Multiple sequence alignment - TraesCS6A01G316400

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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 TraesCS6A01G316400 chr6A 100.000 3074 0 0 1 3074 552834355 552831282 0.000000e+00 5677.0
1 TraesCS6A01G316400 chr6A 99.625 801 3 0 2274 3074 186485511 186484711 0.000000e+00 1463.0
2 TraesCS6A01G316400 chr6B 88.541 2042 112 61 290 2270 611349973 611347993 0.000000e+00 2362.0
3 TraesCS6A01G316400 chr6B 99.005 804 7 1 2272 3074 278610150 278609347 0.000000e+00 1439.0
4 TraesCS6A01G316400 chr6B 86.111 252 29 5 1 248 611351517 611351268 1.820000e-67 267.0
5 TraesCS6A01G316400 chr6D 89.970 1645 75 52 670 2267 407209234 407207633 0.000000e+00 2041.0
6 TraesCS6A01G316400 chr6D 89.535 774 37 15 796 1556 406345925 406345183 0.000000e+00 941.0
7 TraesCS6A01G316400 chr6D 97.644 382 9 0 2475 2856 127192313 127192694 0.000000e+00 656.0
8 TraesCS6A01G316400 chr6D 86.888 511 26 15 1762 2267 406345178 406344704 4.510000e-148 534.0
9 TraesCS6A01G316400 chr6D 88.312 385 20 9 290 665 407210773 407210405 3.640000e-119 438.0
10 TraesCS6A01G316400 chr6D 94.714 227 7 2 2853 3074 127192761 127192987 6.310000e-92 348.0
11 TraesCS6A01G316400 chr6D 97.688 173 4 0 2275 2447 127191903 127192075 6.440000e-77 298.0
12 TraesCS6A01G316400 chr6D 95.055 182 9 0 1 182 407211787 407211606 1.390000e-73 287.0
13 TraesCS6A01G316400 chr5A 99.750 800 2 0 2275 3074 662566276 662565477 0.000000e+00 1467.0
14 TraesCS6A01G316400 chr7A 99.625 801 3 0 2274 3074 478378392 478379192 0.000000e+00 1463.0
15 TraesCS6A01G316400 chr7A 78.138 709 120 20 1375 2074 131833684 131833002 4.740000e-113 418.0
16 TraesCS6A01G316400 chr7A 77.258 299 57 10 1022 1316 131835154 131834863 6.820000e-37 165.0
17 TraesCS6A01G316400 chr1A 90.268 411 21 5 2449 2856 96137881 96138275 1.260000e-143 520.0
18 TraesCS6A01G316400 chr1A 87.288 236 15 4 2853 3074 96138343 96138577 3.930000e-64 255.0
19 TraesCS6A01G316400 chr1A 92.179 179 11 3 2270 2447 96137660 96137836 1.830000e-62 250.0
20 TraesCS6A01G316400 chr1A 87.952 166 15 5 2275 2438 568002846 568002684 1.130000e-44 191.0
21 TraesCS6A01G316400 chrUn 89.731 409 23 6 2449 2856 18078240 18077850 3.540000e-139 505.0
22 TraesCS6A01G316400 chrUn 87.554 233 15 3 2856 3074 18077780 18077548 1.090000e-64 257.0
23 TraesCS6A01G316400 chrUn 90.230 174 11 4 2275 2447 18078809 18078641 3.990000e-54 222.0
24 TraesCS6A01G316400 chr3D 89.268 410 26 4 2449 2856 48255307 48254914 5.920000e-137 497.0
25 TraesCS6A01G316400 chr3D 87.727 220 13 3 2856 3061 48254843 48254624 8.510000e-61 244.0
26 TraesCS6A01G316400 chr1B 92.507 347 26 0 2449 2795 206028926 206028580 5.920000e-137 497.0
27 TraesCS6A01G316400 chr1B 91.837 49 4 0 2808 2856 206028583 206028535 5.500000e-08 69.4
28 TraesCS6A01G316400 chr7B 78.138 709 114 24 1375 2074 94310125 94309449 2.210000e-111 412.0
29 TraesCS6A01G316400 chr7B 78.000 300 53 10 1022 1316 94311537 94311246 3.150000e-40 176.0
30 TraesCS6A01G316400 chr7D 77.856 709 116 25 1375 2074 133225331 133224655 4.770000e-108 401.0
31 TraesCS6A01G316400 chr7D 77.258 299 57 10 1022 1316 133226803 133226512 6.820000e-37 165.0


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 TraesCS6A01G316400 chr6A 552831282 552834355 3073 True 5677.000000 5677 100.000000 1 3074 1 chr6A.!!$R2 3073
1 TraesCS6A01G316400 chr6A 186484711 186485511 800 True 1463.000000 1463 99.625000 2274 3074 1 chr6A.!!$R1 800
2 TraesCS6A01G316400 chr6B 278609347 278610150 803 True 1439.000000 1439 99.005000 2272 3074 1 chr6B.!!$R1 802
3 TraesCS6A01G316400 chr6B 611347993 611351517 3524 True 1314.500000 2362 87.326000 1 2270 2 chr6B.!!$R2 2269
4 TraesCS6A01G316400 chr6D 407207633 407211787 4154 True 922.000000 2041 91.112333 1 2267 3 chr6D.!!$R2 2266
5 TraesCS6A01G316400 chr6D 406344704 406345925 1221 True 737.500000 941 88.211500 796 2267 2 chr6D.!!$R1 1471
6 TraesCS6A01G316400 chr6D 127191903 127192987 1084 False 434.000000 656 96.682000 2275 3074 3 chr6D.!!$F1 799
7 TraesCS6A01G316400 chr5A 662565477 662566276 799 True 1467.000000 1467 99.750000 2275 3074 1 chr5A.!!$R1 799
8 TraesCS6A01G316400 chr7A 478378392 478379192 800 False 1463.000000 1463 99.625000 2274 3074 1 chr7A.!!$F1 800
9 TraesCS6A01G316400 chr7A 131833002 131835154 2152 True 291.500000 418 77.698000 1022 2074 2 chr7A.!!$R1 1052
10 TraesCS6A01G316400 chr1A 96137660 96138577 917 False 341.666667 520 89.911667 2270 3074 3 chr1A.!!$F1 804
11 TraesCS6A01G316400 chrUn 18077548 18078809 1261 True 328.000000 505 89.171667 2275 3074 3 chrUn.!!$R1 799
12 TraesCS6A01G316400 chr3D 48254624 48255307 683 True 370.500000 497 88.497500 2449 3061 2 chr3D.!!$R1 612
13 TraesCS6A01G316400 chr7B 94309449 94311537 2088 True 294.000000 412 78.069000 1022 2074 2 chr7B.!!$R1 1052
14 TraesCS6A01G316400 chr7D 133224655 133226803 2148 True 283.000000 401 77.557000 1022 2074 2 chr7D.!!$R1 1052

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
540 2434 0.036732 TCCTTGACCCTGATGTGCAC 59.963 55.0 10.75 10.75 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2196 6502 0.17691 TCACACACACACACACGGAT 59.823 50.0 0.0 0.0 0.0 4.18 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
33 34 0.737715 GGAGCAACAGGAGCAGTACG 60.738 60.000 0.00 0.00 0.00 3.67
56 57 2.749076 TGCACACATCTCCTGCATTTAC 59.251 45.455 0.00 0.00 36.00 2.01
142 143 1.795286 GCCAATACTGCGATAGACTGC 59.205 52.381 0.00 0.00 39.76 4.40
147 150 4.757799 ATACTGCGATAGACTGCTACTG 57.242 45.455 0.00 0.00 39.76 2.74
182 185 5.303165 TGCAATACATGGATCATCAGTCTC 58.697 41.667 0.00 0.00 0.00 3.36
186 189 2.102084 ACATGGATCATCAGTCTCCACG 59.898 50.000 0.00 0.00 41.65 4.94
187 190 1.114627 TGGATCATCAGTCTCCACGG 58.885 55.000 0.00 0.00 34.17 4.94
189 192 1.339610 GGATCATCAGTCTCCACGGAG 59.660 57.143 6.77 6.77 43.21 4.63
202 835 2.099405 CCACGGAGCCATGGTTTTAAT 58.901 47.619 14.67 0.00 0.00 1.40
206 839 4.994217 CACGGAGCCATGGTTTTAATTTTT 59.006 37.500 14.67 0.00 0.00 1.94
207 840 6.159988 CACGGAGCCATGGTTTTAATTTTTA 58.840 36.000 14.67 0.00 0.00 1.52
208 841 6.090223 CACGGAGCCATGGTTTTAATTTTTAC 59.910 38.462 14.67 0.00 0.00 2.01
217 850 8.931775 CATGGTTTTAATTTTTACTAACTGGCC 58.068 33.333 0.00 0.00 0.00 5.36
220 853 8.931775 GGTTTTAATTTTTACTAACTGGCCATG 58.068 33.333 5.51 2.78 0.00 3.66
221 854 9.483916 GTTTTAATTTTTACTAACTGGCCATGT 57.516 29.630 5.51 3.55 0.00 3.21
249 885 4.262463 GCCTAATATCAGGGATCACGTTCA 60.262 45.833 0.00 0.00 36.10 3.18
252 888 4.753516 ATATCAGGGATCACGTTCAACA 57.246 40.909 0.00 0.00 0.00 3.33
254 890 2.489971 TCAGGGATCACGTTCAACAAC 58.510 47.619 0.00 0.00 0.00 3.32
255 891 1.535462 CAGGGATCACGTTCAACAACC 59.465 52.381 0.00 0.00 0.00 3.77
256 892 1.420138 AGGGATCACGTTCAACAACCT 59.580 47.619 0.00 0.00 0.00 3.50
264 980 5.466819 TCACGTTCAACAACCTCTATAGTG 58.533 41.667 0.00 0.00 0.00 2.74
275 2146 9.886132 AACAACCTCTATAGTGGTTTTACTATG 57.114 33.333 28.55 20.80 46.24 2.23
294 2165 7.283625 ACTATGAACAATTTTTACACCAGCA 57.716 32.000 0.00 0.00 0.00 4.41
296 2167 5.843673 TGAACAATTTTTACACCAGCAGA 57.156 34.783 0.00 0.00 0.00 4.26
298 2169 4.243007 ACAATTTTTACACCAGCAGAGC 57.757 40.909 0.00 0.00 0.00 4.09
299 2170 3.636300 ACAATTTTTACACCAGCAGAGCA 59.364 39.130 0.00 0.00 0.00 4.26
300 2171 4.281688 ACAATTTTTACACCAGCAGAGCAT 59.718 37.500 0.00 0.00 0.00 3.79
301 2172 5.221501 ACAATTTTTACACCAGCAGAGCATT 60.222 36.000 0.00 0.00 0.00 3.56
308 2194 1.523258 CAGCAGAGCATTCTCCCCG 60.523 63.158 0.00 0.00 40.22 5.73
397 2284 4.681978 ACGCTCCGGCCACTGTTC 62.682 66.667 2.24 0.00 34.44 3.18
411 2298 0.994995 CTGTTCCTCGCAGATTCACG 59.005 55.000 0.00 0.00 36.12 4.35
412 2299 0.601057 TGTTCCTCGCAGATTCACGA 59.399 50.000 0.00 2.46 33.89 4.35
442 2330 2.494870 ACGAACACACATCTACCCTACC 59.505 50.000 0.00 0.00 0.00 3.18
443 2331 2.159142 CGAACACACATCTACCCTACCC 60.159 54.545 0.00 0.00 0.00 3.69
444 2332 2.942604 ACACACATCTACCCTACCCT 57.057 50.000 0.00 0.00 0.00 4.34
445 2333 4.284178 GAACACACATCTACCCTACCCTA 58.716 47.826 0.00 0.00 0.00 3.53
446 2334 3.639952 ACACACATCTACCCTACCCTAC 58.360 50.000 0.00 0.00 0.00 3.18
447 2335 2.963782 CACACATCTACCCTACCCTACC 59.036 54.545 0.00 0.00 0.00 3.18
448 2336 2.090887 ACACATCTACCCTACCCTACCC 60.091 54.545 0.00 0.00 0.00 3.69
449 2337 2.179424 CACATCTACCCTACCCTACCCT 59.821 54.545 0.00 0.00 0.00 4.34
450 2338 3.400322 CACATCTACCCTACCCTACCCTA 59.600 52.174 0.00 0.00 0.00 3.53
451 2339 3.400662 ACATCTACCCTACCCTACCCTAC 59.599 52.174 0.00 0.00 0.00 3.18
452 2340 2.433031 TCTACCCTACCCTACCCTACC 58.567 57.143 0.00 0.00 0.00 3.18
453 2341 1.430853 CTACCCTACCCTACCCTACCC 59.569 61.905 0.00 0.00 0.00 3.69
454 2342 0.254980 ACCCTACCCTACCCTACCCT 60.255 60.000 0.00 0.00 0.00 4.34
455 2343 1.013836 ACCCTACCCTACCCTACCCTA 59.986 57.143 0.00 0.00 0.00 3.53
456 2344 1.430853 CCCTACCCTACCCTACCCTAC 59.569 61.905 0.00 0.00 0.00 3.18
492 2385 1.133668 AGGCTGAGGCTCAAGTGTTTT 60.134 47.619 19.29 0.00 38.73 2.43
516 2409 0.326927 ATTTCCCACACGTACCCAGG 59.673 55.000 0.00 0.00 0.00 4.45
536 2430 1.280421 GCTTCTCCTTGACCCTGATGT 59.720 52.381 0.00 0.00 0.00 3.06
539 2433 0.325933 CTCCTTGACCCTGATGTGCA 59.674 55.000 0.00 0.00 0.00 4.57
540 2434 0.036732 TCCTTGACCCTGATGTGCAC 59.963 55.000 10.75 10.75 0.00 4.57
541 2435 0.250858 CCTTGACCCTGATGTGCACA 60.251 55.000 24.08 24.08 0.00 4.57
542 2436 0.877071 CTTGACCCTGATGTGCACAC 59.123 55.000 24.37 16.37 0.00 3.82
544 2438 2.032528 ACCCTGATGTGCACACGG 59.967 61.111 24.37 21.36 0.00 4.94
550 2451 1.447838 GATGTGCACACGGACGGAT 60.448 57.895 24.37 2.72 35.97 4.18
660 2562 2.433664 CGTGCCGTTCCTGGTACC 60.434 66.667 4.43 4.43 41.08 3.34
665 2567 1.002017 CCGTTCCTGGTACCCCCTA 59.998 63.158 10.07 0.00 0.00 3.53
668 2592 1.493861 GTTCCTGGTACCCCCTACTC 58.506 60.000 10.07 0.00 0.00 2.59
680 3748 3.087781 CCCCCTACTCGCTATTAGTACC 58.912 54.545 0.00 0.00 0.00 3.34
685 3753 5.642919 CCCTACTCGCTATTAGTACCAGTAG 59.357 48.000 0.00 0.00 34.22 2.57
718 3786 1.027357 CGCCTAATCAAGCTTGCCAT 58.973 50.000 21.99 8.22 0.00 4.40
750 3819 2.739379 GCGCTTCTTATATCTTGCTCCC 59.261 50.000 0.00 0.00 0.00 4.30
765 3844 2.364317 CCCCTCTCGCTTCTCCCA 60.364 66.667 0.00 0.00 0.00 4.37
821 3911 1.205055 TCTGCTCCGAGGAGAGTCTA 58.795 55.000 22.32 0.00 44.53 2.59
837 3927 3.003173 TACCGCTCCCAGCTGCTT 61.003 61.111 8.66 0.00 39.60 3.91
849 3939 1.376553 GCTGCTTCACTGACCCTCC 60.377 63.158 0.00 0.00 0.00 4.30
864 3954 1.480312 CCCTCCAGTGATCGATCTCCT 60.480 57.143 25.02 17.47 0.00 3.69
1035 4140 3.710722 CGGTGCTGGGAGGAGCTT 61.711 66.667 0.00 0.00 39.90 3.74
1337 4463 0.179153 TCAAGCATCTCACTCGCTCG 60.179 55.000 0.00 0.00 34.11 5.03
1339 4465 2.897641 AAGCATCTCACTCGCTCGCC 62.898 60.000 0.00 0.00 34.11 5.54
1386 5670 2.865551 CACGAATTTTGTTTGCTTGGCT 59.134 40.909 0.00 0.00 0.00 4.75
1881 6168 3.154516 GACGACGACGACGACTCT 58.845 61.111 25.15 3.47 42.66 3.24
1882 6169 1.225422 GACGACGACGACGACTCTG 60.225 63.158 25.15 0.00 42.66 3.35
1883 6170 1.612469 GACGACGACGACGACTCTGA 61.612 60.000 25.15 0.00 42.66 3.27
1884 6171 1.225422 CGACGACGACGACTCTGAC 60.225 63.158 15.32 0.00 42.66 3.51
2160 6460 4.157817 CGTTCCTACGGTCGTTGG 57.842 61.111 15.70 15.70 43.94 3.77
2161 6461 2.090524 CGTTCCTACGGTCGTTGGC 61.091 63.158 16.72 5.60 43.94 4.52
2162 6462 2.090524 GTTCCTACGGTCGTTGGCG 61.091 63.158 16.72 0.00 40.07 5.69
2163 6463 2.563798 TTCCTACGGTCGTTGGCGT 61.564 57.895 16.72 0.00 40.07 5.68
2164 6464 2.048877 CCTACGGTCGTTGGCGTT 60.049 61.111 10.57 0.00 39.49 4.84
2194 6500 0.462937 TTTGTGTGCGTGCCAGTAGT 60.463 50.000 0.00 0.00 0.00 2.73
2195 6501 0.389757 TTGTGTGCGTGCCAGTAGTA 59.610 50.000 0.00 0.00 0.00 1.82
2196 6502 0.389757 TGTGTGCGTGCCAGTAGTAA 59.610 50.000 0.00 0.00 0.00 2.24
2197 6503 1.001520 TGTGTGCGTGCCAGTAGTAAT 59.998 47.619 0.00 0.00 0.00 1.89
2198 6504 1.659098 GTGTGCGTGCCAGTAGTAATC 59.341 52.381 0.00 0.00 0.00 1.75
2199 6505 1.287425 GTGCGTGCCAGTAGTAATCC 58.713 55.000 0.00 0.00 0.00 3.01
2200 6506 0.179121 TGCGTGCCAGTAGTAATCCG 60.179 55.000 0.00 0.00 0.00 4.18
2201 6507 0.179119 GCGTGCCAGTAGTAATCCGT 60.179 55.000 0.00 0.00 0.00 4.69
2202 6508 1.556564 CGTGCCAGTAGTAATCCGTG 58.443 55.000 0.00 0.00 0.00 4.94
2203 6509 1.135199 CGTGCCAGTAGTAATCCGTGT 60.135 52.381 0.00 0.00 0.00 4.49
2204 6510 2.268298 GTGCCAGTAGTAATCCGTGTG 58.732 52.381 0.00 0.00 0.00 3.82
2207 6513 2.353406 GCCAGTAGTAATCCGTGTGTGT 60.353 50.000 0.00 0.00 0.00 3.72
2231 6537 7.041440 TGTGTGTGTGATGTAAACTTAATCTGG 60.041 37.037 0.00 0.00 0.00 3.86
2235 6541 7.172532 TGTGTGATGTAAACTTAATCTGGTGTC 59.827 37.037 0.00 0.00 0.00 3.67
2241 6547 8.149973 TGTAAACTTAATCTGGTGTCAAGTTC 57.850 34.615 0.00 0.00 38.21 3.01
2701 7411 9.582431 AATCAAGATCTGCAATGAAAATGTTAG 57.418 29.630 0.00 0.00 0.00 2.34
2967 7779 3.787476 GCACTTGGTTCGTTACAGTTGTG 60.787 47.826 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 5.121105 TCATGAGTAAATGCAGGAGATGTG 58.879 41.667 0.00 0.00 0.00 3.21
56 57 2.096496 GCAGGTGGATTCGTTTCATGAG 59.904 50.000 0.00 0.00 0.00 2.90
142 143 4.630894 TTGCAACAAGTTGGAACAGTAG 57.369 40.909 14.58 0.00 44.10 2.57
186 189 9.146984 GTTAGTAAAAATTAAAACCATGGCTCC 57.853 33.333 13.04 0.00 0.00 4.70
187 190 9.923143 AGTTAGTAAAAATTAAAACCATGGCTC 57.077 29.630 13.04 0.00 0.00 4.70
189 192 8.931775 CCAGTTAGTAAAAATTAAAACCATGGC 58.068 33.333 13.04 0.00 0.00 4.40
202 835 6.403855 GCGAATACATGGCCAGTTAGTAAAAA 60.404 38.462 13.05 0.00 0.00 1.94
206 839 3.493699 GGCGAATACATGGCCAGTTAGTA 60.494 47.826 13.05 11.84 46.13 1.82
207 840 2.561569 GCGAATACATGGCCAGTTAGT 58.438 47.619 13.05 9.84 0.00 2.24
208 841 1.873591 GGCGAATACATGGCCAGTTAG 59.126 52.381 13.05 3.42 46.13 2.34
217 850 5.977635 TCCCTGATATTAGGCGAATACATG 58.022 41.667 8.05 0.00 36.47 3.21
220 853 6.043411 GTGATCCCTGATATTAGGCGAATAC 58.957 44.000 8.05 6.99 36.47 1.89
221 854 5.163550 CGTGATCCCTGATATTAGGCGAATA 60.164 44.000 8.05 2.47 36.47 1.75
222 858 4.382040 CGTGATCCCTGATATTAGGCGAAT 60.382 45.833 8.05 0.00 36.47 3.34
224 860 2.492088 CGTGATCCCTGATATTAGGCGA 59.508 50.000 8.05 7.46 36.47 5.54
225 861 2.231478 ACGTGATCCCTGATATTAGGCG 59.769 50.000 8.05 8.22 36.47 5.52
249 885 9.886132 CATAGTAAAACCACTATAGAGGTTGTT 57.114 33.333 28.48 24.13 45.95 2.83
275 2146 4.681483 GCTCTGCTGGTGTAAAAATTGTTC 59.319 41.667 0.00 0.00 0.00 3.18
286 2157 0.035630 GGAGAATGCTCTGCTGGTGT 60.036 55.000 0.00 0.00 41.06 4.16
289 2160 1.153005 GGGGAGAATGCTCTGCTGG 60.153 63.158 0.00 0.00 39.84 4.85
294 2165 3.483869 GCCCGGGGAGAATGCTCT 61.484 66.667 25.28 0.00 41.06 4.09
298 2169 3.537206 GATCCGCCCGGGGAGAATG 62.537 68.421 25.28 0.56 40.02 2.67
299 2170 3.242291 GATCCGCCCGGGGAGAAT 61.242 66.667 25.28 1.25 40.02 2.40
328 2214 4.570874 GGGGAGAAGATGGCCCGC 62.571 72.222 0.00 0.00 42.99 6.13
387 2274 2.527951 ATCTGCGAGGAACAGTGGCC 62.528 60.000 0.00 0.00 36.50 5.36
397 2284 0.108615 ACCTTCGTGAATCTGCGAGG 60.109 55.000 0.00 11.17 38.40 4.63
411 2298 6.056428 AGATGTGTGTTCGTTTTTACCTTC 57.944 37.500 0.00 0.00 0.00 3.46
412 2299 6.017687 GGTAGATGTGTGTTCGTTTTTACCTT 60.018 38.462 0.00 0.00 0.00 3.50
442 2330 1.430853 GGTAGGGTAGGGTAGGGTAGG 59.569 61.905 0.00 0.00 0.00 3.18
443 2331 1.430853 GGGTAGGGTAGGGTAGGGTAG 59.569 61.905 0.00 0.00 0.00 3.18
444 2332 1.013836 AGGGTAGGGTAGGGTAGGGTA 59.986 57.143 0.00 0.00 0.00 3.69
445 2333 0.254980 AGGGTAGGGTAGGGTAGGGT 60.255 60.000 0.00 0.00 0.00 4.34
446 2334 0.486433 GAGGGTAGGGTAGGGTAGGG 59.514 65.000 0.00 0.00 0.00 3.53
447 2335 1.238615 TGAGGGTAGGGTAGGGTAGG 58.761 60.000 0.00 0.00 0.00 3.18
448 2336 2.449730 TGATGAGGGTAGGGTAGGGTAG 59.550 54.545 0.00 0.00 0.00 3.18
449 2337 2.449730 CTGATGAGGGTAGGGTAGGGTA 59.550 54.545 0.00 0.00 0.00 3.69
450 2338 1.220750 CTGATGAGGGTAGGGTAGGGT 59.779 57.143 0.00 0.00 0.00 4.34
451 2339 1.503784 TCTGATGAGGGTAGGGTAGGG 59.496 57.143 0.00 0.00 0.00 3.53
452 2340 3.235200 CTTCTGATGAGGGTAGGGTAGG 58.765 54.545 0.00 0.00 0.00 3.18
453 2341 3.235200 CCTTCTGATGAGGGTAGGGTAG 58.765 54.545 0.00 0.00 35.03 3.18
454 2342 2.693074 GCCTTCTGATGAGGGTAGGGTA 60.693 54.545 0.00 0.00 41.06 3.69
455 2343 1.972207 GCCTTCTGATGAGGGTAGGGT 60.972 57.143 0.00 0.00 41.06 4.34
456 2344 0.761802 GCCTTCTGATGAGGGTAGGG 59.238 60.000 0.00 0.00 41.06 3.53
492 2385 2.289819 GGGTACGTGTGGGAAATGAAGA 60.290 50.000 0.00 0.00 0.00 2.87
516 2409 1.280421 ACATCAGGGTCAAGGAGAAGC 59.720 52.381 0.00 0.00 0.00 3.86
536 2430 2.048597 GTCATCCGTCCGTGTGCA 60.049 61.111 0.00 0.00 0.00 4.57
539 2433 3.755628 CCCGTCATCCGTCCGTGT 61.756 66.667 0.00 0.00 33.66 4.49
540 2434 2.884087 CTTCCCGTCATCCGTCCGTG 62.884 65.000 0.00 0.00 33.66 4.94
541 2435 2.677524 TTCCCGTCATCCGTCCGT 60.678 61.111 0.00 0.00 33.66 4.69
542 2436 2.104331 CTTCCCGTCATCCGTCCG 59.896 66.667 0.00 0.00 33.66 4.79
544 2438 1.141234 GTCCTTCCCGTCATCCGTC 59.859 63.158 0.00 0.00 33.66 4.79
550 2451 1.052124 ACAGTTGGTCCTTCCCGTCA 61.052 55.000 0.00 0.00 34.77 4.35
557 2458 0.180406 ACGCTTGACAGTTGGTCCTT 59.820 50.000 0.00 0.00 46.38 3.36
660 2562 3.757493 CTGGTACTAATAGCGAGTAGGGG 59.243 52.174 6.27 0.00 30.08 4.79
665 2567 6.825610 ACTACTACTGGTACTAATAGCGAGT 58.174 40.000 0.00 0.00 0.00 4.18
680 3748 3.982058 GGCGCTGCTAATTACTACTACTG 59.018 47.826 7.64 0.00 0.00 2.74
685 3753 5.227908 TGATTAGGCGCTGCTAATTACTAC 58.772 41.667 16.74 7.40 0.00 2.73
718 3786 0.108585 AAGAAGCGCACCAGAAAGGA 59.891 50.000 11.47 0.00 41.22 3.36
750 3819 0.539051 AATGTGGGAGAAGCGAGAGG 59.461 55.000 0.00 0.00 0.00 3.69
765 3844 0.958822 GGTGAGCGAAACCCAAATGT 59.041 50.000 0.00 0.00 0.00 2.71
849 3939 3.481453 TGGAGTAGGAGATCGATCACTG 58.519 50.000 26.47 0.00 0.00 3.66
853 3943 3.492337 ACCTTGGAGTAGGAGATCGATC 58.508 50.000 17.91 17.91 38.73 3.69
854 3944 3.603965 ACCTTGGAGTAGGAGATCGAT 57.396 47.619 0.00 0.00 38.73 3.59
855 3945 4.088056 CTACCTTGGAGTAGGAGATCGA 57.912 50.000 0.00 0.00 38.73 3.59
864 3954 1.410648 CCGCCTACCTACCTTGGAGTA 60.411 57.143 0.00 0.00 0.00 2.59
988 4078 2.761465 CCCCCATTGCTCCTCCTCC 61.761 68.421 0.00 0.00 0.00 4.30
1354 4480 2.393271 AAATTCGTGAGCCCTCAGAG 57.607 50.000 0.00 0.00 40.75 3.35
1356 4669 2.154462 ACAAAATTCGTGAGCCCTCAG 58.846 47.619 0.00 0.00 40.75 3.35
1357 4670 2.270352 ACAAAATTCGTGAGCCCTCA 57.730 45.000 0.00 0.00 37.24 3.86
1359 4672 2.545742 GCAAACAAAATTCGTGAGCCCT 60.546 45.455 0.00 0.00 0.00 5.19
1360 4673 1.792367 GCAAACAAAATTCGTGAGCCC 59.208 47.619 0.00 0.00 0.00 5.19
1365 5305 2.865551 AGCCAAGCAAACAAAATTCGTG 59.134 40.909 0.00 0.00 0.00 4.35
1876 6163 1.225422 CGTCGTCGTCGTCAGAGTC 60.225 63.158 3.67 0.00 38.33 3.36
1877 6164 1.662760 TCGTCGTCGTCGTCAGAGT 60.663 57.895 11.41 0.00 38.33 3.24
1878 6165 1.225422 GTCGTCGTCGTCGTCAGAG 60.225 63.158 11.41 0.00 38.33 3.35
1879 6166 2.849007 GTCGTCGTCGTCGTCAGA 59.151 61.111 11.41 0.00 38.33 3.27
1880 6167 2.567522 CGTCGTCGTCGTCGTCAG 60.568 66.667 12.51 1.64 41.73 3.51
2151 6451 0.457166 TATCTGAACGCCAACGACCG 60.457 55.000 0.00 0.00 43.93 4.79
2159 6459 1.396996 ACAAACGCATATCTGAACGCC 59.603 47.619 0.00 0.00 0.00 5.68
2160 6460 2.159707 ACACAAACGCATATCTGAACGC 60.160 45.455 0.00 0.00 0.00 4.84
2161 6461 3.407252 CACACAAACGCATATCTGAACG 58.593 45.455 0.00 0.00 0.00 3.95
2162 6462 3.163594 GCACACAAACGCATATCTGAAC 58.836 45.455 0.00 0.00 0.00 3.18
2163 6463 2.159720 CGCACACAAACGCATATCTGAA 60.160 45.455 0.00 0.00 0.00 3.02
2164 6464 1.393196 CGCACACAAACGCATATCTGA 59.607 47.619 0.00 0.00 0.00 3.27
2194 6500 2.159085 TCACACACACACACACGGATTA 60.159 45.455 0.00 0.00 0.00 1.75
2195 6501 1.013596 CACACACACACACACGGATT 58.986 50.000 0.00 0.00 0.00 3.01
2196 6502 0.176910 TCACACACACACACACGGAT 59.823 50.000 0.00 0.00 0.00 4.18
2197 6503 0.176910 ATCACACACACACACACGGA 59.823 50.000 0.00 0.00 0.00 4.69
2198 6504 0.304401 CATCACACACACACACACGG 59.696 55.000 0.00 0.00 0.00 4.94
2199 6505 1.006086 ACATCACACACACACACACG 58.994 50.000 0.00 0.00 0.00 4.49
2200 6506 4.094294 AGTTTACATCACACACACACACAC 59.906 41.667 0.00 0.00 0.00 3.82
2201 6507 4.257731 AGTTTACATCACACACACACACA 58.742 39.130 0.00 0.00 0.00 3.72
2202 6508 4.875544 AGTTTACATCACACACACACAC 57.124 40.909 0.00 0.00 0.00 3.82
2203 6509 6.986904 TTAAGTTTACATCACACACACACA 57.013 33.333 0.00 0.00 0.00 3.72
2204 6510 7.798516 CAGATTAAGTTTACATCACACACACAC 59.201 37.037 0.00 0.00 0.00 3.82
2207 6513 6.995686 ACCAGATTAAGTTTACATCACACACA 59.004 34.615 0.00 0.00 0.00 3.72
2270 6577 5.959554 GCACGTGCATAATTACTAGTGTAC 58.040 41.667 34.52 0.00 41.59 2.90
2701 7411 0.664166 CGGGAACACATGCAAAGTGC 60.664 55.000 19.09 4.56 45.29 4.40
2967 7779 4.479619 CAGTAAAGCCTTCTCATTTGTGC 58.520 43.478 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.