Multiple sequence alignment - TraesCS7D01G176800

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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 TraesCS7D01G176800 chr7D 100.000 2558 0 0 1 2558 129493914 129496471 0.000000e+00 4724.0
1 TraesCS7D01G176800 chr7D 89.041 73 8 0 2482 2554 129491678 129491606 9.750000e-15 91.6
2 TraesCS7D01G176800 chr7D 89.041 73 8 0 2482 2554 129492473 129492401 9.750000e-15 91.6
3 TraesCS7D01G176800 chr7A 92.917 2273 103 16 317 2557 128838312 128840558 0.000000e+00 3253.0
4 TraesCS7D01G176800 chr7A 90.441 136 2 4 25 156 128838185 128838313 4.380000e-38 169.0
5 TraesCS7D01G176800 chr7B 92.203 1693 96 13 380 2050 90731382 90733060 0.000000e+00 2362.0
6 TraesCS7D01G176800 chr7B 90.678 472 37 5 1577 2045 90753961 90754428 2.800000e-174 621.0
7 TraesCS7D01G176800 chr7B 90.083 484 31 8 1577 2050 90743557 90744033 1.680000e-171 612.0
8 TraesCS7D01G176800 chr7B 90.062 483 32 6 1577 2050 90747694 90748169 1.680000e-171 612.0
9 TraesCS7D01G176800 chr7B 90.062 483 32 6 1577 2050 90750827 90751302 1.680000e-171 612.0
10 TraesCS7D01G176800 chr7B 89.050 484 32 7 1577 2050 90734153 90734625 4.740000e-162 580.0
11 TraesCS7D01G176800 chr7B 89.050 484 32 7 1577 2050 90735718 90736190 4.740000e-162 580.0
12 TraesCS7D01G176800 chr7B 89.050 484 32 7 1577 2050 90749262 90749734 4.740000e-162 580.0
13 TraesCS7D01G176800 chr7B 89.941 169 16 1 154 321 679620498 679620666 1.540000e-52 217.0
14 TraesCS7D01G176800 chr1D 91.824 159 13 0 163 321 473455951 473456109 3.310000e-54 222.0
15 TraesCS7D01G176800 chr1D 93.182 44 3 0 2510 2553 22617808 22617851 5.910000e-07 65.8
16 TraesCS7D01G176800 chr2D 91.613 155 13 0 167 321 6645246 6645092 5.540000e-52 215.0
17 TraesCS7D01G176800 chr2D 89.759 166 17 0 163 328 87407519 87407354 1.990000e-51 213.0
18 TraesCS7D01G176800 chr4D 90.566 159 15 0 167 325 505988097 505987939 7.170000e-51 211.0
19 TraesCS7D01G176800 chrUn 90.062 161 14 2 163 323 34210760 34210918 9.280000e-50 207.0
20 TraesCS7D01G176800 chr3B 89.634 164 15 2 163 325 403826558 403826720 9.280000e-50 207.0
21 TraesCS7D01G176800 chr5B 89.091 165 18 0 157 321 395709768 395709932 3.340000e-49 206.0
22 TraesCS7D01G176800 chr3D 89.091 165 18 0 163 327 459077275 459077439 3.340000e-49 206.0


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 TraesCS7D01G176800 chr7D 129493914 129496471 2557 False 4724.0 4724 100.000 1 2558 1 chr7D.!!$F1 2557
1 TraesCS7D01G176800 chr7A 128838185 128840558 2373 False 1711.0 3253 91.679 25 2557 2 chr7A.!!$F1 2532
2 TraesCS7D01G176800 chr7B 90731382 90736190 4808 False 1174.0 2362 90.101 380 2050 3 chr7B.!!$F2 1670
3 TraesCS7D01G176800 chr7B 90743557 90754428 10871 False 607.4 621 89.987 1577 2050 5 chr7B.!!$F3 473

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
898 913 0.457035 CTGGTTCCATTTCATGCGGG 59.543 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2294 10459 0.107848 ACCCATGACCCGACGAAATC 60.108 55.0 0.0 0.0 0.0 2.17 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.432980 ACCTAAATGGCTATGTGGTACC 57.567 45.455 4.43 4.43 40.22 3.34
22 23 3.181458 ACCTAAATGGCTATGTGGTACCG 60.181 47.826 7.57 0.00 40.22 4.02
23 24 1.675552 AAATGGCTATGTGGTACCGC 58.324 50.000 18.93 18.93 0.00 5.68
24 25 0.531974 AATGGCTATGTGGTACCGCG 60.532 55.000 20.23 0.00 0.00 6.46
25 26 2.965462 GGCTATGTGGTACCGCGC 60.965 66.667 20.23 16.63 0.00 6.86
28 29 1.069090 CTATGTGGTACCGCGCCAT 59.931 57.895 20.23 14.39 38.40 4.40
156 160 4.279420 TGGCTCACACTATATGCTCACTAG 59.721 45.833 0.00 0.00 0.00 2.57
158 162 5.473846 GGCTCACACTATATGCTCACTAGTA 59.526 44.000 0.00 0.00 0.00 1.82
159 163 6.151985 GGCTCACACTATATGCTCACTAGTAT 59.848 42.308 0.00 0.00 32.30 2.12
160 164 7.309499 GGCTCACACTATATGCTCACTAGTATT 60.309 40.741 0.00 0.00 29.99 1.89
161 165 8.085296 GCTCACACTATATGCTCACTAGTATTT 58.915 37.037 0.00 0.00 29.99 1.40
162 166 9.619316 CTCACACTATATGCTCACTAGTATTTC 57.381 37.037 0.00 0.00 29.99 2.17
165 169 9.581289 ACACTATATGCTCACTAGTATTTCTCT 57.419 33.333 0.00 0.00 29.99 3.10
166 170 9.838975 CACTATATGCTCACTAGTATTTCTCTG 57.161 37.037 0.00 0.00 29.99 3.35
167 171 9.581289 ACTATATGCTCACTAGTATTTCTCTGT 57.419 33.333 0.00 0.00 29.99 3.41
170 174 5.967088 TGCTCACTAGTATTTCTCTGTTCC 58.033 41.667 0.00 0.00 0.00 3.62
174 178 8.251721 GCTCACTAGTATTTCTCTGTTCCTAAA 58.748 37.037 0.00 0.00 0.00 1.85
187 191 9.975218 TCTCTGTTCCTAAATATAAGCCTTTTT 57.025 29.630 0.00 0.00 0.00 1.94
201 205 8.966069 ATAAGCCTTTTTAGAGATTCCACTAC 57.034 34.615 0.00 0.00 0.00 2.73
202 206 6.374417 AGCCTTTTTAGAGATTCCACTACA 57.626 37.500 0.00 0.00 0.00 2.74
204 208 7.231467 AGCCTTTTTAGAGATTCCACTACAAA 58.769 34.615 0.00 0.00 0.00 2.83
205 209 7.175119 AGCCTTTTTAGAGATTCCACTACAAAC 59.825 37.037 0.00 0.00 0.00 2.93
206 210 7.175119 GCCTTTTTAGAGATTCCACTACAAACT 59.825 37.037 0.00 0.00 0.00 2.66
213 217 8.362464 AGAGATTCCACTACAAACTACATACA 57.638 34.615 0.00 0.00 0.00 2.29
214 218 8.470805 AGAGATTCCACTACAAACTACATACAG 58.529 37.037 0.00 0.00 0.00 2.74
216 220 8.982723 AGATTCCACTACAAACTACATACAGAT 58.017 33.333 0.00 0.00 0.00 2.90
220 224 9.027202 TCCACTACAAACTACATACAGATGTAA 57.973 33.333 0.00 0.00 45.74 2.41
221 225 9.647797 CCACTACAAACTACATACAGATGTAAA 57.352 33.333 0.00 0.00 45.74 2.01
254 258 9.941664 CATTTTAGAATGTAGATTCGCTCATTT 57.058 29.630 6.93 0.00 42.61 2.32
258 262 7.383102 AGAATGTAGATTCGCTCATTTTGTT 57.617 32.000 6.93 0.00 42.61 2.83
259 263 7.820648 AGAATGTAGATTCGCTCATTTTGTTT 58.179 30.769 6.93 0.00 42.61 2.83
261 265 5.617609 TGTAGATTCGCTCATTTTGTTTCG 58.382 37.500 0.00 0.00 0.00 3.46
262 266 4.749245 AGATTCGCTCATTTTGTTTCGT 57.251 36.364 0.00 0.00 0.00 3.85
263 267 5.856126 AGATTCGCTCATTTTGTTTCGTA 57.144 34.783 0.00 0.00 0.00 3.43
266 270 5.351233 TTCGCTCATTTTGTTTCGTATGT 57.649 34.783 0.00 0.00 0.00 2.29
268 272 6.089920 TCGCTCATTTTGTTTCGTATGTAG 57.910 37.500 0.00 0.00 0.00 2.74
269 273 5.636121 TCGCTCATTTTGTTTCGTATGTAGT 59.364 36.000 0.00 0.00 0.00 2.73
270 274 5.952064 CGCTCATTTTGTTTCGTATGTAGTC 59.048 40.000 0.00 0.00 0.00 2.59
271 275 6.248631 GCTCATTTTGTTTCGTATGTAGTCC 58.751 40.000 0.00 0.00 0.00 3.85
272 276 6.128391 GCTCATTTTGTTTCGTATGTAGTCCA 60.128 38.462 0.00 0.00 0.00 4.02
274 278 9.093970 CTCATTTTGTTTCGTATGTAGTCCATA 57.906 33.333 0.00 0.00 34.86 2.74
312 316 9.819267 AGAAAGACTTATATTTAGAAACGGAGG 57.181 33.333 0.00 0.00 0.00 4.30
314 318 7.909485 AGACTTATATTTAGAAACGGAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
316 320 7.564292 AGACTTATATTTAGAAACGGAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
317 321 8.773033 ACTTATATTTAGAAACGGAGGGAGTA 57.227 34.615 0.00 0.00 0.00 2.59
371 375 6.085555 CTCGTAGATAAAGGGTATGAGCAA 57.914 41.667 0.00 0.00 33.89 3.91
373 377 7.770366 TCGTAGATAAAGGGTATGAGCAATA 57.230 36.000 0.00 0.00 0.00 1.90
466 474 1.827315 TTGAACTGAAACGGCGAGCG 61.827 55.000 16.62 0.00 0.00 5.03
542 554 6.541641 CCTGGTGATAAAGATCTTTCCTTCTG 59.458 42.308 23.70 13.54 34.23 3.02
646 658 3.887621 TGTATCTCTTCCAAACCCTCG 57.112 47.619 0.00 0.00 0.00 4.63
781 793 0.811616 CGAATTCGAGGCCTTCCTGG 60.812 60.000 23.29 0.00 44.46 4.45
847 859 1.723220 GTTTACGCAGGAGAAGACCC 58.277 55.000 0.00 0.00 0.00 4.46
856 868 1.687297 GGAGAAGACCCCCGATGACC 61.687 65.000 0.00 0.00 0.00 4.02
898 913 0.457035 CTGGTTCCATTTCATGCGGG 59.543 55.000 0.00 0.00 0.00 6.13
906 921 2.581208 ATTTCATGCGGGGCGACGTA 62.581 55.000 0.00 0.00 35.98 3.57
1223 1238 1.271379 TCTGCTTCGGTTCGTGTACAT 59.729 47.619 0.00 0.00 0.00 2.29
1386 1410 0.251354 TGGAGACGGTCGCTACTACT 59.749 55.000 11.61 0.00 0.00 2.57
1407 1431 1.832883 TGGGTTACGCTGAAATGCAT 58.167 45.000 0.00 0.00 0.00 3.96
1409 1433 2.942376 TGGGTTACGCTGAAATGCATAG 59.058 45.455 0.00 0.00 0.00 2.23
1479 1503 2.640316 ACTTCAAGAAGGTGGTGGTC 57.360 50.000 13.83 0.00 42.53 4.02
1598 1622 1.000827 AGTCTTGTGCTGAGTCGACTG 60.001 52.381 25.58 10.96 31.19 3.51
1613 1641 3.968724 GTCGACTGTTGCAACAATTCTTC 59.031 43.478 30.62 19.66 38.66 2.87
1644 1673 6.674694 TGTGCAACATTTTATTTTTGTGCT 57.325 29.167 0.00 0.00 45.67 4.40
1817 1852 9.316859 GATCACAACAAAAACAAAAGAAAACTG 57.683 29.630 0.00 0.00 0.00 3.16
1821 1856 8.134261 ACAACAAAAACAAAAGAAAACTGCAAT 58.866 25.926 0.00 0.00 0.00 3.56
1850 1885 6.320164 TCAGGTAACAGTTGCAACAGTTTAAT 59.680 34.615 35.34 22.19 39.07 1.40
1864 1899 7.148755 GCAACAGTTTAATGCAACAAATCTAGG 60.149 37.037 0.00 0.00 39.81 3.02
1908 1943 4.774124 TGGGAGCTACATCATTTCTTCTG 58.226 43.478 0.00 0.00 0.00 3.02
2018 9323 4.628333 CACACATATTTAAGGTCGACCGTT 59.372 41.667 27.95 22.63 42.08 4.44
2085 9390 3.119849 CGAATGATCTGGTTTGACCCAAC 60.120 47.826 0.00 0.00 37.50 3.77
2115 9420 0.471191 ATGCCAGATTGATCAGCCGA 59.529 50.000 0.00 0.00 0.00 5.54
2168 10321 8.878769 GTTCTAGATTTTTCTTCTCCATGTCTC 58.121 37.037 0.00 0.00 0.00 3.36
2217 10372 4.749099 AGCTACTCATCTTTCATTGATCGC 59.251 41.667 0.00 0.00 0.00 4.58
2254 10409 4.761975 CAGCCAATGCCTTCATATGTTTT 58.238 39.130 1.90 0.00 38.69 2.43
2289 10454 2.173143 TGATGCCTTCATATGTGCCTCA 59.827 45.455 13.79 13.79 31.96 3.86
2294 10459 3.384668 CCTTCATATGTGCCTCAGTACG 58.615 50.000 1.90 0.00 0.00 3.67
2300 10465 1.990799 TGTGCCTCAGTACGATTTCG 58.009 50.000 0.00 0.00 46.33 3.46
2356 10521 0.478072 TCCACTGAACAAGGGCACAT 59.522 50.000 0.00 0.00 0.00 3.21
2430 10595 4.098501 CCCATAGAACAAAAGGCTCATTCC 59.901 45.833 0.00 0.00 0.00 3.01
2503 10669 2.362077 CCTATTTGGCGCCTTTAATGCT 59.638 45.455 29.70 7.11 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.181458 CGGTACCACATAGCCATTTAGGT 60.181 47.826 13.54 0.00 40.61 3.08
3 4 2.803852 CGCGGTACCACATAGCCATTTA 60.804 50.000 13.54 0.00 0.00 1.40
4 5 1.675552 GCGGTACCACATAGCCATTT 58.324 50.000 13.54 0.00 0.00 2.32
5 6 0.531974 CGCGGTACCACATAGCCATT 60.532 55.000 13.54 0.00 0.00 3.16
6 7 1.069090 CGCGGTACCACATAGCCAT 59.931 57.895 13.54 0.00 0.00 4.40
7 8 2.497293 CGCGGTACCACATAGCCA 59.503 61.111 13.54 0.00 0.00 4.75
9 10 2.965462 GGCGCGGTACCACATAGC 60.965 66.667 13.54 5.65 0.00 2.97
10 11 1.069090 ATGGCGCGGTACCACATAG 59.931 57.895 13.54 0.00 40.82 2.23
11 12 1.227409 CATGGCGCGGTACCACATA 60.227 57.895 13.54 0.00 40.82 2.29
12 13 2.513666 CATGGCGCGGTACCACAT 60.514 61.111 13.54 7.58 40.82 3.21
13 14 2.168666 TAACATGGCGCGGTACCACA 62.169 55.000 13.54 5.38 40.82 4.17
14 15 1.426041 CTAACATGGCGCGGTACCAC 61.426 60.000 13.54 0.07 40.82 4.16
15 16 1.153529 CTAACATGGCGCGGTACCA 60.154 57.895 13.54 7.44 42.61 3.25
16 17 0.102844 TACTAACATGGCGCGGTACC 59.897 55.000 8.83 0.16 0.00 3.34
17 18 2.144482 ATACTAACATGGCGCGGTAC 57.856 50.000 8.83 0.00 0.00 3.34
18 19 2.894763 AATACTAACATGGCGCGGTA 57.105 45.000 8.83 0.00 0.00 4.02
21 22 2.478514 TGCATAATACTAACATGGCGCG 59.521 45.455 0.00 0.00 0.00 6.86
22 23 4.481930 TTGCATAATACTAACATGGCGC 57.518 40.909 0.00 0.00 0.00 6.53
23 24 6.742718 GCTAATTGCATAATACTAACATGGCG 59.257 38.462 0.00 0.00 42.31 5.69
24 25 7.029563 GGCTAATTGCATAATACTAACATGGC 58.970 38.462 0.00 0.00 45.15 4.40
25 26 8.340618 AGGCTAATTGCATAATACTAACATGG 57.659 34.615 0.00 0.00 45.15 3.66
159 163 9.975218 AAAGGCTTATATTTAGGAACAGAGAAA 57.025 29.630 0.00 0.00 0.00 2.52
160 164 9.975218 AAAAGGCTTATATTTAGGAACAGAGAA 57.025 29.630 0.00 0.00 0.00 2.87
161 165 9.975218 AAAAAGGCTTATATTTAGGAACAGAGA 57.025 29.630 0.00 0.00 0.00 3.10
176 180 8.548877 TGTAGTGGAATCTCTAAAAAGGCTTAT 58.451 33.333 0.00 0.00 0.00 1.73
177 181 7.913789 TGTAGTGGAATCTCTAAAAAGGCTTA 58.086 34.615 0.00 0.00 0.00 3.09
179 183 6.374417 TGTAGTGGAATCTCTAAAAAGGCT 57.626 37.500 0.00 0.00 0.00 4.58
180 184 7.175119 AGTTTGTAGTGGAATCTCTAAAAAGGC 59.825 37.037 3.22 0.00 30.99 4.35
181 185 8.622948 AGTTTGTAGTGGAATCTCTAAAAAGG 57.377 34.615 3.22 0.00 30.99 3.11
187 191 9.470399 TGTATGTAGTTTGTAGTGGAATCTCTA 57.530 33.333 0.00 0.00 0.00 2.43
188 192 8.362464 TGTATGTAGTTTGTAGTGGAATCTCT 57.638 34.615 0.00 0.00 0.00 3.10
189 193 8.467598 TCTGTATGTAGTTTGTAGTGGAATCTC 58.532 37.037 0.00 0.00 0.00 2.75
191 195 9.035607 CATCTGTATGTAGTTTGTAGTGGAATC 57.964 37.037 0.00 0.00 0.00 2.52
192 196 8.540388 ACATCTGTATGTAGTTTGTAGTGGAAT 58.460 33.333 0.00 0.00 44.66 3.01
194 198 7.476540 ACATCTGTATGTAGTTTGTAGTGGA 57.523 36.000 0.00 0.00 44.66 4.02
195 199 9.647797 TTTACATCTGTATGTAGTTTGTAGTGG 57.352 33.333 0.00 0.00 46.58 4.00
228 232 9.941664 AAATGAGCGAATCTACATTCTAAAATG 57.058 29.630 0.00 0.00 46.42 2.32
230 234 9.773328 CAAAATGAGCGAATCTACATTCTAAAA 57.227 29.630 0.00 0.00 36.93 1.52
231 235 8.946085 ACAAAATGAGCGAATCTACATTCTAAA 58.054 29.630 0.00 0.00 36.93 1.85
232 236 8.492673 ACAAAATGAGCGAATCTACATTCTAA 57.507 30.769 0.00 0.00 36.93 2.10
233 237 8.492673 AACAAAATGAGCGAATCTACATTCTA 57.507 30.769 0.00 0.00 36.93 2.10
235 239 7.045354 CGAAACAAAATGAGCGAATCTACATTC 60.045 37.037 0.00 0.00 35.86 2.67
237 241 6.128282 ACGAAACAAAATGAGCGAATCTACAT 60.128 34.615 0.00 0.00 0.00 2.29
238 242 5.178623 ACGAAACAAAATGAGCGAATCTACA 59.821 36.000 0.00 0.00 0.00 2.74
239 243 5.618561 ACGAAACAAAATGAGCGAATCTAC 58.381 37.500 0.00 0.00 0.00 2.59
240 244 5.856126 ACGAAACAAAATGAGCGAATCTA 57.144 34.783 0.00 0.00 0.00 1.98
242 246 6.021596 ACATACGAAACAAAATGAGCGAATC 58.978 36.000 0.00 0.00 0.00 2.52
243 247 5.938322 ACATACGAAACAAAATGAGCGAAT 58.062 33.333 0.00 0.00 0.00 3.34
244 248 5.351233 ACATACGAAACAAAATGAGCGAA 57.649 34.783 0.00 0.00 0.00 4.70
245 249 5.636121 ACTACATACGAAACAAAATGAGCGA 59.364 36.000 0.00 0.00 0.00 4.93
246 250 5.854157 ACTACATACGAAACAAAATGAGCG 58.146 37.500 0.00 0.00 0.00 5.03
247 251 6.128391 TGGACTACATACGAAACAAAATGAGC 60.128 38.462 0.00 0.00 0.00 4.26
249 253 7.915293 ATGGACTACATACGAAACAAAATGA 57.085 32.000 0.00 0.00 38.26 2.57
286 290 9.819267 CCTCCGTTTCTAAATATAAGTCTTTCT 57.181 33.333 0.00 0.00 0.00 2.52
287 291 9.043079 CCCTCCGTTTCTAAATATAAGTCTTTC 57.957 37.037 0.00 0.00 0.00 2.62
288 292 8.765517 TCCCTCCGTTTCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
290 294 7.564292 ACTCCCTCCGTTTCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
291 295 7.724287 ACTCCCTCCGTTTCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
292 296 7.672122 ACTCCCTCCGTTTCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
293 297 8.636213 TGTACTCCCTCCGTTTCTAAATATAAG 58.364 37.037 0.00 0.00 0.00 1.73
294 298 8.537728 TGTACTCCCTCCGTTTCTAAATATAA 57.462 34.615 0.00 0.00 0.00 0.98
297 301 7.427989 AATGTACTCCCTCCGTTTCTAAATA 57.572 36.000 0.00 0.00 0.00 1.40
298 302 5.952347 ATGTACTCCCTCCGTTTCTAAAT 57.048 39.130 0.00 0.00 0.00 1.40
300 304 5.716228 TGTAATGTACTCCCTCCGTTTCTAA 59.284 40.000 0.00 0.00 0.00 2.10
302 306 4.091549 TGTAATGTACTCCCTCCGTTTCT 58.908 43.478 0.00 0.00 0.00 2.52
303 307 4.460948 TGTAATGTACTCCCTCCGTTTC 57.539 45.455 0.00 0.00 0.00 2.78
304 308 4.766375 CATGTAATGTACTCCCTCCGTTT 58.234 43.478 0.00 0.00 40.20 3.60
371 375 2.372264 CTGCAACAGCCCACAGATTAT 58.628 47.619 0.00 0.00 31.67 1.28
373 377 0.896940 CCTGCAACAGCCCACAGATT 60.897 55.000 0.00 0.00 31.67 2.40
529 540 0.647925 GCGACGCAGAAGGAAAGATC 59.352 55.000 16.42 0.00 0.00 2.75
532 543 3.951332 TGCGACGCAGAAGGAAAG 58.049 55.556 20.50 0.00 33.32 2.62
542 554 2.677573 AAACTTTTGGCCTGCGACGC 62.678 55.000 14.19 14.19 0.00 5.19
1386 1410 1.957177 TGCATTTCAGCGTAACCCAAA 59.043 42.857 0.00 0.00 37.31 3.28
1409 1433 3.612247 TTCTTCAGCTCCGGGCAGC 62.612 63.158 15.92 11.92 44.79 5.25
1479 1503 1.153823 CCAGAAGTAGCCGTCGGTG 60.154 63.158 13.94 0.70 0.00 4.94
1598 1622 5.095691 TCTCGAAGAAGAATTGTTGCAAC 57.904 39.130 22.83 22.83 34.09 4.17
1613 1641 7.801547 AAATAAAATGTTGCACATCTCGAAG 57.198 32.000 0.00 0.00 37.97 3.79
1644 1673 5.187687 TGATGCTTTCTCTGATATGTTGCA 58.812 37.500 0.00 0.00 0.00 4.08
1817 1852 4.155826 TGCAACTGTTACCTGATACATTGC 59.844 41.667 0.00 0.00 38.19 3.56
1821 1856 4.709250 TGTTGCAACTGTTACCTGATACA 58.291 39.130 28.61 2.45 0.00 2.29
1850 1885 8.593945 AAGAATTATTCCCTAGATTTGTTGCA 57.406 30.769 0.78 0.00 0.00 4.08
1858 1893 8.903059 ATCGGTAGAAGAATTATTCCCTAGAT 57.097 34.615 9.16 7.25 0.00 1.98
1864 1899 6.595716 CCCATGATCGGTAGAAGAATTATTCC 59.404 42.308 9.16 0.00 0.00 3.01
1925 1960 5.975410 AACTTGAAGAAGAAGAAGACACG 57.025 39.130 0.00 0.00 32.98 4.49
2032 9337 1.335872 CCCGCAACAAAGTGGTGAATC 60.336 52.381 0.00 0.00 37.20 2.52
2115 9420 9.981460 AATAGATTTTAGGGAAATGTTCTGTCT 57.019 29.630 0.00 0.00 38.06 3.41
2148 9453 5.064071 GGACGAGACATGGAGAAGAAAAATC 59.936 44.000 0.00 0.00 0.00 2.17
2254 10409 5.535783 TGAAGGCATCATTGTCTCAAGAAAA 59.464 36.000 0.00 0.00 36.59 2.29
2274 10439 4.307443 TCGTACTGAGGCACATATGAAG 57.693 45.455 10.38 2.58 0.00 3.02
2294 10459 0.107848 ACCCATGACCCGACGAAATC 60.108 55.000 0.00 0.00 0.00 2.17
2300 10465 2.497770 CGGTACCCATGACCCGAC 59.502 66.667 6.25 0.00 43.01 4.79
2356 10521 2.261671 GGCTCGAGTTTCGCTCCA 59.738 61.111 15.13 0.00 41.10 3.86
2400 10565 3.573967 CCTTTTGTTCTATGGGCTGTGTT 59.426 43.478 0.00 0.00 0.00 3.32
2406 10571 2.446435 TGAGCCTTTTGTTCTATGGGC 58.554 47.619 0.00 0.00 39.82 5.36
2430 10595 3.094572 AGAACAAGATTTGGGCCATCAG 58.905 45.455 7.26 2.47 34.12 2.90


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

AutoCloner maintained by Alex Coulton.