Multiple sequence alignment - TraesCS1A01G199400

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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 TraesCS1A01G199400 chr1A 100.000 2879 0 0 1 2879 358173992 358176870 0.000000e+00 5317.0
1 TraesCS1A01G199400 chr1A 94.788 2072 80 15 104 2162 358150623 358152679 0.000000e+00 3203.0
2 TraesCS1A01G199400 chr1B 93.774 2313 69 27 595 2879 389089427 389091692 0.000000e+00 3404.0
3 TraesCS1A01G199400 chr1B 95.483 1461 48 7 595 2043 389007215 389008669 0.000000e+00 2316.0
4 TraesCS1A01G199400 chr1B 89.781 411 32 7 104 508 388912493 388912899 4.250000e-143 518.0
5 TraesCS1A01G199400 chr1B 96.154 104 4 0 1 104 155161410 155161307 1.370000e-38 171.0
6 TraesCS1A01G199400 chr1B 88.571 105 9 2 504 608 389001658 389001759 1.080000e-24 124.0
7 TraesCS1A01G199400 chr1D 94.873 1814 59 13 104 1908 286749225 286751013 0.000000e+00 2804.0
8 TraesCS1A01G199400 chr1D 90.363 882 37 16 2012 2879 286751068 286751915 0.000000e+00 1114.0
9 TraesCS1A01G199400 chr1D 90.833 120 9 1 1 120 151565159 151565042 2.970000e-35 159.0
10 TraesCS1A01G199400 chr3D 96.154 104 4 0 1 104 303596345 303596242 1.370000e-38 171.0
11 TraesCS1A01G199400 chr3D 94.495 109 6 0 1 109 471237670 471237778 4.930000e-38 169.0
12 TraesCS1A01G199400 chr3D 94.444 108 6 0 1 108 276865612 276865719 1.770000e-37 167.0
13 TraesCS1A01G199400 chr3D 93.750 112 6 1 1 111 457183535 457183646 1.770000e-37 167.0
14 TraesCS1A01G199400 chr3D 73.868 287 65 7 1403 1684 157443216 157442935 3.920000e-19 106.0
15 TraesCS1A01G199400 chr3D 76.879 173 36 4 1403 1573 157540411 157540241 8.490000e-16 95.3
16 TraesCS1A01G199400 chr2D 93.750 112 7 0 1 112 158803383 158803272 4.930000e-38 169.0
17 TraesCS1A01G199400 chr2D 94.444 108 6 0 1 108 102181390 102181497 1.770000e-37 167.0
18 TraesCS1A01G199400 chr7D 92.920 113 6 2 1 113 504352484 504352374 2.300000e-36 163.0
19 TraesCS1A01G199400 chr5B 77.844 167 33 3 1402 1566 700997744 700997908 1.830000e-17 100.0
20 TraesCS1A01G199400 chr4B 86.022 93 13 0 1403 1495 547205193 547205285 1.830000e-17 100.0
21 TraesCS1A01G199400 chr3A 73.540 291 62 11 1403 1684 170811851 170812135 2.360000e-16 97.1
22 TraesCS1A01G199400 chr4A 84.946 93 14 0 1403 1495 26413652 26413560 8.490000e-16 95.3


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 TraesCS1A01G199400 chr1A 358173992 358176870 2878 False 5317 5317 100.000 1 2879 1 chr1A.!!$F2 2878
1 TraesCS1A01G199400 chr1A 358150623 358152679 2056 False 3203 3203 94.788 104 2162 1 chr1A.!!$F1 2058
2 TraesCS1A01G199400 chr1B 389089427 389091692 2265 False 3404 3404 93.774 595 2879 1 chr1B.!!$F4 2284
3 TraesCS1A01G199400 chr1B 389007215 389008669 1454 False 2316 2316 95.483 595 2043 1 chr1B.!!$F3 1448
4 TraesCS1A01G199400 chr1D 286749225 286751915 2690 False 1959 2804 92.618 104 2879 2 chr1D.!!$F1 2775

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
43 44 0.331954 TCCTCTGCTCCTCGTTAGGT 59.668 55.0 0.0 0.0 44.09 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2008 2034 0.460311 CGCGACAGGGTCCTAGAAAT 59.54 55.0 0.0 0.0 0.0 2.17 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
26 27 9.665264 CTTACTGAAAACTACTTGTCATTTTCC 57.335 33.333 14.39 4.19 39.32 3.13
27 28 7.881775 ACTGAAAACTACTTGTCATTTTCCT 57.118 32.000 14.39 3.80 39.32 3.36
28 29 7.931275 ACTGAAAACTACTTGTCATTTTCCTC 58.069 34.615 14.39 0.11 39.32 3.71
29 30 7.775561 ACTGAAAACTACTTGTCATTTTCCTCT 59.224 33.333 14.39 2.01 39.32 3.69
30 31 7.930217 TGAAAACTACTTGTCATTTTCCTCTG 58.070 34.615 14.39 0.00 39.32 3.35
31 32 5.948992 AACTACTTGTCATTTTCCTCTGC 57.051 39.130 0.00 0.00 0.00 4.26
32 33 5.234466 ACTACTTGTCATTTTCCTCTGCT 57.766 39.130 0.00 0.00 0.00 4.24
33 34 5.241662 ACTACTTGTCATTTTCCTCTGCTC 58.758 41.667 0.00 0.00 0.00 4.26
34 35 3.416156 ACTTGTCATTTTCCTCTGCTCC 58.584 45.455 0.00 0.00 0.00 4.70
35 36 3.073650 ACTTGTCATTTTCCTCTGCTCCT 59.926 43.478 0.00 0.00 0.00 3.69
36 37 3.340814 TGTCATTTTCCTCTGCTCCTC 57.659 47.619 0.00 0.00 0.00 3.71
37 38 2.275318 GTCATTTTCCTCTGCTCCTCG 58.725 52.381 0.00 0.00 0.00 4.63
38 39 1.902508 TCATTTTCCTCTGCTCCTCGT 59.097 47.619 0.00 0.00 0.00 4.18
39 40 2.303022 TCATTTTCCTCTGCTCCTCGTT 59.697 45.455 0.00 0.00 0.00 3.85
40 41 3.513912 TCATTTTCCTCTGCTCCTCGTTA 59.486 43.478 0.00 0.00 0.00 3.18
41 42 3.594603 TTTTCCTCTGCTCCTCGTTAG 57.405 47.619 0.00 0.00 0.00 2.34
42 43 1.475403 TTCCTCTGCTCCTCGTTAGG 58.525 55.000 0.00 0.00 45.21 2.69
43 44 0.331954 TCCTCTGCTCCTCGTTAGGT 59.668 55.000 0.00 0.00 44.09 3.08
44 45 1.187087 CCTCTGCTCCTCGTTAGGTT 58.813 55.000 0.00 0.00 44.09 3.50
45 46 1.135333 CCTCTGCTCCTCGTTAGGTTC 59.865 57.143 0.00 0.00 44.09 3.62
46 47 0.809385 TCTGCTCCTCGTTAGGTTCG 59.191 55.000 0.00 0.00 44.09 3.95
47 48 0.809385 CTGCTCCTCGTTAGGTTCGA 59.191 55.000 0.00 0.00 44.09 3.71
48 49 0.524862 TGCTCCTCGTTAGGTTCGAC 59.475 55.000 0.00 0.00 44.09 4.20
49 50 0.524862 GCTCCTCGTTAGGTTCGACA 59.475 55.000 0.00 0.00 44.09 4.35
50 51 1.731750 GCTCCTCGTTAGGTTCGACAC 60.732 57.143 0.00 0.00 44.09 3.67
51 52 1.811359 CTCCTCGTTAGGTTCGACACT 59.189 52.381 0.00 0.00 44.09 3.55
52 53 1.808945 TCCTCGTTAGGTTCGACACTC 59.191 52.381 0.00 0.00 44.09 3.51
53 54 1.811359 CCTCGTTAGGTTCGACACTCT 59.189 52.381 0.00 0.00 38.19 3.24
54 55 2.228343 CCTCGTTAGGTTCGACACTCTT 59.772 50.000 0.00 0.00 38.19 2.85
55 56 3.438087 CCTCGTTAGGTTCGACACTCTTA 59.562 47.826 0.00 0.00 38.19 2.10
56 57 4.401714 CTCGTTAGGTTCGACACTCTTAC 58.598 47.826 0.00 0.00 33.71 2.34
57 58 4.067896 TCGTTAGGTTCGACACTCTTACT 58.932 43.478 0.00 0.00 32.30 2.24
58 59 4.516698 TCGTTAGGTTCGACACTCTTACTT 59.483 41.667 0.00 0.00 32.30 2.24
59 60 5.700832 TCGTTAGGTTCGACACTCTTACTTA 59.299 40.000 0.00 0.00 32.30 2.24
60 61 6.372659 TCGTTAGGTTCGACACTCTTACTTAT 59.627 38.462 0.00 0.00 32.30 1.73
61 62 6.686253 CGTTAGGTTCGACACTCTTACTTATC 59.314 42.308 0.00 0.00 0.00 1.75
62 63 5.232610 AGGTTCGACACTCTTACTTATCG 57.767 43.478 0.00 0.00 0.00 2.92
63 64 4.940046 AGGTTCGACACTCTTACTTATCGA 59.060 41.667 0.00 0.00 36.85 3.59
64 65 5.413833 AGGTTCGACACTCTTACTTATCGAA 59.586 40.000 2.99 2.99 43.90 3.71
65 66 6.072286 AGGTTCGACACTCTTACTTATCGAAA 60.072 38.462 8.30 0.00 46.48 3.46
66 67 6.583806 GGTTCGACACTCTTACTTATCGAAAA 59.416 38.462 8.30 0.00 46.48 2.29
67 68 7.201333 GGTTCGACACTCTTACTTATCGAAAAG 60.201 40.741 8.30 0.00 46.48 2.27
68 69 7.137490 TCGACACTCTTACTTATCGAAAAGA 57.863 36.000 0.00 0.00 35.80 2.52
69 70 7.242079 TCGACACTCTTACTTATCGAAAAGAG 58.758 38.462 16.62 16.62 46.69 2.85
70 71 6.021311 CGACACTCTTACTTATCGAAAAGAGC 60.021 42.308 17.49 7.32 45.71 4.09
71 72 6.926313 ACACTCTTACTTATCGAAAAGAGCT 58.074 36.000 17.49 0.00 45.71 4.09
72 73 8.053026 ACACTCTTACTTATCGAAAAGAGCTA 57.947 34.615 17.49 0.00 45.71 3.32
73 74 8.688151 ACACTCTTACTTATCGAAAAGAGCTAT 58.312 33.333 17.49 0.00 45.71 2.97
84 85 7.730364 TCGAAAAGAGCTATAATTGATTCCC 57.270 36.000 0.00 0.00 0.00 3.97
85 86 7.509546 TCGAAAAGAGCTATAATTGATTCCCT 58.490 34.615 0.00 0.00 0.00 4.20
86 87 8.647796 TCGAAAAGAGCTATAATTGATTCCCTA 58.352 33.333 0.00 0.00 0.00 3.53
87 88 9.442047 CGAAAAGAGCTATAATTGATTCCCTAT 57.558 33.333 0.00 0.00 0.00 2.57
94 95 9.950496 AGCTATAATTGATTCCCTATACTTGTG 57.050 33.333 0.00 0.00 0.00 3.33
95 96 9.167311 GCTATAATTGATTCCCTATACTTGTGG 57.833 37.037 0.00 0.00 0.00 4.17
96 97 9.672673 CTATAATTGATTCCCTATACTTGTGGG 57.327 37.037 0.00 0.00 42.20 4.61
97 98 5.994416 ATTGATTCCCTATACTTGTGGGT 57.006 39.130 0.00 0.00 41.58 4.51
98 99 5.367945 TTGATTCCCTATACTTGTGGGTC 57.632 43.478 0.00 0.00 41.58 4.46
99 100 4.367166 TGATTCCCTATACTTGTGGGTCA 58.633 43.478 0.00 0.00 41.58 4.02
100 101 4.975147 TGATTCCCTATACTTGTGGGTCAT 59.025 41.667 0.00 0.00 41.58 3.06
101 102 5.071788 TGATTCCCTATACTTGTGGGTCATC 59.928 44.000 0.00 0.00 41.58 2.92
102 103 4.002256 TCCCTATACTTGTGGGTCATCA 57.998 45.455 0.00 0.00 41.58 3.07
163 164 7.557719 AGCCAAGTCACTAAACATATGCTATTT 59.442 33.333 1.58 0.00 0.00 1.40
179 180 4.142622 TGCTATTTCAAAACATGCCTCTCG 60.143 41.667 0.00 0.00 0.00 4.04
245 246 7.308109 GGACATGTATCAACGACCTTAAACAAA 60.308 37.037 0.00 0.00 0.00 2.83
296 297 3.055819 GGTCATTCTCTTCAGCCTGTGTA 60.056 47.826 0.00 0.00 0.00 2.90
297 298 4.180057 GTCATTCTCTTCAGCCTGTGTAG 58.820 47.826 0.00 0.00 0.00 2.74
298 299 3.834813 TCATTCTCTTCAGCCTGTGTAGT 59.165 43.478 0.00 0.00 0.00 2.73
368 370 6.459923 GGGTCTACATAAAGGCATAGAGAAG 58.540 44.000 0.00 0.00 0.00 2.85
404 411 5.931146 GTGGACAATTTATGTTGGAATTGCA 59.069 36.000 0.00 0.00 44.12 4.08
410 417 7.175293 ACAATTTATGTTGGAATTGCATTGCTT 59.825 29.630 10.49 0.00 43.58 3.91
526 535 1.310933 CGGCCAAGATCAGCTGCTTT 61.311 55.000 9.47 0.00 0.00 3.51
528 537 1.403780 GGCCAAGATCAGCTGCTTTTG 60.404 52.381 9.47 11.35 0.00 2.44
541 550 1.586541 CTTTTGCGGAAAGGGAGCC 59.413 57.895 3.48 0.00 40.87 4.70
579 588 5.245531 CGGGCCTGTTCATTGTATATGTAT 58.754 41.667 2.29 0.00 0.00 2.29
580 589 6.403049 CGGGCCTGTTCATTGTATATGTATA 58.597 40.000 2.29 0.00 0.00 1.47
679 689 2.346766 AGACACAGTTCCAACATGCA 57.653 45.000 0.00 0.00 0.00 3.96
857 867 7.303182 AGATTGAACGATATATGTTCCTCCA 57.697 36.000 17.76 5.18 43.95 3.86
1210 1234 4.980434 GTCAATGACCATGCATGCTTATTC 59.020 41.667 21.69 12.11 0.00 1.75
1211 1235 3.909776 ATGACCATGCATGCTTATTCG 57.090 42.857 21.69 8.18 0.00 3.34
1212 1236 1.948834 TGACCATGCATGCTTATTCGG 59.051 47.619 21.69 12.18 0.00 4.30
1213 1237 1.949525 GACCATGCATGCTTATTCGGT 59.050 47.619 21.69 15.32 0.00 4.69
1214 1238 2.358898 GACCATGCATGCTTATTCGGTT 59.641 45.455 21.69 1.60 0.00 4.44
1692 1716 2.676471 GTGAAGGGCAATGGCGGT 60.676 61.111 0.00 0.00 42.47 5.68
1908 1932 0.673022 GAAGGTCTGAGGCACAGCAG 60.673 60.000 7.09 0.00 45.38 4.24
1965 1989 1.879372 GCGCTATTGCTGGGATGATCA 60.879 52.381 0.00 0.00 36.97 2.92
1969 1993 3.825014 GCTATTGCTGGGATGATCATTGT 59.175 43.478 10.14 0.00 36.03 2.71
1972 1996 1.565288 TGCTGGGATGATCATTGTCCA 59.435 47.619 10.14 15.81 33.62 4.02
1991 2017 2.413634 CCATACCGTTTTCGTTGCTTCC 60.414 50.000 0.00 0.00 42.35 3.46
1994 2020 1.746787 ACCGTTTTCGTTGCTTCCTTT 59.253 42.857 0.00 0.00 42.35 3.11
2008 2034 8.073768 CGTTGCTTCCTTTCTTATTTTCAGTTA 58.926 33.333 0.00 0.00 0.00 2.24
2054 2082 1.079819 CCGTCCATGTGAAGAGCGT 60.080 57.895 0.00 0.00 0.00 5.07
2067 2095 3.819877 GAGCGTGGGGGTTTGACGT 62.820 63.158 0.00 0.00 35.52 4.34
2073 2101 1.597578 GGGGGTTTGACGTACGCAA 60.598 57.895 16.72 17.04 0.00 4.85
2091 2120 3.002656 CGCAATGACAGTGAAAACTCTGT 59.997 43.478 7.16 0.00 0.00 3.41
2223 2253 4.382386 ACAACCCTAATAACACCAAGCT 57.618 40.909 0.00 0.00 0.00 3.74
2237 2267 5.238583 ACACCAAGCTACAAGAATACTGAC 58.761 41.667 0.00 0.00 0.00 3.51
2336 2373 4.093850 CCGTCCCCTTTTTAAAGTCGTATG 59.906 45.833 1.91 0.00 34.20 2.39
2380 2418 6.239915 CCTTACCCACTTCTTTTACCTCTTCT 60.240 42.308 0.00 0.00 0.00 2.85
2393 2431 9.464714 CTTTTACCTCTTCTTTTAAAAGGAAGC 57.535 33.333 24.20 0.00 37.66 3.86
2394 2432 8.762481 TTTACCTCTTCTTTTAAAAGGAAGCT 57.238 30.769 24.20 11.22 36.67 3.74
2395 2433 9.856162 TTTACCTCTTCTTTTAAAAGGAAGCTA 57.144 29.630 24.20 12.00 36.67 3.32
2396 2434 7.747155 ACCTCTTCTTTTAAAAGGAAGCTAC 57.253 36.000 24.20 0.00 36.67 3.58
2397 2435 7.519057 ACCTCTTCTTTTAAAAGGAAGCTACT 58.481 34.615 24.20 9.32 36.67 2.57
2398 2436 7.445707 ACCTCTTCTTTTAAAAGGAAGCTACTG 59.554 37.037 24.20 14.66 36.67 2.74
2399 2437 7.203255 TCTTCTTTTAAAAGGAAGCTACTGC 57.797 36.000 24.20 0.00 36.67 4.40
2741 2785 0.540133 TGCTGGATCCTGCAAAGCAA 60.540 50.000 35.94 17.39 45.40 3.91
2742 2786 0.604578 GCTGGATCCTGCAAAGCAAA 59.395 50.000 32.11 0.00 38.41 3.68
2743 2787 1.001181 GCTGGATCCTGCAAAGCAAAA 59.999 47.619 32.11 0.00 38.41 2.44
2744 2788 2.929592 GCTGGATCCTGCAAAGCAAAAG 60.930 50.000 32.11 10.35 38.41 2.27
2745 2789 2.559668 CTGGATCCTGCAAAGCAAAAGA 59.440 45.455 14.23 0.00 38.41 2.52
2746 2790 2.964464 TGGATCCTGCAAAGCAAAAGAA 59.036 40.909 14.23 0.00 38.41 2.52
2747 2791 3.387374 TGGATCCTGCAAAGCAAAAGAAA 59.613 39.130 14.23 0.00 38.41 2.52
2748 2792 4.141756 TGGATCCTGCAAAGCAAAAGAAAA 60.142 37.500 14.23 0.00 38.41 2.29
2749 2793 4.212004 GGATCCTGCAAAGCAAAAGAAAAC 59.788 41.667 3.84 0.00 38.41 2.43
2750 2794 4.199432 TCCTGCAAAGCAAAAGAAAACA 57.801 36.364 0.00 0.00 38.41 2.83
2751 2795 4.573900 TCCTGCAAAGCAAAAGAAAACAA 58.426 34.783 0.00 0.00 38.41 2.83
2752 2796 5.184711 TCCTGCAAAGCAAAAGAAAACAAT 58.815 33.333 0.00 0.00 38.41 2.71
2753 2797 5.064962 TCCTGCAAAGCAAAAGAAAACAATG 59.935 36.000 0.00 0.00 38.41 2.82
2754 2798 5.163733 CCTGCAAAGCAAAAGAAAACAATGT 60.164 36.000 0.00 0.00 38.41 2.71
2755 2799 5.629097 TGCAAAGCAAAAGAAAACAATGTG 58.371 33.333 0.00 0.00 34.76 3.21
2756 2800 5.410746 TGCAAAGCAAAAGAAAACAATGTGA 59.589 32.000 0.00 0.00 34.76 3.58
2757 2801 6.072838 TGCAAAGCAAAAGAAAACAATGTGAA 60.073 30.769 0.00 0.00 34.76 3.18
2758 2802 6.968335 GCAAAGCAAAAGAAAACAATGTGAAT 59.032 30.769 0.00 0.00 0.00 2.57
2759 2803 7.044576 GCAAAGCAAAAGAAAACAATGTGAATG 60.045 33.333 0.00 0.00 0.00 2.67
2760 2804 7.846644 AAGCAAAAGAAAACAATGTGAATGA 57.153 28.000 0.00 0.00 0.00 2.57
2761 2805 7.473027 AGCAAAAGAAAACAATGTGAATGAG 57.527 32.000 0.00 0.00 0.00 2.90
2762 2806 6.018507 AGCAAAAGAAAACAATGTGAATGAGC 60.019 34.615 0.00 0.00 0.00 4.26
2763 2807 6.652245 CAAAAGAAAACAATGTGAATGAGCC 58.348 36.000 0.00 0.00 0.00 4.70
2764 2808 4.525912 AGAAAACAATGTGAATGAGCCC 57.474 40.909 0.00 0.00 0.00 5.19
2765 2809 4.154942 AGAAAACAATGTGAATGAGCCCT 58.845 39.130 0.00 0.00 0.00 5.19
2769 2813 6.418057 AAACAATGTGAATGAGCCCTAAAA 57.582 33.333 0.00 0.00 0.00 1.52
2827 2872 6.073003 ACGGATGAAAGAATCTTGTTCAGTTC 60.073 38.462 0.00 0.00 34.91 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.665264 GGAAAATGACAAGTAGTTTTCAGTAAG 57.335 33.333 17.06 0.00 40.52 2.34
1 2 9.403583 AGGAAAATGACAAGTAGTTTTCAGTAA 57.596 29.630 17.06 0.00 40.52 2.24
2 3 8.974060 AGGAAAATGACAAGTAGTTTTCAGTA 57.026 30.769 17.06 0.00 40.52 2.74
3 4 7.775561 AGAGGAAAATGACAAGTAGTTTTCAGT 59.224 33.333 17.06 0.00 40.52 3.41
4 5 8.072567 CAGAGGAAAATGACAAGTAGTTTTCAG 58.927 37.037 17.06 6.82 40.52 3.02
5 6 7.468631 GCAGAGGAAAATGACAAGTAGTTTTCA 60.469 37.037 17.06 1.73 40.52 2.69
6 7 6.858478 GCAGAGGAAAATGACAAGTAGTTTTC 59.142 38.462 11.20 11.20 38.94 2.29
7 8 6.547510 AGCAGAGGAAAATGACAAGTAGTTTT 59.452 34.615 0.00 0.00 0.00 2.43
8 9 6.064717 AGCAGAGGAAAATGACAAGTAGTTT 58.935 36.000 0.00 0.00 0.00 2.66
9 10 5.625150 AGCAGAGGAAAATGACAAGTAGTT 58.375 37.500 0.00 0.00 0.00 2.24
10 11 5.234466 AGCAGAGGAAAATGACAAGTAGT 57.766 39.130 0.00 0.00 0.00 2.73
11 12 4.633565 GGAGCAGAGGAAAATGACAAGTAG 59.366 45.833 0.00 0.00 0.00 2.57
12 13 4.287067 AGGAGCAGAGGAAAATGACAAGTA 59.713 41.667 0.00 0.00 0.00 2.24
13 14 3.073650 AGGAGCAGAGGAAAATGACAAGT 59.926 43.478 0.00 0.00 0.00 3.16
14 15 3.683802 AGGAGCAGAGGAAAATGACAAG 58.316 45.455 0.00 0.00 0.00 3.16
15 16 3.679389 GAGGAGCAGAGGAAAATGACAA 58.321 45.455 0.00 0.00 0.00 3.18
16 17 2.354103 CGAGGAGCAGAGGAAAATGACA 60.354 50.000 0.00 0.00 0.00 3.58
17 18 2.275318 CGAGGAGCAGAGGAAAATGAC 58.725 52.381 0.00 0.00 0.00 3.06
18 19 1.902508 ACGAGGAGCAGAGGAAAATGA 59.097 47.619 0.00 0.00 0.00 2.57
19 20 2.393271 ACGAGGAGCAGAGGAAAATG 57.607 50.000 0.00 0.00 0.00 2.32
20 21 4.130286 CTAACGAGGAGCAGAGGAAAAT 57.870 45.455 0.00 0.00 0.00 1.82
21 22 3.594603 CTAACGAGGAGCAGAGGAAAA 57.405 47.619 0.00 0.00 0.00 2.29
34 35 3.555917 AAGAGTGTCGAACCTAACGAG 57.444 47.619 0.00 0.00 40.37 4.18
35 36 4.067896 AGTAAGAGTGTCGAACCTAACGA 58.932 43.478 0.00 0.00 37.43 3.85
36 37 4.416505 AGTAAGAGTGTCGAACCTAACG 57.583 45.455 0.00 0.00 0.00 3.18
37 38 6.686253 CGATAAGTAAGAGTGTCGAACCTAAC 59.314 42.308 0.00 0.00 0.00 2.34
38 39 6.595326 TCGATAAGTAAGAGTGTCGAACCTAA 59.405 38.462 0.00 0.00 35.48 2.69
39 40 6.108687 TCGATAAGTAAGAGTGTCGAACCTA 58.891 40.000 0.00 0.00 35.48 3.08
40 41 4.940046 TCGATAAGTAAGAGTGTCGAACCT 59.060 41.667 0.00 0.00 35.48 3.50
41 42 5.227238 TCGATAAGTAAGAGTGTCGAACC 57.773 43.478 0.00 0.00 35.48 3.62
42 43 7.536622 TCTTTTCGATAAGTAAGAGTGTCGAAC 59.463 37.037 14.15 0.00 44.53 3.95
43 44 7.587629 TCTTTTCGATAAGTAAGAGTGTCGAA 58.412 34.615 14.15 4.17 43.60 3.71
44 45 7.137490 TCTTTTCGATAAGTAAGAGTGTCGA 57.863 36.000 14.15 0.00 36.46 4.20
45 46 6.021311 GCTCTTTTCGATAAGTAAGAGTGTCG 60.021 42.308 14.15 0.00 43.39 4.35
46 47 7.030768 AGCTCTTTTCGATAAGTAAGAGTGTC 58.969 38.462 14.15 3.85 43.39 3.67
47 48 6.926313 AGCTCTTTTCGATAAGTAAGAGTGT 58.074 36.000 14.15 4.97 43.39 3.55
58 59 9.436957 GGGAATCAATTATAGCTCTTTTCGATA 57.563 33.333 0.00 0.00 0.00 2.92
59 60 8.160106 AGGGAATCAATTATAGCTCTTTTCGAT 58.840 33.333 0.00 0.00 0.00 3.59
60 61 7.509546 AGGGAATCAATTATAGCTCTTTTCGA 58.490 34.615 0.00 0.00 0.00 3.71
61 62 7.736447 AGGGAATCAATTATAGCTCTTTTCG 57.264 36.000 0.00 0.00 0.00 3.46
68 69 9.950496 CACAAGTATAGGGAATCAATTATAGCT 57.050 33.333 0.00 0.00 0.00 3.32
69 70 9.167311 CCACAAGTATAGGGAATCAATTATAGC 57.833 37.037 0.00 0.00 0.00 2.97
70 71 9.672673 CCCACAAGTATAGGGAATCAATTATAG 57.327 37.037 0.00 0.00 45.80 1.31
71 72 9.177927 ACCCACAAGTATAGGGAATCAATTATA 57.822 33.333 3.32 0.00 45.80 0.98
72 73 8.057246 ACCCACAAGTATAGGGAATCAATTAT 57.943 34.615 3.32 0.00 45.80 1.28
73 74 7.128109 TGACCCACAAGTATAGGGAATCAATTA 59.872 37.037 3.32 0.00 45.80 1.40
74 75 6.069088 TGACCCACAAGTATAGGGAATCAATT 60.069 38.462 3.32 0.00 45.80 2.32
75 76 5.431731 TGACCCACAAGTATAGGGAATCAAT 59.568 40.000 3.32 0.00 45.80 2.57
76 77 4.785914 TGACCCACAAGTATAGGGAATCAA 59.214 41.667 3.32 0.00 45.80 2.57
77 78 4.367166 TGACCCACAAGTATAGGGAATCA 58.633 43.478 3.32 0.00 45.80 2.57
78 79 5.071788 TGATGACCCACAAGTATAGGGAATC 59.928 44.000 3.32 6.91 45.80 2.52
79 80 4.975147 TGATGACCCACAAGTATAGGGAAT 59.025 41.667 3.32 0.00 45.80 3.01
80 81 4.367166 TGATGACCCACAAGTATAGGGAA 58.633 43.478 3.32 0.00 45.80 3.97
81 82 4.002256 TGATGACCCACAAGTATAGGGA 57.998 45.455 3.32 0.00 45.80 4.20
83 84 5.794894 GGTATGATGACCCACAAGTATAGG 58.205 45.833 0.00 0.00 32.88 2.57
95 96 0.687354 ATGCGAGGGGTATGATGACC 59.313 55.000 0.00 0.00 38.93 4.02
96 97 3.678056 TTATGCGAGGGGTATGATGAC 57.322 47.619 0.00 0.00 0.00 3.06
97 98 3.119137 CGATTATGCGAGGGGTATGATGA 60.119 47.826 0.00 0.00 0.00 2.92
98 99 3.119137 TCGATTATGCGAGGGGTATGATG 60.119 47.826 0.00 0.00 35.01 3.07
99 100 3.096852 TCGATTATGCGAGGGGTATGAT 58.903 45.455 0.00 0.00 35.01 2.45
100 101 2.521126 TCGATTATGCGAGGGGTATGA 58.479 47.619 0.00 0.00 35.01 2.15
101 102 3.119137 TCATCGATTATGCGAGGGGTATG 60.119 47.826 0.00 0.00 44.26 2.39
102 103 3.096852 TCATCGATTATGCGAGGGGTAT 58.903 45.455 0.00 0.00 44.26 2.73
155 156 5.449588 CGAGAGGCATGTTTTGAAATAGCAT 60.450 40.000 0.00 0.00 0.00 3.79
163 164 2.542020 TCACGAGAGGCATGTTTTGA 57.458 45.000 0.00 0.00 0.00 2.69
256 257 9.462606 AGAATGACCTCGAAAAATAATAAGGTT 57.537 29.630 0.00 0.00 37.26 3.50
296 297 5.897377 ACAAACTCAAAACTAGCACAACT 57.103 34.783 0.00 0.00 0.00 3.16
297 298 6.944557 AAACAAACTCAAAACTAGCACAAC 57.055 33.333 0.00 0.00 0.00 3.32
298 299 9.134734 CTTAAAACAAACTCAAAACTAGCACAA 57.865 29.630 0.00 0.00 0.00 3.33
420 427 7.759489 TTTTCAAGCTTATTTCCTTGAGCTA 57.241 32.000 0.00 0.00 45.59 3.32
548 557 3.901797 GAACAGGCCCGGGTGTCTG 62.902 68.421 27.40 27.40 0.00 3.51
557 566 7.883311 AGTTATACATATACAATGAACAGGCCC 59.117 37.037 0.00 0.00 0.00 5.80
579 588 8.660295 TTCTTATTCTAGGTTGGACAGAGTTA 57.340 34.615 0.00 0.00 0.00 2.24
580 589 7.554959 TTCTTATTCTAGGTTGGACAGAGTT 57.445 36.000 0.00 0.00 0.00 3.01
826 836 6.390721 ACATATATCGTTCAATCTTCGGGAG 58.609 40.000 0.00 0.00 0.00 4.30
827 837 6.340962 ACATATATCGTTCAATCTTCGGGA 57.659 37.500 0.00 0.00 0.00 5.14
1210 1234 3.009723 ACATCAGCATAACAAGGAACCG 58.990 45.455 0.00 0.00 0.00 4.44
1211 1235 5.050091 CGATACATCAGCATAACAAGGAACC 60.050 44.000 0.00 0.00 0.00 3.62
1212 1236 5.523916 ACGATACATCAGCATAACAAGGAAC 59.476 40.000 0.00 0.00 0.00 3.62
1213 1237 5.523552 CACGATACATCAGCATAACAAGGAA 59.476 40.000 0.00 0.00 0.00 3.36
1214 1238 5.049828 CACGATACATCAGCATAACAAGGA 58.950 41.667 0.00 0.00 0.00 3.36
1798 1822 2.513666 GGCGGCGATGATGGTCAA 60.514 61.111 12.98 0.00 0.00 3.18
1952 1976 1.565288 TGGACAATGATCATCCCAGCA 59.435 47.619 9.06 0.00 0.00 4.41
1965 1989 3.365565 GCAACGAAAACGGTATGGACAAT 60.366 43.478 0.00 0.00 0.00 2.71
1969 1993 2.172851 AGCAACGAAAACGGTATGGA 57.827 45.000 0.00 0.00 0.00 3.41
1972 1996 2.774687 AGGAAGCAACGAAAACGGTAT 58.225 42.857 0.00 0.00 0.00 2.73
1994 2020 9.901172 GGGTCCTAGAAATAACTGAAAATAAGA 57.099 33.333 0.00 0.00 0.00 2.10
2008 2034 0.460311 CGCGACAGGGTCCTAGAAAT 59.540 55.000 0.00 0.00 0.00 2.17
2010 2036 2.707849 GCGCGACAGGGTCCTAGAA 61.708 63.158 12.10 0.00 0.00 2.10
2035 2062 2.456119 CGCTCTTCACATGGACGGC 61.456 63.158 0.00 0.00 0.00 5.68
2054 2082 2.030862 GCGTACGTCAAACCCCCA 59.969 61.111 17.90 0.00 0.00 4.96
2067 2095 4.211164 CAGAGTTTTCACTGTCATTGCGTA 59.789 41.667 0.00 0.00 34.61 4.42
2073 2101 4.752101 GTGCTACAGAGTTTTCACTGTCAT 59.248 41.667 0.00 0.00 45.76 3.06
2091 2120 5.627499 AATCTTTTGCTTTGATCGTGCTA 57.373 34.783 6.09 0.00 0.00 3.49
2162 2192 0.322277 CAGCCACCTCTGATTGCACT 60.322 55.000 0.00 0.00 36.19 4.40
2336 2373 1.244816 GCAACCCAGTTGAACCCTAC 58.755 55.000 11.50 0.00 45.28 3.18
2393 2431 9.844790 TCAAAAATAATTTGATGTGAGCAGTAG 57.155 29.630 0.00 0.00 33.90 2.57
2395 2433 9.199982 CTTCAAAAATAATTTGATGTGAGCAGT 57.800 29.630 4.62 0.00 38.12 4.40
2396 2434 9.414295 TCTTCAAAAATAATTTGATGTGAGCAG 57.586 29.630 13.22 4.42 38.12 4.24
2397 2435 9.414295 CTCTTCAAAAATAATTTGATGTGAGCA 57.586 29.630 13.22 0.00 38.12 4.26
2398 2436 9.630098 TCTCTTCAAAAATAATTTGATGTGAGC 57.370 29.630 13.22 0.00 38.12 4.26
2446 2489 5.034852 TCCTTGATTGTGTCTTCTGTTGA 57.965 39.130 0.00 0.00 0.00 3.18
2447 2490 4.818546 ACTCCTTGATTGTGTCTTCTGTTG 59.181 41.667 0.00 0.00 0.00 3.33
2448 2491 5.041191 ACTCCTTGATTGTGTCTTCTGTT 57.959 39.130 0.00 0.00 0.00 3.16
2450 2493 4.635223 TGACTCCTTGATTGTGTCTTCTG 58.365 43.478 0.00 0.00 0.00 3.02
2614 2657 4.079253 ACCGCACCTGAAAATATGAAGTT 58.921 39.130 0.00 0.00 0.00 2.66
2660 2703 1.918262 TGCTCTGGTTTGAGGATCCAT 59.082 47.619 15.82 0.00 34.82 3.41
2741 2785 5.070847 AGGGCTCATTCACATTGTTTTCTTT 59.929 36.000 0.00 0.00 0.00 2.52
2742 2786 4.590222 AGGGCTCATTCACATTGTTTTCTT 59.410 37.500 0.00 0.00 0.00 2.52
2743 2787 4.154942 AGGGCTCATTCACATTGTTTTCT 58.845 39.130 0.00 0.00 0.00 2.52
2744 2788 4.525912 AGGGCTCATTCACATTGTTTTC 57.474 40.909 0.00 0.00 0.00 2.29
2745 2789 6.418057 TTTAGGGCTCATTCACATTGTTTT 57.582 33.333 0.00 0.00 0.00 2.43
2746 2790 6.418057 TTTTAGGGCTCATTCACATTGTTT 57.582 33.333 0.00 0.00 0.00 2.83
2747 2791 6.418057 TTTTTAGGGCTCATTCACATTGTT 57.582 33.333 0.00 0.00 0.00 2.83
2769 2813 8.352137 TCAGTATCATCCATTCACATTGTTTT 57.648 30.769 0.00 0.00 0.00 2.43
2827 2872 9.331282 CACCTCTTTATCCAGGTTAGAATTAAG 57.669 37.037 0.00 0.00 41.41 1.85


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

AutoCloner maintained by Alex Coulton.