Multiple sequence alignment - TraesCS5B01G361900

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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 TraesCS5B01G361900 chr5B 100.000 3692 0 0 961 4652 541344723 541341032 0.000000e+00 6818
1 TraesCS5B01G361900 chr5B 100.000 568 0 0 1 568 541345683 541345116 0.000000e+00 1050
2 TraesCS5B01G361900 chr5B 92.353 170 12 1 4184 4352 498885982 498886151 1.670000e-59 241
3 TraesCS5B01G361900 chr5B 90.604 149 11 3 3791 3939 541336119 541335974 1.320000e-45 195
4 TraesCS5B01G361900 chr5D 97.980 3070 39 8 1048 4112 444550823 444547772 0.000000e+00 5304
5 TraesCS5B01G361900 chr5D 93.510 339 13 3 219 556 444551686 444551356 3.230000e-136 496
6 TraesCS5B01G361900 chr5D 94.534 311 10 2 4346 4650 444547080 444546771 1.510000e-129 473
7 TraesCS5B01G361900 chr5D 92.116 241 15 3 1 241 444552495 444552259 2.070000e-88 337
8 TraesCS5B01G361900 chr5D 97.222 72 2 0 4116 4187 444547150 444547079 6.320000e-24 122
9 TraesCS5B01G361900 chr5D 79.365 189 19 6 3787 3975 444540924 444540756 1.060000e-21 115
10 TraesCS5B01G361900 chr5A 96.892 3153 94 3 961 4112 561534975 561531826 0.000000e+00 5276
11 TraesCS5B01G361900 chr5A 89.583 192 1 6 380 552 561535260 561535069 4.680000e-55 226
12 TraesCS5B01G361900 chr5A 93.182 88 4 2 308 395 561535364 561535279 1.360000e-25 128
13 TraesCS5B01G361900 chr3D 92.941 170 11 1 4186 4355 18133703 18133535 3.600000e-61 246
14 TraesCS5B01G361900 chr2D 92.353 170 13 0 4186 4355 352947835 352948004 4.650000e-60 243
15 TraesCS5B01G361900 chr7B 93.210 162 11 0 4186 4347 626602505 626602344 6.020000e-59 239
16 TraesCS5B01G361900 chr7B 89.385 179 17 1 4182 4360 292668368 292668192 1.680000e-54 224
17 TraesCS5B01G361900 chr4B 91.379 174 11 3 4186 4355 646363194 646363367 7.780000e-58 235
18 TraesCS5B01G361900 chr4B 90.805 174 12 3 4186 4355 646335881 646336054 3.620000e-56 230
19 TraesCS5B01G361900 chr4D 92.121 165 13 0 4183 4347 471702481 471702645 2.800000e-57 233
20 TraesCS5B01G361900 chr2B 92.121 165 13 0 4184 4348 798639701 798639537 2.800000e-57 233


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 TraesCS5B01G361900 chr5B 541341032 541345683 4651 True 3934.000000 6818 100.0000 1 4652 2 chr5B.!!$R2 4651
1 TraesCS5B01G361900 chr5D 444546771 444552495 5724 True 1346.400000 5304 95.0724 1 4650 5 chr5D.!!$R2 4649
2 TraesCS5B01G361900 chr5A 561531826 561535364 3538 True 1876.666667 5276 93.2190 308 4112 3 chr5A.!!$R1 3804

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
50 51 0.105778 CTTCTCTCCGCCCTTCATCC 59.894 60.000 0.00 0.0 0.00 3.51 F
65 66 0.673985 CATCCGCCGTTCATCTCCTA 59.326 55.000 0.00 0.0 0.00 2.94 F
79 80 1.178276 CTCCTAGTGCTGAACGGTCT 58.822 55.000 0.33 0.0 0.00 3.85 F
2013 3044 1.147817 ACCTTTGGGTTGATGAGGCTT 59.852 47.619 0.00 0.0 44.73 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1320 2351 2.364448 GAGAAGGGGAGGCGGAGT 60.364 66.667 0.0 0.0 0.00 3.85 R
1683 2714 4.125703 AGTCGGTAATGTAGTAGTCCTCG 58.874 47.826 0.0 0.0 0.00 4.63 R
2196 3227 1.305381 ACCCCTCTCGACCTTCAGG 60.305 63.158 0.0 0.0 42.17 3.86 R
4023 5076 0.392193 CCTCGAATGCTCTGCCAGTT 60.392 55.000 0.0 0.0 0.00 3.16 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
27 28 4.918588 TCTCGCCTTTCCTCCTTTTTATT 58.081 39.130 0.00 0.00 0.00 1.40
50 51 0.105778 CTTCTCTCCGCCCTTCATCC 59.894 60.000 0.00 0.00 0.00 3.51
52 53 3.798954 CTCTCCGCCCTTCATCCGC 62.799 68.421 0.00 0.00 0.00 5.54
65 66 0.673985 CATCCGCCGTTCATCTCCTA 59.326 55.000 0.00 0.00 0.00 2.94
74 75 3.182967 CGTTCATCTCCTAGTGCTGAAC 58.817 50.000 14.46 14.46 41.28 3.18
79 80 1.178276 CTCCTAGTGCTGAACGGTCT 58.822 55.000 0.33 0.00 0.00 3.85
155 156 1.548973 CTACGGATCGAATGCCACGC 61.549 60.000 0.00 0.00 0.00 5.34
162 163 2.753966 CGAATGCCACGCCTTCAGG 61.754 63.158 3.21 0.00 33.87 3.86
183 184 4.820744 CCCCTTGGATGCCGGTGG 62.821 72.222 1.90 0.00 0.00 4.61
233 234 8.053026 TCTACAAGATTCACTACTAGTGGTTC 57.947 38.462 9.48 5.34 45.94 3.62
251 847 2.961522 TCGAGAAAATGCCACGTTTC 57.038 45.000 0.00 0.00 34.57 2.78
252 848 2.489971 TCGAGAAAATGCCACGTTTCT 58.510 42.857 5.19 5.19 44.72 2.52
266 862 1.252015 CGTTTCTATTTCGGCTCGACG 59.748 52.381 0.00 0.00 34.89 5.12
283 880 5.666969 TCGACGAAATGACACATCTTTTT 57.333 34.783 0.00 0.00 33.54 1.94
305 902 8.494016 TTTTTCTCTTTCTTTCTTCTTCTCGT 57.506 30.769 0.00 0.00 0.00 4.18
485 1121 3.672503 GCATCCCCACCCCACCTT 61.673 66.667 0.00 0.00 0.00 3.50
1263 2294 1.982938 CCCTTCCCTCGACGACCTT 60.983 63.158 0.00 0.00 0.00 3.50
1320 2351 1.300620 CACCTTCCGCAACGAGACA 60.301 57.895 0.00 0.00 0.00 3.41
1596 2627 2.029623 GAGTACTACATGGCCTTCGGA 58.970 52.381 3.32 0.00 0.00 4.55
1683 2714 2.178235 GGAAGGTATGCCGTTCGCC 61.178 63.158 0.00 0.00 40.50 5.54
2013 3044 1.147817 ACCTTTGGGTTGATGAGGCTT 59.852 47.619 0.00 0.00 44.73 4.35
2196 3227 1.743252 CAAGAAGGAGGCGCCACTC 60.743 63.158 31.54 18.78 40.02 3.51
2487 3518 5.104360 AGGCCTCAGTGACATGTACAATAAT 60.104 40.000 0.00 0.00 0.00 1.28
2603 3634 1.781025 CTTGCTGTCGCGTTTGGGAA 61.781 55.000 5.77 2.12 38.96 3.97
2754 3785 5.013079 TGTCAGGTGTAAATCAGAAGATGGT 59.987 40.000 0.00 0.00 33.90 3.55
2802 3833 2.838202 TCTTAAGCCTTCCTGTACTGGG 59.162 50.000 17.82 8.78 0.00 4.45
3081 4112 6.153510 GGTATTTGAAAAGCTTGAAGGGAGAT 59.846 38.462 0.00 0.00 0.00 2.75
3219 4250 6.775629 TCAAGTTTGGTTTATCAGCCTTACTT 59.224 34.615 0.00 0.00 33.07 2.24
3438 4469 1.751927 CACCTGGGCCTTGATGCTC 60.752 63.158 4.53 0.00 0.00 4.26
3677 4709 6.189677 AGTAGATAGCGTAGATCAATCTGC 57.810 41.667 2.72 0.57 37.76 4.26
3772 4806 2.110213 AAGCACGGCGACTTTCCA 59.890 55.556 16.62 0.00 0.00 3.53
3942 4976 4.057432 ACAGGCACAATTTGTTACATTGC 58.943 39.130 0.00 0.00 35.36 3.56
3943 4977 3.432933 CAGGCACAATTTGTTACATTGCC 59.567 43.478 15.14 15.14 35.36 4.52
4016 5069 8.883731 AGATATACATTTTGTTATATCCGCAGC 58.116 33.333 0.00 0.00 34.25 5.25
4017 5070 6.875948 ATACATTTTGTTATATCCGCAGCA 57.124 33.333 0.00 0.00 0.00 4.41
4018 5071 4.920376 ACATTTTGTTATATCCGCAGCAC 58.080 39.130 0.00 0.00 0.00 4.40
4019 5072 4.202010 ACATTTTGTTATATCCGCAGCACC 60.202 41.667 0.00 0.00 0.00 5.01
4020 5073 2.700722 TTGTTATATCCGCAGCACCA 57.299 45.000 0.00 0.00 0.00 4.17
4021 5074 2.928801 TGTTATATCCGCAGCACCAT 57.071 45.000 0.00 0.00 0.00 3.55
4022 5075 3.207265 TGTTATATCCGCAGCACCATT 57.793 42.857 0.00 0.00 0.00 3.16
4023 5076 4.344359 TGTTATATCCGCAGCACCATTA 57.656 40.909 0.00 0.00 0.00 1.90
4024 5077 4.709250 TGTTATATCCGCAGCACCATTAA 58.291 39.130 0.00 0.00 0.00 1.40
4025 5078 4.513692 TGTTATATCCGCAGCACCATTAAC 59.486 41.667 0.00 0.00 0.00 2.01
4026 5079 3.492102 ATATCCGCAGCACCATTAACT 57.508 42.857 0.00 0.00 0.00 2.24
4112 5165 6.403049 TCGAGATAAAAGGCAACAGATGTTA 58.597 36.000 0.00 0.00 36.32 2.41
4114 5167 7.011389 TCGAGATAAAAGGCAACAGATGTTATG 59.989 37.037 0.00 0.00 36.32 1.90
4145 5816 7.064371 GTCAGCTGCTATGTCCTGATTATTATG 59.936 40.741 9.47 0.00 36.78 1.90
4193 5864 7.274603 AGACGTTTATGTCTTATACTCCCTC 57.725 40.000 0.00 0.00 46.85 4.30
4194 5865 6.264970 AGACGTTTATGTCTTATACTCCCTCC 59.735 42.308 0.00 0.00 46.85 4.30
4195 5866 5.895534 ACGTTTATGTCTTATACTCCCTCCA 59.104 40.000 0.00 0.00 0.00 3.86
4196 5867 6.553852 ACGTTTATGTCTTATACTCCCTCCAT 59.446 38.462 0.00 0.00 0.00 3.41
4197 5868 7.070821 ACGTTTATGTCTTATACTCCCTCCATT 59.929 37.037 0.00 0.00 0.00 3.16
4198 5869 7.599245 CGTTTATGTCTTATACTCCCTCCATTC 59.401 40.741 0.00 0.00 0.00 2.67
4199 5870 7.554959 TTATGTCTTATACTCCCTCCATTCC 57.445 40.000 0.00 0.00 0.00 3.01
4200 5871 5.157770 TGTCTTATACTCCCTCCATTCCT 57.842 43.478 0.00 0.00 0.00 3.36
4201 5872 6.289482 TGTCTTATACTCCCTCCATTCCTA 57.711 41.667 0.00 0.00 0.00 2.94
4202 5873 6.689561 TGTCTTATACTCCCTCCATTCCTAA 58.310 40.000 0.00 0.00 0.00 2.69
4203 5874 7.136885 TGTCTTATACTCCCTCCATTCCTAAA 58.863 38.462 0.00 0.00 0.00 1.85
4204 5875 7.794683 TGTCTTATACTCCCTCCATTCCTAAAT 59.205 37.037 0.00 0.00 0.00 1.40
4205 5876 9.322769 GTCTTATACTCCCTCCATTCCTAAATA 57.677 37.037 0.00 0.00 0.00 1.40
4210 5881 9.860393 ATACTCCCTCCATTCCTAAATATAAGT 57.140 33.333 0.00 0.00 0.00 2.24
4211 5882 8.208575 ACTCCCTCCATTCCTAAATATAAGTC 57.791 38.462 0.00 0.00 0.00 3.01
4212 5883 8.019652 ACTCCCTCCATTCCTAAATATAAGTCT 58.980 37.037 0.00 0.00 0.00 3.24
4213 5884 8.814448 TCCCTCCATTCCTAAATATAAGTCTT 57.186 34.615 0.00 0.00 0.00 3.01
4214 5885 9.237706 TCCCTCCATTCCTAAATATAAGTCTTT 57.762 33.333 0.00 0.00 0.00 2.52
4215 5886 9.868160 CCCTCCATTCCTAAATATAAGTCTTTT 57.132 33.333 0.00 0.00 0.00 2.27
4243 5914 3.241067 TCCACTATGGACTACAAACGC 57.759 47.619 0.00 0.00 42.67 4.84
4244 5915 2.563620 TCCACTATGGACTACAAACGCA 59.436 45.455 0.00 0.00 42.67 5.24
4245 5916 2.930040 CCACTATGGACTACAAACGCAG 59.070 50.000 0.00 0.00 40.96 5.18
4246 5917 2.348666 CACTATGGACTACAAACGCAGC 59.651 50.000 0.00 0.00 0.00 5.25
4247 5918 2.028476 ACTATGGACTACAAACGCAGCA 60.028 45.455 0.00 0.00 0.00 4.41
4248 5919 1.890876 ATGGACTACAAACGCAGCAA 58.109 45.000 0.00 0.00 0.00 3.91
4249 5920 1.669604 TGGACTACAAACGCAGCAAA 58.330 45.000 0.00 0.00 0.00 3.68
4250 5921 2.017782 TGGACTACAAACGCAGCAAAA 58.982 42.857 0.00 0.00 0.00 2.44
4251 5922 2.621055 TGGACTACAAACGCAGCAAAAT 59.379 40.909 0.00 0.00 0.00 1.82
4252 5923 2.979813 GGACTACAAACGCAGCAAAATG 59.020 45.455 0.00 0.00 0.00 2.32
4253 5924 3.304391 GGACTACAAACGCAGCAAAATGA 60.304 43.478 0.00 0.00 0.00 2.57
4254 5925 3.888934 ACTACAAACGCAGCAAAATGAG 58.111 40.909 0.00 0.00 0.00 2.90
4255 5926 2.869233 ACAAACGCAGCAAAATGAGT 57.131 40.000 0.00 0.00 34.45 3.41
4256 5927 2.462889 ACAAACGCAGCAAAATGAGTG 58.537 42.857 0.00 0.00 33.23 3.51
4257 5928 2.098934 ACAAACGCAGCAAAATGAGTGA 59.901 40.909 0.00 0.00 33.23 3.41
4258 5929 3.114809 CAAACGCAGCAAAATGAGTGAA 58.885 40.909 0.00 0.00 33.23 3.18
4259 5930 3.648339 AACGCAGCAAAATGAGTGAAT 57.352 38.095 0.00 0.00 33.23 2.57
4260 5931 3.207474 ACGCAGCAAAATGAGTGAATC 57.793 42.857 0.00 0.00 31.59 2.52
4261 5932 2.816087 ACGCAGCAAAATGAGTGAATCT 59.184 40.909 0.00 0.00 31.59 2.40
4262 5933 4.002982 ACGCAGCAAAATGAGTGAATCTA 58.997 39.130 0.00 0.00 31.59 1.98
4263 5934 4.142816 ACGCAGCAAAATGAGTGAATCTAC 60.143 41.667 0.00 0.00 31.59 2.59
4264 5935 4.142838 CGCAGCAAAATGAGTGAATCTACA 60.143 41.667 0.00 0.00 0.00 2.74
4265 5936 5.091431 GCAGCAAAATGAGTGAATCTACAC 58.909 41.667 0.00 0.00 40.60 2.90
4279 5950 9.950496 AGTGAATCTACACTCAAAAATATGTCT 57.050 29.630 0.00 0.00 46.36 3.41
4307 5978 6.770746 ACATCCGTATCTAGTTTGTAGTGT 57.229 37.500 0.00 0.00 0.00 3.55
4308 5979 7.870509 ACATCCGTATCTAGTTTGTAGTGTA 57.129 36.000 0.00 0.00 0.00 2.90
4309 5980 8.284945 ACATCCGTATCTAGTTTGTAGTGTAA 57.715 34.615 0.00 0.00 0.00 2.41
4310 5981 8.910944 ACATCCGTATCTAGTTTGTAGTGTAAT 58.089 33.333 0.00 0.00 0.00 1.89
4311 5982 9.395707 CATCCGTATCTAGTTTGTAGTGTAATC 57.604 37.037 0.00 0.00 0.00 1.75
4312 5983 8.743085 TCCGTATCTAGTTTGTAGTGTAATCT 57.257 34.615 0.00 0.00 0.00 2.40
4313 5984 8.834465 TCCGTATCTAGTTTGTAGTGTAATCTC 58.166 37.037 0.00 0.00 0.00 2.75
4314 5985 8.838365 CCGTATCTAGTTTGTAGTGTAATCTCT 58.162 37.037 0.00 0.00 0.00 3.10
4341 6012 7.941795 AAAGACATATATTTACGAACGGAGG 57.058 36.000 0.00 0.00 0.00 4.30
4342 6013 6.022163 AGACATATATTTACGAACGGAGGG 57.978 41.667 0.00 0.00 0.00 4.30
4343 6014 5.771666 AGACATATATTTACGAACGGAGGGA 59.228 40.000 0.00 0.00 0.00 4.20
4344 6015 6.022163 ACATATATTTACGAACGGAGGGAG 57.978 41.667 0.00 0.00 0.00 4.30
4345 6016 5.537674 ACATATATTTACGAACGGAGGGAGT 59.462 40.000 0.00 0.00 0.00 3.85
4354 6025 4.021192 ACGAACGGAGGGAGTATTTGTTTA 60.021 41.667 0.00 0.00 0.00 2.01
4390 6067 2.926200 CCAGAGTTATGAACGAGCAGTG 59.074 50.000 0.00 0.00 36.23 3.66
4407 6084 3.573491 GTCCCGCAGCGGCATTAC 61.573 66.667 29.55 18.19 46.86 1.89
4445 6122 8.622948 ACCAGTTTATTTTCTCCTTTCTAGTG 57.377 34.615 0.00 0.00 0.00 2.74
4502 6179 0.397941 CAGGGTGAACTCTCAAGCCA 59.602 55.000 0.00 0.00 33.82 4.75
4510 6187 3.181445 TGAACTCTCAAGCCAAAAGGCTA 60.181 43.478 9.76 0.00 45.26 3.93
4563 6240 1.181098 GGGGCACATGCTGTCTTGTT 61.181 55.000 3.48 0.00 41.70 2.83
4564 6241 1.533625 GGGCACATGCTGTCTTGTTA 58.466 50.000 3.48 0.00 41.70 2.41
4565 6242 1.470098 GGGCACATGCTGTCTTGTTAG 59.530 52.381 3.48 0.00 41.70 2.34
4567 6244 3.012518 GGCACATGCTGTCTTGTTAGAT 58.987 45.455 3.48 0.00 41.70 1.98
4589 6266 4.404691 CTGTTTCCAGGGAGCACC 57.595 61.111 0.00 0.00 40.67 5.01
4650 6327 4.513442 TGTTATCAACTGCCATGGAGTAC 58.487 43.478 18.40 10.75 0.00 2.73
4651 6328 2.315925 ATCAACTGCCATGGAGTACG 57.684 50.000 18.40 10.78 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.698309 GAGAAGAAAAATAAAAAGGAGGAAAGG 57.302 33.333 0.00 0.00 0.00 3.11
16 17 7.024171 GCGGAGAGAAGAAAAATAAAAAGGAG 58.976 38.462 0.00 0.00 0.00 3.69
27 28 1.697432 TGAAGGGCGGAGAGAAGAAAA 59.303 47.619 0.00 0.00 0.00 2.29
50 51 0.872021 GCACTAGGAGATGAACGGCG 60.872 60.000 4.80 4.80 0.00 6.46
52 53 1.751351 TCAGCACTAGGAGATGAACGG 59.249 52.381 3.32 0.00 0.00 4.44
65 66 2.031163 GGCAGACCGTTCAGCACT 59.969 61.111 0.00 0.00 35.98 4.40
79 80 1.075542 CTTAGAACGCAATCACGGCA 58.924 50.000 0.00 0.00 37.37 5.69
139 140 3.640000 GGCGTGGCATTCGATCCG 61.640 66.667 1.30 0.00 0.00 4.18
199 200 9.778741 AGTAGTGAATCTTGTAGATGAAAAACA 57.221 29.630 0.00 0.00 34.65 2.83
233 234 2.969443 AGAAACGTGGCATTTTCTCG 57.031 45.000 16.96 6.35 37.48 4.04
283 880 7.982354 AGAAACGAGAAGAAGAAAGAAAGAGAA 59.018 33.333 0.00 0.00 0.00 2.87
289 886 6.821665 TCCAAAGAAACGAGAAGAAGAAAGAA 59.178 34.615 0.00 0.00 0.00 2.52
320 917 0.034059 AGAGAGGCAAGGACGTGTTG 59.966 55.000 0.00 0.00 0.00 3.33
484 1120 0.391597 GGCGGTGGATATTCGGAGAA 59.608 55.000 0.00 0.00 45.90 2.87
485 1121 1.469335 GGGCGGTGGATATTCGGAGA 61.469 60.000 0.00 0.00 0.00 3.71
1320 2351 2.364448 GAGAAGGGGAGGCGGAGT 60.364 66.667 0.00 0.00 0.00 3.85
1683 2714 4.125703 AGTCGGTAATGTAGTAGTCCTCG 58.874 47.826 0.00 0.00 0.00 4.63
2196 3227 1.305381 ACCCCTCTCGACCTTCAGG 60.305 63.158 0.00 0.00 42.17 3.86
2487 3518 3.118629 GCTGATCATCCAACAGGACACTA 60.119 47.826 0.00 0.00 33.38 2.74
2603 3634 2.954318 GCATAACTGTTCAGCATCCCAT 59.046 45.455 10.94 0.00 0.00 4.00
2754 3785 8.497554 GGACGTGTAAACTCAAATGTAATAACA 58.502 33.333 0.00 0.00 40.69 2.41
2802 3833 7.283127 TCAATAATATTCTTGCACTCCACCTTC 59.717 37.037 8.35 0.00 0.00 3.46
3081 4112 3.589735 AGACATGTATTTGGTACCACCCA 59.410 43.478 16.04 9.19 37.50 4.51
4007 5060 2.560504 CAGTTAATGGTGCTGCGGATA 58.439 47.619 0.00 0.00 0.00 2.59
4008 5061 1.382522 CAGTTAATGGTGCTGCGGAT 58.617 50.000 0.00 0.00 0.00 4.18
4010 5063 1.802636 CCAGTTAATGGTGCTGCGG 59.197 57.895 0.00 0.00 44.91 5.69
4019 5072 2.938451 TCGAATGCTCTGCCAGTTAATG 59.062 45.455 0.00 0.00 0.00 1.90
4020 5073 3.201290 CTCGAATGCTCTGCCAGTTAAT 58.799 45.455 0.00 0.00 0.00 1.40
4021 5074 2.621338 CTCGAATGCTCTGCCAGTTAA 58.379 47.619 0.00 0.00 0.00 2.01
4022 5075 1.134699 CCTCGAATGCTCTGCCAGTTA 60.135 52.381 0.00 0.00 0.00 2.24
4023 5076 0.392193 CCTCGAATGCTCTGCCAGTT 60.392 55.000 0.00 0.00 0.00 3.16
4024 5077 1.220206 CCTCGAATGCTCTGCCAGT 59.780 57.895 0.00 0.00 0.00 4.00
4025 5078 1.523258 CCCTCGAATGCTCTGCCAG 60.523 63.158 0.00 0.00 0.00 4.85
4026 5079 1.989508 TCCCTCGAATGCTCTGCCA 60.990 57.895 0.00 0.00 0.00 4.92
4089 5142 5.551760 AACATCTGTTGCCTTTTATCTCG 57.448 39.130 0.00 0.00 36.80 4.04
4112 5165 1.836166 ACATAGCAGCTGACAGGACAT 59.164 47.619 20.43 0.00 0.00 3.06
4114 5167 1.472376 GGACATAGCAGCTGACAGGAC 60.472 57.143 20.43 5.75 0.00 3.85
4186 5857 8.019652 AGACTTATATTTAGGAATGGAGGGAGT 58.980 37.037 0.00 0.00 0.00 3.85
4187 5858 8.442660 AGACTTATATTTAGGAATGGAGGGAG 57.557 38.462 0.00 0.00 0.00 4.30
4188 5859 8.814448 AAGACTTATATTTAGGAATGGAGGGA 57.186 34.615 0.00 0.00 0.00 4.20
4189 5860 9.868160 AAAAGACTTATATTTAGGAATGGAGGG 57.132 33.333 0.00 0.00 0.00 4.30
4223 5894 2.563620 TGCGTTTGTAGTCCATAGTGGA 59.436 45.455 0.00 0.00 45.98 4.02
4224 5895 2.930040 CTGCGTTTGTAGTCCATAGTGG 59.070 50.000 0.00 0.00 39.43 4.00
4225 5896 2.348666 GCTGCGTTTGTAGTCCATAGTG 59.651 50.000 0.00 0.00 0.00 2.74
4226 5897 2.028476 TGCTGCGTTTGTAGTCCATAGT 60.028 45.455 0.00 0.00 0.00 2.12
4227 5898 2.616960 TGCTGCGTTTGTAGTCCATAG 58.383 47.619 0.00 0.00 0.00 2.23
4228 5899 2.753055 TGCTGCGTTTGTAGTCCATA 57.247 45.000 0.00 0.00 0.00 2.74
4229 5900 1.890876 TTGCTGCGTTTGTAGTCCAT 58.109 45.000 0.00 0.00 0.00 3.41
4230 5901 1.669604 TTTGCTGCGTTTGTAGTCCA 58.330 45.000 0.00 0.00 0.00 4.02
4231 5902 2.766970 TTTTGCTGCGTTTGTAGTCC 57.233 45.000 0.00 0.00 0.00 3.85
4232 5903 3.884169 TCATTTTGCTGCGTTTGTAGTC 58.116 40.909 0.00 0.00 0.00 2.59
4233 5904 3.315191 ACTCATTTTGCTGCGTTTGTAGT 59.685 39.130 0.00 0.00 0.00 2.73
4234 5905 3.665409 CACTCATTTTGCTGCGTTTGTAG 59.335 43.478 0.00 0.00 0.00 2.74
4235 5906 3.313803 TCACTCATTTTGCTGCGTTTGTA 59.686 39.130 0.00 0.00 0.00 2.41
4236 5907 2.098934 TCACTCATTTTGCTGCGTTTGT 59.901 40.909 0.00 0.00 0.00 2.83
4237 5908 2.730069 TCACTCATTTTGCTGCGTTTG 58.270 42.857 0.00 0.00 0.00 2.93
4238 5909 3.435105 TTCACTCATTTTGCTGCGTTT 57.565 38.095 0.00 0.00 0.00 3.60
4239 5910 3.254166 AGATTCACTCATTTTGCTGCGTT 59.746 39.130 0.00 0.00 0.00 4.84
4240 5911 2.816087 AGATTCACTCATTTTGCTGCGT 59.184 40.909 0.00 0.00 0.00 5.24
4241 5912 3.482722 AGATTCACTCATTTTGCTGCG 57.517 42.857 0.00 0.00 0.00 5.18
4242 5913 5.091431 GTGTAGATTCACTCATTTTGCTGC 58.909 41.667 0.00 0.00 35.68 5.25
4243 5914 6.492007 AGTGTAGATTCACTCATTTTGCTG 57.508 37.500 0.00 0.00 44.07 4.41
4281 5952 9.565090 ACACTACAAACTAGATACGGATGTATA 57.435 33.333 0.00 0.00 41.37 1.47
4282 5953 8.461249 ACACTACAAACTAGATACGGATGTAT 57.539 34.615 0.00 0.00 43.97 2.29
4283 5954 7.870509 ACACTACAAACTAGATACGGATGTA 57.129 36.000 0.00 0.00 34.45 2.29
4284 5955 6.770746 ACACTACAAACTAGATACGGATGT 57.229 37.500 0.00 0.00 0.00 3.06
4285 5956 9.395707 GATTACACTACAAACTAGATACGGATG 57.604 37.037 0.00 0.00 0.00 3.51
4286 5957 9.352191 AGATTACACTACAAACTAGATACGGAT 57.648 33.333 0.00 0.00 0.00 4.18
4287 5958 8.743085 AGATTACACTACAAACTAGATACGGA 57.257 34.615 0.00 0.00 0.00 4.69
4288 5959 8.838365 AGAGATTACACTACAAACTAGATACGG 58.162 37.037 0.00 0.00 0.00 4.02
4315 5986 8.823818 CCTCCGTTCGTAAATATATGTCTTTTT 58.176 33.333 0.00 0.00 0.00 1.94
4316 5987 7.440255 CCCTCCGTTCGTAAATATATGTCTTTT 59.560 37.037 0.00 0.00 0.00 2.27
4317 5988 6.927381 CCCTCCGTTCGTAAATATATGTCTTT 59.073 38.462 0.00 0.00 0.00 2.52
4318 5989 6.266103 TCCCTCCGTTCGTAAATATATGTCTT 59.734 38.462 0.00 0.00 0.00 3.01
4319 5990 5.771666 TCCCTCCGTTCGTAAATATATGTCT 59.228 40.000 0.00 0.00 0.00 3.41
4320 5991 6.017400 TCCCTCCGTTCGTAAATATATGTC 57.983 41.667 0.00 0.00 0.00 3.06
4321 5992 5.537674 ACTCCCTCCGTTCGTAAATATATGT 59.462 40.000 0.00 0.00 0.00 2.29
4322 5993 6.022163 ACTCCCTCCGTTCGTAAATATATG 57.978 41.667 0.00 0.00 0.00 1.78
4323 5994 7.951347 ATACTCCCTCCGTTCGTAAATATAT 57.049 36.000 0.00 0.00 0.00 0.86
4324 5995 7.765695 AATACTCCCTCCGTTCGTAAATATA 57.234 36.000 0.00 0.00 0.00 0.86
4325 5996 6.661304 AATACTCCCTCCGTTCGTAAATAT 57.339 37.500 0.00 0.00 0.00 1.28
4326 5997 6.127366 ACAAATACTCCCTCCGTTCGTAAATA 60.127 38.462 0.00 0.00 0.00 1.40
4327 5998 5.114081 CAAATACTCCCTCCGTTCGTAAAT 58.886 41.667 0.00 0.00 0.00 1.40
4328 5999 4.021192 ACAAATACTCCCTCCGTTCGTAAA 60.021 41.667 0.00 0.00 0.00 2.01
4329 6000 3.511146 ACAAATACTCCCTCCGTTCGTAA 59.489 43.478 0.00 0.00 0.00 3.18
4330 6001 3.091545 ACAAATACTCCCTCCGTTCGTA 58.908 45.455 0.00 0.00 0.00 3.43
4331 6002 1.897802 ACAAATACTCCCTCCGTTCGT 59.102 47.619 0.00 0.00 0.00 3.85
4332 6003 2.667473 ACAAATACTCCCTCCGTTCG 57.333 50.000 0.00 0.00 0.00 3.95
4333 6004 5.240121 TGTAAACAAATACTCCCTCCGTTC 58.760 41.667 0.00 0.00 0.00 3.95
4334 6005 5.012354 TCTGTAAACAAATACTCCCTCCGTT 59.988 40.000 0.00 0.00 0.00 4.44
4335 6006 4.529377 TCTGTAAACAAATACTCCCTCCGT 59.471 41.667 0.00 0.00 0.00 4.69
4336 6007 5.080969 TCTGTAAACAAATACTCCCTCCG 57.919 43.478 0.00 0.00 0.00 4.63
4337 6008 5.189145 TCCTCTGTAAACAAATACTCCCTCC 59.811 44.000 0.00 0.00 0.00 4.30
4338 6009 6.295719 TCCTCTGTAAACAAATACTCCCTC 57.704 41.667 0.00 0.00 0.00 4.30
4339 6010 6.893020 ATCCTCTGTAAACAAATACTCCCT 57.107 37.500 0.00 0.00 0.00 4.20
4340 6011 6.183360 GCAATCCTCTGTAAACAAATACTCCC 60.183 42.308 0.00 0.00 0.00 4.30
4341 6012 6.374333 TGCAATCCTCTGTAAACAAATACTCC 59.626 38.462 0.00 0.00 0.00 3.85
4342 6013 7.119846 AGTGCAATCCTCTGTAAACAAATACTC 59.880 37.037 0.00 0.00 0.00 2.59
4343 6014 6.942576 AGTGCAATCCTCTGTAAACAAATACT 59.057 34.615 0.00 0.00 0.00 2.12
4344 6015 7.145932 AGTGCAATCCTCTGTAAACAAATAC 57.854 36.000 0.00 0.00 0.00 1.89
4345 6016 6.374333 GGAGTGCAATCCTCTGTAAACAAATA 59.626 38.462 25.54 0.00 36.35 1.40
4354 6025 1.554160 CTCTGGAGTGCAATCCTCTGT 59.446 52.381 31.33 0.00 40.29 3.41
4445 6122 4.030452 GCGCTGGCTGTGTGGTTC 62.030 66.667 0.00 0.00 35.83 3.62
4472 6149 3.815962 GAGTTCACCCTGAAAGAAACTCC 59.184 47.826 0.00 0.00 38.22 3.85
4589 6266 4.283678 CAAAATGTTGTTGCTTGCAATGG 58.716 39.130 11.32 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.