Multiple sequence alignment - TraesCS4D01G244800

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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 TraesCS4D01G244800 chr4D 100.000 3120 0 0 1 3120 409481045 409477926 0.000000e+00 5762.0
1 TraesCS4D01G244800 chr4B 93.847 2649 111 29 505 3120 506323076 506325705 0.000000e+00 3941.0
2 TraesCS4D01G244800 chr4B 88.675 468 29 6 4 456 506322630 506323088 1.640000e-152 549.0
3 TraesCS4D01G244800 chr4A 92.495 2665 116 40 505 3120 64567964 64570593 0.000000e+00 3736.0
4 TraesCS4D01G244800 chr4A 86.414 449 26 10 36 463 64567545 64567979 2.840000e-125 459.0
5 TraesCS4D01G244800 chr4A 100.000 36 0 0 3 38 64528698 64528733 2.010000e-07 67.6
6 TraesCS4D01G244800 chr3D 82.222 90 8 7 2686 2771 517809464 517809549 1.550000e-08 71.3
7 TraesCS4D01G244800 chr5A 93.182 44 3 0 413 456 561552019 561552062 7.220000e-07 65.8
8 TraesCS4D01G244800 chr5A 100.000 28 0 0 412 439 28658022 28657995 6.000000e-03 52.8
9 TraesCS4D01G244800 chr3A 86.441 59 6 1 414 472 479095739 479095795 2.600000e-06 63.9
10 TraesCS4D01G244800 chr1A 94.737 38 2 0 412 449 471797964 471798001 3.360000e-05 60.2


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 TraesCS4D01G244800 chr4D 409477926 409481045 3119 True 5762.0 5762 100.0000 1 3120 1 chr4D.!!$R1 3119
1 TraesCS4D01G244800 chr4B 506322630 506325705 3075 False 2245.0 3941 91.2610 4 3120 2 chr4B.!!$F1 3116
2 TraesCS4D01G244800 chr4A 64567545 64570593 3048 False 2097.5 3736 89.4545 36 3120 2 chr4A.!!$F2 3084

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
938 971 0.034186 TAATTGGCCCCTGAGTGCTG 60.034 55.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2334 2415 0.178767 CCATGGGACGAGCATCTTCA 59.821 55.0 2.85 0.0 34.65 3.02 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
36 37 2.755064 TGATGGGTGCGGCATTGG 60.755 61.111 5.72 0.00 0.00 3.16
37 38 2.440065 GATGGGTGCGGCATTGGA 60.440 61.111 5.72 0.00 0.00 3.53
41 42 2.270850 GGTGCGGCATTGGAGGTA 59.729 61.111 5.72 0.00 0.00 3.08
42 43 1.152963 GGTGCGGCATTGGAGGTAT 60.153 57.895 5.72 0.00 0.00 2.73
53 54 6.655003 CGGCATTGGAGGTATATTTTCAGTAT 59.345 38.462 0.00 0.00 0.00 2.12
154 155 6.093495 GGTAAAACAGAGCACATGTAGCATAA 59.907 38.462 18.31 0.00 0.00 1.90
183 184 7.633621 CGGTCCATGATGATACATAATAATGC 58.366 38.462 0.00 0.00 36.50 3.56
187 188 8.482128 TCCATGATGATACATAATAATGCCGTA 58.518 33.333 0.00 0.00 36.50 4.02
366 380 2.682856 GCATCGGCTCAACCTTAATCAA 59.317 45.455 0.00 0.00 36.96 2.57
372 386 3.769300 GGCTCAACCTTAATCAACCCAAT 59.231 43.478 0.00 0.00 34.51 3.16
375 389 6.239036 GGCTCAACCTTAATCAACCCAATATC 60.239 42.308 0.00 0.00 34.51 1.63
376 390 6.239036 GCTCAACCTTAATCAACCCAATATCC 60.239 42.308 0.00 0.00 0.00 2.59
377 391 6.133356 TCAACCTTAATCAACCCAATATCCC 58.867 40.000 0.00 0.00 0.00 3.85
378 392 5.742562 ACCTTAATCAACCCAATATCCCA 57.257 39.130 0.00 0.00 0.00 4.37
382 396 7.012607 CCTTAATCAACCCAATATCCCAAGAT 58.987 38.462 0.00 0.00 36.44 2.40
383 397 7.039504 CCTTAATCAACCCAATATCCCAAGATG 60.040 40.741 0.00 0.00 33.67 2.90
384 398 4.879295 TCAACCCAATATCCCAAGATGT 57.121 40.909 0.00 0.00 33.67 3.06
385 399 5.205517 TCAACCCAATATCCCAAGATGTT 57.794 39.130 0.00 0.00 34.44 2.71
388 402 5.205517 ACCCAATATCCCAAGATGTTCAA 57.794 39.130 0.00 0.00 32.02 2.69
389 403 5.203528 ACCCAATATCCCAAGATGTTCAAG 58.796 41.667 0.00 0.00 32.02 3.02
390 404 5.044179 ACCCAATATCCCAAGATGTTCAAGA 60.044 40.000 0.00 0.00 32.02 3.02
391 405 5.533903 CCCAATATCCCAAGATGTTCAAGAG 59.466 44.000 0.00 0.00 32.02 2.85
392 406 5.009410 CCAATATCCCAAGATGTTCAAGAGC 59.991 44.000 0.00 0.00 32.02 4.09
393 407 2.496899 TCCCAAGATGTTCAAGAGCC 57.503 50.000 0.00 0.00 0.00 4.70
394 408 1.704628 TCCCAAGATGTTCAAGAGCCA 59.295 47.619 0.00 0.00 0.00 4.75
395 409 2.309755 TCCCAAGATGTTCAAGAGCCAT 59.690 45.455 0.00 0.00 0.00 4.40
396 410 2.426024 CCCAAGATGTTCAAGAGCCATG 59.574 50.000 0.00 0.00 0.00 3.66
397 411 2.426024 CCAAGATGTTCAAGAGCCATGG 59.574 50.000 7.63 7.63 0.00 3.66
398 412 2.426024 CAAGATGTTCAAGAGCCATGGG 59.574 50.000 15.13 0.00 0.00 4.00
399 413 1.918262 AGATGTTCAAGAGCCATGGGA 59.082 47.619 15.13 0.00 0.00 4.37
403 417 3.509442 TGTTCAAGAGCCATGGGATTTT 58.491 40.909 15.13 0.00 0.00 1.82
482 503 9.618890 ACTTAATGATCTAAACATACATGCAGT 57.381 29.630 0.00 0.00 0.00 4.40
483 504 9.874215 CTTAATGATCTAAACATACATGCAGTG 57.126 33.333 0.00 0.00 0.00 3.66
484 505 5.739752 TGATCTAAACATACATGCAGTGC 57.260 39.130 8.58 8.58 0.00 4.40
485 506 4.576053 TGATCTAAACATACATGCAGTGCC 59.424 41.667 13.72 0.00 0.00 5.01
486 507 3.949132 TCTAAACATACATGCAGTGCCA 58.051 40.909 13.72 0.69 0.00 4.92
487 508 4.525996 TCTAAACATACATGCAGTGCCAT 58.474 39.130 13.72 3.36 0.00 4.40
488 509 3.513680 AAACATACATGCAGTGCCATG 57.486 42.857 13.72 17.43 46.19 3.66
494 515 2.736144 CATGCAGTGCCATGTTTCTT 57.264 45.000 13.72 0.00 38.19 2.52
495 516 3.034721 CATGCAGTGCCATGTTTCTTT 57.965 42.857 13.72 0.00 38.19 2.52
496 517 4.177165 CATGCAGTGCCATGTTTCTTTA 57.823 40.909 13.72 0.00 38.19 1.85
497 518 3.641437 TGCAGTGCCATGTTTCTTTAC 57.359 42.857 13.72 0.00 0.00 2.01
498 519 2.954989 TGCAGTGCCATGTTTCTTTACA 59.045 40.909 13.72 0.00 0.00 2.41
499 520 3.004629 TGCAGTGCCATGTTTCTTTACAG 59.995 43.478 13.72 0.00 0.00 2.74
500 521 3.253188 GCAGTGCCATGTTTCTTTACAGA 59.747 43.478 2.85 0.00 0.00 3.41
501 522 4.614535 GCAGTGCCATGTTTCTTTACAGAG 60.615 45.833 2.85 0.00 0.00 3.35
502 523 4.516698 CAGTGCCATGTTTCTTTACAGAGT 59.483 41.667 0.00 0.00 0.00 3.24
503 524 4.516698 AGTGCCATGTTTCTTTACAGAGTG 59.483 41.667 0.00 0.00 0.00 3.51
504 525 4.515191 GTGCCATGTTTCTTTACAGAGTGA 59.485 41.667 0.00 0.00 0.00 3.41
505 526 4.756642 TGCCATGTTTCTTTACAGAGTGAG 59.243 41.667 0.00 0.00 0.00 3.51
506 527 4.997395 GCCATGTTTCTTTACAGAGTGAGA 59.003 41.667 0.00 0.00 0.00 3.27
537 558 6.712276 ACTTAATTTGAAGTGGGAGACTAGG 58.288 40.000 0.00 0.00 38.25 3.02
627 654 1.235281 TGGTCCGACTCACACTCTCG 61.235 60.000 0.00 0.00 0.00 4.04
725 752 0.962356 AAATCCTGCCTGTCAAGCCG 60.962 55.000 0.00 0.00 0.00 5.52
905 938 2.357881 CGACAGGCAGAGCAAGCA 60.358 61.111 0.00 0.00 0.00 3.91
908 941 0.670162 GACAGGCAGAGCAAGCAAAA 59.330 50.000 0.00 0.00 0.00 2.44
913 946 2.366266 AGGCAGAGCAAGCAAAATTTGA 59.634 40.909 10.26 0.00 0.00 2.69
926 959 4.640956 CAAAATTTGAGCGCTTAATTGGC 58.359 39.130 23.59 7.48 0.00 4.52
927 960 2.584492 ATTTGAGCGCTTAATTGGCC 57.416 45.000 15.95 0.00 0.00 5.36
936 969 1.106285 CTTAATTGGCCCCTGAGTGC 58.894 55.000 0.00 0.00 0.00 4.40
937 970 0.704076 TTAATTGGCCCCTGAGTGCT 59.296 50.000 0.00 0.00 0.00 4.40
938 971 0.034186 TAATTGGCCCCTGAGTGCTG 60.034 55.000 0.00 0.00 0.00 4.41
939 972 2.085343 AATTGGCCCCTGAGTGCTGT 62.085 55.000 0.00 0.00 0.00 4.40
940 973 2.776370 ATTGGCCCCTGAGTGCTGTG 62.776 60.000 0.00 0.00 0.00 3.66
941 974 3.640407 GGCCCCTGAGTGCTGTGA 61.640 66.667 0.00 0.00 0.00 3.58
943 976 1.001641 GCCCCTGAGTGCTGTGAAT 60.002 57.895 0.00 0.00 0.00 2.57
944 977 0.610232 GCCCCTGAGTGCTGTGAATT 60.610 55.000 0.00 0.00 0.00 2.17
945 978 1.171308 CCCCTGAGTGCTGTGAATTG 58.829 55.000 0.00 0.00 0.00 2.32
946 979 0.524862 CCCTGAGTGCTGTGAATTGC 59.475 55.000 0.00 0.00 0.00 3.56
975 1008 2.216046 CTGAACAAGAAGCAGCTGTGA 58.784 47.619 16.64 0.00 0.00 3.58
1006 1039 2.433145 AGCACGTCGTCATGGCAG 60.433 61.111 7.98 0.00 0.00 4.85
1146 1179 1.153549 GCTCATCCTCTCGCCGTTT 60.154 57.895 0.00 0.00 0.00 3.60
1500 1539 1.512310 GCTCCTCGTCTTCGTCGTG 60.512 63.158 0.00 0.00 38.33 4.35
1695 1734 1.416813 CGCTGCTCGACATGTCCTTC 61.417 60.000 20.03 9.24 41.67 3.46
1715 1754 1.452145 GGCCACTTCACCTTCGCAAA 61.452 55.000 0.00 0.00 0.00 3.68
1733 1772 0.600255 AACTCACAGCAGGTACGCAC 60.600 55.000 0.00 0.00 0.00 5.34
1740 1779 0.670546 AGCAGGTACGCACACATCAC 60.671 55.000 0.00 0.00 0.00 3.06
1741 1780 1.635663 GCAGGTACGCACACATCACC 61.636 60.000 0.00 0.00 0.00 4.02
1742 1781 0.320334 CAGGTACGCACACATCACCA 60.320 55.000 0.00 0.00 0.00 4.17
1743 1782 0.394938 AGGTACGCACACATCACCAA 59.605 50.000 0.00 0.00 0.00 3.67
1785 1829 2.104331 CACGCCCGCCTAGTAGTG 59.896 66.667 0.00 0.00 0.00 2.74
1795 1839 3.005897 CCGCCTAGTAGTGTGCTTATCAT 59.994 47.826 0.00 0.00 0.00 2.45
2118 2162 2.355599 CTCCGCGGCAGCTCTATG 60.356 66.667 23.51 0.00 42.32 2.23
2121 2165 1.521457 CCGCGGCAGCTCTATGAAA 60.521 57.895 14.67 0.00 42.32 2.69
2122 2166 0.882042 CCGCGGCAGCTCTATGAAAT 60.882 55.000 14.67 0.00 42.32 2.17
2133 2177 7.064016 GGCAGCTCTATGAAATATACTACTTGC 59.936 40.741 0.00 0.00 0.00 4.01
2136 2180 9.083422 AGCTCTATGAAATATACTACTTGCTCA 57.917 33.333 0.00 0.00 0.00 4.26
2144 2188 6.884280 ATATACTACTTGCTCATTTTGGCC 57.116 37.500 0.00 0.00 0.00 5.36
2160 2236 0.449388 GGCCACTTTGCATCTCGAAG 59.551 55.000 0.00 0.00 41.14 3.79
2164 2240 3.849911 CCACTTTGCATCTCGAAGTCTA 58.150 45.455 0.00 0.00 45.39 2.59
2165 2241 3.862267 CCACTTTGCATCTCGAAGTCTAG 59.138 47.826 0.00 0.00 45.39 2.43
2166 2242 4.380973 CCACTTTGCATCTCGAAGTCTAGA 60.381 45.833 0.00 0.00 45.39 2.43
2167 2243 5.164233 CACTTTGCATCTCGAAGTCTAGAA 58.836 41.667 0.00 0.00 45.39 2.10
2168 2244 5.809562 CACTTTGCATCTCGAAGTCTAGAAT 59.190 40.000 0.00 0.00 45.39 2.40
2169 2245 6.312426 CACTTTGCATCTCGAAGTCTAGAATT 59.688 38.462 4.86 4.86 45.39 2.17
2170 2246 6.533367 ACTTTGCATCTCGAAGTCTAGAATTC 59.467 38.462 20.37 20.37 44.19 2.17
2171 2247 5.843673 TGCATCTCGAAGTCTAGAATTCT 57.156 39.130 25.54 13.56 33.67 2.40
2172 2248 6.944234 TGCATCTCGAAGTCTAGAATTCTA 57.056 37.500 25.54 16.70 33.67 2.10
2173 2249 6.964908 TGCATCTCGAAGTCTAGAATTCTAG 58.035 40.000 29.34 29.34 45.57 2.43
2294 2370 8.396272 ACTTGTGCAAAATTTCTACTGAGTAT 57.604 30.769 0.00 0.00 0.00 2.12
2295 2371 9.502091 ACTTGTGCAAAATTTCTACTGAGTATA 57.498 29.630 0.00 0.00 0.00 1.47
2298 2374 9.448438 TGTGCAAAATTTCTACTGAGTATATGT 57.552 29.630 0.00 0.00 0.00 2.29
2333 2414 7.274447 TCTGAAATTTGTGCAAAAATCTTCCT 58.726 30.769 15.22 0.00 33.56 3.36
2334 2415 7.769970 TCTGAAATTTGTGCAAAAATCTTCCTT 59.230 29.630 15.22 5.68 33.56 3.36
2372 2461 0.724785 GACAAGCGCGTTTAAGCACC 60.725 55.000 8.18 0.00 36.85 5.01
2376 2466 1.226295 GCGCGTTTAAGCACCCATC 60.226 57.895 8.43 0.00 36.85 3.51
2379 2469 0.179200 GCGTTTAAGCACCCATCGTG 60.179 55.000 0.00 0.00 46.03 4.35
2413 2503 1.197910 GTATGTAGTTGGCGCTCGAC 58.802 55.000 7.64 7.79 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.433404 CCCATCAGATTAAGCTATTGCATTCT 59.567 38.462 1.12 0.00 42.74 2.40
6 7 4.083643 CGCACCCATCAGATTAAGCTATTG 60.084 45.833 0.00 0.00 0.00 1.90
22 23 4.738998 CCTCCAATGCCGCACCCA 62.739 66.667 0.00 0.00 0.00 4.51
154 155 3.490439 TGTATCATCATGGACCGCAAT 57.510 42.857 0.00 0.00 0.00 3.56
187 188 2.741486 AATACAACACCCCGTGCGCT 62.741 55.000 9.73 0.00 36.98 5.92
199 201 6.936374 GCACATGGCAATTATCAAATACAAC 58.064 36.000 0.00 0.00 43.97 3.32
309 311 2.156917 TCTTGGCAGAAGCTGAACATG 58.843 47.619 0.00 0.00 41.70 3.21
332 346 1.226802 CGATGCACTCGGGTCTGAG 60.227 63.158 5.34 5.34 43.82 3.35
366 380 4.879295 TGAACATCTTGGGATATTGGGT 57.121 40.909 0.00 0.00 0.00 4.51
372 386 3.523157 TGGCTCTTGAACATCTTGGGATA 59.477 43.478 0.00 0.00 0.00 2.59
375 389 2.205022 TGGCTCTTGAACATCTTGGG 57.795 50.000 0.00 0.00 0.00 4.12
376 390 2.426024 CCATGGCTCTTGAACATCTTGG 59.574 50.000 0.00 0.00 0.00 3.61
377 391 2.426024 CCCATGGCTCTTGAACATCTTG 59.574 50.000 6.09 0.00 0.00 3.02
378 392 2.309755 TCCCATGGCTCTTGAACATCTT 59.690 45.455 6.09 0.00 0.00 2.40
382 396 2.905415 AATCCCATGGCTCTTGAACA 57.095 45.000 6.09 0.00 0.00 3.18
383 397 4.541973 AAAAATCCCATGGCTCTTGAAC 57.458 40.909 6.09 0.00 0.00 3.18
456 477 9.618890 ACTGCATGTATGTTTAGATCATTAAGT 57.381 29.630 0.00 0.00 0.00 2.24
457 478 9.874215 CACTGCATGTATGTTTAGATCATTAAG 57.126 33.333 0.00 0.00 0.00 1.85
458 479 8.344831 GCACTGCATGTATGTTTAGATCATTAA 58.655 33.333 0.00 0.00 0.00 1.40
459 480 7.041167 GGCACTGCATGTATGTTTAGATCATTA 60.041 37.037 2.82 0.00 0.00 1.90
460 481 6.238842 GGCACTGCATGTATGTTTAGATCATT 60.239 38.462 2.82 0.00 0.00 2.57
461 482 5.240183 GGCACTGCATGTATGTTTAGATCAT 59.760 40.000 2.82 0.00 0.00 2.45
462 483 4.576053 GGCACTGCATGTATGTTTAGATCA 59.424 41.667 2.82 0.00 0.00 2.92
463 484 4.576053 TGGCACTGCATGTATGTTTAGATC 59.424 41.667 2.82 0.00 0.00 2.75
464 485 4.525996 TGGCACTGCATGTATGTTTAGAT 58.474 39.130 2.82 0.00 0.00 1.98
465 486 3.949132 TGGCACTGCATGTATGTTTAGA 58.051 40.909 2.82 0.00 0.00 2.10
466 487 4.096833 ACATGGCACTGCATGTATGTTTAG 59.903 41.667 13.96 0.00 39.91 1.85
467 488 4.015764 ACATGGCACTGCATGTATGTTTA 58.984 39.130 13.96 0.00 39.91 2.01
468 489 2.827322 ACATGGCACTGCATGTATGTTT 59.173 40.909 13.96 0.00 39.91 2.83
469 490 2.449464 ACATGGCACTGCATGTATGTT 58.551 42.857 13.96 0.03 39.91 2.71
470 491 2.133281 ACATGGCACTGCATGTATGT 57.867 45.000 13.96 10.29 39.91 2.29
471 492 3.129813 AGAAACATGGCACTGCATGTATG 59.870 43.478 15.20 10.51 40.71 2.39
472 493 3.359033 AGAAACATGGCACTGCATGTAT 58.641 40.909 15.20 6.40 40.71 2.29
473 494 2.794103 AGAAACATGGCACTGCATGTA 58.206 42.857 15.20 0.00 40.71 2.29
474 495 1.624336 AGAAACATGGCACTGCATGT 58.376 45.000 2.82 8.08 43.09 3.21
475 496 2.736144 AAGAAACATGGCACTGCATG 57.264 45.000 2.82 7.49 35.13 4.06
476 497 3.573538 TGTAAAGAAACATGGCACTGCAT 59.426 39.130 2.82 0.00 0.00 3.96
477 498 2.954989 TGTAAAGAAACATGGCACTGCA 59.045 40.909 2.82 0.00 0.00 4.41
478 499 3.253188 TCTGTAAAGAAACATGGCACTGC 59.747 43.478 0.00 0.00 0.00 4.40
479 500 4.516698 ACTCTGTAAAGAAACATGGCACTG 59.483 41.667 0.00 0.00 0.00 3.66
480 501 4.516698 CACTCTGTAAAGAAACATGGCACT 59.483 41.667 0.00 0.00 0.00 4.40
481 502 4.515191 TCACTCTGTAAAGAAACATGGCAC 59.485 41.667 0.00 0.00 0.00 5.01
482 503 4.713553 TCACTCTGTAAAGAAACATGGCA 58.286 39.130 0.00 0.00 0.00 4.92
483 504 4.997395 TCTCACTCTGTAAAGAAACATGGC 59.003 41.667 0.00 0.00 0.00 4.40
484 505 6.226787 AGTCTCACTCTGTAAAGAAACATGG 58.773 40.000 0.00 0.00 0.00 3.66
485 506 6.925718 TGAGTCTCACTCTGTAAAGAAACATG 59.074 38.462 0.00 0.00 45.27 3.21
486 507 6.926272 GTGAGTCTCACTCTGTAAAGAAACAT 59.074 38.462 23.25 0.00 45.27 2.71
487 508 6.273825 GTGAGTCTCACTCTGTAAAGAAACA 58.726 40.000 23.25 0.00 45.27 2.83
488 509 6.757026 GTGAGTCTCACTCTGTAAAGAAAC 57.243 41.667 23.25 0.00 45.27 2.78
501 522 8.704234 CACTTCAAATTAAGTAGTGAGTCTCAC 58.296 37.037 23.11 23.11 41.33 3.51
502 523 7.872993 CCACTTCAAATTAAGTAGTGAGTCTCA 59.127 37.037 14.91 0.00 37.61 3.27
503 524 7.332182 CCCACTTCAAATTAAGTAGTGAGTCTC 59.668 40.741 14.91 0.00 37.61 3.36
504 525 7.016268 TCCCACTTCAAATTAAGTAGTGAGTCT 59.984 37.037 14.91 0.00 37.61 3.24
505 526 7.159372 TCCCACTTCAAATTAAGTAGTGAGTC 58.841 38.462 14.91 0.00 37.61 3.36
506 527 7.016268 TCTCCCACTTCAAATTAAGTAGTGAGT 59.984 37.037 14.91 0.00 37.61 3.41
564 585 2.166870 AGTTTGTGTATGCATGCATGGG 59.833 45.455 37.43 4.09 37.82 4.00
627 654 0.107993 TGCTATGGCAGTGAGTGAGC 60.108 55.000 0.00 0.00 44.28 4.26
725 752 6.690528 GCTAGTACAGTACGAGATTACAAACC 59.309 42.308 21.47 0.62 33.88 3.27
905 938 3.684305 GGCCAATTAAGCGCTCAAATTTT 59.316 39.130 21.61 4.57 0.00 1.82
908 941 1.136891 GGGCCAATTAAGCGCTCAAAT 59.863 47.619 12.06 11.47 39.86 2.32
913 946 1.754234 CAGGGGCCAATTAAGCGCT 60.754 57.895 2.64 2.64 42.40 5.92
926 959 1.171308 CAATTCACAGCACTCAGGGG 58.829 55.000 0.00 0.00 0.00 4.79
927 960 0.524862 GCAATTCACAGCACTCAGGG 59.475 55.000 0.00 0.00 0.00 4.45
960 993 1.263484 CACAGTCACAGCTGCTTCTTG 59.737 52.381 15.27 8.84 39.96 3.02
962 995 0.755079 TCACAGTCACAGCTGCTTCT 59.245 50.000 15.27 6.47 39.96 2.85
965 998 0.389556 CGATCACAGTCACAGCTGCT 60.390 55.000 15.27 0.00 39.96 4.24
975 1008 0.248255 CGTGCTCGATCGATCACAGT 60.248 55.000 36.73 0.00 40.16 3.55
1062 1095 1.141234 GGGGCTCTGCACGTAGTAC 59.859 63.158 0.00 0.00 41.61 2.73
1089 1122 3.321648 TGGCTCAGGGTGTGCGAT 61.322 61.111 0.00 0.00 37.71 4.58
1695 1734 3.423154 GCGAAGGTGAAGTGGCCG 61.423 66.667 0.00 0.00 0.00 6.13
1715 1754 1.006102 GTGCGTACCTGCTGTGAGT 60.006 57.895 0.00 0.00 35.36 3.41
1733 1772 2.159430 CGTGTACATGGTTGGTGATGTG 59.841 50.000 7.22 0.00 34.60 3.21
1740 1779 1.164411 ATGCACGTGTACATGGTTGG 58.836 50.000 18.38 6.93 0.00 3.77
1741 1780 2.583739 CAATGCACGTGTACATGGTTG 58.416 47.619 18.38 9.81 0.00 3.77
1742 1781 1.068610 GCAATGCACGTGTACATGGTT 60.069 47.619 18.38 0.00 0.00 3.67
1743 1782 0.521291 GCAATGCACGTGTACATGGT 59.479 50.000 18.38 8.25 0.00 3.55
1785 1829 3.362401 CGATCACGCAAGATGATAAGCAC 60.362 47.826 0.00 0.00 37.92 4.40
1975 2019 4.197498 CCTACCACGCGGTACCGG 62.197 72.222 33.98 25.18 46.71 5.28
2111 2155 9.868277 ATGAGCAAGTAGTATATTTCATAGAGC 57.132 33.333 0.00 0.00 0.00 4.09
2118 2162 7.862873 GGCCAAAATGAGCAAGTAGTATATTTC 59.137 37.037 0.00 0.00 0.00 2.17
2121 2165 6.263168 GTGGCCAAAATGAGCAAGTAGTATAT 59.737 38.462 7.24 0.00 0.00 0.86
2122 2166 5.588648 GTGGCCAAAATGAGCAAGTAGTATA 59.411 40.000 7.24 0.00 0.00 1.47
2133 2177 2.529780 TGCAAAGTGGCCAAAATGAG 57.470 45.000 7.24 0.00 0.00 2.90
2136 2180 2.353011 CGAGATGCAAAGTGGCCAAAAT 60.353 45.455 7.24 0.00 0.00 1.82
2144 2188 4.738124 TCTAGACTTCGAGATGCAAAGTG 58.262 43.478 5.48 0.00 33.54 3.16
2164 2240 9.270640 CAAATGAAATCCTCGATCTAGAATTCT 57.729 33.333 13.56 13.56 0.00 2.40
2165 2241 8.014517 GCAAATGAAATCCTCGATCTAGAATTC 58.985 37.037 0.00 0.00 0.00 2.17
2166 2242 7.040823 GGCAAATGAAATCCTCGATCTAGAATT 60.041 37.037 0.00 0.00 0.00 2.17
2167 2243 6.429385 GGCAAATGAAATCCTCGATCTAGAAT 59.571 38.462 0.00 0.00 0.00 2.40
2168 2244 5.760253 GGCAAATGAAATCCTCGATCTAGAA 59.240 40.000 0.00 0.00 0.00 2.10
2169 2245 5.163311 TGGCAAATGAAATCCTCGATCTAGA 60.163 40.000 0.00 0.00 0.00 2.43
2170 2246 5.049818 GTGGCAAATGAAATCCTCGATCTAG 60.050 44.000 0.00 0.00 0.00 2.43
2171 2247 4.816385 GTGGCAAATGAAATCCTCGATCTA 59.184 41.667 0.00 0.00 0.00 1.98
2172 2248 3.629398 GTGGCAAATGAAATCCTCGATCT 59.371 43.478 0.00 0.00 0.00 2.75
2173 2249 3.629398 AGTGGCAAATGAAATCCTCGATC 59.371 43.478 0.00 0.00 0.00 3.69
2214 2290 5.008217 TCCAATTCCACACGTAAAAACTGAG 59.992 40.000 0.00 0.00 0.00 3.35
2294 2370 9.986833 CACAAATTTCAGATCATACGAAACATA 57.013 29.630 0.00 0.00 31.87 2.29
2295 2371 7.485913 GCACAAATTTCAGATCATACGAAACAT 59.514 33.333 0.00 0.00 31.87 2.71
2296 2372 6.801377 GCACAAATTTCAGATCATACGAAACA 59.199 34.615 0.00 0.00 31.87 2.83
2297 2373 6.801377 TGCACAAATTTCAGATCATACGAAAC 59.199 34.615 0.00 0.00 31.87 2.78
2298 2374 6.907741 TGCACAAATTTCAGATCATACGAAA 58.092 32.000 0.00 0.00 33.48 3.46
2299 2375 6.493449 TGCACAAATTTCAGATCATACGAA 57.507 33.333 0.00 0.00 0.00 3.85
2301 2377 7.565450 TTTTGCACAAATTTCAGATCATACG 57.435 32.000 0.00 0.00 0.00 3.06
2333 2414 1.407299 CCATGGGACGAGCATCTTCAA 60.407 52.381 2.85 0.00 34.65 2.69
2334 2415 0.178767 CCATGGGACGAGCATCTTCA 59.821 55.000 2.85 0.00 34.65 3.02
2358 2447 1.226295 GATGGGTGCTTAAACGCGC 60.226 57.895 5.73 0.00 39.59 6.86
2359 2448 1.060308 CGATGGGTGCTTAAACGCG 59.940 57.895 3.53 3.53 35.86 6.01
2397 2487 2.260434 GGTCGAGCGCCAACTACA 59.740 61.111 2.29 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.