Multiple sequence alignment - TraesCS2B01G529400

Loading Multiple Alignment...

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 TraesCS2B01G529400 chr2B 100.000 2966 0 0 1 2966 724409281 724412246 0.000000e+00 5478.0
1 TraesCS2B01G529400 chr2B 97.605 668 16 0 2299 2966 724423807 724424474 0.000000e+00 1146.0
2 TraesCS2B01G529400 chr2B 94.918 669 31 3 2299 2966 22332873 22332207 0.000000e+00 1044.0
3 TraesCS2B01G529400 chr2D 88.272 2251 135 45 29 2178 596028506 596030728 0.000000e+00 2575.0
4 TraesCS2B01G529400 chr2A 85.355 2267 146 85 1 2171 729687074 729689250 0.000000e+00 2176.0
5 TraesCS2B01G529400 chr1B 95.366 669 29 2 2299 2966 579806641 579807308 0.000000e+00 1062.0
6 TraesCS2B01G529400 chr7B 95.067 669 31 2 2299 2966 657001650 657000983 0.000000e+00 1051.0
7 TraesCS2B01G529400 chr7B 94.918 669 32 2 2299 2966 598145791 598146458 0.000000e+00 1046.0
8 TraesCS2B01G529400 chr3B 95.188 665 30 2 2303 2966 113583423 113584086 0.000000e+00 1050.0
9 TraesCS2B01G529400 chr6B 94.933 671 30 3 2299 2966 79179198 79178529 0.000000e+00 1048.0
10 TraesCS2B01G529400 chr6B 94.933 671 30 3 2299 2966 79191252 79190583 0.000000e+00 1048.0
11 TraesCS2B01G529400 chr5B 94.910 668 32 2 2299 2966 211844802 211844137 0.000000e+00 1044.0
12 TraesCS2B01G529400 chr5B 83.117 77 9 3 1028 1102 308110203 308110277 1.910000e-07 67.6
13 TraesCS2B01G529400 chr5D 83.117 77 9 3 1028 1102 271900001 271900075 1.910000e-07 67.6
14 TraesCS2B01G529400 chr5A 83.117 77 9 3 1028 1102 361709268 361709342 1.910000e-07 67.6


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 TraesCS2B01G529400 chr2B 724409281 724412246 2965 False 5478 5478 100.000 1 2966 1 chr2B.!!$F1 2965
1 TraesCS2B01G529400 chr2B 724423807 724424474 667 False 1146 1146 97.605 2299 2966 1 chr2B.!!$F2 667
2 TraesCS2B01G529400 chr2B 22332207 22332873 666 True 1044 1044 94.918 2299 2966 1 chr2B.!!$R1 667
3 TraesCS2B01G529400 chr2D 596028506 596030728 2222 False 2575 2575 88.272 29 2178 1 chr2D.!!$F1 2149
4 TraesCS2B01G529400 chr2A 729687074 729689250 2176 False 2176 2176 85.355 1 2171 1 chr2A.!!$F1 2170
5 TraesCS2B01G529400 chr1B 579806641 579807308 667 False 1062 1062 95.366 2299 2966 1 chr1B.!!$F1 667
6 TraesCS2B01G529400 chr7B 657000983 657001650 667 True 1051 1051 95.067 2299 2966 1 chr7B.!!$R1 667
7 TraesCS2B01G529400 chr7B 598145791 598146458 667 False 1046 1046 94.918 2299 2966 1 chr7B.!!$F1 667
8 TraesCS2B01G529400 chr3B 113583423 113584086 663 False 1050 1050 95.188 2303 2966 1 chr3B.!!$F1 663
9 TraesCS2B01G529400 chr6B 79178529 79179198 669 True 1048 1048 94.933 2299 2966 1 chr6B.!!$R1 667
10 TraesCS2B01G529400 chr6B 79190583 79191252 669 True 1048 1048 94.933 2299 2966 1 chr6B.!!$R2 667
11 TraesCS2B01G529400 chr5B 211844137 211844802 665 True 1044 1044 94.910 2299 2966 1 chr5B.!!$R1 667

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
313 325 0.597568 CGGTCATGCAGAAAAAGGCA 59.402 50.0 0.0 0.0 45.23 4.75 F
1437 1556 0.035458 CCTTTTCCCTCTGTCGTGCT 59.965 55.0 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 1734 0.035458 AGCTGTCAGCCAGTTACCAC 59.965 55.0 21.32 0.0 43.77 4.16 R
2664 2816 0.530744 CTGTACCTACGCTCCAGCAA 59.469 55.0 0.00 0.0 42.21 3.91 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
93 95 4.912586 TCGATTTGGTTTCTACCCAATGA 58.087 39.130 0.00 0.00 44.35 2.57
183 186 7.055378 ACTCCACACTACTACTAGTATCCTTG 58.945 42.308 2.33 2.09 31.46 3.61
262 273 2.734673 GAAGTCGCTGGCTGCTTCG 61.735 63.158 14.58 0.99 40.11 3.79
276 287 4.778415 TTCGACGGCTCTGCTCGC 62.778 66.667 0.00 0.00 0.00 5.03
284 296 2.507992 CTCTGCTCGCGGTCAAGG 60.508 66.667 6.13 0.00 0.00 3.61
294 306 2.126031 GGTCAAGGCGGACTCGAC 60.126 66.667 11.22 0.00 46.68 4.20
303 315 2.571757 GGACTCGACGGTCATGCA 59.428 61.111 9.10 0.00 37.91 3.96
305 317 1.506718 GACTCGACGGTCATGCAGA 59.493 57.895 9.10 0.00 36.35 4.26
308 320 1.270094 ACTCGACGGTCATGCAGAAAA 60.270 47.619 9.10 0.00 0.00 2.29
309 321 1.798223 CTCGACGGTCATGCAGAAAAA 59.202 47.619 9.10 0.00 0.00 1.94
310 322 1.798223 TCGACGGTCATGCAGAAAAAG 59.202 47.619 9.10 0.00 0.00 2.27
311 323 1.135972 CGACGGTCATGCAGAAAAAGG 60.136 52.381 9.10 0.00 0.00 3.11
312 324 0.598065 ACGGTCATGCAGAAAAAGGC 59.402 50.000 0.00 0.00 0.00 4.35
313 325 0.597568 CGGTCATGCAGAAAAAGGCA 59.402 50.000 0.00 0.00 45.23 4.75
314 326 1.401931 CGGTCATGCAGAAAAAGGCAG 60.402 52.381 0.00 0.00 44.24 4.85
315 327 1.888512 GGTCATGCAGAAAAAGGCAGA 59.111 47.619 0.00 0.00 44.24 4.26
380 393 2.097104 GCGAACTTTGAATCACGTCGAA 60.097 45.455 0.00 0.00 0.00 3.71
460 494 6.106003 TCGACAGCTCAGAAAAATGCTAATA 58.894 36.000 0.00 0.00 34.10 0.98
512 554 6.310764 TGATTGATTGGTGGCCATTTTTAT 57.689 33.333 9.72 0.00 31.53 1.40
547 589 2.793278 AATTCGACAAAAGCCACACC 57.207 45.000 0.00 0.00 0.00 4.16
551 593 1.156736 CGACAAAAGCCACACCCTAG 58.843 55.000 0.00 0.00 0.00 3.02
583 625 4.730966 TGATAGGATCGTTCTAGGCTTCT 58.269 43.478 0.00 0.00 0.00 2.85
589 631 3.361281 TCGTTCTAGGCTTCTAGTGGA 57.639 47.619 0.00 0.00 40.90 4.02
626 668 2.350522 CAACCAAATCTGGACGAGAGG 58.649 52.381 0.00 0.00 46.92 3.69
660 702 2.586425 ACTGTGAATTTGGGAGTGGTG 58.414 47.619 0.00 0.00 0.00 4.17
661 703 1.888512 CTGTGAATTTGGGAGTGGTGG 59.111 52.381 0.00 0.00 0.00 4.61
662 704 1.216678 TGTGAATTTGGGAGTGGTGGT 59.783 47.619 0.00 0.00 0.00 4.16
703 769 1.065647 TTCACCCCCAACGGAATGTA 58.934 50.000 0.00 0.00 0.00 2.29
749 815 1.828979 TCCACCCGGCAAGATAAAAC 58.171 50.000 0.00 0.00 0.00 2.43
833 912 1.756375 CGTTGTCTCATAGCAGGCGC 61.756 60.000 0.00 0.00 38.99 6.53
840 919 3.933722 ATAGCAGGCGCCGCTCAT 61.934 61.111 36.75 26.70 40.96 2.90
896 983 1.901085 CGGAGGGTGGAGAGAAAGG 59.099 63.158 0.00 0.00 0.00 3.11
1147 1260 2.021457 CGGTCTCCTCTCCTCTCTTTC 58.979 57.143 0.00 0.00 0.00 2.62
1149 1262 2.024369 GGTCTCCTCTCCTCTCTTTCCT 60.024 54.545 0.00 0.00 0.00 3.36
1190 1308 1.977009 ACCGTCGATCTGCCTGTCA 60.977 57.895 0.00 0.00 0.00 3.58
1239 1357 2.821991 AGAATTAATCGCCTCTCCGG 57.178 50.000 0.00 0.00 0.00 5.14
1285 1403 3.309296 TCCTGATTATTCTCCTCCGCTT 58.691 45.455 0.00 0.00 0.00 4.68
1316 1435 1.932604 CAGAAGCTGAAGACGCGAGTT 60.933 52.381 15.93 5.01 37.98 3.01
1328 1447 1.612463 ACGCGAGTTGTAAGGAAGAGT 59.388 47.619 15.93 0.00 46.40 3.24
1349 1468 7.233883 GAGTATCAATCCGGAGTGGAACGAT 62.234 48.000 29.89 18.26 43.32 3.73
1352 1471 2.661054 TCCGGAGTGGAACGATGAA 58.339 52.632 0.00 0.00 46.38 2.57
1376 1495 1.219213 ACCCTCTCCATCGAAGATCCT 59.781 52.381 0.00 0.00 45.12 3.24
1406 1525 3.135225 TGTCAAACTGGTATGTGTTCCG 58.865 45.455 0.00 0.00 0.00 4.30
1430 1549 1.710809 TCTTTCCCCCTTTTCCCTCTG 59.289 52.381 0.00 0.00 0.00 3.35
1437 1556 0.035458 CCTTTTCCCTCTGTCGTGCT 59.965 55.000 0.00 0.00 0.00 4.40
1494 1616 7.351981 CCTAAATCGAATCATGAAACGCAATA 58.648 34.615 16.41 9.76 0.00 1.90
1508 1631 3.088532 ACGCAATAAATTTCTCCCTGCA 58.911 40.909 0.00 0.00 0.00 4.41
1605 1734 1.071605 GTACAGACAAGCAGCCGAAG 58.928 55.000 0.00 0.00 0.00 3.79
1647 1784 2.229784 CCTGACAACCCATTGCTTCTTC 59.770 50.000 0.00 0.00 39.66 2.87
1653 1790 4.651045 ACAACCCATTGCTTCTTCTTCTTT 59.349 37.500 0.00 0.00 39.66 2.52
1654 1791 5.221322 ACAACCCATTGCTTCTTCTTCTTTC 60.221 40.000 0.00 0.00 39.66 2.62
1828 1965 4.443266 AGAACTGCCTCGCCGAGC 62.443 66.667 9.01 5.08 0.00 5.03
1969 2111 5.063880 AGGGCGTATCAGGCTTTTAATTAG 58.936 41.667 0.00 0.00 36.85 1.73
2023 2165 4.780815 TCTTTCTCAAGTGAAAAGCTGGA 58.219 39.130 0.00 0.00 35.79 3.86
2031 2173 6.970484 TCAAGTGAAAAGCTGGAGTAAATTC 58.030 36.000 0.00 0.00 0.00 2.17
2034 2176 6.299141 AGTGAAAAGCTGGAGTAAATTCTGA 58.701 36.000 0.00 0.00 0.00 3.27
2077 2219 9.862371 AGTTAGGATTTAGATTATGTGCGATAG 57.138 33.333 0.00 0.00 0.00 2.08
2078 2220 9.856488 GTTAGGATTTAGATTATGTGCGATAGA 57.144 33.333 0.00 0.00 39.76 1.98
2081 2223 8.753133 AGGATTTAGATTATGTGCGATAGATGA 58.247 33.333 0.00 0.00 39.76 2.92
2083 2225 9.579768 GATTTAGATTATGTGCGATAGATGACT 57.420 33.333 0.00 0.00 39.76 3.41
2105 2253 3.576982 TGTGTGGTCGAACTTCCTAAGAT 59.423 43.478 0.33 0.00 0.00 2.40
2110 2258 3.447944 GGTCGAACTTCCTAAGATGGACT 59.552 47.826 10.33 0.00 38.48 3.85
2114 2262 5.245301 TCGAACTTCCTAAGATGGACTGAAA 59.755 40.000 0.00 0.00 35.58 2.69
2117 2265 7.360438 CGAACTTCCTAAGATGGACTGAAAAAG 60.360 40.741 0.00 0.00 35.58 2.27
2123 2272 6.942576 CCTAAGATGGACTGAAAAAGGAAGAA 59.057 38.462 0.00 0.00 0.00 2.52
2127 2276 4.207165 TGGACTGAAAAAGGAAGAACTGG 58.793 43.478 0.00 0.00 0.00 4.00
2144 2293 3.922640 GTGGCAGGGGCGCAAAAA 61.923 61.111 10.83 0.00 42.47 1.94
2145 2294 2.921972 TGGCAGGGGCGCAAAAAT 60.922 55.556 10.83 0.00 42.47 1.82
2152 2301 0.887933 GGGGCGCAAAAATTCTCAGA 59.112 50.000 10.83 0.00 0.00 3.27
2167 2316 5.365021 TTCTCAGAATTCCATCCTCCTTC 57.635 43.478 0.65 0.00 0.00 3.46
2172 2321 4.643784 CAGAATTCCATCCTCCTTCCTTTG 59.356 45.833 0.65 0.00 0.00 2.77
2173 2322 4.541714 AGAATTCCATCCTCCTTCCTTTGA 59.458 41.667 0.65 0.00 0.00 2.69
2174 2323 5.195349 AGAATTCCATCCTCCTTCCTTTGAT 59.805 40.000 0.65 0.00 0.00 2.57
2175 2324 3.939740 TCCATCCTCCTTCCTTTGATG 57.060 47.619 0.00 0.00 34.10 3.07
2176 2325 3.192944 TCCATCCTCCTTCCTTTGATGT 58.807 45.455 0.00 0.00 32.78 3.06
2177 2326 3.054139 TCCATCCTCCTTCCTTTGATGTG 60.054 47.826 0.00 0.00 32.78 3.21
2178 2327 3.285484 CATCCTCCTTCCTTTGATGTGG 58.715 50.000 0.00 0.00 0.00 4.17
2179 2328 2.348472 TCCTCCTTCCTTTGATGTGGT 58.652 47.619 0.00 0.00 0.00 4.16
2180 2329 2.305927 TCCTCCTTCCTTTGATGTGGTC 59.694 50.000 0.00 0.00 0.00 4.02
2181 2330 2.040278 CCTCCTTCCTTTGATGTGGTCA 59.960 50.000 0.00 0.00 34.25 4.02
2182 2331 3.341823 CTCCTTCCTTTGATGTGGTCAG 58.658 50.000 0.00 0.00 38.29 3.51
2183 2332 1.815003 CCTTCCTTTGATGTGGTCAGC 59.185 52.381 0.00 0.00 38.29 4.26
2184 2333 2.553904 CCTTCCTTTGATGTGGTCAGCT 60.554 50.000 0.00 0.00 38.29 4.24
2185 2334 2.479566 TCCTTTGATGTGGTCAGCTC 57.520 50.000 0.00 0.00 38.29 4.09
2186 2335 1.003580 TCCTTTGATGTGGTCAGCTCC 59.996 52.381 0.00 0.00 38.29 4.70
2187 2336 1.004044 CCTTTGATGTGGTCAGCTCCT 59.996 52.381 0.00 0.00 38.29 3.69
2188 2337 2.553904 CCTTTGATGTGGTCAGCTCCTT 60.554 50.000 0.00 0.00 38.29 3.36
2189 2338 2.189594 TTGATGTGGTCAGCTCCTTG 57.810 50.000 0.00 0.00 38.29 3.61
2190 2339 1.351076 TGATGTGGTCAGCTCCTTGA 58.649 50.000 0.00 0.00 31.80 3.02
2191 2340 1.911357 TGATGTGGTCAGCTCCTTGAT 59.089 47.619 0.00 0.00 31.80 2.57
2192 2341 2.286872 GATGTGGTCAGCTCCTTGATG 58.713 52.381 0.00 0.00 0.00 3.07
2193 2342 0.321919 TGTGGTCAGCTCCTTGATGC 60.322 55.000 0.00 0.00 31.07 3.91
2194 2343 1.078918 TGGTCAGCTCCTTGATGCG 60.079 57.895 0.00 0.00 31.07 4.73
2195 2344 1.817099 GGTCAGCTCCTTGATGCGG 60.817 63.158 0.00 0.00 31.07 5.69
2196 2345 1.078848 GTCAGCTCCTTGATGCGGT 60.079 57.895 0.00 0.00 31.07 5.68
2197 2346 1.086634 GTCAGCTCCTTGATGCGGTC 61.087 60.000 0.00 0.00 31.07 4.79
2198 2347 1.220206 CAGCTCCTTGATGCGGTCT 59.780 57.895 0.00 0.00 0.00 3.85
2199 2348 0.809241 CAGCTCCTTGATGCGGTCTC 60.809 60.000 0.00 0.00 0.00 3.36
2200 2349 1.219124 GCTCCTTGATGCGGTCTCA 59.781 57.895 0.00 0.00 0.00 3.27
2201 2350 0.809241 GCTCCTTGATGCGGTCTCAG 60.809 60.000 0.00 0.00 0.00 3.35
2202 2351 0.820226 CTCCTTGATGCGGTCTCAGA 59.180 55.000 0.00 0.00 0.00 3.27
2203 2352 1.205655 CTCCTTGATGCGGTCTCAGAA 59.794 52.381 0.00 0.00 0.00 3.02
2204 2353 1.066858 TCCTTGATGCGGTCTCAGAAC 60.067 52.381 0.00 0.00 0.00 3.01
2205 2354 1.338105 CCTTGATGCGGTCTCAGAACA 60.338 52.381 0.00 0.00 0.00 3.18
2206 2355 2.416747 CTTGATGCGGTCTCAGAACAA 58.583 47.619 0.00 0.00 0.00 2.83
2207 2356 2.768253 TGATGCGGTCTCAGAACAAT 57.232 45.000 0.00 0.00 0.00 2.71
2208 2357 2.349590 TGATGCGGTCTCAGAACAATG 58.650 47.619 0.00 0.00 0.00 2.82
2209 2358 1.667724 GATGCGGTCTCAGAACAATGG 59.332 52.381 0.00 0.00 0.00 3.16
2210 2359 0.955428 TGCGGTCTCAGAACAATGGC 60.955 55.000 0.00 0.00 0.00 4.40
2211 2360 0.674895 GCGGTCTCAGAACAATGGCT 60.675 55.000 0.00 0.00 0.00 4.75
2212 2361 1.081892 CGGTCTCAGAACAATGGCTG 58.918 55.000 0.00 0.00 0.00 4.85
2213 2362 0.807496 GGTCTCAGAACAATGGCTGC 59.193 55.000 0.00 0.00 32.27 5.25
2214 2363 1.527034 GTCTCAGAACAATGGCTGCA 58.473 50.000 0.50 0.00 32.27 4.41
2215 2364 1.881973 GTCTCAGAACAATGGCTGCAA 59.118 47.619 0.50 0.00 32.27 4.08
2216 2365 2.490903 GTCTCAGAACAATGGCTGCAAT 59.509 45.455 0.50 0.00 32.27 3.56
2217 2366 3.691118 GTCTCAGAACAATGGCTGCAATA 59.309 43.478 0.50 0.00 32.27 1.90
2218 2367 4.337555 GTCTCAGAACAATGGCTGCAATAT 59.662 41.667 0.50 0.00 32.27 1.28
2219 2368 4.337274 TCTCAGAACAATGGCTGCAATATG 59.663 41.667 0.50 0.05 32.27 1.78
2220 2369 3.120792 CAGAACAATGGCTGCAATATGC 58.879 45.455 0.50 0.00 45.29 3.14
2221 2370 3.028850 AGAACAATGGCTGCAATATGCT 58.971 40.909 0.50 0.00 45.31 3.79
2222 2371 2.882927 ACAATGGCTGCAATATGCTG 57.117 45.000 0.50 4.45 45.31 4.41
2223 2372 2.380941 ACAATGGCTGCAATATGCTGA 58.619 42.857 12.56 0.00 45.31 4.26
2224 2373 2.963101 ACAATGGCTGCAATATGCTGAT 59.037 40.909 12.56 0.00 45.31 2.90
2225 2374 3.243737 ACAATGGCTGCAATATGCTGATG 60.244 43.478 12.56 7.83 45.31 3.07
2226 2375 2.351706 TGGCTGCAATATGCTGATGA 57.648 45.000 12.56 0.00 45.31 2.92
2227 2376 2.227194 TGGCTGCAATATGCTGATGAG 58.773 47.619 12.56 0.00 45.31 2.90
2228 2377 2.228059 GGCTGCAATATGCTGATGAGT 58.772 47.619 12.56 0.00 45.31 3.41
2229 2378 3.181452 TGGCTGCAATATGCTGATGAGTA 60.181 43.478 12.56 0.00 45.31 2.59
2230 2379 3.436015 GGCTGCAATATGCTGATGAGTAG 59.564 47.826 12.56 0.00 45.31 2.57
2231 2380 3.436015 GCTGCAATATGCTGATGAGTAGG 59.564 47.826 12.56 0.00 45.31 3.18
2232 2381 4.639334 CTGCAATATGCTGATGAGTAGGT 58.361 43.478 3.78 0.00 45.31 3.08
2233 2382 4.635223 TGCAATATGCTGATGAGTAGGTC 58.365 43.478 3.78 0.00 45.31 3.85
2234 2383 4.346127 TGCAATATGCTGATGAGTAGGTCT 59.654 41.667 3.78 0.00 45.31 3.85
2235 2384 5.539955 TGCAATATGCTGATGAGTAGGTCTA 59.460 40.000 3.78 0.00 45.31 2.59
2236 2385 6.041979 TGCAATATGCTGATGAGTAGGTCTAA 59.958 38.462 3.78 0.00 45.31 2.10
2237 2386 7.102346 GCAATATGCTGATGAGTAGGTCTAAT 58.898 38.462 0.00 0.00 40.96 1.73
2238 2387 7.605691 GCAATATGCTGATGAGTAGGTCTAATT 59.394 37.037 0.00 0.00 40.96 1.40
2239 2388 9.499479 CAATATGCTGATGAGTAGGTCTAATTT 57.501 33.333 0.00 0.00 0.00 1.82
2241 2390 9.717942 ATATGCTGATGAGTAGGTCTAATTTTC 57.282 33.333 0.00 0.00 0.00 2.29
2242 2391 7.187824 TGCTGATGAGTAGGTCTAATTTTCT 57.812 36.000 0.00 0.00 0.00 2.52
2243 2392 7.044181 TGCTGATGAGTAGGTCTAATTTTCTG 58.956 38.462 0.00 0.00 0.00 3.02
2244 2393 6.018343 GCTGATGAGTAGGTCTAATTTTCTGC 60.018 42.308 0.00 0.00 0.00 4.26
2245 2394 6.946340 TGATGAGTAGGTCTAATTTTCTGCA 58.054 36.000 0.00 0.00 0.00 4.41
2246 2395 7.044181 TGATGAGTAGGTCTAATTTTCTGCAG 58.956 38.462 7.63 7.63 0.00 4.41
2247 2396 5.178797 TGAGTAGGTCTAATTTTCTGCAGC 58.821 41.667 9.47 0.00 0.00 5.25
2248 2397 5.165961 AGTAGGTCTAATTTTCTGCAGCA 57.834 39.130 9.47 0.00 0.00 4.41
2249 2398 5.560724 AGTAGGTCTAATTTTCTGCAGCAA 58.439 37.500 9.47 0.30 0.00 3.91
2250 2399 6.183347 AGTAGGTCTAATTTTCTGCAGCAAT 58.817 36.000 9.47 6.99 0.00 3.56
2251 2400 5.990120 AGGTCTAATTTTCTGCAGCAATT 57.010 34.783 20.85 20.85 0.00 2.32
2252 2401 6.350629 AGGTCTAATTTTCTGCAGCAATTT 57.649 33.333 21.75 16.39 0.00 1.82
2253 2402 6.762333 AGGTCTAATTTTCTGCAGCAATTTT 58.238 32.000 21.75 12.25 0.00 1.82
2254 2403 7.219322 AGGTCTAATTTTCTGCAGCAATTTTT 58.781 30.769 21.75 10.31 0.00 1.94
2255 2404 7.386025 AGGTCTAATTTTCTGCAGCAATTTTTC 59.614 33.333 21.75 14.36 0.00 2.29
2256 2405 7.171337 GGTCTAATTTTCTGCAGCAATTTTTCA 59.829 33.333 21.75 8.97 0.00 2.69
2257 2406 8.219105 GTCTAATTTTCTGCAGCAATTTTTCAG 58.781 33.333 21.75 15.44 0.00 3.02
2258 2407 5.934935 ATTTTCTGCAGCAATTTTTCAGG 57.065 34.783 9.47 0.00 0.00 3.86
2259 2408 4.669206 TTTCTGCAGCAATTTTTCAGGA 57.331 36.364 9.47 0.00 0.00 3.86
2260 2409 4.669206 TTCTGCAGCAATTTTTCAGGAA 57.331 36.364 9.47 0.00 0.00 3.36
2261 2410 4.669206 TCTGCAGCAATTTTTCAGGAAA 57.331 36.364 9.47 0.00 0.00 3.13
2262 2411 5.021033 TCTGCAGCAATTTTTCAGGAAAA 57.979 34.783 9.47 3.19 41.20 2.29
2273 2422 5.850557 TTTTCAGGAAAATTCTGCAGTGA 57.149 34.783 14.67 4.36 35.57 3.41
2274 2423 6.409524 TTTTCAGGAAAATTCTGCAGTGAT 57.590 33.333 14.67 6.57 35.57 3.06
2275 2424 5.633830 TTCAGGAAAATTCTGCAGTGATC 57.366 39.130 14.67 6.42 32.63 2.92
2276 2425 4.914983 TCAGGAAAATTCTGCAGTGATCT 58.085 39.130 14.67 1.11 32.63 2.75
2277 2426 5.319453 TCAGGAAAATTCTGCAGTGATCTT 58.681 37.500 14.67 2.40 32.63 2.40
2278 2427 5.182570 TCAGGAAAATTCTGCAGTGATCTTG 59.817 40.000 14.67 12.22 32.63 3.02
2279 2428 5.182570 CAGGAAAATTCTGCAGTGATCTTGA 59.817 40.000 14.67 0.00 0.00 3.02
2280 2429 5.182760 AGGAAAATTCTGCAGTGATCTTGAC 59.817 40.000 14.67 0.00 0.00 3.18
2281 2430 5.182760 GGAAAATTCTGCAGTGATCTTGACT 59.817 40.000 14.67 0.00 0.00 3.41
2282 2431 6.294397 GGAAAATTCTGCAGTGATCTTGACTT 60.294 38.462 14.67 0.00 0.00 3.01
2283 2432 7.094634 GGAAAATTCTGCAGTGATCTTGACTTA 60.095 37.037 14.67 0.00 0.00 2.24
2284 2433 6.734104 AATTCTGCAGTGATCTTGACTTAC 57.266 37.500 14.67 0.00 0.00 2.34
2285 2434 4.871933 TCTGCAGTGATCTTGACTTACA 57.128 40.909 14.67 0.00 0.00 2.41
2286 2435 5.213891 TCTGCAGTGATCTTGACTTACAA 57.786 39.130 14.67 0.00 36.97 2.41
2287 2436 4.991056 TCTGCAGTGATCTTGACTTACAAC 59.009 41.667 14.67 0.00 34.56 3.32
2288 2437 3.740832 TGCAGTGATCTTGACTTACAACG 59.259 43.478 0.00 0.00 34.56 4.10
2289 2438 3.423645 GCAGTGATCTTGACTTACAACGC 60.424 47.826 0.00 0.00 34.56 4.84
2290 2439 2.987149 AGTGATCTTGACTTACAACGCG 59.013 45.455 3.53 3.53 34.56 6.01
2291 2440 2.729882 GTGATCTTGACTTACAACGCGT 59.270 45.455 5.58 5.58 34.56 6.01
2292 2441 3.916172 GTGATCTTGACTTACAACGCGTA 59.084 43.478 14.46 0.00 34.56 4.42
2293 2442 4.383649 GTGATCTTGACTTACAACGCGTAA 59.616 41.667 14.46 1.58 37.76 3.18
2294 2443 4.383649 TGATCTTGACTTACAACGCGTAAC 59.616 41.667 14.46 0.00 35.09 2.50
2295 2444 3.704512 TCTTGACTTACAACGCGTAACA 58.295 40.909 14.46 2.46 35.09 2.41
2296 2445 4.300803 TCTTGACTTACAACGCGTAACAT 58.699 39.130 14.46 0.18 35.09 2.71
2297 2446 4.746115 TCTTGACTTACAACGCGTAACATT 59.254 37.500 14.46 0.00 35.09 2.71
2301 2450 4.053295 ACTTACAACGCGTAACATTCTGT 58.947 39.130 14.46 14.26 35.09 3.41
2312 2461 4.919168 CGTAACATTCTGTTAACGAGACCA 59.081 41.667 0.26 0.00 43.57 4.02
2326 2475 2.750948 GAGACCAAGCGTGAGTGTTTA 58.249 47.619 0.00 0.00 0.00 2.01
2389 2541 5.440610 CTTTTATATGCTCAAGGGGTCACT 58.559 41.667 0.00 0.00 0.00 3.41
2395 2547 1.342074 CTCAAGGGGTCACTGACAGA 58.658 55.000 10.08 0.66 33.68 3.41
2421 2573 4.320641 GCAACGCAGACAAGGGTAAAAATA 60.321 41.667 0.00 0.00 33.96 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.523072 TACGGTTGACACGCTCCTAC 59.477 55.000 0.00 0.00 34.00 3.18
93 95 2.825861 CTGGCAAGCAAAAACCTCAT 57.174 45.000 0.00 0.00 0.00 2.90
179 182 5.705609 TTGCTTAAGCTTTAAGGACAAGG 57.294 39.130 26.90 0.00 42.66 3.61
183 186 9.908152 TTTTAGAATTGCTTAAGCTTTAAGGAC 57.092 29.630 26.90 10.80 42.66 3.85
276 287 3.744719 TCGAGTCCGCCTTGACCG 61.745 66.667 0.00 0.00 35.83 4.79
284 296 2.579787 CATGACCGTCGAGTCCGC 60.580 66.667 10.19 0.00 35.83 5.54
294 306 0.597568 TGCCTTTTTCTGCATGACCG 59.402 50.000 0.00 0.00 31.31 4.79
303 315 4.819630 TCGTTTACATGTCTGCCTTTTTCT 59.180 37.500 0.00 0.00 0.00 2.52
305 317 4.578928 ACTCGTTTACATGTCTGCCTTTTT 59.421 37.500 0.00 0.00 0.00 1.94
308 320 3.067106 CACTCGTTTACATGTCTGCCTT 58.933 45.455 0.00 0.00 0.00 4.35
309 321 2.299013 TCACTCGTTTACATGTCTGCCT 59.701 45.455 0.00 0.00 0.00 4.75
310 322 2.668457 CTCACTCGTTTACATGTCTGCC 59.332 50.000 0.00 0.00 0.00 4.85
311 323 2.092838 GCTCACTCGTTTACATGTCTGC 59.907 50.000 0.00 0.00 0.00 4.26
312 324 2.342651 CGCTCACTCGTTTACATGTCTG 59.657 50.000 0.00 0.00 0.00 3.51
313 325 2.596452 CGCTCACTCGTTTACATGTCT 58.404 47.619 0.00 0.00 0.00 3.41
314 326 1.059264 GCGCTCACTCGTTTACATGTC 59.941 52.381 0.00 0.00 0.00 3.06
315 327 1.068474 GCGCTCACTCGTTTACATGT 58.932 50.000 2.69 2.69 0.00 3.21
356 368 0.789383 CGTGATTCAAAGTTCGCCGC 60.789 55.000 0.00 0.00 0.00 6.53
380 393 2.952310 GCAAGTTTCAGGAAGGTGAGTT 59.048 45.455 0.00 0.00 0.00 3.01
437 471 4.668576 TTAGCATTTTTCTGAGCTGTCG 57.331 40.909 0.00 0.00 37.94 4.35
484 522 2.761767 TGGCCACCAATCAATCAATCTG 59.238 45.455 0.00 0.00 0.00 2.90
512 554 7.200778 TGTCGAATTTGTCATCATCAAGAAA 57.799 32.000 0.00 0.00 0.00 2.52
547 589 5.636965 CGATCCTATCAAGATGCAAACTAGG 59.363 44.000 0.00 0.00 0.00 3.02
551 593 5.525378 AGAACGATCCTATCAAGATGCAAAC 59.475 40.000 0.00 0.00 0.00 2.93
583 625 3.585862 GCTCACGAGAAACATTCCACTA 58.414 45.455 0.00 0.00 0.00 2.74
589 631 1.880027 GTTGGGCTCACGAGAAACATT 59.120 47.619 0.00 0.00 0.00 2.71
626 668 3.357079 CAGTTGGTGCCCGCACTC 61.357 66.667 18.60 9.94 45.52 3.51
660 702 4.302559 AGTACATTTCTTCCCCTCAACC 57.697 45.455 0.00 0.00 0.00 3.77
661 703 7.610305 TGAAATAGTACATTTCTTCCCCTCAAC 59.390 37.037 21.08 3.53 38.47 3.18
662 704 7.610305 GTGAAATAGTACATTTCTTCCCCTCAA 59.390 37.037 21.08 5.60 38.47 3.02
703 769 1.633432 TGGGTGTCTCCATCGGAAAAT 59.367 47.619 0.00 0.00 38.11 1.82
749 815 2.063266 TCCAGTTTTGCTAGTAACGCG 58.937 47.619 3.53 3.53 0.00 6.01
833 912 1.457643 TACTCCCCAGGATGAGCGG 60.458 63.158 5.99 0.00 39.69 5.52
840 919 4.223953 CTGCTAAATACTACTCCCCAGGA 58.776 47.826 0.00 0.00 0.00 3.86
843 922 4.223953 CTCCTGCTAAATACTACTCCCCA 58.776 47.826 0.00 0.00 0.00 4.96
923 1010 0.861837 GACTGACTGGTTGAGTTGCG 59.138 55.000 0.00 0.00 33.83 4.85
1014 1126 2.526873 ACCTTCACCAGCCCGACT 60.527 61.111 0.00 0.00 0.00 4.18
1134 1246 3.954258 GAGAAGGAGGAAAGAGAGGAGAG 59.046 52.174 0.00 0.00 0.00 3.20
1135 1247 3.596046 AGAGAAGGAGGAAAGAGAGGAGA 59.404 47.826 0.00 0.00 0.00 3.71
1147 1260 1.403679 CTACACAGCGAGAGAAGGAGG 59.596 57.143 0.00 0.00 0.00 4.30
1149 1262 2.491675 TCTACACAGCGAGAGAAGGA 57.508 50.000 0.00 0.00 0.00 3.36
1190 1308 4.514401 AGAGGACTAAAATTCGCGGAATT 58.486 39.130 6.13 8.45 43.07 2.17
1285 1403 6.142817 GTCTTCAGCTTCTGCGAAAAATTAA 58.857 36.000 0.00 0.00 45.42 1.40
1316 1435 5.205821 TCCGGATTGATACTCTTCCTTACA 58.794 41.667 0.00 0.00 0.00 2.41
1319 1438 4.100189 CACTCCGGATTGATACTCTTCCTT 59.900 45.833 16.44 0.00 0.00 3.36
1328 1447 2.380941 TCGTTCCACTCCGGATTGATA 58.619 47.619 22.46 7.92 45.80 2.15
1349 1468 1.186200 CGATGGAGAGGGTCAGTTCA 58.814 55.000 0.00 0.00 0.00 3.18
1352 1471 1.006043 TCTTCGATGGAGAGGGTCAGT 59.994 52.381 0.00 0.00 0.00 3.41
1376 1495 5.013704 ACATACCAGTTTGACAGGAATGGTA 59.986 40.000 17.17 17.17 44.82 3.25
1406 1525 2.110188 AGGGAAAAGGGGGAAAGAGAAC 59.890 50.000 0.00 0.00 0.00 3.01
1430 1549 4.024893 TCAGTTGAATTTCTGAAGCACGAC 60.025 41.667 0.00 0.00 37.69 4.34
1468 1587 4.035091 TGCGTTTCATGATTCGATTTAGGG 59.965 41.667 19.34 0.00 0.00 3.53
1482 1604 6.332630 CAGGGAGAAATTTATTGCGTTTCAT 58.667 36.000 0.00 0.00 35.00 2.57
1605 1734 0.035458 AGCTGTCAGCCAGTTACCAC 59.965 55.000 21.32 0.00 43.77 4.16
1647 1784 2.032549 CACGTCCTGCACAAGAAAGAAG 60.033 50.000 0.00 0.00 0.00 2.85
1653 1790 0.874175 CGAACACGTCCTGCACAAGA 60.874 55.000 0.00 0.00 0.00 3.02
1654 1791 0.874175 TCGAACACGTCCTGCACAAG 60.874 55.000 0.00 0.00 0.00 3.16
1745 1882 2.191641 GCAGCTGGACCCTCATCC 59.808 66.667 17.12 0.00 39.45 3.51
1773 1910 0.537653 TCTTCACCACGGTGTTGTCA 59.462 50.000 15.65 0.00 45.55 3.58
1828 1965 0.249238 GACAGGTAGATGGCGCTCTG 60.249 60.000 7.64 6.70 0.00 3.35
1952 2089 7.712639 CACAGAGAGCTAATTAAAAGCCTGATA 59.287 37.037 17.19 0.00 41.02 2.15
1969 2111 3.422122 CAGAGAGTGCACAGAGAGC 57.578 57.895 21.04 1.86 0.00 4.09
2031 2173 9.050601 CCTAACTTAAGCTTGGATTCTAATCAG 57.949 37.037 9.86 0.00 37.15 2.90
2066 2208 4.499696 CCACACAGTCATCTATCGCACATA 60.500 45.833 0.00 0.00 0.00 2.29
2067 2209 3.451526 CACACAGTCATCTATCGCACAT 58.548 45.455 0.00 0.00 0.00 3.21
2070 2212 1.824852 ACCACACAGTCATCTATCGCA 59.175 47.619 0.00 0.00 0.00 5.10
2072 2214 2.354821 TCGACCACACAGTCATCTATCG 59.645 50.000 0.00 0.00 36.52 2.92
2073 2215 4.106197 GTTCGACCACACAGTCATCTATC 58.894 47.826 0.00 0.00 36.52 2.08
2075 2217 3.154710 AGTTCGACCACACAGTCATCTA 58.845 45.455 0.00 0.00 36.52 1.98
2076 2218 1.964223 AGTTCGACCACACAGTCATCT 59.036 47.619 0.00 0.00 36.52 2.90
2077 2219 2.440539 AGTTCGACCACACAGTCATC 57.559 50.000 0.00 0.00 36.52 2.92
2078 2220 2.548067 GGAAGTTCGACCACACAGTCAT 60.548 50.000 0.00 0.00 36.52 3.06
2079 2221 1.202486 GGAAGTTCGACCACACAGTCA 60.202 52.381 0.00 0.00 36.52 3.41
2081 2223 1.120530 AGGAAGTTCGACCACACAGT 58.879 50.000 0.00 0.00 0.00 3.55
2083 2225 2.960384 TCTTAGGAAGTTCGACCACACA 59.040 45.455 0.00 0.00 0.00 3.72
2105 2253 4.207165 CCAGTTCTTCCTTTTTCAGTCCA 58.793 43.478 0.00 0.00 0.00 4.02
2110 2258 2.693074 GCCACCAGTTCTTCCTTTTTCA 59.307 45.455 0.00 0.00 0.00 2.69
2114 2262 1.479389 CCTGCCACCAGTTCTTCCTTT 60.479 52.381 0.00 0.00 37.38 3.11
2117 2265 1.303643 CCCTGCCACCAGTTCTTCC 60.304 63.158 0.00 0.00 37.38 3.46
2127 2276 2.730066 AATTTTTGCGCCCCTGCCAC 62.730 55.000 4.18 0.00 0.00 5.01
2139 2288 7.123847 AGGAGGATGGAATTCTGAGAATTTTTG 59.876 37.037 20.27 0.00 26.50 2.44
2143 2292 5.990713 AGGAGGATGGAATTCTGAGAATT 57.009 39.130 19.51 19.51 26.50 2.17
2144 2293 5.163109 GGAAGGAGGATGGAATTCTGAGAAT 60.163 44.000 0.97 0.97 26.50 2.40
2145 2294 4.164988 GGAAGGAGGATGGAATTCTGAGAA 59.835 45.833 5.23 0.00 26.50 2.87
2152 2301 4.953781 TCAAAGGAAGGAGGATGGAATT 57.046 40.909 0.00 0.00 0.00 2.17
2167 2316 1.004044 AGGAGCTGACCACATCAAAGG 59.996 52.381 0.00 0.00 36.69 3.11
2172 2321 2.286872 CATCAAGGAGCTGACCACATC 58.713 52.381 0.00 0.00 0.00 3.06
2173 2322 1.681166 GCATCAAGGAGCTGACCACAT 60.681 52.381 0.00 0.00 0.00 3.21
2174 2323 0.321919 GCATCAAGGAGCTGACCACA 60.322 55.000 0.00 0.00 0.00 4.17
2175 2324 1.364626 CGCATCAAGGAGCTGACCAC 61.365 60.000 0.00 0.00 0.00 4.16
2176 2325 1.078918 CGCATCAAGGAGCTGACCA 60.079 57.895 0.00 0.00 0.00 4.02
2177 2326 1.817099 CCGCATCAAGGAGCTGACC 60.817 63.158 0.00 0.00 0.00 4.02
2178 2327 1.078848 ACCGCATCAAGGAGCTGAC 60.079 57.895 0.00 0.00 0.00 3.51
2179 2328 1.219124 GACCGCATCAAGGAGCTGA 59.781 57.895 0.00 0.00 0.00 4.26
2180 2329 0.809241 GAGACCGCATCAAGGAGCTG 60.809 60.000 0.00 0.00 0.00 4.24
2181 2330 1.260538 TGAGACCGCATCAAGGAGCT 61.261 55.000 0.00 0.00 0.00 4.09
2182 2331 0.809241 CTGAGACCGCATCAAGGAGC 60.809 60.000 0.00 0.00 0.00 4.70
2183 2332 0.820226 TCTGAGACCGCATCAAGGAG 59.180 55.000 0.00 0.00 0.00 3.69
2184 2333 1.066858 GTTCTGAGACCGCATCAAGGA 60.067 52.381 0.00 0.00 0.00 3.36
2185 2334 1.338105 TGTTCTGAGACCGCATCAAGG 60.338 52.381 0.00 0.00 0.00 3.61
2186 2335 2.084610 TGTTCTGAGACCGCATCAAG 57.915 50.000 0.00 0.00 0.00 3.02
2187 2336 2.542020 TTGTTCTGAGACCGCATCAA 57.458 45.000 0.00 0.00 0.00 2.57
2188 2337 2.349590 CATTGTTCTGAGACCGCATCA 58.650 47.619 0.00 0.00 0.00 3.07
2189 2338 1.667724 CCATTGTTCTGAGACCGCATC 59.332 52.381 0.00 0.00 0.00 3.91
2190 2339 1.742761 CCATTGTTCTGAGACCGCAT 58.257 50.000 0.00 0.00 0.00 4.73
2191 2340 0.955428 GCCATTGTTCTGAGACCGCA 60.955 55.000 0.00 0.00 0.00 5.69
2192 2341 0.674895 AGCCATTGTTCTGAGACCGC 60.675 55.000 0.00 0.00 0.00 5.68
2193 2342 1.081892 CAGCCATTGTTCTGAGACCG 58.918 55.000 0.00 0.00 32.26 4.79
2194 2343 0.807496 GCAGCCATTGTTCTGAGACC 59.193 55.000 7.19 0.00 32.26 3.85
2195 2344 1.527034 TGCAGCCATTGTTCTGAGAC 58.473 50.000 7.19 0.00 32.26 3.36
2196 2345 2.275134 TTGCAGCCATTGTTCTGAGA 57.725 45.000 7.19 0.00 32.26 3.27
2197 2346 4.607955 CATATTGCAGCCATTGTTCTGAG 58.392 43.478 7.19 0.00 32.26 3.35
2198 2347 3.181484 GCATATTGCAGCCATTGTTCTGA 60.181 43.478 7.19 0.00 44.26 3.27
2199 2348 3.120792 GCATATTGCAGCCATTGTTCTG 58.879 45.455 0.00 0.37 44.26 3.02
2200 2349 3.447918 GCATATTGCAGCCATTGTTCT 57.552 42.857 0.00 0.00 44.26 3.01
2212 2361 4.892433 AGACCTACTCATCAGCATATTGC 58.108 43.478 0.00 0.00 45.46 3.56
2213 2362 9.499479 AAATTAGACCTACTCATCAGCATATTG 57.501 33.333 0.00 0.00 0.00 1.90
2215 2364 9.717942 GAAAATTAGACCTACTCATCAGCATAT 57.282 33.333 0.00 0.00 0.00 1.78
2216 2365 8.928448 AGAAAATTAGACCTACTCATCAGCATA 58.072 33.333 0.00 0.00 0.00 3.14
2217 2366 7.714377 CAGAAAATTAGACCTACTCATCAGCAT 59.286 37.037 0.00 0.00 0.00 3.79
2218 2367 7.044181 CAGAAAATTAGACCTACTCATCAGCA 58.956 38.462 0.00 0.00 0.00 4.41
2219 2368 6.018343 GCAGAAAATTAGACCTACTCATCAGC 60.018 42.308 0.00 0.00 0.00 4.26
2220 2369 7.044181 TGCAGAAAATTAGACCTACTCATCAG 58.956 38.462 0.00 0.00 0.00 2.90
2221 2370 6.946340 TGCAGAAAATTAGACCTACTCATCA 58.054 36.000 0.00 0.00 0.00 3.07
2222 2371 6.018343 GCTGCAGAAAATTAGACCTACTCATC 60.018 42.308 20.43 0.00 0.00 2.92
2223 2372 5.819901 GCTGCAGAAAATTAGACCTACTCAT 59.180 40.000 20.43 0.00 0.00 2.90
2224 2373 5.178797 GCTGCAGAAAATTAGACCTACTCA 58.821 41.667 20.43 0.00 0.00 3.41
2225 2374 5.178797 TGCTGCAGAAAATTAGACCTACTC 58.821 41.667 20.43 0.00 0.00 2.59
2226 2375 5.165961 TGCTGCAGAAAATTAGACCTACT 57.834 39.130 20.43 0.00 0.00 2.57
2227 2376 5.880054 TTGCTGCAGAAAATTAGACCTAC 57.120 39.130 20.43 0.00 0.00 3.18
2228 2377 7.466746 AAATTGCTGCAGAAAATTAGACCTA 57.533 32.000 20.43 0.00 0.00 3.08
2229 2378 5.990120 AATTGCTGCAGAAAATTAGACCT 57.010 34.783 20.43 0.00 0.00 3.85
2230 2379 7.171337 TGAAAAATTGCTGCAGAAAATTAGACC 59.829 33.333 20.43 11.99 0.00 3.85
2231 2380 8.075593 TGAAAAATTGCTGCAGAAAATTAGAC 57.924 30.769 20.43 14.98 0.00 2.59
2232 2381 7.385752 CCTGAAAAATTGCTGCAGAAAATTAGA 59.614 33.333 20.43 0.00 0.00 2.10
2233 2382 7.385752 TCCTGAAAAATTGCTGCAGAAAATTAG 59.614 33.333 20.43 14.63 0.00 1.73
2234 2383 7.215789 TCCTGAAAAATTGCTGCAGAAAATTA 58.784 30.769 20.43 6.61 0.00 1.40
2235 2384 6.056884 TCCTGAAAAATTGCTGCAGAAAATT 58.943 32.000 20.43 18.55 0.00 1.82
2236 2385 5.613329 TCCTGAAAAATTGCTGCAGAAAAT 58.387 33.333 20.43 13.44 0.00 1.82
2237 2386 5.021033 TCCTGAAAAATTGCTGCAGAAAA 57.979 34.783 20.43 11.50 0.00 2.29
2238 2387 4.669206 TCCTGAAAAATTGCTGCAGAAA 57.331 36.364 20.43 15.35 0.00 2.52
2239 2388 4.669206 TTCCTGAAAAATTGCTGCAGAA 57.331 36.364 20.43 2.96 0.00 3.02
2240 2389 4.669206 TTTCCTGAAAAATTGCTGCAGA 57.331 36.364 20.43 0.00 0.00 4.26
2241 2390 5.934935 ATTTTCCTGAAAAATTGCTGCAG 57.065 34.783 10.11 10.11 43.51 4.41
2250 2399 6.219417 TCACTGCAGAATTTTCCTGAAAAA 57.781 33.333 23.35 0.00 42.71 1.94
2251 2400 5.850557 TCACTGCAGAATTTTCCTGAAAA 57.149 34.783 23.35 7.45 43.48 2.29
2252 2401 5.771666 AGATCACTGCAGAATTTTCCTGAAA 59.228 36.000 23.35 0.00 33.65 2.69
2253 2402 5.319453 AGATCACTGCAGAATTTTCCTGAA 58.681 37.500 23.35 0.00 33.65 3.02
2254 2403 4.914983 AGATCACTGCAGAATTTTCCTGA 58.085 39.130 23.35 11.38 33.65 3.86
2255 2404 5.182570 TCAAGATCACTGCAGAATTTTCCTG 59.817 40.000 23.35 5.45 34.88 3.86
2256 2405 5.182760 GTCAAGATCACTGCAGAATTTTCCT 59.817 40.000 23.35 4.89 0.00 3.36
2257 2406 5.182760 AGTCAAGATCACTGCAGAATTTTCC 59.817 40.000 23.35 7.68 0.00 3.13
2258 2407 6.251655 AGTCAAGATCACTGCAGAATTTTC 57.748 37.500 23.35 9.49 0.00 2.29
2259 2408 6.645790 AAGTCAAGATCACTGCAGAATTTT 57.354 33.333 23.35 11.71 0.00 1.82
2260 2409 6.712095 TGTAAGTCAAGATCACTGCAGAATTT 59.288 34.615 23.35 5.90 0.00 1.82
2261 2410 6.233434 TGTAAGTCAAGATCACTGCAGAATT 58.767 36.000 23.35 3.36 0.00 2.17
2262 2411 5.798132 TGTAAGTCAAGATCACTGCAGAAT 58.202 37.500 23.35 13.42 0.00 2.40
2263 2412 5.213891 TGTAAGTCAAGATCACTGCAGAA 57.786 39.130 23.35 8.50 0.00 3.02
2264 2413 4.871933 TGTAAGTCAAGATCACTGCAGA 57.128 40.909 23.35 0.00 0.00 4.26
2265 2414 4.143242 CGTTGTAAGTCAAGATCACTGCAG 60.143 45.833 13.48 13.48 36.66 4.41
2266 2415 3.740832 CGTTGTAAGTCAAGATCACTGCA 59.259 43.478 0.00 0.00 36.66 4.41
2267 2416 3.423645 GCGTTGTAAGTCAAGATCACTGC 60.424 47.826 0.00 0.00 36.66 4.40
2268 2417 3.181540 CGCGTTGTAAGTCAAGATCACTG 60.182 47.826 0.00 0.00 36.66 3.66
2269 2418 2.987149 CGCGTTGTAAGTCAAGATCACT 59.013 45.455 0.00 0.00 36.66 3.41
2270 2419 2.729882 ACGCGTTGTAAGTCAAGATCAC 59.270 45.455 5.58 0.00 36.66 3.06
2271 2420 3.021269 ACGCGTTGTAAGTCAAGATCA 57.979 42.857 5.58 0.00 36.66 2.92
2272 2421 4.383649 TGTTACGCGTTGTAAGTCAAGATC 59.616 41.667 20.78 0.00 43.52 2.75
2273 2422 4.300803 TGTTACGCGTTGTAAGTCAAGAT 58.699 39.130 20.78 0.00 43.52 2.40
2274 2423 3.704512 TGTTACGCGTTGTAAGTCAAGA 58.295 40.909 20.78 0.00 43.52 3.02
2275 2424 4.640805 ATGTTACGCGTTGTAAGTCAAG 57.359 40.909 20.78 0.00 43.52 3.02
2276 2425 4.746115 AGAATGTTACGCGTTGTAAGTCAA 59.254 37.500 20.78 0.00 43.52 3.18
2277 2426 4.149221 CAGAATGTTACGCGTTGTAAGTCA 59.851 41.667 20.78 7.07 43.52 3.41
2278 2427 4.625135 CAGAATGTTACGCGTTGTAAGTC 58.375 43.478 20.78 10.09 43.52 3.01
2279 2428 4.640805 CAGAATGTTACGCGTTGTAAGT 57.359 40.909 20.78 0.00 43.52 2.24
2293 2442 7.966117 ACGCTTGGTCTCGTTAACAGAATGT 62.966 44.000 6.39 0.03 44.58 2.71
2294 2443 3.181530 CGCTTGGTCTCGTTAACAGAATG 60.182 47.826 6.39 0.00 46.00 2.67
2295 2444 2.993899 CGCTTGGTCTCGTTAACAGAAT 59.006 45.455 6.39 0.00 0.00 2.40
2296 2445 2.223876 ACGCTTGGTCTCGTTAACAGAA 60.224 45.455 6.39 0.00 35.09 3.02
2297 2446 1.338973 ACGCTTGGTCTCGTTAACAGA 59.661 47.619 6.39 5.17 35.09 3.41
2301 2450 1.338973 ACTCACGCTTGGTCTCGTTAA 59.661 47.619 0.00 0.00 36.73 2.01
2312 2461 1.202651 AGGCAGTAAACACTCACGCTT 60.203 47.619 0.00 0.00 0.00 4.68
2326 2475 3.647771 GGGGGTTCGGAAGGCAGT 61.648 66.667 0.00 0.00 0.00 4.40
2389 2541 0.950555 GTCTGCGTTGCCATCTGTCA 60.951 55.000 0.00 0.00 0.00 3.58
2395 2547 1.973281 CCCTTGTCTGCGTTGCCAT 60.973 57.895 0.00 0.00 0.00 4.40
2421 2573 1.318576 CCAACCGCAACTCCTTTTCT 58.681 50.000 0.00 0.00 0.00 2.52
2664 2816 0.530744 CTGTACCTACGCTCCAGCAA 59.469 55.000 0.00 0.00 42.21 3.91
2817 2969 2.665000 CAAGAGGAGCTTGCCGGA 59.335 61.111 5.05 0.00 46.67 5.14


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

AutoCloner maintained by Alex Coulton.