Multiple sequence alignment - TraesCS2A01G169500

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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 TraesCS2A01G169500 chr2A 100.000 3308 0 0 1 3308 124377631 124380938 0.000000e+00 6109.0
1 TraesCS2A01G169500 chr2A 94.643 56 3 0 1 56 78335768 78335823 1.640000e-13 87.9
2 TraesCS2A01G169500 chr2A 93.220 59 4 0 1 59 235675497 235675439 1.640000e-13 87.9
3 TraesCS2A01G169500 chr2D 95.187 3283 115 21 45 3308 120550375 120553633 0.000000e+00 5147.0
4 TraesCS2A01G169500 chr2B 94.734 3285 109 28 45 3308 173463486 173466727 0.000000e+00 5049.0
5 TraesCS2A01G169500 chr3A 82.440 2221 358 27 698 2896 9606851 9604641 0.000000e+00 1912.0
6 TraesCS2A01G169500 chr3D 83.594 1981 310 13 926 2896 4068298 4066323 0.000000e+00 1844.0
7 TraesCS2A01G169500 chrUn 81.292 2213 392 19 698 2893 242439605 242441812 0.000000e+00 1773.0
8 TraesCS2A01G169500 chrUn 81.292 2213 392 19 698 2893 242452640 242454847 0.000000e+00 1773.0
9 TraesCS2A01G169500 chr3B 81.273 2216 393 19 698 2896 6309733 6307523 0.000000e+00 1773.0
10 TraesCS2A01G169500 chr3B 82.338 2027 345 12 879 2896 6380871 6378849 0.000000e+00 1748.0
11 TraesCS2A01G169500 chr1D 100.000 50 0 0 1 50 367413227 367413178 3.510000e-15 93.5
12 TraesCS2A01G169500 chr5B 98.039 51 1 0 1 51 254944438 254944388 4.550000e-14 89.8
13 TraesCS2A01G169500 chr5B 90.769 65 5 1 1 64 285935694 285935630 5.880000e-13 86.1
14 TraesCS2A01G169500 chr1A 98.039 51 1 0 1 51 83819903 83819953 4.550000e-14 89.8
15 TraesCS2A01G169500 chr5A 93.220 59 4 0 1 59 3813783 3813841 1.640000e-13 87.9
16 TraesCS2A01G169500 chr6A 96.154 52 2 0 1 52 268571383 268571434 5.880000e-13 86.1
17 TraesCS2A01G169500 chr5D 91.228 57 3 2 2 57 180472113 180472168 3.540000e-10 76.8


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 TraesCS2A01G169500 chr2A 124377631 124380938 3307 False 6109 6109 100.000 1 3308 1 chr2A.!!$F2 3307
1 TraesCS2A01G169500 chr2D 120550375 120553633 3258 False 5147 5147 95.187 45 3308 1 chr2D.!!$F1 3263
2 TraesCS2A01G169500 chr2B 173463486 173466727 3241 False 5049 5049 94.734 45 3308 1 chr2B.!!$F1 3263
3 TraesCS2A01G169500 chr3A 9604641 9606851 2210 True 1912 1912 82.440 698 2896 1 chr3A.!!$R1 2198
4 TraesCS2A01G169500 chr3D 4066323 4068298 1975 True 1844 1844 83.594 926 2896 1 chr3D.!!$R1 1970
5 TraesCS2A01G169500 chrUn 242439605 242441812 2207 False 1773 1773 81.292 698 2893 1 chrUn.!!$F1 2195
6 TraesCS2A01G169500 chrUn 242452640 242454847 2207 False 1773 1773 81.292 698 2893 1 chrUn.!!$F2 2195
7 TraesCS2A01G169500 chr3B 6307523 6309733 2210 True 1773 1773 81.273 698 2896 1 chr3B.!!$R1 2198
8 TraesCS2A01G169500 chr3B 6378849 6380871 2022 True 1748 1748 82.338 879 2896 1 chr3B.!!$R2 2017

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
462 472 0.616371 TCAGGTACAATGGTTCCCGG 59.384 55.0 0.0 0.0 35.20 5.73 F
1747 1794 0.865111 TGACGTGCTTGTCGAAATGG 59.135 50.0 0.0 0.0 41.87 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2160 2207 1.234821 TTCCAAGCTGGCGTACTTTG 58.765 50.0 0.0 0.0 37.47 2.77 R
2665 2717 1.243902 TTTCTTCCATCAACCACCGC 58.756 50.0 0.0 0.0 0.00 5.68 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
33 34 8.621286 AGTACAAAGTTGAGTCACTTATTTTGG 58.379 33.333 12.94 0.78 35.87 3.28
34 35 6.805713 ACAAAGTTGAGTCACTTATTTTGGG 58.194 36.000 12.94 0.00 35.87 4.12
35 36 6.605594 ACAAAGTTGAGTCACTTATTTTGGGA 59.394 34.615 12.94 0.00 35.87 4.37
36 37 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
37 38 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
38 39 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
39 40 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
40 41 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
41 42 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
42 43 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
43 44 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
64 65 4.096682 GGAGTAGTAGTGAGTACTGGCAAG 59.903 50.000 10.13 0.00 42.37 4.01
122 126 5.354234 CCATCCGACTGCATATAATTTACCC 59.646 44.000 0.00 0.00 0.00 3.69
126 130 5.995282 CCGACTGCATATAATTTACCCTTGA 59.005 40.000 0.00 0.00 0.00 3.02
146 150 7.041644 CCCTTGATGCCTAAATTGCAATATTTG 60.042 37.037 13.39 9.85 42.92 2.32
159 163 3.736126 GCAATATTTGTGCTCCCAGCTTC 60.736 47.826 0.00 0.00 42.97 3.86
187 192 5.719085 TGGCCCAAGTTGTAATGTCATATTT 59.281 36.000 0.00 0.00 0.00 1.40
218 223 5.615289 AGCAATGGTGGATATACTCTGAAC 58.385 41.667 0.00 0.00 0.00 3.18
226 231 2.154567 TATACTCTGAACCGTGCCCT 57.845 50.000 0.00 0.00 0.00 5.19
332 341 6.590292 TGTAGCTGCTCTCTAACAATAAACAC 59.410 38.462 4.91 0.00 0.00 3.32
344 353 6.918892 AACAATAAACACGCTATATCTGCA 57.081 33.333 0.00 0.00 0.00 4.41
373 382 4.803452 TCCCTTCATGTTTGAGTCCTTTT 58.197 39.130 0.00 0.00 32.27 2.27
462 472 0.616371 TCAGGTACAATGGTTCCCGG 59.384 55.000 0.00 0.00 35.20 5.73
694 710 2.758423 TCTTCGGCTTATGCTGTCAGTA 59.242 45.455 9.10 0.00 45.38 2.74
876 903 3.727970 GCAGCGAGTATAAAAACCAGTGC 60.728 47.826 0.00 0.00 0.00 4.40
933 960 3.260297 TGGAGCAAGGCCAGGAAA 58.740 55.556 5.01 0.00 0.00 3.13
1132 1159 3.081804 GTCAGTAATTTGGGTGGGTCAG 58.918 50.000 0.00 0.00 0.00 3.51
1317 1344 2.548057 TGCGAGGAGTTTGTTTGATGAC 59.452 45.455 0.00 0.00 0.00 3.06
1393 1420 4.932200 GTGCTTATACACATGGAGATAGGC 59.068 45.833 0.00 4.15 40.40 3.93
1605 1632 4.639078 TCATGGTTTCTGTCATGAGGAA 57.361 40.909 0.00 0.97 43.09 3.36
1747 1794 0.865111 TGACGTGCTTGTCGAAATGG 59.135 50.000 0.00 0.00 41.87 3.16
1748 1795 0.865769 GACGTGCTTGTCGAAATGGT 59.134 50.000 0.00 0.00 0.00 3.55
1749 1796 2.063266 GACGTGCTTGTCGAAATGGTA 58.937 47.619 0.00 0.00 0.00 3.25
1750 1797 2.477375 GACGTGCTTGTCGAAATGGTAA 59.523 45.455 0.00 0.00 0.00 2.85
1751 1798 2.478894 ACGTGCTTGTCGAAATGGTAAG 59.521 45.455 0.00 0.00 0.00 2.34
1752 1799 2.734606 CGTGCTTGTCGAAATGGTAAGA 59.265 45.455 0.00 0.00 0.00 2.10
1753 1800 3.185594 CGTGCTTGTCGAAATGGTAAGAA 59.814 43.478 0.00 0.00 0.00 2.52
1754 1801 4.319190 CGTGCTTGTCGAAATGGTAAGAAA 60.319 41.667 0.00 0.00 0.00 2.52
1755 1802 5.616866 CGTGCTTGTCGAAATGGTAAGAAAT 60.617 40.000 0.00 0.00 0.00 2.17
1756 1803 5.569059 GTGCTTGTCGAAATGGTAAGAAATG 59.431 40.000 0.00 0.00 0.00 2.32
1935 1982 6.615088 CCAACATTTTGATCTAGAGGTTGTG 58.385 40.000 18.48 10.04 34.24 3.33
1941 1988 9.334947 CATTTTGATCTAGAGGTTGTGTATGAT 57.665 33.333 0.00 0.00 0.00 2.45
1950 1997 6.176183 AGAGGTTGTGTATGATCTTTGGAAG 58.824 40.000 0.00 0.00 0.00 3.46
2160 2207 1.418264 GAAGCCCTCCTATTCCTGGAC 59.582 57.143 0.00 0.00 0.00 4.02
2292 2339 2.264005 TAAAAAGAGGCTGCGTTCCA 57.736 45.000 0.00 0.00 0.00 3.53
2300 2347 2.100916 GAGGCTGCGTTCCAGATACTTA 59.899 50.000 0.00 0.00 44.64 2.24
2307 2354 6.036735 GCTGCGTTCCAGATACTTACATTTAA 59.963 38.462 0.00 0.00 44.64 1.52
2339 2391 2.035066 GGCTGTGTGAAAGCACTGAAAT 59.965 45.455 7.16 0.00 45.36 2.17
2344 2396 5.904941 TGTGTGAAAGCACTGAAATTTCAT 58.095 33.333 20.76 5.40 45.36 2.57
2583 2635 7.038048 GCTTTGGAAATTTTTAGAGAGATGGG 58.962 38.462 0.00 0.00 0.00 4.00
2635 2687 7.931578 TGTCTATACTTGTTTAATTGGTGGG 57.068 36.000 0.00 0.00 0.00 4.61
2638 2690 8.799367 GTCTATACTTGTTTAATTGGTGGGTTT 58.201 33.333 0.00 0.00 0.00 3.27
2665 2717 2.711311 CTTGCGATGGATGGTGCG 59.289 61.111 0.00 0.00 0.00 5.34
2702 2754 7.623278 TGGAAGAAATGATAAATAAGGGGCTTT 59.377 33.333 0.00 0.00 0.00 3.51
2871 2923 7.921041 ATGATGGAGATAGTTTTCAGGACTA 57.079 36.000 0.00 0.00 34.38 2.59
2921 2973 9.678260 AAGTTTTCATATTGAGCTCTATGAACT 57.322 29.630 26.26 21.40 41.59 3.01
2922 2974 9.678260 AGTTTTCATATTGAGCTCTATGAACTT 57.322 29.630 26.26 16.86 41.59 2.66
2925 2977 9.453572 TTTCATATTGAGCTCTATGAACTTTGT 57.546 29.630 26.26 3.45 41.59 2.83
2926 2978 8.429493 TCATATTGAGCTCTATGAACTTTGTG 57.571 34.615 19.24 2.63 32.77 3.33
2927 2979 7.496920 TCATATTGAGCTCTATGAACTTTGTGG 59.503 37.037 19.24 0.00 32.77 4.17
2928 2980 4.890158 TGAGCTCTATGAACTTTGTGGA 57.110 40.909 16.19 0.00 0.00 4.02
2929 2981 5.426689 TGAGCTCTATGAACTTTGTGGAT 57.573 39.130 16.19 0.00 0.00 3.41
2930 2982 6.544928 TGAGCTCTATGAACTTTGTGGATA 57.455 37.500 16.19 0.00 0.00 2.59
2960 3012 2.692557 CAACAATTCACTGGTGGTGGAA 59.307 45.455 0.70 0.00 45.38 3.53
2977 3029 2.376518 TGGAAAGGGAGAGCAGTTGAAT 59.623 45.455 0.00 0.00 0.00 2.57
3046 3099 7.489160 TGTACAAGTGATACTAGAATTGCGAT 58.511 34.615 0.00 0.00 0.00 4.58
3048 3101 6.341316 ACAAGTGATACTAGAATTGCGATGT 58.659 36.000 0.00 0.00 0.00 3.06
3049 3102 6.818644 ACAAGTGATACTAGAATTGCGATGTT 59.181 34.615 0.00 0.00 0.00 2.71
3050 3103 7.334421 ACAAGTGATACTAGAATTGCGATGTTT 59.666 33.333 0.00 0.00 0.00 2.83
3082 3135 4.576330 AAGTGGCCTAAAGACATAAGCT 57.424 40.909 3.32 0.00 0.00 3.74
3084 3137 3.519510 AGTGGCCTAAAGACATAAGCTCA 59.480 43.478 3.32 0.00 0.00 4.26
3085 3138 4.164988 AGTGGCCTAAAGACATAAGCTCAT 59.835 41.667 3.32 0.00 0.00 2.90
3086 3139 4.884164 GTGGCCTAAAGACATAAGCTCATT 59.116 41.667 3.32 0.00 0.00 2.57
3087 3140 5.008118 GTGGCCTAAAGACATAAGCTCATTC 59.992 44.000 3.32 0.00 0.00 2.67
3088 3141 5.126067 GGCCTAAAGACATAAGCTCATTCA 58.874 41.667 0.00 0.00 0.00 2.57
3101 3154 3.119291 GCTCATTCAGTCTATCCACGTG 58.881 50.000 9.08 9.08 0.00 4.49
3108 3161 3.192844 TCAGTCTATCCACGTGTTCCTTC 59.807 47.826 15.65 1.05 0.00 3.46
3157 3210 3.549299 AGCATTTTCGTTGAGCTGAAG 57.451 42.857 0.00 0.00 33.67 3.02
3236 3289 3.572255 GGATCAGATCTAGACTGGTGTCC 59.428 52.174 10.36 16.68 43.91 4.02
3258 3311 2.009051 TGTGTCAAGTGAACAGTGCTG 58.991 47.619 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.621286 CCAAAATAAGTGACTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
8 9 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
9 10 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
10 11 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
11 12 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
12 13 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
13 14 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
14 15 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
15 16 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
16 17 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
17 18 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
18 19 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
19 20 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
20 21 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
21 22 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
22 23 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
23 24 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
24 25 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
25 26 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
26 27 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
27 28 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
28 29 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
29 30 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
30 31 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
31 32 0.549950 CTACTACTCCCTCCGTCCCA 59.450 60.000 0.00 0.00 0.00 4.37
32 33 0.550432 ACTACTACTCCCTCCGTCCC 59.450 60.000 0.00 0.00 0.00 4.46
33 34 1.211457 TCACTACTACTCCCTCCGTCC 59.789 57.143 0.00 0.00 0.00 4.79
34 35 2.093021 ACTCACTACTACTCCCTCCGTC 60.093 54.545 0.00 0.00 0.00 4.79
35 36 1.914798 ACTCACTACTACTCCCTCCGT 59.085 52.381 0.00 0.00 0.00 4.69
36 37 2.713863 ACTCACTACTACTCCCTCCG 57.286 55.000 0.00 0.00 0.00 4.63
37 38 4.453751 CAGTACTCACTACTACTCCCTCC 58.546 52.174 0.00 0.00 33.53 4.30
38 39 4.453751 CCAGTACTCACTACTACTCCCTC 58.546 52.174 0.00 0.00 33.53 4.30
39 40 3.371810 GCCAGTACTCACTACTACTCCCT 60.372 52.174 0.00 0.00 33.53 4.20
40 41 2.950975 GCCAGTACTCACTACTACTCCC 59.049 54.545 0.00 0.00 33.53 4.30
41 42 3.618351 TGCCAGTACTCACTACTACTCC 58.382 50.000 0.00 0.00 33.53 3.85
42 43 4.096682 CCTTGCCAGTACTCACTACTACTC 59.903 50.000 0.00 0.00 33.53 2.59
43 44 4.017808 CCTTGCCAGTACTCACTACTACT 58.982 47.826 0.00 0.00 33.53 2.57
64 65 7.826744 CCTAGGCATCTTATAGGAAAAATCTCC 59.173 40.741 0.00 0.00 38.73 3.71
122 126 8.332464 CACAAATATTGCAATTTAGGCATCAAG 58.668 33.333 18.75 0.72 41.58 3.02
126 130 6.350906 AGCACAAATATTGCAATTTAGGCAT 58.649 32.000 18.75 0.25 42.83 4.40
146 150 2.777969 CAGATGAAGCTGGGAGCAC 58.222 57.895 0.00 0.00 45.56 4.40
159 163 3.091545 ACATTACAACTTGGGCCAGATG 58.908 45.455 6.23 9.97 0.00 2.90
187 192 0.770499 TCCACCATTGCTCCTGACAA 59.230 50.000 0.00 0.00 0.00 3.18
218 223 1.526575 ATGTTTTCAGCAGGGCACGG 61.527 55.000 0.00 0.00 0.00 4.94
226 231 5.826601 TTTGTACACAGATGTTTTCAGCA 57.173 34.783 0.00 0.00 40.48 4.41
352 361 5.535753 AAAAAGGACTCAAACATGAAGGG 57.464 39.130 0.00 0.00 0.00 3.95
378 387 3.324846 ACAGTGGAAATCTGTCTGTAGCA 59.675 43.478 0.00 0.00 41.52 3.49
462 472 5.846203 ACATATGGTGCAGGATTAAATTGC 58.154 37.500 7.80 3.14 38.30 3.56
560 576 8.729805 AGTTACATGAAAATTTCCTGCAAAAA 57.270 26.923 10.23 0.00 0.00 1.94
615 631 6.033966 AGCAAACTTCCTTGAAAAGTTAACG 58.966 36.000 0.00 0.00 44.13 3.18
694 710 2.069165 GCCGCCAATCCCCTCCTTAT 62.069 60.000 0.00 0.00 0.00 1.73
876 903 1.912043 AGTGTGATCAAGGGAGGAAGG 59.088 52.381 0.00 0.00 0.00 3.46
933 960 3.650942 TCACACACTCCCTGAAGGTAATT 59.349 43.478 0.00 0.00 36.75 1.40
1132 1159 6.727824 AGCATGAACTTGTAGTAATGTCAC 57.272 37.500 0.00 0.00 29.80 3.67
1317 1344 5.210845 GGTGACGGACCAGAAGTATTCATG 61.211 50.000 1.14 0.00 44.44 3.07
1605 1632 1.425066 TCCATGGCTTTCTGAACCTGT 59.575 47.619 6.96 0.00 0.00 4.00
1747 1794 5.685728 AGTAGGAGCAATCCCATTTCTTAC 58.314 41.667 0.00 0.00 0.00 2.34
1748 1795 5.667626 AGAGTAGGAGCAATCCCATTTCTTA 59.332 40.000 0.00 0.00 0.00 2.10
1749 1796 4.476479 AGAGTAGGAGCAATCCCATTTCTT 59.524 41.667 0.00 0.00 0.00 2.52
1750 1797 4.043596 AGAGTAGGAGCAATCCCATTTCT 58.956 43.478 0.00 0.00 0.00 2.52
1751 1798 4.133078 CAGAGTAGGAGCAATCCCATTTC 58.867 47.826 0.00 0.00 0.00 2.17
1752 1799 3.117738 CCAGAGTAGGAGCAATCCCATTT 60.118 47.826 0.00 0.00 0.00 2.32
1753 1800 2.441001 CCAGAGTAGGAGCAATCCCATT 59.559 50.000 0.00 0.00 0.00 3.16
1754 1801 2.053244 CCAGAGTAGGAGCAATCCCAT 58.947 52.381 0.00 0.00 0.00 4.00
1755 1802 1.273838 ACCAGAGTAGGAGCAATCCCA 60.274 52.381 0.00 0.00 0.00 4.37
1756 1803 1.414550 GACCAGAGTAGGAGCAATCCC 59.585 57.143 0.00 0.00 0.00 3.85
1920 1967 7.904558 AAGATCATACACAACCTCTAGATCA 57.095 36.000 0.00 0.00 34.58 2.92
1935 1982 7.121168 TGAACCATGTTCTTCCAAAGATCATAC 59.879 37.037 11.11 0.00 42.89 2.39
1941 1988 5.384336 TGATGAACCATGTTCTTCCAAAGA 58.616 37.500 15.83 0.00 35.26 2.52
2160 2207 1.234821 TTCCAAGCTGGCGTACTTTG 58.765 50.000 0.00 0.00 37.47 2.77
2300 2347 9.970395 CACACAGCCATCAATAATATTAAATGT 57.030 29.630 0.00 0.00 0.00 2.71
2307 2354 6.321945 TGCTTTCACACAGCCATCAATAATAT 59.678 34.615 0.00 0.00 36.33 1.28
2339 2391 6.040729 TGAAACAATCTGAAAGCCTCATGAAA 59.959 34.615 0.00 0.00 32.14 2.69
2344 2396 7.523293 TTTATGAAACAATCTGAAAGCCTCA 57.477 32.000 0.00 0.00 0.00 3.86
2583 2635 2.025321 TCTGCTGATAAACCCCCTTTCC 60.025 50.000 0.00 0.00 0.00 3.13
2635 2687 4.153475 TCCATCGCAAGCACTTTACTAAAC 59.847 41.667 0.00 0.00 37.18 2.01
2638 2690 3.603158 TCCATCGCAAGCACTTTACTA 57.397 42.857 0.00 0.00 37.18 1.82
2665 2717 1.243902 TTTCTTCCATCAACCACCGC 58.756 50.000 0.00 0.00 0.00 5.68
2667 2719 6.773976 TTATCATTTCTTCCATCAACCACC 57.226 37.500 0.00 0.00 0.00 4.61
2745 2797 5.695851 TTTCTTCTCATCTCCAGTTTTGC 57.304 39.130 0.00 0.00 0.00 3.68
2871 2923 9.265862 CTTATGATATATCCTTCTCTTCCTGGT 57.734 37.037 10.25 0.00 0.00 4.00
2918 2970 8.514330 TGTTGAAAGTAGTTATCCACAAAGTT 57.486 30.769 0.00 0.00 0.00 2.66
2919 2971 8.514330 TTGTTGAAAGTAGTTATCCACAAAGT 57.486 30.769 8.40 0.00 29.16 2.66
2920 2972 9.965824 AATTGTTGAAAGTAGTTATCCACAAAG 57.034 29.630 12.05 0.00 33.96 2.77
2921 2973 9.959749 GAATTGTTGAAAGTAGTTATCCACAAA 57.040 29.630 12.05 0.24 33.96 2.83
2922 2974 9.126151 TGAATTGTTGAAAGTAGTTATCCACAA 57.874 29.630 11.15 11.15 34.51 3.33
2923 2975 8.564574 GTGAATTGTTGAAAGTAGTTATCCACA 58.435 33.333 0.00 0.00 0.00 4.17
2924 2976 8.784043 AGTGAATTGTTGAAAGTAGTTATCCAC 58.216 33.333 0.00 0.00 0.00 4.02
2925 2977 8.783093 CAGTGAATTGTTGAAAGTAGTTATCCA 58.217 33.333 0.00 0.00 0.00 3.41
2926 2978 8.237267 CCAGTGAATTGTTGAAAGTAGTTATCC 58.763 37.037 0.00 0.00 0.00 2.59
2927 2979 8.784043 ACCAGTGAATTGTTGAAAGTAGTTATC 58.216 33.333 0.00 0.00 0.00 1.75
2928 2980 8.567948 CACCAGTGAATTGTTGAAAGTAGTTAT 58.432 33.333 0.00 0.00 0.00 1.89
2929 2981 7.012894 CCACCAGTGAATTGTTGAAAGTAGTTA 59.987 37.037 0.00 0.00 0.00 2.24
2930 2982 6.183360 CCACCAGTGAATTGTTGAAAGTAGTT 60.183 38.462 0.00 0.00 0.00 2.24
2960 3012 4.917906 AGTTATTCAACTGCTCTCCCTT 57.082 40.909 0.00 0.00 43.50 3.95
2977 3029 4.466370 AGCTGCTCACTGTATACCAAGTTA 59.534 41.667 0.00 0.00 0.00 2.24
3009 3061 3.057019 CACTTGTACAAGCTCGCTACAA 58.943 45.455 30.97 9.35 41.99 2.41
3046 3099 4.404073 AGGCCACTTTGATACACAAAAACA 59.596 37.500 5.01 0.00 45.97 2.83
3048 3101 6.716934 TTAGGCCACTTTGATACACAAAAA 57.283 33.333 5.01 0.00 45.97 1.94
3049 3102 6.547880 TCTTTAGGCCACTTTGATACACAAAA 59.452 34.615 5.01 0.00 45.97 2.44
3050 3103 6.016610 GTCTTTAGGCCACTTTGATACACAAA 60.017 38.462 5.01 0.00 44.79 2.83
3082 3135 4.381612 GGAACACGTGGATAGACTGAATGA 60.382 45.833 21.57 0.00 0.00 2.57
3084 3137 3.769844 AGGAACACGTGGATAGACTGAAT 59.230 43.478 21.57 0.00 0.00 2.57
3085 3138 3.162666 AGGAACACGTGGATAGACTGAA 58.837 45.455 21.57 0.00 0.00 3.02
3086 3139 2.803956 AGGAACACGTGGATAGACTGA 58.196 47.619 21.57 0.00 0.00 3.41
3087 3140 3.056821 TGAAGGAACACGTGGATAGACTG 60.057 47.826 21.57 0.00 0.00 3.51
3088 3141 3.162666 TGAAGGAACACGTGGATAGACT 58.837 45.455 21.57 6.09 0.00 3.24
3146 3199 1.724429 CTCTCTGCCTTCAGCTCAAC 58.276 55.000 0.00 0.00 44.23 3.18
3236 3289 1.267532 GCACTGTTCACTTGACACACG 60.268 52.381 0.00 0.00 0.00 4.49
3258 3311 1.872313 GAGATTGCCTAGATGCTGCAC 59.128 52.381 3.57 0.00 34.16 4.57
3259 3312 1.487558 TGAGATTGCCTAGATGCTGCA 59.512 47.619 4.13 4.13 0.00 4.41


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

AutoCloner maintained by Alex Coulton.