Multiple sequence alignment - TraesCS2A01G002200

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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 TraesCS2A01G002200 chr2A 100.000 2474 0 0 1 2474 1188268 1185795 0.000000e+00 4569.0
1 TraesCS2A01G002200 chr2A 87.556 1551 159 21 349 1886 766405390 766403861 0.000000e+00 1764.0
2 TraesCS2A01G002200 chr2A 85.619 598 58 16 1223 1801 766401585 766400997 9.790000e-169 603.0
3 TraesCS2A01G002200 chr2A 83.634 666 77 17 867 1524 1090680 1090039 4.550000e-167 597.0
4 TraesCS2A01G002200 chr2A 88.196 449 47 5 1880 2325 766403835 766403390 4.680000e-147 531.0
5 TraesCS2A01G002200 chr2A 82.895 532 84 6 1416 1943 766406221 766405693 2.880000e-129 472.0
6 TraesCS2A01G002200 chr2A 98.611 144 1 1 2332 2474 1177661 1177518 1.140000e-63 254.0
7 TraesCS2A01G002200 chr2A 90.000 120 12 0 2033 2152 972416 972297 3.290000e-34 156.0
8 TraesCS2A01G002200 chr2D 96.404 2336 72 9 1 2331 1784285 1781957 0.000000e+00 3838.0
9 TraesCS2A01G002200 chr2D 89.354 1099 97 14 1245 2331 641114287 641113197 0.000000e+00 1363.0
10 TraesCS2A01G002200 chr2D 88.537 916 86 15 349 1256 641116781 641115877 0.000000e+00 1092.0
11 TraesCS2A01G002200 chr2D 83.525 959 103 22 867 1801 641111690 641110763 0.000000e+00 845.0
12 TraesCS2A01G002200 chr2D 81.732 947 127 19 867 1797 1673084 1672168 0.000000e+00 749.0
13 TraesCS2A01G002200 chr2D 82.584 712 90 13 870 1576 1762497 1761815 4.550000e-167 597.0
14 TraesCS2A01G002200 chr2D 82.051 624 94 11 1342 1958 641117677 641117065 1.310000e-142 516.0
15 TraesCS2A01G002200 chr2D 81.303 476 60 12 885 1355 641120475 641120024 2.340000e-95 359.0
16 TraesCS2A01G002200 chr2D 85.315 143 19 2 130 272 1622272 1622412 1.980000e-31 147.0
17 TraesCS2A01G002200 chr2D 88.350 103 11 1 130 231 1817443 1817341 3.340000e-24 122.0
18 TraesCS2A01G002200 chr2B 85.714 1295 121 29 358 1630 10085915 10087167 0.000000e+00 1308.0
19 TraesCS2A01G002200 chr2B 96.689 151 3 2 2325 2474 301919140 301918991 1.470000e-62 250.0
20 TraesCS2A01G002200 chr2B 88.961 154 7 2 201 354 10085708 10085851 5.440000e-42 182.0
21 TraesCS2A01G002200 chr2B 88.525 122 12 2 2033 2152 10171657 10171778 1.980000e-31 147.0
22 TraesCS2A01G002200 chr2B 91.667 72 6 0 1 72 10085577 10085648 1.570000e-17 100.0
23 TraesCS2A01G002200 chr2B 97.500 40 1 0 15 54 10074000 10073961 4.410000e-08 69.4
24 TraesCS2A01G002200 chr6B 97.959 147 1 2 2328 2474 566265506 566265362 1.140000e-63 254.0
25 TraesCS2A01G002200 chr6B 95.597 159 4 3 2318 2474 479823015 479822858 4.080000e-63 252.0
26 TraesCS2A01G002200 chr6B 96.104 154 5 1 2321 2474 474028730 474028578 1.470000e-62 250.0
27 TraesCS2A01G002200 chr4B 98.601 143 2 0 2332 2474 30300392 30300250 1.140000e-63 254.0
28 TraesCS2A01G002200 chr4B 98.601 143 1 1 2332 2474 480033274 480033133 4.080000e-63 252.0
29 TraesCS2A01G002200 chr7B 96.667 150 4 1 2325 2474 127078831 127078979 5.280000e-62 248.0
30 TraesCS2A01G002200 chr5B 96.053 152 4 2 2324 2474 163165848 163165998 1.900000e-61 246.0


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 TraesCS2A01G002200 chr2A 1185795 1188268 2473 True 4569.0 4569 100.000000 1 2474 1 chr2A.!!$R4 2473
1 TraesCS2A01G002200 chr2A 766400997 766406221 5224 True 842.5 1764 86.066500 349 2325 4 chr2A.!!$R5 1976
2 TraesCS2A01G002200 chr2A 1090039 1090680 641 True 597.0 597 83.634000 867 1524 1 chr2A.!!$R2 657
3 TraesCS2A01G002200 chr2D 1781957 1784285 2328 True 3838.0 3838 96.404000 1 2331 1 chr2D.!!$R3 2330
4 TraesCS2A01G002200 chr2D 641110763 641120475 9712 True 835.0 1363 84.954000 349 2331 5 chr2D.!!$R5 1982
5 TraesCS2A01G002200 chr2D 1672168 1673084 916 True 749.0 749 81.732000 867 1797 1 chr2D.!!$R1 930
6 TraesCS2A01G002200 chr2D 1761815 1762497 682 True 597.0 597 82.584000 870 1576 1 chr2D.!!$R2 706
7 TraesCS2A01G002200 chr2B 10085577 10087167 1590 False 530.0 1308 88.780667 1 1630 3 chr2B.!!$F2 1629

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
168 169 0.035881 ATGCGTGGCCTCCATATGAG 59.964 55.0 3.32 0.0 41.07 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 12708 0.319813 TATGTCAGGCGGCGATGATG 60.32 55.0 12.98 2.56 0.0 3.07 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
168 169 0.035881 ATGCGTGGCCTCCATATGAG 59.964 55.000 3.32 0.00 41.07 2.90
196 197 6.072508 AGCACAAATCTCATCGTTACATGTTT 60.073 34.615 2.30 0.00 0.00 2.83
392 3744 5.486526 TGACCAAATAATTGTTTGATGGCC 58.513 37.500 24.34 6.41 40.64 5.36
514 3868 9.410556 AGTGTTGAAATGTGTTATTAATTGCTC 57.589 29.630 0.00 0.00 0.00 4.26
710 4067 5.508200 AGTGTTGGAACTTTTTATTGCGA 57.492 34.783 0.00 0.00 0.00 5.10
716 4073 6.221858 TGGAACTTTTTATTGCGAAAATGC 57.778 33.333 0.00 0.00 30.45 3.56
750 4107 8.460428 AGTGTTACGTTGGAATCTGTTTTTAAA 58.540 29.630 0.00 0.00 0.00 1.52
806 4167 5.234972 GCTTTATTGTTGGCATGCCTTATTC 59.765 40.000 35.53 20.50 36.94 1.75
808 4169 4.822685 ATTGTTGGCATGCCTTATTCAA 57.177 36.364 35.53 27.92 36.94 2.69
1146 4524 5.691754 CCTTTCATTGCCTGTTACTTGTTTC 59.308 40.000 0.00 0.00 0.00 2.78
1159 4540 6.932400 TGTTACTTGTTTCGTTATCAGTCCAT 59.068 34.615 0.00 0.00 0.00 3.41
1236 4618 7.112452 TGTTCCATATATAGGTCGGATCATG 57.888 40.000 0.00 0.00 0.00 3.07
1320 6304 1.318158 GCAAAGCTGGATGGGTCTGG 61.318 60.000 0.00 0.00 0.00 3.86
1441 12318 2.722201 CGCTCTCCTTTACCCGCCT 61.722 63.158 0.00 0.00 0.00 5.52
1455 12332 2.680352 GCCTCCTCTCCCACGTCA 60.680 66.667 0.00 0.00 0.00 4.35
1630 12512 5.516090 TGCCGATAACTCAGTTTTTCAAAC 58.484 37.500 0.00 0.00 0.00 2.93
1642 12538 5.296283 CAGTTTTTCAAACATTGATGCCCAA 59.704 36.000 2.38 0.00 39.84 4.12
1693 12589 1.426215 TGGTGGGCATGCTCATGATAT 59.574 47.619 25.81 0.00 41.20 1.63
1757 12653 8.373048 TCGCTTCTAAGATTTTTCTTTGTGTA 57.627 30.769 0.00 0.00 0.00 2.90
1782 12678 6.906157 AAATTGATCCTGTGACATGTTTCT 57.094 33.333 0.00 0.00 0.00 2.52
1798 12694 8.408043 ACATGTTTCTGGTGAATCAAGATTAA 57.592 30.769 0.00 0.00 36.06 1.40
1812 12708 5.357257 TCAAGATTAAATCAGACGGGTAGC 58.643 41.667 0.00 0.00 0.00 3.58
1833 12729 1.106944 TCATCGCCGCCTGACATAGA 61.107 55.000 0.00 0.00 0.00 1.98
1841 12737 1.402259 CGCCTGACATAGAACGTCTCT 59.598 52.381 0.00 0.00 38.28 3.10
1888 12784 8.512800 AGCATCATTAGCGTCAATATATATCG 57.487 34.615 0.00 0.00 37.01 2.92
1922 12818 1.402456 GCAGACTCGTATGTGAACGGT 60.402 52.381 0.00 0.00 43.05 4.83
1946 12842 4.516698 CCCTAATTCAAATGGGACTGATCG 59.483 45.833 0.00 0.00 42.11 3.69
1957 12853 0.666274 GACTGATCGTCGGCAACACA 60.666 55.000 0.00 0.00 32.04 3.72
1964 12860 0.726827 CGTCGGCAACACATTAGCAT 59.273 50.000 0.00 0.00 0.00 3.79
1986 12882 5.815233 TTTTTCCCATCTGCAACCATTAA 57.185 34.783 0.00 0.00 0.00 1.40
1992 12888 4.380867 CCCATCTGCAACCATTAAAGTGTC 60.381 45.833 0.00 0.00 0.00 3.67
2065 12961 1.167781 TTCAGGTTTTCGCCGGAACC 61.168 55.000 5.05 10.61 44.47 3.62
2073 12969 4.351938 CGCCGGAACCGAGACACA 62.352 66.667 15.07 0.00 42.83 3.72
2076 12972 2.805353 CGGAACCGAGACACAGCG 60.805 66.667 7.53 0.00 42.83 5.18
2208 13104 2.160813 CGTATGGTGTGGCAAAACTACC 59.839 50.000 0.00 0.00 0.00 3.18
2217 13113 2.360801 TGGCAAAACTACCAGCAAAGTC 59.639 45.455 0.00 0.00 0.00 3.01
2261 13157 1.304713 AAGGGCTCAACCATGGCTG 60.305 57.895 13.04 10.84 42.05 4.85
2272 13168 1.746615 CATGGCTGGTAGTGCGCTT 60.747 57.895 9.73 0.00 0.00 4.68
2331 13227 2.306341 CGAAGCACATGGACATCTCT 57.694 50.000 0.00 0.00 0.00 3.10
2332 13228 1.931841 CGAAGCACATGGACATCTCTG 59.068 52.381 0.00 0.00 0.00 3.35
2333 13229 2.676176 CGAAGCACATGGACATCTCTGT 60.676 50.000 0.00 0.00 38.67 3.41
2334 13230 3.429410 CGAAGCACATGGACATCTCTGTA 60.429 47.826 0.00 0.00 35.14 2.74
2335 13231 3.815856 AGCACATGGACATCTCTGTAG 57.184 47.619 0.00 0.00 35.14 2.74
2336 13232 2.433604 AGCACATGGACATCTCTGTAGG 59.566 50.000 0.00 0.00 35.14 3.18
2337 13233 2.432146 GCACATGGACATCTCTGTAGGA 59.568 50.000 0.00 0.00 35.14 2.94
2338 13234 3.739519 GCACATGGACATCTCTGTAGGAC 60.740 52.174 0.00 0.00 35.14 3.85
2339 13235 3.034635 ACATGGACATCTCTGTAGGACC 58.965 50.000 0.00 0.00 35.14 4.46
2340 13236 3.303938 CATGGACATCTCTGTAGGACCT 58.696 50.000 0.00 0.00 35.14 3.85
2341 13237 3.474798 TGGACATCTCTGTAGGACCTT 57.525 47.619 0.00 0.00 35.14 3.50
2342 13238 3.099905 TGGACATCTCTGTAGGACCTTG 58.900 50.000 0.00 0.00 35.14 3.61
2343 13239 3.245622 TGGACATCTCTGTAGGACCTTGA 60.246 47.826 0.00 0.00 35.14 3.02
2344 13240 3.769844 GGACATCTCTGTAGGACCTTGAA 59.230 47.826 0.00 0.00 35.14 2.69
2345 13241 4.142049 GGACATCTCTGTAGGACCTTGAAG 60.142 50.000 0.00 0.00 35.14 3.02
2346 13242 4.421131 ACATCTCTGTAGGACCTTGAAGT 58.579 43.478 0.00 0.00 32.49 3.01
2347 13243 5.580998 ACATCTCTGTAGGACCTTGAAGTA 58.419 41.667 0.00 0.00 32.49 2.24
2348 13244 6.198639 ACATCTCTGTAGGACCTTGAAGTAT 58.801 40.000 0.00 0.00 32.49 2.12
2349 13245 6.097554 ACATCTCTGTAGGACCTTGAAGTATG 59.902 42.308 0.00 6.77 32.49 2.39
2350 13246 5.580998 TCTCTGTAGGACCTTGAAGTATGT 58.419 41.667 0.00 0.00 0.00 2.29
2351 13247 5.652891 TCTCTGTAGGACCTTGAAGTATGTC 59.347 44.000 0.00 0.00 0.00 3.06
2352 13248 5.580998 TCTGTAGGACCTTGAAGTATGTCT 58.419 41.667 0.00 0.00 0.00 3.41
2353 13249 6.728411 TCTGTAGGACCTTGAAGTATGTCTA 58.272 40.000 0.00 0.00 0.00 2.59
2354 13250 6.829298 TCTGTAGGACCTTGAAGTATGTCTAG 59.171 42.308 0.00 0.00 0.00 2.43
2355 13251 6.728411 TGTAGGACCTTGAAGTATGTCTAGA 58.272 40.000 0.00 0.00 0.00 2.43
2356 13252 6.829298 TGTAGGACCTTGAAGTATGTCTAGAG 59.171 42.308 0.00 0.00 0.00 2.43
2357 13253 5.205056 AGGACCTTGAAGTATGTCTAGAGG 58.795 45.833 0.00 0.00 0.00 3.69
2358 13254 4.342665 GGACCTTGAAGTATGTCTAGAGGG 59.657 50.000 0.00 0.00 0.00 4.30
2359 13255 4.290942 ACCTTGAAGTATGTCTAGAGGGG 58.709 47.826 0.00 0.00 0.00 4.79
2360 13256 3.643792 CCTTGAAGTATGTCTAGAGGGGG 59.356 52.174 0.00 0.00 0.00 5.40
2383 13279 4.403585 GGGGGTGATTAGACTACTTGAC 57.596 50.000 0.00 0.00 0.00 3.18
2384 13280 3.134262 GGGGGTGATTAGACTACTTGACC 59.866 52.174 0.00 0.00 0.00 4.02
2385 13281 3.773119 GGGGTGATTAGACTACTTGACCA 59.227 47.826 0.00 0.00 0.00 4.02
2386 13282 4.224370 GGGGTGATTAGACTACTTGACCAA 59.776 45.833 0.00 0.00 0.00 3.67
2387 13283 5.104485 GGGGTGATTAGACTACTTGACCAAT 60.104 44.000 0.00 0.00 0.00 3.16
2388 13284 6.099269 GGGGTGATTAGACTACTTGACCAATA 59.901 42.308 0.00 0.00 0.00 1.90
2389 13285 7.365295 GGGGTGATTAGACTACTTGACCAATAA 60.365 40.741 0.00 0.00 0.00 1.40
2390 13286 8.044908 GGGTGATTAGACTACTTGACCAATAAA 58.955 37.037 0.00 0.00 0.00 1.40
2391 13287 9.444600 GGTGATTAGACTACTTGACCAATAAAA 57.555 33.333 0.00 0.00 0.00 1.52
2418 13314 8.777578 ACTTAACCTTTTCCCAATTTTAGAGT 57.222 30.769 0.00 0.00 0.00 3.24
2419 13315 9.209048 ACTTAACCTTTTCCCAATTTTAGAGTT 57.791 29.630 0.00 0.00 0.00 3.01
2421 13317 9.825109 TTAACCTTTTCCCAATTTTAGAGTTTG 57.175 29.630 0.00 0.00 0.00 2.93
2422 13318 6.826668 ACCTTTTCCCAATTTTAGAGTTTGG 58.173 36.000 0.00 0.00 39.69 3.28
2423 13319 5.700832 CCTTTTCCCAATTTTAGAGTTTGGC 59.299 40.000 0.00 0.00 38.85 4.52
2424 13320 5.878406 TTTCCCAATTTTAGAGTTTGGCA 57.122 34.783 0.00 0.00 38.85 4.92
2425 13321 5.467035 TTCCCAATTTTAGAGTTTGGCAG 57.533 39.130 0.00 0.00 38.85 4.85
2426 13322 4.735369 TCCCAATTTTAGAGTTTGGCAGA 58.265 39.130 0.00 0.00 38.85 4.26
2427 13323 5.332743 TCCCAATTTTAGAGTTTGGCAGAT 58.667 37.500 0.00 0.00 38.85 2.90
2428 13324 5.779771 TCCCAATTTTAGAGTTTGGCAGATT 59.220 36.000 0.00 0.00 38.85 2.40
2429 13325 6.269769 TCCCAATTTTAGAGTTTGGCAGATTT 59.730 34.615 0.00 0.00 38.85 2.17
2430 13326 6.936335 CCCAATTTTAGAGTTTGGCAGATTTT 59.064 34.615 0.00 0.00 38.85 1.82
2431 13327 8.093927 CCCAATTTTAGAGTTTGGCAGATTTTA 58.906 33.333 0.00 0.00 38.85 1.52
2432 13328 9.143631 CCAATTTTAGAGTTTGGCAGATTTTAG 57.856 33.333 0.00 0.00 34.03 1.85
2433 13329 8.650714 CAATTTTAGAGTTTGGCAGATTTTAGC 58.349 33.333 0.00 0.00 0.00 3.09
2434 13330 7.524717 TTTTAGAGTTTGGCAGATTTTAGCT 57.475 32.000 0.00 0.00 0.00 3.32
2435 13331 8.630054 TTTTAGAGTTTGGCAGATTTTAGCTA 57.370 30.769 0.00 0.00 0.00 3.32
2436 13332 8.807948 TTTAGAGTTTGGCAGATTTTAGCTAT 57.192 30.769 0.00 0.00 0.00 2.97
2437 13333 8.807948 TTAGAGTTTGGCAGATTTTAGCTATT 57.192 30.769 0.00 0.00 0.00 1.73
2438 13334 7.709149 AGAGTTTGGCAGATTTTAGCTATTT 57.291 32.000 0.00 0.00 0.00 1.40
2439 13335 8.127150 AGAGTTTGGCAGATTTTAGCTATTTT 57.873 30.769 0.00 0.00 0.00 1.82
2440 13336 9.243105 AGAGTTTGGCAGATTTTAGCTATTTTA 57.757 29.630 0.00 0.00 0.00 1.52
2441 13337 9.508567 GAGTTTGGCAGATTTTAGCTATTTTAG 57.491 33.333 0.00 0.00 0.00 1.85
2442 13338 8.470002 AGTTTGGCAGATTTTAGCTATTTTAGG 58.530 33.333 0.00 0.00 0.00 2.69
2443 13339 8.466798 GTTTGGCAGATTTTAGCTATTTTAGGA 58.533 33.333 0.00 0.00 0.00 2.94
2444 13340 7.568199 TGGCAGATTTTAGCTATTTTAGGAC 57.432 36.000 0.00 0.00 0.00 3.85
2445 13341 7.116075 TGGCAGATTTTAGCTATTTTAGGACA 58.884 34.615 0.00 0.00 0.00 4.02
2446 13342 7.613801 TGGCAGATTTTAGCTATTTTAGGACAA 59.386 33.333 0.00 0.00 0.00 3.18
2447 13343 8.131731 GGCAGATTTTAGCTATTTTAGGACAAG 58.868 37.037 0.00 0.00 0.00 3.16
2448 13344 8.678199 GCAGATTTTAGCTATTTTAGGACAAGT 58.322 33.333 0.00 0.00 0.00 3.16
2450 13346 9.959721 AGATTTTAGCTATTTTAGGACAAGTCA 57.040 29.630 0.00 0.00 0.00 3.41
2453 13349 7.611213 TTAGCTATTTTAGGACAAGTCAAGC 57.389 36.000 0.00 0.00 0.00 4.01
2454 13350 5.560724 AGCTATTTTAGGACAAGTCAAGCA 58.439 37.500 2.29 0.00 0.00 3.91
2455 13351 6.003950 AGCTATTTTAGGACAAGTCAAGCAA 58.996 36.000 2.29 0.00 0.00 3.91
2456 13352 6.660949 AGCTATTTTAGGACAAGTCAAGCAAT 59.339 34.615 2.29 0.00 0.00 3.56
2457 13353 6.969473 GCTATTTTAGGACAAGTCAAGCAATC 59.031 38.462 2.29 0.00 0.00 2.67
2458 13354 6.899393 ATTTTAGGACAAGTCAAGCAATCA 57.101 33.333 2.29 0.00 0.00 2.57
2459 13355 6.899393 TTTTAGGACAAGTCAAGCAATCAT 57.101 33.333 2.29 0.00 0.00 2.45
2460 13356 6.500684 TTTAGGACAAGTCAAGCAATCATC 57.499 37.500 2.29 0.00 0.00 2.92
2461 13357 4.025040 AGGACAAGTCAAGCAATCATCA 57.975 40.909 2.29 0.00 0.00 3.07
2462 13358 3.755378 AGGACAAGTCAAGCAATCATCAC 59.245 43.478 2.29 0.00 0.00 3.06
2463 13359 3.503363 GGACAAGTCAAGCAATCATCACA 59.497 43.478 2.29 0.00 0.00 3.58
2464 13360 4.157289 GGACAAGTCAAGCAATCATCACAT 59.843 41.667 2.29 0.00 0.00 3.21
2465 13361 5.355071 GGACAAGTCAAGCAATCATCACATA 59.645 40.000 2.29 0.00 0.00 2.29
2466 13362 6.127925 GGACAAGTCAAGCAATCATCACATAA 60.128 38.462 2.29 0.00 0.00 1.90
2467 13363 7.400599 ACAAGTCAAGCAATCATCACATAAT 57.599 32.000 0.00 0.00 0.00 1.28
2468 13364 7.833786 ACAAGTCAAGCAATCATCACATAATT 58.166 30.769 0.00 0.00 0.00 1.40
2469 13365 7.972277 ACAAGTCAAGCAATCATCACATAATTC 59.028 33.333 0.00 0.00 0.00 2.17
2470 13366 7.634671 AGTCAAGCAATCATCACATAATTCA 57.365 32.000 0.00 0.00 0.00 2.57
2471 13367 8.058667 AGTCAAGCAATCATCACATAATTCAA 57.941 30.769 0.00 0.00 0.00 2.69
2472 13368 8.188799 AGTCAAGCAATCATCACATAATTCAAG 58.811 33.333 0.00 0.00 0.00 3.02
2473 13369 6.976349 TCAAGCAATCATCACATAATTCAAGC 59.024 34.615 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
168 169 2.907910 ACGATGAGATTTGTGCTTGC 57.092 45.000 0.00 0.00 0.00 4.01
196 197 3.056107 CCTCGATCCTCTGTTGGTTGTTA 60.056 47.826 0.00 0.00 0.00 2.41
710 4067 6.628919 ACGTAACACTTAAGAAGGCATTTT 57.371 33.333 10.09 0.00 0.00 1.82
716 4073 6.649557 AGATTCCAACGTAACACTTAAGAAGG 59.350 38.462 10.09 0.78 0.00 3.46
750 4107 6.844696 ACACGTGATAAGCGATTTCATTAT 57.155 33.333 25.01 0.00 0.00 1.28
808 4169 7.329226 CCGAGCAATCAAAACATATTTCAGTTT 59.671 33.333 0.00 0.00 39.46 2.66
914 4280 7.126733 GGCCTGTATATATAGAGAAGGGAGAA 58.873 42.308 16.53 0.00 0.00 2.87
1146 4524 7.953158 AACTGATCATTATGGACTGATAACG 57.047 36.000 0.00 0.00 32.36 3.18
1236 4618 1.084370 CATCCACGTCTTCTTCGCCC 61.084 60.000 0.00 0.00 0.00 6.13
1320 6304 4.816385 TCTTGATTGAGGAGACAACACAAC 59.184 41.667 0.00 0.00 32.50 3.32
1415 9336 2.355818 GGTAAAGGAGAGCGGGTCATTT 60.356 50.000 10.15 9.51 32.92 2.32
1441 12318 1.866015 AATGATGACGTGGGAGAGGA 58.134 50.000 0.00 0.00 0.00 3.71
1488 12365 2.910319 CAATATCCATTAGGTCCCGGGA 59.090 50.000 22.63 22.63 35.89 5.14
1693 12589 9.607988 AACACAATACCGATAATCAACATTCTA 57.392 29.630 0.00 0.00 0.00 2.10
1757 12653 8.464404 CAGAAACATGTCACAGGATCAATTTAT 58.536 33.333 0.00 0.00 0.00 1.40
1782 12678 6.316140 CCGTCTGATTTAATCTTGATTCACCA 59.684 38.462 6.50 0.00 0.00 4.17
1798 12694 2.288457 CGATGATGCTACCCGTCTGATT 60.288 50.000 0.00 0.00 0.00 2.57
1812 12708 0.319813 TATGTCAGGCGGCGATGATG 60.320 55.000 12.98 2.56 0.00 3.07
1833 12729 7.782049 TCTAATATTGATTCACCAGAGACGTT 58.218 34.615 0.00 0.00 0.00 3.99
1841 12737 7.744733 TGCTACCATCTAATATTGATTCACCA 58.255 34.615 0.00 0.00 0.00 4.17
1888 12784 3.124297 CGAGTCTGCTGACATTTTCCTTC 59.876 47.826 23.61 10.09 45.20 3.46
1946 12842 2.919666 AATGCTAATGTGTTGCCGAC 57.080 45.000 0.00 0.00 0.00 4.79
1957 12853 5.422145 GTTGCAGATGGGAAAAATGCTAAT 58.578 37.500 0.00 0.00 37.76 1.73
1964 12860 5.815233 TTAATGGTTGCAGATGGGAAAAA 57.185 34.783 0.00 0.00 0.00 1.94
1986 12882 1.075536 GGTTGATTGAGGGGGACACTT 59.924 52.381 0.00 0.00 0.00 3.16
1992 12888 0.611896 GTGGTGGTTGATTGAGGGGG 60.612 60.000 0.00 0.00 0.00 5.40
2065 12961 1.071239 CACAAGAAACGCTGTGTCTCG 60.071 52.381 0.00 0.00 27.27 4.04
2073 12969 6.986231 TCATATACATGATCACAAGAAACGCT 59.014 34.615 0.00 0.00 36.22 5.07
2195 13091 2.100749 ACTTTGCTGGTAGTTTTGCCAC 59.899 45.455 0.00 0.00 33.78 5.01
2208 13104 1.135575 GCCTTCCATTCGACTTTGCTG 60.136 52.381 0.00 0.00 0.00 4.41
2217 13113 1.661341 CTCTTCCAGCCTTCCATTCG 58.339 55.000 0.00 0.00 0.00 3.34
2261 13157 1.741770 CAGACCCAAGCGCACTACC 60.742 63.158 11.47 0.00 0.00 3.18
2331 13227 6.728411 TCTAGACATACTTCAAGGTCCTACA 58.272 40.000 0.00 0.00 0.00 2.74
2332 13228 6.263617 CCTCTAGACATACTTCAAGGTCCTAC 59.736 46.154 0.00 0.00 0.00 3.18
2333 13229 6.366340 CCTCTAGACATACTTCAAGGTCCTA 58.634 44.000 0.00 0.00 0.00 2.94
2334 13230 5.205056 CCTCTAGACATACTTCAAGGTCCT 58.795 45.833 0.00 0.00 0.00 3.85
2335 13231 4.342665 CCCTCTAGACATACTTCAAGGTCC 59.657 50.000 0.00 0.00 0.00 4.46
2336 13232 4.342665 CCCCTCTAGACATACTTCAAGGTC 59.657 50.000 0.00 0.00 0.00 3.85
2337 13233 4.290942 CCCCTCTAGACATACTTCAAGGT 58.709 47.826 0.00 0.00 0.00 3.50
2338 13234 3.643792 CCCCCTCTAGACATACTTCAAGG 59.356 52.174 0.00 0.00 0.00 3.61
2339 13235 4.946478 CCCCCTCTAGACATACTTCAAG 57.054 50.000 0.00 0.00 0.00 3.02
2362 13258 3.134262 GGTCAAGTAGTCTAATCACCCCC 59.866 52.174 0.00 0.00 0.00 5.40
2363 13259 3.773119 TGGTCAAGTAGTCTAATCACCCC 59.227 47.826 6.13 0.00 0.00 4.95
2364 13260 5.416271 TTGGTCAAGTAGTCTAATCACCC 57.584 43.478 6.13 0.00 0.00 4.61
2365 13261 9.444600 TTTTATTGGTCAAGTAGTCTAATCACC 57.555 33.333 2.72 2.72 0.00 4.02
2392 13288 9.209048 ACTCTAAAATTGGGAAAAGGTTAAGTT 57.791 29.630 0.00 0.00 0.00 2.66
2393 13289 8.777578 ACTCTAAAATTGGGAAAAGGTTAAGT 57.222 30.769 0.00 0.00 0.00 2.24
2395 13291 9.825109 CAAACTCTAAAATTGGGAAAAGGTTAA 57.175 29.630 0.00 0.00 0.00 2.01
2396 13292 8.425703 CCAAACTCTAAAATTGGGAAAAGGTTA 58.574 33.333 0.00 0.00 39.92 2.85
2397 13293 7.279615 CCAAACTCTAAAATTGGGAAAAGGTT 58.720 34.615 0.00 0.00 39.92 3.50
2398 13294 6.687901 GCCAAACTCTAAAATTGGGAAAAGGT 60.688 38.462 5.97 0.00 43.06 3.50
2399 13295 5.700832 GCCAAACTCTAAAATTGGGAAAAGG 59.299 40.000 5.97 0.00 43.06 3.11
2400 13296 6.287525 TGCCAAACTCTAAAATTGGGAAAAG 58.712 36.000 5.97 0.00 40.90 2.27
2401 13297 6.098982 TCTGCCAAACTCTAAAATTGGGAAAA 59.901 34.615 5.97 0.00 42.81 2.29
2402 13298 5.600484 TCTGCCAAACTCTAAAATTGGGAAA 59.400 36.000 5.97 0.00 42.81 3.13
2403 13299 5.144100 TCTGCCAAACTCTAAAATTGGGAA 58.856 37.500 5.97 0.00 42.81 3.97
2404 13300 4.735369 TCTGCCAAACTCTAAAATTGGGA 58.265 39.130 5.97 2.20 43.06 4.37
2405 13301 5.665916 ATCTGCCAAACTCTAAAATTGGG 57.334 39.130 5.97 0.00 43.06 4.12
2406 13302 7.967890 AAAATCTGCCAAACTCTAAAATTGG 57.032 32.000 0.00 0.00 45.11 3.16
2407 13303 8.650714 GCTAAAATCTGCCAAACTCTAAAATTG 58.349 33.333 0.00 0.00 0.00 2.32
2408 13304 8.588472 AGCTAAAATCTGCCAAACTCTAAAATT 58.412 29.630 0.00 0.00 0.00 1.82
2409 13305 8.127150 AGCTAAAATCTGCCAAACTCTAAAAT 57.873 30.769 0.00 0.00 0.00 1.82
2410 13306 7.524717 AGCTAAAATCTGCCAAACTCTAAAA 57.475 32.000 0.00 0.00 0.00 1.52
2411 13307 8.807948 ATAGCTAAAATCTGCCAAACTCTAAA 57.192 30.769 0.00 0.00 0.00 1.85
2412 13308 8.807948 AATAGCTAAAATCTGCCAAACTCTAA 57.192 30.769 0.00 0.00 0.00 2.10
2413 13309 8.807948 AAATAGCTAAAATCTGCCAAACTCTA 57.192 30.769 0.00 0.00 0.00 2.43
2414 13310 7.709149 AAATAGCTAAAATCTGCCAAACTCT 57.291 32.000 0.00 0.00 0.00 3.24
2415 13311 9.508567 CTAAAATAGCTAAAATCTGCCAAACTC 57.491 33.333 0.00 0.00 0.00 3.01
2416 13312 8.470002 CCTAAAATAGCTAAAATCTGCCAAACT 58.530 33.333 0.00 0.00 0.00 2.66
2417 13313 8.466798 TCCTAAAATAGCTAAAATCTGCCAAAC 58.533 33.333 0.00 0.00 0.00 2.93
2418 13314 8.466798 GTCCTAAAATAGCTAAAATCTGCCAAA 58.533 33.333 0.00 0.00 0.00 3.28
2419 13315 7.613801 TGTCCTAAAATAGCTAAAATCTGCCAA 59.386 33.333 0.00 0.00 0.00 4.52
2420 13316 7.116075 TGTCCTAAAATAGCTAAAATCTGCCA 58.884 34.615 0.00 0.00 0.00 4.92
2421 13317 7.568199 TGTCCTAAAATAGCTAAAATCTGCC 57.432 36.000 0.00 0.00 0.00 4.85
2422 13318 8.678199 ACTTGTCCTAAAATAGCTAAAATCTGC 58.322 33.333 0.00 0.00 0.00 4.26
2424 13320 9.959721 TGACTTGTCCTAAAATAGCTAAAATCT 57.040 29.630 0.00 0.00 0.00 2.40
2427 13323 8.512138 GCTTGACTTGTCCTAAAATAGCTAAAA 58.488 33.333 0.00 0.00 0.00 1.52
2428 13324 7.663905 TGCTTGACTTGTCCTAAAATAGCTAAA 59.336 33.333 0.00 0.00 0.00 1.85
2429 13325 7.165485 TGCTTGACTTGTCCTAAAATAGCTAA 58.835 34.615 0.00 0.00 0.00 3.09
2430 13326 6.707290 TGCTTGACTTGTCCTAAAATAGCTA 58.293 36.000 0.00 0.00 0.00 3.32
2431 13327 5.560724 TGCTTGACTTGTCCTAAAATAGCT 58.439 37.500 0.00 0.00 0.00 3.32
2432 13328 5.880054 TGCTTGACTTGTCCTAAAATAGC 57.120 39.130 0.00 0.00 0.00 2.97
2433 13329 8.044060 TGATTGCTTGACTTGTCCTAAAATAG 57.956 34.615 0.00 0.00 0.00 1.73
2434 13330 7.994425 TGATTGCTTGACTTGTCCTAAAATA 57.006 32.000 0.00 0.00 0.00 1.40
2435 13331 6.899393 TGATTGCTTGACTTGTCCTAAAAT 57.101 33.333 0.00 0.00 0.00 1.82
2436 13332 6.489700 TGATGATTGCTTGACTTGTCCTAAAA 59.510 34.615 0.00 0.00 0.00 1.52
2437 13333 6.003326 TGATGATTGCTTGACTTGTCCTAAA 58.997 36.000 0.00 0.00 0.00 1.85
2438 13334 5.412594 GTGATGATTGCTTGACTTGTCCTAA 59.587 40.000 0.00 0.00 0.00 2.69
2439 13335 4.937620 GTGATGATTGCTTGACTTGTCCTA 59.062 41.667 0.00 0.00 0.00 2.94
2440 13336 3.755378 GTGATGATTGCTTGACTTGTCCT 59.245 43.478 0.00 0.00 0.00 3.85
2441 13337 3.503363 TGTGATGATTGCTTGACTTGTCC 59.497 43.478 0.00 0.00 0.00 4.02
2442 13338 4.754372 TGTGATGATTGCTTGACTTGTC 57.246 40.909 0.00 0.00 0.00 3.18
2443 13339 6.822667 TTATGTGATGATTGCTTGACTTGT 57.177 33.333 0.00 0.00 0.00 3.16
2444 13340 7.971722 TGAATTATGTGATGATTGCTTGACTTG 59.028 33.333 0.00 0.00 0.00 3.16
2445 13341 8.058667 TGAATTATGTGATGATTGCTTGACTT 57.941 30.769 0.00 0.00 0.00 3.01
2446 13342 7.634671 TGAATTATGTGATGATTGCTTGACT 57.365 32.000 0.00 0.00 0.00 3.41
2447 13343 7.043590 GCTTGAATTATGTGATGATTGCTTGAC 60.044 37.037 0.00 0.00 0.00 3.18
2448 13344 6.976349 GCTTGAATTATGTGATGATTGCTTGA 59.024 34.615 0.00 0.00 0.00 3.02
2449 13345 7.161829 GCTTGAATTATGTGATGATTGCTTG 57.838 36.000 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.