Multiple sequence alignment - TraesCS7D01G500500

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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 TraesCS7D01G500500 chr7D 100.000 2468 0 0 1 2468 606683879 606686346 0.000000e+00 4558
1 TraesCS7D01G500500 chr7D 86.042 1655 161 26 244 1886 606657335 606658931 0.000000e+00 1712
2 TraesCS7D01G500500 chr7A 96.012 1605 50 6 451 2054 698744470 698746061 0.000000e+00 2597
3 TraesCS7D01G500500 chr7A 95.825 1557 53 6 920 2468 698822542 698824094 0.000000e+00 2505
4 TraesCS7D01G500500 chr7A 95.443 1558 58 6 920 2468 698954845 698956398 0.000000e+00 2471
5 TraesCS7D01G500500 chr7A 87.328 1381 125 19 244 1603 698729345 698730696 0.000000e+00 1535
6 TraesCS7D01G500500 chr7A 96.977 397 12 0 2054 2450 698747110 698747506 0.000000e+00 667
7 TraesCS7D01G500500 chr7A 93.983 349 19 2 107 455 698738908 698739254 6.050000e-146 527
8 TraesCS7D01G500500 chr7A 88.055 293 23 4 1598 1883 698731062 698731349 1.090000e-88 337
9 TraesCS7D01G500500 chr7A 80.726 441 71 7 183 616 699024988 699025421 5.090000e-87 331
10 TraesCS7D01G500500 chr7A 86.096 187 19 3 2021 2201 698731625 698731810 6.960000e-46 195
11 TraesCS7D01G500500 chr7A 84.574 188 24 4 2273 2460 698731835 698732017 5.420000e-42 182
12 TraesCS7D01G500500 chr7B 87.382 1585 135 28 296 1870 690904412 690905941 0.000000e+00 1759
13 TraesCS7D01G500500 chr7B 81.111 450 57 8 2021 2460 690906246 690906677 3.930000e-88 335
14 TraesCS7D01G500500 chr7B 81.840 413 58 14 203 605 690934424 690934829 5.090000e-87 331
15 TraesCS7D01G500500 chr7B 79.861 432 50 13 2033 2458 690936775 690937175 5.200000e-72 281
16 TraesCS7D01G500500 chr7B 87.879 198 21 3 1689 1883 690936274 690936471 1.910000e-56 230
17 TraesCS7D01G500500 chr7B 85.821 134 16 3 750 881 690935215 690935347 3.310000e-29 139
18 TraesCS7D01G500500 chr3A 81.232 682 116 8 905 1583 563395071 563395743 7.760000e-150 540
19 TraesCS7D01G500500 chrUn 80.922 477 75 9 183 647 92703143 92702671 1.800000e-96 363
20 TraesCS7D01G500500 chr6A 76.768 297 63 3 930 1225 616989705 616989414 7.060000e-36 161
21 TraesCS7D01G500500 chr2A 73.282 393 90 12 967 1353 753433698 753433315 1.990000e-26 130


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 TraesCS7D01G500500 chr7D 606683879 606686346 2467 False 4558.00 4558 100.00000 1 2468 1 chr7D.!!$F2 2467
1 TraesCS7D01G500500 chr7D 606657335 606658931 1596 False 1712.00 1712 86.04200 244 1886 1 chr7D.!!$F1 1642
2 TraesCS7D01G500500 chr7A 698822542 698824094 1552 False 2505.00 2505 95.82500 920 2468 1 chr7A.!!$F2 1548
3 TraesCS7D01G500500 chr7A 698954845 698956398 1553 False 2471.00 2471 95.44300 920 2468 1 chr7A.!!$F3 1548
4 TraesCS7D01G500500 chr7A 698744470 698747506 3036 False 1632.00 2597 96.49450 451 2450 2 chr7A.!!$F6 1999
5 TraesCS7D01G500500 chr7A 698729345 698732017 2672 False 562.25 1535 86.51325 244 2460 4 chr7A.!!$F5 2216
6 TraesCS7D01G500500 chr7B 690904412 690906677 2265 False 1047.00 1759 84.24650 296 2460 2 chr7B.!!$F1 2164
7 TraesCS7D01G500500 chr7B 690934424 690937175 2751 False 245.25 331 83.85025 203 2458 4 chr7B.!!$F2 2255
8 TraesCS7D01G500500 chr3A 563395071 563395743 672 False 540.00 540 81.23200 905 1583 1 chr3A.!!$F1 678

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
167 168 0.179018 ATGGAATAGCTGGGCCGAAC 60.179 55.0 0.0 0.0 0.0 3.95 F
175 176 0.316841 GCTGGGCCGAACAATTTCAA 59.683 50.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1018 1321 2.047939 ACCGTAAAACTCCGCCCG 60.048 61.111 0.0 0.0 0.0 6.13 R
1732 2685 5.067413 GTGGTCATGGAAGATAGTTACTCGA 59.933 44.000 0.0 0.0 0.0 4.04 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
17 18 4.519610 AAGGGCGCCTGTTTGATT 57.480 50.000 28.56 7.13 32.13 2.57
18 19 2.267045 AAGGGCGCCTGTTTGATTC 58.733 52.632 28.56 5.83 32.13 2.52
19 20 1.250840 AAGGGCGCCTGTTTGATTCC 61.251 55.000 28.56 4.97 32.13 3.01
20 21 1.678970 GGGCGCCTGTTTGATTCCT 60.679 57.895 28.56 0.00 0.00 3.36
21 22 1.508088 GGCGCCTGTTTGATTCCTG 59.492 57.895 22.15 0.00 0.00 3.86
22 23 1.153958 GCGCCTGTTTGATTCCTGC 60.154 57.895 0.00 0.00 0.00 4.85
23 24 1.865788 GCGCCTGTTTGATTCCTGCA 61.866 55.000 0.00 0.00 0.00 4.41
24 25 0.813184 CGCCTGTTTGATTCCTGCAT 59.187 50.000 0.00 0.00 0.00 3.96
25 26 1.468565 CGCCTGTTTGATTCCTGCATG 60.469 52.381 0.00 0.00 0.00 4.06
26 27 1.738030 GCCTGTTTGATTCCTGCATGC 60.738 52.381 11.82 11.82 0.00 4.06
27 28 1.822990 CCTGTTTGATTCCTGCATGCT 59.177 47.619 20.33 0.00 0.00 3.79
28 29 2.416836 CCTGTTTGATTCCTGCATGCTG 60.417 50.000 20.33 18.55 0.00 4.41
29 30 1.067425 TGTTTGATTCCTGCATGCTGC 60.067 47.619 20.33 6.13 45.29 5.25
43 44 3.782244 CTGCAGCGCGACCACTTC 61.782 66.667 12.10 0.00 0.00 3.01
44 45 4.299547 TGCAGCGCGACCACTTCT 62.300 61.111 12.10 0.00 0.00 2.85
45 46 3.044305 GCAGCGCGACCACTTCTT 61.044 61.111 12.10 0.00 0.00 2.52
46 47 2.607892 GCAGCGCGACCACTTCTTT 61.608 57.895 12.10 0.00 0.00 2.52
47 48 1.941812 CAGCGCGACCACTTCTTTT 59.058 52.632 12.10 0.00 0.00 2.27
48 49 0.307760 CAGCGCGACCACTTCTTTTT 59.692 50.000 12.10 0.00 0.00 1.94
75 76 9.747293 TTAAATTTTTCGAATTTTTAGGACGGT 57.253 25.926 0.00 0.00 32.64 4.83
77 78 9.917129 AAATTTTTCGAATTTTTAGGACGGTAT 57.083 25.926 0.00 0.00 0.00 2.73
78 79 9.917129 AATTTTTCGAATTTTTAGGACGGTATT 57.083 25.926 0.00 0.00 0.00 1.89
79 80 8.953507 TTTTTCGAATTTTTAGGACGGTATTC 57.046 30.769 0.00 0.00 0.00 1.75
80 81 7.670009 TTTCGAATTTTTAGGACGGTATTCA 57.330 32.000 0.00 0.00 0.00 2.57
81 82 7.670009 TTCGAATTTTTAGGACGGTATTCAA 57.330 32.000 0.00 0.00 0.00 2.69
82 83 7.852971 TCGAATTTTTAGGACGGTATTCAAT 57.147 32.000 0.00 0.00 0.00 2.57
83 84 8.271312 TCGAATTTTTAGGACGGTATTCAATT 57.729 30.769 0.00 0.00 0.00 2.32
84 85 8.732531 TCGAATTTTTAGGACGGTATTCAATTT 58.267 29.630 0.00 0.00 0.00 1.82
85 86 9.349145 CGAATTTTTAGGACGGTATTCAATTTT 57.651 29.630 0.00 0.00 0.00 1.82
106 107 6.993786 TTTTTCAGGGTTCACCAAAATTTC 57.006 33.333 0.00 0.00 43.89 2.17
107 108 4.314740 TTCAGGGTTCACCAAAATTTCG 57.685 40.909 0.00 0.00 43.89 3.46
108 109 3.292460 TCAGGGTTCACCAAAATTTCGT 58.708 40.909 0.00 0.00 43.89 3.85
109 110 3.316868 TCAGGGTTCACCAAAATTTCGTC 59.683 43.478 0.00 0.00 43.89 4.20
110 111 3.317993 CAGGGTTCACCAAAATTTCGTCT 59.682 43.478 0.00 0.00 43.89 4.18
111 112 3.958147 AGGGTTCACCAAAATTTCGTCTT 59.042 39.130 0.00 0.00 43.89 3.01
112 113 4.048504 GGGTTCACCAAAATTTCGTCTTG 58.951 43.478 0.00 0.00 39.85 3.02
113 114 4.048504 GGTTCACCAAAATTTCGTCTTGG 58.951 43.478 4.60 4.60 44.35 3.61
118 119 4.568152 CCAAAATTTCGTCTTGGTCAGT 57.432 40.909 0.00 0.00 35.80 3.41
119 120 4.932146 CCAAAATTTCGTCTTGGTCAGTT 58.068 39.130 0.00 0.00 35.80 3.16
120 121 5.348164 CCAAAATTTCGTCTTGGTCAGTTT 58.652 37.500 0.00 0.00 35.80 2.66
121 122 5.810074 CCAAAATTTCGTCTTGGTCAGTTTT 59.190 36.000 0.00 0.00 35.80 2.43
122 123 6.312672 CCAAAATTTCGTCTTGGTCAGTTTTT 59.687 34.615 0.00 0.00 35.80 1.94
144 145 6.524101 TTTGGTAAGCTGTAATTGGAATCC 57.476 37.500 0.00 0.00 0.00 3.01
145 146 4.196193 TGGTAAGCTGTAATTGGAATCCG 58.804 43.478 0.00 0.00 0.00 4.18
146 147 4.196971 GGTAAGCTGTAATTGGAATCCGT 58.803 43.478 0.00 0.00 0.00 4.69
147 148 4.272748 GGTAAGCTGTAATTGGAATCCGTC 59.727 45.833 0.00 0.00 0.00 4.79
148 149 3.627395 AGCTGTAATTGGAATCCGTCA 57.373 42.857 0.00 0.00 0.00 4.35
149 150 4.156455 AGCTGTAATTGGAATCCGTCAT 57.844 40.909 0.00 0.00 0.00 3.06
150 151 3.879295 AGCTGTAATTGGAATCCGTCATG 59.121 43.478 0.00 0.00 0.00 3.07
151 152 3.003689 GCTGTAATTGGAATCCGTCATGG 59.996 47.826 0.00 0.00 40.09 3.66
161 162 0.758734 TCCGTCATGGAATAGCTGGG 59.241 55.000 0.00 0.00 46.38 4.45
162 163 0.886490 CCGTCATGGAATAGCTGGGC 60.886 60.000 0.00 0.00 42.00 5.36
163 164 0.886490 CGTCATGGAATAGCTGGGCC 60.886 60.000 0.00 0.00 0.00 5.80
164 165 0.886490 GTCATGGAATAGCTGGGCCG 60.886 60.000 0.00 0.00 0.00 6.13
165 166 1.053835 TCATGGAATAGCTGGGCCGA 61.054 55.000 0.00 0.00 0.00 5.54
166 167 0.179020 CATGGAATAGCTGGGCCGAA 60.179 55.000 0.00 0.00 0.00 4.30
167 168 0.179018 ATGGAATAGCTGGGCCGAAC 60.179 55.000 0.00 0.00 0.00 3.95
168 169 1.223487 GGAATAGCTGGGCCGAACA 59.777 57.895 0.00 0.00 0.00 3.18
169 170 0.393808 GGAATAGCTGGGCCGAACAA 60.394 55.000 0.00 0.00 0.00 2.83
170 171 1.680338 GAATAGCTGGGCCGAACAAT 58.320 50.000 0.00 0.00 0.00 2.71
171 172 2.024414 GAATAGCTGGGCCGAACAATT 58.976 47.619 0.00 0.00 0.00 2.32
172 173 2.143876 ATAGCTGGGCCGAACAATTT 57.856 45.000 0.00 0.00 0.00 1.82
173 174 1.459450 TAGCTGGGCCGAACAATTTC 58.541 50.000 0.00 0.00 0.00 2.17
174 175 0.539438 AGCTGGGCCGAACAATTTCA 60.539 50.000 0.00 0.00 0.00 2.69
175 176 0.316841 GCTGGGCCGAACAATTTCAA 59.683 50.000 0.00 0.00 0.00 2.69
176 177 1.934849 GCTGGGCCGAACAATTTCAAC 60.935 52.381 0.00 0.00 0.00 3.18
177 178 1.339610 CTGGGCCGAACAATTTCAACA 59.660 47.619 0.00 0.00 0.00 3.33
178 179 1.967066 TGGGCCGAACAATTTCAACAT 59.033 42.857 0.00 0.00 0.00 2.71
179 180 3.157881 TGGGCCGAACAATTTCAACATA 58.842 40.909 0.00 0.00 0.00 2.29
180 181 3.766591 TGGGCCGAACAATTTCAACATAT 59.233 39.130 0.00 0.00 0.00 1.78
181 182 4.950475 TGGGCCGAACAATTTCAACATATA 59.050 37.500 0.00 0.00 0.00 0.86
182 183 5.419155 TGGGCCGAACAATTTCAACATATAA 59.581 36.000 0.00 0.00 0.00 0.98
183 184 6.097554 TGGGCCGAACAATTTCAACATATAAT 59.902 34.615 0.00 0.00 0.00 1.28
184 185 6.983890 GGGCCGAACAATTTCAACATATAATT 59.016 34.615 0.00 0.00 0.00 1.40
185 186 7.042791 GGGCCGAACAATTTCAACATATAATTG 60.043 37.037 0.00 0.00 42.24 2.32
186 187 7.336975 GCCGAACAATTTCAACATATAATTGC 58.663 34.615 7.50 0.00 40.95 3.56
187 188 7.009999 GCCGAACAATTTCAACATATAATTGCA 59.990 33.333 7.50 0.00 40.95 4.08
188 189 8.320295 CCGAACAATTTCAACATATAATTGCAC 58.680 33.333 7.50 3.07 40.95 4.57
189 190 8.858186 CGAACAATTTCAACATATAATTGCACA 58.142 29.630 7.50 0.00 40.95 4.57
199 200 9.463003 CAACATATAATTGCACAATTGTTTTCG 57.537 29.630 16.87 0.00 40.83 3.46
200 201 7.674564 ACATATAATTGCACAATTGTTTTCGC 58.325 30.769 16.87 9.98 40.83 4.70
201 202 3.876242 AATTGCACAATTGTTTTCGCC 57.124 38.095 8.77 0.00 39.36 5.54
208 209 3.616379 CACAATTGTTTTCGCCAACTTGT 59.384 39.130 8.77 0.00 30.68 3.16
209 210 4.800993 CACAATTGTTTTCGCCAACTTGTA 59.199 37.500 8.77 0.00 30.11 2.41
210 211 4.801516 ACAATTGTTTTCGCCAACTTGTAC 59.198 37.500 4.92 0.00 29.78 2.90
221 222 3.120304 GCCAACTTGTACTCGATTGTTCC 60.120 47.826 0.00 0.00 0.00 3.62
228 229 1.056660 ACTCGATTGTTCCCACCACT 58.943 50.000 0.00 0.00 0.00 4.00
232 233 1.303317 ATTGTTCCCACCACTCGCC 60.303 57.895 0.00 0.00 0.00 5.54
233 234 3.818121 TTGTTCCCACCACTCGCCG 62.818 63.158 0.00 0.00 0.00 6.46
235 236 4.308458 TTCCCACCACTCGCCGTG 62.308 66.667 0.00 0.00 43.41 4.94
795 1087 9.476202 TTGGAGAGTATATTATTGACGACATTG 57.524 33.333 0.00 0.00 0.00 2.82
893 1196 0.524392 GAGTGCCGTCGTCATCAGAG 60.524 60.000 0.00 0.00 0.00 3.35
894 1197 2.161486 GTGCCGTCGTCATCAGAGC 61.161 63.158 0.00 0.00 0.00 4.09
895 1198 2.343426 TGCCGTCGTCATCAGAGCT 61.343 57.895 0.00 0.00 0.00 4.09
896 1199 1.029947 TGCCGTCGTCATCAGAGCTA 61.030 55.000 0.00 0.00 0.00 3.32
1055 1358 3.433306 TCCAATGAGGGACGAACAAAT 57.567 42.857 0.00 0.00 38.24 2.32
1531 1889 6.258230 TGAAACATTAGCAACCTGAGATTG 57.742 37.500 0.00 0.00 0.00 2.67
1732 2685 4.004982 GCACATTTCATTTCCCAAAGCAT 58.995 39.130 0.00 0.00 0.00 3.79
1733 2686 4.093850 GCACATTTCATTTCCCAAAGCATC 59.906 41.667 0.00 0.00 0.00 3.91
1795 2748 7.138736 TGAGTTAAAACTTCAGCAAATAGCAC 58.861 34.615 0.00 0.00 42.47 4.40
2101 4300 6.090898 TCGAAAATGAAAGCTAGACTAGTTGC 59.909 38.462 11.15 2.53 0.00 4.17
2325 4525 3.814625 TCCACATTTGTGTTGCTCTGTA 58.185 40.909 9.66 0.00 44.21 2.74
2326 4526 4.203226 TCCACATTTGTGTTGCTCTGTAA 58.797 39.130 9.66 0.00 44.21 2.41
2327 4527 4.642437 TCCACATTTGTGTTGCTCTGTAAA 59.358 37.500 9.66 0.00 44.21 2.01
2384 4593 9.258826 CTTCACTCATTGTCAGGATTTCTATAG 57.741 37.037 0.00 0.00 0.00 1.31
2458 4667 5.693814 GACTGAGAGTCATTTCGCATTTTT 58.306 37.500 0.00 0.00 44.45 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.250840 GGAATCAAACAGGCGCCCTT 61.251 55.000 26.15 12.57 0.00 3.95
1 2 1.678970 GGAATCAAACAGGCGCCCT 60.679 57.895 26.15 7.86 0.00 5.19
2 3 1.678970 AGGAATCAAACAGGCGCCC 60.679 57.895 26.15 5.07 0.00 6.13
3 4 1.508088 CAGGAATCAAACAGGCGCC 59.492 57.895 21.89 21.89 0.00 6.53
4 5 1.153958 GCAGGAATCAAACAGGCGC 60.154 57.895 0.00 0.00 0.00 6.53
6 7 1.738030 GCATGCAGGAATCAAACAGGC 60.738 52.381 14.21 0.00 0.00 4.85
8 9 2.876091 CAGCATGCAGGAATCAAACAG 58.124 47.619 21.98 0.00 0.00 3.16
26 27 3.782244 GAAGTGGTCGCGCTGCAG 61.782 66.667 10.11 10.11 0.00 4.41
27 28 3.807631 AAGAAGTGGTCGCGCTGCA 62.808 57.895 5.56 0.00 0.00 4.41
28 29 2.117941 AAAAGAAGTGGTCGCGCTGC 62.118 55.000 5.56 0.00 0.00 5.25
29 30 0.307760 AAAAAGAAGTGGTCGCGCTG 59.692 50.000 5.56 0.00 0.00 5.18
30 31 2.702847 AAAAAGAAGTGGTCGCGCT 58.297 47.368 5.56 0.00 0.00 5.92
49 50 9.747293 ACCGTCCTAAAAATTCGAAAAATTTAA 57.253 25.926 0.00 0.00 30.38 1.52
51 52 9.917129 ATACCGTCCTAAAAATTCGAAAAATTT 57.083 25.926 0.00 6.67 0.00 1.82
52 53 9.917129 AATACCGTCCTAAAAATTCGAAAAATT 57.083 25.926 0.00 0.00 0.00 1.82
53 54 9.563898 GAATACCGTCCTAAAAATTCGAAAAAT 57.436 29.630 0.00 0.00 0.00 1.82
54 55 8.566260 TGAATACCGTCCTAAAAATTCGAAAAA 58.434 29.630 0.00 0.00 0.00 1.94
55 56 8.097078 TGAATACCGTCCTAAAAATTCGAAAA 57.903 30.769 0.00 0.00 0.00 2.29
56 57 7.670009 TGAATACCGTCCTAAAAATTCGAAA 57.330 32.000 0.00 0.00 0.00 3.46
57 58 7.670009 TTGAATACCGTCCTAAAAATTCGAA 57.330 32.000 0.00 0.00 0.00 3.71
58 59 7.852971 ATTGAATACCGTCCTAAAAATTCGA 57.147 32.000 0.00 0.00 0.00 3.71
59 60 8.905103 AAATTGAATACCGTCCTAAAAATTCG 57.095 30.769 0.00 0.00 0.00 3.34
83 84 5.582665 CGAAATTTTGGTGAACCCTGAAAAA 59.417 36.000 0.00 0.00 34.29 1.94
84 85 5.112686 CGAAATTTTGGTGAACCCTGAAAA 58.887 37.500 0.00 0.00 34.29 2.29
85 86 4.160626 ACGAAATTTTGGTGAACCCTGAAA 59.839 37.500 10.22 0.00 34.29 2.69
86 87 3.702045 ACGAAATTTTGGTGAACCCTGAA 59.298 39.130 10.22 0.00 34.29 3.02
87 88 3.292460 ACGAAATTTTGGTGAACCCTGA 58.708 40.909 10.22 0.00 34.29 3.86
88 89 3.317993 AGACGAAATTTTGGTGAACCCTG 59.682 43.478 10.22 0.00 34.29 4.45
89 90 3.562182 AGACGAAATTTTGGTGAACCCT 58.438 40.909 10.22 0.00 34.29 4.34
90 91 4.048504 CAAGACGAAATTTTGGTGAACCC 58.951 43.478 10.22 0.00 34.29 4.11
91 92 4.048504 CCAAGACGAAATTTTGGTGAACC 58.951 43.478 10.22 0.00 37.24 3.62
97 98 4.568152 ACTGACCAAGACGAAATTTTGG 57.432 40.909 10.22 7.27 45.37 3.28
98 99 6.885735 AAAACTGACCAAGACGAAATTTTG 57.114 33.333 3.73 3.73 0.00 2.44
119 120 7.382898 GGATTCCAATTACAGCTTACCAAAAA 58.617 34.615 0.00 0.00 0.00 1.94
120 121 6.349777 CGGATTCCAATTACAGCTTACCAAAA 60.350 38.462 3.09 0.00 0.00 2.44
121 122 5.124776 CGGATTCCAATTACAGCTTACCAAA 59.875 40.000 3.09 0.00 0.00 3.28
122 123 4.638421 CGGATTCCAATTACAGCTTACCAA 59.362 41.667 3.09 0.00 0.00 3.67
123 124 4.196193 CGGATTCCAATTACAGCTTACCA 58.804 43.478 3.09 0.00 0.00 3.25
124 125 4.196971 ACGGATTCCAATTACAGCTTACC 58.803 43.478 3.09 0.00 0.00 2.85
125 126 4.873827 TGACGGATTCCAATTACAGCTTAC 59.126 41.667 3.09 0.00 0.00 2.34
126 127 5.092554 TGACGGATTCCAATTACAGCTTA 57.907 39.130 3.09 0.00 0.00 3.09
127 128 3.950397 TGACGGATTCCAATTACAGCTT 58.050 40.909 3.09 0.00 0.00 3.74
128 129 3.627395 TGACGGATTCCAATTACAGCT 57.373 42.857 3.09 0.00 0.00 4.24
129 130 3.003689 CCATGACGGATTCCAATTACAGC 59.996 47.826 3.09 0.00 36.56 4.40
130 131 4.450976 TCCATGACGGATTCCAATTACAG 58.549 43.478 3.09 0.00 39.64 2.74
131 132 4.495690 TCCATGACGGATTCCAATTACA 57.504 40.909 3.09 0.00 39.64 2.41
132 133 6.348540 GCTATTCCATGACGGATTCCAATTAC 60.349 42.308 3.09 0.00 45.80 1.89
133 134 5.705441 GCTATTCCATGACGGATTCCAATTA 59.295 40.000 3.09 0.00 45.80 1.40
134 135 4.520492 GCTATTCCATGACGGATTCCAATT 59.480 41.667 3.09 0.00 45.80 2.32
135 136 4.074970 GCTATTCCATGACGGATTCCAAT 58.925 43.478 3.09 0.00 45.80 3.16
136 137 3.136443 AGCTATTCCATGACGGATTCCAA 59.864 43.478 3.09 0.00 45.80 3.53
137 138 2.705658 AGCTATTCCATGACGGATTCCA 59.294 45.455 3.09 0.00 45.80 3.53
138 139 3.070018 CAGCTATTCCATGACGGATTCC 58.930 50.000 0.00 0.00 45.80 3.01
139 140 3.070018 CCAGCTATTCCATGACGGATTC 58.930 50.000 0.00 0.00 45.80 2.52
140 141 2.224621 CCCAGCTATTCCATGACGGATT 60.225 50.000 0.00 0.00 45.80 3.01
141 142 1.349026 CCCAGCTATTCCATGACGGAT 59.651 52.381 0.00 0.00 45.80 4.18
142 143 0.758734 CCCAGCTATTCCATGACGGA 59.241 55.000 0.00 0.00 44.40 4.69
143 144 0.886490 GCCCAGCTATTCCATGACGG 60.886 60.000 0.00 0.00 0.00 4.79
144 145 0.886490 GGCCCAGCTATTCCATGACG 60.886 60.000 0.00 0.00 0.00 4.35
145 146 0.886490 CGGCCCAGCTATTCCATGAC 60.886 60.000 0.00 0.00 0.00 3.06
146 147 1.053835 TCGGCCCAGCTATTCCATGA 61.054 55.000 0.00 0.00 0.00 3.07
147 148 0.179020 TTCGGCCCAGCTATTCCATG 60.179 55.000 0.00 0.00 0.00 3.66
148 149 0.179018 GTTCGGCCCAGCTATTCCAT 60.179 55.000 0.00 0.00 0.00 3.41
149 150 1.223487 GTTCGGCCCAGCTATTCCA 59.777 57.895 0.00 0.00 0.00 3.53
150 151 0.393808 TTGTTCGGCCCAGCTATTCC 60.394 55.000 0.00 0.00 0.00 3.01
151 152 1.680338 ATTGTTCGGCCCAGCTATTC 58.320 50.000 0.00 0.00 0.00 1.75
152 153 2.143876 AATTGTTCGGCCCAGCTATT 57.856 45.000 0.00 0.00 0.00 1.73
153 154 2.024414 GAAATTGTTCGGCCCAGCTAT 58.976 47.619 0.00 0.00 0.00 2.97
154 155 1.271652 TGAAATTGTTCGGCCCAGCTA 60.272 47.619 0.00 0.00 36.46 3.32
155 156 0.539438 TGAAATTGTTCGGCCCAGCT 60.539 50.000 0.00 0.00 36.46 4.24
156 157 0.316841 TTGAAATTGTTCGGCCCAGC 59.683 50.000 0.00 0.00 36.46 4.85
157 158 1.339610 TGTTGAAATTGTTCGGCCCAG 59.660 47.619 0.00 0.00 36.46 4.45
158 159 1.403814 TGTTGAAATTGTTCGGCCCA 58.596 45.000 0.00 0.00 36.46 5.36
159 160 2.741759 ATGTTGAAATTGTTCGGCCC 57.258 45.000 0.00 0.00 36.46 5.80
160 161 7.516627 GCAATTATATGTTGAAATTGTTCGGCC 60.517 37.037 0.00 0.00 40.87 6.13
161 162 7.009999 TGCAATTATATGTTGAAATTGTTCGGC 59.990 33.333 8.82 0.00 40.87 5.54
162 163 8.320295 GTGCAATTATATGTTGAAATTGTTCGG 58.680 33.333 8.82 0.00 40.87 4.30
163 164 8.858186 TGTGCAATTATATGTTGAAATTGTTCG 58.142 29.630 8.82 0.00 40.87 3.95
173 174 9.463003 CGAAAACAATTGTGCAATTATATGTTG 57.537 29.630 12.82 1.30 38.84 3.33
174 175 8.167985 GCGAAAACAATTGTGCAATTATATGTT 58.832 29.630 12.82 7.97 38.84 2.71
175 176 7.201513 GGCGAAAACAATTGTGCAATTATATGT 60.202 33.333 12.82 2.71 38.84 2.29
176 177 7.118724 GGCGAAAACAATTGTGCAATTATATG 58.881 34.615 12.82 2.14 38.84 1.78
177 178 6.815641 TGGCGAAAACAATTGTGCAATTATAT 59.184 30.769 12.82 0.00 38.84 0.86
178 179 6.159293 TGGCGAAAACAATTGTGCAATTATA 58.841 32.000 12.82 0.00 38.84 0.98
179 180 4.993584 TGGCGAAAACAATTGTGCAATTAT 59.006 33.333 12.82 0.00 38.84 1.28
180 181 4.371786 TGGCGAAAACAATTGTGCAATTA 58.628 34.783 12.82 0.00 38.84 1.40
181 182 3.201290 TGGCGAAAACAATTGTGCAATT 58.799 36.364 12.82 5.43 41.33 2.32
182 183 2.831333 TGGCGAAAACAATTGTGCAAT 58.169 38.095 12.82 0.00 0.00 3.56
183 184 2.299993 TGGCGAAAACAATTGTGCAA 57.700 40.000 12.82 1.33 0.00 4.08
184 185 1.929836 GTTGGCGAAAACAATTGTGCA 59.070 42.857 12.82 0.00 0.00 4.57
185 186 2.200899 AGTTGGCGAAAACAATTGTGC 58.799 42.857 12.82 10.89 32.21 4.57
186 187 3.616379 ACAAGTTGGCGAAAACAATTGTG 59.384 39.130 12.82 0.08 33.06 3.33
187 188 3.855858 ACAAGTTGGCGAAAACAATTGT 58.144 36.364 4.92 4.92 32.21 2.71
188 189 5.040635 AGTACAAGTTGGCGAAAACAATTG 58.959 37.500 7.96 3.24 32.21 2.32
189 190 5.257082 AGTACAAGTTGGCGAAAACAATT 57.743 34.783 7.96 0.00 32.21 2.32
190 191 4.553938 CGAGTACAAGTTGGCGAAAACAAT 60.554 41.667 7.96 0.00 32.21 2.71
191 192 3.242478 CGAGTACAAGTTGGCGAAAACAA 60.242 43.478 7.96 0.00 32.21 2.83
192 193 2.285756 CGAGTACAAGTTGGCGAAAACA 59.714 45.455 7.96 0.00 32.21 2.83
193 194 2.540931 TCGAGTACAAGTTGGCGAAAAC 59.459 45.455 7.96 0.00 0.00 2.43
194 195 2.823984 TCGAGTACAAGTTGGCGAAAA 58.176 42.857 7.96 0.00 0.00 2.29
195 196 2.512485 TCGAGTACAAGTTGGCGAAA 57.488 45.000 7.96 0.00 0.00 3.46
196 197 2.734606 CAATCGAGTACAAGTTGGCGAA 59.265 45.455 7.96 0.00 0.00 4.70
197 198 2.288579 ACAATCGAGTACAAGTTGGCGA 60.289 45.455 7.96 10.70 0.00 5.54
198 199 2.066262 ACAATCGAGTACAAGTTGGCG 58.934 47.619 7.96 5.68 0.00 5.69
199 200 3.120304 GGAACAATCGAGTACAAGTTGGC 60.120 47.826 7.96 0.00 0.00 4.52
200 201 3.435671 GGGAACAATCGAGTACAAGTTGG 59.564 47.826 7.96 0.00 0.00 3.77
201 202 4.062293 TGGGAACAATCGAGTACAAGTTG 58.938 43.478 0.00 0.00 37.44 3.16
208 209 2.232941 GAGTGGTGGGAACAATCGAGTA 59.767 50.000 0.00 0.00 46.06 2.59
209 210 1.002087 GAGTGGTGGGAACAATCGAGT 59.998 52.381 0.00 0.00 46.06 4.18
210 211 1.726853 GAGTGGTGGGAACAATCGAG 58.273 55.000 0.00 0.00 46.06 4.04
306 323 0.605589 GTGGGGCAGAAACTAAGCGT 60.606 55.000 0.00 0.00 0.00 5.07
731 1023 1.604147 ATTTGGTAAAGCCCCAGCGC 61.604 55.000 0.00 0.00 46.67 5.92
732 1024 0.894835 AATTTGGTAAAGCCCCAGCG 59.105 50.000 0.00 0.00 46.67 5.18
893 1196 8.527810 AGTTACTGAGATTATCCAATAGCTAGC 58.472 37.037 6.62 6.62 0.00 3.42
896 1199 7.659390 GCAAGTTACTGAGATTATCCAATAGCT 59.341 37.037 0.00 0.00 0.00 3.32
1018 1321 2.047939 ACCGTAAAACTCCGCCCG 60.048 61.111 0.00 0.00 0.00 6.13
1531 1889 9.490379 TCTAAGAACTTGAGAAATAGACAAACC 57.510 33.333 0.00 0.00 0.00 3.27
1561 1919 9.947433 TTTACGAAACTTATCCTTCTCCAAATA 57.053 29.630 0.00 0.00 0.00 1.40
1562 1920 8.857694 TTTACGAAACTTATCCTTCTCCAAAT 57.142 30.769 0.00 0.00 0.00 2.32
1732 2685 5.067413 GTGGTCATGGAAGATAGTTACTCGA 59.933 44.000 0.00 0.00 0.00 4.04
1733 2686 5.163550 TGTGGTCATGGAAGATAGTTACTCG 60.164 44.000 0.00 0.00 0.00 4.18
2076 4275 6.090898 GCAACTAGTCTAGCTTTCATTTTCGA 59.909 38.462 6.81 0.00 0.00 3.71
2101 4300 7.190920 ACAGAAAATTTCTCCACTAAGAACG 57.809 36.000 5.09 0.00 38.11 3.95
2325 4525 3.327757 TGCTCTGTCACTAGAACCCATTT 59.672 43.478 0.00 0.00 0.00 2.32
2326 4526 2.906389 TGCTCTGTCACTAGAACCCATT 59.094 45.455 0.00 0.00 0.00 3.16
2327 4527 2.540383 TGCTCTGTCACTAGAACCCAT 58.460 47.619 0.00 0.00 0.00 4.00
2368 4571 7.268586 GTTTGCTCTCTATAGAAATCCTGACA 58.731 38.462 3.57 0.00 0.00 3.58
2384 4593 5.048921 GGTAAAGTAAACCAGGTTTGCTCTC 60.049 44.000 29.64 22.04 44.92 3.20


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

AutoCloner maintained by Alex Coulton.