Multiple sequence alignment - TraesCS5B01G084600

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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 TraesCS5B01G084600 chr5B 100.000 7813 0 0 1 7813 107189496 107197308 0.000000e+00 14428
1 TraesCS5B01G084600 chr5D 96.347 5831 141 27 943 6740 97825937 97831728 0.000000e+00 9522
2 TraesCS5B01G084600 chr5D 93.939 1122 35 9 6703 7813 97831839 97832938 0.000000e+00 1664
3 TraesCS5B01G084600 chr5D 83.046 755 87 21 89 830 454030237 454029511 0.000000e+00 647
4 TraesCS5B01G084600 chr5D 85.678 391 42 10 6 382 564504142 564504532 4.390000e-107 399
5 TraesCS5B01G084600 chr5D 94.355 124 4 3 833 953 97820622 97820745 3.720000e-43 187
6 TraesCS5B01G084600 chr5A 94.051 3866 138 28 833 4638 105696172 105692339 0.000000e+00 5781
7 TraesCS5B01G084600 chr5A 96.494 1483 48 4 4637 6117 105691983 105690503 0.000000e+00 2447
8 TraesCS5B01G084600 chr5A 95.523 1519 43 10 6297 7813 105690381 105688886 0.000000e+00 2405
9 TraesCS5B01G084600 chr5A 82.130 554 67 17 6 547 548284036 548284569 5.560000e-121 446
10 TraesCS5B01G084600 chr1D 83.235 847 97 21 5 830 199563891 199563069 0.000000e+00 736
11 TraesCS5B01G084600 chr1D 81.550 813 105 20 37 831 28964277 28963492 5.150000e-176 628
12 TraesCS5B01G084600 chr1D 87.306 386 36 9 5 382 472298129 472298509 5.600000e-116 429
13 TraesCS5B01G084600 chr7A 82.353 782 105 21 5 759 18119854 18120629 0.000000e+00 649
14 TraesCS5B01G084600 chr4D 81.338 852 107 28 6 829 475197590 475196763 0.000000e+00 645
15 TraesCS5B01G084600 chr4D 86.340 388 40 7 4 382 46761358 46761741 2.030000e-110 411
16 TraesCS5B01G084600 chr6D 82.510 749 97 17 90 830 59176298 59177020 1.850000e-175 627
17 TraesCS5B01G084600 chr6D 85.567 388 44 8 6 382 148075371 148075757 5.680000e-106 396
18 TraesCS5B01G084600 chr7D 80.645 837 111 27 5 832 1604370 1605164 1.120000e-167 601
19 TraesCS5B01G084600 chr7D 82.716 648 82 18 191 830 494898862 494899487 4.120000e-152 549
20 TraesCS5B01G084600 chr2A 80.191 838 107 27 5 830 698123424 698124214 2.450000e-159 573
21 TraesCS5B01G084600 chr3D 83.333 510 69 13 337 833 548483806 548484312 2.570000e-124 457
22 TraesCS5B01G084600 chr3D 86.822 387 37 12 6 382 39313299 39312917 3.370000e-113 420
23 TraesCS5B01G084600 chr1A 85.974 385 42 10 7 382 463808779 463809160 1.220000e-107 401
24 TraesCS5B01G084600 chr4B 82.082 413 57 11 100 498 472877879 472877470 3.490000e-88 337


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 TraesCS5B01G084600 chr5B 107189496 107197308 7812 False 14428.000000 14428 100.000 1 7813 1 chr5B.!!$F1 7812
1 TraesCS5B01G084600 chr5D 97825937 97832938 7001 False 5593.000000 9522 95.143 943 7813 2 chr5D.!!$F3 6870
2 TraesCS5B01G084600 chr5D 454029511 454030237 726 True 647.000000 647 83.046 89 830 1 chr5D.!!$R1 741
3 TraesCS5B01G084600 chr5A 105688886 105696172 7286 True 3544.333333 5781 95.356 833 7813 3 chr5A.!!$R1 6980
4 TraesCS5B01G084600 chr5A 548284036 548284569 533 False 446.000000 446 82.130 6 547 1 chr5A.!!$F1 541
5 TraesCS5B01G084600 chr1D 199563069 199563891 822 True 736.000000 736 83.235 5 830 1 chr1D.!!$R2 825
6 TraesCS5B01G084600 chr1D 28963492 28964277 785 True 628.000000 628 81.550 37 831 1 chr1D.!!$R1 794
7 TraesCS5B01G084600 chr7A 18119854 18120629 775 False 649.000000 649 82.353 5 759 1 chr7A.!!$F1 754
8 TraesCS5B01G084600 chr4D 475196763 475197590 827 True 645.000000 645 81.338 6 829 1 chr4D.!!$R1 823
9 TraesCS5B01G084600 chr6D 59176298 59177020 722 False 627.000000 627 82.510 90 830 1 chr6D.!!$F1 740
10 TraesCS5B01G084600 chr7D 1604370 1605164 794 False 601.000000 601 80.645 5 832 1 chr7D.!!$F1 827
11 TraesCS5B01G084600 chr7D 494898862 494899487 625 False 549.000000 549 82.716 191 830 1 chr7D.!!$F2 639
12 TraesCS5B01G084600 chr2A 698123424 698124214 790 False 573.000000 573 80.191 5 830 1 chr2A.!!$F1 825
13 TraesCS5B01G084600 chr3D 548483806 548484312 506 False 457.000000 457 83.333 337 833 1 chr3D.!!$F1 496

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
680 778 0.038983 TTCGAGATTTGGACGCACGA 60.039 50.000 0.0 0.0 0.00 4.35 F
1524 1646 0.523072 CGGAGTTGTGCTTCATTGGG 59.477 55.000 0.0 0.0 0.00 4.12 F
2098 2249 5.055144 TGTTGCTGATAGAGATGAAGCATC 58.945 41.667 0.0 0.0 42.97 3.91 F
3429 3590 2.432510 AGCATTACTAGACCAGTGCCTC 59.567 50.000 0.0 0.0 38.24 4.70 F
4153 4315 0.038599 TGCTCATGCATTGGTCTGGT 59.961 50.000 0.0 0.0 45.31 4.00 F
4886 5419 0.179009 CATGCCCATCAACTCCCGAT 60.179 55.000 0.0 0.0 0.00 4.18 F
6286 6826 1.071987 TGCCTGAGCACTCTTGTGG 59.928 57.895 0.0 0.0 46.52 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 1925 2.697431 TTACGGTTGCTGTTGAATGC 57.303 45.000 0.00 0.00 0.00 3.56 R
2833 2984 1.067060 GGCCGAAATTAAGCCATCCAC 59.933 52.381 8.11 0.00 46.34 4.02 R
3718 3880 2.038952 TGTTCAGCACCAGATACAAGCT 59.961 45.455 0.00 0.00 35.63 3.74 R
5400 5934 0.251354 GCTCATCAGCTCCAGAACCA 59.749 55.000 0.00 0.00 43.09 3.67 R
6119 6654 1.027357 ACTTGCTCACTTGTTGCCTG 58.973 50.000 0.00 0.00 0.00 4.85 R
6454 6994 1.274167 TCTGGCACGTCGAATTAGGTT 59.726 47.619 0.00 0.00 0.00 3.50 R
7187 7891 0.808453 GGATTCGAATTCGGTCGGCA 60.808 55.000 26.47 4.23 41.43 5.69 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
260 289 2.260434 GCGAGAGGCACGGTTGTA 59.740 61.111 0.00 0.00 42.87 2.41
296 325 1.006571 GTCGTGCCTCTCGGAAACA 60.007 57.895 0.00 0.00 0.00 2.83
341 381 0.937699 CGCGAGAGTCACGGTTTTGA 60.938 55.000 11.95 0.00 0.00 2.69
364 406 3.000815 GTGAGAGGCACGGTTTTGA 57.999 52.632 0.00 0.00 37.83 2.69
397 462 1.305201 ACGGTTGTGATTTTGCGAGT 58.695 45.000 0.00 0.00 0.00 4.18
398 463 1.263217 ACGGTTGTGATTTTGCGAGTC 59.737 47.619 0.00 0.00 0.00 3.36
403 468 1.264020 TGTGATTTTGCGAGTCACAGC 59.736 47.619 16.18 0.00 45.10 4.40
404 469 0.874390 TGATTTTGCGAGTCACAGCC 59.126 50.000 0.00 0.00 0.00 4.85
405 470 0.179215 GATTTTGCGAGTCACAGCCG 60.179 55.000 0.00 0.00 0.00 5.52
406 471 0.884704 ATTTTGCGAGTCACAGCCGT 60.885 50.000 0.00 0.00 0.00 5.68
509 588 3.998913 TGTGATTTCATAGGAGGCACA 57.001 42.857 0.00 0.00 31.91 4.57
510 589 4.508551 TGTGATTTCATAGGAGGCACAT 57.491 40.909 0.00 0.00 30.47 3.21
656 754 1.359848 CGAGGAATCCAACGGTGAAG 58.640 55.000 0.00 0.00 0.00 3.02
660 758 2.253414 GAATCCAACGGTGAAGGCGC 62.253 60.000 0.00 0.00 0.00 6.53
680 778 0.038983 TTCGAGATTTGGACGCACGA 60.039 50.000 0.00 0.00 0.00 4.35
692 790 2.789893 GGACGCACGATTTGAGAGATAC 59.210 50.000 0.00 0.00 0.00 2.24
732 832 8.250143 ACAAATCTATGAACAAGGGAAAACTT 57.750 30.769 0.00 0.00 0.00 2.66
753 853 1.153353 CCGATTACAACAAGTGGCGT 58.847 50.000 0.00 0.00 0.00 5.68
772 872 2.998279 GCTGCATGTGGGCCACTTC 61.998 63.158 34.69 23.15 35.11 3.01
774 874 0.896940 CTGCATGTGGGCCACTTCTT 60.897 55.000 34.69 15.87 35.11 2.52
776 876 1.181098 GCATGTGGGCCACTTCTTGT 61.181 55.000 34.69 12.77 35.11 3.16
788 888 3.146847 CACTTCTTGTAACCTGGGGAAC 58.853 50.000 0.00 0.00 0.00 3.62
790 890 4.041198 CACTTCTTGTAACCTGGGGAACTA 59.959 45.833 0.00 0.00 0.00 2.24
796 896 1.657804 AACCTGGGGAACTAGAGTGG 58.342 55.000 0.00 0.00 42.49 4.00
801 901 3.565890 CCTGGGGAACTAGAGTGGTCTTA 60.566 52.174 0.00 0.00 42.49 2.10
806 907 4.282703 GGGAACTAGAGTGGTCTTACAACA 59.717 45.833 0.00 0.00 33.84 3.33
813 914 7.941238 ACTAGAGTGGTCTTACAACAAGTACTA 59.059 37.037 0.00 0.00 33.84 1.82
874 976 2.491693 ACTGAACACACACTTTGTTGGG 59.508 45.455 0.00 0.00 37.31 4.12
1171 1290 5.047164 TCACTAGCATCCGTTAAAACCTACA 60.047 40.000 0.00 0.00 0.00 2.74
1193 1312 4.936685 AAAGCAGAGTTAAATCCCTCCT 57.063 40.909 0.00 0.00 0.00 3.69
1243 1362 0.740868 TCGAGCCAAGCTGTACATGC 60.741 55.000 0.00 2.42 39.88 4.06
1249 1368 1.432514 CAAGCTGTACATGCGAGTGT 58.567 50.000 0.00 0.00 36.13 3.55
1285 1404 1.536073 CGTGGGTGAGCTCAAGGAGA 61.536 60.000 20.19 0.00 0.00 3.71
1359 1481 2.585247 GACGGCACCATCGTAGGC 60.585 66.667 0.00 0.00 41.22 3.93
1390 1512 1.679032 GCGGTTCCCTCACTAATGCTT 60.679 52.381 0.00 0.00 0.00 3.91
1404 1526 7.432869 TCACTAATGCTTTTGTAATGCTTTGT 58.567 30.769 0.00 0.00 33.22 2.83
1406 1528 9.190858 CACTAATGCTTTTGTAATGCTTTGTAA 57.809 29.630 0.00 0.00 33.22 2.41
1427 1549 1.861542 TTTGGTCGCTTTGGCCATCG 61.862 55.000 6.09 11.43 34.44 3.84
1445 1567 3.835378 TCGCTTATGACGACTGTTGTA 57.165 42.857 0.00 0.00 33.96 2.41
1458 1580 3.753272 GACTGTTGTATGTTGCAGATGGT 59.247 43.478 0.00 0.00 33.57 3.55
1524 1646 0.523072 CGGAGTTGTGCTTCATTGGG 59.477 55.000 0.00 0.00 0.00 4.12
1730 1854 5.699097 TCCACATTTTTGGTAGTGCTTAC 57.301 39.130 0.00 0.00 37.93 2.34
2098 2249 5.055144 TGTTGCTGATAGAGATGAAGCATC 58.945 41.667 0.00 0.00 42.97 3.91
2425 2576 8.668510 AAGATAAGCGTGAATTCATGTATCTT 57.331 30.769 27.90 27.90 36.90 2.40
2465 2616 8.754096 TCAATGTTTTGTTCATCATCTTTTTCG 58.246 29.630 0.00 0.00 34.32 3.46
2488 2639 5.449862 CGAAAGGTGAAAACATTCCTGAACA 60.450 40.000 0.00 0.00 0.00 3.18
2521 2672 6.658831 ACTGTGATGTTTCTGAATTTGTACG 58.341 36.000 0.00 0.00 0.00 3.67
2549 2700 9.922305 GCTTTCAATGTTGTAACTCATATCTAC 57.078 33.333 0.00 0.00 0.00 2.59
2844 2995 4.161565 CCTACTGTAACTGTGGATGGCTTA 59.838 45.833 0.00 0.00 0.00 3.09
3082 3243 8.877808 TCATGTTTCAGCACATAGAGTATTAG 57.122 34.615 0.00 0.00 35.51 1.73
3429 3590 2.432510 AGCATTACTAGACCAGTGCCTC 59.567 50.000 0.00 0.00 38.24 4.70
3717 3879 6.183309 ACTTTCGATATTCTTTGCCTTGAC 57.817 37.500 0.00 0.00 0.00 3.18
3718 3880 5.705441 ACTTTCGATATTCTTTGCCTTGACA 59.295 36.000 0.00 0.00 0.00 3.58
3768 3930 6.990798 TGATTTTGTATTGATGCTGGTTTGA 58.009 32.000 0.00 0.00 0.00 2.69
3819 3981 6.347079 CCATCATGTTTCTGTGCAAAATGAAC 60.347 38.462 0.00 0.00 0.00 3.18
3836 3998 7.830099 AAATGAACTCTGGACTCAAATTCTT 57.170 32.000 0.00 0.00 0.00 2.52
3845 4007 4.202040 TGGACTCAAATTCTTGCACTTGTG 60.202 41.667 0.00 0.00 32.14 3.33
3899 4061 8.739039 TGATGAACCTTATGATGTTTACTTTGG 58.261 33.333 0.00 0.00 0.00 3.28
4005 4167 3.300388 TCTTAGTTCCTCGATCATGCCT 58.700 45.455 0.00 0.00 0.00 4.75
4153 4315 0.038599 TGCTCATGCATTGGTCTGGT 59.961 50.000 0.00 0.00 45.31 4.00
4323 4487 7.011482 GTGATGTCACTGATATACCCTTCAAAC 59.989 40.741 5.91 0.00 43.25 2.93
4644 4820 9.408648 ACTAGATCTGTTTGTTAATAATTGGGG 57.591 33.333 5.18 0.00 0.00 4.96
4886 5419 0.179009 CATGCCCATCAACTCCCGAT 60.179 55.000 0.00 0.00 0.00 4.18
4917 5450 1.410224 CCCCATCCCTTCTAACCAAGC 60.410 57.143 0.00 0.00 0.00 4.01
4973 5506 1.201181 GCATTCGTTATGGTGGTTGCA 59.799 47.619 0.00 0.00 34.66 4.08
5400 5934 8.196378 AGTCAACATCTAGAGTCCTTTTAGTT 57.804 34.615 0.00 0.00 0.00 2.24
5485 6019 7.469343 TGGAGGGTATGTATGCATTGATTTAT 58.531 34.615 3.54 0.00 36.58 1.40
5536 6071 7.022979 TGTCGTTTGAGATATTTTTGCAGATG 58.977 34.615 0.00 0.00 0.00 2.90
5675 6210 1.969208 TGCATTTCTGACCATGGCAAA 59.031 42.857 13.04 6.44 0.00 3.68
5697 6232 5.091261 AGAGGTAATCTTCGTCATGCTTT 57.909 39.130 0.00 0.00 32.99 3.51
5902 6437 7.222031 GGTTTGCATTTCGTTTTTCTTAACTCT 59.778 33.333 0.00 0.00 0.00 3.24
5946 6481 5.660417 ACACACTATGTTCTGATCTCCATCT 59.340 40.000 0.00 0.00 38.98 2.90
5960 6495 5.698741 TCTCCATCTCCTTTTGCTGATTA 57.301 39.130 0.00 0.00 0.00 1.75
6045 6580 1.202580 AGCGAGCAATCCAGGTACATC 60.203 52.381 0.00 0.00 0.00 3.06
6122 6657 7.772332 AAAGTTACAGTATTTAGATCGCAGG 57.228 36.000 0.00 0.00 0.00 4.85
6130 6665 2.472695 TTAGATCGCAGGCAACAAGT 57.527 45.000 0.00 0.00 41.41 3.16
6161 6696 1.773856 TTGTGTGAATCGAGGGCCCA 61.774 55.000 27.56 2.74 0.00 5.36
6286 6826 1.071987 TGCCTGAGCACTCTTGTGG 59.928 57.895 0.00 0.00 46.52 4.17
6448 6988 3.053828 CGTAACCACTGACGGGGT 58.946 61.111 0.00 0.00 39.65 4.95
6454 6994 0.838608 ACCACTGACGGGGTAAACAA 59.161 50.000 0.00 0.00 35.09 2.83
6461 7001 4.202493 ACTGACGGGGTAAACAAACCTAAT 60.202 41.667 0.00 0.00 39.65 1.73
6494 7034 0.393448 TGCTGCATTGCCACATGTTT 59.607 45.000 6.12 0.00 0.00 2.83
6533 7073 1.035932 TGATCGGTCCGGTTCCTCTC 61.036 60.000 12.29 5.88 0.00 3.20
6662 7203 5.735285 TTCATTGCAACCATGGATAACAA 57.265 34.783 21.47 14.85 0.00 2.83
6667 7208 4.880759 TGCAACCATGGATAACAAAACAG 58.119 39.130 21.47 0.00 0.00 3.16
6668 7209 4.586421 TGCAACCATGGATAACAAAACAGA 59.414 37.500 21.47 0.00 0.00 3.41
6669 7210 5.163513 GCAACCATGGATAACAAAACAGAG 58.836 41.667 21.47 0.00 0.00 3.35
6872 7564 1.446272 GAAAGAGTCCACGAGGCGG 60.446 63.158 0.00 0.00 33.74 6.13
6899 7591 2.994995 TCCATCGCCACGTGTCCT 60.995 61.111 15.65 0.00 0.00 3.85
6948 7640 2.046314 CGGGATTTCCACACGCCT 60.046 61.111 0.00 0.00 37.91 5.52
7017 7709 4.779733 TCTCCACCTCCCCTCGCC 62.780 72.222 0.00 0.00 0.00 5.54
7141 7845 2.105128 CGCTCTCGATTTCCCGCT 59.895 61.111 0.00 0.00 38.10 5.52
7598 8310 2.507102 CGCTACCTCACGCACCTG 60.507 66.667 0.00 0.00 0.00 4.00
7601 8313 1.982395 CTACCTCACGCACCTGGGA 60.982 63.158 0.00 0.00 0.00 4.37
7766 8478 1.450312 CGTCAAGGACCTCATGGCC 60.450 63.158 0.00 0.00 36.63 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.178944 TGACTCTCGTGAAAGGGGGA 60.179 55.000 0.00 0.00 0.00 4.81
1 2 0.685097 TTGACTCTCGTGAAAGGGGG 59.315 55.000 0.00 0.00 0.00 5.40
2 3 1.338200 CCTTGACTCTCGTGAAAGGGG 60.338 57.143 8.07 0.00 33.16 4.79
3 4 1.344763 ACCTTGACTCTCGTGAAAGGG 59.655 52.381 16.70 6.34 37.66 3.95
223 252 1.656429 CGAAAGCAAAACCGTGACTCG 60.656 52.381 0.00 0.00 39.52 4.18
260 289 2.225963 CGACCGTGACTCTCACTAAAGT 59.774 50.000 1.14 0.00 44.85 2.66
387 452 0.884704 ACGGCTGTGACTCGCAAAAT 60.885 50.000 0.00 0.00 0.00 1.82
391 456 4.357947 GGACGGCTGTGACTCGCA 62.358 66.667 0.80 0.00 0.00 5.10
464 543 0.744771 GCCTCTCGCGGAAGGAAAAT 60.745 55.000 25.65 0.00 0.00 1.82
509 588 2.463589 TTTCCGGAAGAGGCACGCAT 62.464 55.000 17.97 0.00 0.00 4.73
510 589 3.171828 TTTCCGGAAGAGGCACGCA 62.172 57.895 17.97 0.00 0.00 5.24
610 708 9.073368 CGTCGAGATTTTTAAAACTAGATCTCA 57.927 33.333 25.62 16.58 39.45 3.27
611 709 8.051329 GCGTCGAGATTTTTAAAACTAGATCTC 58.949 37.037 20.72 20.72 37.32 2.75
656 754 1.716172 GTCCAAATCTCGAAGCGCC 59.284 57.895 2.29 0.00 0.00 6.53
660 758 0.366871 CGTGCGTCCAAATCTCGAAG 59.633 55.000 0.00 0.00 0.00 3.79
732 832 1.816074 GCCACTTGTTGTAATCGGGA 58.184 50.000 0.00 0.00 0.00 5.14
740 840 3.110139 CAGCACGCCACTTGTTGT 58.890 55.556 0.00 0.00 0.00 3.32
753 853 3.813606 AAGTGGCCCACATGCAGCA 62.814 57.895 17.80 0.00 36.74 4.41
764 864 1.534729 CCAGGTTACAAGAAGTGGCC 58.465 55.000 0.00 0.00 0.00 5.36
772 872 3.838903 ACTCTAGTTCCCCAGGTTACAAG 59.161 47.826 0.00 0.00 0.00 3.16
774 874 3.170717 CACTCTAGTTCCCCAGGTTACA 58.829 50.000 0.00 0.00 0.00 2.41
776 876 2.113052 ACCACTCTAGTTCCCCAGGTTA 59.887 50.000 0.00 0.00 0.00 2.85
788 888 7.216973 AGTACTTGTTGTAAGACCACTCTAG 57.783 40.000 0.00 0.00 32.25 2.43
790 890 7.778185 ATAGTACTTGTTGTAAGACCACTCT 57.222 36.000 0.00 0.00 32.25 3.24
801 901 9.998106 AATCACTAGTTGAATAGTACTTGTTGT 57.002 29.630 0.00 0.00 37.92 3.32
813 914 7.039504 ACCAAGCAATGAAATCACTAGTTGAAT 60.040 33.333 0.00 0.00 37.92 2.57
855 956 1.203523 GCCCAACAAAGTGTGTGTTCA 59.796 47.619 0.00 0.00 40.60 3.18
874 976 2.846754 TTTGGTTGGGGGCTTGGC 60.847 61.111 0.00 0.00 0.00 4.52
883 985 1.459348 AGGCCTTGGGTTTGGTTGG 60.459 57.895 0.00 0.00 0.00 3.77
1112 1225 1.635663 GAACGGTGTTCCAGATGCGG 61.636 60.000 0.00 0.00 0.00 5.69
1113 1226 0.670546 AGAACGGTGTTCCAGATGCG 60.671 55.000 6.09 0.00 0.00 4.73
1119 1238 1.364901 GTCGGAGAACGGTGTTCCA 59.635 57.895 6.09 0.00 44.45 3.53
1171 1290 5.257262 GAGGAGGGATTTAACTCTGCTTTT 58.743 41.667 0.00 0.00 39.08 2.27
1243 1362 2.901042 GCCCTTCCCCTACACTCG 59.099 66.667 0.00 0.00 0.00 4.18
1249 1368 2.686106 GGACACGCCCTTCCCCTA 60.686 66.667 0.00 0.00 0.00 3.53
1390 1512 7.306866 GCGACCAAAATTACAAAGCATTACAAA 60.307 33.333 0.00 0.00 0.00 2.83
1404 1526 1.964223 TGGCCAAAGCGACCAAAATTA 59.036 42.857 0.61 0.00 41.24 1.40
1406 1528 0.975887 ATGGCCAAAGCGACCAAAAT 59.024 45.000 10.96 0.00 41.24 1.82
1427 1549 5.550981 CAACATACAACAGTCGTCATAAGC 58.449 41.667 0.00 0.00 0.00 3.09
1445 1567 4.397103 CACAATCTACACCATCTGCAACAT 59.603 41.667 0.00 0.00 0.00 2.71
1458 1580 2.230508 GTCTCCACCGTCACAATCTACA 59.769 50.000 0.00 0.00 0.00 2.74
1524 1646 3.117171 CTGAGCTGCAGTGTCGCC 61.117 66.667 16.64 0.00 39.85 5.54
1776 1925 2.697431 TTACGGTTGCTGTTGAATGC 57.303 45.000 0.00 0.00 0.00 3.56
2445 2596 7.978975 ACCTTTCGAAAAAGATGATGAACAAAA 59.021 29.630 12.41 0.00 43.90 2.44
2465 2616 5.901552 TGTTCAGGAATGTTTTCACCTTTC 58.098 37.500 0.00 0.00 33.23 2.62
2521 2672 8.454106 AGATATGAGTTACAACATTGAAAGCAC 58.546 33.333 0.00 0.00 0.00 4.40
2549 2700 7.683437 ATATATGAGAATGGACATGCACAAG 57.317 36.000 0.00 0.00 0.00 3.16
2798 2949 5.478332 GGAACTGTTGATTTTCTCTCCCATT 59.522 40.000 0.00 0.00 0.00 3.16
2829 2980 3.443681 CCGAAATTAAGCCATCCACAGTT 59.556 43.478 0.00 0.00 0.00 3.16
2830 2981 3.016736 CCGAAATTAAGCCATCCACAGT 58.983 45.455 0.00 0.00 0.00 3.55
2831 2982 2.223572 GCCGAAATTAAGCCATCCACAG 60.224 50.000 0.00 0.00 0.00 3.66
2832 2983 1.748493 GCCGAAATTAAGCCATCCACA 59.252 47.619 0.00 0.00 0.00 4.17
2833 2984 1.067060 GGCCGAAATTAAGCCATCCAC 59.933 52.381 8.11 0.00 46.34 4.02
2834 2985 1.398692 GGCCGAAATTAAGCCATCCA 58.601 50.000 8.11 0.00 46.34 3.41
2844 2995 1.185315 CAGAACCCATGGCCGAAATT 58.815 50.000 6.09 0.00 0.00 1.82
3082 3243 5.449177 GCATTACAGATTCCCTTAGTGCAAC 60.449 44.000 0.00 0.00 0.00 4.17
3429 3590 6.524239 CACACTTGAACATACATTTGGAATCG 59.476 38.462 0.00 0.00 0.00 3.34
3496 3657 3.802866 AGCAGCTAACTTCCTTGCTATC 58.197 45.455 0.00 0.00 42.81 2.08
3683 3845 7.979444 AGAATATCGAAAGTTCAGGTCAAAA 57.021 32.000 9.50 0.00 0.00 2.44
3718 3880 2.038952 TGTTCAGCACCAGATACAAGCT 59.961 45.455 0.00 0.00 35.63 3.74
3768 3930 9.209175 GAAGTACTGTCTGTCTTTTGATATGTT 57.791 33.333 0.00 0.00 0.00 2.71
3819 3981 4.070716 AGTGCAAGAATTTGAGTCCAGAG 58.929 43.478 0.00 0.00 36.36 3.35
3836 3998 4.561500 TTAGGCTATAACCACAAGTGCA 57.438 40.909 0.00 0.00 0.00 4.57
3845 4007 9.384764 GTATGAGGAATTCATTAGGCTATAACC 57.615 37.037 7.93 0.00 44.14 2.85
3899 4061 5.480642 TCATCTGATGGATAGAAGGCTTC 57.519 43.478 19.53 19.53 32.64 3.86
4005 4167 7.529158 CAACAGAACATTTACAGTGCATGATA 58.471 34.615 0.00 0.00 0.00 2.15
4011 4173 4.228912 AGCAACAGAACATTTACAGTGC 57.771 40.909 0.00 0.00 0.00 4.40
4110 4272 7.542130 GCATAATATTGGCTAGCATGGTAAAAC 59.458 37.037 18.24 0.00 0.00 2.43
4225 4389 1.665679 ACGCCATCTGCAAATAAGACG 59.334 47.619 0.00 0.00 41.33 4.18
4353 4517 8.398665 GGAAACTAACCTAATGAAGCATTAGTG 58.601 37.037 19.89 15.16 46.83 2.74
4550 4726 5.392995 TGTGATCCCAAAAGAAAAGATGGA 58.607 37.500 0.00 0.00 34.82 3.41
4624 4800 6.382570 CCATCCCCCAATTATTAACAAACAGA 59.617 38.462 0.00 0.00 0.00 3.41
4642 4818 2.050918 CCTCCTCTAAACTCCATCCCC 58.949 57.143 0.00 0.00 0.00 4.81
4643 4819 3.047695 TCCTCCTCTAAACTCCATCCC 57.952 52.381 0.00 0.00 0.00 3.85
4644 4820 4.034410 ACTTCCTCCTCTAAACTCCATCC 58.966 47.826 0.00 0.00 0.00 3.51
4886 5419 2.082414 GGATGGGGAATTCGGGGGA 61.082 63.158 0.00 0.00 0.00 4.81
4955 5488 3.620488 AGATGCAACCACCATAACGAAT 58.380 40.909 0.00 0.00 0.00 3.34
4973 5506 2.840651 CCCACAGAACCACTAGGAAGAT 59.159 50.000 0.00 0.00 38.69 2.40
5166 5699 9.978044 CAGATATGTGTGAATGAATAGAGAAGA 57.022 33.333 0.00 0.00 0.00 2.87
5400 5934 0.251354 GCTCATCAGCTCCAGAACCA 59.749 55.000 0.00 0.00 43.09 3.67
5485 6019 7.336679 AGTCACATTATTTAGCATGCAGTACAA 59.663 33.333 21.98 8.43 0.00 2.41
5675 6210 4.744795 AAGCATGACGAAGATTACCTCT 57.255 40.909 0.00 0.00 34.96 3.69
5725 6260 1.553248 TGGGTACACATCAGCCACTAC 59.447 52.381 0.00 0.00 38.60 2.73
5946 6481 7.446931 TGTCACATTACTTAATCAGCAAAAGGA 59.553 33.333 0.00 0.00 0.00 3.36
5960 6495 3.192001 CCTGCAGCATTGTCACATTACTT 59.808 43.478 8.66 0.00 0.00 2.24
6045 6580 9.927668 ACTGAAGGAAACAAATGGTTATAAATG 57.072 29.630 0.00 0.00 39.29 2.32
6081 6616 9.828852 CTGTAACTTTTTAACACACAACACTAA 57.171 29.630 0.00 0.00 0.00 2.24
6117 6652 2.062361 TTGCTCACTTGTTGCCTGCG 62.062 55.000 0.00 0.00 0.00 5.18
6119 6654 1.027357 ACTTGCTCACTTGTTGCCTG 58.973 50.000 0.00 0.00 0.00 4.85
6121 6656 3.708563 TTAACTTGCTCACTTGTTGCC 57.291 42.857 0.00 0.00 0.00 4.52
6122 6657 5.043248 ACAATTAACTTGCTCACTTGTTGC 58.957 37.500 0.00 0.00 38.50 4.17
6130 6665 5.468409 TCGATTCACACAATTAACTTGCTCA 59.532 36.000 0.00 0.00 38.50 4.26
6286 6826 4.474226 GTGAAGACACATGAGTTTCCAC 57.526 45.455 0.00 3.63 45.32 4.02
6448 6988 4.083908 GGCACGTCGAATTAGGTTTGTTTA 60.084 41.667 0.00 0.00 0.00 2.01
6454 6994 1.274167 TCTGGCACGTCGAATTAGGTT 59.726 47.619 0.00 0.00 0.00 3.50
6533 7073 4.848357 ACCCATAACAGGATGAACTGAAG 58.152 43.478 0.00 0.00 40.97 3.02
6634 7175 6.795144 ATCCATGGTTGCAATGAATAAGAA 57.205 33.333 12.58 0.00 0.00 2.52
6872 7564 2.396157 GGCGATGGACGGTTGGTTC 61.396 63.158 0.00 0.00 42.83 3.62
6948 7640 4.439700 CGTCCGCTTGACTTTATAGAGGAA 60.440 45.833 0.00 0.00 42.13 3.36
7186 7890 1.003851 GATTCGAATTCGGTCGGCAA 58.996 50.000 26.47 13.24 41.43 4.52
7187 7891 0.808453 GGATTCGAATTCGGTCGGCA 60.808 55.000 26.47 4.23 41.43 5.69
7466 8178 2.678934 CTCCCGAACTCGTCCCCA 60.679 66.667 0.00 0.00 37.74 4.96
7766 8478 3.403276 GTCCTTGGAGTCGACGAAG 57.597 57.895 10.46 13.01 0.00 3.79


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

AutoCloner maintained by Alex Coulton.