Multiple sequence alignment - TraesCS5A01G094500

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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 TraesCS5A01G094500 chr5A 100.000 2568 0 0 1 2568 131568315 131565748 0.000000e+00 4743
1 TraesCS5A01G094500 chr5D 92.138 1908 82 25 636 2511 120773643 120771772 0.000000e+00 2630
2 TraesCS5A01G094500 chr5D 88.957 489 24 13 1 487 120776134 120775674 6.160000e-161 577
3 TraesCS5A01G094500 chr5D 97.222 72 2 0 461 532 120775587 120775516 3.470000e-24 122
4 TraesCS5A01G094500 chr5D 95.775 71 3 0 570 640 120774262 120774192 5.810000e-22 115
5 TraesCS5A01G094500 chr5B 88.981 1080 65 31 900 1970 133862368 133861334 0.000000e+00 1286
6 TraesCS5A01G094500 chr5B 95.871 557 17 5 406 956 133862916 133862360 0.000000e+00 896
7 TraesCS5A01G094500 chr5B 90.952 420 10 4 1 420 133864470 133864079 8.080000e-150 540


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 TraesCS5A01G094500 chr5A 131565748 131568315 2567 True 4743.000000 4743 100.000000 1 2568 1 chr5A.!!$R1 2567
1 TraesCS5A01G094500 chr5D 120771772 120776134 4362 True 861.000000 2630 93.523000 1 2511 4 chr5D.!!$R1 2510
2 TraesCS5A01G094500 chr5B 133861334 133864470 3136 True 907.333333 1286 91.934667 1 1970 3 chr5B.!!$R1 1969

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
196 199 1.067295 AAGACCTGATCAACCCTGCA 58.933 50.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2104 5234 0.322187 TTTTTCCTCGCACTAGGGCC 60.322 55.0 12.39 0.0 37.24 5.8 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
189 192 8.762645 ACAACTAGATCAATAAGACCTGATCAA 58.237 33.333 13.03 0.00 46.92 2.57
190 193 9.039870 CAACTAGATCAATAAGACCTGATCAAC 57.960 37.037 13.03 0.00 46.92 3.18
191 194 7.731054 ACTAGATCAATAAGACCTGATCAACC 58.269 38.462 13.03 0.00 46.92 3.77
192 195 5.934781 AGATCAATAAGACCTGATCAACCC 58.065 41.667 13.03 0.00 46.92 4.11
193 196 5.669447 AGATCAATAAGACCTGATCAACCCT 59.331 40.000 13.03 0.00 46.92 4.34
194 197 5.102953 TCAATAAGACCTGATCAACCCTG 57.897 43.478 0.00 0.00 0.00 4.45
195 198 3.567478 ATAAGACCTGATCAACCCTGC 57.433 47.619 0.00 0.00 0.00 4.85
196 199 1.067295 AAGACCTGATCAACCCTGCA 58.933 50.000 0.00 0.00 0.00 4.41
197 200 1.067295 AGACCTGATCAACCCTGCAA 58.933 50.000 0.00 0.00 0.00 4.08
198 201 1.425066 AGACCTGATCAACCCTGCAAA 59.575 47.619 0.00 0.00 0.00 3.68
199 202 2.158475 AGACCTGATCAACCCTGCAAAA 60.158 45.455 0.00 0.00 0.00 2.44
200 203 2.627699 GACCTGATCAACCCTGCAAAAA 59.372 45.455 0.00 0.00 0.00 1.94
230 233 6.586344 ACCTGATCAGTTGTATGACATAAGG 58.414 40.000 21.11 3.63 30.46 2.69
250 253 8.840321 CATAAGGGTGATATCACTAAAAAGTGG 58.160 37.037 29.87 11.80 45.73 4.00
373 376 5.887035 TGATTGATATGTTTGCATCACAGGA 59.113 36.000 5.55 0.00 36.58 3.86
420 423 3.695830 TCACTATGAAACAGGTGGGAC 57.304 47.619 0.00 0.00 0.00 4.46
538 1859 2.941720 GCAAGAAGATTAGTGGAGCCTG 59.058 50.000 0.00 0.00 0.00 4.85
695 3757 6.668133 TTCCCTGGAAATAGGTTTTATCCT 57.332 37.500 0.00 0.00 41.20 3.24
1001 4121 4.811024 CGCACCATACTCTAAACACATCAT 59.189 41.667 0.00 0.00 0.00 2.45
1036 4156 8.403236 CAAAACCACTAAGTAACACTAGCTTTT 58.597 33.333 0.00 0.00 0.00 2.27
1063 4183 9.838339 TTTCTCTGAGAAAAACACTAGATTTCT 57.162 29.630 26.04 13.41 40.89 2.52
1064 4184 9.838339 TTCTCTGAGAAAAACACTAGATTTCTT 57.162 29.630 17.32 5.74 41.96 2.52
1065 4185 9.838339 TCTCTGAGAAAAACACTAGATTTCTTT 57.162 29.630 4.57 2.02 41.96 2.52
1080 4200 7.043961 AGATTTCTTTCCAGAGAAAAACACC 57.956 36.000 4.40 0.00 45.68 4.16
1095 4215 2.568623 ACACCAGCTTTCCAACTAGG 57.431 50.000 0.00 0.00 39.47 3.02
1168 4288 1.734137 GCTATCGACGGAGAAGGCA 59.266 57.895 0.00 0.00 0.00 4.75
1231 4351 1.202952 ACAGTGACGACCCTCTTCTCT 60.203 52.381 0.00 0.00 0.00 3.10
1500 4620 3.763897 ACTCCCACGTATAAGTACCGTTT 59.236 43.478 0.00 0.00 0.00 3.60
1501 4621 4.947388 ACTCCCACGTATAAGTACCGTTTA 59.053 41.667 0.00 0.00 0.00 2.01
1728 4855 3.001939 AGCACCGAGTTTACGTTTTGAAG 59.998 43.478 0.00 0.00 0.00 3.02
1857 4985 6.349300 GGCAGAGTCTCCAAATTCATTACTA 58.651 40.000 0.00 0.00 0.00 1.82
1899 5028 5.659440 AAATAACATTTGCCGAGTTCCAT 57.341 34.783 0.00 0.00 0.00 3.41
1903 5032 2.424601 ACATTTGCCGAGTTCCATGATG 59.575 45.455 0.00 0.00 0.00 3.07
1913 5042 5.171476 CGAGTTCCATGATGAAACACTAGT 58.829 41.667 0.00 0.00 0.00 2.57
1930 5059 5.053145 CACTAGTCAAAAGAACAGCACTCT 58.947 41.667 0.00 0.00 0.00 3.24
1959 5088 1.238439 CATGTTTGCCGAGTTCCTGT 58.762 50.000 0.00 0.00 0.00 4.00
1971 5100 3.201290 GAGTTCCTGTCATATGGCACTG 58.799 50.000 5.74 0.65 30.40 3.66
1997 5126 6.324561 ACAAACACAAATTTTGCCAAGTTT 57.675 29.167 9.04 11.32 37.45 2.66
2005 5134 3.701532 TTTTGCCAAGTTTCTACCACG 57.298 42.857 0.00 0.00 0.00 4.94
2009 5138 1.730612 GCCAAGTTTCTACCACGCTAC 59.269 52.381 0.00 0.00 0.00 3.58
2042 5172 5.449177 GGATTTCACCGAGTTCAATTCATCC 60.449 44.000 0.00 0.00 0.00 3.51
2047 5177 1.594862 CGAGTTCAATTCATCCGGAGC 59.405 52.381 11.34 0.00 0.00 4.70
2071 5201 4.631377 CGAGTTGTTGATAATTGAGCTCCA 59.369 41.667 12.15 0.00 0.00 3.86
2085 5215 2.029288 CTCCACAGTGACGCGCAAT 61.029 57.895 5.73 0.97 0.00 3.56
2093 5223 1.667510 TGACGCGCAATTCAGCAGA 60.668 52.632 5.73 0.00 0.00 4.26
2099 5229 1.727213 GCGCAATTCAGCAGACTTCAC 60.727 52.381 0.30 0.00 0.00 3.18
2104 5234 4.534168 CAATTCAGCAGACTTCACTGTTG 58.466 43.478 0.00 0.00 45.68 3.33
2106 5236 0.590195 CAGCAGACTTCACTGTTGGC 59.410 55.000 0.00 0.00 42.47 4.52
2167 5304 0.503117 GTCGCATATTCGCCGAGTTC 59.497 55.000 0.00 0.00 0.00 3.01
2172 5309 0.597637 ATATTCGCCGAGTTCTGCCG 60.598 55.000 0.00 0.00 0.00 5.69
2184 5321 3.978687 AGTTCTGCCGGATATAAACTCG 58.021 45.455 5.05 0.00 0.00 4.18
2189 5326 2.814280 CCGGATATAAACTCGGCAGT 57.186 50.000 0.00 0.00 35.95 4.40
2190 5327 2.404215 CCGGATATAAACTCGGCAGTG 58.596 52.381 0.00 0.00 35.95 3.66
2191 5328 1.792949 CGGATATAAACTCGGCAGTGC 59.207 52.381 6.55 6.55 31.06 4.40
2240 5379 1.600663 CCAGATGTGACGGCGATCTAC 60.601 57.143 16.62 7.27 0.00 2.59
2247 5386 0.638746 GACGGCGATCTACGTTTGTG 59.361 55.000 16.62 0.00 44.24 3.33
2254 5393 2.809696 CGATCTACGTTTGTGGGGTTTT 59.190 45.455 0.00 0.00 37.22 2.43
2273 5412 2.450609 TCACTAACGGAAACTCAGCC 57.549 50.000 0.00 0.00 0.00 4.85
2277 5416 3.314080 CACTAACGGAAACTCAGCCAAAA 59.686 43.478 0.00 0.00 0.00 2.44
2315 5454 6.950545 TCATTACGAAATTTCAACGTTCACT 58.049 32.000 17.99 0.00 40.61 3.41
2322 5461 6.519761 CGAAATTTCAACGTTCACTTCTATGG 59.480 38.462 17.99 0.00 0.00 2.74
2328 5467 1.735700 CGTTCACTTCTATGGCGAGCA 60.736 52.381 0.00 0.00 0.00 4.26
2329 5468 2.346803 GTTCACTTCTATGGCGAGCAA 58.653 47.619 0.00 0.00 0.00 3.91
2334 5473 1.524355 CTTCTATGGCGAGCAATCGTG 59.476 52.381 0.00 0.00 35.26 4.35
2343 5482 2.159517 GCGAGCAATCGTGGAGAAAAAT 60.160 45.455 0.00 0.00 35.26 1.82
2345 5484 3.372206 CGAGCAATCGTGGAGAAAAATCT 59.628 43.478 0.00 0.00 0.00 2.40
2348 5487 4.154918 AGCAATCGTGGAGAAAAATCTGAC 59.845 41.667 0.00 0.00 0.00 3.51
2350 5489 5.392380 GCAATCGTGGAGAAAAATCTGACAT 60.392 40.000 0.00 0.00 0.00 3.06
2361 5500 9.376075 GAGAAAAATCTGACATAGATCTGACAA 57.624 33.333 5.18 0.00 45.41 3.18
2364 5503 8.945481 AAAATCTGACATAGATCTGACAAGAG 57.055 34.615 5.18 0.00 45.41 2.85
2399 5538 0.455410 TGGCAATGGCTATTTGACGC 59.545 50.000 8.59 0.00 40.87 5.19
2400 5539 0.455410 GGCAATGGCTATTTGACGCA 59.545 50.000 0.00 0.00 40.87 5.24
2401 5540 1.548986 GCAATGGCTATTTGACGCAC 58.451 50.000 0.00 0.00 36.96 5.34
2402 5541 1.813896 CAATGGCTATTTGACGCACG 58.186 50.000 0.00 0.00 0.00 5.34
2419 5558 0.182775 ACGGTTGGGATTCCTATGCC 59.817 55.000 2.01 1.76 42.30 4.40
2426 5565 1.343069 GGATTCCTATGCCGAGTCCT 58.657 55.000 0.00 0.00 34.25 3.85
2432 5571 3.101437 TCCTATGCCGAGTCCTAAAACA 58.899 45.455 0.00 0.00 0.00 2.83
2443 5582 0.038618 CCTAAAACACGGCAAAGGGC 60.039 55.000 0.00 0.00 43.74 5.19
2508 5648 1.286880 CTCCTGGCAACCGCAAAAG 59.713 57.895 0.00 0.00 41.24 2.27
2511 5651 1.950630 CTGGCAACCGCAAAAGCAC 60.951 57.895 0.00 0.00 41.24 4.40
2512 5652 2.354074 CTGGCAACCGCAAAAGCACT 62.354 55.000 0.00 0.00 41.24 4.40
2513 5653 1.661509 GGCAACCGCAAAAGCACTC 60.662 57.895 0.00 0.00 41.24 3.51
2514 5654 2.010817 GCAACCGCAAAAGCACTCG 61.011 57.895 0.00 0.00 38.36 4.18
2515 5655 2.010817 CAACCGCAAAAGCACTCGC 61.011 57.895 0.00 0.00 38.99 5.03
2516 5656 3.194272 AACCGCAAAAGCACTCGCC 62.194 57.895 0.00 0.00 39.83 5.54
2517 5657 4.404654 CCGCAAAAGCACTCGCCC 62.405 66.667 0.00 0.00 39.83 6.13
2518 5658 3.659092 CGCAAAAGCACTCGCCCA 61.659 61.111 0.00 0.00 39.83 5.36
2519 5659 2.050077 GCAAAAGCACTCGCCCAC 60.050 61.111 0.00 0.00 39.83 4.61
2520 5660 2.644992 CAAAAGCACTCGCCCACC 59.355 61.111 0.00 0.00 39.83 4.61
2521 5661 2.597510 AAAAGCACTCGCCCACCC 60.598 61.111 0.00 0.00 39.83 4.61
2522 5662 4.660938 AAAGCACTCGCCCACCCC 62.661 66.667 0.00 0.00 39.83 4.95
2535 5675 4.312152 ACCCCGGTCGTCTCCCTT 62.312 66.667 0.00 0.00 0.00 3.95
2536 5676 3.459063 CCCCGGTCGTCTCCCTTC 61.459 72.222 0.00 0.00 0.00 3.46
2537 5677 2.362632 CCCGGTCGTCTCCCTTCT 60.363 66.667 0.00 0.00 0.00 2.85
2538 5678 2.416432 CCCGGTCGTCTCCCTTCTC 61.416 68.421 0.00 0.00 0.00 2.87
2539 5679 2.416432 CCGGTCGTCTCCCTTCTCC 61.416 68.421 0.00 0.00 0.00 3.71
2540 5680 2.762234 CGGTCGTCTCCCTTCTCCG 61.762 68.421 0.00 0.00 0.00 4.63
2541 5681 1.378250 GGTCGTCTCCCTTCTCCGA 60.378 63.158 0.00 0.00 0.00 4.55
2542 5682 0.752376 GGTCGTCTCCCTTCTCCGAT 60.752 60.000 0.00 0.00 0.00 4.18
2543 5683 0.382515 GTCGTCTCCCTTCTCCGATG 59.617 60.000 0.00 0.00 0.00 3.84
2544 5684 1.066587 CGTCTCCCTTCTCCGATGC 59.933 63.158 0.00 0.00 0.00 3.91
2545 5685 1.667154 CGTCTCCCTTCTCCGATGCA 61.667 60.000 0.00 0.00 0.00 3.96
2546 5686 0.179097 GTCTCCCTTCTCCGATGCAC 60.179 60.000 0.00 0.00 0.00 4.57
2547 5687 1.144936 CTCCCTTCTCCGATGCACC 59.855 63.158 0.00 0.00 0.00 5.01
2548 5688 1.306141 TCCCTTCTCCGATGCACCT 60.306 57.895 0.00 0.00 0.00 4.00
2549 5689 1.144936 CCCTTCTCCGATGCACCTC 59.855 63.158 0.00 0.00 0.00 3.85
2550 5690 1.144936 CCTTCTCCGATGCACCTCC 59.855 63.158 0.00 0.00 0.00 4.30
2551 5691 1.333636 CCTTCTCCGATGCACCTCCT 61.334 60.000 0.00 0.00 0.00 3.69
2552 5692 0.539051 CTTCTCCGATGCACCTCCTT 59.461 55.000 0.00 0.00 0.00 3.36
2553 5693 0.537188 TTCTCCGATGCACCTCCTTC 59.463 55.000 0.00 0.00 0.00 3.46
2554 5694 1.227089 CTCCGATGCACCTCCTTCG 60.227 63.158 0.00 0.00 33.67 3.79
2555 5695 2.892425 CCGATGCACCTCCTTCGC 60.892 66.667 0.00 0.00 32.86 4.70
2556 5696 2.892425 CGATGCACCTCCTTCGCC 60.892 66.667 0.00 0.00 0.00 5.54
2557 5697 2.892425 GATGCACCTCCTTCGCCG 60.892 66.667 0.00 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
198 201 7.389053 GTCATACAACTGATCAGGTCTCTTTTT 59.611 37.037 26.08 6.41 0.00 1.94
199 202 6.876257 GTCATACAACTGATCAGGTCTCTTTT 59.124 38.462 26.08 7.14 0.00 2.27
200 203 6.014242 TGTCATACAACTGATCAGGTCTCTTT 60.014 38.462 26.08 7.86 0.00 2.52
201 204 5.481824 TGTCATACAACTGATCAGGTCTCTT 59.518 40.000 26.08 8.59 0.00 2.85
202 205 5.019470 TGTCATACAACTGATCAGGTCTCT 58.981 41.667 26.08 7.44 0.00 3.10
203 206 5.330455 TGTCATACAACTGATCAGGTCTC 57.670 43.478 26.08 6.97 0.00 3.36
204 207 5.946942 ATGTCATACAACTGATCAGGTCT 57.053 39.130 26.08 10.85 0.00 3.85
205 208 6.703607 CCTTATGTCATACAACTGATCAGGTC 59.296 42.308 26.08 7.76 0.00 3.85
206 209 6.408548 CCCTTATGTCATACAACTGATCAGGT 60.409 42.308 26.08 18.36 0.00 4.00
207 210 5.994054 CCCTTATGTCATACAACTGATCAGG 59.006 44.000 26.08 12.13 0.00 3.86
208 211 6.481313 CACCCTTATGTCATACAACTGATCAG 59.519 42.308 21.37 21.37 0.00 2.90
209 212 6.156083 TCACCCTTATGTCATACAACTGATCA 59.844 38.462 0.00 0.00 0.00 2.92
210 213 6.582636 TCACCCTTATGTCATACAACTGATC 58.417 40.000 0.00 0.00 0.00 2.92
211 214 6.560003 TCACCCTTATGTCATACAACTGAT 57.440 37.500 0.00 0.00 0.00 2.90
212 215 6.560003 ATCACCCTTATGTCATACAACTGA 57.440 37.500 0.00 0.00 0.00 3.41
213 216 8.150296 TGATATCACCCTTATGTCATACAACTG 58.850 37.037 0.00 0.00 0.00 3.16
214 217 8.150945 GTGATATCACCCTTATGTCATACAACT 58.849 37.037 22.97 0.00 40.85 3.16
230 233 8.573035 TCAAAACCACTTTTTAGTGATATCACC 58.427 33.333 28.26 13.32 40.31 4.02
373 376 7.505585 TCCAATCATTCTTGTCCAAAACTACTT 59.494 33.333 0.00 0.00 0.00 2.24
538 1859 0.669625 AGCTTACACGACCGAAAGCC 60.670 55.000 17.70 7.29 44.24 4.35
695 3757 6.757897 ATGCTCAGAATTCGGAAATTACAA 57.242 33.333 9.61 0.00 35.21 2.41
741 3803 0.684479 GCTCCCTGGGTCCATTTTCC 60.684 60.000 13.56 0.00 0.00 3.13
1001 4121 4.528920 ACTTAGTGGTTTTGCCTTGTGTA 58.471 39.130 0.00 0.00 38.35 2.90
1042 4162 8.840321 TGGAAAGAAATCTAGTGTTTTTCTCAG 58.160 33.333 10.74 0.00 38.42 3.35
1043 4163 8.746052 TGGAAAGAAATCTAGTGTTTTTCTCA 57.254 30.769 10.74 5.41 38.42 3.27
1044 4164 9.057089 TCTGGAAAGAAATCTAGTGTTTTTCTC 57.943 33.333 10.74 3.86 38.42 2.87
1045 4165 8.980481 TCTGGAAAGAAATCTAGTGTTTTTCT 57.020 30.769 0.00 0.00 40.47 2.52
1046 4166 9.057089 TCTCTGGAAAGAAATCTAGTGTTTTTC 57.943 33.333 0.00 0.00 30.61 2.29
1047 4167 8.980481 TCTCTGGAAAGAAATCTAGTGTTTTT 57.020 30.769 0.00 0.00 30.61 1.94
1048 4168 8.980481 TTCTCTGGAAAGAAATCTAGTGTTTT 57.020 30.769 0.00 0.00 32.42 2.43
1049 4169 8.980481 TTTCTCTGGAAAGAAATCTAGTGTTT 57.020 30.769 0.00 0.00 39.67 2.83
1050 4170 8.980481 TTTTCTCTGGAAAGAAATCTAGTGTT 57.020 30.769 0.35 0.00 43.02 3.32
1051 4171 8.841300 GTTTTTCTCTGGAAAGAAATCTAGTGT 58.159 33.333 0.35 0.00 43.02 3.55
1052 4172 8.840321 TGTTTTTCTCTGGAAAGAAATCTAGTG 58.160 33.333 0.35 0.00 43.02 2.74
1053 4173 8.841300 GTGTTTTTCTCTGGAAAGAAATCTAGT 58.159 33.333 0.35 0.00 43.02 2.57
1054 4174 8.293157 GGTGTTTTTCTCTGGAAAGAAATCTAG 58.707 37.037 0.35 0.00 43.02 2.43
1055 4175 7.777910 TGGTGTTTTTCTCTGGAAAGAAATCTA 59.222 33.333 0.35 0.00 43.02 1.98
1056 4176 6.607198 TGGTGTTTTTCTCTGGAAAGAAATCT 59.393 34.615 0.35 0.00 43.02 2.40
1057 4177 6.805713 TGGTGTTTTTCTCTGGAAAGAAATC 58.194 36.000 0.35 0.00 43.02 2.17
1058 4178 6.683861 GCTGGTGTTTTTCTCTGGAAAGAAAT 60.684 38.462 0.35 0.00 43.02 2.17
1059 4179 5.394115 GCTGGTGTTTTTCTCTGGAAAGAAA 60.394 40.000 0.00 0.00 42.12 2.52
1060 4180 4.097892 GCTGGTGTTTTTCTCTGGAAAGAA 59.902 41.667 0.00 0.00 41.66 2.52
1061 4181 3.632145 GCTGGTGTTTTTCTCTGGAAAGA 59.368 43.478 0.00 0.00 41.66 2.52
1062 4182 3.633986 AGCTGGTGTTTTTCTCTGGAAAG 59.366 43.478 0.00 0.00 41.66 2.62
1063 4183 3.631250 AGCTGGTGTTTTTCTCTGGAAA 58.369 40.909 0.00 0.00 39.38 3.13
1064 4184 3.297134 AGCTGGTGTTTTTCTCTGGAA 57.703 42.857 0.00 0.00 0.00 3.53
1065 4185 3.297134 AAGCTGGTGTTTTTCTCTGGA 57.703 42.857 0.00 0.00 0.00 3.86
1066 4186 3.243535 GGAAAGCTGGTGTTTTTCTCTGG 60.244 47.826 0.00 0.00 32.74 3.86
1080 4200 3.425162 AAGGACCTAGTTGGAAAGCTG 57.575 47.619 0.00 0.00 39.71 4.24
1095 4215 5.707298 TCTTCTTGATGGATTGTGAAAGGAC 59.293 40.000 0.00 0.00 0.00 3.85
1168 4288 1.079819 CGGCGTGAAGATCACCACT 60.080 57.895 13.30 0.00 44.20 4.00
1500 4620 9.866798 TGCATGCAGTGTAAAATTTTGATTATA 57.133 25.926 18.46 0.00 0.00 0.98
1501 4621 8.774890 TGCATGCAGTGTAAAATTTTGATTAT 57.225 26.923 18.46 0.00 0.00 1.28
1728 4855 5.640732 ACGAGTTCATTATTTGTGAATGGC 58.359 37.500 0.00 0.00 37.84 4.40
1824 4951 2.156051 GAGACTCTGCCGACCGGTTT 62.156 60.000 9.42 0.00 37.65 3.27
1857 4985 4.329462 TTTGCGGGCAAAGTTAGAATTT 57.671 36.364 14.35 0.00 40.51 1.82
1899 5028 7.467267 GCTGTTCTTTTGACTAGTGTTTCATCA 60.467 37.037 0.00 0.00 0.00 3.07
1903 5032 5.965918 GTGCTGTTCTTTTGACTAGTGTTTC 59.034 40.000 0.00 0.00 0.00 2.78
1913 5042 3.872696 TGTCAGAGTGCTGTTCTTTTGA 58.127 40.909 0.00 0.00 42.84 2.69
1930 5059 1.665448 CGGCAAACATGCGATTTGTCA 60.665 47.619 11.13 0.00 40.86 3.58
1959 5088 2.040947 TGTTTGTCCCAGTGCCATATGA 59.959 45.455 3.65 0.00 0.00 2.15
1971 5100 3.274288 TGGCAAAATTTGTGTTTGTCCC 58.726 40.909 7.60 0.00 39.34 4.46
1997 5126 2.029623 GGATTCCAGTAGCGTGGTAGA 58.970 52.381 0.00 0.00 38.88 2.59
2005 5134 2.872858 GTGAAATCCGGATTCCAGTAGC 59.127 50.000 29.32 8.06 0.00 3.58
2009 5138 1.299541 CGGTGAAATCCGGATTCCAG 58.700 55.000 29.32 17.20 45.88 3.86
2042 5172 2.004583 TTATCAACAACTCGGCTCCG 57.995 50.000 1.14 1.14 41.35 4.63
2047 5177 4.034510 GGAGCTCAATTATCAACAACTCGG 59.965 45.833 17.19 0.00 0.00 4.63
2071 5201 1.862123 CTGAATTGCGCGTCACTGT 59.138 52.632 8.43 0.00 0.00 3.55
2085 5215 2.564771 CCAACAGTGAAGTCTGCTGAA 58.435 47.619 0.00 0.00 38.84 3.02
2093 5223 1.072331 CACTAGGGCCAACAGTGAAGT 59.928 52.381 21.69 3.01 41.80 3.01
2099 5229 1.448540 CTCGCACTAGGGCCAACAG 60.449 63.158 12.39 1.78 0.00 3.16
2104 5234 0.322187 TTTTTCCTCGCACTAGGGCC 60.322 55.000 12.39 0.00 37.24 5.80
2106 5236 1.076332 CGTTTTTCCTCGCACTAGGG 58.924 55.000 0.00 0.00 37.24 3.53
2126 5256 2.540101 ACTGCTGAGTTTCTTTCGTTCG 59.460 45.455 0.00 0.00 0.00 3.95
2128 5258 3.270877 ACACTGCTGAGTTTCTTTCGTT 58.729 40.909 0.00 0.00 0.00 3.85
2129 5259 2.866762 GACACTGCTGAGTTTCTTTCGT 59.133 45.455 0.00 0.00 0.00 3.85
2172 5309 2.143925 GGCACTGCCGAGTTTATATCC 58.856 52.381 3.73 0.00 39.62 2.59
2187 5324 3.958860 GGTCCACCTGCAGGCACT 61.959 66.667 33.06 11.05 43.88 4.40
2210 5349 1.134670 GTCACATCTGGCCTGGTAGTC 60.135 57.143 10.07 0.00 0.00 2.59
2235 5374 3.566742 GTGAAAACCCCACAAACGTAGAT 59.433 43.478 0.00 0.00 34.81 1.98
2240 5379 3.697982 GTTAGTGAAAACCCCACAAACG 58.302 45.455 0.00 0.00 37.01 3.60
2247 5386 3.216800 AGTTTCCGTTAGTGAAAACCCC 58.783 45.455 0.00 0.00 33.80 4.95
2254 5393 1.689813 TGGCTGAGTTTCCGTTAGTGA 59.310 47.619 0.00 0.00 0.00 3.41
2292 5431 7.586300 AGAAGTGAACGTTGAAATTTCGTAATG 59.414 33.333 5.00 10.46 36.80 1.90
2298 5437 6.305638 GCCATAGAAGTGAACGTTGAAATTTC 59.694 38.462 5.00 11.41 0.00 2.17
2299 5438 6.149633 GCCATAGAAGTGAACGTTGAAATTT 58.850 36.000 5.00 0.00 0.00 1.82
2328 5467 7.331026 TCTATGTCAGATTTTTCTCCACGATT 58.669 34.615 0.00 0.00 0.00 3.34
2329 5468 6.878317 TCTATGTCAGATTTTTCTCCACGAT 58.122 36.000 0.00 0.00 0.00 3.73
2334 5473 7.984050 TGTCAGATCTATGTCAGATTTTTCTCC 59.016 37.037 0.00 0.00 44.41 3.71
2343 5482 4.892345 CCCTCTTGTCAGATCTATGTCAGA 59.108 45.833 0.00 0.00 37.79 3.27
2345 5484 3.386078 GCCCTCTTGTCAGATCTATGTCA 59.614 47.826 0.00 0.00 0.00 3.58
2348 5487 2.038295 GGGCCCTCTTGTCAGATCTATG 59.962 54.545 17.04 0.00 0.00 2.23
2350 5489 1.794714 GGGCCCTCTTGTCAGATCTA 58.205 55.000 17.04 0.00 0.00 1.98
2376 5515 3.287222 GTCAAATAGCCATTGCCAGGTA 58.713 45.455 0.00 0.00 38.69 3.08
2379 5518 1.534595 GCGTCAAATAGCCATTGCCAG 60.535 52.381 0.00 0.00 38.69 4.85
2386 5525 0.604243 AACCGTGCGTCAAATAGCCA 60.604 50.000 0.00 0.00 0.00 4.75
2399 5538 1.308998 GCATAGGAATCCCAACCGTG 58.691 55.000 0.00 0.00 33.88 4.94
2400 5539 0.182775 GGCATAGGAATCCCAACCGT 59.817 55.000 0.00 0.00 33.88 4.83
2401 5540 0.884704 CGGCATAGGAATCCCAACCG 60.885 60.000 6.30 6.30 33.88 4.44
2402 5541 0.472471 TCGGCATAGGAATCCCAACC 59.528 55.000 0.00 0.00 33.88 3.77
2419 5558 1.504359 TTGCCGTGTTTTAGGACTCG 58.496 50.000 0.00 0.00 36.57 4.18
2426 5565 1.333177 ATGCCCTTTGCCGTGTTTTA 58.667 45.000 0.00 0.00 40.16 1.52
2482 5622 4.560743 TTGCCAGGAGTGCGCACA 62.561 61.111 39.21 16.81 31.88 4.57
2503 5643 2.644992 GGTGGGCGAGTGCTTTTG 59.355 61.111 0.00 0.00 42.25 2.44
2518 5658 4.312152 AAGGGAGACGACCGGGGT 62.312 66.667 6.32 2.45 0.00 4.95
2519 5659 3.459063 GAAGGGAGACGACCGGGG 61.459 72.222 6.32 0.00 0.00 5.73
2520 5660 2.362632 AGAAGGGAGACGACCGGG 60.363 66.667 6.32 0.00 0.00 5.73
2521 5661 2.416432 GGAGAAGGGAGACGACCGG 61.416 68.421 0.00 0.00 0.00 5.28
2522 5662 2.762234 CGGAGAAGGGAGACGACCG 61.762 68.421 0.00 0.00 0.00 4.79
2523 5663 0.752376 ATCGGAGAAGGGAGACGACC 60.752 60.000 0.00 0.00 43.58 4.79
2524 5664 0.382515 CATCGGAGAAGGGAGACGAC 59.617 60.000 0.00 0.00 43.58 4.34
2525 5665 1.384989 GCATCGGAGAAGGGAGACGA 61.385 60.000 0.00 0.00 43.58 4.20
2526 5666 1.066587 GCATCGGAGAAGGGAGACG 59.933 63.158 0.00 0.00 43.58 4.18
2527 5667 0.179097 GTGCATCGGAGAAGGGAGAC 60.179 60.000 0.00 0.00 43.58 3.36
2528 5668 1.330655 GGTGCATCGGAGAAGGGAGA 61.331 60.000 0.00 0.00 43.58 3.71
2529 5669 1.144936 GGTGCATCGGAGAAGGGAG 59.855 63.158 0.00 0.00 43.58 4.30
2530 5670 1.306141 AGGTGCATCGGAGAAGGGA 60.306 57.895 0.00 0.00 43.58 4.20
2531 5671 1.144936 GAGGTGCATCGGAGAAGGG 59.855 63.158 0.00 0.00 43.58 3.95
2532 5672 1.144936 GGAGGTGCATCGGAGAAGG 59.855 63.158 0.00 0.00 43.58 3.46
2533 5673 0.539051 AAGGAGGTGCATCGGAGAAG 59.461 55.000 0.00 0.00 43.58 2.85
2534 5674 0.537188 GAAGGAGGTGCATCGGAGAA 59.463 55.000 0.00 0.00 43.58 2.87
2535 5675 1.667154 CGAAGGAGGTGCATCGGAGA 61.667 60.000 0.00 0.00 45.75 3.71
2536 5676 1.227089 CGAAGGAGGTGCATCGGAG 60.227 63.158 0.00 0.00 0.00 4.63
2537 5677 2.892640 CGAAGGAGGTGCATCGGA 59.107 61.111 0.00 0.00 0.00 4.55
2538 5678 2.892425 GCGAAGGAGGTGCATCGG 60.892 66.667 7.20 0.00 35.91 4.18
2539 5679 2.892425 GGCGAAGGAGGTGCATCG 60.892 66.667 0.85 0.85 38.28 3.84
2540 5680 2.892425 CGGCGAAGGAGGTGCATC 60.892 66.667 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.