Multiple sequence alignment - TraesCS6D01G397000

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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 TraesCS6D01G397000 chr6D 100.000 1754 0 0 841 2594 469205245 469206998 0.000000e+00 3240
1 TraesCS6D01G397000 chr6D 100.000 458 0 0 1 458 469204405 469204862 0.000000e+00 846
2 TraesCS6D01G397000 chr6D 81.761 477 32 26 2103 2544 469224345 469224801 5.310000e-92 348
3 TraesCS6D01G397000 chr6D 86.275 204 28 0 956 1159 306129277 306129480 3.360000e-54 222
4 TraesCS6D01G397000 chr6B 88.448 1740 82 52 890 2561 715448826 715450514 0.000000e+00 1989
5 TraesCS6D01G397000 chr6B 92.268 194 14 1 177 369 715448166 715448359 9.150000e-70 274
6 TraesCS6D01G397000 chr6B 84.753 223 33 1 956 1178 473055963 473056184 3.360000e-54 222
7 TraesCS6D01G397000 chr6B 94.406 143 7 1 1 142 715448021 715448163 4.350000e-53 219
8 TraesCS6D01G397000 chr6B 85.784 204 29 0 956 1159 563805927 563805724 1.560000e-52 217
9 TraesCS6D01G397000 chr6A 84.801 1783 125 75 867 2594 614381484 614383175 0.000000e+00 1657
10 TraesCS6D01G397000 chr6A 86.158 419 31 7 1 417 614380782 614381175 6.630000e-116 427
11 TraesCS6D01G397000 chr6A 86.979 192 25 0 956 1147 441486255 441486446 1.560000e-52 217
12 TraesCS6D01G397000 chr7A 89.193 694 51 17 860 1541 165448449 165447768 0.000000e+00 845
13 TraesCS6D01G397000 chr2B 83.978 181 29 0 958 1138 30145543 30145363 9.540000e-40 174
14 TraesCS6D01G397000 chr2D 82.383 193 33 1 947 1138 18210830 18210638 1.600000e-37 167


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 TraesCS6D01G397000 chr6D 469204405 469206998 2593 False 2043.000000 3240 100.000000 1 2594 2 chr6D.!!$F3 2593
1 TraesCS6D01G397000 chr6B 715448021 715450514 2493 False 827.333333 1989 91.707333 1 2561 3 chr6B.!!$F2 2560
2 TraesCS6D01G397000 chr6A 614380782 614383175 2393 False 1042.000000 1657 85.479500 1 2594 2 chr6A.!!$F2 2593
3 TraesCS6D01G397000 chr7A 165447768 165448449 681 True 845.000000 845 89.193000 860 1541 1 chr7A.!!$R1 681

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
442 448 0.108615 CTCTCCACCACCATGACGAC 60.109 60.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2396 2517 0.171455 GGATGCGAGACAGAGACGTT 59.829 55.0 0.0 0.0 0.0 3.99 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
26 27 5.116882 CGGTTCCTCTAGGTAAAATCCAAG 58.883 45.833 0.00 0.00 36.34 3.61
107 112 1.687563 AAAACGTCACCCCTGGAAAG 58.312 50.000 0.00 0.00 0.00 2.62
108 113 0.841289 AAACGTCACCCCTGGAAAGA 59.159 50.000 0.00 0.00 0.00 2.52
109 114 0.841289 AACGTCACCCCTGGAAAGAA 59.159 50.000 0.00 0.00 0.00 2.52
110 115 0.841289 ACGTCACCCCTGGAAAGAAA 59.159 50.000 0.00 0.00 0.00 2.52
157 163 2.544069 GGCTCCGCTATAGACAACTCAC 60.544 54.545 3.21 0.00 0.00 3.51
158 164 2.099263 GCTCCGCTATAGACAACTCACA 59.901 50.000 3.21 0.00 0.00 3.58
159 165 3.793801 GCTCCGCTATAGACAACTCACAG 60.794 52.174 3.21 0.00 0.00 3.66
160 166 2.099263 TCCGCTATAGACAACTCACAGC 59.901 50.000 3.21 0.00 0.00 4.40
161 167 2.159240 CCGCTATAGACAACTCACAGCA 60.159 50.000 3.21 0.00 0.00 4.41
162 168 2.854777 CGCTATAGACAACTCACAGCAC 59.145 50.000 3.21 0.00 0.00 4.40
163 169 3.190874 GCTATAGACAACTCACAGCACC 58.809 50.000 3.21 0.00 0.00 5.01
164 170 3.118956 GCTATAGACAACTCACAGCACCT 60.119 47.826 3.21 0.00 0.00 4.00
165 171 3.601443 ATAGACAACTCACAGCACCTC 57.399 47.619 0.00 0.00 0.00 3.85
166 172 1.123077 AGACAACTCACAGCACCTCA 58.877 50.000 0.00 0.00 0.00 3.86
167 173 1.696336 AGACAACTCACAGCACCTCAT 59.304 47.619 0.00 0.00 0.00 2.90
168 174 2.105477 AGACAACTCACAGCACCTCATT 59.895 45.455 0.00 0.00 0.00 2.57
169 175 3.324846 AGACAACTCACAGCACCTCATTA 59.675 43.478 0.00 0.00 0.00 1.90
170 176 3.668447 ACAACTCACAGCACCTCATTAG 58.332 45.455 0.00 0.00 0.00 1.73
171 177 3.071602 ACAACTCACAGCACCTCATTAGT 59.928 43.478 0.00 0.00 0.00 2.24
172 178 3.601443 ACTCACAGCACCTCATTAGTC 57.399 47.619 0.00 0.00 0.00 2.59
173 179 2.899900 ACTCACAGCACCTCATTAGTCA 59.100 45.455 0.00 0.00 0.00 3.41
185 191 2.436542 TCATTAGTCATTACCCCACCCG 59.563 50.000 0.00 0.00 0.00 5.28
193 199 2.119484 TTACCCCACCCGCACAGAAG 62.119 60.000 0.00 0.00 0.00 2.85
194 200 3.636231 CCCCACCCGCACAGAAGA 61.636 66.667 0.00 0.00 0.00 2.87
196 202 2.738521 CCACCCGCACAGAAGACG 60.739 66.667 0.00 0.00 0.00 4.18
200 206 2.259818 CCGCACAGAAGACGCTCT 59.740 61.111 0.00 0.00 0.00 4.09
207 213 1.539388 ACAGAAGACGCTCTCTGACAG 59.461 52.381 13.41 0.00 34.59 3.51
259 265 7.118496 CAGTCATGGAAAGAGAGTAGGTATT 57.882 40.000 0.00 0.00 0.00 1.89
277 283 2.320681 TTAGTGCTGTAGGGTCCAGT 57.679 50.000 0.00 0.00 32.41 4.00
432 438 4.024984 CCCCCTCCCTCTCCACCA 62.025 72.222 0.00 0.00 0.00 4.17
433 439 2.689034 CCCCTCCCTCTCCACCAC 60.689 72.222 0.00 0.00 0.00 4.16
434 440 2.689034 CCCTCCCTCTCCACCACC 60.689 72.222 0.00 0.00 0.00 4.61
435 441 2.122729 CCTCCCTCTCCACCACCA 59.877 66.667 0.00 0.00 0.00 4.17
436 442 1.307343 CCTCCCTCTCCACCACCAT 60.307 63.158 0.00 0.00 0.00 3.55
437 443 1.630126 CCTCCCTCTCCACCACCATG 61.630 65.000 0.00 0.00 0.00 3.66
438 444 0.618680 CTCCCTCTCCACCACCATGA 60.619 60.000 0.00 0.00 0.00 3.07
439 445 0.909610 TCCCTCTCCACCACCATGAC 60.910 60.000 0.00 0.00 0.00 3.06
440 446 1.219124 CCTCTCCACCACCATGACG 59.781 63.158 0.00 0.00 0.00 4.35
441 447 1.257750 CCTCTCCACCACCATGACGA 61.258 60.000 0.00 0.00 0.00 4.20
442 448 0.108615 CTCTCCACCACCATGACGAC 60.109 60.000 0.00 0.00 0.00 4.34
443 449 1.446099 CTCCACCACCATGACGACG 60.446 63.158 0.00 0.00 0.00 5.12
444 450 1.873270 CTCCACCACCATGACGACGA 61.873 60.000 0.00 0.00 0.00 4.20
445 451 1.446099 CCACCACCATGACGACGAG 60.446 63.158 0.00 0.00 0.00 4.18
446 452 1.446099 CACCACCATGACGACGAGG 60.446 63.158 0.00 0.08 0.00 4.63
447 453 2.509336 CCACCATGACGACGAGGC 60.509 66.667 0.00 0.00 0.00 4.70
448 454 2.509336 CACCATGACGACGAGGCC 60.509 66.667 0.00 0.00 0.00 5.19
449 455 3.771160 ACCATGACGACGAGGCCC 61.771 66.667 0.00 0.00 0.00 5.80
450 456 4.873129 CCATGACGACGAGGCCCG 62.873 72.222 11.48 11.48 45.44 6.13
451 457 3.822192 CATGACGACGAGGCCCGA 61.822 66.667 18.74 0.00 41.76 5.14
452 458 3.823330 ATGACGACGAGGCCCGAC 61.823 66.667 18.74 12.19 41.76 4.79
891 897 3.060615 GAGGGCAAGCAGCTGGTG 61.061 66.667 20.97 14.36 44.79 4.17
1594 1646 2.681778 AGGAGACCGCCCACTGAG 60.682 66.667 0.00 0.00 0.00 3.35
1641 1693 0.623723 TTAGGCAGGGCTAGGGTTTG 59.376 55.000 2.72 0.00 0.00 2.93
1642 1694 0.549169 TAGGCAGGGCTAGGGTTTGT 60.549 55.000 0.00 0.00 0.00 2.83
1669 1721 2.099062 GTCGGCGCAGATTGCTTG 59.901 61.111 14.65 0.00 42.25 4.01
1682 1734 0.752054 TTGCTTGCTTTTGGGGTCAG 59.248 50.000 0.00 0.00 0.00 3.51
1683 1735 0.396974 TGCTTGCTTTTGGGGTCAGT 60.397 50.000 0.00 0.00 0.00 3.41
1684 1736 0.315251 GCTTGCTTTTGGGGTCAGTC 59.685 55.000 0.00 0.00 0.00 3.51
1685 1737 1.691196 CTTGCTTTTGGGGTCAGTCA 58.309 50.000 0.00 0.00 0.00 3.41
1691 1743 3.321968 GCTTTTGGGGTCAGTCAATTTCT 59.678 43.478 0.00 0.00 0.00 2.52
1744 1796 3.565482 TGAAAGTGTTCATCAGACAAGGC 59.435 43.478 0.00 0.00 38.88 4.35
1747 1808 0.396435 TGTTCATCAGACAAGGCGGT 59.604 50.000 0.00 0.00 0.00 5.68
1748 1809 0.798776 GTTCATCAGACAAGGCGGTG 59.201 55.000 0.00 0.00 0.00 4.94
1749 1810 0.955428 TTCATCAGACAAGGCGGTGC 60.955 55.000 0.00 0.00 0.00 5.01
1750 1811 1.376424 CATCAGACAAGGCGGTGCT 60.376 57.895 0.00 0.00 0.00 4.40
1751 1812 1.376424 ATCAGACAAGGCGGTGCTG 60.376 57.895 0.00 0.00 0.00 4.41
1752 1813 2.809861 ATCAGACAAGGCGGTGCTGG 62.810 60.000 12.12 0.00 0.00 4.85
1753 1814 3.560251 AGACAAGGCGGTGCTGGT 61.560 61.111 0.00 0.00 0.00 4.00
1754 1815 2.214216 AGACAAGGCGGTGCTGGTA 61.214 57.895 0.00 0.00 0.00 3.25
1755 1816 2.032071 ACAAGGCGGTGCTGGTAC 59.968 61.111 0.00 0.00 0.00 3.34
1802 1866 2.653726 CTTGCTCCTCTGCTCTCTCTA 58.346 52.381 0.00 0.00 0.00 2.43
1804 1868 3.311167 TGCTCCTCTGCTCTCTCTATT 57.689 47.619 0.00 0.00 0.00 1.73
1805 1869 3.221771 TGCTCCTCTGCTCTCTCTATTC 58.778 50.000 0.00 0.00 0.00 1.75
1807 1871 3.503748 GCTCCTCTGCTCTCTCTATTCTC 59.496 52.174 0.00 0.00 0.00 2.87
1808 1872 4.747931 GCTCCTCTGCTCTCTCTATTCTCT 60.748 50.000 0.00 0.00 0.00 3.10
1812 1876 5.829924 CCTCTGCTCTCTCTATTCTCTTCTT 59.170 44.000 0.00 0.00 0.00 2.52
1813 1877 6.016777 CCTCTGCTCTCTCTATTCTCTTCTTC 60.017 46.154 0.00 0.00 0.00 2.87
1814 1878 5.827797 TCTGCTCTCTCTATTCTCTTCTTCC 59.172 44.000 0.00 0.00 0.00 3.46
1815 1879 4.892934 TGCTCTCTCTATTCTCTTCTTCCC 59.107 45.833 0.00 0.00 0.00 3.97
1816 1880 4.892934 GCTCTCTCTATTCTCTTCTTCCCA 59.107 45.833 0.00 0.00 0.00 4.37
1817 1881 5.010012 GCTCTCTCTATTCTCTTCTTCCCAG 59.990 48.000 0.00 0.00 0.00 4.45
1818 1882 6.086011 TCTCTCTATTCTCTTCTTCCCAGT 57.914 41.667 0.00 0.00 0.00 4.00
1819 1883 6.498538 TCTCTCTATTCTCTTCTTCCCAGTT 58.501 40.000 0.00 0.00 0.00 3.16
1820 1884 6.605594 TCTCTCTATTCTCTTCTTCCCAGTTC 59.394 42.308 0.00 0.00 0.00 3.01
1821 1885 6.256819 TCTCTATTCTCTTCTTCCCAGTTCA 58.743 40.000 0.00 0.00 0.00 3.18
1848 1928 1.073763 TCAGGTCAGGTCAATTGGGTG 59.926 52.381 5.42 1.13 0.00 4.61
1949 2029 6.350780 CGTGTGGGTTCCTATTACTTTCTAGT 60.351 42.308 0.00 0.00 38.44 2.57
1954 2034 7.456902 TGGGTTCCTATTACTTTCTAGTCAGTT 59.543 37.037 2.51 0.00 35.78 3.16
1955 2035 7.764901 GGGTTCCTATTACTTTCTAGTCAGTTG 59.235 40.741 2.51 0.00 35.78 3.16
1989 2076 0.669619 TGGTGCTGCTGTCAAATGTG 59.330 50.000 0.00 0.00 0.00 3.21
2054 2141 8.462016 TCCAAGAAAGAAAGAAGAACAAGAAAG 58.538 33.333 0.00 0.00 0.00 2.62
2056 2143 6.800543 AGAAAGAAAGAAGAACAAGAAAGGC 58.199 36.000 0.00 0.00 0.00 4.35
2057 2144 6.605194 AGAAAGAAAGAAGAACAAGAAAGGCT 59.395 34.615 0.00 0.00 0.00 4.58
2086 2192 2.401568 TCTGCAGCAAGATGGAGGATA 58.598 47.619 9.47 0.00 38.99 2.59
2087 2193 2.367894 TCTGCAGCAAGATGGAGGATAG 59.632 50.000 9.47 0.00 38.99 2.08
2203 2313 6.096001 GGATTGAATTAGTGCTTGGTGAGAAT 59.904 38.462 0.00 0.00 0.00 2.40
2204 2314 7.283127 GGATTGAATTAGTGCTTGGTGAGAATA 59.717 37.037 0.00 0.00 0.00 1.75
2205 2315 7.994425 TTGAATTAGTGCTTGGTGAGAATAA 57.006 32.000 0.00 0.00 0.00 1.40
2236 2346 4.642429 AGTAACTGTTGGTTTAGCTCAGG 58.358 43.478 2.69 0.00 39.17 3.86
2334 2455 7.043391 GGACAAAAATAAGCACACAGAAGAAAC 60.043 37.037 0.00 0.00 0.00 2.78
2337 2458 8.482429 CAAAAATAAGCACACAGAAGAAACATC 58.518 33.333 0.00 0.00 0.00 3.06
2343 2464 1.466167 CACAGAAGAAACATCTGCCCG 59.534 52.381 3.57 0.00 46.56 6.13
2347 2468 0.400213 AAGAAACATCTGCCCGTCCA 59.600 50.000 0.00 0.00 0.00 4.02
2348 2469 0.620556 AGAAACATCTGCCCGTCCAT 59.379 50.000 0.00 0.00 0.00 3.41
2349 2470 1.017387 GAAACATCTGCCCGTCCATC 58.983 55.000 0.00 0.00 0.00 3.51
2350 2471 0.327924 AAACATCTGCCCGTCCATCA 59.672 50.000 0.00 0.00 0.00 3.07
2358 2479 1.971505 GCCCGTCCATCATCCTGTCA 61.972 60.000 0.00 0.00 0.00 3.58
2359 2480 0.761187 CCCGTCCATCATCCTGTCAT 59.239 55.000 0.00 0.00 0.00 3.06
2360 2481 1.541889 CCCGTCCATCATCCTGTCATG 60.542 57.143 0.00 0.00 0.00 3.07
2361 2482 1.139654 CCGTCCATCATCCTGTCATGT 59.860 52.381 0.00 0.00 0.00 3.21
2362 2483 2.420547 CCGTCCATCATCCTGTCATGTT 60.421 50.000 0.00 0.00 0.00 2.71
2363 2484 3.273434 CGTCCATCATCCTGTCATGTTT 58.727 45.455 0.00 0.00 0.00 2.83
2365 2486 4.012374 GTCCATCATCCTGTCATGTTTGT 58.988 43.478 0.00 0.00 0.00 2.83
2366 2487 4.460382 GTCCATCATCCTGTCATGTTTGTT 59.540 41.667 0.00 0.00 0.00 2.83
2367 2488 5.047802 GTCCATCATCCTGTCATGTTTGTTT 60.048 40.000 0.00 0.00 0.00 2.83
2368 2489 5.047872 TCCATCATCCTGTCATGTTTGTTTG 60.048 40.000 0.00 0.00 0.00 2.93
2387 2508 0.798776 GTGAATTGTGACCGCTCCTG 59.201 55.000 0.00 0.00 0.00 3.86
2388 2509 0.955428 TGAATTGTGACCGCTCCTGC 60.955 55.000 0.00 0.00 0.00 4.85
2389 2510 0.674895 GAATTGTGACCGCTCCTGCT 60.675 55.000 0.00 0.00 36.97 4.24
2390 2511 0.674895 AATTGTGACCGCTCCTGCTC 60.675 55.000 0.00 0.00 36.97 4.26
2391 2512 2.527951 ATTGTGACCGCTCCTGCTCC 62.528 60.000 0.00 0.00 36.97 4.70
2392 2513 3.386237 GTGACCGCTCCTGCTCCT 61.386 66.667 0.00 0.00 36.97 3.69
2393 2514 2.604686 TGACCGCTCCTGCTCCTT 60.605 61.111 0.00 0.00 36.97 3.36
2409 2531 1.000163 TCCTTGCAACGTCTCTGTCTC 60.000 52.381 0.00 0.00 0.00 3.36
2421 2543 3.249080 GTCTCTGTCTCGCATCCTAGTAC 59.751 52.174 0.00 0.00 0.00 2.73
2439 2561 4.557705 AGTACCCTGCCACTCATACTTAT 58.442 43.478 0.00 0.00 0.00 1.73
2442 2564 5.291905 ACCCTGCCACTCATACTTATTAC 57.708 43.478 0.00 0.00 0.00 1.89
2443 2565 4.102681 ACCCTGCCACTCATACTTATTACC 59.897 45.833 0.00 0.00 0.00 2.85
2445 2567 5.221925 CCCTGCCACTCATACTTATTACCAT 60.222 44.000 0.00 0.00 0.00 3.55
2446 2568 6.013725 CCCTGCCACTCATACTTATTACCATA 60.014 42.308 0.00 0.00 0.00 2.74
2448 2570 7.766278 CCTGCCACTCATACTTATTACCATATC 59.234 40.741 0.00 0.00 0.00 1.63
2449 2571 8.201242 TGCCACTCATACTTATTACCATATCA 57.799 34.615 0.00 0.00 0.00 2.15
2477 2603 6.259608 CCACTACCATTGTTTGCAAAATTCAA 59.740 34.615 14.67 14.25 38.21 2.69
2495 2630 4.404691 GCACCCAGCAGCTACTTT 57.595 55.556 0.00 0.00 44.79 2.66
2496 2631 2.175236 GCACCCAGCAGCTACTTTC 58.825 57.895 0.00 0.00 44.79 2.62
2502 2638 3.055747 ACCCAGCAGCTACTTTCTAGAAC 60.056 47.826 4.18 0.00 0.00 3.01
2518 2654 5.721232 TCTAGAACGGAATCAGACCTTTTC 58.279 41.667 0.00 0.00 0.00 2.29
2523 2659 2.417933 CGGAATCAGACCTTTTCAGCAG 59.582 50.000 0.00 0.00 0.00 4.24
2566 2702 2.784356 TTTTGCGGCTGCTGTTGCT 61.784 52.632 20.27 0.00 43.34 3.91
2581 2722 1.670811 GTTGCTGCTACTGTGTTGTGT 59.329 47.619 6.98 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.900194 TCATTCCTTGGATTTTACCTAGAGG 58.100 40.000 0.00 0.00 42.17 3.69
107 112 3.119602 GGGAAACGGCAATTACCTCTTTC 60.120 47.826 6.32 6.32 0.00 2.62
108 113 2.823747 GGGAAACGGCAATTACCTCTTT 59.176 45.455 0.00 0.00 0.00 2.52
109 114 2.443416 GGGAAACGGCAATTACCTCTT 58.557 47.619 0.00 0.00 0.00 2.85
110 115 1.677820 CGGGAAACGGCAATTACCTCT 60.678 52.381 0.00 0.00 39.42 3.69
157 163 4.130118 GGGTAATGACTAATGAGGTGCTG 58.870 47.826 0.00 0.00 0.00 4.41
158 164 3.136626 GGGGTAATGACTAATGAGGTGCT 59.863 47.826 0.00 0.00 0.00 4.40
159 165 3.118038 TGGGGTAATGACTAATGAGGTGC 60.118 47.826 0.00 0.00 0.00 5.01
160 166 4.451900 GTGGGGTAATGACTAATGAGGTG 58.548 47.826 0.00 0.00 0.00 4.00
161 167 3.458487 GGTGGGGTAATGACTAATGAGGT 59.542 47.826 0.00 0.00 0.00 3.85
162 168 3.181443 GGGTGGGGTAATGACTAATGAGG 60.181 52.174 0.00 0.00 0.00 3.86
163 169 3.494398 CGGGTGGGGTAATGACTAATGAG 60.494 52.174 0.00 0.00 0.00 2.90
164 170 2.436542 CGGGTGGGGTAATGACTAATGA 59.563 50.000 0.00 0.00 0.00 2.57
165 171 2.846193 CGGGTGGGGTAATGACTAATG 58.154 52.381 0.00 0.00 0.00 1.90
166 172 1.142262 GCGGGTGGGGTAATGACTAAT 59.858 52.381 0.00 0.00 0.00 1.73
167 173 0.542805 GCGGGTGGGGTAATGACTAA 59.457 55.000 0.00 0.00 0.00 2.24
168 174 0.618107 TGCGGGTGGGGTAATGACTA 60.618 55.000 0.00 0.00 0.00 2.59
169 175 1.921346 TGCGGGTGGGGTAATGACT 60.921 57.895 0.00 0.00 0.00 3.41
170 176 1.747745 GTGCGGGTGGGGTAATGAC 60.748 63.158 0.00 0.00 0.00 3.06
171 177 2.191786 CTGTGCGGGTGGGGTAATGA 62.192 60.000 0.00 0.00 0.00 2.57
172 178 1.748879 CTGTGCGGGTGGGGTAATG 60.749 63.158 0.00 0.00 0.00 1.90
173 179 1.493854 TTCTGTGCGGGTGGGGTAAT 61.494 55.000 0.00 0.00 0.00 1.89
185 191 0.242286 TCAGAGAGCGTCTTCTGTGC 59.758 55.000 10.49 0.00 38.12 4.57
193 199 1.153862 CCAGCTGTCAGAGAGCGTC 60.154 63.158 13.81 0.00 41.61 5.19
194 200 2.644212 CCCAGCTGTCAGAGAGCGT 61.644 63.158 13.81 0.22 41.61 5.07
196 202 2.125188 GCCCAGCTGTCAGAGAGC 60.125 66.667 11.73 11.73 36.65 4.09
200 206 2.203832 TGGAGCCCAGCTGTCAGA 60.204 61.111 13.81 0.00 39.88 3.27
256 262 3.704566 CACTGGACCCTACAGCACTAATA 59.295 47.826 0.00 0.00 39.55 0.98
259 265 1.203137 ACACTGGACCCTACAGCACTA 60.203 52.381 0.00 0.00 39.55 2.74
416 422 2.689034 GTGGTGGAGAGGGAGGGG 60.689 72.222 0.00 0.00 0.00 4.79
417 423 2.689034 GGTGGTGGAGAGGGAGGG 60.689 72.222 0.00 0.00 0.00 4.30
418 424 1.307343 ATGGTGGTGGAGAGGGAGG 60.307 63.158 0.00 0.00 0.00 4.30
419 425 0.618680 TCATGGTGGTGGAGAGGGAG 60.619 60.000 0.00 0.00 0.00 4.30
420 426 0.909610 GTCATGGTGGTGGAGAGGGA 60.910 60.000 0.00 0.00 0.00 4.20
421 427 1.604378 GTCATGGTGGTGGAGAGGG 59.396 63.158 0.00 0.00 0.00 4.30
422 428 1.219124 CGTCATGGTGGTGGAGAGG 59.781 63.158 0.00 0.00 0.00 3.69
423 429 0.108615 GTCGTCATGGTGGTGGAGAG 60.109 60.000 0.00 0.00 0.00 3.20
424 430 1.873270 CGTCGTCATGGTGGTGGAGA 61.873 60.000 0.00 0.00 0.00 3.71
425 431 1.446099 CGTCGTCATGGTGGTGGAG 60.446 63.158 0.00 0.00 0.00 3.86
426 432 1.873270 CTCGTCGTCATGGTGGTGGA 61.873 60.000 0.00 0.00 0.00 4.02
427 433 1.446099 CTCGTCGTCATGGTGGTGG 60.446 63.158 0.00 0.00 0.00 4.61
428 434 1.446099 CCTCGTCGTCATGGTGGTG 60.446 63.158 0.00 0.00 0.00 4.17
429 435 2.970639 CCTCGTCGTCATGGTGGT 59.029 61.111 0.00 0.00 0.00 4.16
430 436 2.509336 GCCTCGTCGTCATGGTGG 60.509 66.667 0.00 0.00 0.00 4.61
431 437 2.509336 GGCCTCGTCGTCATGGTG 60.509 66.667 0.00 0.00 0.00 4.17
432 438 3.771160 GGGCCTCGTCGTCATGGT 61.771 66.667 0.84 0.00 0.00 3.55
433 439 4.873129 CGGGCCTCGTCGTCATGG 62.873 72.222 0.84 0.00 0.00 3.66
434 440 3.822192 TCGGGCCTCGTCGTCATG 61.822 66.667 0.84 0.00 40.32 3.07
435 441 3.823330 GTCGGGCCTCGTCGTCAT 61.823 66.667 0.84 0.00 40.32 3.06
1610 1662 0.598065 CTGCCTAAAACCCTGCACAC 59.402 55.000 0.00 0.00 0.00 3.82
1641 1693 3.116531 CGCCGACGGGGAAGAAAC 61.117 66.667 25.56 0.00 37.91 2.78
1669 1721 3.321968 AGAAATTGACTGACCCCAAAAGC 59.678 43.478 0.00 0.00 0.00 3.51
1747 1808 0.973632 ATTGACTGACGGTACCAGCA 59.026 50.000 13.54 8.10 35.14 4.41
1748 1809 2.000447 GAATTGACTGACGGTACCAGC 59.000 52.381 13.54 3.18 35.14 4.85
1749 1810 3.254060 CTGAATTGACTGACGGTACCAG 58.746 50.000 13.54 7.45 37.64 4.00
1750 1811 2.631062 ACTGAATTGACTGACGGTACCA 59.369 45.455 13.54 0.00 0.00 3.25
1751 1812 2.993899 CACTGAATTGACTGACGGTACC 59.006 50.000 0.16 0.16 0.00 3.34
1752 1813 2.412089 GCACTGAATTGACTGACGGTAC 59.588 50.000 0.00 0.00 0.00 3.34
1753 1814 2.683968 GCACTGAATTGACTGACGGTA 58.316 47.619 0.00 0.00 0.00 4.02
1754 1815 1.512926 GCACTGAATTGACTGACGGT 58.487 50.000 0.00 0.00 0.00 4.83
1755 1816 0.439985 CGCACTGAATTGACTGACGG 59.560 55.000 0.00 0.00 0.00 4.79
1802 1866 5.574970 AACTGAACTGGGAAGAAGAGAAT 57.425 39.130 0.00 0.00 0.00 2.40
1804 1868 4.528596 CCTAACTGAACTGGGAAGAAGAGA 59.471 45.833 0.00 0.00 0.00 3.10
1805 1869 4.284746 ACCTAACTGAACTGGGAAGAAGAG 59.715 45.833 0.00 0.00 0.00 2.85
1807 1871 4.040461 TGACCTAACTGAACTGGGAAGAAG 59.960 45.833 0.00 0.00 0.00 2.85
1808 1872 3.971305 TGACCTAACTGAACTGGGAAGAA 59.029 43.478 0.00 0.00 0.00 2.52
1812 1876 2.257207 CCTGACCTAACTGAACTGGGA 58.743 52.381 0.00 0.00 0.00 4.37
1813 1877 1.978580 ACCTGACCTAACTGAACTGGG 59.021 52.381 0.00 0.00 0.00 4.45
1814 1878 2.632996 TGACCTGACCTAACTGAACTGG 59.367 50.000 0.00 0.00 0.00 4.00
1815 1879 3.306364 CCTGACCTGACCTAACTGAACTG 60.306 52.174 0.00 0.00 0.00 3.16
1816 1880 2.900546 CCTGACCTGACCTAACTGAACT 59.099 50.000 0.00 0.00 0.00 3.01
1817 1881 2.633481 ACCTGACCTGACCTAACTGAAC 59.367 50.000 0.00 0.00 0.00 3.18
1818 1882 2.897969 GACCTGACCTGACCTAACTGAA 59.102 50.000 0.00 0.00 0.00 3.02
1819 1883 2.158370 TGACCTGACCTGACCTAACTGA 60.158 50.000 0.00 0.00 0.00 3.41
1820 1884 2.248248 TGACCTGACCTGACCTAACTG 58.752 52.381 0.00 0.00 0.00 3.16
1821 1885 2.696526 TGACCTGACCTGACCTAACT 57.303 50.000 0.00 0.00 0.00 2.24
1848 1928 3.267483 TGCTACCCGCAGAAATTTAGAC 58.733 45.455 0.00 0.00 45.47 2.59
1949 2029 0.829990 TGCACTCACTGACCAACTGA 59.170 50.000 0.00 0.00 0.00 3.41
1954 2034 1.337384 ACCACTGCACTCACTGACCA 61.337 55.000 0.00 0.00 0.00 4.02
1955 2035 0.882042 CACCACTGCACTCACTGACC 60.882 60.000 0.00 0.00 0.00 4.02
2059 2146 2.259618 CATCTTGCTGCAGAATTGTGC 58.740 47.619 20.43 20.04 44.27 4.57
2072 2178 2.502295 CTTGCCTATCCTCCATCTTGC 58.498 52.381 0.00 0.00 0.00 4.01
2146 2253 9.586435 ACAAAAGAAACGAAAAATCTCAAGAAT 57.414 25.926 0.00 0.00 0.00 2.40
2152 2259 8.737648 CAGAGAACAAAAGAAACGAAAAATCTC 58.262 33.333 0.00 0.00 0.00 2.75
2236 2346 3.829601 AGATACATACAGGAGCTGGCTAC 59.170 47.826 0.00 0.00 35.51 3.58
2334 2455 0.604780 GGATGATGGACGGGCAGATG 60.605 60.000 0.00 0.00 0.00 2.90
2337 2458 1.227764 CAGGATGATGGACGGGCAG 60.228 63.158 0.00 0.00 39.69 4.85
2343 2464 4.012374 ACAAACATGACAGGATGATGGAC 58.988 43.478 0.00 0.00 39.69 4.02
2347 2468 5.535783 TCACAAACAAACATGACAGGATGAT 59.464 36.000 0.00 0.00 39.69 2.45
2348 2469 4.886489 TCACAAACAAACATGACAGGATGA 59.114 37.500 0.00 0.00 39.69 2.92
2349 2470 5.185668 TCACAAACAAACATGACAGGATG 57.814 39.130 0.00 0.00 46.00 3.51
2350 2471 5.850557 TTCACAAACAAACATGACAGGAT 57.149 34.783 0.00 0.00 0.00 3.24
2358 2479 4.803088 CGGTCACAATTCACAAACAAACAT 59.197 37.500 0.00 0.00 0.00 2.71
2359 2480 4.169508 CGGTCACAATTCACAAACAAACA 58.830 39.130 0.00 0.00 0.00 2.83
2360 2481 3.000177 GCGGTCACAATTCACAAACAAAC 60.000 43.478 0.00 0.00 0.00 2.93
2361 2482 3.119316 AGCGGTCACAATTCACAAACAAA 60.119 39.130 0.00 0.00 0.00 2.83
2362 2483 2.425312 AGCGGTCACAATTCACAAACAA 59.575 40.909 0.00 0.00 0.00 2.83
2363 2484 2.020720 AGCGGTCACAATTCACAAACA 58.979 42.857 0.00 0.00 0.00 2.83
2365 2486 1.606668 GGAGCGGTCACAATTCACAAA 59.393 47.619 17.59 0.00 0.00 2.83
2366 2487 1.202758 AGGAGCGGTCACAATTCACAA 60.203 47.619 17.59 0.00 0.00 3.33
2367 2488 0.396435 AGGAGCGGTCACAATTCACA 59.604 50.000 17.59 0.00 0.00 3.58
2368 2489 0.798776 CAGGAGCGGTCACAATTCAC 59.201 55.000 17.59 0.00 0.00 3.18
2387 2508 0.601311 ACAGAGACGTTGCAAGGAGC 60.601 55.000 24.88 15.49 45.96 4.70
2388 2509 1.000283 AGACAGAGACGTTGCAAGGAG 60.000 52.381 24.88 10.26 0.00 3.69
2389 2510 1.000163 GAGACAGAGACGTTGCAAGGA 60.000 52.381 24.88 0.00 0.00 3.36
2390 2511 1.423395 GAGACAGAGACGTTGCAAGG 58.577 55.000 17.21 17.21 0.00 3.61
2391 2512 1.056103 CGAGACAGAGACGTTGCAAG 58.944 55.000 0.00 0.00 0.00 4.01
2392 2513 0.939577 GCGAGACAGAGACGTTGCAA 60.940 55.000 0.00 0.00 0.00 4.08
2393 2514 1.371758 GCGAGACAGAGACGTTGCA 60.372 57.895 0.00 0.00 0.00 4.08
2396 2517 0.171455 GGATGCGAGACAGAGACGTT 59.829 55.000 0.00 0.00 0.00 3.99
2409 2531 1.367840 GGCAGGGTACTAGGATGCG 59.632 63.158 0.00 0.00 37.76 4.73
2421 2543 4.102524 TGGTAATAAGTATGAGTGGCAGGG 59.897 45.833 0.00 0.00 0.00 4.45
2439 2561 8.270137 ACAATGGTAGTGGTATGATATGGTAA 57.730 34.615 0.00 0.00 0.00 2.85
2442 2564 7.522073 GCAAACAATGGTAGTGGTATGATATGG 60.522 40.741 0.00 0.00 0.00 2.74
2443 2565 7.013178 TGCAAACAATGGTAGTGGTATGATATG 59.987 37.037 0.00 0.00 0.00 1.78
2445 2567 6.418946 TGCAAACAATGGTAGTGGTATGATA 58.581 36.000 0.00 0.00 0.00 2.15
2446 2568 5.260424 TGCAAACAATGGTAGTGGTATGAT 58.740 37.500 0.00 0.00 0.00 2.45
2448 2570 5.384063 TTGCAAACAATGGTAGTGGTATG 57.616 39.130 0.00 0.00 0.00 2.39
2449 2571 6.412362 TTTTGCAAACAATGGTAGTGGTAT 57.588 33.333 12.39 0.00 35.21 2.73
2451 2573 4.744795 TTTTGCAAACAATGGTAGTGGT 57.255 36.364 12.39 0.00 35.21 4.16
2452 2574 5.757320 TGAATTTTGCAAACAATGGTAGTGG 59.243 36.000 12.39 0.00 35.21 4.00
2455 2577 6.018098 TGCTTGAATTTTGCAAACAATGGTAG 60.018 34.615 12.39 5.14 35.21 3.18
2477 2603 0.322008 GAAAGTAGCTGCTGGGTGCT 60.322 55.000 13.43 0.00 43.37 4.40
2491 2626 4.773149 AGGTCTGATTCCGTTCTAGAAAGT 59.227 41.667 15.85 0.00 0.00 2.66
2492 2627 5.331876 AGGTCTGATTCCGTTCTAGAAAG 57.668 43.478 6.78 9.21 0.00 2.62
2495 2630 5.245301 TGAAAAGGTCTGATTCCGTTCTAGA 59.755 40.000 0.00 0.00 0.00 2.43
2496 2631 5.479306 TGAAAAGGTCTGATTCCGTTCTAG 58.521 41.667 0.00 0.00 0.00 2.43
2502 2638 2.417933 CTGCTGAAAAGGTCTGATTCCG 59.582 50.000 0.00 0.00 0.00 4.30
2518 2654 0.734309 TGCGATGCAATTACCTGCTG 59.266 50.000 0.00 0.00 43.07 4.41
2566 2702 1.743996 TGCAACACAACACAGTAGCA 58.256 45.000 0.00 0.00 0.00 3.49
2568 2704 3.620761 CACATGCAACACAACACAGTAG 58.379 45.455 0.00 0.00 0.00 2.57
2569 2705 2.223456 GCACATGCAACACAACACAGTA 60.223 45.455 0.00 0.00 41.59 2.74


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

AutoCloner maintained by Alex Coulton.