Multiple sequence alignment - TraesCS2D01G283500

Loading Multiple Alignment...

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 TraesCS2D01G283500 chr2D 100.000 2192 0 0 1 2192 357702778 357700587 0.000000e+00 4048.0
1 TraesCS2D01G283500 chr2D 84.851 1208 168 13 973 2177 34988092 34989287 0.000000e+00 1203.0
2 TraesCS2D01G283500 chr2D 85.150 1165 160 12 973 2134 585517370 585516216 0.000000e+00 1181.0
3 TraesCS2D01G283500 chr2D 84.365 1196 172 12 973 2165 34994847 34996030 0.000000e+00 1158.0
4 TraesCS2D01G283500 chr2D 87.013 77 10 0 360 436 193590652 193590728 1.080000e-13 87.9
5 TraesCS2D01G283500 chr2A 95.921 1618 50 10 579 2192 478763189 478761584 0.000000e+00 2608.0
6 TraesCS2D01G283500 chr2A 85.017 1208 166 13 973 2177 38309367 38310562 0.000000e+00 1214.0
7 TraesCS2D01G283500 chr2A 84.821 1199 165 13 968 2165 719541238 719540056 0.000000e+00 1190.0
8 TraesCS2D01G283500 chr2A 88.259 247 11 7 5 236 478763588 478763345 1.660000e-71 279.0
9 TraesCS2D01G283500 chr2A 89.706 68 7 0 369 436 718971733 718971800 1.080000e-13 87.9
10 TraesCS2D01G283500 chr2B 95.727 1568 34 11 643 2192 425353784 425352232 0.000000e+00 2494.0
11 TraesCS2D01G283500 chr2B 85.182 1208 164 13 973 2177 57664597 57665792 0.000000e+00 1225.0
12 TraesCS2D01G283500 chr2B 84.127 1197 173 14 973 2165 57672650 57673833 0.000000e+00 1142.0
13 TraesCS2D01G283500 chr2B 91.781 219 8 6 5 215 425354274 425354058 1.650000e-76 296.0
14 TraesCS2D01G283500 chr3B 88.462 52 5 1 359 410 16342516 16342566 6.530000e-06 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 TraesCS2D01G283500 chr2D 357700587 357702778 2191 True 4048.0 4048 100.000 1 2192 1 chr2D.!!$R1 2191
1 TraesCS2D01G283500 chr2D 34988092 34989287 1195 False 1203.0 1203 84.851 973 2177 1 chr2D.!!$F1 1204
2 TraesCS2D01G283500 chr2D 585516216 585517370 1154 True 1181.0 1181 85.150 973 2134 1 chr2D.!!$R2 1161
3 TraesCS2D01G283500 chr2D 34994847 34996030 1183 False 1158.0 1158 84.365 973 2165 1 chr2D.!!$F2 1192
4 TraesCS2D01G283500 chr2A 478761584 478763588 2004 True 1443.5 2608 92.090 5 2192 2 chr2A.!!$R2 2187
5 TraesCS2D01G283500 chr2A 38309367 38310562 1195 False 1214.0 1214 85.017 973 2177 1 chr2A.!!$F1 1204
6 TraesCS2D01G283500 chr2A 719540056 719541238 1182 True 1190.0 1190 84.821 968 2165 1 chr2A.!!$R1 1197
7 TraesCS2D01G283500 chr2B 425352232 425354274 2042 True 1395.0 2494 93.754 5 2192 2 chr2B.!!$R1 2187
8 TraesCS2D01G283500 chr2B 57664597 57665792 1195 False 1225.0 1225 85.182 973 2177 1 chr2B.!!$F1 1204
9 TraesCS2D01G283500 chr2B 57672650 57673833 1183 False 1142.0 1142 84.127 973 2165 1 chr2B.!!$F2 1192

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
534 681 0.108138 AGCACTAACCGGCATCTGTC 60.108 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1341 1508 1.81806 CGTGAGATGGCAATTTTGGGA 59.182 47.619 0.0 0.0 0.0 4.37 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
85 92 5.125097 GTGCTGTTCTCATTCTCATTTGGAT 59.875 40.000 0.00 0.00 0.00 3.41
140 155 3.119291 CTCGTGATCTGTATGCTCAACC 58.881 50.000 0.00 0.00 0.00 3.77
143 158 3.684305 CGTGATCTGTATGCTCAACCAAA 59.316 43.478 0.00 0.00 0.00 3.28
144 159 4.201753 CGTGATCTGTATGCTCAACCAAAG 60.202 45.833 0.00 0.00 0.00 2.77
145 160 4.697352 GTGATCTGTATGCTCAACCAAAGT 59.303 41.667 0.00 0.00 0.00 2.66
146 161 4.937620 TGATCTGTATGCTCAACCAAAGTC 59.062 41.667 0.00 0.00 0.00 3.01
147 162 4.350368 TCTGTATGCTCAACCAAAGTCA 57.650 40.909 0.00 0.00 0.00 3.41
284 410 2.754552 CCCACAATTCGAACCATCACAT 59.245 45.455 0.00 0.00 0.00 3.21
326 454 8.461222 CAAATTTGTGGAGCTTTGATCACTATA 58.539 33.333 10.15 0.00 31.76 1.31
336 464 6.752351 AGCTTTGATCACTATAACTGTGTACG 59.248 38.462 0.00 0.00 36.83 3.67
349 496 4.444536 ACTGTGTACGAACTTTTTAGGCA 58.555 39.130 0.00 0.00 0.00 4.75
359 506 6.016276 ACGAACTTTTTAGGCATGTGAGATTT 60.016 34.615 0.00 0.00 0.00 2.17
360 507 7.174253 ACGAACTTTTTAGGCATGTGAGATTTA 59.826 33.333 0.00 0.00 0.00 1.40
361 508 7.693951 CGAACTTTTTAGGCATGTGAGATTTAG 59.306 37.037 0.00 0.00 0.00 1.85
362 509 8.635765 AACTTTTTAGGCATGTGAGATTTAGA 57.364 30.769 0.00 0.00 0.00 2.10
363 510 8.273780 ACTTTTTAGGCATGTGAGATTTAGAG 57.726 34.615 0.00 0.00 0.00 2.43
364 511 7.337942 ACTTTTTAGGCATGTGAGATTTAGAGG 59.662 37.037 0.00 0.00 0.00 3.69
365 512 6.560003 TTTAGGCATGTGAGATTTAGAGGA 57.440 37.500 0.00 0.00 0.00 3.71
366 513 6.753913 TTAGGCATGTGAGATTTAGAGGAT 57.246 37.500 0.00 0.00 0.00 3.24
367 514 7.855784 TTAGGCATGTGAGATTTAGAGGATA 57.144 36.000 0.00 0.00 0.00 2.59
368 515 6.753913 AGGCATGTGAGATTTAGAGGATAA 57.246 37.500 0.00 0.00 0.00 1.75
369 516 7.327064 AGGCATGTGAGATTTAGAGGATAAT 57.673 36.000 0.00 0.00 0.00 1.28
370 517 7.753630 AGGCATGTGAGATTTAGAGGATAATT 58.246 34.615 0.00 0.00 0.00 1.40
371 518 7.664731 AGGCATGTGAGATTTAGAGGATAATTG 59.335 37.037 0.00 0.00 0.00 2.32
372 519 7.094463 GGCATGTGAGATTTAGAGGATAATTGG 60.094 40.741 0.00 0.00 0.00 3.16
373 520 7.446625 GCATGTGAGATTTAGAGGATAATTGGT 59.553 37.037 0.00 0.00 0.00 3.67
374 521 9.347240 CATGTGAGATTTAGAGGATAATTGGTT 57.653 33.333 0.00 0.00 0.00 3.67
375 522 9.927081 ATGTGAGATTTAGAGGATAATTGGTTT 57.073 29.630 0.00 0.00 0.00 3.27
376 523 9.177608 TGTGAGATTTAGAGGATAATTGGTTTG 57.822 33.333 0.00 0.00 0.00 2.93
377 524 8.131731 GTGAGATTTAGAGGATAATTGGTTTGC 58.868 37.037 0.00 0.00 0.00 3.68
378 525 8.055181 TGAGATTTAGAGGATAATTGGTTTGCT 58.945 33.333 0.00 0.00 0.00 3.91
379 526 8.230472 AGATTTAGAGGATAATTGGTTTGCTG 57.770 34.615 0.00 0.00 0.00 4.41
380 527 5.835113 TTAGAGGATAATTGGTTTGCTGC 57.165 39.130 0.00 0.00 0.00 5.25
381 528 3.026694 AGAGGATAATTGGTTTGCTGCC 58.973 45.455 0.00 0.00 0.00 4.85
382 529 2.760092 GAGGATAATTGGTTTGCTGCCA 59.240 45.455 0.00 0.00 0.00 4.92
388 535 2.706339 TTGGTTTGCTGCCAACATTT 57.294 40.000 17.00 0.00 40.69 2.32
389 536 1.950828 TGGTTTGCTGCCAACATTTG 58.049 45.000 17.00 0.00 32.29 2.32
409 556 2.276472 GCATTGCCAATACTTCGCAA 57.724 45.000 0.00 0.00 45.77 4.85
410 557 2.605030 GCATTGCCAATACTTCGCAAA 58.395 42.857 0.00 0.00 44.94 3.68
411 558 2.345341 GCATTGCCAATACTTCGCAAAC 59.655 45.455 0.00 0.00 44.94 2.93
412 559 2.715737 TTGCCAATACTTCGCAAACC 57.284 45.000 0.00 0.00 39.43 3.27
413 560 1.610363 TGCCAATACTTCGCAAACCA 58.390 45.000 0.00 0.00 0.00 3.67
414 561 1.957177 TGCCAATACTTCGCAAACCAA 59.043 42.857 0.00 0.00 0.00 3.67
415 562 2.287909 TGCCAATACTTCGCAAACCAAC 60.288 45.455 0.00 0.00 0.00 3.77
416 563 2.287909 GCCAATACTTCGCAAACCAACA 60.288 45.455 0.00 0.00 0.00 3.33
417 564 3.797184 GCCAATACTTCGCAAACCAACAA 60.797 43.478 0.00 0.00 0.00 2.83
418 565 4.555262 CCAATACTTCGCAAACCAACAAT 58.445 39.130 0.00 0.00 0.00 2.71
419 566 4.987912 CCAATACTTCGCAAACCAACAATT 59.012 37.500 0.00 0.00 0.00 2.32
420 567 5.107530 CCAATACTTCGCAAACCAACAATTG 60.108 40.000 3.24 3.24 0.00 2.32
462 609 7.894376 AAAAGAATGGCAATATCACAAGTTG 57.106 32.000 0.00 0.00 0.00 3.16
463 610 5.002464 AGAATGGCAATATCACAAGTTGC 57.998 39.130 1.81 0.97 45.54 4.17
469 616 5.921004 GCAATATCACAAGTTGCCAAAAA 57.079 34.783 1.81 0.00 41.67 1.94
470 617 6.484818 GCAATATCACAAGTTGCCAAAAAT 57.515 33.333 1.81 0.00 41.67 1.82
471 618 6.901265 GCAATATCACAAGTTGCCAAAAATT 58.099 32.000 1.81 0.00 41.67 1.82
472 619 8.027440 GCAATATCACAAGTTGCCAAAAATTA 57.973 30.769 1.81 0.00 41.67 1.40
473 620 8.502387 GCAATATCACAAGTTGCCAAAAATTAA 58.498 29.630 1.81 0.00 41.67 1.40
474 621 9.810231 CAATATCACAAGTTGCCAAAAATTAAC 57.190 29.630 1.81 0.00 0.00 2.01
475 622 9.553064 AATATCACAAGTTGCCAAAAATTAACA 57.447 25.926 1.81 0.00 0.00 2.41
476 623 7.856145 ATCACAAGTTGCCAAAAATTAACAA 57.144 28.000 1.81 0.00 0.00 2.83
477 624 7.066374 TCACAAGTTGCCAAAAATTAACAAC 57.934 32.000 1.81 0.00 40.65 3.32
496 643 5.362556 CAACTTATTGTGAGGTTGACAGG 57.637 43.478 0.00 0.00 40.74 4.00
497 644 4.706842 ACTTATTGTGAGGTTGACAGGT 57.293 40.909 0.00 0.00 0.00 4.00
498 645 5.818678 ACTTATTGTGAGGTTGACAGGTA 57.181 39.130 0.00 0.00 0.00 3.08
499 646 6.182507 ACTTATTGTGAGGTTGACAGGTAA 57.817 37.500 0.00 0.00 0.00 2.85
500 647 5.995897 ACTTATTGTGAGGTTGACAGGTAAC 59.004 40.000 0.00 0.00 0.00 2.50
501 648 3.916359 TTGTGAGGTTGACAGGTAACA 57.084 42.857 0.00 0.00 41.41 2.41
502 649 4.431416 TTGTGAGGTTGACAGGTAACAT 57.569 40.909 0.00 0.00 41.41 2.71
503 650 3.738982 TGTGAGGTTGACAGGTAACATG 58.261 45.455 0.00 0.00 41.41 3.21
504 651 3.074412 GTGAGGTTGACAGGTAACATGG 58.926 50.000 0.00 0.00 41.41 3.66
505 652 2.708861 TGAGGTTGACAGGTAACATGGT 59.291 45.455 0.00 0.00 41.41 3.55
506 653 3.904965 TGAGGTTGACAGGTAACATGGTA 59.095 43.478 0.00 0.00 41.41 3.25
507 654 4.348461 TGAGGTTGACAGGTAACATGGTAA 59.652 41.667 0.00 0.00 41.41 2.85
508 655 4.648651 AGGTTGACAGGTAACATGGTAAC 58.351 43.478 0.00 0.00 41.41 2.50
509 656 3.754850 GGTTGACAGGTAACATGGTAACC 59.245 47.826 1.05 3.71 41.41 2.85
510 657 4.391155 GTTGACAGGTAACATGGTAACCA 58.609 43.478 1.05 0.00 38.19 3.67
511 658 4.708576 TGACAGGTAACATGGTAACCAA 57.291 40.909 1.05 0.00 36.95 3.67
512 659 4.391155 TGACAGGTAACATGGTAACCAAC 58.609 43.478 1.05 0.00 36.95 3.77
513 660 3.754850 GACAGGTAACATGGTAACCAACC 59.245 47.826 1.05 0.00 45.18 3.77
524 671 3.909776 GTAACCAACCAAGCACTAACC 57.090 47.619 0.00 0.00 0.00 2.85
525 672 1.314730 AACCAACCAAGCACTAACCG 58.685 50.000 0.00 0.00 0.00 4.44
526 673 0.536460 ACCAACCAAGCACTAACCGG 60.536 55.000 0.00 0.00 0.00 5.28
527 674 1.579429 CAACCAAGCACTAACCGGC 59.421 57.895 0.00 0.00 0.00 6.13
528 675 1.149627 AACCAAGCACTAACCGGCA 59.850 52.632 0.00 0.00 0.00 5.69
529 676 0.251165 AACCAAGCACTAACCGGCAT 60.251 50.000 0.00 0.00 0.00 4.40
530 677 0.676782 ACCAAGCACTAACCGGCATC 60.677 55.000 0.00 0.00 0.00 3.91
531 678 0.392998 CCAAGCACTAACCGGCATCT 60.393 55.000 0.00 0.00 0.00 2.90
532 679 0.729116 CAAGCACTAACCGGCATCTG 59.271 55.000 0.00 0.00 0.00 2.90
533 680 0.324943 AAGCACTAACCGGCATCTGT 59.675 50.000 0.00 0.00 0.00 3.41
534 681 0.108138 AGCACTAACCGGCATCTGTC 60.108 55.000 0.00 0.00 0.00 3.51
535 682 0.391130 GCACTAACCGGCATCTGTCA 60.391 55.000 0.00 0.00 0.00 3.58
536 683 1.943968 GCACTAACCGGCATCTGTCAA 60.944 52.381 0.00 0.00 0.00 3.18
537 684 2.422597 CACTAACCGGCATCTGTCAAA 58.577 47.619 0.00 0.00 0.00 2.69
538 685 3.009723 CACTAACCGGCATCTGTCAAAT 58.990 45.455 0.00 0.00 0.00 2.32
539 686 3.440173 CACTAACCGGCATCTGTCAAATT 59.560 43.478 0.00 0.00 0.00 1.82
540 687 4.079253 ACTAACCGGCATCTGTCAAATTT 58.921 39.130 0.00 0.00 0.00 1.82
541 688 4.522789 ACTAACCGGCATCTGTCAAATTTT 59.477 37.500 0.00 0.00 0.00 1.82
542 689 3.302365 ACCGGCATCTGTCAAATTTTG 57.698 42.857 0.00 2.59 0.00 2.44
543 690 2.029110 ACCGGCATCTGTCAAATTTTGG 60.029 45.455 0.00 0.00 0.00 3.28
544 691 1.994779 CGGCATCTGTCAAATTTTGGC 59.005 47.619 6.79 6.79 35.37 4.52
545 692 2.609984 CGGCATCTGTCAAATTTTGGCA 60.610 45.455 15.16 15.16 44.14 4.92
546 693 3.602483 GGCATCTGTCAAATTTTGGCAT 58.398 40.909 16.20 0.63 45.37 4.40
547 694 3.372822 GGCATCTGTCAAATTTTGGCATG 59.627 43.478 16.20 13.44 45.37 4.06
548 695 3.181514 GCATCTGTCAAATTTTGGCATGC 60.182 43.478 20.32 20.32 45.37 4.06
549 696 3.042871 TCTGTCAAATTTTGGCATGCC 57.957 42.857 30.54 30.54 45.37 4.40
550 697 2.367894 TCTGTCAAATTTTGGCATGCCA 59.632 40.909 35.59 35.59 45.37 4.92
563 710 4.903054 TGGCATGCCAATTTTTAACATCA 58.097 34.783 36.95 8.36 44.12 3.07
564 711 5.311265 TGGCATGCCAATTTTTAACATCAA 58.689 33.333 36.95 7.62 44.12 2.57
565 712 5.766670 TGGCATGCCAATTTTTAACATCAAA 59.233 32.000 36.95 7.19 44.12 2.69
566 713 6.085573 GGCATGCCAATTTTTAACATCAAAC 58.914 36.000 32.08 0.00 35.81 2.93
567 714 6.085573 GCATGCCAATTTTTAACATCAAACC 58.914 36.000 6.36 0.00 0.00 3.27
568 715 6.293845 GCATGCCAATTTTTAACATCAAACCA 60.294 34.615 6.36 0.00 0.00 3.67
569 716 7.646314 CATGCCAATTTTTAACATCAAACCAA 58.354 30.769 0.00 0.00 0.00 3.67
570 717 7.814264 TGCCAATTTTTAACATCAAACCAAT 57.186 28.000 0.00 0.00 0.00 3.16
571 718 7.869800 TGCCAATTTTTAACATCAAACCAATC 58.130 30.769 0.00 0.00 0.00 2.67
572 719 7.500227 TGCCAATTTTTAACATCAAACCAATCA 59.500 29.630 0.00 0.00 0.00 2.57
573 720 8.513774 GCCAATTTTTAACATCAAACCAATCAT 58.486 29.630 0.00 0.00 0.00 2.45
574 721 9.828852 CCAATTTTTAACATCAAACCAATCATG 57.171 29.630 0.00 0.00 0.00 3.07
575 722 9.332301 CAATTTTTAACATCAAACCAATCATGC 57.668 29.630 0.00 0.00 0.00 4.06
576 723 8.851541 ATTTTTAACATCAAACCAATCATGCT 57.148 26.923 0.00 0.00 0.00 3.79
577 724 7.887996 TTTTAACATCAAACCAATCATGCTC 57.112 32.000 0.00 0.00 0.00 4.26
578 725 6.839124 TTAACATCAAACCAATCATGCTCT 57.161 33.333 0.00 0.00 0.00 4.09
611 758 6.894103 AGGATAATCAAGCAAGTTCTGGAATT 59.106 34.615 0.00 0.00 0.00 2.17
726 873 1.141449 GCGCCCAAGCATATGCAAA 59.859 52.632 28.62 0.00 45.16 3.68
728 875 1.807377 GCGCCCAAGCATATGCAAATT 60.807 47.619 28.62 12.34 45.16 1.82
731 878 2.807837 GCCCAAGCATATGCAAATTCCC 60.808 50.000 28.62 7.61 45.16 3.97
771 936 3.381272 ACACTAGCTCAAGCAAGCAAAAA 59.619 39.130 4.59 0.00 45.00 1.94
875 1040 4.032703 CTGCTATTTTTGCCGCAGTATT 57.967 40.909 0.00 0.00 43.53 1.89
912 1079 9.157104 TGTGTGAAATAAATATGTACACGATGT 57.843 29.630 0.00 0.00 39.66 3.06
925 1092 5.417894 TGTACACGATGTGGTTCTCTTCTAT 59.582 40.000 0.00 0.00 37.94 1.98
946 1113 4.963318 TTTGTGGCATCCCAATAAAACA 57.037 36.364 0.00 0.00 44.33 2.83
963 1130 9.065871 CAATAAAACAAACATTCTAGCTACAGC 57.934 33.333 0.00 0.00 42.49 4.40
1212 1379 1.686800 GGGAACAGCCATGGCCATT 60.687 57.895 33.14 26.13 43.17 3.16
1341 1508 1.677637 GGGCCGAGAATCCTTCGACT 61.678 60.000 0.00 0.00 34.02 4.18
1421 1588 3.680156 GCCAACATCAAAGGCCGA 58.320 55.556 0.00 0.00 42.58 5.54
1479 1646 2.731572 CCAAGAGCAGTCCCAATCAAT 58.268 47.619 0.00 0.00 0.00 2.57
1517 1684 3.323775 ACCTTGGTGAAGAGAGGGTAAA 58.676 45.455 0.00 0.00 33.51 2.01
1581 1748 3.459232 ACTATGGACATCATGACACCG 57.541 47.619 0.00 0.00 37.30 4.94
2165 2338 6.659242 TGGGATGGAGAGACAATTTAGTTTTC 59.341 38.462 0.00 0.00 0.00 2.29
2183 2356 2.873170 TCGCGAAACATAAGCTTGTG 57.127 45.000 20.36 20.36 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 105 2.294233 GTCCACTTTGCTGCATGAGAAA 59.706 45.455 17.12 2.59 0.00 2.52
107 114 1.728971 GATCACGAGTCCACTTTGCTG 59.271 52.381 0.00 0.00 0.00 4.41
140 155 2.878580 TGCTTGTGCAGTTTGACTTTG 58.121 42.857 0.00 0.00 45.31 2.77
262 388 2.159382 GTGATGGTTCGAATTGTGGGT 58.841 47.619 0.00 0.00 0.00 4.51
305 433 6.595326 CAGTTATAGTGATCAAAGCTCCACAA 59.405 38.462 0.00 0.00 32.35 3.33
326 454 4.877251 TGCCTAAAAAGTTCGTACACAGTT 59.123 37.500 0.00 0.00 0.00 3.16
336 464 8.730680 TCTAAATCTCACATGCCTAAAAAGTTC 58.269 33.333 0.00 0.00 0.00 3.01
349 496 9.927081 AAACCAATTATCCTCTAAATCTCACAT 57.073 29.630 0.00 0.00 0.00 3.21
359 506 4.207165 GGCAGCAAACCAATTATCCTCTA 58.793 43.478 0.00 0.00 0.00 2.43
360 507 3.026694 GGCAGCAAACCAATTATCCTCT 58.973 45.455 0.00 0.00 0.00 3.69
361 508 2.760092 TGGCAGCAAACCAATTATCCTC 59.240 45.455 0.00 0.00 33.12 3.71
362 509 2.818921 TGGCAGCAAACCAATTATCCT 58.181 42.857 0.00 0.00 33.12 3.24
363 510 3.608316 TTGGCAGCAAACCAATTATCC 57.392 42.857 0.00 0.00 42.23 2.59
369 516 2.286872 CAAATGTTGGCAGCAAACCAA 58.713 42.857 8.44 1.35 44.86 3.67
370 517 1.474677 CCAAATGTTGGCAGCAAACCA 60.475 47.619 8.44 0.00 45.17 3.67
371 518 1.228533 CCAAATGTTGGCAGCAAACC 58.771 50.000 8.44 0.00 45.17 3.27
396 543 3.634568 TGTTGGTTTGCGAAGTATTGG 57.365 42.857 0.00 0.00 0.00 3.16
397 544 5.107530 CCAATTGTTGGTTTGCGAAGTATTG 60.108 40.000 4.43 0.00 45.93 1.90
398 545 4.987912 CCAATTGTTGGTTTGCGAAGTATT 59.012 37.500 4.43 0.00 45.93 1.89
399 546 4.555262 CCAATTGTTGGTTTGCGAAGTAT 58.445 39.130 4.43 0.00 45.93 2.12
400 547 3.971150 CCAATTGTTGGTTTGCGAAGTA 58.029 40.909 4.43 0.00 45.93 2.24
401 548 2.820330 CCAATTGTTGGTTTGCGAAGT 58.180 42.857 4.43 0.00 45.93 3.01
436 583 9.590451 CAACTTGTGATATTGCCATTCTTTTAT 57.410 29.630 0.00 0.00 0.00 1.40
437 584 7.545265 GCAACTTGTGATATTGCCATTCTTTTA 59.455 33.333 0.00 0.00 42.32 1.52
438 585 6.369615 GCAACTTGTGATATTGCCATTCTTTT 59.630 34.615 0.00 0.00 42.32 2.27
439 586 5.870978 GCAACTTGTGATATTGCCATTCTTT 59.129 36.000 0.00 0.00 42.32 2.52
440 587 5.413499 GCAACTTGTGATATTGCCATTCTT 58.587 37.500 0.00 0.00 42.32 2.52
441 588 5.002464 GCAACTTGTGATATTGCCATTCT 57.998 39.130 0.00 0.00 42.32 2.40
447 594 5.921004 TTTTTGGCAACTTGTGATATTGC 57.079 34.783 0.00 0.00 46.39 3.56
448 595 9.810231 GTTAATTTTTGGCAACTTGTGATATTG 57.190 29.630 0.00 0.00 37.61 1.90
449 596 9.553064 TGTTAATTTTTGGCAACTTGTGATATT 57.447 25.926 0.00 0.00 37.61 1.28
450 597 9.553064 TTGTTAATTTTTGGCAACTTGTGATAT 57.447 25.926 0.00 0.00 37.61 1.63
451 598 8.821894 GTTGTTAATTTTTGGCAACTTGTGATA 58.178 29.630 0.00 0.00 37.17 2.15
452 599 7.552330 AGTTGTTAATTTTTGGCAACTTGTGAT 59.448 29.630 0.00 0.00 44.79 3.06
453 600 6.876257 AGTTGTTAATTTTTGGCAACTTGTGA 59.124 30.769 0.00 0.00 44.79 3.58
454 601 7.071014 AGTTGTTAATTTTTGGCAACTTGTG 57.929 32.000 0.00 0.00 44.79 3.33
458 605 9.389755 ACAATAAGTTGTTAATTTTTGGCAACT 57.610 25.926 0.00 0.00 46.07 3.16
459 606 9.432077 CACAATAAGTTGTTAATTTTTGGCAAC 57.568 29.630 0.00 0.00 46.07 4.17
460 607 9.383519 TCACAATAAGTTGTTAATTTTTGGCAA 57.616 25.926 0.00 0.00 46.07 4.52
461 608 8.948631 TCACAATAAGTTGTTAATTTTTGGCA 57.051 26.923 0.00 0.00 46.07 4.92
462 609 8.495148 CCTCACAATAAGTTGTTAATTTTTGGC 58.505 33.333 0.00 0.00 46.07 4.52
463 610 9.541143 ACCTCACAATAAGTTGTTAATTTTTGG 57.459 29.630 0.00 0.00 46.07 3.28
467 614 9.744468 GTCAACCTCACAATAAGTTGTTAATTT 57.256 29.630 0.00 0.00 46.07 1.82
468 615 8.908903 TGTCAACCTCACAATAAGTTGTTAATT 58.091 29.630 0.00 0.00 46.07 1.40
469 616 8.458573 TGTCAACCTCACAATAAGTTGTTAAT 57.541 30.769 0.00 0.00 46.07 1.40
470 617 7.012894 CCTGTCAACCTCACAATAAGTTGTTAA 59.987 37.037 0.00 0.00 46.07 2.01
471 618 6.485313 CCTGTCAACCTCACAATAAGTTGTTA 59.515 38.462 0.00 0.00 46.07 2.41
472 619 5.299279 CCTGTCAACCTCACAATAAGTTGTT 59.701 40.000 0.00 0.00 46.07 2.83
474 621 4.821805 ACCTGTCAACCTCACAATAAGTTG 59.178 41.667 0.00 0.00 40.72 3.16
475 622 5.048846 ACCTGTCAACCTCACAATAAGTT 57.951 39.130 0.00 0.00 0.00 2.66
476 623 4.706842 ACCTGTCAACCTCACAATAAGT 57.293 40.909 0.00 0.00 0.00 2.24
477 624 5.995282 TGTTACCTGTCAACCTCACAATAAG 59.005 40.000 0.00 0.00 0.00 1.73
478 625 5.931294 TGTTACCTGTCAACCTCACAATAA 58.069 37.500 0.00 0.00 0.00 1.40
479 626 5.554437 TGTTACCTGTCAACCTCACAATA 57.446 39.130 0.00 0.00 0.00 1.90
480 627 4.431416 TGTTACCTGTCAACCTCACAAT 57.569 40.909 0.00 0.00 0.00 2.71
481 628 3.916359 TGTTACCTGTCAACCTCACAA 57.084 42.857 0.00 0.00 0.00 3.33
482 629 3.495983 CCATGTTACCTGTCAACCTCACA 60.496 47.826 0.00 0.00 0.00 3.58
483 630 3.074412 CCATGTTACCTGTCAACCTCAC 58.926 50.000 0.00 0.00 0.00 3.51
484 631 2.708861 ACCATGTTACCTGTCAACCTCA 59.291 45.455 0.00 0.00 0.00 3.86
485 632 3.418684 ACCATGTTACCTGTCAACCTC 57.581 47.619 0.00 0.00 0.00 3.85
486 633 4.506095 GGTTACCATGTTACCTGTCAACCT 60.506 45.833 0.00 0.00 33.13 3.50
487 634 3.754850 GGTTACCATGTTACCTGTCAACC 59.245 47.826 0.00 5.42 33.13 3.77
488 635 4.391155 TGGTTACCATGTTACCTGTCAAC 58.609 43.478 0.00 0.00 36.36 3.18
489 636 4.708576 TGGTTACCATGTTACCTGTCAA 57.291 40.909 0.00 0.00 36.36 3.18
490 637 4.391155 GTTGGTTACCATGTTACCTGTCA 58.609 43.478 4.38 0.00 36.36 3.58
491 638 3.754850 GGTTGGTTACCATGTTACCTGTC 59.245 47.826 14.00 0.00 46.92 3.51
492 639 3.758425 GGTTGGTTACCATGTTACCTGT 58.242 45.455 14.00 0.00 46.92 4.00
504 651 2.224784 CGGTTAGTGCTTGGTTGGTTAC 59.775 50.000 0.00 0.00 0.00 2.50
505 652 2.496111 CGGTTAGTGCTTGGTTGGTTA 58.504 47.619 0.00 0.00 0.00 2.85
506 653 1.314730 CGGTTAGTGCTTGGTTGGTT 58.685 50.000 0.00 0.00 0.00 3.67
507 654 0.536460 CCGGTTAGTGCTTGGTTGGT 60.536 55.000 0.00 0.00 0.00 3.67
508 655 1.862602 GCCGGTTAGTGCTTGGTTGG 61.863 60.000 1.90 0.00 0.00 3.77
509 656 1.169661 TGCCGGTTAGTGCTTGGTTG 61.170 55.000 1.90 0.00 0.00 3.77
510 657 0.251165 ATGCCGGTTAGTGCTTGGTT 60.251 50.000 1.90 0.00 0.00 3.67
511 658 0.676782 GATGCCGGTTAGTGCTTGGT 60.677 55.000 1.90 0.00 0.00 3.67
512 659 0.392998 AGATGCCGGTTAGTGCTTGG 60.393 55.000 1.90 0.00 0.00 3.61
513 660 0.729116 CAGATGCCGGTTAGTGCTTG 59.271 55.000 1.90 0.00 0.00 4.01
514 661 0.324943 ACAGATGCCGGTTAGTGCTT 59.675 50.000 1.90 0.00 0.00 3.91
515 662 0.108138 GACAGATGCCGGTTAGTGCT 60.108 55.000 1.90 0.00 0.00 4.40
516 663 0.391130 TGACAGATGCCGGTTAGTGC 60.391 55.000 1.90 0.00 0.00 4.40
517 664 2.093306 TTGACAGATGCCGGTTAGTG 57.907 50.000 1.90 0.00 0.00 2.74
518 665 2.851263 TTTGACAGATGCCGGTTAGT 57.149 45.000 1.90 0.00 0.00 2.24
519 666 4.701956 AAATTTGACAGATGCCGGTTAG 57.298 40.909 1.90 0.00 0.00 2.34
520 667 4.321601 CCAAAATTTGACAGATGCCGGTTA 60.322 41.667 7.37 0.00 0.00 2.85
521 668 3.554752 CCAAAATTTGACAGATGCCGGTT 60.555 43.478 7.37 0.00 0.00 4.44
522 669 2.029110 CCAAAATTTGACAGATGCCGGT 60.029 45.455 7.37 0.00 0.00 5.28
523 670 2.609350 CCAAAATTTGACAGATGCCGG 58.391 47.619 7.37 0.00 0.00 6.13
524 671 1.994779 GCCAAAATTTGACAGATGCCG 59.005 47.619 7.37 0.00 0.00 5.69
525 672 3.042871 TGCCAAAATTTGACAGATGCC 57.957 42.857 7.37 0.00 0.00 4.40
526 673 3.181514 GCATGCCAAAATTTGACAGATGC 60.182 43.478 6.36 6.10 0.00 3.91
527 674 3.372822 GGCATGCCAAAATTTGACAGATG 59.627 43.478 32.08 0.00 35.81 2.90
528 675 3.008157 TGGCATGCCAAAATTTGACAGAT 59.992 39.130 36.95 0.00 44.12 2.90
529 676 2.367894 TGGCATGCCAAAATTTGACAGA 59.632 40.909 36.95 8.86 44.12 3.41
530 677 2.768698 TGGCATGCCAAAATTTGACAG 58.231 42.857 36.95 0.00 44.12 3.51
531 678 2.924757 TGGCATGCCAAAATTTGACA 57.075 40.000 36.95 9.68 44.12 3.58
541 688 4.903054 TGATGTTAAAAATTGGCATGCCA 58.097 34.783 35.59 35.59 45.63 4.92
542 689 5.876612 TTGATGTTAAAAATTGGCATGCC 57.123 34.783 30.54 30.54 0.00 4.40
543 690 6.085573 GGTTTGATGTTAAAAATTGGCATGC 58.914 36.000 9.90 9.90 0.00 4.06
544 691 7.199541 TGGTTTGATGTTAAAAATTGGCATG 57.800 32.000 0.00 0.00 0.00 4.06
545 692 7.814264 TTGGTTTGATGTTAAAAATTGGCAT 57.186 28.000 0.00 0.00 0.00 4.40
546 693 7.500227 TGATTGGTTTGATGTTAAAAATTGGCA 59.500 29.630 0.00 0.00 0.00 4.92
547 694 7.869800 TGATTGGTTTGATGTTAAAAATTGGC 58.130 30.769 0.00 0.00 0.00 4.52
548 695 9.828852 CATGATTGGTTTGATGTTAAAAATTGG 57.171 29.630 0.00 0.00 0.00 3.16
549 696 9.332301 GCATGATTGGTTTGATGTTAAAAATTG 57.668 29.630 0.00 0.00 0.00 2.32
550 697 9.287373 AGCATGATTGGTTTGATGTTAAAAATT 57.713 25.926 0.00 0.00 0.00 1.82
551 698 8.851541 AGCATGATTGGTTTGATGTTAAAAAT 57.148 26.923 0.00 0.00 0.00 1.82
552 699 8.149647 AGAGCATGATTGGTTTGATGTTAAAAA 58.850 29.630 0.00 0.00 32.62 1.94
553 700 7.669427 AGAGCATGATTGGTTTGATGTTAAAA 58.331 30.769 0.00 0.00 32.62 1.52
554 701 7.230849 AGAGCATGATTGGTTTGATGTTAAA 57.769 32.000 0.00 0.00 32.62 1.52
555 702 6.839124 AGAGCATGATTGGTTTGATGTTAA 57.161 33.333 0.00 0.00 32.62 2.01
556 703 6.839124 AAGAGCATGATTGGTTTGATGTTA 57.161 33.333 0.00 0.00 32.62 2.41
557 704 5.733620 AAGAGCATGATTGGTTTGATGTT 57.266 34.783 0.00 0.00 32.62 2.71
558 705 5.948162 ACTAAGAGCATGATTGGTTTGATGT 59.052 36.000 0.00 0.00 32.62 3.06
559 706 6.446781 ACTAAGAGCATGATTGGTTTGATG 57.553 37.500 0.00 0.00 32.62 3.07
560 707 6.183360 CGAACTAAGAGCATGATTGGTTTGAT 60.183 38.462 12.78 0.00 34.76 2.57
561 708 5.122239 CGAACTAAGAGCATGATTGGTTTGA 59.878 40.000 12.78 0.00 34.76 2.69
562 709 5.122239 TCGAACTAAGAGCATGATTGGTTTG 59.878 40.000 0.00 6.41 34.37 2.93
563 710 5.245531 TCGAACTAAGAGCATGATTGGTTT 58.754 37.500 0.00 0.00 31.26 3.27
564 711 4.832248 TCGAACTAAGAGCATGATTGGTT 58.168 39.130 0.00 1.97 33.44 3.67
565 712 4.437239 CTCGAACTAAGAGCATGATTGGT 58.563 43.478 0.00 0.00 35.95 3.67
566 713 3.806521 CCTCGAACTAAGAGCATGATTGG 59.193 47.826 0.00 0.00 34.56 3.16
567 714 4.686972 TCCTCGAACTAAGAGCATGATTG 58.313 43.478 0.00 0.00 34.56 2.67
568 715 5.543507 ATCCTCGAACTAAGAGCATGATT 57.456 39.130 0.00 0.00 34.56 2.57
569 716 6.656632 TTATCCTCGAACTAAGAGCATGAT 57.343 37.500 0.00 0.00 34.56 2.45
570 717 6.265422 TGATTATCCTCGAACTAAGAGCATGA 59.735 38.462 0.00 0.00 34.56 3.07
571 718 6.450545 TGATTATCCTCGAACTAAGAGCATG 58.549 40.000 0.00 0.00 34.56 4.06
572 719 6.656632 TGATTATCCTCGAACTAAGAGCAT 57.343 37.500 0.00 0.00 34.56 3.79
573 720 6.465439 TTGATTATCCTCGAACTAAGAGCA 57.535 37.500 0.00 0.00 34.56 4.26
574 721 5.404066 GCTTGATTATCCTCGAACTAAGAGC 59.596 44.000 0.00 0.00 34.56 4.09
575 722 6.507900 TGCTTGATTATCCTCGAACTAAGAG 58.492 40.000 0.00 0.00 35.60 2.85
576 723 6.465439 TGCTTGATTATCCTCGAACTAAGA 57.535 37.500 0.00 0.00 0.00 2.10
577 724 6.758886 ACTTGCTTGATTATCCTCGAACTAAG 59.241 38.462 0.00 0.00 0.00 2.18
578 725 6.640518 ACTTGCTTGATTATCCTCGAACTAA 58.359 36.000 0.00 0.00 0.00 2.24
611 758 2.807967 CGATGGCTCTGTTCTGAAAACA 59.192 45.455 0.00 0.00 0.00 2.83
621 768 2.388735 TCCACTATTCGATGGCTCTGT 58.611 47.619 0.00 0.00 35.81 3.41
771 936 2.309613 TCCAATGCTGCAGTTTTCACT 58.690 42.857 16.64 0.00 0.00 3.41
803 968 1.541233 CCCTCTCTGTTGTCTTGCGTT 60.541 52.381 0.00 0.00 0.00 4.84
804 969 0.034059 CCCTCTCTGTTGTCTTGCGT 59.966 55.000 0.00 0.00 0.00 5.24
816 981 3.117474 TGTTGATATCTCGACCCCTCTCT 60.117 47.826 3.98 0.00 35.23 3.10
817 982 3.223435 TGTTGATATCTCGACCCCTCTC 58.777 50.000 3.98 0.00 35.23 3.20
912 1079 4.365514 TGCCACAAATAGAAGAGAACCA 57.634 40.909 0.00 0.00 0.00 3.67
925 1092 4.963318 TGTTTTATTGGGATGCCACAAA 57.037 36.364 4.96 6.79 0.00 2.83
946 1113 7.438459 CGTAAATAGGCTGTAGCTAGAATGTTT 59.562 37.037 0.00 0.00 41.70 2.83
1212 1379 1.999295 TCCAAATTCATCCCACTCCCA 59.001 47.619 0.00 0.00 0.00 4.37
1341 1508 1.818060 CGTGAGATGGCAATTTTGGGA 59.182 47.619 0.00 0.00 0.00 4.37
1421 1588 3.117663 TCTCACCTTTTGGCTTTACTGGT 60.118 43.478 0.00 0.00 45.59 4.00
1479 1646 3.011566 AGGTCCATGTTTGTGTCACAA 57.988 42.857 14.48 14.48 36.11 3.33
1517 1684 3.244249 GCAGGACTTCAAGACTGGTTACT 60.244 47.826 13.31 0.00 0.00 2.24
1581 1748 4.185059 GCCGGCTTAGCAGCTTGC 62.185 66.667 22.15 5.84 46.44 4.01
2165 2338 2.873170 TCACAAGCTTATGTTTCGCG 57.127 45.000 4.34 0.00 0.00 5.87


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

AutoCloner maintained by Alex Coulton.