Multiple sequence alignment - TraesCS4D01G047700

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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 TraesCS4D01G047700 chr4D 100.000 2602 0 0 1 2602 23420874 23418273 0.000000e+00 4806
1 TraesCS4D01G047700 chr4B 95.060 830 35 4 1 829 35520979 35520155 0.000000e+00 1301
2 TraesCS4D01G047700 chr4B 91.346 936 47 22 1629 2559 35515247 35514341 0.000000e+00 1249
3 TraesCS4D01G047700 chr4B 84.176 771 80 24 932 1692 35516007 35515269 0.000000e+00 710
4 TraesCS4D01G047700 chr4A 94.175 824 34 7 1739 2559 578540693 578541505 0.000000e+00 1243
5 TraesCS4D01G047700 chr4A 94.379 765 24 9 1 763 578538685 578539432 0.000000e+00 1157
6 TraesCS4D01G047700 chr4A 85.063 395 27 19 940 1334 578539749 578540111 8.790000e-100 374
7 TraesCS4D01G047700 chr4A 89.161 286 15 10 1328 1613 578540230 578540499 2.480000e-90 342


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 TraesCS4D01G047700 chr4D 23418273 23420874 2601 True 4806.0 4806 100.0000 1 2602 1 chr4D.!!$R1 2601
1 TraesCS4D01G047700 chr4B 35520155 35520979 824 True 1301.0 1301 95.0600 1 829 1 chr4B.!!$R1 828
2 TraesCS4D01G047700 chr4B 35514341 35516007 1666 True 979.5 1249 87.7610 932 2559 2 chr4B.!!$R2 1627
3 TraesCS4D01G047700 chr4A 578538685 578541505 2820 False 779.0 1243 90.6945 1 2559 4 chr4A.!!$F1 2558

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
857 863 0.036105 ATGAGCGTGAGACCATTGCA 60.036 50.0 0.0 0.0 0.0 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1814 2321 0.1023 ACACCGTTGCTTCTTTTGGC 59.898 50.0 0.0 0.0 0.0 4.52 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
219 220 2.750637 GTCGACGAGAGGGAGCCA 60.751 66.667 0.00 0.00 0.00 4.75
361 365 2.516930 AGTGCAGCGCAACCTTGT 60.517 55.556 11.47 0.00 41.47 3.16
362 366 2.120909 AGTGCAGCGCAACCTTGTT 61.121 52.632 11.47 0.00 41.47 2.83
363 367 1.945662 GTGCAGCGCAACCTTGTTG 60.946 57.895 11.47 2.65 41.47 3.33
374 378 3.627577 GCAACCTTGTTGAAGAAGTGAGA 59.372 43.478 10.94 0.00 0.00 3.27
379 383 3.475566 TGTTGAAGAAGTGAGACCCTG 57.524 47.619 0.00 0.00 0.00 4.45
391 396 2.299521 GAGACCCTGCTCTATGTACGT 58.700 52.381 0.00 0.00 32.16 3.57
455 461 3.318839 TGCTTTTCCATTTCACTCACCAG 59.681 43.478 0.00 0.00 0.00 4.00
456 462 3.319122 GCTTTTCCATTTCACTCACCAGT 59.681 43.478 0.00 0.00 0.00 4.00
457 463 4.202151 GCTTTTCCATTTCACTCACCAGTT 60.202 41.667 0.00 0.00 0.00 3.16
642 648 8.014517 CCGCAAGCAAATAATTTTGTTGTATTT 58.985 29.630 0.97 0.00 43.43 1.40
766 772 1.075374 TGGCACATAGCTTTGGACCTT 59.925 47.619 15.32 0.00 44.79 3.50
773 779 0.610687 AGCTTTGGACCTTCCTCTCG 59.389 55.000 0.00 0.00 37.46 4.04
791 797 6.017934 TCCTCTCGTTGTTCTTTCTTTGAATG 60.018 38.462 0.00 0.00 0.00 2.67
798 804 8.690840 CGTTGTTCTTTCTTTGAATGGTTTATC 58.309 33.333 0.00 0.00 0.00 1.75
799 805 8.978539 GTTGTTCTTTCTTTGAATGGTTTATCC 58.021 33.333 0.00 0.00 0.00 2.59
805 811 4.338118 TCTTTGAATGGTTTATCCGGATGC 59.662 41.667 27.55 15.86 39.52 3.91
807 813 3.476552 TGAATGGTTTATCCGGATGCTC 58.523 45.455 27.55 15.27 39.52 4.26
809 815 2.620251 TGGTTTATCCGGATGCTCTG 57.380 50.000 27.55 0.00 39.52 3.35
816 822 0.462581 TCCGGATGCTCTGTCAATGC 60.463 55.000 0.00 0.00 0.00 3.56
823 829 0.525668 GCTCTGTCAATGCTGCATGC 60.526 55.000 17.00 11.82 43.25 4.06
829 835 0.389296 TCAATGCTGCATGCTTGTGC 60.389 50.000 20.33 17.08 45.25 4.57
830 836 0.389817 CAATGCTGCATGCTTGTGCT 60.390 50.000 20.33 0.00 45.27 4.40
831 837 0.389817 AATGCTGCATGCTTGTGCTG 60.390 50.000 20.33 13.28 45.27 4.41
832 838 2.126071 GCTGCATGCTTGTGCTGG 60.126 61.111 20.33 0.36 45.27 4.85
833 839 2.126071 CTGCATGCTTGTGCTGGC 60.126 61.111 20.33 0.00 45.27 4.85
834 840 2.913060 TGCATGCTTGTGCTGGCA 60.913 55.556 20.33 0.00 45.27 4.92
835 841 2.340809 GCATGCTTGTGCTGGCAA 59.659 55.556 11.37 0.00 41.90 4.52
836 842 1.301087 GCATGCTTGTGCTGGCAAA 60.301 52.632 11.37 0.00 41.90 3.68
837 843 1.289109 GCATGCTTGTGCTGGCAAAG 61.289 55.000 11.37 5.25 41.90 2.77
838 844 0.315886 CATGCTTGTGCTGGCAAAGA 59.684 50.000 15.86 6.78 41.90 2.52
840 846 0.315886 TGCTTGTGCTGGCAAAGATG 59.684 50.000 15.86 1.90 40.48 2.90
842 848 1.402456 GCTTGTGCTGGCAAAGATGAG 60.402 52.381 15.86 1.47 36.03 2.90
843 849 0.599558 TTGTGCTGGCAAAGATGAGC 59.400 50.000 0.00 0.00 0.00 4.26
845 851 1.302752 TGCTGGCAAAGATGAGCGT 60.303 52.632 0.00 0.00 30.92 5.07
846 852 1.136147 GCTGGCAAAGATGAGCGTG 59.864 57.895 0.00 0.00 0.00 5.34
848 854 0.725686 CTGGCAAAGATGAGCGTGAG 59.274 55.000 0.00 0.00 0.00 3.51
849 855 0.321346 TGGCAAAGATGAGCGTGAGA 59.679 50.000 0.00 0.00 0.00 3.27
850 856 0.723981 GGCAAAGATGAGCGTGAGAC 59.276 55.000 0.00 0.00 0.00 3.36
851 857 0.723981 GCAAAGATGAGCGTGAGACC 59.276 55.000 0.00 0.00 0.00 3.85
852 858 1.941209 GCAAAGATGAGCGTGAGACCA 60.941 52.381 0.00 0.00 0.00 4.02
854 860 3.005554 CAAAGATGAGCGTGAGACCATT 58.994 45.455 0.00 0.00 0.00 3.16
855 861 2.306341 AGATGAGCGTGAGACCATTG 57.694 50.000 0.00 0.00 0.00 2.82
857 863 0.036105 ATGAGCGTGAGACCATTGCA 60.036 50.000 0.00 0.00 0.00 4.08
858 864 0.950555 TGAGCGTGAGACCATTGCAC 60.951 55.000 0.00 0.00 0.00 4.57
859 865 0.950555 GAGCGTGAGACCATTGCACA 60.951 55.000 0.00 0.00 32.96 4.57
863 869 1.135603 CGTGAGACCATTGCACATTGG 60.136 52.381 9.47 9.47 37.73 3.16
865 871 0.889994 GAGACCATTGCACATTGGCA 59.110 50.000 10.69 0.00 43.19 4.92
878 1038 5.996513 TGCACATTGGCAAATAATTTCTTGT 59.003 32.000 3.01 0.00 41.65 3.16
881 1041 7.622672 GCACATTGGCAAATAATTTCTTGTCAG 60.623 37.037 3.01 0.00 38.32 3.51
884 1044 5.083122 TGGCAAATAATTTCTTGTCAGGGA 58.917 37.500 3.17 0.00 32.42 4.20
887 1047 6.097412 GGCAAATAATTTCTTGTCAGGGAGAT 59.903 38.462 0.35 0.00 0.00 2.75
888 1048 7.199078 GCAAATAATTTCTTGTCAGGGAGATC 58.801 38.462 0.00 0.00 0.00 2.75
891 1051 5.527026 AATTTCTTGTCAGGGAGATCCTT 57.473 39.130 0.00 0.00 45.47 3.36
892 1052 3.988976 TTCTTGTCAGGGAGATCCTTG 57.011 47.619 4.66 4.66 45.47 3.61
893 1053 1.556911 TCTTGTCAGGGAGATCCTTGC 59.443 52.381 6.13 2.97 45.47 4.01
900 1060 0.747283 GGGAGATCCTTGCTGTGCTG 60.747 60.000 0.00 0.00 35.95 4.41
901 1061 1.375098 GGAGATCCTTGCTGTGCTGC 61.375 60.000 0.00 0.00 0.00 5.25
904 1064 1.012841 GATCCTTGCTGTGCTGCTAC 58.987 55.000 0.00 0.00 0.00 3.58
905 1065 0.393537 ATCCTTGCTGTGCTGCTACC 60.394 55.000 0.00 0.00 0.00 3.18
906 1066 2.042831 CCTTGCTGTGCTGCTACCC 61.043 63.158 0.00 0.00 0.00 3.69
907 1067 1.002868 CTTGCTGTGCTGCTACCCT 60.003 57.895 0.00 0.00 0.00 4.34
913 1073 2.103042 GTGCTGCTACCCTTGCGAG 61.103 63.158 0.00 0.00 0.00 5.03
914 1074 2.266055 GCTGCTACCCTTGCGAGT 59.734 61.111 0.00 0.00 0.00 4.18
915 1075 1.254975 TGCTGCTACCCTTGCGAGTA 61.255 55.000 0.00 0.00 0.00 2.59
916 1076 0.806492 GCTGCTACCCTTGCGAGTAC 60.806 60.000 0.00 0.00 0.00 2.73
917 1077 0.179108 CTGCTACCCTTGCGAGTACC 60.179 60.000 0.00 0.00 0.00 3.34
918 1078 0.901114 TGCTACCCTTGCGAGTACCA 60.901 55.000 0.00 0.00 0.00 3.25
919 1079 0.459759 GCTACCCTTGCGAGTACCAC 60.460 60.000 0.00 0.00 0.00 4.16
921 1081 0.542467 TACCCTTGCGAGTACCACCA 60.542 55.000 0.00 0.00 0.00 4.17
923 1083 0.673644 CCCTTGCGAGTACCACCAAG 60.674 60.000 0.00 9.02 35.61 3.61
928 1088 0.948678 GCGAGTACCACCAAGCAAAA 59.051 50.000 0.00 0.00 0.00 2.44
929 1089 1.334689 GCGAGTACCACCAAGCAAAAC 60.335 52.381 0.00 0.00 0.00 2.43
960 1120 1.223487 GCGCCTTATCCTCCCAACA 59.777 57.895 0.00 0.00 0.00 3.33
966 1126 2.308866 CCTTATCCTCCCAACACAACCT 59.691 50.000 0.00 0.00 0.00 3.50
1081 1243 4.922026 GTCAACACCACCGCCGGT 62.922 66.667 1.02 1.02 41.07 5.28
1096 1258 3.982241 GGTGTGCTGTGCCAAGGC 61.982 66.667 3.61 3.61 42.35 4.35
1098 1260 4.519612 TGTGCTGTGCCAAGGCCA 62.520 61.111 5.01 5.43 41.09 5.36
1137 1299 4.265056 GGCCTGACAACCACCGGT 62.265 66.667 0.00 0.00 37.65 5.28
1194 1359 2.657143 GTGAGGTACGAGGAAGAGGAT 58.343 52.381 0.00 0.00 0.00 3.24
1257 1422 2.442272 GAGGCCTACAGCGAGGGA 60.442 66.667 4.42 0.00 45.17 4.20
1357 1647 3.490759 GATCCACCAGCGCACACG 61.491 66.667 11.47 0.00 44.07 4.49
1380 1670 2.766313 TGCACGTTGCTTCTTCTACAT 58.234 42.857 10.54 0.00 45.31 2.29
1385 1675 3.927142 ACGTTGCTTCTTCTACATGTAGC 59.073 43.478 25.31 16.98 33.32 3.58
1402 1692 1.762708 AGCCCATTTGGTTACGGATG 58.237 50.000 0.00 0.00 36.04 3.51
1403 1693 0.744281 GCCCATTTGGTTACGGATGG 59.256 55.000 0.00 0.00 38.98 3.51
1506 1796 1.068250 GAGAGGGCCGTCATACAGC 59.932 63.158 26.40 5.61 0.00 4.40
1507 1797 2.279517 GAGGGCCGTCATACAGCG 60.280 66.667 20.47 0.00 0.00 5.18
1550 1840 1.375396 CGACCCCAGCAACATCGAA 60.375 57.895 0.00 0.00 34.77 3.71
1603 1893 1.626356 AAGAGCCGCCTCCAATAGCA 61.626 55.000 0.00 0.00 38.96 3.49
1614 1931 5.450412 CGCCTCCAATAGCAAAACATGTAAT 60.450 40.000 0.00 0.00 0.00 1.89
1615 1932 6.238621 CGCCTCCAATAGCAAAACATGTAATA 60.239 38.462 0.00 0.00 0.00 0.98
1616 1933 7.141363 GCCTCCAATAGCAAAACATGTAATAG 58.859 38.462 0.00 0.00 0.00 1.73
1617 1934 7.013274 GCCTCCAATAGCAAAACATGTAATAGA 59.987 37.037 0.00 0.00 0.00 1.98
1618 1935 8.902806 CCTCCAATAGCAAAACATGTAATAGAA 58.097 33.333 0.00 0.00 0.00 2.10
1627 1944 9.840427 GCAAAACATGTAATAGAATTGTACTGT 57.160 29.630 0.00 0.00 0.00 3.55
1654 1971 4.037208 CAGGTTGTGAATCTTCTGCTGTTT 59.963 41.667 0.00 0.00 0.00 2.83
1665 1982 2.929641 TCTGCTGTTTGTGACCAATCA 58.070 42.857 0.00 0.00 0.00 2.57
1669 1986 3.066621 TGCTGTTTGTGACCAATCAGTTC 59.933 43.478 12.52 1.96 44.67 3.01
1692 2192 5.481122 TCAATTGGAGATCAAGGCATGAAAA 59.519 36.000 5.42 0.00 42.54 2.29
1693 2193 6.014413 TCAATTGGAGATCAAGGCATGAAAAA 60.014 34.615 5.42 0.00 42.54 1.94
1694 2194 5.395682 TTGGAGATCAAGGCATGAAAAAG 57.604 39.130 0.00 0.00 42.54 2.27
1695 2195 4.665451 TGGAGATCAAGGCATGAAAAAGA 58.335 39.130 0.00 0.00 42.54 2.52
1696 2196 5.266788 TGGAGATCAAGGCATGAAAAAGAT 58.733 37.500 0.00 0.00 42.54 2.40
1697 2197 5.126545 TGGAGATCAAGGCATGAAAAAGATG 59.873 40.000 0.00 0.00 42.54 2.90
1698 2198 5.359009 GGAGATCAAGGCATGAAAAAGATGA 59.641 40.000 0.00 0.00 42.54 2.92
1699 2199 6.040616 GGAGATCAAGGCATGAAAAAGATGAT 59.959 38.462 0.00 0.00 42.54 2.45
1700 2200 6.806751 AGATCAAGGCATGAAAAAGATGATG 58.193 36.000 0.00 0.00 42.54 3.07
1701 2201 6.605995 AGATCAAGGCATGAAAAAGATGATGA 59.394 34.615 0.00 0.00 42.54 2.92
1703 2203 7.177832 TCAAGGCATGAAAAAGATGATGAAT 57.822 32.000 0.00 0.00 34.30 2.57
1704 2204 8.296211 TCAAGGCATGAAAAAGATGATGAATA 57.704 30.769 0.00 0.00 34.30 1.75
1705 2205 8.192774 TCAAGGCATGAAAAAGATGATGAATAC 58.807 33.333 0.00 0.00 34.30 1.89
1706 2206 6.732154 AGGCATGAAAAAGATGATGAATACG 58.268 36.000 0.00 0.00 0.00 3.06
1707 2207 5.400485 GGCATGAAAAAGATGATGAATACGC 59.600 40.000 0.00 0.00 0.00 4.42
1708 2208 5.972973 GCATGAAAAAGATGATGAATACGCA 59.027 36.000 0.00 0.00 0.00 5.24
1709 2209 6.639686 GCATGAAAAAGATGATGAATACGCAT 59.360 34.615 0.00 0.00 0.00 4.73
1710 2210 7.358105 GCATGAAAAAGATGATGAATACGCATG 60.358 37.037 0.00 0.00 0.00 4.06
1711 2211 6.497437 TGAAAAAGATGATGAATACGCATGG 58.503 36.000 0.00 0.00 0.00 3.66
1712 2212 6.318396 TGAAAAAGATGATGAATACGCATGGA 59.682 34.615 0.00 0.00 0.00 3.41
1713 2213 6.698008 AAAAGATGATGAATACGCATGGAA 57.302 33.333 0.00 0.00 0.00 3.53
1714 2214 5.679734 AAGATGATGAATACGCATGGAAC 57.320 39.130 0.00 0.00 0.00 3.62
1715 2215 4.965814 AGATGATGAATACGCATGGAACT 58.034 39.130 0.00 0.00 0.00 3.01
1767 2272 8.804743 CAATTGAACAAAGAATACATCATCTGC 58.195 33.333 0.00 0.00 0.00 4.26
1773 2278 9.793252 AACAAAGAATACATCATCTGCATTAAC 57.207 29.630 0.00 0.00 0.00 2.01
1774 2279 8.959548 ACAAAGAATACATCATCTGCATTAACA 58.040 29.630 0.00 0.00 0.00 2.41
1775 2280 9.961265 CAAAGAATACATCATCTGCATTAACAT 57.039 29.630 0.00 0.00 0.00 2.71
1845 2352 0.034896 AACGGTGTCTGTCCATGTCC 59.965 55.000 0.00 0.00 0.00 4.02
2267 2777 2.564561 TTTGCCCACTGACTGGTGCA 62.565 55.000 0.00 0.00 41.73 4.57
2332 2843 5.718649 TGTGCGAAAATAGTAGATTCAGC 57.281 39.130 0.00 0.00 0.00 4.26
2489 3000 9.412460 ACCATGTTGATGTAAGATGATACATTT 57.588 29.630 1.87 0.00 44.44 2.32
2503 3014 9.417561 AGATGATACATTTGATCCTGAAACAAT 57.582 29.630 0.00 0.00 0.00 2.71
2559 3070 3.973657 TGTTGTCGACTCTGTTAAGGTC 58.026 45.455 17.92 0.00 0.00 3.85
2566 3077 4.086199 GACTCTGTTAAGGTCGACTCTG 57.914 50.000 16.46 5.83 0.00 3.35
2567 3078 3.488363 ACTCTGTTAAGGTCGACTCTGT 58.512 45.455 16.46 0.90 0.00 3.41
2568 3079 3.890147 ACTCTGTTAAGGTCGACTCTGTT 59.110 43.478 16.46 6.85 0.00 3.16
2569 3080 5.068636 ACTCTGTTAAGGTCGACTCTGTTA 58.931 41.667 16.46 5.90 0.00 2.41
2570 3081 5.533903 ACTCTGTTAAGGTCGACTCTGTTAA 59.466 40.000 16.46 11.22 0.00 2.01
2571 3082 6.010294 TCTGTTAAGGTCGACTCTGTTAAG 57.990 41.667 16.46 5.96 0.00 1.85
2572 3083 5.766670 TCTGTTAAGGTCGACTCTGTTAAGA 59.233 40.000 16.46 11.34 0.00 2.10
2573 3084 5.766222 TGTTAAGGTCGACTCTGTTAAGAC 58.234 41.667 16.46 5.71 0.00 3.01
2574 3085 3.555917 AAGGTCGACTCTGTTAAGACG 57.444 47.619 16.46 0.00 36.09 4.18
2575 3086 2.502295 AGGTCGACTCTGTTAAGACGT 58.498 47.619 16.46 0.00 36.17 4.34
2576 3087 3.668447 AGGTCGACTCTGTTAAGACGTA 58.332 45.455 16.46 0.00 36.17 3.57
2577 3088 4.260170 AGGTCGACTCTGTTAAGACGTAT 58.740 43.478 16.46 0.00 36.17 3.06
2578 3089 5.423015 AGGTCGACTCTGTTAAGACGTATA 58.577 41.667 16.46 0.00 36.17 1.47
2579 3090 5.293079 AGGTCGACTCTGTTAAGACGTATAC 59.707 44.000 16.46 0.00 36.17 1.47
2580 3091 5.186766 GTCGACTCTGTTAAGACGTATACG 58.813 45.833 23.24 23.24 46.33 3.06
2596 3107 6.045698 CGTATACGTAGTGATTGACTCTGT 57.954 41.667 17.16 0.00 45.73 3.41
2597 3108 6.484540 CGTATACGTAGTGATTGACTCTGTT 58.515 40.000 17.16 0.00 45.73 3.16
2598 3109 7.624661 CGTATACGTAGTGATTGACTCTGTTA 58.375 38.462 17.16 0.00 45.73 2.41
2599 3110 8.118607 CGTATACGTAGTGATTGACTCTGTTAA 58.881 37.037 17.16 0.00 45.73 2.01
2600 3111 9.219497 GTATACGTAGTGATTGACTCTGTTAAC 57.781 37.037 0.08 0.00 45.73 2.01
2601 3112 6.080648 ACGTAGTGATTGACTCTGTTAACA 57.919 37.500 8.28 8.28 42.51 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
249 250 1.528129 GGCTCACTTGCTGCTTTACT 58.472 50.000 0.00 0.00 0.00 2.24
252 253 2.263741 CGGGCTCACTTGCTGCTTT 61.264 57.895 0.00 0.00 0.00 3.51
273 274 1.444895 CACGGCAGCTTTGAATGGC 60.445 57.895 0.00 0.00 38.54 4.40
361 365 2.037772 GAGCAGGGTCTCACTTCTTCAA 59.962 50.000 0.00 0.00 33.41 2.69
362 366 1.620819 GAGCAGGGTCTCACTTCTTCA 59.379 52.381 0.00 0.00 33.41 3.02
363 367 1.899142 AGAGCAGGGTCTCACTTCTTC 59.101 52.381 0.00 0.00 35.59 2.87
374 378 1.400737 GGACGTACATAGAGCAGGGT 58.599 55.000 0.00 0.00 0.00 4.34
379 383 2.029623 TCAAGGGGACGTACATAGAGC 58.970 52.381 0.00 0.00 0.00 4.09
391 396 5.880332 CGATGATTTAACTTCTTCAAGGGGA 59.120 40.000 0.00 0.00 33.37 4.81
455 461 2.378445 ACCAACCAAGCAACAACAAC 57.622 45.000 0.00 0.00 0.00 3.32
456 462 2.613977 CCAACCAACCAAGCAACAACAA 60.614 45.455 0.00 0.00 0.00 2.83
457 463 1.066573 CCAACCAACCAAGCAACAACA 60.067 47.619 0.00 0.00 0.00 3.33
642 648 2.258013 CGAGCAGGCGAAAACCCAA 61.258 57.895 0.00 0.00 0.00 4.12
766 772 5.018539 TCAAAGAAAGAACAACGAGAGGA 57.981 39.130 0.00 0.00 0.00 3.71
773 779 8.978539 GGATAAACCATTCAAAGAAAGAACAAC 58.021 33.333 0.00 0.00 38.79 3.32
791 797 2.158957 TGACAGAGCATCCGGATAAACC 60.159 50.000 18.63 6.90 33.66 3.27
798 804 0.463295 AGCATTGACAGAGCATCCGG 60.463 55.000 0.00 0.00 33.66 5.14
799 805 0.656259 CAGCATTGACAGAGCATCCG 59.344 55.000 4.34 0.00 33.66 4.18
805 811 3.624305 GCATGCAGCATTGACAGAG 57.376 52.632 14.21 0.00 44.79 3.35
823 829 1.402456 GCTCATCTTTGCCAGCACAAG 60.402 52.381 0.00 0.37 0.00 3.16
829 835 0.725686 CTCACGCTCATCTTTGCCAG 59.274 55.000 0.00 0.00 0.00 4.85
830 836 0.321346 TCTCACGCTCATCTTTGCCA 59.679 50.000 0.00 0.00 0.00 4.92
831 837 0.723981 GTCTCACGCTCATCTTTGCC 59.276 55.000 0.00 0.00 0.00 4.52
832 838 0.723981 GGTCTCACGCTCATCTTTGC 59.276 55.000 0.00 0.00 0.00 3.68
833 839 2.084610 TGGTCTCACGCTCATCTTTG 57.915 50.000 0.00 0.00 0.00 2.77
834 840 3.005554 CAATGGTCTCACGCTCATCTTT 58.994 45.455 0.00 0.00 0.00 2.52
835 841 2.625737 CAATGGTCTCACGCTCATCTT 58.374 47.619 0.00 0.00 0.00 2.40
836 842 1.741732 GCAATGGTCTCACGCTCATCT 60.742 52.381 0.00 0.00 0.00 2.90
837 843 0.654683 GCAATGGTCTCACGCTCATC 59.345 55.000 0.00 0.00 0.00 2.92
838 844 0.036105 TGCAATGGTCTCACGCTCAT 60.036 50.000 0.00 0.00 0.00 2.90
840 846 0.950555 TGTGCAATGGTCTCACGCTC 60.951 55.000 0.00 0.00 33.69 5.03
842 848 0.523072 AATGTGCAATGGTCTCACGC 59.477 50.000 0.00 0.00 33.69 5.34
843 849 1.135603 CCAATGTGCAATGGTCTCACG 60.136 52.381 6.33 0.00 33.69 4.35
845 851 0.889994 GCCAATGTGCAATGGTCTCA 59.110 50.000 14.03 0.00 39.00 3.27
846 852 0.889994 TGCCAATGTGCAATGGTCTC 59.110 50.000 14.03 1.47 38.56 3.36
848 854 3.910817 TTGCCAATGTGCAATGGTC 57.089 47.368 14.03 8.38 45.77 4.02
854 860 5.996513 ACAAGAAATTATTTGCCAATGTGCA 59.003 32.000 0.00 0.00 40.07 4.57
855 861 6.147492 TGACAAGAAATTATTTGCCAATGTGC 59.853 34.615 0.00 0.00 0.00 4.57
857 863 6.875195 CCTGACAAGAAATTATTTGCCAATGT 59.125 34.615 0.00 0.00 0.00 2.71
858 864 6.314400 CCCTGACAAGAAATTATTTGCCAATG 59.686 38.462 0.00 0.00 0.00 2.82
859 865 6.213195 TCCCTGACAAGAAATTATTTGCCAAT 59.787 34.615 0.00 0.00 0.00 3.16
863 869 6.515272 TCTCCCTGACAAGAAATTATTTGC 57.485 37.500 0.00 0.00 0.00 3.68
865 871 7.646884 AGGATCTCCCTGACAAGAAATTATTT 58.353 34.615 0.00 0.00 45.61 1.40
866 872 7.218314 AGGATCTCCCTGACAAGAAATTATT 57.782 36.000 0.00 0.00 45.61 1.40
867 873 6.838401 AGGATCTCCCTGACAAGAAATTAT 57.162 37.500 0.00 0.00 45.61 1.28
881 1041 0.747283 CAGCACAGCAAGGATCTCCC 60.747 60.000 0.00 0.00 36.42 4.30
884 1044 0.907486 TAGCAGCACAGCAAGGATCT 59.093 50.000 0.00 0.00 36.85 2.75
887 1047 1.003355 GGTAGCAGCACAGCAAGGA 60.003 57.895 0.00 0.00 36.85 3.36
888 1048 2.042831 GGGTAGCAGCACAGCAAGG 61.043 63.158 0.00 0.00 36.85 3.61
891 1051 1.302752 CAAGGGTAGCAGCACAGCA 60.303 57.895 0.00 0.00 36.85 4.41
892 1052 2.694760 GCAAGGGTAGCAGCACAGC 61.695 63.158 0.00 0.00 0.00 4.40
893 1053 2.393768 CGCAAGGGTAGCAGCACAG 61.394 63.158 0.00 0.00 0.00 3.66
905 1065 1.298859 GCTTGGTGGTACTCGCAAGG 61.299 60.000 0.00 0.00 33.78 3.61
906 1066 0.602638 TGCTTGGTGGTACTCGCAAG 60.603 55.000 0.00 0.00 35.14 4.01
907 1067 0.179043 TTGCTTGGTGGTACTCGCAA 60.179 50.000 0.00 0.00 35.30 4.85
913 1073 2.801699 GCCTTGTTTTGCTTGGTGGTAC 60.802 50.000 0.00 0.00 0.00 3.34
914 1074 1.410882 GCCTTGTTTTGCTTGGTGGTA 59.589 47.619 0.00 0.00 0.00 3.25
915 1075 0.177836 GCCTTGTTTTGCTTGGTGGT 59.822 50.000 0.00 0.00 0.00 4.16
916 1076 0.465287 AGCCTTGTTTTGCTTGGTGG 59.535 50.000 0.00 0.00 32.94 4.61
917 1077 1.856802 GAGCCTTGTTTTGCTTGGTG 58.143 50.000 0.00 0.00 38.11 4.17
918 1078 0.385390 CGAGCCTTGTTTTGCTTGGT 59.615 50.000 0.00 0.00 38.11 3.67
919 1079 0.385390 ACGAGCCTTGTTTTGCTTGG 59.615 50.000 0.00 0.00 42.24 3.61
921 1081 1.607148 GGTACGAGCCTTGTTTTGCTT 59.393 47.619 0.00 0.00 38.11 3.91
923 1083 3.767287 GGTACGAGCCTTGTTTTGC 57.233 52.632 0.00 0.00 0.00 3.68
960 1120 4.496670 GCGATGAGCGTAGGTTGT 57.503 55.556 0.00 0.00 43.41 3.32
985 1147 2.046988 CATGCTCACGGTGCTGGA 60.047 61.111 2.51 0.43 0.00 3.86
992 1154 4.465512 GCAACGCCATGCTCACGG 62.466 66.667 1.30 0.00 43.06 4.94
994 1156 2.126734 GTGCAACGCCATGCTCAC 60.127 61.111 9.49 0.00 46.54 3.51
1061 1223 2.358247 GGCGGTGGTGTTGACGAT 60.358 61.111 0.00 0.00 0.00 3.73
1081 1243 4.519612 TGGCCTTGGCACAGCACA 62.520 61.111 14.04 0.00 42.39 4.57
1194 1359 0.107800 CGTACTCCTCCTCGTCCTCA 60.108 60.000 0.00 0.00 0.00 3.86
1309 1474 1.738099 CCTTGAAGACGAGCACGGG 60.738 63.158 8.74 0.00 44.46 5.28
1344 1634 3.792047 CATCCGTGTGCGCTGGTG 61.792 66.667 9.73 3.33 36.67 4.17
1363 1653 3.927142 GCTACATGTAGAAGAAGCAACGT 59.073 43.478 32.39 0.00 35.21 3.99
1380 1670 1.629353 TCCGTAACCAAATGGGCTACA 59.371 47.619 4.17 0.00 42.05 2.74
1385 1675 2.428544 TCCATCCGTAACCAAATGGG 57.571 50.000 4.17 0.00 39.33 4.00
1402 1692 1.081242 CACGCACAACAAGGCATCC 60.081 57.895 0.00 0.00 0.00 3.51
1403 1693 1.081242 CCACGCACAACAAGGCATC 60.081 57.895 0.00 0.00 0.00 3.91
1506 1796 3.458579 CTTGACCACGTCGACGCG 61.459 66.667 35.92 27.39 44.43 6.01
1507 1797 3.103911 CCTTGACCACGTCGACGC 61.104 66.667 35.92 20.72 44.43 5.19
1550 1840 2.243810 GGCAGATCCTTCTCGAGGTAT 58.756 52.381 13.56 1.00 46.39 2.73
1614 1931 7.231925 TCACAACCTGTCTACAGTACAATTCTA 59.768 37.037 9.17 0.00 42.27 2.10
1615 1932 6.041637 TCACAACCTGTCTACAGTACAATTCT 59.958 38.462 9.17 0.00 42.27 2.40
1616 1933 6.220930 TCACAACCTGTCTACAGTACAATTC 58.779 40.000 9.17 0.00 42.27 2.17
1617 1934 6.169557 TCACAACCTGTCTACAGTACAATT 57.830 37.500 9.17 0.00 42.27 2.32
1618 1935 5.801531 TCACAACCTGTCTACAGTACAAT 57.198 39.130 9.17 0.00 42.27 2.71
1619 1936 5.601583 TTCACAACCTGTCTACAGTACAA 57.398 39.130 9.17 0.00 42.27 2.41
1620 1937 5.538813 AGATTCACAACCTGTCTACAGTACA 59.461 40.000 9.17 0.00 42.27 2.90
1621 1938 6.026947 AGATTCACAACCTGTCTACAGTAC 57.973 41.667 9.17 0.00 42.27 2.73
1622 1939 6.493802 AGAAGATTCACAACCTGTCTACAGTA 59.506 38.462 9.17 0.00 42.27 2.74
1623 1940 5.305644 AGAAGATTCACAACCTGTCTACAGT 59.694 40.000 9.17 0.00 42.27 3.55
1624 1941 5.636965 CAGAAGATTCACAACCTGTCTACAG 59.363 44.000 3.02 3.02 43.40 2.74
1625 1942 5.541845 CAGAAGATTCACAACCTGTCTACA 58.458 41.667 0.00 0.00 0.00 2.74
1626 1943 4.390297 GCAGAAGATTCACAACCTGTCTAC 59.610 45.833 0.00 0.00 0.00 2.59
1627 1944 4.284490 AGCAGAAGATTCACAACCTGTCTA 59.716 41.667 0.00 0.00 0.00 2.59
1628 1945 3.072184 AGCAGAAGATTCACAACCTGTCT 59.928 43.478 0.00 0.00 0.00 3.41
1629 1946 3.188048 CAGCAGAAGATTCACAACCTGTC 59.812 47.826 0.00 0.00 0.00 3.51
1630 1947 3.144506 CAGCAGAAGATTCACAACCTGT 58.855 45.455 0.00 0.00 0.00 4.00
1631 1948 3.144506 ACAGCAGAAGATTCACAACCTG 58.855 45.455 0.00 0.00 0.00 4.00
1632 1949 3.498774 ACAGCAGAAGATTCACAACCT 57.501 42.857 0.00 0.00 0.00 3.50
1633 1950 4.202050 ACAAACAGCAGAAGATTCACAACC 60.202 41.667 0.00 0.00 0.00 3.77
1634 1951 4.736793 CACAAACAGCAGAAGATTCACAAC 59.263 41.667 0.00 0.00 0.00 3.32
1635 1952 4.639755 TCACAAACAGCAGAAGATTCACAA 59.360 37.500 0.00 0.00 0.00 3.33
1636 1953 4.035558 GTCACAAACAGCAGAAGATTCACA 59.964 41.667 0.00 0.00 0.00 3.58
1637 1954 4.531332 GTCACAAACAGCAGAAGATTCAC 58.469 43.478 0.00 0.00 0.00 3.18
1638 1955 3.565482 GGTCACAAACAGCAGAAGATTCA 59.435 43.478 0.00 0.00 0.00 2.57
1639 1956 3.565482 TGGTCACAAACAGCAGAAGATTC 59.435 43.478 0.00 0.00 0.00 2.52
1640 1957 3.554934 TGGTCACAAACAGCAGAAGATT 58.445 40.909 0.00 0.00 0.00 2.40
1641 1958 3.213206 TGGTCACAAACAGCAGAAGAT 57.787 42.857 0.00 0.00 0.00 2.40
1654 1971 4.852134 CCAATTGAACTGATTGGTCACA 57.148 40.909 7.12 0.00 42.93 3.58
1665 1982 4.038271 TGCCTTGATCTCCAATTGAACT 57.962 40.909 7.12 0.00 33.68 3.01
1669 1986 4.994907 TTCATGCCTTGATCTCCAATTG 57.005 40.909 0.00 0.00 33.34 2.32
1676 1993 6.605995 TCATCATCTTTTTCATGCCTTGATCT 59.394 34.615 0.00 0.00 33.34 2.75
1692 2192 5.371526 AGTTCCATGCGTATTCATCATCTT 58.628 37.500 0.00 0.00 0.00 2.40
1693 2193 4.965814 AGTTCCATGCGTATTCATCATCT 58.034 39.130 0.00 0.00 0.00 2.90
1694 2194 5.679734 AAGTTCCATGCGTATTCATCATC 57.320 39.130 0.00 0.00 0.00 2.92
1695 2195 5.221106 CCAAAGTTCCATGCGTATTCATCAT 60.221 40.000 0.00 0.00 0.00 2.45
1696 2196 4.096231 CCAAAGTTCCATGCGTATTCATCA 59.904 41.667 0.00 0.00 0.00 3.07
1697 2197 4.335315 TCCAAAGTTCCATGCGTATTCATC 59.665 41.667 0.00 0.00 0.00 2.92
1698 2198 4.269183 TCCAAAGTTCCATGCGTATTCAT 58.731 39.130 0.00 0.00 0.00 2.57
1699 2199 3.680490 TCCAAAGTTCCATGCGTATTCA 58.320 40.909 0.00 0.00 0.00 2.57
1700 2200 3.065371 CCTCCAAAGTTCCATGCGTATTC 59.935 47.826 0.00 0.00 0.00 1.75
1701 2201 3.016736 CCTCCAAAGTTCCATGCGTATT 58.983 45.455 0.00 0.00 0.00 1.89
1703 2203 1.626321 TCCTCCAAAGTTCCATGCGTA 59.374 47.619 0.00 0.00 0.00 4.42
1704 2204 0.400213 TCCTCCAAAGTTCCATGCGT 59.600 50.000 0.00 0.00 0.00 5.24
1705 2205 1.672881 GATCCTCCAAAGTTCCATGCG 59.327 52.381 0.00 0.00 0.00 4.73
1706 2206 1.672881 CGATCCTCCAAAGTTCCATGC 59.327 52.381 0.00 0.00 0.00 4.06
1707 2207 2.679837 CACGATCCTCCAAAGTTCCATG 59.320 50.000 0.00 0.00 0.00 3.66
1708 2208 2.571653 TCACGATCCTCCAAAGTTCCAT 59.428 45.455 0.00 0.00 0.00 3.41
1709 2209 1.974957 TCACGATCCTCCAAAGTTCCA 59.025 47.619 0.00 0.00 0.00 3.53
1710 2210 2.233922 TCTCACGATCCTCCAAAGTTCC 59.766 50.000 0.00 0.00 0.00 3.62
1711 2211 3.594603 TCTCACGATCCTCCAAAGTTC 57.405 47.619 0.00 0.00 0.00 3.01
1712 2212 4.319177 CTTTCTCACGATCCTCCAAAGTT 58.681 43.478 0.00 0.00 0.00 2.66
1713 2213 3.866449 GCTTTCTCACGATCCTCCAAAGT 60.866 47.826 0.00 0.00 0.00 2.66
1714 2214 2.675348 GCTTTCTCACGATCCTCCAAAG 59.325 50.000 0.00 0.00 0.00 2.77
1715 2215 2.038426 TGCTTTCTCACGATCCTCCAAA 59.962 45.455 0.00 0.00 0.00 3.28
1731 2231 8.842358 ATTCTTTGTTCAATTGATGATGCTTT 57.158 26.923 9.40 0.00 38.03 3.51
1733 2233 8.525316 TGTATTCTTTGTTCAATTGATGATGCT 58.475 29.630 9.40 0.00 38.03 3.79
1773 2278 7.645735 CCTCCTGTATGATTCGTATCGATTATG 59.354 40.741 1.71 0.00 35.23 1.90
1774 2279 7.682261 GCCTCCTGTATGATTCGTATCGATTAT 60.682 40.741 1.71 0.00 35.23 1.28
1775 2280 6.404403 GCCTCCTGTATGATTCGTATCGATTA 60.404 42.308 1.71 0.00 35.23 1.75
1776 2281 5.622460 GCCTCCTGTATGATTCGTATCGATT 60.622 44.000 1.71 0.00 35.23 3.34
1811 2318 0.103937 CCGTTGCTTCTTTTGGCCAA 59.896 50.000 16.05 16.05 0.00 4.52
1812 2319 1.040339 ACCGTTGCTTCTTTTGGCCA 61.040 50.000 0.00 0.00 0.00 5.36
1813 2320 0.597377 CACCGTTGCTTCTTTTGGCC 60.597 55.000 0.00 0.00 0.00 5.36
1814 2321 0.102300 ACACCGTTGCTTCTTTTGGC 59.898 50.000 0.00 0.00 0.00 4.52
1815 2322 1.676006 AGACACCGTTGCTTCTTTTGG 59.324 47.619 0.00 0.00 0.00 3.28
1816 2323 2.097466 ACAGACACCGTTGCTTCTTTTG 59.903 45.455 0.00 0.00 0.00 2.44
1817 2324 2.354821 GACAGACACCGTTGCTTCTTTT 59.645 45.455 0.00 0.00 0.00 2.27
1861 2368 1.334149 GCTTTCTTGCCGAGTGTTGTC 60.334 52.381 0.00 0.00 0.00 3.18
2008 2515 1.185618 TGGAGCTGTACAAGTCCGCT 61.186 55.000 15.27 11.40 32.01 5.52
2218 2728 6.849588 ATTTTCACCAGACTTCAATTTTGC 57.150 33.333 0.00 0.00 0.00 3.68
2226 2736 7.852454 GCAAATTGAAAATTTTCACCAGACTTC 59.148 33.333 28.78 12.34 45.99 3.01
2267 2777 6.493166 TGATCTTCCACTTCAATTTACCCAT 58.507 36.000 0.00 0.00 0.00 4.00
2332 2843 8.324163 AGAGGTATGTTTTTGCTAACTACTTG 57.676 34.615 0.00 0.00 0.00 3.16
2489 3000 2.617788 CCGTCCCATTGTTTCAGGATCA 60.618 50.000 0.00 0.00 0.00 2.92
2500 3011 1.374560 TTAATGACGCCGTCCCATTG 58.625 50.000 15.60 0.00 33.21 2.82
2503 3014 1.758280 AGTATTAATGACGCCGTCCCA 59.242 47.619 15.60 0.00 0.00 4.37
2573 3084 6.045698 ACAGAGTCAATCACTACGTATACG 57.954 41.667 23.24 23.24 39.66 3.06
2574 3085 9.219497 GTTAACAGAGTCAATCACTACGTATAC 57.781 37.037 0.00 0.00 34.41 1.47
2575 3086 8.949177 TGTTAACAGAGTCAATCACTACGTATA 58.051 33.333 3.59 0.00 34.41 1.47
2576 3087 7.823665 TGTTAACAGAGTCAATCACTACGTAT 58.176 34.615 3.59 0.00 34.41 3.06
2577 3088 7.205737 TGTTAACAGAGTCAATCACTACGTA 57.794 36.000 3.59 0.00 34.41 3.57
2578 3089 6.080648 TGTTAACAGAGTCAATCACTACGT 57.919 37.500 3.59 0.00 34.41 3.57


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

AutoCloner maintained by Alex Coulton.