Multiple sequence alignment - TraesCS5D01G200200

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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 TraesCS5D01G200200 chr5D 100.000 2498 0 0 1 2498 302875582 302878079 0.000000e+00 4614
1 TraesCS5D01G200200 chr5A 95.316 790 33 3 910 1698 395063199 395062413 0.000000e+00 1251
2 TraesCS5D01G200200 chr5A 84.770 696 45 26 238 919 395063802 395063154 2.090000e-180 641
3 TraesCS5D01G200200 chr5A 88.911 514 43 10 1976 2477 395061415 395060904 2.730000e-174 621
4 TraesCS5D01G200200 chr5A 87.220 446 40 10 1060 1498 395001420 395000985 2.230000e-135 492
5 TraesCS5D01G200200 chr5A 92.935 184 11 2 22 203 395063981 395063798 1.470000e-67 267
6 TraesCS5D01G200200 chr5B 90.642 919 35 21 7 910 347676578 347677460 0.000000e+00 1173
7 TraesCS5D01G200200 chr5B 91.547 698 40 5 910 1607 347677424 347678102 0.000000e+00 944
8 TraesCS5D01G200200 chr5B 83.369 938 94 39 1597 2495 347687027 347687941 0.000000e+00 811
9 TraesCS5D01G200200 chr5B 88.089 403 40 7 1103 1498 347928228 347928629 2.910000e-129 472


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 TraesCS5D01G200200 chr5D 302875582 302878079 2497 False 4614.0 4614 100.0000 1 2498 1 chr5D.!!$F1 2497
1 TraesCS5D01G200200 chr5A 395060904 395063981 3077 True 695.0 1251 90.4830 22 2477 4 chr5A.!!$R2 2455
2 TraesCS5D01G200200 chr5B 347676578 347678102 1524 False 1058.5 1173 91.0945 7 1607 2 chr5B.!!$F3 1600
3 TraesCS5D01G200200 chr5B 347687027 347687941 914 False 811.0 811 83.3690 1597 2495 1 chr5B.!!$F1 898

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
902 923 0.306228 ACTCGCTCTGATCACGATCG 59.694 55.0 14.88 14.88 40.63 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2310 3097 0.035458 AGCTCACCTACAAGCACACC 59.965 55.0 0.0 0.0 41.06 4.16 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
96 100 4.430908 CCGAGTGACCTAATTCTGGTTAC 58.569 47.826 13.90 13.90 42.26 2.50
225 232 1.051556 TCCCAACAAAACAAGGGGCC 61.052 55.000 0.00 0.00 41.77 5.80
288 296 4.074970 CCATCTCACAGCCAGTAGTTTTT 58.925 43.478 0.00 0.00 0.00 1.94
507 523 3.204827 CCGGGCGCTTCTTCCATG 61.205 66.667 7.64 0.00 0.00 3.66
586 602 5.753921 CCGAAGAAACTGACTCTTAAACAGT 59.246 40.000 0.00 0.00 45.02 3.55
591 609 4.755266 ACTGACTCTTAAACAGTGGTGT 57.245 40.909 0.00 0.00 42.18 4.16
842 860 6.826668 TCCAATCGCCTATATATTATGGGTG 58.173 40.000 4.59 4.59 0.00 4.61
843 861 5.997746 CCAATCGCCTATATATTATGGGTGG 59.002 44.000 9.66 1.81 0.00 4.61
844 862 6.409234 CCAATCGCCTATATATTATGGGTGGT 60.409 42.308 9.66 1.49 0.00 4.16
848 866 6.208007 TCGCCTATATATTATGGGTGGTATCG 59.792 42.308 9.66 0.41 0.00 2.92
851 869 6.269077 CCTATATATTATGGGTGGTATCGCCA 59.731 42.308 8.10 0.00 46.95 5.69
883 904 1.152860 ACCATCCGCCACAACACAA 60.153 52.632 0.00 0.00 0.00 3.33
887 908 1.227999 ATCCGCCACAACACAACTCG 61.228 55.000 0.00 0.00 0.00 4.18
888 909 2.052237 CGCCACAACACAACTCGC 60.052 61.111 0.00 0.00 0.00 5.03
889 910 2.534019 CGCCACAACACAACTCGCT 61.534 57.895 0.00 0.00 0.00 4.93
890 911 1.279840 GCCACAACACAACTCGCTC 59.720 57.895 0.00 0.00 0.00 5.03
891 912 1.160329 GCCACAACACAACTCGCTCT 61.160 55.000 0.00 0.00 0.00 4.09
892 913 0.583438 CCACAACACAACTCGCTCTG 59.417 55.000 0.00 0.00 0.00 3.35
893 914 1.570813 CACAACACAACTCGCTCTGA 58.429 50.000 0.00 0.00 0.00 3.27
894 915 2.138320 CACAACACAACTCGCTCTGAT 58.862 47.619 0.00 0.00 0.00 2.90
895 916 2.156504 CACAACACAACTCGCTCTGATC 59.843 50.000 0.00 0.00 0.00 2.92
896 917 2.224042 ACAACACAACTCGCTCTGATCA 60.224 45.455 0.00 0.00 0.00 2.92
897 918 2.071688 ACACAACTCGCTCTGATCAC 57.928 50.000 0.00 0.00 0.00 3.06
898 919 0.987715 CACAACTCGCTCTGATCACG 59.012 55.000 0.00 0.00 0.00 4.35
899 920 0.881796 ACAACTCGCTCTGATCACGA 59.118 50.000 6.71 6.71 0.00 4.35
900 921 1.474478 ACAACTCGCTCTGATCACGAT 59.526 47.619 7.28 0.00 34.94 3.73
901 922 2.115595 CAACTCGCTCTGATCACGATC 58.884 52.381 7.28 0.00 34.94 3.69
902 923 0.306228 ACTCGCTCTGATCACGATCG 59.694 55.000 14.88 14.88 40.63 3.69
903 924 0.996229 CTCGCTCTGATCACGATCGC 60.996 60.000 16.60 0.00 40.63 4.58
904 925 2.013483 CGCTCTGATCACGATCGCC 61.013 63.158 16.60 2.68 40.63 5.54
905 926 1.361993 GCTCTGATCACGATCGCCT 59.638 57.895 16.60 0.00 40.63 5.52
906 927 0.938637 GCTCTGATCACGATCGCCTG 60.939 60.000 16.60 7.25 40.63 4.85
907 928 0.665298 CTCTGATCACGATCGCCTGA 59.335 55.000 16.60 13.07 40.63 3.86
908 929 0.382158 TCTGATCACGATCGCCTGAC 59.618 55.000 16.60 7.94 40.63 3.51
909 930 0.596083 CTGATCACGATCGCCTGACC 60.596 60.000 16.60 3.85 40.63 4.02
910 931 1.300233 GATCACGATCGCCTGACCC 60.300 63.158 16.60 4.80 0.00 4.46
911 932 2.016393 GATCACGATCGCCTGACCCA 62.016 60.000 16.60 0.00 0.00 4.51
912 933 2.298158 ATCACGATCGCCTGACCCAC 62.298 60.000 16.60 0.00 0.00 4.61
913 934 2.994995 ACGATCGCCTGACCCACA 60.995 61.111 16.60 0.00 0.00 4.17
914 935 2.264480 CGATCGCCTGACCCACAA 59.736 61.111 0.26 0.00 0.00 3.33
915 936 2.100631 CGATCGCCTGACCCACAAC 61.101 63.158 0.26 0.00 0.00 3.32
916 937 1.003839 GATCGCCTGACCCACAACA 60.004 57.895 0.00 0.00 0.00 3.33
917 938 1.298859 GATCGCCTGACCCACAACAC 61.299 60.000 0.00 0.00 0.00 3.32
918 939 2.050836 ATCGCCTGACCCACAACACA 62.051 55.000 0.00 0.00 0.00 3.72
919 940 1.821759 CGCCTGACCCACAACACAA 60.822 57.895 0.00 0.00 0.00 3.33
920 941 1.733526 GCCTGACCCACAACACAAC 59.266 57.895 0.00 0.00 0.00 3.32
921 942 0.751643 GCCTGACCCACAACACAACT 60.752 55.000 0.00 0.00 0.00 3.16
922 943 1.762708 CCTGACCCACAACACAACTT 58.237 50.000 0.00 0.00 0.00 2.66
978 999 9.012161 AGATTTCTTGATTTCTTCTTCTTCCTG 57.988 33.333 0.00 0.00 0.00 3.86
991 1012 0.804989 CTTCCTGTGTTTCATCGGCC 59.195 55.000 0.00 0.00 0.00 6.13
1029 1050 3.241530 AGCTCCAGTTCCGCCACA 61.242 61.111 0.00 0.00 0.00 4.17
1179 1200 1.302832 CAAGGTGCTGTCCCTGGAC 60.303 63.158 9.44 9.44 44.77 4.02
1357 1378 0.098376 GAGGGTACAGTACGACGCTG 59.902 60.000 16.17 0.00 38.80 5.18
1362 1383 0.446616 TACAGTACGACGCTGAGCTG 59.553 55.000 1.78 0.00 37.40 4.24
1413 1434 1.762460 AGATGGGTTCGCGAGGGAT 60.762 57.895 9.59 0.00 0.00 3.85
1504 1525 1.813786 GCCGCCGATTCTAGAGTAGAT 59.186 52.381 0.00 0.00 34.22 1.98
1522 1543 7.601886 AGAGTAGATTTGAACAGAGTGAACATG 59.398 37.037 0.00 0.00 0.00 3.21
1589 1610 2.353323 CTACTCTGGGGCGTTAAAACC 58.647 52.381 0.00 0.00 0.00 3.27
1698 1720 8.953990 GGCATTATATTTGTCAAATCAACGTAC 58.046 33.333 14.07 1.29 32.38 3.67
1722 1759 4.573607 AGTATAGAGTGAACATACGACGCA 59.426 41.667 0.00 0.00 31.76 5.24
1730 1767 3.002965 TGAACATACGACGCACTATCGAT 59.997 43.478 2.16 2.16 42.25 3.59
1731 1768 3.184649 ACATACGACGCACTATCGATC 57.815 47.619 0.00 0.00 42.25 3.69
1733 1770 3.188667 ACATACGACGCACTATCGATCAT 59.811 43.478 0.00 0.00 42.25 2.45
1736 1775 2.237526 CGACGCACTATCGATCATGAG 58.762 52.381 0.00 6.09 42.25 2.90
1739 1778 1.344458 GCACTATCGATCATGAGGCG 58.656 55.000 0.00 12.95 0.00 5.52
1741 1780 2.590073 CACTATCGATCATGAGGCGTC 58.410 52.381 17.06 0.00 0.00 5.19
1772 1811 6.650807 ACTTCGTCAATCTCAATATGTTGTGT 59.349 34.615 1.86 0.00 36.69 3.72
1777 1827 5.882000 TCAATCTCAATATGTTGTGTCCCAG 59.118 40.000 1.86 0.00 36.69 4.45
1795 1845 7.179338 GTGTCCCAGAGGTATTCATAGACATAT 59.821 40.741 0.00 0.00 34.65 1.78
1841 1892 6.237901 TCATAGGGGTAAATGTATGTGCATC 58.762 40.000 0.00 0.00 0.00 3.91
1845 1896 7.568128 AGGGGTAAATGTATGTGCATCTATA 57.432 36.000 0.00 0.00 0.00 1.31
1872 1924 4.757657 ACATCTGCAATTGTACCGTGTTAA 59.242 37.500 7.40 0.00 0.00 2.01
1904 1956 5.826643 AGAATTGTAAGGTGGGCTAATTGA 58.173 37.500 0.00 0.00 0.00 2.57
1910 2414 6.905736 TGTAAGGTGGGCTAATTGATGAATA 58.094 36.000 0.00 0.00 0.00 1.75
1932 2436 1.425448 CCCAAGGGAGTCCACTCTTTT 59.575 52.381 12.30 0.00 42.48 2.27
1933 2437 2.158460 CCCAAGGGAGTCCACTCTTTTT 60.158 50.000 12.30 0.00 42.48 1.94
1934 2438 3.149981 CCAAGGGAGTCCACTCTTTTTC 58.850 50.000 12.30 0.00 42.48 2.29
1940 2444 5.360999 AGGGAGTCCACTCTTTTTCAAAAAG 59.639 40.000 15.46 15.46 42.48 2.27
1942 2446 6.320418 GGGAGTCCACTCTTTTTCAAAAAGTA 59.680 38.462 19.82 8.12 42.48 2.24
1959 2739 9.421806 TCAAAAAGTATCATAGCCAAAATGTTG 57.578 29.630 0.00 0.00 34.25 3.33
1972 2752 5.539582 CAAAATGTTGGCAATCATCCAAG 57.460 39.130 1.92 0.00 43.57 3.61
1973 2753 3.899052 AATGTTGGCAATCATCCAAGG 57.101 42.857 1.92 0.00 43.57 3.61
1995 2775 5.127682 AGGGAGTATTTGTTTGGATGATTGC 59.872 40.000 0.00 0.00 0.00 3.56
1999 2779 6.165577 AGTATTTGTTTGGATGATTGCCAAC 58.834 36.000 0.00 0.00 44.58 3.77
2031 2811 7.683437 CATGTATCCATGCAGACTTATCATT 57.317 36.000 0.00 0.00 41.88 2.57
2034 2814 6.712095 TGTATCCATGCAGACTTATCATTTCC 59.288 38.462 0.00 0.00 0.00 3.13
2094 2879 3.860641 AGCAAAACCTTGACCAAAGTTG 58.139 40.909 0.00 0.00 34.14 3.16
2096 2881 4.000325 GCAAAACCTTGACCAAAGTTGTT 59.000 39.130 0.00 0.00 34.14 2.83
2097 2882 4.454161 GCAAAACCTTGACCAAAGTTGTTT 59.546 37.500 0.00 0.00 33.97 2.83
2098 2883 5.049060 GCAAAACCTTGACCAAAGTTGTTTT 60.049 36.000 0.00 0.00 39.14 2.43
2099 2884 6.514212 GCAAAACCTTGACCAAAGTTGTTTTT 60.514 34.615 0.00 0.00 37.77 1.94
2149 2934 0.030638 CTCAAACCAAACAGCACCGG 59.969 55.000 0.00 0.00 0.00 5.28
2196 2983 0.689080 CTCAGCCTCCAGCCTCCTTA 60.689 60.000 0.00 0.00 45.47 2.69
2271 3058 4.492160 CGTTGCTCGCGGCTCCTA 62.492 66.667 18.14 0.00 42.39 2.94
2290 3077 7.014038 GGCTCCTAATACAGCTAGTGTTTAGTA 59.986 40.741 3.77 0.00 40.94 1.82
2307 3094 7.737311 GTGTTTAGTAGCGTTGTATTGTAACAC 59.263 37.037 0.00 0.00 35.38 3.32
2310 3097 2.070783 AGCGTTGTATTGTAACACCGG 58.929 47.619 0.00 0.00 36.00 5.28
2318 3105 0.107116 TTGTAACACCGGGTGTGCTT 60.107 50.000 31.96 19.48 46.79 3.91
2350 3137 8.150945 TGAGCTTGTACAAACTCTTCTTCTATT 58.849 33.333 29.59 0.68 35.25 1.73
2373 3160 4.489679 ACGAATTGAAAGGCAAGACTTC 57.510 40.909 0.00 0.00 40.42 3.01
2375 3162 5.305585 ACGAATTGAAAGGCAAGACTTCTA 58.694 37.500 0.00 0.00 40.42 2.10
2430 3222 4.079253 GCCTTCACATTTTCCACCTCTTA 58.921 43.478 0.00 0.00 0.00 2.10
2444 3236 4.956700 CCACCTCTTACTTCAGATCCACTA 59.043 45.833 0.00 0.00 0.00 2.74
2445 3237 5.600484 CCACCTCTTACTTCAGATCCACTAT 59.400 44.000 0.00 0.00 0.00 2.12
2468 3260 4.702831 GGAACACCACAATTCCAACAAAT 58.297 39.130 0.00 0.00 43.40 2.32
2472 3264 7.443879 GGAACACCACAATTCCAACAAATAAAT 59.556 33.333 0.00 0.00 43.40 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.543756 TCGTAATCTGTTCATGATGACTTGTA 58.456 34.615 0.00 0.00 0.00 2.41
5 6 6.398095 TCGTAATCTGTTCATGATGACTTGT 58.602 36.000 0.00 0.00 0.00 3.16
9 10 6.893958 AACTCGTAATCTGTTCATGATGAC 57.106 37.500 0.00 0.00 0.00 3.06
18 19 4.024048 CAGGCACAAAACTCGTAATCTGTT 60.024 41.667 0.00 0.00 0.00 3.16
225 232 0.108709 CCAATGTCAAATGCACCCCG 60.109 55.000 0.00 0.00 0.00 5.73
251 259 6.653020 TGTGAGATGGCAGTATAAGTTGAAT 58.347 36.000 0.00 0.00 0.00 2.57
372 380 2.069273 CTCGATGTTCACACCCAACTC 58.931 52.381 0.00 0.00 0.00 3.01
373 381 1.691976 TCTCGATGTTCACACCCAACT 59.308 47.619 0.00 0.00 0.00 3.16
380 388 0.526211 CCCTCGTCTCGATGTTCACA 59.474 55.000 0.00 0.00 34.61 3.58
454 463 3.319122 CCATAATTTAAGGTGGGCTGAGC 59.681 47.826 0.00 0.00 0.00 4.26
507 523 0.608856 TGCATGGTGTCATGGTGACC 60.609 55.000 7.55 0.00 46.40 4.02
551 567 3.184581 CAGTTTCTTCGGGAAAGTTCGAG 59.815 47.826 8.61 0.00 42.89 4.04
597 615 6.148948 GGCGGTAAGGTTTAAACGTTAATTT 58.851 36.000 26.54 10.19 39.88 1.82
805 823 0.681243 GATTGGAAGCTGGGGGTGAC 60.681 60.000 0.00 0.00 0.00 3.67
806 824 1.691219 GATTGGAAGCTGGGGGTGA 59.309 57.895 0.00 0.00 0.00 4.02
807 825 1.750399 CGATTGGAAGCTGGGGGTG 60.750 63.158 0.00 0.00 0.00 4.61
808 826 2.677228 CGATTGGAAGCTGGGGGT 59.323 61.111 0.00 0.00 0.00 4.95
809 827 2.830370 GCGATTGGAAGCTGGGGG 60.830 66.667 0.00 0.00 0.00 5.40
810 828 1.983119 TAGGCGATTGGAAGCTGGGG 61.983 60.000 0.00 0.00 0.00 4.96
811 829 0.109342 ATAGGCGATTGGAAGCTGGG 59.891 55.000 0.00 0.00 0.00 4.45
812 830 2.839486 TATAGGCGATTGGAAGCTGG 57.161 50.000 0.00 0.00 0.00 4.85
813 831 7.172190 CCATAATATATAGGCGATTGGAAGCTG 59.828 40.741 0.00 0.00 0.00 4.24
814 832 7.220030 CCATAATATATAGGCGATTGGAAGCT 58.780 38.462 0.00 0.00 0.00 3.74
815 833 6.428159 CCCATAATATATAGGCGATTGGAAGC 59.572 42.308 0.00 0.00 0.00 3.86
816 834 7.442364 CACCCATAATATATAGGCGATTGGAAG 59.558 40.741 0.00 0.00 0.00 3.46
842 860 3.126001 TGGAGAATGAATGGCGATACC 57.874 47.619 0.00 0.00 39.84 2.73
843 861 4.153117 GTGATGGAGAATGAATGGCGATAC 59.847 45.833 0.00 0.00 0.00 2.24
844 862 4.318332 GTGATGGAGAATGAATGGCGATA 58.682 43.478 0.00 0.00 0.00 2.92
848 866 2.658285 TGGTGATGGAGAATGAATGGC 58.342 47.619 0.00 0.00 0.00 4.40
851 869 3.748083 CGGATGGTGATGGAGAATGAAT 58.252 45.455 0.00 0.00 0.00 2.57
887 908 0.938637 CAGGCGATCGTGATCAGAGC 60.939 60.000 17.81 5.40 37.69 4.09
888 909 0.665298 TCAGGCGATCGTGATCAGAG 59.335 55.000 17.81 0.00 37.69 3.35
889 910 0.382158 GTCAGGCGATCGTGATCAGA 59.618 55.000 17.81 4.04 39.04 3.27
890 911 0.596083 GGTCAGGCGATCGTGATCAG 60.596 60.000 17.81 1.65 37.94 2.90
891 912 1.437573 GGTCAGGCGATCGTGATCA 59.562 57.895 17.81 0.00 37.94 2.92
892 913 1.300233 GGGTCAGGCGATCGTGATC 60.300 63.158 17.81 13.30 39.04 2.92
893 914 2.058001 TGGGTCAGGCGATCGTGAT 61.058 57.895 17.81 0.00 39.04 3.06
894 915 2.678580 TGGGTCAGGCGATCGTGA 60.679 61.111 17.81 10.69 35.02 4.35
895 916 2.509336 GTGGGTCAGGCGATCGTG 60.509 66.667 17.81 8.23 0.00 4.35
896 917 2.579657 TTGTGGGTCAGGCGATCGT 61.580 57.895 17.81 0.00 0.00 3.73
897 918 2.100631 GTTGTGGGTCAGGCGATCG 61.101 63.158 11.69 11.69 0.00 3.69
898 919 1.003839 TGTTGTGGGTCAGGCGATC 60.004 57.895 0.00 0.00 0.00 3.69
899 920 1.302511 GTGTTGTGGGTCAGGCGAT 60.303 57.895 0.00 0.00 0.00 4.58
900 921 2.110213 GTGTTGTGGGTCAGGCGA 59.890 61.111 0.00 0.00 0.00 5.54
901 922 1.821759 TTGTGTTGTGGGTCAGGCG 60.822 57.895 0.00 0.00 0.00 5.52
902 923 0.751643 AGTTGTGTTGTGGGTCAGGC 60.752 55.000 0.00 0.00 0.00 4.85
903 924 1.405105 CAAGTTGTGTTGTGGGTCAGG 59.595 52.381 0.00 0.00 0.00 3.86
904 925 1.202290 GCAAGTTGTGTTGTGGGTCAG 60.202 52.381 4.48 0.00 0.00 3.51
905 926 0.814457 GCAAGTTGTGTTGTGGGTCA 59.186 50.000 4.48 0.00 0.00 4.02
906 927 1.065551 GAGCAAGTTGTGTTGTGGGTC 59.934 52.381 4.48 0.00 0.00 4.46
907 928 1.102978 GAGCAAGTTGTGTTGTGGGT 58.897 50.000 4.48 0.00 0.00 4.51
908 929 1.066002 CAGAGCAAGTTGTGTTGTGGG 59.934 52.381 4.48 0.00 29.24 4.61
909 930 2.016318 TCAGAGCAAGTTGTGTTGTGG 58.984 47.619 4.48 0.00 33.18 4.17
910 931 3.313249 TGATCAGAGCAAGTTGTGTTGTG 59.687 43.478 4.48 0.50 33.57 3.33
911 932 3.313526 GTGATCAGAGCAAGTTGTGTTGT 59.686 43.478 4.48 0.00 0.00 3.32
912 933 3.605461 CGTGATCAGAGCAAGTTGTGTTG 60.605 47.826 4.48 0.97 0.00 3.33
913 934 2.545526 CGTGATCAGAGCAAGTTGTGTT 59.454 45.455 4.48 0.00 0.00 3.32
914 935 2.138320 CGTGATCAGAGCAAGTTGTGT 58.862 47.619 4.48 0.00 0.00 3.72
915 936 2.407090 TCGTGATCAGAGCAAGTTGTG 58.593 47.619 4.48 0.00 0.00 3.33
916 937 2.820059 TCGTGATCAGAGCAAGTTGT 57.180 45.000 4.48 0.00 0.00 3.32
917 938 3.256558 TGATCGTGATCAGAGCAAGTTG 58.743 45.455 8.43 0.00 42.42 3.16
918 939 3.599730 TGATCGTGATCAGAGCAAGTT 57.400 42.857 8.43 0.00 42.42 2.66
961 982 7.264373 TGAAACACAGGAAGAAGAAGAAATC 57.736 36.000 0.00 0.00 0.00 2.17
962 983 7.308229 CGATGAAACACAGGAAGAAGAAGAAAT 60.308 37.037 0.00 0.00 0.00 2.17
963 984 6.017934 CGATGAAACACAGGAAGAAGAAGAAA 60.018 38.462 0.00 0.00 0.00 2.52
970 991 2.151202 GCCGATGAAACACAGGAAGAA 58.849 47.619 0.00 0.00 0.00 2.52
972 993 0.804989 GGCCGATGAAACACAGGAAG 59.195 55.000 0.00 0.00 0.00 3.46
973 994 0.109532 TGGCCGATGAAACACAGGAA 59.890 50.000 0.00 0.00 0.00 3.36
978 999 1.315257 ATGGCTGGCCGATGAAACAC 61.315 55.000 7.14 0.00 39.42 3.32
991 1012 1.996786 GCGGTGTTCATGGATGGCTG 61.997 60.000 0.00 0.00 0.00 4.85
1344 1365 1.210413 CAGCTCAGCGTCGTACTGT 59.790 57.895 0.00 0.00 36.50 3.55
1491 1512 9.249053 TCACTCTGTTCAAATCTACTCTAGAAT 57.751 33.333 0.00 0.00 38.50 2.40
1504 1525 2.622942 GGGCATGTTCACTCTGTTCAAA 59.377 45.455 0.00 0.00 0.00 2.69
1570 1591 1.980036 AGGTTTTAACGCCCCAGAGTA 59.020 47.619 0.00 0.00 0.00 2.59
1572 1593 1.165270 CAGGTTTTAACGCCCCAGAG 58.835 55.000 0.00 0.00 0.00 3.35
1589 1610 6.389091 ACACCAAATAAACATGCATACACAG 58.611 36.000 0.00 0.00 0.00 3.66
1698 1720 4.904724 GCGTCGTATGTTCACTCTATACTG 59.095 45.833 0.00 0.00 0.00 2.74
1700 1722 4.669728 GTGCGTCGTATGTTCACTCTATAC 59.330 45.833 0.00 0.00 0.00 1.47
1702 1724 3.377485 AGTGCGTCGTATGTTCACTCTAT 59.623 43.478 0.00 0.00 33.16 1.98
1722 1759 2.509569 AGACGCCTCATGATCGATAGT 58.490 47.619 19.96 5.57 37.40 2.12
1730 1767 3.064958 CGAAGTAACTAGACGCCTCATGA 59.935 47.826 0.00 0.00 0.00 3.07
1731 1768 3.181499 ACGAAGTAACTAGACGCCTCATG 60.181 47.826 0.00 0.00 41.94 3.07
1733 1770 2.430465 ACGAAGTAACTAGACGCCTCA 58.570 47.619 0.00 0.00 41.94 3.86
1772 1811 6.669591 CCATATGTCTATGAATACCTCTGGGA 59.330 42.308 1.24 0.00 37.51 4.37
1777 1827 6.591834 GCACACCATATGTCTATGAATACCTC 59.408 42.308 1.24 0.00 40.64 3.85
1813 1863 6.570378 GCACATACATTTACCCCTATGAATGC 60.570 42.308 0.00 0.00 33.84 3.56
1818 1869 6.240894 AGATGCACATACATTTACCCCTATG 58.759 40.000 0.00 0.00 0.00 2.23
1841 1892 8.988934 ACGGTACAATTGCAGATGTTTATATAG 58.011 33.333 5.05 1.67 0.00 1.31
1845 1896 5.414454 ACACGGTACAATTGCAGATGTTTAT 59.586 36.000 5.05 0.00 0.00 1.40
1872 1924 6.345298 CCCACCTTACAATTCTTGTGTTTTT 58.655 36.000 2.85 0.00 45.03 1.94
1877 1929 3.157087 AGCCCACCTTACAATTCTTGTG 58.843 45.455 2.85 0.00 45.03 3.33
1889 1941 5.598417 GGTTATTCATCAATTAGCCCACCTT 59.402 40.000 0.00 0.00 0.00 3.50
1904 1956 3.053619 GTGGACTCCCTTGGGTTATTCAT 60.054 47.826 5.51 0.00 0.00 2.57
1910 2414 0.104409 AGAGTGGACTCCCTTGGGTT 60.104 55.000 5.51 0.00 43.88 4.11
1932 2436 9.995003 AACATTTTGGCTATGATACTTTTTGAA 57.005 25.926 0.00 0.00 0.00 2.69
1933 2437 9.421806 CAACATTTTGGCTATGATACTTTTTGA 57.578 29.630 0.00 0.00 0.00 2.69
1934 2438 8.658609 CCAACATTTTGGCTATGATACTTTTTG 58.341 33.333 0.00 0.00 46.09 2.44
1956 2736 1.753073 CTCCCTTGGATGATTGCCAAC 59.247 52.381 0.00 0.00 40.32 3.77
1959 2739 3.515602 ATACTCCCTTGGATGATTGCC 57.484 47.619 0.00 0.00 0.00 4.52
1960 2740 4.646492 ACAAATACTCCCTTGGATGATTGC 59.354 41.667 0.00 0.00 0.00 3.56
1961 2741 6.780457 AACAAATACTCCCTTGGATGATTG 57.220 37.500 0.00 0.00 0.00 2.67
1962 2742 6.155049 CCAAACAAATACTCCCTTGGATGATT 59.845 38.462 0.00 0.00 36.26 2.57
1964 2744 5.016173 CCAAACAAATACTCCCTTGGATGA 58.984 41.667 0.00 0.00 36.26 2.92
1965 2745 5.016173 TCCAAACAAATACTCCCTTGGATG 58.984 41.667 0.00 0.00 37.88 3.51
1966 2746 5.269554 TCCAAACAAATACTCCCTTGGAT 57.730 39.130 0.00 0.00 37.88 3.41
1967 2747 4.733077 TCCAAACAAATACTCCCTTGGA 57.267 40.909 0.00 0.00 39.91 3.53
1968 2748 5.016173 TCATCCAAACAAATACTCCCTTGG 58.984 41.667 0.00 0.00 35.65 3.61
1969 2749 6.780457 ATCATCCAAACAAATACTCCCTTG 57.220 37.500 0.00 0.00 0.00 3.61
1970 2750 6.351286 GCAATCATCCAAACAAATACTCCCTT 60.351 38.462 0.00 0.00 0.00 3.95
1971 2751 5.127682 GCAATCATCCAAACAAATACTCCCT 59.872 40.000 0.00 0.00 0.00 4.20
1972 2752 5.351458 GCAATCATCCAAACAAATACTCCC 58.649 41.667 0.00 0.00 0.00 4.30
1973 2753 5.105392 TGGCAATCATCCAAACAAATACTCC 60.105 40.000 0.00 0.00 0.00 3.85
2058 2838 4.563374 GGTTTTGCTTGCCTATGATTTGGT 60.563 41.667 0.00 0.00 0.00 3.67
2096 2881 9.261035 TCACCCTATCAAATATTTGGCTAAAAA 57.739 29.630 24.40 7.07 38.66 1.94
2097 2882 8.830915 TCACCCTATCAAATATTTGGCTAAAA 57.169 30.769 24.40 7.73 38.66 1.52
2098 2883 8.691797 GTTCACCCTATCAAATATTTGGCTAAA 58.308 33.333 24.40 8.40 38.66 1.85
2099 2884 7.836685 TGTTCACCCTATCAAATATTTGGCTAA 59.163 33.333 24.40 8.74 38.66 3.09
2114 2899 3.737559 TTGAGCCAATGTTCACCCTAT 57.262 42.857 0.00 0.00 30.81 2.57
2149 2934 1.062587 CCGTCAAAGGTGATCGCATTC 59.937 52.381 6.63 0.00 35.80 2.67
2196 2983 2.559668 TGACTTCCGTCCTAATCGTGTT 59.440 45.455 0.00 0.00 39.47 3.32
2271 3058 6.205101 ACGCTACTAAACACTAGCTGTATT 57.795 37.500 0.00 0.00 34.36 1.89
2298 3085 0.109723 AGCACACCCGGTGTTACAAT 59.890 50.000 21.11 2.50 45.08 2.71
2307 3094 1.671054 CACCTACAAGCACACCCGG 60.671 63.158 0.00 0.00 0.00 5.73
2310 3097 0.035458 AGCTCACCTACAAGCACACC 59.965 55.000 0.00 0.00 41.06 4.16
2318 3105 4.344102 AGAGTTTGTACAAGCTCACCTACA 59.656 41.667 37.74 9.66 46.73 2.74
2350 3137 5.763204 AGAAGTCTTGCCTTTCAATTCGTTA 59.237 36.000 0.00 0.00 33.57 3.18
2358 3145 3.746045 ACGTAGAAGTCTTGCCTTTCA 57.254 42.857 0.00 0.00 0.00 2.69
2363 3150 4.056050 TGAGAAAACGTAGAAGTCTTGCC 58.944 43.478 0.00 0.00 0.00 4.52
2390 3177 2.038557 AGGCGGCGATAATATGGTCTTT 59.961 45.455 12.98 0.00 0.00 2.52
2393 3180 2.000447 GAAGGCGGCGATAATATGGTC 59.000 52.381 12.98 0.00 0.00 4.02
2394 3181 1.346395 TGAAGGCGGCGATAATATGGT 59.654 47.619 12.98 0.00 0.00 3.55
2395 3182 1.732259 GTGAAGGCGGCGATAATATGG 59.268 52.381 12.98 0.00 0.00 2.74
2468 3260 5.073008 TGCTGGTGCCATTCTCCTATATTTA 59.927 40.000 0.00 0.00 38.71 1.40
2472 3264 2.369860 CTGCTGGTGCCATTCTCCTATA 59.630 50.000 0.00 0.00 38.71 1.31
2477 3274 1.001641 ACCTGCTGGTGCCATTCTC 60.002 57.895 15.36 0.00 46.51 2.87


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

AutoCloner maintained by Alex Coulton.