Multiple sequence alignment - TraesCS2D01G391400

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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 TraesCS2D01G391400 chr2D 100.000 2840 0 0 1 2840 498534001 498531162 0.000000e+00 5245.0
1 TraesCS2D01G391400 chr2D 84.456 193 30 0 1393 1585 569853853 569853661 1.040000e-44 191.0
2 TraesCS2D01G391400 chr2D 88.506 87 10 0 2247 2333 109129687 109129601 3.870000e-19 106.0
3 TraesCS2D01G391400 chr2A 91.466 2156 130 19 1 2126 643232187 643230056 0.000000e+00 2913.0
4 TraesCS2D01G391400 chr2A 95.238 42 2 0 21 62 686378597 686378556 1.830000e-07 67.6
5 TraesCS2D01G391400 chr2B 94.762 1050 49 4 794 1840 585757650 585756604 0.000000e+00 1629.0
6 TraesCS2D01G391400 chr2B 97.297 37 1 0 2239 2275 768375609 768375645 2.360000e-06 63.9
7 TraesCS2D01G391400 chr4D 97.500 600 13 1 2241 2840 366977085 366976488 0.000000e+00 1024.0
8 TraesCS2D01G391400 chr4D 90.331 362 35 0 61 422 231646708 231646347 2.560000e-130 475.0
9 TraesCS2D01G391400 chr4D 85.714 168 24 0 1393 1560 30755426 30755593 8.080000e-41 178.0
10 TraesCS2D01G391400 chr4B 90.391 614 46 6 2239 2840 643652318 643651706 0.000000e+00 795.0
11 TraesCS2D01G391400 chr1B 90.344 611 44 4 2241 2840 59540108 59539502 0.000000e+00 787.0
12 TraesCS2D01G391400 chr1B 89.394 132 14 0 657 788 278698005 278698136 1.750000e-37 167.0
13 TraesCS2D01G391400 chr4A 81.525 774 94 36 1037 1790 613544311 613543567 2.440000e-165 592.0
14 TraesCS2D01G391400 chr4A 85.882 170 24 0 1393 1562 571971976 571972145 6.250000e-42 182.0
15 TraesCS2D01G391400 chr5D 80.723 830 98 36 1034 1841 556423358 556424147 8.760000e-165 590.0
16 TraesCS2D01G391400 chr5D 90.244 369 35 1 60 427 349067442 349067810 5.500000e-132 481.0
17 TraesCS2D01G391400 chr5D 80.851 470 77 10 1377 1840 556449723 556450185 9.680000e-95 357.0
18 TraesCS2D01G391400 chr5D 82.688 439 37 9 2439 2840 482763208 482762772 1.250000e-93 353.0
19 TraesCS2D01G391400 chr5D 87.500 168 21 0 2595 2762 553870503 553870670 8.030000e-46 195.0
20 TraesCS2D01G391400 chr5D 80.833 240 33 6 1025 1264 556449439 556449665 2.910000e-40 176.0
21 TraesCS2D01G391400 chr5D 92.784 97 7 0 2241 2337 482763351 482763255 1.060000e-29 141.0
22 TraesCS2D01G391400 chr6D 90.761 368 32 2 61 427 392115216 392115582 9.140000e-135 490.0
23 TraesCS2D01G391400 chr6D 82.540 63 11 0 2243 2305 28286121 28286183 3.950000e-04 56.5
24 TraesCS2D01G391400 chr1D 85.177 479 51 11 1379 1841 421226616 421227090 9.210000e-130 473.0
25 TraesCS2D01G391400 chr1D 78.920 389 38 18 427 785 198756733 198757107 1.020000e-54 224.0
26 TraesCS2D01G391400 chr5B 81.279 641 68 15 2240 2838 510534716 510535346 3.310000e-129 472.0
27 TraesCS2D01G391400 chr5B 89.459 370 36 3 60 427 293884872 293884504 5.540000e-127 464.0
28 TraesCS2D01G391400 chr5B 80.811 641 70 18 2241 2838 9080107 9079477 1.200000e-123 453.0
29 TraesCS2D01G391400 chr5B 85.475 179 25 1 1382 1560 491173622 491173445 4.830000e-43 185.0
30 TraesCS2D01G391400 chr5B 92.157 51 3 1 13 62 526595875 526595925 1.410000e-08 71.3
31 TraesCS2D01G391400 chr5A 89.702 369 36 2 61 427 350076256 350075888 1.190000e-128 470.0
32 TraesCS2D01G391400 chr5A 78.246 285 50 12 1382 1662 520532042 520531766 3.760000e-39 172.0
33 TraesCS2D01G391400 chr7D 89.674 368 37 1 61 427 315498741 315499108 4.280000e-128 468.0
34 TraesCS2D01G391400 chr7D 80.926 367 58 10 436 798 593954755 593955113 2.150000e-71 279.0
35 TraesCS2D01G391400 chr3B 89.431 369 37 2 61 427 412868777 412869145 5.540000e-127 464.0
36 TraesCS2D01G391400 chr3D 89.402 368 37 2 61 427 263827413 263827047 1.990000e-126 462.0
37 TraesCS2D01G391400 chr3A 79.656 639 57 28 2241 2840 701141264 701141868 2.650000e-105 392.0
38 TraesCS2D01G391400 chr3A 79.316 643 56 29 2240 2840 696202413 696203020 2.060000e-101 379.0
39 TraesCS2D01G391400 chr3A 78.288 631 70 27 2271 2838 733265007 733264381 7.530000e-91 344.0
40 TraesCS2D01G391400 chr1A 80.964 394 38 15 428 789 76760948 76760560 7.750000e-71 278.0
41 TraesCS2D01G391400 chr7A 78.804 368 62 14 434 798 686339756 686340110 1.700000e-57 233.0
42 TraesCS2D01G391400 chr6A 90.099 101 6 1 2241 2337 502924782 502924682 8.260000e-26 128.0


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 TraesCS2D01G391400 chr2D 498531162 498534001 2839 True 5245.0 5245 100.000 1 2840 1 chr2D.!!$R2 2839
1 TraesCS2D01G391400 chr2A 643230056 643232187 2131 True 2913.0 2913 91.466 1 2126 1 chr2A.!!$R1 2125
2 TraesCS2D01G391400 chr2B 585756604 585757650 1046 True 1629.0 1629 94.762 794 1840 1 chr2B.!!$R1 1046
3 TraesCS2D01G391400 chr4D 366976488 366977085 597 True 1024.0 1024 97.500 2241 2840 1 chr4D.!!$R2 599
4 TraesCS2D01G391400 chr4B 643651706 643652318 612 True 795.0 795 90.391 2239 2840 1 chr4B.!!$R1 601
5 TraesCS2D01G391400 chr1B 59539502 59540108 606 True 787.0 787 90.344 2241 2840 1 chr1B.!!$R1 599
6 TraesCS2D01G391400 chr4A 613543567 613544311 744 True 592.0 592 81.525 1037 1790 1 chr4A.!!$R1 753
7 TraesCS2D01G391400 chr5D 556423358 556424147 789 False 590.0 590 80.723 1034 1841 1 chr5D.!!$F3 807
8 TraesCS2D01G391400 chr5D 556449439 556450185 746 False 266.5 357 80.842 1025 1840 2 chr5D.!!$F4 815
9 TraesCS2D01G391400 chr5D 482762772 482763351 579 True 247.0 353 87.736 2241 2840 2 chr5D.!!$R1 599
10 TraesCS2D01G391400 chr5B 510534716 510535346 630 False 472.0 472 81.279 2240 2838 1 chr5B.!!$F1 598
11 TraesCS2D01G391400 chr5B 9079477 9080107 630 True 453.0 453 80.811 2241 2838 1 chr5B.!!$R1 597
12 TraesCS2D01G391400 chr3A 701141264 701141868 604 False 392.0 392 79.656 2241 2840 1 chr3A.!!$F2 599
13 TraesCS2D01G391400 chr3A 696202413 696203020 607 False 379.0 379 79.316 2240 2840 1 chr3A.!!$F1 600
14 TraesCS2D01G391400 chr3A 733264381 733265007 626 True 344.0 344 78.288 2271 2838 1 chr3A.!!$R1 567

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
38 39 0.320374 ATGTTTCGGGTCTCGCTTCA 59.68 50.0 0.0 0.0 39.05 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2081 0.107081 ACCGACGATTTCCACAACCA 59.893 50.0 0.0 0.0 0.0 3.67 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 1.439679 AATGTTTCGGGTCTCGCTTC 58.560 50.000 0.00 0.00 39.05 3.86
38 39 0.320374 ATGTTTCGGGTCTCGCTTCA 59.680 50.000 0.00 0.00 39.05 3.02
46 47 1.157585 GGTCTCGCTTCAAGGGTTTC 58.842 55.000 0.72 0.00 0.00 2.78
47 48 1.270893 GGTCTCGCTTCAAGGGTTTCT 60.271 52.381 0.72 0.00 0.00 2.52
55 56 4.396166 CGCTTCAAGGGTTTCTGAATATGT 59.604 41.667 0.00 0.00 0.00 2.29
68 69 8.739972 GTTTCTGAATATGTGGGAATACTTTGT 58.260 33.333 0.00 0.00 0.00 2.83
71 72 7.888021 TCTGAATATGTGGGAATACTTTGTGTT 59.112 33.333 0.00 0.00 0.00 3.32
82 83 7.330946 GGGAATACTTTGTGTTAAAAAGATGGC 59.669 37.037 5.36 0.00 37.91 4.40
84 85 4.616953 ACTTTGTGTTAAAAAGATGGCGG 58.383 39.130 5.36 0.00 37.91 6.13
134 135 7.502561 AGGGATAGCGTTCTTTAGCATTTTTAT 59.497 33.333 0.00 0.00 35.48 1.40
139 140 8.810652 AGCGTTCTTTAGCATTTTTATTTTGA 57.189 26.923 0.00 0.00 35.48 2.69
141 142 9.856803 GCGTTCTTTAGCATTTTTATTTTGAAA 57.143 25.926 0.00 0.00 0.00 2.69
166 167 6.835488 AGACATGATTATTTGTTGGTATGCCT 59.165 34.615 0.00 0.00 35.27 4.75
181 182 9.338622 GTTGGTATGCCTAAGTATTAATGTCTT 57.661 33.333 0.16 5.71 35.27 3.01
182 183 9.914834 TTGGTATGCCTAAGTATTAATGTCTTT 57.085 29.630 0.16 0.00 35.27 2.52
282 283 9.353431 TGAACATGTTATATAGCATTCCACATT 57.647 29.630 11.95 0.00 0.00 2.71
313 314 8.687824 ATTTGTTTTTATCATTTGCCTACTCG 57.312 30.769 0.00 0.00 0.00 4.18
316 317 6.876789 TGTTTTTATCATTTGCCTACTCGAGA 59.123 34.615 21.68 1.61 0.00 4.04
341 343 3.294214 AGCAGGAATTAAGCTTGGGATG 58.706 45.455 9.86 1.72 34.37 3.51
350 352 0.957395 AGCTTGGGATGCTTGACACG 60.957 55.000 0.00 0.00 37.52 4.49
354 356 0.396435 TGGGATGCTTGACACGTCTT 59.604 50.000 0.00 0.00 0.00 3.01
479 481 5.493133 TCTTCACTTTTGCAACATACGTT 57.507 34.783 0.00 0.00 35.01 3.99
480 482 6.606234 TCTTCACTTTTGCAACATACGTTA 57.394 33.333 0.00 0.00 32.75 3.18
514 516 3.713858 TTTTGCAACAGAGGTCATGTG 57.286 42.857 0.00 0.00 0.00 3.21
530 532 8.121305 AGGTCATGTGCAGAAAATATTTGTAA 57.879 30.769 0.39 0.00 0.00 2.41
580 582 6.426980 TTTGCAACAGAGATTATGTAGCAG 57.573 37.500 0.00 0.00 0.00 4.24
581 583 5.089970 TGCAACAGAGATTATGTAGCAGT 57.910 39.130 0.00 0.00 0.00 4.40
582 584 5.491070 TGCAACAGAGATTATGTAGCAGTT 58.509 37.500 0.00 0.00 0.00 3.16
607 609 4.710423 TTTTGCAACAGAGCTTGTGTTA 57.290 36.364 13.40 0.00 40.74 2.41
611 613 2.614057 GCAACAGAGCTTGTGTTACAGT 59.386 45.455 13.40 0.00 40.74 3.55
614 616 5.640732 CAACAGAGCTTGTGTTACAGTTTT 58.359 37.500 13.40 0.00 40.74 2.43
644 646 5.772825 AACAGAGTTTATGCTGCAAAAGA 57.227 34.783 6.36 0.00 35.57 2.52
645 647 5.113502 ACAGAGTTTATGCTGCAAAAGAC 57.886 39.130 6.36 3.68 35.57 3.01
648 650 6.154445 CAGAGTTTATGCTGCAAAAGACATT 58.846 36.000 6.36 0.00 0.00 2.71
657 659 3.976169 TGCAAAAGACATTAACTGCACC 58.024 40.909 0.00 0.00 35.02 5.01
665 693 4.328983 AGACATTAACTGCACCGTATTTCG 59.671 41.667 0.00 0.00 39.52 3.46
695 723 5.586339 TGAACGATGTTGCAAAATCTTGAA 58.414 33.333 23.92 7.31 34.14 2.69
709 737 3.550339 TTGAATTGCGGTGCGTGGC 62.550 57.895 0.00 0.00 0.00 5.01
720 748 2.276869 TGCGTGGCACTAGACTGAT 58.723 52.632 16.72 0.00 31.71 2.90
738 766 2.159099 TGATACATGGTTGGCTCTCGAC 60.159 50.000 0.00 0.00 0.00 4.20
741 769 2.650116 ATGGTTGGCTCTCGACGCT 61.650 57.895 2.40 0.00 0.00 5.07
760 788 1.299468 GCGGACGTGGAGCATAGAG 60.299 63.158 0.00 0.00 0.00 2.43
775 803 3.583806 CATAGAGTCGGCCAGATGATTC 58.416 50.000 2.24 0.00 0.00 2.52
779 807 3.900601 AGAGTCGGCCAGATGATTCTAAT 59.099 43.478 2.24 0.00 30.46 1.73
850 879 4.271049 CGCTATCACAATTGTCTGTTAGGG 59.729 45.833 8.48 11.30 0.00 3.53
853 882 6.037610 GCTATCACAATTGTCTGTTAGGGAAG 59.962 42.308 8.48 3.03 0.00 3.46
960 989 2.938451 GCCACCGGTACCAGTATAAAAC 59.062 50.000 6.87 0.00 0.00 2.43
999 1028 3.306364 CCAGAACTTCCAACTCGACATCT 60.306 47.826 0.00 0.00 0.00 2.90
1355 1402 1.684049 CCAGCGAAGAGGAGGAGGT 60.684 63.158 0.00 0.00 0.00 3.85
1569 1616 1.752694 CAATTTCCCCGCCGACCAT 60.753 57.895 0.00 0.00 0.00 3.55
1690 1758 1.603678 GGGCGTCTACAACACGAAAGA 60.604 52.381 0.00 0.00 39.75 2.52
1693 1761 2.793232 GCGTCTACAACACGAAAGACTT 59.207 45.455 0.00 0.00 39.75 3.01
1695 1763 3.361724 CGTCTACAACACGAAAGACTTGC 60.362 47.826 0.00 0.00 39.75 4.01
1854 1925 5.691896 TCCATCTGATTCTGAAATCTGCAT 58.308 37.500 0.00 0.00 41.63 3.96
1924 1995 4.929211 GTGTTTTTCTTTCTTGCCTGTTGT 59.071 37.500 0.00 0.00 0.00 3.32
1930 2001 2.957491 TTCTTGCCTGTTGTTGTTGG 57.043 45.000 0.00 0.00 0.00 3.77
1932 2003 1.748493 TCTTGCCTGTTGTTGTTGGTC 59.252 47.619 0.00 0.00 0.00 4.02
1977 2048 5.640147 AGTTCAGCTGGACTAGATAGCTAT 58.360 41.667 26.78 5.76 45.37 2.97
2006 2077 6.510799 CGAGCATTAGGTTCTTTAGCATTGAG 60.511 42.308 0.00 0.00 0.00 3.02
2010 2081 7.201857 GCATTAGGTTCTTTAGCATTGAGGAAT 60.202 37.037 0.00 0.00 0.00 3.01
2046 2117 2.030701 TCGGTTGTGTACGTTTTGAAGC 59.969 45.455 0.00 0.00 0.00 3.86
2049 2120 3.024313 GTTGTGTACGTTTTGAAGCGTC 58.976 45.455 8.84 0.00 44.59 5.19
2053 2124 4.507021 TGTGTACGTTTTGAAGCGTCAATA 59.493 37.500 15.88 8.61 44.59 1.90
2065 2136 5.010112 TGAAGCGTCAATATTTGGGTTTGAA 59.990 36.000 0.00 0.00 31.66 2.69
2074 2145 8.306038 TCAATATTTGGGTTTGAATTCAGTCAG 58.694 33.333 8.41 0.00 0.00 3.51
2095 2166 4.954092 GAACTGATGGTTCCTTCACATC 57.046 45.455 3.75 0.00 46.17 3.06
2108 2179 5.895928 TCCTTCACATCATCTTAAGAGACG 58.104 41.667 11.53 4.23 33.99 4.18
2126 2197 2.011947 ACGCTCATGACATGACATTGG 58.988 47.619 14.24 5.72 35.06 3.16
2127 2198 1.268386 CGCTCATGACATGACATTGGC 60.268 52.381 14.24 13.98 35.06 4.52
2128 2199 1.268386 GCTCATGACATGACATTGGCG 60.268 52.381 14.24 4.33 35.06 5.69
2129 2200 0.734309 TCATGACATGACATTGGCGC 59.266 50.000 14.24 0.00 33.59 6.53
2130 2201 0.248743 CATGACATGACATTGGCGCC 60.249 55.000 22.73 22.73 0.00 6.53
2131 2202 0.680601 ATGACATGACATTGGCGCCA 60.681 50.000 29.03 29.03 0.00 5.69
2132 2203 0.892814 TGACATGACATTGGCGCCAA 60.893 50.000 41.54 41.54 40.47 4.52
2133 2204 0.179156 GACATGACATTGGCGCCAAG 60.179 55.000 41.38 33.21 39.47 3.61
2144 2215 2.544726 GCGCCAAGCTTGTACTTCT 58.455 52.632 24.35 0.00 44.04 2.85
2145 2216 0.444260 GCGCCAAGCTTGTACTTCTC 59.556 55.000 24.35 3.47 44.04 2.87
2146 2217 1.941668 GCGCCAAGCTTGTACTTCTCT 60.942 52.381 24.35 0.00 44.04 3.10
2147 2218 1.728971 CGCCAAGCTTGTACTTCTCTG 59.271 52.381 24.35 7.38 0.00 3.35
2148 2219 2.079925 GCCAAGCTTGTACTTCTCTGG 58.920 52.381 24.35 7.53 0.00 3.86
2149 2220 2.289694 GCCAAGCTTGTACTTCTCTGGA 60.290 50.000 24.35 0.00 0.00 3.86
2150 2221 3.330267 CCAAGCTTGTACTTCTCTGGAC 58.670 50.000 24.35 0.00 0.00 4.02
2151 2222 3.330267 CAAGCTTGTACTTCTCTGGACC 58.670 50.000 18.65 0.00 0.00 4.46
2152 2223 2.609747 AGCTTGTACTTCTCTGGACCA 58.390 47.619 0.00 0.00 0.00 4.02
2153 2224 2.564947 AGCTTGTACTTCTCTGGACCAG 59.435 50.000 15.99 15.99 0.00 4.00
2154 2225 2.300437 GCTTGTACTTCTCTGGACCAGT 59.700 50.000 21.06 4.97 32.61 4.00
2155 2226 3.862642 GCTTGTACTTCTCTGGACCAGTG 60.863 52.174 21.06 18.45 32.61 3.66
2156 2227 2.958818 TGTACTTCTCTGGACCAGTGT 58.041 47.619 21.06 16.42 32.61 3.55
2157 2228 2.628178 TGTACTTCTCTGGACCAGTGTG 59.372 50.000 21.06 16.51 32.61 3.82
2158 2229 1.051812 ACTTCTCTGGACCAGTGTGG 58.948 55.000 21.06 16.14 45.02 4.17
2159 2230 0.322975 CTTCTCTGGACCAGTGTGGG 59.677 60.000 21.06 9.38 43.37 4.61
2165 2236 3.798758 GACCAGTGTGGGCTCTCT 58.201 61.111 0.00 0.00 44.12 3.10
2166 2237 1.594310 GACCAGTGTGGGCTCTCTC 59.406 63.158 0.00 0.00 44.12 3.20
2167 2238 1.893919 GACCAGTGTGGGCTCTCTCC 61.894 65.000 0.00 0.00 44.12 3.71
2168 2239 1.611851 CCAGTGTGGGCTCTCTCCT 60.612 63.158 0.00 0.00 32.67 3.69
2169 2240 1.595882 CAGTGTGGGCTCTCTCCTG 59.404 63.158 0.00 0.00 0.00 3.86
2170 2241 0.902048 CAGTGTGGGCTCTCTCCTGA 60.902 60.000 1.17 0.00 0.00 3.86
2171 2242 0.042431 AGTGTGGGCTCTCTCCTGAT 59.958 55.000 0.00 0.00 0.00 2.90
2172 2243 1.289231 AGTGTGGGCTCTCTCCTGATA 59.711 52.381 0.00 0.00 0.00 2.15
2173 2244 2.090831 AGTGTGGGCTCTCTCCTGATAT 60.091 50.000 0.00 0.00 0.00 1.63
2174 2245 2.036992 GTGTGGGCTCTCTCCTGATATG 59.963 54.545 0.00 0.00 0.00 1.78
2175 2246 2.091111 TGTGGGCTCTCTCCTGATATGA 60.091 50.000 0.00 0.00 0.00 2.15
2176 2247 2.968574 GTGGGCTCTCTCCTGATATGAA 59.031 50.000 0.00 0.00 0.00 2.57
2177 2248 3.389329 GTGGGCTCTCTCCTGATATGAAA 59.611 47.826 0.00 0.00 0.00 2.69
2178 2249 4.040047 TGGGCTCTCTCCTGATATGAAAA 58.960 43.478 0.00 0.00 0.00 2.29
2179 2250 4.102210 TGGGCTCTCTCCTGATATGAAAAG 59.898 45.833 0.00 0.00 0.00 2.27
2180 2251 4.504689 GGGCTCTCTCCTGATATGAAAAGG 60.505 50.000 0.00 0.00 0.00 3.11
2181 2252 4.504689 GGCTCTCTCCTGATATGAAAAGGG 60.505 50.000 0.00 0.00 0.00 3.95
2182 2253 4.346418 GCTCTCTCCTGATATGAAAAGGGA 59.654 45.833 0.00 0.00 0.00 4.20
2183 2254 5.163258 GCTCTCTCCTGATATGAAAAGGGAA 60.163 44.000 0.00 0.00 0.00 3.97
2184 2255 6.465607 GCTCTCTCCTGATATGAAAAGGGAAT 60.466 42.308 0.00 0.00 0.00 3.01
2185 2256 7.256475 GCTCTCTCCTGATATGAAAAGGGAATA 60.256 40.741 0.00 0.00 0.00 1.75
2186 2257 8.748179 TCTCTCCTGATATGAAAAGGGAATAT 57.252 34.615 0.00 0.00 0.00 1.28
2187 2258 9.843704 TCTCTCCTGATATGAAAAGGGAATATA 57.156 33.333 0.00 0.00 0.00 0.86
2191 2262 9.466497 TCCTGATATGAAAAGGGAATATAATGC 57.534 33.333 0.00 0.00 0.00 3.56
2192 2263 9.246670 CCTGATATGAAAAGGGAATATAATGCA 57.753 33.333 0.00 0.00 0.00 3.96
2194 2265 9.812347 TGATATGAAAAGGGAATATAATGCAGT 57.188 29.630 0.00 0.00 0.00 4.40
2198 2269 9.603921 ATGAAAAGGGAATATAATGCAGTTTTG 57.396 29.630 0.00 0.00 0.00 2.44
2199 2270 8.040132 TGAAAAGGGAATATAATGCAGTTTTGG 58.960 33.333 0.00 0.00 0.00 3.28
2200 2271 7.494922 AAAGGGAATATAATGCAGTTTTGGT 57.505 32.000 0.00 0.00 0.00 3.67
2201 2272 6.469782 AGGGAATATAATGCAGTTTTGGTG 57.530 37.500 0.00 0.00 0.00 4.17
2202 2273 5.957774 AGGGAATATAATGCAGTTTTGGTGT 59.042 36.000 0.00 0.00 0.00 4.16
2203 2274 6.042143 GGGAATATAATGCAGTTTTGGTGTG 58.958 40.000 0.00 0.00 0.00 3.82
2204 2275 6.350949 GGGAATATAATGCAGTTTTGGTGTGT 60.351 38.462 0.00 0.00 0.00 3.72
2205 2276 7.096551 GGAATATAATGCAGTTTTGGTGTGTT 58.903 34.615 0.00 0.00 0.00 3.32
2206 2277 7.602265 GGAATATAATGCAGTTTTGGTGTGTTT 59.398 33.333 0.00 0.00 0.00 2.83
2207 2278 8.900983 AATATAATGCAGTTTTGGTGTGTTTT 57.099 26.923 0.00 0.00 0.00 2.43
2208 2279 8.900983 ATATAATGCAGTTTTGGTGTGTTTTT 57.099 26.923 0.00 0.00 0.00 1.94
2229 2300 6.677781 TTTTAACATAGTACAGATGCAGGC 57.322 37.500 7.50 0.00 0.00 4.85
2230 2301 2.515926 ACATAGTACAGATGCAGGCG 57.484 50.000 7.50 0.00 0.00 5.52
2231 2302 1.757118 ACATAGTACAGATGCAGGCGT 59.243 47.619 7.50 0.00 0.00 5.68
2232 2303 2.168521 ACATAGTACAGATGCAGGCGTT 59.831 45.455 7.50 0.00 0.00 4.84
2233 2304 2.579207 TAGTACAGATGCAGGCGTTC 57.421 50.000 0.00 0.00 0.00 3.95
2234 2305 0.608130 AGTACAGATGCAGGCGTTCA 59.392 50.000 0.00 0.00 0.00 3.18
2235 2306 1.208052 AGTACAGATGCAGGCGTTCAT 59.792 47.619 0.00 0.00 0.00 2.57
2236 2307 2.430694 AGTACAGATGCAGGCGTTCATA 59.569 45.455 0.00 0.00 0.00 2.15
2237 2308 1.656652 ACAGATGCAGGCGTTCATAC 58.343 50.000 0.00 0.00 0.00 2.39
2569 2684 3.774766 TGCATCCTCTAGTGAAAAGCCTA 59.225 43.478 0.00 0.00 0.00 3.93
2574 2689 4.466726 TCCTCTAGTGAAAAGCCTAAGACC 59.533 45.833 0.00 0.00 0.00 3.85
2700 2831 2.154139 TGGAGGACACAAGCATGGT 58.846 52.632 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.615496 AGACCCGAAACATTTTATCGTCG 59.385 43.478 0.00 0.00 34.90 5.12
11 12 3.615496 CGAGACCCGAAACATTTTATCGT 59.385 43.478 0.00 0.00 41.76 3.73
18 19 1.270625 TGAAGCGAGACCCGAAACATT 60.271 47.619 0.00 0.00 41.76 2.71
37 38 4.599041 TCCCACATATTCAGAAACCCTTG 58.401 43.478 0.00 0.00 0.00 3.61
38 39 4.946160 TCCCACATATTCAGAAACCCTT 57.054 40.909 0.00 0.00 0.00 3.95
46 47 7.630242 ACACAAAGTATTCCCACATATTCAG 57.370 36.000 0.00 0.00 0.00 3.02
47 48 9.521841 TTAACACAAAGTATTCCCACATATTCA 57.478 29.630 0.00 0.00 0.00 2.57
55 56 8.364142 CCATCTTTTTAACACAAAGTATTCCCA 58.636 33.333 0.00 0.00 33.61 4.37
68 69 4.075682 TGTCATCCGCCATCTTTTTAACA 58.924 39.130 0.00 0.00 0.00 2.41
71 72 4.394920 GTCTTGTCATCCGCCATCTTTTTA 59.605 41.667 0.00 0.00 0.00 1.52
74 75 2.026822 AGTCTTGTCATCCGCCATCTTT 60.027 45.455 0.00 0.00 0.00 2.52
114 115 8.810652 TCAAAATAAAAATGCTAAAGAACGCT 57.189 26.923 0.00 0.00 0.00 5.07
134 135 9.829507 ACCAACAAATAATCATGTCTTTCAAAA 57.170 25.926 0.00 0.00 0.00 2.44
139 140 7.981225 GGCATACCAACAAATAATCATGTCTTT 59.019 33.333 0.00 0.00 35.26 2.52
141 142 6.835488 AGGCATACCAACAAATAATCATGTCT 59.165 34.615 0.00 0.00 39.06 3.41
142 143 7.042797 AGGCATACCAACAAATAATCATGTC 57.957 36.000 0.00 0.00 39.06 3.06
143 144 8.532186 TTAGGCATACCAACAAATAATCATGT 57.468 30.769 0.00 0.00 39.06 3.21
144 145 8.632679 ACTTAGGCATACCAACAAATAATCATG 58.367 33.333 0.00 0.00 39.06 3.07
145 146 8.766994 ACTTAGGCATACCAACAAATAATCAT 57.233 30.769 0.00 0.00 39.06 2.45
146 147 9.860650 ATACTTAGGCATACCAACAAATAATCA 57.139 29.630 0.00 0.00 39.06 2.57
152 153 9.469097 ACATTAATACTTAGGCATACCAACAAA 57.531 29.630 0.00 0.00 39.06 2.83
153 154 9.116067 GACATTAATACTTAGGCATACCAACAA 57.884 33.333 0.00 0.00 39.06 2.83
183 184 9.890629 TCAAAGCAATAGTCTATAGTTTGACAT 57.109 29.630 14.48 0.00 35.81 3.06
254 255 7.228507 TGTGGAATGCTATATAACATGTTCACC 59.771 37.037 15.85 5.07 0.00 4.02
288 289 8.519526 TCGAGTAGGCAAATGATAAAAACAAAT 58.480 29.630 0.00 0.00 0.00 2.32
289 290 7.877003 TCGAGTAGGCAAATGATAAAAACAAA 58.123 30.769 0.00 0.00 0.00 2.83
291 292 6.876789 TCTCGAGTAGGCAAATGATAAAAACA 59.123 34.615 13.13 0.00 0.00 2.83
292 293 7.303634 TCTCGAGTAGGCAAATGATAAAAAC 57.696 36.000 13.13 0.00 0.00 2.43
294 295 6.035650 CGTTCTCGAGTAGGCAAATGATAAAA 59.964 38.462 13.13 0.00 39.71 1.52
295 296 5.518847 CGTTCTCGAGTAGGCAAATGATAAA 59.481 40.000 13.13 0.00 39.71 1.40
313 314 3.526534 AGCTTAATTCCTGCTCGTTCTC 58.473 45.455 0.00 0.00 30.41 2.87
316 317 2.749621 CCAAGCTTAATTCCTGCTCGTT 59.250 45.455 0.00 0.00 35.85 3.85
341 343 3.710233 CGTTGAAGACGTGTCAAGC 57.290 52.632 10.70 6.39 46.49 4.01
451 453 3.438781 TGTTGCAAAAGTGAAGAACGACT 59.561 39.130 0.00 0.00 0.00 4.18
454 456 4.375698 CGTATGTTGCAAAAGTGAAGAACG 59.624 41.667 0.00 0.00 0.00 3.95
614 616 9.973450 TTGCAGCATAAACTCTGTTATTAAAAA 57.027 25.926 0.00 0.00 33.09 1.94
619 621 7.809806 GTCTTTTGCAGCATAAACTCTGTTATT 59.190 33.333 0.00 0.00 33.09 1.40
626 628 7.809806 AGTTAATGTCTTTTGCAGCATAAACTC 59.190 33.333 0.00 0.00 0.00 3.01
628 630 7.619982 GCAGTTAATGTCTTTTGCAGCATAAAC 60.620 37.037 0.00 0.46 0.00 2.01
644 646 4.593597 CGAAATACGGTGCAGTTAATGT 57.406 40.909 0.00 0.00 38.46 2.71
657 659 4.571375 TCGTTCATGTTTCCGAAATACG 57.429 40.909 0.00 3.70 42.18 3.06
670 698 5.630264 TCAAGATTTTGCAACATCGTTCATG 59.370 36.000 17.55 13.05 34.98 3.07
709 737 4.122776 GCCAACCATGTATCAGTCTAGTG 58.877 47.826 0.00 0.00 0.00 2.74
720 748 0.172578 CGTCGAGAGCCAACCATGTA 59.827 55.000 0.00 0.00 0.00 2.29
741 769 2.004808 CTCTATGCTCCACGTCCGCA 62.005 60.000 5.54 5.54 38.14 5.69
751 779 0.965439 ATCTGGCCGACTCTATGCTC 59.035 55.000 0.00 0.00 0.00 4.26
755 783 3.505386 AGAATCATCTGGCCGACTCTAT 58.495 45.455 0.00 0.00 33.59 1.98
760 788 3.995199 TGATTAGAATCATCTGGCCGAC 58.005 45.455 0.00 0.00 40.32 4.79
817 845 9.190317 AGACAATTGTGATAGCGATATATCCTA 57.810 33.333 17.58 9.57 32.18 2.94
840 868 3.559384 CCTGGTTTCCTTCCCTAACAGAC 60.559 52.174 0.00 0.00 0.00 3.51
850 879 2.554462 GCTCTGTTTCCTGGTTTCCTTC 59.446 50.000 0.00 0.00 0.00 3.46
853 882 1.981256 TGCTCTGTTTCCTGGTTTCC 58.019 50.000 0.00 0.00 0.00 3.13
950 979 2.878406 CGCCTCCATGGGTTTTATACTG 59.122 50.000 13.02 0.00 36.00 2.74
960 989 2.825836 GAAGTGCGCCTCCATGGG 60.826 66.667 13.02 2.26 36.00 4.00
999 1028 2.236893 TGTGCTGCTTGGATCAGACATA 59.763 45.455 0.00 0.00 33.54 2.29
1063 1092 2.690778 GGCGCGCCAAGAAGTTGAT 61.691 57.895 43.55 0.00 35.46 2.57
1266 1307 3.446570 GTGTGCATGGCCTCCTGC 61.447 66.667 15.80 15.80 38.87 4.85
1267 1308 2.753043 GGTGTGCATGGCCTCCTG 60.753 66.667 3.32 0.00 0.00 3.86
1268 1309 4.415150 CGGTGTGCATGGCCTCCT 62.415 66.667 3.32 0.00 0.00 3.69
1274 1315 3.792047 CTGACGCGGTGTGCATGG 61.792 66.667 12.47 0.00 46.97 3.66
1288 1329 4.424711 GGTGGGAATGGGCGCTGA 62.425 66.667 7.64 0.00 0.00 4.26
1297 1344 4.752879 CGCCGTCGTGGTGGGAAT 62.753 66.667 2.63 0.00 44.97 3.01
1690 1758 4.388499 CCGTACGGCCCTGCAAGT 62.388 66.667 23.44 0.00 0.00 3.16
1854 1925 0.817013 GCCATCGCCATTTTTCTGGA 59.183 50.000 0.00 0.00 38.69 3.86
1924 1995 1.364901 GAGACCGGACGACCAACAA 59.635 57.895 9.46 0.00 35.59 2.83
1930 2001 2.202272 CGAACGAGACCGGACGAC 60.202 66.667 21.66 14.98 39.36 4.34
1932 2003 1.795177 GAACGAACGAGACCGGACG 60.795 63.158 9.46 13.68 41.33 4.79
1977 2048 5.109903 GCTAAAGAACCTAATGCTCGAAGA 58.890 41.667 0.00 0.00 0.00 2.87
2006 2077 2.159572 CGACGATTTCCACAACCATTCC 60.160 50.000 0.00 0.00 0.00 3.01
2010 2081 0.107081 ACCGACGATTTCCACAACCA 59.893 50.000 0.00 0.00 0.00 3.67
2046 2117 7.090173 ACTGAATTCAAACCCAAATATTGACG 58.910 34.615 9.88 0.00 33.13 4.35
2049 2120 8.306038 TCTGACTGAATTCAAACCCAAATATTG 58.694 33.333 9.88 0.00 0.00 1.90
2053 2124 6.324770 AGTTCTGACTGAATTCAAACCCAAAT 59.675 34.615 9.88 0.00 36.99 2.32
2079 2150 7.050377 TCTTAAGATGATGTGAAGGAACCATC 58.950 38.462 0.00 0.00 36.40 3.51
2087 2158 5.347342 AGCGTCTCTTAAGATGATGTGAAG 58.653 41.667 5.44 2.52 40.43 3.02
2095 2166 4.676546 TGTCATGAGCGTCTCTTAAGATG 58.323 43.478 5.44 0.00 40.86 2.90
2108 2179 1.268386 CGCCAATGTCATGTCATGAGC 60.268 52.381 15.96 13.62 40.53 4.26
2126 2197 0.444260 GAGAAGTACAAGCTTGGCGC 59.556 55.000 29.18 17.97 39.57 6.53
2127 2198 1.728971 CAGAGAAGTACAAGCTTGGCG 59.271 52.381 29.18 6.05 0.00 5.69
2128 2199 2.079925 CCAGAGAAGTACAAGCTTGGC 58.920 52.381 29.18 20.65 0.00 4.52
2129 2200 3.330267 GTCCAGAGAAGTACAAGCTTGG 58.670 50.000 29.18 9.36 0.00 3.61
2130 2201 3.244215 TGGTCCAGAGAAGTACAAGCTTG 60.244 47.826 24.84 24.84 0.00 4.01
2131 2202 2.972713 TGGTCCAGAGAAGTACAAGCTT 59.027 45.455 0.00 0.00 0.00 3.74
2132 2203 2.564947 CTGGTCCAGAGAAGTACAAGCT 59.435 50.000 14.26 0.00 32.44 3.74
2133 2204 2.300437 ACTGGTCCAGAGAAGTACAAGC 59.700 50.000 26.18 0.00 35.18 4.01
2134 2205 3.322254 ACACTGGTCCAGAGAAGTACAAG 59.678 47.826 26.18 4.46 35.18 3.16
2135 2206 3.069586 CACACTGGTCCAGAGAAGTACAA 59.930 47.826 26.18 0.00 35.18 2.41
2136 2207 2.628178 CACACTGGTCCAGAGAAGTACA 59.372 50.000 26.18 0.00 35.18 2.90
2137 2208 2.028930 CCACACTGGTCCAGAGAAGTAC 60.029 54.545 26.18 0.00 35.18 2.73
2138 2209 2.248248 CCACACTGGTCCAGAGAAGTA 58.752 52.381 26.18 0.00 35.18 2.24
2139 2210 1.051812 CCACACTGGTCCAGAGAAGT 58.948 55.000 26.18 14.22 35.18 3.01
2140 2211 0.322975 CCCACACTGGTCCAGAGAAG 59.677 60.000 26.18 14.60 35.17 2.85
2141 2212 1.768684 GCCCACACTGGTCCAGAGAA 61.769 60.000 26.18 0.00 35.17 2.87
2142 2213 2.217038 GCCCACACTGGTCCAGAGA 61.217 63.158 26.18 0.00 35.17 3.10
2143 2214 2.177594 GAGCCCACACTGGTCCAGAG 62.178 65.000 26.18 19.92 35.17 3.35
2144 2215 2.122413 AGCCCACACTGGTCCAGA 60.122 61.111 26.18 0.00 35.17 3.86
2145 2216 2.177594 GAGAGCCCACACTGGTCCAG 62.178 65.000 17.88 17.88 35.17 3.86
2146 2217 2.122413 AGAGCCCACACTGGTCCA 60.122 61.111 0.00 0.00 35.17 4.02
2147 2218 1.893919 GAGAGAGCCCACACTGGTCC 61.894 65.000 0.00 0.00 35.17 4.46
2148 2219 1.594310 GAGAGAGCCCACACTGGTC 59.406 63.158 0.00 0.00 35.17 4.02
2149 2220 1.915769 GGAGAGAGCCCACACTGGT 60.916 63.158 0.00 0.00 35.17 4.00
2150 2221 1.611851 AGGAGAGAGCCCACACTGG 60.612 63.158 0.00 0.00 37.25 4.00
2151 2222 0.902048 TCAGGAGAGAGCCCACACTG 60.902 60.000 0.00 0.00 0.00 3.66
2152 2223 0.042431 ATCAGGAGAGAGCCCACACT 59.958 55.000 0.00 0.00 0.00 3.55
2153 2224 1.781786 TATCAGGAGAGAGCCCACAC 58.218 55.000 0.00 0.00 0.00 3.82
2154 2225 2.091111 TCATATCAGGAGAGAGCCCACA 60.091 50.000 0.00 0.00 0.00 4.17
2155 2226 2.603021 TCATATCAGGAGAGAGCCCAC 58.397 52.381 0.00 0.00 0.00 4.61
2156 2227 3.334910 TTCATATCAGGAGAGAGCCCA 57.665 47.619 0.00 0.00 0.00 5.36
2157 2228 4.504689 CCTTTTCATATCAGGAGAGAGCCC 60.505 50.000 0.00 0.00 0.00 5.19
2158 2229 4.504689 CCCTTTTCATATCAGGAGAGAGCC 60.505 50.000 0.00 0.00 0.00 4.70
2159 2230 4.346418 TCCCTTTTCATATCAGGAGAGAGC 59.654 45.833 0.00 0.00 0.00 4.09
2160 2231 6.491714 TTCCCTTTTCATATCAGGAGAGAG 57.508 41.667 0.00 0.00 0.00 3.20
2161 2232 8.748179 ATATTCCCTTTTCATATCAGGAGAGA 57.252 34.615 0.00 0.00 0.00 3.10
2165 2236 9.466497 GCATTATATTCCCTTTTCATATCAGGA 57.534 33.333 0.00 0.00 0.00 3.86
2166 2237 9.246670 TGCATTATATTCCCTTTTCATATCAGG 57.753 33.333 0.00 0.00 0.00 3.86
2168 2239 9.812347 ACTGCATTATATTCCCTTTTCATATCA 57.188 29.630 0.00 0.00 0.00 2.15
2172 2243 9.603921 CAAAACTGCATTATATTCCCTTTTCAT 57.396 29.630 0.00 0.00 0.00 2.57
2173 2244 8.040132 CCAAAACTGCATTATATTCCCTTTTCA 58.960 33.333 0.00 0.00 0.00 2.69
2174 2245 8.040727 ACCAAAACTGCATTATATTCCCTTTTC 58.959 33.333 0.00 0.00 0.00 2.29
2175 2246 7.823799 CACCAAAACTGCATTATATTCCCTTTT 59.176 33.333 0.00 0.00 0.00 2.27
2176 2247 7.038373 ACACCAAAACTGCATTATATTCCCTTT 60.038 33.333 0.00 0.00 0.00 3.11
2177 2248 6.440328 ACACCAAAACTGCATTATATTCCCTT 59.560 34.615 0.00 0.00 0.00 3.95
2178 2249 5.957774 ACACCAAAACTGCATTATATTCCCT 59.042 36.000 0.00 0.00 0.00 4.20
2179 2250 6.042143 CACACCAAAACTGCATTATATTCCC 58.958 40.000 0.00 0.00 0.00 3.97
2180 2251 6.630071 ACACACCAAAACTGCATTATATTCC 58.370 36.000 0.00 0.00 0.00 3.01
2181 2252 8.532977 AAACACACCAAAACTGCATTATATTC 57.467 30.769 0.00 0.00 0.00 1.75
2182 2253 8.900983 AAAACACACCAAAACTGCATTATATT 57.099 26.923 0.00 0.00 0.00 1.28
2183 2254 8.900983 AAAAACACACCAAAACTGCATTATAT 57.099 26.923 0.00 0.00 0.00 0.86
2205 2276 6.183360 CGCCTGCATCTGTACTATGTTAAAAA 60.183 38.462 9.55 0.00 0.00 1.94
2206 2277 5.293324 CGCCTGCATCTGTACTATGTTAAAA 59.707 40.000 9.55 0.00 0.00 1.52
2207 2278 4.808895 CGCCTGCATCTGTACTATGTTAAA 59.191 41.667 9.55 0.00 0.00 1.52
2208 2279 4.142026 ACGCCTGCATCTGTACTATGTTAA 60.142 41.667 9.55 0.00 0.00 2.01
2209 2280 3.383505 ACGCCTGCATCTGTACTATGTTA 59.616 43.478 9.55 1.46 0.00 2.41
2210 2281 2.168521 ACGCCTGCATCTGTACTATGTT 59.831 45.455 9.55 0.00 0.00 2.71
2211 2282 1.757118 ACGCCTGCATCTGTACTATGT 59.243 47.619 9.55 0.00 0.00 2.29
2212 2283 2.515926 ACGCCTGCATCTGTACTATG 57.484 50.000 0.00 0.00 0.00 2.23
2213 2284 2.430694 TGAACGCCTGCATCTGTACTAT 59.569 45.455 0.00 0.00 0.00 2.12
2214 2285 1.822371 TGAACGCCTGCATCTGTACTA 59.178 47.619 0.00 0.00 0.00 1.82
2215 2286 0.608130 TGAACGCCTGCATCTGTACT 59.392 50.000 0.00 0.00 0.00 2.73
2216 2287 1.656652 ATGAACGCCTGCATCTGTAC 58.343 50.000 0.00 0.00 0.00 2.90
2217 2288 2.167487 TGTATGAACGCCTGCATCTGTA 59.833 45.455 0.00 0.00 0.00 2.74
2218 2289 1.066215 TGTATGAACGCCTGCATCTGT 60.066 47.619 0.00 0.00 0.00 3.41
2219 2290 1.655484 TGTATGAACGCCTGCATCTG 58.345 50.000 0.00 0.00 0.00 2.90
2220 2291 2.158914 TCATGTATGAACGCCTGCATCT 60.159 45.455 0.00 0.00 33.08 2.90
2221 2292 2.212652 TCATGTATGAACGCCTGCATC 58.787 47.619 0.00 0.00 33.08 3.91
2222 2293 2.216046 CTCATGTATGAACGCCTGCAT 58.784 47.619 0.00 0.00 36.18 3.96
2223 2294 1.655484 CTCATGTATGAACGCCTGCA 58.345 50.000 0.00 0.00 36.18 4.41
2224 2295 0.305922 GCTCATGTATGAACGCCTGC 59.694 55.000 0.00 0.00 36.18 4.85
2225 2296 1.945387 AGCTCATGTATGAACGCCTG 58.055 50.000 0.00 0.00 36.18 4.85
2226 2297 2.698855 AAGCTCATGTATGAACGCCT 57.301 45.000 0.00 0.00 36.18 5.52
2227 2298 3.764885 AAAAGCTCATGTATGAACGCC 57.235 42.857 0.00 0.00 36.18 5.68
2569 2684 1.689273 GCGGATGGATAGACAGGTCTT 59.311 52.381 7.33 0.00 40.93 3.01
2574 2689 0.390492 TGCAGCGGATGGATAGACAG 59.610 55.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.