Multiple sequence alignment - TraesCS7B01G212000

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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 TraesCS7B01G212000 chr7B 100.000 2594 0 0 1 2594 388158679 388161272 0.000000e+00 4791.0
1 TraesCS7B01G212000 chr7B 86.111 72 4 6 1831 1899 118638704 118638636 3.580000e-09 73.1
2 TraesCS7B01G212000 chr7A 92.475 1196 47 12 623 1808 443338509 443339671 0.000000e+00 1670.0
3 TraesCS7B01G212000 chr7A 85.920 348 28 5 300 626 443338122 443338469 4.110000e-93 351.0
4 TraesCS7B01G212000 chr7D 95.139 864 27 7 896 1750 391574702 391575559 0.000000e+00 1349.0
5 TraesCS7B01G212000 chr7D 88.764 712 69 4 1887 2594 547483398 547482694 0.000000e+00 861.0
6 TraesCS7B01G212000 chr7D 91.749 303 15 5 623 915 391574379 391574681 1.860000e-111 412.0
7 TraesCS7B01G212000 chr7D 83.333 492 33 12 146 618 391573859 391574320 2.400000e-110 409.0
8 TraesCS7B01G212000 chr2A 86.381 771 91 11 1831 2594 657061169 657060406 0.000000e+00 830.0
9 TraesCS7B01G212000 chr4D 86.863 746 85 7 1855 2594 418386639 418385901 0.000000e+00 822.0
10 TraesCS7B01G212000 chr3D 87.607 702 75 6 1897 2594 352780593 352779900 0.000000e+00 804.0
11 TraesCS7B01G212000 chr6A 85.271 774 100 11 1825 2594 522454732 522455495 0.000000e+00 785.0
12 TraesCS7B01G212000 chr2D 86.733 701 83 6 1903 2594 366056423 366055724 0.000000e+00 771.0
13 TraesCS7B01G212000 chr4B 85.032 775 95 11 1827 2594 464541077 464540317 0.000000e+00 769.0
14 TraesCS7B01G212000 chr3A 85.428 748 96 8 1855 2594 603922070 603921328 0.000000e+00 765.0
15 TraesCS7B01G212000 chr4A 84.987 746 102 7 1855 2594 697376501 697375760 0.000000e+00 749.0


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 TraesCS7B01G212000 chr7B 388158679 388161272 2593 False 4791.000000 4791 100.000000 1 2594 1 chr7B.!!$F1 2593
1 TraesCS7B01G212000 chr7A 443338122 443339671 1549 False 1010.500000 1670 89.197500 300 1808 2 chr7A.!!$F1 1508
2 TraesCS7B01G212000 chr7D 547482694 547483398 704 True 861.000000 861 88.764000 1887 2594 1 chr7D.!!$R1 707
3 TraesCS7B01G212000 chr7D 391573859 391575559 1700 False 723.333333 1349 90.073667 146 1750 3 chr7D.!!$F1 1604
4 TraesCS7B01G212000 chr2A 657060406 657061169 763 True 830.000000 830 86.381000 1831 2594 1 chr2A.!!$R1 763
5 TraesCS7B01G212000 chr4D 418385901 418386639 738 True 822.000000 822 86.863000 1855 2594 1 chr4D.!!$R1 739
6 TraesCS7B01G212000 chr3D 352779900 352780593 693 True 804.000000 804 87.607000 1897 2594 1 chr3D.!!$R1 697
7 TraesCS7B01G212000 chr6A 522454732 522455495 763 False 785.000000 785 85.271000 1825 2594 1 chr6A.!!$F1 769
8 TraesCS7B01G212000 chr2D 366055724 366056423 699 True 771.000000 771 86.733000 1903 2594 1 chr2D.!!$R1 691
9 TraesCS7B01G212000 chr4B 464540317 464541077 760 True 769.000000 769 85.032000 1827 2594 1 chr4B.!!$R1 767
10 TraesCS7B01G212000 chr3A 603921328 603922070 742 True 765.000000 765 85.428000 1855 2594 1 chr3A.!!$R1 739
11 TraesCS7B01G212000 chr4A 697375760 697376501 741 True 749.000000 749 84.987000 1855 2594 1 chr4A.!!$R1 739

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
96 97 0.036388 GGCAGAATTCGGTGTCTGGA 60.036 55.0 7.44 0.0 41.36 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 2003 0.106066 TCGAGGGGCCGGATTTACTA 60.106 55.0 5.05 0.0 0.0 1.82 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
39 40 4.619227 CCCACAGTGCGTCGGGTT 62.619 66.667 0.00 0.00 33.55 4.11
40 41 3.041940 CCACAGTGCGTCGGGTTC 61.042 66.667 0.00 0.00 0.00 3.62
41 42 2.279851 CACAGTGCGTCGGGTTCA 60.280 61.111 0.00 0.00 0.00 3.18
42 43 2.029073 ACAGTGCGTCGGGTTCAG 59.971 61.111 0.00 0.00 0.00 3.02
43 44 3.414700 CAGTGCGTCGGGTTCAGC 61.415 66.667 0.00 0.00 0.00 4.26
44 45 4.681978 AGTGCGTCGGGTTCAGCC 62.682 66.667 0.00 0.00 0.00 4.85
45 46 4.681978 GTGCGTCGGGTTCAGCCT 62.682 66.667 0.00 0.00 37.43 4.58
46 47 4.680237 TGCGTCGGGTTCAGCCTG 62.680 66.667 0.00 0.00 45.18 4.85
49 50 4.373116 GTCGGGTTCAGCCTGCGA 62.373 66.667 0.00 0.00 43.46 5.10
50 51 3.390521 TCGGGTTCAGCCTGCGAT 61.391 61.111 0.00 0.00 43.46 4.58
51 52 2.055633 TCGGGTTCAGCCTGCGATA 61.056 57.895 0.00 0.00 43.46 2.92
52 53 1.592669 CGGGTTCAGCCTGCGATAG 60.593 63.158 0.00 0.00 36.72 2.08
64 65 2.124487 CGATAGCCGGGCCCAAAA 60.124 61.111 24.92 3.72 33.91 2.44
65 66 1.751162 CGATAGCCGGGCCCAAAAA 60.751 57.895 24.92 4.16 33.91 1.94
66 67 1.813859 GATAGCCGGGCCCAAAAAC 59.186 57.895 24.92 5.40 0.00 2.43
67 68 2.000215 GATAGCCGGGCCCAAAAACG 62.000 60.000 24.92 6.17 0.00 3.60
71 72 3.676605 CGGGCCCAAAAACGGACC 61.677 66.667 24.92 0.00 46.41 4.46
72 73 3.676605 GGGCCCAAAAACGGACCG 61.677 66.667 19.95 13.61 39.37 4.79
73 74 2.595172 GGCCCAAAAACGGACCGA 60.595 61.111 23.38 0.00 0.00 4.69
74 75 2.622962 GGCCCAAAAACGGACCGAG 61.623 63.158 23.38 4.55 0.00 4.63
75 76 2.622962 GCCCAAAAACGGACCGAGG 61.623 63.158 23.38 13.19 0.00 4.63
76 77 2.622962 CCCAAAAACGGACCGAGGC 61.623 63.158 23.38 0.00 0.00 4.70
77 78 2.554272 CAAAAACGGACCGAGGCG 59.446 61.111 23.38 0.53 0.00 5.52
87 88 3.264897 CCGAGGCGGCAGAATTCG 61.265 66.667 13.08 11.32 41.17 3.34
88 89 3.264897 CGAGGCGGCAGAATTCGG 61.265 66.667 13.08 0.69 0.00 4.30
89 90 2.125106 GAGGCGGCAGAATTCGGT 60.125 61.111 13.08 0.00 0.00 4.69
90 91 2.436646 AGGCGGCAGAATTCGGTG 60.437 61.111 13.08 0.00 0.00 4.94
91 92 2.746277 GGCGGCAGAATTCGGTGT 60.746 61.111 3.07 0.00 0.00 4.16
92 93 2.750888 GGCGGCAGAATTCGGTGTC 61.751 63.158 3.07 0.00 0.00 3.67
93 94 1.741770 GCGGCAGAATTCGGTGTCT 60.742 57.895 7.44 0.00 0.00 3.41
94 95 1.970917 GCGGCAGAATTCGGTGTCTG 61.971 60.000 7.44 5.97 43.46 3.51
95 96 1.361668 CGGCAGAATTCGGTGTCTGG 61.362 60.000 7.44 0.00 41.36 3.86
96 97 0.036388 GGCAGAATTCGGTGTCTGGA 60.036 55.000 7.44 0.00 41.36 3.86
97 98 1.363744 GCAGAATTCGGTGTCTGGAG 58.636 55.000 7.44 0.00 41.36 3.86
98 99 1.066858 GCAGAATTCGGTGTCTGGAGA 60.067 52.381 7.44 0.00 41.36 3.71
99 100 2.611518 CAGAATTCGGTGTCTGGAGAC 58.388 52.381 0.00 0.00 44.97 3.36
107 108 2.179517 GTCTGGAGACGCGACTGG 59.820 66.667 17.32 6.17 35.12 4.00
108 109 3.062466 TCTGGAGACGCGACTGGG 61.062 66.667 17.32 5.81 0.00 4.45
109 110 4.135153 CTGGAGACGCGACTGGGG 62.135 72.222 17.32 1.46 0.00 4.96
136 137 2.360553 TCGGTACCGATGCGTAAAAA 57.639 45.000 32.61 6.92 44.01 1.94
137 138 2.261345 TCGGTACCGATGCGTAAAAAG 58.739 47.619 32.61 0.17 44.01 2.27
138 139 1.994779 CGGTACCGATGCGTAAAAAGT 59.005 47.619 30.64 0.00 42.83 2.66
139 140 2.028404 CGGTACCGATGCGTAAAAAGTC 59.972 50.000 30.64 0.00 42.83 3.01
140 141 2.028404 GGTACCGATGCGTAAAAAGTCG 59.972 50.000 0.00 0.00 0.00 4.18
156 157 0.966370 GTCGCCTGGGTACTCTCTGT 60.966 60.000 0.00 0.00 0.00 3.41
160 161 1.348036 GCCTGGGTACTCTCTGTTGTT 59.652 52.381 0.00 0.00 0.00 2.83
167 168 4.262463 GGGTACTCTCTGTTGTTCACATGA 60.262 45.833 0.00 0.00 33.76 3.07
198 199 0.904649 TAGCACAGATCCACACAGGG 59.095 55.000 0.00 0.00 38.24 4.45
230 231 0.665972 GATGCCACGCTAGCTAGCTC 60.666 60.000 36.02 24.41 46.85 4.09
245 246 5.669477 AGCTAGCTCTTCAATTCCTTACTG 58.331 41.667 12.68 0.00 0.00 2.74
247 248 4.917906 AGCTCTTCAATTCCTTACTGGT 57.082 40.909 0.00 0.00 37.07 4.00
248 249 4.583871 AGCTCTTCAATTCCTTACTGGTG 58.416 43.478 0.00 0.00 37.07 4.17
249 250 3.127721 GCTCTTCAATTCCTTACTGGTGC 59.872 47.826 0.00 0.00 37.07 5.01
250 251 3.334691 TCTTCAATTCCTTACTGGTGCG 58.665 45.455 0.00 0.00 37.07 5.34
251 252 2.107950 TCAATTCCTTACTGGTGCGG 57.892 50.000 0.00 0.00 37.07 5.69
252 253 0.451783 CAATTCCTTACTGGTGCGGC 59.548 55.000 0.00 0.00 37.07 6.53
253 254 0.328258 AATTCCTTACTGGTGCGGCT 59.672 50.000 0.00 0.00 37.07 5.52
254 255 0.107654 ATTCCTTACTGGTGCGGCTC 60.108 55.000 0.00 0.00 37.07 4.70
255 256 1.476845 TTCCTTACTGGTGCGGCTCA 61.477 55.000 0.00 0.00 37.07 4.26
256 257 1.003839 CCTTACTGGTGCGGCTCAA 60.004 57.895 0.00 0.00 0.00 3.02
257 258 0.605319 CCTTACTGGTGCGGCTCAAA 60.605 55.000 0.00 0.00 0.00 2.69
258 259 1.234821 CTTACTGGTGCGGCTCAAAA 58.765 50.000 0.00 0.00 0.00 2.44
259 260 1.606668 CTTACTGGTGCGGCTCAAAAA 59.393 47.619 0.00 0.00 0.00 1.94
291 292 8.491152 CCTTACTGATGAAAACTATTAGCATCG 58.509 37.037 0.00 0.00 38.48 3.84
310 311 4.893424 TCGGGCAAGTAAATGAAATAGC 57.107 40.909 0.00 0.00 0.00 2.97
355 361 1.070821 CTTGCAGCGAAATCGACTCA 58.929 50.000 7.06 0.00 43.02 3.41
357 363 1.725641 TGCAGCGAAATCGACTCATT 58.274 45.000 7.06 0.00 43.02 2.57
375 381 8.475331 GACTCATTCGAAGGTTACTTTTCATA 57.525 34.615 9.94 0.00 36.97 2.15
398 404 9.590451 CATAACAATAACCAATCAGATTTTGCT 57.410 29.630 0.00 0.00 0.00 3.91
438 446 0.250467 ATGTGCAAGTCTGAGCGGTT 60.250 50.000 0.00 0.00 0.00 4.44
461 469 7.921214 GGTTCATGTCTCGTTGATAAGAAGATA 59.079 37.037 0.00 0.00 27.32 1.98
471 479 4.989044 TGATAAGAAGATACGCGTTGTGA 58.011 39.130 20.78 0.00 0.00 3.58
494 517 1.233019 GCTAGCAATGCACCATCGAT 58.767 50.000 10.63 0.00 0.00 3.59
504 527 6.267817 CAATGCACCATCGATTTAGACATTT 58.732 36.000 0.00 0.00 0.00 2.32
506 529 4.335315 TGCACCATCGATTTAGACATTTCC 59.665 41.667 0.00 0.00 0.00 3.13
521 545 3.253230 CATTTCCAAATCTTTGCCGACC 58.747 45.455 0.00 0.00 36.86 4.79
523 547 0.610785 TCCAAATCTTTGCCGACCCC 60.611 55.000 0.00 0.00 36.86 4.95
638 719 1.172180 ATAATGGCATCGCAACCCCG 61.172 55.000 0.00 0.00 0.00 5.73
642 723 4.778143 GCATCGCAACCCCGTCCT 62.778 66.667 0.00 0.00 0.00 3.85
681 762 1.963338 AGTGAGGACGCAAGCAAGC 60.963 57.895 0.00 0.00 45.62 4.01
715 806 1.293818 CATGCCATGCCAAGTTGCA 59.706 52.632 0.00 0.00 46.94 4.08
831 922 4.446413 CGACGCGGCCTTTACCCT 62.446 66.667 12.47 0.00 0.00 4.34
832 923 2.510918 GACGCGGCCTTTACCCTC 60.511 66.667 12.47 0.00 0.00 4.30
833 924 3.305177 GACGCGGCCTTTACCCTCA 62.305 63.158 12.47 0.00 0.00 3.86
834 925 2.818274 CGCGGCCTTTACCCTCAC 60.818 66.667 0.00 0.00 0.00 3.51
835 926 2.818274 GCGGCCTTTACCCTCACG 60.818 66.667 0.00 0.00 0.00 4.35
836 927 2.818274 CGGCCTTTACCCTCACGC 60.818 66.667 0.00 0.00 0.00 5.34
838 929 2.349755 GCCTTTACCCTCACGCCA 59.650 61.111 0.00 0.00 0.00 5.69
936 1078 3.100658 TCTAGTCTCCTGATCTCGTCG 57.899 52.381 0.00 0.00 0.00 5.12
937 1079 2.431419 TCTAGTCTCCTGATCTCGTCGT 59.569 50.000 0.00 0.00 0.00 4.34
938 1080 1.658994 AGTCTCCTGATCTCGTCGTC 58.341 55.000 0.00 0.00 0.00 4.20
1014 1156 1.898330 TAGCCATGTCCTGCTTCGCA 61.898 55.000 0.00 0.00 39.00 5.10
1305 1447 2.666190 GTGCACGAGGAGCAGCAA 60.666 61.111 0.00 0.00 43.63 3.91
1402 1544 4.347453 CCGGTGGCAGCAAAGCAC 62.347 66.667 17.80 0.00 35.83 4.40
1545 1687 0.325484 AGGAGATGAGGCTGCAGAGT 60.325 55.000 20.43 2.16 0.00 3.24
1701 1852 0.033228 TTTGGTTTGCGGCTTGGATG 59.967 50.000 0.00 0.00 0.00 3.51
1729 1880 1.202348 CGATTGGGAGCTTGGTTTTCC 59.798 52.381 0.00 0.00 41.14 3.13
1730 1881 2.529632 GATTGGGAGCTTGGTTTTCCT 58.470 47.619 0.00 0.00 41.38 3.36
1798 1949 9.420118 ACATGTATTGTTGGGTATTCATTACAT 57.580 29.630 0.00 0.00 38.24 2.29
1801 1952 9.639563 TGTATTGTTGGGTATTCATTACATGAT 57.360 29.630 0.00 0.00 39.39 2.45
1808 1959 8.821686 TGGGTATTCATTACATGATGAAAAGT 57.178 30.769 12.36 1.88 45.96 2.66
1809 1960 9.253832 TGGGTATTCATTACATGATGAAAAGTT 57.746 29.630 12.36 1.59 45.96 2.66
1810 1961 9.520204 GGGTATTCATTACATGATGAAAAGTTG 57.480 33.333 12.36 0.00 45.96 3.16
1815 1966 9.462174 TTCATTACATGATGAAAAGTTGACAAC 57.538 29.630 10.47 10.47 41.65 3.32
1816 1967 8.628280 TCATTACATGATGAAAAGTTGACAACA 58.372 29.630 20.08 0.00 33.31 3.33
1817 1968 9.247126 CATTACATGATGAAAAGTTGACAACAA 57.753 29.630 20.08 1.70 0.00 2.83
1818 1969 9.814899 ATTACATGATGAAAAGTTGACAACAAA 57.185 25.926 20.08 1.56 37.77 2.83
1819 1970 9.645059 TTACATGATGAAAAGTTGACAACAAAA 57.355 25.926 20.08 1.91 37.77 2.44
1820 1971 8.545229 ACATGATGAAAAGTTGACAACAAAAA 57.455 26.923 20.08 2.59 37.77 1.94
1821 1972 8.658609 ACATGATGAAAAGTTGACAACAAAAAG 58.341 29.630 20.08 2.66 37.77 2.27
1822 1973 8.658609 CATGATGAAAAGTTGACAACAAAAAGT 58.341 29.630 20.08 2.44 37.77 2.66
1823 1974 8.600449 TGATGAAAAGTTGACAACAAAAAGTT 57.400 26.923 20.08 1.99 42.42 2.66
1853 2006 5.398603 GAGCATCTACAGCCACATATAGT 57.601 43.478 0.00 0.00 0.00 2.12
1868 2021 0.974383 ATAGTAAATCCGGCCCCTCG 59.026 55.000 0.00 0.00 0.00 4.63
1910 2073 2.217038 ATGTCCGTGGGCAGTGACT 61.217 57.895 0.00 0.00 0.00 3.41
1956 2119 2.112522 GCATCCGCGTATCTCATATCG 58.887 52.381 4.92 0.00 0.00 2.92
2079 2248 6.150307 TGCAAACGGACATAAACATACTTCAT 59.850 34.615 0.00 0.00 0.00 2.57
2308 2488 4.262036 GGATTTGGAGTTGGAAAGGACAAC 60.262 45.833 0.00 0.00 46.44 3.32
2313 2493 1.594331 GTTGGAAAGGACAACGAGCT 58.406 50.000 0.00 0.00 38.83 4.09
2363 2545 2.979676 CGCTTCAGCCTTGCCACA 60.980 61.111 0.00 0.00 37.91 4.17
2366 2548 1.893808 CTTCAGCCTTGCCACACGT 60.894 57.895 0.00 0.00 0.00 4.49
2371 2553 3.357079 CCTTGCCACACGTGCCTC 61.357 66.667 17.22 4.97 0.00 4.70
2387 2570 2.525629 TCCTCCACCGTTGCCTCA 60.526 61.111 0.00 0.00 0.00 3.86
2452 2635 2.654877 GTTCTTCCGTCGGAGGCA 59.345 61.111 18.11 4.96 31.21 4.75
2464 2650 2.048127 GAGGCAAGCGTCCGTCTT 60.048 61.111 3.50 0.00 0.00 3.01
2467 2653 2.430244 GCAAGCGTCCGTCTTCGA 60.430 61.111 0.00 0.00 39.71 3.71
2580 2766 4.517934 CCGCCTCCCTCTCCCGTA 62.518 72.222 0.00 0.00 0.00 4.02
2585 2771 1.378250 CTCCCTCTCCCGTACACGT 60.378 63.158 0.58 0.00 37.74 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.619227 AACCCGACGCACTGTGGG 62.619 66.667 21.50 21.50 45.45 4.61
23 24 3.041940 GAACCCGACGCACTGTGG 61.042 66.667 10.21 2.45 0.00 4.17
24 25 2.279851 TGAACCCGACGCACTGTG 60.280 61.111 2.76 2.76 0.00 3.66
25 26 2.029073 CTGAACCCGACGCACTGT 59.971 61.111 0.00 0.00 0.00 3.55
26 27 3.414700 GCTGAACCCGACGCACTG 61.415 66.667 0.00 0.00 0.00 3.66
27 28 4.681978 GGCTGAACCCGACGCACT 62.682 66.667 0.00 0.00 0.00 4.40
28 29 4.681978 AGGCTGAACCCGACGCAC 62.682 66.667 0.00 0.00 40.58 5.34
29 30 4.680237 CAGGCTGAACCCGACGCA 62.680 66.667 9.42 0.00 40.58 5.24
32 33 2.292794 TATCGCAGGCTGAACCCGAC 62.293 60.000 20.86 0.00 40.58 4.79
33 34 2.016393 CTATCGCAGGCTGAACCCGA 62.016 60.000 20.86 17.65 40.58 5.14
34 35 1.592669 CTATCGCAGGCTGAACCCG 60.593 63.158 20.86 12.40 40.58 5.28
35 36 1.889573 GCTATCGCAGGCTGAACCC 60.890 63.158 20.86 0.00 40.58 4.11
36 37 1.889573 GGCTATCGCAGGCTGAACC 60.890 63.158 20.86 5.43 46.26 3.62
37 38 3.724494 GGCTATCGCAGGCTGAAC 58.276 61.111 20.86 0.00 46.26 3.18
46 47 4.868116 TTTGGGCCCGGCTATCGC 62.868 66.667 19.37 0.00 37.59 4.58
47 48 1.751162 TTTTTGGGCCCGGCTATCG 60.751 57.895 19.37 0.00 38.88 2.92
48 49 1.813859 GTTTTTGGGCCCGGCTATC 59.186 57.895 19.37 1.81 0.00 2.08
49 50 2.049767 CGTTTTTGGGCCCGGCTAT 61.050 57.895 19.37 0.00 0.00 2.97
50 51 2.673687 CGTTTTTGGGCCCGGCTA 60.674 61.111 19.37 0.00 0.00 3.93
53 54 3.676605 GTCCGTTTTTGGGCCCGG 61.677 66.667 19.37 13.77 41.75 5.73
57 58 2.622962 CCTCGGTCCGTTTTTGGGC 61.623 63.158 11.88 0.00 0.00 5.36
58 59 2.622962 GCCTCGGTCCGTTTTTGGG 61.623 63.158 11.88 6.50 0.00 4.12
59 60 2.951458 GCCTCGGTCCGTTTTTGG 59.049 61.111 11.88 8.18 0.00 3.28
60 61 2.554272 CGCCTCGGTCCGTTTTTG 59.446 61.111 11.88 0.00 0.00 2.44
61 62 2.667199 CCGCCTCGGTCCGTTTTT 60.667 61.111 11.88 0.00 42.73 1.94
71 72 3.264897 CCGAATTCTGCCGCCTCG 61.265 66.667 3.52 0.00 0.00 4.63
72 73 2.125106 ACCGAATTCTGCCGCCTC 60.125 61.111 3.52 0.00 0.00 4.70
73 74 2.436646 CACCGAATTCTGCCGCCT 60.437 61.111 3.52 0.00 0.00 5.52
74 75 2.746277 ACACCGAATTCTGCCGCC 60.746 61.111 3.52 0.00 0.00 6.13
75 76 1.741770 AGACACCGAATTCTGCCGC 60.742 57.895 3.52 0.00 0.00 6.53
76 77 1.361668 CCAGACACCGAATTCTGCCG 61.362 60.000 3.52 0.00 38.36 5.69
77 78 0.036388 TCCAGACACCGAATTCTGCC 60.036 55.000 3.52 0.00 38.36 4.85
78 79 1.066858 TCTCCAGACACCGAATTCTGC 60.067 52.381 3.52 0.00 38.36 4.26
79 80 2.611518 GTCTCCAGACACCGAATTCTG 58.388 52.381 3.52 0.00 44.18 3.02
80 81 1.202582 CGTCTCCAGACACCGAATTCT 59.797 52.381 7.48 0.00 44.99 2.40
81 82 1.630148 CGTCTCCAGACACCGAATTC 58.370 55.000 7.48 0.00 44.99 2.17
82 83 0.389948 GCGTCTCCAGACACCGAATT 60.390 55.000 7.48 0.00 44.99 2.17
83 84 1.215647 GCGTCTCCAGACACCGAAT 59.784 57.895 7.48 0.00 44.99 3.34
84 85 2.649034 GCGTCTCCAGACACCGAA 59.351 61.111 7.48 0.00 44.99 4.30
85 86 3.733960 CGCGTCTCCAGACACCGA 61.734 66.667 7.48 0.00 44.99 4.69
86 87 3.733960 TCGCGTCTCCAGACACCG 61.734 66.667 5.77 8.56 44.99 4.94
87 88 2.126424 GTCGCGTCTCCAGACACC 60.126 66.667 5.77 0.00 44.99 4.16
88 89 1.442857 CAGTCGCGTCTCCAGACAC 60.443 63.158 5.77 0.00 44.99 3.67
89 90 2.626780 CCAGTCGCGTCTCCAGACA 61.627 63.158 5.77 0.00 44.99 3.41
90 91 2.179517 CCAGTCGCGTCTCCAGAC 59.820 66.667 5.77 0.00 41.47 3.51
91 92 3.062466 CCCAGTCGCGTCTCCAGA 61.062 66.667 5.77 0.00 0.00 3.86
92 93 4.135153 CCCCAGTCGCGTCTCCAG 62.135 72.222 5.77 0.00 0.00 3.86
118 119 1.994779 ACTTTTTACGCATCGGTACCG 59.005 47.619 28.66 28.66 41.35 4.02
119 120 2.028404 CGACTTTTTACGCATCGGTACC 59.972 50.000 0.16 0.16 0.00 3.34
120 121 3.279528 CGACTTTTTACGCATCGGTAC 57.720 47.619 0.00 0.00 0.00 3.34
129 130 1.728425 GTACCCAGGCGACTTTTTACG 59.272 52.381 0.00 0.00 40.21 3.18
130 131 2.998670 GAGTACCCAGGCGACTTTTTAC 59.001 50.000 0.00 0.00 40.21 2.01
131 132 2.901839 AGAGTACCCAGGCGACTTTTTA 59.098 45.455 0.00 0.00 40.21 1.52
132 133 1.697982 AGAGTACCCAGGCGACTTTTT 59.302 47.619 0.00 0.00 40.21 1.94
133 134 1.275573 GAGAGTACCCAGGCGACTTTT 59.724 52.381 0.00 0.00 40.21 2.27
134 135 0.896226 GAGAGTACCCAGGCGACTTT 59.104 55.000 0.00 0.00 40.21 2.66
135 136 0.039911 AGAGAGTACCCAGGCGACTT 59.960 55.000 0.00 0.00 40.21 3.01
136 137 0.681564 CAGAGAGTACCCAGGCGACT 60.682 60.000 0.00 0.00 46.44 4.18
137 138 0.966370 ACAGAGAGTACCCAGGCGAC 60.966 60.000 0.00 0.00 0.00 5.19
138 139 0.251653 AACAGAGAGTACCCAGGCGA 60.252 55.000 0.00 0.00 0.00 5.54
139 140 0.108615 CAACAGAGAGTACCCAGGCG 60.109 60.000 0.00 0.00 0.00 5.52
140 141 0.977395 ACAACAGAGAGTACCCAGGC 59.023 55.000 0.00 0.00 0.00 4.85
141 142 2.632996 TGAACAACAGAGAGTACCCAGG 59.367 50.000 0.00 0.00 0.00 4.45
142 143 3.069586 TGTGAACAACAGAGAGTACCCAG 59.930 47.826 0.00 0.00 33.78 4.45
143 144 3.035363 TGTGAACAACAGAGAGTACCCA 58.965 45.455 0.00 0.00 33.78 4.51
144 145 3.746045 TGTGAACAACAGAGAGTACCC 57.254 47.619 0.00 0.00 33.78 3.69
160 161 3.367806 GCTAGCTGTCTCTGTTCATGTGA 60.368 47.826 7.70 0.00 0.00 3.58
167 168 2.242926 TCTGTGCTAGCTGTCTCTGTT 58.757 47.619 17.23 0.00 0.00 3.16
171 172 1.753649 TGGATCTGTGCTAGCTGTCTC 59.246 52.381 17.23 6.34 0.00 3.36
198 199 3.102097 GCATCGCCAGGTAGCAAC 58.898 61.111 0.00 0.00 0.00 4.17
230 231 2.420022 CCGCACCAGTAAGGAATTGAAG 59.580 50.000 0.00 0.00 41.22 3.02
262 263 9.905713 TGCTAATAGTTTTCATCAGTAAGGATT 57.094 29.630 0.00 0.00 0.00 3.01
264 265 9.547753 GATGCTAATAGTTTTCATCAGTAAGGA 57.452 33.333 0.00 0.00 35.06 3.36
265 266 8.491152 CGATGCTAATAGTTTTCATCAGTAAGG 58.509 37.037 6.48 0.00 34.73 2.69
266 267 8.491152 CCGATGCTAATAGTTTTCATCAGTAAG 58.509 37.037 6.48 0.00 34.73 2.34
267 268 7.441157 CCCGATGCTAATAGTTTTCATCAGTAA 59.559 37.037 6.48 0.00 34.73 2.24
268 269 6.929049 CCCGATGCTAATAGTTTTCATCAGTA 59.071 38.462 6.48 0.00 34.73 2.74
269 270 5.760253 CCCGATGCTAATAGTTTTCATCAGT 59.240 40.000 6.48 0.00 34.73 3.41
270 271 5.334414 GCCCGATGCTAATAGTTTTCATCAG 60.334 44.000 6.48 0.00 34.73 2.90
271 272 4.515191 GCCCGATGCTAATAGTTTTCATCA 59.485 41.667 6.48 0.00 34.73 3.07
272 273 4.515191 TGCCCGATGCTAATAGTTTTCATC 59.485 41.667 0.00 0.00 42.00 2.92
273 274 4.460263 TGCCCGATGCTAATAGTTTTCAT 58.540 39.130 0.00 0.00 42.00 2.57
285 286 2.418368 TCATTTACTTGCCCGATGCT 57.582 45.000 0.00 0.00 42.00 3.79
291 292 7.716612 AGTAATGCTATTTCATTTACTTGCCC 58.283 34.615 0.00 0.00 37.75 5.36
336 342 1.070821 TGAGTCGATTTCGCTGCAAG 58.929 50.000 0.00 0.00 39.60 4.01
375 381 9.643693 CTTAGCAAAATCTGATTGGTTATTGTT 57.356 29.630 3.22 5.23 39.12 2.83
398 404 7.275183 CACATATCTCTGGTGAATTGGACTTA 58.725 38.462 0.00 0.00 34.52 2.24
438 446 7.132863 CGTATCTTCTTATCAACGAGACATGA 58.867 38.462 0.00 0.00 32.35 3.07
471 479 0.680921 ATGGTGCATTGCTAGCCGTT 60.681 50.000 13.29 0.00 0.00 4.44
494 517 6.015856 TCGGCAAAGATTTGGAAATGTCTAAA 60.016 34.615 7.38 0.00 38.44 1.85
504 527 0.610785 GGGGTCGGCAAAGATTTGGA 60.611 55.000 7.38 0.00 38.57 3.53
506 529 1.506262 CGGGGTCGGCAAAGATTTG 59.494 57.895 0.84 0.84 41.03 2.32
521 545 4.065281 GAGTCCGTCCACACCGGG 62.065 72.222 6.32 0.00 45.51 5.73
523 547 2.258591 CAGAGTCCGTCCACACCG 59.741 66.667 0.00 0.00 0.00 4.94
535 559 5.527214 TGTTGAACGATTGATTTGTCAGAGT 59.473 36.000 0.00 0.00 0.00 3.24
618 644 0.314935 GGGGTTGCGATGCCATTATG 59.685 55.000 0.00 0.00 0.00 1.90
681 762 2.401766 ATGGCCTCGCTTTGCTTCG 61.402 57.895 3.32 0.00 0.00 3.79
715 806 4.066139 GGCTCTGGGGGTTGGCAT 62.066 66.667 0.00 0.00 0.00 4.40
936 1078 3.886505 AGTGATCTACGGGATTGAGAGAC 59.113 47.826 0.00 0.00 34.33 3.36
937 1079 4.171878 AGTGATCTACGGGATTGAGAGA 57.828 45.455 0.00 0.00 34.33 3.10
938 1080 4.261825 GGAAGTGATCTACGGGATTGAGAG 60.262 50.000 0.00 0.00 34.33 3.20
1545 1687 3.578968 TTCCTCGGCCGACCTCTGA 62.579 63.158 27.28 12.85 0.00 3.27
1638 1780 5.221641 ACGCATCCTCATGGCTAATTAACTA 60.222 40.000 0.00 0.00 0.00 2.24
1639 1781 4.067896 CGCATCCTCATGGCTAATTAACT 58.932 43.478 0.00 0.00 0.00 2.24
1640 1782 3.815401 ACGCATCCTCATGGCTAATTAAC 59.185 43.478 0.00 0.00 0.00 2.01
1679 1821 1.227205 CAAGCCGCAAACCAAAGCA 60.227 52.632 0.00 0.00 0.00 3.91
1681 1823 0.318120 ATCCAAGCCGCAAACCAAAG 59.682 50.000 0.00 0.00 0.00 2.77
1701 1852 3.428045 CCAAGCTCCCAATCGAAACATTC 60.428 47.826 0.00 0.00 0.00 2.67
1730 1881 9.970553 ACGGATACTACAATCCTATATACAAGA 57.029 33.333 1.70 0.00 42.91 3.02
1798 1949 8.600449 AACTTTTTGTTGTCAACTTTTCATCA 57.400 26.923 16.45 0.00 37.52 3.07
1801 1952 8.202745 ACAAACTTTTTGTTGTCAACTTTTCA 57.797 26.923 16.45 0.00 39.13 2.69
1808 1959 9.296400 GCTCTTATACAAACTTTTTGTTGTCAA 57.704 29.630 9.44 0.00 39.13 3.18
1809 1960 8.462811 TGCTCTTATACAAACTTTTTGTTGTCA 58.537 29.630 9.44 0.00 39.13 3.58
1810 1961 8.850454 TGCTCTTATACAAACTTTTTGTTGTC 57.150 30.769 9.44 0.00 39.13 3.18
1811 1962 9.463443 GATGCTCTTATACAAACTTTTTGTTGT 57.537 29.630 9.44 0.00 39.13 3.32
1812 1963 9.683069 AGATGCTCTTATACAAACTTTTTGTTG 57.317 29.630 9.44 0.00 39.13 3.33
1817 1968 8.669243 GCTGTAGATGCTCTTATACAAACTTTT 58.331 33.333 0.00 0.00 0.00 2.27
1818 1969 7.281100 GGCTGTAGATGCTCTTATACAAACTTT 59.719 37.037 0.00 0.00 0.00 2.66
1819 1970 6.763610 GGCTGTAGATGCTCTTATACAAACTT 59.236 38.462 0.00 0.00 0.00 2.66
1820 1971 6.127054 TGGCTGTAGATGCTCTTATACAAACT 60.127 38.462 0.00 0.00 0.00 2.66
1821 1972 6.018669 GTGGCTGTAGATGCTCTTATACAAAC 60.019 42.308 0.00 0.00 0.00 2.93
1822 1973 6.049149 GTGGCTGTAGATGCTCTTATACAAA 58.951 40.000 0.00 0.00 0.00 2.83
1823 1974 5.128663 TGTGGCTGTAGATGCTCTTATACAA 59.871 40.000 0.00 0.00 0.00 2.41
1845 1996 3.518303 GAGGGGCCGGATTTACTATATGT 59.482 47.826 5.05 0.00 0.00 2.29
1847 2000 2.764572 CGAGGGGCCGGATTTACTATAT 59.235 50.000 5.05 0.00 0.00 0.86
1850 2003 0.106066 TCGAGGGGCCGGATTTACTA 60.106 55.000 5.05 0.00 0.00 1.82
1851 2004 0.979187 TTCGAGGGGCCGGATTTACT 60.979 55.000 5.05 0.00 0.00 2.24
1852 2005 0.812811 GTTCGAGGGGCCGGATTTAC 60.813 60.000 5.05 0.00 0.00 2.01
1853 2006 1.523524 GTTCGAGGGGCCGGATTTA 59.476 57.895 5.05 0.00 0.00 1.40
1910 2073 2.294791 CGACAAATTTAAGGTGTGCCCA 59.705 45.455 0.00 0.00 34.66 5.36
1956 2119 4.099113 GGGTAGTATGGATATAAGACGCCC 59.901 50.000 0.00 0.00 0.00 6.13
2079 2248 3.469008 ACTGTGATCTTTTGGACGTGA 57.531 42.857 0.00 0.00 0.00 4.35
2218 2392 1.313812 ACCAGTCTCGGACGCCTAAG 61.314 60.000 0.00 0.00 37.67 2.18
2219 2393 1.303888 ACCAGTCTCGGACGCCTAA 60.304 57.895 0.00 0.00 37.67 2.69
2281 2455 2.940994 TTCCAACTCCAAATCCGACA 57.059 45.000 0.00 0.00 0.00 4.35
2288 2462 2.685897 CGTTGTCCTTTCCAACTCCAAA 59.314 45.455 0.00 0.00 39.98 3.28
2308 2488 1.298713 CGTCGGATGAAGGAGCTCG 60.299 63.158 7.83 0.00 0.00 5.03
2366 2548 4.329545 GCAACGGTGGAGGAGGCA 62.330 66.667 0.90 0.00 0.00 4.75
2371 2553 1.002134 AATGAGGCAACGGTGGAGG 60.002 57.895 0.90 0.00 46.39 4.30
2464 2650 3.749064 GCTCCCTCACAGCGTCGA 61.749 66.667 0.00 0.00 0.00 4.20
2470 2656 1.982395 TACCACCGCTCCCTCACAG 60.982 63.158 0.00 0.00 0.00 3.66
2471 2657 2.118732 TACCACCGCTCCCTCACA 59.881 61.111 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.