Multiple sequence alignment - TraesCS5B01G351000

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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 TraesCS5B01G351000 chr5B 100.000 3958 0 0 1 3958 531547218 531543261 0.000000e+00 7310.0
1 TraesCS5B01G351000 chr5B 78.014 564 103 12 292 845 405497124 405497676 6.340000e-88 335.0
2 TraesCS5B01G351000 chr5D 92.866 3210 137 23 782 3958 437350067 437346917 0.000000e+00 4575.0
3 TraesCS5B01G351000 chr5A 94.092 1388 57 14 864 2245 552531084 552529716 0.000000e+00 2085.0
4 TraesCS5B01G351000 chr5A 94.356 1063 33 7 2907 3958 552528832 552527786 0.000000e+00 1605.0
5 TraesCS5B01G351000 chr5A 88.794 821 70 13 40 849 552531879 552531070 0.000000e+00 987.0
6 TraesCS5B01G351000 chr5A 86.090 266 24 4 2474 2726 552529607 552529342 1.400000e-69 274.0
7 TraesCS5B01G351000 chr5A 90.000 120 5 3 2288 2407 552529716 552529604 8.860000e-32 148.0
8 TraesCS5B01G351000 chr5A 92.857 56 4 0 2792 2847 552528907 552528852 9.120000e-12 82.4
9 TraesCS5B01G351000 chr5A 72.059 272 62 8 576 845 649808857 649808598 7.100000e-08 69.4
10 TraesCS5B01G351000 chr3A 72.079 856 193 31 7 845 488115387 488114561 8.610000e-52 215.0
11 TraesCS5B01G351000 chr3A 96.875 32 1 0 583 614 19784037 19784068 2.000000e-03 54.7
12 TraesCS5B01G351000 chr4D 100.000 32 0 0 3582 3613 56719339 56719308 4.270000e-05 60.2
13 TraesCS5B01G351000 chr1D 100.000 32 0 0 3582 3613 49604547 49604578 4.270000e-05 60.2
14 TraesCS5B01G351000 chr4B 97.059 34 0 1 3580 3612 143312873 143312906 5.530000e-04 56.5
15 TraesCS5B01G351000 chr1B 94.444 36 2 0 786 821 163704564 163704599 5.530000e-04 56.5
16 TraesCS5B01G351000 chr4A 100.000 29 0 0 3585 3613 200093505 200093533 2.000000e-03 54.7
17 TraesCS5B01G351000 chr3D 100.000 28 0 0 783 810 61848368 61848341 7.000000e-03 52.8
18 TraesCS5B01G351000 chr2D 100.000 28 0 0 3586 3613 608200169 608200142 7.000000e-03 52.8


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 TraesCS5B01G351000 chr5B 531543261 531547218 3957 True 7310.000000 7310 100.0000 1 3958 1 chr5B.!!$R1 3957
1 TraesCS5B01G351000 chr5B 405497124 405497676 552 False 335.000000 335 78.0140 292 845 1 chr5B.!!$F1 553
2 TraesCS5B01G351000 chr5D 437346917 437350067 3150 True 4575.000000 4575 92.8660 782 3958 1 chr5D.!!$R1 3176
3 TraesCS5B01G351000 chr5A 552527786 552531879 4093 True 863.566667 2085 91.0315 40 3958 6 chr5A.!!$R2 3918
4 TraesCS5B01G351000 chr3A 488114561 488115387 826 True 215.000000 215 72.0790 7 845 1 chr3A.!!$R1 838

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
978 1032 0.533755 CTTCTGCGAAGGCCCATAGG 60.534 60.0 0.0 0.0 38.85 2.57 F
2075 2138 0.039764 ACCTGGTCTCATCTGTCCGA 59.960 55.0 0.0 0.0 0.00 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 2280 0.541392 ACCGCTGTAATGAGGATGCA 59.459 50.000 0.00 0.00 0.00 3.96 R
3127 3658 1.302511 CCACGGAACCAAGGGTCAG 60.303 63.158 6.47 4.49 33.12 3.51 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
21 22 2.416547 CCTGCAGATCTTGGTTGTAACG 59.583 50.000 17.39 0.00 0.00 3.18
23 24 3.325870 TGCAGATCTTGGTTGTAACGAG 58.674 45.455 0.00 0.00 0.00 4.18
27 28 5.109210 CAGATCTTGGTTGTAACGAGCATA 58.891 41.667 0.00 0.00 0.00 3.14
28 29 5.005779 CAGATCTTGGTTGTAACGAGCATAC 59.994 44.000 0.00 0.00 0.00 2.39
30 31 1.999048 TGGTTGTAACGAGCATACGG 58.001 50.000 0.00 0.00 37.61 4.02
33 34 3.111098 GGTTGTAACGAGCATACGGTAG 58.889 50.000 0.00 0.00 36.13 3.18
37 38 1.683943 AACGAGCATACGGTAGGCTA 58.316 50.000 25.19 0.00 46.96 3.93
39 40 1.336125 ACGAGCATACGGTAGGCTAAC 59.664 52.381 25.19 13.99 46.96 2.34
63 64 6.183361 ACCTTACTAAGAATGTTCCCTTTGGT 60.183 38.462 0.00 0.00 0.00 3.67
111 112 3.247006 ACTTGCCTTGTACATACGGAG 57.753 47.619 0.00 0.00 0.00 4.63
130 131 4.023107 CGGAGATAGACAAAATAGCCTCGA 60.023 45.833 0.00 0.00 0.00 4.04
140 141 5.106157 ACAAAATAGCCTCGACATCAAAAGG 60.106 40.000 0.00 0.00 0.00 3.11
172 173 5.032846 TGTTTCAGACCAGATCCCTATTCT 58.967 41.667 0.00 0.00 0.00 2.40
175 176 5.004361 TCAGACCAGATCCCTATTCTAGG 57.996 47.826 0.00 0.00 45.81 3.02
231 236 5.398603 ACTGTGGTGAATTTTGTGACAAA 57.601 34.783 6.66 6.66 0.00 2.83
234 239 5.788450 TGTGGTGAATTTTGTGACAAACTT 58.212 33.333 10.72 11.75 0.00 2.66
247 252 2.673368 GACAAACTTGTGATAGGCCTCG 59.327 50.000 9.68 0.00 42.43 4.63
255 260 4.801330 TGTGATAGGCCTCGTATTATGG 57.199 45.455 9.68 0.00 0.00 2.74
285 290 4.202151 GGAAGCCAATTATCTCGCCAAATT 60.202 41.667 0.00 0.00 0.00 1.82
321 327 3.217626 CCATTGCCCACTCTTCTAATCC 58.782 50.000 0.00 0.00 0.00 3.01
350 361 3.555966 AGCCAATATTCCTTTCCCTTCG 58.444 45.455 0.00 0.00 0.00 3.79
371 382 1.647545 CTATTGCACGCCACACCTGG 61.648 60.000 0.00 0.00 41.13 4.45
449 460 5.477984 TGCTTTGAGGATTCTTGCACTTAAT 59.522 36.000 0.00 0.00 0.00 1.40
450 461 5.803967 GCTTTGAGGATTCTTGCACTTAATG 59.196 40.000 0.00 0.00 0.00 1.90
471 482 4.631234 TGAGTTTGGGTCCTGGAGTATAT 58.369 43.478 0.00 0.00 0.00 0.86
479 494 3.557898 GGTCCTGGAGTATATGCCATGTG 60.558 52.174 0.00 0.00 32.89 3.21
495 510 1.189752 TGTGGAGCCAACAAAGCAAA 58.810 45.000 0.00 0.00 0.00 3.68
561 578 4.356405 TGTCTTGTCATGACCTCACAAT 57.644 40.909 22.85 0.00 33.83 2.71
570 587 4.764823 TCATGACCTCACAATAAACCCAAC 59.235 41.667 0.00 0.00 0.00 3.77
634 655 9.941325 CCTGATAAGAGAATTAATATGCTGAGT 57.059 33.333 0.00 0.00 0.00 3.41
641 662 9.624373 AGAGAATTAATATGCTGAGTTGTTGAT 57.376 29.630 0.00 0.00 0.00 2.57
652 673 5.649557 CTGAGTTGTTGATAGAGTCCTCTG 58.350 45.833 7.08 0.00 40.71 3.35
680 701 5.406780 AGTTTGAAGCAAGACATCGAGTAAG 59.593 40.000 0.00 0.00 0.00 2.34
714 735 6.888632 ACTTGAGCAACAGATTTTATGAGGAT 59.111 34.615 0.00 0.00 0.00 3.24
770 792 8.519799 TCATCCATCCTTTTAACTTATTCCAC 57.480 34.615 0.00 0.00 0.00 4.02
833 887 2.726821 CCAACATCACTTGGCATACCT 58.273 47.619 0.00 0.00 34.50 3.08
845 899 7.450014 TCACTTGGCATACCTAAAATTTTCTCA 59.550 33.333 6.72 0.00 36.63 3.27
846 900 7.542130 CACTTGGCATACCTAAAATTTTCTCAC 59.458 37.037 6.72 0.00 36.63 3.51
847 901 7.232534 ACTTGGCATACCTAAAATTTTCTCACA 59.767 33.333 6.72 0.00 36.63 3.58
848 902 7.716799 TGGCATACCTAAAATTTTCTCACAT 57.283 32.000 6.72 0.00 36.63 3.21
849 903 8.133024 TGGCATACCTAAAATTTTCTCACATT 57.867 30.769 6.72 0.00 36.63 2.71
850 904 8.592809 TGGCATACCTAAAATTTTCTCACATTT 58.407 29.630 6.72 0.00 36.63 2.32
851 905 9.435688 GGCATACCTAAAATTTTCTCACATTTT 57.564 29.630 6.72 0.00 36.69 1.82
899 953 3.713248 TGGATGACTAGTCTGATGCCATT 59.287 43.478 23.01 0.00 0.00 3.16
978 1032 0.533755 CTTCTGCGAAGGCCCATAGG 60.534 60.000 0.00 0.00 38.85 2.57
1043 1097 2.541120 CCTCTACCGTACCGCCTCG 61.541 68.421 0.00 0.00 0.00 4.63
1779 1842 2.785921 CAGTCGGACGAGGACGAG 59.214 66.667 1.89 0.00 40.09 4.18
1902 1965 2.264794 GCGGCGAGGAAGGAGAAA 59.735 61.111 12.98 0.00 0.00 2.52
1903 1966 2.101233 GCGGCGAGGAAGGAGAAAC 61.101 63.158 12.98 0.00 0.00 2.78
1941 2004 2.400402 GAGAGCGACGAGGACGAC 59.600 66.667 0.00 0.00 42.66 4.34
1972 2035 1.560292 GCGTATGCTTCTAGCGTGC 59.440 57.895 0.00 1.63 46.26 5.34
2068 2131 1.079503 GTTGCGAACCTGGTCTCATC 58.920 55.000 0.00 0.00 0.00 2.92
2075 2138 0.039764 ACCTGGTCTCATCTGTCCGA 59.960 55.000 0.00 0.00 0.00 4.55
2077 2140 1.468985 CTGGTCTCATCTGTCCGAGT 58.531 55.000 0.00 0.00 0.00 4.18
2078 2141 1.821753 CTGGTCTCATCTGTCCGAGTT 59.178 52.381 0.00 0.00 0.00 3.01
2191 2257 9.710818 TGTTTAGGGTTATAGAGAGTGTAGATT 57.289 33.333 0.00 0.00 0.00 2.40
2198 2264 9.073475 GGTTATAGAGAGTGTAGATTGATGAGT 57.927 37.037 0.00 0.00 0.00 3.41
2214 2280 3.014304 TGAGTTATCGGCCTACTGTCT 57.986 47.619 0.00 0.00 0.00 3.41
2216 2282 1.409427 AGTTATCGGCCTACTGTCTGC 59.591 52.381 0.00 0.00 0.00 4.26
2217 2283 1.136305 GTTATCGGCCTACTGTCTGCA 59.864 52.381 0.00 0.00 0.00 4.41
2232 2298 1.202568 TCTGCATCCTCATTACAGCGG 60.203 52.381 0.00 0.00 0.00 5.52
2237 2303 3.119495 GCATCCTCATTACAGCGGTTTTT 60.119 43.478 0.00 0.00 0.00 1.94
2247 2313 8.898761 TCATTACAGCGGTTTTTGATATATTGT 58.101 29.630 0.00 0.00 0.00 2.71
2256 2322 9.347934 CGGTTTTTGATATATTGTTGCTTGTTA 57.652 29.630 0.00 0.00 0.00 2.41
2271 2337 4.003648 GCTTGTTACTTGTGGCAGACTAT 58.996 43.478 0.00 0.00 0.00 2.12
2273 2339 5.817816 GCTTGTTACTTGTGGCAGACTATAT 59.182 40.000 0.00 0.00 0.00 0.86
2274 2340 6.316390 GCTTGTTACTTGTGGCAGACTATATT 59.684 38.462 0.00 0.00 0.00 1.28
2284 2355 4.100963 TGGCAGACTATATTGGTACCTGTG 59.899 45.833 14.36 0.48 0.00 3.66
2320 2391 4.044444 ACCCCATATGTGATATGCATTCCA 59.956 41.667 3.54 0.00 40.96 3.53
2341 2412 6.065374 TCCACAGCAACCTTAATTTGTTCTA 58.935 36.000 0.00 0.00 0.00 2.10
2360 2431 9.500785 TTGTTCTATTCAATCTATGTGTTGTGA 57.499 29.630 0.00 0.00 0.00 3.58
2361 2432 9.671279 TGTTCTATTCAATCTATGTGTTGTGAT 57.329 29.630 0.00 0.00 0.00 3.06
2366 2437 8.975410 ATTCAATCTATGTGTTGTGATTTGTG 57.025 30.769 0.00 0.00 0.00 3.33
2411 2482 8.807667 ATATTGCATTAAGAACTATTTGCAGC 57.192 30.769 0.00 0.00 32.51 5.25
2412 2483 5.641783 TGCATTAAGAACTATTTGCAGCA 57.358 34.783 0.00 0.00 0.00 4.41
2413 2484 6.023357 TGCATTAAGAACTATTTGCAGCAA 57.977 33.333 2.83 2.83 0.00 3.91
2414 2485 6.632909 TGCATTAAGAACTATTTGCAGCAAT 58.367 32.000 9.12 2.06 0.00 3.56
2415 2486 7.770201 TGCATTAAGAACTATTTGCAGCAATA 58.230 30.769 9.12 0.40 0.00 1.90
2416 2487 8.249638 TGCATTAAGAACTATTTGCAGCAATAA 58.750 29.630 9.12 2.38 0.00 1.40
2417 2488 8.749499 GCATTAAGAACTATTTGCAGCAATAAG 58.251 33.333 9.12 11.73 0.00 1.73
2418 2489 9.793252 CATTAAGAACTATTTGCAGCAATAAGT 57.207 29.630 9.12 12.38 0.00 2.24
2424 2495 9.387123 GAACTATTTGCAGCAATAAGTTATAGC 57.613 33.333 24.89 14.72 32.63 2.97
2425 2496 7.576236 ACTATTTGCAGCAATAAGTTATAGCG 58.424 34.615 9.12 0.00 0.00 4.26
2426 2497 3.878086 TGCAGCAATAAGTTATAGCGC 57.122 42.857 0.00 0.00 0.00 5.92
2427 2498 3.466836 TGCAGCAATAAGTTATAGCGCT 58.533 40.909 17.26 17.26 0.00 5.92
2428 2499 4.627058 TGCAGCAATAAGTTATAGCGCTA 58.373 39.130 21.30 21.30 0.00 4.26
2429 2500 5.053811 TGCAGCAATAAGTTATAGCGCTAA 58.946 37.500 22.98 4.55 0.00 3.09
2430 2501 5.177511 TGCAGCAATAAGTTATAGCGCTAAG 59.822 40.000 22.98 4.32 0.00 2.18
2431 2502 5.405571 GCAGCAATAAGTTATAGCGCTAAGA 59.594 40.000 22.98 9.90 0.00 2.10
2432 2503 6.616682 GCAGCAATAAGTTATAGCGCTAAGAC 60.617 42.308 22.98 21.13 0.00 3.01
2433 2504 6.642950 CAGCAATAAGTTATAGCGCTAAGACT 59.357 38.462 22.98 22.93 0.00 3.24
2434 2505 6.864165 AGCAATAAGTTATAGCGCTAAGACTC 59.136 38.462 26.42 17.56 0.00 3.36
2435 2506 6.641314 GCAATAAGTTATAGCGCTAAGACTCA 59.359 38.462 26.42 18.13 0.00 3.41
2436 2507 7.169308 GCAATAAGTTATAGCGCTAAGACTCAA 59.831 37.037 26.42 20.29 0.00 3.02
2437 2508 9.031360 CAATAAGTTATAGCGCTAAGACTCAAA 57.969 33.333 26.42 18.57 0.00 2.69
2438 2509 9.765795 AATAAGTTATAGCGCTAAGACTCAAAT 57.234 29.630 26.42 19.50 0.00 2.32
2439 2510 9.765795 ATAAGTTATAGCGCTAAGACTCAAATT 57.234 29.630 26.42 17.30 0.00 1.82
2441 2512 9.765795 AAGTTATAGCGCTAAGACTCAAATTAT 57.234 29.630 26.42 13.10 0.00 1.28
2442 2513 9.413048 AGTTATAGCGCTAAGACTCAAATTATC 57.587 33.333 22.98 4.50 0.00 1.75
2443 2514 9.413048 GTTATAGCGCTAAGACTCAAATTATCT 57.587 33.333 22.98 0.97 0.00 1.98
2446 2517 7.938563 AGCGCTAAGACTCAAATTATCTAAG 57.061 36.000 8.99 0.00 0.00 2.18
2447 2518 7.717568 AGCGCTAAGACTCAAATTATCTAAGA 58.282 34.615 8.99 0.00 0.00 2.10
2448 2519 8.198109 AGCGCTAAGACTCAAATTATCTAAGAA 58.802 33.333 8.99 0.00 0.00 2.52
2449 2520 8.818057 GCGCTAAGACTCAAATTATCTAAGAAA 58.182 33.333 0.00 0.00 0.00 2.52
2457 2528 9.804758 ACTCAAATTATCTAAGAAACGTAGAGG 57.195 33.333 0.00 0.00 31.27 3.69
2458 2529 8.644318 TCAAATTATCTAAGAAACGTAGAGGC 57.356 34.615 0.00 0.00 31.27 4.70
2459 2530 8.255206 TCAAATTATCTAAGAAACGTAGAGGCA 58.745 33.333 0.00 0.00 31.27 4.75
2460 2531 8.543774 CAAATTATCTAAGAAACGTAGAGGCAG 58.456 37.037 0.00 0.00 31.27 4.85
2461 2532 7.584122 ATTATCTAAGAAACGTAGAGGCAGA 57.416 36.000 0.00 0.00 31.27 4.26
2462 2533 5.916661 ATCTAAGAAACGTAGAGGCAGAA 57.083 39.130 0.00 0.00 31.27 3.02
2463 2534 5.916661 TCTAAGAAACGTAGAGGCAGAAT 57.083 39.130 0.00 0.00 0.00 2.40
2464 2535 6.282199 TCTAAGAAACGTAGAGGCAGAATT 57.718 37.500 0.00 0.00 0.00 2.17
2465 2536 7.400599 TCTAAGAAACGTAGAGGCAGAATTA 57.599 36.000 0.00 0.00 0.00 1.40
2466 2537 8.008513 TCTAAGAAACGTAGAGGCAGAATTAT 57.991 34.615 0.00 0.00 0.00 1.28
2467 2538 9.128404 TCTAAGAAACGTAGAGGCAGAATTATA 57.872 33.333 0.00 0.00 0.00 0.98
2468 2539 9.915629 CTAAGAAACGTAGAGGCAGAATTATAT 57.084 33.333 0.00 0.00 0.00 0.86
2533 2674 7.805071 CACATTTAAGCTCGTTCTTCAATTCTT 59.195 33.333 0.00 0.00 0.00 2.52
2534 2675 8.999431 ACATTTAAGCTCGTTCTTCAATTCTTA 58.001 29.630 0.00 0.00 0.00 2.10
2575 2726 4.579869 AGAAGCAAATGTACATTCGGTCT 58.420 39.130 21.02 16.71 0.00 3.85
2577 2728 3.009723 AGCAAATGTACATTCGGTCTGG 58.990 45.455 21.02 6.80 0.00 3.86
2642 2796 6.150307 TGTTCTTACACAATGTTGTCTGTTGT 59.850 34.615 0.00 0.00 39.91 3.32
2669 2823 7.993101 CATTCTTGATGGTTGTAGTTGATCAT 58.007 34.615 0.00 0.00 31.83 2.45
2710 2864 3.928727 ATGTGTTTCTGCTGTCCATTG 57.071 42.857 0.00 0.00 0.00 2.82
2808 3331 1.640917 ACATACGTCCAGACTGGGTT 58.359 50.000 21.56 8.46 38.32 4.11
2847 3370 1.376037 AGTTGGCTCGCAGGCTTAC 60.376 57.895 10.22 8.48 41.96 2.34
3272 3803 3.754965 CTGTCCTTCACTTGGGATTTGA 58.245 45.455 0.00 0.00 33.89 2.69
3350 3881 5.423931 ACAAAAGTTTAACATGTCTTGGGGT 59.576 36.000 0.00 0.00 0.00 4.95
3773 4314 4.513442 TCCATGTACCAAATGTAGCTGTC 58.487 43.478 0.00 0.00 0.00 3.51
3784 4325 6.036517 CCAAATGTAGCTGTCACATACTTCTC 59.963 42.308 0.00 0.00 35.58 2.87
3808 4349 9.552114 CTCTTCTTTGTATTTGTTATTGCTCTG 57.448 33.333 0.00 0.00 0.00 3.35
3855 4396 8.718102 TTCTACTATGTTTCATCTTGTAAGCC 57.282 34.615 0.00 0.00 0.00 4.35
3877 4418 4.219033 CGAATAGTTTGCTGGTTGTTGTC 58.781 43.478 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.094417 GCTCGTTACAACCAAGATCTGC 59.906 50.000 0.00 0.00 0.00 4.26
4 5 3.325870 TGCTCGTTACAACCAAGATCTG 58.674 45.455 0.00 0.00 0.00 2.90
5 6 3.678056 TGCTCGTTACAACCAAGATCT 57.322 42.857 0.00 0.00 0.00 2.75
12 13 2.000429 ACCGTATGCTCGTTACAACC 58.000 50.000 0.00 0.00 0.00 3.77
18 19 1.683943 TAGCCTACCGTATGCTCGTT 58.316 50.000 11.15 0.00 36.57 3.85
21 22 1.962100 AGGTTAGCCTACCGTATGCTC 59.038 52.381 11.15 0.00 44.90 4.26
23 24 2.904697 AAGGTTAGCCTACCGTATGC 57.095 50.000 0.00 0.00 46.33 3.14
27 28 4.860022 TCTTAGTAAGGTTAGCCTACCGT 58.140 43.478 10.02 0.00 46.33 4.83
28 29 5.841957 TTCTTAGTAAGGTTAGCCTACCG 57.158 43.478 10.02 0.00 46.33 4.02
30 31 7.710044 GGAACATTCTTAGTAAGGTTAGCCTAC 59.290 40.741 10.02 0.00 46.33 3.18
33 34 5.821470 GGGAACATTCTTAGTAAGGTTAGCC 59.179 44.000 10.02 5.29 33.83 3.93
37 38 6.719829 CCAAAGGGAACATTCTTAGTAAGGTT 59.280 38.462 10.02 6.42 36.17 3.50
39 40 6.246163 ACCAAAGGGAACATTCTTAGTAAGG 58.754 40.000 10.02 0.00 38.05 2.69
63 64 2.673775 TTTGGGCTTGGAGTCATGAA 57.326 45.000 0.00 0.00 0.00 2.57
111 112 6.216569 TGATGTCGAGGCTATTTTGTCTATC 58.783 40.000 0.00 0.00 0.00 2.08
140 141 9.220767 GGGATCTGGTCTGAAACATATTTATAC 57.779 37.037 0.00 0.00 0.00 1.47
172 173 2.836636 TTGCATAACATTGGGGCCTA 57.163 45.000 0.84 0.00 0.00 3.93
175 176 4.281688 ACTCATATTGCATAACATTGGGGC 59.718 41.667 0.00 0.00 0.00 5.80
207 211 6.516739 TTGTCACAAAATTCACCACAGTTA 57.483 33.333 0.00 0.00 0.00 2.24
231 236 5.279506 CCATAATACGAGGCCTATCACAAGT 60.280 44.000 4.42 0.00 0.00 3.16
234 239 4.157246 ACCATAATACGAGGCCTATCACA 58.843 43.478 4.42 0.00 0.00 3.58
247 252 3.181469 TGGCTTCCACGAGACCATAATAC 60.181 47.826 0.00 0.00 0.00 1.89
255 260 3.798202 AGATAATTGGCTTCCACGAGAC 58.202 45.455 0.00 0.00 30.78 3.36
321 327 3.199880 AGGAATATTGGCTCAAGGTCG 57.800 47.619 0.00 0.00 0.00 4.79
350 361 0.673644 AGGTGTGGCGTGCAATAGTC 60.674 55.000 0.00 0.00 0.00 2.59
371 382 2.027385 GAATTGGGAAGCTCACCATCC 58.973 52.381 9.85 1.51 36.48 3.51
407 418 8.846943 TCAAAGCAAAATATCTCTCTACAACA 57.153 30.769 0.00 0.00 0.00 3.33
418 429 7.009907 GTGCAAGAATCCTCAAAGCAAAATATC 59.990 37.037 0.00 0.00 31.78 1.63
422 433 4.099881 AGTGCAAGAATCCTCAAAGCAAAA 59.900 37.500 0.00 0.00 31.78 2.44
449 460 2.409064 TACTCCAGGACCCAAACTCA 57.591 50.000 0.00 0.00 0.00 3.41
450 461 4.743955 GCATATACTCCAGGACCCAAACTC 60.744 50.000 0.00 0.00 0.00 3.01
471 482 0.758310 TTTGTTGGCTCCACATGGCA 60.758 50.000 0.00 0.00 38.22 4.92
479 494 2.602257 AACTTTGCTTTGTTGGCTCC 57.398 45.000 0.00 0.00 0.00 4.70
540 557 3.836365 TTGTGAGGTCATGACAAGACA 57.164 42.857 26.47 20.15 37.74 3.41
561 578 2.696187 GTGAAAAGGCCAGTTGGGTTTA 59.304 45.455 5.01 0.00 39.65 2.01
570 587 0.113190 AAGGAGGGTGAAAAGGCCAG 59.887 55.000 5.01 0.00 0.00 4.85
627 648 3.834813 AGGACTCTATCAACAACTCAGCA 59.165 43.478 0.00 0.00 0.00 4.41
628 649 4.159506 AGAGGACTCTATCAACAACTCAGC 59.840 45.833 0.00 0.00 38.35 4.26
629 650 5.394005 CCAGAGGACTCTATCAACAACTCAG 60.394 48.000 0.82 0.00 37.98 3.35
630 651 4.464244 CCAGAGGACTCTATCAACAACTCA 59.536 45.833 0.82 0.00 37.98 3.41
631 652 4.142049 CCCAGAGGACTCTATCAACAACTC 60.142 50.000 0.82 0.00 37.98 3.01
632 653 3.772025 CCCAGAGGACTCTATCAACAACT 59.228 47.826 0.82 0.00 37.98 3.16
633 654 3.769844 TCCCAGAGGACTCTATCAACAAC 59.230 47.826 0.82 0.00 37.19 3.32
634 655 4.061131 TCCCAGAGGACTCTATCAACAA 57.939 45.455 0.82 0.00 37.19 2.83
637 658 4.338795 ACTTCCCAGAGGACTCTATCAA 57.661 45.455 0.82 0.00 43.90 2.57
641 662 4.127918 TCAAACTTCCCAGAGGACTCTA 57.872 45.455 0.82 0.00 43.90 2.43
643 664 3.669536 CTTCAAACTTCCCAGAGGACTC 58.330 50.000 0.00 0.00 43.90 3.36
652 673 3.365364 CGATGTCTTGCTTCAAACTTCCC 60.365 47.826 0.00 0.00 0.00 3.97
680 701 1.405105 TGTTGCTCAAGTTGTTCCAGC 59.595 47.619 2.11 5.09 0.00 4.85
714 735 5.773091 TGATGTCTACAGGTGGTAAGGATA 58.227 41.667 0.00 0.00 0.00 2.59
770 792 5.605564 TCAAATATTTGTGTGACCGAGTG 57.394 39.130 23.95 0.00 39.18 3.51
850 904 7.092846 TGTGAGAAATTTTTACCCCCTCAAAAA 60.093 33.333 5.38 0.00 37.84 1.94
851 905 6.384305 TGTGAGAAATTTTTACCCCCTCAAAA 59.616 34.615 5.38 0.00 31.98 2.44
852 906 5.900123 TGTGAGAAATTTTTACCCCCTCAAA 59.100 36.000 5.38 0.00 31.98 2.69
853 907 5.459505 TGTGAGAAATTTTTACCCCCTCAA 58.540 37.500 5.38 0.00 31.98 3.02
854 908 5.068215 TGTGAGAAATTTTTACCCCCTCA 57.932 39.130 0.00 0.00 0.00 3.86
855 909 5.105351 CCATGTGAGAAATTTTTACCCCCTC 60.105 44.000 0.00 0.00 0.00 4.30
856 910 4.777366 CCATGTGAGAAATTTTTACCCCCT 59.223 41.667 0.00 0.00 0.00 4.79
857 911 4.775253 TCCATGTGAGAAATTTTTACCCCC 59.225 41.667 0.00 0.00 0.00 5.40
858 912 5.993748 TCCATGTGAGAAATTTTTACCCC 57.006 39.130 0.00 0.00 0.00 4.95
859 913 7.035612 GTCATCCATGTGAGAAATTTTTACCC 58.964 38.462 0.00 0.00 0.00 3.69
860 914 7.830739 AGTCATCCATGTGAGAAATTTTTACC 58.169 34.615 0.00 0.00 0.00 2.85
861 915 9.994432 CTAGTCATCCATGTGAGAAATTTTTAC 57.006 33.333 0.00 0.00 0.00 2.01
862 916 9.739276 ACTAGTCATCCATGTGAGAAATTTTTA 57.261 29.630 0.00 0.00 0.00 1.52
863 917 8.641498 ACTAGTCATCCATGTGAGAAATTTTT 57.359 30.769 0.00 0.00 0.00 1.94
864 918 8.105829 AGACTAGTCATCCATGTGAGAAATTTT 58.894 33.333 24.44 0.00 0.00 1.82
865 919 7.551974 CAGACTAGTCATCCATGTGAGAAATTT 59.448 37.037 24.44 0.00 0.00 1.82
866 920 7.046652 CAGACTAGTCATCCATGTGAGAAATT 58.953 38.462 24.44 0.00 0.00 1.82
867 921 6.382282 TCAGACTAGTCATCCATGTGAGAAAT 59.618 38.462 24.44 0.00 0.00 2.17
868 922 5.716703 TCAGACTAGTCATCCATGTGAGAAA 59.283 40.000 24.44 0.00 0.00 2.52
869 923 5.264395 TCAGACTAGTCATCCATGTGAGAA 58.736 41.667 24.44 0.00 0.00 2.87
870 924 4.860022 TCAGACTAGTCATCCATGTGAGA 58.140 43.478 24.44 4.13 0.00 3.27
871 925 5.530712 CATCAGACTAGTCATCCATGTGAG 58.469 45.833 24.44 7.94 0.00 3.51
872 926 4.202192 GCATCAGACTAGTCATCCATGTGA 60.202 45.833 24.44 16.63 0.00 3.58
873 927 4.056740 GCATCAGACTAGTCATCCATGTG 58.943 47.826 24.44 12.00 0.00 3.21
914 968 4.927267 TTCGGCCCATCATATATTTCCT 57.073 40.909 0.00 0.00 0.00 3.36
978 1032 3.126000 GTGAAAGAGCAGAATAGTGGTGC 59.874 47.826 0.00 0.00 37.48 5.01
1043 1097 1.834896 GAGAACCCCTCTTTCTCCTCC 59.165 57.143 1.34 0.00 42.17 4.30
1105 1162 4.715523 TTTCGCCTTCCTGCCCCG 62.716 66.667 0.00 0.00 0.00 5.73
1767 1830 4.176851 GCGTCCTCGTCCTCGTCC 62.177 72.222 0.00 0.00 39.49 4.79
1941 2004 1.195347 CATACGCTGAAGCTCAGTCG 58.805 55.000 18.39 18.39 45.94 4.18
1970 2033 4.464244 ACAGACACTATCTTAGAAGCAGCA 59.536 41.667 0.00 0.00 34.41 4.41
1971 2034 5.004922 ACAGACACTATCTTAGAAGCAGC 57.995 43.478 0.00 0.00 34.41 5.25
1972 2035 8.629158 AGAATACAGACACTATCTTAGAAGCAG 58.371 37.037 0.00 0.00 34.41 4.24
2068 2131 3.062639 GCATGATAACACAACTCGGACAG 59.937 47.826 0.00 0.00 0.00 3.51
2075 2138 9.060347 CCTGATAATAAGCATGATAACACAACT 57.940 33.333 0.00 0.00 0.00 3.16
2077 2140 8.978874 ACCTGATAATAAGCATGATAACACAA 57.021 30.769 0.00 0.00 0.00 3.33
2078 2141 9.710900 CTACCTGATAATAAGCATGATAACACA 57.289 33.333 0.00 0.00 0.00 3.72
2151 2217 2.483877 CCTAAACAGAACAATGCGAGCA 59.516 45.455 0.00 0.00 0.00 4.26
2191 2257 3.296854 ACAGTAGGCCGATAACTCATCA 58.703 45.455 0.00 0.00 32.71 3.07
2198 2264 1.480789 TGCAGACAGTAGGCCGATAA 58.519 50.000 0.00 0.00 0.00 1.75
2214 2280 0.541392 ACCGCTGTAATGAGGATGCA 59.459 50.000 0.00 0.00 0.00 3.96
2216 2282 4.155826 TCAAAAACCGCTGTAATGAGGATG 59.844 41.667 0.00 0.00 0.00 3.51
2217 2283 4.331968 TCAAAAACCGCTGTAATGAGGAT 58.668 39.130 0.00 0.00 0.00 3.24
2237 2303 8.458052 CCACAAGTAACAAGCAACAATATATCA 58.542 33.333 0.00 0.00 0.00 2.15
2247 2313 2.357637 GTCTGCCACAAGTAACAAGCAA 59.642 45.455 0.00 0.00 0.00 3.91
2256 2322 4.844349 ACCAATATAGTCTGCCACAAGT 57.156 40.909 0.00 0.00 0.00 3.16
2271 2337 4.594062 ACCAAGTACACACAGGTACCAATA 59.406 41.667 15.94 0.00 43.66 1.90
2273 2339 2.773087 ACCAAGTACACACAGGTACCAA 59.227 45.455 15.94 0.00 43.66 3.67
2274 2340 2.103432 CACCAAGTACACACAGGTACCA 59.897 50.000 15.94 0.00 43.66 3.25
2284 2355 2.579410 ATGGGGTTCACCAAGTACAC 57.421 50.000 0.00 0.00 45.13 2.90
2320 2391 8.177119 TGAATAGAACAAATTAAGGTTGCTGT 57.823 30.769 2.39 0.00 0.00 4.40
2341 2412 8.795513 TCACAAATCACAACACATAGATTGAAT 58.204 29.630 0.00 0.00 31.58 2.57
2350 2421 6.455360 AAGAGTTCACAAATCACAACACAT 57.545 33.333 0.00 0.00 0.00 3.21
2360 2431 8.655935 ATGATTAGGGAAAAGAGTTCACAAAT 57.344 30.769 0.00 0.00 0.00 2.32
2361 2432 9.753674 ATATGATTAGGGAAAAGAGTTCACAAA 57.246 29.630 0.00 0.00 0.00 2.83
2407 2478 5.405571 TCTTAGCGCTATAACTTATTGCTGC 59.594 40.000 19.60 16.33 37.04 5.25
2408 2479 6.642950 AGTCTTAGCGCTATAACTTATTGCTG 59.357 38.462 19.60 7.66 35.28 4.41
2409 2480 6.750148 AGTCTTAGCGCTATAACTTATTGCT 58.250 36.000 19.60 9.53 35.28 3.91
2410 2481 6.641314 TGAGTCTTAGCGCTATAACTTATTGC 59.359 38.462 24.66 15.84 34.32 3.56
2411 2482 8.575565 TTGAGTCTTAGCGCTATAACTTATTG 57.424 34.615 24.66 7.67 0.00 1.90
2412 2483 9.765795 ATTTGAGTCTTAGCGCTATAACTTATT 57.234 29.630 24.66 13.53 0.00 1.40
2413 2484 9.765795 AATTTGAGTCTTAGCGCTATAACTTAT 57.234 29.630 24.66 17.75 0.00 1.73
2415 2486 9.765795 ATAATTTGAGTCTTAGCGCTATAACTT 57.234 29.630 24.66 15.27 0.00 2.66
2416 2487 9.413048 GATAATTTGAGTCTTAGCGCTATAACT 57.587 33.333 24.32 24.32 0.00 2.24
2417 2488 9.413048 AGATAATTTGAGTCTTAGCGCTATAAC 57.587 33.333 19.60 18.32 0.00 1.89
2420 2491 9.632807 CTTAGATAATTTGAGTCTTAGCGCTAT 57.367 33.333 19.60 2.28 0.00 2.97
2421 2492 8.847196 TCTTAGATAATTTGAGTCTTAGCGCTA 58.153 33.333 14.45 14.45 0.00 4.26
2422 2493 7.717568 TCTTAGATAATTTGAGTCTTAGCGCT 58.282 34.615 17.26 17.26 0.00 5.92
2423 2494 7.932120 TCTTAGATAATTTGAGTCTTAGCGC 57.068 36.000 0.00 0.00 0.00 5.92
2431 2502 9.804758 CCTCTACGTTTCTTAGATAATTTGAGT 57.195 33.333 0.00 0.00 0.00 3.41
2432 2503 8.756864 GCCTCTACGTTTCTTAGATAATTTGAG 58.243 37.037 0.00 0.00 0.00 3.02
2433 2504 8.255206 TGCCTCTACGTTTCTTAGATAATTTGA 58.745 33.333 0.00 0.00 0.00 2.69
2434 2505 8.420374 TGCCTCTACGTTTCTTAGATAATTTG 57.580 34.615 0.00 0.00 0.00 2.32
2435 2506 8.475639 TCTGCCTCTACGTTTCTTAGATAATTT 58.524 33.333 0.00 0.00 0.00 1.82
2436 2507 8.008513 TCTGCCTCTACGTTTCTTAGATAATT 57.991 34.615 0.00 0.00 0.00 1.40
2437 2508 7.584122 TCTGCCTCTACGTTTCTTAGATAAT 57.416 36.000 0.00 0.00 0.00 1.28
2438 2509 7.400599 TTCTGCCTCTACGTTTCTTAGATAA 57.599 36.000 0.00 0.00 0.00 1.75
2439 2510 7.584122 ATTCTGCCTCTACGTTTCTTAGATA 57.416 36.000 0.00 0.00 0.00 1.98
2440 2511 5.916661 TTCTGCCTCTACGTTTCTTAGAT 57.083 39.130 0.00 0.00 0.00 1.98
2441 2512 5.916661 ATTCTGCCTCTACGTTTCTTAGA 57.083 39.130 0.00 0.00 0.00 2.10
2442 2513 9.915629 ATATAATTCTGCCTCTACGTTTCTTAG 57.084 33.333 0.00 0.00 0.00 2.18
2469 2540 9.754382 CATGCTATGGTGCTAAGAAAAATTAAT 57.246 29.630 0.00 0.00 0.00 1.40
2470 2541 8.748412 ACATGCTATGGTGCTAAGAAAAATTAA 58.252 29.630 0.00 0.00 33.60 1.40
2471 2542 8.292444 ACATGCTATGGTGCTAAGAAAAATTA 57.708 30.769 0.00 0.00 33.60 1.40
2472 2543 7.174107 ACATGCTATGGTGCTAAGAAAAATT 57.826 32.000 0.00 0.00 33.60 1.82
2473 2544 6.780457 ACATGCTATGGTGCTAAGAAAAAT 57.220 33.333 0.00 0.00 33.60 1.82
2474 2545 6.183360 GCTACATGCTATGGTGCTAAGAAAAA 60.183 38.462 0.00 0.00 38.95 1.94
2475 2546 5.296780 GCTACATGCTATGGTGCTAAGAAAA 59.703 40.000 0.00 0.00 38.95 2.29
2476 2547 4.816385 GCTACATGCTATGGTGCTAAGAAA 59.184 41.667 0.00 0.00 38.95 2.52
2575 2726 4.842574 TGCTGATTAGTATGACTTTGCCA 58.157 39.130 0.00 0.00 0.00 4.92
2577 2728 6.092670 TCAACTGCTGATTAGTATGACTTTGC 59.907 38.462 0.00 0.00 0.00 3.68
2627 2781 5.443185 AGAATGGACAACAGACAACATTG 57.557 39.130 0.00 0.00 0.00 2.82
2631 2785 5.455392 CATCAAGAATGGACAACAGACAAC 58.545 41.667 0.00 0.00 0.00 3.32
2669 2823 8.470805 ACACATTTATCAACAAAAACACCACTA 58.529 29.630 0.00 0.00 0.00 2.74
2710 2864 3.802948 ACGTTCCAGGACAGATATCAC 57.197 47.619 5.32 0.00 0.00 3.06
2847 3370 3.440173 CCTATGGTATAATTTGCCAGGCG 59.560 47.826 7.03 0.00 43.96 5.52
3127 3658 1.302511 CCACGGAACCAAGGGTCAG 60.303 63.158 6.47 4.49 33.12 3.51
3128 3659 2.833227 CCACGGAACCAAGGGTCA 59.167 61.111 6.47 0.00 33.12 4.02
3272 3803 3.379372 CGTTGCAAATCCCAAGAGATCAT 59.621 43.478 0.00 0.00 0.00 2.45
3350 3881 3.975982 TCCTCATGCCTTCAAGGATATCA 59.024 43.478 7.98 0.00 37.67 2.15
3717 4248 5.453567 AAGGCCTATGTTCACTGAAAAAC 57.546 39.130 5.16 0.00 0.00 2.43
3718 4249 7.001674 TCTAAAGGCCTATGTTCACTGAAAAA 58.998 34.615 5.16 0.00 0.00 1.94
3784 4325 9.683069 AACAGAGCAATAACAAATACAAAGAAG 57.317 29.630 0.00 0.00 0.00 2.85
3855 4396 4.024048 AGACAACAACCAGCAAACTATTCG 60.024 41.667 0.00 0.00 0.00 3.34
3877 4418 3.519579 CCTTGCTGATGACACAGACTAG 58.480 50.000 8.62 0.00 39.94 2.57


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

AutoCloner maintained by Alex Coulton.