Multiple sequence alignment - TraesCS5A01G413400

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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 TraesCS5A01G413400 chr5A 100.000 3419 0 0 1 3419 601642002 601645420 0.000000e+00 6314
1 TraesCS5A01G413400 chr2A 98.319 2736 46 0 1 2736 202781350 202778615 0.000000e+00 4798
2 TraesCS5A01G413400 chr2A 97.480 2738 55 3 1 2737 28781967 28784691 0.000000e+00 4662
3 TraesCS5A01G413400 chr2A 97.184 2450 67 2 288 2737 120716244 120718691 0.000000e+00 4141
4 TraesCS5A01G413400 chr2A 74.892 2322 523 51 2 2293 351425957 351428248 0.000000e+00 1003
5 TraesCS5A01G413400 chr6A 98.136 2736 44 2 1 2736 570451068 570453796 0.000000e+00 4763
6 TraesCS5A01G413400 chr6A 83.932 529 77 8 2895 3419 344694315 344693791 1.830000e-137 499
7 TraesCS5A01G413400 chr7B 97.078 2738 79 1 1 2737 317881598 317878861 0.000000e+00 4612
8 TraesCS5A01G413400 chr7B 93.182 88 6 0 2734 2821 481947811 481947898 2.770000e-26 130
9 TraesCS5A01G413400 chr7A 97.848 1812 38 1 1 1811 709792064 709793875 0.000000e+00 3129
10 TraesCS5A01G413400 chr7A 97.535 933 23 0 1805 2737 709807577 709808509 0.000000e+00 1596
11 TraesCS5A01G413400 chr7A 83.752 597 78 15 2837 3419 363594045 363593454 6.450000e-152 547
12 TraesCS5A01G413400 chr7A 96.324 272 10 0 2464 2735 67504573 67504302 6.730000e-122 448
13 TraesCS5A01G413400 chr2B 78.009 2310 468 33 1 2289 46074682 46072392 0.000000e+00 1415
14 TraesCS5A01G413400 chr2D 78.061 2311 458 41 1 2289 288231573 288229290 0.000000e+00 1413
15 TraesCS5A01G413400 chr5B 81.592 1646 298 5 51 1694 556944427 556946069 0.000000e+00 1356
16 TraesCS5A01G413400 chr5B 81.395 1376 249 6 367 1739 609851317 609852688 0.000000e+00 1116
17 TraesCS5A01G413400 chr3A 74.860 2319 523 50 2 2293 507635842 507633557 0.000000e+00 998
18 TraesCS5A01G413400 chr1A 85.980 592 74 5 2837 3419 284759210 284758619 2.900000e-175 625
19 TraesCS5A01G413400 chr1A 85.642 592 75 7 2837 3419 284869407 284868817 6.270000e-172 614
20 TraesCS5A01G413400 chr1A 86.832 524 66 3 2897 3419 285248922 285248401 1.770000e-162 582
21 TraesCS5A01G413400 chr1A 85.799 507 69 3 2914 3419 285260190 285259686 5.020000e-148 534
22 TraesCS5A01G413400 chr1A 83.779 524 80 5 2896 3417 135679398 135678878 3.070000e-135 492
23 TraesCS5A01G413400 chr4A 87.356 522 64 2 2898 3419 262468286 262467767 6.320000e-167 597
24 TraesCS5A01G413400 chr1D 82.197 528 88 6 2894 3417 216974676 216975201 1.870000e-122 449
25 TraesCS5A01G413400 chr4B 93.684 95 6 0 2737 2831 624425403 624425309 3.560000e-30 143


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 TraesCS5A01G413400 chr5A 601642002 601645420 3418 False 6314 6314 100.000 1 3419 1 chr5A.!!$F1 3418
1 TraesCS5A01G413400 chr2A 202778615 202781350 2735 True 4798 4798 98.319 1 2736 1 chr2A.!!$R1 2735
2 TraesCS5A01G413400 chr2A 28781967 28784691 2724 False 4662 4662 97.480 1 2737 1 chr2A.!!$F1 2736
3 TraesCS5A01G413400 chr2A 120716244 120718691 2447 False 4141 4141 97.184 288 2737 1 chr2A.!!$F2 2449
4 TraesCS5A01G413400 chr2A 351425957 351428248 2291 False 1003 1003 74.892 2 2293 1 chr2A.!!$F3 2291
5 TraesCS5A01G413400 chr6A 570451068 570453796 2728 False 4763 4763 98.136 1 2736 1 chr6A.!!$F1 2735
6 TraesCS5A01G413400 chr6A 344693791 344694315 524 True 499 499 83.932 2895 3419 1 chr6A.!!$R1 524
7 TraesCS5A01G413400 chr7B 317878861 317881598 2737 True 4612 4612 97.078 1 2737 1 chr7B.!!$R1 2736
8 TraesCS5A01G413400 chr7A 709792064 709793875 1811 False 3129 3129 97.848 1 1811 1 chr7A.!!$F1 1810
9 TraesCS5A01G413400 chr7A 709807577 709808509 932 False 1596 1596 97.535 1805 2737 1 chr7A.!!$F2 932
10 TraesCS5A01G413400 chr7A 363593454 363594045 591 True 547 547 83.752 2837 3419 1 chr7A.!!$R2 582
11 TraesCS5A01G413400 chr2B 46072392 46074682 2290 True 1415 1415 78.009 1 2289 1 chr2B.!!$R1 2288
12 TraesCS5A01G413400 chr2D 288229290 288231573 2283 True 1413 1413 78.061 1 2289 1 chr2D.!!$R1 2288
13 TraesCS5A01G413400 chr5B 556944427 556946069 1642 False 1356 1356 81.592 51 1694 1 chr5B.!!$F1 1643
14 TraesCS5A01G413400 chr5B 609851317 609852688 1371 False 1116 1116 81.395 367 1739 1 chr5B.!!$F2 1372
15 TraesCS5A01G413400 chr3A 507633557 507635842 2285 True 998 998 74.860 2 2293 1 chr3A.!!$R1 2291
16 TraesCS5A01G413400 chr1A 284758619 284759210 591 True 625 625 85.980 2837 3419 1 chr1A.!!$R2 582
17 TraesCS5A01G413400 chr1A 284868817 284869407 590 True 614 614 85.642 2837 3419 1 chr1A.!!$R3 582
18 TraesCS5A01G413400 chr1A 285248401 285248922 521 True 582 582 86.832 2897 3419 1 chr1A.!!$R4 522
19 TraesCS5A01G413400 chr1A 285259686 285260190 504 True 534 534 85.799 2914 3419 1 chr1A.!!$R5 505
20 TraesCS5A01G413400 chr1A 135678878 135679398 520 True 492 492 83.779 2896 3417 1 chr1A.!!$R1 521
21 TraesCS5A01G413400 chr4A 262467767 262468286 519 True 597 597 87.356 2898 3419 1 chr4A.!!$R1 521
22 TraesCS5A01G413400 chr1D 216974676 216975201 525 False 449 449 82.197 2894 3417 1 chr1D.!!$F1 523

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
286 287 1.676678 GGCTCAGACGATGGCCAGTA 61.677 60.0 13.05 0.0 42.0 2.74 F
1592 1603 2.096496 GTCACTCTTCAATGCATTCCCG 59.904 50.0 9.53 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1993 2040 0.328258 GGGCCTGAAGCTTGAACCTA 59.672 55.0 2.1 0.0 43.05 3.08 R
2910 2966 0.034059 AGGCGGATGCTTATCTTCGG 59.966 55.0 0.0 0.0 42.25 4.30 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
113 114 3.260884 TGTCCCATGTCTCCTTACTTGTC 59.739 47.826 0.00 0.00 0.00 3.18
150 151 9.860898 ATTAATGAACTTTCCATCTTGCTTAAC 57.139 29.630 0.00 0.00 0.00 2.01
175 176 2.932187 GCTTTGCAGGCTAACCAATTGG 60.932 50.000 23.31 23.31 39.06 3.16
245 246 4.824479 TTGCAGATGATCTTCTGGTGTA 57.176 40.909 29.67 10.57 42.78 2.90
286 287 1.676678 GGCTCAGACGATGGCCAGTA 61.677 60.000 13.05 0.00 42.00 2.74
302 303 8.588290 ATGGCCAGTATTATTCAACACTTTTA 57.412 30.769 13.05 0.00 0.00 1.52
676 681 4.563374 GGAATTTTTGGTGGACAGGGATTG 60.563 45.833 0.00 0.00 0.00 2.67
1067 1078 4.706476 TCCTCAACCATCAGGCTTTATTTG 59.294 41.667 0.00 0.00 39.06 2.32
1448 1459 6.183360 GCAGGCCATTTTTCTATTCACATTTG 60.183 38.462 5.01 0.00 0.00 2.32
1592 1603 2.096496 GTCACTCTTCAATGCATTCCCG 59.904 50.000 9.53 0.00 0.00 5.14
1810 1856 2.371841 TCTTTGCAGGCTTCTCAACCTA 59.628 45.455 0.00 0.00 33.38 3.08
2152 2199 3.295585 TTGCTGCTGCCAGGAATATTA 57.704 42.857 13.47 0.00 43.32 0.98
2339 2386 3.768215 TGCTCTTCTCACTCTCATGTCAT 59.232 43.478 0.00 0.00 0.00 3.06
2353 2400 6.420638 TCTCATGTCATTGAATCATGTCCTT 58.579 36.000 13.79 0.00 39.61 3.36
2479 2526 7.012661 ACATGATATGATGGTCTATGCTTGA 57.987 36.000 7.11 0.00 0.00 3.02
2501 2548 6.070656 TGATTGTTGGAAAGAAGGAGATTGT 58.929 36.000 0.00 0.00 30.39 2.71
2709 2756 9.499479 CTGTGAGCTGAATATATTGGTATCTTT 57.501 33.333 1.78 0.00 0.00 2.52
2757 2804 8.937634 AAAAATGTAGCCATGAGAAATGATTC 57.062 30.769 0.00 0.00 35.70 2.52
2759 2806 7.893124 AATGTAGCCATGAGAAATGATTCTT 57.107 32.000 0.00 0.00 45.91 2.52
2760 2807 6.932356 TGTAGCCATGAGAAATGATTCTTC 57.068 37.500 0.00 0.00 45.91 2.87
2761 2808 6.656902 TGTAGCCATGAGAAATGATTCTTCT 58.343 36.000 0.00 0.00 45.91 2.85
2762 2809 6.765036 TGTAGCCATGAGAAATGATTCTTCTC 59.235 38.462 0.00 8.14 45.91 2.87
2763 2810 5.131784 AGCCATGAGAAATGATTCTTCTCC 58.868 41.667 11.20 0.17 45.91 3.71
2764 2811 4.885907 GCCATGAGAAATGATTCTTCTCCA 59.114 41.667 11.20 3.37 45.91 3.86
2765 2812 5.221009 GCCATGAGAAATGATTCTTCTCCAC 60.221 44.000 11.20 0.00 45.91 4.02
2766 2813 6.120905 CCATGAGAAATGATTCTTCTCCACT 58.879 40.000 11.20 0.00 45.91 4.00
2767 2814 6.602406 CCATGAGAAATGATTCTTCTCCACTT 59.398 38.462 11.20 0.00 45.91 3.16
2768 2815 7.415318 CCATGAGAAATGATTCTTCTCCACTTG 60.415 40.741 11.20 6.00 45.91 3.16
2769 2816 6.537355 TGAGAAATGATTCTTCTCCACTTGT 58.463 36.000 11.20 0.00 45.91 3.16
2770 2817 6.652481 TGAGAAATGATTCTTCTCCACTTGTC 59.348 38.462 11.20 0.00 45.91 3.18
2771 2818 5.942826 AGAAATGATTCTTCTCCACTTGTCC 59.057 40.000 0.00 0.00 43.43 4.02
2772 2819 4.916041 ATGATTCTTCTCCACTTGTCCA 57.084 40.909 0.00 0.00 0.00 4.02
2773 2820 4.008074 TGATTCTTCTCCACTTGTCCAC 57.992 45.455 0.00 0.00 0.00 4.02
2774 2821 3.648067 TGATTCTTCTCCACTTGTCCACT 59.352 43.478 0.00 0.00 0.00 4.00
2775 2822 4.838423 TGATTCTTCTCCACTTGTCCACTA 59.162 41.667 0.00 0.00 0.00 2.74
2776 2823 4.873746 TTCTTCTCCACTTGTCCACTAG 57.126 45.455 0.00 0.00 0.00 2.57
2777 2824 3.845860 TCTTCTCCACTTGTCCACTAGT 58.154 45.455 0.00 0.00 32.36 2.57
2778 2825 3.574396 TCTTCTCCACTTGTCCACTAGTG 59.426 47.826 16.34 16.34 45.09 2.74
2779 2826 2.958818 TCTCCACTTGTCCACTAGTGT 58.041 47.619 21.18 0.00 44.40 3.55
2780 2827 2.891580 TCTCCACTTGTCCACTAGTGTC 59.108 50.000 21.18 13.87 44.40 3.67
2781 2828 2.628178 CTCCACTTGTCCACTAGTGTCA 59.372 50.000 21.18 16.12 44.40 3.58
2782 2829 3.239449 TCCACTTGTCCACTAGTGTCAT 58.761 45.455 21.18 4.28 44.40 3.06
2783 2830 3.006859 TCCACTTGTCCACTAGTGTCATG 59.993 47.826 21.18 20.21 44.40 3.07
2784 2831 3.329386 CACTTGTCCACTAGTGTCATGG 58.671 50.000 21.18 15.57 42.16 3.66
2785 2832 2.972713 ACTTGTCCACTAGTGTCATGGT 59.027 45.455 21.18 16.07 34.89 3.55
2786 2833 3.006967 ACTTGTCCACTAGTGTCATGGTC 59.993 47.826 21.18 4.57 34.89 4.02
2787 2834 2.604139 TGTCCACTAGTGTCATGGTCA 58.396 47.619 21.18 7.09 34.89 4.02
2788 2835 2.299013 TGTCCACTAGTGTCATGGTCAC 59.701 50.000 21.18 11.93 34.89 3.67
2789 2836 1.899814 TCCACTAGTGTCATGGTCACC 59.100 52.381 21.18 0.00 36.58 4.02
2790 2837 1.623311 CCACTAGTGTCATGGTCACCA 59.377 52.381 21.18 0.00 38.19 4.17
2791 2838 2.354103 CCACTAGTGTCATGGTCACCAG 60.354 54.545 21.18 13.68 36.75 4.00
2792 2839 1.902508 ACTAGTGTCATGGTCACCAGG 59.097 52.381 0.63 0.63 36.75 4.45
2793 2840 0.613260 TAGTGTCATGGTCACCAGGC 59.387 55.000 2.71 0.00 36.75 4.85
2794 2841 1.073025 GTGTCATGGTCACCAGGCA 59.927 57.895 2.71 2.31 36.75 4.75
2795 2842 1.073025 TGTCATGGTCACCAGGCAC 59.927 57.895 2.71 3.92 36.75 5.01
2796 2843 2.034879 GTCATGGTCACCAGGCACG 61.035 63.158 2.71 0.00 36.75 5.34
2797 2844 2.032528 CATGGTCACCAGGCACGT 59.967 61.111 1.19 0.00 36.75 4.49
2798 2845 1.188871 TCATGGTCACCAGGCACGTA 61.189 55.000 2.71 0.00 36.75 3.57
2799 2846 1.019278 CATGGTCACCAGGCACGTAC 61.019 60.000 1.19 0.00 36.75 3.67
2800 2847 2.431942 GGTCACCAGGCACGTACG 60.432 66.667 15.01 15.01 0.00 3.67
2801 2848 2.646719 GTCACCAGGCACGTACGA 59.353 61.111 24.41 0.00 0.00 3.43
2802 2849 1.443872 GTCACCAGGCACGTACGAG 60.444 63.158 24.41 16.14 0.00 4.18
2803 2850 1.900016 TCACCAGGCACGTACGAGT 60.900 57.895 24.41 6.16 0.00 4.18
2804 2851 1.006571 CACCAGGCACGTACGAGTT 60.007 57.895 24.41 4.10 0.00 3.01
2805 2852 0.599204 CACCAGGCACGTACGAGTTT 60.599 55.000 24.41 3.71 0.00 2.66
2806 2853 0.319297 ACCAGGCACGTACGAGTTTC 60.319 55.000 24.41 8.34 0.00 2.78
2807 2854 0.038526 CCAGGCACGTACGAGTTTCT 60.039 55.000 24.41 10.47 0.00 2.52
2808 2855 1.604693 CCAGGCACGTACGAGTTTCTT 60.605 52.381 24.41 0.00 0.00 2.52
2809 2856 1.455786 CAGGCACGTACGAGTTTCTTG 59.544 52.381 24.41 8.91 0.00 3.02
2810 2857 1.068127 AGGCACGTACGAGTTTCTTGT 59.932 47.619 24.41 0.00 32.27 3.16
2811 2858 2.294233 AGGCACGTACGAGTTTCTTGTA 59.706 45.455 24.41 0.00 29.93 2.41
2812 2859 3.052036 GGCACGTACGAGTTTCTTGTAA 58.948 45.455 24.41 0.00 32.83 2.41
2813 2860 3.676646 GGCACGTACGAGTTTCTTGTAAT 59.323 43.478 24.41 0.00 32.83 1.89
2814 2861 4.201561 GGCACGTACGAGTTTCTTGTAATC 60.202 45.833 24.41 0.00 32.83 1.75
2815 2862 4.201561 GCACGTACGAGTTTCTTGTAATCC 60.202 45.833 24.41 0.00 32.83 3.01
2816 2863 4.029861 CACGTACGAGTTTCTTGTAATCCG 59.970 45.833 24.41 2.60 32.83 4.18
2817 2864 3.001365 CGTACGAGTTTCTTGTAATCCGC 60.001 47.826 10.44 0.00 32.83 5.54
2818 2865 3.314541 ACGAGTTTCTTGTAATCCGCT 57.685 42.857 0.00 0.00 0.00 5.52
2819 2866 3.660865 ACGAGTTTCTTGTAATCCGCTT 58.339 40.909 0.00 0.00 0.00 4.68
2820 2867 4.813027 ACGAGTTTCTTGTAATCCGCTTA 58.187 39.130 0.00 0.00 0.00 3.09
2821 2868 4.624452 ACGAGTTTCTTGTAATCCGCTTAC 59.376 41.667 0.00 0.57 40.21 2.34
2822 2869 4.032558 CGAGTTTCTTGTAATCCGCTTACC 59.967 45.833 4.33 0.00 39.23 2.85
2823 2870 4.901868 AGTTTCTTGTAATCCGCTTACCA 58.098 39.130 4.33 0.00 39.23 3.25
2824 2871 5.310451 AGTTTCTTGTAATCCGCTTACCAA 58.690 37.500 4.33 0.00 39.23 3.67
2825 2872 5.944007 AGTTTCTTGTAATCCGCTTACCAAT 59.056 36.000 4.33 0.00 39.23 3.16
2826 2873 5.811399 TTCTTGTAATCCGCTTACCAATG 57.189 39.130 4.33 0.00 39.23 2.82
2827 2874 3.625764 TCTTGTAATCCGCTTACCAATGC 59.374 43.478 4.33 0.00 39.23 3.56
2828 2875 2.992593 TGTAATCCGCTTACCAATGCA 58.007 42.857 0.00 0.00 39.23 3.96
2829 2876 2.680841 TGTAATCCGCTTACCAATGCAC 59.319 45.455 0.00 0.00 39.23 4.57
2830 2877 0.732571 AATCCGCTTACCAATGCACG 59.267 50.000 0.00 0.00 0.00 5.34
2831 2878 0.107897 ATCCGCTTACCAATGCACGA 60.108 50.000 0.00 0.00 0.00 4.35
2832 2879 1.017177 TCCGCTTACCAATGCACGAC 61.017 55.000 0.00 0.00 0.00 4.34
2833 2880 1.295357 CCGCTTACCAATGCACGACA 61.295 55.000 0.00 0.00 0.00 4.35
2834 2881 0.726827 CGCTTACCAATGCACGACAT 59.273 50.000 0.00 0.00 42.30 3.06
2835 2882 1.529622 CGCTTACCAATGCACGACATG 60.530 52.381 0.00 0.00 39.60 3.21
2857 2904 1.203052 GTCGGAGTAAATGACCACGGA 59.797 52.381 0.00 0.00 0.00 4.69
2861 2908 3.067742 CGGAGTAAATGACCACGGATAGT 59.932 47.826 0.00 0.00 0.00 2.12
2873 2920 1.464376 CGGATAGTCACATCGGCCCT 61.464 60.000 0.00 0.00 0.00 5.19
2879 2926 1.612146 TCACATCGGCCCTCCTTGA 60.612 57.895 0.00 0.00 0.00 3.02
2882 2929 1.140852 CACATCGGCCCTCCTTGATAA 59.859 52.381 0.00 0.00 0.00 1.75
2885 2932 2.638480 TCGGCCCTCCTTGATAAATG 57.362 50.000 0.00 0.00 0.00 2.32
2886 2933 0.954452 CGGCCCTCCTTGATAAATGC 59.046 55.000 0.00 0.00 0.00 3.56
2887 2934 1.477558 CGGCCCTCCTTGATAAATGCT 60.478 52.381 0.00 0.00 0.00 3.79
2888 2935 2.670939 GGCCCTCCTTGATAAATGCTT 58.329 47.619 0.00 0.00 0.00 3.91
2891 2938 3.570125 GCCCTCCTTGATAAATGCTTACC 59.430 47.826 0.00 0.00 0.00 2.85
2910 2966 3.741476 CTGCGCCCCTCAAAGCAC 61.741 66.667 4.18 0.00 35.59 4.40
2932 2988 3.390135 CGAAGATAAGCATCCGCCTTTA 58.610 45.455 0.00 0.00 39.83 1.85
3026 3082 3.554342 CTAGCAGGCGGCCTCCAT 61.554 66.667 20.97 10.46 46.50 3.41
3121 3180 1.065418 GGCTACAGTACAACCTGCCAT 60.065 52.381 10.57 0.00 38.79 4.40
3163 3222 1.152398 ACCACAGTGTCCCGTACCT 60.152 57.895 0.00 0.00 0.00 3.08
3301 3360 1.131638 ACCTGTCTGTGAGAAGCCAA 58.868 50.000 0.00 0.00 0.00 4.52
3381 3440 0.969894 CCCTTCCTCGAAGTCTGTGT 59.030 55.000 1.05 0.00 37.92 3.72
3383 3442 1.341531 CCTTCCTCGAAGTCTGTGTGT 59.658 52.381 1.05 0.00 37.92 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 114 7.652909 TGGAAAGTTCATTAATTGCAAGAACAG 59.347 33.333 22.84 10.02 40.63 3.16
150 151 0.169009 GGTTAGCCTGCAAAGCTTCG 59.831 55.000 15.45 0.00 41.83 3.79
175 176 3.721087 TGGTCCAAGAGAAATTCCCTC 57.279 47.619 0.00 0.85 0.00 4.30
245 246 1.070758 CCTGATAAGTAGCGTGCCCAT 59.929 52.381 0.00 0.00 0.00 4.00
302 303 3.073650 AGGAGTTTGACCAGAAAGAGCAT 59.926 43.478 0.00 0.00 0.00 3.79
676 681 6.379988 AGACTCCTCTTAGAATCTGTTTCTCC 59.620 42.308 4.34 0.00 43.75 3.71
1362 1373 5.182487 CAAGCAAAAGTTTTAACCTTGGGT 58.818 37.500 18.50 4.10 37.65 4.51
1448 1459 3.441572 AGCACATCTACAACAATTCTGCC 59.558 43.478 0.00 0.00 0.00 4.85
1592 1603 5.065731 CCCATAGAAGCAAAGTGAATCAGAC 59.934 44.000 0.00 0.00 0.00 3.51
1993 2040 0.328258 GGGCCTGAAGCTTGAACCTA 59.672 55.000 2.10 0.00 43.05 3.08
2339 2386 3.696051 GGCAGCTAAAGGACATGATTCAA 59.304 43.478 0.00 0.00 0.00 2.69
2353 2400 3.988976 ATCAACAAGAGAGGCAGCTAA 57.011 42.857 0.00 0.00 0.00 3.09
2479 2526 6.324770 ACAACAATCTCCTTCTTTCCAACAAT 59.675 34.615 0.00 0.00 0.00 2.71
2501 2548 6.538381 GGAAAAGAAAATTCCAGCTTTGACAA 59.462 34.615 0.56 0.00 44.70 3.18
2709 2756 0.843309 TGAACAGAGAAAGGCACCCA 59.157 50.000 0.00 0.00 0.00 4.51
2737 2784 6.656902 AGAAGAATCATTTCTCATGGCTACA 58.343 36.000 0.00 0.00 41.42 2.74
2738 2785 7.188468 GAGAAGAATCATTTCTCATGGCTAC 57.812 40.000 9.46 0.00 46.22 3.58
2746 2793 6.093357 GGACAAGTGGAGAAGAATCATTTCTC 59.907 42.308 6.47 6.47 46.23 2.87
2747 2794 5.942826 GGACAAGTGGAGAAGAATCATTTCT 59.057 40.000 0.00 0.00 44.20 2.52
2748 2795 5.707298 TGGACAAGTGGAGAAGAATCATTTC 59.293 40.000 0.00 0.00 0.00 2.17
2749 2796 5.474876 GTGGACAAGTGGAGAAGAATCATTT 59.525 40.000 0.00 0.00 0.00 2.32
2750 2797 5.006386 GTGGACAAGTGGAGAAGAATCATT 58.994 41.667 0.00 0.00 0.00 2.57
2751 2798 4.288105 AGTGGACAAGTGGAGAAGAATCAT 59.712 41.667 0.00 0.00 0.00 2.45
2752 2799 3.648067 AGTGGACAAGTGGAGAAGAATCA 59.352 43.478 0.00 0.00 0.00 2.57
2753 2800 4.278975 AGTGGACAAGTGGAGAAGAATC 57.721 45.455 0.00 0.00 0.00 2.52
2754 2801 4.841246 ACTAGTGGACAAGTGGAGAAGAAT 59.159 41.667 0.00 0.00 0.00 2.40
2755 2802 4.039245 CACTAGTGGACAAGTGGAGAAGAA 59.961 45.833 15.49 0.00 39.55 2.52
2756 2803 3.574396 CACTAGTGGACAAGTGGAGAAGA 59.426 47.826 15.49 0.00 39.55 2.87
2757 2804 3.322254 ACACTAGTGGACAAGTGGAGAAG 59.678 47.826 26.12 0.00 45.94 2.85
2758 2805 3.305720 ACACTAGTGGACAAGTGGAGAA 58.694 45.455 26.12 0.00 45.94 2.87
2759 2806 2.891580 GACACTAGTGGACAAGTGGAGA 59.108 50.000 26.12 0.00 45.94 3.71
2760 2807 2.628178 TGACACTAGTGGACAAGTGGAG 59.372 50.000 26.12 0.00 45.94 3.86
2761 2808 2.673258 TGACACTAGTGGACAAGTGGA 58.327 47.619 26.12 1.54 45.94 4.02
2762 2809 3.329386 CATGACACTAGTGGACAAGTGG 58.671 50.000 26.12 12.62 45.94 4.00
2763 2810 3.244215 ACCATGACACTAGTGGACAAGTG 60.244 47.826 26.12 18.62 46.84 3.16
2764 2811 2.972713 ACCATGACACTAGTGGACAAGT 59.027 45.455 26.12 20.57 36.82 3.16
2765 2812 3.006859 TGACCATGACACTAGTGGACAAG 59.993 47.826 26.12 19.86 35.38 3.16
2766 2813 2.969262 TGACCATGACACTAGTGGACAA 59.031 45.455 26.12 9.36 35.38 3.18
2767 2814 2.299013 GTGACCATGACACTAGTGGACA 59.701 50.000 26.12 23.27 35.81 4.02
2768 2815 2.353803 GGTGACCATGACACTAGTGGAC 60.354 54.545 26.12 18.90 38.20 4.02
2769 2816 1.899814 GGTGACCATGACACTAGTGGA 59.100 52.381 26.12 13.05 38.20 4.02
2770 2817 1.623311 TGGTGACCATGACACTAGTGG 59.377 52.381 26.12 11.09 38.20 4.00
2771 2818 2.354103 CCTGGTGACCATGACACTAGTG 60.354 54.545 21.44 21.44 42.46 2.74
2772 2819 1.902508 CCTGGTGACCATGACACTAGT 59.097 52.381 23.13 0.00 42.46 2.57
2773 2820 1.406069 GCCTGGTGACCATGACACTAG 60.406 57.143 20.46 20.46 43.21 2.57
2774 2821 0.613260 GCCTGGTGACCATGACACTA 59.387 55.000 11.24 13.05 38.20 2.74
2775 2822 1.376466 GCCTGGTGACCATGACACT 59.624 57.895 11.24 0.00 38.20 3.55
2776 2823 1.073025 TGCCTGGTGACCATGACAC 59.927 57.895 11.24 12.38 37.51 3.67
2777 2824 1.073025 GTGCCTGGTGACCATGACA 59.927 57.895 11.24 4.24 30.82 3.58
2778 2825 2.034879 CGTGCCTGGTGACCATGAC 61.035 63.158 11.24 4.59 30.82 3.06
2779 2826 1.188871 TACGTGCCTGGTGACCATGA 61.189 55.000 11.24 0.00 30.82 3.07
2780 2827 1.019278 GTACGTGCCTGGTGACCATG 61.019 60.000 4.03 3.01 30.82 3.66
2781 2828 1.295423 GTACGTGCCTGGTGACCAT 59.705 57.895 4.03 0.00 30.82 3.55
2782 2829 2.738480 GTACGTGCCTGGTGACCA 59.262 61.111 3.40 3.40 0.00 4.02
2783 2830 2.431942 CGTACGTGCCTGGTGACC 60.432 66.667 7.22 0.00 0.00 4.02
2784 2831 1.443872 CTCGTACGTGCCTGGTGAC 60.444 63.158 16.05 0.00 0.00 3.67
2785 2832 1.457823 AACTCGTACGTGCCTGGTGA 61.458 55.000 16.05 0.00 0.00 4.02
2786 2833 0.599204 AAACTCGTACGTGCCTGGTG 60.599 55.000 16.05 0.00 0.00 4.17
2787 2834 0.319297 GAAACTCGTACGTGCCTGGT 60.319 55.000 16.05 3.45 0.00 4.00
2788 2835 0.038526 AGAAACTCGTACGTGCCTGG 60.039 55.000 16.05 0.00 0.00 4.45
2789 2836 1.455786 CAAGAAACTCGTACGTGCCTG 59.544 52.381 16.05 4.54 0.00 4.85
2790 2837 1.068127 ACAAGAAACTCGTACGTGCCT 59.932 47.619 16.05 8.22 0.00 4.75
2791 2838 1.494824 ACAAGAAACTCGTACGTGCC 58.505 50.000 16.05 6.07 0.00 5.01
2792 2839 4.201561 GGATTACAAGAAACTCGTACGTGC 60.202 45.833 16.05 0.00 0.00 5.34
2793 2840 4.029861 CGGATTACAAGAAACTCGTACGTG 59.970 45.833 16.05 15.64 0.00 4.49
2794 2841 4.161333 CGGATTACAAGAAACTCGTACGT 58.839 43.478 16.05 0.00 0.00 3.57
2795 2842 3.001365 GCGGATTACAAGAAACTCGTACG 60.001 47.826 9.53 9.53 0.00 3.67
2796 2843 4.171754 AGCGGATTACAAGAAACTCGTAC 58.828 43.478 0.00 0.00 0.00 3.67
2797 2844 4.445452 AGCGGATTACAAGAAACTCGTA 57.555 40.909 0.00 0.00 0.00 3.43
2798 2845 3.314541 AGCGGATTACAAGAAACTCGT 57.685 42.857 0.00 0.00 0.00 4.18
2799 2846 4.032558 GGTAAGCGGATTACAAGAAACTCG 59.967 45.833 16.93 0.00 44.81 4.18
2800 2847 4.933400 TGGTAAGCGGATTACAAGAAACTC 59.067 41.667 16.93 0.00 44.81 3.01
2801 2848 4.901868 TGGTAAGCGGATTACAAGAAACT 58.098 39.130 16.93 0.00 44.81 2.66
2802 2849 5.616488 TTGGTAAGCGGATTACAAGAAAC 57.384 39.130 16.93 0.55 44.81 2.78
2803 2850 5.392595 GCATTGGTAAGCGGATTACAAGAAA 60.393 40.000 16.93 6.82 44.81 2.52
2804 2851 4.095782 GCATTGGTAAGCGGATTACAAGAA 59.904 41.667 16.93 7.50 44.81 2.52
2805 2852 3.625764 GCATTGGTAAGCGGATTACAAGA 59.374 43.478 16.93 3.68 44.81 3.02
2806 2853 3.376859 TGCATTGGTAAGCGGATTACAAG 59.623 43.478 16.93 5.52 44.81 3.16
2807 2854 3.127895 GTGCATTGGTAAGCGGATTACAA 59.872 43.478 16.93 3.77 44.81 2.41
2808 2855 2.680841 GTGCATTGGTAAGCGGATTACA 59.319 45.455 16.93 0.00 44.81 2.41
2809 2856 2.286184 CGTGCATTGGTAAGCGGATTAC 60.286 50.000 7.59 7.59 42.68 1.89
2810 2857 1.937223 CGTGCATTGGTAAGCGGATTA 59.063 47.619 0.00 0.00 0.00 1.75
2811 2858 0.732571 CGTGCATTGGTAAGCGGATT 59.267 50.000 0.00 0.00 0.00 3.01
2812 2859 0.107897 TCGTGCATTGGTAAGCGGAT 60.108 50.000 0.00 0.00 0.00 4.18
2813 2860 1.017177 GTCGTGCATTGGTAAGCGGA 61.017 55.000 0.00 0.00 0.00 5.54
2814 2861 1.295357 TGTCGTGCATTGGTAAGCGG 61.295 55.000 0.00 0.00 0.00 5.52
2815 2862 0.726827 ATGTCGTGCATTGGTAAGCG 59.273 50.000 0.00 0.00 33.14 4.68
2816 2863 1.468520 ACATGTCGTGCATTGGTAAGC 59.531 47.619 0.00 0.00 35.19 3.09
2817 2864 3.121559 CACATGTCGTGCATTGGTAAG 57.878 47.619 0.00 0.00 39.19 2.34
2830 2877 3.617263 GGTCATTTACTCCGACACATGTC 59.383 47.826 0.00 1.70 41.47 3.06
2831 2878 3.007506 TGGTCATTTACTCCGACACATGT 59.992 43.478 0.00 0.00 0.00 3.21
2832 2879 3.370978 GTGGTCATTTACTCCGACACATG 59.629 47.826 0.00 0.00 0.00 3.21
2833 2880 3.596214 GTGGTCATTTACTCCGACACAT 58.404 45.455 0.00 0.00 0.00 3.21
2834 2881 2.608506 CGTGGTCATTTACTCCGACACA 60.609 50.000 0.00 0.00 0.00 3.72
2835 2882 1.990563 CGTGGTCATTTACTCCGACAC 59.009 52.381 0.00 0.00 0.00 3.67
2857 2904 0.105453 AGGAGGGCCGATGTGACTAT 60.105 55.000 0.00 0.00 39.96 2.12
2861 2908 0.982852 ATCAAGGAGGGCCGATGTGA 60.983 55.000 0.00 1.29 39.96 3.58
2873 2920 5.126067 GCAGAGGTAAGCATTTATCAAGGA 58.874 41.667 0.00 0.00 0.00 3.36
2879 2926 2.222027 GGCGCAGAGGTAAGCATTTAT 58.778 47.619 10.83 0.00 0.00 1.40
2882 2929 1.452108 GGGCGCAGAGGTAAGCATT 60.452 57.895 10.83 0.00 0.00 3.56
2885 2932 3.741830 GAGGGGCGCAGAGGTAAGC 62.742 68.421 10.83 0.00 0.00 3.09
2886 2933 1.899437 TTGAGGGGCGCAGAGGTAAG 61.899 60.000 10.83 0.00 0.00 2.34
2887 2934 1.485294 TTTGAGGGGCGCAGAGGTAA 61.485 55.000 10.83 0.00 0.00 2.85
2888 2935 1.899437 CTTTGAGGGGCGCAGAGGTA 61.899 60.000 10.83 0.00 0.00 3.08
2891 2938 3.130160 GCTTTGAGGGGCGCAGAG 61.130 66.667 10.83 0.00 0.00 3.35
2910 2966 0.034059 AGGCGGATGCTTATCTTCGG 59.966 55.000 0.00 0.00 42.25 4.30
2954 3010 4.473520 CGCCTTCCAGCATCCGGT 62.474 66.667 0.00 0.00 0.00 5.28
3121 3180 3.154473 CCGCCCTGGATTCGAGGA 61.154 66.667 15.68 0.00 42.00 3.71
3145 3204 1.152398 AGGTACGGGACACTGTGGT 60.152 57.895 13.09 2.80 36.70 4.16
3179 3238 2.587753 CAACAGTGTCGCACCGGT 60.588 61.111 0.00 0.00 34.49 5.28
3312 3371 4.643387 GCGCCAACTGGTCAGGGT 62.643 66.667 0.00 0.00 37.57 4.34
3381 3440 3.056107 CCCGTCTCTTCTGGTTAATGACA 60.056 47.826 0.00 0.00 0.00 3.58
3383 3442 2.500098 CCCCGTCTCTTCTGGTTAATGA 59.500 50.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.