Multiple sequence alignment - TraesCS6A01G233800

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 TraesCS6A01G233800 chr6A 100.000 2742 0 0 1 2742 441484984 441487725 0.000000e+00 5064
1 TraesCS6A01G233800 chr6A 77.083 432 83 11 47 465 560618156 560617728 4.560000e-58 235
2 TraesCS6A01G233800 chr6A 88.021 192 23 0 1272 1463 614381579 614381770 7.640000e-56 228
3 TraesCS6A01G233800 chr6A 82.072 251 36 7 594 838 602683907 602684154 3.580000e-49 206
4 TraesCS6A01G233800 chr6D 91.546 1656 94 18 1001 2624 306129006 306130647 0.000000e+00 2241
5 TraesCS6A01G233800 chr6D 93.824 1020 50 9 1 1009 306127814 306128831 0.000000e+00 1522
6 TraesCS6A01G233800 chr6D 86.979 192 25 0 1272 1463 469205360 469205551 1.650000e-52 217
7 TraesCS6A01G233800 chr6B 87.894 1842 127 48 951 2742 473055642 473057437 0.000000e+00 2078
8 TraesCS6A01G233800 chr6B 91.988 986 65 8 1237 2210 563805962 563804979 0.000000e+00 1371
9 TraesCS6A01G233800 chr6B 88.745 231 23 3 1981 2210 563814508 563814280 2.080000e-71 279
10 TraesCS6A01G233800 chr6B 85.909 220 27 2 1272 1490 715448892 715449108 5.910000e-57 231
11 TraesCS6A01G233800 chrUn 78.974 585 113 8 1 581 115096997 115097575 9.210000e-105 390
12 TraesCS6A01G233800 chr5A 78.846 572 113 8 13 579 258035644 258036212 1.990000e-101 379
13 TraesCS6A01G233800 chr3A 77.649 519 103 13 1 513 53223404 53223915 1.230000e-78 303
14 TraesCS6A01G233800 chr2B 89.954 219 22 0 1272 1490 557227660 557227442 1.610000e-72 283
15 TraesCS6A01G233800 chr2A 89.498 219 23 0 1272 1490 618267349 618267131 7.480000e-71 278
16 TraesCS6A01G233800 chr2D 88.584 219 25 0 1272 1490 476345879 476345661 1.620000e-67 267
17 TraesCS6A01G233800 chr2D 84.800 250 35 3 594 841 374103840 374104088 5.860000e-62 248
18 TraesCS6A01G233800 chr4B 76.715 481 100 12 40 517 128019905 128020376 9.740000e-65 257
19 TraesCS6A01G233800 chr3D 76.145 524 97 22 1 513 41721435 41721941 1.630000e-62 250
20 TraesCS6A01G233800 chr7D 84.362 243 37 1 594 835 564170609 564170851 1.270000e-58 237
21 TraesCS6A01G233800 chr5B 75.000 544 119 13 47 582 234089604 234090138 4.560000e-58 235
22 TraesCS6A01G233800 chr1D 83.740 246 37 3 591 834 23328316 23328072 2.120000e-56 230
23 TraesCS6A01G233800 chr7A 82.213 253 40 5 588 835 717839033 717838781 2.140000e-51 213
24 TraesCS6A01G233800 chr5D 81.746 252 43 3 582 833 488387123 488386875 9.950000e-50 207
25 TraesCS6A01G233800 chr5D 77.676 327 62 9 4 325 376273238 376272918 3.600000e-44 189
26 TraesCS6A01G233800 chr4D 81.967 244 41 3 591 832 35358739 35358497 1.290000e-48 204
27 TraesCS6A01G233800 chr4A 82.128 235 40 1 595 827 685323134 685323368 1.670000e-47 200


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 TraesCS6A01G233800 chr6A 441484984 441487725 2741 False 5064.0 5064 100.000 1 2742 1 chr6A.!!$F1 2741
1 TraesCS6A01G233800 chr6D 306127814 306130647 2833 False 1881.5 2241 92.685 1 2624 2 chr6D.!!$F2 2623
2 TraesCS6A01G233800 chr6B 473055642 473057437 1795 False 2078.0 2078 87.894 951 2742 1 chr6B.!!$F1 1791
3 TraesCS6A01G233800 chr6B 563804979 563805962 983 True 1371.0 1371 91.988 1237 2210 1 chr6B.!!$R1 973
4 TraesCS6A01G233800 chrUn 115096997 115097575 578 False 390.0 390 78.974 1 581 1 chrUn.!!$F1 580
5 TraesCS6A01G233800 chr5A 258035644 258036212 568 False 379.0 379 78.846 13 579 1 chr5A.!!$F1 566
6 TraesCS6A01G233800 chr3A 53223404 53223915 511 False 303.0 303 77.649 1 513 1 chr3A.!!$F1 512
7 TraesCS6A01G233800 chr3D 41721435 41721941 506 False 250.0 250 76.145 1 513 1 chr3D.!!$F1 512
8 TraesCS6A01G233800 chr5B 234089604 234090138 534 False 235.0 235 75.000 47 582 1 chr5B.!!$F1 535

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
816 846 0.170116 AACGTGGGCGCATTACATTG 59.83 50.0 10.83 2.36 42.83 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 2167 0.17897 GATGCAGCTGGGATTGGGAT 60.179 55.0 17.12 0.0 0.0 3.85 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
198 203 1.227497 GCGAAGGAGAGGCATGGAG 60.227 63.158 0.00 0.00 0.00 3.86
218 223 2.659610 GCAGTGGAGGAGAAGCGT 59.340 61.111 0.00 0.00 0.00 5.07
407 430 1.266446 GGGAGTATCGGAGTCTTACGC 59.734 57.143 0.00 0.00 34.37 4.42
557 586 2.660490 CGAACAGTTACGGACGGTTTA 58.340 47.619 10.06 0.00 44.89 2.01
601 630 6.744622 GCCCTTCCATATTTTACTACTCCCTC 60.745 46.154 0.00 0.00 0.00 4.30
622 651 5.041951 TCCATTTCAAATTGTAGTGCGTC 57.958 39.130 0.00 0.00 0.00 5.19
624 653 3.907894 TTTCAAATTGTAGTGCGTCCC 57.092 42.857 0.00 0.00 0.00 4.46
642 671 2.239654 TCCCCGCTTCTTGAGATTCAAT 59.760 45.455 0.00 0.00 35.59 2.57
671 700 7.094975 TGACCGTAAATTTAACCAATGAGACTG 60.095 37.037 0.00 0.00 0.00 3.51
746 776 3.186409 CGGTGATATAATTGTTGCTCCCG 59.814 47.826 0.00 0.00 0.00 5.14
754 784 0.390124 TTGTTGCTCCCGTCGTAGTT 59.610 50.000 0.00 0.00 0.00 2.24
782 812 7.530525 GTCTCGTTGGTTAAATTTACGGTTAAC 59.469 37.037 9.79 0.00 38.78 2.01
790 820 8.900511 GTTAAATTTACGGTTAACCTTGGATC 57.099 34.615 22.12 0.00 35.21 3.36
791 821 8.733458 GTTAAATTTACGGTTAACCTTGGATCT 58.267 33.333 22.12 5.15 35.21 2.75
801 831 3.771577 ACCTTGGATCTCAGAAAACGT 57.228 42.857 0.00 0.00 0.00 3.99
809 839 1.577328 CTCAGAAAACGTGGGCGCAT 61.577 55.000 10.83 0.00 42.83 4.73
816 846 0.170116 AACGTGGGCGCATTACATTG 59.830 50.000 10.83 2.36 42.83 2.82
820 850 0.322906 TGGGCGCATTACATTGTGGA 60.323 50.000 10.83 0.00 0.00 4.02
827 857 3.627123 CGCATTACATTGTGGAATGGAGA 59.373 43.478 14.78 0.00 46.30 3.71
895 926 9.587772 GAAGTACATGATTACACACATTCTACT 57.412 33.333 0.00 0.00 0.00 2.57
898 929 9.797556 GTACATGATTACACACATTCTACTACA 57.202 33.333 0.00 0.00 0.00 2.74
900 931 9.719355 ACATGATTACACACATTCTACTACAAA 57.281 29.630 0.00 0.00 0.00 2.83
922 953 9.323985 ACAAATACAATTGCACATAAACAAACT 57.676 25.926 5.05 0.00 33.52 2.66
1204 1440 1.040893 ACCTACCGATGACGATGGCA 61.041 55.000 0.00 0.00 42.66 4.92
1492 1728 3.785859 GCGCCATCCACCTCCTCA 61.786 66.667 0.00 0.00 0.00 3.86
1750 1986 2.119655 CGAGGAGTAGACCCGGTGG 61.120 68.421 0.00 0.00 37.80 4.61
1757 1993 0.899720 GTAGACCCGGTGGATCAACA 59.100 55.000 1.86 0.00 34.81 3.33
1760 1996 0.391263 GACCCGGTGGATCAACAGTC 60.391 60.000 1.86 2.29 34.81 3.51
1768 2004 1.546029 TGGATCAACAGTCCTGACGAG 59.454 52.381 0.40 0.00 36.68 4.18
1777 2013 2.034685 CAGTCCTGACGAGTGTTCTTGA 59.965 50.000 0.00 0.00 37.18 3.02
1780 2016 4.523173 AGTCCTGACGAGTGTTCTTGATTA 59.477 41.667 0.00 0.00 36.20 1.75
1823 2062 1.486726 GATCCTGGGTGTACTTCCCTG 59.513 57.143 21.21 20.04 44.84 4.45
1826 2065 2.198304 CTGGGTGTACTTCCCTGCCC 62.198 65.000 21.21 10.25 44.84 5.36
1832 2071 1.607178 TACTTCCCTGCCCGTCGAA 60.607 57.895 0.00 0.00 0.00 3.71
1882 2124 5.356882 TTCTTTCTGCAGTTTAATCGGTG 57.643 39.130 14.67 0.00 0.00 4.94
1890 2132 5.698832 TGCAGTTTAATCGGTGAAGATTTG 58.301 37.500 0.00 0.00 40.83 2.32
1892 2134 4.788100 CAGTTTAATCGGTGAAGATTTGCG 59.212 41.667 0.00 0.00 40.83 4.85
1895 2137 5.811399 TTAATCGGTGAAGATTTGCGATT 57.189 34.783 0.00 0.00 40.83 3.34
1896 2138 4.701956 AATCGGTGAAGATTTGCGATTT 57.298 36.364 0.00 0.00 37.56 2.17
1902 2144 5.563842 GGTGAAGATTTGCGATTTCACTAG 58.436 41.667 18.40 0.00 45.32 2.57
1903 2145 5.351465 GGTGAAGATTTGCGATTTCACTAGA 59.649 40.000 18.40 0.00 45.32 2.43
1924 2167 5.738909 AGACGCTTACTTAGGAGTACTACA 58.261 41.667 8.10 0.00 38.07 2.74
1925 2168 6.355747 AGACGCTTACTTAGGAGTACTACAT 58.644 40.000 8.10 0.00 38.07 2.29
1926 2169 6.482973 AGACGCTTACTTAGGAGTACTACATC 59.517 42.308 8.10 0.00 38.07 3.06
1927 2170 5.530543 ACGCTTACTTAGGAGTACTACATCC 59.469 44.000 8.10 0.00 38.07 3.51
1928 2171 5.048852 CGCTTACTTAGGAGTACTACATCCC 60.049 48.000 8.10 0.00 38.07 3.85
1929 2172 5.832060 GCTTACTTAGGAGTACTACATCCCA 59.168 44.000 8.10 0.00 38.07 4.37
1943 2196 0.178970 ATCCCAATCCCAGCTGCATC 60.179 55.000 8.66 0.00 0.00 3.91
1954 2207 2.421424 CCAGCTGCATCTGTTAGAAACC 59.579 50.000 15.94 0.00 32.32 3.27
1956 2209 3.755378 CAGCTGCATCTGTTAGAAACCTT 59.245 43.478 9.43 0.00 0.00 3.50
1977 2230 5.063564 CCTTTTAGTATCTGTCGTTGGCTTC 59.936 44.000 0.00 0.00 0.00 3.86
1994 2247 4.081365 TGGCTTCAAGTGGATCGTGTAATA 60.081 41.667 0.00 0.00 0.00 0.98
2024 2277 4.072131 TCATGGAACCTGTTTCACTTAGC 58.928 43.478 0.00 0.00 35.70 3.09
2028 2281 3.821033 GGAACCTGTTTCACTTAGCATGT 59.179 43.478 0.00 0.00 35.70 3.21
2034 2287 3.183574 TGTTTCACTTAGCATGTTCGTCG 59.816 43.478 0.00 0.00 0.00 5.12
2038 2291 2.597305 CACTTAGCATGTTCGTCGGTAC 59.403 50.000 0.00 0.00 0.00 3.34
2082 2343 1.877637 AACGCAGTGTAGCATTCACA 58.122 45.000 8.23 0.00 45.00 3.58
2107 2368 2.670905 TGTGCCGTCATTATCTTCGTTG 59.329 45.455 0.00 0.00 0.00 4.10
2118 2379 3.868757 ATCTTCGTTGGTCTCGATCAA 57.131 42.857 0.00 0.00 37.18 2.57
2152 2413 3.382546 CCATTCGGGAGCATGAAATTCTT 59.617 43.478 0.00 0.00 40.01 2.52
2162 2425 6.585322 GGAGCATGAAATTCTTTGTTCAAGAG 59.415 38.462 0.00 0.00 42.76 2.85
2166 2429 4.039124 TGAAATTCTTTGTTCAAGAGCCCC 59.961 41.667 0.00 0.00 42.76 5.80
2167 2430 1.995376 TTCTTTGTTCAAGAGCCCCC 58.005 50.000 0.00 0.00 42.76 5.40
2168 2431 0.850100 TCTTTGTTCAAGAGCCCCCA 59.150 50.000 0.00 0.00 36.51 4.96
2171 2434 3.075283 TCTTTGTTCAAGAGCCCCCATTA 59.925 43.478 0.00 0.00 36.51 1.90
2173 2436 1.707989 TGTTCAAGAGCCCCCATTACA 59.292 47.619 0.00 0.00 0.00 2.41
2175 2438 2.492088 GTTCAAGAGCCCCCATTACAAC 59.508 50.000 0.00 0.00 0.00 3.32
2180 2443 3.123273 AGAGCCCCCATTACAACTGTAT 58.877 45.455 0.00 0.00 0.00 2.29
2203 2466 4.351407 TGTTGATTGTTGAGGTAGGGGTAA 59.649 41.667 0.00 0.00 0.00 2.85
2216 2490 0.837940 GGGGTAAGAGGAATCGGCTT 59.162 55.000 0.00 0.00 0.00 4.35
2219 2493 2.289565 GGTAAGAGGAATCGGCTTTGG 58.710 52.381 0.00 0.00 0.00 3.28
2242 2516 2.154854 ATCTCGGTTATCCATGCACG 57.845 50.000 0.00 0.00 0.00 5.34
2258 2532 3.204119 CGCATGGCCGCAGATTGA 61.204 61.111 0.00 0.00 0.00 2.57
2260 2534 1.226773 GCATGGCCGCAGATTGAAC 60.227 57.895 0.00 0.00 0.00 3.18
2275 2549 5.228635 CAGATTGAACAAATGATAACGCTGC 59.771 40.000 0.00 0.00 0.00 5.25
2304 2587 0.321830 GGATTCCGTCGTTTCCCCAA 60.322 55.000 0.00 0.00 0.00 4.12
2305 2588 0.800631 GATTCCGTCGTTTCCCCAAC 59.199 55.000 0.00 0.00 0.00 3.77
2306 2589 0.607217 ATTCCGTCGTTTCCCCAACC 60.607 55.000 0.00 0.00 30.65 3.77
2307 2590 2.670592 CCGTCGTTTCCCCAACCC 60.671 66.667 0.00 0.00 30.65 4.11
2308 2591 2.670592 CGTCGTTTCCCCAACCCC 60.671 66.667 0.00 0.00 30.65 4.95
2309 2592 2.516909 GTCGTTTCCCCAACCCCA 59.483 61.111 0.00 0.00 30.65 4.96
2319 2602 0.106015 CCCAACCCCATGGATTCTCC 60.106 60.000 15.22 0.00 43.54 3.71
2321 2604 0.630673 CAACCCCATGGATTCTCCCA 59.369 55.000 15.22 0.00 41.05 4.37
2338 2621 1.202336 CCCATGAATTGGCTTCGCTTC 60.202 52.381 0.00 0.00 44.97 3.86
2367 2650 3.473647 CATGCTCCGAGGGCAGGA 61.474 66.667 4.67 0.00 42.98 3.86
2568 2859 1.609072 GGTTGACCTGGTTCTTCTTGC 59.391 52.381 0.00 0.00 0.00 4.01
2622 2913 4.932799 TGTTTACTAGTAACGCATGCATGT 59.067 37.500 26.79 10.85 0.00 3.21
2624 2915 6.035220 TGTTTACTAGTAACGCATGCATGTAC 59.965 38.462 26.79 20.18 0.00 2.90
2625 2916 3.113322 ACTAGTAACGCATGCATGTACG 58.887 45.455 26.79 23.40 0.00 3.67
2626 2917 2.287393 AGTAACGCATGCATGTACGA 57.713 45.000 26.58 10.61 0.00 3.43
2627 2918 2.193447 AGTAACGCATGCATGTACGAG 58.807 47.619 26.58 16.37 0.00 4.18
2628 2919 1.924524 GTAACGCATGCATGTACGAGT 59.075 47.619 26.58 17.83 0.00 4.18
2629 2920 2.287393 AACGCATGCATGTACGAGTA 57.713 45.000 26.58 0.00 0.00 2.59
2630 2921 2.509052 ACGCATGCATGTACGAGTAT 57.491 45.000 26.58 7.49 0.00 2.12
2631 2922 3.636282 ACGCATGCATGTACGAGTATA 57.364 42.857 26.58 0.00 0.00 1.47
2632 2923 4.174411 ACGCATGCATGTACGAGTATAT 57.826 40.909 26.58 6.58 0.00 0.86
2660 2951 4.754114 TGGTAATTTTAACCGTGCGTTACT 59.246 37.500 0.00 0.00 40.08 2.24
2662 2953 6.128688 TGGTAATTTTAACCGTGCGTTACTAC 60.129 38.462 0.00 0.00 40.08 2.73
2663 2954 6.090763 GGTAATTTTAACCGTGCGTTACTACT 59.909 38.462 0.00 0.00 36.65 2.57
2664 2955 7.274686 GGTAATTTTAACCGTGCGTTACTACTA 59.725 37.037 0.00 0.00 36.65 1.82
2665 2956 7.650834 AATTTTAACCGTGCGTTACTACTAA 57.349 32.000 0.00 0.00 36.65 2.24
2666 2957 7.650834 ATTTTAACCGTGCGTTACTACTAAA 57.349 32.000 0.00 0.00 36.65 1.85
2667 2958 6.446659 TTTAACCGTGCGTTACTACTAAAC 57.553 37.500 0.00 0.00 36.65 2.01
2668 2959 3.641437 ACCGTGCGTTACTACTAAACA 57.359 42.857 0.00 0.00 0.00 2.83
2669 2960 3.568538 ACCGTGCGTTACTACTAAACAG 58.431 45.455 0.00 0.00 0.00 3.16
2670 2961 3.004734 ACCGTGCGTTACTACTAAACAGT 59.995 43.478 0.00 0.00 0.00 3.55
2671 2962 3.362831 CCGTGCGTTACTACTAAACAGTG 59.637 47.826 0.00 0.00 0.00 3.66
2672 2963 3.976942 CGTGCGTTACTACTAAACAGTGT 59.023 43.478 0.00 0.00 0.00 3.55
2673 2964 5.146460 CGTGCGTTACTACTAAACAGTGTA 58.854 41.667 0.00 0.00 0.00 2.90
2674 2965 5.058492 CGTGCGTTACTACTAAACAGTGTAC 59.942 44.000 0.00 0.00 0.00 2.90
2675 2966 6.145535 GTGCGTTACTACTAAACAGTGTACT 58.854 40.000 0.00 0.00 0.00 2.73
2676 2967 7.298122 GTGCGTTACTACTAAACAGTGTACTA 58.702 38.462 0.00 0.00 0.00 1.82
2677 2968 7.269297 GTGCGTTACTACTAAACAGTGTACTAC 59.731 40.741 0.00 0.00 0.00 2.73
2678 2969 7.041440 TGCGTTACTACTAAACAGTGTACTACA 60.041 37.037 0.00 0.00 0.00 2.74
2679 2970 7.965107 GCGTTACTACTAAACAGTGTACTACAT 59.035 37.037 0.00 0.00 0.00 2.29
2696 2987 6.452494 ACTACATAGTACGATATGATGGCC 57.548 41.667 8.65 0.00 36.76 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
198 203 2.125350 CTTCTCCTCCACTGCCGC 60.125 66.667 0.00 0.00 0.00 6.53
218 223 2.363795 CTACACCCGGGCTCCAGA 60.364 66.667 24.08 0.00 0.00 3.86
326 333 4.784838 TCCTCCCATCTTTCTCTGAATCAA 59.215 41.667 0.00 0.00 0.00 2.57
327 334 4.365368 TCCTCCCATCTTTCTCTGAATCA 58.635 43.478 0.00 0.00 0.00 2.57
407 430 1.216710 GGAGTCCAGACAGAAGCCG 59.783 63.158 3.60 0.00 0.00 5.52
557 586 2.165998 GCATCTTCAAAGCAGACCCTT 58.834 47.619 0.00 0.00 0.00 3.95
601 630 4.165779 GGACGCACTACAATTTGAAATGG 58.834 43.478 2.79 0.00 0.00 3.16
622 651 2.113860 TTGAATCTCAAGAAGCGGGG 57.886 50.000 0.00 0.00 31.83 5.73
624 653 5.570589 GTCAAAATTGAATCTCAAGAAGCGG 59.429 40.000 0.00 0.00 40.05 5.52
627 656 6.672147 ACGGTCAAAATTGAATCTCAAGAAG 58.328 36.000 0.00 0.00 40.05 2.85
642 671 8.630917 TCTCATTGGTTAAATTTACGGTCAAAA 58.369 29.630 0.00 0.00 0.00 2.44
671 700 2.570442 TTTTTATTCCCGCCGCAATC 57.430 45.000 0.00 0.00 0.00 2.67
746 776 1.000938 ACCAACGAGACCAACTACGAC 60.001 52.381 0.00 0.00 0.00 4.34
754 784 4.451774 CCGTAAATTTAACCAACGAGACCA 59.548 41.667 11.09 0.00 35.66 4.02
782 812 2.744202 CCACGTTTTCTGAGATCCAAGG 59.256 50.000 0.00 0.00 0.00 3.61
790 820 1.577328 ATGCGCCCACGTTTTCTGAG 61.577 55.000 4.18 0.00 42.83 3.35
791 821 1.169661 AATGCGCCCACGTTTTCTGA 61.170 50.000 4.18 0.00 42.83 3.27
801 831 0.322906 TCCACAATGTAATGCGCCCA 60.323 50.000 4.18 0.00 0.00 5.36
809 839 5.762179 ACTCTCTCCATTCCACAATGTAA 57.238 39.130 0.00 0.00 38.22 2.41
816 846 7.500559 AGCAATTTTATACTCTCTCCATTCCAC 59.499 37.037 0.00 0.00 0.00 4.02
874 905 9.719355 TTTGTAGTAGAATGTGTGTAATCATGT 57.281 29.630 0.00 0.00 0.00 3.21
896 927 9.323985 AGTTTGTTTATGTGCAATTGTATTTGT 57.676 25.926 7.40 0.00 0.00 2.83
935 981 7.640240 GCGCTAGATTTTTCGAGTTTTCATATT 59.360 33.333 0.00 0.00 0.00 1.28
1088 1317 1.218316 GCTGTACGTTGGAGGGAGG 59.782 63.158 0.00 0.00 0.00 4.30
1258 1494 4.680237 TCCTTCACGCTGCCACCG 62.680 66.667 0.00 0.00 0.00 4.94
1465 1701 4.593864 GATGGCGCGGAGGAGGAC 62.594 72.222 8.83 0.00 0.00 3.85
1492 1728 1.133419 GGGTACGAGAAGGAGGAGGAT 60.133 57.143 0.00 0.00 0.00 3.24
1730 1966 3.217743 CCGGGTCTACTCCTCGGC 61.218 72.222 0.00 0.00 35.68 5.54
1739 1975 1.191535 CTGTTGATCCACCGGGTCTA 58.808 55.000 6.32 0.00 34.93 2.59
1750 1986 2.029828 ACACTCGTCAGGACTGTTGATC 60.030 50.000 0.00 0.00 0.00 2.92
1757 1993 2.307768 TCAAGAACACTCGTCAGGACT 58.692 47.619 0.00 0.00 0.00 3.85
1760 1996 5.655488 AGATAATCAAGAACACTCGTCAGG 58.345 41.667 0.00 0.00 0.00 3.86
1768 2004 9.185192 CCAAAACAGAAAGATAATCAAGAACAC 57.815 33.333 0.00 0.00 0.00 3.32
1777 2013 5.903923 AGACCCCCAAAACAGAAAGATAAT 58.096 37.500 0.00 0.00 0.00 1.28
1780 2016 3.903530 AGACCCCCAAAACAGAAAGAT 57.096 42.857 0.00 0.00 0.00 2.40
1851 2090 4.622701 ACTGCAGAAAGAAAGAACACAC 57.377 40.909 23.35 0.00 0.00 3.82
1882 2124 5.484958 CGTCTAGTGAAATCGCAAATCTTC 58.515 41.667 0.00 0.00 0.00 2.87
1890 2132 3.436496 AGTAAGCGTCTAGTGAAATCGC 58.564 45.455 0.00 0.00 45.82 4.58
1892 2134 6.793349 TCCTAAGTAAGCGTCTAGTGAAATC 58.207 40.000 0.00 0.00 0.00 2.17
1895 2137 5.251764 ACTCCTAAGTAAGCGTCTAGTGAA 58.748 41.667 0.00 0.00 32.59 3.18
1896 2138 4.841422 ACTCCTAAGTAAGCGTCTAGTGA 58.159 43.478 0.00 0.00 32.59 3.41
1902 2144 6.293353 GGATGTAGTACTCCTAAGTAAGCGTC 60.293 46.154 0.00 0.00 39.66 5.19
1903 2145 5.530543 GGATGTAGTACTCCTAAGTAAGCGT 59.469 44.000 0.00 0.00 39.66 5.07
1924 2167 0.178970 GATGCAGCTGGGATTGGGAT 60.179 55.000 17.12 0.00 0.00 3.85
1925 2168 1.228228 GATGCAGCTGGGATTGGGA 59.772 57.895 17.12 0.00 0.00 4.37
1926 2169 1.107538 CAGATGCAGCTGGGATTGGG 61.108 60.000 24.22 0.00 32.26 4.12
1927 2170 0.395311 ACAGATGCAGCTGGGATTGG 60.395 55.000 33.28 9.25 40.20 3.16
1928 2171 1.471119 AACAGATGCAGCTGGGATTG 58.529 50.000 33.28 10.92 40.20 2.67
1929 2172 2.507058 TCTAACAGATGCAGCTGGGATT 59.493 45.455 33.28 21.48 40.20 3.01
1943 2196 8.861101 CGACAGATACTAAAAGGTTTCTAACAG 58.139 37.037 0.00 0.00 0.00 3.16
1954 2207 5.637810 TGAAGCCAACGACAGATACTAAAAG 59.362 40.000 0.00 0.00 0.00 2.27
1956 2209 5.142061 TGAAGCCAACGACAGATACTAAA 57.858 39.130 0.00 0.00 0.00 1.85
1994 2247 1.971357 ACAGGTTCCATGAGAAGTCGT 59.029 47.619 0.00 0.00 34.29 4.34
2082 2343 2.698855 AGATAATGACGGCACAGCTT 57.301 45.000 0.00 0.00 0.00 3.74
2107 2368 5.449177 GGGAAATTGATGTTTGATCGAGACC 60.449 44.000 0.00 0.00 0.00 3.85
2148 2409 1.216678 TGGGGGCTCTTGAACAAAGAA 59.783 47.619 0.00 0.00 44.38 2.52
2149 2410 0.850100 TGGGGGCTCTTGAACAAAGA 59.150 50.000 0.00 0.00 42.83 2.52
2152 2413 2.109128 TGTAATGGGGGCTCTTGAACAA 59.891 45.455 0.00 0.00 0.00 2.83
2162 2425 3.012934 ACATACAGTTGTAATGGGGGC 57.987 47.619 0.00 0.00 33.76 5.80
2173 2436 6.655003 CCTACCTCAACAATCAACATACAGTT 59.345 38.462 0.00 0.00 42.42 3.16
2175 2438 5.586243 CCCTACCTCAACAATCAACATACAG 59.414 44.000 0.00 0.00 0.00 2.74
2180 2443 2.714250 ACCCCTACCTCAACAATCAACA 59.286 45.455 0.00 0.00 0.00 3.33
2191 2454 2.892215 CGATTCCTCTTACCCCTACCTC 59.108 54.545 0.00 0.00 0.00 3.85
2203 2466 2.879103 TTTCCAAAGCCGATTCCTCT 57.121 45.000 0.00 0.00 0.00 3.69
2216 2490 4.338118 GCATGGATAACCGAGATTTTCCAA 59.662 41.667 9.15 0.00 41.28 3.53
2219 2493 4.552767 CGTGCATGGATAACCGAGATTTTC 60.553 45.833 0.00 0.00 39.42 2.29
2242 2516 1.226773 GTTCAATCTGCGGCCATGC 60.227 57.895 2.24 0.00 0.00 4.06
2252 2526 5.335127 GCAGCGTTATCATTTGTTCAATCT 58.665 37.500 0.00 0.00 0.00 2.40
2258 2532 2.742053 ACTCGCAGCGTTATCATTTGTT 59.258 40.909 15.93 0.00 0.00 2.83
2260 2534 2.697363 CACTCGCAGCGTTATCATTTG 58.303 47.619 15.93 0.00 0.00 2.32
2275 2549 2.202932 CGGAATCCAGGGCACTCG 60.203 66.667 0.00 0.00 0.00 4.18
2568 2859 3.896133 GTGATGCCCTGCCATGCG 61.896 66.667 0.00 0.00 0.00 4.73
2629 2920 8.071368 CGCACGGTTAAAATTACCAATACATAT 58.929 33.333 0.00 0.00 35.31 1.78
2630 2921 7.065563 ACGCACGGTTAAAATTACCAATACATA 59.934 33.333 0.00 0.00 35.31 2.29
2631 2922 6.127952 ACGCACGGTTAAAATTACCAATACAT 60.128 34.615 0.00 0.00 35.31 2.29
2632 2923 5.180868 ACGCACGGTTAAAATTACCAATACA 59.819 36.000 0.00 0.00 35.31 2.29
2650 2941 3.976942 ACACTGTTTAGTAGTAACGCACG 59.023 43.478 0.00 0.00 34.74 5.34
2652 2943 6.317789 AGTACACTGTTTAGTAGTAACGCA 57.682 37.500 0.00 0.00 34.74 5.24
2672 2963 7.114095 TGGCCATCATATCGTACTATGTAGTA 58.886 38.462 0.00 0.00 37.73 1.82
2673 2964 5.949952 TGGCCATCATATCGTACTATGTAGT 59.050 40.000 0.00 0.00 40.24 2.73
2674 2965 6.451064 TGGCCATCATATCGTACTATGTAG 57.549 41.667 0.00 0.00 32.13 2.74
2675 2966 8.706322 ATATGGCCATCATATCGTACTATGTA 57.294 34.615 24.80 0.00 43.54 2.29
2676 2967 5.939764 ATGGCCATCATATCGTACTATGT 57.060 39.130 14.09 0.00 33.61 2.29
2677 2968 8.143835 TGAATATGGCCATCATATCGTACTATG 58.856 37.037 24.80 0.00 45.54 2.23
2678 2969 8.250143 TGAATATGGCCATCATATCGTACTAT 57.750 34.615 24.80 1.94 45.54 2.12
2679 2970 7.201911 CCTGAATATGGCCATCATATCGTACTA 60.202 40.741 24.80 0.00 45.54 1.82
2695 2986 6.039047 CACTCATTTTCCAGTCCTGAATATGG 59.961 42.308 0.00 0.00 0.00 2.74
2696 2987 6.825213 TCACTCATTTTCCAGTCCTGAATATG 59.175 38.462 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.