Multiple sequence alignment - TraesCS7A01G195700

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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 TraesCS7A01G195700 chr7A 100.000 2918 0 0 1 2918 155645543 155642626 0.000000e+00 5389
1 TraesCS7A01G195700 chr7D 96.760 1389 40 3 782 2170 153769272 153767889 0.000000e+00 2311
2 TraesCS7A01G195700 chr7D 84.203 690 43 22 30 689 153772829 153772176 6.910000e-171 610
3 TraesCS7A01G195700 chr7D 89.460 389 34 4 2530 2918 153767437 153767056 4.370000e-133 484
4 TraesCS7A01G195700 chr7D 86.557 305 27 6 2240 2538 153767764 153767468 1.010000e-84 324
5 TraesCS7A01G195700 chr7B 93.404 1410 57 12 780 2178 115526260 115524876 0.000000e+00 2056
6 TraesCS7A01G195700 chr7B 84.349 722 42 32 3 694 115559989 115559309 2.450000e-180 641
7 TraesCS7A01G195700 chr7B 88.889 306 26 5 2530 2835 115524404 115524107 1.280000e-98 370


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 TraesCS7A01G195700 chr7A 155642626 155645543 2917 True 5389.00 5389 100.0000 1 2918 1 chr7A.!!$R1 2917
1 TraesCS7A01G195700 chr7D 153767056 153772829 5773 True 932.25 2311 89.2450 30 2918 4 chr7D.!!$R1 2888
2 TraesCS7A01G195700 chr7B 115524107 115526260 2153 True 1213.00 2056 91.1465 780 2835 2 chr7B.!!$R2 2055
3 TraesCS7A01G195700 chr7B 115559309 115559989 680 True 641.00 641 84.3490 3 694 1 chr7B.!!$R1 691

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
242 255 0.045419 CGTGCGTTGTTGTTTTTCGC 60.045 50.0 0.0 0.0 45.7 4.70 F
767 3281 0.391927 TGGAATTTGTACCTCCCGCG 60.392 55.0 0.0 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 4751 0.102120 GTGTCTGCTCGGAGATCTGG 59.898 60.0 9.69 0.0 33.89 3.86 R
2711 5704 0.249573 CCAGTTTGCAGCCCACTTTG 60.250 55.0 0.00 0.0 0.00 2.77 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
70 75 5.594317 ACTTTGCTCTAGGATTTGTGTTGTT 59.406 36.000 0.00 0.00 0.00 2.83
71 76 5.437289 TTGCTCTAGGATTTGTGTTGTTG 57.563 39.130 0.00 0.00 0.00 3.33
72 77 4.460263 TGCTCTAGGATTTGTGTTGTTGT 58.540 39.130 0.00 0.00 0.00 3.32
120 125 6.039382 TGTGCAAGATAGTGTAGATACGTGAT 59.961 38.462 0.00 0.00 0.00 3.06
122 127 6.918022 TGCAAGATAGTGTAGATACGTGATTG 59.082 38.462 0.00 0.00 0.00 2.67
127 132 9.339850 AGATAGTGTAGATACGTGATTGTTAGT 57.660 33.333 0.00 0.00 0.00 2.24
128 133 9.383462 GATAGTGTAGATACGTGATTGTTAGTG 57.617 37.037 0.00 0.00 0.00 2.74
129 134 6.034591 AGTGTAGATACGTGATTGTTAGTGC 58.965 40.000 0.00 0.00 0.00 4.40
130 135 5.803461 GTGTAGATACGTGATTGTTAGTGCA 59.197 40.000 0.00 0.00 0.00 4.57
139 144 6.697455 ACGTGATTGTTAGTGCATGTATAGAG 59.303 38.462 0.00 0.00 0.00 2.43
142 147 3.977427 TGTTAGTGCATGTATAGAGCGG 58.023 45.455 0.00 0.00 0.00 5.52
152 157 6.015940 TGCATGTATAGAGCGGATCATATAGG 60.016 42.308 0.00 0.00 0.00 2.57
153 158 6.207614 GCATGTATAGAGCGGATCATATAGGA 59.792 42.308 0.00 0.00 0.00 2.94
154 159 7.589395 CATGTATAGAGCGGATCATATAGGAC 58.411 42.308 0.00 0.00 0.00 3.85
155 160 6.659824 TGTATAGAGCGGATCATATAGGACA 58.340 40.000 0.00 0.00 0.00 4.02
156 161 7.290813 TGTATAGAGCGGATCATATAGGACAT 58.709 38.462 0.00 0.00 0.00 3.06
157 162 6.892658 ATAGAGCGGATCATATAGGACATC 57.107 41.667 0.00 0.00 0.00 3.06
158 163 4.865905 AGAGCGGATCATATAGGACATCT 58.134 43.478 0.00 0.00 0.00 2.90
159 164 4.644234 AGAGCGGATCATATAGGACATCTG 59.356 45.833 0.00 0.00 0.00 2.90
160 165 4.348486 AGCGGATCATATAGGACATCTGT 58.652 43.478 0.00 0.00 0.00 3.41
161 166 4.774726 AGCGGATCATATAGGACATCTGTT 59.225 41.667 0.00 0.00 0.00 3.16
162 167 5.952347 AGCGGATCATATAGGACATCTGTTA 59.048 40.000 0.00 0.00 0.00 2.41
163 168 6.437477 AGCGGATCATATAGGACATCTGTTAA 59.563 38.462 0.00 0.00 0.00 2.01
164 169 7.039011 AGCGGATCATATAGGACATCTGTTAAA 60.039 37.037 0.00 0.00 0.00 1.52
165 170 7.602644 GCGGATCATATAGGACATCTGTTAAAA 59.397 37.037 0.00 0.00 0.00 1.52
166 171 9.489084 CGGATCATATAGGACATCTGTTAAAAA 57.511 33.333 0.00 0.00 0.00 1.94
223 228 7.148255 TGTGGTATCATATGAGTTTTGCAGAAC 60.148 37.037 12.01 12.01 0.00 3.01
235 248 1.061887 GCAGAACGTGCGTTGTTGT 59.938 52.632 14.89 0.00 43.99 3.32
242 255 0.045419 CGTGCGTTGTTGTTTTTCGC 60.045 50.000 0.00 0.00 45.70 4.70
244 257 3.752831 GCGTTGTTGTTTTTCGCAC 57.247 47.368 0.00 0.00 45.01 5.34
245 258 1.264672 GCGTTGTTGTTTTTCGCACT 58.735 45.000 0.00 0.00 45.01 4.40
246 259 2.442424 GCGTTGTTGTTTTTCGCACTA 58.558 42.857 0.00 0.00 45.01 2.74
247 260 2.462565 GCGTTGTTGTTTTTCGCACTAG 59.537 45.455 0.00 0.00 45.01 2.57
248 261 3.033185 CGTTGTTGTTTTTCGCACTAGG 58.967 45.455 0.00 0.00 0.00 3.02
249 262 3.242478 CGTTGTTGTTTTTCGCACTAGGA 60.242 43.478 0.00 0.00 0.00 2.94
250 263 4.279659 GTTGTTGTTTTTCGCACTAGGAG 58.720 43.478 0.00 0.00 0.00 3.69
252 265 3.942748 TGTTGTTTTTCGCACTAGGAGTT 59.057 39.130 0.00 0.00 0.00 3.01
253 266 4.034742 TGTTGTTTTTCGCACTAGGAGTTC 59.965 41.667 0.00 0.00 0.00 3.01
254 267 3.799366 TGTTTTTCGCACTAGGAGTTCA 58.201 40.909 0.00 0.00 0.00 3.18
255 268 3.558418 TGTTTTTCGCACTAGGAGTTCAC 59.442 43.478 0.00 0.00 0.00 3.18
256 269 3.746045 TTTTCGCACTAGGAGTTCACT 57.254 42.857 0.00 0.00 0.00 3.41
257 270 4.859304 TTTTCGCACTAGGAGTTCACTA 57.141 40.909 0.00 0.00 0.00 2.74
258 271 3.844577 TTCGCACTAGGAGTTCACTAC 57.155 47.619 0.00 0.00 0.00 2.73
259 272 1.736126 TCGCACTAGGAGTTCACTACG 59.264 52.381 0.00 0.00 0.00 3.51
260 273 1.736126 CGCACTAGGAGTTCACTACGA 59.264 52.381 0.00 0.00 0.00 3.43
261 274 2.161012 CGCACTAGGAGTTCACTACGAA 59.839 50.000 0.00 0.00 0.00 3.85
262 275 3.728268 CGCACTAGGAGTTCACTACGAAG 60.728 52.174 0.00 0.00 33.09 3.79
266 279 4.877251 ACTAGGAGTTCACTACGAAGCTAG 59.123 45.833 0.00 0.00 33.09 3.42
326 345 1.597797 ATGTGGCATTTGGACGGCAG 61.598 55.000 0.00 0.00 38.50 4.85
426 452 4.082136 GTCTTGACCCGTTTAGAGTCTGAT 60.082 45.833 1.86 0.00 0.00 2.90
427 453 3.868757 TGACCCGTTTAGAGTCTGATG 57.131 47.619 1.86 0.00 0.00 3.07
429 455 3.444034 TGACCCGTTTAGAGTCTGATGAG 59.556 47.826 1.86 0.00 0.00 2.90
430 456 3.432378 ACCCGTTTAGAGTCTGATGAGT 58.568 45.455 1.86 0.00 0.00 3.41
431 457 3.444388 ACCCGTTTAGAGTCTGATGAGTC 59.556 47.826 1.86 0.00 41.68 3.36
465 492 1.394618 TCAGAACCAAAAACACGGGG 58.605 50.000 0.00 0.00 0.00 5.73
482 509 2.855370 CGGGGAAAGAAACAAAAACACG 59.145 45.455 0.00 0.00 0.00 4.49
503 535 3.188460 CGGGAACAGAAAATGTGGTACAG 59.812 47.826 0.00 0.00 43.00 2.74
513 545 5.607119 AAATGTGGTACAGAAATGTCGTC 57.393 39.130 0.00 0.00 41.80 4.20
547 592 7.433680 ACATGATTTGTAGACCCAAGAAAAAC 58.566 34.615 0.00 0.00 36.57 2.43
693 1338 6.190346 TCTCTATAGAGTAGTCCCTTGGTC 57.810 45.833 25.54 0.00 42.60 4.02
701 1346 5.046231 AGAGTAGTCCCTTGGTCTGAAATTC 60.046 44.000 0.00 0.00 0.00 2.17
707 1352 2.229784 CCTTGGTCTGAAATTCCTGTGC 59.770 50.000 0.00 0.00 0.00 4.57
708 1353 2.655090 TGGTCTGAAATTCCTGTGCA 57.345 45.000 0.00 0.00 0.00 4.57
709 1354 3.159213 TGGTCTGAAATTCCTGTGCAT 57.841 42.857 0.00 0.00 0.00 3.96
710 1355 4.299586 TGGTCTGAAATTCCTGTGCATA 57.700 40.909 0.00 0.00 0.00 3.14
711 1356 4.858850 TGGTCTGAAATTCCTGTGCATAT 58.141 39.130 0.00 0.00 0.00 1.78
715 1516 5.587844 GTCTGAAATTCCTGTGCATATCAGT 59.412 40.000 8.69 0.00 35.66 3.41
722 1523 4.323417 TCCTGTGCATATCAGTTTCGTTT 58.677 39.130 0.00 0.00 0.00 3.60
723 1524 5.483811 TCCTGTGCATATCAGTTTCGTTTA 58.516 37.500 0.00 0.00 0.00 2.01
729 1530 8.941977 TGTGCATATCAGTTTCGTTTACTAAAT 58.058 29.630 0.00 0.00 0.00 1.40
730 1531 9.769093 GTGCATATCAGTTTCGTTTACTAAATT 57.231 29.630 0.00 0.00 0.00 1.82
731 1532 9.767684 TGCATATCAGTTTCGTTTACTAAATTG 57.232 29.630 0.00 0.00 0.00 2.32
732 1533 9.221775 GCATATCAGTTTCGTTTACTAAATTGG 57.778 33.333 3.68 0.00 0.00 3.16
749 3263 0.681887 TGGTGCTCTTCCCATGCATG 60.682 55.000 20.19 20.19 39.00 4.06
764 3278 2.733956 TGCATGGAATTTGTACCTCCC 58.266 47.619 0.00 0.00 0.00 4.30
765 3279 1.676006 GCATGGAATTTGTACCTCCCG 59.324 52.381 0.00 0.00 0.00 5.14
767 3281 0.391927 TGGAATTTGTACCTCCCGCG 60.392 55.000 0.00 0.00 0.00 6.46
768 3282 1.093496 GGAATTTGTACCTCCCGCGG 61.093 60.000 21.04 21.04 0.00 6.46
769 3283 1.712018 GAATTTGTACCTCCCGCGGC 61.712 60.000 22.85 5.24 0.00 6.53
770 3284 3.692370 ATTTGTACCTCCCGCGGCC 62.692 63.158 22.85 2.81 0.00 6.13
796 3654 2.022129 CGGACGAGTTGTGTGAGGC 61.022 63.158 0.00 0.00 0.00 4.70
925 3791 2.504032 GATCCGATCACCCCGCAA 59.496 61.111 3.33 0.00 0.00 4.85
928 3794 2.869503 ATCCGATCACCCCGCAACAC 62.870 60.000 0.00 0.00 0.00 3.32
942 3808 1.181786 CAACACAACCACCAACCAGT 58.818 50.000 0.00 0.00 0.00 4.00
943 3809 1.134175 CAACACAACCACCAACCAGTC 59.866 52.381 0.00 0.00 0.00 3.51
944 3810 0.746563 ACACAACCACCAACCAGTCG 60.747 55.000 0.00 0.00 0.00 4.18
945 3811 1.822186 ACAACCACCAACCAGTCGC 60.822 57.895 0.00 0.00 0.00 5.19
981 3851 4.247380 GCCCCCAGCTCAGATCCG 62.247 72.222 0.00 0.00 38.99 4.18
1412 4282 3.060615 CTTCCTCGTCCCCGTCGT 61.061 66.667 0.00 0.00 35.01 4.34
1754 4624 2.109799 CGGCTACAGGATGCTGGG 59.890 66.667 19.22 11.57 42.53 4.45
1761 4631 1.000521 CAGGATGCTGGGCAAGGAA 60.001 57.895 6.28 0.00 43.62 3.36
1764 4634 1.318158 GGATGCTGGGCAAGGAAGTG 61.318 60.000 0.00 0.00 43.62 3.16
1785 4655 0.469331 AGATGGAGGGCATGCCATTG 60.469 55.000 36.56 0.00 44.60 2.82
1837 4707 3.244044 GGAGAAGGAAGATGAAGGGATCG 60.244 52.174 0.00 0.00 0.00 3.69
1931 4801 1.064825 AAGTGACGGGGATGGAGTTT 58.935 50.000 0.00 0.00 0.00 2.66
2193 5096 8.644318 AAGTTAACTCTTGTTACTGTACTGTG 57.356 34.615 15.01 0.00 38.26 3.66
2197 5100 7.578310 AACTCTTGTTACTGTACTGTGTCTA 57.422 36.000 15.01 4.89 34.15 2.59
2251 5188 0.940126 GGCATAAGCATGTCAGGTCG 59.060 55.000 0.00 0.00 44.61 4.79
2259 5196 4.737855 AGCATGTCAGGTCGTAGTTATT 57.262 40.909 0.00 0.00 0.00 1.40
2282 5219 7.862512 TTTGAATTTTGGTTTCAGAAGCATT 57.137 28.000 0.00 0.00 42.32 3.56
2285 5222 7.695820 TGAATTTTGGTTTCAGAAGCATTTTG 58.304 30.769 0.00 0.00 42.32 2.44
2289 5226 4.219115 TGGTTTCAGAAGCATTTTGGGTA 58.781 39.130 0.00 0.00 38.28 3.69
2312 5251 4.722361 TTGAGCTGAATAATGCATTGCA 57.278 36.364 22.27 14.72 44.86 4.08
2348 5288 7.837863 TGTTATCTTAAGTAGGTCTTCTGTGG 58.162 38.462 1.63 0.00 37.56 4.17
2366 5306 1.780309 TGGTTCTGTCCTGATGGGTTT 59.220 47.619 0.00 0.00 36.25 3.27
2373 5313 1.546029 GTCCTGATGGGTTTTGCCTTC 59.454 52.381 0.00 0.00 37.43 3.46
2374 5314 0.527565 CCTGATGGGTTTTGCCTTCG 59.472 55.000 0.00 0.00 37.43 3.79
2380 5320 1.203001 TGGGTTTTGCCTTCGGAGATT 60.203 47.619 0.00 0.00 35.04 2.40
2407 5347 1.808343 GAAGTAAAACCATCGGGCGTT 59.192 47.619 0.00 0.00 37.90 4.84
2408 5348 1.161843 AGTAAAACCATCGGGCGTTG 58.838 50.000 0.00 0.00 37.90 4.10
2438 5378 2.427095 GGTGGAGGGATGTACAAATTGC 59.573 50.000 0.00 0.00 0.00 3.56
2441 5381 4.576463 GTGGAGGGATGTACAAATTGCTAG 59.424 45.833 0.00 0.00 0.00 3.42
2442 5382 3.565902 GGAGGGATGTACAAATTGCTAGC 59.434 47.826 8.10 8.10 0.00 3.42
2455 5395 8.310406 ACAAATTGCTAGCCATTTAAAAGTTC 57.690 30.769 22.33 0.00 0.00 3.01
2489 5440 6.183360 TGTCTGTCTGTTTGGTTAATTGTTCC 60.183 38.462 0.00 0.00 0.00 3.62
2536 5529 4.018050 AGGAGGAATGCTGGTAATTCAGTT 60.018 41.667 0.00 0.00 36.03 3.16
2541 5534 5.507985 GGAATGCTGGTAATTCAGTTATGCC 60.508 44.000 0.00 0.00 36.03 4.40
2545 5538 3.202906 TGGTAATTCAGTTATGCCGAGC 58.797 45.455 0.00 0.00 0.00 5.03
2546 5539 3.202906 GGTAATTCAGTTATGCCGAGCA 58.797 45.455 1.01 1.01 44.86 4.26
2556 5549 2.642139 ATGCCGAGCAAAGATTTGTG 57.358 45.000 7.12 0.00 43.62 3.33
2693 5686 3.372206 CCATTTCTGGTCGTCTCATCAAC 59.628 47.826 0.00 0.00 37.79 3.18
2694 5687 2.743636 TTCTGGTCGTCTCATCAACC 57.256 50.000 0.00 0.00 0.00 3.77
2698 5691 2.480419 CTGGTCGTCTCATCAACCAAAC 59.520 50.000 0.00 0.00 41.07 2.93
2701 5694 3.564225 GGTCGTCTCATCAACCAAACTTT 59.436 43.478 0.00 0.00 0.00 2.66
2702 5695 4.036380 GGTCGTCTCATCAACCAAACTTTT 59.964 41.667 0.00 0.00 0.00 2.27
2706 5699 7.698970 GTCGTCTCATCAACCAAACTTTTAAAA 59.301 33.333 0.00 0.00 0.00 1.52
2707 5700 8.244802 TCGTCTCATCAACCAAACTTTTAAAAA 58.755 29.630 1.66 0.00 0.00 1.94
2708 5701 8.318167 CGTCTCATCAACCAAACTTTTAAAAAC 58.682 33.333 1.66 0.00 0.00 2.43
2709 5702 9.145865 GTCTCATCAACCAAACTTTTAAAAACA 57.854 29.630 1.66 0.00 0.00 2.83
2710 5703 9.364989 TCTCATCAACCAAACTTTTAAAAACAG 57.635 29.630 1.66 0.00 0.00 3.16
2711 5704 7.969314 TCATCAACCAAACTTTTAAAAACAGC 58.031 30.769 1.66 0.00 0.00 4.40
2712 5705 7.604164 TCATCAACCAAACTTTTAAAAACAGCA 59.396 29.630 1.66 0.00 0.00 4.41
2713 5706 7.730364 TCAACCAAACTTTTAAAAACAGCAA 57.270 28.000 1.66 0.00 0.00 3.91
2721 5714 4.479786 TTTAAAAACAGCAAAGTGGGCT 57.520 36.364 0.00 0.00 43.77 5.19
2742 5735 2.760092 TGCAAACTGGTTTTCTTCTGCT 59.240 40.909 0.00 0.00 0.00 4.24
2763 5756 7.719633 TCTGCTGTTTGGAGTTCTTTTAGTATT 59.280 33.333 0.00 0.00 35.48 1.89
2822 5815 6.705825 CCATGTATGTGATTCCTCGTTTATGA 59.294 38.462 0.00 0.00 0.00 2.15
2841 5834 9.233232 GTTTATGAAGTTGTTTTGAGAAATCGT 57.767 29.630 0.00 0.00 0.00 3.73
2850 5843 9.993881 GTTGTTTTGAGAAATCGTTCAAATATG 57.006 29.630 1.07 0.00 41.42 1.78
2880 5873 8.084684 ACCTTGAGATATTTTGCTGAAACTTTC 58.915 33.333 0.00 0.00 0.00 2.62
2894 5887 2.148916 ACTTTCGTCGATGTGCTTCA 57.851 45.000 4.21 0.00 0.00 3.02
2907 5900 2.417586 TGTGCTTCATCGCTTGAATCTG 59.582 45.455 1.79 0.00 43.30 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 75 9.607988 CACCCAATGACTACTAATGTTTATACA 57.392 33.333 0.00 0.00 38.95 2.29
71 76 9.609346 ACACCCAATGACTACTAATGTTTATAC 57.391 33.333 0.00 0.00 0.00 1.47
72 77 9.607988 CACACCCAATGACTACTAATGTTTATA 57.392 33.333 0.00 0.00 0.00 0.98
81 86 3.580895 TCTTGCACACCCAATGACTACTA 59.419 43.478 0.00 0.00 0.00 1.82
82 87 2.371841 TCTTGCACACCCAATGACTACT 59.628 45.455 0.00 0.00 0.00 2.57
83 88 2.778299 TCTTGCACACCCAATGACTAC 58.222 47.619 0.00 0.00 0.00 2.73
90 95 2.949177 ACACTATCTTGCACACCCAA 57.051 45.000 0.00 0.00 0.00 4.12
120 125 4.098807 TCCGCTCTATACATGCACTAACAA 59.901 41.667 0.00 0.00 0.00 2.83
122 127 4.238761 TCCGCTCTATACATGCACTAAC 57.761 45.455 0.00 0.00 0.00 2.34
126 131 3.303881 TGATCCGCTCTATACATGCAC 57.696 47.619 0.00 0.00 0.00 4.57
127 132 5.859205 ATATGATCCGCTCTATACATGCA 57.141 39.130 0.00 0.00 0.00 3.96
128 133 6.207614 TCCTATATGATCCGCTCTATACATGC 59.792 42.308 0.00 0.00 0.00 4.06
129 134 7.229506 TGTCCTATATGATCCGCTCTATACATG 59.770 40.741 0.00 0.00 0.00 3.21
130 135 7.290813 TGTCCTATATGATCCGCTCTATACAT 58.709 38.462 0.00 0.00 0.00 2.29
139 144 4.727507 ACAGATGTCCTATATGATCCGC 57.272 45.455 0.00 0.00 0.00 5.54
163 168 3.427193 GCGCACCATTTTCGTGTATTTTT 59.573 39.130 0.30 0.00 33.61 1.94
164 169 2.983803 GCGCACCATTTTCGTGTATTTT 59.016 40.909 0.30 0.00 33.61 1.82
165 170 2.591133 GCGCACCATTTTCGTGTATTT 58.409 42.857 0.30 0.00 33.61 1.40
166 171 1.135517 GGCGCACCATTTTCGTGTATT 60.136 47.619 10.83 0.00 35.26 1.89
167 172 0.450184 GGCGCACCATTTTCGTGTAT 59.550 50.000 10.83 0.00 35.26 2.29
168 173 1.579084 GGGCGCACCATTTTCGTGTA 61.579 55.000 10.83 0.00 39.85 2.90
169 174 2.642700 GGCGCACCATTTTCGTGT 59.357 55.556 10.83 0.00 35.26 4.49
170 175 2.126502 GGGCGCACCATTTTCGTG 60.127 61.111 10.83 0.00 39.85 4.35
201 206 6.901887 CACGTTCTGCAAAACTCATATGATAC 59.098 38.462 5.72 0.00 0.00 2.24
223 228 0.045419 GCGAAAAACAACAACGCACG 60.045 50.000 0.00 0.00 46.75 5.34
233 246 3.558418 GTGAACTCCTAGTGCGAAAAACA 59.442 43.478 0.00 0.00 0.00 2.83
235 248 4.067972 AGTGAACTCCTAGTGCGAAAAA 57.932 40.909 0.00 0.00 0.00 1.94
242 255 3.440872 AGCTTCGTAGTGAACTCCTAGTG 59.559 47.826 0.00 0.00 31.87 2.74
243 256 3.688235 AGCTTCGTAGTGAACTCCTAGT 58.312 45.455 0.00 0.00 31.87 2.57
244 257 4.260866 GCTAGCTTCGTAGTGAACTCCTAG 60.261 50.000 7.70 0.00 32.81 3.02
245 258 3.626670 GCTAGCTTCGTAGTGAACTCCTA 59.373 47.826 7.70 0.00 31.87 2.94
246 259 2.424246 GCTAGCTTCGTAGTGAACTCCT 59.576 50.000 7.70 0.00 31.87 3.69
247 260 2.791849 CGCTAGCTTCGTAGTGAACTCC 60.792 54.545 13.93 0.00 33.09 3.85
248 261 2.442424 CGCTAGCTTCGTAGTGAACTC 58.558 52.381 13.93 0.00 33.09 3.01
249 262 1.132643 CCGCTAGCTTCGTAGTGAACT 59.867 52.381 13.93 0.00 33.09 3.01
250 263 1.131883 TCCGCTAGCTTCGTAGTGAAC 59.868 52.381 13.93 0.00 33.09 3.18
252 265 1.015109 CTCCGCTAGCTTCGTAGTGA 58.985 55.000 13.93 0.00 33.09 3.41
253 266 3.535691 CTCCGCTAGCTTCGTAGTG 57.464 57.895 13.93 0.00 0.00 2.74
426 452 1.106944 TGAGTGGCACGACAGACTCA 61.107 55.000 12.71 5.67 41.93 3.41
427 453 0.244994 ATGAGTGGCACGACAGACTC 59.755 55.000 20.51 9.53 36.23 3.36
429 455 0.038251 TGATGAGTGGCACGACAGAC 60.038 55.000 20.51 17.24 0.00 3.51
430 456 0.244721 CTGATGAGTGGCACGACAGA 59.755 55.000 21.71 12.83 31.60 3.41
431 457 0.244721 TCTGATGAGTGGCACGACAG 59.755 55.000 20.51 20.70 0.00 3.51
465 492 4.924462 TGTTCCCGTGTTTTTGTTTCTTTC 59.076 37.500 0.00 0.00 0.00 2.62
482 509 4.394729 TCTGTACCACATTTTCTGTTCCC 58.605 43.478 0.00 0.00 35.29 3.97
503 535 5.985530 TCATGTATCATCCAGACGACATTTC 59.014 40.000 0.00 0.00 35.18 2.17
513 545 6.652481 GGGTCTACAAATCATGTATCATCCAG 59.348 42.308 0.00 0.00 43.42 3.86
593 638 5.278604 GTTTGTATGGAACGGGCAATTATC 58.721 41.667 0.00 0.00 0.00 1.75
665 712 9.589461 CCAAGGGACTACTCTATAGAGAAATTA 57.411 37.037 31.91 15.16 41.15 1.40
683 730 3.084786 CAGGAATTTCAGACCAAGGGAC 58.915 50.000 0.00 0.00 0.00 4.46
690 1335 4.883585 TGATATGCACAGGAATTTCAGACC 59.116 41.667 0.00 0.00 0.00 3.85
693 1338 6.446781 AACTGATATGCACAGGAATTTCAG 57.553 37.500 7.62 5.04 41.44 3.02
701 1346 4.685169 AAACGAAACTGATATGCACAGG 57.315 40.909 7.62 0.00 39.38 4.00
709 1354 8.231837 GCACCAATTTAGTAAACGAAACTGATA 58.768 33.333 0.00 0.00 0.00 2.15
710 1355 7.040686 AGCACCAATTTAGTAAACGAAACTGAT 60.041 33.333 0.00 0.00 0.00 2.90
711 1356 6.261381 AGCACCAATTTAGTAAACGAAACTGA 59.739 34.615 0.00 0.00 0.00 3.41
715 1516 6.870971 AGAGCACCAATTTAGTAAACGAAA 57.129 33.333 0.00 0.00 0.00 3.46
722 1523 4.919774 TGGGAAGAGCACCAATTTAGTA 57.080 40.909 0.00 0.00 32.89 1.82
723 1524 3.806949 TGGGAAGAGCACCAATTTAGT 57.193 42.857 0.00 0.00 32.89 2.24
729 1530 0.040058 ATGCATGGGAAGAGCACCAA 59.960 50.000 0.00 0.00 41.60 3.67
730 1531 0.681887 CATGCATGGGAAGAGCACCA 60.682 55.000 19.40 0.00 41.60 4.17
731 1532 1.389609 CCATGCATGGGAAGAGCACC 61.390 60.000 34.31 0.00 44.31 5.01
732 1533 2.112898 CCATGCATGGGAAGAGCAC 58.887 57.895 34.31 0.00 44.31 4.40
749 3263 1.093496 CCGCGGGAGGTACAAATTCC 61.093 60.000 20.10 0.00 0.00 3.01
771 3285 2.126580 CAACTCGTCCGGTCGTCC 60.127 66.667 20.21 0.00 0.00 4.79
772 3286 1.728426 CACAACTCGTCCGGTCGTC 60.728 63.158 20.21 0.21 0.00 4.20
773 3287 2.333938 CACAACTCGTCCGGTCGT 59.666 61.111 20.21 0.00 0.00 4.34
774 3288 2.014554 CACACAACTCGTCCGGTCG 61.015 63.158 15.22 15.22 0.00 4.79
775 3289 0.663568 CTCACACAACTCGTCCGGTC 60.664 60.000 0.00 0.00 0.00 4.79
776 3290 1.362717 CTCACACAACTCGTCCGGT 59.637 57.895 0.00 0.00 0.00 5.28
777 3291 1.372997 CCTCACACAACTCGTCCGG 60.373 63.158 0.00 0.00 0.00 5.14
778 3292 2.022129 GCCTCACACAACTCGTCCG 61.022 63.158 0.00 0.00 0.00 4.79
796 3654 0.732880 GGGATGTGTCACTGTCGTCG 60.733 60.000 4.27 0.00 0.00 5.12
925 3791 0.746563 CGACTGGTTGGTGGTTGTGT 60.747 55.000 0.00 0.00 0.00 3.72
928 3794 1.507141 GAGCGACTGGTTGGTGGTTG 61.507 60.000 0.00 0.00 0.00 3.77
1754 4624 1.093159 CTCCATCTGCACTTCCTTGC 58.907 55.000 0.00 0.00 43.31 4.01
1761 4631 1.226542 CATGCCCTCCATCTGCACT 59.773 57.895 0.00 0.00 37.92 4.40
1764 4634 2.910994 GGCATGCCCTCCATCTGC 60.911 66.667 27.24 0.00 29.71 4.26
1785 4655 1.902508 TCCAGGGTGAACTGAGATGTC 59.097 52.381 0.00 0.00 40.97 3.06
1862 4732 1.298859 GCGATGTGAGTTCACCCCAC 61.299 60.000 9.60 0.00 45.88 4.61
1880 4750 1.067250 GTCTGCTCGGAGATCTGGC 59.933 63.158 9.69 0.00 33.89 4.85
1881 4751 0.102120 GTGTCTGCTCGGAGATCTGG 59.898 60.000 9.69 0.00 33.89 3.86
1931 4801 5.500234 AGCTATTCTACATCAAAAGCACCA 58.500 37.500 0.00 0.00 0.00 4.17
2170 5040 7.919621 AGACACAGTACAGTAACAAGAGTTAAC 59.080 37.037 0.00 0.00 41.58 2.01
2171 5041 8.004087 AGACACAGTACAGTAACAAGAGTTAA 57.996 34.615 0.00 0.00 41.58 2.01
2172 5042 7.578310 AGACACAGTACAGTAACAAGAGTTA 57.422 36.000 0.00 0.00 39.15 2.24
2197 5100 8.402683 AGGGTAGTAGATATCAACTGGTCATAT 58.597 37.037 5.32 0.00 0.00 1.78
2219 5156 0.698238 TTATGCCACAGCTCAAGGGT 59.302 50.000 0.00 0.00 40.80 4.34
2220 5157 1.386533 CTTATGCCACAGCTCAAGGG 58.613 55.000 0.00 0.00 40.80 3.95
2259 5196 7.862512 AAATGCTTCTGAAACCAAAATTCAA 57.137 28.000 0.00 0.00 36.43 2.69
2282 5219 6.154192 TGCATTATTCAGCTCAATTACCCAAA 59.846 34.615 0.00 0.00 0.00 3.28
2285 5222 5.772825 TGCATTATTCAGCTCAATTACCC 57.227 39.130 0.00 0.00 0.00 3.69
2289 5226 5.666462 TGCAATGCATTATTCAGCTCAATT 58.334 33.333 12.53 0.00 31.71 2.32
2312 5251 6.054860 ACTTAAGATAACAGGATGCACACT 57.945 37.500 10.09 0.00 42.53 3.55
2348 5288 2.029918 GCAAAACCCATCAGGACAGAAC 60.030 50.000 0.00 0.00 39.89 3.01
2373 5313 5.353400 GGTTTTACTTCCCAACTAATCTCCG 59.647 44.000 0.00 0.00 0.00 4.63
2374 5314 6.243148 TGGTTTTACTTCCCAACTAATCTCC 58.757 40.000 0.00 0.00 0.00 3.71
2380 5320 4.566070 CCCGATGGTTTTACTTCCCAACTA 60.566 45.833 0.00 0.00 0.00 2.24
2407 5347 2.528818 CCCTCCACCTTGCAGTCCA 61.529 63.158 0.00 0.00 0.00 4.02
2408 5348 1.566298 ATCCCTCCACCTTGCAGTCC 61.566 60.000 0.00 0.00 0.00 3.85
2438 5378 6.681777 AGCAGTTGAACTTTTAAATGGCTAG 58.318 36.000 0.00 0.00 0.00 3.42
2441 5381 6.868339 ACATAGCAGTTGAACTTTTAAATGGC 59.132 34.615 0.00 0.00 0.00 4.40
2442 5382 8.299570 AGACATAGCAGTTGAACTTTTAAATGG 58.700 33.333 0.00 0.00 0.00 3.16
2455 5395 4.083643 CCAAACAGACAGACATAGCAGTTG 60.084 45.833 0.00 0.00 0.00 3.16
2497 5451 3.260884 TCCTCCTGTATTGAGTCAACCAC 59.739 47.826 7.96 9.84 0.00 4.16
2511 5465 3.266772 TGAATTACCAGCATTCCTCCTGT 59.733 43.478 0.00 0.00 30.64 4.00
2536 5529 2.423185 CCACAAATCTTTGCTCGGCATA 59.577 45.455 2.63 0.00 41.79 3.14
2541 5534 1.536766 TCTGCCACAAATCTTTGCTCG 59.463 47.619 2.63 0.00 41.79 5.03
2545 5538 3.054878 GCAGTTCTGCCACAAATCTTTG 58.945 45.455 13.11 1.19 43.62 2.77
2546 5539 3.375782 GCAGTTCTGCCACAAATCTTT 57.624 42.857 13.11 0.00 0.00 2.52
2645 5638 9.270640 GATGCTAGATTGATGATAAAGACAACT 57.729 33.333 0.00 0.00 0.00 3.16
2693 5686 7.020602 CCACTTTGCTGTTTTTAAAAGTTTGG 58.979 34.615 0.14 0.00 0.00 3.28
2694 5687 7.020602 CCCACTTTGCTGTTTTTAAAAGTTTG 58.979 34.615 0.14 0.00 0.00 2.93
2698 5691 4.875536 AGCCCACTTTGCTGTTTTTAAAAG 59.124 37.500 0.14 0.00 37.76 2.27
2709 5702 1.044790 AGTTTGCAGCCCACTTTGCT 61.045 50.000 0.00 0.00 40.87 3.91
2710 5703 0.877213 CAGTTTGCAGCCCACTTTGC 60.877 55.000 0.00 0.00 40.67 3.68
2711 5704 0.249573 CCAGTTTGCAGCCCACTTTG 60.250 55.000 0.00 0.00 0.00 2.77
2712 5705 0.687427 ACCAGTTTGCAGCCCACTTT 60.687 50.000 0.00 0.00 0.00 2.66
2713 5706 0.687427 AACCAGTTTGCAGCCCACTT 60.687 50.000 0.00 0.00 0.00 3.16
2721 5714 2.760092 AGCAGAAGAAAACCAGTTTGCA 59.240 40.909 4.11 0.00 30.40 4.08
2723 5716 4.376340 ACAGCAGAAGAAAACCAGTTTG 57.624 40.909 0.00 0.00 32.36 2.93
2742 5735 8.617809 GTGTGAATACTAAAAGAACTCCAAACA 58.382 33.333 0.00 0.00 0.00 2.83
2763 5756 5.325239 TGAGGAGTGAGAAGATAAGTGTGA 58.675 41.667 0.00 0.00 0.00 3.58
2772 5765 3.098774 AGAGCATGAGGAGTGAGAAGA 57.901 47.619 0.00 0.00 0.00 2.87
2778 5771 3.942829 TGGTAAAAGAGCATGAGGAGTG 58.057 45.455 0.00 0.00 0.00 3.51
2779 5772 4.851639 ATGGTAAAAGAGCATGAGGAGT 57.148 40.909 0.00 0.00 44.67 3.85
2822 5815 8.702163 ATTTGAACGATTTCTCAAAACAACTT 57.298 26.923 1.74 0.00 42.96 2.66
2850 5843 9.508567 GTTTCAGCAAAATATCTCAAGGTAATC 57.491 33.333 0.00 0.00 0.00 1.75
2852 5845 8.635765 AGTTTCAGCAAAATATCTCAAGGTAA 57.364 30.769 0.00 0.00 0.00 2.85
2855 5848 7.272084 CGAAAGTTTCAGCAAAATATCTCAAGG 59.728 37.037 15.67 0.00 0.00 3.61
2894 5887 5.902613 TTGAAAATCCAGATTCAAGCGAT 57.097 34.783 0.00 0.00 39.81 4.58


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

AutoCloner maintained by Alex Coulton.