Multiple sequence alignment - TraesCS1D01G079700

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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 TraesCS1D01G079700 chr1D 100.000 6094 0 0 1 6094 62420618 62414525 0.000000e+00 11254.0
1 TraesCS1D01G079700 chr1B 93.947 5303 200 58 830 6094 99599970 99594751 0.000000e+00 7902.0
2 TraesCS1D01G079700 chr1B 89.525 821 72 10 4 814 99600772 99599956 0.000000e+00 1027.0
3 TraesCS1D01G079700 chr1A 95.575 3571 129 14 827 4387 60359006 60355455 0.000000e+00 5692.0
4 TraesCS1D01G079700 chr1A 88.594 754 33 19 5096 5825 60354710 60353986 0.000000e+00 867.0
5 TraesCS1D01G079700 chr1A 89.740 692 40 15 4387 5066 60355375 60354703 0.000000e+00 856.0
6 TraesCS1D01G079700 chr1A 83.710 620 68 15 120 723 60360688 60360086 6.900000e-154 555.0
7 TraesCS1D01G079700 chr1A 93.443 61 3 1 6035 6094 60353793 60353733 8.410000e-14 89.8


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 TraesCS1D01G079700 chr1D 62414525 62420618 6093 True 11254.00 11254 100.0000 1 6094 1 chr1D.!!$R1 6093
1 TraesCS1D01G079700 chr1B 99594751 99600772 6021 True 4464.50 7902 91.7360 4 6094 2 chr1B.!!$R1 6090
2 TraesCS1D01G079700 chr1A 60353733 60360688 6955 True 1611.96 5692 90.2124 120 6094 5 chr1A.!!$R1 5974

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
189 199 0.179067 TGAACTGACCCGGTTGTGAC 60.179 55.000 0.00 0.0 32.62 3.67 F
585 604 1.111277 AGGCCTTTGAAAGCACGTTT 58.889 45.000 0.00 0.0 0.00 3.60 F
1855 2882 1.064758 ACTGTCTTTGTGTGCTGGGAA 60.065 47.619 0.00 0.0 0.00 3.97 F
1920 2947 1.005630 GGTGCGCAGAGTTCTGTCT 60.006 57.895 12.22 0.0 45.45 3.41 F
3555 4594 1.067060 GTGAAGTGGCCAACAAAGACC 59.933 52.381 7.24 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1559 2585 0.614979 CCTCGTCCTCCTTCTTCCCA 60.615 60.000 0.00 0.00 0.00 4.37 R
1899 2926 1.591703 CAGAACTCTGCGCACCCTA 59.408 57.895 5.66 0.00 37.15 3.53 R
3555 4594 0.249447 TGTCAGTGTCCAGAAGCACG 60.249 55.000 0.00 0.00 40.26 5.34 R
3774 4813 7.066307 TGTCATCAAGCATGTATACATAGGT 57.934 36.000 17.86 14.18 34.26 3.08 R
5438 6590 0.035630 AGAAGAAAGAGCCGCTGCAT 60.036 50.000 0.00 0.00 41.13 3.96 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
88 90 9.507329 AAGCTGATTGAAAATCACTAAACTAGA 57.493 29.630 0.00 0.00 0.00 2.43
157 159 1.135489 CGCTAACTCCACTCGCTACAA 60.135 52.381 0.00 0.00 0.00 2.41
175 185 2.108250 ACAACCCTAGTGCCAATGAACT 59.892 45.455 0.00 0.00 0.00 3.01
189 199 0.179067 TGAACTGACCCGGTTGTGAC 60.179 55.000 0.00 0.00 32.62 3.67
215 226 5.404946 CATGTGCATTTTCCCTCAAGTTAG 58.595 41.667 0.00 0.00 0.00 2.34
216 227 3.255642 TGTGCATTTTCCCTCAAGTTAGC 59.744 43.478 0.00 0.00 0.00 3.09
220 231 4.723248 CATTTTCCCTCAAGTTAGCGAAC 58.277 43.478 0.83 0.83 35.64 3.95
226 237 2.096218 CCTCAAGTTAGCGAACACAAGC 60.096 50.000 12.42 0.00 38.10 4.01
227 238 2.543848 CTCAAGTTAGCGAACACAAGCA 59.456 45.455 12.42 0.00 38.10 3.91
331 343 4.574421 TGATATCCGCAACCATTACAAGTG 59.426 41.667 0.00 0.00 0.00 3.16
359 371 6.700352 TGCTTTGGATCCAAAATTTAGGAAG 58.300 36.000 33.74 22.25 44.07 3.46
371 383 8.244113 CCAAAATTTAGGAAGCTACAAAGTAGG 58.756 37.037 6.34 0.00 0.00 3.18
430 444 6.644347 AGTCATCTTCTCCGTAATGTCAAAT 58.356 36.000 0.00 0.00 0.00 2.32
440 454 7.170828 TCTCCGTAATGTCAAATTATCAATCCG 59.829 37.037 0.00 0.00 0.00 4.18
445 459 4.980590 TGTCAAATTATCAATCCGTGCAC 58.019 39.130 6.82 6.82 0.00 4.57
486 500 4.798882 ACTTCAAAACTACCAATGGACCA 58.201 39.130 6.16 0.00 0.00 4.02
490 504 4.586841 TCAAAACTACCAATGGACCAAAGG 59.413 41.667 6.16 12.71 0.00 3.11
502 516 2.678336 GGACCAAAGGAACGATGATGTC 59.322 50.000 0.00 0.00 0.00 3.06
525 539 1.657181 GTTTGCCCGCACGAACTTG 60.657 57.895 0.00 0.00 32.16 3.16
585 604 1.111277 AGGCCTTTGAAAGCACGTTT 58.889 45.000 0.00 0.00 0.00 3.60
628 647 9.899226 GAAAACTTTGAGCTATGAATGTACTTT 57.101 29.630 0.00 0.00 0.00 2.66
690 709 7.208080 ACTACAAGGTCACCATAATATCGAAC 58.792 38.462 0.00 0.00 0.00 3.95
696 715 7.335627 AGGTCACCATAATATCGAACAAAGAA 58.664 34.615 0.00 0.00 0.00 2.52
709 728 5.530915 TCGAACAAAGAATTCAACTCCACAT 59.469 36.000 8.44 0.00 0.00 3.21
897 1922 3.773418 TTTCATCTTACCCGTCCACAA 57.227 42.857 0.00 0.00 0.00 3.33
1001 2026 3.316283 ACCAAAAACACATGCGCAATAG 58.684 40.909 17.11 10.55 0.00 1.73
1014 2039 1.738365 CGCAATAGTCTGCTGTCTGCT 60.738 52.381 3.20 0.00 43.37 4.24
1015 2040 1.932511 GCAATAGTCTGCTGTCTGCTC 59.067 52.381 3.20 0.00 43.37 4.26
1017 2042 3.188492 CAATAGTCTGCTGTCTGCTCTG 58.812 50.000 3.20 0.00 43.37 3.35
1082 2108 2.180159 CTAGTCCCCACCACAACCCG 62.180 65.000 0.00 0.00 0.00 5.28
1551 2577 3.396570 CGGGGCTAGGGTTTCGGT 61.397 66.667 0.00 0.00 0.00 4.69
1559 2585 3.994853 GGGTTTCGGTCGGACGGT 61.995 66.667 14.30 0.00 0.00 4.83
1715 2741 7.147863 CCCATTCATGAAGGTGATTGTTTCATA 60.148 37.037 18.05 0.00 38.98 2.15
1757 2784 8.918202 ACTTTGACAATTTTGTAGTCTGGATA 57.082 30.769 0.00 0.00 42.43 2.59
1855 2882 1.064758 ACTGTCTTTGTGTGCTGGGAA 60.065 47.619 0.00 0.00 0.00 3.97
1886 2913 7.623630 TGTGGATTGATCTGAATAACTGAGAA 58.376 34.615 0.00 0.00 0.00 2.87
1920 2947 1.005630 GGTGCGCAGAGTTCTGTCT 60.006 57.895 12.22 0.00 45.45 3.41
1938 2965 6.283694 TCTGTCTTTCTATGTGGATGTATGC 58.716 40.000 0.00 0.00 0.00 3.14
1963 2992 6.987992 CCAAGCCATTGCAATTGAAATATACT 59.012 34.615 11.46 6.63 41.13 2.12
2227 3261 7.479980 TCAGGTTCTTACAAAATTGAACACAG 58.520 34.615 0.00 0.00 40.12 3.66
2262 3296 5.240623 CAGTTTTTGTTAGTGGCACATCCTA 59.759 40.000 21.41 0.00 44.52 2.94
3373 4410 5.329399 ACCTTGTGGTCCTTTAATATGCAA 58.671 37.500 0.00 0.00 44.78 4.08
3374 4411 5.777732 ACCTTGTGGTCCTTTAATATGCAAA 59.222 36.000 0.00 0.00 44.78 3.68
3555 4594 1.067060 GTGAAGTGGCCAACAAAGACC 59.933 52.381 7.24 0.00 0.00 3.85
3740 4779 1.522258 GCTTTTGCAACAATGTGGACG 59.478 47.619 0.00 0.00 46.58 4.79
3774 4813 3.313791 TGGATATCCCGGTCATCTTTGA 58.686 45.455 19.34 0.00 37.93 2.69
3866 4905 5.061920 AGAAGCGAGTTTCGAAAGATAGT 57.938 39.130 11.66 0.00 43.74 2.12
4048 5087 7.956420 TGGTCCAAATATATACTTTGCTACG 57.044 36.000 0.00 0.00 33.27 3.51
4284 5330 5.699097 TTGGCTAGTGTTTGTTTGTATCC 57.301 39.130 0.00 0.00 0.00 2.59
4296 5342 5.320549 TGTTTGTATCCGTCTTCTCCTAC 57.679 43.478 0.00 0.00 0.00 3.18
4325 5371 1.667724 CCTCTGCTGCATACTTTTCCG 59.332 52.381 1.31 0.00 0.00 4.30
4355 5401 6.970484 ACATCAACTCAGCGTAAAAGAAAAT 58.030 32.000 0.00 0.00 0.00 1.82
4398 5524 6.429385 GCTAGCATCTGATAACTATTTTGGCT 59.571 38.462 10.63 0.00 0.00 4.75
4405 5531 7.044181 TCTGATAACTATTTTGGCTCTCACAG 58.956 38.462 0.00 0.00 0.00 3.66
4448 5574 5.681954 GCTTGCACCATGCTTTTGGATAATA 60.682 40.000 7.74 0.00 45.31 0.98
4629 5755 1.942657 TCAGACTCAAAGCTTGTGCAC 59.057 47.619 10.75 10.75 42.74 4.57
4649 5775 2.686405 ACAAGGTGACGTTTCTTTTCCC 59.314 45.455 0.00 0.00 0.00 3.97
4668 5798 3.136443 TCCCTACCTCTGGTATGCAAATG 59.864 47.826 0.00 0.00 37.56 2.32
4692 5822 6.757897 CAAGGATGCCTATGTGTTTTTAGA 57.242 37.500 0.00 0.00 31.13 2.10
4693 5823 6.555315 CAAGGATGCCTATGTGTTTTTAGAC 58.445 40.000 0.00 0.00 31.13 2.59
4694 5824 5.815581 AGGATGCCTATGTGTTTTTAGACA 58.184 37.500 0.00 0.00 28.47 3.41
4695 5825 5.648092 AGGATGCCTATGTGTTTTTAGACAC 59.352 40.000 1.41 1.41 40.41 3.67
4696 5826 7.302680 AGGATGCCTATGTGTTTTTAGACACC 61.303 42.308 5.78 0.00 39.81 4.16
4707 5837 7.894847 GTGTTTTTAGACACCTGATTGTTTTG 58.105 34.615 0.00 0.00 43.16 2.44
4803 5933 1.005924 TCCCTTTTGGAAGATCTGGCC 59.994 52.381 0.00 0.00 41.40 5.36
4845 5975 2.939103 CCCGTGGAAGAAGTTCATCATC 59.061 50.000 10.09 2.06 33.93 2.92
4846 5976 3.599343 CCGTGGAAGAAGTTCATCATCA 58.401 45.455 10.09 0.00 33.93 3.07
4847 5977 3.372206 CCGTGGAAGAAGTTCATCATCAC 59.628 47.826 10.09 8.43 33.93 3.06
5031 6171 6.208402 TCACAAATCTTGCTGCTTTACCATTA 59.792 34.615 0.00 0.00 0.00 1.90
5050 6190 8.691661 ACCATTACTTGTTGTATGTTTCTCTT 57.308 30.769 0.00 0.00 0.00 2.85
5066 6206 1.082300 CTTGCGTTGCTGTCAGCTG 60.082 57.895 24.76 7.63 42.97 4.24
5067 6207 3.185082 TTGCGTTGCTGTCAGCTGC 62.185 57.895 24.76 23.31 42.97 5.25
5099 6240 0.961019 GGCAGGCTTGTTTCATGTCA 59.039 50.000 0.00 0.00 0.00 3.58
5101 6242 1.610522 GCAGGCTTGTTTCATGTCACT 59.389 47.619 0.00 0.00 0.00 3.41
5124 6265 1.396996 CGTGGATTTCACCTTTAGCCG 59.603 52.381 0.00 0.00 43.23 5.52
5192 6333 4.794329 GCAGCATCACATCGTAGTGTATCT 60.794 45.833 9.20 3.65 40.37 1.98
5203 6344 5.413969 CGTAGTGTATCTTATCACCACGA 57.586 43.478 9.69 0.00 46.32 4.35
5239 6380 3.004862 TCTCATCGTAGTGCGTCTGTAA 58.995 45.455 0.00 0.00 42.13 2.41
5276 6423 2.958355 ACCATTTGACTCTTGTGGGTTG 59.042 45.455 0.00 0.00 34.27 3.77
5277 6424 2.297033 CCATTTGACTCTTGTGGGTTGG 59.703 50.000 0.00 0.00 0.00 3.77
5278 6425 1.398692 TTTGACTCTTGTGGGTTGGC 58.601 50.000 0.00 0.00 0.00 4.52
5279 6426 0.817634 TTGACTCTTGTGGGTTGGCG 60.818 55.000 0.00 0.00 0.00 5.69
5280 6427 1.070786 GACTCTTGTGGGTTGGCGA 59.929 57.895 0.00 0.00 0.00 5.54
5281 6428 0.534203 GACTCTTGTGGGTTGGCGAA 60.534 55.000 0.00 0.00 0.00 4.70
5282 6429 0.110486 ACTCTTGTGGGTTGGCGAAT 59.890 50.000 0.00 0.00 0.00 3.34
5438 6590 1.477923 CCTTCCCTTCCGTGGTCAAAA 60.478 52.381 0.00 0.00 0.00 2.44
5530 6682 1.180456 TGCATTGAACCCACCTGCTG 61.180 55.000 0.00 0.00 34.21 4.41
5557 6709 2.162408 GCAGCTGATTTTTAGGCGTCTT 59.838 45.455 20.43 0.00 0.00 3.01
5566 6718 8.142994 TGATTTTTAGGCGTCTTATCAGATTC 57.857 34.615 0.00 0.00 0.00 2.52
5569 6721 6.465439 TTTAGGCGTCTTATCAGATTCAGA 57.535 37.500 0.00 0.00 0.00 3.27
5575 6727 6.481644 GGCGTCTTATCAGATTCAGAAAAGAT 59.518 38.462 0.00 0.00 0.00 2.40
5576 6728 7.653713 GGCGTCTTATCAGATTCAGAAAAGATA 59.346 37.037 0.00 0.00 0.00 1.98
5577 6729 9.202273 GCGTCTTATCAGATTCAGAAAAGATAT 57.798 33.333 0.00 0.00 0.00 1.63
5610 6765 6.819146 GGAAAGGTAGAATTCTTCTTGACGAT 59.181 38.462 14.36 3.23 41.14 3.73
5613 6768 9.892130 AAAGGTAGAATTCTTCTTGACGATTAT 57.108 29.630 14.36 0.00 41.14 1.28
5619 6774 9.050601 AGAATTCTTCTTGACGATTATGGATTC 57.949 33.333 0.88 0.00 36.36 2.52
5757 6919 3.311596 CAGCTAAATTTACCACTACCGCC 59.688 47.826 0.00 0.00 0.00 6.13
5759 6921 3.311596 GCTAAATTTACCACTACCGCCAG 59.688 47.826 0.00 0.00 0.00 4.85
5761 6923 0.107361 ATTTACCACTACCGCCAGGC 60.107 55.000 0.00 0.00 42.76 4.85
5805 6971 2.028567 GGCACCTGCTACTCTATGATCC 60.029 54.545 0.00 0.00 41.70 3.36
5818 6984 6.979418 ACTCTATGATCCCTAGCTGATGATA 58.021 40.000 0.00 0.00 0.00 2.15
5819 6985 7.062322 ACTCTATGATCCCTAGCTGATGATAG 58.938 42.308 15.00 15.00 37.60 2.08
5821 6987 7.646884 TCTATGATCCCTAGCTGATGATAGAA 58.353 38.462 18.56 9.15 40.28 2.10
5822 6988 6.795144 ATGATCCCTAGCTGATGATAGAAG 57.205 41.667 0.00 0.00 34.34 2.85
5823 6989 4.465660 TGATCCCTAGCTGATGATAGAAGC 59.534 45.833 0.00 0.00 34.34 3.86
5824 6990 3.849527 TCCCTAGCTGATGATAGAAGCA 58.150 45.455 0.00 0.00 39.47 3.91
5825 6991 4.226384 TCCCTAGCTGATGATAGAAGCAA 58.774 43.478 0.00 0.00 39.47 3.91
5826 6992 4.039730 TCCCTAGCTGATGATAGAAGCAAC 59.960 45.833 0.00 0.00 39.47 4.17
5827 6993 4.040217 CCCTAGCTGATGATAGAAGCAACT 59.960 45.833 0.00 0.00 39.47 3.16
5828 6994 5.229423 CCTAGCTGATGATAGAAGCAACTC 58.771 45.833 0.00 0.00 39.47 3.01
5829 6995 4.750021 AGCTGATGATAGAAGCAACTCA 57.250 40.909 0.00 0.00 39.47 3.41
5830 6996 4.695396 AGCTGATGATAGAAGCAACTCAG 58.305 43.478 0.00 0.00 39.47 3.35
5831 6997 3.808726 GCTGATGATAGAAGCAACTCAGG 59.191 47.826 0.00 0.00 36.91 3.86
5832 6998 3.801698 TGATGATAGAAGCAACTCAGGC 58.198 45.455 0.00 0.00 0.00 4.85
5833 6999 3.198417 TGATGATAGAAGCAACTCAGGCA 59.802 43.478 0.00 0.00 0.00 4.75
5834 7000 3.257469 TGATAGAAGCAACTCAGGCAG 57.743 47.619 0.00 0.00 0.00 4.85
5835 7001 2.833943 TGATAGAAGCAACTCAGGCAGA 59.166 45.455 0.00 0.00 0.00 4.26
5846 7012 2.082231 CTCAGGCAGAGTTTCACCATG 58.918 52.381 0.00 0.00 39.62 3.66
5852 7018 2.648059 CAGAGTTTCACCATGGATCCC 58.352 52.381 21.47 1.78 0.00 3.85
5871 7037 7.038048 GGATCCCAATTTTTCATGAAGAGTTC 58.962 38.462 8.41 0.00 0.00 3.01
5897 7110 7.601073 TTCTATTTTCTCTACTCGTACGTGA 57.399 36.000 22.86 12.20 0.00 4.35
5901 7114 4.658713 TTCTCTACTCGTACGTGACAAG 57.341 45.455 22.86 15.64 0.00 3.16
5903 7116 4.502016 TCTCTACTCGTACGTGACAAGAT 58.498 43.478 22.86 3.00 0.00 2.40
5904 7117 4.329256 TCTCTACTCGTACGTGACAAGATG 59.671 45.833 22.86 14.07 0.00 2.90
5905 7118 4.248058 TCTACTCGTACGTGACAAGATGA 58.752 43.478 22.86 9.56 0.00 2.92
5907 7120 2.161808 ACTCGTACGTGACAAGATGAGG 59.838 50.000 22.86 0.00 0.00 3.86
5908 7121 2.418976 CTCGTACGTGACAAGATGAGGA 59.581 50.000 16.05 0.00 0.00 3.71
5909 7122 2.815503 TCGTACGTGACAAGATGAGGAA 59.184 45.455 16.05 0.00 0.00 3.36
5910 7123 3.442625 TCGTACGTGACAAGATGAGGAAT 59.557 43.478 16.05 0.00 0.00 3.01
5911 7124 4.082408 TCGTACGTGACAAGATGAGGAATT 60.082 41.667 16.05 0.00 0.00 2.17
5913 7126 5.803461 CGTACGTGACAAGATGAGGAATTTA 59.197 40.000 7.22 0.00 0.00 1.40
5914 7127 6.237490 CGTACGTGACAAGATGAGGAATTTAC 60.237 42.308 7.22 0.00 0.00 2.01
5915 7128 5.794894 ACGTGACAAGATGAGGAATTTACT 58.205 37.500 0.00 0.00 0.00 2.24
5918 7131 8.041323 ACGTGACAAGATGAGGAATTTACTATT 58.959 33.333 0.00 0.00 0.00 1.73
5919 7132 8.543774 CGTGACAAGATGAGGAATTTACTATTC 58.456 37.037 0.00 0.00 0.00 1.75
5920 7133 9.606631 GTGACAAGATGAGGAATTTACTATTCT 57.393 33.333 0.00 0.00 0.00 2.40
5921 7134 9.605275 TGACAAGATGAGGAATTTACTATTCTG 57.395 33.333 0.00 0.00 0.00 3.02
5922 7135 9.823647 GACAAGATGAGGAATTTACTATTCTGA 57.176 33.333 0.00 0.00 0.00 3.27
5939 7163 4.743057 TCTGATGAATCGAGTTGACCAT 57.257 40.909 0.00 0.00 0.00 3.55
5946 7170 1.146263 CGAGTTGACCATAGCCCCC 59.854 63.158 0.00 0.00 0.00 5.40
6005 7229 0.394352 AAATCAGGTCCATCCGTGGC 60.394 55.000 0.00 0.00 45.63 5.01
6026 7250 1.858458 CGCAACGGATGTACTACCATG 59.142 52.381 8.96 7.91 0.00 3.66
6027 7251 2.737359 CGCAACGGATGTACTACCATGT 60.737 50.000 8.96 0.00 0.00 3.21
6028 7252 3.489568 CGCAACGGATGTACTACCATGTA 60.490 47.826 8.96 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 49 7.950512 TCAATCAGCTTCTTGTATTCCAAAAA 58.049 30.769 5.23 0.00 31.20 1.94
61 63 9.766277 CTAGTTTAGTGATTTTCAATCAGCTTC 57.234 33.333 0.00 0.00 0.00 3.86
117 119 5.790593 AGCGTACAGGTGATTTTCTTTCTA 58.209 37.500 0.00 0.00 0.00 2.10
133 135 0.169672 GCGAGTGGAGTTAGCGTACA 59.830 55.000 0.00 0.00 0.00 2.90
137 139 0.450583 TGTAGCGAGTGGAGTTAGCG 59.549 55.000 0.00 0.00 0.00 4.26
157 159 1.985159 TCAGTTCATTGGCACTAGGGT 59.015 47.619 0.00 0.00 0.00 4.34
175 185 4.612412 GGCGTCACAACCGGGTCA 62.612 66.667 6.32 0.00 0.00 4.02
215 226 2.405892 ATTTGACTGCTTGTGTTCGC 57.594 45.000 0.00 0.00 0.00 4.70
216 227 3.745975 TCCTATTTGACTGCTTGTGTTCG 59.254 43.478 0.00 0.00 0.00 3.95
220 231 6.292542 CGATACATCCTATTTGACTGCTTGTG 60.293 42.308 0.00 0.00 0.00 3.33
226 237 6.791887 ATTGCGATACATCCTATTTGACTG 57.208 37.500 0.00 0.00 0.00 3.51
227 238 8.774586 GTTTATTGCGATACATCCTATTTGACT 58.225 33.333 0.00 0.00 0.00 3.41
301 313 8.855110 TGTAATGGTTGCGGATATCAATAAATT 58.145 29.630 4.83 0.00 0.00 1.82
309 321 4.554723 GCACTTGTAATGGTTGCGGATATC 60.555 45.833 0.00 0.00 0.00 1.63
331 343 5.632244 AAATTTTGGATCCAAAGCATTGC 57.368 34.783 32.77 0.00 45.15 3.56
424 438 4.793216 GTGTGCACGGATTGATAATTTGAC 59.207 41.667 13.13 0.00 0.00 3.18
440 454 4.671880 TGGTAATATTTCGTGTGTGCAC 57.328 40.909 10.75 10.75 41.97 4.57
445 459 7.359262 TGAAGTCTTGGTAATATTTCGTGTG 57.641 36.000 0.00 0.00 0.00 3.82
475 489 1.144093 TCGTTCCTTTGGTCCATTGGT 59.856 47.619 1.86 0.00 0.00 3.67
580 594 3.320826 CCATCTTTTTGGAAGGGAAACGT 59.679 43.478 0.00 0.00 39.25 3.99
628 647 3.157881 CCTAGAGGATCGTTCCATGCTA 58.842 50.000 14.83 11.08 45.30 3.49
690 709 8.733458 TGATTCTATGTGGAGTTGAATTCTTTG 58.267 33.333 7.05 0.00 0.00 2.77
696 715 6.947733 TGGTTTGATTCTATGTGGAGTTGAAT 59.052 34.615 0.00 0.00 0.00 2.57
781 1806 8.456904 TGTTAGTGTATCGTGTTATTTGTCTC 57.543 34.615 0.00 0.00 0.00 3.36
782 1807 8.997621 ATGTTAGTGTATCGTGTTATTTGTCT 57.002 30.769 0.00 0.00 0.00 3.41
828 1853 8.863086 TGTGGTCTAGTAACTTTATGTTAGTGT 58.137 33.333 8.13 0.00 42.77 3.55
829 1854 9.701098 TTGTGGTCTAGTAACTTTATGTTAGTG 57.299 33.333 8.13 1.15 42.77 2.74
832 1857 9.492973 GGTTTGTGGTCTAGTAACTTTATGTTA 57.507 33.333 0.00 0.00 39.89 2.41
833 1858 7.446319 GGGTTTGTGGTCTAGTAACTTTATGTT 59.554 37.037 0.00 0.00 42.31 2.71
834 1859 6.938596 GGGTTTGTGGTCTAGTAACTTTATGT 59.061 38.462 0.00 0.00 0.00 2.29
835 1860 6.938030 TGGGTTTGTGGTCTAGTAACTTTATG 59.062 38.462 0.00 0.00 0.00 1.90
836 1861 7.081857 TGGGTTTGTGGTCTAGTAACTTTAT 57.918 36.000 0.00 0.00 0.00 1.40
837 1862 6.497624 TGGGTTTGTGGTCTAGTAACTTTA 57.502 37.500 0.00 0.00 0.00 1.85
838 1863 5.376756 TGGGTTTGTGGTCTAGTAACTTT 57.623 39.130 0.00 0.00 0.00 2.66
839 1864 5.376756 TTGGGTTTGTGGTCTAGTAACTT 57.623 39.130 0.00 0.00 0.00 2.66
840 1865 5.376756 TTTGGGTTTGTGGTCTAGTAACT 57.623 39.130 0.00 0.00 0.00 2.24
841 1866 6.443792 CAATTTGGGTTTGTGGTCTAGTAAC 58.556 40.000 0.00 0.00 0.00 2.50
897 1922 4.621087 GTTGTGGGCTGGGGGCTT 62.621 66.667 0.00 0.00 41.46 4.35
1229 2255 4.574271 TCGGCGCGGGAGAGGATA 62.574 66.667 15.48 0.00 0.00 2.59
1532 2558 3.078836 CGAAACCCTAGCCCCGGA 61.079 66.667 0.73 0.00 0.00 5.14
1551 2577 2.280552 CCTTCTTCCCACCGTCCGA 61.281 63.158 0.00 0.00 0.00 4.55
1559 2585 0.614979 CCTCGTCCTCCTTCTTCCCA 60.615 60.000 0.00 0.00 0.00 4.37
1715 2741 8.958119 TGTCAAAGTAAATAACAGAGTTCAGT 57.042 30.769 0.00 0.00 0.00 3.41
1757 2784 8.609176 GCAACATAATCAAATGCAAGAATGAAT 58.391 29.630 0.00 0.00 37.00 2.57
1880 2907 7.466050 GCACCCTAAGACGATAAAATTTCTCAG 60.466 40.741 0.00 0.00 0.00 3.35
1881 2908 6.315393 GCACCCTAAGACGATAAAATTTCTCA 59.685 38.462 0.00 0.00 0.00 3.27
1886 2913 3.311596 GCGCACCCTAAGACGATAAAATT 59.688 43.478 0.30 0.00 0.00 1.82
1899 2926 1.591703 CAGAACTCTGCGCACCCTA 59.408 57.895 5.66 0.00 37.15 3.53
1920 2947 4.580167 GCTTGGCATACATCCACATAGAAA 59.420 41.667 0.00 0.00 32.45 2.52
1938 2965 6.987992 AGTATATTTCAATTGCAATGGCTTGG 59.012 34.615 13.82 0.00 41.91 3.61
2051 3081 6.349363 CCAACAAGCTCCCACTTAGTTTTATC 60.349 42.308 0.00 0.00 0.00 1.75
2254 3288 6.828273 TGAATAGAACCAACCAATAGGATGTG 59.172 38.462 0.00 0.00 36.03 3.21
2262 3296 9.874205 CAACATTATTGAATAGAACCAACCAAT 57.126 29.630 0.00 0.00 0.00 3.16
2648 3685 4.574828 TCTTTGATAGGGTTTTATCTGCGC 59.425 41.667 0.00 0.00 32.44 6.09
2744 3781 7.773224 TGTCATTTCTCTCTTCCAAAACTACAA 59.227 33.333 0.00 0.00 0.00 2.41
3529 4568 2.106566 TGTTGGCCACTTCACAACATT 58.893 42.857 3.88 0.00 46.56 2.71
3555 4594 0.249447 TGTCAGTGTCCAGAAGCACG 60.249 55.000 0.00 0.00 40.26 5.34
3774 4813 7.066307 TGTCATCAAGCATGTATACATAGGT 57.934 36.000 17.86 14.18 34.26 3.08
4048 5087 9.722056 CAATGATATGCAAGTTTAGGACTTTAC 57.278 33.333 0.00 0.00 46.34 2.01
4284 5330 1.835494 TCCAGGTGTAGGAGAAGACG 58.165 55.000 0.00 0.00 0.00 4.18
4296 5342 1.673665 GCAGCAGAGGTTCCAGGTG 60.674 63.158 0.00 0.00 0.00 4.00
4325 5371 1.009829 CGCTGAGTTGATGTTAGCCC 58.990 55.000 0.00 0.00 0.00 5.19
4448 5574 5.367937 AGTGGCAACCAGATACTCTCATTAT 59.632 40.000 0.00 0.00 32.34 1.28
4629 5755 2.949644 AGGGAAAAGAAACGTCACCTTG 59.050 45.455 0.00 0.00 0.00 3.61
4636 5762 3.244457 CCAGAGGTAGGGAAAAGAAACGT 60.244 47.826 0.00 0.00 0.00 3.99
4688 5818 4.469657 AGGCAAAACAATCAGGTGTCTAA 58.530 39.130 0.00 0.00 0.00 2.10
4690 5820 2.949447 AGGCAAAACAATCAGGTGTCT 58.051 42.857 0.00 0.00 0.00 3.41
4691 5821 3.181476 ACAAGGCAAAACAATCAGGTGTC 60.181 43.478 0.00 0.00 0.00 3.67
4692 5822 2.765699 ACAAGGCAAAACAATCAGGTGT 59.234 40.909 0.00 0.00 0.00 4.16
4693 5823 3.125316 CACAAGGCAAAACAATCAGGTG 58.875 45.455 0.00 0.00 0.00 4.00
4694 5824 2.483538 GCACAAGGCAAAACAATCAGGT 60.484 45.455 0.00 0.00 43.97 4.00
4695 5825 2.137523 GCACAAGGCAAAACAATCAGG 58.862 47.619 0.00 0.00 43.97 3.86
4725 5855 2.745515 ACCTGAGCCGAGTTTAAGAC 57.254 50.000 0.00 0.00 0.00 3.01
4728 5858 2.300723 TGCTAACCTGAGCCGAGTTTAA 59.699 45.455 0.00 0.00 42.11 1.52
4769 5899 0.041238 AAGGGAGGATGAGGTCGACA 59.959 55.000 18.91 0.00 0.00 4.35
4803 5933 2.093306 TAACTTGACATGGGCGTCTG 57.907 50.000 0.00 0.00 36.82 3.51
4845 5975 1.066858 ACTGTTCCGCCTGATACTGTG 60.067 52.381 0.00 0.00 0.00 3.66
4846 5976 1.267121 ACTGTTCCGCCTGATACTGT 58.733 50.000 0.00 0.00 0.00 3.55
4847 5977 3.187700 GTTACTGTTCCGCCTGATACTG 58.812 50.000 0.00 0.00 0.00 2.74
5031 6171 4.574828 ACGCAAGAGAAACATACAACAAGT 59.425 37.500 0.00 0.00 43.62 3.16
5050 6190 3.653009 GCAGCTGACAGCAACGCA 61.653 61.111 28.43 0.00 45.56 5.24
5076 6216 0.828762 ATGAAACAAGCCTGCCTGCA 60.829 50.000 0.00 0.00 0.00 4.41
5101 6242 3.596214 GCTAAAGGTGAAATCCACGAGA 58.404 45.455 0.00 0.00 46.62 4.04
5124 6265 2.183679 TCTTTTGCTCTCTCTCCTCCC 58.816 52.381 0.00 0.00 0.00 4.30
5192 6333 3.024423 CGCGAGTTCGTGGTGATAA 57.976 52.632 0.00 0.00 45.14 1.75
5239 6380 6.038936 GTCAAATGGTTACAGGTAACAACAGT 59.961 38.462 20.35 9.29 45.32 3.55
5333 6480 2.025969 CACTGACGACCTGCAGCAG 61.026 63.158 16.23 16.23 35.57 4.24
5334 6481 2.029518 CACTGACGACCTGCAGCA 59.970 61.111 8.66 0.00 35.57 4.41
5335 6482 2.024319 GTCACTGACGACCTGCAGC 61.024 63.158 8.66 0.00 35.57 5.25
5336 6483 0.665670 CAGTCACTGACGACCTGCAG 60.666 60.000 6.78 6.78 37.67 4.41
5337 6484 1.363807 CAGTCACTGACGACCTGCA 59.636 57.895 0.00 0.00 37.67 4.41
5338 6485 1.373497 CCAGTCACTGACGACCTGC 60.373 63.158 6.30 0.00 37.67 4.85
5339 6486 0.039074 GACCAGTCACTGACGACCTG 60.039 60.000 6.30 0.00 37.67 4.00
5340 6487 1.516365 CGACCAGTCACTGACGACCT 61.516 60.000 6.30 0.00 37.67 3.85
5341 6488 1.081376 CGACCAGTCACTGACGACC 60.081 63.158 6.30 0.00 37.67 4.79
5342 6489 0.522180 ATCGACCAGTCACTGACGAC 59.478 55.000 22.40 3.54 40.28 4.34
5343 6490 0.521735 CATCGACCAGTCACTGACGA 59.478 55.000 22.27 22.27 41.04 4.20
5344 6491 1.073216 GCATCGACCAGTCACTGACG 61.073 60.000 6.30 11.90 37.67 4.35
5345 6492 0.737715 GGCATCGACCAGTCACTGAC 60.738 60.000 6.30 0.38 32.44 3.51
5346 6493 1.591703 GGCATCGACCAGTCACTGA 59.408 57.895 6.30 0.00 32.44 3.41
5438 6590 0.035630 AGAAGAAAGAGCCGCTGCAT 60.036 50.000 0.00 0.00 41.13 3.96
5566 6718 6.203723 CCTTTCCGAAGCCTATATCTTTTCTG 59.796 42.308 0.00 0.00 0.00 3.02
5569 6721 6.002653 ACCTTTCCGAAGCCTATATCTTTT 57.997 37.500 0.00 0.00 0.00 2.27
5575 6727 6.553852 AGAATTCTACCTTTCCGAAGCCTATA 59.446 38.462 6.06 0.00 0.00 1.31
5576 6728 5.367060 AGAATTCTACCTTTCCGAAGCCTAT 59.633 40.000 6.06 0.00 0.00 2.57
5577 6729 4.715297 AGAATTCTACCTTTCCGAAGCCTA 59.285 41.667 6.06 0.00 0.00 3.93
5610 6765 3.630892 TTTCCGGAACCGAATCCATAA 57.369 42.857 18.64 0.00 42.83 1.90
5613 6768 2.273538 TTTTTCCGGAACCGAATCCA 57.726 45.000 18.64 0.00 42.83 3.41
5761 6923 2.290514 TGGTGAATGAAGCCAGAGAAGG 60.291 50.000 0.00 0.00 0.00 3.46
5805 6971 5.212532 AGTTGCTTCTATCATCAGCTAGG 57.787 43.478 0.00 0.00 34.42 3.02
5818 6984 3.931768 CTCTGCCTGAGTTGCTTCT 57.068 52.632 0.00 0.00 37.99 2.85
5827 6993 1.271543 CCATGGTGAAACTCTGCCTGA 60.272 52.381 2.57 0.00 36.74 3.86
5828 6994 1.171308 CCATGGTGAAACTCTGCCTG 58.829 55.000 2.57 0.00 36.74 4.85
5829 6995 1.067295 TCCATGGTGAAACTCTGCCT 58.933 50.000 12.58 0.00 36.74 4.75
5830 6996 2.019984 GATCCATGGTGAAACTCTGCC 58.980 52.381 12.58 0.00 36.74 4.85
5831 6997 2.019984 GGATCCATGGTGAAACTCTGC 58.980 52.381 12.58 0.00 36.74 4.26
5832 6998 2.025981 TGGGATCCATGGTGAAACTCTG 60.026 50.000 15.23 0.00 36.74 3.35
5833 6999 2.278245 TGGGATCCATGGTGAAACTCT 58.722 47.619 15.23 0.00 36.74 3.24
5834 7000 2.806945 TGGGATCCATGGTGAAACTC 57.193 50.000 15.23 0.80 36.74 3.01
5835 7001 3.763557 ATTGGGATCCATGGTGAAACT 57.236 42.857 15.23 0.00 31.90 2.66
5836 7002 4.824479 AAATTGGGATCCATGGTGAAAC 57.176 40.909 15.23 0.51 31.53 2.78
5837 7003 5.309020 TGAAAAATTGGGATCCATGGTGAAA 59.691 36.000 15.23 1.27 31.53 2.69
5838 7004 4.842948 TGAAAAATTGGGATCCATGGTGAA 59.157 37.500 15.23 0.00 31.53 3.18
5839 7005 4.423913 TGAAAAATTGGGATCCATGGTGA 58.576 39.130 15.23 0.00 31.53 4.02
5840 7006 4.822685 TGAAAAATTGGGATCCATGGTG 57.177 40.909 15.23 0.00 31.53 4.17
5841 7007 5.031495 TCATGAAAAATTGGGATCCATGGT 58.969 37.500 15.23 0.00 31.53 3.55
5842 7008 5.617528 TCATGAAAAATTGGGATCCATGG 57.382 39.130 15.23 4.97 31.53 3.66
5846 7012 6.535963 ACTCTTCATGAAAAATTGGGATCC 57.464 37.500 9.88 1.92 0.00 3.36
5871 7037 8.121086 TCACGTACGAGTAGAGAAAATAGAATG 58.879 37.037 24.41 2.80 0.00 2.67
5875 7041 6.769076 TGTCACGTACGAGTAGAGAAAATAG 58.231 40.000 24.41 0.00 0.00 1.73
5887 7053 2.418976 TCCTCATCTTGTCACGTACGAG 59.581 50.000 24.41 15.18 40.57 4.18
5903 7116 9.481340 CGATTCATCAGAATAGTAAATTCCTCA 57.519 33.333 0.00 0.00 44.30 3.86
5904 7117 9.698309 TCGATTCATCAGAATAGTAAATTCCTC 57.302 33.333 0.00 0.00 44.30 3.71
5905 7118 9.703892 CTCGATTCATCAGAATAGTAAATTCCT 57.296 33.333 0.00 0.00 44.30 3.36
5910 7123 9.302345 GTCAACTCGATTCATCAGAATAGTAAA 57.698 33.333 0.00 0.00 44.30 2.01
5911 7124 7.921214 GGTCAACTCGATTCATCAGAATAGTAA 59.079 37.037 0.00 0.00 44.30 2.24
5913 7126 6.127338 TGGTCAACTCGATTCATCAGAATAGT 60.127 38.462 0.00 0.00 44.30 2.12
5914 7127 6.276091 TGGTCAACTCGATTCATCAGAATAG 58.724 40.000 0.00 0.00 44.30 1.73
5915 7128 6.220726 TGGTCAACTCGATTCATCAGAATA 57.779 37.500 0.00 0.00 44.30 1.75
5918 7131 4.743057 ATGGTCAACTCGATTCATCAGA 57.257 40.909 0.00 0.00 0.00 3.27
5919 7132 4.447054 GCTATGGTCAACTCGATTCATCAG 59.553 45.833 0.00 0.00 0.00 2.90
5920 7133 4.371786 GCTATGGTCAACTCGATTCATCA 58.628 43.478 0.00 0.00 0.00 3.07
5921 7134 3.743396 GGCTATGGTCAACTCGATTCATC 59.257 47.826 0.00 0.00 0.00 2.92
5922 7135 3.495100 GGGCTATGGTCAACTCGATTCAT 60.495 47.826 0.00 0.00 0.00 2.57
5946 7170 6.646653 TGCTGCTATCTAACAGAAATATTCGG 59.353 38.462 0.00 0.00 35.90 4.30
6019 7243 7.861372 GCTGTTGTACATAGTACTACATGGTAG 59.139 40.741 19.34 11.69 34.00 3.18
6026 7250 6.018994 GCCATTGCTGTTGTACATAGTACTAC 60.019 42.308 4.31 12.68 33.53 2.73
6027 7251 6.046593 GCCATTGCTGTTGTACATAGTACTA 58.953 40.000 4.77 4.77 33.53 1.82
6028 7252 4.876107 GCCATTGCTGTTGTACATAGTACT 59.124 41.667 0.00 0.00 33.53 2.73


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

AutoCloner maintained by Alex Coulton.