Multiple sequence alignment - TraesCS3D01G342100

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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 TraesCS3D01G342100 chr3D 100.000 3198 0 0 1 3198 454982454 454979257 0.000000e+00 5906.0
1 TraesCS3D01G342100 chr3D 88.622 2083 125 53 1 2039 454218245 454220259 0.000000e+00 2431.0
2 TraesCS3D01G342100 chr3D 84.762 210 20 5 2127 2335 454220244 454220442 1.950000e-47 200.0
3 TraesCS3D01G342100 chr3D 89.062 64 7 0 2796 2859 149612007 149611944 2.640000e-11 80.5
4 TraesCS3D01G342100 chr3D 90.909 44 3 1 2127 2169 520863786 520863829 1.240000e-04 58.4
5 TraesCS3D01G342100 chr3A 93.873 1469 48 16 578 2039 596356707 596358140 0.000000e+00 2176.0
6 TraesCS3D01G342100 chr3A 91.912 1496 66 23 583 2039 597235268 597233789 0.000000e+00 2041.0
7 TraesCS3D01G342100 chr3A 90.869 898 61 15 2127 3014 597233804 597232918 0.000000e+00 1184.0
8 TraesCS3D01G342100 chr3A 83.356 745 96 9 1304 2039 32100869 32100144 0.000000e+00 664.0
9 TraesCS3D01G342100 chr3A 85.427 597 41 20 1 577 597235910 597235340 2.140000e-161 579.0
10 TraesCS3D01G342100 chr3A 93.443 183 11 1 1858 2039 596358884 596359066 1.460000e-68 270.0
11 TraesCS3D01G342100 chr3A 88.018 217 20 5 26 236 596356036 596356252 5.300000e-63 252.0
12 TraesCS3D01G342100 chr3A 92.806 139 10 0 3060 3198 597232824 597232686 5.410000e-48 202.0
13 TraesCS3D01G342100 chr3A 86.911 191 9 10 2127 2312 596358125 596358304 1.950000e-47 200.0
14 TraesCS3D01G342100 chr3A 94.681 94 5 0 3105 3198 597232922 597232829 2.570000e-31 147.0
15 TraesCS3D01G342100 chr3A 93.056 72 5 0 2039 2110 691498831 691498760 4.360000e-19 106.0
16 TraesCS3D01G342100 chr3A 89.831 59 6 0 2796 2854 167915640 167915582 3.420000e-10 76.8
17 TraesCS3D01G342100 chr3A 89.474 57 6 0 2796 2852 167957415 167957359 4.430000e-09 73.1
18 TraesCS3D01G342100 chr3A 90.909 44 3 1 2127 2169 656255297 656255340 1.240000e-04 58.4
19 TraesCS3D01G342100 chr3A 90.909 44 3 1 2127 2169 656339733 656339776 1.240000e-04 58.4
20 TraesCS3D01G342100 chr3A 90.909 44 3 1 2127 2169 656424959 656425002 1.240000e-04 58.4
21 TraesCS3D01G342100 chr3B 95.047 1373 35 11 688 2039 597841511 597840151 0.000000e+00 2128.0
22 TraesCS3D01G342100 chr3B 94.234 1370 41 9 697 2039 596852343 596853701 0.000000e+00 2058.0
23 TraesCS3D01G342100 chr3B 90.631 1078 80 8 2127 3198 597840166 597839104 0.000000e+00 1411.0
24 TraesCS3D01G342100 chr3B 91.549 639 27 11 1 622 597859185 597858557 0.000000e+00 856.0
25 TraesCS3D01G342100 chr3B 85.447 749 96 7 999 1739 39581778 39581035 0.000000e+00 767.0
26 TraesCS3D01G342100 chr3B 84.021 388 56 4 1652 2039 39581041 39580660 5.040000e-98 368.0
27 TraesCS3D01G342100 chr3B 86.471 170 13 5 2127 2296 596853686 596853845 9.120000e-41 178.0
28 TraesCS3D01G342100 chr3B 79.193 322 16 26 332 624 596849026 596849325 3.280000e-40 176.0
29 TraesCS3D01G342100 chr3B 87.356 87 8 3 2027 2111 578993272 578993187 2.630000e-16 97.1
30 TraesCS3D01G342100 chr3B 86.207 58 8 0 2785 2842 301364572 301364629 2.660000e-06 63.9
31 TraesCS3D01G342100 chr6A 87.915 422 43 2 1300 1721 34546741 34547154 1.030000e-134 490.0
32 TraesCS3D01G342100 chr6A 84.000 325 32 3 1338 1662 162573599 162573903 8.680000e-76 294.0
33 TraesCS3D01G342100 chr7B 100.000 92 0 0 2036 2127 717890827 717890918 1.530000e-38 171.0
34 TraesCS3D01G342100 chr7B 93.506 77 5 0 2035 2111 720078386 720078462 7.250000e-22 115.0
35 TraesCS3D01G342100 chr7B 94.595 74 4 0 2038 2111 746169538 746169465 7.250000e-22 115.0
36 TraesCS3D01G342100 chr7B 93.151 73 5 0 2035 2107 53621660 53621732 1.210000e-19 108.0
37 TraesCS3D01G342100 chr2B 100.000 89 0 0 2039 2127 61395548 61395460 7.100000e-37 165.0
38 TraesCS3D01G342100 chr2B 94.444 72 4 0 2036 2107 135518579 135518508 9.380000e-21 111.0
39 TraesCS3D01G342100 chr4D 90.909 88 6 2 2583 2668 33236529 33236442 2.020000e-22 117.0
40 TraesCS3D01G342100 chr1B 90.789 76 7 0 2036 2111 588327581 588327656 5.640000e-18 102.0
41 TraesCS3D01G342100 chr1A 90.769 65 6 0 2795 2859 569394869 569394933 1.580000e-13 87.9
42 TraesCS3D01G342100 chr1A 79.464 112 18 2 1921 2031 553956843 553956736 1.230000e-09 75.0
43 TraesCS3D01G342100 chr4A 88.235 68 7 1 2795 2861 624681766 624681699 2.640000e-11 80.5
44 TraesCS3D01G342100 chr1D 80.189 106 16 2 1921 2025 462106345 462106244 1.230000e-09 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 TraesCS3D01G342100 chr3D 454979257 454982454 3197 True 5906.0 5906 100.000000 1 3198 1 chr3D.!!$R2 3197
1 TraesCS3D01G342100 chr3D 454218245 454220442 2197 False 1315.5 2431 86.692000 1 2335 2 chr3D.!!$F2 2334
2 TraesCS3D01G342100 chr3A 597232686 597235910 3224 True 830.6 2041 91.139000 1 3198 5 chr3A.!!$R5 3197
3 TraesCS3D01G342100 chr3A 596356036 596359066 3030 False 724.5 2176 90.561250 26 2312 4 chr3A.!!$F4 2286
4 TraesCS3D01G342100 chr3A 32100144 32100869 725 True 664.0 664 83.356000 1304 2039 1 chr3A.!!$R1 735
5 TraesCS3D01G342100 chr3B 597839104 597841511 2407 True 1769.5 2128 92.839000 688 3198 2 chr3B.!!$R4 2510
6 TraesCS3D01G342100 chr3B 597858557 597859185 628 True 856.0 856 91.549000 1 622 1 chr3B.!!$R2 621
7 TraesCS3D01G342100 chr3B 596849026 596853845 4819 False 804.0 2058 86.632667 332 2296 3 chr3B.!!$F2 1964
8 TraesCS3D01G342100 chr3B 39580660 39581778 1118 True 567.5 767 84.734000 999 2039 2 chr3B.!!$R3 1040

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
204 216 0.251916 ATCAAAATCACTCGGGCCGA 59.748 50.0 29.14 29.14 0.00 5.54 F
641 3624 1.040646 ACCAAGAAGACTGCGTGAGA 58.959 50.0 0.00 0.00 0.00 3.27 F
2080 5538 0.034767 CCCAGCCTCTGCATCAGAAA 60.035 55.0 0.00 0.00 40.18 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2061 5519 0.034767 TTTCTGATGCAGAGGCTGGG 60.035 55.0 0.00 0.0 41.75 4.45 R
2108 5566 0.243907 GCTCTGAGGCTCGTGTGTTA 59.756 55.0 10.42 0.0 0.00 2.41 R
2907 6391 1.030457 CGCAACCGAGTATAGGACCT 58.970 55.0 0.00 0.0 33.72 3.85 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
49 54 0.319900 CTTGCGACATCTATCCCGGG 60.320 60.000 16.85 16.85 0.00 5.73
88 94 2.104144 CGATTCATGCGTAAAGCTTGC 58.896 47.619 0.00 0.00 46.78 4.01
94 100 1.210155 GCGTAAAGCTTGCCACTGG 59.790 57.895 0.00 0.00 44.04 4.00
97 103 1.878102 CGTAAAGCTTGCCACTGGACT 60.878 52.381 0.00 0.00 0.00 3.85
154 161 7.214467 TGAAAAAGTAATGGAAACCTAGCTG 57.786 36.000 0.00 0.00 0.00 4.24
169 180 4.742417 CCTAGCTGGTCGATCTATTGATG 58.258 47.826 0.00 0.00 32.19 3.07
204 216 0.251916 ATCAAAATCACTCGGGCCGA 59.748 50.000 29.14 29.14 0.00 5.54
345 568 1.197721 CGTTGCTGATTGTGGTCTTCC 59.802 52.381 0.00 0.00 0.00 3.46
390 613 2.307768 TCTTTCCGGCGAGATATGAGT 58.692 47.619 9.30 0.00 0.00 3.41
465 713 7.117956 CACAATGCATCCTCAGTTAGATAGATG 59.882 40.741 0.00 0.00 38.76 2.90
469 717 8.427902 TGCATCCTCAGTTAGATAGATGTATT 57.572 34.615 0.00 0.00 38.35 1.89
539 791 2.455032 CGCTACTTCTTCATCTGTCCG 58.545 52.381 0.00 0.00 0.00 4.79
559 811 2.033755 CGTCTCGTCGTCCCACTCT 61.034 63.158 0.00 0.00 0.00 3.24
624 955 4.401202 CCACATTAATCCCACAACCTAACC 59.599 45.833 0.00 0.00 0.00 2.85
639 3622 2.288825 CCTAACCAAGAAGACTGCGTGA 60.289 50.000 0.00 0.00 0.00 4.35
640 3623 1.871080 AACCAAGAAGACTGCGTGAG 58.129 50.000 0.00 0.00 0.00 3.51
641 3624 1.040646 ACCAAGAAGACTGCGTGAGA 58.959 50.000 0.00 0.00 0.00 3.27
642 3625 1.412710 ACCAAGAAGACTGCGTGAGAA 59.587 47.619 0.00 0.00 0.00 2.87
643 3626 2.037772 ACCAAGAAGACTGCGTGAGAAT 59.962 45.455 0.00 0.00 0.00 2.40
644 3627 3.070018 CCAAGAAGACTGCGTGAGAATT 58.930 45.455 0.00 0.00 0.00 2.17
645 3628 3.124297 CCAAGAAGACTGCGTGAGAATTC 59.876 47.826 0.00 0.00 0.00 2.17
646 3629 3.667497 AGAAGACTGCGTGAGAATTCA 57.333 42.857 8.44 0.00 0.00 2.57
684 3678 7.368059 TCCACAACTAGTATGATGCGTATTAG 58.632 38.462 8.33 0.00 0.00 1.73
745 4046 2.083002 TGATGTACTACGTACGTGGCA 58.917 47.619 30.25 20.66 41.41 4.92
824 4136 5.475719 CACCTGAAATTGATTCTTGCATGT 58.524 37.500 0.00 0.00 38.92 3.21
849 4161 2.119801 ATCCATCTTGCCAGTGTGAC 57.880 50.000 0.00 0.00 0.00 3.67
890 4212 5.542779 CCACCACTATATAAGAACCAGCTC 58.457 45.833 0.00 0.00 0.00 4.09
942 4266 3.370846 CCCAGCCATCTCACAACATAAGA 60.371 47.826 0.00 0.00 0.00 2.10
996 4349 1.883021 CGTTGCCAGGTTCCAATCC 59.117 57.895 0.00 0.00 0.00 3.01
1269 4622 3.400054 GCCCCCTACAAGCTCCGT 61.400 66.667 0.00 0.00 0.00 4.69
2041 5499 4.743018 CCATGGAGGCGTCCTTTT 57.257 55.556 24.96 8.43 44.30 2.27
2042 5500 2.961424 CCATGGAGGCGTCCTTTTT 58.039 52.632 24.96 6.05 44.30 1.94
2061 5519 4.359434 TTTTTGGAAAAAGGGCCATACC 57.641 40.909 6.18 2.14 33.29 2.73
2070 5528 2.774351 GGCCATACCCCAGCCTCT 60.774 66.667 0.00 0.00 43.62 3.69
2071 5529 2.512896 GCCATACCCCAGCCTCTG 59.487 66.667 0.00 0.00 0.00 3.35
2072 5530 2.512896 CCATACCCCAGCCTCTGC 59.487 66.667 0.00 0.00 37.95 4.26
2073 5531 2.377810 CCATACCCCAGCCTCTGCA 61.378 63.158 0.00 0.00 41.13 4.41
2074 5532 1.713005 CCATACCCCAGCCTCTGCAT 61.713 60.000 0.00 0.00 41.13 3.96
2075 5533 0.250640 CATACCCCAGCCTCTGCATC 60.251 60.000 0.00 0.00 41.13 3.91
2076 5534 0.695462 ATACCCCAGCCTCTGCATCA 60.695 55.000 0.00 0.00 41.13 3.07
2077 5535 1.340399 TACCCCAGCCTCTGCATCAG 61.340 60.000 0.00 0.00 41.13 2.90
2078 5536 2.372890 CCCCAGCCTCTGCATCAGA 61.373 63.158 0.00 0.00 41.13 3.27
2079 5537 1.605992 CCCAGCCTCTGCATCAGAA 59.394 57.895 0.00 0.00 40.18 3.02
2080 5538 0.034767 CCCAGCCTCTGCATCAGAAA 60.035 55.000 0.00 0.00 40.18 2.52
2081 5539 1.380524 CCAGCCTCTGCATCAGAAAG 58.619 55.000 0.00 0.00 40.18 2.62
2082 5540 1.065636 CCAGCCTCTGCATCAGAAAGA 60.066 52.381 0.00 0.00 40.18 2.52
2083 5541 2.421670 CCAGCCTCTGCATCAGAAAGAT 60.422 50.000 0.00 0.00 40.18 2.40
2092 5550 3.532892 CATCAGAAAGATGCATACGGC 57.467 47.619 0.00 0.00 46.90 5.68
2093 5551 2.988010 TCAGAAAGATGCATACGGCT 57.012 45.000 0.00 0.00 45.15 5.52
2094 5552 2.826428 TCAGAAAGATGCATACGGCTC 58.174 47.619 0.00 0.00 45.15 4.70
2095 5553 2.168313 TCAGAAAGATGCATACGGCTCA 59.832 45.455 0.00 0.00 45.15 4.26
2096 5554 3.136763 CAGAAAGATGCATACGGCTCAT 58.863 45.455 0.00 0.00 45.15 2.90
2097 5555 4.039124 TCAGAAAGATGCATACGGCTCATA 59.961 41.667 0.00 0.00 45.15 2.15
2098 5556 4.934001 CAGAAAGATGCATACGGCTCATAT 59.066 41.667 0.00 0.00 45.15 1.78
2099 5557 5.410746 CAGAAAGATGCATACGGCTCATATT 59.589 40.000 0.00 0.00 45.15 1.28
2100 5558 6.591448 CAGAAAGATGCATACGGCTCATATTA 59.409 38.462 0.00 0.00 45.15 0.98
2101 5559 7.279536 CAGAAAGATGCATACGGCTCATATTAT 59.720 37.037 0.00 0.00 45.15 1.28
2102 5560 7.826252 AGAAAGATGCATACGGCTCATATTATT 59.174 33.333 0.00 0.00 45.15 1.40
2103 5561 9.098355 GAAAGATGCATACGGCTCATATTATTA 57.902 33.333 0.00 0.00 45.15 0.98
2104 5562 9.448438 AAAGATGCATACGGCTCATATTATTAA 57.552 29.630 0.00 0.00 45.15 1.40
2105 5563 9.448438 AAGATGCATACGGCTCATATTATTAAA 57.552 29.630 0.00 0.00 45.15 1.52
2106 5564 9.448438 AGATGCATACGGCTCATATTATTAAAA 57.552 29.630 0.00 0.00 45.15 1.52
2123 5581 6.811253 ATTAAAATTAACACACGAGCCTCA 57.189 33.333 0.00 0.00 0.00 3.86
2124 5582 4.749245 AAAATTAACACACGAGCCTCAG 57.251 40.909 0.00 0.00 0.00 3.35
2125 5583 3.678056 AATTAACACACGAGCCTCAGA 57.322 42.857 0.00 0.00 0.00 3.27
2126 5584 2.724977 TTAACACACGAGCCTCAGAG 57.275 50.000 0.00 0.00 0.00 3.35
2127 5585 0.243907 TAACACACGAGCCTCAGAGC 59.756 55.000 0.00 0.00 0.00 4.09
2128 5586 2.125753 CACACGAGCCTCAGAGCC 60.126 66.667 0.00 0.00 0.00 4.70
2129 5587 2.601666 ACACGAGCCTCAGAGCCA 60.602 61.111 0.00 0.00 0.00 4.75
2130 5588 1.986757 ACACGAGCCTCAGAGCCAT 60.987 57.895 0.00 0.00 0.00 4.40
2131 5589 1.521010 CACGAGCCTCAGAGCCATG 60.521 63.158 0.00 0.00 0.00 3.66
2132 5590 2.108566 CGAGCCTCAGAGCCATGG 59.891 66.667 7.63 7.63 0.00 3.66
2133 5591 2.429767 CGAGCCTCAGAGCCATGGA 61.430 63.158 18.40 0.00 0.00 3.41
2134 5592 1.446791 GAGCCTCAGAGCCATGGAG 59.553 63.158 18.40 2.70 0.00 3.86
2174 5632 0.971386 CTCAGCCAACCCAAAGCATT 59.029 50.000 0.00 0.00 0.00 3.56
2243 5704 5.451354 TCTAACTAATTATTGGCCCCCAAC 58.549 41.667 0.00 0.00 46.95 3.77
2277 5739 3.186909 GGCATTATCGCAAGGGAAAAAC 58.813 45.455 0.00 0.00 38.47 2.43
2396 5861 7.253905 ACGGTTTACATTATATATCCTGCCT 57.746 36.000 0.00 0.00 0.00 4.75
2397 5862 7.686434 ACGGTTTACATTATATATCCTGCCTT 58.314 34.615 0.00 0.00 0.00 4.35
2580 6052 2.543777 AGAGTATGCACGTGGTTTGT 57.456 45.000 18.88 0.00 0.00 2.83
2659 6132 8.762645 TGGAAGACTACATGTTGAGAGAATTAT 58.237 33.333 14.37 0.00 0.00 1.28
2725 6198 3.495377 TCGTGTGTTGCAATAGGTACAAC 59.505 43.478 0.59 0.00 43.10 3.32
2850 6334 4.738252 TGCAAAGACGTCTTATAGTATGCG 59.262 41.667 30.26 15.16 35.90 4.73
2859 6343 3.504906 TCTTATAGTATGCGACGAAGGGG 59.495 47.826 0.00 0.00 0.00 4.79
2878 6362 4.086457 GGGGTTACCATGTGTCATTCTTT 58.914 43.478 2.98 0.00 39.85 2.52
2903 6387 7.775053 AAAACCAAATCACATTTAGCCTAGA 57.225 32.000 0.00 0.00 0.00 2.43
2907 6391 7.630082 ACCAAATCACATTTAGCCTAGACTTA 58.370 34.615 0.00 0.00 0.00 2.24
2920 6404 4.937015 GCCTAGACTTAGGTCCTATACTCG 59.063 50.000 0.00 0.00 46.96 4.18
2949 6433 1.821753 CTCGACTGACCTTGGATGTCT 59.178 52.381 0.00 0.00 33.83 3.41
2997 6481 4.487804 TCCTTGCTATTAGAGGAGATGCT 58.512 43.478 0.00 0.00 34.74 3.79
3025 6509 2.554893 GCCACAAGGAAATAAACACCGA 59.445 45.455 0.00 0.00 36.89 4.69
3038 6522 2.110213 ACCGAAGCGCCAGTTTCA 59.890 55.556 2.29 0.00 37.43 2.69
3040 6524 1.667830 CCGAAGCGCCAGTTTCAGA 60.668 57.895 2.29 0.00 37.43 3.27
3176 6708 2.206576 ACCTCTGCCTTTCCAATCAC 57.793 50.000 0.00 0.00 0.00 3.06
3185 6717 5.263599 TGCCTTTCCAATCACTACATCATT 58.736 37.500 0.00 0.00 0.00 2.57
3194 6726 7.071071 TCCAATCACTACATCATTGAGTCCATA 59.929 37.037 0.00 0.00 30.31 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 54 1.654775 CGCGCATTGATTCTAAGTCGC 60.655 52.381 8.75 0.00 38.20 5.19
87 92 0.388649 CGTCTGTACAGTCCAGTGGC 60.389 60.000 21.99 0.00 0.00 5.01
88 94 0.243907 CCGTCTGTACAGTCCAGTGG 59.756 60.000 21.99 1.40 0.00 4.00
94 100 2.161012 TCATCGAACCGTCTGTACAGTC 59.839 50.000 21.99 15.74 0.00 3.51
97 103 1.881324 TGTCATCGAACCGTCTGTACA 59.119 47.619 0.00 0.00 0.00 2.90
108 114 0.029700 ACGTGTCGTGTGTCATCGAA 59.970 50.000 0.00 0.00 39.18 3.71
204 216 3.952675 CGCAAGCGTGTTGTGCCT 61.953 61.111 6.25 0.00 34.73 4.75
306 507 1.913262 TGGAGTCGTGGACAGGCAT 60.913 57.895 0.00 0.00 34.60 4.40
307 508 2.523168 TGGAGTCGTGGACAGGCA 60.523 61.111 0.00 0.00 34.60 4.75
308 509 2.048127 GTGGAGTCGTGGACAGGC 60.048 66.667 0.00 0.00 34.60 4.85
309 510 2.083835 AACGTGGAGTCGTGGACAGG 62.084 60.000 0.00 0.00 43.38 4.00
345 568 2.826777 ATTGCGGCAACAGGGAGAGG 62.827 60.000 18.94 0.00 0.00 3.69
390 613 1.521457 GCTTCCCGTCGCATCATCA 60.521 57.895 0.00 0.00 0.00 3.07
539 791 2.175322 GTGGGACGACGAGACGAC 59.825 66.667 0.00 0.00 37.03 4.34
559 811 1.133253 GTACGTACGCAGCGAGTGA 59.867 57.895 24.65 0.00 0.00 3.41
579 907 1.011904 GTGCGCTCGATCGTACGTA 60.012 57.895 25.06 20.79 35.59 3.57
580 908 2.277120 GTGCGCTCGATCGTACGT 60.277 61.111 25.06 2.33 35.59 3.57
624 955 3.742882 TGAATTCTCACGCAGTCTTCTTG 59.257 43.478 7.05 0.00 41.61 3.02
639 3622 3.629398 GGATGCCGTGAATTCTGAATTCT 59.371 43.478 31.80 17.94 45.85 2.40
640 3623 3.378112 TGGATGCCGTGAATTCTGAATTC 59.622 43.478 27.97 27.97 45.86 2.17
641 3624 3.129287 GTGGATGCCGTGAATTCTGAATT 59.871 43.478 15.09 15.09 0.00 2.17
642 3625 2.684881 GTGGATGCCGTGAATTCTGAAT 59.315 45.455 7.05 0.00 0.00 2.57
643 3626 2.083774 GTGGATGCCGTGAATTCTGAA 58.916 47.619 7.05 0.00 0.00 3.02
644 3627 1.003003 TGTGGATGCCGTGAATTCTGA 59.997 47.619 7.05 0.00 0.00 3.27
645 3628 1.452110 TGTGGATGCCGTGAATTCTG 58.548 50.000 7.05 0.00 0.00 3.02
646 3629 1.812571 GTTGTGGATGCCGTGAATTCT 59.187 47.619 7.05 0.00 0.00 2.40
684 3678 8.577296 TCATTCATGCTCCATTACTAGTACTAC 58.423 37.037 0.91 0.00 0.00 2.73
705 3996 8.776376 ACATCAAAATGGTGGTTAATTCATTC 57.224 30.769 0.00 0.00 37.19 2.67
745 4046 4.910195 TGTACTGCTCATTCTCATTGGTT 58.090 39.130 0.00 0.00 0.00 3.67
807 4113 9.754382 GGATATGTTACATGCAAGAATCAATTT 57.246 29.630 8.26 0.00 0.00 1.82
824 4136 5.104569 TCACACTGGCAAGATGGATATGTTA 60.105 40.000 0.00 0.00 0.00 2.41
849 4161 2.183811 CGAGCAGAGCAGGAGTGG 59.816 66.667 0.00 0.00 0.00 4.00
942 4266 3.487372 TGGACTCGTGTATGCTAGCTAT 58.513 45.455 17.23 10.27 0.00 2.97
996 4349 1.958205 GATCGCCCTCGCCATTGAG 60.958 63.158 0.00 0.00 35.26 3.02
1077 4430 4.087892 AAGTCCATGGCGCTCGCT 62.088 61.111 6.96 0.00 41.60 4.93
1500 4859 1.227380 GATCGCGTTGATGCCCTCT 60.227 57.895 5.77 0.00 37.47 3.69
2040 5498 4.359434 GGTATGGCCCTTTTTCCAAAAA 57.641 40.909 0.00 0.00 35.75 1.94
2053 5511 2.774351 AGAGGCTGGGGTATGGCC 60.774 66.667 0.00 0.00 45.57 5.36
2054 5512 2.512896 CAGAGGCTGGGGTATGGC 59.487 66.667 0.00 0.00 0.00 4.40
2055 5513 1.713005 ATGCAGAGGCTGGGGTATGG 61.713 60.000 0.00 0.00 41.91 2.74
2056 5514 0.250640 GATGCAGAGGCTGGGGTATG 60.251 60.000 0.00 0.00 41.91 2.39
2057 5515 0.695462 TGATGCAGAGGCTGGGGTAT 60.695 55.000 0.00 0.00 41.91 2.73
2058 5516 1.306911 TGATGCAGAGGCTGGGGTA 60.307 57.895 0.00 0.00 41.91 3.69
2059 5517 2.611800 TGATGCAGAGGCTGGGGT 60.612 61.111 0.00 0.00 41.91 4.95
2060 5518 1.918467 TTCTGATGCAGAGGCTGGGG 61.918 60.000 0.00 0.00 41.75 4.96
2061 5519 0.034767 TTTCTGATGCAGAGGCTGGG 60.035 55.000 0.00 0.00 41.75 4.45
2062 5520 1.065636 TCTTTCTGATGCAGAGGCTGG 60.066 52.381 0.00 0.00 41.75 4.85
2063 5521 2.398252 TCTTTCTGATGCAGAGGCTG 57.602 50.000 0.00 0.00 41.75 4.85
2064 5522 2.920524 CATCTTTCTGATGCAGAGGCT 58.079 47.619 0.00 0.00 44.96 4.58
2073 5531 3.181462 TGAGCCGTATGCATCTTTCTGAT 60.181 43.478 0.19 0.00 44.83 2.90
2074 5532 2.168313 TGAGCCGTATGCATCTTTCTGA 59.832 45.455 0.19 0.00 44.83 3.27
2075 5533 2.554142 TGAGCCGTATGCATCTTTCTG 58.446 47.619 0.19 0.00 44.83 3.02
2076 5534 2.988010 TGAGCCGTATGCATCTTTCT 57.012 45.000 0.19 0.00 44.83 2.52
2077 5535 5.869753 AATATGAGCCGTATGCATCTTTC 57.130 39.130 0.19 0.00 44.83 2.62
2078 5536 7.928307 AATAATATGAGCCGTATGCATCTTT 57.072 32.000 0.19 0.00 44.83 2.52
2079 5537 9.448438 TTTAATAATATGAGCCGTATGCATCTT 57.552 29.630 0.19 0.00 44.83 2.40
2080 5538 9.448438 TTTTAATAATATGAGCCGTATGCATCT 57.552 29.630 0.19 0.00 44.83 2.90
2097 5555 8.952278 TGAGGCTCGTGTGTTAATTTTAATAAT 58.048 29.630 10.42 0.00 0.00 1.28
2098 5556 8.325421 TGAGGCTCGTGTGTTAATTTTAATAA 57.675 30.769 10.42 0.00 0.00 1.40
2099 5557 7.820386 TCTGAGGCTCGTGTGTTAATTTTAATA 59.180 33.333 10.42 0.00 0.00 0.98
2100 5558 6.653320 TCTGAGGCTCGTGTGTTAATTTTAAT 59.347 34.615 10.42 0.00 0.00 1.40
2101 5559 5.992829 TCTGAGGCTCGTGTGTTAATTTTAA 59.007 36.000 10.42 0.00 0.00 1.52
2102 5560 5.543714 TCTGAGGCTCGTGTGTTAATTTTA 58.456 37.500 10.42 0.00 0.00 1.52
2103 5561 4.385825 TCTGAGGCTCGTGTGTTAATTTT 58.614 39.130 10.42 0.00 0.00 1.82
2104 5562 3.997021 CTCTGAGGCTCGTGTGTTAATTT 59.003 43.478 10.42 0.00 0.00 1.82
2105 5563 3.589988 CTCTGAGGCTCGTGTGTTAATT 58.410 45.455 10.42 0.00 0.00 1.40
2106 5564 2.675317 GCTCTGAGGCTCGTGTGTTAAT 60.675 50.000 10.42 0.00 0.00 1.40
2107 5565 1.336887 GCTCTGAGGCTCGTGTGTTAA 60.337 52.381 10.42 0.00 0.00 2.01
2108 5566 0.243907 GCTCTGAGGCTCGTGTGTTA 59.756 55.000 10.42 0.00 0.00 2.41
2109 5567 1.005630 GCTCTGAGGCTCGTGTGTT 60.006 57.895 10.42 0.00 0.00 3.32
2110 5568 2.653702 GCTCTGAGGCTCGTGTGT 59.346 61.111 10.42 0.00 0.00 3.72
2111 5569 2.125753 GGCTCTGAGGCTCGTGTG 60.126 66.667 22.52 7.43 37.85 3.82
2112 5570 1.986757 ATGGCTCTGAGGCTCGTGT 60.987 57.895 28.26 9.57 41.96 4.49
2113 5571 1.521010 CATGGCTCTGAGGCTCGTG 60.521 63.158 28.26 20.24 41.96 4.35
2114 5572 2.729479 CCATGGCTCTGAGGCTCGT 61.729 63.158 28.26 13.97 41.96 4.18
2115 5573 2.108566 CCATGGCTCTGAGGCTCG 59.891 66.667 28.26 19.43 41.96 5.03
2116 5574 1.446791 CTCCATGGCTCTGAGGCTC 59.553 63.158 28.26 7.79 41.96 4.70
2117 5575 2.071262 CCTCCATGGCTCTGAGGCT 61.071 63.158 28.26 13.64 41.96 4.58
2118 5576 2.509916 CCTCCATGGCTCTGAGGC 59.490 66.667 22.95 22.95 39.29 4.70
2127 5585 2.808206 GGGTAGGACGCCTCCATGG 61.808 68.421 4.97 4.97 39.39 3.66
2128 5586 2.808206 GGGGTAGGACGCCTCCATG 61.808 68.421 4.47 0.00 46.55 3.66
2129 5587 2.446036 GGGGTAGGACGCCTCCAT 60.446 66.667 4.47 0.00 46.55 3.41
2134 5592 3.366739 CTTGACGGGGTAGGACGCC 62.367 68.421 2.71 2.71 46.59 5.68
2135 5593 2.183555 CTTGACGGGGTAGGACGC 59.816 66.667 0.00 0.00 0.00 5.19
2136 5594 1.509923 GTCTTGACGGGGTAGGACG 59.490 63.158 0.00 0.00 0.00 4.79
2137 5595 0.614134 AGGTCTTGACGGGGTAGGAC 60.614 60.000 0.00 0.00 0.00 3.85
2138 5596 0.324091 GAGGTCTTGACGGGGTAGGA 60.324 60.000 0.00 0.00 0.00 2.94
2139 5597 0.613853 TGAGGTCTTGACGGGGTAGG 60.614 60.000 0.00 0.00 0.00 3.18
2174 5632 0.900182 AGCTCGTCATGGACACCAGA 60.900 55.000 0.00 0.00 36.75 3.86
2236 5696 1.037493 CTGATCATGCATGTTGGGGG 58.963 55.000 25.43 9.14 0.00 5.40
2243 5704 3.181500 CGATAATGCCCTGATCATGCATG 60.181 47.826 25.11 21.07 44.49 4.06
2277 5739 9.445786 GGGTACATACGATTGATTGTTTATTTG 57.554 33.333 0.00 0.00 0.00 2.32
2659 6132 8.184249 ACATAGATAATTGATCCCCACTACCTA 58.816 37.037 0.00 0.00 34.80 3.08
2680 6153 9.411801 ACGATCATGTTTTGCTAGTATACATAG 57.588 33.333 5.50 5.49 0.00 2.23
2693 6166 3.370276 TGCAACACACGATCATGTTTTG 58.630 40.909 14.71 14.71 41.26 2.44
2778 6262 1.544691 CATTATAGGGCGGAGTAGCGT 59.455 52.381 0.00 0.00 38.18 5.07
2779 6263 1.544691 ACATTATAGGGCGGAGTAGCG 59.455 52.381 0.00 0.00 38.18 4.26
2780 6264 4.461781 TCTTACATTATAGGGCGGAGTAGC 59.538 45.833 0.00 0.00 0.00 3.58
2825 6309 6.237728 CGCATACTATAAGACGTCTTTGCAAA 60.238 38.462 32.89 20.52 33.95 3.68
2842 6326 1.477553 AACCCCTTCGTCGCATACTA 58.522 50.000 0.00 0.00 0.00 1.82
2844 6328 1.564207 GTAACCCCTTCGTCGCATAC 58.436 55.000 0.00 0.00 0.00 2.39
2850 6334 1.002773 ACACATGGTAACCCCTTCGTC 59.997 52.381 0.00 0.00 0.00 4.20
2859 6343 8.138712 TGGTTTTAAAGAATGACACATGGTAAC 58.861 33.333 0.00 0.00 0.00 2.50
2878 6362 8.736244 GTCTAGGCTAAATGTGATTTGGTTTTA 58.264 33.333 0.00 0.00 33.79 1.52
2903 6387 3.635836 GCAACCGAGTATAGGACCTAAGT 59.364 47.826 5.03 0.00 33.72 2.24
2907 6391 1.030457 CGCAACCGAGTATAGGACCT 58.970 55.000 0.00 0.00 33.72 3.85
2920 6404 1.733399 GTCAGTCGAGGACGCAACC 60.733 63.158 1.78 0.00 37.67 3.77
2949 6433 1.171308 GAGATTGCTGCTGCCTCAAA 58.829 50.000 13.47 0.68 38.71 2.69
2997 6481 7.375053 GTGTTTATTTCCTTGTGGCAAATCTA 58.625 34.615 0.00 0.00 30.99 1.98
3025 6509 3.146066 TGTAATTCTGAAACTGGCGCTT 58.854 40.909 7.64 0.00 0.00 4.68
3038 6522 9.476202 TCATCGTCAATTATCGATTGTAATTCT 57.524 29.630 1.71 0.00 44.46 2.40


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

AutoCloner maintained by Alex Coulton.