Multiple sequence alignment - TraesCS5B01G142800

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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 TraesCS5B01G142800 chr5B 100.000 2426 0 0 1 2426 269953849 269951424 0.000000e+00 4481.0
1 TraesCS5B01G142800 chr5B 92.632 190 14 0 753 942 269946783 269946972 8.550000e-70 274.0
2 TraesCS5B01G142800 chr5B 88.021 192 22 1 749 940 524222928 524222738 2.430000e-55 226.0
3 TraesCS5B01G142800 chr5B 93.919 148 7 2 2280 2426 60086230 60086084 3.140000e-54 222.0
4 TraesCS5B01G142800 chr5D 95.312 1536 55 6 756 2276 338408062 338409595 0.000000e+00 2422.0
5 TraesCS5B01G142800 chr5D 95.055 1537 60 5 755 2276 476457964 476456429 0.000000e+00 2403.0
6 TraesCS5B01G142800 chr5D 90.893 582 35 9 1039 1617 565257986 565258552 0.000000e+00 765.0
7 TraesCS5B01G142800 chr5D 85.095 577 68 8 1039 1611 565239015 565238453 7.520000e-160 573.0
8 TraesCS5B01G142800 chr3B 97.786 768 13 4 1 767 51966944 51966180 0.000000e+00 1321.0
9 TraesCS5B01G142800 chr3B 98.141 753 13 1 1 753 776030216 776030967 0.000000e+00 1312.0
10 TraesCS5B01G142800 chr3B 85.347 389 36 8 47 435 741653732 741653365 1.360000e-102 383.0
11 TraesCS5B01G142800 chr3B 97.619 42 1 0 447 488 741653284 741653243 3.350000e-09 73.1
12 TraesCS5B01G142800 chr4B 97.347 754 12 1 1 754 613015839 613015094 0.000000e+00 1275.0
13 TraesCS5B01G142800 chr1B 97.458 708 17 1 47 754 634164010 634163304 0.000000e+00 1206.0
14 TraesCS5B01G142800 chr4A 96.823 661 21 0 1616 2276 689848516 689849176 0.000000e+00 1105.0
15 TraesCS5B01G142800 chr4A 85.590 576 61 9 1039 1611 606648226 606647670 3.480000e-163 584.0
16 TraesCS5B01G142800 chr4A 95.833 72 2 1 970 1041 689847592 689847662 5.480000e-22 115.0
17 TraesCS5B01G142800 chr7D 96.520 661 23 0 1616 2276 35182927 35182267 0.000000e+00 1094.0
18 TraesCS5B01G142800 chr7D 89.637 193 18 2 749 940 207790331 207790140 6.700000e-61 244.0
19 TraesCS5B01G142800 chr7D 89.157 83 6 2 962 1041 35183863 35183781 1.530000e-17 100.0
20 TraesCS5B01G142800 chr7A 96.218 661 25 0 1616 2276 35396703 35396043 0.000000e+00 1083.0
21 TraesCS5B01G142800 chr7A 92.391 368 25 2 1 366 705292905 705293271 2.760000e-144 521.0
22 TraesCS5B01G142800 chr7A 91.667 372 22 3 397 760 705293272 705293642 7.740000e-140 507.0
23 TraesCS5B01G142800 chr7A 90.110 91 4 4 956 1041 35397647 35397557 1.970000e-21 113.0
24 TraesCS5B01G142800 chr2B 91.777 754 45 2 1 754 53731151 53731887 0.000000e+00 1033.0
25 TraesCS5B01G142800 chr2B 91.766 753 45 2 1 753 53729499 53730234 0.000000e+00 1031.0
26 TraesCS5B01G142800 chr2B 92.431 436 33 0 319 754 53754616 53755051 7.370000e-175 623.0
27 TraesCS5B01G142800 chr1A 96.471 510 6 1 245 754 61118369 61118866 0.000000e+00 832.0
28 TraesCS5B01G142800 chr1A 98.095 420 8 0 1 420 61117894 61118313 0.000000e+00 732.0
29 TraesCS5B01G142800 chr1A 90.857 175 16 0 753 927 508205710 508205536 4.030000e-58 235.0
30 TraesCS5B01G142800 chr1A 91.304 138 12 0 1 138 61117189 61117326 3.180000e-44 189.0
31 TraesCS5B01G142800 chr6B 96.599 147 3 2 2281 2426 369526057 369525912 2.410000e-60 243.0
32 TraesCS5B01G142800 chr6B 93.878 147 7 2 2281 2426 305957628 305957773 1.130000e-53 220.0
33 TraesCS5B01G142800 chr7B 88.776 196 20 2 748 942 88338323 88338517 3.120000e-59 239.0
34 TraesCS5B01G142800 chr7B 93.038 158 8 3 2271 2426 578788603 578788447 6.750000e-56 228.0
35 TraesCS5B01G142800 chr7B 91.463 164 9 5 2266 2426 654207720 654207559 1.130000e-53 220.0
36 TraesCS5B01G142800 chr6A 88.144 194 22 1 749 942 91164657 91164465 1.880000e-56 230.0
37 TraesCS5B01G142800 chr4D 87.692 195 23 1 747 940 30392894 30393088 2.430000e-55 226.0
38 TraesCS5B01G142800 chrUn 93.878 147 6 3 2281 2426 344735187 344735043 4.060000e-53 219.0
39 TraesCS5B01G142800 chr3A 93.878 147 6 3 2281 2426 738564523 738564667 4.060000e-53 219.0
40 TraesCS5B01G142800 chr3A 93.197 147 8 2 2281 2426 738664681 738664826 5.250000e-52 215.0
41 TraesCS5B01G142800 chr3A 93.197 147 7 3 2281 2426 738491981 738492125 1.890000e-51 213.0


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 TraesCS5B01G142800 chr5B 269951424 269953849 2425 True 4481.000000 4481 100.0000 1 2426 1 chr5B.!!$R2 2425
1 TraesCS5B01G142800 chr5D 338408062 338409595 1533 False 2422.000000 2422 95.3120 756 2276 1 chr5D.!!$F1 1520
2 TraesCS5B01G142800 chr5D 476456429 476457964 1535 True 2403.000000 2403 95.0550 755 2276 1 chr5D.!!$R1 1521
3 TraesCS5B01G142800 chr5D 565257986 565258552 566 False 765.000000 765 90.8930 1039 1617 1 chr5D.!!$F2 578
4 TraesCS5B01G142800 chr5D 565238453 565239015 562 True 573.000000 573 85.0950 1039 1611 1 chr5D.!!$R2 572
5 TraesCS5B01G142800 chr3B 51966180 51966944 764 True 1321.000000 1321 97.7860 1 767 1 chr3B.!!$R1 766
6 TraesCS5B01G142800 chr3B 776030216 776030967 751 False 1312.000000 1312 98.1410 1 753 1 chr3B.!!$F1 752
7 TraesCS5B01G142800 chr4B 613015094 613015839 745 True 1275.000000 1275 97.3470 1 754 1 chr4B.!!$R1 753
8 TraesCS5B01G142800 chr1B 634163304 634164010 706 True 1206.000000 1206 97.4580 47 754 1 chr1B.!!$R1 707
9 TraesCS5B01G142800 chr4A 689847592 689849176 1584 False 610.000000 1105 96.3280 970 2276 2 chr4A.!!$F1 1306
10 TraesCS5B01G142800 chr4A 606647670 606648226 556 True 584.000000 584 85.5900 1039 1611 1 chr4A.!!$R1 572
11 TraesCS5B01G142800 chr7D 35182267 35183863 1596 True 597.000000 1094 92.8385 962 2276 2 chr7D.!!$R2 1314
12 TraesCS5B01G142800 chr7A 35396043 35397647 1604 True 598.000000 1083 93.1640 956 2276 2 chr7A.!!$R1 1320
13 TraesCS5B01G142800 chr7A 705292905 705293642 737 False 514.000000 521 92.0290 1 760 2 chr7A.!!$F1 759
14 TraesCS5B01G142800 chr2B 53729499 53731887 2388 False 1032.000000 1033 91.7715 1 754 2 chr2B.!!$F2 753
15 TraesCS5B01G142800 chr1A 61117189 61118866 1677 False 584.333333 832 95.2900 1 754 3 chr1A.!!$F1 753

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
693 3273 0.52218 TTGTTCCGTGCGTTTTGTGT 59.478 45.0 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2353 5565 0.319405 CCGACGGTAGACAAAAGGGT 59.681 55.0 5.48 0.0 0.0 4.34 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
45 751 3.526931 TCAGTTAGGCTGGAAATCGAG 57.473 47.619 0.00 0.00 45.08 4.04
412 1121 1.791103 CGTTGGTCGGCAACAATGGT 61.791 55.000 0.00 0.00 35.71 3.55
532 3112 6.400568 TGTTTCCTTATTTACCTGGAGTACG 58.599 40.000 0.00 0.00 0.00 3.67
596 3176 2.268298 CGGTCAGTCAAGGGTATTTCG 58.732 52.381 0.00 0.00 0.00 3.46
693 3273 0.522180 TTGTTCCGTGCGTTTTGTGT 59.478 45.000 0.00 0.00 0.00 3.72
782 3362 9.435688 GATAATTTAGTCCCAAACTTGCAAAAT 57.564 29.630 0.00 0.00 39.55 1.82
783 3363 7.495135 AATTTAGTCCCAAACTTGCAAAATG 57.505 32.000 0.00 0.00 39.55 2.32
785 3365 6.716934 TTAGTCCCAAACTTGCAAAATGTA 57.283 33.333 0.00 0.00 39.55 2.29
788 3368 5.128663 AGTCCCAAACTTGCAAAATGTAACT 59.871 36.000 0.00 3.19 33.03 2.24
789 3369 5.815222 GTCCCAAACTTGCAAAATGTAACTT 59.185 36.000 0.00 0.00 0.00 2.66
798 3378 8.796475 ACTTGCAAAATGTAACTTCATCATACT 58.204 29.630 0.00 0.00 0.00 2.12
799 3379 9.282247 CTTGCAAAATGTAACTTCATCATACTC 57.718 33.333 0.00 0.00 0.00 2.59
811 3391 4.256110 TCATCATACTCCAACTTGCACTG 58.744 43.478 0.00 0.00 0.00 3.66
834 3414 3.495434 TGTGACGTTTTAATCCCAGGT 57.505 42.857 0.00 0.00 0.00 4.00
841 3421 5.261216 ACGTTTTAATCCCAGGTCAATCAT 58.739 37.500 0.00 0.00 0.00 2.45
852 3432 4.183865 CAGGTCAATCATAGCTCGACAAA 58.816 43.478 0.00 0.00 0.00 2.83
902 3482 2.539476 CACACACTTTTGCAGAAACCC 58.461 47.619 0.00 0.00 0.00 4.11
930 3510 4.794655 GCTGTTTTCTTTAATCAACCCGCA 60.795 41.667 0.00 0.00 0.00 5.69
944 3524 2.430921 CGCACTCACCTCCACGTC 60.431 66.667 0.00 0.00 0.00 4.34
947 3527 1.362717 CACTCACCTCCACGTCGTT 59.637 57.895 0.00 0.00 0.00 3.85
1052 3808 1.737838 CTCTACAAGGAAATGGCGCA 58.262 50.000 10.83 0.00 0.00 6.09
1318 4506 1.955778 TCACCTTAACCTCGACGTTCA 59.044 47.619 2.95 0.00 0.00 3.18
1350 4538 1.515020 CCTGGTCTTGGAGCTCTCG 59.485 63.158 14.64 2.41 0.00 4.04
1554 4766 3.452264 TCGATCTCCAAATGATGTGTCCT 59.548 43.478 0.00 0.00 0.00 3.85
1678 4890 1.990060 ATGTCGGTGGCCTACAGCT 60.990 57.895 3.32 0.00 45.25 4.24
1807 5019 3.182887 ACCACTCAGTCCTCATCTTCT 57.817 47.619 0.00 0.00 0.00 2.85
1815 5027 3.037549 AGTCCTCATCTTCTAGGCCTTG 58.962 50.000 12.58 9.98 32.55 3.61
1899 5111 3.260483 GATGACTGCCGCAGCGAG 61.260 66.667 20.56 9.41 44.31 5.03
2253 5465 0.836400 AGGTGGACCAGTTCATCGGT 60.836 55.000 0.00 0.00 38.89 4.69
2282 5494 3.646715 CCTCCCCCTGCGGTCAAA 61.647 66.667 0.00 0.00 0.00 2.69
2283 5495 2.677228 CTCCCCCTGCGGTCAAAT 59.323 61.111 0.00 0.00 0.00 2.32
2284 5496 1.000896 CTCCCCCTGCGGTCAAATT 60.001 57.895 0.00 0.00 0.00 1.82
2285 5497 0.611896 CTCCCCCTGCGGTCAAATTT 60.612 55.000 0.00 0.00 0.00 1.82
2286 5498 0.610785 TCCCCCTGCGGTCAAATTTC 60.611 55.000 0.00 0.00 0.00 2.17
2287 5499 1.506262 CCCCTGCGGTCAAATTTCG 59.494 57.895 0.00 0.00 0.00 3.46
2288 5500 1.241315 CCCCTGCGGTCAAATTTCGT 61.241 55.000 0.00 0.00 0.00 3.85
2289 5501 0.109781 CCCTGCGGTCAAATTTCGTG 60.110 55.000 0.00 0.00 0.00 4.35
2290 5502 0.591170 CCTGCGGTCAAATTTCGTGT 59.409 50.000 0.00 0.00 0.00 4.49
2291 5503 1.001815 CCTGCGGTCAAATTTCGTGTT 60.002 47.619 0.00 0.00 0.00 3.32
2292 5504 2.542824 CCTGCGGTCAAATTTCGTGTTT 60.543 45.455 0.00 0.00 0.00 2.83
2293 5505 3.112580 CTGCGGTCAAATTTCGTGTTTT 58.887 40.909 0.00 0.00 0.00 2.43
2294 5506 3.512680 TGCGGTCAAATTTCGTGTTTTT 58.487 36.364 0.00 0.00 0.00 1.94
2295 5507 3.304559 TGCGGTCAAATTTCGTGTTTTTG 59.695 39.130 0.00 0.00 0.00 2.44
2296 5508 3.548268 GCGGTCAAATTTCGTGTTTTTGA 59.452 39.130 0.00 0.00 37.11 2.69
2299 5511 5.383984 GTCAAATTTCGTGTTTTTGACCC 57.616 39.130 13.92 0.00 46.87 4.46
2300 5512 5.106442 GTCAAATTTCGTGTTTTTGACCCT 58.894 37.500 13.92 0.00 46.87 4.34
2301 5513 5.579119 GTCAAATTTCGTGTTTTTGACCCTT 59.421 36.000 13.92 0.00 46.87 3.95
2302 5514 6.091577 GTCAAATTTCGTGTTTTTGACCCTTT 59.908 34.615 13.92 0.00 46.87 3.11
2303 5515 6.651225 TCAAATTTCGTGTTTTTGACCCTTTT 59.349 30.769 0.00 0.00 35.16 2.27
2304 5516 7.173390 TCAAATTTCGTGTTTTTGACCCTTTTT 59.827 29.630 0.00 0.00 35.16 1.94
2305 5517 5.847670 TTTCGTGTTTTTGACCCTTTTTG 57.152 34.783 0.00 0.00 0.00 2.44
2306 5518 3.254892 TCGTGTTTTTGACCCTTTTTGC 58.745 40.909 0.00 0.00 0.00 3.68
2307 5519 2.996621 CGTGTTTTTGACCCTTTTTGCA 59.003 40.909 0.00 0.00 0.00 4.08
2308 5520 3.433615 CGTGTTTTTGACCCTTTTTGCAA 59.566 39.130 0.00 0.00 0.00 4.08
2309 5521 4.083802 CGTGTTTTTGACCCTTTTTGCAAA 60.084 37.500 8.05 8.05 0.00 3.68
2310 5522 5.150683 GTGTTTTTGACCCTTTTTGCAAAC 58.849 37.500 12.39 0.00 30.77 2.93
2311 5523 4.821805 TGTTTTTGACCCTTTTTGCAAACA 59.178 33.333 12.39 4.32 32.02 2.83
2312 5524 5.299279 TGTTTTTGACCCTTTTTGCAAACAA 59.701 32.000 12.39 8.88 31.65 2.83
2313 5525 6.183360 TGTTTTTGACCCTTTTTGCAAACAAA 60.183 30.769 12.39 14.31 43.97 2.83
2323 5535 4.599047 TTTGCAAACAAAATCGGGATCT 57.401 36.364 8.05 0.00 42.73 2.75
2324 5536 3.574284 TGCAAACAAAATCGGGATCTG 57.426 42.857 0.00 0.00 0.00 2.90
2325 5537 3.153130 TGCAAACAAAATCGGGATCTGA 58.847 40.909 0.00 0.00 0.00 3.27
2326 5538 3.057596 TGCAAACAAAATCGGGATCTGAC 60.058 43.478 0.00 0.00 0.00 3.51
2327 5539 3.673323 GCAAACAAAATCGGGATCTGACC 60.673 47.826 0.00 0.00 0.00 4.02
2328 5540 2.420058 ACAAAATCGGGATCTGACCC 57.580 50.000 0.00 0.00 45.92 4.46
2334 5546 2.499685 GGGATCTGACCCGGTTCG 59.500 66.667 0.00 0.00 40.49 3.95
2366 5578 3.875125 GGGATCTGACCCTTTTGTCTAC 58.125 50.000 7.74 0.00 45.90 2.59
2367 5579 3.370633 GGGATCTGACCCTTTTGTCTACC 60.371 52.174 7.74 0.00 45.90 3.18
2368 5580 3.522553 GATCTGACCCTTTTGTCTACCG 58.477 50.000 0.00 0.00 36.21 4.02
2369 5581 2.322658 TCTGACCCTTTTGTCTACCGT 58.677 47.619 0.00 0.00 36.21 4.83
2370 5582 2.298163 TCTGACCCTTTTGTCTACCGTC 59.702 50.000 0.00 0.00 36.21 4.79
2371 5583 1.000060 TGACCCTTTTGTCTACCGTCG 60.000 52.381 0.00 0.00 36.21 5.12
2372 5584 0.319405 ACCCTTTTGTCTACCGTCGG 59.681 55.000 10.48 10.48 0.00 4.79
2373 5585 0.390735 CCCTTTTGTCTACCGTCGGG 60.391 60.000 17.28 0.00 40.11 5.14
2374 5586 1.017701 CCTTTTGTCTACCGTCGGGC 61.018 60.000 17.28 3.43 36.48 6.13
2375 5587 1.004679 TTTTGTCTACCGTCGGGCC 60.005 57.895 17.28 0.00 36.48 5.80
2376 5588 1.756408 TTTTGTCTACCGTCGGGCCA 61.756 55.000 17.28 3.30 36.48 5.36
2377 5589 2.438951 TTTGTCTACCGTCGGGCCAC 62.439 60.000 17.28 8.89 36.48 5.01
2378 5590 3.376078 GTCTACCGTCGGGCCACA 61.376 66.667 17.28 0.00 36.48 4.17
2379 5591 3.376078 TCTACCGTCGGGCCACAC 61.376 66.667 17.28 0.00 36.48 3.82
2380 5592 4.789075 CTACCGTCGGGCCACACG 62.789 72.222 17.28 16.77 36.48 4.49
2398 5610 3.204827 GCGGTAGGCCTGTGCATG 61.205 66.667 17.99 0.00 40.13 4.06
2399 5611 3.204827 CGGTAGGCCTGTGCATGC 61.205 66.667 17.99 11.82 40.13 4.06
2400 5612 2.273449 GGTAGGCCTGTGCATGCT 59.727 61.111 17.99 0.00 40.13 3.79
2401 5613 1.526887 GGTAGGCCTGTGCATGCTA 59.473 57.895 17.99 7.15 40.13 3.49
2402 5614 0.815615 GGTAGGCCTGTGCATGCTAC 60.816 60.000 17.99 15.34 40.13 3.58
2403 5615 0.815615 GTAGGCCTGTGCATGCTACC 60.816 60.000 17.99 12.45 40.13 3.18
2404 5616 2.310327 TAGGCCTGTGCATGCTACCG 62.310 60.000 17.99 11.27 40.13 4.02
2405 5617 3.880846 GCCTGTGCATGCTACCGC 61.881 66.667 20.33 14.41 37.47 5.68
2406 5618 3.204827 CCTGTGCATGCTACCGCC 61.205 66.667 20.33 0.47 34.43 6.13
2407 5619 2.436469 CTGTGCATGCTACCGCCA 60.436 61.111 20.33 5.08 34.43 5.69
2408 5620 2.033294 TGTGCATGCTACCGCCAA 59.967 55.556 20.33 0.00 34.43 4.52
2409 5621 1.585267 CTGTGCATGCTACCGCCAAA 61.585 55.000 20.33 0.00 34.43 3.28
2410 5622 1.137404 GTGCATGCTACCGCCAAAG 59.863 57.895 20.33 0.00 34.43 2.77
2411 5623 2.045708 TGCATGCTACCGCCAAAGG 61.046 57.895 20.33 0.00 34.43 3.11
2412 5624 2.774799 GCATGCTACCGCCAAAGGG 61.775 63.158 11.37 0.00 35.02 3.95
2413 5625 1.077787 CATGCTACCGCCAAAGGGA 60.078 57.895 0.00 0.00 35.59 4.20
2414 5626 0.466189 CATGCTACCGCCAAAGGGAT 60.466 55.000 0.00 0.00 35.59 3.85
2415 5627 0.179018 ATGCTACCGCCAAAGGGATC 60.179 55.000 0.00 0.00 35.59 3.36
2416 5628 1.271840 TGCTACCGCCAAAGGGATCT 61.272 55.000 0.00 0.00 35.59 2.75
2417 5629 0.815615 GCTACCGCCAAAGGGATCTG 60.816 60.000 0.00 0.00 35.59 2.90
2418 5630 0.815615 CTACCGCCAAAGGGATCTGC 60.816 60.000 0.00 0.00 35.59 4.26
2419 5631 2.587322 TACCGCCAAAGGGATCTGCG 62.587 60.000 0.00 0.00 44.47 5.18
2420 5632 3.204827 CGCCAAAGGGATCTGCGG 61.205 66.667 0.00 0.00 41.42 5.69
2421 5633 2.044946 GCCAAAGGGATCTGCGGT 60.045 61.111 0.00 0.00 35.59 5.68
2422 5634 1.223487 GCCAAAGGGATCTGCGGTA 59.777 57.895 0.00 0.00 35.59 4.02
2423 5635 0.815615 GCCAAAGGGATCTGCGGTAG 60.816 60.000 0.00 0.00 35.59 3.18
2424 5636 0.815615 CCAAAGGGATCTGCGGTAGC 60.816 60.000 0.00 0.00 39.49 3.58
2425 5637 0.815615 CAAAGGGATCTGCGGTAGCC 60.816 60.000 0.00 0.00 44.33 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 751 6.237942 GCACATCACAATACTACACATCTGTC 60.238 42.308 0.00 0.00 0.00 3.51
128 836 3.244561 CCTGCTTCTTCCTTTGACCTGTA 60.245 47.826 0.00 0.00 0.00 2.74
412 1121 1.381522 CACCATCGCCAATGTCATCA 58.618 50.000 0.00 0.00 33.13 3.07
532 3112 1.451387 CACCCCCTACAATCACGCC 60.451 63.158 0.00 0.00 0.00 5.68
596 3176 1.670967 GCCTGTACGGTGTGGACTTAC 60.671 57.143 0.00 0.00 34.25 2.34
693 3273 0.533308 GTACACCCGGCAACTTGTCA 60.533 55.000 0.00 0.00 0.00 3.58
782 3362 6.371548 GCAAGTTGGAGTATGATGAAGTTACA 59.628 38.462 4.75 0.00 0.00 2.41
783 3363 6.371548 TGCAAGTTGGAGTATGATGAAGTTAC 59.628 38.462 4.75 0.00 0.00 2.50
785 3365 5.182001 GTGCAAGTTGGAGTATGATGAAGTT 59.818 40.000 4.75 0.00 0.00 2.66
788 3368 4.696877 CAGTGCAAGTTGGAGTATGATGAA 59.303 41.667 4.20 0.00 0.00 2.57
789 3369 4.256110 CAGTGCAAGTTGGAGTATGATGA 58.744 43.478 4.20 0.00 0.00 2.92
798 3378 0.669619 CACATGCAGTGCAAGTTGGA 59.330 50.000 22.56 0.00 43.62 3.53
799 3379 3.188773 CACATGCAGTGCAAGTTGG 57.811 52.632 22.56 9.60 43.62 3.77
811 3391 3.427503 CCTGGGATTAAAACGTCACATGC 60.428 47.826 0.00 0.00 0.00 4.06
819 3399 5.835113 ATGATTGACCTGGGATTAAAACG 57.165 39.130 0.00 0.00 0.00 3.60
821 3401 6.672593 AGCTATGATTGACCTGGGATTAAAA 58.327 36.000 0.00 0.00 0.00 1.52
826 3406 2.301296 CGAGCTATGATTGACCTGGGAT 59.699 50.000 0.00 0.00 0.00 3.85
834 3414 3.561310 GCCATTTGTCGAGCTATGATTGA 59.439 43.478 0.00 0.00 0.00 2.57
841 3421 0.744414 GGCTGCCATTTGTCGAGCTA 60.744 55.000 15.17 0.00 0.00 3.32
880 3460 1.583404 GTTTCTGCAAAAGTGTGTGCG 59.417 47.619 0.00 0.00 43.93 5.34
882 3462 2.539476 GGGTTTCTGCAAAAGTGTGTG 58.461 47.619 0.00 0.00 0.00 3.82
885 3465 1.119684 GGGGGTTTCTGCAAAAGTGT 58.880 50.000 0.00 0.00 0.00 3.55
902 3482 5.230182 GTTGATTAAAGAAAACAGCAGGGG 58.770 41.667 0.00 0.00 0.00 4.79
930 3510 1.362717 CAACGACGTGGAGGTGAGT 59.637 57.895 3.97 0.00 0.00 3.41
1052 3808 0.618680 TAGGAGGCAGAGCACCACAT 60.619 55.000 7.08 0.00 0.00 3.21
1170 4223 1.592400 CGCTGAGGACGAGGGTGTAA 61.592 60.000 0.00 0.00 0.00 2.41
1203 4289 1.001760 GAGCCAGGAGAGTACCCCA 59.998 63.158 0.00 0.00 0.00 4.96
1318 4506 3.801997 CAGGGCGGAGAGGGCAAT 61.802 66.667 0.00 0.00 0.00 3.56
1678 4890 4.124351 CGCCGCGTACTCCTCCAA 62.124 66.667 4.92 0.00 0.00 3.53
1786 4998 4.323569 AGAAGATGAGGACTGAGTGGTA 57.676 45.455 0.00 0.00 0.00 3.25
1807 5019 4.124351 CGTCGCGGACAAGGCCTA 62.124 66.667 5.16 0.00 32.09 3.93
1899 5111 2.112815 GGCCATGAGGTTGCGGTAC 61.113 63.158 0.00 0.00 37.19 3.34
1980 5192 1.004560 CTCCTTGAACTGCTCGGCA 60.005 57.895 0.00 0.00 36.92 5.69
2278 5490 5.331876 AGGGTCAAAAACACGAAATTTGA 57.668 34.783 0.00 0.00 39.89 2.69
2279 5491 6.415798 AAAGGGTCAAAAACACGAAATTTG 57.584 33.333 0.00 0.00 35.94 2.32
2280 5492 7.301789 CAAAAAGGGTCAAAAACACGAAATTT 58.698 30.769 0.00 0.00 35.94 1.82
2281 5493 6.621812 GCAAAAAGGGTCAAAAACACGAAATT 60.622 34.615 0.00 0.00 35.94 1.82
2282 5494 5.163804 GCAAAAAGGGTCAAAAACACGAAAT 60.164 36.000 0.00 0.00 35.94 2.17
2283 5495 4.152580 GCAAAAAGGGTCAAAAACACGAAA 59.847 37.500 0.00 0.00 35.94 3.46
2284 5496 3.680458 GCAAAAAGGGTCAAAAACACGAA 59.320 39.130 0.00 0.00 35.94 3.85
2285 5497 3.254892 GCAAAAAGGGTCAAAAACACGA 58.745 40.909 0.00 0.00 35.94 4.35
2286 5498 2.996621 TGCAAAAAGGGTCAAAAACACG 59.003 40.909 0.00 0.00 35.94 4.49
2287 5499 5.150683 GTTTGCAAAAAGGGTCAAAAACAC 58.849 37.500 14.67 0.00 31.29 3.32
2288 5500 4.821805 TGTTTGCAAAAAGGGTCAAAAACA 59.178 33.333 14.67 0.13 34.80 2.83
2289 5501 5.363979 TGTTTGCAAAAAGGGTCAAAAAC 57.636 34.783 14.67 0.00 31.29 2.43
2290 5502 6.391227 TTTGTTTGCAAAAAGGGTCAAAAA 57.609 29.167 14.67 0.00 41.15 1.94
2302 5514 4.038522 TCAGATCCCGATTTTGTTTGCAAA 59.961 37.500 8.05 8.05 42.25 3.68
2303 5515 3.571828 TCAGATCCCGATTTTGTTTGCAA 59.428 39.130 0.00 0.00 0.00 4.08
2304 5516 3.057596 GTCAGATCCCGATTTTGTTTGCA 60.058 43.478 0.00 0.00 0.00 4.08
2305 5517 3.501950 GTCAGATCCCGATTTTGTTTGC 58.498 45.455 0.00 0.00 0.00 3.68
2306 5518 3.119495 GGGTCAGATCCCGATTTTGTTTG 60.119 47.826 0.00 0.00 37.93 2.93
2307 5519 3.089284 GGGTCAGATCCCGATTTTGTTT 58.911 45.455 0.00 0.00 37.93 2.83
2308 5520 2.723273 GGGTCAGATCCCGATTTTGTT 58.277 47.619 0.00 0.00 37.93 2.83
2309 5521 2.420058 GGGTCAGATCCCGATTTTGT 57.580 50.000 0.00 0.00 37.93 2.83
2317 5529 2.499685 CGAACCGGGTCAGATCCC 59.500 66.667 21.79 0.00 43.78 3.85
2318 5530 2.499685 CCGAACCGGGTCAGATCC 59.500 66.667 21.79 0.00 44.15 3.36
2346 5558 3.679083 CGGTAGACAAAAGGGTCAGATCC 60.679 52.174 0.00 0.00 40.29 3.36
2347 5559 3.056035 ACGGTAGACAAAAGGGTCAGATC 60.056 47.826 0.00 0.00 40.29 2.75
2348 5560 2.904434 ACGGTAGACAAAAGGGTCAGAT 59.096 45.455 0.00 0.00 40.29 2.90
2349 5561 2.298163 GACGGTAGACAAAAGGGTCAGA 59.702 50.000 0.00 0.00 40.29 3.27
2350 5562 2.685100 GACGGTAGACAAAAGGGTCAG 58.315 52.381 0.00 0.00 40.29 3.51
2351 5563 1.000060 CGACGGTAGACAAAAGGGTCA 60.000 52.381 0.00 0.00 40.29 4.02
2352 5564 1.670967 CCGACGGTAGACAAAAGGGTC 60.671 57.143 5.48 0.00 38.08 4.46
2353 5565 0.319405 CCGACGGTAGACAAAAGGGT 59.681 55.000 5.48 0.00 0.00 4.34
2354 5566 0.390735 CCCGACGGTAGACAAAAGGG 60.391 60.000 13.94 0.00 0.00 3.95
2355 5567 1.017701 GCCCGACGGTAGACAAAAGG 61.018 60.000 13.94 0.00 0.00 3.11
2356 5568 1.017701 GGCCCGACGGTAGACAAAAG 61.018 60.000 13.94 0.00 0.00 2.27
2357 5569 1.004679 GGCCCGACGGTAGACAAAA 60.005 57.895 13.94 0.00 0.00 2.44
2358 5570 2.208619 TGGCCCGACGGTAGACAAA 61.209 57.895 13.94 0.00 0.00 2.83
2359 5571 2.601067 TGGCCCGACGGTAGACAA 60.601 61.111 13.94 0.00 0.00 3.18
2360 5572 3.376078 GTGGCCCGACGGTAGACA 61.376 66.667 13.94 3.52 0.00 3.41
2361 5573 3.376078 TGTGGCCCGACGGTAGAC 61.376 66.667 13.94 6.31 0.00 2.59
2362 5574 3.376078 GTGTGGCCCGACGGTAGA 61.376 66.667 13.94 0.00 0.00 2.59
2363 5575 4.789075 CGTGTGGCCCGACGGTAG 62.789 72.222 13.94 0.00 31.84 3.18
2381 5593 3.204827 CATGCACAGGCCTACCGC 61.205 66.667 3.98 9.35 42.76 5.68
2382 5594 2.310327 TAGCATGCACAGGCCTACCG 62.310 60.000 21.98 0.00 42.76 4.02
2383 5595 0.815615 GTAGCATGCACAGGCCTACC 60.816 60.000 21.98 0.00 39.20 3.18
2384 5596 0.815615 GGTAGCATGCACAGGCCTAC 60.816 60.000 21.98 11.23 39.20 3.18
2385 5597 1.526887 GGTAGCATGCACAGGCCTA 59.473 57.895 21.98 0.00 39.20 3.93
2386 5598 2.273449 GGTAGCATGCACAGGCCT 59.727 61.111 21.98 0.00 39.20 5.19
2387 5599 3.204827 CGGTAGCATGCACAGGCC 61.205 66.667 21.98 12.51 39.20 5.19
2388 5600 3.880846 GCGGTAGCATGCACAGGC 61.881 66.667 21.98 17.19 44.35 4.85
2398 5610 0.815615 CAGATCCCTTTGGCGGTAGC 60.816 60.000 0.00 0.00 44.18 3.58
2399 5611 0.815615 GCAGATCCCTTTGGCGGTAG 60.816 60.000 0.00 0.00 0.00 3.18
2400 5612 1.223487 GCAGATCCCTTTGGCGGTA 59.777 57.895 0.00 0.00 0.00 4.02
2401 5613 2.044946 GCAGATCCCTTTGGCGGT 60.045 61.111 0.00 0.00 0.00 5.68
2402 5614 3.204827 CGCAGATCCCTTTGGCGG 61.205 66.667 0.00 0.00 43.63 6.13
2403 5615 2.587322 TACCGCAGATCCCTTTGGCG 62.587 60.000 0.00 0.00 46.61 5.69
2404 5616 0.815615 CTACCGCAGATCCCTTTGGC 60.816 60.000 0.00 0.00 0.00 4.52
2405 5617 0.815615 GCTACCGCAGATCCCTTTGG 60.816 60.000 0.00 0.00 35.78 3.28
2406 5618 0.815615 GGCTACCGCAGATCCCTTTG 60.816 60.000 0.00 0.00 38.10 2.77
2407 5619 1.527370 GGCTACCGCAGATCCCTTT 59.473 57.895 0.00 0.00 38.10 3.11
2408 5620 3.231298 GGCTACCGCAGATCCCTT 58.769 61.111 0.00 0.00 38.10 3.95


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

AutoCloner maintained by Alex Coulton.