Multiple sequence alignment - TraesCS3D01G317700

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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 TraesCS3D01G317700 chr3D 100.000 3419 0 0 1 3419 431626906 431630324 0.000000e+00 6314
1 TraesCS3D01G317700 chr3D 93.847 2974 133 24 458 3407 431447718 431450665 0.000000e+00 4433
2 TraesCS3D01G317700 chr3D 87.901 2149 208 25 855 2970 431831829 431833958 0.000000e+00 2481
3 TraesCS3D01G317700 chr3D 85.640 1539 192 12 1143 2677 438047162 438048675 0.000000e+00 1591
4 TraesCS3D01G317700 chr3D 90.431 209 18 1 2968 3174 431834107 431834315 1.210000e-69 274
5 TraesCS3D01G317700 chr3D 80.833 360 58 10 463 816 434912895 434913249 4.350000e-69 272
6 TraesCS3D01G317700 chr3D 87.791 172 16 3 3237 3407 431836598 431836765 2.690000e-46 196
7 TraesCS3D01G317700 chr3D 90.909 88 8 0 3043 3130 431834313 431834400 5.990000e-23 119
8 TraesCS3D01G317700 chr3B 94.790 2572 91 17 854 3419 564023129 564025663 0.000000e+00 3967
9 TraesCS3D01G317700 chr3B 88.015 2161 209 20 846 2970 564038006 564040152 0.000000e+00 2510
10 TraesCS3D01G317700 chr3B 84.239 368 49 7 455 819 27380834 27381195 1.950000e-92 350
11 TraesCS3D01G317700 chr3B 88.304 171 16 2 3237 3407 564040618 564040784 5.790000e-48 202
12 TraesCS3D01G317700 chr3B 87.903 124 13 1 3048 3169 564040496 564040619 9.890000e-31 145
13 TraesCS3D01G317700 chr3A 93.575 2179 94 15 412 2548 568971353 568973527 0.000000e+00 3206
14 TraesCS3D01G317700 chr3A 94.011 2037 83 7 650 2673 569167265 569169275 0.000000e+00 3049
15 TraesCS3D01G317700 chr3A 87.175 2152 217 26 855 2970 569229972 569232100 0.000000e+00 2390
16 TraesCS3D01G317700 chr3A 96.937 914 27 1 2507 3419 569169276 569170189 0.000000e+00 1531
17 TraesCS3D01G317700 chr3A 84.414 1450 172 20 860 2284 576270159 576268739 0.000000e+00 1376
18 TraesCS3D01G317700 chr3A 85.147 1360 172 11 1209 2563 576273681 576275015 0.000000e+00 1365
19 TraesCS3D01G317700 chr3A 89.254 335 30 3 2349 2677 576268711 576268377 6.830000e-112 414
20 TraesCS3D01G317700 chr3A 78.727 597 68 32 254 819 728617278 728617846 9.080000e-91 344
21 TraesCS3D01G317700 chr3A 94.444 180 10 0 2546 2725 568973580 568973759 9.340000e-71 278
22 TraesCS3D01G317700 chr3A 88.550 131 15 0 2547 2677 576275198 576275328 3.530000e-35 159
23 TraesCS3D01G317700 chr7D 95.305 213 9 1 1 212 301331446 301331234 1.520000e-88 337
24 TraesCS3D01G317700 chr7D 85.075 268 16 7 1 247 2722502 2722766 5.660000e-63 252
25 TraesCS3D01G317700 chr7D 92.025 163 9 3 37 197 433310426 433310266 3.430000e-55 226
26 TraesCS3D01G317700 chr1A 78.399 537 90 23 250 773 456286855 456287378 3.290000e-85 326
27 TraesCS3D01G317700 chr1A 76.936 607 73 30 263 818 6220046 6219456 2.010000e-72 283
28 TraesCS3D01G317700 chr1A 78.652 356 60 11 428 774 26946368 26946716 4.440000e-54 222
29 TraesCS3D01G317700 chr2B 91.667 228 16 3 1 228 513700080 513699856 2.560000e-81 313
30 TraesCS3D01G317700 chr6A 81.818 363 56 8 462 819 541600939 541600582 2.580000e-76 296
31 TraesCS3D01G317700 chr7B 78.227 519 69 26 260 762 687811428 687810938 3.340000e-75 292
32 TraesCS3D01G317700 chr7A 93.467 199 9 3 1 198 303947431 303947236 3.340000e-75 292
33 TraesCS3D01G317700 chr1B 76.964 560 96 25 260 808 92586600 92586063 4.320000e-74 289
34 TraesCS3D01G317700 chr5D 77.413 518 88 24 261 763 249535855 249536358 7.220000e-72 281
35 TraesCS3D01G317700 chr4A 88.987 227 18 7 5 228 407483664 407483886 1.210000e-69 274
36 TraesCS3D01G317700 chr4D 80.663 362 59 9 462 819 434100938 434101292 1.560000e-68 270
37 TraesCS3D01G317700 chr2D 85.824 261 13 6 1 240 346006594 346006851 4.380000e-64 255
38 TraesCS3D01G317700 chr2D 77.324 441 68 21 260 687 20322295 20321874 7.380000e-57 231
39 TraesCS3D01G317700 chr2D 85.714 217 9 5 1 195 642896252 642896036 3.460000e-50 209
40 TraesCS3D01G317700 chr4B 76.038 530 82 33 261 767 494691394 494690887 2.050000e-57 233
41 TraesCS3D01G317700 chrUn 93.631 157 6 3 37 191 213242601 213242755 7.380000e-57 231
42 TraesCS3D01G317700 chrUn 92.025 163 9 3 37 197 418480739 418480579 3.430000e-55 226
43 TraesCS3D01G317700 chrUn 76.023 513 68 33 265 756 334883981 334884459 7.430000e-52 215
44 TraesCS3D01G317700 chr1D 81.498 227 26 11 260 478 250221798 250221580 4.540000e-39 172


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 TraesCS3D01G317700 chr3D 431626906 431630324 3418 False 6314.000000 6314 100.0000 1 3419 1 chr3D.!!$F2 3418
1 TraesCS3D01G317700 chr3D 431447718 431450665 2947 False 4433.000000 4433 93.8470 458 3407 1 chr3D.!!$F1 2949
2 TraesCS3D01G317700 chr3D 438047162 438048675 1513 False 1591.000000 1591 85.6400 1143 2677 1 chr3D.!!$F4 1534
3 TraesCS3D01G317700 chr3D 431831829 431836765 4936 False 767.500000 2481 89.2580 855 3407 4 chr3D.!!$F5 2552
4 TraesCS3D01G317700 chr3B 564023129 564025663 2534 False 3967.000000 3967 94.7900 854 3419 1 chr3B.!!$F2 2565
5 TraesCS3D01G317700 chr3B 564038006 564040784 2778 False 952.333333 2510 88.0740 846 3407 3 chr3B.!!$F3 2561
6 TraesCS3D01G317700 chr3A 569229972 569232100 2128 False 2390.000000 2390 87.1750 855 2970 1 chr3A.!!$F1 2115
7 TraesCS3D01G317700 chr3A 569167265 569170189 2924 False 2290.000000 3049 95.4740 650 3419 2 chr3A.!!$F4 2769
8 TraesCS3D01G317700 chr3A 568971353 568973759 2406 False 1742.000000 3206 94.0095 412 2725 2 chr3A.!!$F3 2313
9 TraesCS3D01G317700 chr3A 576268377 576270159 1782 True 895.000000 1376 86.8340 860 2677 2 chr3A.!!$R1 1817
10 TraesCS3D01G317700 chr3A 576273681 576275328 1647 False 762.000000 1365 86.8485 1209 2677 2 chr3A.!!$F5 1468
11 TraesCS3D01G317700 chr3A 728617278 728617846 568 False 344.000000 344 78.7270 254 819 1 chr3A.!!$F2 565
12 TraesCS3D01G317700 chr1A 456286855 456287378 523 False 326.000000 326 78.3990 250 773 1 chr1A.!!$F2 523
13 TraesCS3D01G317700 chr1A 6219456 6220046 590 True 283.000000 283 76.9360 263 818 1 chr1A.!!$R1 555
14 TraesCS3D01G317700 chr1B 92586063 92586600 537 True 289.000000 289 76.9640 260 808 1 chr1B.!!$R1 548
15 TraesCS3D01G317700 chr5D 249535855 249536358 503 False 281.000000 281 77.4130 261 763 1 chr5D.!!$F1 502
16 TraesCS3D01G317700 chr4B 494690887 494691394 507 True 233.000000 233 76.0380 261 767 1 chr4B.!!$R1 506

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
357 362 0.977395 AGGAGGTTACAGCCTGTGTC 59.023 55.000 7.83 0.0 40.94 3.67 F
1734 2129 1.449956 CTCAGCTGCTCTTGAGGCC 60.450 63.158 9.47 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 2320 1.818363 ACGGCAGCTGCATCATCAG 60.818 57.895 37.63 20.83 44.36 2.90 R
3150 4259 4.824289 TCGTAATTAAAGGAAGTCGGCTT 58.176 39.130 0.00 0.00 37.71 4.35 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
76 77 9.649167 TTTTTGCCAAATTCATGAACAATTTTT 57.351 22.222 11.07 4.20 32.25 1.94
77 78 8.630278 TTTGCCAAATTCATGAACAATTTTTG 57.370 26.923 11.07 15.79 32.25 2.44
78 79 7.563888 TGCCAAATTCATGAACAATTTTTGA 57.436 28.000 23.59 9.52 32.25 2.69
79 80 7.993101 TGCCAAATTCATGAACAATTTTTGAA 58.007 26.923 23.59 13.69 32.25 2.69
80 81 8.630917 TGCCAAATTCATGAACAATTTTTGAAT 58.369 25.926 23.59 0.00 38.35 2.57
81 82 9.465985 GCCAAATTCATGAACAATTTTTGAATT 57.534 25.926 23.59 5.24 44.57 2.17
86 87 9.703892 ATTCATGAACAATTTTTGAATTACCGA 57.296 25.926 11.07 0.00 34.29 4.69
87 88 8.741101 TCATGAACAATTTTTGAATTACCGAG 57.259 30.769 0.00 0.00 0.00 4.63
88 89 7.328249 TCATGAACAATTTTTGAATTACCGAGC 59.672 33.333 0.00 0.00 0.00 5.03
89 90 6.507900 TGAACAATTTTTGAATTACCGAGCA 58.492 32.000 0.00 0.00 0.00 4.26
90 91 7.151308 TGAACAATTTTTGAATTACCGAGCAT 58.849 30.769 0.00 0.00 0.00 3.79
91 92 7.328249 TGAACAATTTTTGAATTACCGAGCATC 59.672 33.333 0.00 0.00 0.00 3.91
92 93 6.924111 ACAATTTTTGAATTACCGAGCATCT 58.076 32.000 0.00 0.00 0.00 2.90
93 94 7.378181 ACAATTTTTGAATTACCGAGCATCTT 58.622 30.769 0.00 0.00 0.00 2.40
94 95 7.872483 ACAATTTTTGAATTACCGAGCATCTTT 59.128 29.630 0.00 0.00 0.00 2.52
95 96 8.711457 CAATTTTTGAATTACCGAGCATCTTTT 58.289 29.630 0.00 0.00 0.00 2.27
96 97 8.831715 ATTTTTGAATTACCGAGCATCTTTTT 57.168 26.923 0.00 0.00 0.00 1.94
97 98 7.636259 TTTTGAATTACCGAGCATCTTTTTG 57.364 32.000 0.00 0.00 0.00 2.44
98 99 5.309323 TGAATTACCGAGCATCTTTTTGG 57.691 39.130 0.00 0.00 0.00 3.28
99 100 5.007034 TGAATTACCGAGCATCTTTTTGGA 58.993 37.500 0.00 0.00 0.00 3.53
100 101 5.475220 TGAATTACCGAGCATCTTTTTGGAA 59.525 36.000 0.00 0.00 0.00 3.53
101 102 5.975693 ATTACCGAGCATCTTTTTGGAAA 57.024 34.783 0.00 0.00 0.00 3.13
102 103 5.975693 TTACCGAGCATCTTTTTGGAAAT 57.024 34.783 0.00 0.00 0.00 2.17
103 104 4.440839 ACCGAGCATCTTTTTGGAAATC 57.559 40.909 0.00 0.00 0.00 2.17
104 105 3.826157 ACCGAGCATCTTTTTGGAAATCA 59.174 39.130 0.00 0.00 0.00 2.57
105 106 4.463891 ACCGAGCATCTTTTTGGAAATCAT 59.536 37.500 0.00 0.00 0.00 2.45
106 107 4.802039 CCGAGCATCTTTTTGGAAATCATG 59.198 41.667 0.00 0.00 0.00 3.07
107 108 5.393352 CCGAGCATCTTTTTGGAAATCATGA 60.393 40.000 0.00 0.00 0.00 3.07
108 109 6.270815 CGAGCATCTTTTTGGAAATCATGAT 58.729 36.000 1.18 1.18 0.00 2.45
109 110 6.755141 CGAGCATCTTTTTGGAAATCATGATT 59.245 34.615 15.36 15.36 0.00 2.57
110 111 7.253983 CGAGCATCTTTTTGGAAATCATGATTG 60.254 37.037 21.39 6.74 0.00 2.67
111 112 7.391620 AGCATCTTTTTGGAAATCATGATTGT 58.608 30.769 21.39 11.51 0.00 2.71
112 113 7.881232 AGCATCTTTTTGGAAATCATGATTGTT 59.119 29.630 21.39 7.02 0.00 2.83
113 114 8.508875 GCATCTTTTTGGAAATCATGATTGTTT 58.491 29.630 21.39 7.09 0.00 2.83
148 149 9.914131 ATTAGCAACTTTTCTGAAATTTAGGAC 57.086 29.630 3.31 0.00 0.00 3.85
149 150 6.749139 AGCAACTTTTCTGAAATTTAGGACC 58.251 36.000 3.31 0.00 0.00 4.46
150 151 6.551227 AGCAACTTTTCTGAAATTTAGGACCT 59.449 34.615 3.31 0.00 0.00 3.85
151 152 7.069950 AGCAACTTTTCTGAAATTTAGGACCTT 59.930 33.333 0.00 0.00 0.00 3.50
152 153 7.710907 GCAACTTTTCTGAAATTTAGGACCTTT 59.289 33.333 0.00 0.00 0.00 3.11
153 154 9.599866 CAACTTTTCTGAAATTTAGGACCTTTT 57.400 29.630 0.00 0.00 0.00 2.27
154 155 9.817809 AACTTTTCTGAAATTTAGGACCTTTTC 57.182 29.630 0.00 4.70 0.00 2.29
155 156 8.977412 ACTTTTCTGAAATTTAGGACCTTTTCA 58.023 29.630 15.77 15.77 36.80 2.69
156 157 9.987272 CTTTTCTGAAATTTAGGACCTTTTCAT 57.013 29.630 16.61 0.00 37.43 2.57
162 163 8.682710 TGAAATTTAGGACCTTTTCATATTCCG 58.317 33.333 13.55 0.00 34.20 4.30
163 164 8.817092 AAATTTAGGACCTTTTCATATTCCGA 57.183 30.769 0.00 0.00 0.00 4.55
164 165 8.817092 AATTTAGGACCTTTTCATATTCCGAA 57.183 30.769 0.00 0.00 0.00 4.30
165 166 8.996651 ATTTAGGACCTTTTCATATTCCGAAT 57.003 30.769 0.00 0.00 0.00 3.34
166 167 8.817092 TTTAGGACCTTTTCATATTCCGAATT 57.183 30.769 0.00 0.00 0.00 2.17
167 168 9.908747 TTTAGGACCTTTTCATATTCCGAATTA 57.091 29.630 0.00 0.00 0.00 1.40
169 170 8.996651 AGGACCTTTTCATATTCCGAATTATT 57.003 30.769 0.00 0.00 0.00 1.40
170 171 8.850156 AGGACCTTTTCATATTCCGAATTATTG 58.150 33.333 0.00 0.00 0.00 1.90
171 172 8.846211 GGACCTTTTCATATTCCGAATTATTGA 58.154 33.333 0.00 0.00 0.00 2.57
218 219 5.922739 AAAATGAAAAAGGAAACATCCGC 57.077 34.783 0.00 0.00 34.28 5.54
219 220 4.599047 AATGAAAAAGGAAACATCCGCA 57.401 36.364 0.00 0.00 34.28 5.69
220 221 4.599047 ATGAAAAAGGAAACATCCGCAA 57.401 36.364 0.00 0.00 34.28 4.85
221 222 4.392921 TGAAAAAGGAAACATCCGCAAA 57.607 36.364 0.00 0.00 34.28 3.68
222 223 4.759782 TGAAAAAGGAAACATCCGCAAAA 58.240 34.783 0.00 0.00 34.28 2.44
223 224 5.178797 TGAAAAAGGAAACATCCGCAAAAA 58.821 33.333 0.00 0.00 34.28 1.94
224 225 5.293079 TGAAAAAGGAAACATCCGCAAAAAG 59.707 36.000 0.00 0.00 34.28 2.27
225 226 4.664150 AAAGGAAACATCCGCAAAAAGA 57.336 36.364 0.00 0.00 34.28 2.52
226 227 4.664150 AAGGAAACATCCGCAAAAAGAA 57.336 36.364 0.00 0.00 34.28 2.52
227 228 4.664150 AGGAAACATCCGCAAAAAGAAA 57.336 36.364 0.00 0.00 34.28 2.52
228 229 5.017294 AGGAAACATCCGCAAAAAGAAAA 57.983 34.783 0.00 0.00 34.28 2.29
229 230 5.423886 AGGAAACATCCGCAAAAAGAAAAA 58.576 33.333 0.00 0.00 34.28 1.94
246 247 3.292159 AAAAACAGGCGGCGTCCC 61.292 61.111 8.37 0.48 0.00 4.46
247 248 3.785122 AAAAACAGGCGGCGTCCCT 62.785 57.895 8.37 3.53 0.00 4.20
248 249 2.400269 AAAAACAGGCGGCGTCCCTA 62.400 55.000 8.37 0.00 0.00 3.53
249 250 2.193087 AAAACAGGCGGCGTCCCTAT 62.193 55.000 8.37 0.00 0.00 2.57
250 251 1.332144 AAACAGGCGGCGTCCCTATA 61.332 55.000 8.37 0.00 0.00 1.31
251 252 1.745320 AACAGGCGGCGTCCCTATAG 61.745 60.000 8.37 0.00 0.00 1.31
252 253 2.600769 AGGCGGCGTCCCTATAGG 60.601 66.667 8.37 12.27 0.00 2.57
253 254 4.374645 GGCGGCGTCCCTATAGGC 62.375 72.222 13.85 1.59 34.51 3.93
256 257 2.916181 GGCGTCCCTATAGGCGGT 60.916 66.667 13.85 0.00 36.18 5.68
257 258 2.649614 GCGTCCCTATAGGCGGTC 59.350 66.667 13.85 2.46 36.18 4.79
258 259 2.928741 GCGTCCCTATAGGCGGTCC 61.929 68.421 13.85 0.00 36.18 4.46
259 260 2.273912 CGTCCCTATAGGCGGTCCC 61.274 68.421 13.85 0.00 33.26 4.46
355 360 3.540211 CAGGAGGTTACAGCCTGTG 57.460 57.895 7.83 0.00 43.25 3.66
357 362 0.977395 AGGAGGTTACAGCCTGTGTC 59.023 55.000 7.83 0.00 40.94 3.67
1734 2129 1.449956 CTCAGCTGCTCTTGAGGCC 60.450 63.158 9.47 0.00 0.00 5.19
1925 2320 0.110486 TTGGTTGCAGAAGGGAGGAC 59.890 55.000 0.00 0.00 0.00 3.85
2063 2458 5.221185 CCAAGAAGCTGTATGATGATTTGGG 60.221 44.000 0.00 0.00 0.00 4.12
2860 3687 5.923204 AGTATTTCTCTTCGAAGCATGGAT 58.077 37.500 20.56 11.92 32.21 3.41
2863 3690 6.610741 ATTTCTCTTCGAAGCATGGATAAC 57.389 37.500 20.56 0.00 32.21 1.89
2864 3691 4.736126 TCTCTTCGAAGCATGGATAACA 57.264 40.909 20.56 0.00 0.00 2.41
3055 4162 9.098355 CTGATCATATAGTGAGCTAGTAGAGTC 57.902 40.741 0.00 0.00 43.59 3.36
3089 4196 7.617041 ACAAGGAAGAACTGTATGAATTAGC 57.383 36.000 0.00 0.00 0.00 3.09
3150 4259 7.482169 TCTTGCTTTCTAAGAAGATGGTAGA 57.518 36.000 0.00 0.00 31.62 2.59
3158 4267 2.741145 AGAAGATGGTAGAAGCCGACT 58.259 47.619 0.00 0.00 0.00 4.18
3409 6744 6.410942 TGTCAGGACTAGAATCATGTATGG 57.589 41.667 0.00 0.00 32.26 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 9.649167 AAAAATTGTTCATGAATTTGGCAAAAA 57.351 22.222 17.70 6.30 34.09 1.94
51 52 9.084164 CAAAAATTGTTCATGAATTTGGCAAAA 57.916 25.926 17.70 0.38 34.09 2.44
52 53 8.464404 TCAAAAATTGTTCATGAATTTGGCAAA 58.536 25.926 22.21 16.01 34.09 3.68
53 54 7.993101 TCAAAAATTGTTCATGAATTTGGCAA 58.007 26.923 22.21 16.74 34.09 4.52
54 55 7.563888 TCAAAAATTGTTCATGAATTTGGCA 57.436 28.000 22.21 10.41 34.09 4.92
55 56 9.465985 AATTCAAAAATTGTTCATGAATTTGGC 57.534 25.926 22.21 8.32 44.14 4.52
60 61 9.703892 TCGGTAATTCAAAAATTGTTCATGAAT 57.296 25.926 12.12 0.00 41.20 2.57
61 62 9.190858 CTCGGTAATTCAAAAATTGTTCATGAA 57.809 29.630 3.38 3.38 35.84 2.57
62 63 7.328249 GCTCGGTAATTCAAAAATTGTTCATGA 59.672 33.333 0.00 0.00 35.84 3.07
63 64 7.116090 TGCTCGGTAATTCAAAAATTGTTCATG 59.884 33.333 0.00 0.00 35.84 3.07
64 65 7.151308 TGCTCGGTAATTCAAAAATTGTTCAT 58.849 30.769 0.00 0.00 35.84 2.57
65 66 6.507900 TGCTCGGTAATTCAAAAATTGTTCA 58.492 32.000 0.00 0.00 35.84 3.18
66 67 7.542130 AGATGCTCGGTAATTCAAAAATTGTTC 59.458 33.333 0.00 0.00 35.84 3.18
67 68 7.378181 AGATGCTCGGTAATTCAAAAATTGTT 58.622 30.769 0.00 0.00 35.84 2.83
68 69 6.924111 AGATGCTCGGTAATTCAAAAATTGT 58.076 32.000 0.00 0.00 35.84 2.71
69 70 7.816945 AAGATGCTCGGTAATTCAAAAATTG 57.183 32.000 0.00 0.00 35.84 2.32
70 71 8.831715 AAAAGATGCTCGGTAATTCAAAAATT 57.168 26.923 0.00 0.00 38.61 1.82
71 72 8.711457 CAAAAAGATGCTCGGTAATTCAAAAAT 58.289 29.630 0.00 0.00 0.00 1.82
72 73 7.170658 CCAAAAAGATGCTCGGTAATTCAAAAA 59.829 33.333 0.00 0.00 0.00 1.94
73 74 6.644592 CCAAAAAGATGCTCGGTAATTCAAAA 59.355 34.615 0.00 0.00 0.00 2.44
74 75 6.015856 TCCAAAAAGATGCTCGGTAATTCAAA 60.016 34.615 0.00 0.00 0.00 2.69
75 76 5.475220 TCCAAAAAGATGCTCGGTAATTCAA 59.525 36.000 0.00 0.00 0.00 2.69
76 77 5.007034 TCCAAAAAGATGCTCGGTAATTCA 58.993 37.500 0.00 0.00 0.00 2.57
77 78 5.560966 TCCAAAAAGATGCTCGGTAATTC 57.439 39.130 0.00 0.00 0.00 2.17
78 79 5.975693 TTCCAAAAAGATGCTCGGTAATT 57.024 34.783 0.00 0.00 0.00 1.40
79 80 5.975693 TTTCCAAAAAGATGCTCGGTAAT 57.024 34.783 0.00 0.00 0.00 1.89
80 81 5.475220 TGATTTCCAAAAAGATGCTCGGTAA 59.525 36.000 0.00 0.00 0.00 2.85
81 82 5.007034 TGATTTCCAAAAAGATGCTCGGTA 58.993 37.500 0.00 0.00 0.00 4.02
82 83 3.826157 TGATTTCCAAAAAGATGCTCGGT 59.174 39.130 0.00 0.00 0.00 4.69
83 84 4.439305 TGATTTCCAAAAAGATGCTCGG 57.561 40.909 0.00 0.00 0.00 4.63
84 85 5.643664 TCATGATTTCCAAAAAGATGCTCG 58.356 37.500 0.00 0.00 0.00 5.03
85 86 7.548075 ACAATCATGATTTCCAAAAAGATGCTC 59.452 33.333 18.41 0.00 0.00 4.26
86 87 7.391620 ACAATCATGATTTCCAAAAAGATGCT 58.608 30.769 18.41 0.00 0.00 3.79
87 88 7.605410 ACAATCATGATTTCCAAAAAGATGC 57.395 32.000 18.41 0.00 0.00 3.91
122 123 9.914131 GTCCTAAATTTCAGAAAAGTTGCTAAT 57.086 29.630 0.00 0.00 33.92 1.73
123 124 8.357402 GGTCCTAAATTTCAGAAAAGTTGCTAA 58.643 33.333 0.00 0.00 33.92 3.09
124 125 7.724061 AGGTCCTAAATTTCAGAAAAGTTGCTA 59.276 33.333 0.00 0.00 33.92 3.49
125 126 6.551227 AGGTCCTAAATTTCAGAAAAGTTGCT 59.449 34.615 0.00 0.00 33.92 3.91
126 127 6.749139 AGGTCCTAAATTTCAGAAAAGTTGC 58.251 36.000 0.00 0.00 33.92 4.17
127 128 9.599866 AAAAGGTCCTAAATTTCAGAAAAGTTG 57.400 29.630 0.00 0.00 33.92 3.16
128 129 9.817809 GAAAAGGTCCTAAATTTCAGAAAAGTT 57.182 29.630 8.95 0.42 36.67 2.66
129 130 8.977412 TGAAAAGGTCCTAAATTTCAGAAAAGT 58.023 29.630 11.61 0.00 36.99 2.66
130 131 9.987272 ATGAAAAGGTCCTAAATTTCAGAAAAG 57.013 29.630 17.94 0.00 42.89 2.27
136 137 8.682710 CGGAATATGAAAAGGTCCTAAATTTCA 58.317 33.333 16.17 16.17 43.53 2.69
137 138 8.899771 TCGGAATATGAAAAGGTCCTAAATTTC 58.100 33.333 7.37 7.37 33.48 2.17
138 139 8.817092 TCGGAATATGAAAAGGTCCTAAATTT 57.183 30.769 0.00 0.00 0.00 1.82
139 140 8.817092 TTCGGAATATGAAAAGGTCCTAAATT 57.183 30.769 0.00 0.00 0.00 1.82
140 141 8.996651 ATTCGGAATATGAAAAGGTCCTAAAT 57.003 30.769 0.34 0.00 0.00 1.40
141 142 8.817092 AATTCGGAATATGAAAAGGTCCTAAA 57.183 30.769 3.22 0.00 0.00 1.85
144 145 8.850156 CAATAATTCGGAATATGAAAAGGTCCT 58.150 33.333 3.22 0.00 0.00 3.85
145 146 8.846211 TCAATAATTCGGAATATGAAAAGGTCC 58.154 33.333 3.22 0.00 0.00 4.46
195 196 5.819901 TGCGGATGTTTCCTTTTTCATTTTT 59.180 32.000 0.00 0.00 40.17 1.94
196 197 5.363939 TGCGGATGTTTCCTTTTTCATTTT 58.636 33.333 0.00 0.00 40.17 1.82
197 198 4.954875 TGCGGATGTTTCCTTTTTCATTT 58.045 34.783 0.00 0.00 40.17 2.32
198 199 4.599047 TGCGGATGTTTCCTTTTTCATT 57.401 36.364 0.00 0.00 40.17 2.57
199 200 4.599047 TTGCGGATGTTTCCTTTTTCAT 57.401 36.364 0.00 0.00 40.17 2.57
200 201 4.392921 TTTGCGGATGTTTCCTTTTTCA 57.607 36.364 0.00 0.00 40.17 2.69
201 202 5.522097 TCTTTTTGCGGATGTTTCCTTTTTC 59.478 36.000 0.00 0.00 40.17 2.29
202 203 5.423886 TCTTTTTGCGGATGTTTCCTTTTT 58.576 33.333 0.00 0.00 40.17 1.94
203 204 5.017294 TCTTTTTGCGGATGTTTCCTTTT 57.983 34.783 0.00 0.00 40.17 2.27
204 205 4.664150 TCTTTTTGCGGATGTTTCCTTT 57.336 36.364 0.00 0.00 40.17 3.11
205 206 4.664150 TTCTTTTTGCGGATGTTTCCTT 57.336 36.364 0.00 0.00 40.17 3.36
206 207 4.664150 TTTCTTTTTGCGGATGTTTCCT 57.336 36.364 0.00 0.00 40.17 3.36
207 208 5.726729 TTTTTCTTTTTGCGGATGTTTCC 57.273 34.783 0.00 0.00 38.81 3.13
229 230 2.400269 TAGGGACGCCGCCTGTTTTT 62.400 55.000 0.00 0.00 0.00 1.94
230 231 2.193087 ATAGGGACGCCGCCTGTTTT 62.193 55.000 0.00 0.00 0.00 2.43
231 232 1.332144 TATAGGGACGCCGCCTGTTT 61.332 55.000 0.00 0.00 0.00 2.83
232 233 1.745320 CTATAGGGACGCCGCCTGTT 61.745 60.000 0.00 0.00 0.00 3.16
233 234 2.123597 TATAGGGACGCCGCCTGT 60.124 61.111 0.00 0.00 0.00 4.00
234 235 2.651361 CTATAGGGACGCCGCCTG 59.349 66.667 0.00 0.00 0.00 4.85
235 236 2.600769 CCTATAGGGACGCCGCCT 60.601 66.667 11.33 0.00 37.23 5.52
236 237 4.374645 GCCTATAGGGACGCCGCC 62.375 72.222 20.58 0.00 37.23 6.13
237 238 4.719369 CGCCTATAGGGACGCCGC 62.719 72.222 20.58 3.01 37.23 6.53
238 239 4.052229 CCGCCTATAGGGACGCCG 62.052 72.222 20.58 13.85 37.23 6.46
239 240 2.916181 ACCGCCTATAGGGACGCC 60.916 66.667 20.58 2.16 37.23 5.68
240 241 2.649614 GACCGCCTATAGGGACGC 59.350 66.667 20.58 4.84 37.23 5.19
241 242 2.273912 GGGACCGCCTATAGGGACG 61.274 68.421 20.58 15.24 37.23 4.79
242 243 1.912264 GGGGACCGCCTATAGGGAC 60.912 68.421 20.58 3.65 40.86 4.46
243 244 2.529753 GGGGACCGCCTATAGGGA 59.470 66.667 20.58 0.00 40.86 4.20
258 259 3.253432 GCTTAAAGCGAGAAATATGGGGG 59.747 47.826 0.00 0.00 0.00 5.40
259 260 4.489679 GCTTAAAGCGAGAAATATGGGG 57.510 45.455 0.00 0.00 0.00 4.96
767 1081 4.930405 TCAACATTGTCCGAACGCTTATTA 59.070 37.500 0.00 0.00 0.00 0.98
1411 1806 2.182842 GCGCTTCGATGATGGCCTT 61.183 57.895 3.32 0.00 0.00 4.35
1925 2320 1.818363 ACGGCAGCTGCATCATCAG 60.818 57.895 37.63 20.83 44.36 2.90
2538 2941 6.273071 GGCAAGCTAAACCAATACCTTATTG 58.727 40.000 0.00 0.00 43.94 1.90
2863 3690 9.844790 AACTTCATGTATGTCATAACATTTGTG 57.155 29.630 0.00 0.00 43.74 3.33
3055 4162 5.163693 ACAGTTCTTCCTTGTTTGGTTTACG 60.164 40.000 0.00 0.00 0.00 3.18
3150 4259 4.824289 TCGTAATTAAAGGAAGTCGGCTT 58.176 39.130 0.00 0.00 37.71 4.35
3366 6701 5.636121 TGACATTTGACAACACTATCGGTAC 59.364 40.000 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.