Multiple sequence alignment - TraesCS6B01G209200

Loading Multiple Alignment...

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 TraesCS6B01G209200 chr6B 100.000 2857 0 0 1 2857 275311648 275308792 0.000000e+00 5276.0
1 TraesCS6B01G209200 chr6B 85.099 859 111 7 1 847 699612221 699611368 0.000000e+00 861.0
2 TraesCS6B01G209200 chr6B 84.554 505 76 2 349 852 445888393 445887890 1.530000e-137 499.0
3 TraesCS6B01G209200 chr6B 85.393 356 44 2 3 350 445912440 445912085 2.090000e-96 363.0
4 TraesCS6B01G209200 chr6A 92.043 2124 106 35 28 2105 194812182 194810076 0.000000e+00 2928.0
5 TraesCS6B01G209200 chr6A 84.785 861 118 8 2 852 405453538 405452681 0.000000e+00 852.0
6 TraesCS6B01G209200 chr6A 94.708 359 17 2 2376 2732 194801487 194801129 8.940000e-155 556.0
7 TraesCS6B01G209200 chr6A 96.441 281 9 1 2105 2384 194804191 194803911 2.010000e-126 462.0
8 TraesCS6B01G209200 chr6D 95.997 1574 33 13 1101 2672 150155411 150156956 0.000000e+00 2531.0
9 TraesCS6B01G209200 chr6D 88.836 842 76 4 25 857 150154274 150155106 0.000000e+00 1018.0
10 TraesCS6B01G209200 chr6D 84.553 861 106 10 2 853 285025707 285024865 0.000000e+00 828.0
11 TraesCS6B01G209200 chr6D 84.191 272 32 7 852 1118 150155132 150155397 1.310000e-63 254.0
12 TraesCS6B01G209200 chr6D 90.351 114 10 1 2730 2843 42418880 42418768 6.380000e-32 148.0
13 TraesCS6B01G209200 chr6D 94.737 38 1 1 2232 2268 452116907 452116944 1.110000e-04 58.4
14 TraesCS6B01G209200 chr4D 84.813 856 115 6 1 843 11470119 11470972 0.000000e+00 846.0
15 TraesCS6B01G209200 chr4D 91.071 112 10 0 2732 2843 467211635 467211524 4.930000e-33 152.0
16 TraesCS6B01G209200 chr4A 84.104 843 121 4 1 830 624315149 624314307 0.000000e+00 802.0
17 TraesCS6B01G209200 chr7D 82.748 626 76 15 3 618 152640439 152639836 1.950000e-146 529.0
18 TraesCS6B01G209200 chr3B 85.372 417 52 7 422 831 711145476 711145890 9.460000e-115 424.0
19 TraesCS6B01G209200 chr3B 85.366 410 52 6 428 831 710829087 710829494 4.400000e-113 418.0
20 TraesCS6B01G209200 chr1D 86.630 359 39 1 1 350 494852009 494852367 3.450000e-104 388.0
21 TraesCS6B01G209200 chr1D 87.179 117 14 1 2727 2843 329677074 329677189 6.420000e-27 132.0
22 TraesCS6B01G209200 chr1D 86.087 115 15 1 2729 2843 414267190 414267303 3.870000e-24 122.0
23 TraesCS6B01G209200 chr7B 84.868 304 35 4 3 295 110192999 110192696 2.150000e-76 296.0
24 TraesCS6B01G209200 chr7A 89.726 146 13 2 60 204 152974468 152974324 4.860000e-43 185.0
25 TraesCS6B01G209200 chr2D 90.909 110 10 0 2734 2843 453612052 453611943 6.380000e-32 148.0
26 TraesCS6B01G209200 chr2D 87.826 115 14 0 2743 2857 89907303 89907189 4.970000e-28 135.0
27 TraesCS6B01G209200 chr1B 90.909 110 10 0 2734 2843 353765089 353765198 6.380000e-32 148.0
28 TraesCS6B01G209200 chr2B 90.654 107 10 0 2734 2840 121129035 121129141 2.970000e-30 143.0
29 TraesCS6B01G209200 chr2A 90.000 110 11 0 2734 2843 596368286 596368177 2.970000e-30 143.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G209200 chr6B 275308792 275311648 2856 True 5276.000000 5276 100.000000 1 2857 1 chr6B.!!$R1 2856
1 TraesCS6B01G209200 chr6B 699611368 699612221 853 True 861.000000 861 85.099000 1 847 1 chr6B.!!$R4 846
2 TraesCS6B01G209200 chr6B 445887890 445888393 503 True 499.000000 499 84.554000 349 852 1 chr6B.!!$R2 503
3 TraesCS6B01G209200 chr6A 194810076 194812182 2106 True 2928.000000 2928 92.043000 28 2105 1 chr6A.!!$R1 2077
4 TraesCS6B01G209200 chr6A 405452681 405453538 857 True 852.000000 852 84.785000 2 852 1 chr6A.!!$R2 850
5 TraesCS6B01G209200 chr6A 194801129 194804191 3062 True 509.000000 556 95.574500 2105 2732 2 chr6A.!!$R3 627
6 TraesCS6B01G209200 chr6D 150154274 150156956 2682 False 1267.666667 2531 89.674667 25 2672 3 chr6D.!!$F2 2647
7 TraesCS6B01G209200 chr6D 285024865 285025707 842 True 828.000000 828 84.553000 2 853 1 chr6D.!!$R2 851
8 TraesCS6B01G209200 chr4D 11470119 11470972 853 False 846.000000 846 84.813000 1 843 1 chr4D.!!$F1 842
9 TraesCS6B01G209200 chr4A 624314307 624315149 842 True 802.000000 802 84.104000 1 830 1 chr4A.!!$R1 829
10 TraesCS6B01G209200 chr7D 152639836 152640439 603 True 529.000000 529 82.748000 3 618 1 chr7D.!!$R1 615


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
721 746 0.028902 GTTGGTGCAACGAGGAACAC 59.971 55.0 0.0 0.0 33.73 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2626 5158 0.322816 TGCTTGCCCTCCACATCTTC 60.323 55.0 0.0 0.0 0.0 2.87 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
26 27 9.241919 ACTGAGATCTATCATAATACTCTGTGG 57.758 37.037 0.00 0.00 35.19 4.17
55 56 3.244215 ACAACAACCGATGATCAGAGTGT 60.244 43.478 0.09 0.00 0.00 3.55
56 57 2.964740 ACAACCGATGATCAGAGTGTG 58.035 47.619 0.09 0.00 0.00 3.82
82 83 1.594293 CTCGTGAACAACCGCCACT 60.594 57.895 0.00 0.00 0.00 4.00
150 151 1.216930 TCTCTCCCGGATATCACCACA 59.783 52.381 0.73 0.00 0.00 4.17
196 198 3.649277 CTCAACTCCGTCCAGGCCG 62.649 68.421 0.00 0.00 40.77 6.13
236 256 7.870509 TCACTAAAAGCTTGAAGCATATGAT 57.129 32.000 20.45 0.00 45.56 2.45
284 304 9.921637 TTGGCATTAGAATTTCGTTAAAATCTT 57.078 25.926 0.00 0.00 36.47 2.40
324 344 3.494048 CCTGTAGCATCTCCCTTAAGCTG 60.494 52.174 0.00 0.00 36.80 4.24
373 393 1.376037 GTCCCAAGCTGGTTCTCCG 60.376 63.158 0.00 0.00 35.17 4.63
379 400 2.289444 CCAAGCTGGTTCTCCGTAGAAA 60.289 50.000 0.00 0.00 43.30 2.52
461 483 5.041940 GTGTCATATAGTTCGGAACCACTC 58.958 45.833 16.84 3.37 0.00 3.51
464 486 0.822164 ATAGTTCGGAACCACTCCCG 59.178 55.000 16.84 0.00 46.57 5.14
484 507 9.106070 ACTCCCGTCTCATTATTATAAAACAAC 57.894 33.333 0.00 0.00 0.00 3.32
509 532 0.895100 GCCACCAGAGCAACCATCAA 60.895 55.000 0.00 0.00 0.00 2.57
553 576 8.451908 AATCGAACCCTAAATTAATCCTCAAG 57.548 34.615 0.00 0.00 0.00 3.02
643 666 1.204941 AGATCCAACAGCTCACGTACC 59.795 52.381 0.00 0.00 0.00 3.34
677 700 0.109365 CATGCCGCGACAATTCCAAA 60.109 50.000 8.23 0.00 0.00 3.28
682 705 2.096819 GCCGCGACAATTCCAAATAAGA 59.903 45.455 8.23 0.00 0.00 2.10
704 727 6.157211 AGAACTTTCATTATCGTCGACAGTT 58.843 36.000 17.16 13.43 33.55 3.16
721 746 0.028902 GTTGGTGCAACGAGGAACAC 59.971 55.000 0.00 0.00 33.73 3.32
784 811 3.621558 ACAAACCCTAGCTATTCTTGCC 58.378 45.455 0.00 0.00 0.00 4.52
794 824 1.398390 CTATTCTTGCCAGGCGACAAC 59.602 52.381 7.03 0.00 0.00 3.32
795 825 0.537143 ATTCTTGCCAGGCGACAACA 60.537 50.000 7.03 0.00 0.00 3.33
796 826 0.749818 TTCTTGCCAGGCGACAACAA 60.750 50.000 7.03 0.00 0.00 2.83
819 850 4.139038 GTCTATAGAGAAGCCTCCTCGTT 58.861 47.826 1.64 0.00 40.30 3.85
853 884 3.388024 ACCAGCAAACTCTAACAGACAGA 59.612 43.478 0.00 0.00 0.00 3.41
865 928 1.356059 ACAGACAGAGACCTCTAGCCA 59.644 52.381 0.00 0.00 37.98 4.75
869 932 0.827368 CAGAGACCTCTAGCCAACCC 59.173 60.000 0.00 0.00 37.98 4.11
907 970 1.064389 GCCTTCTTTGCTAGGGGACAT 60.064 52.381 0.00 0.00 31.95 3.06
974 1039 2.481289 AGAAGAAACTAGCAGGCCAC 57.519 50.000 5.01 0.00 0.00 5.01
976 1041 0.321653 AAGAAACTAGCAGGCCACCG 60.322 55.000 5.01 0.00 0.00 4.94
1007 1072 2.050350 GGCTGTCCTGCATGCATGT 61.050 57.895 26.79 0.00 34.04 3.21
1023 1088 6.143438 GCATGCATGTGTTTATAGAAATGAGC 59.857 38.462 26.79 2.96 0.00 4.26
1026 1091 5.678483 GCATGTGTTTATAGAAATGAGCGTG 59.322 40.000 0.00 0.00 0.00 5.34
1036 1101 4.177026 AGAAATGAGCGTGTGTATGAGTC 58.823 43.478 0.00 0.00 0.00 3.36
1054 1119 2.537639 TCGTATGCGACTGTACTGTG 57.462 50.000 10.43 4.36 42.81 3.66
1112 1178 9.504708 TTCCGTTCATTATAAGTTCCAACTTTA 57.495 29.630 9.92 1.26 46.52 1.85
1114 1180 9.769093 CCGTTCATTATAAGTTCCAACTTTAAG 57.231 33.333 9.92 0.00 46.52 1.85
1271 1368 4.423209 GCCCTCCACTCCCTCCCT 62.423 72.222 0.00 0.00 0.00 4.20
1274 1371 2.360980 CTCCACTCCCTCCCTCGT 59.639 66.667 0.00 0.00 0.00 4.18
1673 1770 2.105128 GATCTCACCGAGGCCGTG 59.895 66.667 0.00 0.00 0.00 4.94
1887 1984 9.959721 AGCAAACTTACCTTGATTCTTATCTTA 57.040 29.630 0.00 0.00 0.00 2.10
2051 2148 5.331876 ACTGTAGTAAGAAGTCTGATGCC 57.668 43.478 0.00 0.00 0.00 4.40
2064 2161 4.645136 AGTCTGATGCCGAGTACTAAATGA 59.355 41.667 0.00 0.00 0.00 2.57
2136 2234 0.248289 TGGAACGAACGATCCCCTTC 59.752 55.000 17.91 3.47 36.40 3.46
2142 2240 1.204941 CGAACGATCCCCTTCAAGACT 59.795 52.381 0.00 0.00 0.00 3.24
2422 4953 7.663827 AGTTATTTTTGGGTTAGTTTAGCACC 58.336 34.615 0.00 0.00 0.00 5.01
2440 4971 3.624777 CACCCCACATAGAGATGCTTTT 58.375 45.455 0.00 0.00 36.43 2.27
2447 4978 6.127535 CCCACATAGAGATGCTTTTCAACAAT 60.128 38.462 0.00 0.00 36.43 2.71
2519 5050 2.949177 ACATGTTTGGACAGCACCTA 57.051 45.000 0.00 0.00 39.58 3.08
2626 5158 5.873179 ATAATAACACACTTCAACACCCG 57.127 39.130 0.00 0.00 0.00 5.28
2652 5184 0.324943 TGGAGGGCAAGCAAGTACTC 59.675 55.000 0.00 0.00 0.00 2.59
2675 5207 4.318332 TGCTGAATAACTCCACAACTCAG 58.682 43.478 0.00 0.00 33.54 3.35
2676 5208 4.040339 TGCTGAATAACTCCACAACTCAGA 59.960 41.667 0.00 0.00 32.39 3.27
2727 5259 8.480501 TGTAACTAAAGACAACTGATATACCCC 58.519 37.037 0.00 0.00 0.00 4.95
2732 5264 7.939784 AAAGACAACTGATATACCCCTTTTC 57.060 36.000 0.00 0.00 0.00 2.29
2733 5265 6.636454 AGACAACTGATATACCCCTTTTCA 57.364 37.500 0.00 0.00 0.00 2.69
2734 5266 6.653989 AGACAACTGATATACCCCTTTTCAG 58.346 40.000 0.00 0.00 39.70 3.02
2735 5267 6.443849 AGACAACTGATATACCCCTTTTCAGA 59.556 38.462 5.33 0.00 37.75 3.27
2736 5268 6.653989 ACAACTGATATACCCCTTTTCAGAG 58.346 40.000 5.33 0.96 37.75 3.35
2737 5269 5.297569 ACTGATATACCCCTTTTCAGAGC 57.702 43.478 5.33 0.00 37.75 4.09
2738 5270 4.721776 ACTGATATACCCCTTTTCAGAGCA 59.278 41.667 5.33 0.00 37.75 4.26
2739 5271 5.370880 ACTGATATACCCCTTTTCAGAGCAT 59.629 40.000 5.33 0.00 37.75 3.79
2740 5272 5.869579 TGATATACCCCTTTTCAGAGCATC 58.130 41.667 0.00 0.00 0.00 3.91
2753 5285 0.678950 GAGCATCTCTAGCAGACCCC 59.321 60.000 0.00 0.00 32.26 4.95
2754 5286 1.112315 AGCATCTCTAGCAGACCCCG 61.112 60.000 0.00 0.00 32.26 5.73
2755 5287 1.395826 GCATCTCTAGCAGACCCCGT 61.396 60.000 0.00 0.00 32.26 5.28
2756 5288 1.982660 CATCTCTAGCAGACCCCGTA 58.017 55.000 0.00 0.00 32.26 4.02
2757 5289 2.520069 CATCTCTAGCAGACCCCGTAT 58.480 52.381 0.00 0.00 32.26 3.06
2758 5290 3.687125 CATCTCTAGCAGACCCCGTATA 58.313 50.000 0.00 0.00 32.26 1.47
2759 5291 3.420300 TCTCTAGCAGACCCCGTATAG 57.580 52.381 0.00 0.00 0.00 1.31
2760 5292 1.813786 CTCTAGCAGACCCCGTATAGC 59.186 57.143 0.00 0.00 0.00 2.97
2761 5293 0.522180 CTAGCAGACCCCGTATAGCG 59.478 60.000 0.00 0.00 40.95 4.26
2762 5294 1.521450 TAGCAGACCCCGTATAGCGC 61.521 60.000 0.00 0.00 39.71 5.92
2763 5295 2.338984 CAGACCCCGTATAGCGCC 59.661 66.667 2.29 0.00 39.71 6.53
2764 5296 3.292936 AGACCCCGTATAGCGCCG 61.293 66.667 2.29 0.00 39.71 6.46
2765 5297 3.289834 GACCCCGTATAGCGCCGA 61.290 66.667 2.29 0.00 39.71 5.54
2766 5298 3.548793 GACCCCGTATAGCGCCGAC 62.549 68.421 2.29 0.00 39.71 4.79
2767 5299 4.353437 CCCCGTATAGCGCCGACC 62.353 72.222 2.29 0.00 39.71 4.79
2768 5300 4.353437 CCCGTATAGCGCCGACCC 62.353 72.222 2.29 0.00 39.71 4.46
2769 5301 4.695231 CCGTATAGCGCCGACCCG 62.695 72.222 2.29 0.00 39.71 5.28
2790 5322 2.712466 GCAAAACGAGTTTACAGTTCGC 59.288 45.455 1.32 0.00 37.84 4.70
2791 5323 2.916735 AAACGAGTTTACAGTTCGCG 57.083 45.000 0.00 0.00 37.84 5.87
2792 5324 1.134226 AACGAGTTTACAGTTCGCGG 58.866 50.000 6.13 0.00 37.84 6.46
2793 5325 0.311790 ACGAGTTTACAGTTCGCGGA 59.688 50.000 6.13 0.00 37.84 5.54
2794 5326 1.269206 ACGAGTTTACAGTTCGCGGAA 60.269 47.619 6.13 0.00 37.84 4.30
2795 5327 1.788308 CGAGTTTACAGTTCGCGGAAA 59.212 47.619 6.13 0.00 0.00 3.13
2796 5328 2.219216 CGAGTTTACAGTTCGCGGAAAA 59.781 45.455 6.13 0.00 0.00 2.29
2797 5329 3.302610 CGAGTTTACAGTTCGCGGAAAAA 60.303 43.478 6.13 0.00 0.00 1.94
2798 5330 3.943958 AGTTTACAGTTCGCGGAAAAAC 58.056 40.909 6.13 7.02 0.00 2.43
2799 5331 2.649140 TTACAGTTCGCGGAAAAACG 57.351 45.000 6.13 2.76 0.00 3.60
2800 5332 0.860533 TACAGTTCGCGGAAAAACGG 59.139 50.000 6.13 6.64 0.00 4.44
2801 5333 1.724581 CAGTTCGCGGAAAAACGGC 60.725 57.895 6.13 0.00 40.64 5.68
2802 5334 1.890510 AGTTCGCGGAAAAACGGCT 60.891 52.632 6.13 0.00 41.63 5.52
2803 5335 0.600782 AGTTCGCGGAAAAACGGCTA 60.601 50.000 6.13 0.00 41.63 3.93
2804 5336 0.445043 GTTCGCGGAAAAACGGCTAT 59.555 50.000 6.13 0.00 41.63 2.97
2805 5337 0.444651 TTCGCGGAAAAACGGCTATG 59.555 50.000 6.13 0.00 41.63 2.23
2806 5338 1.582680 CGCGGAAAAACGGCTATGC 60.583 57.895 0.00 0.00 41.63 3.14
2807 5339 1.582680 GCGGAAAAACGGCTATGCG 60.583 57.895 0.00 0.00 40.81 4.73
2808 5340 1.061887 CGGAAAAACGGCTATGCGG 59.938 57.895 0.00 0.00 35.02 5.69
2809 5341 1.431845 GGAAAAACGGCTATGCGGG 59.568 57.895 2.48 0.00 33.14 6.13
2810 5342 1.226575 GAAAAACGGCTATGCGGGC 60.227 57.895 2.48 0.00 33.14 6.13
2811 5343 2.607668 GAAAAACGGCTATGCGGGCC 62.608 60.000 0.00 0.00 45.57 5.80
2837 5369 4.803426 CGGCGGCAGAGTCAGACC 62.803 72.222 10.53 0.00 0.00 3.85
2838 5370 4.459089 GGCGGCAGAGTCAGACCC 62.459 72.222 3.07 0.00 0.00 4.46
2839 5371 4.459089 GCGGCAGAGTCAGACCCC 62.459 72.222 0.00 0.00 0.00 4.95
2840 5372 4.135153 CGGCAGAGTCAGACCCCG 62.135 72.222 0.00 1.18 0.00 5.73
2841 5373 4.459089 GGCAGAGTCAGACCCCGC 62.459 72.222 0.00 0.00 0.00 6.13
2842 5374 3.695606 GCAGAGTCAGACCCCGCA 61.696 66.667 0.00 0.00 0.00 5.69
2843 5375 3.023949 GCAGAGTCAGACCCCGCAT 62.024 63.158 0.00 0.00 0.00 4.73
2844 5376 1.676678 GCAGAGTCAGACCCCGCATA 61.677 60.000 0.00 0.00 0.00 3.14
2845 5377 0.387202 CAGAGTCAGACCCCGCATAG 59.613 60.000 0.00 0.00 0.00 2.23
2846 5378 0.033011 AGAGTCAGACCCCGCATAGT 60.033 55.000 0.00 0.00 0.00 2.12
2847 5379 0.103208 GAGTCAGACCCCGCATAGTG 59.897 60.000 0.00 0.00 0.00 2.74
2848 5380 1.144057 GTCAGACCCCGCATAGTGG 59.856 63.158 0.00 0.00 0.00 4.00
2849 5381 1.001120 TCAGACCCCGCATAGTGGA 59.999 57.895 0.00 0.00 34.74 4.02
2850 5382 0.616395 TCAGACCCCGCATAGTGGAA 60.616 55.000 0.00 0.00 34.74 3.53
2851 5383 0.462047 CAGACCCCGCATAGTGGAAC 60.462 60.000 0.00 0.00 34.74 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.536175 TGTTGTTGACCACAGAGTATTATGATA 58.464 33.333 0.00 0.00 36.48 2.15
26 27 3.684103 TCATCGGTTGTTGTTGTTGAC 57.316 42.857 0.00 0.00 0.00 3.18
56 57 0.385974 GTTGTTCACGAGCACCATGC 60.386 55.000 0.00 0.00 45.46 4.06
82 83 4.825085 GGATGGTCAACAAAGTTTCCACTA 59.175 41.667 5.95 0.00 30.68 2.74
150 151 4.971282 TGGGAGATCAGTTTACATGGAGAT 59.029 41.667 0.00 0.00 0.00 2.75
196 198 8.801913 GCTTTTAGTGATTGTCTATTTGAATGC 58.198 33.333 0.00 0.00 0.00 3.56
236 256 2.305927 GTGAGAAGGAAGGTGGGAATCA 59.694 50.000 0.00 0.00 0.00 2.57
284 304 3.455910 ACAGGTCTATGGCTAGCAATTGA 59.544 43.478 18.24 14.63 0.00 2.57
290 310 1.964223 TGCTACAGGTCTATGGCTAGC 59.036 52.381 6.04 6.04 0.00 3.42
324 344 7.328493 GTCATTTGTCTTGGTGTTATTTTAGGC 59.672 37.037 0.00 0.00 0.00 3.93
373 393 2.620242 TGGCGATTAACCGGTTTCTAC 58.380 47.619 27.64 13.02 0.00 2.59
379 400 1.208535 TCAGATTGGCGATTAACCGGT 59.791 47.619 0.00 0.00 0.00 5.28
461 483 7.849026 CGTGTTGTTTTATAATAATGAGACGGG 59.151 37.037 0.00 0.00 0.00 5.28
464 486 9.916397 CCTCGTGTTGTTTTATAATAATGAGAC 57.084 33.333 0.00 0.00 0.00 3.36
484 507 3.535629 TTGCTCTGGTGGCCTCGTG 62.536 63.158 3.32 0.00 0.00 4.35
509 532 7.880160 TCGATTCCCTTCATGTTATTGAAAT 57.120 32.000 0.00 0.00 35.31 2.17
553 576 6.503524 TCTGAACAAAGTTAAGGCAATTCAC 58.496 36.000 0.00 0.00 0.00 3.18
643 666 1.640069 CATGCTCTCAACGATGGCG 59.360 57.895 0.00 0.00 44.79 5.69
677 700 7.974501 ACTGTCGACGATAATGAAAGTTCTTAT 59.025 33.333 11.62 0.00 25.28 1.73
682 705 5.120208 CCAACTGTCGACGATAATGAAAGTT 59.880 40.000 11.62 8.55 40.04 2.66
704 727 4.134623 GTGTTCCTCGTTGCACCA 57.865 55.556 0.00 0.00 0.00 4.17
746 772 2.027625 GTTGTCCTCTGGCGGTTCG 61.028 63.158 0.00 0.00 0.00 3.95
794 824 4.215399 CGAGGAGGCTTCTCTATAGACTTG 59.785 50.000 20.34 0.00 37.65 3.16
795 825 4.141344 ACGAGGAGGCTTCTCTATAGACTT 60.141 45.833 20.34 0.00 37.65 3.01
796 826 3.393278 ACGAGGAGGCTTCTCTATAGACT 59.607 47.826 20.34 0.00 37.65 3.24
819 850 5.188555 AGAGTTTGCTGGTCTTGATGATCTA 59.811 40.000 0.00 0.00 0.00 1.98
853 884 0.684805 CTCGGGTTGGCTAGAGGTCT 60.685 60.000 0.00 0.00 0.00 3.85
865 928 1.228154 GGTTTGCTGTCCTCGGGTT 60.228 57.895 0.00 0.00 0.00 4.11
869 932 0.741221 GCTAGGGTTTGCTGTCCTCG 60.741 60.000 0.00 0.00 32.46 4.63
907 970 3.716872 AGGGTTCTCCTCTTTTGACTTGA 59.283 43.478 0.00 0.00 44.06 3.02
992 1057 1.330234 AAACACATGCATGCAGGACA 58.670 45.000 36.44 8.40 0.00 4.02
1000 1065 6.038603 ACGCTCATTTCTATAAACACATGCAT 59.961 34.615 0.00 0.00 0.00 3.96
1007 1072 7.762159 TCATACACACGCTCATTTCTATAAACA 59.238 33.333 0.00 0.00 0.00 2.83
1023 1088 1.773525 CGCATACGACTCATACACACG 59.226 52.381 0.00 0.00 43.93 4.49
1036 1101 2.257974 ACACAGTACAGTCGCATACG 57.742 50.000 0.00 0.00 42.01 3.06
1051 1116 7.925043 TCTTACCTGAGTTTGTTTTAACACA 57.075 32.000 0.00 0.00 38.92 3.72
1112 1178 3.319405 TCGAGCTCACTCTCTTGAAACTT 59.681 43.478 15.40 0.00 41.09 2.66
1114 1180 2.983803 GTCGAGCTCACTCTCTTGAAAC 59.016 50.000 15.40 0.00 41.09 2.78
1115 1181 2.029828 GGTCGAGCTCACTCTCTTGAAA 60.030 50.000 15.40 0.00 41.09 2.69
1118 1184 0.172352 GGGTCGAGCTCACTCTCTTG 59.828 60.000 15.40 0.00 41.09 3.02
1119 1185 0.251386 TGGGTCGAGCTCACTCTCTT 60.251 55.000 15.40 0.00 41.09 2.85
1120 1186 0.251386 TTGGGTCGAGCTCACTCTCT 60.251 55.000 15.40 0.00 41.09 3.10
1121 1187 0.172352 CTTGGGTCGAGCTCACTCTC 59.828 60.000 15.40 3.65 41.09 3.20
1271 1368 2.180769 CGATGGGCAACTCGACGA 59.819 61.111 0.00 0.00 37.05 4.20
1274 1371 1.511305 GAGACGATGGGCAACTCGA 59.489 57.895 9.14 0.00 38.24 4.04
1976 2073 5.767665 TCGTTTACATAATGCATAAGGCCAT 59.232 36.000 5.01 0.00 43.89 4.40
1979 2076 8.574196 AATTTCGTTTACATAATGCATAAGGC 57.426 30.769 0.00 0.00 45.13 4.35
2051 2148 8.522178 AGAGAAACACTTTCATTTAGTACTCG 57.478 34.615 0.00 0.00 42.10 4.18
2064 2161 6.418946 AGTCCTGAAAAGAGAGAAACACTTT 58.581 36.000 0.00 0.00 40.13 2.66
2422 4953 4.701651 TGTTGAAAAGCATCTCTATGTGGG 59.298 41.667 0.00 0.00 35.38 4.61
2440 4971 6.033341 GCTGTACAAACTTGTTGATTGTTGA 58.967 36.000 0.00 0.00 41.08 3.18
2447 4978 6.017440 GTCCTATTGCTGTACAAACTTGTTGA 60.017 38.462 0.00 0.00 42.86 3.18
2519 5050 1.883926 GAAACGTGTATTGGCCTGGTT 59.116 47.619 3.32 0.00 0.00 3.67
2526 5057 3.437741 GTGGGTAAGGAAACGTGTATTGG 59.562 47.826 0.00 0.00 0.00 3.16
2578 5109 6.591935 TCCATTTGTAGCTTCCGATTATTCT 58.408 36.000 0.00 0.00 0.00 2.40
2626 5158 0.322816 TGCTTGCCCTCCACATCTTC 60.323 55.000 0.00 0.00 0.00 2.87
2652 5184 4.318332 TGAGTTGTGGAGTTATTCAGCAG 58.682 43.478 0.00 0.00 0.00 4.24
2727 5259 4.805192 GTCTGCTAGAGATGCTCTGAAAAG 59.195 45.833 7.19 0.00 41.37 2.27
2732 5264 1.340889 GGGTCTGCTAGAGATGCTCTG 59.659 57.143 7.19 0.00 41.37 3.35
2733 5265 1.703411 GGGTCTGCTAGAGATGCTCT 58.297 55.000 0.00 2.22 43.83 4.09
2734 5266 0.678950 GGGGTCTGCTAGAGATGCTC 59.321 60.000 0.00 0.00 31.63 4.26
2735 5267 1.112315 CGGGGTCTGCTAGAGATGCT 61.112 60.000 0.00 0.00 31.63 3.79
2736 5268 1.365633 CGGGGTCTGCTAGAGATGC 59.634 63.158 0.00 0.00 31.63 3.91
2737 5269 1.982660 TACGGGGTCTGCTAGAGATG 58.017 55.000 0.00 0.00 31.63 2.90
2738 5270 2.982339 ATACGGGGTCTGCTAGAGAT 57.018 50.000 0.00 0.00 31.63 2.75
2739 5271 2.552591 GCTATACGGGGTCTGCTAGAGA 60.553 54.545 0.00 0.00 0.00 3.10
2740 5272 1.813786 GCTATACGGGGTCTGCTAGAG 59.186 57.143 0.00 0.00 0.00 2.43
2741 5273 1.881072 CGCTATACGGGGTCTGCTAGA 60.881 57.143 0.00 0.00 38.44 2.43
2742 5274 0.522180 CGCTATACGGGGTCTGCTAG 59.478 60.000 0.00 0.00 38.44 3.42
2743 5275 1.521450 GCGCTATACGGGGTCTGCTA 61.521 60.000 0.00 0.00 43.93 3.49
2744 5276 2.857744 GCGCTATACGGGGTCTGCT 61.858 63.158 0.00 0.00 43.93 4.24
2745 5277 2.355956 GCGCTATACGGGGTCTGC 60.356 66.667 0.00 0.00 43.93 4.26
2746 5278 2.338984 GGCGCTATACGGGGTCTG 59.661 66.667 7.64 0.00 43.93 3.51
2747 5279 3.292936 CGGCGCTATACGGGGTCT 61.293 66.667 7.64 0.00 43.93 3.85
2748 5280 3.289834 TCGGCGCTATACGGGGTC 61.290 66.667 7.64 0.00 43.93 4.46
2749 5281 3.599704 GTCGGCGCTATACGGGGT 61.600 66.667 7.64 0.00 43.93 4.95
2750 5282 4.353437 GGTCGGCGCTATACGGGG 62.353 72.222 7.64 0.00 43.93 5.73
2751 5283 4.353437 GGGTCGGCGCTATACGGG 62.353 72.222 7.64 0.00 43.93 5.28
2752 5284 4.695231 CGGGTCGGCGCTATACGG 62.695 72.222 7.64 0.00 43.93 4.02
2754 5286 3.778360 TTGCGGGTCGGCGCTATAC 62.778 63.158 7.64 2.79 35.06 1.47
2755 5287 2.575125 TTTTGCGGGTCGGCGCTATA 62.575 55.000 7.64 0.00 35.06 1.31
2756 5288 3.961838 TTTTGCGGGTCGGCGCTAT 62.962 57.895 7.64 0.00 35.06 2.97
2757 5289 4.683721 TTTTGCGGGTCGGCGCTA 62.684 61.111 7.64 0.00 35.06 4.26
2761 5293 4.084888 CTCGTTTTGCGGGTCGGC 62.085 66.667 0.00 0.00 41.72 5.54
2767 5299 3.285745 GAACTGTAAACTCGTTTTGCGG 58.714 45.455 0.00 7.33 40.90 5.69
2768 5300 2.955799 CGAACTGTAAACTCGTTTTGCG 59.044 45.455 0.00 0.00 43.01 4.85
2769 5301 2.712466 GCGAACTGTAAACTCGTTTTGC 59.288 45.455 0.00 0.00 35.06 3.68
2770 5302 2.955799 CGCGAACTGTAAACTCGTTTTG 59.044 45.455 0.00 0.00 35.06 2.44
2771 5303 2.033492 CCGCGAACTGTAAACTCGTTTT 60.033 45.455 8.23 0.00 35.06 2.43
2772 5304 1.523934 CCGCGAACTGTAAACTCGTTT 59.476 47.619 8.23 0.35 35.06 3.60
2773 5305 1.134226 CCGCGAACTGTAAACTCGTT 58.866 50.000 8.23 0.00 35.06 3.85
2774 5306 0.311790 TCCGCGAACTGTAAACTCGT 59.688 50.000 8.23 0.00 35.06 4.18
2775 5307 1.411394 TTCCGCGAACTGTAAACTCG 58.589 50.000 8.23 0.00 35.70 4.18
2776 5308 3.865224 TTTTCCGCGAACTGTAAACTC 57.135 42.857 8.23 0.00 0.00 3.01
2777 5309 3.544637 CGTTTTTCCGCGAACTGTAAACT 60.545 43.478 8.23 0.00 0.00 2.66
2778 5310 2.710460 CGTTTTTCCGCGAACTGTAAAC 59.290 45.455 8.23 8.24 0.00 2.01
2779 5311 2.286301 CCGTTTTTCCGCGAACTGTAAA 60.286 45.455 8.23 0.00 0.00 2.01
2780 5312 1.261089 CCGTTTTTCCGCGAACTGTAA 59.739 47.619 8.23 0.00 0.00 2.41
2781 5313 0.860533 CCGTTTTTCCGCGAACTGTA 59.139 50.000 8.23 0.00 0.00 2.74
2782 5314 1.644913 CCGTTTTTCCGCGAACTGT 59.355 52.632 8.23 0.00 0.00 3.55
2783 5315 1.724581 GCCGTTTTTCCGCGAACTG 60.725 57.895 8.23 1.06 0.00 3.16
2784 5316 0.600782 TAGCCGTTTTTCCGCGAACT 60.601 50.000 8.23 0.00 0.00 3.01
2785 5317 0.445043 ATAGCCGTTTTTCCGCGAAC 59.555 50.000 8.23 2.38 0.00 3.95
2786 5318 0.444651 CATAGCCGTTTTTCCGCGAA 59.555 50.000 8.23 0.00 0.00 4.70
2787 5319 1.973137 GCATAGCCGTTTTTCCGCGA 61.973 55.000 8.23 0.00 0.00 5.87
2788 5320 1.582680 GCATAGCCGTTTTTCCGCG 60.583 57.895 0.00 0.00 0.00 6.46
2789 5321 1.582680 CGCATAGCCGTTTTTCCGC 60.583 57.895 0.00 0.00 0.00 5.54
2790 5322 1.061887 CCGCATAGCCGTTTTTCCG 59.938 57.895 0.00 0.00 0.00 4.30
2791 5323 1.431845 CCCGCATAGCCGTTTTTCC 59.568 57.895 0.00 0.00 0.00 3.13
2792 5324 1.226575 GCCCGCATAGCCGTTTTTC 60.227 57.895 0.00 0.00 0.00 2.29
2793 5325 2.706834 GGCCCGCATAGCCGTTTTT 61.707 57.895 0.00 0.00 41.41 1.94
2794 5326 3.138128 GGCCCGCATAGCCGTTTT 61.138 61.111 0.00 0.00 41.41 2.43
2820 5352 4.803426 GGTCTGACTCTGCCGCCG 62.803 72.222 7.85 0.00 0.00 6.46
2821 5353 4.459089 GGGTCTGACTCTGCCGCC 62.459 72.222 7.85 0.00 0.00 6.13
2822 5354 4.459089 GGGGTCTGACTCTGCCGC 62.459 72.222 7.74 0.00 0.00 6.53
2823 5355 4.135153 CGGGGTCTGACTCTGCCG 62.135 72.222 7.74 0.00 0.00 5.69
2824 5356 4.459089 GCGGGGTCTGACTCTGCC 62.459 72.222 27.39 11.86 45.15 4.85
2826 5358 0.387202 CTATGCGGGGTCTGACTCTG 59.613 60.000 12.25 12.25 0.00 3.35
2827 5359 0.033011 ACTATGCGGGGTCTGACTCT 60.033 55.000 7.74 0.00 0.00 3.24
2828 5360 0.103208 CACTATGCGGGGTCTGACTC 59.897 60.000 7.85 2.89 0.00 3.36
2829 5361 1.330655 CCACTATGCGGGGTCTGACT 61.331 60.000 7.85 0.00 0.00 3.41
2830 5362 1.144057 CCACTATGCGGGGTCTGAC 59.856 63.158 0.00 0.00 0.00 3.51
2831 5363 0.616395 TTCCACTATGCGGGGTCTGA 60.616 55.000 0.00 0.00 0.00 3.27
2832 5364 0.462047 GTTCCACTATGCGGGGTCTG 60.462 60.000 0.00 0.00 0.00 3.51
2833 5365 0.617820 AGTTCCACTATGCGGGGTCT 60.618 55.000 0.00 0.00 0.00 3.85
2834 5366 0.462047 CAGTTCCACTATGCGGGGTC 60.462 60.000 0.00 0.00 0.00 4.46
2835 5367 1.198759 ACAGTTCCACTATGCGGGGT 61.199 55.000 0.00 0.00 0.00 4.95
2836 5368 0.828022 TACAGTTCCACTATGCGGGG 59.172 55.000 0.00 0.00 0.00 5.73
2837 5369 2.684001 TTACAGTTCCACTATGCGGG 57.316 50.000 0.00 0.00 0.00 6.13



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

AutoCloner maintained by Alex Coulton.