Multiple sequence alignment - TraesCS2D01G539000

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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 TraesCS2D01G539000 chr2D 100.000 2822 0 0 1 2822 619669165 619666344 0.000000e+00 5212.0
1 TraesCS2D01G539000 chr2A 89.957 2071 142 27 6 2027 751213964 751211911 0.000000e+00 2612.0
2 TraesCS2D01G539000 chr2A 88.757 676 35 18 2091 2754 751211586 751210940 0.000000e+00 789.0
3 TraesCS2D01G539000 chr2A 78.417 417 84 5 1450 1865 752793262 752792851 1.670000e-67 267.0
4 TraesCS2D01G539000 chr2A 95.238 63 2 1 2026 2088 751211802 751211741 6.430000e-17 99.0
5 TraesCS2D01G539000 chr2B 90.939 1501 89 19 495 1975 759352088 759350615 0.000000e+00 1975.0
6 TraesCS2D01G539000 chr2B 90.162 681 32 12 2091 2764 759349003 759348351 0.000000e+00 854.0
7 TraesCS2D01G539000 chr2B 87.471 431 34 4 1 419 759353000 759352578 1.970000e-131 479.0
8 TraesCS2D01G539000 chr2B 71.500 1000 230 36 871 1835 761721608 761720629 1.700000e-52 217.0
9 TraesCS2D01G539000 chr2B 95.890 73 1 1 2752 2822 159251608 159251536 1.780000e-22 117.0
10 TraesCS2D01G539000 chr2B 92.308 65 4 1 2026 2090 759349242 759349179 1.080000e-14 91.6
11 TraesCS2D01G539000 chr7B 77.079 541 111 9 871 1407 63937809 63938340 1.640000e-77 300.0
12 TraesCS2D01G539000 chr3B 98.611 72 1 0 2751 2822 349269441 349269370 8.210000e-26 128.0
13 TraesCS2D01G539000 chr3A 91.667 84 4 2 2741 2822 430526515 430526433 2.300000e-21 113.0
14 TraesCS2D01G539000 chr6D 94.595 74 1 1 2752 2822 309955223 309955296 8.260000e-21 111.0
15 TraesCS2D01G539000 chr5B 93.151 73 5 0 2750 2822 315165276 315165348 1.070000e-19 108.0
16 TraesCS2D01G539000 chr1D 94.444 72 1 2 2751 2822 8284305 8284237 1.070000e-19 108.0
17 TraesCS2D01G539000 chr6A 93.151 73 3 1 2752 2822 594463517 594463445 3.840000e-19 106.0
18 TraesCS2D01G539000 chr1B 93.243 74 2 1 2752 2822 589766297 589766224 3.840000e-19 106.0
19 TraesCS2D01G539000 chr5A 92.000 75 4 2 2749 2822 659715924 659715997 1.380000e-18 104.0


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 TraesCS2D01G539000 chr2D 619666344 619669165 2821 True 5212.000000 5212 100.000000 1 2822 1 chr2D.!!$R1 2821
1 TraesCS2D01G539000 chr2A 751210940 751213964 3024 True 1166.666667 2612 91.317333 6 2754 3 chr2A.!!$R2 2748
2 TraesCS2D01G539000 chr2B 759348351 759353000 4649 True 849.900000 1975 90.220000 1 2764 4 chr2B.!!$R3 2763
3 TraesCS2D01G539000 chr2B 761720629 761721608 979 True 217.000000 217 71.500000 871 1835 1 chr2B.!!$R2 964
4 TraesCS2D01G539000 chr7B 63937809 63938340 531 False 300.000000 300 77.079000 871 1407 1 chr7B.!!$F1 536

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
268 283 0.040958 CTTGTGGAACGCTGCACTTC 60.041 55.0 11.8 0.0 43.87 3.01 F
857 1299 0.167470 CGAGGTGCTCTGCAATGTTG 59.833 55.0 0.0 0.0 41.47 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1110 1561 0.394899 CCCTGGCTTCCTCCATTGAC 60.395 60.0 0.0 0.0 35.22 3.18 R
1832 2313 1.354040 GTGACTCTGTTCGATGCCTG 58.646 55.0 0.0 0.0 0.00 4.85 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
62 65 2.903357 CCGTGGAGGTGGATCTGG 59.097 66.667 0.00 0.00 34.51 3.86
101 112 3.659334 CTGCGCAGGAGCTTGAAA 58.341 55.556 29.88 0.00 40.50 2.69
124 135 3.483869 GCCAAGGATCTCGCCCCT 61.484 66.667 0.00 0.00 0.00 4.79
202 213 1.134965 CGAGGTAAGAAGGAGCTGGTG 60.135 57.143 0.00 0.00 0.00 4.17
215 226 4.649705 TGGTGGGGCGGAAGGAGA 62.650 66.667 0.00 0.00 0.00 3.71
231 242 1.536662 AGACAGAGGAGGCGGGTTT 60.537 57.895 0.00 0.00 0.00 3.27
268 283 0.040958 CTTGTGGAACGCTGCACTTC 60.041 55.000 11.80 0.00 43.87 3.01
272 287 1.598130 GGAACGCTGCACTTCTGGT 60.598 57.895 0.00 0.00 0.00 4.00
274 289 1.845809 GAACGCTGCACTTCTGGTGG 61.846 60.000 0.00 0.00 45.44 4.61
315 335 2.182030 GACCGAGCTCGACCAAGG 59.818 66.667 36.59 20.71 43.02 3.61
316 336 2.600769 ACCGAGCTCGACCAAGGT 60.601 61.111 36.59 21.39 43.02 3.50
317 337 2.182030 CCGAGCTCGACCAAGGTC 59.818 66.667 36.59 9.22 43.02 3.85
318 338 2.182030 CGAGCTCGACCAAGGTCC 59.818 66.667 32.06 0.11 41.76 4.46
319 339 2.182030 GAGCTCGACCAAGGTCCG 59.818 66.667 13.35 8.80 41.76 4.79
372 397 4.133373 ATGGCAGGGCGGCTTGAT 62.133 61.111 25.57 7.38 41.89 2.57
397 422 4.308458 CGGACGGGAGCACCAACA 62.308 66.667 1.58 0.00 40.22 3.33
398 423 2.358737 GGACGGGAGCACCAACAG 60.359 66.667 1.58 0.00 40.22 3.16
404 429 2.186826 GGAGCACCAACAGCAACGT 61.187 57.895 0.00 0.00 35.97 3.99
468 521 3.194062 CTGAAAAGATCGGCTCTCTTCC 58.806 50.000 0.00 0.00 31.83 3.46
470 523 2.977772 AAAGATCGGCTCTCTTCCAG 57.022 50.000 0.00 0.00 31.83 3.86
478 531 1.515020 CTCTCTTCCAGCACTCCCG 59.485 63.158 0.00 0.00 0.00 5.14
492 545 2.359975 CCCGGTCCAGTCAAAGCC 60.360 66.667 0.00 0.00 0.00 4.35
493 546 2.750350 CCGGTCCAGTCAAAGCCT 59.250 61.111 0.00 0.00 0.00 4.58
627 1066 2.742053 CAAATGGTCAGTGAGGGTTACG 59.258 50.000 0.00 0.00 0.00 3.18
628 1067 0.249398 ATGGTCAGTGAGGGTTACGC 59.751 55.000 0.00 0.00 0.00 4.42
629 1068 1.079336 GGTCAGTGAGGGTTACGCC 60.079 63.158 0.00 0.00 0.00 5.68
730 1172 3.486383 TCTCCAAATCCACAACAAGACC 58.514 45.455 0.00 0.00 0.00 3.85
848 1290 1.018148 CAGTATCGTCGAGGTGCTCT 58.982 55.000 4.85 0.00 0.00 4.09
857 1299 0.167470 CGAGGTGCTCTGCAATGTTG 59.833 55.000 0.00 0.00 41.47 3.33
887 1329 1.215014 GCTCGCAAGGTTTGGCAAAC 61.215 55.000 30.15 30.15 40.65 2.93
975 1417 1.278238 GCCGTGCTAGACATGTACAC 58.722 55.000 0.00 4.56 33.01 2.90
976 1418 1.403647 GCCGTGCTAGACATGTACACA 60.404 52.381 16.38 4.51 33.01 3.72
1039 1490 1.613630 TCTCCAGAAGCCCAGACCC 60.614 63.158 0.00 0.00 0.00 4.46
1048 1499 1.147153 GCCCAGACCCAGAGCATAC 59.853 63.158 0.00 0.00 0.00 2.39
1096 1547 4.379918 GGACAGAAAGAAACAAGCTATGCC 60.380 45.833 0.00 0.00 0.00 4.40
1110 1561 2.739932 GCTATGCCAGGCTATATCCACG 60.740 54.545 14.15 0.00 0.00 4.94
1111 1562 1.352083 ATGCCAGGCTATATCCACGT 58.648 50.000 14.15 0.00 0.00 4.49
1124 1575 0.036388 TCCACGTCAATGGAGGAAGC 60.036 55.000 0.00 0.00 44.14 3.86
1296 1750 3.266772 ACACTGGAAATCTTCATGGCCTA 59.733 43.478 3.32 0.00 0.00 3.93
1349 1803 1.668237 GCTTCTGAGAAAATCGGAGCC 59.332 52.381 0.00 0.00 44.25 4.70
1424 1878 1.586154 GCCACCAGGGACATTGTTCG 61.586 60.000 0.00 0.00 40.01 3.95
1425 1879 0.250727 CCACCAGGGACATTGTTCGT 60.251 55.000 0.00 0.00 40.01 3.85
1427 1881 2.555123 CCAGGGACATTGTTCGTGG 58.445 57.895 19.62 19.62 40.10 4.94
1428 1882 0.960364 CCAGGGACATTGTTCGTGGG 60.960 60.000 23.63 9.48 41.76 4.61
1429 1883 1.303317 AGGGACATTGTTCGTGGGC 60.303 57.895 0.00 0.00 0.00 5.36
1431 1885 1.602323 GGACATTGTTCGTGGGCCA 60.602 57.895 0.00 0.00 0.00 5.36
1433 1887 1.680555 GGACATTGTTCGTGGGCCATA 60.681 52.381 10.70 0.00 0.00 2.74
1434 1888 1.400494 GACATTGTTCGTGGGCCATAC 59.600 52.381 10.70 9.50 0.00 2.39
1435 1889 1.004277 ACATTGTTCGTGGGCCATACT 59.996 47.619 10.70 0.00 0.00 2.12
1470 1936 0.765510 ACCACCAGGGACTTGAACTC 59.234 55.000 0.00 0.00 41.15 3.01
1780 2258 2.281484 GCGGAAACAGCACTCCCA 60.281 61.111 0.00 0.00 34.19 4.37
1832 2313 7.115520 GCTATTTGAAGGCTGAAAACTTCTTTC 59.884 37.037 0.00 0.00 42.67 2.62
1858 2339 4.748892 CATCGAACAGAGTCACCAACTAT 58.251 43.478 0.00 0.00 38.74 2.12
1865 2346 6.919775 ACAGAGTCACCAACTATTAAGAGT 57.080 37.500 0.00 0.00 38.74 3.24
1873 2354 7.122353 GTCACCAACTATTAAGAGTCCAGAGTA 59.878 40.741 2.67 0.00 0.00 2.59
1884 2365 6.865834 AGAGTCCAGAGTAATGTTTCATCT 57.134 37.500 0.00 0.00 0.00 2.90
1887 2368 7.617723 AGAGTCCAGAGTAATGTTTCATCTAGT 59.382 37.037 0.00 0.00 0.00 2.57
1903 2386 8.777865 TTCATCTAGTATTTGAAGTGAGGTTG 57.222 34.615 0.00 0.00 0.00 3.77
1911 2403 2.344592 TGAAGTGAGGTTGTATGGGGT 58.655 47.619 0.00 0.00 0.00 4.95
1936 2428 8.946085 GTGTCTTATTTGACTTGTGATTCCATA 58.054 33.333 0.00 0.00 37.79 2.74
1947 2439 9.167311 GACTTGTGATTCCATATTAAACACTCT 57.833 33.333 0.00 0.00 0.00 3.24
2018 3720 5.182950 ACACGCATATTTTCATCCACTTCAA 59.817 36.000 0.00 0.00 0.00 2.69
2157 4149 4.778534 ATTGAGACCAAACTCAGCAATG 57.221 40.909 0.00 0.00 45.63 2.82
2180 4172 0.111061 TTGCACATCAGGAGCCTGTT 59.889 50.000 15.67 5.39 43.96 3.16
2199 4199 6.666417 CCTGTTTCAAGAATGAACTGAAGAG 58.334 40.000 0.00 0.00 45.01 2.85
2283 4283 2.191128 ACCATTTCTCGAAAGCAGCT 57.809 45.000 0.00 0.00 33.32 4.24
2293 4293 4.769488 TCTCGAAAGCAGCTCTCCATATAT 59.231 41.667 0.00 0.00 0.00 0.86
2294 4294 5.946377 TCTCGAAAGCAGCTCTCCATATATA 59.054 40.000 0.00 0.00 0.00 0.86
2295 4295 6.605194 TCTCGAAAGCAGCTCTCCATATATAT 59.395 38.462 0.00 0.00 0.00 0.86
2297 4297 8.293699 TCGAAAGCAGCTCTCCATATATATTA 57.706 34.615 0.00 0.00 0.00 0.98
2298 4298 8.918116 TCGAAAGCAGCTCTCCATATATATTAT 58.082 33.333 0.00 0.00 0.00 1.28
2299 4299 8.976471 CGAAAGCAGCTCTCCATATATATTATG 58.024 37.037 0.00 0.00 0.00 1.90
2300 4300 9.829507 GAAAGCAGCTCTCCATATATATTATGT 57.170 33.333 0.00 0.00 0.00 2.29
2302 4302 9.610705 AAGCAGCTCTCCATATATATTATGTTG 57.389 33.333 0.00 0.00 0.00 3.33
2352 4358 6.715347 ATTGGGGAGTGTATTTTGCTAATC 57.285 37.500 0.00 0.00 0.00 1.75
2445 4451 6.493189 TCCAGCTGTTCAACCATATACATA 57.507 37.500 13.81 0.00 0.00 2.29
2507 4513 6.238484 GCTGCCAGTGTATAAAGAATAACTGG 60.238 42.308 13.94 13.94 43.45 4.00
2522 4530 7.775120 AGAATAACTGGGTTTGCTAATCATTG 58.225 34.615 0.00 0.00 0.00 2.82
2564 4572 1.210478 CAGGGTACAGGGTTCAGGATG 59.790 57.143 0.00 0.00 37.54 3.51
2593 4601 4.151867 AGAATTTCAAAGAAGCGACGTACC 59.848 41.667 0.00 0.00 0.00 3.34
2594 4602 2.512485 TTCAAAGAAGCGACGTACCA 57.488 45.000 0.00 0.00 0.00 3.25
2595 4603 2.736144 TCAAAGAAGCGACGTACCAT 57.264 45.000 0.00 0.00 0.00 3.55
2596 4604 2.333926 TCAAAGAAGCGACGTACCATG 58.666 47.619 0.00 0.00 0.00 3.66
2597 4605 2.029739 TCAAAGAAGCGACGTACCATGA 60.030 45.455 0.00 0.00 0.00 3.07
2598 4606 2.734606 CAAAGAAGCGACGTACCATGAA 59.265 45.455 0.00 0.00 0.00 2.57
2599 4607 2.279582 AGAAGCGACGTACCATGAAG 57.720 50.000 0.00 0.00 0.00 3.02
2600 4608 1.135083 AGAAGCGACGTACCATGAAGG 60.135 52.381 0.00 0.00 45.67 3.46
2735 4743 8.428852 GTTAATTATAATTCAGGGGGCACATTT 58.571 33.333 13.95 0.00 0.00 2.32
2757 4766 5.036117 TCAGCCACTGAATTAATACTCCC 57.964 43.478 0.00 0.00 37.57 4.30
2759 4768 5.059833 CAGCCACTGAATTAATACTCCCTC 58.940 45.833 0.00 0.00 32.44 4.30
2764 4773 7.635089 GCCACTGAATTAATACTCCCTCTGTAA 60.635 40.741 0.00 0.00 0.00 2.41
2765 4774 8.265055 CCACTGAATTAATACTCCCTCTGTAAA 58.735 37.037 0.00 0.00 0.00 2.01
2766 4775 9.099454 CACTGAATTAATACTCCCTCTGTAAAC 57.901 37.037 0.00 0.00 0.00 2.01
2767 4776 9.047947 ACTGAATTAATACTCCCTCTGTAAACT 57.952 33.333 0.00 0.00 0.00 2.66
2778 4787 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2779 4788 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2780 4789 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2781 4790 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2782 4791 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2816 4825 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
2817 4826 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
2818 4827 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
2819 4828 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2820 4829 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
2821 4830 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.517257 CATCAGGCAGGACGACGAC 60.517 63.158 0.00 0.00 0.00 4.34
101 112 2.586792 GAGATCCTTGGCAGCCGT 59.413 61.111 7.03 0.00 0.00 5.68
124 135 1.076549 GGTGGTCAAAGGCCATGGA 59.923 57.895 18.40 0.00 38.40 3.41
166 177 2.278857 CGACCTCTTCGCCGATGG 60.279 66.667 0.00 0.35 41.87 3.51
176 187 2.946791 GCTCCTTCTTACCTCGACCTCT 60.947 54.545 0.00 0.00 0.00 3.69
180 191 1.135333 CCAGCTCCTTCTTACCTCGAC 59.865 57.143 0.00 0.00 0.00 4.20
181 192 1.272536 ACCAGCTCCTTCTTACCTCGA 60.273 52.381 0.00 0.00 0.00 4.04
202 213 2.683933 TCTGTCTCCTTCCGCCCC 60.684 66.667 0.00 0.00 0.00 5.80
215 226 1.841556 TGAAACCCGCCTCCTCTGT 60.842 57.895 0.00 0.00 0.00 3.41
268 283 2.358737 GGCGGAGTGAACCACCAG 60.359 66.667 0.00 0.00 34.49 4.00
272 287 2.063015 ATTGGTGGCGGAGTGAACCA 62.063 55.000 0.00 0.00 40.90 3.67
273 288 0.035820 TATTGGTGGCGGAGTGAACC 60.036 55.000 0.00 0.00 0.00 3.62
274 289 1.940613 GATATTGGTGGCGGAGTGAAC 59.059 52.381 0.00 0.00 0.00 3.18
315 335 4.222847 GATGGAGGACGCCCGGAC 62.223 72.222 0.73 0.00 37.58 4.79
318 338 3.447025 GAAGGATGGAGGACGCCCG 62.447 68.421 0.00 0.00 37.58 6.13
319 339 2.506472 GAAGGATGGAGGACGCCC 59.494 66.667 0.00 0.00 0.00 6.13
468 521 3.302347 GACTGGACCGGGAGTGCTG 62.302 68.421 6.32 0.00 40.86 4.41
470 523 2.391724 TTTGACTGGACCGGGAGTGC 62.392 60.000 6.32 0.00 37.33 4.40
478 531 1.559682 TGGATAGGCTTTGACTGGACC 59.440 52.381 0.00 0.00 0.00 4.46
492 545 3.034635 AGTGGTTGGAGTAGCTGGATAG 58.965 50.000 0.00 0.00 0.00 2.08
493 546 3.031736 GAGTGGTTGGAGTAGCTGGATA 58.968 50.000 0.00 0.00 0.00 2.59
668 1110 2.556114 CCAAGAACCAATTCTCCAGGCT 60.556 50.000 0.00 0.00 44.82 4.58
730 1172 1.156645 GGAGCTGCTGACATAAGCCG 61.157 60.000 7.01 0.00 42.83 5.52
838 1280 0.167470 CAACATTGCAGAGCACCTCG 59.833 55.000 0.00 0.00 38.71 4.63
848 1290 2.794282 GCAACAACGTCTCAACATTGCA 60.794 45.455 0.00 0.00 40.46 4.08
857 1299 0.111089 CTTGCGAGCAACAACGTCTC 60.111 55.000 6.39 0.00 0.00 3.36
1039 1490 3.422473 CGTATCTCGTCGAGTATGCTCTG 60.422 52.174 21.15 3.13 35.86 3.35
1096 1547 3.006859 TCCATTGACGTGGATATAGCCTG 59.993 47.826 8.79 3.49 43.20 4.85
1110 1561 0.394899 CCCTGGCTTCCTCCATTGAC 60.395 60.000 0.00 0.00 35.22 3.18
1111 1562 2.001803 CCCTGGCTTCCTCCATTGA 58.998 57.895 0.00 0.00 35.22 2.57
1124 1575 1.997311 TCCTCCATGAGTGCCCTGG 60.997 63.158 0.00 0.00 0.00 4.45
1431 1885 5.361285 GTGGTGTTGAGAGTCTCCATAGTAT 59.639 44.000 17.57 0.00 31.48 2.12
1433 1887 3.511934 GTGGTGTTGAGAGTCTCCATAGT 59.488 47.826 17.57 0.00 31.48 2.12
1434 1888 3.118956 GGTGGTGTTGAGAGTCTCCATAG 60.119 52.174 17.57 0.00 31.48 2.23
1435 1889 2.832129 GGTGGTGTTGAGAGTCTCCATA 59.168 50.000 17.57 1.93 31.48 2.74
1470 1936 2.865551 GTGGTTTTTGCATTCAGGTGTG 59.134 45.455 0.00 0.00 0.00 3.82
1671 2149 2.083835 TAGCCCTTCGTAGCGCATCC 62.084 60.000 11.47 0.00 0.00 3.51
1780 2258 2.289694 CCAACATCTCTTCCAAGACGGT 60.290 50.000 0.00 0.00 35.57 4.83
1825 2303 3.329386 TCTGTTCGATGCCTGAAAGAAG 58.671 45.455 0.00 0.00 34.07 2.85
1826 2304 3.244215 ACTCTGTTCGATGCCTGAAAGAA 60.244 43.478 0.00 0.00 34.07 2.52
1827 2305 2.300152 ACTCTGTTCGATGCCTGAAAGA 59.700 45.455 0.00 0.00 34.07 2.52
1832 2313 1.354040 GTGACTCTGTTCGATGCCTG 58.646 55.000 0.00 0.00 0.00 4.85
1858 2339 8.816894 AGATGAAACATTACTCTGGACTCTTAA 58.183 33.333 0.00 0.00 0.00 1.85
1884 2365 7.335627 CCCATACAACCTCACTTCAAATACTA 58.664 38.462 0.00 0.00 0.00 1.82
1887 2368 5.014755 ACCCCATACAACCTCACTTCAAATA 59.985 40.000 0.00 0.00 0.00 1.40
1899 2382 5.124936 GTCAAATAAGACACCCCATACAACC 59.875 44.000 0.00 0.00 38.40 3.77
1903 2386 5.944007 ACAAGTCAAATAAGACACCCCATAC 59.056 40.000 0.00 0.00 40.98 2.39
1911 2403 9.685276 ATATGGAATCACAAGTCAAATAAGACA 57.315 29.630 0.00 0.00 40.98 3.41
1936 2428 9.672673 ACAATTAGCTATGTGAGAGTGTTTAAT 57.327 29.630 10.34 0.00 0.00 1.40
1942 2434 6.760298 ACATGACAATTAGCTATGTGAGAGTG 59.240 38.462 4.72 0.00 31.34 3.51
1947 2439 9.448438 AAGTAAACATGACAATTAGCTATGTGA 57.552 29.630 4.72 0.00 32.75 3.58
2011 3713 7.593875 TTCCAAACAAAGTTTCATTGAAGTG 57.406 32.000 10.18 0.64 0.00 3.16
2139 4131 5.886960 AATACATTGCTGAGTTTGGTCTC 57.113 39.130 0.00 0.00 35.28 3.36
2157 4149 2.357009 CAGGCTCCTGATGTGCAAATAC 59.643 50.000 10.33 0.00 46.30 1.89
2169 4161 3.822735 TTCATTCTTGAAACAGGCTCCTG 59.177 43.478 14.05 14.05 41.87 3.86
2180 4172 7.445402 CCCTAAACTCTTCAGTTCATTCTTGAA 59.555 37.037 0.00 0.00 42.45 2.69
2199 4199 5.936956 CCATGCTTATGAGAGATCCCTAAAC 59.063 44.000 0.00 0.00 0.00 2.01
2293 4293 9.913310 TCCATTCTCCAAATGTACAACATAATA 57.087 29.630 0.00 0.00 37.97 0.98
2294 4294 8.821686 TCCATTCTCCAAATGTACAACATAAT 57.178 30.769 0.00 0.00 37.97 1.28
2295 4295 8.685427 CATCCATTCTCCAAATGTACAACATAA 58.315 33.333 0.00 0.00 37.97 1.90
2297 4297 6.891361 TCATCCATTCTCCAAATGTACAACAT 59.109 34.615 0.00 0.00 41.31 2.71
2298 4298 6.244654 TCATCCATTCTCCAAATGTACAACA 58.755 36.000 0.00 0.00 0.00 3.33
2299 4299 6.599244 TCTCATCCATTCTCCAAATGTACAAC 59.401 38.462 0.00 0.00 0.00 3.32
2300 4300 6.720309 TCTCATCCATTCTCCAAATGTACAA 58.280 36.000 0.00 0.00 0.00 2.41
2301 4301 6.312141 TCTCATCCATTCTCCAAATGTACA 57.688 37.500 0.00 0.00 0.00 2.90
2302 4302 6.038714 GGTTCTCATCCATTCTCCAAATGTAC 59.961 42.308 0.00 0.00 0.00 2.90
2304 4304 4.952335 GGTTCTCATCCATTCTCCAAATGT 59.048 41.667 0.00 0.00 0.00 2.71
2305 4305 4.951715 TGGTTCTCATCCATTCTCCAAATG 59.048 41.667 0.00 0.00 0.00 2.32
2308 4308 4.656100 TTGGTTCTCATCCATTCTCCAA 57.344 40.909 0.00 0.00 34.75 3.53
2314 4320 3.012730 TCCCCAATTGGTTCTCATCCATT 59.987 43.478 22.91 0.00 34.75 3.16
2403 4409 8.946085 CAGCTGGATGTTCTATTTTTAGTGTAA 58.054 33.333 5.57 0.00 0.00 2.41
2458 4464 8.213679 AGCATGTTCTGACCATTATATTACAGT 58.786 33.333 0.00 0.00 0.00 3.55
2459 4465 8.501580 CAGCATGTTCTGACCATTATATTACAG 58.498 37.037 0.00 0.00 36.19 2.74
2460 4466 7.041167 GCAGCATGTTCTGACCATTATATTACA 60.041 37.037 4.68 0.00 39.31 2.41
2461 4467 7.301054 GCAGCATGTTCTGACCATTATATTAC 58.699 38.462 4.68 0.00 39.31 1.89
2462 4468 6.430925 GGCAGCATGTTCTGACCATTATATTA 59.569 38.462 4.68 0.00 36.09 0.98
2522 4530 5.485620 TGACCATTATGAGATGCTATGCTC 58.514 41.667 0.00 0.00 0.00 4.26
2564 4572 4.153117 TCGCTTCTTTGAAATTCTGCTCTC 59.847 41.667 0.00 0.00 0.00 3.20
2566 4574 4.154717 GTCGCTTCTTTGAAATTCTGCTC 58.845 43.478 0.00 0.00 0.00 4.26
2735 4743 4.721776 AGGGAGTATTAATTCAGTGGCTGA 59.278 41.667 0.00 0.00 38.87 4.26
2790 4799 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
2791 4800 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
2792 4801 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
2793 4802 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
2794 4803 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
2795 4804 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
2796 4805 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
2797 4806 7.224522 TCCCTCCGTAAACTAATATAAGAGC 57.775 40.000 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.