Multiple sequence alignment - TraesCS3D01G092400

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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 TraesCS3D01G092400 chr3D 100.000 2502 0 0 1 2502 46539497 46541998 0.000000e+00 4621.0
1 TraesCS3D01G092400 chr3D 92.002 1638 87 22 371 1974 585903803 585902176 0.000000e+00 2259.0
2 TraesCS3D01G092400 chr3D 97.275 367 8 1 2136 2502 585902013 585901649 2.730000e-174 621.0
3 TraesCS3D01G092400 chr6D 97.270 2198 49 6 313 2502 110324319 110322125 0.000000e+00 3716.0
4 TraesCS3D01G092400 chr6D 96.218 1798 46 5 311 2098 80068485 80070270 0.000000e+00 2924.0
5 TraesCS3D01G092400 chr6D 98.321 417 6 1 2087 2502 80081919 80082335 0.000000e+00 730.0
6 TraesCS3D01G092400 chr1D 94.700 2151 95 14 362 2500 467457299 467455156 0.000000e+00 3323.0
7 TraesCS3D01G092400 chr1D 92.270 1022 46 12 961 1974 122263780 122262784 0.000000e+00 1419.0
8 TraesCS3D01G092400 chr1D 96.597 529 18 0 1974 2502 122262753 122262225 0.000000e+00 878.0
9 TraesCS3D01G092400 chr5D 96.329 1798 37 16 313 2104 495476152 495477926 0.000000e+00 2928.0
10 TraesCS3D01G092400 chr7D 93.684 1615 85 11 365 1974 602775777 602777379 0.000000e+00 2401.0
11 TraesCS3D01G092400 chr7D 95.154 1135 46 7 843 1974 590072350 590071222 0.000000e+00 1783.0
12 TraesCS3D01G092400 chr7D 96.975 529 16 0 1974 2502 590071191 590070663 0.000000e+00 889.0
13 TraesCS3D01G092400 chr7D 97.548 367 9 0 2136 2502 602777542 602777908 1.630000e-176 628.0
14 TraesCS3D01G092400 chr5A 95.207 1523 59 8 460 1974 426307127 426305611 0.000000e+00 2396.0
15 TraesCS3D01G092400 chr5A 97.732 529 12 0 1974 2502 426305580 426305052 0.000000e+00 911.0
16 TraesCS3D01G092400 chr5A 96.000 50 2 0 1058 1107 426306289 426306240 5.740000e-12 82.4
17 TraesCS3D01G092400 chr3B 89.318 1011 69 16 973 1974 241928863 241927883 0.000000e+00 1232.0
18 TraesCS3D01G092400 chr3B 88.469 529 37 2 1974 2502 241927852 241927348 3.540000e-173 617.0
19 TraesCS3D01G092400 chr3B 90.847 295 26 1 1 294 72933757 72934051 6.490000e-106 394.0
20 TraesCS3D01G092400 chr2D 95.687 626 25 2 313 937 590221072 590221696 0.000000e+00 1005.0
21 TraesCS3D01G092400 chr2B 87.526 489 48 11 364 845 18196139 18195657 1.010000e-153 553.0
22 TraesCS3D01G092400 chr3A 94.375 320 14 2 1 317 57962389 57962071 2.890000e-134 488.0
23 TraesCS3D01G092400 chr6B 90.141 355 17 5 1974 2323 440764547 440764206 1.770000e-121 446.0
24 TraesCS3D01G092400 chr1B 89.859 355 20 4 1974 2323 571153813 571154156 2.280000e-120 442.0


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 TraesCS3D01G092400 chr3D 46539497 46541998 2501 False 4621.0 4621 100.0000 1 2502 1 chr3D.!!$F1 2501
1 TraesCS3D01G092400 chr3D 585901649 585903803 2154 True 1440.0 2259 94.6385 371 2502 2 chr3D.!!$R1 2131
2 TraesCS3D01G092400 chr6D 110322125 110324319 2194 True 3716.0 3716 97.2700 313 2502 1 chr6D.!!$R1 2189
3 TraesCS3D01G092400 chr6D 80068485 80070270 1785 False 2924.0 2924 96.2180 311 2098 1 chr6D.!!$F1 1787
4 TraesCS3D01G092400 chr1D 467455156 467457299 2143 True 3323.0 3323 94.7000 362 2500 1 chr1D.!!$R1 2138
5 TraesCS3D01G092400 chr1D 122262225 122263780 1555 True 1148.5 1419 94.4335 961 2502 2 chr1D.!!$R2 1541
6 TraesCS3D01G092400 chr5D 495476152 495477926 1774 False 2928.0 2928 96.3290 313 2104 1 chr5D.!!$F1 1791
7 TraesCS3D01G092400 chr7D 602775777 602777908 2131 False 1514.5 2401 95.6160 365 2502 2 chr7D.!!$F1 2137
8 TraesCS3D01G092400 chr7D 590070663 590072350 1687 True 1336.0 1783 96.0645 843 2502 2 chr7D.!!$R1 1659
9 TraesCS3D01G092400 chr5A 426305052 426307127 2075 True 1129.8 2396 96.3130 460 2502 3 chr5A.!!$R1 2042
10 TraesCS3D01G092400 chr3B 241927348 241928863 1515 True 924.5 1232 88.8935 973 2502 2 chr3B.!!$R1 1529
11 TraesCS3D01G092400 chr2D 590221072 590221696 624 False 1005.0 1005 95.6870 313 937 1 chr2D.!!$F1 624

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 0.179113 GGTGCTGTTTGTGGGTGTTG 60.179 55.0 0.0 0.0 0.00 3.33 F
44 45 0.814457 GTGCTGTTTGTGGGTGTTGA 59.186 50.0 0.0 0.0 0.00 3.18 F
253 254 0.976641 AGATTGGAGAAGTGACGCCA 59.023 50.0 0.0 0.0 37.91 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1160 1221 0.179127 CGCACCATCAGATCGAGTGT 60.179 55.000 0.00 0.0 0.00 3.55 R
1165 1226 1.524355 GATGAACGCACCATCAGATCG 59.476 52.381 7.22 0.0 39.98 3.69 R
2030 2186 5.488341 ACCAAGAAGCACAGATAAATACGT 58.512 37.500 0.00 0.0 0.00 3.57 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
17 18 3.246112 AGCTGGGGTGGCGTTACA 61.246 61.111 0.00 0.00 34.52 2.41
18 19 3.053896 GCTGGGGTGGCGTTACAC 61.054 66.667 0.00 0.00 40.60 2.90
24 25 3.481661 GTGGCGTTACACCGATGG 58.518 61.111 0.00 0.00 35.34 3.51
25 26 2.104253 GTGGCGTTACACCGATGGG 61.104 63.158 0.00 0.00 35.34 4.00
35 36 4.079446 CCGATGGGTGCTGTTTGT 57.921 55.556 0.00 0.00 0.00 2.83
36 37 1.580942 CCGATGGGTGCTGTTTGTG 59.419 57.895 0.00 0.00 0.00 3.33
37 38 1.580942 CGATGGGTGCTGTTTGTGG 59.419 57.895 0.00 0.00 0.00 4.17
38 39 1.865788 CGATGGGTGCTGTTTGTGGG 61.866 60.000 0.00 0.00 0.00 4.61
39 40 0.827507 GATGGGTGCTGTTTGTGGGT 60.828 55.000 0.00 0.00 0.00 4.51
40 41 1.114722 ATGGGTGCTGTTTGTGGGTG 61.115 55.000 0.00 0.00 0.00 4.61
41 42 1.756561 GGGTGCTGTTTGTGGGTGT 60.757 57.895 0.00 0.00 0.00 4.16
42 43 1.326951 GGGTGCTGTTTGTGGGTGTT 61.327 55.000 0.00 0.00 0.00 3.32
43 44 0.179113 GGTGCTGTTTGTGGGTGTTG 60.179 55.000 0.00 0.00 0.00 3.33
44 45 0.814457 GTGCTGTTTGTGGGTGTTGA 59.186 50.000 0.00 0.00 0.00 3.18
45 46 1.203523 GTGCTGTTTGTGGGTGTTGAA 59.796 47.619 0.00 0.00 0.00 2.69
46 47 2.106566 TGCTGTTTGTGGGTGTTGAAT 58.893 42.857 0.00 0.00 0.00 2.57
47 48 2.159128 TGCTGTTTGTGGGTGTTGAATG 60.159 45.455 0.00 0.00 0.00 2.67
48 49 2.100584 GCTGTTTGTGGGTGTTGAATGA 59.899 45.455 0.00 0.00 0.00 2.57
49 50 3.705604 CTGTTTGTGGGTGTTGAATGAC 58.294 45.455 0.00 0.00 0.00 3.06
50 51 3.360867 TGTTTGTGGGTGTTGAATGACT 58.639 40.909 0.00 0.00 0.00 3.41
51 52 3.380004 TGTTTGTGGGTGTTGAATGACTC 59.620 43.478 0.00 0.00 0.00 3.36
52 53 3.576078 TTGTGGGTGTTGAATGACTCT 57.424 42.857 0.00 0.00 0.00 3.24
53 54 2.849942 TGTGGGTGTTGAATGACTCTG 58.150 47.619 0.00 0.00 0.00 3.35
54 55 2.154462 GTGGGTGTTGAATGACTCTGG 58.846 52.381 0.00 0.00 0.00 3.86
55 56 1.774254 TGGGTGTTGAATGACTCTGGT 59.226 47.619 0.00 0.00 0.00 4.00
56 57 2.174639 TGGGTGTTGAATGACTCTGGTT 59.825 45.455 0.00 0.00 0.00 3.67
57 58 3.222603 GGGTGTTGAATGACTCTGGTTT 58.777 45.455 0.00 0.00 0.00 3.27
58 59 3.253432 GGGTGTTGAATGACTCTGGTTTC 59.747 47.826 0.00 0.00 0.00 2.78
59 60 4.137543 GGTGTTGAATGACTCTGGTTTCT 58.862 43.478 0.00 0.00 0.00 2.52
60 61 4.023707 GGTGTTGAATGACTCTGGTTTCTG 60.024 45.833 0.00 0.00 0.00 3.02
61 62 4.816385 GTGTTGAATGACTCTGGTTTCTGA 59.184 41.667 0.00 0.00 0.00 3.27
62 63 5.471456 GTGTTGAATGACTCTGGTTTCTGAT 59.529 40.000 0.00 0.00 0.00 2.90
63 64 6.016777 GTGTTGAATGACTCTGGTTTCTGATT 60.017 38.462 0.00 0.00 0.00 2.57
64 65 6.547141 TGTTGAATGACTCTGGTTTCTGATTT 59.453 34.615 0.00 0.00 0.00 2.17
65 66 6.808008 TGAATGACTCTGGTTTCTGATTTC 57.192 37.500 0.00 0.00 0.00 2.17
66 67 5.409520 TGAATGACTCTGGTTTCTGATTTCG 59.590 40.000 0.00 0.00 0.00 3.46
67 68 3.067106 TGACTCTGGTTTCTGATTTCGC 58.933 45.455 0.00 0.00 0.00 4.70
68 69 3.244215 TGACTCTGGTTTCTGATTTCGCT 60.244 43.478 0.00 0.00 0.00 4.93
69 70 3.744660 ACTCTGGTTTCTGATTTCGCTT 58.255 40.909 0.00 0.00 0.00 4.68
70 71 3.748568 ACTCTGGTTTCTGATTTCGCTTC 59.251 43.478 0.00 0.00 0.00 3.86
71 72 3.738982 TCTGGTTTCTGATTTCGCTTCA 58.261 40.909 0.00 0.00 0.00 3.02
72 73 4.326826 TCTGGTTTCTGATTTCGCTTCAT 58.673 39.130 0.00 0.00 0.00 2.57
73 74 4.761739 TCTGGTTTCTGATTTCGCTTCATT 59.238 37.500 0.00 0.00 0.00 2.57
74 75 5.937540 TCTGGTTTCTGATTTCGCTTCATTA 59.062 36.000 0.00 0.00 0.00 1.90
75 76 6.429692 TCTGGTTTCTGATTTCGCTTCATTAA 59.570 34.615 0.00 0.00 0.00 1.40
76 77 7.121168 TCTGGTTTCTGATTTCGCTTCATTAAT 59.879 33.333 0.00 0.00 0.00 1.40
77 78 8.275015 TGGTTTCTGATTTCGCTTCATTAATA 57.725 30.769 0.00 0.00 0.00 0.98
78 79 8.735315 TGGTTTCTGATTTCGCTTCATTAATAA 58.265 29.630 0.00 0.00 0.00 1.40
79 80 9.567848 GGTTTCTGATTTCGCTTCATTAATAAA 57.432 29.630 0.00 0.00 0.00 1.40
83 84 9.734620 TCTGATTTCGCTTCATTAATAAAATGG 57.265 29.630 0.00 0.00 0.00 3.16
84 85 8.870160 TGATTTCGCTTCATTAATAAAATGGG 57.130 30.769 0.00 0.00 0.00 4.00
85 86 7.925483 TGATTTCGCTTCATTAATAAAATGGGG 59.075 33.333 0.00 0.00 0.00 4.96
86 87 5.195001 TCGCTTCATTAATAAAATGGGGC 57.805 39.130 0.00 2.98 0.00 5.80
87 88 3.980775 CGCTTCATTAATAAAATGGGGCG 59.019 43.478 16.65 16.65 39.86 6.13
88 89 4.306600 GCTTCATTAATAAAATGGGGCGG 58.693 43.478 0.00 0.00 0.00 6.13
89 90 4.799255 GCTTCATTAATAAAATGGGGCGGG 60.799 45.833 0.00 0.00 0.00 6.13
90 91 3.235200 TCATTAATAAAATGGGGCGGGG 58.765 45.455 0.00 0.00 0.00 5.73
91 92 2.089600 TTAATAAAATGGGGCGGGGG 57.910 50.000 0.00 0.00 0.00 5.40
177 178 9.492973 AAATATCCCAGAATTGTTTTCTTTGTG 57.507 29.630 0.00 0.00 0.00 3.33
178 179 5.275067 TCCCAGAATTGTTTTCTTTGTGG 57.725 39.130 0.00 0.00 34.48 4.17
179 180 4.714308 TCCCAGAATTGTTTTCTTTGTGGT 59.286 37.500 0.00 0.00 33.22 4.16
180 181 5.894393 TCCCAGAATTGTTTTCTTTGTGGTA 59.106 36.000 0.00 0.00 33.22 3.25
181 182 6.553100 TCCCAGAATTGTTTTCTTTGTGGTAT 59.447 34.615 0.00 0.00 33.22 2.73
182 183 7.726291 TCCCAGAATTGTTTTCTTTGTGGTATA 59.274 33.333 0.00 0.00 33.22 1.47
183 184 8.364142 CCCAGAATTGTTTTCTTTGTGGTATAA 58.636 33.333 0.00 0.00 33.22 0.98
184 185 9.757227 CCAGAATTGTTTTCTTTGTGGTATAAA 57.243 29.630 0.00 0.00 31.14 1.40
212 213 8.795786 TTTGCAACATGAAATACTTACAAGAC 57.204 30.769 0.00 0.00 0.00 3.01
213 214 7.744087 TGCAACATGAAATACTTACAAGACT 57.256 32.000 0.00 0.00 0.00 3.24
214 215 8.165239 TGCAACATGAAATACTTACAAGACTT 57.835 30.769 0.00 0.00 0.00 3.01
215 216 8.289618 TGCAACATGAAATACTTACAAGACTTC 58.710 33.333 0.00 0.00 0.00 3.01
216 217 8.507249 GCAACATGAAATACTTACAAGACTTCT 58.493 33.333 0.00 0.00 0.00 2.85
217 218 9.817365 CAACATGAAATACTTACAAGACTTCTG 57.183 33.333 0.00 0.71 0.00 3.02
218 219 9.561069 AACATGAAATACTTACAAGACTTCTGT 57.439 29.630 0.00 0.00 0.00 3.41
227 228 8.240267 ACTTACAAGACTTCTGTAGAAAGACT 57.760 34.615 0.00 0.00 33.07 3.24
228 229 8.138712 ACTTACAAGACTTCTGTAGAAAGACTG 58.861 37.037 0.00 0.00 33.07 3.51
229 230 6.472686 ACAAGACTTCTGTAGAAAGACTGT 57.527 37.500 0.00 0.00 33.07 3.55
230 231 6.276847 ACAAGACTTCTGTAGAAAGACTGTG 58.723 40.000 0.00 0.00 33.07 3.66
231 232 5.461032 AGACTTCTGTAGAAAGACTGTGG 57.539 43.478 0.00 0.00 33.07 4.17
232 233 4.896482 AGACTTCTGTAGAAAGACTGTGGT 59.104 41.667 0.00 0.00 33.07 4.16
233 234 5.010213 AGACTTCTGTAGAAAGACTGTGGTC 59.990 44.000 0.00 0.00 42.41 4.02
234 235 4.649674 ACTTCTGTAGAAAGACTGTGGTCA 59.350 41.667 0.00 0.00 44.36 4.02
235 236 4.855715 TCTGTAGAAAGACTGTGGTCAG 57.144 45.455 0.00 0.00 44.36 3.51
236 237 4.470602 TCTGTAGAAAGACTGTGGTCAGA 58.529 43.478 2.17 0.00 44.36 3.27
237 238 5.080337 TCTGTAGAAAGACTGTGGTCAGAT 58.920 41.667 2.17 0.00 44.36 2.90
238 239 5.540337 TCTGTAGAAAGACTGTGGTCAGATT 59.460 40.000 2.17 0.00 44.36 2.40
239 240 5.541845 TGTAGAAAGACTGTGGTCAGATTG 58.458 41.667 2.17 0.00 44.36 2.67
240 241 4.013267 AGAAAGACTGTGGTCAGATTGG 57.987 45.455 2.17 0.00 44.36 3.16
241 242 3.648067 AGAAAGACTGTGGTCAGATTGGA 59.352 43.478 2.17 0.00 44.36 3.53
242 243 3.692257 AAGACTGTGGTCAGATTGGAG 57.308 47.619 2.17 0.00 44.36 3.86
243 244 2.894731 AGACTGTGGTCAGATTGGAGA 58.105 47.619 2.17 0.00 44.36 3.71
244 245 3.242867 AGACTGTGGTCAGATTGGAGAA 58.757 45.455 2.17 0.00 44.36 2.87
245 246 3.260380 AGACTGTGGTCAGATTGGAGAAG 59.740 47.826 2.17 0.00 44.36 2.85
246 247 2.975489 ACTGTGGTCAGATTGGAGAAGT 59.025 45.455 2.17 0.00 43.76 3.01
247 248 3.244353 ACTGTGGTCAGATTGGAGAAGTG 60.244 47.826 2.17 0.00 43.76 3.16
248 249 2.972021 TGTGGTCAGATTGGAGAAGTGA 59.028 45.455 0.00 0.00 0.00 3.41
249 250 3.244215 TGTGGTCAGATTGGAGAAGTGAC 60.244 47.826 0.00 0.00 37.41 3.67
250 251 2.029020 TGGTCAGATTGGAGAAGTGACG 60.029 50.000 0.00 0.00 38.74 4.35
251 252 1.996191 GTCAGATTGGAGAAGTGACGC 59.004 52.381 0.00 0.00 0.00 5.19
252 253 1.066858 TCAGATTGGAGAAGTGACGCC 60.067 52.381 0.00 0.00 0.00 5.68
253 254 0.976641 AGATTGGAGAAGTGACGCCA 59.023 50.000 0.00 0.00 37.91 5.69
254 255 1.079503 GATTGGAGAAGTGACGCCAC 58.920 55.000 0.00 0.00 39.26 5.01
269 270 7.709269 GTGACGCCACTCTATAATTATGAAA 57.291 36.000 8.28 0.00 40.10 2.69
270 271 8.311650 GTGACGCCACTCTATAATTATGAAAT 57.688 34.615 8.28 0.00 40.10 2.17
271 272 9.419297 GTGACGCCACTCTATAATTATGAAATA 57.581 33.333 8.28 0.00 40.10 1.40
272 273 9.990360 TGACGCCACTCTATAATTATGAAATAA 57.010 29.630 8.28 0.00 44.01 1.40
473 475 6.707290 ACACTGCTACAATGAATAGTTACCA 58.293 36.000 0.00 0.00 0.00 3.25
543 548 1.256812 GTCATTTCACCAACAGGGGG 58.743 55.000 0.00 0.00 43.74 5.40
630 635 4.467107 GCCTCCTCTCCTCCCCGT 62.467 72.222 0.00 0.00 0.00 5.28
1024 1085 1.627297 GGAGCAACGGGGAGAGGAAT 61.627 60.000 0.00 0.00 0.00 3.01
1160 1221 3.872511 TCCTTATTCTTGCCGTCGTTA 57.127 42.857 0.00 0.00 0.00 3.18
1165 1226 1.774639 TTCTTGCCGTCGTTACACTC 58.225 50.000 0.00 0.00 0.00 3.51
1422 1488 4.837093 TCCAGACCTAGGGTTACATTTG 57.163 45.455 14.81 0.00 35.25 2.32
1423 1489 4.172807 TCCAGACCTAGGGTTACATTTGT 58.827 43.478 14.81 0.00 35.25 2.83
1424 1490 4.019681 TCCAGACCTAGGGTTACATTTGTG 60.020 45.833 14.81 0.00 35.25 3.33
1425 1491 4.019681 CCAGACCTAGGGTTACATTTGTGA 60.020 45.833 14.81 0.00 35.25 3.58
1426 1492 5.514136 CCAGACCTAGGGTTACATTTGTGAA 60.514 44.000 14.81 0.00 35.25 3.18
1427 1493 5.643777 CAGACCTAGGGTTACATTTGTGAAG 59.356 44.000 14.81 0.00 35.25 3.02
1428 1494 5.309806 AGACCTAGGGTTACATTTGTGAAGT 59.690 40.000 14.81 0.00 35.25 3.01
1429 1495 6.499350 AGACCTAGGGTTACATTTGTGAAGTA 59.501 38.462 14.81 0.00 35.25 2.24
1505 1579 1.605992 CAGGCTGGCCAATGAGAGA 59.394 57.895 7.01 0.00 38.92 3.10
2030 2186 2.284754 TTATGTGTTCTGCCCAGCAA 57.715 45.000 0.00 0.00 38.41 3.91
2339 2495 3.130160 CTCGCCTGGGAAAGCAGC 61.130 66.667 0.00 0.00 0.00 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.246112 TGTAACGCCACCCCAGCT 61.246 61.111 0.00 0.00 0.00 4.24
7 8 2.104253 CCCATCGGTGTAACGCCAC 61.104 63.158 0.00 0.00 38.12 5.01
8 9 2.266372 CCCATCGGTGTAACGCCA 59.734 61.111 0.00 0.00 38.12 5.69
9 10 2.266689 ACCCATCGGTGTAACGCC 59.733 61.111 0.00 0.00 42.48 5.68
17 18 1.150536 ACAAACAGCACCCATCGGT 59.849 52.632 0.00 0.00 46.31 4.69
18 19 1.580942 CACAAACAGCACCCATCGG 59.419 57.895 0.00 0.00 0.00 4.18
19 20 1.580942 CCACAAACAGCACCCATCG 59.419 57.895 0.00 0.00 0.00 3.84
20 21 0.827507 ACCCACAAACAGCACCCATC 60.828 55.000 0.00 0.00 0.00 3.51
21 22 1.114722 CACCCACAAACAGCACCCAT 61.115 55.000 0.00 0.00 0.00 4.00
22 23 1.756172 CACCCACAAACAGCACCCA 60.756 57.895 0.00 0.00 0.00 4.51
23 24 1.326951 AACACCCACAAACAGCACCC 61.327 55.000 0.00 0.00 0.00 4.61
24 25 0.179113 CAACACCCACAAACAGCACC 60.179 55.000 0.00 0.00 0.00 5.01
25 26 0.814457 TCAACACCCACAAACAGCAC 59.186 50.000 0.00 0.00 0.00 4.40
26 27 1.550327 TTCAACACCCACAAACAGCA 58.450 45.000 0.00 0.00 0.00 4.41
27 28 2.100584 TCATTCAACACCCACAAACAGC 59.899 45.455 0.00 0.00 0.00 4.40
28 29 3.381272 AGTCATTCAACACCCACAAACAG 59.619 43.478 0.00 0.00 0.00 3.16
29 30 3.360867 AGTCATTCAACACCCACAAACA 58.639 40.909 0.00 0.00 0.00 2.83
30 31 3.632145 AGAGTCATTCAACACCCACAAAC 59.368 43.478 0.00 0.00 0.00 2.93
31 32 3.631686 CAGAGTCATTCAACACCCACAAA 59.368 43.478 0.00 0.00 0.00 2.83
32 33 3.213506 CAGAGTCATTCAACACCCACAA 58.786 45.455 0.00 0.00 0.00 3.33
33 34 2.487086 CCAGAGTCATTCAACACCCACA 60.487 50.000 0.00 0.00 0.00 4.17
34 35 2.154462 CCAGAGTCATTCAACACCCAC 58.846 52.381 0.00 0.00 0.00 4.61
35 36 1.774254 ACCAGAGTCATTCAACACCCA 59.226 47.619 0.00 0.00 0.00 4.51
36 37 2.568623 ACCAGAGTCATTCAACACCC 57.431 50.000 0.00 0.00 0.00 4.61
37 38 4.023707 CAGAAACCAGAGTCATTCAACACC 60.024 45.833 0.00 0.00 0.00 4.16
38 39 4.816385 TCAGAAACCAGAGTCATTCAACAC 59.184 41.667 0.00 0.00 0.00 3.32
39 40 5.034852 TCAGAAACCAGAGTCATTCAACA 57.965 39.130 0.00 0.00 0.00 3.33
40 41 6.566197 AATCAGAAACCAGAGTCATTCAAC 57.434 37.500 0.00 0.00 0.00 3.18
41 42 6.073058 CGAAATCAGAAACCAGAGTCATTCAA 60.073 38.462 0.00 0.00 0.00 2.69
42 43 5.409520 CGAAATCAGAAACCAGAGTCATTCA 59.590 40.000 0.00 0.00 0.00 2.57
43 44 5.672321 GCGAAATCAGAAACCAGAGTCATTC 60.672 44.000 0.00 0.00 0.00 2.67
44 45 4.154918 GCGAAATCAGAAACCAGAGTCATT 59.845 41.667 0.00 0.00 0.00 2.57
45 46 3.686726 GCGAAATCAGAAACCAGAGTCAT 59.313 43.478 0.00 0.00 0.00 3.06
46 47 3.067106 GCGAAATCAGAAACCAGAGTCA 58.933 45.455 0.00 0.00 0.00 3.41
47 48 3.330267 AGCGAAATCAGAAACCAGAGTC 58.670 45.455 0.00 0.00 0.00 3.36
48 49 3.409026 AGCGAAATCAGAAACCAGAGT 57.591 42.857 0.00 0.00 0.00 3.24
49 50 3.748048 TGAAGCGAAATCAGAAACCAGAG 59.252 43.478 0.00 0.00 0.00 3.35
50 51 3.738982 TGAAGCGAAATCAGAAACCAGA 58.261 40.909 0.00 0.00 0.00 3.86
51 52 4.691860 ATGAAGCGAAATCAGAAACCAG 57.308 40.909 0.00 0.00 0.00 4.00
52 53 6.567687 TTAATGAAGCGAAATCAGAAACCA 57.432 33.333 0.00 0.00 0.00 3.67
53 54 9.567848 TTTATTAATGAAGCGAAATCAGAAACC 57.432 29.630 0.00 0.00 0.00 3.27
57 58 9.734620 CCATTTTATTAATGAAGCGAAATCAGA 57.265 29.630 0.00 0.00 0.00 3.27
58 59 8.971321 CCCATTTTATTAATGAAGCGAAATCAG 58.029 33.333 0.00 0.00 0.00 2.90
59 60 7.925483 CCCCATTTTATTAATGAAGCGAAATCA 59.075 33.333 0.00 0.00 0.00 2.57
60 61 7.095649 GCCCCATTTTATTAATGAAGCGAAATC 60.096 37.037 0.00 0.00 0.00 2.17
61 62 6.705825 GCCCCATTTTATTAATGAAGCGAAAT 59.294 34.615 0.00 0.00 0.00 2.17
62 63 6.045955 GCCCCATTTTATTAATGAAGCGAAA 58.954 36.000 0.00 0.00 0.00 3.46
63 64 5.596845 GCCCCATTTTATTAATGAAGCGAA 58.403 37.500 0.00 0.00 0.00 4.70
64 65 4.261405 CGCCCCATTTTATTAATGAAGCGA 60.261 41.667 19.77 0.00 44.24 4.93
65 66 3.980775 CGCCCCATTTTATTAATGAAGCG 59.019 43.478 14.74 14.74 40.07 4.68
66 67 4.306600 CCGCCCCATTTTATTAATGAAGC 58.693 43.478 0.00 0.00 0.00 3.86
67 68 4.262420 CCCCGCCCCATTTTATTAATGAAG 60.262 45.833 0.00 0.00 0.00 3.02
68 69 3.643792 CCCCGCCCCATTTTATTAATGAA 59.356 43.478 0.00 0.00 0.00 2.57
69 70 3.235200 CCCCGCCCCATTTTATTAATGA 58.765 45.455 0.00 0.00 0.00 2.57
70 71 2.301583 CCCCCGCCCCATTTTATTAATG 59.698 50.000 0.00 0.00 0.00 1.90
71 72 2.615391 CCCCCGCCCCATTTTATTAAT 58.385 47.619 0.00 0.00 0.00 1.40
72 73 2.089600 CCCCCGCCCCATTTTATTAA 57.910 50.000 0.00 0.00 0.00 1.40
73 74 3.852558 CCCCCGCCCCATTTTATTA 57.147 52.632 0.00 0.00 0.00 0.98
74 75 4.718143 CCCCCGCCCCATTTTATT 57.282 55.556 0.00 0.00 0.00 1.40
151 152 9.492973 CACAAAGAAAACAATTCTGGGATATTT 57.507 29.630 0.00 0.00 0.00 1.40
152 153 8.096414 CCACAAAGAAAACAATTCTGGGATATT 58.904 33.333 0.00 0.00 0.00 1.28
153 154 7.235399 ACCACAAAGAAAACAATTCTGGGATAT 59.765 33.333 0.00 0.00 0.00 1.63
154 155 6.553100 ACCACAAAGAAAACAATTCTGGGATA 59.447 34.615 0.00 0.00 0.00 2.59
155 156 5.366477 ACCACAAAGAAAACAATTCTGGGAT 59.634 36.000 0.00 0.00 0.00 3.85
156 157 4.714308 ACCACAAAGAAAACAATTCTGGGA 59.286 37.500 0.00 0.00 0.00 4.37
157 158 5.022282 ACCACAAAGAAAACAATTCTGGG 57.978 39.130 0.00 0.00 0.00 4.45
158 159 9.757227 TTTATACCACAAAGAAAACAATTCTGG 57.243 29.630 0.00 0.00 0.00 3.86
186 187 9.410556 GTCTTGTAAGTATTTCATGTTGCAAAT 57.589 29.630 0.00 0.00 0.00 2.32
187 188 8.629158 AGTCTTGTAAGTATTTCATGTTGCAAA 58.371 29.630 0.00 0.00 0.00 3.68
188 189 8.165239 AGTCTTGTAAGTATTTCATGTTGCAA 57.835 30.769 0.00 0.00 0.00 4.08
189 190 7.744087 AGTCTTGTAAGTATTTCATGTTGCA 57.256 32.000 0.00 0.00 0.00 4.08
190 191 8.507249 AGAAGTCTTGTAAGTATTTCATGTTGC 58.493 33.333 0.00 0.00 0.00 4.17
191 192 9.817365 CAGAAGTCTTGTAAGTATTTCATGTTG 57.183 33.333 0.00 0.00 0.00 3.33
192 193 9.561069 ACAGAAGTCTTGTAAGTATTTCATGTT 57.439 29.630 0.00 0.00 0.00 2.71
201 202 9.352191 AGTCTTTCTACAGAAGTCTTGTAAGTA 57.648 33.333 0.00 0.00 35.21 2.24
202 203 8.138712 CAGTCTTTCTACAGAAGTCTTGTAAGT 58.861 37.037 0.00 0.00 35.21 2.24
203 204 8.138712 ACAGTCTTTCTACAGAAGTCTTGTAAG 58.861 37.037 0.00 0.00 35.21 2.34
204 205 7.921214 CACAGTCTTTCTACAGAAGTCTTGTAA 59.079 37.037 0.00 0.00 35.21 2.41
205 206 7.426410 CACAGTCTTTCTACAGAAGTCTTGTA 58.574 38.462 0.00 0.00 35.21 2.41
206 207 6.276847 CACAGTCTTTCTACAGAAGTCTTGT 58.723 40.000 0.00 0.00 35.21 3.16
207 208 5.694006 CCACAGTCTTTCTACAGAAGTCTTG 59.306 44.000 0.00 0.00 35.21 3.02
208 209 5.364157 ACCACAGTCTTTCTACAGAAGTCTT 59.636 40.000 0.00 0.00 35.21 3.01
209 210 4.896482 ACCACAGTCTTTCTACAGAAGTCT 59.104 41.667 0.00 0.00 35.21 3.24
210 211 5.203060 ACCACAGTCTTTCTACAGAAGTC 57.797 43.478 0.00 0.00 35.21 3.01
211 212 4.649674 TGACCACAGTCTTTCTACAGAAGT 59.350 41.667 0.00 0.00 43.91 3.01
212 213 5.010112 TCTGACCACAGTCTTTCTACAGAAG 59.990 44.000 0.00 0.00 43.91 2.85
213 214 4.893524 TCTGACCACAGTCTTTCTACAGAA 59.106 41.667 0.00 0.00 43.91 3.02
214 215 4.470602 TCTGACCACAGTCTTTCTACAGA 58.529 43.478 0.00 0.00 43.91 3.41
215 216 4.855715 TCTGACCACAGTCTTTCTACAG 57.144 45.455 0.00 0.00 43.91 2.74
216 217 5.511373 CCAATCTGACCACAGTCTTTCTACA 60.511 44.000 0.00 0.00 43.91 2.74
217 218 4.932200 CCAATCTGACCACAGTCTTTCTAC 59.068 45.833 0.00 0.00 43.91 2.59
218 219 4.838423 TCCAATCTGACCACAGTCTTTCTA 59.162 41.667 0.00 0.00 43.91 2.10
219 220 3.648067 TCCAATCTGACCACAGTCTTTCT 59.352 43.478 0.00 0.00 43.91 2.52
220 221 3.999663 CTCCAATCTGACCACAGTCTTTC 59.000 47.826 0.00 0.00 43.91 2.62
221 222 3.648067 TCTCCAATCTGACCACAGTCTTT 59.352 43.478 0.00 0.00 43.91 2.52
222 223 3.242867 TCTCCAATCTGACCACAGTCTT 58.757 45.455 0.00 0.00 43.91 3.01
223 224 2.894731 TCTCCAATCTGACCACAGTCT 58.105 47.619 0.00 0.00 43.91 3.24
224 225 3.007398 ACTTCTCCAATCTGACCACAGTC 59.993 47.826 0.00 0.00 43.81 3.51
225 226 2.975489 ACTTCTCCAATCTGACCACAGT 59.025 45.455 0.00 0.00 43.81 3.55
226 227 3.007290 TCACTTCTCCAATCTGACCACAG 59.993 47.826 0.00 0.00 44.66 3.66
227 228 2.972021 TCACTTCTCCAATCTGACCACA 59.028 45.455 0.00 0.00 0.00 4.17
228 229 3.330267 GTCACTTCTCCAATCTGACCAC 58.670 50.000 0.00 0.00 0.00 4.16
229 230 2.029020 CGTCACTTCTCCAATCTGACCA 60.029 50.000 0.00 0.00 0.00 4.02
230 231 2.611518 CGTCACTTCTCCAATCTGACC 58.388 52.381 0.00 0.00 0.00 4.02
231 232 1.996191 GCGTCACTTCTCCAATCTGAC 59.004 52.381 0.00 0.00 0.00 3.51
232 233 1.066858 GGCGTCACTTCTCCAATCTGA 60.067 52.381 0.00 0.00 0.00 3.27
233 234 1.338105 TGGCGTCACTTCTCCAATCTG 60.338 52.381 0.00 0.00 0.00 2.90
234 235 0.976641 TGGCGTCACTTCTCCAATCT 59.023 50.000 0.00 0.00 0.00 2.40
235 236 1.079503 GTGGCGTCACTTCTCCAATC 58.920 55.000 14.12 0.00 40.58 2.67
236 237 3.233355 GTGGCGTCACTTCTCCAAT 57.767 52.632 14.12 0.00 40.58 3.16
237 238 4.771127 GTGGCGTCACTTCTCCAA 57.229 55.556 14.12 0.00 40.58 3.53
245 246 7.709269 TTTCATAATTATAGAGTGGCGTCAC 57.291 36.000 13.44 13.44 43.93 3.67
246 247 9.990360 TTATTTCATAATTATAGAGTGGCGTCA 57.010 29.630 0.00 0.00 0.00 4.35
307 308 9.627123 CCCAACTAACTTATATCTGGATTCAAA 57.373 33.333 0.00 0.00 0.00 2.69
308 309 8.998814 TCCCAACTAACTTATATCTGGATTCAA 58.001 33.333 0.00 0.00 0.00 2.69
309 310 8.561536 TCCCAACTAACTTATATCTGGATTCA 57.438 34.615 0.00 0.00 0.00 2.57
473 475 4.796231 GCGGTGGCACGAGACGAT 62.796 66.667 16.36 0.00 39.62 3.73
543 548 0.306840 GCGCCGCCTCCTTTTTATAC 59.693 55.000 0.00 0.00 0.00 1.47
970 1030 4.889856 CATCCATGGCCGTCGCGA 62.890 66.667 3.71 3.71 35.02 5.87
1024 1085 1.384502 CCTCCCCCATAGCCTCACA 60.385 63.158 0.00 0.00 0.00 3.58
1160 1221 0.179127 CGCACCATCAGATCGAGTGT 60.179 55.000 0.00 0.00 0.00 3.55
1165 1226 1.524355 GATGAACGCACCATCAGATCG 59.476 52.381 7.22 0.00 39.98 3.69
1422 1488 9.654663 AAAGACAAGGAATATACACTACTTCAC 57.345 33.333 0.00 0.00 0.00 3.18
2030 2186 5.488341 ACCAAGAAGCACAGATAAATACGT 58.512 37.500 0.00 0.00 0.00 3.57


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

AutoCloner maintained by Alex Coulton.