Multiple sequence alignment - TraesCS2A01G252600

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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 TraesCS2A01G252600 chr2A 100.000 2488 0 0 1 2488 384332321 384329834 0.000000e+00 4595.0
1 TraesCS2A01G252600 chr2A 78.339 277 35 16 2166 2425 254575079 254575347 3.310000e-34 156.0
2 TraesCS2A01G252600 chr2D 92.593 1809 93 13 684 2470 305506741 305504952 0.000000e+00 2560.0
3 TraesCS2A01G252600 chr2D 90.722 291 17 6 137 426 305507021 305506740 1.810000e-101 379.0
4 TraesCS2A01G252600 chr2D 100.000 50 0 0 1 50 305507328 305507279 2.630000e-15 93.5
5 TraesCS2A01G252600 chr2B 93.853 1155 49 6 755 1890 373747880 373746729 0.000000e+00 1720.0
6 TraesCS2A01G252600 chr2B 94.009 434 17 5 1 426 373748609 373748177 0.000000e+00 649.0
7 TraesCS2A01G252600 chr2B 92.652 313 21 2 2177 2488 373746390 373746079 1.360000e-122 449.0
8 TraesCS2A01G252600 chr2B 88.462 260 25 3 1922 2180 373746726 373746471 2.400000e-80 309.0
9 TraesCS2A01G252600 chr2B 78.445 283 39 14 2223 2488 174788239 174788516 5.510000e-37 165.0
10 TraesCS2A01G252600 chr2B 84.685 111 17 0 2055 2165 637786458 637786348 7.270000e-21 111.0
11 TraesCS2A01G252600 chr2B 85.185 108 16 0 2055 2162 643930085 643930192 7.270000e-21 111.0
12 TraesCS2A01G252600 chr2B 92.308 39 3 0 1803 1841 381345743 381345705 3.460000e-04 56.5
13 TraesCS2A01G252600 chr3A 94.595 259 14 0 427 685 721830416 721830158 3.850000e-108 401.0
14 TraesCS2A01G252600 chr3A 94.186 258 15 0 428 685 468323742 468323485 6.450000e-106 394.0
15 TraesCS2A01G252600 chr3A 92.776 263 19 0 424 686 670825919 670825657 5.020000e-102 381.0
16 TraesCS2A01G252600 chr5A 92.830 265 19 0 421 685 535518766 535518502 3.880000e-103 385.0
17 TraesCS2A01G252600 chr5A 79.231 260 35 12 2226 2470 510476654 510476399 1.980000e-36 163.0
18 TraesCS2A01G252600 chr5A 75.725 276 47 11 2226 2488 633641463 633641195 1.210000e-23 121.0
19 TraesCS2A01G252600 chr5A 97.143 35 1 0 1803 1837 670602857 670602891 2.670000e-05 60.2
20 TraesCS2A01G252600 chr1A 92.720 261 19 0 425 685 537981412 537981152 6.500000e-101 377.0
21 TraesCS2A01G252600 chr1A 88.258 264 30 1 422 685 480593959 480593697 5.170000e-82 315.0
22 TraesCS2A01G252600 chr1A 83.784 111 18 0 2055 2165 22931616 22931506 3.380000e-19 106.0
23 TraesCS2A01G252600 chr6A 90.421 261 25 0 425 685 405665991 405665731 6.590000e-91 344.0
24 TraesCS2A01G252600 chr6B 88.390 267 30 1 419 685 81010777 81010512 1.110000e-83 320.0
25 TraesCS2A01G252600 chr6B 92.857 42 1 1 1802 1841 514678515 514678474 2.670000e-05 60.2
26 TraesCS2A01G252600 chr5D 88.015 267 32 0 419 685 421314559 421314825 1.440000e-82 316.0
27 TraesCS2A01G252600 chr5D 90.000 50 4 1 1803 1851 443840804 443840853 2.070000e-06 63.9
28 TraesCS2A01G252600 chr5D 92.683 41 3 0 1803 1843 338504766 338504726 2.670000e-05 60.2
29 TraesCS2A01G252600 chr4A 81.295 278 35 12 2220 2488 342449476 342449745 2.510000e-50 209.0
30 TraesCS2A01G252600 chr5B 81.132 212 29 5 2226 2428 537958915 537958706 2.560000e-35 159.0
31 TraesCS2A01G252600 chr5B 80.556 216 28 13 2220 2428 477518732 477518940 1.190000e-33 154.0
32 TraesCS2A01G252600 chr6D 79.545 220 29 12 2220 2427 47670363 47670578 2.580000e-30 143.0
33 TraesCS2A01G252600 chr4D 86.667 120 15 1 2223 2341 179857597 179857478 5.580000e-27 132.0
34 TraesCS2A01G252600 chr4D 83.529 85 6 3 1752 1836 7830242 7830318 3.430000e-09 73.1
35 TraesCS2A01G252600 chr3B 78.505 214 30 12 2226 2428 752701259 752701051 2.600000e-25 126.0
36 TraesCS2A01G252600 chr3B 84.259 108 17 0 2055 2162 805847184 805847291 3.380000e-19 106.0
37 TraesCS2A01G252600 chr3B 97.297 37 1 0 1803 1839 667641795 667641831 2.070000e-06 63.9
38 TraesCS2A01G252600 chr7A 83.636 110 16 2 2053 2161 681515187 681515079 4.380000e-18 102.0
39 TraesCS2A01G252600 chr4B 83.486 109 16 2 2055 2162 15453572 15453679 1.570000e-17 100.0
40 TraesCS2A01G252600 chr4B 83.333 108 18 0 2055 2162 565311153 565311260 1.570000e-17 100.0
41 TraesCS2A01G252600 chr4B 82.828 99 7 2 1748 1844 613320096 613320186 2.050000e-11 80.5
42 TraesCS2A01G252600 chr4B 97.222 36 1 0 1802 1837 633620823 633620858 7.430000e-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 TraesCS2A01G252600 chr2A 384329834 384332321 2487 True 4595.000000 4595 100.000000 1 2488 1 chr2A.!!$R1 2487
1 TraesCS2A01G252600 chr2D 305504952 305507328 2376 True 1010.833333 2560 94.438333 1 2470 3 chr2D.!!$R1 2469
2 TraesCS2A01G252600 chr2B 373746079 373748609 2530 True 781.750000 1720 92.244000 1 2488 4 chr2B.!!$R3 2487

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
451 628 0.680618 TCGGTCCTTTTTACTCCGCA 59.319 50.0 0.0 0.0 40.81 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 2277 0.247894 GCGACACGAGTTGTTTTGCA 60.248 50.0 4.26 0.0 39.17 4.08 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
50 51 6.651643 TGTATTTTGTAGGATTTGTAGCGTGT 59.348 34.615 0.00 0.00 0.00 4.49
59 60 1.948104 TTGTAGCGTGTCAGCTTGTT 58.052 45.000 0.00 0.00 46.80 2.83
258 431 8.543862 TGATGATCAATCATTCCTCTTTATCG 57.456 34.615 0.00 0.00 46.84 2.92
259 432 8.152898 TGATGATCAATCATTCCTCTTTATCGT 58.847 33.333 0.00 0.00 46.84 3.73
282 455 4.697514 AGTGATGTCAGGATTGGTATTCG 58.302 43.478 0.00 0.00 0.00 3.34
320 496 2.378445 CCGTCATGGTGTATGTGACA 57.622 50.000 5.70 0.00 41.69 3.58
325 501 4.026886 CGTCATGGTGTATGTGACATTACG 60.027 45.833 2.29 0.00 41.69 3.18
336 513 4.304110 TGTGACATTACGACTTGGAAGAC 58.696 43.478 0.00 0.00 0.00 3.01
372 549 7.440856 ACTTTATTTTCATTGGCAAATTCGTGT 59.559 29.630 3.01 0.00 0.00 4.49
392 569 2.093106 TGTGCCACGTAAAACCAAGTT 58.907 42.857 0.00 0.00 0.00 2.66
430 607 3.990318 GCAGGTTGCAAATATACTCCC 57.010 47.619 0.00 0.00 44.26 4.30
431 608 3.555966 GCAGGTTGCAAATATACTCCCT 58.444 45.455 0.00 0.00 44.26 4.20
432 609 3.954258 GCAGGTTGCAAATATACTCCCTT 59.046 43.478 0.00 0.00 44.26 3.95
433 610 4.036852 GCAGGTTGCAAATATACTCCCTTC 59.963 45.833 0.00 0.00 44.26 3.46
434 611 4.273480 CAGGTTGCAAATATACTCCCTTCG 59.727 45.833 0.00 0.00 0.00 3.79
435 612 3.564225 GGTTGCAAATATACTCCCTTCGG 59.436 47.826 0.00 0.00 0.00 4.30
436 613 4.196971 GTTGCAAATATACTCCCTTCGGT 58.803 43.478 0.00 0.00 0.00 4.69
437 614 4.067972 TGCAAATATACTCCCTTCGGTC 57.932 45.455 0.00 0.00 0.00 4.79
438 615 3.181458 TGCAAATATACTCCCTTCGGTCC 60.181 47.826 0.00 0.00 0.00 4.46
439 616 3.071167 GCAAATATACTCCCTTCGGTCCT 59.929 47.826 0.00 0.00 0.00 3.85
440 617 4.444449 GCAAATATACTCCCTTCGGTCCTT 60.444 45.833 0.00 0.00 0.00 3.36
441 618 5.681639 CAAATATACTCCCTTCGGTCCTTT 58.318 41.667 0.00 0.00 0.00 3.11
442 619 5.970501 AATATACTCCCTTCGGTCCTTTT 57.029 39.130 0.00 0.00 0.00 2.27
443 620 5.970501 ATATACTCCCTTCGGTCCTTTTT 57.029 39.130 0.00 0.00 0.00 1.94
444 621 7.441903 AATATACTCCCTTCGGTCCTTTTTA 57.558 36.000 0.00 0.00 0.00 1.52
445 622 3.413846 ACTCCCTTCGGTCCTTTTTAC 57.586 47.619 0.00 0.00 0.00 2.01
446 623 2.977580 ACTCCCTTCGGTCCTTTTTACT 59.022 45.455 0.00 0.00 0.00 2.24
447 624 3.007723 ACTCCCTTCGGTCCTTTTTACTC 59.992 47.826 0.00 0.00 0.00 2.59
448 625 2.303890 TCCCTTCGGTCCTTTTTACTCC 59.696 50.000 0.00 0.00 0.00 3.85
449 626 2.344025 CCTTCGGTCCTTTTTACTCCG 58.656 52.381 0.00 0.00 42.12 4.63
450 627 1.730612 CTTCGGTCCTTTTTACTCCGC 59.269 52.381 0.00 0.00 40.81 5.54
451 628 0.680618 TCGGTCCTTTTTACTCCGCA 59.319 50.000 0.00 0.00 40.81 5.69
452 629 1.276989 TCGGTCCTTTTTACTCCGCAT 59.723 47.619 0.00 0.00 40.81 4.73
453 630 2.496871 TCGGTCCTTTTTACTCCGCATA 59.503 45.455 0.00 0.00 40.81 3.14
454 631 3.133362 TCGGTCCTTTTTACTCCGCATAT 59.867 43.478 0.00 0.00 40.81 1.78
455 632 3.875134 CGGTCCTTTTTACTCCGCATATT 59.125 43.478 0.00 0.00 35.01 1.28
456 633 5.051816 CGGTCCTTTTTACTCCGCATATTA 58.948 41.667 0.00 0.00 35.01 0.98
457 634 5.176958 CGGTCCTTTTTACTCCGCATATTAG 59.823 44.000 0.00 0.00 35.01 1.73
458 635 6.285990 GGTCCTTTTTACTCCGCATATTAGA 58.714 40.000 0.00 0.00 0.00 2.10
459 636 6.424207 GGTCCTTTTTACTCCGCATATTAGAG 59.576 42.308 0.00 0.00 0.00 2.43
460 637 6.985059 GTCCTTTTTACTCCGCATATTAGAGT 59.015 38.462 0.00 0.00 43.17 3.24
461 638 7.494952 GTCCTTTTTACTCCGCATATTAGAGTT 59.505 37.037 4.78 0.00 41.09 3.01
462 639 7.494625 TCCTTTTTACTCCGCATATTAGAGTTG 59.505 37.037 4.78 0.00 41.09 3.16
463 640 7.280205 CCTTTTTACTCCGCATATTAGAGTTGT 59.720 37.037 4.78 0.00 41.09 3.32
464 641 7.534085 TTTTACTCCGCATATTAGAGTTGTG 57.466 36.000 4.78 0.00 41.09 3.33
465 642 4.737855 ACTCCGCATATTAGAGTTGTGT 57.262 40.909 0.00 0.00 37.60 3.72
466 643 4.683832 ACTCCGCATATTAGAGTTGTGTC 58.316 43.478 0.00 0.00 37.60 3.67
467 644 4.159693 ACTCCGCATATTAGAGTTGTGTCA 59.840 41.667 0.00 0.00 37.60 3.58
468 645 5.079689 TCCGCATATTAGAGTTGTGTCAA 57.920 39.130 0.00 0.00 0.00 3.18
469 646 5.109210 TCCGCATATTAGAGTTGTGTCAAG 58.891 41.667 0.00 0.00 0.00 3.02
470 647 4.870426 CCGCATATTAGAGTTGTGTCAAGT 59.130 41.667 0.00 0.00 0.00 3.16
471 648 5.005779 CCGCATATTAGAGTTGTGTCAAGTC 59.994 44.000 8.68 8.68 0.00 3.01
472 649 5.576774 CGCATATTAGAGTTGTGTCAAGTCA 59.423 40.000 16.26 1.49 0.00 3.41
473 650 6.090763 CGCATATTAGAGTTGTGTCAAGTCAA 59.909 38.462 16.26 10.36 0.00 3.18
474 651 7.360017 CGCATATTAGAGTTGTGTCAAGTCAAA 60.360 37.037 16.26 4.85 0.00 2.69
475 652 8.454106 GCATATTAGAGTTGTGTCAAGTCAAAT 58.546 33.333 16.26 2.80 0.00 2.32
479 656 8.909708 TTAGAGTTGTGTCAAGTCAAATTTTG 57.090 30.769 16.26 2.59 0.00 2.44
480 657 6.924111 AGAGTTGTGTCAAGTCAAATTTTGT 58.076 32.000 16.26 0.00 0.00 2.83
481 658 8.050778 AGAGTTGTGTCAAGTCAAATTTTGTA 57.949 30.769 16.26 0.00 0.00 2.41
482 659 8.519526 AGAGTTGTGTCAAGTCAAATTTTGTAA 58.480 29.630 16.26 0.00 0.00 2.41
483 660 9.134734 GAGTTGTGTCAAGTCAAATTTTGTAAA 57.865 29.630 8.89 0.00 0.00 2.01
484 661 8.921670 AGTTGTGTCAAGTCAAATTTTGTAAAC 58.078 29.630 8.89 0.85 0.00 2.01
485 662 8.921670 GTTGTGTCAAGTCAAATTTTGTAAACT 58.078 29.630 8.89 3.06 0.00 2.66
486 663 9.482627 TTGTGTCAAGTCAAATTTTGTAAACTT 57.517 25.926 8.89 8.51 0.00 2.66
487 664 9.482627 TGTGTCAAGTCAAATTTTGTAAACTTT 57.517 25.926 8.89 0.00 0.00 2.66
488 665 9.739786 GTGTCAAGTCAAATTTTGTAAACTTTG 57.260 29.630 8.89 11.63 38.88 2.77
489 666 9.698309 TGTCAAGTCAAATTTTGTAAACTTTGA 57.302 25.926 14.81 14.81 41.90 2.69
643 820 9.683069 AGTTAAAATAGACATGCTTTGACTTTG 57.317 29.630 0.00 0.00 32.49 2.77
644 821 9.677567 GTTAAAATAGACATGCTTTGACTTTGA 57.322 29.630 0.00 0.00 32.49 2.69
651 828 8.579682 AGACATGCTTTGACTTTGAATAAAAC 57.420 30.769 0.00 0.00 0.00 2.43
652 829 8.416329 AGACATGCTTTGACTTTGAATAAAACT 58.584 29.630 0.00 0.00 0.00 2.66
653 830 8.947055 ACATGCTTTGACTTTGAATAAAACTT 57.053 26.923 0.00 0.00 0.00 2.66
679 856 4.473477 ACAGACTAAAAAGGATCGGAGG 57.527 45.455 0.00 0.00 0.00 4.30
680 857 4.094476 ACAGACTAAAAAGGATCGGAGGA 58.906 43.478 0.00 0.00 0.00 3.71
681 858 4.530946 ACAGACTAAAAAGGATCGGAGGAA 59.469 41.667 0.00 0.00 0.00 3.36
682 859 5.112686 CAGACTAAAAAGGATCGGAGGAAG 58.887 45.833 0.00 0.00 0.00 3.46
683 860 4.778427 AGACTAAAAAGGATCGGAGGAAGT 59.222 41.667 0.00 0.00 0.00 3.01
684 861 5.956563 AGACTAAAAAGGATCGGAGGAAGTA 59.043 40.000 0.00 0.00 0.00 2.24
1005 1409 3.149648 AAATCCGCAGCCATGGCC 61.150 61.111 33.14 17.81 43.17 5.36
1077 1481 1.457643 CTCCTCGCCCAGGTCCATA 60.458 63.158 0.00 0.00 43.95 2.74
1189 1596 5.696822 AGTACTACGTATACATGCGAATGG 58.303 41.667 8.61 0.00 39.23 3.16
1208 1615 3.772387 TGGGTCAGGCATTGATTGTTTA 58.228 40.909 0.00 0.00 38.29 2.01
1209 1616 4.352009 TGGGTCAGGCATTGATTGTTTAT 58.648 39.130 0.00 0.00 38.29 1.40
1212 1619 5.581874 GGGTCAGGCATTGATTGTTTATTTG 59.418 40.000 0.00 0.00 38.29 2.32
1216 1623 7.816995 GTCAGGCATTGATTGTTTATTTGGTTA 59.183 33.333 0.00 0.00 38.29 2.85
1218 1625 8.997323 CAGGCATTGATTGTTTATTTGGTTAAA 58.003 29.630 0.00 0.00 0.00 1.52
1319 1726 3.311110 TCGGCGAACAGGAAGGCT 61.311 61.111 7.35 0.00 0.00 4.58
1335 1742 3.771160 CTACGGCGGGGCTCAAGT 61.771 66.667 13.24 0.00 0.00 3.16
1505 1912 2.563261 AGAACCTTCCTTTTCCGTCC 57.437 50.000 0.00 0.00 0.00 4.79
1521 1928 2.283298 CGTCCATAGCTGTTCTGCATT 58.717 47.619 0.00 0.00 34.99 3.56
1564 1971 5.136105 AGTGGATCAATTAATGCTCCCTTC 58.864 41.667 0.00 1.96 42.58 3.46
1575 1982 2.632377 TGCTCCCTTCGTGATTTGATC 58.368 47.619 0.00 0.00 0.00 2.92
1706 2117 2.672961 TCACATGGTGAAGATCGTCC 57.327 50.000 6.18 0.00 39.78 4.79
1722 2133 5.594725 AGATCGTCCTGTGCTATAGAAAGAA 59.405 40.000 3.21 0.00 0.00 2.52
1766 2177 5.941555 AATAAGTACTCCCTCTGTGAAGG 57.058 43.478 0.00 0.00 36.08 3.46
1774 2185 7.844779 AGTACTCCCTCTGTGAAGGAATATAAA 59.155 37.037 0.00 0.00 38.87 1.40
1777 2188 8.560903 ACTCCCTCTGTGAAGGAATATAAAATT 58.439 33.333 0.00 0.00 38.87 1.82
1815 2239 8.928270 ACTTAGACCAGTTAATGATCTAAACG 57.072 34.615 0.00 0.00 32.86 3.60
1851 2277 9.832445 TTCTTCACAGAGAGTAACAATAAAAGT 57.168 29.630 0.00 0.00 0.00 2.66
1858 2284 8.958043 CAGAGAGTAACAATAAAAGTGCAAAAC 58.042 33.333 0.00 0.00 0.00 2.43
1862 2288 8.996024 AGTAACAATAAAAGTGCAAAACAACT 57.004 26.923 0.00 0.00 0.00 3.16
1865 2291 6.096695 ACAATAAAAGTGCAAAACAACTCGT 58.903 32.000 0.00 0.00 0.00 4.18
1872 2298 0.316689 CAAAACAACTCGTGTCGCCC 60.317 55.000 0.00 0.00 40.60 6.13
1927 2356 0.846870 CTCTTCCACCCCTCCCCTTT 60.847 60.000 0.00 0.00 0.00 3.11
1932 2361 1.229984 CACCCCTCCCCTTTCTCCT 60.230 63.158 0.00 0.00 0.00 3.69
1940 2369 3.391382 CCTTTCTCCTCCCGCCGT 61.391 66.667 0.00 0.00 0.00 5.68
2016 2445 2.577059 GCGTGGTAGTGGCTGCTA 59.423 61.111 0.00 0.00 0.00 3.49
2068 2498 1.543429 GGCTGGTGTTAGAGTTGTGCT 60.543 52.381 0.00 0.00 0.00 4.40
2127 2557 2.417586 CGTCGTATGGTGTGTAGACAGA 59.582 50.000 0.00 0.00 30.74 3.41
2143 2573 3.641436 AGACAGAGTATGTTGTGGTGTCA 59.359 43.478 0.00 0.00 44.17 3.58
2154 2584 4.591498 TGTTGTGGTGTCATAGTAGGACTT 59.409 41.667 15.41 0.00 36.26 3.01
2162 2592 7.399191 TGGTGTCATAGTAGGACTTTTGTATCT 59.601 37.037 15.41 0.00 36.26 1.98
2210 2724 4.854173 TGCCAACATAACAGGACATACAT 58.146 39.130 0.00 0.00 0.00 2.29
2221 2735 0.471617 GACATACATGCAGGGGAGCT 59.528 55.000 2.31 0.00 34.99 4.09
2253 2767 5.105310 GGTATTGTAGCGGTATCATGGAGAT 60.105 44.000 0.00 0.00 40.86 2.75
2317 2831 5.452777 GTGAACCTTGTTAGCAAATCTCAC 58.547 41.667 9.82 9.82 33.35 3.51
2407 2922 0.238553 GCAAGTTTCAAGGAGGTCGC 59.761 55.000 0.00 0.00 0.00 5.19
2428 2943 4.505922 CGCAGATTGTTGATCTAGAGGAAC 59.494 45.833 0.00 4.26 43.32 3.62
2438 2953 1.480954 TCTAGAGGAACGGTGCCAATC 59.519 52.381 8.15 0.00 0.00 2.67
2440 2955 0.693049 AGAGGAACGGTGCCAATCTT 59.307 50.000 8.15 0.00 0.00 2.40
2478 2994 5.245751 GGAAGCAGGAGAGAAGATCATATCA 59.754 44.000 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 5.360714 AGAACAAAAGGATCAAACAAGCTGA 59.639 36.000 0.00 0.00 0.00 4.26
146 318 6.253758 TCTCTCACACTCTGAAAACCCTATA 58.746 40.000 0.00 0.00 0.00 1.31
258 431 5.692204 CGAATACCAATCCTGACATCACTAC 59.308 44.000 0.00 0.00 0.00 2.73
259 432 5.221441 CCGAATACCAATCCTGACATCACTA 60.221 44.000 0.00 0.00 0.00 2.74
282 455 1.477295 GGTAGTACCTCAGAGCACACC 59.523 57.143 12.41 0.36 34.73 4.16
320 496 2.736144 TGCGTCTTCCAAGTCGTAAT 57.264 45.000 7.60 0.00 39.24 1.89
325 501 1.461127 GTGTGATGCGTCTTCCAAGTC 59.539 52.381 7.58 0.00 0.00 3.01
336 513 6.183360 CCAATGAAAATAAAGTGTGTGATGCG 60.183 38.462 0.00 0.00 0.00 4.73
372 549 1.752683 ACTTGGTTTTACGTGGCACA 58.247 45.000 19.09 0.00 0.00 4.57
430 607 1.730612 GCGGAGTAAAAAGGACCGAAG 59.269 52.381 0.00 0.00 45.31 3.79
431 608 1.070445 TGCGGAGTAAAAAGGACCGAA 59.930 47.619 0.00 0.00 45.31 4.30
432 609 0.680618 TGCGGAGTAAAAAGGACCGA 59.319 50.000 0.00 0.00 45.31 4.69
433 610 1.734163 ATGCGGAGTAAAAAGGACCG 58.266 50.000 0.00 0.00 45.26 4.79
434 611 6.285990 TCTAATATGCGGAGTAAAAAGGACC 58.714 40.000 0.00 0.00 0.00 4.46
435 612 6.985059 ACTCTAATATGCGGAGTAAAAAGGAC 59.015 38.462 0.00 0.00 38.37 3.85
436 613 7.120923 ACTCTAATATGCGGAGTAAAAAGGA 57.879 36.000 0.00 0.00 38.37 3.36
437 614 7.280205 ACAACTCTAATATGCGGAGTAAAAAGG 59.720 37.037 6.10 0.00 39.09 3.11
438 615 8.116753 CACAACTCTAATATGCGGAGTAAAAAG 58.883 37.037 6.10 0.00 39.09 2.27
439 616 7.604927 ACACAACTCTAATATGCGGAGTAAAAA 59.395 33.333 6.10 0.00 39.09 1.94
440 617 7.101054 ACACAACTCTAATATGCGGAGTAAAA 58.899 34.615 6.10 0.00 39.09 1.52
441 618 6.636705 ACACAACTCTAATATGCGGAGTAAA 58.363 36.000 6.10 0.00 39.09 2.01
442 619 6.127563 TGACACAACTCTAATATGCGGAGTAA 60.128 38.462 6.10 0.00 39.09 2.24
443 620 5.358725 TGACACAACTCTAATATGCGGAGTA 59.641 40.000 6.10 0.00 39.09 2.59
444 621 4.159693 TGACACAACTCTAATATGCGGAGT 59.840 41.667 0.00 0.00 41.37 3.85
445 622 4.682787 TGACACAACTCTAATATGCGGAG 58.317 43.478 0.00 0.00 0.00 4.63
446 623 4.729227 TGACACAACTCTAATATGCGGA 57.271 40.909 0.00 0.00 0.00 5.54
447 624 4.870426 ACTTGACACAACTCTAATATGCGG 59.130 41.667 0.00 0.00 0.00 5.69
448 625 5.576774 TGACTTGACACAACTCTAATATGCG 59.423 40.000 0.00 0.00 0.00 4.73
449 626 6.968131 TGACTTGACACAACTCTAATATGC 57.032 37.500 0.00 0.00 0.00 3.14
453 630 9.520204 CAAAATTTGACTTGACACAACTCTAAT 57.480 29.630 0.00 0.00 0.00 1.73
454 631 8.519526 ACAAAATTTGACTTGACACAACTCTAA 58.480 29.630 13.19 0.00 0.00 2.10
455 632 8.050778 ACAAAATTTGACTTGACACAACTCTA 57.949 30.769 13.19 0.00 0.00 2.43
456 633 6.924111 ACAAAATTTGACTTGACACAACTCT 58.076 32.000 13.19 0.00 0.00 3.24
457 634 8.682128 TTACAAAATTTGACTTGACACAACTC 57.318 30.769 13.19 0.00 0.00 3.01
458 635 8.921670 GTTTACAAAATTTGACTTGACACAACT 58.078 29.630 13.19 0.00 0.00 3.16
459 636 8.921670 AGTTTACAAAATTTGACTTGACACAAC 58.078 29.630 13.19 2.34 0.00 3.32
460 637 9.482627 AAGTTTACAAAATTTGACTTGACACAA 57.517 25.926 13.19 0.00 0.00 3.33
461 638 9.482627 AAAGTTTACAAAATTTGACTTGACACA 57.517 25.926 13.19 0.00 35.21 3.72
617 794 9.683069 CAAAGTCAAAGCATGTCTATTTTAACT 57.317 29.630 0.00 0.00 0.00 2.24
618 795 9.677567 TCAAAGTCAAAGCATGTCTATTTTAAC 57.322 29.630 0.00 0.00 0.00 2.01
625 802 9.677567 GTTTTATTCAAAGTCAAAGCATGTCTA 57.322 29.630 0.00 0.00 0.00 2.59
626 803 8.416329 AGTTTTATTCAAAGTCAAAGCATGTCT 58.584 29.630 0.00 0.00 0.00 3.41
627 804 8.579682 AGTTTTATTCAAAGTCAAAGCATGTC 57.420 30.769 0.00 0.00 0.00 3.06
628 805 8.947055 AAGTTTTATTCAAAGTCAAAGCATGT 57.053 26.923 0.00 0.00 0.00 3.21
653 830 9.021807 CCTCCGATCCTTTTTAGTCTGTATATA 57.978 37.037 0.00 0.00 0.00 0.86
654 831 7.728981 TCCTCCGATCCTTTTTAGTCTGTATAT 59.271 37.037 0.00 0.00 0.00 0.86
655 832 7.064866 TCCTCCGATCCTTTTTAGTCTGTATA 58.935 38.462 0.00 0.00 0.00 1.47
656 833 5.897824 TCCTCCGATCCTTTTTAGTCTGTAT 59.102 40.000 0.00 0.00 0.00 2.29
657 834 5.266788 TCCTCCGATCCTTTTTAGTCTGTA 58.733 41.667 0.00 0.00 0.00 2.74
658 835 4.094476 TCCTCCGATCCTTTTTAGTCTGT 58.906 43.478 0.00 0.00 0.00 3.41
659 836 4.737855 TCCTCCGATCCTTTTTAGTCTG 57.262 45.455 0.00 0.00 0.00 3.51
660 837 4.778427 ACTTCCTCCGATCCTTTTTAGTCT 59.222 41.667 0.00 0.00 0.00 3.24
661 838 5.087391 ACTTCCTCCGATCCTTTTTAGTC 57.913 43.478 0.00 0.00 0.00 2.59
662 839 5.720520 ACTACTTCCTCCGATCCTTTTTAGT 59.279 40.000 0.00 0.00 0.00 2.24
663 840 6.223351 ACTACTTCCTCCGATCCTTTTTAG 57.777 41.667 0.00 0.00 0.00 1.85
664 841 6.616237 AACTACTTCCTCCGATCCTTTTTA 57.384 37.500 0.00 0.00 0.00 1.52
665 842 5.500546 AACTACTTCCTCCGATCCTTTTT 57.499 39.130 0.00 0.00 0.00 1.94
666 843 6.809976 ATAACTACTTCCTCCGATCCTTTT 57.190 37.500 0.00 0.00 0.00 2.27
667 844 6.809976 AATAACTACTTCCTCCGATCCTTT 57.190 37.500 0.00 0.00 0.00 3.11
668 845 6.809976 AAATAACTACTTCCTCCGATCCTT 57.190 37.500 0.00 0.00 0.00 3.36
669 846 8.493787 AATAAATAACTACTTCCTCCGATCCT 57.506 34.615 0.00 0.00 0.00 3.24
918 1322 5.010282 TCCTTTCTTAAATCTTGTGGAGCC 58.990 41.667 0.00 0.00 0.00 4.70
1189 1596 5.581874 CCAAATAAACAATCAATGCCTGACC 59.418 40.000 0.00 0.00 36.69 4.02
1216 1623 8.866956 GCATCCGCGTATAGTAGTAATTATTTT 58.133 33.333 4.92 0.00 0.00 1.82
1218 1625 7.541162 TGCATCCGCGTATAGTAGTAATTATT 58.459 34.615 4.92 0.00 42.97 1.40
1230 1637 2.417243 CCATGATCTGCATCCGCGTATA 60.417 50.000 4.92 0.00 42.97 1.47
1234 1641 1.596203 ACCATGATCTGCATCCGCG 60.596 57.895 0.00 0.00 42.97 6.46
1319 1726 3.315949 AACTTGAGCCCCGCCGTA 61.316 61.111 0.00 0.00 0.00 4.02
1505 1912 2.380102 GCGAATGCAGAACAGCTATG 57.620 50.000 0.00 0.00 42.15 2.23
1564 1971 4.631377 ACTACACCACATGATCAAATCACG 59.369 41.667 0.00 0.00 43.01 4.35
1575 1982 6.593770 ACACATACATTGTACTACACCACATG 59.406 38.462 0.00 0.00 36.57 3.21
1649 2060 2.230992 TGAAAAACGCATGGGATGAAGG 59.769 45.455 17.76 0.00 0.00 3.46
1706 2117 8.932945 TCTATGTTGTTCTTTCTATAGCACAG 57.067 34.615 0.00 0.00 0.00 3.66
1747 2158 3.544698 TCCTTCACAGAGGGAGTACTT 57.455 47.619 0.00 0.00 32.81 2.24
1832 2258 8.958043 GTTTTGCACTTTTATTGTTACTCTCTG 58.042 33.333 0.00 0.00 0.00 3.35
1851 2277 0.247894 GCGACACGAGTTGTTTTGCA 60.248 50.000 4.26 0.00 39.17 4.08
1858 2284 3.934391 GAGGGGGCGACACGAGTTG 62.934 68.421 0.00 0.00 0.00 3.16
1862 2288 4.671590 TGAGAGGGGGCGACACGA 62.672 66.667 0.00 0.00 0.00 4.35
1885 2311 1.289066 CGTCGCTGGTTTCTCCTCA 59.711 57.895 0.00 0.00 37.07 3.86
2041 2471 1.174078 TCTAACACCAGCCGACGACA 61.174 55.000 0.00 0.00 0.00 4.35
2054 2484 6.710295 ACACAATATTCAGCACAACTCTAACA 59.290 34.615 0.00 0.00 0.00 2.41
2113 2543 4.587262 ACAACATACTCTGTCTACACACCA 59.413 41.667 0.00 0.00 36.98 4.17
2115 2545 4.923871 CCACAACATACTCTGTCTACACAC 59.076 45.833 0.00 0.00 36.98 3.82
2127 2557 5.955959 TCCTACTATGACACCACAACATACT 59.044 40.000 0.00 0.00 0.00 2.12
2162 2592 6.985117 AGGTTGTTACTTCGTGTGTCTATAA 58.015 36.000 0.00 0.00 0.00 0.98
2210 2724 3.957586 CACACCAGCTCCCCTGCA 61.958 66.667 0.00 0.00 40.36 4.41
2221 2735 1.338294 CCGCTACAATACCACACACCA 60.338 52.381 0.00 0.00 0.00 4.17
2253 2767 1.690893 GAGCCTGACTATGGATGCTCA 59.309 52.381 0.00 0.00 43.50 4.26
2302 2816 3.990092 ACGACAGTGAGATTTGCTAACA 58.010 40.909 0.00 0.00 29.42 2.41
2317 2831 0.667487 AATCACACGAGGCACGACAG 60.667 55.000 12.15 3.12 45.77 3.51
2407 2922 5.046529 CCGTTCCTCTAGATCAACAATCTG 58.953 45.833 12.24 0.00 44.69 2.90
2428 2943 1.750193 ACCATACAAGATTGGCACCG 58.250 50.000 0.00 0.00 36.41 4.94
2438 2953 2.159517 GCTTCCAAGCGAACCATACAAG 60.160 50.000 0.00 0.00 42.88 3.16
2440 2955 1.448985 GCTTCCAAGCGAACCATACA 58.551 50.000 0.00 0.00 42.88 2.29


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

AutoCloner maintained by Alex Coulton.