Multiple sequence alignment - TraesCS6B01G124800

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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 TraesCS6B01G124800 chr6B 100.000 2126 0 0 1 2126 119850678 119848553 0.000000e+00 3927.0
1 TraesCS6B01G124800 chr6D 89.512 2174 109 82 2 2126 52725753 52723650 0.000000e+00 2641.0
2 TraesCS6B01G124800 chr6A 93.947 1206 34 19 930 2126 63610778 63609603 0.000000e+00 1786.0
3 TraesCS6B01G124800 chr6A 84.112 856 48 44 2 839 63611604 63610819 0.000000e+00 747.0
4 TraesCS6B01G124800 chr7B 90.000 170 14 1 1421 1590 547711349 547711515 1.280000e-52 217.0
5 TraesCS6B01G124800 chr7B 97.059 34 1 0 1361 1394 547711306 547711339 8.190000e-05 58.4
6 TraesCS6B01G124800 chr5D 88.189 127 4 4 2011 2126 297792759 297792633 7.910000e-30 141.0
7 TraesCS6B01G124800 chr5D 98.039 51 1 0 1072 1122 285247438 285247488 2.910000e-14 89.8
8 TraesCS6B01G124800 chr5D 90.000 50 5 0 1077 1126 113391895 113391846 4.900000e-07 65.8
9 TraesCS6B01G124800 chr3D 88.189 127 4 4 2011 2126 70729664 70729790 7.910000e-30 141.0
10 TraesCS6B01G124800 chr3D 87.402 127 5 4 2011 2126 443945626 443945752 3.680000e-28 135.0
11 TraesCS6B01G124800 chr3D 98.182 55 1 0 1072 1126 252334799 252334853 1.740000e-16 97.1
12 TraesCS6B01G124800 chr2D 88.189 127 4 4 2011 2126 106236306 106236180 7.910000e-30 141.0
13 TraesCS6B01G124800 chr2D 88.189 127 4 4 2011 2126 422777646 422777520 7.910000e-30 141.0
14 TraesCS6B01G124800 chr2D 88.189 127 4 4 2011 2126 503852139 503852265 7.910000e-30 141.0
15 TraesCS6B01G124800 chr2D 88.189 127 4 4 2011 2126 592138012 592138138 7.910000e-30 141.0
16 TraesCS6B01G124800 chr1D 86.667 135 6 3 1364 1498 413940956 413941078 2.840000e-29 139.0
17 TraesCS6B01G124800 chr1A 85.185 135 8 6 1364 1498 467151161 467151283 6.160000e-26 128.0
18 TraesCS6B01G124800 chr3B 98.182 55 1 0 1072 1126 313808032 313808086 1.740000e-16 97.1
19 TraesCS6B01G124800 chr3A 98.182 55 1 0 1072 1126 332220139 332220085 1.740000e-16 97.1
20 TraesCS6B01G124800 chr7D 87.500 88 2 2 1364 1451 420082372 420082450 2.250000e-15 93.5
21 TraesCS6B01G124800 chr5B 98.039 51 1 0 1072 1122 322858711 322858761 2.910000e-14 89.8
22 TraesCS6B01G124800 chr5A 98.039 51 1 0 1072 1122 377119607 377119657 2.910000e-14 89.8
23 TraesCS6B01G124800 chr4A 86.364 88 3 2 1364 1451 613673563 613673485 1.050000e-13 87.9
24 TraesCS6B01G124800 chr2B 94.737 38 2 0 1380 1417 34588163 34588126 2.280000e-05 60.2


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 TraesCS6B01G124800 chr6B 119848553 119850678 2125 True 3927.0 3927 100.0000 1 2126 1 chr6B.!!$R1 2125
1 TraesCS6B01G124800 chr6D 52723650 52725753 2103 True 2641.0 2641 89.5120 2 2126 1 chr6D.!!$R1 2124
2 TraesCS6B01G124800 chr6A 63609603 63611604 2001 True 1266.5 1786 89.0295 2 2126 2 chr6A.!!$R1 2124

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
799 854 0.378257 GCAGCGAGAGAGAGAGACAG 59.622 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1926 2009 0.110238 TCATCTCTTTTGTTGCGCGC 60.11 50.0 27.26 27.26 0.0 6.86 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
43 47 2.276201 CGTGATTCAAATCGTAGCCCA 58.724 47.619 0.00 0.00 38.26 5.36
84 91 5.360591 CCAGTCACCTTGAATACTACCATC 58.639 45.833 0.00 0.00 0.00 3.51
85 92 5.129485 CCAGTCACCTTGAATACTACCATCT 59.871 44.000 0.00 0.00 0.00 2.90
86 93 6.323996 CCAGTCACCTTGAATACTACCATCTA 59.676 42.308 0.00 0.00 0.00 1.98
232 239 4.586235 GGCCGGGGTAGCATGCAT 62.586 66.667 21.98 7.68 0.00 3.96
233 240 3.289834 GCCGGGGTAGCATGCATG 61.290 66.667 22.70 22.70 0.00 4.06
234 241 2.510411 CCGGGGTAGCATGCATGA 59.490 61.111 30.64 7.50 0.00 3.07
235 242 1.073722 CCGGGGTAGCATGCATGAT 59.926 57.895 30.64 26.66 0.00 2.45
253 260 3.367607 TGATTTTTCACTTTTCACCGCG 58.632 40.909 0.00 0.00 0.00 6.46
276 283 2.405191 GCTTTCGGCGCATCTTCC 59.595 61.111 10.83 0.00 0.00 3.46
277 284 3.102097 CTTTCGGCGCATCTTCCC 58.898 61.111 10.83 0.00 0.00 3.97
278 285 2.813179 CTTTCGGCGCATCTTCCCG 61.813 63.158 10.83 0.75 43.21 5.14
279 286 3.599285 TTTCGGCGCATCTTCCCGT 62.599 57.895 10.83 0.00 42.48 5.28
280 287 4.812476 TCGGCGCATCTTCCCGTG 62.812 66.667 10.83 0.00 42.48 4.94
297 304 4.154347 GGGCCGTGGCAGAGAGAG 62.154 72.222 13.76 0.00 44.11 3.20
298 305 3.071206 GGCCGTGGCAGAGAGAGA 61.071 66.667 13.76 0.00 44.11 3.10
299 306 2.493973 GCCGTGGCAGAGAGAGAG 59.506 66.667 5.89 0.00 41.49 3.20
300 307 2.049185 GCCGTGGCAGAGAGAGAGA 61.049 63.158 5.89 0.00 41.49 3.10
302 309 0.393673 CCGTGGCAGAGAGAGAGAGA 60.394 60.000 0.00 0.00 0.00 3.10
332 339 3.058160 CCGGCTGGCAAGTTGGAG 61.058 66.667 0.00 0.00 0.00 3.86
333 340 2.032528 CGGCTGGCAAGTTGGAGA 59.967 61.111 4.75 0.00 0.00 3.71
336 343 0.957888 GGCTGGCAAGTTGGAGAGTC 60.958 60.000 4.75 0.00 0.00 3.36
338 345 1.805869 CTGGCAAGTTGGAGAGTCTG 58.194 55.000 4.75 0.00 0.00 3.51
345 352 0.959553 GTTGGAGAGTCTGGACACGA 59.040 55.000 0.00 0.00 0.00 4.35
346 353 0.959553 TTGGAGAGTCTGGACACGAC 59.040 55.000 0.00 0.00 0.00 4.34
363 372 3.597728 CGGCCTCCTCTAGACGCC 61.598 72.222 0.00 0.00 41.75 5.68
367 376 1.227664 CCTCCTCTAGACGCCTCCA 59.772 63.158 0.00 0.00 0.00 3.86
452 463 4.742201 CGCCTGCACCTGCGTAGT 62.742 66.667 11.27 0.00 45.43 2.73
453 464 2.577059 GCCTGCACCTGCGTAGTA 59.423 61.111 0.00 0.00 45.83 1.82
455 466 1.516386 CCTGCACCTGCGTAGTACG 60.516 63.158 18.37 18.37 45.83 3.67
456 467 1.516386 CTGCACCTGCGTAGTACGG 60.516 63.158 23.29 10.01 45.83 4.02
457 468 2.884207 GCACCTGCGTAGTACGGC 60.884 66.667 23.29 13.95 42.82 5.68
458 469 2.578713 CACCTGCGTAGTACGGCG 60.579 66.667 23.29 4.80 42.82 6.46
507 518 1.648467 GGTCAGCGTGATTTCCAGCC 61.648 60.000 0.00 0.00 0.00 4.85
621 663 3.264159 TGCCGCTGCAATCGATCG 61.264 61.111 9.36 9.36 46.66 3.69
622 664 4.005472 GCCGCTGCAATCGATCGG 62.005 66.667 16.41 15.93 42.68 4.18
623 665 3.341043 CCGCTGCAATCGATCGGG 61.341 66.667 16.41 6.63 36.73 5.14
624 666 3.341043 CGCTGCAATCGATCGGGG 61.341 66.667 16.41 6.25 0.00 5.73
625 667 2.974698 GCTGCAATCGATCGGGGG 60.975 66.667 16.41 5.88 0.00 5.40
626 668 2.505982 CTGCAATCGATCGGGGGT 59.494 61.111 16.41 0.00 0.00 4.95
627 669 1.595382 CTGCAATCGATCGGGGGTC 60.595 63.158 16.41 2.03 0.00 4.46
750 794 3.039526 CCCCTCCTCCTCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
765 809 2.387757 CTCCCTCTCTTCTTCCTCCTG 58.612 57.143 0.00 0.00 0.00 3.86
772 827 0.620121 CTTCTTCCTCCTGCCCTCCT 60.620 60.000 0.00 0.00 0.00 3.69
793 848 2.101965 CACCGCAGCGAGAGAGAG 59.898 66.667 18.75 0.00 0.00 3.20
794 849 2.045829 ACCGCAGCGAGAGAGAGA 60.046 61.111 18.75 0.00 0.00 3.10
795 850 2.112198 ACCGCAGCGAGAGAGAGAG 61.112 63.158 18.75 0.00 0.00 3.20
796 851 1.817520 CCGCAGCGAGAGAGAGAGA 60.818 63.158 18.75 0.00 0.00 3.10
797 852 1.351707 CGCAGCGAGAGAGAGAGAC 59.648 63.158 9.98 0.00 0.00 3.36
798 853 1.365368 CGCAGCGAGAGAGAGAGACA 61.365 60.000 9.98 0.00 0.00 3.41
799 854 0.378257 GCAGCGAGAGAGAGAGACAG 59.622 60.000 0.00 0.00 0.00 3.51
800 855 2.011548 GCAGCGAGAGAGAGAGACAGA 61.012 57.143 0.00 0.00 0.00 3.41
836 891 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
837 892 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
838 893 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
839 894 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
840 895 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
841 896 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
842 897 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
843 898 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
844 899 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
845 900 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
846 901 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
847 902 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
848 903 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
849 904 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
850 905 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
851 906 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
852 907 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
853 908 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
854 909 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
857 912 3.640967 AGAGAGAGAGAGAGAGAGAGAGC 59.359 52.174 0.00 0.00 0.00 4.09
863 918 1.837439 AGAGAGAGAGAGAGCGAGGAA 59.163 52.381 0.00 0.00 0.00 3.36
865 920 1.134098 AGAGAGAGAGAGCGAGGAAGG 60.134 57.143 0.00 0.00 0.00 3.46
872 927 1.153469 GAGCGAGGAAGGGAAGCAG 60.153 63.158 0.00 0.00 0.00 4.24
878 933 1.676967 GGAAGGGAAGCAGGCAGTG 60.677 63.158 0.00 0.00 0.00 3.66
879 934 1.376466 GAAGGGAAGCAGGCAGTGA 59.624 57.895 0.00 0.00 0.00 3.41
881 936 2.749441 GGGAAGCAGGCAGTGAGC 60.749 66.667 0.00 0.00 44.65 4.26
882 937 2.350514 GGAAGCAGGCAGTGAGCT 59.649 61.111 0.00 0.00 44.79 4.09
899 965 4.671590 TGAGAGGTCGGCCGTCCA 62.672 66.667 36.90 18.28 40.50 4.02
909 975 4.404098 GCCGTCCACCCGTCCATT 62.404 66.667 0.00 0.00 0.00 3.16
910 976 2.349755 CCGTCCACCCGTCCATTT 59.650 61.111 0.00 0.00 0.00 2.32
911 977 1.743995 CCGTCCACCCGTCCATTTC 60.744 63.158 0.00 0.00 0.00 2.17
914 980 2.437716 CCACCCGTCCATTTCCCG 60.438 66.667 0.00 0.00 0.00 5.14
915 981 2.437716 CACCCGTCCATTTCCCGG 60.438 66.667 0.00 0.00 41.37 5.73
916 982 4.419921 ACCCGTCCATTTCCCGGC 62.420 66.667 0.00 0.00 40.38 6.13
920 986 4.419921 GTCCATTTCCCGGCCGGT 62.420 66.667 40.52 21.85 0.00 5.28
923 989 4.418328 CATTTCCCGGCCGGTGGA 62.418 66.667 40.52 29.26 0.00 4.02
935 1004 1.684049 CGGTGGAGCTCCCTCTTCT 60.684 63.158 29.95 0.00 38.21 2.85
1168 1238 2.612251 CCCCTCCTCTCCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
1169 1239 2.612251 CCCTCCTCTCCCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
1170 1240 2.018086 CCCTCCTCTCCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
1239 1309 2.486203 CACACACTCGCTTACTCTCTCT 59.514 50.000 0.00 0.00 0.00 3.10
1240 1310 2.745281 ACACACTCGCTTACTCTCTCTC 59.255 50.000 0.00 0.00 0.00 3.20
1241 1311 3.006940 CACACTCGCTTACTCTCTCTCT 58.993 50.000 0.00 0.00 0.00 3.10
1242 1312 3.063452 CACACTCGCTTACTCTCTCTCTC 59.937 52.174 0.00 0.00 0.00 3.20
1256 1326 2.727684 CTCTCTCGTCGTCGTCGCA 61.728 63.158 7.01 0.00 38.33 5.10
1258 1328 3.012936 CTCTCGTCGTCGTCGCAGT 62.013 63.158 7.01 0.00 38.33 4.40
1285 1359 0.889306 GAGTCAGTCCGTAGCTGGTT 59.111 55.000 0.00 0.00 34.89 3.67
1287 1361 1.817447 AGTCAGTCCGTAGCTGGTTAC 59.183 52.381 0.00 0.00 34.89 2.50
1288 1362 0.806868 TCAGTCCGTAGCTGGTTACG 59.193 55.000 9.42 9.42 44.46 3.18
1356 1433 1.963338 GTCTGCTCGCTTGCTTGGT 60.963 57.895 0.00 0.00 0.00 3.67
1921 2004 2.126071 CATGGCAGCAGCACAAGC 60.126 61.111 2.65 0.00 44.61 4.01
1922 2005 2.599281 ATGGCAGCAGCACAAGCA 60.599 55.556 2.65 0.00 45.49 3.91
1926 2009 2.554775 CAGCAGCACAAGCACGAG 59.445 61.111 0.00 0.00 45.49 4.18
1927 2010 3.352222 AGCAGCACAAGCACGAGC 61.352 61.111 0.00 0.00 45.49 5.03
1944 2027 0.110056 AGCGCGCAACAAAAGAGATG 60.110 50.000 35.10 0.00 0.00 2.90
1991 2074 8.611654 TTCTGGTGTTTCAGGTTAATTACTAC 57.388 34.615 0.00 0.00 35.58 2.73
1992 2075 7.737869 TCTGGTGTTTCAGGTTAATTACTACA 58.262 34.615 0.00 0.00 35.58 2.74
1993 2076 7.876068 TCTGGTGTTTCAGGTTAATTACTACAG 59.124 37.037 0.00 0.00 35.58 2.74
1994 2077 7.511268 TGGTGTTTCAGGTTAATTACTACAGT 58.489 34.615 0.00 0.00 0.00 3.55
1995 2078 8.649591 TGGTGTTTCAGGTTAATTACTACAGTA 58.350 33.333 0.00 0.00 0.00 2.74
1996 2079 8.929746 GGTGTTTCAGGTTAATTACTACAGTAC 58.070 37.037 0.00 0.00 0.00 2.73
1997 2080 9.480053 GTGTTTCAGGTTAATTACTACAGTACA 57.520 33.333 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.660560 GGGCGGTAGTCTAGCAACGA 61.661 60.000 9.63 0.00 0.00 3.85
16 17 2.336400 GATTTGAATCACGGGCGGGC 62.336 60.000 0.00 0.00 35.49 6.13
17 18 1.727467 GATTTGAATCACGGGCGGG 59.273 57.895 0.00 0.00 35.49 6.13
68 72 9.915629 GAATGTAGTAGATGGTAGTATTCAAGG 57.084 37.037 0.00 0.00 0.00 3.61
84 91 2.270923 TGCAAGCGCAGAATGTAGTAG 58.729 47.619 11.47 0.00 45.36 2.57
85 92 2.378445 TGCAAGCGCAGAATGTAGTA 57.622 45.000 11.47 0.00 45.36 1.82
86 93 3.231734 TGCAAGCGCAGAATGTAGT 57.768 47.368 11.47 0.00 45.36 2.73
219 226 3.132646 TGAAAAATCATGCATGCTACCCC 59.867 43.478 22.25 9.86 0.00 4.95
230 237 4.143556 CGCGGTGAAAAGTGAAAAATCATG 60.144 41.667 0.00 0.00 0.00 3.07
231 238 3.980775 CGCGGTGAAAAGTGAAAAATCAT 59.019 39.130 0.00 0.00 0.00 2.45
232 239 3.367607 CGCGGTGAAAAGTGAAAAATCA 58.632 40.909 0.00 0.00 0.00 2.57
233 240 2.153057 GCGCGGTGAAAAGTGAAAAATC 59.847 45.455 8.83 0.00 0.00 2.17
234 241 2.124122 GCGCGGTGAAAAGTGAAAAAT 58.876 42.857 8.83 0.00 0.00 1.82
235 242 1.551145 GCGCGGTGAAAAGTGAAAAA 58.449 45.000 8.83 0.00 0.00 1.94
278 285 4.767255 CTCTCTGCCACGGCCCAC 62.767 72.222 5.42 0.00 41.09 4.61
280 287 4.154347 CTCTCTCTGCCACGGCCC 62.154 72.222 5.42 0.00 41.09 5.80
281 288 3.071206 TCTCTCTCTGCCACGGCC 61.071 66.667 5.42 0.00 41.09 6.13
282 289 2.003658 CTCTCTCTCTCTGCCACGGC 62.004 65.000 0.00 0.00 42.35 5.68
319 326 1.610102 CCAGACTCTCCAACTTGCCAG 60.610 57.143 0.00 0.00 0.00 4.85
320 327 0.397941 CCAGACTCTCCAACTTGCCA 59.602 55.000 0.00 0.00 0.00 4.92
321 328 0.687354 TCCAGACTCTCCAACTTGCC 59.313 55.000 0.00 0.00 0.00 4.52
323 330 2.760374 GTGTCCAGACTCTCCAACTTG 58.240 52.381 0.00 0.00 0.00 3.16
324 331 1.341531 CGTGTCCAGACTCTCCAACTT 59.658 52.381 0.00 0.00 0.00 2.66
325 332 0.962489 CGTGTCCAGACTCTCCAACT 59.038 55.000 0.00 0.00 0.00 3.16
327 334 0.959553 GTCGTGTCCAGACTCTCCAA 59.040 55.000 0.00 0.00 35.84 3.53
328 335 1.235281 CGTCGTGTCCAGACTCTCCA 61.235 60.000 0.00 0.00 36.53 3.86
329 336 1.502640 CGTCGTGTCCAGACTCTCC 59.497 63.158 0.00 0.00 36.53 3.71
331 338 2.627737 GCCGTCGTGTCCAGACTCT 61.628 63.158 0.00 0.00 36.53 3.24
332 339 2.126424 GCCGTCGTGTCCAGACTC 60.126 66.667 0.00 0.00 36.53 3.36
333 340 3.681835 GGCCGTCGTGTCCAGACT 61.682 66.667 0.00 0.00 36.53 3.24
336 343 4.436998 GGAGGCCGTCGTGTCCAG 62.437 72.222 0.00 0.00 0.00 3.86
338 345 4.131088 GAGGAGGCCGTCGTGTCC 62.131 72.222 0.00 0.00 0.00 4.02
345 352 2.829458 GCGTCTAGAGGAGGCCGT 60.829 66.667 16.47 0.00 46.45 5.68
363 372 1.300931 CGTGTGGTGACTGGTGGAG 60.301 63.158 0.00 0.00 0.00 3.86
367 376 3.556306 CCCCGTGTGGTGACTGGT 61.556 66.667 0.00 0.00 0.00 4.00
417 428 1.282875 GCGTTCACTTCACTTGGCC 59.717 57.895 0.00 0.00 0.00 5.36
446 457 4.580551 ATGCCCGCCGTACTACGC 62.581 66.667 2.87 0.00 40.91 4.42
470 481 1.739562 CTCACTTGGCCTCACTCGC 60.740 63.158 3.32 0.00 0.00 5.03
471 482 1.079543 CCTCACTTGGCCTCACTCG 60.080 63.158 3.32 0.00 0.00 4.18
472 483 0.036858 GACCTCACTTGGCCTCACTC 60.037 60.000 3.32 0.00 0.00 3.51
473 484 0.764369 TGACCTCACTTGGCCTCACT 60.764 55.000 3.32 0.00 0.00 3.41
515 526 1.739049 GAGTGGATCCGAGGCTGAG 59.261 63.158 7.39 0.00 0.00 3.35
607 649 3.341043 CCCCGATCGATTGCAGCG 61.341 66.667 18.66 1.73 0.00 5.18
608 650 2.974698 CCCCCGATCGATTGCAGC 60.975 66.667 18.66 0.00 0.00 5.25
609 651 1.595382 GACCCCCGATCGATTGCAG 60.595 63.158 18.66 0.00 0.00 4.41
610 652 2.504032 GACCCCCGATCGATTGCA 59.496 61.111 18.66 0.00 0.00 4.08
611 653 2.661866 CGACCCCCGATCGATTGC 60.662 66.667 18.66 0.76 42.25 3.56
612 654 3.125607 TCGACCCCCGATCGATTG 58.874 61.111 18.66 5.59 43.38 2.67
624 666 0.465642 GGTGGGAATGGGAATCGACC 60.466 60.000 0.00 0.00 0.00 4.79
625 667 0.465642 GGGTGGGAATGGGAATCGAC 60.466 60.000 0.00 0.00 0.00 4.20
626 668 0.623324 AGGGTGGGAATGGGAATCGA 60.623 55.000 0.00 0.00 0.00 3.59
627 669 0.179018 GAGGGTGGGAATGGGAATCG 60.179 60.000 0.00 0.00 0.00 3.34
750 794 0.415429 AGGGCAGGAGGAAGAAGAGA 59.585 55.000 0.00 0.00 0.00 3.10
797 852 3.118920 TCTCTCTAGACGGACTCTGTCTG 60.119 52.174 25.23 16.66 45.83 3.51
799 854 3.131577 TCTCTCTCTAGACGGACTCTGTC 59.868 52.174 9.72 9.72 36.60 3.51
800 855 3.101437 TCTCTCTCTAGACGGACTCTGT 58.899 50.000 0.00 0.00 0.00 3.41
836 891 3.551863 CGCTCTCTCTCTCTCTCTCTCTC 60.552 56.522 0.00 0.00 0.00 3.20
837 892 2.363680 CGCTCTCTCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
838 893 2.362397 TCGCTCTCTCTCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
839 894 2.363680 CTCGCTCTCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
840 895 2.546795 CCTCGCTCTCTCTCTCTCTCTC 60.547 59.091 0.00 0.00 0.00 3.20
841 896 1.414181 CCTCGCTCTCTCTCTCTCTCT 59.586 57.143 0.00 0.00 0.00 3.10
842 897 1.412710 TCCTCGCTCTCTCTCTCTCTC 59.587 57.143 0.00 0.00 0.00 3.20
843 898 1.496060 TCCTCGCTCTCTCTCTCTCT 58.504 55.000 0.00 0.00 0.00 3.10
844 899 2.213499 CTTCCTCGCTCTCTCTCTCTC 58.787 57.143 0.00 0.00 0.00 3.20
845 900 1.134098 CCTTCCTCGCTCTCTCTCTCT 60.134 57.143 0.00 0.00 0.00 3.10
846 901 1.308998 CCTTCCTCGCTCTCTCTCTC 58.691 60.000 0.00 0.00 0.00 3.20
847 902 0.106719 CCCTTCCTCGCTCTCTCTCT 60.107 60.000 0.00 0.00 0.00 3.10
848 903 0.106918 TCCCTTCCTCGCTCTCTCTC 60.107 60.000 0.00 0.00 0.00 3.20
849 904 0.333312 TTCCCTTCCTCGCTCTCTCT 59.667 55.000 0.00 0.00 0.00 3.10
850 905 0.744281 CTTCCCTTCCTCGCTCTCTC 59.256 60.000 0.00 0.00 0.00 3.20
851 906 1.326951 GCTTCCCTTCCTCGCTCTCT 61.327 60.000 0.00 0.00 0.00 3.10
852 907 1.142965 GCTTCCCTTCCTCGCTCTC 59.857 63.158 0.00 0.00 0.00 3.20
853 908 1.610673 TGCTTCCCTTCCTCGCTCT 60.611 57.895 0.00 0.00 0.00 4.09
854 909 1.153469 CTGCTTCCCTTCCTCGCTC 60.153 63.158 0.00 0.00 0.00 5.03
857 912 2.124942 GCCTGCTTCCCTTCCTCG 60.125 66.667 0.00 0.00 0.00 4.63
863 918 3.076092 CTCACTGCCTGCTTCCCT 58.924 61.111 0.00 0.00 0.00 4.20
865 920 2.039405 CAGCTCACTGCCTGCTTCC 61.039 63.158 0.00 0.00 44.23 3.46
872 927 1.217779 GACCTCTCAGCTCACTGCC 59.782 63.158 0.00 0.00 44.10 4.85
878 933 4.200283 CGGCCGACCTCTCAGCTC 62.200 72.222 24.07 0.00 0.00 4.09
881 936 3.827898 GGACGGCCGACCTCTCAG 61.828 72.222 34.71 2.97 0.00 3.35
882 937 4.671590 TGGACGGCCGACCTCTCA 62.672 66.667 39.01 21.96 36.79 3.27
893 959 1.743995 GAAATGGACGGGTGGACGG 60.744 63.158 0.00 0.00 38.39 4.79
895 961 1.378119 GGGAAATGGACGGGTGGAC 60.378 63.158 0.00 0.00 0.00 4.02
896 962 2.961893 CGGGAAATGGACGGGTGGA 61.962 63.158 0.00 0.00 0.00 4.02
897 963 2.437716 CGGGAAATGGACGGGTGG 60.438 66.667 0.00 0.00 0.00 4.61
903 969 4.419921 ACCGGCCGGGAAATGGAC 62.420 66.667 44.99 0.00 39.97 4.02
904 970 4.418328 CACCGGCCGGGAAATGGA 62.418 66.667 44.99 0.00 39.97 3.41
906 972 4.418328 TCCACCGGCCGGGAAATG 62.418 66.667 44.99 33.15 39.97 2.32
907 973 4.109675 CTCCACCGGCCGGGAAAT 62.110 66.667 44.99 24.60 39.97 2.17
916 982 2.685380 AAGAGGGAGCTCCACCGG 60.685 66.667 33.29 0.00 38.24 5.28
918 984 0.539518 GAAGAAGAGGGAGCTCCACC 59.460 60.000 33.29 22.94 38.24 4.61
919 985 0.539518 GGAAGAAGAGGGAGCTCCAC 59.460 60.000 33.29 24.81 38.24 4.02
920 986 0.618968 GGGAAGAAGAGGGAGCTCCA 60.619 60.000 33.29 0.00 38.24 3.86
922 988 1.681486 CCGGGAAGAAGAGGGAGCTC 61.681 65.000 4.71 4.71 0.00 4.09
923 989 1.687493 CCGGGAAGAAGAGGGAGCT 60.687 63.158 0.00 0.00 0.00 4.09
925 991 1.045911 CCTCCGGGAAGAAGAGGGAG 61.046 65.000 0.00 0.00 42.98 4.30
927 993 2.736826 GCCTCCGGGAAGAAGAGGG 61.737 68.421 0.00 0.00 46.14 4.30
935 1004 3.179339 TTGGGTTGCCTCCGGGAA 61.179 61.111 0.00 0.00 33.58 3.97
1032 1102 3.694566 GTGTGGAGTTGATCATAAACCCC 59.305 47.826 0.00 0.00 0.00 4.95
1168 1238 0.030603 AGGGCTAAAGGAGGAGGAGG 60.031 60.000 0.00 0.00 0.00 4.30
1169 1239 1.419381 GAGGGCTAAAGGAGGAGGAG 58.581 60.000 0.00 0.00 0.00 3.69
1170 1240 0.031010 GGAGGGCTAAAGGAGGAGGA 60.031 60.000 0.00 0.00 0.00 3.71
1239 1309 2.727684 CTGCGACGACGACGAGAGA 61.728 63.158 22.94 2.95 42.66 3.10
1240 1310 2.276120 CTGCGACGACGACGAGAG 60.276 66.667 22.94 13.15 42.66 3.20
1241 1311 3.008240 GACTGCGACGACGACGAGA 62.008 63.158 22.94 7.68 42.66 4.04
1242 1312 2.571096 GACTGCGACGACGACGAG 60.571 66.667 22.94 17.51 42.66 4.18
1256 1326 2.835764 ACGGACTGACTCTAGAGAGACT 59.164 50.000 26.57 3.24 44.74 3.24
1258 1328 3.181473 GCTACGGACTGACTCTAGAGAGA 60.181 52.174 26.57 10.61 44.74 3.10
1292 1366 4.431809 TGTTGTTGCAAGAACCAAAGATG 58.568 39.130 29.99 0.00 31.74 2.90
1339 1415 1.962822 CACCAAGCAAGCGAGCAGA 60.963 57.895 6.21 0.00 36.85 4.26
1356 1433 2.606213 TGGAGGACGCCATCACCA 60.606 61.111 0.00 0.00 34.37 4.17
1921 2004 2.349376 CTTTTGTTGCGCGCTCGTG 61.349 57.895 33.29 11.70 38.14 4.35
1922 2005 2.052237 CTTTTGTTGCGCGCTCGT 60.052 55.556 33.29 0.00 38.14 4.18
1926 2009 0.110238 TCATCTCTTTTGTTGCGCGC 60.110 50.000 27.26 27.26 0.00 6.86
1927 2010 2.434761 GATCATCTCTTTTGTTGCGCG 58.565 47.619 0.00 0.00 0.00 6.86
2005 2088 0.250770 AAAAACTCCACGGCTCTCCC 60.251 55.000 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.