Multiple sequence alignment - TraesCS5B01G288400

Loading Multiple Alignment...

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 TraesCS5B01G288400 chr5B 100.000 2390 0 0 1 2390 473783483 473781094 0.000000e+00 4414.0
1 TraesCS5B01G288400 chr5B 92.135 1157 64 12 725 1863 473773811 473772664 0.000000e+00 1607.0
2 TraesCS5B01G288400 chr5B 80.507 1262 172 30 625 1858 473766323 473765108 0.000000e+00 900.0
3 TraesCS5B01G288400 chr5B 91.212 330 21 6 292 620 473766692 473766370 2.180000e-120 442.0
4 TraesCS5B01G288400 chr5B 85.459 392 33 14 1890 2275 473770815 473770442 1.040000e-103 387.0
5 TraesCS5B01G288400 chr5B 89.606 279 16 7 332 608 473774072 473773805 2.270000e-90 342.0
6 TraesCS5B01G288400 chr5B 85.380 342 27 12 9 342 473775665 473775339 1.370000e-87 333.0
7 TraesCS5B01G288400 chr5D 88.941 2324 151 51 1 2275 393908718 393906452 0.000000e+00 2771.0
8 TraesCS5B01G288400 chr5D 91.394 1743 116 17 418 2151 393904238 393902521 0.000000e+00 2357.0
9 TraesCS5B01G288400 chr5D 84.851 1307 149 17 656 1940 393901085 393899806 0.000000e+00 1271.0
10 TraesCS5B01G288400 chr5D 81.032 1260 165 28 625 1858 393897360 393896149 0.000000e+00 935.0
11 TraesCS5B01G288400 chr5D 91.451 386 27 5 37 420 393905186 393904805 2.100000e-145 525.0
12 TraesCS5B01G288400 chr5D 80.274 583 70 31 49 620 393897955 393897407 4.790000e-107 398.0
13 TraesCS5B01G288400 chr5D 87.770 139 14 2 2139 2275 360917172 360917309 2.460000e-35 159.0
14 TraesCS5B01G288400 chr5D 84.416 154 21 2 2125 2275 30433115 30432962 5.320000e-32 148.0
15 TraesCS5B01G288400 chr5A 90.566 1431 97 20 429 1835 495927361 495925945 0.000000e+00 1860.0
16 TraesCS5B01G288400 chr5A 85.754 1067 117 16 650 1708 495907039 495906000 0.000000e+00 1096.0
17 TraesCS5B01G288400 chr5A 81.598 1114 151 25 770 1858 495903220 495902136 0.000000e+00 872.0
18 TraesCS5B01G288400 chr5A 84.840 719 67 21 9 703 495918862 495918162 0.000000e+00 686.0
19 TraesCS5B01G288400 chr5A 91.184 397 17 6 9 392 495927748 495927357 7.570000e-145 523.0
20 TraesCS5B01G288400 chr5A 88.889 414 40 4 1834 2244 495925389 495925799 2.740000e-139 505.0
21 TraesCS5B01G288400 chr5A 87.464 351 37 5 688 1037 495912260 495911916 4.790000e-107 398.0
22 TraesCS5B01G288400 chr5A 88.450 329 24 8 292 620 495903746 495903432 3.730000e-103 385.0
23 TraesCS5B01G288400 chr5A 98.077 104 2 0 2286 2389 32133496 32133393 5.250000e-42 182.0
24 TraesCS5B01G288400 chr5A 97.143 105 3 0 2286 2390 417329775 417329671 6.790000e-41 178.0
25 TraesCS5B01G288400 chr2D 90.647 139 9 3 2139 2275 74135678 74135814 5.250000e-42 182.0
26 TraesCS5B01G288400 chr2D 95.575 113 4 1 2277 2389 625091302 625091191 1.890000e-41 180.0
27 TraesCS5B01G288400 chr6D 97.143 105 3 0 2286 2390 315754318 315754422 6.790000e-41 178.0
28 TraesCS5B01G288400 chr1D 89.928 139 12 1 2139 2275 489752079 489752217 6.790000e-41 178.0
29 TraesCS5B01G288400 chr1D 97.115 104 3 0 2286 2389 382756348 382756245 2.440000e-40 176.0
30 TraesCS5B01G288400 chr4D 97.115 104 3 0 2286 2389 372510497 372510394 2.440000e-40 176.0
31 TraesCS5B01G288400 chr1B 97.115 104 3 0 2285 2388 800946 801049 2.440000e-40 176.0
32 TraesCS5B01G288400 chr7B 95.413 109 5 0 2281 2389 145010097 145010205 8.780000e-40 174.0
33 TraesCS5B01G288400 chr6B 93.162 117 8 0 2273 2389 644713509 644713625 3.160000e-39 172.0
34 TraesCS5B01G288400 chr3B 89.706 136 12 1 2142 2275 327942129 327941994 3.160000e-39 172.0
35 TraesCS5B01G288400 chr3B 88.148 135 14 1 2142 2274 736943453 736943587 2.460000e-35 159.0
36 TraesCS5B01G288400 chr3D 87.234 141 14 2 2139 2275 445041075 445041215 8.840000e-35 158.0
37 TraesCS5B01G288400 chr7D 100.000 31 0 0 1900 1930 629651817 629651847 9.230000e-05 58.4


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 TraesCS5B01G288400 chr5B 473781094 473783483 2389 True 4414.000000 4414 100.000000 1 2390 1 chr5B.!!$R1 2389
1 TraesCS5B01G288400 chr5B 473765108 473775665 10557 True 668.500000 1607 87.383167 9 2275 6 chr5B.!!$R2 2266
2 TraesCS5B01G288400 chr5D 393896149 393908718 12569 True 1376.166667 2771 86.323833 1 2275 6 chr5D.!!$R2 2274
3 TraesCS5B01G288400 chr5A 495925945 495927748 1803 True 1191.500000 1860 90.875000 9 1835 2 chr5A.!!$R6 1826
4 TraesCS5B01G288400 chr5A 495902136 495907039 4903 True 784.333333 1096 85.267333 292 1858 3 chr5A.!!$R5 1566
5 TraesCS5B01G288400 chr5A 495918162 495918862 700 True 686.000000 686 84.840000 9 703 1 chr5A.!!$R4 694

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
416 4756 0.325671 GGAGGTCAGTCAGGGATGGA 60.326 60.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2363 12697 0.104304 GCCATATCGGTGAACCTCGT 59.896 55.0 0.0 0.0 36.97 4.18 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
40 42 2.289133 GCTCCCTGAATATCCCTTCGTC 60.289 54.545 0.00 0.00 0.00 4.20
64 66 3.492011 GCACTTGGCAAAGACAATTCAAG 59.508 43.478 8.15 0.00 43.97 3.02
181 192 5.955488 ACACTATCTACTAGCACAAGTGTG 58.045 41.667 14.20 7.08 43.13 3.82
265 284 2.339348 CGCCCAATTGCAAGCACA 59.661 55.556 4.94 0.00 0.00 4.57
268 291 0.668401 GCCCAATTGCAAGCACAGAC 60.668 55.000 4.94 0.00 0.00 3.51
406 4746 2.925170 AGCAAGCGGGAGGTCAGT 60.925 61.111 0.00 0.00 41.46 3.41
410 4750 2.286523 AAGCGGGAGGTCAGTCAGG 61.287 63.158 0.00 0.00 41.46 3.86
413 4753 1.381872 CGGGAGGTCAGTCAGGGAT 60.382 63.158 0.00 0.00 0.00 3.85
416 4756 0.325671 GGAGGTCAGTCAGGGATGGA 60.326 60.000 0.00 0.00 0.00 3.41
639 9070 8.297426 TCTCTGACTGTAAGCGTATTATAATGG 58.703 37.037 8.28 1.56 37.60 3.16
746 9214 5.071788 TGTCCAACTAGTCTCCATCTGTTTT 59.928 40.000 0.00 0.00 0.00 2.43
788 9256 5.649395 TGATGGAATGGTGATCAAAGTCTTC 59.351 40.000 0.00 1.24 0.00 2.87
816 9284 3.619233 TCGCTAAAACAAAGCCTTCAC 57.381 42.857 0.00 0.00 36.60 3.18
859 9327 5.973565 GGATTTCAAATACAGCCTTTCGATG 59.026 40.000 0.00 0.00 0.00 3.84
892 9366 2.284699 CTTGGTCGACCCCTCCCT 60.285 66.667 31.19 0.00 34.29 4.20
919 9394 4.692523 ATAAACCATTCCACCCCTTTCT 57.307 40.909 0.00 0.00 0.00 2.52
991 9468 0.676736 AGCTATAGCCTGCGAGGTTC 59.323 55.000 21.17 0.00 43.38 3.62
1019 9496 0.851469 ATGGGCATGGCTGAGAAGAT 59.149 50.000 19.78 0.00 0.00 2.40
1023 9500 2.652590 GGCATGGCTGAGAAGATTTCT 58.347 47.619 12.86 0.00 44.21 2.52
1050 9527 4.473520 AAGGCCGGGCTGATCACG 62.474 66.667 33.52 0.00 0.00 4.35
1185 9665 3.353836 CACCCGTTGTTCCAGGCG 61.354 66.667 0.00 0.00 0.00 5.52
1337 9822 1.418334 CATGTCCTCCCTAGGGTGAG 58.582 60.000 28.15 18.83 43.84 3.51
1413 9903 7.127012 ACATTTGCATTTGGATTGGATGATA 57.873 32.000 0.00 0.00 0.00 2.15
1419 9909 4.771114 TTTGGATTGGATGATACCGACT 57.229 40.909 0.00 0.00 0.00 4.18
1420 9910 5.880164 TTTGGATTGGATGATACCGACTA 57.120 39.130 0.00 0.00 0.00 2.59
1517 10012 4.423625 AGCTCCCAAGTATGGTATTGTC 57.576 45.455 0.00 0.00 46.01 3.18
1619 10114 6.653320 TGTTAGATGTTAATGTGTGTTCTCCC 59.347 38.462 0.00 0.00 0.00 4.30
1644 10139 4.317671 AAGTTGTAGTAACTGTCTGCGT 57.682 40.909 0.00 0.00 0.00 5.24
1743 10246 3.868077 GCGCACTTCTATTCTTCTCACAT 59.132 43.478 0.30 0.00 0.00 3.21
1819 10323 9.665719 TGTGATTTAGATGAAACTATGCTAACA 57.334 29.630 0.00 0.00 0.00 2.41
1839 10343 7.380602 GCTAACATTGATCAGCCATATTGTTTC 59.619 37.037 0.00 0.00 0.00 2.78
1863 10367 5.610398 TCTGAAGTTCATCTGCTACACAAA 58.390 37.500 5.91 0.00 0.00 2.83
1864 10368 6.054941 TCTGAAGTTCATCTGCTACACAAAA 58.945 36.000 5.91 0.00 0.00 2.44
1942 12269 6.294675 CCTCAACTCACATGGCTAATTTTCAA 60.295 38.462 0.00 0.00 0.00 2.69
2054 12385 9.561069 AGGAGCTTTTTATCGACACATAATATT 57.439 29.630 0.00 0.00 0.00 1.28
2088 12419 1.000607 ACGAGCACAACGAGTACATGT 60.001 47.619 2.69 2.69 34.70 3.21
2092 12423 1.667756 GCACAACGAGTACATGTCCGA 60.668 52.381 18.04 0.00 0.00 4.55
2094 12425 1.884579 ACAACGAGTACATGTCCGACT 59.115 47.619 18.04 10.24 0.00 4.18
2099 12430 2.418976 CGAGTACATGTCCGACTTCTGA 59.581 50.000 0.00 0.00 0.00 3.27
2139 12470 8.499162 ACACACTCAATAAAGAAAAGAAGATCG 58.501 33.333 0.00 0.00 0.00 3.69
2151 12482 4.408182 AAGAAGATCGGACCAACCTATG 57.592 45.455 0.00 0.00 36.31 2.23
2172 12503 2.092914 GGTTGGATGGTTAGGAGGACAG 60.093 54.545 0.00 0.00 0.00 3.51
2181 12512 4.078571 TGGTTAGGAGGACAGTGATATCCT 60.079 45.833 15.62 15.62 42.89 3.24
2198 12530 1.127567 CCTCACCCCACCAGAGTTCA 61.128 60.000 0.00 0.00 0.00 3.18
2203 12535 0.764890 CCCCACCAGAGTTCAAGTCA 59.235 55.000 0.00 0.00 0.00 3.41
2224 12556 1.800805 AGACTTGACATTGGTGCTCG 58.199 50.000 0.00 0.00 0.00 5.03
2235 12567 3.552132 TTGGTGCTCGCATTATTCCTA 57.448 42.857 0.00 0.00 0.00 2.94
2265 12599 0.095417 GCTTCTGGCGATGTTCGTTC 59.905 55.000 0.00 0.00 42.81 3.95
2272 12606 0.669318 GCGATGTTCGTTCAGTGGGA 60.669 55.000 0.00 0.00 42.81 4.37
2274 12608 1.726853 GATGTTCGTTCAGTGGGAGG 58.273 55.000 0.00 0.00 0.00 4.30
2275 12609 1.002087 GATGTTCGTTCAGTGGGAGGT 59.998 52.381 0.00 0.00 0.00 3.85
2276 12610 0.105964 TGTTCGTTCAGTGGGAGGTG 59.894 55.000 0.00 0.00 0.00 4.00
2278 12612 1.407656 TTCGTTCAGTGGGAGGTGCT 61.408 55.000 0.00 0.00 0.00 4.40
2280 12614 1.754745 GTTCAGTGGGAGGTGCTCA 59.245 57.895 0.00 0.00 31.08 4.26
2281 12615 0.326264 GTTCAGTGGGAGGTGCTCAT 59.674 55.000 0.00 0.00 31.08 2.90
2283 12617 1.489481 TCAGTGGGAGGTGCTCATAG 58.511 55.000 0.00 0.00 31.08 2.23
2286 12620 0.179000 GTGGGAGGTGCTCATAGGTG 59.821 60.000 0.00 0.00 31.08 4.00
2287 12621 0.252696 TGGGAGGTGCTCATAGGTGT 60.253 55.000 0.00 0.00 31.08 4.16
2288 12622 0.912486 GGGAGGTGCTCATAGGTGTT 59.088 55.000 0.00 0.00 31.08 3.32
2290 12624 2.103263 GGGAGGTGCTCATAGGTGTTAG 59.897 54.545 0.00 0.00 31.08 2.34
2291 12625 3.031736 GGAGGTGCTCATAGGTGTTAGA 58.968 50.000 0.00 0.00 31.08 2.10
2292 12626 3.451178 GGAGGTGCTCATAGGTGTTAGAA 59.549 47.826 0.00 0.00 31.08 2.10
2293 12627 4.101741 GGAGGTGCTCATAGGTGTTAGAAT 59.898 45.833 0.00 0.00 31.08 2.40
2294 12628 5.304614 GGAGGTGCTCATAGGTGTTAGAATA 59.695 44.000 0.00 0.00 31.08 1.75
2295 12629 6.183360 GGAGGTGCTCATAGGTGTTAGAATAA 60.183 42.308 0.00 0.00 31.08 1.40
2296 12630 7.195374 AGGTGCTCATAGGTGTTAGAATAAA 57.805 36.000 0.00 0.00 0.00 1.40
2297 12631 7.806180 AGGTGCTCATAGGTGTTAGAATAAAT 58.194 34.615 0.00 0.00 0.00 1.40
2299 12633 7.173390 GGTGCTCATAGGTGTTAGAATAAATCC 59.827 40.741 0.00 0.00 0.00 3.01
2300 12634 7.715249 GTGCTCATAGGTGTTAGAATAAATCCA 59.285 37.037 0.00 0.00 0.00 3.41
2301 12635 8.271458 TGCTCATAGGTGTTAGAATAAATCCAA 58.729 33.333 0.00 0.00 0.00 3.53
2302 12636 8.778358 GCTCATAGGTGTTAGAATAAATCCAAG 58.222 37.037 0.00 0.00 0.00 3.61
2304 12638 7.719633 TCATAGGTGTTAGAATAAATCCAAGGC 59.280 37.037 0.00 0.00 0.00 4.35
2306 12640 6.435164 AGGTGTTAGAATAAATCCAAGGCAT 58.565 36.000 0.00 0.00 0.00 4.40
2309 12643 7.255486 GGTGTTAGAATAAATCCAAGGCATACC 60.255 40.741 0.00 0.00 0.00 2.73
2312 12646 5.063880 AGAATAAATCCAAGGCATACCGTC 58.936 41.667 0.00 0.00 42.76 4.79
2313 12647 1.663695 AAATCCAAGGCATACCGTCG 58.336 50.000 0.00 0.00 42.76 5.12
2315 12649 1.048601 ATCCAAGGCATACCGTCGAT 58.951 50.000 0.00 0.00 42.76 3.59
2316 12650 0.828022 TCCAAGGCATACCGTCGATT 59.172 50.000 0.00 0.00 42.76 3.34
2321 12655 1.201647 AGGCATACCGTCGATTATCCG 59.798 52.381 0.00 0.00 42.76 4.18
2328 12662 0.949397 CGTCGATTATCCGAGGACCA 59.051 55.000 0.00 0.00 44.30 4.02
2330 12664 2.604855 CGTCGATTATCCGAGGACCAAG 60.605 54.545 0.00 0.00 44.30 3.61
2331 12665 1.340248 TCGATTATCCGAGGACCAAGC 59.660 52.381 0.00 0.00 34.19 4.01
2333 12667 2.483013 CGATTATCCGAGGACCAAGCAA 60.483 50.000 0.00 0.00 0.00 3.91
2334 12668 3.744660 GATTATCCGAGGACCAAGCAAT 58.255 45.455 0.00 0.00 0.00 3.56
2335 12669 2.910688 TATCCGAGGACCAAGCAATC 57.089 50.000 0.00 0.00 0.00 2.67
2338 12672 0.321564 CCGAGGACCAAGCAATCACA 60.322 55.000 0.00 0.00 0.00 3.58
2339 12673 0.798776 CGAGGACCAAGCAATCACAC 59.201 55.000 0.00 0.00 0.00 3.82
2343 12677 1.069227 GGACCAAGCAATCACACGAAC 60.069 52.381 0.00 0.00 0.00 3.95
2344 12678 1.601903 GACCAAGCAATCACACGAACA 59.398 47.619 0.00 0.00 0.00 3.18
2348 12682 0.859232 AGCAATCACACGAACACGAC 59.141 50.000 0.00 0.00 0.00 4.34
2350 12684 1.194547 GCAATCACACGAACACGACAT 59.805 47.619 0.00 0.00 0.00 3.06
2352 12686 1.336877 ATCACACGAACACGACATCG 58.663 50.000 0.00 0.00 44.33 3.84
2354 12688 0.702924 CACACGAACACGACATCGAG 59.297 55.000 8.54 2.37 41.43 4.04
2355 12689 0.589708 ACACGAACACGACATCGAGA 59.410 50.000 8.54 0.00 41.43 4.04
2356 12690 1.199327 ACACGAACACGACATCGAGAT 59.801 47.619 8.54 0.00 41.43 2.75
2358 12692 2.661675 CACGAACACGACATCGAGATTT 59.338 45.455 8.54 0.00 41.43 2.17
2361 12695 3.121279 CGAACACGACATCGAGATTTGTT 59.879 43.478 8.54 7.54 41.43 2.83
2362 12696 4.322539 CGAACACGACATCGAGATTTGTTA 59.677 41.667 8.54 0.00 41.43 2.41
2363 12697 5.164129 CGAACACGACATCGAGATTTGTTAA 60.164 40.000 8.54 0.00 41.43 2.01
2364 12698 5.511088 ACACGACATCGAGATTTGTTAAC 57.489 39.130 8.54 0.00 43.02 2.01
2365 12699 4.089493 ACACGACATCGAGATTTGTTAACG 59.911 41.667 8.54 0.00 43.02 3.18
2369 12703 4.817517 ACATCGAGATTTGTTAACGAGGT 58.182 39.130 0.00 0.00 41.62 3.85
2370 12704 5.235516 ACATCGAGATTTGTTAACGAGGTT 58.764 37.500 0.00 0.00 43.27 3.50
2382 14371 0.104304 ACGAGGTTCACCGATATGGC 59.896 55.000 0.00 0.00 43.94 4.40
2384 14373 1.611977 CGAGGTTCACCGATATGGCTA 59.388 52.381 0.00 0.00 43.94 3.93
2385 14374 2.607282 CGAGGTTCACCGATATGGCTAC 60.607 54.545 0.00 0.00 43.94 3.58
2386 14375 2.364324 GAGGTTCACCGATATGGCTACA 59.636 50.000 0.00 0.00 43.94 2.74
2387 14376 2.972713 AGGTTCACCGATATGGCTACAT 59.027 45.455 0.00 0.00 43.94 2.29
2388 14377 3.006967 AGGTTCACCGATATGGCTACATC 59.993 47.826 0.00 0.00 43.94 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.803768 CAGGGAGCGAATGTCGACAG 60.804 60.000 24.41 11.58 43.74 3.51
40 42 0.314935 ATTGTCTTTGCCAAGTGCCG 59.685 50.000 0.00 0.00 40.16 5.69
64 66 2.749441 GCTTGAGCCCTGCTGGAC 60.749 66.667 11.88 0.00 39.88 4.02
181 192 8.548721 GTCTAATAATGCACCACTTGTATACAC 58.451 37.037 4.68 0.00 28.95 2.90
183 194 7.172703 GGGTCTAATAATGCACCACTTGTATAC 59.827 40.741 0.00 0.00 28.95 1.47
189 200 4.526970 CTGGGTCTAATAATGCACCACTT 58.473 43.478 0.00 0.00 0.00 3.16
190 201 3.117888 CCTGGGTCTAATAATGCACCACT 60.118 47.826 0.00 0.00 0.00 4.00
191 202 3.214328 CCTGGGTCTAATAATGCACCAC 58.786 50.000 0.00 0.00 0.00 4.16
246 261 3.693471 TGCTTGCAATTGGGCGGG 61.693 61.111 7.72 0.00 36.28 6.13
265 284 1.963515 GCTTTGTTTGATGGGGTGTCT 59.036 47.619 0.00 0.00 0.00 3.41
268 291 1.273327 GAGGCTTTGTTTGATGGGGTG 59.727 52.381 0.00 0.00 0.00 4.61
319 3334 2.584791 GCGTTGTTTAGGTCAGCATTG 58.415 47.619 0.00 0.00 0.00 2.82
399 4739 2.277008 AATCCATCCCTGACTGACCT 57.723 50.000 0.00 0.00 0.00 3.85
416 4756 5.548406 AGATTTAGCCGCGGATTAGTTAAT 58.452 37.500 33.48 17.11 0.00 1.40
428 4768 6.688813 GCTAATAATGCATTAGATTTAGCCGC 59.311 38.462 31.14 19.24 46.29 6.53
481 4826 1.003051 GGGGTAGGAGCTGGAGGAA 59.997 63.158 0.00 0.00 0.00 3.36
598 8987 7.350382 ACAGTCAGAGATTCAGAGTAGGATTA 58.650 38.462 0.00 0.00 0.00 1.75
732 9200 4.699257 AGAGCAATGAAAACAGATGGAGAC 59.301 41.667 0.00 0.00 0.00 3.36
765 9233 5.884792 AGAAGACTTTGATCACCATTCCATC 59.115 40.000 0.00 0.00 0.00 3.51
800 9268 3.129638 AGCAACGTGAAGGCTTTGTTTTA 59.870 39.130 0.00 0.00 33.21 1.52
848 9316 0.108615 CGTCTGTCCATCGAAAGGCT 60.109 55.000 2.54 0.00 0.00 4.58
892 9366 5.491992 AGGGGTGGAATGGTTTATATAGGA 58.508 41.667 0.00 0.00 0.00 2.94
919 9394 1.162505 TGGAATTGGGAGGTTGGGAA 58.837 50.000 0.00 0.00 0.00 3.97
991 9468 2.889617 CATGCCCATGGTGCACAG 59.110 61.111 24.55 17.76 42.38 3.66
1050 9527 2.315386 GCACCGGTCCAACGTCTTC 61.315 63.158 2.59 0.00 0.00 2.87
1413 9903 1.743958 CTCATCAACTCGGTAGTCGGT 59.256 52.381 0.00 0.00 39.77 4.69
1419 9909 2.685388 CTCAGAGCTCATCAACTCGGTA 59.315 50.000 17.77 0.00 37.99 4.02
1420 9910 1.476085 CTCAGAGCTCATCAACTCGGT 59.524 52.381 17.77 0.00 37.99 4.69
1517 10012 5.125257 TGCCAAGTATATGGTGATGTTGTTG 59.875 40.000 0.00 0.00 42.75 3.33
1619 10114 5.169295 GCAGACAGTTACTACAACTTAGGG 58.831 45.833 0.00 0.00 0.00 3.53
1671 10173 4.327357 CGCCATATATAGTCGGCAGAAAAG 59.673 45.833 16.60 1.21 45.14 2.27
1710 10213 7.328157 GAATAGAAGTGCGCTATTCTACTTC 57.672 40.000 26.42 24.23 45.37 3.01
1735 10238 4.583907 TCCAACTTGCAATCAATGTGAGAA 59.416 37.500 0.00 0.00 0.00 2.87
1743 10246 1.266718 GACGCTCCAACTTGCAATCAA 59.733 47.619 0.00 0.00 0.00 2.57
1793 10297 9.665719 TGTTAGCATAGTTTCATCTAAATCACA 57.334 29.630 0.00 0.00 0.00 3.58
1819 10323 7.058525 TCAGAGAAACAATATGGCTGATCAAT 58.941 34.615 0.00 0.00 0.00 2.57
1839 10343 4.814147 TGTGTAGCAGATGAACTTCAGAG 58.186 43.478 0.00 0.00 0.00 3.35
1942 12269 8.964772 CAAACTTTCTATTCATCCTTGGAGATT 58.035 33.333 0.00 0.00 0.00 2.40
1985 12315 1.470805 GCGAGTTTTGCCTTTGGTGTT 60.471 47.619 0.00 0.00 0.00 3.32
2054 12385 6.400621 CGTTGTGCTCGTATTCTTTTGATGTA 60.401 38.462 0.00 0.00 0.00 2.29
2070 12401 1.993370 GGACATGTACTCGTTGTGCTC 59.007 52.381 0.00 0.00 32.31 4.26
2088 12419 5.679894 GCATTCTAGTCATTCAGAAGTCGGA 60.680 44.000 0.00 0.00 34.43 4.55
2092 12423 5.641209 GTGTGCATTCTAGTCATTCAGAAGT 59.359 40.000 0.00 0.00 34.43 3.01
2094 12425 5.409520 GTGTGTGCATTCTAGTCATTCAGAA 59.590 40.000 0.00 0.00 35.37 3.02
2099 12430 4.898320 TGAGTGTGTGCATTCTAGTCATT 58.102 39.130 0.00 0.00 33.21 2.57
2151 12482 1.913419 TGTCCTCCTAACCATCCAACC 59.087 52.381 0.00 0.00 0.00 3.77
2181 12512 0.764890 CTTGAACTCTGGTGGGGTGA 59.235 55.000 0.00 0.00 0.00 4.02
2184 12515 0.764890 TGACTTGAACTCTGGTGGGG 59.235 55.000 0.00 0.00 0.00 4.96
2185 12516 2.867109 ATGACTTGAACTCTGGTGGG 57.133 50.000 0.00 0.00 0.00 4.61
2203 12535 3.525537 CGAGCACCAATGTCAAGTCTAT 58.474 45.455 0.00 0.00 0.00 1.98
2235 12567 4.689612 TCGCCAGAAGCCTAATAAATCT 57.310 40.909 0.00 0.00 38.78 2.40
2251 12585 0.948623 CCACTGAACGAACATCGCCA 60.949 55.000 0.00 0.00 45.12 5.69
2265 12599 0.467384 CCTATGAGCACCTCCCACTG 59.533 60.000 0.00 0.00 0.00 3.66
2272 12606 6.808321 TTATTCTAACACCTATGAGCACCT 57.192 37.500 0.00 0.00 0.00 4.00
2274 12608 7.715249 TGGATTTATTCTAACACCTATGAGCAC 59.285 37.037 0.00 0.00 0.00 4.40
2275 12609 7.801104 TGGATTTATTCTAACACCTATGAGCA 58.199 34.615 0.00 0.00 0.00 4.26
2276 12610 8.677148 TTGGATTTATTCTAACACCTATGAGC 57.323 34.615 0.00 0.00 0.00 4.26
2278 12612 7.719633 GCCTTGGATTTATTCTAACACCTATGA 59.280 37.037 0.00 0.00 0.00 2.15
2280 12614 7.582719 TGCCTTGGATTTATTCTAACACCTAT 58.417 34.615 0.00 0.00 0.00 2.57
2281 12615 6.964464 TGCCTTGGATTTATTCTAACACCTA 58.036 36.000 0.00 0.00 0.00 3.08
2283 12617 6.715347 ATGCCTTGGATTTATTCTAACACC 57.285 37.500 0.00 0.00 0.00 4.16
2286 12620 6.485648 ACGGTATGCCTTGGATTTATTCTAAC 59.514 38.462 0.00 0.00 0.00 2.34
2287 12621 6.597562 ACGGTATGCCTTGGATTTATTCTAA 58.402 36.000 0.00 0.00 0.00 2.10
2288 12622 6.182507 ACGGTATGCCTTGGATTTATTCTA 57.817 37.500 0.00 0.00 0.00 2.10
2290 12624 4.084013 CGACGGTATGCCTTGGATTTATTC 60.084 45.833 0.00 0.00 0.00 1.75
2291 12625 3.813166 CGACGGTATGCCTTGGATTTATT 59.187 43.478 0.00 0.00 0.00 1.40
2292 12626 3.070446 TCGACGGTATGCCTTGGATTTAT 59.930 43.478 0.00 0.00 0.00 1.40
2293 12627 2.431419 TCGACGGTATGCCTTGGATTTA 59.569 45.455 0.00 0.00 0.00 1.40
2294 12628 1.208535 TCGACGGTATGCCTTGGATTT 59.791 47.619 0.00 0.00 0.00 2.17
2295 12629 0.828022 TCGACGGTATGCCTTGGATT 59.172 50.000 0.00 0.00 0.00 3.01
2296 12630 1.048601 ATCGACGGTATGCCTTGGAT 58.951 50.000 0.00 0.00 29.05 3.41
2297 12631 0.828022 AATCGACGGTATGCCTTGGA 59.172 50.000 0.00 0.00 0.00 3.53
2299 12633 2.993899 GGATAATCGACGGTATGCCTTG 59.006 50.000 0.00 0.00 0.00 3.61
2300 12634 2.352421 CGGATAATCGACGGTATGCCTT 60.352 50.000 0.00 0.00 0.00 4.35
2301 12635 1.201647 CGGATAATCGACGGTATGCCT 59.798 52.381 0.00 0.00 0.00 4.75
2302 12636 1.200716 TCGGATAATCGACGGTATGCC 59.799 52.381 0.00 0.00 33.92 4.40
2304 12638 2.745821 TCCTCGGATAATCGACGGTATG 59.254 50.000 0.00 0.00 35.18 2.39
2306 12640 2.146342 GTCCTCGGATAATCGACGGTA 58.854 52.381 0.00 0.00 35.18 4.02
2309 12643 0.949397 TGGTCCTCGGATAATCGACG 59.051 55.000 0.00 0.00 35.18 5.12
2312 12646 1.068588 TGCTTGGTCCTCGGATAATCG 59.931 52.381 0.00 0.00 0.00 3.34
2313 12647 2.910688 TGCTTGGTCCTCGGATAATC 57.089 50.000 0.00 0.00 0.00 1.75
2315 12649 2.503765 TGATTGCTTGGTCCTCGGATAA 59.496 45.455 0.00 0.00 0.00 1.75
2316 12650 2.115427 TGATTGCTTGGTCCTCGGATA 58.885 47.619 0.00 0.00 0.00 2.59
2321 12655 0.798776 CGTGTGATTGCTTGGTCCTC 59.201 55.000 0.00 0.00 0.00 3.71
2328 12662 1.260561 GTCGTGTTCGTGTGATTGCTT 59.739 47.619 0.00 0.00 38.33 3.91
2330 12664 0.579630 TGTCGTGTTCGTGTGATTGC 59.420 50.000 0.00 0.00 38.33 3.56
2331 12665 2.470621 CGATGTCGTGTTCGTGTGATTG 60.471 50.000 0.00 0.00 38.33 2.67
2333 12667 1.068816 TCGATGTCGTGTTCGTGTGAT 60.069 47.619 2.04 0.00 40.80 3.06
2334 12668 0.308376 TCGATGTCGTGTTCGTGTGA 59.692 50.000 2.04 0.00 40.80 3.58
2335 12669 0.702924 CTCGATGTCGTGTTCGTGTG 59.297 55.000 2.04 0.00 40.80 3.82
2338 12672 2.631418 AATCTCGATGTCGTGTTCGT 57.369 45.000 2.04 0.00 40.80 3.85
2339 12673 2.661675 ACAAATCTCGATGTCGTGTTCG 59.338 45.455 2.04 0.00 40.80 3.95
2343 12677 4.322539 TCGTTAACAAATCTCGATGTCGTG 59.677 41.667 6.39 0.17 40.80 4.35
2344 12678 4.478699 TCGTTAACAAATCTCGATGTCGT 58.521 39.130 6.39 0.00 40.80 4.34
2348 12682 5.347635 TGAACCTCGTTAACAAATCTCGATG 59.652 40.000 6.39 0.00 0.00 3.84
2350 12684 4.682860 GTGAACCTCGTTAACAAATCTCGA 59.317 41.667 6.39 0.00 27.94 4.04
2352 12686 4.143179 CGGTGAACCTCGTTAACAAATCTC 60.143 45.833 6.39 0.00 28.88 2.75
2354 12688 3.742369 TCGGTGAACCTCGTTAACAAATC 59.258 43.478 6.39 0.00 28.88 2.17
2355 12689 3.731089 TCGGTGAACCTCGTTAACAAAT 58.269 40.909 6.39 0.00 28.88 2.32
2356 12690 3.176552 TCGGTGAACCTCGTTAACAAA 57.823 42.857 6.39 0.00 28.88 2.83
2358 12692 4.426416 CATATCGGTGAACCTCGTTAACA 58.574 43.478 6.39 0.00 28.88 2.41
2361 12695 2.223876 GCCATATCGGTGAACCTCGTTA 60.224 50.000 0.00 0.00 36.97 3.18
2362 12696 1.472728 GCCATATCGGTGAACCTCGTT 60.473 52.381 0.00 0.00 36.97 3.85
2363 12697 0.104304 GCCATATCGGTGAACCTCGT 59.896 55.000 0.00 0.00 36.97 4.18
2364 12698 0.389391 AGCCATATCGGTGAACCTCG 59.611 55.000 0.00 0.00 36.97 4.63
2365 12699 2.364324 TGTAGCCATATCGGTGAACCTC 59.636 50.000 0.00 0.00 36.97 3.85


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

AutoCloner maintained by Alex Coulton.