Multiple sequence alignment - TraesCS5B01G123100

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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 TraesCS5B01G123100 chr5B 100.000 3227 0 0 1 3227 222128704 222125478 0.000000e+00 5960
1 TraesCS5B01G123100 chr5B 89.474 152 14 2 2845 2996 221913594 221913445 1.180000e-44 191
2 TraesCS5B01G123100 chr5D 92.742 2797 91 36 462 3217 208537672 208534947 0.000000e+00 3938
3 TraesCS5B01G123100 chr5D 88.862 413 15 10 28 417 208538091 208537687 2.250000e-131 479
4 TraesCS5B01G123100 chr5A 94.137 2166 80 19 471 2620 269321318 269319184 0.000000e+00 3253
5 TraesCS5B01G123100 chr5A 95.333 300 12 2 2701 2998 269315818 269315519 2.910000e-130 475
6 TraesCS5B01G123100 chr5A 84.787 447 26 22 1 417 269328417 269327983 8.330000e-111 411
7 TraesCS5B01G123100 chr5A 80.460 174 13 9 2631 2792 269316000 269315836 2.630000e-21 113
8 TraesCS5B01G123100 chr4A 82.081 1038 165 14 1195 2220 501976228 501975200 0.000000e+00 867
9 TraesCS5B01G123100 chr4D 81.967 1037 168 12 1195 2220 89435846 89434818 0.000000e+00 861
10 TraesCS5B01G123100 chr4B 81.310 1038 173 13 1195 2220 126508469 126507441 0.000000e+00 822


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 TraesCS5B01G123100 chr5B 222125478 222128704 3226 True 5960.000000 5960 100.000000 1 3227 1 chr5B.!!$R2 3226
1 TraesCS5B01G123100 chr5D 208534947 208538091 3144 True 2208.500000 3938 90.802000 28 3217 2 chr5D.!!$R1 3189
2 TraesCS5B01G123100 chr5A 269315519 269321318 5799 True 1280.333333 3253 89.976667 471 2998 3 chr5A.!!$R2 2527
3 TraesCS5B01G123100 chr4A 501975200 501976228 1028 True 867.000000 867 82.081000 1195 2220 1 chr4A.!!$R1 1025
4 TraesCS5B01G123100 chr4D 89434818 89435846 1028 True 861.000000 861 81.967000 1195 2220 1 chr4D.!!$R1 1025
5 TraesCS5B01G123100 chr4B 126507441 126508469 1028 True 822.000000 822 81.310000 1195 2220 1 chr4B.!!$R1 1025

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
421 445 0.443869 CGTTGCTCGTTGGGAGATTG 59.556 55.0 0.0 0.0 46.23 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2332 2399 0.445436 AGACGAAGGCACGTACGTAG 59.555 55.0 22.34 16.04 46.52 3.51 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
25 26 8.664669 ACTCCCCTTTTAAATGTGAACATTAT 57.335 30.769 9.01 3.39 45.06 1.28
26 27 8.531146 ACTCCCCTTTTAAATGTGAACATTATG 58.469 33.333 9.01 0.00 45.06 1.90
51 55 9.950680 TGAAAAGAAACTGTGAACATTAGAATC 57.049 29.630 0.00 0.00 0.00 2.52
60 64 8.204160 ACTGTGAACATTAGAATCCGAATCATA 58.796 33.333 0.00 0.00 0.00 2.15
80 84 2.236382 GCCAGCTCGATCTGCTTCG 61.236 63.158 10.79 0.00 38.92 3.79
83 87 1.198767 CAGCTCGATCTGCTTCGAAG 58.801 55.000 21.02 21.02 46.54 3.79
88 92 3.123621 GCTCGATCTGCTTCGAAGAAAAA 59.876 43.478 28.95 9.79 46.54 1.94
111 115 1.271840 ATGGCTGGTGTCACCGGTAT 61.272 55.000 27.97 20.29 46.46 2.73
136 140 4.093952 CCGGCAAGCAAGCGACTG 62.094 66.667 0.00 0.00 34.64 3.51
225 229 3.649277 GACCTGACATGCTCGCCGT 62.649 63.158 0.00 0.00 0.00 5.68
231 235 3.190849 CATGCTCGCCGTGACCTG 61.191 66.667 0.00 0.00 31.89 4.00
232 236 3.695606 ATGCTCGCCGTGACCTGT 61.696 61.111 0.00 0.00 0.00 4.00
283 300 1.106351 AACATTCCCGTGCAGTGCAA 61.106 50.000 21.67 3.70 41.47 4.08
284 301 1.210931 CATTCCCGTGCAGTGCAAG 59.789 57.895 21.67 22.03 41.47 4.01
370 394 2.276409 GCTGCCCCATGTCCATGA 59.724 61.111 8.82 0.00 41.20 3.07
375 399 2.196776 CCCATGTCCATGAGGCCC 59.803 66.667 8.82 0.00 41.20 5.80
376 400 2.196776 CCATGTCCATGAGGCCCC 59.803 66.667 8.82 0.00 41.20 5.80
401 425 2.431430 TCGCGCTCACTGCTTCTG 60.431 61.111 5.56 0.00 40.11 3.02
417 441 2.664851 TGCGTTGCTCGTTGGGAG 60.665 61.111 4.16 0.00 46.06 4.30
418 442 2.357034 GCGTTGCTCGTTGGGAGA 60.357 61.111 0.00 0.00 46.23 3.71
419 443 1.741770 GCGTTGCTCGTTGGGAGAT 60.742 57.895 0.00 0.00 46.23 2.75
420 444 1.298859 GCGTTGCTCGTTGGGAGATT 61.299 55.000 0.00 0.00 46.23 2.40
421 445 0.443869 CGTTGCTCGTTGGGAGATTG 59.556 55.000 0.00 0.00 46.23 2.67
422 446 1.523758 GTTGCTCGTTGGGAGATTGT 58.476 50.000 0.00 0.00 46.23 2.71
424 448 3.071479 GTTGCTCGTTGGGAGATTGTAA 58.929 45.455 0.00 0.00 46.23 2.41
425 449 2.695359 TGCTCGTTGGGAGATTGTAAC 58.305 47.619 0.00 0.00 46.23 2.50
426 450 2.301870 TGCTCGTTGGGAGATTGTAACT 59.698 45.455 0.00 0.00 46.23 2.24
428 452 3.864003 GCTCGTTGGGAGATTGTAACTAC 59.136 47.826 0.00 0.00 46.23 2.73
429 453 4.619863 GCTCGTTGGGAGATTGTAACTACA 60.620 45.833 0.00 0.00 46.23 2.74
430 454 5.661458 CTCGTTGGGAGATTGTAACTACAT 58.339 41.667 0.00 0.00 46.23 2.29
431 455 6.045072 TCGTTGGGAGATTGTAACTACATT 57.955 37.500 0.00 0.00 35.89 2.71
432 456 6.103997 TCGTTGGGAGATTGTAACTACATTC 58.896 40.000 4.35 4.35 37.03 2.67
433 457 5.872617 CGTTGGGAGATTGTAACTACATTCA 59.127 40.000 12.08 0.00 38.41 2.57
434 458 6.370442 CGTTGGGAGATTGTAACTACATTCAA 59.630 38.462 12.08 0.00 38.41 2.69
435 459 7.527457 GTTGGGAGATTGTAACTACATTCAAC 58.473 38.462 12.08 0.00 38.41 3.18
436 460 6.774673 TGGGAGATTGTAACTACATTCAACA 58.225 36.000 12.08 6.70 38.41 3.33
437 461 7.402054 TGGGAGATTGTAACTACATTCAACAT 58.598 34.615 12.08 0.00 38.41 2.71
438 462 8.544622 TGGGAGATTGTAACTACATTCAACATA 58.455 33.333 12.08 0.04 38.41 2.29
439 463 9.046296 GGGAGATTGTAACTACATTCAACATAG 57.954 37.037 12.08 0.00 38.41 2.23
440 464 9.817809 GGAGATTGTAACTACATTCAACATAGA 57.182 33.333 12.08 0.00 38.41 1.98
442 466 9.319143 AGATTGTAACTACATTCAACATAGAGC 57.681 33.333 12.08 0.00 38.41 4.09
443 467 9.098355 GATTGTAACTACATTCAACATAGAGCA 57.902 33.333 6.81 0.00 36.86 4.26
444 468 9.618890 ATTGTAACTACATTCAACATAGAGCAT 57.381 29.630 0.00 0.00 35.89 3.79
445 469 8.424274 TGTAACTACATTCAACATAGAGCATG 57.576 34.615 0.00 0.00 40.78 4.06
446 470 8.257306 TGTAACTACATTCAACATAGAGCATGA 58.743 33.333 0.00 0.00 38.10 3.07
447 471 7.783090 AACTACATTCAACATAGAGCATGAG 57.217 36.000 0.00 0.00 38.10 2.90
448 472 6.882656 ACTACATTCAACATAGAGCATGAGT 58.117 36.000 0.00 0.00 38.10 3.41
449 473 7.334090 ACTACATTCAACATAGAGCATGAGTT 58.666 34.615 0.00 0.00 38.10 3.01
450 474 7.826252 ACTACATTCAACATAGAGCATGAGTTT 59.174 33.333 0.00 0.00 38.10 2.66
451 475 7.458409 ACATTCAACATAGAGCATGAGTTTT 57.542 32.000 0.00 0.00 38.10 2.43
452 476 7.310664 ACATTCAACATAGAGCATGAGTTTTG 58.689 34.615 0.00 0.00 38.10 2.44
453 477 6.882610 TTCAACATAGAGCATGAGTTTTGT 57.117 33.333 0.00 0.00 38.10 2.83
454 478 6.882610 TCAACATAGAGCATGAGTTTTGTT 57.117 33.333 0.00 0.00 38.10 2.83
455 479 6.671190 TCAACATAGAGCATGAGTTTTGTTG 58.329 36.000 17.84 17.84 42.34 3.33
456 480 6.486320 TCAACATAGAGCATGAGTTTTGTTGA 59.514 34.615 20.50 20.50 45.41 3.18
457 481 6.492007 ACATAGAGCATGAGTTTTGTTGAG 57.508 37.500 0.00 0.00 38.10 3.02
458 482 6.000219 ACATAGAGCATGAGTTTTGTTGAGT 59.000 36.000 0.00 0.00 38.10 3.41
459 483 4.825546 AGAGCATGAGTTTTGTTGAGTG 57.174 40.909 0.00 0.00 0.00 3.51
460 484 4.454678 AGAGCATGAGTTTTGTTGAGTGA 58.545 39.130 0.00 0.00 0.00 3.41
468 492 4.432712 AGTTTTGTTGAGTGATTTGTGCC 58.567 39.130 0.00 0.00 0.00 5.01
469 493 3.451141 TTTGTTGAGTGATTTGTGCCC 57.549 42.857 0.00 0.00 0.00 5.36
494 518 4.137116 TGAGTATGGTATGGACAGCAAC 57.863 45.455 0.00 0.00 0.00 4.17
544 572 3.110447 TGCAAAGCAAGGAAATCCAAC 57.890 42.857 1.67 0.00 34.76 3.77
597 631 2.939460 AAAGCAATATCAACACCGGC 57.061 45.000 0.00 0.00 0.00 6.13
603 637 2.951642 CAATATCAACACCGGCAAGGAT 59.048 45.455 0.00 2.63 45.00 3.24
604 638 2.799126 TATCAACACCGGCAAGGATT 57.201 45.000 0.00 0.00 45.00 3.01
613 647 2.224917 ACCGGCAAGGATTTTTCTGGTA 60.225 45.455 0.00 0.00 45.00 3.25
614 648 2.163613 CCGGCAAGGATTTTTCTGGTAC 59.836 50.000 0.00 0.00 45.00 3.34
634 668 5.829391 GGTACTAAAACAACCCAAAAGGAGA 59.171 40.000 0.00 0.00 39.89 3.71
638 677 1.675552 ACAACCCAAAAGGAGACGTG 58.324 50.000 0.00 0.00 39.89 4.49
646 685 3.129638 CCAAAAGGAGACGTGGAAAACAA 59.870 43.478 0.00 0.00 34.66 2.83
647 686 4.381079 CCAAAAGGAGACGTGGAAAACAAA 60.381 41.667 0.00 0.00 34.66 2.83
648 687 5.164954 CAAAAGGAGACGTGGAAAACAAAA 58.835 37.500 0.00 0.00 0.00 2.44
697 753 2.947652 AGCATTTCATGATTAGCGCACT 59.052 40.909 11.47 0.00 0.00 4.40
747 803 8.960591 ACAAGCTCATTATTAAACACTGCTAAT 58.039 29.630 0.00 0.00 0.00 1.73
748 804 9.443283 CAAGCTCATTATTAAACACTGCTAATC 57.557 33.333 0.00 0.00 0.00 1.75
749 805 8.159344 AGCTCATTATTAAACACTGCTAATCC 57.841 34.615 0.00 0.00 0.00 3.01
816 872 5.527214 CACGCCTTCATATAAAACTCCATCA 59.473 40.000 0.00 0.00 0.00 3.07
817 873 5.527582 ACGCCTTCATATAAAACTCCATCAC 59.472 40.000 0.00 0.00 0.00 3.06
818 874 5.049405 CGCCTTCATATAAAACTCCATCACC 60.049 44.000 0.00 0.00 0.00 4.02
819 875 5.241728 GCCTTCATATAAAACTCCATCACCC 59.758 44.000 0.00 0.00 0.00 4.61
820 876 6.605119 CCTTCATATAAAACTCCATCACCCT 58.395 40.000 0.00 0.00 0.00 4.34
821 877 6.712547 CCTTCATATAAAACTCCATCACCCTC 59.287 42.308 0.00 0.00 0.00 4.30
838 899 4.148825 CCTCCCTTCCCACTCGCG 62.149 72.222 0.00 0.00 0.00 5.87
875 936 1.935913 TCCCATTCCCATTCCATTCCA 59.064 47.619 0.00 0.00 0.00 3.53
877 938 3.051187 TCCCATTCCCATTCCATTCCATT 60.051 43.478 0.00 0.00 0.00 3.16
885 946 3.374540 CCATTCCATTCCATTCCCTTCCT 60.375 47.826 0.00 0.00 0.00 3.36
1668 1735 1.682451 CGTCCCATTTCCGCTCCCTA 61.682 60.000 0.00 0.00 0.00 3.53
1800 1867 0.698238 TGGGCTGCATACTCCACTTT 59.302 50.000 0.50 0.00 0.00 2.66
1935 2002 1.003839 CACCCTGCAAGAACGCCTA 60.004 57.895 0.00 0.00 34.07 3.93
2028 2095 1.446792 CACACAGAAGCTCGCCGAT 60.447 57.895 0.00 0.00 0.00 4.18
2071 2138 1.000486 CTCTTCGGGGACAGGGAGA 60.000 63.158 0.00 0.00 0.00 3.71
2207 2274 2.066393 TGGAGGGCCTCGATTCCTG 61.066 63.158 26.54 0.00 34.31 3.86
2243 2310 1.427809 TGATTCATCCCATCTCGCCT 58.572 50.000 0.00 0.00 0.00 5.52
2295 2362 4.037327 AGCTTTCTTCTTCTTGGTTTGCTC 59.963 41.667 0.00 0.00 0.00 4.26
2383 2456 3.786450 GGAAGGAAGGGGATTAGAAAGGA 59.214 47.826 0.00 0.00 0.00 3.36
2469 2542 6.326064 TGCCTTTTGGTATATATGTTGCCAAT 59.674 34.615 9.70 0.00 42.99 3.16
2530 2603 4.207891 TGAGTTTATGTTCCAGAGCTCC 57.792 45.455 10.93 0.00 0.00 4.70
2536 2609 2.623418 TGTTCCAGAGCTCCCTAAGA 57.377 50.000 10.93 0.00 0.00 2.10
2562 2635 5.814705 CACTTTGATCTCTCTCATGGTTACC 59.185 44.000 0.00 0.00 0.00 2.85
2620 2694 2.613977 GGGGTGTGAGATTGTCTGTCTG 60.614 54.545 0.00 0.00 0.00 3.51
2621 2695 2.613977 GGGTGTGAGATTGTCTGTCTGG 60.614 54.545 0.00 0.00 0.00 3.86
2623 2697 3.258372 GGTGTGAGATTGTCTGTCTGGTA 59.742 47.826 0.00 0.00 0.00 3.25
2625 2699 4.867047 GTGTGAGATTGTCTGTCTGGTATG 59.133 45.833 0.00 0.00 0.00 2.39
2626 2700 4.081476 TGTGAGATTGTCTGTCTGGTATGG 60.081 45.833 0.00 0.00 0.00 2.74
2687 5934 2.623878 TACTGCGTTCCAAAGTTCCA 57.376 45.000 0.00 0.00 0.00 3.53
2762 6122 3.306613 AGGCCTGGTAATGTAGGAGTAC 58.693 50.000 3.11 0.00 36.11 2.73
2853 6213 5.047235 ACGTATATTCCTCCCTACTGAATGC 60.047 44.000 0.00 0.00 31.55 3.56
2882 6242 1.494721 TGCTGAAAGGGGTGAAAGTCT 59.505 47.619 0.00 0.00 0.00 3.24
3014 6376 2.095263 CCAATTAACCTTCACAGCCGTG 60.095 50.000 0.00 0.00 45.08 4.94
3028 6390 0.320771 GCCGTGTGATCTTGTCCAGT 60.321 55.000 0.00 0.00 0.00 4.00
3029 6391 1.878102 GCCGTGTGATCTTGTCCAGTT 60.878 52.381 0.00 0.00 0.00 3.16
3030 6392 2.611971 GCCGTGTGATCTTGTCCAGTTA 60.612 50.000 0.00 0.00 0.00 2.24
3031 6393 3.254060 CCGTGTGATCTTGTCCAGTTAG 58.746 50.000 0.00 0.00 0.00 2.34
3032 6394 2.668457 CGTGTGATCTTGTCCAGTTAGC 59.332 50.000 0.00 0.00 0.00 3.09
3033 6395 3.615110 CGTGTGATCTTGTCCAGTTAGCT 60.615 47.826 0.00 0.00 0.00 3.32
3034 6396 3.929610 GTGTGATCTTGTCCAGTTAGCTC 59.070 47.826 0.00 0.00 0.00 4.09
3035 6397 3.834813 TGTGATCTTGTCCAGTTAGCTCT 59.165 43.478 0.00 0.00 0.00 4.09
3036 6398 5.016831 TGTGATCTTGTCCAGTTAGCTCTA 58.983 41.667 0.00 0.00 0.00 2.43
3037 6399 5.126222 TGTGATCTTGTCCAGTTAGCTCTAG 59.874 44.000 0.00 0.00 0.00 2.43
3038 6400 5.358442 GTGATCTTGTCCAGTTAGCTCTAGA 59.642 44.000 0.00 0.00 0.00 2.43
3048 6410 8.251721 GTCCAGTTAGCTCTAGAAAAATGACTA 58.748 37.037 9.79 0.00 0.00 2.59
3086 6449 5.163447 GGTTTCTTTACCTGCTTTGGTCTTT 60.163 40.000 0.18 0.00 41.22 2.52
3087 6450 5.514274 TTCTTTACCTGCTTTGGTCTTTG 57.486 39.130 0.18 0.00 41.22 2.77
3088 6451 4.532834 TCTTTACCTGCTTTGGTCTTTGT 58.467 39.130 0.18 0.00 41.22 2.83
3089 6452 4.953579 TCTTTACCTGCTTTGGTCTTTGTT 59.046 37.500 0.18 0.00 41.22 2.83
3090 6453 6.123651 TCTTTACCTGCTTTGGTCTTTGTTA 58.876 36.000 0.18 0.00 41.22 2.41
3118 6481 4.088634 TCTCCAACAGCAGCCATATTTTT 58.911 39.130 0.00 0.00 0.00 1.94
3130 6493 2.631267 CATATTTTTGGGCAAGGCACC 58.369 47.619 0.00 0.00 0.00 5.01
3159 6522 2.755952 AAAAAGGGTCTCCAACAGCT 57.244 45.000 0.00 0.00 34.83 4.24
3160 6523 1.986882 AAAAGGGTCTCCAACAGCTG 58.013 50.000 13.48 13.48 34.83 4.24
3162 6525 0.846693 AAGGGTCTCCAACAGCTGTT 59.153 50.000 26.36 26.36 39.12 3.16
3218 6581 3.577805 GCCCTAAAAATAGGCTCCTCA 57.422 47.619 0.00 0.00 43.62 3.86
3219 6582 4.105754 GCCCTAAAAATAGGCTCCTCAT 57.894 45.455 0.00 0.00 43.62 2.90
3220 6583 3.823304 GCCCTAAAAATAGGCTCCTCATG 59.177 47.826 0.00 0.00 43.62 3.07
3221 6584 3.823304 CCCTAAAAATAGGCTCCTCATGC 59.177 47.826 0.00 0.00 35.90 4.06
3222 6585 3.499918 CCTAAAAATAGGCTCCTCATGCG 59.500 47.826 0.00 0.00 0.00 4.73
3223 6586 1.972872 AAAATAGGCTCCTCATGCGG 58.027 50.000 0.00 0.00 0.00 5.69
3224 6587 0.839946 AAATAGGCTCCTCATGCGGT 59.160 50.000 0.77 0.00 0.00 5.68
3225 6588 1.717032 AATAGGCTCCTCATGCGGTA 58.283 50.000 0.77 0.00 0.00 4.02
3226 6589 1.717032 ATAGGCTCCTCATGCGGTAA 58.283 50.000 0.77 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.994421 AATGTTCACATTTAAAAGGGGAGT 57.006 33.333 0.00 0.00 43.48 3.85
1 2 8.748412 TCATAATGTTCACATTTAAAAGGGGAG 58.252 33.333 10.38 0.00 43.48 4.30
2 3 8.657387 TCATAATGTTCACATTTAAAAGGGGA 57.343 30.769 10.38 0.00 43.48 4.81
3 4 9.717942 TTTCATAATGTTCACATTTAAAAGGGG 57.282 29.630 10.38 0.00 43.48 4.79
13 14 9.467258 CACAGTTTCTTTTCATAATGTTCACAT 57.533 29.630 0.00 0.00 38.41 3.21
14 15 8.681806 TCACAGTTTCTTTTCATAATGTTCACA 58.318 29.630 0.00 0.00 0.00 3.58
15 16 9.515020 TTCACAGTTTCTTTTCATAATGTTCAC 57.485 29.630 0.00 0.00 0.00 3.18
16 17 9.515020 GTTCACAGTTTCTTTTCATAATGTTCA 57.485 29.630 0.00 0.00 0.00 3.18
17 18 9.515020 TGTTCACAGTTTCTTTTCATAATGTTC 57.485 29.630 0.00 0.00 0.00 3.18
25 26 9.950680 GATTCTAATGTTCACAGTTTCTTTTCA 57.049 29.630 0.00 0.00 0.00 2.69
26 27 9.399403 GGATTCTAATGTTCACAGTTTCTTTTC 57.601 33.333 0.00 0.00 0.00 2.29
51 55 1.073964 CGAGCTGGCATATGATTCGG 58.926 55.000 6.97 1.47 0.00 4.30
60 64 0.532417 GAAGCAGATCGAGCTGGCAT 60.532 55.000 30.05 16.13 42.53 4.40
88 92 0.673437 CGGTGACACCAGCCATTTTT 59.327 50.000 24.18 0.00 38.47 1.94
89 93 1.178534 CCGGTGACACCAGCCATTTT 61.179 55.000 24.18 0.00 38.47 1.82
90 94 1.603455 CCGGTGACACCAGCCATTT 60.603 57.895 24.18 0.00 38.47 2.32
91 95 1.485294 TACCGGTGACACCAGCCATT 61.485 55.000 24.18 0.00 38.47 3.16
92 96 1.271840 ATACCGGTGACACCAGCCAT 61.272 55.000 24.18 7.48 38.47 4.40
93 97 1.916273 ATACCGGTGACACCAGCCA 60.916 57.895 24.18 5.38 38.47 4.75
135 139 1.346395 ACAGTTATGTCGGTTGGAGCA 59.654 47.619 0.00 0.00 32.99 4.26
136 140 2.000447 GACAGTTATGTCGGTTGGAGC 59.000 52.381 0.00 0.00 46.01 4.70
211 215 2.432456 GTCACGGCGAGCATGTCA 60.432 61.111 16.62 0.00 0.00 3.58
225 229 4.269523 GCACCCCAGCACAGGTCA 62.270 66.667 0.00 0.00 32.72 4.02
231 235 3.677648 CAGCAAGCACCCCAGCAC 61.678 66.667 0.00 0.00 36.85 4.40
232 236 4.980702 CCAGCAAGCACCCCAGCA 62.981 66.667 0.00 0.00 36.85 4.41
401 425 1.298859 AATCTCCCAACGAGCAACGC 61.299 55.000 0.00 0.00 46.94 4.84
417 441 9.098355 TGCTCTATGTTGAATGTAGTTACAATC 57.902 33.333 0.00 0.00 39.99 2.67
418 442 9.618890 ATGCTCTATGTTGAATGTAGTTACAAT 57.381 29.630 0.00 0.00 39.99 2.71
419 443 8.882736 CATGCTCTATGTTGAATGTAGTTACAA 58.117 33.333 0.00 0.00 34.44 2.41
420 444 8.257306 TCATGCTCTATGTTGAATGTAGTTACA 58.743 33.333 0.00 0.00 38.05 2.41
421 445 8.648557 TCATGCTCTATGTTGAATGTAGTTAC 57.351 34.615 0.00 0.00 38.01 2.50
422 446 8.478066 ACTCATGCTCTATGTTGAATGTAGTTA 58.522 33.333 0.00 0.00 38.01 2.24
424 448 6.882656 ACTCATGCTCTATGTTGAATGTAGT 58.117 36.000 0.00 0.00 38.01 2.73
425 449 7.783090 AACTCATGCTCTATGTTGAATGTAG 57.217 36.000 0.00 0.00 38.01 2.74
426 450 8.453320 CAAAACTCATGCTCTATGTTGAATGTA 58.547 33.333 0.00 0.00 38.01 2.29
428 452 7.310664 ACAAAACTCATGCTCTATGTTGAATG 58.689 34.615 0.00 0.00 38.01 2.67
429 453 7.458409 ACAAAACTCATGCTCTATGTTGAAT 57.542 32.000 0.00 0.00 38.01 2.57
430 454 6.882610 ACAAAACTCATGCTCTATGTTGAA 57.117 33.333 0.00 0.00 38.01 2.69
431 455 6.671190 CAACAAAACTCATGCTCTATGTTGA 58.329 36.000 19.74 0.00 45.55 3.18
432 456 6.671190 TCAACAAAACTCATGCTCTATGTTG 58.329 36.000 18.98 18.98 44.62 3.33
433 457 6.488006 ACTCAACAAAACTCATGCTCTATGTT 59.512 34.615 0.00 0.00 38.01 2.71
434 458 6.000219 ACTCAACAAAACTCATGCTCTATGT 59.000 36.000 0.00 0.00 38.01 2.29
435 459 6.148315 TCACTCAACAAAACTCATGCTCTATG 59.852 38.462 0.00 0.00 38.17 2.23
436 460 6.233434 TCACTCAACAAAACTCATGCTCTAT 58.767 36.000 0.00 0.00 0.00 1.98
437 461 5.610398 TCACTCAACAAAACTCATGCTCTA 58.390 37.500 0.00 0.00 0.00 2.43
438 462 4.454678 TCACTCAACAAAACTCATGCTCT 58.545 39.130 0.00 0.00 0.00 4.09
439 463 4.818534 TCACTCAACAAAACTCATGCTC 57.181 40.909 0.00 0.00 0.00 4.26
440 464 5.779529 AATCACTCAACAAAACTCATGCT 57.220 34.783 0.00 0.00 0.00 3.79
441 465 5.750067 ACAAATCACTCAACAAAACTCATGC 59.250 36.000 0.00 0.00 0.00 4.06
442 466 6.291955 GCACAAATCACTCAACAAAACTCATG 60.292 38.462 0.00 0.00 0.00 3.07
443 467 5.750067 GCACAAATCACTCAACAAAACTCAT 59.250 36.000 0.00 0.00 0.00 2.90
444 468 5.101628 GCACAAATCACTCAACAAAACTCA 58.898 37.500 0.00 0.00 0.00 3.41
445 469 4.504097 GGCACAAATCACTCAACAAAACTC 59.496 41.667 0.00 0.00 0.00 3.01
446 470 4.432712 GGCACAAATCACTCAACAAAACT 58.567 39.130 0.00 0.00 0.00 2.66
447 471 3.555547 GGGCACAAATCACTCAACAAAAC 59.444 43.478 0.00 0.00 0.00 2.43
448 472 3.196469 TGGGCACAAATCACTCAACAAAA 59.804 39.130 0.00 0.00 0.00 2.44
449 473 2.762887 TGGGCACAAATCACTCAACAAA 59.237 40.909 0.00 0.00 0.00 2.83
450 474 2.361757 CTGGGCACAAATCACTCAACAA 59.638 45.455 0.00 0.00 0.00 2.83
451 475 1.955778 CTGGGCACAAATCACTCAACA 59.044 47.619 0.00 0.00 0.00 3.33
452 476 1.956477 ACTGGGCACAAATCACTCAAC 59.044 47.619 0.00 0.00 0.00 3.18
453 477 2.361757 CAACTGGGCACAAATCACTCAA 59.638 45.455 0.00 0.00 0.00 3.02
454 478 1.955778 CAACTGGGCACAAATCACTCA 59.044 47.619 0.00 0.00 0.00 3.41
455 479 2.227388 CTCAACTGGGCACAAATCACTC 59.773 50.000 0.00 0.00 0.00 3.51
456 480 2.233271 CTCAACTGGGCACAAATCACT 58.767 47.619 0.00 0.00 0.00 3.41
457 481 1.956477 ACTCAACTGGGCACAAATCAC 59.044 47.619 0.00 0.00 0.00 3.06
458 482 2.363306 ACTCAACTGGGCACAAATCA 57.637 45.000 0.00 0.00 0.00 2.57
459 483 3.129287 CCATACTCAACTGGGCACAAATC 59.871 47.826 0.00 0.00 0.00 2.17
460 484 3.091545 CCATACTCAACTGGGCACAAAT 58.908 45.455 0.00 0.00 0.00 2.32
468 492 4.697514 CTGTCCATACCATACTCAACTGG 58.302 47.826 0.00 0.00 38.55 4.00
469 493 4.122776 GCTGTCCATACCATACTCAACTG 58.877 47.826 0.00 0.00 0.00 3.16
597 631 9.244799 GTTGTTTTAGTACCAGAAAAATCCTTG 57.755 33.333 0.00 0.00 0.00 3.61
603 637 7.477945 TTGGGTTGTTTTAGTACCAGAAAAA 57.522 32.000 0.00 0.00 33.51 1.94
604 638 7.477945 TTTGGGTTGTTTTAGTACCAGAAAA 57.522 32.000 0.00 0.00 33.51 2.29
613 647 4.337274 CGTCTCCTTTTGGGTTGTTTTAGT 59.663 41.667 0.00 0.00 40.87 2.24
614 648 4.337274 ACGTCTCCTTTTGGGTTGTTTTAG 59.663 41.667 0.00 0.00 40.87 1.85
634 668 4.442332 GGGGAATTCTTTTGTTTTCCACGT 60.442 41.667 5.23 0.00 39.52 4.49
638 677 4.065088 GCTGGGGAATTCTTTTGTTTTCC 58.935 43.478 5.23 0.00 37.49 3.13
646 685 8.289544 ACTTATTTATAGGCTGGGGAATTCTTT 58.710 33.333 5.23 0.00 0.00 2.52
647 686 7.725844 CACTTATTTATAGGCTGGGGAATTCTT 59.274 37.037 5.23 0.00 0.00 2.52
648 687 7.234355 CACTTATTTATAGGCTGGGGAATTCT 58.766 38.462 5.23 0.00 0.00 2.40
697 753 3.092511 GAGGCTGGGATGGCAGGA 61.093 66.667 0.00 0.00 34.73 3.86
816 872 2.125225 GTGGGAAGGGAGGAGGGT 59.875 66.667 0.00 0.00 0.00 4.34
817 873 1.690985 GAGTGGGAAGGGAGGAGGG 60.691 68.421 0.00 0.00 0.00 4.30
818 874 2.060980 CGAGTGGGAAGGGAGGAGG 61.061 68.421 0.00 0.00 0.00 4.30
819 875 2.726351 GCGAGTGGGAAGGGAGGAG 61.726 68.421 0.00 0.00 0.00 3.69
820 876 2.683933 GCGAGTGGGAAGGGAGGA 60.684 66.667 0.00 0.00 0.00 3.71
821 877 4.148825 CGCGAGTGGGAAGGGAGG 62.149 72.222 0.00 0.00 0.00 4.30
838 899 0.536724 GGAATGGGGAATGTGGCAAC 59.463 55.000 0.00 0.00 0.00 4.17
875 936 1.623542 CGACGGGGAAGGAAGGGAAT 61.624 60.000 0.00 0.00 0.00 3.01
877 938 2.682494 CGACGGGGAAGGAAGGGA 60.682 66.667 0.00 0.00 0.00 4.20
1639 1706 1.910580 AAATGGGACGCGGATGAGGT 61.911 55.000 12.47 0.00 0.00 3.85
1668 1735 3.461773 CGGGACACGCTCCAGGAT 61.462 66.667 0.00 0.00 41.63 3.24
1914 1981 2.970974 GCGTTCTTGCAGGGTGAGC 61.971 63.158 0.00 0.00 34.15 4.26
2139 2206 2.345244 CGCACCTGCTTCTCCAGT 59.655 61.111 0.00 0.00 39.32 4.00
2243 2310 1.274728 CCACCAAATTGCCCGATCAAA 59.725 47.619 0.00 0.00 0.00 2.69
2332 2399 0.445436 AGACGAAGGCACGTACGTAG 59.555 55.000 22.34 16.04 46.52 3.51
2383 2456 3.956199 CCATCTTTAACATCATGGTGGCT 59.044 43.478 11.45 0.00 32.49 4.75
2536 2609 5.954153 ACCATGAGAGAGATCAAAGTGAT 57.046 39.130 0.00 0.00 40.34 3.06
2562 2635 8.487176 GTGTAATTACAGAACAAGGCATTTTTG 58.513 33.333 18.56 0.00 36.78 2.44
2620 2694 5.425630 ACGGAGACAGATAAAAACCATACC 58.574 41.667 0.00 0.00 0.00 2.73
2621 2695 6.036844 GGAACGGAGACAGATAAAAACCATAC 59.963 42.308 0.00 0.00 0.00 2.39
2623 2697 4.941873 GGAACGGAGACAGATAAAAACCAT 59.058 41.667 0.00 0.00 0.00 3.55
2625 2699 4.392138 CAGGAACGGAGACAGATAAAAACC 59.608 45.833 0.00 0.00 0.00 3.27
2626 2700 4.142881 GCAGGAACGGAGACAGATAAAAAC 60.143 45.833 0.00 0.00 0.00 2.43
2657 5904 5.957910 TGGAACGCAGTAAAAATGTTTTG 57.042 34.783 0.00 0.00 45.00 2.44
2658 5905 6.592220 ACTTTGGAACGCAGTAAAAATGTTTT 59.408 30.769 0.00 0.00 45.00 2.43
2687 5934 2.744202 CCTTACAATGTCAGCGCTCTTT 59.256 45.455 7.13 0.00 0.00 2.52
2853 6213 1.511305 CCTTTCAGCAGCATGGCAG 59.489 57.895 0.00 0.00 35.86 4.85
2870 6230 3.898741 CTCCTCCTATAGACTTTCACCCC 59.101 52.174 0.00 0.00 0.00 4.95
3014 6376 4.464069 AGAGCTAACTGGACAAGATCAC 57.536 45.455 0.00 0.00 0.00 3.06
3074 6437 3.550820 TGCTCTAACAAAGACCAAAGCA 58.449 40.909 0.00 0.00 30.38 3.91
3081 6444 5.538067 GTTGGAGATGCTCTAACAAAGAC 57.462 43.478 15.79 0.00 46.43 3.01
3088 6451 2.679059 GCTGCTGTTGGAGATGCTCTAA 60.679 50.000 0.00 0.00 33.10 2.10
3089 6452 1.134580 GCTGCTGTTGGAGATGCTCTA 60.135 52.381 0.00 0.00 33.10 2.43
3090 6453 0.392729 GCTGCTGTTGGAGATGCTCT 60.393 55.000 0.00 0.00 33.10 4.09
3118 6481 4.619320 CCCTTGGTGCCTTGCCCA 62.619 66.667 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.