Multiple sequence alignment - TraesCS3D01G146500

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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 TraesCS3D01G146500 chr3D 100.000 3743 0 0 1 3743 110397934 110394192 0.000000e+00 6913
1 TraesCS3D01G146500 chr3B 92.420 2810 109 44 733 3528 161636853 161634134 0.000000e+00 3914
2 TraesCS3D01G146500 chr3B 93.971 680 23 4 1 662 161637695 161637016 0.000000e+00 1013
3 TraesCS3D01G146500 chr3B 98.013 151 3 0 3593 3743 161634141 161633991 2.870000e-66 263
4 TraesCS3D01G146500 chr3A 92.019 1942 120 20 938 2861 119694037 119695961 0.000000e+00 2695
5 TraesCS3D01G146500 chr3A 92.988 656 27 5 9 649 119692950 119693601 0.000000e+00 939
6 TraesCS3D01G146500 chr3A 87.674 576 45 13 2892 3458 119695959 119696517 0.000000e+00 647
7 TraesCS3D01G146500 chr3A 83.448 145 16 3 3530 3673 119696522 119696659 1.090000e-25 128


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 TraesCS3D01G146500 chr3D 110394192 110397934 3742 True 6913.00 6913 100.000000 1 3743 1 chr3D.!!$R1 3742
1 TraesCS3D01G146500 chr3B 161633991 161637695 3704 True 1730.00 3914 94.801333 1 3743 3 chr3B.!!$R1 3742
2 TraesCS3D01G146500 chr3A 119692950 119696659 3709 False 1102.25 2695 89.032250 9 3673 4 chr3A.!!$F1 3664


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
931 1153 0.093535 CGTTGACGTGTGCATAGCAG 59.906 55.0 0.00 0.0 35.11 4.24 F
932 1154 0.179215 GTTGACGTGTGCATAGCAGC 60.179 55.0 0.00 0.0 40.08 5.25 F
938 1160 0.238289 GTGTGCATAGCAGCGTTGTT 59.762 50.0 0.00 0.0 40.08 2.83 F
1640 1878 0.392998 GGAGATGGCTTCTTTGCGGA 60.393 55.0 4.23 0.0 33.74 5.54 F
1930 2186 0.804989 GAGGGAGTGTGCAAAATCCG 59.195 55.0 16.90 0.0 32.30 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1906 2162 0.257328 TTTGCACACTCCCTCCACAA 59.743 50.000 0.00 0.0 0.00 3.33 R
2573 2837 0.721718 CTTCAGGTTTAAGCGCCTCG 59.278 55.000 2.29 0.0 31.73 4.63 R
2577 2841 1.001815 TGCAACTTCAGGTTTAAGCGC 60.002 47.619 0.00 0.0 35.74 5.92 R
2603 2867 1.132849 TGGTCCCTCACCTCTGAAAGA 60.133 52.381 0.00 0.0 46.98 2.52 R
3677 3959 1.212935 GCCCCACATGACATCCTTACT 59.787 52.381 0.00 0.0 0.00 2.24 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
98 100 9.778741 TTGTTATCTAAAATGTATCTAGCCCTG 57.221 33.333 0.00 0.00 0.00 4.45
158 160 6.604795 CCAAAATGATGAACCTAACATCTCCT 59.395 38.462 0.00 0.00 42.89 3.69
168 170 6.051179 ACCTAACATCTCCTGTTTCCTTAC 57.949 41.667 0.00 0.00 45.98 2.34
417 423 8.420374 TTGCAGTTATGTAACTATTGTAGAGC 57.580 34.615 5.19 3.64 44.19 4.09
665 721 5.183140 TGCTCTAAGCTGAAACATTTTACCC 59.817 40.000 0.11 0.00 42.97 3.69
674 730 4.901849 TGAAACATTTTACCCCAATGTGGA 59.098 37.500 0.00 0.00 42.80 4.02
695 782 4.315803 GAGGCAGTAGAAAAGTAGCACAA 58.684 43.478 0.00 0.00 0.00 3.33
715 802 5.743398 CACAATCGTTTTGCTTTTCTGAAGA 59.257 36.000 0.00 0.00 0.00 2.87
716 803 6.418819 CACAATCGTTTTGCTTTTCTGAAGAT 59.581 34.615 0.00 0.00 0.00 2.40
717 804 6.418819 ACAATCGTTTTGCTTTTCTGAAGATG 59.581 34.615 0.00 0.00 0.00 2.90
718 805 4.858935 TCGTTTTGCTTTTCTGAAGATGG 58.141 39.130 0.00 0.00 0.00 3.51
719 806 3.983344 CGTTTTGCTTTTCTGAAGATGGG 59.017 43.478 0.00 0.00 0.00 4.00
720 807 4.309933 GTTTTGCTTTTCTGAAGATGGGG 58.690 43.478 0.00 0.00 0.00 4.96
722 809 1.203038 TGCTTTTCTGAAGATGGGGCA 60.203 47.619 0.00 0.00 0.00 5.36
723 810 1.475682 GCTTTTCTGAAGATGGGGCAG 59.524 52.381 0.00 0.00 0.00 4.85
724 811 2.097825 CTTTTCTGAAGATGGGGCAGG 58.902 52.381 0.00 0.00 0.00 4.85
725 812 0.332632 TTTCTGAAGATGGGGCAGGG 59.667 55.000 0.00 0.00 0.00 4.45
727 814 3.728292 CTGAAGATGGGGCAGGGGC 62.728 68.421 0.00 0.00 40.13 5.80
764 955 2.338809 TCTGAGTTTGTCTCCCCACAT 58.661 47.619 0.00 0.00 42.12 3.21
774 965 2.497273 GTCTCCCCACATTTCCAATTGG 59.503 50.000 19.08 19.08 0.00 3.16
778 969 3.326297 TCCCCACATTTCCAATTGGTTTC 59.674 43.478 23.76 0.00 36.34 2.78
784 975 6.989169 CCACATTTCCAATTGGTTTCACTTTA 59.011 34.615 23.76 0.00 36.34 1.85
815 1037 6.332630 GGTGAATAAGTTGTGCTATGCAAAT 58.667 36.000 0.00 0.00 41.47 2.32
817 1039 6.473455 GTGAATAAGTTGTGCTATGCAAATCC 59.527 38.462 0.00 0.00 41.47 3.01
823 1045 5.048364 AGTTGTGCTATGCAAATCCGTTTTA 60.048 36.000 0.00 0.00 41.47 1.52
824 1046 4.728534 TGTGCTATGCAAATCCGTTTTAC 58.271 39.130 0.00 0.00 41.47 2.01
846 1068 5.600696 ACTAGTTTGTTTCCCTGCAAAATG 58.399 37.500 0.00 0.00 36.51 2.32
848 1070 3.199727 AGTTTGTTTCCCTGCAAAATGGT 59.800 39.130 0.00 0.00 36.51 3.55
851 1073 0.965439 TTTCCCTGCAAAATGGTCCG 59.035 50.000 0.00 0.00 0.00 4.79
855 1077 0.523072 CCTGCAAAATGGTCCGACTG 59.477 55.000 0.00 0.00 0.00 3.51
858 1080 1.234821 GCAAAATGGTCCGACTGACA 58.765 50.000 0.00 0.00 46.38 3.58
867 1089 0.894184 TCCGACTGACAGTGGACCTC 60.894 60.000 18.20 0.00 0.00 3.85
886 1108 1.463553 CGCCTTTGACCTGGCCTTTT 61.464 55.000 3.32 0.00 45.90 2.27
904 1126 1.462616 TTTTGTGGCCATCTCATCGG 58.537 50.000 9.72 0.00 0.00 4.18
909 1131 2.824546 GCCATCTCATCGGCTGGA 59.175 61.111 0.00 0.00 45.29 3.86
910 1132 1.596477 GCCATCTCATCGGCTGGAC 60.596 63.158 0.00 0.00 45.29 4.02
911 1133 1.300465 CCATCTCATCGGCTGGACG 60.300 63.158 0.00 0.00 0.00 4.79
912 1134 1.953138 CATCTCATCGGCTGGACGC 60.953 63.158 0.00 0.00 38.13 5.19
913 1135 3.490793 ATCTCATCGGCTGGACGCG 62.491 63.158 3.53 3.53 40.44 6.01
914 1136 4.498520 CTCATCGGCTGGACGCGT 62.499 66.667 13.85 13.85 40.44 6.01
915 1137 3.989698 CTCATCGGCTGGACGCGTT 62.990 63.158 15.53 0.00 40.44 4.84
916 1138 3.853330 CATCGGCTGGACGCGTTG 61.853 66.667 15.53 8.42 40.44 4.10
917 1139 4.063967 ATCGGCTGGACGCGTTGA 62.064 61.111 15.53 5.45 40.44 3.18
927 1149 3.151798 CGCGTTGACGTGTGCATA 58.848 55.556 8.78 0.00 44.02 3.14
928 1150 1.057208 CGCGTTGACGTGTGCATAG 59.943 57.895 8.78 0.00 44.02 2.23
929 1151 1.225745 GCGTTGACGTGTGCATAGC 60.226 57.895 0.00 0.00 42.22 2.97
930 1152 1.896339 GCGTTGACGTGTGCATAGCA 61.896 55.000 0.00 0.00 42.22 3.49
931 1153 0.093535 CGTTGACGTGTGCATAGCAG 59.906 55.000 0.00 0.00 35.11 4.24
932 1154 0.179215 GTTGACGTGTGCATAGCAGC 60.179 55.000 0.00 0.00 40.08 5.25
933 1155 1.625759 TTGACGTGTGCATAGCAGCG 61.626 55.000 0.00 12.22 40.08 5.18
934 1156 2.048222 ACGTGTGCATAGCAGCGT 60.048 55.556 13.25 13.25 42.87 5.07
935 1157 1.626654 GACGTGTGCATAGCAGCGTT 61.627 55.000 17.88 6.76 45.70 4.84
936 1158 1.225827 CGTGTGCATAGCAGCGTTG 60.226 57.895 0.00 0.00 40.08 4.10
937 1159 1.868997 GTGTGCATAGCAGCGTTGT 59.131 52.632 0.00 0.00 40.08 3.32
938 1160 0.238289 GTGTGCATAGCAGCGTTGTT 59.762 50.000 0.00 0.00 40.08 2.83
939 1161 1.463056 GTGTGCATAGCAGCGTTGTTA 59.537 47.619 0.00 0.00 40.08 2.41
940 1162 2.095853 GTGTGCATAGCAGCGTTGTTAT 59.904 45.455 2.82 2.82 40.08 1.89
941 1163 2.351418 TGTGCATAGCAGCGTTGTTATC 59.649 45.455 5.67 3.03 40.08 1.75
942 1164 1.939934 TGCATAGCAGCGTTGTTATCC 59.060 47.619 5.67 0.00 37.31 2.59
943 1165 2.213499 GCATAGCAGCGTTGTTATCCT 58.787 47.619 5.67 0.00 29.42 3.24
944 1166 3.181470 TGCATAGCAGCGTTGTTATCCTA 60.181 43.478 5.67 0.00 37.31 2.94
945 1167 3.430218 GCATAGCAGCGTTGTTATCCTAG 59.570 47.826 5.67 0.00 29.42 3.02
946 1168 1.941325 AGCAGCGTTGTTATCCTAGC 58.059 50.000 0.00 0.00 0.00 3.42
1188 1420 1.890041 CGCCCCGAACACTGACAAA 60.890 57.895 0.00 0.00 0.00 2.83
1194 1426 0.878523 CGAACACTGACAAAGCGGGA 60.879 55.000 0.00 0.00 0.00 5.14
1195 1427 0.586802 GAACACTGACAAAGCGGGAC 59.413 55.000 0.00 0.00 0.00 4.46
1197 1429 1.071471 CACTGACAAAGCGGGACCT 59.929 57.895 0.00 0.00 0.00 3.85
1208 1440 4.475135 GGGACCTCCAGAAGCCGC 62.475 72.222 0.00 0.00 37.91 6.53
1450 1688 0.881118 TTTCATCGAGCAAGTTGGGC 59.119 50.000 4.75 0.00 0.00 5.36
1632 1870 1.225704 CACCCTGGGAGATGGCTTC 59.774 63.158 22.23 0.00 0.00 3.86
1633 1871 1.083706 ACCCTGGGAGATGGCTTCT 59.916 57.895 22.23 2.05 37.41 2.85
1634 1872 0.551131 ACCCTGGGAGATGGCTTCTT 60.551 55.000 22.23 0.00 33.74 2.52
1635 1873 0.627986 CCCTGGGAGATGGCTTCTTT 59.372 55.000 7.01 0.00 33.74 2.52
1636 1874 1.684248 CCCTGGGAGATGGCTTCTTTG 60.684 57.143 7.01 0.00 33.74 2.77
1637 1875 1.101331 CTGGGAGATGGCTTCTTTGC 58.899 55.000 4.23 0.00 33.74 3.68
1638 1876 0.677731 TGGGAGATGGCTTCTTTGCG 60.678 55.000 4.23 0.00 33.74 4.85
1639 1877 1.379642 GGGAGATGGCTTCTTTGCGG 61.380 60.000 4.23 0.00 33.74 5.69
1640 1878 0.392998 GGAGATGGCTTCTTTGCGGA 60.393 55.000 4.23 0.00 33.74 5.54
1724 1972 0.890996 CTTGGGTTCAGGTGAGTGCC 60.891 60.000 0.00 0.00 0.00 5.01
1726 1974 2.358737 GGTTCAGGTGAGTGCCCG 60.359 66.667 0.00 0.00 0.00 6.13
1732 1980 0.951040 CAGGTGAGTGCCCGAAGAAC 60.951 60.000 0.00 0.00 0.00 3.01
1759 2007 6.567050 GGCAGTGTGAATATTGAATTGATGT 58.433 36.000 0.00 0.00 0.00 3.06
1906 2162 4.641989 GTGATATGCCTGTCCACAATCTTT 59.358 41.667 0.00 0.00 0.00 2.52
1930 2186 0.804989 GAGGGAGTGTGCAAAATCCG 59.195 55.000 16.90 0.00 32.30 4.18
1985 2241 2.625790 CTCTAGTACAGGTGCCAGATCC 59.374 54.545 0.00 0.00 0.00 3.36
2014 2270 6.538742 TCCTTCTCTGTTACACTGTCAAAAAG 59.461 38.462 0.00 0.00 0.00 2.27
2496 2755 6.726490 ATACCTCGAGAATGGTAAGCTTTA 57.274 37.500 15.71 0.00 41.48 1.85
2573 2837 9.341899 GTATTGTTGATGTTTTTCAGGTATGAC 57.658 33.333 0.00 0.00 34.35 3.06
2577 2841 4.935205 TGATGTTTTTCAGGTATGACGAGG 59.065 41.667 0.00 0.00 34.35 4.63
2603 2867 3.825143 AAACCTGAAGTTGCAAGCAAT 57.175 38.095 11.00 0.00 39.19 3.56
2755 3019 5.759059 TGAATGGCTAAAATCTCACCTGAT 58.241 37.500 0.00 0.00 0.00 2.90
2833 3097 7.992608 ACCTTTTTCTTGGTTTATTTTGATGCT 59.007 29.630 0.00 0.00 31.62 3.79
2895 3159 1.605753 GGTTGGTCACCTTGTCCTTC 58.394 55.000 0.00 0.00 43.29 3.46
2957 3221 5.349543 TGCATGATCACATCTATTATGTCGC 59.650 40.000 0.00 0.00 34.15 5.19
2979 3243 9.507280 GTCGCATTATCATTATGGAAATTATGG 57.493 33.333 0.00 0.00 0.00 2.74
2980 3244 9.460019 TCGCATTATCATTATGGAAATTATGGA 57.540 29.630 0.00 0.00 0.00 3.41
3064 3328 6.922957 GTGCACTTTGAATGATTGTAGGAAAA 59.077 34.615 10.32 0.00 0.00 2.29
3178 3443 2.037641 GCCTCAAAGTTTTTGATGGGCT 59.962 45.455 19.44 0.00 37.03 5.19
3180 3445 4.809673 CCTCAAAGTTTTTGATGGGCTAC 58.190 43.478 4.85 0.00 0.00 3.58
3181 3446 4.280677 CCTCAAAGTTTTTGATGGGCTACA 59.719 41.667 4.85 0.00 0.00 2.74
3272 3544 7.822334 CACAACTAATACAAGGACTATGGACAA 59.178 37.037 0.00 0.00 0.00 3.18
3318 3590 5.468746 CCAATTGAATGAAATGGATGGATGC 59.531 40.000 7.12 0.00 0.00 3.91
3326 3598 5.849510 TGAAATGGATGGATGCATTGATTC 58.150 37.500 0.00 5.30 46.12 2.52
3398 3670 7.041721 CAGTCTAATATACACCTGCTCAAACA 58.958 38.462 0.00 0.00 0.00 2.83
3419 3691 4.218417 ACATCAAGGACAAAATGTACCTGC 59.782 41.667 0.00 0.00 29.22 4.85
3484 3766 7.377766 TGCAGACCTCATGTAGTAATTTTTC 57.622 36.000 0.00 0.00 0.00 2.29
3531 3813 7.630242 AGTTTGAATCTTCACTGAAGTTTCA 57.370 32.000 27.17 27.17 46.95 2.69
3544 3826 4.358851 TGAAGTTTCATTTGTTGGCTTCG 58.641 39.130 0.00 0.00 34.63 3.79
3560 3842 2.413837 CTTCGTTCTCAAATGGGACGT 58.586 47.619 0.00 0.00 0.00 4.34
3563 3845 1.234821 GTTCTCAAATGGGACGTGCA 58.765 50.000 9.96 0.00 0.00 4.57
3567 3849 2.086869 CTCAAATGGGACGTGCATCTT 58.913 47.619 9.96 0.00 0.00 2.40
3568 3850 2.489329 CTCAAATGGGACGTGCATCTTT 59.511 45.455 9.96 2.20 0.00 2.52
3587 3869 7.115378 GCATCTTTTGCCCTTATATTTTGATCG 59.885 37.037 0.00 0.00 46.15 3.69
3640 3922 4.971008 GGAAACTCTCCTAATGTTTTCGC 58.029 43.478 0.00 0.00 41.61 4.70
3677 3959 5.772825 GCATTAGCTCAATACCATCCAAA 57.227 39.130 0.00 0.00 37.91 3.28
3685 3967 6.064717 GCTCAATACCATCCAAAGTAAGGAT 58.935 40.000 0.00 0.00 46.61 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 100 7.834068 TTCTATCATTCTAAAGACTGCACAC 57.166 36.000 0.00 0.00 0.00 3.82
158 160 4.385825 AGATCTGCAAACGTAAGGAAACA 58.614 39.130 0.00 0.00 46.39 2.83
417 423 3.539592 CGAATGACTAAGTAAACGCAGCG 60.540 47.826 14.82 14.82 0.00 5.18
558 564 8.107399 ACTAGCTAGTTCCAAAATAAAACCAC 57.893 34.615 20.95 0.00 31.13 4.16
599 618 5.863965 TGAATTATCCATGCTATTCCGACA 58.136 37.500 0.00 0.00 0.00 4.35
665 721 2.787473 TTCTACTGCCTCCACATTGG 57.213 50.000 0.00 0.00 39.43 3.16
674 730 4.351874 TTGTGCTACTTTTCTACTGCCT 57.648 40.909 0.00 0.00 0.00 4.75
695 782 5.464168 CCATCTTCAGAAAAGCAAAACGAT 58.536 37.500 0.00 0.00 0.00 3.73
723 810 1.070445 CATGAGATCAGGTCGCCCC 59.930 63.158 0.00 0.00 0.00 5.80
724 811 0.683973 ATCATGAGATCAGGTCGCCC 59.316 55.000 0.09 0.00 0.00 6.13
725 812 2.036992 AGAATCATGAGATCAGGTCGCC 59.963 50.000 12.37 0.00 31.90 5.54
727 814 4.581077 TCAGAATCATGAGATCAGGTCG 57.419 45.455 12.37 0.00 31.90 4.79
742 920 2.711009 TGTGGGGAGACAAACTCAGAAT 59.289 45.455 0.00 0.00 46.54 2.40
764 955 9.213799 GCATAATAAAGTGAAACCAATTGGAAA 57.786 29.630 31.22 9.99 37.80 3.13
774 965 9.221775 CTTATTCACCGCATAATAAAGTGAAAC 57.778 33.333 7.84 0.00 46.91 2.78
778 969 8.181573 ACAACTTATTCACCGCATAATAAAGTG 58.818 33.333 0.00 0.00 29.62 3.16
784 975 4.640201 AGCACAACTTATTCACCGCATAAT 59.360 37.500 0.00 0.00 0.00 1.28
815 1037 5.528320 CAGGGAAACAAACTAGTAAAACGGA 59.472 40.000 0.00 0.00 0.00 4.69
817 1039 5.209977 GCAGGGAAACAAACTAGTAAAACG 58.790 41.667 0.00 0.00 0.00 3.60
823 1045 5.453198 CCATTTTGCAGGGAAACAAACTAGT 60.453 40.000 0.00 0.00 35.60 2.57
824 1046 4.990426 CCATTTTGCAGGGAAACAAACTAG 59.010 41.667 0.00 0.00 35.60 2.57
846 1068 1.289380 GTCCACTGTCAGTCGGACC 59.711 63.158 27.46 17.37 46.38 4.46
848 1070 0.894184 GAGGTCCACTGTCAGTCGGA 60.894 60.000 15.92 15.92 0.00 4.55
851 1073 1.080434 GCGAGGTCCACTGTCAGTC 60.080 63.158 1.37 0.00 0.00 3.51
855 1077 0.951040 CAAAGGCGAGGTCCACTGTC 60.951 60.000 0.00 0.00 0.00 3.51
858 1080 1.371558 GTCAAAGGCGAGGTCCACT 59.628 57.895 0.00 0.00 0.00 4.00
886 1108 1.031571 GCCGATGAGATGGCCACAAA 61.032 55.000 8.16 0.00 45.73 2.83
894 1116 1.953138 GCGTCCAGCCGATGAGATG 60.953 63.158 0.00 0.00 40.81 2.90
895 1117 2.419198 GCGTCCAGCCGATGAGAT 59.581 61.111 0.00 0.00 40.81 2.75
896 1118 4.193334 CGCGTCCAGCCGATGAGA 62.193 66.667 0.00 0.00 44.76 3.27
897 1119 3.989698 AACGCGTCCAGCCGATGAG 62.990 63.158 14.44 0.00 44.76 2.90
900 1122 4.063967 TCAACGCGTCCAGCCGAT 62.064 61.111 14.44 0.00 44.76 4.18
904 1126 4.059459 CACGTCAACGCGTCCAGC 62.059 66.667 14.44 2.32 43.83 4.85
905 1127 2.657296 ACACGTCAACGCGTCCAG 60.657 61.111 14.44 6.03 43.83 3.86
906 1128 2.957489 CACACGTCAACGCGTCCA 60.957 61.111 14.44 0.00 43.83 4.02
907 1129 4.349871 GCACACGTCAACGCGTCC 62.350 66.667 14.44 2.36 43.83 4.79
908 1130 1.610715 TATGCACACGTCAACGCGTC 61.611 55.000 14.44 0.00 43.83 5.19
909 1131 1.614227 CTATGCACACGTCAACGCGT 61.614 55.000 5.58 5.58 46.88 6.01
910 1132 1.057208 CTATGCACACGTCAACGCG 59.943 57.895 3.53 3.53 44.43 6.01
911 1133 1.225745 GCTATGCACACGTCAACGC 60.226 57.895 1.81 0.00 44.43 4.84
912 1134 0.093535 CTGCTATGCACACGTCAACG 59.906 55.000 0.12 0.12 38.81 4.10
913 1135 0.179215 GCTGCTATGCACACGTCAAC 60.179 55.000 0.00 0.00 33.79 3.18
914 1136 1.625759 CGCTGCTATGCACACGTCAA 61.626 55.000 0.00 0.00 33.79 3.18
915 1137 2.094066 CGCTGCTATGCACACGTCA 61.094 57.895 0.00 0.00 33.79 4.35
916 1138 1.626654 AACGCTGCTATGCACACGTC 61.627 55.000 13.59 0.00 42.59 4.34
917 1139 1.667830 AACGCTGCTATGCACACGT 60.668 52.632 9.19 9.19 44.34 4.49
918 1140 1.225827 CAACGCTGCTATGCACACG 60.226 57.895 0.00 8.15 38.45 4.49
919 1141 0.238289 AACAACGCTGCTATGCACAC 59.762 50.000 0.00 0.00 33.79 3.82
920 1142 1.802069 TAACAACGCTGCTATGCACA 58.198 45.000 0.00 0.00 33.79 4.57
921 1143 2.286418 GGATAACAACGCTGCTATGCAC 60.286 50.000 0.00 0.00 33.79 4.57
922 1144 1.939934 GGATAACAACGCTGCTATGCA 59.060 47.619 0.00 0.00 36.92 3.96
923 1145 2.213499 AGGATAACAACGCTGCTATGC 58.787 47.619 0.00 0.00 0.00 3.14
924 1146 3.430218 GCTAGGATAACAACGCTGCTATG 59.570 47.826 0.00 0.00 0.00 2.23
925 1147 3.555168 GGCTAGGATAACAACGCTGCTAT 60.555 47.826 0.00 0.00 0.00 2.97
926 1148 2.223971 GGCTAGGATAACAACGCTGCTA 60.224 50.000 0.00 0.00 0.00 3.49
927 1149 1.473434 GGCTAGGATAACAACGCTGCT 60.473 52.381 0.00 0.00 0.00 4.24
928 1150 0.938008 GGCTAGGATAACAACGCTGC 59.062 55.000 0.00 0.00 0.00 5.25
929 1151 1.583054 GGGCTAGGATAACAACGCTG 58.417 55.000 0.00 0.00 0.00 5.18
930 1152 0.104304 CGGGCTAGGATAACAACGCT 59.896 55.000 0.00 0.00 0.00 5.07
931 1153 0.179092 ACGGGCTAGGATAACAACGC 60.179 55.000 0.00 0.00 0.00 4.84
932 1154 3.441496 TTACGGGCTAGGATAACAACG 57.559 47.619 0.00 0.00 0.00 4.10
933 1155 3.873361 GGTTTACGGGCTAGGATAACAAC 59.127 47.826 0.00 0.00 0.00 3.32
934 1156 3.776417 AGGTTTACGGGCTAGGATAACAA 59.224 43.478 0.00 0.00 0.00 2.83
935 1157 3.377573 AGGTTTACGGGCTAGGATAACA 58.622 45.455 0.00 0.00 0.00 2.41
936 1158 3.244009 GGAGGTTTACGGGCTAGGATAAC 60.244 52.174 0.00 0.00 0.00 1.89
937 1159 2.967887 GGAGGTTTACGGGCTAGGATAA 59.032 50.000 0.00 0.00 0.00 1.75
938 1160 2.601905 GGAGGTTTACGGGCTAGGATA 58.398 52.381 0.00 0.00 0.00 2.59
939 1161 1.421480 GGAGGTTTACGGGCTAGGAT 58.579 55.000 0.00 0.00 0.00 3.24
940 1162 0.688749 GGGAGGTTTACGGGCTAGGA 60.689 60.000 0.00 0.00 0.00 2.94
941 1163 0.979187 TGGGAGGTTTACGGGCTAGG 60.979 60.000 0.00 0.00 0.00 3.02
942 1164 0.177373 GTGGGAGGTTTACGGGCTAG 59.823 60.000 0.00 0.00 0.00 3.42
943 1165 0.544833 TGTGGGAGGTTTACGGGCTA 60.545 55.000 0.00 0.00 0.00 3.93
944 1166 1.844289 TGTGGGAGGTTTACGGGCT 60.844 57.895 0.00 0.00 0.00 5.19
945 1167 1.673337 GTGTGGGAGGTTTACGGGC 60.673 63.158 0.00 0.00 0.00 6.13
946 1168 1.002990 GGTGTGGGAGGTTTACGGG 60.003 63.158 0.00 0.00 0.00 5.28
1182 1414 2.111999 CTGGAGGTCCCGCTTTGTCA 62.112 60.000 0.00 0.00 37.93 3.58
1188 1420 3.394836 GCTTCTGGAGGTCCCGCT 61.395 66.667 0.00 0.00 37.93 5.52
1443 1680 4.189580 AGCACCACACGCCCAACT 62.190 61.111 0.00 0.00 0.00 3.16
1450 1688 2.941333 CAGCAAGAGCACCACACG 59.059 61.111 0.00 0.00 45.49 4.49
1637 1875 4.368808 CCACACGCGCAAAGTCCG 62.369 66.667 5.73 0.00 0.00 4.79
1638 1876 4.683334 GCCACACGCGCAAAGTCC 62.683 66.667 5.73 0.00 0.00 3.85
1639 1877 3.649986 AGCCACACGCGCAAAGTC 61.650 61.111 5.73 0.00 44.76 3.01
1640 1878 3.952675 CAGCCACACGCGCAAAGT 61.953 61.111 5.73 0.00 44.76 2.66
1726 1974 1.495584 TTCACACTGCCGCGTTCTTC 61.496 55.000 4.92 0.00 0.00 2.87
1732 1980 1.006086 TCAATATTCACACTGCCGCG 58.994 50.000 0.00 0.00 0.00 6.46
1759 2007 6.438741 AGAACTATCAGTGGACAGAGATTTCA 59.561 38.462 0.00 0.00 0.00 2.69
1906 2162 0.257328 TTTGCACACTCCCTCCACAA 59.743 50.000 0.00 0.00 0.00 3.33
1930 2186 1.664016 CCGTGCAGAAACATCACTTGC 60.664 52.381 0.00 0.00 0.00 4.01
1985 2241 5.010112 TGACAGTGTAACAGAGAAGGAAGAG 59.990 44.000 0.00 0.00 41.43 2.85
2014 2270 5.824904 ATTGAGCAGGTTATGACAATGTC 57.175 39.130 6.41 6.41 36.66 3.06
2496 2755 7.770897 ACTTCAAGATTCAGTCACAGTTTAGTT 59.229 33.333 0.00 0.00 0.00 2.24
2547 2808 9.341899 GTCATACCTGAAAAACATCAACAATAC 57.658 33.333 0.00 0.00 31.85 1.89
2573 2837 0.721718 CTTCAGGTTTAAGCGCCTCG 59.278 55.000 2.29 0.00 31.73 4.63
2577 2841 1.001815 TGCAACTTCAGGTTTAAGCGC 60.002 47.619 0.00 0.00 35.74 5.92
2603 2867 1.132849 TGGTCCCTCACCTCTGAAAGA 60.133 52.381 0.00 0.00 46.98 2.52
2755 3019 6.017192 ACCTACCAAGTCTCTCAAGTATTCA 58.983 40.000 0.00 0.00 0.00 2.57
2833 3097 4.492604 GCAGCTTGGTGGTGGTTA 57.507 55.556 1.97 0.00 43.78 2.85
3064 3328 7.882179 ACAACTTGAACACTTAGTGAGTTTTT 58.118 30.769 20.07 1.89 36.10 1.94
3178 3443 7.617723 ACTTGCATTCCTAATTATGGGTTTGTA 59.382 33.333 0.00 0.00 0.00 2.41
3180 3445 6.877236 ACTTGCATTCCTAATTATGGGTTTG 58.123 36.000 0.00 0.00 0.00 2.93
3181 3446 7.330262 CAACTTGCATTCCTAATTATGGGTTT 58.670 34.615 0.00 0.00 0.00 3.27
3272 3544 4.765339 GGTGGTTTACTTCCTGCTAATTGT 59.235 41.667 0.00 0.00 0.00 2.71
3318 3590 4.441079 GGGATGAAAGTGGCTGAATCAATG 60.441 45.833 0.00 0.00 0.00 2.82
3326 3598 1.547372 CAAAGGGGATGAAAGTGGCTG 59.453 52.381 0.00 0.00 0.00 4.85
3398 3670 4.406456 TGCAGGTACATTTTGTCCTTGAT 58.594 39.130 0.00 0.00 29.55 2.57
3514 3796 7.205297 CCAACAAATGAAACTTCAGTGAAGAT 58.795 34.615 34.16 22.81 41.71 2.40
3520 3802 5.343307 AAGCCAACAAATGAAACTTCAGT 57.657 34.783 0.00 0.00 41.08 3.41
3521 3803 4.442073 CGAAGCCAACAAATGAAACTTCAG 59.558 41.667 0.00 0.00 41.08 3.02
3522 3804 4.142271 ACGAAGCCAACAAATGAAACTTCA 60.142 37.500 0.00 0.00 42.14 3.02
3523 3805 4.359706 ACGAAGCCAACAAATGAAACTTC 58.640 39.130 0.00 0.00 0.00 3.01
3524 3806 4.385358 ACGAAGCCAACAAATGAAACTT 57.615 36.364 0.00 0.00 0.00 2.66
3525 3807 4.097892 AGAACGAAGCCAACAAATGAAACT 59.902 37.500 0.00 0.00 0.00 2.66
3526 3808 4.359706 AGAACGAAGCCAACAAATGAAAC 58.640 39.130 0.00 0.00 0.00 2.78
3527 3809 4.097135 TGAGAACGAAGCCAACAAATGAAA 59.903 37.500 0.00 0.00 0.00 2.69
3528 3810 3.629855 TGAGAACGAAGCCAACAAATGAA 59.370 39.130 0.00 0.00 0.00 2.57
3529 3811 3.210227 TGAGAACGAAGCCAACAAATGA 58.790 40.909 0.00 0.00 0.00 2.57
3530 3812 3.624326 TGAGAACGAAGCCAACAAATG 57.376 42.857 0.00 0.00 0.00 2.32
3531 3813 4.647424 TTTGAGAACGAAGCCAACAAAT 57.353 36.364 0.00 0.00 0.00 2.32
3532 3814 4.358851 CATTTGAGAACGAAGCCAACAAA 58.641 39.130 0.00 0.00 0.00 2.83
3533 3815 3.243367 CCATTTGAGAACGAAGCCAACAA 60.243 43.478 0.00 0.00 0.00 2.83
3534 3816 2.293122 CCATTTGAGAACGAAGCCAACA 59.707 45.455 0.00 0.00 0.00 3.33
3544 3826 1.234821 TGCACGTCCCATTTGAGAAC 58.765 50.000 0.00 0.00 0.00 3.01
3563 3845 7.287696 ACCGATCAAAATATAAGGGCAAAAGAT 59.712 33.333 0.00 0.00 0.00 2.40
3567 3849 6.783708 AACCGATCAAAATATAAGGGCAAA 57.216 33.333 0.00 0.00 0.00 3.68
3568 3850 7.558444 AGTTAACCGATCAAAATATAAGGGCAA 59.442 33.333 0.88 0.00 0.00 4.52
3587 3869 8.912658 GCAAATGCTTTCTTACTTTAGTTAACC 58.087 33.333 0.88 0.00 38.21 2.85
3677 3959 1.212935 GCCCCACATGACATCCTTACT 59.787 52.381 0.00 0.00 0.00 2.24
3685 3967 2.605607 CCTCAGGCCCCACATGACA 61.606 63.158 0.00 0.00 0.00 3.58



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

AutoCloner maintained by Alex Coulton.