Multiple sequence alignment - TraesCS3D01G390200

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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 TraesCS3D01G390200 chr3D 100.000 2972 0 0 1 2972 505320898 505317927 0.000000e+00 5489
1 TraesCS3D01G390200 chr3D 87.382 531 54 8 1 528 513894721 513894201 5.480000e-167 597
2 TraesCS3D01G390200 chr3A 92.337 1853 96 19 663 2496 643461557 643459732 0.000000e+00 2593
3 TraesCS3D01G390200 chr3A 90.952 210 17 1 2488 2697 643459464 643459257 6.270000e-72 281
4 TraesCS3D01G390200 chr3A 94.853 136 7 0 2699 2834 643458972 643458837 2.320000e-51 213
5 TraesCS3D01G390200 chr3A 94.505 91 5 0 548 638 643461634 643461544 1.110000e-29 141
6 TraesCS3D01G390200 chr3A 95.455 66 3 0 2904 2969 643458526 643458461 4.050000e-19 106
7 TraesCS3D01G390200 chr3B 89.457 1584 91 43 528 2091 667113705 667112178 0.000000e+00 1930
8 TraesCS3D01G390200 chr3B 91.837 147 8 4 2171 2316 667112177 667112034 5.020000e-48 202
9 TraesCS3D01G390200 chr7A 94.549 532 22 5 1 526 679842928 679843458 0.000000e+00 815
10 TraesCS3D01G390200 chr2A 92.669 532 25 8 1 525 683220448 683219924 0.000000e+00 754
11 TraesCS3D01G390200 chr2A 87.640 89 10 1 2592 2680 59597112 59597025 5.240000e-18 102
12 TraesCS3D01G390200 chr4B 92.614 528 30 6 1 527 618407127 618407646 0.000000e+00 750
13 TraesCS3D01G390200 chr4B 88.805 527 53 2 7 527 286321443 286321969 2.500000e-180 641
14 TraesCS3D01G390200 chr4B 86.754 536 54 11 1 527 70727278 70726751 5.520000e-162 580
15 TraesCS3D01G390200 chr6A 95.532 470 14 3 61 524 3682575 3683043 0.000000e+00 745
16 TraesCS3D01G390200 chr6A 91.139 79 6 1 1318 1395 582265077 582265155 4.050000e-19 106
17 TraesCS3D01G390200 chr6A 91.139 79 6 1 1318 1395 582631048 582630970 4.050000e-19 106
18 TraesCS3D01G390200 chr6A 100.000 40 0 0 1 40 3682537 3682576 1.140000e-09 75
19 TraesCS3D01G390200 chr4D 92.120 533 26 5 1 527 404668071 404667549 0.000000e+00 737
20 TraesCS3D01G390200 chr7D 93.496 492 24 3 46 529 40836989 40836498 0.000000e+00 725
21 TraesCS3D01G390200 chr7D 74.532 534 118 12 1 528 476777781 476777260 1.790000e-52 217
22 TraesCS3D01G390200 chr2D 89.865 148 15 0 2716 2863 34338977 34339124 1.090000e-44 191
23 TraesCS3D01G390200 chr2D 86.550 171 14 4 366 529 87799054 87799222 2.350000e-41 180
24 TraesCS3D01G390200 chr6D 89.873 79 7 1 1318 1395 435351403 435351481 1.880000e-17 100
25 TraesCS3D01G390200 chr6B 89.873 79 7 1 1318 1395 658403357 658403435 1.880000e-17 100


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 TraesCS3D01G390200 chr3D 505317927 505320898 2971 True 5489.0 5489 100.0000 1 2972 1 chr3D.!!$R1 2971
1 TraesCS3D01G390200 chr3D 513894201 513894721 520 True 597.0 597 87.3820 1 528 1 chr3D.!!$R2 527
2 TraesCS3D01G390200 chr3A 643458461 643461634 3173 True 666.8 2593 93.6204 548 2969 5 chr3A.!!$R1 2421
3 TraesCS3D01G390200 chr3B 667112034 667113705 1671 True 1066.0 1930 90.6470 528 2316 2 chr3B.!!$R1 1788
4 TraesCS3D01G390200 chr7A 679842928 679843458 530 False 815.0 815 94.5490 1 526 1 chr7A.!!$F1 525
5 TraesCS3D01G390200 chr2A 683219924 683220448 524 True 754.0 754 92.6690 1 525 1 chr2A.!!$R2 524
6 TraesCS3D01G390200 chr4B 618407127 618407646 519 False 750.0 750 92.6140 1 527 1 chr4B.!!$F2 526
7 TraesCS3D01G390200 chr4B 286321443 286321969 526 False 641.0 641 88.8050 7 527 1 chr4B.!!$F1 520
8 TraesCS3D01G390200 chr4B 70726751 70727278 527 True 580.0 580 86.7540 1 527 1 chr4B.!!$R1 526
9 TraesCS3D01G390200 chr6A 3682537 3683043 506 False 410.0 745 97.7660 1 524 2 chr6A.!!$F2 523
10 TraesCS3D01G390200 chr4D 404667549 404668071 522 True 737.0 737 92.1200 1 527 1 chr4D.!!$R1 526
11 TraesCS3D01G390200 chr7D 476777260 476777781 521 True 217.0 217 74.5320 1 528 1 chr7D.!!$R2 527

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
915 964 0.460811 TGTGCACATCTCTCGCATCC 60.461 55.0 17.42 0.0 38.07 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2175 0.108615 CCTGACTCCACGTGTCATCC 60.109 60.0 15.65 0.17 42.57 3.51 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
358 364 2.047844 CGTGTGGGGCTCTGTCTG 60.048 66.667 0.00 0.00 0.00 3.51
401 431 4.691685 TCGTCGGCAATGTAATGTTTTAGT 59.308 37.500 0.00 0.00 0.00 2.24
490 530 5.103000 CGGGAGACTCTATGTAACTTTGTG 58.897 45.833 1.74 0.00 0.00 3.33
769 817 6.488769 TCTTTATGCCTACTCCCGAATAAA 57.511 37.500 0.00 0.00 0.00 1.40
781 829 2.925563 CCCGAATAAACACGTACTCCAC 59.074 50.000 0.00 0.00 0.00 4.02
889 938 6.160576 TCTACGGCGGTATAAATAAACCTT 57.839 37.500 13.24 0.00 33.34 3.50
897 946 5.238650 CGGTATAAATAAACCTTCCAGCCTG 59.761 44.000 0.00 0.00 33.34 4.85
915 964 0.460811 TGTGCACATCTCTCGCATCC 60.461 55.000 17.42 0.00 38.07 3.51
963 1017 2.891580 TGGAGACCGACCTATTGCTATC 59.108 50.000 0.00 0.00 0.00 2.08
989 1045 3.364023 CACAGTAGTAGTACAACAAGCGC 59.636 47.826 10.33 0.00 0.00 5.92
1007 1068 1.745827 CGCCACCGGTAAGATGGAATT 60.746 52.381 6.87 0.00 34.46 2.17
1203 1264 4.878774 CGCTCTCTCTTCTTGCGT 57.121 55.556 0.00 0.00 41.45 5.24
1225 1286 1.458445 CAATGCATCGATCGGCTGTAG 59.542 52.381 16.41 0.43 0.00 2.74
1261 1327 4.037446 ACTGCCATTGACACGTTGTTATTT 59.963 37.500 0.00 0.00 0.00 1.40
1289 1355 6.607970 TGGCTAGCCTAGTACTATCAAACTA 58.392 40.000 33.07 4.80 36.94 2.24
1380 1455 4.446023 GGCATCAAGGAGAAGATCAAGGAT 60.446 45.833 0.00 0.00 0.00 3.24
1769 1844 1.146930 CAGGGCACGCTGGTATGAT 59.853 57.895 6.81 0.00 0.00 2.45
1883 1958 2.357760 GACCGGCGGTGCTTACAA 60.358 61.111 39.41 0.00 35.25 2.41
2002 2077 3.003275 CAGCGTGTTTGTGAACAATAGGT 59.997 43.478 0.00 0.00 46.62 3.08
2004 2079 4.212636 AGCGTGTTTGTGAACAATAGGTAC 59.787 41.667 0.00 0.00 46.62 3.34
2087 2162 3.096852 TGGTATGCTGCAGTACTGTACT 58.903 45.455 23.44 14.53 40.28 2.73
2100 2175 6.134688 AGTACTGTACTGTGACGTAGTGCG 62.135 50.000 19.09 0.00 38.36 5.34
2109 2184 1.154093 ACGTAGTGCGGATGACACG 60.154 57.895 5.41 0.00 46.52 4.49
2112 2187 1.076533 GTAGTGCGGATGACACGTGG 61.077 60.000 21.57 1.25 42.94 4.94
2113 2188 1.245376 TAGTGCGGATGACACGTGGA 61.245 55.000 21.57 6.22 42.94 4.02
2115 2190 2.261671 GCGGATGACACGTGGAGT 59.738 61.111 21.57 4.38 0.00 3.85
2125 2200 2.268022 ACGTGGAGTCAGGTGCTAG 58.732 57.895 0.00 0.00 40.08 3.42
2126 2201 0.251209 ACGTGGAGTCAGGTGCTAGA 60.251 55.000 0.00 0.00 40.08 2.43
2145 2220 2.529005 AGTCCACACGACAGCGATCG 62.529 60.000 11.69 11.69 44.66 3.69
2248 2323 9.982291 ACTATGTTAAATATTACTTTGTGTGCG 57.018 29.630 0.00 0.00 0.00 5.34
2249 2324 7.734538 ATGTTAAATATTACTTTGTGTGCGC 57.265 32.000 0.00 0.00 0.00 6.09
2270 2346 2.295349 CACAATAATGATGCAGAGGCCC 59.705 50.000 0.00 0.00 40.13 5.80
2338 2414 6.618770 TGTGTGTTGTTTGTATTTGTTTCG 57.381 33.333 0.00 0.00 0.00 3.46
2339 2415 5.061064 TGTGTGTTGTTTGTATTTGTTTCGC 59.939 36.000 0.00 0.00 0.00 4.70
2419 2495 7.703298 TCTTTTAATCTGAAAAGTCGAACGA 57.297 32.000 8.13 0.00 43.77 3.85
2420 2496 8.133754 TCTTTTAATCTGAAAAGTCGAACGAA 57.866 30.769 8.13 0.00 43.77 3.85
2437 2513 6.633634 TCGAACGAAAATTGTAATTGTCCAAC 59.366 34.615 0.00 0.00 30.40 3.77
2443 2519 8.061268 CGAAAATTGTAATTGTCCAACAAAAGG 58.939 33.333 0.00 0.00 41.96 3.11
2444 2520 8.800370 AAAATTGTAATTGTCCAACAAAAGGT 57.200 26.923 0.00 0.00 41.96 3.50
2445 2521 9.892130 AAAATTGTAATTGTCCAACAAAAGGTA 57.108 25.926 0.00 0.00 41.96 3.08
2451 2527 5.570234 TTGTCCAACAAAAGGTAAGACAC 57.430 39.130 0.00 0.00 39.80 3.67
2461 2537 1.075050 AGGTAAGACACTCCCACTCGA 59.925 52.381 0.00 0.00 0.00 4.04
2464 2540 2.223803 AAGACACTCCCACTCGATCT 57.776 50.000 0.00 0.00 0.00 2.75
2486 2562 4.448210 TGAGTCTTAAGTTGGTTGGTCAC 58.552 43.478 1.63 0.00 0.00 3.67
2532 2884 3.653352 TGCTAGAGATGCTACTCCCTCTA 59.347 47.826 0.00 0.00 37.25 2.43
2536 2888 4.672899 AGAGATGCTACTCCCTCTAATCC 58.327 47.826 7.01 0.00 37.60 3.01
2537 2889 4.107149 AGAGATGCTACTCCCTCTAATCCA 59.893 45.833 7.01 0.00 37.60 3.41
2551 2903 8.781951 TCCCTCTAATCCATATTAATCAATCCC 58.218 37.037 0.00 0.00 0.00 3.85
2565 2917 9.790344 ATTAATCAATCCCTCTACATTTCTCTG 57.210 33.333 0.00 0.00 0.00 3.35
2588 2940 6.866480 TGTTTAATGTAACTACTACCTCCGG 58.134 40.000 0.00 0.00 0.00 5.14
2591 2943 1.035923 GTAACTACTACCTCCGGCCC 58.964 60.000 0.00 0.00 0.00 5.80
2653 3005 1.679977 AAGGCCGCTGACATGCATT 60.680 52.632 0.00 0.00 0.00 3.56
2675 3027 3.237628 GTTGCTTTTTCTCTCAATCCGC 58.762 45.455 0.00 0.00 0.00 5.54
2688 3040 1.298859 AATCCGCGTCTGAAGGCAAC 61.299 55.000 4.92 0.00 36.04 4.17
2689 3041 2.449031 ATCCGCGTCTGAAGGCAACA 62.449 55.000 4.92 0.00 36.04 3.33
2697 3049 2.162921 CTGAAGGCAACACACGCGAG 62.163 60.000 15.93 7.88 41.41 5.03
2708 3343 4.478195 ACGCGAGTGACTACATGC 57.522 55.556 15.93 0.00 46.97 4.06
2714 3349 2.596452 CGAGTGACTACATGCGAAAGT 58.404 47.619 0.00 0.00 0.00 2.66
2748 3383 2.025981 TCACTGCATGCATTAACTCCCT 60.026 45.455 22.97 0.00 0.00 4.20
2772 3407 5.102313 GCTAATTTCATTGGTGGTTACTGC 58.898 41.667 0.00 0.00 0.00 4.40
2786 3421 3.113322 GTTACTGCGCTCGAATATCACA 58.887 45.455 9.73 0.00 0.00 3.58
2811 3446 5.666969 TCCTCAAAATTAATATCGTGCCG 57.333 39.130 0.00 0.00 0.00 5.69
2818 3453 1.112950 TAATATCGTGCCGTGGTCCA 58.887 50.000 0.00 0.00 0.00 4.02
2853 3764 0.538118 TGGACCTTTAATCCCGGACG 59.462 55.000 0.73 0.00 35.12 4.79
2857 3768 0.106149 CCTTTAATCCCGGACGGAGG 59.894 60.000 13.13 5.93 46.60 4.30
2858 3769 0.828677 CTTTAATCCCGGACGGAGGT 59.171 55.000 13.13 0.00 46.60 3.85
2859 3770 2.034124 CTTTAATCCCGGACGGAGGTA 58.966 52.381 13.13 0.00 46.60 3.08
2860 3771 1.696063 TTAATCCCGGACGGAGGTAG 58.304 55.000 13.13 0.00 46.60 3.18
2861 3772 0.552848 TAATCCCGGACGGAGGTAGT 59.447 55.000 13.13 0.00 46.60 2.73
2862 3773 0.552848 AATCCCGGACGGAGGTAGTA 59.447 55.000 13.13 0.00 46.60 1.82
2863 3774 0.552848 ATCCCGGACGGAGGTAGTAA 59.447 55.000 13.13 0.00 46.60 2.24
2864 3775 0.394352 TCCCGGACGGAGGTAGTAAC 60.394 60.000 13.13 0.00 34.86 2.50
2865 3776 0.394899 CCCGGACGGAGGTAGTAACT 60.395 60.000 13.13 0.00 37.50 2.24
2866 3777 1.134098 CCCGGACGGAGGTAGTAACTA 60.134 57.143 13.13 0.00 37.50 2.24
2867 3778 2.216898 CCGGACGGAGGTAGTAACTAG 58.783 57.143 4.40 0.00 37.50 2.57
2868 3779 2.420687 CCGGACGGAGGTAGTAACTAGT 60.421 54.545 4.40 0.00 37.50 2.57
2869 3780 3.274288 CGGACGGAGGTAGTAACTAGTT 58.726 50.000 13.68 13.68 0.00 2.24
2870 3781 3.691609 CGGACGGAGGTAGTAACTAGTTT 59.308 47.826 14.49 0.00 0.00 2.66
2871 3782 4.201861 CGGACGGAGGTAGTAACTAGTTTC 60.202 50.000 14.49 8.92 0.00 2.78
2872 3783 4.702131 GGACGGAGGTAGTAACTAGTTTCA 59.298 45.833 14.49 0.00 0.00 2.69
2873 3784 5.163673 GGACGGAGGTAGTAACTAGTTTCAG 60.164 48.000 14.49 7.32 0.00 3.02
2874 3785 5.320277 ACGGAGGTAGTAACTAGTTTCAGT 58.680 41.667 14.49 7.96 0.00 3.41
2875 3786 6.476378 ACGGAGGTAGTAACTAGTTTCAGTA 58.524 40.000 14.49 1.06 0.00 2.74
2876 3787 6.597280 ACGGAGGTAGTAACTAGTTTCAGTAG 59.403 42.308 14.49 0.92 0.00 2.57
2877 3788 6.038050 CGGAGGTAGTAACTAGTTTCAGTAGG 59.962 46.154 14.49 0.00 0.00 3.18
2878 3789 6.889177 GGAGGTAGTAACTAGTTTCAGTAGGT 59.111 42.308 14.49 0.00 0.00 3.08
2879 3790 7.066887 GGAGGTAGTAACTAGTTTCAGTAGGTC 59.933 44.444 14.49 3.94 0.00 3.85
2880 3791 7.465116 AGGTAGTAACTAGTTTCAGTAGGTCA 58.535 38.462 14.49 0.00 0.00 4.02
2881 3792 7.392953 AGGTAGTAACTAGTTTCAGTAGGTCAC 59.607 40.741 14.49 1.57 0.00 3.67
2882 3793 7.175641 GGTAGTAACTAGTTTCAGTAGGTCACA 59.824 40.741 14.49 0.00 0.00 3.58
2883 3794 7.592885 AGTAACTAGTTTCAGTAGGTCACAA 57.407 36.000 14.49 0.00 0.00 3.33
2884 3795 8.191534 AGTAACTAGTTTCAGTAGGTCACAAT 57.808 34.615 14.49 0.00 0.00 2.71
2885 3796 8.648693 AGTAACTAGTTTCAGTAGGTCACAATT 58.351 33.333 14.49 0.00 0.00 2.32
2886 3797 7.730364 AACTAGTTTCAGTAGGTCACAATTG 57.270 36.000 1.12 3.24 0.00 2.32
2887 3798 6.827727 ACTAGTTTCAGTAGGTCACAATTGT 58.172 36.000 4.92 4.92 0.00 2.71
2888 3799 7.280356 ACTAGTTTCAGTAGGTCACAATTGTT 58.720 34.615 8.77 0.00 0.00 2.83
2889 3800 6.377327 AGTTTCAGTAGGTCACAATTGTTG 57.623 37.500 8.77 2.99 0.00 3.33
2890 3801 5.885912 AGTTTCAGTAGGTCACAATTGTTGT 59.114 36.000 8.77 0.00 46.75 3.32
2891 3802 6.377146 AGTTTCAGTAGGTCACAATTGTTGTT 59.623 34.615 8.77 0.00 43.23 2.83
2892 3803 5.749596 TCAGTAGGTCACAATTGTTGTTG 57.250 39.130 8.77 0.00 43.23 3.33
2893 3804 5.189928 TCAGTAGGTCACAATTGTTGTTGT 58.810 37.500 8.77 0.00 43.23 3.32
2894 3805 5.295787 TCAGTAGGTCACAATTGTTGTTGTC 59.704 40.000 8.77 0.00 43.23 3.18
2895 3806 5.296780 CAGTAGGTCACAATTGTTGTTGTCT 59.703 40.000 8.77 3.96 43.23 3.41
2896 3807 5.885912 AGTAGGTCACAATTGTTGTTGTCTT 59.114 36.000 8.77 0.00 43.23 3.01
2897 3808 5.248870 AGGTCACAATTGTTGTTGTCTTC 57.751 39.130 8.77 0.00 43.23 2.87
2898 3809 4.949856 AGGTCACAATTGTTGTTGTCTTCT 59.050 37.500 8.77 0.00 43.23 2.85
2899 3810 5.066505 AGGTCACAATTGTTGTTGTCTTCTC 59.933 40.000 8.77 0.00 43.23 2.87
2900 3811 5.163663 GGTCACAATTGTTGTTGTCTTCTCA 60.164 40.000 8.77 0.00 43.23 3.27
2901 3812 6.460123 GGTCACAATTGTTGTTGTCTTCTCAT 60.460 38.462 8.77 0.00 43.23 2.90
2902 3813 6.974622 GTCACAATTGTTGTTGTCTTCTCATT 59.025 34.615 8.77 0.00 43.23 2.57
2959 3870 5.528043 TCATATAATGCACCGCCATTTTT 57.472 34.783 0.00 0.00 36.80 1.94
2969 3880 2.817844 ACCGCCATTTTTCTCAACCTAC 59.182 45.455 0.00 0.00 0.00 3.18
2970 3881 3.081804 CCGCCATTTTTCTCAACCTACT 58.918 45.455 0.00 0.00 0.00 2.57
2971 3882 4.258543 CCGCCATTTTTCTCAACCTACTA 58.741 43.478 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 1.477558 GGCCCGAATGTCTTGGATCAT 60.478 52.381 0.00 0.00 0.00 2.45
112 113 1.002134 ACTGGCCCGAATGTCTTGG 60.002 57.895 0.00 0.00 0.00 3.61
175 180 1.377725 CCATCGCCTCTGCCACTTT 60.378 57.895 0.00 0.00 0.00 2.66
292 298 0.179100 ACAATGGAGCGATCTCGTGG 60.179 55.000 0.00 0.00 40.26 4.94
358 364 3.303406 GAACATGCTTGAAAGTCACAGC 58.697 45.455 6.60 5.84 33.90 4.40
490 530 3.001330 CGTCGGTCTTTATTGATCAAGCC 59.999 47.826 14.54 7.81 0.00 4.35
534 574 1.192803 ACTGTTTCCCCTCGGACTCC 61.193 60.000 0.00 0.00 38.14 3.85
535 575 0.037232 CACTGTTTCCCCTCGGACTC 60.037 60.000 0.00 0.00 38.14 3.36
536 576 1.481056 CCACTGTTTCCCCTCGGACT 61.481 60.000 0.00 0.00 38.14 3.85
537 577 1.003718 CCACTGTTTCCCCTCGGAC 60.004 63.158 0.00 0.00 38.14 4.79
538 578 2.890766 GCCACTGTTTCCCCTCGGA 61.891 63.158 0.00 0.00 35.88 4.55
539 579 2.359975 GCCACTGTTTCCCCTCGG 60.360 66.667 0.00 0.00 0.00 4.63
540 580 1.228124 TTGCCACTGTTTCCCCTCG 60.228 57.895 0.00 0.00 0.00 4.63
541 581 1.179174 GGTTGCCACTGTTTCCCCTC 61.179 60.000 0.00 0.00 0.00 4.30
542 582 1.152546 GGTTGCCACTGTTTCCCCT 60.153 57.895 0.00 0.00 0.00 4.79
543 583 2.207229 GGGTTGCCACTGTTTCCCC 61.207 63.158 0.00 0.00 0.00 4.81
859 908 0.659957 ATACCGCCGTAGAGTTCGAC 59.340 55.000 0.00 0.00 0.00 4.20
889 938 1.196766 AGAGATGTGCACAGGCTGGA 61.197 55.000 25.84 0.00 41.91 3.86
897 946 1.156645 GGGATGCGAGAGATGTGCAC 61.157 60.000 10.75 10.75 42.11 4.57
915 964 3.983044 AGGGAGTTGTTTGTAGCTAGG 57.017 47.619 0.00 0.00 0.00 3.02
963 1017 5.629849 GCTTGTTGTACTACTACTGTGACAG 59.370 44.000 11.70 11.70 37.52 3.51
989 1045 2.092646 TGGAATTCCATCTTACCGGTGG 60.093 50.000 23.63 9.89 42.01 4.61
1115 1176 1.376553 GTCTTGTGCTCCTCCCTGC 60.377 63.158 0.00 0.00 0.00 4.85
1203 1264 1.524393 AGCCGATCGATGCATTGCA 60.524 52.632 18.66 14.72 44.86 4.08
1261 1327 4.044191 TGATAGTACTAGGCTAGCCATGGA 59.956 45.833 34.70 20.58 38.92 3.41
1289 1355 7.552687 TCAATCAAAACGGAGCAGATTAATACT 59.447 33.333 0.00 0.00 0.00 2.12
1298 1371 6.073548 GGACTATATCAATCAAAACGGAGCAG 60.074 42.308 0.00 0.00 0.00 4.24
1380 1455 3.467226 CGAGCCCCGGGAAGCTTA 61.467 66.667 26.32 0.00 40.11 3.09
1683 1758 3.402681 CCAGTCATCCCGGGCTGT 61.403 66.667 23.26 2.69 0.00 4.40
1769 1844 2.741985 CATGCGTTCCAGTGCCGA 60.742 61.111 0.00 0.00 0.00 5.54
1807 1882 2.213499 GTGCCCTTGATGATCGTAAGG 58.787 52.381 12.91 12.91 40.48 2.69
2002 2077 3.138798 GCTCCACCTCCGCTCGTA 61.139 66.667 0.00 0.00 0.00 3.43
2004 2079 2.016393 TATTGCTCCACCTCCGCTCG 62.016 60.000 0.00 0.00 0.00 5.03
2028 2103 3.743911 CACACAAACGTGAGCCACTTATA 59.256 43.478 0.00 0.00 39.34 0.98
2038 2113 1.325037 CAACGCTACACACAAACGTGA 59.675 47.619 0.00 0.00 39.34 4.35
2087 2162 0.109458 GTCATCCGCACTACGTCACA 60.109 55.000 0.00 0.00 41.42 3.58
2091 2166 1.154093 CGTGTCATCCGCACTACGT 60.154 57.895 0.00 0.00 41.42 3.57
2100 2175 0.108615 CCTGACTCCACGTGTCATCC 60.109 60.000 15.65 0.17 42.57 3.51
2109 2184 1.474879 GACTCTAGCACCTGACTCCAC 59.525 57.143 0.00 0.00 0.00 4.02
2112 2187 1.474879 GTGGACTCTAGCACCTGACTC 59.525 57.143 0.00 0.00 0.00 3.36
2113 2188 1.203063 TGTGGACTCTAGCACCTGACT 60.203 52.381 0.00 0.00 0.00 3.41
2115 2190 1.257743 GTGTGGACTCTAGCACCTGA 58.742 55.000 0.00 0.00 0.00 3.86
2117 2192 0.251209 TCGTGTGGACTCTAGCACCT 60.251 55.000 0.00 0.00 0.00 4.00
2119 2194 0.596577 TGTCGTGTGGACTCTAGCAC 59.403 55.000 0.00 0.00 46.24 4.40
2125 2200 0.798771 GATCGCTGTCGTGTGGACTC 60.799 60.000 0.00 0.00 46.24 3.36
2126 2201 1.213013 GATCGCTGTCGTGTGGACT 59.787 57.895 0.00 0.00 46.24 3.85
2145 2220 5.425577 TGAGATCTTCTGCAGTACGATAC 57.574 43.478 14.67 11.25 0.00 2.24
2148 2223 3.119459 GGTTGAGATCTTCTGCAGTACGA 60.119 47.826 14.67 9.06 0.00 3.43
2149 2224 3.182967 GGTTGAGATCTTCTGCAGTACG 58.817 50.000 14.67 3.49 0.00 3.67
2154 2229 3.776969 ACATAGGGTTGAGATCTTCTGCA 59.223 43.478 0.00 0.00 0.00 4.41
2248 2323 2.288030 GGCCTCTGCATCATTATTGTGC 60.288 50.000 0.00 0.00 40.13 4.57
2249 2324 2.295349 GGGCCTCTGCATCATTATTGTG 59.705 50.000 0.84 0.00 40.13 3.33
2338 2414 7.926555 TGTAGAAGCCAGTGATACTTTTATAGC 59.073 37.037 0.00 0.00 0.00 2.97
2339 2415 9.988815 ATGTAGAAGCCAGTGATACTTTTATAG 57.011 33.333 0.00 0.00 0.00 1.31
2405 2481 8.738554 CAATTACAATTTTCGTTCGACTTTTCA 58.261 29.630 0.00 0.00 0.00 2.69
2419 2495 8.800370 ACCTTTTGTTGGACAATTACAATTTT 57.200 26.923 0.00 0.00 38.00 1.82
2420 2496 9.892130 TTACCTTTTGTTGGACAATTACAATTT 57.108 25.926 0.00 0.00 38.00 1.82
2437 2513 4.065789 GAGTGGGAGTGTCTTACCTTTTG 58.934 47.826 0.00 0.00 0.00 2.44
2443 2519 3.018149 AGATCGAGTGGGAGTGTCTTAC 58.982 50.000 0.00 0.00 0.00 2.34
2444 2520 3.017442 CAGATCGAGTGGGAGTGTCTTA 58.983 50.000 0.00 0.00 0.00 2.10
2445 2521 1.821753 CAGATCGAGTGGGAGTGTCTT 59.178 52.381 0.00 0.00 0.00 3.01
2461 2537 5.071788 TGACCAACCAACTTAAGACTCAGAT 59.928 40.000 10.09 0.00 0.00 2.90
2464 2540 4.448210 GTGACCAACCAACTTAAGACTCA 58.552 43.478 10.09 0.00 0.00 3.41
2486 2562 2.286365 TGGAAGCAAGTTAGGTTGGG 57.714 50.000 0.00 0.00 0.00 4.12
2549 2901 9.667107 TTACATTAAACAGAGAAATGTAGAGGG 57.333 33.333 7.08 0.00 43.31 4.30
2588 2940 2.342648 CGGGCTTACTATCCGGGC 59.657 66.667 0.00 0.00 40.07 6.13
2591 2943 2.049433 CGCCGGGCTTACTATCCG 60.049 66.667 18.34 0.00 43.05 4.18
2653 3005 3.304659 GCGGATTGAGAGAAAAAGCAACA 60.305 43.478 0.00 0.00 0.00 3.33
2675 3027 1.564622 CGTGTGTTGCCTTCAGACG 59.435 57.895 7.77 7.77 43.55 4.18
2688 3040 0.984829 CATGTAGTCACTCGCGTGTG 59.015 55.000 29.93 29.93 41.89 3.82
2689 3041 0.732880 GCATGTAGTCACTCGCGTGT 60.733 55.000 8.21 8.21 41.89 4.49
2697 3049 2.412847 GGCAACTTTCGCATGTAGTCAC 60.413 50.000 0.00 0.00 0.00 3.67
2708 3343 0.872388 AGTTTAGCGGGCAACTTTCG 59.128 50.000 0.00 0.00 28.27 3.46
2714 3349 1.234615 GCAGTGAGTTTAGCGGGCAA 61.235 55.000 0.00 0.00 0.00 4.52
2748 3383 5.336372 GCAGTAACCACCAATGAAATTAGCA 60.336 40.000 0.00 0.00 32.46 3.49
2772 3407 2.983136 GAGGATGTGTGATATTCGAGCG 59.017 50.000 0.00 0.00 0.00 5.03
2786 3421 6.970484 GGCACGATATTAATTTTGAGGATGT 58.030 36.000 0.00 0.00 0.00 3.06
2811 3446 2.861147 AGCCTAAACTCTTGGACCAC 57.139 50.000 0.00 0.00 0.00 4.16
2818 3453 4.168883 AGGTCCACTTAGCCTAAACTCTT 58.831 43.478 0.00 0.00 0.00 2.85
2853 3764 6.889177 ACCTACTGAAACTAGTTACTACCTCC 59.111 42.308 8.92 0.00 32.19 4.30
2857 3768 8.103948 TGTGACCTACTGAAACTAGTTACTAC 57.896 38.462 8.92 2.21 32.19 2.73
2858 3769 8.696043 TTGTGACCTACTGAAACTAGTTACTA 57.304 34.615 8.92 0.00 32.19 1.82
2859 3770 7.592885 TTGTGACCTACTGAAACTAGTTACT 57.407 36.000 8.92 0.00 32.19 2.24
2860 3771 8.709646 CAATTGTGACCTACTGAAACTAGTTAC 58.290 37.037 8.92 0.00 32.19 2.50
2861 3772 8.426489 ACAATTGTGACCTACTGAAACTAGTTA 58.574 33.333 11.07 0.00 32.19 2.24
2862 3773 7.280356 ACAATTGTGACCTACTGAAACTAGTT 58.720 34.615 11.07 1.12 32.19 2.24
2863 3774 6.827727 ACAATTGTGACCTACTGAAACTAGT 58.172 36.000 11.07 0.00 34.71 2.57
2864 3775 7.226720 ACAACAATTGTGACCTACTGAAACTAG 59.773 37.037 12.82 0.00 43.48 2.57
2865 3776 7.051623 ACAACAATTGTGACCTACTGAAACTA 58.948 34.615 12.82 0.00 43.48 2.24
2866 3777 5.885912 ACAACAATTGTGACCTACTGAAACT 59.114 36.000 12.82 0.00 43.48 2.66
2867 3778 6.131544 ACAACAATTGTGACCTACTGAAAC 57.868 37.500 12.82 0.00 43.48 2.78
2868 3779 6.151985 ACAACAACAATTGTGACCTACTGAAA 59.848 34.615 12.82 0.00 44.59 2.69
2869 3780 5.650266 ACAACAACAATTGTGACCTACTGAA 59.350 36.000 12.82 0.00 44.59 3.02
2870 3781 5.189928 ACAACAACAATTGTGACCTACTGA 58.810 37.500 12.82 0.00 44.59 3.41
2871 3782 5.296780 AGACAACAACAATTGTGACCTACTG 59.703 40.000 12.82 7.23 44.59 2.74
2872 3783 5.437060 AGACAACAACAATTGTGACCTACT 58.563 37.500 12.82 5.87 44.59 2.57
2873 3784 5.751243 AGACAACAACAATTGTGACCTAC 57.249 39.130 12.82 3.64 44.59 3.18
2874 3785 6.119536 AGAAGACAACAACAATTGTGACCTA 58.880 36.000 12.82 0.00 44.59 3.08
2875 3786 4.949856 AGAAGACAACAACAATTGTGACCT 59.050 37.500 12.82 1.50 44.59 3.85
2876 3787 5.163663 TGAGAAGACAACAACAATTGTGACC 60.164 40.000 12.82 0.00 44.59 4.02
2877 3788 5.879237 TGAGAAGACAACAACAATTGTGAC 58.121 37.500 12.82 0.00 44.59 3.67
2878 3789 6.698008 ATGAGAAGACAACAACAATTGTGA 57.302 33.333 12.82 0.00 44.59 3.58
2879 3790 6.753279 ACAATGAGAAGACAACAACAATTGTG 59.247 34.615 12.82 8.99 44.59 3.33
2881 3792 8.854979 TTACAATGAGAAGACAACAACAATTG 57.145 30.769 3.24 3.24 35.59 2.32
2902 3813 9.584008 ACGGGAGAGTAGAAGAATATAATTACA 57.416 33.333 0.00 0.00 0.00 2.41
2909 3820 7.419711 TCAAAACGGGAGAGTAGAAGAATAT 57.580 36.000 0.00 0.00 0.00 1.28
2927 3838 6.360681 GCGGTGCATTATATGATCTTCAAAAC 59.639 38.462 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.