Multiple sequence alignment - TraesCS4D01G127500

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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 TraesCS4D01G127500 chr4D 100.000 5455 0 0 1 5455 111939194 111944648 0.000000e+00 10074.0
1 TraesCS4D01G127500 chr4D 92.857 56 1 2 1773 1828 121077002 121076950 1.630000e-10 78.7
2 TraesCS4D01G127500 chr4A 94.273 2043 65 21 51 2057 465408370 465406344 0.000000e+00 3077.0
3 TraesCS4D01G127500 chr4A 97.482 1787 29 9 2073 3854 465406359 465404584 0.000000e+00 3037.0
4 TraesCS4D01G127500 chr4A 91.092 1392 69 22 3907 5249 465404585 465403200 0.000000e+00 1832.0
5 TraesCS4D01G127500 chr4A 94.211 190 11 0 5266 5455 465344621 465344432 1.920000e-74 291.0
6 TraesCS4D01G127500 chr4A 97.561 41 1 0 1713 1753 581757230 581757270 2.730000e-08 71.3
7 TraesCS4D01G127500 chr4B 97.165 1799 28 6 2076 3854 172509024 172510819 0.000000e+00 3018.0
8 TraesCS4D01G127500 chr4B 93.102 2015 56 21 73 2059 172507079 172509038 0.000000e+00 2874.0
9 TraesCS4D01G127500 chr4B 94.607 853 25 6 3907 4753 172510818 172511655 0.000000e+00 1301.0
10 TraesCS4D01G127500 chr4B 94.241 191 10 1 5266 5455 172517395 172517585 1.920000e-74 291.0
11 TraesCS4D01G127500 chr4B 83.708 178 14 8 4741 4903 172514105 172514282 2.630000e-33 154.0
12 TraesCS4D01G127500 chr4B 82.051 195 18 7 4876 5054 172517012 172517205 3.400000e-32 150.0
13 TraesCS4D01G127500 chr4B 94.643 56 3 0 1 56 172507026 172507081 2.710000e-13 87.9
14 TraesCS4D01G127500 chr4B 90.769 65 1 4 1767 1829 578509610 578509671 1.260000e-11 82.4
15 TraesCS4D01G127500 chr4B 90.769 65 1 4 1767 1829 578518771 578518832 1.260000e-11 82.4
16 TraesCS4D01G127500 chr5D 78.313 415 57 19 5059 5449 511451231 511451636 2.540000e-58 237.0
17 TraesCS4D01G127500 chr5D 82.963 135 17 3 5059 5192 511450655 511450784 3.450000e-22 117.0
18 TraesCS4D01G127500 chr5D 93.750 48 3 0 1706 1753 9467007 9467054 7.580000e-09 73.1
19 TraesCS4D01G127500 chr5D 85.915 71 6 4 1742 1811 411995003 411995070 7.580000e-09 73.1
20 TraesCS4D01G127500 chr5A 74.138 232 52 8 1706 1931 7599615 7599844 7.530000e-14 89.8
21 TraesCS4D01G127500 chr2B 90.909 66 6 0 1706 1771 583411881 583411816 7.530000e-14 89.8
22 TraesCS4D01G127500 chr7A 96.154 52 1 1 1760 1811 63057078 63057128 3.500000e-12 84.2
23 TraesCS4D01G127500 chr7A 85.507 69 10 0 1969 2037 227997088 227997020 7.580000e-09 73.1
24 TraesCS4D01G127500 chr7B 86.301 73 7 2 1765 1835 530676601 530676672 5.860000e-10 76.8
25 TraesCS4D01G127500 chr3B 85.897 78 4 6 1734 1811 324235550 324235480 5.860000e-10 76.8
26 TraesCS4D01G127500 chr3B 97.436 39 1 0 1733 1771 633130299 633130337 3.530000e-07 67.6
27 TraesCS4D01G127500 chr1A 87.692 65 8 0 1707 1771 547563096 547563160 5.860000e-10 76.8


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 TraesCS4D01G127500 chr4D 111939194 111944648 5454 False 10074.000000 10074 100.000000 1 5455 1 chr4D.!!$F1 5454
1 TraesCS4D01G127500 chr4A 465403200 465408370 5170 True 2648.666667 3077 94.282333 51 5249 3 chr4A.!!$R2 5198
2 TraesCS4D01G127500 chr4B 172507026 172517585 10559 False 1125.128571 3018 91.359571 1 5455 7 chr4B.!!$F3 5454

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
317 322 0.391263 ACCTCGGCGAAAAGGATGTC 60.391 55.000 19.08 0.0 36.46 3.06 F
679 691 0.546122 ATTAAGCCATCAGCCCGTCA 59.454 50.000 0.00 0.0 45.47 4.35 F
1130 1151 0.632294 GTAGAGGAGGAGGTGGAGGT 59.368 60.000 0.00 0.0 0.00 3.85 F
1172 1193 1.288335 GGAAGTGGAGGAGGTAGAGGA 59.712 57.143 0.00 0.0 0.00 3.71 F
2949 2996 1.776667 TGGGCAGATCCTAAGAATGGG 59.223 52.381 0.00 0.0 34.39 4.00 F
4053 4119 1.704628 TCTTTCTTGGCACAGGATGGA 59.295 47.619 0.00 0.0 45.92 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1171 1192 0.336737 TCAGGGTCTTCCTCCTCCTC 59.663 60.000 0.00 0.00 46.12 3.71 R
2581 2628 1.003696 AGCTTGTTCTTAGCCTGGGAC 59.996 52.381 0.00 0.00 39.47 4.46 R
2734 2781 2.613506 GGGTGCACGGTGTAGTTGC 61.614 63.158 11.45 0.00 0.00 4.17 R
2973 3020 3.499918 CAGATGTTTCAGGAACCTGTGAC 59.500 47.826 18.60 17.17 43.96 3.67 R
4322 4390 0.602562 CACCATGGCGACCAATTTGT 59.397 50.000 13.04 0.00 36.95 2.83 R
5321 10692 0.173255 GGATTGGTCCAACAATGCCG 59.827 55.000 6.41 0.00 44.42 5.69 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
23 24 4.574828 GCTGACAAGACAAAGGTAAACTCA 59.425 41.667 0.00 0.00 0.00 3.41
26 27 3.875134 ACAAGACAAAGGTAAACTCACCG 59.125 43.478 0.00 0.00 43.84 4.94
134 136 3.869866 CGATTCGGTCGCGATTTTT 57.130 47.368 14.06 0.00 44.33 1.94
248 253 1.878775 CTTGGGCTTTCTGCTTCGG 59.121 57.895 0.00 0.00 42.39 4.30
275 280 1.594331 AGTTGTGTTTCTCCGGCTTC 58.406 50.000 0.00 0.00 0.00 3.86
302 307 3.065575 CCGTAGTGGCATGAACCTC 57.934 57.895 0.00 0.00 0.00 3.85
317 322 0.391263 ACCTCGGCGAAAAGGATGTC 60.391 55.000 19.08 0.00 36.46 3.06
358 363 7.517320 TGCTTTATCCAATCTGTATGTATGGT 58.483 34.615 0.00 0.00 32.90 3.55
521 533 3.326297 AGATTCTTACCTAGCTCCATGCC 59.674 47.826 0.00 0.00 44.23 4.40
679 691 0.546122 ATTAAGCCATCAGCCCGTCA 59.454 50.000 0.00 0.00 45.47 4.35
785 797 4.271807 TGAGAACCTCCCTGTATCATCT 57.728 45.455 0.00 0.00 0.00 2.90
861 873 2.175878 GCACCTATGGCTACATCCAG 57.824 55.000 0.00 0.00 39.89 3.86
942 954 1.004745 TGTCCTCAATTTGCTCTCCCC 59.995 52.381 0.00 0.00 0.00 4.81
1020 1032 1.919240 TGCCTAGACGGACAGAAGAA 58.081 50.000 0.00 0.00 33.16 2.52
1130 1151 0.632294 GTAGAGGAGGAGGTGGAGGT 59.368 60.000 0.00 0.00 0.00 3.85
1171 1192 1.289530 AGGAAGTGGAGGAGGTAGAGG 59.710 57.143 0.00 0.00 0.00 3.69
1172 1193 1.288335 GGAAGTGGAGGAGGTAGAGGA 59.712 57.143 0.00 0.00 0.00 3.71
1173 1194 2.661718 GAAGTGGAGGAGGTAGAGGAG 58.338 57.143 0.00 0.00 0.00 3.69
1465 1486 6.374333 TCTTAGGGTTAGCATTTCAATGTGTC 59.626 38.462 1.59 0.00 38.65 3.67
1898 1944 1.813513 GCGCTAGCATGGATATTGGT 58.186 50.000 16.45 0.00 44.35 3.67
2067 2113 9.507329 AAGTAAATTAGATCAGAGCTTGTCAAA 57.493 29.630 0.00 0.00 0.00 2.69
2068 2114 9.507329 AGTAAATTAGATCAGAGCTTGTCAAAA 57.493 29.630 0.00 0.00 0.00 2.44
2226 2272 7.578310 TTACACGCTTATCTTATGTACTCCT 57.422 36.000 0.00 0.00 0.00 3.69
2342 2389 8.822105 CACTTGAAAACTAAGTGTACTGTTTC 57.178 34.615 9.14 0.00 46.13 2.78
2550 2597 6.064846 ACTTAACTTTGTCATGTGCTTCTG 57.935 37.500 0.00 0.00 0.00 3.02
2741 2788 5.857822 AACTTGAATAGTTCCGCAACTAC 57.142 39.130 0.00 0.00 45.90 2.73
2754 2801 2.144738 AACTACACCGTGCACCCCT 61.145 57.895 12.15 0.00 0.00 4.79
2755 2802 2.047274 CTACACCGTGCACCCCTG 60.047 66.667 12.15 6.39 0.00 4.45
2949 2996 1.776667 TGGGCAGATCCTAAGAATGGG 59.223 52.381 0.00 0.00 34.39 4.00
3792 3858 5.914898 ATTTTCCTGAAAACCCGATAAGG 57.085 39.130 7.18 0.00 42.32 2.69
3812 3878 5.269505 AGGTACTCTTATTAGCTGCTGTG 57.730 43.478 13.43 0.00 0.00 3.66
3855 3921 6.615264 CTGCATCAGACTGCTGTTATTATT 57.385 37.500 8.04 0.00 42.75 1.40
3856 3922 6.367686 TGCATCAGACTGCTGTTATTATTG 57.632 37.500 8.04 0.00 42.75 1.90
3857 3923 5.882000 TGCATCAGACTGCTGTTATTATTGT 59.118 36.000 8.04 0.00 42.75 2.71
3858 3924 6.183360 TGCATCAGACTGCTGTTATTATTGTG 60.183 38.462 8.04 0.00 42.75 3.33
3859 3925 6.037500 GCATCAGACTGCTGTTATTATTGTGA 59.962 38.462 8.04 0.00 42.84 3.58
3860 3926 6.968131 TCAGACTGCTGTTATTATTGTGAC 57.032 37.500 0.00 0.00 42.84 3.67
3861 3927 5.576774 TCAGACTGCTGTTATTATTGTGACG 59.423 40.000 0.00 0.00 42.84 4.35
3862 3928 5.348724 CAGACTGCTGTTATTATTGTGACGT 59.651 40.000 0.00 0.00 37.37 4.34
3863 3929 5.348724 AGACTGCTGTTATTATTGTGACGTG 59.651 40.000 0.00 0.00 0.00 4.49
3864 3930 4.994852 ACTGCTGTTATTATTGTGACGTGT 59.005 37.500 0.00 0.00 0.00 4.49
3865 3931 5.468746 ACTGCTGTTATTATTGTGACGTGTT 59.531 36.000 0.00 0.00 0.00 3.32
3866 3932 6.647481 ACTGCTGTTATTATTGTGACGTGTTA 59.353 34.615 0.00 0.00 0.00 2.41
3867 3933 7.056002 TGCTGTTATTATTGTGACGTGTTAG 57.944 36.000 0.00 0.00 0.00 2.34
3868 3934 6.647481 TGCTGTTATTATTGTGACGTGTTAGT 59.353 34.615 0.00 0.00 0.00 2.24
3869 3935 7.171848 TGCTGTTATTATTGTGACGTGTTAGTT 59.828 33.333 0.00 0.00 0.00 2.24
3870 3936 8.013378 GCTGTTATTATTGTGACGTGTTAGTTT 58.987 33.333 0.00 0.00 0.00 2.66
3874 3940 9.976255 TTATTATTGTGACGTGTTAGTTTATGC 57.024 29.630 0.00 0.00 0.00 3.14
3875 3941 5.933187 ATTGTGACGTGTTAGTTTATGCA 57.067 34.783 0.00 0.00 0.00 3.96
3876 3942 5.736486 TTGTGACGTGTTAGTTTATGCAA 57.264 34.783 0.00 0.00 0.00 4.08
3877 3943 5.337219 TGTGACGTGTTAGTTTATGCAAG 57.663 39.130 0.00 0.00 0.00 4.01
3878 3944 4.812091 TGTGACGTGTTAGTTTATGCAAGT 59.188 37.500 0.00 0.00 0.00 3.16
3879 3945 5.050634 TGTGACGTGTTAGTTTATGCAAGTC 60.051 40.000 0.00 0.00 39.53 3.01
3880 3946 4.449743 TGACGTGTTAGTTTATGCAAGTCC 59.550 41.667 0.00 0.00 38.77 3.85
3881 3947 4.638304 ACGTGTTAGTTTATGCAAGTCCT 58.362 39.130 0.00 0.00 0.00 3.85
3882 3948 4.451096 ACGTGTTAGTTTATGCAAGTCCTG 59.549 41.667 0.00 0.00 0.00 3.86
3883 3949 4.451096 CGTGTTAGTTTATGCAAGTCCTGT 59.549 41.667 0.00 0.00 0.00 4.00
3884 3950 5.614668 CGTGTTAGTTTATGCAAGTCCTGTG 60.615 44.000 0.00 0.00 0.00 3.66
3885 3951 5.468746 GTGTTAGTTTATGCAAGTCCTGTGA 59.531 40.000 0.00 0.00 0.00 3.58
3886 3952 6.017440 GTGTTAGTTTATGCAAGTCCTGTGAA 60.017 38.462 0.00 0.00 0.00 3.18
3887 3953 6.544197 TGTTAGTTTATGCAAGTCCTGTGAAA 59.456 34.615 0.00 0.00 0.00 2.69
3888 3954 7.230510 TGTTAGTTTATGCAAGTCCTGTGAAAT 59.769 33.333 0.00 0.00 0.00 2.17
3889 3955 8.726988 GTTAGTTTATGCAAGTCCTGTGAAATA 58.273 33.333 0.00 0.00 0.00 1.40
3890 3956 7.759489 AGTTTATGCAAGTCCTGTGAAATAA 57.241 32.000 0.00 0.00 0.00 1.40
3891 3957 8.177119 AGTTTATGCAAGTCCTGTGAAATAAA 57.823 30.769 0.00 0.00 0.00 1.40
3892 3958 8.299570 AGTTTATGCAAGTCCTGTGAAATAAAG 58.700 33.333 0.00 0.00 0.00 1.85
3893 3959 7.994425 TTATGCAAGTCCTGTGAAATAAAGA 57.006 32.000 0.00 0.00 0.00 2.52
3894 3960 6.899393 ATGCAAGTCCTGTGAAATAAAGAA 57.101 33.333 0.00 0.00 0.00 2.52
3895 3961 6.899393 TGCAAGTCCTGTGAAATAAAGAAT 57.101 33.333 0.00 0.00 0.00 2.40
3896 3962 6.680810 TGCAAGTCCTGTGAAATAAAGAATG 58.319 36.000 0.00 0.00 0.00 2.67
3897 3963 6.265196 TGCAAGTCCTGTGAAATAAAGAATGT 59.735 34.615 0.00 0.00 0.00 2.71
3898 3964 7.446931 TGCAAGTCCTGTGAAATAAAGAATGTA 59.553 33.333 0.00 0.00 0.00 2.29
3899 3965 8.296713 GCAAGTCCTGTGAAATAAAGAATGTAA 58.703 33.333 0.00 0.00 0.00 2.41
3902 3968 9.793259 AGTCCTGTGAAATAAAGAATGTAAAGA 57.207 29.630 0.00 0.00 0.00 2.52
4002 4068 7.702785 AGTAACAAAGATATGCATGGGGATAT 58.297 34.615 10.16 0.00 40.31 1.63
4026 4092 5.576774 TCACAGAATAAACATCAGTACAGCG 59.423 40.000 0.00 0.00 0.00 5.18
4053 4119 1.704628 TCTTTCTTGGCACAGGATGGA 59.295 47.619 0.00 0.00 45.92 3.41
4060 4126 2.323599 TGGCACAGGATGGATAGAGAG 58.676 52.381 0.00 0.00 43.62 3.20
4082 4148 3.560636 ATTCCGTTTGCCTAGCTATGT 57.439 42.857 0.00 0.00 0.00 2.29
4145 4213 3.090210 TGAATGGTGCTGATGGATGTT 57.910 42.857 0.00 0.00 0.00 2.71
4331 4399 0.667993 CACAGGCACGACAAATTGGT 59.332 50.000 0.00 0.00 0.00 3.67
4523 4591 3.867493 GTGTAATAAGTACTTGTCGCCCC 59.133 47.826 18.56 0.72 33.46 5.80
4641 4716 3.680937 TGGTTTGTCTAGGCGTAATTTCG 59.319 43.478 0.00 0.00 0.00 3.46
4646 4721 4.414852 TGTCTAGGCGTAATTTCGTGTAC 58.585 43.478 6.34 0.00 0.00 2.90
4738 4817 2.831565 AGAAGAACCCAGAGCTGATCT 58.168 47.619 0.00 0.00 39.56 2.75
4754 7295 5.567552 GCTGATCTCAGAATAACAGCAAAC 58.432 41.667 11.34 0.00 46.59 2.93
4797 7338 0.381801 CCATTTACATGTCGCCCAGC 59.618 55.000 0.00 0.00 0.00 4.85
4857 7412 9.276590 CAGGAGAACTGCATGTAATATATGAAA 57.723 33.333 1.02 0.00 40.97 2.69
4883 7438 2.655090 TCAGGATGCAGGAAAACACA 57.345 45.000 0.00 0.00 34.76 3.72
4891 7446 3.626930 TGCAGGAAAACACAAACTACCT 58.373 40.909 0.00 0.00 0.00 3.08
4945 10258 4.564406 CCTTGGTCAGAACAACTGCTCTAT 60.564 45.833 0.00 0.00 45.38 1.98
4950 10263 5.932303 GGTCAGAACAACTGCTCTATACAAA 59.068 40.000 0.00 0.00 45.38 2.83
4951 10264 6.091441 GGTCAGAACAACTGCTCTATACAAAG 59.909 42.308 0.00 0.00 45.38 2.77
4952 10265 5.639506 TCAGAACAACTGCTCTATACAAAGC 59.360 40.000 0.00 0.00 45.38 3.51
4953 10266 4.627467 AGAACAACTGCTCTATACAAAGCG 59.373 41.667 0.00 0.00 41.51 4.68
4954 10267 4.188247 ACAACTGCTCTATACAAAGCGA 57.812 40.909 0.00 0.00 41.51 4.93
4957 10270 2.496070 ACTGCTCTATACAAAGCGACCA 59.504 45.455 0.00 0.00 41.51 4.02
4958 10271 3.056107 ACTGCTCTATACAAAGCGACCAA 60.056 43.478 0.00 0.00 41.51 3.67
4959 10272 4.122776 CTGCTCTATACAAAGCGACCAAT 58.877 43.478 0.00 0.00 41.51 3.16
4960 10273 4.513442 TGCTCTATACAAAGCGACCAATT 58.487 39.130 0.00 0.00 41.51 2.32
4961 10274 4.332543 TGCTCTATACAAAGCGACCAATTG 59.667 41.667 0.00 0.00 41.51 2.32
4963 10276 4.257731 TCTATACAAAGCGACCAATTGCA 58.742 39.130 0.00 0.00 37.75 4.08
4977 10303 4.114073 CCAATTGCACGCATCACATTTAT 58.886 39.130 0.00 0.00 0.00 1.40
4990 10316 7.205297 GCATCACATTTATTTAGGACAATGCT 58.795 34.615 0.00 0.00 33.62 3.79
5004 10330 2.687425 ACAATGCTTGTGTGTTGCTACA 59.313 40.909 0.00 0.00 43.48 2.74
5029 10355 8.605746 CAGGCAATATTTAACAATTTCATGTGG 58.394 33.333 0.00 0.00 32.81 4.17
5100 10442 7.096106 CGCAAGAAAGACAAAAATCAAGCATAA 60.096 33.333 0.00 0.00 43.02 1.90
5124 10466 6.767456 ACCAAATATTTCTCCAACAATTGCA 58.233 32.000 5.05 0.00 0.00 4.08
5184 10526 5.582269 CCGAGAGCATGACTTTCAAATTAGA 59.418 40.000 0.00 0.00 29.82 2.10
5239 10581 7.637631 TTCTAAATATGCCAAGTACAATGCA 57.362 32.000 5.81 5.81 38.23 3.96
5245 10587 9.664332 AAATATGCCAAGTACAATGCATAAAAA 57.336 25.926 20.05 6.70 46.31 1.94
5269 10640 1.763968 TACCTCGTGAGATCAGGTGG 58.236 55.000 17.53 17.53 45.51 4.61
5317 10688 6.912591 GCCTTAAATGACATACAACTATGCAC 59.087 38.462 0.00 0.00 34.08 4.57
5321 10692 6.668541 AATGACATACAACTATGCACTGTC 57.331 37.500 0.00 0.00 34.08 3.51
5339 10710 1.135402 GTCGGCATTGTTGGACCAATC 60.135 52.381 10.83 5.10 32.81 2.67
5349 10720 5.715439 TGTTGGACCAATCCTAGATCAAT 57.285 39.130 10.83 0.00 46.43 2.57
5377 10748 6.715347 ACTGAAGTTTGCCTTTGAGTAATT 57.285 33.333 0.00 0.00 32.03 1.40
5378 10749 7.112452 ACTGAAGTTTGCCTTTGAGTAATTT 57.888 32.000 0.00 0.00 32.03 1.82
5383 10754 8.691661 AAGTTTGCCTTTGAGTAATTTCTCTA 57.308 30.769 12.61 3.21 35.68 2.43
5450 10822 6.300354 ACAAACTACACAAACATAGACAGC 57.700 37.500 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.283722 AGATCTCGGTGAGTTTACCTTTGT 59.716 41.667 0.00 0.00 38.62 2.83
23 24 2.625790 GGAGCAATAGACAGATCTCGGT 59.374 50.000 0.00 0.00 36.29 4.69
26 27 4.935352 ACTGGAGCAATAGACAGATCTC 57.065 45.455 0.00 0.00 36.29 2.75
151 153 3.936203 TCGGCGACTTGGCACCTT 61.936 61.111 4.99 0.00 45.16 3.50
155 157 2.970324 GTTGTCGGCGACTTGGCA 60.970 61.111 36.17 16.79 45.16 4.92
248 253 3.060070 CGGAGAAACACAACTACGGAAAC 60.060 47.826 0.00 0.00 36.90 2.78
302 307 2.384203 GGAGACATCCTTTTCGCCG 58.616 57.895 0.00 0.00 42.94 6.46
317 322 3.312709 GCAATCGGCGAAAAAGGAG 57.687 52.632 15.93 0.00 0.00 3.69
358 363 3.521560 CCATAGCAAGTAAAGCGACTGA 58.478 45.455 0.00 0.00 37.01 3.41
508 520 5.171339 AGTAAATATGGCATGGAGCTAGG 57.829 43.478 10.98 0.00 44.79 3.02
785 797 2.281498 CGAAGAAATTGCGTATGCTCGA 59.719 45.455 8.69 0.00 43.34 4.04
861 873 8.876275 ACAATTGGTATGCAATGATATCAAAC 57.124 30.769 9.99 2.89 33.60 2.93
942 954 4.205587 AGAGCAGAGGAGGCAAAAATATG 58.794 43.478 0.00 0.00 0.00 1.78
1020 1032 3.243975 CCAAGCATTCTTTTGGTTCAGCT 60.244 43.478 0.00 0.00 39.18 4.24
1130 1151 4.487804 CTCTGAAATATCCTCCTCCTCCA 58.512 47.826 0.00 0.00 0.00 3.86
1171 1192 0.336737 TCAGGGTCTTCCTCCTCCTC 59.663 60.000 0.00 0.00 46.12 3.71
1172 1193 0.793617 TTCAGGGTCTTCCTCCTCCT 59.206 55.000 0.00 0.00 46.12 3.69
1173 1194 1.199615 CTTCAGGGTCTTCCTCCTCC 58.800 60.000 0.00 0.00 46.12 4.30
1280 1301 4.555262 CTTCTCTTTATCGCTCCCATCTC 58.445 47.826 0.00 0.00 0.00 2.75
1969 2015 2.231964 TGGCCAAGATTCAATGTTCTGC 59.768 45.455 0.61 0.00 0.00 4.26
1970 2016 4.730949 ATGGCCAAGATTCAATGTTCTG 57.269 40.909 10.96 0.00 0.00 3.02
1971 2017 4.142315 CGAATGGCCAAGATTCAATGTTCT 60.142 41.667 10.96 0.00 31.26 3.01
1972 2018 4.107622 CGAATGGCCAAGATTCAATGTTC 58.892 43.478 10.96 3.66 31.26 3.18
2069 2115 8.170730 ACCACCCTCTGATCTAATTTACTTTTT 58.829 33.333 0.00 0.00 0.00 1.94
2070 2116 7.611855 CACCACCCTCTGATCTAATTTACTTTT 59.388 37.037 0.00 0.00 0.00 2.27
2071 2117 7.112779 CACCACCCTCTGATCTAATTTACTTT 58.887 38.462 0.00 0.00 0.00 2.66
2072 2118 6.353082 CCACCACCCTCTGATCTAATTTACTT 60.353 42.308 0.00 0.00 0.00 2.24
2073 2119 5.131142 CCACCACCCTCTGATCTAATTTACT 59.869 44.000 0.00 0.00 0.00 2.24
2074 2120 5.130477 TCCACCACCCTCTGATCTAATTTAC 59.870 44.000 0.00 0.00 0.00 2.01
2226 2272 1.307778 TGGCTATCAGGGGAGGCAA 60.308 57.895 0.00 0.00 44.43 4.52
2342 2389 8.532408 TCGCACTTTAAACTTACTTTTTAACG 57.468 30.769 0.00 0.00 30.02 3.18
2550 2597 6.645306 ACTCTTAGCTTCTTTCCCTGTTATC 58.355 40.000 0.00 0.00 0.00 1.75
2581 2628 1.003696 AGCTTGTTCTTAGCCTGGGAC 59.996 52.381 0.00 0.00 39.47 4.46
2734 2781 2.613506 GGGTGCACGGTGTAGTTGC 61.614 63.158 11.45 0.00 0.00 4.17
2754 2801 6.183360 TTACAAGGGTAAAAAGCAGATTTGCA 60.183 34.615 11.25 0.00 43.28 4.08
2755 2802 6.220201 TTACAAGGGTAAAAAGCAGATTTGC 58.780 36.000 0.00 0.00 42.24 3.68
2973 3020 3.499918 CAGATGTTTCAGGAACCTGTGAC 59.500 47.826 18.60 17.17 43.96 3.67
3062 3110 8.938883 ACATATACAGATTTGACCTAGAACCAT 58.061 33.333 0.00 0.00 0.00 3.55
3792 3858 4.372656 CCCACAGCAGCTAATAAGAGTAC 58.627 47.826 0.00 0.00 0.00 2.73
3854 3920 5.294799 ACTTGCATAAACTAACACGTCACAA 59.705 36.000 0.00 0.00 0.00 3.33
3855 3921 4.812091 ACTTGCATAAACTAACACGTCACA 59.188 37.500 0.00 0.00 0.00 3.58
3856 3922 5.338614 ACTTGCATAAACTAACACGTCAC 57.661 39.130 0.00 0.00 0.00 3.67
3857 3923 4.449743 GGACTTGCATAAACTAACACGTCA 59.550 41.667 0.00 0.00 34.13 4.35
3858 3924 4.689345 AGGACTTGCATAAACTAACACGTC 59.311 41.667 0.00 0.00 32.33 4.34
3859 3925 4.451096 CAGGACTTGCATAAACTAACACGT 59.549 41.667 0.00 0.00 0.00 4.49
3860 3926 4.451096 ACAGGACTTGCATAAACTAACACG 59.549 41.667 0.00 0.00 0.00 4.49
3861 3927 5.468746 TCACAGGACTTGCATAAACTAACAC 59.531 40.000 0.00 0.00 0.00 3.32
3862 3928 5.616270 TCACAGGACTTGCATAAACTAACA 58.384 37.500 0.00 0.00 0.00 2.41
3863 3929 6.554334 TTCACAGGACTTGCATAAACTAAC 57.446 37.500 0.00 0.00 0.00 2.34
3864 3930 7.759489 ATTTCACAGGACTTGCATAAACTAA 57.241 32.000 0.00 0.00 0.00 2.24
3865 3931 8.856153 TTATTTCACAGGACTTGCATAAACTA 57.144 30.769 0.00 0.00 0.00 2.24
3866 3932 7.759489 TTATTTCACAGGACTTGCATAAACT 57.241 32.000 0.00 0.00 0.00 2.66
3867 3933 8.296713 TCTTTATTTCACAGGACTTGCATAAAC 58.703 33.333 0.00 0.00 0.00 2.01
3868 3934 8.402798 TCTTTATTTCACAGGACTTGCATAAA 57.597 30.769 0.00 0.00 0.00 1.40
3869 3935 7.994425 TCTTTATTTCACAGGACTTGCATAA 57.006 32.000 0.00 0.00 0.00 1.90
3870 3936 7.994425 TTCTTTATTTCACAGGACTTGCATA 57.006 32.000 0.00 0.00 0.00 3.14
3871 3937 6.899393 TTCTTTATTTCACAGGACTTGCAT 57.101 33.333 0.00 0.00 0.00 3.96
3872 3938 6.265196 ACATTCTTTATTTCACAGGACTTGCA 59.735 34.615 0.00 0.00 0.00 4.08
3873 3939 6.681777 ACATTCTTTATTTCACAGGACTTGC 58.318 36.000 0.00 0.00 0.00 4.01
3876 3942 9.793259 TCTTTACATTCTTTATTTCACAGGACT 57.207 29.630 0.00 0.00 0.00 3.85
3888 3954 9.515226 AGCACCTTACATTCTTTACATTCTTTA 57.485 29.630 0.00 0.00 0.00 1.85
3889 3955 8.409358 AGCACCTTACATTCTTTACATTCTTT 57.591 30.769 0.00 0.00 0.00 2.52
3890 3956 7.885399 AGAGCACCTTACATTCTTTACATTCTT 59.115 33.333 0.00 0.00 0.00 2.52
3891 3957 7.398024 AGAGCACCTTACATTCTTTACATTCT 58.602 34.615 0.00 0.00 0.00 2.40
3892 3958 7.201652 GGAGAGCACCTTACATTCTTTACATTC 60.202 40.741 0.00 0.00 0.00 2.67
3893 3959 6.599638 GGAGAGCACCTTACATTCTTTACATT 59.400 38.462 0.00 0.00 0.00 2.71
3894 3960 6.069963 AGGAGAGCACCTTACATTCTTTACAT 60.070 38.462 0.00 0.00 36.86 2.29
3895 3961 5.248477 AGGAGAGCACCTTACATTCTTTACA 59.752 40.000 0.00 0.00 36.86 2.41
3896 3962 5.582665 CAGGAGAGCACCTTACATTCTTTAC 59.417 44.000 0.00 0.00 38.32 2.01
3897 3963 5.248477 ACAGGAGAGCACCTTACATTCTTTA 59.752 40.000 0.00 0.00 38.32 1.85
3898 3964 4.042187 ACAGGAGAGCACCTTACATTCTTT 59.958 41.667 0.00 0.00 38.32 2.52
3899 3965 3.584848 ACAGGAGAGCACCTTACATTCTT 59.415 43.478 0.00 0.00 38.32 2.52
3900 3966 3.177228 ACAGGAGAGCACCTTACATTCT 58.823 45.455 0.00 0.00 38.32 2.40
3901 3967 3.618690 ACAGGAGAGCACCTTACATTC 57.381 47.619 0.00 0.00 38.32 2.67
3902 3968 4.074970 CAAACAGGAGAGCACCTTACATT 58.925 43.478 0.00 0.00 38.32 2.71
3903 3969 3.073062 ACAAACAGGAGAGCACCTTACAT 59.927 43.478 0.00 0.00 38.32 2.29
3904 3970 2.438021 ACAAACAGGAGAGCACCTTACA 59.562 45.455 0.00 0.00 38.32 2.41
3905 3971 3.127425 ACAAACAGGAGAGCACCTTAC 57.873 47.619 0.00 0.00 38.32 2.34
3906 3972 3.644265 TGTACAAACAGGAGAGCACCTTA 59.356 43.478 0.00 0.00 38.32 2.69
3907 3973 2.438021 TGTACAAACAGGAGAGCACCTT 59.562 45.455 0.00 0.00 38.32 3.50
3994 4060 7.147320 ACTGATGTTTATTCTGTGATATCCCCA 60.147 37.037 0.00 0.00 0.00 4.96
4002 4068 5.576774 CGCTGTACTGATGTTTATTCTGTGA 59.423 40.000 3.61 0.00 0.00 3.58
4026 4092 4.081087 TCCTGTGCCAAGAAAGAGGTATAC 60.081 45.833 0.00 0.00 0.00 1.47
4053 4119 4.762289 AGGCAAACGGAATTCTCTCTAT 57.238 40.909 5.23 0.00 0.00 1.98
4060 4126 3.877508 ACATAGCTAGGCAAACGGAATTC 59.122 43.478 5.07 0.00 0.00 2.17
4082 4148 4.274950 CCGTTTGCTGTAAAAGAAAGAGGA 59.725 41.667 5.81 0.00 30.52 3.71
4145 4213 6.871492 TCAGTCACGATAGCAGATTTAAAACA 59.129 34.615 0.00 0.00 42.67 2.83
4322 4390 0.602562 CACCATGGCGACCAATTTGT 59.397 50.000 13.04 0.00 36.95 2.83
4523 4591 2.417586 GGTTTGTAGGAAAATCCGACCG 59.582 50.000 7.11 0.00 40.83 4.79
4641 4716 8.230486 CCATTTCTAAACTTGATCACAGTACAC 58.770 37.037 0.00 0.00 0.00 2.90
4646 4721 6.258230 TGCCATTTCTAAACTTGATCACAG 57.742 37.500 0.00 0.00 0.00 3.66
4738 4817 2.225491 GTGCCGTTTGCTGTTATTCTGA 59.775 45.455 0.00 0.00 42.00 3.27
4754 7295 2.513204 CCTCAGCTGGATGTGCCG 60.513 66.667 15.13 0.00 40.66 5.69
4797 7338 7.148523 GCATGGGCTCAAAAAGAAAAATCTAAG 60.149 37.037 0.00 0.00 36.96 2.18
4848 7389 9.887629 CTGCATCCTGAAGACTATTTCATATAT 57.112 33.333 0.00 0.00 36.55 0.86
4851 7392 6.327365 TCCTGCATCCTGAAGACTATTTCATA 59.673 38.462 0.00 0.00 36.55 2.15
4852 7393 5.131642 TCCTGCATCCTGAAGACTATTTCAT 59.868 40.000 0.00 0.00 36.55 2.57
4853 7394 4.471025 TCCTGCATCCTGAAGACTATTTCA 59.529 41.667 0.00 0.00 35.83 2.69
4857 7412 5.189180 GTTTTCCTGCATCCTGAAGACTAT 58.811 41.667 0.00 0.00 0.00 2.12
4858 7413 4.041567 TGTTTTCCTGCATCCTGAAGACTA 59.958 41.667 0.00 0.00 0.00 2.59
4871 7426 5.761165 TTAGGTAGTTTGTGTTTTCCTGC 57.239 39.130 0.00 0.00 0.00 4.85
4891 7446 6.692486 TGTGCCTGAAGTTTTTGTTTCTTTA 58.308 32.000 0.00 0.00 0.00 1.85
4945 10258 1.069568 CGTGCAATTGGTCGCTTTGTA 60.070 47.619 7.72 0.00 0.00 2.41
4952 10265 0.794229 GTGATGCGTGCAATTGGTCG 60.794 55.000 7.72 0.00 0.00 4.79
4953 10266 0.240678 TGTGATGCGTGCAATTGGTC 59.759 50.000 7.72 0.00 0.00 4.02
4954 10267 0.889994 ATGTGATGCGTGCAATTGGT 59.110 45.000 7.72 0.00 0.00 3.67
4957 10270 6.476380 CCTAAATAAATGTGATGCGTGCAATT 59.524 34.615 0.00 0.00 0.00 2.32
4958 10271 5.978919 CCTAAATAAATGTGATGCGTGCAAT 59.021 36.000 0.00 0.00 0.00 3.56
4959 10272 5.124617 TCCTAAATAAATGTGATGCGTGCAA 59.875 36.000 0.00 0.00 0.00 4.08
4960 10273 4.637977 TCCTAAATAAATGTGATGCGTGCA 59.362 37.500 0.00 0.00 0.00 4.57
4961 10274 4.970003 GTCCTAAATAAATGTGATGCGTGC 59.030 41.667 0.00 0.00 0.00 5.34
4963 10276 6.751514 TTGTCCTAAATAAATGTGATGCGT 57.248 33.333 0.00 0.00 0.00 5.24
5004 10330 8.538701 TCCACATGAAATTGTTAAATATTGCCT 58.461 29.630 0.00 0.00 0.00 4.75
5016 10342 9.520515 AAGTAGTAATTCTCCACATGAAATTGT 57.479 29.630 0.00 0.00 0.00 2.71
5064 10406 0.311790 CTTTCTTGCGCCTTTGCTCA 59.688 50.000 4.18 0.00 35.36 4.26
5100 10442 6.767456 TGCAATTGTTGGAGAAATATTTGGT 58.233 32.000 5.17 0.00 0.00 3.67
5184 10526 9.715121 AAGTTAAATCATGCATCTGTTCAAAAT 57.285 25.926 0.00 0.00 0.00 1.82
5221 10563 9.835389 AATTTTTATGCATTGTACTTGGCATAT 57.165 25.926 19.29 8.84 45.49 1.78
5245 10587 5.011125 CCACCTGATCTCACGAGGTAATAAT 59.989 44.000 1.57 0.00 38.07 1.28
5256 10598 7.445121 TCATATTTCATACCACCTGATCTCAC 58.555 38.462 0.00 0.00 0.00 3.51
5269 10640 8.784043 AGGCCGTCTAAATTTCATATTTCATAC 58.216 33.333 0.00 0.00 0.00 2.39
5317 10688 0.888736 TGGTCCAACAATGCCGACAG 60.889 55.000 0.00 0.00 0.00 3.51
5321 10692 0.173255 GGATTGGTCCAACAATGCCG 59.827 55.000 6.41 0.00 44.42 5.69
5339 10710 8.394121 GCAAACTTCAGTTAAGATTGATCTAGG 58.606 37.037 10.32 0.00 45.87 3.02
5349 10720 5.885912 ACTCAAAGGCAAACTTCAGTTAAGA 59.114 36.000 0.00 0.00 38.85 2.10
5422 10794 8.731605 TGTCTATGTTTGTGTAGTTTGTTTCAA 58.268 29.630 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.