Multiple sequence alignment - TraesCS2A01G116900

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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 TraesCS2A01G116900 chr2A 100.000 2900 0 0 1 2900 66847770 66850669 0.000000e+00 5356.0
1 TraesCS2A01G116900 chr2D 90.028 2898 107 78 1 2778 67497977 67495142 0.000000e+00 3583.0
2 TraesCS2A01G116900 chr2B 91.489 1598 58 23 739 2274 103195392 103196973 0.000000e+00 2126.0
3 TraesCS2A01G116900 chr2B 96.262 535 15 2 1 535 103194058 103194587 0.000000e+00 872.0
4 TraesCS2A01G116900 chr2B 90.476 210 13 5 531 736 103194882 103195088 1.320000e-68 270.0
5 TraesCS2A01G116900 chr2B 90.710 183 8 5 2380 2561 103197092 103197266 4.830000e-58 235.0
6 TraesCS2A01G116900 chr2B 86.207 58 6 2 2809 2865 797515370 797515314 8.680000e-06 62.1
7 TraesCS2A01G116900 chr3D 84.270 89 8 4 2779 2866 123319460 123319543 6.660000e-12 82.4
8 TraesCS2A01G116900 chr7D 93.023 43 2 1 2824 2865 611664843 611664801 8.680000e-06 62.1


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 TraesCS2A01G116900 chr2A 66847770 66850669 2899 False 5356.00 5356 100.00000 1 2900 1 chr2A.!!$F1 2899
1 TraesCS2A01G116900 chr2D 67495142 67497977 2835 True 3583.00 3583 90.02800 1 2778 1 chr2D.!!$R1 2777
2 TraesCS2A01G116900 chr2B 103194058 103197266 3208 False 875.75 2126 92.23425 1 2561 4 chr2B.!!$F1 2560

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
908 1540 0.107456 CACAGTCTCAGCAACCACCT 59.893 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2590 3387 0.040058 TTTGTGCATGGCCCTCTGAT 59.96 50.0 0.0 0.0 0.0 2.9 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
68 69 9.999009 CATTTTGGCATGTATCATAATAGCTAG 57.001 33.333 0.00 0.00 0.00 3.42
315 317 2.684881 ACAACAAGCTATGCATGTAGGC 59.315 45.455 10.16 8.43 39.58 3.93
325 327 5.652014 GCTATGCATGTAGGCCCATTAATAA 59.348 40.000 10.16 0.00 0.00 1.40
326 328 6.322201 GCTATGCATGTAGGCCCATTAATAAT 59.678 38.462 10.16 0.00 0.00 1.28
327 329 7.147846 GCTATGCATGTAGGCCCATTAATAATT 60.148 37.037 10.16 0.00 0.00 1.40
374 376 0.107993 TCAATCGGCTCTGGCTTCAG 60.108 55.000 0.00 0.00 39.78 3.02
422 424 4.381932 GCTGGTTGATTAATTTGGAGTGGG 60.382 45.833 0.00 0.00 0.00 4.61
646 953 4.947883 TCCTCATCTCTTTGGTCCTAAGA 58.052 43.478 14.09 14.09 0.00 2.10
769 1379 2.367512 GCATGTCCCTCCCCTCCT 60.368 66.667 0.00 0.00 0.00 3.69
770 1380 2.447714 GCATGTCCCTCCCCTCCTC 61.448 68.421 0.00 0.00 0.00 3.71
771 1381 1.768077 CATGTCCCTCCCCTCCTCC 60.768 68.421 0.00 0.00 0.00 4.30
908 1540 0.107456 CACAGTCTCAGCAACCACCT 59.893 55.000 0.00 0.00 0.00 4.00
981 1622 3.321111 GCAGTAGTATAGTAGCCAGCCAA 59.679 47.826 0.00 0.00 0.00 4.52
1556 2238 4.738998 TTCCATGCCGGTGCCCAG 62.739 66.667 1.90 0.00 36.33 4.45
1903 2606 1.941668 GCTTCCTCTCCCACTGAAACG 60.942 57.143 0.00 0.00 0.00 3.60
1904 2607 0.685097 TTCCTCTCCCACTGAAACGG 59.315 55.000 0.00 0.00 0.00 4.44
1905 2608 0.178944 TCCTCTCCCACTGAAACGGA 60.179 55.000 0.00 0.00 0.00 4.69
1906 2609 0.037232 CCTCTCCCACTGAAACGGAC 60.037 60.000 0.00 0.00 0.00 4.79
1907 2610 0.388649 CTCTCCCACTGAAACGGACG 60.389 60.000 0.00 0.00 0.00 4.79
1908 2611 2.027625 CTCCCACTGAAACGGACGC 61.028 63.158 0.00 0.00 0.00 5.19
1909 2612 3.411351 CCCACTGAAACGGACGCG 61.411 66.667 3.53 3.53 0.00 6.01
1910 2613 4.072088 CCACTGAAACGGACGCGC 62.072 66.667 5.73 0.00 0.00 6.86
1911 2614 3.036084 CACTGAAACGGACGCGCT 61.036 61.111 5.73 0.00 0.00 5.92
1912 2615 3.036084 ACTGAAACGGACGCGCTG 61.036 61.111 5.73 6.95 0.00 5.18
1913 2616 3.777925 CTGAAACGGACGCGCTGG 61.778 66.667 5.73 0.00 0.00 4.85
2040 2781 2.910688 TCGTGAAGAAGAGTGGCTTT 57.089 45.000 0.00 0.00 36.83 3.51
2041 2782 2.483876 TCGTGAAGAAGAGTGGCTTTG 58.516 47.619 0.00 0.00 36.83 2.77
2042 2783 2.158957 TCGTGAAGAAGAGTGGCTTTGT 60.159 45.455 0.00 0.00 36.83 2.83
2043 2784 2.614057 CGTGAAGAAGAGTGGCTTTGTT 59.386 45.455 0.00 0.00 36.83 2.83
2090 2831 3.774766 TGCTCACATCCATGTACTTAGGT 59.225 43.478 0.00 0.00 39.39 3.08
2130 2874 9.685828 AGCACTATTACTACGTACTACTAGTAC 57.314 37.037 14.27 14.27 45.71 2.73
2215 2967 6.261381 ACAGCCTCTCTCTAATTAGTTAGTCG 59.739 42.308 12.19 6.86 38.72 4.18
2258 3014 2.124236 AGTACTCGAGAGGCCCGG 60.124 66.667 21.68 0.00 0.00 5.73
2273 3029 0.529119 CCCGGGAATGTAGTACGCAC 60.529 60.000 18.48 0.00 0.00 5.34
2279 3035 1.058695 GAATGTAGTACGCACACGCAC 59.941 52.381 5.61 0.00 45.53 5.34
2301 3057 4.202050 ACACTGTTGTTGATCCTTGAAAGC 60.202 41.667 0.00 0.00 28.43 3.51
2313 3069 3.384467 TCCTTGAAAGCTTCAGTTTTGGG 59.616 43.478 0.00 0.00 41.38 4.12
2327 3083 6.760291 TCAGTTTTGGGTTGTAGTTTTGTTT 58.240 32.000 0.00 0.00 0.00 2.83
2388 3184 4.742659 CGTACTCTCCTACGTACTTACCTC 59.257 50.000 0.00 0.00 35.74 3.85
2406 3202 4.699994 ACCTCAAGGAAGAAGATAAGGGA 58.300 43.478 2.30 0.00 38.94 4.20
2561 3358 1.402968 TGATTCTAGGGTACGTCACGC 59.597 52.381 0.00 0.00 40.33 5.34
2563 3360 1.089920 TTCTAGGGTACGTCACGCTC 58.910 55.000 14.64 0.00 46.91 5.03
2564 3361 0.036105 TCTAGGGTACGTCACGCTCA 60.036 55.000 14.64 4.75 46.91 4.26
2565 3362 0.377554 CTAGGGTACGTCACGCTCAG 59.622 60.000 14.64 9.34 46.91 3.35
2566 3363 0.036105 TAGGGTACGTCACGCTCAGA 60.036 55.000 14.64 0.78 46.91 3.27
2567 3364 1.136984 GGGTACGTCACGCTCAGAG 59.863 63.158 0.00 0.00 37.14 3.35
2568 3365 1.514443 GGTACGTCACGCTCAGAGC 60.514 63.158 12.94 12.94 38.02 4.09
2569 3366 1.514443 GTACGTCACGCTCAGAGCC 60.514 63.158 17.16 1.50 38.18 4.70
2580 3377 1.202330 CTCAGAGCCTCAGACCCATT 58.798 55.000 0.00 0.00 0.00 3.16
2588 3385 2.106166 GCCTCAGACCCATTCATCAGAT 59.894 50.000 0.00 0.00 0.00 2.90
2589 3386 3.741249 CCTCAGACCCATTCATCAGATG 58.259 50.000 3.71 3.71 0.00 2.90
2590 3387 3.390311 CCTCAGACCCATTCATCAGATGA 59.610 47.826 9.21 9.21 37.55 2.92
2591 3388 4.041815 CCTCAGACCCATTCATCAGATGAT 59.958 45.833 14.11 0.00 39.39 2.45
2592 3389 5.224821 TCAGACCCATTCATCAGATGATC 57.775 43.478 14.11 8.22 39.39 2.92
2593 3390 4.657039 TCAGACCCATTCATCAGATGATCA 59.343 41.667 14.11 0.00 39.39 2.92
2594 3391 4.998033 CAGACCCATTCATCAGATGATCAG 59.002 45.833 14.11 7.03 39.39 2.90
2595 3392 4.906060 AGACCCATTCATCAGATGATCAGA 59.094 41.667 14.11 0.00 39.39 3.27
2690 3487 2.997986 GCTTGCTTGGATTTGTTGGATG 59.002 45.455 0.00 0.00 0.00 3.51
2756 3553 9.970395 ATATAAATGTGCATGTAACCATTTGAG 57.030 29.630 17.14 0.00 37.87 3.02
2778 3575 9.829507 TTGAGTTTATTGGACAATCAAACAAAT 57.170 25.926 19.75 9.20 32.78 2.32
2779 3576 9.829507 TGAGTTTATTGGACAATCAAACAAATT 57.170 25.926 19.75 8.01 32.78 1.82
2781 3578 9.829507 AGTTTATTGGACAATCAAACAAATTCA 57.170 25.926 19.75 0.00 32.78 2.57
2783 3580 9.829507 TTTATTGGACAATCAAACAAATTCAGT 57.170 25.926 0.03 0.00 32.50 3.41
2784 3581 9.829507 TTATTGGACAATCAAACAAATTCAGTT 57.170 25.926 0.03 0.00 32.50 3.16
2785 3582 8.735692 ATTGGACAATCAAACAAATTCAGTTT 57.264 26.923 3.81 3.81 39.61 2.66
2786 3583 8.558973 TTGGACAATCAAACAAATTCAGTTTT 57.441 26.923 6.31 0.00 37.10 2.43
2787 3584 7.972527 TGGACAATCAAACAAATTCAGTTTTG 58.027 30.769 6.31 5.95 41.37 2.44
2788 3585 6.906678 GGACAATCAAACAAATTCAGTTTTGC 59.093 34.615 6.31 0.00 39.65 3.68
2789 3586 6.784176 ACAATCAAACAAATTCAGTTTTGCC 58.216 32.000 6.31 0.00 39.65 4.52
2790 3587 6.373774 ACAATCAAACAAATTCAGTTTTGCCA 59.626 30.769 6.31 0.00 39.65 4.92
2791 3588 6.607735 ATCAAACAAATTCAGTTTTGCCAG 57.392 33.333 6.31 0.00 39.65 4.85
2792 3589 5.728471 TCAAACAAATTCAGTTTTGCCAGA 58.272 33.333 6.31 0.11 39.65 3.86
2793 3590 6.347696 TCAAACAAATTCAGTTTTGCCAGAT 58.652 32.000 6.31 0.00 39.65 2.90
2794 3591 6.479660 TCAAACAAATTCAGTTTTGCCAGATC 59.520 34.615 6.31 0.00 39.65 2.75
2795 3592 4.549458 ACAAATTCAGTTTTGCCAGATCG 58.451 39.130 0.00 0.00 39.65 3.69
2796 3593 2.927553 ATTCAGTTTTGCCAGATCGC 57.072 45.000 0.00 0.00 0.00 4.58
2797 3594 1.896220 TTCAGTTTTGCCAGATCGCT 58.104 45.000 0.00 0.00 0.00 4.93
2798 3595 2.760634 TCAGTTTTGCCAGATCGCTA 57.239 45.000 0.00 0.00 0.00 4.26
2799 3596 3.266510 TCAGTTTTGCCAGATCGCTAT 57.733 42.857 0.00 0.00 0.00 2.97
2800 3597 4.400529 TCAGTTTTGCCAGATCGCTATA 57.599 40.909 0.00 0.00 0.00 1.31
2801 3598 4.960938 TCAGTTTTGCCAGATCGCTATAT 58.039 39.130 0.00 0.00 0.00 0.86
2802 3599 6.096673 TCAGTTTTGCCAGATCGCTATATA 57.903 37.500 0.00 0.00 0.00 0.86
2803 3600 6.159293 TCAGTTTTGCCAGATCGCTATATAG 58.841 40.000 5.30 5.30 0.00 1.31
2804 3601 5.928839 CAGTTTTGCCAGATCGCTATATAGT 59.071 40.000 11.38 0.00 0.00 2.12
2805 3602 5.928839 AGTTTTGCCAGATCGCTATATAGTG 59.071 40.000 15.86 15.86 35.21 2.74
2806 3603 3.510388 TGCCAGATCGCTATATAGTGC 57.490 47.619 16.96 5.77 33.96 4.40
2807 3604 3.092301 TGCCAGATCGCTATATAGTGCT 58.908 45.455 16.96 8.75 33.96 4.40
2808 3605 3.511540 TGCCAGATCGCTATATAGTGCTT 59.488 43.478 16.96 8.07 33.96 3.91
2809 3606 3.862267 GCCAGATCGCTATATAGTGCTTG 59.138 47.826 16.96 13.70 33.96 4.01
2810 3607 4.380973 GCCAGATCGCTATATAGTGCTTGA 60.381 45.833 16.96 2.13 33.96 3.02
2811 3608 5.098893 CCAGATCGCTATATAGTGCTTGAC 58.901 45.833 16.96 7.39 33.96 3.18
2812 3609 5.105957 CCAGATCGCTATATAGTGCTTGACT 60.106 44.000 16.96 9.12 38.88 3.41
2813 3610 6.385843 CAGATCGCTATATAGTGCTTGACTT 58.614 40.000 16.96 0.00 35.96 3.01
2814 3611 6.307558 CAGATCGCTATATAGTGCTTGACTTG 59.692 42.308 16.96 6.09 35.96 3.16
2815 3612 5.515797 TCGCTATATAGTGCTTGACTTGT 57.484 39.130 16.96 0.00 35.96 3.16
2816 3613 6.628919 TCGCTATATAGTGCTTGACTTGTA 57.371 37.500 16.96 0.00 35.96 2.41
2817 3614 6.436261 TCGCTATATAGTGCTTGACTTGTAC 58.564 40.000 16.96 0.00 35.96 2.90
2818 3615 6.038936 TCGCTATATAGTGCTTGACTTGTACA 59.961 38.462 16.96 0.00 35.96 2.90
2819 3616 6.695713 CGCTATATAGTGCTTGACTTGTACAA 59.304 38.462 10.27 8.28 35.96 2.41
2820 3617 7.382488 CGCTATATAGTGCTTGACTTGTACAAT 59.618 37.037 9.13 0.00 35.96 2.71
2821 3618 9.692749 GCTATATAGTGCTTGACTTGTACAATA 57.307 33.333 9.13 0.00 35.96 1.90
2826 3623 7.986085 AGTGCTTGACTTGTACAATATTTCT 57.014 32.000 9.13 0.00 0.00 2.52
2827 3624 8.396272 AGTGCTTGACTTGTACAATATTTCTT 57.604 30.769 9.13 0.00 0.00 2.52
2828 3625 9.502091 AGTGCTTGACTTGTACAATATTTCTTA 57.498 29.630 9.13 0.00 0.00 2.10
2857 3654 8.786898 ACATAAATGAGACATGTATTACCATGC 58.213 33.333 0.00 0.00 44.88 4.06
2858 3655 8.785946 CATAAATGAGACATGTATTACCATGCA 58.214 33.333 0.00 0.00 44.88 3.96
2859 3656 6.624352 AATGAGACATGTATTACCATGCAC 57.376 37.500 0.00 0.00 44.88 4.57
2860 3657 5.096443 TGAGACATGTATTACCATGCACA 57.904 39.130 0.00 0.00 44.88 4.57
2861 3658 5.495640 TGAGACATGTATTACCATGCACAA 58.504 37.500 0.00 0.00 44.88 3.33
2862 3659 5.942826 TGAGACATGTATTACCATGCACAAA 59.057 36.000 0.00 0.00 44.88 2.83
2863 3660 6.432472 TGAGACATGTATTACCATGCACAAAA 59.568 34.615 0.00 0.00 44.88 2.44
2864 3661 7.040132 TGAGACATGTATTACCATGCACAAAAA 60.040 33.333 0.00 0.00 44.88 1.94
2865 3662 7.315142 AGACATGTATTACCATGCACAAAAAG 58.685 34.615 0.00 0.00 44.88 2.27
2866 3663 6.991938 ACATGTATTACCATGCACAAAAAGT 58.008 32.000 0.00 0.00 44.88 2.66
2867 3664 8.116651 ACATGTATTACCATGCACAAAAAGTA 57.883 30.769 0.00 0.00 44.88 2.24
2868 3665 8.748412 ACATGTATTACCATGCACAAAAAGTAT 58.252 29.630 0.00 0.00 44.88 2.12
2874 3671 6.832520 ACCATGCACAAAAAGTATATCACA 57.167 33.333 0.00 0.00 0.00 3.58
2875 3672 6.620678 ACCATGCACAAAAAGTATATCACAC 58.379 36.000 0.00 0.00 0.00 3.82
2876 3673 6.208402 ACCATGCACAAAAAGTATATCACACA 59.792 34.615 0.00 0.00 0.00 3.72
2877 3674 7.089538 CCATGCACAAAAAGTATATCACACAA 58.910 34.615 0.00 0.00 0.00 3.33
2878 3675 7.598118 CCATGCACAAAAAGTATATCACACAAA 59.402 33.333 0.00 0.00 0.00 2.83
2879 3676 8.976471 CATGCACAAAAAGTATATCACACAAAA 58.024 29.630 0.00 0.00 0.00 2.44
2880 3677 8.572828 TGCACAAAAAGTATATCACACAAAAG 57.427 30.769 0.00 0.00 0.00 2.27
2881 3678 8.409371 TGCACAAAAAGTATATCACACAAAAGA 58.591 29.630 0.00 0.00 0.00 2.52
2882 3679 9.243637 GCACAAAAAGTATATCACACAAAAGAA 57.756 29.630 0.00 0.00 0.00 2.52
2887 3684 9.463443 AAAAGTATATCACACAAAAGAACAAGC 57.537 29.630 0.00 0.00 0.00 4.01
2888 3685 7.744087 AGTATATCACACAAAAGAACAAGCA 57.256 32.000 0.00 0.00 0.00 3.91
2889 3686 8.165239 AGTATATCACACAAAAGAACAAGCAA 57.835 30.769 0.00 0.00 0.00 3.91
2890 3687 8.796475 AGTATATCACACAAAAGAACAAGCAAT 58.204 29.630 0.00 0.00 0.00 3.56
2891 3688 9.410556 GTATATCACACAAAAGAACAAGCAATT 57.589 29.630 0.00 0.00 0.00 2.32
2892 3689 6.592798 ATCACACAAAAGAACAAGCAATTG 57.407 33.333 0.00 0.00 0.00 2.32
2893 3690 4.869297 TCACACAAAAGAACAAGCAATTGG 59.131 37.500 7.72 0.00 0.00 3.16
2894 3691 4.034279 CACACAAAAGAACAAGCAATTGGG 59.966 41.667 7.72 0.00 0.00 4.12
2895 3692 4.190772 CACAAAAGAACAAGCAATTGGGT 58.809 39.130 7.72 0.00 0.00 4.51
2896 3693 4.635324 CACAAAAGAACAAGCAATTGGGTT 59.365 37.500 7.72 0.00 37.82 4.11
2897 3694 4.875536 ACAAAAGAACAAGCAATTGGGTTC 59.124 37.500 7.72 0.00 39.83 3.62
2898 3695 4.751767 AAAGAACAAGCAATTGGGTTCA 57.248 36.364 7.72 0.00 41.49 3.18
2899 3696 4.751767 AAGAACAAGCAATTGGGTTCAA 57.248 36.364 7.72 0.00 41.49 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 6.659745 ATGATACATGCCAAAATGCTACAT 57.340 33.333 0.00 0.00 0.00 2.29
68 69 6.939132 TGCTCCAAGATACTAGTACTACAC 57.061 41.667 4.31 0.00 0.00 2.90
325 327 7.378181 CCTGCCAAGACAAACACTTTAATAAT 58.622 34.615 0.00 0.00 0.00 1.28
326 328 6.239176 CCCTGCCAAGACAAACACTTTAATAA 60.239 38.462 0.00 0.00 0.00 1.40
327 329 5.242838 CCCTGCCAAGACAAACACTTTAATA 59.757 40.000 0.00 0.00 0.00 0.98
374 376 7.116948 GCATATGAGTATATGACACACTGGTTC 59.883 40.741 6.97 0.00 45.92 3.62
476 478 1.608542 GCATGCCACAATCCTTGCAAA 60.609 47.619 6.36 0.00 37.27 3.68
548 850 8.911918 TGCTAGAAAAATAACACTTGGAAGTA 57.088 30.769 0.00 0.00 37.08 2.24
613 917 5.495926 AAGAGATGAGGAGAATGTTGTGT 57.504 39.130 0.00 0.00 0.00 3.72
646 953 3.900601 TGTTTGGATTTGTGTGCCCTAAT 59.099 39.130 0.00 0.00 0.00 1.73
759 1369 2.615773 GTAGGGGAGGAGGGGAGG 59.384 72.222 0.00 0.00 0.00 4.30
769 1379 1.152525 GAGATGGCGAGGTAGGGGA 60.153 63.158 0.00 0.00 0.00 4.81
770 1380 0.833834 ATGAGATGGCGAGGTAGGGG 60.834 60.000 0.00 0.00 0.00 4.79
771 1381 0.605589 GATGAGATGGCGAGGTAGGG 59.394 60.000 0.00 0.00 0.00 3.53
908 1540 2.959707 GCTAGCTAGCTTAGGTTGAGGA 59.040 50.000 33.71 0.00 45.62 3.71
955 1596 3.759618 CTGGCTACTATACTACTGCTCCC 59.240 52.174 0.00 0.00 0.00 4.30
981 1622 1.131638 TGGCAGAAGTGAAGTGAGGT 58.868 50.000 0.00 0.00 0.00 3.85
1030 1685 1.150081 CCATCATCTGGGAGGCACC 59.850 63.158 0.00 0.00 41.82 5.01
1031 1686 1.527844 GCCATCATCTGGGAGGCAC 60.528 63.158 0.00 0.00 46.06 5.01
1536 2206 3.747976 GGCACCGGCATGGAACAC 61.748 66.667 0.00 0.00 43.71 3.32
1780 2462 4.778143 GAAGCCGGCCACCATCGT 62.778 66.667 26.15 0.00 0.00 3.73
1860 2563 2.582978 GGGGAGTAGCCGTTGTCC 59.417 66.667 0.00 0.00 37.63 4.02
1904 2607 4.527157 GAGCAATGCCAGCGCGTC 62.527 66.667 8.43 0.00 38.08 5.19
1906 2609 2.370824 CTAAGAGCAATGCCAGCGCG 62.371 60.000 0.00 0.00 38.08 6.86
1907 2610 1.354506 CTAAGAGCAATGCCAGCGC 59.645 57.895 0.00 0.00 37.01 5.92
1908 2611 1.354506 GCTAAGAGCAATGCCAGCG 59.645 57.895 0.00 0.00 41.89 5.18
1909 2612 1.732308 GGCTAAGAGCAATGCCAGC 59.268 57.895 0.00 5.91 44.75 4.85
1912 2615 2.049888 AAGAGGCTAAGAGCAATGCC 57.950 50.000 0.00 0.00 44.75 4.40
1913 2616 2.541762 CGTAAGAGGCTAAGAGCAATGC 59.458 50.000 0.00 0.00 41.87 3.56
1916 2619 4.015084 AGTACGTAAGAGGCTAAGAGCAA 58.985 43.478 0.00 0.00 42.27 3.91
1917 2620 3.618351 AGTACGTAAGAGGCTAAGAGCA 58.382 45.455 0.00 0.00 42.27 4.26
1918 2621 3.626670 TGAGTACGTAAGAGGCTAAGAGC 59.373 47.826 0.00 0.00 40.38 4.09
1919 2622 4.877251 ACTGAGTACGTAAGAGGCTAAGAG 59.123 45.833 0.00 0.00 43.62 2.85
1967 2677 5.109903 CGAAGCAAACACTACCTAGCTAAT 58.890 41.667 0.00 0.00 0.00 1.73
2090 2831 8.792830 AGTAATAGTGCTGCTAATTGAAAGAA 57.207 30.769 0.00 0.00 32.72 2.52
2130 2874 5.023920 CGTGCATGCATGAAAACTTACTAG 58.976 41.667 31.95 7.10 35.09 2.57
2194 2943 7.411274 CACACGACTAACTAATTAGAGAGAGG 58.589 42.308 19.38 12.93 40.38 3.69
2215 2967 2.156098 TCCGCCACTTTAATTCCACAC 58.844 47.619 0.00 0.00 0.00 3.82
2255 3011 0.173935 TGTGCGTACTACATTCCCGG 59.826 55.000 4.97 0.00 0.00 5.73
2258 3014 0.643820 GCGTGTGCGTACTACATTCC 59.356 55.000 4.97 0.00 40.81 3.01
2273 3029 1.334059 GGATCAACAACAGTGTGCGTG 60.334 52.381 0.00 0.00 38.27 5.34
2279 3035 4.037208 AGCTTTCAAGGATCAACAACAGTG 59.963 41.667 0.00 0.00 0.00 3.66
2301 3057 6.394809 ACAAAACTACAACCCAAAACTGAAG 58.605 36.000 0.00 0.00 0.00 3.02
2313 3069 9.612620 CCTATCTGAATCAAACAAAACTACAAC 57.387 33.333 0.00 0.00 0.00 3.32
2327 3083 1.754745 GGCCGGCCTATCTGAATCA 59.245 57.895 38.76 0.00 0.00 2.57
2388 3184 9.549078 GTACTATTTCCCTTATCTTCTTCCTTG 57.451 37.037 0.00 0.00 0.00 3.61
2445 3241 3.551846 ACCTTTCCGTTGAACTGTCAAT 58.448 40.909 0.00 0.00 45.38 2.57
2516 3313 3.755628 GTACCTGGCGAGTGGCGA 61.756 66.667 0.00 0.00 44.92 5.54
2517 3314 3.296709 AAGTACCTGGCGAGTGGCG 62.297 63.158 0.00 0.00 44.92 5.69
2518 3315 1.741770 CAAGTACCTGGCGAGTGGC 60.742 63.158 0.00 0.00 42.51 5.01
2519 3316 1.079127 CCAAGTACCTGGCGAGTGG 60.079 63.158 0.00 0.00 0.00 4.00
2520 3317 0.670546 CACCAAGTACCTGGCGAGTG 60.671 60.000 10.60 0.00 40.45 3.51
2521 3318 1.671742 CACCAAGTACCTGGCGAGT 59.328 57.895 10.60 0.00 40.45 4.18
2522 3319 1.741770 GCACCAAGTACCTGGCGAG 60.742 63.158 10.60 2.45 40.45 5.03
2561 3358 1.138661 GAATGGGTCTGAGGCTCTGAG 59.861 57.143 22.47 9.75 0.00 3.35
2562 3359 1.198713 GAATGGGTCTGAGGCTCTGA 58.801 55.000 18.78 18.78 0.00 3.27
2563 3360 0.907486 TGAATGGGTCTGAGGCTCTG 59.093 55.000 16.72 15.59 0.00 3.35
2564 3361 1.767681 GATGAATGGGTCTGAGGCTCT 59.232 52.381 16.72 0.00 0.00 4.09
2565 3362 1.487976 TGATGAATGGGTCTGAGGCTC 59.512 52.381 7.79 7.79 0.00 4.70
2566 3363 1.489649 CTGATGAATGGGTCTGAGGCT 59.510 52.381 0.00 0.00 0.00 4.58
2567 3364 1.487976 TCTGATGAATGGGTCTGAGGC 59.512 52.381 0.00 0.00 0.00 4.70
2568 3365 3.390311 TCATCTGATGAATGGGTCTGAGG 59.610 47.826 17.56 0.00 36.11 3.86
2569 3366 4.684484 TCATCTGATGAATGGGTCTGAG 57.316 45.455 17.56 0.00 36.11 3.35
2580 3377 1.976404 GGCCCTCTGATCATCTGATGA 59.024 52.381 21.55 21.55 44.55 2.92
2588 3385 1.225426 GTGCATGGCCCTCTGATCA 59.775 57.895 0.00 0.00 0.00 2.92
2589 3386 0.394762 TTGTGCATGGCCCTCTGATC 60.395 55.000 0.00 0.00 0.00 2.92
2590 3387 0.040058 TTTGTGCATGGCCCTCTGAT 59.960 50.000 0.00 0.00 0.00 2.90
2591 3388 0.178967 TTTTGTGCATGGCCCTCTGA 60.179 50.000 0.00 0.00 0.00 3.27
2592 3389 0.899720 ATTTTGTGCATGGCCCTCTG 59.100 50.000 0.00 0.00 0.00 3.35
2593 3390 0.899720 CATTTTGTGCATGGCCCTCT 59.100 50.000 0.00 0.00 0.00 3.69
2594 3391 0.609662 ACATTTTGTGCATGGCCCTC 59.390 50.000 0.00 0.00 0.00 4.30
2595 3392 1.935799 TACATTTTGTGCATGGCCCT 58.064 45.000 0.00 0.00 0.00 5.19
2720 3517 8.757982 ACATGCACATTTATATCTTCTCCTTT 57.242 30.769 0.00 0.00 0.00 3.11
2722 3519 9.277783 GTTACATGCACATTTATATCTTCTCCT 57.722 33.333 0.00 0.00 0.00 3.69
2723 3520 8.507249 GGTTACATGCACATTTATATCTTCTCC 58.493 37.037 0.00 0.00 0.00 3.71
2724 3521 9.056005 TGGTTACATGCACATTTATATCTTCTC 57.944 33.333 0.00 0.00 0.00 2.87
2725 3522 8.978874 TGGTTACATGCACATTTATATCTTCT 57.021 30.769 0.00 0.00 0.00 2.85
2728 3525 9.970395 CAAATGGTTACATGCACATTTATATCT 57.030 29.630 9.56 0.00 40.43 1.98
2729 3526 9.964303 TCAAATGGTTACATGCACATTTATATC 57.036 29.630 9.56 0.00 40.43 1.63
2730 3527 9.970395 CTCAAATGGTTACATGCACATTTATAT 57.030 29.630 9.56 0.00 40.43 0.86
2731 3528 8.965819 ACTCAAATGGTTACATGCACATTTATA 58.034 29.630 9.56 2.86 40.43 0.98
2733 3530 7.225784 ACTCAAATGGTTACATGCACATTTA 57.774 32.000 9.56 1.24 40.43 1.40
2735 3532 5.726980 ACTCAAATGGTTACATGCACATT 57.273 34.783 0.00 0.00 37.40 2.71
2736 3533 5.726980 AACTCAAATGGTTACATGCACAT 57.273 34.783 0.00 0.00 37.40 3.21
2737 3534 5.528043 AAACTCAAATGGTTACATGCACA 57.472 34.783 0.00 0.00 37.40 4.57
2738 3535 7.063308 CCAATAAACTCAAATGGTTACATGCAC 59.937 37.037 0.00 0.00 37.40 4.57
2739 3536 7.039434 TCCAATAAACTCAAATGGTTACATGCA 60.039 33.333 0.00 0.00 37.40 3.96
2778 3575 1.896220 AGCGATCTGGCAAAACTGAA 58.104 45.000 0.00 0.00 34.64 3.02
2779 3576 2.760634 TAGCGATCTGGCAAAACTGA 57.239 45.000 0.00 0.00 34.64 3.41
2780 3577 5.928839 ACTATATAGCGATCTGGCAAAACTG 59.071 40.000 9.78 0.00 34.64 3.16
2781 3578 5.928839 CACTATATAGCGATCTGGCAAAACT 59.071 40.000 9.78 0.00 34.64 2.66
2782 3579 5.389935 GCACTATATAGCGATCTGGCAAAAC 60.390 44.000 9.78 0.00 34.64 2.43
2783 3580 4.690748 GCACTATATAGCGATCTGGCAAAA 59.309 41.667 9.78 0.00 34.64 2.44
2784 3581 4.021104 AGCACTATATAGCGATCTGGCAAA 60.021 41.667 9.78 0.00 35.48 3.68
2785 3582 3.511540 AGCACTATATAGCGATCTGGCAA 59.488 43.478 9.78 0.00 35.48 4.52
2786 3583 3.092301 AGCACTATATAGCGATCTGGCA 58.908 45.455 9.78 0.00 35.48 4.92
2787 3584 3.791973 AGCACTATATAGCGATCTGGC 57.208 47.619 9.78 3.14 35.48 4.85
2788 3585 5.098893 GTCAAGCACTATATAGCGATCTGG 58.901 45.833 9.78 0.47 35.48 3.86
2789 3586 5.948588 AGTCAAGCACTATATAGCGATCTG 58.051 41.667 9.78 1.64 31.37 2.90
2790 3587 6.015856 ACAAGTCAAGCACTATATAGCGATCT 60.016 38.462 9.78 0.00 32.30 2.75
2791 3588 6.153067 ACAAGTCAAGCACTATATAGCGATC 58.847 40.000 9.78 0.00 32.30 3.69
2792 3589 6.090483 ACAAGTCAAGCACTATATAGCGAT 57.910 37.500 9.78 0.00 32.30 4.58
2793 3590 5.515797 ACAAGTCAAGCACTATATAGCGA 57.484 39.130 9.78 0.00 32.30 4.93
2794 3591 6.206498 TGTACAAGTCAAGCACTATATAGCG 58.794 40.000 9.78 1.29 32.30 4.26
2795 3592 8.594881 ATTGTACAAGTCAAGCACTATATAGC 57.405 34.615 14.65 0.00 32.30 2.97
2800 3597 9.672673 AGAAATATTGTACAAGTCAAGCACTAT 57.327 29.630 14.65 0.99 32.30 2.12
2801 3598 9.502091 AAGAAATATTGTACAAGTCAAGCACTA 57.498 29.630 14.65 0.00 32.30 2.74
2802 3599 7.986085 AGAAATATTGTACAAGTCAAGCACT 57.014 32.000 14.65 3.53 36.64 4.40
2848 3645 8.965819 TGTGATATACTTTTTGTGCATGGTAAT 58.034 29.630 0.00 0.00 0.00 1.89
2849 3646 8.240682 GTGTGATATACTTTTTGTGCATGGTAA 58.759 33.333 0.00 0.00 0.00 2.85
2850 3647 7.391833 TGTGTGATATACTTTTTGTGCATGGTA 59.608 33.333 0.00 0.00 0.00 3.25
2851 3648 6.208402 TGTGTGATATACTTTTTGTGCATGGT 59.792 34.615 0.00 0.00 0.00 3.55
2852 3649 6.619744 TGTGTGATATACTTTTTGTGCATGG 58.380 36.000 0.00 0.00 0.00 3.66
2853 3650 8.518151 TTTGTGTGATATACTTTTTGTGCATG 57.482 30.769 0.00 0.00 0.00 4.06
2854 3651 9.195411 CTTTTGTGTGATATACTTTTTGTGCAT 57.805 29.630 0.00 0.00 0.00 3.96
2855 3652 8.409371 TCTTTTGTGTGATATACTTTTTGTGCA 58.591 29.630 0.00 0.00 0.00 4.57
2856 3653 8.795786 TCTTTTGTGTGATATACTTTTTGTGC 57.204 30.769 0.00 0.00 0.00 4.57
2861 3658 9.463443 GCTTGTTCTTTTGTGTGATATACTTTT 57.537 29.630 0.00 0.00 0.00 2.27
2862 3659 8.629158 TGCTTGTTCTTTTGTGTGATATACTTT 58.371 29.630 0.00 0.00 0.00 2.66
2863 3660 8.165239 TGCTTGTTCTTTTGTGTGATATACTT 57.835 30.769 0.00 0.00 0.00 2.24
2864 3661 7.744087 TGCTTGTTCTTTTGTGTGATATACT 57.256 32.000 0.00 0.00 0.00 2.12
2865 3662 8.970691 ATTGCTTGTTCTTTTGTGTGATATAC 57.029 30.769 0.00 0.00 0.00 1.47
2866 3663 9.409312 CAATTGCTTGTTCTTTTGTGTGATATA 57.591 29.630 0.00 0.00 0.00 0.86
2867 3664 7.385752 CCAATTGCTTGTTCTTTTGTGTGATAT 59.614 33.333 0.00 0.00 0.00 1.63
2868 3665 6.700960 CCAATTGCTTGTTCTTTTGTGTGATA 59.299 34.615 0.00 0.00 0.00 2.15
2869 3666 5.524646 CCAATTGCTTGTTCTTTTGTGTGAT 59.475 36.000 0.00 0.00 0.00 3.06
2870 3667 4.869297 CCAATTGCTTGTTCTTTTGTGTGA 59.131 37.500 0.00 0.00 0.00 3.58
2871 3668 4.034279 CCCAATTGCTTGTTCTTTTGTGTG 59.966 41.667 0.00 0.00 0.00 3.82
2872 3669 4.190772 CCCAATTGCTTGTTCTTTTGTGT 58.809 39.130 0.00 0.00 0.00 3.72
2873 3670 4.190772 ACCCAATTGCTTGTTCTTTTGTG 58.809 39.130 0.00 0.00 0.00 3.33
2874 3671 4.486125 ACCCAATTGCTTGTTCTTTTGT 57.514 36.364 0.00 0.00 0.00 2.83
2875 3672 4.874966 TGAACCCAATTGCTTGTTCTTTTG 59.125 37.500 22.87 0.96 38.29 2.44
2876 3673 5.096443 TGAACCCAATTGCTTGTTCTTTT 57.904 34.783 22.87 0.92 38.29 2.27
2877 3674 4.751767 TGAACCCAATTGCTTGTTCTTT 57.248 36.364 22.87 2.37 38.29 2.52
2878 3675 4.751767 TTGAACCCAATTGCTTGTTCTT 57.248 36.364 22.87 1.45 38.29 2.52


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

AutoCloner maintained by Alex Coulton.