Multiple sequence alignment - TraesCS2A01G578000

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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 TraesCS2A01G578000 chr2A 100.000 3097 0 0 1 3097 771608449 771611545 0.000000e+00 5720
1 TraesCS2A01G578000 chr2A 99.749 796 2 0 1 796 24046171 24046966 0.000000e+00 1459
2 TraesCS2A01G578000 chr2A 82.475 1010 102 24 842 1821 771712712 771713676 0.000000e+00 815
3 TraesCS2A01G578000 chr2A 80.683 849 106 32 1069 1877 771547102 771547932 9.500000e-170 606
4 TraesCS2A01G578000 chr2D 93.211 1694 61 20 842 2510 645893176 645894840 0.000000e+00 2442
5 TraesCS2A01G578000 chr2D 83.152 1009 111 23 842 1821 645947647 645948625 0.000000e+00 867
6 TraesCS2A01G578000 chr2D 85.333 300 42 2 1545 1843 645853143 645853441 3.000000e-80 309
7 TraesCS2A01G578000 chr2D 87.379 103 12 1 842 944 645931981 645932082 1.950000e-22 117
8 TraesCS2A01G578000 chr6A 100.000 799 0 0 1 799 77146007 77145209 0.000000e+00 1476
9 TraesCS2A01G578000 chr6B 99.874 796 1 0 1 796 41207165 41206370 0.000000e+00 1465
10 TraesCS2A01G578000 chr5B 99.874 796 1 0 1 796 469108879 469108084 0.000000e+00 1465
11 TraesCS2A01G578000 chr5B 99.749 796 2 0 1 796 699567812 699567017 0.000000e+00 1459
12 TraesCS2A01G578000 chr5B 99.500 800 4 0 1 800 587777213 587778012 0.000000e+00 1456
13 TraesCS2A01G578000 chr5B 100.000 537 0 0 2561 3097 63274801 63275337 0.000000e+00 992
14 TraesCS2A01G578000 chr5B 100.000 522 0 0 2576 3097 362948304 362948825 0.000000e+00 965
15 TraesCS2A01G578000 chr2B 99.749 797 2 0 1 797 712055246 712054450 0.000000e+00 1461
16 TraesCS2A01G578000 chr2B 99.829 584 1 0 2514 3097 199159680 199160263 0.000000e+00 1074
17 TraesCS2A01G578000 chr2B 90.909 792 51 6 1100 1878 789670346 789669563 0.000000e+00 1044
18 TraesCS2A01G578000 chr2B 100.000 503 0 0 2595 3097 528837741 528837239 0.000000e+00 929
19 TraesCS2A01G578000 chr2B 96.364 495 18 0 2603 3097 727722929 727723423 0.000000e+00 815
20 TraesCS2A01G578000 chr2B 83.439 791 91 17 1061 1821 789602116 789601336 0.000000e+00 699
21 TraesCS2A01G578000 chr2B 89.326 534 20 16 1873 2397 789669454 789668949 1.210000e-178 636
22 TraesCS2A01G578000 chr2B 87.029 239 31 0 1092 1330 789609676 789609438 1.420000e-68 270
23 TraesCS2A01G578000 chr2B 84.831 178 12 9 842 1018 789602279 789602116 6.870000e-37 165
24 TraesCS2A01G578000 chr7A 99.624 798 3 0 1 798 682217437 682218234 0.000000e+00 1458
25 TraesCS2A01G578000 chr5A 99.624 798 3 0 1 798 670590589 670589792 0.000000e+00 1458
26 TraesCS2A01G578000 chr7B 99.798 495 1 0 2603 3097 748190683 748190189 0.000000e+00 909
27 TraesCS2A01G578000 chrUn 99.394 495 3 0 2603 3097 2009608 2009114 0.000000e+00 898
28 TraesCS2A01G578000 chr7D 96.364 495 18 0 2603 3097 166480345 166479851 0.000000e+00 815
29 TraesCS2A01G578000 chr1D 95.758 495 14 2 2603 3097 474291675 474292162 0.000000e+00 791


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 TraesCS2A01G578000 chr2A 771608449 771611545 3096 False 5720 5720 100.0000 1 3097 1 chr2A.!!$F3 3096
1 TraesCS2A01G578000 chr2A 24046171 24046966 795 False 1459 1459 99.7490 1 796 1 chr2A.!!$F1 795
2 TraesCS2A01G578000 chr2A 771712712 771713676 964 False 815 815 82.4750 842 1821 1 chr2A.!!$F4 979
3 TraesCS2A01G578000 chr2A 771547102 771547932 830 False 606 606 80.6830 1069 1877 1 chr2A.!!$F2 808
4 TraesCS2A01G578000 chr2D 645893176 645894840 1664 False 2442 2442 93.2110 842 2510 1 chr2D.!!$F2 1668
5 TraesCS2A01G578000 chr2D 645947647 645948625 978 False 867 867 83.1520 842 1821 1 chr2D.!!$F4 979
6 TraesCS2A01G578000 chr6A 77145209 77146007 798 True 1476 1476 100.0000 1 799 1 chr6A.!!$R1 798
7 TraesCS2A01G578000 chr6B 41206370 41207165 795 True 1465 1465 99.8740 1 796 1 chr6B.!!$R1 795
8 TraesCS2A01G578000 chr5B 469108084 469108879 795 True 1465 1465 99.8740 1 796 1 chr5B.!!$R1 795
9 TraesCS2A01G578000 chr5B 699567017 699567812 795 True 1459 1459 99.7490 1 796 1 chr5B.!!$R2 795
10 TraesCS2A01G578000 chr5B 587777213 587778012 799 False 1456 1456 99.5000 1 800 1 chr5B.!!$F3 799
11 TraesCS2A01G578000 chr5B 63274801 63275337 536 False 992 992 100.0000 2561 3097 1 chr5B.!!$F1 536
12 TraesCS2A01G578000 chr5B 362948304 362948825 521 False 965 965 100.0000 2576 3097 1 chr5B.!!$F2 521
13 TraesCS2A01G578000 chr2B 712054450 712055246 796 True 1461 1461 99.7490 1 797 1 chr2B.!!$R2 796
14 TraesCS2A01G578000 chr2B 199159680 199160263 583 False 1074 1074 99.8290 2514 3097 1 chr2B.!!$F1 583
15 TraesCS2A01G578000 chr2B 528837239 528837741 502 True 929 929 100.0000 2595 3097 1 chr2B.!!$R1 502
16 TraesCS2A01G578000 chr2B 789668949 789670346 1397 True 840 1044 90.1175 1100 2397 2 chr2B.!!$R5 1297
17 TraesCS2A01G578000 chr2B 789601336 789602279 943 True 432 699 84.1350 842 1821 2 chr2B.!!$R4 979
18 TraesCS2A01G578000 chr7A 682217437 682218234 797 False 1458 1458 99.6240 1 798 1 chr7A.!!$F1 797
19 TraesCS2A01G578000 chr5A 670589792 670590589 797 True 1458 1458 99.6240 1 798 1 chr5A.!!$R1 797

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
833 834 0.033642 TAACCGGTGCGTGTCAATGA 59.966 50.0 8.52 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2319 2518 0.469917 CCGTGGGGTGCTAGATTCAT 59.53 55.0 0.0 0.0 0.0 2.57 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
800 801 4.714632 CCTCTTTTTCTACCAGTGTTCCA 58.285 43.478 0.00 0.00 0.00 3.53
801 802 5.130350 CCTCTTTTTCTACCAGTGTTCCAA 58.870 41.667 0.00 0.00 0.00 3.53
802 803 5.239525 CCTCTTTTTCTACCAGTGTTCCAAG 59.760 44.000 0.00 0.00 0.00 3.61
803 804 5.751586 TCTTTTTCTACCAGTGTTCCAAGT 58.248 37.500 0.00 0.00 0.00 3.16
804 805 5.588648 TCTTTTTCTACCAGTGTTCCAAGTG 59.411 40.000 0.00 0.00 0.00 3.16
805 806 4.764050 TTTCTACCAGTGTTCCAAGTGA 57.236 40.909 0.00 0.00 0.00 3.41
806 807 4.764050 TTCTACCAGTGTTCCAAGTGAA 57.236 40.909 0.00 0.00 0.00 3.18
819 820 6.548441 TTCCAAGTGAACAAGTATTAACCG 57.452 37.500 0.00 0.00 0.00 4.44
820 821 4.998672 TCCAAGTGAACAAGTATTAACCGG 59.001 41.667 0.00 0.00 0.00 5.28
821 822 4.758165 CCAAGTGAACAAGTATTAACCGGT 59.242 41.667 0.00 0.00 0.00 5.28
822 823 5.334569 CCAAGTGAACAAGTATTAACCGGTG 60.335 44.000 8.52 0.00 0.00 4.94
823 824 3.749609 AGTGAACAAGTATTAACCGGTGC 59.250 43.478 8.52 0.00 0.00 5.01
824 825 2.737783 TGAACAAGTATTAACCGGTGCG 59.262 45.455 8.52 0.00 0.00 5.34
825 826 2.460757 ACAAGTATTAACCGGTGCGT 57.539 45.000 8.52 0.00 0.00 5.24
826 827 2.070783 ACAAGTATTAACCGGTGCGTG 58.929 47.619 8.52 7.73 0.00 5.34
827 828 2.070783 CAAGTATTAACCGGTGCGTGT 58.929 47.619 8.52 0.00 0.00 4.49
828 829 2.000429 AGTATTAACCGGTGCGTGTC 58.000 50.000 8.52 0.00 0.00 3.67
829 830 1.273048 AGTATTAACCGGTGCGTGTCA 59.727 47.619 8.52 0.00 0.00 3.58
830 831 2.067766 GTATTAACCGGTGCGTGTCAA 58.932 47.619 8.52 0.00 0.00 3.18
831 832 1.816074 ATTAACCGGTGCGTGTCAAT 58.184 45.000 8.52 0.00 0.00 2.57
832 833 0.869068 TTAACCGGTGCGTGTCAATG 59.131 50.000 8.52 0.00 0.00 2.82
833 834 0.033642 TAACCGGTGCGTGTCAATGA 59.966 50.000 8.52 0.00 0.00 2.57
834 835 0.816018 AACCGGTGCGTGTCAATGAA 60.816 50.000 8.52 0.00 0.00 2.57
835 836 0.605319 ACCGGTGCGTGTCAATGAAT 60.605 50.000 6.12 0.00 0.00 2.57
836 837 1.338294 ACCGGTGCGTGTCAATGAATA 60.338 47.619 6.12 0.00 0.00 1.75
837 838 1.939934 CCGGTGCGTGTCAATGAATAT 59.060 47.619 0.00 0.00 0.00 1.28
838 839 2.354510 CCGGTGCGTGTCAATGAATATT 59.645 45.455 0.00 0.00 0.00 1.28
839 840 3.558006 CCGGTGCGTGTCAATGAATATTA 59.442 43.478 0.00 0.00 0.00 0.98
840 841 4.034626 CCGGTGCGTGTCAATGAATATTAA 59.965 41.667 0.00 0.00 0.00 1.40
951 957 0.890996 CAGTGGAGCTGGTTGGTTCC 60.891 60.000 0.00 0.00 41.42 3.62
975 981 7.742213 TCCCCTATATATAAATCCCAGTTGTGT 59.258 37.037 0.00 0.00 0.00 3.72
976 982 7.829211 CCCCTATATATAAATCCCAGTTGTGTG 59.171 40.741 0.00 0.00 0.00 3.82
977 983 7.336931 CCCTATATATAAATCCCAGTTGTGTGC 59.663 40.741 0.00 0.00 0.00 4.57
978 984 7.882791 CCTATATATAAATCCCAGTTGTGTGCA 59.117 37.037 0.00 0.00 0.00 4.57
979 985 9.283768 CTATATATAAATCCCAGTTGTGTGCAA 57.716 33.333 0.00 0.00 0.00 4.08
994 1000 4.513519 CAATGCATGCTGCCTTGG 57.486 55.556 20.33 0.00 42.62 3.61
1040 1046 2.892852 TGCAATTCTTCCCACCTTGAAG 59.107 45.455 0.00 0.00 40.45 3.02
1041 1047 3.157087 GCAATTCTTCCCACCTTGAAGA 58.843 45.455 0.00 0.00 44.79 2.87
1042 1048 3.192212 GCAATTCTTCCCACCTTGAAGAG 59.808 47.826 0.00 0.00 46.38 2.85
1043 1049 4.655963 CAATTCTTCCCACCTTGAAGAGA 58.344 43.478 0.00 0.00 46.38 3.10
1044 1050 4.566426 ATTCTTCCCACCTTGAAGAGAG 57.434 45.455 0.00 0.00 46.38 3.20
1045 1051 2.260822 TCTTCCCACCTTGAAGAGAGG 58.739 52.381 0.00 0.00 42.38 3.69
1046 1052 2.158158 TCTTCCCACCTTGAAGAGAGGA 60.158 50.000 0.00 0.00 42.38 3.71
1047 1053 1.645710 TCCCACCTTGAAGAGAGGAC 58.354 55.000 0.00 0.00 37.72 3.85
1048 1054 1.132849 TCCCACCTTGAAGAGAGGACA 60.133 52.381 0.00 0.00 37.72 4.02
1049 1055 1.277557 CCCACCTTGAAGAGAGGACAG 59.722 57.143 0.00 0.00 37.72 3.51
1083 1095 1.377202 GGAGAAAGCCATGGACGCA 60.377 57.895 18.40 0.00 0.00 5.24
1110 1122 4.363990 AGCGAGGTGACCTGCGTG 62.364 66.667 9.89 0.00 34.52 5.34
1439 1472 5.116882 ACTGTCACTTTTCTGTTGGAGTAC 58.883 41.667 0.00 0.00 0.00 2.73
1464 1505 3.628053 TGTTTCGTCGATGCGTTAATC 57.372 42.857 0.00 0.00 0.00 1.75
1469 1510 6.859508 TGTTTCGTCGATGCGTTAATCTATAT 59.140 34.615 0.00 0.00 0.00 0.86
1473 1514 9.859692 TTCGTCGATGCGTTAATCTATATATAG 57.140 33.333 12.84 12.84 0.00 1.31
1474 1515 8.493547 TCGTCGATGCGTTAATCTATATATAGG 58.506 37.037 17.81 4.02 0.00 2.57
1475 1516 8.281194 CGTCGATGCGTTAATCTATATATAGGT 58.719 37.037 17.81 9.63 0.00 3.08
1476 1517 9.383462 GTCGATGCGTTAATCTATATATAGGTG 57.617 37.037 17.81 2.49 0.00 4.00
1618 1695 0.164002 GCTTCTTTTCTGGCGACGAC 59.836 55.000 0.00 0.00 0.00 4.34
1854 1931 0.930742 CAGTAGCTAGCTGTACGCGC 60.931 60.000 27.68 0.00 45.59 6.86
1890 2081 4.082190 AGTGTGCTATCGTTGTCATACAGT 60.082 41.667 0.00 0.00 0.00 3.55
1925 2116 2.156446 GCGATGCATGCACTTGTGC 61.156 57.895 25.37 17.97 41.61 4.57
1926 2117 1.866059 CGATGCATGCACTTGTGCG 60.866 57.895 25.37 15.38 44.11 5.34
1987 2181 7.544566 AGACACCGGCATATATACTTATTTTCG 59.455 37.037 0.00 0.00 0.00 3.46
2042 2236 6.238648 GCTATGAGAGTGACTCTTTCCTACTC 60.239 46.154 17.31 1.96 41.35 2.59
2061 2255 1.115467 CGTAGAGAGGGTTGAGGCAT 58.885 55.000 0.00 0.00 0.00 4.40
2105 2299 7.390823 TGCTGTTTAATCTTGTAGTGGATGTA 58.609 34.615 0.00 0.00 0.00 2.29
2272 2471 0.036022 GTCCTCACCTGCTTTGAGCT 59.964 55.000 1.29 0.00 42.97 4.09
2319 2518 4.206375 TGACAAAAGTGAGCTCATTCCAA 58.794 39.130 21.47 0.00 0.00 3.53
2342 2541 1.623542 ATCTAGCACCCCACGGAACC 61.624 60.000 0.00 0.00 0.00 3.62
2426 2628 4.621068 TGCTCTTCACTTTGACAAGTTG 57.379 40.909 0.00 0.00 40.66 3.16
2510 2712 3.725490 GGGGGAAAGTGCTTACGTATAG 58.275 50.000 0.00 0.00 0.00 1.31
2511 2713 3.385755 GGGGGAAAGTGCTTACGTATAGA 59.614 47.826 0.00 0.00 0.00 1.98
2512 2714 4.141869 GGGGGAAAGTGCTTACGTATAGAA 60.142 45.833 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
800 801 4.214758 GCACCGGTTAATACTTGTTCACTT 59.785 41.667 2.97 0.0 0.00 3.16
801 802 3.749609 GCACCGGTTAATACTTGTTCACT 59.250 43.478 2.97 0.0 0.00 3.41
802 803 3.423907 CGCACCGGTTAATACTTGTTCAC 60.424 47.826 2.97 0.0 0.00 3.18
803 804 2.737783 CGCACCGGTTAATACTTGTTCA 59.262 45.455 2.97 0.0 0.00 3.18
804 805 2.738314 ACGCACCGGTTAATACTTGTTC 59.262 45.455 2.97 0.0 0.00 3.18
805 806 2.481185 CACGCACCGGTTAATACTTGTT 59.519 45.455 2.97 0.0 0.00 2.83
806 807 2.070783 CACGCACCGGTTAATACTTGT 58.929 47.619 2.97 0.0 0.00 3.16
807 808 2.070783 ACACGCACCGGTTAATACTTG 58.929 47.619 2.97 0.0 0.00 3.16
808 809 2.288948 TGACACGCACCGGTTAATACTT 60.289 45.455 2.97 0.0 0.00 2.24
809 810 1.273048 TGACACGCACCGGTTAATACT 59.727 47.619 2.97 0.0 0.00 2.12
810 811 1.712401 TGACACGCACCGGTTAATAC 58.288 50.000 2.97 0.0 0.00 1.89
811 812 2.452295 TTGACACGCACCGGTTAATA 57.548 45.000 2.97 0.0 0.00 0.98
812 813 1.466950 CATTGACACGCACCGGTTAAT 59.533 47.619 2.97 0.0 0.00 1.40
813 814 0.869068 CATTGACACGCACCGGTTAA 59.131 50.000 2.97 0.0 0.00 2.01
814 815 0.033642 TCATTGACACGCACCGGTTA 59.966 50.000 2.97 0.0 0.00 2.85
815 816 0.816018 TTCATTGACACGCACCGGTT 60.816 50.000 2.97 0.0 0.00 4.44
816 817 0.605319 ATTCATTGACACGCACCGGT 60.605 50.000 0.00 0.0 0.00 5.28
817 818 1.364721 TATTCATTGACACGCACCGG 58.635 50.000 0.00 0.0 0.00 5.28
818 819 3.673746 AATATTCATTGACACGCACCG 57.326 42.857 0.00 0.0 0.00 4.94
819 820 6.119144 ACTTAATATTCATTGACACGCACC 57.881 37.500 0.00 0.0 0.00 5.01
820 821 7.123830 GGTACTTAATATTCATTGACACGCAC 58.876 38.462 0.00 0.0 0.00 5.34
821 822 6.259167 GGGTACTTAATATTCATTGACACGCA 59.741 38.462 0.00 0.0 0.00 5.24
822 823 6.482308 AGGGTACTTAATATTCATTGACACGC 59.518 38.462 0.00 0.0 0.00 5.34
823 824 8.433421 AAGGGTACTTAATATTCATTGACACG 57.567 34.615 0.00 0.0 34.49 4.49
824 825 8.837389 GGAAGGGTACTTAATATTCATTGACAC 58.163 37.037 0.00 0.0 36.97 3.67
825 826 7.996644 GGGAAGGGTACTTAATATTCATTGACA 59.003 37.037 0.00 0.0 36.97 3.58
826 827 8.218488 AGGGAAGGGTACTTAATATTCATTGAC 58.782 37.037 0.00 0.0 36.97 3.18
827 828 8.217799 CAGGGAAGGGTACTTAATATTCATTGA 58.782 37.037 0.00 0.0 36.97 2.57
828 829 8.217799 TCAGGGAAGGGTACTTAATATTCATTG 58.782 37.037 0.00 0.0 36.97 2.82
829 830 8.344939 TCAGGGAAGGGTACTTAATATTCATT 57.655 34.615 0.00 0.0 36.97 2.57
830 831 7.947782 TCAGGGAAGGGTACTTAATATTCAT 57.052 36.000 0.00 0.0 36.97 2.57
831 832 7.256190 CGATCAGGGAAGGGTACTTAATATTCA 60.256 40.741 0.00 0.0 36.97 2.57
832 833 7.039223 TCGATCAGGGAAGGGTACTTAATATTC 60.039 40.741 0.00 0.0 36.97 1.75
833 834 6.785963 TCGATCAGGGAAGGGTACTTAATATT 59.214 38.462 0.00 0.0 36.97 1.28
834 835 6.320518 TCGATCAGGGAAGGGTACTTAATAT 58.679 40.000 0.00 0.0 36.97 1.28
835 836 5.708544 TCGATCAGGGAAGGGTACTTAATA 58.291 41.667 0.00 0.0 36.97 0.98
836 837 4.553678 TCGATCAGGGAAGGGTACTTAAT 58.446 43.478 0.00 0.0 36.97 1.40
837 838 3.985127 TCGATCAGGGAAGGGTACTTAA 58.015 45.455 0.00 0.0 36.97 1.85
838 839 3.675348 TCGATCAGGGAAGGGTACTTA 57.325 47.619 0.00 0.0 36.97 2.24
839 840 2.544844 TCGATCAGGGAAGGGTACTT 57.455 50.000 0.00 0.0 40.34 2.24
840 841 2.320781 CATCGATCAGGGAAGGGTACT 58.679 52.381 0.00 0.0 0.00 2.73
951 957 7.336931 GCACACAACTGGGATTTATATATAGGG 59.663 40.741 0.00 0.0 0.00 3.53
994 1000 0.744771 GGATTGGGTCGAACTCTGGC 60.745 60.000 0.00 0.0 0.00 4.85
1040 1046 1.181786 CTGTCCTGTCCTGTCCTCTC 58.818 60.000 0.00 0.0 0.00 3.20
1041 1047 0.252012 CCTGTCCTGTCCTGTCCTCT 60.252 60.000 0.00 0.0 0.00 3.69
1042 1048 1.261238 CCCTGTCCTGTCCTGTCCTC 61.261 65.000 0.00 0.0 0.00 3.71
1043 1049 1.229336 CCCTGTCCTGTCCTGTCCT 60.229 63.158 0.00 0.0 0.00 3.85
1044 1050 2.960688 GCCCTGTCCTGTCCTGTCC 61.961 68.421 0.00 0.0 0.00 4.02
1045 1051 1.557269 ATGCCCTGTCCTGTCCTGTC 61.557 60.000 0.00 0.0 0.00 3.51
1046 1052 1.539869 ATGCCCTGTCCTGTCCTGT 60.540 57.895 0.00 0.0 0.00 4.00
1047 1053 1.077930 CATGCCCTGTCCTGTCCTG 60.078 63.158 0.00 0.0 0.00 3.86
1048 1054 2.304056 CCATGCCCTGTCCTGTCCT 61.304 63.158 0.00 0.0 0.00 3.85
1049 1055 2.262774 CTCCATGCCCTGTCCTGTCC 62.263 65.000 0.00 0.0 0.00 4.02
1110 1122 1.376037 CTCGTTGGCCCAGAAGTCC 60.376 63.158 0.00 0.0 0.00 3.85
1439 1472 2.570169 ACGCATCGACGAAACAAAATG 58.430 42.857 0.00 0.0 36.70 2.32
1469 1510 7.616528 TTCATTCAGGTCATCATCACCTATA 57.383 36.000 0.00 0.0 42.85 1.31
1473 1514 6.461110 AATTTCATTCAGGTCATCATCACC 57.539 37.500 0.00 0.0 0.00 4.02
1474 1515 7.284034 ACCTAATTTCATTCAGGTCATCATCAC 59.716 37.037 0.00 0.0 36.69 3.06
1475 1516 7.283807 CACCTAATTTCATTCAGGTCATCATCA 59.716 37.037 0.00 0.0 39.40 3.07
1476 1517 7.284034 ACACCTAATTTCATTCAGGTCATCATC 59.716 37.037 0.00 0.0 39.40 2.92
1618 1695 6.496571 AGTAACGATGTCTAAGAATCCGAAG 58.503 40.000 0.00 0.0 0.00 3.79
1854 1931 7.148641 ACGATAGCACACTAGATTAATTCAGG 58.851 38.462 0.00 0.0 42.67 3.86
1925 2116 7.006742 GCCAAAACTTATTCACGTTATGTTACG 59.993 37.037 0.00 0.0 46.52 3.18
1926 2117 7.804129 TGCCAAAACTTATTCACGTTATGTTAC 59.196 33.333 0.00 0.0 0.00 2.50
2010 2204 5.505780 AGAGTCACTCTCATAGCTGTTAGT 58.494 41.667 0.00 0.0 44.98 2.24
2011 2205 6.449635 AAGAGTCACTCTCATAGCTGTTAG 57.550 41.667 8.09 0.0 44.98 2.34
2042 2236 1.115467 ATGCCTCAACCCTCTCTACG 58.885 55.000 0.00 0.0 0.00 3.51
2049 2243 1.566298 GGTCTCCATGCCTCAACCCT 61.566 60.000 0.00 0.0 0.00 4.34
2272 2471 6.525578 AGTTAATCTTCATCACGGACACTA 57.474 37.500 0.00 0.0 0.00 2.74
2319 2518 0.469917 CCGTGGGGTGCTAGATTCAT 59.530 55.000 0.00 0.0 0.00 2.57
2342 2541 5.088739 CCAAAAACATTAGCAAGCTCTACG 58.911 41.667 0.00 0.0 0.00 3.51
2426 2628 5.360649 AAGGCTGTAAATCTTCCCTAGAC 57.639 43.478 0.00 0.0 35.19 2.59
2457 2659 9.373450 TCCAGCTATTCTCTTCAGTATCTTATT 57.627 33.333 0.00 0.0 0.00 1.40
2458 2660 8.948401 TCCAGCTATTCTCTTCAGTATCTTAT 57.052 34.615 0.00 0.0 0.00 1.73
2459 2661 8.801299 CATCCAGCTATTCTCTTCAGTATCTTA 58.199 37.037 0.00 0.0 0.00 2.10
2493 2695 6.744537 TCGACTTTCTATACGTAAGCACTTTC 59.255 38.462 0.00 0.0 45.62 2.62
2497 2699 5.052502 GCTTCGACTTTCTATACGTAAGCAC 60.053 44.000 0.00 0.0 45.62 4.40
2503 2705 3.858238 GCTTGCTTCGACTTTCTATACGT 59.142 43.478 0.00 0.0 0.00 3.57
2505 2707 5.779806 TTGCTTGCTTCGACTTTCTATAC 57.220 39.130 0.00 0.0 0.00 1.47
2510 2712 3.549574 CTCTTTGCTTGCTTCGACTTTC 58.450 45.455 0.00 0.0 0.00 2.62
2511 2713 2.291741 CCTCTTTGCTTGCTTCGACTTT 59.708 45.455 0.00 0.0 0.00 2.66
2512 2714 1.876156 CCTCTTTGCTTGCTTCGACTT 59.124 47.619 0.00 0.0 0.00 3.01


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

AutoCloner maintained by Alex Coulton.