Multiple sequence alignment - TraesCS5D01G028100

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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 TraesCS5D01G028100 chr5D 100.000 3737 0 0 1 3737 26793374 26789638 0.000000e+00 6902
1 TraesCS5D01G028100 chr5A 93.401 3046 127 45 1 3012 18640099 18637094 0.000000e+00 4444
2 TraesCS5D01G028100 chr5A 88.488 582 34 17 3189 3737 18635224 18634643 0.000000e+00 673
3 TraesCS5D01G028100 chr5B 95.916 1763 55 4 1120 2878 19440090 19438341 0.000000e+00 2841
4 TraesCS5D01G028100 chr5B 91.454 667 36 11 474 1123 19440800 19440138 0.000000e+00 896
5 TraesCS5D01G028100 chr5B 86.207 290 15 11 1 267 19441467 19441180 1.310000e-74 291
6 TraesCS5D01G028100 chr5B 85.862 290 16 3 3420 3703 19437878 19437608 6.110000e-73 285
7 TraesCS5D01G028100 chr5B 82.031 256 31 7 2939 3191 19438334 19438091 1.760000e-48 204
8 TraesCS5D01G028100 chr5B 90.265 113 11 0 351 463 19441024 19440912 8.360000e-32 148
9 TraesCS5D01G028100 chr1A 93.293 164 10 1 1854 2016 60280876 60280713 1.340000e-59 241
10 TraesCS5D01G028100 chr4A 92.683 164 11 1 1854 2016 541739194 541739031 6.240000e-58 235
11 TraesCS5D01G028100 chr3B 93.168 161 10 1 1854 2013 606328111 606328271 6.240000e-58 235
12 TraesCS5D01G028100 chr3B 92.073 164 12 1 1854 2016 8696956 8696793 2.900000e-56 230
13 TraesCS5D01G028100 chr2A 92.547 161 11 1 1854 2013 635593566 635593726 2.900000e-56 230
14 TraesCS5D01G028100 chr6B 91.463 164 13 1 1854 2016 691829693 691829530 1.350000e-54 224


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 TraesCS5D01G028100 chr5D 26789638 26793374 3736 True 6902.0 6902 100.0000 1 3737 1 chr5D.!!$R1 3736
1 TraesCS5D01G028100 chr5A 18634643 18640099 5456 True 2558.5 4444 90.9445 1 3737 2 chr5A.!!$R1 3736
2 TraesCS5D01G028100 chr5B 19437608 19441467 3859 True 777.5 2841 88.6225 1 3703 6 chr5B.!!$R1 3702

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
143 146 0.038526 GGTTTCTTCTCGCAGACCGA 60.039 55.0 0.0 0.0 45.15 4.69 F
715 916 1.076332 ATACGTGACTGAAAAGCCGC 58.924 50.0 0.0 0.0 0.00 6.53 F
2169 2439 1.388547 GTGGTTTCTGGTTGCACTCA 58.611 50.0 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2346 0.602638 CCGGAAGTGCTGCTGTACAA 60.603 55.0 13.86 0.0 0.0 2.41 R
2285 2555 0.872021 CCCGTAGCGTGATCTCTTGC 60.872 60.0 0.00 0.0 0.0 4.01 R
3043 3383 0.257616 TAAAAAGGGGGCCGATCTGG 59.742 55.0 0.00 0.0 42.5 3.86 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
54 55 2.035783 GTCAAGCCAAGGTCCCCC 59.964 66.667 0.00 0.00 0.00 5.40
55 56 2.121506 TCAAGCCAAGGTCCCCCT 60.122 61.111 0.00 0.00 45.63 4.79
70 71 0.637195 CCCCTCCCACTTCTCCTCTA 59.363 60.000 0.00 0.00 0.00 2.43
86 89 3.089874 TATCTGCAGCCGCCCCTT 61.090 61.111 9.47 0.00 37.32 3.95
98 101 2.626780 GCCCCTTGCTTGGTTCGAC 61.627 63.158 0.00 0.00 36.87 4.20
130 133 2.839486 TCTTCACTGATGCGGTTTCT 57.161 45.000 0.00 0.00 0.00 2.52
141 144 2.446341 CGGTTTCTTCTCGCAGACC 58.554 57.895 0.00 0.00 0.00 3.85
142 145 1.344942 CGGTTTCTTCTCGCAGACCG 61.345 60.000 0.00 0.00 43.12 4.79
143 146 0.038526 GGTTTCTTCTCGCAGACCGA 60.039 55.000 0.00 0.00 45.15 4.69
263 290 3.971245 AAGCTACTTGTTCCTCTCCTG 57.029 47.619 0.00 0.00 0.00 3.86
287 354 2.151202 CGTGGTAGATTTTGTGCTGGT 58.849 47.619 0.00 0.00 0.00 4.00
289 356 2.488153 GTGGTAGATTTTGTGCTGGTCC 59.512 50.000 0.00 0.00 0.00 4.46
306 393 1.076777 CCTCGCCCCATGGATTTGT 60.077 57.895 15.22 0.00 0.00 2.83
315 402 3.371487 CCCCATGGATTTGTGCTGTAGTA 60.371 47.826 15.22 0.00 0.00 1.82
321 408 5.754782 TGGATTTGTGCTGTAGTAATGGAT 58.245 37.500 0.00 0.00 0.00 3.41
329 416 4.469586 TGCTGTAGTAATGGATTGTCCTGA 59.530 41.667 0.00 0.00 37.46 3.86
335 422 9.559732 TGTAGTAATGGATTGTCCTGATATTTG 57.440 33.333 0.00 0.00 37.46 2.32
336 423 7.516198 AGTAATGGATTGTCCTGATATTTGC 57.484 36.000 0.00 0.00 37.46 3.68
337 424 7.293073 AGTAATGGATTGTCCTGATATTTGCT 58.707 34.615 0.00 0.00 37.46 3.91
339 426 4.209538 TGGATTGTCCTGATATTTGCTGG 58.790 43.478 0.00 0.00 37.46 4.85
340 427 3.005155 GGATTGTCCTGATATTTGCTGGC 59.995 47.826 0.00 0.00 32.53 4.85
343 430 2.091720 TGTCCTGATATTTGCTGGCCAT 60.092 45.455 5.51 0.00 0.00 4.40
344 431 2.555757 GTCCTGATATTTGCTGGCCATC 59.444 50.000 5.51 1.26 0.00 3.51
346 433 2.295349 CCTGATATTTGCTGGCCATCAC 59.705 50.000 9.25 0.69 0.00 3.06
348 435 2.953648 TGATATTTGCTGGCCATCACTG 59.046 45.455 9.25 0.00 0.00 3.66
349 436 1.105457 TATTTGCTGGCCATCACTGC 58.895 50.000 9.25 7.98 0.00 4.40
358 457 1.590932 GCCATCACTGCATGGAGTAG 58.409 55.000 20.32 13.93 45.79 2.57
360 459 2.420547 GCCATCACTGCATGGAGTAGAA 60.421 50.000 20.32 8.98 45.79 2.10
415 514 7.487189 GGAAATTATCACTCAAACTTGCTCATG 59.513 37.037 0.00 0.00 0.00 3.07
430 529 6.755141 ACTTGCTCATGTTGCATCAATAATTC 59.245 34.615 14.61 0.00 40.34 2.17
433 532 6.532302 TGCTCATGTTGCATCAATAATTCAAC 59.468 34.615 11.00 0.00 40.59 3.18
468 570 8.879427 ACCATACTGATGTACTATATGCTACA 57.121 34.615 0.00 0.00 0.00 2.74
715 916 1.076332 ATACGTGACTGAAAAGCCGC 58.924 50.000 0.00 0.00 0.00 6.53
1188 1458 4.876107 GTGGTCCTTGTGTACATATTCTGG 59.124 45.833 0.00 0.00 0.00 3.86
1199 1469 9.040939 TGTGTACATATTCTGGATGATAAAACG 57.959 33.333 0.00 0.00 0.00 3.60
1207 1477 4.122776 CTGGATGATAAAACGAGGGACAG 58.877 47.826 0.00 0.00 0.00 3.51
1298 1568 3.058016 CGAGCAAATTCAGCCTTTCTTCA 60.058 43.478 0.00 0.00 0.00 3.02
1341 1611 4.637276 TCAAGTATGACGGTGTCAACAAT 58.363 39.130 3.47 0.00 45.96 2.71
1536 1806 4.721776 AGTATTCCAGAAGCCCTAATCACA 59.278 41.667 0.00 0.00 0.00 3.58
1932 2202 2.301346 GTGAATTGGGGCCTGTATCTG 58.699 52.381 0.84 0.00 0.00 2.90
1959 2229 5.765182 CACTCTGTTTTGGAACCTCAACTAT 59.235 40.000 0.00 0.00 34.80 2.12
2076 2346 4.202631 GGATACCTCTACCCTCTGATCACT 60.203 50.000 0.00 0.00 0.00 3.41
2169 2439 1.388547 GTGGTTTCTGGTTGCACTCA 58.611 50.000 0.00 0.00 0.00 3.41
2235 2505 5.997129 TGTTACTGAAATGAGCAGTGATTCA 59.003 36.000 0.00 0.00 45.52 2.57
2247 2517 3.311871 GCAGTGATTCATACCAGCTTCTG 59.688 47.826 0.00 0.00 0.00 3.02
2285 2555 0.539051 ATGCTCCCTGAGTTCTTCGG 59.461 55.000 0.00 0.00 31.39 4.30
2331 2601 0.465705 TGATCGGCATCCTGTTCTCC 59.534 55.000 0.00 0.00 0.00 3.71
2382 2652 0.942962 GCTTCCAGGAGATCATTGCG 59.057 55.000 0.00 0.00 0.00 4.85
2385 2655 1.147824 CCAGGAGATCATTGCGGCT 59.852 57.895 0.00 0.00 0.00 5.52
2535 2805 3.169099 CATCCCTCCGACTATCCTGATT 58.831 50.000 0.00 0.00 0.00 2.57
2695 2965 2.765807 ATCTGCTGGACCCCTCGG 60.766 66.667 0.00 0.00 0.00 4.63
2724 2994 1.064296 CGAAGATGAGACGACCCCG 59.936 63.158 0.00 0.00 42.50 5.73
2733 3003 2.918802 ACGACCCCGCTTGTGGTA 60.919 61.111 0.00 0.00 39.95 3.25
2774 3044 8.451908 AGTGTAATAAAAGGATAGGAACATGC 57.548 34.615 0.00 0.00 0.00 4.06
2834 3104 6.474819 TTGTATACCAACTTGTTCGTCATG 57.525 37.500 0.00 0.00 0.00 3.07
2835 3105 5.785243 TGTATACCAACTTGTTCGTCATGA 58.215 37.500 0.00 0.00 0.00 3.07
2864 3137 2.821688 GAAGAGCATGCTGAGCGCC 61.822 63.158 28.27 9.57 38.05 6.53
2913 3186 6.556495 TCAGACTCTATTTGGCCTAATCTCAT 59.444 38.462 16.00 1.36 0.00 2.90
2921 3194 3.378512 TGGCCTAATCTCATCTGTGACT 58.621 45.455 3.32 0.00 0.00 3.41
2922 3195 3.133542 TGGCCTAATCTCATCTGTGACTG 59.866 47.826 3.32 0.00 0.00 3.51
2923 3196 3.133721 GGCCTAATCTCATCTGTGACTGT 59.866 47.826 0.00 0.00 0.00 3.55
2928 3201 7.255625 GCCTAATCTCATCTGTGACTGTATGTA 60.256 40.741 0.00 0.00 0.00 2.29
2931 3204 8.476064 AATCTCATCTGTGACTGTATGTAGAT 57.524 34.615 0.00 0.00 0.00 1.98
2962 3238 5.121105 TGATAGACGTCCGATTAACTGAGA 58.879 41.667 13.01 0.00 0.00 3.27
3008 3348 2.289882 TGCTGGGATATAGTGCATGCTC 60.290 50.000 20.33 15.94 0.00 4.26
3009 3349 2.027377 GCTGGGATATAGTGCATGCTCT 60.027 50.000 24.28 24.28 0.00 4.09
3010 3350 3.597255 CTGGGATATAGTGCATGCTCTG 58.403 50.000 27.98 8.49 0.00 3.35
3011 3351 2.303890 TGGGATATAGTGCATGCTCTGG 59.696 50.000 27.98 0.00 0.00 3.86
3012 3352 2.355513 GGGATATAGTGCATGCTCTGGG 60.356 54.545 27.98 0.00 0.00 4.45
3013 3353 2.304180 GGATATAGTGCATGCTCTGGGT 59.696 50.000 27.98 17.30 0.00 4.51
3014 3354 3.244700 GGATATAGTGCATGCTCTGGGTT 60.245 47.826 27.98 14.41 0.00 4.11
3015 3355 2.814805 ATAGTGCATGCTCTGGGTTT 57.185 45.000 27.98 7.27 0.00 3.27
3016 3356 2.584835 TAGTGCATGCTCTGGGTTTT 57.415 45.000 27.98 6.59 0.00 2.43
3017 3357 2.584835 AGTGCATGCTCTGGGTTTTA 57.415 45.000 20.86 0.00 0.00 1.52
3018 3358 2.162681 AGTGCATGCTCTGGGTTTTAC 58.837 47.619 20.86 5.46 0.00 2.01
3019 3359 2.162681 GTGCATGCTCTGGGTTTTACT 58.837 47.619 20.33 0.00 0.00 2.24
3020 3360 2.162408 GTGCATGCTCTGGGTTTTACTC 59.838 50.000 20.33 0.00 0.00 2.59
3022 3362 3.019564 GCATGCTCTGGGTTTTACTCAT 58.980 45.455 11.37 0.00 0.00 2.90
3024 3364 4.274459 GCATGCTCTGGGTTTTACTCATAG 59.726 45.833 11.37 0.00 0.00 2.23
3025 3365 3.873910 TGCTCTGGGTTTTACTCATAGC 58.126 45.455 9.40 9.40 45.68 2.97
3026 3366 3.206964 GCTCTGGGTTTTACTCATAGCC 58.793 50.000 5.94 0.00 41.37 3.93
3027 3367 3.458189 CTCTGGGTTTTACTCATAGCCG 58.542 50.000 0.00 0.00 32.18 5.52
3028 3368 2.169769 TCTGGGTTTTACTCATAGCCGG 59.830 50.000 0.00 0.00 37.20 6.13
3030 3370 0.935196 GGTTTTACTCATAGCCGGCG 59.065 55.000 23.20 9.03 0.00 6.46
3031 3371 0.303796 GTTTTACTCATAGCCGGCGC 59.696 55.000 23.20 0.00 0.00 6.53
3032 3372 0.812412 TTTTACTCATAGCCGGCGCC 60.812 55.000 23.20 19.07 34.57 6.53
3033 3373 1.682451 TTTACTCATAGCCGGCGCCT 61.682 55.000 26.68 8.66 34.57 5.52
3034 3374 0.824595 TTACTCATAGCCGGCGCCTA 60.825 55.000 26.68 11.02 34.57 3.93
3035 3375 1.521450 TACTCATAGCCGGCGCCTAC 61.521 60.000 26.68 16.51 34.57 3.18
3039 3379 1.227556 ATAGCCGGCGCCTACAAAG 60.228 57.895 26.68 7.40 34.57 2.77
3040 3380 1.968050 ATAGCCGGCGCCTACAAAGT 61.968 55.000 26.68 0.95 34.57 2.66
3041 3381 2.845752 TAGCCGGCGCCTACAAAGTG 62.846 60.000 26.68 5.71 34.57 3.16
3042 3382 3.799755 CCGGCGCCTACAAAGTGC 61.800 66.667 26.68 0.00 40.04 4.40
3045 3385 2.671619 GCGCCTACAAAGTGCCCA 60.672 61.111 0.00 0.00 34.66 5.36
3047 3387 1.003839 CGCCTACAAAGTGCCCAGA 60.004 57.895 0.00 0.00 0.00 3.86
3048 3388 0.392998 CGCCTACAAAGTGCCCAGAT 60.393 55.000 0.00 0.00 0.00 2.90
3049 3389 1.383523 GCCTACAAAGTGCCCAGATC 58.616 55.000 0.00 0.00 0.00 2.75
3050 3390 1.656652 CCTACAAAGTGCCCAGATCG 58.343 55.000 0.00 0.00 0.00 3.69
3051 3391 1.656652 CTACAAAGTGCCCAGATCGG 58.343 55.000 0.00 0.00 0.00 4.18
3092 4975 5.034797 GGATTAAAGCAAATACAGCCGTTC 58.965 41.667 0.00 0.00 0.00 3.95
3109 4992 3.541711 CGTTCGATGAAACAGTCAAACC 58.458 45.455 0.00 0.00 40.50 3.27
3125 5008 1.811645 AACCCGCCCCAAAATCGTTG 61.812 55.000 0.00 0.00 0.00 4.10
3202 5174 4.351938 ACGCCGTTGTCGCAGCTA 62.352 61.111 0.00 0.00 35.54 3.32
3203 5175 3.838795 CGCCGTTGTCGCAGCTAC 61.839 66.667 0.00 0.00 35.54 3.58
3232 5204 2.883253 GTCGCAGCTTCTCGCCTC 60.883 66.667 0.00 0.00 40.39 4.70
3254 5226 4.104417 GAGCTCGACGTCGTGGCT 62.104 66.667 38.34 38.34 45.41 4.75
3258 5230 4.994201 TCGACGTCGTGGCTGTGC 62.994 66.667 34.40 0.00 40.80 4.57
3347 5340 3.927163 TTTTCGCCTCGTCGGAGCC 62.927 63.158 0.00 0.00 39.06 4.70
3400 5397 2.788191 CTTTTCACCTCGCCGGAGCT 62.788 60.000 5.05 0.00 39.06 4.09
3405 5402 1.966451 ACCTCGCCGGAGCTTTTTG 60.966 57.895 5.05 0.00 39.06 2.44
3409 5406 1.207593 CGCCGGAGCTTTTTGTCAG 59.792 57.895 5.05 0.00 36.60 3.51
3462 5481 2.572095 CTATGCACCTCGCCGGTTGA 62.572 60.000 1.90 0.00 46.37 3.18
3524 5544 2.554272 CCGGTCGCAACTTTTCGG 59.446 61.111 0.00 0.00 0.00 4.30
3554 5574 2.022195 GCATCTAGGACGGTGTACTCA 58.978 52.381 0.00 0.00 0.00 3.41
3647 5672 3.587061 TCAATAATCACTGGACACACCCT 59.413 43.478 0.00 0.00 38.00 4.34
3695 5720 5.335819 CCACAAACAACACATATCAGCATCA 60.336 40.000 0.00 0.00 0.00 3.07
3714 5739 6.038382 AGCATCAGATTAACAGATTTGAGCTG 59.962 38.462 0.00 0.00 39.26 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 2.627699 GCAGATAGAGGAGAAGTGGGAG 59.372 54.545 0.00 0.00 0.00 4.30
55 56 2.023984 TGCAGATAGAGGAGAAGTGGGA 60.024 50.000 0.00 0.00 0.00 4.37
70 71 4.809496 CAAGGGGCGGCTGCAGAT 62.809 66.667 20.43 0.05 45.35 2.90
86 89 0.179067 AAACGGAGTCGAACCAAGCA 60.179 50.000 9.94 0.00 45.00 3.91
98 101 2.478134 CAGTGAAGAAGAGCAAACGGAG 59.522 50.000 0.00 0.00 0.00 4.63
130 133 4.415332 GGCGTCGGTCTGCGAGAA 62.415 66.667 0.00 0.00 0.00 2.87
157 176 3.699134 AAGAAGAATCCCCCGCGCC 62.699 63.158 0.00 0.00 0.00 6.53
213 237 2.159099 TGCCGGAGTATAAGAAGCACAG 60.159 50.000 5.05 0.00 0.00 3.66
215 239 2.202566 GTGCCGGAGTATAAGAAGCAC 58.797 52.381 5.05 0.00 41.86 4.40
216 240 1.828595 TGTGCCGGAGTATAAGAAGCA 59.171 47.619 5.05 0.00 0.00 3.91
217 241 2.474816 CTGTGCCGGAGTATAAGAAGC 58.525 52.381 5.05 0.00 0.00 3.86
263 290 1.401018 GCACAAAATCTACCACGGCAC 60.401 52.381 0.00 0.00 0.00 5.01
287 354 1.227102 CAAATCCATGGGGCGAGGA 59.773 57.895 13.02 0.00 35.59 3.71
289 356 2.008268 GCACAAATCCATGGGGCGAG 62.008 60.000 13.02 1.19 0.00 5.03
306 393 4.469586 TCAGGACAATCCATTACTACAGCA 59.530 41.667 0.00 0.00 39.61 4.41
315 402 5.303589 CCAGCAAATATCAGGACAATCCATT 59.696 40.000 0.00 0.00 39.61 3.16
321 408 2.291475 TGGCCAGCAAATATCAGGACAA 60.291 45.455 0.00 0.00 33.62 3.18
329 416 1.684983 GCAGTGATGGCCAGCAAATAT 59.315 47.619 28.14 9.46 0.00 1.28
335 422 2.782222 CCATGCAGTGATGGCCAGC 61.782 63.158 15.83 15.83 36.69 4.85
336 423 1.077285 TCCATGCAGTGATGGCCAG 60.077 57.895 13.05 0.00 42.52 4.85
337 424 1.077285 CTCCATGCAGTGATGGCCA 60.077 57.895 8.56 8.56 42.52 5.36
339 426 1.139654 TCTACTCCATGCAGTGATGGC 59.860 52.381 0.00 0.00 42.52 4.40
340 427 3.464907 CTTCTACTCCATGCAGTGATGG 58.535 50.000 0.00 12.77 43.96 3.51
343 430 2.182827 AGCTTCTACTCCATGCAGTGA 58.817 47.619 0.00 0.00 0.00 3.41
344 431 2.687700 AGCTTCTACTCCATGCAGTG 57.312 50.000 0.00 0.00 0.00 3.66
346 433 5.423015 TCTAAAAGCTTCTACTCCATGCAG 58.577 41.667 0.00 0.00 0.00 4.41
348 435 6.743575 TTTCTAAAAGCTTCTACTCCATGC 57.256 37.500 0.00 0.00 0.00 4.06
349 436 7.772757 AGGATTTCTAAAAGCTTCTACTCCATG 59.227 37.037 0.00 0.00 0.00 3.66
430 529 8.213518 ACATCAGTATGGTATTTAAGCTGTTG 57.786 34.615 0.00 0.00 37.43 3.33
468 570 9.174166 GAATTTTCGTATGGCCATATAAGGTAT 57.826 33.333 27.84 14.21 0.00 2.73
560 761 6.362820 GCCTATAAGATAGCAGTCGTGTTAAC 59.637 42.308 0.00 0.00 0.00 2.01
715 916 7.798516 TGTCTACACGTACTACTAAAAGAAACG 59.201 37.037 0.00 0.00 36.32 3.60
838 1053 8.807581 GTTGGAAAGCCGATTATCAATAAAAAG 58.192 33.333 0.00 0.00 36.79 2.27
1188 1458 3.531538 TGCTGTCCCTCGTTTTATCATC 58.468 45.455 0.00 0.00 0.00 2.92
1199 1469 3.073274 ACAAACCTTATGCTGTCCCTC 57.927 47.619 0.00 0.00 0.00 4.30
1298 1568 5.928976 TGAAATCAACACGATCCTCCATAT 58.071 37.500 0.00 0.00 31.11 1.78
1341 1611 1.066858 CCCTTACGCTCTTTGCTCTCA 60.067 52.381 0.00 0.00 40.11 3.27
1449 1719 1.071987 TCCAGCAGCCTTGACACTG 59.928 57.895 0.00 0.00 36.96 3.66
1536 1806 4.101741 GGAAACATAGTACCCATCTCAGCT 59.898 45.833 0.00 0.00 0.00 4.24
1702 1972 2.041265 ACCCCCGAGAGCTGGAAT 59.959 61.111 0.00 0.00 0.00 3.01
1872 2142 7.831691 TTCAAACCATCTTGAAGGTTCAATA 57.168 32.000 10.18 0.00 46.92 1.90
1932 2202 3.945285 TGAGGTTCCAAAACAGAGTGTTC 59.055 43.478 0.00 0.00 40.14 3.18
1959 2229 4.402155 GCCAATGTACTGATTGAATCCCAA 59.598 41.667 2.26 0.00 35.65 4.12
2076 2346 0.602638 CCGGAAGTGCTGCTGTACAA 60.603 55.000 13.86 0.00 0.00 2.41
2169 2439 3.211963 GCCGCCGCTTGAATCCAT 61.212 61.111 0.00 0.00 0.00 3.41
2196 2466 4.037446 TCAGTAACAAAGTTGCCCATGTTC 59.963 41.667 0.00 0.00 37.25 3.18
2247 2517 4.864334 CCACGCTCAGCCATCCCC 62.864 72.222 0.00 0.00 0.00 4.81
2285 2555 0.872021 CCCGTAGCGTGATCTCTTGC 60.872 60.000 0.00 0.00 0.00 4.01
2331 2601 4.657824 AGGACCACACCGAACGCG 62.658 66.667 3.53 3.53 34.73 6.01
2340 2610 2.519622 CCAGGACAGCAGGACCACA 61.520 63.158 0.00 0.00 0.00 4.17
2382 2652 2.100087 GCAGTAGAGGTAGTTCTCAGCC 59.900 54.545 0.00 0.00 36.30 4.85
2385 2655 3.690139 CGAAGCAGTAGAGGTAGTTCTCA 59.310 47.826 0.00 0.00 36.30 3.27
2535 2805 1.301637 CAGCACCATCACCACGACA 60.302 57.895 0.00 0.00 0.00 4.35
2715 2985 2.234913 ATACCACAAGCGGGGTCGTC 62.235 60.000 0.00 0.00 38.60 4.20
2724 2994 6.075762 TGCATCATAAATCATACCACAAGC 57.924 37.500 0.00 0.00 0.00 4.01
2774 3044 2.555325 CACATGGCATTATACAGGGCAG 59.445 50.000 0.00 0.00 40.58 4.85
2823 3093 9.663904 CTTCTATTTCTTTTTCATGACGAACAA 57.336 29.630 0.00 0.00 31.73 2.83
2828 3098 7.521529 TGCTCTTCTATTTCTTTTTCATGACG 58.478 34.615 0.00 0.00 0.00 4.35
2829 3099 9.286946 CATGCTCTTCTATTTCTTTTTCATGAC 57.713 33.333 0.00 0.00 31.01 3.06
2830 3100 7.972277 GCATGCTCTTCTATTTCTTTTTCATGA 59.028 33.333 11.37 0.00 31.01 3.07
2831 3101 7.974501 AGCATGCTCTTCTATTTCTTTTTCATG 59.025 33.333 16.30 0.00 0.00 3.07
2832 3102 7.974501 CAGCATGCTCTTCTATTTCTTTTTCAT 59.025 33.333 19.68 0.00 0.00 2.57
2833 3103 7.175467 TCAGCATGCTCTTCTATTTCTTTTTCA 59.825 33.333 19.68 0.00 34.76 2.69
2834 3104 7.533426 TCAGCATGCTCTTCTATTTCTTTTTC 58.467 34.615 19.68 0.00 34.76 2.29
2835 3105 7.458409 TCAGCATGCTCTTCTATTTCTTTTT 57.542 32.000 19.68 0.00 34.76 1.94
2864 3137 3.914364 GTGCGCCTTTGATGTTTCTAAAG 59.086 43.478 4.18 0.00 0.00 1.85
2882 3155 2.544685 CCAAATAGAGTCTGAGGTGCG 58.455 52.381 1.86 0.00 0.00 5.34
2928 3201 8.684386 ATCGGACGTCTATCATAATGATATCT 57.316 34.615 16.46 0.00 38.54 1.98
2931 3204 9.999009 GTTAATCGGACGTCTATCATAATGATA 57.001 33.333 16.46 0.00 38.26 2.15
2941 3214 4.515944 CCTCTCAGTTAATCGGACGTCTAT 59.484 45.833 16.46 6.82 0.00 1.98
2950 3226 4.184629 CCAAACCTCCTCTCAGTTAATCG 58.815 47.826 0.00 0.00 0.00 3.34
2962 3238 2.310930 TTTGGGCTGCCAAACCTCCT 62.311 55.000 22.05 0.00 35.16 3.69
3008 3348 2.561569 CCGGCTATGAGTAAAACCCAG 58.438 52.381 0.00 0.00 0.00 4.45
3009 3349 1.407712 GCCGGCTATGAGTAAAACCCA 60.408 52.381 22.15 0.00 0.00 4.51
3010 3350 1.306148 GCCGGCTATGAGTAAAACCC 58.694 55.000 22.15 0.00 0.00 4.11
3011 3351 0.935196 CGCCGGCTATGAGTAAAACC 59.065 55.000 26.68 0.00 0.00 3.27
3012 3352 0.303796 GCGCCGGCTATGAGTAAAAC 59.696 55.000 26.68 0.00 35.83 2.43
3013 3353 0.812412 GGCGCCGGCTATGAGTAAAA 60.812 55.000 26.68 0.00 39.81 1.52
3014 3354 1.227438 GGCGCCGGCTATGAGTAAA 60.227 57.895 26.68 0.00 39.81 2.01
3015 3355 0.824595 TAGGCGCCGGCTATGAGTAA 60.825 55.000 26.68 0.00 39.70 2.24
3016 3356 1.228337 TAGGCGCCGGCTATGAGTA 60.228 57.895 26.68 0.65 39.70 2.59
3017 3357 2.520982 TAGGCGCCGGCTATGAGT 60.521 61.111 26.68 1.83 39.70 3.41
3018 3358 2.049063 GTAGGCGCCGGCTATGAG 60.049 66.667 26.68 9.69 42.43 2.90
3019 3359 1.962321 TTTGTAGGCGCCGGCTATGA 61.962 55.000 26.68 12.21 42.43 2.15
3020 3360 1.498865 CTTTGTAGGCGCCGGCTATG 61.499 60.000 26.68 10.55 42.43 2.23
3022 3362 2.185867 CTTTGTAGGCGCCGGCTA 59.814 61.111 26.68 17.07 39.70 3.93
3024 3364 3.799755 CACTTTGTAGGCGCCGGC 61.800 66.667 23.20 19.07 38.90 6.13
3025 3365 3.799755 GCACTTTGTAGGCGCCGG 61.800 66.667 23.20 10.62 0.00 6.13
3026 3366 3.799755 GGCACTTTGTAGGCGCCG 61.800 66.667 23.20 8.17 35.28 6.46
3027 3367 3.440415 GGGCACTTTGTAGGCGCC 61.440 66.667 21.89 21.89 41.14 6.53
3028 3368 2.671619 TGGGCACTTTGTAGGCGC 60.672 61.111 0.00 0.00 40.46 6.53
3030 3370 1.383523 GATCTGGGCACTTTGTAGGC 58.616 55.000 0.00 0.00 0.00 3.93
3031 3371 1.656652 CGATCTGGGCACTTTGTAGG 58.343 55.000 0.00 0.00 0.00 3.18
3032 3372 1.656652 CCGATCTGGGCACTTTGTAG 58.343 55.000 0.00 0.00 0.00 2.74
3033 3373 3.853104 CCGATCTGGGCACTTTGTA 57.147 52.632 0.00 0.00 0.00 2.41
3034 3374 4.722193 CCGATCTGGGCACTTTGT 57.278 55.556 0.00 0.00 0.00 2.83
3042 3382 2.514516 AAAAAGGGGGCCGATCTGGG 62.515 60.000 0.00 0.00 38.63 4.45
3043 3383 0.257616 TAAAAAGGGGGCCGATCTGG 59.742 55.000 0.00 0.00 42.50 3.86
3044 3384 1.749063 GTTAAAAAGGGGGCCGATCTG 59.251 52.381 0.00 0.00 0.00 2.90
3045 3385 1.341679 GGTTAAAAAGGGGGCCGATCT 60.342 52.381 0.00 0.00 0.00 2.75
3047 3387 0.681887 CGGTTAAAAAGGGGGCCGAT 60.682 55.000 0.00 0.00 41.45 4.18
3048 3388 1.303480 CGGTTAAAAAGGGGGCCGA 60.303 57.895 0.00 0.00 41.45 5.54
3049 3389 1.604308 ACGGTTAAAAAGGGGGCCG 60.604 57.895 0.00 0.00 44.10 6.13
3050 3390 1.537814 CCACGGTTAAAAAGGGGGCC 61.538 60.000 0.00 0.00 0.00 5.80
3051 3391 1.537814 CCCACGGTTAAAAAGGGGGC 61.538 60.000 1.04 0.00 42.36 5.80
3052 3392 2.661054 CCCACGGTTAAAAAGGGGG 58.339 57.895 0.00 0.00 42.95 5.40
3092 4975 1.399727 GCGGGTTTGACTGTTTCATCG 60.400 52.381 0.00 0.00 32.84 3.84
3109 4992 2.126110 GCAACGATTTTGGGGCGG 60.126 61.111 0.00 0.00 0.00 6.13
3211 5183 4.421479 CGAGAAGCTGCGACCGGT 62.421 66.667 6.92 6.92 0.00 5.28
3400 5397 2.637025 GCGCGGCTCTGACAAAAA 59.363 55.556 8.83 0.00 0.00 1.94
3524 5544 0.740868 TCCTAGATGCAACTGCGTGC 60.741 55.000 6.76 0.18 45.83 5.34
3554 5574 3.006323 GGATATGCACGGTCTCATCTCTT 59.994 47.826 0.00 0.00 0.00 2.85
3565 5585 3.705604 GGTTCATTTTGGATATGCACGG 58.294 45.455 0.00 0.00 0.00 4.94
3647 5672 1.330234 TATAGCGGGGCACGTTCATA 58.670 50.000 12.27 3.09 46.52 2.15
3695 5720 5.494724 TGCTCAGCTCAAATCTGTTAATCT 58.505 37.500 0.00 0.00 33.48 2.40
3714 5739 5.762825 TCAATTAATCTCCATGCTTGCTC 57.237 39.130 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.