Multiple sequence alignment - TraesCS5A01G246500

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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 TraesCS5A01G246500 chr5A 100.000 2894 0 0 1 2894 459777340 459774447 0.000000e+00 5345
1 TraesCS5A01G246500 chr5B 89.019 2978 123 86 1 2894 425092621 425095478 0.000000e+00 3500
2 TraesCS5A01G246500 chr5D 91.443 2501 83 54 435 2894 359474258 359476668 0.000000e+00 3312
3 TraesCS5A01G246500 chr5D 83.333 402 36 17 1 401 359473675 359474046 2.760000e-90 342
4 TraesCS5A01G246500 chr4A 82.653 196 34 0 1690 1885 535035691 535035886 1.070000e-39 174
5 TraesCS5A01G246500 chr4D 82.967 182 31 0 1690 1871 61852301 61852482 6.420000e-37 165
6 TraesCS5A01G246500 chr4B 81.538 195 36 0 1691 1885 90892349 90892155 8.300000e-36 161
7 TraesCS5A01G246500 chr6B 80.769 208 29 11 1664 1864 539195275 539195072 4.990000e-33 152
8 TraesCS5A01G246500 chr1B 80.925 173 31 2 1693 1864 667750250 667750421 5.030000e-28 135
9 TraesCS5A01G246500 chr1D 79.885 174 31 4 1693 1864 479540798 479540969 1.090000e-24 124
10 TraesCS5A01G246500 chr3A 79.191 173 32 4 1693 1863 423672120 423672290 1.820000e-22 117


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 TraesCS5A01G246500 chr5A 459774447 459777340 2893 True 5345 5345 100.000 1 2894 1 chr5A.!!$R1 2893
1 TraesCS5A01G246500 chr5B 425092621 425095478 2857 False 3500 3500 89.019 1 2894 1 chr5B.!!$F1 2893
2 TraesCS5A01G246500 chr5D 359473675 359476668 2993 False 1827 3312 87.388 1 2894 2 chr5D.!!$F1 2893

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
413 415 0.108992 ATTTGCTTGACGCTGCATGG 60.109 50.0 0.0 0.0 39.07 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 2279 0.039437 GCGAATGCGGTAGCTAGCTA 60.039 55.0 20.67 20.67 45.42 3.32 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
58 59 2.417719 GTCCTGCTTCAGTACTTGGTG 58.582 52.381 0.00 0.00 0.00 4.17
68 69 1.003580 AGTACTTGGTGTGCATGGAGG 59.996 52.381 0.00 0.00 33.54 4.30
69 70 0.322456 TACTTGGTGTGCATGGAGGC 60.322 55.000 0.00 0.00 0.00 4.70
70 71 1.303888 CTTGGTGTGCATGGAGGCT 60.304 57.895 0.00 0.00 34.04 4.58
71 72 0.896940 CTTGGTGTGCATGGAGGCTT 60.897 55.000 0.00 0.00 34.04 4.35
72 73 1.180456 TTGGTGTGCATGGAGGCTTG 61.180 55.000 0.00 0.00 34.04 4.01
73 74 2.345760 GGTGTGCATGGAGGCTTGG 61.346 63.158 0.00 0.00 34.04 3.61
74 75 2.036098 TGTGCATGGAGGCTTGGG 59.964 61.111 0.00 0.00 34.04 4.12
75 76 2.356278 GTGCATGGAGGCTTGGGA 59.644 61.111 0.00 0.00 34.04 4.37
76 77 1.304381 GTGCATGGAGGCTTGGGAA 60.304 57.895 0.00 0.00 34.04 3.97
77 78 1.000521 TGCATGGAGGCTTGGGAAG 60.001 57.895 0.00 0.00 34.04 3.46
78 79 1.000396 GCATGGAGGCTTGGGAAGT 60.000 57.895 0.00 0.00 0.00 3.01
79 80 1.318158 GCATGGAGGCTTGGGAAGTG 61.318 60.000 0.00 0.00 0.00 3.16
80 81 1.000396 ATGGAGGCTTGGGAAGTGC 60.000 57.895 0.00 0.00 0.00 4.40
81 82 2.747855 GGAGGCTTGGGAAGTGCG 60.748 66.667 0.00 0.00 0.00 5.34
82 83 2.347490 GAGGCTTGGGAAGTGCGA 59.653 61.111 0.00 0.00 0.00 5.10
83 84 1.743252 GAGGCTTGGGAAGTGCGAG 60.743 63.158 0.00 0.00 0.00 5.03
86 87 2.684843 GCTTGGGAAGTGCGAGCTG 61.685 63.158 0.00 0.00 0.00 4.24
95 96 1.026718 AGTGCGAGCTGGTTTATGGC 61.027 55.000 0.00 0.00 0.00 4.40
96 97 1.026718 GTGCGAGCTGGTTTATGGCT 61.027 55.000 0.00 0.00 39.16 4.75
98 99 1.723870 CGAGCTGGTTTATGGCTGC 59.276 57.895 0.00 0.00 36.37 5.25
99 100 1.723870 GAGCTGGTTTATGGCTGCG 59.276 57.895 0.00 0.00 36.37 5.18
104 105 0.250945 TGGTTTATGGCTGCGTCCAA 60.251 50.000 0.63 0.00 39.96 3.53
105 106 0.885196 GGTTTATGGCTGCGTCCAAA 59.115 50.000 0.63 0.00 39.96 3.28
106 107 1.271102 GGTTTATGGCTGCGTCCAAAA 59.729 47.619 0.63 1.87 39.96 2.44
107 108 2.324860 GTTTATGGCTGCGTCCAAAAC 58.675 47.619 0.63 9.00 39.96 2.43
117 118 0.306533 CGTCCAAAACGTGAACCTGG 59.693 55.000 0.00 0.00 46.42 4.45
140 141 0.167470 CGAGCGAGTGGTAGAAACGA 59.833 55.000 0.00 0.00 0.00 3.85
146 147 3.610114 GCGAGTGGTAGAAACGAACTGTA 60.610 47.826 0.00 0.00 0.00 2.74
147 148 4.730657 CGAGTGGTAGAAACGAACTGTAT 58.269 43.478 0.00 0.00 0.00 2.29
148 149 5.159209 CGAGTGGTAGAAACGAACTGTATT 58.841 41.667 0.00 0.00 0.00 1.89
149 150 6.317088 CGAGTGGTAGAAACGAACTGTATTA 58.683 40.000 0.00 0.00 0.00 0.98
156 157 8.811378 GGTAGAAACGAACTGTATTATTACCAC 58.189 37.037 0.00 0.00 0.00 4.16
168 169 2.375173 ATTACCACCCTCGACGTTTC 57.625 50.000 0.00 0.00 0.00 2.78
207 208 2.126734 ACGGACGGTAGAAACGCG 60.127 61.111 3.53 3.53 34.00 6.01
229 230 1.750930 CACAGTGTGCAGGAGGAGT 59.249 57.895 10.97 0.00 0.00 3.85
230 231 0.602106 CACAGTGTGCAGGAGGAGTG 60.602 60.000 10.97 0.00 0.00 3.51
231 232 1.670406 CAGTGTGCAGGAGGAGTGC 60.670 63.158 0.00 0.00 41.59 4.40
237 238 1.072159 GCAGGAGGAGTGCAACAGT 59.928 57.895 0.00 0.00 41.43 3.55
240 241 1.131638 AGGAGGAGTGCAACAGTGAA 58.868 50.000 0.00 0.00 41.43 3.18
250 251 4.102649 GTGCAACAGTGAAGGTTTTGTAC 58.897 43.478 0.00 0.00 36.32 2.90
258 259 1.262151 GAAGGTTTTGTACGCTTGCGA 59.738 47.619 22.03 2.66 0.00 5.10
274 275 2.510238 GAGCGGTGCAGGTGCTAG 60.510 66.667 7.20 0.00 39.49 3.42
275 276 4.767255 AGCGGTGCAGGTGCTAGC 62.767 66.667 8.10 8.10 42.66 3.42
288 289 3.713764 AGGTGCTAGCACTTAATCAGGAT 59.286 43.478 38.82 14.90 45.52 3.24
301 302 6.540189 ACTTAATCAGGATCTGAAAATGACGG 59.460 38.462 1.53 0.00 44.04 4.79
338 339 2.119495 CTCTGGGGAAAGGCTAGCTTA 58.881 52.381 15.72 0.00 0.00 3.09
368 369 3.309436 TTGCATCACTCGACCCGGG 62.309 63.158 22.25 22.25 0.00 5.73
379 380 1.026584 CGACCCGGGAAACAGTTTTT 58.973 50.000 32.02 0.00 0.00 1.94
383 384 1.067974 CCCGGGAAACAGTTTTTGGTC 59.932 52.381 18.48 0.00 0.00 4.02
387 389 2.946990 GGGAAACAGTTTTTGGTCGAGA 59.053 45.455 0.00 0.00 0.00 4.04
410 412 3.574284 ATAAATTTGCTTGACGCTGCA 57.426 38.095 0.00 0.00 40.11 4.41
411 413 2.443887 AAATTTGCTTGACGCTGCAT 57.556 40.000 0.00 0.00 39.07 3.96
413 415 0.108992 ATTTGCTTGACGCTGCATGG 60.109 50.000 0.00 0.00 39.07 3.66
414 416 2.752322 TTTGCTTGACGCTGCATGGC 62.752 55.000 0.00 0.00 39.07 4.40
415 417 4.487412 GCTTGACGCTGCATGGCC 62.487 66.667 0.00 0.00 35.14 5.36
416 418 2.749044 CTTGACGCTGCATGGCCT 60.749 61.111 3.32 0.00 0.00 5.19
423 453 1.143183 GCTGCATGGCCTTTCATGG 59.857 57.895 3.32 0.00 43.34 3.66
430 460 3.369681 GCATGGCCTTTCATGGATTTCAA 60.370 43.478 3.32 0.00 43.34 2.69
432 462 4.475051 TGGCCTTTCATGGATTTCAATG 57.525 40.909 3.32 0.00 0.00 2.82
448 646 0.606401 AATGCACCTCCTGGAACACG 60.606 55.000 0.00 0.00 37.04 4.49
478 676 3.560025 GGATCCTGTGTTGACCATGTTCT 60.560 47.826 3.84 0.00 0.00 3.01
479 677 3.576078 TCCTGTGTTGACCATGTTCTT 57.424 42.857 0.00 0.00 0.00 2.52
480 678 3.213506 TCCTGTGTTGACCATGTTCTTG 58.786 45.455 0.00 0.00 0.00 3.02
481 679 2.287788 CCTGTGTTGACCATGTTCTTGC 60.288 50.000 0.00 0.00 0.00 4.01
541 742 5.107337 CCAGATGTCACGATCAAATATTCCG 60.107 44.000 0.00 0.00 0.00 4.30
542 743 5.691754 CAGATGTCACGATCAAATATTCCGA 59.308 40.000 0.00 0.00 0.00 4.55
543 744 5.923114 AGATGTCACGATCAAATATTCCGAG 59.077 40.000 0.00 0.00 0.00 4.63
544 745 5.257082 TGTCACGATCAAATATTCCGAGA 57.743 39.130 0.00 0.00 0.00 4.04
564 765 3.509967 AGAGAACCCCAATTTAAAAGGCG 59.490 43.478 4.88 0.21 0.00 5.52
620 821 2.617274 GGACGGCCAGCAAAGACAC 61.617 63.158 0.00 0.00 0.00 3.67
623 824 2.034879 CGGCCAGCAAAGACACGAT 61.035 57.895 2.24 0.00 0.00 3.73
644 845 5.163953 CGATCACGAAGCAAAAGAACATACT 60.164 40.000 0.00 0.00 42.66 2.12
645 846 6.034577 CGATCACGAAGCAAAAGAACATACTA 59.965 38.462 0.00 0.00 42.66 1.82
646 847 6.462073 TCACGAAGCAAAAGAACATACTAC 57.538 37.500 0.00 0.00 0.00 2.73
661 862 3.792053 CTACATCACGCCTCGGCCC 62.792 68.421 0.00 0.00 37.98 5.80
675 876 4.722700 GCCCGGGCACACACAGAT 62.723 66.667 40.73 0.00 41.49 2.90
684 885 3.020274 GGCACACACAGATAGAGAGAGA 58.980 50.000 0.00 0.00 0.00 3.10
685 886 3.066621 GGCACACACAGATAGAGAGAGAG 59.933 52.174 0.00 0.00 0.00 3.20
686 887 3.066621 GCACACACAGATAGAGAGAGAGG 59.933 52.174 0.00 0.00 0.00 3.69
687 888 4.522114 CACACACAGATAGAGAGAGAGGA 58.478 47.826 0.00 0.00 0.00 3.71
691 892 4.103153 ACACAGATAGAGAGAGAGGAGAGG 59.897 50.000 0.00 0.00 0.00 3.69
693 894 3.652869 CAGATAGAGAGAGAGGAGAGGGT 59.347 52.174 0.00 0.00 0.00 4.34
728 929 3.213402 GCGACTCGAGAGGGAGGG 61.213 72.222 21.68 0.85 38.39 4.30
729 930 2.590645 CGACTCGAGAGGGAGGGA 59.409 66.667 21.68 0.00 38.39 4.20
730 931 1.525077 CGACTCGAGAGGGAGGGAG 60.525 68.421 21.68 0.00 38.39 4.30
731 932 1.152839 GACTCGAGAGGGAGGGAGG 60.153 68.421 21.68 0.00 38.39 4.30
812 1013 1.608283 GGTTACATCATCGCCTAGGCC 60.608 57.143 28.09 10.55 37.98 5.19
813 1014 0.317160 TTACATCATCGCCTAGGCCG 59.683 55.000 28.09 21.60 37.98 6.13
814 1015 2.154798 TACATCATCGCCTAGGCCGC 62.155 60.000 28.09 3.58 37.98 6.53
815 1016 2.919856 ATCATCGCCTAGGCCGCT 60.920 61.111 28.09 11.78 37.98 5.52
1647 1872 4.220413 CTGAGCAGCATGTCCCTG 57.780 61.111 0.00 0.00 39.31 4.45
1842 2067 2.432628 CGCCACGTCCTCAAGGTC 60.433 66.667 0.00 0.00 36.34 3.85
2034 2276 2.005451 GCATGTGCTTCTCTCGTTCAT 58.995 47.619 0.00 0.00 38.21 2.57
2037 2279 3.667497 TGTGCTTCTCTCGTTCATCTT 57.333 42.857 0.00 0.00 0.00 2.40
2038 2280 4.783764 TGTGCTTCTCTCGTTCATCTTA 57.216 40.909 0.00 0.00 0.00 2.10
2039 2281 4.738124 TGTGCTTCTCTCGTTCATCTTAG 58.262 43.478 0.00 0.00 0.00 2.18
2040 2282 3.549873 GTGCTTCTCTCGTTCATCTTAGC 59.450 47.826 0.00 0.00 0.00 3.09
2047 2289 5.467399 TCTCTCGTTCATCTTAGCTAGCTAC 59.533 44.000 24.09 12.35 0.00 3.58
2048 2290 4.515944 TCTCGTTCATCTTAGCTAGCTACC 59.484 45.833 24.09 5.60 0.00 3.18
2084 2326 4.222847 GTTCCCCTCCGCGGCTAG 62.223 72.222 23.51 14.27 0.00 3.42
2133 2375 0.109272 TCTGTAGCGAGCGTTCCTTG 60.109 55.000 0.00 0.00 0.00 3.61
2175 2417 9.547279 AATTTAGGTGGTCCTCTATTTTCATTT 57.453 29.630 0.00 0.00 43.94 2.32
2176 2418 8.575649 TTTAGGTGGTCCTCTATTTTCATTTC 57.424 34.615 0.00 0.00 43.94 2.17
2177 2419 6.139679 AGGTGGTCCTCTATTTTCATTTCA 57.860 37.500 0.00 0.00 40.58 2.69
2181 2423 7.976175 GGTGGTCCTCTATTTTCATTTCATTTC 59.024 37.037 0.00 0.00 0.00 2.17
2213 2455 3.668447 ACTGTTGCTCATGTAACTCCTG 58.332 45.455 0.00 0.00 39.12 3.86
2217 2459 2.466846 TGCTCATGTAACTCCTGGCTA 58.533 47.619 0.00 0.00 0.00 3.93
2353 2595 1.515088 CGTGCGTGCTCCTGAGTAG 60.515 63.158 0.00 0.00 0.00 2.57
2354 2596 1.153745 GTGCGTGCTCCTGAGTAGG 60.154 63.158 1.29 1.29 46.06 3.18
2452 2694 0.037232 GTCCAGGTTTGCTAGTCGCT 60.037 55.000 0.00 0.00 40.11 4.93
2453 2695 1.203994 GTCCAGGTTTGCTAGTCGCTA 59.796 52.381 0.00 0.00 40.11 4.26
2454 2696 1.203994 TCCAGGTTTGCTAGTCGCTAC 59.796 52.381 0.00 0.00 40.11 3.58
2459 2705 2.165030 GGTTTGCTAGTCGCTACTACCA 59.835 50.000 3.11 0.00 40.11 3.25
2475 2721 4.424566 CACCTGCGTGCCATTGCC 62.425 66.667 0.00 0.00 36.33 4.52
2478 2724 3.672447 CTGCGTGCCATTGCCACA 61.672 61.111 0.00 0.00 36.33 4.17
2537 2783 0.395173 TTAGCCATTTTCCTCCCCGC 60.395 55.000 0.00 0.00 0.00 6.13
2538 2784 2.279037 TAGCCATTTTCCTCCCCGCC 62.279 60.000 0.00 0.00 0.00 6.13
2539 2785 2.683475 CCATTTTCCTCCCCGCCT 59.317 61.111 0.00 0.00 0.00 5.52
2552 2798 1.216710 CCGCCTCCTCACTCACTTC 59.783 63.158 0.00 0.00 0.00 3.01
2568 2814 2.542211 CTTCGGGCATTTGTTCGGGC 62.542 60.000 0.00 0.00 0.00 6.13
2569 2815 3.369400 CGGGCATTTGTTCGGGCA 61.369 61.111 0.00 0.00 0.00 5.36
2570 2816 2.261361 GGGCATTTGTTCGGGCAC 59.739 61.111 0.00 0.00 0.00 5.01
2571 2817 2.126502 GGCATTTGTTCGGGCACG 60.127 61.111 0.00 0.00 42.74 5.34
2572 2818 2.126502 GCATTTGTTCGGGCACGG 60.127 61.111 9.32 0.00 41.39 4.94
2573 2819 2.566010 CATTTGTTCGGGCACGGG 59.434 61.111 9.32 0.00 41.39 5.28
2574 2820 2.675075 ATTTGTTCGGGCACGGGG 60.675 61.111 9.32 0.00 41.39 5.73
2575 2821 3.501040 ATTTGTTCGGGCACGGGGT 62.501 57.895 9.32 0.00 41.39 4.95
2576 2822 2.127027 ATTTGTTCGGGCACGGGGTA 62.127 55.000 9.32 0.00 41.39 3.69
2585 2831 1.683938 GGGCACGGGGTAGCTTAATTT 60.684 52.381 0.00 0.00 0.00 1.82
2606 2852 0.895100 GCACAGACCAATGCTTCCCA 60.895 55.000 0.00 0.00 38.84 4.37
2623 2869 0.037303 CCATCCCCTCCATTGATCCG 59.963 60.000 0.00 0.00 0.00 4.18
2628 2874 1.131638 CCCTCCATTGATCCGAGGAA 58.868 55.000 13.89 0.00 45.15 3.36
2660 2921 1.806461 GCCATGATCCATGCAGCAGG 61.806 60.000 0.00 0.00 40.20 4.85
2774 3037 1.613061 CCCCCGCATTTAACTCCCT 59.387 57.895 0.00 0.00 0.00 4.20
2813 3076 2.543037 AGGTTCTTCTCCTCCTCCTC 57.457 55.000 0.00 0.00 0.00 3.71
2814 3077 1.007842 AGGTTCTTCTCCTCCTCCTCC 59.992 57.143 0.00 0.00 0.00 4.30
2815 3078 1.007842 GGTTCTTCTCCTCCTCCTCCT 59.992 57.143 0.00 0.00 0.00 3.69
2816 3079 2.384828 GTTCTTCTCCTCCTCCTCCTC 58.615 57.143 0.00 0.00 0.00 3.71
2817 3080 0.930726 TCTTCTCCTCCTCCTCCTCC 59.069 60.000 0.00 0.00 0.00 4.30
2818 3081 0.933700 CTTCTCCTCCTCCTCCTCCT 59.066 60.000 0.00 0.00 0.00 3.69
2819 3082 0.930726 TTCTCCTCCTCCTCCTCCTC 59.069 60.000 0.00 0.00 0.00 3.71
2820 3083 0.996762 TCTCCTCCTCCTCCTCCTCC 60.997 65.000 0.00 0.00 0.00 4.30
2821 3084 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
2826 3089 1.219213 TCCTCCTCCTCCTCCTTGATC 59.781 57.143 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 1.304381 TTCCCAAGCCTCCATGCAC 60.304 57.895 0.00 0.00 0.00 4.57
68 69 2.359230 AGCTCGCACTTCCCAAGC 60.359 61.111 0.00 0.00 0.00 4.01
69 70 2.037136 CCAGCTCGCACTTCCCAAG 61.037 63.158 0.00 0.00 0.00 3.61
70 71 2.032528 CCAGCTCGCACTTCCCAA 59.967 61.111 0.00 0.00 0.00 4.12
71 72 2.337879 AAACCAGCTCGCACTTCCCA 62.338 55.000 0.00 0.00 0.00 4.37
72 73 0.321298 TAAACCAGCTCGCACTTCCC 60.321 55.000 0.00 0.00 0.00 3.97
73 74 1.398390 CATAAACCAGCTCGCACTTCC 59.602 52.381 0.00 0.00 0.00 3.46
74 75 1.398390 CCATAAACCAGCTCGCACTTC 59.602 52.381 0.00 0.00 0.00 3.01
75 76 1.453155 CCATAAACCAGCTCGCACTT 58.547 50.000 0.00 0.00 0.00 3.16
76 77 1.026718 GCCATAAACCAGCTCGCACT 61.027 55.000 0.00 0.00 0.00 4.40
77 78 1.026718 AGCCATAAACCAGCTCGCAC 61.027 55.000 0.00 0.00 28.40 5.34
78 79 1.026182 CAGCCATAAACCAGCTCGCA 61.026 55.000 0.00 0.00 33.70 5.10
79 80 1.723870 CAGCCATAAACCAGCTCGC 59.276 57.895 0.00 0.00 33.70 5.03
80 81 1.723870 GCAGCCATAAACCAGCTCG 59.276 57.895 0.00 0.00 33.70 5.03
81 82 1.026718 ACGCAGCCATAAACCAGCTC 61.027 55.000 0.00 0.00 33.70 4.09
82 83 1.002134 ACGCAGCCATAAACCAGCT 60.002 52.632 0.00 0.00 37.32 4.24
83 84 1.429423 GACGCAGCCATAAACCAGC 59.571 57.895 0.00 0.00 0.00 4.85
86 87 0.885196 TTTGGACGCAGCCATAAACC 59.115 50.000 0.00 0.00 37.86 3.27
99 100 1.602377 CTCCAGGTTCACGTTTTGGAC 59.398 52.381 0.00 0.00 34.42 4.02
104 105 1.597027 CGGCTCCAGGTTCACGTTT 60.597 57.895 0.00 0.00 0.00 3.60
105 106 2.030562 CGGCTCCAGGTTCACGTT 59.969 61.111 0.00 0.00 0.00 3.99
106 107 2.915659 TCGGCTCCAGGTTCACGT 60.916 61.111 0.00 0.00 0.00 4.49
107 108 2.125912 CTCGGCTCCAGGTTCACG 60.126 66.667 0.00 0.00 0.00 4.35
108 109 2.435059 GCTCGGCTCCAGGTTCAC 60.435 66.667 0.00 0.00 0.00 3.18
109 110 4.069232 CGCTCGGCTCCAGGTTCA 62.069 66.667 0.00 0.00 0.00 3.18
110 111 3.708220 CTCGCTCGGCTCCAGGTTC 62.708 68.421 0.00 0.00 0.00 3.62
117 118 1.654954 TTCTACCACTCGCTCGGCTC 61.655 60.000 0.00 0.00 0.00 4.70
129 130 8.530311 TGGTAATAATACAGTTCGTTTCTACCA 58.470 33.333 0.00 0.00 33.45 3.25
140 141 5.450965 CGTCGAGGGTGGTAATAATACAGTT 60.451 44.000 0.00 0.00 33.45 3.16
146 147 4.436332 GAAACGTCGAGGGTGGTAATAAT 58.564 43.478 10.27 0.00 0.00 1.28
147 148 3.368323 GGAAACGTCGAGGGTGGTAATAA 60.368 47.826 10.27 0.00 0.00 1.40
148 149 2.166254 GGAAACGTCGAGGGTGGTAATA 59.834 50.000 10.27 0.00 0.00 0.98
149 150 1.066645 GGAAACGTCGAGGGTGGTAAT 60.067 52.381 10.27 0.00 0.00 1.89
168 169 2.794981 CGACCATGTAGTGTAGCGAAGG 60.795 54.545 0.00 0.00 0.00 3.46
229 230 3.181505 CGTACAAAACCTTCACTGTTGCA 60.182 43.478 0.00 0.00 0.00 4.08
230 231 3.359654 CGTACAAAACCTTCACTGTTGC 58.640 45.455 0.00 0.00 0.00 4.17
231 232 3.064820 AGCGTACAAAACCTTCACTGTTG 59.935 43.478 0.00 0.00 0.00 3.33
232 233 3.275999 AGCGTACAAAACCTTCACTGTT 58.724 40.909 0.00 0.00 0.00 3.16
237 238 1.003331 CGCAAGCGTACAAAACCTTCA 60.003 47.619 6.25 0.00 34.35 3.02
240 241 0.865769 CTCGCAAGCGTACAAAACCT 59.134 50.000 14.57 0.00 40.74 3.50
258 259 4.767255 GCTAGCACCTGCACCGCT 62.767 66.667 10.63 5.23 45.16 5.52
268 269 4.749099 CAGATCCTGATTAAGTGCTAGCAC 59.251 45.833 35.56 35.56 39.30 4.40
269 270 4.651045 TCAGATCCTGATTAAGTGCTAGCA 59.349 41.667 14.93 14.93 35.39 3.49
270 271 5.207110 TCAGATCCTGATTAAGTGCTAGC 57.793 43.478 8.10 8.10 35.39 3.42
274 275 7.192232 GTCATTTTCAGATCCTGATTAAGTGC 58.808 38.462 0.00 0.00 40.39 4.40
275 276 7.404985 CGTCATTTTCAGATCCTGATTAAGTG 58.595 38.462 0.00 0.00 40.39 3.16
288 289 0.871722 CGCAACCCGTCATTTTCAGA 59.128 50.000 0.00 0.00 0.00 3.27
301 302 2.202349 GCATCGAAGTGCGCAACC 60.202 61.111 14.00 0.00 40.61 3.77
338 339 0.034767 TGATGCAAGCAAGGCTAGCT 60.035 50.000 15.72 0.00 45.97 3.32
345 346 0.445436 GGTCGAGTGATGCAAGCAAG 59.555 55.000 0.00 0.00 28.10 4.01
368 369 8.623310 TTATTTTCTCGACCAAAAACTGTTTC 57.377 30.769 6.20 0.00 0.00 2.78
379 380 6.861055 GTCAAGCAAATTTATTTTCTCGACCA 59.139 34.615 0.00 0.00 0.00 4.02
410 412 4.685030 GCATTGAAATCCATGAAAGGCCAT 60.685 41.667 5.01 0.00 0.00 4.40
411 413 3.369681 GCATTGAAATCCATGAAAGGCCA 60.370 43.478 5.01 0.00 0.00 5.36
413 415 3.619929 GTGCATTGAAATCCATGAAAGGC 59.380 43.478 0.00 0.00 0.00 4.35
414 416 4.081309 AGGTGCATTGAAATCCATGAAAGG 60.081 41.667 0.00 0.00 0.00 3.11
415 417 5.080969 AGGTGCATTGAAATCCATGAAAG 57.919 39.130 0.00 0.00 0.00 2.62
416 418 4.081531 GGAGGTGCATTGAAATCCATGAAA 60.082 41.667 0.00 0.00 0.00 2.69
423 453 2.726821 TCCAGGAGGTGCATTGAAATC 58.273 47.619 0.00 0.00 35.89 2.17
430 460 1.003355 CGTGTTCCAGGAGGTGCAT 60.003 57.895 0.00 0.00 35.89 3.96
432 462 1.374758 CTCGTGTTCCAGGAGGTGC 60.375 63.158 6.13 0.00 41.07 5.01
448 646 0.250513 AACACAGGATCCCGCTTCTC 59.749 55.000 8.55 0.00 0.00 2.87
461 659 2.620115 AGCAAGAACATGGTCAACACAG 59.380 45.455 14.46 0.00 0.00 3.66
478 676 5.593968 TCTTTTGTTACTCGTGTCTAGCAA 58.406 37.500 0.00 0.00 0.00 3.91
479 677 5.190992 TCTTTTGTTACTCGTGTCTAGCA 57.809 39.130 0.00 0.00 0.00 3.49
480 678 6.520792 TTTCTTTTGTTACTCGTGTCTAGC 57.479 37.500 0.00 0.00 0.00 3.42
481 679 8.348983 TCTTTTCTTTTGTTACTCGTGTCTAG 57.651 34.615 0.00 0.00 0.00 2.43
541 742 4.380550 CGCCTTTTAAATTGGGGTTCTCTC 60.381 45.833 13.25 0.00 0.00 3.20
542 743 3.509967 CGCCTTTTAAATTGGGGTTCTCT 59.490 43.478 13.25 0.00 0.00 3.10
543 744 3.257375 ACGCCTTTTAAATTGGGGTTCTC 59.743 43.478 18.33 0.39 43.06 2.87
544 745 3.236047 ACGCCTTTTAAATTGGGGTTCT 58.764 40.909 18.33 3.87 43.06 3.01
564 765 2.203437 ACCCGGTTTGGCTCCAAC 60.203 61.111 0.00 0.00 35.46 3.77
606 807 0.955428 TGATCGTGTCTTTGCTGGCC 60.955 55.000 0.00 0.00 0.00 5.36
620 821 3.519908 TGTTCTTTTGCTTCGTGATCG 57.480 42.857 0.00 0.00 38.55 3.69
623 824 5.986741 TGTAGTATGTTCTTTTGCTTCGTGA 59.013 36.000 0.00 0.00 0.00 4.35
644 845 3.845259 GGGCCGAGGCGTGATGTA 61.845 66.667 8.14 0.00 43.06 2.29
661 862 0.817654 TCTCTATCTGTGTGTGCCCG 59.182 55.000 0.00 0.00 0.00 6.13
664 865 3.066621 CCTCTCTCTCTATCTGTGTGTGC 59.933 52.174 0.00 0.00 0.00 4.57
674 875 2.716424 CCACCCTCTCCTCTCTCTCTAT 59.284 54.545 0.00 0.00 0.00 1.98
675 876 2.131854 CCACCCTCTCCTCTCTCTCTA 58.868 57.143 0.00 0.00 0.00 2.43
684 885 1.063266 GTCTGATCTCCACCCTCTCCT 60.063 57.143 0.00 0.00 0.00 3.69
685 886 1.342474 TGTCTGATCTCCACCCTCTCC 60.342 57.143 0.00 0.00 0.00 3.71
686 887 2.151502 TGTCTGATCTCCACCCTCTC 57.848 55.000 0.00 0.00 0.00 3.20
687 888 2.225496 ACTTGTCTGATCTCCACCCTCT 60.225 50.000 0.00 0.00 0.00 3.69
691 892 1.731720 GCACTTGTCTGATCTCCACC 58.268 55.000 0.00 0.00 0.00 4.61
693 894 0.390340 GCGCACTTGTCTGATCTCCA 60.390 55.000 0.30 0.00 0.00 3.86
728 929 1.216710 CTCTCCTGTTCACCGCCTC 59.783 63.158 0.00 0.00 0.00 4.70
729 930 0.832135 TTCTCTCCTGTTCACCGCCT 60.832 55.000 0.00 0.00 0.00 5.52
730 931 0.034896 TTTCTCTCCTGTTCACCGCC 59.965 55.000 0.00 0.00 0.00 6.13
731 932 1.433534 CTTTCTCTCCTGTTCACCGC 58.566 55.000 0.00 0.00 0.00 5.68
814 1015 4.834453 CCGAGGAGGCTGCTGCAG 62.834 72.222 24.80 24.80 41.91 4.41
955 1157 1.750780 GGCTAAGCCTCTGGGTTGC 60.751 63.158 10.82 11.24 46.69 4.17
1040 1259 2.205152 GGCATGGGCATGGACATCC 61.205 63.158 0.00 0.00 43.71 3.51
1127 1346 2.674380 CACCACCAGGAGGCTTGC 60.674 66.667 2.09 0.00 39.06 4.01
1429 1648 2.738521 CGAGAACTGGTGGTGCGG 60.739 66.667 0.00 0.00 0.00 5.69
1430 1649 3.414700 GCGAGAACTGGTGGTGCG 61.415 66.667 0.00 0.00 0.00 5.34
1431 1650 3.050275 GGCGAGAACTGGTGGTGC 61.050 66.667 0.00 0.00 0.00 5.01
1842 2067 1.067364 TGCTTGTTGTTGTGCATCCAG 59.933 47.619 0.00 0.00 0.00 3.86
1918 2143 4.101790 GGTTGCATGCGGACGGTG 62.102 66.667 14.09 0.00 0.00 4.94
2034 2276 2.031069 CGAATGCGGTAGCTAGCTAAGA 60.031 50.000 25.74 10.39 45.42 2.10
2037 2279 0.039437 GCGAATGCGGTAGCTAGCTA 60.039 55.000 20.67 20.67 45.42 3.32
2038 2280 1.300233 GCGAATGCGGTAGCTAGCT 60.300 57.895 23.12 23.12 45.42 3.32
2039 2281 3.235355 GCGAATGCGGTAGCTAGC 58.765 61.111 13.03 13.03 45.42 3.42
2081 2323 4.350620 CTAGCCATGCACCGCTAG 57.649 61.111 22.65 22.65 46.20 3.42
2082 2324 1.971505 AAGCTAGCCATGCACCGCTA 61.972 55.000 12.13 14.17 36.53 4.26
2083 2325 1.971505 TAAGCTAGCCATGCACCGCT 61.972 55.000 12.13 13.44 39.17 5.52
2084 2326 1.523711 TAAGCTAGCCATGCACCGC 60.524 57.895 12.13 0.00 0.00 5.68
2133 2375 5.656859 ACCTAAATTAATCCAGCCAAGAACC 59.343 40.000 0.00 0.00 0.00 3.62
2176 2418 9.844790 TGAGCAACAGTAAATAGAAATGAAATG 57.155 29.630 0.00 0.00 0.00 2.32
2226 2468 0.247185 ACCAAATCAGCAAATGGCCG 59.753 50.000 0.00 0.00 46.50 6.13
2243 2485 2.092323 GTACATTCCCCAGCAAGAACC 58.908 52.381 0.00 0.00 0.00 3.62
2402 2644 3.741830 TTGTCCCAACGCAGACGCA 62.742 57.895 0.00 0.00 45.53 5.24
2403 2645 1.852067 AATTGTCCCAACGCAGACGC 61.852 55.000 0.00 0.00 45.53 5.19
2405 2647 2.793278 AAAATTGTCCCAACGCAGAC 57.207 45.000 0.00 0.00 0.00 3.51
2406 2648 3.482436 AGTAAAATTGTCCCAACGCAGA 58.518 40.909 0.00 0.00 0.00 4.26
2407 2649 3.252215 TGAGTAAAATTGTCCCAACGCAG 59.748 43.478 0.00 0.00 0.00 5.18
2452 2694 1.261938 ATGGCACGCAGGTGGTAGTA 61.262 55.000 0.00 0.00 44.54 1.82
2453 2695 2.124507 AATGGCACGCAGGTGGTAGT 62.125 55.000 0.00 0.00 44.54 2.73
2454 2696 1.377202 AATGGCACGCAGGTGGTAG 60.377 57.895 0.00 0.00 44.54 3.18
2459 2705 4.972733 TGGCAATGGCACGCAGGT 62.973 61.111 5.05 0.00 43.71 4.00
2475 2721 7.155328 ACAGTTGTCTATCTTCTTTAGGTGTG 58.845 38.462 0.00 0.00 0.00 3.82
2478 2724 6.651225 GCAACAGTTGTCTATCTTCTTTAGGT 59.349 38.462 14.88 0.00 0.00 3.08
2537 2783 1.893786 CCCGAAGTGAGTGAGGAGG 59.106 63.158 0.00 0.00 0.00 4.30
2538 2784 1.216710 GCCCGAAGTGAGTGAGGAG 59.783 63.158 0.00 0.00 0.00 3.69
2539 2785 0.904865 ATGCCCGAAGTGAGTGAGGA 60.905 55.000 0.00 0.00 0.00 3.71
2552 2798 3.369400 TGCCCGAACAAATGCCCG 61.369 61.111 0.00 0.00 0.00 6.13
2568 2814 2.490115 TGCAAAATTAAGCTACCCCGTG 59.510 45.455 0.00 0.00 0.00 4.94
2569 2815 2.490509 GTGCAAAATTAAGCTACCCCGT 59.509 45.455 0.00 0.00 0.00 5.28
2570 2816 2.490115 TGTGCAAAATTAAGCTACCCCG 59.510 45.455 0.00 0.00 0.00 5.73
2571 2817 3.761752 TCTGTGCAAAATTAAGCTACCCC 59.238 43.478 0.00 0.00 0.00 4.95
2572 2818 4.380550 GGTCTGTGCAAAATTAAGCTACCC 60.381 45.833 0.00 0.00 0.00 3.69
2573 2819 4.217550 TGGTCTGTGCAAAATTAAGCTACC 59.782 41.667 0.00 6.56 0.00 3.18
2574 2820 5.371115 TGGTCTGTGCAAAATTAAGCTAC 57.629 39.130 0.00 2.19 0.00 3.58
2575 2821 6.389091 CATTGGTCTGTGCAAAATTAAGCTA 58.611 36.000 0.00 0.00 0.00 3.32
2576 2822 4.935352 TTGGTCTGTGCAAAATTAAGCT 57.065 36.364 0.00 0.00 0.00 3.74
2585 2831 0.961019 GGAAGCATTGGTCTGTGCAA 59.039 50.000 0.00 0.00 43.63 4.08
2606 2852 1.356124 CTCGGATCAATGGAGGGGAT 58.644 55.000 0.00 0.00 0.00 3.85
2636 2882 1.895231 GCATGGATCATGGCGCTCA 60.895 57.895 7.64 3.81 41.64 4.26
2637 2883 1.853114 CTGCATGGATCATGGCGCTC 61.853 60.000 7.64 0.00 41.64 5.03
2813 3076 2.419851 GCAGAACTGATCAAGGAGGAGG 60.420 54.545 5.97 0.00 0.00 4.30
2814 3077 2.419851 GGCAGAACTGATCAAGGAGGAG 60.420 54.545 5.97 0.00 0.00 3.69
2815 3078 1.556911 GGCAGAACTGATCAAGGAGGA 59.443 52.381 5.97 0.00 0.00 3.71
2816 3079 1.407989 GGGCAGAACTGATCAAGGAGG 60.408 57.143 5.97 0.00 0.00 4.30
2817 3080 1.741732 CGGGCAGAACTGATCAAGGAG 60.742 57.143 5.97 0.00 0.00 3.69
2818 3081 0.250234 CGGGCAGAACTGATCAAGGA 59.750 55.000 5.97 0.00 0.00 3.36
2819 3082 1.372087 GCGGGCAGAACTGATCAAGG 61.372 60.000 5.97 0.00 0.00 3.61
2820 3083 0.674581 TGCGGGCAGAACTGATCAAG 60.675 55.000 5.97 0.00 0.00 3.02
2821 3084 0.035152 ATGCGGGCAGAACTGATCAA 60.035 50.000 5.97 0.00 0.00 2.57
2826 3089 0.734889 CCTTAATGCGGGCAGAACTG 59.265 55.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.