Multiple sequence alignment - TraesCS4D01G277700

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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 TraesCS4D01G277700 chr4D 100.000 2567 0 0 1 2567 449855552 449852986 0.000000e+00 4741.0
1 TraesCS4D01G277700 chr4D 87.716 578 48 9 1120 1688 449739472 449738909 0.000000e+00 652.0
2 TraesCS4D01G277700 chr4D 85.321 327 32 9 1179 1501 449876086 449875772 8.860000e-85 324.0
3 TraesCS4D01G277700 chr4D 86.517 267 20 8 813 1069 449739725 449739465 1.940000e-71 279.0
4 TraesCS4D01G277700 chr4D 85.366 123 10 4 2211 2327 449969078 449969198 1.250000e-23 121.0
5 TraesCS4D01G277700 chr4D 85.593 118 9 5 2216 2327 449947810 449947925 1.610000e-22 117.0
6 TraesCS4D01G277700 chr4B 89.865 888 39 20 807 1690 562419689 562418849 0.000000e+00 1094.0
7 TraesCS4D01G277700 chr4B 84.729 812 55 32 900 1688 562361493 562360728 0.000000e+00 749.0
8 TraesCS4D01G277700 chr4B 84.298 363 37 13 1143 1501 562436363 562436017 1.140000e-88 337.0
9 TraesCS4D01G277700 chr4B 90.850 153 11 3 765 916 562361660 562361510 4.330000e-48 202.0
10 TraesCS4D01G277700 chr4B 88.136 118 12 2 2211 2327 562685847 562685963 3.440000e-29 139.0
11 TraesCS4D01G277700 chr4B 88.182 110 7 5 2209 2313 562360107 562359999 2.680000e-25 126.0
12 TraesCS4D01G277700 chr4A 88.047 937 60 27 767 1688 17256201 17257100 0.000000e+00 1062.0
13 TraesCS4D01G277700 chr4A 84.615 1040 62 52 665 1689 17032163 17033119 0.000000e+00 944.0
14 TraesCS4D01G277700 chr4A 87.763 523 27 10 1695 2211 17033163 17033654 6.160000e-161 577.0
15 TraesCS4D01G277700 chr4A 91.521 401 26 6 1153 1553 17253374 17253766 1.740000e-151 545.0
16 TraesCS4D01G277700 chr4A 91.398 372 17 3 2210 2567 17033687 17034057 1.770000e-136 496.0
17 TraesCS4D01G277700 chr4A 86.544 327 28 9 1179 1501 17024259 17024573 1.890000e-91 346.0
18 TraesCS4D01G277700 chr4A 100.000 28 0 0 2211 2238 16986701 16986674 5.000000e-03 52.8
19 TraesCS4D01G277700 chr5D 94.378 587 21 4 1 587 503076308 503076882 0.000000e+00 891.0
20 TraesCS4D01G277700 chr5D 94.646 579 18 3 1 579 8404355 8404920 0.000000e+00 885.0
21 TraesCS4D01G277700 chr5D 93.986 582 21 3 1 582 69415878 69416445 0.000000e+00 869.0
22 TraesCS4D01G277700 chr5D 93.266 594 24 6 1 593 231231369 231230791 0.000000e+00 861.0
23 TraesCS4D01G277700 chr5D 92.955 582 33 4 1 581 374397526 374398100 0.000000e+00 841.0
24 TraesCS4D01G277700 chr6D 93.127 582 29 4 1 582 450665845 450666415 0.000000e+00 843.0
25 TraesCS4D01G277700 chr6D 93.878 49 3 0 544 592 22061607 22061655 9.850000e-10 75.0
26 TraesCS4D01G277700 chr2D 92.967 583 27 6 1 583 43346206 43346774 0.000000e+00 837.0
27 TraesCS4D01G277700 chr2D 94.659 543 23 2 1 543 79278378 79278914 0.000000e+00 837.0
28 TraesCS4D01G277700 chr2D 97.561 41 1 0 543 583 585918326 585918286 1.270000e-08 71.3
29 TraesCS4D01G277700 chr7A 92.401 579 34 3 3 581 643976325 643975757 0.000000e+00 817.0
30 TraesCS4D01G277700 chr5A 75.920 598 93 28 4 585 12584584 12584022 2.530000e-65 259.0
31 TraesCS4D01G277700 chr1B 97.500 40 1 0 545 584 134466426 134466387 4.580000e-08 69.4


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 TraesCS4D01G277700 chr4D 449852986 449855552 2566 True 4741.000000 4741 100.000000 1 2567 1 chr4D.!!$R1 2566
1 TraesCS4D01G277700 chr4D 449738909 449739725 816 True 465.500000 652 87.116500 813 1688 2 chr4D.!!$R3 875
2 TraesCS4D01G277700 chr4B 562418849 562419689 840 True 1094.000000 1094 89.865000 807 1690 1 chr4B.!!$R1 883
3 TraesCS4D01G277700 chr4B 562359999 562361660 1661 True 359.000000 749 87.920333 765 2313 3 chr4B.!!$R3 1548
4 TraesCS4D01G277700 chr4A 17253374 17257100 3726 False 803.500000 1062 89.784000 767 1688 2 chr4A.!!$F3 921
5 TraesCS4D01G277700 chr4A 17032163 17034057 1894 False 672.333333 944 87.925333 665 2567 3 chr4A.!!$F2 1902
6 TraesCS4D01G277700 chr5D 503076308 503076882 574 False 891.000000 891 94.378000 1 587 1 chr5D.!!$F4 586
7 TraesCS4D01G277700 chr5D 8404355 8404920 565 False 885.000000 885 94.646000 1 579 1 chr5D.!!$F1 578
8 TraesCS4D01G277700 chr5D 69415878 69416445 567 False 869.000000 869 93.986000 1 582 1 chr5D.!!$F2 581
9 TraesCS4D01G277700 chr5D 231230791 231231369 578 True 861.000000 861 93.266000 1 593 1 chr5D.!!$R1 592
10 TraesCS4D01G277700 chr5D 374397526 374398100 574 False 841.000000 841 92.955000 1 581 1 chr5D.!!$F3 580
11 TraesCS4D01G277700 chr6D 450665845 450666415 570 False 843.000000 843 93.127000 1 582 1 chr6D.!!$F2 581
12 TraesCS4D01G277700 chr2D 43346206 43346774 568 False 837.000000 837 92.967000 1 583 1 chr2D.!!$F1 582
13 TraesCS4D01G277700 chr2D 79278378 79278914 536 False 837.000000 837 94.659000 1 543 1 chr2D.!!$F2 542
14 TraesCS4D01G277700 chr7A 643975757 643976325 568 True 817.000000 817 92.401000 3 581 1 chr7A.!!$R1 578
15 TraesCS4D01G277700 chr5A 12584022 12584584 562 True 259.000000 259 75.920000 4 585 1 chr5A.!!$R1 581

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
711 733 0.033405 CTCGTGGGAGGTAAGGAGGA 60.033 60.0 0.0 0.0 36.61 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1766 3973 0.179045 CCCTTGGCCTAGTCGATTGG 60.179 60.0 13.38 2.17 0.0 3.16 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 1.048601 TGCTCTTCTTCCTGGACGTT 58.951 50.000 0.00 0.00 0.00 3.99
514 530 0.822121 GACTGGGGCGTTTTCTTGGT 60.822 55.000 0.00 0.00 0.00 3.67
538 555 4.050934 GCCGAAAAAGTGGCCGGG 62.051 66.667 2.18 0.00 45.73 5.73
539 556 3.370231 CCGAAAAAGTGGCCGGGG 61.370 66.667 2.18 0.00 38.42 5.73
540 557 3.370231 CGAAAAAGTGGCCGGGGG 61.370 66.667 2.18 0.00 0.00 5.40
595 617 4.927978 GCTCTTAGCATAGAGGTCTCAA 57.072 45.455 14.61 0.00 41.89 3.02
596 618 5.467035 GCTCTTAGCATAGAGGTCTCAAT 57.533 43.478 14.61 0.00 41.89 2.57
597 619 5.852827 GCTCTTAGCATAGAGGTCTCAATT 58.147 41.667 14.61 0.00 41.89 2.32
598 620 5.695816 GCTCTTAGCATAGAGGTCTCAATTG 59.304 44.000 14.61 0.00 41.89 2.32
599 621 6.166984 TCTTAGCATAGAGGTCTCAATTGG 57.833 41.667 5.42 0.00 0.00 3.16
600 622 5.899547 TCTTAGCATAGAGGTCTCAATTGGA 59.100 40.000 5.42 0.00 0.00 3.53
601 623 6.384015 TCTTAGCATAGAGGTCTCAATTGGAA 59.616 38.462 5.42 0.00 0.00 3.53
602 624 5.441718 AGCATAGAGGTCTCAATTGGAAA 57.558 39.130 5.42 0.00 0.00 3.13
603 625 5.819991 AGCATAGAGGTCTCAATTGGAAAA 58.180 37.500 5.42 0.00 0.00 2.29
604 626 6.248433 AGCATAGAGGTCTCAATTGGAAAAA 58.752 36.000 5.42 0.00 0.00 1.94
605 627 6.376581 AGCATAGAGGTCTCAATTGGAAAAAG 59.623 38.462 5.42 0.00 0.00 2.27
607 629 7.094205 GCATAGAGGTCTCAATTGGAAAAAGAA 60.094 37.037 5.42 0.00 0.00 2.52
608 630 8.964772 CATAGAGGTCTCAATTGGAAAAAGAAT 58.035 33.333 5.42 0.00 0.00 2.40
609 631 7.224522 AGAGGTCTCAATTGGAAAAAGAATG 57.775 36.000 5.42 0.00 0.00 2.67
610 632 6.779539 AGAGGTCTCAATTGGAAAAAGAATGT 59.220 34.615 5.42 0.00 0.00 2.71
611 633 6.986250 AGGTCTCAATTGGAAAAAGAATGTC 58.014 36.000 5.42 0.00 0.00 3.06
612 634 6.550854 AGGTCTCAATTGGAAAAAGAATGTCA 59.449 34.615 5.42 0.00 0.00 3.58
614 636 7.710475 GGTCTCAATTGGAAAAAGAATGTCAAA 59.290 33.333 5.42 0.00 0.00 2.69
615 637 9.264719 GTCTCAATTGGAAAAAGAATGTCAAAT 57.735 29.630 5.42 0.00 0.00 2.32
640 662 9.791801 ATATGTTACAACTATTGCCATATGTCA 57.208 29.630 1.24 0.00 32.88 3.58
641 663 7.315247 TGTTACAACTATTGCCATATGTCAC 57.685 36.000 1.24 0.00 0.00 3.67
642 664 7.109501 TGTTACAACTATTGCCATATGTCACT 58.890 34.615 1.24 0.00 0.00 3.41
643 665 8.261522 TGTTACAACTATTGCCATATGTCACTA 58.738 33.333 1.24 0.00 0.00 2.74
644 666 9.104965 GTTACAACTATTGCCATATGTCACTAA 57.895 33.333 1.24 0.00 0.00 2.24
645 667 7.792374 ACAACTATTGCCATATGTCACTAAG 57.208 36.000 1.24 0.00 0.00 2.18
646 668 6.260936 ACAACTATTGCCATATGTCACTAAGC 59.739 38.462 1.24 0.00 0.00 3.09
647 669 6.179906 ACTATTGCCATATGTCACTAAGCT 57.820 37.500 1.24 0.00 0.00 3.74
648 670 5.994054 ACTATTGCCATATGTCACTAAGCTG 59.006 40.000 1.24 0.00 0.00 4.24
649 671 4.486125 TTGCCATATGTCACTAAGCTGA 57.514 40.909 1.24 0.00 0.00 4.26
659 681 6.096673 TGTCACTAAGCTGACATGTTTAGA 57.903 37.500 17.81 0.00 44.54 2.10
660 682 6.701340 TGTCACTAAGCTGACATGTTTAGAT 58.299 36.000 17.81 8.56 44.54 1.98
661 683 7.836842 TGTCACTAAGCTGACATGTTTAGATA 58.163 34.615 17.81 8.50 44.54 1.98
662 684 7.976175 TGTCACTAAGCTGACATGTTTAGATAG 59.024 37.037 17.81 16.27 44.54 2.08
663 685 6.980978 TCACTAAGCTGACATGTTTAGATAGC 59.019 38.462 17.81 12.50 35.33 2.97
664 686 6.201806 CACTAAGCTGACATGTTTAGATAGCC 59.798 42.308 17.81 0.00 35.33 3.93
666 688 5.102953 AGCTGACATGTTTAGATAGCCAA 57.897 39.130 13.42 0.00 0.00 4.52
667 689 5.500234 AGCTGACATGTTTAGATAGCCAAA 58.500 37.500 13.42 0.00 0.00 3.28
670 692 7.123247 AGCTGACATGTTTAGATAGCCAAAATT 59.877 33.333 13.42 0.00 0.00 1.82
671 693 8.405531 GCTGACATGTTTAGATAGCCAAAATTA 58.594 33.333 13.42 0.00 0.00 1.40
711 733 0.033405 CTCGTGGGAGGTAAGGAGGA 60.033 60.000 0.00 0.00 36.61 3.71
712 734 0.410663 TCGTGGGAGGTAAGGAGGAA 59.589 55.000 0.00 0.00 0.00 3.36
909 2983 6.206498 CAGATCGTACAATCAAATCCGTAGA 58.794 40.000 0.00 0.00 0.00 2.59
923 3030 1.962100 CCGTAGAATAGACCTGGTCCC 59.038 57.143 22.81 10.11 32.18 4.46
1043 3152 1.971357 TCTCTCCTCCAACAACCACTC 59.029 52.381 0.00 0.00 0.00 3.51
1069 3179 2.224378 CCAGCCATTCATCCATCGTACT 60.224 50.000 0.00 0.00 0.00 2.73
1118 3232 4.536364 CAACATTTGCTCCATACCGTAG 57.464 45.455 0.00 0.00 0.00 3.51
1140 3254 1.463444 ACCGTACGTACCGTAGTTGTC 59.537 52.381 19.67 0.00 43.06 3.18
1161 3281 6.884832 TGTCCTCAGAGACTCAAAAGTTAAA 58.115 36.000 5.02 0.00 37.66 1.52
1162 3282 6.761714 TGTCCTCAGAGACTCAAAAGTTAAAC 59.238 38.462 5.02 0.00 37.66 2.01
1163 3283 5.983720 TCCTCAGAGACTCAAAAGTTAAACG 59.016 40.000 5.02 0.00 35.28 3.60
1168 3291 6.202954 CAGAGACTCAAAAGTTAAACGACCAT 59.797 38.462 5.02 0.00 35.28 3.55
1217 3340 4.221422 GCGAGGGCGGTGCTGATA 62.221 66.667 0.00 0.00 38.16 2.15
1218 3341 2.028190 CGAGGGCGGTGCTGATAG 59.972 66.667 0.00 0.00 0.00 2.08
1219 3342 2.280457 GAGGGCGGTGCTGATAGC 60.280 66.667 0.00 0.00 42.82 2.97
1468 3597 5.188434 ACTAGTCAATTAGCATGCATGTGT 58.812 37.500 26.79 17.10 0.00 3.72
1516 3660 2.543238 GGTCGTCTCTTGTTCGTCTTGT 60.543 50.000 0.00 0.00 0.00 3.16
1564 3719 7.340743 TGGTTCCTTCATTCTTTCAAGTGTAAA 59.659 33.333 0.00 0.00 0.00 2.01
1591 3749 3.366052 AGGGCTTCCGTTAAATGATGT 57.634 42.857 0.00 0.00 35.17 3.06
1650 3808 7.684670 AGTACGTACTACATGAATTTGCAATG 58.315 34.615 26.36 0.00 34.13 2.82
1691 3851 4.642429 GTCTGTGACCACTAACCAAATCT 58.358 43.478 1.62 0.00 0.00 2.40
1727 3934 7.095910 TGTTGCACGATGATTTGGAATATTTT 58.904 30.769 0.00 0.00 0.00 1.82
1743 3950 8.796475 TGGAATATTTTGAAGGAGAGAAACAAG 58.204 33.333 0.00 0.00 0.00 3.16
1753 3960 5.380043 AGGAGAGAAACAAGCTCATTTTCA 58.620 37.500 13.97 0.00 34.85 2.69
1756 3963 4.023707 AGAGAAACAAGCTCATTTTCACCG 60.024 41.667 13.97 0.00 34.85 4.94
1759 3966 4.647424 AACAAGCTCATTTTCACCGAAA 57.353 36.364 0.00 0.00 0.00 3.46
1760 3967 4.228912 ACAAGCTCATTTTCACCGAAAG 57.771 40.909 0.00 0.00 32.93 2.62
1779 3986 1.413077 AGGCTTACCAATCGACTAGGC 59.587 52.381 0.00 0.00 39.06 3.93
1796 4003 1.678970 GCCAAGGGACCAAAGCGAT 60.679 57.895 0.00 0.00 0.00 4.58
1842 4054 6.119536 TCTGTATTATGGATGTGTGGGTTTC 58.880 40.000 0.00 0.00 0.00 2.78
1852 4064 1.071228 GTGTGGGTTTCTACGAGGGTT 59.929 52.381 0.00 0.00 0.00 4.11
1857 4069 3.073356 TGGGTTTCTACGAGGGTTTCAAT 59.927 43.478 0.00 0.00 0.00 2.57
1905 4123 5.885230 TTATCTCTTTGCCACTTGTGATG 57.115 39.130 1.89 0.00 0.00 3.07
1916 4134 5.874810 TGCCACTTGTGATGAGTATCTTAAC 59.125 40.000 1.89 0.00 34.92 2.01
1958 4267 5.973565 GGGCGACTTGAAATGAATATCTTTG 59.026 40.000 0.00 0.00 0.00 2.77
2001 4314 4.481930 TCGAATTCGAATTGCAGTGTTT 57.518 36.364 27.36 0.98 46.30 2.83
2002 4315 4.218265 TCGAATTCGAATTGCAGTGTTTG 58.782 39.130 27.36 6.45 46.30 2.93
2003 4316 3.974401 CGAATTCGAATTGCAGTGTTTGT 59.026 39.130 27.27 0.00 43.02 2.83
2004 4317 4.440758 CGAATTCGAATTGCAGTGTTTGTT 59.559 37.500 27.27 0.00 43.02 2.83
2005 4318 5.623264 CGAATTCGAATTGCAGTGTTTGTTA 59.377 36.000 27.27 0.00 43.02 2.41
2006 4319 6.397480 CGAATTCGAATTGCAGTGTTTGTTAC 60.397 38.462 27.27 7.17 43.02 2.50
2007 4320 4.884458 TCGAATTGCAGTGTTTGTTACA 57.116 36.364 0.00 0.00 0.00 2.41
2008 4321 5.431420 TCGAATTGCAGTGTTTGTTACAT 57.569 34.783 0.00 0.00 39.39 2.29
2009 4322 5.826586 TCGAATTGCAGTGTTTGTTACATT 58.173 33.333 0.00 0.00 39.39 2.71
2010 4323 6.269315 TCGAATTGCAGTGTTTGTTACATTT 58.731 32.000 0.00 0.00 39.39 2.32
2017 4330 8.795786 TGCAGTGTTTGTTACATTTATTTCTC 57.204 30.769 0.00 0.00 39.39 2.87
2049 4362 4.007659 CCCCATAATATCCTGTTAACGCC 58.992 47.826 0.26 0.00 0.00 5.68
2151 4465 6.064846 ACCAATATTTAATCAAGCGAGCAG 57.935 37.500 0.00 0.00 0.00 4.24
2187 4505 1.366111 AATCACATAACGCGGCGCTT 61.366 50.000 30.54 23.16 0.00 4.68
2207 4525 2.024176 AGCTGGTGCGTAGTATTTGG 57.976 50.000 0.00 0.00 45.42 3.28
2250 4602 2.479049 GCATGTCAACACATCATCTGCC 60.479 50.000 0.00 0.00 41.69 4.85
2251 4603 2.565046 TGTCAACACATCATCTGCCA 57.435 45.000 0.00 0.00 0.00 4.92
2258 4610 1.063616 CACATCATCTGCCAAAGAGCG 59.936 52.381 0.00 0.00 38.67 5.03
2320 4677 0.528924 CCATAGTTGGACGTGACCGA 59.471 55.000 0.00 0.00 46.92 4.69
2324 4681 0.031721 AGTTGGACGTGACCGAGAAC 59.968 55.000 0.00 0.00 37.88 3.01
2348 4705 2.516695 CATGCGGTGGCCATAGCA 60.517 61.111 31.08 31.08 44.13 3.49
2430 4800 9.820229 TTATAATCATTCAGTTTGTTCACGAAC 57.180 29.630 2.89 2.89 39.88 3.95
2441 4811 3.162666 TGTTCACGAACTCCCTATGACT 58.837 45.455 11.01 0.00 41.67 3.41
2486 4856 8.615878 AATTTGCGGTAGATTATATACTTGCA 57.384 30.769 11.24 11.24 34.80 4.08
2487 4857 7.652300 TTTGCGGTAGATTATATACTTGCAG 57.348 36.000 13.56 0.00 36.54 4.41
2488 4858 6.584185 TGCGGTAGATTATATACTTGCAGA 57.416 37.500 11.24 0.00 33.07 4.26
2493 4863 9.809096 CGGTAGATTATATACTTGCAGATCATT 57.191 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 4.722535 AGGAGGAAGCCGAGGCCA 62.723 66.667 10.95 0.00 43.17 5.36
587 609 6.550854 TGACATTCTTTTTCCAATTGAGACCT 59.449 34.615 7.12 0.00 0.00 3.85
588 610 6.748132 TGACATTCTTTTTCCAATTGAGACC 58.252 36.000 7.12 0.00 0.00 3.85
589 611 8.647143 TTTGACATTCTTTTTCCAATTGAGAC 57.353 30.769 7.12 0.00 0.00 3.36
607 629 8.965819 TGGCAATAGTTGTAACATATTTGACAT 58.034 29.630 0.00 0.00 0.00 3.06
608 630 8.341892 TGGCAATAGTTGTAACATATTTGACA 57.658 30.769 0.00 1.59 0.00 3.58
614 636 9.791801 TGACATATGGCAATAGTTGTAACATAT 57.208 29.630 9.39 0.00 36.25 1.78
615 637 9.051679 GTGACATATGGCAATAGTTGTAACATA 57.948 33.333 14.28 0.00 32.99 2.29
616 638 7.775093 AGTGACATATGGCAATAGTTGTAACAT 59.225 33.333 14.28 0.00 32.99 2.71
617 639 7.109501 AGTGACATATGGCAATAGTTGTAACA 58.890 34.615 14.28 0.00 32.99 2.41
619 641 9.325198 CTTAGTGACATATGGCAATAGTTGTAA 57.675 33.333 17.52 4.39 34.87 2.41
620 642 7.441157 GCTTAGTGACATATGGCAATAGTTGTA 59.559 37.037 17.52 3.35 34.87 2.41
622 644 6.484643 AGCTTAGTGACATATGGCAATAGTTG 59.515 38.462 17.52 13.05 34.87 3.16
623 645 6.484643 CAGCTTAGTGACATATGGCAATAGTT 59.515 38.462 17.52 8.67 34.87 2.24
624 646 5.994054 CAGCTTAGTGACATATGGCAATAGT 59.006 40.000 17.52 5.50 34.87 2.12
627 649 4.818546 GTCAGCTTAGTGACATATGGCAAT 59.181 41.667 16.87 16.87 45.34 3.56
629 651 3.797039 GTCAGCTTAGTGACATATGGCA 58.203 45.455 7.32 7.32 45.34 4.92
637 659 7.043059 GCTATCTAAACATGTCAGCTTAGTGAC 60.043 40.741 12.53 7.61 46.08 3.67
640 662 6.127054 TGGCTATCTAAACATGTCAGCTTAGT 60.127 38.462 12.53 5.63 0.00 2.24
641 663 6.283694 TGGCTATCTAAACATGTCAGCTTAG 58.716 40.000 0.00 3.68 0.00 2.18
642 664 6.233905 TGGCTATCTAAACATGTCAGCTTA 57.766 37.500 0.00 0.00 0.00 3.09
643 665 5.102953 TGGCTATCTAAACATGTCAGCTT 57.897 39.130 0.00 0.00 0.00 3.74
644 666 4.760530 TGGCTATCTAAACATGTCAGCT 57.239 40.909 0.00 0.00 0.00 4.24
645 667 5.818136 TTTGGCTATCTAAACATGTCAGC 57.182 39.130 0.00 1.62 0.00 4.26
646 668 9.722056 GTAATTTTGGCTATCTAAACATGTCAG 57.278 33.333 0.00 0.00 0.00 3.51
647 669 8.682710 GGTAATTTTGGCTATCTAAACATGTCA 58.317 33.333 0.00 0.00 0.00 3.58
648 670 8.903820 AGGTAATTTTGGCTATCTAAACATGTC 58.096 33.333 0.00 0.00 0.00 3.06
649 671 8.823220 AGGTAATTTTGGCTATCTAAACATGT 57.177 30.769 0.00 0.00 0.00 3.21
661 683 8.491134 GGGGATAATTTAAAGGTAATTTTGGCT 58.509 33.333 0.00 0.00 32.01 4.75
662 684 8.491134 AGGGGATAATTTAAAGGTAATTTTGGC 58.509 33.333 0.00 0.00 32.01 4.52
670 692 7.348011 ACGAGGTAAGGGGATAATTTAAAGGTA 59.652 37.037 0.00 0.00 0.00 3.08
671 693 6.159222 ACGAGGTAAGGGGATAATTTAAAGGT 59.841 38.462 0.00 0.00 0.00 3.50
909 2983 3.459969 GGAAATGAGGGACCAGGTCTATT 59.540 47.826 19.57 11.63 32.47 1.73
923 3030 4.513442 TCCTGTAACGAATGGGAAATGAG 58.487 43.478 0.00 0.00 0.00 2.90
1043 3152 0.685131 TGGATGAATGGCTGGCTTGG 60.685 55.000 2.00 0.00 0.00 3.61
1136 3250 5.359194 AACTTTTGAGTCTCTGAGGACAA 57.641 39.130 4.59 6.44 38.57 3.18
1140 3254 5.983720 TCGTTTAACTTTTGAGTCTCTGAGG 59.016 40.000 4.59 0.00 0.00 3.86
1161 3281 4.444876 CCCCATAGAAATCTTCATGGTCGT 60.445 45.833 10.06 0.00 36.99 4.34
1162 3282 4.067896 CCCCATAGAAATCTTCATGGTCG 58.932 47.826 10.06 0.00 36.99 4.79
1163 3283 5.053978 ACCCCATAGAAATCTTCATGGTC 57.946 43.478 10.06 0.00 36.99 4.02
1168 3291 3.181479 CGACGACCCCATAGAAATCTTCA 60.181 47.826 0.00 0.00 0.00 3.02
1223 3349 2.429058 CACTGGACCAGCAGCACT 59.571 61.111 21.95 0.00 34.37 4.40
1468 3597 0.238025 ACGCATGTACGTACGTCACA 59.762 50.000 26.53 24.44 46.19 3.58
1516 3660 8.961294 ACCAATGAACAAAGAATCAATCAAAA 57.039 26.923 0.00 0.00 0.00 2.44
1564 3719 8.576442 CATCATTTAACGGAAGCCCTTAAATAT 58.424 33.333 10.65 5.61 35.90 1.28
1570 3725 3.697166 ACATCATTTAACGGAAGCCCTT 58.303 40.909 0.00 0.00 0.00 3.95
1591 3749 1.200760 TTGAGCAGCTTCCAGGGCTA 61.201 55.000 0.00 0.00 38.03 3.93
1629 3787 7.216881 CACTTCATTGCAAATTCATGTAGTACG 59.783 37.037 1.71 0.00 0.00 3.67
1633 3791 6.392354 ACCACTTCATTGCAAATTCATGTAG 58.608 36.000 1.71 2.57 0.00 2.74
1634 3792 6.209192 AGACCACTTCATTGCAAATTCATGTA 59.791 34.615 1.71 0.00 0.00 2.29
1635 3793 5.011329 AGACCACTTCATTGCAAATTCATGT 59.989 36.000 1.71 0.00 0.00 3.21
1650 3808 4.020543 AGACCTACATCAGAGACCACTTC 58.979 47.826 0.00 0.00 0.00 3.01
1690 3850 2.743664 TCGTGCAACAATCTTCCATGAG 59.256 45.455 0.00 0.00 35.74 2.90
1691 3851 2.777094 TCGTGCAACAATCTTCCATGA 58.223 42.857 0.00 0.00 35.74 3.07
1727 3934 4.630644 ATGAGCTTGTTTCTCTCCTTCA 57.369 40.909 0.00 0.00 0.00 3.02
1743 3950 1.541588 AGCCTTTCGGTGAAAATGAGC 59.458 47.619 0.00 0.00 30.84 4.26
1753 3960 1.276989 TCGATTGGTAAGCCTTTCGGT 59.723 47.619 0.00 0.00 39.01 4.69
1756 3963 4.120589 CCTAGTCGATTGGTAAGCCTTTC 58.879 47.826 0.00 0.00 35.27 2.62
1759 3966 1.413077 GCCTAGTCGATTGGTAAGCCT 59.587 52.381 0.00 0.00 35.27 4.58
1760 3967 1.540580 GGCCTAGTCGATTGGTAAGCC 60.541 57.143 0.00 0.00 0.00 4.35
1761 3968 1.138266 TGGCCTAGTCGATTGGTAAGC 59.862 52.381 3.32 0.00 0.00 3.09
1762 3969 3.458189 CTTGGCCTAGTCGATTGGTAAG 58.542 50.000 3.32 0.00 0.00 2.34
1763 3970 2.169769 CCTTGGCCTAGTCGATTGGTAA 59.830 50.000 13.38 0.00 0.00 2.85
1764 3971 1.760613 CCTTGGCCTAGTCGATTGGTA 59.239 52.381 13.38 0.00 0.00 3.25
1765 3972 0.541863 CCTTGGCCTAGTCGATTGGT 59.458 55.000 13.38 0.00 0.00 3.67
1766 3973 0.179045 CCCTTGGCCTAGTCGATTGG 60.179 60.000 13.38 2.17 0.00 3.16
1767 3974 0.830648 TCCCTTGGCCTAGTCGATTG 59.169 55.000 13.38 0.00 0.00 2.67
1768 3975 0.831307 GTCCCTTGGCCTAGTCGATT 59.169 55.000 13.38 0.00 0.00 3.34
1769 3976 1.049289 GGTCCCTTGGCCTAGTCGAT 61.049 60.000 13.38 0.00 0.00 3.59
1770 3977 1.684734 GGTCCCTTGGCCTAGTCGA 60.685 63.158 13.38 5.38 0.00 4.20
1771 3978 1.550130 TTGGTCCCTTGGCCTAGTCG 61.550 60.000 13.38 3.01 0.00 4.18
1772 3979 0.696501 TTTGGTCCCTTGGCCTAGTC 59.303 55.000 13.38 3.50 0.00 2.59
1773 3980 0.698818 CTTTGGTCCCTTGGCCTAGT 59.301 55.000 13.38 0.00 0.00 2.57
1779 3986 0.609131 ACATCGCTTTGGTCCCTTGG 60.609 55.000 0.00 0.00 0.00 3.61
1810 4017 9.424319 CACACATCCATAATACAGATTACTACC 57.576 37.037 0.00 0.00 30.24 3.18
1842 4054 1.379527 GGGCATTGAAACCCTCGTAG 58.620 55.000 0.00 0.00 43.36 3.51
1852 4064 0.971959 GCATGACCCTGGGCATTGAA 60.972 55.000 14.08 0.00 0.00 2.69
1857 4069 0.544833 ATTTTGCATGACCCTGGGCA 60.545 50.000 14.08 12.49 0.00 5.36
1893 4111 5.874810 TGTTAAGATACTCATCACAAGTGGC 59.125 40.000 0.00 0.00 33.21 5.01
1929 4238 4.759516 TTCATTTCAAGTCGCCCTTAAC 57.240 40.909 0.00 0.00 0.00 2.01
1958 4267 1.804151 TGGACACGCTTCTTTGCATAC 59.196 47.619 0.00 0.00 0.00 2.39
2002 4315 9.698617 GGACATGTAACGAGAAATAAATGTAAC 57.301 33.333 0.00 0.00 31.62 2.50
2003 4316 8.885722 GGGACATGTAACGAGAAATAAATGTAA 58.114 33.333 0.00 0.00 31.62 2.41
2004 4317 7.496591 GGGGACATGTAACGAGAAATAAATGTA 59.503 37.037 0.00 0.00 31.62 2.29
2005 4318 6.317893 GGGGACATGTAACGAGAAATAAATGT 59.682 38.462 0.00 0.00 33.63 2.71
2006 4319 6.317642 TGGGGACATGTAACGAGAAATAAATG 59.682 38.462 0.00 0.00 33.40 2.32
2007 4320 6.419791 TGGGGACATGTAACGAGAAATAAAT 58.580 36.000 0.00 0.00 33.40 1.40
2008 4321 5.806818 TGGGGACATGTAACGAGAAATAAA 58.193 37.500 0.00 0.00 33.40 1.40
2009 4322 5.423704 TGGGGACATGTAACGAGAAATAA 57.576 39.130 0.00 0.00 33.40 1.40
2187 4505 2.761767 TCCAAATACTACGCACCAGCTA 59.238 45.455 0.00 0.00 39.10 3.32
2250 4602 2.338813 CGTTCGAGTTAGACGCTCTTTG 59.661 50.000 0.00 0.00 0.00 2.77
2251 4603 2.582687 CGTTCGAGTTAGACGCTCTTT 58.417 47.619 0.00 0.00 0.00 2.52
2258 4610 3.189287 TGTTAGACCCGTTCGAGTTAGAC 59.811 47.826 0.00 0.00 0.00 2.59
2320 4677 1.229428 CACCGCATGTTGACTGTTCT 58.771 50.000 0.00 0.00 0.00 3.01
2324 4681 2.562912 GCCACCGCATGTTGACTG 59.437 61.111 0.00 0.00 34.03 3.51
2348 4705 8.664669 AATGTAATACTCCCCAGATTGTTTTT 57.335 30.769 0.00 0.00 0.00 1.94
2498 4868 5.070313 GGCATTGGCAGGGATATCTTTAAAA 59.930 40.000 5.17 0.00 43.71 1.52
2500 4870 4.151883 GGCATTGGCAGGGATATCTTTAA 58.848 43.478 5.17 0.00 43.71 1.52
2501 4871 3.139957 TGGCATTGGCAGGGATATCTTTA 59.860 43.478 9.11 0.00 43.71 1.85
2505 4875 1.822990 CATGGCATTGGCAGGGATATC 59.177 52.381 18.37 0.00 42.43 1.63


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

AutoCloner maintained by Alex Coulton.