Multiple sequence alignment - TraesCS4D01G300600

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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 TraesCS4D01G300600 chr4D 100.000 2983 0 0 1 2983 469101330 469104312 0.000000e+00 5509.0
1 TraesCS4D01G300600 chr4D 95.830 1199 20 2 1708 2894 414635005 414633825 0.000000e+00 1910.0
2 TraesCS4D01G300600 chr4D 100.000 310 0 0 3108 3417 469104437 469104746 1.060000e-159 573.0
3 TraesCS4D01G300600 chr4D 98.065 310 5 1 3108 3417 414633289 414632981 3.880000e-149 538.0
4 TraesCS4D01G300600 chr4D 97.849 93 2 0 1 93 469156895 469156987 9.810000e-36 161.0
5 TraesCS4D01G300600 chr1A 93.510 2373 85 13 639 2983 1315705 1318036 0.000000e+00 3465.0
6 TraesCS4D01G300600 chr1A 85.586 444 29 9 216 643 307059457 307059033 1.880000e-117 433.0
7 TraesCS4D01G300600 chr7D 98.197 1276 23 0 1708 2983 370965134 370963859 0.000000e+00 2230.0
8 TraesCS4D01G300600 chr7D 98.206 1059 15 4 643 1701 370966230 370965176 0.000000e+00 1847.0
9 TraesCS4D01G300600 chr6D 96.853 1271 18 4 1708 2978 81149435 81148187 0.000000e+00 2106.0
10 TraesCS4D01G300600 chr6D 98.687 1066 7 1 643 1701 81150542 81149477 0.000000e+00 1884.0
11 TraesCS4D01G300600 chr6D 98.680 1061 11 2 643 1701 469310012 469311071 0.000000e+00 1879.0
12 TraesCS4D01G300600 chr6D 79.268 246 33 15 138 373 100842421 100842184 4.570000e-34 156.0
13 TraesCS4D01G300600 chr7A 96.121 1289 37 2 1707 2983 652924722 652926009 0.000000e+00 2091.0
14 TraesCS4D01G300600 chr7A 94.357 1276 30 2 1708 2983 100754941 100753708 0.000000e+00 1919.0
15 TraesCS4D01G300600 chr7A 95.806 310 12 1 3108 3417 652926632 652926940 1.830000e-137 499.0
16 TraesCS4D01G300600 chr2D 96.160 1276 17 1 1708 2983 459831957 459833200 0.000000e+00 2056.0
17 TraesCS4D01G300600 chr2D 98.867 1059 11 1 643 1701 114802129 114803186 0.000000e+00 1888.0
18 TraesCS4D01G300600 chr2D 98.688 1067 9 4 638 1701 459830851 459831915 0.000000e+00 1888.0
19 TraesCS4D01G300600 chr2D 98.643 884 12 0 1708 2591 155548076 155547193 0.000000e+00 1567.0
20 TraesCS4D01G300600 chr2D 98.065 310 6 0 3108 3417 632022449 632022140 1.080000e-149 540.0
21 TraesCS4D01G300600 chr1D 96.965 1219 25 1 1777 2983 276512390 276511172 0.000000e+00 2036.0
22 TraesCS4D01G300600 chr1D 98.214 1064 16 2 641 1701 276513482 276512419 0.000000e+00 1857.0
23 TraesCS4D01G300600 chr1D 94.625 614 21 2 2360 2961 414457592 414456979 0.000000e+00 941.0
24 TraesCS4D01G300600 chr1D 98.710 310 4 0 3108 3417 276510691 276510382 4.980000e-153 551.0
25 TraesCS4D01G300600 chr1D 96.452 310 11 0 3108 3417 414456547 414456238 2.350000e-141 512.0
26 TraesCS4D01G300600 chr5D 96.555 1219 30 1 1777 2983 384157595 384158813 0.000000e+00 2008.0
27 TraesCS4D01G300600 chr5D 99.245 1059 8 0 643 1701 58672898 58671840 0.000000e+00 1912.0
28 TraesCS4D01G300600 chr5D 98.387 310 5 0 3108 3417 384159517 384159826 2.320000e-151 545.0
29 TraesCS4D01G300600 chr3D 93.972 1294 50 24 1708 2983 114396527 114395244 0.000000e+00 1932.0
30 TraesCS4D01G300600 chr3D 95.659 1221 19 3 1708 2927 595952586 595951399 0.000000e+00 1930.0
31 TraesCS4D01G300600 chr3D 98.777 1063 8 2 643 1701 114397630 114396569 0.000000e+00 1886.0
32 TraesCS4D01G300600 chr3D 98.496 1064 9 4 643 1701 406153653 406152592 0.000000e+00 1869.0
33 TraesCS4D01G300600 chr3D 95.943 419 17 0 2565 2983 114395613 114395195 0.000000e+00 680.0
34 TraesCS4D01G300600 chr6A 96.182 969 22 7 1708 2664 555216130 555215165 0.000000e+00 1570.0
35 TraesCS4D01G300600 chr6A 94.516 310 17 0 3108 3417 555214383 555214074 2.390000e-131 479.0
36 TraesCS4D01G300600 chr5B 95.091 937 24 11 1708 2644 74639785 74640699 0.000000e+00 1456.0
37 TraesCS4D01G300600 chr2B 88.046 527 47 3 133 643 470513564 470514090 8.110000e-171 610.0
38 TraesCS4D01G300600 chr2B 81.973 527 52 18 138 643 73632525 73632021 1.140000e-109 407.0
39 TraesCS4D01G300600 chr1B 87.833 526 48 8 133 642 268594319 268593794 1.360000e-168 603.0
40 TraesCS4D01G300600 chr1B 84.820 527 45 9 133 643 198754679 198755186 6.590000e-137 497.0
41 TraesCS4D01G300600 chr2A 85.579 527 41 9 133 643 261671313 261671820 1.410000e-143 520.0
42 TraesCS4D01G300600 chr2A 85.579 527 41 9 133 643 279502783 279503290 1.410000e-143 520.0
43 TraesCS4D01G300600 chr2A 95.793 309 13 0 3109 3417 624982766 624983074 1.830000e-137 499.0
44 TraesCS4D01G300600 chr7B 92.903 310 22 0 3108 3417 598646717 598646408 5.200000e-123 451.0
45 TraesCS4D01G300600 chr7B 79.923 518 77 16 138 643 689971492 689970990 4.190000e-94 355.0
46 TraesCS4D01G300600 chr4A 80.309 518 78 13 135 643 466142857 466143359 1.500000e-98 370.0
47 TraesCS4D01G300600 chr4A 93.333 60 4 0 34 93 2576540 2576481 4.700000e-14 89.8
48 TraesCS4D01G300600 chr3B 77.083 144 30 3 137 279 594662741 594662882 2.830000e-11 80.5


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 TraesCS4D01G300600 chr4D 469101330 469104746 3416 False 3041.000000 5509 100.000000 1 3417 2 chr4D.!!$F2 3416
1 TraesCS4D01G300600 chr4D 414632981 414635005 2024 True 1224.000000 1910 96.947500 1708 3417 2 chr4D.!!$R1 1709
2 TraesCS4D01G300600 chr1A 1315705 1318036 2331 False 3465.000000 3465 93.510000 639 2983 1 chr1A.!!$F1 2344
3 TraesCS4D01G300600 chr7D 370963859 370966230 2371 True 2038.500000 2230 98.201500 643 2983 2 chr7D.!!$R1 2340
4 TraesCS4D01G300600 chr6D 81148187 81150542 2355 True 1995.000000 2106 97.770000 643 2978 2 chr6D.!!$R2 2335
5 TraesCS4D01G300600 chr6D 469310012 469311071 1059 False 1879.000000 1879 98.680000 643 1701 1 chr6D.!!$F1 1058
6 TraesCS4D01G300600 chr7A 100753708 100754941 1233 True 1919.000000 1919 94.357000 1708 2983 1 chr7A.!!$R1 1275
7 TraesCS4D01G300600 chr7A 652924722 652926940 2218 False 1295.000000 2091 95.963500 1707 3417 2 chr7A.!!$F1 1710
8 TraesCS4D01G300600 chr2D 459830851 459833200 2349 False 1972.000000 2056 97.424000 638 2983 2 chr2D.!!$F2 2345
9 TraesCS4D01G300600 chr2D 114802129 114803186 1057 False 1888.000000 1888 98.867000 643 1701 1 chr2D.!!$F1 1058
10 TraesCS4D01G300600 chr2D 155547193 155548076 883 True 1567.000000 1567 98.643000 1708 2591 1 chr2D.!!$R1 883
11 TraesCS4D01G300600 chr1D 276510382 276513482 3100 True 1481.333333 2036 97.963000 641 3417 3 chr1D.!!$R1 2776
12 TraesCS4D01G300600 chr1D 414456238 414457592 1354 True 726.500000 941 95.538500 2360 3417 2 chr1D.!!$R2 1057
13 TraesCS4D01G300600 chr5D 58671840 58672898 1058 True 1912.000000 1912 99.245000 643 1701 1 chr5D.!!$R1 1058
14 TraesCS4D01G300600 chr5D 384157595 384159826 2231 False 1276.500000 2008 97.471000 1777 3417 2 chr5D.!!$F1 1640
15 TraesCS4D01G300600 chr3D 595951399 595952586 1187 True 1930.000000 1930 95.659000 1708 2927 1 chr3D.!!$R2 1219
16 TraesCS4D01G300600 chr3D 406152592 406153653 1061 True 1869.000000 1869 98.496000 643 1701 1 chr3D.!!$R1 1058
17 TraesCS4D01G300600 chr3D 114395195 114397630 2435 True 1499.333333 1932 96.230667 643 2983 3 chr3D.!!$R3 2340
18 TraesCS4D01G300600 chr6A 555214074 555216130 2056 True 1024.500000 1570 95.349000 1708 3417 2 chr6A.!!$R1 1709
19 TraesCS4D01G300600 chr5B 74639785 74640699 914 False 1456.000000 1456 95.091000 1708 2644 1 chr5B.!!$F1 936
20 TraesCS4D01G300600 chr2B 470513564 470514090 526 False 610.000000 610 88.046000 133 643 1 chr2B.!!$F1 510
21 TraesCS4D01G300600 chr2B 73632021 73632525 504 True 407.000000 407 81.973000 138 643 1 chr2B.!!$R1 505
22 TraesCS4D01G300600 chr1B 268593794 268594319 525 True 603.000000 603 87.833000 133 642 1 chr1B.!!$R1 509
23 TraesCS4D01G300600 chr1B 198754679 198755186 507 False 497.000000 497 84.820000 133 643 1 chr1B.!!$F1 510
24 TraesCS4D01G300600 chr2A 261671313 261671820 507 False 520.000000 520 85.579000 133 643 1 chr2A.!!$F1 510
25 TraesCS4D01G300600 chr2A 279502783 279503290 507 False 520.000000 520 85.579000 133 643 1 chr2A.!!$F2 510
26 TraesCS4D01G300600 chr7B 689970990 689971492 502 True 355.000000 355 79.923000 138 643 1 chr7B.!!$R2 505
27 TraesCS4D01G300600 chr4A 466142857 466143359 502 False 370.000000 370 80.309000 135 643 1 chr4A.!!$F1 508

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
193 194 0.249911 CCCGCAGTCCCTATGTAAGC 60.250 60.0 0.00 0.0 0.00 3.09 F
295 315 1.143305 CTGTGACAGAGAAGGTTGCG 58.857 55.0 6.79 0.0 32.44 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 2068 0.697658 TGTTCCAGACATGCCATCCA 59.302 50.000 0.00 0.0 32.0 3.41 R
2552 2650 7.446931 ACAACATAGTTAACATCATGACACCAA 59.553 33.333 16.95 0.0 0.0 3.67 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
22 23 4.671377 GGATTCGCAAAGCATGATAAACA 58.329 39.130 0.00 0.00 0.00 2.83
23 24 4.736793 GGATTCGCAAAGCATGATAAACAG 59.263 41.667 0.00 0.00 0.00 3.16
24 25 3.135414 TCGCAAAGCATGATAAACAGC 57.865 42.857 0.00 0.00 0.00 4.40
25 26 2.749076 TCGCAAAGCATGATAAACAGCT 59.251 40.909 0.00 0.00 35.62 4.24
26 27 3.191162 TCGCAAAGCATGATAAACAGCTT 59.809 39.130 0.00 0.00 41.19 3.74
27 28 4.394610 TCGCAAAGCATGATAAACAGCTTA 59.605 37.500 0.00 0.00 39.81 3.09
28 29 5.066375 TCGCAAAGCATGATAAACAGCTTAT 59.934 36.000 0.00 0.00 39.81 1.73
29 30 5.397534 CGCAAAGCATGATAAACAGCTTATC 59.602 40.000 0.00 0.00 44.35 1.75
39 40 7.194607 GATAAACAGCTTATCATGCTTAGCA 57.805 36.000 10.09 10.09 43.77 3.49
40 41 7.814642 GATAAACAGCTTATCATGCTTAGCAT 58.185 34.615 14.63 14.63 43.77 3.79
41 42 8.295288 GATAAACAGCTTATCATGCTTAGCATT 58.705 33.333 17.91 6.80 43.77 3.56
53 54 4.753233 TGCTTAGCATTGTGTTTGTTTGT 58.247 34.783 1.39 0.00 31.71 2.83
54 55 5.174395 TGCTTAGCATTGTGTTTGTTTGTT 58.826 33.333 1.39 0.00 31.71 2.83
55 56 6.333416 TGCTTAGCATTGTGTTTGTTTGTTA 58.667 32.000 1.39 0.00 31.71 2.41
56 57 6.983307 TGCTTAGCATTGTGTTTGTTTGTTAT 59.017 30.769 1.39 0.00 31.71 1.89
57 58 8.138074 TGCTTAGCATTGTGTTTGTTTGTTATA 58.862 29.630 1.39 0.00 31.71 0.98
58 59 8.424731 GCTTAGCATTGTGTTTGTTTGTTATAC 58.575 33.333 0.00 0.00 0.00 1.47
59 60 8.804688 TTAGCATTGTGTTTGTTTGTTATACC 57.195 30.769 0.00 0.00 0.00 2.73
60 61 6.810911 AGCATTGTGTTTGTTTGTTATACCA 58.189 32.000 0.00 0.00 0.00 3.25
61 62 7.441017 AGCATTGTGTTTGTTTGTTATACCAT 58.559 30.769 0.00 0.00 0.00 3.55
62 63 7.930865 AGCATTGTGTTTGTTTGTTATACCATT 59.069 29.630 0.00 0.00 0.00 3.16
63 64 8.555361 GCATTGTGTTTGTTTGTTATACCATTT 58.445 29.630 0.00 0.00 0.00 2.32
64 65 9.861138 CATTGTGTTTGTTTGTTATACCATTTG 57.139 29.630 0.00 0.00 0.00 2.32
65 66 8.425577 TTGTGTTTGTTTGTTATACCATTTGG 57.574 30.769 0.00 0.00 42.17 3.28
66 67 7.782049 TGTGTTTGTTTGTTATACCATTTGGA 58.218 30.769 3.01 0.00 38.94 3.53
67 68 8.258007 TGTGTTTGTTTGTTATACCATTTGGAA 58.742 29.630 3.01 0.00 38.94 3.53
68 69 9.099454 GTGTTTGTTTGTTATACCATTTGGAAA 57.901 29.630 3.01 0.00 38.94 3.13
69 70 9.667107 TGTTTGTTTGTTATACCATTTGGAAAA 57.333 25.926 3.01 0.00 38.94 2.29
71 72 9.892130 TTTGTTTGTTATACCATTTGGAAAAGT 57.108 25.926 3.01 0.00 38.94 2.66
78 79 9.550811 GTTATACCATTTGGAAAAGTAGAAACG 57.449 33.333 3.01 0.00 38.94 3.60
79 80 5.447624 ACCATTTGGAAAAGTAGAAACGG 57.552 39.130 3.01 0.00 38.94 4.44
80 81 4.891168 ACCATTTGGAAAAGTAGAAACGGT 59.109 37.500 3.01 0.00 38.94 4.83
81 82 5.219633 CCATTTGGAAAAGTAGAAACGGTG 58.780 41.667 0.00 0.00 37.39 4.94
82 83 3.974871 TTGGAAAAGTAGAAACGGTGC 57.025 42.857 0.00 0.00 0.00 5.01
83 84 3.202829 TGGAAAAGTAGAAACGGTGCT 57.797 42.857 0.00 0.00 0.00 4.40
84 85 3.547746 TGGAAAAGTAGAAACGGTGCTT 58.452 40.909 0.00 0.00 0.00 3.91
85 86 3.314080 TGGAAAAGTAGAAACGGTGCTTG 59.686 43.478 0.00 0.00 0.00 4.01
86 87 3.297472 GAAAAGTAGAAACGGTGCTTGC 58.703 45.455 0.00 0.00 0.00 4.01
87 88 2.256117 AAGTAGAAACGGTGCTTGCT 57.744 45.000 0.00 0.00 0.00 3.91
88 89 2.256117 AGTAGAAACGGTGCTTGCTT 57.744 45.000 0.00 0.00 0.00 3.91
89 90 2.572290 AGTAGAAACGGTGCTTGCTTT 58.428 42.857 0.00 0.00 0.00 3.51
90 91 3.735591 AGTAGAAACGGTGCTTGCTTTA 58.264 40.909 0.00 0.00 0.00 1.85
91 92 4.131596 AGTAGAAACGGTGCTTGCTTTAA 58.868 39.130 0.00 0.00 0.00 1.52
92 93 4.760204 AGTAGAAACGGTGCTTGCTTTAAT 59.240 37.500 0.00 0.00 0.00 1.40
93 94 4.160736 AGAAACGGTGCTTGCTTTAATC 57.839 40.909 0.00 0.00 0.00 1.75
94 95 3.821033 AGAAACGGTGCTTGCTTTAATCT 59.179 39.130 0.00 0.00 0.00 2.40
95 96 4.278419 AGAAACGGTGCTTGCTTTAATCTT 59.722 37.500 0.00 0.00 0.00 2.40
96 97 4.584327 AACGGTGCTTGCTTTAATCTTT 57.416 36.364 0.00 0.00 0.00 2.52
97 98 5.699097 AACGGTGCTTGCTTTAATCTTTA 57.301 34.783 0.00 0.00 0.00 1.85
98 99 5.043189 ACGGTGCTTGCTTTAATCTTTAC 57.957 39.130 0.00 0.00 0.00 2.01
99 100 4.082949 ACGGTGCTTGCTTTAATCTTTACC 60.083 41.667 0.00 0.00 0.00 2.85
100 101 4.156008 CGGTGCTTGCTTTAATCTTTACCT 59.844 41.667 0.00 0.00 0.00 3.08
101 102 5.641709 GGTGCTTGCTTTAATCTTTACCTC 58.358 41.667 0.00 0.00 0.00 3.85
102 103 5.416013 GGTGCTTGCTTTAATCTTTACCTCT 59.584 40.000 0.00 0.00 0.00 3.69
103 104 6.071896 GGTGCTTGCTTTAATCTTTACCTCTT 60.072 38.462 0.00 0.00 0.00 2.85
104 105 7.371159 GTGCTTGCTTTAATCTTTACCTCTTT 58.629 34.615 0.00 0.00 0.00 2.52
105 106 8.512138 GTGCTTGCTTTAATCTTTACCTCTTTA 58.488 33.333 0.00 0.00 0.00 1.85
106 107 9.243105 TGCTTGCTTTAATCTTTACCTCTTTAT 57.757 29.630 0.00 0.00 0.00 1.40
107 108 9.723447 GCTTGCTTTAATCTTTACCTCTTTATC 57.277 33.333 0.00 0.00 0.00 1.75
147 148 7.075674 AGAAAATTGGACAGTTTTGCAAAAG 57.924 32.000 24.46 16.03 31.68 2.27
193 194 0.249911 CCCGCAGTCCCTATGTAAGC 60.250 60.000 0.00 0.00 0.00 3.09
204 207 3.119316 CCCTATGTAAGCGGATCTAGCAG 60.119 52.174 14.28 3.92 37.01 4.24
214 217 3.304257 CGGATCTAGCAGAACGATTCAG 58.696 50.000 0.00 0.00 32.70 3.02
239 242 7.882271 AGTTTTGCAAATTAATCCCTGCATTTA 59.118 29.630 13.65 4.26 43.83 1.40
277 282 4.446371 CGCTCCTTTGTTCATCTTATCCT 58.554 43.478 0.00 0.00 0.00 3.24
279 284 5.189180 GCTCCTTTGTTCATCTTATCCTGT 58.811 41.667 0.00 0.00 0.00 4.00
281 286 6.373005 TCCTTTGTTCATCTTATCCTGTGA 57.627 37.500 0.00 0.00 0.00 3.58
286 291 5.970592 TGTTCATCTTATCCTGTGACAGAG 58.029 41.667 15.33 3.26 32.44 3.35
291 311 4.678256 TCTTATCCTGTGACAGAGAAGGT 58.322 43.478 15.33 0.00 32.44 3.50
295 315 1.143305 CTGTGACAGAGAAGGTTGCG 58.857 55.000 6.79 0.00 32.44 4.85
377 401 1.602237 CCCCATGTAGGTGCGTCTT 59.398 57.895 0.00 0.00 34.66 3.01
389 413 1.734465 GTGCGTCTTCATTCCCAAGAG 59.266 52.381 0.00 0.00 30.32 2.85
414 438 4.671590 TCCCCTGTGCTCGTCGGA 62.672 66.667 0.00 0.00 0.00 4.55
550 591 4.373116 ACATGGACGCCGCGAAGT 62.373 61.111 21.79 6.96 0.00 3.01
1970 2068 0.740737 GGATTGCCAGCGTGCTAATT 59.259 50.000 0.00 0.00 0.00 1.40
2552 2650 8.451908 AACTATGTCTTGTAAGCTTTGAACTT 57.548 30.769 3.20 0.00 0.00 2.66
2793 3174 8.685257 ATGGAATGAGGATATGTTGGATACTA 57.315 34.615 0.00 0.00 37.61 1.82
2796 3177 8.762645 GGAATGAGGATATGTTGGATACTATCA 58.237 37.037 0.00 0.00 37.61 2.15
2889 4832 8.169977 TGATCAAATTAGGTTATCTTGGATGC 57.830 34.615 0.00 0.00 0.00 3.91
2891 4834 6.430864 TCAAATTAGGTTATCTTGGATGCCA 58.569 36.000 0.00 0.00 0.00 4.92
3136 5288 4.753662 ACGCCGAGGCACCCTAGA 62.754 66.667 15.03 0.00 42.06 2.43
3155 5307 8.606830 ACCCTAGATGATCAAATTAGGTTATCC 58.393 37.037 20.38 0.00 31.06 2.59
3292 6199 6.653020 AGCCACATTCATCACACTTATTAGA 58.347 36.000 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.671377 TGTTTATCATGCTTTGCGAATCC 58.329 39.130 0.00 0.00 0.00 3.01
1 2 4.205792 GCTGTTTATCATGCTTTGCGAATC 59.794 41.667 0.00 0.00 0.00 2.52
3 4 3.191162 AGCTGTTTATCATGCTTTGCGAA 59.809 39.130 0.00 0.00 30.56 4.70
6 7 6.744550 GATAAGCTGTTTATCATGCTTTGC 57.255 37.500 16.37 0.00 44.66 3.68
15 16 7.194607 TGCTAAGCATGATAAGCTGTTTATC 57.805 36.000 14.93 14.93 42.53 1.75
31 32 4.753233 ACAAACAAACACAATGCTAAGCA 58.247 34.783 0.00 0.00 44.86 3.91
32 33 5.717038 AACAAACAAACACAATGCTAAGC 57.283 34.783 0.00 0.00 0.00 3.09
33 34 8.911662 GGTATAACAAACAAACACAATGCTAAG 58.088 33.333 0.00 0.00 0.00 2.18
34 35 8.414003 TGGTATAACAAACAAACACAATGCTAA 58.586 29.630 0.00 0.00 0.00 3.09
35 36 7.941919 TGGTATAACAAACAAACACAATGCTA 58.058 30.769 0.00 0.00 0.00 3.49
36 37 6.810911 TGGTATAACAAACAAACACAATGCT 58.189 32.000 0.00 0.00 0.00 3.79
37 38 7.650834 ATGGTATAACAAACAAACACAATGC 57.349 32.000 0.00 0.00 0.00 3.56
38 39 9.861138 CAAATGGTATAACAAACAAACACAATG 57.139 29.630 0.00 0.00 0.00 2.82
39 40 9.050601 CCAAATGGTATAACAAACAAACACAAT 57.949 29.630 0.00 0.00 0.00 2.71
40 41 8.258007 TCCAAATGGTATAACAAACAAACACAA 58.742 29.630 0.00 0.00 36.34 3.33
41 42 7.782049 TCCAAATGGTATAACAAACAAACACA 58.218 30.769 0.00 0.00 36.34 3.72
42 43 8.649973 TTCCAAATGGTATAACAAACAAACAC 57.350 30.769 0.00 0.00 36.34 3.32
43 44 9.667107 TTTTCCAAATGGTATAACAAACAAACA 57.333 25.926 0.00 0.00 36.34 2.83
45 46 9.892130 ACTTTTCCAAATGGTATAACAAACAAA 57.108 25.926 0.00 0.00 36.34 2.83
52 53 9.550811 CGTTTCTACTTTTCCAAATGGTATAAC 57.449 33.333 0.00 0.00 36.34 1.89
53 54 8.732531 CCGTTTCTACTTTTCCAAATGGTATAA 58.267 33.333 0.00 0.00 32.38 0.98
54 55 7.884354 ACCGTTTCTACTTTTCCAAATGGTATA 59.116 33.333 5.52 0.00 43.36 1.47
55 56 6.717997 ACCGTTTCTACTTTTCCAAATGGTAT 59.282 34.615 5.52 0.00 43.36 2.73
56 57 6.016943 CACCGTTTCTACTTTTCCAAATGGTA 60.017 38.462 6.79 0.00 43.34 3.25
57 58 4.891168 ACCGTTTCTACTTTTCCAAATGGT 59.109 37.500 0.00 1.99 41.37 3.55
58 59 5.219633 CACCGTTTCTACTTTTCCAAATGG 58.780 41.667 0.00 0.00 39.75 3.16
59 60 4.679654 GCACCGTTTCTACTTTTCCAAATG 59.320 41.667 0.00 0.00 0.00 2.32
60 61 4.583073 AGCACCGTTTCTACTTTTCCAAAT 59.417 37.500 0.00 0.00 0.00 2.32
61 62 3.949113 AGCACCGTTTCTACTTTTCCAAA 59.051 39.130 0.00 0.00 0.00 3.28
62 63 3.547746 AGCACCGTTTCTACTTTTCCAA 58.452 40.909 0.00 0.00 0.00 3.53
63 64 3.202829 AGCACCGTTTCTACTTTTCCA 57.797 42.857 0.00 0.00 0.00 3.53
64 65 3.852205 GCAAGCACCGTTTCTACTTTTCC 60.852 47.826 0.00 0.00 0.00 3.13
65 66 3.003378 AGCAAGCACCGTTTCTACTTTTC 59.997 43.478 0.00 0.00 0.00 2.29
66 67 2.949644 AGCAAGCACCGTTTCTACTTTT 59.050 40.909 0.00 0.00 0.00 2.27
67 68 2.572290 AGCAAGCACCGTTTCTACTTT 58.428 42.857 0.00 0.00 0.00 2.66
68 69 2.256117 AGCAAGCACCGTTTCTACTT 57.744 45.000 0.00 0.00 0.00 2.24
69 70 2.256117 AAGCAAGCACCGTTTCTACT 57.744 45.000 0.00 0.00 0.00 2.57
70 71 4.477302 TTAAAGCAAGCACCGTTTCTAC 57.523 40.909 0.00 0.00 0.00 2.59
71 72 5.001232 AGATTAAAGCAAGCACCGTTTCTA 58.999 37.500 0.00 0.00 0.00 2.10
72 73 3.821033 AGATTAAAGCAAGCACCGTTTCT 59.179 39.130 0.00 0.00 0.00 2.52
73 74 4.160736 AGATTAAAGCAAGCACCGTTTC 57.839 40.909 0.00 0.00 0.00 2.78
74 75 4.584327 AAGATTAAAGCAAGCACCGTTT 57.416 36.364 0.00 0.00 0.00 3.60
75 76 4.584327 AAAGATTAAAGCAAGCACCGTT 57.416 36.364 0.00 0.00 0.00 4.44
76 77 4.082949 GGTAAAGATTAAAGCAAGCACCGT 60.083 41.667 0.00 0.00 0.00 4.83
77 78 4.156008 AGGTAAAGATTAAAGCAAGCACCG 59.844 41.667 0.00 0.00 0.00 4.94
78 79 5.416013 AGAGGTAAAGATTAAAGCAAGCACC 59.584 40.000 0.00 0.00 0.00 5.01
79 80 6.502136 AGAGGTAAAGATTAAAGCAAGCAC 57.498 37.500 0.00 0.00 0.00 4.40
80 81 7.524717 AAAGAGGTAAAGATTAAAGCAAGCA 57.475 32.000 0.00 0.00 0.00 3.91
81 82 9.723447 GATAAAGAGGTAAAGATTAAAGCAAGC 57.277 33.333 0.00 0.00 0.00 4.01
111 112 9.100197 ACTGTCCAATTTTCTTTATTATTGGGT 57.900 29.630 11.54 1.53 44.52 4.51
112 113 9.942850 AACTGTCCAATTTTCTTTATTATTGGG 57.057 29.630 11.54 1.01 44.52 4.12
117 118 9.823647 TGCAAAACTGTCCAATTTTCTTTATTA 57.176 25.926 0.00 0.00 0.00 0.98
118 119 8.729805 TGCAAAACTGTCCAATTTTCTTTATT 57.270 26.923 0.00 0.00 0.00 1.40
119 120 8.729805 TTGCAAAACTGTCCAATTTTCTTTAT 57.270 26.923 0.00 0.00 0.00 1.40
120 121 8.553459 TTTGCAAAACTGTCCAATTTTCTTTA 57.447 26.923 10.02 0.00 0.00 1.85
121 122 7.446001 TTTGCAAAACTGTCCAATTTTCTTT 57.554 28.000 10.02 0.00 0.00 2.52
122 123 7.390162 TCTTTTGCAAAACTGTCCAATTTTCTT 59.610 29.630 20.46 0.00 0.00 2.52
123 124 6.878389 TCTTTTGCAAAACTGTCCAATTTTCT 59.122 30.769 20.46 0.00 0.00 2.52
124 125 7.071014 TCTTTTGCAAAACTGTCCAATTTTC 57.929 32.000 20.46 0.00 0.00 2.29
125 126 6.654582 ACTCTTTTGCAAAACTGTCCAATTTT 59.345 30.769 20.46 0.00 0.00 1.82
126 127 6.172630 ACTCTTTTGCAAAACTGTCCAATTT 58.827 32.000 20.46 0.00 0.00 1.82
127 128 5.733676 ACTCTTTTGCAAAACTGTCCAATT 58.266 33.333 20.46 0.00 0.00 2.32
128 129 5.343307 ACTCTTTTGCAAAACTGTCCAAT 57.657 34.783 20.46 0.00 0.00 3.16
129 130 4.381505 GGACTCTTTTGCAAAACTGTCCAA 60.382 41.667 36.40 16.58 40.76 3.53
130 131 3.130340 GGACTCTTTTGCAAAACTGTCCA 59.870 43.478 36.40 17.12 40.76 4.02
131 132 3.490933 GGGACTCTTTTGCAAAACTGTCC 60.491 47.826 35.25 35.25 40.57 4.02
147 148 9.847224 TTCAATTATCTAAAACCATAGGGACTC 57.153 33.333 0.00 0.00 41.75 3.36
193 194 3.243234 ACTGAATCGTTCTGCTAGATCCG 60.243 47.826 0.00 0.00 32.51 4.18
204 207 8.162245 GGATTAATTTGCAAAACTGAATCGTTC 58.838 33.333 17.19 6.78 0.00 3.95
239 242 1.063488 GCGCGGGCGAAATTGTTAT 59.937 52.632 18.30 0.00 42.83 1.89
277 282 0.880278 GCGCAACCTTCTCTGTCACA 60.880 55.000 0.30 0.00 0.00 3.58
279 284 0.319900 GAGCGCAACCTTCTCTGTCA 60.320 55.000 11.47 0.00 0.00 3.58
281 286 1.373497 CGAGCGCAACCTTCTCTGT 60.373 57.895 11.47 0.00 0.00 3.41
286 291 2.430244 TCGACGAGCGCAACCTTC 60.430 61.111 11.47 0.00 40.61 3.46
363 384 2.420129 GGGAATGAAGACGCACCTACAT 60.420 50.000 0.00 0.00 0.00 2.29
377 401 0.469917 GATCGGGCTCTTGGGAATGA 59.530 55.000 0.00 0.00 0.00 2.57
389 413 4.554036 GCACAGGGGAGATCGGGC 62.554 72.222 0.00 0.00 0.00 6.13
579 620 4.210093 TTGACCACGTCCGTGCGT 62.210 61.111 14.06 12.77 46.88 5.24
595 636 2.688666 TGCTCGATCCCCTGCCTT 60.689 61.111 0.00 0.00 0.00 4.35
916 966 0.535102 GAGGGGCGAGAGAGAGAGAG 60.535 65.000 0.00 0.00 0.00 3.20
917 967 0.986019 AGAGGGGCGAGAGAGAGAGA 60.986 60.000 0.00 0.00 0.00 3.10
1701 1762 9.062524 ACAGCATACTACACTGAATTTTTAACA 57.937 29.630 0.00 0.00 35.38 2.41
1702 1763 9.893305 AACAGCATACTACACTGAATTTTTAAC 57.107 29.630 0.00 0.00 35.38 2.01
1970 2068 0.697658 TGTTCCAGACATGCCATCCA 59.302 50.000 0.00 0.00 32.00 3.41
2552 2650 7.446931 ACAACATAGTTAACATCATGACACCAA 59.553 33.333 16.95 0.00 0.00 3.67
2793 3174 0.968901 TAGGGTGCCTCGACGTTGAT 60.969 55.000 5.82 0.00 34.61 2.57
2796 3177 0.683504 ATCTAGGGTGCCTCGACGTT 60.684 55.000 0.00 0.00 34.61 3.99
3118 5061 4.208686 CTAGGGTGCCTCGGCGTC 62.209 72.222 6.85 0.00 45.51 5.19
3119 5062 4.753662 TCTAGGGTGCCTCGGCGT 62.754 66.667 6.85 0.00 45.51 5.68
3120 5063 3.227276 ATCTAGGGTGCCTCGGCG 61.227 66.667 0.00 0.00 45.51 6.46
3121 5064 1.476007 ATCATCTAGGGTGCCTCGGC 61.476 60.000 0.00 0.00 42.35 5.54
3122 5065 0.605589 GATCATCTAGGGTGCCTCGG 59.394 60.000 0.00 0.00 34.61 4.63
3136 5288 7.395489 GCATCCAGGATAACCTAATTTGATCAT 59.605 37.037 0.00 0.00 45.94 2.45
3292 6199 8.646900 TGTGGCTCCTAATTTTCTTATTGTTTT 58.353 29.630 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.