Multiple sequence alignment - TraesCS5A01G253800

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 TraesCS5A01G253800 chr5A 100.000 3275 0 0 1 3275 469895377 469898651 0.000000e+00 6048
1 TraesCS5A01G253800 chr5A 86.606 769 35 28 2526 3275 469905379 469906098 0.000000e+00 787
2 TraesCS5A01G253800 chr5D 94.107 1697 83 10 818 2510 367808928 367810611 0.000000e+00 2564
3 TraesCS5A01G253800 chr5D 90.705 624 32 13 2572 3188 367811367 367811971 0.000000e+00 808
4 TraesCS5A01G253800 chr5D 95.111 225 8 1 505 729 367808576 367808797 5.200000e-93 351
5 TraesCS5A01G253800 chr5D 79.158 475 59 21 41 489 367808068 367808528 3.200000e-75 292
6 TraesCS5A01G253800 chr5B 92.323 1498 84 15 779 2273 435767971 435769440 0.000000e+00 2100
7 TraesCS5A01G253800 chr5B 91.964 560 34 10 2720 3274 435769822 435770375 0.000000e+00 774
8 TraesCS5A01G253800 chr5B 81.641 463 50 16 41 489 435767157 435767598 5.200000e-93 351
9 TraesCS5A01G253800 chr5B 88.889 171 9 4 486 651 435767630 435767795 5.540000e-48 202
10 TraesCS5A01G253800 chr5B 81.095 201 13 14 2268 2467 435769484 435769660 1.580000e-28 137
11 TraesCS5A01G253800 chr7A 89.489 333 30 4 959 1287 191919141 191918810 1.820000e-112 416
12 TraesCS5A01G253800 chr7A 86.585 246 16 8 486 729 191919631 191919401 4.190000e-64 255
13 TraesCS5A01G253800 chr7A 91.398 93 8 0 395 487 191919757 191919665 9.540000e-26 128


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 TraesCS5A01G253800 chr5A 469895377 469898651 3274 False 6048.000000 6048 100.000000 1 3275 1 chr5A.!!$F1 3274
1 TraesCS5A01G253800 chr5A 469905379 469906098 719 False 787.000000 787 86.606000 2526 3275 1 chr5A.!!$F2 749
2 TraesCS5A01G253800 chr5D 367808068 367811971 3903 False 1003.750000 2564 89.770250 41 3188 4 chr5D.!!$F1 3147
3 TraesCS5A01G253800 chr5B 435767157 435770375 3218 False 712.800000 2100 87.182400 41 3274 5 chr5B.!!$F1 3233
4 TraesCS5A01G253800 chr7A 191918810 191919757 947 True 266.333333 416 89.157333 395 1287 3 chr7A.!!$R1 892

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
34 35 0.039180 TAACGCTGGACTCCTGGAGA 59.961 55.0 29.71 7.06 33.32 3.71 F
38 39 0.248843 GCTGGACTCCTGGAGACTTG 59.751 60.0 29.71 18.93 33.32 3.16 F
1743 1906 0.374758 CGGTCATGGCGTTTGATCTG 59.625 55.0 0.00 0.00 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1029 1189 0.179189 GATTTTCGGTTGCCTGCTCG 60.179 55.0 0.0 0.0 0.0 5.03 R
1856 2019 0.951040 CACCAGGCACGTCTTCTTCC 60.951 60.0 0.0 0.0 0.0 3.46 R
2900 3858 1.151760 CATGGGATTGGGATGGGAGA 58.848 55.0 0.0 0.0 0.0 3.71 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
30 31 4.913126 GGTAACGCTGGACTCCTG 57.087 61.111 0.00 0.00 0.00 3.86
31 32 1.218316 GGTAACGCTGGACTCCTGG 59.782 63.158 4.27 0.00 0.00 4.45
32 33 1.255667 GGTAACGCTGGACTCCTGGA 61.256 60.000 0.00 0.00 0.00 3.86
33 34 0.173708 GTAACGCTGGACTCCTGGAG 59.826 60.000 22.00 22.00 35.52 3.86
34 35 0.039180 TAACGCTGGACTCCTGGAGA 59.961 55.000 29.71 7.06 33.32 3.71
35 36 1.536943 AACGCTGGACTCCTGGAGAC 61.537 60.000 29.71 22.77 33.32 3.36
36 37 1.680651 CGCTGGACTCCTGGAGACT 60.681 63.158 29.71 8.74 33.32 3.24
37 38 1.254284 CGCTGGACTCCTGGAGACTT 61.254 60.000 29.71 7.93 33.32 3.01
38 39 0.248843 GCTGGACTCCTGGAGACTTG 59.751 60.000 29.71 18.93 33.32 3.16
39 40 0.901124 CTGGACTCCTGGAGACTTGG 59.099 60.000 29.71 13.23 33.32 3.61
56 57 2.401766 GGTGGAGTGCGATGCTTGG 61.402 63.158 0.00 0.00 0.00 3.61
64 65 2.264480 CGATGCTTGGGTCCACGA 59.736 61.111 0.00 0.00 0.00 4.35
65 66 1.375396 CGATGCTTGGGTCCACGAA 60.375 57.895 0.00 0.00 0.00 3.85
101 105 2.444010 AGAGAGGAGGCCGATAAGTAGT 59.556 50.000 0.00 0.00 0.00 2.73
104 108 2.488937 GAGGAGGCCGATAAGTAGTAGC 59.511 54.545 0.00 0.00 0.00 3.58
105 109 2.158505 AGGAGGCCGATAAGTAGTAGCA 60.159 50.000 0.00 0.00 0.00 3.49
107 111 2.885894 GAGGCCGATAAGTAGTAGCACT 59.114 50.000 0.00 0.00 0.00 4.40
108 112 2.885894 AGGCCGATAAGTAGTAGCACTC 59.114 50.000 0.00 0.00 0.00 3.51
109 113 2.885894 GGCCGATAAGTAGTAGCACTCT 59.114 50.000 0.00 0.00 0.00 3.24
110 114 3.058085 GGCCGATAAGTAGTAGCACTCTC 60.058 52.174 0.00 0.00 0.00 3.20
111 115 3.058085 GCCGATAAGTAGTAGCACTCTCC 60.058 52.174 0.00 0.00 0.00 3.71
127 131 2.108362 CCGAGGATAACGGTGGGC 59.892 66.667 0.00 0.00 44.57 5.36
160 170 3.188786 CGGGCGGCTTCTTCTTCG 61.189 66.667 9.56 0.00 0.00 3.79
193 203 1.592223 GGAAGATAGATCCCGCCGG 59.408 63.158 0.00 0.00 0.00 6.13
194 204 1.592223 GAAGATAGATCCCGCCGGG 59.408 63.158 18.41 18.41 46.11 5.73
206 216 2.646175 CGCCGGGAGTTGGAGAGAA 61.646 63.158 2.18 0.00 0.00 2.87
236 246 5.409826 CGCTGTAAGTTTTCTTCAGATTCCT 59.590 40.000 0.00 0.00 40.91 3.36
283 310 2.028125 GCCGCCATGTCAGCTAGGTA 62.028 60.000 0.00 0.00 0.00 3.08
289 316 3.623510 GCCATGTCAGCTAGGTAGTTTTC 59.376 47.826 0.00 0.00 0.00 2.29
294 321 5.539048 TGTCAGCTAGGTAGTTTTCAAGTC 58.461 41.667 0.00 0.00 0.00 3.01
298 325 4.082136 AGCTAGGTAGTTTTCAAGTCGAGG 60.082 45.833 0.00 0.00 0.00 4.63
299 326 4.082354 GCTAGGTAGTTTTCAAGTCGAGGA 60.082 45.833 0.00 0.00 0.00 3.71
300 327 5.394333 GCTAGGTAGTTTTCAAGTCGAGGAT 60.394 44.000 0.00 0.00 0.00 3.24
301 328 5.074584 AGGTAGTTTTCAAGTCGAGGATC 57.925 43.478 0.00 0.00 0.00 3.36
322 355 4.445453 TCGATGAACTGGAATCTGGAATG 58.555 43.478 0.00 0.00 0.00 2.67
330 363 4.202609 ACTGGAATCTGGAATGAACTTGGT 60.203 41.667 0.00 0.00 0.00 3.67
369 402 3.187700 GTGTGAGTGATGGGTTCGTATC 58.812 50.000 0.00 0.00 0.00 2.24
374 407 4.038763 TGAGTGATGGGTTCGTATCCATAC 59.961 45.833 6.83 6.37 43.20 2.39
499 577 1.956477 ACTCGTTTCATTTGCAGCCTT 59.044 42.857 0.00 0.00 0.00 4.35
500 578 2.287788 ACTCGTTTCATTTGCAGCCTTG 60.288 45.455 0.00 0.00 0.00 3.61
518 596 0.393402 TGCAGTGCAGGGCTATTCTG 60.393 55.000 15.37 2.10 33.32 3.02
549 630 8.539770 TTCAAGTTGAAAATCAGAGCTAGTAG 57.460 34.615 15.92 0.00 32.71 2.57
559 640 5.560722 TCAGAGCTAGTAGATGCTAGACT 57.439 43.478 8.90 5.64 40.54 3.24
569 650 6.837312 AGTAGATGCTAGACTAGTGACTGAT 58.163 40.000 11.15 0.00 0.00 2.90
575 656 7.441890 TGCTAGACTAGTGACTGATAATAGC 57.558 40.000 11.15 3.80 0.00 2.97
635 718 3.421844 CCGGTTCTCTTGGAAGGAATTT 58.578 45.455 0.00 0.00 34.23 1.82
642 725 7.230712 GGTTCTCTTGGAAGGAATTTTGTTCTA 59.769 37.037 0.00 0.00 34.23 2.10
708 791 8.494016 ACTTAGTCAGCATAACCAAATACTTC 57.506 34.615 0.00 0.00 0.00 3.01
729 813 7.676947 ACTTCTACTACTTGTTTGGCAGAATA 58.323 34.615 0.00 0.00 0.00 1.75
730 814 8.322091 ACTTCTACTACTTGTTTGGCAGAATAT 58.678 33.333 0.00 0.00 0.00 1.28
731 815 8.492673 TTCTACTACTTGTTTGGCAGAATATG 57.507 34.615 0.00 0.00 0.00 1.78
737 821 7.944729 ACTTGTTTGGCAGAATATGAATACT 57.055 32.000 0.00 0.00 0.00 2.12
738 822 7.989826 ACTTGTTTGGCAGAATATGAATACTC 58.010 34.615 0.00 0.00 0.00 2.59
740 824 5.827797 TGTTTGGCAGAATATGAATACTCCC 59.172 40.000 0.00 0.00 0.00 4.30
741 825 5.912149 TTGGCAGAATATGAATACTCCCT 57.088 39.130 0.00 0.00 0.00 4.20
744 828 4.499183 GCAGAATATGAATACTCCCTCCG 58.501 47.826 0.00 0.00 0.00 4.63
745 829 4.021016 GCAGAATATGAATACTCCCTCCGT 60.021 45.833 0.00 0.00 0.00 4.69
746 830 5.473931 CAGAATATGAATACTCCCTCCGTG 58.526 45.833 0.00 0.00 0.00 4.94
747 831 3.963428 ATATGAATACTCCCTCCGTGC 57.037 47.619 0.00 0.00 0.00 5.34
748 832 0.389391 ATGAATACTCCCTCCGTGCG 59.611 55.000 0.00 0.00 0.00 5.34
749 833 0.681887 TGAATACTCCCTCCGTGCGA 60.682 55.000 0.00 0.00 0.00 5.10
751 835 0.395311 AATACTCCCTCCGTGCGAGA 60.395 55.000 0.00 0.00 41.63 4.04
752 836 0.395311 ATACTCCCTCCGTGCGAGAA 60.395 55.000 0.00 0.00 41.63 2.87
753 837 0.395311 TACTCCCTCCGTGCGAGAAT 60.395 55.000 0.00 0.00 41.63 2.40
756 840 1.136305 CTCCCTCCGTGCGAGAATAAA 59.864 52.381 0.00 0.00 41.63 1.40
759 843 1.468565 CCTCCGTGCGAGAATAAACGA 60.469 52.381 0.00 0.00 41.63 3.85
760 844 1.582502 CTCCGTGCGAGAATAAACGAC 59.417 52.381 0.00 0.00 41.63 4.34
762 846 1.582502 CCGTGCGAGAATAAACGACTC 59.417 52.381 0.00 0.00 38.27 3.36
763 847 2.247637 CGTGCGAGAATAAACGACTCA 58.752 47.619 0.00 0.00 38.27 3.41
764 848 2.659757 CGTGCGAGAATAAACGACTCAA 59.340 45.455 0.00 0.00 38.27 3.02
765 849 3.479866 CGTGCGAGAATAAACGACTCAAC 60.480 47.826 0.00 0.00 38.27 3.18
767 851 4.150098 GTGCGAGAATAAACGACTCAACTT 59.850 41.667 0.00 0.00 0.00 2.66
770 854 6.588756 TGCGAGAATAAACGACTCAACTTTAT 59.411 34.615 0.00 0.00 0.00 1.40
771 855 7.756272 TGCGAGAATAAACGACTCAACTTTATA 59.244 33.333 0.00 0.00 0.00 0.98
772 856 8.753175 GCGAGAATAAACGACTCAACTTTATAT 58.247 33.333 0.00 0.00 0.00 0.86
831 988 3.130340 TGGCTGTTTCTGTCAAAAGTTCC 59.870 43.478 0.00 0.00 0.00 3.62
834 991 5.167845 GCTGTTTCTGTCAAAAGTTCCAAA 58.832 37.500 0.00 0.00 0.00 3.28
861 1018 3.672397 CGCATGATCCTAGAACTGAATCG 59.328 47.826 0.00 0.00 0.00 3.34
867 1024 6.743110 TGATCCTAGAACTGAATCGATCTTG 58.257 40.000 0.00 0.00 0.00 3.02
870 1027 8.642935 ATCCTAGAACTGAATCGATCTTGATA 57.357 34.615 0.00 0.00 0.00 2.15
909 1067 3.858503 GCACCTCCATTTCTGAAAGCAAC 60.859 47.826 8.95 0.00 0.00 4.17
914 1072 2.053627 CATTTCTGAAAGCAACGCACC 58.946 47.619 8.95 0.00 0.00 5.01
919 1077 2.419673 TCTGAAAGCAACGCACCATATG 59.580 45.455 0.00 0.00 0.00 1.78
920 1078 2.158559 TGAAAGCAACGCACCATATGT 58.841 42.857 1.24 0.00 0.00 2.29
921 1079 3.339141 TGAAAGCAACGCACCATATGTA 58.661 40.909 1.24 0.00 0.00 2.29
922 1080 3.944650 TGAAAGCAACGCACCATATGTAT 59.055 39.130 1.24 0.00 0.00 2.29
923 1081 3.969117 AAGCAACGCACCATATGTATG 57.031 42.857 1.24 0.98 0.00 2.39
1013 1173 2.173519 CTTGGAAATGGCCAGTGACAT 58.826 47.619 13.05 0.00 39.52 3.06
1020 1180 1.803334 TGGCCAGTGACATAAACGAC 58.197 50.000 0.00 0.00 0.00 4.34
1029 1189 1.059264 GACATAAACGACGCAGAGCAC 59.941 52.381 0.00 0.00 0.00 4.40
1290 1453 1.156645 GCCGCATGAAGCTCTTCGAT 61.157 55.000 0.00 0.00 42.28 3.59
1362 1525 1.448540 CCTCTTCGCGTCCTGCAAT 60.449 57.895 5.77 0.00 46.97 3.56
1381 1544 1.194121 TGGCCTGCTCTGCTTCTACA 61.194 55.000 3.32 0.00 0.00 2.74
1473 1636 2.031360 GCTCCGCGACCTGTACTAT 58.969 57.895 8.23 0.00 0.00 2.12
1743 1906 0.374758 CGGTCATGGCGTTTGATCTG 59.625 55.000 0.00 0.00 0.00 2.90
1856 2019 0.677731 TACTACGTGACGGAGGTGGG 60.678 60.000 22.53 0.00 42.90 4.61
1864 2027 0.903454 GACGGAGGTGGGGAAGAAGA 60.903 60.000 0.00 0.00 0.00 2.87
2149 2315 0.957888 GGTGAGGCTGCTGAACTTCC 60.958 60.000 0.00 0.00 0.00 3.46
2319 2533 0.391661 CCTTCTGTGGTCATGGTCCG 60.392 60.000 0.00 0.00 0.00 4.79
2369 2583 9.228636 GTATTTTGTACAAACTTTCGAACATGT 57.771 29.630 20.43 3.52 0.00 3.21
2376 2590 7.734538 ACAAACTTTCGAACATGTTTACTTG 57.265 32.000 13.36 11.40 32.29 3.16
2410 2624 6.560253 ATGAATTATGGTGTAATTCTCGGC 57.440 37.500 16.81 0.00 41.81 5.54
2470 2684 3.069586 GCTAATAAGGATTTTGTGCCCCC 59.930 47.826 0.00 0.00 0.00 5.40
2473 2687 4.128388 GGATTTTGTGCCCCCGCG 62.128 66.667 0.00 0.00 38.08 6.46
2501 2715 9.981114 AAAAATAAGTATTTTGTGCAGTAAGCT 57.019 25.926 9.26 0.00 43.06 3.74
2502 2716 9.981114 AAAATAAGTATTTTGTGCAGTAAGCTT 57.019 25.926 3.48 3.48 42.47 3.74
2503 2717 9.981114 AAATAAGTATTTTGTGCAGTAAGCTTT 57.019 25.926 3.20 0.00 37.04 3.51
2504 2718 9.981114 AATAAGTATTTTGTGCAGTAAGCTTTT 57.019 25.926 3.20 0.00 45.94 2.27
2505 2719 7.930513 AAGTATTTTGTGCAGTAAGCTTTTC 57.069 32.000 3.20 0.00 45.94 2.29
2506 2720 7.277174 AGTATTTTGTGCAGTAAGCTTTTCT 57.723 32.000 3.20 0.63 45.94 2.52
2507 2721 7.141363 AGTATTTTGTGCAGTAAGCTTTTCTG 58.859 34.615 20.03 20.03 45.94 3.02
2508 2722 4.981806 TTTGTGCAGTAAGCTTTTCTGT 57.018 36.364 22.94 0.00 45.94 3.41
2509 2723 4.981806 TTGTGCAGTAAGCTTTTCTGTT 57.018 36.364 22.94 0.00 45.94 3.16
2510 2724 4.981806 TGTGCAGTAAGCTTTTCTGTTT 57.018 36.364 22.94 0.00 45.94 2.83
2511 2725 5.323371 TGTGCAGTAAGCTTTTCTGTTTT 57.677 34.783 22.94 0.00 45.94 2.43
2512 2726 5.719173 TGTGCAGTAAGCTTTTCTGTTTTT 58.281 33.333 22.94 0.00 45.94 1.94
2580 3530 6.316140 GCGCAAATTCTACCCATGATATATCA 59.684 38.462 17.56 17.56 41.70 2.15
2581 3531 7.148255 GCGCAAATTCTACCCATGATATATCAA 60.148 37.037 19.03 1.91 40.69 2.57
2650 3600 6.806739 CGAATTTTTAGATCCACCAAAGTTCC 59.193 38.462 0.00 0.00 0.00 3.62
2816 3773 1.160137 CTTGTTCCTCTTGGGCGAAG 58.840 55.000 2.45 2.45 34.39 3.79
2839 3796 4.660938 GAGCCGGCACAAAGGGGT 62.661 66.667 31.54 3.33 0.00 4.95
2840 3797 4.660938 AGCCGGCACAAAGGGGTC 62.661 66.667 31.54 0.00 0.00 4.46
2843 3800 2.281208 CGGCACAAAGGGGTCGAA 60.281 61.111 0.00 0.00 0.00 3.71
2844 3801 2.325082 CGGCACAAAGGGGTCGAAG 61.325 63.158 0.00 0.00 0.00 3.79
2845 3802 1.072505 GGCACAAAGGGGTCGAAGA 59.927 57.895 0.00 0.00 0.00 2.87
2846 3803 0.955919 GGCACAAAGGGGTCGAAGAG 60.956 60.000 0.00 0.00 36.95 2.85
2883 3841 1.298339 GCGGCGGGAAATCATTTCG 60.298 57.895 9.78 0.00 40.57 3.46
2947 3913 3.834726 CGGAGCTCGTCTGATCCT 58.165 61.111 7.83 0.00 40.11 3.24
2971 3937 1.132453 CGTGCTTGTGAGTCCTCGATA 59.868 52.381 0.00 0.00 0.00 2.92
2974 3940 1.751924 GCTTGTGAGTCCTCGATACCT 59.248 52.381 0.00 0.00 0.00 3.08
2975 3941 2.166664 GCTTGTGAGTCCTCGATACCTT 59.833 50.000 0.00 0.00 0.00 3.50
2984 3950 4.020128 AGTCCTCGATACCTTCTTTTGCTT 60.020 41.667 0.00 0.00 0.00 3.91
3152 4118 2.237143 CTGTAGTTGAGGGATTGAGGCA 59.763 50.000 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.312973 CAGCGTTACCGTTATCTCTCTCT 59.687 47.826 0.00 0.00 36.15 3.10
1 2 3.548415 CCAGCGTTACCGTTATCTCTCTC 60.548 52.174 0.00 0.00 36.15 3.20
2 3 2.358267 CCAGCGTTACCGTTATCTCTCT 59.642 50.000 0.00 0.00 36.15 3.10
3 4 2.357009 TCCAGCGTTACCGTTATCTCTC 59.643 50.000 0.00 0.00 36.15 3.20
4 5 2.098770 GTCCAGCGTTACCGTTATCTCT 59.901 50.000 0.00 0.00 36.15 3.10
5 6 2.098770 AGTCCAGCGTTACCGTTATCTC 59.901 50.000 0.00 0.00 36.15 2.75
6 7 2.097825 AGTCCAGCGTTACCGTTATCT 58.902 47.619 0.00 0.00 36.15 1.98
7 8 2.457970 GAGTCCAGCGTTACCGTTATC 58.542 52.381 0.00 0.00 36.15 1.75
8 9 1.135721 GGAGTCCAGCGTTACCGTTAT 59.864 52.381 3.60 0.00 36.15 1.89
9 10 0.527565 GGAGTCCAGCGTTACCGTTA 59.472 55.000 3.60 0.00 36.15 3.18
10 11 1.183676 AGGAGTCCAGCGTTACCGTT 61.184 55.000 12.86 0.00 36.15 4.44
11 12 1.605738 AGGAGTCCAGCGTTACCGT 60.606 57.895 12.86 0.00 36.15 4.83
12 13 1.153823 CAGGAGTCCAGCGTTACCG 60.154 63.158 12.86 0.00 37.07 4.02
13 14 1.218316 CCAGGAGTCCAGCGTTACC 59.782 63.158 12.86 0.00 0.00 2.85
14 15 0.173708 CTCCAGGAGTCCAGCGTTAC 59.826 60.000 12.86 0.00 0.00 2.50
15 16 0.039180 TCTCCAGGAGTCCAGCGTTA 59.961 55.000 16.65 0.00 0.00 3.18
16 17 1.228894 TCTCCAGGAGTCCAGCGTT 60.229 57.895 16.65 0.00 0.00 4.84
17 18 1.979693 GTCTCCAGGAGTCCAGCGT 60.980 63.158 16.65 0.00 0.00 5.07
18 19 1.254284 AAGTCTCCAGGAGTCCAGCG 61.254 60.000 16.65 0.00 0.00 5.18
19 20 0.248843 CAAGTCTCCAGGAGTCCAGC 59.751 60.000 16.65 3.46 0.00 4.85
20 21 0.901124 CCAAGTCTCCAGGAGTCCAG 59.099 60.000 16.65 2.60 0.00 3.86
21 22 0.191064 ACCAAGTCTCCAGGAGTCCA 59.809 55.000 16.65 0.00 0.00 4.02
22 23 0.610687 CACCAAGTCTCCAGGAGTCC 59.389 60.000 16.65 0.00 0.00 3.85
23 24 0.610687 CCACCAAGTCTCCAGGAGTC 59.389 60.000 16.65 11.04 0.00 3.36
24 25 0.191064 TCCACCAAGTCTCCAGGAGT 59.809 55.000 16.65 0.00 0.00 3.85
25 26 0.901124 CTCCACCAAGTCTCCAGGAG 59.099 60.000 10.70 10.70 36.98 3.69
26 27 0.191064 ACTCCACCAAGTCTCCAGGA 59.809 55.000 0.00 0.00 0.00 3.86
27 28 0.322975 CACTCCACCAAGTCTCCAGG 59.677 60.000 0.00 0.00 0.00 4.45
28 29 0.321122 GCACTCCACCAAGTCTCCAG 60.321 60.000 0.00 0.00 0.00 3.86
29 30 1.754745 GCACTCCACCAAGTCTCCA 59.245 57.895 0.00 0.00 0.00 3.86
30 31 1.374758 CGCACTCCACCAAGTCTCC 60.375 63.158 0.00 0.00 0.00 3.71
31 32 0.247736 ATCGCACTCCACCAAGTCTC 59.752 55.000 0.00 0.00 0.00 3.36
32 33 0.036952 CATCGCACTCCACCAAGTCT 60.037 55.000 0.00 0.00 0.00 3.24
33 34 1.639298 GCATCGCACTCCACCAAGTC 61.639 60.000 0.00 0.00 0.00 3.01
34 35 1.672356 GCATCGCACTCCACCAAGT 60.672 57.895 0.00 0.00 0.00 3.16
35 36 0.957395 AAGCATCGCACTCCACCAAG 60.957 55.000 0.00 0.00 0.00 3.61
36 37 1.073025 AAGCATCGCACTCCACCAA 59.927 52.632 0.00 0.00 0.00 3.67
37 38 1.672030 CAAGCATCGCACTCCACCA 60.672 57.895 0.00 0.00 0.00 4.17
38 39 2.401766 CCAAGCATCGCACTCCACC 61.402 63.158 0.00 0.00 0.00 4.61
39 40 2.401766 CCCAAGCATCGCACTCCAC 61.402 63.158 0.00 0.00 0.00 4.02
56 57 1.823610 AGTAACTAGCCTTCGTGGACC 59.176 52.381 0.00 0.00 38.35 4.46
90 94 3.186817 CGGAGAGTGCTACTACTTATCGG 59.813 52.174 0.00 0.00 0.00 4.18
111 115 0.748450 TAAGCCCACCGTTATCCTCG 59.252 55.000 0.00 0.00 0.00 4.63
149 153 2.091432 GCGAAGAAGACGAAGAAGAAGC 59.909 50.000 0.00 0.00 0.00 3.86
160 170 0.391793 CTTCCCCAGGCGAAGAAGAC 60.392 60.000 8.04 0.00 39.29 3.01
188 198 2.564553 CTTCTCTCCAACTCCCGGCG 62.565 65.000 0.00 0.00 0.00 6.46
190 200 1.490574 ATCTTCTCTCCAACTCCCGG 58.509 55.000 0.00 0.00 0.00 5.73
191 201 2.159028 GGAATCTTCTCTCCAACTCCCG 60.159 54.545 0.00 0.00 0.00 5.14
193 203 2.740256 GCGGAATCTTCTCTCCAACTCC 60.740 54.545 0.00 0.00 0.00 3.85
194 204 2.167487 AGCGGAATCTTCTCTCCAACTC 59.833 50.000 0.00 0.00 0.00 3.01
199 209 3.131400 ACTTACAGCGGAATCTTCTCTCC 59.869 47.826 0.00 0.00 0.00 3.71
206 216 5.305585 TGAAGAAAACTTACAGCGGAATCT 58.694 37.500 0.00 0.00 0.00 2.40
283 310 3.936372 TCGATCCTCGACTTGAAAACT 57.064 42.857 0.00 0.00 44.82 2.66
294 321 2.871182 TTCCAGTTCATCGATCCTCG 57.129 50.000 0.00 0.00 42.10 4.63
298 325 4.327982 TCCAGATTCCAGTTCATCGATC 57.672 45.455 0.00 0.00 0.00 3.69
299 326 4.760530 TTCCAGATTCCAGTTCATCGAT 57.239 40.909 0.00 0.00 0.00 3.59
300 327 4.162131 TCATTCCAGATTCCAGTTCATCGA 59.838 41.667 0.00 0.00 0.00 3.59
301 328 4.445453 TCATTCCAGATTCCAGTTCATCG 58.555 43.478 0.00 0.00 0.00 3.84
330 363 4.823442 TCACACGTTCTACAAGGTTCTAGA 59.177 41.667 0.00 0.00 0.00 2.43
347 380 0.319555 ACGAACCCATCACTCACACG 60.320 55.000 0.00 0.00 0.00 4.49
374 407 4.424430 GCCACTAACACGCGTGCG 62.424 66.667 37.35 26.79 46.03 5.34
375 408 2.113131 AAAGCCACTAACACGCGTGC 62.113 55.000 37.35 22.32 0.00 5.34
376 409 0.384230 CAAAGCCACTAACACGCGTG 60.384 55.000 35.99 35.99 0.00 5.34
377 410 0.812412 ACAAAGCCACTAACACGCGT 60.812 50.000 5.58 5.58 0.00 6.01
378 411 0.306533 AACAAAGCCACTAACACGCG 59.693 50.000 3.53 3.53 0.00 6.01
455 496 5.354234 TGCATGGCTAACTTTTTCTAGTAGC 59.646 40.000 0.00 0.00 0.00 3.58
499 577 0.393402 CAGAATAGCCCTGCACTGCA 60.393 55.000 3.11 3.11 36.92 4.41
500 578 0.107508 TCAGAATAGCCCTGCACTGC 60.108 55.000 0.00 0.00 0.00 4.40
501 579 1.661341 GTCAGAATAGCCCTGCACTG 58.339 55.000 0.00 0.00 0.00 3.66
502 580 0.543749 GGTCAGAATAGCCCTGCACT 59.456 55.000 0.00 0.00 0.00 4.40
503 581 0.253044 TGGTCAGAATAGCCCTGCAC 59.747 55.000 0.00 0.00 0.00 4.57
518 596 6.364435 GCTCTGATTTTCAACTTGAATTGGTC 59.636 38.462 5.03 3.05 36.11 4.02
549 630 8.181573 GCTATTATCAGTCACTAGTCTAGCATC 58.818 40.741 6.81 0.00 0.00 3.91
559 640 5.010112 GGCACTCTGCTATTATCAGTCACTA 59.990 44.000 0.00 0.00 44.28 2.74
569 650 5.186198 GGAAAAGAAGGCACTCTGCTATTA 58.814 41.667 0.00 0.00 44.28 0.98
575 656 2.072298 CTCGGAAAAGAAGGCACTCTG 58.928 52.381 0.00 0.00 38.49 3.35
635 718 9.665719 TCAACATAATATGTGCTTCTAGAACAA 57.334 29.630 6.67 0.00 44.07 2.83
642 725 7.686438 TGTGTTCAACATAATATGTGCTTCT 57.314 32.000 6.67 0.00 44.07 2.85
708 791 8.492673 TTCATATTCTGCCAAACAAGTAGTAG 57.507 34.615 0.00 0.00 0.00 2.57
729 813 0.389391 CGCACGGAGGGAGTATTCAT 59.611 55.000 0.00 0.00 0.00 2.57
730 814 0.681887 TCGCACGGAGGGAGTATTCA 60.682 55.000 0.00 0.00 34.74 2.57
731 815 2.112898 TCGCACGGAGGGAGTATTC 58.887 57.895 0.00 0.00 34.74 1.75
737 821 1.134907 GTTTATTCTCGCACGGAGGGA 60.135 52.381 0.00 0.00 43.34 4.20
738 822 1.287425 GTTTATTCTCGCACGGAGGG 58.713 55.000 0.00 0.00 43.34 4.30
740 824 1.582502 GTCGTTTATTCTCGCACGGAG 59.417 52.381 0.00 0.00 44.58 4.63
741 825 1.200716 AGTCGTTTATTCTCGCACGGA 59.799 47.619 0.00 0.00 33.39 4.69
744 828 3.673809 AGTTGAGTCGTTTATTCTCGCAC 59.326 43.478 0.00 0.00 0.00 5.34
745 829 3.909430 AGTTGAGTCGTTTATTCTCGCA 58.091 40.909 0.00 0.00 0.00 5.10
746 830 4.905412 AAGTTGAGTCGTTTATTCTCGC 57.095 40.909 0.00 0.00 0.00 5.03
756 840 8.943002 CCCAAAGTTAATATAAAGTTGAGTCGT 58.057 33.333 0.00 0.00 0.00 4.34
759 843 9.802039 TGACCCAAAGTTAATATAAAGTTGAGT 57.198 29.630 0.00 0.00 0.00 3.41
767 851 9.569122 GGCTTATCTGACCCAAAGTTAATATAA 57.431 33.333 0.00 0.00 0.00 0.98
770 854 6.053005 CGGCTTATCTGACCCAAAGTTAATA 58.947 40.000 0.00 0.00 0.00 0.98
771 855 4.881850 CGGCTTATCTGACCCAAAGTTAAT 59.118 41.667 0.00 0.00 0.00 1.40
772 856 4.258543 CGGCTTATCTGACCCAAAGTTAA 58.741 43.478 0.00 0.00 0.00 2.01
773 857 3.262405 ACGGCTTATCTGACCCAAAGTTA 59.738 43.478 0.00 0.00 0.00 2.24
774 858 2.039879 ACGGCTTATCTGACCCAAAGTT 59.960 45.455 0.00 0.00 0.00 2.66
775 859 1.628846 ACGGCTTATCTGACCCAAAGT 59.371 47.619 0.00 0.00 0.00 2.66
776 860 2.403252 ACGGCTTATCTGACCCAAAG 57.597 50.000 0.00 0.00 0.00 2.77
777 861 2.617021 GGAACGGCTTATCTGACCCAAA 60.617 50.000 0.00 0.00 0.00 3.28
895 1053 1.680735 TGGTGCGTTGCTTTCAGAAAT 59.319 42.857 0.00 0.00 0.00 2.17
909 1067 4.152402 GCTTAGGAACATACATATGGTGCG 59.848 45.833 7.80 0.00 45.08 5.34
914 1072 8.627208 ATTGGAAGCTTAGGAACATACATATG 57.373 34.615 0.00 0.00 39.55 1.78
919 1077 9.736023 CATAAAATTGGAAGCTTAGGAACATAC 57.264 33.333 0.00 0.00 0.00 2.39
920 1078 8.912988 CCATAAAATTGGAAGCTTAGGAACATA 58.087 33.333 0.00 0.00 39.25 2.29
921 1079 7.633553 GCCATAAAATTGGAAGCTTAGGAACAT 60.634 37.037 0.00 0.00 39.25 2.71
922 1080 6.350949 GCCATAAAATTGGAAGCTTAGGAACA 60.351 38.462 0.00 0.00 39.25 3.18
923 1081 6.042777 GCCATAAAATTGGAAGCTTAGGAAC 58.957 40.000 0.00 0.00 39.25 3.62
1013 1173 0.728129 CTCGTGCTCTGCGTCGTTTA 60.728 55.000 0.00 0.00 32.60 2.01
1029 1189 0.179189 GATTTTCGGTTGCCTGCTCG 60.179 55.000 0.00 0.00 0.00 5.03
1275 1435 5.277393 CCATTTCTCATCGAAGAGCTTCATG 60.277 44.000 12.74 10.68 43.63 3.07
1290 1453 2.489971 GTTGACACGGACCATTTCTCA 58.510 47.619 0.00 0.00 0.00 3.27
1362 1525 1.194121 TGTAGAAGCAGAGCAGGCCA 61.194 55.000 5.01 0.00 0.00 5.36
1381 1544 2.159366 CGATCTTCAGCGTGTACTTCCT 60.159 50.000 0.00 0.00 0.00 3.36
1425 1588 2.817396 GGCTTCGAGAGGTGCAGC 60.817 66.667 8.11 8.11 0.00 5.25
1461 1624 4.735662 GCTGTAGAGATAGTACAGGTCG 57.264 50.000 11.24 0.00 45.14 4.79
1473 1636 1.183549 GGAACCCGAAGCTGTAGAGA 58.816 55.000 0.00 0.00 0.00 3.10
1743 1906 3.060602 CGTCACAAAGGTCTCTTCCTTC 58.939 50.000 0.00 0.00 45.79 3.46
1856 2019 0.951040 CACCAGGCACGTCTTCTTCC 60.951 60.000 0.00 0.00 0.00 3.46
2259 2425 2.893489 AGAAATTCAGGAACCTGGTTGC 59.107 45.455 21.88 21.88 43.75 4.17
2261 2427 4.453480 TCAGAAATTCAGGAACCTGGTT 57.547 40.909 12.82 12.82 43.75 3.67
2319 2533 6.776603 ACATCTCTGTTACCTACACCTATACC 59.223 42.308 0.00 0.00 32.10 2.73
2376 2590 9.853555 TTACACCATAATTCATTCATGTTTCAC 57.146 29.630 0.00 0.00 0.00 3.18
2410 2624 6.761714 ACAATAACCAGTAGCTTAAATCTCCG 59.238 38.462 0.00 0.00 0.00 4.63
2447 2661 3.704061 GGGGCACAAAATCCTTATTAGCA 59.296 43.478 0.00 0.00 0.00 3.49
2448 2662 3.069586 GGGGGCACAAAATCCTTATTAGC 59.930 47.826 0.00 0.00 0.00 3.09
2514 2728 5.838521 ACAGAAAAGCTTATCCCCTCAAAAA 59.161 36.000 0.00 0.00 0.00 1.94
2515 2729 5.393866 ACAGAAAAGCTTATCCCCTCAAAA 58.606 37.500 0.00 0.00 0.00 2.44
2516 2730 4.998051 ACAGAAAAGCTTATCCCCTCAAA 58.002 39.130 0.00 0.00 0.00 2.69
2517 2731 4.657814 ACAGAAAAGCTTATCCCCTCAA 57.342 40.909 0.00 0.00 0.00 3.02
2518 2732 4.042809 TGAACAGAAAAGCTTATCCCCTCA 59.957 41.667 0.00 0.00 0.00 3.86
2519 2733 4.396478 GTGAACAGAAAAGCTTATCCCCTC 59.604 45.833 0.00 0.00 0.00 4.30
2520 2734 4.043435 AGTGAACAGAAAAGCTTATCCCCT 59.957 41.667 0.00 0.00 0.00 4.79
2521 2735 4.336280 AGTGAACAGAAAAGCTTATCCCC 58.664 43.478 0.00 0.00 0.00 4.81
2522 2736 4.093556 CGAGTGAACAGAAAAGCTTATCCC 59.906 45.833 0.00 0.00 0.00 3.85
2523 2737 4.691216 ACGAGTGAACAGAAAAGCTTATCC 59.309 41.667 0.00 0.00 0.00 2.59
2524 2738 5.177696 ACACGAGTGAACAGAAAAGCTTATC 59.822 40.000 10.50 0.00 0.00 1.75
2580 3530 3.192541 AGCTTTGCCGTTTTCCATTTT 57.807 38.095 0.00 0.00 0.00 1.82
2581 3531 2.908688 AGCTTTGCCGTTTTCCATTT 57.091 40.000 0.00 0.00 0.00 2.32
2591 3541 1.207593 CTGGACGAAAGCTTTGCCG 59.792 57.895 18.30 17.05 0.00 5.69
2834 3791 3.394836 GCTGGCTCTTCGACCCCT 61.395 66.667 0.00 0.00 0.00 4.79
2838 3795 2.507324 GTCGGCTGGCTCTTCGAC 60.507 66.667 0.00 0.00 43.62 4.20
2839 3796 4.116328 CGTCGGCTGGCTCTTCGA 62.116 66.667 0.00 0.00 0.00 3.71
2840 3797 4.116328 TCGTCGGCTGGCTCTTCG 62.116 66.667 0.00 0.00 0.00 3.79
2841 3798 2.202676 CTCGTCGGCTGGCTCTTC 60.203 66.667 0.00 0.00 0.00 2.87
2900 3858 1.151760 CATGGGATTGGGATGGGAGA 58.848 55.000 0.00 0.00 0.00 3.71
2947 3913 2.415491 CGAGGACTCACAAGCACGATTA 60.415 50.000 0.00 0.00 0.00 1.75
2971 3937 1.398692 TTCCGCAAGCAAAAGAAGGT 58.601 45.000 0.00 0.00 0.00 3.50
2974 3940 1.782044 GCATTCCGCAAGCAAAAGAA 58.218 45.000 0.00 0.00 41.79 2.52
2975 3941 3.495124 GCATTCCGCAAGCAAAAGA 57.505 47.368 0.00 0.00 41.79 2.52
3180 4147 4.940046 AGTGCAGATTACTGTCAAATCCAG 59.060 41.667 0.00 0.00 45.04 3.86


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

AutoCloner maintained by Alex Coulton.