Multiple sequence alignment - TraesCS6D01G342000

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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 TraesCS6D01G342000 chr6D 100.000 2726 0 0 1 2726 441396725 441399450 0.000000e+00 5035.0
1 TraesCS6D01G342000 chr6D 94.212 2246 102 12 29 2274 441315919 441318136 0.000000e+00 3402.0
2 TraesCS6D01G342000 chr6D 92.304 1949 113 17 29 1969 441290431 441292350 0.000000e+00 2734.0
3 TraesCS6D01G342000 chr6D 85.213 940 97 31 1792 2726 441101311 441102213 0.000000e+00 928.0
4 TraesCS6D01G342000 chr6D 94.444 558 21 1 2018 2565 441292348 441292905 0.000000e+00 850.0
5 TraesCS6D01G342000 chr6D 98.265 461 5 1 2266 2726 441325665 441326122 0.000000e+00 804.0
6 TraesCS6D01G342000 chr6D 80.802 698 100 16 241 932 441304791 441305460 1.450000e-142 516.0
7 TraesCS6D01G342000 chr6D 80.802 698 100 16 241 932 441312773 441313442 1.450000e-142 516.0
8 TraesCS6D01G342000 chr6D 91.239 331 27 2 1957 2286 441292904 441293233 1.490000e-122 449.0
9 TraesCS6D01G342000 chr6D 89.423 104 11 0 139 242 441316127 441316230 6.120000e-27 132.0
10 TraesCS6D01G342000 chr6D 89.655 58 4 1 2320 2375 441293244 441293301 3.770000e-09 73.1
11 TraesCS6D01G342000 chr6A 93.058 2708 153 16 29 2726 589174401 589177083 0.000000e+00 3927.0
12 TraesCS6D01G342000 chr6A 92.614 2708 150 18 29 2726 589193263 589190596 0.000000e+00 3847.0
13 TraesCS6D01G342000 chr6A 88.630 343 28 7 2386 2726 589089490 589089823 9.090000e-110 407.0
14 TraesCS6D01G342000 chr6B 86.703 2399 243 29 29 2382 666219126 666221493 0.000000e+00 2593.0
15 TraesCS6D01G342000 chr6B 86.705 2106 213 35 79 2157 666306403 666308468 0.000000e+00 2276.0
16 TraesCS6D01G342000 chr6B 86.610 2106 215 32 79 2157 666274278 666276343 0.000000e+00 2265.0
17 TraesCS6D01G342000 chr6B 87.508 1561 156 16 855 2382 666176384 666177938 0.000000e+00 1766.0
18 TraesCS6D01G342000 chr6B 87.326 789 74 15 1952 2726 666276351 666277127 0.000000e+00 880.0
19 TraesCS6D01G342000 chr6B 87.326 789 74 15 1952 2726 666308476 666309252 0.000000e+00 880.0
20 TraesCS6D01G342000 chr6B 87.917 720 70 6 545 1248 666054680 666055398 0.000000e+00 832.0
21 TraesCS6D01G342000 chr6B 83.437 803 87 22 29 819 666175615 666176383 0.000000e+00 704.0
22 TraesCS6D01G342000 chr6B 89.143 525 50 6 1760 2278 666055413 666055936 0.000000e+00 647.0
23 TraesCS6D01G342000 chr6B 85.851 417 40 12 2315 2726 666055941 666056343 2.510000e-115 425.0
24 TraesCS6D01G342000 chrUn 87.446 1163 117 16 1007 2157 349101524 349100379 0.000000e+00 1312.0
25 TraesCS6D01G342000 chrUn 87.326 789 74 15 1952 2726 349100371 349099595 0.000000e+00 880.0
26 TraesCS6D01G342000 chr7A 89.189 148 15 1 881 1027 731292009 731291862 1.670000e-42 183.0


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 TraesCS6D01G342000 chr6D 441396725 441399450 2725 False 5035.000000 5035 100.000000 1 2726 1 chr6D.!!$F4 2725
1 TraesCS6D01G342000 chr6D 441312773 441318136 5363 False 1350.000000 3402 88.145667 29 2274 3 chr6D.!!$F6 2245
2 TraesCS6D01G342000 chr6D 441290431 441293301 2870 False 1026.525000 2734 91.910500 29 2565 4 chr6D.!!$F5 2536
3 TraesCS6D01G342000 chr6D 441101311 441102213 902 False 928.000000 928 85.213000 1792 2726 1 chr6D.!!$F1 934
4 TraesCS6D01G342000 chr6D 441304791 441305460 669 False 516.000000 516 80.802000 241 932 1 chr6D.!!$F2 691
5 TraesCS6D01G342000 chr6A 589174401 589177083 2682 False 3927.000000 3927 93.058000 29 2726 1 chr6A.!!$F2 2697
6 TraesCS6D01G342000 chr6A 589190596 589193263 2667 True 3847.000000 3847 92.614000 29 2726 1 chr6A.!!$R1 2697
7 TraesCS6D01G342000 chr6B 666219126 666221493 2367 False 2593.000000 2593 86.703000 29 2382 1 chr6B.!!$F1 2353
8 TraesCS6D01G342000 chr6B 666306403 666309252 2849 False 1578.000000 2276 87.015500 79 2726 2 chr6B.!!$F5 2647
9 TraesCS6D01G342000 chr6B 666274278 666277127 2849 False 1572.500000 2265 86.968000 79 2726 2 chr6B.!!$F4 2647
10 TraesCS6D01G342000 chr6B 666175615 666177938 2323 False 1235.000000 1766 85.472500 29 2382 2 chr6B.!!$F3 2353
11 TraesCS6D01G342000 chr6B 666054680 666056343 1663 False 634.666667 832 87.637000 545 2726 3 chr6B.!!$F2 2181
12 TraesCS6D01G342000 chrUn 349099595 349101524 1929 True 1096.000000 1312 87.386000 1007 2726 2 chrUn.!!$R1 1719

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
203 3334 0.251634 CTGAGAAAGCCAGGTCCTCC 59.748 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 5568 0.81401 GCCAACACACGAGACCAAGT 60.814 55.0 0.0 0.0 0.0 3.16 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
22 23 3.870274 CCTAAAGGTAGGGGAAAAGTCG 58.130 50.000 0.00 0.00 43.07 4.18
23 24 3.516700 CCTAAAGGTAGGGGAAAAGTCGA 59.483 47.826 0.00 0.00 43.07 4.20
24 25 4.163649 CCTAAAGGTAGGGGAAAAGTCGAT 59.836 45.833 0.00 0.00 43.07 3.59
25 26 4.652679 AAAGGTAGGGGAAAAGTCGATT 57.347 40.909 0.00 0.00 0.00 3.34
26 27 3.629142 AGGTAGGGGAAAAGTCGATTG 57.371 47.619 0.00 0.00 0.00 2.67
27 28 2.238898 AGGTAGGGGAAAAGTCGATTGG 59.761 50.000 0.00 0.00 0.00 3.16
49 3168 1.053424 AGTAGGGGAAAAGTCGCACA 58.947 50.000 0.00 0.00 38.45 4.57
77 3208 5.655532 CCTACTTCAGCCTAAAGGTACACTA 59.344 44.000 0.00 0.00 37.57 2.74
89 3220 4.456662 AGGTACACTAGAGGGTAGATGG 57.543 50.000 0.00 0.00 0.00 3.51
151 3282 1.566703 TCCTGTTTGGAAGGTGGTCAA 59.433 47.619 0.00 0.00 42.94 3.18
159 3290 2.224769 TGGAAGGTGGTCAAATGGTCTC 60.225 50.000 0.00 0.00 0.00 3.36
187 3318 5.304686 ACTCAAAGGTTGTGGTATTCTGA 57.695 39.130 0.00 0.00 0.00 3.27
188 3319 5.308825 ACTCAAAGGTTGTGGTATTCTGAG 58.691 41.667 0.00 0.00 35.12 3.35
189 3320 5.071788 ACTCAAAGGTTGTGGTATTCTGAGA 59.928 40.000 0.00 0.00 33.60 3.27
190 3321 5.935945 TCAAAGGTTGTGGTATTCTGAGAA 58.064 37.500 0.00 0.00 0.00 2.87
191 3322 6.361433 TCAAAGGTTGTGGTATTCTGAGAAA 58.639 36.000 0.00 0.00 0.00 2.52
192 3323 6.486657 TCAAAGGTTGTGGTATTCTGAGAAAG 59.513 38.462 0.00 0.00 0.00 2.62
193 3324 4.327680 AGGTTGTGGTATTCTGAGAAAGC 58.672 43.478 0.00 0.00 0.00 3.51
194 3325 3.440522 GGTTGTGGTATTCTGAGAAAGCC 59.559 47.826 0.00 5.25 0.00 4.35
195 3326 4.072131 GTTGTGGTATTCTGAGAAAGCCA 58.928 43.478 14.36 14.36 0.00 4.75
196 3327 3.942829 TGTGGTATTCTGAGAAAGCCAG 58.057 45.455 17.45 0.00 0.00 4.85
197 3328 3.274288 GTGGTATTCTGAGAAAGCCAGG 58.726 50.000 17.45 0.00 32.73 4.45
198 3329 2.912956 TGGTATTCTGAGAAAGCCAGGT 59.087 45.455 14.36 0.00 32.73 4.00
199 3330 3.055094 TGGTATTCTGAGAAAGCCAGGTC 60.055 47.826 14.36 0.00 32.73 3.85
200 3331 2.797177 ATTCTGAGAAAGCCAGGTCC 57.203 50.000 0.00 0.00 32.73 4.46
201 3332 1.734655 TTCTGAGAAAGCCAGGTCCT 58.265 50.000 0.00 0.00 32.73 3.85
202 3333 1.270907 TCTGAGAAAGCCAGGTCCTC 58.729 55.000 0.00 0.00 32.73 3.71
203 3334 0.251634 CTGAGAAAGCCAGGTCCTCC 59.748 60.000 0.00 0.00 0.00 4.30
204 3335 1.201429 TGAGAAAGCCAGGTCCTCCC 61.201 60.000 0.00 0.00 0.00 4.30
205 3336 2.245438 GAGAAAGCCAGGTCCTCCCG 62.245 65.000 0.00 0.00 38.74 5.14
206 3337 3.330720 AAAGCCAGGTCCTCCCGG 61.331 66.667 0.00 0.00 38.74 5.73
210 3341 2.445845 CCAGGTCCTCCCGGCATA 60.446 66.667 0.00 0.00 38.74 3.14
211 3342 1.843376 CCAGGTCCTCCCGGCATAT 60.843 63.158 0.00 0.00 38.74 1.78
212 3343 0.544357 CCAGGTCCTCCCGGCATATA 60.544 60.000 0.00 0.00 38.74 0.86
213 3344 0.608640 CAGGTCCTCCCGGCATATAC 59.391 60.000 0.00 0.00 38.74 1.47
214 3345 0.487772 AGGTCCTCCCGGCATATACT 59.512 55.000 0.00 0.00 38.74 2.12
215 3346 1.714787 AGGTCCTCCCGGCATATACTA 59.285 52.381 0.00 0.00 38.74 1.82
216 3347 2.100989 GGTCCTCCCGGCATATACTAG 58.899 57.143 0.00 0.00 0.00 2.57
217 3348 2.100989 GTCCTCCCGGCATATACTAGG 58.899 57.143 0.00 0.00 0.00 3.02
218 3349 1.714787 TCCTCCCGGCATATACTAGGT 59.285 52.381 0.00 0.00 0.00 3.08
219 3350 1.825474 CCTCCCGGCATATACTAGGTG 59.175 57.143 0.00 0.00 0.00 4.00
220 3351 1.825474 CTCCCGGCATATACTAGGTGG 59.175 57.143 0.00 0.00 0.00 4.61
221 3352 0.902531 CCCGGCATATACTAGGTGGG 59.097 60.000 0.00 0.00 0.00 4.61
222 3353 1.551560 CCCGGCATATACTAGGTGGGA 60.552 57.143 0.00 0.00 37.61 4.37
223 3354 2.467880 CCGGCATATACTAGGTGGGAT 58.532 52.381 0.00 0.00 0.00 3.85
224 3355 2.168521 CCGGCATATACTAGGTGGGATG 59.831 54.545 0.00 0.00 0.00 3.51
225 3356 3.096852 CGGCATATACTAGGTGGGATGA 58.903 50.000 0.00 0.00 0.00 2.92
226 3357 3.513912 CGGCATATACTAGGTGGGATGAA 59.486 47.826 0.00 0.00 0.00 2.57
227 3358 4.020573 CGGCATATACTAGGTGGGATGAAA 60.021 45.833 0.00 0.00 0.00 2.69
228 3359 5.512404 CGGCATATACTAGGTGGGATGAAAA 60.512 44.000 0.00 0.00 0.00 2.29
229 3360 6.485171 GGCATATACTAGGTGGGATGAAAAT 58.515 40.000 0.00 0.00 0.00 1.82
230 3361 7.580688 CGGCATATACTAGGTGGGATGAAAATA 60.581 40.741 0.00 0.00 0.00 1.40
231 3362 8.107095 GGCATATACTAGGTGGGATGAAAATAA 58.893 37.037 0.00 0.00 0.00 1.40
232 3363 8.947115 GCATATACTAGGTGGGATGAAAATAAC 58.053 37.037 0.00 0.00 0.00 1.89
233 3364 9.449719 CATATACTAGGTGGGATGAAAATAACC 57.550 37.037 0.00 0.00 0.00 2.85
234 3365 5.789574 ACTAGGTGGGATGAAAATAACCA 57.210 39.130 0.00 0.00 0.00 3.67
235 3366 6.147437 ACTAGGTGGGATGAAAATAACCAA 57.853 37.500 0.00 0.00 32.19 3.67
236 3367 6.741724 ACTAGGTGGGATGAAAATAACCAAT 58.258 36.000 0.00 0.00 32.19 3.16
237 3368 5.937975 AGGTGGGATGAAAATAACCAATG 57.062 39.130 0.00 0.00 32.19 2.82
238 3369 4.162131 AGGTGGGATGAAAATAACCAATGC 59.838 41.667 0.00 0.00 32.19 3.56
239 3370 4.081198 GGTGGGATGAAAATAACCAATGCA 60.081 41.667 0.00 0.00 32.19 3.96
252 3383 1.843368 CAATGCATGGAAGGTGGTCT 58.157 50.000 0.00 0.00 0.00 3.85
253 3384 2.173519 CAATGCATGGAAGGTGGTCTT 58.826 47.619 0.00 0.00 38.65 3.01
261 3392 4.286297 TGGAAGGTGGTCTTATGTTCTG 57.714 45.455 0.00 0.00 35.50 3.02
263 3394 3.559171 GGAAGGTGGTCTTATGTTCTGCA 60.559 47.826 0.00 0.00 35.50 4.41
276 3407 2.159254 TGTTCTGCAACAACTCAAAGGC 60.159 45.455 9.10 0.00 39.69 4.35
319 3553 1.688772 TCCTCCCGTCATGTACTAGC 58.311 55.000 0.00 0.00 0.00 3.42
320 3554 1.214673 TCCTCCCGTCATGTACTAGCT 59.785 52.381 0.00 0.00 0.00 3.32
321 3555 2.440627 TCCTCCCGTCATGTACTAGCTA 59.559 50.000 0.00 0.00 0.00 3.32
322 3556 2.814919 CCTCCCGTCATGTACTAGCTAG 59.185 54.545 19.44 19.44 0.00 3.42
346 3580 2.227865 GGGACGAAAATAAGCACTGCAA 59.772 45.455 3.30 0.00 0.00 4.08
425 3659 2.829720 AGTTGACCCACTAGCGATAACA 59.170 45.455 0.00 0.00 0.00 2.41
524 3764 4.361451 ACAAACATCATCGATGGCTTTC 57.639 40.909 24.61 0.00 43.60 2.62
581 3822 2.861462 TCTTTCTTTTGCGTGTTGGG 57.139 45.000 0.00 0.00 0.00 4.12
656 3901 2.104132 TGCGATCACATCCGTCGG 59.896 61.111 4.39 4.39 36.00 4.79
707 3952 3.039202 GCGTGGAAACCATCTGCGG 62.039 63.158 0.00 0.00 35.28 5.69
748 3993 1.377987 GCGATACAAGGGGCCAACA 60.378 57.895 4.39 0.00 0.00 3.33
758 4003 2.899838 GGCCAACAGTCACACGCA 60.900 61.111 0.00 0.00 0.00 5.24
827 4074 1.074889 AGGACGGTTTAAATGGGTGCT 59.925 47.619 0.00 0.00 0.00 4.40
1182 4444 0.995024 CTCAGGTGTTCCCTTCCCAT 59.005 55.000 0.00 0.00 42.73 4.00
1722 4984 0.466124 CGAGTCCTTTCCCTCCCATC 59.534 60.000 0.00 0.00 0.00 3.51
1949 5227 3.004106 GCTGTTTGTTTGATCTCTGCTGT 59.996 43.478 0.00 0.00 0.00 4.40
2078 5568 1.819305 GCTGTCAGGGCCTCAAAGAAA 60.819 52.381 0.95 0.00 0.00 2.52
2210 5701 2.200081 TCTCCTGGAGCCAGCTAAATT 58.800 47.619 19.08 0.00 42.35 1.82
2513 6020 6.149474 AGCTATTTCCATGTTGTGTTGACTAC 59.851 38.462 0.00 0.00 0.00 2.73
2523 6030 7.209471 TGTTGTGTTGACTACTTCTTTTTGT 57.791 32.000 0.00 0.00 0.00 2.83
2596 6245 7.639113 TTATAGCGTTCCTTCAAATTCCATT 57.361 32.000 0.00 0.00 0.00 3.16
2652 6398 3.056304 CACCAAACGCCCACTTTAATTG 58.944 45.455 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.618351 GACTTTTCCCCTACCTTTAGGC 58.382 50.000 0.00 0.00 43.56 3.93
1 2 3.516700 TCGACTTTTCCCCTACCTTTAGG 59.483 47.826 0.00 0.00 44.43 2.69
2 3 4.813750 TCGACTTTTCCCCTACCTTTAG 57.186 45.455 0.00 0.00 0.00 1.85
3 4 5.493809 CAATCGACTTTTCCCCTACCTTTA 58.506 41.667 0.00 0.00 0.00 1.85
5 6 3.308188 CCAATCGACTTTTCCCCTACCTT 60.308 47.826 0.00 0.00 0.00 3.50
6 7 2.238898 CCAATCGACTTTTCCCCTACCT 59.761 50.000 0.00 0.00 0.00 3.08
7 8 2.026542 ACCAATCGACTTTTCCCCTACC 60.027 50.000 0.00 0.00 0.00 3.18
9 10 4.533311 ACTAACCAATCGACTTTTCCCCTA 59.467 41.667 0.00 0.00 0.00 3.53
10 11 2.971901 AACCAATCGACTTTTCCCCT 57.028 45.000 0.00 0.00 0.00 4.79
11 12 3.682696 ACTAACCAATCGACTTTTCCCC 58.317 45.455 0.00 0.00 0.00 4.81
12 13 4.874396 CCTACTAACCAATCGACTTTTCCC 59.126 45.833 0.00 0.00 0.00 3.97
13 14 4.874396 CCCTACTAACCAATCGACTTTTCC 59.126 45.833 0.00 0.00 0.00 3.13
14 15 4.874396 CCCCTACTAACCAATCGACTTTTC 59.126 45.833 0.00 0.00 0.00 2.29
15 16 4.533311 TCCCCTACTAACCAATCGACTTTT 59.467 41.667 0.00 0.00 0.00 2.27
16 17 4.098894 TCCCCTACTAACCAATCGACTTT 58.901 43.478 0.00 0.00 0.00 2.66
17 18 3.716431 TCCCCTACTAACCAATCGACTT 58.284 45.455 0.00 0.00 0.00 3.01
18 19 3.393426 TCCCCTACTAACCAATCGACT 57.607 47.619 0.00 0.00 0.00 4.18
19 20 4.476628 TTTCCCCTACTAACCAATCGAC 57.523 45.455 0.00 0.00 0.00 4.20
22 23 4.874396 CGACTTTTCCCCTACTAACCAATC 59.126 45.833 0.00 0.00 0.00 2.67
23 24 4.840271 CGACTTTTCCCCTACTAACCAAT 58.160 43.478 0.00 0.00 0.00 3.16
24 25 3.557686 GCGACTTTTCCCCTACTAACCAA 60.558 47.826 0.00 0.00 0.00 3.67
25 26 2.027837 GCGACTTTTCCCCTACTAACCA 60.028 50.000 0.00 0.00 0.00 3.67
26 27 2.027837 TGCGACTTTTCCCCTACTAACC 60.028 50.000 0.00 0.00 0.00 2.85
27 28 2.998670 GTGCGACTTTTCCCCTACTAAC 59.001 50.000 0.00 0.00 0.00 2.34
77 3208 2.481441 TGCATTGACCATCTACCCTCT 58.519 47.619 0.00 0.00 0.00 3.69
133 3264 3.243839 CCATTTGACCACCTTCCAAACAG 60.244 47.826 0.00 0.00 33.33 3.16
151 3282 4.351111 ACCTTTGAGTTGTAGGAGACCATT 59.649 41.667 0.00 0.00 33.21 3.16
179 3310 3.198853 AGGACCTGGCTTTCTCAGAATAC 59.801 47.826 0.00 0.00 34.36 1.89
187 3318 2.294078 CGGGAGGACCTGGCTTTCT 61.294 63.158 0.00 0.00 38.80 2.52
188 3319 2.269241 CGGGAGGACCTGGCTTTC 59.731 66.667 0.00 0.00 38.80 2.62
200 3331 1.825474 CCACCTAGTATATGCCGGGAG 59.175 57.143 2.18 0.00 0.00 4.30
201 3332 1.551560 CCCACCTAGTATATGCCGGGA 60.552 57.143 2.18 0.00 34.10 5.14
202 3333 0.902531 CCCACCTAGTATATGCCGGG 59.097 60.000 2.18 0.00 0.00 5.73
203 3334 1.933021 TCCCACCTAGTATATGCCGG 58.067 55.000 0.00 0.00 0.00 6.13
204 3335 3.096852 TCATCCCACCTAGTATATGCCG 58.903 50.000 0.00 0.00 0.00 5.69
205 3336 5.499004 TTTCATCCCACCTAGTATATGCC 57.501 43.478 0.00 0.00 0.00 4.40
206 3337 8.947115 GTTATTTTCATCCCACCTAGTATATGC 58.053 37.037 0.00 0.00 0.00 3.14
207 3338 9.449719 GGTTATTTTCATCCCACCTAGTATATG 57.550 37.037 0.00 0.00 0.00 1.78
208 3339 9.177927 TGGTTATTTTCATCCCACCTAGTATAT 57.822 33.333 0.00 0.00 0.00 0.86
209 3340 8.570038 TGGTTATTTTCATCCCACCTAGTATA 57.430 34.615 0.00 0.00 0.00 1.47
210 3341 7.460214 TGGTTATTTTCATCCCACCTAGTAT 57.540 36.000 0.00 0.00 0.00 2.12
211 3342 6.894735 TGGTTATTTTCATCCCACCTAGTA 57.105 37.500 0.00 0.00 0.00 1.82
212 3343 5.789574 TGGTTATTTTCATCCCACCTAGT 57.210 39.130 0.00 0.00 0.00 2.57
213 3344 6.461509 GCATTGGTTATTTTCATCCCACCTAG 60.462 42.308 0.00 0.00 0.00 3.02
214 3345 5.362430 GCATTGGTTATTTTCATCCCACCTA 59.638 40.000 0.00 0.00 0.00 3.08
215 3346 4.162131 GCATTGGTTATTTTCATCCCACCT 59.838 41.667 0.00 0.00 0.00 4.00
216 3347 4.081198 TGCATTGGTTATTTTCATCCCACC 60.081 41.667 0.00 0.00 0.00 4.61
217 3348 5.083533 TGCATTGGTTATTTTCATCCCAC 57.916 39.130 0.00 0.00 0.00 4.61
218 3349 5.396548 CCATGCATTGGTTATTTTCATCCCA 60.397 40.000 0.00 0.00 40.99 4.37
219 3350 5.058490 CCATGCATTGGTTATTTTCATCCC 58.942 41.667 0.00 0.00 40.99 3.85
220 3351 5.916318 TCCATGCATTGGTTATTTTCATCC 58.084 37.500 0.00 0.00 46.52 3.51
221 3352 6.480981 CCTTCCATGCATTGGTTATTTTCATC 59.519 38.462 0.00 0.00 46.52 2.92
222 3353 6.070078 ACCTTCCATGCATTGGTTATTTTCAT 60.070 34.615 0.00 0.00 46.52 2.57
223 3354 5.248020 ACCTTCCATGCATTGGTTATTTTCA 59.752 36.000 0.00 0.00 46.52 2.69
224 3355 5.581874 CACCTTCCATGCATTGGTTATTTTC 59.418 40.000 0.00 0.00 46.52 2.29
225 3356 5.490159 CACCTTCCATGCATTGGTTATTTT 58.510 37.500 0.00 0.00 46.52 1.82
226 3357 4.080975 CCACCTTCCATGCATTGGTTATTT 60.081 41.667 0.00 0.00 46.52 1.40
227 3358 3.451902 CCACCTTCCATGCATTGGTTATT 59.548 43.478 0.00 0.00 46.52 1.40
228 3359 3.033184 CCACCTTCCATGCATTGGTTAT 58.967 45.455 0.00 0.00 46.52 1.89
229 3360 2.225242 ACCACCTTCCATGCATTGGTTA 60.225 45.455 11.86 3.65 46.52 2.85
230 3361 1.269012 CCACCTTCCATGCATTGGTT 58.731 50.000 0.00 0.00 46.52 3.67
231 3362 0.114954 ACCACCTTCCATGCATTGGT 59.885 50.000 11.86 11.86 46.52 3.67
233 3364 1.843368 AGACCACCTTCCATGCATTG 58.157 50.000 0.00 0.00 0.00 2.82
234 3365 2.610438 AAGACCACCTTCCATGCATT 57.390 45.000 0.00 0.00 0.00 3.56
235 3366 3.053395 ACATAAGACCACCTTCCATGCAT 60.053 43.478 0.00 0.00 36.34 3.96
236 3367 2.308570 ACATAAGACCACCTTCCATGCA 59.691 45.455 0.00 0.00 36.34 3.96
237 3368 3.004752 ACATAAGACCACCTTCCATGC 57.995 47.619 0.00 0.00 36.34 4.06
238 3369 4.637534 CAGAACATAAGACCACCTTCCATG 59.362 45.833 0.00 0.00 36.34 3.66
239 3370 4.848357 CAGAACATAAGACCACCTTCCAT 58.152 43.478 0.00 0.00 36.34 3.41
252 3383 5.735922 GCCTTTGAGTTGTTGCAGAACATAA 60.736 40.000 11.90 5.09 41.77 1.90
253 3384 4.261572 GCCTTTGAGTTGTTGCAGAACATA 60.262 41.667 11.90 0.05 41.77 2.29
261 3392 1.536709 CCACAGCCTTTGAGTTGTTGC 60.537 52.381 0.00 0.00 0.00 4.17
263 3394 2.143876 ACCACAGCCTTTGAGTTGTT 57.856 45.000 0.00 0.00 0.00 2.83
276 3407 2.926200 CGACTTGCTCAGAATACCACAG 59.074 50.000 0.00 0.00 0.00 3.66
312 3546 2.338577 TCGTCCCACCTAGCTAGTAC 57.661 55.000 19.31 8.29 0.00 2.73
319 3553 3.621715 GTGCTTATTTTCGTCCCACCTAG 59.378 47.826 0.00 0.00 0.00 3.02
320 3554 3.262405 AGTGCTTATTTTCGTCCCACCTA 59.738 43.478 0.00 0.00 0.00 3.08
321 3555 2.039879 AGTGCTTATTTTCGTCCCACCT 59.960 45.455 0.00 0.00 0.00 4.00
322 3556 2.161609 CAGTGCTTATTTTCGTCCCACC 59.838 50.000 0.00 0.00 0.00 4.61
346 3580 1.106351 TGCACGCCAAATTGGTCACT 61.106 50.000 14.17 0.00 40.46 3.41
387 3621 3.545124 CTGCACCAACGGGCCTGTA 62.545 63.158 20.05 0.00 37.90 2.74
481 3719 1.014352 CACACGCCCCATTACTAAGC 58.986 55.000 0.00 0.00 0.00 3.09
482 3720 2.396590 ACACACGCCCCATTACTAAG 57.603 50.000 0.00 0.00 0.00 2.18
484 3722 2.566279 TGTAACACACGCCCCATTACTA 59.434 45.455 0.00 0.00 0.00 1.82
487 3725 2.553172 GTTTGTAACACACGCCCCATTA 59.447 45.455 0.00 0.00 0.00 1.90
488 3726 1.338655 GTTTGTAACACACGCCCCATT 59.661 47.619 0.00 0.00 0.00 3.16
561 3801 2.693074 ACCCAACACGCAAAAGAAAGAT 59.307 40.909 0.00 0.00 0.00 2.40
581 3822 1.272769 ACAAGTCTCCGTTGCTCCTAC 59.727 52.381 0.00 0.00 0.00 3.18
656 3901 5.004726 GGTTCGTTTTGCAATGCTTCATATC 59.995 40.000 6.82 0.00 0.00 1.63
748 3993 5.406767 TTTAAATTTACGTGCGTGTGACT 57.593 34.783 7.55 0.00 0.00 3.41
1722 4984 1.055040 CCTCATCCCTCCTGGCTTAG 58.945 60.000 0.00 0.00 0.00 2.18
1913 5191 2.001076 AACAGCCTTTTGGGAAGAGG 57.999 50.000 0.00 0.00 40.82 3.69
1949 5227 6.811253 ACTTAAGATTTACGACCAATTGCA 57.189 33.333 10.09 0.00 0.00 4.08
2078 5568 0.814010 GCCAACACACGAGACCAAGT 60.814 55.000 0.00 0.00 0.00 3.16
2159 5650 6.866770 TCTTCAACTCGTTTATACCACAGAAG 59.133 38.462 0.00 0.00 0.00 2.85
2210 5701 7.784073 TCCAGGAAAATATTAATCATCCAGCAA 59.216 33.333 0.00 0.00 0.00 3.91
2267 5760 5.728351 TTGCCTGTCGCTATGTAATTAAC 57.272 39.130 0.00 0.00 38.78 2.01
2513 6020 6.892691 AGAGTTCATCGCTAACAAAAAGAAG 58.107 36.000 0.00 0.00 0.00 2.85
2523 6030 4.424626 CAGCTTGTAGAGTTCATCGCTAA 58.575 43.478 0.00 0.00 30.82 3.09
2652 6398 0.733909 GATTGCTTCGTTGCCAAGCC 60.734 55.000 3.63 0.00 44.90 4.35


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

AutoCloner maintained by Alex Coulton.