Multiple sequence alignment - TraesCS4A01G140900

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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 TraesCS4A01G140900 chr4A 100.000 2363 0 0 1 2363 218050778 218053140 0.000000e+00 4364
1 TraesCS4A01G140900 chr4A 95.664 2260 77 10 1 2243 602465167 602462912 0.000000e+00 3611
2 TraesCS4A01G140900 chr5A 95.706 2259 79 4 1 2243 692979192 692981448 0.000000e+00 3618
3 TraesCS4A01G140900 chr5A 95.502 2001 71 4 261 2243 693957649 693959648 0.000000e+00 3179
4 TraesCS4A01G140900 chr5A 94.167 120 7 0 2244 2363 303149254 303149135 1.440000e-42 183
5 TraesCS4A01G140900 chr5A 91.045 134 9 3 2231 2363 415886471 415886340 6.710000e-41 178
6 TraesCS4A01G140900 chr6B 95.579 2262 81 5 1 2244 617028554 617030814 0.000000e+00 3605
7 TraesCS4A01G140900 chr6B 94.523 2264 86 8 1 2247 399208530 399206288 0.000000e+00 3459
8 TraesCS4A01G140900 chr2B 95.362 2264 83 8 1 2244 435353333 435351072 0.000000e+00 3579
9 TraesCS4A01G140900 chr5B 94.790 2265 94 8 1 2243 576501418 576503680 0.000000e+00 3507
10 TraesCS4A01G140900 chr1B 94.292 2260 91 12 2 2243 651732030 651729791 0.000000e+00 3424
11 TraesCS4A01G140900 chr1B 95.163 2026 75 8 1 2006 17134731 17136753 0.000000e+00 3177
12 TraesCS4A01G140900 chr1B 94.515 1896 83 11 371 2248 41212305 41214197 0.000000e+00 2905
13 TraesCS4A01G140900 chr1B 94.360 1897 85 7 371 2248 41174293 41176186 0.000000e+00 2891
14 TraesCS4A01G140900 chr1B 95.041 121 5 1 2244 2363 599389030 599388910 3.100000e-44 189
15 TraesCS4A01G140900 chr1B 92.969 128 7 2 2238 2363 628479366 628479239 4.010000e-43 185
16 TraesCS4A01G140900 chr1B 94.167 120 6 1 2244 2363 446919472 446919354 5.190000e-42 182
17 TraesCS4A01G140900 chr7B 95.392 2040 75 5 223 2244 709654254 709656292 0.000000e+00 3229
18 TraesCS4A01G140900 chr3A 89.909 2319 125 29 1 2244 224968248 224970532 0.000000e+00 2885
19 TraesCS4A01G140900 chr3A 93.600 125 7 1 2239 2363 123146791 123146914 4.010000e-43 185
20 TraesCS4A01G140900 chr6A 94.167 120 7 0 2244 2363 123152774 123152655 1.440000e-42 183
21 TraesCS4A01G140900 chr5D 94.167 120 7 0 2244 2363 338459000 338458881 1.440000e-42 183
22 TraesCS4A01G140900 chr4D 94.167 120 7 0 2244 2363 124866358 124866239 1.440000e-42 183


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 TraesCS4A01G140900 chr4A 218050778 218053140 2362 False 4364 4364 100.000 1 2363 1 chr4A.!!$F1 2362
1 TraesCS4A01G140900 chr4A 602462912 602465167 2255 True 3611 3611 95.664 1 2243 1 chr4A.!!$R1 2242
2 TraesCS4A01G140900 chr5A 692979192 692981448 2256 False 3618 3618 95.706 1 2243 1 chr5A.!!$F1 2242
3 TraesCS4A01G140900 chr5A 693957649 693959648 1999 False 3179 3179 95.502 261 2243 1 chr5A.!!$F2 1982
4 TraesCS4A01G140900 chr6B 617028554 617030814 2260 False 3605 3605 95.579 1 2244 1 chr6B.!!$F1 2243
5 TraesCS4A01G140900 chr6B 399206288 399208530 2242 True 3459 3459 94.523 1 2247 1 chr6B.!!$R1 2246
6 TraesCS4A01G140900 chr2B 435351072 435353333 2261 True 3579 3579 95.362 1 2244 1 chr2B.!!$R1 2243
7 TraesCS4A01G140900 chr5B 576501418 576503680 2262 False 3507 3507 94.790 1 2243 1 chr5B.!!$F1 2242
8 TraesCS4A01G140900 chr1B 651729791 651732030 2239 True 3424 3424 94.292 2 2243 1 chr1B.!!$R4 2241
9 TraesCS4A01G140900 chr1B 17134731 17136753 2022 False 3177 3177 95.163 1 2006 1 chr1B.!!$F1 2005
10 TraesCS4A01G140900 chr1B 41212305 41214197 1892 False 2905 2905 94.515 371 2248 1 chr1B.!!$F3 1877
11 TraesCS4A01G140900 chr1B 41174293 41176186 1893 False 2891 2891 94.360 371 2248 1 chr1B.!!$F2 1877
12 TraesCS4A01G140900 chr7B 709654254 709656292 2038 False 3229 3229 95.392 223 2244 1 chr7B.!!$F1 2021
13 TraesCS4A01G140900 chr3A 224968248 224970532 2284 False 2885 2885 89.909 1 2244 1 chr3A.!!$F2 2243

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
435 438 1.905894 TGTTGCAGTCCAGCAGGTATA 59.094 47.619 0.0 0.0 46.54 1.47 F
1090 1116 1.293062 ATGTCCCTCCAGCACATTCT 58.707 50.000 0.0 0.0 0.00 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1265 1292 0.458543 CTGATACTCTGCCACGCGTT 60.459 55.0 10.22 0.0 0.0 4.84 R
2085 2171 0.801836 GAATTTTGGTCATGGCCGCG 60.802 55.0 12.67 0.0 0.0 6.46 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
93 96 4.602340 TTTCAGAAAGAGGCTCGTAAGT 57.398 40.909 9.22 0.00 39.48 2.24
195 198 9.790344 AGAAGGCGATAGTAAGTTTCTAGTATA 57.210 33.333 0.00 0.00 39.35 1.47
435 438 1.905894 TGTTGCAGTCCAGCAGGTATA 59.094 47.619 0.00 0.00 46.54 1.47
442 446 2.840651 AGTCCAGCAGGTATAGCTTGTT 59.159 45.455 0.55 0.00 41.14 2.83
453 457 5.247564 AGGTATAGCTTGTTGTTGGACACTA 59.752 40.000 0.00 0.00 0.00 2.74
526 530 4.019860 GCCTGAAGCATCTATCTTCCCATA 60.020 45.833 0.00 0.00 42.97 2.74
608 614 5.982356 TGTGGAAGTGGATTTCTCTGATAG 58.018 41.667 0.00 0.00 0.00 2.08
751 757 6.183360 ACAATGGTTTGTTGTGTATGCTTACA 60.183 34.615 8.29 8.29 43.57 2.41
836 844 8.063770 AGTGATTCCCAAGGATGATTAATTCTT 58.936 33.333 0.00 0.00 34.03 2.52
995 1006 6.265196 TGTGCATCTTTCTTTAAATGTCAGGT 59.735 34.615 0.00 0.00 0.00 4.00
1090 1116 1.293062 ATGTCCCTCCAGCACATTCT 58.707 50.000 0.00 0.00 0.00 2.40
1265 1292 2.509166 TTAGAGGAGACCGAAGCTGA 57.491 50.000 0.00 0.00 0.00 4.26
1272 1299 3.000080 GACCGAAGCTGAACGCGTG 62.000 63.158 14.98 0.24 45.59 5.34
1310 1337 1.202976 ACTGCAAAGAGTTGAGGCCAT 60.203 47.619 5.01 0.00 36.83 4.40
1332 1380 1.594862 GATGCTAGATTTGCGCGTCTT 59.405 47.619 8.43 0.00 36.89 3.01
1346 1394 2.794981 CGCGTCTTATGGATCTGTTCGT 60.795 50.000 0.00 0.00 0.00 3.85
1620 1669 4.589908 ACTGTTGGGCCTAAGTTAATGAG 58.410 43.478 0.00 0.00 0.00 2.90
1641 1712 6.359804 TGAGATCTTGGAGAATTGTATTGGG 58.640 40.000 0.00 0.00 0.00 4.12
1642 1713 5.699143 AGATCTTGGAGAATTGTATTGGGG 58.301 41.667 0.00 0.00 0.00 4.96
1804 1890 1.203313 TGGTTAGAGAGAAGGGCTGGT 60.203 52.381 0.00 0.00 0.00 4.00
1870 1956 6.025749 AGCCCAAGAACTAACATTAAAAGC 57.974 37.500 0.00 0.00 0.00 3.51
1899 1985 6.205658 TGGCCCAAAAGTAAATGTAAAAATGC 59.794 34.615 0.00 0.00 0.00 3.56
1946 2032 7.382218 CCATTAAAACAACTGATTTGGACTGAC 59.618 37.037 0.00 0.00 39.84 3.51
1988 2074 2.629210 TTTTTCCACGTCAGCGCG 59.371 55.556 0.00 0.00 42.83 6.86
2085 2171 7.917720 TTAACTACGAAAATTTTGGTCAAGC 57.082 32.000 20.06 0.00 31.50 4.01
2131 2217 6.540914 AGAAAAGGTCACGTTTGTTCATTCTA 59.459 34.615 0.00 0.00 0.00 2.10
2224 2311 5.127031 CGACCAAAATGGGGAGTCATAATTT 59.873 40.000 0.87 0.00 43.37 1.82
2248 2335 4.817464 ACCGTATTTCTTGTAGTGTTTGCA 59.183 37.500 0.00 0.00 0.00 4.08
2249 2336 5.297278 ACCGTATTTCTTGTAGTGTTTGCAA 59.703 36.000 0.00 0.00 0.00 4.08
2250 2337 6.183360 ACCGTATTTCTTGTAGTGTTTGCAAA 60.183 34.615 8.05 8.05 30.72 3.68
2251 2338 6.861055 CCGTATTTCTTGTAGTGTTTGCAAAT 59.139 34.615 16.21 1.69 30.72 2.32
2252 2339 7.381139 CCGTATTTCTTGTAGTGTTTGCAAATT 59.619 33.333 16.21 7.06 30.72 1.82
2253 2340 8.751335 CGTATTTCTTGTAGTGTTTGCAAATTT 58.249 29.630 16.21 6.71 30.72 1.82
2255 2342 8.947055 ATTTCTTGTAGTGTTTGCAAATTTCT 57.053 26.923 16.21 15.19 30.72 2.52
2258 2345 9.462174 TTCTTGTAGTGTTTGCAAATTTCTATG 57.538 29.630 16.21 11.52 30.72 2.23
2259 2346 8.629158 TCTTGTAGTGTTTGCAAATTTCTATGT 58.371 29.630 16.21 0.00 30.72 2.29
2260 2347 8.795786 TTGTAGTGTTTGCAAATTTCTATGTC 57.204 30.769 16.21 0.00 0.00 3.06
2261 2348 8.165239 TGTAGTGTTTGCAAATTTCTATGTCT 57.835 30.769 16.21 6.27 0.00 3.41
2262 2349 9.278978 TGTAGTGTTTGCAAATTTCTATGTCTA 57.721 29.630 16.21 5.44 0.00 2.59
2263 2350 9.543018 GTAGTGTTTGCAAATTTCTATGTCTAC 57.457 33.333 16.21 12.29 0.00 2.59
2264 2351 8.165239 AGTGTTTGCAAATTTCTATGTCTACA 57.835 30.769 16.21 1.16 0.00 2.74
2265 2352 8.629158 AGTGTTTGCAAATTTCTATGTCTACAA 58.371 29.630 16.21 0.00 0.00 2.41
2266 2353 9.410556 GTGTTTGCAAATTTCTATGTCTACAAT 57.589 29.630 16.21 0.00 0.00 2.71
2267 2354 9.409312 TGTTTGCAAATTTCTATGTCTACAATG 57.591 29.630 16.21 0.00 0.00 2.82
2268 2355 8.375465 GTTTGCAAATTTCTATGTCTACAATGC 58.625 33.333 16.21 0.00 0.00 3.56
2269 2356 7.395190 TGCAAATTTCTATGTCTACAATGCT 57.605 32.000 0.00 0.00 0.00 3.79
2270 2357 7.475015 TGCAAATTTCTATGTCTACAATGCTC 58.525 34.615 0.00 0.00 0.00 4.26
2271 2358 7.121020 TGCAAATTTCTATGTCTACAATGCTCA 59.879 33.333 0.00 0.00 0.00 4.26
2272 2359 7.970061 GCAAATTTCTATGTCTACAATGCTCAA 59.030 33.333 0.00 0.00 0.00 3.02
2273 2360 9.282247 CAAATTTCTATGTCTACAATGCTCAAC 57.718 33.333 0.00 0.00 0.00 3.18
2274 2361 8.565896 AATTTCTATGTCTACAATGCTCAACA 57.434 30.769 0.00 0.00 0.00 3.33
2275 2362 8.743085 ATTTCTATGTCTACAATGCTCAACAT 57.257 30.769 0.00 0.00 42.30 2.71
2276 2363 7.543947 TTCTATGTCTACAATGCTCAACATG 57.456 36.000 0.00 0.00 39.60 3.21
2277 2364 6.051074 TCTATGTCTACAATGCTCAACATGG 58.949 40.000 0.00 0.00 39.60 3.66
2278 2365 4.284829 TGTCTACAATGCTCAACATGGA 57.715 40.909 0.00 0.00 39.60 3.41
2279 2366 4.256110 TGTCTACAATGCTCAACATGGAG 58.744 43.478 0.00 0.00 39.60 3.86
2307 2394 2.128771 GCTAATTGCTCCCACCTTCA 57.871 50.000 0.00 0.00 38.95 3.02
2308 2395 2.446435 GCTAATTGCTCCCACCTTCAA 58.554 47.619 0.00 0.00 38.95 2.69
2309 2396 3.026694 GCTAATTGCTCCCACCTTCAAT 58.973 45.455 0.00 0.00 38.95 2.57
2310 2397 4.207165 GCTAATTGCTCCCACCTTCAATA 58.793 43.478 0.00 0.00 38.95 1.90
2311 2398 4.829492 GCTAATTGCTCCCACCTTCAATAT 59.171 41.667 0.00 0.00 38.95 1.28
2312 2399 5.278660 GCTAATTGCTCCCACCTTCAATATG 60.279 44.000 0.00 0.00 38.95 1.78
2313 2400 3.737559 TTGCTCCCACCTTCAATATGT 57.262 42.857 0.00 0.00 0.00 2.29
2314 2401 4.853468 TTGCTCCCACCTTCAATATGTA 57.147 40.909 0.00 0.00 0.00 2.29
2315 2402 5.387113 TTGCTCCCACCTTCAATATGTAT 57.613 39.130 0.00 0.00 0.00 2.29
2316 2403 4.973168 TGCTCCCACCTTCAATATGTATC 58.027 43.478 0.00 0.00 0.00 2.24
2317 2404 4.202461 TGCTCCCACCTTCAATATGTATCC 60.202 45.833 0.00 0.00 0.00 2.59
2318 2405 4.202461 GCTCCCACCTTCAATATGTATCCA 60.202 45.833 0.00 0.00 0.00 3.41
2319 2406 5.555017 CTCCCACCTTCAATATGTATCCAG 58.445 45.833 0.00 0.00 0.00 3.86
2320 2407 5.223655 TCCCACCTTCAATATGTATCCAGA 58.776 41.667 0.00 0.00 0.00 3.86
2321 2408 5.851693 TCCCACCTTCAATATGTATCCAGAT 59.148 40.000 0.00 0.00 0.00 2.90
2322 2409 6.332635 TCCCACCTTCAATATGTATCCAGATT 59.667 38.462 0.00 0.00 32.85 2.40
2323 2410 6.432162 CCCACCTTCAATATGTATCCAGATTG 59.568 42.308 0.00 0.00 46.71 2.67
2332 2419 8.718158 AATATGTATCCAGATTGAGACTCTGA 57.282 34.615 3.68 0.00 42.22 3.27
2333 2420 6.653526 ATGTATCCAGATTGAGACTCTGAG 57.346 41.667 2.45 2.45 42.22 3.35
2334 2421 5.514169 TGTATCCAGATTGAGACTCTGAGT 58.486 41.667 10.66 10.66 42.22 3.41
2335 2422 5.592282 TGTATCCAGATTGAGACTCTGAGTC 59.408 44.000 26.43 26.43 45.38 3.36
2346 2433 4.057406 GACTCTGAGTCATCTGGATTGG 57.943 50.000 28.18 0.00 44.45 3.16
2347 2434 3.448934 ACTCTGAGTCATCTGGATTGGT 58.551 45.455 4.06 0.00 0.00 3.67
2348 2435 3.197333 ACTCTGAGTCATCTGGATTGGTG 59.803 47.826 4.06 0.00 0.00 4.17
2349 2436 3.176411 TCTGAGTCATCTGGATTGGTGT 58.824 45.455 0.00 0.00 0.00 4.16
2350 2437 4.352893 TCTGAGTCATCTGGATTGGTGTA 58.647 43.478 0.00 0.00 0.00 2.90
2351 2438 4.777366 TCTGAGTCATCTGGATTGGTGTAA 59.223 41.667 0.00 0.00 0.00 2.41
2352 2439 5.248248 TCTGAGTCATCTGGATTGGTGTAAA 59.752 40.000 0.00 0.00 0.00 2.01
2353 2440 5.875224 TGAGTCATCTGGATTGGTGTAAAA 58.125 37.500 0.00 0.00 0.00 1.52
2354 2441 5.939883 TGAGTCATCTGGATTGGTGTAAAAG 59.060 40.000 0.00 0.00 0.00 2.27
2355 2442 4.702131 AGTCATCTGGATTGGTGTAAAAGC 59.298 41.667 0.00 0.00 0.00 3.51
2356 2443 4.016444 TCATCTGGATTGGTGTAAAAGCC 58.984 43.478 0.00 0.00 33.59 4.35
2357 2444 3.806949 TCTGGATTGGTGTAAAAGCCT 57.193 42.857 0.00 0.00 34.13 4.58
2358 2445 3.420893 TCTGGATTGGTGTAAAAGCCTG 58.579 45.455 0.00 0.00 34.13 4.85
2359 2446 1.892474 TGGATTGGTGTAAAAGCCTGC 59.108 47.619 0.00 0.00 34.13 4.85
2360 2447 1.892474 GGATTGGTGTAAAAGCCTGCA 59.108 47.619 0.00 0.00 30.26 4.41
2361 2448 2.497273 GGATTGGTGTAAAAGCCTGCAT 59.503 45.455 0.00 0.00 30.26 3.96
2362 2449 3.429410 GGATTGGTGTAAAAGCCTGCATC 60.429 47.826 0.00 0.00 30.26 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 96 4.198530 TCAAATGCAGTCAACTCTTCACA 58.801 39.130 0.00 0.00 0.00 3.58
195 198 7.054491 ACAAGCCTCATAAACATGAAAAAGT 57.946 32.000 0.00 0.00 0.00 2.66
435 438 7.524717 AATTAATAGTGTCCAACAACAAGCT 57.475 32.000 0.00 0.00 0.00 3.74
453 457 7.928706 AGCATACAACGCTCTCTCTTAATTAAT 59.071 33.333 0.00 0.00 33.35 1.40
526 530 5.053978 ACAGAGTTTCTCCACTCCAAAAT 57.946 39.130 0.00 0.00 43.89 1.82
751 757 5.626578 GCATGGCACCAGGTTTATTAAACAT 60.627 40.000 18.41 10.54 43.15 2.71
836 844 5.021033 TGAAAATTTTGAAGCAGGCAAGA 57.979 34.783 8.47 0.00 0.00 3.02
995 1006 5.538053 TGTTCCATAGCTTTTTCCATGTCAA 59.462 36.000 0.00 0.00 0.00 3.18
1040 1066 2.689471 AGAATGTCAGCAACAACAGCAA 59.311 40.909 0.00 0.00 42.37 3.91
1090 1116 4.692228 GACTCAAGGCCAACATTTTGAAA 58.308 39.130 5.01 0.00 34.24 2.69
1247 1274 2.093106 GTTCAGCTTCGGTCTCCTCTA 58.907 52.381 0.00 0.00 0.00 2.43
1265 1292 0.458543 CTGATACTCTGCCACGCGTT 60.459 55.000 10.22 0.00 0.00 4.84
1272 1299 3.619038 GCAGTAACAACTGATACTCTGCC 59.381 47.826 9.63 0.00 40.39 4.85
1310 1337 0.527600 ACGCGCAAATCTAGCATCGA 60.528 50.000 5.73 0.00 33.69 3.59
1332 1380 9.139734 ACTATTTTACCTACGAACAGATCCATA 57.860 33.333 0.00 0.00 0.00 2.74
1346 1394 6.972328 CACGCCGTACTAAACTATTTTACCTA 59.028 38.462 0.00 0.00 0.00 3.08
1620 1669 4.829492 CCCCCAATACAATTCTCCAAGATC 59.171 45.833 0.00 0.00 0.00 2.75
1641 1712 1.391157 TTGCACAGTTTGGCAGTCCC 61.391 55.000 0.00 0.00 41.68 4.46
1642 1713 0.675633 ATTGCACAGTTTGGCAGTCC 59.324 50.000 0.00 0.00 41.68 3.85
1870 1956 1.067213 CATTTACTTTTGGGCCACGGG 60.067 52.381 5.23 0.83 0.00 5.28
1899 1985 2.030805 GGCTGAGCCCAATAATTTAGCG 60.031 50.000 13.77 0.00 44.06 4.26
2066 2152 3.301706 GCGCTTGACCAAAATTTTCGTA 58.698 40.909 0.00 0.00 0.00 3.43
2085 2171 0.801836 GAATTTTGGTCATGGCCGCG 60.802 55.000 12.67 0.00 0.00 6.46
2224 2311 5.990386 TGCAAACACTACAAGAAATACGGTA 59.010 36.000 0.00 0.00 0.00 4.02
2248 2335 9.013229 TGTTGAGCATTGTAGACATAGAAATTT 57.987 29.630 0.00 0.00 0.00 1.82
2249 2336 8.565896 TGTTGAGCATTGTAGACATAGAAATT 57.434 30.769 0.00 0.00 0.00 1.82
2250 2337 8.618677 CATGTTGAGCATTGTAGACATAGAAAT 58.381 33.333 0.00 0.00 35.19 2.17
2251 2338 7.066163 CCATGTTGAGCATTGTAGACATAGAAA 59.934 37.037 0.00 0.00 35.19 2.52
2252 2339 6.539826 CCATGTTGAGCATTGTAGACATAGAA 59.460 38.462 0.00 0.00 35.19 2.10
2253 2340 6.051074 CCATGTTGAGCATTGTAGACATAGA 58.949 40.000 0.00 0.00 35.19 1.98
2254 2341 6.051074 TCCATGTTGAGCATTGTAGACATAG 58.949 40.000 0.00 0.00 35.19 2.23
2255 2342 5.988287 TCCATGTTGAGCATTGTAGACATA 58.012 37.500 0.00 0.00 35.19 2.29
2256 2343 4.847198 TCCATGTTGAGCATTGTAGACAT 58.153 39.130 0.00 0.00 35.19 3.06
2257 2344 4.256110 CTCCATGTTGAGCATTGTAGACA 58.744 43.478 0.00 0.00 35.19 3.41
2258 2345 4.871993 CTCCATGTTGAGCATTGTAGAC 57.128 45.455 0.00 0.00 35.19 2.59
2288 2375 2.128771 TGAAGGTGGGAGCAATTAGC 57.871 50.000 0.00 0.00 46.19 3.09
2289 2376 5.829924 ACATATTGAAGGTGGGAGCAATTAG 59.170 40.000 0.00 0.00 33.45 1.73
2290 2377 5.765510 ACATATTGAAGGTGGGAGCAATTA 58.234 37.500 0.00 0.00 33.45 1.40
2291 2378 4.613437 ACATATTGAAGGTGGGAGCAATT 58.387 39.130 0.00 0.00 33.45 2.32
2292 2379 4.255510 ACATATTGAAGGTGGGAGCAAT 57.744 40.909 0.00 0.00 35.38 3.56
2293 2380 3.737559 ACATATTGAAGGTGGGAGCAA 57.262 42.857 0.00 0.00 0.00 3.91
2294 2381 4.202461 GGATACATATTGAAGGTGGGAGCA 60.202 45.833 0.00 0.00 0.00 4.26
2295 2382 4.202461 TGGATACATATTGAAGGTGGGAGC 60.202 45.833 0.00 0.00 46.17 4.70
2296 2383 5.567037 TGGATACATATTGAAGGTGGGAG 57.433 43.478 0.00 0.00 46.17 4.30
2309 2396 7.446931 GACTCAGAGTCTCAATCTGGATACATA 59.553 40.741 21.67 0.00 43.93 2.29
2310 2397 6.265196 GACTCAGAGTCTCAATCTGGATACAT 59.735 42.308 21.67 0.00 43.93 2.29
2311 2398 5.592282 GACTCAGAGTCTCAATCTGGATACA 59.408 44.000 21.67 0.00 43.21 2.29
2312 2399 5.592282 TGACTCAGAGTCTCAATCTGGATAC 59.408 44.000 27.42 1.21 45.27 2.24
2313 2400 5.760131 TGACTCAGAGTCTCAATCTGGATA 58.240 41.667 27.42 3.74 45.27 2.59
2314 2401 4.608269 TGACTCAGAGTCTCAATCTGGAT 58.392 43.478 27.42 0.00 45.27 3.41
2315 2402 4.039603 TGACTCAGAGTCTCAATCTGGA 57.960 45.455 27.42 4.92 45.27 3.86
2316 2403 4.646040 AGATGACTCAGAGTCTCAATCTGG 59.354 45.833 27.42 0.00 45.27 3.86
2317 2404 5.450826 CCAGATGACTCAGAGTCTCAATCTG 60.451 48.000 31.04 31.04 44.46 2.90
2318 2405 4.646040 CCAGATGACTCAGAGTCTCAATCT 59.354 45.833 27.42 23.04 45.27 2.40
2319 2406 4.644234 TCCAGATGACTCAGAGTCTCAATC 59.356 45.833 27.42 21.50 45.27 2.67
2320 2407 4.608269 TCCAGATGACTCAGAGTCTCAAT 58.392 43.478 27.42 15.24 45.27 2.57
2321 2408 4.039603 TCCAGATGACTCAGAGTCTCAA 57.960 45.455 27.42 11.26 45.27 3.02
2322 2409 3.728385 TCCAGATGACTCAGAGTCTCA 57.272 47.619 27.42 12.54 45.27 3.27
2323 2410 4.202141 CCAATCCAGATGACTCAGAGTCTC 60.202 50.000 27.42 21.30 45.27 3.36
2324 2411 3.705579 CCAATCCAGATGACTCAGAGTCT 59.294 47.826 27.42 15.22 45.27 3.24
2325 2412 3.450457 ACCAATCCAGATGACTCAGAGTC 59.550 47.826 22.09 22.09 45.26 3.36
2326 2413 3.197333 CACCAATCCAGATGACTCAGAGT 59.803 47.826 1.46 1.46 0.00 3.24
2327 2414 3.197333 ACACCAATCCAGATGACTCAGAG 59.803 47.826 0.00 0.00 0.00 3.35
2328 2415 3.176411 ACACCAATCCAGATGACTCAGA 58.824 45.455 0.00 0.00 0.00 3.27
2329 2416 3.623906 ACACCAATCCAGATGACTCAG 57.376 47.619 0.00 0.00 0.00 3.35
2330 2417 5.497464 TTTACACCAATCCAGATGACTCA 57.503 39.130 0.00 0.00 0.00 3.41
2331 2418 5.163713 GCTTTTACACCAATCCAGATGACTC 60.164 44.000 0.00 0.00 0.00 3.36
2332 2419 4.702131 GCTTTTACACCAATCCAGATGACT 59.298 41.667 0.00 0.00 0.00 3.41
2333 2420 4.142381 GGCTTTTACACCAATCCAGATGAC 60.142 45.833 0.00 0.00 0.00 3.06
2334 2421 4.016444 GGCTTTTACACCAATCCAGATGA 58.984 43.478 0.00 0.00 0.00 2.92
2335 2422 4.019174 AGGCTTTTACACCAATCCAGATG 58.981 43.478 0.00 0.00 0.00 2.90
2336 2423 4.019174 CAGGCTTTTACACCAATCCAGAT 58.981 43.478 0.00 0.00 0.00 2.90
2337 2424 3.420893 CAGGCTTTTACACCAATCCAGA 58.579 45.455 0.00 0.00 0.00 3.86
2338 2425 2.094545 GCAGGCTTTTACACCAATCCAG 60.095 50.000 0.00 0.00 0.00 3.86
2339 2426 1.892474 GCAGGCTTTTACACCAATCCA 59.108 47.619 0.00 0.00 0.00 3.41
2340 2427 1.892474 TGCAGGCTTTTACACCAATCC 59.108 47.619 0.00 0.00 0.00 3.01
2341 2428 3.774066 GATGCAGGCTTTTACACCAATC 58.226 45.455 0.00 0.00 0.00 2.67
2342 2429 3.874392 GATGCAGGCTTTTACACCAAT 57.126 42.857 0.00 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.