Multiple sequence alignment - TraesCS5A01G157400

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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 TraesCS5A01G157400 chr5A 100.000 2781 0 0 1 2781 337634966 337632186 0.000000 5136.0
1 TraesCS5A01G157400 chr5D 91.822 2568 147 24 1 2547 254430643 254428118 0.000000 3520.0
2 TraesCS5A01G157400 chr5B 90.974 2238 158 19 572 2780 288440009 288442231 0.000000 2974.0
3 TraesCS5A01G157400 chr4D 82.667 75 8 5 200 272 112722445 112722374 0.000008 62.1


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 TraesCS5A01G157400 chr5A 337632186 337634966 2780 True 5136 5136 100.000 1 2781 1 chr5A.!!$R1 2780
1 TraesCS5A01G157400 chr5D 254428118 254430643 2525 True 3520 3520 91.822 1 2547 1 chr5D.!!$R1 2546
2 TraesCS5A01G157400 chr5B 288440009 288442231 2222 False 2974 2974 90.974 572 2780 1 chr5B.!!$F1 2208

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
62 63 0.038343 GCTCATCTCCTCTCATCGGC 60.038 60.0 0.0 0.0 0.00 5.54 F
1168 1171 0.179161 CGTTGACGAAGAGCGAGGAT 60.179 55.0 0.0 0.0 44.57 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 1608 0.250513 GGAAGGGTCACTAGCACAGG 59.749 60.0 0.00 0.0 0.0 4.00 R
2255 2271 0.099259 CTATGCAATGCCACACACGG 59.901 55.0 1.53 0.0 0.0 4.94 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
18 19 3.569827 TCTTCTCTTCCCACCACCA 57.430 52.632 0.00 0.00 0.00 4.17
40 41 3.473647 CCCATGCCGCTCCTCTCA 61.474 66.667 0.00 0.00 0.00 3.27
52 53 0.753479 TCCTCTCACCGCTCATCTCC 60.753 60.000 0.00 0.00 0.00 3.71
61 62 0.240678 CGCTCATCTCCTCTCATCGG 59.759 60.000 0.00 0.00 0.00 4.18
62 63 0.038343 GCTCATCTCCTCTCATCGGC 60.038 60.000 0.00 0.00 0.00 5.54
69 70 4.271816 CTCTCATCGGCCCGACGG 62.272 72.222 8.62 6.99 39.18 4.79
83 84 2.606519 ACGGCCTAGCTTGGACCA 60.607 61.111 19.07 0.00 0.00 4.02
133 134 7.229306 TGTTAACCATTGGATTGATGCTCTATC 59.771 37.037 10.37 0.00 36.29 2.08
149 150 7.587037 TGCTCTATCAAAAATATGGAAAGGG 57.413 36.000 0.00 0.00 0.00 3.95
166 167 6.126478 TGGAAAGGGAAATATCTAAGGGAGTG 60.126 42.308 0.00 0.00 0.00 3.51
177 178 1.892209 AAGGGAGTGGCTACAAAACG 58.108 50.000 2.02 0.00 0.00 3.60
179 180 1.583495 GGGAGTGGCTACAAAACGGC 61.583 60.000 2.02 0.00 0.00 5.68
220 221 7.704472 AGTTATCAGTCGATTTCTAGCTTTCAG 59.296 37.037 0.00 0.00 32.73 3.02
229 230 4.955811 TTCTAGCTTTCAGTCTCAACCA 57.044 40.909 0.00 0.00 0.00 3.67
232 233 5.240891 TCTAGCTTTCAGTCTCAACCATTG 58.759 41.667 0.00 0.00 0.00 2.82
265 266 2.391678 ACATCCAGGGCATCATTTTCC 58.608 47.619 0.00 0.00 0.00 3.13
271 272 1.358787 AGGGCATCATTTTCCACCTCA 59.641 47.619 0.00 0.00 0.00 3.86
290 291 1.206849 CAGCTCTCTTCTTCCTCACCC 59.793 57.143 0.00 0.00 0.00 4.61
291 292 1.203237 AGCTCTCTTCTTCCTCACCCA 60.203 52.381 0.00 0.00 0.00 4.51
296 297 4.171234 TCTCTTCTTCCTCACCCAATCTT 58.829 43.478 0.00 0.00 0.00 2.40
297 298 4.599241 TCTCTTCTTCCTCACCCAATCTTT 59.401 41.667 0.00 0.00 0.00 2.52
301 302 1.753903 TCCTCACCCAATCTTTCCCA 58.246 50.000 0.00 0.00 0.00 4.37
306 307 0.482446 ACCCAATCTTTCCCACAGCA 59.518 50.000 0.00 0.00 0.00 4.41
313 314 2.981914 CTTTCCCACAGCAGCCACCA 62.982 60.000 0.00 0.00 0.00 4.17
314 315 3.790416 TTCCCACAGCAGCCACCAC 62.790 63.158 0.00 0.00 0.00 4.16
316 317 4.935495 CCACAGCAGCCACCACGT 62.935 66.667 0.00 0.00 0.00 4.49
383 384 4.821589 CTCCCGAACAGCCTCGCC 62.822 72.222 0.00 0.00 37.51 5.54
405 406 2.669240 CCGAAACCTCCTCCCACC 59.331 66.667 0.00 0.00 0.00 4.61
407 408 2.669240 GAAACCTCCTCCCACCGG 59.331 66.667 0.00 0.00 0.00 5.28
409 410 4.974438 AACCTCCTCCCACCGGCA 62.974 66.667 0.00 0.00 0.00 5.69
413 414 4.954118 TCCTCCCACCGGCACACT 62.954 66.667 0.00 0.00 0.00 3.55
464 465 2.004583 GGCCTTGCCGGTTTATTTTC 57.995 50.000 1.90 0.00 39.62 2.29
467 468 2.416836 GCCTTGCCGGTTTATTTTCCTC 60.417 50.000 1.90 0.00 34.25 3.71
509 510 4.039092 CTGCCTCCCCCACCACAG 62.039 72.222 0.00 0.00 0.00 3.66
541 542 1.417506 CCCACCCCCACCCTAAGATAT 60.418 57.143 0.00 0.00 0.00 1.63
603 605 4.996758 CCAAAATTGACTGACCCAAATTCC 59.003 41.667 0.00 0.00 0.00 3.01
615 617 1.067635 CCAAATTCCAAAGTCAGGCGG 60.068 52.381 0.00 0.00 0.00 6.13
627 629 1.522355 CAGGCGGCTGACATGTAGG 60.522 63.158 33.59 2.54 0.00 3.18
632 634 2.036733 GGCGGCTGACATGTAGGTATTA 59.963 50.000 0.00 0.00 0.00 0.98
638 640 6.091305 CGGCTGACATGTAGGTATTATGAATG 59.909 42.308 0.00 0.00 0.00 2.67
641 643 7.148738 GCTGACATGTAGGTATTATGAATGACG 60.149 40.741 0.00 0.00 0.00 4.35
886 888 3.054875 ACACTCTGTACCATGCATGTCAT 60.055 43.478 24.58 12.49 35.31 3.06
958 960 7.416213 GCAACCTGTTTCCATATATTTGTAGCA 60.416 37.037 0.00 0.00 0.00 3.49
959 961 7.807977 ACCTGTTTCCATATATTTGTAGCAG 57.192 36.000 0.00 0.00 0.00 4.24
963 965 7.513856 TGTTTCCATATATTTGTAGCAGCCTA 58.486 34.615 0.00 0.00 0.00 3.93
964 966 7.661437 TGTTTCCATATATTTGTAGCAGCCTAG 59.339 37.037 0.00 0.00 0.00 3.02
965 967 5.734720 TCCATATATTTGTAGCAGCCTAGC 58.265 41.667 0.00 0.00 0.00 3.42
966 968 5.248248 TCCATATATTTGTAGCAGCCTAGCA 59.752 40.000 0.00 0.00 36.85 3.49
980 983 6.428159 AGCAGCCTAGCAATGTGTATATAAAC 59.572 38.462 0.00 0.00 36.85 2.01
1029 1032 1.107114 GACATCCAGAAGAGCGAGGA 58.893 55.000 0.00 0.00 34.12 3.71
1168 1171 0.179161 CGTTGACGAAGAGCGAGGAT 60.179 55.000 0.00 0.00 44.57 3.24
1280 1283 3.548668 CGTACGTATTTGCTTTCCGATCA 59.451 43.478 7.22 0.00 0.00 2.92
1391 1394 0.244178 GGATAGACGGCGAAGGATCC 59.756 60.000 16.62 15.63 0.00 3.36
1423 1426 0.539051 CACAAGCCGGAGAGGAAGAT 59.461 55.000 5.05 0.00 45.00 2.40
1470 1473 0.595095 GACCAAGGTTCAAGCAGCAG 59.405 55.000 0.00 0.00 0.00 4.24
1597 1600 1.101635 TCGTCTCATACCTCGGCCTG 61.102 60.000 0.00 0.00 0.00 4.85
1605 1608 0.683504 TACCTCGGCCTGAACCTCTC 60.684 60.000 0.00 0.00 0.00 3.20
1627 1630 1.985159 TGTGCTAGTGACCCTTCCAAT 59.015 47.619 0.00 0.00 0.00 3.16
1643 1646 2.440627 TCCAATCATCCATCCACCTGAG 59.559 50.000 0.00 0.00 0.00 3.35
1706 1709 8.507249 ACAAGATTGAATTCCGAAGTTAAAGAG 58.493 33.333 2.27 0.00 0.00 2.85
1784 1787 9.465199 TGAAATGAACTTTTGATCCATCTATGA 57.535 29.630 0.00 0.00 0.00 2.15
1793 1796 7.707624 TTTGATCCATCTATGAAAGCTGTTT 57.292 32.000 0.00 0.00 0.00 2.83
1794 1797 8.806429 TTTGATCCATCTATGAAAGCTGTTTA 57.194 30.769 0.00 0.00 0.00 2.01
1838 1843 4.380843 TGGAAGCTGTAGGAATTGGAAA 57.619 40.909 0.00 0.00 0.00 3.13
1853 1858 2.238521 TGGAAATTCTGGCCAACTCAC 58.761 47.619 7.01 0.00 0.00 3.51
1864 1869 1.501741 CAACTCACGGGCCAAATCG 59.498 57.895 4.39 0.10 0.00 3.34
1889 1894 4.340381 ACTTGGGCTATGCATCTCAAATTC 59.660 41.667 0.19 0.00 0.00 2.17
1907 1920 2.177394 TCTTGTATCTTTGCGGTGCA 57.823 45.000 0.00 0.00 36.47 4.57
1910 1923 4.257731 TCTTGTATCTTTGCGGTGCATAA 58.742 39.130 0.00 0.00 38.76 1.90
1914 1927 5.339177 TGTATCTTTGCGGTGCATAATTTG 58.661 37.500 0.00 0.00 38.76 2.32
1962 1975 2.436646 GGATGTGGTCCGGCACAG 60.437 66.667 18.04 0.00 37.23 3.66
1965 1978 4.927782 TGTGGTCCGGCACAGCAC 62.928 66.667 15.06 15.06 41.68 4.40
1975 1988 2.477176 GCACAGCACGTTTGGTCCA 61.477 57.895 0.00 0.00 0.00 4.02
1984 1997 1.010462 GTTTGGTCCACGCGTTGTC 60.010 57.895 10.22 3.49 0.00 3.18
1985 1998 1.449778 TTTGGTCCACGCGTTGTCA 60.450 52.632 10.22 7.03 0.00 3.58
2057 2070 4.040095 GGGTAGTTGTCCTCTTTGTGTAGT 59.960 45.833 0.00 0.00 0.00 2.73
2064 2077 4.280174 TGTCCTCTTTGTGTAGTGACCTAC 59.720 45.833 0.00 0.00 43.30 3.18
2194 2208 5.359576 TGTTGCACCACATTAAGAGAACTTT 59.640 36.000 0.00 0.00 37.53 2.66
2195 2209 6.127479 TGTTGCACCACATTAAGAGAACTTTT 60.127 34.615 0.00 0.00 37.53 2.27
2239 2255 1.873698 TCTACAACACGGCCTTTGAC 58.126 50.000 13.80 0.00 0.00 3.18
2249 2265 2.281761 CCTTTGACTGCGTGGGCT 60.282 61.111 0.00 0.00 40.82 5.19
2274 2290 0.099259 CCGTGTGTGGCATTGCATAG 59.901 55.000 11.39 0.00 0.00 2.23
2277 2297 1.811965 GTGTGTGGCATTGCATAGTCA 59.188 47.619 11.39 0.00 0.00 3.41
2292 2312 1.136828 AGTCACTTGGTACCTTGCCA 58.863 50.000 14.36 0.00 0.00 4.92
2325 2345 4.754411 AAGCCTCCCATCAATTATCCAT 57.246 40.909 0.00 0.00 0.00 3.41
2390 2410 4.311208 ACCTATGGGGAGAAGGGATTTA 57.689 45.455 0.00 0.00 38.76 1.40
2392 2412 5.243566 ACCTATGGGGAGAAGGGATTTATT 58.756 41.667 0.00 0.00 38.76 1.40
2537 2562 1.455383 CGGTCTGGCAAAGCTTGGTT 61.455 55.000 0.00 0.00 0.00 3.67
2540 2565 0.396974 TCTGGCAAAGCTTGGTTGGT 60.397 50.000 0.00 0.00 0.00 3.67
2574 2599 1.519246 CCAGCTTCATCTCCTCGCA 59.481 57.895 0.00 0.00 0.00 5.10
2581 2606 0.178767 TCATCTCCTCGCATGTTGGG 59.821 55.000 0.00 0.00 0.00 4.12
2584 2609 3.329889 TCCTCGCATGTTGGGGCT 61.330 61.111 1.40 0.00 0.00 5.19
2587 2612 2.359850 TCGCATGTTGGGGCTGAC 60.360 61.111 0.00 0.00 0.00 3.51
2648 2673 2.431942 AACCACGACGCGACATCC 60.432 61.111 15.93 0.00 0.00 3.51
2651 2676 2.126463 CACGACGCGACATCCTGT 60.126 61.111 15.93 0.00 0.00 4.00
2653 2678 0.861866 CACGACGCGACATCCTGTAG 60.862 60.000 15.93 0.00 0.00 2.74
2674 2699 2.903547 GCGTTTGCGGTGTGATGGT 61.904 57.895 0.00 0.00 38.78 3.55
2677 2702 1.264557 CGTTTGCGGTGTGATGGTTAA 59.735 47.619 0.00 0.00 0.00 2.01
2679 2704 1.968704 TTGCGGTGTGATGGTTAACA 58.031 45.000 8.10 0.00 0.00 2.41
2755 2795 1.617947 GCTACTGGGGGTGAGGACTG 61.618 65.000 0.00 0.00 0.00 3.51
2763 2803 2.300967 GGTGAGGACTGGGGATGCA 61.301 63.158 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.049627 GAGGAGCGGCATGGGAGAAT 62.050 60.000 1.45 0.00 0.00 2.40
40 41 1.327303 GATGAGAGGAGATGAGCGGT 58.673 55.000 0.00 0.00 0.00 5.68
52 53 4.271816 CCGTCGGGCCGATGAGAG 62.272 72.222 41.57 25.23 44.49 3.20
62 63 4.530857 CCAAGCTAGGCCGTCGGG 62.531 72.222 14.38 0.00 0.00 5.14
69 70 1.474077 CACATTTGGTCCAAGCTAGGC 59.526 52.381 4.09 0.00 0.00 3.93
83 84 7.339466 ACAGGAGAAACTAGAAACAACACATTT 59.661 33.333 0.00 0.00 0.00 2.32
149 150 6.420913 TGTAGCCACTCCCTTAGATATTTC 57.579 41.667 0.00 0.00 0.00 2.17
155 156 3.306502 CGTTTTGTAGCCACTCCCTTAGA 60.307 47.826 0.00 0.00 0.00 2.10
166 167 4.111016 GGCGGCCGTTTTGTAGCC 62.111 66.667 28.70 13.03 43.53 3.93
177 178 3.313012 AACTTTAAATTTCAGGCGGCC 57.687 42.857 12.11 12.11 0.00 6.13
179 180 6.852664 ACTGATAACTTTAAATTTCAGGCGG 58.147 36.000 15.41 5.21 35.93 6.13
181 182 7.748847 TCGACTGATAACTTTAAATTTCAGGC 58.251 34.615 15.41 13.03 36.18 4.85
212 213 3.152341 CCAATGGTTGAGACTGAAAGCT 58.848 45.455 0.00 0.00 37.60 3.74
220 221 4.578105 GGATCTTGATCCAATGGTTGAGAC 59.422 45.833 21.11 0.00 40.43 3.36
232 233 3.484407 CCTGGATGTTGGATCTTGATCC 58.516 50.000 19.70 19.70 41.10 3.36
251 252 1.358787 TGAGGTGGAAAATGATGCCCT 59.641 47.619 0.00 0.00 0.00 5.19
265 266 2.166254 GAGGAAGAAGAGAGCTGAGGTG 59.834 54.545 0.00 0.00 0.00 4.00
271 272 1.203237 TGGGTGAGGAAGAAGAGAGCT 60.203 52.381 0.00 0.00 0.00 4.09
290 291 0.529378 GGCTGCTGTGGGAAAGATTG 59.471 55.000 0.00 0.00 0.00 2.67
291 292 0.112995 TGGCTGCTGTGGGAAAGATT 59.887 50.000 0.00 0.00 0.00 2.40
296 297 3.497115 TGGTGGCTGCTGTGGGAA 61.497 61.111 0.00 0.00 0.00 3.97
297 298 4.269523 GTGGTGGCTGCTGTGGGA 62.270 66.667 0.00 0.00 0.00 4.37
301 302 2.030562 GTACGTGGTGGCTGCTGT 59.969 61.111 0.00 0.00 0.00 4.40
306 307 3.688159 GGTCCGTACGTGGTGGCT 61.688 66.667 15.21 0.00 0.00 4.75
370 371 4.821589 GGAGGGCGAGGCTGTTCG 62.822 72.222 0.00 0.00 43.23 3.95
371 372 4.475135 GGGAGGGCGAGGCTGTTC 62.475 72.222 0.00 0.00 0.00 3.18
380 381 4.468689 GAGGTTTCGGGGAGGGCG 62.469 72.222 0.00 0.00 0.00 6.13
383 384 2.368011 GGAGGAGGTTTCGGGGAGG 61.368 68.421 0.00 0.00 0.00 4.30
391 392 3.647771 GCCGGTGGGAGGAGGTTT 61.648 66.667 1.90 0.00 34.06 3.27
518 519 3.589627 TTAGGGTGGGGGTGGGAGG 62.590 68.421 0.00 0.00 0.00 4.30
519 520 2.001269 CTTAGGGTGGGGGTGGGAG 61.001 68.421 0.00 0.00 0.00 4.30
520 521 1.844296 ATCTTAGGGTGGGGGTGGGA 61.844 60.000 0.00 0.00 0.00 4.37
521 522 0.029474 TATCTTAGGGTGGGGGTGGG 60.029 60.000 0.00 0.00 0.00 4.61
522 523 2.133858 ATATCTTAGGGTGGGGGTGG 57.866 55.000 0.00 0.00 0.00 4.61
523 524 4.435137 TCATATATCTTAGGGTGGGGGTG 58.565 47.826 0.00 0.00 0.00 4.61
524 525 4.796185 TCATATATCTTAGGGTGGGGGT 57.204 45.455 0.00 0.00 0.00 4.95
525 526 4.413520 CCATCATATATCTTAGGGTGGGGG 59.586 50.000 0.00 0.00 0.00 5.40
526 527 4.413520 CCCATCATATATCTTAGGGTGGGG 59.586 50.000 9.55 0.00 40.00 4.96
563 564 2.838637 TGGTTGAAGGGGAAACAACT 57.161 45.000 0.00 0.00 42.06 3.16
615 617 7.148738 CGTCATTCATAATACCTACATGTCAGC 60.149 40.741 0.00 0.00 0.00 4.26
838 840 5.238432 TCATTTGGTATGACAGTTGTGACAC 59.762 40.000 0.00 0.00 30.95 3.67
886 888 0.099259 CCGACGGACTATGTACGCAA 59.901 55.000 8.64 0.00 44.66 4.85
919 921 0.536006 AGGTTGCAAGAGCTCACACC 60.536 55.000 17.77 13.24 42.74 4.16
922 924 1.312815 AACAGGTTGCAAGAGCTCAC 58.687 50.000 17.77 4.40 42.74 3.51
958 960 7.657761 GTCAGTTTATATACACATTGCTAGGCT 59.342 37.037 2.04 0.00 0.00 4.58
959 961 7.441157 TGTCAGTTTATATACACATTGCTAGGC 59.559 37.037 2.04 0.00 0.00 3.93
963 965 9.008965 TGTTTGTCAGTTTATATACACATTGCT 57.991 29.630 2.04 0.00 0.00 3.91
964 966 9.061610 GTGTTTGTCAGTTTATATACACATTGC 57.938 33.333 2.04 0.00 35.82 3.56
965 967 9.554724 GGTGTTTGTCAGTTTATATACACATTG 57.445 33.333 0.00 0.00 37.08 2.82
966 968 9.515226 AGGTGTTTGTCAGTTTATATACACATT 57.485 29.630 0.00 0.00 37.08 2.71
980 983 7.494625 TCTCTACAAAACTAAGGTGTTTGTCAG 59.505 37.037 4.41 3.55 39.71 3.51
1029 1032 2.525124 TTGCTCCGGGGACACATGT 61.525 57.895 4.80 0.00 0.00 3.21
1168 1171 4.735132 GCGCTGTACCTCCGCACA 62.735 66.667 14.41 0.00 46.32 4.57
1280 1283 4.618927 CGAATGAATGCAAATCAACCAGGT 60.619 41.667 9.32 0.00 0.00 4.00
1384 1387 3.017581 AAGCGCCCCTGGATCCTT 61.018 61.111 14.23 0.00 0.00 3.36
1408 1411 1.573108 TTTGATCTTCCTCTCCGGCT 58.427 50.000 0.00 0.00 0.00 5.52
1470 1473 3.488090 GCACCGCACTTCCGCTAC 61.488 66.667 0.00 0.00 0.00 3.58
1597 1600 2.094442 GTCACTAGCACAGGAGAGGTTC 60.094 54.545 0.00 0.00 0.00 3.62
1605 1608 0.250513 GGAAGGGTCACTAGCACAGG 59.749 60.000 0.00 0.00 0.00 4.00
1627 1630 1.288188 TTGCTCAGGTGGATGGATGA 58.712 50.000 0.00 0.00 0.00 2.92
1643 1646 2.342354 GCGTTTGATTGCACTACATTGC 59.658 45.455 0.00 0.00 43.31 3.56
1757 1760 9.731819 CATAGATGGATCAAAAGTTCATTTCAG 57.268 33.333 0.00 0.00 0.00 3.02
1838 1843 1.002134 CCCGTGAGTTGGCCAGAAT 60.002 57.895 5.11 0.00 0.00 2.40
1853 1858 1.506262 CCAAGTTCGATTTGGCCCG 59.494 57.895 14.13 0.00 38.73 6.13
1864 1869 2.923121 TGAGATGCATAGCCCAAGTTC 58.077 47.619 0.00 0.00 0.00 3.01
1889 1894 4.614555 TTATGCACCGCAAAGATACAAG 57.385 40.909 0.00 0.00 43.62 3.16
1962 1975 4.659874 CGCGTGGACCAAACGTGC 62.660 66.667 0.00 0.00 43.57 5.34
1965 1978 2.052590 CAACGCGTGGACCAAACG 60.053 61.111 14.98 14.20 43.81 3.60
1984 1997 2.098280 CACTCCAGTCTACTCCATCGTG 59.902 54.545 0.00 0.00 0.00 4.35
1985 1998 2.026169 TCACTCCAGTCTACTCCATCGT 60.026 50.000 0.00 0.00 0.00 3.73
1998 2011 1.901591 AGTGTTGGCATTCACTCCAG 58.098 50.000 16.43 0.00 40.28 3.86
2064 2077 1.173444 CGGAGATCCCTACCGGACTG 61.173 65.000 9.46 0.00 46.09 3.51
2194 2208 5.319043 ACTTTGGAGAGACCCATGTAAAA 57.681 39.130 0.00 0.00 35.87 1.52
2195 2209 4.993705 ACTTTGGAGAGACCCATGTAAA 57.006 40.909 0.00 0.00 35.87 2.01
2255 2271 0.099259 CTATGCAATGCCACACACGG 59.901 55.000 1.53 0.00 0.00 4.94
2266 2282 4.844349 AGGTACCAAGTGACTATGCAAT 57.156 40.909 15.94 0.00 0.00 3.56
2274 2290 2.200373 ATGGCAAGGTACCAAGTGAC 57.800 50.000 15.94 11.77 41.49 3.67
2277 2297 4.270008 GAACATATGGCAAGGTACCAAGT 58.730 43.478 15.94 0.00 41.49 3.16
2292 2312 3.248024 TGGGAGGCTTATCGGAACATAT 58.752 45.455 0.00 0.00 0.00 1.78
2390 2410 6.405842 GGTGGTTTTCTGTTTTCTGTCTGAAT 60.406 38.462 0.00 0.00 34.24 2.57
2392 2412 4.398044 GGTGGTTTTCTGTTTTCTGTCTGA 59.602 41.667 0.00 0.00 0.00 3.27
2469 2490 3.650950 GAGGAGCTTGGGGTGGCA 61.651 66.667 0.00 0.00 0.00 4.92
2513 2538 2.042831 GCTTTGCCAGACCGAGCAT 61.043 57.895 0.00 0.00 39.11 3.79
2554 2579 1.227497 CGAGGAGATGAAGCTGGCC 60.227 63.158 0.00 0.00 0.00 5.36
2557 2582 1.218763 CATGCGAGGAGATGAAGCTG 58.781 55.000 0.00 0.00 0.00 4.24
2592 2617 4.457496 TGGCTCGTAGCAGCTGCC 62.457 66.667 34.39 19.42 44.75 4.85
2613 2638 3.179265 CTAGTTGTCCGCGCCACG 61.179 66.667 0.00 0.00 43.15 4.94
2624 2649 0.386352 TCGCGTCGTGGTTCTAGTTG 60.386 55.000 5.77 0.00 0.00 3.16
2629 2654 1.443872 GATGTCGCGTCGTGGTTCT 60.444 57.895 5.77 0.00 0.00 3.01
2648 2673 1.959226 ACCGCAAACGCACCTACAG 60.959 57.895 0.00 0.00 38.22 2.74
2651 2676 2.109387 ACACCGCAAACGCACCTA 59.891 55.556 0.00 0.00 38.22 3.08
2653 2678 2.903547 ATCACACCGCAAACGCACC 61.904 57.895 0.00 0.00 38.22 5.01
2666 2691 2.708861 ACCCTCTGTGTTAACCATCACA 59.291 45.455 2.48 0.00 41.37 3.58
2674 2699 0.109723 GCCACCACCCTCTGTGTTAA 59.890 55.000 0.00 0.00 43.85 2.01
2677 2702 3.570212 GGCCACCACCCTCTGTGT 61.570 66.667 0.00 0.00 43.85 3.72
2679 2704 2.450502 AAGGCCACCACCCTCTGT 60.451 61.111 5.01 0.00 0.00 3.41
2725 2765 3.121030 CAGTAGCCACTGCACGCC 61.121 66.667 0.00 0.00 45.44 5.68
2744 2784 3.049080 GCATCCCCAGTCCTCACCC 62.049 68.421 0.00 0.00 0.00 4.61
2745 2785 1.639635 ATGCATCCCCAGTCCTCACC 61.640 60.000 0.00 0.00 0.00 4.02
2755 2795 3.839353 CTCCGGCTCATGCATCCCC 62.839 68.421 0.00 0.00 41.91 4.81


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

AutoCloner maintained by Alex Coulton.