Multiple sequence alignment - TraesCS3B01G136000

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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 TraesCS3B01G136000 chr3B 100.000 2685 0 0 1 2685 118758932 118761616 0.000000e+00 4959
1 TraesCS3B01G136000 chr3D 91.107 2249 115 38 248 2474 73393348 73395533 0.000000e+00 2966
2 TraesCS3B01G136000 chr3D 94.872 234 9 2 1 231 73393131 73393364 1.960000e-96 363
3 TraesCS3B01G136000 chr3D 91.566 166 14 0 2520 2685 73395521 73395686 2.080000e-56 230
4 TraesCS3B01G136000 chr3A 89.258 2439 159 56 248 2648 86373123 86375496 0.000000e+00 2957
5 TraesCS3B01G136000 chr3A 92.340 235 14 3 1 231 86372905 86373139 5.540000e-87 331
6 TraesCS3B01G136000 chr2D 91.304 782 32 15 1398 2171 66077207 66076454 0.000000e+00 1035
7 TraesCS3B01G136000 chrUn 90.723 733 31 16 1447 2171 105815339 105816042 0.000000e+00 942
8 TraesCS3B01G136000 chrUn 90.450 733 34 15 1447 2171 106336592 106337296 0.000000e+00 933
9 TraesCS3B01G136000 chr5D 90.314 733 35 15 1447 2171 187522747 187523451 0.000000e+00 928
10 TraesCS3B01G136000 chr5D 90.191 734 35 20 1447 2171 180244278 180244983 0.000000e+00 922


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 TraesCS3B01G136000 chr3B 118758932 118761616 2684 False 4959.000000 4959 100.000 1 2685 1 chr3B.!!$F1 2684
1 TraesCS3B01G136000 chr3D 73393131 73395686 2555 False 1186.333333 2966 92.515 1 2685 3 chr3D.!!$F1 2684
2 TraesCS3B01G136000 chr3A 86372905 86375496 2591 False 1644.000000 2957 90.799 1 2648 2 chr3A.!!$F1 2647
3 TraesCS3B01G136000 chr2D 66076454 66077207 753 True 1035.000000 1035 91.304 1398 2171 1 chr2D.!!$R1 773
4 TraesCS3B01G136000 chrUn 105815339 105816042 703 False 942.000000 942 90.723 1447 2171 1 chrUn.!!$F1 724
5 TraesCS3B01G136000 chrUn 106336592 106337296 704 False 933.000000 933 90.450 1447 2171 1 chrUn.!!$F2 724
6 TraesCS3B01G136000 chr5D 187522747 187523451 704 False 928.000000 928 90.314 1447 2171 1 chr5D.!!$F2 724
7 TraesCS3B01G136000 chr5D 180244278 180244983 705 False 922.000000 922 90.191 1447 2171 1 chr5D.!!$F1 724

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
239 244 0.249657 CCAGCTACGATGCTCCCTTC 60.250 60.0 4.15 0.0 41.98 3.46 F
240 245 0.461548 CAGCTACGATGCTCCCTTCA 59.538 55.0 4.15 0.0 41.98 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1637 1664 0.551396 AGGGGCTACCATTTACAGGC 59.449 55.000 0.97 0.0 43.89 4.85 R
1943 1989 1.226101 CCTAATTGCTGCGCACACG 60.226 57.895 5.66 0.0 38.71 4.49 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
70 72 9.142515 TCTGCATTATGAAAAACAAGCAAATAG 57.857 29.630 0.00 0.00 0.00 1.73
116 120 1.175654 TGCCAGTTGTATGCATGGTG 58.824 50.000 10.16 0.00 35.17 4.17
120 124 2.819019 CCAGTTGTATGCATGGTGTTGA 59.181 45.455 10.16 0.00 0.00 3.18
218 223 1.067354 GGGGAAGCACAGCATGAAAAG 60.067 52.381 0.00 0.00 39.69 2.27
219 224 1.615392 GGGAAGCACAGCATGAAAAGT 59.385 47.619 0.00 0.00 39.69 2.66
220 225 2.352127 GGGAAGCACAGCATGAAAAGTC 60.352 50.000 0.00 0.00 39.69 3.01
221 226 2.352127 GGAAGCACAGCATGAAAAGTCC 60.352 50.000 0.00 0.00 39.69 3.85
222 227 1.985473 AGCACAGCATGAAAAGTCCA 58.015 45.000 0.00 0.00 39.69 4.02
223 228 1.884579 AGCACAGCATGAAAAGTCCAG 59.115 47.619 0.00 0.00 39.69 3.86
224 229 1.668047 GCACAGCATGAAAAGTCCAGC 60.668 52.381 0.00 0.00 39.69 4.85
225 230 1.884579 CACAGCATGAAAAGTCCAGCT 59.115 47.619 0.00 0.00 39.69 4.24
226 231 3.076621 CACAGCATGAAAAGTCCAGCTA 58.923 45.455 0.00 0.00 39.69 3.32
227 232 3.077359 ACAGCATGAAAAGTCCAGCTAC 58.923 45.455 0.00 0.00 39.69 3.58
228 233 2.094894 CAGCATGAAAAGTCCAGCTACG 59.905 50.000 0.00 0.00 39.69 3.51
229 234 2.028112 AGCATGAAAAGTCCAGCTACGA 60.028 45.455 0.00 0.00 32.82 3.43
230 235 2.939103 GCATGAAAAGTCCAGCTACGAT 59.061 45.455 0.00 0.00 0.00 3.73
231 236 3.242543 GCATGAAAAGTCCAGCTACGATG 60.243 47.826 0.00 0.00 0.00 3.84
232 237 2.346803 TGAAAAGTCCAGCTACGATGC 58.653 47.619 0.00 0.00 0.00 3.91
233 238 2.028112 TGAAAAGTCCAGCTACGATGCT 60.028 45.455 0.00 0.00 45.18 3.79
234 239 2.301577 AAAGTCCAGCTACGATGCTC 57.698 50.000 4.15 0.00 41.98 4.26
235 240 0.461961 AAGTCCAGCTACGATGCTCC 59.538 55.000 4.15 0.00 41.98 4.70
236 241 1.068250 GTCCAGCTACGATGCTCCC 59.932 63.158 4.15 0.00 41.98 4.30
237 242 1.075970 TCCAGCTACGATGCTCCCT 60.076 57.895 4.15 0.00 41.98 4.20
238 243 0.687757 TCCAGCTACGATGCTCCCTT 60.688 55.000 4.15 0.00 41.98 3.95
239 244 0.249657 CCAGCTACGATGCTCCCTTC 60.250 60.000 4.15 0.00 41.98 3.46
240 245 0.461548 CAGCTACGATGCTCCCTTCA 59.538 55.000 4.15 0.00 41.98 3.02
241 246 1.134699 CAGCTACGATGCTCCCTTCAA 60.135 52.381 4.15 0.00 41.98 2.69
242 247 1.555075 AGCTACGATGCTCCCTTCAAA 59.445 47.619 0.00 0.00 39.34 2.69
243 248 2.027192 AGCTACGATGCTCCCTTCAAAA 60.027 45.455 0.00 0.00 39.34 2.44
244 249 2.747446 GCTACGATGCTCCCTTCAAAAA 59.253 45.455 0.00 0.00 0.00 1.94
245 250 3.181506 GCTACGATGCTCCCTTCAAAAAG 60.182 47.826 0.00 0.00 0.00 2.27
246 251 3.140325 ACGATGCTCCCTTCAAAAAGA 57.860 42.857 0.00 0.00 34.14 2.52
247 252 3.486383 ACGATGCTCCCTTCAAAAAGAA 58.514 40.909 0.00 0.00 34.14 2.52
248 253 3.888930 ACGATGCTCCCTTCAAAAAGAAA 59.111 39.130 0.00 0.00 35.40 2.52
249 254 4.340950 ACGATGCTCCCTTCAAAAAGAAAA 59.659 37.500 0.00 0.00 35.40 2.29
250 255 5.163457 ACGATGCTCCCTTCAAAAAGAAAAA 60.163 36.000 0.00 0.00 35.40 1.94
278 283 1.822506 ACGATCCTTCACTCAGACGA 58.177 50.000 0.00 0.00 0.00 4.20
306 311 8.338259 GCAACGAGATATTCTGTAATTGATGTT 58.662 33.333 0.00 0.00 0.00 2.71
308 313 7.855545 ACGAGATATTCTGTAATTGATGTTGC 58.144 34.615 0.00 0.00 0.00 4.17
355 361 5.978814 ACATCTAGTAGGTGGTTGATGAAC 58.021 41.667 14.91 0.00 36.25 3.18
409 415 4.979197 TGTGTTTAGCAATGCGTTTTTAGG 59.021 37.500 0.00 0.00 0.00 2.69
416 422 3.821841 CAATGCGTTTTTAGGAGTCACC 58.178 45.455 0.00 0.00 39.35 4.02
439 445 6.852664 CCTAGGTGGTTGATGAAACATAAAC 58.147 40.000 0.00 0.00 40.86 2.01
442 448 6.690530 AGGTGGTTGATGAAACATAAACATG 58.309 36.000 12.24 0.00 40.86 3.21
487 495 6.995686 CCATATAATATATAACAAGCCCCGCA 59.004 38.462 0.00 0.00 0.00 5.69
495 503 0.538516 ACAAGCCCCGCACAAACATA 60.539 50.000 0.00 0.00 0.00 2.29
538 552 1.062047 TCGACGCATACTCGACAGC 59.938 57.895 0.00 0.00 35.26 4.40
541 555 3.289629 CGCATACTCGACAGCGTG 58.710 61.111 7.59 0.00 44.67 5.34
542 556 1.226295 CGCATACTCGACAGCGTGA 60.226 57.895 7.59 0.00 44.67 4.35
574 588 6.728200 TGAGAACATCATGTTTCAAGTTGTC 58.272 36.000 4.04 0.00 41.28 3.18
653 667 3.307782 CCGCGTGAGTAATTCGGTTTAAT 59.692 43.478 4.92 0.00 35.75 1.40
831 845 9.683870 ACAGTACTTATTTACTAGCAGTACTCT 57.316 33.333 7.22 0.00 44.42 3.24
1014 1032 3.491792 CGCTACCTCCTCTTCTTGATTCC 60.492 52.174 0.00 0.00 0.00 3.01
1168 1186 3.751470 GACGACTTCGACGGCTTC 58.249 61.111 5.47 0.00 43.02 3.86
1574 1601 7.328157 TGTTTTCGTTCTTTGTTTCTTGTTC 57.672 32.000 0.00 0.00 0.00 3.18
1637 1664 3.385193 AAAAGGAATGTTCTTTGCCCG 57.615 42.857 0.00 0.00 34.99 6.13
1697 1728 3.130516 CAGCATCTGCACCAATCTTCATT 59.869 43.478 4.79 0.00 45.16 2.57
1714 1746 2.039613 TCATTGATTTTGCCCCAAACCC 59.960 45.455 0.00 0.00 32.79 4.11
1776 1808 5.112220 TGTCTTGCAATGTTGAATCAGAC 57.888 39.130 0.00 0.00 0.00 3.51
1789 1821 6.818142 TGTTGAATCAGACATACATACTGTGG 59.182 38.462 0.00 0.00 33.93 4.17
1832 1871 8.637099 TCCAACATCTATCAAACATGTGAAAAA 58.363 29.630 0.00 0.00 31.00 1.94
1834 1873 9.247126 CAACATCTATCAAACATGTGAAAAACA 57.753 29.630 0.00 0.00 44.79 2.83
1835 1874 9.467258 AACATCTATCAAACATGTGAAAAACAG 57.533 29.630 0.00 0.00 43.64 3.16
1836 1875 8.632679 ACATCTATCAAACATGTGAAAAACAGT 58.367 29.630 0.00 0.00 43.64 3.55
1859 1905 2.548057 TGTTTCGAGAATCCAAGTGCAC 59.452 45.455 9.40 9.40 0.00 4.57
1889 1935 7.170393 ACCAGAAAATGCTTATCCCTTTTAC 57.830 36.000 0.00 0.00 0.00 2.01
1892 1938 4.649088 AAATGCTTATCCCTTTTACGCC 57.351 40.909 0.00 0.00 0.00 5.68
1906 1952 4.877378 TTTACGCCCTCTCTTTACAGAA 57.123 40.909 0.00 0.00 0.00 3.02
1943 1989 6.392354 TGAACAATCTCATCCAATTCAAAGC 58.608 36.000 0.00 0.00 0.00 3.51
1984 2030 4.267928 GTGTAAAGTGCAGATAACCTAGCG 59.732 45.833 0.00 0.00 0.00 4.26
2160 2208 6.017109 ACCATCTACAGAAAATTCACACACAC 60.017 38.462 0.00 0.00 0.00 3.82
2171 2219 2.360844 TCACACACACCAACGACAATT 58.639 42.857 0.00 0.00 0.00 2.32
2205 2253 7.588488 GCAAATTTCATTCCATTGACAGTTTTG 59.412 33.333 0.00 0.00 0.00 2.44
2206 2254 8.614346 CAAATTTCATTCCATTGACAGTTTTGT 58.386 29.630 0.00 0.00 41.18 2.83
2207 2255 7.718272 ATTTCATTCCATTGACAGTTTTGTG 57.282 32.000 0.00 0.00 37.76 3.33
2223 2272 7.706179 ACAGTTTTGTGTCACAAATTAATGGAG 59.294 33.333 27.28 15.25 46.17 3.86
2237 2286 7.989416 AATTAATGGAGAAAACTCGGTACAA 57.011 32.000 0.00 0.00 0.00 2.41
2242 2291 6.067263 TGGAGAAAACTCGGTACAATTTTG 57.933 37.500 0.00 0.00 0.00 2.44
2245 2294 6.445357 AGAAAACTCGGTACAATTTTGTGT 57.555 33.333 6.21 0.00 42.31 3.72
2247 2296 5.570234 AAACTCGGTACAATTTTGTGTGT 57.430 34.783 6.21 0.00 42.31 3.72
2248 2297 4.545823 ACTCGGTACAATTTTGTGTGTG 57.454 40.909 6.21 0.63 42.31 3.82
2268 2317 1.138464 GTGGGAATTAGGACGGAGGAC 59.862 57.143 0.00 0.00 0.00 3.85
2312 2361 1.107114 TGCCGACCTCATCTCTCTTC 58.893 55.000 0.00 0.00 0.00 2.87
2430 2486 0.889186 ACCACTTTGGCACCGTGATC 60.889 55.000 14.83 0.00 42.67 2.92
2462 2518 6.418819 GTGTATTTGCAAGTGGATTATCATGC 59.581 38.462 4.47 0.13 0.00 4.06
2471 2527 5.931441 GTGGATTATCATGCACTACTTCC 57.069 43.478 4.42 0.00 45.83 3.46
2475 2531 2.231215 ATCATGCACTACTTCCTCGC 57.769 50.000 0.00 0.00 0.00 5.03
2477 2533 1.135139 TCATGCACTACTTCCTCGCTC 59.865 52.381 0.00 0.00 0.00 5.03
2478 2534 1.134995 CATGCACTACTTCCTCGCTCA 60.135 52.381 0.00 0.00 0.00 4.26
2479 2535 0.528017 TGCACTACTTCCTCGCTCAG 59.472 55.000 0.00 0.00 0.00 3.35
2482 2538 2.797792 GCACTACTTCCTCGCTCAGATG 60.798 54.545 0.00 0.00 0.00 2.90
2483 2539 1.407258 ACTACTTCCTCGCTCAGATGC 59.593 52.381 0.00 0.00 0.00 3.91
2487 2543 2.584261 TTCCTCGCTCAGATGCAGGC 62.584 60.000 0.00 0.00 33.98 4.85
2488 2544 2.588314 CTCGCTCAGATGCAGGCC 60.588 66.667 0.00 0.00 0.00 5.19
2489 2545 3.381333 CTCGCTCAGATGCAGGCCA 62.381 63.158 5.01 0.00 0.00 5.36
2490 2546 2.895865 CGCTCAGATGCAGGCCAG 60.896 66.667 5.01 0.00 0.00 4.85
2492 2548 2.192443 CTCAGATGCAGGCCAGGG 59.808 66.667 5.01 0.00 0.00 4.45
2493 2549 2.285592 TCAGATGCAGGCCAGGGA 60.286 61.111 5.01 0.00 0.00 4.20
2494 2550 1.695239 TCAGATGCAGGCCAGGGAT 60.695 57.895 5.01 2.65 0.00 3.85
2495 2551 0.400381 TCAGATGCAGGCCAGGGATA 60.400 55.000 5.01 0.00 0.00 2.59
2496 2552 0.475475 CAGATGCAGGCCAGGGATAA 59.525 55.000 5.01 0.00 0.00 1.75
2498 2554 1.353694 AGATGCAGGCCAGGGATAATC 59.646 52.381 5.01 0.00 0.00 1.75
2499 2555 0.407139 ATGCAGGCCAGGGATAATCC 59.593 55.000 5.01 0.00 35.23 3.01
2503 2559 2.061061 CAGGCCAGGGATAATCCTTCT 58.939 52.381 5.01 0.00 36.57 2.85
2504 2560 2.444766 CAGGCCAGGGATAATCCTTCTT 59.555 50.000 5.01 0.00 36.57 2.52
2505 2561 3.117360 CAGGCCAGGGATAATCCTTCTTT 60.117 47.826 5.01 0.00 36.57 2.52
2506 2562 3.533487 AGGCCAGGGATAATCCTTCTTTT 59.467 43.478 5.01 0.00 36.57 2.27
2508 2564 4.386873 GGCCAGGGATAATCCTTCTTTTCT 60.387 45.833 0.00 0.00 36.57 2.52
2509 2565 5.163088 GGCCAGGGATAATCCTTCTTTTCTA 60.163 44.000 0.00 0.00 36.57 2.10
2511 2567 6.833933 GCCAGGGATAATCCTTCTTTTCTAAA 59.166 38.462 0.00 0.00 36.57 1.85
2512 2568 7.342026 GCCAGGGATAATCCTTCTTTTCTAAAA 59.658 37.037 0.00 0.00 36.57 1.52
2513 2569 9.255029 CCAGGGATAATCCTTCTTTTCTAAAAA 57.745 33.333 0.00 0.00 36.57 1.94
2594 2650 9.557061 AAGTCTCTAAAACGAACCTAAAATTCT 57.443 29.630 0.00 0.00 0.00 2.40
2648 2704 0.529773 TACTGCGGCGGATCATGAAC 60.530 55.000 17.15 0.00 0.00 3.18
2680 2736 2.223711 CCAGTTCCGTTTGTTCCAAAGG 60.224 50.000 3.16 3.16 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 72 5.171476 TGGAAATGAAGAGAACGTGATCTC 58.829 41.667 8.89 8.89 45.06 2.75
116 120 8.074370 GTGTCTTTACTATTTCAAACCCTCAAC 58.926 37.037 0.00 0.00 0.00 3.18
120 124 7.287810 AGTGTGTCTTTACTATTTCAAACCCT 58.712 34.615 0.00 0.00 0.00 4.34
209 214 2.346803 TCGTAGCTGGACTTTTCATGC 58.653 47.619 0.00 0.00 0.00 4.06
218 223 1.068250 GGGAGCATCGTAGCTGGAC 59.932 63.158 8.97 0.00 46.75 4.02
219 224 0.687757 AAGGGAGCATCGTAGCTGGA 60.688 55.000 8.97 0.00 46.75 3.86
220 225 0.249657 GAAGGGAGCATCGTAGCTGG 60.250 60.000 8.97 0.00 46.75 4.85
221 226 0.461548 TGAAGGGAGCATCGTAGCTG 59.538 55.000 8.97 0.00 46.75 4.24
223 228 2.024176 TTTGAAGGGAGCATCGTAGC 57.976 50.000 0.00 0.00 34.37 3.58
224 229 4.253685 TCTTTTTGAAGGGAGCATCGTAG 58.746 43.478 0.00 0.00 34.37 3.51
225 230 4.280436 TCTTTTTGAAGGGAGCATCGTA 57.720 40.909 0.00 0.00 34.37 3.43
226 231 3.140325 TCTTTTTGAAGGGAGCATCGT 57.860 42.857 0.00 0.00 34.37 3.73
227 232 4.503741 TTTCTTTTTGAAGGGAGCATCG 57.496 40.909 0.00 0.00 35.89 3.84
228 233 6.283694 ACTTTTTCTTTTTGAAGGGAGCATC 58.716 36.000 0.00 0.00 35.89 3.91
229 234 6.239217 ACTTTTTCTTTTTGAAGGGAGCAT 57.761 33.333 0.00 0.00 35.89 3.79
230 235 5.395214 GGACTTTTTCTTTTTGAAGGGAGCA 60.395 40.000 0.00 0.00 35.89 4.26
231 236 5.050490 GGACTTTTTCTTTTTGAAGGGAGC 58.950 41.667 0.00 0.00 35.89 4.70
232 237 6.220726 TGGACTTTTTCTTTTTGAAGGGAG 57.779 37.500 0.00 0.00 35.89 4.30
233 238 5.395214 GCTGGACTTTTTCTTTTTGAAGGGA 60.395 40.000 0.00 0.00 35.89 4.20
234 239 4.811024 GCTGGACTTTTTCTTTTTGAAGGG 59.189 41.667 0.00 0.00 35.89 3.95
235 240 5.664457 AGCTGGACTTTTTCTTTTTGAAGG 58.336 37.500 0.00 0.00 35.89 3.46
236 241 6.414987 CGTAGCTGGACTTTTTCTTTTTGAAG 59.585 38.462 0.00 0.00 35.89 3.02
237 242 6.094325 TCGTAGCTGGACTTTTTCTTTTTGAA 59.906 34.615 0.00 0.00 0.00 2.69
238 243 5.587043 TCGTAGCTGGACTTTTTCTTTTTGA 59.413 36.000 0.00 0.00 0.00 2.69
239 244 5.816919 TCGTAGCTGGACTTTTTCTTTTTG 58.183 37.500 0.00 0.00 0.00 2.44
240 245 6.294010 GGATCGTAGCTGGACTTTTTCTTTTT 60.294 38.462 0.00 0.00 0.00 1.94
241 246 5.181433 GGATCGTAGCTGGACTTTTTCTTTT 59.819 40.000 0.00 0.00 0.00 2.27
242 247 4.695928 GGATCGTAGCTGGACTTTTTCTTT 59.304 41.667 0.00 0.00 0.00 2.52
243 248 4.020128 AGGATCGTAGCTGGACTTTTTCTT 60.020 41.667 0.00 0.00 0.00 2.52
244 249 3.515901 AGGATCGTAGCTGGACTTTTTCT 59.484 43.478 0.00 0.00 0.00 2.52
245 250 3.863041 AGGATCGTAGCTGGACTTTTTC 58.137 45.455 0.00 0.00 0.00 2.29
246 251 3.983044 AGGATCGTAGCTGGACTTTTT 57.017 42.857 0.00 0.00 0.00 1.94
247 252 3.260884 TGAAGGATCGTAGCTGGACTTTT 59.739 43.478 0.00 0.00 0.00 2.27
248 253 2.832129 TGAAGGATCGTAGCTGGACTTT 59.168 45.455 0.00 0.00 0.00 2.66
249 254 2.166664 GTGAAGGATCGTAGCTGGACTT 59.833 50.000 0.00 0.00 0.00 3.01
250 255 1.751924 GTGAAGGATCGTAGCTGGACT 59.248 52.381 0.00 0.00 0.00 3.85
278 283 8.501580 CATCAATTACAGAATATCTCGTTGCAT 58.498 33.333 0.00 0.00 0.00 3.96
306 311 6.855914 CTTCTAAAGAAACATTGCTAAACGCA 59.144 34.615 0.00 0.00 39.25 5.24
308 313 8.067784 TGTCTTCTAAAGAAACATTGCTAAACG 58.932 33.333 0.00 0.00 39.67 3.60
320 325 8.750298 CCACCTACTAGATGTCTTCTAAAGAAA 58.250 37.037 0.00 0.00 39.67 2.52
323 328 7.648039 ACCACCTACTAGATGTCTTCTAAAG 57.352 40.000 0.00 0.00 36.50 1.85
416 422 7.447374 TGTTTATGTTTCATCAACCACCTAG 57.553 36.000 4.94 0.00 33.97 3.02
475 483 1.398958 ATGTTTGTGCGGGGCTTGTT 61.399 50.000 0.00 0.00 0.00 2.83
531 539 4.757554 CGTACATCACGCTGTCGA 57.242 55.556 0.00 0.00 45.03 4.20
541 555 4.115516 ACATGATGTTCTCAGCGTACATC 58.884 43.478 0.00 0.00 45.22 3.06
542 556 4.128925 ACATGATGTTCTCAGCGTACAT 57.871 40.909 0.00 0.00 37.28 2.29
549 563 6.732154 ACAACTTGAAACATGATGTTCTCAG 58.268 36.000 11.70 9.62 40.14 3.35
574 588 5.639757 TCGCATGAAAATTGTTACATGGAG 58.360 37.500 0.00 0.00 39.96 3.86
653 667 3.050089 TGACTGGAGTACCCTGGAAAAA 58.950 45.455 0.00 0.00 38.11 1.94
692 706 9.094578 AGTGAGAATAGCTGGCTAGAATTAATA 57.905 33.333 0.00 0.00 31.45 0.98
873 889 6.544197 GGGTTAGGATGGAAATCTTCTTCTTC 59.456 42.308 0.00 0.00 0.00 2.87
1014 1032 3.655810 GAGAGGCGGACAGTGGCAG 62.656 68.421 0.00 0.00 0.00 4.85
1170 1188 3.851845 TTGTCGAAGTGCCCGTCGG 62.852 63.158 3.60 3.60 41.94 4.79
1171 1189 2.355363 TTGTCGAAGTGCCCGTCG 60.355 61.111 0.00 0.00 42.82 5.12
1172 1190 2.027625 CCTTGTCGAAGTGCCCGTC 61.028 63.158 0.00 0.00 0.00 4.79
1357 1384 0.649910 CGTAGCTGTACGCGTCGTAG 60.650 60.000 18.63 14.06 45.22 3.51
1530 1557 3.242188 ACAAAAGAAAGAAACGACGGTCG 60.242 43.478 27.33 27.33 46.93 4.79
1539 1566 9.036671 ACAAAGAACGAAAACAAAAGAAAGAAA 57.963 25.926 0.00 0.00 0.00 2.52
1540 1567 8.582433 ACAAAGAACGAAAACAAAAGAAAGAA 57.418 26.923 0.00 0.00 0.00 2.52
1541 1568 8.582433 AACAAAGAACGAAAACAAAAGAAAGA 57.418 26.923 0.00 0.00 0.00 2.52
1542 1569 9.301606 GAAACAAAGAACGAAAACAAAAGAAAG 57.698 29.630 0.00 0.00 0.00 2.62
1574 1601 5.638657 CCAAAACTGAGACAGAGATGAGAAG 59.361 44.000 5.76 0.00 35.18 2.85
1637 1664 0.551396 AGGGGCTACCATTTACAGGC 59.449 55.000 0.97 0.00 43.89 4.85
1697 1728 1.813102 AAGGGTTTGGGGCAAAATCA 58.187 45.000 0.00 0.00 35.03 2.57
1789 1821 8.462016 AGATGTTGGAACTAAGCAAATCATTAC 58.538 33.333 0.00 0.00 0.00 1.89
1832 1871 4.881850 ACTTGGATTCTCGAAACAAACTGT 59.118 37.500 0.00 0.00 0.00 3.55
1834 1873 4.261197 GCACTTGGATTCTCGAAACAAACT 60.261 41.667 0.00 0.00 0.00 2.66
1835 1874 3.975035 GCACTTGGATTCTCGAAACAAAC 59.025 43.478 0.00 0.00 0.00 2.93
1836 1875 3.629855 TGCACTTGGATTCTCGAAACAAA 59.370 39.130 0.00 0.00 0.00 2.83
1842 1883 2.234661 AGATGTGCACTTGGATTCTCGA 59.765 45.455 19.41 0.00 0.00 4.04
1844 1885 4.333926 GGTAAGATGTGCACTTGGATTCTC 59.666 45.833 19.41 0.00 0.00 2.87
1859 1905 6.774656 AGGGATAAGCATTTTCTGGTAAGATG 59.225 38.462 0.00 0.00 33.48 2.90
1889 1935 8.608844 AATAATAATTCTGTAAAGAGAGGGCG 57.391 34.615 0.00 0.00 0.00 6.13
1943 1989 1.226101 CCTAATTGCTGCGCACACG 60.226 57.895 5.66 0.00 38.71 4.49
1984 2030 4.111916 CACCAAGAAACATGTTTGACCAC 58.888 43.478 27.85 13.05 32.11 4.16
2056 2102 3.060339 CGTTTGGTGCATTGAAAAAGAGC 60.060 43.478 0.00 0.00 0.00 4.09
2171 2219 5.287674 TGGAATGAAATTTGCTTCACCAA 57.712 34.783 0.00 0.00 36.07 3.67
2205 2253 7.323656 CGAGTTTTCTCCATTAATTTGTGACAC 59.676 37.037 0.00 0.00 43.49 3.67
2206 2254 7.359595 CGAGTTTTCTCCATTAATTTGTGACA 58.640 34.615 0.00 0.00 43.49 3.58
2207 2255 6.801862 CCGAGTTTTCTCCATTAATTTGTGAC 59.198 38.462 0.00 0.00 43.49 3.67
2223 2272 6.020995 CACACACAAAATTGTACCGAGTTTTC 60.021 38.462 0.00 0.00 39.91 2.29
2237 2286 5.010617 GTCCTAATTCCCACACACACAAAAT 59.989 40.000 0.00 0.00 0.00 1.82
2242 2291 2.073816 CGTCCTAATTCCCACACACAC 58.926 52.381 0.00 0.00 0.00 3.82
2245 2294 1.553248 CTCCGTCCTAATTCCCACACA 59.447 52.381 0.00 0.00 0.00 3.72
2247 2296 1.200519 CCTCCGTCCTAATTCCCACA 58.799 55.000 0.00 0.00 0.00 4.17
2248 2297 1.138464 GTCCTCCGTCCTAATTCCCAC 59.862 57.143 0.00 0.00 0.00 4.61
2268 2317 3.430862 CGTGTGATGCCAACCCCG 61.431 66.667 0.00 0.00 0.00 5.73
2288 2337 1.079503 GAGATGAGGTCGGCAACAAC 58.920 55.000 0.00 0.00 0.00 3.32
2312 2361 0.807667 CTGCGACATCTCCCTTTCGG 60.808 60.000 0.00 0.00 32.04 4.30
2324 2373 1.899814 AGACCCAGATTAACTGCGACA 59.100 47.619 0.00 0.00 44.52 4.35
2341 2390 5.864628 AGATTGCCTCTTCGTTTAAAGAC 57.135 39.130 0.00 0.00 32.03 3.01
2439 2495 6.418819 GTGCATGATAATCCACTTGCAAATAC 59.581 38.462 0.00 0.00 44.33 1.89
2462 2518 2.797792 GCATCTGAGCGAGGAAGTAGTG 60.798 54.545 0.00 0.00 0.00 2.74
2464 2520 1.406898 TGCATCTGAGCGAGGAAGTAG 59.593 52.381 0.00 0.00 37.31 2.57
2465 2521 1.406898 CTGCATCTGAGCGAGGAAGTA 59.593 52.381 0.00 0.00 37.31 2.24
2466 2522 0.175302 CTGCATCTGAGCGAGGAAGT 59.825 55.000 0.00 0.00 37.31 3.01
2467 2523 0.530211 CCTGCATCTGAGCGAGGAAG 60.530 60.000 0.00 0.00 35.91 3.46
2469 2525 3.086391 GCCTGCATCTGAGCGAGGA 62.086 63.158 14.90 0.00 35.91 3.71
2471 2527 2.588314 GGCCTGCATCTGAGCGAG 60.588 66.667 0.00 0.00 37.31 5.03
2475 2531 1.706995 ATCCCTGGCCTGCATCTGAG 61.707 60.000 3.32 0.00 0.00 3.35
2477 2533 0.475475 TTATCCCTGGCCTGCATCTG 59.525 55.000 3.32 0.00 0.00 2.90
2478 2534 1.353694 GATTATCCCTGGCCTGCATCT 59.646 52.381 3.32 0.00 0.00 2.90
2479 2535 1.615384 GGATTATCCCTGGCCTGCATC 60.615 57.143 3.32 0.36 0.00 3.91
2482 2538 0.480252 AAGGATTATCCCTGGCCTGC 59.520 55.000 7.76 0.00 37.19 4.85
2483 2539 2.061061 AGAAGGATTATCCCTGGCCTG 58.939 52.381 7.76 2.54 37.19 4.85
2487 2543 8.823220 TTTTAGAAAAGAAGGATTATCCCTGG 57.177 34.615 7.76 0.00 37.19 4.45
2514 2570 7.500141 TGTTTACCGAGGAAGTAGTACTTTTT 58.500 34.615 16.56 8.24 38.80 1.94
2515 2571 7.054491 TGTTTACCGAGGAAGTAGTACTTTT 57.946 36.000 16.56 8.58 38.80 2.27
2516 2572 6.655078 TGTTTACCGAGGAAGTAGTACTTT 57.345 37.500 16.56 1.94 38.80 2.66
2594 2650 4.853196 CGTAGAACCGTTCGTTAGATTTGA 59.147 41.667 5.62 0.00 33.74 2.69
2608 2664 0.096976 CAAATGCAGCCGTAGAACCG 59.903 55.000 0.00 0.00 0.00 4.44
2648 2704 5.586243 ACAAACGGAACTGGATTATCATGAG 59.414 40.000 0.09 0.00 0.00 2.90
2653 2709 4.698304 TGGAACAAACGGAACTGGATTATC 59.302 41.667 0.00 0.00 31.92 1.75


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

AutoCloner maintained by Alex Coulton.