Multiple sequence alignment - TraesCS3B01G225500

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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 TraesCS3B01G225500 chr3B 100.000 3002 0 0 1 3002 309614083 309617084 0.000000e+00 5544.0
1 TraesCS3B01G225500 chr3B 92.135 267 16 3 2688 2954 309616355 309616616 3.650000e-99 372.0
2 TraesCS3B01G225500 chr3B 92.135 267 16 3 2273 2534 309616770 309617036 3.650000e-99 372.0
3 TraesCS3B01G225500 chr3D 95.231 2097 51 20 872 2954 253520033 253517972 0.000000e+00 3273.0
4 TraesCS3B01G225500 chr3D 96.239 771 18 6 2233 3002 253518266 253517506 0.000000e+00 1253.0
5 TraesCS3B01G225500 chr3D 82.087 508 77 11 260 764 46521697 46522193 3.580000e-114 422.0
6 TraesCS3B01G225500 chr3D 88.344 326 17 8 2632 2954 253518671 253518364 3.650000e-99 372.0
7 TraesCS3B01G225500 chr3D 92.075 265 18 2 2273 2534 253517818 253517554 1.310000e-98 370.0
8 TraesCS3B01G225500 chr3A 95.891 1947 43 9 872 2791 336598391 336596455 0.000000e+00 3118.0
9 TraesCS3B01G225500 chr3A 89.568 278 17 4 2688 2955 336596986 336596711 2.870000e-90 342.0
10 TraesCS3B01G225500 chr3A 93.902 164 7 3 2821 2984 336596454 336596294 8.310000e-61 244.0
11 TraesCS3B01G225500 chr3A 93.798 129 6 2 2407 2534 336596451 336596324 3.050000e-45 193.0
12 TraesCS3B01G225500 chr3A 94.231 104 4 1 2273 2374 336596558 336596455 1.110000e-34 158.0
13 TraesCS3B01G225500 chr6B 83.421 760 101 11 6 764 492195161 492194426 0.000000e+00 682.0
14 TraesCS3B01G225500 chr2D 82.225 782 102 15 3 783 33362176 33362921 9.070000e-180 640.0
15 TraesCS3B01G225500 chr5D 82.307 763 102 14 3 763 466525398 466526129 5.460000e-177 630.0
16 TraesCS3B01G225500 chr5D 82.848 653 78 12 112 763 210683174 210682555 3.380000e-154 555.0
17 TraesCS3B01G225500 chr2B 80.407 786 114 19 3 783 682863960 682863210 2.020000e-156 562.0
18 TraesCS3B01G225500 chr6D 79.735 755 130 13 3 754 56077159 56077893 2.650000e-145 525.0
19 TraesCS3B01G225500 chr1B 82.214 551 79 15 245 781 529711199 529710654 9.810000e-125 457.0
20 TraesCS3B01G225500 chr1B 93.023 43 3 0 787 829 487022267 487022225 2.500000e-06 63.9
21 TraesCS3B01G225500 chr5B 80.561 535 93 9 255 781 321438949 321439480 4.660000e-108 401.0
22 TraesCS3B01G225500 chr5B 93.333 45 3 0 783 827 591757908 591757864 1.930000e-07 67.6
23 TraesCS3B01G225500 chr1A 82.046 479 61 9 3 481 51685081 51684628 4.690000e-103 385.0
24 TraesCS3B01G225500 chr7B 97.561 41 1 0 787 827 637572789 637572749 1.490000e-08 71.3
25 TraesCS3B01G225500 chr7B 90.698 43 4 0 787 829 641178219 641178177 1.160000e-04 58.4
26 TraesCS3B01G225500 chr2A 92.683 41 3 0 2946 2986 417747411 417747451 3.230000e-05 60.2
27 TraesCS3B01G225500 chr6A 100.000 28 0 0 800 827 572974297 572974324 5.000000e-03 52.8


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 TraesCS3B01G225500 chr3B 309614083 309617084 3001 False 2096 5544 94.756667 1 3002 3 chr3B.!!$F1 3001
1 TraesCS3B01G225500 chr3D 253517506 253520033 2527 True 1317 3273 92.972250 872 3002 4 chr3D.!!$R1 2130
2 TraesCS3B01G225500 chr3A 336596294 336598391 2097 True 811 3118 93.478000 872 2984 5 chr3A.!!$R1 2112
3 TraesCS3B01G225500 chr6B 492194426 492195161 735 True 682 682 83.421000 6 764 1 chr6B.!!$R1 758
4 TraesCS3B01G225500 chr2D 33362176 33362921 745 False 640 640 82.225000 3 783 1 chr2D.!!$F1 780
5 TraesCS3B01G225500 chr5D 466525398 466526129 731 False 630 630 82.307000 3 763 1 chr5D.!!$F1 760
6 TraesCS3B01G225500 chr5D 210682555 210683174 619 True 555 555 82.848000 112 763 1 chr5D.!!$R1 651
7 TraesCS3B01G225500 chr2B 682863210 682863960 750 True 562 562 80.407000 3 783 1 chr2B.!!$R1 780
8 TraesCS3B01G225500 chr6D 56077159 56077893 734 False 525 525 79.735000 3 754 1 chr6D.!!$F1 751
9 TraesCS3B01G225500 chr1B 529710654 529711199 545 True 457 457 82.214000 245 781 1 chr1B.!!$R2 536
10 TraesCS3B01G225500 chr5B 321438949 321439480 531 False 401 401 80.561000 255 781 1 chr5B.!!$F1 526

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
69 70 0.028902 GTATTTCCAACGCCGCCATC 59.971 55.0 0.0 0.0 0.0 3.51 F
875 916 0.107831 TTACCAAACAGCCTGCGAGT 59.892 50.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1465 1520 0.984230 ATCAGCCCCGTCTCTTTCAA 59.016 50.000 0.0 0.0 0.00 2.69 R
2189 2246 3.561143 ACAACAACCAACTGGCTTATGA 58.439 40.909 0.0 0.0 39.32 2.15 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
68 69 1.711060 CGTATTTCCAACGCCGCCAT 61.711 55.000 0.00 0.00 33.04 4.40
69 70 0.028902 GTATTTCCAACGCCGCCATC 59.971 55.000 0.00 0.00 0.00 3.51
82 83 2.108566 CCATCAGGAGCAGCTCGG 59.891 66.667 16.47 11.03 36.89 4.63
149 150 2.508928 CGTCTGTGGTGGGGTGTT 59.491 61.111 0.00 0.00 0.00 3.32
330 352 3.237741 CCTCCTCCCGCTCATCCC 61.238 72.222 0.00 0.00 0.00 3.85
331 353 2.444706 CTCCTCCCGCTCATCCCA 60.445 66.667 0.00 0.00 0.00 4.37
387 415 4.227134 CCGAGCCCGTGGAGATGG 62.227 72.222 0.00 0.00 0.00 3.51
388 416 3.147595 CGAGCCCGTGGAGATGGA 61.148 66.667 0.00 0.00 0.00 3.41
428 456 2.435938 GGCGCCCTCGTCATCAAA 60.436 61.111 18.11 0.00 40.61 2.69
431 459 1.019278 GCGCCCTCGTCATCAAAGAA 61.019 55.000 0.00 0.00 38.14 2.52
491 519 3.470888 CCGAAGATGGAGCCGGGT 61.471 66.667 5.45 5.45 38.42 5.28
497 525 2.683933 ATGGAGCCGGGTCTCGTT 60.684 61.111 31.09 12.19 37.11 3.85
499 527 3.692406 GGAGCCGGGTCTCGTTGT 61.692 66.667 31.09 0.00 37.11 3.32
525 553 2.181777 GCGAGCACGAGGACATGA 59.818 61.111 8.01 0.00 42.66 3.07
622 656 1.035923 CTAGAGGAGATTGCCGCTCA 58.964 55.000 0.00 0.00 39.00 4.26
643 677 3.506096 CCGCGGCTGAGACGAGTA 61.506 66.667 14.07 0.00 35.20 2.59
646 680 2.747822 GCGGCTGAGACGAGTACGA 61.748 63.158 14.07 0.00 42.66 3.43
755 793 1.006571 GGTGTCGGCGTGAAGAAGA 60.007 57.895 6.85 0.00 0.00 2.87
764 805 1.000955 GCGTGAAGAAGAAGGAGGACA 59.999 52.381 0.00 0.00 0.00 4.02
767 808 3.492656 CGTGAAGAAGAAGGAGGACAACA 60.493 47.826 0.00 0.00 0.00 3.33
796 837 4.111375 CGACTACAATAGTTGTGAGGCT 57.889 45.455 5.64 0.00 45.03 4.58
797 838 4.495422 CGACTACAATAGTTGTGAGGCTT 58.505 43.478 5.64 0.00 45.03 4.35
798 839 4.929808 CGACTACAATAGTTGTGAGGCTTT 59.070 41.667 5.64 0.00 45.03 3.51
799 840 5.062308 CGACTACAATAGTTGTGAGGCTTTC 59.938 44.000 5.64 0.00 45.03 2.62
800 841 4.929808 ACTACAATAGTTGTGAGGCTTTCG 59.070 41.667 5.64 0.00 45.03 3.46
801 842 4.002906 ACAATAGTTGTGAGGCTTTCGA 57.997 40.909 0.00 0.00 43.48 3.71
802 843 4.385825 ACAATAGTTGTGAGGCTTTCGAA 58.614 39.130 0.00 0.00 43.48 3.71
803 844 4.819630 ACAATAGTTGTGAGGCTTTCGAAA 59.180 37.500 10.71 10.71 43.48 3.46
804 845 5.298276 ACAATAGTTGTGAGGCTTTCGAAAA 59.702 36.000 12.41 0.00 43.48 2.29
805 846 6.183360 ACAATAGTTGTGAGGCTTTCGAAAAA 60.183 34.615 12.41 0.00 43.48 1.94
806 847 4.292977 AGTTGTGAGGCTTTCGAAAAAG 57.707 40.909 12.41 2.02 43.99 2.27
813 854 3.729004 CTTTCGAAAAAGCGCTCGT 57.271 47.368 12.06 0.00 35.79 4.18
814 855 2.018717 CTTTCGAAAAAGCGCTCGTT 57.981 45.000 12.06 7.99 35.79 3.85
815 856 3.163642 CTTTCGAAAAAGCGCTCGTTA 57.836 42.857 12.06 0.20 35.79 3.18
816 857 3.537806 CTTTCGAAAAAGCGCTCGTTAA 58.462 40.909 12.06 8.41 35.79 2.01
817 858 3.799137 TTCGAAAAAGCGCTCGTTAAT 57.201 38.095 12.06 0.00 36.46 1.40
818 859 3.799137 TCGAAAAAGCGCTCGTTAATT 57.201 38.095 12.06 0.00 36.46 1.40
819 860 4.907188 TCGAAAAAGCGCTCGTTAATTA 57.093 36.364 12.06 0.00 36.46 1.40
820 861 4.877942 TCGAAAAAGCGCTCGTTAATTAG 58.122 39.130 12.06 0.70 36.46 1.73
821 862 4.386652 TCGAAAAAGCGCTCGTTAATTAGT 59.613 37.500 12.06 0.00 36.46 2.24
822 863 5.077424 CGAAAAAGCGCTCGTTAATTAGTT 58.923 37.500 12.06 0.00 0.00 2.24
823 864 5.001267 CGAAAAAGCGCTCGTTAATTAGTTG 59.999 40.000 12.06 0.00 0.00 3.16
824 865 3.385079 AAGCGCTCGTTAATTAGTTGC 57.615 42.857 12.06 0.00 0.00 4.17
825 866 2.618053 AGCGCTCGTTAATTAGTTGCT 58.382 42.857 2.64 0.00 0.00 3.91
826 867 2.603560 AGCGCTCGTTAATTAGTTGCTC 59.396 45.455 2.64 0.00 0.00 4.26
827 868 2.285660 GCGCTCGTTAATTAGTTGCTCC 60.286 50.000 0.00 0.00 0.00 4.70
828 869 2.284417 CGCTCGTTAATTAGTTGCTCCC 59.716 50.000 0.00 0.00 0.00 4.30
829 870 2.612672 GCTCGTTAATTAGTTGCTCCCC 59.387 50.000 0.00 0.00 0.00 4.81
830 871 3.681874 GCTCGTTAATTAGTTGCTCCCCT 60.682 47.826 0.00 0.00 0.00 4.79
831 872 4.514401 CTCGTTAATTAGTTGCTCCCCTT 58.486 43.478 0.00 0.00 0.00 3.95
832 873 4.258543 TCGTTAATTAGTTGCTCCCCTTG 58.741 43.478 0.00 0.00 0.00 3.61
833 874 3.377172 CGTTAATTAGTTGCTCCCCTTGG 59.623 47.826 0.00 0.00 0.00 3.61
834 875 4.595986 GTTAATTAGTTGCTCCCCTTGGA 58.404 43.478 0.00 0.00 38.75 3.53
842 883 3.702048 TCCCCTTGGAGGCGAACG 61.702 66.667 0.00 0.00 35.03 3.95
843 884 4.778143 CCCCTTGGAGGCGAACGG 62.778 72.222 0.00 0.00 32.73 4.44
844 885 4.778143 CCCTTGGAGGCGAACGGG 62.778 72.222 0.00 0.00 32.73 5.28
845 886 4.016706 CCTTGGAGGCGAACGGGT 62.017 66.667 0.00 0.00 0.00 5.28
846 887 2.742372 CTTGGAGGCGAACGGGTG 60.742 66.667 0.00 0.00 0.00 4.61
847 888 4.323477 TTGGAGGCGAACGGGTGG 62.323 66.667 0.00 0.00 0.00 4.61
849 890 4.452733 GGAGGCGAACGGGTGGAG 62.453 72.222 0.00 0.00 0.00 3.86
850 891 3.379445 GAGGCGAACGGGTGGAGA 61.379 66.667 0.00 0.00 0.00 3.71
851 892 2.683933 AGGCGAACGGGTGGAGAT 60.684 61.111 0.00 0.00 0.00 2.75
852 893 1.380785 AGGCGAACGGGTGGAGATA 60.381 57.895 0.00 0.00 0.00 1.98
853 894 1.227176 GGCGAACGGGTGGAGATAC 60.227 63.158 0.00 0.00 0.00 2.24
854 895 1.673808 GGCGAACGGGTGGAGATACT 61.674 60.000 0.00 0.00 0.00 2.12
855 896 0.248949 GCGAACGGGTGGAGATACTC 60.249 60.000 0.00 0.00 0.00 2.59
856 897 1.390565 CGAACGGGTGGAGATACTCT 58.609 55.000 0.00 0.00 0.00 3.24
857 898 1.749634 CGAACGGGTGGAGATACTCTT 59.250 52.381 0.00 0.00 0.00 2.85
858 899 2.947652 CGAACGGGTGGAGATACTCTTA 59.052 50.000 0.00 0.00 0.00 2.10
859 900 3.243002 CGAACGGGTGGAGATACTCTTAC 60.243 52.174 0.00 0.00 0.00 2.34
860 901 2.664015 ACGGGTGGAGATACTCTTACC 58.336 52.381 13.15 13.15 37.15 2.85
861 902 2.024655 ACGGGTGGAGATACTCTTACCA 60.025 50.000 18.81 0.00 38.46 3.25
862 903 3.028850 CGGGTGGAGATACTCTTACCAA 58.971 50.000 18.81 0.00 38.46 3.67
863 904 3.449737 CGGGTGGAGATACTCTTACCAAA 59.550 47.826 18.81 0.00 38.46 3.28
864 905 4.679905 CGGGTGGAGATACTCTTACCAAAC 60.680 50.000 18.81 8.13 38.46 2.93
865 906 4.224370 GGGTGGAGATACTCTTACCAAACA 59.776 45.833 18.81 0.00 38.46 2.83
866 907 5.420409 GGTGGAGATACTCTTACCAAACAG 58.580 45.833 15.17 0.00 37.51 3.16
867 908 4.870991 GTGGAGATACTCTTACCAAACAGC 59.129 45.833 0.00 0.00 32.32 4.40
868 909 4.081087 TGGAGATACTCTTACCAAACAGCC 60.081 45.833 0.00 0.00 0.00 4.85
869 910 4.162509 GGAGATACTCTTACCAAACAGCCT 59.837 45.833 0.00 0.00 0.00 4.58
870 911 5.091261 AGATACTCTTACCAAACAGCCTG 57.909 43.478 0.00 0.00 0.00 4.85
871 912 1.897560 ACTCTTACCAAACAGCCTGC 58.102 50.000 0.00 0.00 0.00 4.85
872 913 0.798776 CTCTTACCAAACAGCCTGCG 59.201 55.000 0.00 0.00 0.00 5.18
873 914 0.394938 TCTTACCAAACAGCCTGCGA 59.605 50.000 0.00 0.00 0.00 5.10
874 915 0.798776 CTTACCAAACAGCCTGCGAG 59.201 55.000 0.00 0.00 0.00 5.03
875 916 0.107831 TTACCAAACAGCCTGCGAGT 59.892 50.000 0.00 0.00 0.00 4.18
876 917 0.107831 TACCAAACAGCCTGCGAGTT 59.892 50.000 0.00 0.00 0.00 3.01
877 918 1.166531 ACCAAACAGCCTGCGAGTTC 61.167 55.000 0.00 0.00 0.00 3.01
878 919 0.886490 CCAAACAGCCTGCGAGTTCT 60.886 55.000 0.00 0.00 0.00 3.01
890 931 4.213270 CCTGCGAGTTCTTTTGTATGACAA 59.787 41.667 0.00 0.00 36.11 3.18
895 936 6.511121 GCGAGTTCTTTTGTATGACAAGTTGA 60.511 38.462 10.54 0.00 39.53 3.18
1066 1121 0.179936 CCTGCTGGGTGGAGAATCTC 59.820 60.000 0.71 0.71 36.08 2.75
1296 1351 3.441290 GGGAAGCAGCAGCAGCAG 61.441 66.667 12.92 0.00 45.49 4.24
1311 1366 2.048222 CAGCAGCGTCCGGAAAGA 60.048 61.111 5.23 0.00 0.00 2.52
1465 1520 1.104630 GGACGAGATCTTCCGGAAGT 58.895 55.000 36.74 26.21 39.38 3.01
1554 1609 1.372087 CGGAGGCCATGAAGCTGTTC 61.372 60.000 5.01 0.00 0.00 3.18
1860 1915 1.075151 GGGGGTAGAGGAGGGTGAG 60.075 68.421 0.00 0.00 0.00 3.51
2363 2425 6.116126 AGAGAACTAATAGGAAACATGGTGC 58.884 40.000 0.00 0.00 0.00 5.01
2370 2432 2.787994 AGGAAACATGGTGCTTCTGAG 58.212 47.619 0.00 0.00 0.00 3.35
2731 3193 9.500785 TGTTGAGTTGTATTTCATCACTATCAA 57.499 29.630 0.00 0.00 0.00 2.57
2840 3302 1.022982 CGCTGGCATGCAGAAAGAGA 61.023 55.000 21.36 0.00 0.00 3.10
2899 3361 2.766263 AGATTATCCTTGCTCACCGTCA 59.234 45.455 0.00 0.00 0.00 4.35
2900 3362 3.389329 AGATTATCCTTGCTCACCGTCAT 59.611 43.478 0.00 0.00 0.00 3.06
2929 3391 9.262358 GATAATATTTCTTACTCTCCGCTGTTT 57.738 33.333 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 2.281831 TGATGGCGGCGTTGGAAA 60.282 55.556 9.37 0.00 0.00 3.13
82 83 2.331451 GCGTGTTGTTGGTGGAGC 59.669 61.111 0.00 0.00 0.00 4.70
153 154 4.008933 GGAGTGGAGTGTGCGGCT 62.009 66.667 0.00 0.00 0.00 5.52
155 156 3.991051 ACGGAGTGGAGTGTGCGG 61.991 66.667 0.00 0.00 42.51 5.69
306 313 2.364448 GCGGGAGGAGGAGGAAGT 60.364 66.667 0.00 0.00 0.00 3.01
330 352 4.135153 CGACCCAGAGGAGCGGTG 62.135 72.222 0.00 0.00 36.73 4.94
351 379 3.036084 CTTGACGTTGGCGAGCGT 61.036 61.111 10.84 10.84 44.50 5.07
491 519 0.385598 CGCTCTTCACGACAACGAGA 60.386 55.000 0.00 0.00 42.66 4.04
497 525 1.371758 GTGCTCGCTCTTCACGACA 60.372 57.895 0.00 0.00 35.35 4.35
546 577 2.434884 CTCACGCGCCCACTTGAT 60.435 61.111 5.73 0.00 0.00 2.57
741 776 0.243907 CTCCTTCTTCTTCACGCCGA 59.756 55.000 0.00 0.00 0.00 5.54
755 793 0.106918 TTGCCGTTGTTGTCCTCCTT 60.107 50.000 0.00 0.00 0.00 3.36
764 805 1.654317 TTGTAGTCGTTGCCGTTGTT 58.346 45.000 0.00 0.00 35.01 2.83
767 808 3.308438 ACTATTGTAGTCGTTGCCGTT 57.692 42.857 0.00 0.00 32.47 4.44
783 824 6.002062 CTTTTTCGAAAGCCTCACAACTAT 57.998 37.500 10.98 0.00 0.00 2.12
784 825 5.418310 CTTTTTCGAAAGCCTCACAACTA 57.582 39.130 10.98 0.00 0.00 2.24
785 826 4.292977 CTTTTTCGAAAGCCTCACAACT 57.707 40.909 10.98 0.00 0.00 3.16
795 836 2.018717 AACGAGCGCTTTTTCGAAAG 57.981 45.000 21.54 1.29 39.93 2.62
796 837 3.589061 TTAACGAGCGCTTTTTCGAAA 57.411 38.095 21.54 6.47 39.93 3.46
797 838 3.799137 ATTAACGAGCGCTTTTTCGAA 57.201 38.095 21.54 8.28 39.93 3.71
798 839 3.799137 AATTAACGAGCGCTTTTTCGA 57.201 38.095 21.54 6.99 39.93 3.71
799 840 4.634991 ACTAATTAACGAGCGCTTTTTCG 58.365 39.130 13.26 13.91 42.26 3.46
800 841 5.219786 GCAACTAATTAACGAGCGCTTTTTC 60.220 40.000 13.26 0.00 0.00 2.29
801 842 4.615541 GCAACTAATTAACGAGCGCTTTTT 59.384 37.500 13.26 10.70 0.00 1.94
802 843 4.083484 AGCAACTAATTAACGAGCGCTTTT 60.083 37.500 13.26 11.11 0.00 2.27
803 844 3.435671 AGCAACTAATTAACGAGCGCTTT 59.564 39.130 13.26 5.26 0.00 3.51
804 845 3.000727 AGCAACTAATTAACGAGCGCTT 58.999 40.909 13.26 0.00 0.00 4.68
805 846 2.603560 GAGCAACTAATTAACGAGCGCT 59.396 45.455 11.27 11.27 0.00 5.92
806 847 2.285660 GGAGCAACTAATTAACGAGCGC 60.286 50.000 0.00 0.00 0.00 5.92
807 848 2.284417 GGGAGCAACTAATTAACGAGCG 59.716 50.000 0.00 0.00 0.00 5.03
808 849 2.612672 GGGGAGCAACTAATTAACGAGC 59.387 50.000 0.00 0.00 0.00 5.03
809 850 4.138487 AGGGGAGCAACTAATTAACGAG 57.862 45.455 0.00 0.00 0.00 4.18
810 851 4.258543 CAAGGGGAGCAACTAATTAACGA 58.741 43.478 0.00 0.00 0.00 3.85
811 852 3.377172 CCAAGGGGAGCAACTAATTAACG 59.623 47.826 0.00 0.00 35.59 3.18
812 853 4.595986 TCCAAGGGGAGCAACTAATTAAC 58.404 43.478 0.00 0.00 38.64 2.01
813 854 4.938575 TCCAAGGGGAGCAACTAATTAA 57.061 40.909 0.00 0.00 38.64 1.40
827 868 4.778143 CCCGTTCGCCTCCAAGGG 62.778 72.222 0.00 0.00 35.37 3.95
828 869 4.016706 ACCCGTTCGCCTCCAAGG 62.017 66.667 0.00 0.00 38.80 3.61
829 870 2.742372 CACCCGTTCGCCTCCAAG 60.742 66.667 0.00 0.00 0.00 3.61
830 871 4.323477 CCACCCGTTCGCCTCCAA 62.323 66.667 0.00 0.00 0.00 3.53
832 873 4.452733 CTCCACCCGTTCGCCTCC 62.453 72.222 0.00 0.00 0.00 4.30
833 874 1.389609 TATCTCCACCCGTTCGCCTC 61.390 60.000 0.00 0.00 0.00 4.70
834 875 1.380785 TATCTCCACCCGTTCGCCT 60.381 57.895 0.00 0.00 0.00 5.52
835 876 1.227176 GTATCTCCACCCGTTCGCC 60.227 63.158 0.00 0.00 0.00 5.54
836 877 0.248949 GAGTATCTCCACCCGTTCGC 60.249 60.000 0.00 0.00 0.00 4.70
837 878 3.940723 GAGTATCTCCACCCGTTCG 57.059 57.895 0.00 0.00 0.00 3.95
849 890 3.623510 GCAGGCTGTTTGGTAAGAGTATC 59.376 47.826 17.16 0.00 0.00 2.24
850 891 3.610911 GCAGGCTGTTTGGTAAGAGTAT 58.389 45.455 17.16 0.00 0.00 2.12
851 892 2.611971 CGCAGGCTGTTTGGTAAGAGTA 60.612 50.000 17.16 0.00 0.00 2.59
852 893 1.878102 CGCAGGCTGTTTGGTAAGAGT 60.878 52.381 17.16 0.00 0.00 3.24
853 894 0.798776 CGCAGGCTGTTTGGTAAGAG 59.201 55.000 17.16 0.00 0.00 2.85
854 895 0.394938 TCGCAGGCTGTTTGGTAAGA 59.605 50.000 17.16 0.81 0.00 2.10
855 896 0.798776 CTCGCAGGCTGTTTGGTAAG 59.201 55.000 17.16 0.02 0.00 2.34
856 897 0.107831 ACTCGCAGGCTGTTTGGTAA 59.892 50.000 17.16 0.00 0.00 2.85
857 898 0.107831 AACTCGCAGGCTGTTTGGTA 59.892 50.000 17.16 0.00 0.00 3.25
858 899 1.152963 AACTCGCAGGCTGTTTGGT 60.153 52.632 17.16 7.46 0.00 3.67
859 900 0.886490 AGAACTCGCAGGCTGTTTGG 60.886 55.000 17.16 6.84 0.00 3.28
860 901 0.947244 AAGAACTCGCAGGCTGTTTG 59.053 50.000 17.16 8.62 0.00 2.93
861 902 1.680338 AAAGAACTCGCAGGCTGTTT 58.320 45.000 17.16 3.77 0.00 2.83
862 903 1.334869 CAAAAGAACTCGCAGGCTGTT 59.665 47.619 17.16 1.59 0.00 3.16
863 904 0.947244 CAAAAGAACTCGCAGGCTGT 59.053 50.000 17.16 0.00 0.00 4.40
864 905 0.947244 ACAAAAGAACTCGCAGGCTG 59.053 50.000 10.94 10.94 0.00 4.85
865 906 2.543777 TACAAAAGAACTCGCAGGCT 57.456 45.000 0.00 0.00 0.00 4.58
866 907 2.742053 TCATACAAAAGAACTCGCAGGC 59.258 45.455 0.00 0.00 0.00 4.85
867 908 3.745975 TGTCATACAAAAGAACTCGCAGG 59.254 43.478 0.00 0.00 0.00 4.85
868 909 4.990543 TGTCATACAAAAGAACTCGCAG 57.009 40.909 0.00 0.00 0.00 5.18
869 910 4.814234 ACTTGTCATACAAAAGAACTCGCA 59.186 37.500 0.00 0.00 37.69 5.10
870 911 5.344207 ACTTGTCATACAAAAGAACTCGC 57.656 39.130 0.00 0.00 37.69 5.03
871 912 6.846283 GTCAACTTGTCATACAAAAGAACTCG 59.154 38.462 0.00 0.00 37.69 4.18
872 913 7.132863 GGTCAACTTGTCATACAAAAGAACTC 58.867 38.462 0.00 0.00 37.69 3.01
873 914 6.039382 GGGTCAACTTGTCATACAAAAGAACT 59.961 38.462 0.00 0.00 37.69 3.01
874 915 6.206498 GGGTCAACTTGTCATACAAAAGAAC 58.794 40.000 0.00 0.00 37.69 3.01
875 916 5.008217 CGGGTCAACTTGTCATACAAAAGAA 59.992 40.000 0.00 0.00 37.69 2.52
876 917 4.513692 CGGGTCAACTTGTCATACAAAAGA 59.486 41.667 0.00 0.00 37.69 2.52
877 918 4.320202 CCGGGTCAACTTGTCATACAAAAG 60.320 45.833 0.00 0.00 37.69 2.27
878 919 3.566322 CCGGGTCAACTTGTCATACAAAA 59.434 43.478 0.00 0.00 37.69 2.44
890 931 3.057337 CTTCGTCCCGGGTCAACT 58.943 61.111 22.86 0.00 0.00 3.16
970 1015 5.255397 TCTCTCTCTCTCTTCTTCTGGTT 57.745 43.478 0.00 0.00 0.00 3.67
978 1031 3.711704 TCTCTCCCTCTCTCTCTCTCTTC 59.288 52.174 0.00 0.00 0.00 2.87
1080 1135 3.612251 CGGTCACCGGTGGAGTAT 58.388 61.111 33.40 0.00 44.15 2.12
1295 1350 1.374758 CTTCTTTCCGGACGCTGCT 60.375 57.895 1.83 0.00 0.00 4.24
1296 1351 3.028366 GCTTCTTTCCGGACGCTGC 62.028 63.158 1.83 1.23 0.00 5.25
1297 1352 2.730672 CGCTTCTTTCCGGACGCTG 61.731 63.158 1.83 0.00 0.00 5.18
1298 1353 2.432628 CGCTTCTTTCCGGACGCT 60.433 61.111 1.83 0.00 0.00 5.07
1299 1354 4.148645 GCGCTTCTTTCCGGACGC 62.149 66.667 17.44 17.44 39.49 5.19
1300 1355 2.432628 AGCGCTTCTTTCCGGACG 60.433 61.111 2.64 4.21 0.00 4.79
1465 1520 0.984230 ATCAGCCCCGTCTCTTTCAA 59.016 50.000 0.00 0.00 0.00 2.69
1554 1609 2.202610 TTCTCGCGCATCAGACCG 60.203 61.111 8.75 0.00 0.00 4.79
1578 1633 3.206639 TGTAGATGACCACCTCTGGGATA 59.793 47.826 0.00 0.00 42.74 2.59
2189 2246 3.561143 ACAACAACCAACTGGCTTATGA 58.439 40.909 0.00 0.00 39.32 2.15
2731 3193 8.680903 GTCAAGATTGTTCATCATGTAGGAAAT 58.319 33.333 0.00 0.00 33.12 2.17
2840 3302 4.679373 AGAGGTGATGATAAGTTCGCAT 57.321 40.909 0.00 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.