Multiple sequence alignment - TraesCS1D01G250100

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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 TraesCS1D01G250100 chr1D 100.000 2694 0 0 1 2694 342488578 342491271 0.000000e+00 4975
1 TraesCS1D01G250100 chr1B 90.046 1738 112 32 448 2147 458726041 458727755 0.000000e+00 2194
2 TraesCS1D01G250100 chr1B 94.167 480 28 0 2215 2694 458727764 458728243 0.000000e+00 732
3 TraesCS1D01G250100 chr1B 84.086 421 51 8 10 424 458684789 458685199 2.510000e-105 392
4 TraesCS1D01G250100 chr1A 88.697 1159 80 24 1 1139 442153974 442155101 0.000000e+00 1367
5 TraesCS1D01G250100 chr1A 92.137 903 47 12 1211 2100 442155205 442156096 0.000000e+00 1253
6 TraesCS1D01G250100 chr1A 96.258 481 16 2 2214 2694 442156208 442156686 0.000000e+00 787


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 TraesCS1D01G250100 chr1D 342488578 342491271 2693 False 4975.000000 4975 100.0000 1 2694 1 chr1D.!!$F1 2693
1 TraesCS1D01G250100 chr1B 458726041 458728243 2202 False 1463.000000 2194 92.1065 448 2694 2 chr1B.!!$F2 2246
2 TraesCS1D01G250100 chr1A 442153974 442156686 2712 False 1135.666667 1367 92.3640 1 2694 3 chr1A.!!$F1 2693

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
213 218 0.390860 ATGCAGGATCGGTACAGAGC 59.609 55.0 2.39 2.39 0.00 4.09 F
945 966 0.462581 CATAGCAAAGGGAGCGAGCA 60.463 55.0 0.00 0.00 37.01 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1519 1583 0.037303 CACACAAGCACAGGAGGGAT 59.963 55.0 0.00 0.0 0.0 3.85 R
2128 2270 0.761187 AGAGCTGCTTGTGTTCCTCA 59.239 50.0 2.53 0.0 0.0 3.86 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
32 33 6.150332 TGTAATGGATCCTAGGAATGGAGAA 58.850 40.000 17.30 0.00 36.99 2.87
41 42 4.101741 CCTAGGAATGGAGAAGATCGGTTT 59.898 45.833 1.05 0.00 0.00 3.27
42 43 3.878778 AGGAATGGAGAAGATCGGTTTG 58.121 45.455 0.00 0.00 0.00 2.93
53 54 2.500504 AGATCGGTTTGTAGGGTCTTCC 59.499 50.000 0.00 0.00 0.00 3.46
55 56 1.897802 TCGGTTTGTAGGGTCTTCCTC 59.102 52.381 0.00 0.00 44.06 3.71
56 57 1.066358 CGGTTTGTAGGGTCTTCCTCC 60.066 57.143 0.00 0.00 44.06 4.30
57 58 1.982958 GGTTTGTAGGGTCTTCCTCCA 59.017 52.381 0.00 0.00 44.06 3.86
58 59 2.576648 GGTTTGTAGGGTCTTCCTCCAT 59.423 50.000 0.00 0.00 44.06 3.41
59 60 3.370633 GGTTTGTAGGGTCTTCCTCCATC 60.371 52.174 0.00 0.00 44.06 3.51
70 71 3.450817 TCTTCCTCCATCGTTATCAGCAA 59.549 43.478 0.00 0.00 0.00 3.91
109 110 1.202592 TCTCAAAGTTGTAGCGTGCCA 60.203 47.619 0.00 0.00 0.00 4.92
119 120 0.804544 TAGCGTGCCACTATTGCGTC 60.805 55.000 0.00 0.00 0.00 5.19
120 121 2.100631 GCGTGCCACTATTGCGTCT 61.101 57.895 0.00 0.00 0.00 4.18
121 122 1.709760 CGTGCCACTATTGCGTCTG 59.290 57.895 0.00 0.00 0.00 3.51
122 123 0.735978 CGTGCCACTATTGCGTCTGA 60.736 55.000 0.00 0.00 0.00 3.27
123 124 1.656652 GTGCCACTATTGCGTCTGAT 58.343 50.000 0.00 0.00 0.00 2.90
124 125 1.594862 GTGCCACTATTGCGTCTGATC 59.405 52.381 0.00 0.00 0.00 2.92
133 134 6.920210 CACTATTGCGTCTGATCTTGATCTTA 59.080 38.462 11.31 0.00 0.00 2.10
140 141 3.447229 TCTGATCTTGATCTTACACCGCA 59.553 43.478 11.31 0.00 0.00 5.69
148 149 2.922740 TCTTACACCGCAGAACCTTT 57.077 45.000 0.00 0.00 0.00 3.11
188 193 4.924305 AGCAACTTGTGATTGACATTGT 57.076 36.364 0.00 0.00 33.40 2.71
195 200 9.414295 CAACTTGTGATTGACATTGTATTTGAT 57.586 29.630 0.00 0.00 33.40 2.57
196 201 8.975410 ACTTGTGATTGACATTGTATTTGATG 57.025 30.769 0.00 0.00 33.40 3.07
198 203 6.921914 TGTGATTGACATTGTATTTGATGCA 58.078 32.000 0.00 0.00 0.00 3.96
201 206 6.377712 TGATTGACATTGTATTTGATGCAGGA 59.622 34.615 0.00 0.00 0.00 3.86
202 207 6.778834 TTGACATTGTATTTGATGCAGGAT 57.221 33.333 0.00 0.00 0.00 3.24
203 208 6.381481 TGACATTGTATTTGATGCAGGATC 57.619 37.500 0.00 0.00 0.00 3.36
204 209 5.007921 TGACATTGTATTTGATGCAGGATCG 59.992 40.000 0.00 0.00 33.17 3.69
206 211 3.558931 TGTATTTGATGCAGGATCGGT 57.441 42.857 0.00 0.00 33.17 4.69
207 212 4.681074 TGTATTTGATGCAGGATCGGTA 57.319 40.909 0.00 0.00 33.17 4.02
208 213 4.377021 TGTATTTGATGCAGGATCGGTAC 58.623 43.478 0.00 1.74 33.17 3.34
209 214 3.558931 ATTTGATGCAGGATCGGTACA 57.441 42.857 0.00 0.00 33.17 2.90
210 215 2.602257 TTGATGCAGGATCGGTACAG 57.398 50.000 0.00 0.00 33.17 2.74
212 217 1.683385 TGATGCAGGATCGGTACAGAG 59.317 52.381 1.40 0.00 33.17 3.35
213 218 0.390860 ATGCAGGATCGGTACAGAGC 59.609 55.000 2.39 2.39 0.00 4.09
214 219 0.684479 TGCAGGATCGGTACAGAGCT 60.684 55.000 11.00 0.00 0.00 4.09
215 220 1.319541 GCAGGATCGGTACAGAGCTA 58.680 55.000 11.00 0.00 0.00 3.32
283 288 1.767289 TCGTCTTGAGCGTCAAACTC 58.233 50.000 2.82 0.00 35.73 3.01
284 289 1.066454 TCGTCTTGAGCGTCAAACTCA 59.934 47.619 0.00 0.00 42.30 3.41
318 324 6.365970 TCTAGCCAAGTTCTCTCATTCTTT 57.634 37.500 0.00 0.00 0.00 2.52
330 336 6.565234 TCTCTCATTCTTTAGATCGTGGAAC 58.435 40.000 0.00 0.00 0.00 3.62
366 372 1.382522 CAACCCCGTGATCATCTTGG 58.617 55.000 0.00 0.15 0.00 3.61
373 379 3.815401 CCCGTGATCATCTTGGTATTTCC 59.185 47.826 0.00 0.00 0.00 3.13
378 384 6.073385 CGTGATCATCTTGGTATTTCCATCTG 60.073 42.308 0.00 0.00 46.60 2.90
408 414 3.949754 CCTGATCAATAAAGCTTGGCTGA 59.050 43.478 0.00 3.27 39.62 4.26
409 415 4.583489 CCTGATCAATAAAGCTTGGCTGAT 59.417 41.667 14.15 14.15 39.62 2.90
410 416 5.068723 CCTGATCAATAAAGCTTGGCTGATT 59.931 40.000 14.98 3.12 39.62 2.57
503 512 6.073819 GGTCAATTGCCAAGTTGTCATAAAAC 60.074 38.462 12.35 0.00 0.00 2.43
506 515 8.417106 TCAATTGCCAAGTTGTCATAAAACTTA 58.583 29.630 0.00 0.00 44.11 2.24
518 527 9.575868 TTGTCATAAAACTTATTGTTCCACCTA 57.424 29.630 0.00 0.00 38.03 3.08
532 541 7.286667 TGTTCCACCTAAATAATCCCCTTAA 57.713 36.000 0.00 0.00 0.00 1.85
537 546 8.008332 TCCACCTAAATAATCCCCTTAATTTCC 58.992 37.037 0.00 0.00 0.00 3.13
541 550 9.090103 CCTAAATAATCCCCTTAATTTCCTTCC 57.910 37.037 0.00 0.00 0.00 3.46
542 551 7.597288 AAATAATCCCCTTAATTTCCTTCCG 57.403 36.000 0.00 0.00 0.00 4.30
554 563 9.129209 CTTAATTTCCTTCCGAAAAGATTGTTC 57.871 33.333 0.00 0.00 43.61 3.18
697 712 2.999185 AGAAAAGAATTCCTGGCCCA 57.001 45.000 0.00 0.00 0.00 5.36
731 751 1.002274 AGGAGATCCGTCCCTTGCT 59.998 57.895 0.00 0.00 42.08 3.91
732 752 1.045911 AGGAGATCCGTCCCTTGCTC 61.046 60.000 0.00 0.00 42.08 4.26
761 781 2.037136 CAGCAGACCCCGAGCAAAG 61.037 63.158 0.00 0.00 0.00 2.77
762 782 2.747855 GCAGACCCCGAGCAAAGG 60.748 66.667 0.00 0.00 0.00 3.11
763 783 2.747855 CAGACCCCGAGCAAAGGC 60.748 66.667 0.00 0.00 41.61 4.35
764 784 3.249189 AGACCCCGAGCAAAGGCA 61.249 61.111 0.00 0.00 44.61 4.75
765 785 2.044946 GACCCCGAGCAAAGGCAT 60.045 61.111 0.00 0.00 44.61 4.40
766 786 1.223487 GACCCCGAGCAAAGGCATA 59.777 57.895 0.00 0.00 44.61 3.14
767 787 1.077716 ACCCCGAGCAAAGGCATAC 60.078 57.895 0.00 0.00 44.61 2.39
768 788 1.823899 CCCCGAGCAAAGGCATACC 60.824 63.158 0.00 0.00 44.61 2.73
852 872 2.742372 CGCCGACCTTTCCACCAG 60.742 66.667 0.00 0.00 0.00 4.00
866 887 1.402968 CCACCAGAGGAATGCATTTCG 59.597 52.381 14.33 0.90 34.98 3.46
873 894 1.873572 GAATGCATTTCGGTGGCGC 60.874 57.895 14.33 0.00 0.00 6.53
903 924 4.429212 CCGATCACCACGCCGTGA 62.429 66.667 20.57 7.53 46.36 4.35
910 931 2.890474 CCACGCCGTGATAGCACC 60.890 66.667 20.57 0.00 42.09 5.01
945 966 0.462581 CATAGCAAAGGGAGCGAGCA 60.463 55.000 0.00 0.00 37.01 4.26
976 997 3.036084 CGTACGGCGCATCCATCC 61.036 66.667 10.83 0.00 34.01 3.51
1135 1164 2.125673 CCCACTCACGTAAGCCCG 60.126 66.667 0.00 0.00 45.62 6.13
1289 1353 3.234630 CTGGCGACGGGGTTCTTCA 62.235 63.158 0.00 0.00 0.00 3.02
1384 1448 3.274586 CCCGCCAGCATGATGTCG 61.275 66.667 7.52 7.52 39.69 4.35
1519 1583 7.706607 CAGTAAATCAATGGAGAATCTGTCGTA 59.293 37.037 0.00 0.00 33.73 3.43
1526 1592 2.559231 GGAGAATCTGTCGTATCCCTCC 59.441 54.545 0.00 0.00 33.73 4.30
1530 1596 1.763968 TCTGTCGTATCCCTCCTGTG 58.236 55.000 0.00 0.00 0.00 3.66
1538 1604 0.037303 ATCCCTCCTGTGCTTGTGTG 59.963 55.000 0.00 0.00 0.00 3.82
1675 1743 4.101448 GAGCAGACGCCCATGGGT 62.101 66.667 31.58 13.70 39.83 4.51
1745 1816 3.758554 GTGTGGTCTATTTGAAGGTGCAT 59.241 43.478 0.00 0.00 0.00 3.96
1753 1824 6.261603 GTCTATTTGAAGGTGCATCATCATCA 59.738 38.462 5.61 0.00 0.00 3.07
1755 1826 5.509716 TTTGAAGGTGCATCATCATCATC 57.490 39.130 5.61 0.00 0.00 2.92
1757 1828 4.725490 TGAAGGTGCATCATCATCATCAT 58.275 39.130 0.00 0.00 0.00 2.45
1758 1829 4.760204 TGAAGGTGCATCATCATCATCATC 59.240 41.667 0.00 0.00 0.00 2.92
1759 1830 4.642466 AGGTGCATCATCATCATCATCT 57.358 40.909 0.00 0.00 0.00 2.90
1760 1831 4.986783 AGGTGCATCATCATCATCATCTT 58.013 39.130 0.00 0.00 0.00 2.40
1761 1832 4.762251 AGGTGCATCATCATCATCATCTTG 59.238 41.667 0.00 0.00 0.00 3.02
1762 1833 4.082733 GGTGCATCATCATCATCATCTTGG 60.083 45.833 0.00 0.00 0.00 3.61
1763 1834 3.506067 TGCATCATCATCATCATCTTGGC 59.494 43.478 0.00 0.00 0.00 4.52
1764 1835 3.506067 GCATCATCATCATCATCTTGGCA 59.494 43.478 0.00 0.00 0.00 4.92
1765 1836 4.022329 GCATCATCATCATCATCTTGGCAA 60.022 41.667 0.00 0.00 0.00 4.52
1766 1837 5.703876 CATCATCATCATCATCTTGGCAAG 58.296 41.667 21.17 21.17 0.00 4.01
1767 1838 4.142038 TCATCATCATCATCTTGGCAAGG 58.858 43.478 25.92 11.90 0.00 3.61
1770 1841 3.457012 TCATCATCATCTTGGCAAGGAGA 59.543 43.478 25.92 22.31 0.00 3.71
1880 1969 1.313091 GGTGAAATTGTCTCCGGCCC 61.313 60.000 0.00 0.00 30.44 5.80
1978 2071 9.515020 CAAAATCTGGCAAATATATAACGTTGT 57.485 29.630 11.99 6.97 0.00 3.32
1998 2091 3.808726 TGTTCATGCAAAATCTGGCAAAC 59.191 39.130 0.00 0.00 44.20 2.93
2006 2099 6.753180 TGCAAAATCTGGCAAACATTACTAA 58.247 32.000 0.00 0.00 37.03 2.24
2010 2103 9.643693 CAAAATCTGGCAAACATTACTAATTCT 57.356 29.630 0.00 0.00 0.00 2.40
2110 2252 3.893720 AGCTTTCACAAATTCAGAAGCG 58.106 40.909 0.00 0.00 0.00 4.68
2149 2291 0.471617 AGGAACACAAGCAGCTCTGT 59.528 50.000 0.00 0.00 0.00 3.41
2174 2316 5.679734 TTTTAGACAAAGAAGCAGCTCTG 57.320 39.130 0.00 0.00 0.00 3.35
2184 2326 2.559840 CAGCTCTGCTTGCGTTGG 59.440 61.111 0.00 0.00 36.40 3.77
2185 2327 1.962822 CAGCTCTGCTTGCGTTGGA 60.963 57.895 0.00 0.00 36.40 3.53
2186 2328 1.963338 AGCTCTGCTTGCGTTGGAC 60.963 57.895 0.00 0.00 33.89 4.02
2187 2329 2.253758 GCTCTGCTTGCGTTGGACA 61.254 57.895 0.00 0.00 0.00 4.02
2188 2330 1.571460 CTCTGCTTGCGTTGGACAC 59.429 57.895 0.00 0.00 0.00 3.67
2189 2331 1.845809 CTCTGCTTGCGTTGGACACC 61.846 60.000 0.00 0.00 0.00 4.16
2190 2332 2.904866 TGCTTGCGTTGGACACCC 60.905 61.111 0.00 0.00 0.00 4.61
2191 2333 2.904866 GCTTGCGTTGGACACCCA 60.905 61.111 0.00 0.00 41.64 4.51
2192 2334 3.030652 CTTGCGTTGGACACCCAC 58.969 61.111 0.00 0.00 43.41 4.61
2193 2335 2.892334 CTTGCGTTGGACACCCACG 61.892 63.158 9.49 9.49 43.41 4.94
2194 2336 3.387225 TTGCGTTGGACACCCACGA 62.387 57.895 16.38 1.83 43.41 4.35
2195 2337 3.343421 GCGTTGGACACCCACGAC 61.343 66.667 16.38 6.02 43.41 4.34
2196 2338 2.663852 CGTTGGACACCCACGACC 60.664 66.667 8.38 0.00 43.41 4.79
2197 2339 2.506962 GTTGGACACCCACGACCA 59.493 61.111 0.00 0.00 43.41 4.02
2198 2340 1.890510 GTTGGACACCCACGACCAC 60.891 63.158 0.00 0.00 43.41 4.16
2199 2341 3.448533 TTGGACACCCACGACCACG 62.449 63.158 0.00 0.00 43.41 4.94
2200 2342 3.608662 GGACACCCACGACCACGA 61.609 66.667 0.00 0.00 42.66 4.35
2201 2343 2.049433 GACACCCACGACCACGAG 60.049 66.667 0.00 0.00 42.66 4.18
2202 2344 2.836360 ACACCCACGACCACGAGT 60.836 61.111 0.00 0.00 42.66 4.18
2203 2345 2.359570 GACACCCACGACCACGAGTT 62.360 60.000 0.00 0.00 42.66 3.01
2204 2346 1.663702 CACCCACGACCACGAGTTC 60.664 63.158 0.00 0.00 42.66 3.01
2205 2347 2.430244 CCCACGACCACGAGTTCG 60.430 66.667 0.00 0.00 46.33 3.95
2206 2348 3.103911 CCACGACCACGAGTTCGC 61.104 66.667 0.00 0.00 44.43 4.70
2207 2349 2.050351 CACGACCACGAGTTCGCT 60.050 61.111 0.00 0.00 44.43 4.93
2208 2350 2.081212 CACGACCACGAGTTCGCTC 61.081 63.158 0.00 0.00 44.43 5.03
2240 2382 0.616395 TTACATCAGACGGAGGCCCA 60.616 55.000 0.00 0.00 0.00 5.36
2409 2552 2.281761 CAGTTGGGACGCCTGCTT 60.282 61.111 0.00 0.00 0.00 3.91
2457 2600 2.332514 CCGCACAGCCTGTTGTTG 59.667 61.111 0.00 0.00 0.00 3.33
2474 2617 6.597562 TGTTGTTGTCAAAGTTATACTCCCT 58.402 36.000 0.00 0.00 35.20 4.20
2571 2714 1.811860 GAGGTAGGCGGCGAAGTAA 59.188 57.895 12.98 0.00 0.00 2.24
2673 2816 0.679505 CCAGGACGTTGAAGGAGACA 59.320 55.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.826252 CCATTCCTAGGATCCATTACATGTTAG 59.174 40.741 13.57 3.26 0.00 2.34
13 14 4.559576 TCTTCTCCATTCCTAGGATCCA 57.440 45.455 13.57 0.00 33.99 3.41
32 33 2.500504 GGAAGACCCTACAAACCGATCT 59.499 50.000 0.00 0.00 0.00 2.75
70 71 4.141846 TGAGAGTAGTAGGATCCGTTACGT 60.142 45.833 5.98 0.00 0.00 3.57
75 76 4.857679 ACTTTGAGAGTAGTAGGATCCGT 58.142 43.478 5.98 0.00 36.65 4.69
104 105 1.594862 GATCAGACGCAATAGTGGCAC 59.405 52.381 10.29 10.29 35.03 5.01
109 110 5.528043 AGATCAAGATCAGACGCAATAGT 57.472 39.130 12.21 0.00 40.22 2.12
119 120 3.785486 TGCGGTGTAAGATCAAGATCAG 58.215 45.455 12.21 0.00 40.22 2.90
120 121 3.447229 TCTGCGGTGTAAGATCAAGATCA 59.553 43.478 12.21 0.00 40.22 2.92
121 122 4.046938 TCTGCGGTGTAAGATCAAGATC 57.953 45.455 1.81 1.81 38.09 2.75
122 123 4.184629 GTTCTGCGGTGTAAGATCAAGAT 58.815 43.478 0.00 0.00 0.00 2.40
123 124 3.585862 GTTCTGCGGTGTAAGATCAAGA 58.414 45.455 0.00 0.00 0.00 3.02
124 125 2.673368 GGTTCTGCGGTGTAAGATCAAG 59.327 50.000 0.00 0.00 0.00 3.02
133 134 2.224426 TGATGTAAAGGTTCTGCGGTGT 60.224 45.455 0.00 0.00 0.00 4.16
140 141 3.763897 GGCCAATGTGATGTAAAGGTTCT 59.236 43.478 0.00 0.00 0.00 3.01
148 149 2.754552 GCTTTGAGGCCAATGTGATGTA 59.245 45.455 5.01 0.00 32.06 2.29
188 193 4.343814 TCTGTACCGATCCTGCATCAAATA 59.656 41.667 0.00 0.00 0.00 1.40
195 200 0.684479 AGCTCTGTACCGATCCTGCA 60.684 55.000 0.00 0.00 0.00 4.41
196 201 1.319541 TAGCTCTGTACCGATCCTGC 58.680 55.000 0.00 0.00 0.00 4.85
198 203 4.041815 TCACTATAGCTCTGTACCGATCCT 59.958 45.833 0.00 0.00 0.00 3.24
201 206 4.762765 CCTTCACTATAGCTCTGTACCGAT 59.237 45.833 0.00 0.00 0.00 4.18
202 207 4.135306 CCTTCACTATAGCTCTGTACCGA 58.865 47.826 0.00 0.00 0.00 4.69
203 208 4.135306 TCCTTCACTATAGCTCTGTACCG 58.865 47.826 0.00 0.00 0.00 4.02
204 209 6.466885 TTTCCTTCACTATAGCTCTGTACC 57.533 41.667 0.00 0.00 0.00 3.34
206 211 7.898014 TGATTTCCTTCACTATAGCTCTGTA 57.102 36.000 0.00 0.00 0.00 2.74
207 212 6.798427 TGATTTCCTTCACTATAGCTCTGT 57.202 37.500 0.00 0.00 0.00 3.41
208 213 6.705381 CCTTGATTTCCTTCACTATAGCTCTG 59.295 42.308 0.00 0.00 0.00 3.35
209 214 6.687647 GCCTTGATTTCCTTCACTATAGCTCT 60.688 42.308 0.00 0.00 0.00 4.09
210 215 5.468409 GCCTTGATTTCCTTCACTATAGCTC 59.532 44.000 0.00 0.00 0.00 4.09
212 217 5.372373 AGCCTTGATTTCCTTCACTATAGC 58.628 41.667 0.00 0.00 0.00 2.97
213 218 7.118971 GCATAGCCTTGATTTCCTTCACTATAG 59.881 40.741 0.00 0.00 0.00 1.31
214 219 6.936900 GCATAGCCTTGATTTCCTTCACTATA 59.063 38.462 0.00 0.00 0.00 1.31
215 220 5.767168 GCATAGCCTTGATTTCCTTCACTAT 59.233 40.000 0.00 0.00 0.00 2.12
283 288 2.957402 TGGCTAGATTATGGGCCTTG 57.043 50.000 4.53 0.00 44.36 3.61
284 289 2.785857 ACTTGGCTAGATTATGGGCCTT 59.214 45.455 4.53 0.00 44.36 4.35
334 340 3.423154 GGTTGGGCAAGCGAGACG 61.423 66.667 0.00 0.00 0.00 4.18
366 372 6.184789 TCAGGGTTTAACCAGATGGAAATAC 58.815 40.000 16.58 0.00 41.02 1.89
373 379 7.880160 TTATTGATCAGGGTTTAACCAGATG 57.120 36.000 20.62 13.95 41.02 2.90
378 384 6.775594 AGCTTTATTGATCAGGGTTTAACC 57.224 37.500 5.40 5.40 37.60 2.85
437 444 7.513371 TTTGGACACTTTAACGATAAACCAT 57.487 32.000 6.21 0.00 28.97 3.55
488 497 9.743057 TGGAACAATAAGTTTTATGACAACTTG 57.257 29.630 8.06 0.00 39.18 3.16
503 512 8.004801 AGGGGATTATTTAGGTGGAACAATAAG 58.995 37.037 0.00 0.00 44.16 1.73
506 515 6.355588 AGGGGATTATTTAGGTGGAACAAT 57.644 37.500 0.00 0.00 44.16 2.71
518 527 7.359056 TCGGAAGGAAATTAAGGGGATTATTT 58.641 34.615 0.00 0.00 0.00 1.40
532 541 5.472137 TCGAACAATCTTTTCGGAAGGAAAT 59.528 36.000 0.00 0.00 43.82 2.17
537 546 5.344207 ACTTCGAACAATCTTTTCGGAAG 57.656 39.130 0.00 8.96 44.79 3.46
541 550 5.974300 TCAGAACTTCGAACAATCTTTTCG 58.026 37.500 0.00 0.00 45.81 3.46
542 551 6.366630 CCTCAGAACTTCGAACAATCTTTTC 58.633 40.000 0.00 0.00 0.00 2.29
554 563 0.977395 AAGGACCCCTCAGAACTTCG 59.023 55.000 0.00 0.00 30.89 3.79
564 573 2.122954 AGCCTCGAAAGGACCCCT 59.877 61.111 0.00 0.00 46.67 4.79
565 574 2.269241 CAGCCTCGAAAGGACCCC 59.731 66.667 0.00 0.00 46.67 4.95
697 712 0.411452 TCCTCTCCTCTCCTTGCACT 59.589 55.000 0.00 0.00 0.00 4.40
731 751 3.417224 CTGCTGCTTTCGCGCTGA 61.417 61.111 5.56 1.08 39.65 4.26
732 752 3.417224 TCTGCTGCTTTCGCGCTG 61.417 61.111 5.56 0.00 39.65 5.18
738 758 1.743252 CTCGGGGTCTGCTGCTTTC 60.743 63.158 0.00 0.00 0.00 2.62
761 781 1.892391 GTAAGCCAGCCGGTATGCC 60.892 63.158 1.90 0.00 33.28 4.40
762 782 0.880718 GAGTAAGCCAGCCGGTATGC 60.881 60.000 1.90 2.83 33.28 3.14
763 783 0.597637 CGAGTAAGCCAGCCGGTATG 60.598 60.000 1.90 2.03 33.28 2.39
764 784 1.740285 CGAGTAAGCCAGCCGGTAT 59.260 57.895 1.90 0.00 33.28 2.73
765 785 3.072486 GCGAGTAAGCCAGCCGGTA 62.072 63.158 1.90 0.00 33.28 4.02
766 786 4.452733 GCGAGTAAGCCAGCCGGT 62.453 66.667 1.90 0.00 33.28 5.28
767 787 3.950794 TTGCGAGTAAGCCAGCCGG 62.951 63.158 0.00 0.00 36.02 6.13
768 788 1.970917 CTTTGCGAGTAAGCCAGCCG 61.971 60.000 0.00 0.00 36.02 5.52
852 872 0.101219 GCCACCGAAATGCATTCCTC 59.899 55.000 13.38 6.73 34.34 3.71
866 887 1.006832 CGGCATATATAAGCGCCACC 58.993 55.000 2.29 0.00 45.14 4.61
873 894 3.123804 GGTGATCGGCGGCATATATAAG 58.876 50.000 10.53 0.00 0.00 1.73
902 923 2.106332 CGGTCGTGGGGTGCTATC 59.894 66.667 0.00 0.00 0.00 2.08
903 924 3.467226 CCGGTCGTGGGGTGCTAT 61.467 66.667 0.00 0.00 0.00 2.97
904 925 4.682334 TCCGGTCGTGGGGTGCTA 62.682 66.667 0.00 0.00 0.00 3.49
961 982 4.293648 CGGGATGGATGCGCCGTA 62.294 66.667 4.18 0.00 40.66 4.02
972 993 0.108186 TAGCTGCTGAACACGGGATG 60.108 55.000 13.43 0.00 0.00 3.51
976 997 0.950555 TTGCTAGCTGCTGAACACGG 60.951 55.000 17.23 0.00 43.37 4.94
1183 1212 3.127548 CGGCTCAGCAAATCAAACATACT 59.872 43.478 0.00 0.00 0.00 2.12
1201 1265 1.376424 CCTCACTGCATCAACGGCT 60.376 57.895 0.00 0.00 0.00 5.52
1289 1353 1.068753 CCAGGAGCGCGAAGATGAT 59.931 57.895 12.10 0.00 0.00 2.45
1310 1374 4.521062 GGAGATGCCGACTGCGCT 62.521 66.667 9.73 0.00 45.60 5.92
1315 1379 2.418910 CGAGGTGGAGATGCCGACT 61.419 63.158 0.00 0.00 40.66 4.18
1406 1470 2.450243 GAGGGTGAGGGTCCAGGA 59.550 66.667 0.00 0.00 0.00 3.86
1519 1583 0.037303 CACACAAGCACAGGAGGGAT 59.963 55.000 0.00 0.00 0.00 3.85
1526 1592 1.151668 GCTAGGTCACACAAGCACAG 58.848 55.000 0.00 0.00 35.05 3.66
1530 1596 1.993370 CGTTAGCTAGGTCACACAAGC 59.007 52.381 0.00 0.00 35.16 4.01
1538 1604 1.299240 GAGCCGCGTTAGCTAGGTC 60.299 63.158 8.36 0.61 41.75 3.85
1659 1727 4.415150 CACCCATGGGCGTCTGCT 62.415 66.667 31.73 6.30 42.25 4.24
1675 1743 1.552337 GATCAGACCCTTGCTCTGACA 59.448 52.381 4.87 0.00 45.43 3.58
1721 1792 3.189287 GCACCTTCAAATAGACCACACTG 59.811 47.826 0.00 0.00 0.00 3.66
1745 1816 4.141344 TCCTTGCCAAGATGATGATGATGA 60.141 41.667 5.89 0.00 0.00 2.92
1753 1824 6.267014 CCAATAATTCTCCTTGCCAAGATGAT 59.733 38.462 5.89 0.00 0.00 2.45
1755 1826 5.361857 ACCAATAATTCTCCTTGCCAAGATG 59.638 40.000 5.89 0.00 0.00 2.90
1757 1828 4.934356 ACCAATAATTCTCCTTGCCAAGA 58.066 39.130 5.89 0.00 0.00 3.02
1758 1829 5.665916 AACCAATAATTCTCCTTGCCAAG 57.334 39.130 0.00 0.00 0.00 3.61
1759 1830 5.792741 CAAACCAATAATTCTCCTTGCCAA 58.207 37.500 0.00 0.00 0.00 4.52
1760 1831 4.322650 GCAAACCAATAATTCTCCTTGCCA 60.323 41.667 0.00 0.00 33.50 4.92
1761 1832 4.183865 GCAAACCAATAATTCTCCTTGCC 58.816 43.478 0.00 0.00 33.50 4.52
1762 1833 3.859386 CGCAAACCAATAATTCTCCTTGC 59.141 43.478 0.00 0.00 35.67 4.01
1763 1834 4.858692 CACGCAAACCAATAATTCTCCTTG 59.141 41.667 0.00 0.00 0.00 3.61
1764 1835 4.522789 ACACGCAAACCAATAATTCTCCTT 59.477 37.500 0.00 0.00 0.00 3.36
1765 1836 4.079253 ACACGCAAACCAATAATTCTCCT 58.921 39.130 0.00 0.00 0.00 3.69
1766 1837 4.165779 CACACGCAAACCAATAATTCTCC 58.834 43.478 0.00 0.00 0.00 3.71
1767 1838 3.608073 GCACACGCAAACCAATAATTCTC 59.392 43.478 0.00 0.00 38.36 2.87
1770 1841 2.287909 ACGCACACGCAAACCAATAATT 60.288 40.909 0.00 0.00 45.53 1.40
1835 1924 1.498865 GCACACACACCCTGAGAACG 61.499 60.000 0.00 0.00 0.00 3.95
1880 1969 1.674322 GTGATTGTCACCCCCACCG 60.674 63.158 0.00 0.00 41.37 4.94
1887 1976 6.701841 ACTCGACATATTATGTGATTGTCACC 59.298 38.462 13.93 0.00 46.40 4.02
1978 2071 4.069300 TGTTTGCCAGATTTTGCATGAA 57.931 36.364 0.00 0.00 37.33 2.57
1998 2091 6.966534 AAATGGAGCCCAGAATTAGTAATG 57.033 37.500 0.00 0.00 36.75 1.90
2006 2099 5.765510 TGTTGTATAAATGGAGCCCAGAAT 58.234 37.500 0.41 0.00 36.75 2.40
2010 2103 3.287222 GCTGTTGTATAAATGGAGCCCA 58.713 45.455 0.00 0.00 38.19 5.36
2043 2136 1.202627 ACCCAGTTGCGTACCGTTTAA 60.203 47.619 0.00 0.00 0.00 1.52
2057 2155 1.751924 GTCTCTATTCAGCGACCCAGT 59.248 52.381 0.00 0.00 31.52 4.00
2061 2159 3.316588 TCATCTGTCTCTATTCAGCGACC 59.683 47.826 0.00 0.00 35.96 4.79
2065 2163 4.691175 TGCTTCATCTGTCTCTATTCAGC 58.309 43.478 0.00 0.00 0.00 4.26
2127 2269 1.141657 AGAGCTGCTTGTGTTCCTCAA 59.858 47.619 2.53 0.00 0.00 3.02
2128 2270 0.761187 AGAGCTGCTTGTGTTCCTCA 59.239 50.000 2.53 0.00 0.00 3.86
2132 2274 3.427161 AAAACAGAGCTGCTTGTGTTC 57.573 42.857 23.40 4.39 31.94 3.18
2168 2310 1.963338 GTCCAACGCAAGCAGAGCT 60.963 57.895 0.00 0.00 42.56 4.09
2169 2311 2.253758 TGTCCAACGCAAGCAGAGC 61.254 57.895 0.00 0.00 45.62 4.09
2170 2312 1.571460 GTGTCCAACGCAAGCAGAG 59.429 57.895 0.00 0.00 45.62 3.35
2171 2313 1.891919 GGTGTCCAACGCAAGCAGA 60.892 57.895 0.00 0.00 45.62 4.26
2172 2314 2.639286 GGTGTCCAACGCAAGCAG 59.361 61.111 0.00 0.00 45.62 4.24
2173 2315 2.904866 GGGTGTCCAACGCAAGCA 60.905 61.111 0.00 0.00 41.30 3.91
2178 2320 3.343421 GTCGTGGGTGTCCAACGC 61.343 66.667 10.44 3.29 46.04 4.84
2179 2321 2.663852 GGTCGTGGGTGTCCAACG 60.664 66.667 9.17 9.17 46.04 4.10
2180 2322 1.890510 GTGGTCGTGGGTGTCCAAC 60.891 63.158 0.00 0.00 46.04 3.77
2181 2323 2.506962 GTGGTCGTGGGTGTCCAA 59.493 61.111 0.00 0.00 46.04 3.53
2182 2324 3.918977 CGTGGTCGTGGGTGTCCA 61.919 66.667 0.00 0.00 41.58 4.02
2183 2325 3.569049 CTCGTGGTCGTGGGTGTCC 62.569 68.421 0.00 0.00 38.33 4.02
2184 2326 2.049433 CTCGTGGTCGTGGGTGTC 60.049 66.667 0.00 0.00 38.33 3.67
2185 2327 2.359570 GAACTCGTGGTCGTGGGTGT 62.360 60.000 0.00 0.00 38.33 4.16
2186 2328 1.663702 GAACTCGTGGTCGTGGGTG 60.664 63.158 0.00 0.00 38.33 4.61
2187 2329 2.732658 GAACTCGTGGTCGTGGGT 59.267 61.111 0.00 0.00 38.33 4.51
2188 2330 2.430244 CGAACTCGTGGTCGTGGG 60.430 66.667 16.33 0.00 38.33 4.61
2189 2331 3.103911 GCGAACTCGTGGTCGTGG 61.104 66.667 23.95 0.00 42.22 4.94
2190 2332 2.050351 AGCGAACTCGTGGTCGTG 60.050 61.111 23.95 0.13 42.22 4.35
2191 2333 2.254651 GAGCGAACTCGTGGTCGT 59.745 61.111 23.95 12.25 42.22 4.34
2199 2341 1.298859 ACATTTGGGCGAGCGAACTC 61.299 55.000 0.00 0.00 39.75 3.01
2200 2342 1.302511 ACATTTGGGCGAGCGAACT 60.303 52.632 0.00 0.00 0.00 3.01
2201 2343 1.154225 CACATTTGGGCGAGCGAAC 60.154 57.895 0.00 0.00 0.00 3.95
2202 2344 2.331893 CCACATTTGGGCGAGCGAA 61.332 57.895 0.00 0.00 39.57 4.70
2203 2345 2.745884 CCACATTTGGGCGAGCGA 60.746 61.111 0.00 0.00 39.57 4.93
2211 2353 3.126858 CCGTCTGATGTAACCACATTTGG 59.873 47.826 0.00 0.00 45.58 3.28
2212 2354 4.000325 TCCGTCTGATGTAACCACATTTG 59.000 43.478 0.00 0.00 45.58 2.32
2226 2368 1.072505 GTTTTGGGCCTCCGTCTGA 59.927 57.895 4.53 0.00 35.24 3.27
2240 2382 1.619983 GTCACGTTTGTTGGCGTTTT 58.380 45.000 0.00 0.00 39.48 2.43
2395 2538 4.659172 CCCAAGCAGGCGTCCCAA 62.659 66.667 0.00 0.00 35.39 4.12
2457 2600 3.195661 CGGCAGGGAGTATAACTTTGAC 58.804 50.000 0.00 0.00 0.00 3.18
2587 2730 4.101790 GTCGTACCCGGACGCGAA 62.102 66.667 15.93 0.00 42.62 4.70


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

AutoCloner maintained by Alex Coulton.