Multiple sequence alignment - TraesCS7A01G331600

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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 TraesCS7A01G331600 chr7A 100.000 2288 0 0 1 2288 484599241 484596954 0.000000e+00 4226.0
1 TraesCS7A01G331600 chr7B 87.841 1283 137 10 128 1395 451361217 451359939 0.000000e+00 1487.0
2 TraesCS7A01G331600 chr7B 91.837 147 11 1 1674 1819 451359908 451359762 1.070000e-48 204.0
3 TraesCS7A01G331600 chr7B 89.873 158 9 1 1817 1974 451359333 451359183 1.790000e-46 196.0
4 TraesCS7A01G331600 chr7B 82.143 224 14 17 2085 2288 451355635 451355418 3.910000e-38 169.0
5 TraesCS7A01G331600 chr7D 84.802 1237 138 27 617 1819 434152125 434150905 0.000000e+00 1197.0
6 TraesCS7A01G331600 chr7D 86.859 624 75 5 1 619 434161471 434160850 0.000000e+00 691.0
7 TraesCS7A01G331600 chr7D 89.767 215 15 1 1817 2031 434150390 434150183 3.750000e-68 268.0
8 TraesCS7A01G331600 chr7D 80.184 217 27 13 2078 2288 434150061 434149855 5.090000e-32 148.0
9 TraesCS7A01G331600 chr2D 81.830 776 124 9 1 768 613060776 613061542 8.920000e-179 636.0
10 TraesCS7A01G331600 chr3B 78.282 1036 170 37 60 1077 71814940 71813942 1.160000e-172 616.0
11 TraesCS7A01G331600 chr2B 79.530 894 148 18 766 1634 748417281 748418164 2.510000e-169 604.0
12 TraesCS7A01G331600 chr2B 79.106 895 150 20 766 1634 748330966 748331849 1.180000e-162 582.0
13 TraesCS7A01G331600 chr2B 75.455 330 60 8 344 667 129259763 129260077 8.520000e-30 141.0
14 TraesCS7A01G331600 chr4D 80.422 664 111 12 98 750 209102558 209101903 2.640000e-134 488.0
15 TraesCS7A01G331600 chr4D 88.571 70 8 0 1417 1486 209101060 209100991 4.050000e-13 86.1
16 TraesCS7A01G331600 chr5A 79.701 670 101 16 991 1634 408460830 408460170 3.470000e-123 451.0
17 TraesCS7A01G331600 chr3D 77.027 518 110 9 768 1280 303589524 303590037 2.880000e-74 289.0
18 TraesCS7A01G331600 chr6D 78.526 312 54 9 421 721 82095559 82095250 2.320000e-45 193.0
19 TraesCS7A01G331600 chr6A 77.244 312 61 9 420 721 98711617 98711306 8.400000e-40 174.0
20 TraesCS7A01G331600 chr4B 90.000 70 7 0 1417 1486 310983300 310983231 8.700000e-15 91.6


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 TraesCS7A01G331600 chr7A 484596954 484599241 2287 True 4226.000000 4226 100.000000 1 2288 1 chr7A.!!$R1 2287
1 TraesCS7A01G331600 chr7B 451355418 451361217 5799 True 514.000000 1487 87.923500 128 2288 4 chr7B.!!$R1 2160
2 TraesCS7A01G331600 chr7D 434160850 434161471 621 True 691.000000 691 86.859000 1 619 1 chr7D.!!$R1 618
3 TraesCS7A01G331600 chr7D 434149855 434152125 2270 True 537.666667 1197 84.917667 617 2288 3 chr7D.!!$R2 1671
4 TraesCS7A01G331600 chr2D 613060776 613061542 766 False 636.000000 636 81.830000 1 768 1 chr2D.!!$F1 767
5 TraesCS7A01G331600 chr3B 71813942 71814940 998 True 616.000000 616 78.282000 60 1077 1 chr3B.!!$R1 1017
6 TraesCS7A01G331600 chr2B 748417281 748418164 883 False 604.000000 604 79.530000 766 1634 1 chr2B.!!$F3 868
7 TraesCS7A01G331600 chr2B 748330966 748331849 883 False 582.000000 582 79.106000 766 1634 1 chr2B.!!$F2 868
8 TraesCS7A01G331600 chr4D 209100991 209102558 1567 True 287.050000 488 84.496500 98 1486 2 chr4D.!!$R1 1388
9 TraesCS7A01G331600 chr5A 408460170 408460830 660 True 451.000000 451 79.701000 991 1634 1 chr5A.!!$R1 643
10 TraesCS7A01G331600 chr3D 303589524 303590037 513 False 289.000000 289 77.027000 768 1280 1 chr3D.!!$F1 512

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
731 751 0.843984 GGCTTTGGGCTAGATGGGTA 59.156 55.0 0.0 0.0 41.46 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1564 1801 0.033781 GCCTGGTTGAGCAAATGCAA 59.966 50.0 8.28 0.0 45.16 4.08 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 6.993902 GGTACCGATGAATTTTAGGGTTCATA 59.006 38.462 0.00 0.00 43.16 2.15
58 59 3.267551 GGGATTGAGTACAAGGGGGTTAA 59.732 47.826 0.00 0.00 39.46 2.01
82 84 2.231348 TGGGGATGGGGGTAAATCAAT 58.769 47.619 0.00 0.00 0.00 2.57
93 95 6.957020 TGGGGGTAAATCAATCTTACAAACAT 59.043 34.615 0.00 0.00 31.99 2.71
94 96 7.456269 TGGGGGTAAATCAATCTTACAAACATT 59.544 33.333 0.00 0.00 31.99 2.71
121 123 1.671742 CTACCCGCAGTGACCTTGT 59.328 57.895 0.00 0.00 0.00 3.16
219 221 1.092348 TCATCGTCGTCGTCCAGAAT 58.908 50.000 1.33 0.00 38.33 2.40
235 237 3.205338 CAGAATGATGGGCATTGTACGA 58.795 45.455 0.00 0.00 46.90 3.43
244 246 1.378531 GCATTGTACGATTGCCTGGA 58.621 50.000 0.00 0.00 0.00 3.86
246 248 2.287188 GCATTGTACGATTGCCTGGATG 60.287 50.000 0.00 0.00 0.00 3.51
286 290 2.805353 CGCTTCGTGGTCGTCCTG 60.805 66.667 0.00 0.00 38.33 3.86
316 321 4.612412 GACGGTCGGTTGGGCACA 62.612 66.667 0.00 0.00 0.00 4.57
352 357 1.215173 CCTGTATTTGGCCCATCTGGA 59.785 52.381 0.00 0.00 37.39 3.86
415 420 2.358267 AGCGTAGTATGTCCACTAGCAC 59.642 50.000 0.00 0.00 31.73 4.40
417 422 3.428452 GCGTAGTATGTCCACTAGCACAA 60.428 47.826 0.00 0.00 31.73 3.33
450 455 3.317149 TGGGTTAGGTATCATCGTCTTCG 59.683 47.826 0.00 0.00 38.55 3.79
478 486 1.541147 CATCGGCTTCAACACCACATT 59.459 47.619 0.00 0.00 0.00 2.71
583 592 1.211190 GCAGCCAAGGAAGAAAGCG 59.789 57.895 0.00 0.00 0.00 4.68
615 625 2.940124 GTTGGGGAAGGGGTTGGT 59.060 61.111 0.00 0.00 0.00 3.67
645 655 2.118679 CATGGTGATGGAGAGGTGGTA 58.881 52.381 0.00 0.00 0.00 3.25
655 666 2.756207 GGAGAGGTGGTAAGACAGAGTC 59.244 54.545 0.00 0.00 0.00 3.36
693 713 5.765576 AGACAGAGAGAAGTAGTGGAGTA 57.234 43.478 0.00 0.00 0.00 2.59
695 715 4.591929 ACAGAGAGAAGTAGTGGAGTACC 58.408 47.826 0.00 0.00 0.00 3.34
720 740 3.230976 GTGGATAATTAGGGGCTTTGGG 58.769 50.000 0.00 0.00 0.00 4.12
731 751 0.843984 GGCTTTGGGCTAGATGGGTA 59.156 55.000 0.00 0.00 41.46 3.69
778 799 1.774110 TGGTGTGTTGCATTTGTCCT 58.226 45.000 0.00 0.00 0.00 3.85
792 813 4.829064 TTTGTCCTTTCATTGACCTTCG 57.171 40.909 0.00 0.00 0.00 3.79
804 825 3.961477 TGACCTTCGTTTGTGATGTTG 57.039 42.857 0.00 0.00 0.00 3.33
818 839 6.613755 TGTGATGTTGATAATGCAGATCAG 57.386 37.500 12.43 0.00 34.85 2.90
854 875 1.466851 AACTCCAAGGGCAAAGCAGC 61.467 55.000 0.00 0.00 0.00 5.25
933 1102 1.165270 CGAGGAACTTCGGCCATTTT 58.835 50.000 2.24 0.00 41.55 1.82
987 1156 0.901827 TCATCCTTGCACCGAAGCTA 59.098 50.000 0.00 0.00 34.99 3.32
1003 1172 0.179100 GCTAGAGTGCTTGCCGATGA 60.179 55.000 0.00 0.00 36.98 2.92
1077 1246 2.330254 CAACATCGGTTGCACCTGT 58.670 52.632 0.00 0.00 46.98 4.00
1079 1248 1.876799 CAACATCGGTTGCACCTGTAA 59.123 47.619 0.00 0.00 46.98 2.41
1092 1261 2.260247 CTGTAAGGTGACGGTCCGA 58.740 57.895 20.51 0.00 0.00 4.55
1136 1305 4.261501 CCAAGGTTGGTCCCCCTA 57.738 61.111 0.09 0.00 43.43 3.53
1140 1309 3.007323 GGTTGGTCCCCCTACGCT 61.007 66.667 0.00 0.00 37.35 5.07
1162 1331 6.568462 CGCTACTGTTCACCAAATCAAGATTT 60.568 38.462 2.31 2.31 41.33 2.17
1193 1362 2.103771 TCACTTTCAAGCTGCTGACTCT 59.896 45.455 1.35 0.00 0.00 3.24
1194 1363 2.223611 CACTTTCAAGCTGCTGACTCTG 59.776 50.000 1.35 0.00 0.00 3.35
1227 1396 6.934645 TCAAGTTGACCGTCTTCAATAAAGAT 59.065 34.615 0.08 0.00 45.57 2.40
1343 1513 3.608474 GCGTTGAGCGGTTTGTTTAAGAT 60.608 43.478 0.00 0.00 41.69 2.40
1379 1549 2.304470 TGCCACTATGTTGAACTGGCTA 59.696 45.455 21.77 9.81 46.46 3.93
1391 1603 6.607600 TGTTGAACTGGCTACTATCTATGTCT 59.392 38.462 0.00 0.00 0.00 3.41
1395 1607 4.895889 ACTGGCTACTATCTATGTCTTGCA 59.104 41.667 0.00 0.00 0.00 4.08
1399 1633 6.212187 TGGCTACTATCTATGTCTTGCATCAT 59.788 38.462 0.00 0.00 38.94 2.45
1406 1640 5.614308 TCTATGTCTTGCATCATTCCGAAT 58.386 37.500 0.00 0.00 38.94 3.34
1411 1646 8.815087 ATGTCTTGCATCATTCCGAATGGAGA 62.815 42.308 18.91 12.15 38.41 3.71
1456 1691 4.703897 TCTAACCAAACAGTCTGACTTGG 58.296 43.478 24.77 24.77 38.72 3.61
1457 1692 1.680338 ACCAAACAGTCTGACTTGGC 58.320 50.000 25.63 0.00 37.37 4.52
1493 1728 1.107114 TCCGCAACCAAACAACATGT 58.893 45.000 0.00 0.00 0.00 3.21
1499 1734 2.865551 CAACCAAACAACATGTCTTGCC 59.134 45.455 0.00 0.00 0.00 4.52
1509 1744 1.808945 CATGTCTTGCCTTTCTTCGCT 59.191 47.619 0.00 0.00 0.00 4.93
1529 1765 2.771321 CCAGGCTGGGGGTATGCAT 61.771 63.158 26.34 3.79 32.67 3.96
1536 1772 2.489275 GGGGGTATGCATGCAACCG 61.489 63.158 29.38 0.00 33.89 4.44
1539 1775 1.032014 GGGTATGCATGCAACCGAAT 58.968 50.000 29.38 16.69 33.89 3.34
1544 1781 0.179132 TGCATGCAACCGAATGATGC 60.179 50.000 20.30 0.00 39.90 3.91
1594 1831 3.620966 GCTCAACCAGGCTCAACTAAGAT 60.621 47.826 0.00 0.00 0.00 2.40
1634 1873 1.305201 AACGACGCAGACAACCAAAT 58.695 45.000 0.00 0.00 0.00 2.32
1635 1874 0.586319 ACGACGCAGACAACCAAATG 59.414 50.000 0.00 0.00 0.00 2.32
1636 1875 0.586319 CGACGCAGACAACCAAATGT 59.414 50.000 0.00 0.00 35.90 2.71
1637 1876 1.002900 CGACGCAGACAACCAAATGTT 60.003 47.619 0.00 0.00 37.80 2.71
1638 1877 2.540769 CGACGCAGACAACCAAATGTTT 60.541 45.455 0.00 0.00 34.00 2.83
1639 1878 2.788786 GACGCAGACAACCAAATGTTTG 59.211 45.455 0.00 0.00 38.18 2.93
1644 1883 4.685924 CAGACAACCAAATGTTTGCTCTT 58.314 39.130 0.00 0.00 36.86 2.85
1650 1889 7.500141 ACAACCAAATGTTTGCTCTTAAGAAT 58.500 30.769 6.63 0.00 36.86 2.40
1663 1902 7.106239 TGCTCTTAAGAATTAAAGTGGAGGAG 58.894 38.462 6.63 0.00 40.54 3.69
1685 1925 2.401017 TCAAACTGTGACTCGAGACG 57.599 50.000 21.68 6.96 0.00 4.18
1690 1930 1.282875 TGTGACTCGAGACGCACAG 59.717 57.895 23.74 0.00 36.44 3.66
1718 1958 2.820178 TCTGTTATGGCCTCACTCTCA 58.180 47.619 3.32 0.00 0.00 3.27
1719 1959 2.497675 TCTGTTATGGCCTCACTCTCAC 59.502 50.000 3.32 0.00 0.00 3.51
1761 2001 2.680312 ACTCGAGGACCATGTTCATG 57.320 50.000 18.41 5.88 0.00 3.07
1771 2011 4.946157 GGACCATGTTCATGTCATTTCTCT 59.054 41.667 11.13 0.00 0.00 3.10
1773 2013 6.769822 GGACCATGTTCATGTCATTTCTCTAT 59.230 38.462 11.13 0.00 0.00 1.98
1799 2039 2.548480 ACTTAGTTTTCACGCTCCTTGC 59.452 45.455 0.00 0.00 38.57 4.01
1850 2607 2.126031 GTTGGTCCTCGAGCGGTC 60.126 66.667 6.99 4.06 32.15 4.79
1870 2627 1.325640 CAAGCTGATCGGACGAATGTG 59.674 52.381 5.48 0.00 0.00 3.21
1874 2631 2.415168 GCTGATCGGACGAATGTGAAAA 59.585 45.455 5.48 0.00 0.00 2.29
1876 2633 4.783450 GCTGATCGGACGAATGTGAAAATC 60.783 45.833 5.48 0.00 0.00 2.17
1884 2641 5.235186 GGACGAATGTGAAAATCGAGATCAT 59.765 40.000 1.03 0.00 39.73 2.45
1919 2676 7.878477 TTTCGAGTAGTAGTGTTGGTTTATG 57.122 36.000 0.00 0.00 0.00 1.90
1933 2690 4.742417 TGGTTTATGAATTGCCAACATCG 58.258 39.130 0.00 0.00 0.00 3.84
1934 2691 4.460731 TGGTTTATGAATTGCCAACATCGA 59.539 37.500 0.00 0.00 0.00 3.59
1935 2692 5.126869 TGGTTTATGAATTGCCAACATCGAT 59.873 36.000 0.00 0.00 0.00 3.59
1936 2693 5.687285 GGTTTATGAATTGCCAACATCGATC 59.313 40.000 0.00 0.00 0.00 3.69
1937 2694 6.460123 GGTTTATGAATTGCCAACATCGATCT 60.460 38.462 0.00 0.00 0.00 2.75
2007 6136 5.388890 GCAACGAGTCAGAATTTCTGTACAG 60.389 44.000 22.44 17.17 44.58 2.74
2025 6154 6.884832 TGTACAGTTAACCTTCCCATATGAG 58.115 40.000 3.65 0.00 0.00 2.90
2063 6244 2.093106 AGGTACGTTCCTCAGCTACAG 58.907 52.381 8.09 0.00 31.32 2.74
2075 6256 2.568956 TCAGCTACAGAATTGACCTGCT 59.431 45.455 0.00 0.00 35.14 4.24
2078 6259 4.331168 CAGCTACAGAATTGACCTGCTTAC 59.669 45.833 0.00 0.00 35.14 2.34
2079 6260 4.020218 AGCTACAGAATTGACCTGCTTACA 60.020 41.667 0.00 0.00 35.14 2.41
2080 6261 4.331168 GCTACAGAATTGACCTGCTTACAG 59.669 45.833 0.00 0.00 44.05 2.74
2081 6262 4.357918 ACAGAATTGACCTGCTTACAGT 57.642 40.909 0.00 0.00 42.81 3.55
2083 6264 4.067896 CAGAATTGACCTGCTTACAGTGT 58.932 43.478 0.00 0.00 42.81 3.55
2157 6395 2.610433 TCTTGCACTTCGTAGCTGATG 58.390 47.619 0.00 0.00 0.00 3.07
2158 6396 1.662629 CTTGCACTTCGTAGCTGATGG 59.337 52.381 0.00 0.00 0.00 3.51
2159 6397 0.740868 TGCACTTCGTAGCTGATGGC 60.741 55.000 0.00 0.00 42.19 4.40
2204 6442 1.277326 TTTCGCAACTGATCGATCGG 58.723 50.000 28.73 28.73 39.11 4.18
2237 6475 2.417379 CGATCGATTTCCTGACCACACT 60.417 50.000 10.26 0.00 0.00 3.55
2239 6477 2.248248 TCGATTTCCTGACCACACTCT 58.752 47.619 0.00 0.00 0.00 3.24
2240 6478 2.029020 TCGATTTCCTGACCACACTCTG 60.029 50.000 0.00 0.00 0.00 3.35
2241 6479 2.079925 GATTTCCTGACCACACTCTGC 58.920 52.381 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 0.909623 CCCTTGTACTCAATCCCCGT 59.090 55.000 0.00 0.00 32.82 5.28
58 59 0.480796 TTTACCCCCATCCCCAACCT 60.481 55.000 0.00 0.00 0.00 3.50
82 84 7.990886 GGGTAGGATGTATCAATGTTTGTAAGA 59.009 37.037 0.00 0.00 0.00 2.10
93 95 2.102420 CACTGCGGGTAGGATGTATCAA 59.898 50.000 0.00 0.00 0.00 2.57
94 96 1.686587 CACTGCGGGTAGGATGTATCA 59.313 52.381 0.00 0.00 0.00 2.15
106 108 1.079127 CCTACAAGGTCACTGCGGG 60.079 63.158 0.00 0.00 0.00 6.13
219 221 1.675483 GCAATCGTACAATGCCCATCA 59.325 47.619 3.76 0.00 34.03 3.07
235 237 0.033796 CAGGGTGACATCCAGGCAAT 60.034 55.000 7.68 0.00 36.65 3.56
246 248 2.032681 GCTGGTGGTCAGGGTGAC 59.967 66.667 0.00 0.00 46.23 3.67
315 320 2.873797 GGCTTGTTAGGCCTCCTTG 58.126 57.895 9.68 0.00 45.57 3.61
338 343 2.042842 TCAAAGATCCAGATGGGCCAAA 59.957 45.455 11.89 0.00 36.21 3.28
352 357 0.179073 CGGCGATCCTGGTCAAAGAT 60.179 55.000 0.00 0.00 0.00 2.40
415 420 2.493278 CCTAACCCAGTCAAAGGCATTG 59.507 50.000 0.00 0.00 40.58 2.82
417 422 1.710809 ACCTAACCCAGTCAAAGGCAT 59.289 47.619 0.00 0.00 0.00 4.40
450 455 2.003301 GTTGAAGCCGATGAAGGAGTC 58.997 52.381 0.00 0.00 0.00 3.36
555 563 2.047844 TTGGCTGCTCGCTCAGTC 60.048 61.111 0.00 2.07 39.06 3.51
583 592 3.334078 CAACGGCATTGGATGAAGC 57.666 52.632 0.00 0.00 34.34 3.86
615 625 1.063792 CCATCACCATGAACCCCATCA 60.064 52.381 0.00 0.00 31.94 3.07
645 655 3.784178 TCCTCTTCCATGACTCTGTCTT 58.216 45.455 0.00 0.00 33.15 3.01
655 666 5.832595 TCTCTGTCTTCTATCCTCTTCCATG 59.167 44.000 0.00 0.00 0.00 3.66
693 713 1.772453 CCCCTAATTATCCACCACGGT 59.228 52.381 0.00 0.00 35.57 4.83
695 715 1.420138 AGCCCCTAATTATCCACCACG 59.580 52.381 0.00 0.00 0.00 4.94
720 740 6.402222 CATTCATTAGTCCTACCCATCTAGC 58.598 44.000 0.00 0.00 0.00 3.42
731 751 8.256356 ACTACTTATCAGCATTCATTAGTCCT 57.744 34.615 0.00 0.00 0.00 3.85
778 799 5.067153 ACATCACAAACGAAGGTCAATGAAA 59.933 36.000 0.00 0.00 0.00 2.69
792 813 7.252708 TGATCTGCATTATCAACATCACAAAC 58.747 34.615 8.93 0.00 30.52 2.93
804 825 5.353678 GGGAGCATTACTGATCTGCATTATC 59.646 44.000 6.65 0.00 37.92 1.75
846 867 0.671781 AGCCGACACTAGCTGCTTTG 60.672 55.000 7.79 8.46 38.11 2.77
854 875 2.159310 CCTTCTCTTCAGCCGACACTAG 60.159 54.545 0.00 0.00 0.00 2.57
933 1102 3.092511 GGCCCAGCCTCCTCATGA 61.093 66.667 0.00 0.00 46.69 3.07
951 1120 3.119352 GGATGATCTTGCAAAAGTGGGTC 60.119 47.826 0.00 0.00 0.00 4.46
987 1156 0.671781 GTGTCATCGGCAAGCACTCT 60.672 55.000 0.00 0.00 0.00 3.24
994 1163 0.396435 AAGTCCAGTGTCATCGGCAA 59.604 50.000 0.00 0.00 0.00 4.52
1003 1172 0.546122 TGCTTGGTGAAGTCCAGTGT 59.454 50.000 0.00 0.00 38.80 3.55
1077 1246 0.250858 TCACTCGGACCGTCACCTTA 60.251 55.000 14.79 0.00 0.00 2.69
1079 1248 1.304217 ATCACTCGGACCGTCACCT 60.304 57.895 14.79 0.00 0.00 4.00
1092 1261 1.549170 GTGACCCTACCGTTGATCACT 59.451 52.381 0.00 0.00 34.86 3.41
1136 1305 3.120321 TGATTTGGTGAACAGTAGCGT 57.880 42.857 0.00 0.00 0.00 5.07
1162 1331 2.547218 GCTTGAAAGTGACGAGGTACCA 60.547 50.000 15.94 0.00 0.00 3.25
1193 1362 1.228245 GTCAACTTGAGGCTGCCCA 60.228 57.895 16.57 10.46 0.00 5.36
1194 1363 1.973812 GGTCAACTTGAGGCTGCCC 60.974 63.158 16.57 7.66 0.00 5.36
1199 1368 1.149148 GAAGACGGTCAACTTGAGGC 58.851 55.000 11.27 0.00 0.00 4.70
1280 1449 3.122111 GCAAGAGTGAACTTTCTAGACGC 59.878 47.826 0.00 0.00 0.00 5.19
1281 1450 3.362237 CGCAAGAGTGAACTTTCTAGACG 59.638 47.826 0.00 0.00 43.02 4.18
1343 1513 8.518430 ACATAGTGGCACATAATTCAACATAA 57.482 30.769 21.41 0.00 44.52 1.90
1379 1549 6.015095 TCGGAATGATGCAAGACATAGATAGT 60.015 38.462 0.00 0.00 39.84 2.12
1391 1603 3.280197 TCTCCATTCGGAATGATGCAA 57.720 42.857 27.77 9.04 42.21 4.08
1395 1607 7.720957 TGTTTGATAATCTCCATTCGGAATGAT 59.279 33.333 27.77 14.37 42.21 2.45
1399 1633 6.657117 TGTTGTTTGATAATCTCCATTCGGAA 59.343 34.615 0.00 0.00 42.21 4.30
1406 1640 4.699735 ACGCATGTTGTTTGATAATCTCCA 59.300 37.500 0.00 0.00 0.00 3.86
1456 1691 2.095718 CGGACTTGTTTAGGCAGAAAGC 60.096 50.000 0.00 0.00 44.65 3.51
1457 1692 2.095718 GCGGACTTGTTTAGGCAGAAAG 60.096 50.000 0.00 0.00 31.29 2.62
1474 1709 1.066303 GACATGTTGTTTGGTTGCGGA 59.934 47.619 0.00 0.00 0.00 5.54
1493 1728 1.237285 GGCAGCGAAGAAAGGCAAGA 61.237 55.000 0.00 0.00 0.00 3.02
1499 1734 1.673665 AGCCTGGCAGCGAAGAAAG 60.674 57.895 22.65 0.00 38.01 2.62
1509 1744 3.419580 CATACCCCCAGCCTGGCA 61.420 66.667 22.65 0.00 35.79 4.92
1529 1765 2.255994 CTGCGCATCATTCGGTTGCA 62.256 55.000 12.24 0.00 41.35 4.08
1536 1772 4.421033 AATCATCATCTGCGCATCATTC 57.579 40.909 12.24 0.00 0.00 2.67
1539 1775 4.642445 AAAAATCATCATCTGCGCATCA 57.358 36.364 12.24 0.00 0.00 3.07
1564 1801 0.033781 GCCTGGTTGAGCAAATGCAA 59.966 50.000 8.28 0.00 45.16 4.08
1620 1859 1.522258 GCAAACATTTGGTTGTCTGCG 59.478 47.619 9.87 0.00 44.25 5.18
1634 1873 8.458573 TCCACTTTAATTCTTAAGAGCAAACA 57.541 30.769 5.12 0.00 0.00 2.83
1635 1874 8.023706 CCTCCACTTTAATTCTTAAGAGCAAAC 58.976 37.037 5.12 0.00 0.00 2.93
1636 1875 7.942341 TCCTCCACTTTAATTCTTAAGAGCAAA 59.058 33.333 5.12 6.65 0.00 3.68
1637 1876 7.458397 TCCTCCACTTTAATTCTTAAGAGCAA 58.542 34.615 5.12 0.00 0.00 3.91
1638 1877 7.016153 TCCTCCACTTTAATTCTTAAGAGCA 57.984 36.000 5.12 0.00 0.00 4.26
1639 1878 6.037720 GCTCCTCCACTTTAATTCTTAAGAGC 59.962 42.308 5.12 0.00 31.19 4.09
1640 1879 7.334858 AGCTCCTCCACTTTAATTCTTAAGAG 58.665 38.462 5.12 0.00 0.00 2.85
1641 1880 7.259088 AGCTCCTCCACTTTAATTCTTAAGA 57.741 36.000 0.00 0.00 0.00 2.10
1644 1883 7.016153 TGAAGCTCCTCCACTTTAATTCTTA 57.984 36.000 0.00 0.00 0.00 2.10
1650 1889 4.821805 CAGTTTGAAGCTCCTCCACTTTAA 59.178 41.667 0.00 0.00 0.00 1.52
1663 1902 2.473235 GTCTCGAGTCACAGTTTGAAGC 59.527 50.000 13.13 0.00 35.39 3.86
1690 1930 4.333926 GTGAGGCCATAACAGAAAGTCATC 59.666 45.833 5.01 0.00 0.00 2.92
1718 1958 3.882888 TCTTTCTTCTTTGTTGCATCCGT 59.117 39.130 0.00 0.00 0.00 4.69
1719 1959 4.488126 TCTTTCTTCTTTGTTGCATCCG 57.512 40.909 0.00 0.00 0.00 4.18
1771 2011 7.553334 AGGAGCGTGAAAACTAAGTGATTATA 58.447 34.615 0.00 0.00 0.00 0.98
1773 2013 5.790593 AGGAGCGTGAAAACTAAGTGATTA 58.209 37.500 0.00 0.00 0.00 1.75
1777 2017 3.607078 GCAAGGAGCGTGAAAACTAAGTG 60.607 47.826 0.00 0.00 0.00 3.16
1799 2039 6.649557 ACTTGATTACTAGGAACTGGAAAACG 59.350 38.462 0.00 0.00 40.33 3.60
1850 2607 1.325640 CACATTCGTCCGATCAGCTTG 59.674 52.381 0.00 0.00 0.00 4.01
1860 2617 4.566759 TGATCTCGATTTTCACATTCGTCC 59.433 41.667 0.00 0.00 34.60 4.79
1919 2676 5.753438 TGTAGTAGATCGATGTTGGCAATTC 59.247 40.000 0.54 3.07 0.00 2.17
1931 2688 5.583854 GCTCCCGTATTATGTAGTAGATCGA 59.416 44.000 0.00 0.00 0.00 3.59
1932 2689 5.353400 TGCTCCCGTATTATGTAGTAGATCG 59.647 44.000 0.00 0.00 0.00 3.69
1933 2690 6.754702 TGCTCCCGTATTATGTAGTAGATC 57.245 41.667 0.00 0.00 0.00 2.75
1934 2691 8.998277 ATATGCTCCCGTATTATGTAGTAGAT 57.002 34.615 0.00 0.00 0.00 1.98
1937 2694 9.636789 ACATATATGCTCCCGTATTATGTAGTA 57.363 33.333 12.79 0.00 0.00 1.82
2025 6154 4.785511 ACCTACGCACTGATATCCATAC 57.214 45.455 0.00 0.00 0.00 2.39
2053 6230 2.935201 GCAGGTCAATTCTGTAGCTGAG 59.065 50.000 0.00 0.00 40.34 3.35
2063 6244 5.701290 AGTAACACTGTAAGCAGGTCAATTC 59.299 40.000 0.00 0.00 46.62 2.17
2075 6256 7.333423 GGATGCACAAGATTAGTAACACTGTAA 59.667 37.037 0.00 0.00 0.00 2.41
2078 6259 5.643348 TGGATGCACAAGATTAGTAACACTG 59.357 40.000 0.00 0.00 0.00 3.66
2079 6260 5.643777 GTGGATGCACAAGATTAGTAACACT 59.356 40.000 13.07 0.00 0.00 3.55
2080 6261 5.411361 TGTGGATGCACAAGATTAGTAACAC 59.589 40.000 18.56 0.00 31.35 3.32
2081 6262 5.555966 TGTGGATGCACAAGATTAGTAACA 58.444 37.500 18.56 0.00 31.35 2.41
2083 6264 6.488344 TGTTTGTGGATGCACAAGATTAGTAA 59.512 34.615 28.19 11.97 44.57 2.24
2130 6341 3.968724 GCTACGAAGTGCAAGAAAACAAG 59.031 43.478 0.00 0.00 45.73 3.16
2138 6376 1.662629 CCATCAGCTACGAAGTGCAAG 59.337 52.381 0.00 0.00 45.73 4.01
2139 6377 1.725641 CCATCAGCTACGAAGTGCAA 58.274 50.000 0.00 0.00 45.73 4.08
2158 6396 3.127533 AAGAACCGCGCCATCAGC 61.128 61.111 0.00 0.00 38.52 4.26
2159 6397 2.753966 CCAAGAACCGCGCCATCAG 61.754 63.158 0.00 0.00 0.00 2.90
2160 6398 2.745884 CCAAGAACCGCGCCATCA 60.746 61.111 0.00 0.00 0.00 3.07
2161 6399 4.179579 GCCAAGAACCGCGCCATC 62.180 66.667 0.00 0.00 0.00 3.51
2210 6448 1.658717 AGGAAATCGATCGAGCGCG 60.659 57.895 23.84 2.41 39.35 6.86
2237 6475 0.323816 ATCGAGGTGTGAGGAGCAGA 60.324 55.000 0.00 0.00 0.00 4.26
2239 6477 1.893062 CATCGAGGTGTGAGGAGCA 59.107 57.895 0.00 0.00 0.00 4.26
2240 6478 1.520342 GCATCGAGGTGTGAGGAGC 60.520 63.158 0.00 0.00 0.00 4.70
2241 6479 1.142748 GGCATCGAGGTGTGAGGAG 59.857 63.158 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.