Multiple sequence alignment - TraesCS3D01G180600

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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 TraesCS3D01G180600 chr3D 100.000 4724 0 0 1 4724 162845560 162850283 0.000000e+00 8724.0
1 TraesCS3D01G180600 chr3D 97.030 101 2 1 4005 4104 34701590 34701690 8.130000e-38 169.0
2 TraesCS3D01G180600 chr3A 95.737 1384 36 11 3346 4724 195182897 195184262 0.000000e+00 2207.0
3 TraesCS3D01G180600 chr3A 95.871 1114 30 6 783 1895 195171569 195172667 0.000000e+00 1788.0
4 TraesCS3D01G180600 chr3A 98.507 804 11 1 2537 3340 195181899 195182701 0.000000e+00 1417.0
5 TraesCS3D01G180600 chr3A 98.058 618 11 1 1930 2546 195172653 195173270 0.000000e+00 1074.0
6 TraesCS3D01G180600 chr3A 95.455 44 1 1 740 783 195171511 195171553 8.480000e-08 69.4
7 TraesCS3D01G180600 chr3B 98.259 1206 20 1 1930 3134 239883327 239884532 0.000000e+00 2109.0
8 TraesCS3D01G180600 chr3B 95.652 1173 36 10 734 1895 239882173 239883341 0.000000e+00 1869.0
9 TraesCS3D01G180600 chr3B 96.279 1075 25 6 3349 4420 239884589 239885651 0.000000e+00 1749.0
10 TraesCS3D01G180600 chr3B 94.099 322 15 4 4404 4722 239885796 239886116 1.980000e-133 486.0
11 TraesCS3D01G180600 chr6D 91.311 679 39 12 1 670 396520225 396520892 0.000000e+00 909.0
12 TraesCS3D01G180600 chr6D 88.355 687 61 16 1 672 411247974 411248656 0.000000e+00 808.0
13 TraesCS3D01G180600 chr2D 90.909 682 51 10 1 673 34535678 34536357 0.000000e+00 905.0
14 TraesCS3D01G180600 chr2D 90.365 685 48 15 1 672 431918457 431919136 0.000000e+00 883.0
15 TraesCS3D01G180600 chr2D 88.791 678 65 10 1 670 642833633 642834307 0.000000e+00 821.0
16 TraesCS3D01G180600 chr2D 97.436 39 0 1 1899 1937 322968600 322968563 1.100000e-06 65.8
17 TraesCS3D01G180600 chr7D 89.312 683 60 12 1 673 569024438 569023759 0.000000e+00 845.0
18 TraesCS3D01G180600 chr5D 88.743 684 55 20 1 673 315686225 315685553 0.000000e+00 817.0
19 TraesCS3D01G180600 chr5D 88.192 686 60 16 1 672 274783760 274784438 0.000000e+00 798.0
20 TraesCS3D01G180600 chr4D 88.416 682 66 12 1 672 72526048 72526726 0.000000e+00 809.0
21 TraesCS3D01G180600 chr7B 82.292 192 22 8 1043 1229 333406136 333406320 6.330000e-34 156.0
22 TraesCS3D01G180600 chr6A 97.778 45 0 1 1893 1937 61530735 61530778 5.070000e-10 76.8


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 TraesCS3D01G180600 chr3D 162845560 162850283 4723 False 8724.000000 8724 100.000000 1 4724 1 chr3D.!!$F2 4723
1 TraesCS3D01G180600 chr3A 195181899 195184262 2363 False 1812.000000 2207 97.122000 2537 4724 2 chr3A.!!$F2 2187
2 TraesCS3D01G180600 chr3A 195171511 195173270 1759 False 977.133333 1788 96.461333 740 2546 3 chr3A.!!$F1 1806
3 TraesCS3D01G180600 chr3B 239882173 239886116 3943 False 1553.250000 2109 96.072250 734 4722 4 chr3B.!!$F1 3988
4 TraesCS3D01G180600 chr6D 396520225 396520892 667 False 909.000000 909 91.311000 1 670 1 chr6D.!!$F1 669
5 TraesCS3D01G180600 chr6D 411247974 411248656 682 False 808.000000 808 88.355000 1 672 1 chr6D.!!$F2 671
6 TraesCS3D01G180600 chr2D 34535678 34536357 679 False 905.000000 905 90.909000 1 673 1 chr2D.!!$F1 672
7 TraesCS3D01G180600 chr2D 431918457 431919136 679 False 883.000000 883 90.365000 1 672 1 chr2D.!!$F2 671
8 TraesCS3D01G180600 chr2D 642833633 642834307 674 False 821.000000 821 88.791000 1 670 1 chr2D.!!$F3 669
9 TraesCS3D01G180600 chr7D 569023759 569024438 679 True 845.000000 845 89.312000 1 673 1 chr7D.!!$R1 672
10 TraesCS3D01G180600 chr5D 315685553 315686225 672 True 817.000000 817 88.743000 1 673 1 chr5D.!!$R1 672
11 TraesCS3D01G180600 chr5D 274783760 274784438 678 False 798.000000 798 88.192000 1 672 1 chr5D.!!$F1 671
12 TraesCS3D01G180600 chr4D 72526048 72526726 678 False 809.000000 809 88.416000 1 672 1 chr4D.!!$F1 671

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
681 706 0.249120 ATGATTTGGGAGTCGTGCGA 59.751 50.000 0.00 0.0 0.0 5.10 F
683 708 0.652592 GATTTGGGAGTCGTGCGATG 59.347 55.000 0.00 0.0 0.0 3.84 F
872 913 0.673437 CCCACACAAGCCACGAAATT 59.327 50.000 0.00 0.0 0.0 1.82 F
1795 1837 1.144093 ACCAAGGGATCGAACCAAACA 59.856 47.619 14.28 0.0 0.0 2.83 F
1928 1970 0.179048 CCTGGGAGCGTATCATTGCA 60.179 55.000 0.00 0.0 0.0 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1909 1951 0.179048 TGCAATGATACGCTCCCAGG 60.179 55.000 0.0 0.0 0.00 4.45 R
1910 1952 1.888215 ATGCAATGATACGCTCCCAG 58.112 50.000 0.0 0.0 0.00 4.45 R
1911 1953 1.948834 CAATGCAATGATACGCTCCCA 59.051 47.619 0.0 0.0 0.00 4.37 R
3234 3278 3.219176 TGCAATTCCCCTCATCTGATC 57.781 47.619 0.0 0.0 0.00 2.92 R
3894 4129 0.313987 GCCCACAGGTTACACTTTGC 59.686 55.000 0.0 0.0 34.57 3.68 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
180 181 2.039624 AGGTGATGGAGGAGGCGT 59.960 61.111 0.00 0.00 0.00 5.68
259 262 2.815308 GGAGATGGCCGACGATGT 59.185 61.111 0.00 0.00 0.00 3.06
331 334 2.923035 CACGGGAGGAGGTGGTGT 60.923 66.667 0.00 0.00 0.00 4.16
441 446 2.564975 GATGACGACACCGACGGT 59.435 61.111 15.37 15.37 39.50 4.83
470 477 2.432456 GCGACAGCCACGACATCA 60.432 61.111 0.00 0.00 37.42 3.07
479 486 1.305219 CCACGACATCAACGGGCATT 61.305 55.000 0.00 0.00 32.49 3.56
481 488 0.321210 ACGACATCAACGGGCATTGA 60.321 50.000 5.96 5.96 42.62 2.57
484 491 2.083774 GACATCAACGGGCATTGAAGA 58.916 47.619 11.43 0.00 41.78 2.87
485 492 1.812571 ACATCAACGGGCATTGAAGAC 59.187 47.619 11.43 0.00 41.78 3.01
487 494 0.953471 TCAACGGGCATTGAAGACGG 60.953 55.000 1.30 0.00 35.65 4.79
488 495 2.332654 AACGGGCATTGAAGACGGC 61.333 57.895 0.00 0.00 0.00 5.68
489 496 3.864686 CGGGCATTGAAGACGGCG 61.865 66.667 4.80 4.80 0.00 6.46
491 498 3.508840 GGCATTGAAGACGGCGGG 61.509 66.667 13.24 0.00 0.00 6.13
492 499 4.179579 GCATTGAAGACGGCGGGC 62.180 66.667 13.24 2.27 0.00 6.13
493 500 3.508840 CATTGAAGACGGCGGGCC 61.509 66.667 13.24 0.00 0.00 5.80
659 684 7.915293 TTTATCTTAATCACATCCAACACGT 57.085 32.000 0.00 0.00 0.00 4.49
673 698 3.126858 CCAACACGTACATGATTTGGGAG 59.873 47.826 0.00 0.00 31.60 4.30
674 699 3.695830 ACACGTACATGATTTGGGAGT 57.304 42.857 0.00 0.00 0.00 3.85
675 700 3.596214 ACACGTACATGATTTGGGAGTC 58.404 45.455 0.00 0.00 0.00 3.36
676 701 2.603110 CACGTACATGATTTGGGAGTCG 59.397 50.000 0.00 0.00 0.00 4.18
677 702 2.232941 ACGTACATGATTTGGGAGTCGT 59.767 45.455 0.00 0.00 0.00 4.34
678 703 2.603110 CGTACATGATTTGGGAGTCGTG 59.397 50.000 0.00 0.00 37.38 4.35
679 704 1.453155 ACATGATTTGGGAGTCGTGC 58.547 50.000 0.00 0.00 35.31 5.34
680 705 0.374758 CATGATTTGGGAGTCGTGCG 59.625 55.000 0.00 0.00 0.00 5.34
681 706 0.249120 ATGATTTGGGAGTCGTGCGA 59.751 50.000 0.00 0.00 0.00 5.10
682 707 0.249120 TGATTTGGGAGTCGTGCGAT 59.751 50.000 0.00 0.00 0.00 4.58
683 708 0.652592 GATTTGGGAGTCGTGCGATG 59.347 55.000 0.00 0.00 0.00 3.84
684 709 0.744414 ATTTGGGAGTCGTGCGATGG 60.744 55.000 0.00 0.00 0.00 3.51
685 710 1.822114 TTTGGGAGTCGTGCGATGGA 61.822 55.000 0.00 0.00 0.00 3.41
686 711 2.105128 GGGAGTCGTGCGATGGAG 59.895 66.667 0.00 0.00 0.00 3.86
687 712 2.711922 GGGAGTCGTGCGATGGAGT 61.712 63.158 0.00 0.00 0.00 3.85
688 713 1.226717 GGAGTCGTGCGATGGAGTC 60.227 63.158 0.00 0.00 32.94 3.36
696 721 4.303853 CGATGGAGTCGGCGTAAG 57.696 61.111 6.85 0.00 46.47 2.34
710 735 1.878953 CGTAAGCAACTTGGACCAGT 58.121 50.000 0.00 0.00 0.00 4.00
711 736 3.034721 CGTAAGCAACTTGGACCAGTA 57.965 47.619 0.00 0.00 0.00 2.74
712 737 3.395639 CGTAAGCAACTTGGACCAGTAA 58.604 45.455 0.00 0.00 0.00 2.24
713 738 3.810941 CGTAAGCAACTTGGACCAGTAAA 59.189 43.478 0.00 0.00 0.00 2.01
714 739 4.454504 CGTAAGCAACTTGGACCAGTAAAT 59.545 41.667 0.00 0.00 0.00 1.40
715 740 4.853924 AAGCAACTTGGACCAGTAAATG 57.146 40.909 0.00 0.00 0.00 2.32
716 741 2.558359 AGCAACTTGGACCAGTAAATGC 59.442 45.455 10.19 10.19 0.00 3.56
717 742 2.295909 GCAACTTGGACCAGTAAATGCA 59.704 45.455 12.24 0.00 0.00 3.96
718 743 3.056607 GCAACTTGGACCAGTAAATGCAT 60.057 43.478 12.24 0.00 0.00 3.96
719 744 4.157656 GCAACTTGGACCAGTAAATGCATA 59.842 41.667 0.00 0.00 0.00 3.14
720 745 5.163519 GCAACTTGGACCAGTAAATGCATAT 60.164 40.000 0.00 0.00 0.00 1.78
721 746 6.267817 CAACTTGGACCAGTAAATGCATATG 58.732 40.000 0.00 0.00 0.00 1.78
722 747 4.339247 ACTTGGACCAGTAAATGCATATGC 59.661 41.667 21.09 21.09 42.50 3.14
723 748 2.877786 TGGACCAGTAAATGCATATGCG 59.122 45.455 22.21 8.17 45.83 4.73
724 749 2.226437 GGACCAGTAAATGCATATGCGG 59.774 50.000 22.21 16.82 45.83 5.69
725 750 1.608590 ACCAGTAAATGCATATGCGGC 59.391 47.619 22.21 10.25 45.83 6.53
726 751 1.608109 CCAGTAAATGCATATGCGGCA 59.392 47.619 22.21 4.58 46.66 5.69
727 752 2.351060 CCAGTAAATGCATATGCGGCAG 60.351 50.000 22.21 8.42 45.68 4.85
728 753 2.291465 CAGTAAATGCATATGCGGCAGT 59.709 45.455 22.21 7.87 45.68 4.40
729 754 2.549754 AGTAAATGCATATGCGGCAGTC 59.450 45.455 22.21 10.95 45.68 3.51
730 755 1.683943 AAATGCATATGCGGCAGTCT 58.316 45.000 22.21 0.00 45.68 3.24
731 756 1.683943 AATGCATATGCGGCAGTCTT 58.316 45.000 22.21 4.84 45.68 3.01
732 757 1.233019 ATGCATATGCGGCAGTCTTC 58.767 50.000 22.21 0.00 45.68 2.87
872 913 0.673437 CCCACACAAGCCACGAAATT 59.327 50.000 0.00 0.00 0.00 1.82
943 984 3.274067 CGCAAGCTACCCCCAAAC 58.726 61.111 0.00 0.00 0.00 2.93
954 995 1.692428 CCCCAAACCCACCGGATAA 59.308 57.895 9.46 0.00 0.00 1.75
958 999 2.424234 CCCAAACCCACCGGATAATCAT 60.424 50.000 9.46 0.00 0.00 2.45
959 1000 2.884639 CCAAACCCACCGGATAATCATC 59.115 50.000 9.46 0.00 0.00 2.92
968 1009 1.168714 GGATAATCATCCCTTGCGCC 58.831 55.000 4.18 0.00 44.55 6.53
1266 1308 4.813526 CTCGTCGGCGACCTCGTG 62.814 72.222 31.86 18.61 42.81 4.35
1368 1410 3.192212 GCTCCTTGCTAAGATTGCTGTTT 59.808 43.478 0.00 0.00 38.95 2.83
1369 1411 4.673841 GCTCCTTGCTAAGATTGCTGTTTC 60.674 45.833 0.00 0.00 38.95 2.78
1405 1447 1.525077 GCAGGTGTTCGTGGTTGGA 60.525 57.895 0.00 0.00 0.00 3.53
1706 1748 1.520590 CGTGGCAAAACAATTGAACCG 59.479 47.619 13.59 0.00 0.00 4.44
1733 1775 6.550843 TCATAGTTGTTGGCATAATTTCGTG 58.449 36.000 0.00 0.00 0.00 4.35
1795 1837 1.144093 ACCAAGGGATCGAACCAAACA 59.856 47.619 14.28 0.00 0.00 2.83
1891 1933 6.681729 TTAGATTGGAGGTTGAGTAGTGTT 57.318 37.500 0.00 0.00 0.00 3.32
1892 1934 5.568620 AGATTGGAGGTTGAGTAGTGTTT 57.431 39.130 0.00 0.00 0.00 2.83
1893 1935 5.941788 AGATTGGAGGTTGAGTAGTGTTTT 58.058 37.500 0.00 0.00 0.00 2.43
1894 1936 6.365520 AGATTGGAGGTTGAGTAGTGTTTTT 58.634 36.000 0.00 0.00 0.00 1.94
1914 1956 2.122783 TTTTCTCCAATACGCCTGGG 57.877 50.000 0.00 0.00 34.46 4.45
1915 1957 1.281419 TTTCTCCAATACGCCTGGGA 58.719 50.000 0.00 0.00 34.46 4.37
1916 1958 0.830648 TTCTCCAATACGCCTGGGAG 59.169 55.000 7.30 7.30 46.61 4.30
1917 1959 1.227674 CTCCAATACGCCTGGGAGC 60.228 63.158 0.00 0.00 40.37 4.70
1926 1968 2.621763 GCCTGGGAGCGTATCATTG 58.378 57.895 0.00 0.00 0.00 2.82
1927 1969 1.510480 GCCTGGGAGCGTATCATTGC 61.510 60.000 0.00 0.00 0.00 3.56
1928 1970 0.179048 CCTGGGAGCGTATCATTGCA 60.179 55.000 0.00 0.00 0.00 4.08
1929 1971 1.544093 CCTGGGAGCGTATCATTGCAT 60.544 52.381 0.00 0.00 0.00 3.96
1930 1972 2.224606 CTGGGAGCGTATCATTGCATT 58.775 47.619 0.00 0.00 0.00 3.56
1931 1973 1.948834 TGGGAGCGTATCATTGCATTG 59.051 47.619 2.08 2.08 0.00 2.82
1932 1974 2.221169 GGGAGCGTATCATTGCATTGA 58.779 47.619 13.30 13.30 0.00 2.57
1933 1975 2.225019 GGGAGCGTATCATTGCATTGAG 59.775 50.000 15.80 5.01 0.00 3.02
1934 1976 2.874701 GGAGCGTATCATTGCATTGAGT 59.125 45.455 15.80 7.74 0.00 3.41
1935 1977 4.058124 GGAGCGTATCATTGCATTGAGTA 58.942 43.478 15.80 6.94 0.00 2.59
1936 1978 4.151335 GGAGCGTATCATTGCATTGAGTAG 59.849 45.833 15.80 10.30 0.00 2.57
1937 1979 4.697514 AGCGTATCATTGCATTGAGTAGT 58.302 39.130 15.80 3.12 0.00 2.73
1938 1980 4.509230 AGCGTATCATTGCATTGAGTAGTG 59.491 41.667 15.80 6.21 0.00 2.74
1939 1981 4.271049 GCGTATCATTGCATTGAGTAGTGT 59.729 41.667 15.80 2.15 0.00 3.55
2522 2565 5.424121 AAACATCTCTGTAACAAGCACAC 57.576 39.130 0.00 0.00 33.36 3.82
2740 2784 6.995686 AGTATCTCCTGACACAGTACTAGATG 59.004 42.308 9.72 5.42 0.00 2.90
2872 2916 2.125350 CCTGGAGTCGCTGAAGCC 60.125 66.667 0.00 0.00 37.91 4.35
3140 3184 8.617809 TCTCACTGTCTTGGTTTTACAATTTAC 58.382 33.333 0.00 0.00 0.00 2.01
3214 3258 6.247727 ACTGATGATATACTCTGTACTGCG 57.752 41.667 0.00 0.00 0.00 5.18
3234 3278 4.143200 TGCGTAACTTTATGCTTTCGAGTG 60.143 41.667 13.09 0.00 44.10 3.51
3297 3341 6.375455 CGTAACCTACAAAGACTAGGAACCTA 59.625 42.308 0.00 0.50 35.23 3.08
3753 3988 1.031029 AGAGTCTCGGCGAACCTACC 61.031 60.000 12.13 0.00 0.00 3.18
3763 3998 1.875157 GCGAACCTACCTGTTTCGGTT 60.875 52.381 5.24 0.00 42.11 4.44
3812 4047 6.827762 TGATTACACATGCCATGATACTGAAA 59.172 34.615 12.53 0.00 0.00 2.69
3855 4090 6.768483 TGGTCTGATTGTCACAGAAGAATTA 58.232 36.000 0.00 0.00 44.29 1.40
3894 4129 1.839994 TCCTGTTTCTATGCAGAGGGG 59.160 52.381 8.78 4.05 34.87 4.79
3999 4236 0.402121 GGGCTGTCTTTTGGACCTCT 59.598 55.000 0.00 0.00 43.89 3.69
4394 4632 4.697352 AGTAGTTGATGAACATGCTGAACC 59.303 41.667 0.00 0.00 34.17 3.62
4420 4658 7.305475 CGCGAGTAACTTCACATTGTAGAATAG 60.305 40.741 0.00 0.00 0.00 1.73
4421 4659 7.515371 GCGAGTAACTTCACATTGTAGAATAGC 60.515 40.741 0.00 0.00 0.00 2.97
4422 4660 7.305475 CGAGTAACTTCACATTGTAGAATAGCG 60.305 40.741 0.00 0.00 0.00 4.26
4424 4662 3.871594 ACTTCACATTGTAGAATAGCGCC 59.128 43.478 2.29 0.00 0.00 6.53
4425 4663 3.819564 TCACATTGTAGAATAGCGCCT 57.180 42.857 2.29 0.00 0.00 5.52
4501 4899 3.924073 GCGTTGTTCACTGGTTTTCTTTT 59.076 39.130 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
256 257 0.612732 CACCAGTTCATGCCCCACAT 60.613 55.000 0.00 0.00 40.66 3.21
259 262 2.283101 GCACCAGTTCATGCCCCA 60.283 61.111 0.00 0.00 35.73 4.96
426 430 2.901339 TGACCGTCGGTGTCGTCA 60.901 61.111 24.45 10.38 35.25 4.35
441 446 1.285950 CTGTCGCCGTCTTCAGTGA 59.714 57.895 0.00 0.00 0.00 3.41
470 477 2.332654 GCCGTCTTCAATGCCCGTT 61.333 57.895 0.00 0.00 0.00 4.44
635 660 7.915293 ACGTGTTGGATGTGATTAAGATAAA 57.085 32.000 0.00 0.00 0.00 1.40
640 665 6.312672 TCATGTACGTGTTGGATGTGATTAAG 59.687 38.462 14.63 0.00 0.00 1.85
649 674 3.694072 CCCAAATCATGTACGTGTTGGAT 59.306 43.478 27.24 9.33 38.20 3.41
659 684 2.627945 GCACGACTCCCAAATCATGTA 58.372 47.619 0.00 0.00 0.00 2.29
680 705 0.459585 TTGCTTACGCCGACTCCATC 60.460 55.000 0.00 0.00 34.43 3.51
681 706 0.739813 GTTGCTTACGCCGACTCCAT 60.740 55.000 0.00 0.00 34.43 3.41
682 707 1.373748 GTTGCTTACGCCGACTCCA 60.374 57.895 0.00 0.00 34.43 3.86
683 708 0.669625 AAGTTGCTTACGCCGACTCC 60.670 55.000 0.00 0.00 32.50 3.85
684 709 0.438830 CAAGTTGCTTACGCCGACTC 59.561 55.000 0.00 0.00 32.50 3.36
685 710 0.949105 CCAAGTTGCTTACGCCGACT 60.949 55.000 0.00 0.00 34.32 4.18
686 711 0.947180 TCCAAGTTGCTTACGCCGAC 60.947 55.000 0.00 0.00 34.43 4.79
687 712 0.947180 GTCCAAGTTGCTTACGCCGA 60.947 55.000 0.00 0.00 34.43 5.54
688 713 1.495951 GTCCAAGTTGCTTACGCCG 59.504 57.895 0.00 0.00 34.43 6.46
689 714 0.887387 TGGTCCAAGTTGCTTACGCC 60.887 55.000 0.00 0.00 34.43 5.68
690 715 0.517316 CTGGTCCAAGTTGCTTACGC 59.483 55.000 0.00 0.00 0.00 4.42
691 716 1.878953 ACTGGTCCAAGTTGCTTACG 58.121 50.000 0.00 0.00 0.00 3.18
692 717 5.699839 CATTTACTGGTCCAAGTTGCTTAC 58.300 41.667 0.00 0.00 0.00 2.34
693 718 4.217550 GCATTTACTGGTCCAAGTTGCTTA 59.782 41.667 0.00 0.00 31.60 3.09
694 719 3.005791 GCATTTACTGGTCCAAGTTGCTT 59.994 43.478 0.00 0.00 31.60 3.91
695 720 2.558359 GCATTTACTGGTCCAAGTTGCT 59.442 45.455 0.00 0.00 31.60 3.91
696 721 2.295909 TGCATTTACTGGTCCAAGTTGC 59.704 45.455 0.00 2.03 33.80 4.17
697 722 4.789012 ATGCATTTACTGGTCCAAGTTG 57.211 40.909 0.00 0.00 0.00 3.16
698 723 5.163519 GCATATGCATTTACTGGTCCAAGTT 60.164 40.000 22.84 0.00 41.59 2.66
699 724 4.339247 GCATATGCATTTACTGGTCCAAGT 59.661 41.667 22.84 0.00 41.59 3.16
700 725 4.555313 CGCATATGCATTTACTGGTCCAAG 60.555 45.833 26.52 1.35 42.21 3.61
701 726 3.314913 CGCATATGCATTTACTGGTCCAA 59.685 43.478 26.52 0.00 42.21 3.53
702 727 2.877786 CGCATATGCATTTACTGGTCCA 59.122 45.455 26.52 0.00 42.21 4.02
703 728 2.226437 CCGCATATGCATTTACTGGTCC 59.774 50.000 26.52 0.00 42.21 4.46
704 729 2.350772 GCCGCATATGCATTTACTGGTC 60.351 50.000 26.52 10.32 42.21 4.02
705 730 1.608590 GCCGCATATGCATTTACTGGT 59.391 47.619 26.52 0.00 42.21 4.00
706 731 1.608109 TGCCGCATATGCATTTACTGG 59.392 47.619 26.52 17.83 42.21 4.00
707 732 2.291465 ACTGCCGCATATGCATTTACTG 59.709 45.455 26.52 15.33 42.21 2.74
708 733 2.549754 GACTGCCGCATATGCATTTACT 59.450 45.455 26.52 4.61 42.21 2.24
709 734 2.549754 AGACTGCCGCATATGCATTTAC 59.450 45.455 26.52 12.75 42.21 2.01
710 735 2.849942 AGACTGCCGCATATGCATTTA 58.150 42.857 26.52 9.25 42.21 1.40
711 736 1.683943 AGACTGCCGCATATGCATTT 58.316 45.000 26.52 6.27 42.21 2.32
712 737 1.605710 GAAGACTGCCGCATATGCATT 59.394 47.619 26.52 9.30 42.21 3.56
713 738 1.233019 GAAGACTGCCGCATATGCAT 58.767 50.000 26.52 3.79 42.21 3.96
714 739 0.107752 TGAAGACTGCCGCATATGCA 60.108 50.000 26.52 7.26 42.21 3.96
715 740 1.003116 CTTGAAGACTGCCGCATATGC 60.003 52.381 18.08 18.08 37.78 3.14
716 741 2.283298 ACTTGAAGACTGCCGCATATG 58.717 47.619 0.00 0.00 0.00 1.78
717 742 2.169352 AGACTTGAAGACTGCCGCATAT 59.831 45.455 0.00 0.00 0.00 1.78
718 743 1.550524 AGACTTGAAGACTGCCGCATA 59.449 47.619 0.00 0.00 0.00 3.14
719 744 0.322975 AGACTTGAAGACTGCCGCAT 59.677 50.000 0.00 0.00 0.00 4.73
720 745 0.966179 TAGACTTGAAGACTGCCGCA 59.034 50.000 7.42 0.00 0.00 5.69
721 746 1.351153 GTAGACTTGAAGACTGCCGC 58.649 55.000 7.42 0.00 0.00 6.53
722 747 1.199327 TCGTAGACTTGAAGACTGCCG 59.801 52.381 7.42 9.20 0.00 5.69
723 748 2.987821 GTTCGTAGACTTGAAGACTGCC 59.012 50.000 7.42 0.00 34.32 4.85
724 749 2.657372 CGTTCGTAGACTTGAAGACTGC 59.343 50.000 7.42 5.16 34.32 4.40
725 750 3.907194 GTCGTTCGTAGACTTGAAGACTG 59.093 47.826 7.42 0.00 34.32 3.51
726 751 3.363772 CGTCGTTCGTAGACTTGAAGACT 60.364 47.826 0.00 0.00 34.32 3.24
727 752 2.901264 CGTCGTTCGTAGACTTGAAGAC 59.099 50.000 0.00 0.00 34.32 3.01
728 753 2.802247 TCGTCGTTCGTAGACTTGAAGA 59.198 45.455 0.00 0.00 40.80 2.87
729 754 3.154489 CTCGTCGTTCGTAGACTTGAAG 58.846 50.000 0.00 0.00 40.80 3.02
730 755 2.096069 CCTCGTCGTTCGTAGACTTGAA 60.096 50.000 0.00 0.00 40.80 2.69
731 756 1.462283 CCTCGTCGTTCGTAGACTTGA 59.538 52.381 0.00 0.00 40.80 3.02
732 757 1.462283 TCCTCGTCGTTCGTAGACTTG 59.538 52.381 0.00 0.66 40.80 3.16
856 897 1.531149 CGAGAATTTCGTGGCTTGTGT 59.469 47.619 2.97 0.00 44.27 3.72
872 913 4.143333 GTGGCTAAGCGGGCGAGA 62.143 66.667 0.00 0.00 34.31 4.04
881 922 2.393768 CGCTGGCTGTGTGGCTAAG 61.394 63.158 0.00 0.00 42.34 2.18
930 971 2.544745 GGTGGGTTTGGGGGTAGCT 61.545 63.158 0.00 0.00 0.00 3.32
937 978 1.064314 TGATTATCCGGTGGGTTTGGG 60.064 52.381 0.00 0.00 33.83 4.12
1368 1410 3.449227 ACGCGAGCCCGAGAATGA 61.449 61.111 15.93 0.00 38.94 2.57
1369 1411 3.257561 CACGCGAGCCCGAGAATG 61.258 66.667 15.93 0.00 38.94 2.67
1706 1748 6.472163 CGAAATTATGCCAACAACTATGAACC 59.528 38.462 0.00 0.00 0.00 3.62
1795 1837 6.821665 TGGAATTCCGAAGTTCGAATAATCTT 59.178 34.615 26.37 9.46 43.74 2.40
1870 1912 5.568620 AAACACTACTCAACCTCCAATCT 57.431 39.130 0.00 0.00 0.00 2.40
1894 1936 2.040545 TCCCAGGCGTATTGGAGAAAAA 59.959 45.455 3.93 0.00 37.96 1.94
1895 1937 1.631388 TCCCAGGCGTATTGGAGAAAA 59.369 47.619 3.93 0.00 37.96 2.29
1896 1938 1.209504 CTCCCAGGCGTATTGGAGAAA 59.790 52.381 11.42 0.00 45.93 2.52
1897 1939 0.830648 CTCCCAGGCGTATTGGAGAA 59.169 55.000 11.42 0.00 45.93 2.87
1898 1940 1.686325 GCTCCCAGGCGTATTGGAGA 61.686 60.000 17.98 5.62 45.93 3.71
1899 1941 1.227674 GCTCCCAGGCGTATTGGAG 60.228 63.158 12.17 12.17 45.83 3.86
1900 1942 2.908015 GCTCCCAGGCGTATTGGA 59.092 61.111 3.93 0.00 37.96 3.53
1908 1950 1.510480 GCAATGATACGCTCCCAGGC 61.510 60.000 0.00 0.00 0.00 4.85
1909 1951 0.179048 TGCAATGATACGCTCCCAGG 60.179 55.000 0.00 0.00 0.00 4.45
1910 1952 1.888215 ATGCAATGATACGCTCCCAG 58.112 50.000 0.00 0.00 0.00 4.45
1911 1953 1.948834 CAATGCAATGATACGCTCCCA 59.051 47.619 0.00 0.00 0.00 4.37
1912 1954 2.221169 TCAATGCAATGATACGCTCCC 58.779 47.619 0.00 0.00 0.00 4.30
1913 1955 2.874701 ACTCAATGCAATGATACGCTCC 59.125 45.455 4.61 0.00 0.00 4.70
1914 1956 4.747108 ACTACTCAATGCAATGATACGCTC 59.253 41.667 4.61 0.00 0.00 5.03
1915 1957 4.509230 CACTACTCAATGCAATGATACGCT 59.491 41.667 4.61 0.00 0.00 5.07
1916 1958 4.271049 ACACTACTCAATGCAATGATACGC 59.729 41.667 4.61 0.00 0.00 4.42
1917 1959 5.973651 ACACTACTCAATGCAATGATACG 57.026 39.130 4.61 0.00 0.00 3.06
1918 1960 8.970691 AAAAACACTACTCAATGCAATGATAC 57.029 30.769 4.61 0.00 0.00 2.24
1919 1961 8.791675 TGAAAAACACTACTCAATGCAATGATA 58.208 29.630 4.61 0.05 0.00 2.15
1920 1962 7.596248 GTGAAAAACACTACTCAATGCAATGAT 59.404 33.333 4.61 0.00 45.13 2.45
1921 1963 6.917477 GTGAAAAACACTACTCAATGCAATGA 59.083 34.615 4.04 4.04 45.13 2.57
1922 1964 7.097342 GTGAAAAACACTACTCAATGCAATG 57.903 36.000 0.00 0.00 45.13 2.82
2101 2144 6.747414 AGGACATAGGTGTAATTGCATAGA 57.253 37.500 0.00 0.00 39.09 1.98
2652 2696 3.486383 ACTCGAAAAAGAAATCCAGGCA 58.514 40.909 0.00 0.00 0.00 4.75
2740 2784 9.840427 TCTAAGAATAAGCAATTAAACAGCAAC 57.160 29.630 0.00 0.00 0.00 4.17
2872 2916 7.378728 TGACTATTGTCGTATAGAGCAAATTCG 59.621 37.037 2.86 0.00 45.70 3.34
3140 3184 8.345565 CCTGGCTAACATTAGTAAATAAAGCAG 58.654 37.037 10.80 0.00 33.32 4.24
3214 3258 7.275779 TCTGATCACTCGAAAGCATAAAGTTAC 59.724 37.037 0.00 0.00 0.00 2.50
3234 3278 3.219176 TGCAATTCCCCTCATCTGATC 57.781 47.619 0.00 0.00 0.00 2.92
3297 3341 5.531634 CATGTTTCTGTACATTTTGCCACT 58.468 37.500 0.00 0.00 36.64 4.00
3753 3988 6.780706 AGTACATAAACAGAACCGAAACAG 57.219 37.500 0.00 0.00 0.00 3.16
3787 4022 5.927819 TCAGTATCATGGCATGTGTAATCA 58.072 37.500 25.62 6.31 0.00 2.57
3812 4047 9.753674 TCAGACCATGGTTTTATTTAGAGAAAT 57.246 29.630 20.85 0.00 38.79 2.17
3855 4090 3.392616 AGGAGGACATGAAAGTTCACAGT 59.607 43.478 0.00 0.00 40.49 3.55
3865 4100 4.019411 TGCATAGAAACAGGAGGACATGAA 60.019 41.667 0.00 0.00 0.00 2.57
3894 4129 0.313987 GCCCACAGGTTACACTTTGC 59.686 55.000 0.00 0.00 34.57 3.68
3965 4201 5.501156 AGACAGCCCGAATAAAGAAGAAAT 58.499 37.500 0.00 0.00 0.00 2.17
4394 4632 4.163552 TCTACAATGTGAAGTTACTCGCG 58.836 43.478 0.00 0.00 0.00 5.87
4694 5096 9.936759 AAAATACACGGACATTTATTGGAAAAT 57.063 25.926 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.