Multiple sequence alignment - TraesCS1A01G258500

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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 TraesCS1A01G258500 chr1A 100.000 2907 0 0 1 2907 451619956 451617050 0.000000e+00 5369
1 TraesCS1A01G258500 chr1D 92.044 2627 114 42 248 2832 350654799 350652226 0.000000e+00 3605
2 TraesCS1A01G258500 chr1D 92.350 183 4 3 26 201 350663415 350663236 4.810000e-63 252
3 TraesCS1A01G258500 chr1D 94.366 71 4 0 2831 2901 309084290 309084220 3.060000e-20 110
4 TraesCS1A01G258500 chr1B 91.827 1872 78 36 991 2832 473286179 473284353 0.000000e+00 2540
5 TraesCS1A01G258500 chr1B 89.619 944 52 19 10 938 473287092 473286180 0.000000e+00 1158
6 TraesCS1A01G258500 chr6B 95.714 70 3 0 2832 2901 134208724 134208655 2.370000e-21 113
7 TraesCS1A01G258500 chr3D 94.366 71 4 0 2831 2901 164287485 164287555 3.060000e-20 110
8 TraesCS1A01G258500 chr3D 93.243 74 5 0 2829 2902 579551724 579551651 3.060000e-20 110
9 TraesCS1A01G258500 chr2D 94.366 71 4 0 2831 2901 418074854 418074784 3.060000e-20 110
10 TraesCS1A01G258500 chr2D 94.286 70 4 0 2832 2901 580120448 580120379 1.100000e-19 108
11 TraesCS1A01G258500 chr7D 94.286 70 4 0 2832 2901 615908074 615908005 1.100000e-19 108
12 TraesCS1A01G258500 chr7D 89.157 83 8 1 2820 2901 431036233 431036315 5.130000e-18 102
13 TraesCS1A01G258500 chr4D 92.857 70 5 0 2832 2901 329659889 329659820 5.130000e-18 102


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 TraesCS1A01G258500 chr1A 451617050 451619956 2906 True 5369 5369 100.000 1 2907 1 chr1A.!!$R1 2906
1 TraesCS1A01G258500 chr1D 350652226 350654799 2573 True 3605 3605 92.044 248 2832 1 chr1D.!!$R2 2584
2 TraesCS1A01G258500 chr1B 473284353 473287092 2739 True 1849 2540 90.723 10 2832 2 chr1B.!!$R1 2822

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
237 245 0.033504 TGACCAGGCTTTCTCACGAC 59.966 55.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2027 2065 0.03601 AGTGGTAGCAGCGCAATTCT 60.036 50.0 11.47 2.85 0.0 2.4 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
21 22 4.491234 ACAGAAGAGAACTGTGACTACG 57.509 45.455 0.00 0.00 45.19 3.51
22 23 4.135306 ACAGAAGAGAACTGTGACTACGA 58.865 43.478 0.00 0.00 45.19 3.43
23 24 4.579340 ACAGAAGAGAACTGTGACTACGAA 59.421 41.667 0.00 0.00 45.19 3.85
24 25 5.150683 CAGAAGAGAACTGTGACTACGAAG 58.849 45.833 0.00 0.00 0.00 3.79
36 37 1.126846 ACTACGAAGTACGAACGACGG 59.873 52.381 13.99 7.46 44.65 4.79
45 46 2.856089 CGAACGACGGTAGAGATGC 58.144 57.895 0.00 0.00 38.46 3.91
124 132 1.003866 GTGGTCTTCAGTCAAACGCAC 60.004 52.381 0.00 0.00 0.00 5.34
126 134 0.232303 GTCTTCAGTCAAACGCACCG 59.768 55.000 0.00 0.00 0.00 4.94
159 167 1.135803 CCGGTTTGGTCGCAAACATAG 60.136 52.381 16.92 9.54 44.39 2.23
160 168 1.533731 CGGTTTGGTCGCAAACATAGT 59.466 47.619 16.92 0.00 44.39 2.12
161 169 2.737783 CGGTTTGGTCGCAAACATAGTA 59.262 45.455 16.92 0.00 44.39 1.82
192 200 2.683933 ATCGACCAAGGCTCGGGT 60.684 61.111 10.28 10.28 40.96 5.28
201 209 2.683362 CCAAGGCTCGGGTTTTCTTATC 59.317 50.000 0.00 0.00 0.00 1.75
203 211 4.010349 CAAGGCTCGGGTTTTCTTATCTT 58.990 43.478 0.00 0.00 0.00 2.40
205 213 5.632034 AGGCTCGGGTTTTCTTATCTTAT 57.368 39.130 0.00 0.00 0.00 1.73
206 214 5.368989 AGGCTCGGGTTTTCTTATCTTATG 58.631 41.667 0.00 0.00 0.00 1.90
237 245 0.033504 TGACCAGGCTTTCTCACGAC 59.966 55.000 0.00 0.00 0.00 4.34
265 274 5.907207 TGGCTTTGTCTACACTATCATCTC 58.093 41.667 0.00 0.00 0.00 2.75
408 417 0.107703 CAGCGAGCAGTATTGGGGAA 60.108 55.000 0.00 0.00 0.00 3.97
420 429 0.034896 TTGGGGAACAAGTCGAGAGC 59.965 55.000 0.00 0.00 33.18 4.09
433 442 2.866688 GAGAGCTCTCGATCAACGC 58.133 57.895 27.19 2.64 42.26 4.84
519 528 3.046390 GACTTCTCTGTTGTGACTGTCG 58.954 50.000 2.98 0.00 0.00 4.35
547 563 1.763655 TCCAGCTCGCCATGATCCT 60.764 57.895 0.00 0.00 0.00 3.24
556 572 1.447643 CCATGATCCTCCCCGTGAC 59.552 63.158 0.00 0.00 0.00 3.67
566 582 2.572290 CTCCCCGTGACAACTTCTTTT 58.428 47.619 0.00 0.00 0.00 2.27
606 622 9.946165 AACAAATCACTACAGTAAAAGTAAAGC 57.054 29.630 0.00 0.00 0.00 3.51
608 624 9.382244 CAAATCACTACAGTAAAAGTAAAGCAC 57.618 33.333 0.00 0.00 0.00 4.40
610 626 7.709269 TCACTACAGTAAAAGTAAAGCACTG 57.291 36.000 0.00 0.00 41.83 3.66
612 628 8.415553 TCACTACAGTAAAAGTAAAGCACTGTA 58.584 33.333 11.22 11.22 45.90 2.74
617 633 9.038803 ACAGTAAAAGTAAAGCACTGTAGTTAC 57.961 33.333 3.98 0.00 45.90 2.50
618 634 9.257651 CAGTAAAAGTAAAGCACTGTAGTTACT 57.742 33.333 0.00 0.00 37.63 2.24
622 638 7.886405 AAGTAAAGCACTGTAGTTACTAAGC 57.114 36.000 0.00 0.00 37.63 3.09
623 639 6.989659 AGTAAAGCACTGTAGTTACTAAGCA 58.010 36.000 0.00 0.00 35.54 3.91
624 640 7.091443 AGTAAAGCACTGTAGTTACTAAGCAG 58.909 38.462 8.03 8.03 35.54 4.24
625 641 5.470047 AAGCACTGTAGTTACTAAGCAGT 57.530 39.130 9.08 9.08 40.54 4.40
626 642 6.585695 AAGCACTGTAGTTACTAAGCAGTA 57.414 37.500 13.06 0.00 38.21 2.74
627 643 6.585695 AGCACTGTAGTTACTAAGCAGTAA 57.414 37.500 13.06 0.00 43.46 2.24
643 659 3.733337 CAGTAAGCAGGTTCACACTTCT 58.267 45.455 0.00 0.00 0.00 2.85
660 676 5.365403 ACTTCTCAGTGAGTAGAAAGTCG 57.635 43.478 27.72 6.17 32.61 4.18
683 699 3.386237 GACTCCGAGCCAGCCAGT 61.386 66.667 0.00 0.00 0.00 4.00
684 700 2.037367 ACTCCGAGCCAGCCAGTA 59.963 61.111 0.00 0.00 0.00 2.74
689 705 3.775654 GAGCCAGCCAGTACCGCT 61.776 66.667 0.00 0.00 36.91 5.52
691 707 3.775654 GCCAGCCAGTACCGCTCT 61.776 66.667 2.12 0.00 33.17 4.09
754 773 1.227853 GTCTCCACCCACACACACC 60.228 63.158 0.00 0.00 0.00 4.16
868 889 4.087182 CGCTCTATATAAACCCTCTCCCA 58.913 47.826 0.00 0.00 0.00 4.37
940 961 4.746115 CACTGCAAGCAACAATACAAACAT 59.254 37.500 0.00 0.00 37.60 2.71
943 964 5.539979 TGCAAGCAACAATACAAACATCAT 58.460 33.333 0.00 0.00 0.00 2.45
944 965 5.634439 TGCAAGCAACAATACAAACATCATC 59.366 36.000 0.00 0.00 0.00 2.92
965 986 1.400371 CGAGCATCCTAAGATCGACCG 60.400 57.143 0.00 0.00 46.76 4.79
982 1003 1.078324 ACCGGAGTCCTTCCTTCCTTA 59.922 52.381 9.46 0.00 44.41 2.69
983 1004 1.481363 CCGGAGTCCTTCCTTCCTTAC 59.519 57.143 7.77 0.00 44.41 2.34
984 1005 2.458620 CGGAGTCCTTCCTTCCTTACT 58.541 52.381 7.77 0.00 44.41 2.24
985 1006 2.832733 CGGAGTCCTTCCTTCCTTACTT 59.167 50.000 7.77 0.00 44.41 2.24
1010 1031 4.115199 GCCGGCCATGGAGAAGGT 62.115 66.667 18.11 0.00 0.00 3.50
1032 1053 2.668280 GGAGAACGTTGACGCTGGC 61.668 63.158 5.00 0.00 44.43 4.85
1361 1388 0.810031 GGCGACGACAAGGTATGCAT 60.810 55.000 3.79 3.79 0.00 3.96
1365 1392 2.534349 CGACGACAAGGTATGCATACAC 59.466 50.000 32.19 22.71 34.98 2.90
1370 1401 0.461163 AAGGTATGCATACACGCGCA 60.461 50.000 32.19 0.00 43.45 6.09
1395 1433 2.159184 GGTGCTCGTGATGATTCTCTGA 60.159 50.000 0.00 0.00 0.00 3.27
1396 1434 2.857152 GTGCTCGTGATGATTCTCTGAC 59.143 50.000 0.00 0.00 0.00 3.51
1397 1435 2.115595 GCTCGTGATGATTCTCTGACG 58.884 52.381 0.00 0.00 0.00 4.35
1398 1436 2.115595 CTCGTGATGATTCTCTGACGC 58.884 52.381 0.00 0.00 0.00 5.19
1399 1437 1.202302 TCGTGATGATTCTCTGACGCC 60.202 52.381 0.00 0.00 0.00 5.68
1400 1438 1.576356 GTGATGATTCTCTGACGCCC 58.424 55.000 0.00 0.00 0.00 6.13
1401 1439 0.103026 TGATGATTCTCTGACGCCCG 59.897 55.000 0.00 0.00 0.00 6.13
1407 1445 2.430382 TTCTCTGACGCCCGTGGAAC 62.430 60.000 0.00 0.00 0.00 3.62
1444 1482 3.830192 GGAATGCAGCTTGGGCCG 61.830 66.667 0.00 0.00 39.73 6.13
1594 1632 2.182030 GACGAGGTCGGCTTCCTG 59.818 66.667 4.13 0.00 45.57 3.86
1756 1794 4.227134 CCCTCCATCGACCGCCTG 62.227 72.222 0.00 0.00 0.00 4.85
1907 1945 1.344438 ACATCGCCGTGGACATATGAT 59.656 47.619 10.38 0.00 0.00 2.45
1908 1946 2.560981 ACATCGCCGTGGACATATGATA 59.439 45.455 10.38 0.00 0.00 2.15
1909 1947 3.195610 ACATCGCCGTGGACATATGATAT 59.804 43.478 10.38 0.00 0.00 1.63
1910 1948 3.230743 TCGCCGTGGACATATGATATG 57.769 47.619 10.38 10.75 0.00 1.78
1911 1949 2.823154 TCGCCGTGGACATATGATATGA 59.177 45.455 18.62 0.00 0.00 2.15
2075 2119 0.603569 AGTCTGGCTAGGTGTCGTTG 59.396 55.000 0.00 0.00 0.00 4.10
2094 2138 7.169982 TGTCGTTGATTTCTTTCTCTTCTCTTC 59.830 37.037 0.00 0.00 0.00 2.87
2096 2140 6.425114 CGTTGATTTCTTTCTCTTCTCTTCCA 59.575 38.462 0.00 0.00 0.00 3.53
2100 2144 6.739331 TTTCTTTCTCTTCTCTTCCACTCT 57.261 37.500 0.00 0.00 0.00 3.24
2139 2183 6.072175 TGTGTTTGTAACTGGGAATCTTATGC 60.072 38.462 0.00 0.00 0.00 3.14
2276 2324 0.611200 TGGGTAGTGCGCATTACAGT 59.389 50.000 34.56 10.87 34.97 3.55
2313 2361 0.824759 AACTCTGGCGGACTGGTATC 59.175 55.000 0.00 0.00 0.00 2.24
2380 2430 0.329261 TTGATGCCAAGAGGGAGTGG 59.671 55.000 0.00 0.00 39.29 4.00
2386 2438 1.938585 CCAAGAGGGAGTGGAGTACA 58.061 55.000 0.00 0.00 40.01 2.90
2410 2462 2.099405 CCGGCCCAAGTTGATTTATGT 58.901 47.619 3.87 0.00 0.00 2.29
2422 2474 5.652452 AGTTGATTTATGTTAGTTCTGCCCC 59.348 40.000 0.00 0.00 0.00 5.80
2423 2475 5.186256 TGATTTATGTTAGTTCTGCCCCA 57.814 39.130 0.00 0.00 0.00 4.96
2492 2545 7.201696 CGTGGTAACCATTTAATGCTACTGATT 60.202 37.037 0.00 0.00 35.28 2.57
2493 2546 8.466798 GTGGTAACCATTTAATGCTACTGATTT 58.533 33.333 0.00 0.00 35.28 2.17
2512 2565 4.503741 TTTTATCAACACCTGCTTCTGC 57.496 40.909 0.00 0.00 40.20 4.26
2652 2708 1.452110 CATCATCGTGCCCAACTTGA 58.548 50.000 0.00 0.00 0.00 3.02
2653 2709 1.131126 CATCATCGTGCCCAACTTGAC 59.869 52.381 0.00 0.00 0.00 3.18
2654 2710 0.107643 TCATCGTGCCCAACTTGACA 59.892 50.000 0.00 0.00 0.00 3.58
2655 2711 0.950836 CATCGTGCCCAACTTGACAA 59.049 50.000 0.00 0.00 0.00 3.18
2656 2712 0.951558 ATCGTGCCCAACTTGACAAC 59.048 50.000 0.00 0.00 0.00 3.32
2657 2713 0.107410 TCGTGCCCAACTTGACAACT 60.107 50.000 0.00 0.00 0.00 3.16
2658 2714 0.738389 CGTGCCCAACTTGACAACTT 59.262 50.000 0.00 0.00 0.00 2.66
2721 2778 8.290325 ACGATCAAAGAAACTTATCTCCAAAAC 58.710 33.333 0.00 0.00 0.00 2.43
2730 2787 9.196552 GAAACTTATCTCCAAAACAAATCCAAG 57.803 33.333 0.00 0.00 0.00 3.61
2735 2792 5.912892 TCTCCAAAACAAATCCAAGAAACC 58.087 37.500 0.00 0.00 0.00 3.27
2739 2796 5.827267 CCAAAACAAATCCAAGAAACCCAAT 59.173 36.000 0.00 0.00 0.00 3.16
2740 2797 6.995091 CCAAAACAAATCCAAGAAACCCAATA 59.005 34.615 0.00 0.00 0.00 1.90
2792 2864 2.965147 GCGCTGACGGCAATGAACA 61.965 57.895 7.13 0.00 41.91 3.18
2793 2865 1.573932 CGCTGACGGCAATGAACAA 59.426 52.632 7.13 0.00 41.91 2.83
2804 2876 4.060205 GGCAATGAACAAAAAGAGTGCAT 58.940 39.130 0.00 0.00 36.82 3.96
2805 2877 4.084223 GGCAATGAACAAAAAGAGTGCATG 60.084 41.667 0.00 0.00 35.44 4.06
2841 2913 4.412270 CGCGGGCGGCAAAATTGA 62.412 61.111 17.50 0.00 43.84 2.57
2842 2914 2.184066 GCGGGCGGCAAAATTGAT 59.816 55.556 12.47 0.00 42.87 2.57
2843 2915 1.435515 GCGGGCGGCAAAATTGATA 59.564 52.632 12.47 0.00 42.87 2.15
2844 2916 0.179124 GCGGGCGGCAAAATTGATAA 60.179 50.000 12.47 0.00 42.87 1.75
2845 2917 1.737363 GCGGGCGGCAAAATTGATAAA 60.737 47.619 12.47 0.00 42.87 1.40
2846 2918 2.820330 CGGGCGGCAAAATTGATAAAT 58.180 42.857 12.47 0.00 0.00 1.40
2847 2919 3.194062 CGGGCGGCAAAATTGATAAATT 58.806 40.909 12.47 0.00 0.00 1.82
2848 2920 3.620821 CGGGCGGCAAAATTGATAAATTT 59.379 39.130 12.47 0.00 34.09 1.82
2849 2921 4.806247 CGGGCGGCAAAATTGATAAATTTA 59.194 37.500 12.47 0.00 32.51 1.40
2850 2922 5.292101 CGGGCGGCAAAATTGATAAATTTAA 59.708 36.000 12.47 0.00 32.51 1.52
2851 2923 6.482835 GGGCGGCAAAATTGATAAATTTAAC 58.517 36.000 12.47 0.00 32.51 2.01
2852 2924 6.457663 GGGCGGCAAAATTGATAAATTTAACC 60.458 38.462 12.47 5.53 32.51 2.85
2853 2925 6.315144 GGCGGCAAAATTGATAAATTTAACCT 59.685 34.615 3.07 0.00 32.51 3.50
2854 2926 7.492994 GGCGGCAAAATTGATAAATTTAACCTA 59.507 33.333 3.07 0.00 32.51 3.08
2855 2927 9.040939 GCGGCAAAATTGATAAATTTAACCTAT 57.959 29.630 13.75 0.00 32.51 2.57
2888 2960 8.964476 ATCAAATTATAGAATGAACTGTCCGT 57.036 30.769 0.00 0.00 0.00 4.69
2889 2961 8.196802 TCAAATTATAGAATGAACTGTCCGTG 57.803 34.615 0.00 0.00 0.00 4.94
2890 2962 8.038351 TCAAATTATAGAATGAACTGTCCGTGA 58.962 33.333 0.00 0.00 0.00 4.35
2891 2963 8.664798 CAAATTATAGAATGAACTGTCCGTGAA 58.335 33.333 0.00 0.00 0.00 3.18
2892 2964 8.786826 AATTATAGAATGAACTGTCCGTGAAA 57.213 30.769 0.00 0.00 0.00 2.69
2893 2965 7.591006 TTATAGAATGAACTGTCCGTGAAAC 57.409 36.000 0.00 0.00 0.00 2.78
2894 2966 4.073293 AGAATGAACTGTCCGTGAAACT 57.927 40.909 0.00 0.00 31.75 2.66
2895 2967 5.209818 AGAATGAACTGTCCGTGAAACTA 57.790 39.130 0.00 0.00 31.75 2.24
2896 2968 5.794894 AGAATGAACTGTCCGTGAAACTAT 58.205 37.500 0.00 0.00 31.75 2.12
2897 2969 6.231211 AGAATGAACTGTCCGTGAAACTATT 58.769 36.000 0.00 0.00 31.75 1.73
2898 2970 6.710744 AGAATGAACTGTCCGTGAAACTATTT 59.289 34.615 0.00 0.00 31.75 1.40
2899 2971 5.917541 TGAACTGTCCGTGAAACTATTTC 57.082 39.130 0.00 0.00 40.08 2.17
2900 2972 5.361427 TGAACTGTCCGTGAAACTATTTCA 58.639 37.500 0.00 0.00 46.68 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.750952 TCGTAGTCACAGTTCTCTTCTG 57.249 45.455 0.00 0.00 38.68 3.02
2 3 4.822896 ACTTCGTAGTCACAGTTCTCTTCT 59.177 41.667 0.00 0.00 0.00 2.85
3 4 5.110940 ACTTCGTAGTCACAGTTCTCTTC 57.889 43.478 0.00 0.00 0.00 2.87
4 5 5.333952 CGTACTTCGTAGTCACAGTTCTCTT 60.334 44.000 0.00 0.00 35.78 2.85
5 6 4.152045 CGTACTTCGTAGTCACAGTTCTCT 59.848 45.833 0.00 0.00 35.78 3.10
8 9 4.395581 TCGTACTTCGTAGTCACAGTTC 57.604 45.455 0.00 0.00 40.80 3.01
10 11 3.363378 CGTTCGTACTTCGTAGTCACAGT 60.363 47.826 0.00 0.00 40.80 3.55
11 12 3.120889 TCGTTCGTACTTCGTAGTCACAG 60.121 47.826 0.00 0.00 40.80 3.66
12 13 2.799978 TCGTTCGTACTTCGTAGTCACA 59.200 45.455 0.00 0.00 40.80 3.58
13 14 3.149234 GTCGTTCGTACTTCGTAGTCAC 58.851 50.000 0.00 0.00 40.80 3.67
14 15 2.159973 CGTCGTTCGTACTTCGTAGTCA 60.160 50.000 0.00 0.00 40.80 3.41
15 16 2.413126 CGTCGTTCGTACTTCGTAGTC 58.587 52.381 0.00 0.00 40.80 2.59
16 17 1.126846 CCGTCGTTCGTACTTCGTAGT 59.873 52.381 0.00 0.00 40.80 2.73
17 18 1.126846 ACCGTCGTTCGTACTTCGTAG 59.873 52.381 0.00 0.00 40.80 3.51
18 19 1.144969 ACCGTCGTTCGTACTTCGTA 58.855 50.000 0.00 0.00 40.80 3.43
19 20 1.126846 CTACCGTCGTTCGTACTTCGT 59.873 52.381 0.00 0.00 40.80 3.85
20 21 1.390123 TCTACCGTCGTTCGTACTTCG 59.610 52.381 0.00 0.00 41.41 3.79
21 22 2.668457 TCTCTACCGTCGTTCGTACTTC 59.332 50.000 0.00 0.00 37.94 3.01
22 23 2.688507 TCTCTACCGTCGTTCGTACTT 58.311 47.619 0.00 0.00 37.94 2.24
23 24 2.370281 TCTCTACCGTCGTTCGTACT 57.630 50.000 0.00 0.00 37.94 2.73
24 25 2.848751 GCATCTCTACCGTCGTTCGTAC 60.849 54.545 0.00 0.00 37.94 3.67
36 37 1.373497 CGCCGGGATGCATCTCTAC 60.373 63.158 23.85 14.31 0.00 2.59
124 132 2.279517 CGGAAAGGGATCTCGCGG 60.280 66.667 6.13 0.00 0.00 6.46
126 134 0.392595 AAACCGGAAAGGGATCTCGC 60.393 55.000 9.46 0.00 46.96 5.03
159 167 1.291877 CGATGCGCCCTGGCTAATAC 61.292 60.000 4.18 0.00 39.32 1.89
160 168 1.005037 CGATGCGCCCTGGCTAATA 60.005 57.895 4.18 0.00 39.32 0.98
161 169 2.281070 CGATGCGCCCTGGCTAAT 60.281 61.111 4.18 0.00 39.32 1.73
180 188 2.194201 TAAGAAAACCCGAGCCTTGG 57.806 50.000 0.00 0.00 0.00 3.61
182 190 4.302559 AAGATAAGAAAACCCGAGCCTT 57.697 40.909 0.00 0.00 0.00 4.35
201 209 5.351233 TGGTCAAAGCGTGTTTACATAAG 57.649 39.130 0.00 0.00 0.00 1.73
203 211 3.749088 CCTGGTCAAAGCGTGTTTACATA 59.251 43.478 0.00 0.00 0.00 2.29
205 213 1.944024 CCTGGTCAAAGCGTGTTTACA 59.056 47.619 0.00 0.00 0.00 2.41
206 214 1.334689 GCCTGGTCAAAGCGTGTTTAC 60.335 52.381 0.00 0.00 0.00 2.01
237 245 1.160137 GTGTAGACAAAGCCAGCAGG 58.840 55.000 0.00 0.00 38.23 4.85
265 274 6.262496 ACTGCATCAAGATGGTGAAATATGAG 59.738 38.462 11.66 0.00 39.16 2.90
297 306 0.737367 ACGGCGTGATGATCACTGTG 60.737 55.000 21.83 13.44 44.85 3.66
420 429 2.103143 AGGCGCGTTGATCGAGAG 59.897 61.111 8.43 0.00 41.61 3.20
429 438 2.117941 GAGTCAAAAGCAGGCGCGTT 62.118 55.000 8.43 0.00 45.49 4.84
433 442 0.669318 TACCGAGTCAAAAGCAGGCG 60.669 55.000 0.00 0.00 0.00 5.52
512 521 4.664677 ACCAGCGGTGCGACAGTC 62.665 66.667 9.63 0.00 32.98 3.51
547 563 2.092861 TGAAAAGAAGTTGTCACGGGGA 60.093 45.455 0.00 0.00 0.00 4.81
556 572 1.263217 CCGGTCGGTGAAAAGAAGTTG 59.737 52.381 0.55 0.00 0.00 3.16
566 582 2.835580 TTTGTTTATCCGGTCGGTGA 57.164 45.000 9.36 0.00 36.47 4.02
606 622 6.387465 TGCTTACTGCTTAGTAACTACAGTG 58.613 40.000 14.46 0.00 41.45 3.66
608 624 6.037098 CCTGCTTACTGCTTAGTAACTACAG 58.963 44.000 0.00 0.00 43.37 2.74
610 626 5.963594 ACCTGCTTACTGCTTAGTAACTAC 58.036 41.667 0.00 0.00 43.37 2.73
611 627 6.209986 TGAACCTGCTTACTGCTTAGTAACTA 59.790 38.462 0.00 0.00 43.37 2.24
612 628 5.011738 TGAACCTGCTTACTGCTTAGTAACT 59.988 40.000 0.00 0.00 43.37 2.24
613 629 5.120363 GTGAACCTGCTTACTGCTTAGTAAC 59.880 44.000 0.00 0.00 43.37 2.50
614 630 5.221561 TGTGAACCTGCTTACTGCTTAGTAA 60.222 40.000 0.00 0.00 43.37 2.24
615 631 4.282449 TGTGAACCTGCTTACTGCTTAGTA 59.718 41.667 0.00 0.00 43.37 1.82
616 632 3.071023 TGTGAACCTGCTTACTGCTTAGT 59.929 43.478 0.00 0.00 43.37 2.24
617 633 3.433615 GTGTGAACCTGCTTACTGCTTAG 59.566 47.826 0.00 0.00 43.37 2.18
618 634 3.071023 AGTGTGAACCTGCTTACTGCTTA 59.929 43.478 0.00 0.00 43.37 3.09
619 635 2.158755 AGTGTGAACCTGCTTACTGCTT 60.159 45.455 0.00 0.00 43.37 3.91
620 636 1.417890 AGTGTGAACCTGCTTACTGCT 59.582 47.619 0.00 0.00 43.37 4.24
621 637 1.884235 AGTGTGAACCTGCTTACTGC 58.116 50.000 0.00 0.00 43.25 4.40
622 638 3.733337 AGAAGTGTGAACCTGCTTACTG 58.267 45.455 0.00 0.00 0.00 2.74
623 639 3.388024 TGAGAAGTGTGAACCTGCTTACT 59.612 43.478 0.00 0.00 0.00 2.24
624 640 3.728845 TGAGAAGTGTGAACCTGCTTAC 58.271 45.455 0.00 0.00 0.00 2.34
625 641 3.388024 ACTGAGAAGTGTGAACCTGCTTA 59.612 43.478 0.00 0.00 0.00 3.09
626 642 2.171448 ACTGAGAAGTGTGAACCTGCTT 59.829 45.455 0.00 0.00 0.00 3.91
627 643 1.765314 ACTGAGAAGTGTGAACCTGCT 59.235 47.619 0.00 0.00 0.00 4.24
643 659 3.186001 GTCGTCGACTTTCTACTCACTGA 59.814 47.826 18.09 0.00 0.00 3.41
660 676 3.384014 CTGGCTCGGAGTCGTCGTC 62.384 68.421 4.99 0.00 37.69 4.20
668 684 2.496817 GTACTGGCTGGCTCGGAG 59.503 66.667 0.00 0.00 0.00 4.63
669 685 3.075005 GGTACTGGCTGGCTCGGA 61.075 66.667 2.00 0.00 0.00 4.55
670 686 4.514577 CGGTACTGGCTGGCTCGG 62.515 72.222 2.00 0.00 0.00 4.63
672 688 3.724914 GAGCGGTACTGGCTGGCTC 62.725 68.421 15.10 9.36 41.72 4.70
673 689 3.775654 GAGCGGTACTGGCTGGCT 61.776 66.667 15.10 4.65 41.72 4.75
683 699 0.245539 GCAAGGTACACAGAGCGGTA 59.754 55.000 0.00 0.00 0.00 4.02
684 700 1.004918 GCAAGGTACACAGAGCGGT 60.005 57.895 0.00 0.00 0.00 5.68
688 704 1.079127 CCCGGCAAGGTACACAGAG 60.079 63.158 0.00 0.00 38.74 3.35
689 705 2.589157 CCCCGGCAAGGTACACAGA 61.589 63.158 0.00 0.00 38.74 3.41
691 707 2.119484 CTTCCCCGGCAAGGTACACA 62.119 60.000 0.00 0.00 38.74 3.72
733 752 3.936203 TGTGTGGGTGGAGACGGC 61.936 66.667 0.00 0.00 0.00 5.68
781 802 3.083349 CCCGGGATGTCAGCTGGA 61.083 66.667 18.48 0.70 0.00 3.86
827 848 3.408853 GAGGGTGGTAGGTGGGCC 61.409 72.222 0.00 0.00 0.00 5.80
837 858 2.526888 TATATAGAGCGGGAGGGTGG 57.473 55.000 0.00 0.00 0.00 4.61
868 889 1.538876 TGTGGCTTGGAGCTAGGGT 60.539 57.895 0.00 0.00 41.99 4.34
940 961 2.489722 CGATCTTAGGATGCTCGGATGA 59.510 50.000 6.59 0.00 31.46 2.92
943 964 1.880675 GTCGATCTTAGGATGCTCGGA 59.119 52.381 0.00 0.00 31.46 4.55
944 965 1.068194 GGTCGATCTTAGGATGCTCGG 60.068 57.143 0.00 0.00 31.46 4.63
965 986 4.286291 TGAAAGTAAGGAAGGAAGGACTCC 59.714 45.833 0.00 0.00 45.81 3.85
982 1003 2.047560 GGCCGGCTACGTGAAAGT 60.048 61.111 28.56 0.00 38.78 2.66
983 1004 1.449601 ATGGCCGGCTACGTGAAAG 60.450 57.895 28.56 0.00 38.78 2.62
984 1005 1.743623 CATGGCCGGCTACGTGAAA 60.744 57.895 28.56 2.22 38.78 2.69
985 1006 2.125310 CATGGCCGGCTACGTGAA 60.125 61.111 28.56 3.74 38.78 3.18
1010 1031 2.355363 CGTCAACGTTCTCCGCCA 60.355 61.111 0.00 0.00 41.42 5.69
1178 1205 1.621814 CCTTCTTGTAGACGGGGTTGA 59.378 52.381 0.00 0.00 30.60 3.18
1370 1401 2.835701 AATCATCACGAGCACCGCGT 62.836 55.000 4.92 0.00 41.00 6.01
1376 1407 2.478539 CGTCAGAGAATCATCACGAGCA 60.479 50.000 0.00 0.00 36.24 4.26
1397 1435 3.443045 CAGCCATGTTCCACGGGC 61.443 66.667 0.00 0.00 40.25 6.13
1398 1436 2.040544 GTCAGCCATGTTCCACGGG 61.041 63.158 0.00 0.00 0.00 5.28
1399 1437 2.040544 GGTCAGCCATGTTCCACGG 61.041 63.158 0.00 0.00 34.09 4.94
1400 1438 1.003355 AGGTCAGCCATGTTCCACG 60.003 57.895 0.00 0.00 37.19 4.94
1401 1439 0.250901 ACAGGTCAGCCATGTTCCAC 60.251 55.000 0.00 0.00 37.19 4.02
1407 1445 1.538512 CACAGAAACAGGTCAGCCATG 59.461 52.381 0.00 0.00 37.19 3.66
1885 1923 0.750249 ATATGTCCACGGCGATGTCA 59.250 50.000 16.62 8.37 0.00 3.58
1907 1945 4.830765 GCACGGCCTGCGGTCATA 62.831 66.667 10.76 0.00 35.72 2.15
1920 1958 4.707840 CAGTTCAGCGCGTGCACG 62.708 66.667 34.01 34.01 46.23 5.34
1930 1968 1.330521 CCGACACAAACCACAGTTCAG 59.669 52.381 0.00 0.00 34.19 3.02
2027 2065 0.036010 AGTGGTAGCAGCGCAATTCT 60.036 50.000 11.47 2.85 0.00 2.40
2075 2119 7.386059 AGAGTGGAAGAGAAGAGAAAGAAATC 58.614 38.462 0.00 0.00 0.00 2.17
2094 2138 3.003275 ACACAACGCATAACAAAGAGTGG 59.997 43.478 0.00 0.00 0.00 4.00
2096 2140 3.625764 ACACACAACGCATAACAAAGAGT 59.374 39.130 0.00 0.00 0.00 3.24
2100 2144 4.486090 ACAAACACACAACGCATAACAAA 58.514 34.783 0.00 0.00 0.00 2.83
2234 2278 1.809684 GTTGGTAGGAGGAACACAGC 58.190 55.000 0.00 0.00 0.00 4.40
2260 2304 4.663636 AAGAAACTGTAATGCGCACTAC 57.336 40.909 21.37 21.37 0.00 2.73
2276 2324 5.237779 CAGAGTTACCCGCAGTTAAAAGAAA 59.762 40.000 0.00 0.00 0.00 2.52
2313 2361 3.789224 GTGAAAACCGTTGCTAAACTGTG 59.211 43.478 0.00 0.00 34.41 3.66
2322 2370 0.736053 TGTGAGGTGAAAACCGTTGC 59.264 50.000 0.00 0.00 34.28 4.17
2380 2430 0.391263 CTTGGGCCGGACTTGTACTC 60.391 60.000 7.57 0.00 0.00 2.59
2386 2438 0.112412 AATCAACTTGGGCCGGACTT 59.888 50.000 7.57 0.00 0.00 3.01
2410 2462 2.562298 CAGCATTTTGGGGCAGAACTAA 59.438 45.455 0.00 0.00 0.00 2.24
2422 2474 2.152868 CACGTTTAACCGCAGCATTTTG 59.847 45.455 0.00 0.00 0.00 2.44
2423 2475 2.389998 CACGTTTAACCGCAGCATTTT 58.610 42.857 0.00 0.00 0.00 1.82
2467 2520 6.995511 TCAGTAGCATTAAATGGTTACCAC 57.004 37.500 6.10 0.00 41.83 4.16
2546 2602 0.787787 GACAAACGCACGCACTGATA 59.212 50.000 0.00 0.00 0.00 2.15
2652 2708 1.981256 AACCATCAAGCGGAAGTTGT 58.019 45.000 0.00 0.00 0.00 3.32
2653 2709 2.293122 TGAAACCATCAAGCGGAAGTTG 59.707 45.455 0.00 0.00 34.30 3.16
2654 2710 2.554032 CTGAAACCATCAAGCGGAAGTT 59.446 45.455 0.00 0.00 37.67 2.66
2655 2711 2.154462 CTGAAACCATCAAGCGGAAGT 58.846 47.619 0.00 0.00 37.67 3.01
2656 2712 2.154462 ACTGAAACCATCAAGCGGAAG 58.846 47.619 0.00 0.00 37.67 3.46
2657 2713 2.270352 ACTGAAACCATCAAGCGGAA 57.730 45.000 0.00 0.00 37.67 4.30
2658 2714 2.270352 AACTGAAACCATCAAGCGGA 57.730 45.000 0.00 0.00 37.67 5.54
2721 2778 6.974622 CGAGATTATTGGGTTTCTTGGATTTG 59.025 38.462 0.00 0.00 0.00 2.32
2730 2787 5.465935 TGCAAAACGAGATTATTGGGTTTC 58.534 37.500 0.00 0.00 31.05 2.78
2735 2792 3.100817 CGCTGCAAAACGAGATTATTGG 58.899 45.455 0.00 0.00 0.00 3.16
2739 2796 0.446222 GCCGCTGCAAAACGAGATTA 59.554 50.000 0.00 0.00 37.47 1.75
2740 2797 1.210155 GCCGCTGCAAAACGAGATT 59.790 52.632 0.00 0.00 37.47 2.40
2792 2864 2.380064 TGTCCCCATGCACTCTTTTT 57.620 45.000 0.00 0.00 0.00 1.94
2793 2865 2.380064 TTGTCCCCATGCACTCTTTT 57.620 45.000 0.00 0.00 0.00 2.27
2804 2876 3.686120 GCGGTAGGAATTATTTGTCCCCA 60.686 47.826 0.00 0.00 34.13 4.96
2805 2877 2.882761 GCGGTAGGAATTATTTGTCCCC 59.117 50.000 0.00 0.00 34.13 4.81
2862 2934 9.396022 ACGGACAGTTCATTCTATAATTTGATT 57.604 29.630 0.00 0.00 0.00 2.57
2863 2935 8.830580 CACGGACAGTTCATTCTATAATTTGAT 58.169 33.333 0.00 0.00 0.00 2.57
2864 2936 8.038351 TCACGGACAGTTCATTCTATAATTTGA 58.962 33.333 0.00 0.00 0.00 2.69
2865 2937 8.196802 TCACGGACAGTTCATTCTATAATTTG 57.803 34.615 0.00 0.00 0.00 2.32
2866 2938 8.786826 TTCACGGACAGTTCATTCTATAATTT 57.213 30.769 0.00 0.00 0.00 1.82
2867 2939 8.665685 GTTTCACGGACAGTTCATTCTATAATT 58.334 33.333 0.00 0.00 0.00 1.40
2868 2940 8.041323 AGTTTCACGGACAGTTCATTCTATAAT 58.959 33.333 0.00 0.00 0.00 1.28
2869 2941 7.383687 AGTTTCACGGACAGTTCATTCTATAA 58.616 34.615 0.00 0.00 0.00 0.98
2870 2942 6.931838 AGTTTCACGGACAGTTCATTCTATA 58.068 36.000 0.00 0.00 0.00 1.31
2871 2943 5.794894 AGTTTCACGGACAGTTCATTCTAT 58.205 37.500 0.00 0.00 0.00 1.98
2872 2944 5.209818 AGTTTCACGGACAGTTCATTCTA 57.790 39.130 0.00 0.00 0.00 2.10
2873 2945 4.073293 AGTTTCACGGACAGTTCATTCT 57.927 40.909 0.00 0.00 0.00 2.40
2874 2946 6.481954 AATAGTTTCACGGACAGTTCATTC 57.518 37.500 0.00 0.00 0.00 2.67
2875 2947 6.485313 TGAAATAGTTTCACGGACAGTTCATT 59.515 34.615 1.24 0.00 44.21 2.57
2876 2948 5.995282 TGAAATAGTTTCACGGACAGTTCAT 59.005 36.000 1.24 0.00 44.21 2.57
2877 2949 5.361427 TGAAATAGTTTCACGGACAGTTCA 58.639 37.500 1.24 0.00 44.21 3.18
2878 2950 5.917541 TGAAATAGTTTCACGGACAGTTC 57.082 39.130 1.24 0.00 44.21 3.01


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

AutoCloner maintained by Alex Coulton.