Multiple sequence alignment - TraesCS6B01G284300

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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 TraesCS6B01G284300 chr6B 100.000 2781 0 0 1 2781 512449327 512446547 0.000000e+00 5136.0
1 TraesCS6B01G284300 chr6D 89.303 2440 119 53 222 2601 314055355 314057712 0.000000e+00 2929.0
2 TraesCS6B01G284300 chr6D 88.333 120 9 3 1 117 314055048 314055165 3.730000e-29 139.0
3 TraesCS6B01G284300 chr6D 100.000 28 0 0 117 144 314055179 314055206 5.000000e-03 52.8
4 TraesCS6B01G284300 chr6A 86.007 1951 99 84 280 2169 451659248 451661085 0.000000e+00 1930.0
5 TraesCS6B01G284300 chr6A 86.926 566 37 14 2218 2781 451661096 451661626 3.960000e-168 601.0
6 TraesCS6B01G284300 chr6A 94.828 58 3 0 1 58 451603294 451603351 1.060000e-14 91.6
7 TraesCS6B01G284300 chr6A 95.556 45 0 2 221 263 451659210 451659254 1.380000e-08 71.3
8 TraesCS6B01G284300 chr2D 90.288 278 27 0 1117 1394 492676514 492676791 5.660000e-97 364.0
9 TraesCS6B01G284300 chr2B 89.531 277 29 0 1117 1393 578605289 578605565 4.410000e-93 351.0
10 TraesCS6B01G284300 chr2A 89.531 277 29 0 1117 1393 637984701 637984977 4.410000e-93 351.0
11 TraesCS6B01G284300 chr4D 80.612 196 31 7 1114 1307 457075098 457075288 8.030000e-31 145.0
12 TraesCS6B01G284300 chr4D 100.000 29 0 0 1202 1230 132218614 132218642 1.000000e-03 54.7
13 TraesCS6B01G284300 chr4A 100.000 29 0 0 1202 1230 430071526 430071498 1.000000e-03 54.7


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 TraesCS6B01G284300 chr6B 512446547 512449327 2780 True 5136.000000 5136 100.000000 1 2781 1 chr6B.!!$R1 2780
1 TraesCS6B01G284300 chr6D 314055048 314057712 2664 False 1040.266667 2929 92.545333 1 2601 3 chr6D.!!$F1 2600
2 TraesCS6B01G284300 chr6A 451659210 451661626 2416 False 867.433333 1930 89.496333 221 2781 3 chr6A.!!$F2 2560

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
214 297 0.039764 AGTCCACCTGATCGACTGGA 59.960 55.0 14.58 0.96 40.23 3.86 F
1406 1563 0.306533 CAGGTAACCAACACACGCAC 59.693 55.0 0.00 0.00 37.17 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 1869 0.037590 GTGCAGGTCAACCCCATACA 59.962 55.0 0.0 0.0 36.42 2.29 R
2538 2730 0.314302 AGGTGAGTGAGTCGTTTCCG 59.686 55.0 0.0 0.0 0.00 4.30 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
69 70 9.174166 ACGTCAGCTAGGTTTTCATTTATAAAT 57.826 29.630 4.81 4.81 0.00 1.40
91 95 4.531659 ACGTCAGTGTTCTTTAGCAAAC 57.468 40.909 0.00 0.00 0.00 2.93
95 99 5.198274 GTCAGTGTTCTTTAGCAAACGAAG 58.802 41.667 0.00 0.00 0.00 3.79
97 101 5.583061 TCAGTGTTCTTTAGCAAACGAAGAA 59.417 36.000 0.00 0.00 37.14 2.52
104 108 5.583061 TCTTTAGCAAACGAAGAACTTGACA 59.417 36.000 0.00 0.00 0.00 3.58
144 162 0.166814 CGCCAGCTTGCTCTTTGTAC 59.833 55.000 8.31 0.00 0.00 2.90
145 163 1.528129 GCCAGCTTGCTCTTTGTACT 58.472 50.000 1.78 0.00 0.00 2.73
150 233 4.808364 CCAGCTTGCTCTTTGTACTCTATC 59.192 45.833 0.00 0.00 0.00 2.08
161 244 9.462174 CTCTTTGTACTCTATCTAAGCAGATTG 57.538 37.037 0.00 0.00 41.84 2.67
163 246 9.243637 CTTTGTACTCTATCTAAGCAGATTGAC 57.756 37.037 0.00 0.00 41.84 3.18
170 253 4.193826 TCTAAGCAGATTGACAGTCCAC 57.806 45.455 0.00 0.00 0.00 4.02
174 257 1.002430 GCAGATTGACAGTCCACCTGA 59.998 52.381 0.00 0.00 44.49 3.86
175 258 2.355513 GCAGATTGACAGTCCACCTGAT 60.356 50.000 0.00 0.00 44.49 2.90
176 259 3.529533 CAGATTGACAGTCCACCTGATC 58.470 50.000 0.00 0.00 44.49 2.92
187 270 0.099613 CACCTGATCGACTGGAGACG 59.900 60.000 14.58 0.00 40.23 4.18
188 271 1.032657 ACCTGATCGACTGGAGACGG 61.033 60.000 14.58 0.00 44.60 4.79
189 272 0.748367 CCTGATCGACTGGAGACGGA 60.748 60.000 0.00 0.00 41.09 4.69
190 273 1.313772 CTGATCGACTGGAGACGGAT 58.686 55.000 0.00 0.00 41.09 4.18
191 274 2.495084 CTGATCGACTGGAGACGGATA 58.505 52.381 0.00 0.00 41.09 2.59
192 275 2.879026 CTGATCGACTGGAGACGGATAA 59.121 50.000 0.00 0.00 41.09 1.75
193 276 3.284617 TGATCGACTGGAGACGGATAAA 58.715 45.455 0.00 0.00 41.09 1.40
194 277 3.066342 TGATCGACTGGAGACGGATAAAC 59.934 47.826 0.00 0.00 41.09 2.01
195 278 2.439409 TCGACTGGAGACGGATAAACA 58.561 47.619 0.00 0.00 41.09 2.83
196 279 2.422479 TCGACTGGAGACGGATAAACAG 59.578 50.000 0.00 0.00 41.09 3.16
197 280 2.163815 CGACTGGAGACGGATAAACAGT 59.836 50.000 0.00 0.00 41.40 3.55
198 281 3.731264 CGACTGGAGACGGATAAACAGTC 60.731 52.174 11.43 11.43 46.78 3.51
201 284 2.232941 TGGAGACGGATAAACAGTCCAC 59.767 50.000 0.00 0.00 42.94 4.02
202 285 2.418334 GGAGACGGATAAACAGTCCACC 60.418 54.545 0.00 0.00 42.94 4.61
203 286 2.496470 GAGACGGATAAACAGTCCACCT 59.504 50.000 0.00 0.00 42.94 4.00
205 288 2.232941 GACGGATAAACAGTCCACCTGA 59.767 50.000 0.00 0.00 44.49 3.86
207 290 3.118738 ACGGATAAACAGTCCACCTGATC 60.119 47.826 0.00 0.00 44.49 2.92
208 291 3.458189 GGATAAACAGTCCACCTGATCG 58.542 50.000 0.00 0.00 44.49 3.69
209 292 3.132289 GGATAAACAGTCCACCTGATCGA 59.868 47.826 0.00 0.00 44.49 3.59
210 293 2.457366 AAACAGTCCACCTGATCGAC 57.543 50.000 0.00 0.00 44.49 4.20
211 294 1.633774 AACAGTCCACCTGATCGACT 58.366 50.000 0.00 0.00 44.49 4.18
212 295 3.729356 CAGTCCACCTGATCGACTG 57.271 57.895 11.66 11.66 45.33 3.51
213 296 0.174389 CAGTCCACCTGATCGACTGG 59.826 60.000 15.89 7.63 46.32 4.00
214 297 0.039764 AGTCCACCTGATCGACTGGA 59.960 55.000 14.58 0.96 40.23 3.86
215 298 0.457851 GTCCACCTGATCGACTGGAG 59.542 60.000 14.58 8.71 40.23 3.86
216 299 0.684479 TCCACCTGATCGACTGGAGG 60.684 60.000 15.46 15.46 44.87 4.30
217 300 1.142748 CACCTGATCGACTGGAGGC 59.857 63.158 14.58 0.00 40.23 4.70
219 302 1.326213 ACCTGATCGACTGGAGGCAG 61.326 60.000 14.58 0.00 40.23 4.85
220 303 1.326213 CCTGATCGACTGGAGGCAGT 61.326 60.000 0.00 0.00 39.52 4.40
223 312 1.103803 GATCGACTGGAGGCAGTACA 58.896 55.000 0.00 0.00 35.23 2.90
259 349 1.148310 GTCTAGCACAACGCACATGT 58.852 50.000 0.00 0.00 46.13 3.21
263 353 1.807139 AGCACAACGCACATGTATCA 58.193 45.000 0.00 0.00 46.13 2.15
269 359 0.806102 ACGCACATGTATCAGTCGGC 60.806 55.000 0.00 0.00 0.00 5.54
417 522 4.962362 GGAATTCTCCTCTCCTCTCTTCTT 59.038 45.833 5.23 0.00 38.88 2.52
430 535 2.048222 TTCTTGCCGAGCCGTCAG 60.048 61.111 0.00 0.00 0.00 3.51
431 536 2.771763 CTTCTTGCCGAGCCGTCAGT 62.772 60.000 0.00 0.00 0.00 3.41
432 537 3.114616 CTTGCCGAGCCGTCAGTG 61.115 66.667 0.00 0.00 0.00 3.66
524 645 0.462759 CCACCTCGGCATCTCTTTCC 60.463 60.000 0.00 0.00 0.00 3.13
577 698 2.697761 GGACGCTGTCGACCTAGCA 61.698 63.158 23.00 0.94 44.89 3.49
578 699 1.226435 GACGCTGTCGACCTAGCAG 60.226 63.158 23.00 18.04 39.87 4.24
639 762 5.173854 CGAACATTTCCTTCTTGAACAAAGC 59.826 40.000 0.00 0.00 35.69 3.51
686 822 3.917300 AGAGAGAGGATAACCATTCCGT 58.083 45.455 0.00 0.00 38.36 4.69
978 1131 4.703645 TCTGTCTCTGACGATTCGATTT 57.296 40.909 13.95 0.00 34.95 2.17
980 1133 3.426323 TGTCTCTGACGATTCGATTTCG 58.574 45.455 13.95 14.55 42.20 3.46
981 1134 2.784380 GTCTCTGACGATTCGATTTCGG 59.216 50.000 13.95 5.40 40.83 4.30
1091 1244 2.671963 CCTTCAGCAGCAGCAGCA 60.672 61.111 12.92 0.00 45.49 4.41
1092 1245 2.691771 CCTTCAGCAGCAGCAGCAG 61.692 63.158 12.92 3.97 45.49 4.24
1406 1563 0.306533 CAGGTAACCAACACACGCAC 59.693 55.000 0.00 0.00 37.17 5.34
1414 1571 1.003108 CAACACACGCACGCCATATA 58.997 50.000 0.00 0.00 0.00 0.86
1415 1572 1.597195 CAACACACGCACGCCATATAT 59.403 47.619 0.00 0.00 0.00 0.86
1416 1573 2.797719 CAACACACGCACGCCATATATA 59.202 45.455 0.00 0.00 0.00 0.86
1417 1574 3.313012 ACACACGCACGCCATATATAT 57.687 42.857 0.00 0.00 0.00 0.86
1418 1575 4.443913 ACACACGCACGCCATATATATA 57.556 40.909 0.00 0.00 0.00 0.86
1537 1714 4.749310 CGGCAAGACCAGAGCGCT 62.749 66.667 11.27 11.27 39.03 5.92
1583 1760 3.992636 GACGTAGACGACAAGAGGG 57.007 57.895 9.41 0.00 43.02 4.30
1585 1762 2.015587 GACGTAGACGACAAGAGGGAT 58.984 52.381 9.41 0.00 43.02 3.85
1799 1979 4.671880 TGAACCAACGTTGCATATACAC 57.328 40.909 22.93 7.85 30.30 2.90
1800 1980 3.123790 TGAACCAACGTTGCATATACACG 59.876 43.478 22.93 8.20 30.30 4.49
1801 1981 2.690786 ACCAACGTTGCATATACACGT 58.309 42.857 22.93 7.67 38.76 4.49
1802 1982 3.847542 ACCAACGTTGCATATACACGTA 58.152 40.909 22.93 0.00 35.93 3.57
1803 1983 3.613737 ACCAACGTTGCATATACACGTAC 59.386 43.478 22.93 0.00 35.93 3.67
1804 1984 3.861113 CCAACGTTGCATATACACGTACT 59.139 43.478 22.93 0.00 35.93 2.73
1805 1985 5.036090 CCAACGTTGCATATACACGTACTA 58.964 41.667 22.93 0.00 35.93 1.82
1806 1986 5.052172 CCAACGTTGCATATACACGTACTAC 60.052 44.000 22.93 0.00 35.93 2.73
1828 2008 2.267188 TACATCTGTGTACGCGTTCC 57.733 50.000 20.78 9.65 39.77 3.62
1829 2009 0.601558 ACATCTGTGTACGCGTTCCT 59.398 50.000 20.78 0.00 36.63 3.36
1830 2010 1.814394 ACATCTGTGTACGCGTTCCTA 59.186 47.619 20.78 2.75 36.63 2.94
1850 2030 0.038618 TACGTCGATGCTGTTGCTGT 60.039 50.000 4.06 0.00 40.48 4.40
1851 2031 0.880278 ACGTCGATGCTGTTGCTGTT 60.880 50.000 4.06 0.00 40.48 3.16
1852 2032 0.451628 CGTCGATGCTGTTGCTGTTG 60.452 55.000 0.00 0.00 40.48 3.33
1853 2033 0.727122 GTCGATGCTGTTGCTGTTGC 60.727 55.000 0.00 0.00 40.48 4.17
1854 2034 0.886043 TCGATGCTGTTGCTGTTGCT 60.886 50.000 0.00 0.00 40.48 3.91
1855 2035 0.728129 CGATGCTGTTGCTGTTGCTG 60.728 55.000 0.00 0.00 40.48 4.41
1856 2036 0.313043 GATGCTGTTGCTGTTGCTGT 59.687 50.000 0.00 0.00 40.48 4.40
1881 2061 0.105039 CTAGCTGGTTGATCCGGACC 59.895 60.000 6.12 4.26 45.09 4.46
1892 2072 3.510459 TGATCCGGACCATGTAGATCAT 58.490 45.455 6.12 0.00 38.65 2.45
1893 2073 3.511540 TGATCCGGACCATGTAGATCATC 59.488 47.826 6.12 0.00 38.65 2.92
1894 2074 2.957474 TCCGGACCATGTAGATCATCA 58.043 47.619 0.00 0.00 34.09 3.07
1905 2085 2.278332 AGATCATCAGGTCGATCGGA 57.722 50.000 16.41 0.00 42.36 4.55
1959 2143 2.260434 CCACATGCAAGCAGCCAC 59.740 61.111 0.00 0.00 44.83 5.01
2018 2206 0.590230 CGATCTGCTTCGTCGACTCC 60.590 60.000 14.70 0.00 37.55 3.85
2029 2217 0.744874 GTCGACTCCGGGATTCATGA 59.255 55.000 8.70 0.00 36.24 3.07
2030 2218 1.032794 TCGACTCCGGGATTCATGAG 58.967 55.000 13.96 0.00 36.24 2.90
2031 2219 1.032794 CGACTCCGGGATTCATGAGA 58.967 55.000 13.96 0.00 0.00 3.27
2032 2220 1.615883 CGACTCCGGGATTCATGAGAT 59.384 52.381 13.96 0.00 0.00 2.75
2033 2221 2.352225 CGACTCCGGGATTCATGAGATC 60.352 54.545 13.96 2.70 0.00 2.75
2034 2222 2.630098 GACTCCGGGATTCATGAGATCA 59.370 50.000 9.33 0.00 0.00 2.92
2035 2223 3.246301 ACTCCGGGATTCATGAGATCAT 58.754 45.455 0.00 0.00 36.96 2.45
2053 2242 2.890311 TCATGTCCGTGAAAATGGCTTT 59.110 40.909 0.00 0.00 0.00 3.51
2195 2387 6.161855 TGTCGCTCTAGAAATCCATACATT 57.838 37.500 0.00 0.00 0.00 2.71
2215 2407 1.613925 TCGTTCCTGTGTTCTCCTCTG 59.386 52.381 0.00 0.00 0.00 3.35
2216 2408 1.613925 CGTTCCTGTGTTCTCCTCTGA 59.386 52.381 0.00 0.00 0.00 3.27
2221 2413 1.444553 GTGTTCTCCTCTGACGCGG 60.445 63.158 12.47 0.00 0.00 6.46
2228 2420 2.786495 CCTCTGACGCGGGTGCTAT 61.786 63.158 10.96 0.00 39.65 2.97
2243 2435 2.091541 TGCTATTTTACTGTGGCCTGC 58.908 47.619 3.32 0.00 0.00 4.85
2294 2486 4.621832 GGAGACGACGAGAGGAGT 57.378 61.111 0.00 0.00 0.00 3.85
2296 2488 0.674269 GGAGACGACGAGAGGAGTGT 60.674 60.000 0.00 0.00 0.00 3.55
2297 2489 0.722848 GAGACGACGAGAGGAGTGTC 59.277 60.000 0.00 0.00 0.00 3.67
2300 2492 3.580916 GACGAGAGGAGTGTCGCT 58.419 61.111 0.00 0.00 43.14 4.93
2389 2581 2.427905 CGAGCGTTCGTTCGTCCA 60.428 61.111 19.56 0.00 41.84 4.02
2438 2630 1.177401 GAAAGAGGCAGCGGGAAAAT 58.823 50.000 0.00 0.00 0.00 1.82
2501 2693 2.218603 GCGAGAAAAGGAAGTTGTGGA 58.781 47.619 0.00 0.00 0.00 4.02
2502 2694 2.814336 GCGAGAAAAGGAAGTTGTGGAT 59.186 45.455 0.00 0.00 0.00 3.41
2503 2695 3.365364 GCGAGAAAAGGAAGTTGTGGATG 60.365 47.826 0.00 0.00 0.00 3.51
2504 2696 3.365364 CGAGAAAAGGAAGTTGTGGATGC 60.365 47.826 0.00 0.00 0.00 3.91
2505 2697 2.554032 AGAAAAGGAAGTTGTGGATGCG 59.446 45.455 0.00 0.00 0.00 4.73
2506 2698 2.270352 AAAGGAAGTTGTGGATGCGA 57.730 45.000 0.00 0.00 0.00 5.10
2507 2699 1.523758 AAGGAAGTTGTGGATGCGAC 58.476 50.000 0.00 0.00 0.00 5.19
2508 2700 0.687354 AGGAAGTTGTGGATGCGACT 59.313 50.000 0.00 0.00 34.74 4.18
2509 2701 1.079503 GGAAGTTGTGGATGCGACTC 58.920 55.000 0.00 0.00 32.25 3.36
2563 2755 1.760613 ACGACTCACTCACCTGGAAAA 59.239 47.619 0.00 0.00 0.00 2.29
2609 2801 1.328680 AGCGCGCAGATGTTCTAATTG 59.671 47.619 35.10 0.00 0.00 2.32
2610 2802 1.327460 GCGCGCAGATGTTCTAATTGA 59.673 47.619 29.10 0.00 0.00 2.57
2612 2804 3.546815 GCGCGCAGATGTTCTAATTGATT 60.547 43.478 29.10 0.00 0.00 2.57
2613 2805 4.318760 GCGCGCAGATGTTCTAATTGATTA 60.319 41.667 29.10 0.00 0.00 1.75
2614 2806 5.737353 CGCGCAGATGTTCTAATTGATTAA 58.263 37.500 8.75 0.00 0.00 1.40
2615 2807 6.191661 CGCGCAGATGTTCTAATTGATTAAA 58.808 36.000 8.75 0.00 0.00 1.52
2616 2808 6.355405 CGCGCAGATGTTCTAATTGATTAAAG 59.645 38.462 8.75 0.00 0.00 1.85
2617 2809 7.409697 GCGCAGATGTTCTAATTGATTAAAGA 58.590 34.615 0.30 0.00 0.00 2.52
2618 2810 8.072567 GCGCAGATGTTCTAATTGATTAAAGAT 58.927 33.333 0.30 0.00 0.00 2.40
2619 2811 9.941664 CGCAGATGTTCTAATTGATTAAAGATT 57.058 29.630 0.00 0.00 0.00 2.40
2695 2889 3.435671 CCCTCGTGGACAGTAAATTTGAC 59.564 47.826 4.76 0.00 35.39 3.18
2696 2890 3.122948 CCTCGTGGACAGTAAATTTGACG 59.877 47.826 0.00 0.00 34.57 4.35
2697 2891 3.979948 TCGTGGACAGTAAATTTGACGA 58.020 40.909 0.00 0.00 32.57 4.20
2698 2892 4.370049 TCGTGGACAGTAAATTTGACGAA 58.630 39.130 0.00 0.00 32.12 3.85
2699 2893 4.809958 TCGTGGACAGTAAATTTGACGAAA 59.190 37.500 0.00 0.00 32.12 3.46
2700 2894 5.293814 TCGTGGACAGTAAATTTGACGAAAA 59.706 36.000 0.00 0.00 32.12 2.29
2701 2895 5.966503 CGTGGACAGTAAATTTGACGAAAAA 59.033 36.000 0.00 0.00 0.00 1.94
2702 2896 6.075780 CGTGGACAGTAAATTTGACGAAAAAC 60.076 38.462 0.00 0.00 0.00 2.43
2731 2925 9.590451 AAAATATGGAATGTTGTGACATCAATC 57.410 29.630 0.00 2.02 45.58 2.67
2732 2926 7.885009 ATATGGAATGTTGTGACATCAATCA 57.115 32.000 12.27 6.69 45.58 2.57
2734 2928 6.402456 TGGAATGTTGTGACATCAATCAAA 57.598 33.333 12.27 0.00 45.58 2.69
2736 2930 8.120140 TGGAATGTTGTGACATCAATCAAATA 57.880 30.769 12.27 0.00 45.58 1.40
2737 2931 8.751242 TGGAATGTTGTGACATCAATCAAATAT 58.249 29.630 12.27 0.00 45.58 1.28
2742 2936 9.447157 TGTTGTGACATCAATCAAATATACTCA 57.553 29.630 0.00 0.00 0.00 3.41
2775 2969 4.394729 TGTGATTTGAGGAGGTTTACACC 58.605 43.478 0.00 0.00 44.67 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.107945 CCAACCCCGTTGTCAAGTTT 58.892 50.000 4.00 0.00 41.41 2.66
39 40 4.067972 TGAAAACCTAGCTGACGTTTCT 57.932 40.909 0.00 0.00 0.00 2.52
69 70 4.207635 CGTTTGCTAAAGAACACTGACGTA 59.792 41.667 0.00 0.00 0.00 3.57
84 88 5.053811 TCATGTCAAGTTCTTCGTTTGCTA 58.946 37.500 0.00 0.00 0.00 3.49
91 95 2.159734 GCTGCTCATGTCAAGTTCTTCG 60.160 50.000 0.00 0.00 0.00 3.79
95 99 0.445436 CCGCTGCTCATGTCAAGTTC 59.555 55.000 0.00 0.00 0.00 3.01
97 101 0.671781 GACCGCTGCTCATGTCAAGT 60.672 55.000 0.00 0.00 0.00 3.16
101 105 2.161486 GTCGACCGCTGCTCATGTC 61.161 63.158 3.51 0.00 0.00 3.06
104 108 1.670949 ATGAGTCGACCGCTGCTCAT 61.671 55.000 13.01 10.77 42.00 2.90
144 162 6.040278 TGGACTGTCAATCTGCTTAGATAGAG 59.960 42.308 10.38 0.00 0.00 2.43
145 163 5.893824 TGGACTGTCAATCTGCTTAGATAGA 59.106 40.000 10.38 0.00 0.00 1.98
150 233 3.055530 AGGTGGACTGTCAATCTGCTTAG 60.056 47.826 10.38 0.00 0.00 2.18
170 253 0.748367 TCCGTCTCCAGTCGATCAGG 60.748 60.000 0.00 0.00 0.00 3.86
174 257 3.021695 TGTTTATCCGTCTCCAGTCGAT 58.978 45.455 0.00 0.00 0.00 3.59
175 258 2.422479 CTGTTTATCCGTCTCCAGTCGA 59.578 50.000 0.00 0.00 0.00 4.20
176 259 2.163815 ACTGTTTATCCGTCTCCAGTCG 59.836 50.000 0.00 0.00 0.00 4.18
195 278 0.039764 TCCAGTCGATCAGGTGGACT 59.960 55.000 3.35 0.00 45.46 3.85
196 279 0.457851 CTCCAGTCGATCAGGTGGAC 59.542 60.000 3.35 0.00 35.22 4.02
197 280 0.684479 CCTCCAGTCGATCAGGTGGA 60.684 60.000 13.45 6.72 38.21 4.02
198 281 1.819229 CCTCCAGTCGATCAGGTGG 59.181 63.158 7.24 7.24 31.83 4.61
201 284 1.440893 CTGCCTCCAGTCGATCAGG 59.559 63.158 0.00 0.00 34.31 3.86
210 293 1.873591 GTGTTGTTGTACTGCCTCCAG 59.126 52.381 0.00 0.00 44.80 3.86
211 294 1.210722 TGTGTTGTTGTACTGCCTCCA 59.789 47.619 0.00 0.00 0.00 3.86
212 295 1.602377 GTGTGTTGTTGTACTGCCTCC 59.398 52.381 0.00 0.00 0.00 4.30
213 296 1.260561 CGTGTGTTGTTGTACTGCCTC 59.739 52.381 0.00 0.00 0.00 4.70
214 297 1.134640 TCGTGTGTTGTTGTACTGCCT 60.135 47.619 0.00 0.00 0.00 4.75
215 298 1.292061 TCGTGTGTTGTTGTACTGCC 58.708 50.000 0.00 0.00 0.00 4.85
216 299 3.602390 AATCGTGTGTTGTTGTACTGC 57.398 42.857 0.00 0.00 0.00 4.40
217 300 5.797934 ACAAAAATCGTGTGTTGTTGTACTG 59.202 36.000 0.00 0.00 30.11 2.74
219 302 6.025280 AGACAAAAATCGTGTGTTGTTGTAC 58.975 36.000 0.00 0.00 34.44 2.90
220 303 6.184580 AGACAAAAATCGTGTGTTGTTGTA 57.815 33.333 0.00 0.00 34.44 2.41
223 312 5.163703 TGCTAGACAAAAATCGTGTGTTGTT 60.164 36.000 0.00 0.00 34.44 2.83
269 359 0.108615 CAAGATAGATAGCGGGGCCG 60.109 60.000 0.00 0.00 43.09 6.13
441 550 1.153429 GGGTAGGGTGTCGATGTGC 60.153 63.158 0.00 0.00 0.00 4.57
446 555 1.304713 GGTCTGGGTAGGGTGTCGA 60.305 63.158 0.00 0.00 0.00 4.20
538 659 3.727258 TCAATCGGCCCAGGGGTG 61.727 66.667 7.91 0.04 37.65 4.61
577 698 2.835431 AGGCCGATCGCTGTAGCT 60.835 61.111 10.32 0.00 39.32 3.32
578 699 2.355244 GAGGCCGATCGCTGTAGC 60.355 66.667 10.32 7.20 37.74 3.58
579 700 2.336809 GGAGGCCGATCGCTGTAG 59.663 66.667 10.32 0.00 37.74 2.74
639 762 1.906757 TTGCAACTTTGTTCTGCACG 58.093 45.000 0.00 0.00 45.31 5.34
663 786 5.302059 CACGGAATGGTTATCCTCTCTCTTA 59.698 44.000 0.00 0.00 34.66 2.10
664 787 4.100189 CACGGAATGGTTATCCTCTCTCTT 59.900 45.833 0.00 0.00 34.66 2.85
673 796 1.400494 GGTGTGCACGGAATGGTTATC 59.600 52.381 13.13 0.00 0.00 1.75
674 797 1.271652 TGGTGTGCACGGAATGGTTAT 60.272 47.619 13.13 0.00 0.00 1.89
675 798 0.108774 TGGTGTGCACGGAATGGTTA 59.891 50.000 13.13 0.00 0.00 2.85
676 799 1.152860 TGGTGTGCACGGAATGGTT 60.153 52.632 13.13 0.00 0.00 3.67
677 800 1.896660 GTGGTGTGCACGGAATGGT 60.897 57.895 13.13 0.00 0.00 3.55
678 801 2.953821 GTGGTGTGCACGGAATGG 59.046 61.111 13.13 0.00 0.00 3.16
679 802 2.555782 CGTGGTGTGCACGGAATG 59.444 61.111 13.13 1.28 41.76 2.67
722 858 0.248702 GTCTCGAGATCGACTTGGCC 60.249 60.000 19.90 0.00 44.22 5.36
723 859 0.590230 CGTCTCGAGATCGACTTGGC 60.590 60.000 19.90 0.87 44.22 4.52
724 860 0.028242 CCGTCTCGAGATCGACTTGG 59.972 60.000 27.54 14.92 44.22 3.61
725 861 1.007580 TCCGTCTCGAGATCGACTTG 58.992 55.000 27.54 16.43 44.22 3.16
726 862 1.956297 ATCCGTCTCGAGATCGACTT 58.044 50.000 27.54 14.96 44.22 3.01
727 863 2.801679 GTTATCCGTCTCGAGATCGACT 59.198 50.000 27.54 19.39 44.22 4.18
728 864 2.096318 GGTTATCCGTCTCGAGATCGAC 60.096 54.545 27.54 20.10 44.22 4.20
729 865 2.484241 TGGTTATCCGTCTCGAGATCGA 60.484 50.000 27.54 21.62 40.53 3.59
919 1063 2.639926 GCTAGTAGCGCGTGCATCG 61.640 63.158 24.79 7.50 46.23 3.84
1397 1554 2.804697 TATATATGGCGTGCGTGTGT 57.195 45.000 0.00 0.00 0.00 3.72
1406 1563 5.775195 TGGAGGATGGAGTATATATATGGCG 59.225 44.000 5.44 0.00 0.00 5.69
1514 1691 2.811317 CTGGTCTTGCCGCTCGTC 60.811 66.667 0.00 0.00 41.21 4.20
1525 1702 3.074999 GCAGCTAGCGCTCTGGTCT 62.075 63.158 23.09 9.06 45.15 3.85
1537 1714 4.819761 CAAGAGCCGCCGCAGCTA 62.820 66.667 0.00 0.00 41.75 3.32
1570 1747 2.444421 ACGTTATCCCTCTTGTCGTCT 58.556 47.619 0.00 0.00 0.00 4.18
1582 1759 0.577269 CGCAGCTGCTAACGTTATCC 59.423 55.000 34.22 3.31 39.32 2.59
1583 1760 1.255600 GACGCAGCTGCTAACGTTATC 59.744 52.381 34.22 15.12 39.16 1.75
1585 1762 1.068832 CGACGCAGCTGCTAACGTTA 61.069 55.000 34.22 7.94 39.16 3.18
1605 1782 2.656651 CGCTCTCATCCTTCGCCG 60.657 66.667 0.00 0.00 0.00 6.46
1642 1822 2.126031 GGAGTTGAGCCGTCCGAC 60.126 66.667 0.00 0.00 0.00 4.79
1689 1869 0.037590 GTGCAGGTCAACCCCATACA 59.962 55.000 0.00 0.00 36.42 2.29
1728 1908 1.979693 GACGTCTCCCACAGCTCCT 60.980 63.158 8.70 0.00 0.00 3.69
1819 1999 1.566404 TCGACGTATAGGAACGCGTA 58.434 50.000 14.46 0.00 46.71 4.42
1820 2000 0.940126 ATCGACGTATAGGAACGCGT 59.060 50.000 5.58 5.58 46.71 6.01
1821 2001 1.315497 CATCGACGTATAGGAACGCG 58.685 55.000 3.53 3.53 46.71 6.01
1822 2002 1.050767 GCATCGACGTATAGGAACGC 58.949 55.000 0.00 0.00 46.71 4.84
1824 2004 3.351020 ACAGCATCGACGTATAGGAAC 57.649 47.619 0.00 0.00 0.00 3.62
1825 2005 3.702330 CAACAGCATCGACGTATAGGAA 58.298 45.455 0.00 0.00 0.00 3.36
1826 2006 2.543031 GCAACAGCATCGACGTATAGGA 60.543 50.000 0.00 0.00 0.00 2.94
1827 2007 1.787155 GCAACAGCATCGACGTATAGG 59.213 52.381 0.00 0.00 0.00 2.57
1828 2008 2.469147 CAGCAACAGCATCGACGTATAG 59.531 50.000 0.00 0.00 0.00 1.31
1829 2009 2.159296 ACAGCAACAGCATCGACGTATA 60.159 45.455 0.00 0.00 0.00 1.47
1830 2010 1.280982 CAGCAACAGCATCGACGTAT 58.719 50.000 0.00 0.00 0.00 3.06
1850 2030 1.694150 ACCAGCTAGACAAGACAGCAA 59.306 47.619 0.00 0.00 37.78 3.91
1851 2031 1.342074 ACCAGCTAGACAAGACAGCA 58.658 50.000 0.00 0.00 37.78 4.41
1852 2032 2.072298 CAACCAGCTAGACAAGACAGC 58.928 52.381 0.00 0.00 35.49 4.40
1853 2033 3.667497 TCAACCAGCTAGACAAGACAG 57.333 47.619 0.00 0.00 0.00 3.51
1854 2034 3.055819 GGATCAACCAGCTAGACAAGACA 60.056 47.826 0.00 0.00 38.79 3.41
1855 2035 3.526534 GGATCAACCAGCTAGACAAGAC 58.473 50.000 0.00 0.00 38.79 3.01
1856 2036 2.166459 CGGATCAACCAGCTAGACAAGA 59.834 50.000 0.00 0.00 38.90 3.02
1881 2061 4.410448 CGATCGACCTGATGATCTACATG 58.590 47.826 10.26 0.00 39.56 3.21
1905 2085 4.397103 TGTTCTACGATTCTACATGACGGT 59.603 41.667 0.00 0.00 0.00 4.83
1912 2092 7.660617 CCTACCTATCTGTTCTACGATTCTACA 59.339 40.741 0.00 0.00 0.00 2.74
1959 2143 5.896922 AGATTTCTCGCATGTAGATTTCG 57.103 39.130 0.00 0.00 0.00 3.46
2008 2196 0.750546 ATGAATCCCGGAGTCGACGA 60.751 55.000 10.46 0.76 39.00 4.20
2029 2217 2.684881 GCCATTTTCACGGACATGATCT 59.315 45.455 0.00 0.00 0.00 2.75
2030 2218 2.684881 AGCCATTTTCACGGACATGATC 59.315 45.455 0.00 0.00 0.00 2.92
2031 2219 2.726821 AGCCATTTTCACGGACATGAT 58.273 42.857 0.00 0.00 0.00 2.45
2032 2220 2.198827 AGCCATTTTCACGGACATGA 57.801 45.000 0.00 0.00 0.00 3.07
2033 2221 3.302365 AAAGCCATTTTCACGGACATG 57.698 42.857 0.00 0.00 0.00 3.21
2034 2222 4.331968 TCTAAAGCCATTTTCACGGACAT 58.668 39.130 0.00 0.00 0.00 3.06
2035 2223 3.745799 TCTAAAGCCATTTTCACGGACA 58.254 40.909 0.00 0.00 0.00 4.02
2036 2224 4.759516 TTCTAAAGCCATTTTCACGGAC 57.240 40.909 0.00 0.00 0.00 4.79
2071 2260 4.933064 GACAGCCGCCGGATCGAG 62.933 72.222 7.68 0.00 0.00 4.04
2074 2263 4.148825 AGTGACAGCCGCCGGATC 62.149 66.667 7.68 0.65 0.00 3.36
2075 2264 4.148825 GAGTGACAGCCGCCGGAT 62.149 66.667 7.68 0.00 0.00 4.18
2077 2266 4.457496 ATGAGTGACAGCCGCCGG 62.457 66.667 0.00 0.00 0.00 6.13
2078 2267 3.190849 CATGAGTGACAGCCGCCG 61.191 66.667 0.00 0.00 0.00 6.46
2144 2336 3.714391 ACTGGTGAAACACGTTCTCTAC 58.286 45.455 0.00 0.00 39.98 2.59
2195 2387 1.613925 CAGAGGAGAACACAGGAACGA 59.386 52.381 0.00 0.00 0.00 3.85
2215 2407 1.326548 CAGTAAAATAGCACCCGCGTC 59.673 52.381 4.92 0.00 45.49 5.19
2216 2408 1.338389 ACAGTAAAATAGCACCCGCGT 60.338 47.619 4.92 0.00 45.49 6.01
2221 2413 2.423538 CAGGCCACAGTAAAATAGCACC 59.576 50.000 5.01 0.00 0.00 5.01
2228 2420 4.073052 CCGCAGGCCACAGTAAAA 57.927 55.556 5.01 0.00 46.14 1.52
2243 2435 3.972227 GGATCAATCCATCGCCCG 58.028 61.111 4.09 0.00 46.38 6.13
2255 2447 2.809174 CACGCGCGTTCTGGATCA 60.809 61.111 35.90 0.00 0.00 2.92
2327 2519 3.000674 CAGCAACAGACGATACGAATCAC 60.001 47.826 0.00 0.00 31.93 3.06
2375 2567 3.033764 TGCTGGACGAACGAACGC 61.034 61.111 0.14 0.00 36.70 4.84
2380 2572 2.365068 CGACAGTGCTGGACGAACG 61.365 63.158 12.73 0.00 36.93 3.95
2501 2693 3.197790 GCCACGCATGAGTCGCAT 61.198 61.111 13.83 0.00 37.85 4.73
2538 2730 0.314302 AGGTGAGTGAGTCGTTTCCG 59.686 55.000 0.00 0.00 0.00 4.30
2576 2768 1.198608 GCGCGCTTCTCATTTGATGC 61.199 55.000 26.67 0.00 34.88 3.91
2665 2859 2.682494 TCCACGAGGGGTGTAGCC 60.682 66.667 0.00 0.00 45.52 3.93
2666 2860 2.227089 CTGTCCACGAGGGGTGTAGC 62.227 65.000 0.00 0.00 45.52 3.58
2668 2862 0.405198 TACTGTCCACGAGGGGTGTA 59.595 55.000 0.00 0.00 45.52 2.90
2673 2867 3.435671 GTCAAATTTACTGTCCACGAGGG 59.564 47.826 0.00 0.00 34.83 4.30
2709 2903 7.700022 TTGATTGATGTCACAACATTCCATA 57.300 32.000 7.30 0.00 46.20 2.74
2737 2931 9.658475 CTCAAATCACATAAAACGTTTTGAGTA 57.342 29.630 31.26 15.31 41.42 2.59
2738 2932 7.647715 CCTCAAATCACATAAAACGTTTTGAGT 59.352 33.333 31.26 25.24 43.27 3.41
2739 2933 7.860373 TCCTCAAATCACATAAAACGTTTTGAG 59.140 33.333 31.26 24.60 43.89 3.02
2740 2934 7.708051 TCCTCAAATCACATAAAACGTTTTGA 58.292 30.769 31.26 22.39 32.51 2.69
2741 2935 7.114811 CCTCCTCAAATCACATAAAACGTTTTG 59.885 37.037 31.26 20.96 0.00 2.44
2742 2936 7.145323 CCTCCTCAAATCACATAAAACGTTTT 58.855 34.615 27.65 27.65 0.00 2.43
2753 2947 4.394729 GGTGTAAACCTCCTCAAATCACA 58.605 43.478 0.00 0.00 0.00 3.58
2755 2949 3.396276 TGGGTGTAAACCTCCTCAAATCA 59.604 43.478 1.05 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.