Multiple sequence alignment - TraesCS2B01G207700

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 TraesCS2B01G207700 chr2B 100.000 3180 0 0 1 3180 188459858 188463037 0.000000e+00 5873
1 TraesCS2B01G207700 chr2B 81.644 1302 187 26 888 2170 185769781 185771049 0.000000e+00 1033
2 TraesCS2B01G207700 chr2B 89.074 659 55 7 888 1534 186375593 186374940 0.000000e+00 802
3 TraesCS2B01G207700 chr2D 96.285 2261 51 18 921 3167 132695048 132697289 0.000000e+00 3679
4 TraesCS2B01G207700 chr2D 93.336 2221 96 19 984 3180 132293189 132295381 0.000000e+00 3234
5 TraesCS2B01G207700 chr2D 81.875 1269 187 22 899 2151 131765317 131766558 0.000000e+00 1029
6 TraesCS2B01G207700 chr2A 92.784 2231 106 23 972 3180 140358025 140360222 0.000000e+00 3177
7 TraesCS2B01G207700 chr2A 82.691 1375 182 36 917 2270 139509098 139510437 0.000000e+00 1170
8 TraesCS2B01G207700 chr2A 92.061 655 37 5 2538 3180 139510835 139511486 0.000000e+00 907
9 TraesCS2B01G207700 chr2A 94.366 71 4 0 885 955 140351054 140351124 3.350000e-20 110
10 TraesCS2B01G207700 chr5B 97.328 786 17 4 1 784 672847579 672846796 0.000000e+00 1332
11 TraesCS2B01G207700 chr5B 95.812 788 26 7 1 784 571552217 571553001 0.000000e+00 1266
12 TraesCS2B01G207700 chr5B 88.068 176 19 2 629 804 626424308 626424135 1.160000e-49 207
13 TraesCS2B01G207700 chr4A 96.183 786 25 5 1 784 674447943 674447161 0.000000e+00 1280
14 TraesCS2B01G207700 chrUn 95.674 786 29 5 1 784 60658263 60659045 0.000000e+00 1258
15 TraesCS2B01G207700 chrUn 95.674 786 28 6 1 784 231863704 231862923 0.000000e+00 1258
16 TraesCS2B01G207700 chrUn 95.674 786 25 8 3 784 329543518 329542738 0.000000e+00 1254
17 TraesCS2B01G207700 chrUn 95.414 785 28 7 3 784 369547988 369547209 0.000000e+00 1243
18 TraesCS2B01G207700 chrUn 95.299 787 29 7 1 784 376543220 376542439 0.000000e+00 1242
19 TraesCS2B01G207700 chrUn 95.044 787 29 7 1 784 376689072 376688293 0.000000e+00 1229
20 TraesCS2B01G207700 chr7B 79.912 682 113 11 957 1631 41054516 41053852 2.220000e-131 479
21 TraesCS2B01G207700 chr1B 87.562 402 17 10 417 786 52409586 52409986 4.870000e-118 435
22 TraesCS2B01G207700 chr6B 79.297 256 41 11 546 796 370147687 370147439 5.460000e-38 169


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 TraesCS2B01G207700 chr2B 188459858 188463037 3179 False 5873.0 5873 100.000 1 3180 1 chr2B.!!$F2 3179
1 TraesCS2B01G207700 chr2B 185769781 185771049 1268 False 1033.0 1033 81.644 888 2170 1 chr2B.!!$F1 1282
2 TraesCS2B01G207700 chr2B 186374940 186375593 653 True 802.0 802 89.074 888 1534 1 chr2B.!!$R1 646
3 TraesCS2B01G207700 chr2D 132695048 132697289 2241 False 3679.0 3679 96.285 921 3167 1 chr2D.!!$F3 2246
4 TraesCS2B01G207700 chr2D 132293189 132295381 2192 False 3234.0 3234 93.336 984 3180 1 chr2D.!!$F2 2196
5 TraesCS2B01G207700 chr2D 131765317 131766558 1241 False 1029.0 1029 81.875 899 2151 1 chr2D.!!$F1 1252
6 TraesCS2B01G207700 chr2A 140358025 140360222 2197 False 3177.0 3177 92.784 972 3180 1 chr2A.!!$F2 2208
7 TraesCS2B01G207700 chr2A 139509098 139511486 2388 False 1038.5 1170 87.376 917 3180 2 chr2A.!!$F3 2263
8 TraesCS2B01G207700 chr5B 672846796 672847579 783 True 1332.0 1332 97.328 1 784 1 chr5B.!!$R2 783
9 TraesCS2B01G207700 chr5B 571552217 571553001 784 False 1266.0 1266 95.812 1 784 1 chr5B.!!$F1 783
10 TraesCS2B01G207700 chr4A 674447161 674447943 782 True 1280.0 1280 96.183 1 784 1 chr4A.!!$R1 783
11 TraesCS2B01G207700 chrUn 60658263 60659045 782 False 1258.0 1258 95.674 1 784 1 chrUn.!!$F1 783
12 TraesCS2B01G207700 chrUn 231862923 231863704 781 True 1258.0 1258 95.674 1 784 1 chrUn.!!$R1 783
13 TraesCS2B01G207700 chrUn 329542738 329543518 780 True 1254.0 1254 95.674 3 784 1 chrUn.!!$R2 781
14 TraesCS2B01G207700 chrUn 369547209 369547988 779 True 1243.0 1243 95.414 3 784 1 chrUn.!!$R3 781
15 TraesCS2B01G207700 chrUn 376542439 376543220 781 True 1242.0 1242 95.299 1 784 1 chrUn.!!$R4 783
16 TraesCS2B01G207700 chrUn 376688293 376689072 779 True 1229.0 1229 95.044 1 784 1 chrUn.!!$R5 783
17 TraesCS2B01G207700 chr7B 41053852 41054516 664 True 479.0 479 79.912 957 1631 1 chr7B.!!$R1 674

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
816 824 0.179094 TGGCCGGCTTACTAATCGTG 60.179 55.0 28.56 0.0 0.0 4.35 F
822 830 0.179468 GCTTACTAATCGTGCCCCCA 59.821 55.0 0.00 0.0 0.0 4.96 F
896 904 0.242825 TGCTAGAGGTTGGTTCGTCG 59.757 55.0 0.00 0.0 0.0 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1909 1945 0.036388 ACACGCCAACACCCATCTAG 60.036 55.0 0.0 0.0 0.0 2.43 R
2065 2101 0.247460 TCCTGGACTGCATTGACTCG 59.753 55.0 0.0 0.0 0.0 4.18 R
2411 2475 5.294552 AGCGGAGAATAATAGAAAGCACAAC 59.705 40.0 0.0 0.0 0.0 3.32 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
521 524 5.704217 TTTGTAAAAGCGCGAACATTTTT 57.296 30.435 12.10 10.24 0.00 1.94
522 525 4.684193 TGTAAAAGCGCGAACATTTTTG 57.316 36.364 12.10 0.00 0.00 2.44
766 774 1.082756 GCAGTTTGACGCAACGAGG 60.083 57.895 0.00 0.00 0.00 4.63
784 792 3.610911 GAGGGGCATATAGGATTTTCCG 58.389 50.000 0.00 0.00 42.75 4.30
785 793 2.308866 AGGGGCATATAGGATTTTCCGG 59.691 50.000 0.00 0.00 42.75 5.14
786 794 2.092323 GGGCATATAGGATTTTCCGGC 58.908 52.381 0.00 0.00 42.75 6.13
787 795 2.290960 GGGCATATAGGATTTTCCGGCT 60.291 50.000 0.00 0.00 42.75 5.52
788 796 2.749621 GGCATATAGGATTTTCCGGCTG 59.250 50.000 0.00 0.00 42.75 4.85
789 797 2.749621 GCATATAGGATTTTCCGGCTGG 59.250 50.000 4.71 4.71 42.75 4.85
790 798 2.561478 TATAGGATTTTCCGGCTGGC 57.439 50.000 6.73 0.00 42.75 4.85
791 799 0.550914 ATAGGATTTTCCGGCTGGCA 59.449 50.000 6.73 0.00 42.75 4.92
792 800 0.393808 TAGGATTTTCCGGCTGGCAC 60.394 55.000 6.73 0.00 42.75 5.01
793 801 2.485122 GATTTTCCGGCTGGCACG 59.515 61.111 6.73 0.00 34.14 5.34
810 818 2.508928 GGCATGGCCGGCTTACTA 59.491 61.111 28.56 8.37 39.62 1.82
811 819 1.153046 GGCATGGCCGGCTTACTAA 60.153 57.895 28.56 5.65 39.62 2.24
812 820 0.537371 GGCATGGCCGGCTTACTAAT 60.537 55.000 28.56 7.87 39.62 1.73
813 821 0.875059 GCATGGCCGGCTTACTAATC 59.125 55.000 28.56 7.32 0.00 1.75
814 822 1.148310 CATGGCCGGCTTACTAATCG 58.852 55.000 28.56 0.79 0.00 3.34
815 823 0.756903 ATGGCCGGCTTACTAATCGT 59.243 50.000 28.56 5.03 0.00 3.73
816 824 0.179094 TGGCCGGCTTACTAATCGTG 60.179 55.000 28.56 0.00 0.00 4.35
817 825 1.496403 GGCCGGCTTACTAATCGTGC 61.496 60.000 28.56 0.00 0.00 5.34
818 826 1.496403 GCCGGCTTACTAATCGTGCC 61.496 60.000 22.15 0.00 40.14 5.01
819 827 0.878961 CCGGCTTACTAATCGTGCCC 60.879 60.000 0.00 0.00 40.40 5.36
820 828 0.878961 CGGCTTACTAATCGTGCCCC 60.879 60.000 0.00 0.00 40.40 5.80
821 829 0.534427 GGCTTACTAATCGTGCCCCC 60.534 60.000 0.00 0.00 37.81 5.40
822 830 0.179468 GCTTACTAATCGTGCCCCCA 59.821 55.000 0.00 0.00 0.00 4.96
823 831 1.202770 GCTTACTAATCGTGCCCCCAT 60.203 52.381 0.00 0.00 0.00 4.00
824 832 2.494059 CTTACTAATCGTGCCCCCATG 58.506 52.381 0.00 0.00 0.00 3.66
825 833 0.762418 TACTAATCGTGCCCCCATGG 59.238 55.000 4.14 4.14 37.09 3.66
844 852 4.169696 CCGTGCCTGGCCCGATTA 62.170 66.667 25.01 0.00 0.00 1.75
845 853 2.588877 CGTGCCTGGCCCGATTAG 60.589 66.667 18.95 0.00 0.00 1.73
846 854 2.902343 GTGCCTGGCCCGATTAGC 60.902 66.667 17.53 0.00 0.00 3.09
847 855 3.407083 TGCCTGGCCCGATTAGCA 61.407 61.111 17.53 0.00 0.00 3.49
848 856 2.124320 GCCTGGCCCGATTAGCAA 60.124 61.111 7.66 0.00 0.00 3.91
849 857 2.189499 GCCTGGCCCGATTAGCAAG 61.189 63.158 7.66 0.00 0.00 4.01
850 858 1.526917 CCTGGCCCGATTAGCAAGG 60.527 63.158 0.00 0.00 44.94 3.61
851 859 2.965716 CCTGGCCCGATTAGCAAGGG 62.966 65.000 0.00 0.00 46.29 3.95
854 862 2.591715 CCCGATTAGCAAGGGCCG 60.592 66.667 0.00 0.00 42.56 6.13
855 863 2.591715 CCGATTAGCAAGGGCCGG 60.592 66.667 0.00 0.00 42.56 6.13
856 864 2.591715 CGATTAGCAAGGGCCGGG 60.592 66.667 2.18 0.00 42.56 5.73
857 865 2.907407 GATTAGCAAGGGCCGGGC 60.907 66.667 22.00 22.00 42.56 6.13
876 884 3.365265 GGCCCGTTTGGTCAGCTG 61.365 66.667 7.63 7.63 39.18 4.24
877 885 2.594592 GCCCGTTTGGTCAGCTGT 60.595 61.111 14.67 0.00 36.04 4.40
878 886 2.908073 GCCCGTTTGGTCAGCTGTG 61.908 63.158 14.67 0.00 36.04 3.66
879 887 2.639286 CCGTTTGGTCAGCTGTGC 59.361 61.111 14.67 8.02 0.00 4.57
880 888 1.893808 CCGTTTGGTCAGCTGTGCT 60.894 57.895 14.67 0.00 40.77 4.40
881 889 0.602638 CCGTTTGGTCAGCTGTGCTA 60.603 55.000 14.67 3.27 36.40 3.49
882 890 0.792640 CGTTTGGTCAGCTGTGCTAG 59.207 55.000 14.67 0.00 36.40 3.42
883 891 1.605457 CGTTTGGTCAGCTGTGCTAGA 60.605 52.381 14.67 0.00 36.40 2.43
884 892 2.072298 GTTTGGTCAGCTGTGCTAGAG 58.928 52.381 14.67 0.00 36.40 2.43
885 893 0.610174 TTGGTCAGCTGTGCTAGAGG 59.390 55.000 14.67 0.00 36.40 3.69
886 894 0.542938 TGGTCAGCTGTGCTAGAGGT 60.543 55.000 14.67 0.00 36.40 3.85
887 895 0.610687 GGTCAGCTGTGCTAGAGGTT 59.389 55.000 14.67 0.00 36.40 3.50
888 896 1.674221 GGTCAGCTGTGCTAGAGGTTG 60.674 57.143 14.67 0.00 36.40 3.77
889 897 0.610174 TCAGCTGTGCTAGAGGTTGG 59.390 55.000 14.67 0.00 36.40 3.77
890 898 0.322975 CAGCTGTGCTAGAGGTTGGT 59.677 55.000 5.25 0.00 36.40 3.67
891 899 1.059913 AGCTGTGCTAGAGGTTGGTT 58.940 50.000 0.00 0.00 36.99 3.67
892 900 1.002544 AGCTGTGCTAGAGGTTGGTTC 59.997 52.381 0.00 0.00 36.99 3.62
893 901 1.714794 CTGTGCTAGAGGTTGGTTCG 58.285 55.000 0.00 0.00 0.00 3.95
894 902 1.000955 CTGTGCTAGAGGTTGGTTCGT 59.999 52.381 0.00 0.00 0.00 3.85
895 903 1.000506 TGTGCTAGAGGTTGGTTCGTC 59.999 52.381 0.00 0.00 0.00 4.20
896 904 0.242825 TGCTAGAGGTTGGTTCGTCG 59.757 55.000 0.00 0.00 0.00 5.12
897 905 0.458025 GCTAGAGGTTGGTTCGTCGG 60.458 60.000 0.00 0.00 0.00 4.79
900 908 4.675029 AGGTTGGTTCGTCGGCGG 62.675 66.667 10.62 0.00 38.89 6.13
929 937 4.918810 TGAAAAGAGGCTGAAAACTTCC 57.081 40.909 0.00 0.00 0.00 3.46
1104 1124 2.364317 CTCCTCCTCCCGCCTCAA 60.364 66.667 0.00 0.00 0.00 3.02
1282 1302 0.972983 CGACCCTCCAGACCACATCT 60.973 60.000 0.00 0.00 38.66 2.90
1326 1346 2.158914 AGACATCCGCAGCATGAACATA 60.159 45.455 0.00 0.00 39.69 2.29
1327 1347 2.613595 GACATCCGCAGCATGAACATAA 59.386 45.455 0.00 0.00 39.69 1.90
1486 1513 1.579429 GCCGTGATTTGCGTTTCCT 59.421 52.632 0.00 0.00 0.00 3.36
1488 1515 0.591170 CCGTGATTTGCGTTTCCTGT 59.409 50.000 0.00 0.00 0.00 4.00
1491 1518 2.095768 CGTGATTTGCGTTTCCTGTGAT 60.096 45.455 0.00 0.00 0.00 3.06
1532 1559 1.971167 GCCACGCCAGTCCATTTCA 60.971 57.895 0.00 0.00 0.00 2.69
1533 1560 1.926511 GCCACGCCAGTCCATTTCAG 61.927 60.000 0.00 0.00 0.00 3.02
1534 1561 1.503542 CACGCCAGTCCATTTCAGC 59.496 57.895 0.00 0.00 0.00 4.26
1535 1562 1.675641 ACGCCAGTCCATTTCAGCC 60.676 57.895 0.00 0.00 0.00 4.85
1536 1563 1.377725 CGCCAGTCCATTTCAGCCT 60.378 57.895 0.00 0.00 0.00 4.58
1537 1564 0.962356 CGCCAGTCCATTTCAGCCTT 60.962 55.000 0.00 0.00 0.00 4.35
1538 1565 1.260544 GCCAGTCCATTTCAGCCTTT 58.739 50.000 0.00 0.00 0.00 3.11
1539 1566 1.203287 GCCAGTCCATTTCAGCCTTTC 59.797 52.381 0.00 0.00 0.00 2.62
1653 1683 8.322091 TCTCCATAGAGAATCGTGAGATGTATA 58.678 37.037 0.00 0.00 46.35 1.47
1865 1898 2.349438 CGCCATTTTGTCGCGCTATAAT 60.349 45.455 5.56 0.00 39.39 1.28
1900 1936 4.262635 GGAGAGGAAAGTCAGTTGTGATGA 60.263 45.833 0.00 0.00 34.36 2.92
1903 1939 4.330250 AGGAAAGTCAGTTGTGATGATGG 58.670 43.478 0.00 0.00 34.36 3.51
1906 1942 3.777106 AGTCAGTTGTGATGATGGTGT 57.223 42.857 0.00 0.00 34.36 4.16
1909 1945 2.553602 TCAGTTGTGATGATGGTGTTGC 59.446 45.455 0.00 0.00 0.00 4.17
1910 1946 2.555325 CAGTTGTGATGATGGTGTTGCT 59.445 45.455 0.00 0.00 0.00 3.91
1911 1947 3.752747 CAGTTGTGATGATGGTGTTGCTA 59.247 43.478 0.00 0.00 0.00 3.49
1913 1949 3.979101 TGTGATGATGGTGTTGCTAGA 57.021 42.857 0.00 0.00 0.00 2.43
1914 1950 4.492494 TGTGATGATGGTGTTGCTAGAT 57.508 40.909 0.00 0.00 0.00 1.98
1915 1951 4.193865 TGTGATGATGGTGTTGCTAGATG 58.806 43.478 0.00 0.00 0.00 2.90
1916 1952 3.562973 GTGATGATGGTGTTGCTAGATGG 59.437 47.826 0.00 0.00 0.00 3.51
1917 1953 2.715749 TGATGGTGTTGCTAGATGGG 57.284 50.000 0.00 0.00 0.00 4.00
1918 1954 1.915489 TGATGGTGTTGCTAGATGGGT 59.085 47.619 0.00 0.00 0.00 4.51
1919 1955 2.292267 GATGGTGTTGCTAGATGGGTG 58.708 52.381 0.00 0.00 0.00 4.61
1920 1956 1.064003 TGGTGTTGCTAGATGGGTGT 58.936 50.000 0.00 0.00 0.00 4.16
1921 1957 1.423541 TGGTGTTGCTAGATGGGTGTT 59.576 47.619 0.00 0.00 0.00 3.32
1922 1958 1.812571 GGTGTTGCTAGATGGGTGTTG 59.187 52.381 0.00 0.00 0.00 3.33
1923 1959 1.812571 GTGTTGCTAGATGGGTGTTGG 59.187 52.381 0.00 0.00 0.00 3.77
1924 1960 0.811281 GTTGCTAGATGGGTGTTGGC 59.189 55.000 0.00 0.00 0.00 4.52
2065 2101 1.464997 GGTTTCTGCATGGTTCGACTC 59.535 52.381 0.00 0.00 0.00 3.36
2095 2131 0.539051 AGTCCAGGAATCTCGGCAAG 59.461 55.000 0.00 0.00 0.00 4.01
2411 2475 3.628017 CAAAACTTCCACTGTTTAGGCG 58.372 45.455 0.00 0.00 36.72 5.52
3031 3339 0.708209 TGGGGTGTAGGAGCAGTAGA 59.292 55.000 0.00 0.00 0.00 2.59
3097 3405 5.621193 AGGTAACATACATGTATCTTGGGC 58.379 41.667 15.60 6.03 40.80 5.36
3109 3418 4.972568 TGTATCTTGGGCTTTATGGGTCTA 59.027 41.667 0.00 0.00 0.00 2.59
3170 3479 3.743396 CGATTAGTAGCTGAATTCTGGGC 59.257 47.826 13.50 11.29 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
766 774 2.092323 GCCGGAAAATCCTATATGCCC 58.908 52.381 5.05 0.00 33.30 5.36
793 801 0.537371 ATTAGTAAGCCGGCCATGCC 60.537 55.000 26.15 6.97 46.75 4.40
794 802 0.875059 GATTAGTAAGCCGGCCATGC 59.125 55.000 26.15 16.62 0.00 4.06
795 803 1.148310 CGATTAGTAAGCCGGCCATG 58.852 55.000 26.15 0.00 0.00 3.66
796 804 0.756903 ACGATTAGTAAGCCGGCCAT 59.243 50.000 26.15 15.94 0.00 4.40
797 805 0.179094 CACGATTAGTAAGCCGGCCA 60.179 55.000 26.15 8.93 0.00 5.36
798 806 1.496403 GCACGATTAGTAAGCCGGCC 61.496 60.000 26.15 8.19 0.00 6.13
799 807 1.496403 GGCACGATTAGTAAGCCGGC 61.496 60.000 21.89 21.89 33.12 6.13
800 808 0.878961 GGGCACGATTAGTAAGCCGG 60.879 60.000 0.00 0.00 41.41 6.13
801 809 0.878961 GGGGCACGATTAGTAAGCCG 60.879 60.000 5.15 5.63 41.41 5.52
802 810 0.534427 GGGGGCACGATTAGTAAGCC 60.534 60.000 2.91 2.91 40.20 4.35
803 811 0.179468 TGGGGGCACGATTAGTAAGC 59.821 55.000 0.00 0.00 0.00 3.09
804 812 2.494059 CATGGGGGCACGATTAGTAAG 58.506 52.381 0.00 0.00 0.00 2.34
805 813 1.142060 CCATGGGGGCACGATTAGTAA 59.858 52.381 2.85 0.00 0.00 2.24
806 814 0.762418 CCATGGGGGCACGATTAGTA 59.238 55.000 2.85 0.00 0.00 1.82
807 815 1.531748 CCATGGGGGCACGATTAGT 59.468 57.895 2.85 0.00 0.00 2.24
808 816 4.481195 CCATGGGGGCACGATTAG 57.519 61.111 2.85 0.00 0.00 1.73
829 837 2.902343 GCTAATCGGGCCAGGCAC 60.902 66.667 15.19 9.32 0.00 5.01
830 838 2.891941 CTTGCTAATCGGGCCAGGCA 62.892 60.000 15.19 2.16 0.00 4.75
831 839 2.124320 TTGCTAATCGGGCCAGGC 60.124 61.111 4.39 1.26 0.00 4.85
832 840 1.526917 CCTTGCTAATCGGGCCAGG 60.527 63.158 4.39 0.00 36.52 4.45
833 841 1.526917 CCCTTGCTAATCGGGCCAG 60.527 63.158 4.39 0.00 0.00 4.85
834 842 2.595095 CCCTTGCTAATCGGGCCA 59.405 61.111 4.39 0.00 0.00 5.36
837 845 2.591715 CGGCCCTTGCTAATCGGG 60.592 66.667 0.00 0.00 41.06 5.14
838 846 2.591715 CCGGCCCTTGCTAATCGG 60.592 66.667 0.00 0.00 37.74 4.18
839 847 2.591715 CCCGGCCCTTGCTAATCG 60.592 66.667 0.00 0.00 37.74 3.34
840 848 2.907407 GCCCGGCCCTTGCTAATC 60.907 66.667 0.00 0.00 37.74 1.75
841 849 4.522975 GGCCCGGCCCTTGCTAAT 62.523 66.667 18.83 0.00 44.06 1.73
859 867 3.365265 CAGCTGACCAAACGGGCC 61.365 66.667 8.42 0.00 42.05 5.80
860 868 2.594592 ACAGCTGACCAAACGGGC 60.595 61.111 23.35 0.00 42.05 6.13
861 869 2.908073 GCACAGCTGACCAAACGGG 61.908 63.158 23.35 0.00 44.81 5.28
862 870 0.602638 TAGCACAGCTGACCAAACGG 60.603 55.000 23.35 0.18 40.10 4.44
863 871 0.792640 CTAGCACAGCTGACCAAACG 59.207 55.000 23.35 0.44 40.10 3.60
864 872 2.072298 CTCTAGCACAGCTGACCAAAC 58.928 52.381 23.35 2.53 40.10 2.93
865 873 1.002430 CCTCTAGCACAGCTGACCAAA 59.998 52.381 23.35 0.39 40.10 3.28
866 874 0.610174 CCTCTAGCACAGCTGACCAA 59.390 55.000 23.35 1.93 40.10 3.67
867 875 0.542938 ACCTCTAGCACAGCTGACCA 60.543 55.000 23.35 0.00 40.10 4.02
868 876 0.610687 AACCTCTAGCACAGCTGACC 59.389 55.000 23.35 10.54 40.10 4.02
869 877 1.674221 CCAACCTCTAGCACAGCTGAC 60.674 57.143 23.35 12.21 40.10 3.51
870 878 0.610174 CCAACCTCTAGCACAGCTGA 59.390 55.000 23.35 0.00 40.10 4.26
871 879 0.322975 ACCAACCTCTAGCACAGCTG 59.677 55.000 13.48 13.48 40.10 4.24
872 880 1.002544 GAACCAACCTCTAGCACAGCT 59.997 52.381 0.00 0.00 43.41 4.24
873 881 1.443802 GAACCAACCTCTAGCACAGC 58.556 55.000 0.00 0.00 0.00 4.40
874 882 1.000955 ACGAACCAACCTCTAGCACAG 59.999 52.381 0.00 0.00 0.00 3.66
875 883 1.000506 GACGAACCAACCTCTAGCACA 59.999 52.381 0.00 0.00 0.00 4.57
876 884 1.711206 GACGAACCAACCTCTAGCAC 58.289 55.000 0.00 0.00 0.00 4.40
877 885 0.242825 CGACGAACCAACCTCTAGCA 59.757 55.000 0.00 0.00 0.00 3.49
878 886 0.458025 CCGACGAACCAACCTCTAGC 60.458 60.000 0.00 0.00 0.00 3.42
879 887 0.458025 GCCGACGAACCAACCTCTAG 60.458 60.000 0.00 0.00 0.00 2.43
880 888 1.588082 GCCGACGAACCAACCTCTA 59.412 57.895 0.00 0.00 0.00 2.43
881 889 2.342648 GCCGACGAACCAACCTCT 59.657 61.111 0.00 0.00 0.00 3.69
882 890 3.110178 CGCCGACGAACCAACCTC 61.110 66.667 0.00 0.00 43.93 3.85
883 891 4.675029 CCGCCGACGAACCAACCT 62.675 66.667 0.00 0.00 43.93 3.50
896 904 2.915137 TTTTCAACCAGGGCCGCC 60.915 61.111 0.00 0.00 0.00 6.13
897 905 1.866853 CTCTTTTCAACCAGGGCCGC 61.867 60.000 0.00 0.00 0.00 6.53
900 908 0.540597 AGCCTCTTTTCAACCAGGGC 60.541 55.000 0.00 0.00 38.50 5.19
907 915 4.709397 TGGAAGTTTTCAGCCTCTTTTCAA 59.291 37.500 0.00 0.00 0.00 2.69
1326 1346 3.055719 CCATGGCGGCAGTCGTTT 61.056 61.111 19.29 0.00 41.72 3.60
1486 1513 1.965930 GCACGTGGCCTTCATCACA 60.966 57.895 18.88 0.00 36.11 3.58
1488 1515 1.965930 GTGCACGTGGCCTTCATCA 60.966 57.895 18.88 0.42 43.89 3.07
1535 1562 2.440409 CCCATCAAGACCACCTGAAAG 58.560 52.381 0.00 0.00 0.00 2.62
1536 1563 1.547675 GCCCATCAAGACCACCTGAAA 60.548 52.381 0.00 0.00 0.00 2.69
1537 1564 0.038166 GCCCATCAAGACCACCTGAA 59.962 55.000 0.00 0.00 0.00 3.02
1538 1565 1.133181 TGCCCATCAAGACCACCTGA 61.133 55.000 0.00 0.00 0.00 3.86
1539 1566 0.033796 ATGCCCATCAAGACCACCTG 60.034 55.000 0.00 0.00 0.00 4.00
1653 1683 2.890945 GTGTACTGGGTTGCCTCAAATT 59.109 45.455 0.00 0.00 0.00 1.82
1865 1898 5.208121 ACTTTCCTCTCCCACATTTCAAAA 58.792 37.500 0.00 0.00 0.00 2.44
1900 1936 1.635487 ACACCCATCTAGCAACACCAT 59.365 47.619 0.00 0.00 0.00 3.55
1903 1939 1.812571 CCAACACCCATCTAGCAACAC 59.187 52.381 0.00 0.00 0.00 3.32
1906 1942 0.676466 CGCCAACACCCATCTAGCAA 60.676 55.000 0.00 0.00 0.00 3.91
1909 1945 0.036388 ACACGCCAACACCCATCTAG 60.036 55.000 0.00 0.00 0.00 2.43
1910 1946 0.398696 AACACGCCAACACCCATCTA 59.601 50.000 0.00 0.00 0.00 1.98
1911 1947 1.150536 AACACGCCAACACCCATCT 59.849 52.632 0.00 0.00 0.00 2.90
1913 1949 2.855514 GCAACACGCCAACACCCAT 61.856 57.895 0.00 0.00 32.94 4.00
1914 1950 3.522731 GCAACACGCCAACACCCA 61.523 61.111 0.00 0.00 32.94 4.51
1915 1951 3.483235 CTGCAACACGCCAACACCC 62.483 63.158 0.00 0.00 41.33 4.61
1916 1952 1.999071 TTCTGCAACACGCCAACACC 61.999 55.000 0.00 0.00 41.33 4.16
1917 1953 0.592247 CTTCTGCAACACGCCAACAC 60.592 55.000 0.00 0.00 41.33 3.32
1918 1954 0.746204 TCTTCTGCAACACGCCAACA 60.746 50.000 0.00 0.00 41.33 3.33
1919 1955 0.317020 GTCTTCTGCAACACGCCAAC 60.317 55.000 0.00 0.00 41.33 3.77
1920 1956 1.444119 GGTCTTCTGCAACACGCCAA 61.444 55.000 0.00 0.00 41.33 4.52
1921 1957 1.891919 GGTCTTCTGCAACACGCCA 60.892 57.895 0.00 0.00 41.33 5.69
1922 1958 1.237285 ATGGTCTTCTGCAACACGCC 61.237 55.000 0.00 0.00 41.33 5.68
1923 1959 0.593128 AATGGTCTTCTGCAACACGC 59.407 50.000 0.00 0.00 42.89 5.34
1924 1960 1.872952 TGAATGGTCTTCTGCAACACG 59.127 47.619 0.00 0.00 0.00 4.49
2065 2101 0.247460 TCCTGGACTGCATTGACTCG 59.753 55.000 0.00 0.00 0.00 4.18
2298 2343 5.724328 TGAACATGACATTAGTCCAGTCTC 58.276 41.667 0.00 0.00 44.33 3.36
2411 2475 5.294552 AGCGGAGAATAATAGAAAGCACAAC 59.705 40.000 0.00 0.00 0.00 3.32
3031 3339 1.900486 AGGTAGCTGCTTCGTTACCTT 59.100 47.619 13.90 1.24 45.28 3.50


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

AutoCloner maintained by Alex Coulton.