Multiple sequence alignment - TraesCS4A01G217100

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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 TraesCS4A01G217100 chr4A 100.000 2549 0 0 1 2549 516356404 516353856 0.000000e+00 4708.0
1 TraesCS4A01G217100 chr4A 88.972 671 57 11 899 1563 516370181 516369522 0.000000e+00 813.0
2 TraesCS4A01G217100 chr4D 91.176 1904 135 21 1 1885 67245709 67243820 0.000000e+00 2555.0
3 TraesCS4A01G217100 chr4D 89.067 686 56 13 875 1553 67275147 67274474 0.000000e+00 833.0
4 TraesCS4A01G217100 chr4D 81.583 657 113 6 1 653 319111566 319110914 1.040000e-148 536.0
5 TraesCS4A01G217100 chr4B 94.592 906 42 4 987 1885 99082144 99081239 0.000000e+00 1395.0
6 TraesCS4A01G217100 chr4B 89.542 698 56 10 875 1563 99265967 99265278 0.000000e+00 869.0
7 TraesCS4A01G217100 chr1A 96.203 632 12 6 1924 2549 32857571 32856946 0.000000e+00 1024.0
8 TraesCS4A01G217100 chr1A 79.562 411 40 16 1992 2369 583865851 583866250 1.170000e-63 254.0
9 TraesCS4A01G217100 chr2A 83.053 655 101 8 1 649 665830471 665829821 1.020000e-163 586.0
10 TraesCS4A01G217100 chr2A 82.317 656 95 14 1 653 103832619 103831982 1.330000e-152 549.0
11 TraesCS4A01G217100 chr3D 85.637 557 72 3 1 557 518319570 518320118 1.700000e-161 579.0
12 TraesCS4A01G217100 chr3D 80.263 380 40 20 1947 2301 28365901 28366270 1.170000e-63 254.0
13 TraesCS4A01G217100 chr3D 80.263 380 40 20 1947 2301 28369283 28369652 1.170000e-63 254.0
14 TraesCS4A01G217100 chr3D 80.263 380 40 20 1947 2301 28375076 28375445 1.170000e-63 254.0
15 TraesCS4A01G217100 chr3D 88.000 50 2 2 1134 1183 117814728 117814683 3.540000e-04 56.5
16 TraesCS4A01G217100 chr5D 84.392 551 68 9 1 544 327212195 327211656 2.250000e-145 525.0
17 TraesCS4A01G217100 chr5D 83.032 554 73 14 1 544 458517426 458516884 1.370000e-132 483.0
18 TraesCS4A01G217100 chr5D 81.851 562 78 14 1 557 428530307 428530849 3.870000e-123 451.0
19 TraesCS4A01G217100 chr5D 93.452 168 10 1 2370 2536 23177497 23177330 5.450000e-62 248.0
20 TraesCS4A01G217100 chr5A 83.877 552 81 6 11 556 426111083 426110534 1.050000e-143 520.0
21 TraesCS4A01G217100 chr5A 83.520 358 29 9 2039 2372 17145577 17145226 8.860000e-80 307.0
22 TraesCS4A01G217100 chr6B 83.565 432 53 13 1947 2372 416874187 416874606 3.080000e-104 388.0
23 TraesCS4A01G217100 chr5B 91.111 180 15 1 2370 2549 16877395 16877217 2.530000e-60 243.0
24 TraesCS4A01G217100 chr5B 90.556 180 16 1 2370 2549 16939456 16939278 1.180000e-58 237.0
25 TraesCS4A01G217100 chr5B 90.556 180 16 1 2370 2549 17178704 17178526 1.180000e-58 237.0
26 TraesCS4A01G217100 chr5B 90.556 180 16 1 2370 2549 17249967 17249789 1.180000e-58 237.0
27 TraesCS4A01G217100 chr5B 90.000 180 17 1 2370 2549 16857204 16857026 5.480000e-57 231.0
28 TraesCS4A01G217100 chr5B 90.000 180 17 1 2370 2549 17158306 17158128 5.480000e-57 231.0
29 TraesCS4A01G217100 chr6D 96.032 126 5 0 2424 2549 268334202 268334327 3.320000e-49 206.0
30 TraesCS4A01G217100 chr6D 79.348 92 9 6 1089 1180 291722408 291722489 3.540000e-04 56.5
31 TraesCS4A01G217100 chr3B 81.301 246 33 5 2136 2369 11575760 11575516 1.200000e-43 187.0
32 TraesCS4A01G217100 chr7B 80.080 251 37 7 2133 2372 278100902 278100654 9.370000e-40 174.0
33 TraesCS4A01G217100 chr3A 80.169 237 39 8 2136 2369 745516180 745515949 1.210000e-38 171.0
34 TraesCS4A01G217100 chrUn 95.745 47 1 1 2370 2416 75336864 75336909 9.780000e-10 75.0


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 TraesCS4A01G217100 chr4A 516353856 516356404 2548 True 4708 4708 100.000 1 2549 1 chr4A.!!$R1 2548
1 TraesCS4A01G217100 chr4A 516369522 516370181 659 True 813 813 88.972 899 1563 1 chr4A.!!$R2 664
2 TraesCS4A01G217100 chr4D 67243820 67245709 1889 True 2555 2555 91.176 1 1885 1 chr4D.!!$R1 1884
3 TraesCS4A01G217100 chr4D 67274474 67275147 673 True 833 833 89.067 875 1553 1 chr4D.!!$R2 678
4 TraesCS4A01G217100 chr4D 319110914 319111566 652 True 536 536 81.583 1 653 1 chr4D.!!$R3 652
5 TraesCS4A01G217100 chr4B 99081239 99082144 905 True 1395 1395 94.592 987 1885 1 chr4B.!!$R1 898
6 TraesCS4A01G217100 chr4B 99265278 99265967 689 True 869 869 89.542 875 1563 1 chr4B.!!$R2 688
7 TraesCS4A01G217100 chr1A 32856946 32857571 625 True 1024 1024 96.203 1924 2549 1 chr1A.!!$R1 625
8 TraesCS4A01G217100 chr2A 665829821 665830471 650 True 586 586 83.053 1 649 1 chr2A.!!$R2 648
9 TraesCS4A01G217100 chr2A 103831982 103832619 637 True 549 549 82.317 1 653 1 chr2A.!!$R1 652
10 TraesCS4A01G217100 chr3D 518319570 518320118 548 False 579 579 85.637 1 557 1 chr3D.!!$F2 556
11 TraesCS4A01G217100 chr3D 28365901 28369652 3751 False 254 254 80.263 1947 2301 2 chr3D.!!$F3 354
12 TraesCS4A01G217100 chr5D 327211656 327212195 539 True 525 525 84.392 1 544 1 chr5D.!!$R2 543
13 TraesCS4A01G217100 chr5D 458516884 458517426 542 True 483 483 83.032 1 544 1 chr5D.!!$R3 543
14 TraesCS4A01G217100 chr5D 428530307 428530849 542 False 451 451 81.851 1 557 1 chr5D.!!$F1 556
15 TraesCS4A01G217100 chr5A 426110534 426111083 549 True 520 520 83.877 11 556 1 chr5A.!!$R2 545

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
92 93 0.035739 GTCAAGTCGGGGTAAGGCAA 59.964 55.0 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1933 2001 0.247735 TGTTTGTAACGCACGTGCAC 60.248 50.0 37.03 27.83 42.21 4.57 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
24 25 2.029073 CGCTGTGTCCGTGGAACT 59.971 61.111 0.00 0.00 31.75 3.01
26 27 1.227556 GCTGTGTCCGTGGAACTGT 60.228 57.895 0.00 0.00 31.75 3.55
60 61 3.700970 TGCGGATCGAGGTGCCAA 61.701 61.111 0.00 0.00 0.00 4.52
77 78 1.528076 AATGGTGTGGCAGCGTCAA 60.528 52.632 0.00 0.00 34.27 3.18
92 93 0.035739 GTCAAGTCGGGGTAAGGCAA 59.964 55.000 0.00 0.00 0.00 4.52
152 153 1.374631 GGATGTGCAGACGCTGTCA 60.375 57.895 10.52 8.31 39.64 3.58
280 303 1.706995 TAGGGTTTGGGTTGTCGCCA 61.707 55.000 0.00 0.00 0.00 5.69
408 434 2.570774 TAGTGGGCCCGGTGTCGATA 62.571 60.000 19.37 0.00 39.00 2.92
412 438 2.420568 GGCCCGGTGTCGATAGTCA 61.421 63.158 0.00 0.00 39.00 3.41
428 454 9.776158 GTCGATAGTCATCATAAATTAGACGAT 57.224 33.333 0.00 0.00 34.56 3.73
476 502 4.308458 CCACGGCGGACACCAAGA 62.308 66.667 13.24 0.00 36.56 3.02
513 550 2.202946 TTCACGTCTGCGCCAACA 60.203 55.556 4.18 0.00 42.83 3.33
544 581 3.119779 GCGTAATTTTGGGTCGGAAATGA 60.120 43.478 0.00 0.00 0.00 2.57
545 582 4.439563 GCGTAATTTTGGGTCGGAAATGAT 60.440 41.667 0.00 0.00 0.00 2.45
546 583 5.220892 GCGTAATTTTGGGTCGGAAATGATA 60.221 40.000 0.00 0.00 0.00 2.15
565 602 3.990806 CGCGCGGACACAAAACGA 61.991 61.111 24.84 0.00 0.00 3.85
569 606 1.722677 GCGGACACAAAACGAACCA 59.277 52.632 0.00 0.00 0.00 3.67
582 619 7.009999 CACAAAACGAACCATTTTTGAGATTGA 59.990 33.333 12.46 0.00 42.76 2.57
585 622 6.391227 ACGAACCATTTTTGAGATTGAGTT 57.609 33.333 0.00 0.00 0.00 3.01
586 623 6.805713 ACGAACCATTTTTGAGATTGAGTTT 58.194 32.000 0.00 0.00 0.00 2.66
615 652 0.179124 GCAGGTGTTTTTGTCCGCAA 60.179 50.000 0.00 0.00 0.00 4.85
617 654 1.134175 CAGGTGTTTTTGTCCGCAACT 59.866 47.619 0.00 0.00 33.82 3.16
622 659 1.951602 GTTTTTGTCCGCAACTACCCT 59.048 47.619 0.00 0.00 33.82 4.34
625 662 3.706600 TTTGTCCGCAACTACCCTAAT 57.293 42.857 0.00 0.00 33.82 1.73
626 663 4.822685 TTTGTCCGCAACTACCCTAATA 57.177 40.909 0.00 0.00 33.82 0.98
650 687 1.294138 GGACGGACGAAATGGGTCA 59.706 57.895 0.00 0.00 36.12 4.02
673 719 4.877251 ACCTTGCTCTTACGTGTTTGTAAA 59.123 37.500 0.00 0.00 34.15 2.01
693 739 0.591659 TAGCTATAGTCCTGTGCGCG 59.408 55.000 0.00 0.00 0.00 6.86
719 765 5.882557 AGTACTTCAAAGTATTGATGGCCTG 59.117 40.000 3.32 0.00 44.70 4.85
726 772 2.092212 AGTATTGATGGCCTGACCCAAG 60.092 50.000 3.32 0.00 38.61 3.61
759 806 6.279513 TCCATGCTTTCCGACATTATTTTT 57.720 33.333 0.00 0.00 0.00 1.94
788 835 6.563567 GCATCACACTGAGAAATCATCATACG 60.564 42.308 0.00 0.00 0.00 3.06
789 836 5.965922 TCACACTGAGAAATCATCATACGT 58.034 37.500 0.00 0.00 0.00 3.57
790 837 7.095695 TCACACTGAGAAATCATCATACGTA 57.904 36.000 0.00 0.00 0.00 3.57
791 838 6.972901 TCACACTGAGAAATCATCATACGTAC 59.027 38.462 0.00 0.00 0.00 3.67
832 879 0.313043 TCGAGTGGACACCGAGAAAC 59.687 55.000 10.48 0.00 32.89 2.78
849 896 5.021033 AGAAACAGAGATCGAGCATCATT 57.979 39.130 2.38 0.00 33.29 2.57
850 897 5.049167 AGAAACAGAGATCGAGCATCATTC 58.951 41.667 2.38 0.92 33.29 2.67
852 899 4.241590 ACAGAGATCGAGCATCATTCTC 57.758 45.455 2.38 2.39 40.90 2.87
854 901 3.005578 CAGAGATCGAGCATCATTCTCCA 59.994 47.826 2.38 0.00 41.27 3.86
855 902 3.640498 AGAGATCGAGCATCATTCTCCAA 59.360 43.478 2.38 0.00 41.27 3.53
856 903 4.100653 AGAGATCGAGCATCATTCTCCAAA 59.899 41.667 2.38 0.00 41.27 3.28
940 991 3.244561 CCTCTCCACAAATACACCACACT 60.245 47.826 0.00 0.00 0.00 3.55
1062 1117 2.202987 GCGGCTGCTATGCTGAGT 60.203 61.111 11.21 0.00 41.56 3.41
1064 1119 1.142531 CGGCTGCTATGCTGAGTCA 59.857 57.895 0.00 0.00 41.56 3.41
1577 1635 3.607741 TGCCGGACGGAAAATATTGTAA 58.392 40.909 15.99 0.00 37.50 2.41
1648 1708 4.035441 CGTGATGGATGATGTGCATTTACA 59.965 41.667 0.00 0.00 39.19 2.41
1680 1740 1.131504 TGTTTCGTGTCTGTGGTTTGC 59.868 47.619 0.00 0.00 0.00 3.68
1681 1741 1.131504 GTTTCGTGTCTGTGGTTTGCA 59.868 47.619 0.00 0.00 0.00 4.08
1761 1822 6.548441 AATTTGTGGTTGCTGAAATCAATG 57.452 33.333 0.00 0.00 28.19 2.82
1812 1875 0.681733 ACAGAGCCAGAACGTGTGAT 59.318 50.000 0.00 0.00 0.00 3.06
1877 1945 1.945580 TTTTTATTCCAGGGGCCACC 58.054 50.000 0.00 0.57 40.67 4.61
1878 1946 0.323908 TTTTATTCCAGGGGCCACCG 60.324 55.000 0.00 0.00 46.96 4.94
1885 1953 1.991167 CAGGGGCCACCGTACCTTA 60.991 63.158 0.00 0.00 46.96 2.69
1886 1954 1.991722 AGGGGCCACCGTACCTTAC 60.992 63.158 0.00 0.00 46.96 2.34
1887 1955 1.991722 GGGGCCACCGTACCTTACT 60.992 63.158 4.39 0.00 37.78 2.24
1888 1956 1.556373 GGGGCCACCGTACCTTACTT 61.556 60.000 4.39 0.00 37.78 2.24
1889 1957 0.325933 GGGCCACCGTACCTTACTTT 59.674 55.000 4.39 0.00 0.00 2.66
1890 1958 1.271543 GGGCCACCGTACCTTACTTTT 60.272 52.381 4.39 0.00 0.00 2.27
1891 1959 2.507484 GGCCACCGTACCTTACTTTTT 58.493 47.619 0.00 0.00 0.00 1.94
1912 1980 7.906199 TTTTTAGGGGATCTTTCACTTTTCA 57.094 32.000 0.00 0.00 0.00 2.69
1913 1981 6.894339 TTTAGGGGATCTTTCACTTTTCAC 57.106 37.500 0.00 0.00 0.00 3.18
1914 1982 4.731313 AGGGGATCTTTCACTTTTCACT 57.269 40.909 0.00 0.00 0.00 3.41
1915 1983 5.066913 AGGGGATCTTTCACTTTTCACTT 57.933 39.130 0.00 0.00 0.00 3.16
1916 1984 5.458595 AGGGGATCTTTCACTTTTCACTTT 58.541 37.500 0.00 0.00 0.00 2.66
1917 1985 5.302823 AGGGGATCTTTCACTTTTCACTTTG 59.697 40.000 0.00 0.00 0.00 2.77
1918 1986 5.069119 GGGGATCTTTCACTTTTCACTTTGT 59.931 40.000 0.00 0.00 0.00 2.83
1919 1987 6.406961 GGGGATCTTTCACTTTTCACTTTGTT 60.407 38.462 0.00 0.00 0.00 2.83
1920 1988 6.697455 GGGATCTTTCACTTTTCACTTTGTTC 59.303 38.462 0.00 0.00 0.00 3.18
1921 1989 6.697455 GGATCTTTCACTTTTCACTTTGTTCC 59.303 38.462 0.00 0.00 0.00 3.62
1922 1990 5.961272 TCTTTCACTTTTCACTTTGTTCCC 58.039 37.500 0.00 0.00 0.00 3.97
1923 1991 5.478679 TCTTTCACTTTTCACTTTGTTCCCA 59.521 36.000 0.00 0.00 0.00 4.37
1924 1992 4.712122 TCACTTTTCACTTTGTTCCCAC 57.288 40.909 0.00 0.00 0.00 4.61
1925 1993 4.340617 TCACTTTTCACTTTGTTCCCACT 58.659 39.130 0.00 0.00 0.00 4.00
1926 1994 5.502079 TCACTTTTCACTTTGTTCCCACTA 58.498 37.500 0.00 0.00 0.00 2.74
1927 1995 5.588648 TCACTTTTCACTTTGTTCCCACTAG 59.411 40.000 0.00 0.00 0.00 2.57
1928 1996 5.357032 CACTTTTCACTTTGTTCCCACTAGT 59.643 40.000 0.00 0.00 0.00 2.57
1929 1997 6.540914 CACTTTTCACTTTGTTCCCACTAGTA 59.459 38.462 0.00 0.00 0.00 1.82
1930 1998 7.066525 CACTTTTCACTTTGTTCCCACTAGTAA 59.933 37.037 0.00 0.00 0.00 2.24
1931 1999 7.612633 ACTTTTCACTTTGTTCCCACTAGTAAA 59.387 33.333 0.00 0.00 0.00 2.01
1932 2000 6.930667 TTCACTTTGTTCCCACTAGTAAAC 57.069 37.500 0.00 1.61 0.00 2.01
1933 2001 5.051816 TCACTTTGTTCCCACTAGTAAACG 58.948 41.667 0.00 0.00 0.00 3.60
1934 2002 4.812626 CACTTTGTTCCCACTAGTAAACGT 59.187 41.667 0.00 0.00 0.00 3.99
1935 2003 4.812626 ACTTTGTTCCCACTAGTAAACGTG 59.187 41.667 0.00 0.00 0.00 4.49
1936 2004 2.758009 TGTTCCCACTAGTAAACGTGC 58.242 47.619 0.00 0.00 0.00 5.34
1937 2005 2.102757 TGTTCCCACTAGTAAACGTGCA 59.897 45.455 0.00 0.00 0.00 4.57
1938 2006 2.443887 TCCCACTAGTAAACGTGCAC 57.556 50.000 6.82 6.82 0.00 4.57
1939 2007 1.065358 CCCACTAGTAAACGTGCACG 58.935 55.000 35.99 35.99 46.33 5.34
1957 2025 3.465907 CACGTGCGTTACAAACATACTG 58.534 45.455 0.82 0.00 0.00 2.74
1969 2037 6.709018 ACAAACATACTGTGGCTAAAGTTT 57.291 33.333 0.00 0.00 0.00 2.66
1970 2038 7.107639 ACAAACATACTGTGGCTAAAGTTTT 57.892 32.000 0.00 0.00 0.00 2.43
1971 2039 7.552459 ACAAACATACTGTGGCTAAAGTTTTT 58.448 30.769 0.00 0.00 0.00 1.94
1972 2040 8.688151 ACAAACATACTGTGGCTAAAGTTTTTA 58.312 29.630 0.00 0.00 0.00 1.52
2016 5464 4.558226 ACACATATTCTCTGCACCAAGA 57.442 40.909 0.00 0.00 0.00 3.02
2138 5608 1.150827 CTCCCCCGTCGTTTTGTAAC 58.849 55.000 0.00 0.00 0.00 2.50
2203 5675 8.477419 AAAAACATAAATCTTCACTTCCCAGA 57.523 30.769 0.00 0.00 0.00 3.86
2226 5698 6.660094 AGAGAAAGAAGTATACGAAGGAGTGT 59.340 38.462 0.00 0.00 0.00 3.55
2284 5757 2.320367 GAGCATAACATAGCGTCCTCG 58.680 52.381 0.00 0.00 40.37 4.63
2304 5777 1.937278 CAGTTGTGCCATTTGTTGCA 58.063 45.000 0.00 0.00 34.54 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.308458 CCGGTGCCGACAGTTCCA 62.308 66.667 12.71 0.00 42.83 3.53
60 61 1.968017 CTTGACGCTGCCACACCAT 60.968 57.895 0.00 0.00 0.00 3.55
77 78 2.660802 CGTTGCCTTACCCCGACT 59.339 61.111 0.00 0.00 0.00 4.18
92 93 3.391382 GGGAGTACAGGCAGCCGT 61.391 66.667 5.55 9.93 0.00 5.68
180 195 1.383803 ATCCTCCTGTGCTCCTCCC 60.384 63.158 0.00 0.00 0.00 4.30
280 303 2.262915 CCTTCGTGCTTCCTCGCT 59.737 61.111 0.00 0.00 0.00 4.93
364 390 1.864029 GCCAGTGGAAGCGTTGTTTTC 60.864 52.381 15.20 0.00 0.00 2.29
408 434 6.863645 CGTCCATCGTCTAATTTATGATGACT 59.136 38.462 17.81 1.92 41.08 3.41
412 438 6.097915 ACCGTCCATCGTCTAATTTATGAT 57.902 37.500 0.00 0.00 37.94 2.45
428 454 2.886134 GCCACCCAACTACCGTCCA 61.886 63.158 0.00 0.00 0.00 4.02
499 536 1.444119 AAATGTGTTGGCGCAGACGT 61.444 50.000 10.83 0.00 41.59 4.34
513 550 3.576550 ACCCAAAATTACGCCTGAAATGT 59.423 39.130 0.00 0.00 0.00 2.71
544 581 1.668472 TTTTGTGTCCGCGCGGTAT 60.668 52.632 44.16 0.00 36.47 2.73
545 582 2.279985 TTTTGTGTCCGCGCGGTA 60.280 55.556 44.16 32.11 36.47 4.02
546 583 3.944233 GTTTTGTGTCCGCGCGGT 61.944 61.111 44.16 0.00 36.47 5.68
557 594 7.038659 TCAATCTCAAAAATGGTTCGTTTTGT 58.961 30.769 8.29 0.00 42.63 2.83
562 599 6.391227 AACTCAATCTCAAAAATGGTTCGT 57.609 33.333 0.00 0.00 0.00 3.85
565 602 7.329226 CGCATAAACTCAATCTCAAAAATGGTT 59.671 33.333 0.00 0.00 0.00 3.67
569 606 7.329226 CCAACGCATAAACTCAATCTCAAAAAT 59.671 33.333 0.00 0.00 0.00 1.82
615 652 4.964262 TCCGTCCATGTTTATTAGGGTAGT 59.036 41.667 0.00 0.00 0.00 2.73
617 654 4.202141 CGTCCGTCCATGTTTATTAGGGTA 60.202 45.833 0.00 0.00 0.00 3.69
622 659 5.294799 CCATTTCGTCCGTCCATGTTTATTA 59.705 40.000 0.00 0.00 0.00 0.98
625 662 3.004171 CCATTTCGTCCGTCCATGTTTA 58.996 45.455 0.00 0.00 0.00 2.01
626 663 1.810151 CCATTTCGTCCGTCCATGTTT 59.190 47.619 0.00 0.00 0.00 2.83
650 687 2.914059 ACAAACACGTAAGAGCAAGGT 58.086 42.857 0.00 0.00 43.62 3.50
673 719 1.200252 CGCGCACAGGACTATAGCTAT 59.800 52.381 11.77 11.77 0.00 2.97
693 739 5.297029 GGCCATCAATACTTTGAAGTACTCC 59.703 44.000 0.00 0.00 44.70 3.85
719 765 1.909302 TGGATCTTGTCTCCTTGGGTC 59.091 52.381 0.00 0.00 33.69 4.46
726 772 2.948315 GGAAAGCATGGATCTTGTCTCC 59.052 50.000 0.00 0.00 0.00 3.71
759 806 4.064388 TGATTTCTCAGTGTGATGCGAAA 58.936 39.130 0.00 0.00 38.03 3.46
765 812 6.577103 ACGTATGATGATTTCTCAGTGTGAT 58.423 36.000 0.00 0.00 34.12 3.06
767 814 6.751888 TGTACGTATGATGATTTCTCAGTGTG 59.248 38.462 0.00 0.00 34.12 3.82
775 822 4.154195 GGGGCATGTACGTATGATGATTTC 59.846 45.833 17.34 4.10 0.00 2.17
788 835 3.637714 CGCATACGGGGCATGTAC 58.362 61.111 0.00 0.00 34.97 2.90
832 879 3.005578 TGGAGAATGATGCTCGATCTCTG 59.994 47.826 9.20 0.00 37.33 3.35
850 897 5.391416 GCTCGATCTCCTTTTTCTTTTGGAG 60.391 44.000 0.00 0.00 45.36 3.86
852 899 4.216257 TGCTCGATCTCCTTTTTCTTTTGG 59.784 41.667 0.00 0.00 0.00 3.28
854 901 5.049129 CACTGCTCGATCTCCTTTTTCTTTT 60.049 40.000 0.00 0.00 0.00 2.27
855 902 4.453819 CACTGCTCGATCTCCTTTTTCTTT 59.546 41.667 0.00 0.00 0.00 2.52
856 903 3.999663 CACTGCTCGATCTCCTTTTTCTT 59.000 43.478 0.00 0.00 0.00 2.52
907 957 3.071206 GGAGAGGACAGGCGCTGA 61.071 66.667 7.64 0.00 35.18 4.26
940 991 0.623617 GAAAGAGGGGAGGGGGCTAA 60.624 60.000 0.00 0.00 0.00 3.09
1053 1108 0.461548 CGGAAGCCTGACTCAGCATA 59.538 55.000 0.00 0.00 0.00 3.14
1077 1132 2.027625 GAACTTGGTCAGGTCGCCG 61.028 63.158 0.00 0.00 26.12 6.46
1079 1134 0.868406 CTTGAACTTGGTCAGGTCGC 59.132 55.000 0.00 0.00 43.11 5.19
1553 1611 1.157870 ATATTTTCCGTCCGGCAGCG 61.158 55.000 0.00 0.55 34.68 5.18
1577 1635 8.785946 CAAAAGTCCATTTATTCCAAGCAAAAT 58.214 29.630 0.00 0.00 0.00 1.82
1593 1653 4.060205 GCAACAAATCTGCAAAAGTCCAT 58.940 39.130 0.00 0.00 39.69 3.41
1648 1708 3.206150 ACACGAAACAGCACTCAAATCT 58.794 40.909 0.00 0.00 0.00 2.40
1680 1740 5.642919 AGAGCTGAAGAGATTAGCAAAACTG 59.357 40.000 0.00 0.00 39.84 3.16
1681 1741 5.803552 AGAGCTGAAGAGATTAGCAAAACT 58.196 37.500 0.00 0.00 39.84 2.66
1694 1754 9.911788 AAATTATATCTTCCAAAGAGCTGAAGA 57.088 29.630 13.90 13.90 46.01 2.87
1761 1822 7.154656 ACTTTTTCCTGCATAATCTTTGGTTC 58.845 34.615 0.00 0.00 0.00 3.62
1812 1875 1.603678 GGGTTCTACTTCACGCAACGA 60.604 52.381 0.00 0.00 0.00 3.85
1862 1930 1.003182 TACGGTGGCCCCTGGAATA 59.997 57.895 0.00 0.00 0.00 1.75
1888 1956 7.563556 AGTGAAAAGTGAAAGATCCCCTAAAAA 59.436 33.333 0.00 0.00 0.00 1.94
1889 1957 7.066781 AGTGAAAAGTGAAAGATCCCCTAAAA 58.933 34.615 0.00 0.00 0.00 1.52
1890 1958 6.610830 AGTGAAAAGTGAAAGATCCCCTAAA 58.389 36.000 0.00 0.00 0.00 1.85
1891 1959 6.200878 AGTGAAAAGTGAAAGATCCCCTAA 57.799 37.500 0.00 0.00 0.00 2.69
1892 1960 5.843019 AGTGAAAAGTGAAAGATCCCCTA 57.157 39.130 0.00 0.00 0.00 3.53
1893 1961 4.731313 AGTGAAAAGTGAAAGATCCCCT 57.269 40.909 0.00 0.00 0.00 4.79
1894 1962 5.069119 ACAAAGTGAAAAGTGAAAGATCCCC 59.931 40.000 0.00 0.00 0.00 4.81
1895 1963 6.149129 ACAAAGTGAAAAGTGAAAGATCCC 57.851 37.500 0.00 0.00 0.00 3.85
1896 1964 6.697455 GGAACAAAGTGAAAAGTGAAAGATCC 59.303 38.462 0.00 0.00 0.00 3.36
1897 1965 6.697455 GGGAACAAAGTGAAAAGTGAAAGATC 59.303 38.462 0.00 0.00 0.00 2.75
1898 1966 6.154363 TGGGAACAAAGTGAAAAGTGAAAGAT 59.846 34.615 0.00 0.00 37.44 2.40
1899 1967 5.478679 TGGGAACAAAGTGAAAAGTGAAAGA 59.521 36.000 0.00 0.00 37.44 2.52
1900 1968 5.576774 GTGGGAACAAAGTGAAAAGTGAAAG 59.423 40.000 0.00 0.00 46.06 2.62
1901 1969 5.245075 AGTGGGAACAAAGTGAAAAGTGAAA 59.755 36.000 0.00 0.00 46.06 2.69
1902 1970 4.770010 AGTGGGAACAAAGTGAAAAGTGAA 59.230 37.500 0.00 0.00 46.06 3.18
1903 1971 4.340617 AGTGGGAACAAAGTGAAAAGTGA 58.659 39.130 0.00 0.00 46.06 3.41
1904 1972 4.718940 AGTGGGAACAAAGTGAAAAGTG 57.281 40.909 0.00 0.00 46.06 3.16
1905 1973 5.506708 ACTAGTGGGAACAAAGTGAAAAGT 58.493 37.500 0.00 0.00 46.06 2.66
1906 1974 7.562454 TTACTAGTGGGAACAAAGTGAAAAG 57.438 36.000 5.39 0.00 46.06 2.27
1907 1975 7.414319 CGTTTACTAGTGGGAACAAAGTGAAAA 60.414 37.037 5.39 0.00 46.06 2.29
1908 1976 6.037391 CGTTTACTAGTGGGAACAAAGTGAAA 59.963 38.462 5.39 0.00 46.06 2.69
1909 1977 5.524646 CGTTTACTAGTGGGAACAAAGTGAA 59.475 40.000 5.39 0.00 46.06 3.18
1910 1978 5.051816 CGTTTACTAGTGGGAACAAAGTGA 58.948 41.667 5.39 0.00 46.06 3.41
1911 1979 4.812626 ACGTTTACTAGTGGGAACAAAGTG 59.187 41.667 5.39 0.00 46.06 3.16
1912 1980 4.812626 CACGTTTACTAGTGGGAACAAAGT 59.187 41.667 5.39 0.00 46.06 2.66
1913 1981 4.319261 GCACGTTTACTAGTGGGAACAAAG 60.319 45.833 5.39 2.61 46.06 2.77
1914 1982 3.560896 GCACGTTTACTAGTGGGAACAAA 59.439 43.478 5.39 0.00 46.06 2.83
1915 1983 3.132925 GCACGTTTACTAGTGGGAACAA 58.867 45.455 5.39 0.00 46.06 2.83
1916 1984 2.102757 TGCACGTTTACTAGTGGGAACA 59.897 45.455 5.39 0.00 38.68 3.18
1917 1985 2.477754 GTGCACGTTTACTAGTGGGAAC 59.522 50.000 5.39 7.04 38.68 3.62
1918 1986 2.758009 GTGCACGTTTACTAGTGGGAA 58.242 47.619 5.39 0.00 38.68 3.97
1919 1987 1.336148 CGTGCACGTTTACTAGTGGGA 60.336 52.381 30.50 0.00 38.68 4.37
1920 1988 1.065358 CGTGCACGTTTACTAGTGGG 58.935 55.000 30.50 0.00 38.68 4.61
1932 2000 1.012124 TTTGTAACGCACGTGCACG 60.012 52.632 37.03 35.99 46.33 5.34
1933 2001 0.247735 TGTTTGTAACGCACGTGCAC 60.248 50.000 37.03 27.83 42.21 4.57
1934 2002 0.658368 ATGTTTGTAACGCACGTGCA 59.342 45.000 37.03 18.05 42.21 4.57
1935 2003 2.096614 AGTATGTTTGTAACGCACGTGC 60.097 45.455 30.42 30.42 37.78 5.34
1936 2004 3.465907 CAGTATGTTTGTAACGCACGTG 58.534 45.455 12.28 12.28 0.00 4.49
1937 2005 3.781341 CAGTATGTTTGTAACGCACGT 57.219 42.857 0.00 0.00 0.00 4.49
2016 5464 6.183360 TGGAGTGTGTTCATGCATTAGTTTTT 60.183 34.615 0.00 0.00 0.00 1.94
2138 5608 9.424659 GTTGCATTTTGTTTTTGTAAGAGAATG 57.575 29.630 0.00 0.00 0.00 2.67
2203 5675 6.208994 ACACACTCCTTCGTATACTTCTTTCT 59.791 38.462 0.56 0.00 0.00 2.52
2235 5707 4.151883 ACTATTTTGGTGCTCACATGGTT 58.848 39.130 0.00 0.00 0.00 3.67
2304 5777 6.780457 ATGTCAATATTAGCCTGCAACTTT 57.220 33.333 0.00 0.00 0.00 2.66
2340 5813 6.426937 TCACTAGCAGTTTGAGGTAAATCAAC 59.573 38.462 0.00 0.00 38.87 3.18
2342 5815 6.109156 TCACTAGCAGTTTGAGGTAAATCA 57.891 37.500 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.