Multiple sequence alignment - TraesCS2D01G528700

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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 TraesCS2D01G528700 chr2D 100.000 3131 0 0 1 3131 616501059 616504189 0.000000e+00 5782.0
1 TraesCS2D01G528700 chr2A 96.377 1325 43 4 925 2247 746596524 746597845 0.000000e+00 2176.0
2 TraesCS2D01G528700 chr2A 94.195 913 23 8 2246 3131 746597875 746598784 0.000000e+00 1365.0
3 TraesCS2D01G528700 chr2A 91.969 635 44 4 80 713 749387149 749386521 0.000000e+00 883.0
4 TraesCS2D01G528700 chr2A 95.349 43 2 0 2359 2401 746598045 746598087 5.600000e-08 69.4
5 TraesCS2D01G528700 chr2B 95.987 1246 47 3 982 2226 751255911 751257154 0.000000e+00 2021.0
6 TraesCS2D01G528700 chr2B 91.741 896 59 9 2248 3131 751257216 751258108 0.000000e+00 1230.0
7 TraesCS2D01G528700 chr4B 93.568 653 40 2 62 713 497549265 497549916 0.000000e+00 972.0
8 TraesCS2D01G528700 chr1D 93.643 645 35 4 66 705 336562978 336562335 0.000000e+00 959.0
9 TraesCS2D01G528700 chr6A 92.427 647 43 4 67 712 579973884 579974525 0.000000e+00 918.0
10 TraesCS2D01G528700 chr4A 88.735 577 59 5 141 713 201708364 201707790 0.000000e+00 701.0
11 TraesCS2D01G528700 chrUn 90.546 476 37 5 238 711 16526008 16526477 9.540000e-175 623.0
12 TraesCS2D01G528700 chrUn 91.964 448 26 6 69 514 254880742 254881181 1.230000e-173 619.0
13 TraesCS2D01G528700 chrUn 91.946 447 27 5 69 514 183130444 183130882 4.440000e-173 617.0
14 TraesCS2D01G528700 chrUn 91.946 447 27 5 69 514 183182980 183183418 4.440000e-173 617.0
15 TraesCS2D01G528700 chrUn 93.689 206 11 2 513 717 183131006 183131210 1.090000e-79 307.0
16 TraesCS2D01G528700 chrUn 93.689 206 11 2 513 717 183183542 183183746 1.090000e-79 307.0
17 TraesCS2D01G528700 chrUn 93.689 206 11 2 513 717 254881305 254881509 1.090000e-79 307.0
18 TraesCS2D01G528700 chr5A 82.331 266 46 1 59 324 647649289 647649025 2.430000e-56 230.0


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 TraesCS2D01G528700 chr2D 616501059 616504189 3130 False 5782.000000 5782 100.0000 1 3131 1 chr2D.!!$F1 3130
1 TraesCS2D01G528700 chr2A 746596524 746598784 2260 False 1203.466667 2176 95.3070 925 3131 3 chr2A.!!$F1 2206
2 TraesCS2D01G528700 chr2A 749386521 749387149 628 True 883.000000 883 91.9690 80 713 1 chr2A.!!$R1 633
3 TraesCS2D01G528700 chr2B 751255911 751258108 2197 False 1625.500000 2021 93.8640 982 3131 2 chr2B.!!$F1 2149
4 TraesCS2D01G528700 chr4B 497549265 497549916 651 False 972.000000 972 93.5680 62 713 1 chr4B.!!$F1 651
5 TraesCS2D01G528700 chr1D 336562335 336562978 643 True 959.000000 959 93.6430 66 705 1 chr1D.!!$R1 639
6 TraesCS2D01G528700 chr6A 579973884 579974525 641 False 918.000000 918 92.4270 67 712 1 chr6A.!!$F1 645
7 TraesCS2D01G528700 chr4A 201707790 201708364 574 True 701.000000 701 88.7350 141 713 1 chr4A.!!$R1 572
8 TraesCS2D01G528700 chrUn 254880742 254881509 767 False 463.000000 619 92.8265 69 717 2 chrUn.!!$F4 648
9 TraesCS2D01G528700 chrUn 183130444 183131210 766 False 462.000000 617 92.8175 69 717 2 chrUn.!!$F2 648
10 TraesCS2D01G528700 chrUn 183182980 183183746 766 False 462.000000 617 92.8175 69 717 2 chrUn.!!$F3 648

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
901 1035 0.030705 AGAAGCTGAGGATGGGGCTA 60.031 55.0 0.0 0.0 34.4 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2416 2666 0.613853 TCTCCGGTTCCGATGGACTT 60.614 55.0 13.08 0.0 0.0 3.01 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
25 26 7.389803 TGGGCATATGGTTTTATCGATATTG 57.610 36.000 5.84 0.00 0.00 1.90
26 27 6.945435 TGGGCATATGGTTTTATCGATATTGT 59.055 34.615 5.84 0.00 0.00 2.71
27 28 7.450014 TGGGCATATGGTTTTATCGATATTGTT 59.550 33.333 5.84 0.00 0.00 2.83
28 29 8.303876 GGGCATATGGTTTTATCGATATTGTTT 58.696 33.333 5.84 0.00 0.00 2.83
29 30 9.691362 GGCATATGGTTTTATCGATATTGTTTT 57.309 29.630 5.84 0.00 0.00 2.43
153 154 3.364167 GCACGGTTTTATTTACTGCGACA 60.364 43.478 0.00 0.00 0.00 4.35
162 163 1.598882 TTACTGCGACATGTTTGGCA 58.401 45.000 16.13 16.13 0.00 4.92
182 183 3.000177 GCAAACGCCAAAAACTGTGTTAG 60.000 43.478 0.00 0.00 0.00 2.34
246 247 9.487442 TGCATAATAAAAAGATCCCTAAACCTT 57.513 29.630 0.00 0.00 0.00 3.50
296 300 1.729472 CGAGTCGGCCGCTAGATATTG 60.729 57.143 23.51 0.56 0.00 1.90
359 363 0.981183 TCCTGCGTGTTCCCTAATGT 59.019 50.000 0.00 0.00 0.00 2.71
383 387 7.621285 TGTAAATGAGATAGCTAGGCTGGATAT 59.379 37.037 8.46 8.46 40.10 1.63
417 421 4.437682 AAGGATCCGAAGCAATCCATAA 57.562 40.909 5.98 0.00 43.33 1.90
713 847 4.938226 ACTTTGCTATCAAACAGAGCCTAC 59.062 41.667 0.00 0.00 37.28 3.18
714 848 4.826274 TTGCTATCAAACAGAGCCTACT 57.174 40.909 0.00 0.00 35.24 2.57
715 849 4.392921 TGCTATCAAACAGAGCCTACTC 57.607 45.455 0.00 0.00 43.82 2.59
716 850 5.046304 TTTGCTATCAAACAGAGCCTACTCT 60.046 40.000 0.00 0.00 44.16 3.24
718 852 7.959940 TTTGCTATCAAACAGAGCCTACTCTTT 60.960 37.037 0.00 0.00 42.50 2.52
831 965 9.911788 ATATTTCAGAAGTATATTATGGGCCAG 57.088 33.333 13.78 0.00 0.00 4.85
832 966 6.763715 TTCAGAAGTATATTATGGGCCAGT 57.236 37.500 13.78 2.96 0.00 4.00
833 967 6.763715 TCAGAAGTATATTATGGGCCAGTT 57.236 37.500 13.78 0.00 0.00 3.16
834 968 7.149202 TCAGAAGTATATTATGGGCCAGTTT 57.851 36.000 13.78 0.00 0.00 2.66
835 969 7.582719 TCAGAAGTATATTATGGGCCAGTTTT 58.417 34.615 13.78 0.00 0.00 2.43
836 970 8.058847 TCAGAAGTATATTATGGGCCAGTTTTT 58.941 33.333 13.78 0.00 0.00 1.94
853 987 4.492604 TTTTTGGACGCCTCCCAG 57.507 55.556 0.00 0.00 35.34 4.45
854 988 1.534697 TTTTTGGACGCCTCCCAGT 59.465 52.632 0.00 0.00 35.34 4.00
855 989 0.106419 TTTTTGGACGCCTCCCAGTT 60.106 50.000 0.00 0.00 35.34 3.16
856 990 0.106419 TTTTGGACGCCTCCCAGTTT 60.106 50.000 0.00 0.00 35.34 2.66
857 991 0.536460 TTTGGACGCCTCCCAGTTTC 60.536 55.000 0.00 0.00 35.34 2.78
858 992 1.415672 TTGGACGCCTCCCAGTTTCT 61.416 55.000 0.00 0.00 35.34 2.52
859 993 1.079057 GGACGCCTCCCAGTTTCTC 60.079 63.158 0.00 0.00 0.00 2.87
860 994 1.079057 GACGCCTCCCAGTTTCTCC 60.079 63.158 0.00 0.00 0.00 3.71
861 995 2.125512 CGCCTCCCAGTTTCTCCG 60.126 66.667 0.00 0.00 0.00 4.63
862 996 2.269241 GCCTCCCAGTTTCTCCGG 59.731 66.667 0.00 0.00 0.00 5.14
863 997 2.593956 GCCTCCCAGTTTCTCCGGT 61.594 63.158 0.00 0.00 0.00 5.28
864 998 2.067197 CCTCCCAGTTTCTCCGGTT 58.933 57.895 0.00 0.00 0.00 4.44
865 999 0.400594 CCTCCCAGTTTCTCCGGTTT 59.599 55.000 0.00 0.00 0.00 3.27
866 1000 1.202891 CCTCCCAGTTTCTCCGGTTTT 60.203 52.381 0.00 0.00 0.00 2.43
867 1001 2.583143 CTCCCAGTTTCTCCGGTTTTT 58.417 47.619 0.00 0.00 0.00 1.94
887 1021 5.633830 TTTTGGACAATCATGAGAGAAGC 57.366 39.130 0.09 0.00 0.00 3.86
888 1022 4.564782 TTGGACAATCATGAGAGAAGCT 57.435 40.909 0.09 0.00 0.00 3.74
889 1023 3.870274 TGGACAATCATGAGAGAAGCTG 58.130 45.455 0.09 0.00 0.00 4.24
890 1024 3.516700 TGGACAATCATGAGAGAAGCTGA 59.483 43.478 0.09 0.00 0.00 4.26
891 1025 4.121317 GGACAATCATGAGAGAAGCTGAG 58.879 47.826 0.09 0.00 0.00 3.35
892 1026 4.121317 GACAATCATGAGAGAAGCTGAGG 58.879 47.826 0.09 0.00 0.00 3.86
893 1027 3.773667 ACAATCATGAGAGAAGCTGAGGA 59.226 43.478 0.09 0.00 0.00 3.71
894 1028 4.409574 ACAATCATGAGAGAAGCTGAGGAT 59.590 41.667 0.09 0.00 32.61 3.24
895 1029 4.610605 ATCATGAGAGAAGCTGAGGATG 57.389 45.455 0.09 0.00 30.11 3.51
896 1030 2.699321 TCATGAGAGAAGCTGAGGATGG 59.301 50.000 0.00 0.00 0.00 3.51
897 1031 1.493861 TGAGAGAAGCTGAGGATGGG 58.506 55.000 0.00 0.00 0.00 4.00
898 1032 0.758123 GAGAGAAGCTGAGGATGGGG 59.242 60.000 0.00 0.00 0.00 4.96
899 1033 1.148048 GAGAAGCTGAGGATGGGGC 59.852 63.158 0.00 0.00 0.00 5.80
900 1034 1.307691 AGAAGCTGAGGATGGGGCT 60.308 57.895 0.00 0.00 36.53 5.19
901 1035 0.030705 AGAAGCTGAGGATGGGGCTA 60.031 55.000 0.00 0.00 34.40 3.93
902 1036 1.063183 GAAGCTGAGGATGGGGCTAT 58.937 55.000 0.00 0.00 34.40 2.97
903 1037 1.423161 GAAGCTGAGGATGGGGCTATT 59.577 52.381 0.00 0.00 34.40 1.73
904 1038 1.063183 AGCTGAGGATGGGGCTATTC 58.937 55.000 0.00 0.00 32.94 1.75
905 1039 0.037447 GCTGAGGATGGGGCTATTCC 59.963 60.000 0.00 0.00 0.00 3.01
906 1040 1.739750 CTGAGGATGGGGCTATTCCT 58.260 55.000 2.95 2.95 42.58 3.36
907 1041 1.350351 CTGAGGATGGGGCTATTCCTG 59.650 57.143 7.26 0.00 39.98 3.86
908 1042 0.037447 GAGGATGGGGCTATTCCTGC 59.963 60.000 7.26 0.00 39.98 4.85
915 1049 3.780624 GGCTATTCCTGCCGAAAGA 57.219 52.632 0.00 0.00 41.03 2.52
916 1050 2.038387 GGCTATTCCTGCCGAAAGAA 57.962 50.000 0.00 0.00 41.03 2.52
917 1051 1.671328 GGCTATTCCTGCCGAAAGAAC 59.329 52.381 0.00 0.00 41.03 3.01
918 1052 2.633488 GCTATTCCTGCCGAAAGAACT 58.367 47.619 0.00 0.00 33.08 3.01
919 1053 2.352960 GCTATTCCTGCCGAAAGAACTG 59.647 50.000 0.00 0.00 33.08 3.16
920 1054 1.826385 ATTCCTGCCGAAAGAACTGG 58.174 50.000 0.00 0.00 33.08 4.00
935 1069 5.022227 AGAACTGGCCCTATATCAGATCT 57.978 43.478 0.00 0.00 36.35 2.75
936 1070 5.410602 AGAACTGGCCCTATATCAGATCTT 58.589 41.667 0.00 0.00 37.36 2.40
937 1071 5.483583 AGAACTGGCCCTATATCAGATCTTC 59.516 44.000 0.00 0.00 37.36 2.87
938 1072 3.766591 ACTGGCCCTATATCAGATCTTCG 59.233 47.826 0.00 0.00 33.19 3.79
941 1075 3.100671 GCCCTATATCAGATCTTCGGGT 58.899 50.000 0.00 0.00 33.00 5.28
942 1076 4.279145 GCCCTATATCAGATCTTCGGGTA 58.721 47.826 0.00 0.00 33.00 3.69
943 1077 4.339814 GCCCTATATCAGATCTTCGGGTAG 59.660 50.000 0.00 0.00 33.00 3.18
964 1100 0.105658 CCCCTGCCTGGCTAGTACTA 60.106 60.000 21.03 1.89 0.00 1.82
966 1102 1.411787 CCCTGCCTGGCTAGTACTACT 60.412 57.143 21.03 0.00 0.00 2.57
967 1103 1.683917 CCTGCCTGGCTAGTACTACTG 59.316 57.143 21.03 0.00 0.00 2.74
968 1104 2.656002 CTGCCTGGCTAGTACTACTGA 58.344 52.381 21.03 0.00 0.00 3.41
1097 1234 1.002274 ACCTCCGCCTCTTCTCCAT 59.998 57.895 0.00 0.00 0.00 3.41
1240 1377 2.348998 CCGTGCTTGCCTTCCTCT 59.651 61.111 0.00 0.00 0.00 3.69
1335 1472 3.264845 GCCACCCTCTCCCCCAAA 61.265 66.667 0.00 0.00 0.00 3.28
1705 1842 2.768344 CCAGCCCCGGGATGTACT 60.768 66.667 26.32 8.18 37.40 2.73
1740 1877 3.112075 CTGCACAACGTCGGCGAT 61.112 61.111 20.03 0.00 42.00 4.58
1880 2017 1.228245 GCAAGGTGGAGTTCCTGCA 60.228 57.895 5.52 0.00 35.27 4.41
1883 2020 2.360475 GGTGGAGTTCCTGCAGGC 60.360 66.667 28.91 15.23 31.31 4.85
1890 2027 4.641645 TTCCTGCAGGCCACCGTG 62.642 66.667 28.91 1.49 34.44 4.94
2019 2156 0.530744 TGGACATCGGGAAGACGAAG 59.469 55.000 0.00 0.00 46.92 3.79
2027 2164 1.469940 CGGGAAGACGAAGATGGTGAG 60.470 57.143 0.00 0.00 35.47 3.51
2127 2264 2.159170 GCTGTATCCTCAAGCTCGAGTT 60.159 50.000 15.13 4.78 0.00 3.01
2128 2265 3.677424 GCTGTATCCTCAAGCTCGAGTTT 60.677 47.826 15.13 12.00 0.00 2.66
2132 2269 2.960819 TCCTCAAGCTCGAGTTTAAGC 58.039 47.619 14.51 0.00 38.84 3.09
2282 2474 1.336440 TCGTTCTGCATTTTGTGTGGG 59.664 47.619 0.00 0.00 0.00 4.61
2294 2487 4.657436 TTTGTGTGGGGTTTGAACATAC 57.343 40.909 0.00 0.00 0.00 2.39
2362 2555 6.677781 TTTCAAATTCCATCGTCTGTATCC 57.322 37.500 0.00 0.00 0.00 2.59
2393 2643 4.212636 CGACACCGGTCAAGTTTAAGAAAT 59.787 41.667 2.59 0.00 44.54 2.17
2421 2671 2.778299 TGTGGCATAACACAGAAGTCC 58.222 47.619 0.00 0.00 45.70 3.85
2423 2673 3.244875 TGTGGCATAACACAGAAGTCCAT 60.245 43.478 0.00 0.00 45.70 3.41
2433 2683 0.613853 AGAAGTCCATCGGAACCGGA 60.614 55.000 9.46 0.23 40.25 5.14
2641 2895 7.552687 CCTAATACATTAGCACACTGAAGGAAA 59.447 37.037 3.82 0.00 38.69 3.13
2839 3102 1.526917 GGCAGCAGTTGACACCAGT 60.527 57.895 0.00 0.00 33.76 4.00
2846 3109 2.682856 GCAGTTGACACCAGTTCAAGAA 59.317 45.455 0.00 0.00 0.00 2.52
3055 3318 1.705337 CTATTGCCTTGGCCACGTCG 61.705 60.000 3.88 0.00 0.00 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.391148 ACAATATCGATAAAACCATATGCCC 57.609 36.000 9.61 0.00 0.00 5.36
48 49 9.660544 AGGGCCTAATTTGTAAAAATATCTGAT 57.339 29.630 2.82 0.00 0.00 2.90
49 50 8.912988 CAGGGCCTAATTTGTAAAAATATCTGA 58.087 33.333 5.28 0.00 0.00 3.27
50 51 8.695456 ACAGGGCCTAATTTGTAAAAATATCTG 58.305 33.333 5.28 0.00 0.00 2.90
51 52 8.838649 ACAGGGCCTAATTTGTAAAAATATCT 57.161 30.769 5.28 0.00 0.00 1.98
52 53 9.884636 AAACAGGGCCTAATTTGTAAAAATATC 57.115 29.630 5.28 0.00 0.00 1.63
53 54 9.665719 CAAACAGGGCCTAATTTGTAAAAATAT 57.334 29.630 24.44 0.00 0.00 1.28
54 55 8.871125 TCAAACAGGGCCTAATTTGTAAAAATA 58.129 29.630 28.34 14.02 34.40 1.40
55 56 7.740805 TCAAACAGGGCCTAATTTGTAAAAAT 58.259 30.769 28.34 1.49 34.40 1.82
56 57 7.125792 TCAAACAGGGCCTAATTTGTAAAAA 57.874 32.000 28.34 15.03 34.40 1.94
57 58 6.732896 TCAAACAGGGCCTAATTTGTAAAA 57.267 33.333 28.34 15.30 34.40 1.52
58 59 6.926630 ATCAAACAGGGCCTAATTTGTAAA 57.073 33.333 28.34 17.47 34.40 2.01
59 60 6.696411 CAATCAAACAGGGCCTAATTTGTAA 58.304 36.000 28.34 17.97 34.40 2.41
60 61 5.337169 GCAATCAAACAGGGCCTAATTTGTA 60.337 40.000 28.34 20.21 34.40 2.41
61 62 4.563374 GCAATCAAACAGGGCCTAATTTGT 60.563 41.667 28.34 18.87 34.40 2.83
62 63 3.934579 GCAATCAAACAGGGCCTAATTTG 59.065 43.478 25.85 25.85 34.11 2.32
63 64 3.582208 TGCAATCAAACAGGGCCTAATTT 59.418 39.130 5.28 7.50 0.00 1.82
64 65 3.172339 TGCAATCAAACAGGGCCTAATT 58.828 40.909 5.28 0.00 0.00 1.40
65 66 2.818921 TGCAATCAAACAGGGCCTAAT 58.181 42.857 5.28 0.00 0.00 1.73
125 126 6.192360 GCAGTAAATAAAACCGTGCTATCTG 58.808 40.000 0.00 0.00 0.00 2.90
131 132 3.158268 GTCGCAGTAAATAAAACCGTGC 58.842 45.455 0.00 0.00 0.00 5.34
162 163 4.443913 ACTAACACAGTTTTTGGCGTTT 57.556 36.364 0.00 0.00 31.59 3.60
267 271 0.099968 CGGCCGACTCGTTTCTATCA 59.900 55.000 24.07 0.00 0.00 2.15
270 274 1.026182 TAGCGGCCGACTCGTTTCTA 61.026 55.000 33.48 15.21 0.00 2.10
296 300 4.937620 TGATAGCCAGATGAGTTTGTTGAC 59.062 41.667 0.00 0.00 0.00 3.18
359 363 7.621285 ACATATCCAGCCTAGCTATCTCATTTA 59.379 37.037 0.00 0.00 36.40 1.40
383 387 5.869649 TCGGATCCTTTCTATGATCAACA 57.130 39.130 10.75 0.00 39.30 3.33
417 421 5.306678 CCTTGGCTGATCTCTAAAGGATAGT 59.693 44.000 10.52 0.00 37.02 2.12
464 468 8.067189 GGTGATTAGTAGTAGTACTCGTTAAGC 58.933 40.741 13.60 6.42 40.23 3.09
546 679 8.032451 ACACCATGTAATGCTGTAAAATTTACC 58.968 33.333 12.72 0.12 41.12 2.85
686 820 5.163814 GGCTCTGTTTGATAGCAAAGTACTG 60.164 44.000 6.36 0.72 44.12 2.74
805 939 9.911788 CTGGCCCATAATATACTTCTGAAATAT 57.088 33.333 0.00 0.00 0.00 1.28
806 940 8.890472 ACTGGCCCATAATATACTTCTGAAATA 58.110 33.333 0.00 0.00 0.00 1.40
807 941 7.759607 ACTGGCCCATAATATACTTCTGAAAT 58.240 34.615 0.00 0.00 0.00 2.17
808 942 7.149202 ACTGGCCCATAATATACTTCTGAAA 57.851 36.000 0.00 0.00 0.00 2.69
809 943 6.763715 ACTGGCCCATAATATACTTCTGAA 57.236 37.500 0.00 0.00 0.00 3.02
810 944 6.763715 AACTGGCCCATAATATACTTCTGA 57.236 37.500 0.00 0.00 0.00 3.27
811 945 7.823745 AAAACTGGCCCATAATATACTTCTG 57.176 36.000 0.00 0.00 0.00 3.02
836 970 0.106419 AACTGGGAGGCGTCCAAAAA 60.106 50.000 25.86 8.25 46.07 1.94
837 971 0.106419 AAACTGGGAGGCGTCCAAAA 60.106 50.000 25.86 10.62 46.07 2.44
838 972 0.536460 GAAACTGGGAGGCGTCCAAA 60.536 55.000 25.86 13.03 46.07 3.28
839 973 1.072505 GAAACTGGGAGGCGTCCAA 59.927 57.895 25.86 15.15 46.07 3.53
840 974 1.827399 GAGAAACTGGGAGGCGTCCA 61.827 60.000 25.86 11.76 46.07 4.02
841 975 1.079057 GAGAAACTGGGAGGCGTCC 60.079 63.158 17.33 17.33 43.05 4.79
842 976 1.079057 GGAGAAACTGGGAGGCGTC 60.079 63.158 0.00 0.00 0.00 5.19
843 977 2.943978 CGGAGAAACTGGGAGGCGT 61.944 63.158 0.00 0.00 0.00 5.68
844 978 2.125512 CGGAGAAACTGGGAGGCG 60.126 66.667 0.00 0.00 0.00 5.52
845 979 2.269241 CCGGAGAAACTGGGAGGC 59.731 66.667 0.00 0.00 41.14 4.70
864 998 5.771666 AGCTTCTCTCATGATTGTCCAAAAA 59.228 36.000 0.00 0.00 0.00 1.94
865 999 5.182570 CAGCTTCTCTCATGATTGTCCAAAA 59.817 40.000 0.00 0.00 0.00 2.44
866 1000 4.698780 CAGCTTCTCTCATGATTGTCCAAA 59.301 41.667 0.00 0.00 0.00 3.28
867 1001 4.019950 TCAGCTTCTCTCATGATTGTCCAA 60.020 41.667 0.00 0.00 0.00 3.53
868 1002 3.516700 TCAGCTTCTCTCATGATTGTCCA 59.483 43.478 0.00 0.00 0.00 4.02
869 1003 4.121317 CTCAGCTTCTCTCATGATTGTCC 58.879 47.826 0.00 0.00 0.00 4.02
870 1004 4.121317 CCTCAGCTTCTCTCATGATTGTC 58.879 47.826 0.00 0.00 0.00 3.18
871 1005 3.773667 TCCTCAGCTTCTCTCATGATTGT 59.226 43.478 0.00 0.00 0.00 2.71
872 1006 4.403585 TCCTCAGCTTCTCTCATGATTG 57.596 45.455 0.00 0.00 0.00 2.67
873 1007 4.202377 CCATCCTCAGCTTCTCTCATGATT 60.202 45.833 0.00 0.00 0.00 2.57
874 1008 3.325425 CCATCCTCAGCTTCTCTCATGAT 59.675 47.826 0.00 0.00 0.00 2.45
875 1009 2.699321 CCATCCTCAGCTTCTCTCATGA 59.301 50.000 0.00 0.00 0.00 3.07
876 1010 2.224329 CCCATCCTCAGCTTCTCTCATG 60.224 54.545 0.00 0.00 0.00 3.07
877 1011 2.048601 CCCATCCTCAGCTTCTCTCAT 58.951 52.381 0.00 0.00 0.00 2.90
878 1012 1.493861 CCCATCCTCAGCTTCTCTCA 58.506 55.000 0.00 0.00 0.00 3.27
879 1013 0.758123 CCCCATCCTCAGCTTCTCTC 59.242 60.000 0.00 0.00 0.00 3.20
880 1014 1.344191 GCCCCATCCTCAGCTTCTCT 61.344 60.000 0.00 0.00 0.00 3.10
881 1015 1.148048 GCCCCATCCTCAGCTTCTC 59.852 63.158 0.00 0.00 0.00 2.87
882 1016 0.030705 TAGCCCCATCCTCAGCTTCT 60.031 55.000 0.00 0.00 36.79 2.85
883 1017 1.063183 ATAGCCCCATCCTCAGCTTC 58.937 55.000 0.00 0.00 36.79 3.86
884 1018 1.423161 GAATAGCCCCATCCTCAGCTT 59.577 52.381 0.00 0.00 36.79 3.74
885 1019 1.063183 GAATAGCCCCATCCTCAGCT 58.937 55.000 0.00 0.00 39.37 4.24
886 1020 0.037447 GGAATAGCCCCATCCTCAGC 59.963 60.000 0.00 0.00 0.00 4.26
887 1021 1.350351 CAGGAATAGCCCCATCCTCAG 59.650 57.143 0.00 0.00 41.63 3.35
888 1022 1.438469 CAGGAATAGCCCCATCCTCA 58.562 55.000 0.00 0.00 41.63 3.86
889 1023 0.037447 GCAGGAATAGCCCCATCCTC 59.963 60.000 0.00 0.00 41.63 3.71
890 1024 1.430369 GGCAGGAATAGCCCCATCCT 61.430 60.000 0.00 0.00 46.50 3.24
891 1025 1.075659 GGCAGGAATAGCCCCATCC 59.924 63.158 0.00 0.00 46.50 3.51
892 1026 4.830573 GGCAGGAATAGCCCCATC 57.169 61.111 0.00 0.00 46.50 3.51
898 1032 2.352960 CAGTTCTTTCGGCAGGAATAGC 59.647 50.000 0.00 0.00 33.85 2.97
899 1033 2.939103 CCAGTTCTTTCGGCAGGAATAG 59.061 50.000 0.00 0.00 33.85 1.73
900 1034 2.939640 GCCAGTTCTTTCGGCAGGAATA 60.940 50.000 0.00 0.00 45.52 1.75
901 1035 1.826385 CCAGTTCTTTCGGCAGGAAT 58.174 50.000 0.00 0.00 33.85 3.01
902 1036 0.889186 GCCAGTTCTTTCGGCAGGAA 60.889 55.000 0.00 0.00 45.52 3.36
903 1037 1.302511 GCCAGTTCTTTCGGCAGGA 60.303 57.895 0.00 0.00 45.52 3.86
904 1038 3.267974 GCCAGTTCTTTCGGCAGG 58.732 61.111 0.00 0.00 45.52 4.85
907 1041 0.107165 ATAGGGCCAGTTCTTTCGGC 60.107 55.000 6.18 0.00 45.47 5.54
908 1042 3.071023 TGATATAGGGCCAGTTCTTTCGG 59.929 47.826 6.18 0.00 0.00 4.30
909 1043 4.039245 TCTGATATAGGGCCAGTTCTTTCG 59.961 45.833 6.18 0.00 0.00 3.46
910 1044 5.552870 TCTGATATAGGGCCAGTTCTTTC 57.447 43.478 6.18 0.00 0.00 2.62
911 1045 5.848921 AGATCTGATATAGGGCCAGTTCTTT 59.151 40.000 6.18 0.00 34.92 2.52
912 1046 5.410602 AGATCTGATATAGGGCCAGTTCTT 58.589 41.667 6.18 0.00 34.92 2.52
913 1047 5.022227 AGATCTGATATAGGGCCAGTTCT 57.978 43.478 6.18 0.00 34.16 3.01
914 1048 5.623368 CGAAGATCTGATATAGGGCCAGTTC 60.623 48.000 6.18 0.00 0.00 3.01
915 1049 4.221703 CGAAGATCTGATATAGGGCCAGTT 59.778 45.833 6.18 0.00 0.00 3.16
916 1050 3.766591 CGAAGATCTGATATAGGGCCAGT 59.233 47.826 6.18 0.00 0.00 4.00
917 1051 3.131933 CCGAAGATCTGATATAGGGCCAG 59.868 52.174 6.18 0.00 0.00 4.85
918 1052 3.099905 CCGAAGATCTGATATAGGGCCA 58.900 50.000 6.18 0.00 0.00 5.36
919 1053 2.432510 CCCGAAGATCTGATATAGGGCC 59.567 54.545 11.24 0.00 0.00 5.80
920 1054 3.100671 ACCCGAAGATCTGATATAGGGC 58.899 50.000 19.43 0.00 41.18 5.19
921 1055 4.890581 CCTACCCGAAGATCTGATATAGGG 59.109 50.000 18.46 18.46 43.03 3.53
922 1056 4.339814 GCCTACCCGAAGATCTGATATAGG 59.660 50.000 0.00 6.03 0.00 2.57
923 1057 4.339814 GGCCTACCCGAAGATCTGATATAG 59.660 50.000 0.00 0.00 0.00 1.31
953 1089 1.283029 ACGGGTCAGTAGTACTAGCCA 59.717 52.381 18.46 0.00 0.00 4.75
960 1096 1.538047 GGACACACGGGTCAGTAGTA 58.462 55.000 1.22 0.00 39.59 1.82
964 1100 4.295119 GCGGACACACGGGTCAGT 62.295 66.667 1.22 0.00 39.59 3.41
1097 1234 4.404098 GCGGCTCCTTTTCCCCGA 62.404 66.667 1.67 0.00 43.20 5.14
1230 1367 3.306595 CTGCGAGCAGAGGAAGGCA 62.307 63.158 19.40 0.00 46.30 4.75
1323 1460 0.394352 CGGTGAATTTGGGGGAGAGG 60.394 60.000 0.00 0.00 0.00 3.69
1705 1842 4.717629 CGCGAAGAGGCACCACGA 62.718 66.667 0.00 0.00 0.00 4.35
1906 2043 2.668632 GGGGTTCCTGACGATGCA 59.331 61.111 0.00 0.00 0.00 3.96
2019 2156 1.746220 AGTCTCACTACGCTCACCATC 59.254 52.381 0.00 0.00 0.00 3.51
2027 2164 2.202623 CCGGCAGTCTCACTACGC 60.203 66.667 0.00 0.00 0.00 4.42
2055 2192 3.868757 TTCAGAATGTACCTCTCCACG 57.131 47.619 0.00 0.00 37.40 4.94
2127 2264 4.282195 CCCCTGTTTTATGTTGTGGCTTAA 59.718 41.667 0.00 0.00 0.00 1.85
2128 2265 3.829601 CCCCTGTTTTATGTTGTGGCTTA 59.170 43.478 0.00 0.00 0.00 3.09
2132 2269 2.962421 ACACCCCTGTTTTATGTTGTGG 59.038 45.455 0.00 0.00 0.00 4.17
2282 2474 6.243811 TGTAAATCGGTGTATGTTCAAACC 57.756 37.500 0.00 0.00 0.00 3.27
2393 2643 5.555966 TCTGTGTTATGCCACATTCAGTTA 58.444 37.500 0.00 0.00 43.91 2.24
2416 2666 0.613853 TCTCCGGTTCCGATGGACTT 60.614 55.000 13.08 0.00 0.00 3.01
2421 2671 1.739338 CTCCCTCTCCGGTTCCGATG 61.739 65.000 13.08 5.14 0.00 3.84
2423 2673 2.044252 CTCCCTCTCCGGTTCCGA 60.044 66.667 13.08 0.00 0.00 4.55
2433 2683 3.791320 TGAACATGGTAACTCTCCCTCT 58.209 45.455 0.00 0.00 37.61 3.69
2641 2895 5.657826 TGGCATGCATTTTGTGTATAAGT 57.342 34.783 21.36 0.00 31.44 2.24
3055 3318 4.144703 GGACCTTCGGAGTCGGCC 62.145 72.222 0.00 0.00 34.97 6.13


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

AutoCloner maintained by Alex Coulton.