Multiple sequence alignment - TraesCS5B01G168000

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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 TraesCS5B01G168000 chr5B 100.000 3451 0 0 1 3451 311843843 311847293 0.000000e+00 6373
1 TraesCS5B01G168000 chr5B 90.969 609 46 6 4 610 386868009 386867408 0.000000e+00 811
2 TraesCS5B01G168000 chr1B 98.143 2854 41 2 610 3451 400295118 400297971 0.000000e+00 4966
3 TraesCS5B01G168000 chr1B 90.909 594 44 7 4 594 496659750 496660336 0.000000e+00 789
4 TraesCS5B01G168000 chr1B 87.109 543 59 5 8 548 229495130 229494597 3.810000e-169 604
5 TraesCS5B01G168000 chr1B 87.571 531 53 10 7 527 356988678 356988151 1.370000e-168 603
6 TraesCS5B01G168000 chr5A 98.007 2860 42 4 607 3451 593169437 593166578 0.000000e+00 4951
7 TraesCS5B01G168000 chr5A 97.597 2872 41 5 607 3451 506137835 506134965 0.000000e+00 4896
8 TraesCS5B01G168000 chr3A 97.863 2855 48 2 607 3451 648036389 648033538 0.000000e+00 4922
9 TraesCS5B01G168000 chr3A 97.767 2866 43 4 606 3451 639500587 639497723 0.000000e+00 4918
10 TraesCS5B01G168000 chr7B 97.831 2859 45 5 610 3451 312341953 312339095 0.000000e+00 4920
11 TraesCS5B01G168000 chr7B 97.700 2869 44 7 604 3451 244397987 244400854 0.000000e+00 4913
12 TraesCS5B01G168000 chr2A 97.659 2862 48 2 609 3451 84594388 84591527 0.000000e+00 4896
13 TraesCS5B01G168000 chr2A 97.511 2852 52 6 610 3451 310415268 310412426 0.000000e+00 4855
14 TraesCS5B01G168000 chr2A 93.659 205 4 1 610 805 310410241 310410037 7.240000e-77 298
15 TraesCS5B01G168000 chr3B 97.686 2852 43 6 610 3451 344281159 344278321 0.000000e+00 4879
16 TraesCS5B01G168000 chr1D 92.991 585 37 4 27 610 180046873 180046292 0.000000e+00 850
17 TraesCS5B01G168000 chr2B 94.173 532 30 1 80 610 662905094 662904563 0.000000e+00 809
18 TraesCS5B01G168000 chr6A 87.109 543 58 7 8 548 586061439 586060907 3.810000e-169 604
19 TraesCS5B01G168000 chr6B 87.619 525 54 6 6 525 360615676 360615158 1.770000e-167 599
20 TraesCS5B01G168000 chr6B 86.717 527 55 10 7 525 360584331 360583812 3.860000e-159 571
21 TraesCS5B01G168000 chrUn 84.029 551 49 23 1 547 53048521 53049036 8.600000e-136 494


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 TraesCS5B01G168000 chr5B 311843843 311847293 3450 False 6373.0 6373 100.000 1 3451 1 chr5B.!!$F1 3450
1 TraesCS5B01G168000 chr5B 386867408 386868009 601 True 811.0 811 90.969 4 610 1 chr5B.!!$R1 606
2 TraesCS5B01G168000 chr1B 400295118 400297971 2853 False 4966.0 4966 98.143 610 3451 1 chr1B.!!$F1 2841
3 TraesCS5B01G168000 chr1B 496659750 496660336 586 False 789.0 789 90.909 4 594 1 chr1B.!!$F2 590
4 TraesCS5B01G168000 chr1B 229494597 229495130 533 True 604.0 604 87.109 8 548 1 chr1B.!!$R1 540
5 TraesCS5B01G168000 chr1B 356988151 356988678 527 True 603.0 603 87.571 7 527 1 chr1B.!!$R2 520
6 TraesCS5B01G168000 chr5A 593166578 593169437 2859 True 4951.0 4951 98.007 607 3451 1 chr5A.!!$R2 2844
7 TraesCS5B01G168000 chr5A 506134965 506137835 2870 True 4896.0 4896 97.597 607 3451 1 chr5A.!!$R1 2844
8 TraesCS5B01G168000 chr3A 648033538 648036389 2851 True 4922.0 4922 97.863 607 3451 1 chr3A.!!$R2 2844
9 TraesCS5B01G168000 chr3A 639497723 639500587 2864 True 4918.0 4918 97.767 606 3451 1 chr3A.!!$R1 2845
10 TraesCS5B01G168000 chr7B 312339095 312341953 2858 True 4920.0 4920 97.831 610 3451 1 chr7B.!!$R1 2841
11 TraesCS5B01G168000 chr7B 244397987 244400854 2867 False 4913.0 4913 97.700 604 3451 1 chr7B.!!$F1 2847
12 TraesCS5B01G168000 chr2A 84591527 84594388 2861 True 4896.0 4896 97.659 609 3451 1 chr2A.!!$R1 2842
13 TraesCS5B01G168000 chr2A 310410037 310415268 5231 True 2576.5 4855 95.585 610 3451 2 chr2A.!!$R2 2841
14 TraesCS5B01G168000 chr3B 344278321 344281159 2838 True 4879.0 4879 97.686 610 3451 1 chr3B.!!$R1 2841
15 TraesCS5B01G168000 chr1D 180046292 180046873 581 True 850.0 850 92.991 27 610 1 chr1D.!!$R1 583
16 TraesCS5B01G168000 chr2B 662904563 662905094 531 True 809.0 809 94.173 80 610 1 chr2B.!!$R1 530
17 TraesCS5B01G168000 chr6A 586060907 586061439 532 True 604.0 604 87.109 8 548 1 chr6A.!!$R1 540
18 TraesCS5B01G168000 chr6B 360615158 360615676 518 True 599.0 599 87.619 6 525 1 chr6B.!!$R2 519
19 TraesCS5B01G168000 chr6B 360583812 360584331 519 True 571.0 571 86.717 7 525 1 chr6B.!!$R1 518
20 TraesCS5B01G168000 chrUn 53048521 53049036 515 False 494.0 494 84.029 1 547 1 chrUn.!!$F1 546

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
543 552 0.107459 GAGCAAGAGTGTCATCCCCC 60.107 60.0 0.00 0.00 0.00 5.40 F
832 861 0.332972 GAGCTTGGGTTCCCAATCCT 59.667 55.0 21.61 19.38 44.07 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1643 1683 1.340889 GCTGATGAAACAACCCAGCAA 59.659 47.619 0.0 0.0 46.68 3.91 R
2787 2828 0.534877 AAGTCATGCGAGTGTGGCAA 60.535 50.000 0.0 0.0 44.66 4.52 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
35 36 1.752683 ATTACCCGTTGCGCCAAATA 58.247 45.000 4.18 0.00 0.00 1.40
199 205 6.472686 AGATGTAGTAAGGCGAGAGAAAAT 57.527 37.500 0.00 0.00 0.00 1.82
200 206 6.276847 AGATGTAGTAAGGCGAGAGAAAATG 58.723 40.000 0.00 0.00 0.00 2.32
253 260 4.442073 CGGTTGAGAACTTGAAGCAAAATG 59.558 41.667 0.00 0.00 0.00 2.32
274 282 3.645687 TGGAGCAAAAGCCCAATTAAACT 59.354 39.130 0.00 0.00 0.00 2.66
309 317 7.410120 AGCCATTATTTTTCTCAACTTAGGG 57.590 36.000 0.00 0.00 0.00 3.53
325 333 7.567250 TCAACTTAGGGGTATATGATCTTGACA 59.433 37.037 0.00 0.00 0.00 3.58
329 337 6.770286 AGGGGTATATGATCTTGACATTGT 57.230 37.500 0.00 0.00 0.00 2.71
333 341 8.103305 GGGGTATATGATCTTGACATTGTACAT 58.897 37.037 0.00 0.00 0.00 2.29
346 354 9.715123 TTGACATTGTACATAGAATTATTTGCG 57.285 29.630 0.00 0.00 0.00 4.85
357 365 6.449635 AGAATTATTTGCGTATCAAAGCCA 57.550 33.333 0.00 0.00 46.68 4.75
361 369 9.410556 GAATTATTTGCGTATCAAAGCCATTAT 57.589 29.630 0.00 0.00 46.68 1.28
382 390 3.806949 TTGGTGCTAATGTTTCTCCCT 57.193 42.857 0.00 0.00 0.00 4.20
438 447 4.715527 AAGTAATACTCCTCCGTCACAC 57.284 45.455 0.00 0.00 0.00 3.82
439 448 3.693807 AGTAATACTCCTCCGTCACACA 58.306 45.455 0.00 0.00 0.00 3.72
440 449 4.084287 AGTAATACTCCTCCGTCACACAA 58.916 43.478 0.00 0.00 0.00 3.33
441 450 4.710375 AGTAATACTCCTCCGTCACACAAT 59.290 41.667 0.00 0.00 0.00 2.71
442 451 3.526931 ATACTCCTCCGTCACACAATG 57.473 47.619 0.00 0.00 0.00 2.82
443 452 1.048601 ACTCCTCCGTCACACAATGT 58.951 50.000 0.00 0.00 0.00 2.71
448 457 2.416836 CCTCCGTCACACAATGTACGAT 60.417 50.000 8.55 0.00 32.90 3.73
455 464 5.113381 CGTCACACAATGTACGATGTTTTTG 59.887 40.000 1.32 0.81 32.90 2.44
457 466 4.737279 CACACAATGTACGATGTTTTTGCA 59.263 37.500 0.94 0.00 0.00 4.08
486 495 5.500234 TCATTTACACAAAGGATCTCCCAG 58.500 41.667 0.00 0.00 37.41 4.45
498 507 3.913163 GGATCTCCCAGAACCTATGGAAT 59.087 47.826 0.00 0.00 40.51 3.01
540 549 4.727507 TCTTAGAGCAAGAGTGTCATCC 57.272 45.455 0.00 0.00 38.39 3.51
543 552 0.107459 GAGCAAGAGTGTCATCCCCC 60.107 60.000 0.00 0.00 0.00 5.40
546 555 1.547675 GCAAGAGTGTCATCCCCCAAA 60.548 52.381 0.00 0.00 0.00 3.28
547 556 2.875296 CAAGAGTGTCATCCCCCAAAA 58.125 47.619 0.00 0.00 0.00 2.44
548 557 2.558359 CAAGAGTGTCATCCCCCAAAAC 59.442 50.000 0.00 0.00 0.00 2.43
549 558 1.075536 AGAGTGTCATCCCCCAAAACC 59.924 52.381 0.00 0.00 0.00 3.27
550 559 1.075536 GAGTGTCATCCCCCAAAACCT 59.924 52.381 0.00 0.00 0.00 3.50
551 560 1.503347 AGTGTCATCCCCCAAAACCTT 59.497 47.619 0.00 0.00 0.00 3.50
552 561 2.090775 AGTGTCATCCCCCAAAACCTTT 60.091 45.455 0.00 0.00 0.00 3.11
553 562 2.037121 GTGTCATCCCCCAAAACCTTTG 59.963 50.000 0.00 0.00 0.00 2.77
554 563 2.325484 GTCATCCCCCAAAACCTTTGT 58.675 47.619 0.00 0.00 0.00 2.83
555 564 2.037121 GTCATCCCCCAAAACCTTTGTG 59.963 50.000 0.00 0.00 0.00 3.33
556 565 1.347378 CATCCCCCAAAACCTTTGTGG 59.653 52.381 0.00 0.00 42.93 4.17
568 577 3.663995 CCTTTGTGGTTGCATGAATGA 57.336 42.857 0.00 0.00 0.00 2.57
569 578 3.992643 CCTTTGTGGTTGCATGAATGAA 58.007 40.909 0.00 0.00 0.00 2.57
570 579 4.378774 CCTTTGTGGTTGCATGAATGAAA 58.621 39.130 0.00 0.00 0.00 2.69
571 580 4.211794 CCTTTGTGGTTGCATGAATGAAAC 59.788 41.667 5.68 5.68 44.05 2.78
572 581 4.669206 TTGTGGTTGCATGAATGAAACT 57.331 36.364 12.78 0.00 44.18 2.66
573 582 4.669206 TGTGGTTGCATGAATGAAACTT 57.331 36.364 12.78 0.00 44.18 2.66
574 583 5.781210 TGTGGTTGCATGAATGAAACTTA 57.219 34.783 12.78 1.99 44.18 2.24
575 584 5.771469 TGTGGTTGCATGAATGAAACTTAG 58.229 37.500 12.78 0.00 44.18 2.18
576 585 5.163513 GTGGTTGCATGAATGAAACTTAGG 58.836 41.667 12.78 0.00 44.18 2.69
577 586 4.832266 TGGTTGCATGAATGAAACTTAGGT 59.168 37.500 12.78 0.00 44.18 3.08
578 587 5.163513 GGTTGCATGAATGAAACTTAGGTG 58.836 41.667 12.78 0.00 44.18 4.00
579 588 5.278957 GGTTGCATGAATGAAACTTAGGTGT 60.279 40.000 12.78 0.00 44.18 4.16
580 589 6.215845 GTTGCATGAATGAAACTTAGGTGTT 58.784 36.000 6.87 0.00 42.00 3.32
581 590 5.771469 TGCATGAATGAAACTTAGGTGTTG 58.229 37.500 0.00 0.00 0.00 3.33
582 591 5.301551 TGCATGAATGAAACTTAGGTGTTGT 59.698 36.000 0.00 0.00 0.00 3.32
583 592 6.183360 TGCATGAATGAAACTTAGGTGTTGTT 60.183 34.615 0.00 0.00 0.00 2.83
584 593 6.701400 GCATGAATGAAACTTAGGTGTTGTTT 59.299 34.615 0.00 0.00 36.73 2.83
585 594 7.865385 GCATGAATGAAACTTAGGTGTTGTTTA 59.135 33.333 0.00 0.00 34.55 2.01
586 595 9.398170 CATGAATGAAACTTAGGTGTTGTTTAG 57.602 33.333 0.00 0.00 34.55 1.85
587 596 7.422399 TGAATGAAACTTAGGTGTTGTTTAGC 58.578 34.615 0.00 0.00 34.55 3.09
588 597 5.412526 TGAAACTTAGGTGTTGTTTAGCG 57.587 39.130 0.00 0.00 34.55 4.26
589 598 3.891056 AACTTAGGTGTTGTTTAGCGC 57.109 42.857 0.00 0.00 0.00 5.92
590 599 2.148768 ACTTAGGTGTTGTTTAGCGCC 58.851 47.619 2.29 0.00 37.90 6.53
592 601 3.007182 ACTTAGGTGTTGTTTAGCGCCTA 59.993 43.478 2.29 0.00 44.89 3.93
593 602 1.804601 AGGTGTTGTTTAGCGCCTAC 58.195 50.000 2.29 0.00 44.89 3.18
594 603 1.071071 AGGTGTTGTTTAGCGCCTACA 59.929 47.619 2.29 2.78 44.89 2.74
595 604 1.874872 GGTGTTGTTTAGCGCCTACAA 59.125 47.619 2.29 9.72 35.11 2.41
596 605 4.601765 AGGTGTTGTTTAGCGCCTACAAC 61.602 47.826 28.62 28.62 44.89 3.32
597 606 6.786777 AGGTGTTGTTTAGCGCCTACAACT 62.787 45.833 31.82 22.67 44.89 3.16
598 607 7.476175 AGGTGTTGTTTAGCGCCTACAACTA 62.476 44.000 31.82 22.40 44.89 2.24
599 608 4.317804 GTTGTTTAGCGCCTACAACTAC 57.682 45.455 28.30 18.48 44.98 2.73
600 609 3.947910 TGTTTAGCGCCTACAACTACT 57.052 42.857 2.29 0.00 0.00 2.57
601 610 5.163513 GTTGTTTAGCGCCTACAACTACTA 58.836 41.667 28.30 6.39 44.98 1.82
602 611 5.389859 TGTTTAGCGCCTACAACTACTAA 57.610 39.130 2.29 0.00 0.00 2.24
603 612 5.782047 TGTTTAGCGCCTACAACTACTAAA 58.218 37.500 2.29 0.00 0.00 1.85
604 613 5.865552 TGTTTAGCGCCTACAACTACTAAAG 59.134 40.000 2.29 0.00 32.09 1.85
605 614 3.521947 AGCGCCTACAACTACTAAAGG 57.478 47.619 2.29 0.00 0.00 3.11
629 638 4.093743 TCTGTTGGGCTGTGTCTTATCTA 58.906 43.478 0.00 0.00 0.00 1.98
646 655 8.543774 GTCTTATCTATATTTCAGTGTGTGTGC 58.456 37.037 0.00 0.00 0.00 4.57
654 682 1.375396 AGTGTGTGTGCGTGTGTGT 60.375 52.632 0.00 0.00 0.00 3.72
832 861 0.332972 GAGCTTGGGTTCCCAATCCT 59.667 55.000 21.61 19.38 44.07 3.24
1097 1137 2.281761 CCCAGGTGCGCTTGTTCT 60.282 61.111 9.73 0.00 0.00 3.01
1172 1212 4.018688 GGAAGGGGTCACAAACTACCTAAT 60.019 45.833 0.00 0.00 35.19 1.73
1180 1220 4.081862 TCACAAACTACCTAATCTGGTCCG 60.082 45.833 0.00 0.00 41.22 4.79
1250 1290 1.201424 GGGGAAGTAGATGAACCGGT 58.799 55.000 0.00 0.00 0.00 5.28
1266 1306 1.230635 CGGTGAACAGGGCAAGTGAG 61.231 60.000 0.00 0.00 0.00 3.51
1405 1445 2.714250 ACCCTGGAAACATTGTACTCCA 59.286 45.455 15.96 15.96 41.51 3.86
1592 1632 4.338879 ACTAAGAAGTGGGTAGAGCGTAA 58.661 43.478 0.00 0.00 33.57 3.18
1643 1683 3.087781 GCTCAGAATTTGAAGGAAGGCT 58.912 45.455 0.00 0.00 34.81 4.58
1755 1795 1.065926 ACTGGAGAAGCGAATGCATCA 60.066 47.619 0.00 0.00 46.23 3.07
1775 1815 2.224079 CACGCTCAGCATTTACTGTGTT 59.776 45.455 0.00 0.00 38.84 3.32
1992 2033 1.593196 CAACGCAAGAAGAAGGGACA 58.407 50.000 0.00 0.00 43.62 4.02
2017 2058 3.622514 CCTCTCAAGGGGAGTCGG 58.377 66.667 0.00 0.00 44.40 4.79
2046 2087 0.178990 GCCAGGAGGACAACACCTTT 60.179 55.000 0.00 0.00 40.73 3.11
2501 2542 2.146920 AGGTCTGGTGCTAGTCCTAC 57.853 55.000 0.16 5.95 35.00 3.18
2714 2755 3.056322 ACGAGTATATCCCCGTTTATGCC 60.056 47.826 0.00 0.00 30.41 4.40
2820 2861 3.118408 GCATGACTTGGGTGTACCTCATA 60.118 47.826 0.00 0.00 41.11 2.15
2821 2862 4.444876 GCATGACTTGGGTGTACCTCATAT 60.445 45.833 0.00 0.00 41.11 1.78
3101 3181 4.202151 GCCAAAATTCTTGTGGAGTGAAGT 60.202 41.667 0.09 0.00 34.05 3.01
3181 3261 4.079558 AGTCCCCATGTGAGATGCTATTTT 60.080 41.667 0.00 0.00 0.00 1.82
3250 3330 4.416620 CTTCGTTAGAGATCACAGACCAC 58.583 47.826 0.00 0.00 0.00 4.16
3275 3355 0.250513 GGAAAGCTGGATCCACGAGT 59.749 55.000 11.44 0.00 35.71 4.18
3347 3427 1.376466 GGAGTCCTGCTGAAAGGCA 59.624 57.895 0.41 0.00 40.15 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 0.550914 TTGAACTGGGACCTTGTGCT 59.449 50.000 0.00 0.00 0.00 4.40
220 227 9.724839 CTTCAAGTTCTCAACCGTTTAAATAAA 57.275 29.630 0.00 0.00 0.00 1.40
226 233 4.193090 TGCTTCAAGTTCTCAACCGTTTA 58.807 39.130 0.00 0.00 0.00 2.01
243 250 2.481568 GGCTTTTGCTCCATTTTGCTTC 59.518 45.455 0.00 0.00 46.54 3.86
244 251 2.497138 GGCTTTTGCTCCATTTTGCTT 58.503 42.857 0.00 0.00 46.54 3.91
245 252 1.271001 GGGCTTTTGCTCCATTTTGCT 60.271 47.619 0.00 0.00 46.54 3.91
300 308 7.735917 TGTCAAGATCATATACCCCTAAGTTG 58.264 38.462 0.00 0.00 0.00 3.16
333 341 7.561021 TGGCTTTGATACGCAAATAATTCTA 57.439 32.000 0.00 0.00 44.90 2.10
357 365 6.897413 AGGGAGAAACATTAGCACCAAATAAT 59.103 34.615 0.00 0.00 0.00 1.28
361 369 4.112634 AGGGAGAAACATTAGCACCAAA 57.887 40.909 0.00 0.00 0.00 3.28
421 429 3.260884 ACATTGTGTGACGGAGGAGTATT 59.739 43.478 0.00 0.00 0.00 1.89
438 447 4.681025 AGCTTGCAAAAACATCGTACATTG 59.319 37.500 0.00 0.00 0.00 2.82
439 448 4.870363 AGCTTGCAAAAACATCGTACATT 58.130 34.783 0.00 0.00 0.00 2.71
440 449 4.503741 AGCTTGCAAAAACATCGTACAT 57.496 36.364 0.00 0.00 0.00 2.29
441 450 3.980646 AGCTTGCAAAAACATCGTACA 57.019 38.095 0.00 0.00 0.00 2.90
442 451 5.627172 TGATAGCTTGCAAAAACATCGTAC 58.373 37.500 0.00 0.00 0.00 3.67
443 452 5.871465 TGATAGCTTGCAAAAACATCGTA 57.129 34.783 0.00 0.00 0.00 3.43
448 457 7.205992 TGTGTAAATGATAGCTTGCAAAAACA 58.794 30.769 0.00 0.00 0.00 2.83
455 464 6.194796 TCCTTTGTGTAAATGATAGCTTGC 57.805 37.500 0.00 0.00 0.00 4.01
457 466 7.500559 GGAGATCCTTTGTGTAAATGATAGCTT 59.499 37.037 0.00 0.00 33.21 3.74
510 519 7.727181 ACACTCTTGCTCTAAGAAAAGTTCTA 58.273 34.615 0.00 0.00 44.47 2.10
512 521 6.480320 TGACACTCTTGCTCTAAGAAAAGTTC 59.520 38.462 0.00 0.00 44.47 3.01
515 524 6.091986 GGATGACACTCTTGCTCTAAGAAAAG 59.908 42.308 0.00 0.00 44.47 2.27
516 525 5.934625 GGATGACACTCTTGCTCTAAGAAAA 59.065 40.000 0.00 0.00 44.47 2.29
517 526 5.482908 GGATGACACTCTTGCTCTAAGAAA 58.517 41.667 0.00 0.00 44.47 2.52
519 528 3.449018 GGGATGACACTCTTGCTCTAAGA 59.551 47.826 0.00 0.00 43.01 2.10
520 529 3.431486 GGGGATGACACTCTTGCTCTAAG 60.431 52.174 0.00 0.00 37.76 2.18
523 532 0.908198 GGGGATGACACTCTTGCTCT 59.092 55.000 0.00 0.00 0.00 4.09
524 533 0.107459 GGGGGATGACACTCTTGCTC 60.107 60.000 0.00 0.00 0.00 4.26
525 534 0.842030 TGGGGGATGACACTCTTGCT 60.842 55.000 0.00 0.00 0.00 3.91
526 535 0.038166 TTGGGGGATGACACTCTTGC 59.962 55.000 0.00 0.00 0.00 4.01
527 536 2.558359 GTTTTGGGGGATGACACTCTTG 59.442 50.000 0.00 0.00 0.00 3.02
531 540 1.158007 AGGTTTTGGGGGATGACACT 58.842 50.000 0.00 0.00 0.00 3.55
548 557 3.663995 TCATTCATGCAACCACAAAGG 57.336 42.857 0.00 0.00 45.67 3.11
549 558 5.051816 AGTTTCATTCATGCAACCACAAAG 58.948 37.500 0.00 0.00 35.05 2.77
550 559 5.021033 AGTTTCATTCATGCAACCACAAA 57.979 34.783 0.00 0.00 35.05 2.83
551 560 4.669206 AGTTTCATTCATGCAACCACAA 57.331 36.364 0.00 0.00 35.05 3.33
552 561 4.669206 AAGTTTCATTCATGCAACCACA 57.331 36.364 0.00 0.00 35.05 4.17
553 562 5.163513 CCTAAGTTTCATTCATGCAACCAC 58.836 41.667 0.00 0.00 35.05 4.16
554 563 4.832266 ACCTAAGTTTCATTCATGCAACCA 59.168 37.500 0.00 0.00 35.05 3.67
555 564 5.163513 CACCTAAGTTTCATTCATGCAACC 58.836 41.667 0.00 0.00 35.05 3.77
556 565 5.772521 ACACCTAAGTTTCATTCATGCAAC 58.227 37.500 0.00 0.00 34.77 4.17
557 566 6.183360 ACAACACCTAAGTTTCATTCATGCAA 60.183 34.615 0.00 0.00 0.00 4.08
558 567 5.301551 ACAACACCTAAGTTTCATTCATGCA 59.698 36.000 0.00 0.00 0.00 3.96
559 568 5.772521 ACAACACCTAAGTTTCATTCATGC 58.227 37.500 0.00 0.00 0.00 4.06
560 569 9.398170 CTAAACAACACCTAAGTTTCATTCATG 57.602 33.333 0.00 0.00 36.85 3.07
561 570 8.082242 GCTAAACAACACCTAAGTTTCATTCAT 58.918 33.333 0.00 0.00 36.85 2.57
562 571 7.422399 GCTAAACAACACCTAAGTTTCATTCA 58.578 34.615 0.00 0.00 36.85 2.57
563 572 6.577427 CGCTAAACAACACCTAAGTTTCATTC 59.423 38.462 0.00 0.00 36.85 2.67
564 573 6.435428 CGCTAAACAACACCTAAGTTTCATT 58.565 36.000 0.00 0.00 36.85 2.57
565 574 5.562113 GCGCTAAACAACACCTAAGTTTCAT 60.562 40.000 0.00 0.00 36.85 2.57
566 575 4.260866 GCGCTAAACAACACCTAAGTTTCA 60.261 41.667 0.00 0.00 36.85 2.69
567 576 4.216731 GCGCTAAACAACACCTAAGTTTC 58.783 43.478 0.00 0.00 36.85 2.78
568 577 3.004002 GGCGCTAAACAACACCTAAGTTT 59.996 43.478 7.64 0.00 38.79 2.66
569 578 2.551032 GGCGCTAAACAACACCTAAGTT 59.449 45.455 7.64 0.00 0.00 2.66
570 579 2.148768 GGCGCTAAACAACACCTAAGT 58.851 47.619 7.64 0.00 0.00 2.24
571 580 2.423577 AGGCGCTAAACAACACCTAAG 58.576 47.619 7.64 0.00 0.00 2.18
572 581 2.554370 AGGCGCTAAACAACACCTAA 57.446 45.000 7.64 0.00 0.00 2.69
573 582 2.299582 TGTAGGCGCTAAACAACACCTA 59.700 45.455 7.64 0.00 0.00 3.08
574 583 1.071071 TGTAGGCGCTAAACAACACCT 59.929 47.619 7.64 0.00 0.00 4.00
575 584 1.515081 TGTAGGCGCTAAACAACACC 58.485 50.000 7.64 0.00 0.00 4.16
579 588 4.261578 AGTAGTTGTAGGCGCTAAACAA 57.738 40.909 7.64 12.70 0.00 2.83
580 589 3.947910 AGTAGTTGTAGGCGCTAAACA 57.052 42.857 7.64 6.64 0.00 2.83
581 590 5.290400 CCTTTAGTAGTTGTAGGCGCTAAAC 59.710 44.000 7.64 7.13 0.00 2.01
582 591 5.185635 TCCTTTAGTAGTTGTAGGCGCTAAA 59.814 40.000 7.64 0.00 0.00 1.85
583 592 4.706476 TCCTTTAGTAGTTGTAGGCGCTAA 59.294 41.667 7.64 0.00 0.00 3.09
584 593 4.272489 TCCTTTAGTAGTTGTAGGCGCTA 58.728 43.478 7.64 0.00 0.00 4.26
585 594 3.094572 TCCTTTAGTAGTTGTAGGCGCT 58.905 45.455 7.64 0.00 0.00 5.92
586 595 3.515330 TCCTTTAGTAGTTGTAGGCGC 57.485 47.619 0.00 0.00 0.00 6.53
587 596 5.163540 ACAGATCCTTTAGTAGTTGTAGGCG 60.164 44.000 0.00 0.00 0.00 5.52
588 597 6.223351 ACAGATCCTTTAGTAGTTGTAGGC 57.777 41.667 0.00 0.00 0.00 3.93
589 598 7.042335 CCAACAGATCCTTTAGTAGTTGTAGG 58.958 42.308 0.00 0.00 34.62 3.18
590 599 7.042335 CCCAACAGATCCTTTAGTAGTTGTAG 58.958 42.308 0.00 0.00 34.62 2.74
591 600 6.575649 GCCCAACAGATCCTTTAGTAGTTGTA 60.576 42.308 0.00 0.00 34.62 2.41
592 601 5.803470 GCCCAACAGATCCTTTAGTAGTTGT 60.803 44.000 0.00 0.00 34.62 3.32
593 602 4.636206 GCCCAACAGATCCTTTAGTAGTTG 59.364 45.833 0.00 0.00 35.80 3.16
594 603 4.536489 AGCCCAACAGATCCTTTAGTAGTT 59.464 41.667 0.00 0.00 0.00 2.24
595 604 4.080863 CAGCCCAACAGATCCTTTAGTAGT 60.081 45.833 0.00 0.00 0.00 2.73
596 605 4.080863 ACAGCCCAACAGATCCTTTAGTAG 60.081 45.833 0.00 0.00 0.00 2.57
597 606 3.844211 ACAGCCCAACAGATCCTTTAGTA 59.156 43.478 0.00 0.00 0.00 1.82
598 607 2.644798 ACAGCCCAACAGATCCTTTAGT 59.355 45.455 0.00 0.00 0.00 2.24
599 608 3.012518 CACAGCCCAACAGATCCTTTAG 58.987 50.000 0.00 0.00 0.00 1.85
600 609 2.375174 ACACAGCCCAACAGATCCTTTA 59.625 45.455 0.00 0.00 0.00 1.85
601 610 1.145738 ACACAGCCCAACAGATCCTTT 59.854 47.619 0.00 0.00 0.00 3.11
602 611 0.773644 ACACAGCCCAACAGATCCTT 59.226 50.000 0.00 0.00 0.00 3.36
603 612 0.326264 GACACAGCCCAACAGATCCT 59.674 55.000 0.00 0.00 0.00 3.24
604 613 0.326264 AGACACAGCCCAACAGATCC 59.674 55.000 0.00 0.00 0.00 3.36
605 614 2.191128 AAGACACAGCCCAACAGATC 57.809 50.000 0.00 0.00 0.00 2.75
629 638 3.058983 CACACGCACACACACTGAAATAT 60.059 43.478 0.00 0.00 0.00 1.28
646 655 1.501741 GGCCATAAGCACACACACG 59.498 57.895 0.00 0.00 46.50 4.49
654 682 4.682553 CCACATGGGCCATAAGCA 57.317 55.556 20.73 0.00 46.50 3.91
832 861 1.064003 AACCACCATCACCACTGCTA 58.936 50.000 0.00 0.00 0.00 3.49
1097 1137 2.820178 TCTGTATCACCTCAGGCTGAA 58.180 47.619 19.29 3.60 33.13 3.02
1172 1212 1.923395 AATGCCCTTCCGGACCAGA 60.923 57.895 1.83 0.00 0.00 3.86
1180 1220 4.219288 CCTCAATATTAGCAATGCCCTTCC 59.781 45.833 0.00 0.00 0.00 3.46
1250 1290 0.397941 CTCCTCACTTGCCCTGTTCA 59.602 55.000 0.00 0.00 0.00 3.18
1266 1306 1.694696 ACACTCCACTTCTTCCACTCC 59.305 52.381 0.00 0.00 0.00 3.85
1431 1471 7.289782 AGCTCATTTACTCTATCCTCAATCTGT 59.710 37.037 0.00 0.00 0.00 3.41
1592 1632 6.013032 TCCCTTCAAGAATTTCATCACTCTCT 60.013 38.462 0.00 0.00 0.00 3.10
1643 1683 1.340889 GCTGATGAAACAACCCAGCAA 59.659 47.619 0.00 0.00 46.68 3.91
1755 1795 2.169832 ACACAGTAAATGCTGAGCGT 57.830 45.000 5.49 0.00 39.62 5.07
1775 1815 4.594920 ACTCTCTTGTCTCCTTCCATTCAA 59.405 41.667 0.00 0.00 0.00 2.69
1992 2033 2.307098 CTCCCCTTGAGAGGTTGTTGAT 59.693 50.000 0.00 0.00 44.42 2.57
2017 2058 2.028876 GTCCTCCTGGCTTCTACTCTC 58.971 57.143 0.00 0.00 0.00 3.20
2097 2138 7.389053 GGAAGGAAATCATGTGTGGATATAGAC 59.611 40.741 0.00 0.00 0.00 2.59
2307 2348 1.615392 ACAGGAAAAGCTGGAACATGC 59.385 47.619 0.00 0.00 38.20 4.06
2501 2542 4.273148 ACTCCAACTAGTACAGCCAAAG 57.727 45.455 0.00 0.00 0.00 2.77
2693 2734 3.518590 GGCATAAACGGGGATATACTCG 58.481 50.000 5.41 5.41 0.00 4.18
2714 2755 2.926200 GTCCACACATCAGAGTGAATCG 59.074 50.000 0.57 0.00 42.05 3.34
2787 2828 0.534877 AAGTCATGCGAGTGTGGCAA 60.535 50.000 0.00 0.00 44.66 4.52
2820 2861 9.293404 CATTGGAATACCTCATCTTTATGTCAT 57.707 33.333 0.00 0.00 37.04 3.06
2821 2862 8.274322 ACATTGGAATACCTCATCTTTATGTCA 58.726 33.333 0.00 0.00 37.04 3.58
3101 3181 1.601903 GGAACGTTGCAGTCATGACAA 59.398 47.619 27.02 10.67 0.00 3.18
3181 3261 4.104738 AGGAACTGAGAATTTGTTCTCCCA 59.895 41.667 13.78 0.00 45.16 4.37
3347 3427 6.374333 GGTGACATCCATACTTACAAATGTGT 59.626 38.462 0.00 0.00 42.09 3.72
3416 3496 6.018180 GTGGTCAAGTTCTTCGAATAAAGTGT 60.018 38.462 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.