Multiple sequence alignment - TraesCS7A01G265000

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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 TraesCS7A01G265000 chr7A 100.000 3161 0 0 1 3161 264859888 264856728 0.000000e+00 5838
1 TraesCS7A01G265000 chr7A 80.000 185 25 3 12 185 483258934 483258751 3.310000e-25 126
2 TraesCS7A01G265000 chr7D 94.272 2933 112 17 251 3161 247327418 247324520 0.000000e+00 4434
3 TraesCS7A01G265000 chr7D 84.181 354 50 6 2681 3030 247324632 247324281 3.910000e-89 339
4 TraesCS7A01G265000 chr7B 96.978 2614 74 4 296 2905 223757924 223755312 0.000000e+00 4385
5 TraesCS7A01G265000 chr7B 96.310 271 9 1 2891 3161 223755296 223755027 8.050000e-121 444
6 TraesCS7A01G265000 chr3A 81.098 164 29 2 84 246 58776969 58776807 2.560000e-26 130
7 TraesCS7A01G265000 chr3B 80.982 163 29 2 84 246 511765180 511765340 9.200000e-26 128
8 TraesCS7A01G265000 chr6D 80.982 163 27 4 85 246 427102866 427103025 3.310000e-25 126
9 TraesCS7A01G265000 chr5D 80.588 170 27 6 84 250 174728337 174728503 3.310000e-25 126
10 TraesCS7A01G265000 chr5D 80.982 163 27 4 85 246 302051043 302051202 3.310000e-25 126
11 TraesCS7A01G265000 chr5D 80.864 162 29 2 85 246 478147318 478147477 3.310000e-25 126
12 TraesCS7A01G265000 chr5D 80.864 162 29 2 85 246 486038810 486038651 3.310000e-25 126
13 TraesCS7A01G265000 chr4D 80.982 163 27 4 85 246 254473255 254473096 3.310000e-25 126
14 TraesCS7A01G265000 chr3D 80.723 166 28 4 85 249 414442744 414442582 3.310000e-25 126


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 TraesCS7A01G265000 chr7A 264856728 264859888 3160 True 5838.0 5838 100.0000 1 3161 1 chr7A.!!$R1 3160
1 TraesCS7A01G265000 chr7D 247324281 247327418 3137 True 2386.5 4434 89.2265 251 3161 2 chr7D.!!$R1 2910
2 TraesCS7A01G265000 chr7B 223755027 223757924 2897 True 2414.5 4385 96.6440 296 3161 2 chr7B.!!$R1 2865

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
293 294 0.313672 GAGCATTTGTTCGGCAACCA 59.686 50.0 0.00 0.0 36.72 3.67 F
1134 1139 0.035176 ATGCAAAAACGGGCAATGCT 59.965 45.0 4.82 0.0 44.20 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1400 1405 0.250081 GAGGGCAGCTACAGTATGGC 60.250 60.0 0.00 0.04 43.62 4.40 R
2799 2824 0.108424 GGTAGCTCTCACACAGCTGG 60.108 60.0 19.93 9.66 46.99 4.85 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
24 25 6.874288 TGCCCAAATCAAAAATAAACAAGG 57.126 33.333 0.00 0.00 0.00 3.61
25 26 5.767168 TGCCCAAATCAAAAATAAACAAGGG 59.233 36.000 0.00 0.00 34.56 3.95
26 27 6.252967 CCCAAATCAAAAATAAACAAGGGC 57.747 37.500 0.00 0.00 0.00 5.19
27 28 5.767168 CCCAAATCAAAAATAAACAAGGGCA 59.233 36.000 0.00 0.00 0.00 5.36
28 29 6.264067 CCCAAATCAAAAATAAACAAGGGCAA 59.736 34.615 0.00 0.00 0.00 4.52
29 30 7.039853 CCCAAATCAAAAATAAACAAGGGCAAT 60.040 33.333 0.00 0.00 0.00 3.56
30 31 8.358895 CCAAATCAAAAATAAACAAGGGCAATT 58.641 29.630 0.00 0.00 0.00 2.32
31 32 9.747293 CAAATCAAAAATAAACAAGGGCAATTT 57.253 25.926 0.00 0.00 0.00 1.82
33 34 9.747293 AATCAAAAATAAACAAGGGCAATTTTG 57.253 25.926 0.00 0.00 37.68 2.44
34 35 7.710896 TCAAAAATAAACAAGGGCAATTTTGG 58.289 30.769 0.00 0.00 37.21 3.28
35 36 7.557719 TCAAAAATAAACAAGGGCAATTTTGGA 59.442 29.630 0.00 0.00 37.21 3.53
36 37 7.509141 AAAATAAACAAGGGCAATTTTGGAG 57.491 32.000 0.00 0.00 30.69 3.86
37 38 5.823861 ATAAACAAGGGCAATTTTGGAGT 57.176 34.783 0.00 0.00 0.00 3.85
38 39 4.502105 AAACAAGGGCAATTTTGGAGTT 57.498 36.364 0.00 0.00 0.00 3.01
39 40 4.502105 AACAAGGGCAATTTTGGAGTTT 57.498 36.364 0.00 0.00 0.00 2.66
40 41 4.071961 ACAAGGGCAATTTTGGAGTTTC 57.928 40.909 0.00 0.00 0.00 2.78
41 42 3.454082 ACAAGGGCAATTTTGGAGTTTCA 59.546 39.130 0.00 0.00 0.00 2.69
42 43 4.080638 ACAAGGGCAATTTTGGAGTTTCAA 60.081 37.500 0.00 0.00 0.00 2.69
43 44 4.769345 AGGGCAATTTTGGAGTTTCAAA 57.231 36.364 0.00 0.00 35.15 2.69
44 45 5.109500 AGGGCAATTTTGGAGTTTCAAAA 57.891 34.783 1.06 1.06 46.42 2.44
45 46 5.125356 AGGGCAATTTTGGAGTTTCAAAAG 58.875 37.500 4.77 0.00 45.84 2.27
46 47 5.104569 AGGGCAATTTTGGAGTTTCAAAAGA 60.105 36.000 4.77 0.00 45.84 2.52
47 48 5.588246 GGGCAATTTTGGAGTTTCAAAAGAA 59.412 36.000 4.77 0.00 45.84 2.52
48 49 6.238456 GGGCAATTTTGGAGTTTCAAAAGAAG 60.238 38.462 4.77 0.00 45.84 2.85
49 50 6.538381 GGCAATTTTGGAGTTTCAAAAGAAGA 59.462 34.615 4.77 0.00 45.84 2.87
50 51 7.227314 GGCAATTTTGGAGTTTCAAAAGAAGAT 59.773 33.333 4.77 0.00 45.84 2.40
51 52 8.066000 GCAATTTTGGAGTTTCAAAAGAAGATG 58.934 33.333 4.77 1.26 45.84 2.90
52 53 8.553696 CAATTTTGGAGTTTCAAAAGAAGATGG 58.446 33.333 4.77 0.00 45.84 3.51
53 54 6.790232 TTTGGAGTTTCAAAAGAAGATGGT 57.210 33.333 0.00 0.00 34.17 3.55
54 55 6.790232 TTGGAGTTTCAAAAGAAGATGGTT 57.210 33.333 0.00 0.00 0.00 3.67
55 56 6.391227 TGGAGTTTCAAAAGAAGATGGTTC 57.609 37.500 0.00 0.00 0.00 3.62
56 57 5.890985 TGGAGTTTCAAAAGAAGATGGTTCA 59.109 36.000 0.00 0.00 0.00 3.18
57 58 6.379703 TGGAGTTTCAAAAGAAGATGGTTCAA 59.620 34.615 0.00 0.00 0.00 2.69
58 59 7.069826 TGGAGTTTCAAAAGAAGATGGTTCAAT 59.930 33.333 0.00 0.00 0.00 2.57
59 60 7.596621 GGAGTTTCAAAAGAAGATGGTTCAATC 59.403 37.037 0.00 0.00 0.00 2.67
60 61 7.141363 AGTTTCAAAAGAAGATGGTTCAATCG 58.859 34.615 0.00 0.00 0.00 3.34
61 62 6.875948 TTCAAAAGAAGATGGTTCAATCGA 57.124 33.333 0.00 0.00 0.00 3.59
62 63 7.452880 TTCAAAAGAAGATGGTTCAATCGAT 57.547 32.000 0.00 0.00 0.00 3.59
63 64 7.076842 TCAAAAGAAGATGGTTCAATCGATC 57.923 36.000 0.00 0.00 0.00 3.69
64 65 6.654582 TCAAAAGAAGATGGTTCAATCGATCA 59.345 34.615 0.00 0.00 0.00 2.92
65 66 6.674694 AAAGAAGATGGTTCAATCGATCAG 57.325 37.500 0.00 0.00 0.00 2.90
66 67 4.701765 AGAAGATGGTTCAATCGATCAGG 58.298 43.478 0.00 0.00 0.00 3.86
67 68 3.482156 AGATGGTTCAATCGATCAGGG 57.518 47.619 0.00 0.00 0.00 4.45
68 69 3.041211 AGATGGTTCAATCGATCAGGGA 58.959 45.455 0.00 0.00 0.00 4.20
69 70 3.455910 AGATGGTTCAATCGATCAGGGAA 59.544 43.478 0.00 0.00 0.00 3.97
70 71 3.712016 TGGTTCAATCGATCAGGGAAA 57.288 42.857 0.00 0.00 0.00 3.13
71 72 4.235079 TGGTTCAATCGATCAGGGAAAT 57.765 40.909 0.00 0.00 0.00 2.17
72 73 4.599041 TGGTTCAATCGATCAGGGAAATT 58.401 39.130 0.00 0.00 0.00 1.82
73 74 5.016173 TGGTTCAATCGATCAGGGAAATTT 58.984 37.500 0.00 0.00 0.00 1.82
74 75 6.184068 TGGTTCAATCGATCAGGGAAATTTA 58.816 36.000 0.00 0.00 0.00 1.40
75 76 6.833416 TGGTTCAATCGATCAGGGAAATTTAT 59.167 34.615 0.00 0.00 0.00 1.40
76 77 7.996066 TGGTTCAATCGATCAGGGAAATTTATA 59.004 33.333 0.00 0.00 0.00 0.98
77 78 8.290325 GGTTCAATCGATCAGGGAAATTTATAC 58.710 37.037 0.00 0.00 0.00 1.47
78 79 9.057089 GTTCAATCGATCAGGGAAATTTATACT 57.943 33.333 0.00 0.00 0.00 2.12
84 85 9.760077 TCGATCAGGGAAATTTATACTAAAGTC 57.240 33.333 0.00 0.00 0.00 3.01
85 86 8.989980 CGATCAGGGAAATTTATACTAAAGTCC 58.010 37.037 0.00 4.62 0.00 3.85
86 87 8.904099 ATCAGGGAAATTTATACTAAAGTCCG 57.096 34.615 0.00 0.00 0.00 4.79
87 88 8.081517 TCAGGGAAATTTATACTAAAGTCCGA 57.918 34.615 0.00 0.00 0.00 4.55
88 89 8.542080 TCAGGGAAATTTATACTAAAGTCCGAA 58.458 33.333 0.00 0.00 0.00 4.30
89 90 8.610035 CAGGGAAATTTATACTAAAGTCCGAAC 58.390 37.037 0.00 0.00 0.00 3.95
90 91 8.323567 AGGGAAATTTATACTAAAGTCCGAACA 58.676 33.333 0.00 0.00 0.00 3.18
91 92 9.117183 GGGAAATTTATACTAAAGTCCGAACAT 57.883 33.333 0.00 0.00 0.00 2.71
168 169 8.912988 AGAGTTTAAACAGGTTTTGAATCATCA 58.087 29.630 20.06 0.00 34.23 3.07
169 170 9.696917 GAGTTTAAACAGGTTTTGAATCATCAT 57.303 29.630 20.06 0.00 34.96 2.45
241 242 7.919313 TTACTGTAGCTTAATTATTCGGTCG 57.081 36.000 0.00 0.00 0.00 4.79
242 243 5.899299 ACTGTAGCTTAATTATTCGGTCGT 58.101 37.500 0.00 0.00 0.00 4.34
243 244 5.975939 ACTGTAGCTTAATTATTCGGTCGTC 59.024 40.000 0.00 0.00 0.00 4.20
244 245 5.893687 TGTAGCTTAATTATTCGGTCGTCA 58.106 37.500 0.00 0.00 0.00 4.35
245 246 5.745294 TGTAGCTTAATTATTCGGTCGTCAC 59.255 40.000 0.00 0.00 0.00 3.67
246 247 4.117685 AGCTTAATTATTCGGTCGTCACC 58.882 43.478 0.00 0.00 39.69 4.02
247 248 4.117685 GCTTAATTATTCGGTCGTCACCT 58.882 43.478 0.00 0.00 41.17 4.00
248 249 4.569564 GCTTAATTATTCGGTCGTCACCTT 59.430 41.667 0.00 0.00 41.17 3.50
249 250 5.276726 GCTTAATTATTCGGTCGTCACCTTC 60.277 44.000 0.00 0.00 41.17 3.46
259 260 1.274167 TCGTCACCTTCATAAAGCGGT 59.726 47.619 0.00 0.00 0.00 5.68
261 262 2.601763 CGTCACCTTCATAAAGCGGTAC 59.398 50.000 0.00 0.00 0.00 3.34
278 279 3.602483 GGTACGATTACCCAAAAGAGCA 58.398 45.455 0.00 0.00 42.05 4.26
279 280 4.196971 GGTACGATTACCCAAAAGAGCAT 58.803 43.478 0.00 0.00 42.05 3.79
283 284 4.522789 ACGATTACCCAAAAGAGCATTTGT 59.477 37.500 0.00 0.00 38.37 2.83
285 286 5.572896 CGATTACCCAAAAGAGCATTTGTTC 59.427 40.000 8.28 0.00 38.37 3.18
286 287 3.369546 ACCCAAAAGAGCATTTGTTCG 57.630 42.857 8.28 0.00 38.37 3.95
287 288 2.035832 ACCCAAAAGAGCATTTGTTCGG 59.964 45.455 8.28 5.77 38.37 4.30
288 289 2.061028 CCAAAAGAGCATTTGTTCGGC 58.939 47.619 8.28 0.00 38.37 5.54
289 290 2.545532 CCAAAAGAGCATTTGTTCGGCA 60.546 45.455 8.28 0.00 38.37 5.69
291 292 2.422276 AAGAGCATTTGTTCGGCAAC 57.578 45.000 0.00 0.00 36.72 4.17
292 293 0.598065 AGAGCATTTGTTCGGCAACC 59.402 50.000 0.00 0.00 36.72 3.77
293 294 0.313672 GAGCATTTGTTCGGCAACCA 59.686 50.000 0.00 0.00 36.72 3.67
308 312 3.615056 GGCAACCAAACACACTTACAAAC 59.385 43.478 0.00 0.00 0.00 2.93
316 320 3.284617 ACACACTTACAAACCCTGAACC 58.715 45.455 0.00 0.00 0.00 3.62
598 602 0.384309 CCTTCGTATGGACAGCGCTA 59.616 55.000 10.99 0.00 0.00 4.26
626 630 4.680537 ACTCCCAGTCGGACGCCT 62.681 66.667 1.89 0.00 34.86 5.52
709 713 1.070134 CTCACCTTCACCGTTTCCTCA 59.930 52.381 0.00 0.00 0.00 3.86
961 965 1.375268 GCGTGCAGAGGAGCTCTTT 60.375 57.895 14.64 1.93 38.99 2.52
1084 1089 1.332195 GGCAAAGGGAGCAGAAAACT 58.668 50.000 0.00 0.00 0.00 2.66
1089 1094 0.321996 AGGGAGCAGAAAACTCGGTC 59.678 55.000 0.00 0.00 34.87 4.79
1125 1130 5.422666 TGATATCTGGCTATGCAAAAACG 57.577 39.130 3.98 0.00 0.00 3.60
1134 1139 0.035176 ATGCAAAAACGGGCAATGCT 59.965 45.000 4.82 0.00 44.20 3.79
1312 1317 6.821665 GCCAAACCACACTACAATCTCTATTA 59.178 38.462 0.00 0.00 0.00 0.98
1385 1390 6.611613 ACAGGATTATGTGGATCGTCATAT 57.388 37.500 8.55 0.00 30.46 1.78
1398 1403 6.767423 TGGATCGTCATATGATGTTGTTGAAT 59.233 34.615 21.55 8.40 33.00 2.57
1400 1405 8.438513 GGATCGTCATATGATGTTGTTGAATAG 58.561 37.037 21.55 0.00 33.00 1.73
1521 1526 7.811653 TCTGTTATAGTTCTATGATCTCTGCG 58.188 38.462 0.00 0.00 0.00 5.18
1590 1595 2.183478 TGTGTGACAATGGCTTCGAT 57.817 45.000 0.00 0.00 0.00 3.59
1836 1841 0.109723 TTTGGGGCGCTCTGTTAAGT 59.890 50.000 7.48 0.00 0.00 2.24
1860 1865 4.870991 GCCTGTAGGACTTACTCAAATGTC 59.129 45.833 1.17 0.00 37.39 3.06
2138 2143 4.517285 GAGCTCAAGGATCATGGTTACAA 58.483 43.478 9.40 0.00 0.00 2.41
2162 2167 8.577296 CAAGCCAATCATAGAAGATGAATGAAT 58.423 33.333 4.53 0.00 32.26 2.57
2163 2168 8.707796 AGCCAATCATAGAAGATGAATGAATT 57.292 30.769 4.53 0.00 32.26 2.17
2192 2197 9.025041 TGAAGATACTCATTTCTCAAGAGTGTA 57.975 33.333 0.00 0.00 42.21 2.90
2197 2202 9.950496 ATACTCATTTCTCAAGAGTGTATTGTT 57.050 29.630 0.00 0.00 42.21 2.83
2198 2203 8.316640 ACTCATTTCTCAAGAGTGTATTGTTC 57.683 34.615 0.00 0.00 40.83 3.18
2229 2236 5.901552 TGGTTGTTTCTTTCATCAAAGTCC 58.098 37.500 0.00 0.00 40.16 3.85
2767 2792 4.397417 GCTTTCCTTCTCTGTTGTATGCAT 59.603 41.667 3.79 3.79 0.00 3.96
2799 2824 1.740025 GTCCTTGCTCATTACCACAGC 59.260 52.381 0.00 0.00 0.00 4.40
2939 2994 3.005554 CTGGCTAGTGGATTTCTGTGTG 58.994 50.000 0.00 0.00 0.00 3.82
2965 3020 4.416620 CTCTCTTTAGTGCTACCAACGAG 58.583 47.826 0.00 0.00 0.00 4.18
3098 3153 2.202479 GCATGACCTTTTCCGCGC 60.202 61.111 0.00 0.00 0.00 6.86
3099 3154 2.976840 GCATGACCTTTTCCGCGCA 61.977 57.895 8.75 0.00 0.00 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.264067 CCCTTGTTTATTTTTGATTTGGGCAA 59.736 34.615 0.00 0.00 0.00 4.52
1 2 5.767168 CCCTTGTTTATTTTTGATTTGGGCA 59.233 36.000 0.00 0.00 0.00 5.36
2 3 5.335583 GCCCTTGTTTATTTTTGATTTGGGC 60.336 40.000 0.00 0.00 46.45 5.36
3 4 5.767168 TGCCCTTGTTTATTTTTGATTTGGG 59.233 36.000 0.00 0.00 0.00 4.12
4 5 6.874288 TGCCCTTGTTTATTTTTGATTTGG 57.126 33.333 0.00 0.00 0.00 3.28
5 6 9.747293 AAATTGCCCTTGTTTATTTTTGATTTG 57.253 25.926 0.00 0.00 0.00 2.32
7 8 9.747293 CAAAATTGCCCTTGTTTATTTTTGATT 57.253 25.926 0.00 0.00 0.00 2.57
8 9 8.358895 CCAAAATTGCCCTTGTTTATTTTTGAT 58.641 29.630 0.00 0.00 0.00 2.57
9 10 7.557719 TCCAAAATTGCCCTTGTTTATTTTTGA 59.442 29.630 0.00 0.00 0.00 2.69
10 11 7.710896 TCCAAAATTGCCCTTGTTTATTTTTG 58.289 30.769 0.00 0.00 0.00 2.44
11 12 7.559533 ACTCCAAAATTGCCCTTGTTTATTTTT 59.440 29.630 0.00 0.00 0.00 1.94
12 13 7.059788 ACTCCAAAATTGCCCTTGTTTATTTT 58.940 30.769 0.00 0.00 0.00 1.82
13 14 6.600388 ACTCCAAAATTGCCCTTGTTTATTT 58.400 32.000 0.00 0.00 0.00 1.40
14 15 6.186420 ACTCCAAAATTGCCCTTGTTTATT 57.814 33.333 0.00 0.00 0.00 1.40
15 16 5.823861 ACTCCAAAATTGCCCTTGTTTAT 57.176 34.783 0.00 0.00 0.00 1.40
16 17 5.622346 AACTCCAAAATTGCCCTTGTTTA 57.378 34.783 0.00 0.00 0.00 2.01
17 18 4.502105 AACTCCAAAATTGCCCTTGTTT 57.498 36.364 0.00 0.00 0.00 2.83
18 19 4.080638 TGAAACTCCAAAATTGCCCTTGTT 60.081 37.500 0.00 0.00 0.00 2.83
19 20 3.454082 TGAAACTCCAAAATTGCCCTTGT 59.546 39.130 0.00 0.00 0.00 3.16
20 21 4.070630 TGAAACTCCAAAATTGCCCTTG 57.929 40.909 0.00 0.00 0.00 3.61
21 22 4.769345 TTGAAACTCCAAAATTGCCCTT 57.231 36.364 0.00 0.00 0.00 3.95
22 23 4.769345 TTTGAAACTCCAAAATTGCCCT 57.231 36.364 0.00 0.00 33.56 5.19
23 24 5.122519 TCTTTTGAAACTCCAAAATTGCCC 58.877 37.500 0.00 0.00 42.81 5.36
24 25 6.538381 TCTTCTTTTGAAACTCCAAAATTGCC 59.462 34.615 0.00 0.00 42.81 4.52
25 26 7.538303 TCTTCTTTTGAAACTCCAAAATTGC 57.462 32.000 0.00 0.00 42.81 3.56
26 27 8.553696 CCATCTTCTTTTGAAACTCCAAAATTG 58.446 33.333 0.00 0.00 42.81 2.32
27 28 8.267183 ACCATCTTCTTTTGAAACTCCAAAATT 58.733 29.630 0.00 0.00 42.81 1.82
28 29 7.795047 ACCATCTTCTTTTGAAACTCCAAAAT 58.205 30.769 0.00 0.00 42.81 1.82
29 30 7.181569 ACCATCTTCTTTTGAAACTCCAAAA 57.818 32.000 0.00 0.00 41.92 2.44
30 31 6.790232 ACCATCTTCTTTTGAAACTCCAAA 57.210 33.333 0.00 0.00 38.07 3.28
31 32 6.379703 TGAACCATCTTCTTTTGAAACTCCAA 59.620 34.615 0.00 0.00 38.07 3.53
32 33 5.890985 TGAACCATCTTCTTTTGAAACTCCA 59.109 36.000 0.00 0.00 38.07 3.86
33 34 6.391227 TGAACCATCTTCTTTTGAAACTCC 57.609 37.500 0.00 0.00 38.07 3.85
34 35 7.324616 CGATTGAACCATCTTCTTTTGAAACTC 59.675 37.037 0.00 0.00 38.07 3.01
35 36 7.013274 TCGATTGAACCATCTTCTTTTGAAACT 59.987 33.333 0.00 0.00 38.07 2.66
36 37 7.138736 TCGATTGAACCATCTTCTTTTGAAAC 58.861 34.615 0.00 0.00 38.07 2.78
37 38 7.270757 TCGATTGAACCATCTTCTTTTGAAA 57.729 32.000 0.00 0.00 38.07 2.69
38 39 6.875948 TCGATTGAACCATCTTCTTTTGAA 57.124 33.333 0.00 0.00 36.89 2.69
39 40 6.654582 TGATCGATTGAACCATCTTCTTTTGA 59.345 34.615 0.00 0.00 0.00 2.69
40 41 6.845302 TGATCGATTGAACCATCTTCTTTTG 58.155 36.000 0.00 0.00 0.00 2.44
41 42 6.094603 CCTGATCGATTGAACCATCTTCTTTT 59.905 38.462 0.00 0.00 0.00 2.27
42 43 5.587844 CCTGATCGATTGAACCATCTTCTTT 59.412 40.000 0.00 0.00 0.00 2.52
43 44 5.121811 CCTGATCGATTGAACCATCTTCTT 58.878 41.667 0.00 0.00 0.00 2.52
44 45 4.444022 CCCTGATCGATTGAACCATCTTCT 60.444 45.833 0.00 0.00 0.00 2.85
45 46 3.812053 CCCTGATCGATTGAACCATCTTC 59.188 47.826 0.00 0.00 0.00 2.87
46 47 3.455910 TCCCTGATCGATTGAACCATCTT 59.544 43.478 0.00 0.00 0.00 2.40
47 48 3.041211 TCCCTGATCGATTGAACCATCT 58.959 45.455 0.00 0.00 0.00 2.90
48 49 3.475566 TCCCTGATCGATTGAACCATC 57.524 47.619 0.00 0.00 0.00 3.51
49 50 3.931907 TTCCCTGATCGATTGAACCAT 57.068 42.857 0.00 0.00 0.00 3.55
50 51 3.712016 TTTCCCTGATCGATTGAACCA 57.288 42.857 0.00 0.00 0.00 3.67
51 52 5.582689 AAATTTCCCTGATCGATTGAACC 57.417 39.130 0.00 0.00 0.00 3.62
52 53 9.057089 AGTATAAATTTCCCTGATCGATTGAAC 57.943 33.333 0.00 0.00 0.00 3.18
58 59 9.760077 GACTTTAGTATAAATTTCCCTGATCGA 57.240 33.333 0.00 0.00 0.00 3.59
59 60 8.989980 GGACTTTAGTATAAATTTCCCTGATCG 58.010 37.037 0.00 0.00 0.00 3.69
60 61 8.989980 CGGACTTTAGTATAAATTTCCCTGATC 58.010 37.037 0.00 0.00 0.00 2.92
61 62 8.711170 TCGGACTTTAGTATAAATTTCCCTGAT 58.289 33.333 0.00 0.00 0.00 2.90
62 63 8.081517 TCGGACTTTAGTATAAATTTCCCTGA 57.918 34.615 0.00 0.00 0.00 3.86
63 64 8.610035 GTTCGGACTTTAGTATAAATTTCCCTG 58.390 37.037 0.00 0.00 0.00 4.45
64 65 8.323567 TGTTCGGACTTTAGTATAAATTTCCCT 58.676 33.333 0.00 0.00 0.00 4.20
65 66 8.496707 TGTTCGGACTTTAGTATAAATTTCCC 57.503 34.615 0.00 0.00 0.00 3.97
142 143 8.912988 TGATGATTCAAAACCTGTTTAAACTCT 58.087 29.630 18.72 0.00 31.63 3.24
143 144 9.696917 ATGATGATTCAAAACCTGTTTAAACTC 57.303 29.630 18.72 5.16 34.96 3.01
215 216 9.616634 CGACCGAATAATTAAGCTACAGTAATA 57.383 33.333 0.00 0.00 0.00 0.98
216 217 8.139989 ACGACCGAATAATTAAGCTACAGTAAT 58.860 33.333 0.00 0.00 0.00 1.89
217 218 7.483307 ACGACCGAATAATTAAGCTACAGTAA 58.517 34.615 0.00 0.00 0.00 2.24
218 219 7.031226 ACGACCGAATAATTAAGCTACAGTA 57.969 36.000 0.00 0.00 0.00 2.74
219 220 5.899299 ACGACCGAATAATTAAGCTACAGT 58.101 37.500 0.00 0.00 0.00 3.55
220 221 5.975344 TGACGACCGAATAATTAAGCTACAG 59.025 40.000 0.00 0.00 0.00 2.74
221 222 5.745294 GTGACGACCGAATAATTAAGCTACA 59.255 40.000 0.00 0.00 0.00 2.74
222 223 5.174579 GGTGACGACCGAATAATTAAGCTAC 59.825 44.000 0.00 0.00 30.61 3.58
223 224 5.284079 GGTGACGACCGAATAATTAAGCTA 58.716 41.667 0.00 0.00 30.61 3.32
224 225 4.117685 GGTGACGACCGAATAATTAAGCT 58.882 43.478 0.00 0.00 30.61 3.74
225 226 4.448363 GGTGACGACCGAATAATTAAGC 57.552 45.455 0.00 0.00 30.61 3.09
237 238 1.659098 CGCTTTATGAAGGTGACGACC 59.341 52.381 0.00 0.00 43.52 4.79
238 239 1.659098 CCGCTTTATGAAGGTGACGAC 59.341 52.381 0.00 0.00 33.34 4.34
239 240 1.274167 ACCGCTTTATGAAGGTGACGA 59.726 47.619 0.00 0.00 35.36 4.20
240 241 1.722011 ACCGCTTTATGAAGGTGACG 58.278 50.000 0.00 0.00 35.36 4.35
241 242 2.601763 CGTACCGCTTTATGAAGGTGAC 59.398 50.000 0.00 0.00 37.57 3.67
242 243 2.492881 TCGTACCGCTTTATGAAGGTGA 59.507 45.455 0.00 0.00 37.57 4.02
243 244 2.883574 TCGTACCGCTTTATGAAGGTG 58.116 47.619 0.00 0.00 37.57 4.00
244 245 3.814005 ATCGTACCGCTTTATGAAGGT 57.186 42.857 0.00 0.00 40.52 3.50
245 246 4.446719 GGTAATCGTACCGCTTTATGAAGG 59.553 45.833 0.00 0.00 40.59 3.46
246 247 5.571778 GGTAATCGTACCGCTTTATGAAG 57.428 43.478 0.00 0.00 40.59 3.02
259 260 5.708230 ACAAATGCTCTTTTGGGTAATCGTA 59.292 36.000 11.31 0.00 40.20 3.43
261 262 5.059404 ACAAATGCTCTTTTGGGTAATCG 57.941 39.130 11.31 0.00 40.20 3.34
274 275 0.313672 TGGTTGCCGAACAAATGCTC 59.686 50.000 0.00 0.00 40.82 4.26
275 276 0.749649 TTGGTTGCCGAACAAATGCT 59.250 45.000 0.00 0.00 40.82 3.79
283 284 1.178276 AAGTGTGTTTGGTTGCCGAA 58.822 45.000 0.00 0.00 0.00 4.30
285 286 1.402259 TGTAAGTGTGTTTGGTTGCCG 59.598 47.619 0.00 0.00 0.00 5.69
286 287 3.512033 TTGTAAGTGTGTTTGGTTGCC 57.488 42.857 0.00 0.00 0.00 4.52
287 288 3.615056 GGTTTGTAAGTGTGTTTGGTTGC 59.385 43.478 0.00 0.00 0.00 4.17
288 289 4.081917 AGGGTTTGTAAGTGTGTTTGGTTG 60.082 41.667 0.00 0.00 0.00 3.77
289 290 4.081917 CAGGGTTTGTAAGTGTGTTTGGTT 60.082 41.667 0.00 0.00 0.00 3.67
291 292 3.697045 TCAGGGTTTGTAAGTGTGTTTGG 59.303 43.478 0.00 0.00 0.00 3.28
292 293 4.974368 TCAGGGTTTGTAAGTGTGTTTG 57.026 40.909 0.00 0.00 0.00 2.93
293 294 4.158949 GGTTCAGGGTTTGTAAGTGTGTTT 59.841 41.667 0.00 0.00 0.00 2.83
308 312 1.315257 CGAGCATTTGGGGTTCAGGG 61.315 60.000 0.00 0.00 0.00 4.45
316 320 2.098117 GGATTTCTGTCGAGCATTTGGG 59.902 50.000 0.00 0.00 0.00 4.12
961 965 0.681887 TTACCTCCGGCATCGTCTCA 60.682 55.000 0.00 0.00 33.95 3.27
977 981 6.494893 TTTCCACAAGAGTGTATGCATTAC 57.505 37.500 3.54 5.00 44.39 1.89
978 982 6.095300 CCATTTCCACAAGAGTGTATGCATTA 59.905 38.462 3.54 0.00 44.39 1.90
981 986 3.758023 CCATTTCCACAAGAGTGTATGCA 59.242 43.478 0.00 0.00 44.39 3.96
990 995 2.697751 CCCACAAACCATTTCCACAAGA 59.302 45.455 0.00 0.00 0.00 3.02
999 1004 1.884928 GCGGAGTACCCACAAACCATT 60.885 52.381 0.00 0.00 34.14 3.16
1084 1089 1.529152 ATGGCTGTACACACGACCGA 61.529 55.000 0.00 0.00 0.00 4.69
1089 1094 3.737774 CAGATATCATGGCTGTACACACG 59.262 47.826 5.32 0.00 0.00 4.49
1119 1124 1.617850 TCATCAGCATTGCCCGTTTTT 59.382 42.857 4.70 0.00 0.00 1.94
1125 1130 1.540267 CTAGCATCATCAGCATTGCCC 59.460 52.381 4.70 0.00 35.71 5.36
1134 1139 0.760567 AGACGGCCCTAGCATCATCA 60.761 55.000 0.00 0.00 42.56 3.07
1385 1390 6.179756 ACAGTATGGCTATTCAACAACATCA 58.820 36.000 0.00 0.00 43.62 3.07
1398 1403 1.048601 GGGCAGCTACAGTATGGCTA 58.951 55.000 7.47 0.00 43.62 3.93
1400 1405 0.250081 GAGGGCAGCTACAGTATGGC 60.250 60.000 0.00 0.04 43.62 4.40
1521 1526 4.517815 CGGCCATGCATGCCCAAC 62.518 66.667 25.14 9.81 46.48 3.77
1590 1595 4.141287 ACACAAAACAGATTTCATCGGGA 58.859 39.130 0.00 0.00 0.00 5.14
1836 1841 4.286032 ACATTTGAGTAAGTCCTACAGGCA 59.714 41.667 0.00 0.00 32.37 4.75
1860 1865 2.190578 GCCACCTCCCCAATCTCG 59.809 66.667 0.00 0.00 0.00 4.04
2138 2143 8.707796 AATTCATTCATCTTCTATGATTGGCT 57.292 30.769 8.98 0.00 33.00 4.75
2192 2197 5.422012 AGAAACAACCAACCTTGAGAACAAT 59.578 36.000 0.00 0.00 35.37 2.71
2197 2202 5.013547 TGAAAGAAACAACCAACCTTGAGA 58.986 37.500 0.00 0.00 0.00 3.27
2198 2203 5.323371 TGAAAGAAACAACCAACCTTGAG 57.677 39.130 0.00 0.00 0.00 3.02
2316 2323 2.106684 TGTTAACACACCATGGGCTACA 59.893 45.455 18.09 7.28 0.00 2.74
2389 2396 2.849294 TTTAAATTTGGCAGCCACCC 57.151 45.000 15.89 0.00 30.78 4.61
2767 2792 1.032014 GCAAGGACCAAGAGCAAACA 58.968 50.000 0.00 0.00 0.00 2.83
2799 2824 0.108424 GGTAGCTCTCACACAGCTGG 60.108 60.000 19.93 9.66 46.99 4.85
2920 2975 3.059352 ACACACAGAAATCCACTAGCC 57.941 47.619 0.00 0.00 0.00 3.93
2939 2994 4.803098 TGGTAGCACTAAAGAGAGGAAC 57.197 45.455 0.00 0.00 0.00 3.62
3043 3098 5.046878 TGACATTCCTTTGTATACACTCCGT 60.047 40.000 4.68 0.00 0.00 4.69
3098 3153 4.873129 AGCCTCATACCGCGCGTG 62.873 66.667 29.95 20.61 0.00 5.34
3099 3154 3.659089 AAAGCCTCATACCGCGCGT 62.659 57.895 29.95 18.85 0.00 6.01


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

AutoCloner maintained by Alex Coulton.