Multiple sequence alignment - TraesCS6B01G442500

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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 TraesCS6B01G442500 chr6B 100.000 2990 0 0 1 2990 705940880 705943869 0.000000e+00 5522.0
1 TraesCS6B01G442500 chr6B 94.434 2102 106 7 1 2097 705644409 705646504 0.000000e+00 3223.0
2 TraesCS6B01G442500 chr6B 88.013 2386 254 17 1 2370 705504278 705506647 0.000000e+00 2793.0
3 TraesCS6B01G442500 chr6B 88.263 2096 224 17 43 2124 705842494 705844581 0.000000e+00 2488.0
4 TraesCS6B01G442500 chr6B 86.148 2339 266 38 328 2632 705788802 705791116 0.000000e+00 2471.0
5 TraesCS6B01G442500 chr6B 86.105 2339 267 38 328 2632 706117253 706119567 0.000000e+00 2466.0
6 TraesCS6B01G442500 chr6B 87.948 2066 219 19 43 2097 705552387 705554433 0.000000e+00 2409.0
7 TraesCS6B01G442500 chr6B 85.537 2261 292 28 43 2282 705602436 705604682 0.000000e+00 2331.0
8 TraesCS6B01G442500 chr6B 85.443 2109 287 16 1 2097 705920470 705922570 0.000000e+00 2176.0
9 TraesCS6B01G442500 chr6B 89.951 617 33 4 2373 2989 705830805 705831392 0.000000e+00 769.0
10 TraesCS6B01G442500 chr6B 89.407 472 41 4 2425 2895 705506732 705507195 1.190000e-163 586.0
11 TraesCS6B01G442500 chr6B 90.847 437 32 6 2539 2974 705832463 705832892 2.000000e-161 579.0
12 TraesCS6B01G442500 chr6B 83.089 615 65 20 2391 2974 705508131 705508737 9.500000e-145 523.0
13 TraesCS6B01G442500 chr6B 87.788 434 43 5 2542 2974 706008160 706008584 1.600000e-137 499.0
14 TraesCS6B01G442500 chr6B 87.981 208 20 3 2153 2357 705638439 705638644 1.070000e-59 241.0
15 TraesCS6B01G442500 chr6B 89.474 171 17 1 2371 2540 705809579 705809749 6.490000e-52 215.0
16 TraesCS6B01G442500 chr6B 85.185 162 21 3 2366 2526 706001094 706001253 2.380000e-36 163.0
17 TraesCS6B01G442500 chr6B 85.093 161 23 1 2366 2526 706190445 706190604 2.380000e-36 163.0
18 TraesCS6B01G442500 chr6D 85.949 2128 275 18 1 2112 462857962 462860081 0.000000e+00 2252.0
19 TraesCS6B01G442500 chr6A 85.494 1620 176 33 744 2345 609576275 609577853 0.000000e+00 1635.0
20 TraesCS6B01G442500 chr6A 91.254 606 24 4 2368 2971 609743644 609744222 0.000000e+00 798.0
21 TraesCS6B01G442500 chr6A 87.908 612 53 13 2368 2974 609577942 609578537 0.000000e+00 701.0
22 TraesCS6B01G442500 chr6A 84.098 610 60 16 2393 2974 609638468 609639068 3.370000e-154 555.0
23 TraesCS6B01G442500 chr6A 83.197 613 66 18 2391 2974 609675821 609676425 7.340000e-146 527.0
24 TraesCS6B01G442500 chr6A 84.298 121 15 3 2107 2225 609638213 609638331 6.770000e-22 115.0
25 TraesCS6B01G442500 chr6A 81.579 114 20 1 1959 2071 609746733 609746846 3.170000e-15 93.5


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 TraesCS6B01G442500 chr6B 705940880 705943869 2989 False 5522.000000 5522 100.000000 1 2990 1 chr6B.!!$F9 2989
1 TraesCS6B01G442500 chr6B 705644409 705646504 2095 False 3223.000000 3223 94.434000 1 2097 1 chr6B.!!$F4 2096
2 TraesCS6B01G442500 chr6B 705842494 705844581 2087 False 2488.000000 2488 88.263000 43 2124 1 chr6B.!!$F7 2081
3 TraesCS6B01G442500 chr6B 705788802 705791116 2314 False 2471.000000 2471 86.148000 328 2632 1 chr6B.!!$F5 2304
4 TraesCS6B01G442500 chr6B 706117253 706119567 2314 False 2466.000000 2466 86.105000 328 2632 1 chr6B.!!$F12 2304
5 TraesCS6B01G442500 chr6B 705552387 705554433 2046 False 2409.000000 2409 87.948000 43 2097 1 chr6B.!!$F1 2054
6 TraesCS6B01G442500 chr6B 705602436 705604682 2246 False 2331.000000 2331 85.537000 43 2282 1 chr6B.!!$F2 2239
7 TraesCS6B01G442500 chr6B 705920470 705922570 2100 False 2176.000000 2176 85.443000 1 2097 1 chr6B.!!$F8 2096
8 TraesCS6B01G442500 chr6B 705504278 705508737 4459 False 1300.666667 2793 86.836333 1 2974 3 chr6B.!!$F14 2973
9 TraesCS6B01G442500 chr6B 705830805 705832892 2087 False 674.000000 769 90.399000 2373 2989 2 chr6B.!!$F15 616
10 TraesCS6B01G442500 chr6D 462857962 462860081 2119 False 2252.000000 2252 85.949000 1 2112 1 chr6D.!!$F1 2111
11 TraesCS6B01G442500 chr6A 609576275 609578537 2262 False 1168.000000 1635 86.701000 744 2974 2 chr6A.!!$F2 2230
12 TraesCS6B01G442500 chr6A 609675821 609676425 604 False 527.000000 527 83.197000 2391 2974 1 chr6A.!!$F1 583
13 TraesCS6B01G442500 chr6A 609743644 609746846 3202 False 445.750000 798 86.416500 1959 2971 2 chr6A.!!$F4 1012
14 TraesCS6B01G442500 chr6A 609638213 609639068 855 False 335.000000 555 84.198000 2107 2974 2 chr6A.!!$F3 867

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
227 234 0.032952 TAACTTCAACGGCGTGCTCT 59.967 50.0 15.7 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 2321 1.138859 TCCAATACAGACATCCAGCCG 59.861 52.381 0.0 0.0 0.0 5.52 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
23 24 0.324943 GCCTGTAGGAGTTGGAGCAA 59.675 55.000 1.17 0.00 37.39 3.91
41 42 6.493115 TGGAGCAATGAGTAATTTGAAAAGGA 59.507 34.615 0.00 0.00 0.00 3.36
145 152 2.549754 CAGCCATAATAACTTCAGCGGG 59.450 50.000 0.00 0.00 0.00 6.13
148 155 3.139077 CCATAATAACTTCAGCGGGGTC 58.861 50.000 0.00 0.00 0.00 4.46
177 184 6.804677 TGAAAGAACAATTTGCAAGCTTAGA 58.195 32.000 0.00 0.00 0.00 2.10
195 202 9.975218 AAGCTTAGAAAAATTAGAGGTATTGGA 57.025 29.630 0.00 0.00 0.00 3.53
206 213 8.958060 ATTAGAGGTATTGGATCTTAGCTACA 57.042 34.615 0.00 0.00 0.00 2.74
207 214 8.777578 TTAGAGGTATTGGATCTTAGCTACAA 57.222 34.615 0.00 0.00 0.00 2.41
208 215 7.863901 AGAGGTATTGGATCTTAGCTACAAT 57.136 36.000 10.36 10.36 36.00 2.71
209 216 8.958060 AGAGGTATTGGATCTTAGCTACAATA 57.042 34.615 8.79 8.79 34.08 1.90
210 217 9.381038 AGAGGTATTGGATCTTAGCTACAATAA 57.619 33.333 12.71 0.00 36.23 1.40
211 218 9.425577 GAGGTATTGGATCTTAGCTACAATAAC 57.574 37.037 16.00 16.00 40.32 1.89
212 219 9.160412 AGGTATTGGATCTTAGCTACAATAACT 57.840 33.333 18.82 18.82 43.45 2.24
213 220 9.780186 GGTATTGGATCTTAGCTACAATAACTT 57.220 33.333 16.29 0.00 38.21 2.66
216 223 9.905713 ATTGGATCTTAGCTACAATAACTTCAA 57.094 29.630 5.06 0.00 30.65 2.69
217 224 8.718102 TGGATCTTAGCTACAATAACTTCAAC 57.282 34.615 0.00 0.00 0.00 3.18
218 225 7.491372 TGGATCTTAGCTACAATAACTTCAACG 59.509 37.037 0.00 0.00 0.00 4.10
219 226 7.042658 GGATCTTAGCTACAATAACTTCAACGG 60.043 40.741 0.00 0.00 0.00 4.44
220 227 5.579511 TCTTAGCTACAATAACTTCAACGGC 59.420 40.000 0.00 0.00 0.00 5.68
221 228 2.671396 AGCTACAATAACTTCAACGGCG 59.329 45.455 4.80 4.80 0.00 6.46
222 229 2.414138 GCTACAATAACTTCAACGGCGT 59.586 45.455 6.77 6.77 0.00 5.68
223 230 2.961522 ACAATAACTTCAACGGCGTG 57.038 45.000 15.70 8.32 0.00 5.34
224 231 1.069500 ACAATAACTTCAACGGCGTGC 60.069 47.619 15.70 0.00 0.00 5.34
225 232 1.196808 CAATAACTTCAACGGCGTGCT 59.803 47.619 15.70 0.00 0.00 4.40
226 233 1.076332 ATAACTTCAACGGCGTGCTC 58.924 50.000 15.70 0.00 0.00 4.26
227 234 0.032952 TAACTTCAACGGCGTGCTCT 59.967 50.000 15.70 0.00 0.00 4.09
228 235 0.814010 AACTTCAACGGCGTGCTCTT 60.814 50.000 15.70 0.00 0.00 2.85
229 236 0.814010 ACTTCAACGGCGTGCTCTTT 60.814 50.000 15.70 0.00 0.00 2.52
230 237 1.144969 CTTCAACGGCGTGCTCTTTA 58.855 50.000 15.70 0.00 0.00 1.85
231 238 1.529438 CTTCAACGGCGTGCTCTTTAA 59.471 47.619 15.70 0.00 0.00 1.52
232 239 1.584175 TCAACGGCGTGCTCTTTAAA 58.416 45.000 15.70 0.00 0.00 1.52
233 240 1.529438 TCAACGGCGTGCTCTTTAAAG 59.471 47.619 15.70 9.04 0.00 1.85
234 241 1.529438 CAACGGCGTGCTCTTTAAAGA 59.471 47.619 15.70 16.85 0.00 2.52
235 242 1.873698 ACGGCGTGCTCTTTAAAGAA 58.126 45.000 13.76 2.52 34.03 2.52
236 243 1.529865 ACGGCGTGCTCTTTAAAGAAC 59.470 47.619 13.76 14.54 34.03 3.01
237 244 1.529438 CGGCGTGCTCTTTAAAGAACA 59.471 47.619 18.25 16.90 34.03 3.18
238 245 2.032377 CGGCGTGCTCTTTAAAGAACAA 60.032 45.455 20.05 6.49 33.37 2.83
239 246 3.364964 CGGCGTGCTCTTTAAAGAACAAT 60.365 43.478 20.05 0.00 33.37 2.71
240 247 4.546570 GGCGTGCTCTTTAAAGAACAATT 58.453 39.130 20.05 0.00 33.37 2.32
241 248 4.982295 GGCGTGCTCTTTAAAGAACAATTT 59.018 37.500 20.05 0.00 33.37 1.82
242 249 5.107875 GGCGTGCTCTTTAAAGAACAATTTG 60.108 40.000 20.05 12.54 33.37 2.32
243 250 5.610338 GCGTGCTCTTTAAAGAACAATTTGC 60.610 40.000 20.05 16.55 33.37 3.68
244 251 5.458452 CGTGCTCTTTAAAGAACAATTTGCA 59.542 36.000 20.05 18.56 33.37 4.08
245 252 6.019961 CGTGCTCTTTAAAGAACAATTTGCAA 60.020 34.615 20.05 0.00 33.37 4.08
246 253 7.339953 GTGCTCTTTAAAGAACAATTTGCAAG 58.660 34.615 20.05 5.78 33.37 4.01
247 254 6.018832 TGCTCTTTAAAGAACAATTTGCAAGC 60.019 34.615 16.95 12.86 34.03 4.01
248 255 6.201615 GCTCTTTAAAGAACAATTTGCAAGCT 59.798 34.615 18.25 0.00 34.03 3.74
249 256 7.254556 GCTCTTTAAAGAACAATTTGCAAGCTT 60.255 33.333 18.25 0.00 34.03 3.74
250 257 9.248291 CTCTTTAAAGAACAATTTGCAAGCTTA 57.752 29.630 18.25 0.00 34.03 3.09
251 258 9.248291 TCTTTAAAGAACAATTTGCAAGCTTAG 57.752 29.630 15.57 0.00 30.73 2.18
252 259 7.945033 TTAAAGAACAATTTGCAAGCTTAGG 57.055 32.000 0.00 0.00 0.00 2.69
253 260 3.917988 AGAACAATTTGCAAGCTTAGGC 58.082 40.909 0.00 0.00 39.06 3.93
254 261 3.321682 AGAACAATTTGCAAGCTTAGGCA 59.678 39.130 7.34 7.34 41.70 4.75
262 269 4.970662 TGCAAGCTTAGGCAAATTAGAG 57.029 40.909 8.89 0.00 41.70 2.43
263 270 3.696051 TGCAAGCTTAGGCAAATTAGAGG 59.304 43.478 8.89 0.00 41.70 3.69
264 271 3.696548 GCAAGCTTAGGCAAATTAGAGGT 59.303 43.478 0.00 0.00 41.70 3.85
265 272 4.881850 GCAAGCTTAGGCAAATTAGAGGTA 59.118 41.667 0.00 0.00 41.70 3.08
266 273 5.532779 GCAAGCTTAGGCAAATTAGAGGTAT 59.467 40.000 0.00 0.00 41.70 2.73
267 274 6.039829 GCAAGCTTAGGCAAATTAGAGGTATT 59.960 38.462 0.00 0.00 41.70 1.89
268 275 7.420800 CAAGCTTAGGCAAATTAGAGGTATTG 58.579 38.462 0.00 0.00 41.70 1.90
269 276 6.064717 AGCTTAGGCAAATTAGAGGTATTGG 58.935 40.000 0.00 0.00 41.70 3.16
321 403 5.006941 TGCTCTTCAAAGAAAATTTTGCAGC 59.993 36.000 8.47 4.13 37.83 5.25
386 543 2.238084 TGGTGTGCTCATAGAGGAGT 57.762 50.000 0.00 0.00 37.24 3.85
393 550 6.109359 GTGTGCTCATAGAGGAGTATTTTGT 58.891 40.000 0.00 0.00 37.24 2.83
645 802 1.690352 AGCTTCAACCTTGCAAGCATT 59.310 42.857 21.43 13.97 40.50 3.56
718 875 9.480861 TCAGCTGAGTATATATATATATGGGGC 57.519 37.037 20.93 16.68 31.69 5.80
731 888 4.765195 ATATGGGGCCCAATAAGTTGAT 57.235 40.909 32.57 12.50 36.95 2.57
797 954 7.225734 GGACCTATCTTCAAACTCTTTATCTGC 59.774 40.741 0.00 0.00 0.00 4.26
987 1144 5.258841 TCTGATGCAAACTCCAGAAATCAT 58.741 37.500 0.00 0.00 33.26 2.45
1290 1450 6.019559 GGTCTTTGTCAAACTTGAAAGCAATC 60.020 38.462 0.00 0.00 39.21 2.67
1322 1482 3.389687 GTCGCATGACACGAATGATTT 57.610 42.857 0.00 0.00 44.82 2.17
1328 1488 4.795278 GCATGACACGAATGATTTCTTTCC 59.205 41.667 0.00 0.00 0.00 3.13
1764 1924 0.800631 ACTGCTCAACACATGATGCG 59.199 50.000 0.00 0.00 37.44 4.73
1786 1946 3.190118 GGAGCAAAGTGACCTTGAAGATG 59.810 47.826 0.00 0.00 0.00 2.90
1847 2007 0.850100 TTTGTGGTGGGTCTGTGGAT 59.150 50.000 0.00 0.00 0.00 3.41
1967 2127 0.543277 TGGGCTCACATGATGGAGAC 59.457 55.000 12.96 10.49 38.49 3.36
2011 2171 1.963515 GTGCCCAATTCCTGTGAAAGT 59.036 47.619 0.00 0.00 33.32 2.66
2071 2314 6.708054 CCATGTCCCTATTTGTAGCTCTAAAG 59.292 42.308 0.00 0.00 0.00 1.85
2094 2337 2.827800 CATCGGCTGGATGTCTGTAT 57.172 50.000 9.31 0.00 46.14 2.29
2097 2340 1.138859 TCGGCTGGATGTCTGTATTGG 59.861 52.381 0.00 0.00 0.00 3.16
2140 3912 6.617784 TGAACCATATCTCTATTTGTACCCCA 59.382 38.462 0.00 0.00 0.00 4.96
2144 3916 8.511126 ACCATATCTCTATTTGTACCCCAAAAT 58.489 33.333 0.00 0.00 45.72 1.82
2172 3944 2.300723 TGGCTGGACGTTTGTACTGTAT 59.699 45.455 0.00 0.00 30.88 2.29
2176 3948 4.377022 GCTGGACGTTTGTACTGTATTGTG 60.377 45.833 0.00 0.00 30.88 3.33
2177 3949 3.495377 TGGACGTTTGTACTGTATTGTGC 59.505 43.478 0.00 0.00 0.00 4.57
2188 3960 7.757526 TGTACTGTATTGTGCATTGGTATTTC 58.242 34.615 0.00 0.00 0.00 2.17
2232 4004 6.513806 TGAAGTGTATGCATATGTTTTGCT 57.486 33.333 10.16 0.00 40.77 3.91
2255 4027 6.144563 GCTGGATTGTTTAAGCTGAAGAAAAC 59.855 38.462 0.00 0.00 32.82 2.43
2312 4085 5.578727 TCATGTTGTTTGGTTTGCTTTGTAC 59.421 36.000 0.00 0.00 0.00 2.90
2321 4094 5.381757 TGGTTTGCTTTGTACCATCTACTT 58.618 37.500 0.00 0.00 37.04 2.24
2345 4118 5.525012 TCCAGAGAGTGATAATTCATTTGCG 59.475 40.000 0.00 0.00 33.56 4.85
2350 4123 5.050769 AGAGTGATAATTCATTTGCGTAGCG 60.051 40.000 0.00 0.00 46.79 4.26
2436 4289 2.440409 TCTGAAGCTTCCATTTCAGCC 58.560 47.619 23.42 0.00 46.19 4.85
2444 4297 4.646492 AGCTTCCATTTCAGCCGATATTTT 59.354 37.500 0.00 0.00 36.62 1.82
2731 6086 9.448438 AAGTGTATGCAGTATAAAATTCACTGA 57.552 29.630 5.19 0.00 41.80 3.41
2765 6120 9.185192 GATGGACATTTAGAACAAAGAAACAAG 57.815 33.333 0.00 0.00 0.00 3.16
2789 6145 2.530497 GCAGTCACAAACCGCGTCA 61.530 57.895 4.92 0.00 0.00 4.35
2790 6146 1.841663 GCAGTCACAAACCGCGTCAT 61.842 55.000 4.92 0.00 0.00 3.06
2791 6147 1.424403 CAGTCACAAACCGCGTCATA 58.576 50.000 4.92 0.00 0.00 2.15
2792 6148 1.126113 CAGTCACAAACCGCGTCATAC 59.874 52.381 4.92 0.00 0.00 2.39
2793 6149 1.000506 AGTCACAAACCGCGTCATACT 59.999 47.619 4.92 0.00 0.00 2.12
2794 6150 1.389106 GTCACAAACCGCGTCATACTC 59.611 52.381 4.92 0.00 0.00 2.59
2795 6151 1.000052 TCACAAACCGCGTCATACTCA 60.000 47.619 4.92 0.00 0.00 3.41
2806 6162 3.372206 GCGTCATACTCATATCCCATTGC 59.628 47.826 0.00 0.00 0.00 3.56
2810 6166 5.769662 GTCATACTCATATCCCATTGCCAAA 59.230 40.000 0.00 0.00 0.00 3.28
2820 6176 2.352323 CCCATTGCCAAAACTAACGTCC 60.352 50.000 0.00 0.00 0.00 4.79
2900 6256 8.041323 TCAAAACCACCATTTAAACTTTGCTTA 58.959 29.630 0.00 0.00 0.00 3.09
2949 6306 3.250040 AGACATTTTGGTCTTCGGTTTCG 59.750 43.478 0.00 0.00 45.59 3.46
2962 6319 0.865769 GGTTTCGTGCGAACTCACAT 59.134 50.000 6.52 0.00 36.80 3.21
2982 8017 8.445275 TCACATACTTAAAACATGACACACTT 57.555 30.769 0.00 0.00 0.00 3.16
2983 8018 9.549078 TCACATACTTAAAACATGACACACTTA 57.451 29.630 0.00 0.00 0.00 2.24
2984 8019 9.811655 CACATACTTAAAACATGACACACTTAG 57.188 33.333 0.00 0.00 0.00 2.18
2985 8020 9.772973 ACATACTTAAAACATGACACACTTAGA 57.227 29.630 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 7.184862 AGGTCCATCCTTTTCAAATTACTCAT 58.815 34.615 0.00 0.00 45.67 2.90
41 42 7.016153 TGAAGTTATTGTAGTTGAGGTCCAT 57.984 36.000 0.00 0.00 0.00 3.41
51 52 4.212636 GCACACCGTTGAAGTTATTGTAGT 59.787 41.667 0.00 0.00 0.00 2.73
130 137 2.433239 GAGGACCCCGCTGAAGTTATTA 59.567 50.000 0.00 0.00 0.00 0.98
145 152 4.984785 GCAAATTGTTCTTTCAAGAGGACC 59.015 41.667 0.00 0.00 36.22 4.46
148 155 5.050567 GCTTGCAAATTGTTCTTTCAAGAGG 60.051 40.000 0.00 0.00 36.22 3.69
195 202 6.258068 GCCGTTGAAGTTATTGTAGCTAAGAT 59.742 38.462 0.00 0.00 0.00 2.40
196 203 5.579511 GCCGTTGAAGTTATTGTAGCTAAGA 59.420 40.000 0.00 0.00 0.00 2.10
197 204 5.500290 CGCCGTTGAAGTTATTGTAGCTAAG 60.500 44.000 0.00 0.00 0.00 2.18
198 205 4.327898 CGCCGTTGAAGTTATTGTAGCTAA 59.672 41.667 0.00 0.00 0.00 3.09
199 206 3.861113 CGCCGTTGAAGTTATTGTAGCTA 59.139 43.478 0.00 0.00 0.00 3.32
200 207 2.671396 CGCCGTTGAAGTTATTGTAGCT 59.329 45.455 0.00 0.00 0.00 3.32
201 208 2.414138 ACGCCGTTGAAGTTATTGTAGC 59.586 45.455 0.00 0.00 0.00 3.58
202 209 3.723835 GCACGCCGTTGAAGTTATTGTAG 60.724 47.826 0.00 0.00 0.00 2.74
203 210 2.158058 GCACGCCGTTGAAGTTATTGTA 59.842 45.455 0.00 0.00 0.00 2.41
204 211 1.069500 GCACGCCGTTGAAGTTATTGT 60.069 47.619 0.00 0.00 0.00 2.71
205 212 1.196808 AGCACGCCGTTGAAGTTATTG 59.803 47.619 0.00 0.00 0.00 1.90
206 213 1.463444 GAGCACGCCGTTGAAGTTATT 59.537 47.619 0.00 0.00 0.00 1.40
207 214 1.076332 GAGCACGCCGTTGAAGTTAT 58.924 50.000 0.00 0.00 0.00 1.89
208 215 0.032952 AGAGCACGCCGTTGAAGTTA 59.967 50.000 0.00 0.00 0.00 2.24
209 216 0.814010 AAGAGCACGCCGTTGAAGTT 60.814 50.000 0.00 0.00 0.00 2.66
210 217 0.814010 AAAGAGCACGCCGTTGAAGT 60.814 50.000 0.00 0.00 0.00 3.01
211 218 1.144969 TAAAGAGCACGCCGTTGAAG 58.855 50.000 0.00 0.00 0.00 3.02
212 219 1.584175 TTAAAGAGCACGCCGTTGAA 58.416 45.000 0.00 0.00 0.00 2.69
213 220 1.529438 CTTTAAAGAGCACGCCGTTGA 59.471 47.619 9.77 0.00 0.00 3.18
214 221 1.529438 TCTTTAAAGAGCACGCCGTTG 59.471 47.619 13.99 0.00 0.00 4.10
215 222 1.873698 TCTTTAAAGAGCACGCCGTT 58.126 45.000 13.99 0.00 0.00 4.44
216 223 1.529865 GTTCTTTAAAGAGCACGCCGT 59.470 47.619 22.72 0.00 36.42 5.68
217 224 1.529438 TGTTCTTTAAAGAGCACGCCG 59.471 47.619 25.44 0.00 40.62 6.46
218 225 3.619233 TTGTTCTTTAAAGAGCACGCC 57.381 42.857 28.02 10.66 44.30 5.68
219 226 5.610338 GCAAATTGTTCTTTAAAGAGCACGC 60.610 40.000 28.02 23.11 44.30 5.34
220 227 5.458452 TGCAAATTGTTCTTTAAAGAGCACG 59.542 36.000 28.02 19.03 44.30 5.34
221 228 6.826893 TGCAAATTGTTCTTTAAAGAGCAC 57.173 33.333 28.02 19.70 44.30 4.40
222 229 6.018832 GCTTGCAAATTGTTCTTTAAAGAGCA 60.019 34.615 25.44 25.44 43.20 4.26
223 230 6.201615 AGCTTGCAAATTGTTCTTTAAAGAGC 59.798 34.615 21.36 21.36 36.22 4.09
224 231 7.704789 AGCTTGCAAATTGTTCTTTAAAGAG 57.295 32.000 17.05 6.09 36.22 2.85
225 232 9.248291 CTAAGCTTGCAAATTGTTCTTTAAAGA 57.752 29.630 13.99 13.99 0.00 2.52
226 233 8.490355 CCTAAGCTTGCAAATTGTTCTTTAAAG 58.510 33.333 9.86 9.04 0.00 1.85
227 234 7.042119 GCCTAAGCTTGCAAATTGTTCTTTAAA 60.042 33.333 9.86 0.00 35.50 1.52
228 235 6.423604 GCCTAAGCTTGCAAATTGTTCTTTAA 59.576 34.615 9.86 0.00 35.50 1.52
229 236 5.925969 GCCTAAGCTTGCAAATTGTTCTTTA 59.074 36.000 9.86 0.00 35.50 1.85
230 237 4.751600 GCCTAAGCTTGCAAATTGTTCTTT 59.248 37.500 9.86 0.00 35.50 2.52
231 238 4.202243 TGCCTAAGCTTGCAAATTGTTCTT 60.202 37.500 9.86 0.46 40.80 2.52
232 239 3.321682 TGCCTAAGCTTGCAAATTGTTCT 59.678 39.130 9.86 0.00 40.80 3.01
233 240 3.652274 TGCCTAAGCTTGCAAATTGTTC 58.348 40.909 9.86 0.00 40.80 3.18
234 241 3.749665 TGCCTAAGCTTGCAAATTGTT 57.250 38.095 9.86 0.00 40.80 2.83
235 242 3.749665 TTGCCTAAGCTTGCAAATTGT 57.250 38.095 18.79 0.00 43.94 2.71
240 247 4.158394 CCTCTAATTTGCCTAAGCTTGCAA 59.842 41.667 17.56 17.56 45.12 4.08
241 248 3.696051 CCTCTAATTTGCCTAAGCTTGCA 59.304 43.478 9.86 8.44 40.80 4.08
242 249 3.696548 ACCTCTAATTTGCCTAAGCTTGC 59.303 43.478 9.86 5.41 40.80 4.01
243 250 7.420800 CAATACCTCTAATTTGCCTAAGCTTG 58.579 38.462 9.86 0.00 40.80 4.01
244 251 6.547510 CCAATACCTCTAATTTGCCTAAGCTT 59.452 38.462 3.48 3.48 40.80 3.74
245 252 6.064717 CCAATACCTCTAATTTGCCTAAGCT 58.935 40.000 0.00 0.00 40.80 3.74
246 253 6.017026 GTCCAATACCTCTAATTTGCCTAAGC 60.017 42.308 0.00 0.00 40.48 3.09
247 254 7.283329 AGTCCAATACCTCTAATTTGCCTAAG 58.717 38.462 0.00 0.00 0.00 2.18
248 255 7.208064 AGTCCAATACCTCTAATTTGCCTAA 57.792 36.000 0.00 0.00 0.00 2.69
249 256 6.824958 AGTCCAATACCTCTAATTTGCCTA 57.175 37.500 0.00 0.00 0.00 3.93
250 257 5.717119 AGTCCAATACCTCTAATTTGCCT 57.283 39.130 0.00 0.00 0.00 4.75
251 258 5.885912 TGAAGTCCAATACCTCTAATTTGCC 59.114 40.000 0.00 0.00 0.00 4.52
252 259 6.458888 GCTGAAGTCCAATACCTCTAATTTGC 60.459 42.308 0.00 0.00 0.00 3.68
253 260 6.038714 GGCTGAAGTCCAATACCTCTAATTTG 59.961 42.308 0.00 0.00 0.00 2.32
254 261 6.122964 GGCTGAAGTCCAATACCTCTAATTT 58.877 40.000 0.00 0.00 0.00 1.82
255 262 5.191722 TGGCTGAAGTCCAATACCTCTAATT 59.808 40.000 0.00 0.00 0.00 1.40
256 263 4.721776 TGGCTGAAGTCCAATACCTCTAAT 59.278 41.667 0.00 0.00 0.00 1.73
257 264 4.081087 GTGGCTGAAGTCCAATACCTCTAA 60.081 45.833 0.00 0.00 35.01 2.10
258 265 3.451178 GTGGCTGAAGTCCAATACCTCTA 59.549 47.826 0.00 0.00 35.01 2.43
259 266 2.237392 GTGGCTGAAGTCCAATACCTCT 59.763 50.000 0.00 0.00 35.01 3.69
260 267 2.027192 TGTGGCTGAAGTCCAATACCTC 60.027 50.000 0.00 0.00 35.01 3.85
261 268 1.985159 TGTGGCTGAAGTCCAATACCT 59.015 47.619 0.00 0.00 35.01 3.08
262 269 2.489938 TGTGGCTGAAGTCCAATACC 57.510 50.000 0.00 0.00 35.01 2.73
263 270 5.648092 AGTTATTGTGGCTGAAGTCCAATAC 59.352 40.000 5.75 0.00 35.01 1.89
264 271 5.815581 AGTTATTGTGGCTGAAGTCCAATA 58.184 37.500 0.00 0.00 35.01 1.90
265 272 4.666512 AGTTATTGTGGCTGAAGTCCAAT 58.333 39.130 4.71 4.71 35.01 3.16
266 273 4.098914 AGTTATTGTGGCTGAAGTCCAA 57.901 40.909 0.00 0.00 35.01 3.53
267 274 3.788227 AGTTATTGTGGCTGAAGTCCA 57.212 42.857 0.00 0.00 0.00 4.02
268 275 4.072131 TGAAGTTATTGTGGCTGAAGTCC 58.928 43.478 0.00 0.00 0.00 3.85
269 276 4.378874 GCTGAAGTTATTGTGGCTGAAGTC 60.379 45.833 0.00 0.00 0.00 3.01
321 403 7.753580 GGTCCAATCGTTTTAAATGACCTAAAG 59.246 37.037 1.35 0.00 0.00 1.85
393 550 8.807118 CCAGATACTCTAAATACAATAGCCTCA 58.193 37.037 0.00 0.00 0.00 3.86
570 727 7.776618 ATAACATCATCCAGATTTGCATCAT 57.223 32.000 0.00 0.00 33.72 2.45
645 802 4.724399 TGAGCCACTCAATTTGTTTCCTA 58.276 39.130 0.00 0.00 37.57 2.94
710 867 4.765195 ATCAACTTATTGGGCCCCATAT 57.235 40.909 22.27 12.86 36.39 1.78
711 868 4.044065 CCTATCAACTTATTGGGCCCCATA 59.956 45.833 22.27 16.44 36.39 2.74
712 869 3.181418 CCTATCAACTTATTGGGCCCCAT 60.181 47.826 22.27 17.73 36.39 4.00
718 875 6.318900 GGAACTTGACCTATCAACTTATTGGG 59.681 42.308 0.00 0.00 40.01 4.12
731 888 2.486548 GGCAACTGTGGAACTTGACCTA 60.487 50.000 0.00 0.00 38.04 3.08
797 954 0.533531 TAGCTCTGATGGCAATGGCG 60.534 55.000 1.51 0.00 42.47 5.69
1290 1450 2.042259 ATGCGACACCACTGCCATG 61.042 57.895 0.00 0.00 0.00 3.66
1322 1482 2.503356 GGGATGCTCTCTTCAGGAAAGA 59.497 50.000 0.00 0.00 41.81 2.52
1328 1488 4.100653 TGATTACTGGGATGCTCTCTTCAG 59.899 45.833 0.00 0.00 33.99 3.02
1479 1639 8.137437 CCTGTGAGTTGATTATTTGACAAGTTT 58.863 33.333 0.00 0.00 0.00 2.66
1764 1924 2.851195 TCTTCAAGGTCACTTTGCTCC 58.149 47.619 0.00 0.00 33.81 4.70
1786 1946 9.664332 AAGATAAACAGATGGCATATGATCTAC 57.336 33.333 27.33 14.75 0.00 2.59
1847 2007 5.069318 TCATCAACATGGTGCAGAAAACTA 58.931 37.500 5.66 0.00 0.00 2.24
1967 2127 1.667236 TGGTGCACTGTCTTGAGTTG 58.333 50.000 17.98 0.00 0.00 3.16
2076 2319 2.224378 CCAATACAGACATCCAGCCGAT 60.224 50.000 0.00 0.00 0.00 4.18
2078 2321 1.138859 TCCAATACAGACATCCAGCCG 59.861 52.381 0.00 0.00 0.00 5.52
2094 2337 9.482627 GGTTCAAACATACAAATAACAATCCAA 57.517 29.630 0.00 0.00 0.00 3.53
2117 2365 7.460214 TTGGGGTACAAATAGAGATATGGTT 57.540 36.000 0.00 0.00 35.79 3.67
2172 3944 8.978874 ATAGACATAGAAATACCAATGCACAA 57.021 30.769 0.00 0.00 0.00 3.33
2203 3975 9.709495 AAAACATATGCATACACTTCATTTGTT 57.291 25.926 8.99 9.37 41.02 2.83
2214 3986 6.127394 ACAATCCAGCAAAACATATGCATACA 60.127 34.615 8.99 0.00 46.22 2.29
2219 3991 7.593875 TTAAACAATCCAGCAAAACATATGC 57.406 32.000 1.58 0.00 44.15 3.14
2220 3992 7.546667 AGCTTAAACAATCCAGCAAAACATATG 59.453 33.333 0.00 0.00 34.49 1.78
2232 4004 7.106439 TGTTTTCTTCAGCTTAAACAATCCA 57.894 32.000 0.00 0.00 37.50 3.41
2312 4085 6.968263 TTATCACTCTCTGGAAGTAGATGG 57.032 41.667 0.00 0.00 33.76 3.51
2321 4094 5.525012 CGCAAATGAATTATCACTCTCTGGA 59.475 40.000 0.00 0.00 38.69 3.86
2353 4126 0.109723 TCTACCAACAGGCGCCTTTT 59.890 50.000 30.60 25.89 0.00 2.27
2357 4130 1.923227 GCTTTCTACCAACAGGCGCC 61.923 60.000 21.89 21.89 0.00 6.53
2358 4131 0.955919 AGCTTTCTACCAACAGGCGC 60.956 55.000 0.00 0.00 0.00 6.53
2359 4132 1.079503 GAGCTTTCTACCAACAGGCG 58.920 55.000 0.00 0.00 0.00 5.52
2362 4135 4.212214 GTGAACAGAGCTTTCTACCAACAG 59.788 45.833 0.00 0.00 0.00 3.16
2363 4136 4.127171 GTGAACAGAGCTTTCTACCAACA 58.873 43.478 0.00 0.00 0.00 3.33
2364 4137 3.498777 GGTGAACAGAGCTTTCTACCAAC 59.501 47.826 10.72 0.00 30.62 3.77
2365 4138 3.135712 TGGTGAACAGAGCTTTCTACCAA 59.864 43.478 13.78 4.12 34.25 3.67
2436 4289 7.032580 TGCCTCACCAAAATACAAAAATATCG 58.967 34.615 0.00 0.00 0.00 2.92
2444 4297 4.404073 ACAGTTTGCCTCACCAAAATACAA 59.596 37.500 0.00 0.00 36.55 2.41
2731 6086 5.653330 TGTTCTAAATGTCCATCATGCACAT 59.347 36.000 0.00 0.00 36.81 3.21
2789 6145 6.376248 AGTTTTGGCAATGGGATATGAGTAT 58.624 36.000 0.00 0.00 0.00 2.12
2790 6146 5.765510 AGTTTTGGCAATGGGATATGAGTA 58.234 37.500 0.00 0.00 0.00 2.59
2791 6147 4.613437 AGTTTTGGCAATGGGATATGAGT 58.387 39.130 0.00 0.00 0.00 3.41
2792 6148 6.507023 GTTAGTTTTGGCAATGGGATATGAG 58.493 40.000 0.00 0.00 0.00 2.90
2793 6149 5.067153 CGTTAGTTTTGGCAATGGGATATGA 59.933 40.000 0.00 0.00 0.00 2.15
2794 6150 5.163561 ACGTTAGTTTTGGCAATGGGATATG 60.164 40.000 0.00 0.00 0.00 1.78
2795 6151 4.953579 ACGTTAGTTTTGGCAATGGGATAT 59.046 37.500 0.00 0.00 0.00 1.63
2806 6162 5.406175 TGAAGATTACGGACGTTAGTTTTGG 59.594 40.000 1.57 0.00 0.00 3.28
2810 6166 4.082354 AGCTGAAGATTACGGACGTTAGTT 60.082 41.667 1.57 0.00 0.00 2.24
2820 6176 9.088512 AGACAAGTTTAATAGCTGAAGATTACG 57.911 33.333 0.00 0.00 0.00 3.18
2848 6204 3.328535 ACAACTGAACATTTCCCCCTT 57.671 42.857 0.00 0.00 0.00 3.95
2900 6256 4.261801 CAGTTCATCCGATTTTACCCTGT 58.738 43.478 0.00 0.00 0.00 4.00
2949 6306 5.981174 TGTTTTAAGTATGTGAGTTCGCAC 58.019 37.500 0.00 0.03 39.39 5.34


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

AutoCloner maintained by Alex Coulton.