Multiple sequence alignment - TraesCS2A01G438300

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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 TraesCS2A01G438300 chr2A 100.000 2990 0 0 1 2990 689711548 689708559 0.000000e+00 5522.0
1 TraesCS2A01G438300 chr2A 97.226 2091 50 4 903 2990 690409571 690411656 0.000000e+00 3533.0
2 TraesCS2A01G438300 chr2A 89.580 1142 90 22 986 2112 689631514 689630387 0.000000e+00 1423.0
3 TraesCS2A01G438300 chr2A 87.353 340 22 13 587 912 690408929 690409261 1.310000e-98 370.0
4 TraesCS2A01G438300 chr2A 84.800 250 33 5 997 1242 690534370 690534618 2.300000e-61 246.0
5 TraesCS2A01G438300 chr2A 75.278 360 58 23 2643 2990 699100053 699100393 3.110000e-30 143.0
6 TraesCS2A01G438300 chr2A 76.577 222 37 13 2393 2609 699099869 699100080 1.130000e-19 108.0
7 TraesCS2A01G438300 chr2A 90.164 61 3 2 137 197 689632008 689631951 3.200000e-10 76.8
8 TraesCS2A01G438300 chr2D 91.803 2330 118 33 653 2946 546871805 546874097 0.000000e+00 3177.0
9 TraesCS2A01G438300 chr2D 88.361 1263 111 23 956 2205 546931921 546933160 0.000000e+00 1485.0
10 TraesCS2A01G438300 chr2D 88.817 778 87 0 1154 1931 555133404 555134181 0.000000e+00 955.0
11 TraesCS2A01G438300 chr2D 86.792 477 63 0 1455 1931 547251527 547252003 1.580000e-147 532.0
12 TraesCS2A01G438300 chr2D 81.111 360 63 4 2618 2976 109733038 109733393 1.750000e-72 283.0
13 TraesCS2A01G438300 chr2D 88.793 232 14 5 2 228 546870895 546871119 1.060000e-69 274.0
14 TraesCS2A01G438300 chr2D 81.421 183 14 14 389 554 546871171 546871350 6.730000e-27 132.0
15 TraesCS2A01G438300 chr2D 97.872 47 1 0 253 299 546871121 546871167 6.870000e-12 82.4
16 TraesCS2A01G438300 chr2B 93.010 1445 60 19 656 2083 653610341 653611761 0.000000e+00 2071.0
17 TraesCS2A01G438300 chr2B 87.311 1458 104 51 767 2186 653619070 653620484 0.000000e+00 1592.0
18 TraesCS2A01G438300 chr2B 91.983 237 9 4 1 228 653609742 653609977 1.030000e-84 324.0
19 TraesCS2A01G438300 chr2B 83.000 300 37 9 2242 2530 653612204 653612500 2.960000e-65 259.0
20 TraesCS2A01G438300 chr2B 95.294 85 4 0 303 387 281272244 281272328 5.200000e-28 135.0
21 TraesCS2A01G438300 chr2B 92.308 91 7 0 303 393 55859712 55859802 2.420000e-26 130.0
22 TraesCS2A01G438300 chr2B 77.381 252 27 19 389 619 653610028 653610270 4.050000e-24 122.0
23 TraesCS2A01G438300 chr2B 97.959 49 1 0 253 301 653609979 653610027 5.310000e-13 86.1
24 TraesCS2A01G438300 chr2B 90.625 64 5 1 2124 2186 653611768 653611831 1.910000e-12 84.2
25 TraesCS2A01G438300 chr4A 90.046 1296 91 15 806 2100 33079185 33080443 0.000000e+00 1644.0
26 TraesCS2A01G438300 chr4A 91.327 196 12 4 574 766 33075810 33076003 2.290000e-66 263.0
27 TraesCS2A01G438300 chr4A 79.524 210 36 4 2407 2615 136428945 136428742 3.110000e-30 143.0
28 TraesCS2A01G438300 chr5A 79.558 362 60 10 2619 2976 709197989 709197638 2.300000e-61 246.0
29 TraesCS2A01G438300 chr5A 100.000 28 0 0 225 252 9839301 9839274 5.000000e-03 52.8
30 TraesCS2A01G438300 chr5A 100.000 28 0 0 225 252 414416095 414416122 5.000000e-03 52.8
31 TraesCS2A01G438300 chr5A 96.774 31 1 0 221 251 491937484 491937514 5.000000e-03 52.8
32 TraesCS2A01G438300 chr5A 100.000 28 0 0 225 252 546684265 546684238 5.000000e-03 52.8
33 TraesCS2A01G438300 chr4D 77.259 343 63 9 2640 2979 434103129 434103459 1.420000e-43 187.0
34 TraesCS2A01G438300 chr4D 91.489 94 6 2 299 391 337933198 337933290 8.700000e-26 128.0
35 TraesCS2A01G438300 chr4D 100.000 29 0 0 223 251 34660037 34660009 1.000000e-03 54.7
36 TraesCS2A01G438300 chr6B 81.283 187 29 5 2760 2941 699871821 699872006 2.400000e-31 147.0
37 TraesCS2A01G438300 chr6B 80.749 187 30 5 2760 2941 699832274 699832459 1.120000e-29 141.0
38 TraesCS2A01G438300 chr6B 80.851 188 29 6 2760 2941 699922436 699922622 1.120000e-29 141.0
39 TraesCS2A01G438300 chr6B 100.000 34 0 0 218 251 648804707 648804674 2.490000e-06 63.9
40 TraesCS2A01G438300 chr6B 100.000 29 0 0 224 252 31586277 31586305 1.000000e-03 54.7
41 TraesCS2A01G438300 chr6D 92.079 101 7 1 295 395 268067205 268067106 1.120000e-29 141.0
42 TraesCS2A01G438300 chr6D 85.714 70 10 0 2918 2987 133288634 133288703 1.150000e-09 75.0
43 TraesCS2A01G438300 chr4B 79.070 215 37 5 2407 2619 415511155 415511363 1.120000e-29 141.0
44 TraesCS2A01G438300 chr7B 92.632 95 6 1 303 396 66196621 66196715 5.200000e-28 135.0
45 TraesCS2A01G438300 chr7D 91.753 97 7 1 299 394 626199973 626199877 1.870000e-27 134.0
46 TraesCS2A01G438300 chr7D 83.721 129 20 1 2393 2521 265268430 265268557 1.460000e-23 121.0
47 TraesCS2A01G438300 chr7D 77.473 182 34 5 2407 2587 457419067 457419242 5.270000e-18 102.0
48 TraesCS2A01G438300 chr3B 94.186 86 5 0 302 387 642815847 642815932 6.730000e-27 132.0
49 TraesCS2A01G438300 chr3D 94.118 85 5 0 303 387 11418775 11418691 2.420000e-26 130.0
50 TraesCS2A01G438300 chr3D 80.380 158 26 5 2393 2548 347290860 347291014 6.770000e-22 115.0
51 TraesCS2A01G438300 chr1B 89.216 102 10 1 297 397 325979006 325979107 3.130000e-25 126.0
52 TraesCS2A01G438300 chr1B 100.000 28 0 0 220 247 58711336 58711309 5.000000e-03 52.8
53 TraesCS2A01G438300 chr5D 79.245 159 25 8 2393 2548 385964854 385964701 1.470000e-18 104.0
54 TraesCS2A01G438300 chr1D 100.000 28 0 0 225 252 335365919 335365892 5.000000e-03 52.8


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 TraesCS2A01G438300 chr2A 689708559 689711548 2989 True 5522.00 5522 100.00000 1 2990 1 chr2A.!!$R1 2989
1 TraesCS2A01G438300 chr2A 690408929 690411656 2727 False 1951.50 3533 92.28950 587 2990 2 chr2A.!!$F2 2403
2 TraesCS2A01G438300 chr2A 689630387 689632008 1621 True 749.90 1423 89.87200 137 2112 2 chr2A.!!$R2 1975
3 TraesCS2A01G438300 chr2D 546931921 546933160 1239 False 1485.00 1485 88.36100 956 2205 1 chr2D.!!$F2 1249
4 TraesCS2A01G438300 chr2D 555133404 555134181 777 False 955.00 955 88.81700 1154 1931 1 chr2D.!!$F4 777
5 TraesCS2A01G438300 chr2D 546870895 546874097 3202 False 916.35 3177 89.97225 2 2946 4 chr2D.!!$F5 2944
6 TraesCS2A01G438300 chr2B 653619070 653620484 1414 False 1592.00 1592 87.31100 767 2186 1 chr2B.!!$F3 1419
7 TraesCS2A01G438300 chr2B 653609742 653612500 2758 False 491.05 2071 88.99300 1 2530 6 chr2B.!!$F4 2529
8 TraesCS2A01G438300 chr4A 33075810 33080443 4633 False 953.50 1644 90.68650 574 2100 2 chr4A.!!$F1 1526

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
975 4889 0.390735 AAGCTTTTCGACCGGCGTAT 60.391 50.000 16.0 0.0 41.80 3.06 F
1251 5176 3.391382 GTGCCGAGCTACTGGGGT 61.391 66.667 0.0 0.0 29.82 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1791 5716 1.014044 GCGTGTTCTCGATCAAGCCA 61.014 55.000 10.35 0.0 34.16 4.75 R
2615 6924 4.513318 GGCAACTAGGCAGCTATCTTTTAG 59.487 45.833 0.00 0.0 43.51 1.85 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
25 26 1.237285 CCCAAAGGCGAAGACCAGTG 61.237 60.000 0.00 0.00 31.70 3.66
109 116 1.160329 ACTGCAGGTCAAGTTCGCAC 61.160 55.000 19.93 0.00 0.00 5.34
153 160 1.153086 GCAACCGATGGATGGCTCT 60.153 57.895 0.00 0.00 0.00 4.09
230 253 5.349061 TCCGTTAGGAATCTTTTACTCCC 57.651 43.478 0.00 0.00 45.12 4.30
231 254 5.028131 TCCGTTAGGAATCTTTTACTCCCT 58.972 41.667 0.00 0.00 45.12 4.20
232 255 5.128335 TCCGTTAGGAATCTTTTACTCCCTC 59.872 44.000 0.00 0.00 45.12 4.30
233 256 5.358090 CGTTAGGAATCTTTTACTCCCTCC 58.642 45.833 0.00 0.00 0.00 4.30
234 257 5.358090 GTTAGGAATCTTTTACTCCCTCCG 58.642 45.833 0.00 0.00 0.00 4.63
235 258 3.451890 AGGAATCTTTTACTCCCTCCGT 58.548 45.455 0.00 0.00 0.00 4.69
236 259 3.844804 AGGAATCTTTTACTCCCTCCGTT 59.155 43.478 0.00 0.00 0.00 4.44
237 260 4.288887 AGGAATCTTTTACTCCCTCCGTTT 59.711 41.667 0.00 0.00 0.00 3.60
238 261 4.634883 GGAATCTTTTACTCCCTCCGTTTC 59.365 45.833 0.00 0.00 0.00 2.78
239 262 4.903045 ATCTTTTACTCCCTCCGTTTCA 57.097 40.909 0.00 0.00 0.00 2.69
240 263 4.693042 TCTTTTACTCCCTCCGTTTCAA 57.307 40.909 0.00 0.00 0.00 2.69
241 264 5.038651 TCTTTTACTCCCTCCGTTTCAAA 57.961 39.130 0.00 0.00 0.00 2.69
242 265 5.627135 TCTTTTACTCCCTCCGTTTCAAAT 58.373 37.500 0.00 0.00 0.00 2.32
243 266 6.066032 TCTTTTACTCCCTCCGTTTCAAATT 58.934 36.000 0.00 0.00 0.00 1.82
244 267 7.225725 TCTTTTACTCCCTCCGTTTCAAATTA 58.774 34.615 0.00 0.00 0.00 1.40
245 268 6.806388 TTTACTCCCTCCGTTTCAAATTAC 57.194 37.500 0.00 0.00 0.00 1.89
246 269 4.635699 ACTCCCTCCGTTTCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
247 270 4.981812 ACTCCCTCCGTTTCAAATTACTT 58.018 39.130 0.00 0.00 0.00 2.24
248 271 4.760204 ACTCCCTCCGTTTCAAATTACTTG 59.240 41.667 0.00 0.00 36.25 3.16
249 272 4.721132 TCCCTCCGTTTCAAATTACTTGT 58.279 39.130 0.00 0.00 36.34 3.16
250 273 4.758165 TCCCTCCGTTTCAAATTACTTGTC 59.242 41.667 0.00 0.00 36.34 3.18
251 274 4.760204 CCCTCCGTTTCAAATTACTTGTCT 59.240 41.667 0.00 0.00 36.34 3.41
252 275 5.334879 CCCTCCGTTTCAAATTACTTGTCTG 60.335 44.000 0.00 0.00 36.34 3.51
253 276 5.238650 CCTCCGTTTCAAATTACTTGTCTGT 59.761 40.000 0.00 0.00 36.34 3.41
257 280 7.012894 TCCGTTTCAAATTACTTGTCTGTCAAT 59.987 33.333 0.00 0.00 36.34 2.57
301 324 3.941483 AGCAGTTGATCCCGTTTAGATTG 59.059 43.478 0.00 0.00 0.00 2.67
302 325 3.689649 GCAGTTGATCCCGTTTAGATTGT 59.310 43.478 0.00 0.00 0.00 2.71
303 326 4.873827 GCAGTTGATCCCGTTTAGATTGTA 59.126 41.667 0.00 0.00 0.00 2.41
305 328 6.106673 CAGTTGATCCCGTTTAGATTGTACT 58.893 40.000 0.00 0.00 0.00 2.73
306 329 6.255887 CAGTTGATCCCGTTTAGATTGTACTC 59.744 42.308 0.00 0.00 0.00 2.59
308 331 4.100498 TGATCCCGTTTAGATTGTACTCCC 59.900 45.833 0.00 0.00 0.00 4.30
309 332 3.716431 TCCCGTTTAGATTGTACTCCCT 58.284 45.455 0.00 0.00 0.00 4.20
310 333 3.703052 TCCCGTTTAGATTGTACTCCCTC 59.297 47.826 0.00 0.00 0.00 4.30
312 335 3.490419 CCGTTTAGATTGTACTCCCTCCG 60.490 52.174 0.00 0.00 0.00 4.63
313 336 3.129988 CGTTTAGATTGTACTCCCTCCGT 59.870 47.826 0.00 0.00 0.00 4.69
314 337 4.381292 CGTTTAGATTGTACTCCCTCCGTT 60.381 45.833 0.00 0.00 0.00 4.44
316 339 2.108970 AGATTGTACTCCCTCCGTTCC 58.891 52.381 0.00 0.00 0.00 3.62
317 340 1.829222 GATTGTACTCCCTCCGTTCCA 59.171 52.381 0.00 0.00 0.00 3.53
318 341 1.946984 TTGTACTCCCTCCGTTCCAT 58.053 50.000 0.00 0.00 0.00 3.41
319 342 2.832643 TGTACTCCCTCCGTTCCATA 57.167 50.000 0.00 0.00 0.00 2.74
320 343 3.104519 TGTACTCCCTCCGTTCCATAA 57.895 47.619 0.00 0.00 0.00 1.90
321 344 3.649843 TGTACTCCCTCCGTTCCATAAT 58.350 45.455 0.00 0.00 0.00 1.28
322 345 3.386726 TGTACTCCCTCCGTTCCATAATG 59.613 47.826 0.00 0.00 0.00 1.90
323 346 2.478292 ACTCCCTCCGTTCCATAATGT 58.522 47.619 0.00 0.00 0.00 2.71
324 347 3.649843 ACTCCCTCCGTTCCATAATGTA 58.350 45.455 0.00 0.00 0.00 2.29
325 348 4.035112 ACTCCCTCCGTTCCATAATGTAA 58.965 43.478 0.00 0.00 0.00 2.41
326 349 4.472108 ACTCCCTCCGTTCCATAATGTAAA 59.528 41.667 0.00 0.00 0.00 2.01
327 350 5.045432 ACTCCCTCCGTTCCATAATGTAAAA 60.045 40.000 0.00 0.00 0.00 1.52
328 351 5.187687 TCCCTCCGTTCCATAATGTAAAAC 58.812 41.667 0.00 0.00 0.00 2.43
329 352 4.034742 CCCTCCGTTCCATAATGTAAAACG 59.965 45.833 0.00 0.00 41.60 3.60
330 353 4.632688 CCTCCGTTCCATAATGTAAAACGT 59.367 41.667 5.39 0.00 40.65 3.99
331 354 5.122711 CCTCCGTTCCATAATGTAAAACGTT 59.877 40.000 0.00 0.00 40.65 3.99
332 355 6.348704 CCTCCGTTCCATAATGTAAAACGTTT 60.349 38.462 7.96 7.96 40.65 3.60
333 356 6.968250 TCCGTTCCATAATGTAAAACGTTTT 58.032 32.000 27.65 27.65 40.65 2.43
334 357 7.424001 TCCGTTCCATAATGTAAAACGTTTTT 58.576 30.769 29.42 15.16 40.65 1.94
393 416 2.554564 GGGACAGAGGGGGTACTTTTTG 60.555 54.545 0.00 0.00 0.00 2.44
406 429 5.010617 GGGTACTTTTTGAGCAAAGATTCCA 59.989 40.000 1.59 0.00 37.24 3.53
486 514 4.971125 GAGCCCGCCGCACTATCC 62.971 72.222 0.00 0.00 41.38 2.59
488 516 4.626081 GCCCGCCGCACTATCCAT 62.626 66.667 0.00 0.00 37.47 3.41
500 532 4.260743 CGCACTATCCATTATTGTGTGGTG 60.261 45.833 5.57 0.00 43.63 4.17
512 556 1.305201 GTGTGGTGGGTACAACTGTG 58.695 55.000 0.00 0.00 34.61 3.66
516 560 1.560146 TGGTGGGTACAACTGTGTCAA 59.440 47.619 0.00 0.00 39.30 3.18
517 561 2.026169 TGGTGGGTACAACTGTGTCAAA 60.026 45.455 0.00 0.00 39.30 2.69
519 563 3.634910 GGTGGGTACAACTGTGTCAAATT 59.365 43.478 0.00 0.00 39.30 1.82
528 572 9.619316 GTACAACTGTGTCAAATTAAATATGCA 57.381 29.630 0.00 0.00 39.30 3.96
534 578 8.341892 TGTGTCAAATTAAATATGCACACCTA 57.658 30.769 0.00 0.00 33.45 3.08
554 599 9.531158 ACACCTATCTAAACTAAGTAGTCTGTT 57.469 33.333 0.00 0.00 34.99 3.16
752 1181 3.794399 TCTCCTTCTCTATCCAGGGAGAA 59.206 47.826 6.99 6.50 43.99 2.87
848 4434 5.200483 CCCTATAAAACCATCTCCAGCAAA 58.800 41.667 0.00 0.00 0.00 3.68
849 4435 5.656416 CCCTATAAAACCATCTCCAGCAAAA 59.344 40.000 0.00 0.00 0.00 2.44
866 4453 3.302415 GCAAAAACGTTTCTTGCCATCAC 60.302 43.478 29.90 15.03 39.62 3.06
908 4502 2.886523 CAACAGAAATCACTTCCCAGCA 59.113 45.455 0.00 0.00 34.21 4.41
971 4885 1.497722 CTCAAGCTTTTCGACCGGC 59.502 57.895 0.00 0.00 0.00 6.13
972 4886 2.173382 CAAGCTTTTCGACCGGCG 59.827 61.111 0.00 6.66 42.69 6.46
973 4887 2.280592 AAGCTTTTCGACCGGCGT 60.281 55.556 16.00 0.00 41.80 5.68
974 4888 1.005867 AAGCTTTTCGACCGGCGTA 60.006 52.632 16.00 5.94 41.80 4.42
975 4889 0.390735 AAGCTTTTCGACCGGCGTAT 60.391 50.000 16.00 0.00 41.80 3.06
982 4899 3.773860 TTCGACCGGCGTATTTTAGTA 57.226 42.857 16.00 0.00 41.80 1.82
1251 5176 3.391382 GTGCCGAGCTACTGGGGT 61.391 66.667 0.00 0.00 29.82 4.95
1791 5716 1.684049 CCTCAAGGACCTCGAGGCT 60.684 63.158 31.56 18.29 39.95 4.58
2477 6786 4.261801 AGATGTGTGTATGTTAGTTGGGC 58.738 43.478 0.00 0.00 0.00 5.36
2615 6924 9.262358 GTTGGAGGTAAGAGAATATATTGTCAC 57.738 37.037 21.06 12.82 32.96 3.67
2641 6950 0.761802 ATAGCTGCCTAGTTGCCTCC 59.238 55.000 0.00 0.00 0.00 4.30
2833 7142 9.981114 ACGTAATGACTATATGAAATCATGACA 57.019 29.630 0.00 0.00 33.95 3.58
2984 7296 4.219725 TCATGACCTCGATCACTTGTGTTA 59.780 41.667 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.847328 CCACCTGGTTGGGAAATACC 58.153 55.000 0.00 0.00 41.11 2.73
153 160 3.387947 GCTTCCGGGGGAGTTCGA 61.388 66.667 0.00 0.00 31.21 3.71
228 251 4.760204 AGACAAGTAATTTGAAACGGAGGG 59.240 41.667 0.00 0.00 39.21 4.30
229 252 5.238650 ACAGACAAGTAATTTGAAACGGAGG 59.761 40.000 0.00 0.00 39.21 4.30
230 253 6.018262 TGACAGACAAGTAATTTGAAACGGAG 60.018 38.462 0.00 0.00 39.21 4.63
231 254 5.818336 TGACAGACAAGTAATTTGAAACGGA 59.182 36.000 0.00 0.00 39.21 4.69
232 255 6.055231 TGACAGACAAGTAATTTGAAACGG 57.945 37.500 0.00 0.00 39.21 4.44
233 256 7.855409 TGATTGACAGACAAGTAATTTGAAACG 59.145 33.333 0.00 0.00 42.02 3.60
252 275 3.431572 GTGCAAGTCTCTGTCTGATTGAC 59.568 47.826 0.00 0.00 45.54 3.18
253 276 3.657634 GTGCAAGTCTCTGTCTGATTGA 58.342 45.455 0.00 0.00 0.00 2.57
257 280 0.315251 CCGTGCAAGTCTCTGTCTGA 59.685 55.000 0.00 0.00 0.00 3.27
301 324 3.387050 ACATTATGGAACGGAGGGAGTAC 59.613 47.826 0.00 0.00 0.00 2.73
302 325 3.649843 ACATTATGGAACGGAGGGAGTA 58.350 45.455 0.00 0.00 0.00 2.59
303 326 2.478292 ACATTATGGAACGGAGGGAGT 58.522 47.619 0.00 0.00 0.00 3.85
305 328 5.187687 GTTTTACATTATGGAACGGAGGGA 58.812 41.667 0.00 0.00 0.00 4.20
306 329 4.034742 CGTTTTACATTATGGAACGGAGGG 59.965 45.833 16.84 0.00 39.33 4.30
308 331 5.789710 ACGTTTTACATTATGGAACGGAG 57.210 39.130 23.39 7.32 45.11 4.63
309 332 6.557291 AAACGTTTTACATTATGGAACGGA 57.443 33.333 23.39 0.00 45.11 4.69
310 333 7.626144 AAAAACGTTTTACATTATGGAACGG 57.374 32.000 25.44 12.69 45.11 4.44
354 377 6.938030 TCTGTCCCATAATGTAAGACGTTTTT 59.062 34.615 0.00 0.00 0.00 1.94
355 378 6.469410 TCTGTCCCATAATGTAAGACGTTTT 58.531 36.000 0.00 0.00 0.00 2.43
356 379 6.045072 TCTGTCCCATAATGTAAGACGTTT 57.955 37.500 0.00 0.00 0.00 3.60
357 380 5.395324 CCTCTGTCCCATAATGTAAGACGTT 60.395 44.000 0.00 0.00 0.00 3.99
358 381 4.099573 CCTCTGTCCCATAATGTAAGACGT 59.900 45.833 0.00 0.00 0.00 4.34
359 382 4.501571 CCCTCTGTCCCATAATGTAAGACG 60.502 50.000 0.00 0.00 0.00 4.18
360 383 4.202367 CCCCTCTGTCCCATAATGTAAGAC 60.202 50.000 0.00 0.00 0.00 3.01
361 384 3.973973 CCCCTCTGTCCCATAATGTAAGA 59.026 47.826 0.00 0.00 0.00 2.10
362 385 3.073062 CCCCCTCTGTCCCATAATGTAAG 59.927 52.174 0.00 0.00 0.00 2.34
363 386 3.053077 CCCCCTCTGTCCCATAATGTAA 58.947 50.000 0.00 0.00 0.00 2.41
364 387 2.021441 ACCCCCTCTGTCCCATAATGTA 60.021 50.000 0.00 0.00 0.00 2.29
365 388 1.275002 ACCCCCTCTGTCCCATAATGT 60.275 52.381 0.00 0.00 0.00 2.71
366 389 1.522900 ACCCCCTCTGTCCCATAATG 58.477 55.000 0.00 0.00 0.00 1.90
367 390 2.252945 AGTACCCCCTCTGTCCCATAAT 59.747 50.000 0.00 0.00 0.00 1.28
368 391 1.654997 AGTACCCCCTCTGTCCCATAA 59.345 52.381 0.00 0.00 0.00 1.90
369 392 1.326055 AGTACCCCCTCTGTCCCATA 58.674 55.000 0.00 0.00 0.00 2.74
370 393 0.421904 AAGTACCCCCTCTGTCCCAT 59.578 55.000 0.00 0.00 0.00 4.00
371 394 0.195096 AAAGTACCCCCTCTGTCCCA 59.805 55.000 0.00 0.00 0.00 4.37
372 395 1.369403 AAAAGTACCCCCTCTGTCCC 58.631 55.000 0.00 0.00 0.00 4.46
373 396 2.374170 TCAAAAAGTACCCCCTCTGTCC 59.626 50.000 0.00 0.00 0.00 4.02
374 397 3.676093 CTCAAAAAGTACCCCCTCTGTC 58.324 50.000 0.00 0.00 0.00 3.51
375 398 2.224793 GCTCAAAAAGTACCCCCTCTGT 60.225 50.000 0.00 0.00 0.00 3.41
376 399 2.224769 TGCTCAAAAAGTACCCCCTCTG 60.225 50.000 0.00 0.00 0.00 3.35
377 400 2.062636 TGCTCAAAAAGTACCCCCTCT 58.937 47.619 0.00 0.00 0.00 3.69
378 401 2.579410 TGCTCAAAAAGTACCCCCTC 57.421 50.000 0.00 0.00 0.00 4.30
379 402 3.117284 TCTTTGCTCAAAAAGTACCCCCT 60.117 43.478 0.00 0.00 38.16 4.79
380 403 3.227614 TCTTTGCTCAAAAAGTACCCCC 58.772 45.455 0.00 0.00 38.16 5.40
381 404 5.468540 AATCTTTGCTCAAAAAGTACCCC 57.531 39.130 0.00 0.00 38.16 4.95
382 405 5.010617 TGGAATCTTTGCTCAAAAAGTACCC 59.989 40.000 0.00 0.00 38.16 3.69
383 406 6.084326 TGGAATCTTTGCTCAAAAAGTACC 57.916 37.500 0.00 0.00 38.16 3.34
384 407 8.593492 AAATGGAATCTTTGCTCAAAAAGTAC 57.407 30.769 0.00 0.00 38.16 2.73
385 408 9.912634 CTAAATGGAATCTTTGCTCAAAAAGTA 57.087 29.630 0.00 0.00 38.16 2.24
386 409 8.641541 TCTAAATGGAATCTTTGCTCAAAAAGT 58.358 29.630 0.00 0.00 38.16 2.66
387 410 9.649167 ATCTAAATGGAATCTTTGCTCAAAAAG 57.351 29.630 0.00 0.00 38.31 2.27
393 416 9.113838 TGTCTAATCTAAATGGAATCTTTGCTC 57.886 33.333 0.00 0.00 0.00 4.26
406 429 4.332819 GCACAGCGGTTGTCTAATCTAAAT 59.667 41.667 0.00 0.00 38.16 1.40
484 512 3.330998 TGTACCCACCACACAATAATGGA 59.669 43.478 0.00 0.00 39.46 3.41
485 513 3.691575 TGTACCCACCACACAATAATGG 58.308 45.455 0.00 0.00 42.13 3.16
486 514 4.764823 AGTTGTACCCACCACACAATAATG 59.235 41.667 0.00 0.00 34.89 1.90
487 515 4.764823 CAGTTGTACCCACCACACAATAAT 59.235 41.667 0.00 0.00 34.89 1.28
488 516 4.138290 CAGTTGTACCCACCACACAATAA 58.862 43.478 0.00 0.00 34.89 1.40
500 532 9.567848 CATATTTAATTTGACACAGTTGTACCC 57.432 33.333 0.00 0.00 35.47 3.69
528 572 9.531158 AACAGACTACTTAGTTTAGATAGGTGT 57.469 33.333 0.00 0.00 36.50 4.16
654 1073 7.595311 ATTCTTTTGTGGTTCAGTTCAAAAC 57.405 32.000 0.00 0.00 35.70 2.43
752 1181 1.270274 ACAACATCAACATGTGCGCAT 59.730 42.857 15.91 7.01 42.89 4.73
819 4405 5.104109 TGGAGATGGTTTTATAGGGGAACTG 60.104 44.000 0.00 0.00 0.00 3.16
848 4434 2.948979 TGAGTGATGGCAAGAAACGTTT 59.051 40.909 14.57 14.57 0.00 3.60
849 4435 2.549754 CTGAGTGATGGCAAGAAACGTT 59.450 45.455 0.00 0.00 0.00 3.99
866 4453 4.641396 TGGTGTTGATCTGGTAAACTGAG 58.359 43.478 0.00 0.00 0.00 3.35
908 4502 3.610911 GATCGAATGGGAAGTCTTGGTT 58.389 45.455 0.00 0.00 0.00 3.67
971 4885 6.715344 TGGCTGTTGAACTACTAAAATACG 57.285 37.500 0.00 0.00 0.00 3.06
972 4886 7.801783 GTGTTGGCTGTTGAACTACTAAAATAC 59.198 37.037 0.00 0.00 0.00 1.89
973 4887 7.040961 GGTGTTGGCTGTTGAACTACTAAAATA 60.041 37.037 0.00 0.00 0.00 1.40
974 4888 6.238925 GGTGTTGGCTGTTGAACTACTAAAAT 60.239 38.462 0.00 0.00 0.00 1.82
975 4889 5.066764 GGTGTTGGCTGTTGAACTACTAAAA 59.933 40.000 0.00 0.00 0.00 1.52
982 4899 1.682854 CATGGTGTTGGCTGTTGAACT 59.317 47.619 0.00 0.00 0.00 3.01
1173 5095 0.944386 TTTCAGTGGCTTCTTCGTGC 59.056 50.000 0.00 0.00 0.00 5.34
1176 5098 1.068954 GGCTTTTCAGTGGCTTCTTCG 60.069 52.381 0.00 0.00 0.00 3.79
1251 5176 3.195591 GAGCTTCCGCGGCTCGATA 62.196 63.158 23.51 0.00 45.01 2.92
1791 5716 1.014044 GCGTGTTCTCGATCAAGCCA 61.014 55.000 10.35 0.00 34.16 4.75
2001 5926 1.542030 AGGCATCGATCTATGGTCGTC 59.458 52.381 9.10 0.00 39.91 4.20
2002 5927 1.270826 CAGGCATCGATCTATGGTCGT 59.729 52.381 9.10 0.00 39.91 4.34
2003 5928 1.988063 CAGGCATCGATCTATGGTCG 58.012 55.000 9.10 0.00 40.30 4.79
2206 6402 6.227298 TGTACCCAAATGTCACATGTTTTT 57.773 33.333 0.00 0.00 0.00 1.94
2477 6786 9.522804 GTGAGATAGATTACTGTCAAGGTTAAG 57.477 37.037 0.00 0.00 36.85 1.85
2615 6924 4.513318 GGCAACTAGGCAGCTATCTTTTAG 59.487 45.833 0.00 0.00 43.51 1.85
2641 6950 6.438259 TCTCTTTACCTCTAACTCATCACG 57.562 41.667 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.