Multiple sequence alignment - TraesCS5B01G511300

Loading Multiple Alignment...

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 TraesCS5B01G511300 chr5B 100.000 3640 0 0 1 3640 676539039 676535400 0.000000e+00 6722.0
1 TraesCS5B01G511300 chr5B 84.086 1904 190 51 979 2848 676549483 676547659 0.000000e+00 1733.0
2 TraesCS5B01G511300 chr5B 80.405 296 36 16 976 1259 676466610 676466895 4.760000e-49 206.0
3 TraesCS5B01G511300 chr5D 91.488 2373 131 35 669 3013 536255228 536252899 0.000000e+00 3197.0
4 TraesCS5B01G511300 chr5D 86.278 1902 172 45 982 2866 536025184 536027013 0.000000e+00 1984.0
5 TraesCS5B01G511300 chr5D 85.240 1897 190 40 982 2866 536280186 536278368 0.000000e+00 1869.0
6 TraesCS5B01G511300 chr5D 87.473 926 104 9 2057 2973 536048214 536049136 0.000000e+00 1057.0
7 TraesCS5B01G511300 chr5D 93.492 461 23 5 1 458 536036825 536037281 0.000000e+00 678.0
8 TraesCS5B01G511300 chr5D 93.750 432 23 3 446 876 536037305 536037733 0.000000e+00 645.0
9 TraesCS5B01G511300 chr5D 86.424 523 28 21 3133 3640 536252682 536252188 1.920000e-147 532.0
10 TraesCS5B01G511300 chr5D 77.971 690 110 22 1595 2267 535997159 535997823 9.470000e-106 394.0
11 TraesCS5B01G511300 chr5D 80.051 391 48 21 939 1319 535996550 535996920 2.790000e-66 263.0
12 TraesCS5B01G511300 chr5D 83.908 87 10 3 827 910 536280349 536280264 3.010000e-11 80.5
13 TraesCS5B01G511300 chr5D 76.647 167 16 13 827 980 536025007 536025163 1.810000e-08 71.3
14 TraesCS5B01G511300 chr4A 90.395 2051 122 35 748 2759 635275949 635273935 0.000000e+00 2627.0
15 TraesCS5B01G511300 chr4A 85.757 2008 194 44 982 2973 635744773 635742842 0.000000e+00 2039.0
16 TraesCS5B01G511300 chr4A 85.789 1907 177 45 982 2866 635303325 635301491 0.000000e+00 1934.0
17 TraesCS5B01G511300 chr4A 85.106 658 55 23 3011 3640 635273176 635272534 1.840000e-177 632.0
18 TraesCS5B01G511300 chr4A 83.562 657 63 26 2247 2866 635300330 635299682 1.130000e-159 573.0
19 TraesCS5B01G511300 chr4A 91.797 256 15 4 2763 3013 635273615 635273361 5.780000e-93 351.0
20 TraesCS5B01G511300 chr4A 81.089 349 41 18 977 1319 633378324 633378653 4.660000e-64 255.0
21 TraesCS5B01G511300 chr4A 79.868 303 46 11 967 1261 633488643 633488938 1.320000e-49 207.0
22 TraesCS5B01G511300 chr4A 87.500 104 12 1 646 748 75320521 75320418 6.380000e-23 119.0
23 TraesCS5B01G511300 chr7D 85.981 107 13 2 646 751 111791646 111791751 2.970000e-21 113.0
24 TraesCS5B01G511300 chr2B 87.129 101 12 1 646 745 556216861 556216761 2.970000e-21 113.0
25 TraesCS5B01G511300 chr2A 87.129 101 12 1 646 745 450996518 450996618 2.970000e-21 113.0
26 TraesCS5B01G511300 chr1B 87.368 95 11 1 646 739 482693854 482693948 1.380000e-19 108.0
27 TraesCS5B01G511300 chr4B 84.906 106 15 1 646 750 7037059 7036954 4.970000e-19 106.0
28 TraesCS5B01G511300 chr3D 85.437 103 13 2 646 746 113586164 113586266 4.970000e-19 106.0


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 TraesCS5B01G511300 chr5B 676535400 676539039 3639 True 6722.000000 6722 100.000000 1 3640 1 chr5B.!!$R1 3639
1 TraesCS5B01G511300 chr5B 676547659 676549483 1824 True 1733.000000 1733 84.086000 979 2848 1 chr5B.!!$R2 1869
2 TraesCS5B01G511300 chr5D 536252188 536255228 3040 True 1864.500000 3197 88.956000 669 3640 2 chr5D.!!$R1 2971
3 TraesCS5B01G511300 chr5D 536048214 536049136 922 False 1057.000000 1057 87.473000 2057 2973 1 chr5D.!!$F1 916
4 TraesCS5B01G511300 chr5D 536025007 536027013 2006 False 1027.650000 1984 81.462500 827 2866 2 chr5D.!!$F3 2039
5 TraesCS5B01G511300 chr5D 536278368 536280349 1981 True 974.750000 1869 84.574000 827 2866 2 chr5D.!!$R2 2039
6 TraesCS5B01G511300 chr5D 536036825 536037733 908 False 661.500000 678 93.621000 1 876 2 chr5D.!!$F4 875
7 TraesCS5B01G511300 chr5D 535996550 535997823 1273 False 328.500000 394 79.011000 939 2267 2 chr5D.!!$F2 1328
8 TraesCS5B01G511300 chr4A 635742842 635744773 1931 True 2039.000000 2039 85.757000 982 2973 1 chr4A.!!$R2 1991
9 TraesCS5B01G511300 chr4A 635299682 635303325 3643 True 1253.500000 1934 84.675500 982 2866 2 chr4A.!!$R4 1884
10 TraesCS5B01G511300 chr4A 635272534 635275949 3415 True 1203.333333 2627 89.099333 748 3640 3 chr4A.!!$R3 2892

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
93 94 0.468226 ACGACGTACCGTATAGGGGA 59.532 55.0 15.67 4.16 46.96 4.81 F
1272 1384 0.328926 TAATTTCGTCACCCCACCCC 59.671 55.0 0.00 0.00 0.00 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 1508 0.383949 GAGGAGAGCAAGGTAGCGAG 59.616 60.0 0.0 0.0 40.15 5.03 R
2891 5249 0.877071 CGCACTGCTGGACTGAATTT 59.123 50.0 0.0 0.0 0.00 1.82 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
49 50 4.015084 TCCCGAAGAAGAAAGAGACGTAT 58.985 43.478 0.00 0.00 0.00 3.06
67 68 3.243873 CGTATCAAGCATAGAAGGAGGCA 60.244 47.826 0.00 0.00 0.00 4.75
68 69 2.996249 TCAAGCATAGAAGGAGGCAG 57.004 50.000 0.00 0.00 0.00 4.85
84 85 1.933041 CAGCGATGACGACGTACCG 60.933 63.158 0.00 6.13 42.66 4.02
85 86 2.099062 GCGATGACGACGTACCGT 59.901 61.111 0.00 1.51 46.43 4.83
93 94 0.468226 ACGACGTACCGTATAGGGGA 59.532 55.000 15.67 4.16 46.96 4.81
116 117 0.589229 GACGTATCAGGCAGACGACG 60.589 60.000 12.62 12.62 41.97 5.12
152 153 2.046217 GTCACGAAAGCCCCTCCC 60.046 66.667 0.00 0.00 0.00 4.30
156 157 0.611896 CACGAAAGCCCCTCCCAAAT 60.612 55.000 0.00 0.00 0.00 2.32
177 178 4.479993 GCAGATGGCGGTGGCTCT 62.480 66.667 0.00 0.00 39.81 4.09
264 265 0.883833 CTCGGCAGCCACAAAGAAAT 59.116 50.000 13.30 0.00 0.00 2.17
279 280 5.162870 ACAAAGAAATAGGGAAGGGGAAAGT 60.163 40.000 0.00 0.00 0.00 2.66
353 354 9.319223 GTTTTAGTTTTGTCGAATTTGCAAAAA 57.681 25.926 17.19 1.47 41.69 1.94
428 432 2.187946 GCTGGTGGATCGAGTGGG 59.812 66.667 0.00 0.00 0.00 4.61
526 567 6.456047 GGTCCGTATTTGAGGTATTTCGAAAC 60.456 42.308 13.81 1.55 0.00 2.78
530 571 7.413657 CCGTATTTGAGGTATTTCGAAACACAT 60.414 37.037 20.05 13.89 0.00 3.21
566 607 1.195448 CCAGCGCAAGTTTAGTGACTG 59.805 52.381 11.47 0.00 41.68 3.51
577 618 2.623418 TAGTGACTGTGGGGTGAGAT 57.377 50.000 0.00 0.00 0.00 2.75
578 619 1.734655 AGTGACTGTGGGGTGAGATT 58.265 50.000 0.00 0.00 0.00 2.40
600 641 9.727859 AGATTTTCTCTCTTTAAAACTACTCCC 57.272 33.333 0.00 0.00 0.00 4.30
605 646 4.081807 TCTCTTTAAAACTACTCCCTCCGC 60.082 45.833 0.00 0.00 0.00 5.54
621 662 5.245526 TCCCTCCGCTTCTTAATATAAGTCC 59.754 44.000 0.00 0.00 0.00 3.85
688 729 9.965902 AGAGTGTAGATTCATCCATTTTACTTT 57.034 29.630 0.00 0.00 0.00 2.66
699 742 8.928733 TCATCCATTTTACTTTGTACGTAGTTC 58.071 33.333 0.00 0.00 37.78 3.01
807 855 2.866762 GAGCATAAAGTTCAGGCCGTAG 59.133 50.000 0.00 0.00 0.00 3.51
918 979 2.076863 GTTTCGACATCCACCTTCCTG 58.923 52.381 0.00 0.00 0.00 3.86
919 980 1.348064 TTCGACATCCACCTTCCTGT 58.652 50.000 0.00 0.00 0.00 4.00
921 982 1.697432 TCGACATCCACCTTCCTGTTT 59.303 47.619 0.00 0.00 0.00 2.83
922 983 2.901192 TCGACATCCACCTTCCTGTTTA 59.099 45.455 0.00 0.00 0.00 2.01
923 984 3.056107 TCGACATCCACCTTCCTGTTTAG 60.056 47.826 0.00 0.00 0.00 1.85
1266 1378 1.680860 CCCCAGGTAATTTCGTCACCC 60.681 57.143 0.00 0.00 32.43 4.61
1267 1379 1.680860 CCCAGGTAATTTCGTCACCCC 60.681 57.143 0.00 0.00 32.43 4.95
1268 1380 1.003812 CCAGGTAATTTCGTCACCCCA 59.996 52.381 0.00 0.00 32.43 4.96
1269 1381 2.081462 CAGGTAATTTCGTCACCCCAC 58.919 52.381 0.00 0.00 32.43 4.61
1270 1382 1.003928 AGGTAATTTCGTCACCCCACC 59.996 52.381 0.00 0.00 32.43 4.61
1271 1383 1.456296 GTAATTTCGTCACCCCACCC 58.544 55.000 0.00 0.00 0.00 4.61
1272 1384 0.328926 TAATTTCGTCACCCCACCCC 59.671 55.000 0.00 0.00 0.00 4.95
1360 1497 1.067060 TGTGTAGTAGCTAGCATGCCG 59.933 52.381 18.83 7.19 0.00 5.69
1362 1499 0.667792 GTAGTAGCTAGCATGCCGCC 60.668 60.000 21.74 10.67 44.04 6.13
1363 1500 1.112916 TAGTAGCTAGCATGCCGCCA 61.113 55.000 21.74 9.37 44.04 5.69
1364 1501 1.302033 GTAGCTAGCATGCCGCCAT 60.302 57.895 21.74 10.26 44.04 4.40
1583 1756 2.106332 CGCAAGCCCTACCTACCG 59.894 66.667 0.00 0.00 0.00 4.02
1701 1888 3.011119 GAGAAGCTCTTCGTGGAGACTA 58.989 50.000 10.54 0.00 43.97 2.59
1703 1890 2.500392 AGCTCTTCGTGGAGACTAGT 57.500 50.000 0.00 0.00 35.52 2.57
1728 1915 0.250338 GAGTGTTTCCTGGCGAGGTT 60.250 55.000 15.09 0.00 40.76 3.50
1736 1923 4.269523 TGGCGAGGTTGCTGGCTT 62.270 61.111 0.00 0.00 34.52 4.35
1880 2082 4.255301 AGAATCAGAGCAAGCAGAAGAAG 58.745 43.478 0.00 0.00 0.00 2.85
1949 2151 2.113986 GGCAAGAGGTGGTGCTGT 59.886 61.111 0.00 0.00 40.70 4.40
1975 2177 1.071471 CCGTGAGTGAGCCCAACTT 59.929 57.895 0.00 0.00 0.00 2.66
1976 2178 1.230635 CCGTGAGTGAGCCCAACTTG 61.231 60.000 0.00 0.00 0.00 3.16
2009 2217 2.109774 CACTCAGATCAGAAGCTCCCT 58.890 52.381 0.00 0.00 0.00 4.20
2011 2219 0.829333 TCAGATCAGAAGCTCCCTGC 59.171 55.000 10.31 0.13 43.29 4.85
2045 2253 1.482593 CGTAGGAAGAGGCCAGACATT 59.517 52.381 5.01 0.00 0.00 2.71
2075 2283 3.958798 GTGAGGGGTTCTACTACTATGCA 59.041 47.826 0.00 0.00 0.00 3.96
2123 2331 1.951130 CACGTCAAGCAGCGACAGT 60.951 57.895 1.92 0.00 32.72 3.55
2134 2342 2.029073 CGACAGTGTGCCGGAACT 59.971 61.111 15.35 6.59 0.00 3.01
2223 2431 2.483877 CAGGTACAAGCAGCGAATGAAA 59.516 45.455 0.00 0.00 0.00 2.69
2279 2487 4.057428 GTCGACGAGCCTGGCACT 62.057 66.667 22.65 0.00 0.00 4.40
2310 2518 2.375766 GCGTGTGACAAGGAGAGCG 61.376 63.158 0.00 0.00 0.00 5.03
2417 2625 1.085091 GTCAGGCACAAGCTGATGAG 58.915 55.000 1.67 0.00 41.70 2.90
2432 2640 4.684877 CTGATGAGACAGACCATCAAGAG 58.315 47.826 0.00 0.00 45.68 2.85
2437 2645 0.036952 ACAGACCATCAAGAGGCACG 60.037 55.000 0.00 0.00 0.00 5.34
2439 2647 0.904865 AGACCATCAAGAGGCACGGA 60.905 55.000 0.00 0.00 0.00 4.69
2471 2679 2.345760 GGTCGACAAGCCTACGGGA 61.346 63.158 18.91 0.00 33.58 5.14
2766 3307 5.766174 GTGGATTGTACTGTTTTAACTGGGA 59.234 40.000 0.00 0.00 32.82 4.37
2891 5249 2.407616 CGTCGAGTAGATGCGCCA 59.592 61.111 4.18 0.00 0.00 5.69
2921 5279 2.177531 CAGTGCGTGCCTGAATGC 59.822 61.111 4.87 0.00 31.38 3.56
2922 5280 2.033141 AGTGCGTGCCTGAATGCT 59.967 55.556 0.00 0.00 33.04 3.79
2936 5294 6.183361 TGCCTGAATGCTCTACAATACATACT 60.183 38.462 0.00 0.00 0.00 2.12
2975 5335 0.236711 CGATCTCCCAATTGATGCGC 59.763 55.000 7.12 0.00 0.00 6.09
3047 5594 4.956504 CTTGAAAAGTACTGCCAGAGGCG 61.957 52.174 0.00 1.28 45.70 5.52
3056 5603 2.490217 CCAGAGGCGTCGGTACAG 59.510 66.667 5.84 0.00 0.00 2.74
3058 5605 1.592400 CCAGAGGCGTCGGTACAGAA 61.592 60.000 5.84 0.00 0.00 3.02
3059 5606 0.242825 CAGAGGCGTCGGTACAGAAA 59.757 55.000 0.00 0.00 0.00 2.52
3060 5607 0.963962 AGAGGCGTCGGTACAGAAAA 59.036 50.000 0.00 0.00 0.00 2.29
3061 5608 1.342174 AGAGGCGTCGGTACAGAAAAA 59.658 47.619 0.00 0.00 0.00 1.94
3062 5609 1.458445 GAGGCGTCGGTACAGAAAAAC 59.542 52.381 0.00 0.00 0.00 2.43
3063 5610 0.514255 GGCGTCGGTACAGAAAAACC 59.486 55.000 0.00 0.00 0.00 3.27
3064 5611 1.505425 GCGTCGGTACAGAAAAACCT 58.495 50.000 0.00 0.00 33.34 3.50
3065 5612 2.610232 GGCGTCGGTACAGAAAAACCTA 60.610 50.000 0.00 0.00 33.34 3.08
3066 5613 2.665052 GCGTCGGTACAGAAAAACCTAG 59.335 50.000 0.00 0.00 33.34 3.02
3068 5615 3.656559 GTCGGTACAGAAAAACCTAGCA 58.343 45.455 0.00 0.00 33.34 3.49
3069 5616 3.678548 GTCGGTACAGAAAAACCTAGCAG 59.321 47.826 0.00 0.00 33.34 4.24
3071 5618 3.676093 GGTACAGAAAAACCTAGCAGCT 58.324 45.455 0.00 0.00 32.72 4.24
3072 5619 3.685272 GGTACAGAAAAACCTAGCAGCTC 59.315 47.826 0.00 0.00 32.72 4.09
3073 5620 2.784347 ACAGAAAAACCTAGCAGCTCC 58.216 47.619 0.00 0.00 0.00 4.70
3074 5621 2.087646 CAGAAAAACCTAGCAGCTCCC 58.912 52.381 0.00 0.00 0.00 4.30
3075 5622 1.705186 AGAAAAACCTAGCAGCTCCCA 59.295 47.619 0.00 0.00 0.00 4.37
3076 5623 2.108250 AGAAAAACCTAGCAGCTCCCAA 59.892 45.455 0.00 0.00 0.00 4.12
3077 5624 2.907458 AAAACCTAGCAGCTCCCAAT 57.093 45.000 0.00 0.00 0.00 3.16
3078 5625 4.018415 AGAAAAACCTAGCAGCTCCCAATA 60.018 41.667 0.00 0.00 0.00 1.90
3079 5626 4.526438 AAAACCTAGCAGCTCCCAATAT 57.474 40.909 0.00 0.00 0.00 1.28
3093 5640 1.202290 CCAATATCTGTTGGTTGGCGC 60.202 52.381 0.00 0.00 42.94 6.53
3095 5642 1.095228 ATATCTGTTGGTTGGCGCCG 61.095 55.000 23.90 4.41 0.00 6.46
3121 5668 2.977405 GCATTCACTGCGAAAGAACT 57.023 45.000 0.00 0.00 41.97 3.01
3127 5674 2.287915 TCACTGCGAAAGAACTTCTTGC 59.712 45.455 4.75 2.13 36.71 4.01
3134 5681 4.148871 GCGAAAGAACTTCTTGCATTTTCC 59.851 41.667 9.77 0.00 36.71 3.13
3135 5682 5.523369 CGAAAGAACTTCTTGCATTTTCCT 58.477 37.500 9.77 0.00 36.71 3.36
3138 5701 7.306225 CGAAAGAACTTCTTGCATTTTCCTTTC 60.306 37.037 9.77 0.00 36.71 2.62
3152 5715 6.723298 TTTTCCTTTCAGGCAATGTTCTTA 57.277 33.333 0.00 0.00 34.61 2.10
3229 5792 7.602753 TCTCAATCTCTTCATACGTTCTTCAA 58.397 34.615 0.00 0.00 0.00 2.69
3274 5837 1.215673 TGGTAGAAACTTTGGGTGGCA 59.784 47.619 0.00 0.00 0.00 4.92
3276 5839 2.897326 GGTAGAAACTTTGGGTGGCATT 59.103 45.455 0.00 0.00 0.00 3.56
3287 5850 2.025037 TGGGTGGCATTAGCTCTTTCAT 60.025 45.455 0.00 0.00 41.70 2.57
3296 5859 5.579511 GCATTAGCTCTTTCATGTTGCAAAT 59.420 36.000 0.00 0.00 37.91 2.32
3384 5949 6.889301 TGAAAATCATCAAGAGCTCTGTTT 57.111 33.333 19.06 8.98 0.00 2.83
3390 5955 2.483876 TCAAGAGCTCTGTTTGGTTCG 58.516 47.619 19.06 0.00 0.00 3.95
3391 5956 1.069636 CAAGAGCTCTGTTTGGTTCGC 60.070 52.381 19.06 0.00 0.00 4.70
3418 5983 7.710896 CCAAAGAATGGGTTCTCATAGATTTC 58.289 38.462 0.00 0.00 46.27 2.17
3419 5984 7.559170 CCAAAGAATGGGTTCTCATAGATTTCT 59.441 37.037 0.00 0.00 46.27 2.52
3449 6020 4.526970 ACAATATCAGTAGCAACAAGGGG 58.473 43.478 0.00 0.00 0.00 4.79
3590 6177 5.480422 GGGAAGGTGTATCCATTGTCTTTTT 59.520 40.000 0.00 0.00 38.80 1.94
3613 6200 0.466555 TTTACTTGCCGGTGCTGGTT 60.467 50.000 1.90 0.00 38.71 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 1.134280 GCTGCCTCCTTCTATGCTTGA 60.134 52.381 0.00 0.00 0.00 3.02
84 85 4.158025 CCTGATACGTCATGTCCCCTATAC 59.842 50.000 0.00 0.00 32.98 1.47
85 86 4.341487 CCTGATACGTCATGTCCCCTATA 58.659 47.826 0.00 0.00 32.98 1.31
93 94 1.202302 CGTCTGCCTGATACGTCATGT 60.202 52.381 0.00 0.00 32.98 3.21
116 117 3.717294 TTCCTCCCGCTCCCAAGC 61.717 66.667 0.00 0.00 45.56 4.01
127 128 1.289800 GGCTTTCGTGACGTTCCTCC 61.290 60.000 4.40 0.00 0.00 4.30
160 161 4.479993 AGAGCCACCGCCATCTGC 62.480 66.667 0.00 0.00 34.57 4.26
169 170 2.512515 GTCGGATGCAGAGCCACC 60.513 66.667 0.00 0.00 0.00 4.61
170 171 2.835701 TTCGTCGGATGCAGAGCCAC 62.836 60.000 0.00 0.00 0.00 5.01
171 172 2.563050 CTTCGTCGGATGCAGAGCCA 62.563 60.000 0.00 0.00 0.00 4.75
177 178 1.139734 GAGCTCTTCGTCGGATGCA 59.860 57.895 6.43 0.00 0.00 3.96
225 226 0.674895 GTGGTCACCTGCACCTCATC 60.675 60.000 0.00 0.00 34.66 2.92
257 258 5.075900 TCACTTTCCCCTTCCCTATTTCTTT 59.924 40.000 0.00 0.00 0.00 2.52
264 265 1.557188 CCCTCACTTTCCCCTTCCCTA 60.557 57.143 0.00 0.00 0.00 3.53
279 280 1.003442 CATCACCCTCTCCCCCTCA 59.997 63.158 0.00 0.00 0.00 3.86
394 397 0.667487 AGCGTTGACTGGACACATCG 60.667 55.000 0.00 0.00 33.99 3.84
526 567 7.567571 CGCTGGAACTCATTTTAGTATATGTG 58.432 38.462 0.00 0.00 0.00 3.21
530 571 5.666462 TGCGCTGGAACTCATTTTAGTATA 58.334 37.500 9.73 0.00 0.00 1.47
577 618 8.155510 GGAGGGAGTAGTTTTAAAGAGAGAAAA 58.844 37.037 0.00 0.00 0.00 2.29
578 619 7.525029 CGGAGGGAGTAGTTTTAAAGAGAGAAA 60.525 40.741 0.00 0.00 0.00 2.52
600 641 8.664211 AAAAGGACTTATATTAAGAAGCGGAG 57.336 34.615 1.47 0.00 0.00 4.63
621 662 7.752695 ACGACATTGAAGCCTCTAAATAAAAG 58.247 34.615 0.00 0.00 0.00 2.27
807 855 1.227556 AAGTGAGTGGTGGCACGTC 60.228 57.895 12.17 8.80 39.88 4.34
918 979 5.744666 TTGTGAGGCAGTAAACACTAAAC 57.255 39.130 0.00 0.00 34.81 2.01
919 980 6.770785 AGATTTGTGAGGCAGTAAACACTAAA 59.229 34.615 0.00 0.00 33.64 1.85
921 982 5.865085 AGATTTGTGAGGCAGTAAACACTA 58.135 37.500 0.00 0.00 34.81 2.74
922 983 4.718961 AGATTTGTGAGGCAGTAAACACT 58.281 39.130 0.00 0.00 34.81 3.55
923 984 4.515191 TGAGATTTGTGAGGCAGTAAACAC 59.485 41.667 0.00 0.00 0.00 3.32
1347 1484 1.301953 CATGGCGGCATGCTAGCTA 60.302 57.895 34.94 24.93 45.43 3.32
1367 1504 3.083997 AGCAAGGTAGCGAGGGGG 61.084 66.667 0.00 0.00 40.15 5.40
1368 1505 2.022240 GAGAGCAAGGTAGCGAGGGG 62.022 65.000 0.00 0.00 40.15 4.79
1369 1506 1.439644 GAGAGCAAGGTAGCGAGGG 59.560 63.158 0.00 0.00 40.15 4.30
1370 1507 1.040339 AGGAGAGCAAGGTAGCGAGG 61.040 60.000 0.00 0.00 40.15 4.63
1371 1508 0.383949 GAGGAGAGCAAGGTAGCGAG 59.616 60.000 0.00 0.00 40.15 5.03
1372 1509 1.038130 GGAGGAGAGCAAGGTAGCGA 61.038 60.000 0.00 0.00 40.15 4.93
1373 1510 1.439644 GGAGGAGAGCAAGGTAGCG 59.560 63.158 0.00 0.00 40.15 4.26
1374 1511 1.439644 CGGAGGAGAGCAAGGTAGC 59.560 63.158 0.00 0.00 0.00 3.58
1375 1512 1.439644 GCGGAGGAGAGCAAGGTAG 59.560 63.158 0.00 0.00 0.00 3.18
1376 1513 2.415608 CGCGGAGGAGAGCAAGGTA 61.416 63.158 0.00 0.00 0.00 3.08
1377 1514 3.764466 CGCGGAGGAGAGCAAGGT 61.764 66.667 0.00 0.00 0.00 3.50
1455 1606 3.507009 GCTAGACCTCGACGCGGT 61.507 66.667 9.74 9.74 37.50 5.68
1569 1742 2.767073 GGGCGGTAGGTAGGGCTT 60.767 66.667 0.00 0.00 0.00 4.35
1604 1782 1.863454 CCGCTACTGCTATTGCTGAAG 59.137 52.381 12.54 0.00 40.66 3.02
1623 1801 1.145803 ACGAACGAAAAGTGCTAGCC 58.854 50.000 13.29 3.49 0.00 3.93
1630 1815 1.994779 ACACGTCAACGAACGAAAAGT 59.005 42.857 9.88 6.48 45.37 2.66
1701 1888 2.887152 GCCAGGAAACACTCATGAAACT 59.113 45.455 0.00 0.00 38.11 2.66
1703 1890 1.879380 CGCCAGGAAACACTCATGAAA 59.121 47.619 0.00 0.00 38.11 2.69
1736 1923 1.304381 GGTGATGCCTGCTGGGAAA 60.304 57.895 8.15 0.00 37.19 3.13
1880 2082 4.589908 TCTTCACTTTGAGCCCCTTATTC 58.410 43.478 0.00 0.00 0.00 1.75
2045 2253 1.846124 GAACCCCTCACCCAGGTCA 60.846 63.158 0.00 0.00 41.51 4.02
2054 2262 4.215908 CTGCATAGTAGTAGAACCCCTCA 58.784 47.826 0.00 0.00 0.00 3.86
2123 2331 1.227823 CAGTGGAAGTTCCGGCACA 60.228 57.895 17.13 0.00 40.17 4.57
2134 2342 2.033141 GCTCAGCAGGCAGTGGAA 59.967 61.111 0.00 0.00 0.00 3.53
2279 2487 4.758251 CACGCCGACATCCCAGCA 62.758 66.667 0.00 0.00 0.00 4.41
2417 2625 1.731720 GTGCCTCTTGATGGTCTGTC 58.268 55.000 0.00 0.00 0.00 3.51
2432 2640 3.490759 CGTGCTGATGTCCGTGCC 61.491 66.667 0.00 0.00 0.00 5.01
2437 2645 1.291877 GACCACACGTGCTGATGTCC 61.292 60.000 17.22 0.00 0.00 4.02
2439 2647 1.664649 CGACCACACGTGCTGATGT 60.665 57.895 17.22 5.57 0.00 3.06
2766 3307 1.141881 CGATCTAACGGCCAGCACT 59.858 57.895 2.24 0.00 0.00 4.40
2852 5210 1.131883 AGCAGCGAATTGAATCACAGC 59.868 47.619 0.00 0.00 0.00 4.40
2882 5240 1.098050 GGACTGAATTTGGCGCATCT 58.902 50.000 10.83 0.00 0.00 2.90
2891 5249 0.877071 CGCACTGCTGGACTGAATTT 59.123 50.000 0.00 0.00 0.00 1.82
2921 5279 6.924060 GCAGGTAACCAGTATGTATTGTAGAG 59.076 42.308 0.00 0.00 37.17 2.43
2922 5280 6.610020 AGCAGGTAACCAGTATGTATTGTAGA 59.390 38.462 0.00 0.00 37.17 2.59
2936 5294 4.482030 TCGGGTATATAAGCAGGTAACCA 58.518 43.478 0.00 0.00 37.17 3.67
2975 5335 1.135915 ACATTCAGGAGCTAGCAGTCG 59.864 52.381 18.83 2.54 0.00 4.18
3042 5589 1.458445 GTTTTTCTGTACCGACGCCTC 59.542 52.381 0.00 0.00 0.00 4.70
3047 5594 3.656559 TGCTAGGTTTTTCTGTACCGAC 58.343 45.455 0.00 0.00 39.46 4.79
3048 5595 3.863400 GCTGCTAGGTTTTTCTGTACCGA 60.863 47.826 0.00 0.00 39.46 4.69
3050 5597 3.676093 AGCTGCTAGGTTTTTCTGTACC 58.324 45.455 0.00 0.00 34.54 3.34
3051 5598 3.685272 GGAGCTGCTAGGTTTTTCTGTAC 59.315 47.826 0.15 0.00 0.00 2.90
3052 5599 3.307480 GGGAGCTGCTAGGTTTTTCTGTA 60.307 47.826 0.15 0.00 0.00 2.74
3053 5600 2.553247 GGGAGCTGCTAGGTTTTTCTGT 60.553 50.000 0.15 0.00 0.00 3.41
3054 5601 2.087646 GGGAGCTGCTAGGTTTTTCTG 58.912 52.381 0.15 0.00 0.00 3.02
3056 5603 2.200373 TGGGAGCTGCTAGGTTTTTC 57.800 50.000 0.15 0.00 0.00 2.29
3058 5605 2.907458 ATTGGGAGCTGCTAGGTTTT 57.093 45.000 0.15 0.00 0.00 2.43
3059 5606 3.718956 AGATATTGGGAGCTGCTAGGTTT 59.281 43.478 0.15 0.00 0.00 3.27
3060 5607 3.072184 CAGATATTGGGAGCTGCTAGGTT 59.928 47.826 0.15 0.00 0.00 3.50
3061 5608 2.636893 CAGATATTGGGAGCTGCTAGGT 59.363 50.000 0.15 0.00 0.00 3.08
3062 5609 2.636893 ACAGATATTGGGAGCTGCTAGG 59.363 50.000 0.15 0.00 31.74 3.02
3063 5610 4.063689 CAACAGATATTGGGAGCTGCTAG 58.936 47.826 0.15 0.00 31.74 3.42
3064 5611 3.181451 CCAACAGATATTGGGAGCTGCTA 60.181 47.826 0.15 0.00 44.74 3.49
3065 5612 2.422519 CCAACAGATATTGGGAGCTGCT 60.423 50.000 0.00 0.00 44.74 4.24
3066 5613 1.952296 CCAACAGATATTGGGAGCTGC 59.048 52.381 0.00 0.00 44.74 5.25
3074 5621 1.202290 GGCGCCAACCAACAGATATTG 60.202 52.381 24.80 0.00 0.00 1.90
3075 5622 1.102978 GGCGCCAACCAACAGATATT 58.897 50.000 24.80 0.00 0.00 1.28
3076 5623 1.095228 CGGCGCCAACCAACAGATAT 61.095 55.000 28.98 0.00 0.00 1.63
3077 5624 1.743623 CGGCGCCAACCAACAGATA 60.744 57.895 28.98 0.00 0.00 1.98
3078 5625 3.055719 CGGCGCCAACCAACAGAT 61.056 61.111 28.98 0.00 0.00 2.90
3093 5640 1.210931 CAGTGAATGCTGTTGGCGG 59.789 57.895 0.00 0.00 45.43 6.13
3113 5660 7.492344 TGAAAGGAAAATGCAAGAAGTTCTTTC 59.508 33.333 15.60 11.67 33.78 2.62
3134 5681 7.987458 TCCTACTATAAGAACATTGCCTGAAAG 59.013 37.037 0.00 0.00 0.00 2.62
3135 5682 7.857456 TCCTACTATAAGAACATTGCCTGAAA 58.143 34.615 0.00 0.00 0.00 2.69
3138 5701 6.926272 GTCTCCTACTATAAGAACATTGCCTG 59.074 42.308 0.00 0.00 0.00 4.85
3164 5727 6.072119 ACACACTAGTCGATGACAGAAACATA 60.072 38.462 0.00 0.00 34.60 2.29
3174 5737 2.228103 GTCACCACACACTAGTCGATGA 59.772 50.000 0.00 0.00 0.00 2.92
3175 5738 2.229062 AGTCACCACACACTAGTCGATG 59.771 50.000 0.00 0.00 0.00 3.84
3176 5739 2.515854 AGTCACCACACACTAGTCGAT 58.484 47.619 0.00 0.00 0.00 3.59
3248 5811 2.817258 CCCAAAGTTTCTACCATTCGCA 59.183 45.455 0.00 0.00 0.00 5.10
3249 5812 2.817844 ACCCAAAGTTTCTACCATTCGC 59.182 45.455 0.00 0.00 0.00 4.70
3250 5813 3.190535 CCACCCAAAGTTTCTACCATTCG 59.809 47.826 0.00 0.00 0.00 3.34
3251 5814 3.056821 GCCACCCAAAGTTTCTACCATTC 60.057 47.826 0.00 0.00 0.00 2.67
3253 5816 2.158385 TGCCACCCAAAGTTTCTACCAT 60.158 45.455 0.00 0.00 0.00 3.55
3254 5817 1.215673 TGCCACCCAAAGTTTCTACCA 59.784 47.619 0.00 0.00 0.00 3.25
3256 5819 4.380550 GCTAATGCCACCCAAAGTTTCTAC 60.381 45.833 0.00 0.00 0.00 2.59
3258 5821 2.562738 GCTAATGCCACCCAAAGTTTCT 59.437 45.455 0.00 0.00 0.00 2.52
3274 5837 8.025243 CAAATTTGCAACATGAAAGAGCTAAT 57.975 30.769 5.01 2.09 33.39 1.73
3316 5881 5.449451 GCGAAAGGGTCTTTAACACAAAGAA 60.449 40.000 1.23 0.00 37.93 2.52
3317 5882 4.035909 GCGAAAGGGTCTTTAACACAAAGA 59.964 41.667 0.00 0.00 31.71 2.52
3322 5887 1.538512 GGGCGAAAGGGTCTTTAACAC 59.461 52.381 0.00 0.00 0.00 3.32
3352 5917 8.800332 AGCTCTTGATGATTTTCAAACTACAAT 58.200 29.630 0.00 0.00 35.31 2.71
3355 5920 7.961827 CAGAGCTCTTGATGATTTTCAAACTAC 59.038 37.037 15.27 0.00 35.31 2.73
3384 5949 0.897863 CCATTCTTTGGGGCGAACCA 60.898 55.000 0.00 0.00 42.33 3.67
3431 5996 1.134521 CGCCCCTTGTTGCTACTGATA 60.135 52.381 0.00 0.00 0.00 2.15
3590 6177 0.533308 AGCACCGGCAAGTAAAACGA 60.533 50.000 0.00 0.00 44.61 3.85
3613 6200 2.584064 CACATCCACCTAGCCGCA 59.416 61.111 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.