Multiple sequence alignment - TraesCS2A01G048900

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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 TraesCS2A01G048900 chr2A 100.000 2504 0 0 1 2504 18913538 18911035 0.000000e+00 4625
1 TraesCS2A01G048900 chr2A 97.260 73 2 0 2250 2322 18911219 18911147 9.400000e-25 124
2 TraesCS2A01G048900 chr2A 97.260 73 2 0 2320 2392 18911289 18911217 9.400000e-25 124
3 TraesCS2A01G048900 chr2A 98.361 61 1 0 618 678 419792769 419792829 9.470000e-20 108
4 TraesCS2A01G048900 chr2D 96.554 1654 34 13 679 2318 17500330 17498686 0.000000e+00 2717
5 TraesCS2A01G048900 chr2D 95.290 637 12 5 1 619 17500965 17500329 0.000000e+00 994
6 TraesCS2A01G048900 chr2D 96.757 185 6 0 2320 2504 17498754 17498570 2.420000e-80 309
7 TraesCS2A01G048900 chr2D 98.276 58 1 0 618 675 33932986 33932929 4.410000e-18 102
8 TraesCS2A01G048900 chr2D 96.721 61 2 0 618 678 630263872 630263932 4.410000e-18 102
9 TraesCS2A01G048900 chr2B 92.371 1206 68 12 679 1872 29706335 29707528 0.000000e+00 1696
10 TraesCS2A01G048900 chr2B 91.932 533 37 5 1 529 29705216 29705746 0.000000e+00 741
11 TraesCS2A01G048900 chr2B 86.350 337 22 12 1993 2318 29720044 29720367 1.840000e-91 346
12 TraesCS2A01G048900 chr2B 91.089 101 7 2 521 619 29706236 29706336 4.340000e-28 135
13 TraesCS2A01G048900 chr6D 98.361 61 1 0 618 678 429812157 429812097 9.470000e-20 108
14 TraesCS2A01G048900 chr1D 98.361 61 1 0 618 678 50989776 50989716 9.470000e-20 108
15 TraesCS2A01G048900 chrUn 98.276 58 1 0 618 675 30304424 30304367 4.410000e-18 102
16 TraesCS2A01G048900 chr7D 96.721 61 2 0 618 678 562255765 562255825 4.410000e-18 102
17 TraesCS2A01G048900 chr5B 98.276 58 1 0 618 675 491240025 491240082 4.410000e-18 102
18 TraesCS2A01G048900 chr4A 98.276 58 1 0 618 675 141126165 141126222 4.410000e-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 TraesCS2A01G048900 chr2A 18911035 18913538 2503 True 1624.333333 4625 98.173333 1 2504 3 chr2A.!!$R1 2503
1 TraesCS2A01G048900 chr2D 17498570 17500965 2395 True 1340.000000 2717 96.200333 1 2504 3 chr2D.!!$R2 2503
2 TraesCS2A01G048900 chr2B 29705216 29707528 2312 False 857.333333 1696 91.797333 1 1872 3 chr2B.!!$F2 1871

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
634 1155 0.318762 GGGAGTCGAACTGAACTGCT 59.681 55.0 0.0 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2339 2885 0.107643 TTGTGTCCTCATGCCGTTCA 59.892 50.0 0.0 0.0 0.0 3.18 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
95 97 2.985896 TCAACCATAGCTGCCTACAAC 58.014 47.619 0.00 0.00 0.00 3.32
206 209 2.292828 AGGCTAACTTGTTGCACCAT 57.707 45.000 0.00 0.00 0.00 3.55
308 311 1.006571 TCAGCGTTCCACGTTCTCC 60.007 57.895 0.00 0.00 44.73 3.71
453 456 2.183811 CACTCTCAGGCTCGCCAG 59.816 66.667 11.02 1.89 38.92 4.85
483 487 6.850752 TCTAATGCTATCATTCACCCGATA 57.149 37.500 0.00 0.00 41.68 2.92
503 507 6.373779 CGATAAAGAAGCTGAAGAAAAGCAA 58.626 36.000 0.00 0.00 43.37 3.91
546 1065 7.712204 TCATACCTCTTATCACACTTACACA 57.288 36.000 0.00 0.00 0.00 3.72
618 1139 9.629649 AACTTGATAATATATTCAGGTAGGGGA 57.370 33.333 0.00 0.00 31.76 4.81
619 1140 9.273137 ACTTGATAATATATTCAGGTAGGGGAG 57.727 37.037 0.00 0.00 31.27 4.30
620 1141 9.273137 CTTGATAATATATTCAGGTAGGGGAGT 57.727 37.037 0.00 0.00 0.00 3.85
621 1142 8.840200 TGATAATATATTCAGGTAGGGGAGTC 57.160 38.462 0.00 0.00 0.00 3.36
622 1143 7.560262 TGATAATATATTCAGGTAGGGGAGTCG 59.440 40.741 0.00 0.00 0.00 4.18
623 1144 3.897657 ATATTCAGGTAGGGGAGTCGA 57.102 47.619 0.00 0.00 0.00 4.20
624 1145 2.544844 ATTCAGGTAGGGGAGTCGAA 57.455 50.000 0.00 0.00 0.00 3.71
625 1146 1.553706 TTCAGGTAGGGGAGTCGAAC 58.446 55.000 0.00 0.00 0.00 3.95
626 1147 0.702902 TCAGGTAGGGGAGTCGAACT 59.297 55.000 0.00 0.00 0.00 3.01
627 1148 0.818296 CAGGTAGGGGAGTCGAACTG 59.182 60.000 0.00 0.00 0.00 3.16
628 1149 0.702902 AGGTAGGGGAGTCGAACTGA 59.297 55.000 0.00 0.00 0.00 3.41
629 1150 1.076677 AGGTAGGGGAGTCGAACTGAA 59.923 52.381 0.00 0.00 0.00 3.02
630 1151 1.204231 GGTAGGGGAGTCGAACTGAAC 59.796 57.143 0.00 0.00 0.00 3.18
631 1152 2.169330 GTAGGGGAGTCGAACTGAACT 58.831 52.381 0.00 0.00 0.00 3.01
632 1153 0.969894 AGGGGAGTCGAACTGAACTG 59.030 55.000 0.00 0.00 0.00 3.16
633 1154 0.670854 GGGGAGTCGAACTGAACTGC 60.671 60.000 0.00 0.00 0.00 4.40
634 1155 0.318762 GGGAGTCGAACTGAACTGCT 59.681 55.000 0.00 0.00 0.00 4.24
635 1156 1.544691 GGGAGTCGAACTGAACTGCTA 59.455 52.381 0.00 0.00 0.00 3.49
636 1157 2.416162 GGGAGTCGAACTGAACTGCTAG 60.416 54.545 0.00 0.00 0.00 3.42
637 1158 2.488545 GGAGTCGAACTGAACTGCTAGA 59.511 50.000 0.00 0.00 0.00 2.43
638 1159 3.494232 GAGTCGAACTGAACTGCTAGAC 58.506 50.000 0.00 0.00 0.00 2.59
639 1160 3.150767 AGTCGAACTGAACTGCTAGACT 58.849 45.455 0.00 0.00 33.47 3.24
640 1161 4.325119 AGTCGAACTGAACTGCTAGACTA 58.675 43.478 0.00 0.00 36.15 2.59
641 1162 4.154556 AGTCGAACTGAACTGCTAGACTAC 59.845 45.833 0.00 0.00 36.15 2.73
642 1163 3.124806 TCGAACTGAACTGCTAGACTACG 59.875 47.826 0.00 0.00 0.00 3.51
643 1164 3.120269 CGAACTGAACTGCTAGACTACGT 60.120 47.826 0.00 0.00 0.00 3.57
644 1165 4.613167 CGAACTGAACTGCTAGACTACGTT 60.613 45.833 0.00 0.00 0.00 3.99
645 1166 4.162096 ACTGAACTGCTAGACTACGTTG 57.838 45.455 0.00 0.00 0.00 4.10
646 1167 3.819337 ACTGAACTGCTAGACTACGTTGA 59.181 43.478 3.44 0.00 0.00 3.18
647 1168 4.083217 ACTGAACTGCTAGACTACGTTGAG 60.083 45.833 3.44 0.00 0.00 3.02
648 1169 3.819337 TGAACTGCTAGACTACGTTGAGT 59.181 43.478 3.44 0.00 0.00 3.41
649 1170 3.833545 ACTGCTAGACTACGTTGAGTG 57.166 47.619 3.44 0.00 0.00 3.51
650 1171 3.409570 ACTGCTAGACTACGTTGAGTGA 58.590 45.455 3.44 0.00 0.00 3.41
651 1172 4.011023 ACTGCTAGACTACGTTGAGTGAT 58.989 43.478 3.44 0.00 0.00 3.06
652 1173 4.142578 ACTGCTAGACTACGTTGAGTGATG 60.143 45.833 3.44 0.00 0.00 3.07
653 1174 4.007659 TGCTAGACTACGTTGAGTGATGA 58.992 43.478 3.44 0.00 0.00 2.92
654 1175 4.457949 TGCTAGACTACGTTGAGTGATGAA 59.542 41.667 3.44 0.00 0.00 2.57
655 1176 4.794246 GCTAGACTACGTTGAGTGATGAAC 59.206 45.833 3.44 0.00 0.00 3.18
656 1177 5.392165 GCTAGACTACGTTGAGTGATGAACT 60.392 44.000 3.44 0.00 43.85 3.01
775 1297 8.137437 CAGTAGAACAAACAACCTCATTTTCAT 58.863 33.333 0.00 0.00 0.00 2.57
795 1317 6.441093 TCATGTTTCAGCACTATGGATTTC 57.559 37.500 0.00 0.00 0.00 2.17
952 1474 1.247567 GCACATACAAGCCTTGTGGT 58.752 50.000 20.12 14.45 45.03 4.16
1043 1565 2.094390 TGGGTTTCTAATCCGTCACTCG 60.094 50.000 0.00 0.00 39.52 4.18
1134 1656 3.130633 CGTCATCACACAAGTTCTTCCA 58.869 45.455 0.00 0.00 0.00 3.53
1135 1657 3.748048 CGTCATCACACAAGTTCTTCCAT 59.252 43.478 0.00 0.00 0.00 3.41
1145 1667 1.084370 GTTCTTCCATGCCGTCCTCG 61.084 60.000 0.00 0.00 0.00 4.63
1198 1720 2.486592 GCAACTAGGCACGTTTTATGGT 59.513 45.455 0.00 0.00 0.00 3.55
1272 1799 3.753272 ACGAATCAATATGCATGCTACCC 59.247 43.478 20.33 0.00 0.00 3.69
1519 2046 3.873910 AGACTGATAAAACGTGGATGGG 58.126 45.455 0.00 0.00 0.00 4.00
1574 2101 2.947448 TGGTCTGAGTCACATCGATG 57.053 50.000 23.68 23.68 0.00 3.84
1585 2112 0.107703 ACATCGATGTGCCGTCCATT 60.108 50.000 29.49 0.86 40.03 3.16
1599 2126 3.243569 CCGTCCATTCCTCTGACATACTC 60.244 52.174 0.00 0.00 0.00 2.59
1819 2353 7.958088 ACAGTTATAAGAGAGCTCCCTTTATC 58.042 38.462 16.27 2.93 0.00 1.75
1821 2355 8.303876 CAGTTATAAGAGAGCTCCCTTTATCTC 58.696 40.741 16.27 1.37 38.77 2.75
1931 2466 1.608590 CTGTCTCGTTTTTGGGTGCAT 59.391 47.619 0.00 0.00 0.00 3.96
1950 2485 3.612479 GCATATCCAACCATCCGCATTTC 60.612 47.826 0.00 0.00 0.00 2.17
2053 2589 5.163652 CCTGAACAAAGAACGAGTCCTTTTT 60.164 40.000 0.00 0.00 30.89 1.94
2054 2590 5.636837 TGAACAAAGAACGAGTCCTTTTTG 58.363 37.500 0.00 0.00 30.89 2.44
2118 2664 9.773328 TTATGCATGAAAATACGAGAGAAAAAG 57.227 29.630 10.16 0.00 0.00 2.27
2315 2861 4.219725 ACCTGAGAAACTAGAGCAGAACTC 59.780 45.833 0.00 0.00 46.66 3.01
2323 2869 2.815722 GAGCAGAACTCCACACGTC 58.184 57.895 0.00 0.00 39.75 4.34
2324 2870 0.315568 GAGCAGAACTCCACACGTCT 59.684 55.000 0.00 0.00 39.75 4.18
2325 2871 0.315568 AGCAGAACTCCACACGTCTC 59.684 55.000 0.00 0.00 0.00 3.36
2326 2872 0.315568 GCAGAACTCCACACGTCTCT 59.684 55.000 0.00 0.00 0.00 3.10
2327 2873 1.540267 GCAGAACTCCACACGTCTCTA 59.460 52.381 0.00 0.00 0.00 2.43
2328 2874 2.668834 GCAGAACTCCACACGTCTCTAC 60.669 54.545 0.00 0.00 0.00 2.59
2329 2875 2.552743 CAGAACTCCACACGTCTCTACA 59.447 50.000 0.00 0.00 0.00 2.74
2330 2876 2.553172 AGAACTCCACACGTCTCTACAC 59.447 50.000 0.00 0.00 0.00 2.90
2331 2877 1.245732 ACTCCACACGTCTCTACACC 58.754 55.000 0.00 0.00 0.00 4.16
2332 2878 1.244816 CTCCACACGTCTCTACACCA 58.755 55.000 0.00 0.00 0.00 4.17
2333 2879 1.819288 CTCCACACGTCTCTACACCAT 59.181 52.381 0.00 0.00 0.00 3.55
2334 2880 1.816835 TCCACACGTCTCTACACCATC 59.183 52.381 0.00 0.00 0.00 3.51
2335 2881 1.819288 CCACACGTCTCTACACCATCT 59.181 52.381 0.00 0.00 0.00 2.90
2336 2882 2.416027 CCACACGTCTCTACACCATCTG 60.416 54.545 0.00 0.00 0.00 2.90
2337 2883 1.819288 ACACGTCTCTACACCATCTGG 59.181 52.381 0.00 0.00 42.17 3.86
2338 2884 2.092323 CACGTCTCTACACCATCTGGA 58.908 52.381 2.55 0.00 38.94 3.86
2339 2885 2.690497 CACGTCTCTACACCATCTGGAT 59.310 50.000 2.55 0.00 38.94 3.41
2340 2886 2.690497 ACGTCTCTACACCATCTGGATG 59.310 50.000 2.55 3.79 38.94 3.51
2341 2887 2.952310 CGTCTCTACACCATCTGGATGA 59.048 50.000 11.66 0.00 41.20 2.92
2342 2888 3.381590 CGTCTCTACACCATCTGGATGAA 59.618 47.826 11.66 0.00 41.20 2.57
2343 2889 4.688021 GTCTCTACACCATCTGGATGAAC 58.312 47.826 11.66 0.00 41.20 3.18
2344 2890 3.381590 TCTCTACACCATCTGGATGAACG 59.618 47.826 11.66 3.09 41.20 3.95
2345 2891 2.430694 TCTACACCATCTGGATGAACGG 59.569 50.000 11.66 0.00 41.20 4.44
2346 2892 0.392998 ACACCATCTGGATGAACGGC 60.393 55.000 11.66 0.00 41.20 5.68
2347 2893 0.392863 CACCATCTGGATGAACGGCA 60.393 55.000 11.66 0.00 41.20 5.69
2348 2894 0.548031 ACCATCTGGATGAACGGCAT 59.452 50.000 11.66 0.00 41.20 4.40
2349 2895 0.949397 CCATCTGGATGAACGGCATG 59.051 55.000 11.66 0.00 41.20 4.06
2350 2896 1.475571 CCATCTGGATGAACGGCATGA 60.476 52.381 11.66 0.00 41.20 3.07
2351 2897 1.871676 CATCTGGATGAACGGCATGAG 59.128 52.381 0.00 0.00 41.20 2.90
2352 2898 0.178767 TCTGGATGAACGGCATGAGG 59.821 55.000 0.00 0.00 37.34 3.86
2353 2899 0.178767 CTGGATGAACGGCATGAGGA 59.821 55.000 0.00 0.00 37.34 3.71
2354 2900 0.107703 TGGATGAACGGCATGAGGAC 60.108 55.000 0.00 0.00 37.34 3.85
2355 2901 0.107703 GGATGAACGGCATGAGGACA 60.108 55.000 0.00 0.00 37.34 4.02
2356 2902 1.009829 GATGAACGGCATGAGGACAC 58.990 55.000 0.00 0.00 37.34 3.67
2357 2903 0.324614 ATGAACGGCATGAGGACACA 59.675 50.000 0.00 0.00 35.42 3.72
2358 2904 0.107643 TGAACGGCATGAGGACACAA 59.892 50.000 0.00 0.00 0.00 3.33
2359 2905 1.234821 GAACGGCATGAGGACACAAA 58.765 50.000 0.00 0.00 0.00 2.83
2360 2906 1.606668 GAACGGCATGAGGACACAAAA 59.393 47.619 0.00 0.00 0.00 2.44
2361 2907 1.686355 ACGGCATGAGGACACAAAAA 58.314 45.000 0.00 0.00 0.00 1.94
2383 2929 7.665561 AAAATCTGAGAAACTAGAGCAGAAC 57.334 36.000 0.00 0.00 38.87 3.01
2384 2930 6.603940 AATCTGAGAAACTAGAGCAGAACT 57.396 37.500 0.00 0.00 38.87 3.01
2398 2944 4.961511 AACTCCACGCGAGCGCAA 62.962 61.111 15.93 2.26 43.01 4.85
2464 3010 1.153862 GGCGAGAGAGACTGCTGTG 60.154 63.158 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.525629 TGACGGCTGGAAGTCCCA 60.526 61.111 0.00 0.00 44.25 4.37
95 97 2.917933 TCATCTTTCCGCATGGTTAGG 58.082 47.619 0.00 0.00 36.30 2.69
206 209 2.785540 TGGTATCAGCAGCAATGTGA 57.214 45.000 0.00 0.00 0.00 3.58
308 311 0.741221 GCAGGAAGGTAGCAGTTCCG 60.741 60.000 7.16 4.64 46.01 4.30
453 456 7.118971 GGGTGAATGATAGCATTAGATCTCAAC 59.881 40.741 6.12 1.89 44.47 3.18
483 487 5.586339 GACTTGCTTTTCTTCAGCTTCTTT 58.414 37.500 0.00 0.00 38.19 2.52
617 1138 3.189702 AGTCTAGCAGTTCAGTTCGACTC 59.810 47.826 0.00 0.00 0.00 3.36
618 1139 3.150767 AGTCTAGCAGTTCAGTTCGACT 58.849 45.455 0.00 0.00 0.00 4.18
619 1140 3.562567 AGTCTAGCAGTTCAGTTCGAC 57.437 47.619 0.00 0.00 0.00 4.20
620 1141 3.124806 CGTAGTCTAGCAGTTCAGTTCGA 59.875 47.826 0.00 0.00 0.00 3.71
621 1142 3.120269 ACGTAGTCTAGCAGTTCAGTTCG 60.120 47.826 0.00 0.00 29.74 3.95
622 1143 4.422546 ACGTAGTCTAGCAGTTCAGTTC 57.577 45.455 0.00 0.00 29.74 3.01
623 1144 4.277672 TCAACGTAGTCTAGCAGTTCAGTT 59.722 41.667 0.00 0.00 45.00 3.16
624 1145 3.819337 TCAACGTAGTCTAGCAGTTCAGT 59.181 43.478 0.00 0.00 45.00 3.41
625 1146 4.083217 ACTCAACGTAGTCTAGCAGTTCAG 60.083 45.833 0.00 0.00 45.00 3.02
626 1147 3.819337 ACTCAACGTAGTCTAGCAGTTCA 59.181 43.478 0.00 0.00 45.00 3.18
627 1148 4.083431 TCACTCAACGTAGTCTAGCAGTTC 60.083 45.833 0.00 0.00 45.00 3.01
628 1149 3.819337 TCACTCAACGTAGTCTAGCAGTT 59.181 43.478 0.00 0.00 45.00 3.16
629 1150 3.409570 TCACTCAACGTAGTCTAGCAGT 58.590 45.455 0.00 0.00 45.00 4.40
630 1151 4.095036 TCATCACTCAACGTAGTCTAGCAG 59.905 45.833 0.00 0.00 45.00 4.24
631 1152 4.007659 TCATCACTCAACGTAGTCTAGCA 58.992 43.478 0.00 0.00 45.00 3.49
632 1153 4.617808 TCATCACTCAACGTAGTCTAGC 57.382 45.455 0.00 0.00 45.00 3.42
633 1154 6.184580 AGTTCATCACTCAACGTAGTCTAG 57.815 41.667 0.00 0.00 45.00 2.43
671 1192 0.259356 TCACCGGGGGTTCAGTTTTT 59.741 50.000 2.42 0.00 31.02 1.94
672 1193 0.481128 ATCACCGGGGGTTCAGTTTT 59.519 50.000 2.42 0.00 31.02 2.43
673 1194 0.481128 AATCACCGGGGGTTCAGTTT 59.519 50.000 2.42 0.00 31.02 2.66
674 1195 0.481128 AAATCACCGGGGGTTCAGTT 59.519 50.000 0.55 0.00 31.02 3.16
675 1196 0.037734 GAAATCACCGGGGGTTCAGT 59.962 55.000 0.55 0.00 31.02 3.41
676 1197 0.328258 AGAAATCACCGGGGGTTCAG 59.672 55.000 19.33 0.00 31.02 3.02
677 1198 0.326927 GAGAAATCACCGGGGGTTCA 59.673 55.000 19.33 0.00 31.02 3.18
775 1297 7.337938 TCATAGAAATCCATAGTGCTGAAACA 58.662 34.615 0.00 0.00 0.00 2.83
952 1474 2.163412 GGAATTGCGTTATTGAGCACCA 59.837 45.455 0.00 0.00 43.69 4.17
1043 1565 1.076513 TCCTTAGGGCTGGGAAAAACC 59.923 52.381 0.00 0.00 38.08 3.27
1145 1667 1.673665 CAACCAGCAGCAGGAGGAC 60.674 63.158 11.55 0.00 0.00 3.85
1238 1761 7.983484 TGCATATTGATTCGTATGAGCATAGAT 59.017 33.333 11.10 0.00 31.48 1.98
1519 2046 7.545965 CAGATCTATGGGTATTTACGGTCATTC 59.454 40.741 0.00 0.00 0.00 2.67
1574 2101 0.741221 GTCAGAGGAATGGACGGCAC 60.741 60.000 0.00 0.00 0.00 5.01
1581 2108 3.070734 CCTGGAGTATGTCAGAGGAATGG 59.929 52.174 0.00 0.00 30.68 3.16
1585 2112 3.245622 TGAACCTGGAGTATGTCAGAGGA 60.246 47.826 0.00 0.00 32.68 3.71
1931 2466 2.174639 AGGAAATGCGGATGGTTGGATA 59.825 45.455 0.00 0.00 0.00 2.59
1950 2485 5.530915 TGATTTTATACATGGAGCGGAAAGG 59.469 40.000 0.00 0.00 0.00 3.11
2000 2535 6.546403 GTCACTGTAGATCCTAGTGTCCATAA 59.454 42.308 16.51 0.37 41.82 1.90
2234 2780 3.043586 GAGACGTACGGCATCACAATAG 58.956 50.000 25.52 0.00 0.00 1.73
2309 2855 2.553172 GTGTAGAGACGTGTGGAGTTCT 59.447 50.000 0.00 0.00 0.00 3.01
2315 2861 1.819288 AGATGGTGTAGAGACGTGTGG 59.181 52.381 0.00 0.00 0.00 4.17
2316 2862 2.416027 CCAGATGGTGTAGAGACGTGTG 60.416 54.545 0.00 0.00 0.00 3.82
2317 2863 1.819288 CCAGATGGTGTAGAGACGTGT 59.181 52.381 0.00 0.00 0.00 4.49
2318 2864 2.092323 TCCAGATGGTGTAGAGACGTG 58.908 52.381 0.00 0.00 36.34 4.49
2319 2865 2.509166 TCCAGATGGTGTAGAGACGT 57.491 50.000 0.00 0.00 36.34 4.34
2320 2866 2.952310 TCATCCAGATGGTGTAGAGACG 59.048 50.000 7.76 0.00 39.24 4.18
2321 2867 4.688021 GTTCATCCAGATGGTGTAGAGAC 58.312 47.826 7.76 0.00 39.24 3.36
2322 2868 3.381590 CGTTCATCCAGATGGTGTAGAGA 59.618 47.826 7.76 0.00 39.24 3.10
2323 2869 3.491619 CCGTTCATCCAGATGGTGTAGAG 60.492 52.174 7.76 0.00 39.24 2.43
2324 2870 2.430694 CCGTTCATCCAGATGGTGTAGA 59.569 50.000 7.76 0.00 39.24 2.59
2325 2871 2.826428 CCGTTCATCCAGATGGTGTAG 58.174 52.381 7.76 0.00 39.24 2.74
2326 2872 1.134521 GCCGTTCATCCAGATGGTGTA 60.135 52.381 7.76 0.00 39.24 2.90
2327 2873 0.392998 GCCGTTCATCCAGATGGTGT 60.393 55.000 7.76 0.00 39.24 4.16
2328 2874 0.392863 TGCCGTTCATCCAGATGGTG 60.393 55.000 7.76 0.00 39.24 4.17
2329 2875 0.548031 ATGCCGTTCATCCAGATGGT 59.452 50.000 7.76 0.00 39.24 3.55
2330 2876 0.949397 CATGCCGTTCATCCAGATGG 59.051 55.000 7.76 0.00 39.24 3.51
2331 2877 1.871676 CTCATGCCGTTCATCCAGATG 59.128 52.381 0.98 0.98 40.09 2.90
2332 2878 1.202734 CCTCATGCCGTTCATCCAGAT 60.203 52.381 0.00 0.00 31.79 2.90
2333 2879 0.178767 CCTCATGCCGTTCATCCAGA 59.821 55.000 0.00 0.00 31.79 3.86
2334 2880 0.178767 TCCTCATGCCGTTCATCCAG 59.821 55.000 0.00 0.00 31.79 3.86
2335 2881 0.107703 GTCCTCATGCCGTTCATCCA 60.108 55.000 0.00 0.00 31.79 3.41
2336 2882 0.107703 TGTCCTCATGCCGTTCATCC 60.108 55.000 0.00 0.00 31.79 3.51
2337 2883 1.009829 GTGTCCTCATGCCGTTCATC 58.990 55.000 0.00 0.00 31.79 2.92
2338 2884 0.324614 TGTGTCCTCATGCCGTTCAT 59.675 50.000 0.00 0.00 35.31 2.57
2339 2885 0.107643 TTGTGTCCTCATGCCGTTCA 59.892 50.000 0.00 0.00 0.00 3.18
2340 2886 1.234821 TTTGTGTCCTCATGCCGTTC 58.765 50.000 0.00 0.00 0.00 3.95
2341 2887 1.686355 TTTTGTGTCCTCATGCCGTT 58.314 45.000 0.00 0.00 0.00 4.44
2342 2888 1.686355 TTTTTGTGTCCTCATGCCGT 58.314 45.000 0.00 0.00 0.00 5.68
2358 2904 7.936301 AGTTCTGCTCTAGTTTCTCAGATTTTT 59.064 33.333 0.00 0.00 34.26 1.94
2359 2905 7.449247 AGTTCTGCTCTAGTTTCTCAGATTTT 58.551 34.615 0.00 0.00 34.26 1.82
2360 2906 7.003402 AGTTCTGCTCTAGTTTCTCAGATTT 57.997 36.000 0.00 0.00 34.26 2.17
2361 2907 6.350949 GGAGTTCTGCTCTAGTTTCTCAGATT 60.351 42.308 0.00 0.00 43.62 2.40
2362 2908 5.127031 GGAGTTCTGCTCTAGTTTCTCAGAT 59.873 44.000 0.00 0.00 43.62 2.90
2363 2909 4.461081 GGAGTTCTGCTCTAGTTTCTCAGA 59.539 45.833 0.00 0.00 43.62 3.27
2364 2910 4.219507 TGGAGTTCTGCTCTAGTTTCTCAG 59.780 45.833 0.00 0.00 43.62 3.35
2365 2911 4.021894 GTGGAGTTCTGCTCTAGTTTCTCA 60.022 45.833 0.00 0.00 43.62 3.27
2366 2912 4.490743 GTGGAGTTCTGCTCTAGTTTCTC 58.509 47.826 0.00 0.00 43.62 2.87
2367 2913 3.057174 CGTGGAGTTCTGCTCTAGTTTCT 60.057 47.826 0.00 0.00 43.62 2.52
2368 2914 3.246619 CGTGGAGTTCTGCTCTAGTTTC 58.753 50.000 0.00 0.00 43.62 2.78
2369 2915 2.610727 GCGTGGAGTTCTGCTCTAGTTT 60.611 50.000 0.00 0.00 43.62 2.66
2370 2916 1.067495 GCGTGGAGTTCTGCTCTAGTT 60.067 52.381 0.00 0.00 43.62 2.24
2371 2917 0.528470 GCGTGGAGTTCTGCTCTAGT 59.472 55.000 0.00 0.00 43.62 2.57
2372 2918 0.524392 CGCGTGGAGTTCTGCTCTAG 60.524 60.000 0.00 0.00 43.62 2.43
2373 2919 0.958876 TCGCGTGGAGTTCTGCTCTA 60.959 55.000 5.77 0.00 43.62 2.43
2374 2920 2.206515 CTCGCGTGGAGTTCTGCTCT 62.207 60.000 5.77 0.00 43.62 4.09
2375 2921 1.803519 CTCGCGTGGAGTTCTGCTC 60.804 63.158 5.77 0.00 43.39 4.26
2376 2922 2.259818 CTCGCGTGGAGTTCTGCT 59.740 61.111 5.77 0.00 38.02 4.24
2377 2923 3.482783 GCTCGCGTGGAGTTCTGC 61.483 66.667 5.77 0.00 45.03 4.26
2378 2924 3.175240 CGCTCGCGTGGAGTTCTG 61.175 66.667 5.77 0.00 45.03 3.02
2381 2927 4.961511 TTGCGCTCGCGTGGAGTT 62.962 61.111 9.73 0.00 45.03 3.01
2382 2928 4.961511 TTTGCGCTCGCGTGGAGT 62.962 61.111 9.73 0.00 45.03 3.85
2383 2929 4.139420 CTTTGCGCTCGCGTGGAG 62.139 66.667 9.73 3.49 45.51 3.86
2384 2930 3.932580 ATCTTTGCGCTCGCGTGGA 62.933 57.895 9.73 7.41 45.51 4.02
2388 2934 2.528743 ATGGATCTTTGCGCTCGCG 61.529 57.895 9.73 6.98 45.51 5.87
2464 3010 2.066999 ATCCTCCTCCCCGCTGTTC 61.067 63.158 0.00 0.00 0.00 3.18
2476 3022 2.093235 CCAAGACAACCTCTCATCCTCC 60.093 54.545 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.