Multiple sequence alignment - TraesCS4D01G299900

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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 TraesCS4D01G299900 chr4D 100.000 4066 0 0 1 4066 468607021 468602956 0.000000e+00 7509.0
1 TraesCS4D01G299900 chr4D 96.875 128 4 0 77 204 19910504 19910631 8.850000e-52 215.0
2 TraesCS4D01G299900 chr4A 92.794 2734 135 28 650 3363 2938587 2941278 0.000000e+00 3901.0
3 TraesCS4D01G299900 chr4A 91.102 708 49 9 3365 4066 2941308 2942007 0.000000e+00 946.0
4 TraesCS4D01G299900 chr4A 85.989 364 32 10 204 564 2938209 2938556 4.960000e-99 372.0
5 TraesCS4D01G299900 chr4B 94.291 2102 99 9 1979 4066 588205571 588203477 0.000000e+00 3197.0
6 TraesCS4D01G299900 chr4B 87.752 1837 123 47 204 1989 588207573 588205788 0.000000e+00 2052.0
7 TraesCS4D01G299900 chrUn 97.656 128 3 0 77 204 438112027 438111900 1.900000e-53 220.0
8 TraesCS4D01G299900 chrUn 96.875 128 4 0 77 204 298934096 298933969 8.850000e-52 215.0
9 TraesCS4D01G299900 chrUn 97.183 71 2 0 2 72 223706147 223706217 1.980000e-23 121.0
10 TraesCS4D01G299900 chrUn 97.183 71 2 0 2 72 266187295 266187365 1.980000e-23 121.0
11 TraesCS4D01G299900 chr7B 97.656 128 3 0 77 204 662745210 662745083 1.900000e-53 220.0
12 TraesCS4D01G299900 chr7B 100.000 28 0 0 450 477 527710257 527710230 7.000000e-03 52.8
13 TraesCS4D01G299900 chr1D 97.656 128 3 0 77 204 51822144 51822017 1.900000e-53 220.0
14 TraesCS4D01G299900 chr1D 97.638 127 3 0 77 203 254469237 254469363 6.840000e-53 219.0
15 TraesCS4D01G299900 chr1D 97.183 71 2 0 2 72 141343961 141344031 1.980000e-23 121.0
16 TraesCS4D01G299900 chr1D 97.183 71 2 0 2 72 351042479 351042409 1.980000e-23 121.0
17 TraesCS4D01G299900 chr1D 93.023 43 2 1 437 479 366000558 366000599 1.220000e-05 62.1
18 TraesCS4D01G299900 chr3D 97.638 127 3 0 77 203 24156949 24157075 6.840000e-53 219.0
19 TraesCS4D01G299900 chr3D 97.183 71 2 0 2 72 202650517 202650447 1.980000e-23 121.0
20 TraesCS4D01G299900 chr3D 97.183 71 2 0 2 72 498430746 498430816 1.980000e-23 121.0
21 TraesCS4D01G299900 chr7A 96.875 128 4 0 77 204 537843137 537843264 8.850000e-52 215.0
22 TraesCS4D01G299900 chr7A 83.784 74 11 1 404 477 34709045 34708973 7.290000e-08 69.4
23 TraesCS4D01G299900 chr5A 96.875 128 4 0 77 204 414823062 414823189 8.850000e-52 215.0
24 TraesCS4D01G299900 chr6D 97.183 71 2 0 2 72 41256351 41256421 1.980000e-23 121.0
25 TraesCS4D01G299900 chr1A 97.183 71 2 0 2 72 251533033 251533103 1.980000e-23 121.0
26 TraesCS4D01G299900 chr1A 97.183 71 2 0 2 72 278501622 278501552 1.980000e-23 121.0
27 TraesCS4D01G299900 chr1B 94.737 38 2 0 350 387 679288903 679288866 4.390000e-05 60.2
28 TraesCS4D01G299900 chr2D 76.923 117 16 9 433 546 13568521 13568413 5.680000e-04 56.5
29 TraesCS4D01G299900 chr7D 100.000 28 0 0 450 477 499603645 499603618 7.000000e-03 52.8


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 TraesCS4D01G299900 chr4D 468602956 468607021 4065 True 7509.000000 7509 100.000000 1 4066 1 chr4D.!!$R1 4065
1 TraesCS4D01G299900 chr4A 2938209 2942007 3798 False 1739.666667 3901 89.961667 204 4066 3 chr4A.!!$F1 3862
2 TraesCS4D01G299900 chr4B 588203477 588207573 4096 True 2624.500000 3197 91.021500 204 4066 2 chr4B.!!$R1 3862

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
839 857 0.252197 GGTTACTGGTGAGGCCGAAT 59.748 55.0 0.0 0.0 41.21 3.34 F
1903 1969 0.318120 CAACCACATGAAACAGGGGC 59.682 55.0 0.0 0.0 0.00 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 1992 3.569701 AGCAATTGAAGTGGTAGTTGGTG 59.430 43.478 10.34 0.00 0.00 4.17 R
3366 3669 0.179156 TTGCGTCGGACGGATACTTC 60.179 55.000 29.30 12.92 42.59 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
35 36 9.999009 TTCGGTAATATTAGTAGATGCTATTCG 57.001 33.333 0.00 0.00 0.00 3.34
36 37 9.387257 TCGGTAATATTAGTAGATGCTATTCGA 57.613 33.333 0.00 0.00 0.00 3.71
37 38 9.999009 CGGTAATATTAGTAGATGCTATTCGAA 57.001 33.333 0.00 0.00 0.00 3.71
41 42 6.919775 ATTAGTAGATGCTATTCGAACCCT 57.080 37.500 0.00 0.00 0.00 4.34
42 43 6.726490 TTAGTAGATGCTATTCGAACCCTT 57.274 37.500 0.00 0.00 0.00 3.95
43 44 5.203060 AGTAGATGCTATTCGAACCCTTC 57.797 43.478 0.00 0.00 0.00 3.46
44 45 3.477210 AGATGCTATTCGAACCCTTCC 57.523 47.619 0.00 0.00 0.00 3.46
45 46 3.041946 AGATGCTATTCGAACCCTTCCT 58.958 45.455 0.00 0.00 0.00 3.36
46 47 3.456277 AGATGCTATTCGAACCCTTCCTT 59.544 43.478 0.00 0.00 0.00 3.36
47 48 3.713826 TGCTATTCGAACCCTTCCTTT 57.286 42.857 0.00 0.00 0.00 3.11
48 49 4.829872 TGCTATTCGAACCCTTCCTTTA 57.170 40.909 0.00 0.00 0.00 1.85
49 50 5.168647 TGCTATTCGAACCCTTCCTTTAA 57.831 39.130 0.00 0.00 0.00 1.52
50 51 5.751586 TGCTATTCGAACCCTTCCTTTAAT 58.248 37.500 0.00 0.00 0.00 1.40
51 52 6.184789 TGCTATTCGAACCCTTCCTTTAATT 58.815 36.000 0.00 0.00 0.00 1.40
52 53 7.340256 TGCTATTCGAACCCTTCCTTTAATTA 58.660 34.615 0.00 0.00 0.00 1.40
53 54 7.830201 TGCTATTCGAACCCTTCCTTTAATTAA 59.170 33.333 0.00 0.00 0.00 1.40
54 55 8.343366 GCTATTCGAACCCTTCCTTTAATTAAG 58.657 37.037 0.00 0.00 0.00 1.85
55 56 9.609346 CTATTCGAACCCTTCCTTTAATTAAGA 57.391 33.333 0.00 0.00 35.80 2.10
57 58 8.873186 TTCGAACCCTTCCTTTAATTAAGATT 57.127 30.769 0.00 0.00 35.80 2.40
58 59 9.962809 TTCGAACCCTTCCTTTAATTAAGATTA 57.037 29.630 0.00 0.00 35.80 1.75
59 60 9.609346 TCGAACCCTTCCTTTAATTAAGATTAG 57.391 33.333 0.00 0.00 35.80 1.73
60 61 9.609346 CGAACCCTTCCTTTAATTAAGATTAGA 57.391 33.333 0.00 0.00 35.80 2.10
147 148 5.789643 TTTTTCCCACCTTCAGAAGAATG 57.210 39.130 12.14 9.22 32.31 2.67
148 149 4.722526 TTTCCCACCTTCAGAAGAATGA 57.277 40.909 12.14 0.20 32.31 2.57
149 150 4.722526 TTCCCACCTTCAGAAGAATGAA 57.277 40.909 12.14 6.10 37.60 2.57
159 160 7.712264 CTTCAGAAGAATGAAGCATAGGTAG 57.288 40.000 3.82 0.00 46.95 3.18
160 161 7.423844 TTCAGAAGAATGAAGCATAGGTAGA 57.576 36.000 0.00 0.00 34.31 2.59
161 162 7.609097 TCAGAAGAATGAAGCATAGGTAGAT 57.391 36.000 0.00 0.00 0.00 1.98
162 163 8.712228 TCAGAAGAATGAAGCATAGGTAGATA 57.288 34.615 0.00 0.00 0.00 1.98
163 164 9.319060 TCAGAAGAATGAAGCATAGGTAGATAT 57.681 33.333 0.00 0.00 0.00 1.63
168 169 8.912988 AGAATGAAGCATAGGTAGATATAGAGC 58.087 37.037 0.00 0.00 0.00 4.09
169 170 7.595819 ATGAAGCATAGGTAGATATAGAGCC 57.404 40.000 0.00 0.00 0.00 4.70
170 171 6.736581 TGAAGCATAGGTAGATATAGAGCCT 58.263 40.000 0.00 0.00 0.00 4.58
171 172 7.185565 TGAAGCATAGGTAGATATAGAGCCTT 58.814 38.462 0.00 0.00 0.00 4.35
172 173 7.340743 TGAAGCATAGGTAGATATAGAGCCTTC 59.659 40.741 0.00 0.00 0.00 3.46
173 174 5.825679 AGCATAGGTAGATATAGAGCCTTCG 59.174 44.000 0.00 0.00 0.00 3.79
174 175 5.591067 GCATAGGTAGATATAGAGCCTTCGT 59.409 44.000 0.00 0.00 0.00 3.85
175 176 6.095720 GCATAGGTAGATATAGAGCCTTCGTT 59.904 42.308 0.00 0.00 0.00 3.85
176 177 7.680113 GCATAGGTAGATATAGAGCCTTCGTTC 60.680 44.444 0.00 0.00 0.00 3.95
177 178 5.632118 AGGTAGATATAGAGCCTTCGTTCA 58.368 41.667 0.00 0.00 0.00 3.18
178 179 6.069331 AGGTAGATATAGAGCCTTCGTTCAA 58.931 40.000 0.00 0.00 0.00 2.69
179 180 6.550108 AGGTAGATATAGAGCCTTCGTTCAAA 59.450 38.462 0.00 0.00 0.00 2.69
180 181 7.233757 AGGTAGATATAGAGCCTTCGTTCAAAT 59.766 37.037 0.00 0.00 0.00 2.32
181 182 7.873505 GGTAGATATAGAGCCTTCGTTCAAATT 59.126 37.037 0.00 0.00 0.00 1.82
182 183 9.262358 GTAGATATAGAGCCTTCGTTCAAATTT 57.738 33.333 0.00 0.00 0.00 1.82
183 184 8.738645 AGATATAGAGCCTTCGTTCAAATTTT 57.261 30.769 0.00 0.00 0.00 1.82
184 185 8.831550 AGATATAGAGCCTTCGTTCAAATTTTC 58.168 33.333 0.00 0.00 0.00 2.29
185 186 8.738645 ATATAGAGCCTTCGTTCAAATTTTCT 57.261 30.769 0.00 0.00 0.00 2.52
186 187 5.113502 AGAGCCTTCGTTCAAATTTTCTG 57.886 39.130 0.00 0.00 0.00 3.02
187 188 4.821805 AGAGCCTTCGTTCAAATTTTCTGA 59.178 37.500 0.00 0.00 0.00 3.27
188 189 5.299279 AGAGCCTTCGTTCAAATTTTCTGAA 59.701 36.000 0.00 0.00 0.00 3.02
189 190 5.901552 AGCCTTCGTTCAAATTTTCTGAAA 58.098 33.333 0.00 0.00 34.68 2.69
190 191 5.979517 AGCCTTCGTTCAAATTTTCTGAAAG 59.020 36.000 2.75 0.00 34.68 2.62
191 192 5.175673 GCCTTCGTTCAAATTTTCTGAAAGG 59.824 40.000 2.75 11.46 34.68 3.11
192 193 6.273071 CCTTCGTTCAAATTTTCTGAAAGGT 58.727 36.000 2.75 0.00 34.68 3.50
193 194 7.422399 CCTTCGTTCAAATTTTCTGAAAGGTA 58.578 34.615 2.75 0.00 34.68 3.08
194 195 7.918562 CCTTCGTTCAAATTTTCTGAAAGGTAA 59.081 33.333 2.75 0.00 34.68 2.85
195 196 8.623310 TTCGTTCAAATTTTCTGAAAGGTAAC 57.377 30.769 2.75 4.91 34.68 2.50
211 212 3.508426 GGTAACTATCCCGGAAGATCCT 58.492 50.000 0.73 0.00 33.30 3.24
221 222 1.437986 GAAGATCCTCCACCCGACG 59.562 63.158 0.00 0.00 0.00 5.12
276 277 2.046314 CCCAACCGTCAATCGCCT 60.046 61.111 0.00 0.00 38.35 5.52
279 280 1.663695 CCAACCGTCAATCGCCTAAT 58.336 50.000 0.00 0.00 38.35 1.73
310 311 2.681778 ACTCTGCTAGCGCCACCT 60.682 61.111 10.77 0.00 34.43 4.00
527 531 4.445052 TCGCAGAATTTCAAGCAAACATTG 59.555 37.500 12.38 0.00 0.00 2.82
645 654 7.490962 TCAACGTGTATCAAAGATTTGTTCT 57.509 32.000 5.29 0.00 39.18 3.01
735 753 9.085250 GTAAAACAAGTCCGAAAAACCAATAAA 57.915 29.630 0.00 0.00 0.00 1.40
816 834 2.657143 GGTACAAACCAAGTCCAACCA 58.343 47.619 0.00 0.00 45.98 3.67
839 857 0.252197 GGTTACTGGTGAGGCCGAAT 59.748 55.000 0.00 0.00 41.21 3.34
890 911 1.071471 AGGCCATTTCCCGCGATAG 59.929 57.895 8.23 0.00 0.00 2.08
891 912 1.227853 GGCCATTTCCCGCGATAGT 60.228 57.895 8.23 0.00 39.35 2.12
922 943 1.154035 GCGGGAAAGGCAATTGACG 60.154 57.895 10.34 2.66 0.00 4.35
924 945 1.586154 CGGGAAAGGCAATTGACGCT 61.586 55.000 10.34 0.00 0.00 5.07
1162 1200 4.069232 CCGTCGGCAAGCTCTCCA 62.069 66.667 0.00 0.00 0.00 3.86
1191 1229 1.082679 TCGTCGACGAGCAGGTCTAG 61.083 60.000 34.97 4.40 44.22 2.43
1248 1286 2.481009 GCTTCTCGCGCCCTTTTC 59.519 61.111 0.00 0.00 0.00 2.29
1254 1292 1.067212 TCTCGCGCCCTTTTCTATCTC 59.933 52.381 0.00 0.00 0.00 2.75
1275 1313 3.490896 TCGCTACGATTTGCTGATTGATC 59.509 43.478 0.00 0.00 0.00 2.92
1340 1378 0.809385 CGAAGCACGAGAAGGAGGTA 59.191 55.000 0.00 0.00 45.77 3.08
1352 1390 3.957919 GAGGTAGAGGCCCTCACC 58.042 66.667 14.46 17.29 46.46 4.02
1463 1502 7.327761 CACAAATTTCATTTCTGCTTGGACTAG 59.672 37.037 0.00 0.00 0.00 2.57
1467 1506 5.227569 TCATTTCTGCTTGGACTAGTGAA 57.772 39.130 0.00 0.00 0.00 3.18
1468 1507 5.809001 TCATTTCTGCTTGGACTAGTGAAT 58.191 37.500 0.00 0.00 0.00 2.57
1473 1512 6.299805 TCTGCTTGGACTAGTGAATATGTT 57.700 37.500 0.00 0.00 0.00 2.71
1490 1529 8.685427 TGAATATGTTGATCGAAATGAATGGTT 58.315 29.630 0.00 0.00 0.00 3.67
1517 1556 0.320421 TCTGCTGTAGGTGCGGTTTC 60.320 55.000 0.00 0.00 37.96 2.78
1701 1742 0.898320 TGCTTGCCTCTGTACTCTCC 59.102 55.000 0.00 0.00 0.00 3.71
1722 1763 7.907389 TCTCCTTTAAATGCTTAGAGAACTGA 58.093 34.615 0.00 0.00 0.00 3.41
1783 1824 5.120053 GTCTTTGTGGACAAACAAACCAAAG 59.880 40.000 0.70 0.00 43.34 2.77
1903 1969 0.318120 CAACCACATGAAACAGGGGC 59.682 55.000 0.00 0.00 0.00 5.80
1925 1992 6.019075 GGGCGAACTTTTGCATATTAAAATCC 60.019 38.462 3.62 0.00 39.39 3.01
2041 2335 3.244181 ACACCCAGATTGCCAAATTTGAC 60.244 43.478 19.86 8.78 31.11 3.18
2098 2392 4.201676 TGCTAGATTTGTAACATCAACGCG 60.202 41.667 3.53 3.53 0.00 6.01
2458 2752 4.440826 TGTAAGTTCCTGGCACCTTTAA 57.559 40.909 0.00 0.00 0.00 1.52
2464 2759 3.418684 TCCTGGCACCTTTAACTTCTC 57.581 47.619 0.00 0.00 0.00 2.87
2470 2765 4.340950 TGGCACCTTTAACTTCTCCTTTTG 59.659 41.667 0.00 0.00 0.00 2.44
2484 2779 7.669722 ACTTCTCCTTTTGTAATGCCTTCATTA 59.330 33.333 0.00 0.00 42.51 1.90
2487 2782 8.686334 TCTCCTTTTGTAATGCCTTCATTATTC 58.314 33.333 1.69 0.00 44.33 1.75
2733 3028 6.981762 AGAGTTCTTGCTGAATATCAGTTG 57.018 37.500 8.97 1.01 45.94 3.16
2759 3054 7.210174 GCAAATGAAAAAGAGGAAGGTAAGTT 58.790 34.615 0.00 0.00 0.00 2.66
2768 3063 4.225267 AGAGGAAGGTAAGTTATGTGGTGG 59.775 45.833 0.00 0.00 0.00 4.61
2771 3066 4.698780 GGAAGGTAAGTTATGTGGTGGTTC 59.301 45.833 0.00 0.00 0.00 3.62
2832 3128 8.893563 TTATTTTCCCTGTATGAGTTTCCATT 57.106 30.769 0.00 0.00 0.00 3.16
2876 3172 4.657013 TGTAATGTTTGTCAGGTATGCCA 58.343 39.130 1.54 0.00 37.19 4.92
3110 3406 6.554419 TCGGTTGATTATTTGATTCAGCAAG 58.446 36.000 0.00 0.00 0.00 4.01
3117 3413 9.017509 TGATTATTTGATTCAGCAAGACTCTTT 57.982 29.630 0.00 0.00 0.00 2.52
3118 3414 9.286946 GATTATTTGATTCAGCAAGACTCTTTG 57.713 33.333 0.00 0.00 0.00 2.77
3120 3416 5.936686 TTGATTCAGCAAGACTCTTTGAG 57.063 39.130 0.00 0.00 35.52 3.02
3208 3504 5.610398 TGTTGTACATCGATTATCCAGCAT 58.390 37.500 0.00 0.00 0.00 3.79
3287 3589 6.090628 TCAGCATTTTTGTTGTGAGTTTCAAC 59.909 34.615 0.00 0.00 43.48 3.18
3299 3602 1.340889 AGTTTCAACATGGCATTGCGT 59.659 42.857 0.00 0.00 0.00 5.24
3323 3626 9.326413 CGTAATTTCAATAGGGAACTGTATTCT 57.674 33.333 0.00 0.00 43.88 2.40
3328 3631 6.349300 TCAATAGGGAACTGTATTCTGAAGC 58.651 40.000 0.00 0.00 43.88 3.86
3338 3641 3.193267 TGTATTCTGAAGCCCATGTTTGC 59.807 43.478 0.00 0.00 0.00 3.68
3373 3704 3.885484 CATGGATTGCACCGAAGTATC 57.115 47.619 0.00 0.00 0.00 2.24
3382 3713 1.010350 CCGAAGTATCCGTCCGACG 60.010 63.158 14.15 14.15 42.11 5.12
3613 3948 8.768957 ACTGCAGTATATACATGTCAATGATC 57.231 34.615 20.16 0.00 37.24 2.92
3729 4065 2.947652 GAGCCATAAAAGCATCTCAGCA 59.052 45.455 0.00 0.00 36.85 4.41
3780 4116 3.574396 AGCCTAGTTCCCTTTTTGCTTTC 59.426 43.478 0.00 0.00 0.00 2.62
3983 4323 5.723295 CGGGAAATGAAAACTGAAATCCAT 58.277 37.500 0.00 0.00 0.00 3.41
4056 4396 6.038161 TGTGTTTGTGATATTAGCAGCCATAC 59.962 38.462 0.00 0.00 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.999009 CGAATAGCATCTACTAATATTACCGAA 57.001 33.333 0.00 0.00 0.00 4.30
10 11 9.387257 TCGAATAGCATCTACTAATATTACCGA 57.613 33.333 0.00 0.00 0.00 4.69
11 12 9.999009 TTCGAATAGCATCTACTAATATTACCG 57.001 33.333 0.00 0.00 0.00 4.02
15 16 9.036980 AGGGTTCGAATAGCATCTACTAATATT 57.963 33.333 0.00 0.00 0.00 1.28
16 17 8.596781 AGGGTTCGAATAGCATCTACTAATAT 57.403 34.615 0.00 0.00 0.00 1.28
17 18 8.418597 AAGGGTTCGAATAGCATCTACTAATA 57.581 34.615 0.00 0.00 0.00 0.98
18 19 6.919775 AGGGTTCGAATAGCATCTACTAAT 57.080 37.500 0.00 0.00 0.00 1.73
19 20 6.239232 GGAAGGGTTCGAATAGCATCTACTAA 60.239 42.308 0.00 0.00 0.00 2.24
20 21 5.243283 GGAAGGGTTCGAATAGCATCTACTA 59.757 44.000 0.00 0.00 0.00 1.82
21 22 4.039366 GGAAGGGTTCGAATAGCATCTACT 59.961 45.833 0.00 0.00 0.00 2.57
22 23 4.039366 AGGAAGGGTTCGAATAGCATCTAC 59.961 45.833 0.00 0.00 0.00 2.59
23 24 4.223953 AGGAAGGGTTCGAATAGCATCTA 58.776 43.478 0.00 0.00 0.00 1.98
24 25 3.041946 AGGAAGGGTTCGAATAGCATCT 58.958 45.455 0.00 0.00 0.00 2.90
25 26 3.477210 AGGAAGGGTTCGAATAGCATC 57.523 47.619 0.00 0.00 0.00 3.91
26 27 3.933861 AAGGAAGGGTTCGAATAGCAT 57.066 42.857 0.00 0.00 0.00 3.79
27 28 3.713826 AAAGGAAGGGTTCGAATAGCA 57.286 42.857 0.00 0.00 0.00 3.49
28 29 6.694877 AATTAAAGGAAGGGTTCGAATAGC 57.305 37.500 0.00 0.00 0.00 2.97
29 30 9.609346 TCTTAATTAAAGGAAGGGTTCGAATAG 57.391 33.333 0.00 0.00 35.75 1.73
31 32 9.475620 AATCTTAATTAAAGGAAGGGTTCGAAT 57.524 29.630 0.00 0.00 35.75 3.34
32 33 8.873186 AATCTTAATTAAAGGAAGGGTTCGAA 57.127 30.769 0.00 0.00 35.75 3.71
33 34 9.609346 CTAATCTTAATTAAAGGAAGGGTTCGA 57.391 33.333 0.00 0.00 35.75 3.71
34 35 9.609346 TCTAATCTTAATTAAAGGAAGGGTTCG 57.391 33.333 0.00 0.00 35.75 3.95
125 126 5.454062 TCATTCTTCTGAAGGTGGGAAAAA 58.546 37.500 16.83 2.41 35.69 1.94
126 127 5.060427 TCATTCTTCTGAAGGTGGGAAAA 57.940 39.130 16.83 3.10 35.69 2.29
127 128 4.722526 TCATTCTTCTGAAGGTGGGAAA 57.277 40.909 16.83 3.78 35.69 3.13
128 129 4.655963 CTTCATTCTTCTGAAGGTGGGAA 58.344 43.478 16.83 13.47 45.46 3.97
129 130 4.292186 CTTCATTCTTCTGAAGGTGGGA 57.708 45.455 16.83 7.52 45.46 4.37
136 137 7.423844 TCTACCTATGCTTCATTCTTCTGAA 57.576 36.000 0.00 0.00 36.54 3.02
137 138 7.609097 ATCTACCTATGCTTCATTCTTCTGA 57.391 36.000 0.00 0.00 0.00 3.27
142 143 8.912988 GCTCTATATCTACCTATGCTTCATTCT 58.087 37.037 0.00 0.00 0.00 2.40
143 144 8.141268 GGCTCTATATCTACCTATGCTTCATTC 58.859 40.741 0.00 0.00 0.00 2.67
144 145 7.843760 AGGCTCTATATCTACCTATGCTTCATT 59.156 37.037 0.00 0.00 0.00 2.57
145 146 7.361438 AGGCTCTATATCTACCTATGCTTCAT 58.639 38.462 0.00 0.00 0.00 2.57
146 147 6.736581 AGGCTCTATATCTACCTATGCTTCA 58.263 40.000 0.00 0.00 0.00 3.02
147 148 7.468084 CGAAGGCTCTATATCTACCTATGCTTC 60.468 44.444 0.00 0.00 0.00 3.86
148 149 6.320164 CGAAGGCTCTATATCTACCTATGCTT 59.680 42.308 0.00 0.00 0.00 3.91
149 150 5.825679 CGAAGGCTCTATATCTACCTATGCT 59.174 44.000 0.00 0.00 0.00 3.79
150 151 5.591067 ACGAAGGCTCTATATCTACCTATGC 59.409 44.000 0.00 0.00 0.00 3.14
151 152 7.337184 TGAACGAAGGCTCTATATCTACCTATG 59.663 40.741 0.00 0.00 0.00 2.23
152 153 7.403671 TGAACGAAGGCTCTATATCTACCTAT 58.596 38.462 0.00 0.00 0.00 2.57
153 154 6.776744 TGAACGAAGGCTCTATATCTACCTA 58.223 40.000 0.00 0.00 0.00 3.08
154 155 5.632118 TGAACGAAGGCTCTATATCTACCT 58.368 41.667 0.00 0.00 0.00 3.08
155 156 5.961396 TGAACGAAGGCTCTATATCTACC 57.039 43.478 0.00 0.00 0.00 3.18
156 157 8.819643 AATTTGAACGAAGGCTCTATATCTAC 57.180 34.615 0.00 0.00 0.00 2.59
157 158 9.832445 AAAATTTGAACGAAGGCTCTATATCTA 57.168 29.630 0.00 0.00 0.00 1.98
158 159 8.738645 AAAATTTGAACGAAGGCTCTATATCT 57.261 30.769 0.00 0.00 0.00 1.98
159 160 8.831550 AGAAAATTTGAACGAAGGCTCTATATC 58.168 33.333 0.00 0.00 0.00 1.63
160 161 8.616076 CAGAAAATTTGAACGAAGGCTCTATAT 58.384 33.333 0.00 0.00 0.00 0.86
161 162 7.822334 TCAGAAAATTTGAACGAAGGCTCTATA 59.178 33.333 0.00 0.00 0.00 1.31
162 163 6.655003 TCAGAAAATTTGAACGAAGGCTCTAT 59.345 34.615 0.00 0.00 0.00 1.98
163 164 5.995282 TCAGAAAATTTGAACGAAGGCTCTA 59.005 36.000 0.00 0.00 0.00 2.43
164 165 4.821805 TCAGAAAATTTGAACGAAGGCTCT 59.178 37.500 0.00 0.00 0.00 4.09
165 166 5.108385 TCAGAAAATTTGAACGAAGGCTC 57.892 39.130 0.00 0.00 0.00 4.70
166 167 5.514274 TTCAGAAAATTTGAACGAAGGCT 57.486 34.783 0.00 0.00 30.03 4.58
167 168 5.175673 CCTTTCAGAAAATTTGAACGAAGGC 59.824 40.000 0.00 0.00 34.50 4.35
168 169 6.273071 ACCTTTCAGAAAATTTGAACGAAGG 58.727 36.000 15.70 15.70 36.67 3.46
169 170 8.743099 GTTACCTTTCAGAAAATTTGAACGAAG 58.257 33.333 0.00 0.00 34.50 3.79
170 171 8.463607 AGTTACCTTTCAGAAAATTTGAACGAA 58.536 29.630 0.00 0.00 34.50 3.85
171 172 7.992008 AGTTACCTTTCAGAAAATTTGAACGA 58.008 30.769 0.00 0.00 34.50 3.85
172 173 9.893305 ATAGTTACCTTTCAGAAAATTTGAACG 57.107 29.630 0.00 0.00 34.50 3.95
175 176 9.020731 GGGATAGTTACCTTTCAGAAAATTTGA 57.979 33.333 0.00 0.00 0.00 2.69
176 177 7.968405 CGGGATAGTTACCTTTCAGAAAATTTG 59.032 37.037 0.00 0.00 0.00 2.32
177 178 7.122204 CCGGGATAGTTACCTTTCAGAAAATTT 59.878 37.037 0.00 0.00 0.00 1.82
178 179 6.602009 CCGGGATAGTTACCTTTCAGAAAATT 59.398 38.462 0.00 0.00 0.00 1.82
179 180 6.069847 TCCGGGATAGTTACCTTTCAGAAAAT 60.070 38.462 0.00 0.00 0.00 1.82
180 181 5.248934 TCCGGGATAGTTACCTTTCAGAAAA 59.751 40.000 0.00 0.00 0.00 2.29
181 182 4.778958 TCCGGGATAGTTACCTTTCAGAAA 59.221 41.667 0.00 0.00 0.00 2.52
182 183 4.355549 TCCGGGATAGTTACCTTTCAGAA 58.644 43.478 0.00 0.00 0.00 3.02
183 184 3.985127 TCCGGGATAGTTACCTTTCAGA 58.015 45.455 0.00 0.00 0.00 3.27
184 185 4.404715 TCTTCCGGGATAGTTACCTTTCAG 59.595 45.833 0.00 0.00 0.00 3.02
185 186 4.355549 TCTTCCGGGATAGTTACCTTTCA 58.644 43.478 0.00 0.00 0.00 2.69
186 187 5.511031 GGATCTTCCGGGATAGTTACCTTTC 60.511 48.000 0.00 0.00 0.00 2.62
187 188 4.347292 GGATCTTCCGGGATAGTTACCTTT 59.653 45.833 0.00 0.00 0.00 3.11
188 189 3.902467 GGATCTTCCGGGATAGTTACCTT 59.098 47.826 0.00 0.00 0.00 3.50
189 190 3.142407 AGGATCTTCCGGGATAGTTACCT 59.858 47.826 0.00 0.05 42.75 3.08
190 191 3.508426 AGGATCTTCCGGGATAGTTACC 58.492 50.000 0.00 0.00 42.75 2.85
191 192 3.510753 GGAGGATCTTCCGGGATAGTTAC 59.489 52.174 8.30 0.00 42.75 2.50
192 193 3.141460 TGGAGGATCTTCCGGGATAGTTA 59.859 47.826 18.23 0.00 42.75 2.24
193 194 2.090719 TGGAGGATCTTCCGGGATAGTT 60.091 50.000 18.23 0.00 42.75 2.24
194 195 1.503784 TGGAGGATCTTCCGGGATAGT 59.496 52.381 18.23 0.00 42.75 2.12
195 196 1.896465 GTGGAGGATCTTCCGGGATAG 59.104 57.143 18.23 0.00 42.75 2.08
196 197 1.482553 GGTGGAGGATCTTCCGGGATA 60.483 57.143 18.23 0.00 42.75 2.59
197 198 0.764752 GGTGGAGGATCTTCCGGGAT 60.765 60.000 18.23 0.00 42.75 3.85
198 199 1.382695 GGTGGAGGATCTTCCGGGA 60.383 63.158 18.23 0.00 42.75 5.14
199 200 2.444256 GGGTGGAGGATCTTCCGGG 61.444 68.421 18.23 0.00 42.75 5.73
200 201 2.797278 CGGGTGGAGGATCTTCCGG 61.797 68.421 18.23 0.00 42.75 5.14
201 202 1.756950 TCGGGTGGAGGATCTTCCG 60.757 63.158 18.23 7.77 42.75 4.30
202 203 1.823976 GTCGGGTGGAGGATCTTCC 59.176 63.158 16.81 16.81 37.77 3.46
241 242 1.340991 GGGGCTTGGATGCTAAAGACA 60.341 52.381 0.00 0.00 32.70 3.41
276 277 1.559682 GAGTGGAAGCCCTGGACATTA 59.440 52.381 0.00 0.00 0.00 1.90
279 280 1.152030 AGAGTGGAAGCCCTGGACA 60.152 57.895 0.00 0.00 0.00 4.02
310 311 0.899717 GCCCTTGCCCAGATTTGTCA 60.900 55.000 0.00 0.00 0.00 3.58
435 437 9.912634 ATGAACATATTTTTGAAACGAGTGAAT 57.087 25.926 0.00 0.00 0.00 2.57
518 522 2.481854 TGAATGGTGCACAATGTTTGC 58.518 42.857 20.43 0.00 40.63 3.68
527 531 5.049167 TGAACATTTCTTTGAATGGTGCAC 58.951 37.500 8.80 8.80 37.08 4.57
626 635 8.324163 ACACCTAGAACAAATCTTTGATACAC 57.676 34.615 9.53 0.00 40.55 2.90
816 834 2.955881 GCCTCACCAGTAACCCGCT 61.956 63.158 0.00 0.00 0.00 5.52
826 844 0.608035 GGTTTCATTCGGCCTCACCA 60.608 55.000 0.00 0.00 39.03 4.17
839 857 2.357034 GCTGGCGAGACGGTTTCA 60.357 61.111 0.00 0.00 0.00 2.69
890 911 3.849953 CCGCGCTTCGTTGCCTAC 61.850 66.667 5.56 0.00 36.19 3.18
922 943 1.026718 ACAGGCGGTTAATGCTCAGC 61.027 55.000 0.00 0.00 0.00 4.26
924 945 1.305219 GCACAGGCGGTTAATGCTCA 61.305 55.000 0.00 0.00 33.44 4.26
1162 1200 1.168407 TCGTCGACGAGGTTGAGGTT 61.168 55.000 34.97 0.00 44.22 3.50
1191 1229 1.144936 CCGAGGAGAGGTGGATTGC 59.855 63.158 0.00 0.00 0.00 3.56
1246 1284 4.036380 TCAGCAAATCGTAGCGAGATAGAA 59.964 41.667 0.00 0.00 39.91 2.10
1248 1286 3.890128 TCAGCAAATCGTAGCGAGATAG 58.110 45.455 0.00 0.00 39.91 2.08
1254 1292 3.492383 AGATCAATCAGCAAATCGTAGCG 59.508 43.478 0.00 0.00 35.48 4.26
1275 1313 2.513204 CACCTGCGCAGATCCCAG 60.513 66.667 38.06 22.00 0.00 4.45
1340 1378 2.040278 CTCCTGGTGAGGGCCTCT 59.960 66.667 32.28 0.00 40.25 3.69
1352 1390 1.270907 ACTGGTCCTTGTAGCTCCTG 58.729 55.000 0.00 0.00 0.00 3.86
1463 1502 8.131100 ACCATTCATTTCGATCAACATATTCAC 58.869 33.333 0.00 0.00 0.00 3.18
1467 1506 6.919662 GCAACCATTCATTTCGATCAACATAT 59.080 34.615 0.00 0.00 0.00 1.78
1468 1507 6.264832 GCAACCATTCATTTCGATCAACATA 58.735 36.000 0.00 0.00 0.00 2.29
1473 1512 2.477694 GCGCAACCATTCATTTCGATCA 60.478 45.455 0.30 0.00 0.00 2.92
1490 1529 1.374631 CCTACAGCAGAACAGCGCA 60.375 57.895 11.47 0.00 40.15 6.09
1517 1556 0.464373 AGCCATACATCAACAGGCCG 60.464 55.000 0.00 0.00 46.35 6.13
1646 1685 3.961408 GAGGTCAGTATTAGGCAGAAGGA 59.039 47.826 0.00 0.00 0.00 3.36
1701 1742 7.695618 GTGCATCAGTTCTCTAAGCATTTAAAG 59.304 37.037 0.00 0.00 32.75 1.85
1830 1896 4.944317 AGCTAACAGAGGTTAAAGCCAATC 59.056 41.667 0.00 0.00 38.71 2.67
1903 1969 7.543868 TGGTGGATTTTAATATGCAAAAGTTCG 59.456 33.333 1.86 0.00 0.00 3.95
1925 1992 3.569701 AGCAATTGAAGTGGTAGTTGGTG 59.430 43.478 10.34 0.00 0.00 4.17
1990 2284 3.771577 AGATCACACGGAAACTTCCTT 57.228 42.857 6.91 0.00 45.33 3.36
2098 2392 5.649831 AGAGGCAGAATTGGTACTTCAAATC 59.350 40.000 0.00 0.00 0.00 2.17
2458 2752 5.385198 TGAAGGCATTACAAAAGGAGAAGT 58.615 37.500 0.00 0.00 0.00 3.01
2464 2759 9.090692 CTTGAATAATGAAGGCATTACAAAAGG 57.909 33.333 0.00 0.00 46.54 3.11
2470 2765 8.515414 GGATACCTTGAATAATGAAGGCATTAC 58.485 37.037 0.00 0.00 46.54 1.89
2484 2779 5.450818 TGCCAGTTTAGGATACCTTGAAT 57.549 39.130 0.00 0.00 34.61 2.57
2487 2782 6.828785 AGTAATTGCCAGTTTAGGATACCTTG 59.171 38.462 0.00 0.00 34.61 3.61
2733 3028 4.607293 ACCTTCCTCTTTTTCATTTGCC 57.393 40.909 0.00 0.00 0.00 4.52
2759 3054 5.560722 TTCTCAAGAAGAACCACCACATA 57.439 39.130 0.00 0.00 39.12 2.29
2788 3083 6.840780 AATAAGTTGATAAAACAGGCTGCT 57.159 33.333 15.89 0.00 0.00 4.24
2803 3098 8.244113 GGAAACTCATACAGGGAAAATAAGTTG 58.756 37.037 0.00 0.00 0.00 3.16
2832 3128 9.755804 TTACAAATGTGATTCAGTATGCAAAAA 57.244 25.926 0.00 0.00 34.76 1.94
2840 3136 9.891828 GACAAACATTACAAATGTGATTCAGTA 57.108 29.630 6.07 0.00 31.80 2.74
2844 3140 7.867403 ACCTGACAAACATTACAAATGTGATTC 59.133 33.333 6.07 4.17 31.80 2.52
2856 3152 4.917385 ACTGGCATACCTGACAAACATTA 58.083 39.130 0.00 0.00 40.83 1.90
2876 3172 3.981071 TTGGTATACAAGCTGCTGACT 57.019 42.857 1.35 0.00 33.18 3.41
3110 3406 5.675684 AAATCCTCTCCTCTCAAAGAGTC 57.324 43.478 3.47 0.00 40.72 3.36
3117 3413 4.813809 AGCAGATAAATCCTCTCCTCTCA 58.186 43.478 0.00 0.00 0.00 3.27
3118 3414 5.772672 TGTAGCAGATAAATCCTCTCCTCTC 59.227 44.000 0.00 0.00 0.00 3.20
3120 3416 6.014669 ACATGTAGCAGATAAATCCTCTCCTC 60.015 42.308 0.00 0.00 0.00 3.71
3183 3479 4.084328 GCTGGATAATCGATGTACAACAGC 60.084 45.833 17.93 17.93 40.40 4.40
3208 3504 8.985315 ACATTCAGCCATCTCATAAATCTAAA 57.015 30.769 0.00 0.00 0.00 1.85
3287 3589 5.403166 CCTATTGAAATTACGCAATGCCATG 59.597 40.000 0.00 0.00 36.27 3.66
3323 3626 3.370840 AGATAGCAAACATGGGCTTCA 57.629 42.857 12.95 0.00 41.41 3.02
3328 3631 5.840243 TTGATCAAGATAGCAAACATGGG 57.160 39.130 3.38 0.00 0.00 4.00
3363 3666 1.709147 CGTCGGACGGATACTTCGGT 61.709 60.000 22.18 0.00 38.08 4.69
3366 3669 0.179156 TTGCGTCGGACGGATACTTC 60.179 55.000 29.30 12.92 42.59 3.01
3373 3704 0.236187 TGAAAAATTGCGTCGGACGG 59.764 50.000 29.30 13.13 42.82 4.79
3382 3713 6.675987 TGCACCCAAAAATATGAAAAATTGC 58.324 32.000 0.00 0.00 0.00 3.56
3444 3777 3.888323 TGCATGAGTAGTTGCTTTTGGAA 59.112 39.130 0.00 0.00 39.60 3.53
3613 3948 5.175859 AGACCGTCATGTTTTATGTACTGG 58.824 41.667 0.40 0.00 0.00 4.00
3729 4065 4.884164 CCAAGAAACTTGACTGAAGGTCTT 59.116 41.667 12.25 0.00 44.74 3.01
3780 4116 3.205338 TCAATGGGCGTATTCATGTGAG 58.795 45.455 0.00 0.00 0.00 3.51
3861 4197 5.789643 AACTTGTTTGCATACAGTCCATT 57.210 34.783 9.95 0.26 0.00 3.16
3908 4248 3.518303 ACCCTGTATGTCCCAGTACTTTC 59.482 47.826 0.00 0.00 0.00 2.62
3983 4323 6.427853 CGCTCTGGTTGATTGAAATATATGGA 59.572 38.462 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.