Multiple sequence alignment - TraesCS7D01G381600

Loading Multiple Alignment...

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 TraesCS7D01G381600 chr7D 100.000 2525 0 0 1 2525 495707570 495705046 0.000000e+00 4663
1 TraesCS7D01G381600 chr7B 88.480 1224 65 28 655 1837 524039375 524038187 0.000000e+00 1410
2 TraesCS7D01G381600 chr7B 90.258 349 18 6 1916 2255 524038159 524037818 2.310000e-120 442
3 TraesCS7D01G381600 chr7B 86.572 283 14 8 2253 2525 524037760 524037492 8.840000e-75 291
4 TraesCS7D01G381600 chr7A 90.033 903 47 16 690 1579 561586150 561585278 0.000000e+00 1129
5 TraesCS7D01G381600 chr7A 90.779 629 44 12 1 626 120016592 120017209 0.000000e+00 828
6 TraesCS7D01G381600 chr7A 86.331 278 20 10 2253 2521 561584693 561584425 1.140000e-73 287
7 TraesCS7D01G381600 chr7A 79.890 363 43 19 1897 2255 561585060 561584724 3.250000e-59 239
8 TraesCS7D01G381600 chr7A 90.506 158 7 6 1624 1773 561585268 561585111 4.260000e-48 202
9 TraesCS7D01G381600 chr4A 95.360 625 25 4 1 622 669866990 669866367 0.000000e+00 990
10 TraesCS7D01G381600 chr5A 95.040 625 27 4 1 622 531218015 531218638 0.000000e+00 979
11 TraesCS7D01G381600 chr5A 90.880 625 43 12 1 622 674166726 674167339 0.000000e+00 826
12 TraesCS7D01G381600 chr4B 95.040 625 22 5 1 622 593156977 593156359 0.000000e+00 974
13 TraesCS7D01G381600 chr5B 94.560 625 28 6 2 622 417884777 417885399 0.000000e+00 961
14 TraesCS7D01G381600 chr5B 92.173 626 34 13 1 622 462256671 462257285 0.000000e+00 870
15 TraesCS7D01G381600 chr1A 91.097 629 41 12 1 625 149123445 149122828 0.000000e+00 837
16 TraesCS7D01G381600 chr4D 89.744 624 38 11 1 622 108050373 108049774 0.000000e+00 774
17 TraesCS7D01G381600 chr2B 95.575 113 5 0 2 114 35123593 35123705 5.550000e-42 182


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 TraesCS7D01G381600 chr7D 495705046 495707570 2524 True 4663.000000 4663 100.000000 1 2525 1 chr7D.!!$R1 2524
1 TraesCS7D01G381600 chr7B 524037492 524039375 1883 True 714.333333 1410 88.436667 655 2525 3 chr7B.!!$R1 1870
2 TraesCS7D01G381600 chr7A 120016592 120017209 617 False 828.000000 828 90.779000 1 626 1 chr7A.!!$F1 625
3 TraesCS7D01G381600 chr7A 561584425 561586150 1725 True 464.250000 1129 86.690000 690 2521 4 chr7A.!!$R1 1831
4 TraesCS7D01G381600 chr4A 669866367 669866990 623 True 990.000000 990 95.360000 1 622 1 chr4A.!!$R1 621
5 TraesCS7D01G381600 chr5A 531218015 531218638 623 False 979.000000 979 95.040000 1 622 1 chr5A.!!$F1 621
6 TraesCS7D01G381600 chr5A 674166726 674167339 613 False 826.000000 826 90.880000 1 622 1 chr5A.!!$F2 621
7 TraesCS7D01G381600 chr4B 593156359 593156977 618 True 974.000000 974 95.040000 1 622 1 chr4B.!!$R1 621
8 TraesCS7D01G381600 chr5B 417884777 417885399 622 False 961.000000 961 94.560000 2 622 1 chr5B.!!$F1 620
9 TraesCS7D01G381600 chr5B 462256671 462257285 614 False 870.000000 870 92.173000 1 622 1 chr5B.!!$F2 621
10 TraesCS7D01G381600 chr1A 149122828 149123445 617 True 837.000000 837 91.097000 1 625 1 chr1A.!!$R1 624
11 TraesCS7D01G381600 chr4D 108049774 108050373 599 True 774.000000 774 89.744000 1 622 1 chr4D.!!$R1 621

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
631 641 1.210478 CCTAGTACTGGGCATGCTTGT 59.79 52.381 18.92 15.48 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1967 2025 0.450583 TACGCGACAGCTCAAGTAGG 59.549 55.0 15.93 0.0 42.32 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
105 106 5.822519 GTGAGGTAATTTGCTACATCCATGA 59.177 40.000 0.00 0.00 32.81 3.07
109 110 5.536161 GGTAATTTGCTACATCCATGATGGT 59.464 40.000 11.87 0.00 43.60 3.55
571 580 1.542492 ACTGTACCAGATCGAACGGT 58.458 50.000 12.25 12.25 35.18 4.83
622 632 3.912907 CCGGCGCCTAGTACTGGG 61.913 72.222 26.68 20.49 0.00 4.45
630 640 1.959042 CCTAGTACTGGGCATGCTTG 58.041 55.000 18.92 10.35 0.00 4.01
631 641 1.210478 CCTAGTACTGGGCATGCTTGT 59.790 52.381 18.92 15.48 0.00 3.16
632 642 2.434336 CCTAGTACTGGGCATGCTTGTA 59.566 50.000 18.92 14.50 0.00 2.41
633 643 2.403252 AGTACTGGGCATGCTTGTAC 57.597 50.000 25.72 25.72 35.18 2.90
634 644 1.909302 AGTACTGGGCATGCTTGTACT 59.091 47.619 27.96 27.96 38.95 2.73
635 645 2.305927 AGTACTGGGCATGCTTGTACTT 59.694 45.455 27.96 19.11 40.27 2.24
636 646 2.292828 ACTGGGCATGCTTGTACTTT 57.707 45.000 18.92 0.00 0.00 2.66
637 647 3.433306 ACTGGGCATGCTTGTACTTTA 57.567 42.857 18.92 0.00 0.00 1.85
638 648 3.347216 ACTGGGCATGCTTGTACTTTAG 58.653 45.455 18.92 5.56 0.00 1.85
639 649 3.009033 ACTGGGCATGCTTGTACTTTAGA 59.991 43.478 18.92 0.00 0.00 2.10
640 650 4.202441 CTGGGCATGCTTGTACTTTAGAT 58.798 43.478 18.92 0.00 0.00 1.98
641 651 4.599041 TGGGCATGCTTGTACTTTAGATT 58.401 39.130 18.92 0.00 0.00 2.40
642 652 5.016173 TGGGCATGCTTGTACTTTAGATTT 58.984 37.500 18.92 0.00 0.00 2.17
643 653 5.480073 TGGGCATGCTTGTACTTTAGATTTT 59.520 36.000 18.92 0.00 0.00 1.82
644 654 6.661377 TGGGCATGCTTGTACTTTAGATTTTA 59.339 34.615 18.92 0.00 0.00 1.52
645 655 7.148086 TGGGCATGCTTGTACTTTAGATTTTAG 60.148 37.037 18.92 0.00 0.00 1.85
646 656 7.196331 GGCATGCTTGTACTTTAGATTTTAGG 58.804 38.462 18.92 0.00 0.00 2.69
647 657 7.067008 GGCATGCTTGTACTTTAGATTTTAGGA 59.933 37.037 18.92 0.00 0.00 2.94
648 658 7.910683 GCATGCTTGTACTTTAGATTTTAGGAC 59.089 37.037 11.37 0.00 0.00 3.85
649 659 7.916914 TGCTTGTACTTTAGATTTTAGGACC 57.083 36.000 0.00 0.00 0.00 4.46
650 660 6.882678 TGCTTGTACTTTAGATTTTAGGACCC 59.117 38.462 0.00 0.00 0.00 4.46
651 661 6.882678 GCTTGTACTTTAGATTTTAGGACCCA 59.117 38.462 0.00 0.00 0.00 4.51
652 662 7.556635 GCTTGTACTTTAGATTTTAGGACCCAT 59.443 37.037 0.00 0.00 0.00 4.00
653 663 8.801882 TTGTACTTTAGATTTTAGGACCCATG 57.198 34.615 0.00 0.00 0.00 3.66
663 673 4.666412 TTAGGACCCATGATTTGGTTGA 57.334 40.909 0.00 0.00 44.83 3.18
666 676 3.165071 GGACCCATGATTTGGTTGAGTT 58.835 45.455 0.00 0.00 44.83 3.01
671 681 4.081697 CCCATGATTTGGTTGAGTTTACCC 60.082 45.833 0.00 0.00 44.83 3.69
687 697 6.659824 AGTTTACCCTATGACCCAGTTATTG 58.340 40.000 0.00 0.00 0.00 1.90
688 698 3.577805 ACCCTATGACCCAGTTATTGC 57.422 47.619 0.00 0.00 0.00 3.56
903 917 1.681486 CCAAACGCCAAACCCAACCT 61.681 55.000 0.00 0.00 0.00 3.50
914 928 3.629142 AACCCAACCTAATCCGAGAAG 57.371 47.619 0.00 0.00 0.00 2.85
916 930 1.475213 CCCAACCTAATCCGAGAAGGC 60.475 57.143 0.00 0.00 40.77 4.35
974 988 1.374125 CATCACCGCCACTCGTTCA 60.374 57.895 0.00 0.00 36.19 3.18
1029 1049 2.436109 GTGTCCCTGCACCACCAT 59.564 61.111 0.00 0.00 33.53 3.55
1120 1143 1.674651 CGTCACTCCTCCGTCTCCA 60.675 63.158 0.00 0.00 0.00 3.86
1129 1152 4.554363 CCGTCTCCACGCGCCTAG 62.554 72.222 5.73 0.00 45.29 3.02
1565 1606 2.228822 CCATGCTAGCTTTTCGGTTTGT 59.771 45.455 17.23 0.00 0.00 2.83
1739 1791 0.322816 AACTGCTCGCCACCATGATT 60.323 50.000 0.00 0.00 0.00 2.57
1754 1808 7.066284 GCCACCATGATTATATTGTAGTCCATC 59.934 40.741 0.00 0.00 0.00 3.51
1774 1828 4.188247 TCGAACCCAGATGTTTCTAGTG 57.812 45.455 0.00 0.00 0.00 2.74
1775 1829 3.056107 TCGAACCCAGATGTTTCTAGTGG 60.056 47.826 0.00 0.00 0.00 4.00
1776 1830 3.056107 CGAACCCAGATGTTTCTAGTGGA 60.056 47.826 0.00 0.00 0.00 4.02
1777 1831 4.383118 CGAACCCAGATGTTTCTAGTGGAT 60.383 45.833 0.00 0.00 0.00 3.41
1778 1832 4.762289 ACCCAGATGTTTCTAGTGGATC 57.238 45.455 0.00 0.00 0.00 3.36
1779 1833 4.366267 ACCCAGATGTTTCTAGTGGATCT 58.634 43.478 0.00 0.00 0.00 2.75
1780 1834 4.785376 ACCCAGATGTTTCTAGTGGATCTT 59.215 41.667 0.00 0.00 0.00 2.40
1781 1835 5.121811 CCCAGATGTTTCTAGTGGATCTTG 58.878 45.833 0.00 0.00 0.00 3.02
1782 1836 5.338708 CCCAGATGTTTCTAGTGGATCTTGT 60.339 44.000 0.00 0.00 0.00 3.16
1794 1848 4.346418 AGTGGATCTTGTAGATAAGGCCAG 59.654 45.833 5.01 0.00 34.53 4.85
1800 1858 5.674525 TCTTGTAGATAAGGCCAGTTCATG 58.325 41.667 5.01 0.00 0.00 3.07
1834 1892 6.148150 ACCGCTCGAAACTAAAACAATTCATA 59.852 34.615 0.00 0.00 0.00 2.15
1835 1893 7.148306 ACCGCTCGAAACTAAAACAATTCATAT 60.148 33.333 0.00 0.00 0.00 1.78
1836 1894 7.696453 CCGCTCGAAACTAAAACAATTCATATT 59.304 33.333 0.00 0.00 0.00 1.28
1837 1895 9.061610 CGCTCGAAACTAAAACAATTCATATTT 57.938 29.630 0.00 0.00 0.00 1.40
1874 1932 8.862325 AACAATTCATTATTGAGAGGTGTACA 57.138 30.769 4.64 0.00 45.35 2.90
1875 1933 9.466497 AACAATTCATTATTGAGAGGTGTACAT 57.534 29.630 0.00 0.00 45.35 2.29
1878 1936 9.911788 AATTCATTATTGAGAGGTGTACATCTT 57.088 29.630 10.66 0.16 37.10 2.40
1879 1937 9.911788 ATTCATTATTGAGAGGTGTACATCTTT 57.088 29.630 10.66 4.10 37.10 2.52
1880 1938 9.739276 TTCATTATTGAGAGGTGTACATCTTTT 57.261 29.630 10.66 1.72 37.10 2.27
1905 1963 3.733443 AAAAATGTCCAAGAGGTGCAC 57.267 42.857 8.80 8.80 35.89 4.57
1906 1964 2.363306 AAATGTCCAAGAGGTGCACA 57.637 45.000 20.43 0.00 35.89 4.57
1907 1965 2.592102 AATGTCCAAGAGGTGCACAT 57.408 45.000 20.43 12.71 32.82 3.21
1908 1966 2.119801 ATGTCCAAGAGGTGCACATC 57.880 50.000 23.39 23.39 35.89 3.06
1909 1967 1.059098 TGTCCAAGAGGTGCACATCT 58.941 50.000 27.36 27.36 38.83 2.90
1910 1968 2.256306 TGTCCAAGAGGTGCACATCTA 58.744 47.619 32.06 15.91 35.78 1.98
1911 1969 2.234661 TGTCCAAGAGGTGCACATCTAG 59.765 50.000 32.06 25.22 35.78 2.43
1912 1970 2.497675 GTCCAAGAGGTGCACATCTAGA 59.502 50.000 32.06 26.86 35.78 2.43
1913 1971 2.497675 TCCAAGAGGTGCACATCTAGAC 59.502 50.000 32.06 6.74 35.78 2.59
1914 1972 2.234661 CCAAGAGGTGCACATCTAGACA 59.765 50.000 32.06 0.00 35.78 3.41
1947 2005 0.966875 GTGCCAATCCTGACATGCCA 60.967 55.000 0.00 0.00 0.00 4.92
1956 2014 4.085357 TCCTGACATGCCACCAATATAC 57.915 45.455 0.00 0.00 0.00 1.47
1962 2020 6.755206 TGACATGCCACCAATATACTACTAC 58.245 40.000 0.00 0.00 0.00 2.73
1963 2021 6.553476 TGACATGCCACCAATATACTACTACT 59.447 38.462 0.00 0.00 0.00 2.57
1964 2022 7.726738 TGACATGCCACCAATATACTACTACTA 59.273 37.037 0.00 0.00 0.00 1.82
1965 2023 7.893658 ACATGCCACCAATATACTACTACTAC 58.106 38.462 0.00 0.00 0.00 2.73
1966 2024 7.728981 ACATGCCACCAATATACTACTACTACT 59.271 37.037 0.00 0.00 0.00 2.57
1967 2025 7.756395 TGCCACCAATATACTACTACTACTC 57.244 40.000 0.00 0.00 0.00 2.59
1994 2052 0.730265 AGCTGTCGCGTAGAAGAGAG 59.270 55.000 5.77 0.00 42.32 3.20
2008 2066 7.360101 GCGTAGAAGAGAGCAATTAACTGAAAA 60.360 37.037 0.00 0.00 0.00 2.29
2011 2069 6.714356 AGAAGAGAGCAATTAACTGAAAAGCT 59.286 34.615 0.00 0.00 34.86 3.74
2012 2070 6.890979 AGAGAGCAATTAACTGAAAAGCTT 57.109 33.333 0.00 0.00 33.00 3.74
2027 2086 8.094548 ACTGAAAAGCTTTTAAAAAGGAGTTGT 58.905 29.630 23.90 5.44 0.00 3.32
2042 2101 0.664166 GTTGTGGCTTGGACGCAATG 60.664 55.000 2.67 0.00 43.17 2.82
2165 2242 3.576861 AGACGTAATCCATCCATCTCCA 58.423 45.455 0.00 0.00 0.00 3.86
2275 2417 0.981183 TAATCCTCAACTGCCGTGGT 59.019 50.000 0.00 0.00 0.00 4.16
2290 2432 5.538118 TGCCGTGGTTCTATATATTCTGTG 58.462 41.667 0.00 0.00 0.00 3.66
2348 2494 2.815503 TCACCGTCGATTCTTCTGTGTA 59.184 45.455 0.00 0.00 0.00 2.90
2349 2495 3.253921 TCACCGTCGATTCTTCTGTGTAA 59.746 43.478 0.00 0.00 0.00 2.41
2350 2496 3.608506 CACCGTCGATTCTTCTGTGTAAG 59.391 47.826 0.00 0.00 0.00 2.34
2351 2497 3.255149 ACCGTCGATTCTTCTGTGTAAGT 59.745 43.478 0.00 0.00 0.00 2.24
2354 2500 5.512082 CCGTCGATTCTTCTGTGTAAGTAAG 59.488 44.000 0.00 0.00 0.00 2.34
2356 2502 5.288952 GTCGATTCTTCTGTGTAAGTAAGGC 59.711 44.000 0.00 0.00 0.00 4.35
2373 2523 3.939740 AGGCATGATGAACACATAGGT 57.060 42.857 0.00 0.00 0.00 3.08
2374 2524 4.240881 AGGCATGATGAACACATAGGTT 57.759 40.909 0.00 0.00 0.00 3.50
2394 2544 2.100631 GGAATGGAGTGGACACGCG 61.101 63.158 3.53 3.53 36.20 6.01
2412 2562 1.976474 GCGGATGGCCTTTTGTGGA 60.976 57.895 3.32 0.00 34.80 4.02
2419 2569 2.402564 TGGCCTTTTGTGGATTTGGAA 58.597 42.857 3.32 0.00 0.00 3.53
2420 2570 2.978278 TGGCCTTTTGTGGATTTGGAAT 59.022 40.909 3.32 0.00 0.00 3.01
2421 2571 4.163427 TGGCCTTTTGTGGATTTGGAATA 58.837 39.130 3.32 0.00 0.00 1.75
2422 2572 4.782156 TGGCCTTTTGTGGATTTGGAATAT 59.218 37.500 3.32 0.00 0.00 1.28
2426 2576 8.646900 GGCCTTTTGTGGATTTGGAATATATAA 58.353 33.333 0.00 0.00 0.00 0.98
2476 2626 2.853003 GACGATCGACTTTCTGCCTAAC 59.147 50.000 24.34 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 2.046892 GCGTCACAGCTCCACCAT 60.047 61.111 0.00 0.00 0.00 3.55
622 632 7.910683 GTCCTAAAATCTAAAGTACAAGCATGC 59.089 37.037 10.51 10.51 0.00 4.06
626 636 6.882678 TGGGTCCTAAAATCTAAAGTACAAGC 59.117 38.462 0.00 0.00 0.00 4.01
627 637 8.893727 CATGGGTCCTAAAATCTAAAGTACAAG 58.106 37.037 0.00 0.00 0.00 3.16
628 638 8.607713 TCATGGGTCCTAAAATCTAAAGTACAA 58.392 33.333 0.00 0.00 0.00 2.41
629 639 8.153221 TCATGGGTCCTAAAATCTAAAGTACA 57.847 34.615 0.00 0.00 0.00 2.90
630 640 9.628500 AATCATGGGTCCTAAAATCTAAAGTAC 57.372 33.333 0.00 0.00 0.00 2.73
632 642 8.971073 CAAATCATGGGTCCTAAAATCTAAAGT 58.029 33.333 0.00 0.00 0.00 2.66
633 643 8.416329 CCAAATCATGGGTCCTAAAATCTAAAG 58.584 37.037 0.00 0.00 46.27 1.85
634 644 8.305046 CCAAATCATGGGTCCTAAAATCTAAA 57.695 34.615 0.00 0.00 46.27 1.85
635 645 7.896383 CCAAATCATGGGTCCTAAAATCTAA 57.104 36.000 0.00 0.00 46.27 2.10
650 660 5.982890 AGGGTAAACTCAACCAAATCATG 57.017 39.130 0.00 0.00 38.87 3.07
651 661 7.339466 GTCATAGGGTAAACTCAACCAAATCAT 59.661 37.037 0.00 0.00 38.87 2.45
652 662 6.657541 GTCATAGGGTAAACTCAACCAAATCA 59.342 38.462 0.00 0.00 38.87 2.57
653 663 6.095021 GGTCATAGGGTAAACTCAACCAAATC 59.905 42.308 0.00 0.00 38.87 2.17
663 673 6.659824 CAATAACTGGGTCATAGGGTAAACT 58.340 40.000 0.00 0.00 0.00 2.66
666 676 4.475381 TGCAATAACTGGGTCATAGGGTAA 59.525 41.667 0.00 0.00 0.00 2.85
671 681 2.872245 CGGTGCAATAACTGGGTCATAG 59.128 50.000 0.00 0.00 0.00 2.23
687 697 2.218953 TCGGTAATCTTCATCGGTGC 57.781 50.000 0.00 0.00 0.00 5.01
688 698 3.782046 ACTTCGGTAATCTTCATCGGTG 58.218 45.455 0.00 0.00 0.00 4.94
748 759 1.598685 GGGAAAAGACGCCGGTGAA 60.599 57.895 24.59 0.00 0.00 3.18
872 886 1.758906 CGTTTGGTTGGGGTTGGGT 60.759 57.895 0.00 0.00 0.00 4.51
874 888 2.419620 GCGTTTGGTTGGGGTTGG 59.580 61.111 0.00 0.00 0.00 3.77
875 889 1.961180 TTGGCGTTTGGTTGGGGTTG 61.961 55.000 0.00 0.00 0.00 3.77
876 890 1.265454 TTTGGCGTTTGGTTGGGGTT 61.265 50.000 0.00 0.00 0.00 4.11
877 891 1.686110 TTTGGCGTTTGGTTGGGGT 60.686 52.632 0.00 0.00 0.00 4.95
878 892 1.227409 GTTTGGCGTTTGGTTGGGG 60.227 57.895 0.00 0.00 0.00 4.96
879 893 1.227409 GGTTTGGCGTTTGGTTGGG 60.227 57.895 0.00 0.00 0.00 4.12
880 894 1.227409 GGGTTTGGCGTTTGGTTGG 60.227 57.895 0.00 0.00 0.00 3.77
881 895 0.108138 TTGGGTTTGGCGTTTGGTTG 60.108 50.000 0.00 0.00 0.00 3.77
903 917 2.279252 GCGCGCCTTCTCGGATTA 60.279 61.111 23.24 0.00 33.16 1.75
929 943 0.460811 CTTACGCTGGCTGATCTGCA 60.461 55.000 23.84 10.73 34.04 4.41
954 968 2.781595 GAACGAGTGGCGGTGATGGT 62.782 60.000 0.00 0.00 42.25 3.55
958 972 2.338620 CTGAACGAGTGGCGGTGA 59.661 61.111 0.00 0.00 42.25 4.02
974 988 2.338984 GTGTGGAACGGAGCGACT 59.661 61.111 0.00 0.00 42.39 4.18
1114 1134 4.874977 GGCTAGGCGCGTGGAGAC 62.875 72.222 18.07 3.54 40.44 3.36
1202 1228 4.289101 TGGTGCTGGTGCTGGCAT 62.289 61.111 0.00 0.00 40.66 4.40
1565 1606 4.443457 GCATCAGCCAGTAATCCTCAAGTA 60.443 45.833 0.00 0.00 33.58 2.24
1659 1705 8.883731 AGTGCTCACAGTTAATTATACAATCAC 58.116 33.333 2.63 0.00 0.00 3.06
1739 1791 6.072649 TCTGGGTTCGATGGACTACAATATA 58.927 40.000 0.00 0.00 0.00 0.86
1754 1808 3.056107 TCCACTAGAAACATCTGGGTTCG 60.056 47.826 0.00 0.00 0.00 3.95
1774 1828 4.965200 ACTGGCCTTATCTACAAGATCC 57.035 45.455 3.32 0.00 36.20 3.36
1775 1829 5.918608 TGAACTGGCCTTATCTACAAGATC 58.081 41.667 3.32 0.00 36.20 2.75
1776 1830 5.957771 TGAACTGGCCTTATCTACAAGAT 57.042 39.130 3.32 0.00 38.70 2.40
1777 1831 5.396772 CCATGAACTGGCCTTATCTACAAGA 60.397 44.000 3.32 0.00 38.47 3.02
1778 1832 4.818546 CCATGAACTGGCCTTATCTACAAG 59.181 45.833 3.32 0.00 38.47 3.16
1779 1833 4.780815 CCATGAACTGGCCTTATCTACAA 58.219 43.478 3.32 0.00 38.47 2.41
1780 1834 4.422073 CCATGAACTGGCCTTATCTACA 57.578 45.455 3.32 0.00 38.47 2.74
1794 1848 0.458370 GCGGTTGAATGGCCATGAAC 60.458 55.000 21.63 23.08 0.00 3.18
1800 1858 1.582610 TTTCGAGCGGTTGAATGGCC 61.583 55.000 17.58 0.00 0.00 5.36
1848 1906 9.295825 TGTACACCTCTCAATAATGAATTGTTT 57.704 29.630 0.00 0.00 44.58 2.83
1849 1907 8.862325 TGTACACCTCTCAATAATGAATTGTT 57.138 30.769 0.00 0.00 44.58 2.83
1850 1908 9.113838 GATGTACACCTCTCAATAATGAATTGT 57.886 33.333 0.00 0.00 44.58 2.71
1851 1909 9.334947 AGATGTACACCTCTCAATAATGAATTG 57.665 33.333 0.00 0.00 45.47 2.32
1852 1910 9.911788 AAGATGTACACCTCTCAATAATGAATT 57.088 29.630 0.00 0.00 34.49 2.17
1853 1911 9.911788 AAAGATGTACACCTCTCAATAATGAAT 57.088 29.630 0.00 0.00 34.49 2.57
1854 1912 9.739276 AAAAGATGTACACCTCTCAATAATGAA 57.261 29.630 0.00 0.00 34.49 2.57
1891 1949 2.497675 TCTAGATGTGCACCTCTTGGAC 59.502 50.000 26.51 0.00 46.53 4.02
1892 1950 2.497675 GTCTAGATGTGCACCTCTTGGA 59.502 50.000 26.51 20.97 37.04 3.53
1893 1951 2.234661 TGTCTAGATGTGCACCTCTTGG 59.765 50.000 26.51 19.40 39.83 3.61
1894 1952 3.599730 TGTCTAGATGTGCACCTCTTG 57.400 47.619 26.51 23.73 0.00 3.02
1895 1953 4.833478 AATGTCTAGATGTGCACCTCTT 57.167 40.909 26.51 12.92 0.00 2.85
1896 1954 5.741383 GCATAATGTCTAGATGTGCACCTCT 60.741 44.000 25.05 25.05 0.00 3.69
1897 1955 4.450419 GCATAATGTCTAGATGTGCACCTC 59.550 45.833 15.69 14.57 0.00 3.85
1898 1956 4.141642 TGCATAATGTCTAGATGTGCACCT 60.142 41.667 15.69 3.77 36.33 4.00
1899 1957 4.129380 TGCATAATGTCTAGATGTGCACC 58.871 43.478 15.69 0.00 36.33 5.01
1900 1958 5.686834 CATGCATAATGTCTAGATGTGCAC 58.313 41.667 15.72 10.75 42.93 4.57
1901 1959 4.214758 GCATGCATAATGTCTAGATGTGCA 59.785 41.667 14.21 15.74 44.05 4.57
1902 1960 4.214758 TGCATGCATAATGTCTAGATGTGC 59.785 41.667 18.46 6.61 38.65 4.57
1903 1961 5.934935 TGCATGCATAATGTCTAGATGTG 57.065 39.130 18.46 0.00 38.65 3.21
1904 1962 7.333672 CACTATGCATGCATAATGTCTAGATGT 59.666 37.037 33.71 22.92 38.30 3.06
1905 1963 7.676572 GCACTATGCATGCATAATGTCTAGATG 60.677 40.741 36.01 24.35 44.26 2.90
1906 1964 6.315642 GCACTATGCATGCATAATGTCTAGAT 59.684 38.462 36.01 16.60 44.26 1.98
1907 1965 5.640783 GCACTATGCATGCATAATGTCTAGA 59.359 40.000 36.01 18.69 44.26 2.43
1908 1966 5.866075 GCACTATGCATGCATAATGTCTAG 58.134 41.667 36.01 27.64 44.26 2.43
1909 1967 5.868043 GCACTATGCATGCATAATGTCTA 57.132 39.130 36.01 19.92 44.26 2.59
1910 1968 4.761235 GCACTATGCATGCATAATGTCT 57.239 40.909 36.01 18.97 44.26 3.41
1956 2014 6.350906 ACAGCTCAAGTAGGAGTAGTAGTAG 58.649 44.000 0.00 0.00 37.24 2.57
1962 2020 2.223386 GCGACAGCTCAAGTAGGAGTAG 60.223 54.545 0.00 0.00 41.01 2.57
1963 2021 1.743958 GCGACAGCTCAAGTAGGAGTA 59.256 52.381 0.00 0.00 41.01 2.59
1964 2022 0.528470 GCGACAGCTCAAGTAGGAGT 59.472 55.000 0.00 0.00 41.01 3.85
1965 2023 0.524392 CGCGACAGCTCAAGTAGGAG 60.524 60.000 0.00 0.00 42.32 3.69
1966 2024 1.241990 ACGCGACAGCTCAAGTAGGA 61.242 55.000 15.93 0.00 42.32 2.94
1967 2025 0.450583 TACGCGACAGCTCAAGTAGG 59.549 55.000 15.93 0.00 42.32 3.18
2008 2066 4.405680 AGCCACAACTCCTTTTTAAAAGCT 59.594 37.500 11.59 1.20 0.00 3.74
2011 2069 5.187967 TCCAAGCCACAACTCCTTTTTAAAA 59.812 36.000 0.00 0.00 0.00 1.52
2012 2070 4.712337 TCCAAGCCACAACTCCTTTTTAAA 59.288 37.500 0.00 0.00 0.00 1.52
2018 2077 0.535102 CGTCCAAGCCACAACTCCTT 60.535 55.000 0.00 0.00 0.00 3.36
2020 2079 2.617274 GCGTCCAAGCCACAACTCC 61.617 63.158 0.00 0.00 0.00 3.85
2027 2086 1.368345 CGATCATTGCGTCCAAGCCA 61.368 55.000 0.00 0.00 33.80 4.75
2075 2138 4.394920 GCTATGCTTTACAACAAGGCAGTA 59.605 41.667 0.46 0.00 36.35 2.74
2076 2139 3.191371 GCTATGCTTTACAACAAGGCAGT 59.809 43.478 0.46 0.00 36.35 4.40
2180 2257 0.948623 TCACGTTGATTGGTCGGCTG 60.949 55.000 0.00 0.00 0.00 4.85
2275 2417 7.078249 ACATGTGGCCACAGAATATATAGAA 57.922 36.000 39.29 15.05 45.48 2.10
2348 2494 5.824624 CCTATGTGTTCATCATGCCTTACTT 59.175 40.000 0.00 0.00 35.70 2.24
2349 2495 5.104360 ACCTATGTGTTCATCATGCCTTACT 60.104 40.000 0.00 0.00 35.70 2.24
2350 2496 5.126067 ACCTATGTGTTCATCATGCCTTAC 58.874 41.667 0.00 0.00 35.70 2.34
2351 2497 5.372343 ACCTATGTGTTCATCATGCCTTA 57.628 39.130 0.00 0.00 35.70 2.69
2354 2500 4.516698 CCTAACCTATGTGTTCATCATGCC 59.483 45.833 0.00 0.00 35.70 4.40
2356 2502 7.040892 CCATTCCTAACCTATGTGTTCATCATG 60.041 40.741 0.00 0.00 35.70 3.07
2373 2523 1.066430 GCGTGTCCACTCCATTCCTAA 60.066 52.381 0.00 0.00 0.00 2.69
2374 2524 0.535335 GCGTGTCCACTCCATTCCTA 59.465 55.000 0.00 0.00 0.00 2.94
2394 2544 1.322538 ATCCACAAAAGGCCATCCGC 61.323 55.000 5.01 0.00 37.47 5.54
2426 2576 8.251026 GCATGATCATTCATCCATTCATACATT 58.749 33.333 5.16 0.00 40.70 2.71
2430 2580 7.613801 TCATGCATGATCATTCATCCATTCATA 59.386 33.333 25.42 0.00 37.44 2.15
2476 2626 3.081804 AGTATTTCCTCCGCAAAGTTGG 58.918 45.455 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.