Multiple sequence alignment - TraesCS7D01G436600

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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 TraesCS7D01G436600 chr7D 100.000 4754 0 0 1 4754 555197368 555192615 0.000000e+00 8780
1 TraesCS7D01G436600 chr7D 85.120 2957 414 18 891 3833 89533131 89530187 0.000000e+00 3000
2 TraesCS7D01G436600 chr7D 84.823 2965 424 16 867 3821 20442344 20445292 0.000000e+00 2959
3 TraesCS7D01G436600 chr7D 83.856 3091 452 31 692 3747 20460109 20463187 0.000000e+00 2900
4 TraesCS7D01G436600 chr7D 100.000 58 0 0 1 58 159903338 159903395 1.810000e-19 108
5 TraesCS7D01G436600 chr7B 95.461 4516 141 27 45 4502 601113510 601118019 0.000000e+00 7145
6 TraesCS7D01G436600 chr7B 88.889 207 9 1 4530 4722 601118007 601118213 4.750000e-60 243
7 TraesCS7D01G436600 chr7B 95.588 68 1 2 1 66 15955017 15954950 1.810000e-19 108
8 TraesCS7D01G436600 chr7A 95.255 3646 132 20 893 4502 640662265 640665905 0.000000e+00 5736
9 TraesCS7D01G436600 chr7A 84.870 2895 416 17 863 3747 20779416 20782298 0.000000e+00 2900
10 TraesCS7D01G436600 chr7A 96.056 786 25 6 75 856 640644496 640645279 0.000000e+00 1275
11 TraesCS7D01G436600 chr7A 86.000 150 6 1 4530 4664 640665893 640666042 3.830000e-31 147
12 TraesCS7D01G436600 chr2A 84.148 3211 463 36 654 3833 733087446 733090641 0.000000e+00 3068
13 TraesCS7D01G436600 chr2A 89.157 83 5 4 1 79 54209442 54209524 3.030000e-17 100
14 TraesCS7D01G436600 chr2D 85.240 2954 417 15 894 3838 598813993 598816936 0.000000e+00 3022
15 TraesCS7D01G436600 chr2D 98.276 58 1 0 1 58 112530447 112530504 8.420000e-18 102
16 TraesCS7D01G436600 chr2B 85.212 2901 410 16 894 3786 727685951 727688840 0.000000e+00 2963
17 TraesCS7D01G436600 chr4D 100.000 58 0 0 1 58 31175623 31175680 1.810000e-19 108
18 TraesCS7D01G436600 chr4D 100.000 58 0 0 1 58 39169804 39169747 1.810000e-19 108
19 TraesCS7D01G436600 chr4B 100.000 58 0 0 1 58 226930890 226930947 1.810000e-19 108
20 TraesCS7D01G436600 chr4A 100.000 58 0 0 1 58 716120928 716120871 1.810000e-19 108
21 TraesCS7D01G436600 chr1D 100.000 58 0 0 1 58 216034683 216034626 1.810000e-19 108


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 TraesCS7D01G436600 chr7D 555192615 555197368 4753 True 8780.0 8780 100.0000 1 4754 1 chr7D.!!$R2 4753
1 TraesCS7D01G436600 chr7D 89530187 89533131 2944 True 3000.0 3000 85.1200 891 3833 1 chr7D.!!$R1 2942
2 TraesCS7D01G436600 chr7D 20442344 20445292 2948 False 2959.0 2959 84.8230 867 3821 1 chr7D.!!$F1 2954
3 TraesCS7D01G436600 chr7D 20460109 20463187 3078 False 2900.0 2900 83.8560 692 3747 1 chr7D.!!$F2 3055
4 TraesCS7D01G436600 chr7B 601113510 601118213 4703 False 3694.0 7145 92.1750 45 4722 2 chr7B.!!$F1 4677
5 TraesCS7D01G436600 chr7A 640662265 640666042 3777 False 2941.5 5736 90.6275 893 4664 2 chr7A.!!$F3 3771
6 TraesCS7D01G436600 chr7A 20779416 20782298 2882 False 2900.0 2900 84.8700 863 3747 1 chr7A.!!$F1 2884
7 TraesCS7D01G436600 chr7A 640644496 640645279 783 False 1275.0 1275 96.0560 75 856 1 chr7A.!!$F2 781
8 TraesCS7D01G436600 chr2A 733087446 733090641 3195 False 3068.0 3068 84.1480 654 3833 1 chr2A.!!$F2 3179
9 TraesCS7D01G436600 chr2D 598813993 598816936 2943 False 3022.0 3022 85.2400 894 3838 1 chr2D.!!$F2 2944
10 TraesCS7D01G436600 chr2B 727685951 727688840 2889 False 2963.0 2963 85.2120 894 3786 1 chr2B.!!$F1 2892

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
32 33 0.035036 TCCGTGTCTCTCTGTCTCGT 59.965 55.000 0.0 0.0 0.00 4.18 F
33 34 0.875728 CCGTGTCTCTCTGTCTCGTT 59.124 55.000 0.0 0.0 0.00 3.85 F
1689 1730 0.807496 GAGAGCAATTCCAGTGCCAC 59.193 55.000 0.0 0.0 43.27 5.01 F
2101 2142 2.143925 CGGAGTTGAAGTCTTTGTCCC 58.856 52.381 0.0 0.0 0.00 4.46 F
3285 3327 1.079888 CCCGCCAAATCTGCAAACC 60.080 57.895 0.0 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 1730 1.079127 AGAAATGGAGACCCACGCG 60.079 57.895 3.53 3.53 46.98 6.01 R
1824 1865 7.955918 ACTTATGTTGCTCCAGAAATCTTTTT 58.044 30.769 0.00 0.00 0.00 1.94 R
2927 2969 3.427573 ACAACCCCACTAGGCAAATAAC 58.572 45.455 0.00 0.00 0.00 1.89 R
3738 3781 0.671781 CAGGTCAAAGCCGGAGAGTG 60.672 60.000 5.05 0.00 0.00 3.51 R
4128 4192 0.602638 ACCTCGCAAGCAATCACGAA 60.603 50.000 0.00 0.00 33.61 3.85 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
24 25 4.563524 CACGTAAAAATCCGTGTCTCTC 57.436 45.455 4.17 0.00 46.87 3.20
25 26 4.235360 CACGTAAAAATCCGTGTCTCTCT 58.765 43.478 4.17 0.00 46.87 3.10
26 27 4.090066 CACGTAAAAATCCGTGTCTCTCTG 59.910 45.833 4.17 0.00 46.87 3.35
27 28 4.235360 CGTAAAAATCCGTGTCTCTCTGT 58.765 43.478 0.00 0.00 0.00 3.41
28 29 4.323868 CGTAAAAATCCGTGTCTCTCTGTC 59.676 45.833 0.00 0.00 0.00 3.51
29 30 4.608948 AAAAATCCGTGTCTCTCTGTCT 57.391 40.909 0.00 0.00 0.00 3.41
30 31 3.859411 AAATCCGTGTCTCTCTGTCTC 57.141 47.619 0.00 0.00 0.00 3.36
31 32 1.374560 ATCCGTGTCTCTCTGTCTCG 58.625 55.000 0.00 0.00 0.00 4.04
32 33 0.035036 TCCGTGTCTCTCTGTCTCGT 59.965 55.000 0.00 0.00 0.00 4.18
33 34 0.875728 CCGTGTCTCTCTGTCTCGTT 59.124 55.000 0.00 0.00 0.00 3.85
34 35 1.267261 CCGTGTCTCTCTGTCTCGTTT 59.733 52.381 0.00 0.00 0.00 3.60
35 36 2.483106 CCGTGTCTCTCTGTCTCGTTTA 59.517 50.000 0.00 0.00 0.00 2.01
36 37 3.127203 CCGTGTCTCTCTGTCTCGTTTAT 59.873 47.826 0.00 0.00 0.00 1.40
37 38 4.379603 CCGTGTCTCTCTGTCTCGTTTATT 60.380 45.833 0.00 0.00 0.00 1.40
38 39 5.154932 CGTGTCTCTCTGTCTCGTTTATTT 58.845 41.667 0.00 0.00 0.00 1.40
39 40 5.284188 CGTGTCTCTCTGTCTCGTTTATTTC 59.716 44.000 0.00 0.00 0.00 2.17
40 41 6.383415 GTGTCTCTCTGTCTCGTTTATTTCT 58.617 40.000 0.00 0.00 0.00 2.52
41 42 6.525280 GTGTCTCTCTGTCTCGTTTATTTCTC 59.475 42.308 0.00 0.00 0.00 2.87
42 43 5.735427 GTCTCTCTGTCTCGTTTATTTCTCG 59.265 44.000 0.00 0.00 0.00 4.04
43 44 5.411977 TCTCTCTGTCTCGTTTATTTCTCGT 59.588 40.000 0.00 0.00 0.00 4.18
44 45 6.010294 TCTCTGTCTCGTTTATTTCTCGTT 57.990 37.500 0.00 0.00 0.00 3.85
45 46 7.118825 TCTCTCTGTCTCGTTTATTTCTCGTTA 59.881 37.037 0.00 0.00 0.00 3.18
46 47 7.759465 TCTCTGTCTCGTTTATTTCTCGTTAT 58.241 34.615 0.00 0.00 0.00 1.89
47 48 8.242053 TCTCTGTCTCGTTTATTTCTCGTTATT 58.758 33.333 0.00 0.00 0.00 1.40
48 49 9.499585 CTCTGTCTCGTTTATTTCTCGTTATTA 57.500 33.333 0.00 0.00 0.00 0.98
82 83 9.200817 AGGTGTACATGCCATATTAAGATTTTT 57.799 29.630 0.00 0.00 0.00 1.94
208 211 3.712016 TGCTCCCAAGTAATTGCACTA 57.288 42.857 0.00 0.00 0.00 2.74
217 220 6.404734 CCCAAGTAATTGCACTAATGAACTCC 60.405 42.308 0.00 0.00 29.96 3.85
265 268 7.093421 GCCTTCTTAGGAGTTAGGAGAACTAAA 60.093 40.741 0.00 0.00 45.05 1.85
396 400 2.421073 CACACATGACACAGCCATAAGG 59.579 50.000 0.00 0.00 38.23 2.69
437 441 7.630242 TTCCTTTGTAGCATTTCTCTATTGG 57.370 36.000 0.00 0.00 0.00 3.16
643 648 6.373216 CCTGAATGGATTGCAACATGATTTTT 59.627 34.615 0.00 0.00 38.35 1.94
880 913 6.128363 GGTTTAATGTGTGGTACTAGCAGAAC 60.128 42.308 0.00 0.00 0.00 3.01
991 1031 9.838339 CCCAACAGACAGATATTAGTAATTCTT 57.162 33.333 0.00 0.00 0.00 2.52
1113 1154 6.316390 CGAAGTATGGGAAGCAAAAAGTAGAT 59.684 38.462 0.00 0.00 0.00 1.98
1307 1348 8.685257 ATTGATCAGGAACATGATATAGGGTA 57.315 34.615 0.00 0.00 40.02 3.69
1689 1730 0.807496 GAGAGCAATTCCAGTGCCAC 59.193 55.000 0.00 0.00 43.27 5.01
1744 1785 6.142498 AGAGAAGATGTCCTGAGGAATACAT 58.858 40.000 0.96 2.92 35.34 2.29
1824 1865 3.578282 TCACATGCCTTGAAGAGACACTA 59.422 43.478 0.00 0.00 0.00 2.74
2101 2142 2.143925 CGGAGTTGAAGTCTTTGTCCC 58.856 52.381 0.00 0.00 0.00 4.46
2149 2190 4.156556 GCTTGCCTCTCATTATTGTGTCAA 59.843 41.667 0.00 0.00 0.00 3.18
2206 2247 8.884124 TGTGGAAGAATGGAGAAGAATAAATT 57.116 30.769 0.00 0.00 0.00 1.82
2499 2540 4.302559 AAGGAACTCATTTGGTAGGACC 57.697 45.455 0.00 0.00 38.49 4.46
2927 2969 9.179909 ACTGGACCTTTATAGATCAGATATACG 57.820 37.037 0.00 0.00 0.00 3.06
3285 3327 1.079888 CCCGCCAAATCTGCAAACC 60.080 57.895 0.00 0.00 0.00 3.27
3703 3745 3.222126 TTCTTGACGTTGCTGCGCG 62.222 57.895 0.00 0.00 34.88 6.86
3711 3754 3.803082 TTGCTGCGCGAATGCTCC 61.803 61.111 12.10 0.00 39.65 4.70
3728 3771 2.105128 CGCGATTCGAGGGAAGCT 59.895 61.111 10.88 0.00 41.67 3.74
3738 3781 1.001641 AGGGAAGCTGTGGCATCAC 60.002 57.895 0.00 0.00 39.57 3.06
3854 3905 7.291566 TCCTCCCTCTAATCTCACTAACTTAG 58.708 42.308 0.00 0.00 0.00 2.18
3866 3924 8.116651 TCTCACTAACTTAGGATGCTCATATC 57.883 38.462 0.00 0.00 0.00 1.63
3879 3937 6.376299 GGATGCTCATATCATGCTTCCATAAA 59.624 38.462 15.28 0.00 44.96 1.40
3910 3968 1.333931 CATGTGATGCTGGTCTCATGC 59.666 52.381 12.73 0.00 40.80 4.06
3923 3981 4.415150 CATGCAGGTCACCCGCCT 62.415 66.667 0.00 0.00 36.66 5.52
3956 4014 2.810439 TTATAATTTGGGCCGCATGC 57.190 45.000 7.91 7.91 40.16 4.06
4007 4065 6.659824 TGAGTATATCCAGTGTCTCTGTACA 58.340 40.000 0.00 0.00 42.19 2.90
4011 4069 7.780271 AGTATATCCAGTGTCTCTGTACATTCA 59.220 37.037 0.00 0.00 42.19 2.57
4014 4072 4.528206 TCCAGTGTCTCTGTACATTCATGT 59.472 41.667 0.00 0.00 42.19 3.21
4100 4158 1.000060 CCTGATGGGCACACTGTTTTG 60.000 52.381 0.00 0.00 0.00 2.44
4101 4159 0.388659 TGATGGGCACACTGTTTTGC 59.611 50.000 0.00 3.09 38.06 3.68
4102 4160 0.675633 GATGGGCACACTGTTTTGCT 59.324 50.000 0.00 0.00 38.85 3.91
4103 4161 1.885887 GATGGGCACACTGTTTTGCTA 59.114 47.619 0.00 2.48 38.85 3.49
4105 4163 1.318576 GGGCACACTGTTTTGCTACT 58.681 50.000 10.16 0.00 38.85 2.57
4106 4164 2.158740 TGGGCACACTGTTTTGCTACTA 60.159 45.455 10.16 0.00 38.85 1.82
4107 4165 2.225727 GGGCACACTGTTTTGCTACTAC 59.774 50.000 10.16 0.00 38.85 2.73
4108 4166 3.139077 GGCACACTGTTTTGCTACTACT 58.861 45.455 10.16 0.00 38.85 2.57
4109 4167 3.058914 GGCACACTGTTTTGCTACTACTG 60.059 47.826 10.16 0.00 38.85 2.74
4128 4192 3.134081 ACTGTGCCTGTGTTTACTACTGT 59.866 43.478 0.00 0.00 0.00 3.55
4130 4194 4.124238 TGTGCCTGTGTTTACTACTGTTC 58.876 43.478 0.00 0.00 0.00 3.18
4142 4228 2.480419 ACTACTGTTCGTGATTGCTTGC 59.520 45.455 0.00 0.00 0.00 4.01
4236 4329 6.128929 CGAGTGAGTTGTGTTTTCATATTCGA 60.129 38.462 0.00 0.00 30.63 3.71
4261 4354 9.846248 GAACTAATTTTTGCAGTACATGATTCT 57.154 29.630 0.00 0.00 0.00 2.40
4371 4464 1.228552 AGAGCCCGGCACAATTTGT 60.229 52.632 13.15 0.00 0.00 2.83
4443 4537 9.849166 TTACTGGCTTTAATTAGTTATTGTTGC 57.151 29.630 0.00 0.00 0.00 4.17
4476 4570 3.217626 GCTAATGGGTGGATCCTTGAAG 58.782 50.000 14.23 2.81 36.25 3.02
4496 4590 3.543680 GTGGTATCAGCACATGTACCT 57.456 47.619 13.10 3.95 45.26 3.08
4497 4591 3.198068 GTGGTATCAGCACATGTACCTG 58.802 50.000 15.88 15.88 45.26 4.00
4498 4592 2.837591 TGGTATCAGCACATGTACCTGT 59.162 45.455 19.38 0.00 36.91 4.00
4499 4593 3.263170 TGGTATCAGCACATGTACCTGTT 59.737 43.478 19.38 15.42 36.91 3.16
4500 4594 4.261801 GGTATCAGCACATGTACCTGTTT 58.738 43.478 19.38 13.29 34.92 2.83
4501 4595 4.700213 GGTATCAGCACATGTACCTGTTTT 59.300 41.667 19.38 11.60 34.92 2.43
4502 4596 5.878116 GGTATCAGCACATGTACCTGTTTTA 59.122 40.000 19.38 10.92 34.92 1.52
4503 4597 6.542370 GGTATCAGCACATGTACCTGTTTTAT 59.458 38.462 19.38 11.52 34.92 1.40
4504 4598 7.067008 GGTATCAGCACATGTACCTGTTTTATT 59.933 37.037 19.38 7.10 34.92 1.40
4505 4599 6.892658 TCAGCACATGTACCTGTTTTATTT 57.107 33.333 19.38 0.00 0.00 1.40
4506 4600 7.283625 TCAGCACATGTACCTGTTTTATTTT 57.716 32.000 19.38 0.00 0.00 1.82
4507 4601 7.721402 TCAGCACATGTACCTGTTTTATTTTT 58.279 30.769 19.38 0.00 0.00 1.94
4653 4762 7.765307 ACAATATATTTTGGAGTGCTGAGTTG 58.235 34.615 10.17 0.00 0.00 3.16
4669 4778 0.243636 GTTGGAAACGAAGGGCCATG 59.756 55.000 6.18 0.00 36.92 3.66
4682 4791 4.584327 AGGGCCATGAATAATTTTACGC 57.416 40.909 6.18 0.00 0.00 4.42
4694 4803 8.579600 TGAATAATTTTACGCGTTTGCTATTTG 58.420 29.630 20.78 0.00 39.65 2.32
4722 4831 3.441500 TGCCTCAGTCTCTAGTTCAGA 57.558 47.619 0.00 0.00 0.00 3.27
4723 4832 3.085533 TGCCTCAGTCTCTAGTTCAGAC 58.914 50.000 2.54 2.54 40.67 3.51
4724 4833 2.096819 GCCTCAGTCTCTAGTTCAGACG 59.903 54.545 4.83 1.76 44.40 4.18
4725 4834 2.680841 CCTCAGTCTCTAGTTCAGACGG 59.319 54.545 4.83 4.66 44.40 4.79
4726 4835 2.680841 CTCAGTCTCTAGTTCAGACGGG 59.319 54.545 9.33 5.06 44.40 5.28
4727 4836 2.305052 TCAGTCTCTAGTTCAGACGGGA 59.695 50.000 9.33 6.79 44.40 5.14
4728 4837 3.054287 TCAGTCTCTAGTTCAGACGGGAT 60.054 47.826 9.33 0.00 44.40 3.85
4729 4838 3.066064 CAGTCTCTAGTTCAGACGGGATG 59.934 52.174 4.83 0.00 44.40 3.51
4730 4839 2.025155 TCTCTAGTTCAGACGGGATGC 58.975 52.381 0.00 0.00 0.00 3.91
4731 4840 0.738975 TCTAGTTCAGACGGGATGCG 59.261 55.000 0.00 0.00 0.00 4.73
4732 4841 0.872021 CTAGTTCAGACGGGATGCGC 60.872 60.000 0.00 0.00 0.00 6.09
4733 4842 1.320344 TAGTTCAGACGGGATGCGCT 61.320 55.000 9.73 0.00 0.00 5.92
4734 4843 2.125552 TTCAGACGGGATGCGCTG 60.126 61.111 9.73 0.00 0.00 5.18
4735 4844 4.819761 TCAGACGGGATGCGCTGC 62.820 66.667 9.73 0.00 0.00 5.25
4736 4845 4.827087 CAGACGGGATGCGCTGCT 62.827 66.667 9.73 0.00 0.00 4.24
4737 4846 4.521062 AGACGGGATGCGCTGCTC 62.521 66.667 9.73 2.52 0.00 4.26
4738 4847 4.521062 GACGGGATGCGCTGCTCT 62.521 66.667 9.73 0.00 0.00 4.09
4739 4848 4.087892 ACGGGATGCGCTGCTCTT 62.088 61.111 9.73 0.00 0.00 2.85
4740 4849 3.267860 CGGGATGCGCTGCTCTTC 61.268 66.667 9.73 0.00 0.00 2.87
4741 4850 2.124983 GGGATGCGCTGCTCTTCA 60.125 61.111 9.73 0.00 0.00 3.02
4742 4851 1.746615 GGGATGCGCTGCTCTTCAA 60.747 57.895 9.73 0.00 0.00 2.69
4743 4852 1.308069 GGGATGCGCTGCTCTTCAAA 61.308 55.000 9.73 0.00 0.00 2.69
4744 4853 0.737219 GGATGCGCTGCTCTTCAAAT 59.263 50.000 9.73 0.00 0.00 2.32
4745 4854 1.133790 GGATGCGCTGCTCTTCAAATT 59.866 47.619 9.73 0.00 0.00 1.82
4746 4855 2.355756 GGATGCGCTGCTCTTCAAATTA 59.644 45.455 9.73 0.00 0.00 1.40
4747 4856 3.004106 GGATGCGCTGCTCTTCAAATTAT 59.996 43.478 9.73 0.00 0.00 1.28
4748 4857 3.680642 TGCGCTGCTCTTCAAATTATC 57.319 42.857 9.73 0.00 0.00 1.75
4749 4858 2.030823 TGCGCTGCTCTTCAAATTATCG 59.969 45.455 9.73 0.00 0.00 2.92
4750 4859 2.285220 GCGCTGCTCTTCAAATTATCGA 59.715 45.455 0.00 0.00 0.00 3.59
4751 4860 3.242413 GCGCTGCTCTTCAAATTATCGAA 60.242 43.478 0.00 0.00 0.00 3.71
4752 4861 4.266945 CGCTGCTCTTCAAATTATCGAAC 58.733 43.478 0.00 0.00 0.00 3.95
4753 4862 4.201714 CGCTGCTCTTCAAATTATCGAACA 60.202 41.667 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.471257 AGACAGAGAGACACGGATTTTTAC 58.529 41.667 0.00 0.00 0.00 2.01
7 8 5.619309 CGAGACAGAGAGACACGGATTTTTA 60.619 44.000 0.00 0.00 0.00 1.52
8 9 4.561105 GAGACAGAGAGACACGGATTTTT 58.439 43.478 0.00 0.00 0.00 1.94
9 10 3.366476 CGAGACAGAGAGACACGGATTTT 60.366 47.826 0.00 0.00 0.00 1.82
10 11 2.162608 CGAGACAGAGAGACACGGATTT 59.837 50.000 0.00 0.00 0.00 2.17
11 12 1.740585 CGAGACAGAGAGACACGGATT 59.259 52.381 0.00 0.00 0.00 3.01
12 13 1.339247 ACGAGACAGAGAGACACGGAT 60.339 52.381 0.00 0.00 31.44 4.18
13 14 0.035036 ACGAGACAGAGAGACACGGA 59.965 55.000 0.00 0.00 31.44 4.69
14 15 0.875728 AACGAGACAGAGAGACACGG 59.124 55.000 0.00 0.00 31.44 4.94
15 16 2.690173 AAACGAGACAGAGAGACACG 57.310 50.000 0.00 0.00 33.10 4.49
16 17 6.383415 AGAAATAAACGAGACAGAGAGACAC 58.617 40.000 0.00 0.00 0.00 3.67
17 18 6.576662 AGAAATAAACGAGACAGAGAGACA 57.423 37.500 0.00 0.00 0.00 3.41
18 19 5.735427 CGAGAAATAAACGAGACAGAGAGAC 59.265 44.000 0.00 0.00 0.00 3.36
19 20 5.411977 ACGAGAAATAAACGAGACAGAGAGA 59.588 40.000 0.00 0.00 0.00 3.10
20 21 5.632959 ACGAGAAATAAACGAGACAGAGAG 58.367 41.667 0.00 0.00 0.00 3.20
21 22 5.624344 ACGAGAAATAAACGAGACAGAGA 57.376 39.130 0.00 0.00 0.00 3.10
22 23 7.972623 ATAACGAGAAATAAACGAGACAGAG 57.027 36.000 0.00 0.00 0.00 3.35
35 36 9.886132 ACACCTTGTTAGATAATAACGAGAAAT 57.114 29.630 14.03 0.80 39.93 2.17
37 38 9.793252 GTACACCTTGTTAGATAATAACGAGAA 57.207 33.333 14.03 0.00 39.93 2.87
38 39 8.959548 TGTACACCTTGTTAGATAATAACGAGA 58.040 33.333 14.03 0.00 39.93 4.04
39 40 9.745880 ATGTACACCTTGTTAGATAATAACGAG 57.254 33.333 0.00 7.70 38.21 4.18
40 41 9.524106 CATGTACACCTTGTTAGATAATAACGA 57.476 33.333 0.00 0.00 0.00 3.85
41 42 8.273557 GCATGTACACCTTGTTAGATAATAACG 58.726 37.037 0.00 0.00 0.00 3.18
42 43 8.557029 GGCATGTACACCTTGTTAGATAATAAC 58.443 37.037 0.00 0.00 0.00 1.89
43 44 8.268605 TGGCATGTACACCTTGTTAGATAATAA 58.731 33.333 0.00 0.00 0.00 1.40
44 45 7.797062 TGGCATGTACACCTTGTTAGATAATA 58.203 34.615 0.00 0.00 0.00 0.98
45 46 6.658849 TGGCATGTACACCTTGTTAGATAAT 58.341 36.000 0.00 0.00 0.00 1.28
46 47 6.056090 TGGCATGTACACCTTGTTAGATAA 57.944 37.500 0.00 0.00 0.00 1.75
47 48 5.685520 TGGCATGTACACCTTGTTAGATA 57.314 39.130 0.00 0.00 0.00 1.98
48 49 4.568072 TGGCATGTACACCTTGTTAGAT 57.432 40.909 0.00 0.00 0.00 1.98
49 50 4.568072 ATGGCATGTACACCTTGTTAGA 57.432 40.909 0.00 0.00 0.00 2.10
50 51 6.942532 AATATGGCATGTACACCTTGTTAG 57.057 37.500 10.98 0.00 0.00 2.34
51 52 8.268605 TCTTAATATGGCATGTACACCTTGTTA 58.731 33.333 10.98 1.01 0.00 2.41
52 53 7.116075 TCTTAATATGGCATGTACACCTTGTT 58.884 34.615 10.98 1.96 0.00 2.83
53 54 6.658849 TCTTAATATGGCATGTACACCTTGT 58.341 36.000 10.98 0.00 0.00 3.16
82 83 6.039941 ACACCTGATTTTCACATAACGGAAAA 59.960 34.615 0.00 0.00 44.36 2.29
87 88 6.238374 GGGATACACCTGATTTTCACATAACG 60.238 42.308 0.00 0.00 38.98 3.18
99 100 2.022035 TCAAGGAGGGGATACACCTGAT 60.022 50.000 0.00 0.00 46.76 2.90
100 101 1.364678 TCAAGGAGGGGATACACCTGA 59.635 52.381 0.00 0.00 46.76 3.86
101 102 1.879575 TCAAGGAGGGGATACACCTG 58.120 55.000 0.00 0.00 46.76 4.00
102 103 2.661176 TTCAAGGAGGGGATACACCT 57.339 50.000 0.00 0.00 46.76 4.00
103 104 2.576648 ACTTTCAAGGAGGGGATACACC 59.423 50.000 0.00 0.00 46.76 4.16
208 211 7.394641 GGAGTTCCTTTCTTTATGGAGTTCATT 59.605 37.037 0.00 0.00 37.30 2.57
217 220 5.336770 GGCTTTGGGAGTTCCTTTCTTTATG 60.337 44.000 0.00 0.00 36.20 1.90
280 283 1.623811 GCCCAGGAGTCACTCTACAAA 59.376 52.381 4.40 0.00 0.00 2.83
345 349 4.005650 TGCACTTGAATCTGAGGAACATC 58.994 43.478 0.00 0.00 0.00 3.06
396 400 7.602753 ACAAAGGAAGCACATTTTTATCCTAC 58.397 34.615 0.00 0.00 36.31 3.18
437 441 5.102313 GCTTTGGGTAATGAACATGCTTAC 58.898 41.667 0.00 0.00 0.00 2.34
643 648 6.017109 GCTGACAAGAACAAGTTTCAGGATTA 60.017 38.462 11.96 0.00 32.72 1.75
859 868 4.740268 CGTTCTGCTAGTACCACACATTA 58.260 43.478 0.00 0.00 0.00 1.90
880 913 5.743467 TGTATTAATTAAACCATCAGCGCG 58.257 37.500 0.00 0.00 0.00 6.86
883 916 8.850156 AGGTGATGTATTAATTAAACCATCAGC 58.150 33.333 33.57 33.57 44.40 4.26
991 1031 6.353323 TCACAATCTCCGCCATTATTTTCTA 58.647 36.000 0.00 0.00 0.00 2.10
1113 1154 1.616327 ACCCATGCTGCCCTGTAGA 60.616 57.895 0.00 0.00 0.00 2.59
1605 1646 1.651240 CTCCCATTCCAAGCAGTGCG 61.651 60.000 10.00 0.00 0.00 5.34
1689 1730 1.079127 AGAAATGGAGACCCACGCG 60.079 57.895 3.53 3.53 46.98 6.01
1744 1785 7.992008 ACGTTATCTTTGAAAAGTTCCTTGAA 58.008 30.769 2.88 0.00 37.31 2.69
1824 1865 7.955918 ACTTATGTTGCTCCAGAAATCTTTTT 58.044 30.769 0.00 0.00 0.00 1.94
2101 2142 4.661993 TGCACTTGCTAACTATTTCGTG 57.338 40.909 2.33 0.00 42.66 4.35
2149 2190 2.151202 CACACGCAAGAGGTTACCAAT 58.849 47.619 3.51 0.00 43.62 3.16
2499 2540 9.967346 AAGATATCATGCATTCTCAATTTCTTG 57.033 29.630 5.32 0.00 0.00 3.02
2927 2969 3.427573 ACAACCCCACTAGGCAAATAAC 58.572 45.455 0.00 0.00 0.00 1.89
2954 2996 5.563842 CAAATAAGTGCCTAAGCTTCTTCG 58.436 41.667 0.00 0.00 40.80 3.79
3711 3754 2.105128 AGCTTCCCTCGAATCGCG 59.895 61.111 0.00 0.00 42.69 5.87
3738 3781 0.671781 CAGGTCAAAGCCGGAGAGTG 60.672 60.000 5.05 0.00 0.00 3.51
3854 3905 3.682696 TGGAAGCATGATATGAGCATCC 58.317 45.455 0.00 0.00 44.13 3.51
3888 3946 3.275999 CATGAGACCAGCATCACATGAA 58.724 45.455 13.91 0.00 45.31 2.57
3923 3981 7.417797 GCCCAAATTATAAAGCATCTTCCTTCA 60.418 37.037 0.00 0.00 0.00 3.02
3956 4014 5.052481 TGAGATTCATTGACGCCTTATCAG 58.948 41.667 0.00 0.00 0.00 2.90
4100 4158 2.457366 AACACAGGCACAGTAGTAGC 57.543 50.000 0.00 0.00 0.00 3.58
4101 4159 5.135508 AGTAAACACAGGCACAGTAGTAG 57.864 43.478 0.00 0.00 0.00 2.57
4102 4160 5.771666 AGTAGTAAACACAGGCACAGTAGTA 59.228 40.000 0.00 0.00 0.00 1.82
4103 4161 4.587684 AGTAGTAAACACAGGCACAGTAGT 59.412 41.667 0.00 0.00 0.00 2.73
4105 4163 4.342951 ACAGTAGTAAACACAGGCACAGTA 59.657 41.667 0.00 0.00 0.00 2.74
4106 4164 3.134081 ACAGTAGTAAACACAGGCACAGT 59.866 43.478 0.00 0.00 0.00 3.55
4107 4165 3.728845 ACAGTAGTAAACACAGGCACAG 58.271 45.455 0.00 0.00 0.00 3.66
4108 4166 3.830744 ACAGTAGTAAACACAGGCACA 57.169 42.857 0.00 0.00 0.00 4.57
4109 4167 3.183775 CGAACAGTAGTAAACACAGGCAC 59.816 47.826 0.00 0.00 0.00 5.01
4128 4192 0.602638 ACCTCGCAAGCAATCACGAA 60.603 50.000 0.00 0.00 33.61 3.85
4130 4194 1.133253 CACCTCGCAAGCAATCACG 59.867 57.895 0.00 0.00 37.18 4.35
4142 4228 5.348724 CCCAAATCGATATTATCACACCTCG 59.651 44.000 0.00 0.00 0.00 4.63
4334 4427 3.093057 TCTCCTTGAGCCTTCTGTCTAC 58.907 50.000 0.00 0.00 0.00 2.59
4371 4464 6.394809 TGTCTCAGCGTTATGAATCACTAAA 58.605 36.000 0.00 0.00 0.00 1.85
4443 4537 3.127548 CACCCATTAGCAGCAAGTTACAG 59.872 47.826 0.00 0.00 0.00 2.74
4476 4570 3.198068 CAGGTACATGTGCTGATACCAC 58.802 50.000 13.86 0.00 39.72 4.16
4517 4611 5.446143 AACAGACACATATTCCGCAAAAA 57.554 34.783 0.00 0.00 0.00 1.94
4518 4612 5.446143 AAACAGACACATATTCCGCAAAA 57.554 34.783 0.00 0.00 0.00 2.44
4519 4613 5.240623 AGAAAACAGACACATATTCCGCAAA 59.759 36.000 0.00 0.00 0.00 3.68
4520 4614 4.759693 AGAAAACAGACACATATTCCGCAA 59.240 37.500 0.00 0.00 0.00 4.85
4521 4615 4.323417 AGAAAACAGACACATATTCCGCA 58.677 39.130 0.00 0.00 0.00 5.69
4522 4616 4.946784 AGAAAACAGACACATATTCCGC 57.053 40.909 0.00 0.00 0.00 5.54
4523 4617 7.596749 AGTTAGAAAACAGACACATATTCCG 57.403 36.000 0.00 0.00 38.12 4.30
4524 4618 8.604890 GCTAGTTAGAAAACAGACACATATTCC 58.395 37.037 0.00 0.00 38.12 3.01
4525 4619 8.604890 GGCTAGTTAGAAAACAGACACATATTC 58.395 37.037 0.00 0.00 38.12 1.75
4526 4620 8.322091 AGGCTAGTTAGAAAACAGACACATATT 58.678 33.333 0.00 0.00 38.12 1.28
4527 4621 7.852263 AGGCTAGTTAGAAAACAGACACATAT 58.148 34.615 0.00 0.00 38.12 1.78
4528 4622 7.241042 AGGCTAGTTAGAAAACAGACACATA 57.759 36.000 0.00 0.00 38.12 2.29
4534 4628 6.267928 AGACAGAAGGCTAGTTAGAAAACAGA 59.732 38.462 0.00 0.00 38.12 3.41
4653 4762 1.474330 ATTCATGGCCCTTCGTTTCC 58.526 50.000 0.00 0.00 0.00 3.13
4658 4767 5.212194 CGTAAAATTATTCATGGCCCTTCG 58.788 41.667 0.00 0.00 0.00 3.79
4669 4778 8.580431 ACAAATAGCAAACGCGTAAAATTATTC 58.420 29.630 14.46 0.00 0.00 1.75
4682 4791 4.381566 GGCAACTTGTACAAATAGCAAACG 59.618 41.667 20.48 6.26 0.00 3.60
4722 4831 4.087892 AAGAGCAGCGCATCCCGT 62.088 61.111 11.47 0.00 39.71 5.28
4723 4832 3.267860 GAAGAGCAGCGCATCCCG 61.268 66.667 11.47 0.00 40.75 5.14
4724 4833 1.308069 TTTGAAGAGCAGCGCATCCC 61.308 55.000 11.47 0.00 0.00 3.85
4725 4834 0.737219 ATTTGAAGAGCAGCGCATCC 59.263 50.000 11.47 0.00 0.00 3.51
4726 4835 2.556534 AATTTGAAGAGCAGCGCATC 57.443 45.000 11.47 4.44 0.00 3.91
4727 4836 3.303593 CGATAATTTGAAGAGCAGCGCAT 60.304 43.478 11.47 0.00 0.00 4.73
4728 4837 2.030823 CGATAATTTGAAGAGCAGCGCA 59.969 45.455 11.47 0.00 0.00 6.09
4729 4838 2.285220 TCGATAATTTGAAGAGCAGCGC 59.715 45.455 0.00 0.00 0.00 5.92
4730 4839 4.201714 TGTTCGATAATTTGAAGAGCAGCG 60.202 41.667 0.00 0.00 0.00 5.18
4731 4840 5.221891 TGTTCGATAATTTGAAGAGCAGC 57.778 39.130 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.