Multiple sequence alignment - TraesCS5B01G139800

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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 TraesCS5B01G139800 chr5B 100.000 3975 0 0 1 3975 263547840 263543866 0.000000e+00 7341
1 TraesCS5B01G139800 chr5A 95.721 2664 76 13 1 2654 313907630 313904995 0.000000e+00 4253
2 TraesCS5B01G139800 chr5A 90.789 684 41 11 2652 3315 313904942 313904261 0.000000e+00 894
3 TraesCS5B01G139800 chr5A 90.274 329 24 6 3334 3656 313904273 313903947 1.320000e-114 424
4 TraesCS5B01G139800 chr5A 91.176 238 20 1 3736 3972 313903952 313903715 4.960000e-84 322
5 TraesCS5B01G139800 chr5A 93.333 90 5 1 3653 3742 678232159 678232071 8.960000e-27 132
6 TraesCS5B01G139800 chr5D 97.560 1844 44 1 53 1895 239939269 239941112 0.000000e+00 3155
7 TraesCS5B01G139800 chr5D 96.392 776 18 8 1880 2654 239941130 239941896 0.000000e+00 1269
8 TraesCS5B01G139800 chr5D 91.558 616 36 6 2649 3249 239941944 239942558 0.000000e+00 835
9 TraesCS5B01G139800 chr5D 88.030 401 24 11 3273 3656 239942628 239943021 1.680000e-123 453
10 TraesCS5B01G139800 chr5D 89.837 246 20 4 3733 3974 239943013 239943257 1.070000e-80 311
11 TraesCS5B01G139800 chr1D 97.436 78 1 1 3654 3731 112352031 112352107 8.960000e-27 132
12 TraesCS5B01G139800 chr3B 96.154 78 2 1 3654 3731 823446185 823446109 4.170000e-25 126
13 TraesCS5B01G139800 chr3B 96.104 77 2 1 3655 3731 335839131 335839206 1.500000e-24 124
14 TraesCS5B01G139800 chr2B 96.154 78 2 1 3654 3731 771215134 771215210 4.170000e-25 126
15 TraesCS5B01G139800 chr2A 92.222 90 6 1 3653 3742 678370615 678370527 4.170000e-25 126
16 TraesCS5B01G139800 chr2A 97.297 74 1 1 3653 3726 24217243 24217315 1.500000e-24 124
17 TraesCS5B01G139800 chr6D 96.104 77 2 1 3655 3731 35636477 35636552 1.500000e-24 124
18 TraesCS5B01G139800 chr1B 95.000 80 2 2 3652 3731 40193228 40193305 1.500000e-24 124


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 TraesCS5B01G139800 chr5B 263543866 263547840 3974 True 7341.00 7341 100.0000 1 3975 1 chr5B.!!$R1 3974
1 TraesCS5B01G139800 chr5A 313903715 313907630 3915 True 1473.25 4253 91.9900 1 3972 4 chr5A.!!$R2 3971
2 TraesCS5B01G139800 chr5D 239939269 239943257 3988 False 1204.60 3155 92.6754 53 3974 5 chr5D.!!$F1 3921

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
648 659 1.071299 CCTGCCTTTTGGGTTTGGC 59.929 57.895 0.0 0.0 45.10 4.52 F
1501 1512 3.840666 AGGAACTGGAGAAAGTGCTCATA 59.159 43.478 0.0 0.0 37.18 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 1960 1.198713 ACTGGACCATGCTCCTACAG 58.801 55.0 8.53 0.59 0.0 2.74 R
3084 3202 0.036306 ACAAGATTGTCGGGTGTCCC 59.964 55.0 0.00 0.00 36.5 4.46 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
160 171 5.123027 GCAGAGGTTTTTGTCTCCAATCTAG 59.877 44.000 0.00 0.00 0.00 2.43
259 270 5.124457 ACATTCCATGAAGTATGAGCAACAC 59.876 40.000 0.00 0.00 39.21 3.32
390 401 7.850193 ACCATTTGCATGTCCATACTTTAATT 58.150 30.769 0.00 0.00 0.00 1.40
398 409 7.811236 GCATGTCCATACTTTAATTCCATGATG 59.189 37.037 0.00 0.00 31.21 3.07
444 455 5.367937 AGCACAGTATATGAAGAATGGTCCT 59.632 40.000 0.00 0.00 0.00 3.85
492 503 4.160065 CACTGGTGCCATATGAATTTTCCA 59.840 41.667 3.65 3.55 0.00 3.53
648 659 1.071299 CCTGCCTTTTGGGTTTGGC 59.929 57.895 0.00 0.00 45.10 4.52
1170 1181 4.422073 TGATGACTTTGTGAGGAGTGTT 57.578 40.909 0.00 0.00 0.00 3.32
1501 1512 3.840666 AGGAACTGGAGAAAGTGCTCATA 59.159 43.478 0.00 0.00 37.18 2.15
1915 1960 4.849518 AGGAAAAGGTGAATTAGCTCTCC 58.150 43.478 0.00 0.00 38.31 3.71
2134 2180 9.751542 CCTATTTTACTCATTGTAGGACTACTG 57.248 37.037 10.51 2.43 37.00 2.74
2234 2280 8.134202 TCATTGTAGGATTACTTCTGTTCTGA 57.866 34.615 0.00 0.00 0.00 3.27
2471 2517 5.074584 TGTTTGGTGGAGGTTTGTTTAAC 57.925 39.130 0.00 0.00 35.94 2.01
2474 2520 4.993029 TGGTGGAGGTTTGTTTAACTTG 57.007 40.909 0.00 0.00 36.93 3.16
2660 2761 6.748333 TCTCAAATACTTGATGCTGAAAGG 57.252 37.500 0.00 0.00 40.78 3.11
2809 2912 4.898861 AGTTTTCCCAAGAACCAGCAATTA 59.101 37.500 0.00 0.00 0.00 1.40
2810 2913 5.543790 AGTTTTCCCAAGAACCAGCAATTAT 59.456 36.000 0.00 0.00 0.00 1.28
2833 2936 5.801350 TGCTATGTGCTATTGAAAGTGTC 57.199 39.130 0.00 0.00 43.37 3.67
2834 2937 5.491070 TGCTATGTGCTATTGAAAGTGTCT 58.509 37.500 0.00 0.00 43.37 3.41
2836 2939 5.352569 GCTATGTGCTATTGAAAGTGTCTGT 59.647 40.000 0.00 0.00 38.95 3.41
2837 2940 6.535150 GCTATGTGCTATTGAAAGTGTCTGTA 59.465 38.462 0.00 0.00 38.95 2.74
2838 2941 6.974932 ATGTGCTATTGAAAGTGTCTGTAG 57.025 37.500 0.00 0.00 0.00 2.74
2839 2942 5.853936 TGTGCTATTGAAAGTGTCTGTAGT 58.146 37.500 0.00 0.00 0.00 2.73
2858 2975 8.910944 TCTGTAGTATTACCATTCACCTCTTAC 58.089 37.037 0.00 0.00 0.00 2.34
2868 2985 3.917329 TCACCTCTTACTGACGACAAG 57.083 47.619 0.00 0.00 0.00 3.16
2882 2999 1.194547 CGACAAGGATGTTTCACCACG 59.805 52.381 0.00 0.00 40.74 4.94
2917 3034 5.163854 GGAGTTGGACATGTTATTGAAGTCG 60.164 44.000 0.00 0.00 0.00 4.18
2957 3074 1.079503 AAAGCATCTTCGGAGAACGC 58.920 50.000 9.89 9.89 45.90 4.84
3055 3173 1.813513 AACTATGGAGTGTGTGCAGC 58.186 50.000 0.00 0.00 35.52 5.25
3084 3202 5.132897 TGCTTGTAATTTGTAAAGGCCTG 57.867 39.130 5.69 0.00 0.00 4.85
3217 3336 6.204882 ACTGCGAAGTTTCTTGCTAATACTTT 59.795 34.615 0.00 0.00 0.00 2.66
3259 3380 1.014352 CCTGTAGCCGCATGGTAAAC 58.986 55.000 0.00 0.00 37.67 2.01
3312 3480 1.825474 TCCGTGGGAAGAGAATGTCTC 59.175 52.381 0.00 0.00 43.70 3.36
3313 3481 1.550524 CCGTGGGAAGAGAATGTCTCA 59.449 52.381 7.94 0.00 45.73 3.27
3315 3483 2.611518 GTGGGAAGAGAATGTCTCACG 58.388 52.381 7.94 0.00 45.73 4.35
3343 3511 8.462811 CAGTCTAAGCTGAACTAGAGAATGTTA 58.537 37.037 0.00 0.00 38.70 2.41
3347 3515 5.735766 AGCTGAACTAGAGAATGTTAACCC 58.264 41.667 2.48 0.00 0.00 4.11
3364 3532 3.903530 ACCCAAGAAAATCCCTCTTGT 57.096 42.857 10.70 0.00 45.53 3.16
3367 3535 3.500343 CCAAGAAAATCCCTCTTGTGGT 58.500 45.455 10.70 0.00 45.53 4.16
3368 3536 3.507622 CCAAGAAAATCCCTCTTGTGGTC 59.492 47.826 10.70 0.00 45.53 4.02
3369 3537 4.144297 CAAGAAAATCCCTCTTGTGGTCA 58.856 43.478 4.73 0.00 43.15 4.02
3370 3538 4.664688 AGAAAATCCCTCTTGTGGTCAT 57.335 40.909 0.00 0.00 0.00 3.06
3371 3539 4.593956 AGAAAATCCCTCTTGTGGTCATC 58.406 43.478 0.00 0.00 0.00 2.92
3389 3557 5.456619 GGTCATCTCATTCCCATGTTCCATA 60.457 44.000 0.00 0.00 0.00 2.74
3402 3576 4.356405 TGTTCCATATGCCATCTACCAG 57.644 45.455 0.00 0.00 0.00 4.00
3451 3625 3.426695 CCCAAGAACGTCTCAATGATTGC 60.427 47.826 0.00 0.00 0.00 3.56
3458 3632 3.264947 CGTCTCAATGATTGCAGAGGAA 58.735 45.455 15.63 0.00 31.00 3.36
3460 3634 4.511527 GTCTCAATGATTGCAGAGGAAGA 58.488 43.478 0.00 0.00 0.00 2.87
3461 3635 4.940046 GTCTCAATGATTGCAGAGGAAGAA 59.060 41.667 0.00 0.00 0.00 2.52
3474 3654 3.055891 AGAGGAAGAAGAAGAAGCAGCTC 60.056 47.826 0.00 0.00 0.00 4.09
3502 3682 7.196331 CAGTTAACTTGGCCAATTATTAGCTC 58.804 38.462 20.85 11.54 0.00 4.09
3561 3741 2.191641 GTCCATGGCCAGCCTCTC 59.808 66.667 13.05 0.00 36.94 3.20
3635 3826 6.168389 TCTCTATAGCACGTATCGGAATGTA 58.832 40.000 0.00 0.00 0.00 2.29
3643 3834 5.006358 GCACGTATCGGAATGTACATCTTTT 59.994 40.000 9.23 0.00 0.00 2.27
3649 3840 9.864034 GTATCGGAATGTACATCTTTTGTATTG 57.136 33.333 9.23 0.00 42.63 1.90
3650 3841 7.315247 TCGGAATGTACATCTTTTGTATTGG 57.685 36.000 9.23 0.00 42.63 3.16
3651 3842 7.106890 TCGGAATGTACATCTTTTGTATTGGA 58.893 34.615 9.23 0.00 42.63 3.53
3652 3843 7.608376 TCGGAATGTACATCTTTTGTATTGGAA 59.392 33.333 9.23 0.00 42.63 3.53
3653 3844 8.240682 CGGAATGTACATCTTTTGTATTGGAAA 58.759 33.333 9.23 0.00 42.63 3.13
3664 3855 9.959749 TCTTTTGTATTGGAAATACAGTTTGTC 57.040 29.630 11.48 0.00 36.09 3.18
3665 3856 9.965824 CTTTTGTATTGGAAATACAGTTTGTCT 57.034 29.630 11.48 0.00 36.09 3.41
3673 3864 8.684386 TGGAAATACAGTTTGTCTAATTCACA 57.316 30.769 0.00 0.00 0.00 3.58
3674 3865 9.295825 TGGAAATACAGTTTGTCTAATTCACAT 57.704 29.630 0.00 0.00 0.00 3.21
3675 3866 9.774742 GGAAATACAGTTTGTCTAATTCACATC 57.225 33.333 0.00 0.00 0.00 3.06
3681 3872 9.376075 ACAGTTTGTCTAATTCACATCTAGATG 57.624 33.333 27.63 27.63 44.15 2.90
3710 3901 8.964476 TTTTAAGGATGTCACATCTAATCTCC 57.036 34.615 17.46 0.18 0.00 3.71
3711 3902 5.559148 AAGGATGTCACATCTAATCTCCC 57.441 43.478 17.46 0.00 0.00 4.30
3712 3903 4.560739 AGGATGTCACATCTAATCTCCCA 58.439 43.478 17.46 0.00 0.00 4.37
3713 3904 4.346418 AGGATGTCACATCTAATCTCCCAC 59.654 45.833 17.46 0.00 0.00 4.61
3714 3905 4.101585 GGATGTCACATCTAATCTCCCACA 59.898 45.833 17.46 0.00 0.00 4.17
3715 3906 5.396772 GGATGTCACATCTAATCTCCCACAA 60.397 44.000 17.46 0.00 0.00 3.33
3716 3907 5.497464 TGTCACATCTAATCTCCCACAAA 57.503 39.130 0.00 0.00 0.00 2.83
3717 3908 6.065976 TGTCACATCTAATCTCCCACAAAT 57.934 37.500 0.00 0.00 0.00 2.32
3718 3909 7.194112 TGTCACATCTAATCTCCCACAAATA 57.806 36.000 0.00 0.00 0.00 1.40
3719 3910 7.805163 TGTCACATCTAATCTCCCACAAATAT 58.195 34.615 0.00 0.00 0.00 1.28
3720 3911 8.933653 TGTCACATCTAATCTCCCACAAATATA 58.066 33.333 0.00 0.00 0.00 0.86
3721 3912 9.950496 GTCACATCTAATCTCCCACAAATATAT 57.050 33.333 0.00 0.00 0.00 0.86
3731 3922 9.672673 ATCTCCCACAAATATATAATGTAGCAC 57.327 33.333 4.31 0.00 0.00 4.40
3732 3923 8.880244 TCTCCCACAAATATATAATGTAGCACT 58.120 33.333 4.31 0.00 0.00 4.40
3733 3924 9.507329 CTCCCACAAATATATAATGTAGCACTT 57.493 33.333 4.31 0.00 0.00 3.16
3734 3925 9.283768 TCCCACAAATATATAATGTAGCACTTG 57.716 33.333 4.31 0.00 0.00 3.16
3745 3936 5.545658 ATGTAGCACTTGGAAATAACACG 57.454 39.130 0.00 0.00 0.00 4.49
3748 3939 1.268352 GCACTTGGAAATAACACGCCA 59.732 47.619 0.00 0.00 0.00 5.69
3812 4007 8.522830 ACTATTGTTCGGATCATGTCAATTTTT 58.477 29.630 0.00 0.00 0.00 1.94
3817 4012 5.252547 TCGGATCATGTCAATTTTTCCTCA 58.747 37.500 0.00 0.00 0.00 3.86
3853 4048 3.726557 TGCCATGGGAATATGAGATCC 57.273 47.619 15.13 0.00 34.85 3.36
3860 4055 7.052873 CCATGGGAATATGAGATCCATCTAAC 58.947 42.308 2.85 0.00 37.25 2.34
3864 4059 4.744795 ATATGAGATCCATCTAACCGGC 57.255 45.455 0.00 0.00 37.25 6.13
3866 4061 0.038159 GAGATCCATCTAACCGGCCG 60.038 60.000 21.04 21.04 37.25 6.13
3928 4123 6.324819 CGGAAATTGAGCTGTTTATGTGAAT 58.675 36.000 0.00 0.00 0.00 2.57
3947 4142 7.174413 TGTGAATTTCATATGGAGTTTCCTGA 58.826 34.615 2.13 0.00 37.46 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 9.460019 AAAGAAAATGAAAGACCCATTTGAAAA 57.540 25.926 0.00 0.00 41.71 2.29
50 51 9.546428 AGTTAAAGAAAATGAAAGACCCATTTG 57.454 29.630 0.00 0.00 41.71 2.32
160 171 4.702131 ACAGCATCAATGAAACTACTTCCC 59.298 41.667 0.00 0.00 32.53 3.97
259 270 5.669477 TGGACATGTTTTTCTCCCAAAAAG 58.331 37.500 0.00 0.00 30.69 2.27
344 355 0.464870 AGCAAGCCAATTTGTGTGCA 59.535 45.000 14.71 0.00 34.44 4.57
390 401 9.040939 CGAATAACTTTGTACATACATCATGGA 57.959 33.333 0.00 0.00 39.13 3.41
398 409 5.957796 GCTGCACGAATAACTTTGTACATAC 59.042 40.000 0.00 0.00 0.00 2.39
444 455 3.411446 CAGTGCCACAAAATCTCAGGTA 58.589 45.455 0.00 0.00 0.00 3.08
492 503 9.632638 ATGAAATACTGCAAATACACTTCCTAT 57.367 29.630 0.00 0.00 0.00 2.57
558 569 9.554395 CCAAACAACAGGAAAGGTAATAAAAAT 57.446 29.630 0.00 0.00 0.00 1.82
561 572 7.663043 ACCAAACAACAGGAAAGGTAATAAA 57.337 32.000 0.00 0.00 0.00 1.40
564 575 5.659079 TGAACCAAACAACAGGAAAGGTAAT 59.341 36.000 0.00 0.00 0.00 1.89
565 576 5.017490 TGAACCAAACAACAGGAAAGGTAA 58.983 37.500 0.00 0.00 0.00 2.85
606 617 1.584724 ACCTTATCCTGACCCACTGG 58.415 55.000 0.00 0.00 38.68 4.00
648 659 8.649973 ACTAGACACTAAACTCAAAACTGAAG 57.350 34.615 0.00 0.00 0.00 3.02
1275 1286 1.304713 CTTGCTCAATGGCAGGGGT 60.305 57.895 0.00 0.00 43.39 4.95
1501 1512 1.576577 TCCTGCACTCTGGTCATCAT 58.423 50.000 0.00 0.00 33.50 2.45
1915 1960 1.198713 ACTGGACCATGCTCCTACAG 58.801 55.000 8.53 0.59 0.00 2.74
2134 2180 7.224949 GGTGTAGTAAGATAAATCCAGAACAGC 59.775 40.741 0.00 0.00 0.00 4.40
2234 2280 6.874134 AGTGCTGTCGTGAATTAAGATAAACT 59.126 34.615 0.00 0.00 0.00 2.66
2332 2378 2.073117 TGCATTCGAGCTCGTTTGTA 57.927 45.000 33.33 26.05 40.80 2.41
2380 2426 2.901291 ACCTTCTCTCTCTTCAGCCTT 58.099 47.619 0.00 0.00 0.00 4.35
2501 2547 6.118170 AGTGCAAACTATACAGATGAAGCAT 58.882 36.000 0.00 0.00 0.00 3.79
2548 2594 5.760484 AATTATTTGGTGAAACAGGGCAT 57.240 34.783 0.00 0.00 39.98 4.40
2660 2761 9.382244 GCCAATTTATGTACTCAACGAATATTC 57.618 33.333 5.30 5.30 0.00 1.75
2833 2936 8.915036 AGTAAGAGGTGAATGGTAATACTACAG 58.085 37.037 0.00 0.00 0.00 2.74
2834 2937 8.692710 CAGTAAGAGGTGAATGGTAATACTACA 58.307 37.037 0.00 0.00 0.00 2.74
2836 2939 8.910944 GTCAGTAAGAGGTGAATGGTAATACTA 58.089 37.037 0.00 0.00 0.00 1.82
2837 2940 7.416438 CGTCAGTAAGAGGTGAATGGTAATACT 60.416 40.741 0.00 0.00 0.00 2.12
2838 2941 6.696148 CGTCAGTAAGAGGTGAATGGTAATAC 59.304 42.308 0.00 0.00 0.00 1.89
2839 2942 6.604396 TCGTCAGTAAGAGGTGAATGGTAATA 59.396 38.462 0.00 0.00 33.88 0.98
2858 2975 2.480419 GGTGAAACATCCTTGTCGTCAG 59.520 50.000 0.00 0.00 39.98 3.51
2868 2985 0.110373 GCGAACGTGGTGAAACATCC 60.110 55.000 0.00 0.00 39.98 3.51
2882 2999 0.884704 TCCAACTCCTGCAAGCGAAC 60.885 55.000 0.00 0.00 0.00 3.95
2929 3046 2.851534 CGAAGATGCTTTTTCGGTTCC 58.148 47.619 15.05 0.00 41.69 3.62
2957 3074 5.043903 ACACAATTAGAATGAGGTCGATCG 58.956 41.667 9.36 9.36 0.00 3.69
3055 3173 7.566709 CCTTTACAAATTACAAGCAAAGCAAG 58.433 34.615 0.00 0.00 0.00 4.01
3084 3202 0.036306 ACAAGATTGTCGGGTGTCCC 59.964 55.000 0.00 0.00 36.50 4.46
3093 3211 5.237344 CGGGAGGATATTTCACAAGATTGTC 59.763 44.000 0.00 0.00 39.91 3.18
3188 3307 1.136336 GCAAGAAACTTCGCAGTACGG 60.136 52.381 0.00 0.00 43.89 4.02
3217 3336 2.833794 ACAGCAGCGAAAACTTACAGA 58.166 42.857 0.00 0.00 0.00 3.41
3259 3380 4.148128 AGCAGATACAGGGTTCATTGAG 57.852 45.455 0.00 0.00 0.00 3.02
3294 3462 2.611518 GTGAGACATTCTCTTCCCACG 58.388 52.381 4.87 0.00 43.73 4.94
3312 3480 1.071605 GTTCAGCTTAGACTGCCGTG 58.928 55.000 0.00 0.00 37.59 4.94
3313 3481 0.969894 AGTTCAGCTTAGACTGCCGT 59.030 50.000 0.00 0.00 37.59 5.68
3315 3483 3.697045 TCTCTAGTTCAGCTTAGACTGCC 59.303 47.826 4.15 0.00 37.59 4.85
3364 3532 3.371917 GGAACATGGGAATGAGATGACCA 60.372 47.826 0.00 0.00 35.39 4.02
3402 3576 2.230660 CCCTTTTCTCTTGGACCACAC 58.769 52.381 0.00 0.00 0.00 3.82
3451 3625 3.002102 GCTGCTTCTTCTTCTTCCTCTG 58.998 50.000 0.00 0.00 0.00 3.35
3458 3632 0.390998 GCCGAGCTGCTTCTTCTTCT 60.391 55.000 2.53 0.00 0.00 2.85
3460 3634 0.673022 CTGCCGAGCTGCTTCTTCTT 60.673 55.000 2.53 0.00 0.00 2.52
3461 3635 1.079266 CTGCCGAGCTGCTTCTTCT 60.079 57.895 2.53 0.00 0.00 2.85
3502 3682 5.385617 CAAGTCCAAAGATTAAGCTTGACG 58.614 41.667 9.86 0.00 35.29 4.35
3513 3693 3.652869 TCTCAAGTCCCAAGTCCAAAGAT 59.347 43.478 0.00 0.00 0.00 2.40
3517 3697 2.368875 GTCTCTCAAGTCCCAAGTCCAA 59.631 50.000 0.00 0.00 0.00 3.53
3561 3741 0.617413 AGCTTGGACTCTCACATGGG 59.383 55.000 0.00 0.00 0.00 4.00
3607 3796 6.381481 TCCGATACGTGCTATAGAGAAAAA 57.619 37.500 3.21 0.00 0.00 1.94
3649 3840 9.774742 GATGTGAATTAGACAAACTGTATTTCC 57.225 33.333 0.00 0.00 0.00 3.13
3655 3846 9.376075 CATCTAGATGTGAATTAGACAAACTGT 57.624 33.333 22.42 0.00 34.23 3.55
3684 3875 9.396022 GGAGATTAGATGTGACATCCTTAAAAA 57.604 33.333 21.05 7.53 0.00 1.94
3685 3876 7.993183 GGGAGATTAGATGTGACATCCTTAAAA 59.007 37.037 21.05 9.11 0.00 1.52
3686 3877 7.127186 TGGGAGATTAGATGTGACATCCTTAAA 59.873 37.037 21.05 11.34 0.00 1.52
3687 3878 6.615316 TGGGAGATTAGATGTGACATCCTTAA 59.385 38.462 21.05 14.34 0.00 1.85
3688 3879 6.042093 GTGGGAGATTAGATGTGACATCCTTA 59.958 42.308 21.05 6.22 0.00 2.69
3689 3880 4.971282 TGGGAGATTAGATGTGACATCCTT 59.029 41.667 21.05 7.22 0.00 3.36
3690 3881 4.346418 GTGGGAGATTAGATGTGACATCCT 59.654 45.833 21.05 11.37 0.00 3.24
3691 3882 4.101585 TGTGGGAGATTAGATGTGACATCC 59.898 45.833 21.05 6.28 0.00 3.51
3692 3883 5.282055 TGTGGGAGATTAGATGTGACATC 57.718 43.478 17.46 17.46 0.00 3.06
3693 3884 5.698741 TTGTGGGAGATTAGATGTGACAT 57.301 39.130 0.00 0.00 0.00 3.06
3694 3885 5.497464 TTTGTGGGAGATTAGATGTGACA 57.503 39.130 0.00 0.00 0.00 3.58
3695 3886 9.950496 ATATATTTGTGGGAGATTAGATGTGAC 57.050 33.333 0.00 0.00 0.00 3.67
3705 3896 9.672673 GTGCTACATTATATATTTGTGGGAGAT 57.327 33.333 9.93 0.00 0.00 2.75
3706 3897 8.880244 AGTGCTACATTATATATTTGTGGGAGA 58.120 33.333 9.93 0.00 0.00 3.71
3707 3898 9.507329 AAGTGCTACATTATATATTTGTGGGAG 57.493 33.333 9.93 3.34 0.00 4.30
3708 3899 9.283768 CAAGTGCTACATTATATATTTGTGGGA 57.716 33.333 9.93 6.61 0.00 4.37
3709 3900 8.514594 CCAAGTGCTACATTATATATTTGTGGG 58.485 37.037 9.93 5.64 0.00 4.61
3710 3901 9.283768 TCCAAGTGCTACATTATATATTTGTGG 57.716 33.333 9.93 8.54 0.00 4.17
3719 3910 8.822855 CGTGTTATTTCCAAGTGCTACATTATA 58.177 33.333 0.00 0.00 0.00 0.98
3720 3911 7.678690 GCGTGTTATTTCCAAGTGCTACATTAT 60.679 37.037 0.00 0.00 0.00 1.28
3721 3912 6.402766 GCGTGTTATTTCCAAGTGCTACATTA 60.403 38.462 0.00 0.00 0.00 1.90
3722 3913 5.619086 GCGTGTTATTTCCAAGTGCTACATT 60.619 40.000 0.00 0.00 0.00 2.71
3723 3914 4.142687 GCGTGTTATTTCCAAGTGCTACAT 60.143 41.667 0.00 0.00 0.00 2.29
3724 3915 3.187637 GCGTGTTATTTCCAAGTGCTACA 59.812 43.478 0.00 0.00 0.00 2.74
3725 3916 3.425758 GGCGTGTTATTTCCAAGTGCTAC 60.426 47.826 0.00 0.00 0.00 3.58
3726 3917 2.745281 GGCGTGTTATTTCCAAGTGCTA 59.255 45.455 0.00 0.00 0.00 3.49
3727 3918 1.539827 GGCGTGTTATTTCCAAGTGCT 59.460 47.619 0.00 0.00 0.00 4.40
3728 3919 1.268352 TGGCGTGTTATTTCCAAGTGC 59.732 47.619 0.00 0.00 0.00 4.40
3729 3920 3.634568 TTGGCGTGTTATTTCCAAGTG 57.365 42.857 0.00 0.00 34.01 3.16
3730 3921 4.657436 TTTTGGCGTGTTATTTCCAAGT 57.343 36.364 0.00 0.00 39.46 3.16
3731 3922 6.307800 CACTATTTTGGCGTGTTATTTCCAAG 59.692 38.462 0.00 0.00 39.46 3.61
3732 3923 6.153067 CACTATTTTGGCGTGTTATTTCCAA 58.847 36.000 0.00 0.00 36.86 3.53
3733 3924 5.704888 CACTATTTTGGCGTGTTATTTCCA 58.295 37.500 0.00 0.00 0.00 3.53
3734 3925 4.561213 GCACTATTTTGGCGTGTTATTTCC 59.439 41.667 0.00 0.00 0.00 3.13
3745 3936 2.102161 CCGGCGCACTATTTTGGC 59.898 61.111 10.83 0.00 0.00 4.52
3748 3939 1.528292 TTTGGCCGGCGCACTATTTT 61.528 50.000 22.54 0.00 36.38 1.82
3775 3969 8.970020 TGATCCGAACAATAGTAGTACCTTTTA 58.030 33.333 0.00 0.00 0.00 1.52
3779 3974 6.550108 ACATGATCCGAACAATAGTAGTACCT 59.450 38.462 0.00 0.00 0.00 3.08
3789 3984 6.813152 GGAAAAATTGACATGATCCGAACAAT 59.187 34.615 0.00 0.00 0.00 2.71
3791 3986 5.476599 AGGAAAAATTGACATGATCCGAACA 59.523 36.000 0.00 0.00 0.00 3.18
3792 3987 5.954335 AGGAAAAATTGACATGATCCGAAC 58.046 37.500 0.00 0.00 0.00 3.95
3812 4007 4.157289 GCATGAGCTCAGAAAAATTGAGGA 59.843 41.667 22.96 0.00 41.82 3.71
3817 4012 4.382685 CCATGGCATGAGCTCAGAAAAATT 60.383 41.667 28.43 0.00 41.70 1.82
3823 4018 0.984432 TCCCATGGCATGAGCTCAGA 60.984 55.000 28.43 8.23 41.70 3.27
3853 4048 1.006102 CTAGGCGGCCGGTTAGATG 60.006 63.158 29.38 0.00 0.00 2.90
3860 4055 4.090588 TCCAAACTAGGCGGCCGG 62.091 66.667 29.38 12.94 0.00 6.13
3864 4059 2.100631 CGCACTCCAAACTAGGCGG 61.101 63.158 0.00 0.00 40.70 6.13
3866 4061 0.741221 CCTCGCACTCCAAACTAGGC 60.741 60.000 0.00 0.00 0.00 3.93
3928 4123 6.884295 ACGAATTCAGGAAACTCCATATGAAA 59.116 34.615 3.65 0.00 39.61 2.69
3947 4142 2.347452 CGATGCCGAACACTTACGAATT 59.653 45.455 0.00 0.00 38.22 2.17


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

AutoCloner maintained by Alex Coulton.