Multiple sequence alignment - TraesCS6A01G308400

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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 TraesCS6A01G308400 chr6A 100.000 2946 0 0 1 2946 543217668 543214723 0.000000e+00 5441
1 TraesCS6A01G308400 chr6B 93.821 1327 60 9 8 1327 593364166 593362855 0.000000e+00 1977
2 TraesCS6A01G308400 chr6B 79.540 782 134 15 2027 2805 674414905 674415663 4.320000e-148 534
3 TraesCS6A01G308400 chr6B 84.174 575 59 15 1457 2015 593362669 593362111 2.010000e-146 529
4 TraesCS6A01G308400 chr6B 78.723 282 44 10 2240 2517 183605359 183605090 1.090000e-39 174
5 TraesCS6A01G308400 chr6D 94.613 891 30 9 437 1327 396917526 396916654 0.000000e+00 1363
6 TraesCS6A01G308400 chr6D 95.048 525 22 3 8 532 396918047 396917527 0.000000e+00 822
7 TraesCS6A01G308400 chr6D 87.535 714 62 14 1310 2015 396916620 396915926 0.000000e+00 800
8 TraesCS6A01G308400 chr1D 79.706 951 163 22 2016 2942 481469230 481470174 0.000000e+00 660
9 TraesCS6A01G308400 chr1D 78.769 942 173 20 2014 2940 25416916 25417845 9.030000e-170 606
10 TraesCS6A01G308400 chr5D 81.114 826 143 11 2118 2940 272149540 272150355 0.000000e+00 649
11 TraesCS6A01G308400 chr2D 79.531 938 144 27 2027 2946 306253769 306254676 2.490000e-175 625
12 TraesCS6A01G308400 chr2D 81.649 376 66 3 2268 2643 351362938 351363310 2.850000e-80 309
13 TraesCS6A01G308400 chr3D 80.191 838 146 13 2028 2849 564395370 564396203 6.980000e-171 610
14 TraesCS6A01G308400 chr3D 82.975 511 72 11 2147 2653 171318011 171318510 5.790000e-122 448
15 TraesCS6A01G308400 chr3A 78.468 901 175 16 2056 2946 737815282 737816173 3.290000e-159 571
16 TraesCS6A01G308400 chr5A 78.628 889 165 18 2059 2940 361909615 361910485 1.530000e-157 566
17 TraesCS6A01G308400 chr2A 77.955 939 170 26 2027 2941 572097357 572096432 1.190000e-153 553
18 TraesCS6A01G308400 chr5B 79.129 781 136 17 2185 2946 625091844 625091072 5.630000e-142 514
19 TraesCS6A01G308400 chr5B 79.129 781 136 17 2185 2946 628671394 628670622 5.630000e-142 514
20 TraesCS6A01G308400 chr1B 81.038 501 88 7 2245 2743 190642310 190642805 2.750000e-105 392
21 TraesCS6A01G308400 chr1B 80.000 265 46 7 2014 2274 40702983 40703244 3.880000e-44 189
22 TraesCS6A01G308400 chr3B 78.172 536 103 9 2417 2942 761501063 761501594 2.190000e-86 329
23 TraesCS6A01G308400 chr2B 81.735 219 35 4 2027 2243 476726421 476726636 8.390000e-41 178


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 TraesCS6A01G308400 chr6A 543214723 543217668 2945 True 5441 5441 100.000000 1 2946 1 chr6A.!!$R1 2945
1 TraesCS6A01G308400 chr6B 593362111 593364166 2055 True 1253 1977 88.997500 8 2015 2 chr6B.!!$R2 2007
2 TraesCS6A01G308400 chr6B 674414905 674415663 758 False 534 534 79.540000 2027 2805 1 chr6B.!!$F1 778
3 TraesCS6A01G308400 chr6D 396915926 396918047 2121 True 995 1363 92.398667 8 2015 3 chr6D.!!$R1 2007
4 TraesCS6A01G308400 chr1D 481469230 481470174 944 False 660 660 79.706000 2016 2942 1 chr1D.!!$F2 926
5 TraesCS6A01G308400 chr1D 25416916 25417845 929 False 606 606 78.769000 2014 2940 1 chr1D.!!$F1 926
6 TraesCS6A01G308400 chr5D 272149540 272150355 815 False 649 649 81.114000 2118 2940 1 chr5D.!!$F1 822
7 TraesCS6A01G308400 chr2D 306253769 306254676 907 False 625 625 79.531000 2027 2946 1 chr2D.!!$F1 919
8 TraesCS6A01G308400 chr3D 564395370 564396203 833 False 610 610 80.191000 2028 2849 1 chr3D.!!$F2 821
9 TraesCS6A01G308400 chr3A 737815282 737816173 891 False 571 571 78.468000 2056 2946 1 chr3A.!!$F1 890
10 TraesCS6A01G308400 chr5A 361909615 361910485 870 False 566 566 78.628000 2059 2940 1 chr5A.!!$F1 881
11 TraesCS6A01G308400 chr2A 572096432 572097357 925 True 553 553 77.955000 2027 2941 1 chr2A.!!$R1 914
12 TraesCS6A01G308400 chr5B 625091072 625091844 772 True 514 514 79.129000 2185 2946 1 chr5B.!!$R1 761
13 TraesCS6A01G308400 chr5B 628670622 628671394 772 True 514 514 79.129000 2185 2946 1 chr5B.!!$R2 761
14 TraesCS6A01G308400 chr3B 761501063 761501594 531 False 329 329 78.172000 2417 2942 1 chr3B.!!$F1 525

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
790 890 0.179108 CGAGAGAAACCATCGGTCCC 60.179 60.0 0.00 0.00 33.12 4.46 F
1737 1929 0.026414 ATGACGACGACGACGATGAG 59.974 55.0 25.15 4.59 42.66 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 2017 0.109412 GCCGCCGCGACTATACTTAT 60.109 55.0 15.93 0.00 0.0 1.73 R
2692 2935 0.728466 CTTTCGGAGTCGTCGACCAC 60.728 60.0 21.40 15.24 36.3 4.16 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 1.135199 ACATCGTGCCTTCGTAATCGT 60.135 47.619 0.00 0.00 38.33 3.73
180 181 3.431725 GAAACCCTTGCCCGCGAG 61.432 66.667 8.23 0.00 0.00 5.03
225 226 2.616842 AGCAAACAGACGGGTAAAAGTG 59.383 45.455 0.00 0.00 0.00 3.16
248 249 2.124819 AAGATGAGCAGCTGCCCG 60.125 61.111 34.39 0.00 43.38 6.13
508 601 3.075283 TCATACCATCTCTCCTCTCCTCC 59.925 52.174 0.00 0.00 0.00 4.30
656 756 1.303074 GTTCCGGTTCCCAGGTTCC 60.303 63.158 0.00 0.00 0.00 3.62
760 860 4.057428 GACGGTCGTCAGGCAGCT 62.057 66.667 17.26 0.00 44.02 4.24
790 890 0.179108 CGAGAGAAACCATCGGTCCC 60.179 60.000 0.00 0.00 33.12 4.46
826 926 1.295423 CTCGGGCGGGAAAAAGAGA 59.705 57.895 0.00 0.00 0.00 3.10
853 953 4.514577 ACTTCCGCGCCCATCTCG 62.515 66.667 0.00 0.00 0.00 4.04
873 973 1.442526 GCATGACAGATTCCCAGCCG 61.443 60.000 0.00 0.00 0.00 5.52
918 1018 2.815478 CGATCCTCTTTCTTCTTCCCG 58.185 52.381 0.00 0.00 0.00 5.14
919 1019 2.166664 CGATCCTCTTTCTTCTTCCCGT 59.833 50.000 0.00 0.00 0.00 5.28
922 1022 4.004196 TCCTCTTTCTTCTTCCCGTTTC 57.996 45.455 0.00 0.00 0.00 2.78
1170 1270 3.462678 GCCTCCACCTCCTCGTCC 61.463 72.222 0.00 0.00 0.00 4.79
1296 1396 1.003839 CTCTGCTGGTTACGGGCAA 60.004 57.895 3.05 0.00 35.49 4.52
1367 1518 4.548451 AGAAGAATGTGAGTGCTCATCA 57.452 40.909 5.11 6.15 42.18 3.07
1379 1554 2.994995 TCATCACGGCCACGGACT 60.995 61.111 2.24 0.00 46.48 3.85
1401 1576 4.555348 TTTGTTACGTTTCGGAATGCTT 57.445 36.364 0.00 0.00 30.39 3.91
1402 1577 3.529634 TGTTACGTTTCGGAATGCTTG 57.470 42.857 0.00 0.00 30.39 4.01
1404 1579 0.800012 TACGTTTCGGAATGCTTGGC 59.200 50.000 0.00 0.00 0.00 4.52
1437 1612 1.219522 GGACACCGTTGACTCCGTTG 61.220 60.000 0.00 0.00 0.00 4.10
1443 1632 1.070786 GTTGACTCCGTTGCCCTGA 59.929 57.895 0.00 0.00 0.00 3.86
1444 1633 0.951040 GTTGACTCCGTTGCCCTGAG 60.951 60.000 0.00 0.00 0.00 3.35
1445 1634 1.118965 TTGACTCCGTTGCCCTGAGA 61.119 55.000 0.00 0.00 0.00 3.27
1446 1635 1.118965 TGACTCCGTTGCCCTGAGAA 61.119 55.000 0.00 0.00 0.00 2.87
1447 1636 0.250513 GACTCCGTTGCCCTGAGAAT 59.749 55.000 0.00 0.00 0.00 2.40
1448 1637 0.250513 ACTCCGTTGCCCTGAGAATC 59.749 55.000 0.00 0.00 0.00 2.52
1468 1657 8.804912 AGAATCATCTCTTTGCTGTATTTCTT 57.195 30.769 0.00 0.00 0.00 2.52
1471 1660 7.750229 TCATCTCTTTGCTGTATTTCTTTGT 57.250 32.000 0.00 0.00 0.00 2.83
1476 1665 8.103305 TCTCTTTGCTGTATTTCTTTGTAGGAT 58.897 33.333 0.00 0.00 0.00 3.24
1485 1674 4.713824 TTCTTTGTAGGATGACGACGAT 57.286 40.909 0.00 0.00 0.00 3.73
1491 1680 0.658368 AGGATGACGACGATGACGAG 59.342 55.000 0.00 0.00 42.66 4.18
1494 1683 1.264557 GATGACGACGATGACGAGGAT 59.735 52.381 0.00 0.00 42.66 3.24
1499 1688 0.952280 GACGATGACGAGGATAGGCA 59.048 55.000 0.00 0.00 42.66 4.75
1501 1690 0.387878 CGATGACGAGGATAGGCAGC 60.388 60.000 0.00 0.00 42.66 5.25
1502 1691 0.387878 GATGACGAGGATAGGCAGCG 60.388 60.000 0.00 0.00 0.00 5.18
1506 1695 3.606662 GAGGATAGGCAGCGGCGA 61.607 66.667 12.98 0.00 42.47 5.54
1572 1761 1.995484 CACAAGAAGCACGACGATGAT 59.005 47.619 0.00 0.00 0.00 2.45
1584 1773 0.656259 ACGATGATGACGACGACGAT 59.344 50.000 15.32 0.00 42.66 3.73
1585 1774 1.037998 CGATGATGACGACGACGATG 58.962 55.000 15.32 0.00 42.66 3.84
1586 1775 1.399572 GATGATGACGACGACGATGG 58.600 55.000 15.32 0.00 42.66 3.51
1595 1784 1.989966 GACGACGATGGCGAGAGGAA 61.990 60.000 0.00 0.00 41.64 3.36
1635 1824 2.286418 TGACGACGACGATGATGATGAG 60.286 50.000 15.32 0.00 42.66 2.90
1644 1833 3.006644 ACGATGATGATGAGGATGACAGG 59.993 47.826 0.00 0.00 0.00 4.00
1689 1881 1.520174 GACGACGACGACGATGATAGA 59.480 52.381 25.15 0.00 42.66 1.98
1713 1905 1.191647 CCACGTTACAAGAAGCACGAC 59.808 52.381 0.00 0.00 36.48 4.34
1716 1908 1.121967 CGTTACAAGAAGCACGACGAC 59.878 52.381 0.00 0.00 34.49 4.34
1722 1914 0.454620 AGAAGCACGACGACGATGAC 60.455 55.000 15.32 5.51 42.66 3.06
1737 1929 0.026414 ATGACGACGACGACGATGAG 59.974 55.000 25.15 4.59 42.66 2.90
1864 2057 3.730061 GCTTTGCTTCGATGAATCACCAG 60.730 47.826 1.89 0.00 0.00 4.00
1868 2061 2.029728 GCTTCGATGAATCACCAGTTCG 59.970 50.000 1.89 0.00 0.00 3.95
1912 2105 2.570415 TTTCACTATTCACCGGCCAA 57.430 45.000 0.00 0.00 0.00 4.52
1918 2111 0.322906 TATTCACCGGCCAACATGCA 60.323 50.000 0.00 0.00 0.00 3.96
1929 2125 2.868839 GCCAACATGCATCCAATATGCC 60.869 50.000 0.00 0.00 43.94 4.40
1930 2126 2.631062 CCAACATGCATCCAATATGCCT 59.369 45.455 0.00 0.00 43.94 4.75
1934 2130 3.181437 ACATGCATCCAATATGCCTGAGA 60.181 43.478 18.10 0.00 43.94 3.27
1942 2138 7.392418 CATCCAATATGCCTGAGATTCTCTTA 58.608 38.462 14.54 0.00 0.00 2.10
1944 2140 5.642919 CCAATATGCCTGAGATTCTCTTAGC 59.357 44.000 14.54 13.68 29.63 3.09
1946 2142 4.767578 ATGCCTGAGATTCTCTTAGCAA 57.232 40.909 21.32 11.03 35.48 3.91
1947 2143 4.767578 TGCCTGAGATTCTCTTAGCAAT 57.232 40.909 17.63 0.00 31.56 3.56
1975 2175 3.006323 TGCAGTTTGACCTGTTTGTGTTT 59.994 39.130 0.00 0.00 34.84 2.83
1976 2176 3.612423 GCAGTTTGACCTGTTTGTGTTTC 59.388 43.478 0.00 0.00 34.84 2.78
1983 2183 6.707440 TGACCTGTTTGTGTTTCAATATGT 57.293 33.333 0.00 0.00 35.84 2.29
1984 2184 6.502652 TGACCTGTTTGTGTTTCAATATGTG 58.497 36.000 0.00 0.00 35.84 3.21
1985 2185 6.319911 TGACCTGTTTGTGTTTCAATATGTGA 59.680 34.615 0.00 0.00 35.84 3.58
1986 2186 7.014134 TGACCTGTTTGTGTTTCAATATGTGAT 59.986 33.333 0.00 0.00 35.70 3.06
1987 2187 7.725251 ACCTGTTTGTGTTTCAATATGTGATT 58.275 30.769 0.00 0.00 35.70 2.57
2015 2215 1.688197 CCAAGGGTTGTGAAATGCAGT 59.312 47.619 0.00 0.00 0.00 4.40
2016 2216 2.102925 CCAAGGGTTGTGAAATGCAGTT 59.897 45.455 0.00 0.00 0.00 3.16
2017 2217 3.432046 CCAAGGGTTGTGAAATGCAGTTT 60.432 43.478 0.00 0.00 0.00 2.66
2018 2218 4.190772 CAAGGGTTGTGAAATGCAGTTTT 58.809 39.130 0.00 0.00 0.00 2.43
2019 2219 4.486125 AGGGTTGTGAAATGCAGTTTTT 57.514 36.364 0.00 0.00 0.00 1.94
2054 2256 0.183014 CCAGCCTCTGCATCAGGATT 59.817 55.000 14.75 0.83 41.13 3.01
2071 2273 7.926674 TCAGGATTATGCATACAACCATATG 57.073 36.000 5.74 0.00 35.91 1.78
2111 2313 1.016130 AGCAGCCGAACAACATCGAG 61.016 55.000 0.00 0.00 45.48 4.04
2116 2318 1.683790 CCGAACAACATCGAGTCGGC 61.684 60.000 13.54 0.00 45.48 5.54
2135 2338 5.174216 GTCGGCAATAAAGCGAAAAGAAAAA 59.826 36.000 0.00 0.00 34.64 1.94
2143 2346 4.257267 AGCGAAAAGAAAAATCCAAGGG 57.743 40.909 0.00 0.00 0.00 3.95
2172 2378 1.007336 CGCGACAGTAACTCCACCAC 61.007 60.000 0.00 0.00 0.00 4.16
2196 2403 7.279313 CACATAACCACTAACCCTATGTTACAC 59.721 40.741 0.00 0.00 38.42 2.90
2203 2415 2.161855 ACCCTATGTTACACGACGACA 58.838 47.619 0.00 0.00 0.00 4.35
2210 2423 7.010738 CCCTATGTTACACGACGACAATAAAAT 59.989 37.037 0.00 0.00 0.00 1.82
2274 2489 1.369568 CGTACGTGCGCCGATGATA 60.370 57.895 22.10 4.23 40.70 2.15
2339 2554 1.144708 TCAAGCTTCAATCCACCACCA 59.855 47.619 0.00 0.00 0.00 4.17
2353 2568 0.962356 CCACCATCAGCAAGGACACC 60.962 60.000 0.00 0.00 0.00 4.16
2365 2580 2.108157 GACACCGACACAGGCACA 59.892 61.111 0.00 0.00 33.69 4.57
2432 2648 0.605319 AAAGTCGCCATTGAAGCCGA 60.605 50.000 0.00 0.00 0.00 5.54
2443 2660 3.627395 TTGAAGCCGAATGTACCATCT 57.373 42.857 0.00 0.00 0.00 2.90
2455 2672 3.918566 TGTACCATCTTCCCTTATCCGA 58.081 45.455 0.00 0.00 0.00 4.55
2461 2678 3.675348 TCTTCCCTTATCCGAGTACCA 57.325 47.619 0.00 0.00 0.00 3.25
2484 2703 4.084287 ACGCCTTGATAATCGGATACCTA 58.916 43.478 0.00 0.00 0.00 3.08
2496 2715 4.999310 TCGGATACCTATGGAGAAGACAT 58.001 43.478 0.00 0.00 0.00 3.06
2500 2719 5.186797 GGATACCTATGGAGAAGACATCAGG 59.813 48.000 0.00 0.00 0.00 3.86
2520 2741 2.894126 GGAGACAGATGTCCCATATCGT 59.106 50.000 9.31 0.00 45.85 3.73
2542 2763 2.745884 CTCCCGCCATTGTCGCAA 60.746 61.111 0.00 0.00 0.00 4.85
2556 2777 2.205074 GTCGCAACATCTTCGATCCAT 58.795 47.619 0.00 0.00 34.61 3.41
2581 2802 1.566211 ACAGGCTAGCACATGAGACT 58.434 50.000 18.24 0.00 0.00 3.24
2583 2804 2.304180 ACAGGCTAGCACATGAGACTTT 59.696 45.455 18.24 0.00 0.00 2.66
2692 2935 4.514577 CCTACCGACGGCAGGCAG 62.515 72.222 20.19 6.64 0.00 4.85
2724 2967 3.005554 CTCCGAAAGAGATGCATGTGTT 58.994 45.455 2.46 0.89 46.50 3.32
2729 2972 4.393062 CGAAAGAGATGCATGTGTTACCTT 59.607 41.667 2.46 0.00 0.00 3.50
2747 2990 0.037326 TTCTGAGCCGCATCGAACTT 60.037 50.000 0.00 0.00 0.00 2.66
2811 3055 3.998672 GGCCGTCACCACCTCGAA 61.999 66.667 0.00 0.00 0.00 3.71
2814 3058 0.953960 GCCGTCACCACCTCGAAATT 60.954 55.000 0.00 0.00 0.00 1.82
2824 3068 1.281899 CCTCGAAATTCAGACTCCGC 58.718 55.000 0.00 0.00 0.00 5.54
2825 3069 1.134965 CCTCGAAATTCAGACTCCGCT 60.135 52.381 0.00 0.00 0.00 5.52
2830 3074 0.247736 AATTCAGACTCCGCTTCGCT 59.752 50.000 0.00 0.00 0.00 4.93
2871 3118 1.972978 CCGTCGAAGAAGAGGGGTT 59.027 57.895 0.00 0.00 41.17 4.11
2893 3140 1.372087 CGCCTTGATTCTGGGTGCTC 61.372 60.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.517276 GATGACGATTACGAAGGCACG 59.483 52.381 0.00 2.85 42.66 5.34
18 19 2.218953 GGATGACGATTACGAAGGCA 57.781 50.000 0.00 0.00 42.66 4.75
130 131 3.344215 GCAGCCATGATCTCCGCG 61.344 66.667 0.00 0.00 0.00 6.46
180 181 2.598394 TCTGCCTTGGTGCTTGGC 60.598 61.111 0.00 0.00 46.26 4.52
225 226 1.202009 GCAGCTGCTCATCTTCGTTTC 60.202 52.381 31.33 0.00 38.21 2.78
248 249 1.117150 TTCCTGTAGGTATGGACGCC 58.883 55.000 0.00 0.00 36.34 5.68
277 278 2.073056 CGCATTTGGTGTAGCTGTACA 58.927 47.619 0.00 0.00 36.78 2.90
284 285 0.590682 TGCACACGCATTTGGTGTAG 59.409 50.000 0.00 0.00 46.27 2.74
508 601 1.355720 ACACAAGAGGGAAATGGAGGG 59.644 52.381 0.00 0.00 0.00 4.30
656 756 2.668457 GAGAGTATGCAGTGAAACACCG 59.332 50.000 0.00 0.00 41.43 4.94
760 860 1.806542 GTTTCTCTCGCTCCATTTGCA 59.193 47.619 0.00 0.00 0.00 4.08
818 918 2.127758 CGCGCGCGTTCTCTTTTT 60.128 55.556 42.49 0.00 34.35 1.94
835 935 2.586357 GAGATGGGCGCGGAAGTC 60.586 66.667 8.83 0.00 0.00 3.01
836 936 4.514577 CGAGATGGGCGCGGAAGT 62.515 66.667 8.83 0.00 36.08 3.01
853 953 1.105759 GGCTGGGAATCTGTCATGCC 61.106 60.000 0.00 0.00 32.76 4.40
856 956 0.107508 CACGGCTGGGAATCTGTCAT 60.108 55.000 0.00 0.00 0.00 3.06
861 961 0.322546 GTTTCCACGGCTGGGAATCT 60.323 55.000 14.09 0.00 43.57 2.40
873 973 2.434359 CGCTCGGGGAGTTTCCAC 60.434 66.667 0.00 0.00 38.64 4.02
941 1041 2.042843 AGGGATCGAACGGGCTCT 60.043 61.111 0.00 0.00 0.00 4.09
1170 1270 2.202440 CCGTGGCTGTCGTACGAG 60.202 66.667 20.18 9.32 40.01 4.18
1267 1367 2.919856 AGCAGAGGAGCCGTGTGT 60.920 61.111 0.00 0.00 34.23 3.72
1279 1379 1.003839 CTTGCCCGTAACCAGCAGA 60.004 57.895 0.00 0.00 37.89 4.26
1367 1518 0.179051 TAACAAAAGTCCGTGGCCGT 60.179 50.000 0.00 0.00 0.00 5.68
1379 1554 4.555348 AGCATTCCGAAACGTAACAAAA 57.445 36.364 0.00 0.00 0.00 2.44
1404 1579 4.530857 GTCCGTGGGCCCATCTCG 62.531 72.222 31.45 26.47 0.00 4.04
1418 1593 1.068585 AACGGAGTCAACGGTGTCC 59.931 57.895 0.00 0.00 45.00 4.02
1443 1632 8.804912 AAGAAATACAGCAAAGAGATGATTCT 57.195 30.769 0.00 0.00 36.73 2.40
1444 1633 9.286946 CAAAGAAATACAGCAAAGAGATGATTC 57.713 33.333 0.00 0.00 37.02 2.52
1445 1634 8.800332 ACAAAGAAATACAGCAAAGAGATGATT 58.200 29.630 0.00 0.00 37.02 2.57
1446 1635 8.345724 ACAAAGAAATACAGCAAAGAGATGAT 57.654 30.769 0.00 0.00 37.02 2.45
1447 1636 7.750229 ACAAAGAAATACAGCAAAGAGATGA 57.250 32.000 0.00 0.00 37.02 2.92
1448 1637 8.180267 CCTACAAAGAAATACAGCAAAGAGATG 58.820 37.037 0.00 0.00 40.19 2.90
1449 1638 8.103305 TCCTACAAAGAAATACAGCAAAGAGAT 58.897 33.333 0.00 0.00 0.00 2.75
1450 1639 7.450074 TCCTACAAAGAAATACAGCAAAGAGA 58.550 34.615 0.00 0.00 0.00 3.10
1451 1640 7.672983 TCCTACAAAGAAATACAGCAAAGAG 57.327 36.000 0.00 0.00 0.00 2.85
1452 1641 7.882791 TCATCCTACAAAGAAATACAGCAAAGA 59.117 33.333 0.00 0.00 0.00 2.52
1453 1642 7.965107 GTCATCCTACAAAGAAATACAGCAAAG 59.035 37.037 0.00 0.00 0.00 2.77
1454 1643 7.360861 CGTCATCCTACAAAGAAATACAGCAAA 60.361 37.037 0.00 0.00 0.00 3.68
1455 1644 6.092122 CGTCATCCTACAAAGAAATACAGCAA 59.908 38.462 0.00 0.00 0.00 3.91
1456 1645 5.580691 CGTCATCCTACAAAGAAATACAGCA 59.419 40.000 0.00 0.00 0.00 4.41
1457 1646 5.810587 TCGTCATCCTACAAAGAAATACAGC 59.189 40.000 0.00 0.00 0.00 4.40
1466 1655 3.791887 GTCATCGTCGTCATCCTACAAAG 59.208 47.826 0.00 0.00 0.00 2.77
1468 1657 2.223180 CGTCATCGTCGTCATCCTACAA 60.223 50.000 0.00 0.00 0.00 2.41
1471 1660 1.865340 CTCGTCATCGTCGTCATCCTA 59.135 52.381 0.00 0.00 38.33 2.94
1476 1665 1.865340 CTATCCTCGTCATCGTCGTCA 59.135 52.381 0.00 0.00 38.33 4.35
1485 1674 2.490148 CCGCTGCCTATCCTCGTCA 61.490 63.158 0.00 0.00 0.00 4.35
1491 1680 1.446272 GTATCGCCGCTGCCTATCC 60.446 63.158 0.00 0.00 0.00 2.59
1494 1683 1.067416 CTTGTATCGCCGCTGCCTA 59.933 57.895 0.00 0.00 0.00 3.93
1499 1688 1.878522 CGCTTCTTGTATCGCCGCT 60.879 57.895 0.00 0.00 0.00 5.52
1501 1690 2.621000 GCGCTTCTTGTATCGCCG 59.379 61.111 0.00 0.00 41.53 6.46
1502 1691 1.876714 TCGCGCTTCTTGTATCGCC 60.877 57.895 5.56 0.00 44.12 5.54
1506 1695 1.132199 CGTCGTCGCGCTTCTTGTAT 61.132 55.000 5.56 0.00 0.00 2.29
1572 1761 3.376914 CTCGCCATCGTCGTCGTCA 62.377 63.158 1.33 0.00 38.33 4.35
1595 1784 2.025418 CGTTTCTTGTACCGCGGCT 61.025 57.895 28.58 15.49 0.00 5.52
1626 1815 3.181457 GCTTCCTGTCATCCTCATCATCA 60.181 47.826 0.00 0.00 0.00 3.07
1635 1824 2.892425 CGCGGCTTCCTGTCATCC 60.892 66.667 0.00 0.00 0.00 3.51
1644 1833 0.179222 GCTTCTTGTAACGCGGCTTC 60.179 55.000 12.47 0.00 0.00 3.86
1680 1872 4.109766 TGTAACGTGGCTTTCTATCATCG 58.890 43.478 0.00 0.00 0.00 3.84
1689 1881 2.032924 GTGCTTCTTGTAACGTGGCTTT 59.967 45.455 0.00 0.00 0.00 3.51
1713 1905 1.922220 GTCGTCGTCGTCATCGTCG 60.922 63.158 1.33 1.62 46.06 5.12
1716 1908 1.012562 ATCGTCGTCGTCGTCATCG 60.013 57.895 11.41 4.14 38.33 3.84
1722 1914 1.012124 CCTCTCATCGTCGTCGTCG 60.012 63.158 5.50 5.50 38.33 5.12
1773 1965 4.141959 TGCCTTGATCAGTCATCGTAATCA 60.142 41.667 0.00 0.00 33.61 2.57
1799 1991 2.346847 GCGTCAGCTAAACTCATGTCAG 59.653 50.000 0.00 0.00 41.01 3.51
1824 2017 0.109412 GCCGCCGCGACTATACTTAT 60.109 55.000 15.93 0.00 0.00 1.73
1829 2022 1.590525 CAAAGCCGCCGCGACTATA 60.591 57.895 15.93 0.00 41.18 1.31
1849 2042 3.313012 ACGAACTGGTGATTCATCGAA 57.687 42.857 12.21 0.00 34.62 3.71
1880 2073 8.992073 GGTGAATAGTGAAATGAAAAATGCTTT 58.008 29.630 0.00 0.00 0.00 3.51
1897 2090 1.750193 CATGTTGGCCGGTGAATAGT 58.250 50.000 1.90 0.00 0.00 2.12
1929 2125 8.068977 GCACATTTATTGCTAAGAGAATCTCAG 58.931 37.037 13.29 3.18 40.17 3.35
1930 2126 7.553760 TGCACATTTATTGCTAAGAGAATCTCA 59.446 33.333 13.29 0.00 42.69 3.27
1934 2130 7.636150 ACTGCACATTTATTGCTAAGAGAAT 57.364 32.000 0.00 0.00 40.86 2.40
1942 2138 4.281688 AGGTCAAACTGCACATTTATTGCT 59.718 37.500 0.00 0.00 40.86 3.91
1944 2140 5.531634 ACAGGTCAAACTGCACATTTATTG 58.468 37.500 0.00 0.00 42.21 1.90
1946 2142 5.789643 AACAGGTCAAACTGCACATTTAT 57.210 34.783 0.00 0.00 42.21 1.40
1947 2143 5.105554 ACAAACAGGTCAAACTGCACATTTA 60.106 36.000 0.00 0.00 42.21 1.40
1992 2192 1.000843 GCATTTCACAACCCTTGGGAC 59.999 52.381 13.39 0.00 44.08 4.46
1993 2193 1.337118 GCATTTCACAACCCTTGGGA 58.663 50.000 13.39 0.00 42.37 4.37
2018 2218 5.407936 AGGCTGGGGTTATCCTTTTAAAAA 58.592 37.500 1.66 0.00 35.33 1.94
2019 2219 5.018374 AGGCTGGGGTTATCCTTTTAAAA 57.982 39.130 0.00 0.00 35.33 1.52
2020 2220 4.293901 AGAGGCTGGGGTTATCCTTTTAAA 59.706 41.667 0.00 0.00 35.33 1.52
2021 2221 3.856206 AGAGGCTGGGGTTATCCTTTTAA 59.144 43.478 0.00 0.00 35.33 1.52
2022 2222 3.202151 CAGAGGCTGGGGTTATCCTTTTA 59.798 47.826 0.00 0.00 35.33 1.52
2023 2223 2.024941 CAGAGGCTGGGGTTATCCTTTT 60.025 50.000 0.00 0.00 35.33 2.27
2024 2224 1.566231 CAGAGGCTGGGGTTATCCTTT 59.434 52.381 0.00 0.00 35.33 3.11
2025 2225 1.216990 CAGAGGCTGGGGTTATCCTT 58.783 55.000 0.00 0.00 35.33 3.36
2037 2239 3.420300 CATAATCCTGATGCAGAGGCT 57.580 47.619 9.34 0.00 41.91 4.58
2071 2273 7.305648 GCTGCTCGATTTTGCATTCTTAATAAC 60.306 37.037 0.00 0.00 38.59 1.89
2091 2293 1.014044 TCGATGTTGTTCGGCTGCTC 61.014 55.000 0.00 0.00 39.56 4.26
2111 2313 3.465122 TCTTTTCGCTTTATTGCCGAC 57.535 42.857 0.00 0.00 0.00 4.79
2116 2318 8.223100 CCTTGGATTTTTCTTTTCGCTTTATTG 58.777 33.333 0.00 0.00 0.00 1.90
2135 2338 1.076485 GAGGCATGCACCCTTGGAT 60.076 57.895 21.36 0.00 33.19 3.41
2172 2378 6.477688 CGTGTAACATAGGGTTAGTGGTTATG 59.522 42.308 0.00 0.00 42.44 1.90
2233 2447 4.280436 TGATTCCTTCTTGAAGGCGTAA 57.720 40.909 21.16 12.73 39.80 3.18
2339 2554 0.320771 GTGTCGGTGTCCTTGCTGAT 60.321 55.000 0.00 0.00 0.00 2.90
2353 2568 3.394874 CGACGTGTGCCTGTGTCG 61.395 66.667 0.00 0.00 46.57 4.35
2365 2580 5.001874 TCTATAATCAGGCTATGTCGACGT 58.998 41.667 15.78 15.78 0.00 4.34
2443 2660 2.428171 CGTTGGTACTCGGATAAGGGAA 59.572 50.000 0.00 0.00 0.00 3.97
2455 2672 3.454375 CGATTATCAAGGCGTTGGTACT 58.546 45.455 18.38 10.35 34.09 2.73
2461 2678 3.323979 AGGTATCCGATTATCAAGGCGTT 59.676 43.478 0.00 0.00 0.00 4.84
2484 2703 3.705579 CTGTCTCCTGATGTCTTCTCCAT 59.294 47.826 0.00 0.00 0.00 3.41
2500 2719 6.723489 ACAGACGATATGGGACATCTGTCTC 61.723 48.000 9.98 6.77 46.65 3.36
2524 2745 3.247056 TTGCGACAATGGCGGGAGA 62.247 57.895 11.62 0.00 0.00 3.71
2542 2763 3.201290 GTTGCTGATGGATCGAAGATGT 58.799 45.455 0.00 0.00 45.12 3.06
2571 2792 1.998315 CTCTGGCGAAAGTCTCATGTG 59.002 52.381 0.00 0.00 36.07 3.21
2692 2935 0.728466 CTTTCGGAGTCGTCGACCAC 60.728 60.000 21.40 15.24 36.30 4.16
2695 2938 0.795085 TCTCTTTCGGAGTCGTCGAC 59.205 55.000 17.70 17.70 42.40 4.20
2724 2967 1.035385 TCGATGCGGCTCAGAAGGTA 61.035 55.000 0.00 0.00 0.00 3.08
2729 2972 0.737367 CAAGTTCGATGCGGCTCAGA 60.737 55.000 0.00 0.00 0.00 3.27
2747 2990 3.007940 ACGTCCCTTTCATCAACAGATCA 59.992 43.478 0.00 0.00 0.00 2.92
2775 3018 3.557903 TTCTGAGGCTGGTGGCAGC 62.558 63.158 10.30 10.30 46.78 5.25
2824 3068 1.133253 CGTGGTCATGCAAGCGAAG 59.867 57.895 0.00 0.00 0.00 3.79
2825 3069 2.324330 CCGTGGTCATGCAAGCGAA 61.324 57.895 0.00 0.00 0.00 4.70
2830 3074 1.003839 GGACTCCGTGGTCATGCAA 60.004 57.895 0.00 0.00 37.91 4.08
2871 3118 2.045045 CCCAGAATCAAGGCGGCA 60.045 61.111 13.08 0.00 0.00 5.69
2914 3161 1.964373 GGCGACGACAATGGTTGGT 60.964 57.895 0.00 0.00 32.28 3.67


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

AutoCloner maintained by Alex Coulton.