Multiple sequence alignment - TraesCS2D01G585900

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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 TraesCS2D01G585900 chr2D 100.000 2411 0 0 1 2411 644703264 644700854 0.000000e+00 4453.0
1 TraesCS2D01G585900 chrUn 99.414 2219 11 1 1 2219 261513064 261515280 0.000000e+00 4024.0
2 TraesCS2D01G585900 chrUn 99.414 2219 8 2 1 2219 45100792 45098579 0.000000e+00 4021.0
3 TraesCS2D01G585900 chrUn 99.009 2219 14 3 1 2219 186163779 186161569 0.000000e+00 3969.0
4 TraesCS2D01G585900 chrUn 91.111 90 5 1 2320 2409 422216209 422216123 4.210000e-23 119.0
5 TraesCS2D01G585900 chr5B 99.369 2219 10 1 1 2219 130614901 130612687 0.000000e+00 4017.0
6 TraesCS2D01G585900 chr5B 99.234 2219 17 0 1 2219 130568755 130570973 0.000000e+00 4004.0
7 TraesCS2D01G585900 chr5B 99.234 2219 12 2 1 2219 130609877 130607664 0.000000e+00 3999.0
8 TraesCS2D01G585900 chr3A 99.234 2219 13 2 1 2219 66030313 66032527 0.000000e+00 4000.0
9 TraesCS2D01G585900 chr3A 91.304 92 5 1 2320 2411 667175676 667175588 3.260000e-24 122.0
10 TraesCS2D01G585900 chr3A 100.000 33 0 0 2244 2276 561294109 561294077 7.200000e-06 62.1
11 TraesCS2D01G585900 chr7B 99.100 2223 17 1 1 2223 743033700 743035919 0.000000e+00 3991.0
12 TraesCS2D01G585900 chr5A 98.963 2219 22 1 1 2219 238861455 238859238 0.000000e+00 3969.0
13 TraesCS2D01G585900 chr6D 91.304 92 5 1 2320 2411 354371336 354371248 3.260000e-24 122.0
14 TraesCS2D01G585900 chr6D 90.217 92 6 2 2320 2411 316024698 316024786 1.510000e-22 117.0
15 TraesCS2D01G585900 chr6B 91.111 90 5 1 2320 2409 93584135 93584049 4.210000e-23 119.0
16 TraesCS2D01G585900 chr6B 91.111 90 5 1 2320 2409 93593173 93593087 4.210000e-23 119.0
17 TraesCS2D01G585900 chr6B 91.111 90 5 1 2320 2409 93609931 93609845 4.210000e-23 119.0
18 TraesCS2D01G585900 chr4D 90.217 92 6 1 2320 2411 464180118 464180206 1.510000e-22 117.0
19 TraesCS2D01G585900 chr4A 85.345 116 11 3 2302 2411 612658449 612658334 5.450000e-22 115.0
20 TraesCS2D01G585900 chr3D 100.000 32 0 0 2244 2275 569373342 569373311 2.590000e-05 60.2
21 TraesCS2D01G585900 chr3D 96.875 32 1 0 2244 2275 569342000 569342031 1.000000e-03 54.7
22 TraesCS2D01G585900 chr2B 100.000 32 0 0 2244 2275 41054417 41054448 2.590000e-05 60.2


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 TraesCS2D01G585900 chr2D 644700854 644703264 2410 True 4453 4453 100.0000 1 2411 1 chr2D.!!$R1 2410
1 TraesCS2D01G585900 chrUn 261513064 261515280 2216 False 4024 4024 99.4140 1 2219 1 chrUn.!!$F1 2218
2 TraesCS2D01G585900 chrUn 45098579 45100792 2213 True 4021 4021 99.4140 1 2219 1 chrUn.!!$R1 2218
3 TraesCS2D01G585900 chrUn 186161569 186163779 2210 True 3969 3969 99.0090 1 2219 1 chrUn.!!$R2 2218
4 TraesCS2D01G585900 chr5B 130607664 130614901 7237 True 4008 4017 99.3015 1 2219 2 chr5B.!!$R1 2218
5 TraesCS2D01G585900 chr5B 130568755 130570973 2218 False 4004 4004 99.2340 1 2219 1 chr5B.!!$F1 2218
6 TraesCS2D01G585900 chr3A 66030313 66032527 2214 False 4000 4000 99.2340 1 2219 1 chr3A.!!$F1 2218
7 TraesCS2D01G585900 chr7B 743033700 743035919 2219 False 3991 3991 99.1000 1 2223 1 chr7B.!!$F1 2222
8 TraesCS2D01G585900 chr5A 238859238 238861455 2217 True 3969 3969 98.9630 1 2219 1 chr5A.!!$R1 2218

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
1047 1048 3.476031 AATGGGCGCCACTATCCCG 62.476 63.158 30.85 0.0 42.98 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2352 7380 0.107643 TTCAGCGTTGGTGGACATGA 59.892 50.0 0.0 0.0 0.0 3.07 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
1047 1048 3.476031 AATGGGCGCCACTATCCCG 62.476 63.158 30.85 0.00 42.98 5.14
1564 6591 1.065273 CTGCGTACGATTAGCCGGT 59.935 57.895 21.65 0.00 0.00 5.28
2237 7265 2.891191 TTTCTCCCTTTAATGCCGGT 57.109 45.000 1.90 0.00 0.00 5.28
2238 7266 2.891191 TTCTCCCTTTAATGCCGGTT 57.109 45.000 1.90 0.00 0.00 4.44
2239 7267 2.413310 TCTCCCTTTAATGCCGGTTC 57.587 50.000 1.90 0.00 0.00 3.62
2240 7268 1.913419 TCTCCCTTTAATGCCGGTTCT 59.087 47.619 1.90 0.00 0.00 3.01
2241 7269 2.017049 CTCCCTTTAATGCCGGTTCTG 58.983 52.381 1.90 0.00 0.00 3.02
2242 7270 0.455815 CCCTTTAATGCCGGTTCTGC 59.544 55.000 1.90 0.00 0.00 4.26
2243 7271 1.173043 CCTTTAATGCCGGTTCTGCA 58.827 50.000 1.90 0.00 43.97 4.41
2244 7272 1.543802 CCTTTAATGCCGGTTCTGCAA 59.456 47.619 1.90 0.00 42.92 4.08
2245 7273 2.595386 CTTTAATGCCGGTTCTGCAAC 58.405 47.619 1.90 0.00 42.92 4.17
2255 7283 3.439895 GGTTCTGCAACCGGTTTTAAA 57.560 42.857 19.55 7.09 43.00 1.52
2256 7284 3.377439 GGTTCTGCAACCGGTTTTAAAG 58.623 45.455 19.55 12.60 43.00 1.85
2257 7285 3.067040 GGTTCTGCAACCGGTTTTAAAGA 59.933 43.478 19.55 14.74 43.00 2.52
2258 7286 4.261867 GGTTCTGCAACCGGTTTTAAAGAT 60.262 41.667 19.55 0.00 43.00 2.40
2259 7287 4.759516 TCTGCAACCGGTTTTAAAGATC 57.240 40.909 19.55 0.22 0.00 2.75
2260 7288 3.504520 TCTGCAACCGGTTTTAAAGATCC 59.495 43.478 19.55 0.00 0.00 3.36
2261 7289 2.226912 TGCAACCGGTTTTAAAGATCCG 59.773 45.455 19.55 16.27 42.22 4.18
2262 7290 2.227149 GCAACCGGTTTTAAAGATCCGT 59.773 45.455 19.55 0.00 41.17 4.69
2263 7291 3.304861 GCAACCGGTTTTAAAGATCCGTT 60.305 43.478 19.55 13.71 41.17 4.44
2264 7292 4.793678 GCAACCGGTTTTAAAGATCCGTTT 60.794 41.667 19.55 13.04 41.17 3.60
2265 7293 5.283294 CAACCGGTTTTAAAGATCCGTTTT 58.717 37.500 19.55 12.87 41.17 2.43
2266 7294 5.112220 ACCGGTTTTAAAGATCCGTTTTC 57.888 39.130 0.00 0.00 41.17 2.29
2267 7295 4.823442 ACCGGTTTTAAAGATCCGTTTTCT 59.177 37.500 0.00 0.00 41.17 2.52
2268 7296 5.997129 ACCGGTTTTAAAGATCCGTTTTCTA 59.003 36.000 0.00 0.00 41.17 2.10
2269 7297 6.073058 ACCGGTTTTAAAGATCCGTTTTCTAC 60.073 38.462 0.00 0.44 41.17 2.59
2270 7298 6.148315 CCGGTTTTAAAGATCCGTTTTCTACT 59.852 38.462 19.38 0.00 41.17 2.57
2271 7299 7.331687 CCGGTTTTAAAGATCCGTTTTCTACTA 59.668 37.037 19.38 0.00 41.17 1.82
2272 7300 8.378421 CGGTTTTAAAGATCCGTTTTCTACTAG 58.622 37.037 15.48 0.00 38.45 2.57
2273 7301 9.212641 GGTTTTAAAGATCCGTTTTCTACTAGT 57.787 33.333 0.00 0.00 0.00 2.57
2275 7303 8.767478 TTTAAAGATCCGTTTTCTACTAGTGG 57.233 34.615 5.39 1.87 0.00 4.00
2276 7304 5.340439 AAGATCCGTTTTCTACTAGTGGG 57.660 43.478 5.39 0.00 0.00 4.61
2277 7305 3.705072 AGATCCGTTTTCTACTAGTGGGG 59.295 47.826 5.39 0.00 0.00 4.96
2278 7306 3.173953 TCCGTTTTCTACTAGTGGGGA 57.826 47.619 5.39 1.18 0.00 4.81
2279 7307 3.094572 TCCGTTTTCTACTAGTGGGGAG 58.905 50.000 5.39 0.00 0.00 4.30
2280 7308 3.094572 CCGTTTTCTACTAGTGGGGAGA 58.905 50.000 5.39 0.00 0.00 3.71
2281 7309 3.130693 CCGTTTTCTACTAGTGGGGAGAG 59.869 52.174 5.39 0.00 0.00 3.20
2282 7310 3.130693 CGTTTTCTACTAGTGGGGAGAGG 59.869 52.174 5.39 0.00 0.00 3.69
2283 7311 3.399952 TTTCTACTAGTGGGGAGAGGG 57.600 52.381 5.39 0.00 0.00 4.30
2284 7312 0.556747 TCTACTAGTGGGGAGAGGGC 59.443 60.000 5.39 0.00 0.00 5.19
2285 7313 0.824182 CTACTAGTGGGGAGAGGGCG 60.824 65.000 5.39 0.00 0.00 6.13
2286 7314 1.284111 TACTAGTGGGGAGAGGGCGA 61.284 60.000 5.39 0.00 0.00 5.54
2287 7315 1.381327 CTAGTGGGGAGAGGGCGAA 60.381 63.158 0.00 0.00 0.00 4.70
2288 7316 0.760945 CTAGTGGGGAGAGGGCGAAT 60.761 60.000 0.00 0.00 0.00 3.34
2289 7317 0.559205 TAGTGGGGAGAGGGCGAATA 59.441 55.000 0.00 0.00 0.00 1.75
2290 7318 0.760945 AGTGGGGAGAGGGCGAATAG 60.761 60.000 0.00 0.00 0.00 1.73
2291 7319 0.759436 GTGGGGAGAGGGCGAATAGA 60.759 60.000 0.00 0.00 0.00 1.98
2292 7320 0.191064 TGGGGAGAGGGCGAATAGAT 59.809 55.000 0.00 0.00 0.00 1.98
2293 7321 1.353091 GGGGAGAGGGCGAATAGATT 58.647 55.000 0.00 0.00 0.00 2.40
2294 7322 1.700186 GGGGAGAGGGCGAATAGATTT 59.300 52.381 0.00 0.00 0.00 2.17
2295 7323 2.106684 GGGGAGAGGGCGAATAGATTTT 59.893 50.000 0.00 0.00 0.00 1.82
2296 7324 3.142174 GGGAGAGGGCGAATAGATTTTG 58.858 50.000 0.00 0.00 0.00 2.44
2297 7325 3.142174 GGAGAGGGCGAATAGATTTTGG 58.858 50.000 0.00 0.00 0.00 3.28
2298 7326 3.142174 GAGAGGGCGAATAGATTTTGGG 58.858 50.000 0.00 0.00 0.00 4.12
2299 7327 2.777692 AGAGGGCGAATAGATTTTGGGA 59.222 45.455 0.00 0.00 0.00 4.37
2300 7328 3.202151 AGAGGGCGAATAGATTTTGGGAA 59.798 43.478 0.00 0.00 0.00 3.97
2301 7329 3.555966 AGGGCGAATAGATTTTGGGAAG 58.444 45.455 0.00 0.00 0.00 3.46
2302 7330 2.034685 GGGCGAATAGATTTTGGGAAGC 59.965 50.000 0.00 0.00 0.00 3.86
2303 7331 2.287009 GGCGAATAGATTTTGGGAAGCG 60.287 50.000 0.00 0.00 0.00 4.68
2304 7332 2.612212 GCGAATAGATTTTGGGAAGCGA 59.388 45.455 0.00 0.00 0.00 4.93
2305 7333 3.546218 GCGAATAGATTTTGGGAAGCGAC 60.546 47.826 0.00 0.00 0.00 5.19
2306 7334 3.002348 CGAATAGATTTTGGGAAGCGACC 59.998 47.826 0.00 0.00 0.00 4.79
2307 7335 2.018542 TAGATTTTGGGAAGCGACCG 57.981 50.000 0.00 0.00 0.00 4.79
2308 7336 1.136774 GATTTTGGGAAGCGACCGC 59.863 57.895 6.25 6.25 42.33 5.68
2320 7348 4.632458 GACCGCTCGCCTCCGATC 62.632 72.222 0.00 0.00 43.47 3.69
2323 7351 4.335584 CGCTCGCCTCCGATCCTC 62.336 72.222 0.00 0.00 43.47 3.71
2324 7352 2.909965 GCTCGCCTCCGATCCTCT 60.910 66.667 0.00 0.00 43.47 3.69
2325 7353 1.601197 GCTCGCCTCCGATCCTCTA 60.601 63.158 0.00 0.00 43.47 2.43
2326 7354 1.858372 GCTCGCCTCCGATCCTCTAC 61.858 65.000 0.00 0.00 43.47 2.59
2327 7355 1.570347 CTCGCCTCCGATCCTCTACG 61.570 65.000 0.00 0.00 43.47 3.51
2328 7356 1.892862 CGCCTCCGATCCTCTACGT 60.893 63.158 0.00 0.00 36.29 3.57
2329 7357 1.843734 CGCCTCCGATCCTCTACGTC 61.844 65.000 0.00 0.00 36.29 4.34
2330 7358 1.517210 GCCTCCGATCCTCTACGTCC 61.517 65.000 0.00 0.00 0.00 4.79
2331 7359 0.179026 CCTCCGATCCTCTACGTCCA 60.179 60.000 0.00 0.00 0.00 4.02
2332 7360 0.945813 CTCCGATCCTCTACGTCCAC 59.054 60.000 0.00 0.00 0.00 4.02
2333 7361 0.812811 TCCGATCCTCTACGTCCACG 60.813 60.000 0.00 0.00 46.33 4.94
2343 7371 2.250485 CGTCCACGTCGTCTTCGT 59.750 61.111 0.00 0.00 42.33 3.85
2344 7372 1.791283 CGTCCACGTCGTCTTCGTC 60.791 63.158 0.00 0.00 39.55 4.20
2345 7373 1.280746 GTCCACGTCGTCTTCGTCA 59.719 57.895 0.00 0.00 39.55 4.35
2346 7374 0.109873 GTCCACGTCGTCTTCGTCAT 60.110 55.000 0.00 0.00 39.55 3.06
2347 7375 0.167470 TCCACGTCGTCTTCGTCATC 59.833 55.000 0.00 0.00 39.55 2.92
2348 7376 0.109919 CCACGTCGTCTTCGTCATCA 60.110 55.000 0.00 0.00 39.55 3.07
2349 7377 0.975544 CACGTCGTCTTCGTCATCAC 59.024 55.000 0.00 0.00 39.55 3.06
2350 7378 0.109873 ACGTCGTCTTCGTCATCACC 60.110 55.000 0.00 0.00 36.85 4.02
2351 7379 0.109919 CGTCGTCTTCGTCATCACCA 60.110 55.000 0.00 0.00 38.33 4.17
2352 7380 1.467543 CGTCGTCTTCGTCATCACCAT 60.468 52.381 0.00 0.00 38.33 3.55
2353 7381 2.186076 GTCGTCTTCGTCATCACCATC 58.814 52.381 0.00 0.00 38.33 3.51
2354 7382 1.816224 TCGTCTTCGTCATCACCATCA 59.184 47.619 0.00 0.00 38.33 3.07
2355 7383 2.427095 TCGTCTTCGTCATCACCATCAT 59.573 45.455 0.00 0.00 38.33 2.45
2356 7384 2.537214 CGTCTTCGTCATCACCATCATG 59.463 50.000 0.00 0.00 0.00 3.07
2357 7385 3.525537 GTCTTCGTCATCACCATCATGT 58.474 45.455 0.00 0.00 0.00 3.21
2358 7386 3.553511 GTCTTCGTCATCACCATCATGTC 59.446 47.826 0.00 0.00 0.00 3.06
2359 7387 2.602257 TCGTCATCACCATCATGTCC 57.398 50.000 0.00 0.00 0.00 4.02
2360 7388 1.830477 TCGTCATCACCATCATGTCCA 59.170 47.619 0.00 0.00 0.00 4.02
2361 7389 1.935873 CGTCATCACCATCATGTCCAC 59.064 52.381 0.00 0.00 0.00 4.02
2362 7390 2.292267 GTCATCACCATCATGTCCACC 58.708 52.381 0.00 0.00 0.00 4.61
2363 7391 1.914798 TCATCACCATCATGTCCACCA 59.085 47.619 0.00 0.00 0.00 4.17
2364 7392 2.308275 TCATCACCATCATGTCCACCAA 59.692 45.455 0.00 0.00 0.00 3.67
2365 7393 2.198827 TCACCATCATGTCCACCAAC 57.801 50.000 0.00 0.00 0.00 3.77
2366 7394 0.804364 CACCATCATGTCCACCAACG 59.196 55.000 0.00 0.00 0.00 4.10
2367 7395 0.960364 ACCATCATGTCCACCAACGC 60.960 55.000 0.00 0.00 0.00 4.84
2368 7396 0.677731 CCATCATGTCCACCAACGCT 60.678 55.000 0.00 0.00 0.00 5.07
2369 7397 0.448990 CATCATGTCCACCAACGCTG 59.551 55.000 0.00 0.00 0.00 5.18
2370 7398 0.324614 ATCATGTCCACCAACGCTGA 59.675 50.000 0.00 0.00 0.00 4.26
2371 7399 0.107643 TCATGTCCACCAACGCTGAA 59.892 50.000 0.00 0.00 0.00 3.02
2372 7400 0.238289 CATGTCCACCAACGCTGAAC 59.762 55.000 0.00 0.00 0.00 3.18
2393 7421 3.788766 CCGCCGCCGAGAAAGTTG 61.789 66.667 0.00 0.00 36.29 3.16
2394 7422 2.736995 CGCCGCCGAGAAAGTTGA 60.737 61.111 0.00 0.00 36.29 3.18
2395 7423 2.314647 CGCCGCCGAGAAAGTTGAA 61.315 57.895 0.00 0.00 36.29 2.69
2396 7424 1.497722 GCCGCCGAGAAAGTTGAAG 59.502 57.895 0.00 0.00 0.00 3.02
2397 7425 1.497722 CCGCCGAGAAAGTTGAAGC 59.502 57.895 0.00 0.00 0.00 3.86
2398 7426 1.497722 CGCCGAGAAAGTTGAAGCC 59.502 57.895 0.00 0.00 0.00 4.35
2399 7427 1.497722 GCCGAGAAAGTTGAAGCCG 59.502 57.895 0.00 0.00 0.00 5.52
2400 7428 0.949105 GCCGAGAAAGTTGAAGCCGA 60.949 55.000 0.00 0.00 0.00 5.54
2401 7429 0.790814 CCGAGAAAGTTGAAGCCGAC 59.209 55.000 0.00 0.00 0.00 4.79
2402 7430 1.497991 CGAGAAAGTTGAAGCCGACA 58.502 50.000 0.00 0.00 0.00 4.35
2403 7431 1.864711 CGAGAAAGTTGAAGCCGACAA 59.135 47.619 0.00 0.00 0.00 3.18
2404 7432 2.096713 CGAGAAAGTTGAAGCCGACAAG 60.097 50.000 0.00 0.00 0.00 3.16
2405 7433 3.131396 GAGAAAGTTGAAGCCGACAAGA 58.869 45.455 0.00 0.00 0.00 3.02
2406 7434 3.541632 AGAAAGTTGAAGCCGACAAGAA 58.458 40.909 0.00 0.00 0.00 2.52
2407 7435 3.561725 AGAAAGTTGAAGCCGACAAGAAG 59.438 43.478 0.00 0.00 0.00 2.85
2408 7436 1.884235 AGTTGAAGCCGACAAGAAGG 58.116 50.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1331 1336 2.599677 GCTCTATAGGGATATCGGGGG 58.400 57.143 2.98 0.00 0.00 5.40
1332 1337 2.158652 TCGCTCTATAGGGATATCGGGG 60.159 54.545 2.98 0.00 39.58 5.73
1854 6882 9.706691 TGAAAGTAGAAGAAGTTATCGAAACAT 57.293 29.630 11.33 1.92 0.00 2.71
1855 6883 9.706691 ATGAAAGTAGAAGAAGTTATCGAAACA 57.293 29.630 11.33 0.00 0.00 2.83
2223 7251 0.455815 GCAGAACCGGCATTAAAGGG 59.544 55.000 0.00 0.00 0.00 3.95
2224 7252 1.173043 TGCAGAACCGGCATTAAAGG 58.827 50.000 0.00 0.00 36.11 3.11
2225 7253 2.595386 GTTGCAGAACCGGCATTAAAG 58.405 47.619 0.00 0.00 41.58 1.85
2226 7254 1.271102 GGTTGCAGAACCGGCATTAAA 59.729 47.619 0.00 0.00 42.47 1.52
2227 7255 0.885196 GGTTGCAGAACCGGCATTAA 59.115 50.000 0.00 0.00 42.47 1.40
2228 7256 2.562125 GGTTGCAGAACCGGCATTA 58.438 52.632 0.00 0.00 42.47 1.90
2229 7257 3.365535 GGTTGCAGAACCGGCATT 58.634 55.556 0.00 0.00 42.47 3.56
2236 7264 4.295857 TCTTTAAAACCGGTTGCAGAAC 57.704 40.909 23.08 0.00 0.00 3.01
2237 7265 4.022676 GGATCTTTAAAACCGGTTGCAGAA 60.023 41.667 23.08 12.40 0.00 3.02
2238 7266 3.504520 GGATCTTTAAAACCGGTTGCAGA 59.495 43.478 23.08 18.76 0.00 4.26
2239 7267 3.669557 CGGATCTTTAAAACCGGTTGCAG 60.670 47.826 23.08 14.10 41.41 4.41
2240 7268 2.226912 CGGATCTTTAAAACCGGTTGCA 59.773 45.455 23.08 8.99 41.41 4.08
2241 7269 2.858839 CGGATCTTTAAAACCGGTTGC 58.141 47.619 23.08 0.00 41.41 4.17
2242 7270 4.492791 AACGGATCTTTAAAACCGGTTG 57.507 40.909 23.08 8.05 43.44 3.77
2247 7275 9.212641 ACTAGTAGAAAACGGATCTTTAAAACC 57.787 33.333 3.59 0.00 0.00 3.27
2249 7277 9.211485 CCACTAGTAGAAAACGGATCTTTAAAA 57.789 33.333 3.59 0.00 0.00 1.52
2250 7278 7.820872 CCCACTAGTAGAAAACGGATCTTTAAA 59.179 37.037 3.59 0.00 0.00 1.52
2251 7279 7.325694 CCCACTAGTAGAAAACGGATCTTTAA 58.674 38.462 3.59 0.00 0.00 1.52
2252 7280 6.127253 CCCCACTAGTAGAAAACGGATCTTTA 60.127 42.308 3.59 0.00 0.00 1.85
2253 7281 5.338137 CCCCACTAGTAGAAAACGGATCTTT 60.338 44.000 3.59 0.00 0.00 2.52
2254 7282 4.161754 CCCCACTAGTAGAAAACGGATCTT 59.838 45.833 3.59 0.00 0.00 2.40
2255 7283 3.705072 CCCCACTAGTAGAAAACGGATCT 59.295 47.826 3.59 0.00 0.00 2.75
2256 7284 3.703052 TCCCCACTAGTAGAAAACGGATC 59.297 47.826 3.59 0.00 0.00 3.36
2257 7285 3.705072 CTCCCCACTAGTAGAAAACGGAT 59.295 47.826 3.59 0.00 0.00 4.18
2258 7286 3.094572 CTCCCCACTAGTAGAAAACGGA 58.905 50.000 3.59 0.82 0.00 4.69
2259 7287 3.094572 TCTCCCCACTAGTAGAAAACGG 58.905 50.000 3.59 0.00 0.00 4.44
2260 7288 3.130693 CCTCTCCCCACTAGTAGAAAACG 59.869 52.174 3.59 0.00 0.00 3.60
2261 7289 3.451540 CCCTCTCCCCACTAGTAGAAAAC 59.548 52.174 3.59 0.00 0.00 2.43
2262 7290 3.721021 CCCTCTCCCCACTAGTAGAAAA 58.279 50.000 3.59 0.00 0.00 2.29
2263 7291 2.626149 GCCCTCTCCCCACTAGTAGAAA 60.626 54.545 3.59 0.00 0.00 2.52
2264 7292 1.063114 GCCCTCTCCCCACTAGTAGAA 60.063 57.143 3.59 0.00 0.00 2.10
2265 7293 0.556747 GCCCTCTCCCCACTAGTAGA 59.443 60.000 3.59 0.00 0.00 2.59
2266 7294 0.824182 CGCCCTCTCCCCACTAGTAG 60.824 65.000 0.00 0.00 0.00 2.57
2267 7295 1.229359 CGCCCTCTCCCCACTAGTA 59.771 63.158 0.00 0.00 0.00 1.82
2268 7296 2.042843 CGCCCTCTCCCCACTAGT 60.043 66.667 0.00 0.00 0.00 2.57
2269 7297 0.760945 ATTCGCCCTCTCCCCACTAG 60.761 60.000 0.00 0.00 0.00 2.57
2270 7298 0.559205 TATTCGCCCTCTCCCCACTA 59.441 55.000 0.00 0.00 0.00 2.74
2271 7299 0.760945 CTATTCGCCCTCTCCCCACT 60.761 60.000 0.00 0.00 0.00 4.00
2272 7300 0.759436 TCTATTCGCCCTCTCCCCAC 60.759 60.000 0.00 0.00 0.00 4.61
2273 7301 0.191064 ATCTATTCGCCCTCTCCCCA 59.809 55.000 0.00 0.00 0.00 4.96
2274 7302 1.353091 AATCTATTCGCCCTCTCCCC 58.647 55.000 0.00 0.00 0.00 4.81
2275 7303 3.142174 CAAAATCTATTCGCCCTCTCCC 58.858 50.000 0.00 0.00 0.00 4.30
2276 7304 3.142174 CCAAAATCTATTCGCCCTCTCC 58.858 50.000 0.00 0.00 0.00 3.71
2277 7305 3.142174 CCCAAAATCTATTCGCCCTCTC 58.858 50.000 0.00 0.00 0.00 3.20
2278 7306 2.777692 TCCCAAAATCTATTCGCCCTCT 59.222 45.455 0.00 0.00 0.00 3.69
2279 7307 3.208747 TCCCAAAATCTATTCGCCCTC 57.791 47.619 0.00 0.00 0.00 4.30
2280 7308 3.555966 CTTCCCAAAATCTATTCGCCCT 58.444 45.455 0.00 0.00 0.00 5.19
2281 7309 2.034685 GCTTCCCAAAATCTATTCGCCC 59.965 50.000 0.00 0.00 0.00 6.13
2282 7310 2.287009 CGCTTCCCAAAATCTATTCGCC 60.287 50.000 0.00 0.00 0.00 5.54
2283 7311 2.612212 TCGCTTCCCAAAATCTATTCGC 59.388 45.455 0.00 0.00 0.00 4.70
2284 7312 3.002348 GGTCGCTTCCCAAAATCTATTCG 59.998 47.826 0.00 0.00 0.00 3.34
2285 7313 3.002348 CGGTCGCTTCCCAAAATCTATTC 59.998 47.826 0.00 0.00 0.00 1.75
2286 7314 2.943033 CGGTCGCTTCCCAAAATCTATT 59.057 45.455 0.00 0.00 0.00 1.73
2287 7315 2.561569 CGGTCGCTTCCCAAAATCTAT 58.438 47.619 0.00 0.00 0.00 1.98
2288 7316 2.010043 GCGGTCGCTTCCCAAAATCTA 61.010 52.381 8.20 0.00 38.26 1.98
2289 7317 1.305930 GCGGTCGCTTCCCAAAATCT 61.306 55.000 8.20 0.00 38.26 2.40
2290 7318 1.136774 GCGGTCGCTTCCCAAAATC 59.863 57.895 8.20 0.00 38.26 2.17
2291 7319 3.274067 GCGGTCGCTTCCCAAAAT 58.726 55.556 8.20 0.00 38.26 1.82
2303 7331 4.632458 GATCGGAGGCGAGCGGTC 62.632 72.222 4.06 4.06 0.00 4.79
2306 7334 4.335584 GAGGATCGGAGGCGAGCG 62.336 72.222 0.00 0.00 0.00 5.03
2307 7335 1.601197 TAGAGGATCGGAGGCGAGC 60.601 63.158 0.00 0.00 42.67 5.03
2308 7336 1.570347 CGTAGAGGATCGGAGGCGAG 61.570 65.000 0.00 0.00 42.67 5.03
2309 7337 1.597302 CGTAGAGGATCGGAGGCGA 60.597 63.158 0.00 0.00 42.67 5.54
2310 7338 1.843734 GACGTAGAGGATCGGAGGCG 61.844 65.000 0.00 0.00 42.67 5.52
2311 7339 1.517210 GGACGTAGAGGATCGGAGGC 61.517 65.000 0.00 0.00 42.67 4.70
2312 7340 0.179026 TGGACGTAGAGGATCGGAGG 60.179 60.000 0.00 0.00 42.67 4.30
2313 7341 0.945813 GTGGACGTAGAGGATCGGAG 59.054 60.000 0.00 0.00 42.67 4.63
2314 7342 0.812811 CGTGGACGTAGAGGATCGGA 60.813 60.000 0.00 0.00 35.56 4.55
2315 7343 1.647629 CGTGGACGTAGAGGATCGG 59.352 63.158 0.00 0.00 35.56 4.18
2326 7354 1.791283 GACGAAGACGACGTGGACG 60.791 63.158 4.58 10.31 43.97 4.79
2327 7355 0.109873 ATGACGAAGACGACGTGGAC 60.110 55.000 4.58 0.00 43.97 4.02
2328 7356 0.167470 GATGACGAAGACGACGTGGA 59.833 55.000 4.58 0.00 43.97 4.02
2329 7357 0.109919 TGATGACGAAGACGACGTGG 60.110 55.000 4.58 0.00 43.97 4.94
2330 7358 0.975544 GTGATGACGAAGACGACGTG 59.024 55.000 4.58 0.00 43.97 4.49
2331 7359 0.109873 GGTGATGACGAAGACGACGT 60.110 55.000 0.00 0.00 46.58 4.34
2332 7360 0.109919 TGGTGATGACGAAGACGACG 60.110 55.000 0.00 0.00 42.66 5.12
2333 7361 2.186076 GATGGTGATGACGAAGACGAC 58.814 52.381 0.00 0.00 42.66 4.34
2334 7362 1.816224 TGATGGTGATGACGAAGACGA 59.184 47.619 0.00 0.00 42.66 4.20
2335 7363 2.278026 TGATGGTGATGACGAAGACG 57.722 50.000 0.00 0.00 45.75 4.18
2336 7364 3.525537 ACATGATGGTGATGACGAAGAC 58.474 45.455 0.00 0.00 0.00 3.01
2337 7365 3.430790 GGACATGATGGTGATGACGAAGA 60.431 47.826 0.00 0.00 0.00 2.87
2338 7366 2.868583 GGACATGATGGTGATGACGAAG 59.131 50.000 0.00 0.00 0.00 3.79
2339 7367 2.235898 TGGACATGATGGTGATGACGAA 59.764 45.455 0.00 0.00 0.00 3.85
2340 7368 1.830477 TGGACATGATGGTGATGACGA 59.170 47.619 0.00 0.00 0.00 4.20
2341 7369 1.935873 GTGGACATGATGGTGATGACG 59.064 52.381 0.00 0.00 0.00 4.35
2342 7370 2.292267 GGTGGACATGATGGTGATGAC 58.708 52.381 0.00 0.00 0.00 3.06
2343 7371 1.914798 TGGTGGACATGATGGTGATGA 59.085 47.619 0.00 0.00 0.00 2.92
2344 7372 2.423446 TGGTGGACATGATGGTGATG 57.577 50.000 0.00 0.00 0.00 3.07
2345 7373 2.726821 GTTGGTGGACATGATGGTGAT 58.273 47.619 0.00 0.00 0.00 3.06
2346 7374 1.610363 CGTTGGTGGACATGATGGTGA 60.610 52.381 0.00 0.00 0.00 4.02
2347 7375 0.804364 CGTTGGTGGACATGATGGTG 59.196 55.000 0.00 0.00 0.00 4.17
2348 7376 0.960364 GCGTTGGTGGACATGATGGT 60.960 55.000 0.00 0.00 0.00 3.55
2349 7377 0.677731 AGCGTTGGTGGACATGATGG 60.678 55.000 0.00 0.00 0.00 3.51
2350 7378 0.448990 CAGCGTTGGTGGACATGATG 59.551 55.000 0.00 0.00 0.00 3.07
2351 7379 0.324614 TCAGCGTTGGTGGACATGAT 59.675 50.000 0.00 0.00 0.00 2.45
2352 7380 0.107643 TTCAGCGTTGGTGGACATGA 59.892 50.000 0.00 0.00 0.00 3.07
2353 7381 0.238289 GTTCAGCGTTGGTGGACATG 59.762 55.000 0.00 0.00 39.15 3.21
2354 7382 1.227999 CGTTCAGCGTTGGTGGACAT 61.228 55.000 8.04 0.00 39.27 3.06
2355 7383 1.885388 CGTTCAGCGTTGGTGGACA 60.885 57.895 8.04 0.00 39.27 4.02
2356 7384 2.935955 CGTTCAGCGTTGGTGGAC 59.064 61.111 0.00 0.00 36.32 4.02
2376 7404 3.788766 CAACTTTCTCGGCGGCGG 61.789 66.667 31.73 21.26 0.00 6.13
2377 7405 2.227968 CTTCAACTTTCTCGGCGGCG 62.228 60.000 27.15 27.15 0.00 6.46
2378 7406 1.497722 CTTCAACTTTCTCGGCGGC 59.502 57.895 7.21 0.00 0.00 6.53
2379 7407 1.497722 GCTTCAACTTTCTCGGCGG 59.502 57.895 7.21 0.00 0.00 6.13
2380 7408 1.497722 GGCTTCAACTTTCTCGGCG 59.502 57.895 0.00 0.00 0.00 6.46
2381 7409 0.949105 TCGGCTTCAACTTTCTCGGC 60.949 55.000 0.00 0.00 0.00 5.54
2382 7410 0.790814 GTCGGCTTCAACTTTCTCGG 59.209 55.000 0.00 0.00 0.00 4.63
2383 7411 1.497991 TGTCGGCTTCAACTTTCTCG 58.502 50.000 0.00 0.00 0.00 4.04
2384 7412 3.131396 TCTTGTCGGCTTCAACTTTCTC 58.869 45.455 0.00 0.00 0.00 2.87
2385 7413 3.194005 TCTTGTCGGCTTCAACTTTCT 57.806 42.857 0.00 0.00 0.00 2.52
2386 7414 3.304057 CCTTCTTGTCGGCTTCAACTTTC 60.304 47.826 0.00 0.00 0.00 2.62
2387 7415 2.618709 CCTTCTTGTCGGCTTCAACTTT 59.381 45.455 0.00 0.00 0.00 2.66
2388 7416 2.222027 CCTTCTTGTCGGCTTCAACTT 58.778 47.619 0.00 0.00 0.00 2.66
2389 7417 1.884235 CCTTCTTGTCGGCTTCAACT 58.116 50.000 0.00 0.00 0.00 3.16
2390 7418 0.238553 GCCTTCTTGTCGGCTTCAAC 59.761 55.000 0.00 0.00 42.98 3.18
2391 7419 0.889186 GGCCTTCTTGTCGGCTTCAA 60.889 55.000 0.00 0.00 45.57 2.69
2392 7420 1.302511 GGCCTTCTTGTCGGCTTCA 60.303 57.895 0.00 0.00 45.57 3.02
2393 7421 3.579685 GGCCTTCTTGTCGGCTTC 58.420 61.111 0.00 0.00 45.57 3.86


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

AutoCloner maintained by Alex Coulton.