Multiple sequence alignment - TraesCS4D01G317100

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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 TraesCS4D01G317100 chr4D 100.000 4756 0 0 1 4756 482232002 482236757 0.000000e+00 8783.0
1 TraesCS4D01G317100 chr4B 94.433 4437 152 38 362 4753 612024060 612028446 0.000000e+00 6737.0
2 TraesCS4D01G317100 chr4B 86.364 220 8 4 1 213 612023790 612023994 2.230000e-53 220.0
3 TraesCS4D01G317100 chr5A 95.351 4259 130 24 551 4756 660400478 660396235 0.000000e+00 6706.0
4 TraesCS4D01G317100 chr5A 81.818 550 33 30 29 550 660401042 660400532 2.670000e-107 399.0
5 TraesCS4D01G317100 chr3A 93.897 426 26 0 1220 1645 209601544 209601969 1.120000e-180 643.0
6 TraesCS4D01G317100 chr2A 92.169 166 13 0 1220 1385 617819469 617819634 7.960000e-58 235.0
7 TraesCS4D01G317100 chr2A 98.077 52 1 0 1663 1714 617819632 617819683 1.820000e-14 91.6


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 TraesCS4D01G317100 chr4D 482232002 482236757 4755 False 8783.0 8783 100.0000 1 4756 1 chr4D.!!$F1 4755
1 TraesCS4D01G317100 chr4B 612023790 612028446 4656 False 3478.5 6737 90.3985 1 4753 2 chr4B.!!$F1 4752
2 TraesCS4D01G317100 chr5A 660396235 660401042 4807 True 3552.5 6706 88.5845 29 4756 2 chr5A.!!$R1 4727

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
280 290 0.108804 AATGTACCGCACTCACTCCG 60.109 55.000 0.00 0.0 0.00 4.63 F
299 309 0.727398 GGCTGTCCTGCGAAACATAC 59.273 55.000 0.00 0.0 0.00 2.39 F
591 676 0.968405 ACCACGTCGCCCTTTTACTA 59.032 50.000 0.00 0.0 0.00 1.82 F
2202 2329 0.104855 TGCTCGAGCTGTGAGTGTTT 59.895 50.000 35.27 0.0 42.66 2.83 F
2558 2691 1.138247 GCAGAATTTCGGCAGCAGG 59.862 57.895 15.35 0.0 37.52 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 2212 0.677731 CAATTCCTCCAAGCTCGGCA 60.678 55.000 0.00 0.00 0.00 5.69 R
2187 2314 1.933181 TGAACAAACACTCACAGCTCG 59.067 47.619 0.00 0.00 0.00 5.03 R
2589 2722 1.541147 ACACAGATTGTTCAATGGCGG 59.459 47.619 2.63 0.00 33.09 6.13 R
3221 3354 0.454957 CCGTTCCAAGCGCAATCTTG 60.455 55.000 11.47 4.96 42.23 3.02 R
4308 4457 0.558220 TTGGAATGTGTGGGTTGGGA 59.442 50.000 0.00 0.00 0.00 4.37 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
93 101 1.153529 CGGCGTGGGCACTTATACA 60.154 57.895 0.00 0.00 42.47 2.29
102 110 4.033587 GTGGGCACTTATACATTACACACG 59.966 45.833 0.00 0.00 0.00 4.49
163 172 4.746951 TACTGCACGACGGACGCG 62.747 66.667 3.53 3.53 46.94 6.01
179 188 3.345808 CGACGCAACCACCACCAG 61.346 66.667 0.00 0.00 0.00 4.00
180 189 2.110213 GACGCAACCACCACCAGA 59.890 61.111 0.00 0.00 0.00 3.86
181 190 2.203153 ACGCAACCACCACCAGAC 60.203 61.111 0.00 0.00 0.00 3.51
182 191 2.978010 CGCAACCACCACCAGACC 60.978 66.667 0.00 0.00 0.00 3.85
183 192 2.194597 GCAACCACCACCAGACCA 59.805 61.111 0.00 0.00 0.00 4.02
184 193 2.193536 GCAACCACCACCAGACCAC 61.194 63.158 0.00 0.00 0.00 4.16
185 194 1.528309 CAACCACCACCAGACCACC 60.528 63.158 0.00 0.00 0.00 4.61
228 238 3.285523 TACCCAGCACGTACACGCC 62.286 63.158 0.85 0.00 44.43 5.68
244 254 4.602259 CCTGTCGTGGCGTGGTGT 62.602 66.667 0.00 0.00 0.00 4.16
245 255 2.337170 CTGTCGTGGCGTGGTGTA 59.663 61.111 0.00 0.00 0.00 2.90
246 256 1.080093 CTGTCGTGGCGTGGTGTAT 60.080 57.895 0.00 0.00 0.00 2.29
247 257 0.669318 CTGTCGTGGCGTGGTGTATT 60.669 55.000 0.00 0.00 0.00 1.89
248 258 0.249953 TGTCGTGGCGTGGTGTATTT 60.250 50.000 0.00 0.00 0.00 1.40
249 259 0.165079 GTCGTGGCGTGGTGTATTTG 59.835 55.000 0.00 0.00 0.00 2.32
250 260 0.249953 TCGTGGCGTGGTGTATTTGT 60.250 50.000 0.00 0.00 0.00 2.83
273 283 7.042950 TGTAATGTAATGTAATGTACCGCACT 58.957 34.615 0.00 0.00 0.00 4.40
277 287 3.887621 ATGTAATGTACCGCACTCACT 57.112 42.857 0.00 0.00 0.00 3.41
280 290 0.108804 AATGTACCGCACTCACTCCG 60.109 55.000 0.00 0.00 0.00 4.63
285 295 4.363990 CGCACTCACTCCGGCTGT 62.364 66.667 0.00 0.00 0.00 4.40
286 296 2.433318 GCACTCACTCCGGCTGTC 60.433 66.667 0.00 0.00 0.00 3.51
287 297 2.262915 CACTCACTCCGGCTGTCC 59.737 66.667 0.00 0.00 0.00 4.02
288 298 2.118513 ACTCACTCCGGCTGTCCT 59.881 61.111 0.00 0.00 0.00 3.85
289 299 2.279069 ACTCACTCCGGCTGTCCTG 61.279 63.158 0.00 0.00 0.00 3.86
290 300 3.655810 CTCACTCCGGCTGTCCTGC 62.656 68.421 0.00 0.00 0.00 4.85
293 303 4.069232 CTCCGGCTGTCCTGCGAA 62.069 66.667 0.00 0.00 0.00 4.70
294 304 3.589654 CTCCGGCTGTCCTGCGAAA 62.590 63.158 0.00 0.00 0.00 3.46
295 305 3.423154 CCGGCTGTCCTGCGAAAC 61.423 66.667 0.00 0.00 0.00 2.78
296 306 2.664851 CGGCTGTCCTGCGAAACA 60.665 61.111 0.00 0.00 0.00 2.83
297 307 2.034879 CGGCTGTCCTGCGAAACAT 61.035 57.895 0.00 0.00 0.00 2.71
298 308 0.739462 CGGCTGTCCTGCGAAACATA 60.739 55.000 0.00 0.00 0.00 2.29
299 309 0.727398 GGCTGTCCTGCGAAACATAC 59.273 55.000 0.00 0.00 0.00 2.39
300 310 1.676014 GGCTGTCCTGCGAAACATACT 60.676 52.381 0.00 0.00 0.00 2.12
301 311 2.418197 GGCTGTCCTGCGAAACATACTA 60.418 50.000 0.00 0.00 0.00 1.82
302 312 2.860735 GCTGTCCTGCGAAACATACTAG 59.139 50.000 0.00 0.00 0.00 2.57
303 313 3.676324 GCTGTCCTGCGAAACATACTAGT 60.676 47.826 0.00 0.00 0.00 2.57
304 314 4.439700 GCTGTCCTGCGAAACATACTAGTA 60.440 45.833 4.77 4.77 0.00 1.82
305 315 4.990257 TGTCCTGCGAAACATACTAGTAC 58.010 43.478 4.31 0.00 0.00 2.73
306 316 4.460034 TGTCCTGCGAAACATACTAGTACA 59.540 41.667 4.31 0.00 0.00 2.90
307 317 5.035443 GTCCTGCGAAACATACTAGTACAG 58.965 45.833 4.31 6.14 0.00 2.74
308 318 4.703575 TCCTGCGAAACATACTAGTACAGT 59.296 41.667 4.31 4.38 41.62 3.55
309 319 5.882000 TCCTGCGAAACATACTAGTACAGTA 59.118 40.000 4.31 1.72 43.89 2.74
310 320 5.970023 CCTGCGAAACATACTAGTACAGTAC 59.030 44.000 4.31 2.05 42.56 2.73
311 321 6.403964 CCTGCGAAACATACTAGTACAGTACA 60.404 42.308 13.37 4.12 42.56 2.90
312 322 6.549061 TGCGAAACATACTAGTACAGTACAG 58.451 40.000 13.37 10.24 42.56 2.74
313 323 6.372381 TGCGAAACATACTAGTACAGTACAGA 59.628 38.462 13.37 0.00 42.56 3.41
314 324 6.906143 GCGAAACATACTAGTACAGTACAGAG 59.094 42.308 13.37 11.41 42.56 3.35
405 420 3.782443 GGGAACAGCGGTCCGGAT 61.782 66.667 14.38 0.00 0.00 4.18
587 672 3.284449 GCACCACGTCGCCCTTTT 61.284 61.111 0.00 0.00 0.00 2.27
588 673 1.962306 GCACCACGTCGCCCTTTTA 60.962 57.895 0.00 0.00 0.00 1.52
589 674 1.864176 CACCACGTCGCCCTTTTAC 59.136 57.895 0.00 0.00 0.00 2.01
591 676 0.968405 ACCACGTCGCCCTTTTACTA 59.032 50.000 0.00 0.00 0.00 1.82
703 795 3.281727 TTCCGCCTAGATTTCAGCATT 57.718 42.857 0.00 0.00 0.00 3.56
865 980 4.143333 CCCACCGCCACCTACTCG 62.143 72.222 0.00 0.00 0.00 4.18
866 981 4.814294 CCACCGCCACCTACTCGC 62.814 72.222 0.00 0.00 0.00 5.03
867 982 4.814294 CACCGCCACCTACTCGCC 62.814 72.222 0.00 0.00 0.00 5.54
869 984 4.208686 CCGCCACCTACTCGCCTC 62.209 72.222 0.00 0.00 0.00 4.70
870 985 3.449227 CGCCACCTACTCGCCTCA 61.449 66.667 0.00 0.00 0.00 3.86
871 986 2.184579 GCCACCTACTCGCCTCAC 59.815 66.667 0.00 0.00 0.00 3.51
872 987 2.352032 GCCACCTACTCGCCTCACT 61.352 63.158 0.00 0.00 0.00 3.41
873 988 1.810532 CCACCTACTCGCCTCACTC 59.189 63.158 0.00 0.00 0.00 3.51
1132 1259 1.407989 GGATCCTGCTGGACTTCAAGG 60.408 57.143 15.36 0.00 46.51 3.61
1134 1261 2.037136 CCTGCTGGACTTCAAGGCG 61.037 63.158 2.92 0.00 34.57 5.52
1558 1685 4.342987 TCTCGCTCGCGCACAACT 62.343 61.111 8.75 0.00 39.59 3.16
1908 2035 4.086574 GCAAGTTTTTATACTTCGACGCC 58.913 43.478 0.00 0.00 36.24 5.68
2016 2143 1.515954 CGGAGACATACCGCCAGTT 59.484 57.895 0.00 0.00 43.74 3.16
2026 2153 1.520787 CCGCCAGTTATCGGGACAC 60.521 63.158 0.00 0.00 41.82 3.67
2085 2212 2.025321 AGGCATTACCGGTTCAATTCCT 60.025 45.455 15.04 14.14 46.52 3.36
2187 2314 0.108945 GCAAATGCCAGTTCCTGCTC 60.109 55.000 0.00 0.00 34.31 4.26
2202 2329 0.104855 TGCTCGAGCTGTGAGTGTTT 59.895 50.000 35.27 0.00 42.66 2.83
2215 2342 5.109210 TGTGAGTGTTTGTTCAGTACTCAG 58.891 41.667 5.70 0.00 45.73 3.35
2237 2367 4.840115 AGTTTCACCCAATTCATCCAATGT 59.160 37.500 0.00 0.00 0.00 2.71
2363 2496 3.817084 TGCTTGATCTTCACAAGAACCAG 59.183 43.478 11.08 0.00 44.92 4.00
2557 2690 1.878070 TGCAGAATTTCGGCAGCAG 59.122 52.632 18.38 0.00 42.36 4.24
2558 2691 1.138247 GCAGAATTTCGGCAGCAGG 59.862 57.895 15.35 0.00 37.52 4.85
2591 2724 3.553828 AACCCATTACTATGTGGACCG 57.446 47.619 0.00 0.00 37.72 4.79
2889 3022 1.847088 GGGAGGAAGGAACTAAGGCAT 59.153 52.381 0.00 0.00 38.49 4.40
2897 3030 4.322057 AGGAACTAAGGCATTGGTTGAT 57.678 40.909 17.75 3.00 39.89 2.57
3007 3140 3.195661 AGACACTCGGAAGTTTGACAAC 58.804 45.455 0.00 0.00 31.71 3.32
3053 3186 1.616994 GGGCAGCTTGGTAACCTCAAT 60.617 52.381 0.00 0.00 0.00 2.57
3180 3313 2.547798 GTCGTCGTGCGTTTTCCC 59.452 61.111 0.00 0.00 42.13 3.97
3188 3321 1.505425 GTGCGTTTTCCCGAAGTAGT 58.495 50.000 0.00 0.00 0.00 2.73
3221 3354 0.397254 TCTCCTGGGATCGGAGGTTC 60.397 60.000 13.35 0.00 46.43 3.62
3230 3363 1.594862 GATCGGAGGTTCAAGATTGCG 59.405 52.381 0.00 0.00 0.00 4.85
3371 3504 8.758829 TCTGACTATGGATTTAGAAAGCTGTTA 58.241 33.333 0.00 0.00 0.00 2.41
3506 3639 1.168714 GGGTGGTGTTGCTTGAGATC 58.831 55.000 0.00 0.00 0.00 2.75
3575 3708 1.075542 TTTTGCGCGACTATGTCAGG 58.924 50.000 12.10 0.00 32.09 3.86
3766 3899 7.044798 AGGACTAATTCTTGATGTTCTGCTAC 58.955 38.462 0.00 0.00 0.00 3.58
3917 4058 9.013229 TGTGTTTAGATTTGTCTGCTCATTATT 57.987 29.630 0.00 0.00 0.00 1.40
3963 4105 6.945218 TGCTGAATAAATGGCTATTTTGGTT 58.055 32.000 13.63 6.76 37.64 3.67
4122 4264 4.903049 TGGTCAGACCTAAACACTCCTTTA 59.097 41.667 20.82 0.00 39.58 1.85
4123 4265 5.546499 TGGTCAGACCTAAACACTCCTTTAT 59.454 40.000 20.82 0.00 39.58 1.40
4252 4401 3.561725 GCAGCTCATCTAACCCACAATAC 59.438 47.826 0.00 0.00 0.00 1.89
4275 4424 3.511934 CCTCTCCTACATATACCAGCACC 59.488 52.174 0.00 0.00 0.00 5.01
4289 4438 5.806654 ACCAGCACCAAATACAAGATTTT 57.193 34.783 0.00 0.00 0.00 1.82
4308 4457 6.436532 AGATTTTCAGCAGTCCAGATTTCATT 59.563 34.615 0.00 0.00 0.00 2.57
4485 4641 0.620410 TTCTCATGTCCATCCCCGGT 60.620 55.000 0.00 0.00 0.00 5.28
4627 4783 0.821711 TGAACCCTTTTGTGGCCGAG 60.822 55.000 0.00 0.00 0.00 4.63
4636 4792 0.617935 TTGTGGCCGAGGATGATGAA 59.382 50.000 0.00 0.00 0.00 2.57
4678 4834 1.598685 GGAAGCGTTCGGGTTTCCA 60.599 57.895 10.92 0.00 44.11 3.53
4753 4912 2.047560 GGCGCCTGGTACTCGTTT 60.048 61.111 22.15 0.00 0.00 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.578898 TACTATGCACGGCGCGGG 62.579 66.667 19.75 8.54 46.97 6.13
93 101 5.449041 CCAGCAATTATCAAGCGTGTGTAAT 60.449 40.000 0.00 3.80 0.00 1.89
102 110 2.351157 GCCGATCCAGCAATTATCAAGC 60.351 50.000 0.00 0.00 0.00 4.01
163 172 2.110213 TCTGGTGGTGGTTGCGTC 59.890 61.111 0.00 0.00 0.00 5.19
178 187 5.047021 CGGTATGATGATGATTAGGTGGTCT 60.047 44.000 0.00 0.00 0.00 3.85
179 188 5.047306 TCGGTATGATGATGATTAGGTGGTC 60.047 44.000 0.00 0.00 0.00 4.02
180 189 4.838423 TCGGTATGATGATGATTAGGTGGT 59.162 41.667 0.00 0.00 0.00 4.16
181 190 5.405935 TCGGTATGATGATGATTAGGTGG 57.594 43.478 0.00 0.00 0.00 4.61
182 191 5.414360 CCTCGGTATGATGATGATTAGGTG 58.586 45.833 0.00 0.00 0.00 4.00
183 192 4.081420 GCCTCGGTATGATGATGATTAGGT 60.081 45.833 0.00 0.00 0.00 3.08
184 193 4.081476 TGCCTCGGTATGATGATGATTAGG 60.081 45.833 0.00 0.00 0.00 2.69
185 194 5.077134 TGCCTCGGTATGATGATGATTAG 57.923 43.478 0.00 0.00 0.00 1.73
228 238 0.669318 AATACACCACGCCACGACAG 60.669 55.000 0.00 0.00 0.00 3.51
245 255 8.894731 TGCGGTACATTACATTACATTACAAAT 58.105 29.630 0.00 0.00 0.00 2.32
246 256 8.176365 GTGCGGTACATTACATTACATTACAAA 58.824 33.333 0.00 0.00 0.00 2.83
247 257 7.549842 AGTGCGGTACATTACATTACATTACAA 59.450 33.333 0.00 0.00 0.00 2.41
248 258 7.042950 AGTGCGGTACATTACATTACATTACA 58.957 34.615 0.00 0.00 0.00 2.41
249 259 7.223193 TGAGTGCGGTACATTACATTACATTAC 59.777 37.037 0.00 0.00 0.00 1.89
250 260 7.223193 GTGAGTGCGGTACATTACATTACATTA 59.777 37.037 0.00 0.00 0.00 1.90
270 280 2.262915 GGACAGCCGGAGTGAGTG 59.737 66.667 5.05 0.00 0.00 3.51
273 283 3.695606 GCAGGACAGCCGGAGTGA 61.696 66.667 5.05 0.00 39.96 3.41
277 287 3.621805 TTTCGCAGGACAGCCGGA 61.622 61.111 5.05 0.00 39.96 5.14
280 290 0.727398 GTATGTTTCGCAGGACAGCC 59.273 55.000 0.00 0.00 0.00 4.85
285 295 4.703575 ACTGTACTAGTATGTTTCGCAGGA 59.296 41.667 5.75 0.00 38.04 3.86
286 296 4.995124 ACTGTACTAGTATGTTTCGCAGG 58.005 43.478 5.75 0.00 38.04 4.85
287 297 6.549061 TGTACTGTACTAGTATGTTTCGCAG 58.451 40.000 17.98 9.05 43.44 5.18
288 298 6.372381 TCTGTACTGTACTAGTATGTTTCGCA 59.628 38.462 17.98 0.00 43.44 5.10
289 299 6.779117 TCTGTACTGTACTAGTATGTTTCGC 58.221 40.000 17.98 0.00 43.44 4.70
290 300 7.408123 CCTCTGTACTGTACTAGTATGTTTCG 58.592 42.308 17.98 1.77 43.44 3.46
291 301 7.067251 AGCCTCTGTACTGTACTAGTATGTTTC 59.933 40.741 17.98 6.46 43.44 2.78
292 302 6.890814 AGCCTCTGTACTGTACTAGTATGTTT 59.109 38.462 17.98 0.00 43.44 2.83
293 303 6.424883 AGCCTCTGTACTGTACTAGTATGTT 58.575 40.000 17.98 0.00 43.44 2.71
294 304 6.003859 AGCCTCTGTACTGTACTAGTATGT 57.996 41.667 17.98 10.66 43.44 2.29
295 305 6.542735 TCAAGCCTCTGTACTGTACTAGTATG 59.457 42.308 17.98 5.21 43.44 2.39
296 306 6.543100 GTCAAGCCTCTGTACTGTACTAGTAT 59.457 42.308 17.98 0.00 43.44 2.12
297 307 5.879223 GTCAAGCCTCTGTACTGTACTAGTA 59.121 44.000 17.98 0.00 40.89 1.82
298 308 4.701171 GTCAAGCCTCTGTACTGTACTAGT 59.299 45.833 17.98 0.00 43.56 2.57
299 309 4.201832 CGTCAAGCCTCTGTACTGTACTAG 60.202 50.000 17.98 14.34 0.00 2.57
300 310 3.688185 CGTCAAGCCTCTGTACTGTACTA 59.312 47.826 17.98 6.49 0.00 1.82
301 311 2.488545 CGTCAAGCCTCTGTACTGTACT 59.511 50.000 17.98 0.00 0.00 2.73
302 312 2.486982 TCGTCAAGCCTCTGTACTGTAC 59.513 50.000 10.98 10.98 0.00 2.90
303 313 2.486982 GTCGTCAAGCCTCTGTACTGTA 59.513 50.000 0.00 0.00 0.00 2.74
304 314 1.269998 GTCGTCAAGCCTCTGTACTGT 59.730 52.381 0.00 0.00 0.00 3.55
305 315 1.729472 CGTCGTCAAGCCTCTGTACTG 60.729 57.143 0.00 0.00 0.00 2.74
306 316 0.522180 CGTCGTCAAGCCTCTGTACT 59.478 55.000 0.00 0.00 0.00 2.73
307 317 0.456312 CCGTCGTCAAGCCTCTGTAC 60.456 60.000 0.00 0.00 0.00 2.90
308 318 0.607217 TCCGTCGTCAAGCCTCTGTA 60.607 55.000 0.00 0.00 0.00 2.74
309 319 1.867919 CTCCGTCGTCAAGCCTCTGT 61.868 60.000 0.00 0.00 0.00 3.41
310 320 1.153939 CTCCGTCGTCAAGCCTCTG 60.154 63.158 0.00 0.00 0.00 3.35
311 321 2.995872 GCTCCGTCGTCAAGCCTCT 61.996 63.158 0.00 0.00 0.00 3.69
312 322 2.507324 GCTCCGTCGTCAAGCCTC 60.507 66.667 0.00 0.00 0.00 4.70
313 323 2.867855 TTGCTCCGTCGTCAAGCCT 61.868 57.895 8.47 0.00 35.12 4.58
314 324 2.357034 TTGCTCCGTCGTCAAGCC 60.357 61.111 8.47 0.00 35.12 4.35
351 365 2.664851 CTTCGTTGGAGCGCACCA 60.665 61.111 23.37 23.37 38.24 4.17
353 367 1.901650 CTTCCTTCGTTGGAGCGCAC 61.902 60.000 11.47 1.97 37.43 5.34
355 369 2.391389 CCTTCCTTCGTTGGAGCGC 61.391 63.158 0.00 0.00 37.43 5.92
584 669 4.286549 TGGTGGAGATCGGGTTTAGTAAAA 59.713 41.667 0.00 0.00 0.00 1.52
585 670 3.839490 TGGTGGAGATCGGGTTTAGTAAA 59.161 43.478 0.00 0.00 0.00 2.01
586 671 3.443052 TGGTGGAGATCGGGTTTAGTAA 58.557 45.455 0.00 0.00 0.00 2.24
587 672 3.104519 TGGTGGAGATCGGGTTTAGTA 57.895 47.619 0.00 0.00 0.00 1.82
588 673 1.946984 TGGTGGAGATCGGGTTTAGT 58.053 50.000 0.00 0.00 0.00 2.24
589 674 2.434336 TGATGGTGGAGATCGGGTTTAG 59.566 50.000 0.00 0.00 0.00 1.85
591 676 1.285280 TGATGGTGGAGATCGGGTTT 58.715 50.000 0.00 0.00 0.00 3.27
745 855 2.879039 GATTGACGTCGGTCCGGTCC 62.879 65.000 12.29 7.79 42.73 4.46
748 858 2.578713 CGATTGACGTCGGTCCGG 60.579 66.667 12.29 0.00 42.73 5.14
798 913 1.152963 AACCAACTGCCACTTCGCT 60.153 52.632 0.00 0.00 0.00 4.93
800 915 1.569493 CGAACCAACTGCCACTTCG 59.431 57.895 0.00 0.00 0.00 3.79
865 980 0.672711 GGTTAACCGGTGAGTGAGGC 60.673 60.000 8.52 0.00 0.00 4.70
866 981 0.036671 GGGTTAACCGGTGAGTGAGG 60.037 60.000 18.39 0.00 36.71 3.86
867 982 0.036671 GGGGTTAACCGGTGAGTGAG 60.037 60.000 18.39 0.00 41.60 3.51
868 983 1.482748 GGGGGTTAACCGGTGAGTGA 61.483 60.000 18.39 0.00 41.60 3.41
869 984 1.002990 GGGGGTTAACCGGTGAGTG 60.003 63.158 18.39 0.00 41.60 3.51
870 985 1.151965 AGGGGGTTAACCGGTGAGT 60.152 57.895 18.39 0.00 41.60 3.41
871 986 1.600638 GAGGGGGTTAACCGGTGAG 59.399 63.158 18.39 0.00 41.60 3.51
872 987 1.919816 GGAGGGGGTTAACCGGTGA 60.920 63.158 18.39 0.00 41.60 4.02
873 988 2.672908 GGAGGGGGTTAACCGGTG 59.327 66.667 18.39 0.00 41.60 4.94
958 1073 2.873557 TTAGCTCCTCCTCCGGGGTG 62.874 65.000 0.00 2.13 36.25 4.61
1386 1513 1.578423 GCTGAGGTTGAGCTTGTGC 59.422 57.895 0.00 0.00 40.05 4.57
2016 2143 2.767445 CGACCGCAGTGTCCCGATA 61.767 63.158 0.00 0.00 31.35 2.92
2085 2212 0.677731 CAATTCCTCCAAGCTCGGCA 60.678 55.000 0.00 0.00 0.00 5.69
2187 2314 1.933181 TGAACAAACACTCACAGCTCG 59.067 47.619 0.00 0.00 0.00 5.03
2202 2329 3.452990 TGGGTGAAACTGAGTACTGAACA 59.547 43.478 0.00 0.00 36.74 3.18
2215 2342 5.151297 ACATTGGATGAATTGGGTGAAAC 57.849 39.130 0.00 0.00 0.00 2.78
2557 2690 1.685765 GGGTTTCCCATGAAGGCCC 60.686 63.158 0.00 0.00 44.65 5.80
2558 2691 4.034246 GGGTTTCCCATGAAGGCC 57.966 61.111 0.00 0.00 44.65 5.19
2589 2722 1.541147 ACACAGATTGTTCAATGGCGG 59.459 47.619 2.63 0.00 33.09 6.13
2591 2724 2.297033 ACCACACAGATTGTTCAATGGC 59.703 45.455 2.63 0.00 35.67 4.40
2889 3022 4.469657 ACAAGGCAGTCTTTATCAACCAA 58.530 39.130 0.00 0.00 32.41 3.67
2897 3030 2.173782 TCCACCAACAAGGCAGTCTTTA 59.826 45.455 0.00 0.00 43.14 1.85
3007 3140 2.022195 CATGCTCAAACTCATCCTGGG 58.978 52.381 0.00 0.00 0.00 4.45
3053 3186 1.371467 ATGTGACCAGATTGGGGTGA 58.629 50.000 0.00 0.00 43.37 4.02
3180 3313 1.331138 CTCACCTCCGCTACTACTTCG 59.669 57.143 0.00 0.00 0.00 3.79
3188 3321 1.454111 GGAGAGCTCACCTCCGCTA 60.454 63.158 21.64 0.00 41.74 4.26
3221 3354 0.454957 CCGTTCCAAGCGCAATCTTG 60.455 55.000 11.47 4.96 42.23 3.02
3575 3708 4.120946 AGTACCATCCTCCAGTATCTCC 57.879 50.000 0.00 0.00 0.00 3.71
3766 3899 5.540337 TCCTATTCTGCTACTATGTTCCAGG 59.460 44.000 0.00 0.00 0.00 4.45
3933 4075 4.748277 AGCCATTTATTCAGCAAGCAAT 57.252 36.364 0.00 0.00 0.00 3.56
3934 4076 5.857471 ATAGCCATTTATTCAGCAAGCAA 57.143 34.783 0.00 0.00 0.00 3.91
3937 4079 7.043565 ACCAAAATAGCCATTTATTCAGCAAG 58.956 34.615 0.00 0.00 33.09 4.01
3963 4105 4.977739 AGATCCTGGGGAATCAGTAATTCA 59.022 41.667 0.00 0.00 44.81 2.57
4122 4264 1.376649 ACTCCTCTTTGGCTCCCAAT 58.623 50.000 0.00 0.00 43.55 3.16
4123 4265 1.149101 AACTCCTCTTTGGCTCCCAA 58.851 50.000 0.00 0.00 42.29 4.12
4252 4401 3.511934 GTGCTGGTATATGTAGGAGAGGG 59.488 52.174 0.00 0.00 0.00 4.30
4275 4424 6.680810 TGGACTGCTGAAAATCTTGTATTTG 58.319 36.000 0.00 0.00 0.00 2.32
4289 4438 3.614092 GGAATGAAATCTGGACTGCTGA 58.386 45.455 0.00 0.00 0.00 4.26
4308 4457 0.558220 TTGGAATGTGTGGGTTGGGA 59.442 50.000 0.00 0.00 0.00 4.37
4420 4573 4.069232 CAGTCCCTCTTCGGCGCA 62.069 66.667 10.83 0.00 0.00 6.09
4462 4618 1.141858 GGGGATGGACATGAGAAGACC 59.858 57.143 0.00 0.00 0.00 3.85
4485 4641 1.401552 GCACACTGACAACAAGCTTGA 59.598 47.619 32.50 9.05 0.00 3.02
4627 4783 3.119291 CAGCGTGTACTCTTCATCATCC 58.881 50.000 0.00 0.00 0.00 3.51
4636 4792 1.874345 CGAACCCCAGCGTGTACTCT 61.874 60.000 0.00 0.00 0.00 3.24
4678 4834 2.049063 GACGCCTTGCTGTCGTCT 60.049 61.111 6.74 0.00 46.21 4.18


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

AutoCloner maintained by Alex Coulton.