Multiple sequence alignment - TraesCS6A01G361900

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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 TraesCS6A01G361900 chr6A 100.000 2157 0 0 1 2157 592029283 592031439 0.000000e+00 3984.0
1 TraesCS6A01G361900 chr6A 87.109 256 29 4 941 1195 592010410 592010662 9.740000e-74 287.0
2 TraesCS6A01G361900 chr6A 87.047 193 21 4 1005 1196 596540377 596540188 4.660000e-52 215.0
3 TraesCS6A01G361900 chr6D 96.231 849 30 2 1306 2153 445493685 445494532 0.000000e+00 1389.0
4 TraesCS6A01G361900 chr6D 88.981 363 37 3 947 1306 445493270 445493632 1.520000e-121 446.0
5 TraesCS6A01G361900 chr6D 86.822 258 31 3 939 1195 445192891 445193146 3.500000e-73 285.0
6 TraesCS6A01G361900 chr6D 86.822 258 31 3 939 1195 445265379 445265634 3.500000e-73 285.0
7 TraesCS6A01G361900 chr6D 90.000 70 3 2 1698 1766 445337387 445337453 1.060000e-13 87.9
8 TraesCS6A01G361900 chr6B 95.216 857 33 6 1305 2157 671163267 671162415 0.000000e+00 1349.0
9 TraesCS6A01G361900 chr6B 90.358 363 32 3 947 1306 671163671 671163309 6.970000e-130 473.0
10 TraesCS6A01G361900 chr6B 87.047 193 21 4 1005 1196 684719050 684718861 4.660000e-52 215.0
11 TraesCS6A01G361900 chr2A 87.500 832 78 14 6 827 215391332 215390517 0.000000e+00 937.0
12 TraesCS6A01G361900 chr2D 85.349 860 90 23 1 832 619873115 619872264 0.000000e+00 857.0
13 TraesCS6A01G361900 chr2D 84.155 852 102 24 1 827 37872518 37873361 0.000000e+00 795.0
14 TraesCS6A01G361900 chr2D 83.882 850 104 17 1 827 557440227 557441066 0.000000e+00 780.0
15 TraesCS6A01G361900 chr4D 85.146 855 94 22 1 827 110190392 110191241 0.000000e+00 845.0
16 TraesCS6A01G361900 chr4D 84.736 832 102 14 10 827 489879242 489878422 0.000000e+00 809.0
17 TraesCS6A01G361900 chr7D 86.430 759 73 19 1 744 156212539 156211796 0.000000e+00 804.0
18 TraesCS6A01G361900 chr1D 84.522 827 92 24 1 798 419715829 419715010 0.000000e+00 785.0
19 TraesCS6A01G361900 chr3D 84.829 791 96 17 1 771 524209735 524210521 0.000000e+00 774.0
20 TraesCS6A01G361900 chrUn 87.047 193 21 4 1005 1196 234300454 234300643 4.660000e-52 215.0
21 TraesCS6A01G361900 chrUn 87.047 193 21 4 1005 1196 387880512 387880701 4.660000e-52 215.0


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 TraesCS6A01G361900 chr6A 592029283 592031439 2156 False 3984.0 3984 100.000 1 2157 1 chr6A.!!$F2 2156
1 TraesCS6A01G361900 chr6D 445493270 445494532 1262 False 917.5 1389 92.606 947 2153 2 chr6D.!!$F4 1206
2 TraesCS6A01G361900 chr6B 671162415 671163671 1256 True 911.0 1349 92.787 947 2157 2 chr6B.!!$R2 1210
3 TraesCS6A01G361900 chr2A 215390517 215391332 815 True 937.0 937 87.500 6 827 1 chr2A.!!$R1 821
4 TraesCS6A01G361900 chr2D 619872264 619873115 851 True 857.0 857 85.349 1 832 1 chr2D.!!$R1 831
5 TraesCS6A01G361900 chr2D 37872518 37873361 843 False 795.0 795 84.155 1 827 1 chr2D.!!$F1 826
6 TraesCS6A01G361900 chr2D 557440227 557441066 839 False 780.0 780 83.882 1 827 1 chr2D.!!$F2 826
7 TraesCS6A01G361900 chr4D 110190392 110191241 849 False 845.0 845 85.146 1 827 1 chr4D.!!$F1 826
8 TraesCS6A01G361900 chr4D 489878422 489879242 820 True 809.0 809 84.736 10 827 1 chr4D.!!$R1 817
9 TraesCS6A01G361900 chr7D 156211796 156212539 743 True 804.0 804 86.430 1 744 1 chr7D.!!$R1 743
10 TraesCS6A01G361900 chr1D 419715010 419715829 819 True 785.0 785 84.522 1 798 1 chr1D.!!$R1 797
11 TraesCS6A01G361900 chr3D 524209735 524210521 786 False 774.0 774 84.829 1 771 1 chr3D.!!$F1 770

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
860 922 0.171455 GCTACAGAGACACGACCAGG 59.829 60.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1838 1972 0.249489 AGTGTGTCGACAAGTGGCTC 60.249 55.0 21.95 8.38 32.49 4.7 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
145 155 2.282180 GTCAAGCCGAAGCCCCAA 60.282 61.111 0.00 0.00 41.25 4.12
234 245 3.062466 CTCGTCCTCGTCAGGCCA 61.062 66.667 5.01 0.00 40.12 5.36
372 383 3.237741 CGGGCCCTGGAGGAGATC 61.238 72.222 22.43 0.00 38.24 2.75
575 618 0.461548 CTCGGCATGTAGAGCAAGGA 59.538 55.000 6.63 0.00 0.00 3.36
583 626 3.064987 TAGAGCAAGGACGGCGAGC 62.065 63.158 16.62 9.39 36.08 5.03
678 737 2.788786 CGAACTTTGCTTGAATTTGCGT 59.211 40.909 0.00 0.00 0.00 5.24
689 748 2.159503 TGAATTTGCGTCGTGTTTGTGT 60.160 40.909 0.00 0.00 0.00 3.72
690 749 2.553079 ATTTGCGTCGTGTTTGTGTT 57.447 40.000 0.00 0.00 0.00 3.32
697 756 4.029704 GCGTCGTGTTTGTGTTGAATTTA 58.970 39.130 0.00 0.00 0.00 1.40
700 759 6.291374 GCGTCGTGTTTGTGTTGAATTTAAAT 60.291 34.615 0.00 0.00 0.00 1.40
772 833 3.347405 CGGTTTTGCGCCGGTGTA 61.347 61.111 17.91 9.85 44.98 2.90
776 837 1.003112 TTTTGCGCCGGTGTATCCT 60.003 52.632 17.91 0.00 0.00 3.24
782 843 1.760875 GCCGGTGTATCCTCAGGGA 60.761 63.158 1.90 0.00 46.81 4.20
799 861 2.572104 AGGGACGATTTTTAGCACCTCT 59.428 45.455 0.00 0.00 0.00 3.69
803 865 5.416947 GGACGATTTTTAGCACCTCTTAGA 58.583 41.667 0.00 0.00 0.00 2.10
834 896 4.959723 AGCTGGAGATGCTCTTATTCTTC 58.040 43.478 0.00 0.00 35.67 2.87
835 897 4.655186 AGCTGGAGATGCTCTTATTCTTCT 59.345 41.667 0.00 0.00 35.67 2.85
836 898 4.990426 GCTGGAGATGCTCTTATTCTTCTC 59.010 45.833 0.00 0.00 34.58 2.87
837 899 5.221501 GCTGGAGATGCTCTTATTCTTCTCT 60.222 44.000 0.00 0.00 35.26 3.10
838 900 6.159299 TGGAGATGCTCTTATTCTTCTCTG 57.841 41.667 0.00 0.00 35.26 3.35
839 901 5.070180 TGGAGATGCTCTTATTCTTCTCTGG 59.930 44.000 0.00 0.00 35.26 3.86
840 902 4.959723 AGATGCTCTTATTCTTCTCTGGC 58.040 43.478 0.00 0.00 0.00 4.85
841 903 3.170791 TGCTCTTATTCTTCTCTGGCG 57.829 47.619 0.00 0.00 0.00 5.69
842 904 1.864082 GCTCTTATTCTTCTCTGGCGC 59.136 52.381 0.00 0.00 0.00 6.53
843 905 2.482839 GCTCTTATTCTTCTCTGGCGCT 60.483 50.000 7.64 0.00 0.00 5.92
844 906 3.243569 GCTCTTATTCTTCTCTGGCGCTA 60.244 47.826 7.64 0.00 0.00 4.26
845 907 4.295051 CTCTTATTCTTCTCTGGCGCTAC 58.705 47.826 7.64 0.00 0.00 3.58
846 908 3.699538 TCTTATTCTTCTCTGGCGCTACA 59.300 43.478 7.64 0.00 0.00 2.74
847 909 2.593346 ATTCTTCTCTGGCGCTACAG 57.407 50.000 7.64 7.43 39.84 2.74
848 910 1.545841 TTCTTCTCTGGCGCTACAGA 58.454 50.000 14.47 14.47 44.74 3.41
852 914 4.415783 TCTGGCGCTACAGAGACA 57.584 55.556 11.71 0.00 42.26 3.41
853 915 1.883732 TCTGGCGCTACAGAGACAC 59.116 57.895 11.71 0.00 42.26 3.67
854 916 1.515088 CTGGCGCTACAGAGACACG 60.515 63.158 7.64 0.00 40.97 4.49
855 917 1.923227 CTGGCGCTACAGAGACACGA 61.923 60.000 7.64 0.00 40.97 4.35
856 918 1.514443 GGCGCTACAGAGACACGAC 60.514 63.158 7.64 0.00 0.00 4.34
857 919 1.514443 GCGCTACAGAGACACGACC 60.514 63.158 0.00 0.00 0.00 4.79
858 920 1.873863 CGCTACAGAGACACGACCA 59.126 57.895 0.00 0.00 0.00 4.02
859 921 0.179187 CGCTACAGAGACACGACCAG 60.179 60.000 0.00 0.00 0.00 4.00
860 922 0.171455 GCTACAGAGACACGACCAGG 59.829 60.000 0.00 0.00 0.00 4.45
861 923 1.822506 CTACAGAGACACGACCAGGA 58.177 55.000 0.00 0.00 0.00 3.86
862 924 1.469308 CTACAGAGACACGACCAGGAC 59.531 57.143 0.00 0.00 0.00 3.85
863 925 1.179814 ACAGAGACACGACCAGGACC 61.180 60.000 0.00 0.00 0.00 4.46
864 926 1.153061 AGAGACACGACCAGGACCA 59.847 57.895 0.00 0.00 0.00 4.02
865 927 0.896019 AGAGACACGACCAGGACCAG 60.896 60.000 0.00 0.00 0.00 4.00
866 928 2.048127 GACACGACCAGGACCAGC 60.048 66.667 0.00 0.00 0.00 4.85
867 929 3.591254 GACACGACCAGGACCAGCC 62.591 68.421 0.00 0.00 0.00 4.85
868 930 4.742201 CACGACCAGGACCAGCCG 62.742 72.222 0.00 0.00 43.43 5.52
870 932 4.742201 CGACCAGGACCAGCCGTG 62.742 72.222 0.00 0.00 43.43 4.94
871 933 3.626924 GACCAGGACCAGCCGTGT 61.627 66.667 0.00 0.00 43.43 4.49
872 934 3.883744 GACCAGGACCAGCCGTGTG 62.884 68.421 0.00 0.00 43.43 3.82
873 935 4.704833 CCAGGACCAGCCGTGTGG 62.705 72.222 0.00 0.00 43.43 4.17
885 947 4.980805 GTGTGGCCTCGTGCGGAA 62.981 66.667 3.32 0.00 42.61 4.30
886 948 4.015406 TGTGGCCTCGTGCGGAAT 62.015 61.111 3.32 0.00 42.61 3.01
887 949 3.195698 GTGGCCTCGTGCGGAATC 61.196 66.667 3.32 0.00 42.61 2.52
888 950 4.467084 TGGCCTCGTGCGGAATCC 62.467 66.667 3.32 0.00 42.61 3.01
898 960 3.204827 CGGAATCCGGGCTGCAAG 61.205 66.667 14.91 0.00 44.15 4.01
899 961 2.830370 GGAATCCGGGCTGCAAGG 60.830 66.667 0.00 3.96 0.00 3.61
908 970 3.512516 GCTGCAAGGCATCCGTCC 61.513 66.667 0.00 0.00 38.13 4.79
909 971 3.197790 CTGCAAGGCATCCGTCCG 61.198 66.667 0.00 0.00 38.13 4.79
912 974 3.499737 CAAGGCATCCGTCCGCAC 61.500 66.667 0.00 0.00 0.00 5.34
913 975 4.015406 AAGGCATCCGTCCGCACA 62.015 61.111 0.00 0.00 0.00 4.57
914 976 3.958147 AAGGCATCCGTCCGCACAG 62.958 63.158 0.00 0.00 0.00 3.66
930 992 4.269523 AGCGCCCTCCTGCACAAA 62.270 61.111 2.29 0.00 0.00 2.83
931 993 3.294493 GCGCCCTCCTGCACAAAA 61.294 61.111 0.00 0.00 0.00 2.44
932 994 2.644992 CGCCCTCCTGCACAAAAC 59.355 61.111 0.00 0.00 0.00 2.43
933 995 2.192861 CGCCCTCCTGCACAAAACA 61.193 57.895 0.00 0.00 0.00 2.83
934 996 1.363807 GCCCTCCTGCACAAAACAC 59.636 57.895 0.00 0.00 0.00 3.32
935 997 1.391157 GCCCTCCTGCACAAAACACA 61.391 55.000 0.00 0.00 0.00 3.72
936 998 0.385390 CCCTCCTGCACAAAACACAC 59.615 55.000 0.00 0.00 0.00 3.82
937 999 0.385390 CCTCCTGCACAAAACACACC 59.615 55.000 0.00 0.00 0.00 4.16
938 1000 1.102154 CTCCTGCACAAAACACACCA 58.898 50.000 0.00 0.00 0.00 4.17
939 1001 1.066002 CTCCTGCACAAAACACACCAG 59.934 52.381 0.00 0.00 0.00 4.00
940 1002 0.528249 CCTGCACAAAACACACCAGC 60.528 55.000 0.00 0.00 0.00 4.85
941 1003 0.866906 CTGCACAAAACACACCAGCG 60.867 55.000 0.00 0.00 0.00 5.18
942 1004 2.230264 GCACAAAACACACCAGCGC 61.230 57.895 0.00 0.00 0.00 5.92
943 1005 1.138459 CACAAAACACACCAGCGCA 59.862 52.632 11.47 0.00 0.00 6.09
944 1006 1.138671 ACAAAACACACCAGCGCAC 59.861 52.632 11.47 0.00 0.00 5.34
945 1007 1.938814 CAAAACACACCAGCGCACG 60.939 57.895 11.47 0.00 0.00 5.34
981 1043 3.570212 AGCCGAGTTGCCTTGGGT 61.570 61.111 0.00 0.00 46.23 4.51
1065 1128 2.240162 GACGGCCGATCAAGAAGGGT 62.240 60.000 35.90 3.54 0.00 4.34
1067 1130 1.602237 GGCCGATCAAGAAGGGTCA 59.398 57.895 0.00 0.00 0.00 4.02
1111 1174 1.726865 CACTTGGCAAGCGTGTTGA 59.273 52.632 26.45 0.00 0.00 3.18
1112 1175 0.311790 CACTTGGCAAGCGTGTTGAT 59.688 50.000 26.45 1.84 0.00 2.57
1115 1178 0.592637 TTGGCAAGCGTGTTGATCTG 59.407 50.000 0.00 0.00 0.00 2.90
1202 1265 3.181472 GCCCCTGCCAATTCTAATTCAAG 60.181 47.826 0.00 0.00 0.00 3.02
1206 1269 5.346522 CCTGCCAATTCTAATTCAAGCTTC 58.653 41.667 0.00 0.00 0.00 3.86
1224 1287 8.509690 TCAAGCTTCAAATTCTACAGATTCAAG 58.490 33.333 0.00 0.00 0.00 3.02
1243 1306 5.129634 TCAAGTTTTGACATTGGCACTCTA 58.870 37.500 0.00 0.00 34.08 2.43
1263 1326 3.777106 ACATGAGTGTCAGGACAATGT 57.223 42.857 7.15 9.33 43.77 2.71
1265 1328 4.825422 ACATGAGTGTCAGGACAATGTAG 58.175 43.478 13.67 4.29 43.77 2.74
1291 1354 6.351711 TGCAGATTCAGACTAACATTAGCAT 58.648 36.000 0.00 0.00 34.09 3.79
1293 1356 7.337689 TGCAGATTCAGACTAACATTAGCATTT 59.662 33.333 0.00 0.00 34.09 2.32
1362 1494 1.340405 CCTGATGGAGGTTGACTTGGG 60.340 57.143 0.00 0.00 37.02 4.12
1399 1531 6.612863 CACATGGGGGATACATATAGATCTCA 59.387 42.308 0.00 0.00 39.74 3.27
1549 1681 0.458889 CGCATGTTTCAGCAATGGGG 60.459 55.000 0.00 0.00 0.00 4.96
1605 1737 0.738975 CATGGCTGCAAGAGATGTGG 59.261 55.000 0.50 0.00 34.07 4.17
1663 1796 1.002134 CCGGTGCCAAGGTCTTCAT 60.002 57.895 0.00 0.00 0.00 2.57
1681 1814 1.955778 CATGAGGCAACAACACCTTCA 59.044 47.619 0.00 0.00 36.05 3.02
1807 1940 1.039856 GCCTTTTTGCAACAGGAGGA 58.960 50.000 22.97 0.00 0.00 3.71
1815 1948 3.222173 TGCAACAGGAGGAGCTTTTTA 57.778 42.857 0.00 0.00 0.00 1.52
1989 2123 1.977293 GCATCTCCCAGGACCACTCC 61.977 65.000 0.00 0.00 36.71 3.85
2004 2138 3.071023 ACCACTCCGAATGAAAAGACTCA 59.929 43.478 0.00 0.00 0.00 3.41
2022 2156 6.187682 AGACTCAAACCAGGAAAAAGAAGAA 58.812 36.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
257 268 1.202903 GGGCTATCTCCTCGTACTCCA 60.203 57.143 0.00 0.00 0.00 3.86
505 516 2.479650 GTCGTCGTCACCTCCTCG 59.520 66.667 0.00 0.00 0.00 4.63
636 694 9.998106 AGTTCGGCTAGTTCATACATATTTAAT 57.002 29.630 0.00 0.00 0.00 1.40
654 713 3.383761 CAAATTCAAGCAAAGTTCGGCT 58.616 40.909 0.00 0.00 43.46 5.52
661 720 2.151736 CACGACGCAAATTCAAGCAAAG 59.848 45.455 0.00 0.00 0.00 2.77
724 785 3.002583 TGATGCTCCCCAGTCGCA 61.003 61.111 0.00 0.00 38.14 5.10
771 832 4.407621 TGCTAAAAATCGTCCCTGAGGATA 59.592 41.667 0.00 0.00 46.41 2.59
772 833 3.199946 TGCTAAAAATCGTCCCTGAGGAT 59.800 43.478 0.00 0.00 46.41 3.24
776 837 2.304761 AGGTGCTAAAAATCGTCCCTGA 59.695 45.455 0.00 0.00 0.00 3.86
782 843 5.420409 CCTCTAAGAGGTGCTAAAAATCGT 58.580 41.667 0.00 0.00 44.25 3.73
799 861 0.324368 TCCAGCTCTTCGGCCTCTAA 60.324 55.000 0.00 0.00 0.00 2.10
803 865 1.382420 ATCTCCAGCTCTTCGGCCT 60.382 57.895 0.00 0.00 0.00 5.19
829 891 1.545841 TCTGTAGCGCCAGAGAAGAA 58.454 50.000 11.71 0.00 36.57 2.52
835 897 1.883732 GTGTCTCTGTAGCGCCAGA 59.116 57.895 14.47 14.47 39.11 3.86
836 898 1.515088 CGTGTCTCTGTAGCGCCAG 60.515 63.158 2.29 5.38 0.00 4.85
837 899 1.969589 TCGTGTCTCTGTAGCGCCA 60.970 57.895 2.29 0.00 0.00 5.69
838 900 1.514443 GTCGTGTCTCTGTAGCGCC 60.514 63.158 2.29 0.00 0.00 6.53
839 901 1.514443 GGTCGTGTCTCTGTAGCGC 60.514 63.158 0.00 0.00 0.00 5.92
840 902 0.179187 CTGGTCGTGTCTCTGTAGCG 60.179 60.000 0.00 0.00 0.00 4.26
841 903 0.171455 CCTGGTCGTGTCTCTGTAGC 59.829 60.000 0.00 0.00 0.00 3.58
842 904 1.469308 GTCCTGGTCGTGTCTCTGTAG 59.531 57.143 0.00 0.00 0.00 2.74
843 905 1.531423 GTCCTGGTCGTGTCTCTGTA 58.469 55.000 0.00 0.00 0.00 2.74
844 906 1.179814 GGTCCTGGTCGTGTCTCTGT 61.180 60.000 0.00 0.00 0.00 3.41
845 907 1.179174 TGGTCCTGGTCGTGTCTCTG 61.179 60.000 0.00 0.00 0.00 3.35
846 908 0.896019 CTGGTCCTGGTCGTGTCTCT 60.896 60.000 0.00 0.00 0.00 3.10
847 909 1.587054 CTGGTCCTGGTCGTGTCTC 59.413 63.158 0.00 0.00 0.00 3.36
848 910 2.574955 GCTGGTCCTGGTCGTGTCT 61.575 63.158 0.00 0.00 0.00 3.41
849 911 2.048127 GCTGGTCCTGGTCGTGTC 60.048 66.667 0.00 0.00 0.00 3.67
850 912 3.626924 GGCTGGTCCTGGTCGTGT 61.627 66.667 0.00 0.00 0.00 4.49
851 913 4.742201 CGGCTGGTCCTGGTCGTG 62.742 72.222 0.00 0.00 0.00 4.35
853 915 4.742201 CACGGCTGGTCCTGGTCG 62.742 72.222 0.00 7.64 36.57 4.79
854 916 3.626924 ACACGGCTGGTCCTGGTC 61.627 66.667 0.00 0.00 0.00 4.02
855 917 3.941188 CACACGGCTGGTCCTGGT 61.941 66.667 0.00 0.00 0.00 4.00
856 918 4.704833 CCACACGGCTGGTCCTGG 62.705 72.222 0.00 0.00 0.00 4.45
868 930 4.980805 TTCCGCACGAGGCCACAC 62.981 66.667 5.01 0.00 40.31 3.82
869 931 3.950794 GATTCCGCACGAGGCCACA 62.951 63.158 5.01 0.00 40.31 4.17
870 932 3.195698 GATTCCGCACGAGGCCAC 61.196 66.667 5.01 0.00 40.31 5.01
871 933 4.467084 GGATTCCGCACGAGGCCA 62.467 66.667 5.01 0.00 40.31 5.36
874 936 4.891727 CCCGGATTCCGCACGAGG 62.892 72.222 19.80 10.98 46.86 4.63
882 944 2.830370 CCTTGCAGCCCGGATTCC 60.830 66.667 0.73 0.00 0.00 3.01
883 945 3.521796 GCCTTGCAGCCCGGATTC 61.522 66.667 0.73 0.00 0.00 2.52
884 946 3.667217 ATGCCTTGCAGCCCGGATT 62.667 57.895 0.73 0.00 43.65 3.01
885 947 4.133373 ATGCCTTGCAGCCCGGAT 62.133 61.111 0.73 0.00 43.65 4.18
886 948 4.802051 GATGCCTTGCAGCCCGGA 62.802 66.667 0.73 0.00 43.65 5.14
891 953 3.512516 GGACGGATGCCTTGCAGC 61.513 66.667 0.00 0.00 43.65 5.25
892 954 3.197790 CGGACGGATGCCTTGCAG 61.198 66.667 0.00 0.00 43.65 4.41
895 957 3.499737 GTGCGGACGGATGCCTTG 61.500 66.667 0.00 0.00 0.00 3.61
896 958 3.958147 CTGTGCGGACGGATGCCTT 62.958 63.158 10.88 0.00 0.00 4.35
897 959 4.457496 CTGTGCGGACGGATGCCT 62.457 66.667 10.88 0.00 0.00 4.75
913 975 3.790416 TTTTGTGCAGGAGGGCGCT 62.790 57.895 7.64 1.38 44.39 5.92
914 976 3.294493 TTTTGTGCAGGAGGGCGC 61.294 61.111 0.00 0.00 44.35 6.53
915 977 2.192861 TGTTTTGTGCAGGAGGGCG 61.193 57.895 0.00 0.00 36.28 6.13
916 978 1.363807 GTGTTTTGTGCAGGAGGGC 59.636 57.895 0.00 0.00 0.00 5.19
917 979 0.385390 GTGTGTTTTGTGCAGGAGGG 59.615 55.000 0.00 0.00 0.00 4.30
918 980 0.385390 GGTGTGTTTTGTGCAGGAGG 59.615 55.000 0.00 0.00 0.00 4.30
919 981 1.066002 CTGGTGTGTTTTGTGCAGGAG 59.934 52.381 0.00 0.00 0.00 3.69
920 982 1.102154 CTGGTGTGTTTTGTGCAGGA 58.898 50.000 0.00 0.00 0.00 3.86
921 983 0.528249 GCTGGTGTGTTTTGTGCAGG 60.528 55.000 0.00 0.00 0.00 4.85
922 984 0.866906 CGCTGGTGTGTTTTGTGCAG 60.867 55.000 0.00 0.00 0.00 4.41
923 985 1.138459 CGCTGGTGTGTTTTGTGCA 59.862 52.632 0.00 0.00 0.00 4.57
924 986 2.230264 GCGCTGGTGTGTTTTGTGC 61.230 57.895 0.00 0.00 0.00 4.57
925 987 1.138459 TGCGCTGGTGTGTTTTGTG 59.862 52.632 9.73 0.00 0.00 3.33
926 988 1.138671 GTGCGCTGGTGTGTTTTGT 59.861 52.632 9.73 0.00 0.00 2.83
927 989 1.938814 CGTGCGCTGGTGTGTTTTG 60.939 57.895 9.73 0.00 0.00 2.44
928 990 2.407210 CGTGCGCTGGTGTGTTTT 59.593 55.556 9.73 0.00 0.00 2.43
929 991 3.582120 CCGTGCGCTGGTGTGTTT 61.582 61.111 9.73 0.00 0.00 2.83
930 992 4.849310 ACCGTGCGCTGGTGTGTT 62.849 61.111 21.56 0.00 38.60 3.32
931 993 2.926901 TAAACCGTGCGCTGGTGTGT 62.927 55.000 22.64 14.44 40.35 3.72
932 994 2.170260 CTAAACCGTGCGCTGGTGTG 62.170 60.000 22.64 13.12 40.35 3.82
933 995 1.959226 CTAAACCGTGCGCTGGTGT 60.959 57.895 22.64 19.92 40.35 4.16
934 996 0.668096 TACTAAACCGTGCGCTGGTG 60.668 55.000 22.64 14.06 40.35 4.17
935 997 0.668401 GTACTAAACCGTGCGCTGGT 60.668 55.000 17.55 17.55 42.98 4.00
936 998 1.356527 GGTACTAAACCGTGCGCTGG 61.357 60.000 16.28 16.28 38.88 4.85
937 999 2.075761 GGTACTAAACCGTGCGCTG 58.924 57.895 9.73 0.08 38.88 5.18
938 1000 4.584688 GGTACTAAACCGTGCGCT 57.415 55.556 9.73 0.00 38.88 5.92
981 1043 2.306715 TATGTAGCCGCCCCTCCAGA 62.307 60.000 0.00 0.00 0.00 3.86
1014 1076 7.589954 CGTCCAGGTAAGTAAGTTTCAAATTTG 59.410 37.037 12.15 12.15 0.00 2.32
1015 1077 7.255346 CCGTCCAGGTAAGTAAGTTTCAAATTT 60.255 37.037 0.00 0.00 34.51 1.82
1052 1115 1.303309 GCCATGACCCTTCTTGATCG 58.697 55.000 0.00 0.00 0.00 3.69
1065 1128 2.574006 GCCATTGATCTAGGCCATGA 57.426 50.000 5.01 2.12 42.58 3.07
1101 1164 1.089920 GATGGCAGATCAACACGCTT 58.910 50.000 0.00 0.00 0.00 4.68
1106 1169 0.548031 GGGGAGATGGCAGATCAACA 59.452 55.000 0.00 0.00 0.00 3.33
1111 1174 1.064166 CAACAAGGGGAGATGGCAGAT 60.064 52.381 0.00 0.00 0.00 2.90
1112 1175 0.329261 CAACAAGGGGAGATGGCAGA 59.671 55.000 0.00 0.00 0.00 4.26
1115 1178 4.344237 CCAACAAGGGGAGATGGC 57.656 61.111 0.00 0.00 0.00 4.40
1141 1204 4.452455 CCCCTCTATCACAAATTATGACGC 59.548 45.833 0.00 0.00 0.00 5.19
1202 1265 9.468532 AAAACTTGAATCTGTAGAATTTGAAGC 57.531 29.630 0.00 0.00 0.00 3.86
1206 1269 9.734620 TGTCAAAACTTGAATCTGTAGAATTTG 57.265 29.630 0.00 0.00 42.15 2.32
1224 1287 4.829064 TGTAGAGTGCCAATGTCAAAAC 57.171 40.909 0.00 0.00 0.00 2.43
1243 1306 3.777106 ACATTGTCCTGACACTCATGT 57.223 42.857 9.27 9.27 41.67 3.21
1251 1314 4.128925 TCTGCATCTACATTGTCCTGAC 57.871 45.455 0.00 0.00 0.00 3.51
1263 1326 7.869937 GCTAATGTTAGTCTGAATCTGCATCTA 59.130 37.037 0.00 0.00 33.32 1.98
1265 1328 6.481313 TGCTAATGTTAGTCTGAATCTGCATC 59.519 38.462 0.00 0.00 33.32 3.91
1291 1354 3.360867 TGTGCCTTCCTGAAACTCAAAA 58.639 40.909 0.00 0.00 0.00 2.44
1293 1356 2.727123 TGTGCCTTCCTGAAACTCAA 57.273 45.000 0.00 0.00 0.00 3.02
1352 1484 4.278170 TGACAATGATGAACCCAAGTCAAC 59.722 41.667 0.00 0.00 33.12 3.18
1362 1494 2.428171 CCCCCATGTGACAATGATGAAC 59.572 50.000 0.00 0.00 0.00 3.18
1399 1531 7.601705 AATTTGATCCGATTCCACCATATTT 57.398 32.000 0.00 0.00 0.00 1.40
1536 1668 1.826720 GCTGATTCCCCATTGCTGAAA 59.173 47.619 0.00 0.00 0.00 2.69
1549 1681 0.467804 GGTCTGGAGAGGGCTGATTC 59.532 60.000 0.00 0.00 0.00 2.52
1642 1774 3.133365 AAGACCTTGGCACCGGCTT 62.133 57.895 0.00 0.00 40.87 4.35
1663 1796 1.340502 TGTGAAGGTGTTGTTGCCTCA 60.341 47.619 0.00 0.00 33.24 3.86
1807 1940 8.879427 AATACACAGGTAAGGAATAAAAAGCT 57.121 30.769 0.00 0.00 32.19 3.74
1815 1948 7.121315 GCTCAAAGAAATACACAGGTAAGGAAT 59.879 37.037 0.00 0.00 32.19 3.01
1838 1972 0.249489 AGTGTGTCGACAAGTGGCTC 60.249 55.000 21.95 8.38 32.49 4.70
1989 2123 4.515191 TCCTGGTTTGAGTCTTTTCATTCG 59.485 41.667 0.00 0.00 0.00 3.34
2004 2138 6.806668 TGGATTTCTTCTTTTTCCTGGTTT 57.193 33.333 0.00 0.00 0.00 3.27
2064 2198 5.784390 AGCTATCATAAGTCCCATGTCAGAT 59.216 40.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.