Multiple sequence alignment - TraesCS7A01G378300

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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 TraesCS7A01G378300 chr7A 100.000 3728 0 0 1 3728 553745690 553749417 0.000000e+00 6885
1 TraesCS7A01G378300 chr7B 90.660 3062 147 62 737 3728 513240011 513243003 0.000000e+00 3941
2 TraesCS7A01G378300 chr7D 90.508 3034 159 49 755 3728 485515335 485518299 0.000000e+00 3888
3 TraesCS7A01G378300 chr7D 82.496 697 70 17 1 662 587304686 587304007 6.990000e-157 564
4 TraesCS7A01G378300 chr7D 79.325 711 75 42 1 662 20626744 20626057 2.060000e-117 433
5 TraesCS7A01G378300 chr7D 88.462 156 12 1 1 150 7291384 7291539 2.290000e-42 183
6 TraesCS7A01G378300 chr7D 77.684 354 44 22 1 331 17254110 17253769 2.290000e-42 183
7 TraesCS7A01G378300 chr4D 84.069 634 74 11 55 663 312570629 312569998 1.490000e-163 586
8 TraesCS7A01G378300 chr4D 87.879 132 10 4 11 142 312570697 312570572 2.320000e-32 150
9 TraesCS7A01G378300 chr3D 82.634 691 71 16 1 658 478659440 478660114 1.940000e-157 566
10 TraesCS7A01G378300 chr3D 82.371 641 70 18 55 661 474537828 474537197 5.520000e-143 518
11 TraesCS7A01G378300 chr3D 79.495 673 81 30 1 663 586432977 586432352 3.440000e-115 425
12 TraesCS7A01G378300 chr3D 78.247 616 81 21 1 574 434952878 434953482 2.760000e-91 346
13 TraesCS7A01G378300 chr2B 81.977 688 85 15 9 662 74332269 74332951 7.040000e-152 547
14 TraesCS7A01G378300 chr6D 82.942 639 63 28 1 606 148480295 148479670 5.480000e-148 534
15 TraesCS7A01G378300 chr3B 81.476 637 87 21 1 624 530558022 530558640 9.300000e-136 494
16 TraesCS7A01G378300 chr5B 82.586 580 64 23 109 668 26441390 26441952 9.370000e-131 477
17 TraesCS7A01G378300 chr3A 78.784 707 86 29 2 661 743498744 743499433 2.070000e-112 416
18 TraesCS7A01G378300 chr2D 78.507 670 84 33 27 662 47007723 47007080 5.840000e-103 385
19 TraesCS7A01G378300 chr5D 81.702 470 44 9 1 437 437243279 437242819 1.650000e-93 353
20 TraesCS7A01G378300 chr5A 78.795 415 57 14 11 394 414715008 414714594 2.220000e-62 250
21 TraesCS7A01G378300 chrUn 84.076 157 18 5 1 151 22865508 22865353 1.080000e-30 145


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 TraesCS7A01G378300 chr7A 553745690 553749417 3727 False 6885 6885 100.000 1 3728 1 chr7A.!!$F1 3727
1 TraesCS7A01G378300 chr7B 513240011 513243003 2992 False 3941 3941 90.660 737 3728 1 chr7B.!!$F1 2991
2 TraesCS7A01G378300 chr7D 485515335 485518299 2964 False 3888 3888 90.508 755 3728 1 chr7D.!!$F2 2973
3 TraesCS7A01G378300 chr7D 587304007 587304686 679 True 564 564 82.496 1 662 1 chr7D.!!$R3 661
4 TraesCS7A01G378300 chr7D 20626057 20626744 687 True 433 433 79.325 1 662 1 chr7D.!!$R2 661
5 TraesCS7A01G378300 chr4D 312569998 312570697 699 True 368 586 85.974 11 663 2 chr4D.!!$R1 652
6 TraesCS7A01G378300 chr3D 478659440 478660114 674 False 566 566 82.634 1 658 1 chr3D.!!$F2 657
7 TraesCS7A01G378300 chr3D 474537197 474537828 631 True 518 518 82.371 55 661 1 chr3D.!!$R1 606
8 TraesCS7A01G378300 chr3D 586432352 586432977 625 True 425 425 79.495 1 663 1 chr3D.!!$R2 662
9 TraesCS7A01G378300 chr3D 434952878 434953482 604 False 346 346 78.247 1 574 1 chr3D.!!$F1 573
10 TraesCS7A01G378300 chr2B 74332269 74332951 682 False 547 547 81.977 9 662 1 chr2B.!!$F1 653
11 TraesCS7A01G378300 chr6D 148479670 148480295 625 True 534 534 82.942 1 606 1 chr6D.!!$R1 605
12 TraesCS7A01G378300 chr3B 530558022 530558640 618 False 494 494 81.476 1 624 1 chr3B.!!$F1 623
13 TraesCS7A01G378300 chr5B 26441390 26441952 562 False 477 477 82.586 109 668 1 chr5B.!!$F1 559
14 TraesCS7A01G378300 chr3A 743498744 743499433 689 False 416 416 78.784 2 661 1 chr3A.!!$F1 659
15 TraesCS7A01G378300 chr2D 47007080 47007723 643 True 385 385 78.507 27 662 1 chr2D.!!$R1 635

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
687 865 0.032952 ACGTGTTCGCAGGCTCTAAA 59.967 50.0 0.0 0.0 41.18 1.85 F
1444 1626 0.104777 TCCCTGCCATGCCTAGATCT 60.105 55.0 0.0 0.0 0.00 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2233 2483 0.037303 AACACCTGCACATGAGAGGG 59.963 55.0 0.0 0.0 0.0 4.30 R
2916 3175 0.895100 TGCCATCTGTTGCCACTTCC 60.895 55.0 0.0 0.0 0.0 3.46 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
18 19 3.797353 ATCAATGAGGGCGGGCGT 61.797 61.111 0.00 0.00 0.00 5.68
127 188 1.909141 GAAGACGGAGCTCGACGACA 61.909 60.000 17.62 0.00 42.43 4.35
130 191 4.086178 CGGAGCTCGACGACACGT 62.086 66.667 7.83 0.00 45.10 4.49
184 269 4.295119 AACGCCTCGCCAGTTCGT 62.295 61.111 0.00 0.00 34.63 3.85
388 515 1.429148 CTCAGCGTGTTATTCGGCCC 61.429 60.000 0.00 0.00 0.00 5.80
408 535 2.273179 TAGTCGCGGCCTCTTGTGT 61.273 57.895 7.31 0.00 0.00 3.72
409 536 0.961857 TAGTCGCGGCCTCTTGTGTA 60.962 55.000 7.31 0.00 0.00 2.90
458 604 1.369625 AAGCTATTTCAGTTCGCCGG 58.630 50.000 0.00 0.00 0.00 6.13
489 657 3.754323 TGTTTCGCCGAATATTTTGTCCT 59.246 39.130 0.00 0.00 0.00 3.85
493 661 6.687081 TTCGCCGAATATTTTGTCCTATTT 57.313 33.333 0.00 0.00 0.00 1.40
663 841 1.279271 ACGGCTGGAGATGCTTTAACT 59.721 47.619 0.00 0.00 0.00 2.24
668 846 2.981859 GGAGATGCTTTAACTCCGGA 57.018 50.000 2.93 2.93 40.28 5.14
669 847 2.552031 GGAGATGCTTTAACTCCGGAC 58.448 52.381 0.00 0.00 40.28 4.79
670 848 2.194271 GAGATGCTTTAACTCCGGACG 58.806 52.381 0.00 0.00 0.00 4.79
671 849 1.549170 AGATGCTTTAACTCCGGACGT 59.451 47.619 0.00 0.00 0.00 4.34
672 850 1.659098 GATGCTTTAACTCCGGACGTG 59.341 52.381 0.00 0.00 0.00 4.49
673 851 0.390124 TGCTTTAACTCCGGACGTGT 59.610 50.000 0.00 0.00 0.00 4.49
674 852 1.202557 TGCTTTAACTCCGGACGTGTT 60.203 47.619 11.79 11.79 0.00 3.32
675 853 1.458445 GCTTTAACTCCGGACGTGTTC 59.542 52.381 10.57 0.00 0.00 3.18
676 854 1.717645 CTTTAACTCCGGACGTGTTCG 59.282 52.381 10.57 0.00 43.34 3.95
677 855 0.664166 TTAACTCCGGACGTGTTCGC 60.664 55.000 10.57 0.00 41.18 4.70
678 856 1.794151 TAACTCCGGACGTGTTCGCA 61.794 55.000 10.57 0.00 41.18 5.10
679 857 2.805353 CTCCGGACGTGTTCGCAG 60.805 66.667 0.00 0.00 41.18 5.18
680 858 4.351938 TCCGGACGTGTTCGCAGG 62.352 66.667 0.00 0.00 41.18 4.85
683 861 3.112709 GGACGTGTTCGCAGGCTC 61.113 66.667 0.00 0.00 41.18 4.70
684 862 2.049063 GACGTGTTCGCAGGCTCT 60.049 61.111 0.00 0.00 41.18 4.09
685 863 1.211969 GACGTGTTCGCAGGCTCTA 59.788 57.895 0.00 0.00 41.18 2.43
686 864 0.388134 GACGTGTTCGCAGGCTCTAA 60.388 55.000 0.00 0.00 41.18 2.10
687 865 0.032952 ACGTGTTCGCAGGCTCTAAA 59.967 50.000 0.00 0.00 41.18 1.85
688 866 1.144969 CGTGTTCGCAGGCTCTAAAA 58.855 50.000 0.00 0.00 0.00 1.52
689 867 1.732259 CGTGTTCGCAGGCTCTAAAAT 59.268 47.619 0.00 0.00 0.00 1.82
690 868 2.474526 CGTGTTCGCAGGCTCTAAAATG 60.475 50.000 0.00 0.00 0.00 2.32
691 869 2.742053 GTGTTCGCAGGCTCTAAAATGA 59.258 45.455 0.00 0.00 0.00 2.57
692 870 2.742053 TGTTCGCAGGCTCTAAAATGAC 59.258 45.455 0.00 0.00 0.00 3.06
693 871 2.742053 GTTCGCAGGCTCTAAAATGACA 59.258 45.455 0.00 0.00 0.00 3.58
694 872 3.052455 TCGCAGGCTCTAAAATGACAA 57.948 42.857 0.00 0.00 0.00 3.18
695 873 3.407698 TCGCAGGCTCTAAAATGACAAA 58.592 40.909 0.00 0.00 0.00 2.83
696 874 4.009675 TCGCAGGCTCTAAAATGACAAAT 58.990 39.130 0.00 0.00 0.00 2.32
697 875 5.182487 TCGCAGGCTCTAAAATGACAAATA 58.818 37.500 0.00 0.00 0.00 1.40
698 876 5.822519 TCGCAGGCTCTAAAATGACAAATAT 59.177 36.000 0.00 0.00 0.00 1.28
699 877 6.318648 TCGCAGGCTCTAAAATGACAAATATT 59.681 34.615 0.00 0.00 0.00 1.28
700 878 6.974622 CGCAGGCTCTAAAATGACAAATATTT 59.025 34.615 0.00 0.00 0.00 1.40
701 879 8.128582 CGCAGGCTCTAAAATGACAAATATTTA 58.871 33.333 0.00 0.00 0.00 1.40
702 880 9.455847 GCAGGCTCTAAAATGACAAATATTTAG 57.544 33.333 0.00 0.00 36.93 1.85
703 881 9.956720 CAGGCTCTAAAATGACAAATATTTAGG 57.043 33.333 0.00 0.00 36.48 2.69
704 882 9.920946 AGGCTCTAAAATGACAAATATTTAGGA 57.079 29.630 0.00 0.00 36.48 2.94
715 893 9.261035 TGACAAATATTTAGGAAGAGAGAGAGT 57.739 33.333 0.00 0.00 0.00 3.24
722 900 7.513560 TTTAGGAAGAGAGAGAGTACTACCT 57.486 40.000 0.00 0.00 0.00 3.08
723 901 8.621126 TTTAGGAAGAGAGAGAGTACTACCTA 57.379 38.462 0.00 0.00 0.00 3.08
724 902 8.802057 TTAGGAAGAGAGAGAGTACTACCTAT 57.198 38.462 0.00 0.00 0.00 2.57
725 903 7.701257 AGGAAGAGAGAGAGTACTACCTATT 57.299 40.000 0.00 0.00 0.00 1.73
726 904 7.514721 AGGAAGAGAGAGAGTACTACCTATTG 58.485 42.308 0.00 0.00 0.00 1.90
727 905 7.128263 AGGAAGAGAGAGAGTACTACCTATTGT 59.872 40.741 0.00 0.00 0.00 2.71
728 906 7.227910 GGAAGAGAGAGAGTACTACCTATTGTG 59.772 44.444 0.00 0.00 0.00 3.33
729 907 6.597562 AGAGAGAGAGTACTACCTATTGTGG 58.402 44.000 0.00 0.00 0.00 4.17
730 908 5.134661 AGAGAGAGTACTACCTATTGTGGC 58.865 45.833 0.00 0.00 0.00 5.01
731 909 5.103855 AGAGAGAGTACTACCTATTGTGGCT 60.104 44.000 0.00 0.00 0.00 4.75
732 910 6.101442 AGAGAGAGTACTACCTATTGTGGCTA 59.899 42.308 0.00 0.00 0.00 3.93
733 911 6.300703 AGAGAGTACTACCTATTGTGGCTAG 58.699 44.000 0.00 0.00 0.00 3.42
734 912 6.015991 AGAGTACTACCTATTGTGGCTAGT 57.984 41.667 0.00 0.00 32.70 2.57
735 913 7.072202 AGAGAGTACTACCTATTGTGGCTAGTA 59.928 40.741 0.00 0.00 31.47 1.82
753 931 1.339644 TATTAAACCGCCGGGCCTCT 61.340 55.000 14.55 0.00 36.48 3.69
779 957 0.543174 AACACCCGCCTCTCTCTCTT 60.543 55.000 0.00 0.00 0.00 2.85
865 1043 2.717639 ATCTCAAGGTGGGAAATCCG 57.282 50.000 0.00 0.00 38.76 4.18
893 1071 3.994392 CCAATCGGACGAAAGAAAAGAGA 59.006 43.478 0.00 0.00 0.00 3.10
921 1100 4.337060 CACCGACCGCGTCACTCA 62.337 66.667 4.92 0.00 35.23 3.41
922 1101 4.338539 ACCGACCGCGTCACTCAC 62.339 66.667 4.92 0.00 35.23 3.51
1401 1583 2.881389 CTCAACTCGCTCCTCGCT 59.119 61.111 0.00 0.00 38.27 4.93
1444 1626 0.104777 TCCCTGCCATGCCTAGATCT 60.105 55.000 0.00 0.00 0.00 2.75
1477 1659 1.112315 ACCTAGCTCCTGCCGATCTG 61.112 60.000 0.00 0.00 40.80 2.90
1506 1696 1.276138 CTCCACCAGCAATTTTTCCCC 59.724 52.381 0.00 0.00 0.00 4.81
1509 1699 2.106338 CCACCAGCAATTTTTCCCCTTT 59.894 45.455 0.00 0.00 0.00 3.11
1510 1700 3.434882 CCACCAGCAATTTTTCCCCTTTT 60.435 43.478 0.00 0.00 0.00 2.27
1511 1701 3.565063 CACCAGCAATTTTTCCCCTTTTG 59.435 43.478 0.00 0.00 0.00 2.44
1512 1702 2.553602 CCAGCAATTTTTCCCCTTTTGC 59.446 45.455 0.00 0.00 42.21 3.68
1513 1703 3.862877 AGCAATTTTTCCCCTTTTGCT 57.137 38.095 2.81 2.81 45.92 3.91
1523 1713 2.698274 TCCCCTTTTGCTTTTTGACCTC 59.302 45.455 0.00 0.00 0.00 3.85
1525 1715 3.134623 CCCCTTTTGCTTTTTGACCTCTT 59.865 43.478 0.00 0.00 0.00 2.85
1526 1716 4.122046 CCCTTTTGCTTTTTGACCTCTTG 58.878 43.478 0.00 0.00 0.00 3.02
1542 1732 4.407296 ACCTCTTGATGTTACCCTCTCATC 59.593 45.833 0.00 0.00 38.57 2.92
1563 1759 0.681564 ACCAAACGTGAAGGCAACCA 60.682 50.000 0.00 0.00 37.17 3.67
1585 1781 0.944386 GCTTTCCGTTGAGCAGAACA 59.056 50.000 0.00 0.00 38.73 3.18
1630 1826 4.558538 CAGAAAGTGGAAACTGAACAGG 57.441 45.455 6.76 0.00 32.90 4.00
1636 1847 0.868406 GGAAACTGAACAGGCTCACG 59.132 55.000 6.76 0.00 0.00 4.35
1638 1849 2.210116 GAAACTGAACAGGCTCACGAA 58.790 47.619 6.76 0.00 0.00 3.85
1645 1856 1.148310 ACAGGCTCACGAATTTCACG 58.852 50.000 0.00 0.00 0.00 4.35
1647 1858 2.288579 ACAGGCTCACGAATTTCACGTA 60.289 45.455 0.00 0.00 42.07 3.57
1653 1864 4.378046 GCTCACGAATTTCACGTAACCATT 60.378 41.667 0.00 0.00 42.07 3.16
1660 1871 6.635239 CGAATTTCACGTAACCATTTGTCTTT 59.365 34.615 0.00 0.00 0.00 2.52
1693 1908 6.438763 AGTTTGCTCTCCTTTTCGTATTTTG 58.561 36.000 0.00 0.00 0.00 2.44
1700 1915 7.303634 TCTCCTTTTCGTATTTTGTAGATGC 57.696 36.000 0.00 0.00 0.00 3.91
1708 1923 8.667987 TTCGTATTTTGTAGATGCAATTTGTC 57.332 30.769 0.00 0.00 0.00 3.18
1717 1932 7.660112 TGTAGATGCAATTTGTCTCACATTTT 58.340 30.769 0.00 0.00 0.00 1.82
1718 1933 8.791675 TGTAGATGCAATTTGTCTCACATTTTA 58.208 29.630 0.00 0.00 0.00 1.52
1720 1935 7.660112 AGATGCAATTTGTCTCACATTTTACA 58.340 30.769 0.00 0.00 0.00 2.41
1721 1936 7.596248 AGATGCAATTTGTCTCACATTTTACAC 59.404 33.333 0.00 0.00 0.00 2.90
1722 1937 5.685068 TGCAATTTGTCTCACATTTTACACG 59.315 36.000 0.00 0.00 0.00 4.49
1723 1938 5.912396 GCAATTTGTCTCACATTTTACACGA 59.088 36.000 0.00 0.00 0.00 4.35
1724 1939 6.416455 GCAATTTGTCTCACATTTTACACGAA 59.584 34.615 0.00 0.00 0.00 3.85
1725 1940 7.565073 GCAATTTGTCTCACATTTTACACGAAC 60.565 37.037 0.00 0.00 0.00 3.95
1726 1941 6.424176 TTTGTCTCACATTTTACACGAACA 57.576 33.333 0.00 0.00 0.00 3.18
1727 1942 6.612247 TTGTCTCACATTTTACACGAACAT 57.388 33.333 0.00 0.00 0.00 2.71
1728 1943 7.716768 TTGTCTCACATTTTACACGAACATA 57.283 32.000 0.00 0.00 0.00 2.29
1729 1944 7.112528 TGTCTCACATTTTACACGAACATAC 57.887 36.000 0.00 0.00 0.00 2.39
1730 1945 6.146510 TGTCTCACATTTTACACGAACATACC 59.853 38.462 0.00 0.00 0.00 2.73
1731 1946 6.146510 GTCTCACATTTTACACGAACATACCA 59.853 38.462 0.00 0.00 0.00 3.25
1732 1947 6.876789 TCTCACATTTTACACGAACATACCAT 59.123 34.615 0.00 0.00 0.00 3.55
1733 1948 7.389330 TCTCACATTTTACACGAACATACCATT 59.611 33.333 0.00 0.00 0.00 3.16
1734 1949 7.301789 TCACATTTTACACGAACATACCATTG 58.698 34.615 0.00 0.00 0.00 2.82
1735 1950 6.033407 CACATTTTACACGAACATACCATTGC 59.967 38.462 0.00 0.00 0.00 3.56
1736 1951 4.688511 TTTACACGAACATACCATTGCC 57.311 40.909 0.00 0.00 0.00 4.52
1737 1952 2.192664 ACACGAACATACCATTGCCA 57.807 45.000 0.00 0.00 0.00 4.92
1738 1953 1.810151 ACACGAACATACCATTGCCAC 59.190 47.619 0.00 0.00 0.00 5.01
1739 1954 1.132262 CACGAACATACCATTGCCACC 59.868 52.381 0.00 0.00 0.00 4.61
1745 1960 0.106519 ATACCATTGCCACCTCCTGC 60.107 55.000 0.00 0.00 0.00 4.85
1746 1961 1.496444 TACCATTGCCACCTCCTGCA 61.496 55.000 0.00 0.00 35.27 4.41
1751 1966 0.991146 TTGCCACCTCCTGCATCTAA 59.009 50.000 0.00 0.00 37.33 2.10
1757 1972 4.440663 GCCACCTCCTGCATCTAAATTTTC 60.441 45.833 0.00 0.00 0.00 2.29
1758 1973 4.098501 CCACCTCCTGCATCTAAATTTTCC 59.901 45.833 0.00 0.00 0.00 3.13
1759 1974 3.947834 ACCTCCTGCATCTAAATTTTCCG 59.052 43.478 0.00 0.00 0.00 4.30
1772 1989 8.665643 TCTAAATTTTCCGTAGAACTTTCACA 57.334 30.769 0.00 0.00 0.00 3.58
1774 1991 5.684550 ATTTTCCGTAGAACTTTCACACC 57.315 39.130 0.00 0.00 0.00 4.16
1782 1999 1.157870 AACTTTCACACCCGCTGTCG 61.158 55.000 0.00 0.00 0.00 4.35
1816 2038 8.434392 AGTTTAATCCCAGTTTGAACTAGTACA 58.566 33.333 0.00 0.00 37.08 2.90
1818 2040 6.435292 AATCCCAGTTTGAACTAGTACACT 57.565 37.500 0.00 0.00 37.08 3.55
1820 2042 4.282703 TCCCAGTTTGAACTAGTACACTCC 59.717 45.833 0.00 0.00 37.08 3.85
1921 2143 4.745351 TGATGATGTCTAGGCTCTGGTAT 58.255 43.478 0.00 0.00 0.00 2.73
1952 2174 7.818930 ACAACAAGTGAATCTTTGTGAATTGTT 59.181 29.630 4.91 0.00 38.49 2.83
1953 2175 8.658609 CAACAAGTGAATCTTTGTGAATTGTTT 58.341 29.630 0.00 0.00 36.50 2.83
1954 2176 8.411318 ACAAGTGAATCTTTGTGAATTGTTTC 57.589 30.769 3.62 0.00 33.63 2.78
1955 2177 7.492344 ACAAGTGAATCTTTGTGAATTGTTTCC 59.508 33.333 3.62 0.00 33.63 3.13
1956 2178 7.352079 AGTGAATCTTTGTGAATTGTTTCCT 57.648 32.000 0.00 0.00 0.00 3.36
1963 2185 1.128692 GTGAATTGTTTCCTCGCTCCG 59.871 52.381 0.00 0.00 0.00 4.63
1968 2190 3.702048 TTTCCTCGCTCCGGGTGG 61.702 66.667 0.00 0.00 0.00 4.61
1983 2205 0.673985 GGTGGTGAGGGAAGCAAAAC 59.326 55.000 0.00 0.00 0.00 2.43
1993 2215 3.010420 GGGAAGCAAAACTAGCTGGTAG 58.990 50.000 1.97 12.08 42.53 3.18
1997 2219 2.025887 AGCAAAACTAGCTGGTAGCCAT 60.026 45.455 13.46 0.00 43.77 4.40
2001 2223 5.449177 GCAAAACTAGCTGGTAGCCATAAAG 60.449 44.000 13.46 0.11 43.77 1.85
2002 2224 3.477210 ACTAGCTGGTAGCCATAAAGC 57.523 47.619 13.46 0.00 43.77 3.51
2003 2225 2.771943 ACTAGCTGGTAGCCATAAAGCA 59.228 45.455 13.46 0.00 43.77 3.91
2004 2226 2.806945 AGCTGGTAGCCATAAAGCAA 57.193 45.000 4.31 0.00 43.77 3.91
2005 2227 3.085952 AGCTGGTAGCCATAAAGCAAA 57.914 42.857 4.31 0.00 43.77 3.68
2006 2228 3.019564 AGCTGGTAGCCATAAAGCAAAG 58.980 45.455 4.31 0.00 43.77 2.77
2007 2229 2.099756 GCTGGTAGCCATAAAGCAAAGG 59.900 50.000 0.00 0.00 34.48 3.11
2008 2230 3.620488 CTGGTAGCCATAAAGCAAAGGA 58.380 45.455 0.00 0.00 30.82 3.36
2009 2231 3.352648 TGGTAGCCATAAAGCAAAGGAC 58.647 45.455 0.00 0.00 34.23 3.85
2021 2243 3.837355 AGCAAAGGACCAAGAAACTGAT 58.163 40.909 0.00 0.00 0.00 2.90
2037 2287 2.108075 ACTGATGAATGGTGTTGGGTGA 59.892 45.455 0.00 0.00 0.00 4.02
2038 2288 2.751259 CTGATGAATGGTGTTGGGTGAG 59.249 50.000 0.00 0.00 0.00 3.51
2039 2289 1.474077 GATGAATGGTGTTGGGTGAGC 59.526 52.381 0.00 0.00 0.00 4.26
2041 2291 1.702401 TGAATGGTGTTGGGTGAGCTA 59.298 47.619 0.00 0.00 0.00 3.32
2056 2306 2.236395 TGAGCTAGCTCACCCTAAAACC 59.764 50.000 37.64 13.29 46.80 3.27
2057 2307 2.236395 GAGCTAGCTCACCCTAAAACCA 59.764 50.000 34.70 0.00 42.31 3.67
2058 2308 2.027100 AGCTAGCTCACCCTAAAACCAC 60.027 50.000 12.68 0.00 0.00 4.16
2059 2309 2.027100 GCTAGCTCACCCTAAAACCACT 60.027 50.000 7.70 0.00 0.00 4.00
2060 2310 3.197116 GCTAGCTCACCCTAAAACCACTA 59.803 47.826 7.70 0.00 0.00 2.74
2061 2311 3.697619 AGCTCACCCTAAAACCACTAC 57.302 47.619 0.00 0.00 0.00 2.73
2062 2312 2.305052 AGCTCACCCTAAAACCACTACC 59.695 50.000 0.00 0.00 0.00 3.18
2063 2313 2.039348 GCTCACCCTAAAACCACTACCA 59.961 50.000 0.00 0.00 0.00 3.25
2064 2314 3.308188 GCTCACCCTAAAACCACTACCAT 60.308 47.826 0.00 0.00 0.00 3.55
2065 2315 4.514401 CTCACCCTAAAACCACTACCATC 58.486 47.826 0.00 0.00 0.00 3.51
2066 2316 3.264964 TCACCCTAAAACCACTACCATCC 59.735 47.826 0.00 0.00 0.00 3.51
2067 2317 3.009695 CACCCTAAAACCACTACCATCCA 59.990 47.826 0.00 0.00 0.00 3.41
2068 2318 3.658705 ACCCTAAAACCACTACCATCCAA 59.341 43.478 0.00 0.00 0.00 3.53
2069 2319 4.014406 CCCTAAAACCACTACCATCCAAC 58.986 47.826 0.00 0.00 0.00 3.77
2070 2320 4.263771 CCCTAAAACCACTACCATCCAACT 60.264 45.833 0.00 0.00 0.00 3.16
2071 2321 5.321927 CCTAAAACCACTACCATCCAACTT 58.678 41.667 0.00 0.00 0.00 2.66
2072 2322 5.773176 CCTAAAACCACTACCATCCAACTTT 59.227 40.000 0.00 0.00 0.00 2.66
2073 2323 6.266786 CCTAAAACCACTACCATCCAACTTTT 59.733 38.462 0.00 0.00 0.00 2.27
2074 2324 5.784578 AAACCACTACCATCCAACTTTTC 57.215 39.130 0.00 0.00 0.00 2.29
2075 2325 3.408634 ACCACTACCATCCAACTTTTCG 58.591 45.455 0.00 0.00 0.00 3.46
2109 2359 6.964741 AGAATATCATCGTCATGCATTCTC 57.035 37.500 0.00 0.00 37.14 2.87
2190 2440 1.135286 GCTCCAATTGCCACTAGTTGC 60.135 52.381 11.91 11.91 0.00 4.17
2215 2465 1.066002 GTTGCCATGACGGAATCCATG 59.934 52.381 0.00 0.00 39.72 3.66
2227 2477 3.018856 GGAATCCATGCTGAATGTGACA 58.981 45.455 0.00 0.00 34.11 3.58
2233 2483 0.798159 TGCTGAATGTGACATGCGAC 59.202 50.000 0.00 0.00 0.00 5.19
2235 2485 0.729116 CTGAATGTGACATGCGACCC 59.271 55.000 0.00 0.00 0.00 4.46
2346 2596 0.324614 TCATGATGTTCACCTGCCGT 59.675 50.000 0.00 0.00 0.00 5.68
2598 2848 3.319198 ATTGACCTGGCCGTCGGT 61.319 61.111 13.94 10.61 35.40 4.69
2729 2979 5.069648 TCTCACAGAAGCTTACATCATAGGG 59.930 44.000 0.00 0.00 0.00 3.53
2826 3078 6.524101 AATTGTGTAACTGTGTTTGTCCTT 57.476 33.333 0.00 0.00 38.04 3.36
2829 3081 4.762765 TGTGTAACTGTGTTTGTCCTTTGT 59.237 37.500 0.00 0.00 38.04 2.83
2830 3082 5.938710 TGTGTAACTGTGTTTGTCCTTTGTA 59.061 36.000 0.00 0.00 38.04 2.41
2831 3083 6.430308 TGTGTAACTGTGTTTGTCCTTTGTAA 59.570 34.615 0.00 0.00 38.04 2.41
2832 3084 6.964934 GTGTAACTGTGTTTGTCCTTTGTAAG 59.035 38.462 0.00 0.00 0.00 2.34
2833 3085 6.655848 TGTAACTGTGTTTGTCCTTTGTAAGT 59.344 34.615 0.00 0.00 0.00 2.24
2916 3175 1.228367 AGCACAGGAACCAAGCTGG 60.228 57.895 0.00 0.00 45.02 4.85
3048 3314 5.866633 GCTTAGAGGACATACATATGACAGC 59.133 44.000 10.38 1.49 37.15 4.40
3131 3397 3.306364 GCTTCTTCTACCTCAGTCTTGCA 60.306 47.826 0.00 0.00 0.00 4.08
3240 3506 0.879839 CACACATCTGTCGTGCCACA 60.880 55.000 0.00 0.00 37.93 4.17
3358 3628 2.577059 GCGTCATCGGGGTCTTGA 59.423 61.111 0.00 0.00 37.56 3.02
3373 3643 1.954382 TCTTGATCGGGGATGTCTACG 59.046 52.381 0.00 0.00 0.00 3.51
3508 3778 3.077359 CGAAGCTTTTGATGAACCCTCT 58.923 45.455 0.00 0.00 0.00 3.69
3708 3978 2.217750 CCACGACCACTCAAAACATGA 58.782 47.619 0.00 0.00 36.38 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 188 2.030562 CCACTTCAAGGCCGACGT 59.969 61.111 0.00 0.00 0.00 4.34
168 246 4.719369 GACGAACTGGCGAGGCGT 62.719 66.667 16.21 16.21 37.14 5.68
234 331 3.381212 CGCGTCGTCGTCGTTGTT 61.381 61.111 13.09 0.00 39.49 2.83
388 515 2.579787 CAAGAGGCCGCGACTACG 60.580 66.667 8.23 0.00 42.93 3.51
441 586 0.931005 CTCCGGCGAACTGAAATAGC 59.069 55.000 9.30 0.00 0.00 2.97
458 604 7.404139 AATATTCGGCGAAACAGTAATACTC 57.596 36.000 27.40 0.00 0.00 2.59
493 661 9.872757 GAATATTAATTCGACTAAAATTCGGCA 57.127 29.630 0.00 0.00 37.09 5.69
578 750 1.407712 GCTAAAATCGGCCACAGGGTA 60.408 52.381 2.24 0.00 36.17 3.69
583 755 2.403378 GGCGCTAAAATCGGCCACA 61.403 57.895 7.64 0.00 44.91 4.17
663 841 4.351938 CCTGCGAACACGTCCGGA 62.352 66.667 0.00 0.00 0.00 5.14
667 845 0.388134 TTAGAGCCTGCGAACACGTC 60.388 55.000 0.00 0.00 0.00 4.34
668 846 0.032952 TTTAGAGCCTGCGAACACGT 59.967 50.000 0.00 0.00 0.00 4.49
669 847 1.144969 TTTTAGAGCCTGCGAACACG 58.855 50.000 0.00 0.00 0.00 4.49
670 848 2.742053 TCATTTTAGAGCCTGCGAACAC 59.258 45.455 0.00 0.00 0.00 3.32
671 849 2.742053 GTCATTTTAGAGCCTGCGAACA 59.258 45.455 0.00 0.00 0.00 3.18
672 850 2.742053 TGTCATTTTAGAGCCTGCGAAC 59.258 45.455 0.00 0.00 0.00 3.95
673 851 3.052455 TGTCATTTTAGAGCCTGCGAA 57.948 42.857 0.00 0.00 0.00 4.70
674 852 2.760634 TGTCATTTTAGAGCCTGCGA 57.239 45.000 0.00 0.00 0.00 5.10
675 853 3.829886 TTTGTCATTTTAGAGCCTGCG 57.170 42.857 0.00 0.00 0.00 5.18
676 854 9.455847 CTAAATATTTGTCATTTTAGAGCCTGC 57.544 33.333 11.05 0.00 34.90 4.85
677 855 9.956720 CCTAAATATTTGTCATTTTAGAGCCTG 57.043 33.333 11.05 0.00 34.90 4.85
678 856 9.920946 TCCTAAATATTTGTCATTTTAGAGCCT 57.079 29.630 11.05 0.00 34.90 4.58
689 867 9.261035 ACTCTCTCTCTTCCTAAATATTTGTCA 57.739 33.333 11.05 0.00 0.00 3.58
696 874 9.228077 AGGTAGTACTCTCTCTCTTCCTAAATA 57.772 37.037 0.00 0.00 0.00 1.40
697 875 8.109560 AGGTAGTACTCTCTCTCTTCCTAAAT 57.890 38.462 0.00 0.00 0.00 1.40
698 876 7.513560 AGGTAGTACTCTCTCTCTTCCTAAA 57.486 40.000 0.00 0.00 0.00 1.85
699 877 8.802057 ATAGGTAGTACTCTCTCTCTTCCTAA 57.198 38.462 0.00 0.00 0.00 2.69
700 878 8.653191 CAATAGGTAGTACTCTCTCTCTTCCTA 58.347 40.741 0.00 0.00 0.00 2.94
701 879 7.128263 ACAATAGGTAGTACTCTCTCTCTTCCT 59.872 40.741 0.00 0.00 0.00 3.36
702 880 7.227910 CACAATAGGTAGTACTCTCTCTCTTCC 59.772 44.444 0.00 0.00 0.00 3.46
703 881 7.227910 CCACAATAGGTAGTACTCTCTCTCTTC 59.772 44.444 0.00 0.00 0.00 2.87
704 882 7.057894 CCACAATAGGTAGTACTCTCTCTCTT 58.942 42.308 0.00 0.00 0.00 2.85
705 883 6.597562 CCACAATAGGTAGTACTCTCTCTCT 58.402 44.000 0.00 0.00 0.00 3.10
706 884 5.239963 GCCACAATAGGTAGTACTCTCTCTC 59.760 48.000 0.00 0.00 0.00 3.20
707 885 5.103855 AGCCACAATAGGTAGTACTCTCTCT 60.104 44.000 0.00 0.00 0.00 3.10
708 886 5.134661 AGCCACAATAGGTAGTACTCTCTC 58.865 45.833 0.00 0.00 0.00 3.20
709 887 5.132043 AGCCACAATAGGTAGTACTCTCT 57.868 43.478 0.00 0.50 0.00 3.10
710 888 6.063404 ACTAGCCACAATAGGTAGTACTCTC 58.937 44.000 0.00 0.00 44.47 3.20
711 889 6.015991 ACTAGCCACAATAGGTAGTACTCT 57.984 41.667 0.00 0.00 44.47 3.24
716 894 8.427276 GGTTTAATACTAGCCACAATAGGTAGT 58.573 37.037 7.66 7.66 46.98 2.73
717 895 7.597743 CGGTTTAATACTAGCCACAATAGGTAG 59.402 40.741 0.00 0.00 40.38 3.18
718 896 7.436118 CGGTTTAATACTAGCCACAATAGGTA 58.564 38.462 0.00 0.00 0.00 3.08
719 897 6.285990 CGGTTTAATACTAGCCACAATAGGT 58.714 40.000 0.00 0.00 0.00 3.08
720 898 5.178809 GCGGTTTAATACTAGCCACAATAGG 59.821 44.000 0.00 0.00 0.00 2.57
721 899 5.178809 GGCGGTTTAATACTAGCCACAATAG 59.821 44.000 15.30 0.00 44.32 1.73
722 900 5.058490 GGCGGTTTAATACTAGCCACAATA 58.942 41.667 15.30 0.00 44.32 1.90
723 901 3.881089 GGCGGTTTAATACTAGCCACAAT 59.119 43.478 15.30 0.00 44.32 2.71
724 902 3.272581 GGCGGTTTAATACTAGCCACAA 58.727 45.455 15.30 0.00 44.32 3.33
725 903 2.739287 CGGCGGTTTAATACTAGCCACA 60.739 50.000 0.00 0.00 44.79 4.17
726 904 1.862827 CGGCGGTTTAATACTAGCCAC 59.137 52.381 0.00 0.00 44.79 5.01
727 905 1.202557 CCGGCGGTTTAATACTAGCCA 60.203 52.381 19.97 0.00 44.79 4.75
728 906 1.505425 CCGGCGGTTTAATACTAGCC 58.495 55.000 19.97 12.66 42.75 3.93
729 907 1.505425 CCCGGCGGTTTAATACTAGC 58.495 55.000 26.32 0.00 0.00 3.42
730 908 1.505425 GCCCGGCGGTTTAATACTAG 58.495 55.000 26.32 6.14 0.00 2.57
731 909 0.106521 GGCCCGGCGGTTTAATACTA 59.893 55.000 26.32 0.00 0.00 1.82
732 910 1.153107 GGCCCGGCGGTTTAATACT 60.153 57.895 26.32 0.00 0.00 2.12
733 911 1.153107 AGGCCCGGCGGTTTAATAC 60.153 57.895 26.32 6.40 0.00 1.89
734 912 1.146707 GAGGCCCGGCGGTTTAATA 59.853 57.895 26.32 0.00 0.00 0.98
735 913 2.124445 GAGGCCCGGCGGTTTAAT 60.124 61.111 26.32 5.57 0.00 1.40
753 931 0.037590 AGAGGCGGGTGTTTAATGCA 59.962 50.000 0.00 0.00 0.00 3.96
893 1071 0.891904 CGGTCGGTGGTGGGAATTTT 60.892 55.000 0.00 0.00 0.00 1.82
1377 1559 3.672295 GAGCGAGTTGAGCCAGGGG 62.672 68.421 0.00 0.00 34.64 4.79
1401 1583 2.661537 CTCACCGTGTTGAGCGCA 60.662 61.111 11.47 0.00 36.83 6.09
1444 1626 1.538204 GCTAGGTTCATTCGCCGATCA 60.538 52.381 0.00 0.00 0.00 2.92
1477 1659 2.124403 CTGGTGGAGCAGATGGGC 60.124 66.667 0.00 0.00 0.00 5.36
1497 1687 5.359576 GGTCAAAAAGCAAAAGGGGAAAAAT 59.640 36.000 0.00 0.00 0.00 1.82
1503 1693 2.700371 AGAGGTCAAAAAGCAAAAGGGG 59.300 45.455 0.00 0.00 0.00 4.79
1506 1696 6.044682 ACATCAAGAGGTCAAAAAGCAAAAG 58.955 36.000 0.00 0.00 0.00 2.27
1509 1699 5.596836 AACATCAAGAGGTCAAAAAGCAA 57.403 34.783 0.00 0.00 0.00 3.91
1510 1700 5.009610 GGTAACATCAAGAGGTCAAAAAGCA 59.990 40.000 0.00 0.00 0.00 3.91
1511 1701 5.461526 GGTAACATCAAGAGGTCAAAAAGC 58.538 41.667 0.00 0.00 0.00 3.51
1512 1702 5.770162 AGGGTAACATCAAGAGGTCAAAAAG 59.230 40.000 0.00 0.00 39.74 2.27
1513 1703 5.701224 AGGGTAACATCAAGAGGTCAAAAA 58.299 37.500 0.00 0.00 39.74 1.94
1542 1732 0.316689 GTTGCCTTCACGTTTGGTCG 60.317 55.000 0.00 0.00 0.00 4.79
1563 1759 2.280797 TGCTCAACGGAAAGCGCT 60.281 55.556 2.64 2.64 41.51 5.92
1572 1768 1.071605 GTAGCCTGTTCTGCTCAACG 58.928 55.000 0.00 0.00 40.23 4.10
1603 1799 2.024414 AGTTTCCACTTTCTGGTGTGC 58.976 47.619 0.00 0.00 41.52 4.57
1624 1820 2.411547 CGTGAAATTCGTGAGCCTGTTC 60.412 50.000 0.00 0.00 0.00 3.18
1625 1821 1.531149 CGTGAAATTCGTGAGCCTGTT 59.469 47.619 0.00 0.00 0.00 3.16
1629 1825 2.159747 GGTTACGTGAAATTCGTGAGCC 60.160 50.000 0.00 0.00 41.62 4.70
1630 1826 2.477375 TGGTTACGTGAAATTCGTGAGC 59.523 45.455 0.00 3.64 42.47 4.26
1636 1847 7.924103 AAAGACAAATGGTTACGTGAAATTC 57.076 32.000 0.00 0.00 0.00 2.17
1638 1849 6.635239 CGAAAAGACAAATGGTTACGTGAAAT 59.365 34.615 0.00 0.00 0.00 2.17
1645 1856 4.602995 TGCACGAAAAGACAAATGGTTAC 58.397 39.130 0.00 0.00 0.00 2.50
1647 1858 3.380004 TCTGCACGAAAAGACAAATGGTT 59.620 39.130 0.00 0.00 0.00 3.67
1653 1864 4.014847 CAAACTCTGCACGAAAAGACAA 57.985 40.909 0.00 0.00 0.00 3.18
1675 1886 7.064609 TGCATCTACAAAATACGAAAAGGAGAG 59.935 37.037 0.00 0.00 0.00 3.20
1677 1888 7.072177 TGCATCTACAAAATACGAAAAGGAG 57.928 36.000 0.00 0.00 0.00 3.69
1678 1889 7.441890 TTGCATCTACAAAATACGAAAAGGA 57.558 32.000 0.00 0.00 0.00 3.36
1686 1897 9.065871 GTGAGACAAATTGCATCTACAAAATAC 57.934 33.333 0.00 0.00 32.27 1.89
1693 1908 9.065871 GTAAAATGTGAGACAAATTGCATCTAC 57.934 33.333 0.00 0.00 0.00 2.59
1700 1915 7.430793 TGTTCGTGTAAAATGTGAGACAAATTG 59.569 33.333 0.00 0.00 0.00 2.32
1708 1923 6.474819 TGGTATGTTCGTGTAAAATGTGAG 57.525 37.500 0.00 0.00 0.00 3.51
1717 1932 3.004171 GTGGCAATGGTATGTTCGTGTA 58.996 45.455 0.00 0.00 0.00 2.90
1718 1933 1.810151 GTGGCAATGGTATGTTCGTGT 59.190 47.619 0.00 0.00 0.00 4.49
1720 1935 1.004277 AGGTGGCAATGGTATGTTCGT 59.996 47.619 0.00 0.00 0.00 3.85
1721 1936 1.670811 GAGGTGGCAATGGTATGTTCG 59.329 52.381 0.00 0.00 0.00 3.95
1722 1937 2.024414 GGAGGTGGCAATGGTATGTTC 58.976 52.381 0.00 0.00 0.00 3.18
1723 1938 1.640670 AGGAGGTGGCAATGGTATGTT 59.359 47.619 0.00 0.00 0.00 2.71
1724 1939 1.064463 CAGGAGGTGGCAATGGTATGT 60.064 52.381 0.00 0.00 0.00 2.29
1725 1940 1.683943 CAGGAGGTGGCAATGGTATG 58.316 55.000 0.00 0.00 0.00 2.39
1726 1941 0.106519 GCAGGAGGTGGCAATGGTAT 60.107 55.000 0.00 0.00 0.00 2.73
1727 1942 1.302949 GCAGGAGGTGGCAATGGTA 59.697 57.895 0.00 0.00 0.00 3.25
1728 1943 2.036256 GCAGGAGGTGGCAATGGT 59.964 61.111 0.00 0.00 0.00 3.55
1729 1944 1.380785 ATGCAGGAGGTGGCAATGG 60.381 57.895 0.00 0.00 44.20 3.16
1730 1945 0.395311 AGATGCAGGAGGTGGCAATG 60.395 55.000 0.00 0.00 44.20 2.82
1731 1946 1.216064 TAGATGCAGGAGGTGGCAAT 58.784 50.000 0.00 0.00 44.20 3.56
1732 1947 0.991146 TTAGATGCAGGAGGTGGCAA 59.009 50.000 0.00 0.00 44.20 4.52
1733 1948 0.991146 TTTAGATGCAGGAGGTGGCA 59.009 50.000 0.00 0.00 45.23 4.92
1734 1949 2.355010 ATTTAGATGCAGGAGGTGGC 57.645 50.000 0.00 0.00 0.00 5.01
1735 1950 4.098501 GGAAAATTTAGATGCAGGAGGTGG 59.901 45.833 0.00 0.00 0.00 4.61
1736 1951 4.201950 CGGAAAATTTAGATGCAGGAGGTG 60.202 45.833 0.00 0.00 0.00 4.00
1737 1952 3.947834 CGGAAAATTTAGATGCAGGAGGT 59.052 43.478 0.00 0.00 0.00 3.85
1738 1953 3.947834 ACGGAAAATTTAGATGCAGGAGG 59.052 43.478 0.00 0.00 0.00 4.30
1739 1954 6.049149 TCTACGGAAAATTTAGATGCAGGAG 58.951 40.000 0.00 0.00 0.00 3.69
1745 1960 9.543018 GTGAAAGTTCTACGGAAAATTTAGATG 57.457 33.333 0.00 0.00 32.81 2.90
1746 1961 9.280174 TGTGAAAGTTCTACGGAAAATTTAGAT 57.720 29.630 0.00 0.00 32.81 1.98
1751 1966 5.009310 GGGTGTGAAAGTTCTACGGAAAATT 59.991 40.000 0.00 0.00 32.81 1.82
1757 1972 1.425412 CGGGTGTGAAAGTTCTACGG 58.575 55.000 0.00 0.00 0.00 4.02
1758 1973 0.788391 GCGGGTGTGAAAGTTCTACG 59.212 55.000 0.00 0.00 0.00 3.51
1759 1974 1.798813 CAGCGGGTGTGAAAGTTCTAC 59.201 52.381 0.00 0.00 0.00 2.59
1782 1999 0.393808 TGGGATTAAACTGCTCCGCC 60.394 55.000 0.00 0.00 0.00 6.13
1783 2000 1.017387 CTGGGATTAAACTGCTCCGC 58.983 55.000 0.00 0.00 0.00 5.54
1786 2003 5.241728 AGTTCAAACTGGGATTAAACTGCTC 59.758 40.000 0.00 0.00 37.98 4.26
1793 2010 7.970102 AGTGTACTAGTTCAAACTGGGATTAA 58.030 34.615 0.00 0.00 41.28 1.40
1853 2075 1.303561 ATGTGCAACTGCCACCGAT 60.304 52.632 0.00 0.00 41.18 4.18
1908 2130 4.184629 GTTGTCACAATACCAGAGCCTAG 58.815 47.826 0.00 0.00 0.00 3.02
1921 2143 6.072230 TCACAAAGATTCACTTGTTGTCACAA 60.072 34.615 0.00 0.00 40.82 3.33
1955 2177 4.135153 CTCACCACCCGGAGCGAG 62.135 72.222 0.73 0.00 35.59 5.03
1963 2185 0.469144 TTTTGCTTCCCTCACCACCC 60.469 55.000 0.00 0.00 0.00 4.61
1968 2190 2.485814 CAGCTAGTTTTGCTTCCCTCAC 59.514 50.000 0.00 0.00 38.92 3.51
1983 2205 3.475566 TGCTTTATGGCTACCAGCTAG 57.524 47.619 0.00 0.00 41.99 3.42
1993 2215 2.825532 TCTTGGTCCTTTGCTTTATGGC 59.174 45.455 0.00 0.00 0.00 4.40
1997 2219 5.197451 TCAGTTTCTTGGTCCTTTGCTTTA 58.803 37.500 0.00 0.00 0.00 1.85
2001 2223 3.569701 TCATCAGTTTCTTGGTCCTTTGC 59.430 43.478 0.00 0.00 0.00 3.68
2002 2224 5.772825 TTCATCAGTTTCTTGGTCCTTTG 57.227 39.130 0.00 0.00 0.00 2.77
2003 2225 5.244626 CCATTCATCAGTTTCTTGGTCCTTT 59.755 40.000 0.00 0.00 0.00 3.11
2004 2226 4.768968 CCATTCATCAGTTTCTTGGTCCTT 59.231 41.667 0.00 0.00 0.00 3.36
2005 2227 4.202609 ACCATTCATCAGTTTCTTGGTCCT 60.203 41.667 0.00 0.00 30.38 3.85
2006 2228 4.082125 ACCATTCATCAGTTTCTTGGTCC 58.918 43.478 0.00 0.00 30.38 4.46
2007 2229 4.520492 ACACCATTCATCAGTTTCTTGGTC 59.480 41.667 0.00 0.00 33.88 4.02
2008 2230 4.473444 ACACCATTCATCAGTTTCTTGGT 58.527 39.130 0.00 0.00 36.46 3.67
2009 2231 5.224888 CAACACCATTCATCAGTTTCTTGG 58.775 41.667 0.00 0.00 0.00 3.61
2021 2243 0.478072 AGCTCACCCAACACCATTCA 59.522 50.000 0.00 0.00 0.00 2.57
2037 2287 2.027100 GTGGTTTTAGGGTGAGCTAGCT 60.027 50.000 19.45 19.45 0.00 3.32
2038 2288 2.027100 AGTGGTTTTAGGGTGAGCTAGC 60.027 50.000 6.62 6.62 0.00 3.42
2039 2289 3.983044 AGTGGTTTTAGGGTGAGCTAG 57.017 47.619 0.00 0.00 0.00 3.42
2041 2291 2.305052 GGTAGTGGTTTTAGGGTGAGCT 59.695 50.000 0.00 0.00 0.00 4.09
2050 2300 6.016943 CGAAAAGTTGGATGGTAGTGGTTTTA 60.017 38.462 0.00 0.00 0.00 1.52
2051 2301 5.221165 CGAAAAGTTGGATGGTAGTGGTTTT 60.221 40.000 0.00 0.00 0.00 2.43
2054 2304 3.408634 CGAAAAGTTGGATGGTAGTGGT 58.591 45.455 0.00 0.00 0.00 4.16
2056 2306 3.670625 TCCGAAAAGTTGGATGGTAGTG 58.329 45.455 0.00 0.00 0.00 2.74
2057 2307 4.569719 ATCCGAAAAGTTGGATGGTAGT 57.430 40.909 0.00 0.00 43.30 2.73
2058 2308 6.346096 TCTTATCCGAAAAGTTGGATGGTAG 58.654 40.000 5.84 2.02 44.58 3.18
2059 2309 6.302535 TCTTATCCGAAAAGTTGGATGGTA 57.697 37.500 5.84 0.00 44.58 3.25
2060 2310 5.174037 TCTTATCCGAAAAGTTGGATGGT 57.826 39.130 5.84 0.00 44.58 3.55
2061 2311 5.822519 TGATCTTATCCGAAAAGTTGGATGG 59.177 40.000 5.84 0.31 44.58 3.51
2062 2312 6.925610 TGATCTTATCCGAAAAGTTGGATG 57.074 37.500 5.84 0.00 44.58 3.51
2063 2313 7.338710 TCTTGATCTTATCCGAAAAGTTGGAT 58.661 34.615 0.00 1.21 46.52 3.41
2064 2314 6.707290 TCTTGATCTTATCCGAAAAGTTGGA 58.293 36.000 0.00 0.00 38.95 3.53
2065 2315 6.985188 TCTTGATCTTATCCGAAAAGTTGG 57.015 37.500 0.00 0.00 0.00 3.77
2071 2321 9.358872 CGATGATATTCTTGATCTTATCCGAAA 57.641 33.333 0.00 0.00 0.00 3.46
2072 2322 8.523658 ACGATGATATTCTTGATCTTATCCGAA 58.476 33.333 0.00 0.00 0.00 4.30
2073 2323 8.056407 ACGATGATATTCTTGATCTTATCCGA 57.944 34.615 0.00 0.00 0.00 4.55
2074 2324 7.970614 TGACGATGATATTCTTGATCTTATCCG 59.029 37.037 0.00 0.00 0.00 4.18
2075 2325 9.814899 ATGACGATGATATTCTTGATCTTATCC 57.185 33.333 0.00 0.00 0.00 2.59
2109 2359 3.117550 TCAGGAAATCCATGGGTATGTGG 60.118 47.826 13.02 0.00 38.89 4.17
2215 2465 0.097674 GGTCGCATGTCACATTCAGC 59.902 55.000 0.00 0.00 0.00 4.26
2227 2477 1.153289 GCACATGAGAGGGTCGCAT 60.153 57.895 0.00 0.00 37.38 4.73
2233 2483 0.037303 AACACCTGCACATGAGAGGG 59.963 55.000 0.00 0.00 0.00 4.30
2235 2485 1.073964 CGAACACCTGCACATGAGAG 58.926 55.000 0.00 0.00 0.00 3.20
2729 2979 1.609208 ATTCCACGGCCATTGATAGC 58.391 50.000 2.24 0.00 0.00 2.97
2826 3078 8.128582 CAGAAGATGTTGCAACTTAACTTACAA 58.871 33.333 28.61 6.27 0.00 2.41
2829 3081 8.445275 TTCAGAAGATGTTGCAACTTAACTTA 57.555 30.769 28.61 8.52 0.00 2.24
2830 3082 6.942532 TCAGAAGATGTTGCAACTTAACTT 57.057 33.333 28.61 24.06 0.00 2.66
2831 3083 6.942532 TTCAGAAGATGTTGCAACTTAACT 57.057 33.333 28.61 18.40 0.00 2.24
2832 3084 7.358683 GCATTTCAGAAGATGTTGCAACTTAAC 60.359 37.037 28.61 16.70 33.52 2.01
2833 3085 6.642131 GCATTTCAGAAGATGTTGCAACTTAA 59.358 34.615 28.61 10.80 33.52 1.85
2916 3175 0.895100 TGCCATCTGTTGCCACTTCC 60.895 55.000 0.00 0.00 0.00 3.46
3048 3314 5.048083 ACCTGTTGTATACTTTGGCAATGTG 60.048 40.000 24.20 10.56 0.00 3.21
3240 3506 2.261671 GTCCGTGATGTCAGCGGT 59.738 61.111 17.30 0.00 39.64 5.68
3358 3628 1.040893 TGCACGTAGACATCCCCGAT 61.041 55.000 0.00 0.00 0.00 4.18
3373 3643 1.032014 TCAAGCAGGGTTCTTTGCAC 58.968 50.000 0.00 0.00 42.67 4.57
3477 3747 1.024271 AAAAGCTTCGTTGAGCAGCA 58.976 45.000 0.00 0.00 45.12 4.41
3508 3778 0.901114 TCCCCCATTTCTGTCGACGA 60.901 55.000 11.62 8.49 0.00 4.20


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

AutoCloner maintained by Alex Coulton.