Multiple sequence alignment - TraesCS4A01G216800

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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 TraesCS4A01G216800 chr4A 100.000 2666 0 0 1 2666 515751250 515748585 0.000000e+00 4924
1 TraesCS4A01G216800 chr4A 92.348 1738 88 20 712 2425 516342753 516344469 0.000000e+00 2431
2 TraesCS4A01G216800 chr4A 86.250 720 85 13 3 715 555977112 555977824 0.000000e+00 769
3 TraesCS4A01G216800 chr4A 86.452 155 21 0 2512 2666 516344568 516344722 1.270000e-38 171
4 TraesCS4A01G216800 chr4B 86.119 1340 104 29 766 2052 99048680 99049990 0.000000e+00 1369
5 TraesCS4A01G216800 chr4B 91.323 945 57 11 748 1671 99040375 99041315 0.000000e+00 1267
6 TraesCS4A01G216800 chr4B 89.114 937 59 19 851 1752 99077967 99078895 0.000000e+00 1125
7 TraesCS4A01G216800 chr4B 88.406 276 17 12 1489 1752 99051908 99052180 4.280000e-83 318
8 TraesCS4A01G216800 chr4B 85.461 282 27 6 1772 2052 99041560 99041828 5.620000e-72 281
9 TraesCS4A01G216800 chr4D 89.802 1059 59 19 712 1743 67238623 67239659 0.000000e+00 1312
10 TraesCS4A01G216800 chr4D 89.182 1063 74 20 716 1740 66935626 66934567 0.000000e+00 1288
11 TraesCS4A01G216800 chr4D 88.398 724 67 14 3 715 77312907 77313624 0.000000e+00 856
12 TraesCS4A01G216800 chr7A 88.630 730 67 9 3 717 236460767 236461495 0.000000e+00 874
13 TraesCS4A01G216800 chr1D 87.137 723 68 17 13 725 10374098 10374805 0.000000e+00 797
14 TraesCS4A01G216800 chr7D 86.345 725 73 15 3 717 46854986 46855694 0.000000e+00 767
15 TraesCS4A01G216800 chr3A 85.831 734 89 14 1 726 710404356 710403630 0.000000e+00 765
16 TraesCS4A01G216800 chr3A 85.559 734 91 14 1 726 710343499 710342773 0.000000e+00 754
17 TraesCS4A01G216800 chr3A 85.442 735 91 15 1 726 710464389 710463662 0.000000e+00 750
18 TraesCS4A01G216800 chr5A 82.967 728 104 16 3 717 524635836 524635116 8.050000e-180 640
19 TraesCS4A01G216800 chr5A 81.981 727 107 18 3 717 28422701 28423415 1.770000e-166 595


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 TraesCS4A01G216800 chr4A 515748585 515751250 2665 True 4924.0 4924 100.0000 1 2666 1 chr4A.!!$R1 2665
1 TraesCS4A01G216800 chr4A 516342753 516344722 1969 False 1301.0 2431 89.4000 712 2666 2 chr4A.!!$F2 1954
2 TraesCS4A01G216800 chr4A 555977112 555977824 712 False 769.0 769 86.2500 3 715 1 chr4A.!!$F1 712
3 TraesCS4A01G216800 chr4B 99077967 99078895 928 False 1125.0 1125 89.1140 851 1752 1 chr4B.!!$F1 901
4 TraesCS4A01G216800 chr4B 99048680 99052180 3500 False 843.5 1369 87.2625 766 2052 2 chr4B.!!$F3 1286
5 TraesCS4A01G216800 chr4B 99040375 99041828 1453 False 774.0 1267 88.3920 748 2052 2 chr4B.!!$F2 1304
6 TraesCS4A01G216800 chr4D 67238623 67239659 1036 False 1312.0 1312 89.8020 712 1743 1 chr4D.!!$F1 1031
7 TraesCS4A01G216800 chr4D 66934567 66935626 1059 True 1288.0 1288 89.1820 716 1740 1 chr4D.!!$R1 1024
8 TraesCS4A01G216800 chr4D 77312907 77313624 717 False 856.0 856 88.3980 3 715 1 chr4D.!!$F2 712
9 TraesCS4A01G216800 chr7A 236460767 236461495 728 False 874.0 874 88.6300 3 717 1 chr7A.!!$F1 714
10 TraesCS4A01G216800 chr1D 10374098 10374805 707 False 797.0 797 87.1370 13 725 1 chr1D.!!$F1 712
11 TraesCS4A01G216800 chr7D 46854986 46855694 708 False 767.0 767 86.3450 3 717 1 chr7D.!!$F1 714
12 TraesCS4A01G216800 chr3A 710403630 710404356 726 True 765.0 765 85.8310 1 726 1 chr3A.!!$R2 725
13 TraesCS4A01G216800 chr3A 710342773 710343499 726 True 754.0 754 85.5590 1 726 1 chr3A.!!$R1 725
14 TraesCS4A01G216800 chr3A 710463662 710464389 727 True 750.0 750 85.4420 1 726 1 chr3A.!!$R3 725
15 TraesCS4A01G216800 chr5A 524635116 524635836 720 True 640.0 640 82.9670 3 717 1 chr5A.!!$R1 714
16 TraesCS4A01G216800 chr5A 28422701 28423415 714 False 595.0 595 81.9810 3 717 1 chr5A.!!$F1 714

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
146 147 0.039437 GTCAAGACTCCTGTTCGCGA 60.039 55.0 3.71 3.71 0.0 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 4863 1.476085 CAGACAACTGTTTGGCCAACA 59.524 47.619 20.35 17.94 42.51 3.33 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
44 45 1.974875 GTCGGGCAACGGGGAAATT 60.975 57.895 0.11 0.00 44.45 1.82
45 46 0.677414 GTCGGGCAACGGGGAAATTA 60.677 55.000 0.11 0.00 44.45 1.40
79 80 1.051812 CTGAGTCTCCACCCTGTTGT 58.948 55.000 0.00 0.00 0.00 3.32
118 119 2.499205 CGCCAGGATGTTCGCCTA 59.501 61.111 0.00 0.00 33.51 3.93
146 147 0.039437 GTCAAGACTCCTGTTCGCGA 60.039 55.000 3.71 3.71 0.00 5.87
176 177 2.355363 CCGAAGTCGTTGGTCGCA 60.355 61.111 0.00 0.00 39.67 5.10
185 186 2.125552 TTGGTCGCAGCCTCATCG 60.126 61.111 0.00 0.00 0.00 3.84
207 208 2.108976 GGAATCGCTCGGCCATCA 59.891 61.111 2.24 0.00 0.00 3.07
219 226 1.281925 GGCCATCAGGAAGGAGGGAA 61.282 60.000 0.00 0.00 41.15 3.97
233 244 3.009714 GGAAAGGGAGGGCTCGGT 61.010 66.667 0.00 0.00 0.00 4.69
287 301 0.395862 CGCTTGGGAGAGGTAGAGGA 60.396 60.000 0.00 0.00 0.00 3.71
292 308 1.152715 GGAGAGGTAGAGGACGGGG 60.153 68.421 0.00 0.00 0.00 5.73
391 422 2.680352 GAGGGAGGTGAGGCGTCA 60.680 66.667 4.68 4.68 33.92 4.35
489 525 3.291101 TTCGGGGAAGAAGACGCGG 62.291 63.158 12.47 0.00 42.35 6.46
606 648 2.461110 CGCCAGCGCTAAATTCGGT 61.461 57.895 10.99 0.00 38.25 4.69
687 731 0.685660 GAAGAAACGTCTGGGGAGGT 59.314 55.000 0.00 0.00 41.57 3.85
698 742 4.564821 CGTCTGGGGAGGTTTTTATGAAGA 60.565 45.833 0.00 0.00 0.00 2.87
709 753 0.459585 TTATGAAGACGCGGCTGGAC 60.460 55.000 19.28 11.55 0.00 4.02
748 793 3.715628 AAACCGTCAACTGTACGTACT 57.284 42.857 25.12 4.41 38.67 2.73
763 818 2.490903 ACGTACTTCTAGCATGGTTCGT 59.509 45.455 1.12 0.00 32.66 3.85
775 830 0.323629 TGGTTCGTTGTGATCCCCTC 59.676 55.000 0.00 0.00 35.86 4.30
795 850 2.049063 AGACTCGGCTGCGAACAC 60.049 61.111 0.00 0.00 0.00 3.32
797 852 1.664965 GACTCGGCTGCGAACACTT 60.665 57.895 0.00 0.00 0.00 3.16
798 853 1.618640 GACTCGGCTGCGAACACTTC 61.619 60.000 0.00 0.00 0.00 3.01
799 854 2.357034 TCGGCTGCGAACACTTCC 60.357 61.111 0.00 0.00 0.00 3.46
801 856 3.423154 GGCTGCGAACACTTCCCG 61.423 66.667 0.00 0.00 0.00 5.14
803 858 2.668280 GCTGCGAACACTTCCCGTC 61.668 63.158 0.00 0.00 0.00 4.79
804 859 1.006102 CTGCGAACACTTCCCGTCT 60.006 57.895 0.00 0.00 0.00 4.18
806 861 2.087009 GCGAACACTTCCCGTCTCG 61.087 63.158 0.00 0.00 0.00 4.04
808 863 1.737008 GAACACTTCCCGTCTCGGC 60.737 63.158 2.41 0.00 46.86 5.54
809 864 2.156051 GAACACTTCCCGTCTCGGCT 62.156 60.000 2.41 0.00 46.86 5.52
826 883 2.612221 CGGCTTAGAAACTCTTCCCGTT 60.612 50.000 0.00 0.00 30.73 4.44
1269 1373 1.742900 GCATGGACGACGACATGACG 61.743 60.000 28.21 15.87 45.55 4.35
1418 1522 2.589157 CGTTCTACCAGGGCCACCA 61.589 63.158 6.18 0.00 40.13 4.17
1673 1792 2.159156 TGAAGTTATGGTGATCCGGACG 60.159 50.000 6.12 0.00 36.30 4.79
1702 4296 2.154389 GCCGTTAAACGACACACTAGTG 59.846 50.000 21.44 21.44 46.05 2.74
1907 4672 5.223382 GCATCGTGCTATCGCCTATATATT 58.777 41.667 0.00 0.00 40.96 1.28
1913 4678 6.360947 CGTGCTATCGCCTATATATTCATCAC 59.639 42.308 0.00 0.00 34.43 3.06
1941 4706 4.739793 TGAAAATGTCCCCTCTGTCAATT 58.260 39.130 0.00 0.00 0.00 2.32
1957 4722 4.203226 GTCAATTGATTCTTCCTCCTCCC 58.797 47.826 12.12 0.00 0.00 4.30
2071 4836 2.834113 CCACCTTCTTCCTTCTCCCTA 58.166 52.381 0.00 0.00 0.00 3.53
2082 4847 1.870941 TTCTCCCTACTCCCGCCTCA 61.871 60.000 0.00 0.00 0.00 3.86
2087 4852 1.742768 CTACTCCCGCCTCATCCAC 59.257 63.158 0.00 0.00 0.00 4.02
2116 4882 1.846007 TGTTGGCCAAACAGTTGTCT 58.154 45.000 22.47 0.00 43.96 3.41
2118 4884 0.459489 TTGGCCAAACAGTTGTCTGC 59.541 50.000 17.98 0.00 44.77 4.26
2125 4891 1.103398 AACAGTTGTCTGCTGCCACC 61.103 55.000 0.00 0.00 44.77 4.61
2130 4896 2.670934 GTCTGCTGCCACCCACAG 60.671 66.667 0.00 0.00 38.22 3.66
2177 4943 3.933722 CCGCCCTGCTCGATCCAT 61.934 66.667 0.00 0.00 0.00 3.41
2178 4944 2.574018 CCGCCCTGCTCGATCCATA 61.574 63.158 0.00 0.00 0.00 2.74
2180 4946 1.375268 GCCCTGCTCGATCCATAGC 60.375 63.158 3.08 3.08 39.25 2.97
2195 4961 0.470833 ATAGCCTCCGTCATGCCTCT 60.471 55.000 0.00 0.00 0.00 3.69
2215 4981 1.817099 CCGCACTCAGCCATCCTTC 60.817 63.158 0.00 0.00 41.38 3.46
2226 4992 1.401905 GCCATCCTTCTAAAACCGCAG 59.598 52.381 0.00 0.00 0.00 5.18
2243 5009 2.488153 CGCAGGGAAAAACTAAAGGGAG 59.512 50.000 0.00 0.00 0.00 4.30
2249 5015 4.218635 GGGAAAAACTAAAGGGAGAAGCAG 59.781 45.833 0.00 0.00 0.00 4.24
2254 5020 2.769095 ACTAAAGGGAGAAGCAGCCTAG 59.231 50.000 0.00 0.00 0.00 3.02
2257 5023 0.911525 AGGGAGAAGCAGCCTAGCAA 60.912 55.000 0.00 0.00 36.85 3.91
2258 5024 0.463474 GGGAGAAGCAGCCTAGCAAG 60.463 60.000 0.00 0.00 36.85 4.01
2260 5026 0.251634 GAGAAGCAGCCTAGCAAGGT 59.748 55.000 0.00 0.00 45.64 3.50
2261 5027 0.695347 AGAAGCAGCCTAGCAAGGTT 59.305 50.000 0.00 0.00 45.64 3.50
2262 5028 1.090728 GAAGCAGCCTAGCAAGGTTC 58.909 55.000 7.77 7.77 45.64 3.62
2263 5029 0.401738 AAGCAGCCTAGCAAGGTTCA 59.598 50.000 0.00 0.00 45.64 3.18
2264 5030 0.035630 AGCAGCCTAGCAAGGTTCAG 60.036 55.000 0.00 0.00 45.64 3.02
2305 5071 0.815615 GATAGAAGGGGGCGCAACAG 60.816 60.000 10.83 0.00 0.00 3.16
2307 5073 4.660938 GAAGGGGGCGCAACAGGT 62.661 66.667 10.83 0.00 0.00 4.00
2308 5074 3.253838 AAGGGGGCGCAACAGGTA 61.254 61.111 10.83 0.00 0.00 3.08
2325 5091 1.451567 TAGGGAGAGTGCTCGACCG 60.452 63.158 8.69 0.00 42.25 4.79
2347 5113 0.716591 TGGGGGTGGTCTCTGTATCT 59.283 55.000 0.00 0.00 0.00 1.98
2352 5118 3.108376 GGGTGGTCTCTGTATCTTCCTT 58.892 50.000 0.00 0.00 0.00 3.36
2353 5119 3.118592 GGGTGGTCTCTGTATCTTCCTTG 60.119 52.174 0.00 0.00 0.00 3.61
2371 5138 4.169856 TCCTTGTTTGCCCCCATCTATATT 59.830 41.667 0.00 0.00 0.00 1.28
2432 5261 3.758172 CCAAACCGGGTCACCTTG 58.242 61.111 6.32 0.76 33.28 3.61
2458 5287 1.212751 GCAAGTTTGGATGCGTCCC 59.787 57.895 22.40 7.05 44.41 4.46
2459 5288 1.523154 GCAAGTTTGGATGCGTCCCA 61.523 55.000 22.40 8.77 44.41 4.37
2460 5289 0.958091 CAAGTTTGGATGCGTCCCAA 59.042 50.000 22.40 14.91 44.41 4.12
2461 5290 0.958822 AAGTTTGGATGCGTCCCAAC 59.041 50.000 26.93 26.93 45.80 3.77
2462 5291 2.336341 GTTTGGATGCGTCCCAACA 58.664 52.632 28.45 7.72 45.15 3.33
2463 5292 0.240945 GTTTGGATGCGTCCCAACAG 59.759 55.000 28.45 0.00 45.15 3.16
2464 5293 0.893270 TTTGGATGCGTCCCAACAGG 60.893 55.000 22.40 0.00 44.41 4.00
2465 5294 2.438434 GGATGCGTCCCAACAGGG 60.438 66.667 14.58 0.00 44.52 4.45
2466 5295 2.351276 GATGCGTCCCAACAGGGT 59.649 61.111 0.00 0.00 43.53 4.34
2467 5296 1.745489 GATGCGTCCCAACAGGGTC 60.745 63.158 0.00 0.00 43.53 4.46
2468 5297 2.185310 GATGCGTCCCAACAGGGTCT 62.185 60.000 0.00 0.00 43.53 3.85
2469 5298 1.779061 ATGCGTCCCAACAGGGTCTT 61.779 55.000 0.00 0.00 43.53 3.01
2470 5299 1.671379 GCGTCCCAACAGGGTCTTC 60.671 63.158 0.00 0.00 43.53 2.87
2471 5300 1.003718 CGTCCCAACAGGGTCTTCC 60.004 63.158 0.00 0.00 43.53 3.46
2472 5301 1.764571 CGTCCCAACAGGGTCTTCCA 61.765 60.000 0.00 0.00 43.53 3.53
2473 5302 0.476771 GTCCCAACAGGGTCTTCCAA 59.523 55.000 0.00 0.00 43.53 3.53
2474 5303 1.133606 GTCCCAACAGGGTCTTCCAAA 60.134 52.381 0.00 0.00 43.53 3.28
2475 5304 1.571457 TCCCAACAGGGTCTTCCAAAA 59.429 47.619 0.00 0.00 43.53 2.44
2476 5305 2.178984 TCCCAACAGGGTCTTCCAAAAT 59.821 45.455 0.00 0.00 43.53 1.82
2477 5306 2.299867 CCCAACAGGGTCTTCCAAAATG 59.700 50.000 0.00 0.00 37.83 2.32
2478 5307 2.965147 CCAACAGGGTCTTCCAAAATGT 59.035 45.455 0.00 0.00 38.24 2.71
2479 5308 3.387699 CCAACAGGGTCTTCCAAAATGTT 59.612 43.478 0.00 0.00 38.24 2.71
2480 5309 4.501400 CCAACAGGGTCTTCCAAAATGTTC 60.501 45.833 0.00 0.00 38.24 3.18
2481 5310 4.184649 ACAGGGTCTTCCAAAATGTTCT 57.815 40.909 0.00 0.00 38.24 3.01
2482 5311 4.145052 ACAGGGTCTTCCAAAATGTTCTC 58.855 43.478 0.00 0.00 38.24 2.87
2483 5312 3.189287 CAGGGTCTTCCAAAATGTTCTCG 59.811 47.826 0.00 0.00 38.24 4.04
2484 5313 2.488153 GGGTCTTCCAAAATGTTCTCGG 59.512 50.000 0.00 0.00 35.00 4.63
2485 5314 2.095212 GGTCTTCCAAAATGTTCTCGGC 60.095 50.000 0.00 0.00 0.00 5.54
2486 5315 2.095212 GTCTTCCAAAATGTTCTCGGCC 60.095 50.000 0.00 0.00 0.00 6.13
2487 5316 1.202348 CTTCCAAAATGTTCTCGGCCC 59.798 52.381 0.00 0.00 0.00 5.80
2488 5317 0.404040 TCCAAAATGTTCTCGGCCCT 59.596 50.000 0.00 0.00 0.00 5.19
2489 5318 1.203001 TCCAAAATGTTCTCGGCCCTT 60.203 47.619 0.00 0.00 0.00 3.95
2490 5319 2.040545 TCCAAAATGTTCTCGGCCCTTA 59.959 45.455 0.00 0.00 0.00 2.69
2491 5320 2.163613 CCAAAATGTTCTCGGCCCTTAC 59.836 50.000 0.00 0.00 0.00 2.34
2492 5321 2.817258 CAAAATGTTCTCGGCCCTTACA 59.183 45.455 0.00 0.00 0.00 2.41
2493 5322 2.871096 AATGTTCTCGGCCCTTACAA 57.129 45.000 0.00 0.00 0.00 2.41
2494 5323 2.871096 ATGTTCTCGGCCCTTACAAA 57.129 45.000 0.00 0.00 0.00 2.83
2495 5324 2.642154 TGTTCTCGGCCCTTACAAAA 57.358 45.000 0.00 0.00 0.00 2.44
2496 5325 2.933573 TGTTCTCGGCCCTTACAAAAA 58.066 42.857 0.00 0.00 0.00 1.94
2497 5326 2.619646 TGTTCTCGGCCCTTACAAAAAC 59.380 45.455 0.00 0.00 0.00 2.43
2498 5327 2.882761 GTTCTCGGCCCTTACAAAAACT 59.117 45.455 0.00 0.00 0.00 2.66
2499 5328 3.217681 TCTCGGCCCTTACAAAAACTT 57.782 42.857 0.00 0.00 0.00 2.66
2500 5329 3.558033 TCTCGGCCCTTACAAAAACTTT 58.442 40.909 0.00 0.00 0.00 2.66
2501 5330 3.955551 TCTCGGCCCTTACAAAAACTTTT 59.044 39.130 0.00 0.00 0.00 2.27
2513 5342 4.826556 CAAAAACTTTTGTCACCTTCCCA 58.173 39.130 6.74 0.00 41.87 4.37
2521 5350 5.772393 TTTGTCACCTTCCCATACATACT 57.228 39.130 0.00 0.00 0.00 2.12
2522 5351 4.753516 TGTCACCTTCCCATACATACTG 57.246 45.455 0.00 0.00 0.00 2.74
2523 5352 3.454447 TGTCACCTTCCCATACATACTGG 59.546 47.826 0.00 0.00 0.00 4.00
2545 5374 4.202264 GGAACACTCCATGGTATCACTAGG 60.202 50.000 12.58 0.00 41.96 3.02
2552 5381 0.941963 TGGTATCACTAGGCCCTCCT 59.058 55.000 0.00 0.00 46.57 3.69
2586 5415 2.817258 GGACCATCCAAAACACATTCGA 59.183 45.455 0.00 0.00 36.28 3.71
2594 5423 3.552068 CCAAAACACATTCGAAACCCTCC 60.552 47.826 0.00 0.00 0.00 4.30
2598 5427 0.618981 ACATTCGAAACCCTCCCTCC 59.381 55.000 0.00 0.00 0.00 4.30
2604 5433 1.299939 GAAACCCTCCCTCCCATTCT 58.700 55.000 0.00 0.00 0.00 2.40
2607 5436 2.143419 CCCTCCCTCCCATTCTCCG 61.143 68.421 0.00 0.00 0.00 4.63
2625 5454 4.870426 TCTCCGTTATCTCATGTTTCAAGC 59.130 41.667 0.00 0.00 0.00 4.01
2627 5456 5.245531 TCCGTTATCTCATGTTTCAAGCTT 58.754 37.500 0.00 0.00 0.00 3.74
2629 5458 5.122239 CCGTTATCTCATGTTTCAAGCTTGA 59.878 40.000 25.16 25.16 34.92 3.02
2630 5459 6.183360 CCGTTATCTCATGTTTCAAGCTTGAT 60.183 38.462 28.89 12.17 37.00 2.57
2659 5488 1.002773 ACCATGTACGGAACACCTTCC 59.997 52.381 0.00 0.00 42.09 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.834188 CAACGGGGGAGTGCTAATTT 58.166 50.000 0.00 0.00 0.00 1.82
44 45 2.606519 AGCAACGGGGGAGTGCTA 60.607 61.111 0.00 0.00 33.70 3.49
45 46 4.335647 CAGCAACGGGGGAGTGCT 62.336 66.667 0.00 0.00 36.12 4.40
128 129 0.671796 TTCGCGAACAGGAGTCTTGA 59.328 50.000 19.38 0.00 0.00 3.02
165 166 2.835701 GATGAGGCTGCGACCAACGA 62.836 60.000 0.00 0.00 45.77 3.85
207 208 0.253394 CCTCCCTTTCCCTCCTTCCT 60.253 60.000 0.00 0.00 0.00 3.36
272 286 1.613610 CCGTCCTCTACCTCTCCCA 59.386 63.158 0.00 0.00 0.00 4.37
287 301 4.651516 ACACCAGCCCTACCCCGT 62.652 66.667 0.00 0.00 0.00 5.28
292 308 2.045926 CAGCCACACCAGCCCTAC 60.046 66.667 0.00 0.00 0.00 3.18
359 390 2.728015 CTCGCACGCGTACACACA 60.728 61.111 13.44 0.00 40.74 3.72
414 445 2.125106 GCCGGTCAGCCTTACCAG 60.125 66.667 1.90 0.00 36.78 4.00
585 627 1.498865 CGAATTTAGCGCTGGCGGAT 61.499 55.000 22.90 3.54 46.35 4.18
606 648 2.437716 GATTTTCGCCGGCCTGGA 60.438 61.111 23.46 10.06 42.00 3.86
639 682 1.533625 CAGAAAAATCGGCCCAGTCA 58.466 50.000 0.00 0.00 0.00 3.41
671 714 1.977056 AAAACCTCCCCAGACGTTTC 58.023 50.000 0.00 0.00 32.27 2.78
687 731 1.466950 CCAGCCGCGTCTTCATAAAAA 59.533 47.619 4.92 0.00 0.00 1.94
688 732 1.083489 CCAGCCGCGTCTTCATAAAA 58.917 50.000 4.92 0.00 0.00 1.52
692 736 2.125512 GTCCAGCCGCGTCTTCAT 60.126 61.111 4.92 0.00 0.00 2.57
709 753 3.599730 TTAGGTGTGTCTGAGAGCATG 57.400 47.619 0.00 0.00 0.00 4.06
748 793 3.394674 TCACAACGAACCATGCTAGAA 57.605 42.857 0.00 0.00 0.00 2.10
763 818 2.461695 GAGTCTGAGAGGGGATCACAA 58.538 52.381 0.00 0.00 0.00 3.33
775 830 1.803519 GTTCGCAGCCGAGTCTGAG 60.804 63.158 3.96 1.24 45.35 3.35
799 854 6.967462 GGAAGAGTTTCTAAGCCGAGACGG 62.967 54.167 5.79 5.79 40.53 4.79
801 856 3.513662 GGAAGAGTTTCTAAGCCGAGAC 58.486 50.000 0.00 0.00 33.68 3.36
803 858 2.735762 CGGGAAGAGTTTCTAAGCCGAG 60.736 54.545 0.00 0.00 36.88 4.63
804 859 1.203994 CGGGAAGAGTTTCTAAGCCGA 59.796 52.381 0.00 0.00 36.88 5.54
806 861 2.764439 ACGGGAAGAGTTTCTAAGCC 57.236 50.000 0.00 0.00 33.68 4.35
949 1022 4.834234 TCGTTCTCGATCGATGTCTAAAG 58.166 43.478 19.78 10.24 41.35 1.85
1673 1792 3.652733 GTCGTTTAACGGCAAAGCCCC 62.653 57.143 17.44 0.00 46.84 5.80
1702 4296 2.734606 TGTACGCTTCACATGTAACAGC 59.265 45.455 0.00 5.52 0.00 4.40
1835 4600 7.359262 TGAACTATCGATACAAACAAACCAG 57.641 36.000 0.00 0.00 0.00 4.00
1907 4672 3.334691 GACATTTTCAGTCCCGTGATGA 58.665 45.455 0.00 0.00 0.00 2.92
1941 4706 1.653918 AGGAGGGAGGAGGAAGAATCA 59.346 52.381 0.00 0.00 0.00 2.57
1957 4722 5.106396 GGATTGACATTTGACTGTTGAGGAG 60.106 44.000 0.00 0.00 0.00 3.69
2071 4836 3.083997 GGTGGATGAGGCGGGAGT 61.084 66.667 0.00 0.00 0.00 3.85
2097 4863 1.476085 CAGACAACTGTTTGGCCAACA 59.524 47.619 20.35 17.94 42.51 3.33
2110 4876 2.203337 TGGGTGGCAGCAGACAAC 60.203 61.111 19.48 0.00 40.91 3.32
2160 4926 2.498291 CTATGGATCGAGCAGGGCGG 62.498 65.000 1.84 0.00 0.00 6.13
2161 4927 1.080230 CTATGGATCGAGCAGGGCG 60.080 63.158 1.84 0.00 0.00 6.13
2165 4931 0.246086 GGAGGCTATGGATCGAGCAG 59.754 60.000 1.84 0.00 40.64 4.24
2170 4936 0.891373 ATGACGGAGGCTATGGATCG 59.109 55.000 0.00 0.00 0.00 3.69
2177 4943 1.075970 AGAGGCATGACGGAGGCTA 60.076 57.895 0.00 0.00 41.09 3.93
2178 4944 2.364842 AGAGGCATGACGGAGGCT 60.365 61.111 0.00 0.00 43.98 4.58
2180 4946 2.202987 GCAGAGGCATGACGGAGG 60.203 66.667 0.00 0.00 40.72 4.30
2215 4981 5.441709 TTAGTTTTTCCCTGCGGTTTTAG 57.558 39.130 0.00 0.00 0.00 1.85
2226 4992 4.149598 TGCTTCTCCCTTTAGTTTTTCCC 58.850 43.478 0.00 0.00 0.00 3.97
2228 4994 4.321304 GGCTGCTTCTCCCTTTAGTTTTTC 60.321 45.833 0.00 0.00 0.00 2.29
2237 5003 0.911525 TGCTAGGCTGCTTCTCCCTT 60.912 55.000 0.00 0.00 0.00 3.95
2243 5009 1.090728 GAACCTTGCTAGGCTGCTTC 58.909 55.000 14.60 6.80 46.22 3.86
2249 5015 2.761208 TCTAGACTGAACCTTGCTAGGC 59.239 50.000 14.60 0.00 46.22 3.93
2254 5020 4.727507 TCTCATCTAGACTGAACCTTGC 57.272 45.455 0.00 0.00 0.00 4.01
2280 5046 1.807495 CGCCCCCTTCTATCTCGGTC 61.807 65.000 0.00 0.00 0.00 4.79
2305 5071 1.385756 GGTCGAGCACTCTCCCTACC 61.386 65.000 10.30 0.00 35.94 3.18
2307 5073 1.451567 CGGTCGAGCACTCTCCCTA 60.452 63.158 15.89 0.00 35.94 3.53
2308 5074 2.752238 CGGTCGAGCACTCTCCCT 60.752 66.667 15.89 0.00 35.94 4.20
2325 5091 2.758852 TACAGAGACCACCCCCACCC 62.759 65.000 0.00 0.00 0.00 4.61
2332 5098 3.515901 ACAAGGAAGATACAGAGACCACC 59.484 47.826 0.00 0.00 0.00 4.61
2333 5099 4.810191 ACAAGGAAGATACAGAGACCAC 57.190 45.455 0.00 0.00 0.00 4.16
2334 5100 5.551233 CAAACAAGGAAGATACAGAGACCA 58.449 41.667 0.00 0.00 0.00 4.02
2340 5106 2.755103 GGGGCAAACAAGGAAGATACAG 59.245 50.000 0.00 0.00 0.00 2.74
2347 5113 0.486879 AGATGGGGGCAAACAAGGAA 59.513 50.000 0.00 0.00 0.00 3.36
2353 5119 9.574516 CCTATATAAATATAGATGGGGGCAAAC 57.425 37.037 15.57 0.00 43.02 2.93
2432 5261 1.194121 ATCCAAACTTGCTTGGGGGC 61.194 55.000 2.88 0.00 45.16 5.80
2458 5287 4.342092 AGAACATTTTGGAAGACCCTGTTG 59.658 41.667 0.00 0.00 35.38 3.33
2459 5288 4.546674 AGAACATTTTGGAAGACCCTGTT 58.453 39.130 0.00 0.00 35.38 3.16
2460 5289 4.145052 GAGAACATTTTGGAAGACCCTGT 58.855 43.478 0.00 0.00 35.38 4.00
2461 5290 3.189287 CGAGAACATTTTGGAAGACCCTG 59.811 47.826 0.00 0.00 35.38 4.45
2462 5291 3.412386 CGAGAACATTTTGGAAGACCCT 58.588 45.455 0.00 0.00 35.38 4.34
2463 5292 2.488153 CCGAGAACATTTTGGAAGACCC 59.512 50.000 0.00 0.00 34.81 4.46
2464 5293 2.095212 GCCGAGAACATTTTGGAAGACC 60.095 50.000 0.00 0.00 0.00 3.85
2465 5294 2.095212 GGCCGAGAACATTTTGGAAGAC 60.095 50.000 0.00 0.00 0.00 3.01
2466 5295 2.159382 GGCCGAGAACATTTTGGAAGA 58.841 47.619 0.00 0.00 0.00 2.87
2467 5296 1.202348 GGGCCGAGAACATTTTGGAAG 59.798 52.381 0.00 0.00 0.00 3.46
2468 5297 1.203001 AGGGCCGAGAACATTTTGGAA 60.203 47.619 0.00 0.00 0.00 3.53
2469 5298 0.404040 AGGGCCGAGAACATTTTGGA 59.596 50.000 0.00 0.00 0.00 3.53
2470 5299 1.256812 AAGGGCCGAGAACATTTTGG 58.743 50.000 0.00 0.00 0.00 3.28
2471 5300 2.817258 TGTAAGGGCCGAGAACATTTTG 59.183 45.455 0.00 0.00 0.00 2.44
2472 5301 3.149005 TGTAAGGGCCGAGAACATTTT 57.851 42.857 0.00 0.00 0.00 1.82
2473 5302 2.871096 TGTAAGGGCCGAGAACATTT 57.129 45.000 0.00 0.00 0.00 2.32
2474 5303 2.871096 TTGTAAGGGCCGAGAACATT 57.129 45.000 0.00 0.00 0.00 2.71
2475 5304 2.871096 TTTGTAAGGGCCGAGAACAT 57.129 45.000 0.00 0.00 0.00 2.71
2476 5305 2.619646 GTTTTTGTAAGGGCCGAGAACA 59.380 45.455 0.00 0.00 0.00 3.18
2477 5306 2.882761 AGTTTTTGTAAGGGCCGAGAAC 59.117 45.455 0.00 0.00 0.00 3.01
2478 5307 3.217681 AGTTTTTGTAAGGGCCGAGAA 57.782 42.857 0.00 0.00 0.00 2.87
2479 5308 2.943036 AGTTTTTGTAAGGGCCGAGA 57.057 45.000 0.00 0.00 0.00 4.04
2480 5309 4.048504 CAAAAGTTTTTGTAAGGGCCGAG 58.951 43.478 8.76 0.00 41.87 4.63
2481 5310 4.048241 CAAAAGTTTTTGTAAGGGCCGA 57.952 40.909 8.76 0.00 41.87 5.54
2492 5321 5.692115 ATGGGAAGGTGACAAAAGTTTTT 57.308 34.783 0.00 0.00 0.00 1.94
2493 5322 5.659079 TGTATGGGAAGGTGACAAAAGTTTT 59.341 36.000 0.00 0.00 0.00 2.43
2494 5323 5.205056 TGTATGGGAAGGTGACAAAAGTTT 58.795 37.500 0.00 0.00 0.00 2.66
2495 5324 4.798882 TGTATGGGAAGGTGACAAAAGTT 58.201 39.130 0.00 0.00 0.00 2.66
2496 5325 4.447138 TGTATGGGAAGGTGACAAAAGT 57.553 40.909 0.00 0.00 0.00 2.66
2497 5326 6.094048 CAGTATGTATGGGAAGGTGACAAAAG 59.906 42.308 0.00 0.00 0.00 2.27
2498 5327 5.943416 CAGTATGTATGGGAAGGTGACAAAA 59.057 40.000 0.00 0.00 0.00 2.44
2499 5328 5.496556 CAGTATGTATGGGAAGGTGACAAA 58.503 41.667 0.00 0.00 0.00 2.83
2500 5329 4.080582 CCAGTATGTATGGGAAGGTGACAA 60.081 45.833 0.00 0.00 33.94 3.18
2501 5330 3.454447 CCAGTATGTATGGGAAGGTGACA 59.546 47.826 0.00 0.00 33.94 3.58
2502 5331 3.709653 TCCAGTATGTATGGGAAGGTGAC 59.290 47.826 0.00 0.00 38.44 3.67
2503 5332 4.002256 TCCAGTATGTATGGGAAGGTGA 57.998 45.455 0.00 0.00 38.44 4.02
2504 5333 4.080582 TGTTCCAGTATGTATGGGAAGGTG 60.081 45.833 0.00 0.00 39.91 4.00
2505 5334 4.080526 GTGTTCCAGTATGTATGGGAAGGT 60.081 45.833 0.00 0.00 39.91 3.50
2506 5335 4.164221 AGTGTTCCAGTATGTATGGGAAGG 59.836 45.833 0.00 0.00 39.91 3.46
2507 5336 5.359194 AGTGTTCCAGTATGTATGGGAAG 57.641 43.478 0.00 0.00 39.91 3.46
2508 5337 4.163458 GGAGTGTTCCAGTATGTATGGGAA 59.837 45.833 0.00 0.00 43.45 3.97
2509 5338 3.709653 GGAGTGTTCCAGTATGTATGGGA 59.290 47.826 0.00 0.00 43.45 4.37
2510 5339 4.073293 GGAGTGTTCCAGTATGTATGGG 57.927 50.000 0.00 0.00 43.45 4.00
2522 5351 3.914426 AGTGATACCATGGAGTGTTCC 57.086 47.619 21.47 0.00 44.31 3.62
2523 5352 4.740934 GCCTAGTGATACCATGGAGTGTTC 60.741 50.000 21.47 7.87 0.00 3.18
2545 5374 2.106684 CCCCAAAGTATTCTAGGAGGGC 59.893 54.545 0.00 0.00 33.68 5.19
2552 5381 4.376223 TGGATGGTCCCCAAAGTATTCTA 58.624 43.478 0.00 0.00 36.95 2.10
2554 5383 3.662759 TGGATGGTCCCCAAAGTATTC 57.337 47.619 0.00 0.00 36.95 1.75
2563 5392 1.937191 ATGTGTTTTGGATGGTCCCC 58.063 50.000 0.00 0.00 35.03 4.81
2574 5403 2.626266 GGGAGGGTTTCGAATGTGTTTT 59.374 45.455 0.00 0.00 0.00 2.43
2578 5407 1.679032 GGAGGGAGGGTTTCGAATGTG 60.679 57.143 0.00 0.00 0.00 3.21
2586 5415 1.299939 GAGAATGGGAGGGAGGGTTT 58.700 55.000 0.00 0.00 0.00 3.27
2594 5423 2.965831 TGAGATAACGGAGAATGGGAGG 59.034 50.000 0.00 0.00 0.00 4.30
2598 5427 5.817296 TGAAACATGAGATAACGGAGAATGG 59.183 40.000 0.00 0.00 0.00 3.16
2604 5433 4.832248 AGCTTGAAACATGAGATAACGGA 58.168 39.130 0.00 0.00 0.00 4.69
2625 5454 6.426633 TCCGTACATGGTTGCATATTATCAAG 59.573 38.462 0.00 0.00 0.00 3.02
2627 5456 5.859495 TCCGTACATGGTTGCATATTATCA 58.141 37.500 0.00 0.00 0.00 2.15
2629 5458 6.017440 GTGTTCCGTACATGGTTGCATATTAT 60.017 38.462 0.00 0.00 39.39 1.28
2630 5459 5.294799 GTGTTCCGTACATGGTTGCATATTA 59.705 40.000 0.00 0.00 39.39 0.98


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

AutoCloner maintained by Alex Coulton.