Multiple sequence alignment - TraesCS3D01G248100

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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 TraesCS3D01G248100 chr3D 100.000 4434 0 0 1 4434 346972304 346976737 0.000000e+00 8189.0
1 TraesCS3D01G248100 chr3D 96.966 758 21 2 1 757 19895449 19896205 0.000000e+00 1271.0
2 TraesCS3D01G248100 chr3A 97.191 3489 77 4 946 4434 466106788 466110255 0.000000e+00 5880.0
3 TraesCS3D01G248100 chr3B 97.997 2097 23 4 2351 4434 447004717 447006807 0.000000e+00 3622.0
4 TraesCS3D01G248100 chr3B 97.182 887 23 1 946 1832 447002963 447003847 0.000000e+00 1498.0
5 TraesCS3D01G248100 chr3B 91.034 435 23 3 1923 2350 447003864 447004289 1.380000e-159 573.0
6 TraesCS3D01G248100 chr3B 84.495 574 58 14 1 563 202898120 202898673 5.050000e-149 538.0
7 TraesCS3D01G248100 chr3B 84.762 210 32 0 550 759 202898687 202898896 1.250000e-50 211.0
8 TraesCS3D01G248100 chr7D 97.632 760 17 1 1 759 250950213 250950972 0.000000e+00 1303.0
9 TraesCS3D01G248100 chr7D 96.875 736 21 2 1 735 251815082 251815816 0.000000e+00 1230.0
10 TraesCS3D01G248100 chr1B 82.476 719 86 23 1 711 133167481 133166795 1.060000e-165 593.0
11 TraesCS3D01G248100 chr5A 84.495 574 57 15 1 563 447595749 447596301 5.050000e-149 538.0
12 TraesCS3D01G248100 chr5A 84.360 211 33 0 550 760 447596315 447596525 1.620000e-49 207.0
13 TraesCS3D01G248100 chrUn 85.064 549 51 11 1 536 88937430 88937960 8.440000e-147 531.0
14 TraesCS3D01G248100 chrUn 85.308 211 29 2 550 759 88937999 88938208 2.690000e-52 217.0
15 TraesCS3D01G248100 chrUn 85.308 211 29 2 550 759 238141166 238141375 2.690000e-52 217.0
16 TraesCS3D01G248100 chr1D 88.482 382 36 8 1 378 8410340 8409963 5.230000e-124 455.0
17 TraesCS3D01G248100 chr1D 88.482 382 36 8 1 378 8442006 8441629 5.230000e-124 455.0
18 TraesCS3D01G248100 chr7B 85.455 385 46 8 1 379 586698341 586698721 4.160000e-105 392.0
19 TraesCS3D01G248100 chr7A 86.441 236 31 1 525 760 239778565 239778799 1.580000e-64 257.0
20 TraesCS3D01G248100 chr7A 97.143 35 1 0 759 793 607420419 607420385 4.790000e-05 60.2
21 TraesCS3D01G248100 chr6B 84.762 210 32 0 550 759 20623205 20622996 1.250000e-50 211.0
22 TraesCS3D01G248100 chr5B 91.358 81 7 0 483 563 438215344 438215264 1.300000e-20 111.0
23 TraesCS3D01G248100 chr1A 97.143 35 1 0 759 793 244504290 244504324 4.790000e-05 60.2
24 TraesCS3D01G248100 chr5D 96.875 32 1 0 762 793 44500321 44500290 2.000000e-03 54.7


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 TraesCS3D01G248100 chr3D 346972304 346976737 4433 False 8189.000000 8189 100.000000 1 4434 1 chr3D.!!$F2 4433
1 TraesCS3D01G248100 chr3D 19895449 19896205 756 False 1271.000000 1271 96.966000 1 757 1 chr3D.!!$F1 756
2 TraesCS3D01G248100 chr3A 466106788 466110255 3467 False 5880.000000 5880 97.191000 946 4434 1 chr3A.!!$F1 3488
3 TraesCS3D01G248100 chr3B 447002963 447006807 3844 False 1897.666667 3622 95.404333 946 4434 3 chr3B.!!$F2 3488
4 TraesCS3D01G248100 chr3B 202898120 202898896 776 False 374.500000 538 84.628500 1 759 2 chr3B.!!$F1 758
5 TraesCS3D01G248100 chr7D 250950213 250950972 759 False 1303.000000 1303 97.632000 1 759 1 chr7D.!!$F1 758
6 TraesCS3D01G248100 chr7D 251815082 251815816 734 False 1230.000000 1230 96.875000 1 735 1 chr7D.!!$F2 734
7 TraesCS3D01G248100 chr1B 133166795 133167481 686 True 593.000000 593 82.476000 1 711 1 chr1B.!!$R1 710
8 TraesCS3D01G248100 chr5A 447595749 447596525 776 False 372.500000 538 84.427500 1 760 2 chr5A.!!$F1 759
9 TraesCS3D01G248100 chrUn 88937430 88938208 778 False 374.000000 531 85.186000 1 759 2 chrUn.!!$F2 758

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
771 845 0.038166 ACCCCTACGTACGACCAGAA 59.962 55.0 24.41 0.00 0.00 3.02 F
852 926 0.093535 TGTCATCGACGACGTACGAC 59.906 55.0 24.41 15.62 45.77 4.34 F
2292 2373 0.031857 CTTTTGAATGGCGTGCACCA 59.968 50.0 12.15 4.61 45.82 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2290 2371 1.909700 ACAATGTAGGGTGCAGTTGG 58.090 50.0 0.0 0.0 0.0 3.77 R
2296 2377 2.228822 CCTCAACAACAATGTAGGGTGC 59.771 50.0 0.0 0.0 39.4 5.01 R
4237 4758 2.161012 CAGCAGCTAGACCAATGTTGTG 59.839 50.0 0.0 0.0 0.0 3.33 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
152 157 3.447229 TCATGACTAATGAGAAGGCGTGA 59.553 43.478 0.00 0.00 44.06 4.35
372 389 2.996249 AGAATGCATCGAGACACCAT 57.004 45.000 0.00 0.00 0.00 3.55
505 525 1.912731 TGTGGAGCAGCTATTGGGTTA 59.087 47.619 0.00 0.00 0.00 2.85
514 534 1.071699 GCTATTGGGTTAGGCCGATGA 59.928 52.381 0.00 0.00 38.44 2.92
563 637 2.412089 GCACTACAGGAGCAAACTAACG 59.588 50.000 0.00 0.00 0.00 3.18
564 638 2.993899 CACTACAGGAGCAAACTAACGG 59.006 50.000 0.00 0.00 0.00 4.44
579 653 8.036575 GCAAACTAACGGGGATACATACATATA 58.963 37.037 0.00 0.00 39.74 0.86
646 720 3.688694 ACACCAAACACCTTATAGCGA 57.311 42.857 0.00 0.00 0.00 4.93
651 725 2.936498 CAAACACCTTATAGCGACCAGG 59.064 50.000 0.00 0.00 0.00 4.45
698 772 4.066490 ACACCGAATAAACCGACAAATCA 58.934 39.130 0.00 0.00 0.00 2.57
712 786 6.095720 ACCGACAAATCAGTTAAAAAGGTTCA 59.904 34.615 0.00 0.00 0.00 3.18
760 834 1.674322 CAAAGTGCCCACCCCTACG 60.674 63.158 0.00 0.00 0.00 3.51
761 835 2.151388 AAAGTGCCCACCCCTACGT 61.151 57.895 0.00 0.00 0.00 3.57
762 836 0.837260 AAAGTGCCCACCCCTACGTA 60.837 55.000 0.00 0.00 0.00 3.57
763 837 1.547472 AAGTGCCCACCCCTACGTAC 61.547 60.000 0.00 0.00 0.00 3.67
764 838 3.069946 TGCCCACCCCTACGTACG 61.070 66.667 15.01 15.01 0.00 3.67
765 839 2.755469 GCCCACCCCTACGTACGA 60.755 66.667 24.41 4.69 0.00 3.43
766 840 3.068729 GCCCACCCCTACGTACGAC 62.069 68.421 24.41 0.00 0.00 4.34
767 841 2.418083 CCCACCCCTACGTACGACC 61.418 68.421 24.41 0.00 0.00 4.79
768 842 1.678635 CCACCCCTACGTACGACCA 60.679 63.158 24.41 5.54 0.00 4.02
769 843 1.660560 CCACCCCTACGTACGACCAG 61.661 65.000 24.41 14.83 0.00 4.00
770 844 0.677731 CACCCCTACGTACGACCAGA 60.678 60.000 24.41 0.41 0.00 3.86
771 845 0.038166 ACCCCTACGTACGACCAGAA 59.962 55.000 24.41 0.00 0.00 3.02
772 846 1.176527 CCCCTACGTACGACCAGAAA 58.823 55.000 24.41 0.00 0.00 2.52
773 847 1.135286 CCCCTACGTACGACCAGAAAC 60.135 57.143 24.41 0.00 0.00 2.78
774 848 1.541147 CCCTACGTACGACCAGAAACA 59.459 52.381 24.41 0.00 0.00 2.83
775 849 2.030007 CCCTACGTACGACCAGAAACAA 60.030 50.000 24.41 0.00 0.00 2.83
776 850 3.367703 CCCTACGTACGACCAGAAACAAT 60.368 47.826 24.41 0.00 0.00 2.71
777 851 4.142403 CCCTACGTACGACCAGAAACAATA 60.142 45.833 24.41 0.00 0.00 1.90
778 852 5.032863 CCTACGTACGACCAGAAACAATAG 58.967 45.833 24.41 8.12 0.00 1.73
779 853 3.248266 ACGTACGACCAGAAACAATAGC 58.752 45.455 24.41 0.00 0.00 2.97
780 854 3.057033 ACGTACGACCAGAAACAATAGCT 60.057 43.478 24.41 0.00 0.00 3.32
781 855 3.303495 CGTACGACCAGAAACAATAGCTG 59.697 47.826 10.44 0.00 0.00 4.24
803 877 9.984590 AGCTGGTTTATTATTAAAACTAGGGAA 57.015 29.630 12.13 0.00 42.44 3.97
844 918 6.961359 AAGAAACATAAATGTCATCGACGA 57.039 33.333 0.00 0.00 40.80 4.20
845 919 6.332504 AGAAACATAAATGTCATCGACGAC 57.667 37.500 4.33 4.33 40.80 4.34
846 920 4.755191 AACATAAATGTCATCGACGACG 57.245 40.909 7.18 0.00 40.80 5.12
847 921 3.766151 ACATAAATGTCATCGACGACGT 58.234 40.909 7.18 3.49 38.84 4.34
848 922 4.912214 ACATAAATGTCATCGACGACGTA 58.088 39.130 6.80 0.00 38.84 3.57
849 923 4.731961 ACATAAATGTCATCGACGACGTAC 59.268 41.667 6.80 0.00 38.84 3.67
850 924 6.499514 ACATAAATGTCATCGACGACGTACG 61.500 44.000 15.01 15.01 41.86 3.67
851 925 1.001624 ATGTCATCGACGACGTACGA 58.998 50.000 24.41 19.43 45.77 3.43
852 926 0.093535 TGTCATCGACGACGTACGAC 59.906 55.000 24.41 15.62 45.77 4.34
853 927 0.093535 GTCATCGACGACGTACGACA 59.906 55.000 24.41 0.00 45.77 4.35
854 928 0.789601 TCATCGACGACGTACGACAA 59.210 50.000 24.41 11.11 45.77 3.18
855 929 1.194322 TCATCGACGACGTACGACAAA 59.806 47.619 24.41 2.27 45.77 2.83
856 930 1.971284 CATCGACGACGTACGACAAAA 59.029 47.619 24.41 2.85 45.77 2.44
857 931 2.098215 TCGACGACGTACGACAAAAA 57.902 45.000 24.41 0.00 45.77 1.94
858 932 2.036217 TCGACGACGTACGACAAAAAG 58.964 47.619 24.41 5.15 45.77 2.27
859 933 1.121257 CGACGACGTACGACAAAAAGG 59.879 52.381 24.41 4.39 45.77 3.11
860 934 2.384382 GACGACGTACGACAAAAAGGA 58.616 47.619 24.41 0.00 45.77 3.36
861 935 2.119457 ACGACGTACGACAAAAAGGAC 58.881 47.619 24.41 0.00 45.77 3.85
862 936 2.223572 ACGACGTACGACAAAAAGGACT 60.224 45.455 24.41 0.00 45.77 3.85
863 937 2.791004 CGACGTACGACAAAAAGGACTT 59.209 45.455 24.41 0.00 45.77 3.01
864 938 3.243643 CGACGTACGACAAAAAGGACTTT 59.756 43.478 24.41 0.00 45.77 2.66
865 939 4.259930 CGACGTACGACAAAAAGGACTTTT 60.260 41.667 24.41 4.29 45.77 2.27
866 940 5.051774 CGACGTACGACAAAAAGGACTTTTA 60.052 40.000 24.41 0.00 45.77 1.52
867 941 6.346040 CGACGTACGACAAAAAGGACTTTTAT 60.346 38.462 24.41 2.80 45.77 1.40
868 942 6.652245 ACGTACGACAAAAAGGACTTTTATG 58.348 36.000 24.41 12.07 41.45 1.90
869 943 5.562623 CGTACGACAAAAAGGACTTTTATGC 59.437 40.000 10.44 2.93 41.45 3.14
870 944 5.508200 ACGACAAAAAGGACTTTTATGCA 57.492 34.783 10.16 0.00 41.45 3.96
871 945 5.897050 ACGACAAAAAGGACTTTTATGCAA 58.103 33.333 10.16 0.00 41.45 4.08
872 946 6.512297 ACGACAAAAAGGACTTTTATGCAAT 58.488 32.000 10.16 0.00 41.45 3.56
873 947 6.983890 ACGACAAAAAGGACTTTTATGCAATT 59.016 30.769 10.16 0.00 41.45 2.32
874 948 7.494298 ACGACAAAAAGGACTTTTATGCAATTT 59.506 29.630 10.16 0.00 41.45 1.82
875 949 8.003784 CGACAAAAAGGACTTTTATGCAATTTC 58.996 33.333 10.16 4.76 41.45 2.17
876 950 8.962884 ACAAAAAGGACTTTTATGCAATTTCT 57.037 26.923 10.16 0.00 41.45 2.52
877 951 8.829612 ACAAAAAGGACTTTTATGCAATTTCTG 58.170 29.630 10.16 4.33 41.45 3.02
878 952 7.967890 AAAAGGACTTTTATGCAATTTCTGG 57.032 32.000 8.19 0.00 40.61 3.86
879 953 6.916360 AAGGACTTTTATGCAATTTCTGGA 57.084 33.333 0.00 0.00 0.00 3.86
880 954 6.521151 AGGACTTTTATGCAATTTCTGGAG 57.479 37.500 0.00 0.00 0.00 3.86
881 955 6.012745 AGGACTTTTATGCAATTTCTGGAGT 58.987 36.000 0.00 0.00 0.00 3.85
882 956 7.175104 AGGACTTTTATGCAATTTCTGGAGTA 58.825 34.615 0.00 0.00 0.00 2.59
883 957 7.836183 AGGACTTTTATGCAATTTCTGGAGTAT 59.164 33.333 0.00 0.00 0.00 2.12
884 958 9.120538 GGACTTTTATGCAATTTCTGGAGTATA 57.879 33.333 0.00 0.00 0.00 1.47
890 964 9.851686 TTATGCAATTTCTGGAGTATAAGATGT 57.148 29.630 0.00 0.00 0.00 3.06
891 965 7.792374 TGCAATTTCTGGAGTATAAGATGTC 57.208 36.000 0.00 0.00 0.00 3.06
892 966 6.767902 TGCAATTTCTGGAGTATAAGATGTCC 59.232 38.462 0.00 0.00 0.00 4.02
893 967 6.995091 GCAATTTCTGGAGTATAAGATGTCCT 59.005 38.462 0.00 0.00 0.00 3.85
894 968 7.500559 GCAATTTCTGGAGTATAAGATGTCCTT 59.499 37.037 0.00 0.00 38.87 3.36
895 969 8.834465 CAATTTCTGGAGTATAAGATGTCCTTG 58.166 37.037 0.00 0.00 36.34 3.61
896 970 7.496346 TTTCTGGAGTATAAGATGTCCTTGT 57.504 36.000 0.00 0.00 36.34 3.16
897 971 6.471233 TCTGGAGTATAAGATGTCCTTGTG 57.529 41.667 0.00 0.00 36.34 3.33
898 972 5.023533 TGGAGTATAAGATGTCCTTGTGC 57.976 43.478 0.00 0.00 36.34 4.57
899 973 4.716784 TGGAGTATAAGATGTCCTTGTGCT 59.283 41.667 0.00 0.00 40.48 4.40
900 974 5.897250 TGGAGTATAAGATGTCCTTGTGCTA 59.103 40.000 0.00 0.00 38.59 3.49
901 975 6.554982 TGGAGTATAAGATGTCCTTGTGCTAT 59.445 38.462 0.00 0.00 38.59 2.97
902 976 7.071196 TGGAGTATAAGATGTCCTTGTGCTATT 59.929 37.037 0.00 0.00 38.59 1.73
903 977 7.934120 GGAGTATAAGATGTCCTTGTGCTATTT 59.066 37.037 0.00 0.00 38.59 1.40
904 978 9.331282 GAGTATAAGATGTCCTTGTGCTATTTT 57.669 33.333 0.00 0.00 38.59 1.82
908 982 9.905713 ATAAGATGTCCTTGTGCTATTTTAAGA 57.094 29.630 0.00 0.00 36.34 2.10
909 983 8.635765 AAGATGTCCTTGTGCTATTTTAAGAA 57.364 30.769 0.00 0.00 32.92 2.52
910 984 8.273780 AGATGTCCTTGTGCTATTTTAAGAAG 57.726 34.615 0.00 0.00 0.00 2.85
911 985 7.885399 AGATGTCCTTGTGCTATTTTAAGAAGT 59.115 33.333 0.00 0.00 0.00 3.01
912 986 7.817418 TGTCCTTGTGCTATTTTAAGAAGTT 57.183 32.000 0.00 0.00 0.00 2.66
913 987 7.648142 TGTCCTTGTGCTATTTTAAGAAGTTG 58.352 34.615 0.00 0.00 0.00 3.16
914 988 6.582672 GTCCTTGTGCTATTTTAAGAAGTTGC 59.417 38.462 0.00 0.00 0.00 4.17
915 989 6.490040 TCCTTGTGCTATTTTAAGAAGTTGCT 59.510 34.615 0.00 0.00 0.00 3.91
916 990 6.803807 CCTTGTGCTATTTTAAGAAGTTGCTC 59.196 38.462 0.00 0.00 0.00 4.26
917 991 7.308830 CCTTGTGCTATTTTAAGAAGTTGCTCT 60.309 37.037 0.00 0.00 0.00 4.09
918 992 7.510549 TGTGCTATTTTAAGAAGTTGCTCTT 57.489 32.000 0.00 0.00 39.09 2.85
919 993 8.615878 TGTGCTATTTTAAGAAGTTGCTCTTA 57.384 30.769 0.00 0.00 36.95 2.10
920 994 9.062524 TGTGCTATTTTAAGAAGTTGCTCTTAA 57.937 29.630 2.63 2.63 43.11 1.85
955 1029 3.813724 GGAATCTTAAACCCCATACGAGC 59.186 47.826 0.00 0.00 0.00 5.03
961 1035 2.097110 AACCCCATACGAGCTCCATA 57.903 50.000 8.47 1.07 0.00 2.74
964 1038 2.225394 ACCCCATACGAGCTCCATAGAT 60.225 50.000 8.47 0.00 0.00 1.98
1028 1102 3.567797 GCGTTCTCCTGCCATCGC 61.568 66.667 0.00 0.00 37.17 4.58
1476 1550 4.752594 GGGGAGGTGGGTAGGGCA 62.753 72.222 0.00 0.00 0.00 5.36
1650 1724 4.133078 CTGGATATTGCAAGGAAGGAGAC 58.867 47.826 4.94 0.00 0.00 3.36
1741 1815 2.685388 GCAGGTTGCTATTCCTTTCTCC 59.315 50.000 0.00 0.00 40.96 3.71
2015 2089 6.580791 CAGTGTTTGGTGTCAATTTTATACCG 59.419 38.462 0.00 0.00 34.16 4.02
2249 2330 4.399303 GGATGGTTTGGTTGGACTATTGAG 59.601 45.833 0.00 0.00 0.00 3.02
2290 2371 1.851658 AACTTTTGAATGGCGTGCAC 58.148 45.000 6.82 6.82 0.00 4.57
2291 2372 0.031994 ACTTTTGAATGGCGTGCACC 59.968 50.000 12.15 3.87 0.00 5.01
2292 2373 0.031857 CTTTTGAATGGCGTGCACCA 59.968 50.000 12.15 4.61 45.82 4.17
2293 2374 0.461548 TTTTGAATGGCGTGCACCAA 59.538 45.000 12.15 5.54 44.65 3.67
2294 2375 0.249238 TTTGAATGGCGTGCACCAAC 60.249 50.000 12.15 1.96 44.65 3.77
2295 2376 1.106351 TTGAATGGCGTGCACCAACT 61.106 50.000 12.15 0.00 44.65 3.16
2296 2377 1.081242 GAATGGCGTGCACCAACTG 60.081 57.895 12.15 0.00 44.65 3.16
2297 2378 3.211564 AATGGCGTGCACCAACTGC 62.212 57.895 12.15 8.26 44.65 4.40
2305 2386 1.228124 GCACCAACTGCACCCTACA 60.228 57.895 0.00 0.00 46.29 2.74
2330 2411 3.475566 TGTTGAGGTTCTTGACTGAGG 57.524 47.619 0.00 0.00 0.00 3.86
2845 3357 0.690762 AAACACGTGGGCTGATACCT 59.309 50.000 21.57 0.00 0.00 3.08
2992 3504 7.786178 TGCTTGTATTATCGATATATTGGGC 57.214 36.000 5.84 8.15 0.00 5.36
3531 4052 4.096984 GGATCAAATTTACAGGCCACAGAG 59.903 45.833 5.01 0.00 0.00 3.35
3613 4134 8.157476 GGATGTTAGTATCATGATAAACCTGGT 58.843 37.037 16.97 0.00 0.00 4.00
3875 4396 4.811969 TTTCTAGCGGACCAGTATTTGA 57.188 40.909 0.00 0.00 0.00 2.69
3886 4407 6.407202 GGACCAGTATTTGATACTCAACAGT 58.593 40.000 0.00 0.00 43.93 3.55
4183 4704 5.792741 AGCTGCATATTGGTTTGCTTAAAA 58.207 33.333 1.02 0.00 39.60 1.52
4184 4705 6.229733 AGCTGCATATTGGTTTGCTTAAAAA 58.770 32.000 1.02 0.00 39.60 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
307 324 3.899052 ATAAGTAGTGCGTAAGGCCAA 57.101 42.857 5.01 0.00 42.61 4.52
372 389 4.164981 TCCCTACTGGCTTCTTCAAGTTA 58.835 43.478 0.00 0.00 31.45 2.24
505 525 2.192605 GCCAATTTGTCATCGGCCT 58.807 52.632 0.00 0.00 36.73 5.19
563 637 9.449719 CAAAGAAACCTATATGTATGTATCCCC 57.550 37.037 0.00 0.00 0.00 4.81
564 638 9.449719 CCAAAGAAACCTATATGTATGTATCCC 57.550 37.037 0.00 0.00 0.00 3.85
579 653 6.127281 ACAAACCGAATTAACCAAAGAAACCT 60.127 34.615 0.00 0.00 0.00 3.50
698 772 7.094506 ACAGAACGAAACTGAACCTTTTTAACT 60.095 33.333 12.98 0.00 38.55 2.24
712 786 4.690184 AACCGAAAAACAGAACGAAACT 57.310 36.364 0.00 0.00 0.00 2.66
760 834 3.617263 CCAGCTATTGTTTCTGGTCGTAC 59.383 47.826 0.00 0.00 41.76 3.67
761 835 3.857052 CCAGCTATTGTTTCTGGTCGTA 58.143 45.455 0.00 0.00 41.76 3.43
762 836 2.699954 CCAGCTATTGTTTCTGGTCGT 58.300 47.619 0.00 0.00 41.76 4.34
777 851 9.984590 TTCCCTAGTTTTAATAATAAACCAGCT 57.015 29.630 0.00 0.00 36.40 4.24
818 892 9.093970 TCGTCGATGACATTTATGTTTCTTATT 57.906 29.630 2.39 0.00 41.95 1.40
819 893 8.540492 GTCGTCGATGACATTTATGTTTCTTAT 58.460 33.333 28.64 0.00 41.95 1.73
820 894 7.253519 CGTCGTCGATGACATTTATGTTTCTTA 60.254 37.037 31.32 0.00 39.25 2.10
821 895 6.453791 CGTCGTCGATGACATTTATGTTTCTT 60.454 38.462 31.32 0.00 39.25 2.52
822 896 5.004440 CGTCGTCGATGACATTTATGTTTCT 59.996 40.000 31.32 0.00 39.25 2.52
823 897 5.181084 CGTCGTCGATGACATTTATGTTTC 58.819 41.667 31.32 6.07 39.25 2.78
824 898 4.624024 ACGTCGTCGATGACATTTATGTTT 59.376 37.500 31.32 6.37 39.78 2.83
825 899 4.171005 ACGTCGTCGATGACATTTATGTT 58.829 39.130 31.32 7.27 39.78 2.71
826 900 3.766151 ACGTCGTCGATGACATTTATGT 58.234 40.909 31.32 19.48 41.23 2.29
827 901 4.144088 CGTACGTCGTCGATGACATTTATG 60.144 45.833 31.32 20.86 38.84 1.90
828 902 3.964347 CGTACGTCGTCGATGACATTTAT 59.036 43.478 31.32 16.27 38.84 1.40
829 903 3.061965 TCGTACGTCGTCGATGACATTTA 59.938 43.478 31.32 18.65 38.84 1.40
830 904 2.159667 TCGTACGTCGTCGATGACATTT 60.160 45.455 31.32 19.52 38.84 2.32
831 905 1.394572 TCGTACGTCGTCGATGACATT 59.605 47.619 31.32 21.66 38.84 2.71
832 906 1.001624 TCGTACGTCGTCGATGACAT 58.998 50.000 31.32 22.61 38.84 3.06
833 907 0.093535 GTCGTACGTCGTCGATGACA 59.906 55.000 31.32 14.84 38.84 3.58
834 908 0.093535 TGTCGTACGTCGTCGATGAC 59.906 55.000 24.88 24.88 40.80 3.06
835 909 0.789601 TTGTCGTACGTCGTCGATGA 59.210 50.000 20.97 2.39 40.80 2.92
836 910 1.594517 TTTGTCGTACGTCGTCGATG 58.405 50.000 16.05 12.90 40.80 3.84
837 911 2.314561 TTTTGTCGTACGTCGTCGAT 57.685 45.000 16.05 0.00 40.80 3.59
838 912 2.036217 CTTTTTGTCGTACGTCGTCGA 58.964 47.619 16.05 8.47 40.80 4.20
839 913 1.121257 CCTTTTTGTCGTACGTCGTCG 59.879 52.381 16.05 6.02 40.80 5.12
840 914 2.151924 GTCCTTTTTGTCGTACGTCGTC 59.848 50.000 16.05 5.49 40.80 4.20
841 915 2.119457 GTCCTTTTTGTCGTACGTCGT 58.881 47.619 16.05 2.21 40.80 4.34
842 916 2.388121 AGTCCTTTTTGTCGTACGTCG 58.612 47.619 16.05 0.00 41.41 5.12
843 917 4.783959 AAAGTCCTTTTTGTCGTACGTC 57.216 40.909 16.05 10.62 0.00 4.34
844 918 6.652245 CATAAAAGTCCTTTTTGTCGTACGT 58.348 36.000 16.05 0.00 42.22 3.57
845 919 5.562623 GCATAAAAGTCCTTTTTGTCGTACG 59.437 40.000 9.53 9.53 42.22 3.67
846 920 6.432107 TGCATAAAAGTCCTTTTTGTCGTAC 58.568 36.000 10.05 0.00 42.22 3.67
847 921 6.621316 TGCATAAAAGTCCTTTTTGTCGTA 57.379 33.333 10.05 0.00 42.22 3.43
848 922 5.508200 TGCATAAAAGTCCTTTTTGTCGT 57.492 34.783 10.05 0.00 42.22 4.34
849 923 7.406799 AATTGCATAAAAGTCCTTTTTGTCG 57.593 32.000 10.05 0.00 42.22 4.35
850 924 9.045223 AGAAATTGCATAAAAGTCCTTTTTGTC 57.955 29.630 10.05 0.00 42.22 3.18
851 925 8.829612 CAGAAATTGCATAAAAGTCCTTTTTGT 58.170 29.630 10.05 0.00 42.22 2.83
852 926 8.284693 CCAGAAATTGCATAAAAGTCCTTTTTG 58.715 33.333 10.05 9.30 42.22 2.44
853 927 8.210265 TCCAGAAATTGCATAAAAGTCCTTTTT 58.790 29.630 10.05 0.00 42.22 1.94
854 928 7.734942 TCCAGAAATTGCATAAAAGTCCTTTT 58.265 30.769 9.72 9.72 44.16 2.27
855 929 7.015584 ACTCCAGAAATTGCATAAAAGTCCTTT 59.984 33.333 0.00 0.00 0.00 3.11
856 930 6.494835 ACTCCAGAAATTGCATAAAAGTCCTT 59.505 34.615 0.00 0.00 0.00 3.36
857 931 6.012745 ACTCCAGAAATTGCATAAAAGTCCT 58.987 36.000 0.00 0.00 0.00 3.85
858 932 6.272822 ACTCCAGAAATTGCATAAAAGTCC 57.727 37.500 0.00 0.00 0.00 3.85
864 938 9.851686 ACATCTTATACTCCAGAAATTGCATAA 57.148 29.630 0.00 0.00 0.00 1.90
865 939 9.494271 GACATCTTATACTCCAGAAATTGCATA 57.506 33.333 0.00 0.00 0.00 3.14
866 940 7.446625 GGACATCTTATACTCCAGAAATTGCAT 59.553 37.037 0.00 0.00 0.00 3.96
867 941 6.767902 GGACATCTTATACTCCAGAAATTGCA 59.232 38.462 0.00 0.00 0.00 4.08
868 942 6.995091 AGGACATCTTATACTCCAGAAATTGC 59.005 38.462 0.00 0.00 0.00 3.56
869 943 8.834465 CAAGGACATCTTATACTCCAGAAATTG 58.166 37.037 0.00 0.00 33.68 2.32
870 944 8.552296 ACAAGGACATCTTATACTCCAGAAATT 58.448 33.333 0.00 0.00 33.68 1.82
871 945 7.989741 CACAAGGACATCTTATACTCCAGAAAT 59.010 37.037 0.00 0.00 33.68 2.17
872 946 7.331026 CACAAGGACATCTTATACTCCAGAAA 58.669 38.462 0.00 0.00 33.68 2.52
873 947 6.630413 GCACAAGGACATCTTATACTCCAGAA 60.630 42.308 0.00 0.00 33.68 3.02
874 948 5.163405 GCACAAGGACATCTTATACTCCAGA 60.163 44.000 0.00 0.00 33.68 3.86
875 949 5.053145 GCACAAGGACATCTTATACTCCAG 58.947 45.833 0.00 0.00 33.68 3.86
876 950 4.716784 AGCACAAGGACATCTTATACTCCA 59.283 41.667 0.00 0.00 33.68 3.86
877 951 5.283457 AGCACAAGGACATCTTATACTCC 57.717 43.478 0.00 0.00 33.68 3.85
878 952 8.894768 AAATAGCACAAGGACATCTTATACTC 57.105 34.615 0.00 0.00 33.68 2.59
882 956 9.905713 TCTTAAAATAGCACAAGGACATCTTAT 57.094 29.630 0.00 0.00 33.68 1.73
883 957 9.733556 TTCTTAAAATAGCACAAGGACATCTTA 57.266 29.630 0.00 0.00 33.68 2.10
884 958 8.635765 TTCTTAAAATAGCACAAGGACATCTT 57.364 30.769 0.00 0.00 35.79 2.40
885 959 7.885399 ACTTCTTAAAATAGCACAAGGACATCT 59.115 33.333 0.00 0.00 0.00 2.90
886 960 8.045176 ACTTCTTAAAATAGCACAAGGACATC 57.955 34.615 0.00 0.00 0.00 3.06
887 961 8.299570 CAACTTCTTAAAATAGCACAAGGACAT 58.700 33.333 0.00 0.00 0.00 3.06
888 962 7.648142 CAACTTCTTAAAATAGCACAAGGACA 58.352 34.615 0.00 0.00 0.00 4.02
889 963 6.582672 GCAACTTCTTAAAATAGCACAAGGAC 59.417 38.462 0.00 0.00 0.00 3.85
890 964 6.490040 AGCAACTTCTTAAAATAGCACAAGGA 59.510 34.615 0.00 0.00 0.00 3.36
891 965 6.681777 AGCAACTTCTTAAAATAGCACAAGG 58.318 36.000 0.00 0.00 0.00 3.61
892 966 7.588512 AGAGCAACTTCTTAAAATAGCACAAG 58.411 34.615 0.00 0.00 0.00 3.16
893 967 7.510549 AGAGCAACTTCTTAAAATAGCACAA 57.489 32.000 0.00 0.00 0.00 3.33
894 968 7.510549 AAGAGCAACTTCTTAAAATAGCACA 57.489 32.000 0.00 0.00 35.70 4.57
927 1001 8.108364 TCGTATGGGGTTTAAGATTCCTAAAAA 58.892 33.333 0.00 0.00 0.00 1.94
928 1002 7.631933 TCGTATGGGGTTTAAGATTCCTAAAA 58.368 34.615 0.00 0.00 0.00 1.52
929 1003 7.197901 TCGTATGGGGTTTAAGATTCCTAAA 57.802 36.000 0.00 0.00 0.00 1.85
930 1004 6.687139 GCTCGTATGGGGTTTAAGATTCCTAA 60.687 42.308 0.00 0.00 0.00 2.69
931 1005 5.221581 GCTCGTATGGGGTTTAAGATTCCTA 60.222 44.000 0.00 0.00 0.00 2.94
932 1006 4.444449 GCTCGTATGGGGTTTAAGATTCCT 60.444 45.833 0.00 0.00 0.00 3.36
933 1007 3.813724 GCTCGTATGGGGTTTAAGATTCC 59.186 47.826 0.00 0.00 0.00 3.01
934 1008 4.704965 AGCTCGTATGGGGTTTAAGATTC 58.295 43.478 0.00 0.00 0.00 2.52
935 1009 4.444449 GGAGCTCGTATGGGGTTTAAGATT 60.444 45.833 7.83 0.00 0.00 2.40
936 1010 3.071167 GGAGCTCGTATGGGGTTTAAGAT 59.929 47.826 7.83 0.00 0.00 2.40
937 1011 2.433239 GGAGCTCGTATGGGGTTTAAGA 59.567 50.000 7.83 0.00 0.00 2.10
938 1012 2.169769 TGGAGCTCGTATGGGGTTTAAG 59.830 50.000 7.83 0.00 0.00 1.85
939 1013 2.189676 TGGAGCTCGTATGGGGTTTAA 58.810 47.619 7.83 0.00 0.00 1.52
940 1014 1.868713 TGGAGCTCGTATGGGGTTTA 58.131 50.000 7.83 0.00 0.00 2.01
941 1015 1.213296 ATGGAGCTCGTATGGGGTTT 58.787 50.000 7.83 0.00 0.00 3.27
942 1016 1.971357 CTATGGAGCTCGTATGGGGTT 59.029 52.381 7.83 0.00 0.00 4.11
943 1017 1.147191 TCTATGGAGCTCGTATGGGGT 59.853 52.381 7.83 0.00 0.00 4.95
944 1018 1.924731 TCTATGGAGCTCGTATGGGG 58.075 55.000 7.83 1.27 0.00 4.96
955 1029 0.387878 GCCGTCGAGCATCTATGGAG 60.388 60.000 0.00 0.00 39.18 3.86
961 1035 2.125512 GTTGGCCGTCGAGCATCT 60.126 61.111 0.00 0.00 0.00 2.90
964 1038 4.980805 GGTGTTGGCCGTCGAGCA 62.981 66.667 0.00 0.00 0.00 4.26
1455 1529 3.155167 CTACCCACCTCCCCTCGC 61.155 72.222 0.00 0.00 0.00 5.03
1458 1532 4.433194 GCCCTACCCACCTCCCCT 62.433 72.222 0.00 0.00 0.00 4.79
1476 1550 1.360194 TTTCGTCAAACACCGCACGT 61.360 50.000 0.00 0.00 33.89 4.49
1650 1724 3.997064 CTTCCTGGCGCTCTCCACG 62.997 68.421 7.64 0.00 31.74 4.94
1933 2007 7.381139 ACAAAAATCATTTACAACCGCTAACTG 59.619 33.333 0.00 0.00 0.00 3.16
2050 2124 6.991531 AGTTCATGCCAAGCAAGAAAATTTAA 59.008 30.769 8.62 0.00 45.39 1.52
2172 2253 6.485171 ACAATTAAGGCATGAGTTCCTAACT 58.515 36.000 0.00 0.00 46.38 2.24
2249 2330 3.153919 TGAAACACATTAGTCCAAGGCC 58.846 45.455 0.00 0.00 0.00 5.19
2290 2371 1.909700 ACAATGTAGGGTGCAGTTGG 58.090 50.000 0.00 0.00 0.00 3.77
2291 2372 2.622942 ACAACAATGTAGGGTGCAGTTG 59.377 45.455 7.80 7.80 38.24 3.16
2292 2373 2.944129 ACAACAATGTAGGGTGCAGTT 58.056 42.857 0.00 0.00 38.24 3.16
2293 2374 2.622942 CAACAACAATGTAGGGTGCAGT 59.377 45.455 0.00 0.00 39.40 4.40
2294 2375 2.884012 TCAACAACAATGTAGGGTGCAG 59.116 45.455 0.00 0.00 39.40 4.41
2295 2376 2.884012 CTCAACAACAATGTAGGGTGCA 59.116 45.455 0.00 0.00 39.40 4.57
2296 2377 2.228822 CCTCAACAACAATGTAGGGTGC 59.771 50.000 0.00 0.00 39.40 5.01
2297 2378 3.486383 ACCTCAACAACAATGTAGGGTG 58.514 45.455 4.40 1.00 38.92 4.61
2298 2379 3.876309 ACCTCAACAACAATGTAGGGT 57.124 42.857 4.40 0.00 38.92 4.34
2305 2386 5.192927 TCAGTCAAGAACCTCAACAACAAT 58.807 37.500 0.00 0.00 0.00 2.71
2330 2411 5.302823 CCCCCTAATGAAGTGAAATGATTCC 59.697 44.000 0.00 0.00 34.49 3.01
2845 3357 8.880244 AGCACACTAAGGATGGTAATATCATTA 58.120 33.333 0.00 0.00 33.61 1.90
2992 3504 0.318441 TCTCAAACTGTCCTGCTCGG 59.682 55.000 0.00 0.00 0.00 4.63
3531 4052 4.002906 TCCATGTACCTGAGACAAACAC 57.997 45.455 0.00 0.00 0.00 3.32
4106 4627 3.551485 GCATAATTTTAACTTGCTGCCGG 59.449 43.478 0.00 0.00 0.00 6.13
4183 4704 8.650143 ACCAAAATATACAAGTGACTTCCATT 57.350 30.769 0.00 0.00 0.00 3.16
4184 4705 9.747898 TTACCAAAATATACAAGTGACTTCCAT 57.252 29.630 0.00 0.00 0.00 3.41
4237 4758 2.161012 CAGCAGCTAGACCAATGTTGTG 59.839 50.000 0.00 0.00 0.00 3.33
4340 4861 6.931281 CCCAATCATAAGCTCTCGAGATAAAA 59.069 38.462 17.03 2.82 0.00 1.52
4341 4862 6.042093 ACCCAATCATAAGCTCTCGAGATAAA 59.958 38.462 17.03 2.44 0.00 1.40
4342 4863 5.540337 ACCCAATCATAAGCTCTCGAGATAA 59.460 40.000 17.03 2.06 0.00 1.75
4343 4864 5.080337 ACCCAATCATAAGCTCTCGAGATA 58.920 41.667 17.03 6.12 0.00 1.98


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

AutoCloner maintained by Alex Coulton.