Multiple sequence alignment - TraesCS5B01G059900

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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 TraesCS5B01G059900 chr5B 100.000 2811 0 0 1 2811 66054655 66051845 0.000000e+00 5192.0
1 TraesCS5B01G059900 chr5B 95.062 486 23 1 1105 1589 66036884 66037369 0.000000e+00 763.0
2 TraesCS5B01G059900 chr5B 88.710 62 6 1 2256 2317 188018853 188018793 1.080000e-09 75.0
3 TraesCS5B01G059900 chr5D 92.435 1388 41 30 603 1969 64133805 64135149 0.000000e+00 1923.0
4 TraesCS5B01G059900 chr5D 95.679 486 20 1 1105 1589 64144500 64144015 0.000000e+00 780.0
5 TraesCS5B01G059900 chr5D 94.499 509 15 4 1 500 64133249 64133753 0.000000e+00 773.0
6 TraesCS5B01G059900 chr5D 89.056 466 41 6 2348 2805 64138712 64139175 1.130000e-158 569.0
7 TraesCS5B01G059900 chr5D 97.368 228 6 0 2053 2280 64135329 64135556 3.400000e-104 388.0
8 TraesCS5B01G059900 chr5D 89.524 105 4 2 1953 2050 64135191 64135295 2.940000e-25 126.0
9 TraesCS5B01G059900 chr5D 100.000 43 0 0 2272 2314 64138669 64138711 2.320000e-11 80.5
10 TraesCS5B01G059900 chr5A 91.269 1214 37 27 708 1900 54463676 54464841 0.000000e+00 1591.0
11 TraesCS5B01G059900 chr5A 96.091 486 18 1 1105 1589 54482311 54481826 0.000000e+00 791.0
12 TraesCS5B01G059900 chr5A 89.231 520 19 8 1 498 54463048 54463552 1.430000e-172 616.0
13 TraesCS5B01G059900 chr5A 80.220 273 26 7 2053 2319 54465922 54466172 2.220000e-41 180.0
14 TraesCS5B01G059900 chr5A 93.617 47 3 0 1994 2040 54465832 54465878 1.400000e-08 71.3
15 TraesCS5B01G059900 chr2D 87.748 302 32 5 2514 2811 635653340 635653040 5.760000e-92 348.0
16 TraesCS5B01G059900 chr2B 85.953 299 37 5 2514 2808 793651002 793650705 5.850000e-82 315.0
17 TraesCS5B01G059900 chr2B 82.587 201 35 0 1363 1563 77170461 77170661 8.000000e-41 178.0
18 TraesCS5B01G059900 chr3D 87.546 273 30 2 2543 2811 426983202 426983474 2.100000e-81 313.0
19 TraesCS5B01G059900 chr3A 84.528 265 37 2 2543 2803 560133500 560133236 2.780000e-65 259.0
20 TraesCS5B01G059900 chr2A 83.251 203 34 0 1361 1563 51583709 51583911 1.330000e-43 187.0
21 TraesCS5B01G059900 chr7B 95.122 41 2 0 2313 2353 211970598 211970558 6.500000e-07 65.8


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 TraesCS5B01G059900 chr5B 66051845 66054655 2810 True 5192.000 5192 100.000000 1 2811 1 chr5B.!!$R1 2810
1 TraesCS5B01G059900 chr5D 64133249 64139175 5926 False 643.250 1923 93.813667 1 2805 6 chr5D.!!$F1 2804
2 TraesCS5B01G059900 chr5A 54463048 54466172 3124 False 614.575 1591 88.584250 1 2319 4 chr5A.!!$F1 2318

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
685 716 0.457166 TTTCCCGTACGTGCAGATCG 60.457 55.0 15.21 0.0 0.0 3.69 F
1620 1681 0.250295 TTGAGAGTTTGTCCCTGCCG 60.250 55.0 0.00 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 1692 0.107703 ACGGACGGACGGACTGTATA 60.108 55.0 6.0 0.0 38.34 1.47 R
2465 6589 0.335361 GACAGTGAGGGGAGGTAGGA 59.665 60.0 0.0 0.0 0.00 2.94 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
153 168 6.318648 ACCGATACAATATGCATGTGAACTTT 59.681 34.615 10.16 0.00 32.27 2.66
157 172 6.579666 ACAATATGCATGTGAACTTTGAGT 57.420 33.333 10.16 0.00 0.00 3.41
249 264 6.220726 ACACTTGCCAAATTATATGAACCC 57.779 37.500 0.00 0.00 0.00 4.11
500 526 3.560068 GCCACCAATTTACTACTCCATCG 59.440 47.826 0.00 0.00 0.00 3.84
501 527 3.560068 CCACCAATTTACTACTCCATCGC 59.440 47.826 0.00 0.00 0.00 4.58
502 528 3.245284 CACCAATTTACTACTCCATCGCG 59.755 47.826 0.00 0.00 0.00 5.87
504 530 3.489785 CCAATTTACTACTCCATCGCGTC 59.510 47.826 5.77 0.00 0.00 5.19
505 531 4.360563 CAATTTACTACTCCATCGCGTCT 58.639 43.478 5.77 0.00 0.00 4.18
506 532 4.650754 ATTTACTACTCCATCGCGTCTT 57.349 40.909 5.77 0.00 0.00 3.01
507 533 3.687572 TTACTACTCCATCGCGTCTTC 57.312 47.619 5.77 0.00 0.00 2.87
508 534 1.460504 ACTACTCCATCGCGTCTTCA 58.539 50.000 5.77 0.00 0.00 3.02
509 535 1.816835 ACTACTCCATCGCGTCTTCAA 59.183 47.619 5.77 0.00 0.00 2.69
510 536 2.159366 ACTACTCCATCGCGTCTTCAAG 60.159 50.000 5.77 0.11 0.00 3.02
511 537 0.603569 ACTCCATCGCGTCTTCAAGT 59.396 50.000 5.77 0.78 0.00 3.16
512 538 1.000955 ACTCCATCGCGTCTTCAAGTT 59.999 47.619 5.77 0.00 0.00 2.66
514 540 3.250744 CTCCATCGCGTCTTCAAGTTAA 58.749 45.455 5.77 0.00 0.00 2.01
515 541 2.991190 TCCATCGCGTCTTCAAGTTAAC 59.009 45.455 5.77 0.00 0.00 2.01
516 542 2.734606 CCATCGCGTCTTCAAGTTAACA 59.265 45.455 5.77 0.00 0.00 2.41
518 544 4.142902 CCATCGCGTCTTCAAGTTAACAAT 60.143 41.667 5.77 0.00 0.00 2.71
519 545 4.383774 TCGCGTCTTCAAGTTAACAATG 57.616 40.909 5.77 6.72 0.00 2.82
521 547 2.902484 GCGTCTTCAAGTTAACAATGCG 59.098 45.455 8.61 6.59 0.00 4.73
523 549 4.669197 GCGTCTTCAAGTTAACAATGCGAT 60.669 41.667 8.61 0.00 0.00 4.58
525 551 5.389411 CGTCTTCAAGTTAACAATGCGATCA 60.389 40.000 8.61 0.00 0.00 2.92
526 552 6.370593 GTCTTCAAGTTAACAATGCGATCAA 58.629 36.000 8.61 0.00 0.00 2.57
527 553 6.303259 GTCTTCAAGTTAACAATGCGATCAAC 59.697 38.462 8.61 0.00 0.00 3.18
528 554 5.940192 TCAAGTTAACAATGCGATCAACT 57.060 34.783 8.61 0.00 0.00 3.16
529 555 7.386573 TCTTCAAGTTAACAATGCGATCAACTA 59.613 33.333 8.61 0.00 0.00 2.24
530 556 7.428282 TCAAGTTAACAATGCGATCAACTAA 57.572 32.000 8.61 0.00 0.00 2.24
531 557 7.866729 TCAAGTTAACAATGCGATCAACTAAA 58.133 30.769 8.61 0.00 0.00 1.85
532 558 8.015087 TCAAGTTAACAATGCGATCAACTAAAG 58.985 33.333 8.61 0.00 0.00 1.85
533 559 7.667043 AGTTAACAATGCGATCAACTAAAGA 57.333 32.000 8.61 0.00 0.00 2.52
534 560 8.094798 AGTTAACAATGCGATCAACTAAAGAA 57.905 30.769 8.61 0.00 0.00 2.52
535 561 8.564574 AGTTAACAATGCGATCAACTAAAGAAA 58.435 29.630 8.61 0.00 0.00 2.52
536 562 9.176181 GTTAACAATGCGATCAACTAAAGAAAA 57.824 29.630 0.00 0.00 0.00 2.29
537 563 9.737427 TTAACAATGCGATCAACTAAAGAAAAA 57.263 25.926 0.00 0.00 0.00 1.94
538 564 7.858052 ACAATGCGATCAACTAAAGAAAAAG 57.142 32.000 0.00 0.00 0.00 2.27
539 565 7.648142 ACAATGCGATCAACTAAAGAAAAAGA 58.352 30.769 0.00 0.00 0.00 2.52
540 566 7.805071 ACAATGCGATCAACTAAAGAAAAAGAG 59.195 33.333 0.00 0.00 0.00 2.85
541 567 6.861065 TGCGATCAACTAAAGAAAAAGAGT 57.139 33.333 0.00 0.00 0.00 3.24
542 568 7.259290 TGCGATCAACTAAAGAAAAAGAGTT 57.741 32.000 0.00 0.00 32.38 3.01
543 569 8.373048 TGCGATCAACTAAAGAAAAAGAGTTA 57.627 30.769 0.00 0.00 31.05 2.24
544 570 8.832521 TGCGATCAACTAAAGAAAAAGAGTTAA 58.167 29.630 0.00 0.00 31.05 2.01
545 571 9.104126 GCGATCAACTAAAGAAAAAGAGTTAAC 57.896 33.333 0.00 0.00 31.05 2.01
551 577 8.782533 ACTAAAGAAAAAGAGTTAACAATGCG 57.217 30.769 8.61 0.00 0.00 4.73
552 578 8.617809 ACTAAAGAAAAAGAGTTAACAATGCGA 58.382 29.630 8.61 0.00 0.00 5.10
553 579 9.612620 CTAAAGAAAAAGAGTTAACAATGCGAT 57.387 29.630 8.61 0.00 0.00 4.58
554 580 8.507470 AAAGAAAAAGAGTTAACAATGCGATC 57.493 30.769 8.61 0.00 0.00 3.69
555 581 6.612306 AGAAAAAGAGTTAACAATGCGATCC 58.388 36.000 8.61 0.00 0.00 3.36
556 582 4.965119 AAAGAGTTAACAATGCGATCCC 57.035 40.909 8.61 0.00 0.00 3.85
557 583 3.627395 AGAGTTAACAATGCGATCCCA 57.373 42.857 8.61 0.00 0.00 4.37
558 584 3.270877 AGAGTTAACAATGCGATCCCAC 58.729 45.455 8.61 0.00 0.00 4.61
559 585 3.055094 AGAGTTAACAATGCGATCCCACT 60.055 43.478 8.61 0.00 0.00 4.00
643 672 6.542574 TTCGATTCAAATTGCAAGCATTTT 57.457 29.167 4.94 8.60 32.04 1.82
644 673 6.542574 TCGATTCAAATTGCAAGCATTTTT 57.457 29.167 4.94 0.00 30.23 1.94
684 715 0.997196 GTTTCCCGTACGTGCAGATC 59.003 55.000 15.21 0.00 0.00 2.75
685 716 0.457166 TTTCCCGTACGTGCAGATCG 60.457 55.000 15.21 0.00 0.00 3.69
706 737 8.233190 AGATCGATTTTGCACTTTTAGAAGAAG 58.767 33.333 0.00 0.00 36.69 2.85
707 738 6.668323 TCGATTTTGCACTTTTAGAAGAAGG 58.332 36.000 0.00 0.00 36.69 3.46
708 739 6.485313 TCGATTTTGCACTTTTAGAAGAAGGA 59.515 34.615 0.00 0.00 36.69 3.36
709 740 7.012894 TCGATTTTGCACTTTTAGAAGAAGGAA 59.987 33.333 0.00 0.00 36.69 3.36
710 741 7.324616 CGATTTTGCACTTTTAGAAGAAGGAAG 59.675 37.037 0.00 0.00 36.69 3.46
711 742 7.639113 TTTTGCACTTTTAGAAGAAGGAAGA 57.361 32.000 0.00 0.00 36.69 2.87
712 743 7.639113 TTTGCACTTTTAGAAGAAGGAAGAA 57.361 32.000 0.00 0.00 36.69 2.52
749 780 9.744468 TCCTCTTTAAAACTGTTTAGATTTTGC 57.256 29.630 6.16 0.00 32.14 3.68
750 781 9.528018 CCTCTTTAAAACTGTTTAGATTTTGCA 57.472 29.630 6.16 0.00 32.14 4.08
819 852 3.077359 CGATCTCCTTTGACTTGGCTTT 58.923 45.455 0.00 0.00 0.00 3.51
831 864 4.383861 GGCTTTGCCTTGGCCAGC 62.384 66.667 19.06 19.06 46.69 4.85
832 865 4.383861 GCTTTGCCTTGGCCAGCC 62.384 66.667 13.97 0.38 0.00 4.85
833 866 2.602568 CTTTGCCTTGGCCAGCCT 60.603 61.111 13.97 0.00 36.94 4.58
834 867 1.304381 CTTTGCCTTGGCCAGCCTA 60.304 57.895 13.97 0.80 36.94 3.93
835 868 1.304381 TTTGCCTTGGCCAGCCTAG 60.304 57.895 13.97 12.51 38.40 3.02
847 880 1.419387 CCAGCCTAGGAGGATTGAAGG 59.581 57.143 14.75 0.00 37.67 3.46
877 913 2.576287 ATTAATGCGTGCGCGTGTGG 62.576 55.000 22.18 0.00 45.51 4.17
912 948 2.675056 GCAGCCACACAGCTTCTCG 61.675 63.158 0.00 0.00 42.61 4.04
984 1021 2.102588 CGCCTCCTATATAAATCCCCCG 59.897 54.545 0.00 0.00 0.00 5.73
1042 1080 3.307975 CCTTCAGCTTCATTCCTTCTCCA 60.308 47.826 0.00 0.00 0.00 3.86
1127 1179 2.435586 GGTGCAGCAGCGATCAGT 60.436 61.111 11.86 0.00 46.23 3.41
1481 1533 1.512310 CGAGAAGCTCACCGACGAC 60.512 63.158 0.00 0.00 0.00 4.34
1592 1653 3.432588 GACCAGCAGCAGCAGCAG 61.433 66.667 12.92 3.65 45.49 4.24
1615 1676 1.200948 GCAGCATTGAGAGTTTGTCCC 59.799 52.381 0.00 0.00 0.00 4.46
1616 1677 2.787994 CAGCATTGAGAGTTTGTCCCT 58.212 47.619 0.00 0.00 0.00 4.20
1618 1679 1.200948 GCATTGAGAGTTTGTCCCTGC 59.799 52.381 0.00 0.00 0.00 4.85
1620 1681 0.250295 TTGAGAGTTTGTCCCTGCCG 60.250 55.000 0.00 0.00 0.00 5.69
1623 1684 0.832135 AGAGTTTGTCCCTGCCGAGA 60.832 55.000 0.00 0.00 0.00 4.04
1624 1685 0.250513 GAGTTTGTCCCTGCCGAGAT 59.749 55.000 0.00 0.00 0.00 2.75
1625 1686 1.480954 GAGTTTGTCCCTGCCGAGATA 59.519 52.381 0.00 0.00 0.00 1.98
1626 1687 1.207329 AGTTTGTCCCTGCCGAGATAC 59.793 52.381 0.00 0.00 0.00 2.24
1631 1692 2.108425 TGTCCCTGCCGAGATACTAGAT 59.892 50.000 0.00 0.00 0.00 1.98
1635 1696 5.528320 GTCCCTGCCGAGATACTAGATATAC 59.472 48.000 0.00 0.00 0.00 1.47
2042 3007 0.729116 GGTGTGACTGAATGCATCCG 59.271 55.000 0.00 0.00 0.00 4.18
2181 3183 4.213270 CACGTGTCATGTGGAAATGTAAGT 59.787 41.667 16.21 0.00 30.90 2.24
2225 3227 5.454520 GTTGTTTAGTATTTGAACCCCACG 58.545 41.667 0.00 0.00 0.00 4.94
2242 3244 3.726730 CCCACGTCATGTTTTTGTTTACG 59.273 43.478 0.00 0.00 35.17 3.18
2314 6437 4.588951 AGCTCGTGATTTATCTACCCATGA 59.411 41.667 0.00 0.00 0.00 3.07
2317 6440 6.428159 GCTCGTGATTTATCTACCCATGATTT 59.572 38.462 0.00 0.00 0.00 2.17
2318 6441 7.602644 GCTCGTGATTTATCTACCCATGATTTA 59.397 37.037 0.00 0.00 0.00 1.40
2319 6442 8.827177 TCGTGATTTATCTACCCATGATTTAC 57.173 34.615 0.00 0.00 0.00 2.01
2320 6443 7.876068 TCGTGATTTATCTACCCATGATTTACC 59.124 37.037 0.00 0.00 0.00 2.85
2321 6444 7.878127 CGTGATTTATCTACCCATGATTTACCT 59.122 37.037 0.00 0.00 0.00 3.08
2322 6445 9.574516 GTGATTTATCTACCCATGATTTACCTT 57.425 33.333 0.00 0.00 0.00 3.50
2330 6453 8.582437 TCTACCCATGATTTACCTTATAGTTCG 58.418 37.037 0.00 0.00 0.00 3.95
2331 6454 7.369551 ACCCATGATTTACCTTATAGTTCGA 57.630 36.000 0.00 0.00 0.00 3.71
2332 6455 7.974504 ACCCATGATTTACCTTATAGTTCGAT 58.025 34.615 0.00 0.00 0.00 3.59
2333 6456 7.878127 ACCCATGATTTACCTTATAGTTCGATG 59.122 37.037 0.00 0.00 0.00 3.84
2334 6457 8.094548 CCCATGATTTACCTTATAGTTCGATGA 58.905 37.037 0.00 0.00 0.00 2.92
2335 6458 9.144747 CCATGATTTACCTTATAGTTCGATGAG 57.855 37.037 0.00 0.00 0.00 2.90
2336 6459 9.914131 CATGATTTACCTTATAGTTCGATGAGA 57.086 33.333 0.00 0.00 0.00 3.27
2338 6461 9.967346 TGATTTACCTTATAGTTCGATGAGAAG 57.033 33.333 0.00 0.00 39.95 2.85
2339 6462 9.968870 GATTTACCTTATAGTTCGATGAGAAGT 57.031 33.333 0.00 0.00 44.25 3.01
2342 6465 9.582431 TTACCTTATAGTTCGATGAGAAGTTTG 57.418 33.333 0.00 0.00 42.23 2.93
2343 6466 7.837863 ACCTTATAGTTCGATGAGAAGTTTGA 58.162 34.615 0.00 0.00 42.23 2.69
2344 6467 7.760340 ACCTTATAGTTCGATGAGAAGTTTGAC 59.240 37.037 0.00 0.00 42.23 3.18
2345 6468 7.759886 CCTTATAGTTCGATGAGAAGTTTGACA 59.240 37.037 0.00 0.00 42.23 3.58
2346 6469 9.140286 CTTATAGTTCGATGAGAAGTTTGACAA 57.860 33.333 0.00 0.00 42.23 3.18
2355 6478 8.446273 CGATGAGAAGTTTGACAAGTAAATCAT 58.554 33.333 6.87 6.87 0.00 2.45
2389 6512 1.988107 TCTGCTGATTTCTTCCCACCT 59.012 47.619 0.00 0.00 0.00 4.00
2390 6513 3.181329 TCTGCTGATTTCTTCCCACCTA 58.819 45.455 0.00 0.00 0.00 3.08
2397 6520 0.978907 TTCTTCCCACCTAACCCGTC 59.021 55.000 0.00 0.00 0.00 4.79
2401 6524 3.405318 CCACCTAACCCGTCCCCC 61.405 72.222 0.00 0.00 0.00 5.40
2449 6573 2.487532 CCCTAGATCGAACCGCCGT 61.488 63.158 0.00 0.00 0.00 5.68
2479 6603 0.563173 CCATCTCCTACCTCCCCTCA 59.437 60.000 0.00 0.00 0.00 3.86
2481 6605 1.219213 CATCTCCTACCTCCCCTCACT 59.781 57.143 0.00 0.00 0.00 3.41
2497 6621 2.105128 CTGTCGCCGGATGAGGTC 59.895 66.667 5.05 0.00 0.00 3.85
2498 6622 2.362503 TGTCGCCGGATGAGGTCT 60.363 61.111 5.05 0.00 0.00 3.85
2565 6689 3.251004 CCTTTATCTGCGGCTGGTAAATC 59.749 47.826 20.79 0.00 0.00 2.17
2586 6710 4.779733 GGGTGGAGGGAGGCTCGA 62.780 72.222 8.69 0.00 0.00 4.04
2743 6874 3.650950 GTGCCCCCTCTTCCAGCA 61.651 66.667 0.00 0.00 0.00 4.41
2746 6877 0.918799 TGCCCCCTCTTCCAGCATTA 60.919 55.000 0.00 0.00 0.00 1.90
2801 6932 3.058160 CCTTTGGTGGCCTCTGCG 61.058 66.667 3.32 0.00 38.85 5.18
2806 6937 4.148825 GGTGGCCTCTGCGACGAT 62.149 66.667 3.32 0.00 46.08 3.73
2807 6938 2.887568 GTGGCCTCTGCGACGATG 60.888 66.667 3.32 0.00 36.46 3.84
2808 6939 4.819761 TGGCCTCTGCGACGATGC 62.820 66.667 3.32 0.00 38.85 3.91
2809 6940 4.521062 GGCCTCTGCGACGATGCT 62.521 66.667 0.00 0.00 38.85 3.79
2810 6941 3.260483 GCCTCTGCGACGATGCTG 61.260 66.667 0.00 0.00 35.36 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.973320 CGTAAAATGTTTGAACCGGCG 59.027 47.619 0.00 0.00 0.00 6.46
249 264 4.339247 CCCAAACCAGTGCTCCTAATAATG 59.661 45.833 0.00 0.00 0.00 1.90
296 319 0.958091 CGGATTCGCATCCTCTCTCT 59.042 55.000 12.38 0.00 46.57 3.10
297 320 0.671251 ACGGATTCGCATCCTCTCTC 59.329 55.000 12.38 0.00 46.57 3.20
298 321 0.387202 CACGGATTCGCATCCTCTCT 59.613 55.000 12.38 0.00 46.57 3.10
299 322 0.103208 ACACGGATTCGCATCCTCTC 59.897 55.000 12.38 0.00 46.57 3.20
485 511 4.097437 TGAAGACGCGATGGAGTAGTAAAT 59.903 41.667 15.93 0.00 0.00 1.40
500 526 2.902484 CGCATTGTTAACTTGAAGACGC 59.098 45.455 7.22 0.00 0.00 5.19
501 527 4.383774 TCGCATTGTTAACTTGAAGACG 57.616 40.909 7.22 4.38 0.00 4.18
502 528 5.927030 TGATCGCATTGTTAACTTGAAGAC 58.073 37.500 7.22 0.00 0.00 3.01
504 530 6.373779 AGTTGATCGCATTGTTAACTTGAAG 58.626 36.000 7.22 0.00 0.00 3.02
505 531 6.312399 AGTTGATCGCATTGTTAACTTGAA 57.688 33.333 7.22 0.00 0.00 2.69
506 532 5.940192 AGTTGATCGCATTGTTAACTTGA 57.060 34.783 7.22 0.00 0.00 3.02
507 533 8.015087 TCTTTAGTTGATCGCATTGTTAACTTG 58.985 33.333 7.22 6.01 31.55 3.16
508 534 8.094798 TCTTTAGTTGATCGCATTGTTAACTT 57.905 30.769 7.22 0.00 31.55 2.66
509 535 7.667043 TCTTTAGTTGATCGCATTGTTAACT 57.333 32.000 7.22 0.00 33.46 2.24
510 536 8.722342 TTTCTTTAGTTGATCGCATTGTTAAC 57.278 30.769 0.00 0.00 0.00 2.01
511 537 9.737427 TTTTTCTTTAGTTGATCGCATTGTTAA 57.263 25.926 0.00 0.00 0.00 2.01
512 538 9.393249 CTTTTTCTTTAGTTGATCGCATTGTTA 57.607 29.630 0.00 0.00 0.00 2.41
514 540 7.648142 TCTTTTTCTTTAGTTGATCGCATTGT 58.352 30.769 0.00 0.00 0.00 2.71
515 541 7.805071 ACTCTTTTTCTTTAGTTGATCGCATTG 59.195 33.333 0.00 0.00 0.00 2.82
516 542 7.875971 ACTCTTTTTCTTTAGTTGATCGCATT 58.124 30.769 0.00 0.00 0.00 3.56
518 544 6.861065 ACTCTTTTTCTTTAGTTGATCGCA 57.139 33.333 0.00 0.00 0.00 5.10
519 545 9.104126 GTTAACTCTTTTTCTTTAGTTGATCGC 57.896 33.333 0.00 0.00 34.23 4.58
525 551 9.233232 CGCATTGTTAACTCTTTTTCTTTAGTT 57.767 29.630 7.22 0.00 36.26 2.24
526 552 8.617809 TCGCATTGTTAACTCTTTTTCTTTAGT 58.382 29.630 7.22 0.00 0.00 2.24
527 553 9.612620 ATCGCATTGTTAACTCTTTTTCTTTAG 57.387 29.630 7.22 0.00 0.00 1.85
528 554 9.607285 GATCGCATTGTTAACTCTTTTTCTTTA 57.393 29.630 7.22 0.00 0.00 1.85
529 555 7.595130 GGATCGCATTGTTAACTCTTTTTCTTT 59.405 33.333 7.22 0.00 0.00 2.52
530 556 7.084486 GGATCGCATTGTTAACTCTTTTTCTT 58.916 34.615 7.22 0.00 0.00 2.52
531 557 6.349363 GGGATCGCATTGTTAACTCTTTTTCT 60.349 38.462 7.22 0.00 0.00 2.52
532 558 5.800438 GGGATCGCATTGTTAACTCTTTTTC 59.200 40.000 7.22 0.00 0.00 2.29
533 559 5.242838 TGGGATCGCATTGTTAACTCTTTTT 59.757 36.000 8.63 0.00 0.00 1.94
534 560 4.764823 TGGGATCGCATTGTTAACTCTTTT 59.235 37.500 8.63 0.00 0.00 2.27
535 561 4.156008 GTGGGATCGCATTGTTAACTCTTT 59.844 41.667 16.24 0.00 0.00 2.52
536 562 3.689649 GTGGGATCGCATTGTTAACTCTT 59.310 43.478 16.24 0.00 0.00 2.85
537 563 3.055094 AGTGGGATCGCATTGTTAACTCT 60.055 43.478 16.24 1.97 0.00 3.24
538 564 3.270877 AGTGGGATCGCATTGTTAACTC 58.729 45.455 16.24 0.00 0.00 3.01
539 565 3.350219 AGTGGGATCGCATTGTTAACT 57.650 42.857 16.24 3.44 0.00 2.24
540 566 3.311596 GGTAGTGGGATCGCATTGTTAAC 59.688 47.826 16.24 6.56 0.00 2.01
541 567 3.537580 GGTAGTGGGATCGCATTGTTAA 58.462 45.455 16.24 0.00 0.00 2.01
542 568 2.482316 CGGTAGTGGGATCGCATTGTTA 60.482 50.000 16.24 4.29 0.00 2.41
543 569 1.742411 CGGTAGTGGGATCGCATTGTT 60.742 52.381 16.24 5.21 0.00 2.83
544 570 0.179084 CGGTAGTGGGATCGCATTGT 60.179 55.000 16.24 6.61 0.00 2.71
545 571 0.179084 ACGGTAGTGGGATCGCATTG 60.179 55.000 16.24 6.89 0.00 2.82
546 572 1.405872 TACGGTAGTGGGATCGCATT 58.594 50.000 16.24 14.17 0.00 3.56
547 573 1.629043 ATACGGTAGTGGGATCGCAT 58.371 50.000 16.24 7.69 0.00 4.73
548 574 2.156917 CTATACGGTAGTGGGATCGCA 58.843 52.381 8.63 8.63 0.00 5.10
549 575 2.430465 TCTATACGGTAGTGGGATCGC 58.570 52.381 2.14 2.14 0.00 4.58
550 576 5.443185 TTTTCTATACGGTAGTGGGATCG 57.557 43.478 0.00 0.00 0.00 3.69
551 577 7.229581 AGATTTTCTATACGGTAGTGGGATC 57.770 40.000 0.00 0.00 0.00 3.36
552 578 7.289317 TGAAGATTTTCTATACGGTAGTGGGAT 59.711 37.037 0.00 0.00 34.31 3.85
553 579 6.608405 TGAAGATTTTCTATACGGTAGTGGGA 59.392 38.462 0.00 0.00 34.31 4.37
554 580 6.812998 TGAAGATTTTCTATACGGTAGTGGG 58.187 40.000 0.00 0.00 34.31 4.61
555 581 8.712285 TTTGAAGATTTTCTATACGGTAGTGG 57.288 34.615 0.00 0.00 34.31 4.00
592 618 4.202264 CCTCCTTTGCGGACTATCTACATT 60.202 45.833 0.00 0.00 36.69 2.71
593 619 3.322254 CCTCCTTTGCGGACTATCTACAT 59.678 47.826 0.00 0.00 36.69 2.29
594 620 2.693591 CCTCCTTTGCGGACTATCTACA 59.306 50.000 0.00 0.00 36.69 2.74
595 621 2.694109 ACCTCCTTTGCGGACTATCTAC 59.306 50.000 0.00 0.00 36.69 2.59
596 622 2.693591 CACCTCCTTTGCGGACTATCTA 59.306 50.000 0.00 0.00 36.69 1.98
597 623 1.482593 CACCTCCTTTGCGGACTATCT 59.517 52.381 0.00 0.00 36.69 1.98
598 624 1.207329 ACACCTCCTTTGCGGACTATC 59.793 52.381 0.00 0.00 36.69 2.08
599 625 1.276622 ACACCTCCTTTGCGGACTAT 58.723 50.000 0.00 0.00 36.69 2.12
616 645 5.707931 TGCTTGCAATTTGAATCGAATACA 58.292 33.333 0.00 0.00 0.00 2.29
643 672 1.663135 GAACAAAGCGCAAAGGCAAAA 59.337 42.857 11.47 0.00 41.24 2.44
644 673 1.285578 GAACAAAGCGCAAAGGCAAA 58.714 45.000 11.47 0.00 41.24 3.68
684 715 6.668323 TCCTTCTTCTAAAAGTGCAAAATCG 58.332 36.000 0.00 0.00 33.95 3.34
685 716 8.352942 TCTTCCTTCTTCTAAAAGTGCAAAATC 58.647 33.333 0.00 0.00 33.95 2.17
709 740 7.516450 TTTAAAGAGGAGGAAGATGGATTCT 57.484 36.000 0.00 0.00 35.70 2.40
710 741 7.831690 AGTTTTAAAGAGGAGGAAGATGGATTC 59.168 37.037 0.00 0.00 0.00 2.52
711 742 7.613411 CAGTTTTAAAGAGGAGGAAGATGGATT 59.387 37.037 0.00 0.00 0.00 3.01
712 743 7.115414 CAGTTTTAAAGAGGAGGAAGATGGAT 58.885 38.462 0.00 0.00 0.00 3.41
748 779 2.804931 GCACGCGTTCCCAAATGC 60.805 61.111 10.22 3.04 42.82 3.56
749 780 2.501650 CGCACGCGTTCCCAAATG 60.502 61.111 10.22 0.00 34.35 2.32
824 857 1.004758 AATCCTCCTAGGCTGGCCA 59.995 57.895 14.39 4.71 38.92 5.36
825 858 1.056700 TCAATCCTCCTAGGCTGGCC 61.057 60.000 2.96 3.00 34.61 5.36
826 859 0.839946 TTCAATCCTCCTAGGCTGGC 59.160 55.000 2.96 0.00 34.61 4.85
827 860 1.419387 CCTTCAATCCTCCTAGGCTGG 59.581 57.143 2.96 9.11 34.61 4.85
828 861 1.202746 GCCTTCAATCCTCCTAGGCTG 60.203 57.143 2.96 0.00 46.14 4.85
829 862 1.135960 GCCTTCAATCCTCCTAGGCT 58.864 55.000 2.96 0.00 46.14 4.58
830 863 0.250081 CGCCTTCAATCCTCCTAGGC 60.250 60.000 2.96 0.00 46.16 3.93
831 864 0.394565 CCGCCTTCAATCCTCCTAGG 59.605 60.000 0.82 0.82 36.46 3.02
832 865 0.394565 CCCGCCTTCAATCCTCCTAG 59.605 60.000 0.00 0.00 0.00 3.02
833 866 0.031515 TCCCGCCTTCAATCCTCCTA 60.032 55.000 0.00 0.00 0.00 2.94
834 867 1.306997 TCCCGCCTTCAATCCTCCT 60.307 57.895 0.00 0.00 0.00 3.69
835 868 1.153147 GTCCCGCCTTCAATCCTCC 60.153 63.158 0.00 0.00 0.00 4.30
836 869 0.462759 CAGTCCCGCCTTCAATCCTC 60.463 60.000 0.00 0.00 0.00 3.71
847 880 0.307760 CGCATTAATTCCAGTCCCGC 59.692 55.000 0.00 0.00 0.00 6.13
877 913 0.531974 TGCCGTTGACTTGTCTGTCC 60.532 55.000 2.35 0.00 36.21 4.02
885 921 2.186826 GTGTGGCTGCCGTTGACTT 61.187 57.895 14.98 0.00 0.00 3.01
1042 1080 2.851045 GATGTGGGTGGGTGGGTT 59.149 61.111 0.00 0.00 0.00 4.11
1127 1179 1.315981 ACTCGCTCATCTGCTCCGAA 61.316 55.000 0.00 0.00 0.00 4.30
1481 1533 1.364171 GATCATCCCGTCCACCTCG 59.636 63.158 0.00 0.00 0.00 4.63
1589 1650 1.306642 ACTCTCAATGCTGCTGCTGC 61.307 55.000 22.51 22.51 40.48 5.25
1590 1651 1.166129 AACTCTCAATGCTGCTGCTG 58.834 50.000 17.00 7.75 40.48 4.41
1591 1652 1.540267 CAAACTCTCAATGCTGCTGCT 59.460 47.619 17.00 0.00 40.48 4.24
1592 1653 1.268899 ACAAACTCTCAATGCTGCTGC 59.731 47.619 8.89 8.89 40.20 5.25
1593 1654 2.095364 GGACAAACTCTCAATGCTGCTG 60.095 50.000 0.00 0.00 0.00 4.41
1594 1655 2.157738 GGACAAACTCTCAATGCTGCT 58.842 47.619 0.00 0.00 0.00 4.24
1595 1656 1.200948 GGGACAAACTCTCAATGCTGC 59.799 52.381 0.00 0.00 0.00 5.25
1596 1657 2.486982 CAGGGACAAACTCTCAATGCTG 59.513 50.000 0.00 0.00 0.00 4.41
1597 1658 2.787994 CAGGGACAAACTCTCAATGCT 58.212 47.619 0.00 0.00 0.00 3.79
1598 1659 1.200948 GCAGGGACAAACTCTCAATGC 59.799 52.381 0.00 0.00 0.00 3.56
1599 1660 1.815003 GGCAGGGACAAACTCTCAATG 59.185 52.381 0.00 0.00 0.00 2.82
1600 1661 1.611673 CGGCAGGGACAAACTCTCAAT 60.612 52.381 0.00 0.00 0.00 2.57
1615 1676 6.259167 GGACTGTATATCTAGTATCTCGGCAG 59.741 46.154 0.00 0.00 0.00 4.85
1616 1677 6.114089 GGACTGTATATCTAGTATCTCGGCA 58.886 44.000 0.00 0.00 0.00 5.69
1618 1679 6.339730 ACGGACTGTATATCTAGTATCTCGG 58.660 44.000 0.00 0.00 0.00 4.63
1620 1681 6.476380 CGGACGGACTGTATATCTAGTATCTC 59.524 46.154 0.00 0.00 0.00 2.75
1623 1684 6.047511 ACGGACGGACTGTATATCTAGTAT 57.952 41.667 0.00 0.00 36.20 2.12
1624 1685 5.473931 GACGGACGGACTGTATATCTAGTA 58.526 45.833 0.00 0.00 38.34 1.82
1625 1686 4.314121 GACGGACGGACTGTATATCTAGT 58.686 47.826 0.00 0.00 38.34 2.57
1626 1687 3.683822 GGACGGACGGACTGTATATCTAG 59.316 52.174 0.00 0.00 38.34 2.43
1631 1692 0.107703 ACGGACGGACGGACTGTATA 60.108 55.000 6.00 0.00 38.34 1.47
1635 1696 4.456253 CGACGGACGGACGGACTG 62.456 72.222 6.00 0.00 38.39 3.51
1806 1870 7.338462 CACGTTCAGTTAGTCTTTTCTTCTTC 58.662 38.462 0.00 0.00 0.00 2.87
1812 1876 4.807304 TCACCACGTTCAGTTAGTCTTTTC 59.193 41.667 0.00 0.00 0.00 2.29
1814 1878 4.395959 TCACCACGTTCAGTTAGTCTTT 57.604 40.909 0.00 0.00 0.00 2.52
1817 1881 4.386049 CAGAATCACCACGTTCAGTTAGTC 59.614 45.833 0.00 0.00 0.00 2.59
1922 1988 9.490379 AAGTACTAAGTGGTTTGAGTAATTCTG 57.510 33.333 0.00 0.00 29.36 3.02
1940 2237 9.107177 CAGAGGTTAGAGTTCGATAAGTACTAA 57.893 37.037 0.00 0.00 30.25 2.24
1941 2238 8.263640 ACAGAGGTTAGAGTTCGATAAGTACTA 58.736 37.037 0.00 0.00 30.25 1.82
1942 2239 7.111466 ACAGAGGTTAGAGTTCGATAAGTACT 58.889 38.462 0.00 0.00 32.93 2.73
2042 3007 3.425193 CGTAAAAAGACATTTGCTGCACC 59.575 43.478 0.00 0.00 0.00 5.01
2050 3015 4.823790 AACGAGGCGTAAAAAGACATTT 57.176 36.364 0.00 0.00 39.99 2.32
2051 3016 4.823790 AAACGAGGCGTAAAAAGACATT 57.176 36.364 0.00 0.00 39.99 2.71
2225 3227 5.812652 TGTCCTCGTAAACAAAAACATGAC 58.187 37.500 0.00 0.00 0.00 3.06
2317 6440 8.963725 TCAAACTTCTCATCGAACTATAAGGTA 58.036 33.333 0.00 0.00 0.00 3.08
2318 6441 7.760340 GTCAAACTTCTCATCGAACTATAAGGT 59.240 37.037 0.00 0.00 0.00 3.50
2319 6442 7.759886 TGTCAAACTTCTCATCGAACTATAAGG 59.240 37.037 0.00 0.00 0.00 2.69
2320 6443 8.689251 TGTCAAACTTCTCATCGAACTATAAG 57.311 34.615 0.00 0.00 0.00 1.73
2321 6444 9.140286 CTTGTCAAACTTCTCATCGAACTATAA 57.860 33.333 0.00 0.00 0.00 0.98
2322 6445 8.304596 ACTTGTCAAACTTCTCATCGAACTATA 58.695 33.333 0.00 0.00 0.00 1.31
2323 6446 7.155328 ACTTGTCAAACTTCTCATCGAACTAT 58.845 34.615 0.00 0.00 0.00 2.12
2324 6447 6.513180 ACTTGTCAAACTTCTCATCGAACTA 58.487 36.000 0.00 0.00 0.00 2.24
2325 6448 5.360591 ACTTGTCAAACTTCTCATCGAACT 58.639 37.500 0.00 0.00 0.00 3.01
2326 6449 5.659048 ACTTGTCAAACTTCTCATCGAAC 57.341 39.130 0.00 0.00 0.00 3.95
2327 6450 7.780008 TTTACTTGTCAAACTTCTCATCGAA 57.220 32.000 0.00 0.00 0.00 3.71
2328 6451 7.655732 TGATTTACTTGTCAAACTTCTCATCGA 59.344 33.333 0.00 0.00 0.00 3.59
2329 6452 7.796838 TGATTTACTTGTCAAACTTCTCATCG 58.203 34.615 0.00 0.00 0.00 3.84
2332 6455 9.219603 CCTATGATTTACTTGTCAAACTTCTCA 57.780 33.333 0.00 0.00 0.00 3.27
2333 6456 9.220767 ACCTATGATTTACTTGTCAAACTTCTC 57.779 33.333 0.00 0.00 0.00 2.87
2334 6457 9.003658 CACCTATGATTTACTTGTCAAACTTCT 57.996 33.333 0.00 0.00 0.00 2.85
2335 6458 8.999431 TCACCTATGATTTACTTGTCAAACTTC 58.001 33.333 0.00 0.00 0.00 3.01
2336 6459 8.784043 GTCACCTATGATTTACTTGTCAAACTT 58.216 33.333 0.00 0.00 37.14 2.66
2337 6460 8.157476 AGTCACCTATGATTTACTTGTCAAACT 58.843 33.333 0.00 0.00 37.14 2.66
2338 6461 8.324163 AGTCACCTATGATTTACTTGTCAAAC 57.676 34.615 0.00 0.00 37.14 2.93
2355 6478 8.928448 AGAAATCAGCAGATAATTAGTCACCTA 58.072 33.333 0.00 0.00 33.08 3.08
2449 6573 4.880426 GAGATGGGGGAGGCCCGA 62.880 72.222 0.00 0.00 46.66 5.14
2460 6584 0.563173 TGAGGGGAGGTAGGAGATGG 59.437 60.000 0.00 0.00 0.00 3.51
2465 6589 0.335361 GACAGTGAGGGGAGGTAGGA 59.665 60.000 0.00 0.00 0.00 2.94
2479 6603 2.680352 ACCTCATCCGGCGACAGT 60.680 61.111 9.30 0.00 0.00 3.55
2481 6605 2.362503 AGACCTCATCCGGCGACA 60.363 61.111 9.30 0.00 0.00 4.35
2540 6664 0.394352 CCAGCCGCAGATAAAGGGTT 60.394 55.000 0.00 0.00 32.89 4.11
2541 6665 1.224592 CCAGCCGCAGATAAAGGGT 59.775 57.895 0.00 0.00 35.99 4.34
2551 6675 1.807981 CGTCGATTTACCAGCCGCA 60.808 57.895 0.00 0.00 0.00 5.69
2586 6710 3.322466 CGGCCCACAGAAGAGGGT 61.322 66.667 0.00 0.00 46.42 4.34
2613 6737 1.072505 GAGAACCCAGGCACCGAAA 59.927 57.895 0.00 0.00 0.00 3.46
2729 6853 1.202976 CCATAATGCTGGAAGAGGGGG 60.203 57.143 0.00 0.00 38.69 5.40
2734 6865 1.565759 AGCCACCATAATGCTGGAAGA 59.434 47.619 0.00 0.00 39.73 2.87
2740 6871 1.475751 CGAAGGAGCCACCATAATGCT 60.476 52.381 0.47 0.00 42.04 3.79
2743 6874 0.839946 AGCGAAGGAGCCACCATAAT 59.160 50.000 0.00 0.00 42.04 1.28
2746 6877 2.586792 GAGCGAAGGAGCCACCAT 59.413 61.111 0.00 0.00 42.04 3.55


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

AutoCloner maintained by Alex Coulton.