Multiple sequence alignment - TraesCS6D01G123000

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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 TraesCS6D01G123000 chr6D 100.000 3016 0 0 1 3016 87501846 87504861 0.000000e+00 5570
1 TraesCS6D01G123000 chr6A 92.437 2208 104 23 654 2842 105637635 105639798 0.000000e+00 3094
2 TraesCS6D01G123000 chr6A 89.877 326 22 5 341 662 105636847 105637165 2.800000e-110 409
3 TraesCS6D01G123000 chr6A 93.671 237 14 1 1 237 105636514 105636749 1.330000e-93 353
4 TraesCS6D01G123000 chr6B 90.400 2052 113 42 1 2032 166138404 166140391 0.000000e+00 2621
5 TraesCS6D01G123000 chr6B 92.308 91 6 1 2074 2164 166140520 166140609 8.780000e-26 128
6 TraesCS6D01G123000 chr2D 91.432 817 60 9 2206 3016 552731418 552732230 0.000000e+00 1112
7 TraesCS6D01G123000 chr2D 90.931 816 59 11 2205 3016 126036924 126037728 0.000000e+00 1083
8 TraesCS6D01G123000 chr2D 90.686 816 67 8 2206 3016 1848865 1848054 0.000000e+00 1077
9 TraesCS6D01G123000 chr2D 90.564 816 66 10 2206 3016 593400679 593401488 0.000000e+00 1070
10 TraesCS6D01G123000 chr5D 92.055 793 48 11 2205 2988 362963555 362962769 0.000000e+00 1101
11 TraesCS6D01G123000 chr1D 90.798 815 65 9 2206 3016 107142619 107141811 0.000000e+00 1081
12 TraesCS6D01G123000 chr7A 90.564 816 68 7 2203 3014 533507719 533508529 0.000000e+00 1072
13 TraesCS6D01G123000 chr4D 90.552 815 69 7 2206 3016 96789379 96790189 0.000000e+00 1072
14 TraesCS6D01G123000 chr5B 90.244 820 75 4 2198 3014 133343701 133344518 0.000000e+00 1066


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 TraesCS6D01G123000 chr6D 87501846 87504861 3015 False 5570.000000 5570 100.000 1 3016 1 chr6D.!!$F1 3015
1 TraesCS6D01G123000 chr6A 105636514 105639798 3284 False 1285.333333 3094 91.995 1 2842 3 chr6A.!!$F1 2841
2 TraesCS6D01G123000 chr6B 166138404 166140609 2205 False 1374.500000 2621 91.354 1 2164 2 chr6B.!!$F1 2163
3 TraesCS6D01G123000 chr2D 552731418 552732230 812 False 1112.000000 1112 91.432 2206 3016 1 chr2D.!!$F2 810
4 TraesCS6D01G123000 chr2D 126036924 126037728 804 False 1083.000000 1083 90.931 2205 3016 1 chr2D.!!$F1 811
5 TraesCS6D01G123000 chr2D 1848054 1848865 811 True 1077.000000 1077 90.686 2206 3016 1 chr2D.!!$R1 810
6 TraesCS6D01G123000 chr2D 593400679 593401488 809 False 1070.000000 1070 90.564 2206 3016 1 chr2D.!!$F3 810
7 TraesCS6D01G123000 chr5D 362962769 362963555 786 True 1101.000000 1101 92.055 2205 2988 1 chr5D.!!$R1 783
8 TraesCS6D01G123000 chr1D 107141811 107142619 808 True 1081.000000 1081 90.798 2206 3016 1 chr1D.!!$R1 810
9 TraesCS6D01G123000 chr7A 533507719 533508529 810 False 1072.000000 1072 90.564 2203 3014 1 chr7A.!!$F1 811
10 TraesCS6D01G123000 chr4D 96789379 96790189 810 False 1072.000000 1072 90.552 2206 3016 1 chr4D.!!$F1 810
11 TraesCS6D01G123000 chr5B 133343701 133344518 817 False 1066.000000 1066 90.244 2198 3014 1 chr5B.!!$F1 816

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
963 1523 1.741327 GCCCGCCATGCATGAATTCT 61.741 55.0 28.31 0.0 0.0 2.4 F
1118 1681 0.246635 AACGACGAAGATGGTGAGGG 59.753 55.0 0.00 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1890 2459 0.680061 AGTTTCCTGAGGTCACCGAC 59.320 55.000 0.0 0.0 0.0 4.79 R
2650 3333 1.071471 GCGATCCCATCCCAACGAT 59.929 57.895 0.0 0.0 0.0 3.73 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
62 63 5.010617 GTGGGTGAACATTCTAAATTGTGGT 59.989 40.000 0.00 0.00 0.00 4.16
106 107 6.317857 GCTCTGAAATACAGTGTTGGAAATC 58.682 40.000 0.00 0.00 45.86 2.17
122 123 4.718774 TGGAAATCTCACTAGAATGGCTCT 59.281 41.667 0.00 0.00 34.73 4.09
175 176 5.049167 TGCAGTAAACTGGCTTTGAAATTG 58.951 37.500 11.86 0.00 43.94 2.32
211 212 9.364989 GCTAATACTGCTCCTTGATATTTCTAG 57.635 37.037 0.00 0.00 0.00 2.43
222 223 6.239430 CCTTGATATTTCTAGAGTGCAGGCTA 60.239 42.308 0.00 0.00 0.00 3.93
237 238 3.887716 GCAGGCTATGAAATTGGACTGAT 59.112 43.478 0.00 0.00 36.50 2.90
238 239 4.261489 GCAGGCTATGAAATTGGACTGATG 60.261 45.833 0.00 0.00 36.50 3.07
239 240 5.128205 CAGGCTATGAAATTGGACTGATGA 58.872 41.667 0.00 0.00 36.50 2.92
240 241 5.591472 CAGGCTATGAAATTGGACTGATGAA 59.409 40.000 0.00 0.00 36.50 2.57
241 242 5.826737 AGGCTATGAAATTGGACTGATGAAG 59.173 40.000 0.00 0.00 0.00 3.02
242 243 5.591877 GGCTATGAAATTGGACTGATGAAGT 59.408 40.000 0.00 0.00 43.85 3.01
243 244 6.096001 GGCTATGAAATTGGACTGATGAAGTT 59.904 38.462 0.00 0.00 40.07 2.66
244 245 6.971184 GCTATGAAATTGGACTGATGAAGTTG 59.029 38.462 0.00 0.00 40.07 3.16
245 246 7.148188 GCTATGAAATTGGACTGATGAAGTTGA 60.148 37.037 0.00 0.00 40.07 3.18
246 247 6.957920 TGAAATTGGACTGATGAAGTTGAA 57.042 33.333 0.00 0.00 40.07 2.69
247 248 7.528996 TGAAATTGGACTGATGAAGTTGAAT 57.471 32.000 0.00 0.00 40.07 2.57
248 249 7.954835 TGAAATTGGACTGATGAAGTTGAATT 58.045 30.769 0.00 0.00 40.07 2.17
249 250 8.423349 TGAAATTGGACTGATGAAGTTGAATTT 58.577 29.630 0.00 0.00 40.07 1.82
250 251 8.597662 AAATTGGACTGATGAAGTTGAATTTG 57.402 30.769 0.00 0.00 40.07 2.32
251 252 6.957920 TTGGACTGATGAAGTTGAATTTGA 57.042 33.333 0.00 0.00 40.07 2.69
252 253 6.317789 TGGACTGATGAAGTTGAATTTGAC 57.682 37.500 0.00 0.00 40.07 3.18
253 254 6.064060 TGGACTGATGAAGTTGAATTTGACT 58.936 36.000 0.00 0.00 40.07 3.41
254 255 7.223584 TGGACTGATGAAGTTGAATTTGACTA 58.776 34.615 0.00 0.00 40.07 2.59
255 256 7.719193 TGGACTGATGAAGTTGAATTTGACTAA 59.281 33.333 0.00 0.00 40.07 2.24
256 257 8.567948 GGACTGATGAAGTTGAATTTGACTAAA 58.432 33.333 0.00 0.00 40.07 1.85
257 258 9.950680 GACTGATGAAGTTGAATTTGACTAAAA 57.049 29.630 0.00 0.00 40.07 1.52
280 281 8.658171 AAATTGAATTTGTTATGAAATTGCGC 57.342 26.923 0.00 0.00 36.00 6.09
281 282 7.599630 ATTGAATTTGTTATGAAATTGCGCT 57.400 28.000 9.73 0.00 36.00 5.92
282 283 6.392353 TGAATTTGTTATGAAATTGCGCTG 57.608 33.333 9.73 0.00 36.00 5.18
283 284 5.925397 TGAATTTGTTATGAAATTGCGCTGT 59.075 32.000 9.73 0.00 36.00 4.40
284 285 7.087007 TGAATTTGTTATGAAATTGCGCTGTA 58.913 30.769 9.73 0.00 36.00 2.74
285 286 7.273164 TGAATTTGTTATGAAATTGCGCTGTAG 59.727 33.333 9.73 0.00 36.00 2.74
286 287 5.621197 TTGTTATGAAATTGCGCTGTAGT 57.379 34.783 9.73 0.00 0.00 2.73
287 288 4.968626 TGTTATGAAATTGCGCTGTAGTG 58.031 39.130 9.73 0.00 0.00 2.74
297 298 2.532531 CGCTGTAGTGCTGGAAATTG 57.467 50.000 0.00 0.00 0.00 2.32
298 299 2.076100 CGCTGTAGTGCTGGAAATTGA 58.924 47.619 0.00 0.00 0.00 2.57
299 300 2.483877 CGCTGTAGTGCTGGAAATTGAA 59.516 45.455 0.00 0.00 0.00 2.69
300 301 3.058293 CGCTGTAGTGCTGGAAATTGAAA 60.058 43.478 0.00 0.00 0.00 2.69
301 302 4.379813 CGCTGTAGTGCTGGAAATTGAAAT 60.380 41.667 0.00 0.00 0.00 2.17
302 303 4.860907 GCTGTAGTGCTGGAAATTGAAATG 59.139 41.667 0.00 0.00 0.00 2.32
309 310 4.710865 TGCTGGAAATTGAAATGATGGCTA 59.289 37.500 0.00 0.00 0.00 3.93
310 311 5.364446 TGCTGGAAATTGAAATGATGGCTAT 59.636 36.000 0.00 0.00 0.00 2.97
311 313 5.694910 GCTGGAAATTGAAATGATGGCTATG 59.305 40.000 0.00 0.00 0.00 2.23
315 317 8.487848 TGGAAATTGAAATGATGGCTATGAAAT 58.512 29.630 0.00 0.00 0.00 2.17
319 321 9.893634 AATTGAAATGATGGCTATGAAATTGAA 57.106 25.926 0.00 0.00 0.00 2.69
320 322 9.893634 ATTGAAATGATGGCTATGAAATTGAAA 57.106 25.926 0.00 0.00 0.00 2.69
330 332 8.028354 TGGCTATGAAATTGAAATGTAGTGTTG 58.972 33.333 0.00 0.00 0.00 3.33
336 338 9.474920 TGAAATTGAAATGTAGTGTTGGAAATC 57.525 29.630 0.00 0.00 0.00 2.17
337 339 9.696917 GAAATTGAAATGTAGTGTTGGAAATCT 57.303 29.630 0.00 0.00 0.00 2.40
338 340 9.696917 AAATTGAAATGTAGTGTTGGAAATCTC 57.303 29.630 0.00 0.00 0.00 2.75
339 341 6.817765 TGAAATGTAGTGTTGGAAATCTCC 57.182 37.500 0.00 0.00 42.81 3.71
378 438 7.289395 TGTTATGAAATTGCGCTGAAATTTTG 58.711 30.769 15.49 0.00 37.35 2.44
441 502 5.645497 TGTTGTGAAATTTCAGTTTTTGGGG 59.355 36.000 21.05 0.00 37.98 4.96
442 503 5.683876 TGTGAAATTTCAGTTTTTGGGGA 57.316 34.783 21.05 0.00 37.98 4.81
477 538 6.292596 GCACTGAAACTTGAAAAACAACAACA 60.293 34.615 0.00 0.00 34.56 3.33
565 629 9.221775 CCAAAAATTAATTACGATGTGAGTAGC 57.778 33.333 0.01 0.00 0.00 3.58
612 676 4.830826 GGAACCTCGAACAAACATTTCT 57.169 40.909 0.00 0.00 0.00 2.52
615 679 3.551846 ACCTCGAACAAACATTTCTGGT 58.448 40.909 0.00 0.00 0.00 4.00
636 703 3.430862 GCGCGTGGCATCCTCAAA 61.431 61.111 8.43 0.00 42.87 2.69
637 704 2.976840 GCGCGTGGCATCCTCAAAA 61.977 57.895 8.43 0.00 42.87 2.44
692 1247 3.499918 CACAAACATCTGAGTGGGAAGAC 59.500 47.826 0.00 0.00 0.00 3.01
713 1268 3.821033 ACCATGCTACAGAAAAACCTCAC 59.179 43.478 0.00 0.00 0.00 3.51
855 1415 2.016393 ATCGATCGAGGCTTTCCGCA 62.016 55.000 23.84 0.00 41.67 5.69
963 1523 1.741327 GCCCGCCATGCATGAATTCT 61.741 55.000 28.31 0.00 0.00 2.40
973 1533 4.023739 TGCATGAATTCTTGATGCGAAG 57.976 40.909 21.92 0.00 44.52 3.79
982 1542 4.060038 TCTTGATGCGAAGATAAGGACC 57.940 45.455 0.00 0.00 0.00 4.46
990 1550 3.749404 CGAAGATAAGGACCGATCGATC 58.251 50.000 18.66 15.68 0.00 3.69
991 1551 3.426426 CGAAGATAAGGACCGATCGATCC 60.426 52.174 21.76 21.76 34.98 3.36
992 1552 2.085320 AGATAAGGACCGATCGATCCG 58.915 52.381 22.88 15.33 40.20 4.18
1038 1598 1.819229 GGATCTCAGCTCGCTGGAA 59.181 57.895 17.93 7.67 43.75 3.53
1118 1681 0.246635 AACGACGAAGATGGTGAGGG 59.753 55.000 0.00 0.00 0.00 4.30
1138 1701 2.355502 AGGAAGCCCTCGAGTCGA 59.644 61.111 15.64 15.64 38.86 4.20
1146 1709 4.813526 CTCGAGTCGACACCGCCG 62.814 72.222 19.50 12.33 35.37 6.46
1301 1870 2.418368 TCCGTCCATTCCATTCCAAG 57.582 50.000 0.00 0.00 0.00 3.61
1302 1871 1.633432 TCCGTCCATTCCATTCCAAGT 59.367 47.619 0.00 0.00 0.00 3.16
1303 1872 2.041081 TCCGTCCATTCCATTCCAAGTT 59.959 45.455 0.00 0.00 0.00 2.66
1304 1873 2.825532 CCGTCCATTCCATTCCAAGTTT 59.174 45.455 0.00 0.00 0.00 2.66
1305 1874 3.119495 CCGTCCATTCCATTCCAAGTTTC 60.119 47.826 0.00 0.00 0.00 2.78
1306 1875 3.119495 CGTCCATTCCATTCCAAGTTTCC 60.119 47.826 0.00 0.00 0.00 3.13
1307 1876 3.831911 GTCCATTCCATTCCAAGTTTCCA 59.168 43.478 0.00 0.00 0.00 3.53
1308 1877 4.082026 GTCCATTCCATTCCAAGTTTCCAG 60.082 45.833 0.00 0.00 0.00 3.86
1309 1878 3.368739 CCATTCCATTCCAAGTTTCCAGC 60.369 47.826 0.00 0.00 0.00 4.85
1443 2012 1.671742 GAGGTTTCAGCCTCGGTGA 59.328 57.895 0.00 0.00 44.64 4.02
1694 2263 0.602106 CCGAGCCTCGCATGATGAAT 60.602 55.000 9.01 0.00 38.82 2.57
1703 2272 1.954528 CATGATGAATCTGCCCGGC 59.045 57.895 1.04 1.04 0.00 6.13
1772 2341 3.953887 GGCGGCAGGCGAATTAGC 61.954 66.667 22.52 1.35 44.92 3.09
1829 2398 2.185350 CAGGCGCTCGAGAATGGT 59.815 61.111 18.75 0.00 0.00 3.55
1865 2434 2.433318 GAGCAGAGACCGTGGCAC 60.433 66.667 7.79 7.79 0.00 5.01
1901 2470 2.698763 GGACTCCGTCGGTGACCTC 61.699 68.421 22.20 9.87 32.65 3.85
2062 2735 5.390387 TGTTCAAAAATTAGGTGGGCTACT 58.610 37.500 0.00 0.00 0.00 2.57
2063 2736 6.544650 TGTTCAAAAATTAGGTGGGCTACTA 58.455 36.000 0.00 0.00 0.00 1.82
2064 2737 6.431852 TGTTCAAAAATTAGGTGGGCTACTAC 59.568 38.462 0.00 0.00 0.00 2.73
2065 2738 5.180271 TCAAAAATTAGGTGGGCTACTACG 58.820 41.667 0.00 0.00 0.00 3.51
2066 2739 4.831674 AAAATTAGGTGGGCTACTACGT 57.168 40.909 0.00 0.00 0.00 3.57
2067 2740 5.937975 AAAATTAGGTGGGCTACTACGTA 57.062 39.130 0.00 0.00 0.00 3.57
2068 2741 4.926140 AATTAGGTGGGCTACTACGTAC 57.074 45.455 0.00 0.00 29.87 3.67
2069 2742 3.652057 TTAGGTGGGCTACTACGTACT 57.348 47.619 0.00 0.00 29.87 2.73
2070 2743 1.760192 AGGTGGGCTACTACGTACTG 58.240 55.000 0.00 0.00 0.00 2.74
2071 2744 1.005215 AGGTGGGCTACTACGTACTGT 59.995 52.381 0.00 0.00 0.00 3.55
2072 2745 2.239654 AGGTGGGCTACTACGTACTGTA 59.760 50.000 0.00 0.00 0.00 2.74
2107 2780 7.119699 TGTGAGGCAAATGTTAGAAGTATTGAG 59.880 37.037 0.00 0.00 0.00 3.02
2176 2849 6.202188 CACAAATACTTTCTAGGTGTGTCGTT 59.798 38.462 0.00 0.00 0.00 3.85
2297 2973 5.343593 GCATCTCATACTGATACGTAAGCAC 59.656 44.000 0.00 0.00 45.62 4.40
2515 3197 1.903183 GGAAGTAGTGGAAGCAGAGGT 59.097 52.381 0.00 0.00 0.00 3.85
2548 3230 4.271816 CGGATCGGGAGCAGTCGG 62.272 72.222 0.00 0.00 0.00 4.79
2615 3298 0.824595 TCTCGAACGACAGGGTTCCA 60.825 55.000 0.00 0.00 42.57 3.53
2719 3402 0.034337 GACGGCTAGGGTTGTGTGAA 59.966 55.000 0.00 0.00 0.00 3.18
2723 3406 0.881796 GCTAGGGTTGTGTGAAAGGC 59.118 55.000 0.00 0.00 0.00 4.35
2913 3596 0.391927 TTAACCATTCCTGACCGGCG 60.392 55.000 0.00 0.00 0.00 6.46
2946 3630 1.524621 CTCGGCTCATTCCCGCAAT 60.525 57.895 0.00 0.00 45.19 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 7.446931 TCAGAGCCATTTCAGTGTAATTTTGTA 59.553 33.333 0.00 0.00 0.00 2.41
106 107 5.798125 TTATCCAGAGCCATTCTAGTGAG 57.202 43.478 0.00 0.00 33.83 3.51
175 176 4.998033 GGAGCAGTATTAGCCTGTAAATCC 59.002 45.833 0.00 0.00 32.41 3.01
211 212 3.065925 GTCCAATTTCATAGCCTGCACTC 59.934 47.826 0.00 0.00 0.00 3.51
222 223 7.528996 TTCAACTTCATCAGTCCAATTTCAT 57.471 32.000 0.00 0.00 32.94 2.57
254 255 9.116054 GCGCAATTTCATAACAAATTCAATTTT 57.884 25.926 0.30 0.00 34.37 1.82
255 256 8.505625 AGCGCAATTTCATAACAAATTCAATTT 58.494 25.926 11.47 0.00 34.37 1.82
256 257 7.958567 CAGCGCAATTTCATAACAAATTCAATT 59.041 29.630 11.47 0.00 34.37 2.32
257 258 7.118101 ACAGCGCAATTTCATAACAAATTCAAT 59.882 29.630 11.47 0.00 34.37 2.57
258 259 6.423302 ACAGCGCAATTTCATAACAAATTCAA 59.577 30.769 11.47 0.00 34.37 2.69
259 260 5.925397 ACAGCGCAATTTCATAACAAATTCA 59.075 32.000 11.47 0.00 34.37 2.57
260 261 6.393720 ACAGCGCAATTTCATAACAAATTC 57.606 33.333 11.47 0.00 34.37 2.17
261 262 7.062138 CACTACAGCGCAATTTCATAACAAATT 59.938 33.333 11.47 0.00 36.57 1.82
262 263 6.527722 CACTACAGCGCAATTTCATAACAAAT 59.472 34.615 11.47 0.00 0.00 2.32
263 264 5.855925 CACTACAGCGCAATTTCATAACAAA 59.144 36.000 11.47 0.00 0.00 2.83
264 265 5.389778 CACTACAGCGCAATTTCATAACAA 58.610 37.500 11.47 0.00 0.00 2.83
265 266 4.671508 GCACTACAGCGCAATTTCATAACA 60.672 41.667 11.47 0.00 0.00 2.41
266 267 3.786048 GCACTACAGCGCAATTTCATAAC 59.214 43.478 11.47 0.00 0.00 1.89
267 268 3.689161 AGCACTACAGCGCAATTTCATAA 59.311 39.130 11.47 0.00 40.15 1.90
268 269 3.063861 CAGCACTACAGCGCAATTTCATA 59.936 43.478 11.47 0.00 40.15 2.15
269 270 2.086869 AGCACTACAGCGCAATTTCAT 58.913 42.857 11.47 0.00 40.15 2.57
270 271 1.197492 CAGCACTACAGCGCAATTTCA 59.803 47.619 11.47 0.00 40.15 2.69
271 272 1.466360 CCAGCACTACAGCGCAATTTC 60.466 52.381 11.47 0.00 40.15 2.17
272 273 0.523072 CCAGCACTACAGCGCAATTT 59.477 50.000 11.47 0.00 40.15 1.82
273 274 0.321564 TCCAGCACTACAGCGCAATT 60.322 50.000 11.47 0.00 40.15 2.32
274 275 0.321564 TTCCAGCACTACAGCGCAAT 60.322 50.000 11.47 0.00 40.15 3.56
275 276 0.533978 TTTCCAGCACTACAGCGCAA 60.534 50.000 11.47 0.00 40.15 4.85
276 277 0.321564 ATTTCCAGCACTACAGCGCA 60.322 50.000 11.47 0.00 40.15 6.09
277 278 0.804989 AATTTCCAGCACTACAGCGC 59.195 50.000 0.00 0.00 40.15 5.92
278 279 2.076100 TCAATTTCCAGCACTACAGCG 58.924 47.619 0.00 0.00 40.15 5.18
279 280 4.503741 TTTCAATTTCCAGCACTACAGC 57.496 40.909 0.00 0.00 0.00 4.40
280 281 6.258230 TCATTTCAATTTCCAGCACTACAG 57.742 37.500 0.00 0.00 0.00 2.74
281 282 6.350361 CCATCATTTCAATTTCCAGCACTACA 60.350 38.462 0.00 0.00 0.00 2.74
282 283 6.038356 CCATCATTTCAATTTCCAGCACTAC 58.962 40.000 0.00 0.00 0.00 2.73
283 284 5.394443 GCCATCATTTCAATTTCCAGCACTA 60.394 40.000 0.00 0.00 0.00 2.74
284 285 4.622220 GCCATCATTTCAATTTCCAGCACT 60.622 41.667 0.00 0.00 0.00 4.40
285 286 3.619929 GCCATCATTTCAATTTCCAGCAC 59.380 43.478 0.00 0.00 0.00 4.40
286 287 3.516300 AGCCATCATTTCAATTTCCAGCA 59.484 39.130 0.00 0.00 0.00 4.41
287 288 4.133013 AGCCATCATTTCAATTTCCAGC 57.867 40.909 0.00 0.00 0.00 4.85
288 289 7.046292 TCATAGCCATCATTTCAATTTCCAG 57.954 36.000 0.00 0.00 0.00 3.86
289 290 7.421087 TTCATAGCCATCATTTCAATTTCCA 57.579 32.000 0.00 0.00 0.00 3.53
290 291 8.897872 ATTTCATAGCCATCATTTCAATTTCC 57.102 30.769 0.00 0.00 0.00 3.13
292 293 9.893634 TCAATTTCATAGCCATCATTTCAATTT 57.106 25.926 0.00 0.00 0.00 1.82
293 294 9.893634 TTCAATTTCATAGCCATCATTTCAATT 57.106 25.926 0.00 0.00 0.00 2.32
294 295 9.893634 TTTCAATTTCATAGCCATCATTTCAAT 57.106 25.926 0.00 0.00 0.00 2.57
295 296 9.893634 ATTTCAATTTCATAGCCATCATTTCAA 57.106 25.926 0.00 0.00 0.00 2.69
296 297 9.320352 CATTTCAATTTCATAGCCATCATTTCA 57.680 29.630 0.00 0.00 0.00 2.69
297 298 9.321562 ACATTTCAATTTCATAGCCATCATTTC 57.678 29.630 0.00 0.00 0.00 2.17
299 300 9.976511 CTACATTTCAATTTCATAGCCATCATT 57.023 29.630 0.00 0.00 0.00 2.57
300 301 9.139734 ACTACATTTCAATTTCATAGCCATCAT 57.860 29.630 0.00 0.00 0.00 2.45
301 302 8.407832 CACTACATTTCAATTTCATAGCCATCA 58.592 33.333 0.00 0.00 0.00 3.07
302 303 8.408601 ACACTACATTTCAATTTCATAGCCATC 58.591 33.333 0.00 0.00 0.00 3.51
310 311 9.474920 GATTTCCAACACTACATTTCAATTTCA 57.525 29.630 0.00 0.00 0.00 2.69
311 313 9.696917 AGATTTCCAACACTACATTTCAATTTC 57.303 29.630 0.00 0.00 0.00 2.17
315 317 7.004086 AGGAGATTTCCAACACTACATTTCAA 58.996 34.615 4.89 0.00 46.64 2.69
319 321 6.542821 TCAAGGAGATTTCCAACACTACATT 58.457 36.000 4.89 0.00 46.64 2.71
320 322 6.126863 TCAAGGAGATTTCCAACACTACAT 57.873 37.500 4.89 0.00 46.64 2.29
324 326 5.053978 ACTTCAAGGAGATTTCCAACACT 57.946 39.130 4.89 0.00 46.64 3.55
330 332 7.436933 ACAAATTCAACTTCAAGGAGATTTCC 58.563 34.615 0.00 0.00 44.39 3.13
336 338 9.748708 TTTCATAACAAATTCAACTTCAAGGAG 57.251 29.630 0.00 0.00 0.00 3.69
437 498 5.815233 TTCAGTGCAATTTAAAATCCCCA 57.185 34.783 0.00 0.00 0.00 4.96
533 597 7.600752 CACATCGTAATTAATTTTTGGTGGGTT 59.399 33.333 5.91 0.00 0.00 4.11
592 656 4.036380 ACCAGAAATGTTTGTTCGAGGTTC 59.964 41.667 0.00 0.00 35.87 3.62
609 673 4.680237 CCACGCGCCTCACCAGAA 62.680 66.667 5.73 0.00 0.00 3.02
648 722 3.620300 TAACTCACCACGCGCCTCG 62.620 63.158 5.73 0.00 45.38 4.63
692 1247 4.074970 AGTGAGGTTTTTCTGTAGCATGG 58.925 43.478 0.00 0.00 0.00 3.66
698 1253 5.451908 CGTACGTAGTGAGGTTTTTCTGTA 58.548 41.667 7.22 0.00 45.73 2.74
713 1268 6.703857 CGAATATAGGATCTTCCGTACGTAG 58.296 44.000 15.21 11.09 42.75 3.51
897 1457 1.979469 CGTGATCGATGCGGATTACTC 59.021 52.381 0.54 0.00 39.71 2.59
926 1486 2.224314 GGGCACGTGAGAGAAAAGAAAG 59.776 50.000 22.23 0.00 0.00 2.62
963 1523 2.429250 TCGGTCCTTATCTTCGCATCAA 59.571 45.455 0.00 0.00 0.00 2.57
973 1533 1.132643 CCGGATCGATCGGTCCTTATC 59.867 57.143 37.26 21.22 42.33 1.75
1050 1610 1.153349 GGACCTTCCCATCAGCGAC 60.153 63.158 0.00 0.00 0.00 5.19
1255 1824 4.451150 GTGAGGTGGCGATGGCGA 62.451 66.667 0.00 0.00 41.24 5.54
1256 1825 4.758251 TGTGAGGTGGCGATGGCG 62.758 66.667 0.00 0.00 41.24 5.69
1257 1826 2.359850 TTGTGAGGTGGCGATGGC 60.360 61.111 0.00 0.00 38.90 4.40
1258 1827 1.746615 CCTTGTGAGGTGGCGATGG 60.747 63.158 0.00 0.00 38.32 3.51
1259 1828 3.895025 CCTTGTGAGGTGGCGATG 58.105 61.111 0.00 0.00 38.32 3.84
1301 1870 1.484038 TAATGGGCATGGCTGGAAAC 58.516 50.000 19.78 1.39 0.00 2.78
1302 1871 2.435069 CAATAATGGGCATGGCTGGAAA 59.565 45.455 19.78 1.92 0.00 3.13
1303 1872 2.040939 CAATAATGGGCATGGCTGGAA 58.959 47.619 19.78 3.38 0.00 3.53
1304 1873 1.707106 CAATAATGGGCATGGCTGGA 58.293 50.000 19.78 3.93 0.00 3.86
1305 1874 0.034337 GCAATAATGGGCATGGCTGG 59.966 55.000 19.78 0.00 0.00 4.85
1306 1875 0.034337 GGCAATAATGGGCATGGCTG 59.966 55.000 19.78 9.32 35.66 4.85
1307 1876 0.398806 TGGCAATAATGGGCATGGCT 60.399 50.000 19.78 1.57 38.95 4.75
1308 1877 2.134991 TGGCAATAATGGGCATGGC 58.865 52.632 11.56 11.56 35.74 4.40
1335 1904 0.250640 AGCTCGAATGGATGGATGCC 60.251 55.000 0.00 0.00 0.00 4.40
1443 2012 1.684049 CCTTCCTCTCCAGCTCCGT 60.684 63.158 0.00 0.00 0.00 4.69
1514 2083 4.637489 CTCTCGATCCGCCGCCTG 62.637 72.222 0.00 0.00 0.00 4.85
1703 2272 4.180946 CTCGTCGGTGCCTCCTCG 62.181 72.222 0.00 0.00 34.49 4.63
1844 2413 2.626780 CCACGGTCTCTGCTCGACA 61.627 63.158 0.00 0.00 33.11 4.35
1890 2459 0.680061 AGTTTCCTGAGGTCACCGAC 59.320 55.000 0.00 0.00 0.00 4.79
1901 2470 0.886490 ACTGCGCCTTGAGTTTCCTG 60.886 55.000 4.18 0.00 0.00 3.86
2062 2735 6.128200 CCTCACACAACATACTACAGTACGTA 60.128 42.308 0.00 0.00 32.72 3.57
2063 2736 5.335426 CCTCACACAACATACTACAGTACGT 60.335 44.000 0.00 0.00 32.72 3.57
2064 2737 5.093457 CCTCACACAACATACTACAGTACG 58.907 45.833 0.00 0.00 32.72 3.67
2065 2738 4.863131 GCCTCACACAACATACTACAGTAC 59.137 45.833 0.00 0.00 32.72 2.73
2066 2739 4.525100 TGCCTCACACAACATACTACAGTA 59.475 41.667 0.00 0.00 34.67 2.74
2067 2740 3.323691 TGCCTCACACAACATACTACAGT 59.676 43.478 0.00 0.00 0.00 3.55
2068 2741 3.925379 TGCCTCACACAACATACTACAG 58.075 45.455 0.00 0.00 0.00 2.74
2069 2742 4.344359 TTGCCTCACACAACATACTACA 57.656 40.909 0.00 0.00 0.00 2.74
2070 2743 5.181245 ACATTTGCCTCACACAACATACTAC 59.819 40.000 0.00 0.00 0.00 2.73
2071 2744 5.312895 ACATTTGCCTCACACAACATACTA 58.687 37.500 0.00 0.00 0.00 1.82
2072 2745 4.144297 ACATTTGCCTCACACAACATACT 58.856 39.130 0.00 0.00 0.00 2.12
2142 2815 5.296813 AGAAAGTATTTGTGCCACGATTC 57.703 39.130 0.00 0.00 39.27 2.52
2176 2849 1.466950 CGCGTCCTTGATAAAGGCAAA 59.533 47.619 3.58 0.00 39.80 3.68
2194 2867 3.636282 ATTTTCAACACTAACCACCGC 57.364 42.857 0.00 0.00 0.00 5.68
2233 2906 7.218228 TGTTTACTGTCTACTCGTGGATTAA 57.782 36.000 0.00 0.00 0.00 1.40
2425 3107 4.827087 CGATGCCGAGGCTGCTGT 62.827 66.667 15.75 0.00 42.51 4.40
2515 3197 3.307906 CGTCCCCTTCACCGACCA 61.308 66.667 0.00 0.00 0.00 4.02
2552 3234 3.194005 AGGTTTTTGAAGAGCGTCTCA 57.806 42.857 9.09 0.00 32.06 3.27
2562 3244 5.508320 GGAGAACGGCAATAAGGTTTTTGAA 60.508 40.000 0.00 0.00 0.00 2.69
2615 3298 2.686835 GGGAGAGCAGGTGCCTCT 60.687 66.667 15.58 10.45 43.38 3.69
2650 3333 1.071471 GCGATCCCATCCCAACGAT 59.929 57.895 0.00 0.00 0.00 3.73
2655 3338 4.870618 TCCGGCGATCCCATCCCA 62.871 66.667 9.30 0.00 0.00 4.37
2719 3402 1.765314 ACTCAGTTCACTCACTGCCTT 59.235 47.619 0.00 0.00 43.51 4.35
2723 3406 3.322254 ACCCTAACTCAGTTCACTCACTG 59.678 47.826 0.00 0.00 44.96 3.66
2913 3596 2.930682 AGCCGAGTCGAAGCTTATTTTC 59.069 45.455 15.64 0.00 31.27 2.29


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

AutoCloner maintained by Alex Coulton.