Multiple sequence alignment - TraesCS3A01G519500

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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 TraesCS3A01G519500 chr3A 100.000 2375 0 0 1 2375 737174478 737172104 0.000000e+00 4386
1 TraesCS3A01G519500 chr3A 94.805 539 22 2 1 533 32994450 32993912 0.000000e+00 835
2 TraesCS3A01G519500 chr3A 79.295 879 110 36 743 1584 737122179 737121336 1.240000e-152 549
3 TraesCS3A01G519500 chr3A 85.385 130 18 1 2187 2315 737125234 737125105 1.480000e-27 134
4 TraesCS3A01G519500 chr3B 88.714 1019 63 21 528 1531 813883868 813882887 0.000000e+00 1197
5 TraesCS3A01G519500 chr3B 86.839 889 71 22 1521 2375 813882149 813881273 0.000000e+00 952
6 TraesCS3A01G519500 chr3B 77.686 847 139 30 728 1557 813757466 813756653 2.760000e-129 472
7 TraesCS3A01G519500 chr5A 95.497 533 21 2 1 530 264075227 264074695 0.000000e+00 848
8 TraesCS3A01G519500 chr5A 95.489 532 23 1 1 531 640396170 640395639 0.000000e+00 848
9 TraesCS3A01G519500 chr5A 95.122 533 25 1 1 532 631638414 631637882 0.000000e+00 839
10 TraesCS3A01G519500 chr5A 95.113 532 25 1 1 531 365446599 365446068 0.000000e+00 837
11 TraesCS3A01G519500 chr1A 95.301 532 23 2 1 531 551668230 551667700 0.000000e+00 843
12 TraesCS3A01G519500 chr1A 94.953 535 24 3 1 532 493927542 493928076 0.000000e+00 835
13 TraesCS3A01G519500 chr7A 94.925 532 25 2 1 531 705535508 705534978 0.000000e+00 832
14 TraesCS3A01G519500 chr2A 94.915 531 26 1 1 530 319018539 319019069 0.000000e+00 830
15 TraesCS3A01G519500 chrUn 85.593 708 58 18 884 1572 46189986 46189304 0.000000e+00 702
16 TraesCS3A01G519500 chrUn 80.462 865 112 30 743 1584 46158896 46158066 2.020000e-170 608
17 TraesCS3A01G519500 chrUn 82.105 190 28 5 2187 2375 46161895 46161711 8.790000e-35 158


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 TraesCS3A01G519500 chr3A 737172104 737174478 2374 True 4386.0 4386 100.0000 1 2375 1 chr3A.!!$R2 2374
1 TraesCS3A01G519500 chr3A 32993912 32994450 538 True 835.0 835 94.8050 1 533 1 chr3A.!!$R1 532
2 TraesCS3A01G519500 chr3A 737121336 737125234 3898 True 341.5 549 82.3400 743 2315 2 chr3A.!!$R3 1572
3 TraesCS3A01G519500 chr3B 813881273 813883868 2595 True 1074.5 1197 87.7765 528 2375 2 chr3B.!!$R2 1847
4 TraesCS3A01G519500 chr3B 813756653 813757466 813 True 472.0 472 77.6860 728 1557 1 chr3B.!!$R1 829
5 TraesCS3A01G519500 chr5A 264074695 264075227 532 True 848.0 848 95.4970 1 530 1 chr5A.!!$R1 529
6 TraesCS3A01G519500 chr5A 640395639 640396170 531 True 848.0 848 95.4890 1 531 1 chr5A.!!$R4 530
7 TraesCS3A01G519500 chr5A 631637882 631638414 532 True 839.0 839 95.1220 1 532 1 chr5A.!!$R3 531
8 TraesCS3A01G519500 chr5A 365446068 365446599 531 True 837.0 837 95.1130 1 531 1 chr5A.!!$R2 530
9 TraesCS3A01G519500 chr1A 551667700 551668230 530 True 843.0 843 95.3010 1 531 1 chr1A.!!$R1 530
10 TraesCS3A01G519500 chr1A 493927542 493928076 534 False 835.0 835 94.9530 1 532 1 chr1A.!!$F1 531
11 TraesCS3A01G519500 chr7A 705534978 705535508 530 True 832.0 832 94.9250 1 531 1 chr7A.!!$R1 530
12 TraesCS3A01G519500 chr2A 319018539 319019069 530 False 830.0 830 94.9150 1 530 1 chr2A.!!$F1 529
13 TraesCS3A01G519500 chrUn 46189304 46189986 682 True 702.0 702 85.5930 884 1572 1 chrUn.!!$R1 688
14 TraesCS3A01G519500 chrUn 46158066 46161895 3829 True 383.0 608 81.2835 743 2375 2 chrUn.!!$R2 1632

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
175 176 0.271927 TATGGAGGCTCAAGGGGGAT 59.728 55.0 17.69 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1439 4040 0.037512 CACAGACAGAGACAGGGCAG 60.038 60.0 0.0 0.0 0.0 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
30 31 6.259167 GTGTTTGACACTGAACCATACTACAA 59.741 38.462 4.06 0.00 45.27 2.41
105 106 3.998099 TCTCAATATGCGTCAGGAGAG 57.002 47.619 0.00 0.00 0.00 3.20
175 176 0.271927 TATGGAGGCTCAAGGGGGAT 59.728 55.000 17.69 0.00 0.00 3.85
391 392 4.081917 GGCCCTTTATTCGTTGAAATTGGA 60.082 41.667 0.00 0.00 0.00 3.53
503 510 1.400494 GCGATTTTTATGCGTCCTGGT 59.600 47.619 0.00 0.00 0.00 4.00
591 600 0.517316 GCAAGCCACGTTTCCTGTAG 59.483 55.000 0.00 0.00 0.00 2.74
593 602 0.396811 AAGCCACGTTTCCTGTAGCT 59.603 50.000 0.00 0.00 35.81 3.32
600 609 1.739371 CGTTTCCTGTAGCTAGGGCAC 60.739 57.143 2.62 4.40 41.70 5.01
641 650 5.771153 TTGTGAGAATGTGAAGCAAATGA 57.229 34.783 0.00 0.00 0.00 2.57
642 651 5.366829 TGTGAGAATGTGAAGCAAATGAG 57.633 39.130 0.00 0.00 0.00 2.90
643 652 5.065235 TGTGAGAATGTGAAGCAAATGAGA 58.935 37.500 0.00 0.00 0.00 3.27
644 653 5.180680 TGTGAGAATGTGAAGCAAATGAGAG 59.819 40.000 0.00 0.00 0.00 3.20
645 654 4.698780 TGAGAATGTGAAGCAAATGAGAGG 59.301 41.667 0.00 0.00 0.00 3.69
646 655 4.914983 AGAATGTGAAGCAAATGAGAGGA 58.085 39.130 0.00 0.00 0.00 3.71
647 656 5.319453 AGAATGTGAAGCAAATGAGAGGAA 58.681 37.500 0.00 0.00 0.00 3.36
648 657 5.771666 AGAATGTGAAGCAAATGAGAGGAAA 59.228 36.000 0.00 0.00 0.00 3.13
649 658 6.266103 AGAATGTGAAGCAAATGAGAGGAAAA 59.734 34.615 0.00 0.00 0.00 2.29
650 659 5.186996 TGTGAAGCAAATGAGAGGAAAAC 57.813 39.130 0.00 0.00 0.00 2.43
651 660 4.037923 TGTGAAGCAAATGAGAGGAAAACC 59.962 41.667 0.00 0.00 0.00 3.27
653 662 2.162681 AGCAAATGAGAGGAAAACCGG 58.837 47.619 0.00 0.00 0.00 5.28
654 663 1.886542 GCAAATGAGAGGAAAACCGGT 59.113 47.619 0.00 0.00 0.00 5.28
656 665 3.146066 CAAATGAGAGGAAAACCGGTCA 58.854 45.455 8.04 0.00 0.00 4.02
657 666 3.502123 AATGAGAGGAAAACCGGTCAA 57.498 42.857 8.04 0.00 0.00 3.18
659 668 3.053831 TGAGAGGAAAACCGGTCAATC 57.946 47.619 8.04 6.62 0.00 2.67
660 669 2.000447 GAGAGGAAAACCGGTCAATCG 59.000 52.381 8.04 0.00 0.00 3.34
669 678 4.090588 GGTCAATCGGCGGGGTCA 62.091 66.667 7.21 0.00 0.00 4.02
678 687 1.153229 GGCGGGGTCACCTTATCAC 60.153 63.158 0.00 0.00 36.97 3.06
696 705 8.206867 CCTTATCACATCCTCATGAAGTAAAGA 58.793 37.037 0.00 0.00 33.72 2.52
721 730 0.308993 GCAGTCACAACAGCTTGGAC 59.691 55.000 0.00 0.00 35.22 4.02
722 731 0.947244 CAGTCACAACAGCTTGGACC 59.053 55.000 0.00 0.00 32.29 4.46
737 746 3.900888 ACCATGGACCGGTCAACT 58.099 55.556 34.40 16.23 27.30 3.16
840 3374 1.576920 CTCCATCCGTCCTCGATCG 59.423 63.158 9.36 9.36 39.71 3.69
911 3459 4.256090 GGGCAATGCGATCGGTGC 62.256 66.667 18.30 0.00 36.24 5.01
933 3481 2.598394 ACTGCCACCACACCATGC 60.598 61.111 0.00 0.00 0.00 4.06
934 3482 2.598099 CTGCCACCACACCATGCA 60.598 61.111 0.00 0.00 0.00 3.96
935 3483 1.980232 CTGCCACCACACCATGCAT 60.980 57.895 0.00 0.00 0.00 3.96
936 3484 2.220615 CTGCCACCACACCATGCATG 62.221 60.000 20.19 20.19 0.00 4.06
937 3485 2.277591 GCCACCACACCATGCATGT 61.278 57.895 24.58 10.59 0.00 3.21
940 3488 2.929641 CCACCACACCATGCATGTATA 58.070 47.619 24.58 0.00 0.00 1.47
942 3490 3.544684 CACCACACCATGCATGTATACT 58.455 45.455 24.58 0.37 0.00 2.12
954 3508 4.040461 TGCATGTATACTTCTTAGCCTCCC 59.960 45.833 4.17 0.00 0.00 4.30
971 3525 3.201708 CCTCCCTGTTCAAGAGATGGATT 59.798 47.826 0.00 0.00 0.00 3.01
972 3526 4.410228 CCTCCCTGTTCAAGAGATGGATTA 59.590 45.833 0.00 0.00 0.00 1.75
981 3535 3.550437 AGAGATGGATTAGTGTGCACC 57.450 47.619 15.69 5.76 0.00 5.01
988 3542 2.343101 GATTAGTGTGCACCGCAGTAA 58.657 47.619 15.69 9.77 41.77 2.24
989 3543 1.504359 TTAGTGTGCACCGCAGTAAC 58.496 50.000 15.69 3.54 40.08 2.50
1005 3567 2.762969 TAACACCGGCTGCAATGGCT 62.763 55.000 0.00 0.00 41.91 4.75
1035 3606 0.892063 ACCTGCTCTTCTTCCTCGTC 59.108 55.000 0.00 0.00 0.00 4.20
1385 3970 3.352524 TGCGTGACATGCATTGCA 58.647 50.000 18.38 14.72 44.86 4.08
1400 3992 0.394216 TTGCATAGCCAGTTCGCCAT 60.394 50.000 0.00 0.00 0.00 4.40
1431 4032 2.409152 TTTTTCGTTGGGCTTTAGCG 57.591 45.000 0.00 0.00 43.26 4.26
1432 4033 1.310904 TTTTCGTTGGGCTTTAGCGT 58.689 45.000 0.00 0.00 43.26 5.07
1433 4034 0.589223 TTTCGTTGGGCTTTAGCGTG 59.411 50.000 0.00 0.00 43.26 5.34
1434 4035 1.847890 TTCGTTGGGCTTTAGCGTGC 61.848 55.000 0.00 0.00 43.26 5.34
1439 4040 3.809423 GGCTTTAGCGTGCCCTAC 58.191 61.111 0.00 0.00 43.11 3.18
1464 4065 0.752658 TGTCTCTGTCTGTGGTGTGG 59.247 55.000 0.00 0.00 0.00 4.17
1572 4928 6.833041 TCTCCTGTAACATGTGTTTCCTTAA 58.167 36.000 0.00 0.00 39.31 1.85
1573 4929 7.458397 TCTCCTGTAACATGTGTTTCCTTAAT 58.542 34.615 0.00 0.00 39.31 1.40
1574 4930 7.606456 TCTCCTGTAACATGTGTTTCCTTAATC 59.394 37.037 0.00 0.00 39.31 1.75
1600 4956 3.130160 GCGCCTTGCTCTCCTTGG 61.130 66.667 0.00 0.00 41.73 3.61
1601 4957 2.348998 CGCCTTGCTCTCCTTGGT 59.651 61.111 0.00 0.00 0.00 3.67
1602 4958 1.743252 CGCCTTGCTCTCCTTGGTC 60.743 63.158 0.00 0.00 0.00 4.02
1603 4959 1.743252 GCCTTGCTCTCCTTGGTCG 60.743 63.158 0.00 0.00 0.00 4.79
1605 4961 0.035458 CCTTGCTCTCCTTGGTCGTT 59.965 55.000 0.00 0.00 0.00 3.85
1606 4962 1.151668 CTTGCTCTCCTTGGTCGTTG 58.848 55.000 0.00 0.00 0.00 4.10
1607 4963 0.468226 TTGCTCTCCTTGGTCGTTGT 59.532 50.000 0.00 0.00 0.00 3.32
1608 4964 0.249868 TGCTCTCCTTGGTCGTTGTG 60.250 55.000 0.00 0.00 0.00 3.33
1610 4966 1.810412 GCTCTCCTTGGTCGTTGTGTT 60.810 52.381 0.00 0.00 0.00 3.32
1611 4967 2.547218 GCTCTCCTTGGTCGTTGTGTTA 60.547 50.000 0.00 0.00 0.00 2.41
1612 4968 3.318017 CTCTCCTTGGTCGTTGTGTTAG 58.682 50.000 0.00 0.00 0.00 2.34
1613 4969 1.798813 CTCCTTGGTCGTTGTGTTAGC 59.201 52.381 0.00 0.00 0.00 3.09
1614 4970 0.872388 CCTTGGTCGTTGTGTTAGCC 59.128 55.000 0.00 0.00 0.00 3.93
1623 4979 1.269723 GTTGTGTTAGCCAGGCTTTCC 59.730 52.381 22.26 8.53 40.44 3.13
1654 5010 2.105477 GGTGTAGATGGGCTCATGACAT 59.895 50.000 2.16 0.00 32.10 3.06
1656 5012 4.202357 GGTGTAGATGGGCTCATGACATAA 60.202 45.833 2.16 0.00 32.10 1.90
1861 5224 9.874205 ATTTTCTTTCATGAACTTGTCTTCAAA 57.126 25.926 7.89 0.00 33.85 2.69
1963 5328 3.363341 ACAAAAATACCGTGTGGCTTG 57.637 42.857 0.00 0.00 39.70 4.01
1964 5329 2.691011 ACAAAAATACCGTGTGGCTTGT 59.309 40.909 0.00 0.00 39.70 3.16
1989 5354 3.257469 TCATGAGCAAAGTAGCAGGAG 57.743 47.619 0.00 0.00 36.85 3.69
1997 5362 1.467920 AAGTAGCAGGAGCAAATGGC 58.532 50.000 0.00 0.00 45.49 4.40
2041 5408 1.153989 CCTAGAGCCTCCCGATCCA 59.846 63.158 0.00 0.00 0.00 3.41
2063 5438 2.349376 CCATGGTACCGTGGCACA 59.651 61.111 34.89 4.11 44.87 4.57
2096 5471 1.312371 TAATGCTTGTGCTTCCGGGC 61.312 55.000 0.00 0.00 40.48 6.13
2116 5491 4.097892 GGGCCTTTAAGGATGTGTACAATG 59.902 45.833 16.18 0.00 37.67 2.82
2137 5512 3.003480 GGTGACATCTTAAGAGTGCCAC 58.997 50.000 11.53 15.50 0.00 5.01
2138 5513 3.557054 GGTGACATCTTAAGAGTGCCACA 60.557 47.826 22.69 14.54 0.00 4.17
2143 5518 7.383572 GTGACATCTTAAGAGTGCCACATATAG 59.616 40.741 19.47 0.00 0.00 1.31
2149 5524 9.154632 TCTTAAGAGTGCCACATATAGGATAAA 57.845 33.333 0.00 0.00 0.00 1.40
2150 5525 9.950496 CTTAAGAGTGCCACATATAGGATAAAT 57.050 33.333 0.00 0.00 0.00 1.40
2163 5538 3.197983 AGGATAAATGTTGAGGGGGTGA 58.802 45.455 0.00 0.00 0.00 4.02
2164 5539 3.053619 AGGATAAATGTTGAGGGGGTGAC 60.054 47.826 0.00 0.00 0.00 3.67
2165 5540 3.308832 GGATAAATGTTGAGGGGGTGACA 60.309 47.826 0.00 0.00 0.00 3.58
2172 5547 2.040412 GTTGAGGGGGTGACAAGAGAAT 59.960 50.000 0.00 0.00 0.00 2.40
2178 5553 3.118592 GGGGGTGACAAGAGAATGTAGAG 60.119 52.174 0.00 0.00 32.57 2.43
2197 5572 4.744795 GAGAAAGGCTTATCTCTCACCA 57.255 45.455 21.72 0.00 39.18 4.17
2205 5580 6.904626 AGGCTTATCTCTCACCACATATTTT 58.095 36.000 0.00 0.00 0.00 1.82
2206 5581 6.769822 AGGCTTATCTCTCACCACATATTTTG 59.230 38.462 0.00 0.00 0.00 2.44
2212 5587 3.130869 TCTCACCACATATTTTGGCATGC 59.869 43.478 9.90 9.90 37.69 4.06
2226 5601 7.880160 TTTTGGCATGCTAGTTACTAATGAT 57.120 32.000 18.92 0.00 0.00 2.45
2230 5605 7.161404 TGGCATGCTAGTTACTAATGATAAGG 58.839 38.462 18.92 0.00 0.00 2.69
2233 5608 7.148507 GCATGCTAGTTACTAATGATAAGGCTG 60.149 40.741 11.37 1.80 0.00 4.85
2318 5705 7.245292 AGGATAAGACTATCTTATGAGCCAGT 58.755 38.462 14.32 0.00 46.46 4.00
2329 5717 1.913778 TGAGCCAGTGTACGTCCTAA 58.086 50.000 0.00 0.00 0.00 2.69
2347 5735 3.875727 CCTAAATGAGATGGAGCACACAG 59.124 47.826 0.00 0.00 0.00 3.66
2351 5739 0.107945 GAGATGGAGCACACAGGACC 60.108 60.000 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.443016 CGGCTAGAGGACCCTGCT 60.443 66.667 0.00 0.00 0.00 4.24
155 156 0.045623 TCCCCCTTGAGCCTCCATAA 59.954 55.000 0.00 0.00 0.00 1.90
175 176 2.267426 CTCGTATTTCATCACACGGCA 58.733 47.619 0.00 0.00 35.21 5.69
391 392 1.070601 GAAATTGGCCCACTTTGCAGT 59.929 47.619 3.51 0.00 0.00 4.40
591 600 1.396653 ATGAATTGCAGTGCCCTAGC 58.603 50.000 13.72 0.00 40.48 3.42
593 602 3.544684 CAGTATGAATTGCAGTGCCCTA 58.455 45.455 13.72 0.00 39.69 3.53
600 609 4.565166 CACAAATGGCAGTATGAATTGCAG 59.435 41.667 0.00 0.00 39.96 4.41
641 650 1.338769 CCGATTGACCGGTTTTCCTCT 60.339 52.381 9.42 0.00 44.23 3.69
642 651 1.084289 CCGATTGACCGGTTTTCCTC 58.916 55.000 9.42 0.86 44.23 3.71
643 652 3.243128 CCGATTGACCGGTTTTCCT 57.757 52.632 9.42 0.00 44.23 3.36
653 662 2.818274 GTGACCCCGCCGATTGAC 60.818 66.667 0.00 0.00 0.00 3.18
654 663 4.090588 GGTGACCCCGCCGATTGA 62.091 66.667 0.00 0.00 32.63 2.57
660 669 1.153229 GTGATAAGGTGACCCCGCC 60.153 63.158 0.00 0.00 43.25 6.13
662 671 1.202651 GGATGTGATAAGGTGACCCCG 60.203 57.143 0.00 0.00 38.74 5.73
665 674 4.101585 TCATGAGGATGTGATAAGGTGACC 59.898 45.833 0.00 0.00 0.00 4.02
666 675 5.282055 TCATGAGGATGTGATAAGGTGAC 57.718 43.478 0.00 0.00 0.00 3.67
667 676 5.426509 ACTTCATGAGGATGTGATAAGGTGA 59.573 40.000 12.40 0.00 33.05 4.02
668 677 5.678583 ACTTCATGAGGATGTGATAAGGTG 58.321 41.667 12.40 0.00 33.05 4.00
669 678 5.965033 ACTTCATGAGGATGTGATAAGGT 57.035 39.130 12.40 0.00 33.05 3.50
678 687 6.688637 TGCAATCTTTACTTCATGAGGATG 57.311 37.500 12.40 0.00 0.00 3.51
696 705 0.313043 GCTGTTGTGACTGCTGCAAT 59.687 50.000 3.02 0.00 44.51 3.56
721 730 1.377202 CCAGTTGACCGGTCCATGG 60.377 63.158 31.19 28.26 0.00 3.66
722 731 2.040544 GCCAGTTGACCGGTCCATG 61.041 63.158 31.19 24.10 0.00 3.66
840 3374 0.586802 GAACGGCAGAAAGTGTGACC 59.413 55.000 0.00 0.00 0.00 4.02
911 3459 3.289834 GTGTGGTGGCAGTGGCAG 61.290 66.667 21.25 0.00 43.71 4.85
933 3481 5.305644 ACAGGGAGGCTAAGAAGTATACATG 59.694 44.000 5.50 0.00 0.00 3.21
934 3482 5.468658 ACAGGGAGGCTAAGAAGTATACAT 58.531 41.667 5.50 0.00 0.00 2.29
935 3483 4.880164 ACAGGGAGGCTAAGAAGTATACA 58.120 43.478 5.50 0.00 0.00 2.29
936 3484 5.363005 TGAACAGGGAGGCTAAGAAGTATAC 59.637 44.000 0.00 0.00 0.00 1.47
937 3485 5.525484 TGAACAGGGAGGCTAAGAAGTATA 58.475 41.667 0.00 0.00 0.00 1.47
940 3488 2.621070 TGAACAGGGAGGCTAAGAAGT 58.379 47.619 0.00 0.00 0.00 3.01
942 3490 3.248024 TCTTGAACAGGGAGGCTAAGAA 58.752 45.455 0.00 0.00 0.00 2.52
954 3508 5.064452 GCACACTAATCCATCTCTTGAACAG 59.936 44.000 0.00 0.00 0.00 3.16
971 3525 0.389757 TGTTACTGCGGTGCACACTA 59.610 50.000 20.43 2.44 33.79 2.74
972 3526 1.145156 TGTTACTGCGGTGCACACT 59.855 52.632 20.43 0.00 33.79 3.55
981 3535 3.788766 GCAGCCGGTGTTACTGCG 61.789 66.667 14.06 0.00 46.38 5.18
988 3542 4.666253 AGCCATTGCAGCCGGTGT 62.666 61.111 1.90 0.00 41.13 4.16
989 3543 4.124351 CAGCCATTGCAGCCGGTG 62.124 66.667 1.90 0.89 41.13 4.94
1005 3567 1.891919 GAGCAGGTGGTTGAACGCA 60.892 57.895 0.00 0.00 0.00 5.24
1012 3583 1.349357 GAGGAAGAAGAGCAGGTGGTT 59.651 52.381 0.00 0.00 0.00 3.67
1074 3646 4.221422 TCGTCATAGCCCGCAGCC 62.221 66.667 0.00 0.00 45.47 4.85
1157 3735 2.283676 TCTCCTGGTCGGTGGTCC 60.284 66.667 0.00 0.00 0.00 4.46
1382 3967 0.815213 GATGGCGAACTGGCTATGCA 60.815 55.000 0.00 0.00 45.14 3.96
1383 3968 0.533755 AGATGGCGAACTGGCTATGC 60.534 55.000 0.00 0.00 45.14 3.14
1384 3969 1.069823 AGAGATGGCGAACTGGCTATG 59.930 52.381 0.00 0.00 45.14 2.23
1385 3970 1.069823 CAGAGATGGCGAACTGGCTAT 59.930 52.381 0.00 0.00 45.14 2.97
1386 3971 0.461548 CAGAGATGGCGAACTGGCTA 59.538 55.000 0.00 0.00 45.14 3.93
1387 3972 1.220206 CAGAGATGGCGAACTGGCT 59.780 57.895 0.00 0.00 45.14 4.75
1430 4031 3.665675 GACAGGGCAGTAGGGCACG 62.666 68.421 0.00 0.00 43.62 5.34
1431 4032 2.245438 GAGACAGGGCAGTAGGGCAC 62.245 65.000 0.00 0.00 45.66 5.01
1432 4033 1.990060 GAGACAGGGCAGTAGGGCA 60.990 63.158 0.00 0.00 45.66 5.36
1433 4034 1.687493 AGAGACAGGGCAGTAGGGC 60.687 63.158 0.00 0.00 42.44 5.19
1434 4035 0.616111 ACAGAGACAGGGCAGTAGGG 60.616 60.000 0.00 0.00 0.00 3.53
1435 4036 0.820871 GACAGAGACAGGGCAGTAGG 59.179 60.000 0.00 0.00 0.00 3.18
1436 4037 1.476085 CAGACAGAGACAGGGCAGTAG 59.524 57.143 0.00 0.00 0.00 2.57
1437 4038 1.203063 ACAGACAGAGACAGGGCAGTA 60.203 52.381 0.00 0.00 0.00 2.74
1438 4039 0.470833 ACAGACAGAGACAGGGCAGT 60.471 55.000 0.00 0.00 0.00 4.40
1439 4040 0.037512 CACAGACAGAGACAGGGCAG 60.038 60.000 0.00 0.00 0.00 4.85
1464 4065 2.548480 GGAGCACAAGGACTAACAACAC 59.452 50.000 0.00 0.00 0.00 3.32
1600 4956 0.602905 AGCCTGGCTAACACAACGAC 60.603 55.000 21.98 0.00 36.99 4.34
1601 4957 0.107831 AAGCCTGGCTAACACAACGA 59.892 50.000 23.69 0.00 38.25 3.85
1602 4958 0.951558 AAAGCCTGGCTAACACAACG 59.048 50.000 23.69 0.00 38.25 4.10
1603 4959 1.269723 GGAAAGCCTGGCTAACACAAC 59.730 52.381 23.69 8.14 38.25 3.32
1605 4961 0.771127 AGGAAAGCCTGGCTAACACA 59.229 50.000 23.69 0.00 44.90 3.72
1606 4962 3.652581 AGGAAAGCCTGGCTAACAC 57.347 52.632 23.69 12.64 44.90 3.32
1623 4979 2.947652 CCCATCTACACCAGCAATTCAG 59.052 50.000 0.00 0.00 0.00 3.02
1626 4982 1.285962 AGCCCATCTACACCAGCAATT 59.714 47.619 0.00 0.00 0.00 2.32
1629 4985 0.909133 TGAGCCCATCTACACCAGCA 60.909 55.000 0.00 0.00 0.00 4.41
1694 5050 9.328845 CAAAGAAGAAAAATGGGAAAAGAATGA 57.671 29.630 0.00 0.00 0.00 2.57
1753 5109 9.749490 GCACAAATTAATGTTCATGAATTTCAG 57.251 29.630 12.12 11.81 30.91 3.02
1754 5110 9.269453 TGCACAAATTAATGTTCATGAATTTCA 57.731 25.926 12.12 5.54 30.91 2.69
1933 5298 8.818057 CCACACGGTATTTTTGTTAATTTTGAA 58.182 29.630 0.00 0.00 0.00 2.69
1972 5337 0.686789 TGCTCCTGCTACTTTGCTCA 59.313 50.000 0.00 0.00 40.48 4.26
1981 5346 0.462581 CTCGCCATTTGCTCCTGCTA 60.463 55.000 0.00 0.00 40.48 3.49
1989 5354 2.807878 TTTTTCGCTCGCCATTTGC 58.192 47.368 0.00 0.00 0.00 3.68
2014 5380 0.391228 GAGGCTCTAGGTGCTTAGGC 59.609 60.000 7.40 0.00 39.26 3.93
2019 5385 2.305314 ATCGGGAGGCTCTAGGTGCT 62.305 60.000 15.23 0.00 0.00 4.40
2020 5386 1.811645 GATCGGGAGGCTCTAGGTGC 61.812 65.000 15.23 0.00 0.00 5.01
2041 5408 0.393808 GCCACGGTACCATGGTCAAT 60.394 55.000 26.98 2.47 38.34 2.57
2063 5438 6.400568 CACAAGCATTAATCCTTTGAATGGT 58.599 36.000 9.07 0.00 41.67 3.55
2066 5441 6.290294 AGCACAAGCATTAATCCTTTGAAT 57.710 33.333 9.07 0.00 45.49 2.57
2074 5449 2.223572 CCCGGAAGCACAAGCATTAATC 60.224 50.000 0.73 0.00 45.49 1.75
2096 5471 5.943416 TCACCATTGTACACATCCTTAAAGG 59.057 40.000 0.00 0.00 36.46 3.11
2116 5491 3.003480 GTGGCACTCTTAAGATGTCACC 58.997 50.000 25.87 19.08 41.95 4.02
2137 5512 6.886459 CACCCCCTCAACATTTATCCTATATG 59.114 42.308 0.00 0.00 0.00 1.78
2138 5513 6.797540 TCACCCCCTCAACATTTATCCTATAT 59.202 38.462 0.00 0.00 0.00 0.86
2143 5518 3.288092 GTCACCCCCTCAACATTTATCC 58.712 50.000 0.00 0.00 0.00 2.59
2149 5524 1.352352 CTCTTGTCACCCCCTCAACAT 59.648 52.381 0.00 0.00 0.00 2.71
2150 5525 0.764890 CTCTTGTCACCCCCTCAACA 59.235 55.000 0.00 0.00 0.00 3.33
2163 5538 5.753721 AGCCTTTCTCTACATTCTCTTGT 57.246 39.130 0.00 0.00 0.00 3.16
2164 5539 8.203485 AGATAAGCCTTTCTCTACATTCTCTTG 58.797 37.037 0.00 0.00 0.00 3.02
2165 5540 8.317776 AGATAAGCCTTTCTCTACATTCTCTT 57.682 34.615 0.00 0.00 0.00 2.85
2172 5547 5.361285 GGTGAGAGATAAGCCTTTCTCTACA 59.639 44.000 14.85 12.50 46.67 2.74
2178 5553 4.207891 TGTGGTGAGAGATAAGCCTTTC 57.792 45.455 0.00 0.00 0.00 2.62
2193 5568 3.530265 AGCATGCCAAAATATGTGGTG 57.470 42.857 15.66 1.31 38.50 4.17
2196 5571 7.031226 AGTAACTAGCATGCCAAAATATGTG 57.969 36.000 15.66 0.00 0.00 3.21
2197 5572 8.746052 TTAGTAACTAGCATGCCAAAATATGT 57.254 30.769 15.66 0.00 0.00 2.29
2205 5580 7.161404 CCTTATCATTAGTAACTAGCATGCCA 58.839 38.462 15.66 0.00 0.00 4.92
2206 5581 6.092807 GCCTTATCATTAGTAACTAGCATGCC 59.907 42.308 15.66 0.00 0.00 4.40
2282 5657 6.719370 AGATAGTCTTATCCTAAGCCTGACAG 59.281 42.308 0.00 0.00 37.05 3.51
2318 5705 4.202121 GCTCCATCTCATTTAGGACGTACA 60.202 45.833 0.00 0.00 0.00 2.90
2329 5717 1.911357 TCCTGTGTGCTCCATCTCATT 59.089 47.619 0.00 0.00 0.00 2.57
2347 5735 1.972872 CTGCATAGATGGTTGGGTCC 58.027 55.000 0.00 0.00 0.00 4.46
2351 5739 2.646930 TGAAGCTGCATAGATGGTTGG 58.353 47.619 1.02 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.