Multiple sequence alignment - TraesCS3B01G059600

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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 TraesCS3B01G059600 chr3B 100.000 3810 0 0 1 3810 31101275 31097466 0.000000e+00 7036
1 TraesCS3B01G059600 chr3B 100.000 2129 0 0 472 2600 31107921 31105793 0.000000e+00 3932
2 TraesCS3B01G059600 chr3B 98.104 1213 22 1 2598 3810 701392837 701391626 0.000000e+00 2111
3 TraesCS3B01G059600 chr3B 87.532 385 42 4 1135 1517 539186049 539186429 1.260000e-119 440
4 TraesCS3B01G059600 chr3B 95.890 219 7 2 234 451 723494517 723494300 1.680000e-93 353
5 TraesCS3B01G059600 chr3B 88.430 242 28 0 1 242 31112026 31111785 3.720000e-75 292
6 TraesCS3B01G059600 chr3B 88.841 233 26 0 1 233 31216001 31215769 1.730000e-73 287
7 TraesCS3B01G059600 chr3B 86.695 233 31 0 1 233 31131975 31131743 3.780000e-65 259
8 TraesCS3B01G059600 chr3B 86.134 238 27 5 1 233 31110083 31109847 6.320000e-63 252
9 TraesCS3B01G059600 chr3B 91.150 113 8 2 836 947 157237627 157237738 6.590000e-33 152
10 TraesCS3B01G059600 chr3D 89.641 1699 116 33 957 2600 19362894 19361201 0.000000e+00 2108
11 TraesCS3B01G059600 chr3D 89.442 1648 112 32 986 2600 19537800 19536182 0.000000e+00 2023
12 TraesCS3B01G059600 chr3D 90.638 235 20 2 1 233 19739479 19739245 1.030000e-80 311
13 TraesCS3B01G059600 chr3D 87.554 233 24 2 1 233 19542593 19542366 8.120000e-67 265
14 TraesCS3B01G059600 chr3D 85.052 194 18 2 476 669 19538244 19538062 1.810000e-43 187
15 TraesCS3B01G059600 chr3D 90.000 110 11 0 838 947 513957275 513957384 3.970000e-30 143
16 TraesCS3B01G059600 chr1B 98.023 1214 22 2 2598 3810 33958180 33959392 0.000000e+00 2108
17 TraesCS3B01G059600 chr1B 97.609 1213 25 4 2598 3810 168614648 168613440 0.000000e+00 2076
18 TraesCS3B01G059600 chr1B 96.789 218 6 1 234 451 584797948 584797732 2.800000e-96 363
19 TraesCS3B01G059600 chr1B 96.347 219 7 1 234 451 655807829 655808047 3.620000e-95 359
20 TraesCS3B01G059600 chr5B 97.858 1214 24 2 2598 3810 330858595 330857383 0.000000e+00 2097
21 TraesCS3B01G059600 chr5B 97.527 1213 29 1 2598 3810 54519907 54521118 0.000000e+00 2073
22 TraesCS3B01G059600 chr5B 97.235 217 6 0 235 451 520370948 520371164 6.010000e-98 368
23 TraesCS3B01G059600 chr7B 97.857 1213 25 1 2598 3810 326905052 326906263 0.000000e+00 2095
24 TraesCS3B01G059600 chr2B 97.694 1214 26 2 2598 3810 464971622 464972834 0.000000e+00 2085
25 TraesCS3B01G059600 chr2B 97.529 1214 27 3 2598 3810 212359039 212357828 0.000000e+00 2073
26 TraesCS3B01G059600 chr2B 96.847 222 7 0 230 451 780152331 780152552 4.650000e-99 372
27 TraesCS3B01G059600 chr2B 97.273 220 3 2 233 451 790587331 790587548 1.670000e-98 370
28 TraesCS3B01G059600 chr2B 95.475 221 8 2 232 451 70882702 70882483 6.060000e-93 351
29 TraesCS3B01G059600 chr4B 97.692 1213 27 1 2598 3810 535268913 535267702 0.000000e+00 2084
30 TraesCS3B01G059600 chr4B 95.872 218 9 0 234 451 115547447 115547230 1.680000e-93 353
31 TraesCS3B01G059600 chr4B 95.890 219 7 2 234 451 664964832 664964615 1.680000e-93 353
32 TraesCS3B01G059600 chr4B 91.262 103 9 0 845 947 600919973 600920075 1.430000e-29 141
33 TraesCS3B01G059600 chr3A 87.242 1646 127 47 987 2591 27009678 27008075 0.000000e+00 1799
34 TraesCS3B01G059600 chr3A 89.787 235 22 2 1 233 27287956 27287722 2.220000e-77 300
35 TraesCS3B01G059600 chr3A 88.664 247 23 3 1 242 27014697 27014451 2.880000e-76 296
36 TraesCS3B01G059600 chr3A 92.632 190 13 1 1 190 27217061 27216873 4.850000e-69 272
37 TraesCS3B01G059600 chr3A 86.364 198 19 2 472 669 27010170 27009981 3.860000e-50 209
38 TraesCS3B01G059600 chr2A 91.827 1040 64 11 1124 2149 727622104 727621072 0.000000e+00 1430
39 TraesCS3B01G059600 chr2A 95.980 199 6 2 2402 2599 727620974 727620777 4.750000e-84 322
40 TraesCS3B01G059600 chr5D 86.076 395 32 9 1134 1517 536501165 536501547 1.650000e-108 403
41 TraesCS3B01G059600 chr5D 89.308 159 13 1 987 1145 536500992 536501146 3.000000e-46 196
42 TraesCS3B01G059600 chr4A 91.589 107 9 0 841 947 313632314 313632420 8.530000e-32 148
43 TraesCS3B01G059600 chr4D 90.654 107 10 0 841 947 259497259 259497365 3.970000e-30 143
44 TraesCS3B01G059600 chr1D 89.091 110 12 0 838 947 24714459 24714568 1.850000e-28 137
45 TraesCS3B01G059600 chr6B 88.991 109 10 2 841 948 301608678 301608785 2.390000e-27 134
46 TraesCS3B01G059600 chr2D 87.826 115 13 1 833 947 351973463 351973350 2.390000e-27 134


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 TraesCS3B01G059600 chr3B 31097466 31101275 3809 True 7036.0 7036 100.000000 1 3810 1 chr3B.!!$R1 3809
1 TraesCS3B01G059600 chr3B 701391626 701392837 1211 True 2111.0 2111 98.104000 2598 3810 1 chr3B.!!$R4 1212
2 TraesCS3B01G059600 chr3B 31105793 31112026 6233 True 1492.0 3932 91.521333 1 2600 3 chr3B.!!$R6 2599
3 TraesCS3B01G059600 chr3D 19361201 19362894 1693 True 2108.0 2108 89.641000 957 2600 1 chr3D.!!$R1 1643
4 TraesCS3B01G059600 chr3D 19536182 19538244 2062 True 1105.0 2023 87.247000 476 2600 2 chr3D.!!$R4 2124
5 TraesCS3B01G059600 chr1B 33958180 33959392 1212 False 2108.0 2108 98.023000 2598 3810 1 chr1B.!!$F1 1212
6 TraesCS3B01G059600 chr1B 168613440 168614648 1208 True 2076.0 2076 97.609000 2598 3810 1 chr1B.!!$R1 1212
7 TraesCS3B01G059600 chr5B 330857383 330858595 1212 True 2097.0 2097 97.858000 2598 3810 1 chr5B.!!$R1 1212
8 TraesCS3B01G059600 chr5B 54519907 54521118 1211 False 2073.0 2073 97.527000 2598 3810 1 chr5B.!!$F1 1212
9 TraesCS3B01G059600 chr7B 326905052 326906263 1211 False 2095.0 2095 97.857000 2598 3810 1 chr7B.!!$F1 1212
10 TraesCS3B01G059600 chr2B 464971622 464972834 1212 False 2085.0 2085 97.694000 2598 3810 1 chr2B.!!$F1 1212
11 TraesCS3B01G059600 chr2B 212357828 212359039 1211 True 2073.0 2073 97.529000 2598 3810 1 chr2B.!!$R2 1212
12 TraesCS3B01G059600 chr4B 535267702 535268913 1211 True 2084.0 2084 97.692000 2598 3810 1 chr4B.!!$R2 1212
13 TraesCS3B01G059600 chr3A 27008075 27010170 2095 True 1004.0 1799 86.803000 472 2591 2 chr3A.!!$R4 2119
14 TraesCS3B01G059600 chr2A 727620777 727622104 1327 True 876.0 1430 93.903500 1124 2599 2 chr2A.!!$R1 1475
15 TraesCS3B01G059600 chr5D 536500992 536501547 555 False 299.5 403 87.692000 987 1517 2 chr5D.!!$F1 530

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
259 2207 0.629058 ACACTTTGGTTCCTGGGTGT 59.371 50.000 0.00 0.0 33.82 4.16 F
260 2208 1.847737 ACACTTTGGTTCCTGGGTGTA 59.152 47.619 1.53 0.0 36.37 2.90 F
2771 6628 1.069906 GCAACATCCACAGACAACGAC 60.070 52.381 0.00 0.0 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2771 6628 1.813513 CTTAGTGTGCTGAACCCCAG 58.186 55.000 0.00 0.00 45.67 4.45 R
2802 6659 4.678309 GCGGACAGTAGAAAGCTTATGTCT 60.678 45.833 19.34 13.55 37.96 3.41 R
3669 7527 2.076100 GGAATCACGACTTGCATGTCA 58.924 47.619 26.67 12.26 36.82 3.58 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
37 38 5.163893 CGCATTTAACGTGTTATCTCCAACT 60.164 40.000 0.00 0.00 0.00 3.16
39 40 5.600908 TTTAACGTGTTATCTCCAACTGC 57.399 39.130 0.00 0.00 0.00 4.40
41 42 4.530710 AACGTGTTATCTCCAACTGCTA 57.469 40.909 0.00 0.00 0.00 3.49
60 61 6.061022 TGCTACAGGAGATAAATGGTGAAA 57.939 37.500 0.00 0.00 0.00 2.69
72 73 8.601546 AGATAAATGGTGAAATTTTAAAGGGCA 58.398 29.630 0.00 0.00 32.16 5.36
130 131 3.248363 GCTTTTGAAAAGATGCAACCACC 59.752 43.478 20.91 0.00 0.00 4.61
136 137 1.843368 AAGATGCAACCACCATGAGG 58.157 50.000 0.00 0.00 42.21 3.86
156 157 8.610896 CATGAGGAAGACATAAAGCTTTCTTAG 58.389 37.037 16.57 6.75 30.21 2.18
173 174 9.196552 GCTTTCTTAGTTATGCAAATCAACTTT 57.803 29.630 10.41 0.00 34.48 2.66
182 183 6.588719 ATGCAAATCAACTTTAAGGCACTA 57.411 33.333 0.00 0.00 38.49 2.74
190 191 9.461312 AATCAACTTTAAGGCACTATAACATGA 57.539 29.630 0.00 0.00 38.49 3.07
195 196 2.838736 AGGCACTATAACATGAAGCGG 58.161 47.619 0.00 0.00 36.02 5.52
214 215 2.481276 CGGGAATCACATGCTTCGACTA 60.481 50.000 0.00 0.00 0.00 2.59
215 216 3.531538 GGGAATCACATGCTTCGACTAA 58.468 45.455 0.00 0.00 0.00 2.24
233 2181 6.071463 CGACTAAGAACCACTTCAAATTTCG 58.929 40.000 0.00 0.00 39.72 3.46
234 2182 6.313744 ACTAAGAACCACTTCAAATTTCGG 57.686 37.500 0.00 0.00 39.72 4.30
235 2183 4.584327 AAGAACCACTTCAAATTTCGGG 57.416 40.909 0.00 0.00 32.91 5.14
237 2185 4.211920 AGAACCACTTCAAATTTCGGGAA 58.788 39.130 0.00 0.00 0.00 3.97
241 2189 6.020971 ACCACTTCAAATTTCGGGAAATAC 57.979 37.500 7.05 0.00 39.88 1.89
242 2190 5.536916 ACCACTTCAAATTTCGGGAAATACA 59.463 36.000 7.05 0.00 39.88 2.29
243 2191 5.861787 CCACTTCAAATTTCGGGAAATACAC 59.138 40.000 7.05 0.00 39.88 2.90
245 2193 7.145323 CACTTCAAATTTCGGGAAATACACTT 58.855 34.615 7.05 0.00 39.88 3.16
246 2194 7.651704 CACTTCAAATTTCGGGAAATACACTTT 59.348 33.333 7.05 0.00 39.88 2.66
247 2195 7.651704 ACTTCAAATTTCGGGAAATACACTTTG 59.348 33.333 7.05 8.40 39.88 2.77
248 2196 6.451393 TCAAATTTCGGGAAATACACTTTGG 58.549 36.000 7.05 0.00 39.88 3.28
249 2197 6.041069 TCAAATTTCGGGAAATACACTTTGGT 59.959 34.615 7.05 0.00 39.88 3.67
250 2198 6.413783 AATTTCGGGAAATACACTTTGGTT 57.586 33.333 7.05 0.00 39.88 3.67
251 2199 5.441709 TTTCGGGAAATACACTTTGGTTC 57.558 39.130 0.00 0.00 0.00 3.62
252 2200 3.414269 TCGGGAAATACACTTTGGTTCC 58.586 45.455 0.00 0.00 0.00 3.62
253 2201 3.073356 TCGGGAAATACACTTTGGTTCCT 59.927 43.478 0.00 0.00 0.00 3.36
254 2202 3.190535 CGGGAAATACACTTTGGTTCCTG 59.809 47.826 0.00 0.00 0.00 3.86
257 2205 3.895704 AATACACTTTGGTTCCTGGGT 57.104 42.857 0.00 0.00 0.00 4.51
258 2206 2.649531 TACACTTTGGTTCCTGGGTG 57.350 50.000 0.00 0.00 0.00 4.61
259 2207 0.629058 ACACTTTGGTTCCTGGGTGT 59.371 50.000 0.00 0.00 33.82 4.16
260 2208 1.847737 ACACTTTGGTTCCTGGGTGTA 59.152 47.619 1.53 0.00 36.37 2.90
261 2209 2.445525 ACACTTTGGTTCCTGGGTGTAT 59.554 45.455 1.53 0.00 36.37 2.29
262 2210 3.653836 ACACTTTGGTTCCTGGGTGTATA 59.346 43.478 1.53 0.00 36.37 1.47
264 2212 5.489637 ACACTTTGGTTCCTGGGTGTATATA 59.510 40.000 1.53 0.00 36.37 0.86
265 2213 5.820947 CACTTTGGTTCCTGGGTGTATATAC 59.179 44.000 5.89 5.89 0.00 1.47
338 2286 9.185680 AGGTAAGAACTATTTTGACAAAACACT 57.814 29.630 15.36 3.23 32.37 3.55
339 2287 9.797556 GGTAAGAACTATTTTGACAAAACACTT 57.202 29.630 15.36 15.89 32.37 3.16
343 2291 8.739972 AGAACTATTTTGACAAAACACTTGACT 58.260 29.630 15.36 7.03 32.37 3.41
344 2292 9.353999 GAACTATTTTGACAAAACACTTGACTT 57.646 29.630 15.36 0.00 32.37 3.01
346 2294 9.783256 ACTATTTTGACAAAACACTTGACTTAC 57.217 29.630 15.36 0.00 32.37 2.34
350 2298 9.535878 TTTTGACAAAACACTTGACTTACTTTT 57.464 25.926 9.30 0.00 0.00 2.27
351 2299 8.514136 TTGACAAAACACTTGACTTACTTTTG 57.486 30.769 0.00 0.00 35.61 2.44
352 2300 6.584563 TGACAAAACACTTGACTTACTTTTGC 59.415 34.615 0.00 0.00 33.72 3.68
354 2302 6.364976 ACAAAACACTTGACTTACTTTTGCAC 59.635 34.615 0.00 0.00 33.72 4.57
355 2303 5.897377 AACACTTGACTTACTTTTGCACT 57.103 34.783 0.00 0.00 0.00 4.40
357 2305 6.604735 ACACTTGACTTACTTTTGCACTAG 57.395 37.500 0.00 0.00 0.00 2.57
359 2307 7.270047 ACACTTGACTTACTTTTGCACTAGTA 58.730 34.615 0.00 3.57 0.00 1.82
361 2309 8.609176 CACTTGACTTACTTTTGCACTAGTAAA 58.391 33.333 16.44 1.77 36.66 2.01
363 2311 9.997482 CTTGACTTACTTTTGCACTAGTAAAAA 57.003 29.630 16.44 12.59 38.55 1.94
402 2350 3.782889 AACAAAAGTTGACCTCACAGC 57.217 42.857 0.00 0.00 0.00 4.40
405 2353 3.509575 ACAAAAGTTGACCTCACAGCAAA 59.490 39.130 0.00 0.00 0.00 3.68
406 2354 4.021544 ACAAAAGTTGACCTCACAGCAAAA 60.022 37.500 0.00 0.00 0.00 2.44
446 2394 9.542462 TTTGCTATTATAGGTCACTATTCACAC 57.458 33.333 1.12 0.00 40.35 3.82
447 2395 8.478775 TGCTATTATAGGTCACTATTCACACT 57.521 34.615 1.12 0.00 40.35 3.55
454 2402 6.605471 AGGTCACTATTCACACTATTCACA 57.395 37.500 0.00 0.00 0.00 3.58
456 2404 6.211584 AGGTCACTATTCACACTATTCACACT 59.788 38.462 0.00 0.00 0.00 3.55
458 2406 8.198109 GGTCACTATTCACACTATTCACACTAT 58.802 37.037 0.00 0.00 0.00 2.12
459 2407 9.587772 GTCACTATTCACACTATTCACACTATT 57.412 33.333 0.00 0.00 0.00 1.73
461 2409 9.586435 CACTATTCACACTATTCACACTATTCA 57.414 33.333 0.00 0.00 0.00 2.57
462 2410 9.587772 ACTATTCACACTATTCACACTATTCAC 57.412 33.333 0.00 0.00 0.00 3.18
463 2411 9.586435 CTATTCACACTATTCACACTATTCACA 57.414 33.333 0.00 0.00 0.00 3.58
464 2412 7.652300 TTCACACTATTCACACTATTCACAC 57.348 36.000 0.00 0.00 0.00 3.82
466 2414 8.117813 TCACACTATTCACACTATTCACACTA 57.882 34.615 0.00 0.00 0.00 2.74
468 2416 9.371136 CACACTATTCACACTATTCACACTATT 57.629 33.333 0.00 0.00 0.00 1.73
469 2417 9.944376 ACACTATTCACACTATTCACACTATTT 57.056 29.630 0.00 0.00 0.00 1.40
2657 6514 3.496130 GCCCTCGAAACATCTCATATGTG 59.504 47.826 1.90 0.00 31.80 3.21
2771 6628 1.069906 GCAACATCCACAGACAACGAC 60.070 52.381 0.00 0.00 0.00 4.34
2802 6659 3.822594 CACACTAAGCGGTGCATTAAA 57.177 42.857 0.00 0.00 40.52 1.52
2969 6826 4.916041 TTCATCTCATGAACTCCCACTT 57.084 40.909 0.00 0.00 43.84 3.16
3182 7039 5.006941 GTCAAGTTAACCTAAGTGTTTCGCA 59.993 40.000 0.88 0.00 0.00 5.10
3236 7093 6.071560 TGTGAACGTAAGAATCTATCACACCT 60.072 38.462 9.25 0.00 40.31 4.00
3518 7375 3.638160 TCATGATCTCCATCATCGTGTCA 59.362 43.478 0.00 0.00 45.26 3.58
3652 7510 1.834263 GACAACTCCTATGGCTCCTGT 59.166 52.381 0.00 0.00 0.00 4.00
3669 7527 3.513912 TCCTGTCGGTTGTCATACTCATT 59.486 43.478 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.833545 AACACGTTAAATGCGCCATAA 57.166 38.095 4.18 0.00 0.00 1.90
11 12 3.545426 GGAGATAACACGTTAAATGCGCC 60.545 47.826 4.18 0.00 0.00 6.53
13 14 4.850859 TGGAGATAACACGTTAAATGCG 57.149 40.909 0.00 0.00 0.00 4.73
21 22 3.257375 TGTAGCAGTTGGAGATAACACGT 59.743 43.478 0.00 0.00 33.02 4.49
22 23 3.845178 TGTAGCAGTTGGAGATAACACG 58.155 45.455 0.00 0.00 33.02 4.49
23 24 4.081642 TCCTGTAGCAGTTGGAGATAACAC 60.082 45.833 0.00 0.00 33.02 3.32
37 38 5.692115 TTCACCATTTATCTCCTGTAGCA 57.308 39.130 0.00 0.00 0.00 3.49
60 61 1.068816 GTCGCGTGTGCCCTTTAAAAT 60.069 47.619 5.77 0.00 38.08 1.82
65 66 3.767630 AAGGTCGCGTGTGCCCTTT 62.768 57.895 5.77 0.00 38.99 3.11
90 91 1.068748 AGCAAGACTCGCTGCATTTTG 60.069 47.619 0.00 0.00 38.60 2.44
97 98 3.338818 TTTCAAAAGCAAGACTCGCTG 57.661 42.857 0.00 0.00 40.35 5.18
130 131 6.998968 AGAAAGCTTTATGTCTTCCTCATG 57.001 37.500 12.68 0.00 0.00 3.07
136 137 9.709600 GCATAACTAAGAAAGCTTTATGTCTTC 57.290 33.333 12.68 0.00 35.56 2.87
156 157 6.868339 AGTGCCTTAAAGTTGATTTGCATAAC 59.132 34.615 0.00 0.00 32.09 1.89
173 174 4.377021 CCGCTTCATGTTATAGTGCCTTA 58.623 43.478 0.00 0.00 0.00 2.69
182 183 3.884895 TGTGATTCCCGCTTCATGTTAT 58.115 40.909 0.00 0.00 0.00 1.89
190 191 1.098050 GAAGCATGTGATTCCCGCTT 58.902 50.000 0.00 0.00 45.17 4.68
195 196 4.433615 TCTTAGTCGAAGCATGTGATTCC 58.566 43.478 5.52 0.00 37.16 3.01
214 215 4.211920 TCCCGAAATTTGAAGTGGTTCTT 58.788 39.130 0.00 0.00 39.32 2.52
215 216 3.827722 TCCCGAAATTTGAAGTGGTTCT 58.172 40.909 0.00 0.00 33.38 3.01
233 2181 3.509967 CCAGGAACCAAAGTGTATTTCCC 59.490 47.826 0.00 0.00 37.09 3.97
234 2182 3.509967 CCCAGGAACCAAAGTGTATTTCC 59.490 47.826 0.00 0.00 36.71 3.13
235 2183 4.022329 CACCCAGGAACCAAAGTGTATTTC 60.022 45.833 0.00 0.00 0.00 2.17
237 2185 3.117284 ACACCCAGGAACCAAAGTGTATT 60.117 43.478 9.76 0.00 36.73 1.89
241 2189 2.649531 TACACCCAGGAACCAAAGTG 57.350 50.000 0.00 0.00 0.00 3.16
242 2190 5.489637 TGTATATACACCCAGGAACCAAAGT 59.510 40.000 11.62 0.00 0.00 2.66
243 2191 5.996644 TGTATATACACCCAGGAACCAAAG 58.003 41.667 11.62 0.00 0.00 2.77
312 2260 9.185680 AGTGTTTTGTCAAAATAGTTCTTACCT 57.814 29.630 13.65 0.34 32.22 3.08
313 2261 9.797556 AAGTGTTTTGTCAAAATAGTTCTTACC 57.202 29.630 17.46 2.76 31.98 2.85
316 2264 9.353999 GTCAAGTGTTTTGTCAAAATAGTTCTT 57.646 29.630 19.36 11.77 34.29 2.52
317 2265 8.739972 AGTCAAGTGTTTTGTCAAAATAGTTCT 58.260 29.630 19.36 13.92 34.29 3.01
318 2266 8.911247 AGTCAAGTGTTTTGTCAAAATAGTTC 57.089 30.769 19.36 12.43 34.29 3.01
323 2271 9.705290 AAAGTAAGTCAAGTGTTTTGTCAAAAT 57.295 25.926 13.65 0.00 32.22 1.82
324 2272 9.535878 AAAAGTAAGTCAAGTGTTTTGTCAAAA 57.464 25.926 6.65 6.65 0.00 2.44
326 2274 7.115663 GCAAAAGTAAGTCAAGTGTTTTGTCAA 59.884 33.333 0.00 0.00 37.26 3.18
327 2275 6.584563 GCAAAAGTAAGTCAAGTGTTTTGTCA 59.415 34.615 0.00 0.00 37.26 3.58
328 2276 6.584563 TGCAAAAGTAAGTCAAGTGTTTTGTC 59.415 34.615 0.00 0.00 37.26 3.18
329 2277 6.364976 GTGCAAAAGTAAGTCAAGTGTTTTGT 59.635 34.615 0.00 0.00 37.26 2.83
330 2278 6.586082 AGTGCAAAAGTAAGTCAAGTGTTTTG 59.414 34.615 0.00 0.00 37.74 2.44
331 2279 6.687604 AGTGCAAAAGTAAGTCAAGTGTTTT 58.312 32.000 0.00 0.00 0.00 2.43
333 2281 5.897377 AGTGCAAAAGTAAGTCAAGTGTT 57.103 34.783 0.00 0.00 0.00 3.32
335 2283 6.604735 ACTAGTGCAAAAGTAAGTCAAGTG 57.395 37.500 0.00 0.00 0.00 3.16
336 2284 8.726870 TTTACTAGTGCAAAAGTAAGTCAAGT 57.273 30.769 17.10 0.00 38.89 3.16
337 2285 9.997482 TTTTTACTAGTGCAAAAGTAAGTCAAG 57.003 29.630 17.10 0.00 38.89 3.02
380 2328 4.021544 TGCTGTGAGGTCAACTTTTGTTTT 60.022 37.500 0.00 0.00 41.35 2.43
381 2329 3.509575 TGCTGTGAGGTCAACTTTTGTTT 59.490 39.130 0.00 0.00 41.35 2.83
382 2330 3.088532 TGCTGTGAGGTCAACTTTTGTT 58.911 40.909 0.00 0.00 44.66 2.83
384 2332 3.781079 TTGCTGTGAGGTCAACTTTTG 57.219 42.857 0.00 0.00 0.00 2.44
385 2333 4.799564 TTTTGCTGTGAGGTCAACTTTT 57.200 36.364 0.00 0.00 0.00 2.27
386 2334 4.799564 TTTTTGCTGTGAGGTCAACTTT 57.200 36.364 0.00 0.00 0.00 2.66
420 2368 9.542462 GTGTGAATAGTGACCTATAATAGCAAA 57.458 33.333 0.00 0.00 32.57 3.68
421 2369 8.924303 AGTGTGAATAGTGACCTATAATAGCAA 58.076 33.333 0.00 0.00 32.57 3.91
428 2376 9.416284 TGTGAATAGTGTGAATAGTGACCTATA 57.584 33.333 0.00 0.00 32.57 1.31
431 2379 6.211584 AGTGTGAATAGTGTGAATAGTGACCT 59.788 38.462 0.00 0.00 0.00 3.85
433 2381 9.587772 AATAGTGTGAATAGTGTGAATAGTGAC 57.412 33.333 0.00 0.00 0.00 3.67
434 2382 9.803315 GAATAGTGTGAATAGTGTGAATAGTGA 57.197 33.333 0.00 0.00 0.00 3.41
436 2384 9.587772 GTGAATAGTGTGAATAGTGTGAATAGT 57.412 33.333 0.00 0.00 0.00 2.12
437 2385 9.586435 TGTGAATAGTGTGAATAGTGTGAATAG 57.414 33.333 0.00 0.00 0.00 1.73
439 2387 8.097038 AGTGTGAATAGTGTGAATAGTGTGAAT 58.903 33.333 0.00 0.00 0.00 2.57
443 2391 9.944376 AAATAGTGTGAATAGTGTGAATAGTGT 57.056 29.630 0.00 0.00 0.00 3.55
449 2397 9.990360 TGTCTAAAATAGTGTGAATAGTGTGAA 57.010 29.630 0.00 0.00 0.00 3.18
450 2398 9.639601 CTGTCTAAAATAGTGTGAATAGTGTGA 57.360 33.333 0.00 0.00 0.00 3.58
453 2401 9.862371 AGTCTGTCTAAAATAGTGTGAATAGTG 57.138 33.333 0.00 0.00 0.00 2.74
458 2406 8.638873 TCTGAAGTCTGTCTAAAATAGTGTGAA 58.361 33.333 0.00 0.00 0.00 3.18
459 2407 8.178313 TCTGAAGTCTGTCTAAAATAGTGTGA 57.822 34.615 0.00 0.00 0.00 3.58
461 2409 8.184304 ACTCTGAAGTCTGTCTAAAATAGTGT 57.816 34.615 0.00 0.00 0.00 3.55
462 2410 9.482627 AAACTCTGAAGTCTGTCTAAAATAGTG 57.517 33.333 0.00 0.00 33.48 2.74
466 2414 9.832445 TTGTAAACTCTGAAGTCTGTCTAAAAT 57.168 29.630 0.00 0.00 33.48 1.82
468 2416 8.475639 ACTTGTAAACTCTGAAGTCTGTCTAAA 58.524 33.333 0.00 0.00 33.48 1.85
469 2417 8.008513 ACTTGTAAACTCTGAAGTCTGTCTAA 57.991 34.615 0.00 0.00 33.48 2.10
2771 6628 1.813513 CTTAGTGTGCTGAACCCCAG 58.186 55.000 0.00 0.00 45.67 4.45
2802 6659 4.678309 GCGGACAGTAGAAAGCTTATGTCT 60.678 45.833 19.34 13.55 37.96 3.41
2969 6826 7.822749 AGATGACTAGAGGGATGTCTATCTA 57.177 40.000 0.00 0.00 32.48 1.98
3153 7010 4.038883 ACACTTAGGTTAACTTGACGAGCT 59.961 41.667 5.42 0.00 0.00 4.09
3236 7093 1.725641 GAAGCACCACGTGATGATCA 58.274 50.000 15.96 0.00 35.23 2.92
3423 7280 4.340666 CGAAGATGGAGATCAAGAAGGAGA 59.659 45.833 0.00 0.00 0.00 3.71
3518 7375 2.744202 GTTGGCGAGACAACTTCATGAT 59.256 45.455 14.10 0.00 45.49 2.45
3669 7527 2.076100 GGAATCACGACTTGCATGTCA 58.924 47.619 26.67 12.26 36.82 3.58


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

AutoCloner maintained by Alex Coulton.