Multiple sequence alignment - TraesCS6B01G090900

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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 TraesCS6B01G090900 chr6B 100.000 2228 0 0 1 2228 66780195 66777968 0.000000e+00 4115.0
1 TraesCS6B01G090900 chr6B 94.993 1498 45 10 731 2228 66746879 66745412 0.000000e+00 2324.0
2 TraesCS6B01G090900 chr6B 91.600 250 18 2 470 717 66747458 66747210 2.120000e-90 342.0
3 TraesCS6B01G090900 chrUn 92.420 343 21 2 978 1316 100515558 100515899 3.330000e-133 484.0
4 TraesCS6B01G090900 chrUn 86.828 372 27 9 753 1119 100677425 100677779 1.600000e-106 396.0
5 TraesCS6B01G090900 chrUn 81.898 453 59 16 1553 2000 100515935 100516369 5.850000e-96 361.0
6 TraesCS6B01G090900 chrUn 91.703 229 18 1 1999 2226 100516407 100516635 1.280000e-82 316.0
7 TraesCS6B01G090900 chrUn 90.230 174 16 1 749 922 100508236 100508408 2.230000e-55 226.0
8 TraesCS6B01G090900 chr6A 79.859 710 83 40 1553 2226 35946309 35945624 4.330000e-127 464.0
9 TraesCS6B01G090900 chr6A 83.946 299 24 12 749 1041 35954659 35954379 4.720000e-67 265.0
10 TraesCS6B01G090900 chr6A 89.873 158 11 2 1163 1316 35946501 35946345 4.850000e-47 198.0
11 TraesCS6B01G090900 chr6A 96.667 90 2 1 1066 1154 35954386 35954297 4.960000e-32 148.0
12 TraesCS6B01G090900 chr6A 83.893 149 21 2 1415 1562 543521629 543521775 2.980000e-29 139.0
13 TraesCS6B01G090900 chr6D 86.626 329 39 5 40 365 318810171 318810497 2.100000e-95 359.0
14 TraesCS6B01G090900 chr6D 79.825 114 16 7 1440 1547 82129961 82129849 2.370000e-10 76.8
15 TraesCS6B01G090900 chr2D 77.377 610 94 30 44 633 6660004 6659419 2.760000e-84 322.0
16 TraesCS6B01G090900 chr2D 88.235 68 8 0 1429 1496 640583730 640583797 5.100000e-12 82.4
17 TraesCS6B01G090900 chr2D 86.538 52 5 2 1495 1545 486488540 486488590 3.090000e-04 56.5
18 TraesCS6B01G090900 chr4D 82.934 334 46 9 39 365 507931869 507932198 7.780000e-75 291.0
19 TraesCS6B01G090900 chr1A 82.927 328 49 7 39 362 516065177 516065501 2.800000e-74 289.0
20 TraesCS6B01G090900 chr3D 82.530 332 52 6 39 366 26101650 26101979 1.010000e-73 287.0
21 TraesCS6B01G090900 chr3D 81.381 333 54 8 39 366 56318393 56318064 4.720000e-67 265.0
22 TraesCS6B01G090900 chr7D 82.121 330 54 5 39 365 541521347 541521020 6.060000e-71 278.0
23 TraesCS6B01G090900 chr7D 86.275 51 7 0 1495 1545 181973423 181973473 3.090000e-04 56.5
24 TraesCS6B01G090900 chr4A 82.121 330 50 8 40 365 159475891 159476215 7.840000e-70 274.0
25 TraesCS6B01G090900 chr1D 80.896 335 57 7 35 365 23254595 23254926 7.890000e-65 257.0
26 TraesCS6B01G090900 chr7B 80.208 192 29 9 1373 1557 468110732 468110543 3.860000e-28 135.0
27 TraesCS6B01G090900 chr5D 83.871 124 15 3 1430 1551 557480664 557480544 1.810000e-21 113.0
28 TraesCS6B01G090900 chr4B 79.730 148 23 5 1373 1519 483765903 483766044 1.410000e-17 100.0
29 TraesCS6B01G090900 chr1B 81.915 94 12 5 1458 1548 411177059 411177150 8.530000e-10 75.0
30 TraesCS6B01G090900 chr3A 97.436 39 1 0 1507 1545 630040373 630040335 1.430000e-07 67.6
31 TraesCS6B01G090900 chr2B 100.000 36 0 0 563 598 37083020 37083055 1.430000e-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 TraesCS6B01G090900 chr6B 66777968 66780195 2227 True 4115 4115 100.000000 1 2228 1 chr6B.!!$R1 2227
1 TraesCS6B01G090900 chr6B 66745412 66747458 2046 True 1333 2324 93.296500 470 2228 2 chr6B.!!$R2 1758
2 TraesCS6B01G090900 chrUn 100515558 100516635 1077 False 387 484 88.673667 978 2226 3 chrUn.!!$F3 1248
3 TraesCS6B01G090900 chr6A 35945624 35946501 877 True 331 464 84.866000 1163 2226 2 chr6A.!!$R1 1063
4 TraesCS6B01G090900 chr2D 6659419 6660004 585 True 322 322 77.377000 44 633 1 chr2D.!!$R1 589

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
153 156 0.108756 GTCTCACTAAGGCCACCGAC 60.109 60.0 5.01 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1367 1727 1.480205 AAACGTCAGACGGTGTTACG 58.52 50.0 26.31 10.01 42.91 3.18 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 4.933064 CGTCGGAGCCGGATGAGC 62.933 72.222 5.05 0.00 40.25 4.26
34 35 4.593864 GTCGGAGCCGGATGAGCC 62.594 72.222 5.05 0.00 40.25 4.70
43 44 4.424711 GGATGAGCCGCCACCCAA 62.425 66.667 0.00 0.00 0.00 4.12
44 45 2.361104 GATGAGCCGCCACCCAAA 60.361 61.111 0.00 0.00 0.00 3.28
45 46 2.676471 ATGAGCCGCCACCCAAAC 60.676 61.111 0.00 0.00 0.00 2.93
46 47 3.505790 ATGAGCCGCCACCCAAACA 62.506 57.895 0.00 0.00 0.00 2.83
47 48 3.670377 GAGCCGCCACCCAAACAC 61.670 66.667 0.00 0.00 0.00 3.32
50 51 4.904590 CCGCCACCCAAACACCCA 62.905 66.667 0.00 0.00 0.00 4.51
51 52 3.601685 CGCCACCCAAACACCCAC 61.602 66.667 0.00 0.00 0.00 4.61
52 53 3.230990 GCCACCCAAACACCCACC 61.231 66.667 0.00 0.00 0.00 4.61
60 61 3.383031 AAACACCCACCACCACCCC 62.383 63.158 0.00 0.00 0.00 4.95
65 66 4.329545 CCACCACCACCCCAGACG 62.330 72.222 0.00 0.00 0.00 4.18
66 67 3.238497 CACCACCACCCCAGACGA 61.238 66.667 0.00 0.00 0.00 4.20
71 72 2.758327 CCACCCCAGACGATCCGA 60.758 66.667 0.00 0.00 0.00 4.55
76 77 1.605058 CCCCAGACGATCCGAAGTGT 61.605 60.000 0.00 0.00 0.00 3.55
80 81 0.731417 AGACGATCCGAAGTGTACCG 59.269 55.000 0.00 0.00 0.00 4.02
142 145 0.956633 ACCAACTTCGCGTCTCACTA 59.043 50.000 5.77 0.00 0.00 2.74
143 146 1.338973 ACCAACTTCGCGTCTCACTAA 59.661 47.619 5.77 0.00 0.00 2.24
148 151 1.529152 TTCGCGTCTCACTAAGGCCA 61.529 55.000 5.01 0.00 0.00 5.36
151 154 1.153823 CGTCTCACTAAGGCCACCG 60.154 63.158 5.01 0.00 0.00 4.94
153 156 0.108756 GTCTCACTAAGGCCACCGAC 60.109 60.000 5.01 0.00 0.00 4.79
170 173 1.596895 GACCACGAGACCTGGAGGAC 61.597 65.000 0.00 0.00 38.94 3.85
171 174 2.701780 CCACGAGACCTGGAGGACG 61.702 68.421 0.00 5.13 38.94 4.79
185 188 0.336737 AGGACGGGAGAGGAGACAAT 59.663 55.000 0.00 0.00 0.00 2.71
186 189 0.461961 GGACGGGAGAGGAGACAATG 59.538 60.000 0.00 0.00 0.00 2.82
188 191 0.978146 ACGGGAGAGGAGACAATGGG 60.978 60.000 0.00 0.00 0.00 4.00
190 193 0.985490 GGGAGAGGAGACAATGGGCT 60.985 60.000 0.00 0.00 0.00 5.19
191 194 0.915364 GGAGAGGAGACAATGGGCTT 59.085 55.000 0.00 0.00 0.00 4.35
192 195 2.119495 GGAGAGGAGACAATGGGCTTA 58.881 52.381 0.00 0.00 0.00 3.09
195 198 1.141858 GAGGAGACAATGGGCTTAGGG 59.858 57.143 0.00 0.00 0.00 3.53
196 199 0.466372 GGAGACAATGGGCTTAGGGC 60.466 60.000 0.00 0.00 40.90 5.19
197 200 0.255890 GAGACAATGGGCTTAGGGCA 59.744 55.000 0.00 0.00 44.01 5.36
198 201 0.929244 AGACAATGGGCTTAGGGCAT 59.071 50.000 0.00 0.00 44.01 4.40
201 205 1.151450 AATGGGCTTAGGGCATCCG 59.849 57.895 0.00 0.00 44.01 4.18
206 210 2.823829 GCTTAGGGCATCCGCAACG 61.824 63.158 0.00 0.00 41.24 4.10
208 212 3.613877 TTAGGGCATCCGCAACGCA 62.614 57.895 0.00 0.00 41.24 5.24
210 214 4.776647 GGGCATCCGCAACGCAAC 62.777 66.667 0.00 0.00 41.24 4.17
213 217 3.418913 CATCCGCAACGCAACCGA 61.419 61.111 0.00 0.00 38.29 4.69
266 270 2.502080 GACTGGACGCGACGACAG 60.502 66.667 15.93 16.94 39.58 3.51
278 282 0.323178 GACGACAGGGACCTACCAGA 60.323 60.000 0.00 0.00 41.20 3.86
282 286 1.689582 CAGGGACCTACCAGACCCC 60.690 68.421 0.00 0.00 42.97 4.95
283 287 1.867487 AGGGACCTACCAGACCCCT 60.867 63.158 0.00 0.00 42.97 4.79
285 289 0.566679 GGGACCTACCAGACCCCTAT 59.433 60.000 0.00 0.00 41.20 2.57
286 290 1.061579 GGGACCTACCAGACCCCTATT 60.062 57.143 0.00 0.00 41.20 1.73
292 296 2.006415 CCAGACCCCTATTGGCCCA 61.006 63.158 0.00 0.00 0.00 5.36
306 310 4.278513 CCCAGCCGGACCCAAACA 62.279 66.667 5.05 0.00 0.00 2.83
318 322 1.966451 CCAAACAGGTCCGGACAGC 60.966 63.158 34.40 19.09 0.00 4.40
331 336 4.626081 ACAGCCCCTGTCGCACAC 62.626 66.667 0.00 0.00 41.21 3.82
370 375 4.660938 GCCACCACCGCCTCCTTT 62.661 66.667 0.00 0.00 0.00 3.11
371 376 2.359975 CCACCACCGCCTCCTTTC 60.360 66.667 0.00 0.00 0.00 2.62
380 396 1.384191 GCCTCCTTTCCACCACCAT 59.616 57.895 0.00 0.00 0.00 3.55
381 397 0.967380 GCCTCCTTTCCACCACCATG 60.967 60.000 0.00 0.00 0.00 3.66
392 408 1.379916 CCACCATGAGGGAGCAACA 59.620 57.895 0.00 0.00 41.15 3.33
397 413 2.894257 ATGAGGGAGCAACACCGCA 61.894 57.895 0.00 0.00 40.79 5.69
401 417 3.058160 GGAGCAACACCGCAGCAT 61.058 61.111 0.00 0.00 0.00 3.79
402 418 2.177531 GAGCAACACCGCAGCATG 59.822 61.111 0.00 0.00 40.87 4.06
434 450 2.297895 CCACCCGAACCCAGATGGA 61.298 63.158 0.00 0.00 37.39 3.41
435 451 1.078426 CACCCGAACCCAGATGGAC 60.078 63.158 0.00 0.00 37.39 4.02
440 456 1.847798 CGAACCCAGATGGACCCCAA 61.848 60.000 0.00 0.00 36.95 4.12
455 471 0.404040 CCCAAAAGGGCACAGACCTA 59.596 55.000 0.00 0.00 42.44 3.08
460 476 3.562681 AGGGCACAGACCTAGGCCA 62.563 63.158 9.30 0.00 40.73 5.36
461 477 2.269241 GGCACAGACCTAGGCCAC 59.731 66.667 9.30 0.46 45.70 5.01
463 479 2.125512 CACAGACCTAGGCCACGC 60.126 66.667 9.30 0.00 0.00 5.34
464 480 3.760035 ACAGACCTAGGCCACGCG 61.760 66.667 9.30 3.53 0.00 6.01
559 575 4.596585 CCAAGCCACAACCCCCGT 62.597 66.667 0.00 0.00 0.00 5.28
671 689 0.743345 GGCGGCGATTGTAAGGAAGT 60.743 55.000 12.98 0.00 0.00 3.01
680 698 3.536956 TTGTAAGGAAGTATGGCGAGG 57.463 47.619 0.00 0.00 0.00 4.63
706 724 1.003442 TGGAGGAGAGGTGGGGATG 59.997 63.158 0.00 0.00 0.00 3.51
717 735 3.489513 GGGGATGGAGGGGGTTCG 61.490 72.222 0.00 0.00 0.00 3.95
718 736 4.191015 GGGATGGAGGGGGTTCGC 62.191 72.222 0.00 0.00 0.00 4.70
719 737 4.191015 GGATGGAGGGGGTTCGCC 62.191 72.222 0.00 0.00 36.67 5.54
747 1082 0.994263 GCATCATGCGCTTTTTCACC 59.006 50.000 9.73 0.00 31.71 4.02
756 1091 2.483876 CGCTTTTTCACCAGTCTCTCA 58.516 47.619 0.00 0.00 0.00 3.27
858 1193 4.455606 AGCAAAGTTCAGCTGACTAAACT 58.544 39.130 18.03 14.56 40.13 2.66
865 1200 4.193826 TCAGCTGACTAAACTAGGCAAG 57.806 45.455 13.74 0.00 44.71 4.01
872 1207 4.755123 TGACTAAACTAGGCAAGCAAAGTC 59.245 41.667 0.00 0.00 41.86 3.01
891 1226 2.516930 ATCGGGCGGCAAATCCAG 60.517 61.111 12.47 0.00 34.01 3.86
902 1237 0.179215 CAAATCCAGCGACGCTTCAC 60.179 55.000 21.97 0.00 36.40 3.18
903 1238 1.298859 AAATCCAGCGACGCTTCACC 61.299 55.000 21.97 0.00 36.40 4.02
904 1239 2.449031 AATCCAGCGACGCTTCACCA 62.449 55.000 21.97 2.35 36.40 4.17
905 1240 3.414700 CCAGCGACGCTTCACCAC 61.415 66.667 21.97 0.00 36.40 4.16
906 1241 2.356313 CAGCGACGCTTCACCACT 60.356 61.111 21.97 0.00 36.40 4.00
907 1242 2.356313 AGCGACGCTTCACCACTG 60.356 61.111 18.46 0.00 33.89 3.66
909 1244 2.738521 CGACGCTTCACCACTGGG 60.739 66.667 0.00 0.00 41.29 4.45
910 1245 2.358737 GACGCTTCACCACTGGGG 60.359 66.667 0.00 0.00 44.81 4.96
927 1262 8.488651 CCACTGGGGTACGATATATAATTTTC 57.511 38.462 0.00 0.00 0.00 2.29
928 1263 8.098286 CCACTGGGGTACGATATATAATTTTCA 58.902 37.037 0.00 0.00 0.00 2.69
929 1264 8.932791 CACTGGGGTACGATATATAATTTTCAC 58.067 37.037 0.00 0.00 0.00 3.18
930 1265 8.653191 ACTGGGGTACGATATATAATTTTCACA 58.347 33.333 0.00 0.00 0.00 3.58
931 1266 8.836268 TGGGGTACGATATATAATTTTCACAC 57.164 34.615 0.00 0.00 0.00 3.82
932 1267 8.430431 TGGGGTACGATATATAATTTTCACACA 58.570 33.333 0.00 0.00 0.00 3.72
951 1286 4.250464 CACAAGTACGTATGTGGGTGAAT 58.750 43.478 17.73 0.00 42.46 2.57
952 1287 5.412640 CACAAGTACGTATGTGGGTGAATA 58.587 41.667 17.73 0.00 42.46 1.75
953 1288 6.046593 CACAAGTACGTATGTGGGTGAATAT 58.953 40.000 17.73 0.00 42.46 1.28
954 1289 7.204604 CACAAGTACGTATGTGGGTGAATATA 58.795 38.462 17.73 0.00 42.46 0.86
955 1290 7.870954 CACAAGTACGTATGTGGGTGAATATAT 59.129 37.037 17.73 0.00 42.46 0.86
956 1291 8.426489 ACAAGTACGTATGTGGGTGAATATATT 58.574 33.333 0.00 0.00 0.00 1.28
957 1292 9.268268 CAAGTACGTATGTGGGTGAATATATTT 57.732 33.333 0.00 0.00 0.00 1.40
958 1293 9.841295 AAGTACGTATGTGGGTGAATATATTTT 57.159 29.630 0.00 0.00 0.00 1.82
959 1294 9.841295 AGTACGTATGTGGGTGAATATATTTTT 57.159 29.630 0.00 0.00 0.00 1.94
961 1296 8.740123 ACGTATGTGGGTGAATATATTTTTCA 57.260 30.769 0.00 0.00 0.00 2.69
1331 1691 4.082571 AGCATAATCCGCCAGCATTATTTC 60.083 41.667 0.00 0.00 0.00 2.17
1383 1743 4.929198 ACGTAACACCGTCTGACG 57.071 55.556 22.49 22.49 42.11 4.35
1438 1798 8.356657 AGAAAATTGAACGTATCATCCAAACAA 58.643 29.630 0.00 0.00 38.03 2.83
1524 1884 2.550830 AGGACAGAATTGCTTCGTGT 57.449 45.000 0.00 0.00 36.45 4.49
1529 1889 2.287915 ACAGAATTGCTTCGTGTCACAC 59.712 45.455 0.00 0.00 36.45 3.82
1708 2074 3.639538 CCAGTCATGCGTATGTAGGTAC 58.360 50.000 13.39 3.92 35.73 3.34
1723 2089 5.513233 TGTAGGTACGAGAGGTCCTATTTT 58.487 41.667 0.00 0.00 40.56 1.82
1726 2092 3.450096 GGTACGAGAGGTCCTATTTTGGT 59.550 47.826 0.00 0.00 0.00 3.67
1763 2129 1.672356 ACGGAAGTGGCACTCATGC 60.672 57.895 22.31 10.77 46.97 4.06
1849 2215 1.001048 TCGACCGTTGACGAGTTGAAT 60.001 47.619 4.91 0.00 43.02 2.57
2147 2553 6.163476 ACATATATGGGTGCACGTACTTATG 58.837 40.000 16.96 16.03 0.00 1.90
2153 2560 3.063452 GGGTGCACGTACTTATGTTCATG 59.937 47.826 11.45 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.933064 GCTCATCCGGCTCCGACG 62.933 72.222 10.28 0.00 42.83 5.12
17 18 4.593864 GGCTCATCCGGCTCCGAC 62.594 72.222 10.28 0.00 42.83 4.79
26 27 3.936772 TTTGGGTGGCGGCTCATCC 62.937 63.158 11.43 12.22 38.38 3.51
27 28 2.361104 TTTGGGTGGCGGCTCATC 60.361 61.111 11.43 3.64 0.00 2.92
28 29 2.676471 GTTTGGGTGGCGGCTCAT 60.676 61.111 11.43 0.00 0.00 2.90
29 30 4.196778 TGTTTGGGTGGCGGCTCA 62.197 61.111 11.43 3.20 0.00 4.26
30 31 3.670377 GTGTTTGGGTGGCGGCTC 61.670 66.667 11.43 6.49 0.00 4.70
33 34 4.904590 TGGGTGTTTGGGTGGCGG 62.905 66.667 0.00 0.00 0.00 6.13
34 35 3.601685 GTGGGTGTTTGGGTGGCG 61.602 66.667 0.00 0.00 0.00 5.69
35 36 3.230990 GGTGGGTGTTTGGGTGGC 61.231 66.667 0.00 0.00 0.00 5.01
36 37 2.131067 GTGGTGGGTGTTTGGGTGG 61.131 63.158 0.00 0.00 0.00 4.61
37 38 2.131067 GGTGGTGGGTGTTTGGGTG 61.131 63.158 0.00 0.00 0.00 4.61
38 39 2.280753 GGTGGTGGGTGTTTGGGT 59.719 61.111 0.00 0.00 0.00 4.51
39 40 2.131067 GTGGTGGTGGGTGTTTGGG 61.131 63.158 0.00 0.00 0.00 4.12
40 41 2.131067 GGTGGTGGTGGGTGTTTGG 61.131 63.158 0.00 0.00 0.00 3.28
41 42 2.131067 GGGTGGTGGTGGGTGTTTG 61.131 63.158 0.00 0.00 0.00 2.93
42 43 2.280753 GGGTGGTGGTGGGTGTTT 59.719 61.111 0.00 0.00 0.00 2.83
43 44 3.828023 GGGGTGGTGGTGGGTGTT 61.828 66.667 0.00 0.00 0.00 3.32
45 46 4.284550 CTGGGGTGGTGGTGGGTG 62.285 72.222 0.00 0.00 0.00 4.61
46 47 4.525028 TCTGGGGTGGTGGTGGGT 62.525 66.667 0.00 0.00 0.00 4.51
47 48 3.966543 GTCTGGGGTGGTGGTGGG 61.967 72.222 0.00 0.00 0.00 4.61
48 49 4.329545 CGTCTGGGGTGGTGGTGG 62.330 72.222 0.00 0.00 0.00 4.61
49 50 2.521958 GATCGTCTGGGGTGGTGGTG 62.522 65.000 0.00 0.00 0.00 4.17
50 51 2.203938 ATCGTCTGGGGTGGTGGT 60.204 61.111 0.00 0.00 0.00 4.16
51 52 2.584608 GATCGTCTGGGGTGGTGG 59.415 66.667 0.00 0.00 0.00 4.61
52 53 2.584608 GGATCGTCTGGGGTGGTG 59.415 66.667 0.00 0.00 0.00 4.17
60 61 1.531264 CGGTACACTTCGGATCGTCTG 60.531 57.143 0.00 0.00 0.00 3.51
61 62 0.731417 CGGTACACTTCGGATCGTCT 59.269 55.000 0.00 0.00 0.00 4.18
65 66 1.227176 GGGCGGTACACTTCGGATC 60.227 63.158 0.00 0.00 0.00 3.36
66 67 1.546589 TTGGGCGGTACACTTCGGAT 61.547 55.000 0.00 0.00 0.00 4.18
71 72 1.072505 CAGGTTGGGCGGTACACTT 59.927 57.895 0.00 0.00 0.00 3.16
93 94 4.269523 GTGGCACAGGCTGGTGGA 62.270 66.667 20.34 0.00 41.80 4.02
129 131 1.214589 GGCCTTAGTGAGACGCGAA 59.785 57.895 15.93 0.00 0.00 4.70
134 136 0.108756 GTCGGTGGCCTTAGTGAGAC 60.109 60.000 3.32 0.29 0.00 3.36
142 145 4.003788 CTCGTGGTCGGTGGCCTT 62.004 66.667 3.32 0.00 37.69 4.35
143 146 4.988716 TCTCGTGGTCGGTGGCCT 62.989 66.667 3.32 0.00 37.69 5.19
148 151 2.989824 CCAGGTCTCGTGGTCGGT 60.990 66.667 0.99 0.00 35.03 4.69
151 154 1.304217 TCCTCCAGGTCTCGTGGTC 60.304 63.158 8.07 0.00 39.97 4.02
153 156 2.701780 CGTCCTCCAGGTCTCGTGG 61.702 68.421 2.55 2.55 40.34 4.94
170 173 1.826024 CCCATTGTCTCCTCTCCCG 59.174 63.158 0.00 0.00 0.00 5.14
171 174 0.985490 AGCCCATTGTCTCCTCTCCC 60.985 60.000 0.00 0.00 0.00 4.30
175 178 1.141858 CCCTAAGCCCATTGTCTCCTC 59.858 57.143 0.00 0.00 0.00 3.71
185 188 4.189580 GCGGATGCCCTAAGCCCA 62.190 66.667 0.00 0.00 42.71 5.36
186 189 3.714487 TTGCGGATGCCCTAAGCCC 62.714 63.158 0.00 0.00 42.71 5.19
188 191 2.823829 CGTTGCGGATGCCCTAAGC 61.824 63.158 0.00 0.00 41.78 3.09
190 193 2.822255 GCGTTGCGGATGCCCTAA 60.822 61.111 0.00 0.00 41.78 2.69
191 194 3.613877 TTGCGTTGCGGATGCCCTA 62.614 57.895 0.00 0.00 41.78 3.53
196 199 3.418913 TCGGTTGCGTTGCGGATG 61.419 61.111 0.00 0.00 0.00 3.51
197 200 3.419759 GTCGGTTGCGTTGCGGAT 61.420 61.111 0.00 0.00 0.00 4.18
208 212 4.626402 TGTCCCCTCCCGTCGGTT 62.626 66.667 11.06 0.00 0.00 4.44
266 270 0.566679 ATAGGGGTCTGGTAGGTCCC 59.433 60.000 0.00 0.00 39.22 4.46
292 296 3.175710 ACCTGTTTGGGTCCGGCT 61.176 61.111 0.00 0.00 41.11 5.52
298 302 2.052047 CTGTCCGGACCTGTTTGGGT 62.052 60.000 31.19 0.00 43.07 4.51
356 361 2.852075 TGGAAAGGAGGCGGTGGT 60.852 61.111 0.00 0.00 0.00 4.16
365 370 0.698238 CCTCATGGTGGTGGAAAGGA 59.302 55.000 0.00 0.00 0.00 3.36
366 371 0.323725 CCCTCATGGTGGTGGAAAGG 60.324 60.000 0.00 0.00 0.00 3.11
368 373 0.698238 CTCCCTCATGGTGGTGGAAA 59.302 55.000 0.00 0.00 34.77 3.13
369 374 1.852157 GCTCCCTCATGGTGGTGGAA 61.852 60.000 0.00 0.00 34.77 3.53
370 375 2.300967 GCTCCCTCATGGTGGTGGA 61.301 63.158 0.00 0.00 34.77 4.02
371 376 2.141011 TTGCTCCCTCATGGTGGTGG 62.141 60.000 0.00 0.00 34.77 4.61
380 396 3.535629 CTGCGGTGTTGCTCCCTCA 62.536 63.158 0.00 0.00 35.36 3.86
381 397 2.743928 CTGCGGTGTTGCTCCCTC 60.744 66.667 0.00 0.00 35.36 4.30
392 408 3.058160 GAGTTGGCATGCTGCGGT 61.058 61.111 18.92 0.00 46.21 5.68
397 413 2.360350 CCGGTGAGTTGGCATGCT 60.360 61.111 18.92 0.00 0.00 3.79
418 434 2.298661 GGTCCATCTGGGTTCGGGT 61.299 63.158 0.00 0.00 38.11 5.28
422 438 0.407918 TTTGGGGTCCATCTGGGTTC 59.592 55.000 0.00 0.00 38.11 3.62
440 456 1.685820 GCCTAGGTCTGTGCCCTTT 59.314 57.895 11.31 0.00 33.35 3.11
447 463 3.760035 CGCGTGGCCTAGGTCTGT 61.760 66.667 15.92 0.00 0.00 3.41
650 668 3.269347 CCTTACAATCGCCGCCGG 61.269 66.667 0.00 0.00 34.56 6.13
657 675 3.713288 TCGCCATACTTCCTTACAATCG 58.287 45.455 0.00 0.00 0.00 3.34
660 678 3.101437 TCCTCGCCATACTTCCTTACAA 58.899 45.455 0.00 0.00 0.00 2.41
661 679 2.693591 CTCCTCGCCATACTTCCTTACA 59.306 50.000 0.00 0.00 0.00 2.41
665 683 0.760945 CCCTCCTCGCCATACTTCCT 60.761 60.000 0.00 0.00 0.00 3.36
671 689 4.172232 AGCCCCCTCCTCGCCATA 62.172 66.667 0.00 0.00 0.00 2.74
680 698 2.445654 CTCTCCTCCAGCCCCCTC 60.446 72.222 0.00 0.00 0.00 4.30
728 746 0.994263 GGTGAAAAAGCGCATGATGC 59.006 50.000 11.47 7.49 40.69 3.91
729 747 2.256174 CTGGTGAAAAAGCGCATGATG 58.744 47.619 11.47 0.00 0.00 3.07
747 1082 4.049869 CCATCGACAATCATGAGAGACTG 58.950 47.826 0.09 0.00 0.00 3.51
756 1091 4.400251 ACAAATTGAGCCATCGACAATCAT 59.600 37.500 0.00 0.00 33.90 2.45
858 1193 1.640428 CGATCGACTTTGCTTGCCTA 58.360 50.000 10.26 0.00 0.00 3.93
865 1200 3.564027 CCGCCCGATCGACTTTGC 61.564 66.667 18.66 9.78 0.00 3.68
872 1207 3.649986 GGATTTGCCGCCCGATCG 61.650 66.667 8.51 8.51 0.00 3.69
891 1226 3.414700 CCAGTGGTGAAGCGTCGC 61.415 66.667 9.80 9.80 0.00 5.19
902 1237 8.098286 TGAAAATTATATATCGTACCCCAGTGG 58.902 37.037 0.63 0.63 41.37 4.00
903 1238 8.932791 GTGAAAATTATATATCGTACCCCAGTG 58.067 37.037 0.00 0.00 0.00 3.66
904 1239 8.653191 TGTGAAAATTATATATCGTACCCCAGT 58.347 33.333 0.00 0.00 0.00 4.00
905 1240 8.932791 GTGTGAAAATTATATATCGTACCCCAG 58.067 37.037 0.00 0.00 0.00 4.45
906 1241 8.430431 TGTGTGAAAATTATATATCGTACCCCA 58.570 33.333 0.00 0.00 0.00 4.96
907 1242 8.836268 TGTGTGAAAATTATATATCGTACCCC 57.164 34.615 0.00 0.00 0.00 4.95
919 1254 8.447833 CCACATACGTACTTGTGTGAAAATTAT 58.552 33.333 24.63 0.00 43.41 1.28
920 1255 7.095144 CCCACATACGTACTTGTGTGAAAATTA 60.095 37.037 24.63 0.00 43.41 1.40
921 1256 6.293735 CCCACATACGTACTTGTGTGAAAATT 60.294 38.462 24.63 0.00 43.41 1.82
922 1257 5.180492 CCCACATACGTACTTGTGTGAAAAT 59.820 40.000 24.63 0.00 43.41 1.82
923 1258 4.512198 CCCACATACGTACTTGTGTGAAAA 59.488 41.667 24.63 0.00 43.41 2.29
924 1259 4.059511 CCCACATACGTACTTGTGTGAAA 58.940 43.478 24.63 0.00 43.41 2.69
925 1260 3.069872 ACCCACATACGTACTTGTGTGAA 59.930 43.478 24.63 0.00 43.41 3.18
926 1261 2.629137 ACCCACATACGTACTTGTGTGA 59.371 45.455 24.63 0.00 43.41 3.58
927 1262 2.734606 CACCCACATACGTACTTGTGTG 59.265 50.000 21.71 18.56 41.27 3.82
928 1263 2.629137 TCACCCACATACGTACTTGTGT 59.371 45.455 21.71 10.32 41.27 3.72
929 1264 3.306917 TCACCCACATACGTACTTGTG 57.693 47.619 18.32 18.32 42.25 3.33
930 1265 4.546829 ATTCACCCACATACGTACTTGT 57.453 40.909 0.00 0.00 0.00 3.16
931 1266 8.827177 AATATATTCACCCACATACGTACTTG 57.173 34.615 0.00 0.00 0.00 3.16
932 1267 9.841295 AAAATATATTCACCCACATACGTACTT 57.159 29.630 0.00 0.00 0.00 2.24
954 1289 8.028938 GCTATGGATGTAACTTGTGTGAAAAAT 58.971 33.333 0.00 0.00 0.00 1.82
955 1290 7.367285 GCTATGGATGTAACTTGTGTGAAAAA 58.633 34.615 0.00 0.00 0.00 1.94
956 1291 6.072175 GGCTATGGATGTAACTTGTGTGAAAA 60.072 38.462 0.00 0.00 0.00 2.29
957 1292 5.414454 GGCTATGGATGTAACTTGTGTGAAA 59.586 40.000 0.00 0.00 0.00 2.69
958 1293 4.941263 GGCTATGGATGTAACTTGTGTGAA 59.059 41.667 0.00 0.00 0.00 3.18
959 1294 4.019771 TGGCTATGGATGTAACTTGTGTGA 60.020 41.667 0.00 0.00 0.00 3.58
960 1295 4.260985 TGGCTATGGATGTAACTTGTGTG 58.739 43.478 0.00 0.00 0.00 3.82
961 1296 4.568072 TGGCTATGGATGTAACTTGTGT 57.432 40.909 0.00 0.00 0.00 3.72
962 1297 6.767902 AGTTATGGCTATGGATGTAACTTGTG 59.232 38.462 0.00 0.00 30.58 3.33
963 1298 6.900194 AGTTATGGCTATGGATGTAACTTGT 58.100 36.000 0.00 0.00 30.58 3.16
964 1299 8.902540 TTAGTTATGGCTATGGATGTAACTTG 57.097 34.615 0.00 0.00 35.00 3.16
965 1300 7.661847 GCTTAGTTATGGCTATGGATGTAACTT 59.338 37.037 0.00 0.00 35.00 2.66
966 1301 7.162082 GCTTAGTTATGGCTATGGATGTAACT 58.838 38.462 0.00 0.00 36.61 2.24
967 1302 6.090898 CGCTTAGTTATGGCTATGGATGTAAC 59.909 42.308 0.00 0.00 0.00 2.50
968 1303 6.163476 CGCTTAGTTATGGCTATGGATGTAA 58.837 40.000 0.00 0.00 0.00 2.41
969 1304 5.337250 CCGCTTAGTTATGGCTATGGATGTA 60.337 44.000 0.00 0.00 0.00 2.29
970 1305 4.563580 CCGCTTAGTTATGGCTATGGATGT 60.564 45.833 0.00 0.00 0.00 3.06
971 1306 3.935203 CCGCTTAGTTATGGCTATGGATG 59.065 47.826 0.00 0.00 0.00 3.51
1067 1402 3.670898 AGGATCTTCCTCATGGCCT 57.329 52.632 3.32 0.00 45.66 5.19
1331 1691 9.825972 ACGTATGTCACTTATCATTTGAAAAAG 57.174 29.630 0.00 5.11 0.00 2.27
1367 1727 1.480205 AAACGTCAGACGGTGTTACG 58.520 50.000 26.31 10.01 42.91 3.18
1391 1751 8.665643 TTTCTTTTCGGATGACAACTTTAGTA 57.334 30.769 0.00 0.00 0.00 1.82
1438 1798 3.118665 AGTTGTGAAGCATGGCAACTTTT 60.119 39.130 7.47 0.00 46.18 2.27
1529 1889 2.607187 GTCCCTGATAAGTGTCACACG 58.393 52.381 1.22 0.00 39.64 4.49
1708 2074 2.280628 GCACCAAAATAGGACCTCTCG 58.719 52.381 0.00 0.00 0.00 4.04
1849 2215 8.768957 TCAATGATTTGTTTCAAAAGTCAACA 57.231 26.923 0.00 0.00 34.32 3.33
2116 2522 5.048224 ACGTGCACCCATATATGTAGTCTAC 60.048 44.000 12.15 2.81 0.00 2.59
2147 2553 2.292267 CCACAGTAGGCATCCATGAAC 58.708 52.381 0.00 0.00 0.00 3.18
2153 2560 2.047061 TGATACCCACAGTAGGCATCC 58.953 52.381 0.00 0.00 33.42 3.51


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

AutoCloner maintained by Alex Coulton.