Multiple sequence alignment - TraesCS5D01G238300

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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 TraesCS5D01G238300 chr5D 100.000 2985 0 0 1 2985 346635778 346638762 0.000000e+00 5513.0
1 TraesCS5D01G238300 chr5D 73.469 343 65 16 27 351 447202761 447202427 4.070000e-19 106.0
2 TraesCS5D01G238300 chr5B 90.998 1744 111 26 1 1720 404192187 404190466 0.000000e+00 2309.0
3 TraesCS5D01G238300 chr5B 90.701 1226 71 12 1795 2985 404190451 404189234 0.000000e+00 1592.0
4 TraesCS5D01G238300 chr5A 94.544 1173 46 11 559 1725 444945616 444944456 0.000000e+00 1796.0
5 TraesCS5D01G238300 chr5A 88.860 763 48 15 2256 2985 444944055 444943297 0.000000e+00 904.0
6 TraesCS5D01G238300 chr5A 95.833 456 13 3 1795 2249 444944440 444943990 0.000000e+00 732.0
7 TraesCS5D01G238300 chr3A 96.970 33 0 1 360 391 732615270 732615302 1.000000e-03 54.7


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 TraesCS5D01G238300 chr5D 346635778 346638762 2984 False 5513.0 5513 100.0000 1 2985 1 chr5D.!!$F1 2984
1 TraesCS5D01G238300 chr5B 404189234 404192187 2953 True 1950.5 2309 90.8495 1 2985 2 chr5B.!!$R1 2984
2 TraesCS5D01G238300 chr5A 444943297 444945616 2319 True 1144.0 1796 93.0790 559 2985 3 chr5A.!!$R1 2426


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
488 491 0.027194 CATCACCTTGCATCGCTTCG 59.973 55.0 0.00 0.00 0.00 3.79 F
1228 1244 0.248907 ATGCGCTTCATGCAAGATGC 60.249 50.0 17.14 17.14 46.87 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 1795 0.114560 AACCGAGGGTCCAGAAGAGA 59.885 55.000 0.0 0.0 33.12 3.10 R
2926 2984 1.818674 CACTGGTAAATCCTGTTGGCC 59.181 52.381 0.0 0.0 44.20 5.36 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
40 41 1.602327 GAGAACCCTAGCCCGTCGTT 61.602 60.000 0.00 0.00 0.00 3.85
50 51 2.581409 CCGTCGTTTCGGGATCGG 60.581 66.667 8.13 0.00 45.88 4.18
54 55 3.192922 CGTTTCGGGATCGGTGGC 61.193 66.667 0.00 0.00 36.95 5.01
55 56 2.046700 GTTTCGGGATCGGTGGCA 60.047 61.111 0.00 0.00 36.95 4.92
94 95 3.344703 CCTCTTGGGTGCATTGTCA 57.655 52.632 0.00 0.00 0.00 3.58
123 124 3.068165 TCAGGTATCATCTGGTTACAGCG 59.932 47.826 0.00 0.00 44.54 5.18
157 158 0.540133 TGCTTGCTTTGATCCTGGCA 60.540 50.000 0.00 0.00 0.00 4.92
183 184 1.880027 CTTCTTCGGTTTTGGGTGGAG 59.120 52.381 0.00 0.00 0.00 3.86
190 191 1.893137 GGTTTTGGGTGGAGTGGATTC 59.107 52.381 0.00 0.00 0.00 2.52
197 198 1.156736 GTGGAGTGGATTCGTTGGTG 58.843 55.000 0.00 0.00 0.00 4.17
199 200 1.142060 TGGAGTGGATTCGTTGGTGTT 59.858 47.619 0.00 0.00 0.00 3.32
212 213 4.748102 TCGTTGGTGTTCTCTCATTTACAC 59.252 41.667 0.00 0.00 40.01 2.90
231 234 0.029567 CGTATCCTCGCAGTCAGTCC 59.970 60.000 0.00 0.00 0.00 3.85
247 250 0.945813 GTCCTCGGTCCTCACTATCG 59.054 60.000 0.00 0.00 0.00 2.92
248 251 0.818445 TCCTCGGTCCTCACTATCGC 60.818 60.000 0.00 0.00 0.00 4.58
249 252 1.101635 CCTCGGTCCTCACTATCGCA 61.102 60.000 0.00 0.00 0.00 5.10
255 258 1.123077 TCCTCACTATCGCATTGGCT 58.877 50.000 0.00 0.00 38.10 4.75
262 265 0.678950 TATCGCATTGGCTGGATCGA 59.321 50.000 0.00 0.00 38.10 3.59
270 273 0.036388 TGGCTGGATCGAAACTCCAC 60.036 55.000 2.00 0.97 37.87 4.02
272 275 0.108804 GCTGGATCGAAACTCCACGA 60.109 55.000 2.00 0.00 37.87 4.35
303 306 2.052157 GAGGACATGCGCTTACGATAC 58.948 52.381 9.73 0.00 43.93 2.24
308 311 1.526887 CATGCGCTTACGATACCTTGG 59.473 52.381 9.73 0.00 43.93 3.61
318 321 1.337447 CGATACCTTGGTGTGTTCGGT 60.337 52.381 2.03 0.00 0.00 4.69
320 323 0.533308 TACCTTGGTGTGTTCGGTGC 60.533 55.000 2.03 0.00 0.00 5.01
321 324 1.821759 CCTTGGTGTGTTCGGTGCA 60.822 57.895 0.00 0.00 0.00 4.57
330 333 2.047655 TTCGGTGCATCGGTGTCC 60.048 61.111 21.08 0.00 0.00 4.02
331 334 3.599285 TTCGGTGCATCGGTGTCCC 62.599 63.158 21.08 0.00 0.00 4.46
347 350 2.125269 CCGTGGTTTCCCTAGGCG 60.125 66.667 2.05 0.00 0.00 5.52
362 365 2.354188 GCGGTGCCGTTTTGGTTC 60.354 61.111 12.46 0.00 41.21 3.62
396 399 1.359848 CCTCATGTTAGTGTGGCGAC 58.640 55.000 0.00 0.00 0.00 5.19
397 400 0.992072 CTCATGTTAGTGTGGCGACG 59.008 55.000 0.00 0.00 0.00 5.12
412 415 4.547406 GGCGACGCCTATTTTCTTATTT 57.453 40.909 31.30 0.00 46.69 1.40
417 420 5.235616 CGACGCCTATTTTCTTATTTGGCTA 59.764 40.000 0.00 0.00 37.01 3.93
418 421 6.564125 CGACGCCTATTTTCTTATTTGGCTAG 60.564 42.308 0.00 0.00 37.01 3.42
419 422 5.008712 ACGCCTATTTTCTTATTTGGCTAGC 59.991 40.000 6.04 6.04 37.01 3.42
420 423 5.239525 CGCCTATTTTCTTATTTGGCTAGCT 59.760 40.000 15.72 0.00 37.01 3.32
421 424 6.442112 GCCTATTTTCTTATTTGGCTAGCTG 58.558 40.000 15.72 0.00 36.32 4.24
422 425 6.442112 CCTATTTTCTTATTTGGCTAGCTGC 58.558 40.000 15.72 0.00 41.94 5.25
423 426 4.355543 TTTTCTTATTTGGCTAGCTGCG 57.644 40.909 15.72 0.00 44.05 5.18
429 432 2.404566 TTTGGCTAGCTGCGGGTTGA 62.405 55.000 15.72 0.00 44.05 3.18
467 470 2.110011 ACTGGCTTGTATGGGGTTCTTT 59.890 45.455 0.00 0.00 0.00 2.52
479 482 1.546029 GGGTTCTTTCCATCACCTTGC 59.454 52.381 0.00 0.00 0.00 4.01
484 487 0.810648 TTTCCATCACCTTGCATCGC 59.189 50.000 0.00 0.00 0.00 4.58
488 491 0.027194 CATCACCTTGCATCGCTTCG 59.973 55.000 0.00 0.00 0.00 3.79
489 492 1.091771 ATCACCTTGCATCGCTTCGG 61.092 55.000 0.00 0.00 0.00 4.30
498 501 2.677003 ATCGCTTCGGCCGTTTGTG 61.677 57.895 27.15 21.08 37.76 3.33
510 513 2.416162 GCCGTTTGTGTTTTGTTCAGGA 60.416 45.455 0.00 0.00 0.00 3.86
511 514 3.839293 CCGTTTGTGTTTTGTTCAGGAA 58.161 40.909 0.00 0.00 0.00 3.36
513 516 3.610677 CGTTTGTGTTTTGTTCAGGAACC 59.389 43.478 9.49 0.00 40.46 3.62
514 517 4.561105 GTTTGTGTTTTGTTCAGGAACCA 58.439 39.130 9.49 0.00 40.46 3.67
523 532 5.560722 TTGTTCAGGAACCAGTCTCATAA 57.439 39.130 9.49 0.00 40.46 1.90
607 617 1.106944 AAGCAAACAGACCAACCCGG 61.107 55.000 0.00 0.00 42.50 5.73
645 655 2.793278 TGTACATCATGTCGGATCGG 57.207 50.000 0.00 0.00 0.00 4.18
786 796 2.520120 TGGTCCATCTATCCAGTCTCCT 59.480 50.000 0.00 0.00 0.00 3.69
941 951 1.754745 GAGAGGCAGAACCACCACA 59.245 57.895 0.00 0.00 43.14 4.17
942 952 0.603975 GAGAGGCAGAACCACCACAC 60.604 60.000 0.00 0.00 43.14 3.82
995 1007 0.814410 CGCCGTACCTGCTCTCTAGA 60.814 60.000 0.00 0.00 0.00 2.43
1213 1229 6.414694 GGAACATAACAATAACACATGATGCG 59.585 38.462 0.00 0.00 0.00 4.73
1215 1231 5.066375 ACATAACAATAACACATGATGCGCT 59.934 36.000 9.73 0.00 0.00 5.92
1219 1235 4.096833 ACAATAACACATGATGCGCTTCAT 59.903 37.500 27.68 27.68 36.79 2.57
1223 1239 3.633573 CATGATGCGCTTCATGCAA 57.366 47.368 37.60 15.81 46.87 4.08
1224 1240 1.477105 CATGATGCGCTTCATGCAAG 58.523 50.000 37.60 23.11 46.87 4.01
1227 1243 1.064952 TGATGCGCTTCATGCAAGATG 59.935 47.619 20.86 0.00 46.87 2.90
1228 1244 0.248907 ATGCGCTTCATGCAAGATGC 60.249 50.000 17.14 17.14 46.87 3.91
1238 1254 1.723273 GCAAGATGCAGCGCACATA 59.277 52.632 11.47 0.00 43.04 2.29
1239 1255 0.590732 GCAAGATGCAGCGCACATAC 60.591 55.000 11.47 7.37 43.04 2.39
1240 1256 1.012086 CAAGATGCAGCGCACATACT 58.988 50.000 11.47 9.45 43.04 2.12
1270 1286 6.767902 TGCTAATACTCTTTGTTGGATGGATC 59.232 38.462 0.00 0.00 0.00 3.36
1295 1317 1.603455 CTTGGCGGGTGACAATGGT 60.603 57.895 0.00 0.00 43.73 3.55
1430 1452 4.785453 CTGACCAAGGCGGGGCTC 62.785 72.222 5.68 0.72 40.22 4.70
1493 1515 4.154347 GCCTCCTCCTCCACGCTG 62.154 72.222 0.00 0.00 0.00 5.18
1526 1548 3.444388 AGTTCATCCTCTTCCACTACGTC 59.556 47.826 0.00 0.00 0.00 4.34
1707 1729 2.385803 CCAACGGTACCTCCATAGTCT 58.614 52.381 10.90 0.00 35.57 3.24
1708 1730 2.361438 CCAACGGTACCTCCATAGTCTC 59.639 54.545 10.90 0.00 35.57 3.36
1711 1733 2.778850 ACGGTACCTCCATAGTCTCTCT 59.221 50.000 10.90 0.00 35.57 3.10
1713 1735 3.816523 CGGTACCTCCATAGTCTCTCTTC 59.183 52.174 10.90 0.00 35.57 2.87
1714 1736 4.445162 CGGTACCTCCATAGTCTCTCTTCT 60.445 50.000 10.90 0.00 35.57 2.85
1718 1740 5.837829 ACCTCCATAGTCTCTCTTCTTCTT 58.162 41.667 0.00 0.00 0.00 2.52
1722 1744 7.201821 CCTCCATAGTCTCTCTTCTTCTTCTTC 60.202 44.444 0.00 0.00 0.00 2.87
1723 1745 7.410174 TCCATAGTCTCTCTTCTTCTTCTTCT 58.590 38.462 0.00 0.00 0.00 2.85
1726 1748 9.927668 CATAGTCTCTCTTCTTCTTCTTCTTTT 57.072 33.333 0.00 0.00 0.00 2.27
1748 1770 6.639632 TTTTCAAATATCCAGCTAGATGGC 57.360 37.500 22.56 0.00 40.41 4.40
1749 1771 5.573380 TTCAAATATCCAGCTAGATGGCT 57.427 39.130 22.56 15.57 44.10 4.75
1759 1781 3.415457 GCTAGATGGCTGGCTTCTATT 57.585 47.619 21.63 5.29 44.39 1.73
1760 1782 3.749226 GCTAGATGGCTGGCTTCTATTT 58.251 45.455 21.63 4.99 44.39 1.40
1761 1783 3.750652 GCTAGATGGCTGGCTTCTATTTC 59.249 47.826 21.63 13.01 44.39 2.17
1762 1784 3.939740 AGATGGCTGGCTTCTATTTCA 57.060 42.857 16.42 0.00 0.00 2.69
1763 1785 4.450305 AGATGGCTGGCTTCTATTTCAT 57.550 40.909 16.42 0.00 0.00 2.57
1764 1786 4.142790 AGATGGCTGGCTTCTATTTCATG 58.857 43.478 16.42 0.00 0.00 3.07
1765 1787 3.650281 TGGCTGGCTTCTATTTCATGA 57.350 42.857 2.00 0.00 0.00 3.07
1766 1788 4.174704 TGGCTGGCTTCTATTTCATGAT 57.825 40.909 0.00 0.00 0.00 2.45
1767 1789 4.139786 TGGCTGGCTTCTATTTCATGATC 58.860 43.478 0.00 0.00 0.00 2.92
1768 1790 3.505293 GGCTGGCTTCTATTTCATGATCC 59.495 47.826 0.00 0.00 0.00 3.36
1769 1791 4.139786 GCTGGCTTCTATTTCATGATCCA 58.860 43.478 0.00 0.00 0.00 3.41
1770 1792 4.765856 GCTGGCTTCTATTTCATGATCCAT 59.234 41.667 0.00 0.00 0.00 3.41
1771 1793 5.106237 GCTGGCTTCTATTTCATGATCCATC 60.106 44.000 0.00 0.00 0.00 3.51
1772 1794 4.999311 TGGCTTCTATTTCATGATCCATCG 59.001 41.667 0.00 0.00 0.00 3.84
1773 1795 4.999950 GGCTTCTATTTCATGATCCATCGT 59.000 41.667 0.00 0.00 0.00 3.73
1774 1796 5.121454 GGCTTCTATTTCATGATCCATCGTC 59.879 44.000 0.00 0.00 0.00 4.20
1775 1797 5.931146 GCTTCTATTTCATGATCCATCGTCT 59.069 40.000 0.00 0.00 0.00 4.18
1776 1798 6.090628 GCTTCTATTTCATGATCCATCGTCTC 59.909 42.308 0.00 0.00 0.00 3.36
1777 1799 6.907853 TCTATTTCATGATCCATCGTCTCT 57.092 37.500 0.00 0.00 0.00 3.10
1778 1800 7.295322 TCTATTTCATGATCCATCGTCTCTT 57.705 36.000 0.00 0.00 0.00 2.85
1779 1801 7.374272 TCTATTTCATGATCCATCGTCTCTTC 58.626 38.462 0.00 0.00 0.00 2.87
1780 1802 5.604758 TTTCATGATCCATCGTCTCTTCT 57.395 39.130 0.00 0.00 0.00 2.85
1781 1803 4.581077 TCATGATCCATCGTCTCTTCTG 57.419 45.455 0.00 0.00 0.00 3.02
1782 1804 3.320256 TCATGATCCATCGTCTCTTCTGG 59.680 47.826 0.00 0.00 0.00 3.86
1783 1805 3.018423 TGATCCATCGTCTCTTCTGGA 57.982 47.619 0.00 0.00 41.76 3.86
1784 1806 2.690497 TGATCCATCGTCTCTTCTGGAC 59.310 50.000 0.00 0.00 40.43 4.02
1785 1807 1.475403 TCCATCGTCTCTTCTGGACC 58.525 55.000 0.00 0.00 32.92 4.46
1786 1808 0.461961 CCATCGTCTCTTCTGGACCC 59.538 60.000 0.00 0.00 0.00 4.46
1787 1809 1.479709 CATCGTCTCTTCTGGACCCT 58.520 55.000 0.00 0.00 0.00 4.34
1788 1810 1.407258 CATCGTCTCTTCTGGACCCTC 59.593 57.143 0.00 0.00 0.00 4.30
1789 1811 0.677098 TCGTCTCTTCTGGACCCTCG 60.677 60.000 0.00 0.00 0.00 4.63
1790 1812 1.658686 CGTCTCTTCTGGACCCTCGG 61.659 65.000 0.00 0.00 0.00 4.63
1793 1815 0.533032 CTCTTCTGGACCCTCGGTTC 59.467 60.000 0.00 0.00 35.25 3.62
1817 1839 2.754946 TCGGACGGCTCTTGTTAATT 57.245 45.000 0.00 0.00 0.00 1.40
1825 1847 6.096673 ACGGCTCTTGTTAATTTTTGGATT 57.903 33.333 0.00 0.00 0.00 3.01
1981 2003 2.503061 CAGACCATCTCCGGCCAG 59.497 66.667 2.24 0.00 0.00 4.85
2043 2065 6.209788 GTGGTCTGAATTGTTATTTTGGGGTA 59.790 38.462 0.00 0.00 0.00 3.69
2240 2263 9.302345 CTAGTTTGAAGCATTAGTCTCGAATTA 57.698 33.333 0.00 0.00 0.00 1.40
2271 2294 9.011095 TGATATCACCCGTGTTATTTTAAACAA 57.989 29.630 0.00 0.00 40.85 2.83
2298 2321 7.910683 GGCAAAATATAGTTTGAAGCACTAGTC 59.089 37.037 25.42 6.87 40.29 2.59
2304 2327 5.234466 AGTTTGAAGCACTAGTCCTGAAT 57.766 39.130 0.00 0.00 0.00 2.57
2319 2342 6.219473 AGTCCTGAATTCGATGTGATGATAC 58.781 40.000 0.04 0.00 0.00 2.24
2377 2403 1.737029 GCTCGCAGATGTAGAACAGCA 60.737 52.381 0.00 0.00 36.88 4.41
2401 2432 7.922811 GCAGAATCAAAGAAGAAGAAAAAGGAA 59.077 33.333 0.00 0.00 0.00 3.36
2411 2442 9.454859 AGAAGAAGAAAAAGGAACCAGTATATG 57.545 33.333 0.00 0.00 0.00 1.78
2424 2455 7.868415 GGAACCAGTATATGAAGTCACAGATAC 59.132 40.741 0.00 0.00 41.98 2.24
2437 2468 4.627467 GTCACAGATACACAACATCAGTCC 59.373 45.833 0.00 0.00 0.00 3.85
2449 2480 5.833131 ACAACATCAGTCCCAAAACTACAAT 59.167 36.000 0.00 0.00 0.00 2.71
2455 2486 5.591067 TCAGTCCCAAAACTACAATTTCGTT 59.409 36.000 0.00 0.00 0.00 3.85
2470 2501 4.837896 TTTCGTTGTATGGAATGTGCAA 57.162 36.364 0.00 0.00 0.00 4.08
2552 2584 3.760580 AAGATCCTATTGGAAGAGGCG 57.239 47.619 0.00 0.00 46.80 5.52
2619 2653 8.271458 TCCACATGAGTTTATCCTAATTAGCAA 58.729 33.333 6.99 0.00 0.00 3.91
2621 2655 8.892723 CACATGAGTTTATCCTAATTAGCAACA 58.107 33.333 6.99 0.00 0.00 3.33
2622 2656 9.461312 ACATGAGTTTATCCTAATTAGCAACAA 57.539 29.630 6.99 0.00 0.00 2.83
2624 2658 7.970384 TGAGTTTATCCTAATTAGCAACAACG 58.030 34.615 6.99 0.00 0.00 4.10
2696 2754 6.998112 TGGGGCAGGATAAGTATAGATAGAT 58.002 40.000 0.00 0.00 0.00 1.98
2819 2877 1.273048 TGGCCAAGCAATGTCATGTTC 59.727 47.619 0.61 0.00 0.00 3.18
2874 2932 2.243478 TGGGCCAGCTAAATCAACCATA 59.757 45.455 0.00 0.00 0.00 2.74
2882 2940 7.229506 GCCAGCTAAATCAACCATAATCTAGTT 59.770 37.037 0.00 0.00 0.00 2.24
2926 2984 2.414058 ATCTCGCGAATACAGCAGAG 57.586 50.000 11.33 0.00 36.95 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 3.000819 ACTGCCACCGATCCCGAA 61.001 61.111 0.00 0.00 38.22 4.30
65 66 2.677971 CCAAGAGGGTAATGACGCG 58.322 57.895 3.53 3.53 43.15 6.01
90 91 3.184382 TGATACCTGAGTTCCCTGACA 57.816 47.619 0.00 0.00 0.00 3.58
94 95 3.310954 ACCAGATGATACCTGAGTTCCCT 60.311 47.826 0.00 0.00 33.65 4.20
157 158 2.558359 CCCAAAACCGAAGAAGCTTCAT 59.442 45.455 27.57 17.00 0.00 2.57
183 184 2.737252 GAGAGAACACCAACGAATCCAC 59.263 50.000 0.00 0.00 0.00 4.02
190 191 4.376008 CGTGTAAATGAGAGAACACCAACG 60.376 45.833 0.00 0.00 39.20 4.10
197 198 5.681982 CGAGGATACGTGTAAATGAGAGAAC 59.318 44.000 0.00 0.00 46.39 3.01
199 200 4.261072 GCGAGGATACGTGTAAATGAGAGA 60.261 45.833 0.00 0.00 46.39 3.10
212 213 0.029567 GGACTGACTGCGAGGATACG 59.970 60.000 0.00 0.00 46.39 3.06
231 234 0.955178 ATGCGATAGTGAGGACCGAG 59.045 55.000 0.00 0.00 39.35 4.63
247 250 1.064654 GAGTTTCGATCCAGCCAATGC 59.935 52.381 0.00 0.00 37.95 3.56
248 251 1.672881 GGAGTTTCGATCCAGCCAATG 59.327 52.381 0.00 0.00 36.79 2.82
249 252 1.281867 TGGAGTTTCGATCCAGCCAAT 59.718 47.619 2.00 0.00 41.96 3.16
270 273 2.592001 TCCTCTCGCTCCGGATCG 60.592 66.667 21.30 21.30 0.00 3.69
272 275 1.152652 ATGTCCTCTCGCTCCGGAT 60.153 57.895 3.57 0.00 0.00 4.18
303 306 1.172180 ATGCACCGAACACACCAAGG 61.172 55.000 0.00 0.00 0.00 3.61
308 311 1.959226 ACCGATGCACCGAACACAC 60.959 57.895 0.00 0.00 0.00 3.82
347 350 2.333581 CCGAACCAAAACGGCACC 59.666 61.111 0.00 0.00 42.55 5.01
352 355 3.248266 CCTAGACTACCGAACCAAAACG 58.752 50.000 0.00 0.00 0.00 3.60
362 365 0.463295 TGAGGCGACCTAGACTACCG 60.463 60.000 0.00 0.00 31.76 4.02
396 399 5.239525 AGCTAGCCAAATAAGAAAATAGGCG 59.760 40.000 12.13 0.00 44.97 5.52
397 400 6.442112 CAGCTAGCCAAATAAGAAAATAGGC 58.558 40.000 12.13 0.00 40.85 3.93
409 412 1.000896 AACCCGCAGCTAGCCAAAT 60.001 52.632 12.13 0.00 41.38 2.32
412 415 2.669133 ATCAACCCGCAGCTAGCCA 61.669 57.895 12.13 0.00 41.38 4.75
419 422 3.499737 GACGCCATCAACCCGCAG 61.500 66.667 0.00 0.00 0.00 5.18
421 424 4.778143 AGGACGCCATCAACCCGC 62.778 66.667 0.00 0.00 0.00 6.13
422 425 2.511600 GAGGACGCCATCAACCCG 60.512 66.667 0.00 0.00 0.00 5.28
423 426 2.511600 CGAGGACGCCATCAACCC 60.512 66.667 0.00 0.00 0.00 4.11
444 447 1.004277 GAACCCCATACAAGCCAGTCA 59.996 52.381 0.00 0.00 0.00 3.41
467 470 0.035152 AAGCGATGCAAGGTGATGGA 60.035 50.000 0.00 0.00 0.00 3.41
479 482 2.098298 CAAACGGCCGAAGCGATG 59.902 61.111 35.90 16.26 41.24 3.84
484 487 1.196200 CAAAACACAAACGGCCGAAG 58.804 50.000 35.90 22.51 0.00 3.79
488 491 1.923864 CTGAACAAAACACAAACGGCC 59.076 47.619 0.00 0.00 0.00 6.13
489 492 1.923864 CCTGAACAAAACACAAACGGC 59.076 47.619 0.00 0.00 0.00 5.68
498 501 3.945285 TGAGACTGGTTCCTGAACAAAAC 59.055 43.478 11.78 1.60 42.85 2.43
556 565 0.107831 TCTTCCACACGAAACAGGGG 59.892 55.000 0.00 0.00 0.00 4.79
831 841 3.203442 TCCAGATGGACGGCGTAC 58.797 61.111 17.03 17.03 39.78 3.67
921 931 1.152030 TGGTGGTTCTGCCTCTCCT 60.152 57.895 0.00 0.00 38.35 3.69
941 951 2.335369 GAGAGTGCGTCGGTGTGT 59.665 61.111 0.00 0.00 0.00 3.72
942 952 2.016704 GTGAGAGTGCGTCGGTGTG 61.017 63.158 0.00 0.00 0.00 3.82
984 996 3.376859 ACGACATCTTGTCTAGAGAGCAG 59.623 47.826 0.00 0.00 44.85 4.24
995 1007 2.864097 GCACTGACTGACGACATCTTGT 60.864 50.000 0.00 0.00 0.00 3.16
1220 1236 0.590732 GTATGTGCGCTGCATCTTGC 60.591 55.000 18.37 0.00 41.91 4.01
1221 1237 1.012086 AGTATGTGCGCTGCATCTTG 58.988 50.000 18.37 0.00 41.91 3.02
1222 1238 1.399440 CAAGTATGTGCGCTGCATCTT 59.601 47.619 18.37 16.97 41.91 2.40
1223 1239 1.012086 CAAGTATGTGCGCTGCATCT 58.988 50.000 18.37 13.32 41.91 2.90
1224 1240 0.729116 ACAAGTATGTGCGCTGCATC 59.271 50.000 18.37 11.76 41.91 3.91
1227 1243 1.595489 GCATACAAGTATGTGCGCTGC 60.595 52.381 18.44 0.76 43.57 5.25
1228 1244 1.935873 AGCATACAAGTATGTGCGCTG 59.064 47.619 18.44 0.00 42.96 5.18
1229 1245 2.315925 AGCATACAAGTATGTGCGCT 57.684 45.000 18.44 8.88 43.57 5.92
1230 1246 4.732285 ATTAGCATACAAGTATGTGCGC 57.268 40.909 18.44 0.00 43.57 6.09
1231 1247 6.863645 AGAGTATTAGCATACAAGTATGTGCG 59.136 38.462 18.44 0.00 43.57 5.34
1232 1248 8.594881 AAGAGTATTAGCATACAAGTATGTGC 57.405 34.615 18.44 9.27 43.57 4.57
1238 1254 8.100791 TCCAACAAAGAGTATTAGCATACAAGT 58.899 33.333 0.00 0.00 38.24 3.16
1239 1255 8.492673 TCCAACAAAGAGTATTAGCATACAAG 57.507 34.615 0.00 0.00 38.24 3.16
1240 1256 8.892723 CATCCAACAAAGAGTATTAGCATACAA 58.107 33.333 0.00 0.00 38.24 2.41
1270 1286 3.726517 CACCCGCCAAGCTGAACG 61.727 66.667 0.00 0.00 0.00 3.95
1726 1748 5.945310 AGCCATCTAGCTGGATATTTGAAA 58.055 37.500 16.90 0.00 42.95 2.69
1727 1749 5.573380 AGCCATCTAGCTGGATATTTGAA 57.427 39.130 16.90 0.00 42.95 2.69
1738 1760 2.094100 TAGAAGCCAGCCATCTAGCT 57.906 50.000 0.00 0.00 46.45 3.32
1739 1761 3.415457 AATAGAAGCCAGCCATCTAGC 57.585 47.619 8.27 0.00 0.00 3.42
1740 1762 4.965814 TGAAATAGAAGCCAGCCATCTAG 58.034 43.478 8.27 0.00 0.00 2.43
1741 1763 5.072193 TCATGAAATAGAAGCCAGCCATCTA 59.928 40.000 0.00 5.53 0.00 1.98
1742 1764 3.939740 TGAAATAGAAGCCAGCCATCT 57.060 42.857 1.75 1.75 0.00 2.90
1743 1765 4.139786 TCATGAAATAGAAGCCAGCCATC 58.860 43.478 0.00 0.00 0.00 3.51
1744 1766 4.174704 TCATGAAATAGAAGCCAGCCAT 57.825 40.909 0.00 0.00 0.00 4.40
1745 1767 3.650281 TCATGAAATAGAAGCCAGCCA 57.350 42.857 0.00 0.00 0.00 4.75
1746 1768 3.505293 GGATCATGAAATAGAAGCCAGCC 59.495 47.826 0.00 0.00 0.00 4.85
1747 1769 4.139786 TGGATCATGAAATAGAAGCCAGC 58.860 43.478 0.00 0.00 0.00 4.85
1748 1770 5.121925 CGATGGATCATGAAATAGAAGCCAG 59.878 44.000 0.00 0.00 0.00 4.85
1749 1771 4.999311 CGATGGATCATGAAATAGAAGCCA 59.001 41.667 0.00 0.00 0.00 4.75
1750 1772 4.999950 ACGATGGATCATGAAATAGAAGCC 59.000 41.667 0.00 0.00 0.00 4.35
1751 1773 5.931146 AGACGATGGATCATGAAATAGAAGC 59.069 40.000 0.00 0.00 0.00 3.86
1752 1774 7.377398 AGAGACGATGGATCATGAAATAGAAG 58.623 38.462 0.00 0.00 0.00 2.85
1753 1775 7.295322 AGAGACGATGGATCATGAAATAGAA 57.705 36.000 0.00 0.00 0.00 2.10
1754 1776 6.907853 AGAGACGATGGATCATGAAATAGA 57.092 37.500 0.00 0.00 0.00 1.98
1755 1777 7.328982 CAGAAGAGACGATGGATCATGAAATAG 59.671 40.741 0.00 0.00 0.00 1.73
1756 1778 7.150640 CAGAAGAGACGATGGATCATGAAATA 58.849 38.462 0.00 0.00 0.00 1.40
1757 1779 5.990386 CAGAAGAGACGATGGATCATGAAAT 59.010 40.000 0.00 0.00 0.00 2.17
1758 1780 5.354767 CAGAAGAGACGATGGATCATGAAA 58.645 41.667 0.00 0.00 0.00 2.69
1759 1781 4.202192 CCAGAAGAGACGATGGATCATGAA 60.202 45.833 0.00 0.00 34.60 2.57
1760 1782 3.320256 CCAGAAGAGACGATGGATCATGA 59.680 47.826 0.00 0.00 34.60 3.07
1761 1783 3.320256 TCCAGAAGAGACGATGGATCATG 59.680 47.826 0.00 0.00 36.92 3.07
1762 1784 3.320541 GTCCAGAAGAGACGATGGATCAT 59.679 47.826 0.00 0.00 43.42 2.45
1763 1785 2.690497 GTCCAGAAGAGACGATGGATCA 59.310 50.000 0.00 0.00 43.42 2.92
1764 1786 2.035321 GGTCCAGAAGAGACGATGGATC 59.965 54.545 0.00 0.00 43.42 3.36
1765 1787 2.035632 GGTCCAGAAGAGACGATGGAT 58.964 52.381 0.00 0.00 43.42 3.41
1766 1788 1.475403 GGTCCAGAAGAGACGATGGA 58.525 55.000 0.00 0.00 39.50 3.41
1767 1789 0.461961 GGGTCCAGAAGAGACGATGG 59.538 60.000 0.00 0.00 34.97 3.51
1768 1790 1.407258 GAGGGTCCAGAAGAGACGATG 59.593 57.143 0.00 0.00 34.97 3.84
1769 1791 1.770294 GAGGGTCCAGAAGAGACGAT 58.230 55.000 0.00 0.00 34.97 3.73
1770 1792 0.677098 CGAGGGTCCAGAAGAGACGA 60.677 60.000 0.00 0.00 34.97 4.20
1771 1793 1.658686 CCGAGGGTCCAGAAGAGACG 61.659 65.000 0.00 0.00 34.97 4.18
1772 1794 0.612453 ACCGAGGGTCCAGAAGAGAC 60.612 60.000 0.00 0.00 0.00 3.36
1773 1795 0.114560 AACCGAGGGTCCAGAAGAGA 59.885 55.000 0.00 0.00 33.12 3.10
1774 1796 0.533032 GAACCGAGGGTCCAGAAGAG 59.467 60.000 0.00 0.00 33.12 2.85
1775 1797 0.903454 GGAACCGAGGGTCCAGAAGA 60.903 60.000 20.76 0.00 33.12 2.87
1776 1798 0.905337 AGGAACCGAGGGTCCAGAAG 60.905 60.000 26.49 0.00 33.12 2.85
1777 1799 0.410663 TAGGAACCGAGGGTCCAGAA 59.589 55.000 26.49 10.01 33.12 3.02
1778 1800 0.410663 TTAGGAACCGAGGGTCCAGA 59.589 55.000 26.49 12.29 33.12 3.86
1779 1801 1.413077 GATTAGGAACCGAGGGTCCAG 59.587 57.143 26.49 0.00 33.12 3.86
1780 1802 1.492764 GATTAGGAACCGAGGGTCCA 58.507 55.000 26.49 8.78 33.12 4.02
1781 1803 0.388294 CGATTAGGAACCGAGGGTCC 59.612 60.000 18.27 18.27 33.12 4.46
1782 1804 0.388294 CCGATTAGGAACCGAGGGTC 59.612 60.000 0.00 0.00 45.00 4.46
1783 1805 2.512973 CCGATTAGGAACCGAGGGT 58.487 57.895 0.00 0.00 45.00 4.34
1793 1815 0.460311 ACAAGAGCCGTCCGATTAGG 59.540 55.000 0.00 0.00 42.97 2.69
1831 1853 6.825213 CCAGTCTACCTGAATGAATGAATGAA 59.175 38.462 0.00 0.00 44.49 2.57
1832 1854 6.351711 CCAGTCTACCTGAATGAATGAATGA 58.648 40.000 0.00 0.00 44.49 2.57
1833 1855 5.008415 GCCAGTCTACCTGAATGAATGAATG 59.992 44.000 0.00 0.00 44.49 2.67
1834 1856 5.128919 GCCAGTCTACCTGAATGAATGAAT 58.871 41.667 0.00 0.00 44.49 2.57
1835 1857 4.517285 GCCAGTCTACCTGAATGAATGAA 58.483 43.478 0.00 0.00 44.49 2.57
1836 1858 3.430790 CGCCAGTCTACCTGAATGAATGA 60.431 47.826 0.00 0.00 44.49 2.57
1842 1864 1.202580 GCATCGCCAGTCTACCTGAAT 60.203 52.381 0.00 0.00 44.49 2.57
1849 1871 2.501128 GCCAGCATCGCCAGTCTA 59.499 61.111 0.00 0.00 0.00 2.59
1953 1975 1.773052 AGATGGTCTGGATGATGGTGG 59.227 52.381 0.00 0.00 0.00 4.61
2043 2065 3.646162 TCCACACTTTGTACATCCTCAGT 59.354 43.478 0.00 0.00 0.00 3.41
2271 2294 6.840780 AGTGCTTCAAACTATATTTTGCCT 57.159 33.333 9.98 0.53 36.56 4.75
2298 2321 5.299949 TGGTATCATCACATCGAATTCAGG 58.700 41.667 6.22 0.00 0.00 3.86
2304 2327 9.996554 ATTTACTATTGGTATCATCACATCGAA 57.003 29.630 0.00 0.00 0.00 3.71
2319 2342 8.514594 TGAAGTTCTGCTTTGATTTACTATTGG 58.485 33.333 4.17 0.00 37.59 3.16
2377 2403 8.417106 GGTTCCTTTTTCTTCTTCTTTGATTCT 58.583 33.333 0.00 0.00 0.00 2.40
2401 2432 7.342026 TGTGTATCTGTGACTTCATATACTGGT 59.658 37.037 0.00 0.00 0.00 4.00
2411 2442 5.928839 ACTGATGTTGTGTATCTGTGACTTC 59.071 40.000 0.00 0.00 36.01 3.01
2424 2455 4.578516 TGTAGTTTTGGGACTGATGTTGTG 59.421 41.667 0.00 0.00 0.00 3.33
2449 2480 4.036852 TGTTGCACATTCCATACAACGAAA 59.963 37.500 0.00 0.00 42.68 3.46
2455 2486 2.512705 TGCTGTTGCACATTCCATACA 58.487 42.857 0.00 0.00 45.31 2.29
2470 2501 4.284490 TGAAGGACTCTAATCTTGTGCTGT 59.716 41.667 0.00 0.00 32.89 4.40
2552 2584 5.055812 TGAATTTTGTTGAATCAGTTGGCC 58.944 37.500 0.00 0.00 0.00 5.36
2592 2626 8.439971 TGCTAATTAGGATAAACTCATGTGGAT 58.560 33.333 14.28 0.00 0.00 3.41
2593 2627 7.801104 TGCTAATTAGGATAAACTCATGTGGA 58.199 34.615 14.28 0.00 0.00 4.02
2603 2637 9.656040 TTACTCGTTGTTGCTAATTAGGATAAA 57.344 29.630 14.28 6.25 0.00 1.40
2619 2653 3.728076 TTCTGCTGAGTTACTCGTTGT 57.272 42.857 7.92 0.00 32.35 3.32
2621 2655 4.694339 AGTTTTCTGCTGAGTTACTCGTT 58.306 39.130 7.92 0.00 32.35 3.85
2622 2656 4.299978 GAGTTTTCTGCTGAGTTACTCGT 58.700 43.478 7.92 0.00 32.35 4.18
2624 2658 3.675698 CCGAGTTTTCTGCTGAGTTACTC 59.324 47.826 5.27 5.27 0.00 2.59
2696 2754 4.701663 CTGAGGAAGCCGAAGCAA 57.298 55.556 0.00 0.00 43.56 3.91
2819 2877 3.002348 GGAATTTGAAGACGATAAGGCCG 59.998 47.826 0.00 0.00 0.00 6.13
2863 2921 8.778059 TGGTCCTAACTAGATTATGGTTGATTT 58.222 33.333 0.00 0.00 34.05 2.17
2882 2940 7.808279 TTCTCCTCTTTCTTTATTGGTCCTA 57.192 36.000 0.00 0.00 0.00 2.94
2926 2984 1.818674 CACTGGTAAATCCTGTTGGCC 59.181 52.381 0.00 0.00 44.20 5.36



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

AutoCloner maintained by Alex Coulton.