Multiple sequence alignment - TraesCS2D01G412300

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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 TraesCS2D01G412300 chr2D 100.000 3014 0 0 1 3014 527273818 527270805 0.000000e+00 5566
1 TraesCS2D01G412300 chr2D 88.014 292 32 2 1228 1519 527004248 527003960 2.880000e-90 342
2 TraesCS2D01G412300 chr2A 89.916 3084 165 68 1 3014 672266931 672263924 0.000000e+00 3838
3 TraesCS2D01G412300 chr2A 89.078 293 29 2 1227 1519 672234909 672234620 7.940000e-96 361
4 TraesCS2D01G412300 chr2B 91.973 2342 111 28 1 2321 624288517 624286232 0.000000e+00 3212
5 TraesCS2D01G412300 chr2B 86.753 385 25 12 2648 3014 624285996 624285620 3.620000e-109 405
6 TraesCS2D01G412300 chr2B 87.713 293 33 2 1227 1519 623869995 623869706 3.720000e-89 339
7 TraesCS2D01G412300 chr2B 88.976 254 11 10 2362 2614 624286232 624285995 6.320000e-77 298
8 TraesCS2D01G412300 chr6D 88.040 301 31 3 1224 1520 326572767 326573066 4.780000e-93 351
9 TraesCS2D01G412300 chr6A 88.040 301 31 3 1224 1520 465316661 465316960 4.780000e-93 351
10 TraesCS2D01G412300 chr3A 85.317 252 27 8 1273 1519 552641269 552641023 4.990000e-63 252
11 TraesCS2D01G412300 chr3D 83.922 255 31 8 1270 1519 103621541 103621790 5.020000e-58 235


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 TraesCS2D01G412300 chr2D 527270805 527273818 3013 True 5566 5566 100.000 1 3014 1 chr2D.!!$R2 3013
1 TraesCS2D01G412300 chr2A 672263924 672266931 3007 True 3838 3838 89.916 1 3014 1 chr2A.!!$R2 3013
2 TraesCS2D01G412300 chr2B 624285620 624288517 2897 True 1305 3212 89.234 1 3014 3 chr2B.!!$R2 3013

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
301 308 0.034767 TTCCTCTGCCATCTGCCTTG 60.035 55.0 0.00 0.00 40.16 3.61 F
998 1019 0.458543 TCGCTCCATCACTTCGAAGC 60.459 55.0 24.86 8.24 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1586 1619 0.253327 GGCTCCGAAACCTCCTCAAT 59.747 55.0 0.0 0.0 0.00 2.57 R
2431 2491 0.163788 GCGCATACATACATCGTGCC 59.836 55.0 0.3 0.0 32.39 5.01 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
63 64 3.692593 GCTCGCCCAATTAGGTTTTCTTA 59.307 43.478 0.00 0.00 34.66 2.10
72 73 6.039382 CCAATTAGGTTTTCTTAATCCTCCCG 59.961 42.308 0.00 0.00 35.54 5.14
93 94 2.006772 CTGGAATACCGCAGCGTTC 58.993 57.895 15.05 10.94 39.42 3.95
144 145 0.179000 CAGGGAGAGCCGCATTAGTT 59.821 55.000 0.00 0.00 33.83 2.24
148 149 2.102588 GGGAGAGCCGCATTAGTTTAGA 59.897 50.000 0.00 0.00 33.83 2.10
163 164 9.803130 CATTAGTTTAGAAATGCAGATATGTCG 57.197 33.333 0.00 0.00 0.00 4.35
184 186 6.258947 TGTCGTGAACATGATAGAAAAACACA 59.741 34.615 0.00 0.00 31.20 3.72
185 187 6.573725 GTCGTGAACATGATAGAAAAACACAC 59.426 38.462 0.00 0.00 0.00 3.82
186 188 6.258947 TCGTGAACATGATAGAAAAACACACA 59.741 34.615 0.00 0.00 0.00 3.72
190 192 3.889196 TGATAGAAAAACACACACGGC 57.111 42.857 0.00 0.00 0.00 5.68
191 193 3.472652 TGATAGAAAAACACACACGGCT 58.527 40.909 0.00 0.00 0.00 5.52
194 196 2.218603 AGAAAAACACACACGGCTAGG 58.781 47.619 0.00 0.00 0.00 3.02
195 197 0.666374 AAAAACACACACGGCTAGGC 59.334 50.000 6.15 6.15 0.00 3.93
196 198 0.464735 AAAACACACACGGCTAGGCA 60.465 50.000 17.45 0.00 0.00 4.75
212 219 3.053831 AGGCAGCTTCGCTTTACTTTA 57.946 42.857 0.00 0.00 36.40 1.85
299 306 0.700564 TTTTCCTCTGCCATCTGCCT 59.299 50.000 0.00 0.00 40.16 4.75
301 308 0.034767 TTCCTCTGCCATCTGCCTTG 60.035 55.000 0.00 0.00 40.16 3.61
310 317 1.076192 ATCTGCCTTGTGCCTTGCT 59.924 52.632 0.00 0.00 40.16 3.91
322 329 1.082690 GCCTTGCTCTTGTGCTAGTC 58.917 55.000 0.00 0.00 34.81 2.59
380 387 8.016497 TGCATTAGTTAATTTGCATTTGTGAC 57.984 30.769 0.00 0.00 0.00 3.67
382 389 8.494347 GCATTAGTTAATTTGCATTTGTGACAA 58.506 29.630 0.00 0.00 0.00 3.18
434 442 8.553459 TCTTTTGGATCTAAGAACAGTGATTC 57.447 34.615 0.00 0.00 0.00 2.52
440 448 4.105486 TCTAAGAACAGTGATTCGATGCG 58.895 43.478 0.00 0.00 33.57 4.73
497 505 1.002773 TGGGACTTTCGCTTTAGGGAC 59.997 52.381 0.00 0.00 36.70 4.46
499 507 2.347731 GGACTTTCGCTTTAGGGACAG 58.652 52.381 8.03 8.03 39.67 3.51
500 508 2.028385 GGACTTTCGCTTTAGGGACAGA 60.028 50.000 14.52 0.00 37.94 3.41
501 509 2.994578 GACTTTCGCTTTAGGGACAGAC 59.005 50.000 14.52 6.78 37.94 3.51
502 510 2.367567 ACTTTCGCTTTAGGGACAGACA 59.632 45.455 14.52 0.00 37.94 3.41
564 572 6.421202 CGCCACTTTAATCATTAGTCTACTCC 59.579 42.308 0.00 0.00 0.00 3.85
565 573 7.501844 GCCACTTTAATCATTAGTCTACTCCT 58.498 38.462 0.00 0.00 0.00 3.69
635 646 1.859703 CGCACACACATTTTGCACAAT 59.140 42.857 0.00 0.00 35.93 2.71
684 698 0.685458 GGGTGGTAGTAGGAGGCGAA 60.685 60.000 0.00 0.00 0.00 4.70
719 733 1.091197 CATGTAGCAGCGTGATGGCA 61.091 55.000 0.00 0.00 34.64 4.92
720 734 1.091771 ATGTAGCAGCGTGATGGCAC 61.092 55.000 0.00 0.00 41.67 5.01
811 831 4.914420 CGCTCGCTCGTAGCCTGG 62.914 72.222 0.00 0.00 38.18 4.45
842 862 2.850060 CTGCATGTCATTCACATTTCGC 59.150 45.455 0.00 0.00 43.89 4.70
994 1015 0.994995 CAACTCGCTCCATCACTTCG 59.005 55.000 0.00 0.00 0.00 3.79
998 1019 0.458543 TCGCTCCATCACTTCGAAGC 60.459 55.000 24.86 8.24 0.00 3.86
1011 1035 3.071167 ACTTCGAAGCTCCAAGGTTTAGT 59.929 43.478 24.86 0.00 35.86 2.24
1093 1120 1.133598 ACTTGTCAGTTGTCACGTCGA 59.866 47.619 0.00 0.00 0.00 4.20
1114 1141 2.747436 TCGATCGATCAAATGGAGCAG 58.253 47.619 24.40 4.90 0.00 4.24
1120 1147 2.749076 CGATCAAATGGAGCAGGAACAA 59.251 45.455 0.00 0.00 0.00 2.83
1165 1195 0.886490 GTAACAGCTGCTGCACCTGT 60.886 55.000 28.39 21.62 41.26 4.00
1201 1231 2.979197 CTCCCTGAACGCGTCGTCT 61.979 63.158 14.44 0.00 39.99 4.18
1446 1476 2.359975 GCACCTCAACTTCCCGGG 60.360 66.667 16.85 16.85 0.00 5.73
1586 1619 0.032615 GAAGGAGCAGGAGGAGGAGA 60.033 60.000 0.00 0.00 0.00 3.71
1641 1674 1.153369 CACCATCGCCGGATTGTCT 60.153 57.895 5.05 0.00 0.00 3.41
1672 1705 0.250901 ATGCAGGACCCGAATATGGC 60.251 55.000 0.00 0.00 0.00 4.40
1778 1811 2.818274 GTTCGCCGTGGGATGACC 60.818 66.667 0.00 0.00 40.81 4.02
1874 1907 1.607628 GCATGCATGGACCAGATTCTC 59.392 52.381 27.34 2.90 0.00 2.87
1928 1961 5.776744 AGTGTTACAACTTACTAACCTCGG 58.223 41.667 0.00 0.00 0.00 4.63
1930 1963 4.039004 TGTTACAACTTACTAACCTCGGCA 59.961 41.667 0.00 0.00 0.00 5.69
1934 1967 4.020485 ACAACTTACTAACCTCGGCAATCT 60.020 41.667 0.00 0.00 0.00 2.40
2018 2051 9.013490 CAAATAAAATTGATGTCGCTTTAGGAG 57.987 33.333 0.00 0.00 31.84 3.69
2074 2107 1.972872 AGACCTGACTGCAACTTTGG 58.027 50.000 0.00 0.00 0.00 3.28
2090 2123 2.286365 TTGGTTTCCCGCTTTCATCT 57.714 45.000 0.00 0.00 0.00 2.90
2191 2229 3.907260 TTTGCCCTGCAGCTCGAGG 62.907 63.158 15.58 4.73 40.61 4.63
2254 2313 6.007703 TGTAAGATCCGTTTTCCCATCTTTT 58.992 36.000 0.00 0.00 36.98 2.27
2317 2377 4.543398 GCTTTTGCCTGCATTTTGCGTC 62.543 50.000 0.00 0.00 42.80 5.19
2328 2388 4.537015 GCATTTTGCGTCTTGTTCTTACT 58.463 39.130 0.00 0.00 31.71 2.24
2329 2389 5.685841 GCATTTTGCGTCTTGTTCTTACTA 58.314 37.500 0.00 0.00 31.71 1.82
2330 2390 5.564127 GCATTTTGCGTCTTGTTCTTACTAC 59.436 40.000 0.00 0.00 31.71 2.73
2331 2391 6.565999 GCATTTTGCGTCTTGTTCTTACTACT 60.566 38.462 0.00 0.00 31.71 2.57
2332 2392 7.359765 GCATTTTGCGTCTTGTTCTTACTACTA 60.360 37.037 0.00 0.00 31.71 1.82
2333 2393 6.998258 TTTGCGTCTTGTTCTTACTACTAC 57.002 37.500 0.00 0.00 0.00 2.73
2334 2394 5.954296 TGCGTCTTGTTCTTACTACTACT 57.046 39.130 0.00 0.00 0.00 2.57
2335 2395 5.936054 TGCGTCTTGTTCTTACTACTACTC 58.064 41.667 0.00 0.00 0.00 2.59
2336 2396 5.106396 TGCGTCTTGTTCTTACTACTACTCC 60.106 44.000 0.00 0.00 0.00 3.85
2337 2397 5.558307 CGTCTTGTTCTTACTACTACTCCG 58.442 45.833 0.00 0.00 0.00 4.63
2358 2418 9.110502 ACTCCGTATTAAATTTCCTGAAGAATC 57.889 33.333 0.00 0.00 33.44 2.52
2417 2477 5.661458 ACTTAGTAGCGTATGAAGCAACAT 58.339 37.500 0.00 0.00 37.01 2.71
2418 2478 5.749109 ACTTAGTAGCGTATGAAGCAACATC 59.251 40.000 0.00 0.00 37.01 3.06
2431 2491 5.633601 TGAAGCAACATCTCTAACAGTAACG 59.366 40.000 0.00 0.00 0.00 3.18
2533 2594 5.049060 CGCATGGGGATTATTTTACGATGAA 60.049 40.000 0.89 0.00 0.00 2.57
2659 2730 2.185093 GGTTACCGGCCCACTACG 59.815 66.667 0.00 0.00 0.00 3.51
2680 2756 8.876790 ACTACGGCAATACTATACTTTTTGTTC 58.123 33.333 0.00 0.00 0.00 3.18
2716 2797 0.029834 GCTTGCATGATTGTAGCCGG 59.970 55.000 3.33 0.00 30.89 6.13
2761 2845 2.164219 GCATAAGGATGTGGTTGGTGTG 59.836 50.000 0.00 0.00 35.30 3.82
2789 2873 1.964373 CCGGTGTGGTTAGTGGCAC 60.964 63.158 10.29 10.29 0.00 5.01
2790 2874 1.227704 CGGTGTGGTTAGTGGCACA 60.228 57.895 21.41 2.83 33.88 4.57
2791 2875 1.227999 CGGTGTGGTTAGTGGCACAG 61.228 60.000 21.41 0.00 41.80 3.66
2805 2889 4.451096 AGTGGCACAGTAGTATTTTTCGTG 59.549 41.667 21.41 0.00 42.13 4.35
2829 2913 0.813184 CATGTGGGACGTACGTAGGT 59.187 55.000 22.87 20.04 0.00 3.08
2831 2915 0.537143 TGTGGGACGTACGTAGGTGT 60.537 55.000 24.34 10.00 0.00 4.16
2832 2916 0.169009 GTGGGACGTACGTAGGTGTC 59.831 60.000 24.34 17.41 0.00 3.67
2839 2923 2.299867 ACGTACGTAGGTGTCCCAAAAT 59.700 45.455 21.41 0.00 0.00 1.82
2893 2984 5.742446 GTTAGGTACGAATTACGATCGACT 58.258 41.667 24.34 2.14 45.77 4.18
2894 2985 4.206698 AGGTACGAATTACGATCGACTG 57.793 45.455 24.34 7.49 45.77 3.51
2969 3060 5.586243 TCAATTCTTAATGCTGGCACTAGTC 59.414 40.000 0.00 0.00 0.00 2.59
2970 3061 4.551702 TTCTTAATGCTGGCACTAGTCA 57.448 40.909 0.00 0.00 0.00 3.41
2995 3086 0.390735 GTTACTCCGGCCATGACGTT 60.391 55.000 2.24 0.00 28.54 3.99
3002 3093 1.665442 GGCCATGACGTTGCCTTTT 59.335 52.632 0.00 0.00 42.01 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.226407 GCGCTTTTGAGATTCGGGC 60.226 57.895 0.00 0.00 0.00 6.13
63 64 1.407656 TATTCCAGCGCGGGAGGATT 61.408 55.000 27.90 18.13 38.42 3.01
93 94 8.370940 TGCTATCTGGAGGAATAGTTTAAGATG 58.629 37.037 0.00 0.00 0.00 2.90
117 118 1.233285 CGGCTCTCCCTGCATAATGC 61.233 60.000 0.00 0.00 45.29 3.56
144 145 6.816140 TGTTCACGACATATCTGCATTTCTAA 59.184 34.615 0.00 0.00 32.00 2.10
160 161 6.573725 GTGTGTTTTTCTATCATGTTCACGAC 59.426 38.462 0.00 0.00 0.00 4.34
163 164 6.356977 CGTGTGTGTTTTTCTATCATGTTCAC 59.643 38.462 0.00 0.00 0.00 3.18
201 208 4.737765 TGCAAAGCAAAGTAAAGTAAAGCG 59.262 37.500 0.00 0.00 34.76 4.68
202 209 6.769608 ATGCAAAGCAAAGTAAAGTAAAGC 57.230 33.333 0.00 0.00 43.62 3.51
263 270 3.560668 GGAAAATGGGTTCGTTAGAGGGT 60.561 47.826 0.00 0.00 0.00 4.34
299 306 0.752743 AGCACAAGAGCAAGGCACAA 60.753 50.000 0.00 0.00 36.85 3.33
301 308 0.801251 CTAGCACAAGAGCAAGGCAC 59.199 55.000 0.00 0.00 36.85 5.01
322 329 1.082756 GCAAACGAGTGCCTTGTCG 60.083 57.895 4.07 0.00 42.04 4.35
376 383 4.318831 GCGCCTGCTTACTTATATTGTCAC 60.319 45.833 0.00 0.00 38.39 3.67
377 384 3.807622 GCGCCTGCTTACTTATATTGTCA 59.192 43.478 0.00 0.00 38.39 3.58
378 385 3.807622 TGCGCCTGCTTACTTATATTGTC 59.192 43.478 4.18 0.00 43.34 3.18
380 387 4.058124 TCTGCGCCTGCTTACTTATATTG 58.942 43.478 4.18 0.00 43.34 1.90
382 389 4.499183 GATCTGCGCCTGCTTACTTATAT 58.501 43.478 4.18 0.00 43.34 0.86
383 390 3.611766 CGATCTGCGCCTGCTTACTTATA 60.612 47.826 4.18 0.00 43.34 0.98
384 391 2.760374 GATCTGCGCCTGCTTACTTAT 58.240 47.619 4.18 0.00 43.34 1.73
434 442 4.262045 GTGCCAAGTATTAAAAACGCATCG 59.738 41.667 0.00 0.00 0.00 3.84
440 448 4.163552 GCCTCGTGCCAAGTATTAAAAAC 58.836 43.478 0.00 0.00 0.00 2.43
497 505 1.959985 ACCTGTCTGTCTGTCTGTCTG 59.040 52.381 0.00 0.00 0.00 3.51
499 507 1.604185 GCACCTGTCTGTCTGTCTGTC 60.604 57.143 0.00 0.00 0.00 3.51
500 508 0.390860 GCACCTGTCTGTCTGTCTGT 59.609 55.000 0.00 0.00 0.00 3.41
501 509 0.320247 GGCACCTGTCTGTCTGTCTG 60.320 60.000 0.00 0.00 0.00 3.51
502 510 0.470833 AGGCACCTGTCTGTCTGTCT 60.471 55.000 0.00 0.00 0.00 3.41
564 572 1.299014 GAGCAGGACGATCGAGCAG 60.299 63.158 24.34 9.89 0.00 4.24
565 573 2.775856 GGAGCAGGACGATCGAGCA 61.776 63.158 24.34 0.00 0.00 4.26
635 646 2.247358 GGAAATGGAGTGGCTTTTCCA 58.753 47.619 8.09 7.46 46.79 3.53
641 652 2.225343 TGGAAATGGAAATGGAGTGGCT 60.225 45.455 0.00 0.00 0.00 4.75
642 653 2.178580 TGGAAATGGAAATGGAGTGGC 58.821 47.619 0.00 0.00 0.00 5.01
645 656 3.377573 CCCATGGAAATGGAAATGGAGT 58.622 45.455 15.22 0.00 44.39 3.85
646 657 2.701951 CCCCATGGAAATGGAAATGGAG 59.298 50.000 15.22 0.00 44.39 3.86
647 658 2.045605 ACCCCATGGAAATGGAAATGGA 59.954 45.455 15.22 0.00 44.39 3.41
648 659 2.171027 CACCCCATGGAAATGGAAATGG 59.829 50.000 15.22 3.87 44.39 3.16
649 660 3.547054 CACCCCATGGAAATGGAAATG 57.453 47.619 15.22 0.00 44.39 2.32
719 733 3.077556 CTACAGGGAGCCAGGCGT 61.078 66.667 5.55 0.00 0.00 5.68
720 734 3.077556 ACTACAGGGAGCCAGGCG 61.078 66.667 5.55 0.00 0.00 5.52
721 735 2.904131 GACTACAGGGAGCCAGGC 59.096 66.667 1.84 1.84 0.00 4.85
725 739 1.041437 AATAGCGACTACAGGGAGCC 58.959 55.000 0.00 0.00 0.00 4.70
726 740 1.681793 TCAATAGCGACTACAGGGAGC 59.318 52.381 0.00 0.00 0.00 4.70
811 831 6.313658 TGTGAATGACATGCAGAATACTACAC 59.686 38.462 0.00 0.00 0.00 2.90
842 862 2.866065 GCATTTGTTTTTGTCTCCCCGG 60.866 50.000 0.00 0.00 0.00 5.73
994 1015 5.334957 GCTTGTTACTAAACCTTGGAGCTTC 60.335 44.000 0.00 0.00 34.49 3.86
998 1019 7.224949 GCTATAGCTTGTTACTAAACCTTGGAG 59.775 40.741 17.75 0.00 38.21 3.86
1011 1035 8.861834 GCTACGTGCTCAGCTATAGCTTGTTA 62.862 46.154 24.80 9.21 43.84 2.41
1093 1120 3.324117 CTGCTCCATTTGATCGATCGAT 58.676 45.455 29.76 29.76 37.59 3.59
1114 1141 2.032981 CACCACCAGCACTTGTTCC 58.967 57.895 0.00 0.00 0.00 3.62
1120 1147 3.170672 TGAGGCACCACCAGCACT 61.171 61.111 0.00 0.00 43.14 4.40
1126 1153 2.032681 GACACCTGAGGCACCACC 59.967 66.667 0.00 0.00 39.61 4.61
1165 1195 2.571757 CCGGAGCTCGTGTTGCTA 59.428 61.111 7.83 0.00 41.30 3.49
1201 1231 3.125573 CTGTCGTCGGAGCTCGGA 61.126 66.667 19.12 19.12 39.77 4.55
1586 1619 0.253327 GGCTCCGAAACCTCCTCAAT 59.747 55.000 0.00 0.00 0.00 2.57
1612 1645 4.864334 GATGGTGCCTGCTCGGGG 62.864 72.222 0.00 0.00 0.00 5.73
1625 1658 0.744414 AACAGACAATCCGGCGATGG 60.744 55.000 9.30 0.00 0.00 3.51
1641 1674 2.621338 GTCCTGCATTCTCGATCAACA 58.379 47.619 0.00 0.00 0.00 3.33
1672 1705 1.883084 GTAGTCGAGCCCAATGCCG 60.883 63.158 0.00 0.00 42.71 5.69
1778 1811 3.095016 CGAAGAAGAGATTGTCGTCGAG 58.905 50.000 0.00 0.00 44.93 4.04
1874 1907 1.205655 TCGACCAAGAGATCCAGCAAG 59.794 52.381 0.00 0.00 0.00 4.01
1928 1961 4.806247 AGCGAAGATGTTAGTGTAGATTGC 59.194 41.667 0.00 0.00 0.00 3.56
1930 1963 8.467598 TCTTTAGCGAAGATGTTAGTGTAGATT 58.532 33.333 1.99 0.00 39.44 2.40
1958 1991 8.806177 AGTAACAAATTAAACGAATTGGTTCC 57.194 30.769 6.29 0.00 45.02 3.62
2018 2051 2.826428 ACCGCATGATATGATATCGCC 58.174 47.619 7.85 0.00 0.00 5.54
2191 2229 2.564721 AAAAACCCTGCTGCTCGGC 61.565 57.895 0.00 0.00 0.00 5.54
2254 2313 8.877864 AAAATACTCTGATTTACACCCAATGA 57.122 30.769 0.00 0.00 0.00 2.57
2332 2392 9.110502 GATTCTTCAGGAAATTTAATACGGAGT 57.889 33.333 0.00 0.00 40.42 3.85
2333 2393 9.109393 TGATTCTTCAGGAAATTTAATACGGAG 57.891 33.333 0.00 0.00 37.49 4.63
2334 2394 9.109393 CTGATTCTTCAGGAAATTTAATACGGA 57.891 33.333 0.00 0.00 44.78 4.69
2357 2417 3.531207 CCGATCGAGCTGGCCTGA 61.531 66.667 18.66 0.00 0.00 3.86
2358 2418 3.781770 GACCGATCGAGCTGGCCTG 62.782 68.421 18.66 4.26 0.00 4.85
2393 2453 6.198650 TGTTGCTTCATACGCTACTAAGTA 57.801 37.500 0.00 0.00 34.87 2.24
2394 2454 5.068234 TGTTGCTTCATACGCTACTAAGT 57.932 39.130 0.00 0.00 34.87 2.24
2395 2455 5.980116 AGATGTTGCTTCATACGCTACTAAG 59.020 40.000 0.00 0.00 34.87 2.18
2396 2456 5.902681 AGATGTTGCTTCATACGCTACTAA 58.097 37.500 0.00 0.00 34.87 2.24
2417 2477 2.153645 TCGTGCCGTTACTGTTAGAGA 58.846 47.619 0.00 0.00 0.00 3.10
2418 2478 2.624316 TCGTGCCGTTACTGTTAGAG 57.376 50.000 0.00 0.00 0.00 2.43
2431 2491 0.163788 GCGCATACATACATCGTGCC 59.836 55.000 0.30 0.00 32.39 5.01
2540 2601 0.393077 AAGAGACAGAACGGTGGGTG 59.607 55.000 0.00 0.00 0.00 4.61
2642 2713 2.185093 CGTAGTGGGCCGGTAACC 59.815 66.667 1.90 3.92 0.00 2.85
2659 2730 8.193250 TCTCGAACAAAAAGTATAGTATTGCC 57.807 34.615 6.12 0.47 0.00 4.52
2670 2741 8.837389 AGCTAGTATTTTTCTCGAACAAAAAGT 58.163 29.630 15.92 9.34 36.43 2.66
2671 2742 9.107367 CAGCTAGTATTTTTCTCGAACAAAAAG 57.893 33.333 15.92 7.07 36.43 2.27
2680 2756 4.093408 TGCAAGCAGCTAGTATTTTTCTCG 59.907 41.667 0.00 0.00 45.94 4.04
2716 2797 5.771153 ATACTAAGACTAGTTTCTCGGGC 57.229 43.478 0.00 0.00 39.23 6.13
2745 2826 0.550914 ACACACACCAACCACATCCT 59.449 50.000 0.00 0.00 0.00 3.24
2748 2829 1.388547 GTGACACACACCAACCACAT 58.611 50.000 0.00 0.00 43.05 3.21
2761 2845 2.972505 CACACCGGCCAGTGACAC 60.973 66.667 25.94 0.00 40.34 3.67
2789 2873 7.635973 CACATGCATACACGAAAAATACTACTG 59.364 37.037 0.00 0.00 0.00 2.74
2790 2874 7.201609 CCACATGCATACACGAAAAATACTACT 60.202 37.037 0.00 0.00 0.00 2.57
2791 2875 6.905076 CCACATGCATACACGAAAAATACTAC 59.095 38.462 0.00 0.00 0.00 2.73
2805 2889 1.205657 CGTACGTCCCACATGCATAC 58.794 55.000 7.22 0.00 0.00 2.39
2882 2973 0.454600 GGCTCCACAGTCGATCGTAA 59.545 55.000 15.94 0.00 0.00 3.18
2893 2984 2.970379 ATGGATGCGTGGCTCCACA 61.970 57.895 18.11 1.04 44.06 4.17
2894 2985 2.124570 ATGGATGCGTGGCTCCAC 60.125 61.111 8.95 8.95 44.06 4.02
2969 3060 0.320374 TGGCCGGAGTAACTTGACTG 59.680 55.000 5.05 0.00 0.00 3.51
2970 3061 1.066143 CATGGCCGGAGTAACTTGACT 60.066 52.381 5.05 0.00 0.00 3.41
2971 3062 1.066430 TCATGGCCGGAGTAACTTGAC 60.066 52.381 5.05 0.00 0.00 3.18
2972 3063 1.066430 GTCATGGCCGGAGTAACTTGA 60.066 52.381 5.05 0.34 0.00 3.02
2973 3064 1.369625 GTCATGGCCGGAGTAACTTG 58.630 55.000 5.05 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.