Multiple sequence alignment - TraesCS5A01G254300

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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 TraesCS5A01G254300 chr5A 100.000 4206 0 0 1 4206 470170508 470174713 0.000000e+00 7768
1 TraesCS5A01G254300 chr5A 83.741 2903 392 48 13 2879 470076640 470079498 0.000000e+00 2673
2 TraesCS5A01G254300 chr5B 94.431 3807 125 27 1 3759 436209239 436213006 0.000000e+00 5775
3 TraesCS5A01G254300 chr5B 84.949 2651 338 39 1 2624 436152802 436155418 0.000000e+00 2628
4 TraesCS5A01G254300 chr5B 86.068 1938 241 16 1 1913 436162952 436164885 0.000000e+00 2056
5 TraesCS5A01G254300 chr5B 88.017 1619 172 12 1 1605 436096072 436097682 0.000000e+00 1895
6 TraesCS5A01G254300 chr5B 78.355 1155 177 39 1746 2879 436097691 436098793 0.000000e+00 680
7 TraesCS5A01G254300 chr5B 73.529 714 132 38 2871 3565 436156723 436157398 7.080000e-53 219
8 TraesCS5A01G254300 chr5B 79.688 256 24 12 3951 4181 436213259 436213511 4.350000e-35 159
9 TraesCS5A01G254300 chr5D 95.046 3694 128 28 1 3662 368286111 368289781 0.000000e+00 5757
10 TraesCS5A01G254300 chr5D 82.287 3280 475 66 1 3222 368078694 368081925 0.000000e+00 2741
11 TraesCS5A01G254300 chr5D 83.620 2906 392 52 1 2867 368029565 368032425 0.000000e+00 2652
12 TraesCS5A01G254300 chr5D 86.137 1962 243 13 1 1935 368244641 368246600 0.000000e+00 2089
13 TraesCS5A01G254300 chr5D 74.363 706 133 32 2871 3565 368032832 368033500 1.500000e-64 257
14 TraesCS5A01G254300 chr5D 83.154 279 21 14 3943 4201 368289959 368290231 9.090000e-57 231
15 TraesCS5A01G254300 chr5D 81.749 263 26 14 3951 4196 368298751 368299008 2.560000e-47 200


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 TraesCS5A01G254300 chr5A 470170508 470174713 4205 False 7768.0 7768 100.0000 1 4206 1 chr5A.!!$F2 4205
1 TraesCS5A01G254300 chr5A 470076640 470079498 2858 False 2673.0 2673 83.7410 13 2879 1 chr5A.!!$F1 2866
2 TraesCS5A01G254300 chr5B 436209239 436213511 4272 False 2967.0 5775 87.0595 1 4181 2 chr5B.!!$F4 4180
3 TraesCS5A01G254300 chr5B 436162952 436164885 1933 False 2056.0 2056 86.0680 1 1913 1 chr5B.!!$F1 1912
4 TraesCS5A01G254300 chr5B 436152802 436157398 4596 False 1423.5 2628 79.2390 1 3565 2 chr5B.!!$F3 3564
5 TraesCS5A01G254300 chr5B 436096072 436098793 2721 False 1287.5 1895 83.1860 1 2879 2 chr5B.!!$F2 2878
6 TraesCS5A01G254300 chr5D 368286111 368290231 4120 False 2994.0 5757 89.1000 1 4201 2 chr5D.!!$F5 4200
7 TraesCS5A01G254300 chr5D 368078694 368081925 3231 False 2741.0 2741 82.2870 1 3222 1 chr5D.!!$F1 3221
8 TraesCS5A01G254300 chr5D 368244641 368246600 1959 False 2089.0 2089 86.1370 1 1935 1 chr5D.!!$F2 1934
9 TraesCS5A01G254300 chr5D 368029565 368033500 3935 False 1454.5 2652 78.9915 1 3565 2 chr5D.!!$F4 3564

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
514 544 0.482887 TGTCACCTCTCACCTCCAGA 59.517 55.000 0.0 0.0 0.0 3.86 F
859 892 0.904865 TGGTGATTCTGTCGAGGGCT 60.905 55.000 0.0 0.0 0.0 5.19 F
2065 2113 1.804748 GGTCGTGTGGAGAATTGGAAC 59.195 52.381 0.0 0.0 0.0 3.62 F
2174 2270 1.023502 GTCTACAGGCTACGAGGGAC 58.976 60.000 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1766 1808 2.009774 CCAGTTGAATCGTGTCATCCC 58.990 52.381 0.00 0.0 0.00 3.85 R
2174 2270 2.030946 GCTAAAGATACTGTGCCTTGCG 59.969 50.000 0.00 0.0 0.00 4.85 R
3181 4389 0.103026 TCTTCACATCATCGCCCTCG 59.897 55.000 0.00 0.0 0.00 4.63 R
3776 5004 0.169009 AATTTCTTTCGAGCGCAGGC 59.831 50.000 11.47 0.0 40.37 4.85 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
31 36 8.929827 TTGATATGTATTTCACCATGCTTTTG 57.070 30.769 0.00 0.00 0.00 2.44
49 54 6.432783 TGCTTTTGGTAATAAGCTAGCTTGAA 59.567 34.615 34.98 19.96 45.37 2.69
58 63 9.290483 GTAATAAGCTAGCTTGAATTTTCAACC 57.710 33.333 34.98 11.36 41.88 3.77
129 134 4.371624 CCATACAGGGCTCCATATTTGA 57.628 45.455 0.00 0.00 0.00 2.69
382 412 6.980051 AAGACGAGGAACACATTATAAACC 57.020 37.500 0.00 0.00 0.00 3.27
415 445 5.049818 GGAGAACTCATTGAGCGGATATTTG 60.050 44.000 13.64 0.00 32.04 2.32
447 477 2.017049 GTGAGCACTTTGTTGAGGTGT 58.983 47.619 0.00 0.00 33.96 4.16
514 544 0.482887 TGTCACCTCTCACCTCCAGA 59.517 55.000 0.00 0.00 0.00 3.86
565 595 2.159310 CCACAAGAGTCGATCTCAGGAC 60.159 54.545 14.62 0.00 44.98 3.85
859 892 0.904865 TGGTGATTCTGTCGAGGGCT 60.905 55.000 0.00 0.00 0.00 5.19
891 927 9.941325 CTCCATAATAATAGCAGATTCAGAGTT 57.059 33.333 0.00 0.00 0.00 3.01
1012 1048 3.270877 GGTGGAACAATGTACTGGCTAG 58.729 50.000 0.00 0.00 44.16 3.42
1066 1102 6.070824 TGCAGTTATGACCTTTGATCTCAGTA 60.071 38.462 0.00 0.00 0.00 2.74
1208 1244 2.586425 CTGTTCCTTTCAGCCCAGAAA 58.414 47.619 0.00 0.00 36.21 2.52
1305 1342 5.719563 TCAGTACTCACCTGATTACATTCCA 59.280 40.000 0.00 0.00 34.12 3.53
1383 1420 6.330250 ACCTATATTCCTATGAGTTGCTTGGT 59.670 38.462 0.00 0.00 0.00 3.67
1476 1513 4.650734 TGCAATCCTACATCTGTGTGAAA 58.349 39.130 0.00 0.00 39.39 2.69
1482 1519 5.724328 TCCTACATCTGTGTGAAATCACTC 58.276 41.667 14.15 11.13 46.55 3.51
1766 1808 3.117812 TGTGCTGCCGCGTGTATG 61.118 61.111 4.92 0.00 39.65 2.39
1915 1960 6.406370 TGGTCGACAATCATCTGAAAAGTAT 58.594 36.000 18.91 0.00 0.00 2.12
2051 2099 4.957759 AGGGAAAATTTATTCGGTCGTG 57.042 40.909 0.00 0.00 0.00 4.35
2065 2113 1.804748 GGTCGTGTGGAGAATTGGAAC 59.195 52.381 0.00 0.00 0.00 3.62
2134 2182 3.253188 TGCAACTGTTCCTTAAGACATGC 59.747 43.478 3.36 9.49 0.00 4.06
2174 2270 1.023502 GTCTACAGGCTACGAGGGAC 58.976 60.000 0.00 0.00 0.00 4.46
2271 2367 8.592105 TTTATTCATGTTTTTCCTTTCTGCTG 57.408 30.769 0.00 0.00 0.00 4.41
2362 2458 9.704098 CTTCTTTTGAAATATAAGCGAAGTACC 57.296 33.333 0.00 0.00 38.07 3.34
2469 2566 7.562454 TGTGTACTTTAGTTCCTTTTCCTTG 57.438 36.000 0.00 0.00 0.00 3.61
2829 3608 3.619038 GCTGTCAAGTAATGTAGTGGAGC 59.381 47.826 0.00 0.00 0.00 4.70
2847 3640 3.998341 GGAGCGGTACTTACAATTGTTCA 59.002 43.478 17.78 3.14 0.00 3.18
2950 4155 7.701809 TTGGTAAACGTCAAAATTTCCATTC 57.298 32.000 0.00 0.00 0.00 2.67
3006 4211 3.636282 AACGGCATTGTAAAACAGTCC 57.364 42.857 0.00 0.00 0.00 3.85
3097 4304 1.611673 CCCCTGACTTGCGATGAAAGT 60.612 52.381 0.00 0.00 40.54 2.66
3098 4305 2.354704 CCCCTGACTTGCGATGAAAGTA 60.355 50.000 0.00 0.00 37.98 2.24
3111 4318 8.126871 TGCGATGAAAGTATATTGTCTTGTAC 57.873 34.615 0.00 0.00 0.00 2.90
3181 4389 3.788135 GCATTTCTTCTCAGAATCGCAGC 60.788 47.826 0.00 0.00 38.89 5.25
3225 4433 5.096954 TGATACTTGAGAGCTTATCGTCG 57.903 43.478 0.00 0.00 0.00 5.12
3236 4444 2.473235 GCTTATCGTCGCATTCTTCTCC 59.527 50.000 0.00 0.00 0.00 3.71
3237 4445 3.706698 CTTATCGTCGCATTCTTCTCCA 58.293 45.455 0.00 0.00 0.00 3.86
3238 4446 2.215907 ATCGTCGCATTCTTCTCCAG 57.784 50.000 0.00 0.00 0.00 3.86
3239 4447 0.458543 TCGTCGCATTCTTCTCCAGC 60.459 55.000 0.00 0.00 0.00 4.85
3240 4448 0.459237 CGTCGCATTCTTCTCCAGCT 60.459 55.000 0.00 0.00 0.00 4.24
3241 4449 1.285578 GTCGCATTCTTCTCCAGCTC 58.714 55.000 0.00 0.00 0.00 4.09
3242 4450 0.179127 TCGCATTCTTCTCCAGCTCG 60.179 55.000 0.00 0.00 0.00 5.03
3243 4451 1.760268 CGCATTCTTCTCCAGCTCGC 61.760 60.000 0.00 0.00 0.00 5.03
3483 4701 4.686554 GCCACCGAGTATGTATTGAAGATC 59.313 45.833 0.00 0.00 0.00 2.75
3617 4843 3.694566 GGTACAAATGGGTGAATGAGGAC 59.305 47.826 0.00 0.00 0.00 3.85
3667 4893 9.881529 TTTTTCTTTTATTGCAAAATCAGCATC 57.118 25.926 1.71 0.00 42.33 3.91
3687 4913 2.094675 CAAACAGCCCCACCTAAGATG 58.905 52.381 0.00 0.00 0.00 2.90
3697 4923 3.763897 CCCACCTAAGATGGAAACCAAAG 59.236 47.826 0.00 0.00 39.87 2.77
3704 4930 6.208599 CCTAAGATGGAAACCAAAGCAACTAA 59.791 38.462 0.00 0.00 36.95 2.24
3705 4931 5.712152 AGATGGAAACCAAAGCAACTAAG 57.288 39.130 0.00 0.00 36.95 2.18
3708 4934 6.494835 AGATGGAAACCAAAGCAACTAAGAAT 59.505 34.615 0.00 0.00 36.95 2.40
3728 4956 2.964209 TGCTAACAAATTGGGGTTCCA 58.036 42.857 0.00 0.00 42.25 3.53
3741 4969 2.556559 GGGGTTCCAAGAACAGCCAATA 60.557 50.000 9.50 0.00 0.00 1.90
3745 4973 1.005450 TCCAAGAACAGCCAATACCCC 59.995 52.381 0.00 0.00 0.00 4.95
3746 4974 1.005924 CCAAGAACAGCCAATACCCCT 59.994 52.381 0.00 0.00 0.00 4.79
3747 4975 2.369394 CAAGAACAGCCAATACCCCTC 58.631 52.381 0.00 0.00 0.00 4.30
3748 4976 1.668826 AGAACAGCCAATACCCCTCA 58.331 50.000 0.00 0.00 0.00 3.86
3749 4977 1.282157 AGAACAGCCAATACCCCTCAC 59.718 52.381 0.00 0.00 0.00 3.51
3750 4978 0.035439 AACAGCCAATACCCCTCACG 60.035 55.000 0.00 0.00 0.00 4.35
3752 4980 0.251916 CAGCCAATACCCCTCACGAA 59.748 55.000 0.00 0.00 0.00 3.85
3754 4982 1.087771 GCCAATACCCCTCACGAACG 61.088 60.000 0.00 0.00 0.00 3.95
3755 4983 1.087771 CCAATACCCCTCACGAACGC 61.088 60.000 0.00 0.00 0.00 4.84
3756 4984 0.390603 CAATACCCCTCACGAACGCA 60.391 55.000 0.00 0.00 0.00 5.24
3757 4985 0.539986 AATACCCCTCACGAACGCAT 59.460 50.000 0.00 0.00 0.00 4.73
3761 4989 1.519455 CCCTCACGAACGCATCTCC 60.519 63.158 0.00 0.00 0.00 3.71
3763 4991 1.136774 CTCACGAACGCATCTCCGA 59.863 57.895 0.00 0.00 0.00 4.55
3764 4992 0.456142 CTCACGAACGCATCTCCGAA 60.456 55.000 0.00 0.00 0.00 4.30
3765 4993 0.456142 TCACGAACGCATCTCCGAAG 60.456 55.000 0.00 0.00 0.00 3.79
3801 5102 2.867429 CGCTCGAAAGAAATTTGGCAT 58.133 42.857 0.00 0.00 41.32 4.40
3810 5112 4.019792 AGAAATTTGGCATGGGAAAACC 57.980 40.909 0.00 0.00 40.81 3.27
3832 5134 9.981114 AAACCAAGTATAAAAGGATTTGACTTG 57.019 29.630 16.20 16.20 44.02 3.16
3833 5135 8.706322 ACCAAGTATAAAAGGATTTGACTTGT 57.294 30.769 18.89 11.04 43.55 3.16
3834 5136 8.576442 ACCAAGTATAAAAGGATTTGACTTGTG 58.424 33.333 18.89 15.21 43.55 3.33
3841 5143 7.609760 AAAAGGATTTGACTTGTGAAAAACC 57.390 32.000 0.00 0.00 39.02 3.27
3842 5144 6.544928 AAGGATTTGACTTGTGAAAAACCT 57.455 33.333 8.13 8.13 37.59 3.50
3843 5145 7.654022 AAGGATTTGACTTGTGAAAAACCTA 57.346 32.000 11.96 0.00 35.67 3.08
3844 5146 7.654022 AGGATTTGACTTGTGAAAAACCTAA 57.346 32.000 10.71 0.00 35.16 2.69
3845 5147 8.073467 AGGATTTGACTTGTGAAAAACCTAAA 57.927 30.769 10.71 0.00 35.16 1.85
3846 5148 8.536175 AGGATTTGACTTGTGAAAAACCTAAAA 58.464 29.630 10.71 0.00 35.16 1.52
3847 5149 9.157104 GGATTTGACTTGTGAAAAACCTAAAAA 57.843 29.630 0.00 0.00 0.00 1.94
3871 5173 1.079336 GGTGTCAGGTACCTTCGGC 60.079 63.158 13.15 3.98 35.30 5.54
3881 5206 2.074576 GTACCTTCGGCCTCTTTGAAC 58.925 52.381 0.00 0.00 0.00 3.18
3885 5210 2.494059 CTTCGGCCTCTTTGAACTGAA 58.506 47.619 0.00 0.00 0.00 3.02
3888 5213 2.104111 TCGGCCTCTTTGAACTGAAGAA 59.896 45.455 0.00 0.00 33.10 2.52
3889 5214 2.481952 CGGCCTCTTTGAACTGAAGAAG 59.518 50.000 0.00 0.00 33.10 2.85
3890 5215 3.744660 GGCCTCTTTGAACTGAAGAAGA 58.255 45.455 0.00 0.00 33.10 2.87
3891 5216 3.500299 GGCCTCTTTGAACTGAAGAAGAC 59.500 47.826 0.00 0.00 33.10 3.01
3923 5248 1.310933 ACGAGTGAAGGCGTATCCGT 61.311 55.000 0.00 0.00 39.21 4.69
3927 5252 1.140161 TGAAGGCGTATCCGTTCCG 59.860 57.895 0.00 0.00 40.77 4.30
3932 5257 1.140375 GCGTATCCGTTCCGAACCT 59.860 57.895 5.67 0.00 36.15 3.50
3956 5339 1.544825 GCTGCACCACACTCTCCCTA 61.545 60.000 0.00 0.00 0.00 3.53
3959 5342 1.273267 TGCACCACACTCTCCCTATCT 60.273 52.381 0.00 0.00 0.00 1.98
3968 5351 5.299531 CACACTCTCCCTATCTATGAAACGA 59.700 44.000 0.00 0.00 0.00 3.85
3969 5352 6.015856 CACACTCTCCCTATCTATGAAACGAT 60.016 42.308 0.00 0.00 0.00 3.73
4005 5388 6.111768 TCTTTTATTTCTCTCATCTTGCGC 57.888 37.500 0.00 0.00 0.00 6.09
4006 5389 4.882671 TTTATTTCTCTCATCTTGCGCC 57.117 40.909 4.18 0.00 0.00 6.53
4028 5426 1.554392 CGCGGAAGAGTTCATCTGAG 58.446 55.000 0.00 0.00 38.67 3.35
4060 5468 2.708132 TCCCCTCCCCTCCCCTAG 60.708 72.222 0.00 0.00 0.00 3.02
4084 5492 0.810426 GGATCTCGGTTTTCGCTCCC 60.810 60.000 0.00 0.00 39.05 4.30
4085 5493 0.175989 GATCTCGGTTTTCGCTCCCT 59.824 55.000 0.00 0.00 39.05 4.20
4086 5494 0.175989 ATCTCGGTTTTCGCTCCCTC 59.824 55.000 0.00 0.00 39.05 4.30
4087 5495 0.898789 TCTCGGTTTTCGCTCCCTCT 60.899 55.000 0.00 0.00 39.05 3.69
4088 5496 0.815734 CTCGGTTTTCGCTCCCTCTA 59.184 55.000 0.00 0.00 39.05 2.43
4089 5497 0.529378 TCGGTTTTCGCTCCCTCTAC 59.471 55.000 0.00 0.00 39.05 2.59
4099 5507 2.359531 CGCTCCCTCTACCTTTCTGTAG 59.640 54.545 0.00 0.00 39.67 2.74
4162 5574 7.337689 GGGAATTAATACAAGTCGTTAGGGTTT 59.662 37.037 0.00 0.00 0.00 3.27
4163 5575 8.179615 GGAATTAATACAAGTCGTTAGGGTTTG 58.820 37.037 0.00 0.00 0.00 2.93
4164 5576 6.484818 TTAATACAAGTCGTTAGGGTTTGC 57.515 37.500 0.00 0.00 0.00 3.68
4166 5578 2.645802 ACAAGTCGTTAGGGTTTGCAA 58.354 42.857 0.00 0.00 0.00 4.08
4183 5595 1.028905 CAACCTGCGAGGGAAAAACA 58.971 50.000 7.06 0.00 40.58 2.83
4184 5596 1.613437 CAACCTGCGAGGGAAAAACAT 59.387 47.619 7.06 0.00 40.58 2.71
4201 5613 1.290203 CATCAATCCGTCGGAACCTG 58.710 55.000 19.76 15.50 34.34 4.00
4202 5614 0.178068 ATCAATCCGTCGGAACCTGG 59.822 55.000 19.76 6.38 34.34 4.45
4203 5615 2.106683 CAATCCGTCGGAACCTGGC 61.107 63.158 19.76 0.00 34.34 4.85
4204 5616 2.589157 AATCCGTCGGAACCTGGCA 61.589 57.895 19.76 0.00 34.34 4.92
4205 5617 2.521958 AATCCGTCGGAACCTGGCAG 62.522 60.000 19.76 7.75 34.34 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 36 9.290483 GTTGAAAATTCAAGCTAGCTTATTACC 57.710 33.333 28.87 18.71 46.80 2.85
58 63 7.619964 TCAATATATGTATGATGCCTGCAAG 57.380 36.000 0.00 0.00 0.00 4.01
129 134 0.817654 GAAATAAGCGGCAGGCCTTT 59.182 50.000 0.00 0.00 45.17 3.11
179 194 8.837389 AGTTTAGGTGAAGTTTAACAGATGTTC 58.163 33.333 0.59 0.00 39.31 3.18
415 445 0.871057 GTGCTCACTGGAAGCTTCAC 59.129 55.000 27.02 16.67 37.60 3.18
447 477 2.290260 CCATTCCTTGCAGACACCAGTA 60.290 50.000 0.00 0.00 0.00 2.74
481 511 1.351017 GGTGACAAACTGGGGATCTCA 59.649 52.381 0.00 0.00 0.00 3.27
514 544 1.829523 AAAGCACATTGGGGCGCATT 61.830 50.000 10.83 0.00 34.54 3.56
859 892 5.093677 TCTGCTATTATTATGGAGAGGGCA 58.906 41.667 0.00 0.00 0.00 5.36
1012 1048 2.102252 AGCTAGCTACCATGTCTTCAGC 59.898 50.000 17.69 0.00 0.00 4.26
1066 1102 5.508200 TGTATCCGTGCAAAACTTTCTTT 57.492 34.783 0.00 0.00 0.00 2.52
1383 1420 9.562408 TTACACAATTTAGTATTGGAGTTGTCA 57.438 29.630 0.00 0.00 33.56 3.58
1476 1513 8.336801 TGTATACATCTAAGCGTATGAGTGAT 57.663 34.615 0.08 0.00 31.02 3.06
1482 1519 7.062371 GCCTTCTTGTATACATCTAAGCGTATG 59.938 40.741 6.36 0.39 31.02 2.39
1762 1804 4.271049 CAGTTGAATCGTGTCATCCCATAC 59.729 45.833 0.00 0.00 0.00 2.39
1766 1808 2.009774 CCAGTTGAATCGTGTCATCCC 58.990 52.381 0.00 0.00 0.00 3.85
1882 1926 5.352569 AGATGATTGTCGACCATTCAAACTC 59.647 40.000 14.12 7.98 37.09 3.01
2051 2099 5.036737 CGCAATATTGTTCCAATTCTCCAC 58.963 41.667 16.61 0.00 0.00 4.02
2065 2113 8.394877 TGAAACACTATTACCTTCGCAATATTG 58.605 33.333 11.27 11.27 0.00 1.90
2174 2270 2.030946 GCTAAAGATACTGTGCCTTGCG 59.969 50.000 0.00 0.00 0.00 4.85
2183 2279 8.019669 GCATTAACCATCATGCTAAAGATACTG 58.980 37.037 0.00 0.00 42.25 2.74
2271 2367 4.703093 AGGAGACAAGAACTAGTGAGCTAC 59.297 45.833 0.00 0.00 0.00 3.58
2469 2566 4.058817 AGTAACTAGACAACTTGCACAGC 58.941 43.478 0.00 0.00 0.00 4.40
2578 2676 4.193240 ACCCAGTTCACAAATTTAGGGT 57.807 40.909 0.00 0.00 43.19 4.34
2745 3513 9.683069 CCCAATTTATCATTATTCACTTAGTGC 57.317 33.333 7.61 0.00 32.98 4.40
2829 3608 6.148811 AGGATGTTGAACAATTGTAAGTACCG 59.851 38.462 12.39 0.00 0.00 4.02
2869 3662 6.694877 ACTCTTCGTGTGCTAATATGTCTA 57.305 37.500 0.00 0.00 0.00 2.59
2885 3678 7.602517 ATTCTGAATGTTCCTTAACTCTTCG 57.397 36.000 1.31 0.00 36.51 3.79
2950 4155 4.341366 AAGCTCAAAACAGAAAATGGGG 57.659 40.909 0.00 0.00 0.00 4.96
3006 4211 3.253188 TCCTCGAAAGAAAAAGGTGCATG 59.747 43.478 0.00 0.00 41.32 4.06
3097 4304 9.263446 AGTAGGGTTCAAGTACAAGACAATATA 57.737 33.333 0.00 0.00 0.00 0.86
3098 4305 8.147244 AGTAGGGTTCAAGTACAAGACAATAT 57.853 34.615 0.00 0.00 0.00 1.28
3111 4318 5.551233 TCTGAAACATGAGTAGGGTTCAAG 58.449 41.667 0.00 0.00 42.95 3.02
3181 4389 0.103026 TCTTCACATCATCGCCCTCG 59.897 55.000 0.00 0.00 0.00 4.63
3225 4433 1.435408 GGCGAGCTGGAGAAGAATGC 61.435 60.000 0.00 0.00 0.00 3.56
3237 4445 4.626081 AACAACAGCCGGCGAGCT 62.626 61.111 23.20 13.22 46.45 4.09
3238 4446 4.090057 GAACAACAGCCGGCGAGC 62.090 66.667 23.20 10.73 0.00 5.03
3239 4447 2.250939 TTGAACAACAGCCGGCGAG 61.251 57.895 23.20 20.55 0.00 5.03
3240 4448 2.203084 TTGAACAACAGCCGGCGA 60.203 55.556 23.20 0.00 0.00 5.54
3241 4449 2.051345 GTTGAACAACAGCCGGCG 60.051 61.111 23.20 18.60 40.84 6.46
3242 4450 1.166531 AGAGTTGAACAACAGCCGGC 61.167 55.000 21.89 21.89 43.47 6.13
3243 4451 1.002468 CAAGAGTTGAACAACAGCCGG 60.002 52.381 17.85 0.00 43.47 6.13
3287 4497 6.371809 TGTTTTACAGGTGAAACAGCTAAG 57.628 37.500 15.73 0.00 41.87 2.18
3316 4528 2.611473 GCGCATAGATGGTACTGCAGAT 60.611 50.000 23.35 2.34 34.29 2.90
3407 4623 2.125147 TGCCCCGCAGATTCTTCG 60.125 61.111 0.00 0.00 33.32 3.79
3483 4701 4.744570 TCGCACTTCCAAGTATTCTGTAG 58.255 43.478 0.00 0.00 37.08 2.74
3617 4843 0.322456 TCAAATGTCCTTGGGGAGCG 60.322 55.000 0.00 0.00 43.12 5.03
3646 4872 8.283992 TGTTTGATGCTGATTTTGCAATAAAAG 58.716 29.630 0.00 0.00 44.01 2.27
3650 4876 5.349270 GCTGTTTGATGCTGATTTTGCAATA 59.651 36.000 0.00 0.00 44.01 1.90
3652 4878 3.495377 GCTGTTTGATGCTGATTTTGCAA 59.505 39.130 0.00 0.00 44.01 4.08
3653 4879 3.061322 GCTGTTTGATGCTGATTTTGCA 58.939 40.909 0.00 0.00 44.95 4.08
3654 4880 2.414138 GGCTGTTTGATGCTGATTTTGC 59.586 45.455 0.00 0.00 0.00 3.68
3657 4883 1.551883 GGGGCTGTTTGATGCTGATTT 59.448 47.619 0.00 0.00 0.00 2.17
3658 4884 1.188863 GGGGCTGTTTGATGCTGATT 58.811 50.000 0.00 0.00 0.00 2.57
3663 4889 0.323360 TAGGTGGGGCTGTTTGATGC 60.323 55.000 0.00 0.00 0.00 3.91
3664 4890 2.094675 CTTAGGTGGGGCTGTTTGATG 58.905 52.381 0.00 0.00 0.00 3.07
3665 4891 1.992557 TCTTAGGTGGGGCTGTTTGAT 59.007 47.619 0.00 0.00 0.00 2.57
3666 4892 1.440618 TCTTAGGTGGGGCTGTTTGA 58.559 50.000 0.00 0.00 0.00 2.69
3667 4893 2.094675 CATCTTAGGTGGGGCTGTTTG 58.905 52.381 0.00 0.00 0.00 2.93
3687 4913 4.686091 GCATTCTTAGTTGCTTTGGTTTCC 59.314 41.667 3.45 0.00 35.95 3.13
3697 4923 6.311200 CCCAATTTGTTAGCATTCTTAGTTGC 59.689 38.462 0.00 2.63 39.17 4.17
3704 4930 4.222810 GGAACCCCAATTTGTTAGCATTCT 59.777 41.667 0.00 0.00 0.00 2.40
3705 4931 4.020662 TGGAACCCCAATTTGTTAGCATTC 60.021 41.667 0.00 0.00 40.09 2.67
3708 4934 2.964209 TGGAACCCCAATTTGTTAGCA 58.036 42.857 0.00 0.00 40.09 3.49
3728 4956 1.992557 TGAGGGGTATTGGCTGTTCTT 59.007 47.619 0.00 0.00 0.00 2.52
3741 4969 2.227089 GAGATGCGTTCGTGAGGGGT 62.227 60.000 0.00 0.00 0.00 4.95
3745 4973 0.456142 TTCGGAGATGCGTTCGTGAG 60.456 55.000 0.00 0.00 35.04 3.51
3746 4974 0.456142 CTTCGGAGATGCGTTCGTGA 60.456 55.000 0.00 0.00 35.04 4.35
3747 4975 1.413767 CCTTCGGAGATGCGTTCGTG 61.414 60.000 0.00 0.00 35.04 4.35
3748 4976 1.153823 CCTTCGGAGATGCGTTCGT 60.154 57.895 0.00 0.00 35.04 3.85
3749 4977 0.457853 TTCCTTCGGAGATGCGTTCG 60.458 55.000 0.00 0.00 35.04 3.95
3750 4978 1.941325 ATTCCTTCGGAGATGCGTTC 58.059 50.000 0.00 0.00 35.04 3.95
3752 4980 1.656652 CAATTCCTTCGGAGATGCGT 58.343 50.000 0.00 0.00 35.04 5.24
3754 4982 1.332997 CAGCAATTCCTTCGGAGATGC 59.667 52.381 11.67 11.67 41.91 3.91
3755 4983 1.332997 GCAGCAATTCCTTCGGAGATG 59.667 52.381 0.00 0.00 35.04 2.90
3756 4984 1.673168 GCAGCAATTCCTTCGGAGAT 58.327 50.000 0.00 0.00 35.04 2.75
3757 4985 0.740868 CGCAGCAATTCCTTCGGAGA 60.741 55.000 0.00 0.00 31.21 3.71
3776 5004 0.169009 AATTTCTTTCGAGCGCAGGC 59.831 50.000 11.47 0.00 40.37 4.85
3777 5005 2.245096 CAAATTTCTTTCGAGCGCAGG 58.755 47.619 11.47 0.00 0.00 4.85
3782 5083 2.925563 CCATGCCAAATTTCTTTCGAGC 59.074 45.455 0.00 0.00 0.00 5.03
3786 5087 5.048782 GGTTTTCCCATGCCAAATTTCTTTC 60.049 40.000 0.00 0.00 0.00 2.62
3801 5102 8.371699 CAAATCCTTTTATACTTGGTTTTCCCA 58.628 33.333 0.00 0.00 43.27 4.37
3819 5121 6.544928 AGGTTTTTCACAAGTCAAATCCTT 57.455 33.333 0.00 0.00 29.03 3.36
3831 5133 5.185442 ACCTTCGGTTTTTAGGTTTTTCACA 59.815 36.000 0.00 0.00 39.19 3.58
3832 5134 5.517411 CACCTTCGGTTTTTAGGTTTTTCAC 59.483 40.000 0.00 0.00 40.24 3.18
3833 5135 5.185442 ACACCTTCGGTTTTTAGGTTTTTCA 59.815 36.000 0.00 0.00 40.24 2.69
3834 5136 5.653507 ACACCTTCGGTTTTTAGGTTTTTC 58.346 37.500 0.00 0.00 40.24 2.29
3836 5138 4.705991 TGACACCTTCGGTTTTTAGGTTTT 59.294 37.500 0.00 0.00 40.24 2.43
3837 5139 4.271661 TGACACCTTCGGTTTTTAGGTTT 58.728 39.130 0.00 0.00 40.24 3.27
3838 5140 3.881089 CTGACACCTTCGGTTTTTAGGTT 59.119 43.478 0.00 0.00 40.24 3.50
3839 5141 3.473625 CTGACACCTTCGGTTTTTAGGT 58.526 45.455 0.00 0.00 42.92 3.08
3840 5142 2.812011 CCTGACACCTTCGGTTTTTAGG 59.188 50.000 0.00 0.00 31.02 2.69
3841 5143 3.473625 ACCTGACACCTTCGGTTTTTAG 58.526 45.455 0.00 0.00 31.02 1.85
3842 5144 3.564053 ACCTGACACCTTCGGTTTTTA 57.436 42.857 0.00 0.00 31.02 1.52
3843 5145 2.430248 ACCTGACACCTTCGGTTTTT 57.570 45.000 0.00 0.00 31.02 1.94
3844 5146 2.486013 GGTACCTGACACCTTCGGTTTT 60.486 50.000 4.06 0.00 34.33 2.43
3845 5147 1.071228 GGTACCTGACACCTTCGGTTT 59.929 52.381 4.06 0.00 34.33 3.27
3846 5148 0.683412 GGTACCTGACACCTTCGGTT 59.317 55.000 4.06 0.00 34.33 4.44
3847 5149 0.178941 AGGTACCTGACACCTTCGGT 60.179 55.000 15.42 0.00 44.18 4.69
3866 5168 2.104111 TCTTCAGTTCAAAGAGGCCGAA 59.896 45.455 0.00 0.00 0.00 4.30
3867 5169 1.691976 TCTTCAGTTCAAAGAGGCCGA 59.308 47.619 0.00 0.00 0.00 5.54
3868 5170 2.169832 TCTTCAGTTCAAAGAGGCCG 57.830 50.000 0.00 0.00 0.00 6.13
3869 5171 3.500299 GTCTTCTTCAGTTCAAAGAGGCC 59.500 47.826 0.00 0.00 34.42 5.19
3871 5173 4.621991 TCGTCTTCTTCAGTTCAAAGAGG 58.378 43.478 0.00 0.00 34.42 3.69
3923 5248 4.697756 CAGCGGCCAGGTTCGGAA 62.698 66.667 2.24 0.00 0.00 4.30
3937 5262 1.544825 TAGGGAGAGTGTGGTGCAGC 61.545 60.000 9.47 9.47 0.00 5.25
3938 5263 1.137872 GATAGGGAGAGTGTGGTGCAG 59.862 57.143 0.00 0.00 0.00 4.41
3942 5267 4.816048 TCATAGATAGGGAGAGTGTGGT 57.184 45.455 0.00 0.00 0.00 4.16
3943 5268 5.508153 CGTTTCATAGATAGGGAGAGTGTGG 60.508 48.000 0.00 0.00 0.00 4.17
3945 5270 5.446860 TCGTTTCATAGATAGGGAGAGTGT 58.553 41.667 0.00 0.00 0.00 3.55
3946 5271 6.385843 CATCGTTTCATAGATAGGGAGAGTG 58.614 44.000 0.00 0.00 0.00 3.51
3947 5272 5.478679 CCATCGTTTCATAGATAGGGAGAGT 59.521 44.000 0.00 0.00 0.00 3.24
3948 5273 5.623368 GCCATCGTTTCATAGATAGGGAGAG 60.623 48.000 0.00 0.00 0.00 3.20
3949 5274 4.220821 GCCATCGTTTCATAGATAGGGAGA 59.779 45.833 0.00 0.00 0.00 3.71
3968 5351 8.682936 AGAAATAAAAGATGAGATTACGCCAT 57.317 30.769 0.00 0.00 0.00 4.40
3969 5352 7.987458 AGAGAAATAAAAGATGAGATTACGCCA 59.013 33.333 0.00 0.00 0.00 5.69
4006 5389 2.509336 ATGAACTCTTCCGCGCCG 60.509 61.111 0.00 0.00 0.00 6.46
4015 5413 1.205893 GGGCGAACTCAGATGAACTCT 59.794 52.381 0.00 0.00 33.14 3.24
4028 5426 2.126031 GGAGACTCACGGGCGAAC 60.126 66.667 4.53 0.00 0.00 3.95
4073 5481 2.764439 AAGGTAGAGGGAGCGAAAAC 57.236 50.000 0.00 0.00 0.00 2.43
4077 5485 1.272536 ACAGAAAGGTAGAGGGAGCGA 60.273 52.381 0.00 0.00 0.00 4.93
4079 5487 3.367321 ACTACAGAAAGGTAGAGGGAGC 58.633 50.000 7.30 0.00 42.68 4.70
4080 5488 3.628487 CGACTACAGAAAGGTAGAGGGAG 59.372 52.174 7.30 0.00 42.68 4.30
4084 5492 2.791849 GCGCGACTACAGAAAGGTAGAG 60.792 54.545 12.10 2.77 42.68 2.43
4085 5493 1.131883 GCGCGACTACAGAAAGGTAGA 59.868 52.381 12.10 0.00 42.68 2.59
4086 5494 1.132643 AGCGCGACTACAGAAAGGTAG 59.867 52.381 12.10 0.00 44.97 3.18
4087 5495 1.171308 AGCGCGACTACAGAAAGGTA 58.829 50.000 12.10 0.00 0.00 3.08
4088 5496 0.317479 AAGCGCGACTACAGAAAGGT 59.683 50.000 12.10 0.00 0.00 3.50
4089 5497 0.992802 GAAGCGCGACTACAGAAAGG 59.007 55.000 12.10 0.00 0.00 3.11
4099 5507 1.346538 GATGCAGAAGAAGCGCGAC 59.653 57.895 12.10 0.04 33.85 5.19
4142 5553 5.549347 TGCAAACCCTAACGACTTGTATTA 58.451 37.500 0.00 0.00 0.00 0.98
4143 5554 4.391155 TGCAAACCCTAACGACTTGTATT 58.609 39.130 0.00 0.00 0.00 1.89
4145 5556 3.472283 TGCAAACCCTAACGACTTGTA 57.528 42.857 0.00 0.00 0.00 2.41
4147 5559 2.994849 GTTGCAAACCCTAACGACTTG 58.005 47.619 0.00 0.00 42.21 3.16
4162 5574 0.753479 TTTTTCCCTCGCAGGTTGCA 60.753 50.000 1.69 0.00 45.36 4.08
4163 5575 0.318699 GTTTTTCCCTCGCAGGTTGC 60.319 55.000 2.18 0.00 40.69 4.17
4164 5576 1.028905 TGTTTTTCCCTCGCAGGTTG 58.971 50.000 2.18 0.00 31.93 3.77
4166 5578 1.202879 TGATGTTTTTCCCTCGCAGGT 60.203 47.619 2.18 0.00 31.93 4.00
4168 5580 3.428045 GGATTGATGTTTTTCCCTCGCAG 60.428 47.826 0.00 0.00 0.00 5.18
4169 5581 2.491693 GGATTGATGTTTTTCCCTCGCA 59.508 45.455 0.00 0.00 0.00 5.10
4170 5582 2.477863 CGGATTGATGTTTTTCCCTCGC 60.478 50.000 0.00 0.00 0.00 5.03
4171 5583 2.747446 ACGGATTGATGTTTTTCCCTCG 59.253 45.455 0.00 0.00 0.00 4.63
4172 5584 3.181510 CGACGGATTGATGTTTTTCCCTC 60.182 47.826 0.00 0.00 0.00 4.30
4173 5585 2.747446 CGACGGATTGATGTTTTTCCCT 59.253 45.455 0.00 0.00 0.00 4.20
4174 5586 2.159435 CCGACGGATTGATGTTTTTCCC 60.159 50.000 8.64 0.00 0.00 3.97
4183 5595 0.178068 CCAGGTTCCGACGGATTGAT 59.822 55.000 19.12 1.28 0.00 2.57
4184 5596 1.594833 CCAGGTTCCGACGGATTGA 59.405 57.895 19.12 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.