 38.462 0.00 0.00 0.00 2.52
2324 3974 6.386050 TCCCTCCGTTCCTAAATAGAAATCTT 59.614 38.462 0.00 0.00 0.00 2.40
2328 3978 5.028131 ACTCCCTCCGTTCCTAAATAGAAA 58.972 41.667 0.00 0.00 0.00 2.52
2331 3981 3.705072 ACACTCCCTCCGTTCCTAAATAG 59.295 47.826 0.00 0.00 0.00 1.73
2605 4255 8.730680 GTTCTACAACCATTAATGACTCAATGT 58.269 33.333 17.23 12.87 31.52 2.71
2636 4286 9.801873 CACACAAAATAACCTATAATTGGAAGG 57.198 33.333 0.00 0.00 36.42 3.46
2667 4318 1.450531 AAGGCAGAACAGCACTGTGC 61.451 55.000 24.59 24.59 44.13 4.57
2763 4414 2.437651 TCTATCATGGCATCCCGTTTCA 59.562 45.455 0.00 0.00 0.00 2.69
2902 4553 0.175760 TCGAAGGCGAAGGAAGATGG 59.824 55.000 0.00 0.00 44.78 3.51
2917 4568 4.628160 GACTGTGTGAGCGTCGAA 57.372 55.556 0.00 0.00 0.00 3.71
2943 4594 0.248012 TGCCTTAGCGACGGATTCAA 59.752 50.000 0.00 0.00 44.31 2.69
2944 4595 0.179111 CTGCCTTAGCGACGGATTCA 60.179 55.000 0.00 0.00 44.31 2.57
3185 4844 4.021280 TGCATTTCCATGTTGTATGCACTT 60.021 37.500 14.28 0.00 44.59 3.16
3429 5091 1.725641 TGGCAGCATACTTCAACGAG 58.274 50.000 0.00 0.00 0.00 4.18
3580 5242 3.252284 CTGTGGCTCCCAGGTGGT 61.252 66.667 0.00 0.00 32.34 4.16
3593 5255 3.566261 GTGCGGTCCACATCTGTG 58.434 61.111 3.28 3.28 44.06 3.66
3634 5299 2.369633 ATGGAGCCTCGCCACATGA 61.370 57.895 0.00 0.00 35.91 3.07
3637 5302 4.783621 GCATGGAGCCTCGCCACA 62.784 66.667 0.00 0.00 35.91 4.17
3893 5929 9.574401 AAAAACAATCATTTAAAAACGTATGCG 57.426 25.926 0.19 0.19 44.93 4.73
4288 6635 8.906867 GGCATATATTAATGTACCAATCTGCAT 58.093 33.333 12.40 0.00 0.00 3.96
4318 6665 7.350744 TCATAATGCTATTTGCTTTCACCAT 57.649 32.000 0.00 0.00 43.37 3.55
4462 6809 5.765182 CCAAAACACTGTACTCCAAGATCTT 59.235 40.000 0.88 0.88 0.00 2.40
4486 6834 3.663025 ACAAATATGCAACAGTTTGGCC 58.337 40.909 15.89 0.00 36.23 5.36
4963 7312 9.606631 AAGCGACTATAAGATTCTGATTCTTTT 57.393 29.630 17.08 12.87 35.19 2.27
5098 7447 5.126707 ACGGAGGGAGTATTTACAAGTACAG 59.873 44.000 0.00 0.00 0.00 2.74
5105 7454 6.795144 TTTGATACGGAGGGAGTATTTACA 57.205 37.500 0.00 0.00 35.19 2.41
5196 7548 4.519906 TTCCAAGGAGAAAGAACTGGTT 57.480 40.909 0.00 0.00 0.00 3.67
5204 7556 4.390909 GCAATGCATTTTCCAAGGAGAAAG 59.609 41.667 9.83 0.00 37.09 2.62
5382 7735 8.244802 ACCATATGTAGAAGCTATGTATTCGTC 58.755 37.037 1.24 0.00 0.00 4.20
5430 8517 8.587950 CGATCAAGAAGTCTACATTTAAGTGTC 58.412 37.037 6.91 0.00 33.62 3.67
5565 8659 3.564235 TGAAACATGCAGTGCAATCTC 57.436 42.857 23.90 15.98 43.62 2.75
5599 8693 6.917477 TCAAATTTTCCAACACTTCTCAATCG 59.083 34.615 0.00 0.00 0.00 3.34
5652 8746 8.494433 AGAATCCTTTTACAGTGCCTGATTATA 58.506 33.333 8.91 0.00 35.18 0.98
5714 8808 3.101437 TGACTAGCCATCTTTCCGGTTA 58.899 45.455 0.00 0.00 0.00 2.85
5825 8919 2.959707 ACCAATCAACCGGTTGCTTTAA 59.040 40.909 37.21 23.05 40.24 1.52
5860 8954 3.367025 GCAAGTACAACATCTACACGGTC 59.633 47.826 0.00 0.00 0.00 4.79
5868 8962 4.465632 TGTATCCGCAAGTACAACATCT 57.534 40.909 0.00 0.00 0.00 2.90
5903 8997 9.424319 CAAATCTCTTACGGTAGCATATTACAT 57.576 33.333 0.00 0.00 0.00 2.29
5917 9011 2.744202 AGCCTTGTGCAAATCTCTTACG 59.256 45.455 0.00 0.00 44.83 3.18


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

AutoCloner maintained by Alex Coulton.