Multiple sequence alignment - TraesCS4D01G290100

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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 TraesCS4D01G290100 chr4D 100.000 2990 0 0 1 2990 461273731 461276720 0.000000e+00 5522.0
1 TraesCS4D01G290100 chr4B 92.889 2728 119 24 57 2760 576400744 576403420 0.000000e+00 3893.0
2 TraesCS4D01G290100 chr4B 94.595 148 5 2 2843 2990 576403461 576403605 3.000000e-55 226.0
3 TraesCS4D01G290100 chr4B 95.745 47 2 0 2897 2943 576446355 576446401 3.200000e-10 76.8
4 TraesCS4D01G290100 chr4A 92.323 1980 93 19 389 2346 7326932 7324990 0.000000e+00 2760.0
5 TraesCS4D01G290100 chr4A 85.902 305 30 6 2380 2679 7324988 7324692 2.240000e-81 313.0
6 TraesCS4D01G290100 chr4A 83.974 312 23 7 75 359 7327238 7326927 1.060000e-69 274.0
7 TraesCS4D01G290100 chr2D 84.639 319 25 11 1258 1569 112556189 112556490 2.250000e-76 296.0
8 TraesCS4D01G290100 chr2D 100.000 33 0 0 1638 1670 112556568 112556600 8.950000e-06 62.1
9 TraesCS4D01G290100 chr1D 100.000 28 0 0 2255 2282 194672001 194672028 5.000000e-03 52.8


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 TraesCS4D01G290100 chr4D 461273731 461276720 2989 False 5522.000000 5522 100.000000 1 2990 1 chr4D.!!$F1 2989
1 TraesCS4D01G290100 chr4B 576400744 576403605 2861 False 2059.500000 3893 93.742000 57 2990 2 chr4B.!!$F2 2933
2 TraesCS4D01G290100 chr4A 7324692 7327238 2546 True 1115.666667 2760 87.399667 75 2679 3 chr4A.!!$R1 2604

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
179 185 0.320374 ATGATTGGTGACACGACGGT 59.68 50.0 0.0 0.0 42.67 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 2085 0.326264 ATTGGTCTGAGTCACCTGGC 59.674 55.0 0.0 0.0 34.66 4.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.189693 CAGGCGATCTATCTATCAGTCTATC 57.810 44.000 0.00 0.00 0.00 2.08
25 26 6.992123 CAGGCGATCTATCTATCAGTCTATCT 59.008 42.308 0.00 0.00 0.00 1.98
26 27 7.171508 CAGGCGATCTATCTATCAGTCTATCTC 59.828 44.444 0.00 0.00 0.00 2.75
27 28 7.071196 AGGCGATCTATCTATCAGTCTATCTCT 59.929 40.741 0.00 0.00 0.00 3.10
28 29 8.364894 GGCGATCTATCTATCAGTCTATCTCTA 58.635 40.741 0.00 0.00 0.00 2.43
29 30 9.411801 GCGATCTATCTATCAGTCTATCTCTAG 57.588 40.741 0.00 0.00 0.00 2.43
30 31 9.411801 CGATCTATCTATCAGTCTATCTCTAGC 57.588 40.741 0.00 0.00 0.00 3.42
34 35 9.698309 CTATCTATCAGTCTATCTCTAGCTAGC 57.302 40.741 16.35 6.62 0.00 3.42
35 36 7.733773 TCTATCAGTCTATCTCTAGCTAGCT 57.266 40.000 23.12 23.12 0.00 3.32
36 37 8.832458 TCTATCAGTCTATCTCTAGCTAGCTA 57.168 38.462 22.85 22.85 0.00 3.32
37 38 8.692710 TCTATCAGTCTATCTCTAGCTAGCTAC 58.307 40.741 20.67 10.91 0.00 3.58
38 39 6.045072 TCAGTCTATCTCTAGCTAGCTACC 57.955 45.833 20.67 1.94 0.00 3.18
39 40 4.868171 CAGTCTATCTCTAGCTAGCTACCG 59.132 50.000 20.67 12.15 0.00 4.02
40 41 4.081309 AGTCTATCTCTAGCTAGCTACCGG 60.081 50.000 20.67 11.42 0.00 5.28
41 42 1.828979 ATCTCTAGCTAGCTACCGGC 58.171 55.000 20.67 0.00 42.19 6.13
51 52 4.415332 CTACCGGCTGCGTGTCGT 62.415 66.667 0.00 0.00 43.10 4.34
52 53 4.710695 TACCGGCTGCGTGTCGTG 62.711 66.667 0.00 0.00 43.10 4.35
136 142 1.093496 CCGGGTAAAATCCGCCAGAC 61.093 60.000 0.00 0.00 45.60 3.51
150 156 1.618861 CCAGACGCTTACGAACAGAG 58.381 55.000 0.00 0.00 43.93 3.35
157 163 1.871039 GCTTACGAACAGAGCAACCAA 59.129 47.619 0.00 0.00 36.45 3.67
159 165 1.508632 TACGAACAGAGCAACCAAGC 58.491 50.000 0.00 0.00 0.00 4.01
179 185 0.320374 ATGATTGGTGACACGACGGT 59.680 50.000 0.00 0.00 42.67 4.83
189 195 1.361271 CACGACGGTGTGTAGTGGT 59.639 57.895 0.00 0.00 46.67 4.16
240 246 2.420687 GCCGGAGAGATGGTTTTCAGAT 60.421 50.000 5.05 0.00 0.00 2.90
270 296 4.660938 GGAAGCCACGGCCAAGGT 62.661 66.667 2.24 0.00 43.17 3.50
271 297 3.365265 GAAGCCACGGCCAAGGTG 61.365 66.667 2.24 2.38 43.17 4.00
446 477 1.617850 GATCCAGATCCAGTCTCGCAT 59.382 52.381 0.00 0.00 34.00 4.73
447 478 1.489481 TCCAGATCCAGTCTCGCATT 58.511 50.000 0.00 0.00 34.00 3.56
448 479 2.666317 TCCAGATCCAGTCTCGCATTA 58.334 47.619 0.00 0.00 34.00 1.90
449 480 3.031013 TCCAGATCCAGTCTCGCATTAA 58.969 45.455 0.00 0.00 34.00 1.40
451 482 3.557595 CCAGATCCAGTCTCGCATTAAAC 59.442 47.826 0.00 0.00 34.00 2.01
452 483 4.183865 CAGATCCAGTCTCGCATTAAACA 58.816 43.478 0.00 0.00 34.00 2.83
453 484 4.631377 CAGATCCAGTCTCGCATTAAACAA 59.369 41.667 0.00 0.00 34.00 2.83
455 486 5.352569 AGATCCAGTCTCGCATTAAACAAAG 59.647 40.000 0.00 0.00 28.45 2.77
456 487 3.751175 TCCAGTCTCGCATTAAACAAAGG 59.249 43.478 0.00 0.00 0.00 3.11
461 493 6.142320 CAGTCTCGCATTAAACAAAGGAAAAC 59.858 38.462 0.00 0.00 0.00 2.43
507 544 4.760047 CTTCCCTCCCACACGGCG 62.760 72.222 4.80 4.80 0.00 6.46
516 553 3.041940 CACACGGCGTGTTCCCTC 61.042 66.667 39.92 0.00 45.08 4.30
662 699 1.219124 CATCACGGCTGCTGGTACT 59.781 57.895 13.87 0.00 0.00 2.73
663 700 0.459899 CATCACGGCTGCTGGTACTA 59.540 55.000 13.87 0.00 0.00 1.82
664 701 0.460311 ATCACGGCTGCTGGTACTAC 59.540 55.000 13.87 0.00 0.00 2.73
813 851 2.743928 CACGCTGCCTCCCACTTC 60.744 66.667 0.00 0.00 0.00 3.01
814 852 2.925170 ACGCTGCCTCCCACTTCT 60.925 61.111 0.00 0.00 0.00 2.85
830 868 2.989571 ACTTCTCCCCACTTTCAAGGAT 59.010 45.455 0.00 0.00 0.00 3.24
877 919 1.450491 GCCGGAGAAGCTTCCTTCC 60.450 63.158 22.81 21.19 46.97 3.46
927 969 2.802816 GTGATATGGATCTTGTCACCGC 59.197 50.000 12.03 0.00 34.58 5.68
947 989 3.645884 GCGGATTGATTTGATTGGATGG 58.354 45.455 0.00 0.00 0.00 3.51
998 1049 1.671379 CAGCAGCAGCAGCAGAGAA 60.671 57.895 12.92 0.00 45.49 2.87
1122 1173 1.186267 AGTCCCGCTTCTTCGTCCTT 61.186 55.000 0.00 0.00 0.00 3.36
1773 1824 4.722700 ACCATGCCGCTGGACACC 62.723 66.667 13.75 0.00 39.73 4.16
1890 1941 4.874977 GCGTGCTACCGAGGCCTC 62.875 72.222 23.79 23.79 0.00 4.70
1996 2047 1.617263 GCTCCCTGGGCTAGATCGATA 60.617 57.143 8.22 0.00 0.00 2.92
2000 2051 2.232452 CCCTGGGCTAGATCGATACTTG 59.768 54.545 0.00 0.16 0.00 3.16
2028 2085 1.862147 CCAGTAGCGTCGTCGTTCG 60.862 63.158 3.66 7.85 39.49 3.95
2047 2104 0.326264 GCCAGGTGACTCAGACCAAT 59.674 55.000 0.00 0.00 40.21 3.16
2143 2200 5.055642 TGCTCAAGATCTTTTGCTTCATG 57.944 39.130 22.33 5.28 0.00 3.07
2146 2203 5.287170 TCAAGATCTTTTGCTTCATGTCG 57.713 39.130 4.86 0.00 0.00 4.35
2151 2208 1.710249 CTTTTGCTTCATGTCGCGTTG 59.290 47.619 5.77 2.85 0.00 4.10
2152 2209 0.660005 TTTGCTTCATGTCGCGTTGC 60.660 50.000 5.77 0.00 0.00 4.17
2226 2283 0.483770 GGTGGGTGGGGTTTTAGGAA 59.516 55.000 0.00 0.00 0.00 3.36
2300 2357 6.805271 GCCGATGATGATGATGAAAAATTAGG 59.195 38.462 0.00 0.00 0.00 2.69
2309 2366 9.246670 TGATGATGAAAAATTAGGTGAAGTGAT 57.753 29.630 0.00 0.00 0.00 3.06
2338 2395 8.964476 TTTTCAGTCTGAACTTCTTATGAACT 57.036 30.769 14.98 0.00 35.89 3.01
2367 2424 4.879197 TCTTAGCGATGATGGTGATGAT 57.121 40.909 0.00 0.00 0.00 2.45
2368 2425 5.219343 TCTTAGCGATGATGGTGATGATT 57.781 39.130 0.00 0.00 0.00 2.57
2369 2426 6.345096 TCTTAGCGATGATGGTGATGATTA 57.655 37.500 0.00 0.00 0.00 1.75
2370 2427 6.939622 TCTTAGCGATGATGGTGATGATTAT 58.060 36.000 0.00 0.00 0.00 1.28
2371 2428 6.815142 TCTTAGCGATGATGGTGATGATTATG 59.185 38.462 0.00 0.00 0.00 1.90
2372 2429 4.903054 AGCGATGATGGTGATGATTATGT 58.097 39.130 0.00 0.00 0.00 2.29
2373 2430 4.694037 AGCGATGATGGTGATGATTATGTG 59.306 41.667 0.00 0.00 0.00 3.21
2374 2431 4.670992 GCGATGATGGTGATGATTATGTGC 60.671 45.833 0.00 0.00 0.00 4.57
2375 2432 4.694037 CGATGATGGTGATGATTATGTGCT 59.306 41.667 0.00 0.00 0.00 4.40
2376 2433 5.390567 CGATGATGGTGATGATTATGTGCTG 60.391 44.000 0.00 0.00 0.00 4.41
2377 2434 5.038651 TGATGGTGATGATTATGTGCTGA 57.961 39.130 0.00 0.00 0.00 4.26
2419 2477 7.264221 TGTGCTTTGTTATGTGAATGAAAACT 58.736 30.769 0.00 0.00 0.00 2.66
2435 2494 4.097286 TGAAAACTTTGTGTGCCTAACTCC 59.903 41.667 0.00 0.00 0.00 3.85
2474 2533 1.596603 TCATGGTCACTGTTGTGCTG 58.403 50.000 0.00 0.00 43.49 4.41
2498 2559 1.515088 CTAGCGGCGTCACTGTCAG 60.515 63.158 9.37 0.00 0.00 3.51
2537 2598 0.767375 AGGTGACTTGATGTGCACCT 59.233 50.000 15.69 3.77 44.54 4.00
2542 2603 2.292267 GACTTGATGTGCACCTATGGG 58.708 52.381 15.69 0.00 38.88 4.00
2572 2633 4.913924 CCGCTTCTTTTCATCAGTTTCTTG 59.086 41.667 0.00 0.00 0.00 3.02
2574 2635 5.277974 CGCTTCTTTTCATCAGTTTCTTGGA 60.278 40.000 0.00 0.00 0.00 3.53
2576 2637 5.673337 TCTTTTCATCAGTTTCTTGGACG 57.327 39.130 0.00 0.00 0.00 4.79
2582 2643 3.553828 TCAGTTTCTTGGACGGTTCTT 57.446 42.857 0.00 0.00 0.00 2.52
2612 2673 3.018149 ACTAGAGTTTAGGACAGCGAGG 58.982 50.000 0.00 0.00 0.00 4.63
2645 2706 3.735514 GCTACCTCGATCACTTTCCTGAC 60.736 52.174 0.00 0.00 0.00 3.51
2651 2712 2.478709 CGATCACTTTCCTGACTCCTCG 60.479 54.545 0.00 0.00 0.00 4.63
2669 2730 3.249091 CTCGATGGCATGATAGCACTAC 58.751 50.000 3.81 0.00 35.83 2.73
2672 2733 3.553715 CGATGGCATGATAGCACTACACT 60.554 47.826 3.81 0.00 35.83 3.55
2680 2741 6.524586 GCATGATAGCACTACACTTTTTGTTC 59.475 38.462 0.00 0.00 39.91 3.18
2686 2747 4.785341 GCACTACACTTTTTGTTCGTGAGG 60.785 45.833 9.40 0.00 39.20 3.86
2687 2748 2.844122 ACACTTTTTGTTCGTGAGGC 57.156 45.000 0.00 0.00 33.09 4.70
2715 2776 0.541392 ACCTGCCGCACAAGATATGA 59.459 50.000 0.00 0.00 0.00 2.15
2770 2831 8.559536 TCGTTTAATCTCAGAAATTATCATGCC 58.440 33.333 0.00 0.00 0.00 4.40
2771 2832 8.344831 CGTTTAATCTCAGAAATTATCATGCCA 58.655 33.333 0.00 0.00 0.00 4.92
2774 2835 6.835819 ATCTCAGAAATTATCATGCCATGG 57.164 37.500 7.63 7.63 0.00 3.66
2775 2836 5.944135 TCTCAGAAATTATCATGCCATGGA 58.056 37.500 18.40 0.31 0.00 3.41
2776 2837 6.002082 TCTCAGAAATTATCATGCCATGGAG 58.998 40.000 18.40 4.23 0.00 3.86
2777 2838 5.074804 TCAGAAATTATCATGCCATGGAGG 58.925 41.667 18.40 3.37 41.84 4.30
2778 2839 5.074804 CAGAAATTATCATGCCATGGAGGA 58.925 41.667 18.40 9.51 41.22 3.71
2779 2840 5.537295 CAGAAATTATCATGCCATGGAGGAA 59.463 40.000 18.40 0.00 41.22 3.36
2780 2841 6.210784 CAGAAATTATCATGCCATGGAGGAAT 59.789 38.462 18.40 5.65 41.22 3.01
2781 2842 7.395206 CAGAAATTATCATGCCATGGAGGAATA 59.605 37.037 18.40 4.61 41.22 1.75
2782 2843 8.120538 AGAAATTATCATGCCATGGAGGAATAT 58.879 33.333 18.40 2.99 41.22 1.28
2783 2844 7.893124 AATTATCATGCCATGGAGGAATATC 57.107 36.000 18.40 0.00 41.22 1.63
2784 2845 4.940468 ATCATGCCATGGAGGAATATCA 57.060 40.909 18.40 0.65 41.22 2.15
2785 2846 4.296621 TCATGCCATGGAGGAATATCAG 57.703 45.455 18.40 0.00 41.22 2.90
2786 2847 3.654321 TCATGCCATGGAGGAATATCAGT 59.346 43.478 18.40 0.00 41.22 3.41
2787 2848 3.497103 TGCCATGGAGGAATATCAGTG 57.503 47.619 18.40 0.00 41.22 3.66
2788 2849 2.779430 TGCCATGGAGGAATATCAGTGT 59.221 45.455 18.40 0.00 41.22 3.55
2789 2850 3.144506 GCCATGGAGGAATATCAGTGTG 58.855 50.000 18.40 0.00 41.22 3.82
2795 2856 4.080919 TGGAGGAATATCAGTGTGTGAAGG 60.081 45.833 0.00 0.00 39.19 3.46
2806 2867 4.635765 CAGTGTGTGAAGGTTGAAGAAGAA 59.364 41.667 0.00 0.00 0.00 2.52
2810 2871 3.621268 TGTGAAGGTTGAAGAAGAACACG 59.379 43.478 0.00 0.00 0.00 4.49
2811 2872 2.612212 TGAAGGTTGAAGAAGAACACGC 59.388 45.455 0.00 0.00 0.00 5.34
2812 2873 1.217882 AGGTTGAAGAAGAACACGCG 58.782 50.000 3.53 3.53 0.00 6.01
2813 2874 0.384353 GGTTGAAGAAGAACACGCGC 60.384 55.000 5.73 0.00 0.00 6.86
2814 2875 0.718220 GTTGAAGAAGAACACGCGCG 60.718 55.000 30.96 30.96 0.00 6.86
2815 2876 1.149361 TTGAAGAAGAACACGCGCGT 61.149 50.000 32.73 32.73 0.00 6.01
2824 2885 4.059459 CACGCGCGTGTTGAGGAC 62.059 66.667 45.19 0.00 40.91 3.85
2825 2886 4.578898 ACGCGCGTGTTGAGGACA 62.579 61.111 37.37 0.00 35.42 4.02
2826 2887 3.767230 CGCGCGTGTTGAGGACAG 61.767 66.667 24.19 0.00 39.39 3.51
2827 2888 3.414700 GCGCGTGTTGAGGACAGG 61.415 66.667 8.43 0.00 44.82 4.00
2828 2889 2.029073 CGCGTGTTGAGGACAGGT 59.971 61.111 0.00 0.00 44.08 4.00
2829 2890 1.594293 CGCGTGTTGAGGACAGGTT 60.594 57.895 0.00 0.00 44.08 3.50
2830 2891 0.319211 CGCGTGTTGAGGACAGGTTA 60.319 55.000 0.00 0.00 44.08 2.85
2831 2892 1.429463 GCGTGTTGAGGACAGGTTAG 58.571 55.000 1.58 0.00 44.08 2.34
2832 2893 1.939838 GCGTGTTGAGGACAGGTTAGG 60.940 57.143 1.58 0.00 44.08 2.69
2833 2894 1.809684 GTGTTGAGGACAGGTTAGGC 58.190 55.000 0.00 0.00 39.39 3.93
2834 2895 1.348036 GTGTTGAGGACAGGTTAGGCT 59.652 52.381 0.00 0.00 39.39 4.58
2835 2896 1.623811 TGTTGAGGACAGGTTAGGCTC 59.376 52.381 0.00 0.00 33.40 4.70
2836 2897 1.066071 GTTGAGGACAGGTTAGGCTCC 60.066 57.143 0.00 0.00 0.00 4.70
2837 2898 0.116342 TGAGGACAGGTTAGGCTCCA 59.884 55.000 0.00 0.00 0.00 3.86
2838 2899 0.537653 GAGGACAGGTTAGGCTCCAC 59.462 60.000 0.00 0.00 0.00 4.02
2839 2900 0.178903 AGGACAGGTTAGGCTCCACA 60.179 55.000 0.00 0.00 0.00 4.17
2840 2901 0.690762 GGACAGGTTAGGCTCCACAA 59.309 55.000 0.00 0.00 0.00 3.33
2841 2902 1.339151 GGACAGGTTAGGCTCCACAAG 60.339 57.143 0.00 0.00 0.00 3.16
2857 2918 5.674525 TCCACAAGAGCTGTAAATATCAGG 58.325 41.667 0.00 0.00 36.10 3.86
2873 2934 1.552337 TCAGGCTGTGAGAAGATGGAC 59.448 52.381 15.27 0.00 0.00 4.02
2882 2943 0.635009 AGAAGATGGACGGGGTAGGA 59.365 55.000 0.00 0.00 0.00 2.94
2945 3006 0.104855 CGATCAATTCTGCTCCCGGA 59.895 55.000 0.73 0.00 0.00 5.14
2952 3013 2.308185 TCTGCTCCCGGAGTAGAGA 58.692 57.895 26.46 16.80 44.12 3.10
2953 3014 0.181587 TCTGCTCCCGGAGTAGAGAG 59.818 60.000 26.46 7.08 44.12 3.20
2964 3025 3.069872 CGGAGTAGAGAGTAGACCAGCTA 59.930 52.174 0.00 0.00 0.00 3.32
2985 3046 2.722094 AGCTATTGCACCAAATTCCGA 58.278 42.857 1.12 0.00 42.74 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.992123 AGATAGACTGATAGATAGATCGCCTG 59.008 42.308 0.00 0.00 0.00 4.85
1 2 7.071196 AGAGATAGACTGATAGATAGATCGCCT 59.929 40.741 0.00 0.00 0.00 5.52
2 3 7.217200 AGAGATAGACTGATAGATAGATCGCC 58.783 42.308 0.00 0.00 0.00 5.54
3 4 9.411801 CTAGAGATAGACTGATAGATAGATCGC 57.588 40.741 0.00 0.00 0.00 4.58
4 5 9.411801 GCTAGAGATAGACTGATAGATAGATCG 57.588 40.741 0.00 0.00 0.00 3.69
8 9 9.698309 GCTAGCTAGAGATAGACTGATAGATAG 57.302 40.741 25.15 0.00 36.19 2.08
9 10 9.434275 AGCTAGCTAGAGATAGACTGATAGATA 57.566 37.037 25.15 0.00 36.19 1.98
10 11 8.324191 AGCTAGCTAGAGATAGACTGATAGAT 57.676 38.462 25.15 0.00 36.19 1.98
11 12 7.733773 AGCTAGCTAGAGATAGACTGATAGA 57.266 40.000 25.15 0.00 36.19 1.98
12 13 7.926555 GGTAGCTAGCTAGAGATAGACTGATAG 59.073 44.444 24.78 0.00 36.19 2.08
13 14 7.417003 CGGTAGCTAGCTAGAGATAGACTGATA 60.417 44.444 24.78 0.00 36.19 2.15
14 15 6.629515 CGGTAGCTAGCTAGAGATAGACTGAT 60.630 46.154 24.78 0.00 36.19 2.90
15 16 5.336929 CGGTAGCTAGCTAGAGATAGACTGA 60.337 48.000 24.78 0.00 36.19 3.41
16 17 4.868171 CGGTAGCTAGCTAGAGATAGACTG 59.132 50.000 24.78 13.82 36.19 3.51
17 18 4.081309 CCGGTAGCTAGCTAGAGATAGACT 60.081 50.000 24.78 11.89 36.19 3.24
18 19 4.186159 CCGGTAGCTAGCTAGAGATAGAC 58.814 52.174 24.78 12.69 36.19 2.59
19 20 3.369681 GCCGGTAGCTAGCTAGAGATAGA 60.370 52.174 24.78 0.00 36.19 1.98
20 21 2.940410 GCCGGTAGCTAGCTAGAGATAG 59.060 54.545 24.78 11.33 38.99 2.08
21 22 2.988570 GCCGGTAGCTAGCTAGAGATA 58.011 52.381 24.78 10.39 38.99 1.98
22 23 1.828979 GCCGGTAGCTAGCTAGAGAT 58.171 55.000 24.78 11.39 38.99 2.75
23 24 3.325902 GCCGGTAGCTAGCTAGAGA 57.674 57.895 24.78 7.93 38.99 3.10
34 35 4.415332 ACGACACGCAGCCGGTAG 62.415 66.667 1.90 0.00 39.22 3.18
35 36 4.710695 CACGACACGCAGCCGGTA 62.711 66.667 1.90 0.00 39.22 4.02
39 40 4.961511 TCCACACGACACGCAGCC 62.962 66.667 0.00 0.00 0.00 4.85
40 41 3.406361 CTCCACACGACACGCAGC 61.406 66.667 0.00 0.00 0.00 5.25
41 42 3.406361 GCTCCACACGACACGCAG 61.406 66.667 0.00 0.00 0.00 5.18
44 45 2.235016 AAACGCTCCACACGACACG 61.235 57.895 0.00 0.00 0.00 4.49
45 46 1.275657 CAAACGCTCCACACGACAC 59.724 57.895 0.00 0.00 0.00 3.67
46 47 0.741574 AACAAACGCTCCACACGACA 60.742 50.000 0.00 0.00 0.00 4.35
47 48 0.315869 CAACAAACGCTCCACACGAC 60.316 55.000 0.00 0.00 0.00 4.34
48 49 0.460459 TCAACAAACGCTCCACACGA 60.460 50.000 0.00 0.00 0.00 4.35
49 50 0.315869 GTCAACAAACGCTCCACACG 60.316 55.000 0.00 0.00 0.00 4.49
50 51 1.014352 AGTCAACAAACGCTCCACAC 58.986 50.000 0.00 0.00 0.00 3.82
51 52 1.400142 CAAGTCAACAAACGCTCCACA 59.600 47.619 0.00 0.00 0.00 4.17
52 53 1.268539 CCAAGTCAACAAACGCTCCAC 60.269 52.381 0.00 0.00 0.00 4.02
53 54 1.021202 CCAAGTCAACAAACGCTCCA 58.979 50.000 0.00 0.00 0.00 3.86
54 55 1.002792 GACCAAGTCAACAAACGCTCC 60.003 52.381 0.00 0.00 32.09 4.70
55 56 1.940613 AGACCAAGTCAACAAACGCTC 59.059 47.619 0.00 0.00 34.60 5.03
96 97 3.392595 GACGACGGACGCCTTCGAT 62.393 63.158 23.91 12.67 46.06 3.59
136 142 0.438830 GGTTGCTCTGTTCGTAAGCG 59.561 55.000 0.00 0.00 38.90 4.68
143 149 1.881973 TCATGCTTGGTTGCTCTGTTC 59.118 47.619 0.00 0.00 0.00 3.18
157 163 1.442769 GTCGTGTCACCAATCATGCT 58.557 50.000 0.00 0.00 0.00 3.79
159 165 0.721154 CCGTCGTGTCACCAATCATG 59.279 55.000 0.00 0.00 0.00 3.07
179 185 0.105964 GCCACACTCACCACTACACA 59.894 55.000 0.00 0.00 0.00 3.72
240 246 2.664851 CTTCCTTGACCGCGTGCA 60.665 61.111 4.92 0.00 0.00 4.57
305 331 0.038618 TTCGCTCTGCATACACACGT 60.039 50.000 0.00 0.00 0.00 4.49
414 445 0.395173 TCTGGATCGGTCGATGTGGA 60.395 55.000 10.77 3.25 34.60 4.02
446 477 5.351740 CCCGCTTTTGTTTTCCTTTGTTTAA 59.648 36.000 0.00 0.00 0.00 1.52
447 478 4.870991 CCCGCTTTTGTTTTCCTTTGTTTA 59.129 37.500 0.00 0.00 0.00 2.01
448 479 3.687212 CCCGCTTTTGTTTTCCTTTGTTT 59.313 39.130 0.00 0.00 0.00 2.83
449 480 3.055747 TCCCGCTTTTGTTTTCCTTTGTT 60.056 39.130 0.00 0.00 0.00 2.83
451 482 3.172229 TCCCGCTTTTGTTTTCCTTTG 57.828 42.857 0.00 0.00 0.00 2.77
452 483 3.552068 CGATCCCGCTTTTGTTTTCCTTT 60.552 43.478 0.00 0.00 0.00 3.11
453 484 2.030274 CGATCCCGCTTTTGTTTTCCTT 60.030 45.455 0.00 0.00 0.00 3.36
455 486 1.538075 TCGATCCCGCTTTTGTTTTCC 59.462 47.619 0.00 0.00 35.37 3.13
456 487 2.981400 TCGATCCCGCTTTTGTTTTC 57.019 45.000 0.00 0.00 35.37 2.29
461 493 4.378770 CCATATGATTCGATCCCGCTTTTG 60.379 45.833 3.65 0.00 35.37 2.44
662 699 2.788640 GCGGGGTAGTGGCATCGTA 61.789 63.158 0.00 0.00 0.00 3.43
663 700 4.157120 GCGGGGTAGTGGCATCGT 62.157 66.667 0.00 0.00 0.00 3.73
664 701 2.495409 TAGCGGGGTAGTGGCATCG 61.495 63.158 0.00 0.00 0.00 3.84
729 767 2.032071 GAGGGTTGGTGTCGTGGG 59.968 66.667 0.00 0.00 0.00 4.61
813 851 1.064389 GGGATCCTTGAAAGTGGGGAG 60.064 57.143 12.58 0.00 0.00 4.30
814 852 0.999712 GGGATCCTTGAAAGTGGGGA 59.000 55.000 12.58 0.00 0.00 4.81
927 969 4.924305 ACCATCCAATCAAATCAATCCG 57.076 40.909 0.00 0.00 0.00 4.18
947 989 1.068588 GCCAACCAGAGAAAACCCAAC 59.931 52.381 0.00 0.00 0.00 3.77
988 1030 1.935199 GAAGCTCATCTTCTCTGCTGC 59.065 52.381 0.00 0.00 45.99 5.25
998 1049 1.357258 CGCAACGCTGAAGCTCATCT 61.357 55.000 0.10 0.00 39.32 2.90
1996 2047 2.299297 GCTACTGGTAGTGGTGACAAGT 59.701 50.000 9.16 0.00 46.06 3.16
2000 2051 0.886563 ACGCTACTGGTAGTGGTGAC 59.113 55.000 20.64 0.27 45.31 3.67
2028 2085 0.326264 ATTGGTCTGAGTCACCTGGC 59.674 55.000 0.00 0.00 34.66 4.85
2146 2203 1.574392 GATCGACGAAACGCAACGC 60.574 57.895 0.00 0.00 0.00 4.84
2151 2208 1.702299 CACCAGATCGACGAAACGC 59.298 57.895 0.00 0.00 0.00 4.84
2152 2209 0.732880 AGCACCAGATCGACGAAACG 60.733 55.000 0.00 0.00 0.00 3.60
2154 2211 3.881089 TCTATAGCACCAGATCGACGAAA 59.119 43.478 0.00 0.00 0.00 3.46
2300 2357 8.439286 GTTCAGACTGAAAATCTATCACTTCAC 58.561 37.037 19.32 0.00 38.22 3.18
2338 2395 7.166167 TCACCATCATCGCTAAGATAGTAGTA 58.834 38.462 0.00 0.00 37.52 1.82
2419 2477 2.948979 CAGTTGGAGTTAGGCACACAAA 59.051 45.455 0.00 0.00 0.00 2.83
2435 2494 0.107456 ACAGAGTGGGCAGTCAGTTG 59.893 55.000 0.00 0.00 33.26 3.16
2498 2559 3.317430 CCTCATTCTATGAAGCAAAGCCC 59.683 47.826 0.00 0.00 39.11 5.19
2542 2603 1.094785 TGAAAAGAAGCGGCCATAGC 58.905 50.000 2.24 0.00 38.76 2.97
2572 2633 1.079336 CCCCGAGAAAGAACCGTCC 60.079 63.158 0.00 0.00 0.00 4.79
2574 2635 0.830866 AGTCCCCGAGAAAGAACCGT 60.831 55.000 0.00 0.00 0.00 4.83
2576 2637 2.427812 CTCTAGTCCCCGAGAAAGAACC 59.572 54.545 0.00 0.00 0.00 3.62
2582 2643 3.267812 TCCTAAACTCTAGTCCCCGAGAA 59.732 47.826 0.00 0.00 0.00 2.87
2625 2686 3.695060 GAGTCAGGAAAGTGATCGAGGTA 59.305 47.826 0.00 0.00 0.00 3.08
2645 2706 1.274447 TGCTATCATGCCATCGAGGAG 59.726 52.381 0.00 0.00 41.22 3.69
2651 2712 4.000331 AGTGTAGTGCTATCATGCCATC 58.000 45.455 0.00 0.00 0.00 3.51
2680 2741 1.022735 AGGTATAGTGTCGCCTCACG 58.977 55.000 1.23 0.00 42.40 4.35
2686 2747 4.320971 CGGCAGGTATAGTGTCGC 57.679 61.111 0.00 0.00 36.04 5.19
2687 2748 0.870307 GTGCGGCAGGTATAGTGTCG 60.870 60.000 1.18 4.93 45.80 4.35
2694 2755 2.368548 TCATATCTTGTGCGGCAGGTAT 59.631 45.455 1.18 0.00 0.00 2.73
2695 2756 1.760029 TCATATCTTGTGCGGCAGGTA 59.240 47.619 1.18 0.00 0.00 3.08
2715 2776 4.395959 TGAACGGTTTTCTGTCTAGTGT 57.604 40.909 0.00 0.00 38.64 3.55
2760 2821 6.977104 TGATATTCCTCCATGGCATGATAAT 58.023 36.000 28.43 20.48 35.26 1.28
2761 2822 6.012245 ACTGATATTCCTCCATGGCATGATAA 60.012 38.462 28.43 15.69 35.26 1.75
2762 2823 5.489997 ACTGATATTCCTCCATGGCATGATA 59.510 40.000 28.43 16.98 35.26 2.15
2764 2825 3.654321 ACTGATATTCCTCCATGGCATGA 59.346 43.478 28.43 13.33 35.26 3.07
2766 2827 3.396946 ACACTGATATTCCTCCATGGCAT 59.603 43.478 6.96 0.00 35.26 4.40
2768 2829 3.144506 CACACTGATATTCCTCCATGGC 58.855 50.000 6.96 0.00 35.26 4.40
2770 2831 5.027293 TCACACACTGATATTCCTCCATG 57.973 43.478 0.00 0.00 0.00 3.66
2771 2832 5.397221 CCTTCACACACTGATATTCCTCCAT 60.397 44.000 0.00 0.00 0.00 3.41
2773 2834 4.080863 ACCTTCACACACTGATATTCCTCC 60.081 45.833 0.00 0.00 0.00 4.30
2774 2835 5.091261 ACCTTCACACACTGATATTCCTC 57.909 43.478 0.00 0.00 0.00 3.71
2775 2836 5.013079 TCAACCTTCACACACTGATATTCCT 59.987 40.000 0.00 0.00 0.00 3.36
2776 2837 5.245531 TCAACCTTCACACACTGATATTCC 58.754 41.667 0.00 0.00 0.00 3.01
2777 2838 6.650807 TCTTCAACCTTCACACACTGATATTC 59.349 38.462 0.00 0.00 0.00 1.75
2778 2839 6.533730 TCTTCAACCTTCACACACTGATATT 58.466 36.000 0.00 0.00 0.00 1.28
2779 2840 6.114187 TCTTCAACCTTCACACACTGATAT 57.886 37.500 0.00 0.00 0.00 1.63
2780 2841 5.545063 TCTTCAACCTTCACACACTGATA 57.455 39.130 0.00 0.00 0.00 2.15
2781 2842 4.422073 TCTTCAACCTTCACACACTGAT 57.578 40.909 0.00 0.00 0.00 2.90
2782 2843 3.904800 TCTTCAACCTTCACACACTGA 57.095 42.857 0.00 0.00 0.00 3.41
2783 2844 4.191544 TCTTCTTCAACCTTCACACACTG 58.808 43.478 0.00 0.00 0.00 3.66
2784 2845 4.487714 TCTTCTTCAACCTTCACACACT 57.512 40.909 0.00 0.00 0.00 3.55
2785 2846 4.394920 TGTTCTTCTTCAACCTTCACACAC 59.605 41.667 0.00 0.00 0.00 3.82
2786 2847 4.394920 GTGTTCTTCTTCAACCTTCACACA 59.605 41.667 0.00 0.00 33.68 3.72
2787 2848 4.494199 CGTGTTCTTCTTCAACCTTCACAC 60.494 45.833 0.00 0.00 0.00 3.82
2788 2849 3.621268 CGTGTTCTTCTTCAACCTTCACA 59.379 43.478 0.00 0.00 0.00 3.58
2789 2850 3.546218 GCGTGTTCTTCTTCAACCTTCAC 60.546 47.826 0.00 0.00 0.00 3.18
2795 2856 0.718220 CGCGCGTGTTCTTCTTCAAC 60.718 55.000 24.19 0.00 0.00 3.18
2810 2871 3.414700 CCTGTCCTCAACACGCGC 61.415 66.667 5.73 0.00 33.24 6.86
2811 2872 0.319211 TAACCTGTCCTCAACACGCG 60.319 55.000 3.53 3.53 33.24 6.01
2812 2873 1.429463 CTAACCTGTCCTCAACACGC 58.571 55.000 0.00 0.00 33.24 5.34
2813 2874 1.939838 GCCTAACCTGTCCTCAACACG 60.940 57.143 0.00 0.00 33.24 4.49
2814 2875 1.348036 AGCCTAACCTGTCCTCAACAC 59.652 52.381 0.00 0.00 33.24 3.32
2815 2876 1.623811 GAGCCTAACCTGTCCTCAACA 59.376 52.381 0.00 0.00 36.18 3.33
2816 2877 1.066071 GGAGCCTAACCTGTCCTCAAC 60.066 57.143 0.00 0.00 0.00 3.18
2817 2878 1.276622 GGAGCCTAACCTGTCCTCAA 58.723 55.000 0.00 0.00 0.00 3.02
2818 2879 0.116342 TGGAGCCTAACCTGTCCTCA 59.884 55.000 0.00 0.00 0.00 3.86
2819 2880 0.537653 GTGGAGCCTAACCTGTCCTC 59.462 60.000 0.00 0.00 0.00 3.71
2820 2881 0.178903 TGTGGAGCCTAACCTGTCCT 60.179 55.000 0.00 0.00 0.00 3.85
2821 2882 0.690762 TTGTGGAGCCTAACCTGTCC 59.309 55.000 0.00 0.00 0.00 4.02
2822 2883 1.623811 TCTTGTGGAGCCTAACCTGTC 59.376 52.381 0.00 0.00 0.00 3.51
2823 2884 1.625818 CTCTTGTGGAGCCTAACCTGT 59.374 52.381 0.00 0.00 35.08 4.00
2824 2885 2.393271 CTCTTGTGGAGCCTAACCTG 57.607 55.000 0.00 0.00 35.08 4.00
2833 2894 5.757320 CCTGATATTTACAGCTCTTGTGGAG 59.243 44.000 0.00 0.00 41.10 3.86
2834 2895 5.674525 CCTGATATTTACAGCTCTTGTGGA 58.325 41.667 0.00 0.00 41.10 4.02
2835 2896 4.274459 GCCTGATATTTACAGCTCTTGTGG 59.726 45.833 0.00 0.00 41.10 4.17
2836 2897 5.007430 CAGCCTGATATTTACAGCTCTTGTG 59.993 44.000 0.00 0.00 41.10 3.33
2837 2898 5.121811 CAGCCTGATATTTACAGCTCTTGT 58.878 41.667 0.00 0.00 43.96 3.16
2838 2899 5.007430 CACAGCCTGATATTTACAGCTCTTG 59.993 44.000 0.00 0.00 34.47 3.02
2839 2900 5.104776 TCACAGCCTGATATTTACAGCTCTT 60.105 40.000 0.00 0.00 34.47 2.85
2840 2901 4.406972 TCACAGCCTGATATTTACAGCTCT 59.593 41.667 0.00 0.00 34.47 4.09
2841 2902 4.697514 TCACAGCCTGATATTTACAGCTC 58.302 43.478 0.00 0.00 34.47 4.09
2857 2918 0.460987 CCCGTCCATCTTCTCACAGC 60.461 60.000 0.00 0.00 0.00 4.40
2873 2934 3.834799 GCGTCACCTCCTACCCCG 61.835 72.222 0.00 0.00 0.00 5.73
2882 2943 4.057428 GTCTCGCCAGCGTCACCT 62.057 66.667 12.32 0.00 40.74 4.00
2945 3006 4.165372 AGCTTAGCTGGTCTACTCTCTACT 59.835 45.833 5.70 0.00 37.57 2.57
2952 3013 3.706594 TGCAATAGCTTAGCTGGTCTACT 59.293 43.478 17.97 0.00 40.10 2.57
2953 3014 3.804873 GTGCAATAGCTTAGCTGGTCTAC 59.195 47.826 17.97 6.96 40.10 2.59
2964 3025 3.088532 TCGGAATTTGGTGCAATAGCTT 58.911 40.909 0.00 0.00 42.74 3.74


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

AutoCloner maintained by Alex Coulton.