Multiple sequence alignment - TraesCS1D01G285300

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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 TraesCS1D01G285300 chr1D 100.000 2602 0 0 1 2602 383321434 383318833 0.000000e+00 4806.0
1 TraesCS1D01G285300 chr1A 89.505 1877 119 30 19 1861 483035025 483033193 0.000000e+00 2303.0
2 TraesCS1D01G285300 chr1A 87.811 763 54 19 1866 2602 483033048 483032299 0.000000e+00 857.0
3 TraesCS1D01G285300 chr1B 87.368 1140 86 29 714 1810 513546071 513544947 0.000000e+00 1254.0
4 TraesCS1D01G285300 chr1B 87.333 750 58 20 1858 2602 513544790 513544073 0.000000e+00 824.0
5 TraesCS1D01G285300 chr1B 79.975 794 85 38 5 784 513546813 513546080 3.840000e-143 518.0
6 TraesCS1D01G285300 chr1B 82.000 100 9 5 2512 2602 513543450 513543351 2.780000e-10 76.8
7 TraesCS1D01G285300 chr3A 83.763 388 56 7 993 1375 603803417 603803802 6.850000e-96 361.0
8 TraesCS1D01G285300 chr3A 88.073 109 13 0 1494 1602 603803914 603804022 2.100000e-26 130.0
9 TraesCS1D01G285300 chr3D 83.632 391 49 12 993 1375 461212843 461213226 1.150000e-93 353.0
10 TraesCS1D01G285300 chr3D 88.991 109 12 0 1494 1602 461213340 461213448 4.520000e-28 135.0
11 TraesCS1D01G285300 chr3B 83.505 388 55 9 993 1375 611727461 611727844 1.150000e-93 353.0


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 TraesCS1D01G285300 chr1D 383318833 383321434 2601 True 4806.0 4806 100.0000 1 2602 1 chr1D.!!$R1 2601
1 TraesCS1D01G285300 chr1A 483032299 483035025 2726 True 1580.0 2303 88.6580 19 2602 2 chr1A.!!$R1 2583
2 TraesCS1D01G285300 chr1B 513543351 513546813 3462 True 668.2 1254 84.1690 5 2602 4 chr1B.!!$R1 2597
3 TraesCS1D01G285300 chr3A 603803417 603804022 605 False 245.5 361 85.9180 993 1602 2 chr3A.!!$F1 609
4 TraesCS1D01G285300 chr3D 461212843 461213448 605 False 244.0 353 86.3115 993 1602 2 chr3D.!!$F1 609

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
210 222 0.162294 GTAGGAAACGGTGCGAAACG 59.838 55.0 0.0 0.0 0.0 3.6 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 1953 0.861185 CACACATGACACAGGACACG 59.139 55.0 0.0 0.0 0.0 4.49 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 2.752640 TCTTCCGCGGGTCATCGA 60.753 61.111 27.83 9.91 0.00 3.59
46 47 4.760220 TCCCCTCCTTGCCCCCTC 62.760 72.222 0.00 0.00 0.00 4.30
71 72 1.445716 CGCGTAGAGATCCTTCGGGT 61.446 60.000 0.00 0.00 41.37 5.28
102 103 2.031870 GTTGAAGGTGTTTGCTCCCTT 58.968 47.619 0.00 0.00 41.23 3.95
104 105 3.586470 TGAAGGTGTTTGCTCCCTTTA 57.414 42.857 0.00 0.00 38.68 1.85
107 108 3.525800 AGGTGTTTGCTCCCTTTATGT 57.474 42.857 0.00 0.00 0.00 2.29
112 113 5.010213 GGTGTTTGCTCCCTTTATGTTGTTA 59.990 40.000 0.00 0.00 0.00 2.41
149 161 6.265876 TCCTTGGTTTGGTAGTTGTTTAATCC 59.734 38.462 0.00 0.00 0.00 3.01
175 187 6.072112 TGTTCTTGCTTGTTTTGTCTATCC 57.928 37.500 0.00 0.00 0.00 2.59
176 188 5.147162 GTTCTTGCTTGTTTTGTCTATCCG 58.853 41.667 0.00 0.00 0.00 4.18
177 189 3.751175 TCTTGCTTGTTTTGTCTATCCGG 59.249 43.478 0.00 0.00 0.00 5.14
178 190 2.432444 TGCTTGTTTTGTCTATCCGGG 58.568 47.619 0.00 0.00 0.00 5.73
179 191 2.224670 TGCTTGTTTTGTCTATCCGGGT 60.225 45.455 0.00 0.00 0.00 5.28
180 192 3.008157 TGCTTGTTTTGTCTATCCGGGTA 59.992 43.478 0.00 0.00 0.00 3.69
181 193 3.621715 GCTTGTTTTGTCTATCCGGGTAG 59.378 47.826 16.18 16.18 0.00 3.18
182 194 4.828829 CTTGTTTTGTCTATCCGGGTAGT 58.171 43.478 21.19 0.00 0.00 2.73
183 195 4.895668 TGTTTTGTCTATCCGGGTAGTT 57.104 40.909 21.19 0.00 0.00 2.24
184 196 4.571919 TGTTTTGTCTATCCGGGTAGTTG 58.428 43.478 21.19 0.00 0.00 3.16
185 197 4.040706 TGTTTTGTCTATCCGGGTAGTTGT 59.959 41.667 21.19 0.00 0.00 3.32
186 198 5.245751 TGTTTTGTCTATCCGGGTAGTTGTA 59.754 40.000 21.19 0.00 0.00 2.41
187 199 6.070653 TGTTTTGTCTATCCGGGTAGTTGTAT 60.071 38.462 21.19 0.00 0.00 2.29
188 200 5.524971 TTGTCTATCCGGGTAGTTGTATG 57.475 43.478 21.19 0.00 0.00 2.39
189 201 4.539726 TGTCTATCCGGGTAGTTGTATGT 58.460 43.478 21.19 0.00 0.00 2.29
190 202 5.693961 TGTCTATCCGGGTAGTTGTATGTA 58.306 41.667 21.19 0.00 0.00 2.29
191 203 5.766670 TGTCTATCCGGGTAGTTGTATGTAG 59.233 44.000 21.19 0.00 0.00 2.74
192 204 5.767168 GTCTATCCGGGTAGTTGTATGTAGT 59.233 44.000 21.19 0.00 0.00 2.73
193 205 6.936900 GTCTATCCGGGTAGTTGTATGTAGTA 59.063 42.308 21.19 0.00 0.00 1.82
194 206 7.118971 GTCTATCCGGGTAGTTGTATGTAGTAG 59.881 44.444 21.19 0.00 0.00 2.57
195 207 4.464008 TCCGGGTAGTTGTATGTAGTAGG 58.536 47.826 0.00 0.00 0.00 3.18
196 208 4.165950 TCCGGGTAGTTGTATGTAGTAGGA 59.834 45.833 0.00 0.00 0.00 2.94
197 209 4.889409 CCGGGTAGTTGTATGTAGTAGGAA 59.111 45.833 0.00 0.00 0.00 3.36
198 210 5.360714 CCGGGTAGTTGTATGTAGTAGGAAA 59.639 44.000 0.00 0.00 0.00 3.13
205 217 2.288961 ATGTAGTAGGAAACGGTGCG 57.711 50.000 0.00 0.00 0.00 5.34
210 222 0.162294 GTAGGAAACGGTGCGAAACG 59.838 55.000 0.00 0.00 0.00 3.60
222 234 1.831389 GCGAAACGAGTGCAGCTTCA 61.831 55.000 0.00 0.00 0.00 3.02
229 241 1.228063 AGTGCAGCTTCAGGTGTGG 60.228 57.895 7.79 0.00 44.70 4.17
314 326 3.877508 CCCTTAGTTTCATCCCGTGAATC 59.122 47.826 0.00 0.00 45.77 2.52
329 341 4.435518 CCGTGAATCGTACCAGTCAAATTG 60.436 45.833 0.00 0.00 37.94 2.32
332 344 6.435428 GTGAATCGTACCAGTCAAATTGTTT 58.565 36.000 0.00 0.00 0.00 2.83
355 367 3.832276 GCGTGTTTTTGCCATCATAGAA 58.168 40.909 0.00 0.00 0.00 2.10
358 370 5.220265 GCGTGTTTTTGCCATCATAGAAATG 60.220 40.000 0.00 0.00 0.00 2.32
359 371 6.092092 CGTGTTTTTGCCATCATAGAAATGA 58.908 36.000 0.00 0.00 46.01 2.57
404 417 2.508439 AATGACGCGCGGTACTGG 60.508 61.111 35.22 4.42 0.00 4.00
427 440 2.874086 CTGTGACATCTGTCTGCACAAA 59.126 45.455 11.35 0.00 44.99 2.83
428 441 3.277715 TGTGACATCTGTCTGCACAAAA 58.722 40.909 11.35 0.00 44.99 2.44
429 442 3.693578 TGTGACATCTGTCTGCACAAAAA 59.306 39.130 11.35 0.00 44.99 1.94
442 455 0.249031 ACAAAAAGCTGCCGAGTTGC 60.249 50.000 0.00 0.00 0.00 4.17
464 477 0.541863 CGAAACCTGCCATAGAGGGT 59.458 55.000 0.00 0.00 38.09 4.34
478 491 7.122055 TGCCATAGAGGGTAACAAAATGTTTAG 59.878 37.037 0.54 0.00 38.68 1.85
482 495 7.745620 AGAGGGTAACAAAATGTTTAGTCTG 57.254 36.000 0.54 0.00 41.45 3.51
484 497 7.661847 AGAGGGTAACAAAATGTTTAGTCTGAG 59.338 37.037 0.54 0.00 41.45 3.35
541 554 3.706086 CCCCTTTGTGGCATATTTAGCTT 59.294 43.478 0.00 0.00 0.00 3.74
547 560 5.720371 TGTGGCATATTTAGCTTTTGTGT 57.280 34.783 0.00 0.00 0.00 3.72
575 595 3.449746 TGCTAGGGTTTACTGCCAATT 57.550 42.857 0.00 0.00 0.00 2.32
576 596 4.577988 TGCTAGGGTTTACTGCCAATTA 57.422 40.909 0.00 0.00 0.00 1.40
577 597 4.266714 TGCTAGGGTTTACTGCCAATTAC 58.733 43.478 0.00 0.00 0.00 1.89
578 598 4.263550 TGCTAGGGTTTACTGCCAATTACA 60.264 41.667 0.00 0.00 0.00 2.41
579 599 4.335594 GCTAGGGTTTACTGCCAATTACAG 59.664 45.833 6.19 6.19 41.08 2.74
649 669 5.747342 TGTCCTACTGTTTAAGTTTGTGGT 58.253 37.500 0.00 0.00 40.56 4.16
705 727 1.531149 CTGAAGTAGTGGTGCCAAACG 59.469 52.381 0.00 0.00 0.00 3.60
708 730 1.878953 AGTAGTGGTGCCAAACGAAG 58.121 50.000 0.00 0.00 0.00 3.79
726 826 6.870971 ACGAAGCTTTGATGTTTACCTTTA 57.129 33.333 20.86 0.00 0.00 1.85
727 827 6.899114 ACGAAGCTTTGATGTTTACCTTTAG 58.101 36.000 20.86 0.00 0.00 1.85
728 828 6.485648 ACGAAGCTTTGATGTTTACCTTTAGT 59.514 34.615 20.86 0.00 0.00 2.24
729 829 7.015877 CGAAGCTTTGATGTTTACCTTTAGTC 58.984 38.462 8.08 0.00 0.00 2.59
814 914 6.933521 CACCTAGATTTATTCTATGTGCTGCT 59.066 38.462 0.00 0.00 42.68 4.24
871 990 1.802960 CCAGTGTCAGTTTAGCTGCTG 59.197 52.381 13.43 2.23 44.66 4.41
941 1060 3.854809 TGTTTTAAACTTCGCAGCAACAC 59.145 39.130 9.33 0.00 0.00 3.32
1023 1144 1.207329 GTGAGGGTTAGCGTCCTGAAT 59.793 52.381 1.67 0.00 32.74 2.57
1141 1262 1.508632 GCAGAAGCACGGTTAGTTCA 58.491 50.000 0.00 0.00 41.58 3.18
1142 1263 1.194772 GCAGAAGCACGGTTAGTTCAC 59.805 52.381 0.00 0.00 41.58 3.18
1386 1523 1.977854 TCAGGTCAGCTTCTTTGCCTA 59.022 47.619 0.00 0.00 0.00 3.93
1450 1607 2.038820 TCATGAACTGTGAGCCATGACA 59.961 45.455 0.00 0.00 40.04 3.58
1451 1608 2.636647 TGAACTGTGAGCCATGACAA 57.363 45.000 0.00 0.00 0.00 3.18
1462 1619 5.048083 GTGAGCCATGACAATTTCCAAGTTA 60.048 40.000 0.00 0.00 0.00 2.24
1606 1766 1.087501 GGCTTTTTCTACTGAGCGGG 58.912 55.000 0.00 0.00 36.02 6.13
1784 1953 8.192774 TGAATTATGACTTTGAAGATGCCATTC 58.807 33.333 0.00 1.69 0.00 2.67
1788 1957 3.149196 ACTTTGAAGATGCCATTCGTGT 58.851 40.909 0.00 0.00 0.00 4.49
1829 2014 5.128205 TGCTGTATTTCTGAAGCTGCATAT 58.872 37.500 0.00 0.00 36.60 1.78
1830 2015 6.290605 TGCTGTATTTCTGAAGCTGCATATA 58.709 36.000 0.00 0.00 36.60 0.86
1831 2016 6.203530 TGCTGTATTTCTGAAGCTGCATATAC 59.796 38.462 0.00 4.96 36.60 1.47
1835 2020 4.502105 TTCTGAAGCTGCATATACCCAA 57.498 40.909 0.00 0.00 0.00 4.12
1901 2226 3.683365 ATTTGGTGGGCATTTCAAGTC 57.317 42.857 0.00 0.00 0.00 3.01
1906 2231 1.546029 GTGGGCATTTCAAGTCCTTCC 59.454 52.381 0.00 0.00 0.00 3.46
1928 2253 7.247456 TCCCAACCCTAAAATTTATGTTTCC 57.753 36.000 0.00 0.00 0.00 3.13
1963 2295 9.553064 AAGTAGCATTGTTATAGGATCTTTGAG 57.447 33.333 0.00 0.00 0.00 3.02
1999 2341 5.231991 CCACACGCTTATTTAAATCATTGGC 59.768 40.000 3.39 2.95 0.00 4.52
2042 2384 1.939934 CGTGAACCAGTCTTTGAAGCA 59.060 47.619 0.00 0.00 0.00 3.91
2046 2388 3.817084 TGAACCAGTCTTTGAAGCATCTG 59.183 43.478 0.00 0.00 0.00 2.90
2085 2432 5.715070 ACAGCTAGTAAACATCTCTCACAC 58.285 41.667 0.00 0.00 0.00 3.82
2098 2445 7.995289 ACATCTCTCACACTATTAGAGTCTTG 58.005 38.462 0.00 0.00 38.32 3.02
2172 2519 1.248486 CCAGAACTGGTCTCGTCTGA 58.752 55.000 12.21 0.00 45.53 3.27
2252 2599 4.077184 CCCAGACGCCGTTAGCCA 62.077 66.667 0.00 0.00 38.78 4.75
2260 2607 3.419759 CCGTTAGCCACCGCACAC 61.420 66.667 0.00 0.00 37.52 3.82
2262 2609 3.419759 GTTAGCCACCGCACACCG 61.420 66.667 0.00 0.00 37.52 4.94
2304 2651 3.055675 ACCGGAATACTTCGATTTGACCA 60.056 43.478 9.46 0.00 0.00 4.02
2552 3610 3.790089 TGTTCCCTTTTCTCCTCCTTC 57.210 47.619 0.00 0.00 0.00 3.46
2554 3612 1.670059 TCCCTTTTCTCCTCCTTCCC 58.330 55.000 0.00 0.00 0.00 3.97
2565 3631 1.407437 CCTCCTTCCCAACGAGAATGG 60.407 57.143 0.00 0.00 37.71 3.16
2570 3636 2.691409 TCCCAACGAGAATGGACATC 57.309 50.000 0.00 0.00 40.56 3.06
2574 3641 1.660607 CAACGAGAATGGACATCGGTG 59.339 52.381 0.00 0.00 46.30 4.94
2579 3646 2.932614 GAGAATGGACATCGGTGAAGTG 59.067 50.000 0.65 0.00 0.00 3.16
2581 3648 0.253044 ATGGACATCGGTGAAGTGGG 59.747 55.000 0.65 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.752640 TCGATGACCCGCGGAAGA 60.753 61.111 30.73 13.13 0.00 2.87
1 2 2.582498 GTCGATGACCCGCGGAAG 60.582 66.667 30.73 14.21 0.00 3.46
2 3 4.137872 GGTCGATGACCCGCGGAA 62.138 66.667 30.73 12.71 46.19 4.30
49 50 2.011881 GAAGGATCTCTACGCGCGC 61.012 63.158 32.58 23.91 0.00 6.86
71 72 1.145571 ACCTTCAACACCTGCCCTAA 58.854 50.000 0.00 0.00 0.00 2.69
104 105 7.935755 CCAAGGATCTGATCAGTATAACAACAT 59.064 37.037 21.92 5.10 0.00 2.71
107 108 7.437713 ACCAAGGATCTGATCAGTATAACAA 57.562 36.000 21.92 1.39 0.00 2.83
112 113 5.192522 ACCAAACCAAGGATCTGATCAGTAT 59.807 40.000 21.92 13.82 0.00 2.12
149 161 4.685924 AGACAAAACAAGCAAGAACATGG 58.314 39.130 0.00 0.00 0.00 3.66
175 187 6.268566 GTTTCCTACTACATACAACTACCCG 58.731 44.000 0.00 0.00 0.00 5.28
176 188 6.268566 CGTTTCCTACTACATACAACTACCC 58.731 44.000 0.00 0.00 0.00 3.69
177 189 6.127619 ACCGTTTCCTACTACATACAACTACC 60.128 42.308 0.00 0.00 0.00 3.18
178 190 6.749118 CACCGTTTCCTACTACATACAACTAC 59.251 42.308 0.00 0.00 0.00 2.73
179 191 6.625740 GCACCGTTTCCTACTACATACAACTA 60.626 42.308 0.00 0.00 0.00 2.24
180 192 5.717119 CACCGTTTCCTACTACATACAACT 58.283 41.667 0.00 0.00 0.00 3.16
181 193 4.328169 GCACCGTTTCCTACTACATACAAC 59.672 45.833 0.00 0.00 0.00 3.32
182 194 4.497300 GCACCGTTTCCTACTACATACAA 58.503 43.478 0.00 0.00 0.00 2.41
183 195 3.427909 CGCACCGTTTCCTACTACATACA 60.428 47.826 0.00 0.00 0.00 2.29
184 196 3.111098 CGCACCGTTTCCTACTACATAC 58.889 50.000 0.00 0.00 0.00 2.39
185 197 3.016031 TCGCACCGTTTCCTACTACATA 58.984 45.455 0.00 0.00 0.00 2.29
186 198 1.820519 TCGCACCGTTTCCTACTACAT 59.179 47.619 0.00 0.00 0.00 2.29
187 199 1.246649 TCGCACCGTTTCCTACTACA 58.753 50.000 0.00 0.00 0.00 2.74
188 200 2.352503 TTCGCACCGTTTCCTACTAC 57.647 50.000 0.00 0.00 0.00 2.73
189 201 2.676076 GTTTCGCACCGTTTCCTACTA 58.324 47.619 0.00 0.00 0.00 1.82
190 202 1.505425 GTTTCGCACCGTTTCCTACT 58.495 50.000 0.00 0.00 0.00 2.57
191 203 0.162294 CGTTTCGCACCGTTTCCTAC 59.838 55.000 0.00 0.00 0.00 3.18
192 204 0.031857 TCGTTTCGCACCGTTTCCTA 59.968 50.000 0.00 0.00 0.00 2.94
193 205 1.219522 CTCGTTTCGCACCGTTTCCT 61.220 55.000 0.00 0.00 0.00 3.36
194 206 1.203313 CTCGTTTCGCACCGTTTCC 59.797 57.895 0.00 0.00 0.00 3.13
195 207 0.382636 CACTCGTTTCGCACCGTTTC 60.383 55.000 0.00 0.00 0.00 2.78
196 208 1.639534 CACTCGTTTCGCACCGTTT 59.360 52.632 0.00 0.00 0.00 3.60
197 209 2.877974 GCACTCGTTTCGCACCGTT 61.878 57.895 0.00 0.00 0.00 4.44
198 210 3.335534 GCACTCGTTTCGCACCGT 61.336 61.111 0.00 0.00 0.00 4.83
205 217 0.514691 CCTGAAGCTGCACTCGTTTC 59.485 55.000 1.02 0.00 0.00 2.78
210 222 1.233285 CCACACCTGAAGCTGCACTC 61.233 60.000 1.02 0.00 0.00 3.51
222 234 5.819991 ACATCTTAATTCATCACCACACCT 58.180 37.500 0.00 0.00 0.00 4.00
276 288 1.490574 AGGGATCTACTCCACACAGC 58.509 55.000 0.00 0.00 46.98 4.40
283 295 5.012251 GGGATGAAACTAAGGGATCTACTCC 59.988 48.000 0.00 0.00 44.11 3.85
314 326 3.305110 GCCAAACAATTTGACTGGTACG 58.695 45.455 17.13 0.00 43.26 3.67
355 367 9.309516 GCAACAGAACATAATCAATTCATCATT 57.690 29.630 0.00 0.00 0.00 2.57
358 370 6.415867 CCGCAACAGAACATAATCAATTCATC 59.584 38.462 0.00 0.00 0.00 2.92
359 371 6.095300 TCCGCAACAGAACATAATCAATTCAT 59.905 34.615 0.00 0.00 0.00 2.57
360 372 5.414144 TCCGCAACAGAACATAATCAATTCA 59.586 36.000 0.00 0.00 0.00 2.57
361 373 5.879237 TCCGCAACAGAACATAATCAATTC 58.121 37.500 0.00 0.00 0.00 2.17
362 374 5.895636 TCCGCAACAGAACATAATCAATT 57.104 34.783 0.00 0.00 0.00 2.32
364 376 4.940654 TGATCCGCAACAGAACATAATCAA 59.059 37.500 0.00 0.00 0.00 2.57
368 380 4.940654 TCATTGATCCGCAACAGAACATAA 59.059 37.500 0.00 0.00 39.78 1.90
396 409 1.819288 AGATGTCACAGACCAGTACCG 59.181 52.381 0.00 0.00 0.00 4.02
427 440 1.968540 GGAGCAACTCGGCAGCTTT 60.969 57.895 0.00 0.00 39.02 3.51
428 441 2.359230 GGAGCAACTCGGCAGCTT 60.359 61.111 0.00 0.00 39.02 3.74
429 442 4.749310 CGGAGCAACTCGGCAGCT 62.749 66.667 0.00 0.00 42.17 4.24
442 455 1.202580 CCTCTATGGCAGGTTTCGGAG 60.203 57.143 0.00 0.00 0.00 4.63
464 477 9.841295 AACTACCTCAGACTAAACATTTTGTTA 57.159 29.630 0.00 0.00 40.14 2.41
478 491 2.779506 CCCAAACCAACTACCTCAGAC 58.220 52.381 0.00 0.00 0.00 3.51
482 495 0.111639 TGGCCCAAACCAACTACCTC 59.888 55.000 0.00 0.00 36.55 3.85
484 497 1.183030 GGTGGCCCAAACCAACTACC 61.183 60.000 0.00 0.00 44.56 3.18
541 554 4.148838 ACCCTAGCAAAGCATAACACAAA 58.851 39.130 0.00 0.00 0.00 2.83
547 560 4.398044 GCAGTAAACCCTAGCAAAGCATAA 59.602 41.667 0.00 0.00 0.00 1.90
578 598 5.584253 AGTGCTCGTGAAACAGATATACT 57.416 39.130 0.00 0.00 35.74 2.12
579 599 6.648725 AAAGTGCTCGTGAAACAGATATAC 57.351 37.500 0.00 0.00 35.74 1.47
593 613 4.766404 AAATGGTTTCCTAAAGTGCTCG 57.234 40.909 0.00 0.00 0.00 5.03
705 727 7.871853 TGACTAAAGGTAAACATCAAAGCTTC 58.128 34.615 0.00 0.00 31.02 3.86
708 730 9.476202 AAAATGACTAAAGGTAAACATCAAAGC 57.524 29.630 0.00 0.00 0.00 3.51
726 826 9.093458 AGAATGGTAAGGAAATGAAAAATGACT 57.907 29.630 0.00 0.00 0.00 3.41
727 827 9.710900 AAGAATGGTAAGGAAATGAAAAATGAC 57.289 29.630 0.00 0.00 0.00 3.06
728 828 9.709495 CAAGAATGGTAAGGAAATGAAAAATGA 57.291 29.630 0.00 0.00 0.00 2.57
729 829 9.492973 ACAAGAATGGTAAGGAAATGAAAAATG 57.507 29.630 0.00 0.00 0.00 2.32
871 990 3.319122 AGTGGCAAGATTGGTTTCTGAAC 59.681 43.478 0.00 0.00 34.96 3.18
941 1060 0.944311 GACCACACTACCACTGCACG 60.944 60.000 0.00 0.00 0.00 5.34
949 1068 6.899114 CAAAGATTTGTAAGACCACACTACC 58.101 40.000 0.00 0.00 33.59 3.18
976 1097 4.162320 CCTTGCCTAACCTAATGAGACAGA 59.838 45.833 0.00 0.00 0.00 3.41
984 1105 3.785887 TCACCATCCTTGCCTAACCTAAT 59.214 43.478 0.00 0.00 0.00 1.73
985 1106 3.186283 TCACCATCCTTGCCTAACCTAA 58.814 45.455 0.00 0.00 0.00 2.69
1098 1219 5.852282 TGACGATGAGGAACTTGATGATA 57.148 39.130 0.00 0.00 41.55 2.15
1141 1262 5.439721 TGCATATAGAACATGGCTGAAAGT 58.560 37.500 0.00 0.00 35.30 2.66
1142 1263 6.039047 AGTTGCATATAGAACATGGCTGAAAG 59.961 38.462 0.00 0.00 0.00 2.62
1188 1325 3.540314 CTGCAGATAAGAGAGGCAGTT 57.460 47.619 8.42 0.00 45.11 3.16
1386 1523 5.266733 ACACAGTTTGCAGTGAAATGAAT 57.733 34.783 10.48 0.00 39.03 2.57
1444 1601 9.874205 AATGGTAATAACTTGGAAATTGTCATG 57.126 29.630 0.00 0.00 0.00 3.07
1472 1631 9.449719 AGATCAAACAGGTAAACTTGGTTATAG 57.550 33.333 0.00 0.00 30.68 1.31
1784 1953 0.861185 CACACATGACACAGGACACG 59.139 55.000 0.00 0.00 0.00 4.49
1788 1957 1.675483 GCAAACACACATGACACAGGA 59.325 47.619 0.00 0.00 0.00 3.86
1829 2014 1.001020 CCCTGCATGTGCTTGGGTA 60.001 57.895 20.57 0.00 44.39 3.69
1830 2015 2.283388 CCCTGCATGTGCTTGGGT 60.283 61.111 20.57 0.00 44.39 4.51
1835 2020 4.946157 GCTAATAATATCCCTGCATGTGCT 59.054 41.667 6.55 0.00 42.66 4.40
1861 2046 6.264067 CCAAATAAGATTCTTCCAGCTAAGGG 59.736 42.308 1.27 0.00 0.00 3.95
1862 2047 6.830838 ACCAAATAAGATTCTTCCAGCTAAGG 59.169 38.462 1.27 0.00 0.00 2.69
1901 2226 6.867519 ACATAAATTTTAGGGTTGGGAAGG 57.132 37.500 0.00 0.00 0.00 3.46
1940 2272 8.150945 GTCCTCAAAGATCCTATAACAATGCTA 58.849 37.037 0.00 0.00 0.00 3.49
1942 2274 6.073548 CGTCCTCAAAGATCCTATAACAATGC 60.074 42.308 0.00 0.00 0.00 3.56
1952 2284 0.909610 TGGCCGTCCTCAAAGATCCT 60.910 55.000 0.00 0.00 0.00 3.24
1962 2294 1.303317 GTGTGGAAATGGCCGTCCT 60.303 57.895 18.02 0.61 34.77 3.85
1963 2295 2.686816 CGTGTGGAAATGGCCGTCC 61.687 63.158 12.03 12.03 0.00 4.79
2006 2348 6.007703 TGGTTCACGGGAGAAATCTTAATTT 58.992 36.000 0.00 0.00 37.80 1.82
2007 2349 5.566469 TGGTTCACGGGAGAAATCTTAATT 58.434 37.500 0.00 0.00 0.00 1.40
2009 2351 4.041198 ACTGGTTCACGGGAGAAATCTTAA 59.959 41.667 0.00 0.00 0.00 1.85
2010 2352 3.581332 ACTGGTTCACGGGAGAAATCTTA 59.419 43.478 0.00 0.00 0.00 2.10
2012 2354 1.978580 ACTGGTTCACGGGAGAAATCT 59.021 47.619 0.00 0.00 0.00 2.40
2013 2355 2.028020 AGACTGGTTCACGGGAGAAATC 60.028 50.000 0.00 0.00 0.00 2.17
2014 2356 1.978580 AGACTGGTTCACGGGAGAAAT 59.021 47.619 0.00 0.00 0.00 2.17
2015 2357 1.420430 AGACTGGTTCACGGGAGAAA 58.580 50.000 0.00 0.00 0.00 2.52
2017 2359 1.070134 CAAAGACTGGTTCACGGGAGA 59.930 52.381 0.00 0.00 0.00 3.71
2018 2360 1.070134 TCAAAGACTGGTTCACGGGAG 59.930 52.381 0.00 0.00 0.00 4.30
2019 2361 1.124780 TCAAAGACTGGTTCACGGGA 58.875 50.000 0.00 0.00 0.00 5.14
2020 2362 1.873591 CTTCAAAGACTGGTTCACGGG 59.126 52.381 0.00 0.00 0.00 5.28
2098 2445 2.012673 CACATGCAAGGCTTAGTCCTC 58.987 52.381 0.00 0.00 34.82 3.71
2266 2613 1.139095 GGTGAGGTTACCGCGAGAG 59.861 63.158 8.23 0.00 0.00 3.20
2267 2614 3.281240 GGTGAGGTTACCGCGAGA 58.719 61.111 8.23 0.00 0.00 4.04
2288 2635 3.131396 GCGGATGGTCAAATCGAAGTAT 58.869 45.455 0.00 0.00 0.00 2.12
2290 2637 1.369625 GCGGATGGTCAAATCGAAGT 58.630 50.000 0.00 0.00 0.00 3.01
2291 2638 0.301687 CGCGGATGGTCAAATCGAAG 59.698 55.000 0.00 0.00 0.00 3.79
2304 2651 1.303317 AAAAGGTTGCTCCGCGGAT 60.303 52.632 31.19 10.11 41.99 4.18
2505 2852 1.986698 CAGTGCCAAGCATAAGCAAC 58.013 50.000 0.00 0.00 45.49 4.17
2552 3610 1.290203 CGATGTCCATTCTCGTTGGG 58.710 55.000 0.00 0.00 34.85 4.12
2554 3612 1.660607 CACCGATGTCCATTCTCGTTG 59.339 52.381 0.00 0.00 0.00 4.10
2565 3631 1.156736 CAACCCACTTCACCGATGTC 58.843 55.000 0.00 0.00 0.00 3.06
2570 3636 0.105964 TCACTCAACCCACTTCACCG 59.894 55.000 0.00 0.00 0.00 4.94
2574 3641 3.437049 GCAACTATCACTCAACCCACTTC 59.563 47.826 0.00 0.00 0.00 3.01
2579 3646 2.162408 GCTTGCAACTATCACTCAACCC 59.838 50.000 0.00 0.00 0.00 4.11


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

AutoCloner maintained by Alex Coulton.