Multiple sequence alignment - TraesCS7B01G495000

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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 TraesCS7B01G495000 chr7B 100.000 3032 0 0 1 3032 746296454 746299485 0.000000e+00 5600.0
1 TraesCS7B01G495000 chr7B 100.000 1973 0 0 416 2388 746441180 746439208 0.000000e+00 3644.0
2 TraesCS7B01G495000 chr7B 91.530 366 25 2 2390 2755 747292346 747292705 1.620000e-137 499.0
3 TraesCS7B01G495000 chr7B 90.110 364 25 2 78 430 746441784 746441421 2.130000e-126 462.0
4 TraesCS7B01G495000 chr7B 87.931 348 30 2 94 430 746441577 746441231 1.690000e-107 399.0
5 TraesCS7B01G495000 chr7B 87.500 344 31 3 98 430 746441668 746441326 1.320000e-103 387.0
6 TraesCS7B01G495000 chr7B 86.928 306 28 2 98 392 746441478 746441174 1.740000e-87 333.0
7 TraesCS7B01G495000 chr7B 88.327 257 22 3 2784 3032 745105003 745105259 4.910000e-78 302.0
8 TraesCS7B01G495000 chr7B 85.816 282 27 3 426 694 21313119 21313400 1.380000e-73 287.0
9 TraesCS7B01G495000 chr7B 90.244 205 19 1 94 298 746441387 746441184 1.790000e-67 267.0
10 TraesCS7B01G495000 chr7B 95.862 145 4 1 2268 2410 746298576 746298720 1.820000e-57 233.0
11 TraesCS7B01G495000 chr7B 95.862 145 4 1 2123 2267 746298721 746298863 1.820000e-57 233.0
12 TraesCS7B01G495000 chr7B 95.862 145 4 1 2268 2410 746439473 746439329 1.820000e-57 233.0
13 TraesCS7B01G495000 chr7B 95.935 123 3 1 2123 2245 746439328 746439208 6.630000e-47 198.0
14 TraesCS7B01G495000 chr7B 86.932 176 18 2 2563 2737 745104818 745104989 3.080000e-45 193.0
15 TraesCS7B01G495000 chr7B 72.642 424 105 11 1630 2047 745102916 745103334 2.450000e-26 130.0
16 TraesCS7B01G495000 chr7B 77.209 215 42 4 2417 2626 746666675 746666887 5.310000e-23 119.0
17 TraesCS7B01G495000 chr7B 95.385 65 3 0 2772 2836 747292690 747292754 1.490000e-18 104.0
18 TraesCS7B01G495000 chr7B 100.000 43 0 0 2280 2322 744648162 744648120 2.510000e-11 80.5
19 TraesCS7B01G495000 chr7B 91.525 59 4 1 2271 2328 746382634 746382576 2.510000e-11 80.5
20 TraesCS7B01G495000 chr7D 86.517 356 40 5 2390 2741 633153287 633153638 4.740000e-103 385.0
21 TraesCS7B01G495000 chr7D 86.226 363 40 6 2393 2751 633200497 633200141 4.740000e-103 385.0
22 TraesCS7B01G495000 chr7D 88.889 261 19 2 2772 3032 633028173 633027923 2.270000e-81 313.0
23 TraesCS7B01G495000 chr7D 90.749 227 17 3 2393 2616 633028482 633028257 1.770000e-77 300.0
24 TraesCS7B01G495000 chr7D 92.453 106 6 1 2649 2754 633028262 633028159 1.880000e-32 150.0
25 TraesCS7B01G495000 chr7D 83.824 136 22 0 556 691 75958725 75958860 2.450000e-26 130.0
26 TraesCS7B01G495000 chr7D 78.974 195 31 7 1822 2011 633029811 633029622 1.140000e-24 124.0
27 TraesCS7B01G495000 chr7D 89.744 78 7 1 5 81 287710739 287710816 6.920000e-17 99.0
28 TraesCS7B01G495000 chr7D 94.545 55 2 1 27 81 158311151 158311098 1.940000e-12 84.2
29 TraesCS7B01G495000 chr4A 87.786 262 32 0 430 691 641844510 641844771 1.060000e-79 307.0
30 TraesCS7B01G495000 chr4A 84.643 280 25 11 427 693 81267519 81267793 2.320000e-66 263.0
31 TraesCS7B01G495000 chr3D 87.786 262 28 1 430 691 162844297 162844554 1.370000e-78 303.0
32 TraesCS7B01G495000 chr3D 82.857 140 20 2 556 691 613709870 613709731 4.110000e-24 122.0
33 TraesCS7B01G495000 chr3D 91.045 67 6 0 15 81 12732697 12732763 1.160000e-14 91.6
34 TraesCS7B01G495000 chr2A 86.296 270 29 4 430 691 46843363 46843094 1.380000e-73 287.0
35 TraesCS7B01G495000 chr2A 93.827 81 5 0 1 81 235359944 235360024 4.110000e-24 122.0
36 TraesCS7B01G495000 chr2A 92.593 81 6 0 1 81 235358180 235358260 1.910000e-22 117.0
37 TraesCS7B01G495000 chr2A 89.831 59 6 0 2270 2328 2919832 2919890 3.240000e-10 76.8
38 TraesCS7B01G495000 chr3B 85.992 257 26 7 431 682 546540019 546540270 1.790000e-67 267.0
39 TraesCS7B01G495000 chr3B 75.058 433 95 12 1161 1588 52917277 52916853 3.990000e-44 189.0
40 TraesCS7B01G495000 chr3B 81.159 138 20 2 562 693 86565773 86565910 4.130000e-19 106.0
41 TraesCS7B01G495000 chr2B 84.926 272 29 8 430 694 255579659 255579393 6.450000e-67 265.0
42 TraesCS7B01G495000 chr2B 74.501 451 101 13 1143 1588 8342772 8343213 1.860000e-42 183.0
43 TraesCS7B01G495000 chr2B 88.235 68 7 1 15 81 82501949 82501882 2.510000e-11 80.5
44 TraesCS7B01G495000 chr5B 76.975 443 90 11 1151 1587 663115411 663115847 3.020000e-60 243.0
45 TraesCS7B01G495000 chrUn 86.364 220 29 1 425 643 50069521 50069302 3.910000e-59 239.0
46 TraesCS7B01G495000 chrUn 74.505 455 102 12 1145 1594 15478263 15477818 5.160000e-43 185.0
47 TraesCS7B01G495000 chrUn 74.172 453 104 13 1141 1587 15915811 15915366 3.110000e-40 176.0
48 TraesCS7B01G495000 chrUn 73.843 432 98 11 1169 1594 15492043 15491621 1.130000e-34 158.0
49 TraesCS7B01G495000 chrUn 89.796 49 5 0 2280 2328 364735807 364735855 2.520000e-06 63.9
50 TraesCS7B01G495000 chrUn 89.796 49 5 0 2280 2328 460310151 460310199 2.520000e-06 63.9
51 TraesCS7B01G495000 chr6B 83.895 267 22 9 428 693 135849880 135849634 5.050000e-58 235.0
52 TraesCS7B01G495000 chr2D 74.890 454 89 20 1154 1594 22567784 22567343 1.860000e-42 183.0
53 TraesCS7B01G495000 chr2D 82.778 180 27 4 1407 1584 2731876 2731699 1.130000e-34 158.0
54 TraesCS7B01G495000 chr2D 70.909 440 109 16 1751 2183 22567159 22566732 5.390000e-13 86.1
55 TraesCS7B01G495000 chr2D 88.462 52 6 0 2275 2326 2676708 2676657 2.520000e-06 63.9
56 TraesCS7B01G495000 chr1D 91.045 67 5 1 15 81 170905756 170905691 4.160000e-14 89.8
57 TraesCS7B01G495000 chr4B 92.593 54 2 2 28 81 525327913 525327964 3.240000e-10 76.8
58 TraesCS7B01G495000 chr1B 90.909 55 5 0 27 81 142839496 142839550 1.170000e-09 75.0


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 TraesCS7B01G495000 chr7B 746296454 746299485 3031 False 2022.000000 5600 97.241333 1 3032 3 chr7B.!!$F4 3031
1 TraesCS7B01G495000 chr7B 746439208 746441784 2576 True 740.375000 3644 91.813750 78 2410 8 chr7B.!!$R3 2332
2 TraesCS7B01G495000 chr7B 745102916 745105259 2343 False 208.333333 302 82.633667 1630 3032 3 chr7B.!!$F3 1402
3 TraesCS7B01G495000 chr7D 633027923 633029811 1888 True 221.750000 313 87.766250 1822 3032 4 chr7D.!!$R3 1210

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
28 29 0.102481 CGTACGAGGTGGGATCAAGG 59.898 60.0 10.44 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2388 3655 7.328493 TCGCTTATTATGTGGTGATATTTCGAG 59.672 37.037 0.0 0.0 0.0 4.04 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
20 21 3.829886 TTACTGTTACGTACGAGGTGG 57.170 47.619 24.41 11.04 0.00 4.61
21 22 0.883833 ACTGTTACGTACGAGGTGGG 59.116 55.000 24.41 9.48 0.00 4.61
22 23 1.167851 CTGTTACGTACGAGGTGGGA 58.832 55.000 24.41 0.00 0.00 4.37
23 24 1.747355 CTGTTACGTACGAGGTGGGAT 59.253 52.381 24.41 0.00 0.00 3.85
24 25 1.745087 TGTTACGTACGAGGTGGGATC 59.255 52.381 24.41 2.45 0.00 3.36
25 26 1.745087 GTTACGTACGAGGTGGGATCA 59.255 52.381 24.41 0.00 0.00 2.92
26 27 2.127271 TACGTACGAGGTGGGATCAA 57.873 50.000 24.41 0.00 0.00 2.57
27 28 0.815734 ACGTACGAGGTGGGATCAAG 59.184 55.000 24.41 0.00 0.00 3.02
28 29 0.102481 CGTACGAGGTGGGATCAAGG 59.898 60.000 10.44 0.00 0.00 3.61
29 30 1.481871 GTACGAGGTGGGATCAAGGA 58.518 55.000 0.00 0.00 0.00 3.36
30 31 1.136500 GTACGAGGTGGGATCAAGGAC 59.864 57.143 0.00 0.00 0.00 3.85
31 32 1.141881 CGAGGTGGGATCAAGGACG 59.858 63.158 0.00 0.00 0.00 4.79
32 33 1.320344 CGAGGTGGGATCAAGGACGA 61.320 60.000 0.00 0.00 0.00 4.20
33 34 0.902531 GAGGTGGGATCAAGGACGAA 59.097 55.000 0.00 0.00 0.00 3.85
34 35 1.278127 GAGGTGGGATCAAGGACGAAA 59.722 52.381 0.00 0.00 0.00 3.46
35 36 1.702957 AGGTGGGATCAAGGACGAAAA 59.297 47.619 0.00 0.00 0.00 2.29
36 37 2.308866 AGGTGGGATCAAGGACGAAAAT 59.691 45.455 0.00 0.00 0.00 1.82
37 38 3.521937 AGGTGGGATCAAGGACGAAAATA 59.478 43.478 0.00 0.00 0.00 1.40
38 39 4.018779 AGGTGGGATCAAGGACGAAAATAA 60.019 41.667 0.00 0.00 0.00 1.40
39 40 4.703093 GGTGGGATCAAGGACGAAAATAAA 59.297 41.667 0.00 0.00 0.00 1.40
40 41 5.392703 GGTGGGATCAAGGACGAAAATAAAC 60.393 44.000 0.00 0.00 0.00 2.01
41 42 4.703093 TGGGATCAAGGACGAAAATAAACC 59.297 41.667 0.00 0.00 0.00 3.27
42 43 4.703093 GGGATCAAGGACGAAAATAAACCA 59.297 41.667 0.00 0.00 0.00 3.67
43 44 5.163652 GGGATCAAGGACGAAAATAAACCAG 60.164 44.000 0.00 0.00 0.00 4.00
44 45 5.163652 GGATCAAGGACGAAAATAAACCAGG 60.164 44.000 0.00 0.00 0.00 4.45
45 46 4.076394 TCAAGGACGAAAATAAACCAGGG 58.924 43.478 0.00 0.00 0.00 4.45
46 47 3.801307 AGGACGAAAATAAACCAGGGT 57.199 42.857 0.00 0.00 0.00 4.34
47 48 4.914177 AGGACGAAAATAAACCAGGGTA 57.086 40.909 0.00 0.00 0.00 3.69
48 49 4.840271 AGGACGAAAATAAACCAGGGTAG 58.160 43.478 0.00 0.00 0.00 3.18
49 50 3.943381 GGACGAAAATAAACCAGGGTAGG 59.057 47.826 0.00 0.00 0.00 3.18
50 51 4.566278 GGACGAAAATAAACCAGGGTAGGT 60.566 45.833 0.00 0.00 45.91 3.08
51 52 4.329392 ACGAAAATAAACCAGGGTAGGTG 58.671 43.478 0.00 0.00 42.25 4.00
52 53 3.692593 CGAAAATAAACCAGGGTAGGTGG 59.307 47.826 0.00 0.00 42.25 4.61
53 54 3.750501 AAATAAACCAGGGTAGGTGGG 57.249 47.619 0.00 0.00 42.25 4.61
54 55 2.672703 ATAAACCAGGGTAGGTGGGA 57.327 50.000 0.00 0.00 42.25 4.37
55 56 1.660242 TAAACCAGGGTAGGTGGGAC 58.340 55.000 0.00 0.00 42.25 4.46
56 57 1.486145 AAACCAGGGTAGGTGGGACG 61.486 60.000 0.00 0.00 42.25 4.79
57 58 2.038329 CCAGGGTAGGTGGGACGA 59.962 66.667 0.00 0.00 0.00 4.20
58 59 1.611261 CCAGGGTAGGTGGGACGAA 60.611 63.158 0.00 0.00 0.00 3.85
59 60 1.196104 CCAGGGTAGGTGGGACGAAA 61.196 60.000 0.00 0.00 0.00 3.46
60 61 0.688487 CAGGGTAGGTGGGACGAAAA 59.312 55.000 0.00 0.00 0.00 2.29
61 62 1.280998 CAGGGTAGGTGGGACGAAAAT 59.719 52.381 0.00 0.00 0.00 1.82
62 63 1.990327 AGGGTAGGTGGGACGAAAATT 59.010 47.619 0.00 0.00 0.00 1.82
63 64 3.054948 CAGGGTAGGTGGGACGAAAATTA 60.055 47.826 0.00 0.00 0.00 1.40
64 65 3.588396 AGGGTAGGTGGGACGAAAATTAA 59.412 43.478 0.00 0.00 0.00 1.40
65 66 3.691118 GGGTAGGTGGGACGAAAATTAAC 59.309 47.826 0.00 0.00 0.00 2.01
66 67 3.691118 GGTAGGTGGGACGAAAATTAACC 59.309 47.826 0.00 0.00 0.00 2.85
67 68 2.429478 AGGTGGGACGAAAATTAACCG 58.571 47.619 0.00 0.00 0.00 4.44
68 69 2.038820 AGGTGGGACGAAAATTAACCGA 59.961 45.455 0.00 0.00 0.00 4.69
69 70 2.160219 GGTGGGACGAAAATTAACCGAC 59.840 50.000 0.00 0.00 0.00 4.79
70 71 2.067766 TGGGACGAAAATTAACCGACG 58.932 47.619 0.00 0.00 0.00 5.12
71 72 1.394572 GGGACGAAAATTAACCGACGG 59.605 52.381 13.61 13.61 0.00 4.79
72 73 2.336667 GGACGAAAATTAACCGACGGA 58.663 47.619 23.38 0.00 0.00 4.69
73 74 2.346545 GGACGAAAATTAACCGACGGAG 59.653 50.000 23.38 0.00 0.00 4.63
74 75 3.244976 GACGAAAATTAACCGACGGAGA 58.755 45.455 23.38 4.42 0.00 3.71
75 76 2.989166 ACGAAAATTAACCGACGGAGAC 59.011 45.455 23.38 2.12 0.00 3.36
76 77 3.248266 CGAAAATTAACCGACGGAGACT 58.752 45.455 23.38 4.34 0.00 3.24
115 116 1.737838 CTGCTTTCGGTGGCTCATTA 58.262 50.000 0.00 0.00 0.00 1.90
167 168 4.037089 TCAGCGTACTAACTCAAACAGTGA 59.963 41.667 0.00 0.00 34.56 3.41
214 215 3.270027 TGTCTTCGGTGGCTCATTAATG 58.730 45.455 9.29 9.29 0.00 1.90
215 216 3.055458 TGTCTTCGGTGGCTCATTAATGA 60.055 43.478 17.07 17.07 35.16 2.57
216 217 3.309954 GTCTTCGGTGGCTCATTAATGAC 59.690 47.826 14.23 10.90 32.50 3.06
259 260 8.542497 AATCATCAGCGTACTAACTTAAACAA 57.458 30.769 0.00 0.00 0.00 2.83
299 300 0.658897 GAAACGGTTGCTTTCGGTGA 59.341 50.000 0.00 0.00 0.00 4.02
324 431 3.627577 GGTGTTAGGTGCGATGAATCATT 59.372 43.478 0.00 0.00 0.00 2.57
327 434 4.511454 TGTTAGGTGCGATGAATCATTAGC 59.489 41.667 14.63 14.63 0.00 3.09
333 440 3.981416 TGCGATGAATCATTAGCGTACTC 59.019 43.478 15.83 0.00 33.10 2.59
361 468 2.154462 CAGTGATGTTGTTGGGGAGAC 58.846 52.381 0.00 0.00 0.00 3.36
362 469 1.156736 GTGATGTTGTTGGGGAGACG 58.843 55.000 0.00 0.00 0.00 4.18
368 475 2.105821 TGTTGTTGGGGAGACGAGAAAT 59.894 45.455 0.00 0.00 0.00 2.17
378 485 3.120165 GGAGACGAGAAATGGTTGCTTTC 60.120 47.826 0.00 0.00 33.69 2.62
381 488 1.535462 CGAGAAATGGTTGCTTTCGGT 59.465 47.619 0.00 0.00 37.62 4.69
399 506 2.419990 CGGTGGCTCATTAATGACTGGA 60.420 50.000 14.23 0.00 32.50 3.86
400 507 3.209410 GGTGGCTCATTAATGACTGGAG 58.791 50.000 14.23 5.74 32.50 3.86
2388 3655 4.113354 CGTCCTTGTACATTCTTCTAGCC 58.887 47.826 0.00 0.00 0.00 3.93
2391 3723 4.098044 TCCTTGTACATTCTTCTAGCCTCG 59.902 45.833 0.00 0.00 0.00 4.63
2415 3747 7.115805 TCGAAATATCACCACATAATAAGCGAC 59.884 37.037 0.00 0.00 0.00 5.19
2458 3790 8.815912 ACTGATATTAAGGTTTGCCATTTTCTT 58.184 29.630 0.00 0.00 37.19 2.52
2487 3819 2.763933 CTACATTGCTCTCGATGCCAT 58.236 47.619 7.87 0.69 37.56 4.40
2500 3834 3.313249 TCGATGCCATGTTTTCTAGCATG 59.687 43.478 7.89 0.00 43.86 4.06
2502 3836 1.477700 TGCCATGTTTTCTAGCATGCC 59.522 47.619 15.66 0.00 40.63 4.40
2512 3846 1.143684 TCTAGCATGCCCCATTTCTCC 59.856 52.381 15.66 0.00 0.00 3.71
2529 3863 5.514500 TTCTCCTGGCTTGTTAGGTATTT 57.486 39.130 0.00 0.00 35.54 1.40
2564 3898 3.517901 CTGGTATGGTTCCTGGTACTTCA 59.482 47.826 3.39 0.00 0.00 3.02
2585 3919 1.727857 CGTTTGCAATTGGTCGCTACC 60.728 52.381 7.72 0.00 46.98 3.18
2607 3942 0.250124 CAAGACTTGGCGGTGTACCA 60.250 55.000 7.35 0.00 35.14 3.25
2619 3954 2.223377 CGGTGTACCAAGAAAGTTCAGC 59.777 50.000 1.50 0.00 35.14 4.26
2722 4057 6.209589 ACTCTCAGAAGCTTACATCAGTTACA 59.790 38.462 0.00 0.00 0.00 2.41
2751 4086 9.775854 ATTAATTCAGTTGGTAGAGATCATCTG 57.224 33.333 0.00 0.00 39.20 2.90
2752 4087 4.662468 TCAGTTGGTAGAGATCATCTGC 57.338 45.455 0.00 0.00 39.20 4.26
2753 4088 4.285020 TCAGTTGGTAGAGATCATCTGCT 58.715 43.478 0.00 0.00 40.29 4.24
2754 4089 4.340666 TCAGTTGGTAGAGATCATCTGCTC 59.659 45.833 0.00 0.00 40.29 4.26
2755 4090 3.640967 AGTTGGTAGAGATCATCTGCTCC 59.359 47.826 0.00 0.00 40.29 4.70
2756 4091 2.603021 TGGTAGAGATCATCTGCTCCC 58.397 52.381 0.00 0.00 40.29 4.30
2757 4092 1.899142 GGTAGAGATCATCTGCTCCCC 59.101 57.143 0.00 0.00 40.29 4.81
2758 4093 1.899142 GTAGAGATCATCTGCTCCCCC 59.101 57.143 0.00 0.00 39.20 5.40
2759 4094 0.831288 AGAGATCATCTGCTCCCCCG 60.831 60.000 0.00 0.00 36.69 5.73
2760 4095 2.031768 GATCATCTGCTCCCCCGC 59.968 66.667 0.00 0.00 0.00 6.13
2761 4096 2.769621 ATCATCTGCTCCCCCGCA 60.770 61.111 0.00 0.00 38.40 5.69
2762 4097 2.329539 GATCATCTGCTCCCCCGCAA 62.330 60.000 0.00 0.00 39.80 4.85
2763 4098 1.925285 ATCATCTGCTCCCCCGCAAA 61.925 55.000 0.00 0.00 39.80 3.68
2764 4099 1.678635 CATCTGCTCCCCCGCAAAA 60.679 57.895 0.00 0.00 39.80 2.44
2765 4100 1.076549 ATCTGCTCCCCCGCAAAAA 59.923 52.632 0.00 0.00 39.80 1.94
2901 4237 4.422057 TCTGTATGGAAGGTGGTTCTGTA 58.578 43.478 0.00 0.00 35.25 2.74
2902 4238 4.466370 TCTGTATGGAAGGTGGTTCTGTAG 59.534 45.833 0.00 0.00 35.25 2.74
2903 4239 3.517901 TGTATGGAAGGTGGTTCTGTAGG 59.482 47.826 0.00 0.00 35.25 3.18
2904 4240 2.112279 TGGAAGGTGGTTCTGTAGGT 57.888 50.000 0.00 0.00 35.25 3.08
2905 4241 2.414612 TGGAAGGTGGTTCTGTAGGTT 58.585 47.619 0.00 0.00 35.25 3.50
2907 4243 3.181448 TGGAAGGTGGTTCTGTAGGTTTC 60.181 47.826 0.00 0.00 35.25 2.78
2908 4244 2.833631 AGGTGGTTCTGTAGGTTTCG 57.166 50.000 0.00 0.00 0.00 3.46
2909 4245 1.346722 AGGTGGTTCTGTAGGTTTCGG 59.653 52.381 0.00 0.00 0.00 4.30
2912 4256 0.675837 GGTTCTGTAGGTTTCGGGGC 60.676 60.000 0.00 0.00 0.00 5.80
2929 4273 3.365472 GGGGCAAAAGTAGGAATGTGAT 58.635 45.455 0.00 0.00 0.00 3.06
2936 4280 6.803807 GCAAAAGTAGGAATGTGATTTGACTC 59.196 38.462 0.00 0.00 0.00 3.36
2992 4336 2.304761 TCCTTTTCTTGATAGCCGTGGT 59.695 45.455 0.00 0.00 0.00 4.16
3016 4360 5.927281 TGTGGTATAACTCTGGAACTACC 57.073 43.478 0.00 0.00 39.54 3.18
3026 4370 2.775384 TCTGGAACTACCCAACACAGTT 59.225 45.455 0.00 0.00 35.47 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.487762 CCCACCTCGTACGTAACAGTAA 59.512 50.000 16.05 0.00 0.00 2.24
1 2 2.083774 CCCACCTCGTACGTAACAGTA 58.916 52.381 16.05 0.00 0.00 2.74
2 3 0.883833 CCCACCTCGTACGTAACAGT 59.116 55.000 16.05 4.04 0.00 3.55
3 4 1.167851 TCCCACCTCGTACGTAACAG 58.832 55.000 16.05 4.88 0.00 3.16
4 5 1.745087 GATCCCACCTCGTACGTAACA 59.255 52.381 16.05 0.00 0.00 2.41
5 6 1.745087 TGATCCCACCTCGTACGTAAC 59.255 52.381 16.05 0.00 0.00 2.50
6 7 2.127271 TGATCCCACCTCGTACGTAA 57.873 50.000 16.05 0.00 0.00 3.18
7 8 2.019249 CTTGATCCCACCTCGTACGTA 58.981 52.381 16.05 0.00 0.00 3.57
8 9 0.815734 CTTGATCCCACCTCGTACGT 59.184 55.000 16.05 0.00 0.00 3.57
9 10 0.102481 CCTTGATCCCACCTCGTACG 59.898 60.000 9.53 9.53 0.00 3.67
10 11 1.136500 GTCCTTGATCCCACCTCGTAC 59.864 57.143 0.00 0.00 0.00 3.67
11 12 1.481871 GTCCTTGATCCCACCTCGTA 58.518 55.000 0.00 0.00 0.00 3.43
12 13 1.605058 CGTCCTTGATCCCACCTCGT 61.605 60.000 0.00 0.00 0.00 4.18
13 14 1.141881 CGTCCTTGATCCCACCTCG 59.858 63.158 0.00 0.00 0.00 4.63
14 15 0.902531 TTCGTCCTTGATCCCACCTC 59.097 55.000 0.00 0.00 0.00 3.85
15 16 1.358152 TTTCGTCCTTGATCCCACCT 58.642 50.000 0.00 0.00 0.00 4.00
16 17 2.194201 TTTTCGTCCTTGATCCCACC 57.806 50.000 0.00 0.00 0.00 4.61
17 18 5.392703 GGTTTATTTTCGTCCTTGATCCCAC 60.393 44.000 0.00 0.00 0.00 4.61
18 19 4.703093 GGTTTATTTTCGTCCTTGATCCCA 59.297 41.667 0.00 0.00 0.00 4.37
19 20 4.703093 TGGTTTATTTTCGTCCTTGATCCC 59.297 41.667 0.00 0.00 0.00 3.85
20 21 5.163652 CCTGGTTTATTTTCGTCCTTGATCC 60.164 44.000 0.00 0.00 0.00 3.36
21 22 5.163652 CCCTGGTTTATTTTCGTCCTTGATC 60.164 44.000 0.00 0.00 0.00 2.92
22 23 4.705023 CCCTGGTTTATTTTCGTCCTTGAT 59.295 41.667 0.00 0.00 0.00 2.57
23 24 4.076394 CCCTGGTTTATTTTCGTCCTTGA 58.924 43.478 0.00 0.00 0.00 3.02
24 25 3.824443 ACCCTGGTTTATTTTCGTCCTTG 59.176 43.478 0.00 0.00 0.00 3.61
25 26 4.108501 ACCCTGGTTTATTTTCGTCCTT 57.891 40.909 0.00 0.00 0.00 3.36
26 27 3.801307 ACCCTGGTTTATTTTCGTCCT 57.199 42.857 0.00 0.00 0.00 3.85
27 28 3.943381 CCTACCCTGGTTTATTTTCGTCC 59.057 47.826 0.00 0.00 0.00 4.79
28 29 4.393990 CACCTACCCTGGTTTATTTTCGTC 59.606 45.833 0.00 0.00 38.45 4.20
29 30 4.329392 CACCTACCCTGGTTTATTTTCGT 58.671 43.478 0.00 0.00 38.45 3.85
30 31 3.692593 CCACCTACCCTGGTTTATTTTCG 59.307 47.826 0.00 0.00 38.45 3.46
31 32 4.021229 CCCACCTACCCTGGTTTATTTTC 58.979 47.826 0.00 0.00 38.45 2.29
32 33 3.663632 TCCCACCTACCCTGGTTTATTTT 59.336 43.478 0.00 0.00 38.45 1.82
33 34 3.010920 GTCCCACCTACCCTGGTTTATTT 59.989 47.826 0.00 0.00 38.45 1.40
34 35 2.579400 GTCCCACCTACCCTGGTTTATT 59.421 50.000 0.00 0.00 38.45 1.40
35 36 2.202707 GTCCCACCTACCCTGGTTTAT 58.797 52.381 0.00 0.00 38.45 1.40
36 37 1.660242 GTCCCACCTACCCTGGTTTA 58.340 55.000 0.00 0.00 38.45 2.01
37 38 1.486145 CGTCCCACCTACCCTGGTTT 61.486 60.000 0.00 0.00 38.45 3.27
38 39 1.916777 CGTCCCACCTACCCTGGTT 60.917 63.158 0.00 0.00 38.45 3.67
39 40 2.284405 CGTCCCACCTACCCTGGT 60.284 66.667 0.00 0.00 41.77 4.00
40 41 1.196104 TTTCGTCCCACCTACCCTGG 61.196 60.000 0.00 0.00 0.00 4.45
41 42 0.688487 TTTTCGTCCCACCTACCCTG 59.312 55.000 0.00 0.00 0.00 4.45
42 43 1.665137 ATTTTCGTCCCACCTACCCT 58.335 50.000 0.00 0.00 0.00 4.34
43 44 2.502142 AATTTTCGTCCCACCTACCC 57.498 50.000 0.00 0.00 0.00 3.69
44 45 3.691118 GGTTAATTTTCGTCCCACCTACC 59.309 47.826 0.00 0.00 0.00 3.18
45 46 3.371898 CGGTTAATTTTCGTCCCACCTAC 59.628 47.826 0.00 0.00 0.00 3.18
46 47 3.260380 TCGGTTAATTTTCGTCCCACCTA 59.740 43.478 0.00 0.00 0.00 3.08
47 48 2.038820 TCGGTTAATTTTCGTCCCACCT 59.961 45.455 0.00 0.00 0.00 4.00
48 49 2.160219 GTCGGTTAATTTTCGTCCCACC 59.840 50.000 0.00 0.00 0.00 4.61
49 50 2.159801 CGTCGGTTAATTTTCGTCCCAC 60.160 50.000 0.00 0.00 0.00 4.61
50 51 2.067766 CGTCGGTTAATTTTCGTCCCA 58.932 47.619 0.00 0.00 0.00 4.37
51 52 1.394572 CCGTCGGTTAATTTTCGTCCC 59.605 52.381 2.08 0.00 0.00 4.46
52 53 2.336667 TCCGTCGGTTAATTTTCGTCC 58.663 47.619 11.88 0.00 0.00 4.79
53 54 3.059966 GTCTCCGTCGGTTAATTTTCGTC 59.940 47.826 11.88 0.00 0.00 4.20
54 55 2.989166 GTCTCCGTCGGTTAATTTTCGT 59.011 45.455 11.88 0.00 0.00 3.85
55 56 3.248266 AGTCTCCGTCGGTTAATTTTCG 58.752 45.455 11.88 0.00 0.00 3.46
56 57 4.564372 GGTAGTCTCCGTCGGTTAATTTTC 59.436 45.833 11.88 0.00 0.00 2.29
57 58 4.021192 TGGTAGTCTCCGTCGGTTAATTTT 60.021 41.667 11.88 0.00 0.00 1.82
58 59 3.511146 TGGTAGTCTCCGTCGGTTAATTT 59.489 43.478 11.88 0.00 0.00 1.82
59 60 3.091545 TGGTAGTCTCCGTCGGTTAATT 58.908 45.455 11.88 0.00 0.00 1.40
60 61 2.726821 TGGTAGTCTCCGTCGGTTAAT 58.273 47.619 11.88 2.53 0.00 1.40
61 62 2.198827 TGGTAGTCTCCGTCGGTTAA 57.801 50.000 11.88 0.00 0.00 2.01
62 63 2.019249 CATGGTAGTCTCCGTCGGTTA 58.981 52.381 11.88 0.00 0.00 2.85
63 64 0.815734 CATGGTAGTCTCCGTCGGTT 59.184 55.000 11.88 0.00 0.00 4.44
64 65 1.035932 CCATGGTAGTCTCCGTCGGT 61.036 60.000 11.88 0.00 0.00 4.69
65 66 1.734137 CCATGGTAGTCTCCGTCGG 59.266 63.158 4.39 4.39 0.00 4.79
66 67 0.750546 TCCCATGGTAGTCTCCGTCG 60.751 60.000 11.73 0.00 0.00 5.12
67 68 1.409427 CTTCCCATGGTAGTCTCCGTC 59.591 57.143 11.73 0.00 0.00 4.79
68 69 1.486211 CTTCCCATGGTAGTCTCCGT 58.514 55.000 11.73 0.00 0.00 4.69
69 70 0.753262 CCTTCCCATGGTAGTCTCCG 59.247 60.000 11.73 0.00 0.00 4.63
70 71 1.132500 CCCTTCCCATGGTAGTCTCC 58.868 60.000 11.73 0.00 0.00 3.71
71 72 0.470341 GCCCTTCCCATGGTAGTCTC 59.530 60.000 11.73 0.00 0.00 3.36
72 73 0.044855 AGCCCTTCCCATGGTAGTCT 59.955 55.000 11.73 4.50 0.00 3.24
73 74 0.919710 AAGCCCTTCCCATGGTAGTC 59.080 55.000 11.73 2.36 0.00 2.59
74 75 0.919710 GAAGCCCTTCCCATGGTAGT 59.080 55.000 11.73 0.00 33.64 2.73
75 76 0.179045 CGAAGCCCTTCCCATGGTAG 60.179 60.000 11.73 7.55 36.27 3.18
76 77 1.632018 CCGAAGCCCTTCCCATGGTA 61.632 60.000 11.73 0.00 36.27 3.25
115 116 1.600485 CGCACCTAAAACCACTCGTTT 59.400 47.619 0.00 0.00 46.92 3.60
153 154 5.067153 CCCAACAACATCACTGTTTGAGTTA 59.933 40.000 0.00 0.00 43.05 2.24
167 168 1.444933 TCTGGTCTCCCCAACAACAT 58.555 50.000 0.00 0.00 44.65 2.71
191 192 1.523758 AATGAGCCACCGAAGACAAC 58.476 50.000 0.00 0.00 0.00 3.32
195 196 3.197766 AGTCATTAATGAGCCACCGAAGA 59.802 43.478 18.47 0.00 37.51 2.87
214 215 1.067142 TCATCGCACCTAACACCAGTC 60.067 52.381 0.00 0.00 0.00 3.51
215 216 0.973632 TCATCGCACCTAACACCAGT 59.026 50.000 0.00 0.00 0.00 4.00
216 217 2.093306 TTCATCGCACCTAACACCAG 57.907 50.000 0.00 0.00 0.00 4.00
259 260 1.628340 TCGTCTCCCCAACAACATCAT 59.372 47.619 0.00 0.00 0.00 2.45
273 274 1.499049 AAGCAACCGTTTCTCGTCTC 58.501 50.000 0.00 0.00 37.94 3.36
299 300 0.973632 TCATCGCACCTAACACCAGT 59.026 50.000 0.00 0.00 0.00 4.00
361 468 1.535462 ACCGAAAGCAACCATTTCTCG 59.465 47.619 0.00 0.00 35.05 4.04
362 469 2.351738 CCACCGAAAGCAACCATTTCTC 60.352 50.000 0.00 0.00 35.05 2.87
368 475 1.896660 GAGCCACCGAAAGCAACCA 60.897 57.895 0.00 0.00 0.00 3.67
378 485 1.942657 CCAGTCATTAATGAGCCACCG 59.057 52.381 18.47 0.30 37.51 4.94
381 488 4.574674 AACTCCAGTCATTAATGAGCCA 57.425 40.909 18.47 2.75 37.51 4.75
399 506 4.406648 TGATGATTCATCGCACCTAACT 57.593 40.909 19.15 0.00 43.14 2.24
400 507 4.550831 CGTTGATGATTCATCGCACCTAAC 60.551 45.833 19.15 15.21 43.14 2.34
2388 3655 7.328493 TCGCTTATTATGTGGTGATATTTCGAG 59.672 37.037 0.00 0.00 0.00 4.04
2391 3723 8.009974 GTGTCGCTTATTATGTGGTGATATTTC 58.990 37.037 0.00 0.00 0.00 2.17
2428 3760 5.750524 TGGCAAACCTTAATATCAGTAGCA 58.249 37.500 0.00 0.00 36.63 3.49
2458 3790 2.168521 GAGAGCAATGTAGCAGTGGGTA 59.831 50.000 0.00 0.00 36.85 3.69
2487 3819 2.530460 ATGGGGCATGCTAGAAAACA 57.470 45.000 18.92 6.77 0.00 2.83
2500 3834 1.000866 AAGCCAGGAGAAATGGGGC 59.999 57.895 0.00 0.00 44.92 5.80
2502 3836 1.928868 AACAAGCCAGGAGAAATGGG 58.071 50.000 0.00 0.00 38.33 4.00
2512 3846 7.807977 ACATGATAAATACCTAACAAGCCAG 57.192 36.000 0.00 0.00 0.00 4.85
2529 3863 2.877786 CCATACCAGCGCAAACATGATA 59.122 45.455 11.47 0.00 0.00 2.15
2564 3898 1.069500 GTAGCGACCAATTGCAAACGT 60.069 47.619 1.71 0.00 37.75 3.99
2585 3919 0.250124 TACACCGCCAAGTCTTGTGG 60.250 55.000 15.93 15.93 39.33 4.17
2607 3942 5.380043 TGATCCTCAAAGCTGAACTTTCTT 58.620 37.500 0.00 0.00 45.78 2.52
2632 3967 9.965824 CTGAAAACTGTTGTACCATTCTTTAAT 57.034 29.630 0.00 0.00 0.00 1.40
2633 3968 8.962679 ACTGAAAACTGTTGTACCATTCTTTAA 58.037 29.630 0.00 0.00 0.00 1.52
2634 3969 8.514330 ACTGAAAACTGTTGTACCATTCTTTA 57.486 30.769 0.00 0.00 0.00 1.85
2646 3981 5.942872 AGAGTGAACAACTGAAAACTGTTG 58.057 37.500 14.81 14.81 40.07 3.33
2732 4067 4.501229 GGAGCAGATGATCTCTACCAACTG 60.501 50.000 0.00 0.00 36.61 3.16
2737 4072 1.899142 GGGGAGCAGATGATCTCTACC 59.101 57.143 12.20 12.20 30.32 3.18
2738 4073 1.899142 GGGGGAGCAGATGATCTCTAC 59.101 57.143 0.00 0.00 30.32 2.59
2739 4074 1.548809 CGGGGGAGCAGATGATCTCTA 60.549 57.143 0.00 0.00 30.32 2.43
2740 4075 0.831288 CGGGGGAGCAGATGATCTCT 60.831 60.000 0.00 0.00 30.32 3.10
2741 4076 1.670590 CGGGGGAGCAGATGATCTC 59.329 63.158 0.00 0.00 0.00 2.75
2742 4077 2.515071 GCGGGGGAGCAGATGATCT 61.515 63.158 0.00 0.00 37.05 2.75
2743 4078 2.031768 GCGGGGGAGCAGATGATC 59.968 66.667 0.00 0.00 37.05 2.92
2744 4079 2.769621 TGCGGGGGAGCAGATGAT 60.770 61.111 0.00 0.00 42.92 2.45
2766 4101 5.764192 GGCTGAGCAGATGATCTATCTTTTT 59.236 40.000 6.82 0.00 43.68 1.94
2767 4102 5.163227 TGGCTGAGCAGATGATCTATCTTTT 60.163 40.000 6.82 0.00 43.68 2.27
2768 4103 4.347292 TGGCTGAGCAGATGATCTATCTTT 59.653 41.667 6.82 0.00 43.68 2.52
2769 4104 3.902467 TGGCTGAGCAGATGATCTATCTT 59.098 43.478 6.82 0.00 43.68 2.40
2842 4178 5.753721 AGACAAACCTTTCAGAGATAGCT 57.246 39.130 0.00 0.00 0.00 3.32
2849 4185 4.020485 GGGCTACTAGACAAACCTTTCAGA 60.020 45.833 0.00 0.00 0.00 3.27
2901 4237 1.546998 CCTACTTTTGCCCCGAAACCT 60.547 52.381 0.00 0.00 0.00 3.50
2902 4238 0.885879 CCTACTTTTGCCCCGAAACC 59.114 55.000 0.00 0.00 0.00 3.27
2903 4239 1.900245 TCCTACTTTTGCCCCGAAAC 58.100 50.000 0.00 0.00 0.00 2.78
2904 4240 2.660670 TTCCTACTTTTGCCCCGAAA 57.339 45.000 0.00 0.00 0.00 3.46
2905 4241 2.224917 ACATTCCTACTTTTGCCCCGAA 60.225 45.455 0.00 0.00 0.00 4.30
2907 4243 1.472480 CACATTCCTACTTTTGCCCCG 59.528 52.381 0.00 0.00 0.00 5.73
2908 4244 2.802719 TCACATTCCTACTTTTGCCCC 58.197 47.619 0.00 0.00 0.00 5.80
2909 4245 5.047377 TCAAATCACATTCCTACTTTTGCCC 60.047 40.000 0.00 0.00 0.00 5.36
2912 4256 7.017645 CGAGTCAAATCACATTCCTACTTTTG 58.982 38.462 0.00 0.00 0.00 2.44
2929 4273 4.647424 AAATTTGGAAGCACGAGTCAAA 57.353 36.364 0.00 0.00 0.00 2.69
2936 4280 3.922240 CCATCTGAAAATTTGGAAGCACG 59.078 43.478 0.00 0.00 0.00 5.34
2977 4321 2.102420 CCACATACCACGGCTATCAAGA 59.898 50.000 0.00 0.00 0.00 3.02
2992 4336 6.552350 GGGTAGTTCCAGAGTTATACCACATA 59.448 42.308 0.00 0.00 35.44 2.29


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

AutoCloner maintained by Alex Coulton.