Multiple sequence alignment - TraesCS2D01G598100

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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 TraesCS2D01G598100 chr2D 100.000 2357 0 0 1 2357 650321605 650323961 0.000000e+00 4353
1 TraesCS2D01G598100 chr2B 88.289 2391 178 56 3 2357 786225648 786227972 0.000000e+00 2771
2 TraesCS2D01G598100 chr2A 87.622 1939 155 49 10 1905 774574811 774572915 0.000000e+00 2172
3 TraesCS2D01G598100 chr2A 92.623 122 7 2 2235 2355 774572614 774572494 8.660000e-40 174
4 TraesCS2D01G598100 chrUn 88.251 366 29 10 293 649 96707904 96707544 2.170000e-115 425
5 TraesCS2D01G598100 chrUn 86.545 275 33 3 1 271 96731850 96731576 1.370000e-77 300
6 TraesCS2D01G598100 chrUn 85.714 140 17 2 649 788 96702250 96702114 6.790000e-31 145
7 TraesCS2D01G598100 chr6B 88.650 326 32 5 283 608 47899051 47898731 2.200000e-105 392
8 TraesCS2D01G598100 chr6B 79.310 232 28 14 684 910 47898727 47898511 6.790000e-31 145


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 TraesCS2D01G598100 chr2D 650321605 650323961 2356 False 4353.0 4353 100.0000 1 2357 1 chr2D.!!$F1 2356
1 TraesCS2D01G598100 chr2B 786225648 786227972 2324 False 2771.0 2771 88.2890 3 2357 1 chr2B.!!$F1 2354
2 TraesCS2D01G598100 chr2A 774572494 774574811 2317 True 1173.0 2172 90.1225 10 2355 2 chr2A.!!$R1 2345
3 TraesCS2D01G598100 chr6B 47898511 47899051 540 True 268.5 392 83.9800 283 910 2 chr6B.!!$R1 627

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
93 94 0.395862 ATCAGACCGACGGGATCAGT 60.396 55.0 20.0 0.0 36.97 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1614 1658 0.587768 CACAAGCGATGCTGTGTTCA 59.412 50.0 0.0 0.0 39.62 3.18 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
78 79 0.962356 ACGAGGGCCAGCAAAATCAG 60.962 55.000 6.18 0.00 0.00 2.90
93 94 0.395862 ATCAGACCGACGGGATCAGT 60.396 55.000 20.00 0.00 36.97 3.41
198 203 3.820467 CAGCAATTTACCAGACCTCAACA 59.180 43.478 0.00 0.00 0.00 3.33
220 225 6.064060 ACAGAAAAGATTCAGACATGGAACA 58.936 36.000 0.00 0.00 39.87 3.18
507 516 3.862642 GCCTAGCTCTGGGATATTTGACG 60.863 52.174 3.27 0.00 32.26 4.35
559 568 7.835822 TCTTCTAGAGGATAGCTCATATTTGC 58.164 38.462 0.00 0.00 0.00 3.68
678 687 1.164411 TTATTCGCCAGGCTGTGTTG 58.836 50.000 14.43 0.00 0.00 3.33
679 688 1.305219 TATTCGCCAGGCTGTGTTGC 61.305 55.000 14.43 8.56 0.00 4.17
725 734 7.085116 TGTTTGTATTTCGGCGAAATTGTTAT 58.915 30.769 41.55 25.79 41.64 1.89
730 739 8.024285 TGTATTTCGGCGAAATTGTTATTTTCT 58.976 29.630 41.55 22.81 41.64 2.52
767 776 5.483685 AAACAGAGTAGCATACAACAGGA 57.516 39.130 0.00 0.00 46.26 3.86
841 851 6.104665 AGAACAGATGACACATACACATGAG 58.895 40.000 0.00 0.00 35.96 2.90
842 852 5.411831 ACAGATGACACATACACATGAGT 57.588 39.130 0.00 0.00 38.49 3.41
852 862 4.379174 ACATGAGTGAACACGCCC 57.621 55.556 0.00 0.00 36.20 6.13
853 863 1.449782 ACATGAGTGAACACGCCCA 59.550 52.632 0.00 3.89 36.20 5.36
1062 1074 1.351017 TGCCCCTCTTTGTCAACTAGG 59.649 52.381 0.00 5.67 0.00 3.02
1095 1107 2.509052 TCCATTTGATACGCTCTCCG 57.491 50.000 0.00 0.00 44.21 4.63
1148 1160 3.818787 CAGCGGGGCAGCATTGTC 61.819 66.667 6.94 0.00 40.15 3.18
1240 1255 3.372206 GCTAGCACACACACAGAAATAGG 59.628 47.826 10.63 0.00 0.00 2.57
1245 1260 4.389374 CACACACACAGAAATAGGAAGGT 58.611 43.478 0.00 0.00 0.00 3.50
1246 1261 4.821805 CACACACACAGAAATAGGAAGGTT 59.178 41.667 0.00 0.00 0.00 3.50
1248 1263 5.531287 ACACACACAGAAATAGGAAGGTTTC 59.469 40.000 0.00 0.00 35.18 2.78
1251 1266 6.486993 ACACACAGAAATAGGAAGGTTTCTTC 59.513 38.462 0.00 0.00 46.47 2.87
1376 1391 1.555967 TTGCAGGGGAAAGCCAATAC 58.444 50.000 0.00 0.00 35.15 1.89
1383 1398 2.558800 GGGGAAAGCCAATACCTCCAAA 60.559 50.000 0.00 0.00 35.15 3.28
1420 1436 8.497554 GCAGAAAACATGCAAAGATAAATGAAA 58.502 29.630 0.00 0.00 43.31 2.69
1453 1472 5.562696 CGAAGTACAATGCAAGTGATTTGGT 60.563 40.000 7.69 0.00 34.17 3.67
1468 1487 1.794151 TTGGTCTGCACAATGGCACG 61.794 55.000 0.00 0.00 39.25 5.34
1472 1491 0.950555 TCTGCACAATGGCACGTCTC 60.951 55.000 0.00 0.00 39.25 3.36
1477 1496 0.885879 ACAATGGCACGTCTCGTCTA 59.114 50.000 0.00 0.00 38.32 2.59
1481 1500 0.240145 TGGCACGTCTCGTCTAACTG 59.760 55.000 0.00 0.00 38.32 3.16
1516 1538 3.008375 TCATACTGAAGACTTGCAGCCTT 59.992 43.478 12.02 0.00 35.57 4.35
1529 1551 5.411669 ACTTGCAGCCTTACATAAACTGTAC 59.588 40.000 0.00 0.00 40.06 2.90
1530 1552 3.930229 TGCAGCCTTACATAAACTGTACG 59.070 43.478 0.00 0.00 40.06 3.67
1534 1556 5.815740 CAGCCTTACATAAACTGTACGGATT 59.184 40.000 9.17 5.47 43.59 3.01
1535 1557 6.018994 CAGCCTTACATAAACTGTACGGATTC 60.019 42.308 9.17 0.00 43.59 2.52
1537 1559 8.995111 AGCCTTACATAAACTGTACGGATTCCT 61.995 40.741 9.17 0.00 43.59 3.36
1538 1560 7.695869 CTTACATAAACTGTACGGATTCCTC 57.304 40.000 9.17 0.00 40.06 3.71
1539 1561 5.934402 ACATAAACTGTACGGATTCCTCT 57.066 39.130 9.17 0.00 35.91 3.69
1561 1605 6.412214 TCTTTCTACCACTATTTAGCCCAAC 58.588 40.000 0.00 0.00 0.00 3.77
1563 1607 4.025360 TCTACCACTATTTAGCCCAACGA 58.975 43.478 0.00 0.00 0.00 3.85
1566 1610 4.595986 ACCACTATTTAGCCCAACGATTT 58.404 39.130 0.00 0.00 0.00 2.17
1602 1646 7.556275 TCCAATCTGAAAACTAACTCAACTTGT 59.444 33.333 0.00 0.00 0.00 3.16
1626 1670 8.138074 TGTATAGTTAGAGATGAACACAGCATC 58.862 37.037 0.00 0.00 41.85 3.91
1631 1675 1.736126 AGATGAACACAGCATCGCTTG 59.264 47.619 0.00 0.00 45.18 4.01
1635 1679 0.588252 AACACAGCATCGCTTGTGTC 59.412 50.000 18.01 0.00 43.87 3.67
1650 1694 5.032863 GCTTGTGTCATATCTGTTTGATGC 58.967 41.667 0.00 0.00 36.65 3.91
1653 1697 4.567959 TGTGTCATATCTGTTTGATGCGAG 59.432 41.667 0.00 0.00 36.65 5.03
1679 1723 1.756538 CTGTTGCCCTGGTTCAACTTT 59.243 47.619 21.61 0.00 42.11 2.66
1688 1732 4.519350 CCCTGGTTCAACTTTTAGGACTTC 59.481 45.833 0.00 0.00 0.00 3.01
1690 1734 5.470437 CCTGGTTCAACTTTTAGGACTTCTC 59.530 44.000 0.00 0.00 0.00 2.87
1691 1735 5.996644 TGGTTCAACTTTTAGGACTTCTCA 58.003 37.500 0.00 0.00 0.00 3.27
1692 1736 6.419791 TGGTTCAACTTTTAGGACTTCTCAA 58.580 36.000 0.00 0.00 0.00 3.02
1693 1737 6.317893 TGGTTCAACTTTTAGGACTTCTCAAC 59.682 38.462 0.00 0.00 0.00 3.18
1694 1738 6.317893 GGTTCAACTTTTAGGACTTCTCAACA 59.682 38.462 0.00 0.00 0.00 3.33
1695 1739 7.410485 GTTCAACTTTTAGGACTTCTCAACAG 58.590 38.462 0.00 0.00 0.00 3.16
1696 1740 6.650120 TCAACTTTTAGGACTTCTCAACAGT 58.350 36.000 0.00 0.00 0.00 3.55
1697 1741 6.761714 TCAACTTTTAGGACTTCTCAACAGTC 59.238 38.462 0.00 0.00 40.12 3.51
1698 1742 6.235231 ACTTTTAGGACTTCTCAACAGTCA 57.765 37.500 2.68 0.00 42.28 3.41
1707 1751 3.627395 TCTCAACAGTCAACACCACTT 57.373 42.857 0.00 0.00 0.00 3.16
1708 1752 4.746535 TCTCAACAGTCAACACCACTTA 57.253 40.909 0.00 0.00 0.00 2.24
1746 1790 6.784068 ACGAAAATACAACTTCAAAACACG 57.216 33.333 0.00 0.00 0.00 4.49
1789 1835 1.065636 CCTGAGAAGCCATGCTCTGAA 60.066 52.381 0.00 0.00 38.25 3.02
1798 1844 1.209019 CCATGCTCTGAACAGCTAGGT 59.791 52.381 0.00 0.00 40.39 3.08
1819 1865 1.648116 AGCTACGGGTAAAAGTCCCA 58.352 50.000 1.91 0.00 44.81 4.37
1820 1866 1.277273 AGCTACGGGTAAAAGTCCCAC 59.723 52.381 1.91 0.00 44.81 4.61
1822 1868 0.607620 TACGGGTAAAAGTCCCACGG 59.392 55.000 1.91 0.00 44.81 4.94
1823 1869 1.372307 CGGGTAAAAGTCCCACGGT 59.628 57.895 1.91 0.00 44.81 4.83
1846 1892 6.484308 GGTTTGTTTAGTAAGCAGGTGAAGTA 59.516 38.462 0.00 0.00 0.00 2.24
1864 1910 7.254455 GGTGAAGTATATTCTGTATGCACACAC 60.254 40.741 0.00 0.00 0.00 3.82
1870 1916 9.645059 GTATATTCTGTATGCACACACTATGAT 57.355 33.333 0.00 0.00 0.00 2.45
1878 1926 9.225436 TGTATGCACACACTATGATAAAGAAAA 57.775 29.630 0.00 0.00 0.00 2.29
1882 1930 6.907212 GCACACACTATGATAAAGAAAATCCG 59.093 38.462 0.00 0.00 0.00 4.18
1883 1931 7.414098 GCACACACTATGATAAAGAAAATCCGT 60.414 37.037 0.00 0.00 0.00 4.69
1884 1932 8.116753 CACACACTATGATAAAGAAAATCCGTC 58.883 37.037 0.00 0.00 0.00 4.79
1885 1933 7.822334 ACACACTATGATAAAGAAAATCCGTCA 59.178 33.333 0.00 0.00 0.00 4.35
1895 1943 5.290493 AGAAAATCCGTCAGTGCCATATA 57.710 39.130 0.00 0.00 0.00 0.86
1898 1946 2.455674 TCCGTCAGTGCCATATATGC 57.544 50.000 7.24 3.97 0.00 3.14
1899 1947 1.970640 TCCGTCAGTGCCATATATGCT 59.029 47.619 7.24 0.00 0.00 3.79
1900 1948 2.071540 CCGTCAGTGCCATATATGCTG 58.928 52.381 7.24 9.39 0.00 4.41
1901 1949 2.548707 CCGTCAGTGCCATATATGCTGT 60.549 50.000 7.24 0.00 0.00 4.40
1902 1950 2.477754 CGTCAGTGCCATATATGCTGTG 59.522 50.000 7.24 2.37 0.00 3.66
1903 1951 2.225019 GTCAGTGCCATATATGCTGTGC 59.775 50.000 7.24 6.02 0.00 4.57
1912 1960 1.100510 ATATGCTGTGCTTGTGCTGG 58.899 50.000 0.00 0.00 40.48 4.85
1922 1970 1.787012 CTTGTGCTGGTTGAATTGCC 58.213 50.000 0.00 0.00 0.00 4.52
1928 1976 1.200948 GCTGGTTGAATTGCCTCTGTC 59.799 52.381 0.00 0.00 0.00 3.51
1933 1981 3.507233 GGTTGAATTGCCTCTGTCATGAA 59.493 43.478 0.00 0.00 0.00 2.57
1936 1984 5.571784 TGAATTGCCTCTGTCATGAATTC 57.428 39.130 0.00 0.00 32.73 2.17
1937 1985 5.258841 TGAATTGCCTCTGTCATGAATTCT 58.741 37.500 7.05 0.00 33.11 2.40
1942 1990 3.370315 GCCTCTGTCATGAATTCTCAGGT 60.370 47.826 7.05 0.00 34.89 4.00
1951 2006 5.819379 TCATGAATTCTCAGGTGTTATGAGC 59.181 40.000 7.05 0.00 43.20 4.26
1954 2009 6.003326 TGAATTCTCAGGTGTTATGAGCAAA 58.997 36.000 7.05 0.00 43.20 3.68
1956 2011 4.890158 TCTCAGGTGTTATGAGCAAAGA 57.110 40.909 0.00 0.00 43.20 2.52
1959 2014 3.067106 CAGGTGTTATGAGCAAAGACGT 58.933 45.455 0.00 0.00 0.00 4.34
1960 2015 3.067106 AGGTGTTATGAGCAAAGACGTG 58.933 45.455 0.00 0.00 0.00 4.49
2126 2181 9.304731 CAATGAGATATACAACCAAACCATTTG 57.695 33.333 0.00 0.00 40.32 2.32
2128 2183 8.050778 TGAGATATACAACCAAACCATTTGAC 57.949 34.615 2.86 0.00 43.26 3.18
2129 2184 7.667635 TGAGATATACAACCAAACCATTTGACA 59.332 33.333 2.86 0.00 43.26 3.58
2130 2185 8.593945 AGATATACAACCAAACCATTTGACAT 57.406 30.769 2.86 0.00 43.26 3.06
2146 2206 9.027129 CCATTTGACATCAATCACATCATTTAC 57.973 33.333 0.00 0.00 35.55 2.01
2228 2288 3.196939 AGAGCCGTACAGAGTACCTAG 57.803 52.381 2.06 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.889177 TCATACAATCCCTACAAAGAAATGCA 59.111 34.615 0.00 0.00 0.00 3.96
2 3 7.333528 TCATACAATCCCTACAAAGAAATGC 57.666 36.000 0.00 0.00 0.00 3.56
6 7 8.519799 GGATTTCATACAATCCCTACAAAGAA 57.480 34.615 1.52 0.00 44.71 2.52
33 34 5.235186 CAGATTGTAAGAGCCGGATAAACTG 59.765 44.000 5.05 0.00 0.00 3.16
78 79 1.139095 GACACTGATCCCGTCGGTC 59.861 63.158 11.06 2.48 44.70 4.79
120 121 2.291153 ACCCAGAACACCTCCAATGATG 60.291 50.000 0.00 0.00 0.00 3.07
183 184 5.623956 TCTTTTCTGTTGAGGTCTGGTAA 57.376 39.130 0.00 0.00 0.00 2.85
198 203 7.587037 TTTGTTCCATGTCTGAATCTTTTCT 57.413 32.000 0.00 0.00 32.78 2.52
220 225 6.743575 AAATAAAGTAGATGCACGAGCTTT 57.256 33.333 6.36 11.23 42.74 3.51
254 260 9.755804 TTCTATGCTGTATGATACTCTTTTCTG 57.244 33.333 4.03 0.00 0.00 3.02
256 262 9.757227 ACTTCTATGCTGTATGATACTCTTTTC 57.243 33.333 4.03 0.00 0.00 2.29
259 265 9.757227 GAAACTTCTATGCTGTATGATACTCTT 57.243 33.333 4.03 0.00 0.00 2.85
417 426 2.997315 TCCTGAGCTGGGTGACGG 60.997 66.667 0.00 0.00 0.00 4.79
507 516 0.237235 TCAATGTTGGAACTTCGCGC 59.763 50.000 0.00 0.00 0.00 6.86
559 568 1.064803 CTCGAGAGATGGAAGTGTCGG 59.935 57.143 6.58 0.00 40.84 4.79
662 671 3.286751 GCAACACAGCCTGGCGAA 61.287 61.111 13.96 0.00 0.00 4.70
665 674 2.492773 AACAGCAACACAGCCTGGC 61.493 57.895 11.65 11.65 34.23 4.85
705 714 8.389586 AGAAAATAACAATTTCGCCGAAATAC 57.610 30.769 23.85 8.37 40.77 1.89
725 734 8.744652 TCTGTTTTCTACATGGTGAAAAGAAAA 58.255 29.630 20.71 15.71 41.10 2.29
730 739 7.041372 GCTACTCTGTTTTCTACATGGTGAAAA 60.041 37.037 18.03 18.03 39.09 2.29
841 851 1.308069 ATCATGCTGGGCGTGTTCAC 61.308 55.000 10.83 0.00 44.84 3.18
842 852 1.002257 ATCATGCTGGGCGTGTTCA 60.002 52.632 10.83 0.00 44.84 3.18
843 853 0.745845 AGATCATGCTGGGCGTGTTC 60.746 55.000 10.83 11.61 44.84 3.18
844 854 0.322816 AAGATCATGCTGGGCGTGTT 60.323 50.000 10.83 3.74 44.84 3.32
845 855 0.745845 GAAGATCATGCTGGGCGTGT 60.746 55.000 10.83 0.41 44.84 4.49
847 857 1.153086 GGAAGATCATGCTGGGCGT 60.153 57.895 0.00 0.00 0.00 5.68
849 859 0.822532 CAGGGAAGATCATGCTGGGC 60.823 60.000 0.00 0.00 0.00 5.36
850 860 0.178998 CCAGGGAAGATCATGCTGGG 60.179 60.000 5.61 0.00 0.00 4.45
851 861 0.841961 TCCAGGGAAGATCATGCTGG 59.158 55.000 6.88 6.88 0.00 4.85
852 862 1.767088 TCTCCAGGGAAGATCATGCTG 59.233 52.381 0.00 0.00 0.00 4.41
853 863 2.187239 TCTCCAGGGAAGATCATGCT 57.813 50.000 0.00 0.00 0.00 3.79
1095 1107 2.292292 GTCAGAGAGAGGCGGTCTATTC 59.708 54.545 0.00 0.00 34.71 1.75
1148 1160 2.126071 AGGTCGACGTGAATGGCG 60.126 61.111 10.45 0.00 0.00 5.69
1240 1255 3.963383 TCAAGCAACGAAGAAACCTTC 57.037 42.857 0.00 0.00 37.33 3.46
1245 1260 4.894784 AGGTCTATCAAGCAACGAAGAAA 58.105 39.130 0.00 0.00 0.00 2.52
1246 1261 4.537135 AGGTCTATCAAGCAACGAAGAA 57.463 40.909 0.00 0.00 0.00 2.52
1248 1263 3.181516 GCAAGGTCTATCAAGCAACGAAG 60.182 47.826 0.00 0.00 0.00 3.79
1251 1266 1.061131 CGCAAGGTCTATCAAGCAACG 59.939 52.381 0.00 0.00 0.00 4.10
1252 1267 2.346803 TCGCAAGGTCTATCAAGCAAC 58.653 47.619 0.00 0.00 38.47 4.17
1253 1268 2.760634 TCGCAAGGTCTATCAAGCAA 57.239 45.000 0.00 0.00 38.47 3.91
1254 1269 2.760634 TTCGCAAGGTCTATCAAGCA 57.239 45.000 0.00 0.00 38.47 3.91
1258 1273 5.984725 TCCTATTTTTCGCAAGGTCTATCA 58.015 37.500 0.00 0.00 38.47 2.15
1368 1383 4.881157 ATTAGGTTTGGAGGTATTGGCT 57.119 40.909 0.00 0.00 0.00 4.75
1376 1391 2.165030 CTGCTGCAATTAGGTTTGGAGG 59.835 50.000 3.02 0.00 43.09 4.30
1383 1398 4.813027 CATGTTTTCTGCTGCAATTAGGT 58.187 39.130 3.02 0.00 0.00 3.08
1420 1436 5.940192 TGCATTGTACTTCGTCTTCAATT 57.060 34.783 0.00 0.00 0.00 2.32
1436 1455 2.991190 GCAGACCAAATCACTTGCATTG 59.009 45.455 0.00 0.00 33.27 2.82
1446 1465 1.273048 TGCCATTGTGCAGACCAAATC 59.727 47.619 0.00 0.00 36.04 2.17
1453 1472 0.950555 GAGACGTGCCATTGTGCAGA 60.951 55.000 0.00 0.00 43.02 4.26
1516 1538 7.414222 AAGAGGAATCCGTACAGTTTATGTA 57.586 36.000 0.00 0.00 43.66 2.29
1529 1551 5.793030 ATAGTGGTAGAAAGAGGAATCCG 57.207 43.478 0.00 0.00 0.00 4.18
1530 1552 7.658167 GCTAAATAGTGGTAGAAAGAGGAATCC 59.342 40.741 0.00 0.00 0.00 3.01
1531 1553 7.658167 GGCTAAATAGTGGTAGAAAGAGGAATC 59.342 40.741 0.00 0.00 0.00 2.52
1532 1554 7.420330 GGGCTAAATAGTGGTAGAAAGAGGAAT 60.420 40.741 0.00 0.00 0.00 3.01
1534 1556 5.365895 GGGCTAAATAGTGGTAGAAAGAGGA 59.634 44.000 0.00 0.00 0.00 3.71
1535 1557 5.130477 TGGGCTAAATAGTGGTAGAAAGAGG 59.870 44.000 0.00 0.00 0.00 3.69
1537 1559 6.412214 GTTGGGCTAAATAGTGGTAGAAAGA 58.588 40.000 0.00 0.00 0.00 2.52
1538 1560 5.293569 CGTTGGGCTAAATAGTGGTAGAAAG 59.706 44.000 0.00 0.00 0.00 2.62
1539 1561 5.046448 TCGTTGGGCTAAATAGTGGTAGAAA 60.046 40.000 0.00 0.00 0.00 2.52
1561 1605 7.734924 TCAGATTGGAGATTGGAATAAATCG 57.265 36.000 0.00 0.00 40.75 3.34
1566 1610 9.973661 TTAGTTTTCAGATTGGAGATTGGAATA 57.026 29.630 0.00 0.00 0.00 1.75
1602 1646 7.363431 CGATGCTGTGTTCATCTCTAACTATA 58.637 38.462 0.00 0.00 38.47 1.31
1609 1653 1.206610 AGCGATGCTGTGTTCATCTCT 59.793 47.619 0.00 0.00 37.57 3.10
1612 1656 1.466167 ACAAGCGATGCTGTGTTCATC 59.534 47.619 0.00 0.00 39.62 2.92
1613 1657 1.198408 CACAAGCGATGCTGTGTTCAT 59.802 47.619 0.00 0.00 39.62 2.57
1614 1658 0.587768 CACAAGCGATGCTGTGTTCA 59.412 50.000 0.00 0.00 39.62 3.18
1615 1659 0.588252 ACACAAGCGATGCTGTGTTC 59.412 50.000 5.34 0.00 42.97 3.18
1626 1670 4.926860 TCAAACAGATATGACACAAGCG 57.073 40.909 0.00 0.00 0.00 4.68
1631 1675 4.025396 CCTCGCATCAAACAGATATGACAC 60.025 45.833 0.00 0.00 34.43 3.67
1635 1679 2.874086 TGCCTCGCATCAAACAGATATG 59.126 45.455 0.00 0.00 34.43 1.78
1665 1709 4.100279 AGTCCTAAAAGTTGAACCAGGG 57.900 45.455 0.00 0.00 0.00 4.45
1668 1712 5.996644 TGAGAAGTCCTAAAAGTTGAACCA 58.003 37.500 0.00 0.00 0.00 3.67
1679 1723 5.357257 GTGTTGACTGTTGAGAAGTCCTAA 58.643 41.667 1.40 0.00 42.85 2.69
1688 1732 4.876107 ACTTAAGTGGTGTTGACTGTTGAG 59.124 41.667 7.48 0.00 0.00 3.02
1690 1734 4.876107 AGACTTAAGTGGTGTTGACTGTTG 59.124 41.667 14.14 0.00 0.00 3.33
1691 1735 5.099042 AGACTTAAGTGGTGTTGACTGTT 57.901 39.130 14.14 0.00 0.00 3.16
1692 1736 4.755266 AGACTTAAGTGGTGTTGACTGT 57.245 40.909 14.14 0.00 0.00 3.55
1693 1737 8.827177 TTATAAGACTTAAGTGGTGTTGACTG 57.173 34.615 14.14 0.00 0.00 3.51
1720 1764 7.007546 CGTGTTTTGAAGTTGTATTTTCGTTCA 59.992 33.333 0.00 0.00 0.00 3.18
1722 1766 6.802834 ACGTGTTTTGAAGTTGTATTTTCGTT 59.197 30.769 0.00 0.00 0.00 3.85
1724 1768 6.784068 ACGTGTTTTGAAGTTGTATTTTCG 57.216 33.333 0.00 0.00 0.00 3.46
1733 1777 5.106317 ACATGACTGAACGTGTTTTGAAGTT 60.106 36.000 0.00 0.00 36.76 2.66
1746 1790 7.897864 AGGTATAGGCTTATACATGACTGAAC 58.102 38.462 22.97 6.65 42.21 3.18
1798 1844 3.893326 GGGACTTTTACCCGTAGCTTA 57.107 47.619 0.00 0.00 37.85 3.09
1813 1859 4.383173 CTTACTAAACAAACCGTGGGACT 58.617 43.478 0.00 0.00 0.00 3.85
1814 1860 3.058708 GCTTACTAAACAAACCGTGGGAC 60.059 47.826 0.00 0.00 0.00 4.46
1819 1865 3.562557 CACCTGCTTACTAAACAAACCGT 59.437 43.478 0.00 0.00 0.00 4.83
1820 1866 3.810941 TCACCTGCTTACTAAACAAACCG 59.189 43.478 0.00 0.00 0.00 4.44
1822 1868 6.373186 ACTTCACCTGCTTACTAAACAAAC 57.627 37.500 0.00 0.00 0.00 2.93
1823 1869 9.953565 ATATACTTCACCTGCTTACTAAACAAA 57.046 29.630 0.00 0.00 0.00 2.83
1864 1910 7.348201 GCACTGACGGATTTTCTTTATCATAG 58.652 38.462 0.00 0.00 0.00 2.23
1870 1916 3.745799 TGGCACTGACGGATTTTCTTTA 58.254 40.909 0.00 0.00 0.00 1.85
1872 1920 2.270352 TGGCACTGACGGATTTTCTT 57.730 45.000 0.00 0.00 0.00 2.52
1878 1926 2.568956 AGCATATATGGCACTGACGGAT 59.431 45.455 14.51 0.00 0.00 4.18
1880 1928 2.071540 CAGCATATATGGCACTGACGG 58.928 52.381 14.51 0.00 0.00 4.79
1882 1930 2.225019 GCACAGCATATATGGCACTGAC 59.775 50.000 19.61 10.91 32.67 3.51
1883 1931 2.105306 AGCACAGCATATATGGCACTGA 59.895 45.455 19.61 0.00 32.67 3.41
1884 1932 2.501261 AGCACAGCATATATGGCACTG 58.499 47.619 14.51 14.21 0.00 3.66
1885 1933 2.882761 CAAGCACAGCATATATGGCACT 59.117 45.455 14.51 0.45 0.00 4.40
1895 1943 1.111116 AACCAGCACAAGCACAGCAT 61.111 50.000 0.00 0.00 45.49 3.79
1898 1946 0.740149 TTCAACCAGCACAAGCACAG 59.260 50.000 0.00 0.00 45.49 3.66
1899 1947 1.401761 ATTCAACCAGCACAAGCACA 58.598 45.000 0.00 0.00 45.49 4.57
1900 1948 2.129607 CAATTCAACCAGCACAAGCAC 58.870 47.619 0.00 0.00 45.49 4.40
1901 1949 1.538634 GCAATTCAACCAGCACAAGCA 60.539 47.619 0.00 0.00 45.49 3.91
1902 1950 1.142474 GCAATTCAACCAGCACAAGC 58.858 50.000 0.00 0.00 42.56 4.01
1903 1951 1.342174 AGGCAATTCAACCAGCACAAG 59.658 47.619 0.00 0.00 0.00 3.16
1912 1960 4.771590 TTCATGACAGAGGCAATTCAAC 57.228 40.909 0.00 0.00 0.00 3.18
1922 1970 4.829968 ACACCTGAGAATTCATGACAGAG 58.170 43.478 8.44 9.42 31.68 3.35
1928 1976 5.587443 TGCTCATAACACCTGAGAATTCATG 59.413 40.000 8.44 0.00 42.22 3.07
1933 1981 5.645497 GTCTTTGCTCATAACACCTGAGAAT 59.355 40.000 4.57 0.00 42.22 2.40
1936 1984 3.369147 CGTCTTTGCTCATAACACCTGAG 59.631 47.826 0.00 0.00 42.47 3.35
1937 1985 3.244078 ACGTCTTTGCTCATAACACCTGA 60.244 43.478 0.00 0.00 0.00 3.86
1942 1990 6.533723 CCTTATACACGTCTTTGCTCATAACA 59.466 38.462 0.00 0.00 0.00 2.41
1951 2006 8.697846 TCATTAAGACCTTATACACGTCTTTG 57.302 34.615 11.52 7.09 42.71 2.77
1954 2009 8.308931 TGTTTCATTAAGACCTTATACACGTCT 58.691 33.333 0.00 0.00 38.50 4.18
1956 2011 9.444600 AATGTTTCATTAAGACCTTATACACGT 57.555 29.630 0.00 0.00 0.00 4.49
1972 2027 7.791029 ACCCAAAGTGAGTAAAATGTTTCATT 58.209 30.769 0.00 0.00 0.00 2.57
1990 2045 7.696992 TTGCCTTTACTATAGAAACCCAAAG 57.303 36.000 6.78 5.92 0.00 2.77
2054 2109 8.382030 TCGATGCATCACTTTTATATGTCATT 57.618 30.769 25.70 0.00 0.00 2.57
2146 2206 8.022550 TGCTGAAACTGAACACAATATATGTTG 58.977 33.333 10.37 10.37 41.46 3.33
2189 2249 6.325596 GGCTCTTAACCATTGTTTCTTGATC 58.674 40.000 0.00 0.00 35.87 2.92
2194 2254 3.751518 ACGGCTCTTAACCATTGTTTCT 58.248 40.909 0.00 0.00 35.87 2.52
2228 2288 3.701532 ATCGCAGTAGCTCTAACTGAC 57.298 47.619 17.47 8.74 45.89 3.51


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

AutoCloner maintained by Alex Coulton.