Multiple sequence alignment - TraesCS4B01G276500

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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 TraesCS4B01G276500 chr4B 100.000 5178 0 0 1 5178 556076373 556071196 0 9563
1 TraesCS4B01G276500 chr4D 95.537 4571 133 31 4 4517 445503516 445498960 0 7245
2 TraesCS4B01G276500 chr4D 95.052 667 21 3 4513 5178 445498758 445498103 0 1038
3 TraesCS4B01G276500 chr4A 95.022 4540 154 33 1 4483 21624899 21629423 0 7066


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 TraesCS4B01G276500 chr4B 556071196 556076373 5177 True 9563.0 9563 100.0000 1 5178 1 chr4B.!!$R1 5177
1 TraesCS4B01G276500 chr4D 445498103 445503516 5413 True 4141.5 7245 95.2945 4 5178 2 chr4D.!!$R1 5174
2 TraesCS4B01G276500 chr4A 21624899 21629423 4524 False 7066.0 7066 95.0220 1 4483 1 chr4A.!!$F1 4482

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
918 952 1.093972 TGCTGTCCACACAACAACTG 58.906 50.000 0.0 0.0 29.82 3.16 F
2003 2038 1.077212 ACATGCTGGGAGTGATGCC 60.077 57.895 0.0 0.0 0.00 4.40 F
3840 3887 0.984995 GGGTACAACCAAGAGGAGCT 59.015 55.000 0.0 0.0 41.02 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2843 2879 0.746063 TTCCACACAAAGCTGCCAAG 59.254 50.0 0.00 0.0 0.0 3.61 R
3922 3969 0.322816 GCTTCACCTCAGGCCATTCA 60.323 55.0 5.01 0.0 0.0 2.57 R
4683 4967 0.037232 CTTGTCCTCCTCCGGTTCAC 60.037 60.0 0.00 0.0 0.0 3.18 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
118 119 9.682465 AGAGAATTAACCCTTATTCCTGTTAAC 57.318 33.333 0.00 0.00 36.37 2.01
196 200 3.742248 GACGAGAGAGGGGAGGGGG 62.742 73.684 0.00 0.00 0.00 5.40
218 222 2.735151 GGGAGGGATTGTTAGGGTTTG 58.265 52.381 0.00 0.00 0.00 2.93
265 271 3.492313 GAGACGCCAAAATGTTGTGATC 58.508 45.455 0.00 0.00 32.40 2.92
284 290 7.950803 TGTGATCTGGTTAGGAGGGATATATA 58.049 38.462 0.00 0.00 0.00 0.86
338 352 8.082852 GTCTTGTTGTAGAAGAATCAGTAGTGA 58.917 37.037 1.95 1.95 37.02 3.41
355 369 1.906574 GTGAACTGATGGGGGTCTGTA 59.093 52.381 0.00 0.00 31.19 2.74
370 385 4.072839 GGTCTGTAGTTTTTCCCCTTCTG 58.927 47.826 0.00 0.00 0.00 3.02
379 394 1.681229 TTCCCCTTCTGGTTATGGCT 58.319 50.000 0.00 0.00 0.00 4.75
435 450 2.035961 GCCTAGTTGCCTCGTCATGATA 59.964 50.000 0.00 0.00 0.00 2.15
522 538 5.630121 AGAAATTTGTGTCTATGGGTGTCA 58.370 37.500 0.00 0.00 0.00 3.58
722 755 7.122353 TCACTACTCTGAATTTCTACAGTACCC 59.878 40.741 0.00 0.00 35.84 3.69
737 770 3.815401 CAGTACCCAGACAAGTTCCAAAG 59.185 47.826 0.00 0.00 0.00 2.77
739 772 3.662759 ACCCAGACAAGTTCCAAAGAA 57.337 42.857 0.00 0.00 0.00 2.52
779 812 5.461078 CACAATGCTTCAAAACAAGAGAAGG 59.539 40.000 0.00 0.00 39.24 3.46
792 825 5.312079 ACAAGAGAAGGTCCTGATTTTCTG 58.688 41.667 0.00 0.00 30.49 3.02
794 827 5.419239 AGAGAAGGTCCTGATTTTCTGAG 57.581 43.478 0.00 0.00 30.49 3.35
795 828 4.843516 AGAGAAGGTCCTGATTTTCTGAGT 59.156 41.667 0.00 0.00 30.49 3.41
796 829 6.019748 AGAGAAGGTCCTGATTTTCTGAGTA 58.980 40.000 0.00 0.00 30.49 2.59
797 830 6.043854 AGAAGGTCCTGATTTTCTGAGTAC 57.956 41.667 0.00 0.00 0.00 2.73
838 872 7.147880 CCTTGGTAGCTACAGTAACTATCTTGT 60.148 40.741 24.75 0.00 0.00 3.16
841 875 9.064706 TGGTAGCTACAGTAACTATCTTGTATC 57.935 37.037 24.75 2.10 0.00 2.24
842 876 8.513774 GGTAGCTACAGTAACTATCTTGTATCC 58.486 40.741 24.75 0.00 0.00 2.59
845 879 6.016443 GCTACAGTAACTATCTTGTATCCGGT 60.016 42.308 0.00 0.00 0.00 5.28
918 952 1.093972 TGCTGTCCACACAACAACTG 58.906 50.000 0.00 0.00 29.82 3.16
932 966 1.542030 ACAACTGTCTCTAGACTGGCG 59.458 52.381 17.82 11.84 44.86 5.69
942 976 4.058817 CTCTAGACTGGCGTTCTTGTTTT 58.941 43.478 0.00 0.00 0.00 2.43
955 989 5.290643 CGTTCTTGTTTTTGCTCAATGGAAA 59.709 36.000 0.00 0.00 34.17 3.13
1146 1181 2.899900 GGCTCCTTTCCCTTTTGTGAAT 59.100 45.455 0.00 0.00 0.00 2.57
1225 1260 4.404073 AGAATACCTCTTGTGAGCCTGTAG 59.596 45.833 0.00 0.00 38.93 2.74
1230 1265 4.777896 ACCTCTTGTGAGCCTGTAGATTTA 59.222 41.667 0.00 0.00 38.93 1.40
1352 1387 2.930950 TCTTGGTTTGACTTCTGTGGG 58.069 47.619 0.00 0.00 0.00 4.61
1677 1712 2.768253 TCCGTGAGCTCATTGAATGT 57.232 45.000 21.47 0.00 0.00 2.71
1689 1724 5.163713 GCTCATTGAATGTAAACAGAGACCC 60.164 44.000 4.93 0.00 0.00 4.46
1719 1754 5.185442 CCTATCTGAAGAGCTGAGCATGATA 59.815 44.000 7.39 4.41 0.00 2.15
1800 1835 6.605471 TTTCAGCACCTCTAATACTCTGAA 57.395 37.500 0.00 0.00 37.32 3.02
1846 1881 3.181438 TGTTTGCTAACTTAAGAGGCCCA 60.181 43.478 10.09 4.79 35.24 5.36
1859 1894 2.436109 GCCCACTTGCAGGAGGAA 59.564 61.111 13.97 0.00 0.00 3.36
1868 1903 3.265221 ACTTGCAGGAGGAAATGAGATCA 59.735 43.478 1.40 0.00 0.00 2.92
1886 1921 1.200483 CATACGACATGGAGCGTGTC 58.800 55.000 17.12 0.00 44.25 3.67
1919 1954 5.621193 AGGAGGGGTAATGATTATTTGTCG 58.379 41.667 0.00 0.00 0.00 4.35
1967 2002 2.551270 AGGCCTTCACTAGTTCATGGA 58.449 47.619 0.00 0.00 0.00 3.41
2003 2038 1.077212 ACATGCTGGGAGTGATGCC 60.077 57.895 0.00 0.00 0.00 4.40
2006 2041 1.276859 ATGCTGGGAGTGATGCCAGA 61.277 55.000 18.63 5.42 32.65 3.86
2033 2069 8.361139 CCTTATCAGGTAGTGTACTTTCTATGG 58.639 40.741 0.00 0.00 35.06 2.74
2050 2086 8.991243 TTTCTATGGCATTCAAAAATCTCTTG 57.009 30.769 4.78 0.00 0.00 3.02
2061 2097 7.537596 TCAAAAATCTCTTGGGCATTCTTAA 57.462 32.000 0.00 0.00 0.00 1.85
2264 2300 5.537300 TGAGAAGGCAATATAGGTCTGTC 57.463 43.478 0.00 0.00 0.00 3.51
2300 2336 8.738645 AACTTATTGGACCTGACATTCTATTC 57.261 34.615 0.00 0.00 0.00 1.75
2357 2393 3.161866 GCCATTTAAACCTCTGAACCCA 58.838 45.455 0.00 0.00 0.00 4.51
2622 2658 6.561519 TCTTTAGGCTAAATGCTCCTAGTT 57.438 37.500 19.32 0.00 42.39 2.24
2762 2798 2.237392 GAGTTCATCAACCCTACAGGCT 59.763 50.000 0.00 0.00 40.58 4.58
2843 2879 4.344237 CCAGAGGCAATGGTTCCC 57.656 61.111 0.11 0.00 32.85 3.97
3485 3521 2.978978 TGACAGATTCTTCAACCTGGGA 59.021 45.455 0.00 0.00 0.00 4.37
3500 3536 2.420687 CCTGGGATTCCTGAGCAACTAC 60.421 54.545 2.01 0.00 34.32 2.73
3533 3569 2.031245 TGTTGCAATTACTCGTGCCAAG 60.031 45.455 0.59 0.00 40.14 3.61
3551 3587 4.782195 GCCAAGTCGTTGCTAATTATCGTG 60.782 45.833 0.00 0.00 31.64 4.35
3688 3735 1.065102 GCGTTACTACTGCAGGATCGA 59.935 52.381 19.93 0.00 0.00 3.59
3784 3831 4.938575 AGAGGTCAGATACTCGGGATAT 57.061 45.455 0.00 0.00 38.72 1.63
3840 3887 0.984995 GGGTACAACCAAGAGGAGCT 59.015 55.000 0.00 0.00 41.02 4.09
3921 3968 2.551270 CTCAACCGCACACGAAGC 59.449 61.111 0.00 0.00 43.93 3.86
3922 3969 1.956170 CTCAACCGCACACGAAGCT 60.956 57.895 0.00 0.00 43.93 3.74
3929 3988 1.154150 GCACACGAAGCTGAATGGC 60.154 57.895 0.00 0.00 0.00 4.40
3931 3990 0.957395 CACACGAAGCTGAATGGCCT 60.957 55.000 3.32 0.00 0.00 5.19
3932 3991 0.957395 ACACGAAGCTGAATGGCCTG 60.957 55.000 3.32 0.00 0.00 4.85
3936 3995 0.034670 GAAGCTGAATGGCCTGAGGT 60.035 55.000 3.32 0.00 0.00 3.85
3954 4013 1.077805 TGAAGCCAGACGGGGACTA 59.922 57.895 0.00 0.00 37.04 2.59
3959 4018 2.029307 GCCAGACGGGGACTACCATC 62.029 65.000 0.00 0.00 42.91 3.51
3961 4020 1.455217 AGACGGGGACTACCATCCG 60.455 63.158 0.00 0.00 43.35 4.18
3967 4026 1.264295 GGGACTACCATCCGTATCCC 58.736 60.000 0.00 0.00 39.97 3.85
4036 4095 0.106318 TCGAGGAAGGGGCTACTACC 60.106 60.000 0.00 0.00 0.00 3.18
4039 4101 1.075748 GGAAGGGGCTACTACCGGA 60.076 63.158 9.46 0.00 0.00 5.14
4150 4212 2.863346 CGGTTGGGGTGACGTCTCA 61.863 63.158 17.92 7.19 0.00 3.27
4310 4375 4.302455 CTCGTCGGATGCTAATTCTGAAT 58.698 43.478 0.00 0.00 30.54 2.57
4327 4392 8.682936 ATTCTGAATGTCTCTAGTGTTTGTTT 57.317 30.769 1.31 0.00 0.00 2.83
4461 4538 0.107800 TCTTCTCATCTGCTGGCTGC 60.108 55.000 9.67 9.67 43.25 5.25
4519 4803 1.694693 GGGCCTTAGGGGTGTCTCATA 60.695 57.143 0.84 0.00 37.43 2.15
4595 4879 1.798813 GTGTTTCTACCGAGCAAGTGG 59.201 52.381 0.00 0.00 0.00 4.00
4605 4889 2.558359 CCGAGCAAGTGGATTTCCTTTT 59.442 45.455 0.00 0.00 36.82 2.27
4631 4915 1.998315 CATGTGAGCTTTCCAGTCTCG 59.002 52.381 0.00 0.00 0.00 4.04
4642 4926 0.390492 CCAGTCTCGGCTCATGCATA 59.610 55.000 0.00 0.00 41.91 3.14
4649 4933 1.162181 CGGCTCATGCATAGTGTGGG 61.162 60.000 0.00 0.00 41.91 4.61
4662 4946 1.074926 TGTGGGGTGGGTTTGCAAT 60.075 52.632 0.00 0.00 0.00 3.56
4683 4967 8.651588 TGCAATTTTTACAAGTTACAACAACAG 58.348 29.630 0.00 0.00 0.00 3.16
4733 5017 4.025040 TGTGGCTTTCATGTGAGAGAAT 57.975 40.909 4.88 0.00 0.00 2.40
4758 5042 3.813596 CCAGCGGCAATGAGTACC 58.186 61.111 1.45 0.00 0.00 3.34
4894 5179 7.547227 GGACAAACTCTTAATGGCATGTTTAT 58.453 34.615 0.00 0.00 0.00 1.40
4909 5194 8.028354 TGGCATGTTTATATCTTGAAACAACAG 58.972 33.333 5.79 2.11 45.78 3.16
4910 5195 8.028938 GGCATGTTTATATCTTGAAACAACAGT 58.971 33.333 5.79 0.00 45.78 3.55
4997 5282 2.237393 CTCTGATAGCTCACAAGGGC 57.763 55.000 0.00 0.00 0.00 5.19
4998 5283 1.483827 CTCTGATAGCTCACAAGGGCA 59.516 52.381 0.00 0.00 0.00 5.36
4999 5284 2.104451 CTCTGATAGCTCACAAGGGCAT 59.896 50.000 0.00 0.00 0.00 4.40
5000 5285 2.158856 TCTGATAGCTCACAAGGGCATG 60.159 50.000 0.00 0.00 0.00 4.06
5001 5286 0.950116 GATAGCTCACAAGGGCATGC 59.050 55.000 9.90 9.90 0.00 4.06
5002 5287 0.466922 ATAGCTCACAAGGGCATGCC 60.467 55.000 29.47 29.47 0.00 4.40
5015 5300 1.247567 GCATGCCCTACAACACAAGT 58.752 50.000 6.36 0.00 0.00 3.16
5090 5375 1.938577 CATCCATCGTTGCTTCTCCAG 59.061 52.381 0.00 0.00 0.00 3.86
5117 5402 4.337555 AGTTCCTTGCACAATCATATCTGC 59.662 41.667 0.00 0.00 0.00 4.26
5121 5406 0.239347 GCACAATCATATCTGCCGGC 59.761 55.000 22.73 22.73 0.00 6.13
5126 5411 2.475371 ATCATATCTGCCGGCTGCCC 62.475 60.000 29.70 0.00 40.16 5.36
5173 5458 2.242670 CGCGCGGTTTGATCGATC 59.757 61.111 24.84 18.72 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 156 1.656652 CTTCCGTAGCATCAAGGTGG 58.343 55.000 0.00 0.00 0.00 4.61
196 200 1.148498 CCCTAACAATCCCTCCCGC 59.852 63.158 0.00 0.00 0.00 6.13
218 222 2.590859 GGTTTCGCTATCGGGGGC 60.591 66.667 0.00 0.00 36.13 5.80
253 259 5.256474 CCTCCTAACCAGATCACAACATTT 58.744 41.667 0.00 0.00 0.00 2.32
265 271 9.937876 TTACAGATATATATCCCTCCTAACCAG 57.062 37.037 17.44 0.00 33.17 4.00
338 352 2.344093 ACTACAGACCCCCATCAGTT 57.656 50.000 0.00 0.00 0.00 3.16
355 369 4.416516 CCATAACCAGAAGGGGAAAAACT 58.583 43.478 0.00 0.00 42.91 2.66
379 394 4.528076 ACAGTGAAGGCTAGATCTCCTA 57.472 45.455 0.00 0.00 31.24 2.94
435 450 3.795688 TTCTCCCTCTTTGTGCAAGAT 57.204 42.857 0.00 0.00 40.95 2.40
522 538 1.271597 CCAGCTGTGCTCCCTAAAACT 60.272 52.381 13.81 0.00 36.40 2.66
755 788 5.461078 CCTTCTCTTGTTTTGAAGCATTGTG 59.539 40.000 0.00 0.00 36.73 3.33
757 790 5.594926 ACCTTCTCTTGTTTTGAAGCATTG 58.405 37.500 0.00 0.00 36.73 2.82
758 791 5.221322 GGACCTTCTCTTGTTTTGAAGCATT 60.221 40.000 0.00 0.00 36.73 3.56
765 798 6.396829 AAATCAGGACCTTCTCTTGTTTTG 57.603 37.500 0.00 0.00 30.54 2.44
770 803 5.555017 TCAGAAAATCAGGACCTTCTCTTG 58.445 41.667 0.00 0.00 0.00 3.02
773 806 5.159273 ACTCAGAAAATCAGGACCTTCTC 57.841 43.478 0.00 0.00 0.00 2.87
779 812 2.930682 GGCGTACTCAGAAAATCAGGAC 59.069 50.000 0.00 0.00 0.00 3.85
792 825 0.727398 GAAAGGCACATGGCGTACTC 59.273 55.000 0.00 0.00 46.16 2.59
794 827 1.654023 GGGAAAGGCACATGGCGTAC 61.654 60.000 0.00 0.00 46.16 3.67
795 828 1.377987 GGGAAAGGCACATGGCGTA 60.378 57.895 0.00 0.00 46.16 4.42
796 829 2.676471 GGGAAAGGCACATGGCGT 60.676 61.111 0.00 0.00 46.16 5.68
797 830 1.978617 AAGGGAAAGGCACATGGCG 60.979 57.895 0.00 0.00 46.16 5.69
838 872 2.932855 TCACAACCAAACACCGGATA 57.067 45.000 9.46 0.00 0.00 2.59
841 875 3.078097 TGATATCACAACCAAACACCGG 58.922 45.455 0.00 0.00 0.00 5.28
842 876 3.751175 ACTGATATCACAACCAAACACCG 59.249 43.478 0.00 0.00 0.00 4.94
845 879 7.336679 CCTATGAACTGATATCACAACCAAACA 59.663 37.037 0.00 0.00 0.00 2.83
918 952 2.229302 ACAAGAACGCCAGTCTAGAGAC 59.771 50.000 1.17 1.17 45.08 3.36
932 966 6.660887 TTTCCATTGAGCAAAAACAAGAAC 57.339 33.333 0.00 0.00 0.00 3.01
1146 1181 4.202567 ACAAGGACAGATTTAGGCTTTCCA 60.203 41.667 0.00 0.00 35.23 3.53
1174 1209 1.089920 ATGGCGTCTGCAGATGTTTC 58.910 50.000 31.29 22.18 45.35 2.78
1352 1387 2.480416 CCAGGCTGAAGTGTACGATCTC 60.480 54.545 17.94 0.00 0.00 2.75
1653 1688 3.616956 TCAATGAGCTCACGGATTTCT 57.383 42.857 20.97 0.00 0.00 2.52
1677 1712 2.816411 AGGACATCGGGTCTCTGTTTA 58.184 47.619 7.83 0.00 46.16 2.01
1689 1724 3.567585 TCAGCTCTTCAGATAGGACATCG 59.432 47.826 0.00 0.00 0.00 3.84
1719 1754 7.229506 AGAGTGCTAAAGAACTTTGCATAGTTT 59.770 33.333 21.24 10.19 38.43 2.66
1817 1852 7.276878 GCCTCTTAAGTTAGCAAACAAAACAAA 59.723 33.333 1.63 0.00 38.12 2.83
1818 1853 6.754675 GCCTCTTAAGTTAGCAAACAAAACAA 59.245 34.615 1.63 0.00 38.12 2.83
1819 1854 6.270064 GCCTCTTAAGTTAGCAAACAAAACA 58.730 36.000 1.63 0.00 38.12 2.83
1820 1855 5.690409 GGCCTCTTAAGTTAGCAAACAAAAC 59.310 40.000 1.63 0.00 38.12 2.43
1821 1856 5.221362 GGGCCTCTTAAGTTAGCAAACAAAA 60.221 40.000 0.84 0.00 38.12 2.44
1846 1881 3.265221 TGATCTCATTTCCTCCTGCAAGT 59.735 43.478 0.00 0.00 0.00 3.16
1859 1894 4.564041 GCTCCATGTCGTATGATCTCATT 58.436 43.478 0.00 0.00 37.76 2.57
1868 1903 3.642901 GACACGCTCCATGTCGTAT 57.357 52.632 4.90 0.00 37.34 3.06
1886 1921 4.410228 TCATTACCCCTCCTTCTCATTGAG 59.590 45.833 7.38 7.38 0.00 3.02
1919 1954 0.895559 CCAAACCAGGGACCTCAAGC 60.896 60.000 0.00 0.00 0.00 4.01
1961 1996 7.235399 TGTCTGGCAATTATATAGTCTCCATGA 59.765 37.037 0.00 0.04 0.00 3.07
1967 2002 6.877855 CAGCATGTCTGGCAATTATATAGTCT 59.122 38.462 8.70 0.00 39.15 3.24
2003 2038 6.777213 AAGTACACTACCTGATAAGGTCTG 57.223 41.667 4.48 5.17 42.99 3.51
2006 2041 8.915036 CATAGAAAGTACACTACCTGATAAGGT 58.085 37.037 7.05 7.05 45.46 3.50
2030 2066 4.624604 GCCCAAGAGATTTTTGAATGCCAT 60.625 41.667 0.00 0.00 0.00 4.40
2031 2067 3.306919 GCCCAAGAGATTTTTGAATGCCA 60.307 43.478 0.00 0.00 0.00 4.92
2033 2069 3.929094 TGCCCAAGAGATTTTTGAATGC 58.071 40.909 0.00 0.00 0.00 3.56
2071 2107 5.977725 CACTGGCATCATTTGAGATTGAATC 59.022 40.000 0.00 0.00 0.00 2.52
2073 2109 5.011586 TCACTGGCATCATTTGAGATTGAA 58.988 37.500 0.00 0.00 0.00 2.69
2074 2110 4.591929 TCACTGGCATCATTTGAGATTGA 58.408 39.130 0.00 0.00 0.00 2.57
2077 2113 7.504574 TCATTATTCACTGGCATCATTTGAGAT 59.495 33.333 0.00 0.00 0.00 2.75
2264 2300 4.037208 GGTCCAATAAGTTCTGCATCATGG 59.963 45.833 0.00 0.00 0.00 3.66
2300 2336 2.310945 TCTATACCGTGATAGGGAGGGG 59.689 54.545 0.00 0.00 35.02 4.79
2357 2393 4.580167 TCAGCTTGCTCAGTGTTTATGTTT 59.420 37.500 0.00 0.00 0.00 2.83
2565 2601 2.554893 GGATCGGGTAGCTAGAACTCAG 59.445 54.545 0.00 0.00 0.00 3.35
2843 2879 0.746063 TTCCACACAAAGCTGCCAAG 59.254 50.000 0.00 0.00 0.00 3.61
2924 2960 2.281345 CCATCCTGATCCGCCTGC 60.281 66.667 0.00 0.00 0.00 4.85
2986 3022 1.821088 AGGATCCCCTGAATGGTACC 58.179 55.000 8.55 4.43 42.42 3.34
3485 3521 3.584848 ACCTTCTGTAGTTGCTCAGGAAT 59.415 43.478 0.00 0.00 33.13 3.01
3500 3536 6.449698 AGTAATTGCAACATTGAACCTTCTG 58.550 36.000 0.00 0.00 0.00 3.02
3533 3569 3.450578 TCCCACGATAATTAGCAACGAC 58.549 45.455 1.10 0.00 0.00 4.34
3551 3587 2.025887 AGTGATGATGTGAGGGTTTCCC 60.026 50.000 0.00 0.00 45.90 3.97
3840 3887 3.760738 TGATTGTGGATGTGGTTTGCTA 58.239 40.909 0.00 0.00 0.00 3.49
3921 3968 1.747709 CTTCACCTCAGGCCATTCAG 58.252 55.000 5.01 0.00 0.00 3.02
3922 3969 0.322816 GCTTCACCTCAGGCCATTCA 60.323 55.000 5.01 0.00 0.00 2.57
3929 3988 1.079543 CGTCTGGCTTCACCTCAGG 60.080 63.158 0.00 0.00 40.22 3.86
3931 3990 2.583441 CCCGTCTGGCTTCACCTCA 61.583 63.158 0.00 0.00 40.22 3.86
3932 3991 2.266055 CCCGTCTGGCTTCACCTC 59.734 66.667 0.00 0.00 40.22 3.85
3936 3995 1.077805 TAGTCCCCGTCTGGCTTCA 59.922 57.895 0.00 0.00 0.00 3.02
3959 4018 3.195591 CTCCTGCGTCGGGATACGG 62.196 68.421 7.70 0.00 43.06 4.02
3961 4020 2.027751 GCTCCTGCGTCGGGATAC 59.972 66.667 7.70 1.37 38.36 2.24
3967 4026 2.811317 GGTTCTGCTCCTGCGTCG 60.811 66.667 0.00 0.00 43.34 5.12
4066 4128 1.674611 CGTCGACATCGTTGGCTGAC 61.675 60.000 17.16 11.75 40.80 3.51
4150 4212 4.473520 CCTGTCGCGGGGATGCTT 62.474 66.667 6.13 0.00 0.00 3.91
4266 4331 2.610859 AGTTCAGGATGCCCCCGT 60.611 61.111 0.00 0.00 34.76 5.28
4310 4375 3.312421 GCAGCAAACAAACACTAGAGACA 59.688 43.478 0.00 0.00 0.00 3.41
4327 4392 0.522286 CAAAACAACGTGACGCAGCA 60.522 50.000 4.25 0.00 0.00 4.41
4434 4506 1.403382 GCAGATGAGAAGACGACTGCA 60.403 52.381 0.00 0.00 46.30 4.41
4435 4507 1.276415 GCAGATGAGAAGACGACTGC 58.724 55.000 0.00 0.00 42.44 4.40
4436 4508 2.528125 CAGCAGATGAGAAGACGACTG 58.472 52.381 0.00 0.00 0.00 3.51
4461 4538 5.954296 AAACACATCATCTGAAGGAACAG 57.046 39.130 0.00 0.00 39.02 3.16
4519 4803 3.433615 GCTTCGTGCAGTAGATTTCAAGT 59.566 43.478 0.00 0.00 42.31 3.16
4595 4879 1.824852 ACATGGCCGGAAAAGGAAATC 59.175 47.619 5.05 0.00 0.00 2.17
4605 4889 1.377202 GAAAGCTCACATGGCCGGA 60.377 57.895 5.05 0.00 0.00 5.14
4631 4915 0.820891 CCCCACACTATGCATGAGCC 60.821 60.000 10.16 0.00 41.13 4.70
4642 4926 2.123468 GCAAACCCACCCCACACT 60.123 61.111 0.00 0.00 0.00 3.55
4649 4933 4.878971 ACTTGTAAAAATTGCAAACCCACC 59.121 37.500 1.71 0.00 34.87 4.61
4662 4946 9.182933 GTTCACTGTTGTTGTAACTTGTAAAAA 57.817 29.630 0.00 0.00 0.00 1.94
4683 4967 0.037232 CTTGTCCTCCTCCGGTTCAC 60.037 60.000 0.00 0.00 0.00 3.18
4727 5011 1.683917 CCGCTGGCTGTACTATTCTCT 59.316 52.381 0.00 0.00 0.00 3.10
4758 5042 3.058160 CAGCCCAAGTTCTGCCGG 61.058 66.667 0.00 0.00 0.00 6.13
4894 5179 7.665559 AGAGGCAAATACTGTTGTTTCAAGATA 59.334 33.333 0.00 0.00 0.00 1.98
4897 5182 6.076981 AGAGGCAAATACTGTTGTTTCAAG 57.923 37.500 0.00 0.00 0.00 3.02
4936 5221 5.437289 TGAACAAGGCAAATACTGTTCTG 57.563 39.130 13.23 0.00 37.24 3.02
4997 5282 3.440173 CCTTACTTGTGTTGTAGGGCATG 59.560 47.826 0.00 0.00 31.94 4.06
4998 5283 3.073946 ACCTTACTTGTGTTGTAGGGCAT 59.926 43.478 0.00 0.00 39.74 4.40
4999 5284 2.440253 ACCTTACTTGTGTTGTAGGGCA 59.560 45.455 0.00 0.00 39.74 5.36
5000 5285 2.812011 CACCTTACTTGTGTTGTAGGGC 59.188 50.000 0.00 0.00 39.74 5.19
5001 5286 3.408634 CCACCTTACTTGTGTTGTAGGG 58.591 50.000 0.00 0.00 41.23 3.53
5002 5287 3.408634 CCCACCTTACTTGTGTTGTAGG 58.591 50.000 0.00 0.00 31.71 3.18
5003 5288 3.408634 CCCCACCTTACTTGTGTTGTAG 58.591 50.000 0.00 0.00 31.71 2.74
5004 5289 2.106857 CCCCCACCTTACTTGTGTTGTA 59.893 50.000 0.00 0.00 31.71 2.41
5015 5300 2.228480 GCCAGTGACCCCCACCTTA 61.228 63.158 0.00 0.00 46.87 2.69
5090 5375 2.229792 TGATTGTGCAAGGAACTGGAC 58.770 47.619 0.00 0.00 40.86 4.02
5117 5402 3.209097 CCGTATTTGGGCAGCCGG 61.209 66.667 5.00 0.00 0.00 6.13
5121 5406 1.243902 ACAACACCGTATTTGGGCAG 58.756 50.000 0.00 0.00 0.00 4.85
5126 5411 3.799137 AGCGTAACAACACCGTATTTG 57.201 42.857 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.