Multiple sequence alignment - TraesCS7A01G461000

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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 TraesCS7A01G461000 chr7A 100.000 2588 0 0 1 2588 657154092 657156679 0.000000e+00 4780.0
1 TraesCS7A01G461000 chr7A 90.750 400 32 3 1093 1487 8404208 8403809 1.760000e-146 529.0
2 TraesCS7A01G461000 chr7A 90.750 400 32 3 1093 1487 8411020 8410621 1.760000e-146 529.0
3 TraesCS7A01G461000 chr7A 81.557 244 36 5 1402 1640 657424521 657424760 2.630000e-45 193.0
4 TraesCS7A01G461000 chr7A 89.286 56 4 2 1531 1584 8403746 8403691 4.620000e-08 69.4
5 TraesCS7A01G461000 chr7A 89.286 56 4 2 1531 1584 8410558 8410503 4.620000e-08 69.4
6 TraesCS7A01G461000 chr7D 92.742 2232 94 22 1 2203 568418832 568421024 0.000000e+00 3162.0
7 TraesCS7A01G461000 chr7D 84.380 621 58 26 997 1584 7466117 7465503 8.030000e-160 573.0
8 TraesCS7A01G461000 chr7D 80.717 446 48 24 1150 1571 7458511 7458080 1.930000e-81 313.0
9 TraesCS7A01G461000 chr7D 93.370 181 12 0 2406 2586 568421027 568421207 4.240000e-68 268.0
10 TraesCS7A01G461000 chr7B 91.089 1672 78 32 1 1664 624245394 624247002 0.000000e+00 2196.0
11 TraesCS7A01G461000 chr7B 85.034 147 18 1 1537 1683 624791143 624791285 2.080000e-31 147.0
12 TraesCS7A01G461000 chr4A 81.638 757 86 38 862 1581 732789535 732788795 1.730000e-161 579.0
13 TraesCS7A01G461000 chrUn 76.144 306 44 20 1111 1412 365429950 365429670 1.620000e-27 134.0
14 TraesCS7A01G461000 chr3A 75.000 308 61 11 1108 1413 482184062 482183769 7.520000e-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 TraesCS7A01G461000 chr7A 657154092 657156679 2587 False 4780.0 4780 100.000 1 2588 1 chr7A.!!$F1 2587
1 TraesCS7A01G461000 chr7A 8403691 8404208 517 True 299.2 529 90.018 1093 1584 2 chr7A.!!$R1 491
2 TraesCS7A01G461000 chr7A 8410503 8411020 517 True 299.2 529 90.018 1093 1584 2 chr7A.!!$R2 491
3 TraesCS7A01G461000 chr7D 568418832 568421207 2375 False 1715.0 3162 93.056 1 2586 2 chr7D.!!$F1 2585
4 TraesCS7A01G461000 chr7D 7465503 7466117 614 True 573.0 573 84.380 997 1584 1 chr7D.!!$R2 587
5 TraesCS7A01G461000 chr7B 624245394 624247002 1608 False 2196.0 2196 91.089 1 1664 1 chr7B.!!$F1 1663
6 TraesCS7A01G461000 chr4A 732788795 732789535 740 True 579.0 579 81.638 862 1581 1 chr4A.!!$R1 719

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
661 683 0.032403 TTTCACATGCACCTGCTTGC 59.968 50.0 11.92 0.0 46.34 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2373 2488 0.107993 TCGATCAGCCTGAGCAAAGG 60.108 55.0 10.97 0.36 43.56 3.11 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
32 33 9.982651 TCTAATTTTGCTGGTCTCTATACATAC 57.017 33.333 0.00 0.00 0.00 2.39
73 74 4.706962 GGCATGTCTCTTTATTTTCCAGGT 59.293 41.667 0.00 0.00 0.00 4.00
74 75 5.885912 GGCATGTCTCTTTATTTTCCAGGTA 59.114 40.000 0.00 0.00 0.00 3.08
159 164 3.303938 TCATCCATCCTCTCTTGTCTCC 58.696 50.000 0.00 0.00 0.00 3.71
165 170 0.823460 CCTCTCTTGTCTCCAGAGCC 59.177 60.000 0.00 0.00 33.56 4.70
211 216 0.955919 GTGCCACTGAGCTTGTACCC 60.956 60.000 0.00 0.00 0.00 3.69
232 237 2.286294 CGCAAGTGGCACTGATTATCTC 59.714 50.000 22.83 3.61 45.17 2.75
332 337 5.956642 GTTTAAACCACTGAACTTGACCAA 58.043 37.500 7.12 0.00 0.00 3.67
388 393 3.365820 ACCGCGTTAAGAAGATTTACACG 59.634 43.478 4.92 0.00 0.00 4.49
436 441 6.963049 ACTTGCTAAACTTACGTAGATTGG 57.037 37.500 0.00 0.00 0.00 3.16
475 484 3.266510 TGTGGCATTACTGAGTGATCC 57.733 47.619 0.00 0.00 0.00 3.36
538 553 6.211587 TGTACGGCAATTAGTACATACAGT 57.788 37.500 13.40 0.00 45.49 3.55
539 554 7.332213 TGTACGGCAATTAGTACATACAGTA 57.668 36.000 13.40 0.00 45.49 2.74
602 617 2.128035 CTGACGCCGATTAGCTTTAGG 58.872 52.381 0.00 0.00 0.00 2.69
616 631 2.866762 GCTTTAGGTTGAATCGATCGCT 59.133 45.455 11.09 0.00 0.00 4.93
657 679 0.604578 ATGGTTTCACATGCACCTGC 59.395 50.000 0.00 0.00 42.50 4.85
658 680 0.467844 TGGTTTCACATGCACCTGCT 60.468 50.000 0.00 0.00 42.66 4.24
659 681 0.675633 GGTTTCACATGCACCTGCTT 59.324 50.000 0.00 0.00 42.66 3.91
661 683 0.032403 TTTCACATGCACCTGCTTGC 59.968 50.000 11.92 0.00 46.34 4.01
662 684 0.824595 TTCACATGCACCTGCTTGCT 60.825 50.000 11.92 0.00 46.34 3.91
663 685 1.080772 CACATGCACCTGCTTGCTG 60.081 57.895 11.92 7.04 46.34 4.41
779 801 8.260818 TCTATTGGATCAAAGAGAGTTTGTAGG 58.739 37.037 2.91 0.00 0.00 3.18
800 822 1.404035 CCGTACGTCCTCATGATCACA 59.596 52.381 15.21 0.00 0.00 3.58
803 825 2.015736 ACGTCCTCATGATCACAAGC 57.984 50.000 0.00 0.00 0.00 4.01
828 850 0.108329 ACGGCTGAGATTAACCACCG 60.108 55.000 0.00 0.00 44.49 4.94
836 858 1.134560 AGATTAACCACCGAGCGAGAC 59.865 52.381 0.00 0.00 0.00 3.36
1077 1142 1.890625 GCAGCAATGGTGGCAATGGA 61.891 55.000 14.61 0.00 0.00 3.41
1137 1202 0.537653 TGTTCGACAAGGTGGTGACA 59.462 50.000 0.00 0.00 38.70 3.58
1515 1604 4.498520 CAGCAGGCGACGTCGGAT 62.499 66.667 36.13 18.17 40.23 4.18
1523 1612 0.525668 GCGACGTCGGATGAAGACAT 60.526 55.000 36.13 0.00 38.46 3.06
1596 1685 3.306294 CCGGTGCAGAATGATAGCAGATA 60.306 47.826 0.00 0.00 39.69 1.98
1597 1686 3.925299 CGGTGCAGAATGATAGCAGATAG 59.075 47.826 0.00 0.00 39.69 2.08
1608 1697 5.461526 TGATAGCAGATAGATTACGCACAC 58.538 41.667 0.00 0.00 0.00 3.82
1672 1761 2.839975 TGTACTGTTCGGCAATGACAA 58.160 42.857 0.00 0.00 0.00 3.18
1682 1771 4.574892 TCGGCAATGACAATCTCAAGTTA 58.425 39.130 0.00 0.00 30.60 2.24
1683 1772 4.391830 TCGGCAATGACAATCTCAAGTTAC 59.608 41.667 0.00 0.00 30.60 2.50
1684 1773 4.393062 CGGCAATGACAATCTCAAGTTACT 59.607 41.667 0.00 0.00 30.60 2.24
1685 1774 5.446473 CGGCAATGACAATCTCAAGTTACTC 60.446 44.000 0.00 0.00 30.60 2.59
1686 1775 5.163713 GGCAATGACAATCTCAAGTTACTCC 60.164 44.000 0.00 0.00 30.60 3.85
1740 1840 7.875971 AGTTAAATGACAATCTCAAGTTCCAC 58.124 34.615 0.00 0.00 30.60 4.02
1751 1851 0.892755 AAGTTCCACCGACGATGCTA 59.107 50.000 0.00 0.00 0.00 3.49
1752 1852 0.456221 AGTTCCACCGACGATGCTAG 59.544 55.000 0.00 0.00 0.00 3.42
1777 1877 3.432588 CAGTCGTCGGCGTCTCCT 61.433 66.667 10.18 0.00 39.49 3.69
1804 1904 4.373116 TCCTGCTCGCCGTTGTCC 62.373 66.667 0.00 0.00 0.00 4.02
1836 1936 2.943978 CGGCGGTCTCCTTGGTCTT 61.944 63.158 0.00 0.00 0.00 3.01
1837 1937 1.376037 GGCGGTCTCCTTGGTCTTG 60.376 63.158 0.00 0.00 0.00 3.02
1838 1938 2.035442 GCGGTCTCCTTGGTCTTGC 61.035 63.158 0.00 0.00 0.00 4.01
1860 1960 1.601419 CCCCAGAGGAACGCGTAGAA 61.601 60.000 14.46 0.00 38.24 2.10
1967 2068 2.878406 CAAACGACAGGGAGTTGAACAT 59.122 45.455 0.00 0.00 35.47 2.71
1980 2081 2.046700 AACATGGGCGGGTACACG 60.047 61.111 14.60 14.60 0.00 4.49
2056 2157 2.930562 ACCCCAGAGCAGACCACC 60.931 66.667 0.00 0.00 0.00 4.61
2063 2164 2.524394 AGCAGACCACCGTGACCT 60.524 61.111 0.00 0.00 0.00 3.85
2079 2180 4.767255 CTGGCGCAGGTCCCACTC 62.767 72.222 10.83 0.00 0.00 3.51
2095 2196 4.704103 TCCAGCCTCCACTCCGCT 62.704 66.667 0.00 0.00 0.00 5.52
2114 2215 2.998279 GCCCAGCCATGTCTGTTGC 61.998 63.158 2.64 1.50 32.32 4.17
2115 2216 2.345760 CCCAGCCATGTCTGTTGCC 61.346 63.158 2.64 0.00 32.32 4.52
2116 2217 1.604308 CCAGCCATGTCTGTTGCCA 60.604 57.895 2.64 0.00 32.32 4.92
2122 2223 3.196207 ATGTCTGTTGCCAGCGGGT 62.196 57.895 4.36 0.00 38.66 5.28
2190 2305 4.690719 CGCGGTTGCCCAGTACCA 62.691 66.667 0.00 0.00 38.08 3.25
2195 2310 1.375523 GTTGCCCAGTACCAGGACG 60.376 63.158 0.00 0.00 0.00 4.79
2203 2318 1.080298 GTACCAGGACGGGAACACG 60.080 63.158 0.00 0.00 40.22 4.49
2204 2319 1.228521 TACCAGGACGGGAACACGA 60.229 57.895 2.83 0.00 40.22 4.35
2205 2320 0.827089 TACCAGGACGGGAACACGAA 60.827 55.000 2.83 0.00 40.22 3.85
2206 2321 1.666872 CCAGGACGGGAACACGAAC 60.667 63.158 2.83 0.00 37.61 3.95
2207 2322 1.068417 CAGGACGGGAACACGAACA 59.932 57.895 2.83 0.00 37.61 3.18
2208 2323 1.068585 AGGACGGGAACACGAACAC 59.931 57.895 2.83 0.00 37.61 3.32
2209 2324 1.957695 GGACGGGAACACGAACACC 60.958 63.158 2.83 0.00 37.61 4.16
2210 2325 1.068585 GACGGGAACACGAACACCT 59.931 57.895 2.83 0.00 37.61 4.00
2211 2326 1.219522 GACGGGAACACGAACACCTG 61.220 60.000 2.83 0.00 37.61 4.00
2212 2327 1.959226 CGGGAACACGAACACCTGG 60.959 63.158 0.00 0.00 35.47 4.45
2213 2328 2.258726 GGGAACACGAACACCTGGC 61.259 63.158 0.00 0.00 0.00 4.85
2214 2329 2.604174 GGAACACGAACACCTGGCG 61.604 63.158 0.00 0.00 0.00 5.69
2215 2330 1.593209 GAACACGAACACCTGGCGA 60.593 57.895 0.00 0.00 0.00 5.54
2216 2331 1.828331 GAACACGAACACCTGGCGAC 61.828 60.000 0.00 0.00 0.00 5.19
2217 2332 3.041940 CACGAACACCTGGCGACC 61.042 66.667 0.00 0.00 0.00 4.79
2218 2333 3.231736 ACGAACACCTGGCGACCT 61.232 61.111 0.00 0.00 0.00 3.85
2219 2334 2.738521 CGAACACCTGGCGACCTG 60.739 66.667 0.00 0.00 0.00 4.00
2220 2335 2.358737 GAACACCTGGCGACCTGG 60.359 66.667 16.47 16.47 46.30 4.45
2221 2336 4.643387 AACACCTGGCGACCTGGC 62.643 66.667 17.52 0.00 45.01 4.85
2233 2348 4.680237 CCTGGCCTGCACGACGAA 62.680 66.667 3.32 0.00 0.00 3.85
2234 2349 3.414700 CTGGCCTGCACGACGAAC 61.415 66.667 3.32 0.00 0.00 3.95
2235 2350 4.980805 TGGCCTGCACGACGAACC 62.981 66.667 3.32 0.00 0.00 3.62
2236 2351 4.980805 GGCCTGCACGACGAACCA 62.981 66.667 0.00 0.00 0.00 3.67
2237 2352 3.414700 GCCTGCACGACGAACCAG 61.415 66.667 0.00 4.59 0.00 4.00
2238 2353 2.338620 CCTGCACGACGAACCAGA 59.661 61.111 0.00 0.00 0.00 3.86
2239 2354 1.734477 CCTGCACGACGAACCAGAG 60.734 63.158 0.00 0.00 0.00 3.35
2240 2355 2.355837 TGCACGACGAACCAGAGC 60.356 61.111 0.00 0.00 0.00 4.09
2241 2356 3.470567 GCACGACGAACCAGAGCG 61.471 66.667 0.00 0.00 0.00 5.03
2242 2357 2.050351 CACGACGAACCAGAGCGT 60.050 61.111 0.00 0.00 44.33 5.07
2243 2358 2.050351 ACGACGAACCAGAGCGTG 60.050 61.111 0.00 0.00 41.34 5.34
2244 2359 2.050351 CGACGAACCAGAGCGTGT 60.050 61.111 0.00 0.00 41.34 4.49
2245 2360 1.208358 CGACGAACCAGAGCGTGTA 59.792 57.895 0.00 0.00 41.34 2.90
2246 2361 0.793478 CGACGAACCAGAGCGTGTAG 60.793 60.000 0.00 0.00 41.34 2.74
2264 2379 2.778679 CTAACGCAGCTTCCGCAC 59.221 61.111 3.60 0.00 39.10 5.34
2265 2380 2.027073 CTAACGCAGCTTCCGCACA 61.027 57.895 3.60 0.00 39.10 4.57
2266 2381 1.959899 CTAACGCAGCTTCCGCACAG 61.960 60.000 3.60 0.00 39.10 3.66
2269 2384 2.047274 GCAGCTTCCGCACAGGTA 60.047 61.111 0.00 0.00 41.99 3.08
2270 2385 2.391389 GCAGCTTCCGCACAGGTAC 61.391 63.158 0.00 0.00 41.99 3.34
2271 2386 1.005037 CAGCTTCCGCACAGGTACA 60.005 57.895 0.00 0.00 41.99 2.90
2272 2387 1.016130 CAGCTTCCGCACAGGTACAG 61.016 60.000 0.00 0.00 41.99 2.74
2273 2388 1.741770 GCTTCCGCACAGGTACAGG 60.742 63.158 0.00 0.00 41.99 4.00
2274 2389 1.079127 CTTCCGCACAGGTACAGGG 60.079 63.158 0.00 0.00 41.99 4.45
2275 2390 3.248446 TTCCGCACAGGTACAGGGC 62.248 63.158 1.95 1.95 41.99 5.19
2277 2392 4.373116 CGCACAGGTACAGGGCGT 62.373 66.667 21.58 0.00 42.51 5.68
2278 2393 2.742372 GCACAGGTACAGGGCGTG 60.742 66.667 5.50 5.50 0.00 5.34
2279 2394 2.742372 CACAGGTACAGGGCGTGC 60.742 66.667 7.17 0.00 0.00 5.34
2296 2411 4.838152 CCGGTGGCCATGTCGAGG 62.838 72.222 22.02 10.94 0.00 4.63
2297 2412 4.838152 CGGTGGCCATGTCGAGGG 62.838 72.222 9.72 0.00 0.00 4.30
2342 2457 4.012895 GGCGTGGACGTGCAAGTG 62.013 66.667 22.28 12.00 42.22 3.16
2343 2458 4.012895 GCGTGGACGTGCAAGTGG 62.013 66.667 22.28 9.15 42.22 4.00
2344 2459 2.279851 CGTGGACGTGCAAGTGGA 60.280 61.111 12.69 0.00 34.11 4.02
2345 2460 2.310233 CGTGGACGTGCAAGTGGAG 61.310 63.158 12.69 0.00 34.11 3.86
2346 2461 1.227556 GTGGACGTGCAAGTGGAGT 60.228 57.895 12.69 0.00 0.00 3.85
2347 2462 1.227527 TGGACGTGCAAGTGGAGTG 60.228 57.895 10.87 0.00 0.00 3.51
2348 2463 1.961277 GGACGTGCAAGTGGAGTGG 60.961 63.158 10.87 0.00 0.00 4.00
2349 2464 1.069090 GACGTGCAAGTGGAGTGGA 59.931 57.895 10.87 0.00 0.00 4.02
2350 2465 0.946221 GACGTGCAAGTGGAGTGGAG 60.946 60.000 10.87 0.00 0.00 3.86
2351 2466 1.669115 CGTGCAAGTGGAGTGGAGG 60.669 63.158 0.00 0.00 0.00 4.30
2352 2467 1.451936 GTGCAAGTGGAGTGGAGGT 59.548 57.895 0.00 0.00 0.00 3.85
2353 2468 0.685097 GTGCAAGTGGAGTGGAGGTA 59.315 55.000 0.00 0.00 0.00 3.08
2354 2469 0.685097 TGCAAGTGGAGTGGAGGTAC 59.315 55.000 0.00 0.00 0.00 3.34
2355 2470 0.389948 GCAAGTGGAGTGGAGGTACG 60.390 60.000 0.00 0.00 0.00 3.67
2356 2471 0.246635 CAAGTGGAGTGGAGGTACGG 59.753 60.000 0.00 0.00 0.00 4.02
2357 2472 1.542187 AAGTGGAGTGGAGGTACGGC 61.542 60.000 0.00 0.00 0.00 5.68
2358 2473 2.118732 TGGAGTGGAGGTACGGCA 59.881 61.111 0.00 0.00 0.00 5.69
2359 2474 1.982395 TGGAGTGGAGGTACGGCAG 60.982 63.158 0.00 0.00 0.00 4.85
2360 2475 2.184579 GAGTGGAGGTACGGCAGC 59.815 66.667 0.00 0.00 0.00 5.25
2361 2476 2.603473 AGTGGAGGTACGGCAGCA 60.603 61.111 0.00 0.00 0.00 4.41
2362 2477 2.125512 GTGGAGGTACGGCAGCAG 60.126 66.667 0.00 0.00 0.00 4.24
2363 2478 3.390521 TGGAGGTACGGCAGCAGG 61.391 66.667 0.00 0.00 0.00 4.85
2364 2479 3.075005 GGAGGTACGGCAGCAGGA 61.075 66.667 0.00 0.00 0.00 3.86
2365 2480 2.496817 GAGGTACGGCAGCAGGAG 59.503 66.667 0.00 0.00 0.00 3.69
2366 2481 2.037367 AGGTACGGCAGCAGGAGA 59.963 61.111 0.00 0.00 0.00 3.71
2367 2482 2.184579 GGTACGGCAGCAGGAGAC 59.815 66.667 0.00 0.00 0.00 3.36
2368 2483 2.202623 GTACGGCAGCAGGAGACG 60.203 66.667 0.00 0.00 0.00 4.18
2369 2484 4.129737 TACGGCAGCAGGAGACGC 62.130 66.667 0.00 0.00 0.00 5.19
2377 2492 2.357517 CAGGAGACGCGTGCCTTT 60.358 61.111 20.70 0.00 0.00 3.11
2378 2493 2.357517 AGGAGACGCGTGCCTTTG 60.358 61.111 20.70 0.00 0.00 2.77
2379 2494 4.090057 GGAGACGCGTGCCTTTGC 62.090 66.667 20.70 0.00 38.26 3.68
2380 2495 3.044305 GAGACGCGTGCCTTTGCT 61.044 61.111 20.70 4.95 38.71 3.91
2381 2496 3.016474 GAGACGCGTGCCTTTGCTC 62.016 63.158 20.70 11.70 38.71 4.26
2382 2497 3.345808 GACGCGTGCCTTTGCTCA 61.346 61.111 20.70 0.00 38.71 4.26
2383 2498 3.300667 GACGCGTGCCTTTGCTCAG 62.301 63.158 20.70 0.00 38.71 3.35
2384 2499 4.093952 CGCGTGCCTTTGCTCAGG 62.094 66.667 0.00 0.00 38.71 3.86
2391 2506 2.391469 CCTTTGCTCAGGCTGATCG 58.609 57.895 19.11 8.61 39.59 3.69
2392 2507 0.107993 CCTTTGCTCAGGCTGATCGA 60.108 55.000 19.11 11.21 39.59 3.59
2393 2508 1.005340 CTTTGCTCAGGCTGATCGAC 58.995 55.000 19.11 8.69 39.59 4.20
2394 2509 0.391661 TTTGCTCAGGCTGATCGACC 60.392 55.000 19.11 5.13 39.59 4.79
2395 2510 1.543944 TTGCTCAGGCTGATCGACCA 61.544 55.000 19.11 7.64 39.59 4.02
2396 2511 1.520342 GCTCAGGCTGATCGACCAC 60.520 63.158 19.11 0.00 35.22 4.16
2397 2512 1.142748 CTCAGGCTGATCGACCACC 59.857 63.158 19.11 0.00 0.00 4.61
2398 2513 1.607801 CTCAGGCTGATCGACCACCA 61.608 60.000 19.11 0.00 0.00 4.17
2399 2514 0.977627 TCAGGCTGATCGACCACCAT 60.978 55.000 14.43 0.00 0.00 3.55
2400 2515 0.812811 CAGGCTGATCGACCACCATG 60.813 60.000 9.42 0.00 0.00 3.66
2401 2516 1.524621 GGCTGATCGACCACCATGG 60.525 63.158 11.19 11.19 45.02 3.66
2509 2624 2.361737 GGAGGAAGGTGGCCAAGC 60.362 66.667 7.24 0.78 0.00 4.01
2525 2640 2.842394 AAGCGGCAGATCTCACACGG 62.842 60.000 1.45 0.00 0.00 4.94
2535 2650 2.254546 TCTCACACGGCTCACATTTT 57.745 45.000 0.00 0.00 0.00 1.82
2558 2673 0.598562 AGATACGTGCGAGCTATGGG 59.401 55.000 0.00 0.00 0.00 4.00
2586 2701 0.623723 TGGCCCACCCAGAAGTATTC 59.376 55.000 0.00 0.00 39.18 1.75
2587 2702 2.809137 TGGCCCACCCAGAAGTATTCC 61.809 57.143 0.00 0.00 40.19 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 6.183360 TGGAACAAGTCGGCATAGACATTATA 60.183 38.462 8.54 0.00 43.24 0.98
74 75 5.057149 GGAACAAGTCGGCATAGACATTAT 58.943 41.667 8.54 0.00 43.24 1.28
177 182 7.523873 GCTCAGTGGCACTATACAAGTATATGA 60.524 40.741 21.59 8.42 35.76 2.15
178 183 6.587990 GCTCAGTGGCACTATACAAGTATATG 59.412 42.308 21.59 4.02 35.76 1.78
211 216 2.283298 AGATAATCAGTGCCACTTGCG 58.717 47.619 0.00 0.00 45.60 4.85
232 237 5.414765 TGTGCATAGATAGATAGTGGGTACG 59.585 44.000 0.00 0.00 0.00 3.67
332 337 3.857157 TGTACCTGCAAGAAAAGGTCT 57.143 42.857 0.00 0.00 43.52 3.85
347 352 4.201980 GCGGTAATTTGGGAAGATTGTACC 60.202 45.833 0.00 0.00 0.00 3.34
349 354 3.623960 CGCGGTAATTTGGGAAGATTGTA 59.376 43.478 0.00 0.00 0.00 2.41
388 393 3.560896 TGTAGGTTACGTTTGTTTGCTCC 59.439 43.478 0.00 0.00 0.00 4.70
436 441 6.166982 GCCACATCTACTGGATATCCTTAAC 58.833 44.000 22.35 0.00 36.82 2.01
602 617 4.845387 TCACTAGTAGCGATCGATTCAAC 58.155 43.478 21.57 8.10 0.00 3.18
616 631 6.539826 CCATGAAGCAATGACAATCACTAGTA 59.460 38.462 0.00 0.00 0.00 1.82
657 679 1.080705 GAAGCAGCCAAGCAGCAAG 60.081 57.895 6.73 0.00 43.44 4.01
658 680 2.567497 GGAAGCAGCCAAGCAGCAA 61.567 57.895 6.73 0.00 43.44 3.91
659 681 2.128290 TAGGAAGCAGCCAAGCAGCA 62.128 55.000 6.73 0.00 43.44 4.41
660 682 1.375098 CTAGGAAGCAGCCAAGCAGC 61.375 60.000 0.00 0.00 41.34 5.25
661 683 0.035630 ACTAGGAAGCAGCCAAGCAG 60.036 55.000 0.00 0.00 36.85 4.24
662 684 0.321919 CACTAGGAAGCAGCCAAGCA 60.322 55.000 0.00 0.00 36.85 3.91
663 685 1.652167 GCACTAGGAAGCAGCCAAGC 61.652 60.000 0.00 0.00 0.00 4.01
779 801 0.384309 TGATCATGAGGACGTACGGC 59.616 55.000 21.06 17.96 0.00 5.68
800 822 2.119801 ATCTCAGCCGTTGATTGCTT 57.880 45.000 0.00 0.00 35.12 3.91
803 825 3.689161 TGGTTAATCTCAGCCGTTGATTG 59.311 43.478 0.00 0.00 34.68 2.67
836 858 4.758251 TCCCATGCACGGCACTCG 62.758 66.667 0.00 0.00 43.04 4.18
919 943 1.081906 CACGCCTTCACATGTGTGC 60.082 57.895 24.63 22.07 45.25 4.57
1515 1604 2.741985 CGCGGTGCCATGTCTTCA 60.742 61.111 0.00 0.00 0.00 3.02
1596 1685 5.892160 TCTAACAGTAGTGTGCGTAATCT 57.108 39.130 3.39 0.00 36.84 2.40
1597 1686 6.263344 TGATCTAACAGTAGTGTGCGTAATC 58.737 40.000 3.39 4.78 36.84 1.75
1608 1697 9.232082 CTTCTTTCTTCGATGATCTAACAGTAG 57.768 37.037 1.37 0.00 0.00 2.57
1646 1735 5.293324 GTCATTGCCGAACAGTACATGAATA 59.707 40.000 0.00 0.00 0.00 1.75
1656 1745 2.743664 TGAGATTGTCATTGCCGAACAG 59.256 45.455 0.00 0.00 0.00 3.16
1672 1761 7.635648 AGACTACTAGTGGAGTAACTTGAGAT 58.364 38.462 13.86 0.00 40.23 2.75
1740 1840 3.881092 ATCGCGCTAGCATCGTCGG 62.881 63.158 20.94 3.17 45.49 4.79
1761 1861 3.126225 GAGGAGACGCCGACGACT 61.126 66.667 0.00 0.00 46.76 4.18
1823 1923 0.957888 GGCAGCAAGACCAAGGAGAC 60.958 60.000 0.00 0.00 0.00 3.36
1824 1924 1.376466 GGCAGCAAGACCAAGGAGA 59.624 57.895 0.00 0.00 0.00 3.71
1836 1936 4.020617 CGTTCCTCTGGGGCAGCA 62.021 66.667 0.00 0.00 34.39 4.41
1912 2013 3.767230 CGACGCTGTTGTGCTCGG 61.767 66.667 0.00 0.00 33.44 4.63
2002 2103 3.973516 TTCGTGCTCGTGCCGTCT 61.974 61.111 16.06 0.00 38.71 4.18
2003 2104 3.764049 GTTCGTGCTCGTGCCGTC 61.764 66.667 16.06 9.65 38.71 4.79
2095 2196 1.604308 CAACAGACATGGCTGGGCA 60.604 57.895 31.68 0.00 40.20 5.36
2189 2304 1.068417 TGTTCGTGTTCCCGTCCTG 59.932 57.895 0.00 0.00 0.00 3.86
2190 2305 1.068585 GTGTTCGTGTTCCCGTCCT 59.931 57.895 0.00 0.00 0.00 3.85
2195 2310 2.258726 GCCAGGTGTTCGTGTTCCC 61.259 63.158 0.00 0.00 0.00 3.97
2203 2318 2.358737 CCAGGTCGCCAGGTGTTC 60.359 66.667 0.00 0.00 0.00 3.18
2204 2319 4.643387 GCCAGGTCGCCAGGTGTT 62.643 66.667 0.00 0.00 32.35 3.32
2216 2331 4.680237 TTCGTCGTGCAGGCCAGG 62.680 66.667 5.01 0.00 0.00 4.45
2217 2332 3.414700 GTTCGTCGTGCAGGCCAG 61.415 66.667 5.01 0.00 0.00 4.85
2218 2333 4.980805 GGTTCGTCGTGCAGGCCA 62.981 66.667 5.01 0.00 0.00 5.36
2219 2334 4.980805 TGGTTCGTCGTGCAGGCC 62.981 66.667 0.35 0.00 0.00 5.19
2220 2335 3.414700 CTGGTTCGTCGTGCAGGC 61.415 66.667 0.35 0.00 0.00 4.85
2221 2336 1.734477 CTCTGGTTCGTCGTGCAGG 60.734 63.158 0.00 0.00 0.00 4.85
2222 2337 2.375766 GCTCTGGTTCGTCGTGCAG 61.376 63.158 0.00 0.00 0.00 4.41
2223 2338 2.355837 GCTCTGGTTCGTCGTGCA 60.356 61.111 0.00 0.00 0.00 4.57
2224 2339 3.470567 CGCTCTGGTTCGTCGTGC 61.471 66.667 0.00 0.00 0.00 5.34
2225 2340 2.050351 ACGCTCTGGTTCGTCGTG 60.050 61.111 0.00 0.00 33.09 4.35
2226 2341 1.509644 TACACGCTCTGGTTCGTCGT 61.510 55.000 0.00 0.00 36.73 4.34
2227 2342 0.793478 CTACACGCTCTGGTTCGTCG 60.793 60.000 0.00 0.00 36.73 5.12
2228 2343 1.071567 GCTACACGCTCTGGTTCGTC 61.072 60.000 0.00 0.00 36.73 4.20
2229 2344 1.080705 GCTACACGCTCTGGTTCGT 60.081 57.895 0.00 0.00 39.79 3.85
2230 2345 3.768632 GCTACACGCTCTGGTTCG 58.231 61.111 0.00 0.00 35.14 3.95
2256 2371 1.079127 CCCTGTACCTGTGCGGAAG 60.079 63.158 0.00 0.00 36.31 3.46
2257 2372 3.065306 CCCTGTACCTGTGCGGAA 58.935 61.111 0.00 0.00 36.31 4.30
2258 2373 3.702048 GCCCTGTACCTGTGCGGA 61.702 66.667 0.00 0.00 36.31 5.54
2261 2376 2.742372 CACGCCCTGTACCTGTGC 60.742 66.667 0.00 0.00 0.00 4.57
2262 2377 2.742372 GCACGCCCTGTACCTGTG 60.742 66.667 0.00 0.00 0.00 3.66
2263 2378 4.016706 GGCACGCCCTGTACCTGT 62.017 66.667 0.00 0.00 30.58 4.00
2279 2394 4.838152 CCTCGACATGGCCACCGG 62.838 72.222 8.16 0.00 0.00 5.28
2280 2395 4.838152 CCCTCGACATGGCCACCG 62.838 72.222 8.16 13.01 0.00 4.94
2325 2440 4.012895 CACTTGCACGTCCACGCC 62.013 66.667 0.00 0.00 44.43 5.68
2326 2441 4.012895 CCACTTGCACGTCCACGC 62.013 66.667 0.00 0.00 44.43 5.34
2327 2442 2.279851 TCCACTTGCACGTCCACG 60.280 61.111 0.00 0.00 46.33 4.94
2328 2443 1.227556 ACTCCACTTGCACGTCCAC 60.228 57.895 0.00 0.00 0.00 4.02
2329 2444 1.227527 CACTCCACTTGCACGTCCA 60.228 57.895 0.00 0.00 0.00 4.02
2330 2445 1.961277 CCACTCCACTTGCACGTCC 60.961 63.158 0.00 0.00 0.00 4.79
2331 2446 0.946221 CTCCACTCCACTTGCACGTC 60.946 60.000 0.00 0.00 0.00 4.34
2332 2447 1.069765 CTCCACTCCACTTGCACGT 59.930 57.895 0.00 0.00 0.00 4.49
2333 2448 1.669115 CCTCCACTCCACTTGCACG 60.669 63.158 0.00 0.00 0.00 5.34
2334 2449 0.685097 TACCTCCACTCCACTTGCAC 59.315 55.000 0.00 0.00 0.00 4.57
2335 2450 0.685097 GTACCTCCACTCCACTTGCA 59.315 55.000 0.00 0.00 0.00 4.08
2336 2451 0.389948 CGTACCTCCACTCCACTTGC 60.390 60.000 0.00 0.00 0.00 4.01
2337 2452 0.246635 CCGTACCTCCACTCCACTTG 59.753 60.000 0.00 0.00 0.00 3.16
2338 2453 1.542187 GCCGTACCTCCACTCCACTT 61.542 60.000 0.00 0.00 0.00 3.16
2339 2454 1.982938 GCCGTACCTCCACTCCACT 60.983 63.158 0.00 0.00 0.00 4.00
2340 2455 2.227089 CTGCCGTACCTCCACTCCAC 62.227 65.000 0.00 0.00 0.00 4.02
2341 2456 1.982395 CTGCCGTACCTCCACTCCA 60.982 63.158 0.00 0.00 0.00 3.86
2342 2457 2.893398 CTGCCGTACCTCCACTCC 59.107 66.667 0.00 0.00 0.00 3.85
2343 2458 2.184579 GCTGCCGTACCTCCACTC 59.815 66.667 0.00 0.00 0.00 3.51
2344 2459 2.603473 TGCTGCCGTACCTCCACT 60.603 61.111 0.00 0.00 0.00 4.00
2345 2460 2.125512 CTGCTGCCGTACCTCCAC 60.126 66.667 0.00 0.00 0.00 4.02
2346 2461 3.390521 CCTGCTGCCGTACCTCCA 61.391 66.667 0.00 0.00 0.00 3.86
2347 2462 3.075005 TCCTGCTGCCGTACCTCC 61.075 66.667 0.00 0.00 0.00 4.30
2348 2463 2.052690 TCTCCTGCTGCCGTACCTC 61.053 63.158 0.00 0.00 0.00 3.85
2349 2464 2.037367 TCTCCTGCTGCCGTACCT 59.963 61.111 0.00 0.00 0.00 3.08
2350 2465 2.184579 GTCTCCTGCTGCCGTACC 59.815 66.667 0.00 0.00 0.00 3.34
2351 2466 2.202623 CGTCTCCTGCTGCCGTAC 60.203 66.667 0.00 0.00 0.00 3.67
2352 2467 4.129737 GCGTCTCCTGCTGCCGTA 62.130 66.667 0.00 0.00 0.00 4.02
2360 2475 2.357517 AAAGGCACGCGTCTCCTG 60.358 61.111 25.01 9.58 0.00 3.86
2361 2476 2.357517 CAAAGGCACGCGTCTCCT 60.358 61.111 20.43 20.43 0.00 3.69
2362 2477 4.090057 GCAAAGGCACGCGTCTCC 62.090 66.667 9.86 14.38 40.72 3.71
2363 2478 3.016474 GAGCAAAGGCACGCGTCTC 62.016 63.158 9.86 7.53 44.61 3.36
2364 2479 3.044305 GAGCAAAGGCACGCGTCT 61.044 61.111 9.86 0.22 44.61 4.18
2365 2480 3.300667 CTGAGCAAAGGCACGCGTC 62.301 63.158 9.86 4.20 44.61 5.19
2366 2481 3.349006 CTGAGCAAAGGCACGCGT 61.349 61.111 5.58 5.58 44.61 6.01
2367 2482 4.093952 CCTGAGCAAAGGCACGCG 62.094 66.667 3.53 3.53 44.61 6.01
2373 2488 0.107993 TCGATCAGCCTGAGCAAAGG 60.108 55.000 10.97 0.36 43.56 3.11
2374 2489 1.005340 GTCGATCAGCCTGAGCAAAG 58.995 55.000 10.97 0.00 43.56 2.77
2375 2490 0.391661 GGTCGATCAGCCTGAGCAAA 60.392 55.000 10.97 0.00 43.56 3.68
2376 2491 1.219124 GGTCGATCAGCCTGAGCAA 59.781 57.895 10.97 0.00 43.56 3.91
2377 2492 1.984026 TGGTCGATCAGCCTGAGCA 60.984 57.895 10.97 0.00 43.56 4.26
2378 2493 1.520342 GTGGTCGATCAGCCTGAGC 60.520 63.158 0.00 0.00 40.32 4.26
2379 2494 1.142748 GGTGGTCGATCAGCCTGAG 59.857 63.158 17.05 0.00 0.00 3.35
2380 2495 0.977627 ATGGTGGTCGATCAGCCTGA 60.978 55.000 24.11 7.13 34.56 3.86
2381 2496 0.812811 CATGGTGGTCGATCAGCCTG 60.813 60.000 24.11 20.28 34.56 4.85
2382 2497 1.524002 CATGGTGGTCGATCAGCCT 59.476 57.895 24.11 12.60 34.56 4.58
2383 2498 1.524621 CCATGGTGGTCGATCAGCC 60.525 63.158 24.11 16.22 34.56 4.85
2384 2499 4.131376 CCATGGTGGTCGATCAGC 57.869 61.111 20.75 20.75 35.87 4.26
2419 2534 2.279784 GAAGATCCTCGGCGCAGG 60.280 66.667 10.83 8.91 34.40 4.85
2432 2547 3.797353 GGCCCGGCAGGATGAAGA 61.797 66.667 12.58 0.00 39.69 2.87
2492 2607 2.361737 GCTTGGCCACCTTCCTCC 60.362 66.667 3.88 0.00 0.00 4.30
2509 2624 2.887568 GCCGTGTGAGATCTGCCG 60.888 66.667 0.00 0.00 0.00 5.69
2535 2650 1.375551 TAGCTCGCACGTATCTCACA 58.624 50.000 0.00 0.00 0.00 3.58
2545 2660 0.319125 GCTACTCCCATAGCTCGCAC 60.319 60.000 0.00 0.00 43.62 5.34
2558 2673 1.054406 TGGGTGGGCCATAGCTACTC 61.054 60.000 10.70 0.00 39.73 2.59
2565 2680 2.206322 ATACTTCTGGGTGGGCCATA 57.794 50.000 10.70 0.00 36.17 2.74


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

AutoCloner maintained by Alex Coulton.