Multiple sequence alignment - TraesCS6D01G279800

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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 TraesCS6D01G279800 chr6D 100.000 2222 0 0 1 2222 387779819 387782040 0.000000e+00 4104
1 TraesCS6D01G279800 chr6D 82.150 493 39 16 1749 2219 409744688 409744223 5.790000e-101 377
2 TraesCS6D01G279800 chr6D 81.089 349 32 20 870 1209 387882758 387883081 4.740000e-62 248
3 TraesCS6D01G279800 chr6D 93.750 128 5 1 1475 1599 409753198 409753071 2.910000e-44 189
4 TraesCS6D01G279800 chr3D 97.353 869 20 3 1 867 149936053 149935186 0.000000e+00 1474
5 TraesCS6D01G279800 chr3D 96.889 868 26 1 1 867 376218327 376219194 0.000000e+00 1452
6 TraesCS6D01G279800 chr3D 96.663 869 28 1 1 868 423753894 423754762 0.000000e+00 1443
7 TraesCS6D01G279800 chr3D 96.532 865 29 1 6 869 139080640 139079776 0.000000e+00 1430
8 TraesCS6D01G279800 chr3D 95.490 887 37 3 3 887 231275355 231274470 0.000000e+00 1413
9 TraesCS6D01G279800 chr4D 97.120 868 24 1 1 867 27016289 27015422 0.000000e+00 1463
10 TraesCS6D01G279800 chr4D 79.268 328 46 16 1475 1789 40819674 40819992 2.240000e-50 209
11 TraesCS6D01G279800 chr5D 96.893 869 25 2 1 867 364486914 364487782 0.000000e+00 1454
12 TraesCS6D01G279800 chr5D 96.318 869 30 2 1 867 465692656 465693524 0.000000e+00 1426
13 TraesCS6D01G279800 chr5D 80.547 329 44 14 1474 1789 548627597 548627276 3.690000e-58 235
14 TraesCS6D01G279800 chr2D 96.667 870 28 1 1 869 129776061 129776930 0.000000e+00 1445
15 TraesCS6D01G279800 chr7D 90.495 768 53 6 1474 2221 17214034 17213267 0.000000e+00 996
16 TraesCS6D01G279800 chr6A 94.297 526 26 2 949 1473 532898248 532898770 0.000000e+00 802
17 TraesCS6D01G279800 chr3A 86.511 771 43 24 1475 2221 24460765 24460032 0.000000e+00 791
18 TraesCS6D01G279800 chr3A 79.268 328 48 16 1474 1789 13511357 13511676 6.220000e-51 211
19 TraesCS6D01G279800 chr6B 92.126 508 25 4 868 1371 578950534 578951030 0.000000e+00 702
20 TraesCS6D01G279800 chr4B 75.875 771 106 37 1475 2191 466640907 466641651 9.900000e-84 320
21 TraesCS6D01G279800 chr4B 79.048 420 57 19 1475 1872 75037341 75036931 2.190000e-65 259
22 TraesCS6D01G279800 chr2A 79.940 334 45 16 1470 1789 48551791 48552116 2.220000e-55 226
23 TraesCS6D01G279800 chr5B 80.061 326 45 15 1475 1789 513852856 513853172 7.980000e-55 224


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 TraesCS6D01G279800 chr6D 387779819 387782040 2221 False 4104 4104 100.000 1 2222 1 chr6D.!!$F1 2221
1 TraesCS6D01G279800 chr3D 149935186 149936053 867 True 1474 1474 97.353 1 867 1 chr3D.!!$R2 866
2 TraesCS6D01G279800 chr3D 376218327 376219194 867 False 1452 1452 96.889 1 867 1 chr3D.!!$F1 866
3 TraesCS6D01G279800 chr3D 423753894 423754762 868 False 1443 1443 96.663 1 868 1 chr3D.!!$F2 867
4 TraesCS6D01G279800 chr3D 139079776 139080640 864 True 1430 1430 96.532 6 869 1 chr3D.!!$R1 863
5 TraesCS6D01G279800 chr3D 231274470 231275355 885 True 1413 1413 95.490 3 887 1 chr3D.!!$R3 884
6 TraesCS6D01G279800 chr4D 27015422 27016289 867 True 1463 1463 97.120 1 867 1 chr4D.!!$R1 866
7 TraesCS6D01G279800 chr5D 364486914 364487782 868 False 1454 1454 96.893 1 867 1 chr5D.!!$F1 866
8 TraesCS6D01G279800 chr5D 465692656 465693524 868 False 1426 1426 96.318 1 867 1 chr5D.!!$F2 866
9 TraesCS6D01G279800 chr2D 129776061 129776930 869 False 1445 1445 96.667 1 869 1 chr2D.!!$F1 868
10 TraesCS6D01G279800 chr7D 17213267 17214034 767 True 996 996 90.495 1474 2221 1 chr7D.!!$R1 747
11 TraesCS6D01G279800 chr6A 532898248 532898770 522 False 802 802 94.297 949 1473 1 chr6A.!!$F1 524
12 TraesCS6D01G279800 chr3A 24460032 24460765 733 True 791 791 86.511 1475 2221 1 chr3A.!!$R1 746
13 TraesCS6D01G279800 chr4B 466640907 466641651 744 False 320 320 75.875 1475 2191 1 chr4B.!!$F1 716

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
877 881 0.03213 TCCACGACAGTGTCAGAAGC 59.968 55.0 22.66 0.0 46.56 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1888 1921 0.723981 GCTTCAGTGCGGATGAGTTC 59.276 55.0 0.0 0.0 0.0 3.01 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
50 51 0.257039 GGTGAATGGAGGCTCATGGT 59.743 55.000 17.69 0.00 0.00 3.55
107 109 1.874345 GAGAAACGAGGAGGCCACGA 61.874 60.000 5.01 0.00 39.84 4.35
443 446 1.939934 CAGCACCAAACTTGAAGACGA 59.060 47.619 0.00 0.00 0.00 4.20
648 651 1.810755 GCGGTTTAGGGACAAGAAAGG 59.189 52.381 0.00 0.00 0.00 3.11
722 725 3.248024 TCAATACCACCTCAACTGGACT 58.752 45.455 0.00 0.00 32.55 3.85
730 733 2.303311 ACCTCAACTGGACTTAGGCTTC 59.697 50.000 0.00 0.00 0.00 3.86
757 760 2.348243 CGTAAGGGGCCGAACCAA 59.652 61.111 0.00 0.00 42.05 3.67
871 875 2.221055 GTGACAATTCCACGACAGTGTC 59.779 50.000 13.56 13.56 46.56 3.67
873 877 2.476619 GACAATTCCACGACAGTGTCAG 59.523 50.000 22.66 16.68 46.56 3.51
877 881 0.032130 TCCACGACAGTGTCAGAAGC 59.968 55.000 22.66 0.00 46.56 3.86
880 884 0.032678 ACGACAGTGTCAGAAGCCTG 59.967 55.000 22.66 6.54 41.74 4.85
887 891 3.446873 CAGTGTCAGAAGCCTGTAGATCT 59.553 47.826 0.00 0.00 41.16 2.75
888 892 4.642437 CAGTGTCAGAAGCCTGTAGATCTA 59.358 45.833 0.00 0.00 41.16 1.98
889 893 4.642885 AGTGTCAGAAGCCTGTAGATCTAC 59.357 45.833 23.53 23.53 41.16 2.59
890 894 4.399618 GTGTCAGAAGCCTGTAGATCTACA 59.600 45.833 29.19 29.19 43.14 2.74
891 895 4.399618 TGTCAGAAGCCTGTAGATCTACAC 59.600 45.833 27.96 20.07 40.77 2.90
892 896 3.954904 TCAGAAGCCTGTAGATCTACACC 59.045 47.826 27.96 21.20 40.77 4.16
893 897 3.068873 CAGAAGCCTGTAGATCTACACCC 59.931 52.174 27.96 20.90 40.77 4.61
894 898 1.693627 AGCCTGTAGATCTACACCCG 58.306 55.000 27.96 19.23 40.77 5.28
895 899 1.063867 AGCCTGTAGATCTACACCCGT 60.064 52.381 27.96 12.52 40.77 5.28
896 900 1.337387 GCCTGTAGATCTACACCCGTC 59.663 57.143 27.96 8.44 40.77 4.79
897 901 1.602851 CCTGTAGATCTACACCCGTCG 59.397 57.143 27.96 17.97 40.77 5.12
898 902 2.286872 CTGTAGATCTACACCCGTCGT 58.713 52.381 27.96 0.00 40.77 4.34
899 903 2.283298 TGTAGATCTACACCCGTCGTC 58.717 52.381 27.96 2.47 40.77 4.20
900 904 2.283298 GTAGATCTACACCCGTCGTCA 58.717 52.381 24.97 0.00 36.15 4.35
901 905 1.830279 AGATCTACACCCGTCGTCAA 58.170 50.000 0.00 0.00 0.00 3.18
902 906 1.743958 AGATCTACACCCGTCGTCAAG 59.256 52.381 0.00 0.00 0.00 3.02
903 907 0.172803 ATCTACACCCGTCGTCAAGC 59.827 55.000 0.00 0.00 0.00 4.01
904 908 0.892358 TCTACACCCGTCGTCAAGCT 60.892 55.000 0.00 0.00 0.00 3.74
905 909 0.456312 CTACACCCGTCGTCAAGCTC 60.456 60.000 0.00 0.00 0.00 4.09
906 910 1.870055 TACACCCGTCGTCAAGCTCC 61.870 60.000 0.00 0.00 0.00 4.70
907 911 2.915659 ACCCGTCGTCAAGCTCCA 60.916 61.111 0.00 0.00 0.00 3.86
908 912 2.283529 ACCCGTCGTCAAGCTCCAT 61.284 57.895 0.00 0.00 0.00 3.41
909 913 0.968901 ACCCGTCGTCAAGCTCCATA 60.969 55.000 0.00 0.00 0.00 2.74
910 914 0.249073 CCCGTCGTCAAGCTCCATAG 60.249 60.000 0.00 0.00 0.00 2.23
921 925 2.618442 GCTCCATAGCTGCTTCTTCT 57.382 50.000 7.79 0.00 45.85 2.85
922 926 2.916640 GCTCCATAGCTGCTTCTTCTT 58.083 47.619 7.79 0.00 45.85 2.52
923 927 2.871633 GCTCCATAGCTGCTTCTTCTTC 59.128 50.000 7.79 0.00 45.85 2.87
924 928 3.465871 CTCCATAGCTGCTTCTTCTTCC 58.534 50.000 7.79 0.00 0.00 3.46
925 929 3.110705 TCCATAGCTGCTTCTTCTTCCT 58.889 45.455 7.79 0.00 0.00 3.36
926 930 4.290093 TCCATAGCTGCTTCTTCTTCCTA 58.710 43.478 7.79 0.00 0.00 2.94
927 931 4.343526 TCCATAGCTGCTTCTTCTTCCTAG 59.656 45.833 7.79 0.00 0.00 3.02
928 932 2.689553 AGCTGCTTCTTCTTCCTAGC 57.310 50.000 0.00 0.00 0.00 3.42
929 933 2.187100 AGCTGCTTCTTCTTCCTAGCT 58.813 47.619 0.00 0.00 35.40 3.32
930 934 3.370104 AGCTGCTTCTTCTTCCTAGCTA 58.630 45.455 0.00 0.00 38.17 3.32
931 935 3.772025 AGCTGCTTCTTCTTCCTAGCTAA 59.228 43.478 0.00 0.00 38.17 3.09
932 936 4.408596 AGCTGCTTCTTCTTCCTAGCTAAT 59.591 41.667 0.00 0.00 38.17 1.73
933 937 5.104569 AGCTGCTTCTTCTTCCTAGCTAATT 60.105 40.000 0.00 0.00 38.17 1.40
934 938 5.588246 GCTGCTTCTTCTTCCTAGCTAATTT 59.412 40.000 0.00 0.00 34.77 1.82
935 939 6.763610 GCTGCTTCTTCTTCCTAGCTAATTTA 59.236 38.462 0.00 0.00 34.77 1.40
936 940 7.042119 GCTGCTTCTTCTTCCTAGCTAATTTAG 60.042 40.741 0.00 0.00 34.77 1.85
954 958 2.103143 CGGCAGCACGTAGAGAGG 59.897 66.667 0.00 0.00 0.00 3.69
960 965 0.331954 AGCACGTAGAGAGGGAGGAA 59.668 55.000 0.00 0.00 0.00 3.36
966 971 3.203487 ACGTAGAGAGGGAGGAAAGAGAT 59.797 47.826 0.00 0.00 0.00 2.75
973 978 2.032620 GGGAGGAAAGAGATACGCAGA 58.967 52.381 0.00 0.00 0.00 4.26
974 979 2.431057 GGGAGGAAAGAGATACGCAGAA 59.569 50.000 0.00 0.00 0.00 3.02
1032 1037 0.179124 TTGCAAAGTTCGTTGTGCCC 60.179 50.000 0.00 0.00 36.12 5.36
1045 1050 2.173669 GTGCCCGTGATCGTGATGG 61.174 63.158 0.00 0.00 35.01 3.51
1062 1067 1.745489 GGTCATGGTGTTCTCGGCC 60.745 63.158 0.00 0.00 0.00 6.13
1065 1070 2.047274 ATGGTGTTCTCGGCCGTG 60.047 61.111 27.15 23.87 0.00 4.94
1247 1252 1.855213 GCATGCAGAAACTGGCGACA 61.855 55.000 14.21 0.00 39.59 4.35
1254 1259 2.354510 CAGAAACTGGCGACAAAGTTGA 59.645 45.455 0.00 0.00 42.06 3.18
1323 1328 8.943909 TTGGTTTGTTAATTCGGTTGTAAAAT 57.056 26.923 0.00 0.00 0.00 1.82
1333 1338 8.582433 AATTCGGTTGTAAAATAACAAACTGG 57.418 30.769 3.56 0.00 43.48 4.00
1338 1343 5.203060 TGTAAAATAACAAACTGGTGCCC 57.797 39.130 0.00 0.00 0.00 5.36
1345 1350 6.680148 ATAACAAACTGGTGCCCTTAAAAT 57.320 33.333 0.00 0.00 0.00 1.82
1400 1405 7.825761 TGGTAAGGTTTTAGTAAGGCATAGTTC 59.174 37.037 0.00 0.00 0.00 3.01
1423 1428 1.611977 GGCCCCTTGTTGAAAGTGTAC 59.388 52.381 0.00 0.00 0.00 2.90
1448 1453 8.520351 ACCCTCTATACAATTTTGTTTAAGTGC 58.480 33.333 0.63 0.00 42.35 4.40
1486 1491 4.338379 AATATCACCGAGCTCCTTTACC 57.662 45.455 8.47 0.00 0.00 2.85
1630 1642 7.149973 GGGTAAAAAGGTAAACTGATTCCAAC 58.850 38.462 0.00 0.00 0.00 3.77
1656 1673 2.893895 CAGCGCATCACGGCTGAT 60.894 61.111 11.47 0.00 43.85 2.90
1661 1678 0.509929 CGCATCACGGCTGATACATG 59.490 55.000 0.00 0.00 35.17 3.21
1707 1726 7.228906 GCAAGAACCCTAATTCTAATCCCTAAC 59.771 40.741 0.00 0.00 37.99 2.34
1737 1756 7.254590 GCCTAATTATTCAATAGGATAGCTGCG 60.255 40.741 0.00 0.00 0.00 5.18
1823 1850 0.685458 GGCATCTGCTGGGAATGGTT 60.685 55.000 1.70 0.00 41.70 3.67
1888 1921 0.521291 TGCTTTCTCGCGAAATTGGG 59.479 50.000 11.33 0.00 38.39 4.12
1895 1928 2.009774 CTCGCGAAATTGGGAACTCAT 58.990 47.619 11.33 0.00 0.00 2.90
1948 1998 2.656085 GAAGATCTATCACGTCGGCAG 58.344 52.381 0.00 0.00 0.00 4.85
2036 2086 1.737838 CGGCTGCTTTGATTGGACTA 58.262 50.000 0.00 0.00 0.00 2.59
2075 2134 0.737367 TTCTTGCGAGCCTGATGTCG 60.737 55.000 0.00 0.00 39.25 4.35
2083 2142 3.084579 CCTGATGTCGCTTGCGTC 58.915 61.111 14.70 9.92 0.00 5.19
2090 2149 0.530744 TGTCGCTTGCGTCTATTCCT 59.469 50.000 14.70 0.00 0.00 3.36
2102 2161 5.580691 TGCGTCTATTCCTCAACAATACTTG 59.419 40.000 0.00 0.00 0.00 3.16
2194 2257 6.589830 ATTCTGTTTGATCGATAACTTCCG 57.410 37.500 11.34 0.00 0.00 4.30
2221 2284 7.424803 CGCAAAGAAAACATATCCATCCATTA 58.575 34.615 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.904865 TTCACCTGTCGCCTCCATCT 60.905 55.000 0.00 0.00 0.00 2.90
50 51 3.395639 CGCACTTATAAATAAGCCCGGA 58.604 45.455 0.73 0.00 42.66 5.14
107 109 0.821517 TGGTGGCGAGATAATCACGT 59.178 50.000 0.00 0.00 33.10 4.49
389 392 2.759535 TGACCATTATGACGTAACCCGA 59.240 45.455 0.00 0.00 40.70 5.14
443 446 3.201266 TCTTAAGCCCATTATTGACCCGT 59.799 43.478 0.00 0.00 0.00 5.28
648 651 1.398390 CTGCCTGGTTATCGAGTTTGC 59.602 52.381 0.00 0.00 0.00 3.68
722 725 2.532843 ACGGTGAAGGTAGAAGCCTAA 58.467 47.619 0.00 0.00 38.03 2.69
730 733 0.177373 GCCCCTTACGGTGAAGGTAG 59.823 60.000 10.90 4.79 44.02 3.18
757 760 4.141779 GGACAAGGAACACGAGGGTTATAT 60.142 45.833 0.00 0.00 0.00 0.86
869 873 4.202070 GGTGTAGATCTACAGGCTTCTGAC 60.202 50.000 31.31 17.71 45.61 3.51
871 875 3.068873 GGGTGTAGATCTACAGGCTTCTG 59.931 52.174 31.31 0.00 45.61 3.02
873 877 2.034812 CGGGTGTAGATCTACAGGCTTC 59.965 54.545 31.31 20.21 45.61 3.86
877 881 1.602851 CGACGGGTGTAGATCTACAGG 59.397 57.143 31.31 24.51 45.61 4.00
880 884 2.283298 TGACGACGGGTGTAGATCTAC 58.717 52.381 23.53 23.53 36.63 2.59
887 891 1.582968 GAGCTTGACGACGGGTGTA 59.417 57.895 0.00 0.00 0.00 2.90
888 892 2.338984 GAGCTTGACGACGGGTGT 59.661 61.111 0.00 0.00 0.00 4.16
889 893 2.432628 GGAGCTTGACGACGGGTG 60.433 66.667 0.00 0.00 0.00 4.61
890 894 0.968901 TATGGAGCTTGACGACGGGT 60.969 55.000 0.00 0.00 0.00 5.28
891 895 0.249073 CTATGGAGCTTGACGACGGG 60.249 60.000 0.00 0.00 0.00 5.28
892 896 0.872021 GCTATGGAGCTTGACGACGG 60.872 60.000 0.00 0.00 45.98 4.79
893 897 2.582959 GCTATGGAGCTTGACGACG 58.417 57.895 0.00 0.00 45.98 5.12
903 907 3.134442 AGGAAGAAGAAGCAGCTATGGAG 59.866 47.826 0.00 0.00 0.00 3.86
904 908 3.110705 AGGAAGAAGAAGCAGCTATGGA 58.889 45.455 0.00 0.00 0.00 3.41
905 909 3.557228 AGGAAGAAGAAGCAGCTATGG 57.443 47.619 0.00 0.00 0.00 2.74
906 910 4.057432 GCTAGGAAGAAGAAGCAGCTATG 58.943 47.826 0.00 0.00 35.05 2.23
907 911 3.966665 AGCTAGGAAGAAGAAGCAGCTAT 59.033 43.478 0.00 0.00 36.19 2.97
908 912 3.370104 AGCTAGGAAGAAGAAGCAGCTA 58.630 45.455 0.00 0.00 36.19 3.32
909 913 2.187100 AGCTAGGAAGAAGAAGCAGCT 58.813 47.619 0.00 0.00 37.44 4.24
910 914 2.689553 AGCTAGGAAGAAGAAGCAGC 57.310 50.000 0.00 0.00 37.44 5.25
911 915 8.364129 CTAAATTAGCTAGGAAGAAGAAGCAG 57.636 38.462 0.00 0.00 37.44 4.24
928 932 1.006832 ACGTGCTGCCGCTAAATTAG 58.993 50.000 0.70 0.00 36.97 1.73
929 933 2.159212 TCTACGTGCTGCCGCTAAATTA 60.159 45.455 0.00 0.00 36.97 1.40
930 934 1.006832 CTACGTGCTGCCGCTAAATT 58.993 50.000 0.00 0.00 36.97 1.82
931 935 0.174845 TCTACGTGCTGCCGCTAAAT 59.825 50.000 0.00 0.00 36.97 1.40
932 936 0.457853 CTCTACGTGCTGCCGCTAAA 60.458 55.000 0.00 0.00 36.97 1.85
933 937 1.138883 CTCTACGTGCTGCCGCTAA 59.861 57.895 0.00 0.00 36.97 3.09
934 938 1.715862 CTCTCTACGTGCTGCCGCTA 61.716 60.000 0.00 2.97 36.97 4.26
935 939 3.057547 CTCTCTACGTGCTGCCGCT 62.058 63.158 0.00 2.11 36.97 5.52
936 940 2.580867 CTCTCTACGTGCTGCCGC 60.581 66.667 0.00 0.00 0.00 6.53
937 941 2.103143 CCTCTCTACGTGCTGCCG 59.897 66.667 0.00 8.60 0.00 5.69
938 942 2.010582 CTCCCTCTCTACGTGCTGCC 62.011 65.000 0.00 0.00 0.00 4.85
939 943 1.435515 CTCCCTCTCTACGTGCTGC 59.564 63.158 0.00 0.00 0.00 5.25
940 944 0.394488 TCCTCCCTCTCTACGTGCTG 60.394 60.000 0.00 0.00 0.00 4.41
941 945 0.331954 TTCCTCCCTCTCTACGTGCT 59.668 55.000 0.00 0.00 0.00 4.40
942 946 1.135333 CTTTCCTCCCTCTCTACGTGC 59.865 57.143 0.00 0.00 0.00 5.34
943 947 2.685897 CTCTTTCCTCCCTCTCTACGTG 59.314 54.545 0.00 0.00 0.00 4.49
944 948 2.577105 TCTCTTTCCTCCCTCTCTACGT 59.423 50.000 0.00 0.00 0.00 3.57
945 949 3.284793 TCTCTTTCCTCCCTCTCTACG 57.715 52.381 0.00 0.00 0.00 3.51
946 950 4.758165 CGTATCTCTTTCCTCCCTCTCTAC 59.242 50.000 0.00 0.00 0.00 2.59
947 951 4.747316 GCGTATCTCTTTCCTCCCTCTCTA 60.747 50.000 0.00 0.00 0.00 2.43
954 958 3.802948 TTCTGCGTATCTCTTTCCTCC 57.197 47.619 0.00 0.00 0.00 4.30
960 965 3.215151 TCGGAGATTCTGCGTATCTCTT 58.785 45.455 24.03 0.00 45.16 2.85
966 971 3.252701 GGTTATCTCGGAGATTCTGCGTA 59.747 47.826 24.36 15.34 45.16 4.42
979 984 4.579454 TGACCTTAATCCGGTTATCTCG 57.421 45.455 0.00 0.00 34.19 4.04
992 997 2.124901 CGGCGGCCATGACCTTAA 60.125 61.111 20.71 0.00 0.00 1.85
997 1002 2.824041 AATCACGGCGGCCATGAC 60.824 61.111 21.21 0.00 0.00 3.06
1032 1037 1.211743 CCATGACCATCACGATCACG 58.788 55.000 0.00 0.00 45.75 4.35
1045 1050 2.100631 CGGCCGAGAACACCATGAC 61.101 63.158 24.07 0.00 0.00 3.06
1223 1228 2.793585 CGCCAGTTTCTGCATGCTTATG 60.794 50.000 20.33 8.80 0.00 1.90
1224 1229 1.402968 CGCCAGTTTCTGCATGCTTAT 59.597 47.619 20.33 0.00 0.00 1.73
1225 1230 0.804364 CGCCAGTTTCTGCATGCTTA 59.196 50.000 20.33 3.61 0.00 3.09
1254 1259 2.824041 GGCCACGCCGTTGATCAT 60.824 61.111 0.00 0.00 39.62 2.45
1333 1338 8.088365 AGAACAACTGAAATATTTTAAGGGCAC 58.912 33.333 1.43 0.00 0.00 5.01
1387 1392 2.298610 GGGCCTTGAACTATGCCTTAC 58.701 52.381 0.84 0.00 43.50 2.34
1423 1428 8.519526 TGCACTTAAACAAAATTGTATAGAGGG 58.480 33.333 0.00 0.00 41.31 4.30
1448 1453 7.465111 CGGTGATATTTCTCTGAAGTTGACATG 60.465 40.741 0.00 0.00 0.00 3.21
1451 1456 6.100004 TCGGTGATATTTCTCTGAAGTTGAC 58.900 40.000 0.00 0.00 29.93 3.18
1486 1491 4.935808 GGCTCATATTCATTTAGGGGTACG 59.064 45.833 0.00 0.00 0.00 3.67
1585 1597 0.736325 CCAAGCACGAGGTACTTCCG 60.736 60.000 0.00 0.39 41.55 4.30
1588 1600 1.677552 CCCCAAGCACGAGGTACTT 59.322 57.895 0.00 0.00 41.55 2.24
1642 1659 0.509929 CATGTATCAGCCGTGATGCG 59.490 55.000 0.00 0.00 45.99 4.73
1656 1673 7.244192 CGATCGAGTTGAATAGCTATCATGTA 58.756 38.462 10.26 0.00 0.00 2.29
1661 1678 4.476862 TGCGATCGAGTTGAATAGCTATC 58.523 43.478 21.57 1.67 0.00 2.08
1719 1738 2.616510 GGCCGCAGCTATCCTATTGAAT 60.617 50.000 0.00 0.00 39.73 2.57
1737 1756 1.302033 CAGATCATAGTGGCCGGCC 60.302 63.158 39.40 39.40 0.00 6.13
1790 1817 1.284198 AGATGCCATTCCAGCAAGTCT 59.716 47.619 0.00 0.00 44.83 3.24
1888 1921 0.723981 GCTTCAGTGCGGATGAGTTC 59.276 55.000 0.00 0.00 0.00 3.01
1895 1928 1.078918 CATCCTGCTTCAGTGCGGA 60.079 57.895 0.00 0.00 41.56 5.54
1948 1998 4.920376 ACTGAACATTTGTACAACTGCAC 58.080 39.130 21.91 16.70 0.00 4.57
1983 2033 6.782000 CCTTCCATAATCCATATTGAACCCAA 59.218 38.462 0.00 0.00 36.61 4.12
2036 2086 2.942796 TTCGTCAGCAGCCCGACAT 61.943 57.895 11.98 0.00 32.24 3.06
2075 2134 2.346803 TGTTGAGGAATAGACGCAAGC 58.653 47.619 0.00 0.00 45.62 4.01
2141 2202 4.398044 ACAAGTTCTCGAAAACCACACAAT 59.602 37.500 0.00 0.00 0.00 2.71
2194 2257 3.502191 TGGATATGTTTTCTTTGCGCC 57.498 42.857 4.18 0.00 0.00 6.53


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

AutoCloner maintained by Alex Coulton.