Multiple sequence alignment - TraesCS2D01G444100

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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 TraesCS2D01G444100 chr2D 100.000 2356 0 0 1 2356 555224737 555222382 0.000000e+00 4351.0
1 TraesCS2D01G444100 chr2D 91.111 90 4 3 1392 1481 555234794 555234709 4.110000e-23 119.0
2 TraesCS2D01G444100 chr2B 84.422 1316 102 41 701 1968 661778912 661777652 0.000000e+00 1199.0
3 TraesCS2D01G444100 chr2B 89.341 910 63 20 541 1427 661833836 661832938 0.000000e+00 1112.0
4 TraesCS2D01G444100 chr2B 87.269 542 21 12 98 611 661834506 661833985 2.030000e-160 575.0
5 TraesCS2D01G444100 chr2B 93.980 299 10 5 2066 2356 661777585 661777287 1.660000e-121 446.0
6 TraesCS2D01G444100 chr2B 86.275 102 4 6 1 92 661834642 661834541 4.140000e-18 102.0
7 TraesCS2D01G444100 chr2B 100.000 28 0 0 515 542 781080254 781080281 4.000000e-03 52.8
8 TraesCS2D01G444100 chr2A 81.687 1316 113 47 466 1745 694956078 694954855 0.000000e+00 977.0
9 TraesCS2D01G444100 chr2A 82.877 1022 85 46 651 1647 694976942 694975986 0.000000e+00 835.0
10 TraesCS2D01G444100 chr2A 94.276 297 11 5 2066 2356 694954565 694954269 1.280000e-122 449.0
11 TraesCS2D01G444100 chr2A 84.659 176 11 5 307 466 694956310 694956135 6.740000e-36 161.0


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 TraesCS2D01G444100 chr2D 555222382 555224737 2355 True 4351.000000 4351 100.000000 1 2356 1 chr2D.!!$R1 2355
1 TraesCS2D01G444100 chr2B 661777287 661778912 1625 True 822.500000 1199 89.201000 701 2356 2 chr2B.!!$R1 1655
2 TraesCS2D01G444100 chr2B 661832938 661834642 1704 True 596.333333 1112 87.628333 1 1427 3 chr2B.!!$R2 1426
3 TraesCS2D01G444100 chr2A 694975986 694976942 956 True 835.000000 835 82.877000 651 1647 1 chr2A.!!$R1 996
4 TraesCS2D01G444100 chr2A 694954269 694956310 2041 True 529.000000 977 86.874000 307 2356 3 chr2A.!!$R2 2049

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
648 984 0.61326 TGTAGCCCTGTACTTGCTGG 59.387 55.0 12.59 0.01 36.57 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 2090 0.320421 ACACCGGACATTTGTCGAGG 60.32 55.0 9.46 17.04 45.65 4.63 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
33 34 6.705302 ACAAGAGAGAAGTCAATATTCAGCA 58.295 36.000 0.00 0.00 0.00 4.41
92 103 4.209703 GCAAACATATTTCGCATCCATTGG 59.790 41.667 0.00 0.00 0.00 3.16
93 104 5.590145 CAAACATATTTCGCATCCATTGGA 58.410 37.500 8.08 8.08 35.55 3.53
94 105 5.443185 AACATATTTCGCATCCATTGGAG 57.557 39.130 11.78 4.84 34.05 3.86
95 106 3.822735 ACATATTTCGCATCCATTGGAGG 59.177 43.478 12.98 12.98 36.49 4.30
149 189 8.549548 CAAACTAACATCATCAATCTGCTCTAG 58.450 37.037 0.00 0.00 0.00 2.43
198 238 3.554692 GCACTCGGTTGATCGGCG 61.555 66.667 0.00 0.00 0.00 6.46
223 263 2.873133 GCAGATAGCAGAACGGTAGT 57.127 50.000 0.00 0.00 44.79 2.73
224 264 3.984508 GCAGATAGCAGAACGGTAGTA 57.015 47.619 0.00 0.00 44.79 1.82
225 265 3.891324 GCAGATAGCAGAACGGTAGTAG 58.109 50.000 0.00 0.00 44.79 2.57
236 276 1.544691 ACGGTAGTAGCAGTTGAGGTG 59.455 52.381 0.00 0.00 0.00 4.00
247 287 3.565482 GCAGTTGAGGTGAAGAATGAACA 59.435 43.478 0.00 0.00 0.00 3.18
301 346 3.308705 GACGTCGGGACCCAGGTT 61.309 66.667 12.15 0.00 0.00 3.50
302 347 3.292500 GACGTCGGGACCCAGGTTC 62.293 68.421 12.15 0.00 0.00 3.62
303 348 3.307906 CGTCGGGACCCAGGTTCA 61.308 66.667 12.15 0.00 0.00 3.18
304 349 2.874664 CGTCGGGACCCAGGTTCAA 61.875 63.158 12.15 0.00 0.00 2.69
305 350 1.452801 GTCGGGACCCAGGTTCAAA 59.547 57.895 12.15 0.00 0.00 2.69
378 437 1.066002 CATCTGGGCGCCTTTAATGTG 59.934 52.381 28.56 12.31 0.00 3.21
464 557 2.025013 CACACGACGACGACACCA 59.975 61.111 15.32 0.00 42.66 4.17
533 651 2.104963 GTCTCAGGTTCAGGTTCAGGTT 59.895 50.000 0.00 0.00 0.00 3.50
637 973 1.677552 CCAACGAACCTGTAGCCCT 59.322 57.895 0.00 0.00 0.00 5.19
640 976 1.274167 CAACGAACCTGTAGCCCTGTA 59.726 52.381 0.00 0.00 0.00 2.74
643 979 1.549170 CGAACCTGTAGCCCTGTACTT 59.451 52.381 0.00 0.00 0.00 2.24
644 980 2.674177 CGAACCTGTAGCCCTGTACTTG 60.674 54.545 0.00 0.00 0.00 3.16
645 981 0.613777 ACCTGTAGCCCTGTACTTGC 59.386 55.000 0.00 0.00 0.00 4.01
646 982 0.905357 CCTGTAGCCCTGTACTTGCT 59.095 55.000 8.89 8.89 39.10 3.91
647 983 1.406069 CCTGTAGCCCTGTACTTGCTG 60.406 57.143 12.59 0.00 36.57 4.41
648 984 0.613260 TGTAGCCCTGTACTTGCTGG 59.387 55.000 12.59 0.01 36.57 4.85
649 985 0.613777 GTAGCCCTGTACTTGCTGGT 59.386 55.000 12.59 0.00 36.57 4.00
705 1046 1.409381 GGAGCTGAATCTCCCTTTGGG 60.409 57.143 0.00 0.00 45.40 4.12
755 1104 4.385310 CCCCTTACTTTCTTTCCATCGGAT 60.385 45.833 0.00 0.00 0.00 4.18
825 1186 1.405105 GAAGCACACTCAAAGCCAACA 59.595 47.619 0.00 0.00 0.00 3.33
906 1280 1.474498 GGTGGCCATAAGAAGTACGGG 60.474 57.143 9.72 0.00 0.00 5.28
907 1281 1.483415 GTGGCCATAAGAAGTACGGGA 59.517 52.381 9.72 0.00 0.00 5.14
914 1288 1.625511 AAGAAGTACGGGAACTCGGT 58.374 50.000 0.00 0.00 0.00 4.69
1159 1543 2.089349 GTCGTCGTGCTCTGCTTCC 61.089 63.158 0.00 0.00 0.00 3.46
1224 1608 1.707451 CGTCGCGTGTGTATGCATT 59.293 52.632 3.54 0.00 38.79 3.56
1288 1676 1.858798 GCTCTGCATTATGCTGCGTTG 60.859 52.381 18.44 9.45 45.31 4.10
1374 1771 2.269241 GCGGACCAAGGAAGGAGG 59.731 66.667 0.00 0.00 0.00 4.30
1378 1775 1.079057 GACCAAGGAAGGAGGCGAC 60.079 63.158 0.00 0.00 0.00 5.19
1423 1828 6.182627 TGAGCAAGTGATATGTCAAGGAAAT 58.817 36.000 0.00 0.00 35.80 2.17
1516 1924 2.785477 CTGCAGCAATAATAAAGCGCAC 59.215 45.455 11.47 0.00 35.33 5.34
1520 1928 3.543494 CAGCAATAATAAAGCGCACACAC 59.457 43.478 11.47 0.00 0.00 3.82
1598 2013 4.671766 GCCATTTGGTCACTCGTAATTGTC 60.672 45.833 0.00 0.00 37.57 3.18
1647 2069 7.391620 TCTTCGTTGAAGAGGGTATAAAATGT 58.608 34.615 5.19 0.00 42.78 2.71
1663 2085 9.338622 GTATAAAATGTGGCCTACTTCTACAAT 57.661 33.333 3.32 0.00 0.00 2.71
1665 2087 7.625828 AAAATGTGGCCTACTTCTACAATAC 57.374 36.000 3.32 0.00 0.00 1.89
1666 2088 5.950544 ATGTGGCCTACTTCTACAATACA 57.049 39.130 3.32 0.00 0.00 2.29
1667 2089 5.748670 TGTGGCCTACTTCTACAATACAA 57.251 39.130 3.32 0.00 0.00 2.41
1668 2090 5.484715 TGTGGCCTACTTCTACAATACAAC 58.515 41.667 3.32 0.00 0.00 3.32
1722 2146 2.745884 TGCACTTCCATTCGGCCG 60.746 61.111 22.12 22.12 0.00 6.13
1753 2185 1.855978 CACAGCACAACACAAAGCATG 59.144 47.619 0.00 0.00 0.00 4.06
1755 2187 2.121786 CAGCACAACACAAAGCATGAC 58.878 47.619 0.00 0.00 0.00 3.06
1773 2206 5.526115 CATGACAGAAGTGTTTTCAGCAAT 58.474 37.500 0.00 0.00 36.88 3.56
1774 2207 4.923893 TGACAGAAGTGTTTTCAGCAATG 58.076 39.130 0.00 0.00 36.88 2.82
1775 2208 4.639755 TGACAGAAGTGTTTTCAGCAATGA 59.360 37.500 0.00 0.00 36.88 2.57
1777 2210 6.152932 ACAGAAGTGTTTTCAGCAATGAAT 57.847 33.333 0.00 0.00 30.30 2.57
1778 2211 5.981315 ACAGAAGTGTTTTCAGCAATGAATG 59.019 36.000 0.00 0.00 30.30 2.67
1779 2212 6.183360 ACAGAAGTGTTTTCAGCAATGAATGA 60.183 34.615 0.00 0.00 30.30 2.57
1785 2231 3.581024 TTCAGCAATGAATGAAGCACC 57.419 42.857 0.00 0.00 31.93 5.01
1815 2261 2.670934 CTCTTGCTTGCACGCCCT 60.671 61.111 13.19 0.00 0.00 5.19
1828 2274 1.142748 CGCCCTCACTTCTGGCTAG 59.857 63.158 0.00 0.00 43.12 3.42
1829 2275 1.608717 CGCCCTCACTTCTGGCTAGT 61.609 60.000 0.00 0.00 43.12 2.57
1830 2276 0.615850 GCCCTCACTTCTGGCTAGTT 59.384 55.000 0.00 0.00 42.01 2.24
1831 2277 1.003696 GCCCTCACTTCTGGCTAGTTT 59.996 52.381 0.00 0.00 42.01 2.66
1832 2278 2.553247 GCCCTCACTTCTGGCTAGTTTT 60.553 50.000 0.00 0.00 42.01 2.43
1833 2279 3.339141 CCCTCACTTCTGGCTAGTTTTC 58.661 50.000 0.00 0.00 0.00 2.29
1834 2280 3.008485 CCCTCACTTCTGGCTAGTTTTCT 59.992 47.826 0.00 0.00 0.00 2.52
1835 2281 4.505742 CCCTCACTTCTGGCTAGTTTTCTT 60.506 45.833 0.00 0.00 0.00 2.52
1836 2282 5.066593 CCTCACTTCTGGCTAGTTTTCTTT 58.933 41.667 0.00 0.00 0.00 2.52
1837 2283 5.532779 CCTCACTTCTGGCTAGTTTTCTTTT 59.467 40.000 0.00 0.00 0.00 2.27
1838 2284 6.039829 CCTCACTTCTGGCTAGTTTTCTTTTT 59.960 38.462 0.00 0.00 0.00 1.94
1877 2323 7.862648 GGCTAGTTAATTAGGCAATACAAGTC 58.137 38.462 21.87 0.00 43.55 3.01
1893 2339 4.160329 ACAAGTCTTCCTATCAGTGGTGA 58.840 43.478 0.00 0.00 37.02 4.02
1912 2358 6.152661 GTGGTGAAATTATCCATTCAGTCCAA 59.847 38.462 0.00 0.00 35.05 3.53
1974 2421 6.857437 TGATCTATCAGTTTTGTCCTCTCA 57.143 37.500 0.00 0.00 32.11 3.27
1975 2422 6.871844 TGATCTATCAGTTTTGTCCTCTCAG 58.128 40.000 0.00 0.00 32.11 3.35
1976 2423 6.665248 TGATCTATCAGTTTTGTCCTCTCAGA 59.335 38.462 0.00 0.00 32.11 3.27
1977 2424 6.918067 TCTATCAGTTTTGTCCTCTCAGAA 57.082 37.500 0.00 0.00 0.00 3.02
1978 2425 6.929625 TCTATCAGTTTTGTCCTCTCAGAAG 58.070 40.000 0.00 0.00 0.00 2.85
1979 2426 5.815233 ATCAGTTTTGTCCTCTCAGAAGA 57.185 39.130 0.00 0.00 0.00 2.87
1980 2427 5.614324 TCAGTTTTGTCCTCTCAGAAGAA 57.386 39.130 0.00 0.00 0.00 2.52
1981 2428 5.605534 TCAGTTTTGTCCTCTCAGAAGAAG 58.394 41.667 0.00 0.00 0.00 2.85
1982 2429 5.363868 TCAGTTTTGTCCTCTCAGAAGAAGA 59.636 40.000 0.00 0.00 0.00 2.87
1983 2430 6.051717 CAGTTTTGTCCTCTCAGAAGAAGAA 58.948 40.000 0.00 0.00 0.00 2.52
1984 2431 6.202570 CAGTTTTGTCCTCTCAGAAGAAGAAG 59.797 42.308 0.00 0.00 0.00 2.85
1985 2432 6.098982 AGTTTTGTCCTCTCAGAAGAAGAAGA 59.901 38.462 0.00 0.00 0.00 2.87
1986 2433 6.485830 TTTGTCCTCTCAGAAGAAGAAGAA 57.514 37.500 0.00 0.00 0.00 2.52
1987 2434 6.485830 TTGTCCTCTCAGAAGAAGAAGAAA 57.514 37.500 0.00 0.00 0.00 2.52
1988 2435 6.485830 TGTCCTCTCAGAAGAAGAAGAAAA 57.514 37.500 0.00 0.00 0.00 2.29
1989 2436 6.284459 TGTCCTCTCAGAAGAAGAAGAAAAC 58.716 40.000 0.00 0.00 0.00 2.43
1990 2437 5.699001 GTCCTCTCAGAAGAAGAAGAAAACC 59.301 44.000 0.00 0.00 0.00 3.27
1991 2438 5.366768 TCCTCTCAGAAGAAGAAGAAAACCA 59.633 40.000 0.00 0.00 0.00 3.67
1992 2439 6.043706 TCCTCTCAGAAGAAGAAGAAAACCAT 59.956 38.462 0.00 0.00 0.00 3.55
1993 2440 6.714356 CCTCTCAGAAGAAGAAGAAAACCATT 59.286 38.462 0.00 0.00 0.00 3.16
1994 2441 7.094848 CCTCTCAGAAGAAGAAGAAAACCATTC 60.095 40.741 0.00 0.00 0.00 2.67
1995 2442 7.512992 TCTCAGAAGAAGAAGAAAACCATTCT 58.487 34.615 0.00 0.00 37.36 2.40
1996 2443 7.659390 TCTCAGAAGAAGAAGAAAACCATTCTC 59.341 37.037 0.00 0.00 34.71 2.87
1997 2444 7.282585 TCAGAAGAAGAAGAAAACCATTCTCA 58.717 34.615 0.00 0.00 34.71 3.27
1998 2445 7.775093 TCAGAAGAAGAAGAAAACCATTCTCAA 59.225 33.333 0.00 0.00 34.71 3.02
1999 2446 8.408601 CAGAAGAAGAAGAAAACCATTCTCAAA 58.591 33.333 0.00 0.00 34.71 2.69
2000 2447 8.971073 AGAAGAAGAAGAAAACCATTCTCAAAA 58.029 29.630 0.00 0.00 34.71 2.44
2001 2448 9.586435 GAAGAAGAAGAAAACCATTCTCAAAAA 57.414 29.630 0.00 0.00 34.71 1.94
2038 2485 6.867519 AAAAAGAGAAGAAAACCCCTCAAA 57.132 33.333 0.00 0.00 0.00 2.69
2132 2607 1.133363 TCCAAACTCTTTCGGTCCCA 58.867 50.000 0.00 0.00 0.00 4.37
2229 2706 8.235226 CCATCTCATGTCTATTTACATTCATGC 58.765 37.037 0.00 0.00 38.01 4.06
2281 2764 1.450025 GCAGGTTCCGGTTTCTTAGG 58.550 55.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.905415 TTTGATTCAGCCCACCTCAT 57.095 45.000 0.00 0.00 0.00 2.90
62 65 5.307926 TGCGAAATATGTTTGCTCATCAA 57.692 34.783 0.00 0.00 0.00 2.57
63 66 4.961435 TGCGAAATATGTTTGCTCATCA 57.039 36.364 0.00 0.00 0.00 3.07
64 67 4.913924 GGATGCGAAATATGTTTGCTCATC 59.086 41.667 0.00 2.88 0.00 2.92
69 72 4.209703 CCAATGGATGCGAAATATGTTTGC 59.790 41.667 0.00 0.00 0.00 3.68
72 75 4.279169 CCTCCAATGGATGCGAAATATGTT 59.721 41.667 0.87 0.00 0.00 2.71
73 76 3.822735 CCTCCAATGGATGCGAAATATGT 59.177 43.478 0.87 0.00 0.00 2.29
74 77 3.366679 GCCTCCAATGGATGCGAAATATG 60.367 47.826 13.51 0.00 34.06 1.78
92 103 4.303282 CTCGCTTCCTCTAATAAAGCCTC 58.697 47.826 0.00 0.00 41.83 4.70
93 104 3.493524 GCTCGCTTCCTCTAATAAAGCCT 60.494 47.826 0.00 0.00 41.83 4.58
94 105 2.803386 GCTCGCTTCCTCTAATAAAGCC 59.197 50.000 0.00 0.00 41.83 4.35
95 106 3.458189 TGCTCGCTTCCTCTAATAAAGC 58.542 45.455 0.00 0.00 41.51 3.51
96 107 4.026475 CGTTGCTCGCTTCCTCTAATAAAG 60.026 45.833 0.00 0.00 0.00 1.85
97 108 3.863424 CGTTGCTCGCTTCCTCTAATAAA 59.137 43.478 0.00 0.00 0.00 1.40
98 109 3.444916 CGTTGCTCGCTTCCTCTAATAA 58.555 45.455 0.00 0.00 0.00 1.40
99 110 2.223735 CCGTTGCTCGCTTCCTCTAATA 60.224 50.000 0.00 0.00 38.35 0.98
149 189 1.795768 TCATTCTCGTGTCACTTGCC 58.204 50.000 0.65 0.00 0.00 4.52
183 223 3.066190 TCCGCCGATCAACCGAGT 61.066 61.111 0.00 0.00 0.00 4.18
222 262 4.569943 TCATTCTTCACCTCAACTGCTAC 58.430 43.478 0.00 0.00 0.00 3.58
223 263 4.890158 TCATTCTTCACCTCAACTGCTA 57.110 40.909 0.00 0.00 0.00 3.49
224 264 3.777106 TCATTCTTCACCTCAACTGCT 57.223 42.857 0.00 0.00 0.00 4.24
225 265 3.565482 TGTTCATTCTTCACCTCAACTGC 59.435 43.478 0.00 0.00 0.00 4.40
236 276 3.302092 CGCTGCGTATCTGTTCATTCTTC 60.302 47.826 14.93 0.00 0.00 2.87
287 332 0.887836 GTTTGAACCTGGGTCCCGAC 60.888 60.000 9.72 1.41 0.00 4.79
288 333 1.057851 AGTTTGAACCTGGGTCCCGA 61.058 55.000 9.72 0.00 0.00 5.14
289 334 0.179001 AAGTTTGAACCTGGGTCCCG 60.179 55.000 9.72 0.00 0.00 5.14
292 337 3.490933 GCTTTGAAGTTTGAACCTGGGTC 60.491 47.826 4.33 4.33 0.00 4.46
293 338 2.430694 GCTTTGAAGTTTGAACCTGGGT 59.569 45.455 0.00 0.00 0.00 4.51
294 339 2.430332 TGCTTTGAAGTTTGAACCTGGG 59.570 45.455 0.00 0.00 0.00 4.45
295 340 3.709987 CTGCTTTGAAGTTTGAACCTGG 58.290 45.455 0.00 0.00 0.00 4.45
296 341 3.118542 GCTGCTTTGAAGTTTGAACCTG 58.881 45.455 0.00 0.00 0.00 4.00
297 342 2.760092 TGCTGCTTTGAAGTTTGAACCT 59.240 40.909 0.00 0.00 0.00 3.50
298 343 2.860136 GTGCTGCTTTGAAGTTTGAACC 59.140 45.455 0.00 0.00 0.00 3.62
299 344 2.531508 CGTGCTGCTTTGAAGTTTGAAC 59.468 45.455 0.00 0.00 0.00 3.18
300 345 2.163412 ACGTGCTGCTTTGAAGTTTGAA 59.837 40.909 0.00 0.00 0.00 2.69
301 346 1.742831 ACGTGCTGCTTTGAAGTTTGA 59.257 42.857 0.00 0.00 0.00 2.69
302 347 1.847999 CACGTGCTGCTTTGAAGTTTG 59.152 47.619 0.82 0.00 0.00 2.93
303 348 1.742831 TCACGTGCTGCTTTGAAGTTT 59.257 42.857 11.67 0.00 0.00 2.66
304 349 1.064060 GTCACGTGCTGCTTTGAAGTT 59.936 47.619 11.67 0.00 0.00 2.66
305 350 0.657840 GTCACGTGCTGCTTTGAAGT 59.342 50.000 11.67 0.00 0.00 3.01
351 396 2.409870 GGCGCCCAGATGTCCTTTG 61.410 63.158 18.11 0.00 0.00 2.77
378 437 3.112709 GGTTCACAGGTCGCGAGC 61.113 66.667 29.78 29.78 0.00 5.03
421 481 1.094073 CCTGGCTTCCTCTGCAATCG 61.094 60.000 0.00 0.00 0.00 3.34
464 557 1.733041 CGCAGGAACACGACGATGT 60.733 57.895 0.00 0.00 31.84 3.06
533 651 3.239464 TGCTGAACCTGCACCTGA 58.761 55.556 0.00 0.00 33.63 3.86
645 981 3.730761 GTCCGCTGCAGCAACCAG 61.731 66.667 36.03 20.19 42.21 4.00
646 982 3.848301 ATGTCCGCTGCAGCAACCA 62.848 57.895 36.03 27.06 42.21 3.67
647 983 3.058160 ATGTCCGCTGCAGCAACC 61.058 61.111 36.03 22.67 42.21 3.77
648 984 2.177531 CATGTCCGCTGCAGCAAC 59.822 61.111 36.03 30.65 42.21 4.17
649 985 2.281692 ACATGTCCGCTGCAGCAA 60.282 55.556 36.03 21.96 42.21 3.91
699 1035 1.331214 TCTGAAGCAAAGGCCCAAAG 58.669 50.000 0.00 0.00 42.56 2.77
705 1046 3.665745 TCCATTTTCTGAAGCAAAGGC 57.334 42.857 0.00 0.00 41.61 4.35
825 1186 1.542030 ACGCTTCTCTGAATCTCACGT 59.458 47.619 0.00 0.00 0.00 4.49
906 1280 1.476891 TGGCTGATACTCACCGAGTTC 59.523 52.381 1.36 1.58 40.28 3.01
907 1281 1.478510 CTGGCTGATACTCACCGAGTT 59.521 52.381 1.36 0.00 40.28 3.01
914 1288 1.153568 GCACGCTGGCTGATACTCA 60.154 57.895 0.00 0.00 0.00 3.41
1141 1525 2.089349 GGAAGCAGAGCACGACGAC 61.089 63.158 0.00 0.00 0.00 4.34
1159 1543 0.738389 GAGCAGAGGAAGAGGACGAG 59.262 60.000 0.00 0.00 0.00 4.18
1194 1578 2.429571 GCGACGCACGTACCAGAA 60.430 61.111 16.42 0.00 44.60 3.02
1224 1608 1.378531 AAAGACGTTTGCTGCACTGA 58.621 45.000 0.00 0.00 0.00 3.41
1295 1683 0.033228 AGCTCGACATATCTGCAGGC 59.967 55.000 15.13 5.76 0.00 4.85
1296 1689 2.402305 GAAGCTCGACATATCTGCAGG 58.598 52.381 15.13 0.00 0.00 4.85
1374 1771 1.515304 GAGCTCTTCTCACGGTCGC 60.515 63.158 6.43 0.00 41.51 5.19
1423 1828 8.428186 AAAACAGAAAACGTTCACATCTAGTA 57.572 30.769 0.00 0.00 36.09 1.82
1487 1893 1.211743 TTATTGCTGCAGCGAGATCG 58.788 50.000 31.23 0.00 45.83 3.69
1516 1924 2.736721 AGCAGTACTATTGCGTTGTGTG 59.263 45.455 0.00 0.00 45.98 3.82
1520 1928 3.511699 TCAGAGCAGTACTATTGCGTTG 58.488 45.455 0.00 0.97 45.98 4.10
1557 1967 1.523154 GCACCGGACCATGAAAGCAA 61.523 55.000 9.46 0.00 0.00 3.91
1560 1970 0.680921 ATGGCACCGGACCATGAAAG 60.681 55.000 26.21 0.41 46.27 2.62
1598 2013 1.226746 GTCAGAGGTTTGTTCACCGG 58.773 55.000 0.00 0.00 42.33 5.28
1647 2069 4.781087 AGGTTGTATTGTAGAAGTAGGCCA 59.219 41.667 5.01 0.00 0.00 5.36
1663 2085 2.610976 CCGGACATTTGTCGAGGTTGTA 60.611 50.000 0.00 0.00 45.65 2.41
1664 2086 1.508632 CGGACATTTGTCGAGGTTGT 58.491 50.000 4.72 0.00 45.65 3.32
1665 2087 0.796312 CCGGACATTTGTCGAGGTTG 59.204 55.000 0.00 0.00 45.65 3.77
1666 2088 0.395312 ACCGGACATTTGTCGAGGTT 59.605 50.000 9.46 7.75 46.80 3.50
1667 2089 2.055299 ACCGGACATTTGTCGAGGT 58.945 52.632 9.46 18.01 45.33 3.85
1668 2090 0.320421 ACACCGGACATTTGTCGAGG 60.320 55.000 9.46 17.04 45.65 4.63
1722 2146 1.162181 TGTGCTGTGCTGTGAAGAGC 61.162 55.000 0.00 0.00 39.62 4.09
1753 2185 5.173774 TCATTGCTGAAAACACTTCTGTC 57.826 39.130 0.00 0.00 0.00 3.51
1755 2187 6.210796 TCATTCATTGCTGAAAACACTTCTG 58.789 36.000 0.00 0.00 44.29 3.02
1773 2206 2.290896 CCTTGGTAGGGTGCTTCATTCA 60.291 50.000 0.00 0.00 37.94 2.57
1774 2207 2.369394 CCTTGGTAGGGTGCTTCATTC 58.631 52.381 0.00 0.00 37.94 2.67
1775 2208 2.514458 CCTTGGTAGGGTGCTTCATT 57.486 50.000 0.00 0.00 37.94 2.57
1785 2231 2.115343 GCAAGAGTTCCCTTGGTAGG 57.885 55.000 0.00 0.00 42.73 3.18
1800 2246 2.979676 TGAGGGCGTGCAAGCAAG 60.980 61.111 25.75 3.58 39.27 4.01
1801 2247 3.286751 GTGAGGGCGTGCAAGCAA 61.287 61.111 25.75 5.75 39.27 3.91
1802 2248 3.772853 AAGTGAGGGCGTGCAAGCA 62.773 57.895 25.75 2.34 39.27 3.91
1803 2249 2.970974 GAAGTGAGGGCGTGCAAGC 61.971 63.158 16.86 16.86 0.00 4.01
1835 2281 6.877611 ACTAGCCAGAAATTTCTCGAAAAA 57.122 33.333 17.91 1.72 34.74 1.94
1836 2282 6.877611 AACTAGCCAGAAATTTCTCGAAAA 57.122 33.333 17.91 2.71 34.74 2.29
1837 2283 7.972832 TTAACTAGCCAGAAATTTCTCGAAA 57.027 32.000 17.91 2.99 34.74 3.46
1838 2284 8.561738 AATTAACTAGCCAGAAATTTCTCGAA 57.438 30.769 17.91 1.73 34.74 3.71
1839 2285 9.314321 CTAATTAACTAGCCAGAAATTTCTCGA 57.686 33.333 17.91 3.91 34.74 4.04
1840 2286 8.552034 CCTAATTAACTAGCCAGAAATTTCTCG 58.448 37.037 17.91 12.89 34.74 4.04
1841 2287 8.346300 GCCTAATTAACTAGCCAGAAATTTCTC 58.654 37.037 17.91 8.16 34.74 2.87
1842 2288 7.834181 TGCCTAATTAACTAGCCAGAAATTTCT 59.166 33.333 15.11 15.11 38.25 2.52
1843 2289 7.996385 TGCCTAATTAACTAGCCAGAAATTTC 58.004 34.615 10.33 10.33 0.00 2.17
1844 2290 7.954666 TGCCTAATTAACTAGCCAGAAATTT 57.045 32.000 0.00 0.00 0.00 1.82
1845 2291 7.954666 TTGCCTAATTAACTAGCCAGAAATT 57.045 32.000 0.00 0.00 0.00 1.82
1846 2292 9.067986 GTATTGCCTAATTAACTAGCCAGAAAT 57.932 33.333 0.00 0.00 0.00 2.17
1847 2293 8.050325 TGTATTGCCTAATTAACTAGCCAGAAA 58.950 33.333 0.00 0.00 0.00 2.52
1848 2294 7.570132 TGTATTGCCTAATTAACTAGCCAGAA 58.430 34.615 0.00 0.00 0.00 3.02
1849 2295 7.131907 TGTATTGCCTAATTAACTAGCCAGA 57.868 36.000 0.00 0.00 0.00 3.86
1850 2296 7.499232 ACTTGTATTGCCTAATTAACTAGCCAG 59.501 37.037 0.00 0.00 0.00 4.85
1851 2297 7.343357 ACTTGTATTGCCTAATTAACTAGCCA 58.657 34.615 0.00 0.00 0.00 4.75
1852 2298 7.715686 AGACTTGTATTGCCTAATTAACTAGCC 59.284 37.037 0.00 0.00 0.00 3.93
1853 2299 8.664211 AGACTTGTATTGCCTAATTAACTAGC 57.336 34.615 0.00 0.00 0.00 3.42
1855 2301 9.609346 GGAAGACTTGTATTGCCTAATTAACTA 57.391 33.333 0.00 0.00 0.00 2.24
1856 2302 8.329502 AGGAAGACTTGTATTGCCTAATTAACT 58.670 33.333 0.00 0.00 0.00 2.24
1857 2303 8.507524 AGGAAGACTTGTATTGCCTAATTAAC 57.492 34.615 0.00 0.00 0.00 2.01
1877 2323 7.282585 TGGATAATTTCACCACTGATAGGAAG 58.717 38.462 0.00 0.00 0.00 3.46
1893 2339 6.408434 GCCCAATTGGACTGAATGGATAATTT 60.408 38.462 26.60 0.00 37.39 1.82
1912 2358 3.008923 CCCAGTTATTTTTGTGGCCCAAT 59.991 43.478 0.00 0.00 31.81 3.16
1963 2410 6.485830 TTCTTCTTCTTCTGAGAGGACAAA 57.514 37.500 0.00 0.00 37.69 2.83
1968 2415 5.615289 TGGTTTTCTTCTTCTTCTGAGAGG 58.385 41.667 0.00 0.00 32.44 3.69
1969 2416 7.661027 AGAATGGTTTTCTTCTTCTTCTGAGAG 59.339 37.037 0.00 0.00 32.44 3.20
1970 2417 7.512992 AGAATGGTTTTCTTCTTCTTCTGAGA 58.487 34.615 0.00 0.00 0.00 3.27
1971 2418 7.443575 TGAGAATGGTTTTCTTCTTCTTCTGAG 59.556 37.037 0.00 0.00 31.99 3.35
1972 2419 7.282585 TGAGAATGGTTTTCTTCTTCTTCTGA 58.717 34.615 0.00 0.00 31.99 3.27
1973 2420 7.502120 TGAGAATGGTTTTCTTCTTCTTCTG 57.498 36.000 0.00 0.00 31.99 3.02
1974 2421 8.525290 TTTGAGAATGGTTTTCTTCTTCTTCT 57.475 30.769 0.00 0.00 31.99 2.85
1975 2422 9.586435 TTTTTGAGAATGGTTTTCTTCTTCTTC 57.414 29.630 0.00 0.00 31.99 2.87
2015 2462 6.867519 TTTGAGGGGTTTTCTTCTCTTTTT 57.132 33.333 0.00 0.00 0.00 1.94
2016 2463 6.867519 TTTTGAGGGGTTTTCTTCTCTTTT 57.132 33.333 0.00 0.00 0.00 2.27
2017 2464 6.867519 TTTTTGAGGGGTTTTCTTCTCTTT 57.132 33.333 0.00 0.00 0.00 2.52
2050 2497 4.464008 TGCACTTGGACTTCTCTGATTTT 58.536 39.130 0.00 0.00 0.00 1.82
2052 2499 3.777106 TGCACTTGGACTTCTCTGATT 57.223 42.857 0.00 0.00 0.00 2.57
2064 2511 9.537192 AATCAAACAATATTATCATGCACTTGG 57.463 29.630 0.00 0.00 0.00 3.61
2229 2706 6.875076 TGATACTATGATGATCTGGCTGATG 58.125 40.000 11.90 0.00 35.14 3.07


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

AutoCloner maintained by Alex Coulton.