Multiple sequence alignment - TraesCS4A01G247600

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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 TraesCS4A01G247600 chr4A 100.000 2668 0 0 1 2668 558652111 558649444 0.000000e+00 4927
1 TraesCS4A01G247600 chr4B 86.675 1516 75 56 652 2102 60083131 60084584 0.000000e+00 1563
2 TraesCS4A01G247600 chr4B 89.358 592 26 11 2104 2668 60084623 60085204 0.000000e+00 710
3 TraesCS4A01G247600 chr4B 89.305 187 10 6 78 262 60081418 60081596 2.670000e-55 226
4 TraesCS4A01G247600 chr4B 79.817 327 30 18 271 569 60079156 60079474 3.480000e-49 206
5 TraesCS4A01G247600 chr4B 82.143 196 15 9 271 454 60081656 60081843 1.650000e-32 150
6 TraesCS4A01G247600 chr4D 86.591 1499 79 59 650 2074 40953399 40954849 0.000000e+00 1543
7 TraesCS4A01G247600 chr4D 92.819 557 13 11 2126 2667 40954989 40955533 0.000000e+00 782
8 TraesCS4A01G247600 chr4D 89.005 573 24 21 78 616 40952745 40953312 0.000000e+00 673


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 TraesCS4A01G247600 chr4A 558649444 558652111 2667 True 4927.000000 4927 100.000000 1 2668 1 chr4A.!!$R1 2667
1 TraesCS4A01G247600 chr4B 60079156 60085204 6048 False 571.000000 1563 85.459600 78 2668 5 chr4B.!!$F1 2590
2 TraesCS4A01G247600 chr4D 40952745 40955533 2788 False 999.333333 1543 89.471667 78 2667 3 chr4D.!!$F1 2589

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
456 2713 0.035439 ATGAAATCGCTGGGTTCGGT 60.035 50.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2252 5840 0.602106 CAGTGGCACTGTCCTGTCAG 60.602 60.0 34.0 10.19 41.19 3.51 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
42 43 6.917217 TTTTGCGGAAATTTCAAATCAACT 57.083 29.167 19.49 0.00 30.89 3.16
43 44 6.917217 TTTGCGGAAATTTCAAATCAACTT 57.083 29.167 19.49 0.00 0.00 2.66
44 45 6.523676 TTGCGGAAATTTCAAATCAACTTC 57.476 33.333 19.49 0.00 0.00 3.01
45 46 4.987912 TGCGGAAATTTCAAATCAACTTCC 59.012 37.500 19.49 2.30 0.00 3.46
46 47 5.745653 CGGAAATTTCAAATCAACTTCCG 57.254 39.130 19.49 15.81 45.28 4.30
47 48 5.219633 CGGAAATTTCAAATCAACTTCCGT 58.780 37.500 19.30 0.00 45.41 4.69
48 49 5.116983 CGGAAATTTCAAATCAACTTCCGTG 59.883 40.000 19.30 0.78 45.41 4.94
50 51 6.074356 GGAAATTTCAAATCAACTTCCGTGTG 60.074 38.462 19.49 0.00 0.00 3.82
52 53 5.766150 TTTCAAATCAACTTCCGTGTGAT 57.234 34.783 0.00 0.00 0.00 3.06
53 54 4.747540 TCAAATCAACTTCCGTGTGATG 57.252 40.909 0.00 0.00 0.00 3.07
54 55 4.133820 TCAAATCAACTTCCGTGTGATGT 58.866 39.130 0.00 0.00 33.05 3.06
55 56 4.578516 TCAAATCAACTTCCGTGTGATGTT 59.421 37.500 0.00 0.00 40.80 2.71
57 58 6.261158 TCAAATCAACTTCCGTGTGATGTTTA 59.739 34.615 0.00 0.00 38.80 2.01
58 59 5.607119 ATCAACTTCCGTGTGATGTTTAC 57.393 39.130 0.00 0.00 38.80 2.01
59 60 4.699637 TCAACTTCCGTGTGATGTTTACT 58.300 39.130 0.00 0.00 38.80 2.24
60 61 4.509970 TCAACTTCCGTGTGATGTTTACTG 59.490 41.667 0.00 0.00 38.80 2.74
63 64 0.442310 CCGTGTGATGTTTACTGCGG 59.558 55.000 0.00 0.00 33.69 5.69
64 65 0.442310 CGTGTGATGTTTACTGCGGG 59.558 55.000 0.00 0.00 0.00 6.13
65 66 1.519408 GTGTGATGTTTACTGCGGGT 58.481 50.000 0.00 0.00 0.00 5.28
66 67 1.877443 GTGTGATGTTTACTGCGGGTT 59.123 47.619 0.00 0.00 0.00 4.11
67 68 2.292292 GTGTGATGTTTACTGCGGGTTT 59.708 45.455 0.00 0.00 0.00 3.27
69 70 3.749088 TGTGATGTTTACTGCGGGTTTAG 59.251 43.478 0.00 0.00 0.00 1.85
70 71 2.745281 TGATGTTTACTGCGGGTTTAGC 59.255 45.455 0.00 0.00 0.00 3.09
71 72 2.257691 TGTTTACTGCGGGTTTAGCA 57.742 45.000 0.00 0.00 42.99 3.49
73 74 1.198408 GTTTACTGCGGGTTTAGCACC 59.802 52.381 0.00 0.00 46.46 5.01
81 82 2.578683 GGTTTAGCACCACATGGGG 58.421 57.895 14.08 14.08 46.42 4.96
82 83 0.970427 GGTTTAGCACCACATGGGGG 60.970 60.000 20.68 11.69 46.42 5.40
98 2285 1.098050 GGGGAGTGCAGCTAATGTTG 58.902 55.000 0.00 0.00 0.00 3.33
101 2288 2.162408 GGGAGTGCAGCTAATGTTGTTC 59.838 50.000 0.00 0.00 0.00 3.18
107 2295 1.131126 CAGCTAATGTTGTTCGGCAGG 59.869 52.381 0.00 0.00 0.00 4.85
136 2329 1.746991 GCAAGTAGTCCAGCCAGCC 60.747 63.158 0.00 0.00 0.00 4.85
141 2334 1.762460 TAGTCCAGCCAGCCCTAGC 60.762 63.158 0.00 0.00 40.32 3.42
174 2368 1.964933 GAGACCAGTATCTAGGCACCC 59.035 57.143 0.00 0.00 0.00 4.61
175 2369 1.049402 GACCAGTATCTAGGCACCCC 58.951 60.000 0.00 0.00 0.00 4.95
424 2671 0.448861 CACACACGACGCGAAATGTC 60.449 55.000 15.93 0.00 0.00 3.06
454 2711 0.248215 GCATGAAATCGCTGGGTTCG 60.248 55.000 0.00 0.00 0.00 3.95
456 2713 0.035439 ATGAAATCGCTGGGTTCGGT 60.035 50.000 0.00 0.00 0.00 4.69
457 2714 0.250553 TGAAATCGCTGGGTTCGGTT 60.251 50.000 0.00 0.00 0.00 4.44
458 2715 0.446616 GAAATCGCTGGGTTCGGTTC 59.553 55.000 0.00 0.00 29.06 3.62
521 2810 2.542178 GCCACGGTAAAAAGCCTTTTTG 59.458 45.455 22.22 10.35 42.41 2.44
545 2834 3.674528 TCCAAAGAGAGAGAAGCACAG 57.325 47.619 0.00 0.00 0.00 3.66
602 3926 3.187058 CACGGCATGTGGTAAGCC 58.813 61.111 0.00 0.00 45.21 4.35
631 3984 1.068474 ATAGTGAATAATCGCGCCGC 58.932 50.000 0.00 0.00 41.06 6.53
651 4004 1.857364 CCGAGAAAAACGTGACGGG 59.143 57.895 10.66 0.00 37.28 5.28
654 4007 2.426261 GAAAAACGTGACGGGCGC 60.426 61.111 10.66 0.00 0.00 6.53
757 4146 4.483683 CGCATCGTGTTCACGCCG 62.484 66.667 18.63 15.96 0.00 6.46
763 4152 1.131826 CGTGTTCACGCCGAATTCC 59.868 57.895 12.19 0.00 35.63 3.01
830 4233 4.960866 CTGTGGCCACCAGCAGCA 62.961 66.667 32.62 11.64 46.50 4.41
831 4234 4.960866 TGTGGCCACCAGCAGCAG 62.961 66.667 32.62 0.00 46.50 4.24
849 4252 4.370364 GCAGCTAGCTCCTATCAGTATC 57.630 50.000 16.15 0.00 41.15 2.24
850 4253 3.761218 GCAGCTAGCTCCTATCAGTATCA 59.239 47.826 16.15 0.00 41.15 2.15
851 4254 4.142403 GCAGCTAGCTCCTATCAGTATCAG 60.142 50.000 16.15 0.00 41.15 2.90
852 4255 5.009631 CAGCTAGCTCCTATCAGTATCAGT 58.990 45.833 16.15 0.00 0.00 3.41
853 4256 6.176896 CAGCTAGCTCCTATCAGTATCAGTA 58.823 44.000 16.15 0.00 0.00 2.74
854 4257 6.828273 CAGCTAGCTCCTATCAGTATCAGTAT 59.172 42.308 16.15 0.00 0.00 2.12
855 4258 7.012327 CAGCTAGCTCCTATCAGTATCAGTATC 59.988 44.444 16.15 0.00 0.00 2.24
856 4259 6.826231 GCTAGCTCCTATCAGTATCAGTATCA 59.174 42.308 7.70 0.00 0.00 2.15
857 4260 7.012327 GCTAGCTCCTATCAGTATCAGTATCAG 59.988 44.444 7.70 0.00 0.00 2.90
858 4261 6.789268 AGCTCCTATCAGTATCAGTATCAGT 58.211 40.000 0.00 0.00 0.00 3.41
859 4262 7.923461 AGCTCCTATCAGTATCAGTATCAGTA 58.077 38.462 0.00 0.00 0.00 2.74
860 4263 8.556589 AGCTCCTATCAGTATCAGTATCAGTAT 58.443 37.037 0.00 0.00 0.00 2.12
861 4264 8.836413 GCTCCTATCAGTATCAGTATCAGTATC 58.164 40.741 0.00 0.00 0.00 2.24
862 4265 9.898152 CTCCTATCAGTATCAGTATCAGTATCA 57.102 37.037 0.00 0.00 0.00 2.15
863 4266 9.898152 TCCTATCAGTATCAGTATCAGTATCAG 57.102 37.037 0.00 0.00 0.00 2.90
880 4283 4.855715 ATCAGTATCAGTATCACCACCG 57.144 45.455 0.00 0.00 0.00 4.94
883 4286 2.362397 AGTATCAGTATCACCACCGCAG 59.638 50.000 0.00 0.00 0.00 5.18
971 4381 4.764771 CCCGACCGACCCCCAGTA 62.765 72.222 0.00 0.00 0.00 2.74
972 4382 3.145551 CCGACCGACCCCCAGTAG 61.146 72.222 0.00 0.00 0.00 2.57
973 4383 3.145551 CGACCGACCCCCAGTAGG 61.146 72.222 0.00 0.00 46.20 3.18
974 4384 3.468140 GACCGACCCCCAGTAGGC 61.468 72.222 0.00 0.00 44.72 3.93
975 4385 4.326227 ACCGACCCCCAGTAGGCA 62.326 66.667 0.00 0.00 44.72 4.75
976 4386 3.470888 CCGACCCCCAGTAGGCAG 61.471 72.222 0.00 0.00 34.18 4.85
1597 5010 1.081376 CTCAAGAACCGCGTCGACT 60.081 57.895 14.70 0.00 0.00 4.18
1598 5011 1.066114 CTCAAGAACCGCGTCGACTC 61.066 60.000 14.70 4.41 0.00 3.36
1654 5067 2.203056 CGCCGCTCCATTGATCCA 60.203 61.111 0.00 0.00 0.00 3.41
1655 5068 2.537560 CGCCGCTCCATTGATCCAC 61.538 63.158 0.00 0.00 0.00 4.02
1658 5088 1.889105 CGCTCCATTGATCCACCCG 60.889 63.158 0.00 0.00 0.00 5.28
1671 5101 2.479340 TCCACCCGTCAATTATACCCA 58.521 47.619 0.00 0.00 0.00 4.51
1672 5102 3.050089 TCCACCCGTCAATTATACCCAT 58.950 45.455 0.00 0.00 0.00 4.00
1724 5157 4.389576 CCACTTCGCCGTGCTTGC 62.390 66.667 0.00 0.00 33.60 4.01
1787 5251 6.721704 TGCATGATGAACTCTATACAGACT 57.278 37.500 0.00 0.00 0.00 3.24
1800 5264 7.604927 ACTCTATACAGACTAAGATGGATCGAC 59.395 40.741 0.00 0.00 0.00 4.20
1801 5265 7.681679 TCTATACAGACTAAGATGGATCGACT 58.318 38.462 0.00 0.00 0.00 4.18
1802 5266 4.909696 ACAGACTAAGATGGATCGACTG 57.090 45.455 0.00 0.00 0.00 3.51
1803 5267 3.067461 ACAGACTAAGATGGATCGACTGC 59.933 47.826 0.00 0.00 0.00 4.40
1804 5268 3.067320 CAGACTAAGATGGATCGACTGCA 59.933 47.826 0.00 0.00 0.00 4.41
1805 5269 3.701542 AGACTAAGATGGATCGACTGCAA 59.298 43.478 0.00 0.00 0.00 4.08
1806 5270 4.047822 GACTAAGATGGATCGACTGCAAG 58.952 47.826 0.00 0.00 42.29 4.01
1912 5380 4.828829 ACCAAGTGTACTGTAATACTGCC 58.171 43.478 6.72 0.00 0.00 4.85
1989 5467 2.768527 TCTGTAATCCCAGAGCAGAAGG 59.231 50.000 0.00 0.00 36.57 3.46
1990 5468 1.210478 TGTAATCCCAGAGCAGAAGGC 59.790 52.381 0.00 0.00 45.30 4.35
2044 5529 7.385778 TCCATACTAAAAGTTGCGCTAAATT 57.614 32.000 9.73 4.13 0.00 1.82
2115 5697 7.617041 ATGAAATAGCTGGTAACACTTTCTC 57.383 36.000 0.00 0.00 46.17 2.87
2121 5703 0.788391 GGTAACACTTTCTCGGTGCG 59.212 55.000 0.00 0.00 38.14 5.34
2135 5717 0.889186 GGTGCGAAGTGGTTGGTGAT 60.889 55.000 0.00 0.00 0.00 3.06
2136 5718 1.609580 GGTGCGAAGTGGTTGGTGATA 60.610 52.381 0.00 0.00 0.00 2.15
2137 5719 1.463444 GTGCGAAGTGGTTGGTGATAC 59.537 52.381 0.00 0.00 0.00 2.24
2138 5720 0.719465 GCGAAGTGGTTGGTGATACG 59.281 55.000 0.00 0.00 0.00 3.06
2226 5814 0.947180 GCGAGTTGCGGTACAGGAAA 60.947 55.000 0.86 0.00 41.29 3.13
2252 5840 5.533482 AGAGTACAAACACTGATCAGTCAC 58.467 41.667 25.58 14.99 40.20 3.67
2261 5849 2.560542 ACTGATCAGTCACTGACAGGAC 59.439 50.000 27.17 11.05 43.63 3.85
2281 5869 4.329545 TGCCACTGCCGGAGAACC 62.330 66.667 5.05 0.00 36.33 3.62
2297 5891 0.249489 AACCGGAGCTTATAGCAGCG 60.249 55.000 9.46 0.00 45.56 5.18
2407 6010 0.798776 CATGAACCAGAACTCGTGGC 59.201 55.000 0.00 0.00 38.83 5.01
2525 6128 2.125552 CGCAGCCGGTGAATGAGA 60.126 61.111 1.90 0.00 0.00 3.27
2640 6255 4.509737 GCGTGGTAGGAGACGGGC 62.510 72.222 0.00 0.00 36.09 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 7.313951 AGTTGATTTGAAATTTCCGCAAAAA 57.686 28.000 15.48 9.04 35.44 1.94
19 20 6.917217 AGTTGATTTGAAATTTCCGCAAAA 57.083 29.167 15.48 9.38 35.44 2.44
21 22 5.465056 GGAAGTTGATTTGAAATTTCCGCAA 59.535 36.000 15.48 10.80 34.82 4.85
22 23 4.987912 GGAAGTTGATTTGAAATTTCCGCA 59.012 37.500 15.48 5.66 34.82 5.69
23 24 5.515548 GGAAGTTGATTTGAAATTTCCGC 57.484 39.130 15.48 3.23 34.82 5.54
25 26 5.983118 ACACGGAAGTTGATTTGAAATTTCC 59.017 36.000 15.48 8.39 46.40 3.13
26 27 6.695278 TCACACGGAAGTTGATTTGAAATTTC 59.305 34.615 11.41 11.41 46.40 2.17
27 28 6.568869 TCACACGGAAGTTGATTTGAAATTT 58.431 32.000 0.00 0.00 46.40 1.82
28 29 6.142818 TCACACGGAAGTTGATTTGAAATT 57.857 33.333 0.00 0.00 46.40 1.82
29 30 5.766150 TCACACGGAAGTTGATTTGAAAT 57.234 34.783 0.00 0.00 46.40 2.17
32 33 4.133820 ACATCACACGGAAGTTGATTTGA 58.866 39.130 0.00 0.00 46.40 2.69
33 34 4.488126 ACATCACACGGAAGTTGATTTG 57.512 40.909 0.00 0.00 46.40 2.32
34 35 5.514274 AAACATCACACGGAAGTTGATTT 57.486 34.783 0.00 0.00 46.40 2.17
35 36 5.763204 AGTAAACATCACACGGAAGTTGATT 59.237 36.000 0.00 0.00 46.40 2.57
36 37 5.179368 CAGTAAACATCACACGGAAGTTGAT 59.821 40.000 0.00 0.00 46.40 2.57
37 38 4.509970 CAGTAAACATCACACGGAAGTTGA 59.490 41.667 0.00 0.00 46.40 3.18
38 39 4.772434 CAGTAAACATCACACGGAAGTTG 58.228 43.478 0.00 0.00 46.40 3.16
39 40 3.250040 GCAGTAAACATCACACGGAAGTT 59.750 43.478 0.00 0.00 46.40 2.66
41 42 2.159841 CGCAGTAAACATCACACGGAAG 60.160 50.000 0.00 0.00 0.00 3.46
42 43 1.795872 CGCAGTAAACATCACACGGAA 59.204 47.619 0.00 0.00 0.00 4.30
43 44 1.424403 CGCAGTAAACATCACACGGA 58.576 50.000 0.00 0.00 0.00 4.69
44 45 0.442310 CCGCAGTAAACATCACACGG 59.558 55.000 0.00 0.00 33.48 4.94
45 46 0.442310 CCCGCAGTAAACATCACACG 59.558 55.000 0.00 0.00 0.00 4.49
46 47 1.519408 ACCCGCAGTAAACATCACAC 58.481 50.000 0.00 0.00 0.00 3.82
47 48 2.264005 AACCCGCAGTAAACATCACA 57.736 45.000 0.00 0.00 0.00 3.58
48 49 3.425758 GCTAAACCCGCAGTAAACATCAC 60.426 47.826 0.00 0.00 0.00 3.06
50 51 2.745281 TGCTAAACCCGCAGTAAACATC 59.255 45.455 0.00 0.00 32.80 3.06
52 53 1.874872 GTGCTAAACCCGCAGTAAACA 59.125 47.619 0.00 0.00 38.19 2.83
53 54 1.198408 GGTGCTAAACCCGCAGTAAAC 59.802 52.381 0.00 0.00 44.02 2.01
54 55 1.525941 GGTGCTAAACCCGCAGTAAA 58.474 50.000 0.00 0.00 44.02 2.01
55 56 3.236604 GGTGCTAAACCCGCAGTAA 57.763 52.632 0.00 0.00 44.02 2.24
64 65 0.039035 TCCCCCATGTGGTGCTAAAC 59.961 55.000 0.00 0.00 0.00 2.01
65 66 0.331278 CTCCCCCATGTGGTGCTAAA 59.669 55.000 0.00 0.00 0.00 1.85
66 67 0.844661 ACTCCCCCATGTGGTGCTAA 60.845 55.000 0.00 0.00 0.00 3.09
67 68 1.229820 ACTCCCCCATGTGGTGCTA 60.230 57.895 0.00 0.00 0.00 3.49
69 70 2.361610 CACTCCCCCATGTGGTGC 60.362 66.667 0.00 0.00 0.00 5.01
70 71 2.361610 GCACTCCCCCATGTGGTG 60.362 66.667 0.00 0.00 34.99 4.17
71 72 2.858476 TGCACTCCCCCATGTGGT 60.858 61.111 0.00 0.00 34.99 4.16
73 74 1.913951 TAGCTGCACTCCCCCATGTG 61.914 60.000 1.02 0.00 37.26 3.21
74 75 1.207488 TTAGCTGCACTCCCCCATGT 61.207 55.000 1.02 0.00 0.00 3.21
76 77 0.184451 CATTAGCTGCACTCCCCCAT 59.816 55.000 1.02 0.00 0.00 4.00
79 80 1.098050 CAACATTAGCTGCACTCCCC 58.902 55.000 1.02 0.00 0.00 4.81
80 81 1.826385 ACAACATTAGCTGCACTCCC 58.174 50.000 1.02 0.00 0.00 4.30
81 82 2.159653 CGAACAACATTAGCTGCACTCC 60.160 50.000 1.02 0.00 0.00 3.85
82 83 2.159653 CCGAACAACATTAGCTGCACTC 60.160 50.000 1.02 0.00 0.00 3.51
98 2285 3.189702 TGCTGTAAATTAACCTGCCGAAC 59.810 43.478 0.00 0.00 0.00 3.95
101 2288 3.190535 ACTTGCTGTAAATTAACCTGCCG 59.809 43.478 0.00 0.00 0.00 5.69
107 2295 6.403309 GGCTGGACTACTTGCTGTAAATTAAC 60.403 42.308 0.00 0.00 0.00 2.01
136 2329 2.303022 TCTCCACAAAACCAGAGCTAGG 59.697 50.000 3.20 3.20 0.00 3.02
141 2334 2.638480 TGGTCTCCACAAAACCAGAG 57.362 50.000 0.00 0.00 38.14 3.35
174 2368 4.271816 CGGCTCTGGGATCGTCGG 62.272 72.222 0.00 0.00 0.00 4.79
175 2369 3.471244 GACGGCTCTGGGATCGTCG 62.471 68.421 7.80 0.00 41.60 5.12
304 2549 3.555795 GCTGTGATGAACTGACAGGAGAA 60.556 47.826 7.51 0.00 38.04 2.87
307 2552 1.973515 AGCTGTGATGAACTGACAGGA 59.026 47.619 7.51 0.00 38.04 3.86
308 2553 2.289257 TGAGCTGTGATGAACTGACAGG 60.289 50.000 7.51 0.00 38.04 4.00
309 2554 3.036075 TGAGCTGTGATGAACTGACAG 57.964 47.619 0.00 0.00 40.14 3.51
424 2671 2.282555 CGATTTCATGCGTGTCCTACAG 59.717 50.000 5.68 0.00 0.00 2.74
434 2691 0.248215 GAACCCAGCGATTTCATGCG 60.248 55.000 0.00 0.00 35.87 4.73
521 2810 3.993736 GTGCTTCTCTCTCTTTGGAAGAC 59.006 47.826 0.00 0.00 37.84 3.01
606 3930 6.304126 CGGCGCGATTATTCACTATATTTTT 58.696 36.000 12.10 0.00 0.00 1.94
628 3952 3.708734 ACGTTTTTCTCGGCGCGG 61.709 61.111 8.83 8.94 0.00 6.46
631 3984 1.154908 CGTCACGTTTTTCTCGGCG 60.155 57.895 0.00 0.00 0.00 6.46
757 4146 2.046009 GAGGGCGAGGGAGGGAATTC 62.046 65.000 0.00 0.00 0.00 2.17
779 4168 3.352748 TGAGGCCGAGGTAGGGGA 61.353 66.667 0.00 0.00 0.00 4.81
830 4233 5.255397 ACTGATACTGATAGGAGCTAGCT 57.745 43.478 19.45 19.45 0.00 3.32
831 4234 6.826231 TGATACTGATACTGATAGGAGCTAGC 59.174 42.308 6.62 6.62 0.00 3.42
832 4235 8.046708 ACTGATACTGATACTGATAGGAGCTAG 58.953 40.741 0.00 0.00 0.00 3.42
833 4236 7.923461 ACTGATACTGATACTGATAGGAGCTA 58.077 38.462 0.00 0.00 0.00 3.32
834 4237 6.789268 ACTGATACTGATACTGATAGGAGCT 58.211 40.000 0.00 0.00 0.00 4.09
835 4238 8.746052 ATACTGATACTGATACTGATAGGAGC 57.254 38.462 0.00 0.00 0.00 4.70
837 4240 9.898152 CTGATACTGATACTGATACTGATAGGA 57.102 37.037 0.00 0.00 0.00 2.94
838 4241 9.679661 ACTGATACTGATACTGATACTGATAGG 57.320 37.037 0.00 0.00 0.00 2.57
850 4253 9.456147 GGTGATACTGATACTGATACTGATACT 57.544 37.037 0.00 0.00 0.00 2.12
851 4254 9.232473 TGGTGATACTGATACTGATACTGATAC 57.768 37.037 0.00 0.00 0.00 2.24
852 4255 9.232473 GTGGTGATACTGATACTGATACTGATA 57.768 37.037 0.00 0.00 0.00 2.15
853 4256 7.177568 GGTGGTGATACTGATACTGATACTGAT 59.822 40.741 0.00 0.00 0.00 2.90
854 4257 6.490381 GGTGGTGATACTGATACTGATACTGA 59.510 42.308 0.00 0.00 0.00 3.41
855 4258 6.568653 CGGTGGTGATACTGATACTGATACTG 60.569 46.154 0.00 0.00 0.00 2.74
856 4259 5.473846 CGGTGGTGATACTGATACTGATACT 59.526 44.000 0.00 0.00 0.00 2.12
857 4260 5.700846 CGGTGGTGATACTGATACTGATAC 58.299 45.833 0.00 0.00 0.00 2.24
858 4261 4.217767 GCGGTGGTGATACTGATACTGATA 59.782 45.833 0.00 0.00 0.00 2.15
859 4262 3.005897 GCGGTGGTGATACTGATACTGAT 59.994 47.826 0.00 0.00 0.00 2.90
860 4263 2.361119 GCGGTGGTGATACTGATACTGA 59.639 50.000 0.00 0.00 0.00 3.41
861 4264 2.100749 TGCGGTGGTGATACTGATACTG 59.899 50.000 0.00 0.00 0.00 2.74
862 4265 2.362397 CTGCGGTGGTGATACTGATACT 59.638 50.000 0.00 0.00 0.00 2.12
863 4266 2.743938 CTGCGGTGGTGATACTGATAC 58.256 52.381 0.00 0.00 0.00 2.24
915 4323 0.170339 GAATCGGGGTTTTGAAGCGG 59.830 55.000 0.00 0.00 0.00 5.52
916 4324 1.165270 AGAATCGGGGTTTTGAAGCG 58.835 50.000 0.00 0.00 0.00 4.68
973 4383 3.628646 CTGGGTGGGTGGCTACTGC 62.629 68.421 0.00 0.00 38.76 4.40
974 4384 2.671070 CTGGGTGGGTGGCTACTG 59.329 66.667 0.00 0.00 0.00 2.74
975 4385 3.330720 GCTGGGTGGGTGGCTACT 61.331 66.667 0.00 0.00 0.00 2.57
976 4386 4.426313 GGCTGGGTGGGTGGCTAC 62.426 72.222 0.00 0.00 0.00 3.58
997 4407 3.248266 GCTGGTTCAAGATGTTCATTGC 58.752 45.455 0.00 0.00 0.00 3.56
1302 4715 2.167219 CGCGATGGACGTCATGCTT 61.167 57.895 18.91 0.00 44.60 3.91
1597 5010 2.435586 GTCGTCGAGGTCGGAGGA 60.436 66.667 4.85 0.00 40.29 3.71
1598 5011 3.507009 GGTCGTCGAGGTCGGAGG 61.507 72.222 4.85 0.00 40.29 4.30
1654 5067 7.310858 GGAACTATATGGGTATAATTGACGGGT 60.311 40.741 0.00 0.00 0.00 5.28
1655 5068 7.046033 GGAACTATATGGGTATAATTGACGGG 58.954 42.308 0.00 0.00 0.00 5.28
1658 5088 9.216117 GTGTGGAACTATATGGGTATAATTGAC 57.784 37.037 0.00 0.00 38.04 3.18
1671 5101 6.821665 GGTATGTGTTGTGTGTGGAACTATAT 59.178 38.462 0.00 0.00 38.04 0.86
1672 5102 6.167685 GGTATGTGTTGTGTGTGGAACTATA 58.832 40.000 0.00 0.00 38.04 1.31
1787 5251 4.433615 GAACTTGCAGTCGATCCATCTTA 58.566 43.478 0.00 0.00 0.00 2.10
1811 5275 0.806884 AAAACTGTTGTCGTCGGCGA 60.807 50.000 8.66 8.66 45.79 5.54
1820 5284 5.744666 ACGTTACATAGCAAAACTGTTGT 57.255 34.783 0.00 0.00 32.63 3.32
1910 5378 2.009774 CAGCTTGTACAGTACCATGGC 58.990 52.381 13.04 7.12 0.00 4.40
1912 5380 2.674852 CTGCAGCTTGTACAGTACCATG 59.325 50.000 0.00 3.29 0.00 3.66
1943 5411 2.093869 TGTAACCCTGAACCTCGCATAC 60.094 50.000 0.00 0.00 0.00 2.39
1987 5465 1.348036 GTAGGTTTCTCACACCAGCCT 59.652 52.381 0.00 0.00 36.67 4.58
1989 5467 2.417719 CAGTAGGTTTCTCACACCAGC 58.582 52.381 0.00 0.00 36.67 4.85
1990 5468 2.037772 AGCAGTAGGTTTCTCACACCAG 59.962 50.000 0.00 0.00 36.67 4.00
1991 5469 2.037251 GAGCAGTAGGTTTCTCACACCA 59.963 50.000 0.00 0.00 36.67 4.17
1993 5471 2.613223 GGGAGCAGTAGGTTTCTCACAC 60.613 54.545 0.00 0.00 0.00 3.82
1994 5472 1.623811 GGGAGCAGTAGGTTTCTCACA 59.376 52.381 0.00 0.00 0.00 3.58
2051 5536 4.952335 GGCTCCCTCCAATCCATATTAATG 59.048 45.833 0.00 0.00 0.00 1.90
2115 5697 2.590575 ACCAACCACTTCGCACCG 60.591 61.111 0.00 0.00 0.00 4.94
2121 5703 3.256558 GGTACGTATCACCAACCACTTC 58.743 50.000 0.00 0.00 36.01 3.01
2138 5720 3.116531 GTTGCCTGCCGTCGGTAC 61.117 66.667 13.94 0.00 0.00 3.34
2226 5814 6.040955 TGACTGATCAGTGTTTGTACTCTTCT 59.959 38.462 32.50 1.82 42.66 2.85
2252 5840 0.602106 CAGTGGCACTGTCCTGTCAG 60.602 60.000 34.00 10.19 41.19 3.51
2275 5863 2.864489 GCTGCTATAAGCTCCGGTTCTC 60.864 54.545 0.00 0.00 42.97 2.87
2281 5869 2.024319 GCCGCTGCTATAAGCTCCG 61.024 63.158 0.00 3.15 42.97 4.63
2314 5908 2.123854 TCCCTGACCGATCTCCCG 60.124 66.667 0.00 0.00 0.00 5.14
2315 5909 2.491022 CGTCCCTGACCGATCTCCC 61.491 68.421 0.00 0.00 0.00 4.30
2522 6125 3.056250 TGGCACTCTCAACAATCTCTCTC 60.056 47.826 0.00 0.00 0.00 3.20
2523 6126 2.902486 TGGCACTCTCAACAATCTCTCT 59.098 45.455 0.00 0.00 0.00 3.10
2524 6127 3.325293 TGGCACTCTCAACAATCTCTC 57.675 47.619 0.00 0.00 0.00 3.20
2525 6128 3.072184 ACTTGGCACTCTCAACAATCTCT 59.928 43.478 0.00 0.00 0.00 3.10
2640 6255 3.184683 GCCTTCTGCAGCGACTCG 61.185 66.667 9.47 0.00 40.77 4.18


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

AutoCloner maintained by Alex Coulton.